304 lines
14 KiB
Groff
304 lines
14 KiB
Groff
LAMMPS (27 Jun 2024)
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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# demo for atom style template simulating a cyclohexane methane mixture
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# part 3: continuing from restart file
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# run the first part and write out restart
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include in.molecular-mix
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# demo for atom style template simulating a cyclohexane methane mixture
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units real
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boundary p p p
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molecule cychex cyclohexane.mol
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Read molecule template cychex:
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LAMMPS molecule file. Cyclohexane(UA)
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1 molecules
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0 fragments
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6 atoms with max type 1
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6 bonds with max type 1
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6 angles with max type 1
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6 dihedrals with max type 1
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0 impropers with max type 0
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atom_style molecular
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pair_style lj/cut 12.0
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pair_modify mix geometric tail yes
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bond_style harmonic
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angle_style harmonic
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dihedral_style harmonic
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lattice sc 6.0
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Lattice spacing in x,y,z = 6 6 6
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variable boxlen index 4.0
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region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
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region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
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region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
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region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
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region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
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region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
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region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
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create_box 2 box bond/types 1 angle/types 1 dihedral/types 1 extra/special/per/atom 6 extra/bond/per/atom 2 extra/angle/per/atom 2 extra/dihedral/per/atom 2
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Created orthogonal box = (-24 -24 -24) to (24 24 24)
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1 by 2 by 2 MPI processor grid
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create_atoms 0 box mol cychex 734594
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Created 3072 atoms
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using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
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create_atoms CPU = 0.002 seconds
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create_atoms 2 random 800 495437 box
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Created 800 atoms
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using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
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create_atoms CPU = 0.000 seconds
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mass 1 14.027
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mass 2 16.043
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pair_coeff 1 1 0.1180 3.905
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pair_coeff 2 2 0.2940 3.730
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bond_coeff 1 260.00 1.5260
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angle_coeff 1 63.0 112.40
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dihedral_coeff 1 2.0 1 3
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thermo 100
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minimize 0.001 0.001 500 1000
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Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
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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: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 7 7 7
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 9.623 | 9.719 | 10.01 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 0 7.5430044e+16 341.92144 7.5430044e+16 1.8707026e+17
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100 0 -3410.6986 572.28283 -2838.4158 14603.831
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200 0 -6109.2306 483.67771 -5625.5529 5069.1821
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204 0 -6137.0238 483.1464 -5653.8774 4952.4083
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Loop time of 0.719327 on 4 procs for 204 steps with 3872 atoms
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99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
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Minimization stats:
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Stopping criterion = energy tolerance
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Energy initial, next-to-last, final =
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7.54300441078755e+16 -5648.75822666276 -5653.87742467986
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Force two-norm initial, final = 8.7430661e+18 74.636836
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Force max component initial, final = 4.1468626e+18 8.680078
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Final line search alpha, max atom move = 0.0032186724 0.027938327
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Iterations, force evaluations = 204 328
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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 | 0.60273 | 0.60882 | 0.61181 | 0.5 | 84.64
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Bond | 0.018965 | 0.019154 | 0.019363 | 0.1 | 2.66
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Neigh | 0.054004 | 0.054008 | 0.054012 | 0.0 | 7.51
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Comm | 0.022945 | 0.026108 | 0.032071 | 2.2 | 3.63
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Output | 3.4085e-05 | 3.6968e-05 | 4.5055e-05 | 0.0 | 0.01
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Modify | 0 | 0 | 0 | 0.0 | 0.00
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Other | | 0.0112 | | | 1.56
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Nlocal: 968 ave 980 max 954 min
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Histogram: 1 0 1 0 0 0 0 0 1 1
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Nghost: 6630 ave 6644 max 6616 min
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Histogram: 1 0 1 0 0 0 0 1 0 1
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Neighs: 193550 ave 195957 max 191376 min
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Histogram: 2 0 0 0 0 0 0 0 1 1
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Total # of neighbors = 774200
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Ave neighs/atom = 199.94835
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Ave special neighs/atom = 3.9669421
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Neighbor list builds = 14
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Dangerous builds = 0
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reset_timestep 0
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velocity all create 100.0 6234235
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fix 1 all nvt temp 100.0 300.0 1.0
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# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
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run 2500
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Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
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Per MPI rank memory allocation (min/avg/max) = 8.498 | 8.785 | 8.881 Mbytes
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Step Temp E_pair E_mol TotEng Press
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0 100 -6137.0238 483.1464 -4500.0059 5429.3515
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100 107.18608 -5623.5468 925.13787 -3461.6193 5640.5922
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200 119.37771 -5671.054 1050.9081 -3242.6804 7494.8576
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300 127.21216 -5646.3171 1053.2825 -3125.1696 5661.5841
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400 133.87894 -5674.4359 1139.3079 -2990.337 7202.7
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500 138.76354 -5679.3297 1234.4508 -2843.7258 6745.1519
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600 150.51628 -5665.2143 1210.3078 -2718.142 6301.1312
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700 152.13291 -5680.6166 979.71444 -2945.4837 8424.0062
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800 161.60449 -5579.521 1209.1388 -2505.674 5226.3319
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900 177.80597 -5626.7406 1125.8767 -2449.2113 9035.9218
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1000 181.98782 -5509.1736 924.24027 -2485.0276 5775.8317
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1100 189.93412 -5534.8176 1169.5911 -2173.6307 8072.3434
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1200 194.04459 -5508.0919 1169.0571 -2100.0095 7766.2625
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1300 203.40621 -5400.0439 1229.5897 -1823.4077 6533.8169
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1400 211.36099 -5362.2808 1318.5794 -1604.867 9789.8496
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1500 221.24251 -5263.1861 1410.6972 -1299.6344 6407.5052
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1600 234.83277 -5316.3854 1299.4287 -1307.2882 10199.28
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1700 233.61193 -5187.0022 1246.0158 -1245.4048 7482.5096
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1800 247.00713 -5193.2051 1451.1363 -891.92372 9836.6864
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1900 250.10386 -5165.7314 1259.876 -1019.978 8648.7513
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2000 257.7022 -5083.7142 1486.9813 -623.18058 9076.3674
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2100 273.9293 -5061.7945 1463.3978 -437.60445 10039.49
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2200 276.40166 -4948.9281 1538.5962 -221.01165 9013.3961
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2300 287.28669 -5039.6841 1535.7768 -188.98782 10739.853
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2400 290.35344 -4947.2095 1615.8983 18.994602 8326.4501
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2500 305.29351 -4925.5822 1669.8823 266.99522 11465.135
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Loop time of 4.32954 on 4 procs for 2500 steps with 3872 atoms
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Performance: 49.890 ns/day, 0.481 hours/ns, 577.429 timesteps/s, 2.236 Matom-step/s
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99.5% 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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Pair | 3.8113 | 3.8529 | 3.8893 | 1.7 | 88.99
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Bond | 0.13153 | 0.13433 | 0.13718 | 0.7 | 3.10
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Neigh | 0.13036 | 0.13039 | 0.13042 | 0.0 | 3.01
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Comm | 0.13688 | 0.1751 | 0.21857 | 8.4 | 4.04
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Output | 0.00032606 | 0.00035873 | 0.00045009 | 0.0 | 0.01
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Modify | 0.027754 | 0.028116 | 0.028735 | 0.2 | 0.65
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Other | | 0.008382 | | | 0.19
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Nlocal: 968 ave 986 max 944 min
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Histogram: 1 0 0 1 0 0 0 0 0 2
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Nghost: 6379.75 ave 6407 max 6352 min
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Histogram: 1 0 1 0 0 0 0 1 0 1
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Neighs: 192584 ave 196718 max 188693 min
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Histogram: 1 1 0 0 0 0 0 1 0 1
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Total # of neighbors = 770338
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Ave neighs/atom = 198.95093
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Ave special neighs/atom = 3.9669421
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Neighbor list builds = 34
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Dangerous builds = 0
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#write_data molecular-mix.data
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#write_restart molecular-mix.restart
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write_restart molecular-mix.restart
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System init for write_restart ...
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Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
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# now restart
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clear
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OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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using 1 OpenMP thread(s) per MPI task
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molecule cychex cyclohexane.mol
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Read molecule template cychex:
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LAMMPS molecule file. Cyclohexane(UA)
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1 molecules
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0 fragments
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6 atoms with max type 1
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6 bonds with max type 1
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6 angles with max type 1
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6 dihedrals with max type 1
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0 impropers with max type 0
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read_restart molecular-mix.restart
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Reading restart file ...
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restart file = 27 Jun 2024, LAMMPS = 27 Jun 2024
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restoring atom style molecular from restart
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orthogonal box = (-24 -24 -24) to (24 24 24)
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1 by 2 by 2 MPI processor grid
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restoring pair style lj/cut from restart
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restoring bond style harmonic from restart
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restoring angle style harmonic from restart
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restoring dihedral style harmonic from restart
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3872 atoms
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3072 bonds
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3072 angles
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3072 dihedrals
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Finding 1-2 1-3 1-4 neighbors ...
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special bond factors lj: 0 0 0
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special bond factors coul: 0 0 0
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2 = max # of 1-2 neighbors
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2 = max # of 1-3 neighbors
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4 = max # of 1-4 neighbors
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7 = max # of special neighbors
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special bonds CPU = 0.000 seconds
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read_restart CPU = 0.004 seconds
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thermo 100
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fix 1 all nvt temp 300.0 300.0 1.0
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Resetting global fix info from restart file:
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fix style: nvt, fix ID: 1
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# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
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run 2000
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Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
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All restart file global fix info was re-assigned
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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: 2000, page size: 100000
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master list distance cutoff = 14
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ghost atom cutoff = 14
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binsize = 7, bins = 7 7 7
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1 neighbor lists, perpetual/occasional/extra = 1 0 0
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(1) pair lj/cut, perpetual
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attributes: half, newton on
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pair build: half/bin/newton
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stencil: half/bin/3d
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bin: standard
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Per MPI rank memory allocation (min/avg/max) = 8.475 | 8.571 | 8.857 Mbytes
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Step Temp E_pair E_mol TotEng Press
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2500 305.29351 -4925.5822 1669.8823 266.99522 11465.135
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2600 296.63161 -4937.8377 1616.2295 101.13964 8654.8533
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2700 303.79396 -4951.8442 1732.7298 286.27771 11140.127
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2800 297.39677 -4879.1242 1642.1355 194.58806 8993.2494
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2900 299.13542 -4888.1435 1660.1105 223.60558 10716.3
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3000 298.07888 -4928.2353 1650.6616 161.87369 10088.459
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3100 304.09536 -4901.4853 1614.3116 221.69625 9505.2057
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3200 301.51357 -4930.5129 1628.4386 177.00496 11411.933
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3300 297.45744 -4923.6217 1700.537 209.19205 8189.571
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3400 298.52831 -5012.7313 1736.6929 168.59495 11673.119
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3500 295.66767 -4947.4296 1700.0072 164.20283 8222.3067
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3600 296.7267 -5112.3707 1727.4319 38.906285 10608.481
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3700 302.92855 -4994.4012 1789.7274 290.73255 8829.4479
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3800 296.77191 -5034.2589 1657.2635 47.371248 9968.3521
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3900 299.86962 -4972.7385 1744.2808 231.65266 10076.37
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4000 304.89527 -5011.2464 1664.6779 171.53137 8926.0386
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4100 296.81738 -5013.2169 1727.5801 139.25455 10898.733
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4200 300.67532 -4988.3547 1782.1574 263.20975 8164.1158
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4300 297.74901 -5023.3433 1784.7361 197.03396 11344.862
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4400 302.0571 -5033.3547 1723.2662 175.26243 8016.975
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4500 305.31958 -5062.5597 1767.0048 227.44095 10827.294
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Loop time of 3.58588 on 4 procs for 2000 steps with 3872 atoms
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Performance: 48.189 ns/day, 0.498 hours/ns, 557.743 timesteps/s, 2.160 Matom-step/s
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99.4% 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 | 3.0873 | 3.1383 | 3.2136 | 2.7 | 87.52
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Bond | 0.10381 | 0.10769 | 0.11168 | 0.9 | 3.00
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Neigh | 0.13651 | 0.13652 | 0.13654 | 0.0 | 3.81
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Comm | 0.094882 | 0.1741 | 0.22894 | 12.3 | 4.86
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Output | 0.00024683 | 0.00028387 | 0.00038642 | 0.0 | 0.01
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Modify | 0.021974 | 0.022331 | 0.022623 | 0.2 | 0.62
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Other | | 0.006685 | | | 0.19
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Nlocal: 968 ave 984 max 948 min
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Histogram: 1 0 0 1 0 0 0 0 1 1
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Nghost: 6349.5 ave 6370 max 6330 min
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Histogram: 1 0 1 0 0 0 0 1 0 1
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Neighs: 192457 ave 196654 max 187154 min
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Histogram: 1 0 0 0 1 0 0 0 1 1
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Total # of neighbors = 769828
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Ave neighs/atom = 198.81921
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Ave special neighs/atom = 3.9669421
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Neighbor list builds = 35
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Dangerous builds = 0
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# clean up
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shell rm molecular-mix.restart
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Total wall time: 0:00:08
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