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 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 (../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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500 314.54728 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 40.482557 66607.667
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3000 301.06631 1022.0381 1889.8447 47.582403 66341.947
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3500 297.98353 989.81011 1848.7308 -204.69823 67462.076
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4000 299.03465 1034.6603 1896.6108 89.196235 66457.338
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4500 306.04532 985.37017 1867.5285 -51.094929 67519.735
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5000 304.72903 1014.9543 1893.3184 -127.04402 67238.517
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5500 292.52622 1025.6599 1868.8502 -19.753932 66716.551
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6000 296.82719 1031.5184 1887.1059 -1.2609328 66368.611
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6500 298.63312 1018.4299 1879.2229 -24.75835 66524.898
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7000 303.25389 1005.9283 1880.0404 -96.273504 67349.674
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7500 292.45089 1068.2863 1911.2595 103.23295 65778.08
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8000 301.22765 1040.6294 1908.9011 -0.83635353 66831.038
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8500 300.19765 1047.5856 1912.8883 -31.582343 66316.305
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9000 295.1108 1023.8234 1874.4635 -88.165532 67192.344
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9500 302.1087 1003.6348 1874.4459 -18.707065 66369.361
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10000 296.3083 1004.126 1858.2178 -28.293045 66862.576
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Loop time of 28.8053 on 4 procs for 10000 steps with 968 atoms
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Performance: 29.994 ns/day, 0.800 hours/ns, 347.159 timesteps/s
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95.2% 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 | 19.929 | 21.765 | 23.391 | 27.8 | 75.56
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Neigh | 0.067397 | 0.071231 | 0.077313 | 1.5 | 0.25
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Comm | 3.9226 | 5.5183 | 7.3214 | 53.7 | 19.16
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Output | 0.00069928 | 0.0016099 | 0.0043275 | 3.9 | 0.01
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Modify | 1.0874 | 1.1376 | 1.1888 | 4.2 | 3.95
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Other | | 0.3112 | | | 1.08
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Nlocal: 242 ave 244 max 239 min
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Histogram: 1 0 0 0 0 0 1 0 1 1
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Nghost: 5718.5 ave 5736 max 5702 min
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Histogram: 1 0 0 0 1 1 0 0 0 1
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Neighs: 100703 ave 108064 max 93454 min
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Histogram: 1 0 0 1 0 0 1 0 0 1
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Total # of neighbors = 402813
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Ave neighs/atom = 416.129
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Neighbor list builds = 14
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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: 0:00:28
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