update log files for fix widom
This commit is contained in:
Axel Kohlmeyer
91
examples/mc/log.14Jun23.widom.lj.g++.1
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91
examples/mc/log.14Jun23.widom.lj.g++.1
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LAMMPS (28 Mar 2023 - Development)
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using 1 OpenMP thread(s) per MPI task
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# Kob and Andersen model Phys. Rev. E 51, 4626 (1995)
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units lj
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atom_style atomic
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pair_style lj/cut 2.5
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pair_modify shift yes
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read_data data.widom.lj
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Reading data file ...
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orthogonal box = (0 0 0) to (9.4 9.4 9.4)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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1000 atoms
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reading velocities ...
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1000 velocities
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read_data CPU = 0.006 seconds
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pair_coeff 1 1 1.0 1.0 2.5
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pair_coeff 1 2 1.5 0.8 2.0
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pair_coeff 2 2 0.5 0.88 2.2
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neighbor 0.3 bin
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neigh_modify delay 0 every 5 check yes
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fix mywidom all widom 10 100000 2 29494 0.75
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fix 1 all langevin 0.75 0.75 0.1 48279 zero yes
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fix 2 all nve
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timestep 0.002
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thermo_style custom step temp pe etotal press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
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thermo 10
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run 100
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 5 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 = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 7 7 7
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, 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
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.181 | 3.181 | 3.181 Mbytes
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Step Temp PotEng TotEng Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3]
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0 0.75021245 -6.4204308 -5.2962374 7.2962696 830.584 1.2039721 0 0 830.584
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10 0.7358936 -6.4405082 -5.3377717 7.1699962 830.584 1.2039721 -3.8577501 171.3429 830.584
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20 0.75426414 -6.4267946 -5.2965298 7.2833985 830.584 1.2039721 -4.0708206 227.63895 830.584
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30 0.72947489 -6.4064078 -5.3132896 7.3872583 830.584 1.2039721 -4.4304803 367.7146 830.584
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40 0.73504751 -6.4248725 -5.3234038 7.2927069 830.584 1.2039721 -4.1904189 266.99373 830.584
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50 0.76497439 -6.4352472 -5.2889331 7.3046861 830.584 1.2039721 -3.8628472 172.51133 830.584
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60 0.75752861 -6.4147051 -5.2795485 7.4416 830.584 1.2039721 -3.5355467 111.5042 830.584
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70 0.77775078 -6.4210798 -5.2556202 7.4473703 830.584 1.2039721 -3.4754802 102.92223 830.584
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80 0.80937104 -6.4320008 -5.2191583 7.4121087 830.584 1.2039721 -3.9287513 188.35625 830.584
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90 0.76321255 -6.4203633 -5.2766893 7.4307727 830.584 1.2039721 -4.2257529 279.87337 830.584
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100 0.74561743 -6.4010576 -5.2837499 7.52907 830.584 1.2039721 -3.6817835 135.5099 830.584
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Loop time of 10.2362 on 1 procs for 100 steps with 1000 atoms
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Performance: 1688.128 tau/day, 9.769 timesteps/s, 9.769 katom-step/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 | 0.058411 | 0.058411 | 0.058411 | 0.0 | 0.57
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Neigh | 0.017611 | 0.017611 | 0.017611 | 0.0 | 0.17
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Comm | 0.001774 | 0.001774 | 0.001774 | 0.0 | 0.02
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Output | 0.00029892 | 0.00029892 | 0.00029892 | 0.0 | 0.00
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Modify | 10.158 | 10.158 | 10.158 | 0.0 | 99.23
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Other | | 0.0003838 | | | 0.00
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Nlocal: 1000 ave 1000 max 1000 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 3049 ave 3049 max 3049 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 46176 ave 46176 max 46176 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 46176
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Ave neighs/atom = 46.176
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Neighbor list builds = 10
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Dangerous builds = 0
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Total wall time: 0:00:10
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91
examples/mc/log.14Jun23.widom.lj.g++.4
Normal file
91
examples/mc/log.14Jun23.widom.lj.g++.4
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@ -0,0 +1,91 @@
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LAMMPS (28 Mar 2023 - Development)
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using 1 OpenMP thread(s) per MPI task
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|
# Kob and Andersen model Phys. Rev. E 51, 4626 (1995)
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units lj
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atom_style atomic
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pair_style lj/cut 2.5
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pair_modify shift yes
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read_data data.widom.lj
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Reading data file ...
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orthogonal box = (0 0 0) to (9.4 9.4 9.4)
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1 by 2 by 2 MPI processor grid
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reading atoms ...
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1000 atoms
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reading velocities ...
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1000 velocities
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read_data CPU = 0.009 seconds
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pair_coeff 1 1 1.0 1.0 2.5
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pair_coeff 1 2 1.5 0.8 2.0
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pair_coeff 2 2 0.5 0.88 2.2
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neighbor 0.3 bin
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neigh_modify delay 0 every 5 check yes
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fix mywidom all widom 10 100000 2 29494 0.75
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fix 1 all langevin 0.75 0.75 0.1 48279 zero yes
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fix 2 all nve
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timestep 0.002
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thermo_style custom step temp pe etotal press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
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thermo 10
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run 100
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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Neighbor list info ...
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update: every = 5 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 = 2.8
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ghost atom cutoff = 2.8
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binsize = 1.4, bins = 7 7 7
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, 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
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 3.13 | 3.13 | 3.131 Mbytes
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Step Temp PotEng TotEng Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3]
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0 0.75021245 -6.4204308 -5.2962374 7.2962696 830.584 1.2039721 0 0 830.584
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10 0.74279259 -6.4332442 -5.3201696 7.2071344 830.584 1.2039721 -3.4462258 98.984938 830.584
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20 0.73016272 -6.4222911 -5.3281423 7.2714238 830.584 1.2039721 -4.4887329 397.41346 830.584
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30 0.74416342 -6.429139 -5.3140101 7.2713375 830.584 1.2039721 -4.3313574 322.19056 830.584
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40 0.73295457 -6.4370942 -5.3387618 7.227091 830.584 1.2039721 -4.7419281 557.00309 830.584
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50 0.76914235 -6.4473959 -5.2948361 7.2179148 830.584 1.2039721 -3.1794069 69.352982 830.584
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60 0.74099083 -6.4433012 -5.3329265 7.204973 830.584 1.2039721 -3.5231065 109.66994 830.584
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70 0.74514671 -6.4288463 -5.312244 7.2771269 830.584 1.2039721 -1.0154832 3.8727995 830.584
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80 0.72787097 -6.4457574 -5.3550427 7.1130709 830.584 1.2039721 -3.6691709 133.2501 830.584
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90 0.78452846 -6.5034376 -5.3278217 6.8238659 830.584 1.2039721 -2.0798339 16.008373 830.584
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100 0.77188499 -6.487313 -5.3306433 6.9133194 830.584 1.2039721 -2.066579 15.727938 830.584
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Loop time of 1.59209 on 4 procs for 100 steps with 1000 atoms
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Performance: 10853.637 tau/day, 62.810 timesteps/s, 62.810 katom-step/s
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96.4% 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 | 0.014713 | 0.015481 | 0.016154 | 0.4 | 0.97
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Neigh | 0.0045952 | 0.0047537 | 0.0048917 | 0.2 | 0.30
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Comm | 0.026382 | 0.086811 | 0.14145 | 13.9 | 5.45
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Output | 0.00022704 | 0.0002596 | 0.00035704 | 0.0 | 0.02
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Modify | 1.4299 | 1.4845 | 1.5447 | 3.4 | 93.24
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Other | | 0.0003365 | | | 0.02
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Nlocal: 250 ave 256 max 242 min
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Histogram: 1 0 0 0 1 0 0 0 1 1
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Nghost: 1666 ave 1670 max 1659 min
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Histogram: 1 0 0 0 0 0 1 0 0 2
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Neighs: 11538 ave 11832 max 11091 min
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Histogram: 1 0 0 0 0 0 1 1 0 1
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Total # of neighbors = 46152
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Ave neighs/atom = 46.152
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Neighbor list builds = 10
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Dangerous builds = 0
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Total wall time: 0:00:01
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139
examples/mc/log.14Jun23.widom.spce.g++.1
Normal file
139
examples/mc/log.14Jun23.widom.spce.g++.1
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@ -0,0 +1,139 @@
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LAMMPS (28 Mar 2023 - Development)
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using 1 OpenMP thread(s) per MPI task
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units real
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dimension 3
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boundary p p p
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atom_style full
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pair_style lj/cut/coul/long 10.0
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bond_style harmonic
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angle_style harmonic
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read_data data.spce
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Reading data file ...
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orthogonal box = (-0.031613 -0.023523 -0.085255) to (43.234352 44.939753 42.306533)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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8640 atoms
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scanning bonds ...
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2 = max bonds/atom
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scanning angles ...
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1 = max angles/atom
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reading bonds ...
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5760 bonds
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reading angles ...
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2880 angles
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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2 = max # of 1-2 neighbors
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1 = max # of 1-3 neighbors
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1 = max # of 1-4 neighbors
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2 = max # of special neighbors
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special bonds CPU = 0.002 seconds
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read_data CPU = 0.048 seconds
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molecule h2omol H2O.txt
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Read molecule template h2omol:
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1 molecules
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0 fragments
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3 atoms with max type 2
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2 bonds with max type 1
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1 angles with max type 1
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0 dihedrals with max type 0
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0 impropers with max type 0
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### Flexible SPC/E Potential Parameters ###
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### Zhang et al., Fluid Phase Equilibria, 262 (2007) 210-216 ###
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pair_coeff 1 1 0.1502629 3.1169
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pair_coeff 1 2 0.0341116368 2.04845
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pair_coeff 2 2 0.00774378 0.98
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bond_coeff 1 176.864 0.9611
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angle_coeff 1 42.1845 109.4712
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kspace_style pppm 1.0e-4
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fix mywidom all widom 10 20 0 29494 298 mol h2omol
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fix 2 all nvt temp 298.0 298.0 100.0
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neighbor 2.0 bin
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neigh_modify delay 10 every 2 check yes
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#run variables
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timestep 0.5
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thermo 10
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thermo_style custom step etotal pe temp press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
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run 100
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PPPM initialization ...
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using 12-bit tables for long-range coulomb (src/kspace.cpp:342)
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G vector (1/distance) = 0.2690183
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grid = 24 24 24
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stencil order = 5
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estimated absolute RMS force accuracy = 0.024843102
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estimated relative force accuracy = 7.4814263e-05
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using double precision KISS FFT
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3d grid and FFT values/proc = 29791 13824
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Generated 0 of 1 mixed pair_coeff terms from geometric mixing rule
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WARNING: Fix widom using full_energy option (src/MC/fix_widom.cpp:320)
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0 atoms in group FixWidom:widom_exclusion_group:mywidom
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0 atoms in group FixWidom:rotation_gas_atoms:mywidom
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WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:654)
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Neighbor list info ...
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update: every = 2 steps, delay = 10 steps, check = yes
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max neighbors/atom: 2000, page size: 100000
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master list distance cutoff = 12
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ghost atom cutoff = 12
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binsize = 6, bins = 8 8 8
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut/coul/long, 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
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 29.66 | 29.66 | 29.66 Mbytes
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Step TotEng PotEng Temp Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3]
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0 -29703.973 -29703.973 0 -4764.5901 82468.116 1.0447118 0 0 82468.116
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10 -29718 -32598.944 111.87604 -498.88935 82468.116 1.0447118 200.15526 1.6274344e-147 82468.116
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20 -29698.227 -32625.357 113.6696 -3120.7115 82468.116 1.0447118 -1.0295764 5.6893637 82468.116
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30 -29668.463 -33188.922 136.71037 -8129.0179 82468.116 1.0447118 5.5971294 7.856256e-05 82468.116
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40 -29654.066 -34017.797 169.45726 -5730.6427 82468.116 1.0447118 128.14313 1.0550462e-94 82468.116
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50 -29627.714 -33214.549 139.28799 -3954.0179 82468.116 1.0447118 122.28545 2.0851209e-90 82468.116
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60 -29602.616 -32995.039 131.73836 -8099.2136 82468.116 1.0447118 -1.4752191 12.07497 82468.116
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70 -29591.096 -33872.451 166.25834 -7065.2821 82468.116 1.0447118 17.210054 2.3911575e-13 82468.116
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80 -29553.631 -32971.209 132.7152 -3535.4257 82468.116 1.0447118 11.148921 6.6631697e-09 82468.116
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90 -29530.109 -33346.146 148.18857 -5312.6414 82468.116 1.0447118 51.783293 1.055658e-38 82468.116
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100 -29505.327 -34074.801 177.4469 -5991.0034 82468.116 1.0447118 32.415523 1.6878187e-24 82468.116
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Loop time of 55.4401 on 1 procs for 100 steps with 8640 atoms
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Performance: 0.078 ns/day, 308.000 hours/ns, 1.804 timesteps/s, 15.584 katom-step/s
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99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
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||||||
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|
||||||
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MPI task timing breakdown:
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||||||
|
Section | min time | avg time | max time |%varavg| %total
|
||||||
|
---------------------------------------------------------------
|
||||||
|
Pair | 5.4117 | 5.4117 | 5.4117 | 0.0 | 9.76
|
||||||
|
Bond | 0.029451 | 0.029451 | 0.029451 | 0.0 | 0.05
|
||||||
|
Kspace | 0.73758 | 0.73758 | 0.73758 | 0.0 | 1.33
|
||||||
|
Neigh | 1.4296 | 1.4296 | 1.4296 | 0.0 | 2.58
|
||||||
|
Comm | 0.018593 | 0.018593 | 0.018593 | 0.0 | 0.03
|
||||||
|
Output | 0.00069303 | 0.00069303 | 0.00069303 | 0.0 | 0.00
|
||||||
|
Modify | 47.81 | 47.81 | 47.81 | 0.0 | 86.24
|
||||||
|
Other | | 0.002525 | | | 0.00
|
||||||
|
|
||||||
|
Nlocal: 8640 ave 8640 max 8640 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Nghost: 23534 ave 23534 max 23534 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
Neighs: 3.27356e+06 ave 3.27356e+06 max 3.27356e+06 min
|
||||||
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||||
|
|
||||||
|
Total # of neighbors = 3273560
|
||||||
|
Ave neighs/atom = 378.88426
|
||||||
|
Ave special neighs/atom = 2
|
||||||
|
Neighbor list builds = 220
|
||||||
|
Dangerous builds = 0
|
||||||
|
Total wall time: 0:00:55
|
||||||
@ -1,89 +0,0 @@
|
|||||||
LAMMPS (30 Jun 2020)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Kob and Andersen model Phys. Rev. E 51, 4626 (1995)
|
|
||||||
|
|
||||||
units lj
|
|
||||||
atom_style atomic
|
|
||||||
|
|
||||||
pair_style lj/cut 2.5
|
|
||||||
pair_modify shift yes
|
|
||||||
|
|
||||||
read_data data.widom.lj
|
|
||||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (9.4000000 9.4000000 9.4000000)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
1000 atoms
|
|
||||||
reading velocities ...
|
|
||||||
1000 velocities
|
|
||||||
read_data CPU = 0.003 seconds
|
|
||||||
|
|
||||||
pair_coeff 1 1 1.0 1.0 2.5
|
|
||||||
pair_coeff 1 2 1.5 0.8 2.0
|
|
||||||
pair_coeff 2 2 0.5 0.88 2.2
|
|
||||||
|
|
||||||
neighbor 0.3 bin
|
|
||||||
neigh_modify delay 0 every 5 check yes
|
|
||||||
|
|
||||||
fix mywidom all widom 10 100000 2 29494 0.75
|
|
||||||
|
|
||||||
fix 1 all langevin 0.75 0.75 0.1 48279 zero yes
|
|
||||||
fix 2 all nve
|
|
||||||
|
|
||||||
timestep 0.002
|
|
||||||
|
|
||||||
thermo_style custom step temp pe etotal press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
|
|
||||||
thermo 10
|
|
||||||
|
|
||||||
run 100
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 5 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2.8
|
|
||||||
ghost atom cutoff = 2.8
|
|
||||||
binsize = 1.4, bins = 7 7 7
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair lj/cut, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.181 | 3.181 | 3.181 Mbytes
|
|
||||||
Step Temp PotEng TotEng Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3]
|
|
||||||
0 0.75021245 -6.4204308 -5.2962374 7.2962696 830.584 1.2039721 0 0 830.584
|
|
||||||
10 0.7358936 -6.4405082 -5.3377717 7.1699962 830.584 1.2039721 -3.8577501 171.3429 830.584
|
|
||||||
20 0.75426414 -6.4267946 -5.2965298 7.2833985 830.584 1.2039721 -4.0708206 227.63895 830.584
|
|
||||||
30 0.72947489 -6.4064078 -5.3132896 7.3872583 830.584 1.2039721 -4.4304803 367.7146 830.584
|
|
||||||
40 0.73504751 -6.4248725 -5.3234038 7.2927069 830.584 1.2039721 -4.1904189 266.99373 830.584
|
|
||||||
50 0.76497439 -6.4352472 -5.2889331 7.3046861 830.584 1.2039721 -3.8628472 172.51133 830.584
|
|
||||||
60 0.75752861 -6.4147051 -5.2795485 7.4416 830.584 1.2039721 -3.5355467 111.5042 830.584
|
|
||||||
70 0.77775078 -6.4210798 -5.2556202 7.4473703 830.584 1.2039721 -3.4754802 102.92223 830.584
|
|
||||||
80 0.80937104 -6.4320008 -5.2191583 7.4121087 830.584 1.2039721 -3.9287513 188.35625 830.584
|
|
||||||
90 0.76321255 -6.4203633 -5.2766893 7.4307727 830.584 1.2039721 -4.2257529 279.87337 830.584
|
|
||||||
100 0.74561743 -6.4010576 -5.2837499 7.52907 830.584 1.2039721 -3.6817835 135.5099 830.584
|
|
||||||
Loop time of 25.8264 on 1 procs for 100 steps with 1000 atoms
|
|
||||||
|
|
||||||
Performance: 669.082 tau/day, 3.872 timesteps/s
|
|
||||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.08186 | 0.08186 | 0.08186 | 0.0 | 0.32
|
|
||||||
Neigh | 0.023613 | 0.023613 | 0.023613 | 0.0 | 0.09
|
|
||||||
Comm | 0.0053532 | 0.0053532 | 0.0053532 | 0.0 | 0.02
|
|
||||||
Output | 0.00037837 | 0.00037837 | 0.00037837 | 0.0 | 0.00
|
|
||||||
Modify | 25.715 | 25.715 | 25.715 | 0.0 | 99.57
|
|
||||||
Other | | 0.0005643 | | | 0.00
|
|
||||||
|
|
||||||
Nlocal: 1000.00 ave 1000 max 1000 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 3049.00 ave 3049 max 3049 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 46176.0 ave 46176 max 46176 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 46176
|
|
||||||
Ave neighs/atom = 46.176000
|
|
||||||
Neighbor list builds = 10
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:25
|
|
||||||
@ -1,89 +0,0 @@
|
|||||||
LAMMPS (30 Jun 2020)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
# Kob and Andersen model Phys. Rev. E 51, 4626 (1995)
|
|
||||||
|
|
||||||
units lj
|
|
||||||
atom_style atomic
|
|
||||||
|
|
||||||
pair_style lj/cut 2.5
|
|
||||||
pair_modify shift yes
|
|
||||||
|
|
||||||
read_data data.widom.lj
|
|
||||||
orthogonal box = (0.0000000 0.0000000 0.0000000) to (9.4000000 9.4000000 9.4000000)
|
|
||||||
1 by 2 by 2 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
1000 atoms
|
|
||||||
reading velocities ...
|
|
||||||
1000 velocities
|
|
||||||
read_data CPU = 0.002 seconds
|
|
||||||
|
|
||||||
pair_coeff 1 1 1.0 1.0 2.5
|
|
||||||
pair_coeff 1 2 1.5 0.8 2.0
|
|
||||||
pair_coeff 2 2 0.5 0.88 2.2
|
|
||||||
|
|
||||||
neighbor 0.3 bin
|
|
||||||
neigh_modify delay 0 every 5 check yes
|
|
||||||
|
|
||||||
fix mywidom all widom 10 100000 2 29494 0.75
|
|
||||||
|
|
||||||
fix 1 all langevin 0.75 0.75 0.1 48279 zero yes
|
|
||||||
fix 2 all nve
|
|
||||||
|
|
||||||
timestep 0.002
|
|
||||||
|
|
||||||
thermo_style custom step temp pe etotal press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
|
|
||||||
thermo 10
|
|
||||||
|
|
||||||
run 100
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 5 steps, delay 0 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 2.8
|
|
||||||
ghost atom cutoff = 2.8
|
|
||||||
binsize = 1.4, bins = 7 7 7
|
|
||||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
||||||
(1) pair lj/cut, perpetual
|
|
||||||
attributes: half, newton on
|
|
||||||
pair build: half/bin/atomonly/newton
|
|
||||||
stencil: half/bin/3d/newton
|
|
||||||
bin: standard
|
|
||||||
Per MPI rank memory allocation (min/avg/max) = 3.13 | 3.13 | 3.131 Mbytes
|
|
||||||
Step Temp PotEng TotEng Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3]
|
|
||||||
0 0.75021245 -6.4204308 -5.2962374 7.2962696 830.584 1.2039721 0 0 830.584
|
|
||||||
10 0.74279259 -6.4332442 -5.3201696 7.2071344 830.584 1.2039721 -3.4462258 98.984938 830.584
|
|
||||||
20 0.73016272 -6.4222911 -5.3281423 7.2714238 830.584 1.2039721 -4.4887329 397.41346 830.584
|
|
||||||
30 0.74416342 -6.429139 -5.3140101 7.2713375 830.584 1.2039721 -4.3313574 322.19056 830.584
|
|
||||||
40 0.73295457 -6.4370942 -5.3387618 7.227091 830.584 1.2039721 -4.7419281 557.00309 830.584
|
|
||||||
50 0.76914235 -6.4473959 -5.2948361 7.2179148 830.584 1.2039721 -3.1794069 69.352982 830.584
|
|
||||||
60 0.74099083 -6.4433012 -5.3329265 7.204973 830.584 1.2039721 -3.5231065 109.66994 830.584
|
|
||||||
70 0.74514671 -6.4288463 -5.312244 7.2771269 830.584 1.2039721 -1.0154832 3.8727995 830.584
|
|
||||||
80 0.72787097 -6.4457574 -5.3550427 7.1130709 830.584 1.2039721 -3.6691709 133.2501 830.584
|
|
||||||
90 0.78452846 -6.5034376 -5.3278217 6.8238659 830.584 1.2039721 -2.0798339 16.008373 830.584
|
|
||||||
100 0.77188499 -6.487313 -5.3306433 6.9133194 830.584 1.2039721 -2.066579 15.727938 830.584
|
|
||||||
Loop time of 3.37748 on 4 procs for 100 steps with 1000 atoms
|
|
||||||
|
|
||||||
Performance: 5116.239 tau/day, 29.608 timesteps/s
|
|
||||||
98.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 0.02025 | 0.020952 | 0.021322 | 0.3 | 0.62
|
|
||||||
Neigh | 0.0059071 | 0.0060568 | 0.0061543 | 0.1 | 0.18
|
|
||||||
Comm | 0.016558 | 0.059554 | 0.094282 | 12.2 | 1.76
|
|
||||||
Output | 0.00022173 | 0.00042927 | 0.0010471 | 0.0 | 0.01
|
|
||||||
Modify | 3.2552 | 3.2902 | 3.3335 | 1.7 | 97.42
|
|
||||||
Other | | 0.0003003 | | | 0.01
|
|
||||||
|
|
||||||
Nlocal: 250.000 ave 256 max 242 min
|
|
||||||
Histogram: 1 0 0 0 1 0 0 0 1 1
|
|
||||||
Nghost: 1666.00 ave 1670 max 1659 min
|
|
||||||
Histogram: 1 0 0 0 0 0 1 0 0 2
|
|
||||||
Neighs: 11538.0 ave 11832 max 11091 min
|
|
||||||
Histogram: 1 0 0 0 0 0 1 1 0 1
|
|
||||||
|
|
||||||
Total # of neighbors = 46152
|
|
||||||
Ave neighs/atom = 46.152000
|
|
||||||
Neighbor list builds = 10
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:00:03
|
|
||||||
@ -1,133 +0,0 @@
|
|||||||
LAMMPS (30 Jun 2020)
|
|
||||||
using 1 OpenMP thread(s) per MPI task
|
|
||||||
units real
|
|
||||||
dimension 3
|
|
||||||
boundary p p p
|
|
||||||
atom_style full
|
|
||||||
|
|
||||||
pair_style lj/cut/coul/long 10.0
|
|
||||||
bond_style harmonic
|
|
||||||
angle_style harmonic
|
|
||||||
|
|
||||||
read_data data.spce
|
|
||||||
orthogonal box = (-0.031613 -0.023523 -0.085255) to (43.234352 44.939753 42.306533)
|
|
||||||
1 by 1 by 1 MPI processor grid
|
|
||||||
reading atoms ...
|
|
||||||
8640 atoms
|
|
||||||
scanning bonds ...
|
|
||||||
2 = max bonds/atom
|
|
||||||
scanning angles ...
|
|
||||||
1 = max angles/atom
|
|
||||||
reading bonds ...
|
|
||||||
5760 bonds
|
|
||||||
reading angles ...
|
|
||||||
2880 angles
|
|
||||||
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 CPU = 0.008 seconds
|
|
||||||
read_data CPU = 0.028 seconds
|
|
||||||
|
|
||||||
molecule h2omol H2O.txt
|
|
||||||
Read molecule template h2omol:
|
|
||||||
1 molecules
|
|
||||||
3 atoms with max type 2
|
|
||||||
2 bonds with max type 1
|
|
||||||
1 angles with max type 1
|
|
||||||
0 dihedrals with max type 0
|
|
||||||
0 impropers with max type 0
|
|
||||||
|
|
||||||
### Flexible SPC/E Potential Parameters ###
|
|
||||||
### Zhang et al., Fluid Phase Equilibria, 262 (2007) 210-216 ###
|
|
||||||
pair_coeff 1 1 0.1502629 3.1169
|
|
||||||
pair_coeff 1 2 0.0341116368 2.04845
|
|
||||||
pair_coeff 2 2 0.00774378 0.98
|
|
||||||
|
|
||||||
bond_coeff 1 176.864 0.9611
|
|
||||||
angle_coeff 1 42.1845 109.4712
|
|
||||||
kspace_style pppm 1.0e-4
|
|
||||||
|
|
||||||
fix mywidom all widom 10 20 0 29494 298 mol h2omol
|
|
||||||
|
|
||||||
fix 2 all nvt temp 298.0 298.0 100.0
|
|
||||||
|
|
||||||
neighbor 2.0 bin
|
|
||||||
neigh_modify delay 10 every 2 check yes
|
|
||||||
|
|
||||||
|
|
||||||
#run variables
|
|
||||||
timestep 0.5
|
|
||||||
|
|
||||||
thermo 10
|
|
||||||
thermo_style custom step etotal pe temp press vol density f_mywidom[1] f_mywidom[2] f_mywidom[3]
|
|
||||||
|
|
||||||
run 100
|
|
||||||
PPPM initialization ...
|
|
||||||
using 12-bit tables for long-range coulomb (src/kspace.cpp:330)
|
|
||||||
G vector (1/distance) = 0.2690183
|
|
||||||
grid = 24 24 24
|
|
||||||
stencil order = 5
|
|
||||||
estimated absolute RMS force accuracy = 0.024843102
|
|
||||||
estimated relative force accuracy = 7.4814263e-05
|
|
||||||
using double precision FFTW3
|
|
||||||
3d grid and FFT values/proc = 29791 13824
|
|
||||||
WARNING: Fix Widom using full_energy option (src/MC/fix_widom.cpp:297)
|
|
||||||
0 atoms in group FixWidom:widom_exclusion_group:mywidom
|
|
||||||
0 atoms in group FixWidom:rotation_gas_atoms:mywidom
|
|
||||||
WARNING: Neighbor exclusions used with KSpace solver may give inconsistent Coulombic energies (src/neighbor.cpp:487)
|
|
||||||
Neighbor list info ...
|
|
||||||
update every 2 steps, delay 10 steps, check yes
|
|
||||||
max neighbors/atom: 2000, page size: 100000
|
|
||||||
master list distance cutoff = 12
|
|
||||||
ghost atom cutoff = 12
|
|
||||||
binsize = 6, bins = 8 8 8
|
|
||||||
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) = 29.66 | 29.66 | 29.66 Mbytes
|
|
||||||
Step TotEng PotEng Temp Press Volume Density f_mywidom[1] f_mywidom[2] f_mywidom[3]
|
|
||||||
0 -29703.973 -29703.973 0 -4764.5901 82468.116 1.9140713 0 0 82468.116
|
|
||||||
10 -29712.131 -31110.041 54.285179 -3154.4423 82468.116 1.9140713 241.93348 3.7366217e-178 82468.116
|
|
||||||
20 -29711.939 -32614.429 112.71273 -4216.1592 82468.116 1.9140713 16.095006 1.5716469e-12 82468.116
|
|
||||||
30 -29688.142 -32368.506 104.08688 -4093.6515 82468.116 1.9140713 5.7862327 5.7086352e-05 82468.116
|
|
||||||
40 -29662.343 -32252.144 100.57005 -1458.5339 82468.116 1.9140713 126.68071 1.2467216e-93 82468.116
|
|
||||||
50 -29646.78 -32837.635 123.91081 -4607.1155 82468.116 1.9140713 74.622397 1.8790479e-55 82468.116
|
|
||||||
60 -29628.968 -33001.229 130.9554 -4589.5296 82468.116 1.9140713 3.6575433 0.0020780497 82468.116
|
|
||||||
70 -29602.78 -32816.28 124.79023 -3082.1133 82468.116 1.9140713 13.983097 5.561247e-11 82468.116
|
|
||||||
80 -29577.552 -33141.454 138.39742 -6332.8138 82468.116 1.9140713 41.98931 1.6075608e-31 82468.116
|
|
||||||
90 -29550.865 -33792.115 164.70094 -4607.6419 82468.116 1.9140713 68.690681 4.2082269e-51 82468.116
|
|
||||||
100 -29515.107 -34052.782 176.21207 -3609.5709 82468.116 1.9140713 41.090597 7.3326206e-31 82468.116
|
|
||||||
Loop time of 163.407 on 1 procs for 100 steps with 8640 atoms
|
|
||||||
|
|
||||||
Performance: 0.026 ns/day, 907.819 hours/ns, 0.612 timesteps/s
|
|
||||||
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
||||||
|
|
||||||
MPI task timing breakdown:
|
|
||||||
Section | min time | avg time | max time |%varavg| %total
|
|
||||||
---------------------------------------------------------------
|
|
||||||
Pair | 8.5495 | 8.5495 | 8.5495 | 0.0 | 5.23
|
|
||||||
Bond | 0.031981 | 0.031981 | 0.031981 | 0.0 | 0.02
|
|
||||||
Kspace | 2.3995 | 2.3995 | 2.3995 | 0.0 | 1.47
|
|
||||||
Neigh | 5.0542 | 5.0542 | 5.0542 | 0.0 | 3.09
|
|
||||||
Comm | 0.051965 | 0.051965 | 0.051965 | 0.0 | 0.03
|
|
||||||
Output | 0.0018802 | 0.0018802 | 0.0018802 | 0.0 | 0.00
|
|
||||||
Modify | 147.31 | 147.31 | 147.31 | 0.0 | 90.15
|
|
||||||
Other | | 0.003614 | | | 0.00
|
|
||||||
|
|
||||||
Nlocal: 8640.00 ave 8640 max 8640 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Nghost: 23499.0 ave 23499 max 23499 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
Neighs: 3.27380e+06 ave 3.2738e+06 max 3.2738e+06 min
|
|
||||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
||||||
|
|
||||||
Total # of neighbors = 3273800
|
|
||||||
Ave neighs/atom = 378.91204
|
|
||||||
Ave special neighs/atom = 2.0000000
|
|
||||||
Neighbor list builds = 220
|
|
||||||
Dangerous builds = 0
|
|
||||||
Total wall time: 0:02:44
|
|
||||||
Reference in New Issue
Block a user