forked from lijiext/lammps
git-svn-id: svn://svn.icms.temple.edu/lammps-ro/trunk@11411 f3b2605a-c512-4ea7-a41b-209d697bcdaa
This commit is contained in:
sjplimp
parent
abdec3cb5d
commit
dd122f6a0b
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LAMMPS (1 Feb 2014)
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# 2d polygon nparticle bodies
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units lj
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dimension 2
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atom_style body nparticle 2 6
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read_data data.body
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orthogonal box = (-15.5322 -15.5322 -0.5) to (15.5322 15.5322 0.5)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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100 atoms
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100 bodies
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velocity all create 1.44 87287 loop geom
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pair_style body 5.0
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pair_coeff * * 1.0 1.0
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neighbor 0.3 bin
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fix 1 all nve/body
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fix 2 all enforce2d
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#compute 1 all body/local type 1 2 3
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#dump 1 all local 100 dump.body index c_1[1] c_1[2] c_1[3] c_1[4]
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thermo 500
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run 10000
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Memory usage per processor = 3.22547 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.44 -0.63799525 0 0.78760475 -0.15028724
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500 1.5537157 -1.5243356 0 0.013843001 0.2654775
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1000 1.5681616 -1.8003444 0 -0.2478644 0.07601415
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1500 1.6994347 -1.7246456 0 -0.04220525 0.3664501
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2000 1.6587022 -1.6970163 0 -0.054901081 0.10137795
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2500 1.7859516 -1.8212698 0 -0.053177671 0.35400181
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3000 1.7865459 -1.730183 0 0.038497352 0.28330983
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3500 2.0521408 -1.98222 0 0.049399375 0.088928245
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4000 1.721448 -1.7409775 0 -0.036743968 0.12815274
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4500 1.6189244 -1.7257177 0 -0.12298249 0.21501422
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5000 1.5828072 -1.6501894 0 -0.083210213 0.33447691
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5500 1.8562352 -1.7632936 0 0.074379269 0.24273308
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6000 1.4818079 -1.6942298 0 -0.22723999 0.22470999
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6500 1.5229137 -1.6249423 0 -0.11725778 -0.043041211
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7000 1.5930761 -1.5349749 0 0.04217044 0.072621368
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7500 1.7251412 -1.7620322 0 -0.05414237 -0.052083575
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8000 1.7843737 -1.6422594 0 0.12427062 0.3924994
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8500 1.9344759 -1.7880774 0 0.12705368 0.32652919
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9000 1.6338929 -1.6889133 0 -0.071359354 0.3793827
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9500 1.5180082 -1.7729127 0 -0.27008457 0.27223707
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10000 1.6133128 -1.7939587 0 -0.19677903 0.18983194
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Loop time of 2.02213 on 1 procs for 10000 steps with 100 atoms
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Pair time (%) = 1.79877 (88.9544)
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Neigh time (%) = 0.0161726 (0.799784)
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Comm time (%) = 0.0302939 (1.49812)
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Outpt time (%) = 0.000165939 (0.00820618)
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Other time (%) = 0.176724 (8.7395)
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Nlocal: 100 ave 100 max 100 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 85 ave 85 max 85 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 424 ave 424 max 424 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 424
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Ave neighs/atom = 4.24
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Neighbor list builds = 795
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Dangerous builds = 83
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@ -0,0 +1,71 @@
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LAMMPS (1 Feb 2014)
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# 2d polygon nparticle bodies
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units lj
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dimension 2
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atom_style body nparticle 2 6
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read_data data.body
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orthogonal box = (-15.5322 -15.5322 -0.5) to (15.5322 15.5322 0.5)
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2 by 2 by 1 MPI processor grid
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reading atoms ...
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100 atoms
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100 bodies
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velocity all create 1.44 87287 loop geom
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pair_style body 5.0
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pair_coeff * * 1.0 1.0
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neighbor 0.3 bin
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fix 1 all nve/body
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fix 2 all enforce2d
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#compute 1 all body/local type 1 2 3
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#dump 1 all local 100 dump.body index c_1[1] c_1[2] c_1[3] c_1[4]
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thermo 500
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run 10000
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Memory usage per processor = 3.19797 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 1.44 -0.63799525 0 0.78760475 -0.15028724
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500 1.5537157 -1.5243356 0 0.013843001 0.2654775
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1000 1.5681616 -1.8003444 0 -0.2478644 0.07601415
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1500 1.6994347 -1.7246456 0 -0.042205239 0.36645011
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2000 1.6586974 -1.6970115 0 -0.054901078 0.10137999
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2500 1.7878623 -1.8213737 0 -0.051390011 0.35530747
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3000 1.7043715 -1.6613359 0 0.025991881 0.27048518
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3500 1.6313416 -1.5250929 0 0.089935264 0.10510436
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4000 1.5883641 -1.7692022 0 -0.1967218 0.50882304
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4500 1.5897207 -1.5634198 0 0.010403642 0.24598267
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5000 1.4849734 -1.5512049 0 -0.081081244 -0.028399888
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5500 1.6074988 -1.7000582 0 -0.10863448 0.42879191
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6000 1.6106093 -1.5850749 0 0.0094282394 0.4115976
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6500 1.8169151 -1.7996899 0 -0.00094400747 0.21677584
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7000 1.5487579 -1.6028263 0 -0.069555913 0.23742891
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7500 1.7231927 -1.8001082 0 -0.094147408 -0.016712191
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8000 1.5832288 -1.7242109 0 -0.15681439 0.33204
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8500 1.9002455 -1.866332 0 0.014911066 0.28393405
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9000 1.5916225 -1.6032424 0 -0.027536096 0.48213053
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9500 1.6326075 -1.7974673 0 -0.18118584 0.078132294
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10000 1.3851677 -1.49406 0 -0.12274404 0.18606978
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Loop time of 0.730152 on 4 procs for 10000 steps with 100 atoms
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Pair time (%) = 0.464131 (63.5663)
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Neigh time (%) = 0.00445265 (0.609824)
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Comm time (%) = 0.204234 (27.9714)
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Outpt time (%) = 0.000480056 (0.0657474)
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Other time (%) = 0.0568546 (7.78668)
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Nlocal: 25 ave 25 max 25 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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Nghost: 43.75 ave 48 max 40 min
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Histogram: 1 1 0 0 0 0 0 1 0 1
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Neighs: 101.5 ave 113 max 91 min
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Histogram: 1 1 0 0 0 0 0 1 0 1
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Total # of neighbors = 406
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Ave neighs/atom = 4.06
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Neighbor list builds = 805
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Dangerous builds = 97
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@ -0,0 +1,131 @@
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LAMMPS (1 Feb 2014)
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# Big colloid particles and small LJ particles
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units lj
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atom_style sphere
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dimension 2
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lattice sq 0.01
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Lattice spacing in x,y,z = 10 10 10
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region box block 0 30 0 30 -0.5 0.5
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create_box 2 box
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Created orthogonal box = (0 0 -5) to (300 300 5)
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1 by 1 by 1 MPI processor grid
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create_atoms 1 box
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Created 900 atoms
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set group all type/fraction 2 0.96 23984
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861 settings made for type/fraction
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set type 1 mass 9
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39 settings made for mass
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set type 2 mass 1
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861 settings made for mass
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velocity all create 1.44 87287 loop geom
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# multi neighbor and comm for efficiency
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neighbor 1 multi
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neigh_modify delay 0
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communicate multi
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# colloid potential
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pair_style colloid 12.5
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pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
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pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
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pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5
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fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
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fix 2 all enforce2d
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#dump 1 all atom 1000 dump.colloid
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#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
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#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
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#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
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#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
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thermo_style custom step temp epair etotal press vol
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thermo 1000
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timestep 0.005
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run 50000
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Memory usage per processor = 2.96579 Mbytes
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Step Temp E_pair TotEng Press Volume
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0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
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1000 1.9558819 -0.00044998322 1.9532587 0.01784589 99146.35
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2000 2.0558568 0.011295331 2.0648679 0.021858185 96654.425
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3000 2.1809647 0.0091754217 2.1877168 0.031294876 68756.47
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4000 2.1960934 0.0028186107 2.1964719 0.049318667 42974.984
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5000 2.1463273 0.012748525 2.156691 0.073994939 28660.577
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6000 2.1073992 0.0076702433 2.1127279 0.097655997 21544.211
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7000 2.084579 -0.0022304831 2.0800323 0.11014552 17791.284
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8000 2.0677538 0.00059800188 2.0660543 0.12718796 15494.44
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9000 2.0545977 0.0064465732 2.0587614 0.15002732 13864.665
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10000 2.0482054 0.010661731 2.0565913 0.17497885 12553.11
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11000 2.0360539 0.022283053 2.0560747 0.18608443 11469.573
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12000 2.0488819 0.012601482 2.0592068 0.20752397 10547.355
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13000 2.0307724 0.027945421 2.0564614 0.23492616 9791.6008
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14000 2.0291712 0.024760645 2.0516772 0.25749445 9166.0223
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15000 2.0421329 0.011858836 2.0517227 0.26019128 8645.5059
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16000 2.0321296 0.023089154 2.0529608 0.30100779 8173.8988
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17000 2.0339883 0.020841935 2.0525702 0.31937035 7749.9866
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18000 2.0165994 0.039101369 2.0534601 0.33206939 7399.5633
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19000 2.0174571 0.03075954 2.045975 0.37582663 7115.1621
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20000 2.0235743 0.033645074 2.054971 0.37789661 6779.655
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21000 2.0086918 0.052575979 2.0590359 0.47587927 6468.3757
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22000 2.0186512 0.035185664 2.0515939 0.39489244 6270.2423
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23000 2.0159704 0.037209936 2.0509404 0.42372164 6090.2568
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24000 2.0262103 0.034411154 2.0583702 0.46377965 5878.6019
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25000 2.0136031 0.040396972 2.0517627 0.49998462 5706.6657
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26000 2.0118123 0.04348596 2.0530629 0.52601904 5555.535
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27000 2.0483861 0.010622163 2.0567323 0.46408289 5439.3763
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28000 1.9775694 0.0880593 2.0634314 0.60451974 5303.7986
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29000 2.0161573 0.051647461 2.0655645 0.55856521 5154.8346
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30000 2.0154349 0.045614723 2.0588102 0.55640547 5067.2252
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31000 2.0264636 0.042015926 2.0662279 0.58323212 4966.2146
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32000 1.9946148 0.074464523 2.0668631 0.64405663 4840.3505
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33000 2.016998 0.046624054 2.0613809 0.6520715 4765.5247
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34000 2.0086574 0.060996501 2.067422 0.6530397 4666.4569
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35000 2.0203252 0.05402663 2.0721071 0.69134002 4595.6514
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36000 2.0271451 0.041489394 2.0663822 0.65114797 4526.2978
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37000 2.0183469 0.064565854 2.0806701 0.70724758 4446.6465
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38000 2.0049133 0.065280115 2.0679658 0.76328332 4389.5655
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39000 2.0254497 0.05173788 2.0749371 0.75604831 4332.6535
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40000 2.0019046 0.080413589 2.0800938 0.78175962 4254.5071
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41000 2.0246809 0.05297341 2.0754047 0.77404015 4193.7093
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42000 2.0254595 0.058651302 2.0818603 0.81823656 4135.9705
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43000 2.0007241 0.083353246 2.0818543 0.82002543 4082.2245
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44000 1.994415 0.089912333 2.0821113 0.98373573 4051.5787
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45000 2.0130937 0.07986583 2.0907228 0.97054142 3991.453
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46000 1.9997536 0.094509733 2.0920414 0.90955799 3926.3675
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47000 2.0026833 0.086980098 2.0874382 1.1140455 3885.3495
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48000 2.0217273 0.077640083 2.0971211 0.94719095 3829.7776
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49000 1.9778606 0.11563852 2.0913015 1.1107597 3798.5114
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50000 2.038067 0.060063696 2.0958661 1.0030415 3763.2003
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Loop time of 8.766 on 1 procs for 50000 steps with 900 atoms
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Pair time (%) = 4.14446 (47.2788)
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Neigh time (%) = 1.10557 (12.612)
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Comm time (%) = 0.423719 (4.83366)
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Outpt time (%) = 0.000560045 (0.00638883)
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Other time (%) = 3.09169 (35.2691)
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Nlocal: 900 ave 900 max 900 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 515 ave 515 max 515 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 5990 ave 5990 max 5990 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 5990
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Ave neighs/atom = 6.65556
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Neighbor list builds = 3145
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Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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@ -0,0 +1,131 @@
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LAMMPS (1 Feb 2014)
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# Big colloid particles and small LJ particles
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units lj
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atom_style sphere
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dimension 2
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lattice sq 0.01
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Lattice spacing in x,y,z = 10 10 10
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region box block 0 30 0 30 -0.5 0.5
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create_box 2 box
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Created orthogonal box = (0 0 -5) to (300 300 5)
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2 by 2 by 1 MPI processor grid
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create_atoms 1 box
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Created 900 atoms
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set group all type/fraction 2 0.96 23984
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861 settings made for type/fraction
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set type 1 mass 9
|
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39 settings made for mass
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set type 2 mass 1
|
||||
861 settings made for mass
|
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|
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velocity all create 1.44 87287 loop geom
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# multi neighbor and comm for efficiency
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neighbor 1 multi
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neigh_modify delay 0
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communicate multi
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# colloid potential
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pair_style colloid 12.5
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pair_coeff 1 1 1.0 1.0 5.0 5.0 12.5
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||||
pair_coeff 1 2 5.0 1.0 5.0 0.0 7.0
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||||
pair_coeff 2 2 10.0 1.0 0.0 0.0 2.5
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fix 1 all npt temp 2.0 2.0 1.0 iso 0.0 1.0 10.0 drag 1.0 mtk no pchain 0 tchain 1
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fix 2 all enforce2d
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#dump 1 all atom 1000 dump.colloid
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#dump 2 all image 1000 image.*.jpg type type # zoom 1.5 center d 0.5 0.5 0.5
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#dump_modify 2 pad 5 adiam 1 5.0 adiam 2 1.5
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#dump 3 all movie 1000 movie.mpg type type # zoom 1.5 center d 0.5 0.5 0.5
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#dump_modify 3 pad 5 adiam 1 5.0 adiam 2 1.5
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thermo_style custom step temp epair etotal press vol
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thermo 1000
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timestep 0.005
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run 50000
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Memory usage per processor = 2.8708 Mbytes
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Step Temp E_pair TotEng Press Volume
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0 1.44 -2.2136534e-06 1.4383978 0.014383923 90000
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1000 1.9558819 -0.00044998322 1.9532587 0.01784589 99146.35
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2000 2.0558568 0.011295331 2.0648679 0.021858185 96654.425
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||||
3000 2.1809647 0.0091754217 2.1877168 0.031294876 68756.47
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4000 2.1960934 0.0028186107 2.1964719 0.049318667 42974.984
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5000 2.1463273 0.01274853 2.156691 0.07399494 28660.577
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6000 2.1073955 0.0076740311 2.112728 0.097657373 21544.21
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7000 2.0843684 -0.001996932 2.0800555 0.11036967 17791.247
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8000 2.0640518 0.0014998478 2.0632583 0.1290879 15498.836
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9000 2.0466103 0.010705612 2.0550419 0.15352798 13893.115
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10000 2.0318438 0.028356097 2.0579423 0.18270659 12603.157
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11000 2.0483114 0.011317082 2.0573526 0.18793572 11521.407
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12000 2.0465451 0.011178196 2.0554494 0.20917582 10593.908
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13000 2.0339418 0.020973133 2.052655 0.22462811 9837.666
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14000 2.0352875 0.021186021 2.054212 0.25973065 9169.0201
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15000 2.0397627 0.016745562 2.0542419 0.26379715 8580.3575
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16000 2.0306726 0.019939485 2.0483558 0.30415554 8135.4142
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17000 2.0303715 0.023425678 2.0515413 0.29717285 7732.4398
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18000 2.0091196 0.046353117 2.0532404 0.4201013 7321.9473
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19000 2.0069004 0.044794224 2.0494648 0.37207191 7008.5252
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20000 2.0293906 0.02286811 2.0500038 0.37743862 6770.2412
|
||||
21000 2.0151565 0.035150252 2.0480677 0.42245372 6563.7655
|
||||
22000 1.9931286 0.061233296 2.0521473 0.44215378 6387.0047
|
||||
23000 2.0095257 0.04877004 2.0560629 0.4359382 6146.7894
|
||||
24000 2.0244673 0.041537999 2.0637559 0.47433783 5904.2578
|
||||
25000 2.0411374 0.014657985 2.0535275 0.42934196 5714.3163
|
||||
26000 2.0101343 0.048931921 2.0568327 0.58433419 5557.1491
|
||||
27000 2.010355 0.044833431 2.0529547 0.53172163 5441.607
|
||||
28000 2.0075626 0.056527165 2.0618592 0.54811055 5312.0333
|
||||
29000 2.0279913 0.036953425 2.0626914 0.53888357 5165.8026
|
||||
30000 2.0014479 0.062210877 2.0614349 0.61283256 5028.4409
|
||||
31000 2.0072038 0.060184255 2.0651578 0.62321627 4918.8388
|
||||
32000 2.0250392 0.043276173 2.0660653 0.61454026 4822.6538
|
||||
33000 2.0225382 0.041253335 2.0615443 0.61742775 4746.3484
|
||||
34000 2.0079979 0.060100013 2.0658668 0.7196627 4668.3612
|
||||
35000 1.9869444 0.081389753 2.0661264 0.69301002 4630.1772
|
||||
36000 2.0080612 0.068966773 2.0747968 0.75807989 4524.4316
|
||||
37000 2.016828 0.059785388 2.0743725 0.73797084 4436.8809
|
||||
38000 1.9923438 0.084178865 2.074309 0.83179043 4358.5286
|
||||
39000 2.0144256 0.058962222 2.0711496 0.72841391 4318.0019
|
||||
40000 2.0205458 0.063834805 2.0821355 0.79611444 4233.3053
|
||||
41000 1.9895557 0.088139599 2.0754847 0.77982219 4183.6801
|
||||
42000 1.9862976 0.097665639 2.0817562 0.9527169 4136.6273
|
||||
43000 1.9845679 0.10838021 2.0907431 0.84567001 4063.3971
|
||||
44000 2.0058015 0.079068928 2.0826418 0.87879853 4013.8417
|
||||
45000 2.01267 0.072607353 2.083041 0.84521964 3983.104
|
||||
46000 2.0028119 0.088952749 2.0895393 0.86809738 3907.9426
|
||||
47000 2.0219141 0.069213747 2.0888813 0.88288894 3868.029
|
||||
48000 1.9820914 0.1111149 2.091004 1.0650645 3812.8502
|
||||
49000 2.0161896 0.077389897 2.0913393 0.94940244 3771.6873
|
||||
50000 2.0216994 0.071211384 2.0906645 0.99837694 3771.8545
|
||||
Loop time of 3.69238 on 4 procs for 50000 steps with 900 atoms
|
||||
|
||||
Pair time (%) = 1.08079 (29.2708)
|
||||
Neigh time (%) = 0.286304 (7.75391)
|
||||
Comm time (%) = 0.855729 (23.1756)
|
||||
Outpt time (%) = 0.000957787 (0.0259396)
|
||||
Other time (%) = 1.4686 (39.7738)
|
||||
|
||||
Nlocal: 225 ave 251 max 199 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Nghost: 295.25 ave 304 max 283 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
Neighs: 1477.25 ave 1684 max 1286 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 5909
|
||||
Ave neighs/atom = 6.56556
|
||||
Neighbor list builds = 3138
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,76 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Pure Cu crystal, structure created by LAMMPS, qeq off
|
||||
|
||||
units metal
|
||||
atom_style charge
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
lattice fcc 3.615
|
||||
Lattice spacing in x,y,z = 3.615 3.615 3.615
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (14.46 14.46 14.46)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 256 atoms
|
||||
mass 1 63.54
|
||||
|
||||
pair_style comb
|
||||
pair_coeff * * ffield.comb Cu
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
timestep 0.00020
|
||||
|
||||
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
|
||||
thermo_modify norm yes
|
||||
velocity all create 10.1 2398378
|
||||
thermo 1
|
||||
|
||||
#dump 1 all custom 10 tmp.dump id type xs ys zs q vx vy vz fx fy fz
|
||||
#dump_modify 1 append yes element Cu
|
||||
|
||||
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 2 element Cu
|
||||
|
||||
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 2 element Cu
|
||||
|
||||
run 10
|
||||
Memory usage per processor = 5.13167 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
|
||||
0 10.1 -3.5063151 -3.5076155 -3.5076155 0 27.496055 3023.4645 14.46 14.46 14.46 0
|
||||
1 10.099643 -3.5063151 -3.5076155 -3.5076155 0 27.512983 3023.4645 14.46 14.46 14.46 0
|
||||
2 10.098572 -3.5063151 -3.5076153 -3.5076153 0 27.563765 3023.4645 14.46 14.46 14.46 0
|
||||
3 10.096788 -3.5063151 -3.5076151 -3.5076151 0 27.64839 3023.4645 14.46 14.46 14.46 0
|
||||
4 10.094291 -3.5063151 -3.5076148 -3.5076148 0 27.766843 3023.4645 14.46 14.46 14.46 0
|
||||
5 10.09108 -3.5063151 -3.5076144 -3.5076144 0 27.919101 3023.4645 14.46 14.46 14.46 0
|
||||
6 10.087158 -3.5063151 -3.5076139 -3.5076139 0 28.105138 3023.4645 14.46 14.46 14.46 0
|
||||
7 10.082524 -3.5063151 -3.5076133 -3.5076133 0 28.324919 3023.4645 14.46 14.46 14.46 0
|
||||
8 10.077179 -3.5063151 -3.5076126 -3.5076126 0 28.578403 3023.4645 14.46 14.46 14.46 0
|
||||
9 10.071123 -3.5063151 -3.5076118 -3.5076118 0 28.865545 3023.4645 14.46 14.46 14.46 0
|
||||
10 10.06436 -3.5063151 -3.5076109 -3.5076109 0 29.186292 3023.4645 14.46 14.46 14.46 0
|
||||
Loop time of 0.180117 on 1 procs for 10 steps with 256 atoms
|
||||
|
||||
Pair time (%) = 0.179547 (99.6834)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000333071 (0.184919)
|
||||
Outpt time (%) = 0.000129461 (0.0718762)
|
||||
Other time (%) = 0.000107765 (0.0598306)
|
||||
|
||||
Nlocal: 256 ave 256 max 256 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4375 ave 4375 max 4375 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 172544 ave 172544 max 172544 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 172544
|
||||
Ave neighs/atom = 674
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,76 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Pure Cu crystal, structure created by LAMMPS, qeq off
|
||||
|
||||
units metal
|
||||
atom_style charge
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
lattice fcc 3.615
|
||||
Lattice spacing in x,y,z = 3.615 3.615 3.615
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (14.46 14.46 14.46)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 256 atoms
|
||||
mass 1 63.54
|
||||
|
||||
pair_style comb
|
||||
pair_coeff * * ffield.comb Cu
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
timestep 0.00020
|
||||
|
||||
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
|
||||
thermo_modify norm yes
|
||||
velocity all create 10.1 2398378
|
||||
thermo 1
|
||||
|
||||
#dump 1 all custom 10 tmp.dump id type xs ys zs q vx vy vz fx fy fz
|
||||
#dump_modify 1 append yes element Cu
|
||||
|
||||
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 2 element Cu
|
||||
|
||||
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 2 element Cu
|
||||
|
||||
run 10
|
||||
Memory usage per processor = 4.62535 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
|
||||
0 10.1 -3.5063151 -3.5076155 -3.5076155 0 27.496055 3023.4645 14.46 14.46 14.46 0
|
||||
1 10.099638 -3.5063151 -3.5076155 -3.5076155 0 27.513531 3023.4645 14.46 14.46 14.46 0
|
||||
2 10.098553 -3.5063151 -3.5076153 -3.5076153 0 27.565957 3023.4645 14.46 14.46 14.46 0
|
||||
3 10.096744 -3.5063151 -3.5076151 -3.5076151 0 27.653322 3023.4645 14.46 14.46 14.46 0
|
||||
4 10.094212 -3.5063151 -3.5076148 -3.5076148 0 27.775611 3023.4645 14.46 14.46 14.46 0
|
||||
5 10.090958 -3.5063151 -3.5076144 -3.5076144 0 27.932801 3023.4645 14.46 14.46 14.46 0
|
||||
6 10.086981 -3.5063151 -3.5076139 -3.5076139 0 28.124863 3023.4645 14.46 14.46 14.46 0
|
||||
7 10.082283 -3.5063151 -3.5076132 -3.5076132 0 28.351761 3023.4645 14.46 14.46 14.46 0
|
||||
8 10.076864 -3.5063151 -3.5076125 -3.5076125 0 28.613454 3023.4645 14.46 14.46 14.46 0
|
||||
9 10.070725 -3.5063151 -3.5076118 -3.5076118 0 28.909893 3023.4645 14.46 14.46 14.46 0
|
||||
10 10.063868 -3.5063151 -3.5076109 -3.5076109 0 29.241022 3023.4645 14.46 14.46 14.46 0
|
||||
Loop time of 0.0488312 on 4 procs for 10 steps with 256 atoms
|
||||
|
||||
Pair time (%) = 0.0467316 (95.7003)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.0016737 (3.42752)
|
||||
Outpt time (%) = 0.000292957 (0.599938)
|
||||
Other time (%) = 0.000132918 (0.2722)
|
||||
|
||||
Nlocal: 64 ave 64 max 64 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2971 ave 2971 max 2971 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 43136 ave 43136 max 43136 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 172544
|
||||
Ave neighs/atom = 674
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,316 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Cu2O crystal, qeq on, minimizes, then calculates elastic constants
|
||||
|
||||
units metal
|
||||
atom_style charge
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
read_data data.Cu2O
|
||||
triclinic box = (0 0 0) to (25.62 25.62 25.62) with tilt (0 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1296 atoms
|
||||
mass 1 63.54
|
||||
group type1 type 1
|
||||
864 atoms in group type1
|
||||
compute charge1 type1 property/atom q
|
||||
compute q1 type1 reduce ave c_charge1
|
||||
mass 2 16.00
|
||||
group type2 type 2
|
||||
432 atoms in group type2
|
||||
compute charge2 type2 property/atom q
|
||||
compute q2 type2 reduce ave c_charge2
|
||||
|
||||
velocity all create 1.0 277387
|
||||
|
||||
pair_style comb
|
||||
pair_coeff * * ffield.comb Cu O
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
timestep 0.00020
|
||||
|
||||
thermo_style custom step temp etotal pe evdwl ecoul c_q1 c_q2 lx ly lz vol
|
||||
thermo_modify norm yes
|
||||
thermo 1
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/comb 1 0.0001
|
||||
|
||||
#dump 1 all cfg 1 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
|
||||
#dump_modify 1 element Cu O
|
||||
|
||||
run 2
|
||||
Memory usage per processor = 11.5578 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
|
||||
0 1 -3.8383547 -3.8384838 -1.1478494 -2.6906344 0.7228352 -1.4456704 25.62 25.62 25.62 16816.568
|
||||
1 0.99939067 -3.8453114 -3.8454405 -0.98378996 -2.8616505 0.72283606 -1.4456721 25.62 25.62 25.62 16816.568
|
||||
2 0.9975671 -3.8453114 -3.8454402 -0.98378316 -2.8616571 0.72283727 -1.4456745 25.62 25.62 25.62 16816.568
|
||||
Loop time of 0.302742 on 1 procs for 2 steps with 1296 atoms
|
||||
|
||||
Pair time (%) = 0.102108 (33.7277)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000131845 (0.0435504)
|
||||
Outpt time (%) = 4.91142e-05 (0.0162231)
|
||||
Other time (%) = 0.200453 (66.2125)
|
||||
|
||||
Nlocal: 1296 ave 1296 max 1296 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 8243 ave 8243 max 8243 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 810432 ave 810432 max 810432 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 810432
|
||||
Ave neighs/atom = 625.333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
fix 1 all box/relax aniso 0.0 vmax 0.001
|
||||
minimize 1.0e-14 1.0e-20 1000 10000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
|
||||
Memory usage per processor = 12.8548 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
|
||||
2 0.9975671 -3.8453114 -3.8454402 -0.98377395 -2.8616663 0.72283727 -1.4456745 25.62 25.62 25.62 16816.568
|
||||
3 0.9975671 -3.8453323 -3.8454611 -0.98048803 -2.8649731 0.72283983 -1.4456797 25.59438 25.59438 25.59438 16766.169
|
||||
4 0.9975671 -3.8453323 -3.8454611 -0.98046852 -2.8649926 0.72283983 -1.4456797 25.59438 25.59438 25.59438 16766.169
|
||||
Loop time of 1.30625 on 1 procs for 2 steps with 1296 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = linesearch alpha is zero
|
||||
Energy initial, next-to-last, final =
|
||||
-3.84544021729 -3.84546110694 -3.84546110755
|
||||
Force two-norm initial, final = 14.2445 25.7656
|
||||
Force max component initial, final = 8.22308 14.8753
|
||||
Final line search alpha, max atom move = 1.64125e-08 2.4414e-07
|
||||
Iterations, force evaluations = 2 14
|
||||
|
||||
Pair time (%) = 0.772175 (59.1137)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000988007 (0.0756367)
|
||||
Outpt time (%) = 2.5034e-05 (0.00191647)
|
||||
Other time (%) = 0.533065 (40.8087)
|
||||
|
||||
Nlocal: 1296 ave 1296 max 1296 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 8243 ave 8243 max 8243 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 810432 ave 810432 max 810432 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 810432
|
||||
Ave neighs/atom = 625.333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
min_modify dmax 0.2 line quadratic
|
||||
|
||||
unfix 1
|
||||
fix 1 all nve
|
||||
run 1
|
||||
Memory usage per processor = 11.7345 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
|
||||
4 0.9975671 -3.8453323 -3.8454611 -0.98046852 -2.8649926 0.72283983 -1.4456797 25.59438 25.59438 25.59438 16766.169
|
||||
5 0.9945563 -3.8453323 -3.8454607 -0.98046814 -2.8649926 0.72284124 -1.4456825 25.59438 25.59438 25.59438 16766.169
|
||||
Loop time of 0.169246 on 1 procs for 1 steps with 1296 atoms
|
||||
|
||||
Pair time (%) = 0.0514591 (30.4049)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 6.58035e-05 (0.0388804)
|
||||
Outpt time (%) = 2.40803e-05 (0.014228)
|
||||
Other time (%) = 0.117697 (69.542)
|
||||
|
||||
Nlocal: 1296 ave 1296 max 1296 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 8243 ave 8243 max 8243 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 810432 ave 810432 max 810432 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 810432
|
||||
Ave neighs/atom = 625.333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
unfix 2
|
||||
#undump 1
|
||||
|
||||
### copy lines after this to any input script for elastic calculations ###
|
||||
## Elastic constants calculations: strain box, measure box stress
|
||||
## strain x, measure s_x, s_y, s_z, s_yz:
|
||||
## calculates C11, C12, C13 and C14
|
||||
|
||||
fix 2 all deform 1 x scale 1.0001 remap x
|
||||
compute perfx all stress/atom pair
|
||||
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
|
||||
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:665)
|
||||
run 10
|
||||
Memory usage per processor = 8.71237 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
|
||||
5 25.59438 25.59438 25.59438 0 0 0 -23809505 -23809514 -23809500 -57057.987 -66762.08 -48486.839
|
||||
6 25.594636 25.59438 25.59438 0 0 0 -23809505 -23809514 -23809500 -57057.987 -66762.08 -48486.839
|
||||
7 25.594892 25.59438 25.59438 0 0 0 -23480575 -23788468 -23788455 -57056.844 -66760.744 -48482.078
|
||||
8 25.595148 25.59438 25.59438 0 0 0 -23151645 -23767428 -23767415 -57055.702 -66759.409 -48477.317
|
||||
9 25.595404 25.59438 25.59438 0 0 0 -22822715 -23746393 -23746380 -57054.56 -66758.075 -48472.557
|
||||
10 25.59566 25.59438 25.59438 0 0 0 -22493785 -23725364 -23725351 -57053.418 -66756.741 -48467.797
|
||||
11 25.595916 25.59438 25.59438 0 0 0 -22164855 -23704340 -23704327 -57052.278 -66755.407 -48463.036
|
||||
12 25.596172 25.59438 25.59438 0 0 0 -21835925 -23683322 -23683309 -57051.137 -66754.073 -48458.277
|
||||
13 25.596428 25.59438 25.59438 0 0 0 -21506996 -23662310 -23662296 -57049.997 -66752.739 -48453.517
|
||||
14 25.596684 25.59438 25.59438 0 0 0 -21178067 -23641302 -23641289 -57048.858 -66751.404 -48448.758
|
||||
15 25.59694 25.59438 25.59438 0 0 0 -20849138 -23620300 -23620287 -57047.718 -66750.07 -48443.999
|
||||
Loop time of 0.623819 on 1 procs for 10 steps with 1296 atoms
|
||||
|
||||
Pair time (%) = 0.619949 (99.3796)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000663996 (0.10644)
|
||||
Outpt time (%) = 0.00292301 (0.468567)
|
||||
Other time (%) = 0.000283003 (0.0453662)
|
||||
|
||||
Nlocal: 1296 ave 1296 max 1296 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 8243 ave 8243 max 8243 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 810432 ave 810432 max 810432 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 810432
|
||||
Ave neighs/atom = 625.333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
## strain z, measure s_z: calculates C33
|
||||
|
||||
fix 2 all deform 1 z scale 1.0001 remap x
|
||||
compute perfz all stress/atom pair
|
||||
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
|
||||
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
|
||||
run 10
|
||||
Memory usage per processor = 9.22946 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
|
||||
15 25.59694 25.59438 25.59438 0 0 0 -20520209 -23599304 -23599291 -57046.578 -66748.736 -48439.241
|
||||
16 25.59694 25.59438 25.594636 0 0 0 -20520209 -23599304 -23599291 -57046.578 -66748.736 -48439.241
|
||||
17 25.59694 25.59438 25.594892 0 0 0 -20499216 -23578254 -23270413 -57040.979 -66747.401 -48438.271
|
||||
18 25.59694 25.59438 25.595148 0 0 0 -20478228 -23557209 -22941536 -57035.38 -66746.066 -48437.301
|
||||
19 25.59694 25.59438 25.595404 0 0 0 -20457246 -23536169 -22612658 -57029.782 -66744.731 -48436.331
|
||||
20 25.59694 25.59438 25.59566 0 0 0 -20436270 -23515135 -22283781 -57024.183 -66743.396 -48435.361
|
||||
21 25.59694 25.59438 25.595916 0 0 0 -20415299 -23494106 -21954904 -57018.585 -66742.061 -48434.392
|
||||
22 25.59694 25.59438 25.596172 0 0 0 -20394333 -23473083 -21626027 -57012.986 -66740.726 -48433.423
|
||||
23 25.59694 25.59438 25.596428 0 0 0 -20373373 -23452065 -21297150 -57007.388 -66739.391 -48432.453
|
||||
24 25.59694 25.59438 25.596684 0 0 0 -20352419 -23431053 -20968274 -57001.79 -66738.056 -48431.485
|
||||
25 25.59694 25.59438 25.59694 0 0 0 -20331470 -23410046 -20639397 -56996.192 -66736.721 -48430.516
|
||||
Loop time of 0.623835 on 1 procs for 10 steps with 1296 atoms
|
||||
|
||||
Pair time (%) = 0.620008 (99.3865)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000666618 (0.106858)
|
||||
Outpt time (%) = 0.00287819 (0.46137)
|
||||
Other time (%) = 0.000282288 (0.0452504)
|
||||
|
||||
Nlocal: 1296 ave 1296 max 1296 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 8243 ave 8243 max 8243 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 810432 ave 810432 max 810432 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 810432
|
||||
Ave neighs/atom = 625.333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
## strain yz, measure s_yz: calculates C44
|
||||
|
||||
fix 2 all deform 1 yz erate 0.0001 remap x
|
||||
compute perfyz all stress/atom pair
|
||||
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
|
||||
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
|
||||
run 10
|
||||
Memory usage per processor = 9.74655 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
|
||||
25 25.59694 25.59438 25.59694 0 0 0 -20310526 -23389045 -20310521 -56990.594 -66735.386 -48429.546
|
||||
26 25.59694 25.59438 25.59694 0 0 5.1193879e-07 -20310526 -23389045 -20310521 -56990.594 -66735.386 -48429.546
|
||||
27 25.59694 25.59438 25.59694 0 0 1.0238776e-06 -20310526 -23389045 -20310521 -56990.588 -66735.38 -48165.079
|
||||
28 25.59694 25.59438 25.59694 0 0 1.5358164e-06 -20310526 -23389045 -20310521 -56990.582 -66735.374 -47900.611
|
||||
29 25.59694 25.59438 25.59694 0 0 2.0477552e-06 -20310526 -23389045 -20310521 -56990.577 -66735.368 -47636.143
|
||||
30 25.59694 25.59438 25.59694 0 0 2.559694e-06 -20310526 -23389045 -20310521 -56990.571 -66735.362 -47371.676
|
||||
31 25.59694 25.59438 25.59694 0 0 3.0716328e-06 -20310526 -23389045 -20310521 -56990.565 -66735.356 -47107.208
|
||||
32 25.59694 25.59438 25.59694 0 0 3.5835716e-06 -20310526 -23389045 -20310521 -56990.56 -66735.35 -46842.74
|
||||
33 25.59694 25.59438 25.59694 0 0 4.0955103e-06 -20310526 -23389045 -20310521 -56990.554 -66735.344 -46578.272
|
||||
34 25.59694 25.59438 25.59694 0 0 4.6074491e-06 -20310526 -23389045 -20310521 -56990.548 -66735.338 -46313.805
|
||||
35 25.59694 25.59438 25.59694 0 0 5.1193879e-06 -20310526 -23389045 -20310521 -56990.542 -66735.332 -46049.337
|
||||
Loop time of 0.624007 on 1 procs for 10 steps with 1296 atoms
|
||||
|
||||
Pair time (%) = 0.620168 (99.3848)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000666857 (0.106867)
|
||||
Outpt time (%) = 0.00289488 (0.463918)
|
||||
Other time (%) = 0.000277042 (0.0443973)
|
||||
|
||||
Nlocal: 1296 ave 1296 max 1296 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 8243 ave 8243 max 8243 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 810432 ave 810432 max 810432 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 810432
|
||||
Ave neighs/atom = 625.333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
## strain xy, measure s_xy: calculates C66
|
||||
|
||||
fix 2 all deform 1 xy erate 0.0001 remap x
|
||||
compute perfxy all stress/atom pair
|
||||
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
|
||||
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
|
||||
run 10
|
||||
Memory usage per processor = 10.2636 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
|
||||
35 25.59694 25.59438 25.59694 0 0 5.1193879e-06 -20310526 -23389045 -20310521 -56990.537 -66735.326 -45784.869
|
||||
36 25.59694 25.59438 25.59694 5.118876e-07 0 5.1193879e-06 -20310526 -23389045 -20310521 -56990.537 -66735.326 -45784.869
|
||||
37 25.59694 25.59438 25.59694 1.0237752e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -56726.131 -66735.322 -45784.862
|
||||
38 25.59694 25.59438 25.59694 1.5356628e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -56461.725 -66735.318 -45784.855
|
||||
39 25.59694 25.59438 25.59694 2.0475504e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -56197.318 -66735.314 -45784.848
|
||||
40 25.59694 25.59438 25.59694 2.559438e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55932.912 -66735.31 -45784.841
|
||||
41 25.59694 25.59438 25.59694 3.0713256e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55668.506 -66735.306 -45784.834
|
||||
42 25.59694 25.59438 25.59694 3.5832132e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55404.1 -66735.302 -45784.827
|
||||
43 25.59694 25.59438 25.59694 4.0951008e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55139.694 -66735.298 -45784.82
|
||||
44 25.59694 25.59438 25.59694 4.6069884e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -54875.288 -66735.294 -45784.813
|
||||
45 25.59694 25.59438 25.59694 5.118876e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -54610.882 -66735.29 -45784.806
|
||||
Loop time of 0.623936 on 1 procs for 10 steps with 1296 atoms
|
||||
|
||||
Pair time (%) = 0.620081 (99.3821)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000681162 (0.109172)
|
||||
Outpt time (%) = 0.00288105 (0.461754)
|
||||
Other time (%) = 0.000293016 (0.0469626)
|
||||
|
||||
Nlocal: 1296 ave 1296 max 1296 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 8243 ave 8243 max 8243 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 810432 ave 810432 max 810432 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 810432
|
||||
Ave neighs/atom = 625.333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,316 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Cu2O crystal, qeq on, minimizes, then calculates elastic constants
|
||||
|
||||
units metal
|
||||
atom_style charge
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
read_data data.Cu2O
|
||||
triclinic box = (0 0 0) to (25.62 25.62 25.62) with tilt (0 0 0)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
1296 atoms
|
||||
mass 1 63.54
|
||||
group type1 type 1
|
||||
864 atoms in group type1
|
||||
compute charge1 type1 property/atom q
|
||||
compute q1 type1 reduce ave c_charge1
|
||||
mass 2 16.00
|
||||
group type2 type 2
|
||||
432 atoms in group type2
|
||||
compute charge2 type2 property/atom q
|
||||
compute q2 type2 reduce ave c_charge2
|
||||
|
||||
velocity all create 1.0 277387
|
||||
|
||||
pair_style comb
|
||||
pair_coeff * * ffield.comb Cu O
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
timestep 0.00020
|
||||
|
||||
thermo_style custom step temp etotal pe evdwl ecoul c_q1 c_q2 lx ly lz vol
|
||||
thermo_modify norm yes
|
||||
thermo 1
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/comb 1 0.0001
|
||||
|
||||
#dump 1 all cfg 1 *.cfg id type xs ys zs q f_2 vx vy vz fx fy fz
|
||||
#dump_modify 1 element Cu O
|
||||
|
||||
run 2
|
||||
Memory usage per processor = 6.52912 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
|
||||
0 1 -3.8383547 -3.8384838 -1.1478494 -2.6906344 0.7228352 -1.4456704 25.62 25.62 25.62 16816.568
|
||||
1 0.99939067 -3.8453114 -3.8454405 -0.98378996 -2.8616505 0.72283606 -1.4456721 25.62 25.62 25.62 16816.568
|
||||
2 0.9975671 -3.8453114 -3.8454402 -0.98378316 -2.8616571 0.72283727 -1.4456745 25.62 25.62 25.62 16816.568
|
||||
Loop time of 0.079618 on 4 procs for 2 steps with 1296 atoms
|
||||
|
||||
Pair time (%) = 0.0258412 (32.4565)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000640452 (0.804406)
|
||||
Outpt time (%) = 7.51615e-05 (0.0944026)
|
||||
Other time (%) = 0.0530612 (66.6447)
|
||||
|
||||
Nlocal: 324 ave 324 max 324 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4943 ave 4943 max 4943 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 202608 ave 202608 max 202608 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 810432
|
||||
Ave neighs/atom = 625.333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
fix 1 all box/relax aniso 0.0 vmax 0.001
|
||||
minimize 1.0e-14 1.0e-20 1000 10000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
|
||||
Memory usage per processor = 7.71427 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
|
||||
2 0.9975671 -3.8453114 -3.8454402 -0.98377395 -2.8616663 0.72283727 -1.4456745 25.62 25.62 25.62 16816.568
|
||||
3 0.9975671 -3.8453323 -3.8454611 -0.98048803 -2.8649731 0.72283983 -1.4456797 25.59438 25.59438 25.59438 16766.169
|
||||
4 0.9975671 -3.8453323 -3.8454611 -0.98046852 -2.8649926 0.72283983 -1.4456797 25.59438 25.59438 25.59438 16766.169
|
||||
Loop time of 0.349189 on 4 procs for 2 steps with 1296 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = linesearch alpha is zero
|
||||
Energy initial, next-to-last, final =
|
||||
-3.84544021729 -3.84546110694 -3.84546110755
|
||||
Force two-norm initial, final = 14.2445 25.7656
|
||||
Force max component initial, final = 8.22308 14.8753
|
||||
Final line search alpha, max atom move = 1.64125e-08 2.4414e-07
|
||||
Iterations, force evaluations = 2 14
|
||||
|
||||
Pair time (%) = 0.20012 (57.31)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.00572902 (1.64066)
|
||||
Outpt time (%) = 4.15444e-05 (0.0118974)
|
||||
Other time (%) = 0.143298 (41.0374)
|
||||
|
||||
Nlocal: 324 ave 331 max 321 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
Nghost: 4943 ave 4946 max 4936 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 202608 ave 207074 max 200694 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 810432
|
||||
Ave neighs/atom = 625.333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
min_modify dmax 0.2 line quadratic
|
||||
|
||||
unfix 1
|
||||
fix 1 all nve
|
||||
run 1
|
||||
Memory usage per processor = 6.68714 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul q1 q2 Lx Ly Lz Volume
|
||||
4 0.9975671 -3.8453323 -3.8454611 -0.98046852 -2.8649926 0.72283983 -1.4456797 25.59438 25.59438 25.59438 16766.169
|
||||
5 0.9945563 -3.8453323 -3.8454607 -0.98046814 -2.8649926 0.72284124 -1.4456825 25.59438 25.59438 25.59438 16766.169
|
||||
Loop time of 0.0451097 on 4 procs for 1 steps with 1296 atoms
|
||||
|
||||
Pair time (%) = 0.013331 (29.5524)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000361264 (0.800855)
|
||||
Outpt time (%) = 3.72529e-05 (0.0825828)
|
||||
Other time (%) = 0.0313802 (69.5642)
|
||||
|
||||
Nlocal: 324 ave 331 max 321 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
Nghost: 4943 ave 4946 max 4936 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 202608 ave 207074 max 200694 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 810432
|
||||
Ave neighs/atom = 625.333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
unfix 2
|
||||
#undump 1
|
||||
|
||||
### copy lines after this to any input script for elastic calculations ###
|
||||
## Elastic constants calculations: strain box, measure box stress
|
||||
## strain x, measure s_x, s_y, s_z, s_yz:
|
||||
## calculates C11, C12, C13 and C14
|
||||
|
||||
fix 2 all deform 1 x scale 1.0001 remap x
|
||||
compute perfx all stress/atom pair
|
||||
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
|
||||
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:665)
|
||||
run 10
|
||||
Memory usage per processor = 5.93235 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
|
||||
5 25.59438 25.59438 25.59438 0 0 0 -23809505 -23809514 -23809500 -57057.987 -66762.08 -48486.839
|
||||
6 25.594636 25.59438 25.59438 0 0 0 -23809505 -23809514 -23809500 -57057.987 -66762.08 -48486.839
|
||||
7 25.594892 25.59438 25.59438 0 0 0 -23480575 -23788468 -23788455 -57056.844 -66760.744 -48482.078
|
||||
8 25.595148 25.59438 25.59438 0 0 0 -23151645 -23767428 -23767415 -57055.702 -66759.409 -48477.317
|
||||
9 25.595404 25.59438 25.59438 0 0 0 -22822715 -23746393 -23746380 -57054.56 -66758.075 -48472.557
|
||||
10 25.59566 25.59438 25.59438 0 0 0 -22493785 -23725364 -23725351 -57053.418 -66756.741 -48467.797
|
||||
11 25.595916 25.59438 25.59438 0 0 0 -22164855 -23704340 -23704327 -57052.278 -66755.407 -48463.036
|
||||
12 25.596172 25.59438 25.59438 0 0 0 -21835925 -23683322 -23683309 -57051.137 -66754.073 -48458.277
|
||||
13 25.596428 25.59438 25.59438 0 0 0 -21506996 -23662310 -23662296 -57049.997 -66752.739 -48453.517
|
||||
14 25.596684 25.59438 25.59438 0 0 0 -21178067 -23641302 -23641289 -57048.858 -66751.404 -48448.758
|
||||
15 25.59694 25.59438 25.59438 0 0 0 -20849138 -23620300 -23620287 -57047.718 -66750.07 -48443.999
|
||||
Loop time of 0.168408 on 4 procs for 10 steps with 1296 atoms
|
||||
|
||||
Pair time (%) = 0.161152 (95.6913)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.0040102 (2.38124)
|
||||
Outpt time (%) = 0.00308657 (1.83279)
|
||||
Other time (%) = 0.000159502 (0.0947117)
|
||||
|
||||
Nlocal: 324 ave 331 max 321 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
Nghost: 4943 ave 4946 max 4936 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 202608 ave 207074 max 200694 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 810432
|
||||
Ave neighs/atom = 625.333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
## strain z, measure s_z: calculates C33
|
||||
|
||||
fix 2 all deform 1 z scale 1.0001 remap x
|
||||
compute perfz all stress/atom pair
|
||||
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
|
||||
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
|
||||
run 10
|
||||
Memory usage per processor = 6.40641 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
|
||||
15 25.59694 25.59438 25.59438 0 0 0 -20520209 -23599304 -23599291 -57046.578 -66748.736 -48439.241
|
||||
16 25.59694 25.59438 25.594636 0 0 0 -20520209 -23599304 -23599291 -57046.578 -66748.736 -48439.241
|
||||
17 25.59694 25.59438 25.594892 0 0 0 -20499216 -23578254 -23270413 -57040.979 -66747.401 -48438.271
|
||||
18 25.59694 25.59438 25.595148 0 0 0 -20478228 -23557209 -22941536 -57035.38 -66746.066 -48437.301
|
||||
19 25.59694 25.59438 25.595404 0 0 0 -20457246 -23536169 -22612658 -57029.782 -66744.731 -48436.331
|
||||
20 25.59694 25.59438 25.59566 0 0 0 -20436270 -23515135 -22283781 -57024.183 -66743.396 -48435.361
|
||||
21 25.59694 25.59438 25.595916 0 0 0 -20415299 -23494106 -21954904 -57018.585 -66742.061 -48434.392
|
||||
22 25.59694 25.59438 25.596172 0 0 0 -20394333 -23473083 -21626027 -57012.986 -66740.726 -48433.423
|
||||
23 25.59694 25.59438 25.596428 0 0 0 -20373373 -23452065 -21297150 -57007.388 -66739.391 -48432.453
|
||||
24 25.59694 25.59438 25.596684 0 0 0 -20352419 -23431053 -20968274 -57001.79 -66738.056 -48431.485
|
||||
25 25.59694 25.59438 25.59694 0 0 0 -20331470 -23410046 -20639397 -56996.192 -66736.721 -48430.516
|
||||
Loop time of 0.168435 on 4 procs for 10 steps with 1296 atoms
|
||||
|
||||
Pair time (%) = 0.161198 (95.7033)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.00402051 (2.38698)
|
||||
Outpt time (%) = 0.00305879 (1.81601)
|
||||
Other time (%) = 0.000157833 (0.0937056)
|
||||
|
||||
Nlocal: 324 ave 331 max 321 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
Nghost: 4943 ave 4946 max 4936 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 202608 ave 207074 max 200694 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 810432
|
||||
Ave neighs/atom = 625.333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
## strain yz, measure s_yz: calculates C44
|
||||
|
||||
fix 2 all deform 1 yz erate 0.0001 remap x
|
||||
compute perfyz all stress/atom pair
|
||||
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
|
||||
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
|
||||
run 10
|
||||
Memory usage per processor = 6.88047 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
|
||||
25 25.59694 25.59438 25.59694 0 0 0 -20310526 -23389045 -20310521 -56990.594 -66735.386 -48429.546
|
||||
26 25.59694 25.59438 25.59694 0 0 5.1193879e-07 -20310526 -23389045 -20310521 -56990.594 -66735.386 -48429.546
|
||||
27 25.59694 25.59438 25.59694 0 0 1.0238776e-06 -20310526 -23389045 -20310521 -56990.588 -66735.38 -48165.079
|
||||
28 25.59694 25.59438 25.59694 0 0 1.5358164e-06 -20310526 -23389045 -20310521 -56990.582 -66735.374 -47900.611
|
||||
29 25.59694 25.59438 25.59694 0 0 2.0477552e-06 -20310526 -23389045 -20310521 -56990.577 -66735.368 -47636.143
|
||||
30 25.59694 25.59438 25.59694 0 0 2.559694e-06 -20310526 -23389045 -20310521 -56990.571 -66735.362 -47371.676
|
||||
31 25.59694 25.59438 25.59694 0 0 3.0716328e-06 -20310526 -23389045 -20310521 -56990.565 -66735.356 -47107.208
|
||||
32 25.59694 25.59438 25.59694 0 0 3.5835716e-06 -20310526 -23389045 -20310521 -56990.56 -66735.35 -46842.74
|
||||
33 25.59694 25.59438 25.59694 0 0 4.0955103e-06 -20310526 -23389045 -20310521 -56990.554 -66735.344 -46578.272
|
||||
34 25.59694 25.59438 25.59694 0 0 4.6074491e-06 -20310526 -23389045 -20310521 -56990.548 -66735.338 -46313.805
|
||||
35 25.59694 25.59438 25.59694 0 0 5.1193879e-06 -20310526 -23389045 -20310521 -56990.542 -66735.332 -46049.337
|
||||
Loop time of 0.168295 on 4 procs for 10 steps with 1296 atoms
|
||||
|
||||
Pair time (%) = 0.161186 (95.776)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.0039618 (2.35408)
|
||||
Outpt time (%) = 0.0029906 (1.777)
|
||||
Other time (%) = 0.000156462 (0.0929689)
|
||||
|
||||
Nlocal: 324 ave 331 max 321 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
Nghost: 4943 ave 4946 max 4936 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 202608 ave 207074 max 200694 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 810432
|
||||
Ave neighs/atom = 625.333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
## strain xy, measure s_xy: calculates C66
|
||||
|
||||
fix 2 all deform 1 xy erate 0.0001 remap x
|
||||
compute perfxy all stress/atom pair
|
||||
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
|
||||
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
|
||||
run 10
|
||||
Memory usage per processor = 7.35453 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
|
||||
35 25.59694 25.59438 25.59694 0 0 5.1193879e-06 -20310526 -23389045 -20310521 -56990.537 -66735.326 -45784.869
|
||||
36 25.59694 25.59438 25.59694 5.118876e-07 0 5.1193879e-06 -20310526 -23389045 -20310521 -56990.537 -66735.326 -45784.869
|
||||
37 25.59694 25.59438 25.59694 1.0237752e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -56726.131 -66735.322 -45784.862
|
||||
38 25.59694 25.59438 25.59694 1.5356628e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -56461.725 -66735.318 -45784.855
|
||||
39 25.59694 25.59438 25.59694 2.0475504e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -56197.318 -66735.314 -45784.848
|
||||
40 25.59694 25.59438 25.59694 2.559438e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55932.912 -66735.31 -45784.841
|
||||
41 25.59694 25.59438 25.59694 3.0713256e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55668.506 -66735.306 -45784.834
|
||||
42 25.59694 25.59438 25.59694 3.5832132e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55404.1 -66735.302 -45784.827
|
||||
43 25.59694 25.59438 25.59694 4.0951008e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -55139.694 -66735.298 -45784.82
|
||||
44 25.59694 25.59438 25.59694 4.6069884e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -54875.288 -66735.294 -45784.813
|
||||
45 25.59694 25.59438 25.59694 5.118876e-06 0 5.1193879e-06 -20310526 -23389045 -20310521 -54610.882 -66735.29 -45784.806
|
||||
Loop time of 0.16841 on 4 procs for 10 steps with 1296 atoms
|
||||
|
||||
Pair time (%) = 0.161244 (95.7444)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.00396228 (2.35275)
|
||||
Outpt time (%) = 0.00304365 (1.80728)
|
||||
Other time (%) = 0.000160992 (0.0955951)
|
||||
|
||||
Nlocal: 324 ave 331 max 321 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
Nghost: 4943 ave 4946 max 4936 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 202608 ave 207074 max 200694 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 810432
|
||||
Ave neighs/atom = 625.333
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,185 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
units metal
|
||||
atom_style charge
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
read_data data.m-HfO2
|
||||
triclinic box = (0 0 0) to (25.642 25.957 26.4845) with tilt (0 -4.46691 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1500 atoms
|
||||
#read_data data.t-HfO2
|
||||
#read_data data.c-HfO2
|
||||
|
||||
mass 1 178.0
|
||||
group type1 type 1
|
||||
500 atoms in group type1
|
||||
compute charge1 type1 property/atom q
|
||||
compute q1 type1 reduce ave c_charge1
|
||||
mass 2 16.00
|
||||
group type2 type 2
|
||||
1000 atoms in group type2
|
||||
compute charge2 type2 property/atom q
|
||||
compute q2 type2 reduce ave c_charge2
|
||||
|
||||
pair_style comb
|
||||
pair_coeff * * ffield.comb Hf O
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 10 delay 10 check yes
|
||||
|
||||
timestep 0.00020
|
||||
|
||||
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz c_q1 c_q2
|
||||
thermo_modify norm yes
|
||||
|
||||
fix 1 all nvt temp 300.0 300.0 0.1
|
||||
thermo 1
|
||||
run 1
|
||||
Memory usage per processor = 11.9784 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
|
||||
0 0 -9.4477472 -9.4477472 5.2079787 -14.655726 -34059.556 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
|
||||
1 0.044670898 -9.4477472 -9.4477529 5.207976 -14.655729 -34064.435 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
|
||||
Loop time of 0.121151 on 1 procs for 1 steps with 1500 atoms
|
||||
|
||||
Pair time (%) = 0.120976 (99.8556)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 8.29697e-05 (0.0684845)
|
||||
Outpt time (%) = 3.09944e-05 (0.0255833)
|
||||
Other time (%) = 6.10352e-05 (0.0503794)
|
||||
|
||||
Nlocal: 1500 ave 1500 max 1500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 10100 ave 10100 max 10100 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1037500
|
||||
Ave neighs/atom = 691.667
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
fix 2 all qeq/comb 1 0.003 file fq.out
|
||||
run 5
|
||||
Memory usage per processor = 17.2999 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
|
||||
1 0.044670898 -9.4477472 -9.4477529 5.207976 -14.655729 -34064.435 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
|
||||
2 0.17033122 -10.093906 -10.093928 2.6584859 -12.752413 -258416.14 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
|
||||
3 0.37132596 -10.093907 -10.093955 2.658471 -12.752426 -258451.18 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
|
||||
4 0.65401191 -10.093909 -10.093993 2.6584487 -12.752442 -258502.27 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
|
||||
5 1.0182646 -10.093912 -10.094043 2.6584191 -12.752462 -258569.36 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
|
||||
6 1.4639339 -10.093916 -10.094105 2.6583821 -12.752487 -258652.41 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
|
||||
Loop time of 0.836291 on 1 procs for 5 steps with 1500 atoms
|
||||
|
||||
Pair time (%) = 0.606207 (72.4875)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000421047 (0.050347)
|
||||
Outpt time (%) = 0.000165939 (0.0198423)
|
||||
Other time (%) = 0.229497 (27.4423)
|
||||
|
||||
Nlocal: 1500 ave 1500 max 1500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 10100 ave 10100 max 10100 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1037500
|
||||
Ave neighs/atom = 691.667
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
fix 1 all box/relax aniso 0.0 vmax 0.0002
|
||||
|
||||
# should minimize to higher tolerance in practice
|
||||
|
||||
#minimize 1.0e-12 1.0e-18 1000 10000
|
||||
minimize 1.0e-4 1.0e-6 1000 10000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
|
||||
Memory usage per processor = 18.7762 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
|
||||
6 1.4639339 -10.093916 -10.094105 2.6583821 -12.752487 -258652.41 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
|
||||
7 1.4639339 -10.094807 -10.094996 2.6556904 -12.750686 -259455.34 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
Loop time of 0.471877 on 1 procs for 1 steps with 1500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-10.0941049618 -10.0941049618 -10.0949959801
|
||||
Force two-norm initial, final = 5418.49 5437.46
|
||||
Force max component initial, final = 4082.68 4098.38
|
||||
Final line search alpha, max atom move = 4.89874e-08 0.000200769
|
||||
Iterations, force evaluations = 1 1
|
||||
|
||||
Pair time (%) = 0.242309 (51.35)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000167131 (0.0354184)
|
||||
Outpt time (%) = 0 (0)
|
||||
Other time (%) = 0.229401 (48.6146)
|
||||
|
||||
Nlocal: 1500 ave 1500 max 1500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 10100 ave 10100 max 10100 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1037500
|
||||
Ave neighs/atom = 691.667
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
min_modify dmax 0.005 line quadratic
|
||||
|
||||
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
|
||||
#dump_modify 1 element Hf O
|
||||
|
||||
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 2 element Hf O
|
||||
|
||||
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 2 element Hf O
|
||||
|
||||
velocity all create 300.1 2398378
|
||||
run 10
|
||||
Memory usage per processor = 17.2999 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
|
||||
7 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
8 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
9 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
10 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
11 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
12 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
13 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
14 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
15 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
16 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
17 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
Loop time of 1.66905 on 1 procs for 10 steps with 1500 atoms
|
||||
|
||||
Pair time (%) = 1.20968 (72.4776)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000833511 (0.0499394)
|
||||
Outpt time (%) = 0.000306129 (0.0183416)
|
||||
Other time (%) = 0.458222 (27.4542)
|
||||
|
||||
Nlocal: 1500 ave 1500 max 1500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 10100 ave 10100 max 10100 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.0375e+06 ave 1.0375e+06 max 1.0375e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1037500
|
||||
Ave neighs/atom = 691.667
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,185 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
units metal
|
||||
atom_style charge
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
read_data data.m-HfO2
|
||||
triclinic box = (0 0 0) to (25.642 25.957 26.4845) with tilt (0 -4.46691 0)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
1500 atoms
|
||||
#read_data data.t-HfO2
|
||||
#read_data data.c-HfO2
|
||||
|
||||
mass 1 178.0
|
||||
group type1 type 1
|
||||
500 atoms in group type1
|
||||
compute charge1 type1 property/atom q
|
||||
compute q1 type1 reduce ave c_charge1
|
||||
mass 2 16.00
|
||||
group type2 type 2
|
||||
1000 atoms in group type2
|
||||
compute charge2 type2 property/atom q
|
||||
compute q2 type2 reduce ave c_charge2
|
||||
|
||||
pair_style comb
|
||||
pair_coeff * * ffield.comb Hf O
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 10 delay 10 check yes
|
||||
|
||||
timestep 0.00020
|
||||
|
||||
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz c_q1 c_q2
|
||||
thermo_modify norm yes
|
||||
|
||||
fix 1 all nvt temp 300.0 300.0 0.1
|
||||
thermo 1
|
||||
run 1
|
||||
Memory usage per processor = 5.22718 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
|
||||
0 0 -9.4477472 -9.4477472 5.2079787 -14.655726 -34059.556 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
|
||||
1 0.044670898 -9.4477472 -9.4477529 5.207976 -14.655729 -34064.435 17627.802 25.642 25.957 26.4845 -4.46691 3.6 -1.8
|
||||
Loop time of 0.0313838 on 4 procs for 1 steps with 1500 atoms
|
||||
|
||||
Pair time (%) = 0.0305235 (97.2589)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000760198 (2.42226)
|
||||
Outpt time (%) = 4.77433e-05 (0.152127)
|
||||
Other time (%) = 5.23329e-05 (0.166751)
|
||||
|
||||
Nlocal: 375 ave 375 max 375 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 6075 ave 6075 max 6075 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 259375 ave 259375 max 259375 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1037500
|
||||
Ave neighs/atom = 691.667
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
fix 2 all qeq/comb 1 0.003 file fq.out
|
||||
run 5
|
||||
Memory usage per processor = 6.92136 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
|
||||
1 0.044670898 -9.4477472 -9.4477529 5.207976 -14.655729 -34064.435 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
|
||||
2 0.17033122 -10.093906 -10.093928 2.6584859 -12.752413 -258416.14 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
|
||||
3 0.37132596 -10.093907 -10.093955 2.658471 -12.752426 -258451.18 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
|
||||
4 0.65401191 -10.093909 -10.093993 2.6584487 -12.752442 -258502.27 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
|
||||
5 1.0182646 -10.093912 -10.094043 2.6584191 -12.752462 -258569.36 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
|
||||
6 1.4639339 -10.093916 -10.094105 2.6583821 -12.752487 -258652.41 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
|
||||
Loop time of 0.215946 on 4 procs for 5 steps with 1500 atoms
|
||||
|
||||
Pair time (%) = 0.152745 (70.7329)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.00467187 (2.16344)
|
||||
Outpt time (%) = 0.000242293 (0.112201)
|
||||
Other time (%) = 0.058287 (26.9915)
|
||||
|
||||
Nlocal: 375 ave 375 max 375 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 6075 ave 6075 max 6075 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 259375 ave 259375 max 259375 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1037500
|
||||
Ave neighs/atom = 691.667
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
fix 1 all box/relax aniso 0.0 vmax 0.0002
|
||||
|
||||
# should minimize to higher tolerance in practice
|
||||
|
||||
#minimize 1.0e-12 1.0e-18 1000 10000
|
||||
minimize 1.0e-4 1.0e-6 1000 10000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
|
||||
Memory usage per processor = 7.6363 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
|
||||
6 1.4639339 -10.093916 -10.094105 2.6583821 -12.752487 -258652.41 17627.802 25.642 25.957 26.4845 -4.46691 3.3566023 -1.6783011
|
||||
7 1.4639339 -10.094807 -10.094996 2.6556904 -12.750686 -259455.34 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
Loop time of 0.121192 on 4 procs for 1 steps with 1500 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-10.0941049618 -10.0941049618 -10.0949959801
|
||||
Force two-norm initial, final = 5418.49 5437.46
|
||||
Force max component initial, final = 4082.68 4098.38
|
||||
Final line search alpha, max atom move = 4.89874e-08 0.000200769
|
||||
Iterations, force evaluations = 1 1
|
||||
|
||||
Pair time (%) = 0.0610258 (50.3547)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.00184089 (1.51899)
|
||||
Outpt time (%) = 0 (0)
|
||||
Other time (%) = 0.0583253 (48.1264)
|
||||
|
||||
Nlocal: 375 ave 375 max 375 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 6075 ave 6075 max 6075 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 259375 ave 259375 max 259375 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1037500
|
||||
Ave neighs/atom = 691.667
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
min_modify dmax 0.005 line quadratic
|
||||
|
||||
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
|
||||
#dump_modify 1 element Hf O
|
||||
|
||||
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 2 element Hf O
|
||||
|
||||
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 2 element Hf O
|
||||
|
||||
velocity all create 300.1 2398378
|
||||
run 10
|
||||
Memory usage per processor = 6.92136 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz q1 q2
|
||||
7 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
8 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
9 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
10 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
11 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
12 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
13 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
14 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
15 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
16 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
17 300.1 -10.056231 -10.094996 2.6556904 -12.750686 -255947.73 17620.43 25.636872 25.952673 26.483135 -4.4666797 3.3563361 -1.6781681
|
||||
Loop time of 0.431377 on 4 procs for 10 steps with 1500 atoms
|
||||
|
||||
Pair time (%) = 0.305476 (70.8142)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.00917089 (2.12596)
|
||||
Outpt time (%) = 0.000487924 (0.113108)
|
||||
Other time (%) = 0.116242 (26.9467)
|
||||
|
||||
Nlocal: 375 ave 375 max 375 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 6075 ave 6075 max 6075 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 259375 ave 259375 max 259375 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1037500
|
||||
Ave neighs/atom = 691.667
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,76 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Pure Si crystal, structure created by LAMMPS, qeq off
|
||||
|
||||
units metal
|
||||
atom_style charge
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
lattice diamond 5.43
|
||||
Lattice spacing in x,y,z = 5.43 5.43 5.43
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (21.72 21.72 21.72)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 512 atoms
|
||||
mass 1 29.0
|
||||
|
||||
pair_style comb
|
||||
pair_coeff * * ffield.comb Si
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
timestep 0.00020
|
||||
|
||||
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
|
||||
thermo_modify norm yes
|
||||
velocity all create 10.1 2398378
|
||||
thermo 1
|
||||
|
||||
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
|
||||
#dump_modify 1 append yes element Si
|
||||
|
||||
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 2 element Si
|
||||
|
||||
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 2 element Si
|
||||
|
||||
run 10
|
||||
Memory usage per processor = 5.5122 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
|
||||
0 10.1 -4.6284152 -4.6297182 -4.6297182 0 1140.7851 10246.592 21.72 21.72 21.72 0
|
||||
1 10.097843 -4.6284152 -4.6297179 -4.6297179 0 1140.8131 10246.592 21.72 21.72 21.72 0
|
||||
2 10.091376 -4.6284152 -4.6297171 -4.6297171 0 1140.8972 10246.592 21.72 21.72 21.72 0
|
||||
3 10.080606 -4.6284152 -4.6297157 -4.6297157 0 1141.0373 10246.592 21.72 21.72 21.72 0
|
||||
4 10.065546 -4.6284152 -4.6297137 -4.6297137 0 1141.233 10246.592 21.72 21.72 21.72 0
|
||||
5 10.046214 -4.6284152 -4.6297113 -4.6297113 0 1141.4842 10246.592 21.72 21.72 21.72 0
|
||||
6 10.022634 -4.6284152 -4.6297082 -4.6297082 0 1141.7906 10246.592 21.72 21.72 21.72 0
|
||||
7 9.9948348 -4.6284152 -4.6297046 -4.6297046 0 1142.1515 10246.592 21.72 21.72 21.72 0
|
||||
8 9.9628496 -4.6284152 -4.6297005 -4.6297005 0 1142.5666 10246.592 21.72 21.72 21.72 0
|
||||
9 9.9267173 -4.6284152 -4.6296958 -4.6296958 0 1143.0353 10246.592 21.72 21.72 21.72 0
|
||||
10 9.8864817 -4.6284152 -4.6296906 -4.6296906 0 1143.5568 10246.592 21.72 21.72 21.72 0
|
||||
Loop time of 0.134541 on 1 procs for 10 steps with 512 atoms
|
||||
|
||||
Pair time (%) = 0.13386 (99.4939)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000366688 (0.272547)
|
||||
Outpt time (%) = 0.000138283 (0.102781)
|
||||
Other time (%) = 0.000175953 (0.13078)
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4861 ave 4861 max 4861 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 212992 ave 212992 max 212992 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 212992
|
||||
Ave neighs/atom = 416
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,76 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Pure Si crystal, structure created by LAMMPS, qeq off
|
||||
|
||||
units metal
|
||||
atom_style charge
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
lattice diamond 5.43
|
||||
Lattice spacing in x,y,z = 5.43 5.43 5.43
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (21.72 21.72 21.72)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 512 atoms
|
||||
mass 1 29.0
|
||||
|
||||
pair_style comb
|
||||
pair_coeff * * ffield.comb Si
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 1 delay 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
timestep 0.00020
|
||||
|
||||
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz xz
|
||||
thermo_modify norm yes
|
||||
velocity all create 10.1 2398378
|
||||
thermo 1
|
||||
|
||||
#dump 1 all cfg 10 *.cfg id type xs ys zs q vx vy vz fx fy fz
|
||||
#dump_modify 1 append yes element Si
|
||||
|
||||
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 2 element Si
|
||||
|
||||
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 2 element Si
|
||||
|
||||
run 10
|
||||
Memory usage per processor = 4.66323 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz Xz
|
||||
0 10.1 -4.6284152 -4.6297182 -4.6297182 0 1140.7851 10246.592 21.72 21.72 21.72 0
|
||||
1 10.097841 -4.6284152 -4.6297179 -4.6297179 0 1140.8134 10246.592 21.72 21.72 21.72 0
|
||||
2 10.091367 -4.6284152 -4.6297171 -4.6297171 0 1140.8983 10246.592 21.72 21.72 21.72 0
|
||||
3 10.080586 -4.6284152 -4.6297157 -4.6297157 0 1141.0397 10246.592 21.72 21.72 21.72 0
|
||||
4 10.065511 -4.6284152 -4.6297137 -4.6297137 0 1141.2373 10246.592 21.72 21.72 21.72 0
|
||||
5 10.046161 -4.6284152 -4.6297112 -4.6297112 0 1141.4909 10246.592 21.72 21.72 21.72 0
|
||||
6 10.02256 -4.6284152 -4.6297082 -4.6297082 0 1141.8001 10246.592 21.72 21.72 21.72 0
|
||||
7 9.9947353 -4.6284152 -4.6297046 -4.6297046 0 1142.1645 10246.592 21.72 21.72 21.72 0
|
||||
8 9.9627224 -4.6284152 -4.6297005 -4.6297005 0 1142.5835 10246.592 21.72 21.72 21.72 0
|
||||
9 9.9265602 -4.6284152 -4.6296958 -4.6296958 0 1143.0565 10246.592 21.72 21.72 21.72 0
|
||||
10 9.8862927 -4.6284152 -4.6296906 -4.6296906 0 1143.5829 10246.592 21.72 21.72 21.72 0
|
||||
Loop time of 0.0370951 on 4 procs for 10 steps with 512 atoms
|
||||
|
||||
Pair time (%) = 0.034411 (92.7644)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.00227368 (6.12933)
|
||||
Outpt time (%) = 0.000264704 (0.713583)
|
||||
Other time (%) = 0.000145674 (0.392704)
|
||||
|
||||
Nlocal: 128 ave 128 max 128 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3073 ave 3073 max 3073 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 53248 ave 53248 max 53248 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 212992
|
||||
Ave neighs/atom = 416
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,274 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
|
||||
|
||||
units metal
|
||||
atom_style charge
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
lattice diamond 5.431
|
||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 512 atoms
|
||||
mass 1 29.0
|
||||
change_box all triclinic
|
||||
triclinic box = (0 0 0) to (21.724 21.724 21.724) with tilt (0 0 0)
|
||||
|
||||
velocity all create 1.0 277387
|
||||
|
||||
pair_style comb
|
||||
pair_coeff * * ffield.comb Si
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all box/relax aniso 0.0 vmax 0.001
|
||||
timestep 0.00020
|
||||
|
||||
thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz
|
||||
thermo_modify norm yes
|
||||
thermo 1
|
||||
minimize 1.0e-14 1.0e-20 1000 10000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
|
||||
Memory usage per processor = 6.19884 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul
|
||||
0 1 -4.6295947 -4.6297237 -4.6297237 0
|
||||
1 1 -4.6295963 -4.6297253 -4.6297253 0
|
||||
2 1 -4.6295965 -4.6297255 -4.6297255 0
|
||||
3 1 -4.6295965 -4.6297255 -4.6297255 0
|
||||
Loop time of 0.229516 on 1 procs for 3 steps with 512 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = linesearch alpha is zero
|
||||
Energy initial, next-to-last, final =
|
||||
-4.62972371535 -4.62972550036 -4.62972550036
|
||||
Force two-norm initial, final = 5.86582 0.235602
|
||||
Force max component initial, final = 3.38663 0.136025
|
||||
Final line search alpha, max atom move = 0.000114869 1.5625e-05
|
||||
Iterations, force evaluations = 3 16
|
||||
|
||||
Pair time (%) = 0.22687 (98.8473)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000636816 (0.27746)
|
||||
Outpt time (%) = 1.88351e-05 (0.00820643)
|
||||
Other time (%) = 0.00199008 (0.867077)
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4861 ave 4861 max 4861 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 212992 ave 212992 max 212992 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 212992
|
||||
Ave neighs/atom = 416
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
min_modify dmax 0.2 line quadratic
|
||||
|
||||
unfix 1
|
||||
run 1
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:54)
|
||||
Memory usage per processor = 5.20702 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul
|
||||
3 1 -4.6295965 -4.6297255 -4.6297255 0
|
||||
4 1 -4.6295965 -4.6297255 -4.6297255 0
|
||||
Loop time of 0.0133381 on 1 procs for 1 steps with 512 atoms
|
||||
|
||||
Pair time (%) = 0.0132809 (99.571)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 3.91006e-05 (0.29315)
|
||||
Outpt time (%) = 1.00136e-05 (0.0750751)
|
||||
Other time (%) = 8.10623e-06 (0.0607751)
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4861 ave 4861 max 4861 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 212992 ave 212992 max 212992 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 212992
|
||||
Ave neighs/atom = 416
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
### copy lines after this to any input script for elastic calculations ###
|
||||
## Elastic constants calculations: strain box, measure box stress
|
||||
## strain x, measure s_x, s_y, s_z, s_yz:
|
||||
## calculates C11, C12, C13 and C14
|
||||
|
||||
fix 2 all deform 1 x scale 1.0001 remap x
|
||||
compute perfx all stress/atom pair
|
||||
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
|
||||
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:665)
|
||||
run 10
|
||||
Memory usage per processor = 5.66478 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
|
||||
4 21.728073 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 4.2424409e-06 1.8970431e-06 5.2226895e-06
|
||||
5 21.728291 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 3.0659899e-06 3.6846991e-06 4.9259641e-06
|
||||
6 21.728508 21.728073 21.728073 0 0 0 364177.1 295296.39 295296.39 3.8875089e-06 2.372335e-06 4.6875974e-06
|
||||
7 21.728725 21.728073 21.728073 0 0 0 510377.09 372612.84 372612.84 3.2832708e-06 3.8145125e-06 4.6443213e-06
|
||||
8 21.728942 21.728073 21.728073 0 0 0 656576.36 449925.76 449925.76 4.0254046e-06 3.7666561e-06 1.4753812e-07
|
||||
9 21.72916 21.728073 21.728073 0 0 0 802774.92 527235.13 527235.13 -5.7956471e-06 -1.771899e-06 2.0927452e-06
|
||||
10 21.729377 21.728073 21.728073 0 0 0 948972.76 604540.97 604540.97 3.4378795e-06 3.6072928e-06 1.6693231e-06
|
||||
11 21.729594 21.728073 21.728073 0 0 0 1095169.9 681843.26 681843.26 3.4064842e-06 3.1661348e-06 1.1859415e-06
|
||||
12 21.729811 21.728073 21.728073 0 0 0 1241366.3 759142.02 759142.02 3.3766971e-06 3.2790869e-06 1.2694808e-06
|
||||
13 21.730029 21.728073 21.728073 0 0 0 1387562 836437.23 836437.23 3.7553942e-06 3.4602587e-06 1.8958276e-06
|
||||
14 21.730246 21.728073 21.728073 0 0 0 1533757 913728.91 913728.91 -5.8836668e-06 -5.4578803e-06 1.5156445e-06
|
||||
Loop time of 0.159919 on 1 procs for 10 steps with 512 atoms
|
||||
|
||||
Pair time (%) = 0.157728 (98.63)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000384331 (0.240328)
|
||||
Outpt time (%) = 0.00167108 (1.04495)
|
||||
Other time (%) = 0.000135422 (0.0846815)
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4861 ave 4861 max 4861 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 212992 ave 212992 max 212992 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 212992
|
||||
Ave neighs/atom = 416
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
## strain z, measure s_z: calculates C33
|
||||
|
||||
fix 2 all deform 1 z scale 1.0001 remap x
|
||||
compute perfz all stress/atom pair
|
||||
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
|
||||
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
|
||||
run 10
|
||||
Memory usage per processor = 6.12255 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
|
||||
14 21.730246 21.728073 21.728073 0 0 0 1679951.2 991017.05 991017.05 4.4203553e-06 1.7546449e-06 3.8696804e-06
|
||||
15 21.730246 21.728073 21.728291 0 0 0 1679951.2 991017.05 991017.05 3.4413815e-06 3.2045526e-06 3.765411e-06
|
||||
16 21.730246 21.728073 21.728508 0 0 0 1757243.6 1068312.4 1137190.1 1.9121071e-06 7.2294681e-06 4.3210997e-06
|
||||
17 21.730246 21.728073 21.728725 0 0 0 1834532.4 1145604.2 1283362.4 3.1284508e-06 3.8448888e-06 4.2955743e-06
|
||||
18 21.730246 21.728073 21.728942 0 0 0 1911817.6 1222892.5 1429534 2.6951046e-06 3.4945075e-06 -4.5517214e-06
|
||||
19 21.730246 21.728073 21.72916 0 0 0 1989099.3 1300177.3 1575704.9 -5.9762705e-07 3.542375e-06 -3.0529456e-06
|
||||
20 21.730246 21.728073 21.729377 0 0 0 2066377.5 1377458.5 1721875.1 -6.9439231e-07 3.3859393e-06 4.3147517e-06
|
||||
21 21.730246 21.728073 21.729594 0 0 0 2143652.1 1454736.2 1868044.5 -4.5695573e-07 3.4108162e-06 3.953809e-06
|
||||
22 21.730246 21.728073 21.729811 0 0 0 2220923.2 1532010.3 2014213.3 -6.2504609e-07 4.0351804e-06 4.6966692e-06
|
||||
23 21.730246 21.728073 21.730029 0 0 0 2298190.7 1609280.9 2160381.3 2.5898938e-07 4.0107779e-06 4.6632245e-06
|
||||
24 21.730246 21.728073 21.730246 0 0 0 2375454.8 1686547.9 2306548.6 -4.5460256e-07 3.6194737e-06 3.412469e-06
|
||||
Loop time of 0.160066 on 1 procs for 10 steps with 512 atoms
|
||||
|
||||
Pair time (%) = 0.157902 (98.6478)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000381947 (0.238618)
|
||||
Outpt time (%) = 0.00164986 (1.03074)
|
||||
Other time (%) = 0.000132561 (0.0828164)
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4861 ave 4861 max 4861 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 212992 ave 212992 max 212992 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 212992
|
||||
Ave neighs/atom = 416
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
## strain yz, measure s_yz: calculates C44
|
||||
|
||||
fix 2 all deform 1 yz erate 0.0001 remap x
|
||||
compute perfyz all stress/atom pair
|
||||
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
|
||||
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
|
||||
run 10
|
||||
Memory usage per processor = 6.58031 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
|
||||
24 21.730246 21.728073 21.730246 0 0 0 2452715.2 1763811.4 2452715.2 3.1470723e-06 2.3932875e-06 3.3367488e-06
|
||||
25 21.730246 21.728073 21.730246 0 0 4.3460492e-07 2452715.2 1763811.4 2452715.2 1.7837353e-06 4.8243295e-06 2.5146962e-06
|
||||
26 21.730246 21.728073 21.730246 0 0 8.6920984e-07 2452715.2 1763811.4 2452715.2 2.8016568e-06 5.6512219e-06 243.65137
|
||||
27 21.730246 21.728073 21.730246 0 0 1.3038148e-06 2452715.2 1763811.4 2452715.2 1.9900804e-06 4.0111151e-06 487.30277
|
||||
28 21.730246 21.728073 21.730246 0 0 1.7384197e-06 2452715.2 1763811.4 2452715.2 1.762453e-06 6.1935142e-06 730.9542
|
||||
29 21.730246 21.728073 21.730246 0 0 2.1730246e-06 2452715.2 1763811.4 2452715.2 2.3991797e-06 5.493982e-06 974.60552
|
||||
30 21.730246 21.728073 21.730246 0 0 2.6076295e-06 2452715.2 1763811.4 2452715.2 2.2018322e-06 4.7607643e-06 1218.2569
|
||||
31 21.730246 21.728073 21.730246 0 0 3.0422344e-06 2452715.2 1763811.4 2452715.2 2.8680162e-06 5.6568584e-06 1461.9083
|
||||
32 21.730246 21.728073 21.730246 0 0 3.4768394e-06 2452715.2 1763811.4 2452715.2 2.2450268e-06 8.6579416e-06 1705.5598
|
||||
33 21.730246 21.728073 21.730246 0 0 3.9114443e-06 2452715.2 1763811.4 2452715.2 1.9691724e-06 8.970813e-06 1949.2111
|
||||
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2.9802012e-06 8.483733e-06 2192.8625
|
||||
Loop time of 0.15999 on 1 procs for 10 steps with 512 atoms
|
||||
|
||||
Pair time (%) = 0.157806 (98.635)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000383854 (0.239924)
|
||||
Outpt time (%) = 0.0016675 (1.04225)
|
||||
Other time (%) = 0.000132561 (0.0828556)
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4861 ave 4861 max 4861 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 212992 ave 212992 max 212992 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 212992
|
||||
Ave neighs/atom = 416
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
## strain xy, measure s_xy: calculates C66
|
||||
|
||||
fix 2 all deform 1 xy erate 0.0001 remap x
|
||||
compute perfxy all stress/atom pair
|
||||
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
|
||||
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
|
||||
run 10
|
||||
Memory usage per processor = 7.03807 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
|
||||
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 3.1183118e-06 9.8932292e-06 2436.5139
|
||||
35 21.730246 21.728073 21.730246 4.3456146e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2.5429824e-06 1.089443e-05 2436.5139
|
||||
36 21.730246 21.728073 21.730246 8.6912293e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 243.63759 -0.00011790196 2436.5139
|
||||
37 21.730246 21.728073 21.730246 1.3036844e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 487.27523 -0.00024666123 2436.5139
|
||||
38 21.730246 21.728073 21.730246 1.7382459e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 730.91287 -0.0003778327 2436.5139
|
||||
39 21.730246 21.728073 21.730246 2.1728073e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 974.55045 -0.00050731605 2436.5139
|
||||
40 21.730246 21.728073 21.730246 2.6073688e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1218.188 -0.00063724551 2436.5139
|
||||
41 21.730246 21.728073 21.730246 3.0419303e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1461.8257 -0.00076799013 2436.5139
|
||||
42 21.730246 21.728073 21.730246 3.4764917e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1705.4633 -0.00089693851 2436.5139
|
||||
43 21.730246 21.728073 21.730246 3.9110532e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1949.1009 -0.0010276841 2436.5139
|
||||
44 21.730246 21.728073 21.730246 4.3456146e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2192.7385 -0.0011569482 2436.5139
|
||||
Loop time of 0.16096 on 1 procs for 10 steps with 512 atoms
|
||||
|
||||
Pair time (%) = 0.158687 (98.5875)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.000389814 (0.242181)
|
||||
Outpt time (%) = 0.00174046 (1.0813)
|
||||
Other time (%) = 0.00014329 (0.0890217)
|
||||
|
||||
Nlocal: 512 ave 512 max 512 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4861 ave 4861 max 4861 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 212992 ave 212992 max 212992 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 212992
|
||||
Ave neighs/atom = 416
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,274 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Pure Si crystal, qeq off, calculates stress-strain, no out.*.cfg
|
||||
|
||||
units metal
|
||||
atom_style charge
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
lattice diamond 5.431
|
||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
||||
region box block 0 4 0 4 0 4
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 512 atoms
|
||||
mass 1 29.0
|
||||
change_box all triclinic
|
||||
triclinic box = (0 0 0) to (21.724 21.724 21.724) with tilt (0 0 0)
|
||||
|
||||
velocity all create 1.0 277387
|
||||
|
||||
pair_style comb
|
||||
pair_coeff * * ffield.comb Si
|
||||
|
||||
neighbor 0.5 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all box/relax aniso 0.0 vmax 0.001
|
||||
timestep 0.00020
|
||||
|
||||
thermo_style custom step temp etotal pe evdwl ecoul #lx ly lz vol pxx pyy pzz
|
||||
thermo_modify norm yes
|
||||
thermo 1
|
||||
minimize 1.0e-14 1.0e-20 1000 10000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
|
||||
Memory usage per processor = 5.35368 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul
|
||||
0 1 -4.6295947 -4.6297237 -4.6297237 0
|
||||
1 1 -4.6295963 -4.6297253 -4.6297253 0
|
||||
2 1 -4.6295965 -4.6297255 -4.6297255 0
|
||||
3 1 -4.6295965 -4.6297255 -4.6297255 0
|
||||
Loop time of 0.0760608 on 4 procs for 3 steps with 512 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = linesearch alpha is zero
|
||||
Energy initial, next-to-last, final =
|
||||
-4.62972371535 -4.62972550036 -4.62972550036
|
||||
Force two-norm initial, final = 5.86582 0.235602
|
||||
Force max component initial, final = 3.38663 0.136025
|
||||
Final line search alpha, max atom move = 0.000114869 1.5625e-05
|
||||
Iterations, force evaluations = 3 16
|
||||
|
||||
Pair time (%) = 0.0578517 (76.0599)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.0166439 (21.8823)
|
||||
Outpt time (%) = 3.75509e-05 (0.0493696)
|
||||
Other time (%) = 0.00152761 (2.0084)
|
||||
|
||||
Nlocal: 128 ave 164 max 100 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
Nghost: 3073 ave 3101 max 3037 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 53248 ave 68224 max 41600 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 212992
|
||||
Ave neighs/atom = 416
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
min_modify dmax 0.2 line quadratic
|
||||
|
||||
unfix 1
|
||||
run 1
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:54)
|
||||
Memory usage per processor = 4.36186 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul
|
||||
3 1 -4.6295965 -4.6297255 -4.6297255 0
|
||||
4 1 -4.6295965 -4.6297255 -4.6297255 0
|
||||
Loop time of 0.00442469 on 4 procs for 1 steps with 512 atoms
|
||||
|
||||
Pair time (%) = 0.00335443 (75.8116)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.00102764 (23.2252)
|
||||
Outpt time (%) = 2.20537e-05 (0.498424)
|
||||
Other time (%) = 2.05636e-05 (0.464747)
|
||||
|
||||
Nlocal: 128 ave 164 max 100 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
Nghost: 3073 ave 3101 max 3037 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 53248 ave 68224 max 41600 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 212992
|
||||
Ave neighs/atom = 416
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
### copy lines after this to any input script for elastic calculations ###
|
||||
## Elastic constants calculations: strain box, measure box stress
|
||||
## strain x, measure s_x, s_y, s_z, s_yz:
|
||||
## calculates C11, C12, C13 and C14
|
||||
|
||||
fix 2 all deform 1 x scale 1.0001 remap x
|
||||
compute perfx all stress/atom pair
|
||||
compute fx all reduce sum c_perfx[1] c_perfx[2] c_perfx[3] c_perfx[4] c_perfx[5] c_perfx[6]
|
||||
thermo_style custom step lx ly lz xy xz yz c_fx[1] c_fx[2] c_fx[3] c_fx[4] c_fx[5] c_fx[6]
|
||||
WARNING: New thermo_style command, previous thermo_modify settings will be lost (../output.cpp:665)
|
||||
run 10
|
||||
Memory usage per processor = 4.81962 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fx[1] fx[2] fx[3] fx[4] fx[5] fx[6]
|
||||
4 21.728073 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 3.2585718e-06 8.1180987e-07 4.0306446e-06
|
||||
5 21.728291 21.728073 21.728073 0 0 0 217976.4 217976.4 217976.4 2.5758786e-06 1.8749159e-06 3.2724054e-06
|
||||
6 21.728508 21.728073 21.728073 0 0 0 364177.1 295296.39 295296.39 1.1168843e-07 -1.1628767e-06 4.899012e-06
|
||||
7 21.728725 21.728073 21.728073 0 0 0 510377.09 372612.84 372612.84 3.802339e-06 2.2938022e-06 3.4583539e-06
|
||||
8 21.728942 21.728073 21.728073 0 0 0 656576.36 449925.76 449925.76 3.6215267e-06 1.8435613e-06 -7.4389779e-07
|
||||
9 21.72916 21.728073 21.728073 0 0 0 802774.92 527235.13 527235.13 -5.064601e-06 -6.209123e-06 4.5628869e-07
|
||||
10 21.729377 21.728073 21.728073 0 0 0 948972.76 604540.97 604540.97 3.2041932e-06 1.4500411e-06 5.5267226e-07
|
||||
11 21.729594 21.728073 21.728073 0 0 0 1095169.9 681843.26 681843.26 3.1624105e-06 1.8235057e-06 7.871368e-07
|
||||
12 21.729811 21.728073 21.728073 0 0 0 1241366.3 759142.02 759142.02 2.4485703e-06 1.2810688e-06 2.6866887e-09
|
||||
13 21.730029 21.728073 21.728073 0 0 0 1387562 836437.23 836437.23 3.6571948e-06 2.3701116e-06 6.6957472e-07
|
||||
14 21.730246 21.728073 21.728073 0 0 0 1533757 913728.91 913728.91 -3.6955126e-06 -5.5104616e-06 1.1388559e-06
|
||||
Loop time of 0.0540757 on 4 procs for 10 steps with 512 atoms
|
||||
|
||||
Pair time (%) = 0.0405609 (75.0076)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.0114365 (21.149)
|
||||
Outpt time (%) = 0.00200176 (3.70178)
|
||||
Other time (%) = 7.6592e-05 (0.141638)
|
||||
|
||||
Nlocal: 128 ave 164 max 100 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
Nghost: 3073 ave 3101 max 3037 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 53248 ave 68224 max 41600 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 212992
|
||||
Ave neighs/atom = 416
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
## strain z, measure s_z: calculates C33
|
||||
|
||||
fix 2 all deform 1 z scale 1.0001 remap x
|
||||
compute perfz all stress/atom pair
|
||||
compute fz all reduce sum c_perfz[1] c_perfz[2] c_perfz[3] c_perfz[4] c_perfz[5] c_perfz[6]
|
||||
thermo_style custom step lx ly lz xy xz yz c_fz[1] c_fz[2] c_fz[3] c_fz[4] c_fz[5] c_fz[6]
|
||||
run 10
|
||||
Memory usage per processor = 5.27739 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fz[1] fz[2] fz[3] fz[4] fz[5] fz[6]
|
||||
14 21.730246 21.728073 21.728073 0 0 0 1679951.2 991017.05 991017.05 3.5908688e-06 1.1023465e-06 4.3869032e-06
|
||||
15 21.730246 21.728073 21.728291 0 0 0 1679951.2 991017.05 991017.05 3.1280098e-06 2.3099075e-06 3.2862947e-06
|
||||
16 21.730246 21.728073 21.728508 0 0 0 1757243.6 1068312.4 1137190.1 2.7484085e-06 -8.7020552e-07 2.7979177e-06
|
||||
17 21.730246 21.728073 21.728725 0 0 0 1834532.4 1145604.2 1283362.4 3.6676044e-06 2.2839782e-06 3.5535702e-06
|
||||
18 21.730246 21.728073 21.728942 0 0 0 1911817.6 1222892.5 1429534 3.9701144e-06 2.7405115e-06 -3.8363284e-06
|
||||
19 21.730246 21.728073 21.72916 0 0 0 1989099.3 1300177.3 1575704.9 6.9640455e-07 2.8451033e-06 -2.8508806e-06
|
||||
20 21.730246 21.728073 21.729377 0 0 0 2066377.5 1377458.5 1721875.1 8.7021293e-07 2.342196e-06 3.7774214e-06
|
||||
21 21.730246 21.728073 21.729594 0 0 0 2143652.1 1454736.2 1868044.5 1.346913e-06 2.6670815e-06 3.9313557e-06
|
||||
22 21.730246 21.728073 21.729811 0 0 0 2220923.2 1532010.3 2014213.3 8.4825249e-08 2.741412e-06 3.3674586e-06
|
||||
23 21.730246 21.728073 21.730029 0 0 0 2298190.7 1609280.9 2160381.3 -3.353247e-07 1.6605663e-06 3.3399914e-06
|
||||
24 21.730246 21.728073 21.730246 0 0 0 2375454.8 1686547.9 2306548.6 5.4012079e-07 2.5242571e-06 3.2038115e-06
|
||||
Loop time of 0.054018 on 4 procs for 10 steps with 512 atoms
|
||||
|
||||
Pair time (%) = 0.040496 (74.9676)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.0114477 (21.1924)
|
||||
Outpt time (%) = 0.00199842 (3.69955)
|
||||
Other time (%) = 7.58767e-05 (0.140466)
|
||||
|
||||
Nlocal: 128 ave 164 max 100 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
Nghost: 3073 ave 3101 max 3037 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 53248 ave 68224 max 41600 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 212992
|
||||
Ave neighs/atom = 416
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
## strain yz, measure s_yz: calculates C44
|
||||
|
||||
fix 2 all deform 1 yz erate 0.0001 remap x
|
||||
compute perfyz all stress/atom pair
|
||||
compute fyz all reduce sum c_perfyz[1] c_perfyz[2] c_perfyz[3] c_perfyz[4] c_perfyz[5] c_perfyz[6]
|
||||
thermo_style custom step lx ly lz xy xz yz c_fyz[1] c_fyz[2] c_fyz[3] c_fyz[4] c_fyz[5] c_fyz[6]
|
||||
run 10
|
||||
Memory usage per processor = 5.73515 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fyz[1] fyz[2] fyz[3] fyz[4] fyz[5] fyz[6]
|
||||
24 21.730246 21.728073 21.730246 0 0 0 2452715.2 1763811.4 2452715.2 2.8906214e-06 1.7666628e-06 2.9640551e-06
|
||||
25 21.730246 21.728073 21.730246 0 0 4.3460492e-07 2452715.2 1763811.4 2452715.2 1.9258037e-06 3.6230832e-06 1.33952e-06
|
||||
26 21.730246 21.728073 21.730246 0 0 8.6920984e-07 2452715.2 1763811.4 2452715.2 2.1740797e-06 5.2110496e-06 243.65137
|
||||
27 21.730246 21.728073 21.730246 0 0 1.3038148e-06 2452715.2 1763811.4 2452715.2 2.60027e-06 4.4622713e-06 487.30277
|
||||
28 21.730246 21.728073 21.730246 0 0 1.7384197e-06 2452715.2 1763811.4 2452715.2 2.3749106e-06 4.4580653e-06 730.9542
|
||||
29 21.730246 21.728073 21.730246 0 0 2.1730246e-06 2452715.2 1763811.4 2452715.2 2.3993094e-06 2.1645558e-06 974.60552
|
||||
30 21.730246 21.728073 21.730246 0 0 2.6076295e-06 2452715.2 1763811.4 2452715.2 2.787245e-06 4.7294171e-06 1218.2569
|
||||
31 21.730246 21.728073 21.730246 0 0 3.0422344e-06 2452715.2 1763811.4 2452715.2 2.691321e-06 5.1697154e-06 1461.9083
|
||||
32 21.730246 21.728073 21.730246 0 0 3.4768394e-06 2452715.2 1763811.4 2452715.2 2.9029135e-06 5.9089513e-06 1705.5598
|
||||
33 21.730246 21.728073 21.730246 0 0 3.9114443e-06 2452715.2 1763811.4 2452715.2 2.6120766e-06 3.8685242e-06 1949.2111
|
||||
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2.5647131e-06 4.7043661e-06 2192.8625
|
||||
Loop time of 0.0540408 on 4 procs for 10 steps with 512 atoms
|
||||
|
||||
Pair time (%) = 0.0404646 (74.8779)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.0114999 (21.2801)
|
||||
Outpt time (%) = 0.00199848 (3.6981)
|
||||
Other time (%) = 7.77841e-05 (0.143936)
|
||||
|
||||
Nlocal: 128 ave 164 max 100 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
Nghost: 3073 ave 3101 max 3037 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 53248 ave 68224 max 41600 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 212992
|
||||
Ave neighs/atom = 416
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
## strain xy, measure s_xy: calculates C66
|
||||
|
||||
fix 2 all deform 1 xy erate 0.0001 remap x
|
||||
compute perfxy all stress/atom pair
|
||||
compute fxy all reduce sum c_perfxy[1] c_perfxy[2] c_perfxy[3] c_perfxy[4] c_perfxy[5] c_perfxy[6]
|
||||
thermo_style custom step lx ly lz xy xz yz c_fxy[1] c_fxy[2] c_fxy[3] c_fxy[4] c_fxy[5] c_fxy[6]
|
||||
run 10
|
||||
Memory usage per processor = 6.19291 Mbytes
|
||||
Step Lx Ly Lz Xy Xz Yz fxy[1] fxy[2] fxy[3] fxy[4] fxy[5] fxy[6]
|
||||
34 21.730246 21.728073 21.730246 0 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2.8976957e-06 5.6758319e-06 2436.5139
|
||||
35 21.730246 21.728073 21.730246 4.3456146e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2.1032622e-06 7.408283e-06 2436.5139
|
||||
36 21.730246 21.728073 21.730246 8.6912293e-07 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 243.63759 -0.00012251553 2436.5139
|
||||
37 21.730246 21.728073 21.730246 1.3036844e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 487.27523 -0.00025164456 2436.5139
|
||||
38 21.730246 21.728073 21.730246 1.7382459e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 730.91287 -0.00038452391 2436.5139
|
||||
39 21.730246 21.728073 21.730246 2.1728073e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 974.55045 -0.000513424 2436.5139
|
||||
40 21.730246 21.728073 21.730246 2.6073688e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1218.188 -0.00064410321 2436.5139
|
||||
41 21.730246 21.728073 21.730246 3.0419303e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1461.8257 -0.00077446789 2436.5139
|
||||
42 21.730246 21.728073 21.730246 3.4764917e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1705.4633 -0.0009043182 2436.5139
|
||||
43 21.730246 21.728073 21.730246 3.9110532e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 1949.1009 -0.001034056 2436.5139
|
||||
44 21.730246 21.728073 21.730246 4.3456146e-06 0 4.3460492e-06 2452715.2 1763811.4 2452715.2 2192.7385 -0.0011642879 2436.5139
|
||||
Loop time of 0.0501781 on 4 procs for 10 steps with 512 atoms
|
||||
|
||||
Pair time (%) = 0.0406764 (81.0642)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0.00744313 (14.8334)
|
||||
Outpt time (%) = 0.0019834 (3.95273)
|
||||
Other time (%) = 7.51019e-05 (0.149671)
|
||||
|
||||
Nlocal: 128 ave 152 max 112 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Nghost: 3073 ave 3089 max 3049 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 53248 ave 63232 max 46592 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 212992
|
||||
Ave neighs/atom = 416
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,73 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Graphene-OH on Cu2O (110) surface
|
||||
|
||||
units metal
|
||||
atom_style charge
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
read_data data.comb3-OHCCu
|
||||
triclinic box = (0 0 0) to (21.3 24.6 23.8162) with tilt (0 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
682 atoms
|
||||
|
||||
mass 1 16.0
|
||||
mass 2 63.5
|
||||
mass 3 1.00
|
||||
mass 4 12.0
|
||||
mass 5 12.0
|
||||
|
||||
pair_style comb3 polar_off
|
||||
pair_coeff * * ffield.comb3 O Cu H C C
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
#dump 1 all cfg 10 *.cfg mass type xs ys zs id type q
|
||||
#dump_modify 1 element O Cu H C C
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/comb 10 1e-3 file fq.out
|
||||
|
||||
timestep 0.00020
|
||||
|
||||
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz
|
||||
thermo_modify norm yes
|
||||
velocity all create 300.0 2398378
|
||||
thermo 10
|
||||
run 100
|
||||
Memory usage per processor = 25.3823 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz
|
||||
0 300 -4.3728818 -4.411603 -3.8436746 -0.56792838 -21237.662 12479.212 21.3 24.6 23.8162
|
||||
10 458.94724 -4.372855 -4.4320916 -3.8642354 -0.56785622 -18031.328 12479.212 21.3 24.6 23.8162
|
||||
20 745.4043 -4.3728584 -4.4690682 -3.900652 -0.56841626 -17212.152 12479.212 21.3 24.6 23.8162
|
||||
30 919.29702 -4.3729441 -4.4915983 -3.9225391 -0.56905928 -18506.161 12479.212 21.3 24.6 23.8162
|
||||
40 966.9902 -4.3732198 -4.4980298 -3.9279672 -0.57006265 -27598.629 12479.212 21.3 24.6 23.8162
|
||||
50 954.6119 -4.3732154 -4.4964277 -3.925068 -0.5713597 -23707.986 12479.212 21.3 24.6 23.8162
|
||||
60 1052.8699 -4.3733735 -4.5092681 -3.9366105 -0.57265757 2649.3253 12479.212 21.3 24.6 23.8162
|
||||
70 1183.0233 -4.3735985 -4.526292 -3.9524058 -0.57388625 9391.824 12479.212 21.3 24.6 23.8162
|
||||
80 1248.4286 -4.373826 -4.5349614 -3.9598431 -0.5751183 12244.153 12479.212 21.3 24.6 23.8162
|
||||
90 1294.4259 -4.3741281 -4.5412004 -3.9649553 -0.57624518 17321.594 12479.212 21.3 24.6 23.8162
|
||||
100 1322.0463 -4.37436 -4.5449973 -3.9676616 -0.57733571 21583.518 12479.212 21.3 24.6 23.8162
|
||||
Loop time of 18.5024 on 1 procs for 100 steps with 682 atoms
|
||||
|
||||
Pair time (%) = 8.40819 (45.4438)
|
||||
Neigh time (%) = 0.074784 (0.404186)
|
||||
Comm time (%) = 0.00549436 (0.0296954)
|
||||
Outpt time (%) = 0.000240088 (0.0012976)
|
||||
Other time (%) = 10.0137 (54.121)
|
||||
|
||||
Nlocal: 682 ave 682 max 682 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 6390 ave 6390 max 6390 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 365314 ave 365314 max 365314 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 365314
|
||||
Ave neighs/atom = 535.651
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,73 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Graphene-OH on Cu2O (110) surface
|
||||
|
||||
units metal
|
||||
atom_style charge
|
||||
dimension 3
|
||||
boundary p p p
|
||||
|
||||
read_data data.comb3-OHCCu
|
||||
triclinic box = (0 0 0) to (21.3 24.6 23.8162) with tilt (0 0 0)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
682 atoms
|
||||
|
||||
mass 1 16.0
|
||||
mass 2 63.5
|
||||
mass 3 1.00
|
||||
mass 4 12.0
|
||||
mass 5 12.0
|
||||
|
||||
pair_style comb3 polar_off
|
||||
pair_coeff * * ffield.comb3 O Cu H C C
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 0 check yes
|
||||
|
||||
#dump 1 all cfg 10 *.cfg mass type xs ys zs id type q
|
||||
#dump_modify 1 element O Cu H C C
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/comb 10 1e-3 file fq.out
|
||||
|
||||
timestep 0.00020
|
||||
|
||||
thermo_style custom step temp etotal pe evdwl ecoul press vol lx ly lz
|
||||
thermo_modify norm yes
|
||||
velocity all create 300.0 2398378
|
||||
thermo 10
|
||||
run 100
|
||||
Memory usage per processor = 12.8135 Mbytes
|
||||
Step Temp TotEng PotEng E_vdwl E_coul Press Volume Lx Ly Lz
|
||||
0 300 -4.3728818 -4.411603 -3.8436746 -0.56792838 -21237.662 12479.212 21.3 24.6 23.8162
|
||||
10 458.94724 -4.372855 -4.4320916 -3.8642354 -0.56785622 -18031.328 12479.212 21.3 24.6 23.8162
|
||||
20 745.4043 -4.3728584 -4.4690682 -3.900652 -0.56841626 -17212.152 12479.212 21.3 24.6 23.8162
|
||||
30 919.29702 -4.3729441 -4.4915983 -3.9225391 -0.56905928 -18506.161 12479.212 21.3 24.6 23.8162
|
||||
40 966.9902 -4.3732198 -4.4980298 -3.9279672 -0.57006265 -27598.629 12479.212 21.3 24.6 23.8162
|
||||
50 954.6119 -4.3732154 -4.4964277 -3.925068 -0.5713597 -23707.986 12479.212 21.3 24.6 23.8162
|
||||
60 1052.8699 -4.3733735 -4.5092681 -3.9366105 -0.57265757 2649.3253 12479.212 21.3 24.6 23.8162
|
||||
70 1183.0233 -4.3735985 -4.526292 -3.9524058 -0.57388625 9391.824 12479.212 21.3 24.6 23.8162
|
||||
80 1248.4286 -4.373826 -4.5349614 -3.9598431 -0.5751183 12244.153 12479.212 21.3 24.6 23.8162
|
||||
90 1294.4259 -4.3741281 -4.5412004 -3.9649553 -0.57624518 17321.594 12479.212 21.3 24.6 23.8162
|
||||
100 1322.0463 -4.37436 -4.5449973 -3.9676616 -0.57733571 21583.518 12479.212 21.3 24.6 23.8162
|
||||
Loop time of 8.13762 on 4 procs for 100 steps with 682 atoms
|
||||
|
||||
Pair time (%) = 3.10767 (38.189)
|
||||
Neigh time (%) = 0.038151 (0.468823)
|
||||
Comm time (%) = 0.765678 (9.40911)
|
||||
Outpt time (%) = 0.000375092 (0.00460936)
|
||||
Other time (%) = 4.22574 (51.9285)
|
||||
|
||||
Nlocal: 170.5 ave 234 max 113 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 3861.75 ave 4574 max 3158 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 91328.5 ave 129432 max 56453 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 365314
|
||||
Ave neighs/atom = 535.651
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,138 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 2d LJ crack simulation
|
||||
|
||||
dimension 2
|
||||
boundary s s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.93
|
||||
Lattice spacing in x,y,z = 1.11428 1.92998 1.11428
|
||||
region box block 0 100 0 40 -0.25 0.25
|
||||
create_box 5 box
|
||||
Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 8141 atoms
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
mass 4 1.0
|
||||
mass 5 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
302 atoms in group lower
|
||||
region 2 block INF INF 38.75 INF INF INF
|
||||
group upper region 2
|
||||
302 atoms in group upper
|
||||
group boundary union lower upper
|
||||
604 atoms in group boundary
|
||||
group mobile subtract all boundary
|
||||
7537 atoms in group mobile
|
||||
|
||||
region leftupper block INF 20 20 INF INF INF
|
||||
region leftlower block INF 20 INF 20 INF INF
|
||||
group leftupper region leftupper
|
||||
841 atoms in group leftupper
|
||||
group leftlower region leftlower
|
||||
841 atoms in group leftlower
|
||||
|
||||
set group leftupper type 2
|
||||
841 settings made for type
|
||||
set group leftlower type 3
|
||||
841 settings made for type
|
||||
set group lower type 4
|
||||
302 settings made for type
|
||||
set group upper type 5
|
||||
302 settings made for type
|
||||
|
||||
# initial velocities
|
||||
|
||||
compute new mobile temp
|
||||
velocity mobile create 0.01 887723 temp new
|
||||
velocity upper set 0.0 0.3 0.0
|
||||
velocity mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes
|
||||
|
||||
# fixes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 boundary setforce NULL 0.0 0.0
|
||||
|
||||
# run
|
||||
|
||||
timestep 0.003
|
||||
thermo 200
|
||||
thermo_modify temp new
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
|
||||
neigh_modify exclude type 2 3
|
||||
|
||||
#dump 1 all atom 500 dump.crack
|
||||
|
||||
#dump 2 all image 250 image.*.jpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 250 movie.mpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
run 5000
|
||||
Memory usage per processor = 2.06456 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0.065651733 -3.2595015 0 -3.1987287 -0.036239172 8605.5917
|
||||
200 0.060086376 -3.2531936 0 -3.1975725 -0.23125026 8638.8101
|
||||
400 0.060533553 -3.2509973 0 -3.1949623 -0.4305406 8679.2464
|
||||
600 0.06082965 -3.2466949 0 -3.1903858 -0.6028531 8716.7569
|
||||
800 0.061677224 -3.2413215 0 -3.1842278 -0.7482749 8756.226
|
||||
1000 0.062383731 -3.2349273 0 -3.1771796 -0.87425132 8793.1116
|
||||
1200 0.063709246 -3.2276094 0 -3.1686347 -0.98020161 8828.8863
|
||||
1400 0.065404552 -3.2196608 0 -3.1591168 -1.0695384 8866.4893
|
||||
1600 0.067579602 -3.2110378 0 -3.1484804 -1.1456387 8900.6772
|
||||
1800 0.069324241 -3.2018536 0 -3.1376812 -1.2020999 8933.017
|
||||
2000 0.071014927 -3.1921108 0 -3.1263733 -1.2430105 8963.9853
|
||||
2200 0.072992881 -3.1818701 0 -3.1143017 -1.2701297 9004.4136
|
||||
2400 0.075000723 -3.1712313 0 -3.1018043 -1.2830866 9034.9991
|
||||
2600 0.076843477 -3.1601004 0 -3.0889675 -1.27924 9072.1325
|
||||
2800 0.078671706 -3.1487747 0 -3.0759495 -1.2659604 9103.9526
|
||||
3000 0.080713586 -3.1373277 0 -3.0626123 -1.2440673 9134.552
|
||||
3200 0.08309469 -3.1260242 0 -3.0491047 -1.214547 9169.0003
|
||||
3400 0.085424766 -3.1146623 0 -3.0355859 -1.1839326 9206.909
|
||||
3600 0.087396485 -3.1029493 0 -3.0220477 -1.143412 9233.783
|
||||
3800 0.089007987 -3.090822 0 -3.0084286 -1.1000791 9259.0348
|
||||
4000 0.089813071 -3.0794078 0 -2.9962692 -1.062847 9281.82
|
||||
4200 0.08584753 -3.0668559 0 -2.9873882 -1.037972 9308.8113
|
||||
4400 0.086197517 -3.0559678 0 -2.9761761 -1.028843 9328.9666
|
||||
4600 0.086766447 -3.0437627 0 -2.9634443 -1.0208785 9361.9925
|
||||
4800 0.088195149 -3.0328502 0 -2.9512093 -1.0272063 9395.6122
|
||||
5000 0.089415266 -3.0228825 0 -2.9401122 -1.0215336 9436.1637
|
||||
Loop time of 6.86201 on 1 procs for 5000 steps with 8141 atoms
|
||||
|
||||
Pair time (%) = 5.71043 (83.218)
|
||||
Neigh time (%) = 0.29686 (4.32613)
|
||||
Comm time (%) = 0.00569272 (0.0829599)
|
||||
Outpt time (%) = 0.000731707 (0.0106631)
|
||||
Other time (%) = 0.8483 (12.3623)
|
||||
|
||||
Nlocal: 8141 ave 8141 max 8141 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 71389 ave 71389 max 71389 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 71389
|
||||
Ave neighs/atom = 8.76907
|
||||
Neighbor list builds = 100
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,138 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 2d LJ crack simulation
|
||||
|
||||
dimension 2
|
||||
boundary s s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.93
|
||||
Lattice spacing in x,y,z = 1.11428 1.92998 1.11428
|
||||
region box block 0 100 0 40 -0.25 0.25
|
||||
create_box 5 box
|
||||
Created orthogonal box = (0 0 -0.278569) to (111.428 77.1994 0.278569)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 8141 atoms
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
mass 4 1.0
|
||||
mass 5 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
302 atoms in group lower
|
||||
region 2 block INF INF 38.75 INF INF INF
|
||||
group upper region 2
|
||||
302 atoms in group upper
|
||||
group boundary union lower upper
|
||||
604 atoms in group boundary
|
||||
group mobile subtract all boundary
|
||||
7537 atoms in group mobile
|
||||
|
||||
region leftupper block INF 20 20 INF INF INF
|
||||
region leftlower block INF 20 INF 20 INF INF
|
||||
group leftupper region leftupper
|
||||
841 atoms in group leftupper
|
||||
group leftlower region leftlower
|
||||
841 atoms in group leftlower
|
||||
|
||||
set group leftupper type 2
|
||||
841 settings made for type
|
||||
set group leftlower type 3
|
||||
841 settings made for type
|
||||
set group lower type 4
|
||||
302 settings made for type
|
||||
set group upper type 5
|
||||
302 settings made for type
|
||||
|
||||
# initial velocities
|
||||
|
||||
compute new mobile temp
|
||||
velocity mobile create 0.01 887723 temp new
|
||||
velocity upper set 0.0 0.3 0.0
|
||||
velocity mobile ramp vy 0.0 0.3 y 1.25 38.75 sum yes
|
||||
|
||||
# fixes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 boundary setforce NULL 0.0 0.0
|
||||
|
||||
# run
|
||||
|
||||
timestep 0.003
|
||||
thermo 200
|
||||
thermo_modify temp new
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
|
||||
neigh_modify exclude type 2 3
|
||||
|
||||
#dump 1 all atom 500 dump.crack
|
||||
|
||||
#dump 2 all image 250 image.*.jpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 250 movie.mpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
run 5000
|
||||
Memory usage per processor = 2.06601 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0.065993465 -3.2595015 0 -3.1984123 -0.035939913 8605.5917
|
||||
200 0.060035253 -3.2531886 0 -3.1976149 -0.22757684 8638.5331
|
||||
400 0.06054278 -3.2510706 0 -3.1950271 -0.42811733 8677.8288
|
||||
600 0.060576995 -3.246816 0 -3.1907408 -0.60017647 8717.6131
|
||||
800 0.060802753 -3.2413477 0 -3.1850635 -0.74499308 8756.4512
|
||||
1000 0.061812114 -3.2349942 0 -3.1777756 -0.87130079 8796.9575
|
||||
1200 0.06317147 -3.2277552 0 -3.1692783 -0.98010628 8823.1488
|
||||
1400 0.065125405 -3.2198031 0 -3.1595175 -1.0690179 8858.8358
|
||||
1600 0.06725411 -3.2111272 0 -3.148871 -1.1440993 8892.6607
|
||||
1800 0.069389572 -3.2019689 0 -3.137736 -1.199078 8933.7591
|
||||
2000 0.071276448 -3.1921621 0 -3.1261826 -1.239553 8969.0463
|
||||
2200 0.073243486 -3.1818809 0 -3.1140805 -1.264839 8997.6559
|
||||
2400 0.075063494 -3.1711703 0 -3.1016851 -1.2772278 9038.4932
|
||||
2600 0.076789207 -3.1600658 0 -3.0889832 -1.2754953 9073.4997
|
||||
2800 0.07875979 -3.1487143 0 -3.0758075 -1.2637926 9106.2245
|
||||
3000 0.080591853 -3.1372361 0 -3.0626334 -1.2388824 9142.7862
|
||||
3200 0.08227693 -3.125423 0 -3.0492605 -1.2055283 9169.4322
|
||||
3400 0.084289444 -3.1136554 0 -3.03563 -1.1672422 9204.8205
|
||||
3600 0.086720297 -3.1021183 0 -3.0218427 -1.126381 9233.2656
|
||||
3800 0.089264018 -3.0909262 0 -3.0082959 -1.0899774 9265.4143
|
||||
4000 0.091377688 -3.0795096 0 -2.9949227 -1.0580229 9297.6799
|
||||
4200 0.092665135 -3.0678736 0 -2.9820949 -1.0390124 9331.6135
|
||||
4400 0.09055434 -3.0560482 0 -2.9722234 -1.0323741 9362.2075
|
||||
4600 0.088763719 -3.0446018 0 -2.9624346 -1.027693 9391.6949
|
||||
4800 0.089467982 -3.0337452 0 -2.950926 -1.0232092 9427.4155
|
||||
5000 0.089910902 -3.0237571 0 -2.9405279 -1.0174796 9452.031
|
||||
Loop time of 1.93628 on 4 procs for 5000 steps with 8141 atoms
|
||||
|
||||
Pair time (%) = 1.46785 (75.8079)
|
||||
Neigh time (%) = 0.0816418 (4.21643)
|
||||
Comm time (%) = 0.13282 (6.85954)
|
||||
Outpt time (%) = 0.000654757 (0.0338153)
|
||||
Other time (%) = 0.253311 (13.0823)
|
||||
|
||||
Nlocal: 2035.25 ave 2064 max 2015 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Nghost: 198 ave 248 max 150 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Neighs: 17850 ave 18247 max 17601 min
|
||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 71400
|
||||
Ave neighs/atom = 8.77042
|
||||
Neighbor list builds = 106
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,89 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style hybrid sphere dipole
|
||||
dimension 2
|
||||
|
||||
lattice sq2 0.7
|
||||
Lattice spacing in x,y,z = 1.69031 1.69031 1.69031
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 200 atoms
|
||||
|
||||
# need both mass settings due to hybrid atom style
|
||||
|
||||
mass 1 1.0
|
||||
set group all mass 1.0
|
||||
200 settings made for mass
|
||||
set group all dipole/random 98934 0.75
|
||||
200 settings made for dipole/random
|
||||
|
||||
velocity all create 0.0 87287 mom no
|
||||
|
||||
pair_style lj/cut/dipole/cut 2.5
|
||||
pair_coeff * * 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve/sphere update dipole
|
||||
fix 2 all enforce2d
|
||||
|
||||
timestep 0.005
|
||||
|
||||
compute erot all erotate/sphere
|
||||
thermo_style custom step temp epair c_erot etotal press
|
||||
thermo 500
|
||||
|
||||
#dump 1 all custom 500 dump.dipole id type x y z mux muy
|
||||
|
||||
#dump 1 all image 250 image.*.jpg mux type # zoom 1.6 adiam 1.2
|
||||
#dump_modify 1 pad 5
|
||||
|
||||
run 10000
|
||||
Memory usage per processor = 3.28197 Mbytes
|
||||
Step Temp E_pair erot TotEng Press
|
||||
0 0 -2.1909822 0 -2.1909822 -2.5750971
|
||||
500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899
|
||||
1000 0.45259485 -2.8743423 0.22311811 -2.4240104 -0.14864606
|
||||
1500 0.42110221 -2.8019062 0.19532181 -2.3829095 0.18067141
|
||||
2000 0.39019973 -2.7914873 0.22407026 -2.4032386 -0.40914143
|
||||
2500 0.40242274 -2.8142159 0.24281467 -2.4138053 -0.3391299
|
||||
3000 0.42771065 -2.8535488 0.25848739 -2.4279767 -0.2500108
|
||||
3500 0.44706195 -2.7890555 0.18446345 -2.3442289 -0.1005632
|
||||
4000 0.4041733 -2.7741037 0.22161024 -2.3719512 -0.13373446
|
||||
4500 0.47549052 -2.8368758 0.21740299 -2.3637627 -0.14246916
|
||||
5000 0.42071015 -2.7518085 0.20821432 -2.3332019 -0.047522754
|
||||
5500 0.43520504 -2.8042986 0.24366805 -2.3712696 -0.22180582
|
||||
6000 0.42802195 -2.7822398 0.24060881 -2.3563579 -0.35350862
|
||||
6500 0.4479767 -2.8175363 0.25806495 -2.3717994 0.07885849
|
||||
7000 0.39538519 -2.7246562 0.23766993 -2.331248 -0.098542228
|
||||
7500 0.40716663 -2.7115371 0.21917238 -2.3064063 -0.14844207
|
||||
8000 0.42814546 -2.7318282 0.23188976 -2.3058235 -0.37209482
|
||||
8500 0.46175735 -2.7607768 0.23020837 -2.3013282 -0.33381513
|
||||
9000 0.48360992 -2.758533 0.21927619 -2.2773411 -0.016767257
|
||||
9500 0.47646809 -2.7812073 0.24046809 -2.3071216 -0.12582235
|
||||
10000 0.48207466 -2.7437285 0.20973254 -2.2640642 0.51612253
|
||||
Loop time of 1.03017 on 1 procs for 10000 steps with 200 atoms
|
||||
|
||||
Pair time (%) = 0.838452 (81.3899)
|
||||
Neigh time (%) = 0.03585 (3.48002)
|
||||
Comm time (%) = 0.0484488 (4.703)
|
||||
Outpt time (%) = 0.000171423 (0.0166403)
|
||||
Other time (%) = 0.107245 (10.4105)
|
||||
|
||||
Nlocal: 200 ave 200 max 200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 158 ave 158 max 158 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1673 ave 1673 max 1673 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1673
|
||||
Ave neighs/atom = 8.365
|
||||
Neighbor list builds = 679
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,89 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Point dipoles in a 2d box
|
||||
|
||||
units lj
|
||||
atom_style hybrid sphere dipole
|
||||
dimension 2
|
||||
|
||||
lattice sq2 0.7
|
||||
Lattice spacing in x,y,z = 1.69031 1.69031 1.69031
|
||||
region box block 0 10 0 10 -0.5 0.5
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -0.845154) to (16.9031 16.9031 0.845154)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 200 atoms
|
||||
|
||||
# need both mass settings due to hybrid atom style
|
||||
|
||||
mass 1 1.0
|
||||
set group all mass 1.0
|
||||
200 settings made for mass
|
||||
set group all dipole/random 98934 0.75
|
||||
200 settings made for dipole/random
|
||||
|
||||
velocity all create 0.0 87287 mom no
|
||||
|
||||
pair_style lj/cut/dipole/cut 2.5
|
||||
pair_coeff * * 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
fix 1 all nve/sphere update dipole
|
||||
fix 2 all enforce2d
|
||||
|
||||
timestep 0.005
|
||||
|
||||
compute erot all erotate/sphere
|
||||
thermo_style custom step temp epair c_erot etotal press
|
||||
thermo 500
|
||||
|
||||
#dump 1 all custom 500 dump.dipole id type x y z mux muy
|
||||
|
||||
#dump 1 all image 250 image.*.jpg mux type # zoom 1.6 adiam 1.2
|
||||
#dump_modify 1 pad 5
|
||||
|
||||
run 10000
|
||||
Memory usage per processor = 3.2813 Mbytes
|
||||
Step Temp E_pair erot TotEng Press
|
||||
0 0 -2.1909822 0 -2.1909822 -2.5750971
|
||||
500 0.39335419 -2.7940623 0.20683255 -2.4026749 -0.24768899
|
||||
1000 0.45259485 -2.8743423 0.22311811 -2.4240104 -0.14864606
|
||||
1500 0.42110221 -2.8019062 0.19532181 -2.3829095 0.18067141
|
||||
2000 0.39019968 -2.7914873 0.22407029 -2.4032386 -0.4091395
|
||||
2500 0.40237391 -2.8138968 0.24276582 -2.4135348 -0.33901619
|
||||
3000 0.42595202 -2.8621684 0.26812111 -2.4383462 -0.19493812
|
||||
3500 0.41153448 -2.8070419 0.23860803 -2.397565 -0.032395966
|
||||
4000 0.40867238 -2.7790568 0.22331133 -2.3724278 0.014462986
|
||||
4500 0.39803378 -2.7718651 0.23536245 -2.3758215 -0.25429533
|
||||
5000 0.42736901 -2.8476039 0.2824171 -2.4223718 0.12187395
|
||||
5500 0.41115816 -2.7810177 0.24508517 -2.3719153 -0.1925336
|
||||
6000 0.43184788 -2.8015292 0.24726776 -2.3718406 -0.014489672
|
||||
6500 0.45955478 -2.8340069 0.26105652 -2.3767499 -0.16015969
|
||||
7000 0.43826613 -2.7488226 0.20031236 -2.3127478 0.071480756
|
||||
7500 0.45738321 -2.7892162 0.23337255 -2.3341199 -0.17245012
|
||||
8000 0.46107991 -2.7322063 0.18569571 -2.2734318 -0.21563894
|
||||
8500 0.40367385 -2.7623279 0.27023252 -2.3606724 -0.038576129
|
||||
9000 0.43104207 -2.7672424 0.25452132 -2.3383555 0.044351007
|
||||
9500 0.38924411 -2.7231541 0.24926613 -2.3358562 -0.21910634
|
||||
10000 0.44421944 -2.7677489 0.23376321 -2.3257506 0.034770807
|
||||
Loop time of 0.443194 on 4 procs for 10000 steps with 200 atoms
|
||||
|
||||
Pair time (%) = 0.217619 (49.1024)
|
||||
Neigh time (%) = 0.00970978 (2.19086)
|
||||
Comm time (%) = 0.157952 (35.6394)
|
||||
Outpt time (%) = 0.000405192 (0.0914255)
|
||||
Other time (%) = 0.0575083 (12.9759)
|
||||
|
||||
Nlocal: 50 ave 55 max 41 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 87.75 ave 92 max 78 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
Neighs: 415 ave 481 max 301 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
|
||||
Total # of neighbors = 1660
|
||||
Ave neighs/atom = 8.3
|
||||
Neighbor list builds = 671
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,106 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
units real
|
||||
atom_style full
|
||||
boundary p p p
|
||||
dielectric 1
|
||||
special_bonds lj/coul 0.0 0.0 1.0
|
||||
|
||||
pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style harmonic
|
||||
improper_style none
|
||||
kspace_style pppm 0.001
|
||||
|
||||
read_data data.dreiding
|
||||
orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
384 atoms
|
||||
scanning bonds ...
|
||||
4 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
3 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
320 bonds
|
||||
reading angles ...
|
||||
448 angles
|
||||
reading dihedrals ...
|
||||
192 dihedrals
|
||||
4 = max # of 1-2 neighbors
|
||||
3 = max # of 1-3 neighbors
|
||||
5 = max # of special neighbors
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
|
||||
pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
|
||||
pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
|
||||
pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
|
||||
pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
|
||||
pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
|
||||
pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4
|
||||
pair_modify mix arithmetic
|
||||
neighbor 2.0 multi
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
variable input index in.ch3oh.box.dreiding
|
||||
variable sname index ch3oh.box.dreiding
|
||||
|
||||
compute hb all pair hbond/dreiding/lj
|
||||
variable C_hbond equal c_hb[1] #number hbonds
|
||||
variable E_hbond equal c_hb[2] #hbond energy
|
||||
thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
|
||||
thermo_modify line multi format float %14.6f
|
||||
|
||||
run 0
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:54)
|
||||
PPPM initialization ...
|
||||
WARNING: System is not charge neutral, net charge = -0.00064 (../pppm.cpp:271)
|
||||
G vector (1/distance) = 0.142073
|
||||
grid = 3 3 3
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.154715
|
||||
estimated relative force accuracy = 0.00046592
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 512 27
|
||||
Memory usage per processor = 7.97163 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000
|
||||
PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880
|
||||
E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
|
||||
E_coul = 597.219740 E_long = -361.164864 E_hbond = -69.322152
|
||||
C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335
|
||||
Loop time of 2.14577e-06 on 1 procs for 0 steps with 384 atoms
|
||||
|
||||
Pair time (%) = 0 (0)
|
||||
Bond time (%) = 0 (0)
|
||||
Kspce time (%) = 0 (0)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0 (0)
|
||||
Outpt time (%) = 0 (0)
|
||||
Other time (%) = 2.14577e-06 (100)
|
||||
|
||||
FFT time (% of Kspce) = 0 (0)
|
||||
FFT Gflps 3d (1d only) = 0 0
|
||||
|
||||
Nlocal: 384 ave 384 max 384 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4637 ave 4637 max 4637 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 101854 ave 101854 max 101854 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 203708 ave 203708 max 203708 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 203708
|
||||
Ave neighs/atom = 530.49
|
||||
Ave special neighs/atom = 4
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,106 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
units real
|
||||
atom_style full
|
||||
boundary p p p
|
||||
dielectric 1
|
||||
special_bonds lj/coul 0.0 0.0 1.0
|
||||
|
||||
pair_style hybrid/overlay hbond/dreiding/lj 2 6 6.5 90 lj/cut/coul/long 8.50000 11.5
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style harmonic
|
||||
improper_style none
|
||||
kspace_style pppm 0.001
|
||||
|
||||
read_data data.dreiding
|
||||
orthogonal box = (0 0 0) to (19.9969 19.1282 19.4697)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
384 atoms
|
||||
scanning bonds ...
|
||||
4 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
3 = max dihedrals/atom
|
||||
reading bonds ...
|
||||
320 bonds
|
||||
reading angles ...
|
||||
448 angles
|
||||
reading dihedrals ...
|
||||
192 dihedrals
|
||||
4 = max # of 1-2 neighbors
|
||||
3 = max # of 1-3 neighbors
|
||||
5 = max # of special neighbors
|
||||
|
||||
pair_coeff 1 1 lj/cut/coul/long 0.015200000256300 2.846421344984478
|
||||
pair_coeff 1 2 lj/cut/coul/long 0.001232882795416 2.846421344984478
|
||||
pair_coeff 1 3 lj/cut/coul/long 0.038019995160237 3.159705878878677
|
||||
pair_coeff 1 4 lj/cut/coul/long 0.038139744011598 2.939787518071103
|
||||
pair_coeff 2 2 lj/cut/coul/long 9.99999974737875e-05 2.846421344984478
|
||||
pair_coeff 2 3 lj/cut/coul/long 0.003083828758188 3.159705878878677
|
||||
pair_coeff 2 4 lj/cut/coul/long 0.003093541672406 2.939787518071103
|
||||
pair_coeff 3 3 lj/cut/coul/long 0.095100000500679 3.472990412772877
|
||||
pair_coeff 3 4 lj/cut/coul/long 0.095399530150179 3.253072051965302
|
||||
pair_coeff 4 4 lj/cut/coul/long 0.095700003206730 3.033153691157727
|
||||
pair_coeff 4 4 hbond/dreiding/lj 2 i 0.4000E+01 2.750000000000000 4
|
||||
pair_modify mix arithmetic
|
||||
neighbor 2.0 multi
|
||||
neigh_modify every 2 delay 4 check yes
|
||||
variable input index in.ch3oh.box.dreiding
|
||||
variable sname index ch3oh.box.dreiding
|
||||
|
||||
compute hb all pair hbond/dreiding/lj
|
||||
variable C_hbond equal c_hb[1] #number hbonds
|
||||
variable E_hbond equal c_hb[2] #hbond energy
|
||||
thermo_style custom etotal ke temp pe ebond eangle edihed eimp evdwl ecoul elong v_E_hbond v_C_hbond press vol
|
||||
thermo_modify line multi format float %14.6f
|
||||
|
||||
run 0
|
||||
WARNING: No fixes defined, atoms won't move (../verlet.cpp:54)
|
||||
PPPM initialization ...
|
||||
WARNING: System is not charge neutral, net charge = -0.00064 (../pppm.cpp:271)
|
||||
G vector (1/distance) = 0.142073
|
||||
grid = 3 3 3
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.154715
|
||||
estimated relative force accuracy = 0.00046592
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 392 12
|
||||
Memory usage per processor = 6.52754 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = 113.723601 KinEng = 0.000000 Temp = 0.000000
|
||||
PotEng = 113.723601 E_bond = 0.535673 E_angle = 1.281880
|
||||
E_dihed = 1.232497 E_impro = 0.000000 E_vdwl = -125.381324
|
||||
E_coul = 597.219740 E_long = -361.164864 E_hbond = -69.322152
|
||||
C_hbond = 235.000000 Press = -328.847347 Volume = 7447.236335
|
||||
Loop time of 5.24521e-06 on 4 procs for 0 steps with 384 atoms
|
||||
|
||||
Pair time (%) = 0 (0)
|
||||
Bond time (%) = 0 (0)
|
||||
Kspce time (%) = 0 (0)
|
||||
Neigh time (%) = 0 (0)
|
||||
Comm time (%) = 0 (0)
|
||||
Outpt time (%) = 0 (0)
|
||||
Other time (%) = 5.24521e-06 (100)
|
||||
|
||||
FFT time (% of Kspce) = 0 (0)
|
||||
FFT Gflps 3d (1d only) = 0 0
|
||||
|
||||
Nlocal: 96 ave 104 max 87 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Nghost: 3063.25 ave 3108 max 3024 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Neighs: 25463.5 ave 28799 max 22471 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
FullNghs: 50927 ave 55516 max 46073 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 203708
|
||||
Ave neighs/atom = 530.49
|
||||
Ave special neighs/atom = 4
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,72 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# NaCl test problem for embedded atom method (EIM) potential
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice diamond 5.0
|
||||
Lattice spacing in x,y,z = 5 5 5
|
||||
read_data data.eim
|
||||
orthogonal box = (-0.5 -0.5 -0.5) to (35.54 35.54 35.54)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2000 atoms
|
||||
reading velocities ...
|
||||
2000 velocities
|
||||
|
||||
pair_style eim
|
||||
pair_coeff * * Na Cl ffield.eim Na Cl
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
timestep 0.001
|
||||
thermo_style custom step pe pxx pyy pzz temp
|
||||
thermo 50
|
||||
|
||||
velocity all create 1400.0 43454 dist gaussian mom yes
|
||||
fix int all npt temp 1400.0 300.0 0.1 aniso 0.0 0.0 0.1
|
||||
|
||||
#dump id all atom 100 dump.eim
|
||||
|
||||
#dump 2 all image 25 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3 element Na Cl
|
||||
|
||||
#dump 3 all movie 25 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3 element Na Cl
|
||||
|
||||
run 500
|
||||
Memory usage per processor = 2.19121 Mbytes
|
||||
Step PotEng Pxx Pyy Pzz Temp
|
||||
0 -5660.4738 -118151.29 -117613.39 -118064.41 1400
|
||||
50 -5773.8661 889.73924 898.43321 703.5365 891.68472
|
||||
100 -5742.8192 866.6183 817.86837 889.72898 838.77403
|
||||
150 -5738.752 -335.23317 -345.69716 -123.3196 900.54672
|
||||
200 -5704.2444 -172.01932 -508.83888 -654.45947 834.82705
|
||||
250 -5724.4679 375.50199 546.99196 405.29298 966.14585
|
||||
300 -5718.5442 428.47856 361.93998 752.00729 934.57116
|
||||
350 -5722.7694 -409.40162 -484.53168 42.702482 865.13075
|
||||
400 -5743.6862 173.43552 288.02324 107.96614 840.48912
|
||||
450 -5751.3366 -752.54635 -762.07316 -591.45022 743.42176
|
||||
500 -5780.5266 -157.23981 84.510897 -52.426827 712.64129
|
||||
Loop time of 5.87275 on 1 procs for 500 steps with 2000 atoms
|
||||
|
||||
Pair time (%) = 5.39652 (91.8909)
|
||||
Neigh time (%) = 0.377995 (6.43642)
|
||||
Comm time (%) = 0.023782 (0.404955)
|
||||
Outpt time (%) = 0.000288486 (0.00491229)
|
||||
Other time (%) = 0.0741594 (1.26277)
|
||||
|
||||
Nlocal: 2000 ave 2000 max 2000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 4194 ave 4194 max 4194 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 99537 ave 99537 max 99537 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 99537
|
||||
Ave neighs/atom = 49.7685
|
||||
Neighbor list builds = 89
|
||||
Dangerous builds = 10
|
||||
|
|
@ -0,0 +1,72 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# NaCl test problem for embedded atom method (EIM) potential
|
||||
|
||||
units metal
|
||||
atom_style atomic
|
||||
|
||||
boundary p p p
|
||||
|
||||
lattice diamond 5.0
|
||||
Lattice spacing in x,y,z = 5 5 5
|
||||
read_data data.eim
|
||||
orthogonal box = (-0.5 -0.5 -0.5) to (35.54 35.54 35.54)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2000 atoms
|
||||
reading velocities ...
|
||||
2000 velocities
|
||||
|
||||
pair_style eim
|
||||
pair_coeff * * Na Cl ffield.eim Na Cl
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
timestep 0.001
|
||||
thermo_style custom step pe pxx pyy pzz temp
|
||||
thermo 50
|
||||
|
||||
velocity all create 1400.0 43454 dist gaussian mom yes
|
||||
fix int all npt temp 1400.0 300.0 0.1 aniso 0.0 0.0 0.1
|
||||
|
||||
#dump id all atom 100 dump.eim
|
||||
|
||||
#dump 2 all image 25 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3 element Na Cl
|
||||
|
||||
#dump 3 all movie 25 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3 element Na Cl
|
||||
|
||||
run 500
|
||||
Memory usage per processor = 1.87327 Mbytes
|
||||
Step PotEng Pxx Pyy Pzz Temp
|
||||
0 -5660.4738 -118151.29 -117613.39 -118064.41 1400
|
||||
50 -5773.8661 889.73924 898.43321 703.5365 891.68472
|
||||
100 -5742.8192 866.6183 817.86837 889.72898 838.77403
|
||||
150 -5738.752 -335.23317 -345.69716 -123.3196 900.54672
|
||||
200 -5704.2444 -172.01932 -508.83888 -654.45947 834.82705
|
||||
250 -5724.4679 375.50199 546.99196 405.29298 966.14585
|
||||
300 -5718.5442 428.47856 361.93998 752.00729 934.57116
|
||||
350 -5722.7694 -409.40162 -484.53168 42.702482 865.13075
|
||||
400 -5743.6862 173.43552 288.02324 107.96614 840.48912
|
||||
450 -5751.3366 -752.54635 -762.07316 -591.45022 743.42176
|
||||
500 -5780.5266 -157.23981 84.510897 -52.426827 712.64129
|
||||
Loop time of 1.52681 on 4 procs for 500 steps with 2000 atoms
|
||||
|
||||
Pair time (%) = 1.36826 (89.6153)
|
||||
Neigh time (%) = 0.0933943 (6.11695)
|
||||
Comm time (%) = 0.0370625 (2.42744)
|
||||
Outpt time (%) = 0.000231683 (0.0151743)
|
||||
Other time (%) = 0.0278663 (1.82513)
|
||||
|
||||
Nlocal: 500 ave 501 max 498 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 2179.25 ave 2182 max 2175 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
Neighs: 24884.2 ave 25164 max 24622 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 99537
|
||||
Ave neighs/atom = 49.7685
|
||||
Neighbor list builds = 89
|
||||
Dangerous builds = 10
|
||||
|
|
@ -0,0 +1,163 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# GayBerne ellipsoids in LJ background fluid
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
dimension 2
|
||||
|
||||
lattice sq 0.02
|
||||
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
|
||||
region box block 0 20 0 20 -0.5 0.5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 400 atoms
|
||||
|
||||
set group all type/fraction 2 0.1 95392
|
||||
45 settings made for type/fraction
|
||||
set type 1 mass 1.0
|
||||
355 settings made for mass
|
||||
set type 2 mass 1.5
|
||||
45 settings made for mass
|
||||
set type 1 shape 1 1 1
|
||||
355 settings made for shape
|
||||
set type 2 shape 3 1 1
|
||||
45 settings made for shape
|
||||
set group all quat/random 18238
|
||||
400 settings made for quat/random
|
||||
|
||||
compute rot all temp/asphere
|
||||
group spheroid type 1
|
||||
355 atoms in group spheroid
|
||||
variable dof equal count(spheroid)+2
|
||||
compute_modify rot extra ${dof}
|
||||
compute_modify rot extra 357
|
||||
|
||||
velocity all create 2.4 87287 loop geom
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
|
||||
pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
|
||||
pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
|
||||
|
||||
neighbor 0.8 bin
|
||||
|
||||
thermo_style custom step c_rot epair etotal press vol
|
||||
thermo 100
|
||||
|
||||
timestep 0.002
|
||||
|
||||
compute q all property/atom quatw quati quatj quatk
|
||||
|
||||
#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
|
||||
#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
|
||||
#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
|
||||
|
||||
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
|
||||
fix 2 all enforce2d
|
||||
|
||||
compute_modify 1_temp extra ${dof}
|
||||
compute_modify 1_temp extra 357
|
||||
|
||||
# equilibrate to shrink box around dilute system
|
||||
|
||||
run 2000
|
||||
Memory usage per processor = 3.4108 Mbytes
|
||||
Step rot E_pair TotEng Press Volume
|
||||
0 2.2718861 0 2.394 0.04788 20000
|
||||
100 1.7443002 0 1.8380563 0.03576216 20558.672
|
||||
200 2.2770454 0 2.3994366 0.046545139 20620.298
|
||||
300 1.8573283 0 1.9571597 0.04240689 18460.771
|
||||
400 2.1709963 -0.00050890768 2.2871782 0.066789189 13689.461
|
||||
500 1.987484 -0.043660052 2.0342913 0.099199049 8475.4405
|
||||
600 2.088535 -0.24318266 1.8270941 0.22391583 4674.8592
|
||||
700 2.2604089 -0.73325761 1.481207 0.57184109 2507.095
|
||||
800 1.8731398 -1.6161576 0.22080738 1.3049285 1420.4278
|
||||
900 2.1404423 -3.0146759 -0.84039269 3.3566833 922.07169
|
||||
1000 1.5927835 -4.5754144 -2.9697785 2.5493591 743.19289
|
||||
1100 1.8380043 -4.8820159 -3.0604394 2.2950846 708.014
|
||||
1200 2.05516 -4.5701279 -2.4718822 1.466469 753.52878
|
||||
1300 2.0000364 -4.0755503 -2.031995 0.35675413 842.14053
|
||||
1400 2.1055032 -3.7342781 -1.6632699 0.58193577 925.51606
|
||||
1500 1.9241806 -3.582658 -1.639377 0.24973032 1006.7339
|
||||
1600 2.125676 -3.4733166 -1.3572836 0.72069214 1061.1355
|
||||
1700 1.8811354 -3.2933821 -1.4183258 0.59272021 1119.2646
|
||||
1800 2.1014782 -3.1254259 -1.0248797 0.95254771 1162.1817
|
||||
1900 1.8977855 -3.1905908 -1.2727444 0.7315737 1191.4876
|
||||
2000 2.0794708 -3.253147 -1.2230906 0.49491309 1187.4615
|
||||
Loop time of 0.725952 on 1 procs for 2000 steps with 400 atoms
|
||||
|
||||
Pair time (%) = 0.503768 (69.3941)
|
||||
Neigh time (%) = 0.0126507 (1.74264)
|
||||
Comm time (%) = 0.0136161 (1.87562)
|
||||
Outpt time (%) = 0.000351191 (0.0483765)
|
||||
Other time (%) = 0.195566 (26.9393)
|
||||
|
||||
Nlocal: 400 ave 400 max 400 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 232 ave 232 max 232 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2868 ave 2868 max 2868 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2868
|
||||
Ave neighs/atom = 7.17
|
||||
Neighbor list builds = 138
|
||||
Dangerous builds = 80
|
||||
|
||||
# run dynamics on dense system
|
||||
|
||||
unfix 1
|
||||
fix 1 all nve/asphere
|
||||
|
||||
run 2000
|
||||
Memory usage per processor = 3.42095 Mbytes
|
||||
Step rot E_pair TotEng Press Volume
|
||||
2000 2.0794708 -3.253147 -1.2230906 0.49491309 1187.4615
|
||||
2100 2.0350673 -3.2084761 -1.1823685 0.33981994 1187.4615
|
||||
2200 1.9674878 -3.1385619 -1.1467435 1.1720132 1187.4615
|
||||
2300 2.0160349 -3.191283 -1.1652127 0.98222377 1187.4615
|
||||
2400 2.1323062 -3.3152814 -1.1669961 0.76099841 1187.4615
|
||||
2500 2.0866909 -3.2692047 -1.1766063 0.67971438 1187.4615
|
||||
2600 2.0982853 -3.2774461 -1.1869918 0.9045362 1187.4615
|
||||
2700 2.0482743 -3.2229418 -1.1928883 0.69426343 1187.4615
|
||||
2800 1.9676269 -3.1400321 -1.1685787 0.7578428 1187.4615
|
||||
2900 2.0421127 -3.2182014 -1.1866875 0.79386471 1187.4615
|
||||
3000 2.1074286 -3.2870176 -1.2012732 0.18871121 1187.4615
|
||||
3100 2.0466481 -3.2227223 -1.1821678 0.70482646 1187.4615
|
||||
3200 2.1159694 -3.2976371 -1.1588561 0.52105755 1187.4615
|
||||
3300 2.150544 -3.3366154 -1.179448 0.45837229 1187.4615
|
||||
3400 2.1035378 -3.2868896 -1.1614884 0.72339226 1187.4615
|
||||
3500 2.0665964 -3.2481259 -1.1351878 0.77887358 1187.4615
|
||||
3600 2.0079794 -3.183204 -1.1647668 0.49419048 1187.4615
|
||||
3700 2.0028597 -3.1740178 -1.1738107 0.38011763 1187.4615
|
||||
3800 1.9501131 -3.1191211 -1.1785414 0.77609881 1187.4615
|
||||
3900 2.0648034 -3.2412864 -1.1750708 0.55412858 1187.4615
|
||||
4000 2.0161932 -3.1865719 -1.1939133 0.6656145 1187.4615
|
||||
Loop time of 0.763192 on 1 procs for 2000 steps with 400 atoms
|
||||
|
||||
Pair time (%) = 0.621734 (81.4649)
|
||||
Neigh time (%) = 0.0058322 (0.764184)
|
||||
Comm time (%) = 0.0142851 (1.87175)
|
||||
Outpt time (%) = 0.000369549 (0.0484215)
|
||||
Other time (%) = 0.120971 (15.8507)
|
||||
|
||||
Nlocal: 400 ave 400 max 400 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 220 ave 220 max 220 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2901 ave 2901 max 2901 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2901
|
||||
Ave neighs/atom = 7.2525
|
||||
Neighbor list builds = 47
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,163 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# GayBerne ellipsoids in LJ background fluid
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
dimension 2
|
||||
|
||||
lattice sq 0.02
|
||||
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
|
||||
region box block 0 20 0 20 -0.5 0.5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 400 atoms
|
||||
|
||||
set group all type/fraction 2 0.1 95392
|
||||
45 settings made for type/fraction
|
||||
set type 1 mass 1.0
|
||||
355 settings made for mass
|
||||
set type 2 mass 1.5
|
||||
45 settings made for mass
|
||||
set type 1 shape 1 1 1
|
||||
355 settings made for shape
|
||||
set type 2 shape 3 1 1
|
||||
45 settings made for shape
|
||||
set group all quat/random 18238
|
||||
400 settings made for quat/random
|
||||
|
||||
compute rot all temp/asphere
|
||||
group spheroid type 1
|
||||
355 atoms in group spheroid
|
||||
variable dof equal count(spheroid)+2
|
||||
compute_modify rot extra ${dof}
|
||||
compute_modify rot extra 357
|
||||
|
||||
velocity all create 2.4 87287 loop geom
|
||||
|
||||
pair_style gayberne 1.0 3.0 1.0 4.0
|
||||
pair_coeff 1 1 3.0 1.0 1 1 1 1 1 1 2.5
|
||||
pair_coeff 1 2 3.0 1.0 1 1 1 0 0 0
|
||||
pair_coeff 2 2 1.0 1.0 1 1 0.2 0 0 0
|
||||
|
||||
neighbor 0.8 bin
|
||||
|
||||
thermo_style custom step c_rot epair etotal press vol
|
||||
thermo 100
|
||||
|
||||
timestep 0.002
|
||||
|
||||
compute q all property/atom quatw quati quatj quatk
|
||||
|
||||
#dump 1 all custom 100 dump.ellipse.gayberne # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
|
||||
#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
|
||||
#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
|
||||
|
||||
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
|
||||
fix 2 all enforce2d
|
||||
|
||||
compute_modify 1_temp extra ${dof}
|
||||
compute_modify 1_temp extra 357
|
||||
|
||||
# equilibrate to shrink box around dilute system
|
||||
|
||||
run 2000
|
||||
Memory usage per processor = 3.39986 Mbytes
|
||||
Step rot E_pair TotEng Press Volume
|
||||
0 2.2718861 0 2.394 0.04788 20000
|
||||
100 1.7443002 0 1.8380563 0.03576216 20558.672
|
||||
200 2.2770454 0 2.3994366 0.046545139 20620.298
|
||||
300 1.8573283 0 1.9571597 0.04240689 18460.771
|
||||
400 2.1709963 -0.00050890768 2.2871782 0.066789189 13689.461
|
||||
500 1.987484 -0.043660052 2.0342913 0.099199049 8475.4405
|
||||
600 2.088535 -0.24318266 1.8270941 0.22391583 4674.8592
|
||||
700 2.2604089 -0.73325761 1.481207 0.57184109 2507.095
|
||||
800 1.8731398 -1.6161576 0.22080738 1.3049285 1420.4278
|
||||
900 2.1404423 -3.0146759 -0.84039269 3.3566833 922.07169
|
||||
1000 1.5927835 -4.5754144 -2.9697785 2.5493591 743.19289
|
||||
1100 1.8380043 -4.8820159 -3.0604394 2.2950846 708.014
|
||||
1200 2.05516 -4.5701279 -2.4718822 1.466469 753.52878
|
||||
1300 2.0000364 -4.0755503 -2.031995 0.35675413 842.14053
|
||||
1400 2.1055032 -3.7342781 -1.6632699 0.58193577 925.51606
|
||||
1500 1.9241806 -3.582658 -1.639377 0.24973032 1006.7339
|
||||
1600 2.125676 -3.4733166 -1.3572836 0.72069214 1061.1355
|
||||
1700 1.8811354 -3.2933821 -1.4183258 0.59272021 1119.2646
|
||||
1800 2.1014782 -3.1254259 -1.0248797 0.9525477 1162.1817
|
||||
1900 1.8977855 -3.1905908 -1.2727444 0.7315737 1191.4876
|
||||
2000 2.0794708 -3.2531471 -1.2230906 0.49491309 1187.4615
|
||||
Loop time of 0.247263 on 4 procs for 2000 steps with 400 atoms
|
||||
|
||||
Pair time (%) = 0.132236 (53.4797)
|
||||
Neigh time (%) = 0.00340456 (1.3769)
|
||||
Comm time (%) = 0.0404702 (16.3672)
|
||||
Outpt time (%) = 0.000372708 (0.150733)
|
||||
Other time (%) = 0.0707802 (28.6254)
|
||||
|
||||
Nlocal: 100 ave 113 max 79 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
Nghost: 139.75 ave 151 max 132 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Neighs: 717 ave 880 max 487 min
|
||||
Histogram: 1 0 0 0 0 1 0 1 0 1
|
||||
|
||||
Total # of neighbors = 2868
|
||||
Ave neighs/atom = 7.17
|
||||
Neighbor list builds = 138
|
||||
Dangerous builds = 80
|
||||
|
||||
# run dynamics on dense system
|
||||
|
||||
unfix 1
|
||||
fix 1 all nve/asphere
|
||||
|
||||
run 2000
|
||||
Memory usage per processor = 3.4007 Mbytes
|
||||
Step rot E_pair TotEng Press Volume
|
||||
2000 2.0794708 -3.2531471 -1.2230906 0.49491309 1187.4615
|
||||
2100 2.0350673 -3.2084761 -1.1823685 0.33981993 1187.4615
|
||||
2200 1.9674878 -3.1385619 -1.1467435 1.1720132 1187.4615
|
||||
2300 2.0160349 -3.191283 -1.1652127 0.98222388 1187.4615
|
||||
2400 2.1323062 -3.3152814 -1.1669961 0.76099822 1187.4615
|
||||
2500 2.0866909 -3.2692048 -1.1766063 0.67971376 1187.4615
|
||||
2600 2.098286 -3.2774469 -1.1869922 0.90453433 1187.4615
|
||||
2700 2.0482737 -3.2229412 -1.1928882 0.69426669 1187.4615
|
||||
2800 1.9676254 -3.1400305 -1.1685788 0.75785389 1187.4615
|
||||
2900 2.0421207 -3.2182098 -1.1866861 0.79382733 1187.4615
|
||||
3000 2.1074356 -3.2870234 -1.2012809 0.18867661 1187.4615
|
||||
3100 2.0466079 -3.2226774 -1.1821925 0.7048821 1187.4615
|
||||
3200 2.1158976 -3.2976855 -1.1589624 0.5209376 1187.4615
|
||||
3300 2.1508115 -3.3368934 -1.1793489 0.45871464 1187.4615
|
||||
3400 2.1046063 -3.2881336 -1.1615171 0.71895972 1187.4615
|
||||
3500 2.066052 -3.2475413 -1.1359344 0.77760912 1187.4615
|
||||
3600 2.0042504 -3.1791312 -1.1647191 0.50555439 1187.4615
|
||||
3700 1.9888544 -3.1596354 -1.1679759 0.4059197 1187.4615
|
||||
3800 1.9919683 -3.1636959 -1.1860197 0.70259722 1187.4615
|
||||
3900 2.056542 -3.2325648 -1.1700712 0.43059703 1187.4615
|
||||
4000 1.9958145 -3.1666798 -1.2556316 0.87469089 1187.4615
|
||||
Loop time of 0.272762 on 4 procs for 2000 steps with 400 atoms
|
||||
|
||||
Pair time (%) = 0.159981 (58.6524)
|
||||
Neigh time (%) = 0.00155282 (0.569295)
|
||||
Comm time (%) = 0.0710112 (26.0341)
|
||||
Outpt time (%) = 0.000505924 (0.185482)
|
||||
Other time (%) = 0.0397106 (14.5587)
|
||||
|
||||
Nlocal: 100 ave 118 max 69 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||
Nghost: 139 ave 156 max 130 min
|
||||
Histogram: 2 0 0 1 0 0 0 0 0 1
|
||||
Neighs: 729.75 ave 951 max 409 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
|
||||
Total # of neighbors = 2919
|
||||
Ave neighs/atom = 7.2975
|
||||
Neighbor list builds = 47
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,160 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# RESquared ellipsoids in LJ background fluid
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
dimension 2
|
||||
|
||||
lattice sq 0.02
|
||||
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
|
||||
region box block 0 20 0 20 -0.5 0.5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 400 atoms
|
||||
|
||||
set group all type/fraction 2 0.1 95392
|
||||
45 settings made for type/fraction
|
||||
set type 1 mass 1.0
|
||||
355 settings made for mass
|
||||
set type 2 mass 1.5
|
||||
45 settings made for mass
|
||||
set type 1 shape 1 1 1
|
||||
355 settings made for shape
|
||||
set type 2 shape 3 1 1
|
||||
45 settings made for shape
|
||||
set group all quat/random 18238
|
||||
400 settings made for quat/random
|
||||
|
||||
compute rot all temp/asphere
|
||||
group spheroid type 1
|
||||
355 atoms in group spheroid
|
||||
variable dof equal count(spheroid)+2
|
||||
compute_modify rot extra ${dof}
|
||||
compute_modify rot extra 357
|
||||
|
||||
velocity all create 2.4 87287 loop geom
|
||||
|
||||
pair_style resquared 4.0
|
||||
pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
|
||||
pair_coeff 1 2 3.0 1 1 1 1 0 0 0
|
||||
pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
|
||||
|
||||
neighbor 0.8 bin
|
||||
|
||||
thermo_style custom step c_rot epair etotal press vol
|
||||
thermo 100
|
||||
|
||||
timestep 0.002
|
||||
|
||||
compute q all property/atom quatw quati quatj quatk
|
||||
|
||||
#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
|
||||
#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
|
||||
#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
|
||||
|
||||
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
|
||||
fix 2 all enforce2d
|
||||
|
||||
compute_modify 1_temp extra ${dof}
|
||||
compute_modify 1_temp extra 357
|
||||
|
||||
# equilibrate to shrink box around dilute system
|
||||
|
||||
run 2000
|
||||
Memory usage per processor = 3.4108 Mbytes
|
||||
Step rot E_pair TotEng Press Volume
|
||||
0 2.2718861 0 2.394 0.04788 20000
|
||||
100 1.7443002 0 1.8380563 0.03576216 20558.672
|
||||
200 2.2770454 0 2.3994366 0.046545139 20620.298
|
||||
300 1.8573283 0 1.9571597 0.04240689 18460.771
|
||||
400 2.1708604 -2.7650654e-05 2.2875165 0.066837495 13689.498
|
||||
500 1.997512 0.016920625 2.0564634 0.11517748 8482.9706
|
||||
600 2.0622304 0.078679437 2.0821362 0.28827312 4776.2481
|
||||
700 2.1106581 0.19687916 2.326279 0.85203631 2756.4602
|
||||
800 1.745752 0.29267549 1.978786 1.6290595 1832.812
|
||||
900 1.7925965 0.24064027 2.0273447 1.7295568 1516.7688
|
||||
1000 1.8280597 0.16642381 1.9844257 1.4314533 1517.3656
|
||||
1100 2.157879 0.10561715 2.2607067 0.98795205 1744.9669
|
||||
1200 1.7966771 0.057760855 1.8309261 0.54369976 2182.8259
|
||||
1300 2.2982472 0.036382605 2.3348878 0.45715755 2731.1166
|
||||
1400 1.7666501 0.038109497 1.7892555 0.32977405 3230.78
|
||||
1500 2.3048922 0.081153096 2.376275 0.45835895 3431.9991
|
||||
1600 1.8588345 0.067622658 1.9190878 0.39494686 3276.3398
|
||||
1700 2.1798404 0.1400767 2.3395072 0.71093539 2829.7905
|
||||
1800 1.9307392 0.14286145 2.0646696 0.84046137 2320.9547
|
||||
1900 2.0667728 0.16459518 2.1859494 1.1672332 1900.3276
|
||||
2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242
|
||||
Loop time of 1.42748 on 1 procs for 2000 steps with 400 atoms
|
||||
|
||||
Pair time (%) = 1.20681 (84.541)
|
||||
Neigh time (%) = 0.0122275 (0.856581)
|
||||
Comm time (%) = 0.0100107 (0.701285)
|
||||
Outpt time (%) = 0.000345707 (0.024218)
|
||||
Other time (%) = 0.198091 (13.8769)
|
||||
|
||||
Nlocal: 400 ave 400 max 400 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 207 ave 207 max 207 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1886 ave 1886 max 1886 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1886
|
||||
Ave neighs/atom = 4.715
|
||||
Neighbor list builds = 179
|
||||
Dangerous builds = 148
|
||||
|
||||
# run dynamics on dense system
|
||||
|
||||
unfix 1
|
||||
fix 1 all nve/asphere
|
||||
|
||||
run 2000
|
||||
Memory usage per processor = 3.41282 Mbytes
|
||||
Step rot E_pair TotEng Press Volume
|
||||
2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242
|
||||
2100 1.9516972 0.15050034 2.1113621 1.1750685 1657.9242
|
||||
2200 1.9410444 0.1617683 2.122019 1.2634696 1657.9242
|
||||
2300 1.918524 0.185457 2.1121008 1.3486177 1657.9242
|
||||
2400 1.9148973 0.18929207 2.1281553 1.3450222 1657.9242
|
||||
2500 1.8892245 0.21635013 2.1016576 1.5081781 1657.9242
|
||||
2600 1.9450942 0.15744768 2.0838764 1.2106282 1657.9242
|
||||
2700 1.9229729 0.18066635 2.1170011 1.3384024 1657.9242
|
||||
2800 1.9512215 0.15099705 2.0988077 1.2134331 1657.9242
|
||||
2900 1.9211263 0.18279158 2.0994515 1.3620719 1657.9242
|
||||
3000 1.9067872 0.19775144 2.0931298 1.4157496 1657.9242
|
||||
3100 1.9114595 0.19296361 2.1126574 1.4113475 1657.9242
|
||||
3200 1.9427389 0.15998511 2.0865325 1.3075162 1657.9242
|
||||
3300 1.9111626 0.19317346 2.1216597 1.430974 1657.9242
|
||||
3400 1.9538368 0.14833057 2.1210144 1.2276261 1657.9242
|
||||
3500 1.9244329 0.17929291 2.0825169 1.3186835 1657.9242
|
||||
3600 1.9511869 0.15107062 2.1197982 1.2271623 1657.9242
|
||||
3700 1.9369647 0.16601964 2.0970193 1.2813174 1657.9242
|
||||
3800 1.9418163 0.16093067 2.1231369 1.2354415 1657.9242
|
||||
3900 1.9450511 0.15759761 2.1394612 1.2392 1657.9242
|
||||
4000 1.9350034 0.1681995 2.1142685 1.2676915 1657.9242
|
||||
Loop time of 2.43595 on 1 procs for 2000 steps with 400 atoms
|
||||
|
||||
Pair time (%) = 2.29204 (94.0923)
|
||||
Neigh time (%) = 0.00481176 (0.197532)
|
||||
Comm time (%) = 0.0134215 (0.550978)
|
||||
Outpt time (%) = 0.000373363 (0.0153272)
|
||||
Other time (%) = 0.125302 (5.14388)
|
||||
|
||||
Nlocal: 400 ave 400 max 400 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 209 ave 209 max 209 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1903 ave 1903 max 1903 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1903
|
||||
Ave neighs/atom = 4.7575
|
||||
Neighbor list builds = 49
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,160 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# RESquared ellipsoids in LJ background fluid
|
||||
|
||||
units lj
|
||||
atom_style ellipsoid
|
||||
dimension 2
|
||||
|
||||
lattice sq 0.02
|
||||
Lattice spacing in x,y,z = 7.07107 7.07107 7.07107
|
||||
region box block 0 20 0 20 -0.5 0.5
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 -3.53553) to (141.421 141.421 3.53553)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 400 atoms
|
||||
|
||||
set group all type/fraction 2 0.1 95392
|
||||
45 settings made for type/fraction
|
||||
set type 1 mass 1.0
|
||||
355 settings made for mass
|
||||
set type 2 mass 1.5
|
||||
45 settings made for mass
|
||||
set type 1 shape 1 1 1
|
||||
355 settings made for shape
|
||||
set type 2 shape 3 1 1
|
||||
45 settings made for shape
|
||||
set group all quat/random 18238
|
||||
400 settings made for quat/random
|
||||
|
||||
compute rot all temp/asphere
|
||||
group spheroid type 1
|
||||
355 atoms in group spheroid
|
||||
variable dof equal count(spheroid)+2
|
||||
compute_modify rot extra ${dof}
|
||||
compute_modify rot extra 357
|
||||
|
||||
velocity all create 2.4 87287 loop geom
|
||||
|
||||
pair_style resquared 4.0
|
||||
pair_coeff 1 1 3.0 1 1 1 1 1 1 1 2.5
|
||||
pair_coeff 1 2 3.0 1 1 1 1 0 0 0
|
||||
pair_coeff 2 2 1.0 1 1 1 0.2 0 0 0
|
||||
|
||||
neighbor 0.8 bin
|
||||
|
||||
thermo_style custom step c_rot epair etotal press vol
|
||||
thermo 100
|
||||
|
||||
timestep 0.002
|
||||
|
||||
compute q all property/atom quatw quati quatj quatk
|
||||
|
||||
#dump 1 all custom 100 dump.ellipse.resquared # id type x y z c_q[1] c_q[2] c_q[3] c_q[4]
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 center d 0.5 0.5 0.5
|
||||
#dump_modify 2 pad 4 adiam 1 1.0 adiam 2 2.0
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 center d 0.5 0.5 0.5
|
||||
#dump_modify 3 pad 4 adiam 1 1.0 adiam 2 2.0
|
||||
|
||||
fix 1 all npt/asphere temp 2.0 2.0 0.1 iso 0.0 1.0 1.0 mtk no pchain 0 tchain 1
|
||||
fix 2 all enforce2d
|
||||
|
||||
compute_modify 1_temp extra ${dof}
|
||||
compute_modify 1_temp extra 357
|
||||
|
||||
# equilibrate to shrink box around dilute system
|
||||
|
||||
run 2000
|
||||
Memory usage per processor = 3.39986 Mbytes
|
||||
Step rot E_pair TotEng Press Volume
|
||||
0 2.2718861 0 2.394 0.04788 20000
|
||||
100 1.7443002 0 1.8380563 0.03576216 20558.672
|
||||
200 2.2770454 0 2.3994366 0.046545139 20620.298
|
||||
300 1.8573283 0 1.9571597 0.04240689 18460.771
|
||||
400 2.1708604 -2.7650654e-05 2.2875165 0.066837495 13689.498
|
||||
500 1.997512 0.016920625 2.0564634 0.11517748 8482.9706
|
||||
600 2.0622304 0.078679437 2.0821362 0.28827312 4776.2481
|
||||
700 2.1106581 0.19687916 2.326279 0.85203631 2756.4602
|
||||
800 1.745752 0.29267549 1.978786 1.6290595 1832.812
|
||||
900 1.7925965 0.24064027 2.0273447 1.7295568 1516.7688
|
||||
1000 1.8280597 0.16642381 1.9844257 1.4314533 1517.3656
|
||||
1100 2.157879 0.10561715 2.2607067 0.98795205 1744.9669
|
||||
1200 1.7966771 0.057760855 1.8309261 0.54369976 2182.8259
|
||||
1300 2.2982472 0.036382605 2.3348878 0.45715755 2731.1166
|
||||
1400 1.7666501 0.038109497 1.7892555 0.32977405 3230.78
|
||||
1500 2.3048922 0.081153096 2.376275 0.45835895 3431.9991
|
||||
1600 1.8588345 0.067622658 1.9190878 0.39494686 3276.3398
|
||||
1700 2.1798404 0.1400767 2.3395072 0.71093539 2829.7905
|
||||
1800 1.9307392 0.14286145 2.0646696 0.84046137 2320.9547
|
||||
1900 2.0667728 0.16459518 2.1859494 1.1672332 1900.3276
|
||||
2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242
|
||||
Loop time of 0.435333 on 4 procs for 2000 steps with 400 atoms
|
||||
|
||||
Pair time (%) = 0.307563 (70.65)
|
||||
Neigh time (%) = 0.00319058 (0.732905)
|
||||
Comm time (%) = 0.0498152 (11.443)
|
||||
Outpt time (%) = 0.00043124 (0.0990598)
|
||||
Other time (%) = 0.0743331 (17.075)
|
||||
|
||||
Nlocal: 100 ave 109 max 96 min
|
||||
Histogram: 2 0 1 0 0 0 0 0 0 1
|
||||
Nghost: 116 ave 120 max 109 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Neighs: 471.5 ave 499 max 455 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1886
|
||||
Ave neighs/atom = 4.715
|
||||
Neighbor list builds = 179
|
||||
Dangerous builds = 148
|
||||
|
||||
# run dynamics on dense system
|
||||
|
||||
unfix 1
|
||||
fix 1 all nve/asphere
|
||||
|
||||
run 2000
|
||||
Memory usage per processor = 3.4007 Mbytes
|
||||
Step rot E_pair TotEng Press Volume
|
||||
2000 1.9311181 0.17205165 2.1209583 1.3796723 1657.9242
|
||||
2100 1.9516972 0.15050034 2.1113621 1.1750685 1657.9242
|
||||
2200 1.9410444 0.1617683 2.122019 1.2634696 1657.9242
|
||||
2300 1.918524 0.185457 2.1121008 1.3486177 1657.9242
|
||||
2400 1.9148973 0.18929207 2.1281553 1.3450222 1657.9242
|
||||
2500 1.8892245 0.21635014 2.1016576 1.5081781 1657.9242
|
||||
2600 1.9450941 0.15744769 2.0838764 1.2106283 1657.9242
|
||||
2700 1.9229729 0.18066636 2.1170012 1.3384025 1657.9242
|
||||
2800 1.9512215 0.15099706 2.0988077 1.2134331 1657.9242
|
||||
2900 1.9211263 0.18279161 2.0994515 1.362072 1657.9242
|
||||
3000 1.9067874 0.19775131 2.0931298 1.415749 1657.9242
|
||||
3100 1.9114597 0.1929634 2.1126573 1.4113467 1657.9242
|
||||
3200 1.9427391 0.15998497 2.0865325 1.3075156 1657.9242
|
||||
3300 1.9111628 0.19317321 2.1216596 1.4309722 1657.9242
|
||||
3400 1.9538367 0.14833072 2.1210148 1.2276275 1657.9242
|
||||
3500 1.9244321 0.17929374 2.0825174 1.3186878 1657.9242
|
||||
3600 1.9511866 0.15107093 2.1197989 1.2271649 1657.9242
|
||||
3700 1.9369592 0.16602536 2.0970215 1.2813456 1657.9242
|
||||
3800 1.9418194 0.16092741 2.1231381 1.2354327 1657.9242
|
||||
3900 1.9450474 0.15760145 2.1394611 1.2392217 1657.9242
|
||||
4000 1.9350001 0.16820285 2.114271 1.2677094 1657.9242
|
||||
Loop time of 0.68978 on 4 procs for 2000 steps with 400 atoms
|
||||
|
||||
Pair time (%) = 0.582906 (84.5062)
|
||||
Neigh time (%) = 0.0012635 (0.183174)
|
||||
Comm time (%) = 0.0669423 (9.70488)
|
||||
Outpt time (%) = 0.000495672 (0.0718595)
|
||||
Other time (%) = 0.0381718 (5.53392)
|
||||
|
||||
Nlocal: 100 ave 107 max 97 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
Nghost: 117.5 ave 121 max 115 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Neighs: 475.75 ave 511 max 446 min
|
||||
Histogram: 1 0 0 1 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1903
|
||||
Ave neighs/atom = 4.7575
|
||||
Neighbor list builds = 49
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,130 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 2-d LJ flow simulation
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.7
|
||||
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
create_box 3 box
|
||||
Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 420 atoms
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 1.12246
|
||||
pair_coeff * * 1.0 1.0 1.12246
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
60 atoms in group lower
|
||||
region 2 block INF INF 8.75 INF INF INF
|
||||
group upper region 2
|
||||
60 atoms in group upper
|
||||
group boundary union lower upper
|
||||
120 atoms in group boundary
|
||||
group flow subtract all boundary
|
||||
300 atoms in group flow
|
||||
|
||||
set group lower type 2
|
||||
60 settings made for type
|
||||
set group upper type 3
|
||||
60 settings made for type
|
||||
|
||||
# initial velocities
|
||||
|
||||
compute mobile flow temp
|
||||
velocity flow create 1.0 482748 temp mobile
|
||||
fix 1 all nve
|
||||
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
|
||||
fix_modify 2 temp mobile
|
||||
|
||||
# Couette flow
|
||||
|
||||
velocity lower set 0.0 0.0 0.0
|
||||
velocity upper set 3.0 0.0 0.0
|
||||
fix 3 boundary setforce 0.0 0.0 0.0
|
||||
fix 4 all enforce2d
|
||||
|
||||
# Poiseuille flow
|
||||
|
||||
#velocity boundary set 0.0 0.0 0.0
|
||||
#fix 3 lower setforce 0.0 0.0 0.0
|
||||
#fix 4 upper setforce 0.0 NULL 0.0
|
||||
#fix 5 upper aveforce 0.0 -1.0 0.0
|
||||
#fix 6 flow addforce 0.5 0.0 0.0
|
||||
#fix 7 all enforce2d
|
||||
|
||||
# Run
|
||||
|
||||
timestep 0.003
|
||||
thermo 500
|
||||
thermo_modify temp mobile
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
|
||||
#dump 1 all atom 500 dump.flow
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 adiam 1.2
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 adiam 1.2
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
run 10000
|
||||
Memory usage per processor = 2.05833 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1 0 0 0.71190476 0.52314537 571.54286
|
||||
500 1.0644427 -0.31382888 0 0.44395296 3.0013076 571.54286
|
||||
1000 1 -0.42965445 0 0.28225032 2.9612165 571.54286
|
||||
1500 1.0739874 -0.41189772 0 0.35267901 2.5621951 571.54286
|
||||
2000 1 -0.40814276 0 0.303762 2.9229578 571.54286
|
||||
2500 1.193111 -0.38495952 0 0.46442186 2.8338993 571.54286
|
||||
3000 1 -0.45584623 0 0.25605853 2.6569248 571.54286
|
||||
3500 0.98858828 -0.44619629 0 0.25758441 2.6526913 571.54286
|
||||
4000 1 -0.43273535 0 0.27916941 2.4570212 571.54286
|
||||
4500 1.0805289 -0.34947719 0 0.41975647 2.5797635 571.54286
|
||||
5000 1 -0.44623035 0 0.26567441 2.3488673 571.54286
|
||||
5500 1.0821688 -0.41710054 0 0.35330058 2.6341553 571.54286
|
||||
6000 1 -0.435398 0 0.27650676 2.496566 571.54286
|
||||
6500 1.0788214 -0.46009514 0 0.30792295 2.3714035 571.54286
|
||||
7000 1 -0.46345696 0 0.2484478 2.5780441 571.54286
|
||||
7500 1.0331063 -0.436765 0 0.29870828 2.2415868 571.54286
|
||||
8000 1 -0.42418776 0 0.287717 2.3469791 571.54286
|
||||
8500 1.0898295 -0.42615905 0 0.3496958 2.6162262 571.54286
|
||||
9000 1 -0.42341477 0 0.28849 2.5134824 571.54286
|
||||
9500 1.0851884 -0.4442208 0 0.32833001 2.4872143 571.54286
|
||||
10000 1 -0.39800556 0 0.3138992 2.5008138 571.54286
|
||||
Loop time of 0.281453 on 1 procs for 10000 steps with 420 atoms
|
||||
|
||||
Pair time (%) = 0.123218 (43.7794)
|
||||
Neigh time (%) = 0.0488372 (17.3518)
|
||||
Comm time (%) = 0.00895357 (3.1812)
|
||||
Outpt time (%) = 0.000183105 (0.0650572)
|
||||
Other time (%) = 0.100261 (35.6226)
|
||||
|
||||
Nlocal: 420 ave 420 max 420 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 48 ave 48 max 48 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 943 ave 943 max 943 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 943
|
||||
Ave neighs/atom = 2.24524
|
||||
Neighbor list builds = 983
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,130 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 2-d LJ flow simulation
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.7
|
||||
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
create_box 3 box
|
||||
Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 420 atoms
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 1.12246
|
||||
pair_coeff * * 1.0 1.0 1.12246
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
60 atoms in group lower
|
||||
region 2 block INF INF 8.75 INF INF INF
|
||||
group upper region 2
|
||||
60 atoms in group upper
|
||||
group boundary union lower upper
|
||||
120 atoms in group boundary
|
||||
group flow subtract all boundary
|
||||
300 atoms in group flow
|
||||
|
||||
set group lower type 2
|
||||
60 settings made for type
|
||||
set group upper type 3
|
||||
60 settings made for type
|
||||
|
||||
# initial velocities
|
||||
|
||||
compute mobile flow temp
|
||||
velocity flow create 1.0 482748 temp mobile
|
||||
fix 1 all nve
|
||||
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
|
||||
fix_modify 2 temp mobile
|
||||
|
||||
# Couette flow
|
||||
|
||||
velocity lower set 0.0 0.0 0.0
|
||||
velocity upper set 3.0 0.0 0.0
|
||||
fix 3 boundary setforce 0.0 0.0 0.0
|
||||
fix 4 all enforce2d
|
||||
|
||||
# Poiseuille flow
|
||||
|
||||
#velocity boundary set 0.0 0.0 0.0
|
||||
#fix 3 lower setforce 0.0 0.0 0.0
|
||||
#fix 4 upper setforce 0.0 NULL 0.0
|
||||
#fix 5 upper aveforce 0.0 -1.0 0.0
|
||||
#fix 6 flow addforce 0.5 0.0 0.0
|
||||
#fix 7 all enforce2d
|
||||
|
||||
# Run
|
||||
|
||||
timestep 0.003
|
||||
thermo 500
|
||||
thermo_modify temp mobile
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
|
||||
#dump 1 all atom 500 dump.flow
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 adiam 1.2
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 adiam 1.2
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
run 10000
|
||||
Memory usage per processor = 2.06206 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1 0 0 0.71190476 0.52314537 571.54286
|
||||
500 1.0951876 -0.33403931 0 0.44562996 3.2502319 571.54286
|
||||
1000 1 -0.3731019 0 0.33880286 2.8561715 571.54286
|
||||
1500 1.0366879 -0.36031105 0 0.37771198 3.0196355 571.54286
|
||||
2000 1 -0.41052955 0 0.30137522 2.865194 571.54286
|
||||
2500 1.1228407 -0.37042187 0 0.4289338 2.9445246 571.54286
|
||||
3000 1 -0.38445444 0 0.32745032 2.5935182 571.54286
|
||||
3500 0.9837004 -0.45271556 0 0.24758544 2.7982195 571.54286
|
||||
4000 1 -0.39733214 0 0.31457262 2.5610834 571.54286
|
||||
4500 1.1185501 -0.40471335 0 0.39158777 2.4136693 571.54286
|
||||
5000 1 -0.41474863 0 0.29715613 2.5475686 571.54286
|
||||
5500 1.0417966 -0.3742507 0 0.36740927 2.4667154 571.54286
|
||||
6000 1 -0.45012825 0 0.26177652 2.569894 571.54286
|
||||
6500 1.1544519 -0.3964682 0 0.42539161 2.5635202 571.54286
|
||||
7000 1 -0.44665963 0 0.26524513 2.4335307 571.54286
|
||||
7500 0.97729968 -0.47377977 0 0.22196453 2.7482936 571.54286
|
||||
8000 1 -0.42864525 0 0.28325951 2.3927949 571.54286
|
||||
8500 1.0967901 -0.40513897 0 0.37567113 2.612602 571.54286
|
||||
9000 1 -0.3847711 0 0.32713366 2.6900106 571.54286
|
||||
9500 1.0085423 -0.4393538 0 0.27863229 2.4411599 571.54286
|
||||
10000 1 -0.44847346 0 0.26343131 2.4997148 571.54286
|
||||
Loop time of 0.163524 on 4 procs for 10000 steps with 420 atoms
|
||||
|
||||
Pair time (%) = 0.0304542 (18.6237)
|
||||
Neigh time (%) = 0.0127853 (7.81863)
|
||||
Comm time (%) = 0.0743965 (45.4959)
|
||||
Outpt time (%) = 0.00036943 (0.225918)
|
||||
Other time (%) = 0.0455183 (27.8359)
|
||||
|
||||
Nlocal: 105 ave 115 max 94 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 40.25 ave 43 max 39 min
|
||||
Histogram: 2 0 1 0 0 0 0 0 0 1
|
||||
Neighs: 235.75 ave 297 max 170 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 943
|
||||
Ave neighs/atom = 2.24524
|
||||
Neighbor list builds = 965
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,130 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 2-d LJ flow simulation
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.7
|
||||
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
create_box 3 box
|
||||
Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 420 atoms
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 1.12246
|
||||
pair_coeff * * 1.0 1.0 1.12246
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
60 atoms in group lower
|
||||
region 2 block INF INF 8.75 INF INF INF
|
||||
group upper region 2
|
||||
60 atoms in group upper
|
||||
group boundary union lower upper
|
||||
120 atoms in group boundary
|
||||
group flow subtract all boundary
|
||||
300 atoms in group flow
|
||||
|
||||
set group lower type 2
|
||||
60 settings made for type
|
||||
set group upper type 3
|
||||
60 settings made for type
|
||||
|
||||
# initial velocities
|
||||
|
||||
compute mobile flow temp
|
||||
velocity flow create 1.0 482748 temp mobile
|
||||
fix 1 all nve
|
||||
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
|
||||
fix_modify 2 temp mobile
|
||||
|
||||
# Couette flow
|
||||
|
||||
#velocity lower set 0.0 0.0 0.0
|
||||
#velocity upper set 3.0 0.0 0.0
|
||||
#fix 3 boundary setforce 0.0 0.0 0.0
|
||||
#fix 4 all enforce2d
|
||||
|
||||
# Poiseuille flow
|
||||
|
||||
velocity boundary set 0.0 0.0 0.0
|
||||
fix 3 lower setforce 0.0 0.0 0.0
|
||||
fix 4 upper setforce 0.0 NULL 0.0
|
||||
fix 5 upper aveforce 0.0 -1.0 0.0
|
||||
fix 6 flow addforce 0.5 0.0 0.0
|
||||
fix 7 all enforce2d
|
||||
|
||||
# Run
|
||||
|
||||
timestep 0.003
|
||||
thermo 500
|
||||
thermo_modify temp mobile
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
|
||||
#dump 1 all atom 500 dump.flow
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
run 10000
|
||||
Memory usage per processor = 2.05833 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1 0 0 0.71190476 0.52314537 571.54286
|
||||
500 1.0990751 -0.36396768 0 0.41846911 2.522517 575.55806
|
||||
1000 1 -0.34609791 0 0.36580685 1.9736175 584.67179
|
||||
1500 1.2112861 -0.39062708 0 0.47169327 1.521881 587.24778
|
||||
2000 1 -0.39956949 0 0.31233527 1.2496669 583.00676
|
||||
2500 1.2236323 -0.40128446 0 0.46982521 1.4276891 570.03729
|
||||
3000 1 -0.48849341 0 0.22341135 1.5091366 553.64637
|
||||
3500 1.2404531 -0.63017461 0 0.25290984 1.7681313 535.22607
|
||||
4000 1 -0.71551407 0 -0.003609313 2.2075137 516.73151
|
||||
4500 1.2253143 -0.76279415 0 0.10951296 2.6154841 503.20466
|
||||
5000 1 -0.79031519 0 -0.078410425 3.0914492 499.10917
|
||||
5500 1.2025432 -0.74031121 0 0.115785 2.5889437 502.17138
|
||||
6000 1 -0.64454518 0 0.067359583 2.0907022 510.47702
|
||||
6500 1.2112733 -0.65703634 0 0.20527486 2.054449 515.41213
|
||||
7000 1 -0.61856581 0 0.093338954 1.9843361 516.79512
|
||||
7500 1.2212907 -0.67431193 0 0.19513077 1.9939559 517.17301
|
||||
8000 1 -0.69966668 0 0.012238083 2.1559293 510.52934
|
||||
8500 1.2245982 -0.73461969 0 0.13717758 2.4482542 506.2679
|
||||
9000 1 -0.697338 0 0.014566762 2.4757604 503.86953
|
||||
9500 1.1882 -0.66622491 0 0.17966032 2.3295348 505.67684
|
||||
10000 1 -0.70364194 0 0.008262826 2.218568 507.64681
|
||||
Loop time of 0.325207 on 1 procs for 10000 steps with 420 atoms
|
||||
|
||||
Pair time (%) = 0.13604 (41.8317)
|
||||
Neigh time (%) = 0.0279303 (8.58846)
|
||||
Comm time (%) = 0.00756764 (2.32702)
|
||||
Outpt time (%) = 0.00018692 (0.0574773)
|
||||
Other time (%) = 0.153482 (47.1953)
|
||||
|
||||
Nlocal: 420 ave 420 max 420 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 50 ave 50 max 50 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1116 ave 1116 max 1116 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1116
|
||||
Ave neighs/atom = 2.65714
|
||||
Neighbor list builds = 563
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,130 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 2-d LJ flow simulation
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.7
|
||||
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
create_box 3 box
|
||||
Created orthogonal box = (0 0 -0.321089) to (25.6871 22.2457 0.321089)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 420 atoms
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 1.12246
|
||||
pair_coeff * * 1.0 1.0 1.12246
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
60 atoms in group lower
|
||||
region 2 block INF INF 8.75 INF INF INF
|
||||
group upper region 2
|
||||
60 atoms in group upper
|
||||
group boundary union lower upper
|
||||
120 atoms in group boundary
|
||||
group flow subtract all boundary
|
||||
300 atoms in group flow
|
||||
|
||||
set group lower type 2
|
||||
60 settings made for type
|
||||
set group upper type 3
|
||||
60 settings made for type
|
||||
|
||||
# initial velocities
|
||||
|
||||
compute mobile flow temp
|
||||
velocity flow create 1.0 482748 temp mobile
|
||||
fix 1 all nve
|
||||
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
|
||||
fix_modify 2 temp mobile
|
||||
|
||||
# Couette flow
|
||||
|
||||
#velocity lower set 0.0 0.0 0.0
|
||||
#velocity upper set 3.0 0.0 0.0
|
||||
#fix 3 boundary setforce 0.0 0.0 0.0
|
||||
#fix 4 all enforce2d
|
||||
|
||||
# Poiseuille flow
|
||||
|
||||
velocity boundary set 0.0 0.0 0.0
|
||||
fix 3 lower setforce 0.0 0.0 0.0
|
||||
fix 4 upper setforce 0.0 NULL 0.0
|
||||
fix 5 upper aveforce 0.0 -1.0 0.0
|
||||
fix 6 flow addforce 0.5 0.0 0.0
|
||||
fix 7 all enforce2d
|
||||
|
||||
# Run
|
||||
|
||||
timestep 0.003
|
||||
thermo 500
|
||||
thermo_modify temp mobile
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
|
||||
#dump 1 all atom 500 dump.flow
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
run 10000
|
||||
Memory usage per processor = 2.06206 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1 0 0 0.71190476 0.52314537 571.54286
|
||||
500 1.0758737 -0.36090417 0 0.40501541 2.7822308 575.0659
|
||||
1000 1 -0.35701441 0 0.35489035 2.0575313 585.71407
|
||||
1500 1.2368663 -0.37709732 0 0.50343367 1.4865879 587.193
|
||||
2000 1 -0.39362939 0 0.31827537 1.4236 578.9418
|
||||
2500 1.2272957 -0.423819 0 0.44989866 1.454461 570.15856
|
||||
3000 1 -0.49143403 0 0.22047073 1.5345951 554.98633
|
||||
3500 1.2444908 -0.59761803 0 0.28834092 1.875379 537.01606
|
||||
4000 1 -0.70133161 0 0.010573147 2.1395416 521.46845
|
||||
4500 1.2212352 -0.74763375 0 0.1217694 2.7598268 507.63512
|
||||
5000 1 -0.7889135 0 -0.077008742 2.9809426 501.21601
|
||||
5500 1.1965673 -0.78262115 0 0.069220825 2.8192028 505.3984
|
||||
6000 1 -0.71434201 0 -0.0024372499 2.346053 512.05291
|
||||
6500 1.203859 -0.67621716 0 0.18081576 2.1621043 518.624
|
||||
7000 1 -0.66493592 0 0.046968842 1.8459166 519.01312
|
||||
7500 1.2065975 -0.69903932 0 0.15994317 2.0439995 515.42888
|
||||
8000 1 -0.71320172 0 -0.0012969589 2.1303566 511.98833
|
||||
8500 1.2146567 -0.72062191 0 0.144098 2.4268382 504.80659
|
||||
9000 1 -0.74806158 0 -0.036156822 2.5758196 502.43487
|
||||
9500 1.1970932 -0.73220717 0 0.1200092 2.585169 504.06803
|
||||
10000 1 -0.71105178 0 0.00085297794 2.3528576 507.92052
|
||||
Loop time of 0.221735 on 4 procs for 10000 steps with 420 atoms
|
||||
|
||||
Pair time (%) = 0.0346093 (15.6084)
|
||||
Neigh time (%) = 0.0078088 (3.52168)
|
||||
Comm time (%) = 0.0817159 (36.8529)
|
||||
Outpt time (%) = 0.000392079 (0.176823)
|
||||
Other time (%) = 0.097209 (43.8402)
|
||||
|
||||
Nlocal: 105 ave 107 max 103 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 42.75 ave 46 max 37 min
|
||||
Histogram: 1 0 0 0 0 0 0 2 0 1
|
||||
Neighs: 276.5 ave 295 max 257 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 1106
|
||||
Ave neighs/atom = 2.63333
|
||||
Neighbor list builds = 564
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,149 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 2d friction simulation
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.9
|
||||
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
|
||||
region box block 0 50 0 22 -0.25 0.25
|
||||
create_box 4 box
|
||||
Created orthogonal box = (0 0 -0.283174) to (56.6348 43.1615 0.283174)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
mass 4 1.0
|
||||
|
||||
# atom regions
|
||||
|
||||
region lo-fixed block INF INF INF 1.1 INF INF
|
||||
region lo-slab block INF INF INF 7 INF INF
|
||||
region above-lo block INF INF INF 7 INF INF side out
|
||||
region hi-fixed block INF INF 20.9 INF INF INF
|
||||
region hi-slab block INF INF 15 INF INF INF
|
||||
region below-hi block INF INF 15 INF INF INF side out
|
||||
region lo-asperity sphere 32 7 0 8
|
||||
region hi-asperity sphere 18 15 0 8
|
||||
region lo-half-sphere intersect 2 lo-asperity above-lo
|
||||
region hi-half-sphere intersect 2 hi-asperity below-hi
|
||||
|
||||
# create 2 surfaces with asperities
|
||||
|
||||
create_atoms 1 region lo-slab
|
||||
Created 750 atoms
|
||||
create_atoms 1 region hi-slab
|
||||
Created 750 atoms
|
||||
create_atoms 2 region lo-half-sphere
|
||||
Created 112 atoms
|
||||
create_atoms 3 region hi-half-sphere
|
||||
Created 112 atoms
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
|
||||
# define groups
|
||||
|
||||
group lo region lo-slab
|
||||
750 atoms in group lo
|
||||
group lo type 2
|
||||
862 atoms in group lo
|
||||
group hi region hi-slab
|
||||
750 atoms in group hi
|
||||
group hi type 3
|
||||
862 atoms in group hi
|
||||
group lo-fixed region lo-fixed
|
||||
150 atoms in group lo-fixed
|
||||
group hi-fixed region hi-fixed
|
||||
150 atoms in group hi-fixed
|
||||
group boundary union lo-fixed hi-fixed
|
||||
300 atoms in group boundary
|
||||
group mobile subtract all boundary
|
||||
1424 atoms in group mobile
|
||||
|
||||
set group lo-fixed type 4
|
||||
150 settings made for type
|
||||
set group hi-fixed type 4
|
||||
150 settings made for type
|
||||
|
||||
# initial velocities
|
||||
|
||||
compute new mobile temp/partial 0 1 0
|
||||
velocity mobile create 0.1 482748 temp new
|
||||
velocity hi set 1.0 0.0 0.0 sum yes
|
||||
|
||||
# fixes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 boundary setforce 0.0 0.0 0.0
|
||||
fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0
|
||||
fix_modify 3 temp new
|
||||
fix 4 all enforce2d
|
||||
|
||||
# Run
|
||||
|
||||
timestep 0.0025
|
||||
thermo 1000
|
||||
thermo_modify temp new
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
|
||||
#dump 1 all atom 500 dump.friction
|
||||
|
||||
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
run 20000
|
||||
Memory usage per processor = 2.05872 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0.1 -3.1333672 0 -3.0921259 -1.1437867 2444.9333
|
||||
1000 0.1 -3.0915465 0 -3.0503052 0.010015559 2444.9333
|
||||
2000 0.1 -3.0826487 0 -3.0414074 -0.42012889 2444.9333
|
||||
3000 0.089819692 -3.07584 0 -3.0387972 -0.25252108 2444.9333
|
||||
4000 0.098489874 -3.0667093 0 -3.0260907 -0.25506538 2444.9333
|
||||
5000 0.11379986 -3.0557087 0 -3.0087762 -0.080871179 2444.9333
|
||||
6000 0.11269179 -3.04532 0 -2.9988445 -0.33381202 2444.9333
|
||||
7000 0.1 -3.0380598 0 -2.9968185 -0.32423909 2444.9333
|
||||
8000 0.1 -3.0346453 0 -2.993404 -0.38015347 2444.9333
|
||||
9000 0.1 -3.0324305 0 -2.9911892 -0.42940009 2444.9333
|
||||
10000 0.11811429 -3.0334969 0 -2.984785 -0.32538147 2444.9333
|
||||
11000 0.11627653 -3.0344827 0 -2.9865288 -0.45037424 2444.9333
|
||||
12000 0.11250787 -3.0472157 0 -3.000816 -0.27347069 2444.9333
|
||||
13000 0.11429889 -3.0455404 0 -2.9984021 -0.28832736 2444.9333
|
||||
14000 0.11292741 -3.0466673 0 -3.0000946 -0.38939496 2444.9333
|
||||
15000 0.11239299 -3.0460428 0 -2.9996905 -0.35437935 2444.9333
|
||||
16000 0.11775554 -3.0457709 0 -2.997207 -0.14263984 2444.9333
|
||||
17000 0.11456908 -3.0459128 0 -2.998663 -0.3686153 2444.9333
|
||||
18000 0.1165453 -3.0454305 0 -2.9973657 -0.3572725 2444.9333
|
||||
19000 0.11403056 -3.0440495 0 -2.9970218 -0.25462158 2444.9333
|
||||
20000 0.11801421 -3.0462201 0 -2.9975495 -0.23484136 2444.9333
|
||||
Loop time of 5.81332 on 1 procs for 20000 steps with 1724 atoms
|
||||
|
||||
Pair time (%) = 4.61616 (79.4065)
|
||||
Neigh time (%) = 0.319022 (5.48777)
|
||||
Comm time (%) = 0.0435834 (0.749715)
|
||||
Outpt time (%) = 0.000309229 (0.00531931)
|
||||
Other time (%) = 0.834251 (14.3507)
|
||||
|
||||
Nlocal: 1724 ave 1724 max 1724 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 147 ave 147 max 147 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 14384 ave 14384 max 14384 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 14384
|
||||
Ave neighs/atom = 8.34339
|
||||
Neighbor list builds = 723
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,149 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 2d friction simulation
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.9
|
||||
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
|
||||
region box block 0 50 0 22 -0.25 0.25
|
||||
create_box 4 box
|
||||
Created orthogonal box = (0 0 -0.283174) to (56.6348 43.1615 0.283174)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
mass 4 1.0
|
||||
|
||||
# atom regions
|
||||
|
||||
region lo-fixed block INF INF INF 1.1 INF INF
|
||||
region lo-slab block INF INF INF 7 INF INF
|
||||
region above-lo block INF INF INF 7 INF INF side out
|
||||
region hi-fixed block INF INF 20.9 INF INF INF
|
||||
region hi-slab block INF INF 15 INF INF INF
|
||||
region below-hi block INF INF 15 INF INF INF side out
|
||||
region lo-asperity sphere 32 7 0 8
|
||||
region hi-asperity sphere 18 15 0 8
|
||||
region lo-half-sphere intersect 2 lo-asperity above-lo
|
||||
region hi-half-sphere intersect 2 hi-asperity below-hi
|
||||
|
||||
# create 2 surfaces with asperities
|
||||
|
||||
create_atoms 1 region lo-slab
|
||||
Created 750 atoms
|
||||
create_atoms 1 region hi-slab
|
||||
Created 750 atoms
|
||||
create_atoms 2 region lo-half-sphere
|
||||
Created 112 atoms
|
||||
create_atoms 3 region hi-half-sphere
|
||||
Created 112 atoms
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
|
||||
# define groups
|
||||
|
||||
group lo region lo-slab
|
||||
750 atoms in group lo
|
||||
group lo type 2
|
||||
862 atoms in group lo
|
||||
group hi region hi-slab
|
||||
750 atoms in group hi
|
||||
group hi type 3
|
||||
862 atoms in group hi
|
||||
group lo-fixed region lo-fixed
|
||||
150 atoms in group lo-fixed
|
||||
group hi-fixed region hi-fixed
|
||||
150 atoms in group hi-fixed
|
||||
group boundary union lo-fixed hi-fixed
|
||||
300 atoms in group boundary
|
||||
group mobile subtract all boundary
|
||||
1424 atoms in group mobile
|
||||
|
||||
set group lo-fixed type 4
|
||||
150 settings made for type
|
||||
set group hi-fixed type 4
|
||||
150 settings made for type
|
||||
|
||||
# initial velocities
|
||||
|
||||
compute new mobile temp/partial 0 1 0
|
||||
velocity mobile create 0.1 482748 temp new
|
||||
velocity hi set 1.0 0.0 0.0 sum yes
|
||||
|
||||
# fixes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 boundary setforce 0.0 0.0 0.0
|
||||
fix 3 mobile temp/rescale 200 0.1 0.1 0.02 1.0
|
||||
fix_modify 3 temp new
|
||||
fix 4 all enforce2d
|
||||
|
||||
# Run
|
||||
|
||||
timestep 0.0025
|
||||
thermo 1000
|
||||
thermo_modify temp new
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
|
||||
#dump 1 all atom 500 dump.friction
|
||||
|
||||
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
run 20000
|
||||
Memory usage per processor = 2.06213 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0.1 -3.1333672 0 -3.0921259 -1.1437867 2444.9333
|
||||
1000 0.081958665 -3.0927273 0 -3.0589265 -0.021846131 2444.9333
|
||||
2000 0.082641883 -3.0850764 0 -3.0509938 -0.44960195 2444.9333
|
||||
3000 0.092293442 -3.0748001 0 -3.0367371 -0.25353161 2444.9333
|
||||
4000 0.096012911 -3.0565129 0 -3.0169159 -0.027669541 2444.9333
|
||||
5000 0.1 -3.0465555 0 -3.0053142 -0.099323956 2444.9333
|
||||
6000 0.11642983 -3.0390782 0 -2.991061 -0.21034609 2444.9333
|
||||
7000 0.11597774 -3.0331763 0 -2.9853456 -0.46345898 2444.9333
|
||||
8000 0.11937899 -3.0305561 0 -2.9813226 -0.30773083 2444.9333
|
||||
9000 0.111108 -3.0274067 0 -2.9815843 -0.5243749 2444.9333
|
||||
10000 0.11666452 -3.0170603 0 -2.9689463 -0.37436916 2444.9333
|
||||
11000 0.11005147 -3.0140407 0 -2.9686541 -0.46293236 2444.9333
|
||||
12000 0.11286668 -3.0174735 0 -2.9709258 -0.28406396 2444.9333
|
||||
13000 0.11280782 -3.0238036 0 -2.9772802 -0.41208934 2444.9333
|
||||
14000 0.1 -3.0332072 0 -2.9919659 -0.1785001 2444.9333
|
||||
15000 0.1148413 -3.0339717 0 -2.9866096 -0.4418584 2444.9333
|
||||
16000 0.11194137 -3.0322089 0 -2.9860428 -0.29354474 2444.9333
|
||||
17000 0.10699902 -3.0395654 0 -2.9954376 -0.37176577 2444.9333
|
||||
18000 0.11091428 -3.0400366 0 -2.9942941 -0.19329155 2444.9333
|
||||
19000 0.1094118 -3.0432032 0 -2.9980803 -0.38516174 2444.9333
|
||||
20000 0.11137857 -3.0442022 0 -2.9982683 -0.37419199 2444.9333
|
||||
Loop time of 1.88423 on 4 procs for 20000 steps with 1724 atoms
|
||||
|
||||
Pair time (%) = 1.16936 (62.0606)
|
||||
Neigh time (%) = 0.0789706 (4.19113)
|
||||
Comm time (%) = 0.359838 (19.0974)
|
||||
Outpt time (%) = 0.00038904 (0.0206471)
|
||||
Other time (%) = 0.275667 (14.6302)
|
||||
|
||||
Nlocal: 431 ave 493 max 377 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
Nghost: 96 ave 125 max 77 min
|
||||
Histogram: 1 1 0 0 1 0 0 0 0 1
|
||||
Neighs: 3596 ave 4228 max 3139 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 14384
|
||||
Ave neighs/atom = 8.34339
|
||||
Neighbor list builds = 700
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,80 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*2
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*2
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*2
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 40 0 ${zz}
|
||||
region box block 0 40 0 40 0 40
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 256000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut/gpu 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 46.8462 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733683 0 -4.6133768 -5.0196737
|
||||
100 0.75865617 -5.760326 0 -4.6223462 0.19586079
|
||||
200 0.75643086 -5.7572859 0 -4.6226441 0.22641241
|
||||
300 0.74927423 -5.7463997 0 -4.6224927 0.29737707
|
||||
400 0.74049393 -5.7329259 0 -4.6221893 0.3776681
|
||||
500 0.73092107 -5.7182622 0 -4.6218849 0.46900655
|
||||
600 0.72320925 -5.7064076 0 -4.6215979 0.53444495
|
||||
700 0.71560947 -5.6946702 0 -4.6212602 0.59905402
|
||||
800 0.71306623 -5.6906095 0 -4.6210143 0.62859381
|
||||
900 0.70675364 -5.6807352 0 -4.6206089 0.68471945
|
||||
1000 0.7044073 -5.6771664 0 -4.6205596 0.70033364
|
||||
Loop time of 21.016 on 1 procs for 1000 steps with 256000 atoms
|
||||
|
||||
Pair time (%) = 13.4638 (64.0646)
|
||||
Neigh time (%) = 6.74725e-05 (0.000321052)
|
||||
Comm time (%) = 1.09447 (5.20779)
|
||||
Outpt time (%) = 0.0103211 (0.0491108)
|
||||
Other time (%) = 6.44732 (30.6781)
|
||||
|
||||
Nlocal: 256000 ave 256000 max 256000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 69917 ave 69917 max 69917 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,80 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*2
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*2
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*2
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 40 0 ${zz}
|
||||
region box block 0 40 0 40 0 40
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 256000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut/gpu 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 14.5208 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -6.7733683 0 -4.6133768 -5.0196737
|
||||
100 0.75865617 -5.760326 0 -4.6223462 0.19586079
|
||||
200 0.75643087 -5.7572859 0 -4.6226441 0.2264124
|
||||
300 0.74927423 -5.7463997 0 -4.6224927 0.29737713
|
||||
400 0.7404939 -5.7329258 0 -4.6221893 0.37766836
|
||||
500 0.73092104 -5.7182626 0 -4.6218853 0.46900587
|
||||
600 0.72320865 -5.7064076 0 -4.6215989 0.53444677
|
||||
700 0.71560468 -5.6946635 0 -4.6212607 0.59907258
|
||||
800 0.7130474 -5.6905859 0 -4.621019 0.62875333
|
||||
900 0.70683795 -5.680864 0 -4.6206112 0.6839564
|
||||
1000 0.70454326 -5.6773491 0 -4.6205384 0.69975744
|
||||
Loop time of 8.72938 on 4 procs for 1000 steps with 256000 atoms
|
||||
|
||||
Pair time (%) = 5.30046 (60.7198)
|
||||
Neigh time (%) = 5.78761e-05 (0.000663004)
|
||||
Comm time (%) = 1.62433 (18.6076)
|
||||
Outpt time (%) = 0.0129588 (0.14845)
|
||||
Other time (%) = 1.79157 (20.5235)
|
||||
|
||||
Nlocal: 64000 ave 64066 max 63924 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Nghost: 30535 ave 30559 max 30518 min
|
||||
Histogram: 1 0 1 0 1 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,80 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1 threads_per_atom 8
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*2
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*2
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*2
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 40 0 ${zz}
|
||||
region box block 0 40 0 40 0 40
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 256000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut/gpu 5.0
|
||||
pair_coeff 1 1 1.0 1.0 5.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 58.5717 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -7.1616931 0 -5.0017016 -5.6743465
|
||||
100 0.75998441 -6.1430228 0 -5.0030506 -0.43702263
|
||||
200 0.75772859 -6.1397321 0 -5.0031437 -0.40563811
|
||||
300 0.75030002 -6.1286578 0 -5.0032122 -0.33104717
|
||||
400 0.73999054 -6.1132463 0 -5.0032649 -0.24001424
|
||||
500 0.73224838 -6.1016938 0 -5.0033255 -0.16524979
|
||||
600 0.72455889 -6.0902001 0 -5.003366 -0.099949772
|
||||
700 0.71911385 -6.0820798 0 -5.0034133 -0.046759186
|
||||
800 0.71253787 -6.0722342 0 -5.0034316 0.0019671065
|
||||
900 0.70835425 -6.0659819 0 -5.0034546 0.037482543
|
||||
1000 0.70648171 -6.0631852 0 -5.0034668 0.057159495
|
||||
Loop time of 53.1575 on 1 procs for 1000 steps with 256000 atoms
|
||||
|
||||
Pair time (%) = 45.4859 (85.5682)
|
||||
Neigh time (%) = 7.9155e-05 (0.000148907)
|
||||
Comm time (%) = 1.40304 (2.63941)
|
||||
Outpt time (%) = 0.00999498 (0.0188026)
|
||||
Other time (%) = 6.25847 (11.7734)
|
||||
|
||||
Nlocal: 256000 ave 256000 max 256000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 141542 ave 141542 max 141542 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,80 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1 threads_per_atom 8
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
variable xx equal 20*$x
|
||||
variable xx equal 20*2
|
||||
variable yy equal 20*$y
|
||||
variable yy equal 20*2
|
||||
variable zz equal 20*$z
|
||||
variable zz equal 20*2
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 ${yy} 0 ${zz}
|
||||
region box block 0 40 0 40 0 ${zz}
|
||||
region box block 0 40 0 40 0 40
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (67.1838 67.1838 67.1838)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 256000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
pair_style lj/cut/gpu 5.0
|
||||
pair_coeff 1 1 1.0 1.0 5.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 20 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
thermo 100
|
||||
run 1000
|
||||
Memory usage per processor = 20.382 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1.44 -7.1616931 0 -5.0017016 -5.6743465
|
||||
100 0.75998441 -6.1430228 0 -5.0030506 -0.43702263
|
||||
200 0.75772859 -6.1397321 0 -5.0031437 -0.40563811
|
||||
300 0.75030002 -6.1286578 0 -5.0032122 -0.33104718
|
||||
400 0.73999055 -6.1132463 0 -5.0032649 -0.24001425
|
||||
500 0.73224835 -6.1016938 0 -5.0033256 -0.16524973
|
||||
600 0.72455878 -6.0902 0 -5.0033661 -0.099949172
|
||||
700 0.71911606 -6.0820833 0 -5.0034134 -0.046771469
|
||||
800 0.71253754 -6.0722337 0 -5.0034316 0.0019725827
|
||||
900 0.70832904 -6.0659437 0 -5.0034543 0.03758241
|
||||
1000 0.70634002 -6.062973 0 -5.0034671 0.057951142
|
||||
Loop time of 26.0448 on 4 procs for 1000 steps with 256000 atoms
|
||||
|
||||
Pair time (%) = 18.6673 (71.674)
|
||||
Neigh time (%) = 6.55651e-05 (0.00025174)
|
||||
Comm time (%) = 5.797 (22.2578)
|
||||
Outpt time (%) = 0.0719919 (0.276416)
|
||||
Other time (%) = 1.50839 (5.79152)
|
||||
|
||||
Nlocal: 64000 ave 64092 max 63823 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 64384.2 ave 64490 max 64211 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 50
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,80 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# GI-System
|
||||
|
||||
units metal
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1
|
||||
|
||||
atom_style charge
|
||||
read_data data.phosphate
|
||||
orthogonal box = (33.0201 33.0201 33.0201) to (86.9799 86.9799 86.9799)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
10950 atoms
|
||||
reading velocities ...
|
||||
10950 velocities
|
||||
|
||||
replicate 3 3 3
|
||||
orthogonal box = (33.0201 33.0201 33.0201) to (194.899 194.899 194.899)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
295650 atoms
|
||||
|
||||
pair_style lj/cut/coul/long/gpu 15.0
|
||||
|
||||
pair_coeff 1 1 0.0 0.29
|
||||
pair_coeff 1 2 0.0 0.29
|
||||
pair_coeff 1 3 0.000668 2.5738064
|
||||
pair_coeff 2 2 0.0 0.29
|
||||
pair_coeff 2 3 0.004251 1.91988674
|
||||
pair_coeff 3 3 0.012185 2.91706967
|
||||
|
||||
kspace_style pppm/gpu 1e-5
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
thermo 100
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
|
||||
run 200
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.210051
|
||||
grid = 108 108 108
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000178801
|
||||
estimated relative force accuracy = 1.24171e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 1520875 1259712
|
||||
Memory usage per processor = 266.927 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 400.30257 -2381941.6 0 -2366643.8 -449.96842 4242016.4
|
||||
100 411.69681 -2392428.5 0 -2376695.3 7046.698 4308883.5
|
||||
200 401.28392 -2394152.5 0 -2378817.2 3243.2685 4334284.4
|
||||
Loop time of 154.943 on 1 procs for 200 steps with 295650 atoms
|
||||
|
||||
Pair time (%) = 12.0178 (7.75625)
|
||||
Kspce time (%) = 80.3771 (51.8753)
|
||||
Neigh time (%) = 0.0138304 (0.00892614)
|
||||
Comm time (%) = 0.348981 (0.225232)
|
||||
Outpt time (%) = 0.00180006 (0.00116176)
|
||||
Other time (%) = 62.1834 (40.1331)
|
||||
|
||||
FFT time (% of Kspce) = 56.9885 (70.9013)
|
||||
FFT Gflps 3d (1d only) = 1.24196 3.00739
|
||||
|
||||
Nlocal: 295650 ave 295650 max 295650 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 226982 ave 226982 max 226982 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,80 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# GI-System
|
||||
|
||||
units metal
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1
|
||||
|
||||
atom_style charge
|
||||
read_data data.phosphate
|
||||
orthogonal box = (33.0201 33.0201 33.0201) to (86.9799 86.9799 86.9799)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
10950 atoms
|
||||
reading velocities ...
|
||||
10950 velocities
|
||||
|
||||
replicate 3 3 3
|
||||
orthogonal box = (33.0201 33.0201 33.0201) to (194.899 194.899 194.899)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
295650 atoms
|
||||
|
||||
pair_style lj/cut/coul/long/gpu 15.0
|
||||
|
||||
pair_coeff 1 1 0.0 0.29
|
||||
pair_coeff 1 2 0.0 0.29
|
||||
pair_coeff 1 3 0.000668 2.5738064
|
||||
pair_coeff 2 2 0.0 0.29
|
||||
pair_coeff 2 3 0.004251 1.91988674
|
||||
pair_coeff 3 3 0.012185 2.91706967
|
||||
|
||||
kspace_style pppm/gpu 1e-5
|
||||
|
||||
neighbor 2.0 bin
|
||||
|
||||
thermo 100
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all npt temp 400 400 0.01 iso 1000.0 1000.0 1.0
|
||||
run 200
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.210051
|
||||
grid = 108 108 108
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000178801
|
||||
estimated relative force accuracy = 1.24171e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 427915 314928
|
||||
Memory usage per processor = 80.0769 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 400.30257 -2381941.6 0 -2366643.8 -449.96842 4242016.4
|
||||
100 411.69681 -2392428.5 0 -2376695.3 7046.698 4308883.5
|
||||
200 401.28392 -2394152.5 0 -2378817.2 3243.2685 4334284.4
|
||||
Loop time of 56.1151 on 4 procs for 200 steps with 295650 atoms
|
||||
|
||||
Pair time (%) = 4.55937 (8.12503)
|
||||
Kspce time (%) = 34.5442 (61.5596)
|
||||
Neigh time (%) = 0.00624901 (0.0111361)
|
||||
Comm time (%) = 0.470437 (0.838343)
|
||||
Outpt time (%) = 0.000446558 (0.000795789)
|
||||
Other time (%) = 16.5344 (29.4651)
|
||||
|
||||
FFT time (% of Kspce) = 22.6526 (65.5758)
|
||||
FFT Gflps 3d (1d only) = 3.12448 11.5533
|
||||
|
||||
Nlocal: 73912.5 ave 74223 max 73638 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Nghost: 105257 ave 105797 max 104698 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Neighbor list builds = 6
|
||||
Dangerous builds = 0
|
||||
unfix 1
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,135 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Rhodopsin model
|
||||
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
units real
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
pair_style lj/charmm/coul/long/gpu 8.0 10.0
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm/gpu 1e-4
|
||||
|
||||
read_data data.rhodo
|
||||
orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
32000 atoms
|
||||
reading velocities ...
|
||||
32000 velocities
|
||||
scanning bonds ...
|
||||
4 = max bonds/atom
|
||||
scanning angles ...
|
||||
18 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
40 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
4 = max impropers/atom
|
||||
reading bonds ...
|
||||
27723 bonds
|
||||
reading angles ...
|
||||
40467 angles
|
||||
reading dihedrals ...
|
||||
56829 dihedrals
|
||||
reading impropers ...
|
||||
1034 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
12 = max # of 1-3 neighbors
|
||||
24 = max # of 1-4 neighbors
|
||||
26 = max # of special neighbors
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 2 $y $z
|
||||
replicate 2 2 $z
|
||||
replicate 2 2 2
|
||||
orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
256000 atoms
|
||||
221784 bonds
|
||||
323736 angles
|
||||
454632 dihedrals
|
||||
8272 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
12 = max # of 1-3 neighbors
|
||||
24 = max # of 1-4 neighbors
|
||||
26 = max # of special neighbors
|
||||
|
||||
fix 1 all shake 0.0001 5 0 m 1.0 a 232
|
||||
12936 = # of size 2 clusters
|
||||
29064 = # of size 3 clusters
|
||||
5976 = # of size 4 clusters
|
||||
33864 = # of frozen angles
|
||||
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
|
||||
|
||||
special_bonds charmm
|
||||
|
||||
thermo 100
|
||||
thermo_style multi
|
||||
timestep 2.0
|
||||
|
||||
run 200
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.245959
|
||||
grid = 48 64 60
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0410392
|
||||
estimated relative force accuracy = 0.000123588
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 237705 184320
|
||||
Memory usage per processor = 760.048 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = 157024.0504 KinEng = 172792.6155 Temp = 301.1796
|
||||
PotEng = -15768.5651 E_bond = 28164.9917 E_angle = 117224.0742
|
||||
E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6323
|
||||
E_coul = 1894295.6635 E_long = -2130488.8032 Press = 9562.1557
|
||||
Volume = 2457390.7959
|
||||
---------------- Step 100 ----- CPU = 36.3779 (sec) ----------------
|
||||
TotEng = -233301.6813 KinEng = 123222.9259 Temp = 214.7790
|
||||
PotEng = -356524.6072 E_bond = 13098.4672 E_angle = 56766.9111
|
||||
E_dihed = 45556.8240 E_impro = 1313.9378 E_vdwl = -40863.9278
|
||||
E_coul = 1705084.7672 E_long = -2137481.5867 Press = -1634.3912
|
||||
Volume = 2522232.6302
|
||||
---------------- Step 200 ----- CPU = 70.7784 (sec) ----------------
|
||||
TotEng = -308342.0030 KinEng = 108937.4160 Temp = 189.8792
|
||||
PotEng = -417279.4189 E_bond = 9579.0134 E_angle = 47373.6274
|
||||
E_dihed = 39847.4817 E_impro = 967.6755 E_vdwl = -23635.2960
|
||||
E_coul = 1646633.4711 E_long = -2138045.3918 Press = -1185.9327
|
||||
Volume = 2554683.1533
|
||||
Loop time of 70.7784 on 1 procs for 200 steps with 256000 atoms
|
||||
|
||||
Pair time (%) = 10.0374 (14.1815)
|
||||
Bond time (%) = 27.2471 (38.4963)
|
||||
Kspce time (%) = 7.19169 (10.1608)
|
||||
Neigh time (%) = 5.43951 (7.68527)
|
||||
Comm time (%) = 0.681534 (0.962912)
|
||||
Outpt time (%) = 0.00139809 (0.0019753)
|
||||
Other time (%) = 20.1798 (28.5112)
|
||||
|
||||
FFT time (% of Kspce) = 5.17983 (72.0253)
|
||||
FFT Gflps 3d (1d only) = 1.72575 2.95071
|
||||
|
||||
Nlocal: 256000 ave 256000 max 256000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 161662 ave 161662 max 161662 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 7.43187
|
||||
Neighbor list builds = 31
|
||||
Dangerous builds = 12
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,135 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Rhodopsin model
|
||||
|
||||
newton off
|
||||
package gpu force/neigh 0 1 1
|
||||
|
||||
variable x index 2
|
||||
variable y index 2
|
||||
variable z index 2
|
||||
|
||||
units real
|
||||
neigh_modify delay 5 every 1
|
||||
|
||||
atom_style full
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
pair_style lj/charmm/coul/long/gpu 8.0 10.0
|
||||
pair_modify mix arithmetic
|
||||
kspace_style pppm/gpu 1e-4
|
||||
|
||||
read_data data.rhodo
|
||||
orthogonal box = (-27.5 -38.5 -36.2676) to (27.5 38.5 36.2645)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
32000 atoms
|
||||
reading velocities ...
|
||||
32000 velocities
|
||||
scanning bonds ...
|
||||
4 = max bonds/atom
|
||||
scanning angles ...
|
||||
18 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
40 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
4 = max impropers/atom
|
||||
reading bonds ...
|
||||
27723 bonds
|
||||
reading angles ...
|
||||
40467 angles
|
||||
reading dihedrals ...
|
||||
56829 dihedrals
|
||||
reading impropers ...
|
||||
1034 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
12 = max # of 1-3 neighbors
|
||||
24 = max # of 1-4 neighbors
|
||||
26 = max # of special neighbors
|
||||
|
||||
replicate $x $y $z
|
||||
replicate 2 $y $z
|
||||
replicate 2 2 $z
|
||||
replicate 2 2 2
|
||||
orthogonal box = (-27.5 -38.5 -36.2676) to (82.5 115.5 108.797)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
256000 atoms
|
||||
221784 bonds
|
||||
323736 angles
|
||||
454632 dihedrals
|
||||
8272 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
12 = max # of 1-3 neighbors
|
||||
24 = max # of 1-4 neighbors
|
||||
26 = max # of special neighbors
|
||||
|
||||
fix 1 all shake 0.0001 5 0 m 1.0 a 232
|
||||
12936 = # of size 2 clusters
|
||||
29064 = # of size 3 clusters
|
||||
5976 = # of size 4 clusters
|
||||
33864 = # of frozen angles
|
||||
fix 2 all npt temp 300.0 300.0 100.0 z 0.0 0.0 1000.0 mtk no pchain 0 tchain 1
|
||||
|
||||
special_bonds charmm
|
||||
|
||||
thermo 100
|
||||
thermo_style multi
|
||||
timestep 2.0
|
||||
|
||||
run 200
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.245959
|
||||
grid = 48 64 60
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0410392
|
||||
estimated relative force accuracy = 0.000123588
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 68635 46080
|
||||
Memory usage per processor = 250.358 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = 157024.0504 KinEng = 172792.6155 Temp = 301.1796
|
||||
PotEng = -15768.5651 E_bond = 28164.9917 E_angle = 117224.0742
|
||||
E_dihed = 61174.8491 E_impro = 3752.0273 E_vdwl = 10108.6323
|
||||
E_coul = 1894295.6635 E_long = -2130488.8032 Press = 9562.1557
|
||||
Volume = 2457390.7959
|
||||
---------------- Step 100 ----- CPU = 12.3409 (sec) ----------------
|
||||
TotEng = -233301.6797 KinEng = 123222.9259 Temp = 214.7790
|
||||
PotEng = -356524.6057 E_bond = 13098.4672 E_angle = 56766.9111
|
||||
E_dihed = 45556.8240 E_impro = 1313.9378 E_vdwl = -40863.9278
|
||||
E_coul = 1705084.7688 E_long = -2137481.5867 Press = -1634.3910
|
||||
Volume = 2522232.6302
|
||||
---------------- Step 200 ----- CPU = 23.6590 (sec) ----------------
|
||||
TotEng = -308341.9699 KinEng = 108937.4196 Temp = 189.8792
|
||||
PotEng = -417279.3895 E_bond = 9579.0134 E_angle = 47373.6274
|
||||
E_dihed = 39847.4807 E_impro = 967.6755 E_vdwl = -23635.2996
|
||||
E_coul = 1646633.5046 E_long = -2138045.3916 Press = -1185.9299
|
||||
Volume = 2554683.1519
|
||||
Loop time of 23.6591 on 4 procs for 200 steps with 256000 atoms
|
||||
|
||||
Pair time (%) = 4.81669 (20.3587)
|
||||
Bond time (%) = 6.52579 (27.5826)
|
||||
Kspce time (%) = 4.48765 (18.968)
|
||||
Neigh time (%) = 1.3238 (5.5953)
|
||||
Comm time (%) = 0.490551 (2.07342)
|
||||
Outpt time (%) = 0.000454485 (0.00192098)
|
||||
Other time (%) = 6.01414 (25.42)
|
||||
|
||||
FFT time (% of Kspce) = 1.77734 (39.6051)
|
||||
FFT Gflps 3d (1d only) = 5.02949 11.6654
|
||||
|
||||
Nlocal: 64000 ave 64001 max 63999 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 70656.5 ave 70660 max 70654 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 0
|
||||
Ave neighs/atom = 0
|
||||
Ave special neighs/atom = 7.43187
|
||||
Neighbor list builds = 31
|
||||
Dangerous builds = 12
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,90 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# This script reproduces stress trajectories from Fig. 1 in
|
||||
# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
|
||||
#
|
||||
# Three thermostatting scenarios are visited: undamped (nodrag),
|
||||
# damped (drag) and Nose-Hoover chain (nhchains).
|
||||
#
|
||||
# The axial and shear stress trajectories are printed to the
|
||||
# file "stress_vs_t.dat". For the damped case, the original figure
|
||||
# seems to be a plot of 2*tau, rather than tau.
|
||||
#
|
||||
# The script also demonstrates how to
|
||||
# orient a crystal along <110>,
|
||||
# and how to use the lj/cubic pair style.
|
||||
|
||||
units lj
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
# Set up FCC lattice with z axis along <110>
|
||||
|
||||
lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
|
||||
Lattice spacing in x,y,z = 1.41421 2 2
|
||||
|
||||
region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
|
||||
create_box 1 mycell
|
||||
Created orthogonal box = (0 0 0) to (7.07107 10 10)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
mass * 1.0
|
||||
create_atoms 1 box
|
||||
Created 1000 atoms
|
||||
|
||||
# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
|
||||
|
||||
pair_style lj/cubic
|
||||
pair_coeff * * 1.0 0.8908987
|
||||
|
||||
# Relax box dimensions
|
||||
|
||||
fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
|
||||
|
||||
min_modify line quadratic
|
||||
minimize 0.0 1.0e-6 10000 100000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
|
||||
Memory usage per processor = 2.80047 Mbytes
|
||||
Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
|
||||
0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999
|
||||
100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999
|
||||
134 0 -6.3344257 -6.3344257 -4.4827806e-13 -4.9289339e-13 -4.9887818e-13 6.9780266 9.8684199 9.8684199
|
||||
Loop time of 0.0800641 on 1 procs for 134 steps with 1000 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = force tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-6.2937539309 -6.33442568056 -6.33442568056
|
||||
Force two-norm initial, final = 3395.29 5.85376e-10
|
||||
Force max component initial, final = 1960.27 3.43538e-10
|
||||
Final line search alpha, max atom move = 1 3.43538e-10
|
||||
Iterations, force evaluations = 134 137
|
||||
|
||||
Pair time (%) = 0.0630546 (78.7551)
|
||||
Neigh time (%) = 0.00099206 (1.23908)
|
||||
Comm time (%) = 0.00194621 (2.43082)
|
||||
Outpt time (%) = 2.00272e-05 (0.0250139)
|
||||
Other time (%) = 0.0140512 (17.5499)
|
||||
|
||||
Nlocal: 1000 ave 1000 max 1000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1724 ave 1724 max 1724 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 21000 ave 21000 max 21000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 21000
|
||||
Ave neighs/atom = 21
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
# Define initial velocity
|
||||
|
||||
velocity all create 0.01 87287 mom yes rot yes dist gaussian
|
||||
write_restart restart.equil
|
||||
|
||||
# Start Run #1
|
||||
|
||||
log log.nodrag
|
||||
|
|
@ -0,0 +1,90 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# This script reproduces stress trajectories from Fig. 1 in
|
||||
# Ravelo, Holian, Germann, and Lomdahl, PRB 70 014103 (2004)
|
||||
#
|
||||
# Three thermostatting scenarios are visited: undamped (nodrag),
|
||||
# damped (drag) and Nose-Hoover chain (nhchains).
|
||||
#
|
||||
# The axial and shear stress trajectories are printed to the
|
||||
# file "stress_vs_t.dat". For the damped case, the original figure
|
||||
# seems to be a plot of 2*tau, rather than tau.
|
||||
#
|
||||
# The script also demonstrates how to
|
||||
# orient a crystal along <110>,
|
||||
# and how to use the lj/cubic pair style.
|
||||
|
||||
units lj
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
# Set up FCC lattice with z axis along <110>
|
||||
|
||||
lattice fcc 1.4142136 orient x 0 0 1 orient y 1 -1 0 orient z 1 1 0
|
||||
Lattice spacing in x,y,z = 1.41421 2 2
|
||||
|
||||
region mycell block 0.0 5.0 0.0 5.0 0.0 5.0 units lattice
|
||||
create_box 1 mycell
|
||||
Created orthogonal box = (0 0 0) to (7.07107 10 10)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
mass * 1.0
|
||||
create_atoms 1 box
|
||||
Created 1000 atoms
|
||||
|
||||
# Using units of Rmin, so sigma = 2^-1/6 = 0.8908987
|
||||
|
||||
pair_style lj/cubic
|
||||
pair_coeff * * 1.0 0.8908987
|
||||
|
||||
# Relax box dimensions
|
||||
|
||||
fix 3 all box/relax aniso 0.0 vmax 1.0e-4 nreset 100
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step temp pe etotal pxx pyy pzz lx ly lz
|
||||
|
||||
min_modify line quadratic
|
||||
minimize 0.0 1.0e-6 10000 100000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
|
||||
Memory usage per processor = 2.77703 Mbytes
|
||||
Step Temp PotEng TotEng Pxx Pyy Pzz Lx Ly Lz
|
||||
0 0 -6.2937539 -6.2937539 -2.7722431 -2.7722431 -2.7722431 7.0710677 9.9999999 9.9999999
|
||||
100 0 -6.3319018 -6.3319018 -0.75971321 -0.75971321 -0.75971321 7.0003571 9.8999999 9.8999999
|
||||
134 0 -6.3344257 -6.3344257 -4.4436885e-13 -4.8889278e-13 -4.8955934e-13 6.9780266 9.8684199 9.8684199
|
||||
Loop time of 0.0301411 on 4 procs for 134 steps with 1000 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = force tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-6.2937539309 -6.33442568056 -6.33442568056
|
||||
Force two-norm initial, final = 3395.29 5.75073e-10
|
||||
Force max component initial, final = 1960.27 3.37121e-10
|
||||
Final line search alpha, max atom move = 1 3.37121e-10
|
||||
Iterations, force evaluations = 134 137
|
||||
|
||||
Pair time (%) = 0.0164203 (54.4781)
|
||||
Neigh time (%) = 0.000260174 (0.863187)
|
||||
Comm time (%) = 0.00554258 (18.3888)
|
||||
Outpt time (%) = 2.22921e-05 (0.0739592)
|
||||
Other time (%) = 0.00789577 (26.196)
|
||||
|
||||
Nlocal: 250 ave 305 max 205 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
Nghost: 829 ave 874 max 774 min
|
||||
Histogram: 1 0 0 0 0 0 2 0 0 1
|
||||
Neighs: 5250 ave 6445 max 4305 min
|
||||
Histogram: 1 0 0 2 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 21000
|
||||
Ave neighs/atom = 21
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
# Define initial velocity
|
||||
|
||||
velocity all create 0.01 87287 mom yes rot yes dist gaussian
|
||||
write_restart restart.equil
|
||||
|
||||
# Start Run #1
|
||||
|
||||
log log.nodrag
|
||||
|
|
@ -0,0 +1,179 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 2d indenter simulation
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.9
|
||||
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 420 atoms
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
60 atoms in group lower
|
||||
group mobile subtract all lower
|
||||
360 atoms in group mobile
|
||||
set group lower type 2
|
||||
60 settings made for type
|
||||
|
||||
# initial velocities
|
||||
|
||||
compute new mobile temp
|
||||
velocity mobile create 0.2 482748 temp new
|
||||
fix 1 all nve
|
||||
fix 2 lower setforce 0.0 0.0 0.0
|
||||
fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0
|
||||
|
||||
# run with indenter
|
||||
|
||||
timestep 0.003
|
||||
variable k equal 1000.0/xlat
|
||||
variable y equal "13.0*ylat - step*dt*0.02*ylat"
|
||||
|
||||
fix 4 all indent $k sphere 10 v_y 0 5.0
|
||||
fix 4 all indent 882.849286914813 sphere 10 v_y 0 5.0
|
||||
fix 5 all enforce2d
|
||||
|
||||
thermo 1000
|
||||
thermo_modify temp new
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
|
||||
#dump 1 all atom 250 dump.indent
|
||||
|
||||
#dump 2 all image 1000 image.*.jpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 1000 movie.mpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
run 30000
|
||||
Memory usage per processor = 2.05408 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0.2 -3.1727576 0 -3.0018052 -1.436185 444.53333
|
||||
1000 0.11974254 -3.0876892 0 -2.9853378 -0.037059247 440.78771
|
||||
2000 0.12086797 -3.0886512 0 -2.9853378 -0.39883289 444.3556
|
||||
3000 0.11671309 -3.0840074 0 -2.9842455 -0.34859991 442.95428
|
||||
4000 0.12339115 -3.1000529 0 -2.9945828 -0.049696765 438.99297
|
||||
5000 0.10860594 -3.0866045 0 -2.9937722 -0.47973882 443.99855
|
||||
6000 0.11839788 -3.0929689 0 -2.9917669 -0.033454196 442.70339
|
||||
7000 0.12194527 -3.0835584 0 -2.9793242 -0.13981611 443.36261
|
||||
8000 0.11671309 -3.0862884 0 -2.9865265 0.073952568 441.71327
|
||||
9000 0.12449823 -3.0880806 0 -2.9816643 0.28647997 439.28167
|
||||
10000 0.12475263 -3.0830722 0 -2.9764384 0.38101457 440.50309
|
||||
11000 0.11198118 -3.0743549 0 -2.9786377 0.67583952 438.50252
|
||||
12000 0.10823034 -3.0621355 0 -2.9696244 0.66485024 441.13781
|
||||
13000 0.1194298 -3.0579575 0 -2.9558734 1.0884087 437.72805
|
||||
14000 0.12310403 -3.051382 0 -2.9461573 0.87077702 445.54011
|
||||
15000 0.11148462 -3.0402208 0 -2.944928 1.0040645 451.90788
|
||||
16000 0.12322336 -3.041552 0 -2.9362254 0.75818853 456.90372
|
||||
17000 0.12311108 -3.0300339 0 -2.9248033 1.0483106 452.91666
|
||||
18000 0.12062525 -3.0261654 0 -2.9230595 1.3983603 451.71885
|
||||
19000 0.11959317 -3.0143074 0 -2.9120838 1.3960468 457.92611
|
||||
20000 0.122338 -3.001592 0 -2.8970221 1.1237176 470.12398
|
||||
21000 0.1209773 -3.028491 0 -2.9250842 0.76640926 472.90657
|
||||
22000 0.11587369 -3.0270707 0 -2.9280263 0.5800164 474.83158
|
||||
23000 0.11060033 -3.0277028 0 -2.9331659 0.96792829 471.43258
|
||||
24000 0.11282983 -3.0192428 0 -2.9228001 1.3053189 467.06167
|
||||
25000 0.11096642 -3.0068579 0 -2.912008 1.4340346 468.26071
|
||||
26000 0.12109501 -3.0023534 0 -2.898846 1.2871412 469.14748
|
||||
27000 0.12624077 -3.0033907 0 -2.8954849 1.3874279 469.76742
|
||||
28000 0.1267503 -3.0016483 0 -2.893307 1.4306934 469.29832
|
||||
29000 0.11992821 -2.9799464 0 -2.8774363 1.4301585 478.04046
|
||||
30000 0.1193433 -2.9677931 0 -2.865783 1.7313522 478.97844
|
||||
Loop time of 2.34072 on 1 procs for 30000 steps with 420 atoms
|
||||
|
||||
Pair time (%) = 1.74973 (74.752)
|
||||
Neigh time (%) = 0.0712562 (3.0442)
|
||||
Comm time (%) = 0.0313151 (1.33784)
|
||||
Outpt time (%) = 0.000312567 (0.0133535)
|
||||
Other time (%) = 0.488101 (20.8526)
|
||||
|
||||
Nlocal: 420 ave 420 max 420 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 110 ave 110 max 110 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3703 ave 3703 max 3703 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3703
|
||||
Ave neighs/atom = 8.81667
|
||||
Neighbor list builds = 619
|
||||
Dangerous builds = 0
|
||||
|
||||
# run without indenter
|
||||
|
||||
unfix 4
|
||||
run 30000
|
||||
Memory usage per processor = 2.05417 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
30000 0.1193433 -2.9677931 0 -2.865783 1.728905 479.6564
|
||||
31000 0.10869597 -3.0331255 0 -2.9402164 -0.36614133 491.53109
|
||||
32000 0.11671309 -3.003635 0 -2.903873 -0.37717771 490.3049
|
||||
33000 0.11357386 -3.0277987 0 -2.9307201 0.46609243 478.52907
|
||||
34000 0.11325318 -3.0277136 0 -2.9309091 0.14887789 487.01132
|
||||
35000 0.11614873 -3.0302671 0 -2.9309876 -0.36332093 487.84102
|
||||
36000 0.11196694 -3.0411493 0 -2.9454442 -0.067640849 486.96511
|
||||
37000 0.12006386 -3.0481451 0 -2.945519 -0.23342373 480.40191
|
||||
38000 0.11842139 -3.0466238 0 -2.9454017 -0.34243775 488.71437
|
||||
39000 0.1198706 -3.0605588 0 -2.9580979 -0.19385979 484.35217
|
||||
40000 0.11191157 -3.0647812 0 -2.9691234 -0.48040337 491.82885
|
||||
41000 0.11291708 -3.065682 0 -2.9691648 -0.2494499 487.47298
|
||||
42000 0.12242643 -3.0738126 0 -2.9691672 -0.36376783 487.84689
|
||||
43000 0.12095077 -3.0725493 0 -2.9691652 -0.36977815 488.33432
|
||||
44000 0.11671309 -3.0789107 0 -2.9791488 -0.22354617 486.65601
|
||||
45000 0.11671309 -3.0688305 0 -2.9690686 -0.25626357 486.86098
|
||||
46000 0.12233634 -3.0703788 0 -2.9658103 -0.26550413 487.14029
|
||||
47000 0.11077381 -3.0604929 0 -2.9658077 -0.1338011 487.70423
|
||||
48000 0.11616048 -3.0761007 0 -2.9768111 -0.26861141 487.1961
|
||||
49000 0.11232937 -3.0728268 0 -2.976812 -0.27614358 488.13299
|
||||
50000 0.11890619 -3.0784515 0 -2.9768151 -0.35807475 488.7576
|
||||
51000 0.1139473 -3.0742097 0 -2.9768119 -0.3599846 488.14034
|
||||
52000 0.11570005 -3.0757089 0 -2.9768129 -0.20273147 488.2635
|
||||
53000 0.11622085 -3.0761556 0 -2.9768145 -0.29363039 485.22966
|
||||
54000 0.11721028 -3.0770006 0 -2.9768137 -0.35379322 486.02806
|
||||
55000 0.11816386 -3.0778183 0 -2.9768164 -0.26890935 486.25412
|
||||
56000 0.12138263 -3.0805663 0 -2.976813 -0.43809353 486.45992
|
||||
57000 0.11368036 -3.0739797 0 -2.9768101 -0.3784405 487.68779
|
||||
58000 0.12624247 -3.0714284 0 -2.9635212 -0.28330741 487.44043
|
||||
59000 0.10749507 -3.0655101 0 -2.9736274 -0.30239742 490.08649
|
||||
60000 0.11976607 -3.0760024 0 -2.9736309 -0.22323075 486.62515
|
||||
Loop time of 2.11157 on 1 procs for 30000 steps with 420 atoms
|
||||
|
||||
Pair time (%) = 1.71606 (81.2693)
|
||||
Neigh time (%) = 0.0706546 (3.34607)
|
||||
Comm time (%) = 0.0320117 (1.51602)
|
||||
Outpt time (%) = 0.000283957 (0.0134476)
|
||||
Other time (%) = 0.292562 (13.8552)
|
||||
|
||||
Nlocal: 420 ave 420 max 420 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 111 ave 111 max 111 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3561 ave 3561 max 3561 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3561
|
||||
Ave neighs/atom = 8.47857
|
||||
Neighbor list builds = 629
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,179 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 2d indenter simulation
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.9
|
||||
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 420 atoms
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
60 atoms in group lower
|
||||
group mobile subtract all lower
|
||||
360 atoms in group mobile
|
||||
set group lower type 2
|
||||
60 settings made for type
|
||||
|
||||
# initial velocities
|
||||
|
||||
compute new mobile temp
|
||||
velocity mobile create 0.2 482748 temp new
|
||||
fix 1 all nve
|
||||
fix 2 lower setforce 0.0 0.0 0.0
|
||||
fix 3 all temp/rescale 100 0.1 0.1 0.01 1.0
|
||||
|
||||
# run with indenter
|
||||
|
||||
timestep 0.003
|
||||
variable k equal 1000.0/xlat
|
||||
variable y equal "13.0*ylat - step*dt*0.02*ylat"
|
||||
|
||||
fix 4 all indent $k sphere 10 v_y 0 5.0
|
||||
fix 4 all indent 882.849286914813 sphere 10 v_y 0 5.0
|
||||
fix 5 all enforce2d
|
||||
|
||||
thermo 1000
|
||||
thermo_modify temp new
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
|
||||
#dump 1 all atom 250 dump.indent
|
||||
|
||||
#dump 2 all image 1000 image.*.jpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 1000 movie.mpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
run 30000
|
||||
Memory usage per processor = 2.06074 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0.2 -3.1727576 0 -3.0018052 -1.436185 444.53333
|
||||
1000 0.11573595 -3.0964873 0 -2.9975606 -0.20448672 441.83732
|
||||
2000 0.11519605 -3.0960246 0 -2.9975594 -0.38133491 442.33058
|
||||
3000 0.11367906 -3.0839597 0 -2.9867912 -0.42579765 444.59119
|
||||
4000 0.11618844 -3.0860897 0 -2.9867762 -0.041580916 439.84614
|
||||
5000 0.11327789 -3.0848614 0 -2.9880358 -0.48898867 446.19202
|
||||
6000 0.12058424 -3.0869438 0 -2.983873 0.011477134 440.56887
|
||||
7000 0.11772522 -3.0833477 0 -2.9827207 -0.090378245 442.56787
|
||||
8000 0.12533514 -3.0970033 0 -2.9898715 0.13263189 441.23478
|
||||
9000 0.1198683 -3.0867062 0 -2.9842473 0.34046664 439.4706
|
||||
10000 0.12234014 -3.0835007 0 -2.9789291 0.28399731 441.94307
|
||||
11000 0.11082436 -3.0754796 0 -2.9807511 0.62194284 441.32012
|
||||
12000 0.10842719 -3.0646379 0 -2.9719584 0.65383569 442.64668
|
||||
13000 0.11686417 -3.0600388 0 -2.9601477 1.0041123 438.50135
|
||||
14000 0.12557378 -3.0570017 0 -2.949666 0.85709167 442.10189
|
||||
15000 0.11934084 -3.0498848 0 -2.9478768 1.0392199 451.74396
|
||||
16000 0.12576904 -3.0452178 0 -2.9377152 1.3479499 441.27019
|
||||
17000 0.11546522 -3.0348362 0 -2.936141 1.6318206 439.4846
|
||||
18000 0.12148312 -3.0221147 0 -2.9182755 1.6088803 449.25447
|
||||
19000 0.11884301 -3.0036771 0 -2.9020946 1.5201596 447.11858
|
||||
20000 0.11165616 -3.0037969 0 -2.9083575 1.4074721 461.75507
|
||||
21000 0.11360221 -2.9898243 0 -2.8927215 1.1326553 473.96356
|
||||
22000 0.12149681 -3.024808 0 -2.9209571 0.78922351 473.43584
|
||||
23000 0.11891429 -3.0140734 0 -2.91243 1.2020863 469.92437
|
||||
24000 0.12003368 -3.0195801 0 -2.9169798 0.76069021 473.29691
|
||||
25000 0.12286633 -3.0215711 0 -2.9165496 0.67406806 485.07199
|
||||
26000 0.1177073 -3.0094446 0 -2.9088329 0.33348438 486.6152
|
||||
27000 0.11671309 -3.0183329 0 -2.918571 0.70486163 484.63284
|
||||
28000 0.12675659 -3.0429799 0 -2.9346332 0.66897197 483.34837
|
||||
29000 0.1156808 -3.0381771 0 -2.9392975 0.56595774 485.98334
|
||||
30000 0.11265389 -3.0300644 0 -2.9337722 0.97207041 485.94269
|
||||
Loop time of 1.04821 on 4 procs for 30000 steps with 420 atoms
|
||||
|
||||
Pair time (%) = 0.450331 (42.9618)
|
||||
Neigh time (%) = 0.01888 (1.80116)
|
||||
Comm time (%) = 0.314544 (30.0076)
|
||||
Outpt time (%) = 0.000509083 (0.0485668)
|
||||
Other time (%) = 0.263949 (25.1809)
|
||||
|
||||
Nlocal: 105 ave 120 max 89 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 91.25 ave 99 max 83 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Neighs: 900.5 ave 1089 max 720 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 3602
|
||||
Ave neighs/atom = 8.57619
|
||||
Neighbor list builds = 616
|
||||
Dangerous builds = 0
|
||||
|
||||
# run without indenter
|
||||
|
||||
unfix 4
|
||||
run 30000
|
||||
Memory usage per processor = 2.06085 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
30000 0.11265389 -3.0300644 0 -2.9337722 0.97234223 485.80685
|
||||
31000 0.11759958 -3.0552427 0 -2.954723 -0.45428585 489.01075
|
||||
32000 0.1244223 -3.031587 0 -2.9252355 -0.55586882 497.58671
|
||||
33000 0.11512011 -3.045739 0 -2.9473387 0.20493313 482.45319
|
||||
34000 0.12011045 -3.0498103 0 -2.9471445 -0.20993642 490.60496
|
||||
35000 0.12168423 -3.0402933 0 -2.9362822 -0.56627306 496.84137
|
||||
36000 0.12206115 -3.054588 0 -2.9502548 0.024107079 488.42757
|
||||
37000 0.1183082 -3.0513368 0 -2.9502114 -0.049466566 490.53247
|
||||
38000 0.10909549 -3.043269 0 -2.9500183 -0.4203535 494.85852
|
||||
39000 0.11529806 -3.0486455 0 -2.9500931 0.018737728 493.31601
|
||||
40000 0.11343932 -3.0471365 0 -2.9501729 -0.22971202 492.54675
|
||||
41000 0.11812961 -3.0411142 0 -2.9401415 -0.32514863 495.25905
|
||||
42000 0.12105766 -3.0434615 0 -2.939986 -0.040665394 492.97267
|
||||
43000 0.10525203 -3.0425539 0 -2.9525885 -0.16326985 494.40556
|
||||
44000 0.10613869 -3.0431187 0 -2.9523954 -0.16981593 495.58301
|
||||
45000 0.11561112 -3.0514123 0 -2.9525924 -0.17742887 493.63953
|
||||
46000 0.11018146 -3.046615 0 -2.9524361 -0.32577677 498.4112
|
||||
47000 0.10570042 -3.043205 0 -2.9528564 -0.14894466 491.63488
|
||||
48000 0.11339264 -3.049744 0 -2.9528203 -0.09546935 491.51042
|
||||
49000 0.10630296 -3.0434874 0 -2.9526237 -0.18683154 494.0362
|
||||
50000 0.10854184 -3.0455192 0 -2.9527418 -0.23688088 495.39066
|
||||
51000 0.10953314 -3.0512975 0 -2.9576727 -0.083732144 495.75424
|
||||
52000 0.12374024 -3.0529561 0 -2.9471877 -0.32091022 494.47207
|
||||
53000 0.11492903 -3.0453421 0 -2.9471052 -0.23510307 496.33496
|
||||
54000 0.11401393 -3.0339003 0 -2.9364455 0.0060137449 496.63695
|
||||
55000 0.11651709 -3.0359636 0 -2.9363692 -0.32187304 495.2289
|
||||
56000 0.12583256 -3.0438852 0 -2.9363284 -0.18360885 495.28665
|
||||
57000 0.11188382 -3.0423929 0 -2.9467589 -0.097898762 496.68295
|
||||
58000 0.11603787 -3.045827 0 -2.9466422 -0.31359664 498.05865
|
||||
59000 0.12070545 -3.0496657 0 -2.9464913 -0.17444968 494.22795
|
||||
60000 0.11476903 -3.0445911 0 -2.9464909 -0.146398 493.56692
|
||||
Loop time of 0.943008 on 4 procs for 30000 steps with 420 atoms
|
||||
|
||||
Pair time (%) = 0.442427 (46.9166)
|
||||
Neigh time (%) = 0.0189115 (2.00544)
|
||||
Comm time (%) = 0.326607 (34.6345)
|
||||
Outpt time (%) = 0.000496209 (0.0526198)
|
||||
Other time (%) = 0.154567 (16.3908)
|
||||
|
||||
Nlocal: 105 ave 121 max 86 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
Nghost: 92 ave 99 max 86 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 892.25 ave 1084 max 682 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 3569
|
||||
Ave neighs/atom = 8.49762
|
||||
Neighbor list builds = 620
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,404 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 2d indenter simulation with minimization instead of dynamics
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.9
|
||||
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 420 atoms
|
||||
|
||||
mass * 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
60 atoms in group lower
|
||||
group mobile subtract all lower
|
||||
360 atoms in group mobile
|
||||
set group lower type 2
|
||||
60 settings made for type
|
||||
|
||||
# initial velocities
|
||||
|
||||
fix 2 lower setforce 0.0 0.0 0.0
|
||||
|
||||
# indenter
|
||||
|
||||
fix 5 all enforce2d
|
||||
|
||||
# minimize with indenter
|
||||
|
||||
thermo 10
|
||||
|
||||
#dump 1 all atom 10 dump.indent
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
minimize 1.0e-6 1.0e-6 1000 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
|
||||
Memory usage per processor = 2.74073 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0 -3.1727576 0 -3.1727576 -1.5977027 444.53333
|
||||
10 0 -3.1801584 0 -3.1801584 -1.3055542 441.12964
|
||||
20 0 -3.1831474 0 -3.1831474 -1.2342864 438.61999
|
||||
30 0 -3.1861452 0 -3.1861452 -1.090794 438.86547
|
||||
40 0 -3.1901049 0 -3.1901049 -0.84848785 435.62268
|
||||
50 0 -3.1904808 0 -3.1904808 -0.81494392 435.62268
|
||||
60 0 -3.1906458 0 -3.1906458 -0.7837635 435.62268
|
||||
70 0 -3.190782 0 -3.190782 -0.75163367 435.62268
|
||||
74 0 -3.1908431 0 -3.1908431 -0.73877396 435.62268
|
||||
Loop time of 0.0425239 on 1 procs for 74 steps with 420 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-3.17275755126 -3.19084058073 -3.19084306284
|
||||
Force two-norm initial, final = 6.74302 0.560627
|
||||
Force max component initial, final = 1.46877 0.0659033
|
||||
Final line search alpha, max atom move = 0.00643442 0.00042405
|
||||
Iterations, force evaluations = 74 411
|
||||
|
||||
Pair time (%) = 0.037972 (89.2957)
|
||||
Neigh time (%) = 0.000494957 (1.16395)
|
||||
Comm time (%) = 0.000413179 (0.971641)
|
||||
Outpt time (%) = 7.00951e-05 (0.164837)
|
||||
Other time (%) = 0.00357366 (8.40388)
|
||||
|
||||
Nlocal: 420 ave 420 max 420 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 95 ave 95 max 95 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3580 ave 3580 max 3580 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3580
|
||||
Ave neighs/atom = 8.52381
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
variable k equal 5000.0/xlat
|
||||
variable k1 equal 1000.0/xlat
|
||||
|
||||
fix 4 all indent $k sphere 10 13.0 0 6.0
|
||||
fix 4 all indent 4414.24643457407 sphere 10 13.0 0 6.0
|
||||
fix_modify 4 energy yes
|
||||
minimize 1.0e-6 1.0e-6 1000 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
|
||||
Memory usage per processor = 2.74073 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
74 0 -3.1908431 0 -2.0624129 -0.73807217 436.03689
|
||||
80 0 -3.1521235 0 -3.1418193 -0.26103179 436.03693
|
||||
90 0 -3.172501 0 -3.1715058 -0.36498503 436.19
|
||||
100 0 -3.1770944 0 -3.1759303 -0.36782131 436.15772
|
||||
110 0 -3.179003 0 -3.1778726 -0.34159509 436.07263
|
||||
120 0 -3.1801625 0 -3.1792123 -0.29559493 435.77089
|
||||
130 0 -3.1809815 0 -3.1802941 -0.20023556 434.9421
|
||||
140 0 -3.181069 0 -3.180391 -0.1867988 434.23462
|
||||
149 0 -3.1811854 0 -3.1804775 -0.17149229 434.62963
|
||||
Loop time of 0.0426731 on 1 procs for 75 steps with 420 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-2.06241291025 -3.18047516326 -3.18047748467
|
||||
Force two-norm initial, final = 1731.02 0.601744
|
||||
Force max component initial, final = 1265.65 0.297585
|
||||
Final line search alpha, max atom move = 0.00267208 0.000795171
|
||||
Iterations, force evaluations = 75 368
|
||||
|
||||
Pair time (%) = 0.0337248 (79.0305)
|
||||
Neigh time (%) = 0.00306416 (7.18053)
|
||||
Comm time (%) = 0.000451803 (1.05875)
|
||||
Outpt time (%) = 6.48499e-05 (0.151969)
|
||||
Other time (%) = 0.00536752 (12.5782)
|
||||
|
||||
Nlocal: 420 ave 420 max 420 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 95 ave 95 max 95 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3584 ave 3584 max 3584 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3584
|
||||
Ave neighs/atom = 8.53333
|
||||
Neighbor list builds = 27
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 4 all indent ${k1} sphere 10 12.5 0 6.0
|
||||
fix 4 all indent 882.849286914813 sphere 10 12.5 0 6.0
|
||||
fix_modify 4 energy yes
|
||||
minimize 1.0e-6 1.0e-6 1000 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
|
||||
Memory usage per processor = 2.74073 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
149 0 -3.1811854 0 -0.18581133 -0.1714388 434.76522
|
||||
150 0 -3.1643579 0 -0.9039795 0.013604142 434.76522
|
||||
160 0 -2.9896502 0 -2.8476201 1.7049354 434.75857
|
||||
170 0 -3.0638049 0 -3.0412807 1.3613793 434.71626
|
||||
180 0 -3.0925759 0 -3.0805454 1.2078809 434.84134
|
||||
190 0 -3.0992403 0 -3.0902396 1.1565899 435.28172
|
||||
200 0 -3.1006774 0 -3.0922078 1.1563293 434.85279
|
||||
210 0 -3.1021512 0 -3.0942343 1.1847386 433.5255
|
||||
220 0 -3.1034865 0 -3.0957045 1.2437301 433.5255
|
||||
Loop time of 0.0324862 on 1 procs for 71 steps with 420 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-0.185811329671 -3.09570333014 -3.0957044814
|
||||
Force two-norm initial, final = 1763.73 6.22486
|
||||
Force max component initial, final = 924.34 1.95519
|
||||
Final line search alpha, max atom move = 1.23202e-05 2.40883e-05
|
||||
Iterations, force evaluations = 71 282
|
||||
|
||||
Pair time (%) = 0.0262792 (80.8935)
|
||||
Neigh time (%) = 0.00164843 (5.07423)
|
||||
Comm time (%) = 0.000334263 (1.02894)
|
||||
Outpt time (%) = 6.07967e-05 (0.187146)
|
||||
Other time (%) = 0.0041635 (12.8162)
|
||||
|
||||
Nlocal: 420 ave 420 max 420 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 109 ave 109 max 109 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3633 ave 3633 max 3633 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3633
|
||||
Ave neighs/atom = 8.65
|
||||
Neighbor list builds = 14
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 4 all indent ${k1} sphere 10 12.0 0 6.0
|
||||
fix 4 all indent 882.849286914813 sphere 10 12.0 0 6.0
|
||||
fix_modify 4 energy yes
|
||||
minimize 1.0e-6 1.0e-6 1000 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
|
||||
Memory usage per processor = 2.74073 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
220 0 -3.1034865 0 2.0778483 1.2452636 432.99162
|
||||
230 0 -2.5109892 0 -2.3349564 6.16399 433.43161
|
||||
240 0 -2.8436954 0 -2.7695635 3.9188746 440.0748
|
||||
250 0 -2.8958915 0 -2.859753 3.5873163 443.3911
|
||||
260 0 -2.9335258 0 -2.9180699 3.2586768 446.93395
|
||||
270 0 -2.9587555 0 -2.9449067 3.0495207 450.7898
|
||||
280 0 -2.9632665 0 -2.9508012 2.9704184 455.18424
|
||||
290 0 -2.9663937 0 -2.9548266 2.9251605 455.18424
|
||||
300 0 -2.9815499 0 -2.972728 2.690073 461.16274
|
||||
310 0 -2.998615 0 -2.9900703 2.5025287 462.28498
|
||||
320 0 -3.0171338 0 -3.0096079 2.2589518 464.76762
|
||||
330 0 -3.066495 0 -3.0615455 1.6037908 468.05879
|
||||
340 0 -3.0915645 0 -3.0882311 1.3314881 470.4116
|
||||
350 0 -3.1067793 0 -3.1027465 1.1863784 468.66537
|
||||
360 0 -3.111438 0 -3.1085634 1.133372 471.4241
|
||||
370 0 -3.1144779 0 -3.1118395 1.0503928 471.4241
|
||||
380 0 -3.1187534 0 -3.115652 0.89135021 473.74678
|
||||
390 0 -3.1198286 0 -3.1164385 0.84502104 473.74678
|
||||
400 0 -3.1202166 0 -3.1166667 0.82342171 474.96181
|
||||
410 0 -3.1206604 0 -3.1169627 0.79018217 475.00074
|
||||
418 0 -3.1207429 0 -3.1171141 0.77776922 473.85863
|
||||
Loop time of 0.089386 on 1 procs for 198 steps with 420 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
2.07784826507 -3.11711145486 -3.11711413336
|
||||
Force two-norm initial, final = 2348.2 0.758541
|
||||
Force max component initial, final = 1038.98 0.227243
|
||||
Final line search alpha, max atom move = 0.00310726 0.000706103
|
||||
Iterations, force evaluations = 198 764
|
||||
|
||||
Pair time (%) = 0.0712759 (79.7395)
|
||||
Neigh time (%) = 0.00549102 (6.14304)
|
||||
Comm time (%) = 0.00098896 (1.10639)
|
||||
Outpt time (%) = 0.000168562 (0.188578)
|
||||
Other time (%) = 0.0114615 (12.8225)
|
||||
|
||||
Nlocal: 420 ave 420 max 420 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 107 ave 107 max 107 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3612 ave 3612 max 3612 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3612
|
||||
Ave neighs/atom = 8.6
|
||||
Neighbor list builds = 46
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 4 all indent ${k1} sphere 10 11.4 0 6.0
|
||||
fix 4 all indent 882.849286914813 sphere 10 11.4 0 6.0
|
||||
fix_modify 4 energy yes
|
||||
minimize 1.0e-6 1.0e-6 1000 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
|
||||
Memory usage per processor = 2.74073 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
418 0 -3.1207429 0 4.5511735 0.77738319 474.09394
|
||||
420 0 -3.0629926 0 1.9444704 1.3379171 473.98211
|
||||
430 0 -2.6813506 0 -2.4214349 4.7277839 473.31189
|
||||
440 0 -2.8631611 0 -2.7958919 3.6555407 477.0175
|
||||
450 0 -2.9314239 0 -2.897992 3.1393288 481.94369
|
||||
460 0 -2.9620386 0 -2.9480925 2.7967516 491.0709
|
||||
470 0 -2.9748225 0 -2.9605783 2.6387787 491.13394
|
||||
480 0 -2.984083 0 -2.9712966 2.5491081 491.9717
|
||||
490 0 -2.9886661 0 -2.9779169 2.4836251 493.12793
|
||||
500 0 -2.9929304 0 -2.9843848 2.4179024 493.50247
|
||||
510 0 -3.0014663 0 -2.9928884 2.3117132 495.11638
|
||||
520 0 -3.0255297 0 -3.0197482 2.0516501 496.59829
|
||||
530 0 -3.0475992 0 -3.0428515 1.8691696 496.97347
|
||||
540 0 -3.0552715 0 -3.0499976 1.7904182 496.00133
|
||||
550 0 -3.061395 0 -3.0556631 1.6863886 495.72563
|
||||
560 0 -3.0651 0 -3.0590723 1.6279321 495.24659
|
||||
570 0 -3.0673019 0 -3.0610166 1.5949476 494.64061
|
||||
580 0 -3.0687599 0 -3.0621893 1.5269488 497.3911
|
||||
586 0 -3.0694654 0 -3.0627953 1.5123574 497.3911
|
||||
Loop time of 0.0674939 on 1 procs for 168 steps with 420 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
4.55117353041 -3.06279311906 -3.06279529487
|
||||
Force two-norm initial, final = 2972.98 2.60071
|
||||
Force max component initial, final = 1399.42 0.742189
|
||||
Final line search alpha, max atom move = 0.00013057 9.69073e-05
|
||||
Iterations, force evaluations = 168 577
|
||||
|
||||
Pair time (%) = 0.0539668 (79.958)
|
||||
Neigh time (%) = 0.0038271 (5.67028)
|
||||
Comm time (%) = 0.00071764 (1.06327)
|
||||
Outpt time (%) = 0.000156879 (0.232435)
|
||||
Other time (%) = 0.00882554 (13.0761)
|
||||
|
||||
Nlocal: 420 ave 420 max 420 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 118 ave 118 max 118 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3637 ave 3637 max 3637 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3637
|
||||
Ave neighs/atom = 8.65952
|
||||
Neighbor list builds = 32
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 4 all indent ${k1} sphere 10 11.2 0 6.0
|
||||
fix 4 all indent 882.849286914813 sphere 10 11.2 0 6.0
|
||||
fix_modify 4 energy yes
|
||||
minimize 1.0e-6 1.0e-6 1000 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
|
||||
Memory usage per processor = 2.74081 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
586 0 -3.0694654 0 -2.5610272 1.5148154 496.584
|
||||
590 0 -2.9807015 0 -2.8962768 2.3098422 496.58447
|
||||
600 0 -2.9891378 0 -2.966537 2.3737377 496.58482
|
||||
610 0 -2.9927542 0 -2.9765217 2.3647514 496.68053
|
||||
620 0 -3.0027846 0 -2.9911735 2.3024398 496.99879
|
||||
630 0 -3.0120047 0 -3.0013041 2.2445443 497.3327
|
||||
640 0 -3.0199795 0 -3.0109861 2.2085552 497.48784
|
||||
650 0 -3.0252192 0 -3.0168447 2.1840453 497.61838
|
||||
660 0 -3.0285753 0 -3.020419 2.1577783 498.09493
|
||||
670 0 -3.032151 0 -3.0245432 2.1160278 498.75158
|
||||
680 0 -3.0334423 0 -3.0260628 2.0715843 498.99145
|
||||
690 0 -3.0348442 0 -3.0277896 2.0397454 499.38565
|
||||
700 0 -3.0373291 0 -3.0303879 1.950985 499.35774
|
||||
710 0 -3.0413907 0 -3.034156 1.8600169 501.53756
|
||||
714 0 -3.0418366 0 -3.0343319 1.8536192 501.53756
|
||||
Loop time of 0.060724 on 1 procs for 128 steps with 420 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-2.56102720477 -3.0343306266 -3.03433194949
|
||||
Force two-norm initial, final = 485.313 7.6949
|
||||
Force max component initial, final = 233.682 1.75894
|
||||
Final line search alpha, max atom move = 0.000202561 0.000356292
|
||||
Iterations, force evaluations = 128 518
|
||||
|
||||
Pair time (%) = 0.048727 (80.2434)
|
||||
Neigh time (%) = 0.0034678 (5.71075)
|
||||
Comm time (%) = 0.000708818 (1.16728)
|
||||
Outpt time (%) = 0.000118494 (0.195135)
|
||||
Other time (%) = 0.00770187 (12.6834)
|
||||
|
||||
Nlocal: 420 ave 420 max 420 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 117 ave 117 max 117 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3707 ave 3707 max 3707 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3707
|
||||
Ave neighs/atom = 8.82619
|
||||
Neighbor list builds = 29
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 4 all indent ${k1} sphere 10 11.0 0 6.0
|
||||
fix 4 all indent 882.849286914813 sphere 10 11.0 0 6.0
|
||||
fix_modify 4 energy yes
|
||||
minimize 1.0e-6 1.0e-6 1000 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
|
||||
Memory usage per processor = 2.74081 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
714 0 -3.0418366 0 -2.5647674 1.8523771 501.87385
|
||||
720 0 -2.9615831 0 -2.9005481 2.6557784 501.89551
|
||||
730 0 -2.9642041 0 -2.9367288 2.732803 502.11719
|
||||
740 0 -2.9666385 0 -2.9495445 2.7501461 501.9651
|
||||
750 0 -2.972902 0 -2.9544262 2.6982499 501.913
|
||||
760 0 -2.9761809 0 -2.9613793 2.7071736 501.90871
|
||||
770 0 -2.9840571 0 -2.9666566 2.6500893 501.90871
|
||||
780 0 -2.9871658 0 -2.9704099 2.6464522 501.59836
|
||||
790 0 -2.9969968 0 -2.9807461 2.6151906 501.40924
|
||||
800 0 -3.0051819 0 -2.9894906 2.5702395 501.37371
|
||||
810 0 -3.0071904 0 -2.9916568 2.5671087 501.33912
|
||||
820 0 -3.0079125 0 -2.9925277 2.5615763 502.01846
|
||||
827 0 -3.0081656 0 -2.9928086 2.5580601 502.05698
|
||||
Loop time of 0.0602961 on 1 procs for 113 steps with 420 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-2.56476735837 -2.99280857633 -2.9928086311
|
||||
Force two-norm initial, final = 447.674 1.83102
|
||||
Force max component initial, final = 195.835 0.221915
|
||||
Final line search alpha, max atom move = 6.85287e-06 1.52076e-06
|
||||
Iterations, force evaluations = 113 508
|
||||
|
||||
Pair time (%) = 0.0482583 (80.0356)
|
||||
Neigh time (%) = 0.00370264 (6.14077)
|
||||
Comm time (%) = 0.000731945 (1.21392)
|
||||
Outpt time (%) = 0.000100374 (0.166469)
|
||||
Other time (%) = 0.00750279 (12.4433)
|
||||
|
||||
Nlocal: 420 ave 420 max 420 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 119 ave 119 max 119 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3803 ave 3803 max 3803 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3803
|
||||
Ave neighs/atom = 9.05476
|
||||
Neighbor list builds = 31
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,405 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 2d indenter simulation with minimization instead of dynamics
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.9
|
||||
Lattice spacing in x,y,z = 1.1327 1.96189 1.1327
|
||||
region box block 0 20 0 10 -0.25 0.25
|
||||
create_box 2 box
|
||||
Created orthogonal box = (0 0 -0.283174) to (22.6539 19.6189 0.283174)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 420 atoms
|
||||
|
||||
mass * 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 2.5
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
60 atoms in group lower
|
||||
group mobile subtract all lower
|
||||
360 atoms in group mobile
|
||||
set group lower type 2
|
||||
60 settings made for type
|
||||
|
||||
# initial velocities
|
||||
|
||||
fix 2 lower setforce 0.0 0.0 0.0
|
||||
|
||||
# indenter
|
||||
|
||||
fix 5 all enforce2d
|
||||
|
||||
# minimize with indenter
|
||||
|
||||
thermo 10
|
||||
|
||||
#dump 1 all atom 10 dump.indent
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
minimize 1.0e-6 1.0e-6 1000 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
|
||||
Memory usage per processor = 2.74739 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0 -3.1727576 0 -3.1727576 -1.5977027 444.53333
|
||||
10 0 -3.1801584 0 -3.1801584 -1.3055542 441.12964
|
||||
20 0 -3.1831474 0 -3.1831474 -1.2342864 438.61999
|
||||
30 0 -3.1861452 0 -3.1861452 -1.090794 438.86547
|
||||
40 0 -3.1901049 0 -3.1901049 -0.84848785 435.62268
|
||||
50 0 -3.1904808 0 -3.1904808 -0.81494392 435.62268
|
||||
60 0 -3.1906458 0 -3.1906458 -0.78376348 435.62268
|
||||
70 0 -3.190782 0 -3.190782 -0.75163367 435.62268
|
||||
74 0 -3.1908431 0 -3.1908431 -0.73877366 435.62268
|
||||
Loop time of 0.0168951 on 4 procs for 74 steps with 420 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-3.17275755126 -3.19084058192 -3.19084306553
|
||||
Force two-norm initial, final = 6.74302 0.560405
|
||||
Force max component initial, final = 1.46877 0.0658777
|
||||
Final line search alpha, max atom move = 0.00643452 0.000423891
|
||||
Iterations, force evaluations = 74 411
|
||||
|
||||
Pair time (%) = 0.00975549 (57.7417)
|
||||
Neigh time (%) = 0.000121534 (0.719346)
|
||||
Comm time (%) = 0.00325423 (19.2615)
|
||||
Outpt time (%) = 0.00011605 (0.686889)
|
||||
Other time (%) = 0.00364774 (21.5906)
|
||||
|
||||
Nlocal: 105 ave 110 max 99 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Nghost: 84 ave 90 max 79 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 895 ave 909 max 887 min
|
||||
Histogram: 1 1 1 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 3580
|
||||
Ave neighs/atom = 8.52381
|
||||
Neighbor list builds = 4
|
||||
Dangerous builds = 0
|
||||
|
||||
variable k equal 5000.0/xlat
|
||||
variable k1 equal 1000.0/xlat
|
||||
|
||||
fix 4 all indent $k sphere 10 13.0 0 6.0
|
||||
fix 4 all indent 4414.24643457407 sphere 10 13.0 0 6.0
|
||||
fix_modify 4 energy yes
|
||||
minimize 1.0e-6 1.0e-6 1000 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
|
||||
Memory usage per processor = 2.74739 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
74 0 -3.1908431 0 -2.0624137 -0.73807188 436.03689
|
||||
80 0 -3.1521235 0 -3.1418193 -0.26103149 436.03693
|
||||
90 0 -3.1725009 0 -3.1715057 -0.36498447 436.19
|
||||
100 0 -3.1770919 0 -3.1759284 -0.3678025 436.15756
|
||||
110 0 -3.1795983 0 -3.1785044 -0.32326426 436.06295
|
||||
120 0 -3.180804 0 -3.180035 -0.20918126 435.18508
|
||||
130 0 -3.1809911 0 -3.1802835 -0.19952199 435.02873
|
||||
140 0 -3.1812648 0 -3.1804983 -0.1536603 433.52101
|
||||
146 0 -3.1812507 0 -3.1805455 -0.14792876 435.60369
|
||||
Loop time of 0.0170696 on 4 procs for 72 steps with 420 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-2.06241374157 -3.1805424084 -3.18054549688
|
||||
Force two-norm initial, final = 1731.02 0.648868
|
||||
Force max component initial, final = 1265.65 0.243588
|
||||
Final line search alpha, max atom move = 0.00411247 0.00100175
|
||||
Iterations, force evaluations = 72 345
|
||||
|
||||
Pair time (%) = 0.00818044 (47.9241)
|
||||
Neigh time (%) = 0.000614583 (3.60046)
|
||||
Comm time (%) = 0.00340056 (19.9218)
|
||||
Outpt time (%) = 0.000127673 (0.747957)
|
||||
Other time (%) = 0.00474632 (27.8057)
|
||||
|
||||
Nlocal: 105 ave 110 max 99 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Nghost: 93 ave 95 max 90 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Neighs: 900.5 ave 991 max 795 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 3602
|
||||
Ave neighs/atom = 8.57619
|
||||
Neighbor list builds = 20
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 4 all indent ${k1} sphere 10 12.5 0 6.0
|
||||
fix 4 all indent 882.849286914813 sphere 10 12.5 0 6.0
|
||||
fix_modify 4 energy yes
|
||||
minimize 1.0e-6 1.0e-6 1000 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
|
||||
Memory usage per processor = 2.74739 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
146 0 -3.1812507 0 -0.19362668 -0.14835915 434.34002
|
||||
150 0 -3.0139224 0 -2.1509399 1.2746122 434.3403
|
||||
160 0 -3.0194803 0 -2.9695748 1.6379418 434.34235
|
||||
170 0 -3.0791621 0 -3.0643991 1.2982776 434.34066
|
||||
180 0 -3.0976992 0 -3.0876817 1.1785055 434.99297
|
||||
190 0 -3.1011034 0 -3.0933162 1.177501 434.36151
|
||||
196 0 -3.101384 0 -3.093552 1.1763591 434.56832
|
||||
Loop time of 0.00935769 on 4 procs for 50 steps with 420 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-0.193626681647 -3.09355173343 -3.09355201119
|
||||
Force two-norm initial, final = 1761.84 3.77378
|
||||
Force max component initial, final = 925.281 0.741268
|
||||
Final line search alpha, max atom move = 8.16442e-06 6.05202e-06
|
||||
Iterations, force evaluations = 50 179
|
||||
|
||||
Pair time (%) = 0.00431252 (46.0853)
|
||||
Neigh time (%) = 0.000466645 (4.98675)
|
||||
Comm time (%) = 0.0018518 (19.789)
|
||||
Outpt time (%) = 8.27312e-05 (0.884099)
|
||||
Other time (%) = 0.002644 (28.2549)
|
||||
|
||||
Nlocal: 105 ave 112 max 98 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Nghost: 94.5 ave 97 max 92 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 912.75 ave 1012 max 810 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 3651
|
||||
Ave neighs/atom = 8.69286
|
||||
Neighbor list builds = 15
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 4 all indent ${k1} sphere 10 12.0 0 6.0
|
||||
fix 4 all indent 882.849286914813 sphere 10 12.0 0 6.0
|
||||
fix_modify 4 energy yes
|
||||
minimize 1.0e-6 1.0e-6 1000 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
|
||||
Memory usage per processor = 2.74739 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
196 0 -3.101384 0 2.0685206 1.175426 434.91329
|
||||
200 0 -2.7636455 0 -1.0998236 3.845322 434.90722
|
||||
210 0 -2.7400198 0 -2.5636998 4.5111706 434.85438
|
||||
220 0 -2.8544322 0 -2.8143558 3.8164599 441.10314
|
||||
230 0 -2.9053821 0 -2.8748243 3.4509052 443.16362
|
||||
240 0 -2.9336393 0 -2.9178903 3.1887133 446.32345
|
||||
250 0 -2.9476213 0 -2.9353019 3.0616994 448.49386
|
||||
260 0 -2.9570838 0 -2.9455155 2.9376727 451.97386
|
||||
270 0 -2.9689281 0 -2.9578275 2.8316438 457.18765
|
||||
280 0 -2.9748011 0 -2.9654648 2.7862357 457.989
|
||||
290 0 -2.9889836 0 -2.9806176 2.5953846 459.49997
|
||||
300 0 -3.0041161 0 -2.9952343 2.4349847 462.63608
|
||||
310 0 -3.011901 0 -3.003921 2.3164192 462.63608
|
||||
320 0 -3.0576072 0 -3.0503749 1.6137857 468.46632
|
||||
330 0 -3.0797 0 -3.0755735 1.4331912 469.59287
|
||||
340 0 -3.0978292 0 -3.0935875 1.2415604 471.43131
|
||||
350 0 -3.1030388 0 -3.0994817 1.1855922 471.43131
|
||||
360 0 -3.1128512 0 -3.1097503 1.096837 469.69029
|
||||
370 0 -3.1148659 0 -3.1119534 1.0489288 470.95557
|
||||
380 0 -3.1166378 0 -3.1136569 0.98288209 473.66763
|
||||
390 0 -3.1193105 0 -3.1160328 0.87791426 471.97237
|
||||
400 0 -3.1206215 0 -3.1170125 0.78375684 473.92596
|
||||
410 0 -3.1208112 0 -3.117148 0.76964642 475.39426
|
||||
416 0 -3.1208738 0 -3.1171963 0.763393 474.17968
|
||||
Loop time of 0.0445333 on 4 procs for 220 steps with 420 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
2.06852056346 -3.11719356011 -3.11719629261
|
||||
Force two-norm initial, final = 2343.13 0.489927
|
||||
Force max component initial, final = 1038.51 0.0921925
|
||||
Final line search alpha, max atom move = 0.00296916 0.000273734
|
||||
Iterations, force evaluations = 220 848
|
||||
|
||||
Pair time (%) = 0.0204562 (45.9347)
|
||||
Neigh time (%) = 0.00166583 (3.74064)
|
||||
Comm time (%) = 0.0099439 (22.3292)
|
||||
Outpt time (%) = 0.000369072 (0.828756)
|
||||
Other time (%) = 0.0120983 (27.1668)
|
||||
|
||||
Nlocal: 105 ave 122 max 89 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Nghost: 89.5 ave 98 max 82 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Neighs: 901.5 ave 1096 max 713 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 3606
|
||||
Ave neighs/atom = 8.58571
|
||||
Neighbor list builds = 53
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 4 all indent ${k1} sphere 10 11.4 0 6.0
|
||||
fix 4 all indent 882.849286914813 sphere 10 11.4 0 6.0
|
||||
fix_modify 4 energy yes
|
||||
minimize 1.0e-6 1.0e-6 1000 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
|
||||
Memory usage per processor = 2.74744 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
416 0 -3.1208738 0 4.5726242 0.76329108 474.24299
|
||||
420 0 -2.7921115 0 0.12554168 3.208605 473.97607
|
||||
430 0 -2.7757713 0 -2.5174284 4.1005727 473.9787
|
||||
440 0 -2.8622562 0 -2.8246751 3.6723228 477.12966
|
||||
450 0 -2.937786 0 -2.909592 3.0648237 484.85615
|
||||
460 0 -2.97273 0 -2.9564121 2.7383277 488.78876
|
||||
470 0 -2.9835994 0 -2.9700404 2.563441 491.80148
|
||||
480 0 -2.9879154 0 -2.9761033 2.5160526 491.96498
|
||||
490 0 -2.9916932 0 -2.9820721 2.4627562 493.83702
|
||||
500 0 -3.001486 0 -2.9936395 2.3293593 494.85915
|
||||
510 0 -3.0335777 0 -3.0270601 1.9771348 497.06866
|
||||
520 0 -3.0489472 0 -3.0436257 1.8483891 497.01921
|
||||
530 0 -3.0557407 0 -3.0503519 1.7746631 496.65321
|
||||
540 0 -3.0607842 0 -3.0547376 1.6643506 497.17452
|
||||
550 0 -3.0667068 0 -3.0598216 1.4983736 500.95093
|
||||
560 0 -3.0695111 0 -3.0626813 1.4851269 499.05662
|
||||
570 0 -3.0728017 0 -3.0657511 1.4648801 498.07014
|
||||
580 0 -3.0738418 0 -3.0668835 1.4561546 498.07014
|
||||
590 0 -3.0764099 0 -3.0693885 1.4545514 497.99673
|
||||
600 0 -3.0818748 0 -3.0747706 1.43346 498.38846
|
||||
610 0 -3.0822295 0 -3.0751338 1.4354444 498.38846
|
||||
620 0 -3.082426 0 -3.0753487 1.4397055 497.93724
|
||||
622 0 -3.0824212 0 -3.0753552 1.4395296 497.93724
|
||||
Loop time of 0.038512 on 4 procs for 206 steps with 420 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
4.57262417707 -3.07535244818 -3.07535522656
|
||||
Force two-norm initial, final = 2978.09 1.12104
|
||||
Force max component initial, final = 1400.85 0.44337
|
||||
Final line search alpha, max atom move = 0.00595121 0.00263859
|
||||
Iterations, force evaluations = 206 720
|
||||
|
||||
Pair time (%) = 0.0172448 (44.7778)
|
||||
Neigh time (%) = 0.00121301 (3.14971)
|
||||
Comm time (%) = 0.00913364 (23.7163)
|
||||
Outpt time (%) = 0.000345349 (0.896732)
|
||||
Other time (%) = 0.0105752 (27.4594)
|
||||
|
||||
Nlocal: 105 ave 123 max 89 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 95.5 ave 105 max 87 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Neighs: 904.75 ave 1103 max 718 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 3619
|
||||
Ave neighs/atom = 8.61667
|
||||
Neighbor list builds = 39
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 4 all indent ${k1} sphere 10 11.2 0 6.0
|
||||
fix 4 all indent 882.849286914813 sphere 10 11.2 0 6.0
|
||||
fix_modify 4 energy yes
|
||||
minimize 1.0e-6 1.0e-6 1000 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
|
||||
Memory usage per processor = 2.74744 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
622 0 -3.0824212 0 -2.5558044 1.4393841 497.98759
|
||||
630 0 -2.9990709 0 -2.9502024 2.2860407 498.00801
|
||||
640 0 -3.0064013 0 -2.9810478 2.2922801 497.90024
|
||||
650 0 -3.0097157 0 -2.9948668 2.314644 497.75126
|
||||
660 0 -3.0165998 0 -3.0052994 2.3153482 497.51161
|
||||
670 0 -3.0231017 0 -3.012251 2.2916257 497.00169
|
||||
680 0 -3.0304422 0 -3.0203383 2.2695844 497.00368
|
||||
690 0 -3.0346029 0 -3.0248205 2.2468155 497.00368
|
||||
700 0 -3.036641 0 -3.0270583 2.2296664 497.6363
|
||||
710 0 -3.037401 0 -3.0277122 2.2211151 498.04962
|
||||
711 0 -3.0374016 0 -3.0277127 2.221111 498.04962
|
||||
Loop time of 0.019655 on 4 procs for 89 steps with 420 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-2.55580440685 -3.02771223773 -3.02771273695
|
||||
Force two-norm initial, final = 490.137 4.69177
|
||||
Force max component initial, final = 232.239 2.5669
|
||||
Final line search alpha, max atom move = 9.39778e-06 2.41232e-05
|
||||
Iterations, force evaluations = 89 359
|
||||
|
||||
Pair time (%) = 0.00871509 (44.3404)
|
||||
Neigh time (%) = 0.000852227 (4.33593)
|
||||
Comm time (%) = 0.00470811 (23.9538)
|
||||
Outpt time (%) = 0.0001598 (0.813025)
|
||||
Other time (%) = 0.00521976 (26.5569)
|
||||
|
||||
Nlocal: 105 ave 122 max 88 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 96.75 ave 107 max 86 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Neighs: 935.5 ave 1131 max 760 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 3742
|
||||
Ave neighs/atom = 8.90952
|
||||
Neighbor list builds = 27
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 4 all indent ${k1} sphere 10 11.0 0 6.0
|
||||
fix 4 all indent 882.849286914813 sphere 10 11.0 0 6.0
|
||||
fix_modify 4 energy yes
|
||||
minimize 1.0e-6 1.0e-6 1000 1000
|
||||
WARNING: Resetting reneighboring criteria during minimization (../min.cpp:173)
|
||||
Memory usage per processor = 2.74744 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
711 0 -3.0374016 0 -2.5400948 2.2234368 497.52862
|
||||
720 0 -2.9467221 0 -2.9050784 3.1683023 497.59856
|
||||
730 0 -2.9511837 0 -2.9319657 3.2028566 497.43904
|
||||
740 0 -2.9618885 0 -2.9417829 3.10431 498.05306
|
||||
750 0 -2.9627467 0 -2.9447731 3.0959012 498.05306
|
||||
760 0 -2.9641239 0 -2.9470922 3.0777312 498.32613
|
||||
770 0 -2.9700494 0 -2.9509269 3.0196934 498.5897
|
||||
780 0 -2.9749707 0 -2.9573574 2.997151 498.94648
|
||||
790 0 -2.9845528 0 -2.9661482 2.9379015 499.2991
|
||||
800 0 -2.994962 0 -2.9772454 2.8800592 499.10677
|
||||
810 0 -2.9980155 0 -2.9808077 2.8692662 499.10677
|
||||
820 0 -2.9989391 0 -2.9817793 2.8656279 499.65704
|
||||
825 0 -2.9991788 0 -2.9820879 2.8660089 499.65704
|
||||
Loop time of 0.0272222 on 4 procs for 114 steps with 420 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-2.54009483624 -2.98208743291 -2.98208787345
|
||||
Force two-norm initial, final = 458.759 2.33644
|
||||
Force max component initial, final = 204.211 0.365055
|
||||
Final line search alpha, max atom move = 3.33864e-05 1.21879e-05
|
||||
Iterations, force evaluations = 114 498
|
||||
|
||||
Pair time (%) = 0.0122632 (45.0484)
|
||||
Neigh time (%) = 0.00070715 (2.59769)
|
||||
Comm time (%) = 0.00696242 (25.5762)
|
||||
Outpt time (%) = 0.000183165 (0.672851)
|
||||
Other time (%) = 0.0071063 (26.1048)
|
||||
|
||||
Nlocal: 105 ave 125 max 86 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 99.5 ave 109 max 90 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
Neighs: 948.25 ave 1245 max 710 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 3793
|
||||
Ave neighs/atom = 9.03095
|
||||
Neighbor list builds = 22
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,67 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Test of MEAM potential for SiC system
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
read_data data.meam
|
||||
orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
128 atoms
|
||||
|
||||
pair_style meam
|
||||
pair_coeff * * library.meam Si C SiC.meam Si C
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 10
|
||||
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all atom 50 dump.meam
|
||||
|
||||
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3 element Si C
|
||||
|
||||
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3 element Si C
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 5.10824 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -636.38121 0 -636.38121 -76571.819
|
||||
10 1807.8862 -666.21959 0 -636.54126 -150571.49
|
||||
20 1932.4467 -668.2581 0 -636.53498 -120223.52
|
||||
30 1951.3652 -668.58139 0 -636.54771 -100508.4
|
||||
40 2172.5974 -672.22715 0 -636.5617 -110753.34
|
||||
50 2056.9149 -670.33108 0 -636.56468 -105418.07
|
||||
60 1947.9564 -668.52788 0 -636.55015 -111413.04
|
||||
70 1994.7712 -669.28849 0 -636.54225 -109645.76
|
||||
80 2126.0903 -671.43755 0 -636.53557 -97475.831
|
||||
90 2065.755 -670.4349 0 -636.52338 -95858.837
|
||||
100 2051.4553 -670.20799 0 -636.53122 -107068.9
|
||||
Loop time of 0.0835102 on 1 procs for 100 steps with 128 atoms
|
||||
|
||||
Pair time (%) = 0.0802212 (96.0616)
|
||||
Neigh time (%) = 0.00220895 (2.64513)
|
||||
Comm time (%) = 0.000565529 (0.677198)
|
||||
Outpt time (%) = 0.000127792 (0.153026)
|
||||
Other time (%) = 0.000386715 (0.463075)
|
||||
|
||||
Nlocal: 128 ave 128 max 128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 543 ave 543 max 543 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1526 ave 1526 max 1526 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 3052 ave 3052 max 3052 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3052
|
||||
Ave neighs/atom = 23.8438
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 10
|
||||
|
|
@ -0,0 +1,67 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Test of MEAM potential for SiC system
|
||||
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
|
||||
read_data data.meam
|
||||
orthogonal box = (-6 -6 -6) to (5.97232 5.97232 5.97232)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
128 atoms
|
||||
|
||||
pair_style meam
|
||||
pair_coeff * * library.meam Si C SiC.meam Si C
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 10
|
||||
|
||||
fix 1 all nve
|
||||
thermo 10
|
||||
timestep 0.001
|
||||
|
||||
#dump 1 all atom 50 dump.meam
|
||||
|
||||
#dump 2 all image 10 image.*.jpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3 element Si C
|
||||
|
||||
#dump 3 all movie 10 movie.mpg element element # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3 element Si C
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 4.99306 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -636.38121 0 -636.38121 -76571.819
|
||||
10 1807.8862 -666.21959 0 -636.54126 -150571.49
|
||||
20 1932.4467 -668.2581 0 -636.53498 -120223.52
|
||||
30 1951.3652 -668.58139 0 -636.54771 -100508.4
|
||||
40 2172.5974 -672.22715 0 -636.5617 -110753.34
|
||||
50 2056.9149 -670.33108 0 -636.56468 -105418.07
|
||||
60 1947.9564 -668.52788 0 -636.55015 -111413.04
|
||||
70 1994.7712 -669.28849 0 -636.54225 -109645.76
|
||||
80 2126.0903 -671.43755 0 -636.53557 -97475.831
|
||||
90 2065.755 -670.4349 0 -636.52338 -95858.837
|
||||
100 2051.4553 -670.20799 0 -636.53122 -107068.9
|
||||
Loop time of 0.0331262 on 4 procs for 100 steps with 128 atoms
|
||||
|
||||
Pair time (%) = 0.0293604 (88.6321)
|
||||
Neigh time (%) = 0.000602961 (1.82019)
|
||||
Comm time (%) = 0.00270861 (8.17666)
|
||||
Outpt time (%) = 0.000221252 (0.667908)
|
||||
Other time (%) = 0.000232935 (0.703175)
|
||||
|
||||
Nlocal: 32 ave 36 max 30 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
Nghost: 293.75 ave 305 max 285 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 381.5 ave 413 max 334 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
FullNghs: 763 ave 866 max 678 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 3052
|
||||
Ave neighs/atom = 23.8438
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 10
|
||||
|
|
@ -0,0 +1,172 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 3d metal shear simulation
|
||||
|
||||
units metal
|
||||
boundary s s p
|
||||
|
||||
atom_style atomic
|
||||
lattice fcc 3.52
|
||||
Lattice spacing in x,y,z = 3.52 3.52 3.52
|
||||
region box block 0 16.0 0 10.0 0 2.828427
|
||||
create_box 3 box
|
||||
Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
|
||||
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
|
||||
create_atoms 1 box
|
||||
Created 1912 atoms
|
||||
|
||||
pair_style meam
|
||||
pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
region lower block INF INF INF 0.9 INF INF
|
||||
region upper block INF INF 6.1 INF INF INF
|
||||
group lower region lower
|
||||
264 atoms in group lower
|
||||
group upper region upper
|
||||
264 atoms in group upper
|
||||
group boundary union lower upper
|
||||
528 atoms in group boundary
|
||||
group mobile subtract all boundary
|
||||
1384 atoms in group mobile
|
||||
|
||||
set group lower type 2
|
||||
264 settings made for type
|
||||
set group upper type 3
|
||||
264 settings made for type
|
||||
|
||||
# void
|
||||
|
||||
#region void cylinder z 8 5 2.5 INF INF
|
||||
#delete_atoms region void
|
||||
|
||||
# temp controllers
|
||||
|
||||
compute new3d mobile temp
|
||||
compute new2d mobile temp/partial 0 1 1
|
||||
|
||||
# equilibrate
|
||||
|
||||
velocity mobile create 300.0 5812775 temp new3d
|
||||
fix 1 all nve
|
||||
fix 2 boundary setforce 0.0 0.0 0.0
|
||||
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new3d
|
||||
|
||||
thermo 25
|
||||
thermo_modify temp new3d
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
|
||||
timestep 0.001
|
||||
run 100
|
||||
Memory usage per processor = 6.77654 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02
|
||||
25 222.78953 -8188.1215 0 -8148.2941 9095.9008 19547.02
|
||||
50 300 -8149.7654 0 -8096.1353 10633.141 19684.382
|
||||
75 304.80657 -8163.4557 0 -8108.9665 7045.457 19759.745
|
||||
100 300 -8173.6884 0 -8120.0584 5952.521 19886.589
|
||||
Loop time of 1.5888 on 1 procs for 100 steps with 1912 atoms
|
||||
|
||||
Pair time (%) = 1.56768 (98.671)
|
||||
Neigh time (%) = 0.0145421 (0.915289)
|
||||
Comm time (%) = 0.0015583 (0.0980806)
|
||||
Outpt time (%) = 6.31809e-05 (0.00397665)
|
||||
Other time (%) = 0.00495219 (0.311694)
|
||||
|
||||
Nlocal: 1912 ave 1912 max 1912 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1672 ave 1672 max 1672 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 23806 ave 23806 max 23806 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 47612 ave 47612 max 47612 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 47612
|
||||
Ave neighs/atom = 24.9017
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
||||
# shear
|
||||
|
||||
velocity upper set 1.0 0 0
|
||||
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
|
||||
|
||||
unfix 3
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new2d
|
||||
|
||||
#dump 1 all atom 500 dump.meam.shear
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
thermo 100
|
||||
thermo_modify temp new2d
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
|
||||
reset_timestep 0
|
||||
run 3000
|
||||
Memory usage per processor = 6.95312 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 300.50853 -8173.6884 0 -8137.8874 4992.9811 19894.297
|
||||
100 292.0799 -8177.7235 0 -8142.9266 2566.6872 19871.516
|
||||
200 306.71233 -8177.1504 0 -8140.6103 872.78764 20047.2
|
||||
300 295.7806 -8172.9505 0 -8137.7127 -1053.769 20091.657
|
||||
400 309.18439 -8169.6374 0 -8132.8028 -1784.5443 20122.178
|
||||
500 304.51122 -8163.9147 0 -8127.6369 -160.26993 20183.44
|
||||
600 300 -8158.55 0 -8122.8096 1555.2344 20279.887
|
||||
700 304.32794 -8149.4746 0 -8113.2185 3700.5984 20430.504
|
||||
800 304.79621 -8138.8368 0 -8102.5249 3721.6015 20510.74
|
||||
900 303.87706 -8128.16 0 -8091.9576 4387.1435 20638.992
|
||||
1000 300 -8113.4908 0 -8077.7503 6186.7017 20755.029
|
||||
1100 306.13485 -8097.1731 0 -8060.7018 8904.6623 20879.616
|
||||
1200 309.15674 -8081.8589 0 -8045.0276 10523.683 20996.875
|
||||
1300 304.48415 -8064.5597 0 -8028.2851 10063.026 21126.348
|
||||
1400 300 -8046.7606 0 -8011.0202 10972.46 21238.721
|
||||
1500 300 -8041.3545 0 -8005.614 11939.553 21374.301
|
||||
1600 309.60382 -8035.2271 0 -7998.3425 11340.231 21530.1
|
||||
1700 300 -8029.1688 0 -7993.4284 11298.984 21635.492
|
||||
1800 300 -8034.2178 0 -7998.4773 9635.8998 21737.07
|
||||
1900 299.69156 -8037.3123 0 -8001.6086 6094.2811 21857.993
|
||||
2000 308.23519 -8030.0074 0 -7993.2859 3176.5086 21983.182
|
||||
2100 300 -8031.5977 0 -7995.8573 1352.4566 22112.054
|
||||
2200 300 -8039.3918 0 -8003.6514 2078.9229 22231.755
|
||||
2300 305.77226 -8038.7518 0 -8002.3237 3408.6101 22345.35
|
||||
2400 300 -8034.7719 0 -7999.0314 5324.2456 22468.716
|
||||
2500 300 -8034.9187 0 -7999.1782 7770.9385 22588.417
|
||||
2600 300 -8034.3037 0 -7998.5633 10402.367 22709.34
|
||||
2700 304.22676 -8032.9652 0 -7996.7213 11603.947 22840.035
|
||||
2800 306.55646 -8032.2292 0 -7995.7077 10585.627 22959.736
|
||||
2900 304.12756 -8031.7372 0 -7995.505 7574.3331 23087.988
|
||||
3000 301.87833 -8033.9958 0 -7998.0316 4111.4578 23197.918
|
||||
Loop time of 50.7057 on 1 procs for 3000 steps with 1912 atoms
|
||||
|
||||
Pair time (%) = 49.8856 (98.3827)
|
||||
Neigh time (%) = 0.619792 (1.22233)
|
||||
Comm time (%) = 0.0500011 (0.0986104)
|
||||
Outpt time (%) = 0.00052166 (0.0010288)
|
||||
Other time (%) = 0.14977 (0.295371)
|
||||
|
||||
Nlocal: 1912 ave 1912 max 1912 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1657 ave 1657 max 1657 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 23337 ave 23337 max 23337 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 46674 ave 46674 max 46674 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 46674
|
||||
Ave neighs/atom = 24.4111
|
||||
Neighbor list builds = 219
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,172 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 3d metal shear simulation
|
||||
|
||||
units metal
|
||||
boundary s s p
|
||||
|
||||
atom_style atomic
|
||||
lattice fcc 3.52
|
||||
Lattice spacing in x,y,z = 3.52 3.52 3.52
|
||||
region box block 0 16.0 0 10.0 0 2.828427
|
||||
create_box 3 box
|
||||
Created orthogonal box = (0 0 0) to (56.32 35.2 9.95606)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
|
||||
lattice fcc 3.52 orient x 1 0 0 orient y 0 1 1 orient z 0 -1 1 origin 0.5 0 0
|
||||
Lattice spacing in x,y,z = 3.52 4.97803 4.97803
|
||||
create_atoms 1 box
|
||||
Created 1912 atoms
|
||||
|
||||
pair_style meam
|
||||
pair_coeff * * library.meam Ni4 Ni.meam Ni4 Ni4 Ni4
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
region lower block INF INF INF 0.9 INF INF
|
||||
region upper block INF INF 6.1 INF INF INF
|
||||
group lower region lower
|
||||
264 atoms in group lower
|
||||
group upper region upper
|
||||
264 atoms in group upper
|
||||
group boundary union lower upper
|
||||
528 atoms in group boundary
|
||||
group mobile subtract all boundary
|
||||
1384 atoms in group mobile
|
||||
|
||||
set group lower type 2
|
||||
264 settings made for type
|
||||
set group upper type 3
|
||||
264 settings made for type
|
||||
|
||||
# void
|
||||
|
||||
#region void cylinder z 8 5 2.5 INF INF
|
||||
#delete_atoms region void
|
||||
|
||||
# temp controllers
|
||||
|
||||
compute new3d mobile temp
|
||||
compute new2d mobile temp/partial 0 1 1
|
||||
|
||||
# equilibrate
|
||||
|
||||
velocity mobile create 300.0 5812775 temp new3d
|
||||
fix 1 all nve
|
||||
fix 2 boundary setforce 0.0 0.0 0.0
|
||||
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new3d
|
||||
|
||||
thermo 25
|
||||
thermo_modify temp new3d
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
|
||||
timestep 0.001
|
||||
run 100
|
||||
Memory usage per processor = 5.96074 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 300 -8232.7767 0 -8179.1466 1386.6643 19547.02
|
||||
25 221.59546 -8187.6813 0 -8148.0673 9100.4509 19547.02
|
||||
50 300 -8150.0685 0 -8096.4384 10317.407 19685.743
|
||||
75 307.76021 -8164.6669 0 -8109.6496 6289.7138 19757.814
|
||||
100 300 -8176.5141 0 -8122.884 4162.2559 19873.327
|
||||
Loop time of 0.443615 on 4 procs for 100 steps with 1912 atoms
|
||||
|
||||
Pair time (%) = 0.425855 (95.9965)
|
||||
Neigh time (%) = 0.00376439 (0.848572)
|
||||
Comm time (%) = 0.0119869 (2.7021)
|
||||
Outpt time (%) = 0.000107288 (0.024185)
|
||||
Other time (%) = 0.00190133 (0.428599)
|
||||
|
||||
Nlocal: 478 ave 492 max 465 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Nghost: 809 ave 822 max 795 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Neighs: 5916 ave 6133 max 5658 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
FullNghs: 11832 ave 12277 max 11299 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 47328
|
||||
Ave neighs/atom = 24.7531
|
||||
Neighbor list builds = 5
|
||||
Dangerous builds = 0
|
||||
|
||||
# shear
|
||||
|
||||
velocity upper set 1.0 0 0
|
||||
velocity mobile ramp vx 0.0 1.0 y 1.4 8.6 sum yes
|
||||
|
||||
unfix 3
|
||||
fix 3 mobile temp/rescale 10 300.0 300.0 10.0 1.0
|
||||
fix_modify 3 temp new2d
|
||||
|
||||
#dump 1 all atom 500 dump.meam.shear
|
||||
|
||||
#dump 2 all image 100 image.*.jpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 100 movie.mpg type type # axes yes 0.8 0.02 view 0 0 zoom 1.5 up 0 1 0 adiam 2.0
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
thermo 100
|
||||
thermo_modify temp new2d
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
|
||||
reset_timestep 0
|
||||
run 3000
|
||||
Memory usage per processor = 6.00501 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 295.42794 -8176.5141 0 -8141.3183 3169.3113 19886.93
|
||||
100 292.02876 -8176.5475 0 -8141.7567 -826.45881 19918.758
|
||||
200 306.10676 -8176.7837 0 -8140.3158 -1371.1065 19948.794
|
||||
300 300 -8172.6378 0 -8136.8974 -1736.2602 20086.712
|
||||
400 306.48529 -8168.4581 0 -8131.9451 -957.8783 20111.985
|
||||
500 309.89005 -8166.3097 0 -8129.391 -1024.7828 20200.517
|
||||
600 302.35862 -8157.8008 0 -8121.7794 540.69714 20316.092
|
||||
700 292.46062 -8149.9463 0 -8115.1041 1709.248 20448.424
|
||||
800 306.03297 -8139.326 0 -8102.8669 4197.3195 20522.955
|
||||
900 302.01714 -8127.2712 0 -8091.2905 6337.0018 20634.106
|
||||
1000 300 -8112.4155 0 -8076.675 7383.2425 20759.915
|
||||
1100 303.06207 -8097.0321 0 -8060.9268 7921.3462 20879.616
|
||||
1200 300.99295 -8079.4118 0 -8043.5531 10534.001 20995.654
|
||||
1300 300 -8065.6269 0 -8029.8865 10683.83 21125.127
|
||||
1400 300 -8050.6108 0 -8014.8704 9586.4735 21255.821
|
||||
1500 300 -8041.9686 0 -8006.2281 9655.7424 21365.751
|
||||
1600 308.48003 -8031.9005 0 -7995.1498 10878.449 21496.446
|
||||
1700 300 -8018.8868 0 -7983.1463 11313.466 21610.04
|
||||
1800 300 -8011.819 0 -7976.0786 11545.414 21730.963
|
||||
1900 300 -8008.9295 0 -7973.1891 9195.9922 21861.658
|
||||
2000 300 -8013.4803 0 -7977.7399 5835.8211 21977.695
|
||||
2100 300 -8024.1289 0 -7988.3885 1247.1291 22107.168
|
||||
2200 300 -8035.3879 0 -7999.6475 755.15155 22219.541
|
||||
2300 300 -8039.784 0 -8004.0436 990.04968 22355.121
|
||||
2400 300 -8044.0207 0 -8008.2803 -798.93073 22469.937
|
||||
2500 300 -8045.7015 0 -8009.9611 -2282.7 22588.417
|
||||
2600 309.16599 -8043.0604 0 -8006.228 -1333.726 22713.005
|
||||
2700 297.78976 -8035.0476 0 -7999.5705 -1819.5883 22842.478
|
||||
2800 306.30156 -8029.889 0 -7993.3979 -155.02495 22962.179
|
||||
2900 300 -8028.0102 0 -7992.2698 731.08083 23083.102
|
||||
3000 300 -8025.8905 0 -7990.15 2169.2725 23200.361
|
||||
Loop time of 13.8878 on 4 procs for 3000 steps with 1912 atoms
|
||||
|
||||
Pair time (%) = 13.3534 (96.1521)
|
||||
Neigh time (%) = 0.160926 (1.15876)
|
||||
Comm time (%) = 0.316833 (2.28138)
|
||||
Outpt time (%) = 0.000683129 (0.00491891)
|
||||
Other time (%) = 0.0559426 (0.402818)
|
||||
|
||||
Nlocal: 478 ave 511 max 445 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 787.5 ave 833 max 753 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
Neighs: 5805 ave 6124 max 5486 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
FullNghs: 11610 ave 12225 max 11027 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 46440
|
||||
Ave neighs/atom = 24.2887
|
||||
Neighbor list builds = 222
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,63 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
#dump id all atom 50 dump.melt
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
Memory usage per processor = 2.35377 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3 -6.7733681 0 -2.2744931 -3.7033504
|
||||
50 1.6758903 -4.7955425 0 -2.2823355 5.670064
|
||||
100 1.6458363 -4.7492704 0 -2.2811332 5.8691042
|
||||
150 1.6324555 -4.7286791 0 -2.280608 5.9589514
|
||||
200 1.6630725 -4.7750988 0 -2.2811136 5.7364886
|
||||
250 1.6275257 -4.7224992 0 -2.281821 5.9567365
|
||||
Loop time of 0.723551 on 1 procs for 250 steps with 4000 atoms
|
||||
|
||||
Pair time (%) = 0.608158 (84.0518)
|
||||
Neigh time (%) = 0.0826616 (11.4244)
|
||||
Comm time (%) = 0.0138171 (1.90962)
|
||||
Outpt time (%) = 9.58443e-05 (0.0132464)
|
||||
Other time (%) = 0.0188186 (2.60087)
|
||||
|
||||
Nlocal: 4000 ave 4000 max 4000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5499 ave 5499 max 5499 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 151513 ave 151513 max 151513 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 151513
|
||||
Ave neighs/atom = 37.8783
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,63 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 3d Lennard-Jones melt
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
|
||||
lattice fcc 0.8442
|
||||
Lattice spacing in x,y,z = 1.6796 1.6796 1.6796
|
||||
region box block 0 10 0 10 0 10
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 0) to (16.796 16.796 16.796)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 4000 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 3.0 87287
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify every 20 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
|
||||
#dump id all atom 50 dump.melt
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
thermo 50
|
||||
run 250
|
||||
Memory usage per processor = 1.88303 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 3 -6.7733681 0 -2.2744931 -3.7033504
|
||||
50 1.6754119 -4.7947589 0 -2.2822693 5.6615925
|
||||
100 1.6503357 -4.756014 0 -2.2811293 5.8050524
|
||||
150 1.6596605 -4.7699432 0 -2.2810749 5.7830138
|
||||
200 1.6371874 -4.7365462 0 -2.2813789 5.9246674
|
||||
250 1.6323462 -4.7292021 0 -2.2812949 5.9762238
|
||||
Loop time of 0.209819 on 4 procs for 250 steps with 4000 atoms
|
||||
|
||||
Pair time (%) = 0.159745 (76.1344)
|
||||
Neigh time (%) = 0.0218451 (10.4114)
|
||||
Comm time (%) = 0.0226035 (10.7728)
|
||||
Outpt time (%) = 0.000118613 (0.0565311)
|
||||
Other time (%) = 0.00550741 (2.62483)
|
||||
|
||||
Nlocal: 1000 ave 1010 max 982 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
||||
Nghost: 2703.75 ave 2713 max 2689 min
|
||||
Histogram: 1 0 0 0 0 0 0 2 0 1
|
||||
Neighs: 37915.5 ave 39239 max 36193 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
|
||||
Total # of neighbors = 151662
|
||||
Ave neighs/atom = 37.9155
|
||||
Neighbor list builds = 12
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,215 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 2d micelle simulation
|
||||
|
||||
dimension 2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
atom_style bond
|
||||
|
||||
# Soft potential push-off
|
||||
|
||||
read_data data.micelle
|
||||
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1200 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
300 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special_bonds fene
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
pair_style soft 1.12246
|
||||
pair_coeff * * 0.0 1.12246
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 50.0 0.75
|
||||
|
||||
velocity all create 0.45 2349852
|
||||
|
||||
variable prefactor equal ramp(1.0,20.0)
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 3 all adapt 1 pair soft a * * v_prefactor
|
||||
fix 4 all enforce2d
|
||||
|
||||
thermo 50
|
||||
run 1000
|
||||
Memory usage per processor = 2.47979 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
|
||||
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
|
||||
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
|
||||
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
|
||||
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
|
||||
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
|
||||
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
|
||||
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
|
||||
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
|
||||
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
|
||||
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
|
||||
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
|
||||
600 0.45 0.58193041 0.088386617 1.119942 5.131481
|
||||
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
|
||||
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
|
||||
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
|
||||
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
|
||||
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
|
||||
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
|
||||
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
|
||||
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
|
||||
Loop time of 0.161192 on 1 procs for 1000 steps with 1200 atoms
|
||||
|
||||
Pair time (%) = 0.10344 (64.1721)
|
||||
Bond time (%) = 0.00639391 (3.96664)
|
||||
Neigh time (%) = 0.019408 (12.0403)
|
||||
Comm time (%) = 0.00402379 (2.49627)
|
||||
Outpt time (%) = 0.00023222 (0.144064)
|
||||
Other time (%) = 0.0276937 (17.1806)
|
||||
|
||||
Nlocal: 1200 ave 1200 max 1200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 195 ave 195 max 195 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3136 ave 3136 max 3136 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3136
|
||||
Ave neighs/atom = 2.61333
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 92
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 3
|
||||
|
||||
# Main run
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
# solvent/head - full-size and long-range
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.0 1.0 2.5
|
||||
|
||||
# tail/tail - size-averaged and long-range
|
||||
|
||||
pair_coeff 3 3 1.0 0.75 2.5
|
||||
pair_coeff 4 4 1.0 0.50 2.5
|
||||
pair_coeff 3 4 1.0 0.67 2.5
|
||||
|
||||
# solvent/tail - full-size and repulsive
|
||||
|
||||
pair_coeff 1 3 1.0 1.0 1.12246
|
||||
pair_coeff 1 4 1.0 1.0 1.12246
|
||||
|
||||
# head/tail - size-averaged and repulsive
|
||||
|
||||
pair_coeff 2 3 1.0 0.88 1.12246
|
||||
pair_coeff 2 4 1.0 0.75 1.12246
|
||||
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 2000 dump.micelle
|
||||
|
||||
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
|
||||
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
reset_timestep 0
|
||||
run 60000
|
||||
Memory usage per processor = 2.63238 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
|
||||
1000 0.45 -1.9727753 0.058614052 -1.4645362 1.9980678
|
||||
2000 0.45 -2.001583 0.074586381 -1.4773716 1.677722
|
||||
3000 0.45 -2.01376 0.065369685 -1.4987654 1.5672632
|
||||
4000 0.44978364 -2.0284623 0.069543994 -1.5095095 1.3255914
|
||||
5000 0.4515788 -2.0213579 0.063453981 -1.5067015 1.2898067
|
||||
6000 0.44084238 -2.0220208 0.059857725 -1.5216881 1.3664878
|
||||
7000 0.45280746 -2.0465582 0.056091161 -1.538037 1.1247107
|
||||
8000 0.45575503 -2.0556878 0.056250977 -1.5440615 1.2847641
|
||||
9000 0.45541476 -2.0383734 0.062759047 -1.5205791 1.4205644
|
||||
10000 0.43553889 -2.0491499 0.064724759 -1.5492492 1.2479479
|
||||
11000 0.46199123 -2.0775949 0.05294824 -1.5630404 0.91003048
|
||||
12000 0.45116812 -2.0484232 0.065204884 -1.5324262 1.1225658
|
||||
13000 0.44686952 -2.0599878 0.049287713 -1.564203 1.1154998
|
||||
14000 0.45212998 -2.0625951 0.058683349 -1.5521586 0.98441931
|
||||
15000 0.4556105 -2.0756197 0.059200748 -1.5611881 0.95502443
|
||||
16000 0.45043625 -2.0824009 0.064992475 -1.5673475 1.1101553
|
||||
17000 0.44547914 -2.0937506 0.063134923 -1.5855078 1.0387966
|
||||
18000 0.44560114 -2.0932092 0.063158377 -1.584821 0.92976825
|
||||
19000 0.46409216 -2.0998691 0.063095466 -1.5730682 0.74222038
|
||||
20000 0.43356947 -2.079761 0.058993704 -1.5875591 0.98809322
|
||||
21000 0.43970509 -2.0772972 0.063415284 -1.5745433 1.1679023
|
||||
22000 0.45439796 -2.0869643 0.060942539 -1.5720025 0.95309247
|
||||
23000 0.46436648 -2.0865877 0.062283763 -1.5603244 0.82847808
|
||||
24000 0.45179512 -2.099375 0.057554155 -1.5904022 0.81341216
|
||||
25000 0.45 -2.1028977 0.053292072 -1.5999806 0.8167413
|
||||
26000 0.44379478 -2.0953332 0.065257482 -1.5866508 0.79986647
|
||||
27000 0.45233801 -2.0995326 0.060977813 -1.5865937 0.8732284
|
||||
28000 0.45416333 -2.0995467 0.051944425 -1.5938174 0.84546945
|
||||
29000 0.44235173 -2.0819112 0.063209787 -1.5767183 0.7973497
|
||||
30000 0.463297 -2.1019723 0.052828108 -1.5862333 0.83736896
|
||||
31000 0.46237603 -2.114332 0.059492046 -1.5928492 0.6791076
|
||||
32000 0.46010313 -2.1067583 0.06500768 -1.5820309 0.73245227
|
||||
33000 0.45581512 -2.106217 0.054623133 -1.5961586 0.77209258
|
||||
34000 0.46132621 -2.1005582 0.063679478 -1.5759369 0.79365061
|
||||
35000 0.44457465 -2.1009737 0.063096958 -1.5936726 0.77684088
|
||||
36000 0.46892599 -2.1283119 0.063349886 -1.5964267 0.66757096
|
||||
37000 0.43919893 -2.117133 0.061828288 -1.6164718 0.82728955
|
||||
38000 0.46347483 -2.1095945 0.053697761 -1.5928082 0.6018967
|
||||
39000 0.46560699 -2.134901 0.051889552 -1.6177925 0.61468453
|
||||
40000 0.45486545 -2.1082829 0.05921023 -1.5945863 0.67314005
|
||||
41000 0.46926414 -2.1056671 0.052918097 -1.5838759 0.72673846
|
||||
42000 0.44801848 -2.1122598 0.053198288 -1.6114163 0.7515948
|
||||
43000 0.44733537 -2.1143993 0.048691802 -1.6187449 0.64883126
|
||||
44000 0.44330158 -2.0946395 0.063057453 -1.5886499 0.74170615
|
||||
45000 0.44616358 -2.1212538 0.054840602 -1.6206214 0.72390736
|
||||
46000 0.43298663 -2.0977927 0.063259619 -1.6019073 0.75151063
|
||||
47000 0.45 -2.093575 0.062292347 -1.5816576 0.83230853
|
||||
48000 0.43668769 -2.1011039 0.055608008 -1.6091721 0.81680002
|
||||
49000 0.43402566 -2.1180572 0.0705711 -1.6138221 0.61733524
|
||||
50000 0.45870183 -2.1234461 0.061839249 -1.6032873 0.71893984
|
||||
51000 0.46897063 -2.1240109 0.056638825 -1.5987922 0.57223633
|
||||
52000 0.44547026 -2.114712 0.066830872 -1.6027821 0.88042497
|
||||
53000 0.45698191 -2.1088353 0.055900552 -1.5963336 0.73302935
|
||||
54000 0.46105819 -2.1164732 0.053844244 -1.6019549 0.52305471
|
||||
55000 0.46526131 -2.1168922 0.053629683 -1.5983889 0.74647219
|
||||
56000 0.4610805 -2.1203778 0.060044544 -1.5996369 0.56764901
|
||||
57000 0.43539083 -2.1162246 0.058878039 -1.6223185 0.63599171
|
||||
58000 0.45613812 -2.1341668 0.059717309 -1.6186914 0.5752578
|
||||
59000 0.45035503 -2.1066421 0.056509876 -1.6001524 0.69875083
|
||||
60000 0.46528439 -2.1306197 0.058828427 -1.6068946 0.47995479
|
||||
Loop time of 13.5248 on 1 procs for 60000 steps with 1200 atoms
|
||||
|
||||
Pair time (%) = 9.22542 (68.2113)
|
||||
Bond time (%) = 0.386645 (2.85879)
|
||||
Neigh time (%) = 1.98116 (14.6484)
|
||||
Comm time (%) = 0.342358 (2.53134)
|
||||
Outpt time (%) = 0.000705719 (0.00521797)
|
||||
Other time (%) = 1.58848 (11.745)
|
||||
|
||||
Nlocal: 1200 ave 1200 max 1200 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 450 ave 450 max 450 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 9799 ave 9799 max 9799 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 9799
|
||||
Ave neighs/atom = 8.16583
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 4876
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,215 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 2d micelle simulation
|
||||
|
||||
dimension 2
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
atom_style bond
|
||||
|
||||
# Soft potential push-off
|
||||
|
||||
read_data data.micelle
|
||||
orthogonal box = (0 0 -0.1) to (35.8569 35.8569 0.1)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
1200 atoms
|
||||
scanning bonds ...
|
||||
1 = max bonds/atom
|
||||
reading bonds ...
|
||||
300 bonds
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
special_bonds fene
|
||||
2 = max # of 1-2 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
pair_style soft 1.12246
|
||||
pair_coeff * * 0.0 1.12246
|
||||
|
||||
bond_style harmonic
|
||||
bond_coeff 1 50.0 0.75
|
||||
|
||||
velocity all create 0.45 2349852
|
||||
|
||||
variable prefactor equal ramp(1.0,20.0)
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all temp/rescale 100 0.45 0.45 0.02 1.0
|
||||
fix 3 all adapt 1 pair soft a * * v_prefactor
|
||||
fix 4 all enforce2d
|
||||
|
||||
thermo 50
|
||||
run 1000
|
||||
Memory usage per processor = 2.79957 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 0.40003481 2.2200223e-06 0.84966203 0.78952518
|
||||
50 0.47411013 0.67721272 0.057404514 1.2083323 1.3375852
|
||||
100 0.45 0.73046745 0.054836584 1.234929 2.3196516
|
||||
150 0.67521742 0.72402001 0.043490075 1.4421648 2.8744416
|
||||
200 0.45 0.78481891 0.076931503 1.3113754 3.0412388
|
||||
250 0.66479018 0.69790602 0.081075564 1.4432178 3.6917024
|
||||
300 0.45 0.76820218 0.066727591 1.2845548 3.7861054
|
||||
350 0.67619136 0.625715 0.072722727 1.3740656 4.2861621
|
||||
400 0.45 0.68527759 0.090724527 1.2256271 4.4725214
|
||||
450 0.56702844 0.64402767 0.080555563 1.2911391 4.7402211
|
||||
500 0.45 0.64883009 0.078376672 1.1768318 4.7919294
|
||||
550 0.564664 0.58260368 0.080779475 1.2275766 4.9855705
|
||||
600 0.45 0.58193041 0.088386617 1.119942 5.131481
|
||||
650 0.52110993 0.5415273 0.097683746 1.1598867 5.2500294
|
||||
700 0.45 0.50856787 0.088471208 1.0466641 5.2550165
|
||||
750 0.51510855 0.47441291 0.089429375 1.0785216 5.375763
|
||||
800 0.45 0.49926696 0.085958476 1.0348504 5.4665914
|
||||
850 0.50688494 0.46614429 0.088962292 1.0615691 5.556932
|
||||
900 0.45 0.47785593 0.10150857 1.0289895 5.7765975
|
||||
950 0.49590559 0.46050477 0.096404887 1.052402 5.8649245
|
||||
1000 0.45 0.47691182 0.08808163 1.0146185 6.0177568
|
||||
Loop time of 0.0566852 on 4 procs for 1000 steps with 1200 atoms
|
||||
|
||||
Pair time (%) = 0.0265669 (46.8675)
|
||||
Bond time (%) = 0.00169075 (2.98269)
|
||||
Neigh time (%) = 0.00560409 (9.88633)
|
||||
Comm time (%) = 0.0120407 (21.2413)
|
||||
Outpt time (%) = 0.000412762 (0.728166)
|
||||
Other time (%) = 0.01037 (18.294)
|
||||
|
||||
Nlocal: 300 ave 305 max 292 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
Nghost: 100.25 ave 108 max 93 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Neighs: 784 ave 815 max 739 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
|
||||
Total # of neighbors = 3136
|
||||
Ave neighs/atom = 2.61333
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 92
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 3
|
||||
|
||||
# Main run
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
|
||||
# solvent/head - full-size and long-range
|
||||
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_coeff 2 2 1.0 1.0 2.5
|
||||
pair_coeff 1 2 1.0 1.0 2.5
|
||||
|
||||
# tail/tail - size-averaged and long-range
|
||||
|
||||
pair_coeff 3 3 1.0 0.75 2.5
|
||||
pair_coeff 4 4 1.0 0.50 2.5
|
||||
pair_coeff 3 4 1.0 0.67 2.5
|
||||
|
||||
# solvent/tail - full-size and repulsive
|
||||
|
||||
pair_coeff 1 3 1.0 1.0 1.12246
|
||||
pair_coeff 1 4 1.0 1.0 1.12246
|
||||
|
||||
# head/tail - size-averaged and repulsive
|
||||
|
||||
pair_coeff 2 3 1.0 0.88 1.12246
|
||||
pair_coeff 2 4 1.0 0.75 1.12246
|
||||
|
||||
thermo 1000
|
||||
|
||||
#dump 1 all atom 2000 dump.micelle
|
||||
|
||||
#dump 2 all image 2000 image.*.jpg type type zoom 1.6
|
||||
#dump_modify 2 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
#dump 3 all movie 2000 movie.mpg type type zoom 1.6
|
||||
#dump_modify 3 pad 5 adiam 1 0.5 adiam 2 1.5 adiam 3 1.0 adiam 4 0.75
|
||||
|
||||
reset_timestep 0
|
||||
run 60000
|
||||
Memory usage per processor = 2.79957 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0.45 -1.7056163 0.08808163 -1.1679097 3.9431686
|
||||
1000 0.45 -1.9727852 0.0586182 -1.464542 1.9980664
|
||||
2000 0.46082446 -1.977605 0.057039794 -1.4601247 1.726013
|
||||
3000 0.45 -2.0006402 0.05562923 -1.495386 1.511225
|
||||
4000 0.4623338 -2.0091993 0.059138048 -1.4881127 1.3542907
|
||||
5000 0.45 -2.0395585 0.061066034 -1.5288674 1.1830193
|
||||
6000 0.45905159 -2.0634848 0.058991931 -1.5458239 1.1082099
|
||||
7000 0.45 -2.0508705 0.061559594 -1.5396859 1.2020831
|
||||
8000 0.44666556 -2.0397402 0.066632486 -1.5268144 1.2612013
|
||||
9000 0.45034184 -2.03446 0.064174681 -1.5203188 1.1644088
|
||||
10000 0.44920732 -2.0856804 0.059525789 -1.5773216 0.93583471
|
||||
11000 0.45896474 -2.063989 0.064678373 -1.5407284 1.0732096
|
||||
12000 0.45848122 -2.0752398 0.061533665 -1.555607 1.0281395
|
||||
13000 0.46738009 -2.0629007 0.067132245 -1.5287778 0.96711354
|
||||
14000 0.44988856 -2.062354 0.062693783 -1.5501466 1.0123189
|
||||
15000 0.45098377 -2.072531 0.051120563 -1.5708025 0.97044948
|
||||
16000 0.45 -2.1017479 0.064909547 -1.5872134 0.90299146
|
||||
17000 0.4552102 -2.0765865 0.056648474 -1.5651072 0.91280438
|
||||
18000 0.44824933 -2.0828037 0.058978706 -1.5759492 0.92795752
|
||||
19000 0.44079166 -2.0556475 0.059088524 -1.5561347 1.1454216
|
||||
20000 0.44463382 -2.0859907 0.057486911 -1.5842405 0.92599126
|
||||
21000 0.44406551 -2.0826296 0.056776522 -1.5821577 0.99925665
|
||||
22000 0.44911834 -2.0711967 0.059641892 -1.5628107 0.95834342
|
||||
23000 0.43655144 -2.0909928 0.062696368 -1.5921088 0.91119509
|
||||
24000 0.44867934 -2.1018259 0.055592487 -1.597928 0.76348634
|
||||
25000 0.45260844 -2.0937068 0.059149636 -1.5823259 0.89135412
|
||||
26000 0.44898273 -2.1016995 0.066566046 -1.5865249 0.74284381
|
||||
27000 0.43221936 -2.084773 0.062900549 -1.5900132 0.87821534
|
||||
28000 0.46292457 -2.0965745 0.055816359 -1.5782193 0.74158202
|
||||
29000 0.45 -2.1306418 0.063790424 -1.6172264 0.53967764
|
||||
30000 0.44871717 -2.0907319 0.055486729 -1.586902 0.99873528
|
||||
31000 0.46125755 -2.0755203 0.056517719 -1.5581294 0.9347469
|
||||
32000 0.45941056 -2.0914092 0.057505763 -1.5748757 0.89468013
|
||||
33000 0.46026614 -2.0984679 0.056646234 -1.5819391 0.80740251
|
||||
34000 0.46916633 -2.1193229 0.054211886 -1.5963356 0.61039936
|
||||
35000 0.43884901 -2.0922975 0.061924634 -1.5918896 0.79377862
|
||||
36000 0.43947177 -2.0909805 0.053228588 -1.5986464 0.90484301
|
||||
37000 0.45414812 -2.1030789 0.055686423 -1.5936228 0.87060399
|
||||
38000 0.44280127 -2.0908535 0.058003408 -1.5904178 0.8046892
|
||||
39000 0.45516585 -2.1008067 0.058183565 -1.5878366 0.6089312
|
||||
40000 0.43067796 -2.0848319 0.062869447 -1.5916434 0.74412702
|
||||
41000 0.44165418 -2.1259603 0.064019775 -1.6206544 0.6221064
|
||||
42000 0.43982239 -2.1055547 0.064067567 -1.6020312 0.62130789
|
||||
43000 0.46586098 -2.1382757 0.05819116 -1.6146118 0.54791918
|
||||
44000 0.45469796 -2.1328327 0.066699087 -1.6118146 0.52752596
|
||||
45000 0.45358824 -2.1251041 0.063138554 -1.6087553 0.64714368
|
||||
46000 0.44191865 -2.1041137 0.059520035 -1.6030433 0.62417966
|
||||
47000 0.45804456 -2.1075048 0.066124313 -1.5837176 0.82334648
|
||||
48000 0.45700413 -2.1298865 0.065741607 -1.6075216 0.58174639
|
||||
49000 0.45842123 -2.1362735 0.056849019 -1.6213852 0.51934277
|
||||
50000 0.44239274 -2.1182037 0.053635135 -1.6225444 0.59636555
|
||||
51000 0.45869721 -2.1176213 0.059785615 -1.5995207 0.62467419
|
||||
52000 0.45 -2.1136347 0.062713868 -1.6012959 0.71773796
|
||||
53000 0.44480469 -2.1070829 0.061995737 -1.6006531 0.72790523
|
||||
54000 0.45834924 -2.1352139 0.056517736 -1.6207289 0.64257865
|
||||
55000 0.44776128 -2.1167768 0.051321782 -1.6180669 0.52184371
|
||||
56000 0.46087785 -2.1186123 0.059414538 -1.598704 0.72628855
|
||||
57000 0.44514743 -2.1107461 0.062138072 -1.6038315 0.68847034
|
||||
58000 0.44897344 -2.1218568 0.056966905 -1.6162906 0.66787759
|
||||
59000 0.43532599 -2.1262526 0.062848971 -1.6284404 0.61398862
|
||||
60000 0.44623012 -2.105934 0.05919675 -1.600879 0.73556885
|
||||
Loop time of 4.35988 on 4 procs for 60000 steps with 1200 atoms
|
||||
|
||||
Pair time (%) = 2.35274 (53.9636)
|
||||
Bond time (%) = 0.0979231 (2.24601)
|
||||
Neigh time (%) = 0.561045 (12.8684)
|
||||
Comm time (%) = 0.839245 (19.2493)
|
||||
Outpt time (%) = 0.00117868 (0.0270348)
|
||||
Other time (%) = 0.507739 (11.6457)
|
||||
|
||||
Nlocal: 300 ave 320 max 287 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Nghost: 218.75 ave 232 max 205 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 2461 ave 2617 max 2321 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 9844
|
||||
Ave neighs/atom = 8.20333
|
||||
Ave special neighs/atom = 0.5
|
||||
Neighbor list builds = 4879
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,118 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 2d Lennard-Jones melt and subsequent energy minimization
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box block 0 20 0 20 -0.1 0.1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 800 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 5.0 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_modify shift yes
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 100 dump.min
|
||||
|
||||
#dump 2 all image 50 image.*.jpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 50 movie.mpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
Memory usage per processor = 2.06282 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 5 -2.461717 0 2.532033 5.0190509
|
||||
100 3.2788864 -0.74311698 0 2.5316708 15.912832
|
||||
200 3.3041082 -0.77000277 0 2.5299752 15.602653
|
||||
300 3.3840228 -0.84859211 0 2.5312006 15.188203
|
||||
400 3.3916063 -0.85694601 0 2.5304208 15.383853
|
||||
500 3.3136052 -0.77935263 0 2.5301106 15.833296
|
||||
600 3.3888915 -0.85213741 0 2.532518 15.162759
|
||||
700 3.2123662 -0.67642106 0 2.5319297 16.310578
|
||||
800 3.3016847 -0.76574936 0 2.5318082 15.639067
|
||||
900 3.463125 -0.92707601 0 2.5317201 14.770608
|
||||
1000 3.3134849 -0.7783474 0 2.5309957 15.658702
|
||||
Loop time of 0.199423 on 1 procs for 1000 steps with 800 atoms
|
||||
|
||||
Pair time (%) = 0.127195 (63.7817)
|
||||
Neigh time (%) = 0.0478823 (24.0104)
|
||||
Comm time (%) = 0.00542498 (2.72034)
|
||||
Outpt time (%) = 0.000106335 (0.0533212)
|
||||
Other time (%) = 0.0188138 (9.43415)
|
||||
|
||||
Nlocal: 800 ave 800 max 800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 316 ave 316 max 316 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7747 ave 7747 max 7747 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7747
|
||||
Ave neighs/atom = 9.68375
|
||||
Neighbor list builds = 203
|
||||
Dangerous builds = 0
|
||||
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
#dump_modify 1 every 25
|
||||
|
||||
thermo 50
|
||||
minimize 1.0e-6 0.001 1000 10000
|
||||
Memory usage per processor = 2.74946 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
1000 3.3134849 -0.7783474 0 2.5309957 15.658702
|
||||
1050 3.3134849 -2.808351 0 0.50099208 1.7334413
|
||||
1100 3.3134849 -2.8586611 0 0.45068195 1.6058414
|
||||
1150 3.3134849 -2.8712625 0 0.43808058 1.6049732
|
||||
1200 3.3134849 -2.8785429 0 0.43080018 1.5883814
|
||||
1250 3.3134849 -2.8832131 0 0.42612994 1.6155122
|
||||
1300 3.3134849 -2.8882533 0 0.42108976 1.6323994
|
||||
1350 3.3134849 -2.8953262 0 0.41401689 1.5991374
|
||||
1365 3.3134849 -2.895477 0 0.41386606 1.5988878
|
||||
Loop time of 0.278112 on 1 procs for 365 steps with 800 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-0.778347402608 -2.89547454669 -2.89547702741
|
||||
Force two-norm initial, final = 1921.37 0.684479
|
||||
Force max component initial, final = 298.456 0.229696
|
||||
Final line search alpha, max atom move = 0.00501944 0.00115295
|
||||
Iterations, force evaluations = 365 1305
|
||||
|
||||
Pair time (%) = 0.231226 (83.1415)
|
||||
Neigh time (%) = 0.0193577 (6.96039)
|
||||
Comm time (%) = 0.00456548 (1.6416)
|
||||
Outpt time (%) = 7.00951e-05 (0.0252039)
|
||||
Other time (%) = 0.0228922 (8.2313)
|
||||
|
||||
Nlocal: 800 ave 800 max 800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 319 ave 319 max 319 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7040 ave 7040 max 7040 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7040
|
||||
Ave neighs/atom = 8.8
|
||||
Neighbor list builds = 83
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,118 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 2d Lennard-Jones melt and subsequent energy minimization
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box block 0 20 0 20 -0.1 0.1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 800 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 5.0 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_modify shift yes
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 100 dump.min
|
||||
|
||||
#dump 2 all image 50 image.*.jpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 50 movie.mpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
Memory usage per processor = 2.06115 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 5 -2.461717 0 2.532033 5.0190509
|
||||
100 3.2788864 -0.74311698 0 2.5316708 15.912832
|
||||
200 3.3041082 -0.77000277 0 2.5299752 15.602653
|
||||
300 3.3840228 -0.84859211 0 2.5312006 15.188203
|
||||
400 3.3916063 -0.85694601 0 2.5304208 15.383853
|
||||
500 3.3136052 -0.77935264 0 2.5301106 15.833296
|
||||
600 3.3888915 -0.85213742 0 2.532518 15.162759
|
||||
700 3.2123632 -0.67641807 0 2.5319297 16.310592
|
||||
800 3.3016497 -0.76571656 0 2.531806 15.639198
|
||||
900 3.4621454 -0.9260857 0 2.531732 14.772965
|
||||
1000 3.2803075 -0.74465936 0 2.5315477 15.835597
|
||||
Loop time of 0.066597 on 4 procs for 1000 steps with 800 atoms
|
||||
|
||||
Pair time (%) = 0.0324514 (48.728)
|
||||
Neigh time (%) = 0.012701 (19.0714)
|
||||
Comm time (%) = 0.0137331 (20.6212)
|
||||
Outpt time (%) = 0.000190914 (0.28667)
|
||||
Other time (%) = 0.00752062 (11.2927)
|
||||
|
||||
Nlocal: 200 ave 202 max 198 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Nghost: 170.25 ave 176 max 167 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Neighs: 1936.75 ave 1963 max 1896 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
|
||||
Total # of neighbors = 7747
|
||||
Ave neighs/atom = 9.68375
|
||||
Neighbor list builds = 203
|
||||
Dangerous builds = 0
|
||||
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
#dump_modify 1 every 25
|
||||
|
||||
thermo 50
|
||||
minimize 1.0e-6 0.001 1000 10000
|
||||
Memory usage per processor = 2.7478 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
1000 3.2803075 -0.74465936 0 2.5315477 15.835597
|
||||
1050 3.2803075 -2.8198371 0 0.45636995 1.6553949
|
||||
1100 3.2803075 -2.8554989 0 0.42070813 1.6571551
|
||||
1150 3.2803075 -2.8646695 0 0.41153758 1.7045388
|
||||
1200 3.2803075 -2.8688213 0 0.40738582 1.6922085
|
||||
1250 3.2803075 -2.8764988 0 0.39970826 1.6948532
|
||||
1300 3.2803075 -2.8776606 0 0.39854651 1.6821387
|
||||
1350 3.2803075 -2.8789379 0 0.39726915 1.6715024
|
||||
1365 3.2803075 -2.879076 0 0.3971311 1.66923
|
||||
Loop time of 0.100178 on 4 procs for 365 steps with 800 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-0.744659361981 -2.87907436106 -2.8790759758
|
||||
Force two-norm initial, final = 2006.88 0.477401
|
||||
Force max component initial, final = 395.193 0.0879763
|
||||
Final line search alpha, max atom move = 0.00334856 0.000294593
|
||||
Iterations, force evaluations = 365 1437
|
||||
|
||||
Pair time (%) = 0.0639488 (63.8349)
|
||||
Neigh time (%) = 0.00472444 (4.71603)
|
||||
Comm time (%) = 0.015418 (15.3905)
|
||||
Outpt time (%) = 0.000124454 (0.124233)
|
||||
Other time (%) = 0.0159628 (15.9343)
|
||||
|
||||
Nlocal: 200 ave 204 max 194 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Nghost: 171.75 ave 173 max 170 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
Neighs: 1762.75 ave 1797 max 1711 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
|
||||
Total # of neighbors = 7051
|
||||
Ave neighs/atom = 8.81375
|
||||
Neighbor list builds = 78
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,356 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 2d Lennard-Jones melt and subsequent energy minimization
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box block 0 20 0 20 -0.1 0.1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 800 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 5.0 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_modify shift yes
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 500 dump.min
|
||||
|
||||
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
Memory usage per processor = 2.06282 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 5 -2.461717 0 2.532033 5.0190509
|
||||
100 3.2788864 -0.74311698 0 2.5316708 15.912832
|
||||
200 3.3041082 -0.77000277 0 2.5299752 15.602653
|
||||
300 3.3840228 -0.84859211 0 2.5312006 15.188203
|
||||
400 3.3916063 -0.85694601 0 2.5304208 15.383853
|
||||
500 3.3136052 -0.77935263 0 2.5301106 15.833296
|
||||
600 3.3888915 -0.85213741 0 2.532518 15.162759
|
||||
700 3.2123662 -0.67642106 0 2.5319297 16.310578
|
||||
800 3.3016847 -0.76574936 0 2.5318082 15.639067
|
||||
900 3.463125 -0.92707601 0 2.5317201 14.770608
|
||||
1000 3.3134849 -0.7783474 0 2.5309957 15.658702
|
||||
Loop time of 0.200018 on 1 procs for 1000 steps with 800 atoms
|
||||
|
||||
Pair time (%) = 0.127843 (63.9158)
|
||||
Neigh time (%) = 0.0480146 (24.0052)
|
||||
Comm time (%) = 0.00542927 (2.71439)
|
||||
Outpt time (%) = 0.000105858 (0.0529242)
|
||||
Other time (%) = 0.018625 (9.31168)
|
||||
|
||||
Nlocal: 800 ave 800 max 800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 316 ave 316 max 316 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7747 ave 7747 max 7747 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7747
|
||||
Ave neighs/atom = 9.68375
|
||||
Neighbor list builds = 203
|
||||
Dangerous builds = 0
|
||||
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
velocity all create 0.0 1
|
||||
thermo 50
|
||||
minimize 1.0e-6 0.001 1000 10000
|
||||
Memory usage per processor = 2.74946 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
1000 0 -0.7783474 0 -0.7783474 12.864955
|
||||
1050 0 -2.808351 0 -2.808351 -1.0603061
|
||||
1100 0 -2.8586611 0 -2.8586611 -1.1879061
|
||||
1150 0 -2.8712625 0 -2.8712625 -1.1887742
|
||||
1200 0 -2.8785429 0 -2.8785429 -1.205366
|
||||
1250 0 -2.8832131 0 -2.8832131 -1.1782352
|
||||
1300 0 -2.8882533 0 -2.8882533 -1.1613481
|
||||
1350 0 -2.8953262 0 -2.8953262 -1.19461
|
||||
1365 0 -2.895477 0 -2.895477 -1.1948596
|
||||
Loop time of 0.278073 on 1 procs for 365 steps with 800 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-0.778347402608 -2.89547454669 -2.89547702741
|
||||
Force two-norm initial, final = 1921.37 0.684479
|
||||
Force max component initial, final = 298.456 0.229696
|
||||
Final line search alpha, max atom move = 0.00501944 0.00115295
|
||||
Iterations, force evaluations = 365 1305
|
||||
|
||||
Pair time (%) = 0.231544 (83.2672)
|
||||
Neigh time (%) = 0.0193498 (6.95854)
|
||||
Comm time (%) = 0.00450826 (1.62125)
|
||||
Outpt time (%) = 6.7234e-05 (0.0241786)
|
||||
Other time (%) = 0.022604 (8.12879)
|
||||
|
||||
Nlocal: 800 ave 800 max 800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 319 ave 319 max 319 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7040 ave 7040 max 7040 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7040
|
||||
Ave neighs/atom = 8.8
|
||||
Neighbor list builds = 83
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-4 nreset 100
|
||||
|
||||
thermo_style custom step temp pe pxx pyy pxy
|
||||
|
||||
min_modify line quadratic
|
||||
minimize 0.0 1.0e-6 10000 100000
|
||||
Memory usage per processor = 2.74946 Mbytes
|
||||
Step Temp PotEng Pxx Pyy Pxy
|
||||
1365 0 -2.895477 -1.2253391 -1.16438 0.0029844696
|
||||
1400 0 -2.9030976 -1.037803 -0.93005749 0.0031404612
|
||||
1450 0 -2.9111551 -0.7499331 -0.56417894 0.0034000612
|
||||
1500 0 -2.9156519 -0.43747438 -0.15725876 0.0035241132
|
||||
1550 0 -2.9163188 -0.10113405 0.29275665 0.0032578192
|
||||
1600 0 -2.9129142 0.25786755 0.78857369 0.0031418378
|
||||
1650 0 -2.9052907 0.63122126 1.3305275 0.0027036138
|
||||
1700 0 -2.8938515 0.97940259 1.9066628 0.0017474185
|
||||
1750 0 -2.8934608 0.9929599 1.9909561 0.0022591527
|
||||
1800 0 -2.8938899 1.0037689 2.0049399 0.0031549929
|
||||
1850 0 -2.8950206 0.99253195 1.9899581 0.0044014083
|
||||
1900 0 -2.8954835 0.99574288 1.9942509 0.0052643914
|
||||
1950 0 -2.8957658 1.0003472 2.0004684 0.0058490005
|
||||
2000 0 -2.8970438 0.97690958 1.9714991 0.0067217987
|
||||
2050 0 -2.897073 0.99072137 1.9920898 0.0072873033
|
||||
2100 0 -2.8972746 0.99651146 1.995402 0.0075817227
|
||||
2150 0 -2.8975964 0.99381046 1.991681 0.007627454
|
||||
2200 0 -2.8979803 0.99274725 1.9904104 0.007749339
|
||||
2250 0 -2.8982086 0.99172995 1.9905936 0.0077177074
|
||||
2300 0 -2.8983994 0.99377061 1.9899673 0.0076946648
|
||||
2350 0 -2.8985769 0.99172845 1.9896457 0.0074117889
|
||||
2400 0 -2.8986693 0.99578192 1.992246 0.0071806046
|
||||
2450 0 -2.8988819 0.99128252 1.9903378 0.0069177704
|
||||
2500 0 -2.8989812 0.99522115 1.991489 0.0068121239
|
||||
2550 0 -2.8991564 0.99146083 1.990657 0.0065352609
|
||||
2600 0 -2.8992555 0.99538317 1.9914926 0.0062558371
|
||||
2650 0 -2.8994204 0.99157917 1.9907942 0.0059727799
|
||||
2700 0 -2.8995111 0.9953798 1.9917332 0.0057516669
|
||||
2750 0 -2.899661 0.9919244 1.9913158 0.005332134
|
||||
2800 0 -2.8997549 0.99504761 1.9916688 0.0050046256
|
||||
2850 0 -2.8999018 0.99193526 1.9912547 0.004492394
|
||||
2900 0 -2.8999871 0.99565899 1.9922087 0.0040528402
|
||||
2950 0 -2.9001422 0.99213366 1.9916425 0.0035862563
|
||||
3000 0 -2.9002325 0.99582487 1.9924604 0.0032829497
|
||||
3050 0 -2.9003895 0.99227644 1.9918388 0.0029100217
|
||||
3100 0 -2.9004934 0.9954142 1.9922624 0.0026581626
|
||||
3150 0 -2.9006459 0.99232395 1.9918443 0.0023680976
|
||||
3200 0 -2.9007414 0.99623688 1.99297 0.0020662395
|
||||
3250 0 -2.9009264 0.99256898 1.991983 0.0018040717
|
||||
3300 0 -2.9009986 0.99800399 1.9945846 0.0015930444
|
||||
3350 0 -2.9011372 0.99321268 1.9969898 0.001407703
|
||||
3400 0 -2.9013641 0.99622318 1.9930656 0.0014563979
|
||||
3450 0 -2.9015832 0.99282311 1.9924118 0.0014454286
|
||||
3500 0 -2.9017596 0.99595378 1.992875 0.0016105573
|
||||
3550 0 -2.9020182 0.99269026 1.9918179 0.0017633837
|
||||
3600 0 -2.9022093 0.99607639 1.9930845 0.0020441612
|
||||
3650 0 -2.9024948 0.99278561 1.9922635 0.0022606286
|
||||
3700 0 -2.9027328 0.99606872 1.9930129 0.0026414228
|
||||
3750 0 -2.9030541 0.99270955 1.9922055 0.0030676238
|
||||
3800 0 -2.9033283 0.99509621 1.9917886 0.0034492628
|
||||
3850 0 -2.9036436 0.99265445 1.9918333 0.0039194462
|
||||
3900 0 -2.9039245 0.99611739 1.9930579 0.0043794142
|
||||
3950 0 -2.9043033 0.99262403 1.9918954 0.0048733419
|
||||
4000 0 -2.9046124 0.99585905 1.9928584 0.0054448584
|
||||
4050 0 -2.9050077 0.99265871 1.9918589 0.0059527585
|
||||
4100 0 -2.9053408 0.99596017 1.992967 0.0066819293
|
||||
4150 0 -2.9057612 0.99271888 1.9920143 0.0074538661
|
||||
4200 0 -2.9061208 0.99585342 1.9928494 0.0083030126
|
||||
4250 0 -2.9065583 0.99276056 1.9921715 0.0091760837
|
||||
4300 0 -2.9069587 0.99569608 1.9928109 0.010563215
|
||||
4350 0 -2.9074386 0.99294112 1.9923317 0.012242263
|
||||
4400 0 -2.9079159 0.99617793 1.9929836 0.014425511
|
||||
4450 0 -2.9084828 0.99335369 1.9912818 0.017137841
|
||||
4500 0 -2.9088005 0.99954722 1.9956616 0.019873686
|
||||
4550 0 -2.9092238 0.99844962 1.9944461 0.022380697
|
||||
4600 0 -2.9096299 0.99300644 1.9925264 0.024687168
|
||||
4650 0 -2.9100061 0.99370577 1.9934207 0.027508267
|
||||
4700 0 -2.9104263 0.99565636 1.9926298 0.030664353
|
||||
4750 0 -2.9109614 0.99284169 1.9919846 0.034334378
|
||||
4800 0 -2.9114155 0.9960171 1.9931707 0.038040635
|
||||
4850 0 -2.9119649 0.99287594 1.9919796 0.041618415
|
||||
4900 0 -2.9125125 0.99631202 1.9935981 0.046177605
|
||||
4950 0 -2.9134822 0.99545012 1.9963436 0.055551769
|
||||
5000 0 -2.9138087 1.0016464 1.9978697 0.059129043
|
||||
5050 0 -2.9138895 1.0005328 2.0066685 0.060919794
|
||||
5100 0 -2.9144557 0.99415884 1.9925195 0.062934069
|
||||
5150 0 -2.9143897 0.99900082 2.0070401 0.06446803
|
||||
5200 0 -2.9150165 0.99737915 1.9943189 0.066857536
|
||||
5250 0 -2.9154332 0.9999712 2.0021875 0.069632138
|
||||
5300 0 -2.9157558 0.99795158 1.9974044 0.070422281
|
||||
5350 0 -2.9158439 1.0016699 2.0035502 0.071049397
|
||||
5400 0 -2.9164666 0.99255654 1.9908929 0.071776886
|
||||
5450 0 -2.9168846 1.0018915 1.9938812 0.072677356
|
||||
5500 0 -2.9173241 0.99707078 1.9957969 0.072868177
|
||||
5550 0 -2.9179842 0.99391224 1.9978813 0.073182143
|
||||
5600 0 -2.9184699 0.99532518 1.9933732 0.073208315
|
||||
5650 0 -2.9188477 1.0063118 2.0052442 0.073258803
|
||||
5700 0 -2.919468 1.0026929 2.0041254 0.073010391
|
||||
5750 0 -2.9202844 1.0035994 2.0008607 0.072352512
|
||||
5800 0 -2.9204309 1.0072764 2.008335 0.072056645
|
||||
5850 0 -2.9213742 0.99720824 1.9925634 0.071173036
|
||||
5900 0 -2.9216129 1.0000335 2.001122 0.070609448
|
||||
5950 0 -2.9223916 1.0003501 2.0032975 0.069559273
|
||||
6000 0 -2.9227892 1.0043807 2.0050332 0.069077943
|
||||
6050 0 -2.9233982 1.004802 2.0050324 0.068450588
|
||||
6100 0 -2.9237721 1.0066363 2.0070477 0.06823504
|
||||
6150 0 -2.9245074 1.0063392 2.0068761 0.068112243
|
||||
6200 0 -2.9258589 0.99455185 1.9953413 0.06865518
|
||||
6250 0 -2.9261201 1.0042987 2.0031819 0.069636648
|
||||
6300 0 -2.9270045 0.99564956 1.9901358 0.071020033
|
||||
6350 0 -2.9270282 1.007771 2.0049483 0.072360652
|
||||
6400 0 -2.9279953 0.99228232 1.9927028 0.074781454
|
||||
6450 0 -2.9280616 1.0017566 2.0022453 0.076142216
|
||||
6500 0 -2.9288249 0.99408967 1.9888019 0.078305191
|
||||
6550 0 -2.9286973 1.0065411 2.0049519 0.079618619
|
||||
6600 0 -2.9291183 0.99372953 1.9985414 0.080448942
|
||||
6650 0 -2.9292204 1.0023178 2.0050015 0.081907164
|
||||
6700 0 -2.9301292 0.99992006 2.0016415 0.085917352
|
||||
6750 0 -2.9302372 1.00613 2.004525 0.086946884
|
||||
6800 0 -2.9305702 1.0074557 1.9965127 0.087976601
|
||||
6850 0 -2.9313326 1.0050252 2.0080944 0.092584504
|
||||
6900 0 -2.9317498 1.0087999 1.9958456 0.094058095
|
||||
6950 0 -2.9318279 0.99688134 2.002508 0.094400121
|
||||
7000 0 -2.9318978 1.0034321 2.0052797 0.095451664
|
||||
7050 0 -2.9322652 0.99758568 2.0037109 0.097238969
|
||||
7100 0 -2.9327121 0.99815697 1.9914701 0.098802948
|
||||
7150 0 -2.9327437 1.0038622 2.0011895 0.10050304
|
||||
7200 0 -2.9329063 1.004612 2.0032044 0.10185804
|
||||
7250 0 -2.9335997 0.98168701 1.9864884 0.10300105
|
||||
7300 0 -2.9336515 0.99279141 1.992742 0.10470943
|
||||
7350 0 -2.9337138 1.003092 2.000106 0.10653676
|
||||
7400 0 -2.9340414 1.0023845 1.9946755 0.10808147
|
||||
7450 0 -2.9342536 0.99920061 1.9983417 0.10966697
|
||||
7500 0 -2.9344657 0.99656006 2.002306 0.11134193
|
||||
7550 0 -2.9346812 1.0009774 2.0059445 0.11345836
|
||||
7600 0 -2.9352073 0.99664019 2.0028997 0.116237
|
||||
7650 0 -2.9355092 1.0067299 2.0052137 0.11889963
|
||||
7700 0 -2.9359369 1.000096 2.0038144 0.12089102
|
||||
7750 0 -2.936237 1.0071591 2.0077241 0.12334687
|
||||
7800 0 -2.9367687 1.0047286 2.0037322 0.12562793
|
||||
7850 0 -2.9372513 0.99839299 2.0008738 0.1271966
|
||||
7900 0 -2.93781 1.0013489 1.9924309 0.12900725
|
||||
7950 0 -2.9382206 0.99271028 1.9910513 0.12995672
|
||||
8000 0 -2.9385111 0.99261038 1.9917151 0.13094744
|
||||
8050 0 -2.9388605 0.99256847 1.9933576 0.13194246
|
||||
8100 0 -2.9391752 0.99421545 1.9941225 0.13291935
|
||||
8150 0 -2.9394092 0.9997332 1.9965286 0.13397127
|
||||
8200 0 -2.939821 0.99876146 1.9939496 0.13501447
|
||||
8250 0 -2.9403015 0.99313692 1.9903144 0.13588404
|
||||
8300 0 -2.9406524 0.99504174 1.9916891 0.13709102
|
||||
8350 0 -2.9411077 0.99272049 1.9917049 0.13823709
|
||||
8400 0 -2.9414976 0.99650126 1.9935111 0.13948558
|
||||
8450 0 -2.9419844 0.9928859 1.9921827 0.14058516
|
||||
8500 0 -2.9424055 0.9957698 1.9928898 0.14199174
|
||||
8550 0 -2.9428963 0.99297812 1.9922564 0.14329168
|
||||
8600 0 -2.9431968 0.99693087 1.9947462 0.14458722
|
||||
8650 0 -2.9435631 0.99940154 1.9944064 0.14582129
|
||||
8700 0 -2.9441466 0.99396641 1.9935763 0.14733962
|
||||
8750 0 -2.9449093 0.99592155 1.9932061 0.15025209
|
||||
8800 0 -2.9461707 0.99237436 1.9925136 0.15595847
|
||||
8850 0 -2.9462853 1.000815 2.007233 0.15828028
|
||||
8900 0 -2.9469511 1.0000829 1.9986375 0.16055827
|
||||
8950 0 -2.9473161 1.0004185 1.9954916 0.16178098
|
||||
9000 0 -2.9476848 1.0002902 1.9955333 0.16283909
|
||||
9050 0 -2.9476782 1.0024581 2.0035957 0.16324604
|
||||
9100 0 -2.9477989 1.0030916 2.0059473 0.16365445
|
||||
9150 0 -2.9482536 0.99281175 1.9946546 0.16370039
|
||||
9200 0 -2.9481416 1.00865 2.0073808 0.16435272
|
||||
9250 0 -2.9486901 0.99494204 1.9953024 0.16410446
|
||||
9300 0 -2.9486493 0.99953893 2.0056513 0.16419403
|
||||
9350 0 -2.949079 1.003429 1.997895 0.16444925
|
||||
9400 0 -2.9491509 1.0064853 2.0082985 0.16432267
|
||||
9450 0 -2.9494699 1.0048863 2.001313 0.16433478
|
||||
9500 0 -2.9496103 1.0059455 2.0060809 0.16420418
|
||||
9550 0 -2.9499432 1.0037986 1.9989587 0.16406824
|
||||
9600 0 -2.9501927 1.0010447 2.0005638 0.16375939
|
||||
9650 0 -2.9511285 0.98322543 1.9801177 0.16290463
|
||||
9700 0 -2.9506509 1.0102419 2.0082163 0.16328052
|
||||
9750 0 -2.9511779 0.99511265 1.9950262 0.16251764
|
||||
9800 0 -2.9512164 0.99608392 2.0052439 0.16186521
|
||||
9850 0 -2.9517206 0.99656506 1.9966162 0.16144425
|
||||
9900 0 -2.9519451 1.0066635 2.0043954 0.16101155
|
||||
9950 0 -2.9520952 1.0051178 2.0087197 0.16058558
|
||||
10000 0 -2.9531155 1.0041379 2.0031534 0.15982682
|
||||
10050 0 -2.9537418 0.99448829 1.9904993 0.15928106
|
||||
10100 0 -2.9540875 1.0000256 1.9948928 0.1590648
|
||||
10150 0 -2.9545724 0.99595476 1.9920689 0.15859113
|
||||
10200 0 -2.9550866 0.9945366 1.9940695 0.15788443
|
||||
10250 0 -2.955721 0.99319075 1.9905041 0.15710363
|
||||
10300 0 -2.9560458 0.99598109 1.9939645 0.15650198
|
||||
10350 0 -2.9565093 0.99480453 1.9979782 0.15542386
|
||||
10400 0 -2.9570486 0.99396171 1.9942613 0.15473357
|
||||
10450 0 -2.9576457 0.99301571 1.9922208 0.1541236
|
||||
10500 0 -2.9583596 0.9956042 1.992646 0.15365553
|
||||
10550 0 -2.9591414 0.99318206 1.9923162 0.15326877
|
||||
10600 0 -2.959942 0.99596727 1.9933176 0.15282597
|
||||
10650 0 -2.9609186 0.99353471 1.9930306 0.1521666
|
||||
10700 0 -2.9620307 0.99594782 1.9932886 0.1508232
|
||||
10750 0 -2.9637166 0.99482397 1.9947588 0.14649906
|
||||
10800 0 -2.9662462 0.99407822 1.9953083 0.13351206
|
||||
10850 0 -2.9665593 1.0027673 1.9995492 0.13140588
|
||||
10900 0 -2.9667709 1.0023406 2.0013835 0.12981724
|
||||
10950 0 -2.9670159 1.0033354 2.0040861 0.12797651
|
||||
11000 0 -2.9672441 1.0037572 2.004755 0.12647524
|
||||
11050 0 -2.967593 0.99874092 1.9995822 0.12495147
|
||||
11100 0 -2.9681165 0.99125559 1.9863869 0.1236617
|
||||
11150 0 -2.9679478 1.0024409 2.0014347 0.12298067
|
||||
11200 0 -2.968096 1.0083556 2.0040025 0.12211851
|
||||
11250 0 -2.96854 0.99060368 1.9933029 0.12097655
|
||||
11300 0 -2.968643 0.99899132 2.0034915 0.11986456
|
||||
11350 0 -2.9687697 1.0018133 2.0075949 0.11899469
|
||||
11365 0 -2.9688638 1.0116402 2.005578 0.11895715
|
||||
Loop time of 2.59925 on 1 procs for 10000 steps with 800 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
-2.89547702741 -2.96928950062 -2.96886378746
|
||||
Force two-norm initial, final = 3665.97 11.745
|
||||
Force max component initial, final = 2998.7 10.1406
|
||||
Final line search alpha, max atom move = 6.36291e-05 0.00064524
|
||||
Iterations, force evaluations = 10000 10063
|
||||
|
||||
Pair time (%) = 1.93873 (74.5878)
|
||||
Neigh time (%) = 0.00854492 (0.328745)
|
||||
Comm time (%) = 0.0286736 (1.10315)
|
||||
Outpt time (%) = 0.00297666 (0.11452)
|
||||
Other time (%) = 0.620332 (23.8658)
|
||||
|
||||
Nlocal: 800 ave 800 max 800 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 330 ave 330 max 330 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 7336 ave 7336 max 7336 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 7336
|
||||
Ave neighs/atom = 9.17
|
||||
Neighbor list builds = 36
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,356 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 2d Lennard-Jones melt and subsequent energy minimization
|
||||
|
||||
units lj
|
||||
dimension 2
|
||||
atom_style atomic
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box block 0 20 0 20 -0.1 0.1
|
||||
create_box 1 box
|
||||
Created orthogonal box = (0 0 -0.153919) to (30.7838 30.7838 0.153919)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 800 atoms
|
||||
mass 1 1.0
|
||||
|
||||
velocity all create 5.0 87287 loop geom
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff 1 1 1.0 1.0 2.5
|
||||
pair_modify shift yes
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all enforce2d
|
||||
|
||||
#dump 1 all atom 500 dump.min
|
||||
|
||||
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
thermo 100
|
||||
|
||||
run 1000
|
||||
Memory usage per processor = 2.06115 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 5 -2.461717 0 2.532033 5.0190509
|
||||
100 3.2788864 -0.74311698 0 2.5316708 15.912832
|
||||
200 3.3041082 -0.77000277 0 2.5299752 15.602653
|
||||
300 3.3840228 -0.84859211 0 2.5312006 15.188203
|
||||
400 3.3916063 -0.85694601 0 2.5304208 15.383853
|
||||
500 3.3136052 -0.77935264 0 2.5301106 15.833296
|
||||
600 3.3888915 -0.85213742 0 2.532518 15.162759
|
||||
700 3.2123632 -0.67641807 0 2.5319297 16.310592
|
||||
800 3.3016497 -0.76571656 0 2.531806 15.639198
|
||||
900 3.4621454 -0.9260857 0 2.531732 14.772965
|
||||
1000 3.2803075 -0.74465936 0 2.5315477 15.835597
|
||||
Loop time of 0.0672228 on 4 procs for 1000 steps with 800 atoms
|
||||
|
||||
Pair time (%) = 0.0325756 (48.4591)
|
||||
Neigh time (%) = 0.012749 (18.9652)
|
||||
Comm time (%) = 0.0136126 (20.25)
|
||||
Outpt time (%) = 0.000190377 (0.283203)
|
||||
Other time (%) = 0.00809526 (12.0424)
|
||||
|
||||
Nlocal: 200 ave 202 max 198 min
|
||||
Histogram: 1 0 1 0 0 0 0 1 0 1
|
||||
Nghost: 170.25 ave 176 max 167 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Neighs: 1936.75 ave 1963 max 1896 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
|
||||
Total # of neighbors = 7747
|
||||
Ave neighs/atom = 9.68375
|
||||
Neighbor list builds = 203
|
||||
Dangerous builds = 0
|
||||
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
|
||||
velocity all create 0.0 1
|
||||
thermo 50
|
||||
minimize 1.0e-6 0.001 1000 10000
|
||||
Memory usage per processor = 2.7478 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
1000 0 -0.74465936 0 -0.74465936 13.069823
|
||||
1050 0 -2.8198371 0 -2.8198371 -1.1103791
|
||||
1100 0 -2.8554989 0 -2.8554989 -1.1086189
|
||||
1150 0 -2.8646695 0 -2.8646695 -1.0612352
|
||||
1200 0 -2.8688213 0 -2.8688213 -1.0735655
|
||||
1250 0 -2.8764988 0 -2.8764988 -1.0709208
|
||||
1300 0 -2.8776606 0 -2.8776606 -1.0836353
|
||||
1350 0 -2.8789379 0 -2.8789379 -1.0942716
|
||||
1365 0 -2.879076 0 -2.879076 -1.096544
|
||||
Loop time of 0.103336 on 4 procs for 365 steps with 800 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = energy tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-0.744659361981 -2.87907436106 -2.8790759758
|
||||
Force two-norm initial, final = 2006.88 0.477401
|
||||
Force max component initial, final = 395.193 0.0879763
|
||||
Final line search alpha, max atom move = 0.00334856 0.000294593
|
||||
Iterations, force evaluations = 365 1437
|
||||
|
||||
Pair time (%) = 0.0650657 (62.9653)
|
||||
Neigh time (%) = 0.00482118 (4.66555)
|
||||
Comm time (%) = 0.0168168 (16.2739)
|
||||
Outpt time (%) = 0.000125468 (0.121417)
|
||||
Other time (%) = 0.0165067 (15.9739)
|
||||
|
||||
Nlocal: 200 ave 204 max 194 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Nghost: 171.75 ave 173 max 170 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
Neighs: 1762.75 ave 1797 max 1711 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
|
||||
Total # of neighbors = 7051
|
||||
Ave neighs/atom = 8.81375
|
||||
Neighbor list builds = 78
|
||||
Dangerous builds = 0
|
||||
|
||||
fix 3 all box/relax x 1.0 y 2.0 vmax 1.0e-4 nreset 100
|
||||
|
||||
thermo_style custom step temp pe pxx pyy pxy
|
||||
|
||||
min_modify line quadratic
|
||||
minimize 0.0 1.0e-6 10000 100000
|
||||
Memory usage per processor = 2.7478 Mbytes
|
||||
Step Temp PotEng Pxx Pyy Pxy
|
||||
1365 0 -2.879076 -1.0493949 -1.1436932 0.037565201
|
||||
1400 0 -2.8859021 -0.86433583 -0.91383427 0.038857701
|
||||
1450 0 -2.8929425 -0.58254768 -0.55566103 0.040538566
|
||||
1500 0 -2.8966088 -0.28118754 -0.15988163 0.042020855
|
||||
1550 0 -2.8967125 0.036820191 0.27480302 0.04324269
|
||||
1600 0 -2.8931249 0.36718787 0.74943653 0.044424741
|
||||
1650 0 -2.8858731 0.69688815 1.2623711 0.044835267
|
||||
1700 0 -2.8755822 0.98073679 1.7977638 0.043907813
|
||||
1750 0 -2.8722618 0.99796906 1.9978937 0.040932086
|
||||
1800 0 -2.8731203 0.9972851 1.9960832 0.039723601
|
||||
1850 0 -2.8733692 1.0063823 2.0084146 0.038402341
|
||||
1900 0 -2.8747209 0.98521911 1.9798435 0.03629572
|
||||
1950 0 -2.874625 1.0055823 2.0075042 0.034193545
|
||||
2000 0 -2.8752902 0.99350208 1.9911933 0.03326557
|
||||
2050 0 -2.8752769 1.0018946 2.0024682 0.03231859
|
||||
2100 0 -2.8758319 0.99169935 1.9887983 0.031437471
|
||||
2150 0 -2.8761892 0.99301192 1.9906401 0.029831022
|
||||
2200 0 -2.8765018 0.99825416 1.9982587 0.027754052
|
||||
2250 0 -2.8768461 0.99326761 1.9910275 0.027115046
|
||||
2300 0 -2.8767423 1.0035487 2.0046857 0.026126393
|
||||
2350 0 -2.8770655 0.99795811 1.9973107 0.025614851
|
||||
2400 0 -2.877445 0.99163396 1.9870033 0.025156704
|
||||
2450 0 -2.8774865 0.99148327 1.9905808 0.024719242
|
||||
2500 0 -2.8775546 0.9950178 1.9915017 0.024486868
|
||||
2550 0 -2.877691 0.9916018 1.9905624 0.02421693
|
||||
2600 0 -2.8777627 0.99470414 1.9910618 0.023930399
|
||||
2650 0 -2.8778782 0.99170595 1.9907118 0.023475253
|
||||
2700 0 -2.877945 0.99480447 1.9913566 0.023271004
|
||||
2750 0 -2.8780803 0.99164504 1.9902596 0.023000125
|
||||
2800 0 -2.8781378 0.99501379 1.9915144 0.022773904
|
||||
2850 0 -2.8782474 0.99219164 1.9915607 0.022481218
|
||||
2900 0 -2.8783151 0.99550644 1.9921431 0.022359954
|
||||
2950 0 -2.8784484 0.99224048 1.9913612 0.022193155
|
||||
3000 0 -2.8785175 0.99532849 1.9920577 0.021941569
|
||||
3050 0 -2.8786568 0.99222235 1.9910476 0.021737518
|
||||
3100 0 -2.8787309 0.99525548 1.9920127 0.021688272
|
||||
3150 0 -2.8788689 0.99228052 1.9913905 0.021446146
|
||||
3200 0 -2.8789303 0.99616583 1.992901 0.021394358
|
||||
3250 0 -2.8790946 0.99232091 1.9915574 0.02118161
|
||||
3300 0 -2.8791847 0.99541221 1.9921056 0.021194771
|
||||
3350 0 -2.8793341 0.9922686 1.9915267 0.021013055
|
||||
3400 0 -2.8794452 0.99516725 1.9917199 0.021036976
|
||||
3450 0 -2.8795969 0.99227386 1.9913259 0.021052828
|
||||
3500 0 -2.8797075 0.99538375 1.9920724 0.02124209
|
||||
3550 0 -2.8798796 0.99230271 1.9914458 0.021226686
|
||||
3600 0 -2.8800015 0.99546439 1.9922124 0.02149345
|
||||
3650 0 -2.880188 0.99227706 1.9913914 0.021617113
|
||||
3700 0 -2.880312 0.99546322 1.9922772 0.021954501
|
||||
3750 0 -2.8805126 0.99224941 1.991302 0.02213367
|
||||
3800 0 -2.8806831 0.99459806 1.9906732 0.022675671
|
||||
3850 0 -2.8808636 0.9921438 1.9909899 0.022992462
|
||||
3900 0 -2.8810051 0.99533223 1.9921709 0.023485422
|
||||
3950 0 -2.881225 0.99232174 1.9914377 0.023944603
|
||||
4000 0 -2.8813892 0.99554805 1.992182 0.024545033
|
||||
4050 0 -2.8816257 0.99218933 1.9910408 0.025105298
|
||||
4100 0 -2.8817867 0.99546861 1.9923568 0.025863634
|
||||
4150 0 -2.8820302 0.99242518 1.9914814 0.026365444
|
||||
4200 0 -2.8822192 0.99526027 1.9919315 0.027062527
|
||||
4250 0 -2.8824692 0.99223247 1.9913085 0.027610787
|
||||
4300 0 -2.8826625 0.99537467 1.9921185 0.028217161
|
||||
4350 0 -2.882922 0.99239179 1.9914342 0.028679998
|
||||
4400 0 -2.8831241 0.99556357 1.9922663 0.029235596
|
||||
4450 0 -2.8833989 0.9921938 1.9912448 0.029596184
|
||||
4500 0 -2.8836067 0.99557381 1.9922188 0.030181
|
||||
4550 0 -2.8838874 0.99214405 1.9912047 0.030371361
|
||||
4600 0 -2.8840891 0.99568228 1.9925689 0.030873328
|
||||
4650 0 -2.8843766 0.99222214 1.991537 0.031107839
|
||||
4700 0 -2.8846039 0.99540851 1.9920535 0.031397701
|
||||
4750 0 -2.8849039 0.99221886 1.9907361 0.031483457
|
||||
4800 0 -2.8851163 0.99551704 1.9923517 0.031579764
|
||||
4850 0 -2.8854144 0.99225442 1.9913169 0.031526446
|
||||
4900 0 -2.8856452 0.99550052 1.9922005 0.031417289
|
||||
4950 0 -2.8859485 0.99210587 1.9910919 0.03118115
|
||||
5000 0 -2.8861801 0.99535546 1.9921671 0.030985542
|
||||
5050 0 -2.8864881 0.99209875 1.9911885 0.030438838
|
||||
5100 0 -2.8867336 0.99520939 1.9919538 0.029911151
|
||||
5150 0 -2.8870413 0.99225176 1.9913023 0.029087623
|
||||
5200 0 -2.8873039 0.99488953 1.9914722 0.0283991
|
||||
5250 0 -2.8876062 0.99228521 1.991158 0.027574033
|
||||
5300 0 -2.8878541 0.99556088 1.9922986 0.026813081
|
||||
5350 0 -2.8881769 0.99220208 1.9912481 0.025847812
|
||||
5400 0 -2.8884304 0.99556208 1.9922152 0.02492658
|
||||
5450 0 -2.8887574 0.99219343 1.9912168 0.023790678
|
||||
5500 0 -2.8890085 0.99566139 1.9925529 0.022691755
|
||||
5550 0 -2.8893435 0.99223125 1.9912108 0.021332027
|
||||
5600 0 -2.8895985 0.99555806 1.9925205 0.019969308
|
||||
5650 0 -2.8899325 0.99238332 1.9915515 0.018334611
|
||||
5700 0 -2.8902024 0.9950743 1.9920344 0.016688965
|
||||
5750 0 -2.8905116 0.99266165 1.9920244 0.014675128
|
||||
5800 0 -2.8907908 0.99538343 1.9922424 0.012898355
|
||||
5850 0 -2.8911238 0.99274659 1.9916141 0.010718854
|
||||
5900 0 -2.891395 0.99586743 1.992946 0.0084079793
|
||||
5950 0 -2.8917377 0.99323184 1.9923269 0.0058847015
|
||||
6000 0 -2.8920318 0.99618703 1.9931886 0.0031743443
|
||||
6050 0 -2.8924173 0.99312644 1.9919607 0.00036370652
|
||||
6100 0 -2.8927403 0.99609392 1.9932028 -0.0023282997
|
||||
6150 0 -2.8931582 0.99334969 1.9924865 -0.0052253296
|
||||
6200 0 -2.8931737 1.0044374 2.0036405 -0.0073374891
|
||||
6250 0 -2.8933601 1.0053494 2.0084308 -0.0095543493
|
||||
6300 0 -2.8937021 1.0040228 2.0072436 -0.011528379
|
||||
6350 0 -2.8941162 1.0040963 2.0067291 -0.014066056
|
||||
6400 0 -2.8946376 1.0056964 2.0065238 -0.016998255
|
||||
6450 0 -2.8952383 1.002655 2.0052962 -0.019179448
|
||||
6500 0 -2.8957747 1.0053824 2.0058467 -0.020794074
|
||||
6550 0 -2.8963468 1.0031095 2.0056915 -0.021771701
|
||||
6600 0 -2.8968938 1.0056478 2.0062435 -0.021988194
|
||||
6650 0 -2.8976105 1.0027738 2.0056577 -0.022097734
|
||||
6700 0 -2.8985813 1.0049044 2.0041091 -0.022978826
|
||||
6750 0 -2.8993763 1.0013212 2.0046643 -0.024685401
|
||||
6800 0 -2.8999352 0.99348555 1.9941849 -0.024745246
|
||||
6850 0 -2.9002761 0.99611648 1.9915352 -0.024953484
|
||||
6900 0 -2.9002655 1.0044443 2.0034446 -0.025004427
|
||||
6950 0 -2.9006942 1.0038737 2.0062629 -0.024954287
|
||||
7000 0 -2.9012609 1.0022744 2.0036566 -0.024819334
|
||||
7050 0 -2.9016604 1.0051803 2.0055167 -0.024458964
|
||||
7100 0 -2.9021771 1.0033287 2.0059127 -0.024041683
|
||||
7150 0 -2.9026446 1.0051909 2.0057434 -0.023513487
|
||||
7200 0 -2.9030997 1.003201 2.0057931 -0.022955905
|
||||
7250 0 -2.9035001 1.0053534 2.006177 -0.022222879
|
||||
7300 0 -2.9039398 1.003141 2.0056512 -0.021526869
|
||||
7350 0 -2.9043194 1.0053552 2.0062897 -0.020600969
|
||||
7400 0 -2.9047554 1.0029275 2.0053735 -0.019798089
|
||||
7450 0 -2.9051394 1.0050723 2.0057785 -0.018810517
|
||||
7500 0 -2.9055639 1.0030839 2.0056435 -0.018085221
|
||||
7550 0 -2.9059506 1.00542 2.006424 -0.01743443
|
||||
7600 0 -2.906389 1.0034617 2.0060075 -0.017038562
|
||||
7650 0 -2.9068088 1.0052048 2.0059319 -0.01659861
|
||||
7700 0 -2.907256 1.0032841 2.0057462 -0.016390423
|
||||
7750 0 -2.9076758 1.0050008 2.0056173 -0.01606256
|
||||
7800 0 -2.9081063 1.0033321 2.0058403 -0.016036071
|
||||
7850 0 -2.9085325 1.0050458 2.0057159 -0.015738035
|
||||
7900 0 -2.9089602 1.0033725 2.0057939 -0.015561818
|
||||
7950 0 -2.9093746 1.00496 2.0055106 -0.015498031
|
||||
8000 0 -2.9097997 1.0034291 2.0058947 -0.015471401
|
||||
8050 0 -2.9102208 1.0049791 2.0055274 -0.015258479
|
||||
8100 0 -2.9106489 1.0035304 2.0060557 -0.015178684
|
||||
8150 0 -2.9110829 1.0052492 2.0060114 -0.014964657
|
||||
8200 0 -2.9115393 1.0037164 2.006322 -0.014718896
|
||||
8250 0 -2.9120088 1.0051472 2.0058765 -0.014430597
|
||||
8300 0 -2.912515 1.0035172 2.0062174 -0.014197457
|
||||
8350 0 -2.9130749 1.0054557 2.0059921 -0.013814584
|
||||
8400 0 -2.9137199 1.0035594 2.0063641 -0.013128137
|
||||
8450 0 -2.914514 1.0053008 2.0055891 -0.012076819
|
||||
8500 0 -2.9153923 1.0020887 2.0048249 -0.010873863
|
||||
8550 0 -2.9161681 1.005124 2.0041437 -0.009983199
|
||||
8600 0 -2.9166232 1.0035103 2.0031583 -0.0098656588
|
||||
8650 0 -2.9168935 1.0017735 2.0032739 -0.010137246
|
||||
8700 0 -2.9176075 0.99350983 1.9942491 -0.010568888
|
||||
8750 0 -2.9176655 1.0037509 2.0042507 -0.010929755
|
||||
8800 0 -2.9180335 1.0034837 2.0006008 -0.011388
|
||||
8850 0 -2.9184726 0.99722599 1.9972524 -0.012308771
|
||||
8900 0 -2.9185896 1.0070137 2.0062244 -0.012981266
|
||||
8950 0 -2.9189395 0.99775846 2.0046927 -0.013843916
|
||||
9000 0 -2.9194348 0.99994718 1.9961545 -0.01430817
|
||||
9050 0 -2.9199623 0.99913876 1.9945451 -0.015066366
|
||||
9100 0 -2.9200915 1.0053667 2.0015458 -0.015628169
|
||||
9150 0 -2.9203602 1.0029844 1.9981877 -0.015943776
|
||||
9200 0 -2.9204472 1.007234 2.0012475 -0.01621898
|
||||
9250 0 -2.9207559 1.0000323 1.9994854 -0.01673357
|
||||
9300 0 -2.9208476 1.0070892 2.004772 -0.016969206
|
||||
9350 0 -2.9212065 0.9954353 2.002531 -0.017293607
|
||||
9400 0 -2.9213536 1.011464 1.9987715 -0.016468707
|
||||
9450 0 -2.9216568 1.0004584 1.992812 -0.016331783
|
||||
9500 0 -2.9215087 1.0030182 2.006723 -0.016328481
|
||||
9550 0 -2.9218914 1.0097858 1.9978241 -0.01513886
|
||||
9600 0 -2.9221223 1.0064187 1.9937476 -0.014411434
|
||||
9650 0 -2.9224212 1.0060439 1.9885122 -0.013032442
|
||||
9700 0 -2.9220952 1.00799 2.0115738 -0.012619136
|
||||
9750 0 -2.9226088 0.99323702 1.9948387 -0.011548183
|
||||
9800 0 -2.9225553 0.99626951 2.0047326 -0.010162452
|
||||
9850 0 -2.9227332 1.006235 2.0036748 -0.0075392887
|
||||
9900 0 -2.9232122 0.98911031 1.9917417 -0.0055326528
|
||||
9950 0 -2.9231491 0.99681615 1.9994126 -0.0037310254
|
||||
10000 0 -2.9235123 0.9884299 1.9875481 -0.0021912307
|
||||
10050 0 -2.9237223 0.9999364 1.9825867 0.00099300384
|
||||
10100 0 -2.9235973 0.99000996 1.9970993 0.0021504958
|
||||
10150 0 -2.9233485 1.0077913 2.0121611 0.004525478
|
||||
10200 0 -2.9236768 1.0032927 2.0035362 0.007071254
|
||||
10250 0 -2.9238478 1.0002834 2.003131 0.0096263035
|
||||
10300 0 -2.9240364 0.99131539 2.0026965 0.011952105
|
||||
10350 0 -2.9242833 0.99641849 1.9947521 0.014575055
|
||||
10400 0 -2.9244439 0.99508819 1.9965681 0.018000688
|
||||
10450 0 -2.9243187 1.0124534 2.0090192 0.021804357
|
||||
10500 0 -2.9246558 0.99263574 2.0030149 0.023531827
|
||||
10550 0 -2.9250009 0.99916756 1.9950546 0.027624091
|
||||
10600 0 -2.9248637 1.0079577 2.0069131 0.02964918
|
||||
10650 0 -2.9253535 1.0010931 1.994458 0.032931815
|
||||
10700 0 -2.925576 0.99564043 1.9973125 0.03610588
|
||||
10750 0 -2.9255597 1.0108614 2.0075111 0.0396819
|
||||
10800 0 -2.9261759 0.9865698 1.9969888 0.0427848
|
||||
10850 0 -2.9265088 0.99539121 1.9933442 0.046588103
|
||||
10900 0 -2.9270268 0.9946174 1.9930678 0.052105624
|
||||
10950 0 -2.9270626 1.0042522 2.0070013 0.055801296
|
||||
11000 0 -2.9274337 1.0073265 2.0057225 0.059701269
|
||||
11050 0 -2.927977 0.99674096 1.9951088 0.062406122
|
||||
11100 0 -2.9280496 1.0088979 2.0105292 0.066470787
|
||||
11150 0 -2.928782 0.99018003 1.990749 0.068640734
|
||||
11200 0 -2.9290447 0.99949136 2.0055469 0.073700453
|
||||
11250 0 -2.9297585 1.0015608 1.9941199 0.078090219
|
||||
11300 0 -2.929934 1.0057572 2.0034521 0.080757029
|
||||
11350 0 -2.9305123 0.99951982 1.9941245 0.083214206
|
||||
11365 0 -2.9302543 1.0058576 2.0105109 0.083648804
|
||||
Loop time of 1.01754 on 4 procs for 10000 steps with 800 atoms
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
-2.8790759758 -2.93081588364 -2.93025426371
|
||||
Force two-norm initial, final = 3556.23 12.2587
|
||||
Force max component initial, final = 2979.1 9.18102
|
||||
Final line search alpha, max atom move = 2.99243e-05 0.000274736
|
||||
Iterations, force evaluations = 10000 10062
|
||||
|
||||
Pair time (%) = 0.498018 (48.9434)
|
||||
Neigh time (%) = 0.0017876 (0.175679)
|
||||
Comm time (%) = 0.107307 (10.5457)
|
||||
Outpt time (%) = 0.00365829 (0.359524)
|
||||
Other time (%) = 0.406768 (39.9757)
|
||||
|
||||
Nlocal: 200 ave 205 max 194 min
|
||||
Histogram: 1 0 0 0 0 1 1 0 0 1
|
||||
Nghost: 178 ave 181 max 173 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Neighs: 1857.25 ave 1884 max 1824 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 7429
|
||||
Ave neighs/atom = 9.28625
|
||||
Neighbor list builds = 29
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,138 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# LJ test of msst shock dynamics
|
||||
|
||||
# Energy in eV, time in ps, distance in angstroms.
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
timestep 1e-03
|
||||
|
||||
lattice fcc 5.3589
|
||||
Lattice spacing in x,y,z = 5.3589 5.3589 5.3589
|
||||
|
||||
## Specify the box as a given number of unit cells.
|
||||
region box1 block 0 18 0 18 0 18 units lattice
|
||||
|
||||
## Instantiate the system.
|
||||
create_box 1 box1
|
||||
Created orthogonal box = (0 0 0) to (96.4602 96.4602 96.4602)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region box1
|
||||
Created 23328 atoms
|
||||
|
||||
mass 1 40.00
|
||||
|
||||
# Initial velocities correspond to around 300K.
|
||||
velocity all create 600.0 9999
|
||||
|
||||
pair_style lj/cut 10
|
||||
pair_coeff 1 1 0.01032 3.405
|
||||
|
||||
timestep 2e-3
|
||||
|
||||
# Equilibrate the system
|
||||
fix 2 all nve
|
||||
thermo 10
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 17.139 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 600 -1943.9014 0 -134.75058 992.06384
|
||||
10 586.44651 -1917.3971 0 -149.11346 1306.17
|
||||
20 539.94305 -1778.786 0 -150.72199 2492.7873
|
||||
30 449.49509 -1506.4706 0 -151.12989 4667.6248
|
||||
40 331.86049 -1151.7344 0 -151.09164 7379.764
|
||||
50 258.27083 -929.8024 0 -151.05092 9103.558
|
||||
60 256.1869 -923.58742 0 -151.1195 9252.9158
|
||||
70 281.76061 -1000.7367 0 -151.1576 8739.2518
|
||||
80 300.28534 -1056.589 0 -151.15321 8324.8812
|
||||
90 305.83368 -1073.3097 0 -151.14426 8175.2478
|
||||
100 304.06857 -1067.9843 0 -151.14112 8191.234
|
||||
Loop time of 3.42543 on 1 procs for 100 steps with 23328 atoms
|
||||
|
||||
Pair time (%) = 3.27706 (95.6685)
|
||||
Neigh time (%) = 0.0675609 (1.97233)
|
||||
Comm time (%) = 0.0221717 (0.647268)
|
||||
Outpt time (%) = 0.000853539 (0.0249177)
|
||||
Other time (%) = 0.0577855 (1.68695)
|
||||
|
||||
Nlocal: 23328 ave 23328 max 23328 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 22235 ave 22235 max 22235 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.18372e+06 ave 2.18372e+06 max 2.18372e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2183715
|
||||
Ave neighs/atom = 93.6092
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
unfix 2
|
||||
|
||||
# MSST fix
|
||||
fix msst all msst z 28.0 q 200 mu 3e2 tscale 0.01
|
||||
MSST parameters:
|
||||
Shock in z direction
|
||||
Cell mass-like parameter qmass (units of mass^2/length^4) = 2.00000e+02
|
||||
Shock velocity = 2.80000e+01
|
||||
Artificial viscosity (units of mass/length/time) = 3.00000e+02
|
||||
Initial pressure calculated on first step
|
||||
Initial volume calculated on first step
|
||||
Initial energy calculated on first step
|
||||
|
||||
# this is needed to make etotal equal the MSST conserved quantity
|
||||
fix_modify msst energy yes
|
||||
|
||||
variable dhug equal f_msst[1]
|
||||
variable dray equal f_msst[2]
|
||||
variable lgr_vel equal f_msst[3]
|
||||
variable lgr_pos equal f_msst[4]
|
||||
|
||||
thermo_style custom step temp ke pe lx ly lz pxx pyy pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
|
||||
|
||||
#dump id all atom 50 dump.msst
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
run 100
|
||||
Fix MSST v0 = 8.97521e+05
|
||||
Fix MSST p0 = 8.10679e+03
|
||||
Fix MSST e0 = to be -1.51141e+02
|
||||
Fix MSST initial strain rate of -3.20112e-02 established by reducing temperature by factor of 1.00000e-02
|
||||
Memory usage per processor = 17.1454 Mbytes
|
||||
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz TotEng dhug dray lgr_vel lgr_pos msst
|
||||
100 301.02788 907.67474 -1058.8159 96.4602 96.4602 96.4602 8242.1214 8202.9779 8095.8693 -151.14112 1.5203428 -10.919311 0 0 9.1684318
|
||||
110 297.71411 897.68288 -1048.8859 96.4602 96.4602 96.399397 8347.6253 8303.7121 8220.7572 -151.20299 1.439058 28.652258 0.017649501 -0.55980494 5.7336721
|
||||
120 295.64308 891.43821 -1042.72 96.4602 96.4602 96.340496 8431.6742 8379.2441 8331.5304 -151.28174 1.3655893 56.776734 0.034747125 -1.119263 2.3808018
|
||||
130 296.02228 892.5816 -1043.9407 96.4602 96.4602 96.283468 8456.2492 8412.6368 8392.5853 -151.35912 1.2945465 37.811981 0.05130089 -1.6783851 -0.87840575
|
||||
140 298.19024 899.11855 -1050.5482 96.4602 96.4602 96.228236 8430.5151 8415.6802 8414.2537 -151.42965 1.2243399 -18.01985 0.067333442 -2.2371818 -4.0330712
|
||||
150 300.86421 907.18122 -1058.6966 96.4602 96.4602 96.174681 8399.4697 8396.2236 8420.9004 -151.51534 1.1598278 -86.5197 0.082879112 -2.7956634 -7.0824881
|
||||
160 303.34119 914.64996 -1066.2388 96.4602 96.4602 96.122673 8388.3438 8360.5024 8428.751 -151.58881 1.0977647 -151.64553 0.097975827 -3.353839 -10.033902
|
||||
170 304.87769 919.28288 -1070.961 96.4602 96.4602 96.072088 8408.8694 8333.4337 8449.5665 -151.67812 1.044322 -201.80899 0.11265931 -3.9117174 -12.897768
|
||||
180 304.99 919.62151 -1071.3588 96.4602 96.4602 96.022824 8461.5542 8343.1436 8484.9824 -151.73733 0.99203387 -235.51793 0.12695926 -4.4693063 -15.685622
|
||||
190 305.1148 919.99782 -1071.7807 96.4602 96.4602 95.9748 8498.7562 8371.4217 8514.4473 -151.78288 0.93937416 -273.43964 0.1408996 -5.0266132 -18.403999
|
||||
200 306.45829 924.0488 -1075.8787 96.4602 96.4602 95.927931 8488.9509 8385.2408 8529.6443 -151.82991 0.88654815 -324.00777 0.15450451 -5.583645 -21.055149
|
||||
Loop time of 4.37563 on 1 procs for 100 steps with 23328 atoms
|
||||
|
||||
Pair time (%) = 3.2868 (75.1161)
|
||||
Neigh time (%) = 0.136101 (3.11044)
|
||||
Comm time (%) = 0.0217741 (0.497621)
|
||||
Outpt time (%) = 0.0132105 (0.301912)
|
||||
Other time (%) = 0.917742 (20.974)
|
||||
|
||||
Nlocal: 23328 ave 23328 max 23328 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 22205 ave 22205 max 22205 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.18349e+06 ave 2.18349e+06 max 2.18349e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2183494
|
||||
Ave neighs/atom = 93.5997
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,138 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# LJ test of msst shock dynamics
|
||||
|
||||
# Energy in eV, time in ps, distance in angstroms.
|
||||
units metal
|
||||
boundary p p p
|
||||
|
||||
atom_style atomic
|
||||
timestep 1e-03
|
||||
|
||||
lattice fcc 5.3589
|
||||
Lattice spacing in x,y,z = 5.3589 5.3589 5.3589
|
||||
|
||||
## Specify the box as a given number of unit cells.
|
||||
region box1 block 0 18 0 18 0 18 units lattice
|
||||
|
||||
## Instantiate the system.
|
||||
create_box 1 box1
|
||||
Created orthogonal box = (0 0 0) to (96.4602 96.4602 96.4602)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
create_atoms 1 region box1
|
||||
Created 23328 atoms
|
||||
|
||||
mass 1 40.00
|
||||
|
||||
# Initial velocities correspond to around 300K.
|
||||
velocity all create 600.0 9999
|
||||
|
||||
pair_style lj/cut 10
|
||||
pair_coeff 1 1 0.01032 3.405
|
||||
|
||||
timestep 2e-3
|
||||
|
||||
# Equilibrate the system
|
||||
fix 2 all nve
|
||||
thermo 10
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 5.52772 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 600 -1943.9014 0 -134.75058 992.06384
|
||||
10 586.47212 -1917.4465 0 -149.08565 1305.7368
|
||||
20 540.13678 -1779.3375 0 -150.68935 2488.8545
|
||||
30 450.11466 -1508.2891 0 -151.08028 4655.1306
|
||||
40 332.99843 -1155.1208 0 -151.04685 7357.5162
|
||||
50 259.2571 -932.72753 0 -151.0022 9086.2087
|
||||
60 256.22581 -923.67654 0 -151.0913 9257.1571
|
||||
70 281.12085 -998.79866 0 -151.14863 8759.7887
|
||||
80 299.37658 -1053.8476 0 -151.1519 8352.9467
|
||||
90 304.24026 -1068.4941 0 -151.13319 8218.1594
|
||||
100 301.9683 -1061.6332 0 -151.12284 8244.1277
|
||||
Loop time of 0.88372 on 4 procs for 100 steps with 23328 atoms
|
||||
|
||||
Pair time (%) = 0.820597 (92.8571)
|
||||
Neigh time (%) = 0.0170572 (1.93016)
|
||||
Comm time (%) = 0.0299263 (3.3864)
|
||||
Outpt time (%) = 0.000454426 (0.0514219)
|
||||
Other time (%) = 0.0156853 (1.77492)
|
||||
|
||||
Nlocal: 5832 ave 5850 max 5813 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 10571 ave 10590 max 10553 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 545762 ave 548069 max 543643 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 2183047
|
||||
Ave neighs/atom = 93.5805
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
unfix 2
|
||||
|
||||
# MSST fix
|
||||
fix msst all msst z 28.0 q 200 mu 3e2 tscale 0.01
|
||||
MSST parameters:
|
||||
Shock in z direction
|
||||
Cell mass-like parameter qmass (units of mass^2/length^4) = 2.00000e+02
|
||||
Shock velocity = 2.80000e+01
|
||||
Artificial viscosity (units of mass/length/time) = 3.00000e+02
|
||||
Initial pressure calculated on first step
|
||||
Initial volume calculated on first step
|
||||
Initial energy calculated on first step
|
||||
|
||||
# this is needed to make etotal equal the MSST conserved quantity
|
||||
fix_modify msst energy yes
|
||||
|
||||
variable dhug equal f_msst[1]
|
||||
variable dray equal f_msst[2]
|
||||
variable lgr_vel equal f_msst[3]
|
||||
variable lgr_pos equal f_msst[4]
|
||||
|
||||
thermo_style custom step temp ke pe lx ly lz pxx pyy pzz etotal v_dhug v_dray v_lgr_vel v_lgr_pos f_msst
|
||||
|
||||
#dump id all atom 50 dump.msst
|
||||
|
||||
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
run 100
|
||||
Fix MSST v0 = 8.97521e+05
|
||||
Fix MSST p0 = 8.18624e+03
|
||||
Fix MSST e0 = to be -1.51123e+02
|
||||
Fix MSST initial strain rate of -3.19005e-02 established by reducing temperature by factor of 1.00000e-02
|
||||
Memory usage per processor = 5.52772 Mbytes
|
||||
Step Temp KinEng PotEng Lx Ly Lz Pxx Pyy Pzz TotEng dhug dray lgr_vel lgr_pos msst
|
||||
100 298.94862 901.40524 -1052.5281 96.4602 96.4602 96.4602 8270.9151 8253.4662 8175.4946 -151.12284 1.5098415 -10.744684 0 0 9.1051034
|
||||
110 296.49826 894.01679 -1045.224 96.4602 96.4602 96.399609 8338.4937 8340.5504 8294.9909 -151.20723 1.4327442 23.73173 0.017588167 -0.55980562 5.6560557
|
||||
120 295.97607 892.44225 -1043.7239 96.4602 96.4602 96.340904 8377.6797 8385.921 8378.3042 -151.28169 1.3584606 24.672199 0.034628719 -1.1192655 2.2953307
|
||||
130 297.34893 896.58179 -1047.945 96.4602 96.4602 96.284029 8379.2516 8394.8806 8416.2669 -151.36322 1.2881444 -17.170168 0.051138087 -1.6783905 -0.96527961
|
||||
140 299.71946 903.72952 -1055.1787 96.4602 96.4602 96.22888 8357.0358 8388.6743 8424.3188 -151.44922 1.221125 -86.501161 0.067146366 -2.2371908 -4.1195182
|
||||
150 301.79241 909.97998 -1061.4976 96.4602 96.4602 96.175327 8332.7118 8393.7027 8434.6177 -151.51765 1.1560248 -151.34689 0.082691635 -2.7956762 -7.172084
|
||||
160 303.18249 914.17141 -1065.7667 96.4602 96.4602 96.123244 8321.1154 8413.1248 8454.5596 -151.59527 1.0977348 -204.4864 0.097810061 -3.3538554 -10.134387
|
||||
170 304.34089 917.66428 -1069.3198 96.4602 96.4602 96.072522 8327.6227 8431.1177 8467.92 -151.65554 1.0390628 -262.29751 0.11253339 -3.9117366 -13.01442
|
||||
180 305.86343 922.25514 -1073.9633 96.4602 96.4602 96.023049 8345.1853 8432.5201 8461.3276 -151.70813 0.97863988 -338.30793 0.12689398 -4.4693274 -15.815462
|
||||
190 307.44054 927.01052 -1078.7892 96.4602 96.4602 95.9747 8368.4081 8427.5109 8450.584 -151.77867 0.92329631 -416.89333 0.1409285 -5.0266346 -18.541801
|
||||
200 308.43619 930.01265 -1081.8521 96.4602 96.4602 95.927349 8393.2058 8443.1265 8454.6733 -151.83947 0.8723277 -479.24592 0.1546734 -5.5836644 -21.20378
|
||||
Loop time of 1.15112 on 4 procs for 100 steps with 23328 atoms
|
||||
|
||||
Pair time (%) = 0.834059 (72.4563)
|
||||
Neigh time (%) = 0.0344771 (2.99509)
|
||||
Comm time (%) = 0.0392016 (3.40552)
|
||||
Outpt time (%) = 0.00405097 (0.351916)
|
||||
Other time (%) = 0.239331 (20.7912)
|
||||
|
||||
Nlocal: 5832 ave 5874 max 5803 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Nghost: 10563.8 ave 10588 max 10526 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 0 2
|
||||
Neighs: 545708 ave 550787 max 542668 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 2182834
|
||||
Ave neighs/atom = 93.5714
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,10 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
Running on 4 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 4394.415 2794.6751 0.41279209 4.8987813 4588.501 0.43598632 0.42993506 1.8911387 0 -3.053578 0.33333333 -2.6175917 0.66666667 -2.7448543 1 -3.0475267
|
||||
100 0.12010575 0.088127762 0.064276554 0.094661883 0.20236294 0.007087892 0.002266113 2.3031028 0 -3.0535897 0.31865586 -3.0473542 0.63955795 -3.0465019 1 -3.048768
|
||||
128 0.095281121 0.071078266 0.057687219 0.073871056 0.21277196 0.0070816181 0.0022610401 2.3073292 0 -3.0535911 0.31919352 -3.0473504 0.64407221 -3.0465095 1 -3.0487705
|
||||
Climbing replica = 3
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
128 0.21277196 0.18384896 0.057687219 0.073871056 0.21277196 0.0070816181 0.0022610401 2.3073292 0 -3.0535911 0.31919352 -3.0473504 0.64407221 -3.0465095 1 -3.0487705
|
||||
218 0.098467802 0.080574436 0.040076462 0.045136805 0.098467802 0.0071048579 0.0022855225 2.313949 0 -3.0535941 0.31520301 -3.0473978 0.61524469 -3.0464893 1 -3.0487748
|
||||
|
|
@ -0,0 +1,17 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
Running on 4 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 14.470556 10.654221 0.40467815 5.0039317 14.654382 0.0018497549 0.00068389874 0.98392852 0 -3.0514828 0.33333333 -3.0496331 0.66666667 -3.049639 1 -3.050317
|
||||
100 0.25773742 0.10794413 0.058202133 0.1204961 0.63926975 0.0015165823 0.0015141592 1.165543 0 -3.0514885 0.28878467 -3.0503489 0.5971109 -3.049972 1 -3.0514861
|
||||
200 0.091708973 0.047949395 0.04087138 0.046881211 0.90030228 0.0014426376 0.0014419188 1.1693721 0 -3.0514914 0.30059249 -3.0502986 0.62913825 -3.0500488 1 -3.0514907
|
||||
300 0.087351776 0.023908733 0.02553215 0.02868203 1.0708021 0.0013861206 0.001385853 1.1702524 0 -3.0514932 0.31570889 -3.0502363 0.648515 -3.0501071 1 -3.0514929
|
||||
400 0.031869592 0.010230083 0.015693232 0.017403653 1.155339 0.0013557368 0.00135563 1.1705851 0 -3.0514939 0.32460841 -3.0502022 0.65786761 -3.0501382 1 -3.0514938
|
||||
500 0.10917875 0.024836538 0.010748894 0.01233245 1.1893181 0.0013430399 0.0013429855 1.1707469 0 -3.0514942 0.32832896 -3.0501886 0.66162453 -3.0501511 1 -3.0514941
|
||||
600 0.012590389 0.0038162493 0.0079914045 0.008914885 1.2058147 0.0013369459 0.0013369129 1.1708664 0 -3.0514942 0.33009568 -3.0501823 0.66339859 -3.0501573 1 -3.0514942
|
||||
665 0.0094084415 0.0027101492 0.0063303343 0.0070901332 1.2481697 0.001333519 0.0013334962 1.1709213 0 -3.0514943 0.33101225 -3.0501789 0.66432323 -3.0501608 1 -3.0514943
|
||||
Climbing replica = 3
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
665 1.2481697 1.2178608 0.0063303343 0.0070901332 1.2481697 0.001333519 0.0013334962 1.1709213 0 -3.0514943 0.33101225 -3.0501789 0.66432323 -3.0501608 1 -3.0514943
|
||||
765 0.35231036 0.10879535 0.0044485485 0.0051013174 0.35231036 0.0016026196 0.0016026062 1.1709914 0 -3.0514943 0.29041219 -3.0503427 0.50280437 -3.0498917 1 -3.0514943
|
||||
865 0.043455145 0.03906183 0.0034246938 0.0039095702 0.012409052 0.0016020467 0.0016020372 1.1725604 0 -3.0514943 0.26970162 -3.050445 0.50350952 -3.0498923 1 -3.0514943
|
||||
949 0.0095823197 0.0052451105 0.0018873737 0.0022408434 0.0082719028 0.0016018849 0.0016018802 1.1743779 0 -3.0514943 0.25504606 -3.0505276 0.5048779 -3.0498925 1 -3.0514943
|
||||
|
|
@ -0,0 +1,13 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
Running on 3 partitions of processors
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
0 7.5536378 1.6893472 0.16935037 7.5536378 7.5536378 1.540436 0 1.6222323 0 -2213.3331 0.5 -2212.4078 1 -2211.7927
|
||||
10 0.27719806 0.040877456 0.049231415 0.27719806 0.18261385 0.51235272 0.497037 1.6796853 0 -2213.3354 0.4899442 -2212.8231 1 -2213.3201
|
||||
20 0.2711434 0.032502606 0.029647879 0.2711434 0.08873222 0.51042627 0.5082811 1.7276175 0 -2213.3367 0.49395581 -2212.8263 1 -2213.3345
|
||||
30 0.042752069 0.0054697216 0.022080279 0.042752069 0.04304853 0.51032354 0.50985348 1.7331829 0 -2213.337 0.49678876 -2212.8267 1 -2213.3365
|
||||
40 0.038871653 0.0031613641 0.015252665 0.038871653 0.027570271 0.51023553 0.51005571 1.7372273 0 -2213.3372 0.49860476 -2212.827 1 -2213.337
|
||||
50 0.030191914 0.002117896 0.0089992491 0.030191914 0.01616834 0.51015661 0.51009831 1.7402235 0 -2213.3373 0.49951137 -2212.8272 1 -2213.3373
|
||||
Climbing replica = 2
|
||||
Step MaxReplicaForce MaxAtomForce GradV0 GradV1 GradVc EBF EBR RDT RD1 PE1 RD2 PE2 ... RDN PEN
|
||||
50 0.030191914 0.0034301261 0.0089992491 0.030191914 0.01616834 0.51015661 0.51009831 1.7402235 0 -2213.3373 0.49951137 -2212.8272 1 -2213.3373
|
||||
60 0.0098471086 0.0013684616 0.0068582214 0.009537211 0.0098471086 0.51013932 0.51011266 1.741105 0 -2213.3373 0.50051546 -2212.8272 1 -2213.3373
|
||||
|
|
@ -0,0 +1,115 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 2d NEMD simulation
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 160 atoms
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
region slice block 4 6 INF INF INF INF
|
||||
set region slice type 2
|
||||
40 settings made for type
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1
|
||||
|
||||
fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
|
||||
fix 2 all deform 1 xy erate 0.01 remap v
|
||||
|
||||
#dump 1 all custom 5000 dump.nemd id type x y z
|
||||
|
||||
#dump 2 all image 1000 image.*.jpg type type adiam 1.2
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 1000 movie.mpg type type adiam 1.2
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
thermo 1000
|
||||
|
||||
run 50000
|
||||
Memory usage per processor = 2.06269 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1.44 0 0 1.431 1.2080502 189.52855
|
||||
1000 1.1132807 0.27905278 0 1.3853755 6.5147704 189.52855
|
||||
2000 1.0443617 0.2588631 0 1.2966975 5.8123077 189.52855
|
||||
3000 0.99740048 0.30663122 0 1.2977979 6.7893948 189.52855
|
||||
4000 1.0452154 0.2549558 0 1.2936386 5.9682721 189.52855
|
||||
5000 1.0446171 0.24804329 0 1.2861316 6.0510081 189.52855
|
||||
6000 0.99414736 0.27672942 0 1.2646634 6.1314117 189.52855
|
||||
7000 0.98222339 0.25264497 0 1.2287295 5.835047 189.52855
|
||||
8000 1.0949044 0.21576814 0 1.3038294 5.491461 189.52855
|
||||
9000 1.0926686 0.24221385 0 1.3280532 6.3130763 189.52855
|
||||
10000 1.076097 0.2855754 0 1.3549468 5.8734258 189.52855
|
||||
11000 0.99180114 0.32327904 0 1.3088814 6.7664177 189.52855
|
||||
12000 0.92157563 0.3649801 0 1.2807959 7.1346057 189.52855
|
||||
13000 1.0357975 0.24757954 0 1.2769033 5.1431799 189.52855
|
||||
14000 1.0007104 0.23333402 0 1.22779 5.7856096 189.52855
|
||||
15000 0.99137134 0.24780673 0 1.232982 6.1361025 189.52855
|
||||
16000 0.94735806 0.285215 0 1.2266521 6.5489235 189.52855
|
||||
17000 0.92947519 0.35111458 0 1.2747806 6.8906691 189.52855
|
||||
18000 0.93468492 0.30314528 0 1.2319884 6.7846869 189.52855
|
||||
19000 0.97664561 0.22133285 0 1.1918744 5.1668518 189.52855
|
||||
20000 0.92288444 0.24361535 0 1.1607318 5.8575076 189.52855
|
||||
21000 0.95982212 0.23711835 0 1.1909416 6.1133698 189.52855
|
||||
22000 0.94710657 0.30873344 0 1.2499206 6.7011709 189.52855
|
||||
23000 0.95315902 0.25917016 0 1.2063719 6.436954 189.52855
|
||||
24000 0.92248708 0.25883982 0 1.1755614 6.7367986 189.52855
|
||||
25000 0.90317019 0.26834925 0 1.1658746 5.8271823 189.52855
|
||||
26000 0.91432206 0.29952864 0 1.2081362 7.2639988 189.52855
|
||||
27000 1.0070883 0.25437551 0 1.2551695 5.9319042 189.52855
|
||||
28000 0.90757676 0.33894646 0 1.2408509 6.5341369 189.52855
|
||||
29000 0.93635654 0.27447038 0 1.2049747 5.7410459 189.52855
|
||||
30000 1.0260914 0.26547724 0 1.2851555 6.7175944 189.52855
|
||||
31000 1.0885528 0.22068838 0 1.3024377 5.9614548 189.52855
|
||||
32000 0.99983894 0.26432646 0 1.2579164 5.6537115 189.52855
|
||||
33000 0.98254278 0.25012552 0 1.2265274 6.00352 189.52855
|
||||
34000 1.0461448 0.239846 0 1.2794524 5.8594944 189.52855
|
||||
35000 1.0600085 0.32706153 0 1.3804449 7.1757696 189.52855
|
||||
36000 1.0293724 0.37370741 0 1.3966463 7.1818303 189.52855
|
||||
37000 0.99724062 0.35645069 0 1.3474586 7.3712517 189.52855
|
||||
38000 1.1355196 0.23285267 0 1.3612752 5.9101916 189.52855
|
||||
39000 1.0750755 0.31068535 0 1.3790417 6.7523098 189.52855
|
||||
40000 1.0269017 0.38361397 0 1.4040975 7.532356 189.52855
|
||||
41000 0.98265149 0.34340216 0 1.3199121 6.9652101 189.52855
|
||||
42000 0.95262128 0.36420847 0 1.3108759 7.5380723 189.52855
|
||||
43000 1.0124646 0.25137287 0 1.2575095 6.6275506 189.52855
|
||||
44000 0.95142407 0.29804153 0 1.2435192 5.9780096 189.52855
|
||||
45000 0.99724723 0.19281581 0 1.1838302 5.4332418 189.52855
|
||||
46000 0.90112949 0.29935892 0 1.1948564 7.0600659 189.52855
|
||||
47000 0.8786086 0.34312007 0 1.2162374 6.4678979 189.52855
|
||||
48000 1.0516991 0.17931414 0 1.2244401 5.5158284 189.52855
|
||||
49000 0.98386816 0.26044721 0 1.2381662 5.8913908 189.52855
|
||||
50000 1.0316312 0.19654107 0 1.2217246 5.2461518 189.52855
|
||||
Loop time of 1.10994 on 1 procs for 50000 steps with 160 atoms
|
||||
|
||||
Pair time (%) = 0.192406 (17.3349)
|
||||
Neigh time (%) = 0.139588 (12.5762)
|
||||
Comm time (%) = 0.0557146 (5.01961)
|
||||
Outpt time (%) = 0.000450134 (0.0405549)
|
||||
Other time (%) = 0.721779 (65.0287)
|
||||
|
||||
Nlocal: 160 ave 160 max 160 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 66 ave 66 max 66 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 351 ave 351 max 351 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 351
|
||||
Ave neighs/atom = 2.19375
|
||||
Neighbor list builds = 5281
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,115 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 2d NEMD simulation
|
||||
|
||||
units lj
|
||||
atom_style atomic
|
||||
dimension 2
|
||||
|
||||
lattice sq2 0.8442
|
||||
Lattice spacing in x,y,z = 1.53919 1.53919 1.53919
|
||||
region box prism 0 10 0 8 -0.5 0.5 0 0 0
|
||||
create_box 2 box
|
||||
Created triclinic box = (0 0 -0.769595) to (15.3919 12.3135 0.769595) with tilt (0 0 0)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 160 atoms
|
||||
mass * 1.0
|
||||
|
||||
velocity all create 1.44 87287 loop geom
|
||||
|
||||
region slice block 4 6 INF INF INF INF
|
||||
set region slice type 2
|
||||
40 settings made for type
|
||||
|
||||
pair_style lj/cut 2.5
|
||||
pair_coeff * * 1.0 1.0 1.0
|
||||
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 0 every 1
|
||||
|
||||
fix 1 all nvt/sllod temp 1.0 1.0 1.0 tchain 1
|
||||
fix 2 all deform 1 xy erate 0.01 remap v
|
||||
|
||||
#dump 1 all custom 5000 dump.nemd id type x y z
|
||||
|
||||
#dump 2 all image 1000 image.*.jpg type type adiam 1.2
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 1000 movie.mpg type type adiam 1.2
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
thermo 1000
|
||||
|
||||
run 50000
|
||||
Memory usage per processor = 2.06108 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1.44 0 0 1.431 1.2080502 189.52855
|
||||
1000 1.124295 0.28924371 0 1.4065119 7.0530596 189.52855
|
||||
2000 0.95544082 0.41610026 0 1.3655696 8.2906389 189.52855
|
||||
3000 1.0379332 0.3006166 0 1.3320627 6.6571959 189.52855
|
||||
4000 1.0384606 0.21868978 0 1.25066 5.5810527 189.52855
|
||||
5000 0.94117133 0.28986466 0 1.2251537 6.7004134 189.52855
|
||||
6000 0.8855088 0.29250925 0 1.1724836 6.0234641 189.52855
|
||||
7000 0.89371735 0.22907448 0 1.1172061 6.0996491 189.52855
|
||||
8000 0.91424769 0.21379978 0 1.1223334 5.3165508 189.52855
|
||||
9000 0.90042293 0.21884136 0 1.1136366 5.488714 189.52855
|
||||
10000 0.85048519 0.25030732 0 1.095477 5.6995459 189.52855
|
||||
11000 0.84698813 0.26740545 0 1.1090999 6.0227022 189.52855
|
||||
12000 0.84154976 0.27476871 0 1.1110588 6.1957407 189.52855
|
||||
13000 0.95858623 0.24922085 0 1.2018159 6.1788034 189.52855
|
||||
14000 1.0214286 0.21791039 0 1.2329551 5.4418702 189.52855
|
||||
15000 1.0398737 0.2633112 0 1.2966857 6.4069155 189.52855
|
||||
16000 1.0064086 0.32204447 0 1.322163 6.9037595 189.52855
|
||||
17000 0.95972629 0.32803912 0 1.2817671 6.816773 189.52855
|
||||
18000 0.97474673 0.27514532 0 1.2437999 6.5619061 189.52855
|
||||
19000 0.98058523 0.29730787 0 1.2717644 6.3947579 189.52855
|
||||
20000 1.0096005 0.29191846 0 1.2952089 6.5005373 189.52855
|
||||
21000 1.0340906 0.30603597 0 1.3336635 6.6365016 189.52855
|
||||
22000 1.0986576 0.25246406 0 1.3442551 6.3254116 189.52855
|
||||
23000 1.0118481 0.31753984 0 1.3230639 6.0921359 189.52855
|
||||
24000 1.0766759 0.20245452 0 1.2724012 5.4505434 189.52855
|
||||
25000 1.1081144 0.1941749 0 1.2953635 5.4769844 189.52855
|
||||
26000 1.0100198 0.29200311 0 1.2957102 6.4496868 189.52855
|
||||
27000 1.0780229 0.22518995 0 1.2964752 5.4742933 189.52855
|
||||
28000 0.95411135 0.30374431 0 1.2518925 6.4759593 189.52855
|
||||
29000 0.89919125 0.33340443 0 1.2269757 7.2806173 189.52855
|
||||
30000 1.0252498 0.21740235 0 1.2362443 6.0225096 189.52855
|
||||
31000 0.94842379 0.29574176 0 1.2382379 6.6857537 189.52855
|
||||
32000 0.98564692 0.28884608 0 1.2683327 5.8893159 189.52855
|
||||
33000 1.0203197 0.25128893 0 1.2652316 6.3876672 189.52855
|
||||
34000 0.92927072 0.35791559 0 1.2813784 6.9518532 189.52855
|
||||
35000 1.0595999 0.2526221 0 1.3055995 6.3468891 189.52855
|
||||
36000 1.0080572 0.3373598 0 1.3391167 6.8836622 189.52855
|
||||
37000 1.0371553 0.39107985 0 1.421753 7.8264775 189.52855
|
||||
38000 1.1399348 0.32003125 0 1.4528415 6.7472192 189.52855
|
||||
39000 1.1719539 0.28244065 0 1.4470698 6.1962707 189.52855
|
||||
40000 1.160549 0.2692168 0 1.4225124 6.4898037 189.52855
|
||||
41000 1.082068 0.31445471 0 1.3897598 7.1045082 189.52855
|
||||
42000 1.1200126 0.24056295 0 1.3535754 6.1401582 189.52855
|
||||
43000 1.1131393 0.25879245 0 1.3649747 5.6653752 189.52855
|
||||
44000 1.0584865 0.28294496 0 1.3348159 6.7007718 189.52855
|
||||
45000 1.1250306 0.22801778 0 1.346017 5.5953791 189.52855
|
||||
46000 1.0799948 0.25829243 0 1.3315373 6.2101875 189.52855
|
||||
47000 1.0466019 0.30437314 0 1.3444338 6.5602361 189.52855
|
||||
48000 0.99707221 0.2760815 0 1.266922 6.3946457 189.52855
|
||||
49000 0.96261953 0.29992833 0 1.2565315 6.7358834 189.52855
|
||||
50000 0.91044957 0.33413644 0 1.2388957 6.7732395 189.52855
|
||||
Loop time of 0.905642 on 4 procs for 50000 steps with 160 atoms
|
||||
|
||||
Pair time (%) = 0.0493886 (5.45344)
|
||||
Neigh time (%) = 0.0384813 (4.24906)
|
||||
Comm time (%) = 0.366813 (40.5031)
|
||||
Outpt time (%) = 0.000886261 (0.0978601)
|
||||
Other time (%) = 0.450073 (49.6966)
|
||||
|
||||
Nlocal: 40 ave 42 max 38 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Nghost: 36.25 ave 42 max 34 min
|
||||
Histogram: 2 1 0 0 0 0 0 0 0 1
|
||||
Neighs: 91 ave 103 max 84 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 364
|
||||
Ave neighs/atom = 2.275
|
||||
Neighbor list builds = 5274
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,140 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 2d LJ obstacle flow
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.7
|
||||
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
|
||||
region box block 0 40 0 10 -0.25 0.25
|
||||
create_box 3 box
|
||||
Created orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 840 atoms
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 1.12246
|
||||
pair_coeff * * 1.0 1.0 1.12246
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
120 atoms in group lower
|
||||
region 2 block INF INF 8.75 INF INF INF
|
||||
group upper region 2
|
||||
120 atoms in group upper
|
||||
group boundary union lower upper
|
||||
240 atoms in group boundary
|
||||
group flow subtract all boundary
|
||||
600 atoms in group flow
|
||||
|
||||
set group lower type 2
|
||||
120 settings made for type
|
||||
set group upper type 3
|
||||
120 settings made for type
|
||||
|
||||
# initial velocities
|
||||
|
||||
compute mobile flow temp
|
||||
velocity flow create 1.0 482748 temp mobile
|
||||
fix 1 all nve
|
||||
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
|
||||
fix_modify 2 temp mobile
|
||||
|
||||
# Poiselle flow
|
||||
|
||||
velocity boundary set 0.0 0.0 0.0
|
||||
fix 3 lower setforce 0.0 0.0 0.0
|
||||
fix 4 upper setforce 0.0 NULL 0.0
|
||||
fix 5 upper aveforce 0.0 -0.5 0.0
|
||||
fix 6 flow addforce 1.0 0.0 0.0
|
||||
|
||||
# 2 obstacles
|
||||
|
||||
region void1 sphere 10 4 0 3
|
||||
delete_atoms region void1
|
||||
Deleted 36 atoms, new total = 804
|
||||
region void2 sphere 20 7 0 3
|
||||
delete_atoms region void2
|
||||
Deleted 35 atoms, new total = 769
|
||||
|
||||
fix 7 flow indent 100 sphere 10 4 0 4
|
||||
fix 8 flow indent 100 sphere 20 7 0 4
|
||||
fix 9 all enforce2d
|
||||
|
||||
# Run
|
||||
|
||||
timestep 0.003
|
||||
thermo 1000
|
||||
thermo_modify temp mobile
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
|
||||
#dump 1 all atom 100 dump.obstacle
|
||||
|
||||
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
run 25000
|
||||
Memory usage per processor = 2.06342 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1.0027471 0 0 0.68849216 0.46317653 1143.0857
|
||||
1000 1 -0.33689286 0 0.34971312 1.2905426 1286.7728
|
||||
2000 1 -0.36746164 0 0.31914434 1.1668828 1313.44
|
||||
3000 1 -0.52004751 0 0.16655848 1.4177739 1324.489
|
||||
4000 1 -0.50683869 0 0.17976729 1.4851498 1370.896
|
||||
5000 1 -0.49074513 0 0.19586085 1.2870129 1411.5513
|
||||
6000 1 -0.45051896 0 0.23608702 1.2173953 1441.7581
|
||||
7000 1 -0.44428914 0 0.24231685 1.2136189 1451.7268
|
||||
8000 1 -0.41943736 0 0.26716862 1.0476856 1463.0805
|
||||
9000 1 -0.42143857 0 0.26516741 1.1040812 1449.7584
|
||||
10000 1 -0.40181705 0 0.28478893 0.97148485 1448.5974
|
||||
11000 1 -0.4088962 0 0.27770978 1.1761219 1440.3567
|
||||
12000 1 -0.38630717 0 0.30029881 1.0593811 1444.9934
|
||||
13000 1 -0.37152911 0 0.31507687 0.98075952 1448.0726
|
||||
14000 1 -0.37370096 0 0.31290502 1.0046443 1449.4749
|
||||
15000 1 -0.39915937 0 0.28744662 1.0240313 1452.3583
|
||||
16000 1 -0.37562636 0 0.31097963 1.0053468 1452.3514
|
||||
17000 1 -0.35736161 0 0.32924437 1.070682 1452.898
|
||||
18000 1 -0.38767402 0 0.29893196 1.0418661 1456.1288
|
||||
19000 1 -0.38489181 0 0.30171417 1.0361798 1446.8804
|
||||
20000 1 -0.39521864 0 0.29138735 1.0754044 1447.4619
|
||||
21000 1 -0.37845983 0 0.30814615 1.0072922 1453.8721
|
||||
22000 1 -0.40926684 0 0.27733914 1.0929362 1452.8181
|
||||
23000 1 -0.3586683 0 0.32793768 1.006092 1459.6104
|
||||
24000 1 -0.38908821 0 0.29751777 0.95291948 1464.8522
|
||||
25000 1 -0.38890426 0 0.29770172 0.95284427 1455.9361
|
||||
Loop time of 1.70272 on 1 procs for 25000 steps with 769 atoms
|
||||
|
||||
Pair time (%) = 0.496648 (29.1678)
|
||||
Neigh time (%) = 0.140946 (8.27769)
|
||||
Comm time (%) = 0.0254805 (1.49646)
|
||||
Outpt time (%) = 0.000277758 (0.0163125)
|
||||
Other time (%) = 1.03937 (61.0417)
|
||||
|
||||
Nlocal: 769 ave 769 max 769 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 48 ave 48 max 48 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1624 ave 1624 max 1624 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1624
|
||||
Ave neighs/atom = 2.11183
|
||||
Neighbor list builds = 1642
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,140 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# 2d LJ obstacle flow
|
||||
|
||||
dimension 2
|
||||
boundary p s p
|
||||
|
||||
atom_style atomic
|
||||
neighbor 0.3 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
# create geometry
|
||||
|
||||
lattice hex 0.7
|
||||
Lattice spacing in x,y,z = 1.28436 2.22457 1.28436
|
||||
region box block 0 40 0 10 -0.25 0.25
|
||||
create_box 3 box
|
||||
Created orthogonal box = (0 0 -0.321089) to (51.3743 22.2457 0.321089)
|
||||
4 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 box
|
||||
Created 840 atoms
|
||||
|
||||
mass 1 1.0
|
||||
mass 2 1.0
|
||||
mass 3 1.0
|
||||
|
||||
# LJ potentials
|
||||
|
||||
pair_style lj/cut 1.12246
|
||||
pair_coeff * * 1.0 1.0 1.12246
|
||||
|
||||
# define groups
|
||||
|
||||
region 1 block INF INF INF 1.25 INF INF
|
||||
group lower region 1
|
||||
120 atoms in group lower
|
||||
region 2 block INF INF 8.75 INF INF INF
|
||||
group upper region 2
|
||||
120 atoms in group upper
|
||||
group boundary union lower upper
|
||||
240 atoms in group boundary
|
||||
group flow subtract all boundary
|
||||
600 atoms in group flow
|
||||
|
||||
set group lower type 2
|
||||
120 settings made for type
|
||||
set group upper type 3
|
||||
120 settings made for type
|
||||
|
||||
# initial velocities
|
||||
|
||||
compute mobile flow temp
|
||||
velocity flow create 1.0 482748 temp mobile
|
||||
fix 1 all nve
|
||||
fix 2 flow temp/rescale 200 1.0 1.0 0.02 1.0
|
||||
fix_modify 2 temp mobile
|
||||
|
||||
# Poiselle flow
|
||||
|
||||
velocity boundary set 0.0 0.0 0.0
|
||||
fix 3 lower setforce 0.0 0.0 0.0
|
||||
fix 4 upper setforce 0.0 NULL 0.0
|
||||
fix 5 upper aveforce 0.0 -0.5 0.0
|
||||
fix 6 flow addforce 1.0 0.0 0.0
|
||||
|
||||
# 2 obstacles
|
||||
|
||||
region void1 sphere 10 4 0 3
|
||||
delete_atoms region void1
|
||||
Deleted 36 atoms, new total = 804
|
||||
region void2 sphere 20 7 0 3
|
||||
delete_atoms region void2
|
||||
Deleted 35 atoms, new total = 769
|
||||
|
||||
fix 7 flow indent 100 sphere 10 4 0 4
|
||||
fix 8 flow indent 100 sphere 20 7 0 4
|
||||
fix 9 all enforce2d
|
||||
|
||||
# Run
|
||||
|
||||
timestep 0.003
|
||||
thermo 1000
|
||||
thermo_modify temp mobile
|
||||
WARNING: Temperature for thermo pressure is not for group all (../thermo.cpp:439)
|
||||
|
||||
#dump 1 all atom 100 dump.obstacle
|
||||
|
||||
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
run 25000
|
||||
Memory usage per processor = 2.05581 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 1.0004177 0 0 0.68689281 0.46210058 1143.0857
|
||||
1000 1 -0.32494012 0 0.36166587 1.2240503 1282.5239
|
||||
2000 1 -0.37815616 0 0.30844982 1.0642877 1312.5691
|
||||
3000 1 -0.49062349 0 0.1959825 1.5239344 1322.2627
|
||||
4000 1 -0.50104941 0 0.18555657 1.4605776 1367.6505
|
||||
5000 1 -0.4655479 0 0.22105808 1.3317864 1406.9197
|
||||
6000 1 -0.50936502 0 0.17724096 1.2130158 1424.3621
|
||||
7000 1 -0.44959207 0 0.23701391 1.1070391 1443.1
|
||||
8000 1 -0.42617261 0 0.26043338 1.2005043 1444.8955
|
||||
9000 1 -0.41192389 0 0.2746821 1.0022569 1450.9691
|
||||
10000 1 -0.40940409 0 0.27720189 0.98653582 1447.7805
|
||||
11000 1 -0.4093125 0 0.27729348 1.0625786 1446.6852
|
||||
12000 1 -0.41948268 0 0.26712331 1.1166793 1449.6135
|
||||
13000 1 -0.38874722 0 0.29785877 0.99617473 1456.1633
|
||||
14000 1 -0.40067763 0 0.28592835 0.98191459 1454.6009
|
||||
15000 1 -0.39026612 0 0.29633987 1.0245506 1452.7783
|
||||
16000 1 -0.39139643 0 0.29520955 1.0281029 1451.2662
|
||||
17000 1 -0.37821271 0 0.30839327 1.0108601 1454.1047
|
||||
18000 1 -0.37382372 0 0.31278227 0.93743647 1457.2083
|
||||
19000 1 -0.3737367 0 0.31286928 1.0333603 1458.6131
|
||||
20000 1 -0.37232139 0 0.31428459 1.0471568 1448.6511
|
||||
21000 1 -0.40114891 0 0.28545707 1.0045402 1455.5644
|
||||
22000 1 -0.36552339 0 0.32108259 0.99841802 1459.4723
|
||||
23000 1 -0.35573934 0 0.33086665 0.89283563 1460.8941
|
||||
24000 1 -0.3608262 0 0.32577978 1.0097641 1453.0004
|
||||
25000 1 -0.36649381 0 0.32011217 0.98366691 1451.5444
|
||||
Loop time of 0.843615 on 4 procs for 25000 steps with 769 atoms
|
||||
|
||||
Pair time (%) = 0.125471 (14.873)
|
||||
Neigh time (%) = 0.0379742 (4.50136)
|
||||
Comm time (%) = 0.221488 (26.2546)
|
||||
Outpt time (%) = 0.000505328 (0.0599003)
|
||||
Other time (%) = 0.458177 (54.3111)
|
||||
|
||||
Nlocal: 192.25 ave 242 max 159 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Nghost: 43 ave 45 max 39 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 2 1
|
||||
Neighs: 414 ave 588 max 284 min
|
||||
Histogram: 2 0 0 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 1656
|
||||
Ave neighs/atom = 2.15345
|
||||
Neighbor list builds = 1641
|
||||
Dangerous builds = 1
|
||||
|
|
@ -0,0 +1,177 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
thermo_style multi
|
||||
thermo 50
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
|
||||
#dump 1 peptide atom 10 dump.peptide
|
||||
|
||||
#dump 2 peptide image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 peptide movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
#compute bnd all property/local btype batom1 batom2
|
||||
#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
|
||||
|
||||
run 300
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 10648 3375
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Memory usage per processor = 22.9109 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
|
||||
PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726
|
||||
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
|
||||
E_coul = 26772.2646 E_long = -33907.9271 Press = -845.4774
|
||||
---------------- Step 50 ----- CPU = 0.9759 (sec) ----------------
|
||||
TotEng = -5247.5490 KinEng = 1132.4011 Temp = 281.4748
|
||||
PotEng = -6379.9501 E_bond = 12.2118 E_angle = 31.7365
|
||||
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1771
|
||||
E_coul = 26804.4490 E_long = -33907.7002 Press = -1331.7981
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.111 7.80799e-07
|
||||
6 0.997 1.06209e-06
|
||||
8 1.08 6.20484e-07
|
||||
10 1.111 6.23445e-07
|
||||
12 1.08 2.68063e-07
|
||||
14 0.96 0
|
||||
18 0.957201 5.38018e-06
|
||||
31 104.52 0.000502316
|
||||
---------------- Step 100 ----- CPU = 1.9636 (sec) ----------------
|
||||
TotEng = -5257.9973 KinEng = 1078.0556 Temp = 267.9664
|
||||
PotEng = -6336.0529 E_bond = 14.4828 E_angle = 43.4429
|
||||
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3266
|
||||
E_coul = 26786.6840 E_long = -33906.5620 Press = -648.6639
|
||||
---------------- Step 150 ----- CPU = 2.9816 (sec) ----------------
|
||||
TotEng = -5287.2844 KinEng = 1098.6036 Temp = 273.0739
|
||||
PotEng = -6385.8881 E_bond = 17.4924 E_angle = 32.8593
|
||||
E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9685
|
||||
E_coul = 26717.2584 E_long = -33907.2812 Press = -333.1895
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 2.18836e-07
|
||||
6 0.997 1.50856e-07
|
||||
8 1.08 6.58343e-08
|
||||
10 1.111 5.55349e-07
|
||||
12 1.08 1.99243e-07
|
||||
14 0.96 0
|
||||
18 0.957201 3.59666e-06
|
||||
31 104.52 0.000388184
|
||||
---------------- Step 200 ----- CPU = 3.9551 (sec) ----------------
|
||||
TotEng = -5308.4528 KinEng = 1100.5056 Temp = 273.5467
|
||||
PotEng = -6408.9584 E_bond = 18.2714 E_angle = 33.3035
|
||||
E_dihed = 16.8150 E_impro = 2.6053 E_vdwl = 686.3261
|
||||
E_coul = 26736.1131 E_long = -33902.3928 Press = -1470.3871
|
||||
---------------- Step 250 ----- CPU = 4.9818 (sec) ----------------
|
||||
TotEng = -5294.1808 KinEng = 1071.1623 Temp = 266.2530
|
||||
PotEng = -6365.3431 E_bond = 14.2022 E_angle = 39.1953
|
||||
E_dihed = 19.4555 E_impro = 3.1387 E_vdwl = 753.5411
|
||||
E_coul = 26713.8466 E_long = -33908.7226 Press = -188.8083
|
||||
SHAKE stats (type/ave/delta) on step 300
|
||||
4 1.111 3.78266e-06
|
||||
6 0.997001 3.50137e-06
|
||||
8 1.08 2.09323e-06
|
||||
10 1.111 5.64331e-06
|
||||
12 1.08 2.10401e-06
|
||||
14 0.96 0
|
||||
18 0.957202 7.67992e-06
|
||||
31 104.52 0.000806336
|
||||
---------------- Step 300 ----- CPU = 6.0094 (sec) ----------------
|
||||
TotEng = -5251.4349 KinEng = 1123.6255 Temp = 279.2934
|
||||
PotEng = -6375.0604 E_bond = 14.2249 E_angle = 38.4712
|
||||
E_dihed = 18.1324 E_impro = 2.3700 E_vdwl = 715.4556
|
||||
E_coul = 26745.4104 E_long = -33909.1249 Press = -469.5456
|
||||
Loop time of 6.00943 on 1 procs for 300 steps with 2004 atoms
|
||||
|
||||
Pair time (%) = 4.59488 (76.4612)
|
||||
Bond time (%) = 0.0122511 (0.203865)
|
||||
Kspce time (%) = 0.654233 (10.8868)
|
||||
Neigh time (%) = 0.642603 (10.6932)
|
||||
Comm time (%) = 0.0338275 (0.562907)
|
||||
Outpt time (%) = 0.000135899 (0.00226142)
|
||||
Other time (%) = 0.0715001 (1.1898)
|
||||
|
||||
FFT time (% of Kspce) = 0.0813602 (12.436)
|
||||
FFT Gflps 3d (1d only) = 2.02205 3.15151
|
||||
|
||||
Nlocal: 2004 ave 2004 max 2004 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 11181 ave 11181 max 11181 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 708028 ave 708028 max 708028 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 708028
|
||||
Ave neighs/atom = 353.307
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 26
|
||||
Dangerous builds = 0
|
||||
|
||||
|
|
@ -0,0 +1,177 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Solvated 5-mer peptide
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
pair_style lj/charmm/coul/long 8.0 10.0 10.0
|
||||
bond_style harmonic
|
||||
angle_style charmm
|
||||
dihedral_style charmm
|
||||
improper_style harmonic
|
||||
kspace_style pppm 0.0001
|
||||
|
||||
read_data data.peptide
|
||||
orthogonal box = (36.8402 41.0137 29.7681) to (64.2116 68.3851 57.1395)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
2004 atoms
|
||||
reading velocities ...
|
||||
2004 velocities
|
||||
scanning bonds ...
|
||||
3 = max bonds/atom
|
||||
scanning angles ...
|
||||
6 = max angles/atom
|
||||
scanning dihedrals ...
|
||||
14 = max dihedrals/atom
|
||||
scanning impropers ...
|
||||
1 = max impropers/atom
|
||||
reading bonds ...
|
||||
1365 bonds
|
||||
reading angles ...
|
||||
786 angles
|
||||
reading dihedrals ...
|
||||
207 dihedrals
|
||||
reading impropers ...
|
||||
12 impropers
|
||||
4 = max # of 1-2 neighbors
|
||||
7 = max # of 1-3 neighbors
|
||||
14 = max # of 1-4 neighbors
|
||||
18 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
neigh_modify delay 5
|
||||
|
||||
timestep 2.0
|
||||
|
||||
thermo_style multi
|
||||
thermo 50
|
||||
|
||||
fix 1 all nvt temp 275.0 275.0 100.0 tchain 1
|
||||
fix 2 all shake 0.0001 10 100 b 4 6 8 10 12 14 18 a 31
|
||||
19 = # of size 2 clusters
|
||||
6 = # of size 3 clusters
|
||||
3 = # of size 4 clusters
|
||||
640 = # of frozen angles
|
||||
|
||||
group peptide type <= 12
|
||||
84 atoms in group peptide
|
||||
|
||||
#dump 1 peptide atom 10 dump.peptide
|
||||
|
||||
#dump 2 peptide image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
|
||||
#dump_modify 2 pad 3
|
||||
|
||||
#dump 3 peptide movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30 bond atom 0.5
|
||||
#dump_modify 3 pad 3
|
||||
|
||||
#compute bnd all property/local btype batom1 batom2
|
||||
#dump 2 peptide local 300 dump.bond index c_bnd[1] c_bnd[2] c_bnd[3]
|
||||
|
||||
run 300
|
||||
PPPM initialization ...
|
||||
G vector (1/distance) = 0.268725
|
||||
grid = 15 15 15
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.0228209
|
||||
estimated relative force accuracy = 6.87243e-05
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 4312 960
|
||||
SHAKE stats (type/ave/delta) on step 0
|
||||
4 1.111 1.44264e-05
|
||||
6 0.996998 7.26967e-06
|
||||
8 1.08 1.32536e-05
|
||||
10 1.111 1.22749e-05
|
||||
12 1.08 1.11767e-05
|
||||
14 0.96 0
|
||||
18 0.957206 4.37979e-05
|
||||
31 104.519 0.00396029
|
||||
Memory usage per processor = 10.3307 Mbytes
|
||||
---------------- Step 0 ----- CPU = 0.0000 (sec) ----------------
|
||||
TotEng = -5237.4580 KinEng = 1134.9186 Temp = 282.1005
|
||||
PotEng = -6372.3766 E_bond = 16.5572 E_angle = 36.3726
|
||||
E_dihed = 15.5190 E_impro = 1.9426 E_vdwl = 692.8945
|
||||
E_coul = 26772.2646 E_long = -33907.9271 Press = -845.4774
|
||||
---------------- Step 50 ----- CPU = 0.2818 (sec) ----------------
|
||||
TotEng = -5247.5490 KinEng = 1132.4011 Temp = 281.4748
|
||||
PotEng = -6379.9501 E_bond = 12.2118 E_angle = 31.7365
|
||||
E_dihed = 18.8145 E_impro = 2.3612 E_vdwl = 658.1771
|
||||
E_coul = 26804.4490 E_long = -33907.7002 Press = -1331.7981
|
||||
SHAKE stats (type/ave/delta) on step 100
|
||||
4 1.111 7.80799e-07
|
||||
6 0.997 1.06209e-06
|
||||
8 1.08 6.20484e-07
|
||||
10 1.111 6.23445e-07
|
||||
12 1.08 2.68063e-07
|
||||
14 0.96 0
|
||||
18 0.957201 5.38018e-06
|
||||
31 104.52 0.000502316
|
||||
---------------- Step 100 ----- CPU = 0.5690 (sec) ----------------
|
||||
TotEng = -5257.9973 KinEng = 1078.0556 Temp = 267.9664
|
||||
PotEng = -6336.0529 E_bond = 14.4828 E_angle = 43.4429
|
||||
E_dihed = 15.2569 E_impro = 2.3160 E_vdwl = 708.3266
|
||||
E_coul = 26786.6840 E_long = -33906.5620 Press = -648.6639
|
||||
---------------- Step 150 ----- CPU = 0.8614 (sec) ----------------
|
||||
TotEng = -5287.2845 KinEng = 1098.6036 Temp = 273.0739
|
||||
PotEng = -6385.8881 E_bond = 17.4924 E_angle = 32.8593
|
||||
E_dihed = 15.1623 E_impro = 1.6522 E_vdwl = 736.9685
|
||||
E_coul = 26717.2583 E_long = -33907.2812 Press = -333.1895
|
||||
SHAKE stats (type/ave/delta) on step 200
|
||||
4 1.111 2.18836e-07
|
||||
6 0.997 1.50856e-07
|
||||
8 1.08 6.58343e-08
|
||||
10 1.111 5.55349e-07
|
||||
12 1.08 1.99243e-07
|
||||
14 0.96 0
|
||||
18 0.957201 3.59666e-06
|
||||
31 104.52 0.000388184
|
||||
---------------- Step 200 ----- CPU = 1.1337 (sec) ----------------
|
||||
TotEng = -5308.4528 KinEng = 1100.5056 Temp = 273.5467
|
||||
PotEng = -6408.9584 E_bond = 18.2714 E_angle = 33.3035
|
||||
E_dihed = 16.8150 E_impro = 2.6053 E_vdwl = 686.3261
|
||||
E_coul = 26736.1131 E_long = -33902.3928 Press = -1470.3869
|
||||
---------------- Step 250 ----- CPU = 1.4284 (sec) ----------------
|
||||
TotEng = -5294.1808 KinEng = 1071.1623 Temp = 266.2530
|
||||
PotEng = -6365.3431 E_bond = 14.2022 E_angle = 39.1953
|
||||
E_dihed = 19.4555 E_impro = 3.1387 E_vdwl = 753.5412
|
||||
E_coul = 26713.8465 E_long = -33908.7226 Press = -188.8075
|
||||
SHAKE stats (type/ave/delta) on step 300
|
||||
4 1.111 3.78266e-06
|
||||
6 0.997001 3.50139e-06
|
||||
8 1.08 2.09322e-06
|
||||
10 1.111 5.6433e-06
|
||||
12 1.08 2.10401e-06
|
||||
14 0.96 0
|
||||
18 0.957202 7.6799e-06
|
||||
31 104.52 0.000806335
|
||||
---------------- Step 300 ----- CPU = 1.7292 (sec) ----------------
|
||||
TotEng = -5251.4350 KinEng = 1123.6255 Temp = 279.2935
|
||||
PotEng = -6375.0605 E_bond = 14.2249 E_angle = 38.4712
|
||||
E_dihed = 18.1324 E_impro = 2.3700 E_vdwl = 715.4558
|
||||
E_coul = 26745.4101 E_long = -33909.1248 Press = -469.5428
|
||||
Loop time of 1.72924 on 4 procs for 300 steps with 2004 atoms
|
||||
|
||||
Pair time (%) = 1.18646 (68.6113)
|
||||
Bond time (%) = 0.0033986 (0.196537)
|
||||
Kspce time (%) = 0.24268 (14.0339)
|
||||
Neigh time (%) = 0.165521 (9.5719)
|
||||
Comm time (%) = 0.0693463 (4.01021)
|
||||
Outpt time (%) = 0.000285089 (0.0164864)
|
||||
Other time (%) = 0.0615544 (3.55962)
|
||||
|
||||
FFT time (% of Kspce) = 0.0323979 (13.35)
|
||||
FFT Gflps 3d (1d only) = 5.07792 11.9536
|
||||
|
||||
Nlocal: 501 ave 508 max 490 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
Nghost: 6586.25 ave 6628 max 6548 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
Neighs: 177007 ave 180562 max 170212 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||
|
||||
Total # of neighbors = 708028
|
||||
Ave neighs/atom = 353.307
|
||||
Ave special neighs/atom = 2.34032
|
||||
Neighbor list builds = 26
|
||||
Dangerous builds = 0
|
||||
|
||||
|
|
@ -0,0 +1,90 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# small Peridynamic cylinder hit by projectile
|
||||
|
||||
units si
|
||||
boundary s s s
|
||||
atom_style peri
|
||||
atom_modify map array
|
||||
neighbor 0.0010 bin
|
||||
|
||||
# small target
|
||||
|
||||
lattice sc 0.0005
|
||||
Lattice spacing in x,y,z = 0.0005 0.0005 0.0005
|
||||
region target cylinder y 0.0 0.0 0.0050 -0.0050 0.0 units box
|
||||
create_box 1 target
|
||||
Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region target
|
||||
Created 3487 atoms
|
||||
|
||||
pair_style peri/pmb
|
||||
pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
|
||||
set group all density 2200
|
||||
3487 settings made for density
|
||||
set group all volume 1.25e-10
|
||||
3487 settings made for volume
|
||||
velocity all set 0.0 0.0 0.0 sum no units box
|
||||
fix 1 all nve
|
||||
|
||||
# spherical indenter to shatter target
|
||||
|
||||
variable y0 equal 0.00155
|
||||
variable vy equal -100
|
||||
variable y equal "v_y0 + step*dt*v_vy"
|
||||
|
||||
fix 2 all indent 1e17 sphere 0.0000 v_y 0.0000 0.0015 units box
|
||||
|
||||
compute 1 all damage/atom
|
||||
timestep 1.0e-7
|
||||
thermo 100
|
||||
|
||||
#dump 1 all custom 100 dump.peri id type x y z c_1
|
||||
|
||||
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
run 1000
|
||||
Peridynamic bonds:
|
||||
total # of bonds = 335966
|
||||
bonds/atom = 96.3482
|
||||
Memory usage per processor = 24.2469 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0 0 0 0 0 5.0030006e-07
|
||||
100 1.7890585e+24 552721.8 0 681881.47 1.7210968e+11 5.0030006e-07
|
||||
200 1.3549879e+27 3097027.6 0 1.0091931e+08 1.1829272e+14 5.5130066e-07
|
||||
300 3.3009625e+27 6331254.8 0 2.4464163e+08 1.9647265e+14 8.0862953e-07
|
||||
400 3.815184e+27 6225081.7 0 2.8165928e+08 1.8189267e+14 1.0095118e-06
|
||||
500 4.2580877e+27 20212686 0 3.2762196e+08 1.6249923e+14 1.2611723e-06
|
||||
600 5.5126512e+27 30861342 0 4.2884284e+08 1.7320038e+14 1.531873e-06
|
||||
700 1.1807414e+28 23119941 0 8.7554687e+08 2.9477434e+14 1.9278632e-06
|
||||
800 1.2424839e+28 2407365.2 0 8.994088e+08 2.3787786e+14 2.5138992e-06
|
||||
900 1.2358398e+28 4532421.1 0 8.9673716e+08 1.9097317e+14 3.1145903e-06
|
||||
1000 1.2341036e+28 3219688.2 0 8.9417102e+08 1.596857e+14 3.7196039e-06
|
||||
Loop time of 19.4915 on 1 procs for 1000 steps with 3487 atoms
|
||||
|
||||
Pair time (%) = 18.802 (96.4629)
|
||||
Neigh time (%) = 0.572242 (2.93586)
|
||||
Comm time (%) = 0.00180793 (0.00927548)
|
||||
Outpt time (%) = 0.000235081 (0.00120607)
|
||||
Other time (%) = 0.115146 (0.59075)
|
||||
|
||||
Nlocal: 3487 ave 3487 max 3487 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 567135 ave 567135 max 567135 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 1.20908e+06 ave 1.20908e+06 max 1.20908e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1209076
|
||||
Ave neighs/atom = 346.738
|
||||
Neighbor list builds = 46
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,90 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# small Peridynamic cylinder hit by projectile
|
||||
|
||||
units si
|
||||
boundary s s s
|
||||
atom_style peri
|
||||
atom_modify map array
|
||||
neighbor 0.0010 bin
|
||||
|
||||
# small target
|
||||
|
||||
lattice sc 0.0005
|
||||
Lattice spacing in x,y,z = 0.0005 0.0005 0.0005
|
||||
region target cylinder y 0.0 0.0 0.0050 -0.0050 0.0 units box
|
||||
create_box 1 target
|
||||
Created orthogonal box = (-0.005 -0.005 -0.005) to (0.005 0 0.005)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
create_atoms 1 region target
|
||||
Created 3487 atoms
|
||||
|
||||
pair_style peri/pmb
|
||||
pair_coeff * * 1.6863e22 0.0015001 0.0005 0.25
|
||||
set group all density 2200
|
||||
3487 settings made for density
|
||||
set group all volume 1.25e-10
|
||||
3487 settings made for volume
|
||||
velocity all set 0.0 0.0 0.0 sum no units box
|
||||
fix 1 all nve
|
||||
|
||||
# spherical indenter to shatter target
|
||||
|
||||
variable y0 equal 0.00155
|
||||
variable vy equal -100
|
||||
variable y equal "v_y0 + step*dt*v_vy"
|
||||
|
||||
fix 2 all indent 1e17 sphere 0.0000 v_y 0.0000 0.0015 units box
|
||||
|
||||
compute 1 all damage/atom
|
||||
timestep 1.0e-7
|
||||
thermo 100
|
||||
|
||||
#dump 1 all custom 100 dump.peri id type x y z c_1
|
||||
|
||||
#dump 2 all image 50 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
|
||||
#dump_modify 2 pad 4
|
||||
|
||||
#dump 3 all movie 50 movie.mpg type type # axes yes 0.8 0.02 view 80 -30 adiam 0.0006
|
||||
#dump_modify 3 pad 4
|
||||
|
||||
run 1000
|
||||
Peridynamic bonds:
|
||||
total # of bonds = 335966
|
||||
bonds/atom = 96.3482
|
||||
Memory usage per processor = 18.744 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press Volume
|
||||
0 0 0 0 0 0 5.0030006e-07
|
||||
100 1.7890585e+24 552721.8 0 681881.47 1.7210968e+11 5.0030006e-07
|
||||
200 1.3549879e+27 3097027.6 0 1.0091931e+08 1.1829272e+14 5.5130066e-07
|
||||
300 3.3009625e+27 6331254.8 0 2.4464163e+08 1.9647265e+14 8.0862953e-07
|
||||
400 3.815184e+27 6225081.7 0 2.8165928e+08 1.8189267e+14 1.0095118e-06
|
||||
500 4.2580877e+27 20212686 0 3.2762196e+08 1.6249923e+14 1.2611723e-06
|
||||
600 5.5126512e+27 30861342 0 4.2884284e+08 1.7320038e+14 1.531873e-06
|
||||
700 1.1807414e+28 23119941 0 8.7554687e+08 2.9477434e+14 1.9278632e-06
|
||||
800 1.2424839e+28 2407365.3 0 8.994088e+08 2.3787786e+14 2.5138992e-06
|
||||
900 1.2358398e+28 4532419.8 0 8.9673716e+08 1.9097317e+14 3.1145903e-06
|
||||
1000 1.2341036e+28 3219727.8 0 8.9417105e+08 1.596857e+14 3.7196039e-06
|
||||
Loop time of 5.56029 on 4 procs for 1000 steps with 3487 atoms
|
||||
|
||||
Pair time (%) = 4.77191 (85.8212)
|
||||
Neigh time (%) = 0.146942 (2.64271)
|
||||
Comm time (%) = 0.597594 (10.7475)
|
||||
Outpt time (%) = 0.000327229 (0.00588511)
|
||||
Other time (%) = 0.0435197 (0.782687)
|
||||
|
||||
Nlocal: 871.75 ave 910 max 835 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
Nghost: 1343.25 ave 1380 max 1305 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 141784 ave 170146 max 116083 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
FullNghs: 302269 ave 346070 max 260820 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 1209076
|
||||
Ave neighs/atom = 346.738
|
||||
Neighbor list builds = 46
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,147 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Pour granular particles into chute container, then induce flow
|
||||
|
||||
atom_style sphere
|
||||
boundary p p fm
|
||||
newton off
|
||||
communicate single vel yes
|
||||
|
||||
region reg block -10 10 -10 10 -0.5 16 units box
|
||||
create_box 1 reg
|
||||
Created orthogonal box = (-10 -10 -0.5) to (10 10 16)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
neighbor 0.2 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
|
||||
# are used in this example file to produce a quick simulation and movie.
|
||||
# More appropriate values for realistic simulations would be
|
||||
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
|
||||
|
||||
pair_style gran/hooke/history 2000.0 NULL 50.0 NULL 0.5 0
|
||||
pair_coeff * *
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all nve/sphere
|
||||
fix 2 all gravity 1.0 spherical 0.0 -180.0
|
||||
fix zlower all wall/gran 2000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 2000.0
|
||||
|
||||
region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
|
||||
fix ins all pour 3000 1 300719 vol 0.13 50 region slab
|
||||
Particle insertion: 402 every 3162 steps, 3000 by step 22135
|
||||
|
||||
compute 1 all erotate/sphere
|
||||
thermo_style custom step atoms ke c_1 vol
|
||||
thermo 1000
|
||||
thermo_modify lost ignore norm no
|
||||
compute_modify thermo_temp dynamic yes
|
||||
|
||||
#dump id all atom 1000 dump.pour
|
||||
|
||||
#dump 2 all image 1000 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 1000 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
run 25000
|
||||
Memory usage per processor = 8.27911 Mbytes
|
||||
Step Atoms KinEng 1 Volume
|
||||
0 0 -0 0 6600
|
||||
1000 402 768.04606 0 6600
|
||||
2000 402 1407.1714 0 6600
|
||||
3000 402 1373.819 15.59952 6600
|
||||
4000 804 1737.1399 39.311164 6600
|
||||
5000 804 1571.3184 67.501382 6600
|
||||
6000 804 1318.6439 77.636174 6600
|
||||
7000 1206 1522.1986 68.863683 6600
|
||||
8000 1206 1387.2223 64.067846 6600
|
||||
9000 1206 1265.901 51.727094 6600
|
||||
10000 1608 1460.2854 48.630285 6600
|
||||
11000 1608 1310.6204 52.851955 6600
|
||||
12000 1608 1128.6198 46.139167 6600
|
||||
13000 2010 1178.8622 50.202317 6600
|
||||
14000 2010 1187.0109 39.476651 6600
|
||||
15000 2010 989.72713 38.740987 6600
|
||||
16000 2412 1120.2349 40.342828 6600
|
||||
17000 2412 1075.0554 39.589605 6600
|
||||
18000 2412 855.00318 40.858609 6600
|
||||
19000 2814 950.88458 41.511679 6600
|
||||
20000 2814 923.42023 36.068246 6600
|
||||
21000 2814 794.06955 41.150212 6600
|
||||
22000 2814 548.02348 35.370804 6600
|
||||
23000 3000 463.81576 37.573817 6600
|
||||
24000 3000 336.43523 25.743644 6600
|
||||
25000 3000 234.89941 20.298489 6600
|
||||
Loop time of 9.30611 on 1 procs for 25000 steps with 3000 atoms
|
||||
|
||||
Pair time (%) = 5.33047 (57.2792)
|
||||
Neigh time (%) = 1.05786 (11.3674)
|
||||
Comm time (%) = 0.251292 (2.70029)
|
||||
Outpt time (%) = 0.000475883 (0.00511366)
|
||||
Other time (%) = 2.66602 (28.648)
|
||||
|
||||
Nlocal: 3000 ave 3000 max 3000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 671 ave 671 max 671 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 13616 ave 13616 max 13616 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 13616
|
||||
Ave neighs/atom = 4.53867
|
||||
Neighbor list builds = 1149
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix ins
|
||||
fix 2 all gravity 1.0 chute 26.0
|
||||
run 25000
|
||||
Memory usage per processor = 9.07965 Mbytes
|
||||
Step Atoms KinEng 1 Volume
|
||||
25000 3000 234.89941 20.298489 6600
|
||||
26000 3000 82.315315 21.537116 6600
|
||||
27000 3000 108.89519 11.940364 6600
|
||||
28000 3000 200.16687 11.301946 6600
|
||||
29000 3000 349.26838 15.094407 6600
|
||||
30000 3000 569.81999 18.792925 6600
|
||||
31000 3000 898.94346 28.160958 6600
|
||||
32000 3000 1240.4814 33.875237 6600
|
||||
33000 3000 1731.5017 41.915333 6600
|
||||
34000 3000 2295.7732 48.265714 6600
|
||||
35000 3000 2886.4882 61.48829 6600
|
||||
36000 3000 3662.1785 79.477977 6600
|
||||
37000 3000 4508.9506 87.503245 6600
|
||||
38000 3000 5487.5698 105.18573 6600
|
||||
39000 3000 6502.5504 107.5985 6600
|
||||
40000 3000 7472.1021 126.10799 6600
|
||||
41000 3000 8747.8718 152.09945 6600
|
||||
42000 3000 10083.088 151.89644 6600
|
||||
43000 3000 11433.111 170.87026 6600
|
||||
44000 3000 12876.825 194.58992 6600
|
||||
45000 3000 14274.884 189.94299 6600
|
||||
46000 3000 15664.174 225.06085 6600
|
||||
47000 3000 17213.88 222.67736 6600
|
||||
48000 3000 18826.294 240.96943 6600
|
||||
49000 3000 20558.693 264.45506 6600
|
||||
50000 3000 22270.716 276.57672 6600
|
||||
Loop time of 18.1762 on 1 procs for 25000 steps with 3000 atoms
|
||||
|
||||
Pair time (%) = 11.5992 (63.8153)
|
||||
Neigh time (%) = 1.71333 (9.42624)
|
||||
Comm time (%) = 0.540144 (2.97171)
|
||||
Outpt time (%) = 0.000629663 (0.00346421)
|
||||
Other time (%) = 4.32291 (23.7833)
|
||||
|
||||
Nlocal: 3000 ave 3000 max 3000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 760 ave 760 max 760 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 14151 ave 14151 max 14151 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 14151
|
||||
Ave neighs/atom = 4.717
|
||||
Neighbor list builds = 873
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,147 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Pour granular particles into chute container, then induce flow
|
||||
|
||||
atom_style sphere
|
||||
boundary p p fm
|
||||
newton off
|
||||
communicate single vel yes
|
||||
|
||||
region reg block -10 10 -10 10 -0.5 16 units box
|
||||
create_box 1 reg
|
||||
Created orthogonal box = (-10 -10 -0.5) to (10 10 16)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
|
||||
neighbor 0.2 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
# IMPORTANT NOTE: these values of stiffness (2000) and timestep (0.001)
|
||||
# are used in this example file to produce a quick simulation and movie.
|
||||
# More appropriate values for realistic simulations would be
|
||||
# k = 2.0e5 and dt = 0.0001, as in bench/in.chute.
|
||||
|
||||
pair_style gran/hooke/history 2000.0 NULL 50.0 NULL 0.5 0
|
||||
pair_coeff * *
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all nve/sphere
|
||||
fix 2 all gravity 1.0 spherical 0.0 -180.0
|
||||
fix zlower all wall/gran 2000.0 NULL 50.0 NULL 0.5 0 zplane 0.0 2000.0
|
||||
|
||||
region slab block -9.0 9.0 -9.0 9.0 10.0 15.0 units box
|
||||
fix ins all pour 3000 1 300719 vol 0.13 50 region slab
|
||||
Particle insertion: 402 every 3162 steps, 3000 by step 22135
|
||||
|
||||
compute 1 all erotate/sphere
|
||||
thermo_style custom step atoms ke c_1 vol
|
||||
thermo 1000
|
||||
thermo_modify lost ignore norm no
|
||||
compute_modify thermo_temp dynamic yes
|
||||
|
||||
#dump id all atom 1000 dump.pour
|
||||
|
||||
#dump 2 all image 1000 image.*.jpg type type # axes yes 0.8 0.02 view 80 -30
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 1000 movie.mpg type type # axes yes 0.8 0.02 view 80 -30
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
run 25000
|
||||
Memory usage per processor = 8.15424 Mbytes
|
||||
Step Atoms KinEng 1 Volume
|
||||
0 0 -0 0 6600
|
||||
1000 402 768.04606 0 6600
|
||||
2000 402 1407.1714 0 6600
|
||||
3000 402 1373.819 15.59952 6600
|
||||
4000 804 1737.1399 39.311164 6600
|
||||
5000 804 1571.3184 67.501382 6600
|
||||
6000 804 1318.6439 77.636174 6600
|
||||
7000 1206 1521.8348 69.010381 6600
|
||||
8000 1206 1391.0761 64.407585 6600
|
||||
9000 1206 1264.9766 50.327155 6600
|
||||
10000 1608 1463.0633 49.89601 6600
|
||||
11000 1608 1316.7149 52.402835 6600
|
||||
12000 1608 1114.153 46.872522 6600
|
||||
13000 2010 1205.8869 51.481237 6600
|
||||
14000 2010 1185.8628 42.191907 6600
|
||||
15000 2010 972.77031 43.899414 6600
|
||||
16000 2412 1104.0835 40.181571 6600
|
||||
17000 2412 1071.8592 41.109972 6600
|
||||
18000 2412 855.89199 38.898224 6600
|
||||
19000 2814 974.59266 41.798845 6600
|
||||
20000 2814 949.73588 41.312762 6600
|
||||
21000 2814 785.75949 39.506434 6600
|
||||
22000 2814 568.33487 35.152281 6600
|
||||
23000 3000 469.29459 37.172088 6600
|
||||
24000 3000 335.08614 25.096975 6600
|
||||
25000 3000 235.38783 16.956807 6600
|
||||
Loop time of 2.9825 on 4 procs for 25000 steps with 3000 atoms
|
||||
|
||||
Pair time (%) = 1.36805 (45.8694)
|
||||
Neigh time (%) = 0.27838 (9.33378)
|
||||
Comm time (%) = 0.419477 (14.0646)
|
||||
Outpt time (%) = 0.000649214 (0.0217675)
|
||||
Other time (%) = 0.915936 (30.7104)
|
||||
|
||||
Nlocal: 750 ave 767 max 740 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
Nghost: 389 ave 399 max 379 min
|
||||
Histogram: 1 0 0 0 0 2 0 0 0 1
|
||||
Neighs: 3555.75 ave 3653 max 3498 min
|
||||
Histogram: 2 0 0 0 1 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 14223
|
||||
Ave neighs/atom = 4.741
|
||||
Neighbor list builds = 1151
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix ins
|
||||
fix 2 all gravity 1.0 chute 26.0
|
||||
run 25000
|
||||
Memory usage per processor = 8.928 Mbytes
|
||||
Step Atoms KinEng 1 Volume
|
||||
25000 3000 235.38783 16.956807 6600
|
||||
26000 3000 86.095398 21.734167 6600
|
||||
27000 3000 105.34548 13.070765 6600
|
||||
28000 3000 194.48452 12.668302 6600
|
||||
29000 3000 338.66556 14.53448 6600
|
||||
30000 3000 561.95176 20.01635 6600
|
||||
31000 3000 863.55789 28.935939 6600
|
||||
32000 3000 1245.8566 31.126919 6600
|
||||
33000 3000 1747.0561 43.002491 6600
|
||||
34000 3000 2297.4715 52.916382 6600
|
||||
35000 3000 2979.0692 60.599758 6600
|
||||
36000 3000 3668.5934 70.783571 6600
|
||||
37000 3000 4550.9061 84.848649 6600
|
||||
38000 3000 5458.0534 96.028867 6600
|
||||
39000 3000 6461.8152 108.41301 6600
|
||||
40000 3000 7504.9659 119.17697 6600
|
||||
41000 3000 8622.1932 129.66834 6600
|
||||
42000 3000 9729.2779 150.83916 6600
|
||||
43000 3000 11006.529 161.20608 6600
|
||||
44000 3000 12332.682 172.45763 6600
|
||||
45000 3000 13532.399 168.86419 6600
|
||||
46000 3000 14872.632 194.18978 6600
|
||||
47000 3000 16262.818 209.10627 6600
|
||||
48000 3000 17620.467 204.85493 6600
|
||||
49000 3000 19038.858 242.63587 6600
|
||||
50000 3000 20554.586 248.70106 6600
|
||||
Loop time of 5.60379 on 4 procs for 25000 steps with 3000 atoms
|
||||
|
||||
Pair time (%) = 3.03686 (54.193)
|
||||
Neigh time (%) = 0.445322 (7.94679)
|
||||
Comm time (%) = 0.673944 (12.0266)
|
||||
Outpt time (%) = 0.000772476 (0.0137849)
|
||||
Other time (%) = 1.44689 (25.8198)
|
||||
|
||||
Nlocal: 750 ave 766 max 736 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Nghost: 402.75 ave 414 max 392 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Neighs: 3675.25 ave 3716 max 3594 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 2 1
|
||||
|
||||
Total # of neighbors = 14701
|
||||
Ave neighs/atom = 4.90033
|
||||
Neighbor list builds = 859
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,100 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Pour 2d granular particles into container
|
||||
|
||||
dimension 2
|
||||
atom_style sphere
|
||||
boundary f fm p
|
||||
newton off
|
||||
communicate single vel yes
|
||||
|
||||
region reg block 0 100 0 50 -0.5 0.5 units box
|
||||
create_box 1 reg
|
||||
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
neighbor 0.2 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
|
||||
# are used in this example file to produce a quick simulation and movie.
|
||||
# More appropriate values for realistic simulations would be
|
||||
# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
|
||||
|
||||
pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
|
||||
pair_coeff * *
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all nve/sphere
|
||||
fix 2 all gravity 1.0 spherical 0.0 -180.0
|
||||
fix xwalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
|
||||
fix ywalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
|
||||
|
||||
region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
|
||||
fix ins all pour 1000 1 4767548 vol 0.4 10 diam range 0.5 1.0 region slab
|
||||
Particle insertion: 224 every 3000 steps, 1000 by step 12001
|
||||
|
||||
fix 3 all enforce2d
|
||||
|
||||
compute 1 all erotate/sphere
|
||||
thermo_style custom step atoms ke c_1 vol
|
||||
thermo 1000
|
||||
thermo_modify lost ignore norm no
|
||||
compute_modify thermo_temp dynamic yes
|
||||
|
||||
#dump id all atom 250 dump.pour
|
||||
|
||||
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
run 25000
|
||||
Memory usage per processor = 8.39742 Mbytes
|
||||
Step Atoms KinEng 1 Volume
|
||||
0 0 -0 0 5000
|
||||
1000 224 201.77464 0 5000
|
||||
2000 224 372.42868 0 5000
|
||||
3000 224 599.60221 0 5000
|
||||
4000 448 1084.3752 0 5000
|
||||
5000 448 1592.4543 0 5000
|
||||
6000 448 1763.3153 37.274939 5000
|
||||
7000 672 1805.206 89.331853 5000
|
||||
8000 672 1778.0015 111.58381 5000
|
||||
9000 672 1592.6805 97.550227 5000
|
||||
10000 896 1632.2116 76.952268 5000
|
||||
11000 896 1594.7057 65.263337 5000
|
||||
12000 896 1539.5424 56.179956 5000
|
||||
13000 1000 1502.7779 61.791119 5000
|
||||
14000 1000 1264.0565 50.885098 5000
|
||||
15000 1000 1028.8287 48.271488 5000
|
||||
16000 1000 742.47431 43.031382 5000
|
||||
17000 1000 466.70958 35.374711 5000
|
||||
18000 1000 311.97604 30.342738 5000
|
||||
19000 1000 217.15209 31.325292 5000
|
||||
20000 1000 53.963502 21.545193 5000
|
||||
21000 1000 20.574937 12.436765 5000
|
||||
22000 1000 14.952026 8.8587603 5000
|
||||
23000 1000 12.308193 7.3973013 5000
|
||||
24000 1000 11.398735 5.1815744 5000
|
||||
25000 1000 10.066348 4.0359674 5000
|
||||
Loop time of 2.91316 on 1 procs for 25000 steps with 1000 atoms
|
||||
|
||||
Pair time (%) = 1.21785 (41.8051)
|
||||
Neigh time (%) = 0.312445 (10.7253)
|
||||
Comm time (%) = 0.0109541 (0.376022)
|
||||
Outpt time (%) = 0.000334263 (0.0114742)
|
||||
Other time (%) = 1.37158 (47.0821)
|
||||
|
||||
Nlocal: 1000 ave 1000 max 1000 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2362 ave 2362 max 2362 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2362
|
||||
Ave neighs/atom = 2.362
|
||||
Neighbor list builds = 2038
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,100 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Pour 2d granular particles into container
|
||||
|
||||
dimension 2
|
||||
atom_style sphere
|
||||
boundary f fm p
|
||||
newton off
|
||||
communicate single vel yes
|
||||
|
||||
region reg block 0 100 0 50 -0.5 0.5 units box
|
||||
create_box 1 reg
|
||||
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
|
||||
4 by 1 by 1 MPI processor grid
|
||||
|
||||
neighbor 0.2 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
|
||||
# are used in this example file to produce a quick simulation and movie.
|
||||
# More appropriate values for realistic simulations would be
|
||||
# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
|
||||
|
||||
pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
|
||||
pair_coeff * *
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 1 all nve/sphere
|
||||
fix 2 all gravity 1.0 spherical 0.0 -180.0
|
||||
fix xwalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
|
||||
fix ywalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
|
||||
|
||||
region slab block 1.0 99.0 30 34.5 -0.5 0.5 units box
|
||||
fix ins all pour 1000 1 4767548 vol 0.4 10 diam range 0.5 1.0 region slab
|
||||
Particle insertion: 224 every 3000 steps, 1000 by step 12001
|
||||
|
||||
fix 3 all enforce2d
|
||||
|
||||
compute 1 all erotate/sphere
|
||||
thermo_style custom step atoms ke c_1 vol
|
||||
thermo 1000
|
||||
thermo_modify lost ignore norm no
|
||||
compute_modify thermo_temp dynamic yes
|
||||
|
||||
#dump id all atom 250 dump.pour
|
||||
|
||||
#dump 2 all image 500 image.*.jpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 5
|
||||
|
||||
#dump 3 all movie 500 movie.mpg type type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 5
|
||||
|
||||
run 25000
|
||||
Memory usage per processor = 8.36296 Mbytes
|
||||
Step Atoms KinEng 1 Volume
|
||||
0 0 -0 0 5000
|
||||
1000 224 201.77464 0 5000
|
||||
2000 224 372.42868 0 5000
|
||||
3000 224 599.60221 0 5000
|
||||
4000 448 1084.3752 0 5000
|
||||
5000 448 1592.4543 0 5000
|
||||
6000 448 1763.3153 37.274939 5000
|
||||
7000 672 1805.206 89.331853 5000
|
||||
8000 672 1778.0015 111.58381 5000
|
||||
9000 672 1592.6805 97.550227 5000
|
||||
10000 896 1631.0865 79.644395 5000
|
||||
11000 896 1592.1233 66.618058 5000
|
||||
12000 896 1538.0168 62.305427 5000
|
||||
13000 1000 1504.7663 60.453118 5000
|
||||
14000 1000 1258.4278 56.953463 5000
|
||||
15000 1000 1051.3757 49.481041 5000
|
||||
16000 1000 745.26845 46.064462 5000
|
||||
17000 1000 461.4175 44.190391 5000
|
||||
18000 1000 321.52252 32.000638 5000
|
||||
19000 1000 219.94195 27.786071 5000
|
||||
20000 1000 47.588667 19.150667 5000
|
||||
21000 1000 22.265142 13.29654 5000
|
||||
22000 1000 16.795774 9.1519062 5000
|
||||
23000 1000 14.227042 7.3286667 5000
|
||||
24000 1000 10.712738 5.4385743 5000
|
||||
25000 1000 9.180883 3.4376108 5000
|
||||
Loop time of 0.936714 on 4 procs for 25000 steps with 1000 atoms
|
||||
|
||||
Pair time (%) = 0.304334 (32.4896)
|
||||
Neigh time (%) = 0.0807448 (8.62001)
|
||||
Comm time (%) = 0.0846794 (9.04005)
|
||||
Outpt time (%) = 0.000462651 (0.0493909)
|
||||
Other time (%) = 0.466493 (49.801)
|
||||
|
||||
Nlocal: 250 ave 260 max 230 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
Nghost: 17.5 ave 24 max 12 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 1 1
|
||||
Neighs: 598.25 ave 630 max 546 min
|
||||
Histogram: 1 0 0 0 0 0 1 0 1 1
|
||||
|
||||
Total # of neighbors = 2393
|
||||
Ave neighs/atom = 2.393
|
||||
Neighbor list builds = 2035
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,113 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Pour 2d granular particles into container
|
||||
|
||||
dimension 2
|
||||
atom_style sphere
|
||||
atom_modify map array
|
||||
boundary f fm p
|
||||
newton off
|
||||
communicate single vel yes cutoff 2.5
|
||||
|
||||
fix prop all property/atom mol
|
||||
|
||||
region reg block 0 100 0 50 -0.5 0.5 units box
|
||||
create_box 1 reg
|
||||
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
|
||||
neighbor 0.2 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
|
||||
# are used in this example file to produce a quick simulation and movie.
|
||||
# More appropriate values for realistic simulations would be
|
||||
# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
|
||||
|
||||
pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
|
||||
pair_coeff * *
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 2 all gravity 1.0 spherical 0.0 -180.0
|
||||
fix xwalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
|
||||
fix ywalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
|
||||
|
||||
molecule object molecule.vshape
|
||||
fix 3 all rigid/small molecule mol object
|
||||
0 rigid bodies with 0 atoms
|
||||
2.23607 = max distance from body owner to body atom
|
||||
|
||||
# insure region size + molecule size does not overlap wall
|
||||
|
||||
region slab block 3.0 97.0 30 34.5 -0.5 0.5 units box
|
||||
fix ins all pour 500 0 4767548 vol 0.8 10 region slab mol object rigid 3
|
||||
Particle insertion: 26 every 3000 steps, 500 by step 57001
|
||||
|
||||
fix 4 all enforce2d
|
||||
|
||||
compute 1 all erotate/sphere
|
||||
thermo_style custom step atoms ke c_1 vol
|
||||
thermo 1000
|
||||
thermo_modify lost ignore norm no
|
||||
compute_modify thermo_temp dynamic yes
|
||||
|
||||
#dump id all atom 100 tmp.dump
|
||||
|
||||
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
|
||||
#variable mol2 atom mol%10
|
||||
#dump 2 all image 250 image.*.jpg v_mol2 type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 5 amap 0 10 sa 1 10 ${colors}
|
||||
|
||||
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
|
||||
#variable mol3 atom mol%10
|
||||
#dump 3 all movie 250 movie.mpg v_mol3 type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
|
||||
|
||||
run 25000
|
||||
Memory usage per processor = 8.8613 Mbytes
|
||||
Step Atoms KinEng 1 Volume
|
||||
0 0 -0 0 5000
|
||||
1000 130 208.5324 0.0022531902 5000
|
||||
2000 130 395.40215 0.0022531902 5000
|
||||
3000 130 647.2719 0.0022531902 5000
|
||||
4000 260 1159.1081 0.0026224951 5000
|
||||
5000 260 1718.8157 0.0026515989 5000
|
||||
6000 260 2031.535 10.691958 5000
|
||||
7000 390 2065.2783 21.015337 5000
|
||||
8000 390 1911.4694 10.935944 5000
|
||||
9000 390 1884.4332 7.8649255 5000
|
||||
10000 520 2109.7343 6.3162072 5000
|
||||
11000 520 2055.0964 9.2024202 5000
|
||||
12000 520 1737.7978 3.8651428 5000
|
||||
13000 650 1827.8021 5.4025759 5000
|
||||
14000 650 1714.9891 5.1408637 5000
|
||||
15000 650 1460.3591 1.9883146 5000
|
||||
16000 780 1656.7752 2.6070722 5000
|
||||
17000 780 1487.906 2.9690473 5000
|
||||
18000 780 1508.32 2.4036266 5000
|
||||
19000 910 1508.0974 5.3892045 5000
|
||||
20000 910 1310.8002 4.8125827 5000
|
||||
21000 910 1044.281 2.4533982 5000
|
||||
22000 1040 1188.4887 1.8312293 5000
|
||||
23000 1040 1405.6437 2.4849983 5000
|
||||
24000 1040 1287.8333 2.4405773 5000
|
||||
25000 1170 1190.5047 2.8533518 5000
|
||||
Loop time of 3.16526 on 1 procs for 25000 steps with 1170 atoms
|
||||
|
||||
Pair time (%) = 0.829346 (26.2015)
|
||||
Neigh time (%) = 0.207036 (6.54087)
|
||||
Comm time (%) = 0.0133698 (0.422392)
|
||||
Outpt time (%) = 0.000298738 (0.00943804)
|
||||
Other time (%) = 2.11521 (66.8258)
|
||||
|
||||
Nlocal: 1170 ave 1170 max 1170 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 1707 ave 1707 max 1707 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 1707
|
||||
Ave neighs/atom = 1.45897
|
||||
Neighbor list builds = 1751
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,113 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# Pour 2d granular particles into container
|
||||
|
||||
dimension 2
|
||||
atom_style sphere
|
||||
atom_modify map array
|
||||
boundary f fm p
|
||||
newton off
|
||||
communicate single vel yes cutoff 2.5
|
||||
|
||||
fix prop all property/atom mol
|
||||
|
||||
region reg block 0 100 0 50 -0.5 0.5 units box
|
||||
create_box 1 reg
|
||||
Created orthogonal box = (0 0 -0.5) to (100 50 0.5)
|
||||
4 by 1 by 1 MPI processor grid
|
||||
|
||||
neighbor 0.2 bin
|
||||
neigh_modify delay 0
|
||||
|
||||
# IMPORTANT NOTE: these values of stiffness (4000) and timestep (0.001)
|
||||
# are used in this example file to produce a quick simulation and movie.
|
||||
# More appropriate values for realistic simulations would be
|
||||
# k = 4.0e5 and dt = 0.0001, as in bench/in.chute (if it were Hertzian).
|
||||
|
||||
pair_style gran/hertz/history 4000.0 NULL 100.0 NULL 0.5 0
|
||||
pair_coeff * *
|
||||
|
||||
timestep 0.001
|
||||
|
||||
fix 2 all gravity 1.0 spherical 0.0 -180.0
|
||||
fix xwalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 xplane 0 100
|
||||
fix ywalls all wall/gran 4000.0 NULL 100.0 NULL 0 1 yplane 0 NULL
|
||||
|
||||
molecule object molecule.vshape
|
||||
fix 3 all rigid/small molecule mol object
|
||||
0 rigid bodies with 0 atoms
|
||||
2.23607 = max distance from body owner to body atom
|
||||
|
||||
# insure region size + molecule size does not overlap wall
|
||||
|
||||
region slab block 3.0 97.0 30 34.5 -0.5 0.5 units box
|
||||
fix ins all pour 500 0 4767548 vol 0.8 10 region slab mol object rigid 3
|
||||
Particle insertion: 26 every 3000 steps, 500 by step 57001
|
||||
|
||||
fix 4 all enforce2d
|
||||
|
||||
compute 1 all erotate/sphere
|
||||
thermo_style custom step atoms ke c_1 vol
|
||||
thermo 1000
|
||||
thermo_modify lost ignore norm no
|
||||
compute_modify thermo_temp dynamic yes
|
||||
|
||||
#dump id all atom 100 tmp.dump
|
||||
|
||||
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
|
||||
#variable mol2 atom mol%10
|
||||
#dump 2 all image 250 image.*.jpg v_mol2 type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 2 pad 5 amap 0 10 sa 1 10 ${colors}
|
||||
|
||||
#variable colors string # "red green blue yellow white # purple pink orange lime gray"
|
||||
#variable mol3 atom mol%10
|
||||
#dump 3 all movie 250 movie.mpg v_mol3 type # zoom 1.6 adiam 1.5
|
||||
#dump_modify 3 pad 5 amap 0 10 sa 1 10 ${colors}
|
||||
|
||||
run 25000
|
||||
Memory usage per processor = 8.82364 Mbytes
|
||||
Step Atoms KinEng 1 Volume
|
||||
0 0 -0 0 5000
|
||||
1000 130 208.5324 0.0022531902 5000
|
||||
2000 130 395.40215 0.0022531902 5000
|
||||
3000 130 647.2719 0.0022531902 5000
|
||||
4000 260 1159.1081 0.0026224951 5000
|
||||
5000 260 1718.8157 0.0026515989 5000
|
||||
6000 260 2031.535 10.691958 5000
|
||||
7000 390 2065.2783 21.015337 5000
|
||||
8000 390 1911.4694 10.935944 5000
|
||||
9000 390 1884.4332 7.8649255 5000
|
||||
10000 520 2109.7343 6.3162072 5000
|
||||
11000 520 2055.0964 9.2024202 5000
|
||||
12000 520 1737.7978 3.8651428 5000
|
||||
13000 650 1835.9412 5.4696261 5000
|
||||
14000 650 1705.5968 4.6127934 5000
|
||||
15000 650 1458.6093 2.3324994 5000
|
||||
16000 780 1663.1206 3.4762842 5000
|
||||
17000 780 1448.6268 2.5272414 5000
|
||||
18000 780 1439.06 2.3644535 5000
|
||||
19000 910 1353.2736 3.4079237 5000
|
||||
20000 910 1303.0395 4.7540237 5000
|
||||
21000 910 1037.3662 2.6725377 5000
|
||||
22000 1040 1225.3222 2.0920106 5000
|
||||
23000 1040 1306.8689 2.4710217 5000
|
||||
24000 1040 1304.5309 2.5544338 5000
|
||||
25000 1170 1181.4033 4.5232994 5000
|
||||
Loop time of 1.24255 on 4 procs for 25000 steps with 1170 atoms
|
||||
|
||||
Pair time (%) = 0.219425 (17.6592)
|
||||
Neigh time (%) = 0.0621997 (5.00579)
|
||||
Comm time (%) = 0.0965945 (7.77386)
|
||||
Outpt time (%) = 0.000469327 (0.0377711)
|
||||
Other time (%) = 0.863865 (69.5234)
|
||||
|
||||
Nlocal: 292.5 ave 312 max 278 min
|
||||
Histogram: 1 1 0 0 0 1 0 0 0 1
|
||||
Nghost: 44.5 ave 60 max 28 min
|
||||
Histogram: 1 1 0 0 0 0 0 0 0 2
|
||||
Neighs: 427.5 ave 451 max 399 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 1710
|
||||
Ave neighs/atom = 1.46154
|
||||
Neighbor list builds = 1769
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,631 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
Processor partition = 0
|
||||
# Parallel replica dynamics model for a single vacancy in bulk Si
|
||||
# events occur when a neighboring atom diffuses to the vacant site
|
||||
# run this on multiple partitions as
|
||||
# mpirun -np 4 lmp_g++ -partition 4x1 -in in.prd
|
||||
|
||||
#log none
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# coordination number cutoff
|
||||
|
||||
variable r equal 2.835
|
||||
|
||||
# minimization parameters
|
||||
|
||||
variable etol equal 1.0e-5
|
||||
variable ftol equal 1.0e-5
|
||||
variable maxiter equal 100
|
||||
variable maxeval equal 100
|
||||
variable dmax equal 1.0e-1
|
||||
|
||||
# diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
||||
|
||||
region myreg block 0 4 0 4 0 4
|
||||
create_box 1 myreg
|
||||
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region myreg
|
||||
Created 512 atoms
|
||||
|
||||
mass 1 28.06
|
||||
|
||||
group Si type 1
|
||||
512 atoms in group Si
|
||||
|
||||
velocity all create $t 5287287 mom yes rot yes dist gaussian
|
||||
velocity all create 1800 5287287 mom yes rot yes dist gaussian
|
||||
|
||||
# make a vacancy
|
||||
|
||||
group del id 300
|
||||
1 atoms in group del
|
||||
delete_atoms group del
|
||||
Deleted 1 atoms, new total = 511
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si
|
||||
|
||||
thermo 10
|
||||
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
||||
# equilibrate
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 2.0318 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1802.5039 -2211.666 0 -2092.8401 12351.692
|
||||
10 996.01982 -2158.3093 0 -2092.649 14285.475
|
||||
20 590.09928 -2131.1531 0 -2092.2521 12113.964
|
||||
30 1033.01 -2159.2522 0 -2091.1534 6860.4116
|
||||
40 724.76581 -2137.281 0 -2089.5025 5999.4372
|
||||
50 489.66604 -2120.8082 0 -2088.5281 6403.4234
|
||||
60 960.70653 -2150.7394 0 -2087.407 5687.324
|
||||
70 908.41498 -2145.7665 0 -2085.8813 8220.9655
|
||||
80 796.82286 -2137.1227 0 -2084.5941 11307.153
|
||||
90 1245.9045 -2164.9841 0 -2082.8507 11282.071
|
||||
100 1083.0647 -2152.0805 0 -2080.682 12015.018
|
||||
Loop time of 0.193601 on 1 procs for 100 steps with 511 atoms
|
||||
|
||||
Pair time (%) = 0.189505 (97.8843)
|
||||
Neigh time (%) = 0.001369 (0.707125)
|
||||
Comm time (%) = 0.000830412 (0.42893)
|
||||
Outpt time (%) = 7.77245e-05 (0.0401467)
|
||||
Other time (%) = 0.0018189 (0.939508)
|
||||
|
||||
Nlocal: 511 ave 511 max 511 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1017 ave 1017 max 1017 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 13996 ave 13996 max 13996 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 13996
|
||||
Ave neighs/atom = 27.3894
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
# only output atoms near vacancy
|
||||
|
||||
compute coord all coord/atom $r
|
||||
compute coord all coord/atom 2.835
|
||||
|
||||
#dump events all custom 1 dump.prd id type x y z
|
||||
#dump_modify events thresh c_coord != 4
|
||||
|
||||
compute patom all pe/atom
|
||||
compute pe all reduce sum c_patom
|
||||
compute satom all stress/atom
|
||||
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
|
||||
|
||||
thermo_style custom step temp pe c_pe press v_press
|
||||
|
||||
compute 1 all event/displace 0.5
|
||||
|
||||
prd 2000 100 10 10 100 1 54985 temp $t min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
|
||||
prd 2000 100 10 10 100 1 54985 temp 1800 min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
|
||||
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 ${ftol} ${maxiter} ${maxeval} vel all uniform
|
||||
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 ${maxiter} ${maxeval} vel all uniform
|
||||
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 100 ${maxeval} vel all uniform
|
||||
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 100 100 vel all uniform
|
||||
WARNING: Resetting reneighboring criteria during PRD (../prd.cpp:201)
|
||||
Memory usage per processor = 3.74841 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
|
||||
110 1083.0647 -2211.0684 -2211.0684 7372.2593 -7372.2593
|
||||
119 1083.0647 -2211.6557 -2211.6557 7411.1722 -7411.1722
|
||||
Loop time of 0.0540199 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
|
||||
110 1453.2509 -2126.4979 -2126.4979 16449.583 -16449.583
|
||||
120 1640.3958 -2113.5727 -2113.5727 18469.616 -18469.616
|
||||
130 1765.8167 -2109.1554 -2109.1554 19438.152 -19438.152
|
||||
140 1727.5983 -2102.4557 -2102.4557 18703.763 -18703.763
|
||||
150 1873.8652 -2105.5049 -2105.5049 18700.015 -18700.015
|
||||
160 1740.1521 -2099.9445 -2099.9445 17850.695 -17850.695
|
||||
170 1854.5372 -2101.9702 -2101.9702 17723.367 -17723.367
|
||||
180 1788.5252 -2099.7644 -2099.7644 17796.757 -17796.757
|
||||
190 1782.0313 -2097.2111 -2097.2111 17085.932 -17085.932
|
||||
200 1761.1774 -2093.3215 -2093.3215 16509.756 -16509.756
|
||||
Loop time of 0.219058 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
100 1761.1774 -2093.3215 -2093.3215 16509.756 -16509.756
|
||||
110 1739.6511 -2090.6077 -2090.6077 15948.63 -15948.63
|
||||
120 1712.9864 -2087.5346 -2087.5346 16028.758 -16028.758
|
||||
130 1632.023 -2080.8455 -2080.8455 16292.761 -16292.761
|
||||
140 1733.3057 -2086.0742 -2086.0742 15090.31 -15090.31
|
||||
150 1739.3938 -2084.9124 -2084.9124 15081.918 -15081.918
|
||||
160 1656.2093 -2077.9071 -2077.9071 16611.003 -16611.003
|
||||
170 1734.9792 -2081.5311 -2081.5311 16511.598 -16511.598
|
||||
180 1867.0258 -2088.5786 -2088.5786 16517.663 -16517.663
|
||||
190 1859.2979 -2086.5014 -2086.5014 15835.134 -15835.134
|
||||
200 1868.7353 -2085.7395 -2085.7395 15039.302 -15039.302
|
||||
Loop time of 0.226545 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
200 1868.7353 -2085.7395 -2085.7395 15039.302 -15039.302
|
||||
216 1868.7353 -2213.2677 -2213.2677 9444.9178 -9444.9178
|
||||
Loop time of 0.0423551 on 1 procs for 16 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
200 1868.7353 -2083.245 -2083.245 15572.348 -15572.348
|
||||
210 1881.8867 -2082.857 -2082.857 15333.566 -15333.566
|
||||
220 1935.757 -2085.3056 -2085.3056 15507.872 -15507.872
|
||||
230 1912.3683 -2082.841 -2082.841 14338.661 -14338.661
|
||||
240 1753.2588 -2071.6079 -2071.6079 13605.421 -13605.421
|
||||
250 1728.2117 -2069.2341 -2069.2341 12820.588 -12820.588
|
||||
260 1835.1212 -2075.4787 -2075.4787 11970.037 -11970.037
|
||||
270 1760.8425 -2069.7609 -2069.7609 13431.399 -13431.399
|
||||
280 1819.1145 -2072.7978 -2072.7978 13843.416 -13843.416
|
||||
290 1931.6502 -2079.3975 -2079.3975 14257.316 -14257.316
|
||||
300 1991.315 -2082.6543 -2082.6543 15669.782 -15669.782
|
||||
Loop time of 0.233078 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
300 1991.315 -2082.6543 -2082.6543 15669.782 -15669.782
|
||||
318 1991.315 -2213.2946 -2213.2946 10290.671 -10290.671
|
||||
Loop time of 0.0492001 on 1 procs for 18 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
300 1991.315 -2082.6543 -2082.6543 15669.782 -15669.782
|
||||
310 1912.141 -2083.3513 -2083.3513 14100.457 -14100.457
|
||||
320 1767.1362 -2080.7508 -2080.7508 13738.15 -13738.15
|
||||
330 1893.2627 -2086.4709 -2086.4709 13308.437 -13308.437
|
||||
340 1779.3615 -2084.7222 -2084.7222 11290.367 -11290.367
|
||||
350 1840.5794 -2087.0052 -2087.0052 12245.306 -12245.306
|
||||
360 1712.927 -2080.8869 -2080.8869 11630.287 -11630.287
|
||||
370 1795.1829 -2080.1542 -2080.1542 11903.52 -11903.52
|
||||
380 1828.9719 -2081.6588 -2081.6588 12611.779 -12611.779
|
||||
390 1860.397 -2085.2626 -2085.2626 11645.979 -11645.979
|
||||
400 1720.6814 -2079.6644 -2079.6644 10689.828 -10689.828
|
||||
Loop time of 0.235478 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
300 1720.6814 -2079.6644 -2079.6644 10689.828 -10689.828
|
||||
310 1717.6388 -2079.0268 -2079.0268 10581.957 -10581.957
|
||||
320 1789.9235 -2083.2531 -2083.2531 11258.441 -11258.441
|
||||
330 1764.9794 -2081.0181 -2081.0181 11462.171 -11462.171
|
||||
340 1726.7798 -2077.8759 -2077.8759 11685.977 -11685.977
|
||||
350 1794.5158 -2081.6454 -2081.6454 11583.204 -11583.204
|
||||
360 1808.19 -2081.8003 -2081.8003 12387.732 -12387.732
|
||||
370 1858.3457 -2084.3825 -2084.3825 13197.68 -13197.68
|
||||
380 1906.8872 -2086.92 -2086.92 13054.839 -13054.839
|
||||
390 1848.16 -2082.5114 -2082.5114 13515.286 -13515.286
|
||||
400 1820.8925 -2080.2663 -2080.2663 13488.79 -13488.79
|
||||
Loop time of 0.235724 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
400 1820.8925 -2080.2663 -2080.2663 13488.79 -13488.79
|
||||
417 1820.8925 -2213.2897 -2213.2897 9117.3067 -9117.3067
|
||||
Loop time of 0.0444851 on 1 procs for 17 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
400 1820.8925 -2080.2663 -2080.2663 13488.79 -13488.79
|
||||
410 1847.8771 -2081.6391 -2081.6391 12838.569 -12838.569
|
||||
420 1782.8346 -2076.9831 -2076.9831 12294.226 -12294.226
|
||||
430 1758.055 -2074.9742 -2074.9742 11409.107 -11409.107
|
||||
440 1849.7159 -2080.6063 -2080.6063 11615.729 -11615.729
|
||||
450 1869.1231 -2081.506 -2081.506 12455.826 -12455.826
|
||||
460 1790.313 -2075.9994 -2075.9994 13049.633 -13049.633
|
||||
470 1815.1995 -2077.3516 -2077.3516 13045.061 -13045.061
|
||||
480 1880.6611 -2081.396 -2081.396 11970.764 -11970.764
|
||||
490 1815.7853 -2076.9102 -2076.9102 12251.974 -12251.974
|
||||
500 1864.8064 -2080.0034 -2080.0034 11181.614 -11181.614
|
||||
Loop time of 0.237723 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
500 1864.8064 -2080.0034 -2080.0034 11181.614 -11181.614
|
||||
517 1864.8064 -2213.2124 -2213.2124 9411.2128 -9411.2128
|
||||
Loop time of 0.044066 on 1 procs for 17 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
500 1864.8064 -2080.0034 -2080.0034 11181.614 -11181.614
|
||||
510 1834.5308 -2077.9186 -2077.9186 12623.531 -12623.531
|
||||
520 1821.9414 -2077.0496 -2077.0496 13905.708 -13905.708
|
||||
530 1926.5524 -2083.9748 -2083.9748 14022.223 -14022.223
|
||||
540 1900.0475 -2082.3932 -2082.3932 13519.516 -13519.516
|
||||
550 1844.7474 -2079.0522 -2079.0522 13017.172 -13017.172
|
||||
560 1851.9925 -2079.9135 -2079.9135 12830.136 -12830.136
|
||||
570 1817.9413 -2078.1133 -2078.1133 12446.332 -12446.332
|
||||
580 1765.4615 -2075.1011 -2075.1011 11172.734 -11172.734
|
||||
590 1841.9645 -2080.5964 -2080.5964 11252.344 -11252.344
|
||||
600 1832.5281 -2080.4681 -2080.4681 13212.158 -13212.158
|
||||
Loop time of 0.232043 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
600 1832.5281 -2080.4681 -2080.4681 13212.158 -13212.158
|
||||
619 1832.5281 -2213.2705 -2213.2705 9195.2704 -9195.2704
|
||||
Loop time of 0.0436239 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
600 1832.5281 -2080.4681 -2080.4681 13212.158 -13212.158
|
||||
610 1787.5429 -2078.0256 -2078.0256 13240.463 -13240.463
|
||||
620 1823.7995 -2080.9486 -2080.9486 12375.051 -12375.051
|
||||
630 1853.2062 -2083.4589 -2083.4589 12983.625 -12983.625
|
||||
640 1834.2035 -2082.851 -2082.851 13067.13 -13067.13
|
||||
650 1789.0195 -2080.5378 -2080.5378 12947.796 -12947.796
|
||||
660 1805.2876 -2082.2756 -2082.2756 12528.317 -12528.317
|
||||
670 1839.5253 -2085.2087 -2085.2087 12508.998 -12508.998
|
||||
680 1819.135 -2084.6004 -2084.6004 12615.631 -12615.631
|
||||
690 1742.0477 -2080.2199 -2080.2199 12867.541 -12867.541
|
||||
700 1771.846 -2082.8491 -2082.8491 11627.605 -11627.605
|
||||
Loop time of 0.225684 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
700 1771.846 -2082.8491 -2082.8491 11627.605 -11627.605
|
||||
716 1771.846 -2213.2414 -2213.2414 8780.9495 -8780.9495
|
||||
Loop time of 0.036298 on 1 procs for 16 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
700 1771.846 -2088.3939 -2088.3939 12152.346 -12152.346
|
||||
710 1762.7562 -2088.4048 -2088.4048 11588.828 -11588.828
|
||||
720 1677.307 -2083.3065 -2083.3065 10323.038 -10323.038
|
||||
730 1638.8947 -2081.1322 -2081.1322 10662.708 -10662.708
|
||||
740 1733.4188 -2087.5736 -2087.5736 11190.078 -11190.078
|
||||
750 1745.235 -2088.4473 -2088.4473 12275.541 -12275.541
|
||||
760 1799.948 -2092.108 -2092.108 13287.26 -13287.26
|
||||
770 1805.9054 -2092.5319 -2092.5319 14221.436 -14221.436
|
||||
780 1802.4038 -2092.3583 -2092.3583 13453.411 -13453.411
|
||||
790 1728.5017 -2087.5173 -2087.5173 12749.412 -12749.412
|
||||
800 1695.7727 -2085.3213 -2085.3213 12245.9 -12245.9
|
||||
Loop time of 0.226421 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
800 1695.7727 -2085.3213 -2085.3213 12245.9 -12245.9
|
||||
817 1695.7727 -2213.2643 -2213.2643 8256.0666 -8256.0666
|
||||
Loop time of 0.04529 on 1 procs for 17 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
800 1695.7727 -2085.3213 -2085.3213 12245.9 -12245.9
|
||||
810 1723.8878 -2077.4775 -2077.4775 14056.576 -14056.576
|
||||
820 1819.4569 -2078.5591 -2078.5591 14126.224 -14126.224
|
||||
830 1857.684 -2082.1666 -2082.1666 13988.119 -13988.119
|
||||
840 1817.2451 -2083.1231 -2083.1231 13507.31 -13507.31
|
||||
850 1801.7367 -2083.0485 -2083.0485 13398.987 -13398.987
|
||||
860 1800.2129 -2082.8677 -2082.8677 13538.068 -13538.068
|
||||
870 1829.4598 -2084.6232 -2084.6232 13353.506 -13353.506
|
||||
880 1713.8058 -2078.7287 -2078.7287 12668.351 -12668.351
|
||||
890 1801.1051 -2078.5303 -2078.5303 12620.955 -12620.955
|
||||
900 1878.837 -2083.4562 -2083.4562 12162.469 -12162.469
|
||||
Loop time of 0.227319 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
800 1878.837 -2083.4562 -2083.4562 12162.469 -12162.469
|
||||
810 1875.9494 -2083.067 -2083.067 12404.086 -12404.086
|
||||
820 1765.2324 -2075.6435 -2075.6435 12708.749 -12708.749
|
||||
830 1805.1712 -2078.1447 -2078.1447 12187.198 -12187.198
|
||||
840 1899.9714 -2084.2726 -2084.2726 12555.644 -12555.644
|
||||
850 1823.6926 -2079.2062 -2079.2062 12933.086 -12933.086
|
||||
860 1809.2646 -2078.2623 -2078.2623 11742.131 -11742.131
|
||||
870 1909.7967 -2084.9627 -2084.9627 11229.754 -11229.754
|
||||
880 1764.4244 -2075.5143 -2075.5143 11457.095 -11457.095
|
||||
890 1771.6808 -2076.1399 -2076.1399 11453.854 -11453.854
|
||||
900 1865.5698 -2082.4582 -2082.4582 11659.558 -11659.558
|
||||
Loop time of 0.22751 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
900 1865.5698 -2082.4582 -2082.4582 11659.558 -11659.558
|
||||
919 1865.5698 -2213.3124 -2213.3124 9426.4803 -9426.4803
|
||||
Loop time of 0.0489779 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
900 1865.5698 -2081.8053 -2081.8053 13628.128 -13628.128
|
||||
910 1841.8133 -2080.4515 -2080.4515 13654.3 -13654.3
|
||||
920 1749.7144 -2074.6188 -2074.6188 12839.204 -12839.204
|
||||
930 1821.6017 -2079.6013 -2079.6013 12167.782 -12167.782
|
||||
940 1780.9248 -2077.1578 -2077.1578 12235.554 -12235.554
|
||||
950 1762.8345 -2076.2012 -2076.2012 11833.919 -11833.919
|
||||
960 1806.203 -2079.2727 -2079.2727 12022.387 -12022.387
|
||||
970 1804.2459 -2079.3716 -2079.3716 12365.406 -12365.406
|
||||
980 1761.8387 -2076.7964 -2076.7964 12458.703 -12458.703
|
||||
990 1836.2958 -2081.9304 -2081.9304 12598.164 -12598.164
|
||||
1000 1865.0257 -2084.1008 -2084.1008 13918.459 -13918.459
|
||||
Loop time of 0.227019 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1000 1865.0257 -2084.1008 -2084.1008 13918.459 -13918.459
|
||||
1017 1865.0257 -2213.2668 -2213.2668 9416.317 -9416.317
|
||||
Loop time of 0.0422699 on 1 procs for 17 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1000 1865.0257 -2084.1008 -2084.1008 13918.459 -13918.459
|
||||
1010 1761.782 -2083.3408 -2083.3408 12613.089 -12613.089
|
||||
1020 1770.1696 -2081.6751 -2081.6751 12434.518 -12434.518
|
||||
1030 1768.5769 -2079.8994 -2079.8994 12854.085 -12854.085
|
||||
1040 1792.1357 -2079.6761 -2079.6761 12773.174 -12773.174
|
||||
1050 1806.4749 -2080.3993 -2080.3993 13958.637 -13958.637
|
||||
1060 1845.1324 -2083.7096 -2083.7096 13427.182 -13427.182
|
||||
1070 1876.1853 -2089.1565 -2089.1565 12775.944 -12775.944
|
||||
1080 1765.8044 -2087.3727 -2087.3727 12387.705 -12387.705
|
||||
1090 1838.2298 -2090.426 -2090.426 12939.571 -12939.571
|
||||
1100 1704.553 -2084.6714 -2084.6714 12988.172 -12988.172
|
||||
Loop time of 0.229601 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1000 1704.553 -2084.6714 -2084.6714 12988.172 -12988.172
|
||||
1010 1772.8609 -2089.6666 -2089.6666 12540.188 -12540.188
|
||||
1020 1770.1379 -2089.9786 -2089.9786 12184.488 -12184.488
|
||||
1030 1656.6786 -2082.9255 -2082.9255 12022.316 -12022.316
|
||||
1040 1702.4827 -2086.2684 -2086.2684 10641.654 -10641.654
|
||||
1050 1674.8977 -2084.6421 -2084.6421 11257.979 -11257.979
|
||||
1060 1676.1205 -2084.7766 -2084.7766 12111.764 -12111.764
|
||||
1070 1778.8497 -2091.4724 -2091.4724 12971.534 -12971.534
|
||||
1080 1779.3081 -2091.3613 -2091.3613 12566.776 -12566.776
|
||||
1090 1668.192 -2083.8243 -2083.8243 12813.326 -12813.326
|
||||
1100 1754.5887 -2089.1711 -2089.1711 13090.818 -13090.818
|
||||
Loop time of 0.232132 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1100 1754.5887 -2089.1711 -2089.1711 13090.818 -13090.818
|
||||
1116 1754.5887 -2213.2659 -2213.2659 8660.0106 -8660.0106
|
||||
Loop time of 0.0410199 on 1 procs for 16 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1100 1754.5887 -2089.1711 -2089.1711 13090.818 -13090.818
|
||||
1110 1848.3952 -2094.8662 -2094.8662 12871.151 -12871.151
|
||||
1120 1738.0586 -2087.0603 -2087.0603 13998.616 -13998.616
|
||||
1130 1728.3695 -2085.8036 -2085.8036 14319.362 -14319.362
|
||||
1140 1841.826 -2092.4967 -2092.4967 13691.837 -13691.837
|
||||
1150 1797.9782 -2088.7251 -2088.7251 13942.683 -13942.683
|
||||
1160 1783.6033 -2086.8622 -2086.8622 13738.416 -13738.416
|
||||
1170 1807.3027 -2087.4147 -2087.4147 13420.976 -13420.976
|
||||
1180 1815.9792 -2086.9303 -2086.9303 12722.057 -12722.057
|
||||
1190 1739.4179 -2080.8105 -2080.8105 12854.023 -12854.023
|
||||
1200 1761.8697 -2081.1857 -2081.1857 12092.665 -12092.665
|
||||
Loop time of 0.226831 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1200 1761.8697 -2081.1857 -2081.1857 12092.665 -12092.665
|
||||
1218 1761.8697 -2213.3017 -2213.3017 8713.6317 -8713.6317
|
||||
Loop time of 0.0469732 on 1 procs for 18 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1200 1761.8697 -2081.1857 -2081.1857 12092.665 -12092.665
|
||||
1210 1760.7244 -2079.9528 -2079.9528 12012.593 -12012.593
|
||||
1220 1752.9287 -2078.2871 -2078.2871 11916.806 -11916.806
|
||||
1230 1838.3629 -2082.7918 -2082.7918 12841.149 -12841.149
|
||||
1240 1870.3467 -2083.881 -2083.881 13974.686 -13974.686
|
||||
1250 1781.4455 -2077.1866 -2077.1866 13743.967 -13743.967
|
||||
1260 1829.5891 -2079.6638 -2079.6638 12847.61 -12847.61
|
||||
1270 1859.3421 -2081.0235 -2081.0235 12227.579 -12227.579
|
||||
1280 1778.2976 -2075.2099 -2075.2099 12092.041 -12092.041
|
||||
1290 1802.5006 -2076.4007 -2076.4007 12166.805 -12166.805
|
||||
1300 1858.5552 -2079.7352 -2079.7352 12469.68 -12469.68
|
||||
Loop time of 0.228306 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1300 1858.5552 -2079.7352 -2079.7352 12469.68 -12469.68
|
||||
1319 1858.5552 -2213.2905 -2213.2905 9377.5263 -9377.5263
|
||||
Loop time of 0.052316 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1300 1858.5552 -2079.7352 -2079.7352 12469.68 -12469.68
|
||||
1310 1883.892 -2081.1414 -2081.1414 13154.969 -13154.969
|
||||
1320 1918.1413 -2083.2747 -2083.2747 14133.403 -14133.403
|
||||
1330 1939.2365 -2084.7147 -2084.7147 14302.027 -14302.027
|
||||
1340 1866.4525 -2080.1222 -2080.1222 14374.257 -14374.257
|
||||
1350 1810.4562 -2076.7079 -2076.7079 12997.156 -12997.156
|
||||
1360 1814.6292 -2077.2746 -2077.2746 11910.098 -11910.098
|
||||
1370 1755.1167 -2073.6137 -2073.6137 11855.888 -11855.888
|
||||
1380 1782.5531 -2075.6399 -2075.6399 12156.35 -12156.35
|
||||
1390 1816.7724 -2078.0849 -2078.0849 12765.305 -12765.305
|
||||
1400 1837.2515 -2079.6383 -2079.6383 13124.564 -13124.564
|
||||
Loop time of 0.226051 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1400 1837.2515 -2079.6383 -2079.6383 13124.564 -13124.564
|
||||
1418 1837.2515 -2213.2909 -2213.2909 9231.4256 -9231.4256
|
||||
Loop time of 0.045156 on 1 procs for 18 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1400 1837.2515 -2083.1407 -2083.1407 12986.943 -12986.943
|
||||
1410 1822.713 -2082.4248 -2082.4248 14004.789 -14004.789
|
||||
1420 1832.5229 -2083.3398 -2083.3398 15470.52 -15470.52
|
||||
1430 1914.5807 -2089.0996 -2089.0996 15354.125 -15354.125
|
||||
1440 1857.9286 -2085.8454 -2085.8454 13988.104 -13988.104
|
||||
1450 1754.4226 -2079.5406 -2079.5406 13819.892 -13819.892
|
||||
1460 1818.444 -2084.2673 -2084.2673 12996.924 -12996.924
|
||||
1470 1825.4699 -2085.2741 -2085.2741 12289.466 -12289.466
|
||||
1480 1723.4843 -2079.0743 -2079.0743 12726.17 -12726.17
|
||||
1490 1818.4232 -2085.8377 -2085.8377 12243.424 -12243.424
|
||||
1500 1808.3404 -2085.6948 -2085.6948 11928.53 -11928.53
|
||||
Loop time of 0.228146 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1500 1808.3404 -2085.6948 -2085.6948 11928.53 -11928.53
|
||||
1519 1808.3404 -2213.302 -2213.302 9037.7704 -9037.7704
|
||||
Loop time of 0.0519381 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1500 1808.3404 -2088.1491 -2088.1491 13315.668 -13315.668
|
||||
1510 1935.1323 -2097.1896 -2097.1896 13464.858 -13464.858
|
||||
1520 1678.3356 -2081.0029 -2081.0029 13813.289 -13813.289
|
||||
1530 1740.6495 -2085.7701 -2085.7701 12852.328 -12852.328
|
||||
1540 1858.7458 -2094.2425 -2094.2425 11105.92 -11105.92
|
||||
1550 1599.0288 -2077.7804 -2077.7804 10438.389 -10438.389
|
||||
1560 1555.965 -2075.3756 -2075.3756 11066.476 -11066.476
|
||||
1570 1782.1645 -2090.5618 -2090.5618 11513.89 -11513.89
|
||||
1580 1639.6945 -2081.3242 -2081.3242 13028.031 -13028.031
|
||||
1590 1706.6709 -2085.7625 -2085.7625 13989.78 -13989.78
|
||||
1600 2022.0741 -2106.5216 -2106.5216 14373.472 -14373.472
|
||||
Loop time of 0.226441 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1600 2022.0741 -2106.5216 -2106.5216 14373.472 -14373.472
|
||||
1617 2022.0741 -2213.2036 -2213.2036 10476.808 -10476.808
|
||||
Loop time of 0.0424151 on 1 procs for 17 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1600 2022.0741 -2106.5216 -2106.5216 14373.472 -14373.472
|
||||
1610 1709.9018 -2082.1738 -2082.1738 11779.399 -11779.399
|
||||
1620 1843.2806 -2085.0227 -2085.0227 12079.368 -12079.368
|
||||
1630 1781.7944 -2083.8272 -2083.8272 11339.308 -11339.308
|
||||
1640 1858.9199 -2087.7445 -2087.7445 11680.172 -11680.172
|
||||
1650 1676.4808 -2079.6354 -2079.6354 10807.862 -10807.862
|
||||
1660 1784.4381 -2078.5909 -2078.5909 10825.528 -10825.528
|
||||
1670 1797.7974 -2078.4044 -2078.4044 11402.613 -11402.613
|
||||
1680 1832.5315 -2080.5079 -2080.5079 12031.263 -12031.263
|
||||
1690 1859.9425 -2084.4511 -2084.4511 12027.239 -12027.239
|
||||
1700 1746.6608 -2080.9402 -2080.9402 11194.592 -11194.592
|
||||
Loop time of 0.226718 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1600 1746.6608 -2080.9402 -2080.9402 11194.592 -11194.592
|
||||
1610 1719.0554 -2079.054 -2079.054 11178.847 -11178.847
|
||||
1620 1785.874 -2083.3136 -2083.3136 11151.584 -11151.584
|
||||
1630 1709.212 -2078.0262 -2078.0262 11909.487 -11909.487
|
||||
1640 1724.909 -2078.7337 -2078.7337 12338.207 -12338.207
|
||||
1650 1851.0445 -2086.6016 -2086.6016 13182.101 -13182.101
|
||||
1660 1877.9938 -2087.9289 -2087.9289 13545.96 -13545.96
|
||||
1670 1859.7098 -2086.3587 -2086.3587 13586.735 -13586.735
|
||||
1680 1856.0077 -2085.8266 -2085.8266 13326.439 -13326.439
|
||||
1690 1852.5537 -2085.3781 -2085.3781 12829.132 -12829.132
|
||||
1700 1781.9012 -2080.5479 -2080.5479 11799.182 -11799.182
|
||||
Loop time of 0.229575 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1700 1781.9012 -2080.5479 -2080.5479 11799.182 -11799.182
|
||||
1719 1781.9012 -2213.2828 -2213.2828 8850.0906 -8850.0906
|
||||
Loop time of 0.0428071 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1700 1781.9012 -2080.5479 -2080.5479 11799.182 -11799.182
|
||||
1710 1744.9008 -2077.9268 -2077.9268 11732.091 -11732.091
|
||||
1720 1752.0816 -2078.1361 -2078.1361 11741.531 -11741.531
|
||||
1730 1828.2888 -2082.842 -2082.842 11720.773 -11720.773
|
||||
1740 1786.3351 -2079.7361 -2079.7361 12450.459 -12450.459
|
||||
1750 1778.8339 -2078.8936 -2078.8936 13103.956 -13103.956
|
||||
1760 1869.5607 -2084.4952 -2084.4952 13328.105 -13328.105
|
||||
1770 1901.6696 -2086.2777 -2086.2777 13723.6 -13723.6
|
||||
1780 1863.4556 -2083.5556 -2083.5556 14468.139 -14468.139
|
||||
1790 1783.3884 -2078.1381 -2078.1381 14221.764 -14221.764
|
||||
1800 1808.5452 -2079.6622 -2079.6622 12177.545 -12177.545
|
||||
Loop time of 0.227294 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1800 1808.5452 -2079.6622 -2079.6622 12177.545 -12177.545
|
||||
1819 1808.5452 -2213.309 -2213.309 9036.9782 -9036.9782
|
||||
Loop time of 0.0526731 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1800 1808.5452 -2076.1141 -2076.1141 12641.91 -12641.91
|
||||
1810 1782.0254 -2074.2029 -2074.2029 11987.656 -11987.656
|
||||
1820 1834.1279 -2077.4569 -2077.4569 11478.352 -11478.352
|
||||
1830 1791.6785 -2074.4904 -2074.4904 11268.276 -11268.276
|
||||
1840 1710.0109 -2068.909 -2068.909 10673.193 -10673.193
|
||||
1850 1793.8245 -2074.1497 -2074.1497 11497.954 -11497.954
|
||||
1860 1876.3222 -2079.2504 -2079.2504 12338.777 -12338.777
|
||||
1870 1854.3831 -2077.5204 -2077.5204 13414.981 -13414.981
|
||||
1880 1873.4141 -2078.5705 -2078.5705 13586.534 -13586.534
|
||||
1890 1905.1875 -2080.5343 -2080.5343 13730.745 -13730.745
|
||||
1900 1928.0686 -2082.0735 -2082.0735 13195.816 -13195.816
|
||||
Loop time of 0.228464 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1900 1928.0686 -2082.0735 -2082.0735 13195.816 -13195.816
|
||||
1920 1928.0686 -2213.2849 -2213.2849 9852.9888 -9852.9888
|
||||
Loop time of 0.0547359 on 1 procs for 20 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1900 1928.0686 -2082.0735 -2082.0735 13195.816 -13195.816
|
||||
1910 1792.83 -2084.9923 -2084.9923 14194.264 -14194.264
|
||||
1920 1848.1085 -2088.3062 -2088.3062 14021.427 -14021.427
|
||||
1930 1801.6152 -2088.6097 -2088.6097 12402.211 -12402.211
|
||||
1940 1728.0714 -2084.0635 -2084.0635 12172.687 -12172.687
|
||||
1950 1873.5978 -2089.1424 -2089.1424 12450.15 -12450.15
|
||||
1960 1750.3387 -2086.13 -2086.13 11887.665 -11887.665
|
||||
1970 1810.8301 -2087.1529 -2087.1529 12874.661 -12874.661
|
||||
1980 1698.2365 -2080.73 -2080.73 12126.298 -12126.298
|
||||
1990 1825.6087 -2082.7204 -2082.7204 12862.535 -12862.535
|
||||
2000 1743.674 -2079.3142 -2079.3142 12724.32 -12724.32
|
||||
Loop time of 0.22565 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1900 1743.674 -2079.3142 -2079.3142 12724.32 -12724.32
|
||||
1910 1792.7661 -2082.8528 -2082.8528 12367.878 -12367.878
|
||||
1920 1800.2311 -2083.6545 -2083.6545 11883.087 -11883.087
|
||||
1930 1804.2647 -2084.2645 -2084.2645 12020.625 -12020.625
|
||||
1940 1854.7421 -2088.0162 -2088.0162 12265.553 -12265.553
|
||||
1950 1748.1756 -2081.4807 -2081.4807 12398.959 -12398.959
|
||||
1960 1715.3022 -2079.7847 -2079.7847 11986.482 -11986.482
|
||||
1970 1809.2371 -2086.4247 -2086.4247 11679.461 -11679.461
|
||||
1980 1800.4344 -2086.3399 -2086.3399 12025.457 -12025.457
|
||||
1990 1697.0311 -2080.0216 -2080.0216 12687.338 -12687.338
|
||||
2000 1742.3339 -2083.4435 -2083.4435 11879.588 -11879.588
|
||||
Loop time of 0.225269 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
2000 1742.3339 -2083.4435 -2083.4435 11879.588 -11879.588
|
||||
2019 1742.3339 -2213.2888 -2213.2888 8577.2768 -8577.2768
|
||||
Loop time of 0.0516479 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
2000 1742.3339 -2083.4435 -2083.4435 11879.588 -11879.588
|
||||
2010 1819.1825 -2088.9481 -2088.9481 10969.804 -10969.804
|
||||
2020 1688.1794 -2080.7333 -2080.7333 12075.819 -12075.819
|
||||
2030 1742.9277 -2084.7042 -2084.7042 12353.472 -12353.472
|
||||
2040 1852.3585 -2092.2678 -2092.2678 12215.689 -12215.689
|
||||
2050 1752.6535 -2086.0967 -2086.0967 12274.557 -12274.557
|
||||
2060 1678.177 -2081.5424 -2081.5424 12559.192 -12559.192
|
||||
2070 1796.9922 -2089.6689 -2089.6689 12144.946 -12144.946
|
||||
2080 1801.5169 -2090.2547 -2090.2547 12446.852 -12446.852
|
||||
2090 1759.1092 -2087.7653 -2087.7653 12345.933 -12345.933
|
||||
2100 1761.5053 -2088.2279 -2088.2279 12750.987 -12750.987
|
||||
Loop time of 0.234734 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
2100 1761.5053 -2088.2279 -2088.2279 12750.987 -12750.987
|
||||
2117 1761.5053 -2213.3069 -2213.3069 8711.9275 -8711.9275
|
||||
Loop time of 0.0468659 on 1 procs for 17 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
2100 1761.5053 -2081.5748 -2081.5748 11355.026 -11355.026
|
||||
Loop time of 7.44176 on 1 procs for 17 steps with 511 atoms
|
||||
|
||||
PRD stats:
|
||||
Dephase time (%) = 1.36382 (18.3266)
|
||||
Dynamics time (%) = 4.58499 (61.6117)
|
||||
Quench time (%) = 0.925114 (12.4314)
|
||||
Other time (%) = 0.0727496 (0.977587)
|
||||
|
||||
Nlocal: 511 ave 511 max 511 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1017 ave 1017 max 1017 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 13354 ave 13354 max 13354 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 13354
|
||||
Ave neighs/atom = 26.1331
|
||||
Neighbor list builds = 96
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,631 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
Processor partition = 1
|
||||
# Parallel replica dynamics model for a single vacancy in bulk Si
|
||||
# events occur when a neighboring atom diffuses to the vacant site
|
||||
# run this on multiple partitions as
|
||||
# mpirun -np 4 lmp_g++ -partition 4x1 -in in.prd
|
||||
|
||||
#log none
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# coordination number cutoff
|
||||
|
||||
variable r equal 2.835
|
||||
|
||||
# minimization parameters
|
||||
|
||||
variable etol equal 1.0e-5
|
||||
variable ftol equal 1.0e-5
|
||||
variable maxiter equal 100
|
||||
variable maxeval equal 100
|
||||
variable dmax equal 1.0e-1
|
||||
|
||||
# diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
||||
|
||||
region myreg block 0 4 0 4 0 4
|
||||
create_box 1 myreg
|
||||
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region myreg
|
||||
Created 512 atoms
|
||||
|
||||
mass 1 28.06
|
||||
|
||||
group Si type 1
|
||||
512 atoms in group Si
|
||||
|
||||
velocity all create $t 5287287 mom yes rot yes dist gaussian
|
||||
velocity all create 1800 5287287 mom yes rot yes dist gaussian
|
||||
|
||||
# make a vacancy
|
||||
|
||||
group del id 300
|
||||
1 atoms in group del
|
||||
delete_atoms group del
|
||||
Deleted 1 atoms, new total = 511
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si
|
||||
|
||||
thermo 10
|
||||
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
||||
# equilibrate
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 2.0318 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1802.5039 -2211.666 0 -2092.8401 12351.692
|
||||
10 996.01982 -2158.3093 0 -2092.649 14285.475
|
||||
20 590.09928 -2131.1531 0 -2092.2521 12113.964
|
||||
30 1033.01 -2159.2522 0 -2091.1534 6860.4116
|
||||
40 724.76581 -2137.281 0 -2089.5025 5999.4372
|
||||
50 489.66604 -2120.8082 0 -2088.5281 6403.4234
|
||||
60 960.70653 -2150.7394 0 -2087.407 5687.324
|
||||
70 908.41498 -2145.7665 0 -2085.8813 8220.9655
|
||||
80 796.82286 -2137.1227 0 -2084.5941 11307.153
|
||||
90 1245.9045 -2164.9841 0 -2082.8507 11282.071
|
||||
100 1083.0647 -2152.0805 0 -2080.682 12015.018
|
||||
Loop time of 0.197225 on 1 procs for 100 steps with 511 atoms
|
||||
|
||||
Pair time (%) = 0.19303 (97.8731)
|
||||
Neigh time (%) = 0.00140977 (0.714802)
|
||||
Comm time (%) = 0.000889301 (0.450907)
|
||||
Outpt time (%) = 7.84397e-05 (0.0397717)
|
||||
Other time (%) = 0.00181723 (0.921397)
|
||||
|
||||
Nlocal: 511 ave 511 max 511 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1017 ave 1017 max 1017 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 13996 ave 13996 max 13996 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 13996
|
||||
Ave neighs/atom = 27.3894
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
# only output atoms near vacancy
|
||||
|
||||
compute coord all coord/atom $r
|
||||
compute coord all coord/atom 2.835
|
||||
|
||||
#dump events all custom 1 dump.prd id type x y z
|
||||
#dump_modify events thresh c_coord != 4
|
||||
|
||||
compute patom all pe/atom
|
||||
compute pe all reduce sum c_patom
|
||||
compute satom all stress/atom
|
||||
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
|
||||
|
||||
thermo_style custom step temp pe c_pe press v_press
|
||||
|
||||
compute 1 all event/displace 0.5
|
||||
|
||||
prd 2000 100 10 10 100 1 54985 temp $t min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
|
||||
prd 2000 100 10 10 100 1 54985 temp 1800 min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
|
||||
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 ${ftol} ${maxiter} ${maxeval} vel all uniform
|
||||
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 ${maxiter} ${maxeval} vel all uniform
|
||||
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 100 ${maxeval} vel all uniform
|
||||
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 100 100 vel all uniform
|
||||
WARNING: Resetting reneighboring criteria during PRD (../prd.cpp:201)
|
||||
Memory usage per processor = 3.74841 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
|
||||
110 1083.0647 -2211.0684 -2211.0684 7372.2593 -7372.2593
|
||||
119 1083.0647 -2211.6557 -2211.6557 7411.1722 -7411.1722
|
||||
Loop time of 0.0541139 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
|
||||
110 1407.6264 -2123.5255 -2123.5255 16796.664 -16796.664
|
||||
120 1740.5244 -2117.1258 -2117.1258 18709.166 -18709.166
|
||||
130 1713.1995 -2109.2989 -2109.2989 18919.818 -18919.818
|
||||
140 1779.4809 -2106.0183 -2106.0183 18935.633 -18935.633
|
||||
150 1774.6703 -2102.5814 -2102.5814 18566.259 -18566.259
|
||||
160 1764.4555 -2098.5966 -2098.5966 18247.113 -18247.113
|
||||
170 1807.273 -2097.5073 -2097.5073 19262.305 -19262.305
|
||||
180 1802.9051 -2096.2207 -2096.2207 18967.398 -18967.398
|
||||
190 1818.8653 -2096.042 -2096.042 18419.673 -18419.673
|
||||
200 1807.602 -2095.1974 -2095.1974 18165.399 -18165.399
|
||||
Loop time of 0.220162 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
100 1807.602 -2095.1974 -2095.1974 18165.399 -18165.399
|
||||
110 1745.3032 -2089.8161 -2089.8161 17154.684 -17154.684
|
||||
120 1759.657 -2089.5011 -2089.5011 15296.251 -15296.251
|
||||
130 1716.433 -2085.3645 -2085.3645 14320.132 -14320.132
|
||||
140 1665.0731 -2080.6773 -2080.6773 13663.224 -13663.224
|
||||
150 1673.2986 -2079.8264 -2079.8264 13049.78 -13049.78
|
||||
160 1748.3061 -2083.2698 -2083.2698 13797.007 -13797.007
|
||||
170 1765.6267 -2082.8476 -2082.8476 15017.251 -15017.251
|
||||
180 1819.2949 -2084.8604 -2084.8604 15341.074 -15341.074
|
||||
190 1856.6017 -2085.841 -2085.841 15232.338 -15232.338
|
||||
200 1837.7362 -2083.245 -2083.245 15359.444 -15359.444
|
||||
Loop time of 0.229724 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
200 1837.7362 -2083.245 -2083.245 15359.444 -15359.444
|
||||
222 1837.7362 -2213.2958 -2213.2958 9231.1053 -9231.1053
|
||||
Loop time of 0.05158 on 1 procs for 22 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
200 1837.7362 -2083.245 -2083.245 15359.444 -15359.444
|
||||
210 1840.6293 -2082.2033 -2082.2033 14844.948 -14844.948
|
||||
220 1876.4513 -2083.4211 -2083.4211 14044.573 -14044.573
|
||||
230 1830.1329 -2079.331 -2079.331 13271.066 -13271.066
|
||||
240 1796.9539 -2076.207 -2076.207 13181.701 -13181.701
|
||||
250 1815.7837 -2076.5264 -2076.5264 13920.64 -13920.64
|
||||
260 1864.2627 -2078.8288 -2078.8288 14446.65 -14446.65
|
||||
270 1823.3876 -2075.3079 -2075.3079 14537.612 -14537.612
|
||||
280 1819.1185 -2074.2612 -2074.2612 14161.795 -14161.795
|
||||
290 1917.7731 -2080.0422 -2080.0422 14106.458 -14106.458
|
||||
300 1873.3899 -2076.5024 -2076.5024 15178.622 -15178.622
|
||||
Loop time of 0.232447 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
300 1873.3899 -2076.5024 -2076.5024 15178.622 -15178.622
|
||||
320 1873.3899 -2213.3069 -2213.3069 9479.7746 -9479.7746
|
||||
Loop time of 0.0591488 on 1 procs for 20 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
300 1873.3899 -2076.5024 -2076.5024 15178.622 -15178.622
|
||||
310 1774.8865 -2074.3353 -2074.3353 15109.591 -15109.591
|
||||
320 1909.8713 -2081.0651 -2081.0651 14297.983 -14297.983
|
||||
330 1831.1736 -2082.648 -2082.648 13911.946 -13911.946
|
||||
340 1782.9014 -2081.0633 -2081.0633 12948.277 -12948.277
|
||||
350 1824.5061 -2082.2008 -2082.2008 12862.649 -12862.649
|
||||
360 1872.7321 -2086.5367 -2086.5367 12420.995 -12420.995
|
||||
370 1688.5932 -2078.7564 -2078.7564 11683.93 -11683.93
|
||||
380 1864.9804 -2082.5641 -2082.5641 11669.845 -11669.845
|
||||
390 1781.3406 -2080.8891 -2080.8891 11392.404 -11392.404
|
||||
400 1754.9942 -2077.4471 -2077.4471 11538.936 -11538.936
|
||||
Loop time of 0.237148 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
300 1754.9942 -2077.4471 -2077.4471 11538.936 -11538.936
|
||||
310 1849.1709 -2083.1493 -2083.1493 11171.322 -11171.322
|
||||
320 1830.1419 -2081.4047 -2081.4047 11369.031 -11369.031
|
||||
330 1763.0288 -2076.5299 -2076.5299 12094.669 -12094.669
|
||||
340 1878.1833 -2083.6662 -2083.6662 13264.506 -13264.506
|
||||
350 1917.2697 -2085.8435 -2085.8435 13291.842 -13291.842
|
||||
360 1795.9824 -2077.5749 -2077.5749 13016.539 -13016.539
|
||||
370 1837.3619 -2080.0809 -2080.0809 11654.708 -11654.708
|
||||
380 1885.8321 -2083.0993 -2083.0993 10923.765 -10923.765
|
||||
390 1745.3951 -2073.7224 -2073.7224 11432.075 -11432.075
|
||||
400 1739.6563 -2073.1992 -2073.1992 10901.087 -10901.087
|
||||
Loop time of 0.236909 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
400 1739.6563 -2073.1992 -2073.1992 10901.087 -10901.087
|
||||
420 1739.6563 -2213.2706 -2213.2706 8556.9364 -8556.9364
|
||||
Loop time of 0.0592799 on 1 procs for 20 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
400 1739.6563 -2073.1992 -2073.1992 10901.087 -10901.087
|
||||
410 1865.528 -2081.2965 -2081.2965 11369.72 -11369.72
|
||||
420 1817.039 -2077.9231 -2077.9231 12284.358 -12284.358
|
||||
430 1841.0037 -2079.3779 -2079.3779 12199.662 -12199.662
|
||||
440 1933.3949 -2085.4168 -2085.4168 12571.997 -12571.997
|
||||
450 1824.2691 -2078.3022 -2078.3022 12475.107 -12475.107
|
||||
460 1742.7526 -2073.0352 -2073.0352 13123.36 -13123.36
|
||||
470 1904.6385 -2083.8117 -2083.8117 12367.287 -12367.287
|
||||
480 1900.8084 -2083.7693 -2083.7693 11586.764 -11586.764
|
||||
490 1765.8738 -2075.1817 -2075.1817 11148.626 -11148.626
|
||||
500 1818.1562 -2078.9363 -2078.9363 11026.721 -11026.721
|
||||
Loop time of 0.236481 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
500 1818.1562 -2078.9363 -2078.9363 11026.721 -11026.721
|
||||
520 1818.1562 -2213.3028 -2213.3028 9100.7638 -9100.7638
|
||||
Loop time of 0.057071 on 1 procs for 20 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
500 1818.1562 -2078.9363 -2078.9363 11026.721 -11026.721
|
||||
510 1855.4317 -2081.7363 -2081.7363 10646.37 -10646.37
|
||||
520 1767.2976 -2076.3 -2076.3 11298.884 -11298.884
|
||||
530 1800.7868 -2078.8762 -2078.8762 10799.285 -10799.285
|
||||
540 1817.9627 -2080.3797 -2080.3797 10703.952 -10703.952
|
||||
550 1790.4703 -2078.9532 -2078.9532 11128.572 -11128.572
|
||||
560 1808.189 -2080.5096 -2080.5096 10652.116 -10652.116
|
||||
570 1830.4747 -2082.3843 -2082.3843 10627.271 -10627.271
|
||||
580 1816.8801 -2081.9375 -2081.9375 10664.365 -10664.365
|
||||
590 1746.6186 -2077.7546 -2077.7546 11742.416 -11742.416
|
||||
600 1761.9264 -2079.1576 -2079.1576 12420.9 -12420.9
|
||||
Loop time of 0.233205 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
600 1761.9264 -2079.1576 -2079.1576 12420.9 -12420.9
|
||||
620 1761.9264 -2213.3164 -2213.3164 8715.1081 -8715.1081
|
||||
Loop time of 0.0507669 on 1 procs for 20 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
600 1761.9264 -2079.1576 -2079.1576 12420.9 -12420.9
|
||||
610 1830.7639 -2084.073 -2084.073 11771.278 -11771.278
|
||||
620 1769.7037 -2080.4252 -2080.4252 11979.886 -11979.886
|
||||
630 1822.9172 -2084.3132 -2084.3132 11300.932 -11300.932
|
||||
640 1824.3493 -2084.8166 -2084.8166 10829.863 -10829.863
|
||||
650 1733.4412 -2079.2284 -2079.2284 11599.031 -11599.031
|
||||
660 1789.5315 -2083.281 -2083.281 12317.055 -12317.055
|
||||
670 1854.9044 -2087.957 -2087.957 12396.242 -12396.242
|
||||
680 1770.0585 -2082.762 -2082.762 12312.359 -12312.359
|
||||
690 1791.3498 -2084.5474 -2084.5474 11710.405 -11710.405
|
||||
700 1879.1336 -2090.7525 -2090.7525 10706.781 -10706.781
|
||||
Loop time of 0.227964 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
700 1879.1336 -2090.7525 -2090.7525 10706.781 -10706.781
|
||||
718 1879.1336 -2213.3003 -2213.3003 9517.1887 -9517.1887
|
||||
Loop time of 0.046052 on 1 procs for 18 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
700 1879.1336 -2088.3939 -2088.3939 12889.204 -12889.204
|
||||
710 1814.1237 -2084.5974 -2084.5974 12285.032 -12285.032
|
||||
720 1755.5486 -2081.2365 -2081.2365 12206.775 -12206.775
|
||||
730 1775.9721 -2083.0461 -2083.0461 12733.094 -12733.094
|
||||
740 1774.9985 -2083.4078 -2083.4078 12653.923 -12653.923
|
||||
750 1775.7013 -2083.8599 -2083.8599 12379.764 -12379.764
|
||||
760 1776.7454 -2084.2994 -2084.2994 12627.379 -12627.379
|
||||
770 1819.9834 -2087.5129 -2087.5129 11631.061 -11631.061
|
||||
780 1809.3834 -2087.2039 -2087.2039 11047.665 -11047.665
|
||||
790 1714.0167 -2081.2937 -2081.2937 11340.179 -11340.179
|
||||
800 1712.7589 -2081.4883 -2081.4883 11330.776 -11330.776
|
||||
Loop time of 0.228653 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
800 1712.7589 -2081.4883 -2081.4883 11330.776 -11330.776
|
||||
818 1712.7589 -2213.2955 -2213.2955 8376.1803 -8376.1803
|
||||
Loop time of 0.0476019 on 1 procs for 18 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
800 1712.7589 -2081.4883 -2081.4883 11330.776 -11330.776
|
||||
810 1792.7684 -2082.4358 -2082.4358 13429.873 -13429.873
|
||||
820 1739.1918 -2078.6129 -2078.6129 13178.104 -13178.104
|
||||
830 1864.638 -2083.0747 -2083.0747 12836.897 -12836.897
|
||||
840 1765.781 -2081.0309 -2081.0309 13384.756 -13384.756
|
||||
850 1752.7636 -2078.0967 -2078.0967 14021.396 -14021.396
|
||||
860 1855.6782 -2081.935 -2081.935 13079.266 -13079.266
|
||||
870 1819.6679 -2083.4249 -2083.4249 12377.61 -12377.61
|
||||
880 1847.0607 -2086.7402 -2086.7402 13476.796 -13476.796
|
||||
890 1788.2771 -2086.2175 -2086.2175 12947.672 -12947.672
|
||||
900 1765.1941 -2084.1493 -2084.1493 12560.819 -12560.819
|
||||
Loop time of 0.226079 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
800 1765.1941 -2084.1493 -2084.1493 12560.819 -12560.819
|
||||
810 1817.715 -2087.8364 -2087.8364 11341.557 -11341.557
|
||||
820 1719.0788 -2081.5392 -2081.5392 10897.597 -10897.597
|
||||
830 1676.1893 -2078.8268 -2078.8268 11397.802 -11397.802
|
||||
840 1780.9587 -2085.7277 -2085.7277 10862.292 -10862.292
|
||||
850 1819.7436 -2088.2381 -2088.2381 11156.469 -11156.469
|
||||
860 1718.1718 -2081.4821 -2081.4821 12556.104 -12556.104
|
||||
870 1759.3307 -2084.0658 -2084.0658 13115.925 -13115.925
|
||||
880 1878.3559 -2091.7336 -2091.7336 12178.258 -12178.258
|
||||
890 1807.6117 -2086.9376 -2086.9376 11895.674 -11895.674
|
||||
900 1746.8208 -2082.8174 -2082.8174 11298.18 -11298.18
|
||||
Loop time of 0.227447 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
900 1746.8208 -2082.8174 -2082.8174 11298.18 -11298.18
|
||||
920 1746.8208 -2213.2983 -2213.2983 8611.3134 -8611.3134
|
||||
Loop time of 0.0549731 on 1 procs for 20 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
900 1746.8208 -2081.8053 -2081.8053 12812.552 -12812.552
|
||||
910 1792.6751 -2084.6689 -2084.6689 12725.248 -12725.248
|
||||
920 1789.7336 -2084.2674 -2084.2674 11813.766 -11813.766
|
||||
930 1783.4345 -2083.6379 -2083.6379 11831.318 -11831.318
|
||||
940 1713.795 -2078.7772 -2078.7772 11723.525 -11723.525
|
||||
950 1711.3789 -2078.256 -2078.256 11640.181 -11640.181
|
||||
960 1711.9374 -2077.7861 -2077.7861 12079.854 -12079.854
|
||||
970 1759.9375 -2080.3175 -2080.3175 12605.261 -12605.261
|
||||
980 1794.9009 -2081.8774 -2081.8774 13293.854 -13293.854
|
||||
990 1839.5283 -2084.0415 -2084.0415 14232.329 -14232.329
|
||||
1000 1891.8985 -2086.7244 -2086.7244 13901.493 -13901.493
|
||||
Loop time of 0.229747 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1000 1891.8985 -2086.7244 -2086.7244 13901.493 -13901.493
|
||||
1018 1891.8985 -2213.3115 -2213.3115 9611.9555 -9611.9555
|
||||
Loop time of 0.0494201 on 1 procs for 18 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1000 1891.8985 -2086.7244 -2086.7244 13901.493 -13901.493
|
||||
1010 1807.931 -2085.4113 -2085.4113 13673.347 -13673.347
|
||||
1020 1848.8179 -2087.9387 -2087.9387 12159.14 -12159.14
|
||||
1030 1783.9124 -2086.2028 -2086.2028 12085.317 -12085.317
|
||||
1040 1802.125 -2085.6618 -2085.6618 13060.527 -13060.527
|
||||
1050 1866.9247 -2089.4183 -2089.4183 12550.017 -12550.017
|
||||
1060 1727.9726 -2084.048 -2084.048 12894.09 -12894.09
|
||||
1070 1797.1898 -2083.1976 -2083.1976 13473.224 -13473.224
|
||||
1080 1798.1026 -2082.3986 -2082.3986 13076.343 -13076.343
|
||||
1090 1902.6166 -2088.501 -2088.501 13792.144 -13792.144
|
||||
1100 1698.3979 -2081.1883 -2081.1883 12986.81 -12986.81
|
||||
Loop time of 0.2302 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1000 1698.3979 -2081.1883 -2081.1883 12986.81 -12986.81
|
||||
1010 1750.2024 -2083.9278 -2083.9278 12435.817 -12435.817
|
||||
1020 1790.2529 -2085.7919 -2085.7919 12295.779 -12295.779
|
||||
1030 1770.1234 -2083.6823 -2083.6823 12925.751 -12925.751
|
||||
1040 1766.3321 -2082.6385 -2082.6385 13147.877 -13147.877
|
||||
1050 1791.6431 -2083.5004 -2083.5004 13631.61 -13631.61
|
||||
1060 1829.9027 -2085.2288 -2085.2288 14240.689 -14240.689
|
||||
1070 1859.399 -2086.4419 -2086.4419 14082.458 -14082.458
|
||||
1080 1885.6176 -2087.5558 -2087.5558 14640.987 -14640.987
|
||||
1090 1886.2609 -2087.1345 -2087.1345 15532.317 -15532.317
|
||||
1100 1790.9433 -2080.5091 -2080.5091 14768.821 -14768.821
|
||||
Loop time of 0.233712 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1100 1790.9433 -2080.5091 -2080.5091 14768.821 -14768.821
|
||||
1118 1790.9433 -2213.2987 -2213.2987 8913.1864 -8913.1864
|
||||
Loop time of 0.0476182 on 1 procs for 18 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1100 1790.9433 -2080.5091 -2080.5091 14768.821 -14768.821
|
||||
1110 1814.3939 -2081.769 -2081.769 13689.839 -13689.839
|
||||
1120 1833.7192 -2082.7815 -2082.7815 13519.243 -13519.243
|
||||
1130 1796.837 -2080.1348 -2080.1348 14072.965 -14072.965
|
||||
1140 1818.7494 -2081.3921 -2081.3921 13916.101 -13916.101
|
||||
1150 1818.9994 -2081.2488 -2081.2488 13140.548 -13140.548
|
||||
1160 1761.0556 -2077.2848 -2077.2848 13308.506 -13308.506
|
||||
1170 1805.8494 -2080.0847 -2080.0847 13471.127 -13471.127
|
||||
1180 1865.5836 -2083.8741 -2083.8741 14278.524 -14278.524
|
||||
1190 1890.5694 -2085.4621 -2085.4621 15255.857 -15255.857
|
||||
1200 1871.5608 -2084.2639 -2084.2639 15821.347 -15821.347
|
||||
Loop time of 0.229159 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1200 1871.5608 -2084.2639 -2084.2639 15821.347 -15821.347
|
||||
1219 1871.5608 -2213.3158 -2213.3158 9468.276 -9468.276
|
||||
Loop time of 0.0486791 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1200 1871.5608 -2084.2639 -2084.2639 15821.347 -15821.347
|
||||
1210 1868.7203 -2084.2286 -2084.2286 14757.029 -14757.029
|
||||
1220 1845.9795 -2082.9747 -2082.9747 13416.768 -13416.768
|
||||
1230 1721.0072 -2074.9829 -2074.9829 12653.426 -12653.426
|
||||
1240 1728.2984 -2075.6335 -2075.6335 11904.94 -11904.94
|
||||
1250 1760.6468 -2077.838 -2077.838 12363.743 -12363.743
|
||||
1260 1790.6407 -2079.8354 -2079.8354 13772.489 -13772.489
|
||||
1270 1855.4774 -2084.1181 -2084.1181 14259.348 -14259.348
|
||||
1280 1909.5179 -2087.7772 -2087.7772 14969.305 -14969.305
|
||||
1290 1843.272 -2083.6147 -2083.6147 15655.108 -15655.108
|
||||
1300 1850.0586 -2084.346 -2084.346 15667.554 -15667.554
|
||||
Loop time of 0.227929 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1300 1850.0586 -2084.346 -2084.346 15667.554 -15667.554
|
||||
1320 1850.0586 -2213.3195 -2213.3195 9322.6568 -9322.6568
|
||||
Loop time of 0.052876 on 1 procs for 20 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1300 1850.0586 -2084.346 -2084.346 15667.554 -15667.554
|
||||
1310 1901.2957 -2088.0828 -2088.0828 14348.338 -14348.338
|
||||
1320 1845.8424 -2084.9061 -2084.9061 13222.237 -13222.237
|
||||
1330 1703.2439 -2075.9846 -2075.9846 13160.468 -13160.468
|
||||
1340 1759.3432 -2080.0715 -2080.0715 12678.444 -12678.444
|
||||
1350 1848.0856 -2086.283 -2086.283 12513.213 -12513.213
|
||||
1360 1766.9936 -2081.3221 -2081.3221 13413.575 -13413.575
|
||||
1370 1759.0589 -2081.1569 -2081.1569 14027.4 -14027.4
|
||||
1380 1854.7078 -2087.8131 -2087.8131 13488.284 -13488.284
|
||||
1390 1861.4274 -2088.694 -2088.694 13755.794 -13755.794
|
||||
1400 1786.8881 -2084.3111 -2084.3111 14765.79 -14765.79
|
||||
Loop time of 0.228036 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1400 1786.8881 -2084.3111 -2084.3111 14765.79 -14765.79
|
||||
1418 1786.8881 -2213.2846 -2213.2846 8886.069 -8886.069
|
||||
Loop time of 0.0462029 on 1 procs for 18 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1400 1786.8881 -2083.1407 -2083.1407 12641.043 -12641.043
|
||||
1410 1812.2443 -2085.4259 -2085.4259 13130.596 -13130.596
|
||||
1420 1781.5601 -2084.1148 -2084.1148 13794.095 -13794.095
|
||||
1430 1816.6843 -2087.3261 -2087.3261 14262.13 -14262.13
|
||||
1440 1776.0284 -2085.8037 -2085.8037 13506.678 -13506.678
|
||||
1450 1747.7998 -2085.4471 -2085.4471 13056.821 -13056.821
|
||||
1460 1778.5134 -2089.39 -2089.39 13266.78 -13266.78
|
||||
1470 1840.1712 -2095.8688 -2095.8688 13524.008 -13524.008
|
||||
1480 1746.1558 -2092.2341 -2092.2341 12369.096 -12369.096
|
||||
1490 1661.5852 -2088.7904 -2088.7904 11360.287 -11360.287
|
||||
1500 1655.5694 -2089.9177 -2089.9177 10972.565 -10972.565
|
||||
Loop time of 0.228232 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1500 1655.5694 -2089.9177 -2089.9177 10972.565 -10972.565
|
||||
1519 1655.5694 -2213.2819 -2213.2819 7982.3333 -7982.3333
|
||||
Loop time of 0.053149 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1500 1655.5694 -2088.1491 -2088.1491 12266.426 -12266.426
|
||||
1510 1858.3169 -2102.6683 -2102.6683 11486.74 -11486.74
|
||||
1520 1589.6231 -2085.7524 -2085.7524 12341.834 -12341.834
|
||||
1530 1569.3501 -2084.7933 -2084.7933 11907.599 -11907.599
|
||||
1540 1796.1688 -2099.8918 -2099.8918 10462.273 -10462.273
|
||||
1550 1603.8116 -2087.2233 -2087.2233 11406.623 -11406.623
|
||||
1560 1542.9429 -2083.0325 -2083.0325 12076.743 -12076.743
|
||||
1570 1817.7406 -2100.7606 -2100.7606 11813.995 -11813.995
|
||||
1580 1646.4361 -2088.9642 -2088.9642 13492.322 -13492.322
|
||||
1590 1632.6599 -2087.4811 -2087.4811 14603.481 -14603.481
|
||||
1600 2009.4138 -2111.5732 -2111.5732 13852.416 -13852.416
|
||||
Loop time of 0.226615 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1600 2009.4138 -2111.5732 -2111.5732 13852.416 -13852.416
|
||||
1619 2009.4138 -2213.2965 -2213.2965 10413.156 -10413.156
|
||||
Loop time of 0.0540211 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1600 2009.4138 -2111.5732 -2111.5732 13852.416 -13852.416
|
||||
1610 1697.1733 -2080.6515 -2080.6515 12137.525 -12137.525
|
||||
1620 1884.5359 -2085.4978 -2085.4978 12301.761 -12301.761
|
||||
1630 1799.0114 -2084.7875 -2084.7875 13001.402 -13001.402
|
||||
1640 1822.4374 -2085.6471 -2085.6471 12188.808 -12188.808
|
||||
1650 1813.8575 -2085.9718 -2085.9718 11877.305 -11877.305
|
||||
1660 1784.9861 -2084.4001 -2084.4001 12331.077 -12331.077
|
||||
1670 1847.3065 -2086.9388 -2086.9388 13451.768 -13451.768
|
||||
1680 1758.4974 -2083.6409 -2083.6409 12744.573 -12744.573
|
||||
1690 1865.6773 -2087.3989 -2087.3989 13885.825 -13885.825
|
||||
1700 1807.1864 -2087.345 -2087.345 12271.996 -12271.996
|
||||
Loop time of 0.225843 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1600 1807.1864 -2087.345 -2087.345 12271.996 -12271.996
|
||||
1610 1781.1589 -2085.0991 -2085.0991 11779.473 -11779.473
|
||||
1620 1751.0492 -2082.5729 -2082.5729 12098.338 -12098.338
|
||||
1630 1750.1596 -2081.9145 -2081.9145 11669.766 -11669.766
|
||||
1640 1799.536 -2084.5103 -2084.5103 12073.924 -12073.924
|
||||
1650 1788.3038 -2083.0848 -2083.0848 12401.815 -12401.815
|
||||
1660 1706.9461 -2077.0226 -2077.0226 11867.225 -11867.225
|
||||
1670 1769.7603 -2080.398 -2080.398 11782.054 -11782.054
|
||||
1680 1855.9414 -2085.2452 -2085.2452 11953.771 -11953.771
|
||||
1690 1794.599 -2080.4156 -2080.4156 12986.207 -12986.207
|
||||
1700 1796.6882 -2079.8178 -2079.8178 13336.358 -13336.358
|
||||
Loop time of 0.228274 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1700 1796.6882 -2079.8178 -2079.8178 13336.358 -13336.358
|
||||
1717 1796.6882 -2213.286 -2213.286 8952.1586 -8952.1586
|
||||
Loop time of 0.0419819 on 1 procs for 17 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1700 1796.6882 -2079.8178 -2079.8178 13336.358 -13336.358
|
||||
1710 1908.9407 -2086.4998 -2086.4998 13426.557 -13426.557
|
||||
1720 1895.1818 -2084.9898 -2084.9898 14259.836 -14259.836
|
||||
1730 1821.3737 -2079.6705 -2079.6705 14430.721 -14430.721
|
||||
1740 1891.4293 -2083.9221 -2083.9221 12809.819 -12809.819
|
||||
1750 1839.7569 -2080.2332 -2080.2332 12449.372 -12449.372
|
||||
1760 1742.4817 -2073.6038 -2073.6038 12438.333 -12438.333
|
||||
1770 1747.721 -2073.6808 -2073.6808 12684.968 -12684.968
|
||||
1780 1840.5898 -2079.4792 -2079.4792 12821.365 -12821.365
|
||||
1790 1835.8529 -2078.8524 -2078.8524 12445.058 -12445.058
|
||||
1800 1839.1137 -2078.7997 -2078.7997 12888.228 -12888.228
|
||||
Loop time of 0.22941 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1800 1839.1137 -2078.7997 -2078.7997 12888.228 -12888.228
|
||||
1820 1839.1137 -2213.3043 -2213.3043 9252.8762 -9252.8762
|
||||
Loop time of 0.053638 on 1 procs for 20 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1800 1839.1137 -2076.1141 -2076.1141 12851.856 -12851.856
|
||||
1810 1847.1948 -2076.4193 -2076.4193 12095.243 -12095.243
|
||||
1820 1852.6203 -2076.6095 -2076.6095 12588.549 -12588.549
|
||||
1830 1834.9309 -2075.3368 -2075.3368 12532.297 -12532.297
|
||||
1840 1781.6431 -2071.7471 -2071.7471 11609.17 -11609.17
|
||||
1850 1762.9842 -2070.4212 -2070.4212 11879.69 -11879.69
|
||||
1860 1835.9552 -2075.0851 -2075.0851 12540.983 -12540.983
|
||||
1870 1921.2641 -2080.5952 -2080.5952 13447.361 -13447.361
|
||||
1880 1908.7351 -2079.7868 -2079.7868 13484.028 -13484.028
|
||||
1890 1893.6986 -2078.9917 -2078.9917 13954.252 -13954.252
|
||||
1900 1883.1217 -2078.6692 -2078.6692 14081.928 -14081.928
|
||||
Loop time of 0.230401 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1900 1883.1217 -2078.6692 -2078.6692 14081.928 -14081.928
|
||||
1921 1883.1217 -2213.3197 -2213.3197 9553.4902 -9553.4902
|
||||
Loop time of 0.0578089 on 1 procs for 21 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1900 1883.1217 -2078.6692 -2078.6692 14081.928 -14081.928
|
||||
1910 1784.5237 -2084.6905 -2084.6905 13389.919 -13389.919
|
||||
1920 1731.1905 -2080.6963 -2080.6963 12970.939 -12970.939
|
||||
1930 1850.3131 -2084.6718 -2084.6718 13719.542 -13719.542
|
||||
1940 1831.2993 -2087.5516 -2087.5516 13434.958 -13434.958
|
||||
1950 1743.2339 -2084.7246 -2084.7246 14362.929 -14362.929
|
||||
1960 1853.8244 -2089.3655 -2089.3655 13929.842 -13929.842
|
||||
1970 1699.1334 -2083.859 -2083.859 13684.756 -13684.756
|
||||
1980 1812.1618 -2085.8552 -2085.8552 14478.969 -14478.969
|
||||
1990 1802.7775 -2087.2555 -2087.2555 14695.415 -14695.415
|
||||
2000 1839.2685 -2091.105 -2091.105 14707.233 -14707.233
|
||||
Loop time of 0.22816 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1900 1839.2685 -2091.105 -2091.105 14707.233 -14707.233
|
||||
1910 1758.6133 -2087.016 -2087.016 13616.046 -13616.046
|
||||
1920 1700.711 -2084.2588 -2084.2588 12824.655 -12824.655
|
||||
1930 1751.7857 -2088.5085 -2088.5085 12349.562 -12349.562
|
||||
1940 1754.9537 -2089.478 -2089.478 12280.371 -12280.371
|
||||
1950 1685.603 -2085.509 -2085.509 13197.034 -13197.034
|
||||
1960 1713.2304 -2087.7626 -2087.7626 13267.547 -13267.547
|
||||
1970 1760.9078 -2091.2137 -2091.2137 13458.047 -13458.047
|
||||
1980 1752.4605 -2090.8824 -2090.8824 14025.525 -14025.525
|
||||
1990 1783.2844 -2093.0833 -2093.0833 13878.972 -13878.972
|
||||
2000 1795.4952 -2094.0299 -2094.0299 13749.599 -13749.599
|
||||
Loop time of 0.227002 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
2000 1795.4952 -2094.0299 -2094.0299 13749.599 -13749.599
|
||||
2017 1795.4952 -2213.2891 -2213.2891 8939.1137 -8939.1137
|
||||
Loop time of 0.041914 on 1 procs for 17 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
2000 1795.4952 -2094.0299 -2094.0299 13749.599 -13749.599
|
||||
2010 1716.471 -2088.9279 -2088.9279 13720.493 -13720.493
|
||||
2020 1648.4001 -2084.439 -2084.439 13359.443 -13359.443
|
||||
2030 1677.6114 -2086.2033 -2086.2033 13113.177 -13113.177
|
||||
2040 1698.0201 -2087.2241 -2087.2241 13276.862 -13276.862
|
||||
2050 1732.5808 -2089.0495 -2089.0495 13460.966 -13460.966
|
||||
2060 1779.8938 -2091.6181 -2091.6181 13393.474 -13393.474
|
||||
2070 1764.0047 -2089.9669 -2089.9669 14040.691 -14040.691
|
||||
2080 1777.9135 -2090.2448 -2090.2448 14162.157 -14162.157
|
||||
2090 1772.5816 -2089.2159 -2089.2159 13499.045 -13499.045
|
||||
2100 1714.5393 -2084.6691 -2084.6691 13396.984 -13396.984
|
||||
Loop time of 0.235394 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
2100 1714.5393 -2084.6691 -2084.6691 13396.984 -13396.984
|
||||
2118 1714.5393 -2213.2509 -2213.2509 8384.1471 -8384.1471
|
||||
Loop time of 0.0487101 on 1 procs for 18 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
2100 1714.5393 -2081.5748 -2081.5748 11032.46 -11032.46
|
||||
Loop time of 7.44167 on 1 procs for 18 steps with 511 atoms
|
||||
|
||||
PRD stats:
|
||||
Dephase time (%) = 1.36759 (18.3775)
|
||||
Dynamics time (%) = 4.60674 (61.9046)
|
||||
Quench time (%) = 1.02249 (13.7401)
|
||||
Other time (%) = 0.0763338 (1.02576)
|
||||
|
||||
Nlocal: 511 ave 511 max 511 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1017 ave 1017 max 1017 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 13354 ave 13354 max 13354 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 13354
|
||||
Ave neighs/atom = 26.1331
|
||||
Neighbor list builds = 95
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,12 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
Running on 4 partitions of processors
|
||||
Step CPU Clock Event Correlated Coincident Replica
|
||||
100 0.000 0 0 0 0 0
|
||||
200 0.538 400 1 0 4 1
|
||||
700 2.284 2100 2 0 2 3
|
||||
900 3.105 2600 3 0 1 3
|
||||
1400 4.856 4300 4 0 1 2
|
||||
1500 5.152 4400 5 1 1 2
|
||||
1800 6.287 5300 6 0 2 3
|
||||
2100 7.438 6200 7 0 1 3
|
||||
Loop time of 7.44176 on 4 procs for 2000 steps with 511 atoms
|
||||
|
|
@ -0,0 +1,631 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
Processor partition = 2
|
||||
# Parallel replica dynamics model for a single vacancy in bulk Si
|
||||
# events occur when a neighboring atom diffuses to the vacant site
|
||||
# run this on multiple partitions as
|
||||
# mpirun -np 4 lmp_g++ -partition 4x1 -in in.prd
|
||||
|
||||
#log none
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# coordination number cutoff
|
||||
|
||||
variable r equal 2.835
|
||||
|
||||
# minimization parameters
|
||||
|
||||
variable etol equal 1.0e-5
|
||||
variable ftol equal 1.0e-5
|
||||
variable maxiter equal 100
|
||||
variable maxeval equal 100
|
||||
variable dmax equal 1.0e-1
|
||||
|
||||
# diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
||||
|
||||
region myreg block 0 4 0 4 0 4
|
||||
create_box 1 myreg
|
||||
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region myreg
|
||||
Created 512 atoms
|
||||
|
||||
mass 1 28.06
|
||||
|
||||
group Si type 1
|
||||
512 atoms in group Si
|
||||
|
||||
velocity all create $t 5287287 mom yes rot yes dist gaussian
|
||||
velocity all create 1800 5287287 mom yes rot yes dist gaussian
|
||||
|
||||
# make a vacancy
|
||||
|
||||
group del id 300
|
||||
1 atoms in group del
|
||||
delete_atoms group del
|
||||
Deleted 1 atoms, new total = 511
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si
|
||||
|
||||
thermo 10
|
||||
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
||||
# equilibrate
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 2.0318 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1802.5039 -2211.666 0 -2092.8401 12351.692
|
||||
10 996.01982 -2158.3093 0 -2092.649 14285.475
|
||||
20 590.09928 -2131.1531 0 -2092.2521 12113.964
|
||||
30 1033.01 -2159.2522 0 -2091.1534 6860.4116
|
||||
40 724.76581 -2137.281 0 -2089.5025 5999.4372
|
||||
50 489.66604 -2120.8082 0 -2088.5281 6403.4234
|
||||
60 960.70653 -2150.7394 0 -2087.407 5687.324
|
||||
70 908.41498 -2145.7665 0 -2085.8813 8220.9655
|
||||
80 796.82286 -2137.1227 0 -2084.5941 11307.153
|
||||
90 1245.9045 -2164.9841 0 -2082.8507 11282.071
|
||||
100 1083.0647 -2152.0805 0 -2080.682 12015.018
|
||||
Loop time of 0.199959 on 1 procs for 100 steps with 511 atoms
|
||||
|
||||
Pair time (%) = 0.195735 (97.8875)
|
||||
Neigh time (%) = 0.00142097 (0.710633)
|
||||
Comm time (%) = 0.000902414 (0.4513)
|
||||
Outpt time (%) = 6.91414e-05 (0.0345778)
|
||||
Other time (%) = 0.00183153 (0.915953)
|
||||
|
||||
Nlocal: 511 ave 511 max 511 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1017 ave 1017 max 1017 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 13996 ave 13996 max 13996 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 13996
|
||||
Ave neighs/atom = 27.3894
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
# only output atoms near vacancy
|
||||
|
||||
compute coord all coord/atom $r
|
||||
compute coord all coord/atom 2.835
|
||||
|
||||
#dump events all custom 1 dump.prd id type x y z
|
||||
#dump_modify events thresh c_coord != 4
|
||||
|
||||
compute patom all pe/atom
|
||||
compute pe all reduce sum c_patom
|
||||
compute satom all stress/atom
|
||||
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
|
||||
|
||||
thermo_style custom step temp pe c_pe press v_press
|
||||
|
||||
compute 1 all event/displace 0.5
|
||||
|
||||
prd 2000 100 10 10 100 1 54985 temp $t min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
|
||||
prd 2000 100 10 10 100 1 54985 temp 1800 min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
|
||||
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 ${ftol} ${maxiter} ${maxeval} vel all uniform
|
||||
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 ${maxiter} ${maxeval} vel all uniform
|
||||
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 100 ${maxeval} vel all uniform
|
||||
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 100 100 vel all uniform
|
||||
WARNING: Resetting reneighboring criteria during PRD (../prd.cpp:201)
|
||||
Memory usage per processor = 3.74841 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
|
||||
110 1083.0647 -2211.0684 -2211.0684 7372.2593 -7372.2593
|
||||
119 1083.0647 -2211.6557 -2211.6557 7411.1722 -7411.1722
|
||||
Loop time of 0.0558779 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
|
||||
110 1453.0014 -2126.4815 -2126.4815 17039.938 -17039.938
|
||||
120 1712.5747 -2118.2811 -2118.2811 19245.699 -19245.699
|
||||
130 1816.1055 -2117.2078 -2117.2078 19172.109 -19172.109
|
||||
140 1741.5479 -2111.5113 -2111.5113 18643.317 -18643.317
|
||||
150 1779.1262 -2108.4242 -2108.4242 18055.809 -18055.809
|
||||
160 1708.5416 -2100.8014 -2100.8014 18706.608 -18706.608
|
||||
170 1810.3199 -2099.9306 -2099.9306 18691.592 -18691.592
|
||||
180 1805.675 -2098.8187 -2098.8187 17517.611 -17517.611
|
||||
190 1827.5401 -2099.2194 -2099.2194 17130.547 -17130.547
|
||||
200 1726.2196 -2093.025 -2093.025 16774.098 -16774.098
|
||||
Loop time of 0.22566 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
100 1726.2196 -2093.025 -2093.025 16774.098 -16774.098
|
||||
110 1740.3774 -2092.6139 -2092.6139 15523.606 -15523.606
|
||||
120 1781.5972 -2093.9535 -2093.9535 14428.677 -14428.677
|
||||
130 1684.5193 -2086.1781 -2086.1781 14825.487 -14825.487
|
||||
140 1613.5723 -2080.1384 -2080.1384 14868.993 -14868.993
|
||||
150 1755.5164 -2087.9807 -2087.9807 13748.119 -13748.119
|
||||
160 1738.7712 -2085.2666 -2085.2666 14802.112 -14802.112
|
||||
170 1674.8255 -2079.507 -2079.507 15674.35 -15674.35
|
||||
180 1760.9622 -2083.599 -2083.599 15769.066 -15769.066
|
||||
190 1899.9806 -2091.1229 -2091.1229 16231.019 -16231.019
|
||||
200 1814.7529 -2083.9976 -2083.9976 17122.298 -17122.298
|
||||
Loop time of 0.236051 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
200 1814.7529 -2083.9976 -2083.9976 17122.298 -17122.298
|
||||
217 1814.7529 -2213.2613 -2213.2613 9069.1206 -9069.1206
|
||||
Loop time of 0.038727 on 1 procs for 17 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
200 1814.7529 -2083.245 -2083.245 15201.593 -15201.593
|
||||
210 1801.6419 -2081.0472 -2081.0472 15342.659 -15342.659
|
||||
220 1881.8236 -2085.0669 -2085.0669 14755.087 -14755.087
|
||||
230 1866.0873 -2082.8539 -2082.8539 13894.752 -13894.752
|
||||
240 1792.3297 -2076.96 -2076.96 13354.538 -13354.538
|
||||
250 1787.3004 -2075.652 -2075.652 13316.541 -13316.541
|
||||
260 1830.871 -2077.5427 -2077.5427 12617.353 -12617.353
|
||||
270 1791.7089 -2074.006 -2074.006 13195.786 -13195.786
|
||||
280 1849.0237 -2076.8667 -2076.8667 13418.75 -13418.75
|
||||
290 1929.6949 -2081.3067 -2081.3067 14728.325 -14728.325
|
||||
300 1879.9418 -2077.2916 -2077.2916 16541.913 -16541.913
|
||||
Loop time of 0.235504 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
300 1879.9418 -2077.2916 -2077.2916 16541.913 -16541.913
|
||||
317 1879.9418 -2213.2283 -2213.2283 9516.969 -9516.969
|
||||
Loop time of 0.046042 on 1 procs for 17 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
300 1879.9418 -2077.2916 -2077.2916 16541.913 -16541.913
|
||||
310 1838.8029 -2078.0409 -2078.0409 14753.009 -14753.009
|
||||
320 1789.8725 -2076.7713 -2076.7713 15560.98 -15560.98
|
||||
330 1950.1614 -2086.0999 -2086.0999 13361.512 -13361.512
|
||||
340 1759.3354 -2082.9137 -2082.9137 12750.26 -12750.26
|
||||
350 1857.8525 -2086.2264 -2086.2264 13541.869 -13541.869
|
||||
360 1873.6249 -2090.6161 -2090.6161 12790.402 -12790.402
|
||||
370 1704.2028 -2083.8532 -2083.8532 12022.063 -12022.063
|
||||
380 1824.0288 -2084.9296 -2084.9296 13078.149 -13078.149
|
||||
390 1823.8695 -2086.0185 -2086.0185 12394.039 -12394.039
|
||||
400 1826.7938 -2087.3212 -2087.3212 11456.443 -11456.443
|
||||
Loop time of 0.229793 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
300 1826.7938 -2087.3212 -2087.3212 11456.443 -11456.443
|
||||
310 1790.3054 -2084.4713 -2084.4713 11190.448 -11190.448
|
||||
320 1732.854 -2080.2375 -2080.2375 11020.269 -11020.269
|
||||
330 1679.9775 -2076.2292 -2076.2292 10476.6 -10476.6
|
||||
340 1706.236 -2077.3108 -2077.3108 10973.286 -10973.286
|
||||
350 1798.7321 -2082.6213 -2082.6213 12099.734 -12099.734
|
||||
360 1827.8354 -2083.7164 -2083.7164 12269.553 -12269.553
|
||||
370 1803.5781 -2081.3205 -2081.3205 11882.622 -11882.622
|
||||
380 1831.5584 -2082.4022 -2082.4022 11868.591 -11868.591
|
||||
390 1865.1115 -2083.8776 -2083.8776 12451.163 -12451.163
|
||||
400 1885.8707 -2084.5972 -2084.5972 12777.133 -12777.133
|
||||
Loop time of 0.235168 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
400 1885.8707 -2084.5972 -2084.5972 12777.133 -12777.133
|
||||
421 1885.8707 -2213.3072 -2213.3072 9565.3643 -9565.3643
|
||||
Loop time of 0.0609999 on 1 procs for 21 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
400 1885.8707 -2084.5972 -2084.5972 12777.133 -12777.133
|
||||
410 1840.8997 -2081.0851 -2081.0851 13049.359 -13049.359
|
||||
420 1860.5306 -2081.9195 -2081.9195 12866.668 -12866.668
|
||||
430 1842.0725 -2080.3072 -2080.3072 11967.296 -11967.296
|
||||
440 1778.5284 -2075.7716 -2075.7716 11672.911 -11672.911
|
||||
450 1792.767 -2076.3662 -2076.3662 11362.562 -11362.562
|
||||
460 1812.368 -2077.2861 -2077.2861 11982.449 -11982.449
|
||||
470 1805.4534 -2076.4744 -2076.4744 11355.668 -11355.668
|
||||
480 1771.7109 -2073.8789 -2073.8789 11574.724 -11574.724
|
||||
490 1895.5684 -2081.6811 -2081.6811 10875.512 -10875.512
|
||||
500 1863.4356 -2079.2626 -2079.2626 12022.062 -12022.062
|
||||
Loop time of 0.235502 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
500 1863.4356 -2079.2626 -2079.2626 12022.062 -12022.062
|
||||
519 1863.4356 -2213.2964 -2213.2964 9413.3063 -9413.3063
|
||||
Loop time of 0.0535631 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
500 1863.4356 -2079.2626 -2079.2626 12022.062 -12022.062
|
||||
510 1811.0452 -2075.5953 -2075.5953 12654.915 -12654.915
|
||||
520 1939.3016 -2083.9091 -2083.9091 12699.136 -12699.136
|
||||
530 1865.6263 -2079.0274 -2079.0274 13205.704 -13205.704
|
||||
540 1840.8195 -2077.4842 -2077.4842 13607.888 -13607.888
|
||||
550 1910.185 -2082.2276 -2082.2276 13164.337 -13164.337
|
||||
560 1897.5018 -2081.7046 -2081.7046 12541.871 -12541.871
|
||||
570 1805.2364 -2076.0408 -2076.0408 12518.288 -12518.288
|
||||
580 1820.8895 -2077.5197 -2077.5197 12510.55 -12510.55
|
||||
590 1880.7209 -2081.9748 -2081.9748 11279.988 -11279.988
|
||||
600 1774.2632 -2075.5235 -2075.5235 10905.347 -10905.347
|
||||
Loop time of 0.232401 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
600 1774.2632 -2075.5235 -2075.5235 10905.347 -10905.347
|
||||
621 1774.2632 -2213.3211 -2213.3211 8802.4378 -8802.4378
|
||||
Loop time of 0.061439 on 1 procs for 21 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
600 1774.2632 -2075.5235 -2075.5235 10905.347 -10905.347
|
||||
610 1776.4519 -2076.2072 -2076.2072 11432.057 -11432.057
|
||||
620 1866.4889 -2082.7151 -2082.7151 11939.587 -11939.587
|
||||
630 1757.9348 -2076.135 -2076.135 12794.432 -12794.432
|
||||
640 1821.0434 -2080.8738 -2080.8738 12398.818 -12398.818
|
||||
650 1878.4228 -2085.2725 -2085.2725 13017.551 -13017.551
|
||||
660 1874.4782 -2085.7432 -2085.7432 13297.304 -13297.304
|
||||
670 1796.8744 -2081.4171 -2081.4171 12112.746 -12112.746
|
||||
680 1789.2824 -2081.7003 -2081.7003 11627.391 -11627.391
|
||||
690 1769.7646 -2081.1645 -2081.1645 12468.2 -12468.2
|
||||
700 1781.4831 -2082.6368 -2082.6368 12878.838 -12878.838
|
||||
Loop time of 0.234258 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
700 1781.4831 -2082.6368 -2082.6368 12878.838 -12878.838
|
||||
720 1781.4831 -2213.249 -2213.249 8849.8358 -8849.8358
|
||||
Loop time of 0.0461211 on 1 procs for 20 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
700 1781.4831 -2088.3939 -2088.3939 12218.534 -12218.534
|
||||
710 1724.4898 -2085.2684 -2085.2684 11903.569 -11903.569
|
||||
720 1764.7152 -2088.4829 -2088.4829 11526.3 -11526.3
|
||||
730 1724.9813 -2086.3524 -2086.3524 12129.067 -12129.067
|
||||
740 1711.2186 -2085.8354 -2085.8354 12875.329 -12875.329
|
||||
750 1774.7765 -2090.326 -2090.326 12385.579 -12385.579
|
||||
760 1787.964 -2091.4692 -2091.4692 11889.535 -11889.535
|
||||
770 1711.6992 -2086.6713 -2086.6713 12283.555 -12283.555
|
||||
780 1717.7443 -2087.2139 -2087.2139 11537.044 -11537.044
|
||||
790 1683.3367 -2084.9743 -2084.9743 10800.126 -10800.126
|
||||
800 1631.6415 -2081.4408 -2081.4408 10616.296 -10616.296
|
||||
Loop time of 0.235564 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
800 1631.6415 -2081.4408 -2081.4408 10616.296 -10616.296
|
||||
819 1631.6415 -2213.3087 -2213.3087 7818.8075 -7818.8075
|
||||
Loop time of 0.0506389 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
800 1631.6415 -2081.4408 -2081.4408 10616.296 -10616.296
|
||||
810 1790.007 -2081.8313 -2081.8313 13202.119 -13202.119
|
||||
820 1849.219 -2084.8387 -2084.8387 12576.218 -12576.218
|
||||
830 1792.8687 -2084.1604 -2084.1604 11392.768 -11392.768
|
||||
840 1731.9467 -2079.4445 -2079.4445 12892.679 -12892.679
|
||||
850 1785.6213 -2078.2286 -2078.2286 13776.917 -13776.917
|
||||
860 1831.1149 -2080.0094 -2080.0094 12904.24 -12904.24
|
||||
870 1819.41 -2081.0253 -2081.0253 12547.946 -12547.946
|
||||
880 1758.8325 -2078.0286 -2078.0286 12618.106 -12618.106
|
||||
890 1763.5444 -2075.2871 -2075.2871 13398.793 -13398.793
|
||||
900 1808.5838 -2075.4917 -2075.4917 13281.327 -13281.327
|
||||
Loop time of 0.235009 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
800 1808.5838 -2075.4917 -2075.4917 13281.327 -13281.327
|
||||
810 1851.8312 -2077.9782 -2077.9782 12015.32 -12015.32
|
||||
820 1808.4808 -2074.7871 -2074.7871 11857.883 -11857.883
|
||||
830 1828.2295 -2075.7871 -2075.7871 11715.86 -11715.86
|
||||
840 1836.1989 -2076.03 -2076.03 12095.951 -12095.951
|
||||
850 1806.7992 -2073.8356 -2073.8356 12485.462 -12485.462
|
||||
860 1889.8731 -2079.0926 -2079.0926 12485.696 -12485.696
|
||||
870 1879.6457 -2078.2828 -2078.2828 13039.623 -13039.623
|
||||
880 1832.0939 -2075.1105 -2075.1105 12938.4 -12938.4
|
||||
890 1875.4331 -2078.0004 -2078.0004 12216.702 -12216.702
|
||||
900 1914.4276 -2080.7098 -2080.7098 12144.748 -12144.748
|
||||
Loop time of 0.231472 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
900 1914.4276 -2080.7098 -2080.7098 12144.748 -12144.748
|
||||
919 1914.4276 -2213.3188 -2213.3188 9764.087 -9764.087
|
||||
Loop time of 0.049932 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
900 1914.4276 -2081.8053 -2081.8053 13963.686 -13963.686
|
||||
910 1810.633 -2075.2099 -2075.2099 14043.827 -14043.827
|
||||
920 1839.0572 -2077.3907 -2077.3907 13195.428 -13195.428
|
||||
930 1875.3856 -2080.1678 -2080.1678 12550.917 -12550.917
|
||||
940 1774.6978 -2073.9954 -2073.9954 12878.164 -12878.164
|
||||
950 1739.4586 -2072.1025 -2072.1025 12381.741 -12381.741
|
||||
960 1860.7393 -2080.5553 -2080.5553 11340.855 -11340.855
|
||||
970 1675.5209 -2068.7733 -2068.7733 12264.795 -12264.795
|
||||
980 1794.0159 -2076.9546 -2076.9546 12079.272 -12079.272
|
||||
990 1965.1199 -2088.653 -2088.653 12866.959 -12866.959
|
||||
1000 1860.4796 -2082.3648 -2082.3648 14940.447 -14940.447
|
||||
Loop time of 0.234604 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1000 1860.4796 -2082.3648 -2082.3648 14940.447 -14940.447
|
||||
1016 1860.4796 -2213.2478 -2213.2478 9385.9786 -9385.9786
|
||||
Loop time of 0.0431788 on 1 procs for 16 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1000 1860.4796 -2082.3648 -2082.3648 14940.447 -14940.447
|
||||
1010 1725.5676 -2081.2141 -2081.2141 12659.195 -12659.195
|
||||
1020 1776.6517 -2080.2782 -2080.2782 14283.292 -14283.292
|
||||
1030 1892.8575 -2087.068 -2087.068 14207.132 -14207.132
|
||||
1040 1779.8487 -2086.4423 -2086.4423 13177.279 -13177.279
|
||||
1050 1827.1799 -2088.9648 -2088.9648 12860.512 -12860.512
|
||||
1060 1788.3529 -2088.9653 -2088.9653 12121.719 -12121.719
|
||||
1070 1710.9667 -2083.8206 -2083.8206 12445.746 -12445.746
|
||||
1080 1828.553 -2086.433 -2086.433 12715.209 -12715.209
|
||||
1090 1823.9802 -2088.7607 -2088.7607 12059.344 -12059.344
|
||||
1100 1792.7229 -2089.0486 -2089.0486 11500.622 -11500.622
|
||||
Loop time of 0.232108 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1000 1792.7229 -2089.0486 -2089.0486 11500.622 -11500.622
|
||||
1010 1699.0134 -2083.5757 -2083.5757 11300.601 -11300.601
|
||||
1020 1628.0232 -2079.447 -2079.447 11165.976 -11165.976
|
||||
1030 1649.3552 -2081.1852 -2081.1852 11327.923 -11327.923
|
||||
1040 1780.5559 -2090.032 -2090.032 11432.453 -11432.453
|
||||
1050 1757.6796 -2088.6549 -2088.6549 11052.281 -11052.281
|
||||
1060 1707.3484 -2085.4178 -2085.4178 11557.124 -11557.124
|
||||
1070 1740.6914 -2087.5927 -2087.5927 12294.274 -12294.274
|
||||
1080 1770.6598 -2089.4669 -2089.4669 12907.34 -12907.34
|
||||
1090 1742.39 -2087.4355 -2087.4355 13144.749 -13144.749
|
||||
1100 1806.4889 -2091.4432 -2091.4432 12589.891 -12589.891
|
||||
Loop time of 0.235962 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1100 1806.4889 -2091.4432 -2091.4432 12589.891 -12589.891
|
||||
1116 1806.4889 -2213.2741 -2213.2741 9022.1362 -9022.1362
|
||||
Loop time of 0.042937 on 1 procs for 16 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1100 1806.4889 -2091.4432 -2091.4432 12589.891 -12589.891
|
||||
1110 1759.3742 -2088.0631 -2088.0631 12373.16 -12373.16
|
||||
1120 1741.0508 -2086.5288 -2086.5288 11902.565 -11902.565
|
||||
1130 1752.2435 -2086.8177 -2086.8177 11844.496 -11844.496
|
||||
1140 1786.7182 -2088.5202 -2088.5202 11401.503 -11401.503
|
||||
1150 1760.1379 -2086.0667 -2086.0667 11634.293 -11634.293
|
||||
1160 1737.621 -2083.7432 -2083.7432 12261.472 -12261.472
|
||||
1170 1706.1721 -2080.6152 -2080.6152 11900.384 -11900.384
|
||||
1180 1692.9524 -2078.4392 -2078.4392 11857.894 -11857.894
|
||||
1190 1845.4734 -2086.9009 -2086.9009 12368.868 -12368.868
|
||||
1200 1931.9798 -2090.8563 -2090.8563 13231.297 -13231.297
|
||||
Loop time of 0.23467 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1200 1931.9798 -2090.8563 -2090.8563 13231.297 -13231.297
|
||||
1217 1931.9798 -2213.2743 -2213.2743 9876.9115 -9876.9115
|
||||
Loop time of 0.0452831 on 1 procs for 17 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1200 1931.9798 -2090.8563 -2090.8563 13231.297 -13231.297
|
||||
1210 1844.6662 -2083.5459 -2083.5459 13676.012 -13676.012
|
||||
1220 1823.5246 -2080.8506 -2080.8506 13754.811 -13754.811
|
||||
1230 1855.1817 -2081.8069 -2081.8069 13072.56 -13072.56
|
||||
1240 1817.3161 -2078.3873 -2078.3873 13440.344 -13440.344
|
||||
1250 1846.7917 -2079.601 -2079.601 13176.331 -13176.331
|
||||
1260 1879.5517 -2081.1956 -2081.1956 12521.935 -12521.935
|
||||
1270 1856.8093 -2079.3203 -2079.3203 12606.391 -12606.391
|
||||
1280 1802.8957 -2075.5089 -2075.5089 13433.639 -13433.639
|
||||
1290 1858.5815 -2079.0007 -2079.0007 11938.06 -11938.06
|
||||
1300 1855.8203 -2078.7061 -2078.7061 11790.601 -11790.601
|
||||
Loop time of 0.232873 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1300 1855.8203 -2078.7061 -2078.7061 11790.601 -11790.601
|
||||
1320 1855.8203 -2213.31 -2213.31 9361.0005 -9361.0005
|
||||
Loop time of 0.0529099 on 1 procs for 20 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1300 1855.8203 -2078.7061 -2078.7061 11790.601 -11790.601
|
||||
1310 1874.9965 -2079.9692 -2079.9692 11644.669 -11644.669
|
||||
1320 1769.8025 -2073.0867 -2073.0867 11913.24 -11913.24
|
||||
1330 1767.7322 -2072.9816 -2072.9816 11519.778 -11519.778
|
||||
1340 1877.3892 -2080.2309 -2080.2309 11401.149 -11401.149
|
||||
1350 1832.5468 -2077.3496 -2077.3496 11388.096 -11388.096
|
||||
1360 1824.2863 -2076.9333 -2076.9333 13175.108 -13175.108
|
||||
1370 1878.976 -2080.7152 -2080.7152 13742.012 -13742.012
|
||||
1380 1853.0704 -2079.2587 -2079.2587 13419.479 -13419.479
|
||||
1390 1879.4579 -2081.3358 -2081.3358 13342.696 -13342.696
|
||||
1400 1900.1245 -2083.1407 -2083.1407 13418.759 -13418.759
|
||||
Loop time of 0.231297 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1400 1900.1245 -2083.1407 -2083.1407 13418.759 -13418.759
|
||||
1418 1900.1245 -2213.3012 -2213.3012 9665.7068 -9665.7068
|
||||
Loop time of 0.045877 on 1 procs for 18 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1400 1900.1245 -2083.1407 -2083.1407 13418.759 -13418.759
|
||||
1410 1901.6666 -2083.8299 -2083.8299 13518.235 -13518.235
|
||||
1420 1818.6697 -2079.0462 -2079.0462 13733.805 -13733.805
|
||||
1430 1760.3629 -2075.8907 -2075.8907 13140.244 -13140.244
|
||||
1440 1797.4632 -2078.982 -2078.982 11102.802 -11102.802
|
||||
1450 1787.354 -2078.9476 -2078.9476 11338.448 -11338.448
|
||||
1460 1762.8326 -2077.925 -2077.925 11770.958 -11770.958
|
||||
1470 1798.49 -2080.8371 -2080.8371 11559.353 -11559.353
|
||||
1480 1811.1557 -2082.2118 -2082.2118 13113.303 -13113.303
|
||||
1490 1874.659 -2086.985 -2086.985 13079.855 -13079.855
|
||||
1500 1882.075 -2088.1491 -2088.1491 13822.082 -13822.082
|
||||
Loop time of 0.235105 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1500 1882.075 -2088.1491 -2088.1491 13822.082 -13822.082
|
||||
1519 1882.075 -2213.3023 -2213.3023 9541.1899 -9541.1899
|
||||
Loop time of 0.0446088 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1500 1882.075 -2088.1491 -2088.1491 13822.082 -13822.082
|
||||
1510 1847.5745 -2086.6473 -2086.6473 13865.395 -13865.395
|
||||
1520 1776.4045 -2082.7466 -2082.7466 12604.819 -12604.819
|
||||
1530 1744.8455 -2081.3864 -2081.3864 11823.185 -11823.185
|
||||
1540 1769.32 -2083.6389 -2083.6389 10753.254 -10753.254
|
||||
1550 1767.1256 -2084.0617 -2084.0617 10187.637 -10187.637
|
||||
1560 1736.4738 -2082.5362 -2082.5362 11049.891 -11049.891
|
||||
1570 1700.4926 -2080.5399 -2080.5399 12042.247 -12042.247
|
||||
1580 1696.0678 -2080.4908 -2080.4908 11552.055 -11552.055
|
||||
1590 1720.0071 -2082.1654 -2082.1654 11110.307 -11110.307
|
||||
1600 1810.361 -2088.1464 -2088.1464 11402.751 -11402.751
|
||||
Loop time of 0.23611 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1600 1810.361 -2088.1464 -2088.1464 11402.751 -11402.751
|
||||
1617 1810.361 -2213.2909 -2213.2909 9047.1326 -9047.1326
|
||||
Loop time of 0.0470579 on 1 procs for 17 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1600 1810.361 -2088.1464 -2088.1464 11402.751 -11402.751
|
||||
1610 1738.2296 -2084.0656 -2084.0656 11367.025 -11367.025
|
||||
1620 1732.2548 -2079.551 -2079.551 11352.482 -11352.482
|
||||
1630 1823.6067 -2081.0447 -2081.0447 11759.019 -11759.019
|
||||
1640 1747.0418 -2077.4773 -2077.4773 11967.929 -11967.929
|
||||
1650 1811.7099 -2078.1627 -2078.1627 11353.138 -11353.138
|
||||
1660 1706.9977 -2071.9188 -2071.9188 10638.169 -10638.169
|
||||
1670 1829.7223 -2073.7338 -2073.7338 11869.478 -11869.478
|
||||
1680 1811.4357 -2074.3495 -2074.3495 12307.737 -12307.737
|
||||
1690 1714.1408 -2068.5122 -2068.5122 13422.716 -13422.716
|
||||
1700 1889.8094 -2074.2435 -2074.2435 13671.805 -13671.805
|
||||
Loop time of 0.233786 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1600 1889.8094 -2074.2435 -2074.2435 13671.805 -13671.805
|
||||
1610 1960.8575 -2078.866 -2078.866 12934.864 -12934.864
|
||||
1620 1923.6166 -2076.54 -2076.54 14112.707 -14112.707
|
||||
1630 1944.7555 -2078.2457 -2078.2457 13865.325 -13865.325
|
||||
1640 1902.2989 -2075.9002 -2075.9002 13297.512 -13297.512
|
||||
1650 1849.5907 -2072.9273 -2072.9273 13933.385 -13933.385
|
||||
1660 1926.326 -2078.5135 -2078.5135 13981.854 -13981.854
|
||||
1670 1920.9614 -2078.7358 -2078.7358 13767.146 -13767.146
|
||||
1680 1850.6527 -2074.6766 -2074.6766 13812.372 -13812.372
|
||||
1690 1863.9535 -2076.0517 -2076.0517 12782.004 -12782.004
|
||||
1700 1893.9231 -2078.4898 -2078.4898 12720.592 -12720.592
|
||||
Loop time of 0.236353 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1700 1893.9231 -2078.4898 -2078.4898 12720.592 -12720.592
|
||||
1716 1893.9231 -2213.2837 -2213.2837 9620.0072 -9620.0072
|
||||
Loop time of 0.040257 on 1 procs for 16 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1700 1893.9231 -2078.4898 -2078.4898 12720.592 -12720.592
|
||||
1710 1875.7299 -2077.7377 -2077.7377 13345.116 -13345.116
|
||||
1720 1898.0515 -2079.6613 -2079.6613 14132.452 -14132.452
|
||||
1730 1882.8777 -2079.146 -2079.146 13699.059 -13699.059
|
||||
1740 1816.9287 -2075.2717 -2075.2717 13073.965 -13073.965
|
||||
1750 1862.4091 -2078.7296 -2078.7296 12789.163 -12789.163
|
||||
1760 1893.0397 -2081.2522 -2081.2522 13312.699 -13312.699
|
||||
1770 1834.7444 -2077.9575 -2077.9575 14033.233 -14033.233
|
||||
1780 1864.6391 -2080.5104 -2080.5104 13228.094 -13228.094
|
||||
1790 1854.6185 -2080.4852 -2080.4852 12156.34 -12156.34
|
||||
1800 1783.2906 -2076.4283 -2076.4283 12334.453 -12334.453
|
||||
Loop time of 0.236237 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1800 1783.2906 -2076.4283 -2076.4283 12334.453 -12334.453
|
||||
1817 1783.2906 -2213.2924 -2213.2924 8858.239 -8858.239
|
||||
Loop time of 0.044467 on 1 procs for 17 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1800 1783.2906 -2076.1141 -2076.1141 12468.46 -12468.46
|
||||
1810 1845.4581 -2080.8627 -2080.8627 12506.58 -12506.58
|
||||
1820 1801.3296 -2078.6098 -2078.6098 13055.572 -13055.572
|
||||
1830 1777.9523 -2077.7188 -2077.7188 12729.867 -12729.867
|
||||
1840 1758.541 -2077.0154 -2077.0154 12518.443 -12518.443
|
||||
1850 1828.6136 -2082.1861 -2082.1861 11837.329 -11837.329
|
||||
1860 1826.6839 -2082.6205 -2082.6205 12848.747 -12848.747
|
||||
1870 1848.9771 -2084.6985 -2084.6985 14273.245 -14273.245
|
||||
1880 1859.0854 -2086.037 -2086.037 13956.23 -13956.23
|
||||
1890 1826.3509 -2084.6002 -2084.6002 13737.356 -13737.356
|
||||
1900 1856.0966 -2087.3351 -2087.3351 13759.117 -13759.117
|
||||
Loop time of 0.233077 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1900 1856.0966 -2087.3351 -2087.3351 13759.117 -13759.117
|
||||
1921 1856.0966 -2213.3256 -2213.3256 9364.6843 -9364.6843
|
||||
Loop time of 0.058537 on 1 procs for 21 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1900 1856.0966 -2087.3351 -2087.3351 13759.117 -13759.117
|
||||
1910 1732.1651 -2081.2025 -2081.2025 13648.771 -13648.771
|
||||
1920 1791.3554 -2081.3056 -2081.3056 13652.014 -13652.014
|
||||
1930 1824.4855 -2083.5698 -2083.5698 13761.469 -13761.469
|
||||
1940 1789.0389 -2083.4838 -2083.4838 12938.14 -12938.14
|
||||
1950 1754.5722 -2081.062 -2081.062 13678.133 -13678.133
|
||||
1960 1790.0373 -2080.9357 -2080.9357 13972.404 -13972.404
|
||||
1970 1815.9084 -2082.4892 -2082.4892 13423.516 -13423.516
|
||||
1980 1741.0456 -2079.056 -2079.056 13024.446 -13024.446
|
||||
1990 1845.2042 -2082.4853 -2082.4853 12369.149 -12369.149
|
||||
2000 1726.2212 -2078.0219 -2078.0219 12670.669 -12670.669
|
||||
Loop time of 0.235034 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1900 1726.2212 -2078.0219 -2078.0219 12670.669 -12670.669
|
||||
1910 1859.235 -2087.1634 -2087.1634 12382.624 -12382.624
|
||||
1920 1859.3456 -2087.6091 -2087.6091 12482.545 -12482.545
|
||||
1930 1748.0548 -2080.7392 -2080.7392 13217.457 -13217.457
|
||||
1940 1876.5822 -2089.6972 -2089.6972 12827.369 -12827.369
|
||||
1950 1858.9549 -2089.1237 -2089.1237 12267.563 -12267.563
|
||||
1960 1661.6597 -2076.6976 -2076.6976 13069.247 -13069.247
|
||||
1970 1739.6756 -2082.3166 -2082.3166 13000.655 -13000.655
|
||||
1980 1831.8527 -2088.8393 -2088.8393 11823.386 -11823.386
|
||||
1990 1661.818 -2078.0492 -2078.0492 12159.308 -12159.308
|
||||
2000 1700.7919 -2080.912 -2080.912 11889.457 -11889.457
|
||||
Loop time of 0.237266 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
2000 1700.7919 -2080.912 -2080.912 11889.457 -11889.457
|
||||
2019 1700.7919 -2213.3012 -2213.3012 8294.8879 -8294.8879
|
||||
Loop time of 0.0530901 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
2000 1700.7919 -2080.912 -2080.912 11889.457 -11889.457
|
||||
2010 1861.3608 -2091.7401 -2091.7401 11627.567 -11627.567
|
||||
2020 1723.5921 -2082.9109 -2082.9109 11679.426 -11679.426
|
||||
2030 1715.155 -2082.5582 -2082.5582 12295.003 -12295.003
|
||||
2040 1850.4844 -2091.6449 -2091.6449 12563.959 -12563.959
|
||||
2050 1761.29 -2085.9529 -2085.9529 13011.92 -13011.92
|
||||
2060 1706.9101 -2082.541 -2082.541 13421.673 -13421.673
|
||||
2070 1819.5707 -2090.0959 -2090.0959 12744.935 -12744.935
|
||||
2080 1798.901 -2088.8739 -2088.8739 12477.746 -12477.746
|
||||
2090 1722.8968 -2084.0198 -2084.0198 12266.395 -12266.395
|
||||
2100 1780.5329 -2087.9446 -2087.9446 12351.983 -12351.983
|
||||
Loop time of 0.233801 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
2100 1780.5329 -2087.9446 -2087.9446 12351.983 -12351.983
|
||||
2118 1780.5329 -2213.3048 -2213.3048 8843.7542 -8843.7542
|
||||
Loop time of 0.0496428 on 1 procs for 18 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
2100 1780.5329 -2081.5748 -2081.5748 11485.708 -11485.708
|
||||
Loop time of 7.43975 on 1 procs for 18 steps with 511 atoms
|
||||
|
||||
PRD stats:
|
||||
Dephase time (%) = 1.39139 (18.7021)
|
||||
Dynamics time (%) = 4.69327 (63.0838)
|
||||
Quench time (%) = 0.975309 (13.1094)
|
||||
Other time (%) = 0.0743728 (0.999668)
|
||||
|
||||
Nlocal: 511 ave 511 max 511 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1017 ave 1017 max 1017 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 13354 ave 13354 max 13354 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 13354
|
||||
Ave neighs/atom = 26.1331
|
||||
Neighbor list builds = 98
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,631 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
Processor partition = 3
|
||||
# Parallel replica dynamics model for a single vacancy in bulk Si
|
||||
# events occur when a neighboring atom diffuses to the vacant site
|
||||
# run this on multiple partitions as
|
||||
# mpirun -np 4 lmp_g++ -partition 4x1 -in in.prd
|
||||
|
||||
#log none
|
||||
|
||||
units metal
|
||||
|
||||
atom_style atomic
|
||||
atom_modify map array
|
||||
boundary p p p
|
||||
atom_modify sort 0 0.0
|
||||
|
||||
# temperature
|
||||
|
||||
variable t equal 1800.0
|
||||
|
||||
# coordination number cutoff
|
||||
|
||||
variable r equal 2.835
|
||||
|
||||
# minimization parameters
|
||||
|
||||
variable etol equal 1.0e-5
|
||||
variable ftol equal 1.0e-5
|
||||
variable maxiter equal 100
|
||||
variable maxeval equal 100
|
||||
variable dmax equal 1.0e-1
|
||||
|
||||
# diamond unit cell
|
||||
|
||||
variable a equal 5.431
|
||||
lattice custom $a a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
lattice custom 5.431 a1 1.0 0.0 0.0 a2 0.0 1.0 0.0 a3 0.0 0.0 1.0 basis 0.0 0.0 0.0 basis 0.0 0.5 0.5 basis 0.5 0.0 0.5 basis 0.5 0.5 0.0 basis 0.25 0.25 0.25 basis 0.25 0.75 0.75 basis 0.75 0.25 0.75 basis 0.75 0.75 0.25
|
||||
Lattice spacing in x,y,z = 5.431 5.431 5.431
|
||||
|
||||
region myreg block 0 4 0 4 0 4
|
||||
create_box 1 myreg
|
||||
Created orthogonal box = (0 0 0) to (21.724 21.724 21.724)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
create_atoms 1 region myreg
|
||||
Created 512 atoms
|
||||
|
||||
mass 1 28.06
|
||||
|
||||
group Si type 1
|
||||
512 atoms in group Si
|
||||
|
||||
velocity all create $t 5287287 mom yes rot yes dist gaussian
|
||||
velocity all create 1800 5287287 mom yes rot yes dist gaussian
|
||||
|
||||
# make a vacancy
|
||||
|
||||
group del id 300
|
||||
1 atoms in group del
|
||||
delete_atoms group del
|
||||
Deleted 1 atoms, new total = 511
|
||||
|
||||
pair_style sw
|
||||
pair_coeff * * Si.sw Si
|
||||
|
||||
thermo 10
|
||||
|
||||
fix 1 all nvt temp $t $t 0.1
|
||||
fix 1 all nvt temp 1800 $t 0.1
|
||||
fix 1 all nvt temp 1800 1800 0.1
|
||||
|
||||
timestep 1.0e-3
|
||||
neighbor 1.0 bin
|
||||
neigh_modify every 1 delay 10 check yes
|
||||
|
||||
# equilibrate
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 2.0318 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 1802.5039 -2211.666 0 -2092.8401 12351.692
|
||||
10 996.01982 -2158.3093 0 -2092.649 14285.475
|
||||
20 590.09928 -2131.1531 0 -2092.2521 12113.964
|
||||
30 1033.01 -2159.2522 0 -2091.1534 6860.4116
|
||||
40 724.76581 -2137.281 0 -2089.5025 5999.4372
|
||||
50 489.66604 -2120.8082 0 -2088.5281 6403.4234
|
||||
60 960.70653 -2150.7394 0 -2087.407 5687.324
|
||||
70 908.41498 -2145.7665 0 -2085.8813 8220.9655
|
||||
80 796.82286 -2137.1227 0 -2084.5941 11307.153
|
||||
90 1245.9045 -2164.9841 0 -2082.8507 11282.071
|
||||
100 1083.0647 -2152.0805 0 -2080.682 12015.018
|
||||
Loop time of 0.203028 on 1 procs for 100 steps with 511 atoms
|
||||
|
||||
Pair time (%) = 0.198757 (97.8963)
|
||||
Neigh time (%) = 0.00147486 (0.726431)
|
||||
Comm time (%) = 0.000895977 (0.441307)
|
||||
Outpt time (%) = 6.69956e-05 (0.0329982)
|
||||
Other time (%) = 0.0018332 (0.90293)
|
||||
|
||||
Nlocal: 511 ave 511 max 511 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1017 ave 1017 max 1017 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 13996 ave 13996 max 13996 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 13996
|
||||
Ave neighs/atom = 27.3894
|
||||
Neighbor list builds = 2
|
||||
Dangerous builds = 0
|
||||
|
||||
# only output atoms near vacancy
|
||||
|
||||
compute coord all coord/atom $r
|
||||
compute coord all coord/atom 2.835
|
||||
|
||||
#dump events all custom 1 dump.prd id type x y z
|
||||
#dump_modify events thresh c_coord != 4
|
||||
|
||||
compute patom all pe/atom
|
||||
compute pe all reduce sum c_patom
|
||||
compute satom all stress/atom
|
||||
compute str all reduce sum c_satom[1] c_satom[2] c_satom[3]
|
||||
variable press equal (c_str[1]+c_str[2]+c_str[3])/(3*vol)
|
||||
|
||||
thermo_style custom step temp pe c_pe press v_press
|
||||
|
||||
compute 1 all event/displace 0.5
|
||||
|
||||
prd 2000 100 10 10 100 1 54985 temp $t min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
|
||||
prd 2000 100 10 10 100 1 54985 temp 1800 min ${etol} ${ftol} ${maxiter} ${maxeval} vel all uniform
|
||||
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 ${ftol} ${maxiter} ${maxeval} vel all uniform
|
||||
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 ${maxiter} ${maxeval} vel all uniform
|
||||
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 100 ${maxeval} vel all uniform
|
||||
prd 2000 100 10 10 100 1 54985 temp 1800 min 1e-05 1e-05 100 100 vel all uniform
|
||||
WARNING: Resetting reneighboring criteria during PRD (../prd.cpp:201)
|
||||
Memory usage per processor = 3.74841 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
|
||||
110 1083.0647 -2211.0684 -2211.0684 7372.2593 -7372.2593
|
||||
119 1083.0647 -2211.6557 -2211.6557 7411.1722 -7411.1722
|
||||
Loop time of 0.0573561 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
100 1083.0647 -2152.0805 -2152.0805 12015.018 -12015.018
|
||||
110 1495.0763 -2129.2427 -2129.2427 17292.034 -17292.034
|
||||
120 1695.6936 -2119.9568 -2119.9568 19395.276 -19395.276
|
||||
130 1720.2165 -2112.5918 -2112.5918 19379.647 -19379.647
|
||||
140 1792.9012 -2110.2027 -2110.2027 20162.681 -20162.681
|
||||
150 1826.4633 -2110.1906 -2110.1906 19821.473 -19821.473
|
||||
160 1707.1346 -2102.4592 -2102.4592 19283.638 -19283.638
|
||||
170 1889.7308 -2106.7875 -2106.7875 19121.04 -19121.04
|
||||
180 1726.1399 -2100.5051 -2100.5051 17912.961 -17912.961
|
||||
190 1725.2909 -2094.183 -2094.183 17836.706 -17836.706
|
||||
200 1797.4072 -2092.6159 -2092.6159 17749.283 -17749.283
|
||||
Loop time of 0.233799 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
100 1797.4072 -2092.6159 -2092.6159 17749.283 -17749.283
|
||||
110 1749.1865 -2088.09 -2088.09 17886.987 -17886.987
|
||||
120 1730.091 -2085.5138 -2085.5138 16298.238 -16298.238
|
||||
130 1725.5695 -2083.8602 -2083.8602 14810.515 -14810.515
|
||||
140 1742.8337 -2083.604 -2083.604 14304.4 -14304.4
|
||||
150 1755.1691 -2082.9974 -2082.9974 14289.749 -14289.749
|
||||
160 1730.1652 -2079.9294 -2079.9294 14796.483 -14796.483
|
||||
170 1746.47 -2079.5667 -2079.5667 14891.286 -14891.286
|
||||
180 1867.6791 -2086.0994 -2086.0994 15143.089 -15143.089
|
||||
190 1826.3577 -2081.9693 -2081.9693 14842.324 -14842.324
|
||||
200 1890.4086 -2084.9324 -2084.9324 15298.464 -15298.464
|
||||
Loop time of 0.243497 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
200 1890.4086 -2084.9324 -2084.9324 15298.464 -15298.464
|
||||
218 1890.4086 -2213.3051 -2213.3051 9595.2117 -9595.2117
|
||||
Loop time of 0.049082 on 1 procs for 18 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
200 1890.4086 -2083.245 -2083.245 15721.201 -15721.201
|
||||
210 1895.0321 -2082.3794 -2082.3794 16182.652 -16182.652
|
||||
220 1967.6529 -2086.173 -2086.173 15532.872 -15532.872
|
||||
230 1820.3126 -2075.6591 -2075.6591 15093.435 -15093.435
|
||||
240 1713.4056 -2067.9324 -2067.9324 14623.702 -14623.702
|
||||
250 1806.5325 -2073.3192 -2073.3192 13241.861 -13241.861
|
||||
260 1838.2185 -2074.62 -2074.62 12793.039 -12793.039
|
||||
270 1796.1907 -2071.1002 -2071.1002 13382.202 -13382.202
|
||||
280 1855.3253 -2074.2821 -2074.2821 14014.125 -14014.125
|
||||
290 1915.1832 -2077.5543 -2077.5543 15817.805 -15817.805
|
||||
300 1943.8007 -2078.9069 -2078.9069 17664.976 -17664.976
|
||||
Loop time of 0.246055 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
300 1943.8007 -2078.9069 -2078.9069 17664.976 -17664.976
|
||||
320 1943.8007 -2213.3262 -2213.3262 9968.2615 -9968.2615
|
||||
Loop time of 0.056031 on 1 procs for 20 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
300 1943.8007 -2078.9069 -2078.9069 17664.976 -17664.976
|
||||
310 1830.358 -2077.8168 -2077.8168 14980.856 -14980.856
|
||||
320 1816.8748 -2078.525 -2078.525 14548.875 -14548.875
|
||||
330 1812.5384 -2078.949 -2078.949 13614.012 -13614.012
|
||||
340 1854.3003 -2082.1223 -2082.1223 13185.902 -13185.902
|
||||
350 1853.1764 -2085.2567 -2085.2567 12110.408 -12110.408
|
||||
360 1853.1119 -2088.4344 -2088.4344 12224.055 -12224.055
|
||||
370 1837.6042 -2090.6376 -2090.6376 11312.576 -11312.576
|
||||
380 1790.0042 -2089.7364 -2089.7364 11726.39 -11726.39
|
||||
390 1704.071 -2083.1405 -2083.1405 11697.254 -11697.254
|
||||
400 1828.0893 -2084.6844 -2084.6844 12331.728 -12331.728
|
||||
Loop time of 0.229254 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
300 1828.0893 -2084.6844 -2084.6844 12331.728 -12331.728
|
||||
310 1818.7058 -2083.7777 -2083.7777 13364.201 -13364.201
|
||||
320 1784.6932 -2081.2738 -2081.2738 13319.356 -13319.356
|
||||
330 1781.3136 -2080.7661 -2080.7661 12726.586 -12726.586
|
||||
340 1850.504 -2085.0411 -2085.0411 12804.72 -12804.72
|
||||
350 1806.9896 -2081.9086 -2081.9086 12799.418 -12799.418
|
||||
360 1797.0754 -2081.008 -2081.008 12932.182 -12932.182
|
||||
370 1939.3485 -2090.1815 -2090.1815 12022.081 -12022.081
|
||||
380 1833.459 -2083.0989 -2083.0989 12722.114 -12722.114
|
||||
390 1767.2468 -2078.7079 -2078.7079 12994.83 -12994.83
|
||||
400 1840.9497 -2083.5253 -2083.5253 12470.362 -12470.362
|
||||
Loop time of 0.235618 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
400 1840.9497 -2083.5253 -2083.5253 12470.362 -12470.362
|
||||
418 1840.9497 -2213.3059 -2213.3059 9257.8757 -9257.8757
|
||||
Loop time of 0.0489299 on 1 procs for 18 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
400 1840.9497 -2083.5253 -2083.5253 12470.362 -12470.362
|
||||
410 1825.8375 -2082.5217 -2082.5217 12012.844 -12012.844
|
||||
420 1723.3215 -2075.7602 -2075.7602 11394.557 -11394.557
|
||||
430 1764.1446 -2078.4055 -2078.4055 9429.6621 -9429.6621
|
||||
440 1722.8256 -2075.5423 -2075.5423 10622.932 -10622.932
|
||||
450 1746.9424 -2076.92 -2076.92 11529.679 -11529.679
|
||||
460 1837.7686 -2082.6258 -2082.6258 12192.008 -12192.008
|
||||
470 1853.9148 -2083.4249 -2083.4249 13244.632 -13244.632
|
||||
480 1853.6885 -2083.2159 -2083.2159 14116.299 -14116.299
|
||||
490 1915.2224 -2087.1642 -2087.1642 14632.565 -14632.565
|
||||
500 1936.7625 -2088.6317 -2088.6317 14188.134 -14188.134
|
||||
Loop time of 0.234017 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
500 1936.7625 -2088.6317 -2088.6317 14188.134 -14188.134
|
||||
519 1936.7625 -2213.3032 -2213.3032 9913.4596 -9913.4596
|
||||
Loop time of 0.047586 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
500 1936.7625 -2088.6317 -2088.6317 14188.134 -14188.134
|
||||
510 1834.5516 -2082.0916 -2082.0916 13945.662 -13945.662
|
||||
520 1805.8538 -2080.48 -2080.48 11915.304 -11915.304
|
||||
530 1719.5829 -2075.0416 -2075.0416 10641.83 -10641.83
|
||||
540 1700.9425 -2073.9843 -2073.9843 10638.084 -10638.084
|
||||
550 1721.0296 -2075.3479 -2075.3479 10855.732 -10855.732
|
||||
560 1792.256 -2080.0028 -2080.0028 10718.277 -10718.277
|
||||
570 1816.469 -2081.5215 -2081.5215 12281.721 -12281.721
|
||||
580 1898.1645 -2086.8779 -2086.8779 13891.519 -13891.519
|
||||
590 1909.9896 -2087.7381 -2087.7381 15407.945 -15407.945
|
||||
600 1905.9376 -2087.7136 -2087.7136 15536.218 -15536.218
|
||||
Loop time of 0.234394 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
600 1905.9376 -2087.7136 -2087.7136 15536.218 -15536.218
|
||||
620 1905.9376 -2213.3226 -2213.3226 9705.2581 -9705.2581
|
||||
Loop time of 0.053184 on 1 procs for 20 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
600 1905.9376 -2087.7136 -2087.7136 15536.218 -15536.218
|
||||
610 1898.495 -2087.6161 -2087.6161 13863.644 -13863.644
|
||||
620 1873.699 -2086.5202 -2086.5202 11778.817 -11778.817
|
||||
630 1744.3676 -2078.5837 -2078.5837 11019.865 -11019.865
|
||||
640 1681.2181 -2074.9263 -2074.9263 9815.9404 -9815.9404
|
||||
650 1707.9678 -2077.065 -2077.065 10236.708 -10236.708
|
||||
660 1719.4888 -2078.0855 -2078.0855 10716.295 -10716.295
|
||||
670 1694.7476 -2076.6002 -2076.6002 10237.649 -10237.649
|
||||
680 1773.8128 -2081.8591 -2081.8591 12034.22 -12034.22
|
||||
690 1832.6905 -2085.7381 -2085.7381 12268.403 -12268.403
|
||||
700 1872.2418 -2088.3939 -2088.3939 12841.871 -12841.871
|
||||
Loop time of 0.23455 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
700 1872.2418 -2088.3939 -2088.3939 12841.871 -12841.871
|
||||
718 1872.2418 -2213.2732 -2213.2732 9469.3455 -9469.3455
|
||||
Loop time of 0.048511 on 1 procs for 18 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
700 1872.2418 -2088.3939 -2088.3939 12841.871 -12841.871
|
||||
710 1856.1726 -2087.4734 -2087.4734 12587.6 -12587.6
|
||||
720 1809.0844 -2084.5719 -2084.5719 11962.825 -11962.825
|
||||
730 1813.7498 -2085.1228 -2085.1228 12275.918 -12275.918
|
||||
740 1778.4404 -2083.0339 -2083.0339 12609.945 -12609.945
|
||||
750 1793.7621 -2084.2846 -2084.2846 12022.021 -12022.021
|
||||
760 1756.218 -2082.0146 -2082.0146 11970.105 -11970.105
|
||||
770 1788.1399 -2084.3038 -2084.3038 11486.204 -11486.204
|
||||
780 1752.5386 -2082.1061 -2082.1061 11773.768 -11773.768
|
||||
790 1737.5719 -2081.2139 -2081.2139 12812.397 -12812.397
|
||||
800 1760.5292 -2082.7503 -2082.7503 13832.216 -13832.216
|
||||
Loop time of 0.237893 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
800 1760.5292 -2082.7503 -2082.7503 13832.216 -13832.216
|
||||
817 1760.5292 -2213.2818 -2213.2818 8701.2542 -8701.2542
|
||||
Loop time of 0.0461509 on 1 procs for 17 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
800 1760.5292 -2082.7503 -2082.7503 13832.216 -13832.216
|
||||
810 1824.7855 -2084.3929 -2084.3929 13668.719 -13668.719
|
||||
820 1712.4425 -2078.6074 -2078.6074 12847.66 -12847.66
|
||||
830 1875.2236 -2083.5586 -2083.5586 12721.192 -12721.192
|
||||
840 1802.2145 -2083.7392 -2083.7392 11989.282 -11989.282
|
||||
850 1820.2177 -2085.1324 -2085.1324 11057.193 -11057.193
|
||||
860 1730.3595 -2080.5914 -2080.5914 11507.405 -11507.405
|
||||
870 1809.9784 -2081.2823 -2081.2823 12298.894 -12298.894
|
||||
880 1803.9222 -2081.5723 -2081.5723 11947.359 -11947.359
|
||||
890 1757.0085 -2078.7491 -2078.7491 12561.76 -12561.76
|
||||
900 1809.447 -2079.3762 -2079.3762 12554.534 -12554.534
|
||||
Loop time of 0.236594 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
800 1809.447 -2079.3762 -2079.3762 12554.534 -12554.534
|
||||
810 1806.5101 -2079.1895 -2079.1895 11903.119 -11903.119
|
||||
820 1785.2438 -2077.8038 -2077.8038 11702.485 -11702.485
|
||||
830 1781.1685 -2077.5303 -2077.5303 12703.961 -12703.961
|
||||
840 1863.47 -2082.9537 -2082.9537 13361.794 -13361.794
|
||||
850 1879.7765 -2084.0849 -2084.0849 14480.503 -14480.503
|
||||
860 1906.2551 -2086.0185 -2086.0185 14752.263 -14752.263
|
||||
870 1882.1344 -2084.7545 -2084.7545 15091.996 -15091.996
|
||||
880 1868.6595 -2084.3355 -2084.3355 14227.917 -14227.917
|
||||
890 1806.8883 -2080.8098 -2080.8098 13418.625 -13418.625
|
||||
900 1813.034 -2081.8053 -2081.8053 13267.308 -13267.308
|
||||
Loop time of 0.231518 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
900 1813.034 -2081.8053 -2081.8053 13267.308 -13267.308
|
||||
917 1813.034 -2213.2328 -2213.2328 9058.7627 -9058.7627
|
||||
Loop time of 0.0442312 on 1 procs for 17 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
900 1813.034 -2081.8053 -2081.8053 13267.308 -13267.308
|
||||
910 1790.47 -2080.925 -2080.925 13187.347 -13187.347
|
||||
920 1773.8688 -2080.4392 -2080.4392 12634.894 -12634.894
|
||||
930 1785.9855 -2081.8252 -2081.8252 12561.505 -12561.505
|
||||
940 1801.3588 -2083.4277 -2083.4277 12028.691 -12028.691
|
||||
950 1778.6138 -2082.521 -2082.521 12646.355 -12646.355
|
||||
960 1764.4699 -2082.1518 -2082.1518 11945.626 -11945.626
|
||||
970 1778.2914 -2083.5962 -2083.5962 11676.59 -11676.59
|
||||
980 1763.0077 -2083.0977 -2083.0977 12675.07 -12675.07
|
||||
990 1724.8156 -2081.0275 -2081.0275 12706.385 -12706.385
|
||||
1000 1789.1021 -2085.6571 -2085.6571 12733.814 -12733.814
|
||||
Loop time of 0.236168 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1000 1789.1021 -2085.6571 -2085.6571 12733.814 -12733.814
|
||||
1019 1789.1021 -2213.3142 -2213.3142 8903.9364 -8903.9364
|
||||
Loop time of 0.0571361 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1000 1789.1021 -2085.6571 -2085.6571 12733.814 -12733.814
|
||||
1010 1803.5662 -2086.2788 -2086.2788 12296.832 -12296.832
|
||||
1020 1721.4631 -2081.4632 -2081.4632 12617.022 -12617.022
|
||||
1030 1901.5059 -2088.5616 -2088.5616 13322.949 -13322.949
|
||||
1040 1790.4919 -2088.3943 -2088.3943 11842.661 -11842.661
|
||||
1050 1728.9375 -2084.1491 -2084.1491 11186.843 -11186.843
|
||||
1060 1822.9805 -2086.1115 -2086.1115 11654.623 -11654.623
|
||||
1070 1793.5987 -2086.1655 -2086.1655 11565.879 -11565.879
|
||||
1080 1774.9684 -2085.0099 -2085.0099 11788.082 -11788.082
|
||||
1090 1875.45 -2090.5357 -2090.5357 12023.082 -12023.082
|
||||
1100 1770.2149 -2089.1678 -2089.1678 11314.012 -11314.012
|
||||
Loop time of 0.240704 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1000 1770.2149 -2089.1678 -2089.1678 11314.012 -11314.012
|
||||
1010 1751.5551 -2088.5144 -2088.5144 11418.611 -11418.611
|
||||
1020 1783.4529 -2091.1906 -2091.1906 11869.563 -11869.563
|
||||
1030 1724.468 -2087.853 -2087.853 11660.095 -11660.095
|
||||
1040 1700.0952 -2086.721 -2086.721 10696.55 -10696.55
|
||||
1050 1760.1423 -2091.0982 -2091.0982 9178.1354 -9178.1354
|
||||
1060 1644.0734 -2083.7826 -2083.7826 9093.1125 -9093.1125
|
||||
1070 1613.8056 -2081.9631 -2081.9631 9591.8493 -9591.8493
|
||||
1080 1709.8502 -2088.2878 -2088.2878 9538.5577 -9538.5577
|
||||
1090 1676.8021 -2085.9346 -2085.9346 10766.925 -10766.925
|
||||
1100 1718.403 -2088.3484 -2088.3484 10949.517 -10949.517
|
||||
Loop time of 0.240443 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1100 1718.403 -2088.3484 -2088.3484 10949.517 -10949.517
|
||||
1117 1718.403 -2213.2587 -2213.2587 8409.3544 -8409.3544
|
||||
Loop time of 0.0466011 on 1 procs for 17 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1100 1718.403 -2088.3484 -2088.3484 10949.517 -10949.517
|
||||
1110 1765.1951 -2090.924 -2090.924 10989.261 -10989.261
|
||||
1120 1739.4922 -2088.58 -2088.58 11689.558 -11689.558
|
||||
1130 1727.0447 -2086.942 -2086.942 12283.035 -12283.035
|
||||
1140 1785.7915 -2089.784 -2089.784 11818.431 -11818.431
|
||||
1150 1809.8869 -2090.1546 -2090.1546 10879.76 -10879.76
|
||||
1160 1744.4121 -2084.5197 -2084.5197 11286.034 -11286.034
|
||||
1170 1757.7394 -2084.0004 -2084.0004 11548.282 -11548.282
|
||||
1180 1821.8601 -2086.7401 -2086.7401 11282.746 -11282.746
|
||||
1190 1801.9718 -2084.0004 -2084.0004 11879.914 -11879.914
|
||||
1200 1778.413 -2081.1797 -2081.1797 11763.504 -11763.504
|
||||
Loop time of 0.24151 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1200 1778.413 -2081.1797 -2081.1797 11763.504 -11763.504
|
||||
1220 1778.413 -2213.2935 -2213.2935 8826.8778 -8826.8778
|
||||
Loop time of 0.0589371 on 1 procs for 20 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1200 1778.413 -2081.1797 -2081.1797 11763.504 -11763.504
|
||||
1210 1779.9735 -2080.1523 -2080.1523 11767.914 -11767.914
|
||||
1220 1761.523 -2077.9508 -2077.9508 12102.479 -12102.479
|
||||
1230 1799.751 -2079.6111 -2079.6111 11976.738 -11976.738
|
||||
1240 1852.8341 -2082.3812 -2082.3812 12122.449 -12122.449
|
||||
1250 1835.3624 -2080.6598 -2080.6598 12594.439 -12594.439
|
||||
1260 1822.3142 -2079.3754 -2079.3754 12980.571 -12980.571
|
||||
1270 1824.7898 -2079.2048 -2079.2048 13133.515 -13133.515
|
||||
1280 1835.3097 -2079.6291 -2079.6291 13141.016 -13141.016
|
||||
1290 1918.3152 -2084.9315 -2084.9315 12831.552 -12831.552
|
||||
1300 1872.0268 -2081.8383 -2081.8383 12855.872 -12855.872
|
||||
Loop time of 0.237981 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1300 1872.0268 -2081.8383 -2081.8383 12855.872 -12855.872
|
||||
1320 1872.0268 -2213.3016 -2213.3016 9471.4837 -9471.4837
|
||||
Loop time of 0.0573471 on 1 procs for 20 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1300 1872.0268 -2081.8383 -2081.8383 12855.872 -12855.872
|
||||
1310 1842.2091 -2079.9447 -2079.9447 11930.547 -11930.547
|
||||
1320 1839.1324 -2079.8702 -2079.8702 11520.211 -11520.211
|
||||
1330 1781.5944 -2076.2294 -2076.2294 12517.772 -12517.772
|
||||
1340 1808.2791 -2078.1377 -2078.1377 12331.797 -12331.797
|
||||
1350 1825.5011 -2079.4214 -2079.4214 12959.817 -12959.817
|
||||
1360 1805.1617 -2078.2612 -2078.2612 12283.097 -12283.097
|
||||
1370 1794.2198 -2077.7174 -2077.7174 11854.379 -11854.379
|
||||
1380 1856.0315 -2081.9959 -2081.9959 12222.656 -12222.656
|
||||
1390 1830.6929 -2080.5837 -2080.5837 12676.219 -12676.219
|
||||
1400 1787.3453 -2078.0218 -2078.0218 12795.723 -12795.723
|
||||
Loop time of 0.238381 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1400 1787.3453 -2078.0218 -2078.0218 12795.723 -12795.723
|
||||
1419 1787.3453 -2213.3099 -2213.3099 8888.2838 -8888.2838
|
||||
Loop time of 0.054687 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1400 1787.3453 -2083.1407 -2083.1407 12644.184 -12644.184
|
||||
1410 1858.6264 -2088.1699 -2088.1699 13665.536 -13665.536
|
||||
1420 1836.7078 -2087.1342 -2087.1342 13718.627 -13718.627
|
||||
1430 1761.5946 -2082.6238 -2082.6238 13729.715 -13729.715
|
||||
1440 1825.9335 -2087.3258 -2087.3258 13009.414 -13009.414
|
||||
1450 1817.7629 -2087.2906 -2087.2906 12876.965 -12876.965
|
||||
1460 1773.2189 -2084.9022 -2084.9022 12124.77 -12124.77
|
||||
1470 1742.8153 -2083.4385 -2083.4385 11686.602 -11686.602
|
||||
1480 1741.4145 -2083.843 -2083.843 11494.225 -11494.225
|
||||
1490 1765.3668 -2085.8995 -2085.8995 11215.781 -11215.781
|
||||
1500 1760.2197 -2086.0116 -2086.0116 11232.652 -11232.652
|
||||
Loop time of 0.240801 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1500 1760.2197 -2086.0116 -2086.0116 11232.652 -11232.652
|
||||
1517 1760.2197 -2213.245 -2213.245 8696.1847 -8696.1847
|
||||
Loop time of 0.0474579 on 1 procs for 17 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1500 1760.2197 -2088.1491 -2088.1491 12985.172 -12985.172
|
||||
1510 1927.1878 -2099.7308 -2099.7308 12023.236 -12023.236
|
||||
1520 1616.4053 -2079.8776 -2079.8776 12507.037 -12507.037
|
||||
1530 1598.2599 -2079.1598 -2079.1598 11597.301 -11597.301
|
||||
1540 1792.8199 -2092.3519 -2092.3519 10302.629 -10302.629
|
||||
1550 1633.2272 -2082.1258 -2082.1258 11028.733 -11028.733
|
||||
1560 1596.4787 -2079.8411 -2079.8411 11401.206 -11401.206
|
||||
1570 1803.3749 -2093.4571 -2093.4571 11211.847 -11211.847
|
||||
1580 1632.0154 -2081.9939 -2081.9939 13381.635 -13381.635
|
||||
1590 1718.3971 -2087.372 -2087.372 14772.258 -14772.258
|
||||
1600 2048.734 -2108.6472 -2108.6472 14338.8 -14338.8
|
||||
Loop time of 0.244154 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1600 2048.734 -2108.6472 -2108.6472 14338.8 -14338.8
|
||||
1618 2048.734 -2213.2799 -2213.2799 10685.447 -10685.447
|
||||
Loop time of 0.0417359 on 1 procs for 18 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1600 2048.734 -2108.6472 -2108.6472 14338.8 -14338.8
|
||||
1610 1699.675 -2080.9037 -2080.9037 11840.386 -11840.386
|
||||
1620 1817.4828 -2081.4111 -2081.4111 13490.885 -13490.885
|
||||
1630 1813.0686 -2081.5266 -2081.5266 13881.909 -13881.909
|
||||
1640 1779.9893 -2079.3276 -2079.3276 13857.386 -13857.386
|
||||
1650 1937.4396 -2087.3853 -2087.3853 13788.514 -13788.514
|
||||
1660 1762.8309 -2083.9296 -2083.9296 12151.903 -12151.903
|
||||
1670 1791.277 -2082.2407 -2082.2407 12210.144 -12210.144
|
||||
1680 1803.435 -2081.2765 -2081.2765 12398.317 -12398.317
|
||||
1690 1802.7286 -2080.2585 -2080.2585 12311.1 -12311.1
|
||||
1700 1825.8738 -2080.7812 -2080.7812 12487.488 -12487.488
|
||||
Loop time of 0.245493 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1600 1825.8738 -2080.7812 -2080.7812 12487.488 -12487.488
|
||||
1610 1818.7567 -2079.2051 -2079.2051 12961.247 -12961.247
|
||||
1620 1853.2617 -2080.4774 -2080.4774 13334.998 -13334.998
|
||||
1630 1845.6923 -2079.1003 -2079.1003 14024.126 -14024.126
|
||||
1640 1842.4692 -2078.142 -2078.142 13972.69 -13972.69
|
||||
1650 1932.9485 -2083.4976 -2083.4976 13927.397 -13927.397
|
||||
1660 1891.8513 -2080.3519 -2080.3519 14382.688 -14382.688
|
||||
1670 1871.3356 -2078.7396 -2078.7396 15250.018 -15250.018
|
||||
1680 1889.0458 -2079.7669 -2079.7669 14923.552 -14923.552
|
||||
1690 1896.2267 -2080.2296 -2080.2296 13037.903 -13037.903
|
||||
1700 1836.5539 -2076.3875 -2076.3875 12688.151 -12688.151
|
||||
Loop time of 0.244405 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1700 1836.5539 -2076.3875 -2076.3875 12688.151 -12688.151
|
||||
1716 1836.5539 -2213.2588 -2213.2588 9221.7377 -9221.7377
|
||||
Loop time of 0.0448401 on 1 procs for 16 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1700 1836.5539 -2076.3875 -2076.3875 12688.151 -12688.151
|
||||
1710 1859.5138 -2078.0746 -2078.0746 12410.243 -12410.243
|
||||
1720 1819.1932 -2075.6335 -2075.6335 12724.601 -12724.601
|
||||
1730 1813.3698 -2075.501 -2075.501 12702.894 -12702.894
|
||||
1740 1840.4368 -2077.5556 -2077.5556 13145.533 -13145.533
|
||||
1750 1872.195 -2079.983 -2079.983 13220.848 -13220.848
|
||||
1760 1847.9633 -2078.804 -2078.804 13870.064 -13870.064
|
||||
1770 1887.8505 -2081.9384 -2081.9384 15041.963 -15041.963
|
||||
1780 1967.1648 -2087.8474 -2087.8474 14594.014 -14594.014
|
||||
1790 1866.7002 -2082.0986 -2082.0986 13615.248 -13615.248
|
||||
1800 1761.77 -2076.1141 -2076.1141 12320.655 -12320.655
|
||||
Loop time of 0.242938 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1800 1761.77 -2076.1141 -2076.1141 12320.655 -12320.655
|
||||
1819 1761.77 -2213.2705 -2213.2705 8712.9668 -8712.9668
|
||||
Loop time of 0.0457761 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1800 1761.77 -2076.1141 -2076.1141 12320.655 -12320.655
|
||||
1810 1703.4947 -2073.1063 -2073.1063 12008.391 -12008.391
|
||||
1820 1780.1034 -2078.8985 -2078.8985 11424.159 -11424.159
|
||||
1830 1792.3191 -2080.4109 -2080.4109 11527.375 -11527.375
|
||||
1840 1740.7982 -2077.6542 -2077.6542 13041.565 -13041.565
|
||||
1850 1860.8658 -2086.1706 -2086.1706 14356.817 -14356.817
|
||||
1860 1942.1014 -2092.2204 -2092.2204 14527.618 -14527.618
|
||||
1870 1830.8975 -2085.683 -2085.683 15024.292 -15024.292
|
||||
1880 1809.0262 -2085.0269 -2085.0269 14356.631 -14356.631
|
||||
1890 1832.6706 -2087.3315 -2087.3315 13353.932 -13353.932
|
||||
1900 1791.352 -2085.3156 -2085.3156 12909.588 -12909.588
|
||||
Loop time of 0.241951 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1900 1791.352 -2085.3156 -2085.3156 12909.588 -12909.588
|
||||
1917 1791.352 -2213.2561 -2213.2561 8912.2973 -8912.2973
|
||||
Loop time of 0.04723 on 1 procs for 17 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1900 1791.352 -2085.3156 -2085.3156 12909.588 -12909.588
|
||||
1910 1839.8996 -2088.5949 -2088.5949 13946.912 -13946.912
|
||||
1920 1728.8047 -2084.4404 -2084.4404 13398.47 -13398.47
|
||||
1930 1844.6379 -2087.8523 -2087.8523 12606.037 -12606.037
|
||||
1940 1750.4698 -2084.9552 -2084.9552 12830.245 -12830.245
|
||||
1950 1777.4189 -2083.7326 -2083.7326 12890.868 -12890.868
|
||||
1960 1757.0139 -2081.0743 -2081.0743 12928.49 -12928.49
|
||||
1970 1815.4975 -2082.2189 -2082.2189 12590.606 -12590.606
|
||||
1980 1820.5692 -2083.6914 -2083.6914 11259.175 -11259.175
|
||||
1990 1760.8482 -2081.178 -2081.178 12204.966 -12204.966
|
||||
2000 1888.8176 -2087.1036 -2087.1036 12717.455 -12717.455
|
||||
Loop time of 0.241486 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
1900 1888.8176 -2087.1036 -2087.1036 12717.455 -12717.455
|
||||
1910 1835.8382 -2083.7475 -2083.7475 13543.202 -13543.202
|
||||
1920 1838.6207 -2084.1142 -2084.1142 13995.434 -13995.434
|
||||
1930 1844.8228 -2084.7395 -2084.7395 14254.28 -14254.28
|
||||
1940 1809.1821 -2082.6216 -2082.6216 14113.256 -14113.256
|
||||
1950 1866.6498 -2086.6639 -2086.6639 13152.916 -13152.916
|
||||
1960 1854.176 -2086.1617 -2086.1617 11993.967 -11993.967
|
||||
1970 1710.438 -2077.0061 -2077.0061 12356.799 -12356.799
|
||||
1980 1713.8796 -2077.4442 -2077.4442 12066.558 -12066.558
|
||||
1990 1830.1984 -2085.2536 -2085.2536 11224.423 -11224.423
|
||||
2000 1745.1241 -2079.7516 -2079.7516 12000.282 -12000.282
|
||||
Loop time of 0.24176 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
2000 1745.1241 -2079.7516 -2079.7516 12000.282 -12000.282
|
||||
2018 1745.1241 -2213.2723 -2213.2723 8595.2359 -8595.2359
|
||||
Loop time of 0.050736 on 1 procs for 18 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
2000 1745.1241 -2079.7516 -2079.7516 12000.282 -12000.282
|
||||
2010 1764.5303 -2081.1092 -2081.1092 12533.707 -12533.707
|
||||
2020 1803.9081 -2083.7299 -2083.7299 12751.448 -12751.448
|
||||
2030 1839.3617 -2086.0949 -2086.0949 12814.216 -12814.216
|
||||
2040 1868.2548 -2088.0926 -2088.0926 13020.533 -13020.533
|
||||
2050 1793.5586 -2083.3252 -2083.3252 13251.553 -13251.553
|
||||
2060 1775.5342 -2082.3028 -2082.3028 12783.678 -12783.678
|
||||
2070 1851.6766 -2087.482 -2087.482 12508.389 -12508.389
|
||||
2080 1855.9094 -2087.9994 -2087.9994 12382.735 -12382.735
|
||||
2090 1728.9486 -2079.9079 -2079.9079 12119.774 -12119.774
|
||||
2100 1750.5079 -2081.5748 -2081.5748 11279.495 -11279.495
|
||||
Loop time of 0.242399 on 1 procs for 100 steps with 511 atoms
|
||||
Memory usage per processor = 4.28247 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
2100 1750.5079 -2081.5748 -2081.5748 11279.495 -11279.495
|
||||
2119 1750.5079 -2213.2837 -2213.2837 8634.903 -8634.903
|
||||
Loop time of 0.0566661 on 1 procs for 19 steps with 511 atoms
|
||||
Memory usage per processor = 3.59582 Mbytes
|
||||
Step Temp PotEng pe Press press
|
||||
2100 1750.5079 -2081.5748 -2081.5748 11279.495 -11279.495
|
||||
Loop time of 7.43815 on 1 procs for 19 steps with 511 atoms
|
||||
|
||||
PRD stats:
|
||||
Dephase time (%) = 1.42733 (19.1893)
|
||||
Dynamics time (%) = 4.79043 (64.4036)
|
||||
Quench time (%) = 1.00286 (13.4826)
|
||||
Other time (%) = 0.0750105 (1.00846)
|
||||
|
||||
Nlocal: 511 ave 511 max 511 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 1017 ave 1017 max 1017 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 13354 ave 13354 max 13354 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 13354
|
||||
Ave neighs/atom = 26.1331
|
||||
Neighbor list builds = 98
|
||||
Dangerous builds = 0
|
||||
|
|
@ -0,0 +1,54 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# REAX potential for Nitroamines system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.AB
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
104 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.AB H B N
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.ab
|
||||
|
||||
run 3000
|
||||
Memory usage per processor = 17.5352 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -8505.1816 0 -8505.1816 -673.36566
|
||||
3000 523.60359 -8415.8532 0 -8255.0946 1497.0172
|
||||
Loop time of 9.70984 on 1 procs for 3000 steps with 104 atoms
|
||||
|
||||
Pair time (%) = 8.40115 (86.522)
|
||||
Neigh time (%) = 0.296464 (3.05323)
|
||||
Comm time (%) = 0.0213256 (0.219629)
|
||||
Outpt time (%) = 1.69277e-05 (0.000174336)
|
||||
Other time (%) = 0.990889 (10.205)
|
||||
|
||||
Nlocal: 104 ave 104 max 104 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 694 ave 694 max 694 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2874 ave 2874 max 2874 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2874
|
||||
Ave neighs/atom = 27.6346
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,54 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# REAX potential for Nitroamines system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.AB
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
104 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.AB H B N
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.ab
|
||||
|
||||
run 3000
|
||||
Memory usage per processor = 11.7224 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -8505.1816 0 -8505.1816 -673.36566
|
||||
3000 505.80651 -8408.2747 0 -8252.9802 851.95508
|
||||
Loop time of 5.95516 on 4 procs for 3000 steps with 104 atoms
|
||||
|
||||
Pair time (%) = 4.26086 (71.5491)
|
||||
Neigh time (%) = 0.158922 (2.66865)
|
||||
Comm time (%) = 0.090479 (1.51934)
|
||||
Outpt time (%) = 2.29478e-05 (0.000385343)
|
||||
Other time (%) = 1.44487 (24.2626)
|
||||
|
||||
Nlocal: 26 ave 35 max 13 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 1 1
|
||||
Nghost: 422.5 ave 452 max 377 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Neighs: 868 ave 1168 max 440 min
|
||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 3472
|
||||
Ave neighs/atom = 33.3846
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,54 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# REAX potential for AuO system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.AuO
|
||||
orthogonal box = (0 0 0) to (26.1562 21.5425 24.0025)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
960 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.AuO O Au
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.auo
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 154.444 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -72201.743 0 -72201.743 -166.20471
|
||||
100 69.043383 -72076.311 0 -71878.944 22701.376
|
||||
Loop time of 13.9279 on 1 procs for 100 steps with 960 atoms
|
||||
|
||||
Pair time (%) = 11.6061 (83.3297)
|
||||
Neigh time (%) = 0.486255 (3.49123)
|
||||
Comm time (%) = 0.00758123 (0.0544319)
|
||||
Outpt time (%) = 2.09808e-05 (0.000150639)
|
||||
Other time (%) = 1.82796 (13.1244)
|
||||
|
||||
Nlocal: 960 ave 960 max 960 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 6708 ave 6708 max 6708 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 369128 ave 369128 max 369128 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 369128
|
||||
Ave neighs/atom = 384.508
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,54 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# REAX potential for AuO system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.AuO
|
||||
orthogonal box = (0 0 0) to (26.1562 21.5425 24.0025)
|
||||
2 by 1 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
960 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.AuO O Au
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.auo
|
||||
|
||||
run 100
|
||||
Memory usage per processor = 84.6159 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -72201.743 0 -72201.743 -166.19729
|
||||
100 69.043332 -72076.31 0 -71878.942 22702.488
|
||||
Loop time of 6.28791 on 4 procs for 100 steps with 960 atoms
|
||||
|
||||
Pair time (%) = 5.49054 (87.319)
|
||||
Neigh time (%) = 0.240415 (3.82344)
|
||||
Comm time (%) = 0.0205393 (0.326648)
|
||||
Outpt time (%) = 2.40207e-05 (0.000382014)
|
||||
Other time (%) = 0.536393 (8.53055)
|
||||
|
||||
Nlocal: 240 ave 240 max 240 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 3981 ave 3981 max 3981 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 105979 ave 105979 max 105979 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 423916
|
||||
Ave neighs/atom = 441.579
|
||||
Neighbor list builds = 10
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,54 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# REAX potential for CHO system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.CHO
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.cho H C O
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.cho
|
||||
|
||||
run 3000
|
||||
Memory usage per processor = 16.9172 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -10226.557 0 -10226.557 -106.0979
|
||||
3000 548.68937 -10170.445 0 -10000.349 35.642615
|
||||
Loop time of 9.15138 on 1 procs for 3000 steps with 105 atoms
|
||||
|
||||
Pair time (%) = 7.81796 (85.4293)
|
||||
Neigh time (%) = 0.272822 (2.98121)
|
||||
Comm time (%) = 0.019613 (0.214318)
|
||||
Outpt time (%) = 1.69277e-05 (0.000184974)
|
||||
Other time (%) = 1.04097 (11.375)
|
||||
|
||||
Nlocal: 105 ave 105 max 105 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 643 ave 643 max 643 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 4237 ave 4237 max 4237 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 4237
|
||||
Ave neighs/atom = 40.3524
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,54 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# REAX potential for CHO system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.CHO
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.cho H C O
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.cho
|
||||
|
||||
run 3000
|
||||
Memory usage per processor = 12.0941 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -10226.557 0 -10226.557 -106.0979
|
||||
3000 548.88663 -10170.509 0 -10000.351 28.08502
|
||||
Loop time of 5.30386 on 4 procs for 3000 steps with 105 atoms
|
||||
|
||||
Pair time (%) = 3.85278 (72.641)
|
||||
Neigh time (%) = 0.143526 (2.70607)
|
||||
Comm time (%) = 0.115977 (2.18665)
|
||||
Outpt time (%) = 2.19345e-05 (0.000413557)
|
||||
Other time (%) = 1.19156 (22.4659)
|
||||
|
||||
Nlocal: 26.25 ave 45 max 6 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Nghost: 380.75 ave 495 max 261 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 1269.5 ave 2197 max 179 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
|
||||
Total # of neighbors = 5078
|
||||
Ave neighs/atom = 48.3619
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,107 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# REAX potential for Nitroamines system
|
||||
# .....
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.FC
|
||||
orthogonal box = (-82.62 -79.5011 -50) to (82.62 79.5011 50)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
17280 atoms
|
||||
|
||||
pair_style reax/c NULL
|
||||
pair_coeff * * ffield.reax.FC C F
|
||||
neighbor 2. bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
|
||||
|
||||
# should equilibrate much longer in practice
|
||||
|
||||
fix 1 all npt temp 100.0 100.0 10.0 iso 1.0 1. 2000.0
|
||||
timestep 0.2
|
||||
thermo_style custom step temp epair etotal press
|
||||
thermo 1
|
||||
dump 4 all xyz 5000 dumpnpt.xyz
|
||||
run 10
|
||||
Memory usage per processor = 463.475 Mbytes
|
||||
Step Temp E_pair TotEng Press
|
||||
0 0 -808525.04 -808525.04 58194.694
|
||||
1 4.9935726 -808803.89 -808546.69 58205.825
|
||||
2 19.98696 -809640.54 -808611.1 58239.155
|
||||
3 45.012616 -811035.31 -808716.91 58294.499
|
||||
4 80.103613 -812988.6 -808862.83 58371.547
|
||||
5 125.26228 -815500.71 -809049.03 58469.871
|
||||
6 180.4316 -818571.61 -809278.4 58588.935
|
||||
7 245.47913 -822200.79 -809557.28 58728.142
|
||||
8 320.17692 -826387.27 -809896.43 58886.877
|
||||
9 404.17073 -831129.48 -810312.5 59064.551
|
||||
10 497.02486 -836425.19 -810825.72 59260.714
|
||||
Loop time of 12.1099 on 1 procs for 10 steps with 17280 atoms
|
||||
|
||||
Pair time (%) = 10.4781 (86.5251)
|
||||
Neigh time (%) = 0.0671439 (0.554454)
|
||||
Comm time (%) = 0.000841141 (0.00694588)
|
||||
Outpt time (%) = 0.000734806 (0.0060678)
|
||||
Other time (%) = 1.56308 (12.9074)
|
||||
|
||||
Nlocal: 17280 ave 17280 max 17280 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5352 ave 5352 max 5352 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.62136e+06 ave 2.62136e+06 max 2.62136e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2621360
|
||||
Ave neighs/atom = 151.699
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
|
||||
fix 1 all nvt temp 100.0 100.0 100.0
|
||||
thermo_style custom step temp epair etotal press
|
||||
timestep 0.2
|
||||
|
||||
#dump 5 all xyz 5000 dumpnvt.xyz
|
||||
#dump 6 all custom 5000 dumpidtype.dat id type x y z
|
||||
|
||||
run 10
|
||||
Memory usage per processor = 463.475 Mbytes
|
||||
Step Temp E_pair TotEng Press
|
||||
10 497.02486 -836425.19 -810825.72 59260.714
|
||||
11 601.65141 -841814.22 -810825.91 59489.422
|
||||
12 716.37599 -847724.72 -810827.48 59738.295
|
||||
13 841.27961 -854161.75 -810831.29 60008.162
|
||||
14 976.46663 -861131.81 -810838.49 60300.362
|
||||
15 1122.0668 -868643.09 -810850.57 60616.791
|
||||
16 1278.2373 -876705.56 -810869.41 60959.94
|
||||
17 1445.1655 -885331.16 -810897.31 61332.931
|
||||
18 1623.072 -894534.04 -810937.04 61739.541
|
||||
19 1812.1865 -904337.99 -811000.57 62200.561
|
||||
20 2011.5899 -915379.19 -811771.41 63361.151
|
||||
Loop time of 12.1846 on 1 procs for 10 steps with 17280 atoms
|
||||
|
||||
Pair time (%) = 10.3822 (85.207)
|
||||
Neigh time (%) = 0.063045 (0.517414)
|
||||
Comm time (%) = 0.000839949 (0.0068935)
|
||||
Outpt time (%) = 0.000734806 (0.00603059)
|
||||
Other time (%) = 1.73786 (14.2627)
|
||||
|
||||
Nlocal: 17280 ave 17280 max 17280 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 5352 ave 5352 max 5352 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.62136e+06 ave 2.62136e+06 max 2.62136e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2621360
|
||||
Ave neighs/atom = 151.699
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,107 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# REAX potential for Nitroamines system
|
||||
# .....
|
||||
|
||||
dimension 3
|
||||
boundary p p p
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.FC
|
||||
orthogonal box = (-82.62 -79.5011 -50) to (82.62 79.5011 50)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
17280 atoms
|
||||
|
||||
pair_style reax/c NULL
|
||||
pair_coeff * * ffield.reax.FC C F
|
||||
neighbor 2. bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 reax/c
|
||||
|
||||
# should equilibrate much longer in practice
|
||||
|
||||
fix 1 all npt temp 100.0 100.0 10.0 iso 1.0 1. 2000.0
|
||||
timestep 0.2
|
||||
thermo_style custom step temp epair etotal press
|
||||
thermo 1
|
||||
dump 4 all xyz 5000 dumpnpt.xyz
|
||||
run 10
|
||||
Memory usage per processor = 147.326 Mbytes
|
||||
Step Temp E_pair TotEng Press
|
||||
0 0 -808525.04 -808525.04 58194.694
|
||||
1 4.9935726 -808803.89 -808546.69 58205.825
|
||||
2 19.98696 -809640.54 -808611.1 58239.155
|
||||
3 45.012616 -811035.31 -808716.91 58294.499
|
||||
4 80.103613 -812988.6 -808862.83 58371.547
|
||||
5 125.26228 -815500.71 -809049.03 58469.871
|
||||
6 180.4316 -818571.61 -809278.4 58588.935
|
||||
7 245.47913 -822200.79 -809557.28 58728.142
|
||||
8 320.17692 -826387.27 -809896.43 58886.877
|
||||
9 404.17073 -831129.48 -810312.5 59064.551
|
||||
10 497.02486 -836425.19 -810825.72 59260.714
|
||||
Loop time of 3.31889 on 4 procs for 10 steps with 17280 atoms
|
||||
|
||||
Pair time (%) = 2.80212 (84.4296)
|
||||
Neigh time (%) = 0.0203807 (0.614083)
|
||||
Comm time (%) = 0.0764048 (2.30212)
|
||||
Outpt time (%) = 0.00042671 (0.012857)
|
||||
Other time (%) = 0.419553 (12.6414)
|
||||
|
||||
Nlocal: 4320 ave 4320 max 4320 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2856 ave 2856 max 2856 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 691892 ave 691892 max 691892 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2767568
|
||||
Ave neighs/atom = 160.16
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
|
||||
fix 1 all nvt temp 100.0 100.0 100.0
|
||||
thermo_style custom step temp epair etotal press
|
||||
timestep 0.2
|
||||
|
||||
#dump 5 all xyz 5000 dumpnvt.xyz
|
||||
#dump 6 all custom 5000 dumpidtype.dat id type x y z
|
||||
|
||||
run 10
|
||||
Memory usage per processor = 147.326 Mbytes
|
||||
Step Temp E_pair TotEng Press
|
||||
10 497.02486 -836425.19 -810825.72 59260.714
|
||||
11 601.65141 -841814.22 -810825.91 59489.422
|
||||
12 716.37599 -847724.72 -810827.48 59738.295
|
||||
13 841.27961 -854161.75 -810831.29 60008.162
|
||||
14 976.46663 -861131.81 -810838.49 60300.362
|
||||
15 1122.0668 -868643.09 -810850.57 60616.791
|
||||
16 1278.2373 -876705.56 -810869.41 60959.94
|
||||
17 1445.1655 -885331.16 -810897.31 61332.931
|
||||
18 1623.072 -894534.04 -810937.04 61739.541
|
||||
19 1812.1865 -904337.99 -811000.57 62200.561
|
||||
20 2011.5899 -915379.19 -811771.41 63361.151
|
||||
Loop time of 3.35651 on 4 procs for 10 steps with 17280 atoms
|
||||
|
||||
Pair time (%) = 2.78306 (82.9152)
|
||||
Neigh time (%) = 0.0192913 (0.574744)
|
||||
Comm time (%) = 0.0874793 (2.60626)
|
||||
Outpt time (%) = 0.000434279 (0.0129384)
|
||||
Other time (%) = 0.466248 (13.8909)
|
||||
|
||||
Nlocal: 4320 ave 4320 max 4320 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 2856 ave 2856 max 2856 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 691892 ave 691892 max 691892 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2767568
|
||||
Ave neighs/atom = 160.16
|
||||
Neighbor list builds = 1
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,54 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# REAX potential for Fe/O/H system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.FeOH3
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.Fe_O_C_H H O Fe
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.feoh
|
||||
|
||||
run 3000
|
||||
Memory usage per processor = 16.853 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -9715.3326 0 -9715.3326 -139.61126
|
||||
3000 527.99277 -9636.2117 0 -9472.5317 114.79608
|
||||
Loop time of 6.54228 on 1 procs for 3000 steps with 105 atoms
|
||||
|
||||
Pair time (%) = 5.61412 (85.8128)
|
||||
Neigh time (%) = 0.290443 (4.43947)
|
||||
Comm time (%) = 0.02038 (0.311512)
|
||||
Outpt time (%) = 1.78814e-05 (0.00027332)
|
||||
Other time (%) = 0.617324 (9.43591)
|
||||
|
||||
Nlocal: 105 ave 105 max 105 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 651 ave 651 max 651 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3391 ave 3391 max 3391 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3391
|
||||
Ave neighs/atom = 32.2952
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,54 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# REAX potential for Fe/O/H system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.FeOH3
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.Fe_O_C_H H O Fe
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.feoh
|
||||
|
||||
run 3000
|
||||
Memory usage per processor = 11.4214 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -9715.3326 0 -9715.3326 -139.61126
|
||||
3000 525.49762 -9635.4571 0 -9472.5506 115.12726
|
||||
Loop time of 3.92556 on 4 procs for 3000 steps with 105 atoms
|
||||
|
||||
Pair time (%) = 2.93981 (74.8889)
|
||||
Neigh time (%) = 0.16493 (4.20144)
|
||||
Comm time (%) = 0.10089 (2.57008)
|
||||
Outpt time (%) = 2.30074e-05 (0.000586091)
|
||||
Other time (%) = 0.719909 (18.339)
|
||||
|
||||
Nlocal: 26.25 ave 34 max 12 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 1 1
|
||||
Nghost: 408 ave 462 max 347 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Neighs: 1108.5 ave 1418 max 453 min
|
||||
Histogram: 1 0 0 0 0 0 0 1 0 2
|
||||
|
||||
Total # of neighbors = 4434
|
||||
Ave neighs/atom = 42.2286
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,54 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# REAX potential for high energy CHON systems
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.RDX
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.rdx H C O N
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.rdx
|
||||
|
||||
run 3000
|
||||
Memory usage per processor = 17.2352 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -10197.932 0 -10197.932 38.347492
|
||||
3000 504.09091 -10089.419 0 -9933.149 1731.8291
|
||||
Loop time of 13.4566 on 1 procs for 3000 steps with 105 atoms
|
||||
|
||||
Pair time (%) = 12.4014 (92.1588)
|
||||
Neigh time (%) = 0.272146 (2.02239)
|
||||
Comm time (%) = 0.0201037 (0.149396)
|
||||
Outpt time (%) = 1.69277e-05 (0.000125795)
|
||||
Other time (%) = 0.762898 (5.66932)
|
||||
|
||||
Nlocal: 105 ave 105 max 105 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 645 ave 645 max 645 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3064 ave 3064 max 3064 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3064
|
||||
Ave neighs/atom = 29.181
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,54 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# REAX potential for high energy CHON systems
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.RDX
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.rdx H C O N
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.rdx
|
||||
|
||||
run 3000
|
||||
Memory usage per processor = 11.3106 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -10197.932 0 -10197.932 38.347492
|
||||
3000 507.49026 -10090.537 0 -9933.2131 1583.9314
|
||||
Loop time of 7.30982 on 4 procs for 3000 steps with 105 atoms
|
||||
|
||||
Pair time (%) = 6.12492 (83.7903)
|
||||
Neigh time (%) = 0.14891 (2.03712)
|
||||
Comm time (%) = 0.127078 (1.73846)
|
||||
Outpt time (%) = 2.09808e-05 (0.000287023)
|
||||
Other time (%) = 0.908887 (12.4338)
|
||||
|
||||
Nlocal: 26.25 ave 46 max 8 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
Nghost: 399.5 ave 512 max 288 min
|
||||
Histogram: 1 0 0 1 0 0 1 0 0 1
|
||||
Neighs: 1011.75 ave 1820 max 420 min
|
||||
Histogram: 1 0 1 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 4047
|
||||
Ave neighs/atom = 38.5429
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,54 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# REAX potential for VOH system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.VOH
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
100 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.V_O_C_H H C O V
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.voh
|
||||
|
||||
run 3000
|
||||
Memory usage per processor = 16.0432 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -10246.825 0 -10246.825 42.256092
|
||||
3000 513.11061 -10194.584 0 -10043.165 -549.30256
|
||||
Loop time of 7.8996 on 1 procs for 3000 steps with 100 atoms
|
||||
|
||||
Pair time (%) = 6.80957 (86.2014)
|
||||
Neigh time (%) = 0.270939 (3.42979)
|
||||
Comm time (%) = 0.0194738 (0.246516)
|
||||
Outpt time (%) = 1.69277e-05 (0.000214286)
|
||||
Other time (%) = 0.799604 (10.1221)
|
||||
|
||||
Nlocal: 100 ave 100 max 100 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 598 ave 598 max 598 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3382 ave 3382 max 3382 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3382
|
||||
Ave neighs/atom = 33.82
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,54 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# REAX potential for VOH system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.VOH
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
100 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.V_O_C_H H C O V
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.voh
|
||||
|
||||
run 3000
|
||||
Memory usage per processor = 11.277 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -10246.825 0 -10246.825 42.256091
|
||||
3000 470.82008 -10184.008 0 -10045.069 -743.16301
|
||||
Loop time of 4.36637 on 4 procs for 3000 steps with 100 atoms
|
||||
|
||||
Pair time (%) = 3.21483 (73.6271)
|
||||
Neigh time (%) = 0.142588 (3.26559)
|
||||
Comm time (%) = 0.0947427 (2.16983)
|
||||
Outpt time (%) = 1.96695e-05 (0.000450478)
|
||||
Other time (%) = 0.914186 (20.937)
|
||||
|
||||
Nlocal: 25 ave 39 max 11 min
|
||||
Histogram: 1 0 0 0 1 1 0 0 0 1
|
||||
Nghost: 368.25 ave 449 max 282 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
Neighs: 1081 ave 1819 max 421 min
|
||||
Histogram: 1 0 1 0 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 4324
|
||||
Ave neighs/atom = 43.24
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,54 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# REAX potential for ZnOH2 system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.ZnOH2
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.ZnOH H O Zn
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.znoh
|
||||
|
||||
run 3000
|
||||
Memory usage per processor = 16.6086 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -7900.2668 0 -7900.2668 60.076093
|
||||
3000 552.32683 -7938.8249 0 -7767.6013 -842.20715
|
||||
Loop time of 5.25412 on 1 procs for 3000 steps with 105 atoms
|
||||
|
||||
Pair time (%) = 4.29984 (81.8375)
|
||||
Neigh time (%) = 0.310224 (5.9044)
|
||||
Comm time (%) = 0.0198703 (0.378185)
|
||||
Outpt time (%) = 1.69277e-05 (0.00032218)
|
||||
Other time (%) = 0.624167 (11.8796)
|
||||
|
||||
Nlocal: 105 ave 105 max 105 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 649 ave 649 max 649 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 3948 ave 3948 max 3948 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 3948
|
||||
Ave neighs/atom = 37.6
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
|
|
@ -0,0 +1,54 @@
|
|||
LAMMPS (1 Feb 2014)
|
||||
# REAX potential for ZnOH2 system
|
||||
# .....
|
||||
|
||||
units real
|
||||
|
||||
atom_style charge
|
||||
read_data data.ZnOH2
|
||||
orthogonal box = (0 0 0) to (25 25 25)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
105 atoms
|
||||
|
||||
pair_style reax/c lmp_control
|
||||
pair_coeff * * ffield.reax.ZnOH H O Zn
|
||||
|
||||
neighbor 2 bin
|
||||
neigh_modify every 10 delay 0 check no
|
||||
|
||||
fix 1 all nve
|
||||
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
|
||||
fix 3 all temp/berendsen 500.0 500.0 100.0
|
||||
|
||||
timestep 0.25
|
||||
|
||||
#dump 1 all atom 30 dump.reax.znoh
|
||||
|
||||
run 3000
|
||||
Memory usage per processor = 11.107 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -7900.2668 0 -7900.2668 60.076093
|
||||
3000 546.98979 -7938.2646 0 -7768.6954 -691.04429
|
||||
Loop time of 3.31566 on 4 procs for 3000 steps with 105 atoms
|
||||
|
||||
Pair time (%) = 2.29327 (69.1648)
|
||||
Neigh time (%) = 0.165577 (4.99379)
|
||||
Comm time (%) = 0.111848 (3.37334)
|
||||
Outpt time (%) = 2.29478e-05 (0.000692104)
|
||||
Other time (%) = 0.744942 (22.4674)
|
||||
|
||||
Nlocal: 26.25 ave 45 max 15 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Nghost: 399 ave 509 max 295 min
|
||||
Histogram: 1 0 0 0 2 0 0 0 0 1
|
||||
Neighs: 1149.25 ave 2060 max 702 min
|
||||
Histogram: 1 2 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 4597
|
||||
Ave neighs/atom = 43.781
|
||||
Neighbor list builds = 300
|
||||
Dangerous builds = 0
|
||||
|
||||
Please see the log.cite file for references relevant to this simulation
|
||||
|
||||
Some files were not shown because too many files have changed in this diff Show More
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Reference in New Issue