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make filenames comply with LAMMPS conventions and add reference log files

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This commit is contained in:
Axel Kohlmeyer
2018-05-03 16:03:37 -04:00
parent c8a0689d78
commit 53cc609c4c
6 changed files with 1073 additions and 3 deletions
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4
examples/USER/misc/bond_react/nylon,6-6_melt/infromdata.class2 → examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt
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@ -6,7 +6,7 @@ boundary p p p
atom_style full
kspace_style pppm 1.0e-2 # actually, this appears required to check 1-3 neighbors
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
@ -46,7 +46,7 @@ thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative
# restart 100 restart1 restart2
run 200000
run 200
# write_restart restart_longrun
# write_data restart_longrun.data

170
examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 Normal file
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@ -0,0 +1,170 @@
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
# 35,000 atom nylon melt example
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 large_nylon_melt.data.gz
orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065)
1 by 1 by 1 MPI processor grid
reading atoms ...
35200 atoms
reading velocities ...
35200 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
31 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
33600 bonds
reading angles ...
59200 angles
reading dihedrals ...
80000 dihedrals
reading impropers ...
35200 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 800.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 12
25 angles with max type 24
23 dihedrals with max type 33
14 impropers with max type 9
molecule mol2 rxn1_stp1_reacted.data_template
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 11
31 angles with max type 23
39 dihedrals with max type 30
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 11
25 angles with max type 23
30 dihedrals with max type 30
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 13
19 angles with max type 25
16 dihedrals with max type 29
10 impropers with max type 11
thermo 50
# dump 1 all xyz 100 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
# stable at 800K
fix 1 statted_grp nvt temp 800 800 100
# in order to customize behavior of reacting atoms,
# you can use the internally created 'bond_react_MASTER_group', like so:
# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
# restart 100 restart1 restart2
run 200
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.20765
grid = 18 18 18
stencil order = 5
estimated absolute RMS force accuracy = 0.0333156
estimated relative force accuracy = 0.000100329
using double precision FFTs
3d grid and FFT values/proc = 12167 5832
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 = 15 15 15
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
Per MPI rank memory allocation (min/avg/max) = 209.1 | 209.1 | 209.1 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 800 3666.3948 0.80366765 0 0
50 673.95238 -9670.9169 0.80366765 31 0
100 693.69241 -4696.4359 0.80366765 57 22
150 715.44689 -14740.892 0.80366765 77 50
200 721.16898 -1411.95 0.80366765 84 66
Loop time of 107.389 on 1 procs for 200 steps with 35200 atoms
Performance: 0.161 ns/day, 149.151 hours/ns, 1.862 timesteps/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 | 27.191 | 27.191 | 27.191 | 0.0 | 25.32
Bond | 11.46 | 11.46 | 11.46 | 0.0 | 10.67
Kspace | 4.2507 | 4.2507 | 4.2507 | 0.0 | 3.96
Neigh | 55.544 | 55.544 | 55.544 | 0.0 | 51.72
Comm | 0.41715 | 0.41715 | 0.41715 | 0.0 | 0.39
Output | 0.0011044 | 0.0011044 | 0.0011044 | 0.0 | 0.00
Modify | 8.4756 | 8.4756 | 8.4756 | 0.0 | 7.89
Other | | 0.04897 | | | 0.05
Nlocal: 35200 ave 35200 max 35200 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 38406 ave 38406 max 38406 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 6.92787e+06 ave 6.92787e+06 max 6.92787e+06 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 6927872
Ave neighs/atom = 196.815
Ave special neighs/atom = 9.83489
Neighbor list builds = 200
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:01:48

170
examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 Normal file
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@ -0,0 +1,170 @@
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
# 35,000 atom nylon melt example
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 large_nylon_melt.data.gz
orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065)
2 by 1 by 2 MPI processor grid
reading atoms ...
35200 atoms
reading velocities ...
35200 velocities
scanning bonds ...
9 = max bonds/atom
scanning angles ...
21 = max angles/atom
scanning dihedrals ...
31 = max dihedrals/atom
scanning impropers ...
29 = max impropers/atom
reading bonds ...
33600 bonds
reading angles ...
59200 angles
reading dihedrals ...
80000 dihedrals
reading impropers ...
35200 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 800.0 4928459 dist gaussian
molecule mol1 rxn1_stp1_unreacted.data_template
Read molecule mol1:
18 atoms with max type 8
16 bonds with max type 12
25 angles with max type 24
23 dihedrals with max type 33
14 impropers with max type 9
molecule mol2 rxn1_stp1_reacted.data_template
Read molecule mol2:
18 atoms with max type 9
17 bonds with max type 11
31 angles with max type 23
39 dihedrals with max type 30
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 11
25 angles with max type 23
30 dihedrals with max type 30
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 13
19 angles with max type 25
16 dihedrals with max type 29
10 impropers with max type 11
thermo 50
# dump 1 all xyz 100 test_vis.xyz
fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
dynamic group bond_react_MASTER_group defined
dynamic group statted_grp defined
# stable at 800K
fix 1 statted_grp nvt temp 800 800 100
# in order to customize behavior of reacting atoms,
# you can use the internally created 'bond_react_MASTER_group', like so:
# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
# restart 100 restart1 restart2
run 200
PPPM initialization ...
using 12-bit tables for long-range coulomb (../kspace.cpp:321)
G vector (1/distance) = 0.20765
grid = 18 18 18
stencil order = 5
estimated absolute RMS force accuracy = 0.0333156
estimated relative force accuracy = 0.000100329
using double precision FFTs
3d grid and FFT values/proc = 4508 1620
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 = 15 15 15
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
Per MPI rank memory allocation (min/avg/max) = 81.11 | 81.13 | 81.15 Mbytes
Step Temp Press Density f_myrxns[1] f_myrxns[2]
0 800 3666.3948 0.80366765 0 0
50 673.95238 -9670.9169 0.80366765 31 0
100 693.69241 -4696.4359 0.80366765 57 22
150 715.43654 -14742.205 0.80366765 77 50
200 721.1906 -1411.4303 0.80366765 84 66
Loop time of 56.2311 on 4 procs for 200 steps with 35200 atoms
Performance: 0.307 ns/day, 78.099 hours/ns, 3.557 timesteps/s
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 | 13.86 | 14.034 | 14.406 | 5.8 | 24.96
Bond | 5.5592 | 5.5952 | 5.6492 | 1.4 | 9.95
Kspace | 2.3969 | 2.7523 | 2.9203 | 12.5 | 4.89
Neigh | 27.265 | 27.268 | 27.271 | 0.0 | 48.49
Comm | 0.75523 | 0.77355 | 0.79381 | 1.7 | 1.38
Output | 0.00051904 | 0.0007363 | 0.0013669 | 0.0 | 0.00
Modify | 5.7629 | 5.7634 | 5.7641 | 0.0 | 10.25
Other | | 0.04441 | | | 0.08
Nlocal: 8800 ave 8912 max 8666 min
Histogram: 1 0 0 1 0 0 0 0 1 1
Nghost: 18358.8 ave 18432 max 18189 min
Histogram: 1 0 0 0 0 0 0 0 1 2
Neighs: 1.73197e+06 ave 1.77209e+06 max 1.68475e+06 min
Histogram: 1 0 1 0 0 0 0 0 0 2
Total # of neighbors = 6927873
Ave neighs/atom = 196.815
Ave special neighs/atom = 9.83489
Neighbor list builds = 200
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:57

2
examples/USER/misc/bond_react/tiny_nylon/infromdata.class2 → examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon
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@ -7,7 +7,7 @@ boundary p p p
atom_style full
kspace_style pppm 1.0e-2 # actually, this appears required to make LAMMPS to check 1-3 neighbors
kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5

365
examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 Normal file
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@ -0,0 +1,365 @@
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 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
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
100 275.26011 39.120329 0.0034851739 1 1
150 438.68516 35.257539 0.0034851739 1 1
200 394.48971 15.444537 0.0034851739 1 1
250 356.00369 50.185792 0.0034851739 1 1
300 301.25816 -26.891497 0.0034851739 1 1
350 279.17264 12.694513 0.0034851739 1 1
400 248.71641 10.684558 0.0034851739 1 1
450 240.30602 12.963034 0.0034851739 1 1
500 252.71279 0.91620356 0.0034851739 1 1
550 300.56824 18.541436 0.0034851739 1 1
600 306.46441 -1.9736081 0.0034851739 1 1
650 336.4537 21.474831 0.0034851739 1 1
700 323.46217 8.486376 0.0034851739 1 1
750 271.87146 5.9615231 0.0034851739 1 1
800 268.43041 36.676068 0.0034851739 1 1
850 269.02683 7.6295416 0.0034851739 1 1
900 282.03605 -1.4688833 0.0034851739 1 1
950 243.69136 -22.771489 0.0034851739 1 1
1000 285.01348 17.925748 0.0034851739 1 1
1050 383.47985 0.70536985 0.0034851739 1 1
1100 368.97167 -4.3046933 0.0034851739 1 1
1150 373.64459 6.3491837 0.0034851739 1 1
1200 332.90575 -36.501095 0.0034851739 1 1
1250 314.04078 -13.382767 0.0034851739 1 1
1300 305.84166 4.7713641 0.0034851739 1 1
1350 286.22145 37.621803 0.0034851739 1 1
1400 265.52855 23.621002 0.0034851739 1 1
1450 281.807 -31.266828 0.0034851739 1 1
1500 275.33855 33.495565 0.0034851739 1 1
1550 273.04973 -22.913871 0.0034851739 1 1
1600 308.18478 -17.98151 0.0034851739 1 1
1650 333.27664 28.987529 0.0034851739 1 1
1700 296.16091 -1.1440455 0.0034851739 1 1
1750 365.75611 34.574845 0.0034851739 1 1
1800 292.83503 -33.199654 0.0034851739 1 1
1850 261.50282 42.608703 0.0034851739 1 1
1900 315.14188 -31.058803 0.0034851739 1 1
1950 335.12895 12.40597 0.0034851739 1 1
2000 278.08586 -5.3178633 0.0034851739 1 1
2050 283.23847 -3.3974302 0.0034851739 1 1
2100 281.38904 0.70263324 0.0034851739 1 1
2150 302.23197 23.372316 0.0034851739 1 1
2200 337.49259 -4.8716803 0.0034851739 1 1
2250 409.64134 -12.043721 0.0034851739 1 1
2300 309.21764 -21.824645 0.0034851739 1 1
2350 290.97879 18.690281 0.0034851739 1 1
2400 341.816 -16.967741 0.0034851739 1 1
2450 310.28034 27.375518 0.0034851739 1 1
2500 248.89429 17.061192 0.0034851739 1 1
2550 273.10927 0.10481657 0.0034851739 1 1
2600 289.56101 -9.7239939 0.0034851739 1 1
2650 298.99719 -33.140576 0.0034851739 1 1
2700 326.05198 -24.509827 0.0034851739 1 1
2750 319.20612 24.305526 0.0034851739 1 1
2800 304.8715 -15.076941 0.0034851739 1 1
2850 374.38923 2.0874883 0.0034851739 1 1
2900 354.01554 -20.595102 0.0034851739 1 1
2950 289.89296 48.39731 0.0034851739 1 1
3000 312.10013 -8.5105997 0.0034851739 1 1
3050 296.97004 -31.008446 0.0034851739 1 1
3100 251.72228 35.710197 0.0034851739 1 1
3150 315.35895 -43.331536 0.0034851739 1 1
3200 334.67773 13.331058 0.0034851739 1 1
3250 308.1669 37.236121 0.0034851739 1 1
3300 329.47601 30.798598 0.0034851739 1 1
3350 299.40055 2.0785585 0.0034851739 1 1
3400 272.41031 32.744922 0.0034851739 1 1
3450 279.34594 -26.181793 0.0034851739 1 1
3500 288.89969 8.935052 0.0034851739 1 1
3550 253.4967 9.7244709 0.0034851739 1 1
3600 294.83266 19.33305 0.0034851739 1 1
3650 290.23794 -5.4939069 0.0034851739 1 1
3700 332.5222 -29.834229 0.0034851739 1 1
3750 364.63024 20.706191 0.0034851739 1 1
3800 295.3842 -6.9434004 0.0034851739 1 1
3850 346.84424 37.796066 0.0034851739 1 1
3900 265.67286 -0.31628068 0.0034851739 1 1
3950 260.455 -2.2571902 0.0034851739 1 1
4000 259.82636 -2.2286205 0.0034851739 1 1
4050 257.79848 24.520293 0.0034851739 1 1
4100 295.58626 -0.42318936 0.0034851739 1 1
4150 265.81353 -49.092436 0.0034851739 1 1
4200 302.10333 51.715259 0.0034851739 1 1
4250 258.98448 -4.8516655 0.0034851739 1 1
4300 327.83401 33.717282 0.0034851739 1 1
4350 311.59571 23.580382 0.0034851739 1 1
4400 300.64237 -31.866661 0.0034851739 1 1
4450 294.15643 -0.11927421 0.0034851739 1 1
4500 299.83605 -17.560873 0.0034851739 1 1
4550 326.83265 32.818482 0.0034851739 1 1
4600 260.39068 -8.0567902 0.0034851739 1 1
4650 247.93553 19.462991 0.0034851739 1 1
4700 214.22252 -34.118303 0.0034851739 1 1
4750 203.15329 27.356205 0.0034851739 1 1
4800 257.761 -10.407989 0.0034851739 1 1
4850 307.1923 11.71101 0.0034851739 1 1
4900 319.00942 4.7808306 0.0034851739 1 1
4950 282.23989 24.996151 0.0034851739 1 1
5000 311.53284 -3.0012665 0.0034851739 1 1
5050 317.58212 32.567832 0.0034851739 1 1
5100 267.51501 -47.695087 0.0034851739 1 1
5150 260.19048 29.046388 0.0034851739 1 1
5200 239.83552 -5.4890385 0.0034851739 1 1
5250 234.8852 -18.172633 0.0034851739 1 1
5300 236.43277 -39.06212 0.0034851739 1 1
5350 280.90079 -2.6932923 0.0034851739 1 1
5400 316.65266 23.071362 0.0034851739 1 1
5450 345.63226 19.573323 0.0034851739 1 1
5500 384.57334 41.507217 0.0034851739 1 1
5550 317.14278 9.6992897 0.0034851739 1 1
5600 279.93243 -12.076895 0.0034851739 1 1
5650 268.06471 1.6196401 0.0034851739 1 1
5700 271.85714 -40.378455 0.0034851739 1 1
5750 313.88363 10.722639 0.0034851739 1 1
5800 281.54495 31.914889 0.0034851739 1 1
5850 293.34821 -8.3154922 0.0034851739 1 1
5900 249.25216 -17.307353 0.0034851739 1 1
5950 268.18639 -4.7222512 0.0034851739 1 1
6000 302.99398 -52.615528 0.0034851739 1 1
6050 314.57931 34.51318 0.0034851739 1 1
6100 345.70348 30.334721 0.0034851739 1 1
6150 316.59329 31.862519 0.0034851739 1 1
6200 317.85346 -32.235221 0.0034851739 1 1
6250 282.97676 0.2936745 0.0034851739 1 1
6300 267.91814 19.265567 0.0034851739 1 1
6350 226.20967 -13.093547 0.0034851739 1 1
6400 307.73316 17.439598 0.0034851739 1 1
6450 292.16253 -23.275163 0.0034851739 1 1
6500 335.05939 26.936463 0.0034851739 1 1
6550 380.73546 19.532416 0.0034851739 1 1
6600 373.0103 30.879532 0.0034851739 1 1
6650 335.37975 -2.1762828 0.0034851739 1 1
6700 298.94272 -10.578587 0.0034851739 1 1
6750 255.11531 -50.576215 0.0034851739 1 1
6800 222.87459 3.0499548 0.0034851739 1 1
6850 268.57213 -43.675945 0.0034851739 1 1
6900 260.3024 4.7483005 0.0034851739 1 1
6950 289.15855 31.62106 0.0034851739 1 1
7000 289.11874 21.635533 0.0034851739 1 1
7050 361.08776 22.445996 0.0034851739 1 1
7100 368.95003 4.8383881 0.0034851739 1 1
7150 331.47448 -36.200495 0.0034851739 1 1
7200 304.7251 13.982693 0.0034851739 1 1
7250 284.09747 0.53758275 0.0034851739 1 1
7300 269.17023 -41.571482 0.0034851739 1 1
7350 222.07071 25.564662 0.0034851739 1 1
7400 304.09598 15.482955 0.0034851739 1 1
7450 298.78752 -7.4335841 0.0034851739 1 1
7500 328.78697 14.666097 0.0034851739 1 1
7550 347.07038 -37.165295 0.0034851739 1 1
7600 362.85673 20.52268 0.0034851739 1 1
7650 347.15141 2.3383775 0.0034851739 1 1
7700 262.10132 33.898374 0.0034851739 1 1
7750 275.84724 -33.534813 0.0034851739 1 1
7800 281.14075 -18.284372 0.0034851739 1 1
7850 264.83337 -30.580199 0.0034851739 1 1
7900 257.35275 -35.080567 0.0034851739 1 1
7950 286.32446 26.594779 0.0034851739 1 1
8000 248.36889 15.605894 0.0034851739 1 1
8050 292.55015 28.811985 0.0034851739 1 1
8100 312.47888 0.83990451 0.0034851739 1 1
8150 285.58532 -15.258185 0.0034851739 1 1
8200 292.22819 -38.233195 0.0034851739 1 1
8250 321.6208 -19.052143 0.0034851739 1 1
8300 319.41332 54.97437 0.0034851739 1 1
8350 307.95647 32.009591 0.0034851739 1 1
8400 345.58105 8.8535539 0.0034851739 1 1
8450 357.75168 12.416896 0.0034851739 1 1
8500 370.049 4.3288665 0.0034851739 1 1
8550 360.62882 12.618614 0.0034851739 1 1
8600 290.10834 -4.8081765 0.0034851739 1 1
8650 297.7575 -5.1976816 0.0034851739 1 1
8700 286.57505 -31.469549 0.0034851739 1 1
8750 307.77059 19.338001 0.0034851739 1 1
8800 231.68316 12.159459 0.0034851739 1 1
8850 329.13623 -8.7262592 0.0034851739 1 1
8900 286.40715 10.326025 0.0034851739 1 1
8950 339.43101 2.7809618 0.0034851739 1 1
9000 402.53799 19.481869 0.0034851739 1 1
9050 349.56449 -4.8450179 0.0034851739 1 1
9100 307.64739 16.889327 0.0034851739 1 1
9150 276.54451 -34.808372 0.0034851739 1 1
9200 233.18668 4.9409791 0.0034851739 1 1
9250 266.48384 -19.850366 0.0034851739 1 1
9300 289.14808 13.520201 0.0034851739 1 1
9350 295.08335 17.156468 0.0034851739 1 1
9400 338.08757 -31.112278 0.0034851739 1 1
9450 336.64739 -25.697747 0.0034851739 1 1
9500 338.10622 1.9241797 0.0034851739 1 1
9550 294.82158 -12.043972 0.0034851739 1 1
9600 268.9836 12.235553 0.0034851739 1 1
9650 279.6269 28.710734 0.0034851739 1 1
9700 279.88562 -10.865604 0.0034851739 1 1
9750 287.56565 12.975819 0.0034851739 1 1
9800 278.39949 4.2088595 0.0034851739 1 1
9850 307.61259 9.341169 0.0034851739 1 1
9900 317.53581 2.3948493 0.0034851739 1 1
9950 332.52938 -14.809185 0.0034851739 1 1
10000 401.93365 -7.637581 0.0034851739 1 1
Loop time of 1.94139 on 1 procs for 10000 steps with 44 atoms
Performance: 445.042 ns/day, 0.054 hours/ns, 5150.945 timesteps/s
99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.26479 | 0.26479 | 0.26479 | 0.0 | 13.64
Bond | 0.76875 | 0.76875 | 0.76875 | 0.0 | 39.60
Kspace | 0.32111 | 0.32111 | 0.32111 | 0.0 | 16.54
Neigh | 0.41333 | 0.41333 | 0.41333 | 0.0 | 21.29
Comm | 0.025956 | 0.025956 | 0.025956 | 0.0 | 1.34
Output | 0.0043445 | 0.0043445 | 0.0043445 | 0.0 | 0.22
Modify | 0.12526 | 0.12526 | 0.12526 | 0.0 | 6.45
Other | | 0.01786 | | | 0.92
Nlocal: 44 ave 44 max 44 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 62 ave 62 max 62 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 812 ave 812 max 812 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 812
Ave neighs/atom = 18.4545
Ave special neighs/atom = 9.77273
Neighbor list builds = 10000
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:01

365
examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 Normal file
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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 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
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
100 275.26011 39.120329 0.0034851739 1 1
150 438.68516 35.257539 0.0034851739 1 1
200 394.48971 15.444537 0.0034851739 1 1
250 356.00369 50.185792 0.0034851739 1 1
300 301.25816 -26.891497 0.0034851739 1 1
350 279.17264 12.694513 0.0034851739 1 1
400 248.71641 10.684558 0.0034851739 1 1
450 240.30602 12.963034 0.0034851739 1 1
500 252.71279 0.91620356 0.0034851739 1 1
550 300.56824 18.541436 0.0034851739 1 1
600 306.46441 -1.9736081 0.0034851739 1 1
650 336.4537 21.474831 0.0034851739 1 1
700 323.46217 8.486376 0.0034851739 1 1
750 271.87146 5.9615231 0.0034851739 1 1
800 268.43041 36.676068 0.0034851739 1 1
850 269.02683 7.6295416 0.0034851739 1 1
900 282.03605 -1.4688833 0.0034851739 1 1
950 243.69136 -22.771489 0.0034851739 1 1
1000 285.01348 17.925748 0.0034851739 1 1
1050 383.47985 0.70536985 0.0034851739 1 1
1100 368.97167 -4.3046933 0.0034851739 1 1
1150 373.64459 6.3491837 0.0034851739 1 1
1200 332.90575 -36.501095 0.0034851739 1 1
1250 314.04078 -13.382767 0.0034851739 1 1
1300 305.84166 4.7713641 0.0034851739 1 1
1350 286.22145 37.621803 0.0034851739 1 1
1400 265.52855 23.621002 0.0034851739 1 1
1450 281.807 -31.266828 0.0034851739 1 1
1500 275.33855 33.495565 0.0034851739 1 1
1550 273.04973 -22.913871 0.0034851739 1 1
1600 308.18478 -17.98151 0.0034851739 1 1
1650 333.27664 28.987529 0.0034851739 1 1
1700 296.16091 -1.1440455 0.0034851739 1 1
1750 365.75611 34.574845 0.0034851739 1 1
1800 292.83503 -33.199654 0.0034851739 1 1
1850 261.50282 42.608703 0.0034851739 1 1
1900 315.14188 -31.058803 0.0034851739 1 1
1950 335.12895 12.40597 0.0034851739 1 1
2000 278.08586 -5.3178633 0.0034851739 1 1
2050 283.23847 -3.3974302 0.0034851739 1 1
2100 281.38904 0.70263324 0.0034851739 1 1
2150 302.23197 23.372316 0.0034851739 1 1
2200 337.49259 -4.8716803 0.0034851739 1 1
2250 409.64134 -12.043721 0.0034851739 1 1
2300 309.21764 -21.824645 0.0034851739 1 1
2350 290.97879 18.690281 0.0034851739 1 1
2400 341.816 -16.967741 0.0034851739 1 1
2450 310.28034 27.375518 0.0034851739 1 1
2500 248.89429 17.061192 0.0034851739 1 1
2550 273.10927 0.1048166 0.0034851739 1 1
2600 289.56101 -9.7239939 0.0034851739 1 1
2650 298.99719 -33.140576 0.0034851739 1 1
2700 326.05198 -24.509827 0.0034851739 1 1
2750 319.20612 24.305526 0.0034851739 1 1
2800 304.8715 -15.076941 0.0034851739 1 1
2850 374.38923 2.0874883 0.0034851739 1 1
2900 354.01554 -20.595102 0.0034851739 1 1
2950 289.89296 48.39731 0.0034851739 1 1
3000 312.10013 -8.5105996 0.0034851739 1 1
3050 296.97004 -31.008446 0.0034851739 1 1
3100 251.72228 35.710197 0.0034851739 1 1
3150 315.35895 -43.331536 0.0034851739 1 1
3200 334.67773 13.331058 0.0034851739 1 1
3250 308.1669 37.236121 0.0034851739 1 1
3300 329.47601 30.798598 0.0034851739 1 1
3350 299.40055 2.0785585 0.0034851739 1 1
3400 272.41031 32.744921 0.0034851739 1 1
3450 279.34594 -26.181793 0.0034851739 1 1
3500 288.89969 8.935052 0.0034851739 1 1
3550 253.4967 9.724471 0.0034851739 1 1
3600 294.83266 19.33305 0.0034851739 1 1
3650 290.23794 -5.493907 0.0034851739 1 1
3700 332.5222 -29.83423 0.0034851739 1 1
3750 364.63024 20.706191 0.0034851739 1 1
3800 295.3842 -6.9434003 0.0034851739 1 1
3850 346.84424 37.796066 0.0034851739 1 1
3900 265.67286 -0.3162804 0.0034851739 1 1
3950 260.455 -2.2571901 0.0034851739 1 1
4000 259.82636 -2.2286207 0.0034851739 1 1
4050 257.79848 24.520293 0.0034851739 1 1
4100 295.58626 -0.42318895 0.0034851739 1 1
4150 265.81352 -49.092436 0.0034851739 1 1
4200 302.10333 51.715258 0.0034851739 1 1
4250 258.98448 -4.8516657 0.0034851739 1 1
4300 327.83401 33.717283 0.0034851739 1 1
4350 311.59571 23.580382 0.0034851739 1 1
4400 300.64237 -31.866661 0.0034851739 1 1
4450 294.15642 -0.11927262 0.0034851739 1 1
4500 299.83605 -17.560872 0.0034851739 1 1
4550 326.83265 32.818481 0.0034851739 1 1
4600 260.39068 -8.0567907 0.0034851739 1 1
4650 247.93553 19.462991 0.0034851739 1 1
4700 214.22252 -34.118304 0.0034851739 1 1
4750 203.15329 27.356204 0.0034851739 1 1
4800 257.761 -10.407986 0.0034851739 1 1
4850 307.1923 11.711008 0.0034851739 1 1
4900 319.00942 4.7808342 0.0034851739 1 1
4950 282.2399 24.996151 0.0034851739 1 1
5000 311.53284 -3.0012669 0.0034851739 1 1
5050 317.58213 32.56782 0.0034851739 1 1
5100 267.51502 -47.695103 0.0034851739 1 1
5150 260.19047 29.046394 0.0034851739 1 1
5200 239.8355 -5.4890372 0.0034851739 1 1
5250 234.88522 -18.172649 0.0034851739 1 1
5300 236.43278 -39.062111 0.0034851739 1 1
5350 280.90083 -2.6932604 0.0034851739 1 1
5400 316.65269 23.071363 0.0034851739 1 1
5450 345.6322 19.573305 0.0034851739 1 1
5500 384.57334 41.50729 0.0034851739 1 1
5550 317.14286 9.6992981 0.0034851739 1 1
5600 279.93246 -12.076859 0.0034851739 1 1
5650 268.06471 1.6196502 0.0034851739 1 1
5700 271.85714 -40.378489 0.0034851739 1 1
5750 313.88361 10.722652 0.0034851739 1 1
5800 281.54499 31.914883 0.0034851739 1 1
5850 293.34819 -8.3155887 0.0034851739 1 1
5900 249.25215 -17.307228 0.0034851739 1 1
5950 268.18645 -4.7223601 0.0034851739 1 1
6000 302.99402 -52.615432 0.0034851739 1 1
6050 314.57946 34.513152 0.0034851739 1 1
6100 345.70342 30.33474 0.0034851739 1 1
6150 316.59329 31.862566 0.0034851739 1 1
6200 317.85341 -32.23511 0.0034851739 1 1
6250 282.97674 0.29367434 0.0034851739 1 1
6300 267.91823 19.265617 0.0034851739 1 1
6350 226.2098 -13.093573 0.0034851739 1 1
6400 307.73307 17.439662 0.0034851739 1 1
6450 292.16311 -23.275251 0.0034851739 1 1
6500 335.05972 26.936588 0.0034851739 1 1
6550 380.7351 19.532324 0.0034851739 1 1
6600 373.01041 30.879146 0.0034851739 1 1
6650 335.37897 -2.1766711 0.0034851739 1 1
6700 298.94275 -10.578361 0.0034851739 1 1
6750 255.11449 -50.575851 0.0034851739 1 1
6800 222.87598 3.0488985 0.0034851739 1 1
6850 268.57268 -43.676136 0.0034851739 1 1
6900 260.30442 4.7484508 0.0034851739 1 1
6950 289.15739 31.622589 0.0034851739 1 1
7000 289.11733 21.636361 0.0034851739 1 1
7050 361.08905 22.442487 0.0034851739 1 1
7100 368.95006 4.8393179 0.0034851739 1 1
7150 331.47878 -36.202032 0.0034851739 1 1
7200 304.72518 13.982604 0.0034851739 1 1
7250 284.0996 0.53900966 0.0034851739 1 1
7300 269.17156 -41.572215 0.0034851739 1 1
7350 222.06563 25.56579 0.0034851739 1 1
7400 304.09479 15.48238 0.0034851739 1 1
7450 298.79046 -7.4369454 0.0034851739 1 1
7500 328.78217 14.672853 0.0034851739 1 1
7550 347.06589 -37.168123 0.0034851739 1 1
7600 362.84157 20.514912 0.0034851739 1 1
7650 347.15916 2.3477485 0.0034851739 1 1
7700 262.09822 33.901831 0.0034851739 1 1
7750 275.85921 -33.536059 0.0034851739 1 1
7800 281.16159 -18.288414 0.0034851739 1 1
7850 264.83553 -30.566284 0.0034851739 1 1
7900 257.35224 -35.087067 0.0034851739 1 1
7950 286.30756 26.586163 0.0034851739 1 1
8000 248.38175 15.601961 0.0034851739 1 1
8050 292.59171 28.784541 0.0034851739 1 1
8100 312.52852 0.87995053 0.0034851739 1 1
8150 285.62346 -15.337252 0.0034851739 1 1
8200 292.24175 -38.192576 0.0034851739 1 1
8250 321.61618 -19.030398 0.0034851739 1 1
8300 319.42189 55.078305 0.0034851739 1 1
8350 308.00357 32.050518 0.0034851739 1 1
8400 345.68186 8.7983733 0.0034851739 1 1
8450 358.00849 12.434592 0.0034851739 1 1
8500 370.14359 4.2184721 0.0034851739 1 1
8550 360.6511 12.580836 0.0034851739 1 1
8600 290.04938 -4.8422589 0.0034851739 1 1
8650 297.95745 -5.3185591 0.0034851739 1 1
8700 286.54284 -31.490479 0.0034851739 1 1
8750 308.08791 19.24417 0.0034851739 1 1
8800 231.72534 12.262217 0.0034851739 1 1
8850 329.2349 -8.9133933 0.0034851739 1 1
8900 287.64023 10.525164 0.0034851739 1 1
8950 341.08296 2.80127 0.0034851739 1 1
9000 403.71266 17.88418 0.0034851739 1 1
9050 348.95132 -4.5813611 0.0034851739 1 1
9100 307.98322 16.707575 0.0034851739 1 1
9150 276.75719 -35.563923 0.0034851739 1 1
9200 230.15547 3.8091656 0.0034851739 1 1
9250 264.64479 -20.97438 0.0034851739 1 1
9300 285.70467 13.881735 0.0034851739 1 1
9350 297.515 13.599319 0.0034851739 1 1
9400 341.45203 -28.494544 0.0034851739 1 1
9450 319.29703 -27.907344 0.0034851739 1 1
9500 332.50473 4.9891138 0.0034851739 1 1
9550 293.10499 -8.3244772 0.0034851739 1 1
9600 255.31174 2.2568315 0.0034851739 1 1
9650 250.01932 5.7005159 0.0034851739 1 1
9700 278.37409 -8.5970424 0.0034851739 1 1
9750 294.86737 17.686447 0.0034851739 1 1
9800 277.07345 -2.0856886 0.0034851739 1 1
9850 295.54707 2.8365471 0.0034851739 1 1
9900 311.51074 29.885116 0.0034851739 1 1
9950 296.01363 12.206068 0.0034851739 1 1
10000 341.35187 -3.0045464 0.0034851739 1 1
Loop time of 3.64332 on 4 procs for 10000 steps with 44 atoms
Performance: 237.146 ns/day, 0.101 hours/ns, 2744.751 timesteps/s
94.5% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.0029962 | 0.10426 | 0.34564 | 43.9 | 2.86
Bond | 0.005929 | 0.29803 | 0.95305 | 71.2 | 8.18
Kspace | 0.83969 | 1.5992 | 1.9344 | 35.6 | 43.89
Neigh | 0.65468 | 0.66443 | 0.67431 | 0.9 | 18.24
Comm | 0.1727 | 0.23754 | 0.2745 | 8.0 | 6.52
Output | 0.0048738 | 0.010774 | 0.028434 | 9.8 | 0.30
Modify | 0.62478 | 0.70376 | 0.779 | 6.5 | 19.32
Other | | 0.02531 | | | 0.69
Nlocal: 11 ave 40 max 0 min
Histogram: 2 1 0 0 0 0 0 0 0 1
Nghost: 36 ave 47 max 7 min
Histogram: 1 0 0 0 0 0 0 0 0 3
Neighs: 203 ave 809 max 0 min
Histogram: 3 0 0 0 0 0 0 0 0 1
Total # of neighbors = 812
Ave neighs/atom = 18.4545
Ave special neighs/atom = 9.77273
Neighbor list builds = 10000
Dangerous builds = 0
# write_restart restart_longrun
# write_data restart_longrun.data
Total wall time: 0:00:03