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update log files

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This commit is contained in:
Jacob Gissinger
2021-02-04 21:00:46 -05:00
parent 9a0805529c
commit dde3a8cebb
4 changed files with 400 additions and 4140 deletions
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4137
examples/USER/reaction/create_atoms_polystyrene/8procs_out.lammps
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11
examples/USER/reaction/create_atoms_polystyrene/in.grow_styrene
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@ -1,4 +1,4 @@
# use bond/react 'create atoms' feature to add 50 new styrene monomers to chain
# use bond/react 'create atoms' feature to add 30 new styrene monomers to chain
units real
@ -20,7 +20,12 @@ improper_style class2
variable T equal 530
read_data trimer.data
read_data trimer.data &
extra/bond/per/atom 5 &
extra/angle/per/atom 15 &
extra/dihedral/per/atom 15 &
extra/improper/per/atom 25 &
extra/special/per/atom 25
molecule mol1 grow_styrene_pre.data_template
molecule mol2 grow_styrene_post.data_template
@ -28,7 +33,7 @@ molecule mol2 grow_styrene_post.data_template
fix myrxns all bond/react stabilization yes statted_grp .03 &
react rxn1 all 1 0 3.0 mol1 mol2 grow_styrene.map &
modify_create fit create_fit overlap 2.0 &
stabilize_steps 100 max_rxn 50
stabilize_steps 100 max_rxn 30
fix 1 statted_grp_REACT nvt temp $T $T 100

196
examples/USER/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.1 Normal file
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LAMMPS (24 Dec 2020)
Reading data file ...
orthogonal box = (50.000000 50.000000 50.000000) to (250.00000 250.00000 250.00000)
1 by 1 by 1 MPI processor grid
reading atoms ...
48 atoms
reading velocities ...
48 velocities
scanning bonds ...
8 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
33 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
50 bonds
reading angles ...
84 angles
reading dihedrals ...
127 dihedrals
reading impropers ...
36 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
8 = max # of 1-3 neighbors
17 = max # of 1-4 neighbors
46 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.077 seconds
Read molecule template mol1:
1 molecules
30 atoms with max type 6
31 bonds with max type 10
51 angles with max type 16
73 dihedrals with max type 19
21 impropers with max type 7
Read molecule template mol2:
1 molecules
46 atoms with max type 6
48 bonds with max type 13
81 angles with max type 22
121 dihedrals with max type 36
35 impropers with max type 9
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00060000000 (../kspace.cpp:324)
using 12-bit tables for long-range coulomb (../kspace.cpp:339)
G vector (1/distance) = 0.20144813
grid = 45 45 45
stencil order = 5
estimated absolute RMS force accuracy = 0.00053712952
estimated relative force accuracy = 1.6175496e-06
using double precision KISS FFT
3d grid and FFT values/proc = 125000 91125
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 = 39 39 39
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
Per MPI rank memory allocation (min/avg/max) = 48.02 | 48.02 | 48.02 Mbytes
Step Temp Press Density f_myrxns[1]
0 496.23742 0.9983211 6.4856516e-05 0
100 534.05394 -0.76952227 6.4856516e-05 0
200 552.2225 -0.55375493 6.4856516e-05 0
300 857.52834 -0.4272061 8.6475354e-05 1
400 714.10681 1.5004615 8.6475354e-05 1
500 678.19171 0.21965471 8.6475354e-05 1
600 572.3234 0.87879933 8.6475354e-05 1
700 996.17398 -0.24269717 0.00010809419 2
800 904.50395 1.3662054 0.00010809419 2
900 1097.1568 -2.2909907 0.00012971303 3
1000 954.08892 1.7705672 0.00012971303 3
1100 1102.0377 -1.7018446 0.00015133187 4
1200 1239.785 -0.30442903 0.00015133187 4
1300 1388.4127 1.3301175 0.00017295071 5
1400 1559.3853 1.6709729 0.00017295071 5
1500 1471.8623 0.8268427 0.00017295071 5
1600 1543.6793 2.1987908 0.00019456955 6
1700 1694.5595 0.48852817 0.00019456955 6
1800 1632.7737 -1.4617692 0.00021618839 7
1900 1922.6502 1.1664257 0.00021618839 7
2000 2223.503 -0.95799878 0.00023780722 8
2100 2142.6035 0.88444463 0.00025942606 9
2200 2298.8636 3.4239313 0.00025942606 9
2300 2252.4355 0.82167302 0.00025942606 9
2400 2321.0788 1.7499714 0.00025942606 9
2500 2095.6715 0.55288444 0.00025942606 9
2600 2136.0316 -3.833114 0.00025942606 9
2700 2466.3134 -2.2519511 0.00025942606 9
2800 2294.3454 1.0637304 0.00025942606 9
2900 2340.3891 1.3997049 0.0002810449 10
3000 2272.0013 -0.27591886 0.0002810449 10
3100 2333.9696 -0.11772138 0.0002810449 10
3200 2409.0946 -1.025473 0.0002810449 10
3300 2148.023 1.6752329 0.0002810449 10
3400 2267.636 -0.45297583 0.0002810449 10
3500 2457.622 0.35627297 0.0002810449 10
3600 2288.008 -15.516626 0.00030266374 11
3700 2458.2681 1.4571773 0.00030266374 11
3800 2566.7623 -29.140553 0.00032428258 12
3900 2839.4062 0.64583638 0.00032428258 12
4000 2893.9852 -52.954497 0.00034590142 13
4100 3021.3611 -65.03731 0.00036752025 14
4200 3002.7136 1.5750081 0.00036752025 14
4300 3218.6248 -120.74039 0.00038913909 15
4400 3345.1482 -0.96545269 0.00038913909 15
4500 3603.2429 1.2438833 0.00038913909 15
4600 3129.8814 -249.91806 0.00041075793 16
4700 3769.052 -289.24351 0.00043237677 17
4800 3560.4714 -3.1655406 0.00043237677 17
4900 3452.2717 -2.1270765 0.00043237677 17
5000 3594.3247 -523.48506 0.00045399561 18
5100 3578.4199 1.0009097 0.00045399561 18
5200 3822.1566 1.0526914 0.00047561445 19
5300 3901.8883 -0.14607602 0.00047561445 19
5400 4059.3644 -1.7789927 0.00049723329 20
5500 4163.6847 1.0240127 0.00049723329 20
5600 4109.1649 0.80199787 0.00049723329 20
5700 4391.2091 2.8730036 0.00049723329 20
5800 4279.6579 -0.36499822 0.00051885212 21
5900 4296.2695 -1.3064528 0.00051885212 21
6000 4065.3758 -2.0483224 0.00051885212 21
6100 4772.5362 -2.6814694 0.00054047096 22
6200 4627.029 2.999215 0.0005620898 23
6300 5120.7881 0.65372968 0.00058370864 24
6400 4588.9559 3.7570705 0.00058370864 24
6500 5008.7814 2.3595833 0.00060532748 25
6600 5195.0053 1.4641612 0.00060532748 25
6700 5622.293 -0.33396047 0.00062694632 26
6800 5515.1957 -4.234874 0.00062694632 26
6900 5156.7455 0.40171954 0.00064856516 27
7000 5120.1639 -1.6065245 0.00064856516 27
7100 5650.0327 0.94436323 0.00067018399 28
7200 5985.1115 -3.8940347 0.00069180283 29
7300 5983.197 0.5293568 0.00069180283 29
7400 6001.1559 -0.13712834 0.00071342167 30
7500 5889.2134 0.17230892 0.00071342167 30
7600 5797.31 2.0920058 0.00071342167 30
7700 5865.2783 -0.18556395 0.00071342167 30
7800 6207.0659 -5.6237083 0.00071342167 30
7900 5627.5108 -2.3718942 0.00071342167 30
8000 5823.9502 -0.85418578 0.00071342167 30
Loop time of 184.87 on 1 procs for 8000 steps with 528 atoms
Performance: 3.739 ns/day, 6.419 hours/ns, 43.274 timesteps/s
99.9% CPU use with 1 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 3.3043 | 3.3043 | 3.3043 | 0.0 | 1.79
Bond | 8.0003 | 8.0003 | 8.0003 | 0.0 | 4.33
Kspace | 168.33 | 168.33 | 168.33 | 0.0 | 91.05
Neigh | 4.6322 | 4.6322 | 4.6322 | 0.0 | 2.51
Comm | 0.077927 | 0.077927 | 0.077927 | 0.0 | 0.04
Output | 0.0020548 | 0.0020548 | 0.0020548 | 0.0 | 0.00
Modify | 0.5005 | 0.5005 | 0.5005 | 0.0 | 0.27
Other | | 0.02483 | | | 0.01
Nlocal: 528.000 ave 528 max 528 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 341.000 ave 341 max 341 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 35111.0 ave 35111 max 35111 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 35111
Ave neighs/atom = 66.498106
Ave special neighs/atom = 11.409091
Neighbor list builds = 8000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:03:05

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examples/USER/reaction/create_atoms_polystyrene/log.24Dec20.grow_styrene.g++.4 Normal file
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LAMMPS (24 Dec 2020)
Reading data file ...
orthogonal box = (50.000000 50.000000 50.000000) to (250.00000 250.00000 250.00000)
1 by 2 by 2 MPI processor grid
reading atoms ...
48 atoms
reading velocities ...
48 velocities
scanning bonds ...
8 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
33 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
50 bonds
reading angles ...
84 angles
reading dihedrals ...
127 dihedrals
reading impropers ...
36 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
8 = max # of 1-3 neighbors
17 = max # of 1-4 neighbors
46 = max # of special neighbors
special bonds CPU = 0.000 seconds
read_data CPU = 0.007 seconds
Read molecule template mol1:
1 molecules
30 atoms with max type 6
31 bonds with max type 10
51 angles with max type 16
73 dihedrals with max type 19
21 impropers with max type 7
Read molecule template mol2:
1 molecules
46 atoms with max type 6
48 bonds with max type 13
81 angles with max type 22
121 dihedrals with max type 36
35 impropers with max type 9
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp_REACT defined
PPPM initialization ...
WARNING: System is not charge neutral, net charge = -0.00060000000 (../kspace.cpp:324)
using 12-bit tables for long-range coulomb (../kspace.cpp:339)
G vector (1/distance) = 0.20144813
grid = 45 45 45
stencil order = 5
estimated absolute RMS force accuracy = 0.00053712952
estimated relative force accuracy = 1.6175496e-06
using double precision KISS FFT
3d grid and FFT values/proc = 39200 24300
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 = 39 39 39
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
Per MPI rank memory allocation (min/avg/max) = 38.70 | 38.92 | 39.43 Mbytes
Step Temp Press Density f_myrxns[1]
0 496.23742 0.9983211 6.4856516e-05 0
100 534.05394 -0.76952227 6.4856516e-05 0
200 552.2225 -0.55375493 6.4856516e-05 0
300 857.52834 -0.4272061 8.6475354e-05 1
400 714.10681 1.5004615 8.6475354e-05 1
500 678.19171 0.21965471 8.6475354e-05 1
600 572.3234 0.87879933 8.6475354e-05 1
700 996.17398 -0.24269717 0.00010809419 2
800 904.50395 1.3662054 0.00010809419 2
900 1097.1568 -2.2909907 0.00012971303 3
1000 954.08892 1.7705672 0.00012971303 3
1100 1102.0377 -1.7018446 0.00015133187 4
1200 1239.785 -0.30442903 0.00015133187 4
1300 1388.4127 1.3301175 0.00017295071 5
1400 1559.3853 1.6709729 0.00017295071 5
1500 1471.8623 0.8268427 0.00017295071 5
1600 1543.6793 2.1987908 0.00019456955 6
1700 1694.5595 0.48852817 0.00019456955 6
1800 1632.7737 -1.4617692 0.00021618839 7
1900 1922.6502 1.1664257 0.00021618839 7
2000 2223.503 -0.95799878 0.00023780722 8
2100 2142.6035 0.88444463 0.00025942606 9
2200 2298.8636 3.4239313 0.00025942606 9
2300 2252.4355 0.82167302 0.00025942606 9
2400 2321.0788 1.7499714 0.00025942606 9
2500 2095.6715 0.55288444 0.00025942606 9
2600 2136.0316 -3.833114 0.00025942606 9
2700 2466.3134 -2.2519511 0.00025942606 9
2800 2294.3454 1.0637304 0.00025942606 9
2900 2340.3891 1.3997049 0.0002810449 10
3000 2272.0013 -0.27591886 0.0002810449 10
3100 2333.9696 -0.11772138 0.0002810449 10
3200 2409.0946 -1.025473 0.0002810449 10
3300 2148.023 1.6752329 0.0002810449 10
3400 2267.636 -0.45297583 0.0002810449 10
3500 2457.622 0.35627297 0.0002810449 10
3600 2288.008 -15.516626 0.00030266374 11
3700 2458.2681 1.4571773 0.00030266374 11
3800 2566.7623 -29.140553 0.00032428258 12
3900 2839.4062 0.64583638 0.00032428258 12
4000 2893.2204 -53.187892 0.00034590142 13
4100 3024.6375 -65.068146 0.00036752025 14
4200 3004.6784 1.4155214 0.00036752025 14
4300 3033.1895 1.8572273 0.00036752025 14
4400 3157.2542 -0.92462977 0.00036752025 14
4500 3557.7137 -194.46498 0.00038913909 15
4600 3096.485 -1.830492 0.00038913909 15
4700 3488.088 -286.81055 0.00041075793 16
4800 3390.5493 -372.77818 0.00043237677 17
4900 3773.7226 -446.58574 0.00045399561 18
5000 3703.0159 -0.81188551 0.00045399561 18
5100 4051.3067 1.2567439 0.00045399561 18
5200 3813.3682 0.92945737 0.00047561445 19
5300 4036.0078 -2.5336258 0.00049723329 20
5400 4219.803 -0.96928261 0.00049723329 20
5500 4433.7447 -0.026762463 0.00051885212 21
5600 4477.4505 -1.417316 0.00054047096 22
5700 4500.0306 -1.0551443 0.00054047096 22
5800 4600.3507 -4.9580056 0.00054047096 22
5900 4765.4978 -2.2546941 0.0005620898 23
6000 5442.6193 0.91161284 0.00058370864 24
6100 5086.8047 -0.9875332 0.00060532748 25
6200 5485.3437 -2.8296626 0.00062694632 26
6300 4988.0396 -0.15179023 0.00064856516 27
6400 5597.3703 4.2941885 0.00067018399 28
6500 5677.0263 -2.8611595 0.00069180283 29
6600 6058.0009 1.4111778 0.00071342167 30
6700 5859.0817 -2.5782466 0.00071342167 30
6800 5879.3941 -4.5681807 0.00071342167 30
6900 6398.288 2.5259412 0.00071342167 30
7000 6250.1096 -2.6049627 0.00071342167 30
7100 5849.651 -0.44062578 0.00071342167 30
7200 5778.6532 -0.27299118 0.00071342167 30
7300 5977.6661 4.2483639 0.00071342167 30
7400 5862.4231 1.0289519 0.00071342167 30
7500 6482.376 7.5412373 0.00071342167 30
7600 5810.4325 1.0343075 0.00071342167 30
7700 5916.7304 2.304302 0.00071342167 30
7800 5869.9504 -0.5946555 0.00071342167 30
7900 5804.0522 -4.1207689 0.00071342167 30
8000 6077.1704 0.52211243 0.00071342167 30
Loop time of 60.5603 on 4 procs for 8000 steps with 528 atoms
Performance: 11.413 ns/day, 2.103 hours/ns, 132.100 timesteps/s
99.9% CPU use with 4 MPI tasks x no OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0041695 | 0.90113 | 2.3423 | 102.8 | 1.49
Bond | 0.011606 | 2.1188 | 5.8107 | 163.9 | 3.50
Kspace | 47.987 | 52.817 | 55.679 | 43.7 | 87.21
Neigh | 3.5961 | 3.6262 | 3.6496 | 1.2 | 5.99
Comm | 0.11097 | 0.16569 | 0.26369 | 15.3 | 0.27
Output | 0.0020366 | 0.0023427 | 0.0032469 | 1.1 | 0.00
Modify | 0.62302 | 0.91659 | 1.1227 | 21.5 | 1.51
Other | | 0.0126 | | | 0.02
Nlocal: 132.000 ave 295 max 0 min
Histogram: 2 0 0 0 0 0 0 1 0 1
Nghost: 133.000 ave 349 max 0 min
Histogram: 2 0 0 0 0 1 0 0 0 1
Neighs: 8383.50 ave 20143 max 0 min
Histogram: 2 0 0 0 0 0 1 0 0 1
Total # of neighbors = 33534
Ave neighs/atom = 63.511364
Ave special neighs/atom = 11.409091
Neighbor list builds = 8000
Dangerous builds = 0
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:01:00