Merge branch 'develop' into small-patches
This commit is contained in:
Axel Kohlmeyer
@ -16,7 +16,7 @@ variable mass equal $a*$a*$a*${rho_0}
|
||||
variable dt equal 1e-3 # timestep microseconds
|
||||
variable skin equal 0.2*$h
|
||||
|
||||
region box block -${Lb} ${Lb} -${Lb} ${Lb} 0 ${a} units box
|
||||
region box block -${Lb} ${Lb} -${Lb} ${Lb} -0.5 0.5 units box
|
||||
create_box 4 box
|
||||
lattice sq $a
|
||||
|
||||
|
||||
@ -14,7 +14,7 @@ variable mass equal $a*$a*$a*${rho_0}
|
||||
variable dt equal 1e-3 # timestep microseconds
|
||||
variable skin equal 0.2*$h
|
||||
|
||||
region box block -$L $L -$L $L 0 $a units box
|
||||
region box block -$L $L -$L $L -0.5 0.5 units box
|
||||
create_box 2 box
|
||||
lattice sq $a
|
||||
|
||||
|
||||
@ -1,40 +1,40 @@
|
||||
variable sname index ch4
|
||||
variable sname index ch4
|
||||
|
||||
units electron
|
||||
newton on
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 100.0
|
||||
pair_coeff * *
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
comm_modify vel yes
|
||||
|
||||
# Minimize
|
||||
min_style cg
|
||||
compute 1 all property/atom spin eradius
|
||||
dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
#dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
min_modify line quadratic dmax 0.1
|
||||
minimize 0 1.0e-6 1000 10000
|
||||
|
||||
# Dynamics
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effTemp all temp/eff
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step pe temp press
|
||||
thermo_modify temp effTemp
|
||||
thermo 1000
|
||||
thermo_style custom step pe temp press
|
||||
thermo_modify temp effTemp
|
||||
|
||||
velocity all create 300.0 4928459 dist gaussian rot yes mom yes
|
||||
velocity all create 300.0 4928459 dist gaussian rot yes mom yes
|
||||
|
||||
timestep 0.005
|
||||
fix 1 all nve/eff
|
||||
timestep 0.005
|
||||
fix 1 all nve/eff
|
||||
|
||||
# the custom dump includes the radii
|
||||
dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 3 all xyz 1000 ${sname}.nve.xyz
|
||||
#dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
#dump 3 all xyz 1000 ${sname}.nve.xyz
|
||||
|
||||
run 100000
|
||||
run 100000
|
||||
|
||||
@ -1,17 +1,17 @@
|
||||
variable sname index ch4
|
||||
variable sname index ch4
|
||||
|
||||
units electron
|
||||
newton on
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 100.0
|
||||
pair_coeff * *
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
comm_modify vel yes
|
||||
|
||||
compute effTemp all temp/eff
|
||||
|
||||
@ -24,8 +24,8 @@ variable erres equal c_energies[4]
|
||||
thermo 1
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_ecoul v_erres
|
||||
|
||||
min_style cg
|
||||
min_style cg
|
||||
compute 1 all property/atom spin eradius erforce
|
||||
dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
minimize 0 1e-6 2000 4000
|
||||
#dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
minimize 0 1e-6 2000 4000
|
||||
|
||||
|
||||
@ -1,17 +1,17 @@
|
||||
variable sname index ch4_ionized
|
||||
variable sname index ch4_ionized
|
||||
|
||||
units electron
|
||||
newton on
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 5000.0 0 0
|
||||
pair_coeff * *
|
||||
pair_style eff/cut 5000.0
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
comm_modify vel yes
|
||||
|
||||
# minimize
|
||||
|
||||
@ -20,23 +20,23 @@ min_modify line quadratic
|
||||
minimize 0 1.0e-6 10000 100000
|
||||
|
||||
# dynamics
|
||||
compute effTemp all temp/eff
|
||||
compute effTemp all temp/eff
|
||||
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke temp press
|
||||
thermo_modify temp effTemp
|
||||
thermo 100
|
||||
thermo_style custom step etotal pe ke temp press
|
||||
thermo_modify temp effTemp
|
||||
|
||||
# equilibrate
|
||||
timestep 0.001
|
||||
fix 1 all nvt/eff temp 300.0 300.0 0.1
|
||||
timestep 0.001
|
||||
fix 1 all nvt/eff temp 300.0 300.0 0.1
|
||||
|
||||
# the custom dump includes the radii
|
||||
compute 1 all property/atom spin eradius
|
||||
dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1[2]
|
||||
dump 2 all xyz 100 ${sname}.nvt.xyz
|
||||
#dump 1 all custom 100 ${sname}.nvt.lammpstrj id type x y z c_1[1] c_1[2]
|
||||
#dump 2 all xyz 100 ${sname}.nvt.xyz
|
||||
|
||||
run 1000000
|
||||
run 1000000
|
||||
|
||||
fix 2 all nve/eff
|
||||
fix 2 all nve/eff
|
||||
|
||||
run 1000000
|
||||
run 1000000
|
||||
|
||||
266
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.dynamics.g++.1
Normal file
266
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.dynamics.g++.1
Normal file
@ -0,0 +1,266 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
variable sname index ch4
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.ch4
|
||||
Reading data file ...
|
||||
orthogonal box = (-500 -500 -500) to (500 500 500)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
15 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
pair_style eff/cut 100.0
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
# Minimize
|
||||
min_style cg
|
||||
compute 1 all property/atom spin eradius
|
||||
dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 1 all custom 1 ch4.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
min_modify line quadratic dmax 0.1
|
||||
minimize 0 1.0e-6 1000 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
|
||||
@Article{Jaramillo-Botero11,
|
||||
author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
|
||||
title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
|
||||
journal = {J.~Comp.\ Chem.},
|
||||
year = 2011,
|
||||
volume = 32,
|
||||
number = 3,
|
||||
pages = {497--512}
|
||||
}
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 3 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 = 102
|
||||
ghost atom cutoff = 102
|
||||
binsize = 51, bins = 20 20 20
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.405 | 5.405 | 5.405 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -27.314082 0 -27.314082 -56588.53
|
||||
1000 0 -34.07448 0 -34.07448 1.3464499
|
||||
Loop time of 0.0308104 on 1 procs for 1000 steps with 15 atoms
|
||||
|
||||
88.9% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
-27.3140820331247 -34.0744796893375 -34.0744796893447
|
||||
Force two-norm initial, final = 10.728716 0.00017815706
|
||||
Force max component initial, final = 6.1727999 8.2675815e-05
|
||||
Final line search alpha, max atom move = 1 8.2675815e-05
|
||||
Iterations, force evaluations = 1000 1943
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.012522 | 0.012522 | 0.012522 | 0.0 | 40.64
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00012209 | 0.00012209 | 0.00012209 | 0.0 | 0.40
|
||||
Output | 0.016563 | 0.016563 | 0.016563 | 0.0 | 53.76
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.001604 | | | 5.20
|
||||
|
||||
Nlocal: 15 ave 15 max 15 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 105 ave 105 max 105 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 105
|
||||
Ave neighs/atom = 7
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
# Dynamics
|
||||
|
||||
compute effTemp all temp/eff
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step pe temp press
|
||||
thermo_modify temp effTemp
|
||||
|
||||
velocity all create 300.0 4928459 dist gaussian rot yes mom yes
|
||||
|
||||
timestep 0.005
|
||||
fix 1 all nve/eff
|
||||
|
||||
# the custom dump includes the radii
|
||||
dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 2 all custom 1000 ch4.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 3 all xyz 1000 ${sname}.nve.xyz
|
||||
dump 3 all xyz 1000 ch4.nve.xyz
|
||||
|
||||
run 100000
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.406 | 5.406 | 5.406 Mbytes
|
||||
Step PotEng Temp Press
|
||||
1000 -34.07448 1050 392.66426
|
||||
2000 -34.065618 583.71716 -618.55027
|
||||
3000 -34.063563 475.54605 661.95076
|
||||
4000 -34.06119 350.76183 -449.64687
|
||||
5000 -34.0652 561.71223 -131.2575
|
||||
6000 -34.065798 593.21728 754.38406
|
||||
7000 -34.067408 677.86019 -409.21139
|
||||
8000 -34.065663 586.03411 446.32573
|
||||
9000 -34.06294 442.71136 414.41408
|
||||
10000 -34.060101 293.33406 -1203.0131
|
||||
11000 -34.064946 548.39598 345.29601
|
||||
12000 -34.067323 673.49043 444.55927
|
||||
13000 -34.063275 460.43973 -854.83884
|
||||
14000 -34.064666 533.57265 1542.0127
|
||||
15000 -34.063343 463.97449 -778.73252
|
||||
16000 -34.064462 522.77625 -1.5339614
|
||||
17000 -34.061203 351.37068 -148.19163
|
||||
18000 -34.066534 631.87837 -237.0746
|
||||
19000 -34.065169 560.16772 1360.7348
|
||||
20000 -34.063042 448.13104 -664.72128
|
||||
21000 -34.060696 324.68723 -167.83333
|
||||
22000 -34.065376 570.90279 -831.73853
|
||||
23000 -34.063127 452.61143 766.59984
|
||||
24000 -34.064572 528.62282 -107.80755
|
||||
25000 -34.06584 595.42175 610.33075
|
||||
26000 -34.066886 650.43579 -894.20521
|
||||
27000 -34.062035 395.20224 1754.7666
|
||||
28000 -34.060696 324.66878 -2622.013
|
||||
29000 -34.066777 644.66282 1551.3147
|
||||
30000 -34.066421 625.94614 -507.44173
|
||||
31000 -34.066163 612.36658 610.11907
|
||||
32000 -34.063109 451.70185 -47.463209
|
||||
33000 -34.062833 437.16794 -607.25848
|
||||
34000 -34.061657 375.30056 -158.28097
|
||||
35000 -34.064937 547.86519 272.75585
|
||||
36000 -34.067509 683.23088 359.91072
|
||||
37000 -34.067582 686.96461 -384.97405
|
||||
38000 -34.063213 457.13191 411.86349
|
||||
39000 -34.06272 431.13187 -594.23723
|
||||
40000 -34.062286 408.41212 456.09079
|
||||
41000 -34.064078 502.64096 -1149.8496
|
||||
42000 -34.066408 625.33334 1403.4937
|
||||
43000 -34.065948 601.03876 -773.40678
|
||||
44000 -34.064113 504.49498 179.93456
|
||||
45000 -34.060573 318.11433 223.38679
|
||||
46000 -34.063614 478.24588 -409.99081
|
||||
47000 -34.064814 541.38544 614.25246
|
||||
48000 -34.065602 582.87984 -743.92184
|
||||
49000 -34.063923 494.52673 474.88127
|
||||
50000 -34.064616 530.94533 288.81199
|
||||
51000 -34.062038 395.2991 -480.07513
|
||||
52000 -34.06497 549.5123 -305.53764
|
||||
53000 -34.065578 581.59919 964.80956
|
||||
54000 -34.06766 691.12707 -437.99603
|
||||
55000 -34.064707 535.85658 1058.6734
|
||||
56000 -34.062481 418.58003 -1011.5341
|
||||
57000 -34.064997 551.06731 -32.91724
|
||||
58000 -34.064281 513.25358 374.91628
|
||||
59000 -34.066177 613.1188 -464.85124
|
||||
60000 -34.064718 536.29803 1011.6698
|
||||
61000 -34.065746 590.46955 -1057.9241
|
||||
62000 -34.063253 459.23293 1526.2698
|
||||
63000 -34.062261 407.08636 -1743.6652
|
||||
64000 -34.063835 489.88286 761.60266
|
||||
65000 -34.069569 791.614 323.26812
|
||||
66000 -34.065557 580.45685 874.52459
|
||||
67000 -34.064917 546.77223 -1349.3606
|
||||
68000 -34.062963 443.96697 1178.4319
|
||||
69000 -34.063063 449.26418 -1660.686
|
||||
70000 -34.063597 477.39716 1323.13
|
||||
71000 -34.065424 573.47914 -131.55428
|
||||
72000 -34.065211 562.31067 -415.56361
|
||||
73000 -34.06339 466.38097 724.92885
|
||||
74000 -34.062286 408.34027 -1094.3845
|
||||
75000 -34.065545 579.79767 587.58121
|
||||
76000 -34.066774 644.61685 -357.22241
|
||||
77000 -34.064479 523.74831 1545.6628
|
||||
78000 -34.065506 577.88405 -1013.2409
|
||||
79000 -34.062874 439.24856 240.66725
|
||||
80000 -34.06306 449.09678 -799.14252
|
||||
81000 -34.063338 463.66067 1528.3351
|
||||
82000 -34.066812 646.52985 -1351.1758
|
||||
83000 -34.064724 536.65114 1338.595
|
||||
84000 -34.063774 486.67172 -876.0475
|
||||
85000 -34.06156 370.19256 617.89915
|
||||
86000 -34.063628 478.95398 -134.40164
|
||||
87000 -34.065141 558.60424 -758.03942
|
||||
88000 -34.066732 642.27865 1159.5992
|
||||
89000 -34.067349 674.83453 -301.45201
|
||||
90000 -34.063623 478.69626 386.87752
|
||||
91000 -34.061885 387.30728 -774.32296
|
||||
92000 -34.061363 359.77745 500.06117
|
||||
93000 -34.065724 589.32209 -469.10399
|
||||
94000 -34.065006 551.42796 818.92294
|
||||
95000 -34.06541 572.75191 -677.20865
|
||||
96000 -34.062331 410.64868 1383.8935
|
||||
97000 -34.061499 366.95753 -1715.2058
|
||||
98000 -34.061153 348.68703 353.63545
|
||||
99000 -34.066217 615.27816 193.79593
|
||||
100000 -34.067739 695.36238 205.35389
|
||||
101000 -34.067314 672.94727 929.41223
|
||||
Loop time of 2.23163 on 1 procs for 100000 steps with 15 atoms
|
||||
|
||||
Performance: 19358038.198 fs/day, 0.000 hours/fs, 44810.274 timesteps/s, 672.154 katom-step/s
|
||||
85.0% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.59187 | 0.59187 | 0.59187 | 0.0 | 26.52
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0061524 | 0.0061524 | 0.0061524 | 0.0 | 0.28
|
||||
Output | 1.5983 | 1.5983 | 1.5983 | 0.0 | 71.62
|
||||
Modify | 0.017759 | 0.017759 | 0.017759 | 0.0 | 0.80
|
||||
Other | | 0.01755 | | | 0.79
|
||||
|
||||
Nlocal: 15 ave 15 max 15 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 105 ave 105 max 105 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 105
|
||||
Ave neighs/atom = 7
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:02
|
||||
266
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.dynamics.g++.4
Normal file
266
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.dynamics.g++.4
Normal file
@ -0,0 +1,266 @@
|
||||
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
|
||||
variable sname index ch4
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.ch4
|
||||
Reading data file ...
|
||||
orthogonal box = (-500 -500 -500) to (500 500 500)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
15 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
pair_style eff/cut 100.0
|
||||
pair_coeff * *
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
# Minimize
|
||||
min_style cg
|
||||
compute 1 all property/atom spin eradius
|
||||
dump 1 all custom 1 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 1 all custom 1 ch4.min.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
min_modify line quadratic dmax 0.1
|
||||
minimize 0 1.0e-6 1000 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
|
||||
@Article{Jaramillo-Botero11,
|
||||
author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
|
||||
title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
|
||||
journal = {J.~Comp.\ Chem.},
|
||||
year = 2011,
|
||||
volume = 32,
|
||||
number = 3,
|
||||
pages = {497--512}
|
||||
}
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 3 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 = 102
|
||||
ghost atom cutoff = 102
|
||||
binsize = 51, bins = 20 20 20
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.385 | 5.385 | 5.385 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 -27.314082 0 -27.314082 -56588.53
|
||||
1000 0 -34.07448 0 -34.07448 0.39495391
|
||||
Loop time of 0.0230482 on 4 procs for 1000 steps with 15 atoms
|
||||
|
||||
97.7% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
-27.3140820331249 -34.0744796901924 -34.0744796901707
|
||||
Force two-norm initial, final = 10.728716 0.00024139276
|
||||
Force max component initial, final = 6.1727999 0.00017091779
|
||||
Final line search alpha, max atom move = 1 0.00017091779
|
||||
Iterations, force evaluations = 1000 1946
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0015331 | 0.0032095 | 0.0046681 | 2.0 | 13.93
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0037211 | 0.0053887 | 0.0069902 | 1.6 | 23.38
|
||||
Output | 0.0062087 | 0.0079064 | 0.011172 | 2.2 | 34.30
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.006544 | | | 28.39
|
||||
|
||||
Nlocal: 3.75 ave 6 max 3 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 11.25 ave 12 max 9 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 3
|
||||
Neighs: 26.25 ave 39 max 12 min
|
||||
Histogram: 1 0 0 0 1 0 1 0 0 1
|
||||
|
||||
Total # of neighbors = 105
|
||||
Ave neighs/atom = 7
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
# Dynamics
|
||||
|
||||
compute effTemp all temp/eff
|
||||
|
||||
thermo 1000
|
||||
thermo_style custom step pe temp press
|
||||
thermo_modify temp effTemp
|
||||
|
||||
velocity all create 300.0 4928459 dist gaussian rot yes mom yes
|
||||
|
||||
timestep 0.005
|
||||
fix 1 all nve/eff
|
||||
|
||||
# the custom dump includes the radii
|
||||
dump 2 all custom 1000 ${sname}.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 2 all custom 1000 ch4.nve.lammpstrj id type q c_1[1] c_1[2] x y z
|
||||
dump 3 all xyz 1000 ${sname}.nve.xyz
|
||||
dump 3 all xyz 1000 ch4.nve.xyz
|
||||
|
||||
run 100000
|
||||
Generated 0 of 3 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 5.401 | 5.401 | 5.401 Mbytes
|
||||
Step PotEng Temp Press
|
||||
1000 -34.07448 1050 391.71277
|
||||
2000 -34.065618 583.70724 -617.78946
|
||||
3000 -34.063563 475.53779 661.75865
|
||||
4000 -34.06119 350.74901 -449.8917
|
||||
5000 -34.065201 561.76559 -130.73147
|
||||
6000 -34.065798 593.21893 753.94281
|
||||
7000 -34.067408 677.86552 -409.14034
|
||||
8000 -34.065662 586.02658 446.74947
|
||||
9000 -34.062939 442.6953 413.93386
|
||||
10000 -34.060101 293.35262 -1202.4169
|
||||
11000 -34.064946 548.37877 344.89658
|
||||
12000 -34.067324 673.52389 444.40605
|
||||
13000 -34.063275 460.44923 -854.41022
|
||||
14000 -34.064667 533.59655 1541.2922
|
||||
15000 -34.063344 464.01572 -777.83895
|
||||
16000 -34.064461 522.76554 -2.2050586
|
||||
17000 -34.061202 351.31261 -148.09486
|
||||
18000 -34.066534 631.89021 -236.72076
|
||||
19000 -34.065169 560.16576 1359.8928
|
||||
20000 -34.063042 448.14707 -663.76152
|
||||
21000 -34.060695 324.66945 -168.3252
|
||||
22000 -34.065376 570.90677 -831.8481
|
||||
23000 -34.063127 452.62391 767.31463
|
||||
24000 -34.064572 528.62018 -108.63204
|
||||
25000 -34.06584 595.41818 610.87995
|
||||
26000 -34.066885 650.4263 -894.11862
|
||||
27000 -34.062035 395.1876 1754.1737
|
||||
28000 -34.060697 324.71187 -2621.333
|
||||
29000 -34.066777 644.68166 1550.7046
|
||||
30000 -34.066421 625.9368 -507.12512
|
||||
31000 -34.066163 612.3605 610.12993
|
||||
32000 -34.063108 451.66459 -48.049967
|
||||
33000 -34.062834 437.21062 -606.58502
|
||||
34000 -34.061656 375.26971 -158.76936
|
||||
35000 -34.064938 547.90576 273.26572
|
||||
36000 -34.067508 683.20936 360.05973
|
||||
37000 -34.067582 686.96938 -385.62265
|
||||
38000 -34.063213 457.13708 412.74004
|
||||
39000 -34.06272 431.16474 -595.05437
|
||||
40000 -34.062285 408.38247 456.29631
|
||||
41000 -34.064078 502.65934 -1149.196
|
||||
42000 -34.066408 625.33356 1402.5676
|
||||
43000 -34.065948 601.04311 -772.96544
|
||||
44000 -34.064113 504.47553 179.83988
|
||||
45000 -34.060572 318.08821 222.85125
|
||||
46000 -34.063614 478.25613 -409.06152
|
||||
47000 -34.064813 541.37361 613.37159
|
||||
48000 -34.065602 582.88704 -743.72019
|
||||
49000 -34.063922 494.52189 475.22811
|
||||
50000 -34.064616 530.95516 288.46302
|
||||
51000 -34.062038 395.30091 -479.68548
|
||||
52000 -34.06497 549.50477 -305.82851
|
||||
53000 -34.065577 581.56927 964.95886
|
||||
54000 -34.06766 691.14533 -437.95563
|
||||
55000 -34.064707 535.85441 1058.0886
|
||||
56000 -34.062481 418.62259 -1010.5517
|
||||
57000 -34.064996 551.02074 -33.54291
|
||||
58000 -34.064281 513.27818 375.07194
|
||||
59000 -34.066177 613.11494 -464.71576
|
||||
60000 -34.064718 536.306 1010.9545
|
||||
61000 -34.065746 590.47317 -1056.9192
|
||||
62000 -34.063252 459.22005 1525.6789
|
||||
63000 -34.06226 407.05859 -1743.9974
|
||||
64000 -34.063836 489.91026 762.61836
|
||||
65000 -34.069569 791.63831 322.35333
|
||||
66000 -34.065557 580.46799 875.11714
|
||||
67000 -34.064916 546.74052 -1349.5741
|
||||
68000 -34.062962 443.93438 1178.1978
|
||||
69000 -34.063064 449.3052 -1659.8695
|
||||
70000 -34.063596 477.36452 1322.0559
|
||||
71000 -34.065424 573.49586 -131.11749
|
||||
72000 -34.06521 562.24612 -415.25895
|
||||
73000 -34.06339 466.38351 724.08642
|
||||
74000 -34.062286 408.37673 -1093.6751
|
||||
75000 -34.065545 579.81257 586.8907
|
||||
76000 -34.066774 644.62609 -356.7044
|
||||
77000 -34.064479 523.75235 1545.8498
|
||||
78000 -34.065506 577.88123 -1014.0878
|
||||
79000 -34.062875 439.30997 241.55748
|
||||
80000 -34.06306 449.06553 -799.58139
|
||||
81000 -34.063338 463.64261 1528.4412
|
||||
82000 -34.066812 646.55603 -1350.9377
|
||||
83000 -34.064724 536.63793 1338.2148
|
||||
84000 -34.063774 486.717 -875.60363
|
||||
85000 -34.06156 370.19433 617.85579
|
||||
86000 -34.063628 478.9961 -135.13703
|
||||
87000 -34.065141 558.62541 -756.91518
|
||||
88000 -34.066732 642.27743 1158.5797
|
||||
89000 -34.067351 674.92164 -300.79164
|
||||
90000 -34.063624 478.70378 386.44004
|
||||
91000 -34.061884 387.27577 -774.22945
|
||||
92000 -34.061364 359.79856 500.36442
|
||||
93000 -34.065723 589.31234 -469.57015
|
||||
94000 -34.065006 551.46665 819.01826
|
||||
95000 -34.065409 572.7351 -676.74519
|
||||
96000 -34.06233 410.60509 1382.9732
|
||||
97000 -34.0615 366.99019 -1714.2302
|
||||
98000 -34.061152 348.67783 352.89211
|
||||
99000 -34.066217 615.29222 193.8722
|
||||
100000 -34.067739 695.32836 206.03841
|
||||
101000 -34.067313 672.90918 928.0541
|
||||
Loop time of 1.62544 on 4 procs for 100000 steps with 15 atoms
|
||||
|
||||
Performance: 26577371.575 fs/day, 0.000 hours/fs, 61521.693 timesteps/s, 922.825 katom-step/s
|
||||
93.6% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.066581 | 0.15332 | 0.25928 | 21.7 | 9.43
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.18521 | 0.29733 | 0.3879 | 16.1 | 18.29
|
||||
Output | 0.66513 | 0.81838 | 1.1333 | 20.4 | 50.35
|
||||
Modify | 0.01285 | 0.014237 | 0.016092 | 1.0 | 0.88
|
||||
Other | | 0.3422 | | | 21.05
|
||||
|
||||
Nlocal: 3.75 ave 5 max 3 min
|
||||
Histogram: 2 0 0 0 0 1 0 0 0 1
|
||||
Nghost: 11.25 ave 12 max 10 min
|
||||
Histogram: 1 0 0 0 0 1 0 0 0 2
|
||||
Neighs: 26.25 ave 47 max 10 min
|
||||
Histogram: 2 0 0 0 0 0 0 1 0 1
|
||||
|
||||
Total # of neighbors = 105
|
||||
Ave neighs/atom = 7
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
Total wall time: 0:00:01
|
||||
2124
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.min.g++.1
Normal file
2124
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.min.g++.1
Normal file
File diff suppressed because it is too large
Load Diff
2124
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.min.g++.4
Normal file
2124
examples/PACKAGES/eff/CH4/log.12Aug24.ch4.min.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
20200
examples/PACKAGES/eff/CH4/log.12Aug24.ch4_ionized.dynamics.g++.1
Normal file
20200
examples/PACKAGES/eff/CH4/log.12Aug24.ch4_ionized.dynamics.g++.1
Normal file
File diff suppressed because it is too large
Load Diff
20200
examples/PACKAGES/eff/CH4/log.12Aug24.ch4_ionized.dynamics.g++.4
Normal file
20200
examples/PACKAGES/eff/CH4/log.12Aug24.ch4_ionized.dynamics.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
@ -3,12 +3,11 @@
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index Si2H6
|
||||
log ${sname}.log
|
||||
variable sname index Si2H6
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
@ -23,7 +22,7 @@ variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
comm_modify vel yes
|
||||
comm_modify vel yes
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
@ -39,12 +38,12 @@ thermo_modify temp effTemp press effPress
|
||||
# Minimization
|
||||
|
||||
min_style cg
|
||||
dump 1 all xyz 2 ${sname}.min.xyz
|
||||
#dump 1 all xyz 2 ${sname}.min.xyz
|
||||
compute 1 all property/atom spin eradius erforce
|
||||
dump 2 all custom 2 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
#dump 2 all custom 2 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
min_modify line quadratic
|
||||
minimize 0 1.0e-5 1000 10000
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
#undump 1
|
||||
#undump 2
|
||||
|
||||
|
||||
@ -3,18 +3,17 @@
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index Si2H6.ang
|
||||
log ${sname}.log
|
||||
variable sname index Si2H6.ang
|
||||
|
||||
units real
|
||||
newton on
|
||||
boundary f f f
|
||||
units real
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
|
||||
pair_style eff/cut 529.177249
|
||||
pair_style eff/cut 529.177249 ecp 1 Si
|
||||
pair_coeff * *
|
||||
|
||||
compute energies all pair eff/cut
|
||||
@ -23,7 +22,7 @@ variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
comm_modify vel yes
|
||||
comm_modify vel yes
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
@ -39,21 +38,21 @@ thermo_modify temp effTemp press effPress
|
||||
# Minimization
|
||||
|
||||
min_style cg
|
||||
dump 1 all xyz 10 ${sname}.min.xyz
|
||||
#dump 1 all xyz 10 ${sname}.min.xyz
|
||||
compute 1 all property/atom spin eradius erforce
|
||||
dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
#dump 2 all custom 10 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
min_modify line quadratic
|
||||
minimize 0 1.0e-6 2000 10000
|
||||
|
||||
undump 1
|
||||
undump 2
|
||||
#undump 1
|
||||
#undump 2
|
||||
|
||||
# Equilibrate at 300K
|
||||
velocity all create 300.0 4928459 rot yes mom yes dist gaussian
|
||||
|
||||
timestep 0.001
|
||||
|
||||
dump 1 all custom 1000 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
#dump 1 all custom 1000 ${sname}.nvt.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
#fix 0 all langevin/eff 300.0 300.0 0.1
|
||||
fix 1 all nvt/eff temp 300.0 300.0 0.1
|
||||
|
||||
|
||||
20189
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.ang.g++.1
Normal file
20189
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.ang.g++.1
Normal file
File diff suppressed because it is too large
Load Diff
20189
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.ang.g++.4
Normal file
20189
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.ang.g++.4
Normal file
File diff suppressed because it is too large
Load Diff
185
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.g++.1
Normal file
185
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.g++.1
Normal file
@ -0,0 +1,185 @@
|
||||
LAMMPS (27 Jun 2024)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
|
||||
# Created 2011-01-07
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index Si2H6
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.Si2H6
|
||||
Reading data file ...
|
||||
orthogonal box = (-1000 -1000 -1000) to (1000 1000 1000)
|
||||
1 by 1 by 1 MPI processor grid
|
||||
reading atoms ...
|
||||
22 atoms
|
||||
read_data CPU = 0.000 seconds
|
||||
|
||||
pair_style eff/cut 1000.0 ecp 1 Si
|
||||
pair_coeff * *
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
thermo 2
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
# Minimization
|
||||
|
||||
min_style cg
|
||||
#dump 1 all xyz 2 ${sname}.min.xyz
|
||||
compute 1 all property/atom spin eradius erforce
|
||||
#dump 2 all custom 2 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
min_modify line quadratic
|
||||
minimize 0 1.0e-5 1000 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
|
||||
@Article{Jaramillo-Botero11,
|
||||
author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
|
||||
title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
|
||||
journal = {J.~Comp.\ Chem.},
|
||||
year = 2011,
|
||||
volume = 32,
|
||||
number = 3,
|
||||
pages = {497--512}
|
||||
}
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 3 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 = 1002
|
||||
ghost atom cutoff = 1002
|
||||
binsize = 501, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.098 | 6.098 | 6.098 Mbytes
|
||||
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||
0 -8.5010994 -8.5010994 0 5.4885963 1.6463577 -15.636053 0 0 3948.0425 3948.0425
|
||||
2 -8.67691 -8.67691 0 5.5258385 1.589403 -15.792152 0 0 3880.1721 3880.1721
|
||||
4 -8.848848 -8.848848 0 5.5663359 1.5311327 -15.946317 0 0 3788.6697 3788.6697
|
||||
6 -9.0177692 -9.0177692 0 5.6106795 1.4710658 -16.099514 0 0 3671.1737 3671.1737
|
||||
8 -9.185303 -9.185303 0 5.6598348 1.4083124 -16.25345 0 0 3523.4287 3523.4287
|
||||
10 -9.3547798 -9.3547798 0 5.7155927 1.3410774 -16.41145 0 0 3336.9891 3336.9891
|
||||
12 -9.5342746 -9.5342746 0 5.7820671 1.2650232 -16.581365 0 0 3091.6153 3091.6153
|
||||
14 -9.753773 -9.753773 0 5.8743943 1.1639 -16.792067 0 0 2711.1247 2711.1247
|
||||
16 -10.097143 -10.097143 0 6.0386279 0.98467639 -17.120448 0 0 1912.0559 1912.0559
|
||||
18 -10.206415 -10.206415 0 6.0972556 0.92111471 -17.224785 0 0 1604.9272 1604.9272
|
||||
20 -10.28471 -10.28471 0 6.1543746 0.86786676 -17.306951 0 0 1325.3681 1325.3681
|
||||
22 -10.343227 -10.343227 0 6.2122367 0.82042286 -17.375887 0 0 1062.6534 1062.6534
|
||||
24 -10.386164 -10.386164 0 6.2699963 0.77763016 -17.43379 0 0 820.84479 820.84479
|
||||
26 -10.416263 -10.416263 0 6.3255676 0.73934069 -17.481171 0 0 608.7375 608.7375
|
||||
28 -10.436521 -10.436521 0 6.3761026 0.70612619 -17.51875 0 0 434.68899 434.68899
|
||||
30 -10.450247 -10.450247 0 6.4147546 0.68147364 -17.546475 0 0 302.62232 302.62232
|
||||
32 -10.456683 -10.456683 0 6.416721 0.67361461 -17.547019 0 0 223.07929 223.07929
|
||||
34 -10.458069 -10.458069 0 6.3974543 0.66990042 -17.525424 0 0 164.78914 164.78914
|
||||
36 -10.458558 -10.458558 0 6.3763802 0.66472241 -17.49966 0 0 100.618 100.618
|
||||
38 -10.459231 -10.459231 0 6.3293189 0.66038284 -17.448933 0 0 -3.1075375 -3.1075375
|
||||
40 -10.459346 -10.459346 0 6.3132377 0.65807627 -17.43066 0 0 -29.981737 -29.981737
|
||||
42 -10.459366 -10.459366 0 6.3179452 0.65719131 -17.434503 0 0 -45.500522 -45.500522
|
||||
44 -10.459413 -10.459413 0 6.2985544 0.66239121 -17.420359 0 0 14.638842 14.638842
|
||||
46 -10.459499 -10.459499 0 6.3129457 0.65696218 -17.429407 0 0 -46.926115 -46.926115
|
||||
48 -10.459522 -10.459522 0 6.3120038 0.65909539 -17.430621 0 0 -27.058486 -27.058486
|
||||
50 -10.459532 -10.459532 0 6.3113769 0.65958039 -17.430489 0 0 -16.067028 -16.067028
|
||||
52 -10.459536 -10.459536 0 6.3181474 0.65939215 -17.437076 0 0 -15.311526 -15.311526
|
||||
54 -10.459539 -10.459539 0 6.3204818 0.66055005 -17.440571 0 0 -0.10049441 -0.10049441
|
||||
56 -10.459539 -10.459539 0 6.320264 0.6605463 -17.440349 0 0 -0.12138433 -0.12138433
|
||||
58 -10.459539 -10.459539 0 6.3204128 0.66045741 -17.440409 0 0 -1.2175181 -1.2175181
|
||||
60 -10.459539 -10.459539 0 6.3201688 0.66048114 -17.440189 0 0 -0.80979907 -0.80979907
|
||||
62 -10.459539 -10.459539 0 6.3201369 0.6605348 -17.440211 0 0 -0.85945578 -0.85945578
|
||||
64 -10.459539 -10.459539 0 6.3201036 0.66047761 -17.44012 0 0 -0.95534716 -0.95534716
|
||||
66 -10.459539 -10.459539 0 6.3201475 0.66049137 -17.440178 0 0 -0.89220676 -0.89220676
|
||||
68 -10.459539 -10.459539 0 6.3201605 0.6605388 -17.440238 0 0 -0.44630696 -0.44630696
|
||||
70 -10.459539 -10.459539 0 6.3202978 0.66049413 -17.440331 0 0 -0.72919073 -0.72919073
|
||||
72 -10.459539 -10.459539 0 6.3202928 0.66056004 -17.440392 0 0 -0.049410442 -0.049410442
|
||||
74 -10.459539 -10.459539 0 6.3204368 0.66055883 -17.440535 0 0 -0.025063323 -0.025063323
|
||||
76 -10.459539 -10.459539 0 6.3204403 0.66054902 -17.440528 0 0 -0.010779864 -0.010779864
|
||||
78 -10.459539 -10.459539 0 6.3203876 0.66056716 -17.440494 0 0 0.087251782 0.087251782
|
||||
80 -10.459539 -10.459539 0 6.3203944 0.66054525 -17.440479 0 0 -0.13822668 -0.13822668
|
||||
82 -10.459539 -10.459539 0 6.3203511 0.66055332 -17.440443 0 0 -0.043786214 -0.043786214
|
||||
84 -10.459539 -10.459539 0 6.32037 0.66054938 -17.440458 0 0 -0.10833476 -0.10833476
|
||||
86 -10.459539 -10.459539 0 6.3203586 0.66055472 -17.440452 0 0 -0.04772439 -0.04772439
|
||||
88 -10.459539 -10.459539 0 6.3203709 0.66055294 -17.440463 0 0 -0.055815521 -0.055815521
|
||||
Loop time of 0.00236996 on 1 procs for 88 steps with 22 atoms
|
||||
|
||||
99.5% CPU use with 1 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = force tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-8.50109938620961 -10.4595390706544 -10.459539070672
|
||||
Force two-norm initial, final = 3.2945156 4.8001667e-06
|
||||
Force max component initial, final = 1.8019385 2.1391495e-06
|
||||
Final line search alpha, max atom move = 1 2.1391495e-06
|
||||
Iterations, force evaluations = 88 127
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0019013 | 0.0019013 | 0.0019013 | 0.0 | 80.23
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 7.926e-06 | 7.926e-06 | 7.926e-06 | 0.0 | 0.33
|
||||
Output | 0.00027587 | 0.00027587 | 0.00027587 | 0.0 | 11.64
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.0001848 | | | 7.80
|
||||
|
||||
Nlocal: 22 ave 22 max 22 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 231 ave 231 max 231 min
|
||||
Histogram: 1 0 0 0 0 0 0 0 0 0
|
||||
|
||||
Total # of neighbors = 231
|
||||
Ave neighs/atom = 10.5
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
#undump 2
|
||||
|
||||
Total wall time: 0:00:00
|
||||
185
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.g++.4
Normal file
185
examples/PACKAGES/eff/ECP/Si2H6/log.12Aug24.Si2H6.g++.4
Normal file
@ -0,0 +1,185 @@
|
||||
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
|
||||
|
||||
# Created 2011-01-07
|
||||
|
||||
# General parameters
|
||||
|
||||
variable sname index Si2H6
|
||||
|
||||
units electron
|
||||
newton on
|
||||
boundary f f f
|
||||
|
||||
atom_style electron
|
||||
|
||||
read_data data.${sname}
|
||||
read_data data.Si2H6
|
||||
Reading data file ...
|
||||
orthogonal box = (-1000 -1000 -1000) to (1000 1000 1000)
|
||||
1 by 2 by 2 MPI processor grid
|
||||
reading atoms ...
|
||||
22 atoms
|
||||
read_data CPU = 0.001 seconds
|
||||
|
||||
pair_style eff/cut 1000.0 ecp 1 Si
|
||||
pair_coeff * *
|
||||
|
||||
compute energies all pair eff/cut
|
||||
variable eke equal c_energies[1]
|
||||
variable epauli equal c_energies[2]
|
||||
variable estatics equal c_energies[3]
|
||||
variable errestrain equal c_energies[4]
|
||||
|
||||
comm_modify vel yes
|
||||
|
||||
compute peratom all stress/atom NULL
|
||||
compute p all reduce sum c_peratom[1] c_peratom[2] c_peratom[3]
|
||||
variable press equal -(c_p[1]+c_p[2]+c_p[3])/(3*vol)
|
||||
|
||||
compute effTemp all temp/eff
|
||||
compute effPress all pressure effTemp
|
||||
|
||||
thermo 2
|
||||
thermo_style custom step etotal pe ke v_eke v_epauli v_estatics v_errestrain temp press v_press
|
||||
thermo_modify temp effTemp press effPress
|
||||
|
||||
# Minimization
|
||||
|
||||
min_style cg
|
||||
#dump 1 all xyz 2 ${sname}.min.xyz
|
||||
compute 1 all property/atom spin eradius erforce
|
||||
#dump 2 all custom 2 ${sname}.min.lammpstrj id type q c_1[1] c_1[2] x y z fx fy fz c_1[3]
|
||||
min_modify line quadratic
|
||||
minimize 0 1.0e-5 1000 10000
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- EFF package: doi:10.1002/jcc.21637
|
||||
|
||||
@Article{Jaramillo-Botero11,
|
||||
author = {A. Jaramillo-Botero and J. Su and A. Qi and Goddard, III, W. A.},
|
||||
title = {Large-Scale, Long-Term Nonadiabatic Electron Molecular Dynamics for Describing Material Properties and Phenomena in Extreme Environments},
|
||||
journal = {J.~Comp.\ Chem.},
|
||||
year = 2011,
|
||||
volume = 32,
|
||||
number = 3,
|
||||
pages = {497--512}
|
||||
}
|
||||
|
||||
- Type Label Framework: https://doi.org/10.1021/acs.jpcb.3c08419
|
||||
|
||||
@Article{Gissinger24,
|
||||
author = {Jacob R. Gissinger, Ilia Nikiforov, Yaser Afshar, Brendon Waters, Moon-ki Choi, Daniel S. Karls, Alexander Stukowski, Wonpil Im, Hendrik Heinz, Axel Kohlmeyer, and Ellad B. Tadmor},
|
||||
title = {Type Label Framework for Bonded Force Fields in LAMMPS},
|
||||
journal = {J. Phys. Chem. B},
|
||||
year = 2024,
|
||||
volume = 128,
|
||||
number = 13,
|
||||
pages = {3282–-3297}
|
||||
}
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Generated 0 of 3 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 = 1002
|
||||
ghost atom cutoff = 1002
|
||||
binsize = 501, bins = 4 4 4
|
||||
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
||||
(1) pair eff/cut, perpetual
|
||||
attributes: half, newton on
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 6.113 | 6.113 | 6.113 Mbytes
|
||||
Step TotEng PotEng KinEng v_eke v_epauli v_estatics v_errestrain Temp Press v_press
|
||||
0 -8.5010994 -8.5010994 0 5.4885963 1.6463577 -15.636053 0 0 3948.0425 3948.0425
|
||||
2 -8.67691 -8.67691 0 5.5258385 1.589403 -15.792152 0 0 3880.1721 3880.1721
|
||||
4 -8.848848 -8.848848 0 5.5663359 1.5311327 -15.946317 0 0 3788.6697 3788.6697
|
||||
6 -9.0177692 -9.0177692 0 5.6106795 1.4710658 -16.099514 0 0 3671.1737 3671.1737
|
||||
8 -9.185303 -9.185303 0 5.6598348 1.4083124 -16.25345 0 0 3523.4287 3523.4287
|
||||
10 -9.3547798 -9.3547798 0 5.7155927 1.3410774 -16.41145 0 0 3336.9891 3336.9891
|
||||
12 -9.5342746 -9.5342746 0 5.7820671 1.2650232 -16.581365 0 0 3091.6153 3091.6153
|
||||
14 -9.753773 -9.753773 0 5.8743943 1.1639 -16.792067 0 0 2711.1247 2711.1247
|
||||
16 -10.097143 -10.097143 0 6.0386279 0.98467639 -17.120448 0 0 1912.0559 1912.0559
|
||||
18 -10.206415 -10.206415 0 6.0972556 0.92111471 -17.224785 0 0 1604.9272 1604.9272
|
||||
20 -10.28471 -10.28471 0 6.1543746 0.86786676 -17.306951 0 0 1325.3681 1325.3681
|
||||
22 -10.343227 -10.343227 0 6.2122367 0.82042286 -17.375887 0 0 1062.6534 1062.6534
|
||||
24 -10.386164 -10.386164 0 6.2699963 0.77763016 -17.43379 0 0 820.84479 820.84479
|
||||
26 -10.416263 -10.416263 0 6.3255676 0.73934069 -17.481171 0 0 608.7375 608.7375
|
||||
28 -10.436521 -10.436521 0 6.3761026 0.70612619 -17.51875 0 0 434.68899 434.68899
|
||||
30 -10.450247 -10.450247 0 6.4147546 0.68147364 -17.546475 0 0 302.62232 302.62232
|
||||
32 -10.456683 -10.456683 0 6.416721 0.67361461 -17.547019 0 0 223.07929 223.07929
|
||||
34 -10.458069 -10.458069 0 6.3974543 0.66990042 -17.525424 0 0 164.78914 164.78914
|
||||
36 -10.458558 -10.458558 0 6.3763802 0.66472241 -17.49966 0 0 100.618 100.618
|
||||
38 -10.459231 -10.459231 0 6.3293189 0.66038284 -17.448933 0 0 -3.1075375 -3.1075375
|
||||
40 -10.459346 -10.459346 0 6.3132377 0.65807627 -17.43066 0 0 -29.981737 -29.981737
|
||||
42 -10.459366 -10.459366 0 6.3179452 0.65719131 -17.434503 0 0 -45.500522 -45.500522
|
||||
44 -10.459413 -10.459413 0 6.2985544 0.66239121 -17.420359 0 0 14.638842 14.638842
|
||||
46 -10.459499 -10.459499 0 6.3129457 0.65696218 -17.429407 0 0 -46.926115 -46.926115
|
||||
48 -10.459522 -10.459522 0 6.3120038 0.65909539 -17.430621 0 0 -27.058486 -27.058486
|
||||
50 -10.459532 -10.459532 0 6.3113769 0.65958039 -17.430489 0 0 -16.067028 -16.067028
|
||||
52 -10.459536 -10.459536 0 6.3181474 0.65939215 -17.437076 0 0 -15.311525 -15.311525
|
||||
54 -10.459539 -10.459539 0 6.3204818 0.66055005 -17.440571 0 0 -0.1004938 -0.1004938
|
||||
56 -10.459539 -10.459539 0 6.320264 0.6605463 -17.440349 0 0 -0.12138436 -0.12138436
|
||||
58 -10.459539 -10.459539 0 6.3204128 0.66045741 -17.440409 0 0 -1.2175176 -1.2175176
|
||||
60 -10.459539 -10.459539 0 6.3201688 0.66048114 -17.440189 0 0 -0.80979946 -0.80979946
|
||||
62 -10.459539 -10.459539 0 6.3201369 0.6605348 -17.440211 0 0 -0.85945162 -0.85945162
|
||||
64 -10.459539 -10.459539 0 6.3201036 0.66047761 -17.44012 0 0 -0.95534903 -0.95534903
|
||||
66 -10.459539 -10.459539 0 6.3201475 0.66049137 -17.440178 0 0 -0.89220297 -0.89220297
|
||||
68 -10.459539 -10.459539 0 6.3201605 0.6605388 -17.440238 0 0 -0.44631358 -0.44631358
|
||||
70 -10.459539 -10.459539 0 6.3202978 0.66049413 -17.440331 0 0 -0.72919322 -0.72919322
|
||||
72 -10.459539 -10.459539 0 6.3202928 0.66056005 -17.440392 0 0 -0.049401694 -0.049401694
|
||||
74 -10.459539 -10.459539 0 6.3204368 0.66055883 -17.440535 0 0 -0.025056381 -0.025056381
|
||||
76 -10.459539 -10.459539 0 6.3204403 0.66054902 -17.440528 0 0 -0.010774653 -0.010774653
|
||||
78 -10.459539 -10.459539 0 6.3203876 0.66056716 -17.440494 0 0 0.087250755 0.087250755
|
||||
80 -10.459539 -10.459539 0 6.3203944 0.66054525 -17.440479 0 0 -0.13822694 -0.13822694
|
||||
82 -10.459539 -10.459539 0 6.3203511 0.66055332 -17.440443 0 0 -0.043784806 -0.043784806
|
||||
84 -10.459539 -10.459539 0 6.32037 0.66054937 -17.440458 0 0 -0.10833935 -0.10833935
|
||||
86 -10.459539 -10.459539 0 6.3203586 0.66055472 -17.440452 0 0 -0.047719128 -0.047719128
|
||||
88 -10.459539 -10.459539 0 6.3203709 0.66055294 -17.440463 0 0 -0.055818341 -0.055818341
|
||||
Loop time of 0.00213866 on 4 procs for 88 steps with 22 atoms
|
||||
|
||||
95.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = force tolerance
|
||||
Energy initial, next-to-last, final =
|
||||
-8.50109938620958 -10.4595390706543 -10.459539070672
|
||||
Force two-norm initial, final = 3.2945156 4.7997573e-06
|
||||
Force max component initial, final = 1.8019385 2.1386971e-06
|
||||
Final line search alpha, max atom move = 1 2.1386971e-06
|
||||
Iterations, force evaluations = 88 127
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.00027642 | 0.00052972 | 0.00096856 | 0.0 | 24.77
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.00035997 | 0.00081245 | 0.0010746 | 0.0 | 37.99
|
||||
Output | 0.00037064 | 0.00039193 | 0.00045231 | 0.0 | 18.33
|
||||
Modify | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Other | | 0.0004046 | | | 18.92
|
||||
|
||||
Nlocal: 5.5 ave 7 max 3 min
|
||||
Histogram: 1 0 0 0 0 0 0 2 0 1
|
||||
Nghost: 16.5 ave 19 max 15 min
|
||||
Histogram: 1 0 2 0 0 0 0 0 0 1
|
||||
Neighs: 57.75 ave 109 max 29 min
|
||||
Histogram: 1 1 0 1 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 231
|
||||
Ave neighs/atom = 10.5
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
#undump 1
|
||||
#undump 2
|
||||
|
||||
Total wall time: 0:00:00
|
||||
1
examples/PACKAGES/electron_stopping/AlCu.eam.alloy
Symbolic link
1
examples/PACKAGES/electron_stopping/AlCu.eam.alloy
Symbolic link
@ -0,0 +1 @@
|
||||
../../../potentials/AlCu.eam.alloy
|
||||
1
examples/PACKAGES/electron_stopping/SiC.tersoff.zbl
Symbolic link
1
examples/PACKAGES/electron_stopping/SiC.tersoff.zbl
Symbolic link
@ -0,0 +1 @@
|
||||
../../../potentials/SiC.tersoff.zbl
|
||||
@ -12,8 +12,8 @@ region box block -10 10 -10 10 -10 10
|
||||
create_box 2 box
|
||||
create_atoms 1 box
|
||||
|
||||
pair_style eam/alloy
|
||||
pair_coeff * * ../../../../potentials/AlCu.eam.alloy Al Cu
|
||||
pair_style eam/alloy
|
||||
pair_coeff * * AlCu.eam.alloy Al Cu
|
||||
|
||||
mass 1 26.982
|
||||
mass 2 63.546
|
||||
|
||||
@ -13,7 +13,7 @@ create_box 1 box
|
||||
create_atoms 1 box
|
||||
|
||||
pair_style tersoff/zbl
|
||||
pair_coeff * * ../../../../potentials/SiC.tersoff.zbl Si
|
||||
pair_coeff * * SiC.tersoff.zbl Si
|
||||
|
||||
mass 1 28.0855
|
||||
|
||||
|
||||
1
examples/PACKAGES/interlayer/aip_water_2dm/COH.DMC.aip.water.2dm
Symbolic link
1
examples/PACKAGES/interlayer/aip_water_2dm/COH.DMC.aip.water.2dm
Symbolic link
@ -0,0 +1 @@
|
||||
../../../../potentials/COH.DMC.aip.water.2dm
|
||||
@ -4,26 +4,26 @@ boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
read_data ./gra_water.data
|
||||
mass 1 12.0107 # carbon mass (g/mole)
|
||||
mass 1 12.0107 # carbon mass (g/mole)
|
||||
mass 2 15.9994 # oxygen mass (g/mole)
|
||||
mass 3 1.008 # hydrogen mass (g/mole)
|
||||
mass 3 1.008 # hydrogen mass (g/mole)
|
||||
# Separate atom groups
|
||||
group gr molecule 1
|
||||
group water molecule 2
|
||||
group gr molecule 1
|
||||
group water molecule 2
|
||||
######################## Potential defition ##############################
|
||||
# Interlayer potential
|
||||
pair_style hybrid/overlay aip/water/2dm 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
|
||||
####################################################################
|
||||
pair_coeff 1 1 none
|
||||
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
|
||||
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
||||
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
||||
pair_coeff * * aip/water/2dm COH.aip.water.2dm C Ow Hw # C-H2O
|
||||
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
||||
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
||||
pair_coeff * * aip/water/2dm COH.DMC.aip.water.2dm C Ow Hw # C-H2O
|
||||
# bond and angle
|
||||
bond_style harmonic
|
||||
bond_coeff 1 0.0 0.9572
|
||||
angle_style harmonic
|
||||
angle_coeff 1 0.0 104.52
|
||||
bond_style harmonic
|
||||
bond_coeff 1 0.0 0.9572
|
||||
angle_style harmonic
|
||||
angle_coeff 1 0.0 104.52
|
||||
# define kspace calculation
|
||||
kspace_style pppm/tip4p 1E-5
|
||||
# Neighbor update settings
|
||||
@ -31,21 +31,21 @@ neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
|
||||
####################################################################
|
||||
# Calculate pair energy
|
||||
compute 1 all pair lj/cut/tip4p/long
|
||||
compute 2 all pair aip/water/2dm
|
||||
compute wt water temp
|
||||
variable TIP4P equal c_1
|
||||
variable EILP equal c_2 # total interlayer energy
|
||||
variable temp_wt equal c_wt
|
||||
compute 1 all pair lj/cut/tip4p/long
|
||||
compute 2 all pair aip/water/2dm
|
||||
compute wt water temp
|
||||
variable TIP4P equal c_1
|
||||
variable EILP equal c_2 # total interlayer energy
|
||||
variable temp_wt equal c_wt
|
||||
############# Output ##############
|
||||
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
|
||||
thermo 100
|
||||
thermo_modify lost error
|
||||
|
||||
fix subf gr setforce 0.0 0.0 0.0
|
||||
fix 1 water shake 0.0001 20 100 b 1 a 1
|
||||
fix subf gr setforce 0.0 0.0 0.0
|
||||
fix 1 water shake 0.0001 20 100 b 1 a 1
|
||||
|
||||
timestep 1e-3
|
||||
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
||||
fix 2 water nve
|
||||
run 1000
|
||||
timestep 1e-3
|
||||
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
||||
fix 2 water nve
|
||||
run 1000
|
||||
|
||||
@ -4,26 +4,26 @@ boundary p p p
|
||||
atom_style full
|
||||
processors * * 1 # domain decomposition over x and y
|
||||
read_data ./gra_water.data
|
||||
mass 1 12.0107 # carbon mass (g/mole)
|
||||
mass 1 12.0107 # carbon mass (g/mole)
|
||||
mass 2 15.9994 # oxygen mass (g/mole)
|
||||
mass 3 1.008 # hydrogen mass (g/mole)
|
||||
mass 3 1.008 # hydrogen mass (g/mole)
|
||||
# Separate atom groups
|
||||
group gr molecule 1
|
||||
group water molecule 2
|
||||
group gr molecule 1
|
||||
group water molecule 2
|
||||
######################## Potential defition ##############################
|
||||
# Interlayer potential
|
||||
pair_style hybrid/overlay aip/water/2dm/opt 16.0 lj/cut/tip4p/long 2 3 1 1 0.1546 10 8.5
|
||||
####################################################################
|
||||
pair_coeff 1 1 none
|
||||
pair_coeff 2 2 lj/cut/tip4p/long 8.0313e-3 3.1589 # O-O
|
||||
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
||||
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
||||
pair_coeff * * aip/water/2dm/opt COH.aip.water.2dm C Ow Hw # C-H2O
|
||||
pair_coeff 2 3 lj/cut/tip4p/long 0.0 0.0 # O-H
|
||||
pair_coeff 3 3 lj/cut/tip4p/long 0.0 0.0 # H-H
|
||||
pair_coeff * * aip/water/2dm/opt COH.DMC.aip.water.2dm C Ow Hw # C-H2O
|
||||
# bond and angle
|
||||
bond_style harmonic
|
||||
bond_coeff 1 0.0 0.9572
|
||||
angle_style harmonic
|
||||
angle_coeff 1 0.0 104.52
|
||||
bond_style harmonic
|
||||
bond_coeff 1 0.0 0.9572
|
||||
angle_style harmonic
|
||||
angle_coeff 1 0.0 104.52
|
||||
# define kspace calculation
|
||||
kspace_style pppm/tip4p 1E-5
|
||||
# Neighbor update settings
|
||||
@ -31,21 +31,21 @@ neighbor 2.0 bin
|
||||
neigh_modify every 1 delay 5 check yes page 1000000 one 100000
|
||||
####################################################################
|
||||
# Calculate pair energy
|
||||
compute 1 all pair lj/cut/tip4p/long
|
||||
compute 2 all pair aip/water/2dm/opt
|
||||
compute wt water temp
|
||||
variable TIP4P equal c_1
|
||||
variable EILP equal c_2 # total interlayer energy
|
||||
variable temp_wt equal c_wt
|
||||
compute 1 all pair lj/cut/tip4p/long
|
||||
compute 2 all pair aip/water/2dm/opt
|
||||
compute wt water temp
|
||||
variable TIP4P equal c_1
|
||||
variable EILP equal c_2 # total interlayer energy
|
||||
variable temp_wt equal c_wt
|
||||
############# Output ##############
|
||||
thermo_style custom step etotal pe ke v_TIP4P v_EILP v_temp_wt
|
||||
thermo 100
|
||||
thermo_modify lost error
|
||||
|
||||
fix subf gr setforce 0.0 0.0 0.0
|
||||
fix 1 water shake 0.0001 20 100 b 1 a 1
|
||||
fix subf gr setforce 0.0 0.0 0.0
|
||||
fix 1 water shake 0.0001 20 100 b 1 a 1
|
||||
|
||||
timestep 1e-3
|
||||
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
||||
fix 2 water nve
|
||||
run 1000
|
||||
timestep 1e-3
|
||||
velocity water create 300.0 12345 dist gaussian mom yes rot yes
|
||||
fix 2 water nve
|
||||
run 1000
|
||||
|
||||
@ -457,9 +457,9 @@ mass *4 ${wheel_mass}
|
||||
variable dx equal 1.0
|
||||
variable density equal 0.001184
|
||||
|
||||
neighbor 0.5 bin
|
||||
neighbor 0.5 bin
|
||||
neigh_modify delay 0 every 1 check yes
|
||||
comm_modify cutoff 3.0
|
||||
comm_modify cutoff 3.0
|
||||
|
||||
pair_style lj/cut 1.2
|
||||
pair_coeff * * 0.0 0.0
|
||||
@ -474,7 +474,7 @@ reset_timestep 0
|
||||
#variable node_force equal "v_total_force / 178"
|
||||
#fix drag all addforce 0.0 0.0 0.0
|
||||
|
||||
velocity all set 0.0 -7.5.0 0.0 units box
|
||||
velocity all set 0.0 -7.5 0.0 units box
|
||||
|
||||
# viscosity of air is 0.0001847
|
||||
|
||||
|
||||
@ -1,4 +1,6 @@
|
||||
LAMMPS (17 Feb 2022)
|
||||
LAMMPS (27 Jun 2024 - Development - patch_27Jun2024-653-ge4a654c7cd-modified)
|
||||
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
||||
using 1 OpenMP thread(s) per MPI task
|
||||
#===========================================================================#
|
||||
# Toy car driving down a system with a floor and ceiling. #
|
||||
# #
|
||||
@ -12,6 +14,7 @@ units cgs
|
||||
dimension 3
|
||||
boundary p p f
|
||||
atom_style atomic
|
||||
processors * 1 *
|
||||
|
||||
#-------------------------------------------------------------------------#
|
||||
# Set up the simulation box
|
||||
@ -36,7 +39,7 @@ region mybox block -48 48 -90 630 -9 ${zh}
|
||||
region mybox block -48 48 -90 630 -9 87
|
||||
create_box 14 mybox
|
||||
Created orthogonal box = (-48 -90 -9) to (48 630 87)
|
||||
1 by 4 by 1 MPI processor grid
|
||||
2 by 1 by 2 MPI processor grid
|
||||
|
||||
#-------------------------------------------------------------------------#
|
||||
# Creating the regions and filling them with atoms assigned to surge_group
|
||||
@ -647,9 +650,9 @@ fix 2 all nve
|
||||
#restart 100000 ParticleRestart
|
||||
|
||||
run 100000
|
||||
generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 2.5255396
|
||||
ghost atom cutoff = 2.5255396
|
||||
@ -660,53 +663,53 @@ Neighbor list info ...
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.245 | 5.007 | 7.291 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 0 0 0 0
|
||||
5000 29877588 4.6948567e-06 0 3.6195804e-05 3.987621e-12
|
||||
10000 27827776 7.2619763e-06 0 3.6601737e-05 4.407525e-12
|
||||
15000 26336751 8.3045873e-06 0 3.6072311e-05 4.7591238e-12
|
||||
20000 25052655 8.3618019e-06 0 3.477566e-05 5.0138704e-12
|
||||
25000 23854604 8.149944e-06 0 3.3300657e-05 5.1772301e-12
|
||||
30000 21629039 8.0369285e-06 0 3.0841153e-05 5.3056994e-12
|
||||
35000 20550367 7.0527369e-06 0 2.8719681e-05 5.253199e-12
|
||||
40000 18310227 6.4085866e-06 0 2.5713675e-05 5.1263402e-12
|
||||
45000 16963286 5.9460113e-06 0 2.3830975e-05 5.0913287e-12
|
||||
50000 15639408 5.1326227e-06 0 2.1621777e-05 4.8649712e-12
|
||||
55000 14004560 4.550004e-06 0 1.9315483e-05 4.6920784e-12
|
||||
60000 12777371 3.941146e-06 0 1.7412759e-05 4.4574594e-12
|
||||
65000 10919170 3.3361501e-06 0 1.4848599e-05 4.1051819e-12
|
||||
70000 9469421.4 2.7031575e-06 0 1.2687087e-05 3.7302586e-12
|
||||
75000 7926062.4 2.054775e-06 0 1.0411489e-05 3.3099123e-12
|
||||
80000 6314071.7 1.5118865e-06 0 8.169025e-06 2.8050899e-12
|
||||
85000 4847441.7 1.0803078e-06 0 6.1911288e-06 2.3005982e-12
|
||||
90000 3260324.1 6.858841e-07 0 4.1233536e-06 1.7789287e-12
|
||||
95000 1724645.4 3.1351302e-07 0 2.1318647e-06 1.1211538e-12
|
||||
100000 218390.81 4.4631827e-08 0 2.7488861e-07 3.8685559e-13
|
||||
Loop time of 647.752 on 4 procs for 100000 steps with 5092 atoms
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.685 | 6.044 | 7.403 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
0 0 0 0 0 0
|
||||
5000 29842261 4.7942025e-06 0 3.6257904e-05 3.9879238e-12
|
||||
10000 28098061 7.2385794e-06 0 3.6863311e-05 4.4347259e-12
|
||||
15000 26888635 8.1191579e-06 0 3.6468752e-05 4.7939026e-12
|
||||
20000 24887991 8.3385518e-06 0 3.4578799e-05 4.9862342e-12
|
||||
25000 23265144 8.3946029e-06 0 3.2923828e-05 5.1750035e-12
|
||||
30000 21711263 7.6172235e-06 0 3.0508139e-05 5.2324506e-12
|
||||
35000 20102910 7.2232838e-06 0 2.8418459e-05 5.2342282e-12
|
||||
40000 18634097 6.5402802e-06 0 2.6186836e-05 5.2128024e-12
|
||||
45000 17486541 5.6292406e-06 0 2.4065889e-05 5.0867315e-12
|
||||
50000 15741195 4.96711e-06 0 2.1563581e-05 4.8546007e-12
|
||||
55000 14195280 4.6806146e-06 0 1.9647177e-05 4.7201162e-12
|
||||
60000 12378448 3.8806954e-06 0 1.693171e-05 4.3985323e-12
|
||||
65000 10976639 3.3069428e-06 0 1.4879983e-05 4.1055737e-12
|
||||
70000 9434340 2.6574414e-06 0 1.2604384e-05 3.703813e-12
|
||||
75000 7827664.3 2.1262358e-06 0 1.0379206e-05 3.3234802e-12
|
||||
80000 6487719.3 1.6234085e-06 0 8.4636294e-06 2.878629e-12
|
||||
85000 4761145.2 1.1556952e-06 0 6.175531e-06 2.3647084e-12
|
||||
90000 3196900 6.7497651e-07 0 4.0455759e-06 1.7461024e-12
|
||||
95000 1711466.2 3.2662861e-07 0 2.1310851e-06 1.1318791e-12
|
||||
100000 217597.05 4.394432e-08 0 2.7336422e-07 3.7619707e-13
|
||||
Loop time of 131.294 on 4 procs for 100000 steps with 5092 atoms
|
||||
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.036284 | 19.922 | 79.572 | 771.6 | 3.08
|
||||
Neigh | 10.175 | 17.392 | 38.739 | 295.5 | 2.69
|
||||
Comm | 0.97616 | 1.0979 | 1.2312 | 8.6 | 0.17
|
||||
Output | 0.0043794 | 0.098646 | 0.13021 | 17.3 | 0.02
|
||||
Modify | 1.2262 | 132.11 | 524.58 |1971.4 | 20.39
|
||||
Other | | 477.1 | | | 73.66
|
||||
Pair | 0.0045648 | 9.3721 | 18.946 | 306.0 | 7.14
|
||||
Neigh | 2.8643 | 5.951 | 9.063 | 125.7 | 4.53
|
||||
Comm | 0.3616 | 0.90559 | 1.7801 | 61.8 | 0.69
|
||||
Output | 0.00058742 | 0.013642 | 0.026668 | 11.2 | 0.01
|
||||
Modify | 0.17841 | 50.602 | 101.42 | 708.8 | 38.54
|
||||
Other | | 64.45 | | | 49.09
|
||||
|
||||
Nlocal: 1273 ave 5092 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19856 ave 79424 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nlocal: 1273 ave 2549 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 247 ave 496 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 19929 ave 39908 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 79424
|
||||
Ave neighs/atom = 15.5978
|
||||
Neighbor list builds = 4946
|
||||
Total # of neighbors = 79716
|
||||
Ave neighs/atom = 15.655145
|
||||
Neighbor list builds = 4954
|
||||
Dangerous builds = 0
|
||||
|
||||
unfix 1
|
||||
@ -743,114 +746,114 @@ fix 3 all langevin 100000.0 5000.0 100.0 5678
|
||||
fix 2 all nve
|
||||
|
||||
run 200000
|
||||
generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.418 | 5.179 | 7.463 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100000 218390.81 0 0 2.3025679e-07 2.3133759e-14
|
||||
105000 103860.18 6.708614e-08 0 1.7658943e-07 6.9220989e-13
|
||||
110000 97287.339 7.0116647e-08 0 1.7268996e-07 7.4104867e-13
|
||||
115000 92211.102 6.7456604e-08 0 1.6467788e-07 7.2196879e-13
|
||||
120000 91577.119 6.8360083e-08 0 1.6491292e-07 7.3664397e-13
|
||||
125000 89670.176 6.7876707e-08 0 1.6241899e-07 7.29547e-13
|
||||
130000 87135.819 6.6698539e-08 0 1.5856877e-07 7.296178e-13
|
||||
135000 84795.008 6.3054439e-08 0 1.5245667e-07 7.1371044e-13
|
||||
140000 81222.266 6.4732255e-08 0 1.5036763e-07 7.2429578e-13
|
||||
145000 78548.301 6.3633278e-08 0 1.464494e-07 7.1795316e-13
|
||||
150000 76597.034 6.3093645e-08 0 1.4385248e-07 7.1457515e-13
|
||||
155000 73820.896 6.0685032e-08 0 1.3851689e-07 7.1093329e-13
|
||||
160000 71360.569 6.2615029e-08 0 1.3785288e-07 7.2019292e-13
|
||||
165000 67879.165 5.9691015e-08 0 1.3125831e-07 7.0403501e-13
|
||||
170000 66641.482 5.9273104e-08 0 1.2953546e-07 7.0719355e-13
|
||||
175000 65623.831 6.011737e-08 0 1.2930679e-07 7.1498836e-13
|
||||
180000 63627.376 5.8380162e-08 0 1.2546465e-07 7.0457247e-13
|
||||
185000 60865.93 5.8039489e-08 0 1.2221249e-07 7.1190327e-13
|
||||
190000 57329.276 5.8432616e-08 0 1.188768e-07 7.1940596e-13
|
||||
195000 54829.503 5.6354458e-08 0 1.1416305e-07 7.0364147e-13
|
||||
200000 52720.064 5.4124289e-08 0 1.0970883e-07 6.935829e-13
|
||||
205000 50368.95 5.4872306e-08 0 1.0797799e-07 7.0426031e-13
|
||||
210000 47452.093 5.3729225e-08 0 1.0375956e-07 6.994635e-13
|
||||
215000 45119.016 5.4481066e-08 0 1.0205156e-07 7.1418206e-13
|
||||
220000 43023.929 5.2752651e-08 0 9.8114229e-08 6.9834508e-13
|
||||
225000 40153.742 5.1097395e-08 0 9.3432837e-08 6.9738856e-13
|
||||
230000 39369.117 5.0504151e-08 0 9.2012337e-08 6.894872e-13
|
||||
235000 36113.296 4.9984145e-08 0 8.8059609e-08 6.9525606e-13
|
||||
240000 33557.343 4.74199e-08 0 8.2800537e-08 6.782253e-13
|
||||
245000 31543.784 4.6897571e-08 0 8.0155245e-08 6.7496202e-13
|
||||
250000 29448.798 4.5972171e-08 0 7.702103e-08 6.6988749e-13
|
||||
255000 26258.805 4.522174e-08 0 7.2907283e-08 6.7773348e-13
|
||||
260000 24024.155 4.4693255e-08 0 7.002273e-08 6.7584518e-13
|
||||
265000 22118.293 4.3984189e-08 0 6.730425e-08 6.7927214e-13
|
||||
270000 20024.409 4.2544987e-08 0 6.3657396e-08 6.8136681e-13
|
||||
275000 17107.549 4.1072236e-08 0 5.9109301e-08 6.666371e-13
|
||||
280000 14749.603 4.0000425e-08 0 5.5551428e-08 6.613669e-13
|
||||
285000 12500.706 4.0279102e-08 0 5.3459018e-08 6.8142024e-13
|
||||
290000 10030.224 3.8370444e-08 0 4.8945647e-08 6.7352743e-13
|
||||
295000 7601.7068 3.723413e-08 0 4.5248866e-08 6.6989317e-13
|
||||
300000 5231.1956 3.5917594e-08 0 4.143302e-08 6.6679331e-13
|
||||
Loop time of 1070.02 on 4 procs for 200000 steps with 5092 atoms
|
||||
Generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.966 | 6.325 | 7.684 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
100000 217597.05 0 0 2.294199e-07 2.3049678e-14
|
||||
105000 105542.67 6.5899047e-08 0 1.7717623e-07 6.9064382e-13
|
||||
110000 96801.947 6.6329049e-08 0 1.683906e-07 7.0960381e-13
|
||||
115000 93283.767 6.4052852e-08 0 1.6240507e-07 7.0033324e-13
|
||||
120000 90930.59 6.3799892e-08 0 1.5967108e-07 7.0244972e-13
|
||||
125000 90114.178 6.3511381e-08 0 1.5852179e-07 7.1128852e-13
|
||||
130000 83917.505 6.279089e-08 0 1.5126794e-07 6.9980391e-13
|
||||
135000 84057.326 6.269189e-08 0 1.5131636e-07 7.1046329e-13
|
||||
140000 80989.747 6.2166941e-08 0 1.4755716e-07 7.0822238e-13
|
||||
145000 79082.787 5.999291e-08 0 1.4337256e-07 7.0169908e-13
|
||||
150000 76377.704 6.0983734e-08 0 1.4151132e-07 7.0803269e-13
|
||||
155000 74642.465 5.8016291e-08 0 1.3671435e-07 6.8979034e-13
|
||||
160000 71320.499 5.8203836e-08 0 1.3339944e-07 6.9671842e-13
|
||||
165000 69769.632 5.8523021e-08 0 1.3208349e-07 6.9774909e-13
|
||||
170000 67002.509 5.6265118e-08 0 1.2690812e-07 6.8640935e-13
|
||||
175000 65045.732 5.5231406e-08 0 1.2381131e-07 6.8623008e-13
|
||||
180000 62633.05 5.3858988e-08 0 1.1989512e-07 6.7679278e-13
|
||||
185000 60510.328 5.3138189e-08 0 1.1693627e-07 6.7838603e-13
|
||||
190000 56958.939 5.3092173e-08 0 1.131459e-07 6.7336019e-13
|
||||
195000 55591.155 5.1736031e-08 0 1.1034766e-07 6.6906721e-13
|
||||
200000 53009.069 5.0934685e-08 0 1.0682393e-07 6.7160648e-13
|
||||
205000 50806.268 5.1266492e-08 0 1.0483325e-07 6.7042981e-13
|
||||
210000 47438.734 4.9024426e-08 0 9.9040681e-08 6.6234011e-13
|
||||
215000 45998.084 4.7751227e-08 0 9.6248556e-08 6.5536559e-13
|
||||
220000 43057.946 4.7441717e-08 0 9.2839159e-08 6.6414744e-13
|
||||
225000 41339.318 4.6636471e-08 0 9.0221906e-08 6.5621184e-13
|
||||
230000 37991.695 4.5885529e-08 0 8.5941452e-08 6.5311348e-13
|
||||
235000 36765.626 4.4005371e-08 0 8.2768609e-08 6.4411688e-13
|
||||
240000 33633.564 4.3031845e-08 0 7.8492844e-08 6.411006e-13
|
||||
245000 31441.462 4.186446e-08 0 7.5014252e-08 6.3558893e-13
|
||||
250000 28346.474 4.1330305e-08 0 7.1216947e-08 6.3547167e-13
|
||||
255000 26485.436 4.0303887e-08 0 6.8228374e-08 6.3491378e-13
|
||||
260000 24251.816 3.8404659e-08 0 6.3974165e-08 6.2184492e-13
|
||||
265000 21588.99 3.8470221e-08 0 6.1232221e-08 6.3046737e-13
|
||||
270000 19476.088 3.7190768e-08 0 5.7725063e-08 6.2042977e-13
|
||||
275000 17402.215 3.719862e-08 0 5.5546362e-08 6.3332028e-13
|
||||
280000 14911.078 3.5602533e-08 0 5.1323785e-08 6.2734446e-13
|
||||
285000 12478.751 3.4819713e-08 0 4.7976481e-08 6.2920228e-13
|
||||
290000 10052.548 3.3720905e-08 0 4.4319645e-08 6.2607642e-13
|
||||
295000 7653.5468 3.190337e-08 0 3.9972762e-08 6.210325e-13
|
||||
300000 5240.5437 3.0902841e-08 0 3.6428123e-08 6.2021355e-13
|
||||
Loop time of 240.576 on 4 procs for 200000 steps with 5092 atoms
|
||||
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.057981 | 36.178 | 144.53 |1040.0 | 3.38
|
||||
Neigh | 0.25871 | 0.37261 | 0.69124 | 30.2 | 0.03
|
||||
Comm | 0.47965 | 0.49514 | 0.51697 | 2.1 | 0.05
|
||||
Output | 0.0064233 | 0.16356 | 0.21598 | 22.4 | 0.02
|
||||
Modify | 0.21709 | 229.82 | 918.61 |2623.2 | 21.48
|
||||
Other | | 803 | | | 75.04
|
||||
Pair | 0.0094455 | 19.351 | 39.054 | 439.7 | 8.04
|
||||
Neigh | 0.069968 | 0.11626 | 0.16266 | 13.6 | 0.05
|
||||
Comm | 0.10053 | 0.88025 | 1.9201 | 85.4 | 0.37
|
||||
Output | 0.0012827 | 0.02596 | 0.050595 | 15.3 | 0.01
|
||||
Modify | 0.03084 | 98.954 | 197.96 | 994.4 | 41.13
|
||||
Other | | 121.2 | | | 50.40
|
||||
|
||||
Nlocal: 1273 ave 5092 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19214.5 ave 76858 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nlocal: 1273 ave 2547 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 175 ave 360 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 19108 ave 38228 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 76858
|
||||
Ave neighs/atom = 15.093873
|
||||
Neighbor list builds = 116
|
||||
Total # of neighbors = 76432
|
||||
Ave neighs/atom = 15.010212
|
||||
Neighbor list builds = 114
|
||||
Dangerous builds = 0
|
||||
|
||||
minimize 0.0 1.0e-8 1000 100000
|
||||
generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.418 | 5.461 | 8.588 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
300000 5231.1956 3.5917594e-08 0 4.143302e-08 6.6679331e-13
|
||||
301000 5231.1956 3.591074e-08 0 4.1426165e-08 6.6674716e-13
|
||||
Loop time of 5.73822 on 4 procs for 1000 steps with 5092 atoms
|
||||
Generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Per MPI rank memory allocation (min/avg/max) = 4.966 | 6.887 | 8.809 Mbytes
|
||||
Step Temp E_pair E_mol TotEng Press
|
||||
300000 5240.5437 3.0902841e-08 0 3.6428123e-08 6.2021355e-13
|
||||
301000 5240.5437 3.0896022e-08 0 3.6421304e-08 6.2016488e-13
|
||||
Loop time of 1.30229 on 4 procs for 1000 steps with 5092 atoms
|
||||
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
99.2% CPU use with 4 MPI tasks x 1 OpenMP threads
|
||||
|
||||
Minimization stats:
|
||||
Stopping criterion = max iterations
|
||||
Energy initial, next-to-last, final =
|
||||
3.59175937800124e-08 3.59107465269502e-08 3.59107396814365e-08
|
||||
Force two-norm initial, final = 8.3566626e-08 8.3465615e-08
|
||||
Force max component initial, final = 3.1363101e-09 3.1301201e-09
|
||||
Final line search alpha, max atom move = 1 3.1301201e-09
|
||||
3.09028409031651e-08 3.08960287166428e-08 3.08960219060082e-08
|
||||
Force two-norm initial, final = 8.2667468e-08 8.2568929e-08
|
||||
Force max component initial, final = 2.9188021e-09 2.9146337e-09
|
||||
Final line search alpha, max atom move = 1 2.9146337e-09
|
||||
Iterations, force evaluations = 1000 1000
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.0003564 | 0.3119 | 1.2465 | 96.6 | 5.44
|
||||
Pair | 5.6358e-05 | 0.14395 | 0.28791 | 37.9 | 11.05
|
||||
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
||||
Comm | 0.0007532 | 0.00080708 | 0.000957 | 0.0 | 0.01
|
||||
Output | 4.88e-05 | 6.4775e-05 | 0.0001121 | 0.0 | 0.00
|
||||
Modify | 0.0004412 | 1.0758 | 4.3017 | 179.6 | 18.75
|
||||
Other | | 4.35 | | | 75.80
|
||||
Comm | 0.00010928 | 0.0035209 | 0.0074675 | 5.8 | 0.27
|
||||
Output | 1.9357e-05 | 2.0372e-05 | 2.2403e-05 | 0.0 | 0.00
|
||||
Modify | 4.6032e-05 | 0.4419 | 0.88539 | 66.5 | 33.93
|
||||
Other | | 0.7129 | | | 54.74
|
||||
|
||||
Nlocal: 1273 ave 5092 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 19216 ave 76864 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nlocal: 1273 ave 2547 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Nghost: 175 ave 360 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
Neighs: 19105.5 ave 38227 max 0 min
|
||||
Histogram: 2 0 0 0 0 0 0 0 0 2
|
||||
|
||||
Total # of neighbors = 76864
|
||||
Ave neighs/atom = 15.095051
|
||||
Total # of neighbors = 76422
|
||||
Ave neighs/atom = 15.008248
|
||||
Neighbor list builds = 0
|
||||
Dangerous builds = 0
|
||||
|
||||
@ -884,22 +887,25 @@ pair_style lj/cut 1.2
|
||||
pair_coeff * * 0.0 0.0
|
||||
|
||||
timestep 0.025
|
||||
if "$(is_defined(dump,mydump))" then "undump mydump"
|
||||
|
||||
reset_timestep 0
|
||||
|
||||
#dump mydump all atom 10000 run.lammpstrj
|
||||
#variable total_force equal 0.2
|
||||
#variable node_force equal "v_total_force / 178"
|
||||
#fix drag all addforce 0.0 0.0 0.0
|
||||
|
||||
velocity all set 0.0 -7.5.0 0.0 units box
|
||||
velocity all set 0.0 -7.5 0.0 units box
|
||||
|
||||
# viscosity of air is 0.0001847
|
||||
|
||||
fix FL all lb/fluid 1 0.0002 ${density} stencil 2 dx ${dx} zwall_velocity 0 0 # dumpxdmf 1000 sflow 0
|
||||
fix FL all lb/fluid 1 0.0002 0.001184 stencil 2 dx ${dx} zwall_velocity 0 0
|
||||
fix FL all lb/fluid 1 0.0002 0.001184 stencil 2 dx 1 zwall_velocity 0 0
|
||||
Using a lattice-Boltzmann grid of 96 by 720 by 97 total grid points. (../fix_lb_fluid.cpp:486)
|
||||
Local Grid Geometry created. (../fix_lb_fluid.cpp:1018)
|
||||
Using a lattice-Boltzmann grid of 96 by 720 by 97 points.
|
||||
Local Grid Geometry created.
|
||||
First Run initialized
|
||||
|
||||
variable vx equal vcm(all,x)
|
||||
variable vy equal vcm(all,y)
|
||||
@ -925,11 +931,11 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
Your simulation uses code contributions which should be cited:
|
||||
|
||||
- fix lb/fluid command:
|
||||
- fix lb/fluid command: doi:10.1016/j.cpc.2022.108318
|
||||
|
||||
@Article{Denniston et al.,
|
||||
author = {C. Denniston, N. Afrasiabian, M.G. Cole-Andre,F.E. Mackay, S.T.T. Ollila, T. Whitehead},
|
||||
title = {LAMMPS lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into LAMMPS through a lattice-Boltzmann fluid}, journal = {Comp.~Phys.~Comm.},
|
||||
author = {C. Denniston and N. Afrasiabian and M. G. Cole-Andre, F. E. Mackay and S. T. T. Ollila and T. Whitehead},
|
||||
title = {{LAMMPS} lb/fluid fix version 2: Improved Hydrodynamic Forces Implemented into {LAMMPS} Through a Lattice-{B}oltzmann Fluid}, journal = {Comput.\ Phys.\ Commun.},
|
||||
year = 2022,
|
||||
volume = 275,
|
||||
pages = {108318}
|
||||
@ -937,9 +943,9 @@ Your simulation uses code contributions which should be cited:
|
||||
|
||||
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
||||
|
||||
generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Generated 0 of 91 mixed pair_coeff terms from geometric mixing rule
|
||||
Neighbor list info ...
|
||||
update every 1 steps, delay 0 steps, check yes
|
||||
update: every = 1 steps, delay = 0 steps, check = yes
|
||||
max neighbors/atom: 2000, page size: 100000
|
||||
master list distance cutoff = 1.7
|
||||
ghost atom cutoff = 3
|
||||
@ -950,85 +956,15 @@ Neighbor list info ...
|
||||
pair build: half/bin/atomonly/newton
|
||||
stencil: half/bin/3d
|
||||
bin: standard
|
||||
Per MPI rank memory allocation (min/avg/max) = 13.03 | 14.01 | 16.94 Mbytes
|
||||
Step v_number_all v_node_mass f_FL[2] f_5[1] f_5[2] f_5[3]
|
||||
0 5092 98.193244 265447.33 0 0 0
|
||||
100 5092 98.193244 265447.33 -0.62398934 11.636864 -1.4385266
|
||||
200 5092 98.193244 265447.33 -0.0067390379 12.774129 0.77152356
|
||||
300 5092 98.193244 265447.33 -0.016866727 11.816838 0.164604
|
||||
400 5092 98.193244 265447.33 -0.099751559 14.292633 3.5403419
|
||||
500 5092 98.193244 265447.33 0.020826826 12.371064 3.4680188
|
||||
600 5092 98.193244 265447.33 -0.12187023 10.702747 0.7831029
|
||||
700 5092 98.193244 265447.33 -0.075493864 10.829418 0.98211649
|
||||
800 5092 98.193244 265447.33 -0.11468917 12.399304 1.7926202
|
||||
900 5092 98.193244 265447.33 -0.068927619 11.055182 2.4723876
|
||||
1000 5092 98.193244 265447.33 -0.069248548 10.39473 1.5087726
|
||||
1100 5092 98.193244 265447.33 0.065523336 9.4891653 1.3947719
|
||||
1200 5092 98.193244 265447.33 -0.044004235 11.847192 2.5397604
|
||||
1300 5092 98.193244 265447.33 0.040137088 10.997654 2.8832378
|
||||
1400 5092 98.193244 265447.33 0.067812628 10.154351 3.4014094
|
||||
1500 5092 98.193244 265447.33 0.026101525 10.034855 2.5467227
|
||||
1600 5092 98.193244 265447.33 0.023101669 11.834913 2.9961902
|
||||
1700 5092 98.193244 265447.33 -0.016678555 11.057297 1.1303356
|
||||
1800 5092 98.193244 265447.33 0.038804941 9.2005261 3.2383612
|
||||
1900 5092 98.193244 265447.33 0.045475707 8.592855 2.7327399
|
||||
2000 5092 98.193244 265447.33 0.0029052791 11.37239 1.650534
|
||||
2100 5092 98.193244 265447.33 0.0021721335 10.534175 1.4627128
|
||||
2200 5092 98.193244 265447.33 0.033545767 9.6499738 1.7555886
|
||||
2300 5092 98.193244 265447.33 0.037477935 10.604272 2.6811451
|
||||
2400 5092 98.193244 265447.33 0.013734867 9.5032009 3.4535601
|
||||
2500 5092 98.193244 265447.33 -0.074779755 10.655833 2.4798429
|
||||
2600 5092 98.193244 265447.33 -0.03912509 9.9731913 1.3805939
|
||||
2700 5092 98.193244 265447.33 0.084748343 9.6155874 1.9680204
|
||||
2800 5092 98.193244 265447.33 0.004716293 11.060178 2.3097572
|
||||
2900 5092 98.193244 265447.33 -0.01716838 10.851167 1.2315357
|
||||
3000 5092 98.193244 265447.33 0.0089978545 10.101686 1.6655875
|
||||
3100 5092 98.193244 265447.33 0.10214007 9.8489205 1.3991661
|
||||
3200 5092 98.193244 265447.33 0.030416619 10.303674 2.8620249
|
||||
3300 5092 98.193244 265447.33 -0.080891033 10.665193 1.6805084
|
||||
3400 5092 98.193244 265447.33 0.011781712 10.916621 0.79341262
|
||||
3500 5092 98.193244 265447.33 0.050815855 9.5573732 0.40493186
|
||||
3600 5092 98.193244 265447.33 -0.017225395 10.438887 2.303509
|
||||
3700 5092 98.193244 265447.33 0.0042521202 9.8119963 3.1057822
|
||||
3800 5092 98.193244 265447.33 0.037295562 9.3673981 2.2084367
|
||||
3900 5092 98.193244 265447.33 0.053448378 8.9799381 1.9075618
|
||||
4000 5092 98.193244 265447.33 0.039518888 10.999985 2.2441035
|
||||
4100 5092 98.193244 265447.33 -0.022548252 10.07084 1.7986935
|
||||
4200 5092 98.193244 265447.33 0.093070808 8.8837865 1.8491384
|
||||
4300 5092 98.193244 265447.33 0.16605392 10.080625 2.3851261
|
||||
4400 5092 98.193244 265447.33 0.071707012 11.041363 1.3512251
|
||||
4500 5092 98.193244 265447.33 -0.044985642 10.590977 0.89464128
|
||||
4600 5092 98.193244 265447.33 0.010801743 9.745945 1.3254718
|
||||
4700 5092 98.193244 265447.33 0.11301693 9.8629299 1.2450238
|
||||
4800 5092 98.193244 265447.33 0.29083508 10.35163 1.6481913
|
||||
4900 5092 98.193244 265447.33 0.274316 9.7650593 1.6979411
|
||||
5000 5092 98.193244 265447.33 -0.041118665 9.9508487 1.7688687
|
||||
Loop time of 5880.47 on 4 procs for 5000 steps with 5092 atoms
|
||||
|
||||
100.0% CPU use with 4 MPI tasks x no OpenMP threads
|
||||
|
||||
MPI task timing breakdown:
|
||||
Section | min time | avg time | max time |%varavg| %total
|
||||
---------------------------------------------------------------
|
||||
Pair | 0.8823 | 1.2112 | 1.6656 | 29.1 | 0.02
|
||||
Neigh | 22.261 | 23.161 | 24.045 | 15.0 | 0.39
|
||||
Comm | 1.1838 | 1.3636 | 1.6084 | 14.2 | 0.02
|
||||
Output | 0.99304 | 0.99848 | 1.0061 | 0.5 | 0.02
|
||||
Modify | 5850 | 5851.7 | 5853.1 | 1.6 | 99.51
|
||||
Other | | 2.046 | | | 0.03
|
||||
|
||||
Nlocal: 1273 ave 5092 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
Nghost: 0 ave 0 max 0 min
|
||||
Histogram: 4 0 0 0 0 0 0 0 0 0
|
||||
Neighs: 8835 ave 35340 max 0 min
|
||||
Histogram: 3 0 0 0 0 0 0 0 0 1
|
||||
|
||||
Total # of neighbors = 35340
|
||||
Ave neighs/atom = 6.9402985
|
||||
Neighbor list builds = 2500
|
||||
Dangerous builds = 0
|
||||
|
||||
|
||||
#-------------------------------------------------------------------------#
|
||||
Total wall time: 2:06:45
|
||||
Per MPI rank memory allocation (min/avg/max) = 14.67 | 16.66 | 18.64 Mbytes
|
||||
Step v_number_all v_node_mass f_FL[2] f_5[1] f_5[2] f_5[3]
|
||||
0 5092 98.193244 265447.33 0 0 0
|
||||
100 5092 98.193244 265447.33 0.42848502 10.910894 -2.3324154
|
||||
200 5092 98.193244 265447.33 -0.02627078 13.323497 0.5134388
|
||||
300 5092 98.193244 265447.33 0.33955198 12.017917 0.07308431
|
||||
400 5092 98.193244 265447.33 0.28511704 14.563626 3.4626969
|
||||
500 5092 98.193244 265447.33 -0.080267505 11.795121 3.266271
|
||||
600 5092 98.193244 265447.33 0.11024837 10.763593 0.68027763
|
||||
700 5092 98.193244 265447.33 0.22058041 10.773118 1.1020572
|
||||
800 5092 98.193244 265447.33 0.26569373 12.841207 1.7015156
|
||||
900 5092
|
||||
1
examples/PACKAGES/pafi/Fe_mm.eam.fs
Symbolic link
1
examples/PACKAGES/pafi/Fe_mm.eam.fs
Symbolic link
@ -0,0 +1 @@
|
||||
../../../potentials/Fe_mm.eam.fs
|
||||
1
examples/PACKAGES/ti/Cu_mishin1.eam.alloy
Symbolic link
1
examples/PACKAGES/ti/Cu_mishin1.eam.alloy
Symbolic link
@ -0,0 +1 @@
|
||||
../../../potentials/Cu_mishin1.eam.alloy
|
||||
@ -5,7 +5,7 @@ LAMMPS data file via write_data, version 24 Dec 2020, timestep = 400000
|
||||
|
||||
9.95143358025075 331.8139610404791 xlo xhi
|
||||
9.95143358025075 331.8139610404791 ylo yhi
|
||||
0 1 zlo zhi
|
||||
-0.5 0.5 zlo zhi
|
||||
0 0 0 xy xz yz
|
||||
|
||||
Atoms # sphere
|
||||
|
||||
@ -1,6 +1,12 @@
|
||||
# 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
|
||||
write_restart molecular-mix.restart
|
||||
|
||||
# now restart
|
||||
clear
|
||||
molecule cychex cyclohexane.mol
|
||||
read_restart molecular-mix.restart
|
||||
|
||||
@ -9,3 +15,6 @@ 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
|
||||
|
||||
# clean up
|
||||
shell rm molecular-mix.restart
|
||||
|
||||
@ -1,6 +1,12 @@
|
||||
# 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
|
||||
write_restart template-mix.restart
|
||||
|
||||
# now restart
|
||||
clear
|
||||
molecule cychex cyclohexane.mol
|
||||
read_restart template-mix.restart
|
||||
|
||||
@ -9,3 +15,6 @@ 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
|
||||
|
||||
# clean up
|
||||
shell rm template-mix.restart
|
||||
|
||||
302
examples/template/log.12Aug24.mol-restart-mix.g++.1
Normal file
302
examples/template/log.12Aug24.mol-restart-mix.g++.1
Normal file
@ -0,0 +1,302 @@
|
||||
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
|
||||
303
examples/template/log.12Aug24.mol-restart-mix.g++.4
Normal file
303
examples/template/log.12Aug24.mol-restart-mix.g++.4
Normal file
@ -0,0 +1,303 @@
|
||||
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
examples/template/log.12Aug24.tmpl-restart-mix.g++.1
Normal file
295
examples/template/log.12Aug24.tmpl-restart-mix.g++.1
Normal file
@ -0,0 +1,295 @@
|
||||
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
examples/template/log.12Aug24.tmpl-restart-mix.g++.4
Normal file
296
examples/template/log.12Aug24.tmpl-restart-mix.g++.4
Normal file
@ -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
|
||||
@ -1,106 +0,0 @@
|
||||
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
|
||||
@ -1,107 +0,0 @@
|
||||
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
|
||||
@ -1,102 +0,0 @@
|
||||
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
|
||||
@ -1,101 +0,0 @@
|
||||
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
|
||||
Reference in New Issue
Block a user