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cleanly demo/test using restart files without leaving binary files behind

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This commit is contained in:
Axel Kohlmeyer
2024-08-12 21:19:46 -04:00
parent a1adf5d2d1
commit 8a77949db2
10 changed files with 1214 additions and 416 deletions
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9
examples/template/in.mol-restart-mix
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# demo for atom style template simulating a cyclohexane methane mixture # demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file # part 3: continuing from restart file
# run the first part and write out restart
include in.molecular-mix
write_restart molecular-mix.restart
# now restart
clear
molecule cychex cyclohexane.mol molecule cychex cyclohexane.mol
read_restart molecular-mix.restart read_restart molecular-mix.restart
@ -9,3 +15,6 @@ thermo 100
fix 1 all nvt temp 300.0 300.0 1.0 fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu # dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000 run 2000
# clean up
shell rm molecular-mix.restart

9
examples/template/in.tmpl-restart-mix
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@ -1,6 +1,12 @@
# demo for atom style template simulating a cyclohexane methane mixture # demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file # part 3: continuing from restart file
# run the first part and write out restart
include in.template-mix
write_restart template-mix.restart
# now restart
clear
molecule cychex cyclohexane.mol molecule cychex cyclohexane.mol
read_restart template-mix.restart read_restart template-mix.restart
@ -9,3 +15,6 @@ thermo 100
fix 1 all nvt temp 300.0 300.0 1.0 fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu # dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000 run 2000
# clean up
shell rm template-mix.restart

302
examples/template/log.12Aug24.mol-restart-mix.g++.1 Normal file
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LAMMPS (27 Jun 2024)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file
# run the first part and write out restart
include in.molecular-mix
# demo for atom style template simulating a cyclohexane methane mixture
units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
LAMMPS molecule file. Cyclohexane(UA)
1 molecules
0 fragments
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
atom_style molecular
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
lattice sc 6.0
Lattice spacing in x,y,z = 6 6 6
variable boxlen index 4.0
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
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
Created orthogonal box = (-24 -24 -24) to (24 24 24)
1 by 1 by 1 MPI processor grid
create_atoms 0 box mol cychex 734594
Created 3072 atoms
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
create_atoms CPU = 0.004 seconds
create_atoms 2 random 800 495437 box
Created 800 atoms
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
create_atoms CPU = 0.000 seconds
mass 1 14.027
mass 2 16.043
pair_coeff 1 1 0.1180 3.905
pair_coeff 2 2 0.2940 3.730
bond_coeff 1 260.00 1.5260
angle_coeff 1 63.0 112.40
dihedral_coeff 1 2.0 1 3
thermo 100
minimize 0.001 0.001 500 1000
Generated 1 of 1 mixed pair_coeff terms from geometric 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 = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 12.28 | 12.28 | 12.28 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 4.3897851e+13 341.92144 4.3897851e+13 1.0886888e+14
100 0 -4351.8383 516.49891 -3835.3394 11635.037
190 0 -6191.8196 457.61266 -5734.2069 4365.4279
Loop time of 2.5667 on 1 procs for 190 steps with 3872 atoms
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
43897850768892.8 -5729.17409504969 -5734.20694761353
Force two-norm initial, final = 1.1080994e+15 72.745546
Force max component initial, final = 4.6607099e+14 17.390179
Final line search alpha, max atom move = 0.0041638487 0.072410076
Iterations, force evaluations = 190 297
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.2379 | 2.2379 | 2.2379 | 0.0 | 87.19
Bond | 0.070658 | 0.070658 | 0.070658 | 0.0 | 2.75
Neigh | 0.21093 | 0.21093 | 0.21093 | 0.0 | 8.22
Comm | 0.012111 | 0.012111 | 0.012111 | 0.0 | 0.47
Output | 3.0458e-05 | 3.0458e-05 | 3.0458e-05 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.03504 | | | 1.37
Nlocal: 3872 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 12122 ave 12122 max 12122 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 774375 ave 774375 max 774375 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 774375
Ave neighs/atom = 199.99354
Ave special neighs/atom = 3.9669421
Neighbor list builds = 14
Dangerous builds = 0
reset_timestep 0
velocity all create 100.0 6234235
fix 1 all nvt temp 100.0 300.0 1.0
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
run 2500
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 11.16 | 11.16 | 11.16 Mbytes
Step Temp E_pair E_mol TotEng Press
0 100 -6191.8196 457.61266 -4580.3354 4842.371
100 106.81292 -5670.2785 921.2043 -3516.5903 5959.4321
200 119.24063 -5701.0127 1040.0231 -3285.1059 6755.2619
300 127.28216 -5706.3887 1026.2838 -3211.4322 6076.6123
400 133.79038 -5734.0279 1113.6088 -3076.65 6583.9393
500 138.77685 -5756.2532 1192.1349 -2962.8117 6436.3524
600 149.39857 -5730.563 1206.6372 -2800.0582 6357.5889
700 155.5825 -5671.0161 929.50406 -2946.2899 7697.5164
800 161.24677 -5628.3833 1186.5533 -2581.2493 5840.6503
900 172.81747 -5638.6453 1148.683 -2495.8707 8169.3352
1000 182.2048 -5579.5767 909.90783 -2567.2594 6270.7354
1100 188.95766 -5548.999 1183.6644 -2185.0058 7711.9244
1200 195.22147 -5511.6798 1111.3361 -2147.7386 7656.4439
1300 205.15867 -5431.6966 1195.8143 -1868.6148 7021.8716
1400 211.44641 -5410.5687 1299.0501 -1671.6986 8903.0061
1500 223.70124 -5359.4567 1388.4189 -1389.8128 6919.2408
1600 231.75318 -5288.3343 1348.829 -1265.3712 9409.2728
1700 229.61746 -5259.4318 1194.5663 -1415.375 7387.4923
1800 245.62483 -5281.0755 1389.3362 -1057.5441 9421.7241
1900 250.69445 -5158.7006 1236.5167 -1029.4919 8649.4835
2000 259.50657 -5148.4153 1485.1392 -668.90355 9130.4701
2100 270.77108 -5092.6634 1418.7937 -549.51913 9666.5632
2200 272.30152 -5079.7585 1514.5708 -423.17779 8568.2546
2300 285.20945 -5085.6197 1492.5671 -302.10191 10281.574
2400 286.95799 -4979.8608 1544.6159 -124.11819 8797.7435
2500 296.10218 -4928.5152 1698.282 186.40572 10946.864
Loop time of 17.2353 on 1 procs for 2500 steps with 3872 atoms
Performance: 12.532 ns/day, 1.915 hours/ns, 145.052 timesteps/s, 561.639 katom-step/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 15.936 | 15.936 | 15.936 | 0.0 | 92.46
Bond | 0.5636 | 0.5636 | 0.5636 | 0.0 | 3.27
Neigh | 0.51213 | 0.51213 | 0.51213 | 0.0 | 2.97
Comm | 0.098127 | 0.098127 | 0.098127 | 0.0 | 0.57
Output | 0.00072478 | 0.00072478 | 0.00072478 | 0.0 | 0.00
Modify | 0.10177 | 0.10177 | 0.10177 | 0.0 | 0.59
Other | | 0.02248 | | | 0.13
Nlocal: 3872 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11821 ave 11821 max 11821 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 770416 ave 770416 max 770416 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 770416
Ave neighs/atom = 198.97107
Ave special neighs/atom = 3.9669421
Neighbor list builds = 34
Dangerous builds = 0
#write_data molecular-mix.data
#write_restart molecular-mix.restart
write_restart molecular-mix.restart
System init for write_restart ...
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
# now restart
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
molecule cychex cyclohexane.mol
Read molecule template cychex:
LAMMPS molecule file. Cyclohexane(UA)
1 molecules
0 fragments
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
read_restart molecular-mix.restart
Reading restart file ...
restart file = 27 Jun 2024, LAMMPS = 27 Jun 2024
restoring atom style molecular from restart
orthogonal box = (-24 -24 -24) to (24 24 24)
1 by 1 by 1 MPI processor grid
restoring pair style lj/cut from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style harmonic from restart
3872 atoms
3072 bonds
3072 angles
3072 dihedrals
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
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
7 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_restart CPU = 0.003 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
All restart file global fix info was re-assigned
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 11.12 | 11.12 | 11.12 Mbytes
Step Temp E_pair E_mol TotEng Press
2500 296.10218 -4928.5152 1698.282 186.40572 10946.864
2600 302.98473 -4910.6997 1585.9276 171.28257 9066.357
2700 300.75989 -4935.1005 1723.6514 258.9337 10755.67
2800 294.26086 -4904.3072 1594.9394 86.02469 9420.9997
2900 296.15059 -4961.5041 1594.1004 49.793724 10129.823
3000 296.65334 -4934.6622 1596.9704 85.306731 10112.636
3100 301.62361 -4975.5261 1671.8512 176.67422 9500.7576
3200 297.34385 -5017.986 1603.4388 16.419054 10451.2
3300 297.01108 -4882.1137 1651.6426 196.65525 9124.096
3400 298.13642 -4983.4532 1742.3589 199.01715 10808.599
3500 315.91146 -4952.209 1651.2231 344.22669 8677.2632
3600 295.12433 -4950.6158 1721.3273 176.06725 10904.222
3700 300.65909 -4967.4001 1770.4243 272.244 9230.4292
3800 302.15034 -4991.9549 1644.8366 139.30847 10154.524
3900 302.16277 -5017.0117 1672.2353 141.79397 9705.6697
4000 303.1458 -4946.2517 1679.8498 231.51137 9527.8793
4100 303.54737 -5003.8276 1639.7221 138.44129 10406.442
4200 291.62491 -5009.3438 1707.6 63.233087 8645.4116
4300 306.17115 -5084.7139 1727.9528 176.0607 10563.216
4400 302.65581 -5004.4302 1747.5309 235.36003 8717.1253
4500 296.42334 -5014.9791 1723.2084 128.57389 10492.246
Loop time of 13.288 on 1 procs for 2000 steps with 3872 atoms
Performance: 13.004 ns/day, 1.846 hours/ns, 150.512 timesteps/s, 582.781 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.191 | 12.191 | 12.191 | 0.0 | 91.74
Bond | 0.4224 | 0.4224 | 0.4224 | 0.0 | 3.18
Neigh | 0.50894 | 0.50894 | 0.50894 | 0.0 | 3.83
Comm | 0.07309 | 0.07309 | 0.07309 | 0.0 | 0.55
Output | 0.00057158 | 0.00057158 | 0.00057158 | 0.0 | 0.00
Modify | 0.077778 | 0.077778 | 0.077778 | 0.0 | 0.59
Other | | 0.01451 | | | 0.11
Nlocal: 3872 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11685 ave 11685 max 11685 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 770346 ave 770346 max 770346 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 770346
Ave neighs/atom = 198.953
Ave special neighs/atom = 3.9669421
Neighbor list builds = 34
Dangerous builds = 0
# clean up
shell rm molecular-mix.restart
Total wall time: 0:00:33

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examples/template/log.12Aug24.mol-restart-mix.g++.4 Normal file
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LAMMPS (27 Jun 2024)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file
# run the first part and write out restart
include in.molecular-mix
# demo for atom style template simulating a cyclohexane methane mixture
units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
LAMMPS molecule file. Cyclohexane(UA)
1 molecules
0 fragments
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
atom_style molecular
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
lattice sc 6.0
Lattice spacing in x,y,z = 6 6 6
variable boxlen index 4.0
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
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
Created orthogonal box = (-24 -24 -24) to (24 24 24)
1 by 2 by 2 MPI processor grid
create_atoms 0 box mol cychex 734594
Created 3072 atoms
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
create_atoms CPU = 0.002 seconds
create_atoms 2 random 800 495437 box
Created 800 atoms
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
create_atoms CPU = 0.000 seconds
mass 1 14.027
mass 2 16.043
pair_coeff 1 1 0.1180 3.905
pair_coeff 2 2 0.2940 3.730
bond_coeff 1 260.00 1.5260
angle_coeff 1 63.0 112.40
dihedral_coeff 1 2.0 1 3
thermo 100
minimize 0.001 0.001 500 1000
Generated 1 of 1 mixed pair_coeff terms from geometric 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 = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.623 | 9.719 | 10.01 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 7.5430044e+16 341.92144 7.5430044e+16 1.8707026e+17
100 0 -3410.6986 572.28283 -2838.4158 14603.831
200 0 -6109.2306 483.67771 -5625.5529 5069.1821
204 0 -6137.0238 483.1464 -5653.8774 4952.4083
Loop time of 0.719327 on 4 procs for 204 steps with 3872 atoms
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
7.54300441078755e+16 -5648.75822666276 -5653.87742467986
Force two-norm initial, final = 8.7430661e+18 74.636836
Force max component initial, final = 4.1468626e+18 8.680078
Final line search alpha, max atom move = 0.0032186724 0.027938327
Iterations, force evaluations = 204 328
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.60273 | 0.60882 | 0.61181 | 0.5 | 84.64
Bond | 0.018965 | 0.019154 | 0.019363 | 0.1 | 2.66
Neigh | 0.054004 | 0.054008 | 0.054012 | 0.0 | 7.51
Comm | 0.022945 | 0.026108 | 0.032071 | 2.2 | 3.63
Output | 3.4085e-05 | 3.6968e-05 | 4.5055e-05 | 0.0 | 0.01
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.0112 | | | 1.56
Nlocal: 968 ave 980 max 954 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 6630 ave 6644 max 6616 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 193550 ave 195957 max 191376 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 774200
Ave neighs/atom = 199.94835
Ave special neighs/atom = 3.9669421
Neighbor list builds = 14
Dangerous builds = 0
reset_timestep 0
velocity all create 100.0 6234235
fix 1 all nvt temp 100.0 300.0 1.0
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
run 2500
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 8.498 | 8.785 | 8.881 Mbytes
Step Temp E_pair E_mol TotEng Press
0 100 -6137.0238 483.1464 -4500.0059 5429.3515
100 107.18608 -5623.5468 925.13787 -3461.6193 5640.5922
200 119.37771 -5671.054 1050.9081 -3242.6804 7494.8576
300 127.21216 -5646.3171 1053.2825 -3125.1696 5661.5841
400 133.87894 -5674.4359 1139.3079 -2990.337 7202.7
500 138.76354 -5679.3297 1234.4508 -2843.7258 6745.1519
600 150.51628 -5665.2143 1210.3078 -2718.142 6301.1312
700 152.13291 -5680.6166 979.71444 -2945.4837 8424.0062
800 161.60449 -5579.521 1209.1388 -2505.674 5226.3319
900 177.80597 -5626.7406 1125.8767 -2449.2113 9035.9218
1000 181.98782 -5509.1736 924.24027 -2485.0276 5775.8317
1100 189.93412 -5534.8176 1169.5911 -2173.6307 8072.3434
1200 194.04459 -5508.0919 1169.0571 -2100.0095 7766.2625
1300 203.40621 -5400.0439 1229.5897 -1823.4077 6533.8169
1400 211.36099 -5362.2808 1318.5794 -1604.867 9789.8496
1500 221.24251 -5263.1861 1410.6972 -1299.6344 6407.5052
1600 234.83277 -5316.3854 1299.4287 -1307.2882 10199.28
1700 233.61193 -5187.0022 1246.0158 -1245.4048 7482.5096
1800 247.00713 -5193.2051 1451.1363 -891.92372 9836.6864
1900 250.10386 -5165.7314 1259.876 -1019.978 8648.7513
2000 257.7022 -5083.7142 1486.9813 -623.18058 9076.3674
2100 273.9293 -5061.7945 1463.3978 -437.60445 10039.49
2200 276.40166 -4948.9281 1538.5962 -221.01165 9013.3961
2300 287.28669 -5039.6841 1535.7768 -188.98782 10739.853
2400 290.35344 -4947.2095 1615.8983 18.994602 8326.4501
2500 305.29351 -4925.5822 1669.8823 266.99522 11465.135
Loop time of 4.32954 on 4 procs for 2500 steps with 3872 atoms
Performance: 49.890 ns/day, 0.481 hours/ns, 577.429 timesteps/s, 2.236 Matom-step/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.8113 | 3.8529 | 3.8893 | 1.7 | 88.99
Bond | 0.13153 | 0.13433 | 0.13718 | 0.7 | 3.10
Neigh | 0.13036 | 0.13039 | 0.13042 | 0.0 | 3.01
Comm | 0.13688 | 0.1751 | 0.21857 | 8.4 | 4.04
Output | 0.00032606 | 0.00035873 | 0.00045009 | 0.0 | 0.01
Modify | 0.027754 | 0.028116 | 0.028735 | 0.2 | 0.65
Other | | 0.008382 | | | 0.19
Nlocal: 968 ave 986 max 944 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 6379.75 ave 6407 max 6352 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 192584 ave 196718 max 188693 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Total # of neighbors = 770338
Ave neighs/atom = 198.95093
Ave special neighs/atom = 3.9669421
Neighbor list builds = 34
Dangerous builds = 0
#write_data molecular-mix.data
#write_restart molecular-mix.restart
write_restart molecular-mix.restart
System init for write_restart ...
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
# now restart
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
molecule cychex cyclohexane.mol
Read molecule template cychex:
LAMMPS molecule file. Cyclohexane(UA)
1 molecules
0 fragments
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
read_restart molecular-mix.restart
Reading restart file ...
restart file = 27 Jun 2024, LAMMPS = 27 Jun 2024
restoring atom style molecular from restart
orthogonal box = (-24 -24 -24) to (24 24 24)
1 by 2 by 2 MPI processor grid
restoring pair style lj/cut from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style harmonic from restart
3872 atoms
3072 bonds
3072 angles
3072 dihedrals
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
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
7 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_restart CPU = 0.004 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
All restart file global fix info was re-assigned
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.475 | 8.571 | 8.857 Mbytes
Step Temp E_pair E_mol TotEng Press
2500 305.29351 -4925.5822 1669.8823 266.99522 11465.135
2600 296.63161 -4937.8377 1616.2295 101.13964 8654.8533
2700 303.79396 -4951.8442 1732.7298 286.27771 11140.127
2800 297.39677 -4879.1242 1642.1355 194.58806 8993.2494
2900 299.13542 -4888.1435 1660.1105 223.60558 10716.3
3000 298.07888 -4928.2353 1650.6616 161.87369 10088.459
3100 304.09536 -4901.4853 1614.3116 221.69625 9505.2057
3200 301.51357 -4930.5129 1628.4386 177.00496 11411.933
3300 297.45744 -4923.6217 1700.537 209.19205 8189.571
3400 298.52831 -5012.7313 1736.6929 168.59495 11673.119
3500 295.66767 -4947.4296 1700.0072 164.20283 8222.3067
3600 296.7267 -5112.3707 1727.4319 38.906285 10608.481
3700 302.92855 -4994.4012 1789.7274 290.73255 8829.4479
3800 296.77191 -5034.2589 1657.2635 47.371248 9968.3521
3900 299.86962 -4972.7385 1744.2808 231.65266 10076.37
4000 304.89527 -5011.2464 1664.6779 171.53137 8926.0386
4100 296.81738 -5013.2169 1727.5801 139.25455 10898.733
4200 300.67532 -4988.3547 1782.1574 263.20975 8164.1158
4300 297.74901 -5023.3433 1784.7361 197.03396 11344.862
4400 302.0571 -5033.3547 1723.2662 175.26243 8016.975
4500 305.31958 -5062.5597 1767.0048 227.44095 10827.294
Loop time of 3.58588 on 4 procs for 2000 steps with 3872 atoms
Performance: 48.189 ns/day, 0.498 hours/ns, 557.743 timesteps/s, 2.160 Matom-step/s
99.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.0873 | 3.1383 | 3.2136 | 2.7 | 87.52
Bond | 0.10381 | 0.10769 | 0.11168 | 0.9 | 3.00
Neigh | 0.13651 | 0.13652 | 0.13654 | 0.0 | 3.81
Comm | 0.094882 | 0.1741 | 0.22894 | 12.3 | 4.86
Output | 0.00024683 | 0.00028387 | 0.00038642 | 0.0 | 0.01
Modify | 0.021974 | 0.022331 | 0.022623 | 0.2 | 0.62
Other | | 0.006685 | | | 0.19
Nlocal: 968 ave 984 max 948 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 6349.5 ave 6370 max 6330 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 192457 ave 196654 max 187154 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Total # of neighbors = 769828
Ave neighs/atom = 198.81921
Ave special neighs/atom = 3.9669421
Neighbor list builds = 35
Dangerous builds = 0
# clean up
shell rm molecular-mix.restart
Total wall time: 0:00:08

295
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LAMMPS (27 Jun 2024)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file
# run the first part and write out restart
include in.template-mix
# demo for atom style template simulating a cyclohexane methane mixture
# part 1: creating system with create_atoms
units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
LAMMPS molecule file. Cyclohexane(UA)
1 molecules
0 fragments
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
atom_style template cychex
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
lattice sc 6.0
Lattice spacing in x,y,z = 6 6 6
variable boxlen index 4.0
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1
Created orthogonal box = (-24 -24 -24) to (24 24 24)
1 by 1 by 1 MPI processor grid
create_atoms 0 box mol cychex 734594
Created 3072 atoms
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
create_atoms CPU = 0.000 seconds
create_atoms 2 random 800 495437 box
Created 800 atoms
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
create_atoms CPU = 0.000 seconds
mass 1 14.027
mass 2 16.043
pair_coeff 1 1 0.1180 3.905
pair_coeff 2 2 0.2940 3.730
bond_coeff 1 260.00 1.5260
angle_coeff 1 63.0 112.40
dihedral_coeff 1 2.0 1 3
thermo 100
minimize 0.001 0.001 500 1000
Generated 1 of 1 mixed pair_coeff terms from geometric 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 = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.05 | 8.05 | 8.05 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 4.3897851e+13 341.92144 4.3897851e+13 1.0886888e+14
100 0 -4351.8383 516.49891 -3835.3394 11635.037
190 0 -6191.8196 457.61266 -5734.2069 4365.4279
Loop time of 2.46574 on 1 procs for 190 steps with 3872 atoms
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
43897850768892.8 -5729.17409504969 -5734.20694761353
Force two-norm initial, final = 1.1080994e+15 72.745546
Force max component initial, final = 4.6607099e+14 17.390179
Final line search alpha, max atom move = 0.0041638487 0.072410076
Iterations, force evaluations = 190 297
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.1376 | 2.1376 | 2.1376 | 0.0 | 86.69
Bond | 0.068456 | 0.068456 | 0.068456 | 0.0 | 2.78
Neigh | 0.21212 | 0.21212 | 0.21212 | 0.0 | 8.60
Comm | 0.012436 | 0.012436 | 0.012436 | 0.0 | 0.50
Output | 2.9907e-05 | 2.9907e-05 | 2.9907e-05 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.03511 | | | 1.42
Nlocal: 3872 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 12122 ave 12122 max 12122 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 774375 ave 774375 max 774375 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 774375
Ave neighs/atom = 199.99354
Ave special neighs/atom = 3.9669421
Neighbor list builds = 14
Dangerous builds = 0
reset_timestep 0
velocity all create 100.0 6234235
fix 1 all nvt temp 100.0 300.0 1.0
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
run 2500
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 6.925 | 6.925 | 6.925 Mbytes
Step Temp E_pair E_mol TotEng Press
0 100 -6191.8196 457.61266 -4580.3354 4842.371
100 106.81292 -5670.2785 921.2043 -3516.5903 5959.4321
200 119.24063 -5701.0127 1040.0231 -3285.1059 6755.2619
300 127.28216 -5706.3887 1026.2838 -3211.4322 6076.6123
400 133.79038 -5734.0279 1113.6088 -3076.65 6583.9393
500 138.77685 -5756.2532 1192.1349 -2962.8117 6436.3524
600 149.39857 -5730.563 1206.6372 -2800.0582 6357.5889
700 155.5825 -5671.0161 929.50406 -2946.2899 7697.5164
800 161.24677 -5628.3833 1186.5533 -2581.2493 5840.6503
900 172.81747 -5638.6453 1148.683 -2495.8707 8169.3352
1000 182.2048 -5579.5767 909.90783 -2567.2594 6270.7354
1100 188.95766 -5548.999 1183.6644 -2185.0058 7711.9244
1200 195.22147 -5511.6798 1111.3361 -2147.7386 7656.4439
1300 205.15867 -5431.6966 1195.8143 -1868.6148 7021.8716
1400 211.44641 -5410.5687 1299.0501 -1671.6986 8903.0061
1500 223.70124 -5359.4567 1388.4189 -1389.8128 6919.2408
1600 231.75318 -5288.3343 1348.829 -1265.3712 9409.2728
1700 229.61746 -5259.4318 1194.5663 -1415.375 7387.4923
1800 245.62483 -5281.0755 1389.3362 -1057.5441 9421.7241
1900 250.69445 -5158.7006 1236.5167 -1029.4919 8649.4835
2000 259.50657 -5148.4153 1485.1392 -668.90355 9130.4701
2100 270.77108 -5092.6634 1418.7937 -549.51913 9666.5632
2200 272.30152 -5079.7585 1514.5708 -423.17779 8568.2546
2300 285.20945 -5085.6197 1492.5671 -302.10191 10281.574
2400 286.95799 -4979.8608 1544.6159 -124.11819 8797.7435
2500 296.10218 -4928.5152 1698.282 186.40572 10946.864
Loop time of 16.1773 on 1 procs for 2500 steps with 3872 atoms
Performance: 13.352 ns/day, 1.797 hours/ns, 154.537 timesteps/s, 598.368 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 14.927 | 14.927 | 14.927 | 0.0 | 92.27
Bond | 0.52161 | 0.52161 | 0.52161 | 0.0 | 3.22
Neigh | 0.52299 | 0.52299 | 0.52299 | 0.0 | 3.23
Comm | 0.090871 | 0.090871 | 0.090871 | 0.0 | 0.56
Output | 0.00059782 | 0.00059782 | 0.00059782 | 0.0 | 0.00
Modify | 0.096104 | 0.096104 | 0.096104 | 0.0 | 0.59
Other | | 0.01791 | | | 0.11
Nlocal: 3872 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11821 ave 11821 max 11821 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 770416 ave 770416 max 770416 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 770416
Ave neighs/atom = 198.97107
Ave special neighs/atom = 3.9669421
Neighbor list builds = 34
Dangerous builds = 0
#write_data template-mix.data
#write_restart template-mix.restart
write_restart template-mix.restart
System init for write_restart ...
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
# now restart
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
molecule cychex cyclohexane.mol
Read molecule template cychex:
LAMMPS molecule file. Cyclohexane(UA)
1 molecules
0 fragments
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
read_restart template-mix.restart
Reading restart file ...
restart file = 27 Jun 2024, LAMMPS = 27 Jun 2024
restoring atom style template from restart
orthogonal box = (-24 -24 -24) to (24 24 24)
1 by 1 by 1 MPI processor grid
restoring pair style lj/cut from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style harmonic from restart
3872 atoms
3072 template bonds
3072 template angles
3072 template dihedrals
read_restart CPU = 0.001 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
All restart file global fix info was re-assigned
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.88 | 6.88 | 6.88 Mbytes
Step Temp E_pair E_mol TotEng Press
2500 296.10218 -4928.5152 1698.282 186.40572 10946.864
2600 302.98473 -4910.6997 1585.9276 171.28257 9066.357
2700 300.75989 -4935.1005 1723.6514 258.9337 10755.67
2800 294.26086 -4904.3072 1594.9394 86.02469 9420.9997
2900 296.15059 -4961.5041 1594.1004 49.793724 10129.823
3000 296.65334 -4934.6622 1596.9704 85.306731 10112.636
3100 301.62361 -4975.5261 1671.8512 176.67422 9500.7576
3200 297.34385 -5017.986 1603.4388 16.419054 10451.2
3300 297.01108 -4882.1137 1651.6426 196.65525 9124.096
3400 298.13642 -4983.4532 1742.3589 199.01715 10808.599
3500 315.91146 -4952.209 1651.2231 344.22669 8677.2632
3600 295.12433 -4950.6158 1721.3273 176.06725 10904.222
3700 300.65909 -4967.4001 1770.4243 272.244 9230.4292
3800 302.15034 -4991.9549 1644.8366 139.30847 10154.524
3900 302.16277 -5017.0117 1672.2353 141.79397 9705.6697
4000 303.1458 -4946.2517 1679.8498 231.51137 9527.8793
4100 303.54737 -5003.8276 1639.7221 138.44129 10406.442
4200 291.62491 -5009.3438 1707.6 63.233087 8645.4116
4300 306.17115 -5084.7139 1727.9528 176.0607 10563.216
4400 302.65581 -5004.4302 1747.5309 235.36003 8717.1253
4500 296.42334 -5014.9791 1723.2084 128.57389 10492.246
Loop time of 13.2399 on 1 procs for 2000 steps with 3872 atoms
Performance: 13.051 ns/day, 1.839 hours/ns, 151.058 timesteps/s, 584.898 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 12.13 | 12.13 | 12.13 | 0.0 | 91.61
Bond | 0.42044 | 0.42044 | 0.42044 | 0.0 | 3.18
Neigh | 0.52469 | 0.52469 | 0.52469 | 0.0 | 3.96
Comm | 0.072857 | 0.072857 | 0.072857 | 0.0 | 0.55
Output | 0.00053188 | 0.00053188 | 0.00053188 | 0.0 | 0.00
Modify | 0.076918 | 0.076918 | 0.076918 | 0.0 | 0.58
Other | | 0.0148 | | | 0.11
Nlocal: 3872 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11685 ave 11685 max 11685 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 770346 ave 770346 max 770346 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 770346
Ave neighs/atom = 198.953
Ave special neighs/atom = 3.9669421
Neighbor list builds = 34
Dangerous builds = 0
# clean up
shell rm template-mix.restart
Total wall time: 0:00:31

296
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@ -0,0 +1,296 @@
LAMMPS (27 Jun 2024)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file
# run the first part and write out restart
include in.template-mix
# demo for atom style template simulating a cyclohexane methane mixture
# part 1: creating system with create_atoms
units real
boundary p p p
molecule cychex cyclohexane.mol
Read molecule template cychex:
LAMMPS molecule file. Cyclohexane(UA)
1 molecules
0 fragments
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
atom_style template cychex
pair_style lj/cut 12.0
pair_modify mix geometric tail yes
bond_style harmonic
angle_style harmonic
dihedral_style harmonic
lattice sc 6.0
Lattice spacing in x,y,z = 6 6 6
variable boxlen index 4.0
region box block -${boxlen} ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 ${boxlen} -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -${boxlen} ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 ${boxlen} -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -${boxlen} ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 ${boxlen} units lattice
region box block -4.0 4.0 -4.0 4.0 -4.0 4.0 units lattice
create_box 2 box bond/types 1 angle/types 1 dihedral/types 1
Created orthogonal box = (-24 -24 -24) to (24 24 24)
1 by 2 by 2 MPI processor grid
create_atoms 0 box mol cychex 734594
Created 3072 atoms
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
create_atoms CPU = 0.001 seconds
create_atoms 2 random 800 495437 box
Created 800 atoms
using lattice units in orthogonal box = (-24 -24 -24) to (24 24 24)
create_atoms CPU = 0.000 seconds
mass 1 14.027
mass 2 16.043
pair_coeff 1 1 0.1180 3.905
pair_coeff 2 2 0.2940 3.730
bond_coeff 1 260.00 1.5260
angle_coeff 1 63.0 112.40
dihedral_coeff 1 2.0 1 3
thermo 100
minimize 0.001 0.001 500 1000
Generated 1 of 1 mixed pair_coeff terms from geometric 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 = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 5.345 | 5.441 | 5.728 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 7.5430044e+16 341.92144 7.5430044e+16 1.8707026e+17
100 0 -3410.6986 572.28283 -2838.4158 14603.831
200 0 -6109.2306 483.67771 -5625.5529 5069.1821
204 0 -6137.0238 483.1464 -5653.8774 4952.4083
Loop time of 0.719475 on 4 procs for 204 steps with 3872 atoms
99.6% CPU use with 4 MPI tasks x 1 OpenMP threads
Minimization stats:
Stopping criterion = energy tolerance
Energy initial, next-to-last, final =
7.54300441078755e+16 -5648.75822666276 -5653.87742467986
Force two-norm initial, final = 8.7430661e+18 74.636836
Force max component initial, final = 4.1468626e+18 8.680078
Final line search alpha, max atom move = 0.0032186724 0.027938327
Iterations, force evaluations = 204 328
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.59281 | 0.6027 | 0.60956 | 0.8 | 83.77
Bond | 0.018776 | 0.020785 | 0.026388 | 2.2 | 2.89
Neigh | 0.054209 | 0.054242 | 0.054273 | 0.0 | 7.54
Comm | 0.018189 | 0.03064 | 0.042206 | 4.9 | 4.26
Output | 3.3034e-05 | 3.5624e-05 | 4.3263e-05 | 0.0 | 0.00
Modify | 0 | 0 | 0 | 0.0 | 0.00
Other | | 0.01107 | | | 1.54
Nlocal: 968 ave 980 max 954 min
Histogram: 1 0 1 0 0 0 0 0 1 1
Nghost: 6630 ave 6644 max 6616 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 193550 ave 195957 max 191376 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 774200
Ave neighs/atom = 199.94835
Ave special neighs/atom = 3.9669421
Neighbor list builds = 14
Dangerous builds = 0
reset_timestep 0
velocity all create 100.0 6234235
fix 1 all nvt temp 100.0 300.0 1.0
# dump 1 all custom 100 cychex-methane.lammpstrj id xu yu zu
run 2500
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
Per MPI rank memory allocation (min/avg/max) = 4.22 | 4.507 | 4.603 Mbytes
Step Temp E_pair E_mol TotEng Press
0 100 -6137.0238 483.1464 -4500.0059 5429.3515
100 107.18608 -5623.5468 925.13787 -3461.6193 5640.5922
200 119.37771 -5671.054 1050.9081 -3242.6804 7494.8576
300 127.21216 -5646.3171 1053.2825 -3125.1696 5661.5841
400 133.87894 -5674.4359 1139.3079 -2990.337 7202.7
500 138.76354 -5679.3297 1234.4508 -2843.7258 6745.1519
600 150.51628 -5665.2143 1210.3078 -2718.142 6301.1312
700 152.13291 -5680.6166 979.71444 -2945.4837 8424.0062
800 161.60449 -5579.521 1209.1388 -2505.674 5226.3319
900 177.80597 -5626.7406 1125.8767 -2449.2113 9035.9218
1000 181.98782 -5509.1736 924.24027 -2485.0276 5775.8317
1100 189.93412 -5534.8176 1169.5911 -2173.6307 8072.3434
1200 194.04459 -5508.0919 1169.0571 -2100.0095 7766.2625
1300 203.40621 -5400.0439 1229.5897 -1823.4077 6533.8169
1400 211.36099 -5362.2808 1318.5794 -1604.867 9789.8496
1500 221.24251 -5263.1861 1410.6972 -1299.6344 6407.5052
1600 234.83277 -5316.3854 1299.4287 -1307.2882 10199.28
1700 233.61193 -5187.0022 1246.0158 -1245.4048 7482.5096
1800 247.00713 -5193.2051 1451.1363 -891.92372 9836.6864
1900 250.10386 -5165.7314 1259.876 -1019.978 8648.7513
2000 257.7022 -5083.7142 1486.9813 -623.18058 9076.3674
2100 273.9293 -5061.7945 1463.3978 -437.60445 10039.49
2200 276.40166 -4948.9281 1538.5962 -221.01165 9013.3961
2300 287.28669 -5039.6841 1535.7768 -188.98782 10739.853
2400 290.35344 -4947.2095 1615.8983 18.994602 8326.4501
2500 305.29351 -4925.5822 1669.8823 266.99522 11465.135
Loop time of 4.32742 on 4 procs for 2500 steps with 3872 atoms
Performance: 49.914 ns/day, 0.481 hours/ns, 577.711 timesteps/s, 2.237 Matom-step/s
99.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.7864 | 3.836 | 3.8948 | 2.2 | 88.64
Bond | 0.13058 | 0.13362 | 0.13735 | 0.8 | 3.09
Neigh | 0.13597 | 0.13601 | 0.13605 | 0.0 | 3.14
Comm | 0.12304 | 0.18542 | 0.23763 | 10.5 | 4.28
Output | 0.00033524 | 0.00036705 | 0.00045513 | 0.0 | 0.01
Modify | 0.027504 | 0.027917 | 0.028571 | 0.3 | 0.65
Other | | 0.008118 | | | 0.19
Nlocal: 968 ave 986 max 944 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 6379.75 ave 6407 max 6352 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 192584 ave 196718 max 188693 min
Histogram: 1 1 0 0 0 0 0 1 0 1
Total # of neighbors = 770338
Ave neighs/atom = 198.95093
Ave special neighs/atom = 3.9669421
Neighbor list builds = 34
Dangerous builds = 0
#write_data template-mix.data
#write_restart template-mix.restart
write_restart template-mix.restart
System init for write_restart ...
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
# now restart
clear
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
molecule cychex cyclohexane.mol
Read molecule template cychex:
LAMMPS molecule file. Cyclohexane(UA)
1 molecules
0 fragments
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
read_restart template-mix.restart
Reading restart file ...
restart file = 27 Jun 2024, LAMMPS = 27 Jun 2024
restoring atom style template from restart
orthogonal box = (-24 -24 -24) to (24 24 24)
1 by 2 by 2 MPI processor grid
restoring pair style lj/cut from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style harmonic from restart
3872 atoms
3072 template bonds
3072 template angles
3072 template dihedrals
read_restart CPU = 0.001 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
Generated 1 of 1 mixed pair_coeff terms from geometric mixing rule
All restart file global fix info was re-assigned
Neighbor list info ...
update: every = 1 steps, delay = 0 steps, check = yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.192 | 4.288 | 4.574 Mbytes
Step Temp E_pair E_mol TotEng Press
2500 305.29351 -4925.5822 1669.8823 266.99522 11465.135
2600 296.63161 -4937.8377 1616.2295 101.13964 8654.8533
2700 303.79396 -4951.8442 1732.7298 286.27771 11140.127
2800 297.39677 -4879.1242 1642.1355 194.58806 8993.2494
2900 299.13542 -4888.1435 1660.1105 223.60558 10716.3
3000 298.07888 -4928.2353 1650.6616 161.87369 10088.459
3100 304.09536 -4901.4853 1614.3116 221.69625 9505.2057
3200 301.51357 -4930.5129 1628.4386 177.00496 11411.933
3300 297.45744 -4923.6217 1700.537 209.19205 8189.571
3400 298.52831 -5012.7313 1736.6929 168.59495 11673.119
3500 295.66767 -4947.4296 1700.0072 164.20283 8222.3067
3600 296.7267 -5112.3707 1727.4319 38.906285 10608.481
3700 302.92855 -4994.4012 1789.7274 290.73255 8829.4479
3800 296.77191 -5034.2589 1657.2635 47.371248 9968.3521
3900 299.86962 -4972.7385 1744.2808 231.65266 10076.37
4000 304.89527 -5011.2464 1664.6779 171.53137 8926.0386
4100 296.81738 -5013.2169 1727.5801 139.25455 10898.733
4200 300.67532 -4988.3547 1782.1574 263.20975 8164.1158
4300 297.74901 -5023.3433 1784.7361 197.03396 11344.862
4400 302.0571 -5033.3547 1723.2662 175.26243 8016.975
4500 305.31958 -5062.5597 1767.0048 227.44095 10827.294
Loop time of 3.5798 on 4 procs for 2000 steps with 3872 atoms
Performance: 48.271 ns/day, 0.497 hours/ns, 558.691 timesteps/s, 2.163 Matom-step/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.0514 | 3.1162 | 3.2058 | 3.3 | 87.05
Bond | 0.10377 | 0.10776 | 0.11194 | 1.0 | 3.01
Neigh | 0.14121 | 0.14125 | 0.1413 | 0.0 | 3.95
Comm | 0.092144 | 0.18542 | 0.25437 | 14.1 | 5.18
Output | 0.00025632 | 0.00028151 | 0.00035298 | 0.0 | 0.01
Modify | 0.02193 | 0.022227 | 0.022584 | 0.2 | 0.62
Other | | 0.006618 | | | 0.18
Nlocal: 968 ave 984 max 948 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 6349.5 ave 6370 max 6330 min
Histogram: 1 0 1 0 0 0 0 1 0 1
Neighs: 192457 ave 196654 max 187154 min
Histogram: 1 0 0 0 1 0 0 0 1 1
Total # of neighbors = 769828
Ave neighs/atom = 198.81921
Ave special neighs/atom = 3.9669421
Neighbor list builds = 35
Dangerous builds = 0
# clean up
shell rm template-mix.restart
Total wall time: 0:00:08

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
read_restart molecular-mix.restart
Reading restart file ...
restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020
restoring atom style molecular from restart
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 1 by 1 MPI processor grid
restoring pair style lj/cut from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style harmonic from restart
3872 atoms
3072 bonds
3072 angles
3072 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.0
special bond factors coul: 0.0 0.0 0.0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
5 = max # of special neighbors
special bonds CPU = 0.002 seconds
read_restart CPU = 0.008 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 10.74 | 10.74 | 10.74 Mbytes
Step Temp E_pair E_mol TotEng Press
0 297.79426 -4928.7403 1686.5107 193.93377 11481.089
100 298.75004 -4870.5672 1619.1613 195.7859 8813.1304
200 296.49886 -4884.3039 1747.4798 284.39198 11537.322
300 295.24937 -4850.2788 1642.4584 198.97822 9160.666
400 297.73321 -4952.9967 1660.6439 143.10604 10751.859
500 293.58308 -4984.2337 1625.8355 29.173529 9530.8826
600 299.50756 -4999.965 1588.0327 44.000269 9233.8621
700 295.64728 -4958.2253 1646.2011 99.365838 11089.418
800 303.5841 -4895.0575 1719.7373 327.65045 8451.8685
900 300.80754 -5033.4853 1727.4591 164.90648 11497.526
1000 300.66472 -4887.4356 1763.3231 345.17233 8454.9551
1100 300.94922 -5003.5731 1766.1276 235.12197 11176.28
1200 299.81632 -4944.4257 1705.2357 220.30525 8879.3201
1300 299.95466 -5009.4367 1637.1947 88.849661 10379.762
1400 300.32601 -4999.539 1735.8132 201.65057 9698.2178
1500 304.10398 -4997.213 1627.5651 139.32157 9299.5337
1600 299.2676 -4960.8958 1746.7172 238.98516 10914.415
1700 293.13408 -5034.7742 1742.2452 89.861851 8213.6882
1800 301.9386 -5068.1221 1755.577 171.43863 11229.315
1900 297.67412 -5012.48 1734.5634 156.86041 8116.1348
2000 296.14819 -5089.1034 1774.3987 102.46517 10858.209
Loop time of 15.5879 on 1 procs for 2000 steps with 3872 atoms
Performance: 11.086 ns/day, 2.165 hours/ns, 128.305 timesteps/s
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 14.116 | 14.116 | 14.116 | 0.0 | 90.56
Bond | 0.58742 | 0.58742 | 0.58742 | 0.0 | 3.77
Neigh | 0.68543 | 0.68543 | 0.68543 | 0.0 | 4.40
Comm | 0.082574 | 0.082574 | 0.082574 | 0.0 | 0.53
Output | 0.00054698 | 0.00054698 | 0.00054698 | 0.0 | 0.00
Modify | 0.078446 | 0.078446 | 0.078446 | 0.0 | 0.50
Other | | 0.03761 | | | 0.24
Nlocal: 3872.00 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11633.0 ave 11633 max 11633 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 770365.0 ave 770365 max 770365 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 770365
Ave neighs/atom = 198.95790
Ave special neighs/atom = 3.9669421
Neighbor list builds = 35
Dangerous builds = 0
Total wall time: 0:00:15

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
read_restart molecular-mix.restart
Reading restart file ...
restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020
WARNING: Restart file used different # of processors: 1 vs. 4 (src/read_restart.cpp:697)
restoring atom style molecular from restart
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 2 by 2 MPI processor grid
restoring pair style lj/cut from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style harmonic from restart
3872 atoms
3072 bonds
3072 angles
3072 dihedrals
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0.0 0.0 0.0
special bond factors coul: 0.0 0.0 0.0
2 = max # of 1-2 neighbors
2 = max # of 1-3 neighbors
4 = max # of 1-4 neighbors
5 = max # of special neighbors
special bonds CPU = 0.001 seconds
read_restart CPU = 0.031 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 8.101 | 8.197 | 8.483 Mbytes
Step Temp E_pair E_mol TotEng Press
0 297.79426 -4928.7403 1686.5107 193.93377 11481.089
100 298.75001 -4870.5672 1619.1613 195.78563 8813.1303
200 301.9265 -4884.8594 1745.0359 344.02042 11561.79
300 298.78957 -4854.0769 1638.3567 231.92774 9180.5245
400 302 -4951.4895 1664.5419 197.74463 10784.638
500 299.17946 -4983.7996 1615.0068 83.354011 9578.745
600 294.32777 -5000.7554 1591.1992 -13.391775 9181.3926
700 300.90925 -4959.9309 1653.6347 165.81003 11121.514
800 293.14833 -4895.5912 1707.8754 194.83943 8397.927
900 299.0508 -5032.8395 1726.0885 143.91128 11478.847
1000 295.15206 -4888.4533 1777.4719 294.69437 8388.738
1100 301.13534 -5004.2113 1761.645 232.14877 11246.198
1200 296.93159 -4944.3223 1703.1744 185.06123 8808.4178
1300 300.79377 -5011.7826 1642.093 101.08422 10390.705
1400 295.85952 -4987.9927 1708.8415 134.68768 9680.88
1500 296.37146 -5009.887 1637.2239 47.082942 9235.3487
1600 298.68972 -4962.1273 1747.402 231.77054 10941.114
1700 299.03141 -5022.0046 1755.8881 184.32195 8248.312
1800 297.26645 -5023.9459 1740.9512 147.07837 11357.02
1900 293.16007 -5023.8887 1754.1333 112.93534 7969.1102
2000 307.66497 -5046.5928 1803.9999 307.46576 11249.704
Loop time of 5.2142 on 4 procs for 2000 steps with 3872 atoms
Performance: 33.140 ns/day, 0.724 hours/ns, 383.568 timesteps/s
94.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.5706 | 3.6724 | 3.7809 | 4.9 | 70.43
Bond | 0.14654 | 0.1524 | 0.15708 | 1.2 | 2.92
Neigh | 0.18217 | 0.1822 | 0.18221 | 0.0 | 3.49
Comm | 0.74346 | 0.8715 | 0.9808 | 10.9 | 16.71
Output | 0.00034776 | 0.00084716 | 0.0023413 | 0.0 | 0.02
Modify | 0.12457 | 0.18985 | 0.31013 | 17.4 | 3.64
Other | | 0.145 | | | 2.78
Nlocal: 968.000 ave 979 max 948 min
Histogram: 1 0 0 0 0 0 0 1 1 1
Nghost: 6321.25 ave 6336 max 6309 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Neighs: 192540.0 ave 195406 max 187182 min
Histogram: 1 0 0 0 0 0 1 0 0 2
Total # of neighbors = 770161
Ave neighs/atom = 198.90522
Ave special neighs/atom = 3.9669421
Neighbor list builds = 35
Dangerous builds = 0
Total wall time: 0:00:05

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
read_restart template-mix.restart
Reading restart file ...
restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020
WARNING: Restart file used different # of processors: 4 vs. 1 (src/read_restart.cpp:697)
restoring atom style template from restart
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 1 by 1 MPI processor grid
restoring pair style lj/cut from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style harmonic from restart
3872 atoms
3072 template bonds
3072 template angles
3072 template dihedrals
read_restart CPU = 0.002 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 6.879 | 6.879 | 6.879 Mbytes
Step Temp E_pair E_mol TotEng Press
2500 297.79426 -4928.7403 1686.5107 193.93377 11481.089
2600 303.69861 -4872.1658 1620.5986 252.72467 8824.1501
2700 304.64827 -4885.5903 1747.1956 376.85504 11560.748
2800 298.79617 -4851.2752 1644.5913 241.04014 9198.1133
2900 302.323 -4949.4247 1661.0637 200.05824 10788.039
3000 302.8192 -4983.7441 1617.1412 127.5418 9606.2027
3100 305.27495 -4999.5335 1589.7081 112.65547 9258.8096
3200 294.9932 -4960.8253 1650.5396 93.556955 11103.25
3300 299.8705 -4896.6757 1711.6029 275.0477 8404.2758
3400 308.43113 -5035.583 1732.7837 256.09989 11520.651
3500 302.54 -4887.2016 1770.4336 374.15506 8359.8351
3600 294.00064 -5011.409 1768.0298 149.01058 11257.53
3700 303.26654 -4942.0636 1690.4493 247.69209 8749.4281
3800 294.7064 -5009.5839 1638.6276 29.577045 10460.396
3900 300.34826 -5011.778 1699.4384 153.29355 9558.3891
4000 298.76709 -5014.8089 1613.1902 45.769836 9254.1067
4100 297.77294 -4978.3228 1736.8967 194.49122 10810.757
4200 302.14768 -5049.4356 1713.0187 149.97929 8258.5093
4300 295.1467 -5094.2287 1757.8215 69.206733 11022.023
4400 305.24677 -4967.1951 1762.3252 317.28577 8423.2256
4500 305.53119 -5047.7285 1775.2795 252.98852 11178.338
Loop time of 15.3536 on 1 procs for 2000 steps with 3872 atoms
Performance: 11.255 ns/day, 2.132 hours/ns, 130.263 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 13.88 | 13.88 | 13.88 | 0.0 | 90.40
Bond | 0.58065 | 0.58065 | 0.58065 | 0.0 | 3.78
Neigh | 0.69518 | 0.69518 | 0.69518 | 0.0 | 4.53
Comm | 0.0826 | 0.0826 | 0.0826 | 0.0 | 0.54
Output | 0.00053438 | 0.00053438 | 0.00053438 | 0.0 | 0.00
Modify | 0.07779 | 0.07779 | 0.07779 | 0.0 | 0.51
Other | | 0.03687 | | | 0.24
Nlocal: 3872.00 ave 3872 max 3872 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 11670.0 ave 11670 max 11670 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 770032.0 ave 770032 max 770032 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 770032
Ave neighs/atom = 198.87190
Ave special neighs/atom = 3.9669421
Neighbor list builds = 35
Dangerous builds = 0
Total wall time: 0:00:15

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LAMMPS (22 Oct 2020)
using 1 OpenMP thread(s) per MPI task
# demo for atom style template simulating a cyclohexane methane mixture
# part 3: continuing from restart file
molecule cychex cyclohexane.mol
Read molecule template cychex:
1 molecules
6 atoms with max type 1
6 bonds with max type 1
6 angles with max type 1
6 dihedrals with max type 1
0 impropers with max type 0
read_restart template-mix.restart
Reading restart file ...
restart file = 22 Oct 2020, LAMMPS = 22 Oct 2020
restoring atom style template from restart
orthogonal box = (-24.000000 -24.000000 -24.000000) to (24.000000 24.000000 24.000000)
1 by 2 by 2 MPI processor grid
restoring pair style lj/cut from restart
restoring bond style harmonic from restart
restoring angle style harmonic from restart
restoring dihedral style harmonic from restart
3872 atoms
3072 template bonds
3072 template angles
3072 template dihedrals
read_restart CPU = 0.006 seconds
thermo 100
fix 1 all nvt temp 300.0 300.0 1.0
Resetting global fix info from restart file:
fix style: nvt, fix ID: 1
# dump 1 all custom 100 custom template-mix.lammpstrj id xu yu zu
run 2000
All restart file global fix info was re-assigned
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 14
ghost atom cutoff = 14
binsize = 7, bins = 7 7 7
1 neighbor lists, perpetual/occasional/extra = 1 0 0
(1) pair lj/cut, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
Per MPI rank memory allocation (min/avg/max) = 4.193 | 4.289 | 4.575 Mbytes
Step Temp E_pair E_mol TotEng Press
2500 297.79426 -4928.7403 1686.5107 193.93377 11481.089
2600 303.6986 -4872.1658 1620.5986 252.72458 8824.1501
2700 296.80713 -4884.3012 1753.5243 293.99628 11523.482
2800 298.88856 -4849.1995 1639.5709 239.1615 9214.1261
2900 297.12578 -4949.9958 1657.7582 136.2123 10727.69
3000 298.19234 -4984.9797 1618.0356 73.812582 9576.9074
3100 301.54182 -4999.9775 1588.997 68.424766 9225.9502
3200 294.07259 -4962.8351 1646.3012 76.686125 11080.923
3300 303.55697 -4900.0696 1721.4077 323.99573 8433.7992
3400 297.80636 -5036.3758 1735.0734 135.00054 11440.101
3500 303.96121 -4882.4297 1757.4268 382.31908 8497.7685
3600 298.21153 -5006.6599 1759.9584 194.27658 11184.938
3700 300.77921 -4941.495 1688.3988 217.50964 8820.5666
3800 294.33206 -5011.7746 1653.7511 38.190478 10418.208
3900 304.38175 -5004.4071 1719.9139 227.68132 9632.0557
4000 302.44152 -5029.0544 1610.1577 70.889929 9237.6379
4100 298.82638 -4971.4109 1755.8272 232.48883 10814.056
4200 297.77273 -5040.0028 1718.5112 114.42322 8287.605
4300 300.50984 -5082.4128 1742.354 127.43881 11003.298
4400 310.02885 -4971.4191 1749.1209 355.03646 8502.7004
4500 302.62639 -5033.3284 1753.488 212.07956 11150.514
Loop time of 4.39645 on 4 procs for 2000 steps with 3872 atoms
Performance: 39.304 ns/day, 0.611 hours/ns, 454.913 timesteps/s
98.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.6185 | 3.6709 | 3.7028 | 1.7 | 83.50
Bond | 0.14772 | 0.15338 | 0.1621 | 1.5 | 3.49
Neigh | 0.17739 | 0.17747 | 0.17756 | 0.0 | 4.04
Comm | 0.29637 | 0.33265 | 0.39131 | 6.7 | 7.57
Output | 0.00034028 | 0.0006627 | 0.0016284 | 0.0 | 0.02
Modify | 0.039076 | 0.041988 | 0.043469 | 0.9 | 0.96
Other | | 0.01937 | | | 0.44
Nlocal: 968.000 ave 977 max 956 min
Histogram: 1 0 0 1 0 0 0 0 0 2
Nghost: 6322.75 ave 6345 max 6308 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 192555.0 ave 195249 max 188636 min
Histogram: 1 0 0 0 0 1 0 0 1 1
Total # of neighbors = 770221
Ave neighs/atom = 198.92071
Ave special neighs/atom = 3.9669421
Neighbor list builds = 34
Dangerous builds = 0
Total wall time: 0:00:04