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 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 (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) = 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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500 314.70267 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 -34.076658 66487.327
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3000 291.76224 1053.524 1894.5121 45.522865 65879.535
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3500 297.65795 1017.1028 1875.085 -79.41965 67185.19
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4000 285.98779 1042.3622 1866.7058 88.549172 66357.051
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4500 295.35 1071.4505 1922.7801 -16.75965 65378.949
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5000 293.20958 1009.9943 1855.1543 -270.58058 67555.38
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5500 292.40422 1085.3901 1928.2287 161.88502 65677.644
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6000 318.79663 1012.4832 1931.3964 -65.692451 67458.05
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6500 308.03807 1046.1413 1934.0436 249.70237 66052.045
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7000 289.33716 1037.9657 1871.9636 47.662734 66782.578
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7500 297.3092 1032.356 1889.3329 -24.049617 66129.95
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8000 298.27827 1044.118 1903.8882 -26.61809 66720.381
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8500 299.52706 1026.7068 1890.0766 -128.14995 67695.559
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9000 304.67694 1018.2095 1896.4236 -61.360724 65942.4
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9500 293.81117 1019.2221 1866.1162 -47.726496 66843.848
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10000 309.9256 1043.5321 1936.875 -103.81403 66222.21
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Loop time of 42.5056 on 1 procs for 10000 steps with 968 atoms
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Performance: 20.327 ns/day, 1.181 hours/ns, 235.263 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 | 40.972 | 40.972 | 40.972 | 0.0 | 96.39
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Neigh | 0.18576 | 0.18576 | 0.18576 | 0.0 | 0.44
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Comm | 0.71338 | 0.71338 | 0.71338 | 0.0 | 1.68
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Output | 0.00050306 | 0.00050306 | 0.00050306 | 0.0 | 0.00
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Modify | 0.52926 | 0.52926 | 0.52926 | 0.0 | 1.25
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Other | | 0.1042 | | | 0.25
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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: 9215 ave 9215 max 9215 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Neighs: 411837 ave 411837 max 411837 min
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Histogram: 1 0 0 0 0 0 0 0 0 0
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Total # of neighbors = 411837
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Ave neighs/atom = 425.451
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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: 0:00:42
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