2017-09-20 06:27:25 +08:00
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LAMMPS (1 Sep 2017)
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# simple water model with LATTE
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units metal
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atom_style full
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atom_modify sort 0 0.0 # turn off sorting of the coordinates
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read_data data.water
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orthogonal box = (0 0 0) to (6.267 6.267 6.267)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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24 atoms
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0 = max # of 1-2 neighbors
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0 = max # of 1-3 neighbors
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0 = max # of 1-4 neighbors
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1 = max # of special neighbors
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# replicate system if requested
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variable x index 1
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variable y index 1
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variable z index 1
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variable nrep equal v_x*v_y*v_z
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if "${nrep} > 1" then "replicate $x $y $z"
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# initialize system
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velocity all create 0.0 87287 loop geom
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pair_style zero 1.0
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pair_coeff * *
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neighbor 1.0 bin
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neigh_modify every 1 delay 0 check yes
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timestep 0.00025
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fix 1 all nve
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fix 2 all latte NULL
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fix_modify 2 energy yes
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2017-09-22 00:40:54 +08:00
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thermo_style custom step temp pe etotal press
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2017-09-20 06:27:25 +08:00
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# minimization
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2017-09-22 00:40:54 +08:00
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thermo 10
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2017-09-20 06:27:25 +08:00
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min_style fire
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2017-09-22 00:40:54 +08:00
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minimize 1.0e-9 1.0e-9 500 500
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2017-09-20 06:27:25 +08:00
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Neighbor list info ...
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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 = 2
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ghost atom cutoff = 2
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binsize = 1, bins = 7 7 7
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair zero, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d/newton
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 5.629 | 5.629 | 5.629 Mbytes
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2017-09-22 00:40:54 +08:00
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Step Temp PotEng TotEng Press
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0 0 -104.95614 -104.95614 48229.712
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10 349.44219 -105.50971 -104.47083 62149.591
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20 1253.6752 -107.00898 -103.28182 116444.44
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30 134.63588 -107.56184 -107.16157 59854.143
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40 2.4043703 -108.15301 -108.14586 32685.77
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50 162.13426 -108.40551 -107.92349 62104.273
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60 134.03149 -108.70118 -108.30271 49400.525
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70 64.159014 -108.78034 -108.5896 37243.303
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80 240.49926 -109.10766 -108.39266 42158.884
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90 0.60467192 -109.61818 -109.61639 14107.515
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100 1.4691163 -109.65556 -109.65119 21596.775
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110 30.500628 -109.69267 -109.602 16104.639
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120 120.62379 -109.83749 -109.47888 9474.971
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130 8.4742975 -109.99986 -109.97467 10104.102
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140 3.4732679 -110.01209 -110.00176 11990.442
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150 24.749482 -110.04313 -109.96955 10851.569
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160 4.1106505 -110.13288 -110.12066 8257.3969
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170 0.0065628716 -110.18061 -110.18059 7876.8748
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180 2.0542078 -110.1837 -110.17759 7996.0533
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190 20.134782 -110.21071 -110.15085 7556.1811
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200 2.3397267 -110.3244 -110.31745 3767.062
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210 4.3544709 -110.34438 -110.33143 4889.145
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220 1.1872367 -110.37457 -110.37104 4162.6543
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230 2.2798399 -110.38081 -110.37403 4321.0943
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240 11.835907 -110.39611 -110.36092 4187.5757
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250 0.13741849 -110.41453 -110.41412 3720.7527
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260 4.2283185 -110.42036 -110.40779 3743.3494
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270 0.47243724 -110.44349 -110.44208 3172.1866
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280 0.06090137 -110.45428 -110.4541 3065.9348
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290 5.3413962 -110.46285 -110.44697 3121.2924
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300 8.2032986 -110.48519 -110.4608 2705.5001
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310 2.0783529 -110.48807 -110.48189 2740.7989
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320 16.629185 -110.51002 -110.46058 2581.7434
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330 0.19723065 -110.53444 -110.53385 1942.0228
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340 6.2758334 -110.54361 -110.52495 1924.0965
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350 1.4539052 -110.59108 -110.58676 -449.41056
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360 0.0514233 -110.60143 -110.60128 1284.8259
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370 1.7240145 -110.60394 -110.59881 1468.0004
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380 13.28516 -110.62337 -110.58387 1573.4714
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390 1.2247432 -110.63525 -110.63161 1113.4557
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400 0.3946985 -110.63694 -110.63576 1083.0801
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410 2.9831433 -110.641 -110.63213 1112.419
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420 0.068550589 -110.66029 -110.66009 897.09211
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430 0.83976182 -110.66259 -110.66009 918.69832
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440 4.4760907 -110.66844 -110.65513 915.24435
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450 1.2841241 -110.67482 -110.671 953.30422
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460 2.5707455 -110.68509 -110.67745 775.21273
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470 0.99721544 -110.68646 -110.6835 812.74984
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480 6.8379261 -110.69468 -110.67435 787.9705
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490 0.18134438 -110.69628 -110.69574 675.52792
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500 2.0946523 -110.69918 -110.69295 696.82065
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Loop time of 31.775 on 1 procs for 500 steps with 24 atoms
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884.8% CPU use with 1 MPI tasks x no OpenMP threads
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2017-09-20 06:27:25 +08:00
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Minimization stats:
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Stopping criterion = max iterations
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Energy initial, next-to-last, final =
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2017-09-22 00:40:54 +08:00
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-104.95614332 -110.698546127 -110.699182193
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Force two-norm initial, final = 19.119 0.234621
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Force max component initial, final = 11.7759 0.0903198
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2017-09-20 06:27:25 +08:00
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Final line search alpha, max atom move = 0 0
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2017-09-22 00:40:54 +08:00
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Iterations, force evaluations = 500 500
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2017-09-20 06:27:25 +08:00
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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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2017-09-22 00:40:54 +08:00
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Pair | 0.00016952 | 0.00016952 | 0.00016952 | 0.0 | 0.00
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Bond | 2.8372e-05 | 2.8372e-05 | 2.8372e-05 | 0.0 | 0.00
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Neigh | 3.0994e-05 | 3.0994e-05 | 3.0994e-05 | 0.0 | 0.00
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Comm | 0.00060034 | 0.00060034 | 0.00060034 | 0.0 | 0.00
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Output | 0.00057817 | 0.00057817 | 0.00057817 | 0.0 | 0.00
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Modify | 31.771 | 31.771 | 31.771 | 0.0 | 99.99
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Other | | 0.002469 | | | 0.01
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2017-09-20 06:27:25 +08:00
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Nlocal: 24 ave 24 max 24 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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2017-09-22 00:40:54 +08:00
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Nghost: 71 ave 71 max 71 min
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2017-09-20 06:27:25 +08:00
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Histogram: 1 0 0 0 0 0 0 0 0 0
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2017-09-22 00:40:54 +08:00
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Neighs: 27 ave 27 max 27 min
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2017-09-20 06:27:25 +08:00
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Histogram: 1 0 0 0 0 0 0 0 0 0
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2017-09-22 00:40:54 +08:00
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Total # of neighbors = 27
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Ave neighs/atom = 1.125
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2017-09-20 06:27:25 +08:00
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Ave special neighs/atom = 0
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2017-09-22 00:40:54 +08:00
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Neighbor list builds = 2
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2017-09-20 06:27:25 +08:00
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Dangerous builds = 0
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2017-09-22 00:40:54 +08:00
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Total wall time: 0:00:31
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