MCP LAMMPS Server

LAMMPS (29 Aug 2024 - Update 3) OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/src/comm.cpp:99) using 1 OpenMP thread(s) per MPI task # LAMMPS input script for water simulation with 10 TIP3P water molecules # NVT ensemble at 300K # Initialize simulation units real boundary p p p atom_style full bond_style harmonic angle_style harmonic dihedral_style none improper_style none pair_style lj/cut/coul/long 10.0 pair_modify mix arithmetic kspace_style pppm 1.0e-4 # Read data file read_data water_10.data Reading data file ... orthogonal box = (-7.5 -7.5 -7.5) to (7.5 7.5 7.5) 1 by 1 by 1 MPI processor grid reading atoms ... 30 atoms scanning bonds ... 2 = max bonds/atom scanning angles ... 1 = max angles/atom orthogonal box = (-7.5 -7.5 -7.5) to (7.5 7.5 7.5) 1 by 1 by 1 MPI processor grid reading bonds ... 20 bonds reading angles ... 10 angles Finding 1-2 1-3 1-4 neighbors ... special bond factors lj: 0 0 0 special bond factors coul: 0 0 0 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 = 0.000 seconds read_data CPU = 0.005 seconds # Set up groups group water type 1 2 3 30 atoms in group water group O type 1 10 atoms in group O group H type 2 3 20 atoms in group H # Set up pair coefficients for TIP3P water pair_coeff 1 1 0.1521 3.188 pair_coeff 2 2 0.0000 0.000 pair_coeff 3 3 0.0000 0.000 pair_coeff 1 2 0.0000 0.000 pair_coeff 1 3 0.0000 0.000 pair_coeff 2 3 0.0000 0.000 # Set up bond coefficients for TIP3P water bond_coeff 1 450.0 0.9572 angle_coeff 1 55.0 104.52 # Set up charges for TIP3P water set type 1 charge -0.830 Setting atom values ... 10 settings made for charge set type 2 charge 0.415 Setting atom values ... 10 settings made for charge set type 3 charge 0.415 Setting atom values ... 10 settings made for charge # Set up neighbor list neighbor 2.0 bin neigh_modify every 1 delay 0 check yes # Set up output thermo 100 thermo_style custom step temp pe ke etotal press vol density dump myDump all custom 500 water_10.lammpstrj id type x y z vx vy vz dump_modify myDump sort id # Minimization minimize 1.0e-4 1.0e-6 1000 10000 PPPM initialization ... using 12-bit tables for long-range coulomb (src/src/kspace.cpp:342) G vector (1/distance) = 0.26644093 grid = 8 8 8 stencil order = 5 estimated absolute RMS force accuracy = 0.0079656343 estimated relative force accuracy = 2.3988271e-05 using double precision KISS FFT 3d grid and FFT values/proc = 3375 512 Generated 0 of 3 mixed pair_coeff terms from arithmetic mixing rule Neighbor list info ... update: every = 1 steps, delay = 0 steps, check = yes max neighbors/atom: 2000, page size: 100000 master list distance cutoff = 12 ghost atom cutoff = 12 binsize = 6, bins = 3 3 3 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 bin: standard Per MPI rank memory allocation (min/avg/max) = 8.293 | 8.293 | 8.293 Mbytes Step Temp PotEng KinEng TotEng Press Volume Density 0 0 53.569206 0 53.569206 6635.0224 3375 0.088637846 100 0 -65.990913 0 -65.990913 150.82928 3375 0.088637846 200 0 -76.40757 0 -76.40757 -1.8016162 3375 0.088637846 220 0 -77.217662 0 -77.217662 -4.5055382 3375 0.088637846 Loop time of 0.0821544 on 1 procs for 220 steps with 30 atoms 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads Minimization stats: Stopping criterion = energy tolerance Energy initial, next-to-last, final = 53.5692064001527 -77.2137983139505 -77.2176621147712 Force two-norm initial, final = 156.04208 3.0114825 Force max component initial, final = 63.95743 0.85493802 Final line search alpha, max atom move = 0.13871089 0.11858921 Iterations, force evaluations = 220 430 MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.011574 | 0.011574 | 0.011574 | 0.0 | 14.09 Bond | 0.00074193 | 0.00074193 | 0.00074193 | 0.0 | 0.90 Kspace | 0.06654 | 0.06654 | 0.06654 | 0.0 | 80.99 Neigh | 0.00037423 | 0.00037423 | 0.00037423 | 0.0 | 0.46 Comm | 0.0019701 | 0.0019701 | 0.0019701 | 0.0 | 2.40 Output | 4.1346e-05 | 4.1346e-05 | 4.1346e-05 | 0.0 | 0.05 Modify | 0 | 0 | 0 | 0.0 | 0.00 Other | | 0.0009126 | | | 1.11 Nlocal: 30 ave 30 max 30 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 744 ave 744 max 744 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 693 ave 693 max 693 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 693 Ave neighs/atom = 23.1 Ave special neighs/atom = 2 Neighbor list builds = 4 Dangerous builds = 0 undump myDump reset_timestep 0 # Equilibration at 300K (NVT) timestep 1.0 fix nvt all nvt temp 300.0 300.0 100.0 run 1000 PPPM initialization ... using 12-bit tables for long-range coulomb (src/src/kspace.cpp:342) G vector (1/distance) = 0.26644093 grid = 8 8 8 stencil order = 5 estimated absolute RMS force accuracy = 0.0079656343 estimated relative force accuracy = 2.3988271e-05 using double precision KISS FFT 3d grid and FFT values/proc = 3375 512 Generated 0 of 3 mixed pair_coeff terms from arithmetic mixing rule Per MPI rank memory allocation (min/avg/max) = 7.168 | 7.168 | 7.168 Mbytes Step Temp PotEng KinEng TotEng Press Volume Density 0 0 -77.217662 0 -77.217662 -4.5055382 3375 0.088637846 100 5.6033798 -77.560141 0.48437571 -77.075765 -26.18836 3375 0.088637846 200 23.641543 -78.15248 2.0436575 -76.108823 -23.302597 3375 0.088637846 300 42.809101 -77.110665 3.7005681 -73.410097 -68.837219 3375 0.088637846 400 67.50521 -74.940251 5.835386 -69.104865 -2.7742029 3375 0.088637846 500 157.33479 -74.165979 13.600568 -60.56541 93.895523 3375 0.088637846 600 220.76445 -66.245172 19.08365 -47.161522 265.24764 3375 0.088637846 700 368.15772 -63.520075 31.824839 -31.695236 147.42106 3375 0.088637846 800 400.25368 -60.871876 34.599325 -26.272551 22.636507 3375 0.088637846 900 304.21146 -60.374867 26.2971 -34.077767 -275.8583 3375 0.088637846 1000 224.97432 -59.328741 19.447566 -39.881175 -116.16996 3375 0.088637846 Loop time of 0.17908 on 1 procs for 1000 steps with 30 atoms Performance: 482.466 ns/day, 0.050 hours/ns, 5584.093 timesteps/s, 167.523 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.016482 | 0.016482 | 0.016482 | 0.0 | 9.20 Bond | 0.0014049 | 0.0014049 | 0.0014049 | 0.0 | 0.78 Kspace | 0.15277 | 0.15277 | 0.15277 | 0.0 | 85.31 Neigh | 0.0015071 | 0.0015071 | 0.0015071 | 0.0 | 0.84 Comm | 0.0045374 | 0.0045374 | 0.0045374 | 0.0 | 2.53 Output | 0.00015549 | 0.00015549 | 0.00015549 | 0.0 | 0.09 Modify | 0.0014619 | 0.0014619 | 0.0014619 | 0.0 | 0.82 Other | | 0.0007655 | | | 0.43 Nlocal: 30 ave 30 max 30 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 642 ave 642 max 642 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 790 ave 790 max 790 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 790 Ave neighs/atom = 26.333333 Ave special neighs/atom = 2 Neighbor list builds = 18 Dangerous builds = 0 unfix nvt # Production run at 300K (NVT) fix nvt_prod all nvt temp 300.0 300.0 100.0 run 5000 PPPM initialization ... using 12-bit tables for long-range coulomb (src/src/kspace.cpp:342) G vector (1/distance) = 0.26644093 grid = 8 8 8 stencil order = 5 estimated absolute RMS force accuracy = 0.0079656343 estimated relative force accuracy = 2.3988271e-05 using double precision KISS FFT 3d grid and FFT values/proc = 3375 512 Generated 0 of 3 mixed pair_coeff terms from arithmetic mixing rule Per MPI rank memory allocation (min/avg/max) = 7.168 | 7.168 | 7.168 Mbytes Step Temp PotEng KinEng TotEng Press Volume Density 1000 224.97432 -59.328741 19.447566 -39.881175 -116.16996 3375 0.088637846 1100 247.20358 -56.065042 21.36914 -34.695901 -97.419681 3375 0.088637846 1200 302.33211 -55.061704 26.134643 -28.92706 184.05055 3375 0.088637846 1300 293.69242 -54.094554 25.387799 -28.706755 -72.041169 3375 0.088637846 1400 271.74209 -48.65904 23.490335 -25.168705 -39.569516 3375 0.088637846 1500 321.16373 -45.01169 27.762514 -17.249176 279.39342 3375 0.088637846 1600 287.49815 -45.145269 24.852344 -20.292925 71.510438 3375 0.088637846 1700 282.65072 -46.177249 24.433315 -21.743934 -79.196836 3375 0.088637846 1800 325.14236 -48.537477 28.106441 -20.431036 107.51812 3375 0.088637846 1900 354.60584 -51.872445 30.653367 -21.219078 -88.340845 3375 0.088637846 2000 193.86391 -44.271481 16.758274 -27.513207 -197.12269 3375 0.088637846 2100 230.20741 -48.948945 19.899932 -29.049013 -614.71564 3375 0.088637846 2200 353.48096 -49.543694 30.556128 -18.987566 849.79333 3375 0.088637846 2300 349.86226 -51.308677 30.243315 -21.065362 308.32314 3375 0.088637846 2400 232.05596 -46.971928 20.059727 -26.912201 -242.20131 3375 0.088637846 2500 246.07757 -44.443956 21.271804 -23.172152 -200.78993 3375 0.088637846 2600 330.36107 -45.647626 28.557564 -17.090062 -233.37493 3375 0.088637846 2700 328.86902 -45.805745 28.428586 -17.377159 -160.07417 3375 0.088637846 2800 267.25478 -44.258087 23.102436 -21.155651 -471.12129 3375 0.088637846 2900 372.76425 -53.032416 32.223043 -20.809373 262.58197 3375 0.088637846 3000 297.4828 -55.561042 25.715452 -29.84559 -60.651219 3375 0.088637846 3100 207.39144 -50.491233 17.92764 -32.563593 -226.92476 3375 0.088637846 3200 241.06483 -46.550407 20.838485 -25.711922 565.9051 3375 0.088637846 3300 271.47936 -46.253523 23.467624 -22.785898 232.80436 3375 0.088637846 3400 279.59281 -46.211927 24.168979 -22.042948 -550.89949 3375 0.088637846 3500 351.91113 -47.619272 30.420427 -17.198845 -202.10011 3375 0.088637846 3600 414.7775 -46.312845 35.854815 -10.458029 -101.81345 3375 0.088637846 3700 335.30928 -46.838419 28.985305 -17.853114 -197.4345 3375 0.088637846 3800 200.71727 -42.787017 17.350702 -25.436315 57.402279 3375 0.088637846 3900 322.93571 -50.98226 27.915691 -23.066569 -100.35569 3375 0.088637846 4000 329.62866 -52.268814 28.494252 -23.774562 597.74635 3375 0.088637846 4100 221.03126 -49.80205 19.106714 -30.695336 -362.13115 3375 0.088637846 4200 237.39981 -48.137429 20.521669 -27.61576 423.53702 3375 0.088637846 4300 373.12841 -48.786682 32.254523 -16.53216 7.166109 3375 0.088637846 4400 306.5307 -49.303687 26.497584 -22.806104 -304.28698 3375 0.088637846 4500 272.33074 -48.71261 23.54122 -25.171391 311.004 3375 0.088637846 4600 275.28899 -47.859935 23.796942 -24.062993 126.38157 3375 0.088637846 4700 214.21236 -44.903536 18.517265 -26.386272 -0.35053211 3375 0.088637846 4800 240.70515 -42.762528 20.807393 -21.955135 93.805694 3375 0.088637846 4900 329.71959 -42.584948 28.502113 -14.082835 398.48823 3375 0.088637846 5000 306.89463 -42.577878 26.529043 -16.048835 180.77413 3375 0.088637846 5100 216.40995 -39.137724 18.707232 -20.430492 -0.22183737 3375 0.088637846 5200 271.43014 -37.844226 23.463369 -14.380857 -102.55716 3375 0.088637846 5300 407.53819 -42.449241 35.229024 -7.2202164 -124.80902 3375 0.088637846 5400 343.77603 -44.526614 29.7172 -14.809414 -208.5972 3375 0.088637846 5500 303.97855 -45.824795 26.276968 -19.547827 -261.17033 3375 0.088637846 5600 290.39278 -45.056884 25.102566 -19.954318 427.53862 3375 0.088637846 5700 260.2855 -45.487543 22.499987 -22.987556 241.34737 3375 0.088637846 5800 235.49714 -48.098192 20.357195 -27.740997 27.056555 3375 0.088637846 5900 284.31902 -52.773732 24.577529 -28.196203 193.72163 3375 0.088637846 6000 333.59994 -49.545374 28.837544 -20.707831 -1.708147 3375 0.088637846 Loop time of 0.894012 on 1 procs for 5000 steps with 30 atoms Performance: 483.215 ns/day, 0.050 hours/ns, 5592.769 timesteps/s, 167.783 katom-step/s 100.0% CPU use with 1 MPI tasks x 1 OpenMP threads MPI task timing breakdown: Section | min time | avg time | max time |%varavg| %total --------------------------------------------------------------- Pair | 0.089248 | 0.089248 | 0.089248 | 0.0 | 9.98 Bond | 0.0071031 | 0.0071031 | 0.0071031 | 0.0 | 0.79 Kspace | 0.75412 | 0.75412 | 0.75412 | 0.0 | 84.35 Neigh | 0.013143 | 0.013143 | 0.013143 | 0.0 | 1.47 Comm | 0.017888 | 0.017888 | 0.017888 | 0.0 | 2.00 Output | 0.0012794 | 0.0012794 | 0.0012794 | 0.0 | 0.14 Modify | 0.0074421 | 0.0074421 | 0.0074421 | 0.0 | 0.83 Other | | 0.003784 | | | 0.42 Nlocal: 30 ave 30 max 30 min Histogram: 1 0 0 0 0 0 0 0 0 0 Nghost: 330 ave 330 max 330 min Histogram: 1 0 0 0 0 0 0 0 0 0 Neighs: 829 ave 829 max 829 min Histogram: 1 0 0 0 0 0 0 0 0 0 Total # of neighbors = 829 Ave neighs/atom = 27.633333 Ave special neighs/atom = 2 Neighbor list builds = 176 Dangerous builds = 0 unfix nvt_prod # Final output print "Simulation completed successfully" Simulation completed successfully Total wall time: 0:00:01