143 lines
5.8 KiB
Groff
143 lines
5.8 KiB
Groff
LAMMPS (27 Nov 2018)
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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 2 by 2 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 (src/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) = 3.37 | 3.37 | 3.371 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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500 314.70267 1036.3305 1943.4431 205.83301 65603.85
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1000 304.99804 1034.15 1913.2896 -79.521176 66268.87
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1500 305.2621 996.9303 1876.831 -97.93992 67090.442
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2000 311.29317 1083.9171 1981.2021 119.28085 65589.674
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2500 305.51905 1051.59 1932.2314 -34.076657 66487.327
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3000 291.76224 1053.524 1894.5121 45.522919 65879.535
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3500 297.65792 1017.1041 1875.0862 -79.411904 67185.183
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4000 285.99141 1042.379 1866.733 88.735986 66356.756
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4500 295.34218 1071.2977 1922.6048 -17.479073 65381.597
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5000 292.47 1012.3769 1855.405 -255.07433 67527.215
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5500 294.04431 1080.4547 1928.0208 192.6588 65811.742
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6000 300.45893 986.16669 1852.2225 -167.3405 67858.175
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6500 305.59738 1022.5276 1903.3947 -116.41298 66612.704
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7000 312.11968 1032.7392 1932.4065 152.17956 66016.299
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7500 306.80585 1032.1157 1916.4662 51.07705 66875.727
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8000 292.30957 1048.9003 1891.4661 61.280503 65894.103
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8500 297.79592 1013.4061 1871.786 -133.01136 66842.574
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9000 290.36753 1043.7732 1880.7412 65.208248 66010.86
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9500 288.92211 1077.8835 1910.6851 46.291982 65674.639
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10000 311.51608 1015.3567 1913.2842 -146.49492 66882.692
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Loop time of 13.9823 on 4 procs for 10000 steps with 968 atoms
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Performance: 61.792 ns/day, 0.388 hours/ns, 715.190 timesteps/s
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98.2% 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 | 10.131 | 11.235 | 12.333 | 23.2 | 80.35
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Neigh | 0.044854 | 0.046303 | 0.047541 | 0.5 | 0.33
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Comm | 1.1939 | 2.2964 | 3.4087 | 51.7 | 16.42
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Output | 0.0004735 | 0.0032033 | 0.01137 | 8.3 | 0.02
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Modify | 0.30542 | 0.31846 | 0.32508 | 1.4 | 2.28
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Other | | 0.08323 | | | 0.60
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Nlocal: 242 ave 248 max 232 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Nghost: 5845.75 ave 5877 max 5808 min
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Histogram: 1 0 0 0 1 0 0 1 0 1
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Neighs: 104313 ave 113860 max 95507 min
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Histogram: 1 1 0 0 0 0 0 1 0 1
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Total # of neighbors = 417252
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Ave neighs/atom = 431.045
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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: 0:00:14
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