forked from lijiext/lammps
144 lines
5.8 KiB
Groff
144 lines
5.8 KiB
Groff
LAMMPS (20 Apr 2018)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
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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 atomic
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newton on
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timestep 1.0
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read_data methanol.data
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orthogonal box = (0 0 0) to (40.4635 40.4635 40.4635)
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1 by 1 by 1 MPI processor grid
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reading atoms ...
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968 atoms
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velocity all create 300.0 16802 dist gaussian
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pair_style table spline 15000
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pair_coeff 1 1 lammps_nb_MET-MET.table nb_METMET 12.0
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WARNING: 78 of 2500 force values in table are inconsistent with -dE/dr.
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Should only be flagged at inflection points (../pair_table.cpp:481)
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neigh_modify delay 0 every 1 check yes one 10000
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neighbor 12.0 bin
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thermo 500
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thermo_style custom step temp pe etotal press vol
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variable STEP equal step
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variable TEMP equal temp
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## volume from cubic angstroms to cubic nm
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variable VOL equal vol/1000.0
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## pressure from atm to bar
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variable PRESS equal press*1.01325
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variable PXX equal pxx*1.01325
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variable PYY equal pyy*1.01325
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variable PZZ equal pzz*1.01325
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variable PXY equal pxy*1.01325
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variable PXZ equal pxz*1.01325
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variable PYZ equal pyz*1.01325
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## energy from kcal/mol to kJ/mol
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variable KE equal ke*4.184
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variable PE equal pe*4.184
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variable UVDW equal evdwl*4.184
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##### SPECIAL COMMANDS FOR FIX_BOCS #####
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# ID group-ID style_name thermostat T_init T_end T_couple barostat P_start P_end P_couple pmatch_basis avg_vol N_sites N_coeffs coeff1 coeff2
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fix 1 all bocs temp 300.0 300.0 100.0 cgiso 0.986 0.986 1000.0 analytic 66476.015 968 2 245030.10 8962.20
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# Report the modified pressure
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thermo_modify press 1_press
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## Uncomment to save some data from simulation to files
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#fix print_temp all print 500 "${STEP} ${TEMP}" file temp.dat screen no
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#fix print_vol all print 500 "${STEP} ${VOL}" file vol.dat screen no
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#fix print_press all print 500 "${STEP} ${PRESS}" file press.dat screen no
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#fix print_ke all print 500 "${STEP} ${KE}" file kinetic_E.dat screen no
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#fix print_pe all print 500 "${STEP} ${PE}" file potential_E.dat screen no
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#fix print_ve all print 500 "${STEP} ${UVDW}" file vdw_E.dat screen no
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#fix print_press_tens all print 500 "${STEP} ${PXX} ${PYY} ${PZZ} ${PXY} ${PXZ} ${PYZ}" file press_tens.dat screen no
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#fix print_PV_eos all print 500 "${VOL} ${PRESS}" file pv_eos.dat screen no
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## Prints a configuration to dump.txt every 500 steps
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#dump 1 all custom 500 dump.txt id type x y z fx fy fz
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# Write restart files to continue simulations
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#restart 10000 state1.restart state2.restart
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## Run for this many steps
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run_style verlet
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run 10000
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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: 10000, page size: 100000
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master list distance cutoff = 24
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ghost atom cutoff = 24
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binsize = 12, bins = 4 4 4
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair table, 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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Per MPI rank memory allocation (min/avg/max) = 4.691 | 4.691 | 4.691 Mbytes
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Step Temp PotEng TotEng Press Volume
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0 300 1061.5961 1926.3291 107.006 66250.679
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500 314.54728 1034.1091 1940.7738 194.42689 65660.282
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1000 301.41603 1030.7027 1899.5173 -91.966709 66262.543
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1500 298.8308 1014.8276 1876.1905 -80.178606 67053.605
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2000 294.78476 1046.8207 1896.521 50.592942 66316.735
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2500 301.18564 1033.9214 1902.0719 40.48255 66607.667
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3000 301.06632 1022.0381 1889.8447 47.582344 66341.947
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3500 297.98361 989.80983 1848.7307 -204.69879 67462.078
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4000 299.03493 1034.6571 1896.6083 89.188888 66457.385
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4500 306.03351 985.4121 1867.5363 -51.102407 67519.446
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5000 305.6903 1013.8613 1894.9963 -141.13704 67240.467
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5500 292.23444 1029.5558 1871.905 20.764579 66683.876
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6000 287.87735 1017.7325 1847.5226 -35.288049 66630.031
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6500 305.26461 960.08118 1839.9891 -352.42596 67612.317
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7000 300.34449 1055.0664 1920.7923 22.04027 66187.27
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7500 305.48612 1038.6651 1919.2115 17.807254 66324.168
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8000 316.03232 1034.6809 1945.6262 27.482857 66502.198
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8500 294.28636 1038.8213 1887.085 -72.840559 66851.661
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9000 316.69029 1065.7481 1978.5899 245.61677 65678.385
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9500 297.46127 1034.5547 1891.97 54.23428 66892.627
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10000 301.24799 1036.5432 1904.8735 7.7134029 66150.506
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Loop time of 34.426 on 1 procs for 10000 steps with 968 atoms
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Performance: 25.097 ns/day, 0.956 hours/ns, 290.478 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 | 33.324 | 33.324 | 33.324 | 0.0 | 96.80
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Neigh | 0.12198 | 0.12198 | 0.12198 | 0.0 | 0.35
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Comm | 0.42865 | 0.42865 | 0.42865 | 0.0 | 1.25
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Output | 0.00059938 | 0.00059938 | 0.00059938 | 0.0 | 0.00
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Modify | 0.42553 | 0.42553 | 0.42553 | 0.0 | 1.24
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Other | | 0.1252 | | | 0.36
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Nlocal: 968 ave 968 max 968 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Nghost: 9112 ave 9112 max 9112 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 404392 ave 404392 max 404392 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 404392
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Ave neighs/atom = 417.76
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Neighbor list builds = 13
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Dangerous builds = 0
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Please see the log.cite file for references relevant to this simulation
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Total wall time: 0:00:34
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