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add stabilized vs unstabilized examples

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This commit is contained in:
jrgissing
2019-06-30 22:13:12 -06:00
parent 483b1dbef5
commit af8103433c
8 changed files with 640 additions and 740 deletions
Download Patch File Download Diff File Expand all files Collapse all files

2
examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon → examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.stabilized
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@ -38,6 +38,8 @@ fix myrxns all bond/react stabilization yes statted_grp .03 &
fix 1 statted_grp_REACT nvt temp 300 300 100
# optionally, you can customize behavior of reacting atoms,
# by using the internally-created 'bond_react_MASTER_group', like so:
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]

48
examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon.unstabilized Normal file
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@ -0,0 +1,48 @@
# two monomer nylon example
# reaction produces a condensed water molecule
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_nylon.data
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
molecule mol2 rxn1_stp1_reacted.data_template
molecule mol3 rxn1_stp2_unreacted.data_template
molecule mol4 rxn1_stp2_reacted.data_template
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization no &
react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map &
react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
fix 1 all nve/limit .03
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run 1000
# write_restart restart_longrun
# write_data restart_longrun.data

370
examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1
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@ -1,370 +0,0 @@
LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# two monomer nylon example
# reaction produces a condensed water molecule
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_nylon.data
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
molecule mol2 rxn1_stp1_reacted.data_template
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
molecule mol3 rxn1_stp2_unreacted.data_template
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
molecule mol4 rxn1_stp2_reacted.data_template
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
fix 1 statted_grp nvt temp 300 300 100
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run 10000
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTs
3d grid and FFT values/proc = 343 8
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
WARNING: Inconsistent image flags (../domain.cpp:786)
Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.34 | 33.34 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 296.70408 -51.30066 0.0034851739 1 0
100 274.25324 46.715512 0.0034851739 1 1
150 471.61579 31.321598 0.0034851739 1 1
200 362.87766 42.061118 0.0034851739 1 1
250 367.58058 65.303109 0.0034851739 1 1
300 372.38236 -52.421725 0.0034851739 1 1
350 297.69957 17.869945 0.0034851739 1 1
400 258.30433 49.19156 0.0034851739 1 1
450 253.34384 -5.8162637 0.0034851739 1 1
500 269.96465 -43.337517 0.0034851739 1 1
550 303.23718 10.180246 0.0034851739 1 1
600 329.59579 -48.97461 0.0034851739 1 1
650 350.42568 50.983183 0.0034851739 1 1
700 342.03272 35.43465 0.0034851739 1 1
750 269.23405 -41.873166 0.0034851739 1 1
800 245.15025 13.953092 0.0034851739 1 1
850 257.85421 -3.1492141 0.0034851739 1 1
900 316.15644 7.7798301 0.0034851739 1 1
950 299.9124 -15.77014 0.0034851739 1 1
1000 302.89968 -17.049693 0.0034851739 1 1
1050 308.91651 71.84632 0.0034851739 1 1
1100 348.43932 -18.742012 0.0034851739 1 1
1150 309.03036 50.536311 0.0034851739 1 1
1200 318.9761 -16.905746 0.0034851739 1 1
1250 320.42806 -0.057975092 0.0034851739 1 1
1300 289.7824 18.200772 0.0034851739 1 1
1350 284.79836 -9.1978427 0.0034851739 1 1
1400 325.43292 42.082833 0.0034851739 1 1
1450 261.5041 -37.823325 0.0034851739 1 1
1500 298.88723 -5.1647385 0.0034851739 1 1
1550 291.37403 -7.7764201 0.0034851739 1 1
1600 293.83475 22.2458 0.0034851739 1 1
1650 293.80611 24.202512 0.0034851739 1 1
1700 291.70205 -23.397884 0.0034851739 1 1
1750 292.32437 -10.671214 0.0034851739 1 1
1800 302.01367 -11.671025 0.0034851739 1 1
1850 322.1651 24.438331 0.0034851739 1 1
1900 310.45076 45.343592 0.0034851739 1 1
1950 325.91745 -19.847809 0.0034851739 1 1
2000 276.89662 63.387098 0.0034851739 1 1
2050 311.33783 -24.683247 0.0034851739 1 1
2100 346.2336 -27.526891 0.0034851739 1 1
2150 345.30604 -15.722411 0.0034851739 1 1
2200 346.7718 -17.857633 0.0034851739 1 1
2250 304.28676 -1.9965581 0.0034851739 1 1
2300 322.56372 -31.786868 0.0034851739 1 1
2350 282.64326 6.1982735 0.0034851739 1 1
2400 286.65759 -63.207781 0.0034851739 1 1
2450 257.05528 32.931491 0.0034851739 1 1
2500 283.64386 26.912373 0.0034851739 1 1
2550 299.54005 27.277039 0.0034851739 1 1
2600 283.92503 14.660972 0.0034851739 1 1
2650 321.93453 -18.977358 0.0034851739 1 1
2700 376.7189 31.826935 0.0034851739 1 1
2750 372.20075 -32.821697 0.0034851739 1 1
2800 361.40604 83.035183 0.0034851739 1 1
2850 332.27269 -23.927452 0.0034851739 1 1
2900 331.14638 -0.12328446 0.0034851739 1 1
2950 303.67489 -24.078857 0.0034851739 1 1
3000 311.40462 21.563537 0.0034851739 1 1
3050 284.72849 -23.849667 0.0034851739 1 1
3100 303.48477 39.347763 0.0034851739 1 1
3150 264.2739 -0.22299879 0.0034851739 1 1
3200 300.03351 31.545323 0.0034851739 1 1
3250 288.56663 5.7225228 0.0034851739 1 1
3300 200.13238 -31.239655 0.0034851739 1 1
3350 231.32512 16.631728 0.0034851739 1 1
3400 260.57402 2.1717992 0.0034851739 1 1
3450 301.47128 -42.210623 0.0034851739 1 1
3500 321.77414 40.074365 0.0034851739 1 1
3550 353.21858 28.387783 0.0034851739 1 1
3600 331.45989 -57.800858 0.0034851739 1 1
3650 303.88123 44.86596 0.0034851739 1 1
3700 329.73833 -0.80615652 0.0034851739 1 1
3750 297.55588 -0.49626039 0.0034851739 1 1
3800 286.38794 -10.010003 0.0034851739 1 1
3850 290.17417 -43.51187 0.0034851739 1 1
3900 247.88933 51.23735 0.0034851739 1 1
3950 332.31324 -18.194985 0.0034851739 1 1
4000 325.56802 18.402825 0.0034851739 1 1
4050 338.37593 36.430977 0.0034851739 1 1
4100 370.95478 39.290285 0.0034851739 1 1
4150 348.47859 -7.0779678 0.0034851739 1 1
4200 241.30632 -33.371788 0.0034851739 1 1
4250 242.17258 -9.986197 0.0034851739 1 1
4300 300.85311 -7.9244294 0.0034851739 1 1
4350 273.15684 -21.257283 0.0034851739 1 1
4400 305.77463 -5.8720722 0.0034851739 1 1
4450 314.97697 45.0373 0.0034851739 1 1
4500 310.77723 16.958773 0.0034851739 1 1
4550 302.1742 12.156862 0.0034851739 1 1
4600 319.74799 6.84889 0.0034851739 1 1
4650 270.86805 -13.767905 0.0034851739 1 1
4700 249.81731 -31.197487 0.0034851739 1 1
4750 285.86481 -9.8916364 0.0034851739 1 1
4800 233.98321 7.1338571 0.0034851739 1 1
4850 302.60551 49.262889 0.0034851739 1 1
4900 316.55056 34.663247 0.0034851739 1 1
4950 357.32741 11.583006 0.0034851739 1 1
5000 400.21045 -8.1781061 0.0034851739 1 1
5050 390.01845 -20.490275 0.0034851739 1 1
5100 378.84247 -41.328757 0.0034851739 1 1
5150 324.02038 -15.023862 0.0034851739 1 1
5200 262.08429 10.937354 0.0034851739 1 1
5250 255.75508 16.381455 0.0034851739 1 1
5300 277.84989 40.68232 0.0034851739 1 1
5350 302.92832 9.1989494 0.0034851739 1 1
5400 283.7196 -1.6584671 0.0034851739 1 1
5450 300.71266 -4.7030295 0.0034851739 1 1
5500 343.5499 -0.30550044 0.0034851739 1 1
5550 369.51271 21.691649 0.0034851739 1 1
5600 372.69789 -38.67994 0.0034851739 1 1
5650 327.41266 11.352137 0.0034851739 1 1
5700 278.98614 -23.827304 0.0034851739 1 1
5750 308.30054 -20.756187 0.0034851739 1 1
5800 341.45594 28.058441 0.0034851739 1 1
5850 322.97844 -10.731921 0.0034851739 1 1
5900 304.53591 32.825279 0.0034851739 1 1
5950 287.1752 -36.780091 0.0034851739 1 1
6000 296.52681 18.781896 0.0034851739 1 1
6050 314.25442 15.992829 0.0034851739 1 1
6100 313.86576 3.4342714 0.0034851739 1 1
6150 325.64196 32.392039 0.0034851739 1 1
6200 367.42931 -27.160706 0.0034851739 1 1
6250 369.30798 39.020934 0.0034851739 1 1
6300 328.92285 -23.175157 0.0034851739 1 1
6350 305.63077 4.9024453 0.0034851739 1 1
6400 241.70341 -13.676629 0.0034851739 1 1
6450 265.66717 2.40612 0.0034851739 1 1
6500 249.36037 13.420255 0.0034851739 1 1
6550 294.53814 10.853462 0.0034851739 1 1
6600 308.2025 18.995308 0.0034851739 1 1
6650 305.43797 -49.56785 0.0034851739 1 1
6700 320.27344 11.336281 0.0034851739 1 1
6750 321.78666 -23.463899 0.0034851739 1 1
6800 303.40388 7.6224553 0.0034851739 1 1
6850 297.18966 51.52256 0.0034851739 1 1
6900 284.18909 -8.4947203 0.0034851739 1 1
6950 331.03663 13.233655 0.0034851739 1 1
7000 311.37928 -43.265479 0.0034851739 1 1
7050 286.81661 -14.174683 0.0034851739 1 1
7100 302.84119 12.048954 0.0034851739 1 1
7150 297.19357 -43.111968 0.0034851739 1 1
7200 332.47359 26.048249 0.0034851739 1 1
7250 262.70677 41.176242 0.0034851739 1 1
7300 250.61405 -23.413982 0.0034851739 1 1
7350 296.91117 35.88133 0.0034851739 1 1
7400 245.09229 -13.447194 0.0034851739 1 1
7450 272.28131 -23.322585 0.0034851739 1 1
7500 209.04985 13.871239 0.0034851739 1 1
7550 255.00955 4.9325621 0.0034851739 1 1
7600 312.30937 -37.368274 0.0034851739 1 1
7650 305.65903 55.245496 0.0034851739 1 1
7700 325.09504 -18.347711 0.0034851739 1 1
7750 363.28282 -22.479686 0.0034851739 1 1
7800 350.17429 26.849547 0.0034851739 1 1
7850 271.70853 -17.764575 0.0034851739 1 1
7900 272.66484 -11.701967 0.0034851739 1 1
7950 298.60202 -12.765675 0.0034851739 1 1
8000 274.58852 49.641532 0.0034851739 1 1
8050 304.72347 -0.55414183 0.0034851739 1 1
8100 328.30757 -39.861301 0.0034851739 1 1
8150 406.67601 2.8999409 0.0034851739 1 1
8200 332.20083 -51.217399 0.0034851739 1 1
8250 354.50609 53.128769 0.0034851739 1 1
8300 337.2758 20.68562 0.0034851739 1 1
8350 361.89708 -54.185869 0.0034851739 1 1
8400 305.63496 24.058529 0.0034851739 1 1
8450 303.27461 4.304683 0.0034851739 1 1
8500 253.53694 -10.909021 0.0034851739 1 1
8550 277.03017 23.241479 0.0034851739 1 1
8600 291.41844 -22.240665 0.0034851739 1 1
8650 307.85368 31.919587 0.0034851739 1 1
8700 309.19724 0.53529642 0.0034851739 1 1
8750 354.6583 11.565515 0.0034851739 1 1
8800 329.78598 19.5996 0.0034851739 1 1
8850 240.79198 21.803515 0.0034851739 1 1
8900 318.40749 -59.816923 0.0034851739 1 1
8950 308.47211 -57.808635 0.0034851739 1 1
9000 271.51207 50.943482 0.0034851739 1 1
9050 249.4005 6.7529187 0.0034851739 1 1
9100 221.8772 47.196092 0.0034851739 1 1
9150 297.9351 4.0058184 0.0034851739 1 1
9200 274.85051 -24.774393 0.0034851739 1 1
9250 336.04757 5.3799028 0.0034851739 1 1
9300 380.44956 -22.389381 0.0034851739 1 1
9350 336.9824 23.050616 0.0034851739 1 1
9400 304.46425 32.530218 0.0034851739 1 1
9450 317.55591 -22.265425 0.0034851739 1 1
9500 323.70901 -7.0159787 0.0034851739 1 1
9550 316.07308 28.062131 0.0034851739 1 1
9600 262.74608 -0.78519192 0.0034851739 1 1
9650 271.55045 -21.430123 0.0034851739 1 1
9700 239.6022 14.483637 0.0034851739 1 1
9750 338.1437 -0.72765302 0.0034851739 1 1
9800 334.50189 19.495144 0.0034851739 1 1
9850 354.87554 19.272719 0.0034851739 1 1
9900 334.02141 -22.393457 0.0034851739 1 1
9950 293.63651 19.178873 0.0034851739 1 1
10000 319.81736 21.904414 0.0034851739 1 1
Loop time of 1.84987 on 1 procs for 10000 steps with 44 atoms
Performance: 467.059 ns/day, 0.051 hours/ns, 5405.774 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 | 0.26152 | 0.26152 | 0.26152 | 0.0 | 14.14
Bond | 0.74069 | 0.74069 | 0.74069 | 0.0 | 40.04
Kspace | 0.30505 | 0.30505 | 0.30505 | 0.0 | 16.49
Neigh | 0.39991 | 0.39991 | 0.39991 | 0.0 | 21.62
Comm | 0.02261 | 0.02261 | 0.02261 | 0.0 | 1.22
Output | 0.0034585 | 0.0034585 | 0.0034585 | 0.0 | 0.19
Modify | 0.099979 | 0.099979 | 0.099979 | 0.0 | 5.40
Other | | 0.01666 | | | 0.90
Nlocal: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 823 ave 823 max 823 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 823
Ave neighs/atom = 18.7045
Ave special neighs/atom = 9.77273
Neighbor list builds = 10000
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:01

370
examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4
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@ -1,370 +0,0 @@
LAMMPS (20 Apr 2018)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
using 1 OpenMP thread(s) per MPI task
# two monomer nylon example
# reaction produces a condensed water molecule
units real
boundary p p p
atom_style full
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
angle_style class2
bond_style class2
dihedral_style class2
improper_style class2
read_data tiny_nylon.data
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
velocity all create 300.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
molecule mol2 rxn1_stp1_reacted.data_template
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
molecule mol3 rxn1_stp2_unreacted.data_template
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
molecule mol4 rxn1_stp2_reacted.data_template
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
thermo 50
# dump 1 all xyz 1 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 0.0 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 0.0 5.0 mol3 mol4 rxn1_stp2_map
WARNING: An atom in 'react #1' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
WARNING: An atom in 'react #2' changes bond connectivity but not atom type (../fix_bond_react.cpp:1489)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
fix 1 statted_grp nvt temp 300 300 100
fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
# restart 100 restart1 restart2
run 10000
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTs
3d grid and FFT values/proc = 252 2
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
WARNING: Inconsistent image flags (../domain.cpp:786)
Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 296.70408 -51.30066 0.0034851739 1 0
100 274.25324 46.715512 0.0034851739 1 1
150 471.61579 31.321598 0.0034851739 1 1
200 362.87766 42.061118 0.0034851739 1 1
250 367.58058 65.303109 0.0034851739 1 1
300 372.38236 -52.421725 0.0034851739 1 1
350 297.69957 17.869945 0.0034851739 1 1
400 258.30433 49.19156 0.0034851739 1 1
450 253.34384 -5.8162637 0.0034851739 1 1
500 269.96465 -43.337517 0.0034851739 1 1
550 303.23718 10.180246 0.0034851739 1 1
600 329.59579 -48.97461 0.0034851739 1 1
650 350.42568 50.983183 0.0034851739 1 1
700 342.03272 35.43465 0.0034851739 1 1
750 269.23405 -41.873166 0.0034851739 1 1
800 245.15025 13.953092 0.0034851739 1 1
850 257.85421 -3.1492141 0.0034851739 1 1
900 316.15644 7.7798301 0.0034851739 1 1
950 299.9124 -15.77014 0.0034851739 1 1
1000 302.89968 -17.049693 0.0034851739 1 1
1050 308.91651 71.84632 0.0034851739 1 1
1100 348.43932 -18.742012 0.0034851739 1 1
1150 309.03036 50.536311 0.0034851739 1 1
1200 318.9761 -16.905746 0.0034851739 1 1
1250 320.42806 -0.057975092 0.0034851739 1 1
1300 289.7824 18.200772 0.0034851739 1 1
1350 284.79836 -9.1978427 0.0034851739 1 1
1400 325.43292 42.082833 0.0034851739 1 1
1450 261.5041 -37.823325 0.0034851739 1 1
1500 298.88723 -5.1647385 0.0034851739 1 1
1550 291.37403 -7.7764201 0.0034851739 1 1
1600 293.83475 22.2458 0.0034851739 1 1
1650 293.80611 24.202512 0.0034851739 1 1
1700 291.70205 -23.397884 0.0034851739 1 1
1750 292.32437 -10.671214 0.0034851739 1 1
1800 302.01367 -11.671025 0.0034851739 1 1
1850 322.1651 24.438331 0.0034851739 1 1
1900 310.45076 45.343592 0.0034851739 1 1
1950 325.91745 -19.847809 0.0034851739 1 1
2000 276.89662 63.387098 0.0034851739 1 1
2050 311.33783 -24.683247 0.0034851739 1 1
2100 346.2336 -27.526891 0.0034851739 1 1
2150 345.30604 -15.722411 0.0034851739 1 1
2200 346.7718 -17.857633 0.0034851739 1 1
2250 304.28676 -1.9965581 0.0034851739 1 1
2300 322.56372 -31.786868 0.0034851739 1 1
2350 282.64326 6.1982735 0.0034851739 1 1
2400 286.65759 -63.207781 0.0034851739 1 1
2450 257.05528 32.931491 0.0034851739 1 1
2500 283.64386 26.912373 0.0034851739 1 1
2550 299.54005 27.277039 0.0034851739 1 1
2600 283.92503 14.660972 0.0034851739 1 1
2650 321.93453 -18.977358 0.0034851739 1 1
2700 376.7189 31.826935 0.0034851739 1 1
2750 372.20075 -32.821697 0.0034851739 1 1
2800 361.40604 83.035183 0.0034851739 1 1
2850 332.27269 -23.927452 0.0034851739 1 1
2900 331.14638 -0.12328446 0.0034851739 1 1
2950 303.67489 -24.078857 0.0034851739 1 1
3000 311.40462 21.563537 0.0034851739 1 1
3050 284.72849 -23.849667 0.0034851739 1 1
3100 303.48477 39.347763 0.0034851739 1 1
3150 264.2739 -0.22299878 0.0034851739 1 1
3200 300.03351 31.545323 0.0034851739 1 1
3250 288.56663 5.7225229 0.0034851739 1 1
3300 200.13238 -31.239655 0.0034851739 1 1
3350 231.32512 16.631728 0.0034851739 1 1
3400 260.57402 2.1717992 0.0034851739 1 1
3450 301.47128 -42.210623 0.0034851739 1 1
3500 321.77414 40.074365 0.0034851739 1 1
3550 353.21858 28.387783 0.0034851739 1 1
3600 331.45989 -57.800858 0.0034851739 1 1
3650 303.88123 44.86596 0.0034851739 1 1
3700 329.73833 -0.8061567 0.0034851739 1 1
3750 297.55588 -0.49626022 0.0034851739 1 1
3800 286.38794 -10.010003 0.0034851739 1 1
3850 290.17417 -43.51187 0.0034851739 1 1
3900 247.88933 51.23735 0.0034851739 1 1
3950 332.31324 -18.194985 0.0034851739 1 1
4000 325.56802 18.402825 0.0034851739 1 1
4050 338.37594 36.430977 0.0034851739 1 1
4100 370.95478 39.290285 0.0034851739 1 1
4150 348.47859 -7.0779683 0.0034851739 1 1
4200 241.30632 -33.371789 0.0034851739 1 1
4250 242.17258 -9.9861962 0.0034851739 1 1
4300 300.85311 -7.924429 0.0034851739 1 1
4350 273.15684 -21.257282 0.0034851739 1 1
4400 305.77464 -5.8720712 0.0034851739 1 1
4450 314.97697 45.037299 0.0034851739 1 1
4500 310.77723 16.958771 0.0034851739 1 1
4550 302.17421 12.156862 0.0034851739 1 1
4600 319.74799 6.8488914 0.0034851739 1 1
4650 270.86805 -13.767907 0.0034851739 1 1
4700 249.81731 -31.197484 0.0034851739 1 1
4750 285.86481 -9.8916332 0.0034851739 1 1
4800 233.98321 7.1338518 0.0034851739 1 1
4850 302.60551 49.262886 0.0034851739 1 1
4900 316.55055 34.663238 0.0034851739 1 1
4950 357.32741 11.583013 0.0034851739 1 1
5000 400.21044 -8.1780861 0.0034851739 1 1
5050 390.01845 -20.490268 0.0034851739 1 1
5100 378.84249 -41.328772 0.0034851739 1 1
5150 324.02039 -15.023852 0.0034851739 1 1
5200 262.08427 10.937367 0.0034851739 1 1
5250 255.75506 16.381495 0.0034851739 1 1
5300 277.84991 40.682283 0.0034851739 1 1
5350 302.92834 9.1989644 0.0034851739 1 1
5400 283.71964 -1.6583895 0.0034851739 1 1
5450 300.71261 -4.703054 0.0034851739 1 1
5500 343.54987 -0.30546396 0.0034851739 1 1
5550 369.51272 21.691639 0.0034851739 1 1
5600 372.69786 -38.679919 0.0034851739 1 1
5650 327.41256 11.352201 0.0034851739 1 1
5700 278.9861 -23.82728 0.0034851739 1 1
5750 308.30037 -20.756238 0.0034851739 1 1
5800 341.4559 28.058314 0.0034851739 1 1
5850 322.9786 -10.731862 0.0034851739 1 1
5900 304.53598 32.825105 0.0034851739 1 1
5950 287.17515 -36.780057 0.0034851739 1 1
6000 296.52688 18.782156 0.0034851739 1 1
6050 314.25411 15.99272 0.0034851739 1 1
6100 313.86572 3.4344108 0.0034851739 1 1
6150 325.64197 32.39212 0.0034851739 1 1
6200 367.4298 -27.161154 0.0034851739 1 1
6250 369.30937 39.020881 0.0034851739 1 1
6300 328.92245 -23.175612 0.0034851739 1 1
6350 305.6293 4.9011587 0.0034851739 1 1
6400 241.70456 -13.675247 0.0034851739 1 1
6450 265.66574 2.4049735 0.0034851739 1 1
6500 249.3592 13.420453 0.0034851739 1 1
6550 294.5367 10.856753 0.0034851739 1 1
6600 308.20246 18.992923 0.0034851739 1 1
6650 305.43756 -49.57151 0.0034851739 1 1
6700 320.27395 11.339101 0.0034851739 1 1
6750 321.7875 -23.463361 0.0034851739 1 1
6800 303.40316 7.6256997 0.0034851739 1 1
6850 297.18652 51.52186 0.0034851739 1 1
6900 284.19084 -8.496294 0.0034851739 1 1
6950 331.04173 13.227745 0.0034851739 1 1
7000 311.38027 -43.26105 0.0034851739 1 1
7050 286.82046 -14.171194 0.0034851739 1 1
7100 302.81691 12.058085 0.0034851739 1 1
7150 297.18018 -43.110658 0.0034851739 1 1
7200 332.46131 26.051496 0.0034851739 1 1
7250 262.72288 41.161451 0.0034851739 1 1
7300 250.62739 -23.440907 0.0034851739 1 1
7350 296.92141 35.869216 0.0034851739 1 1
7400 245.06807 -13.467896 0.0034851739 1 1
7450 272.2659 -23.292836 0.0034851739 1 1
7500 209.05776 13.888665 0.0034851739 1 1
7550 255.03716 4.9662624 0.0034851739 1 1
7600 312.26011 -37.350427 0.0034851739 1 1
7650 305.5823 55.208039 0.0034851739 1 1
7700 325.13382 -18.370791 0.0034851739 1 1
7750 363.24898 -22.473126 0.0034851739 1 1
7800 350.19254 26.792307 0.0034851739 1 1
7850 271.76418 -17.843445 0.0034851739 1 1
7900 272.70301 -11.709349 0.0034851739 1 1
7950 298.5993 -12.736235 0.0034851739 1 1
8000 274.52611 49.657345 0.0034851739 1 1
8050 304.73711 -0.52485689 0.0034851739 1 1
8100 328.29239 -39.901891 0.0034851739 1 1
8150 406.52096 2.8669076 0.0034851739 1 1
8200 332.17309 -51.168754 0.0034851739 1 1
8250 354.68419 53.003157 0.0034851739 1 1
8300 337.28934 20.766408 0.0034851739 1 1
8350 361.81133 -54.159227 0.0034851739 1 1
8400 305.59597 24.011667 0.0034851739 1 1
8450 303.25823 4.423341 0.0034851739 1 1
8500 253.50747 -11.026949 0.0034851739 1 1
8550 277.13504 23.204625 0.0034851739 1 1
8600 291.40211 -22.253861 0.0034851739 1 1
8650 307.93765 32.14162 0.0034851739 1 1
8700 309.1529 0.36279434 0.0034851739 1 1
8750 355.10326 11.677219 0.0034851739 1 1
8800 330.21328 19.235269 0.0034851739 1 1
8850 241.29109 21.707386 0.0034851739 1 1
8900 319.15363 -60.010115 0.0034851739 1 1
8950 308.88552 -57.637014 0.0034851739 1 1
9000 272.22373 51.15837 0.0034851739 1 1
9050 248.84947 7.3390565 0.0034851739 1 1
9100 221.91564 48.387079 0.0034851739 1 1
9150 298.03506 2.9058639 0.0034851739 1 1
9200 274.25114 -24.597819 0.0034851739 1 1
9250 334.08373 5.1079577 0.0034851739 1 1
9300 383.07285 -23.274763 0.0034851739 1 1
9350 335.00581 20.94212 0.0034851739 1 1
9400 309.23862 34.074744 0.0034851739 1 1
9450 312.62262 -28.468057 0.0034851739 1 1
9500 324.54274 2.851136 0.0034851739 1 1
9550 313.32781 22.468182 0.0034851739 1 1
9600 269.04372 4.064934 0.0034851739 1 1
9650 270.98476 -21.520127 0.0034851739 1 1
9700 236.8736 16.250728 0.0034851739 1 1
9750 333.94686 1.6864148 0.0034851739 1 1
9800 330.91875 12.150018 0.0034851739 1 1
9850 343.8603 25.338853 0.0034851739 1 1
9900 330.93364 -28.292992 0.0034851739 1 1
9950 291.25518 25.795948 0.0034851739 1 1
10000 319.25565 25.323846 0.0034851739 1 1
Loop time of 3.55353 on 4 procs for 10000 steps with 44 atoms
Performance: 243.139 ns/day, 0.099 hours/ns, 2814.105 timesteps/s
93.4% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0030422 | 0.10454 | 0.35211 | 44.8 | 2.94
Bond | 0.0063896 | 0.29222 | 0.94356 | 71.3 | 8.22
Kspace | 0.88508 | 1.6486 | 1.979 | 35.1 | 46.39
Neigh | 0.61154 | 0.62212 | 0.63307 | 1.0 | 17.51
Comm | 0.18944 | 0.24549 | 0.29196 | 7.9 | 6.91
Output | 0.0050066 | 0.011804 | 0.032134 | 10.8 | 0.33
Modify | 0.52282 | 0.60522 | 0.69588 | 7.9 | 17.03
Other | | 0.02359 | | | 0.66
Nlocal: 11 ave 44 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Nghost: 33 ave 44 max 0 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 205.75 ave 823 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 823
Ave neighs/atom = 18.7045
Ave special neighs/atom = 9.77273
Neighbor list builds = 10000
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:03

148
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@ -0,0 +1,148 @@
LAMMPS (5 Jun 2019)
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000181113 secs
read_data CPU = 0.0251833 secs
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTs
3d grid and FFT values/proc = 343 8
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
WARNING: Inconsistent image flags (../domain.cpp:784)
Per MPI rank memory allocation (min/avg/max) = 34.41 | 34.41 | 34.41 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 293.70542 -52.547388 0.0034851739 1 0
100 276.36755 54.81826 0.0034851739 1 1
150 448.65869 16.874435 0.0034851739 1 1
200 379.84257 11.578545 0.0034851739 1 1
250 298.21983 90.656585 0.0034851739 1 1
300 333.3111 -30.139607 0.0034851739 1 1
350 266.57108 6.4505134 0.0034851739 1 1
400 264.05476 10.513204 0.0034851739 1 1
450 250.70418 -18.635379 0.0034851739 1 1
500 261.21632 10.231013 0.0034851739 1 1
550 309.89024 -8.8299506 0.0034851739 1 1
600 373.45851 30.368993 0.0034851739 1 1
650 338.26242 9.0362267 0.0034851739 1 1
700 295.67794 -5.6007538 0.0034851739 1 1
750 310.86563 -59.228181 0.0034851739 1 1
800 286.22678 -9.9022407 0.0034851739 1 1
850 218.42135 27.845352 0.0034851739 1 1
900 259.62551 24.216336 0.0034851739 1 1
950 250.21307 -14.560985 0.0034851739 1 1
1000 274.29245 -0.38768626 0.0034851739 1 1
Loop time of 0.341061 on 1 procs for 1000 steps with 44 atoms
Performance: 253.327 ns/day, 0.095 hours/ns, 2932.025 timesteps/s
87.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.031135 | 0.031135 | 0.031135 | 0.0 | 9.13
Bond | 0.12623 | 0.12623 | 0.12623 | 0.0 | 37.01
Kspace | 0.036491 | 0.036491 | 0.036491 | 0.0 | 10.70
Neigh | 0.046395 | 0.046395 | 0.046395 | 0.0 | 13.60
Comm | 0.0025396 | 0.0025396 | 0.0025396 | 0.0 | 0.74
Output | 0.07775 | 0.07775 | 0.07775 | 0.0 | 22.80
Modify | 0.019219 | 0.019219 | 0.019219 | 0.0 | 5.64
Other | | 0.001306 | | | 0.38
Nlocal: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 2 ave 2 max 2 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 740 ave 740 max 740 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 740
Ave neighs/atom = 16.8182
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

148
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@ -0,0 +1,148 @@
LAMMPS (5 Jun 2019)
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000178751 secs
read_data CPU = 0.0385782 secs
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTs
3d grid and FFT values/proc = 252 2
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
WARNING: Inconsistent image flags (../domain.cpp:784)
Per MPI rank memory allocation (min/avg/max) = 34.42 | 34.77 | 35.45 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 293.70542 -52.547388 0.0034851739 1 0
100 276.36755 54.81826 0.0034851739 1 1
150 448.65869 16.874435 0.0034851739 1 1
200 379.84257 11.578545 0.0034851739 1 1
250 298.21983 90.656585 0.0034851739 1 1
300 333.3111 -30.139607 0.0034851739 1 1
350 266.57108 6.4505134 0.0034851739 1 1
400 264.05476 10.513204 0.0034851739 1 1
450 250.70418 -18.635379 0.0034851739 1 1
500 261.21632 10.231013 0.0034851739 1 1
550 309.89024 -8.8299506 0.0034851739 1 1
600 373.45851 30.368993 0.0034851739 1 1
650 338.26242 9.0362267 0.0034851739 1 1
700 295.67794 -5.6007538 0.0034851739 1 1
750 310.86563 -59.228181 0.0034851739 1 1
800 286.22678 -9.9022407 0.0034851739 1 1
850 218.42135 27.845352 0.0034851739 1 1
900 259.62551 24.216336 0.0034851739 1 1
950 250.21307 -14.560985 0.0034851739 1 1
1000 274.29245 -0.38768626 0.0034851739 1 1
Loop time of 0.271242 on 4 procs for 1000 steps with 44 atoms
Performance: 318.535 ns/day, 0.075 hours/ns, 3686.747 timesteps/s
98.6% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00023773 | 0.0077322 | 0.016042 | 8.4 | 2.85
Bond | 0.00073385 | 0.032108 | 0.08446 | 19.4 | 11.84
Kspace | 0.041659 | 0.098095 | 0.13373 | 12.3 | 36.16
Neigh | 0.028894 | 0.029247 | 0.029558 | 0.1 | 10.78
Comm | 0.012367 | 0.013642 | 0.01503 | 0.9 | 5.03
Output | 0.032475 | 0.040504 | 0.061019 | 5.9 | 14.93
Modify | 0.032934 | 0.049086 | 0.0577 | 4.3 | 18.10
Other | | 0.0008281 | | | 0.31
Nlocal: 11 ave 21 max 0 min
Histogram: 1 1 0 0 0 0 0 0 0 2
Nghost: 32.5 ave 43 max 23 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Neighs: 185 ave 376 max 0 min
Histogram: 2 0 0 0 0 0 0 0 0 2
Total # of neighbors = 740
Ave neighs/atom = 16.8182
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

147
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LAMMPS (5 Jun 2019)
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000217102 secs
read_data CPU = 0.00630778 secs
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
dynamic group bond_react_MASTER_group defined
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTs
3d grid and FFT values/proc = 343 8
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
WARNING: Inconsistent image flags (../domain.cpp:784)
Per MPI rank memory allocation (min/avg/max) = 34.35 | 34.35 | 34.35 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 416.49412 -20.293038 0.0034851739 1 0
100 746.49323 91.912227 0.0034851739 1 1
150 515.15907 -1.4024709 0.0034851739 1 1
200 441.14572 -19.333087 0.0034851739 1 1
250 376.40996 30.717679 0.0034851739 1 1
300 326.15127 -3.0433799 0.0034851739 1 1
350 326.21116 6.235391 0.0034851739 1 1
400 366.48556 3.9807338 0.0034851739 1 1
450 313.79097 7.6674629 0.0034851739 1 1
500 278.89836 14.102052 0.0034851739 1 1
550 267.50214 18.241417 0.0034851739 1 1
600 276.28064 7.4649611 0.0034851739 1 1
650 255.26713 -8.5258573 0.0034851739 1 1
700 258.59752 -5.3341215 0.0034851739 1 1
750 263.71264 33.369869 0.0034851739 1 1
800 246.22976 -15.349137 0.0034851739 1 1
850 255.93887 16.331669 0.0034851739 1 1
900 239.72525 -0.20075789 0.0034851739 1 1
950 213.73064 12.17619 0.0034851739 1 1
1000 218.25094 -9.0955642 0.0034851739 1 1
Loop time of 0.348252 on 1 procs for 1000 steps with 44 atoms
Performance: 248.096 ns/day, 0.097 hours/ns, 2871.483 timesteps/s
91.8% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.031941 | 0.031941 | 0.031941 | 0.0 | 9.17
Bond | 0.13031 | 0.13031 | 0.13031 | 0.0 | 37.42
Kspace | 0.037554 | 0.037554 | 0.037554 | 0.0 | 10.78
Neigh | 0.047397 | 0.047397 | 0.047397 | 0.0 | 13.61
Comm | 0.0025814 | 0.0025814 | 0.0025814 | 0.0 | 0.74
Output | 0.083526 | 0.083526 | 0.083526 | 0.0 | 23.98
Modify | 0.013602 | 0.013602 | 0.013602 | 0.0 | 3.91
Other | | 0.001336 | | | 0.38
Nlocal: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 3 ave 3 max 3 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 818 ave 818 max 818 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 818
Ave neighs/atom = 18.5909
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00

147
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LAMMPS (5 Jun 2019)
Reading data file ...
orthogonal box = (-25 -25 -25) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
44 atoms
reading velocities ...
44 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
29 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
42 bonds
reading angles ...
74 angles
reading dihedrals ...
100 dihedrals
reading impropers ...
44 impropers
Finding 1-2 1-3 1-4 neighbors ...
special bond factors lj: 0 0 0
special bond factors coul: 0 0 0
4 = max # of 1-2 neighbors
6 = max # of 1-3 neighbors
12 = max # of 1-4 neighbors
41 = max # of special neighbors
special bonds CPU = 0.000163256 secs
read_data CPU = 0.0244579 secs
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 14
25 angles with max type 28
23 dihedrals with max type 36
14 impropers with max type 11
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 13
31 angles with max type 27
39 dihedrals with max type 33
20 impropers with max type 1
Read molecule mol3:
15 atoms with max type 9
14 bonds with max type 13
25 angles with max type 27
30 dihedrals with max type 33
16 impropers with max type 1
Read molecule mol4:
15 atoms with max type 11
13 bonds with max type 15
19 angles with max type 29
16 dihedrals with max type 32
10 impropers with max type 13
WARNING: Bond/react: Atom affected by reaction rxn1 too close to template edge (../fix_bond_react.cpp:1785)
WARNING: Bond/react: Atom affected by reaction rxn2 too close to template edge (../fix_bond_react.cpp:1785)
dynamic group bond_react_MASTER_group defined
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:319)
G vector (1/distance) = 0.0534597
grid = 2 2 2
stencil order = 5
estimated absolute RMS force accuracy = 0.0402256
estimated relative force accuracy = 0.000121138
using double precision FFTs
3d grid and FFT values/proc = 252 2
Neighbor list info ...
update every 1 steps, delay 10 steps, check yes
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 10.5
ghost atom cutoff = 10.5
binsize = 5.25, bins = 10 10 10
2 neighbor lists, perpetual/occasional/extra = 1 1 0
(1) pair lj/class2/coul/long, perpetual
attributes: half, newton on
pair build: half/bin/newton
stencil: half/bin/3d/newton
bin: standard
(2) fix bond/react, occasional, copy from (1)
attributes: half, newton on
pair build: copy
stencil: none
bin: none
Setting up Verlet run ...
Unit style : real
Current step : 0
Time step : 1
WARNING: Inconsistent image flags (../domain.cpp:784)
Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 300 346.78165 0.0034851739 0 0
50 416.49412 -20.293038 0.0034851739 1 0
100 746.49323 91.912227 0.0034851739 1 1
150 515.15907 -1.4024709 0.0034851739 1 1
200 441.14572 -19.333087 0.0034851739 1 1
250 376.40996 30.717679 0.0034851739 1 1
300 326.15127 -3.0433799 0.0034851739 1 1
350 326.21116 6.235391 0.0034851739 1 1
400 366.48556 3.9807338 0.0034851739 1 1
450 313.79097 7.6674629 0.0034851739 1 1
500 278.89836 14.102052 0.0034851739 1 1
550 267.50214 18.241417 0.0034851739 1 1
600 276.28064 7.4649611 0.0034851739 1 1
650 255.26713 -8.5258573 0.0034851739 1 1
700 258.59752 -5.3341215 0.0034851739 1 1
750 263.71264 33.369869 0.0034851739 1 1
800 246.22976 -15.349137 0.0034851739 1 1
850 255.93887 16.331669 0.0034851739 1 1
900 239.72525 -0.20075789 0.0034851739 1 1
950 213.73064 12.17619 0.0034851739 1 1
1000 218.25094 -9.0955642 0.0034851739 1 1
Loop time of 0.254903 on 4 procs for 1000 steps with 44 atoms
Performance: 338.952 ns/day, 0.071 hours/ns, 3923.053 timesteps/s
99.8% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.00014252 | 0.0090715 | 0.021332 | 9.6 | 3.56
Bond | 0.00047028 | 0.037261 | 0.10789 | 22.7 | 14.62
Kspace | 0.051006 | 0.12756 | 0.1693 | 13.6 | 50.04
Neigh | 0.035644 | 0.036088 | 0.036523 | 0.2 | 14.16
Comm | 0.013984 | 0.016074 | 0.018676 | 1.6 | 6.31
Output | 0.0002816 | 0.00033726 | 0.00044251 | 0.0 | 0.13
Modify | 0.023697 | 0.027803 | 0.033552 | 2.5 | 10.91
Other | | 0.0007123 | | | 0.28
Nlocal: 11 ave 29 max 0 min
Histogram: 1 1 0 0 1 0 0 0 0 1
Nghost: 25 ave 31 max 12 min
Histogram: 1 0 0 0 0 0 0 0 2 1
Neighs: 204.5 ave 443 max 0 min
Histogram: 2 0 0 0 0 0 0 0 1 1
Total # of neighbors = 818
Ave neighs/atom = 18.5909
Ave special neighs/atom = 9.77273
Neighbor list builds = 1000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:00