forked from lijiext/lammps
update log files for qeq and rdf-adf examples
This commit is contained in:
Axel Kohlmeyer
parent
46bf4b7efb
commit
4b8c6d40e2
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@ -1,4 +1,5 @@
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LAMMPS (5 Oct 2016)
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# This example demonstrates the use of various fix qeq variants with
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# that defines and uses charges, in this case pair_style buck/coul/long
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@ -14,6 +15,7 @@ replicate 2 2 2
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orthogonal box = (0 0 0) to (50.3166 50.3166 56.0405)
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1 by 1 by 1 MPI processor grid
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9600 atoms
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Time spent = 0.00114894 secs
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pair_style buck/coul/long 12.0
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pair_coeff 2 2 1388.77 .3623188 175.0
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@ -50,47 +52,57 @@ fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2
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run 100
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Ewald initialization ...
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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
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using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
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G vector (1/distance) = 0.305064
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estimated absolute RMS force accuracy = 2.07629e-05
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estimated relative force accuracy = 1.44191e-06
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KSpace vectors: actual max1d max3d = 13556 20 34460
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kxmax kymax kzmax = 18 18 20
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Neighbor list info ...
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2 neighbor list requests
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 13
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ghost atom cutoff = 13
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binsize = 6.5 -> bins = 8 8 9
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Memory usage per processor = 110.875 Mbytes
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binsize = 6.5, bins = 8 8 9
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair buck/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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(2) fix qeq/fire, perpetual, copy from (1)
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attributes: half, newton on
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 134 | 134 | 134 Mbytes
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Step PotEng c_q1 c_q2 v_qtot S/CPU
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0 -27457.219 0.85227886 -0.42613943 -2.1827873e-10 0
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10 -27626.057 0.85486228 -0.42743114 -2.0372681e-10 0.64960264
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20 -27975.085 0.85968531 -0.42984266 -8.8220986e-11 0.55300005
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30 -28552.628 0.86755661 -0.4337783 1.4142643e-10 0.52434987
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40 -29133.643 0.87426387 -0.43713193 1.6871127e-10 0.52326849
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50 -29697.011 0.8794039 -0.43970195 1.2460077e-10 0.52083626
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60 -30342.001 0.88478594 -0.44239297 -4.3655746e-11 0.52824882
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70 -31081.138 0.8906973 -0.44534865 -4.7293724e-11 0.56010601
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80 -31792.732 0.89506635 -0.44753317 -3.774403e-11 0.60040973
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90 -32424.749 0.89714841 -0.44857421 -1.0004442e-10 0.57758717
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100 -32998.353 0.89755721 -0.44877861 -1.0231815e-10 0.59560798
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Loop time of 178.401 on 1 procs for 100 steps with 9600 atoms
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10 -27626.057 0.85486228 -0.42743114 -2.0372681e-10 0.64313877
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20 -27975.085 0.85968531 -0.42984266 -1.036824e-10 0.55119179
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30 -28552.628 0.86755661 -0.4337783 1.3051249e-10 0.53160643
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40 -29133.643 0.87426387 -0.43713193 1.1368684e-10 0.53075341
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50 -29697.011 0.8794039 -0.43970195 1.200533e-10 0.52358127
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60 -30342.001 0.88478594 -0.44239297 6.002665e-11 0.5366762
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70 -31081.138 0.8906973 -0.44534865 -4.7293724e-11 0.55904546
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80 -31792.732 0.89506635 -0.44753317 -4.3200998e-11 0.59606079
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90 -32424.749 0.89714841 -0.44857421 -1.1596057e-10 0.58047419
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100 -32998.353 0.89755721 -0.44877861 -1.0231815e-10 0.59444001
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Loop time of 177.79 on 1 procs for 100 steps with 9600 atoms
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Performance: 0.005 ns/day, 4955.597 hours/ns, 0.561 timesteps/s
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99.9% CPU use with 1 MPI tasks x no OpenMP threads
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Performance: 0.005 ns/day, 4938.612 hours/ns, 0.562 timesteps/s
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99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 15.042 | 15.042 | 15.042 | 0.0 | 8.43
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Kspace | 98.245 | 98.245 | 98.245 | 0.0 | 55.07
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Pair | 11.518 | 11.518 | 11.518 | 0.0 | 6.48
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Kspace | 107.37 | 107.37 | 107.37 | 0.0 | 60.39
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.019511 | 0.019511 | 0.019511 | 0.0 | 0.01
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Output | 0.0020375 | 0.0020375 | 0.0020375 | 0.0 | 0.00
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Modify | 65.083 | 65.083 | 65.083 | 0.0 | 36.48
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Other | | 0.009152 | | | 0.01
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Comm | 0.019721 | 0.019721 | 0.019721 | 0.0 | 0.01
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Output | 0.002218 | 0.002218 | 0.002218 | 0.0 | 0.00
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Modify | 58.869 | 58.869 | 58.869 | 0.0 | 33.11
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Other | | 0.007197 | | | 0.00
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Nlocal: 9600 ave 9600 max 9600 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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@ -103,4 +115,4 @@ Total # of neighbors = 2940800
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Ave neighs/atom = 306.333
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:03:02
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Total wall time: 0:03:01
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@ -1,4 +1,5 @@
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LAMMPS (5 Oct 2016)
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# This example demonstrates the use of various fix qeq variants with
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# that defines and uses charges, in this case pair_style buck/coul/long
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@ -14,6 +15,7 @@ replicate 2 2 2
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orthogonal box = (0 0 0) to (50.3166 50.3166 56.0405)
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1 by 2 by 2 MPI processor grid
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9600 atoms
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Time spent = 0.000675201 secs
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pair_style buck/coul/long 12.0
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pair_coeff 2 2 1388.77 .3623188 175.0
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@ -50,47 +52,57 @@ fix 2 all qeq/fire 1 10 1.0e-4 100 param.qeq2
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run 100
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Ewald initialization ...
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WARNING: Using 12-bit tables for long-range coulomb (../kspace.cpp:316)
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using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
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G vector (1/distance) = 0.305064
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estimated absolute RMS force accuracy = 2.07629e-05
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estimated relative force accuracy = 1.44191e-06
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KSpace vectors: actual max1d max3d = 13556 20 34460
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kxmax kymax kzmax = 18 18 20
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Neighbor list info ...
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2 neighbor list requests
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 13
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ghost atom cutoff = 13
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binsize = 6.5 -> bins = 8 8 9
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Memory usage per processor = 46.867 Mbytes
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binsize = 6.5, bins = 8 8 9
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair buck/coul/long, perpetual
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attributes: half, newton on
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pair build: half/bin/atomonly/newton
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stencil: half/bin/3d/newton
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bin: standard
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(2) fix qeq/fire, perpetual, copy from (1)
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attributes: half, newton on
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 53.06 | 53.13 | 53.21 Mbytes
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Step PotEng c_q1 c_q2 v_qtot S/CPU
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0 -27457.215 0.85227886 -0.42613943 2.1373125e-11 0
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10 -27626.057 0.85486228 -0.42743114 3.0468073e-11 2.561772
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20 -27975.085 0.85968531 -0.42984266 9.777068e-11 2.1470405
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30 -28552.627 0.86755661 -0.4337783 1.2823875e-10 2.0585052
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40 -29133.643 0.87426387 -0.43713193 1.5506885e-10 2.0319632
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50 -29697.01 0.8794039 -0.43970195 2.1873348e-10 2.0350244
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60 -30342 0.88478594 -0.44239297 1.891749e-10 2.0793976
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70 -31081.139 0.89069733 -0.44534866 1.4688339e-10 2.1759002
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80 -31792.732 0.89506635 -0.44753317 1.4142643e-10 2.3320978
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90 -32424.752 0.89714841 -0.44857421 9.9134922e-11 2.2673305
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100 -32998.353 0.89755721 -0.44877861 1.5097612e-10 2.3389389
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Loop time of 45.6331 on 4 procs for 100 steps with 9600 atoms
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10 -27626.057 0.85486228 -0.42743114 3.0468073e-11 2.4245312
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20 -27975.085 0.85968531 -0.42984266 1.0095391e-10 2.0185316
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30 -28552.627 0.86755661 -0.4337783 1.3096724e-10 1.9605335
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40 -29133.643 0.87426387 -0.43713193 1.5279511e-10 1.9624139
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50 -29697.01 0.8794039 -0.43970195 1.6461854e-10 1.8113263
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60 -30342 0.88478594 -0.44239297 1.7826096e-10 1.9537722
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70 -31081.139 0.89069733 -0.44534866 1.4733814e-10 2.058406
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80 -31792.732 0.89506635 -0.44753317 1.3824319e-10 2.2160813
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90 -32424.752 0.89714841 -0.44857421 1.2914825e-10 2.0952145
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100 -32998.353 0.89755721 -0.44877861 1.4824764e-10 2.1292486
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Loop time of 48.7541 on 4 procs for 100 steps with 9600 atoms
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Performance: 0.019 ns/day, 1267.586 hours/ns, 2.191 timesteps/s
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99.9% CPU use with 4 MPI tasks x no OpenMP threads
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Performance: 0.018 ns/day, 1354.281 hours/ns, 2.051 timesteps/s
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97.4% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 3.8297 | 3.8983 | 3.938 | 2.1 | 8.54
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Kspace | 24.434 | 24.579 | 24.78 | 2.9 | 53.86
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Pair | 2.9747 | 3.0315 | 3.0758 | 2.1 | 6.22
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Kspace | 27.873 | 28.264 | 28.63 | 5.3 | 57.97
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.078239 | 0.31795 | 0.53069 | 30.8 | 0.70
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Output | 0.00097322 | 0.0010365 | 0.0011294 | 0.2 | 0.00
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Modify | 16.831 | 16.832 | 16.832 | 0.0 | 36.88
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Other | | 0.005259 | | | 0.01
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Comm | 0.53835 | 0.8523 | 1.2286 | 28.2 | 1.75
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Output | 0.0012984 | 0.001591 | 0.0024178 | 1.2 | 0.00
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Modify | 16.58 | 16.59 | 16.601 | 0.3 | 34.03
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Other | | 0.01409 | | | 0.03
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Nlocal: 2400 ave 2400 max 2400 min
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Histogram: 4 0 0 0 0 0 0 0 0 0
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@ -103,4 +115,4 @@ Total # of neighbors = 2940800
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Ave neighs/atom = 306.333
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Neighbor list builds = 0
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Dangerous builds = 0
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Total wall time: 0:00:46
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Total wall time: 0:00:49
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@ -1,4 +1,5 @@
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LAMMPS (5 Oct 2016)
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# This example demonstrates the use of various fix qeq variants with pair reax/c
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# You can comment in/out various versions below
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#
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@ -54,13 +55,23 @@ timestep 0.25
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run 10
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Neighbor list info ...
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2 neighbor list requests
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 11
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ghost atom cutoff = 11
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binsize = 5.5 -> bins = 5 5 5
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Memory usage per processor = 15.8004 Mbytes
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binsize = 5.5, bins = 5 5 5
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair reax/c, perpetual
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attributes: half, newton off, ghost
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pair build: half/bin/newtoff/ghost
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stencil: half/ghost/bin/3d/newtoff
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bin: standard
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(2) fix qeq/reax, perpetual, copy from (1)
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attributes: half, newton off, ghost
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 16.65 | 16.65 | 16.65 Mbytes
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Step PotEng c_q1 c_q2 c_q3 v_qtot
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0 -10226.557 0.095634063 -0.15658793 -0.091167279 4.4408921e-16
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1 -10225.799 0.095649584 -0.1566219 -0.091171371 7.1054274e-15
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@ -73,20 +84,20 @@ Step PotEng c_q1 c_q2 c_q3 v_qtot
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8 -10194.646 0.095767243 -0.15689184 -0.091186932 -2.4424907e-15
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9 -10190.016 0.095760528 -0.15687664 -0.091185782 -4.4408921e-16
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10 -10186.168 0.095748006 -0.15684815 -0.09118383 1.110223e-15
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Loop time of 0.0398569 on 1 procs for 10 steps with 105 atoms
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Loop time of 0.0322483 on 1 procs for 10 steps with 105 atoms
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Performance: 5.419 ns/day, 4.429 hours/ns, 250.898 timesteps/s
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100.3% CPU use with 1 MPI tasks x no OpenMP threads
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Performance: 6.698 ns/day, 3.583 hours/ns, 310.094 timesteps/s
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99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.034917 | 0.034917 | 0.034917 | 0.0 | 87.61
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Pair | 0.026229 | 0.026229 | 0.026229 | 0.0 | 81.34
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 3.2663e-05 | 3.2663e-05 | 3.2663e-05 | 0.0 | 0.08
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Output | 0.00016952 | 0.00016952 | 0.00016952 | 0.0 | 0.43
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Modify | 0.0047123 | 0.0047123 | 0.0047123 | 0.0 | 11.82
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Other | | 2.527e-05 | | | 0.06
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Comm | 5.2214e-05 | 5.2214e-05 | 5.2214e-05 | 0.0 | 0.16
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Output | 0.00027299 | 0.00027299 | 0.00027299 | 0.0 | 0.85
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Modify | 0.0056667 | 0.0056667 | 0.0056667 | 0.0 | 17.57
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Other | | 2.694e-05 | | | 0.08
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Nlocal: 105 ave 105 max 105 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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@ -1,4 +1,5 @@
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LAMMPS (5 Oct 2016)
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LAMMPS (27 Nov 2018)
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using 1 OpenMP thread(s) per MPI task
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# This example demonstrates the use of various fix qeq variants with pair reax/c
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# You can comment in/out various versions below
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#
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@ -54,13 +55,23 @@ timestep 0.25
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run 10
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Neighbor list info ...
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2 neighbor list requests
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update every 1 steps, delay 0 steps, check yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 11
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ghost atom cutoff = 11
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binsize = 5.5 -> bins = 5 5 5
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Memory usage per processor = 11.6046 Mbytes
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binsize = 5.5, bins = 5 5 5
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2 neighbor lists, perpetual/occasional/extra = 2 0 0
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(1) pair reax/c, perpetual
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attributes: half, newton off, ghost
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pair build: half/bin/newtoff/ghost
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stencil: half/ghost/bin/3d/newtoff
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bin: standard
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(2) fix qeq/reax, perpetual, copy from (1)
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attributes: half, newton off, ghost
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pair build: copy
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stencil: none
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bin: none
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Per MPI rank memory allocation (min/avg/max) = 10.83 | 11.69 | 12.52 Mbytes
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Step PotEng c_q1 c_q2 c_q3 v_qtot
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0 -10226.557 0.095633919 -0.15658765 -0.091167194 1.7763568e-15
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1 -10225.799 0.0956503 -0.15662357 -0.09117143 2.8865799e-15
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@ -73,20 +84,20 @@ Step PotEng c_q1 c_q2 c_q3 v_qtot
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8 -10194.646 0.095766449 -0.15689014 -0.091186673 -4.4408921e-16
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9 -10190.016 0.095761078 -0.15687818 -0.09118551 -4.4408921e-16
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10 -10186.168 0.095747223 -0.15684634 -0.091183742 0
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Loop time of 0.0217528 on 4 procs for 10 steps with 105 atoms
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Loop time of 0.0185181 on 4 procs for 10 steps with 105 atoms
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Performance: 9.930 ns/day, 2.417 hours/ns, 459.710 timesteps/s
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93.1% CPU use with 4 MPI tasks x no OpenMP threads
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Performance: 11.664 ns/day, 2.058 hours/ns, 540.011 timesteps/s
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92.5% CPU use with 4 MPI tasks x 1 OpenMP threads
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MPI task timing breakdown:
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Section | min time | avg time | max time |%varavg| %total
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---------------------------------------------------------------
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Pair | 0.012203 | 0.014022 | 0.015427 | 1.0 | 64.46
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Pair | 0.0097179 | 0.01078 | 0.012052 | 0.8 | 58.21
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Neigh | 0 | 0 | 0 | 0.0 | 0.00
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Comm | 0.00011754 | 0.0015323 | 0.0033445 | 3.0 | 7.04
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Output | 0.00041366 | 0.00044626 | 0.00048447 | 0.1 | 2.05
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Modify | 0.0056725 | 0.0056758 | 0.0056815 | 0.0 | 26.09
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Other | | 7.629e-05 | | | 0.35
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Comm | 0.00041604 | 0.0017492 | 0.0028496 | 2.1 | 9.45
|
||||
Output | 0.00041103 | 0.00046283 | 0.00051498 | 0.0 | 2.50
|
||||
Modify | 0.0051849 | 0.0052357 | 0.0052917 | 0.1 | 28.27
|
||||
Other | | 0.0002902 | | | 1.57
|
||||
|
||||
Nlocal: 26.25 ave 35 max 15 min
|
||||
Histogram: 1 0 0 1 0 0 0 0 0 2
|
||||
|
|
@ -1,12 +1,13 @@
|
|||
LAMMPS (10 Oct 2018)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:87)
|
||||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Liquid water RDFs and ADFs (~12 O-O-O/atom, ~1 O-H...O/atom)
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
read_data data.spce
|
||||
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
|
||||
1 by 2 by 1 MPI processor grid
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
4500 atoms
|
||||
scanning bonds ...
|
||||
|
|
@ -65,7 +66,7 @@ PPPM initialization ...
|
|||
estimated absolute RMS force accuracy = 0.000394674
|
||||
estimated relative force accuracy = 1.18855e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 59643 32000
|
||||
3d grid and FFT values/proc = 103823 64000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 2 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
|
|
@ -78,39 +79,39 @@ Neighbor list info ...
|
|||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 25.06 | 25.25 | 25.44 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 35.36 | 35.36 | 35.36 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -16692.369 0 -14010.534 -112.83562
|
||||
100 283.44729 -17008.717 0 -14474.854 -162.06374
|
||||
200 298.75279 -16765.544 0 -14094.858 428.79127
|
||||
300 296.6501 -16589.155 0 -13937.267 547.40768
|
||||
400 303.83151 -16625.028 0 -13908.942 237.9775
|
||||
500 298.01615 -16717.015 0 -14052.915 230.7095
|
||||
Loop time of 21.4041 on 2 procs for 500 steps with 4500 atoms
|
||||
100 283.44729 -17008.717 0 -14474.854 -162.06378
|
||||
200 298.75279 -16765.543 0 -14094.858 428.7917
|
||||
300 296.65014 -16589.155 0 -13937.267 547.40796
|
||||
400 303.82963 -16625.011 0 -13908.942 237.93694
|
||||
500 298.00057 -16716.887 0 -14052.926 231.55014
|
||||
Loop time of 38.2796 on 1 procs for 500 steps with 4500 atoms
|
||||
|
||||
Performance: 4.037 ns/day, 5.946 hours/ns, 23.360 timesteps/s
|
||||
94.8% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
Performance: 2.257 ns/day, 10.633 hours/ns, 13.062 timesteps/s
|
||||
99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 14.892 | 15.034 | 15.176 | 3.7 | 70.24
|
||||
Bond | 0.00056624 | 0.00059342 | 0.0006206 | 0.0 | 0.00
|
||||
Kspace | 3.987 | 4.1321 | 4.2773 | 7.1 | 19.31
|
||||
Neigh | 1.7494 | 1.7496 | 1.7497 | 0.0 | 8.17
|
||||
Comm | 0.20554 | 0.20637 | 0.2072 | 0.2 | 0.96
|
||||
Output | 0.00015688 | 0.00036144 | 0.00056601 | 0.0 | 0.00
|
||||
Modify | 0.25707 | 0.2606 | 0.26413 | 0.7 | 1.22
|
||||
Other | | 0.02059 | | | 0.10
|
||||
Pair | 28.428 | 28.428 | 28.428 | 0.0 | 74.26
|
||||
Bond | 0.00056672 | 0.00056672 | 0.00056672 | 0.0 | 0.00
|
||||
Kspace | 5.3161 | 5.3161 | 5.3161 | 0.0 | 13.89
|
||||
Neigh | 4.1185 | 4.1185 | 4.1185 | 0.0 | 10.76
|
||||
Comm | 0.12788 | 0.12788 | 0.12788 | 0.0 | 0.33
|
||||
Output | 0.00021887 | 0.00021887 | 0.00021887 | 0.0 | 0.00
|
||||
Modify | 0.26748 | 0.26748 | 0.26748 | 0.0 | 0.70
|
||||
Other | | 0.02102 | | | 0.05
|
||||
|
||||
Nlocal: 2250 ave 2258 max 2242 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 16319 ave 16381 max 16257 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 1.30073e+06 ave 1.32386e+06 max 1.2776e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nlocal: 4500 ave 4500 max 4500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 21248 ave 21248 max 21248 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.60146e+06 ave 2.60146e+06 max 2.60146e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 2601457
|
||||
Total # of neighbors = 2601459
|
||||
Ave neighs/atom = 578.102
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 45
|
||||
|
|
@ -119,7 +120,7 @@ Dangerous builds = 0
|
|||
reset_timestep 0
|
||||
|
||||
compute gofr all rdf 100 1 1 2 2 1 2 # O-O, H-H, O-H
|
||||
compute gofa all adf 45 1 1 1 2.0 3.5 2.0 3.5 1 2 1 0.0 1.2 1.5 2.5
|
||||
compute gofa all adf 45 1 1 1 2.0 3.5 2.0 3.5 2 1 1 0.0 1.2 1.5 2.5 # O-O-O, O-H...O
|
||||
fix rdf all ave/time 100 10 1000 c_gofr[*] file spce-rdf.dat mode vector
|
||||
fix adf all ave/time 10 100 1000 c_gofa[*] file spce-adf.dat mode vector
|
||||
|
||||
|
|
@ -132,7 +133,7 @@ PPPM initialization ...
|
|||
estimated absolute RMS force accuracy = 0.000394674
|
||||
estimated relative force accuracy = 1.18855e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 59643 32000
|
||||
3d grid and FFT values/proc = 103823 64000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 2 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
|
|
@ -155,48 +156,48 @@ Neighbor list info ...
|
|||
pair build: full/bin
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 26.78 | 26.78 | 26.78 Mbytes
|
||||
Per MPI rank memory allocation (min/avg/max) = 36.67 | 36.67 | 36.67 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 298.01615 -16717.015 0 -14052.915 230.81371
|
||||
100 307.1766 -16759.33 0 -14013.341 454.2771
|
||||
200 298.94628 -16674.186 0 -14001.771 114.20846
|
||||
300 293.13091 -16581.542 0 -13961.113 272.85574
|
||||
400 294.47017 -16556.872 0 -13924.471 180.3252
|
||||
500 305.57174 -16647.976 0 -13916.333 -444.14856
|
||||
600 302.53992 -16670.304 0 -13965.764 114.82353
|
||||
700 306.56761 -16616.508 0 -13875.962 534.02537
|
||||
800 299.06297 -16644.133 0 -13970.675 83.643063
|
||||
900 301.15522 -16674.021 0 -13981.859 325.04538
|
||||
1000 298.14963 -16701.663 0 -14036.369 356.0601
|
||||
Loop time of 53.3181 on 2 procs for 1000 steps with 4500 atoms
|
||||
0 298.00057 -16716.887 0 -14052.926 231.6595
|
||||
100 307.31045 -16761.022 0 -14013.835 449.26027
|
||||
200 299.52847 -16679.165 0 -14001.546 148.44719
|
||||
300 293.68499 -16583.548 0 -13958.166 140.79069
|
||||
400 306.76266 -16658.573 0 -13916.284 481.26934
|
||||
500 294.75648 -16640.446 0 -14005.485 585.05479
|
||||
600 303.19282 -16629.985 0 -13919.608 328.23667
|
||||
700 300.28233 -16590.155 0 -13905.797 -176.71076
|
||||
800 292.36899 -16620.826 0 -14007.208 -194.83408
|
||||
900 304.92802 -16633.331 0 -13907.443 479.49808
|
||||
1000 300.64529 -16598.233 0 -13910.63 904.96137
|
||||
Loop time of 107.579 on 1 procs for 1000 steps with 4500 atoms
|
||||
|
||||
Performance: 3.241 ns/day, 7.405 hours/ns, 18.755 timesteps/s
|
||||
97.3% CPU use with 2 MPI tasks x 1 OpenMP threads
|
||||
Performance: 1.606 ns/day, 14.942 hours/ns, 9.295 timesteps/s
|
||||
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 28.831 | 29.365 | 29.899 | 9.9 | 55.07
|
||||
Bond | 0.00097084 | 0.0010794 | 0.001188 | 0.3 | 0.00
|
||||
Kspace | 7.3086 | 7.8356 | 8.3626 | 18.8 | 14.70
|
||||
Neigh | 3.7241 | 3.7245 | 3.7248 | 0.0 | 6.99
|
||||
Comm | 0.32839 | 0.33495 | 0.34151 | 1.1 | 0.63
|
||||
Output | 0.00043344 | 0.0015392 | 0.002645 | 2.8 | 0.00
|
||||
Modify | 12.013 | 12.014 | 12.015 | 0.0 | 22.53
|
||||
Other | | 0.04153 | | | 0.08
|
||||
Pair | 58.928 | 58.928 | 58.928 | 0.0 | 54.78
|
||||
Bond | 0.0012271 | 0.0012271 | 0.0012271 | 0.0 | 0.00
|
||||
Kspace | 10.698 | 10.698 | 10.698 | 0.0 | 9.94
|
||||
Neigh | 8.7649 | 8.7649 | 8.7649 | 0.0 | 8.15
|
||||
Comm | 0.2608 | 0.2608 | 0.2608 | 0.0 | 0.24
|
||||
Output | 0.00043702 | 0.00043702 | 0.00043702 | 0.0 | 0.00
|
||||
Modify | 28.883 | 28.883 | 28.883 | 0.0 | 26.85
|
||||
Other | | 0.04301 | | | 0.04
|
||||
|
||||
Nlocal: 2250 ave 2251 max 2249 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 16300 ave 16358 max 16242 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Neighs: 1.301e+06 ave 1.31594e+06 max 1.28606e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
FullNghs: 2.602e+06 ave 2.60923e+06 max 2.59476e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 1
|
||||
Nlocal: 4500 ave 4500 max 4500 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 21275 ave 21275 max 21275 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 2.60217e+06 ave 2.60217e+06 max 2.60217e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
FullNghs: 5.20478e+06 ave 5.20478e+06 max 5.20478e+06 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 5203998
|
||||
Ave neighs/atom = 1156.44
|
||||
Total # of neighbors = 5204784
|
||||
Ave neighs/atom = 1156.62
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 93
|
||||
Neighbor list builds = 94
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:01:14
|
||||
Total wall time: 0:02:26
|
||||
|
|
@ -0,0 +1,203 @@
|
|||
LAMMPS (27 Nov 2018)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
# Liquid water RDFs and ADFs (~12 O-O-O/atom, ~1 O-H...O/atom)
|
||||
|
||||
units real
|
||||
atom_style full
|
||||
|
||||
read_data data.spce
|
||||
orthogonal box = (0.02645 0.02645 0.02641) to (35.5328 35.5328 35.4736)
|
||||
2 by 2 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
4500 atoms
|
||||
scanning bonds ...
|
||||
2 = max bonds/atom
|
||||
scanning angles ...
|
||||
1 = max angles/atom
|
||||
reading bonds ...
|
||||
3000 bonds
|
||||
reading angles ...
|
||||
1500 angles
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
1 = max # of 1-4 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
pair_style lj/cut/coul/long 12.0 12.0
|
||||
pair_coeff * * 0.0 1.0
|
||||
pair_coeff 1 1 0.15535 3.166
|
||||
kspace_style pppm 1.0e-6
|
||||
|
||||
bond_style harmonic
|
||||
angle_style harmonic
|
||||
dihedral_style none
|
||||
improper_style none
|
||||
|
||||
bond_coeff 1 1000.00 1.000
|
||||
angle_coeff 1 100.0 109.47
|
||||
|
||||
# need to set bond/angle inclusion to > 0.0
|
||||
# so that intramolecular pairs are included in neighbor lists (required for second ADF)
|
||||
special_bonds lj/coul 1.0e-100 1.0e-100 1.0
|
||||
2 = max # of 1-2 neighbors
|
||||
1 = max # of 1-3 neighbors
|
||||
2 = max # of special neighbors
|
||||
|
||||
neighbor 2.0 bin
|
||||
timestep 2.0
|
||||
neigh_modify every 1 delay 2 check yes
|
||||
|
||||
fix 1 all shake 0.0001 20 0 b 1 a 1
|
||||
0 = # of size 2 clusters
|
||||
0 = # of size 3 clusters
|
||||
0 = # of size 4 clusters
|
||||
1500 = # of frozen angles
|
||||
fix 2 all nvt temp 300.0 300.0 100.0
|
||||
|
||||
velocity all create 300.0 6244325
|
||||
|
||||
thermo 100
|
||||
run 500
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.279652
|
||||
grid = 40 40 40
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000394674
|
||||
estimated relative force accuracy = 1.18855e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 34263 16000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 2 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 6 6 6
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 13.1 | 13.1 | 13.1 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 300 -16692.369 0 -14010.534 -112.83562
|
||||
100 283.44729 -17008.717 0 -14474.854 -162.06378
|
||||
200 298.75279 -16765.543 0 -14094.858 428.79175
|
||||
300 296.65013 -16589.155 0 -13937.267 547.40809
|
||||
400 303.82993 -16625.014 0 -13908.942 237.957
|
||||
500 298.00206 -16716.893 0 -14052.919 231.33112
|
||||
Loop time of 12.5516 on 4 procs for 500 steps with 4500 atoms
|
||||
|
||||
Performance: 6.884 ns/day, 3.487 hours/ns, 39.836 timesteps/s
|
||||
94.9% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 7.739 | 7.9051 | 8.2663 | 7.5 | 62.98
|
||||
Bond | 0.00061631 | 0.00064486 | 0.00070524 | 0.0 | 0.01
|
||||
Kspace | 2.7001 | 3.0573 | 3.2239 | 11.9 | 24.36
|
||||
Neigh | 1.1736 | 1.174 | 1.1743 | 0.0 | 9.35
|
||||
Comm | 0.18222 | 0.1869 | 0.19248 | 0.8 | 1.49
|
||||
Output | 0.00017595 | 0.00032246 | 0.00076079 | 0.0 | 0.00
|
||||
Modify | 0.20354 | 0.20467 | 0.20652 | 0.2 | 1.63
|
||||
Other | | 0.02259 | | | 0.18
|
||||
|
||||
Nlocal: 1125 ave 1132 max 1114 min
|
||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
||||
Nghost: 12241 ave 12298 max 12196 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
Neighs: 650366 ave 671163 max 631441 min
|
||||
Histogram: 1 0 0 1 0 1 0 0 0 1
|
||||
|
||||
Total # of neighbors = 2601464
|
||||
Ave neighs/atom = 578.103
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 45
|
||||
Dangerous builds = 0
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
compute gofr all rdf 100 1 1 2 2 1 2 # O-O, H-H, O-H
|
||||
compute gofa all adf 45 1 1 1 2.0 3.5 2.0 3.5 2 1 1 0.0 1.2 1.5 2.5 # O-O-O, O-H...O
|
||||
fix rdf all ave/time 100 10 1000 c_gofr[*] file spce-rdf.dat mode vector
|
||||
fix adf all ave/time 10 100 1000 c_gofa[*] file spce-adf.dat mode vector
|
||||
|
||||
run 1000
|
||||
PPPM initialization ...
|
||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:321)
|
||||
G vector (1/distance) = 0.279652
|
||||
grid = 40 40 40
|
||||
stencil order = 5
|
||||
estimated absolute RMS force accuracy = 0.000394674
|
||||
estimated relative force accuracy = 1.18855e-06
|
||||
using double precision FFTs
|
||||
3d grid and FFT values/proc = 34263 16000
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 2 steps, check yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 14
|
||||
ghost atom cutoff = 14
|
||||
binsize = 7, bins = 6 6 6
|
||||
3 neighbor lists, perpetual/occasional/extra = 1 2 0
|
||||
(1) pair lj/cut/coul/long, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/newton
|
||||
stencil: half/bin/3d/newton
|
||||
bin: standard
|
||||
(2) compute rdf, occasional, copy from (1)
|
||||
attributes: half, newton on
|
||||
pair build: copy
|
||||
stencil: none
|
||||
bin: none
|
||||
(3) compute adf, occasional
|
||||
attributes: full, newton on
|
||||
pair build: full/bin
|
||||
stencil: full/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 13.96 | 13.96 | 13.96 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 298.00206 -16716.893 0 -14052.919 231.44272
|
||||
100 307.28155 -16760.647 0 -14013.72 452.38436
|
||||
200 299.05168 -16674.695 0 -14001.338 177.44237
|
||||
300 292.7564 -16573.946 0 -13956.865 122.27796
|
||||
400 299.2644 -16578.318 0 -13903.059 482.03304
|
||||
500 296.04028 -16623.179 0 -13976.742 89.968145
|
||||
600 300.30911 -16664.206 0 -13979.608 132.70079
|
||||
700 292.39517 -16703.749 0 -14089.897 825.267
|
||||
800 298.75851 -16661.684 0 -13990.948 468.68671
|
||||
900 301.55689 -16644.846 0 -13949.093 -72.16965
|
||||
1000 298.2852 -16682.077 0 -14015.572 0.69725342
|
||||
Loop time of 32.3106 on 4 procs for 1000 steps with 4500 atoms
|
||||
|
||||
Performance: 5.348 ns/day, 4.488 hours/ns, 30.950 timesteps/s
|
||||
96.8% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 15.647 | 15.876 | 16.119 | 4.3 | 49.13
|
||||
Bond | 0.0011718 | 0.0012704 | 0.001348 | 0.2 | 0.00
|
||||
Kspace | 5.286 | 5.5364 | 5.7729 | 7.5 | 17.13
|
||||
Neigh | 2.3892 | 2.3962 | 2.3991 | 0.3 | 7.42
|
||||
Comm | 0.34641 | 0.35514 | 0.35988 | 0.9 | 1.10
|
||||
Output | 0.00047851 | 0.00069892 | 0.0013568 | 0.0 | 0.00
|
||||
Modify | 8.0882 | 8.0963 | 8.1047 | 0.3 | 25.06
|
||||
Other | | 0.04887 | | | 0.15
|
||||
|
||||
Nlocal: 1125 ave 1137 max 1114 min
|
||||
Histogram: 1 1 0 0 0 0 0 1 0 1
|
||||
Nghost: 12206.2 ave 12239 max 12169 min
|
||||
Histogram: 1 0 1 0 0 0 0 0 1 1
|
||||
Neighs: 650464 ave 655962 max 641444 min
|
||||
Histogram: 1 0 0 0 0 0 0 2 0 1
|
||||
FullNghs: 1.30095e+06 ave 1.31925e+06 max 1.28413e+06 min
|
||||
Histogram: 1 0 1 0 0 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 5203786
|
||||
Ave neighs/atom = 1156.4
|
||||
Ave special neighs/atom = 2
|
||||
Neighbor list builds = 94
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:45
|
||||
Loading…
Reference in New Issue