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update example inputs and logs for change in ReaxFF required name

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This commit is contained in:
Axel Kohlmeyer
2023-11-30 07:20:33 -05:00
parent 6ff87f5c39
commit 00be75e084
71 changed files with 4207 additions and 2369 deletions
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24
examples/reaxff/RDX/in.RDX
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# REAX potential for high energy CHON systems
# .....
units real
units real
atom_style charge
read_data data.RDX
atom_style charge
read_data data.RDX
pair_style reax/c lmp_control
pair_coeff * * ffield.reax.rdx H C O N
pair_style reaxff lmp_control
pair_coeff * * ffield.reax.rdx H C O N
neighbor 2 bin
neigh_modify every 10 delay 0 check no
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
timestep 0.25
thermo 100
#dump 1 all atom 30 dump.reax.rdx
#dump 1 all atom 30 dump.reax.rdx
run 3000
run 3000

19
examples/reaxff/RDX/lmp_control
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simulation_name RDX_example ! output files will carry this name + their specific ext
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
energy_update_freq 1
tabulate_long_range 10000 ! denotes the granularity of long range tabulation, 0 means no tabulation
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
thb_cutoff 0.001 ! cutoff value for three body interactions
nbrhood_cutoff 4.5 ! near neighbors cutoff for bond calculations in A
hbond_cutoff 6.0 ! cutoff distance for hydrogen bond interactions
bond_graph_cutoff 0.3 ! bond strength cutoff for bond graphs
thb_cutoff 0.001 ! cutoff value for three body interactions
write_freq 1 ! write trajectory after so many steps
traj_title RDX ! (no white spaces)
atom_info 1 ! 0: no atom info, 1: print basic atom info in the trajectory file
atom_forces 1 ! 0: basic atom format, 1: print force on each atom in the trajectory file
atom_velocities 0 ! 0: basic atom format, 1: print the velocity of each atom in the trajectory file
bond_info 1 ! 0: do not print bonds, 1: print bonds in the trajectory file
angle_info 1 ! 0: do not print angles, 1: print angles in the trajectory file

140
examples/reaxff/RDX/log.30Nov23.RDX.g++.1 Normal file
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LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# REAX potential for high energy CHON systems
# .....
units real
atom_style charge
read_data data.RDX
Reading data file ...
orthogonal box = (0 0 0) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
105 atoms
read_data CPU = 0.001 seconds
pair_style reaxff lmp_control
pair_coeff * * ffield.reax.rdx H C O N
Reading potential file ffield.reax.rdx with DATE: 2010-02-19
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
thermo 100
#dump 1 all atom 30 dump.reax.rdx
run 3000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 16.3 | 16.3 | 16.3 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -10197.932 0 -10197.932 38.347492
100 47.478574 -10176.425 0 -10161.706 632.99863
200 166.95277 -10181.513 0 -10129.757 -27.107717
300 142.53594 -10148.039 0 -10103.853 5120.6794
400 322.68495 -10178.868 0 -10078.834 2342.89
500 193.81476 -10117.984 0 -10057.901 8412.5289
600 300.27155 -10134.473 0 -10041.388 -2801.8661
700 272.63426 -10110.146 0 -10025.629 10749.023
800 339.99867 -10114.124 0 -10008.723 5122.9966
900 231.65547 -10068.587 0 -9996.7728 5306.059
1000 329.92918 -10088.776 0 -9986.4964 3190.1697
1100 376.60905 -10092.398 0 -9975.6476 2921.9605
1200 361.98746 -10076.599 0 -9964.3813 3612.0455
1300 358.65631 -10069.365 0 -9958.1802 4339.8435
1400 470.15262 -10098.553 0 -9952.8035 -146.0811
1500 509.62274 -10106.57 0 -9948.5844 2356.8592
1600 417.89364 -10075.274 0 -9945.7249 1760.5655
1700 453.21317 -10084.329 0 -9943.8306 -570.32375
1800 472.92112 -10087.83 0 -9941.2221 1550.3495
1900 507.18794 -10096.441 0 -9939.2102 -460.65809
2000 443.55347 -10076.832 0 -9939.3281 -145.14295
2100 485.44451 -10088.451 0 -9937.9611 -614.40787
2200 507.52411 -10095.157 0 -9937.8226 1308.3869
2300 496.44961 -10089.637 0 -9935.7354 206.44147
2400 457.99343 -10078.114 0 -9936.1344 810.80538
2500 507.88115 -10092.692 0 -9935.2463 -464.87873
2600 437.84198 -10069.789 0 -9934.0561 1323.4191
2700 503.09017 -10088.945 0 -9932.9853 1133.3561
2800 481.73908 -10082.193 0 -9932.852 -27.838881
2900 487.56555 -10082.752 0 -9931.6045 1772.2131
3000 510.30601 -10091.368 0 -9933.1706 1273.0501
Loop time of 5.35022 on 1 procs for 3000 steps with 105 atoms
Performance: 12.112 ns/day, 1.982 hours/ns, 560.725 timesteps/s, 58.876 katom-step/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 4.7927 | 4.7927 | 4.7927 | 0.0 | 89.58
Neigh | 0.15169 | 0.15169 | 0.15169 | 0.0 | 2.84
Comm | 0.011036 | 0.011036 | 0.011036 | 0.0 | 0.21
Output | 0.00080628 | 0.00080628 | 0.00080628 | 0.0 | 0.02
Modify | 0.3906 | 0.3906 | 0.3906 | 0.0 | 7.30
Other | | 0.003436 | | | 0.06
Nlocal: 105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 645 ave 645 max 645 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3065 ave 3065 max 3065 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3065
Ave neighs/atom = 29.190476
Neighbor list builds = 300
Dangerous builds not checked
Total wall time: 0:00:05

140
examples/reaxff/RDX/log.30Nov23.RDX.g++.4 Normal file
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LAMMPS (21 Nov 2023)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# REAX potential for high energy CHON systems
# .....
units real
atom_style charge
read_data data.RDX
Reading data file ...
orthogonal box = (0 0 0) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
105 atoms
read_data CPU = 0.001 seconds
pair_style reaxff lmp_control
pair_coeff * * ffield.reax.rdx H C O N
Reading potential file ffield.reax.rdx with DATE: 2010-02-19
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
thermo 100
#dump 1 all atom 30 dump.reax.rdx
run 3000
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited:
- pair reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
number = {4--5},
pages = {245--259}
}
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
@Article{Aktulga12,
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update: every = 10 steps, delay = 0 steps, check = no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reaxff, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: full/ghost/bin/3d
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 10.78 | 11.56 | 12.26 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -10197.932 0 -10197.932 38.347492
100 47.47852 -10176.425 0 -10161.706 632.97359
200 166.95287 -10181.513 0 -10129.757 -27.146803
300 142.53582 -10148.039 0 -10103.852 5120.6397
400 322.68523 -10178.868 0 -10078.834 2342.7187
500 193.81484 -10117.984 0 -10057.901 8412.4559
600 300.27165 -10134.473 0 -10041.388 -2801.9143
700 272.63408 -10110.146 0 -10025.629 10749.2
800 339.99669 -10114.123 0 -10008.723 5123.2489
900 231.65632 -10068.587 0 -9996.7729 5306.0392
1000 329.93324 -10088.777 0 -9986.4967 3190.4707
1100 376.60924 -10092.398 0 -9975.6478 2920.8475
1200 361.98231 -10076.598 0 -9964.3816 3612.0573
1300 358.6599 -10069.366 0 -9958.1803 4341.9871
1400 470.14856 -10098.552 0 -9952.8036 -146.9069
1500 509.6454 -10106.577 0 -9948.5847 2355.4022
1600 417.9276 -10075.284 0 -9945.7249 1749.565
1700 453.25817 -10084.343 0 -9943.8306 -570.48011
1800 472.9517 -10087.84 0 -9941.2226 1532.6424
1900 507.14171 -10096.428 0 -9939.212 -404.84948
2000 443.62843 -10076.86 0 -9939.3329 -132.17302
2100 485.441 -10088.414 0 -9937.925 -609.75758
2200 507.23914 -10095.067 0 -9937.8209 1288.5372
2300 499.64956 -10090.665 0 -9935.7719 149.06622
2400 457.97848 -10078.107 0 -9936.1317 2065.2075
2500 510.58254 -10093.537 0 -9935.2543 -559.75965
2600 440.97503 -10070.865 0 -9934.1605 1164.1078
2700 500.4945 -10088.165 0 -9933.0096 1051.9016
2800 485.77814 -10083.543 0 -9932.9498 294.64404
2900 487.73983 -10082.939 0 -9931.7373 2208.263
3000 504.69717 -10089.803 0 -9933.3447 1723.6386
Loop time of 2.81192 on 4 procs for 3000 steps with 105 atoms
Performance: 23.045 ns/day, 1.041 hours/ns, 1066.887 timesteps/s, 112.023 katom-step/s
99.3% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 2.0513 | 2.1567 | 2.2232 | 4.3 | 76.70
Neigh | 0.072125 | 0.087048 | 0.10214 | 3.7 | 3.10
Comm | 0.086792 | 0.15326 | 0.25749 | 16.2 | 5.45
Output | 0.00058533 | 0.00064027 | 0.00080207 | 0.0 | 0.02
Modify | 0.39587 | 0.41124 | 0.42647 | 1.7 | 14.62
Other | | 0.003062 | | | 0.11
Nlocal: 26.25 ave 46 max 8 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 399.5 ave 512 max 288 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 1011.25 ave 1819 max 420 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 4045
Ave neighs/atom = 38.52381
Neighbor list builds = 300
Dangerous builds not checked
Total wall time: 0:00:02

81
examples/reaxff/RDX/log.8Mar18.RDX.g++.1
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@ -1,81 +0,0 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for high energy CHON systems
# .....
units real
atom_style charge
read_data data.RDX
orthogonal box = (0 0 0) to (25 25 25)
1 by 1 by 1 MPI processor grid
reading atoms ...
105 atoms
pair_style reax/c lmp_control
pair_coeff * * ffield.reax.rdx H C O N
Reading potential file ffield.reax.rdx with DATE: 2010-02-19
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
#dump 1 all atom 30 dump.reax.rdx
run 3000
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 19 | 19 | 19 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -10197.932 0 -10197.932 38.347492
3000 510.63767 -10091.537 0 -9933.2374 1144.545
Loop time of 21.2931 on 1 procs for 3000 steps with 105 atoms
Performance: 3.043 ns/day, 7.886 hours/ns, 140.891 timesteps/s
97.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 19.887 | 19.887 | 19.887 | 0.0 | 93.40
Neigh | 0.33143 | 0.33143 | 0.33143 | 0.0 | 1.56
Comm | 0.02079 | 0.02079 | 0.02079 | 0.0 | 0.10
Output | 2.5272e-05 | 2.5272e-05 | 2.5272e-05 | 0.0 | 0.00
Modify | 1.0478 | 1.0478 | 1.0478 | 0.0 | 4.92
Other | | 0.006125 | | | 0.03
Nlocal: 105 ave 105 max 105 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 645 ave 645 max 645 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 3063 ave 3063 max 3063 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 3063
Ave neighs/atom = 29.1714
Neighbor list builds = 300
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:21

81
examples/reaxff/RDX/log.8Mar18.RDX.g++.4
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@ -1,81 +0,0 @@
LAMMPS (8 Mar 2018)
using 1 OpenMP thread(s) per MPI task
# REAX potential for high energy CHON systems
# .....
units real
atom_style charge
read_data data.RDX
orthogonal box = (0 0 0) to (25 25 25)
1 by 2 by 2 MPI processor grid
reading atoms ...
105 atoms
pair_style reax/c lmp_control
pair_coeff * * ffield.reax.rdx H C O N
Reading potential file ffield.reax.rdx with DATE: 2010-02-19
neighbor 2 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq
fix 3 all temp/berendsen 500.0 500.0 100.0
timestep 0.25
#dump 1 all atom 30 dump.reax.rdx
run 3000
Neighbor list info ...
update every 10 steps, delay 0 steps, check no
max neighbors/atom: 2000, page size: 100000
master list distance cutoff = 12
ghost atom cutoff = 12
binsize = 6, bins = 5 5 5
2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual
attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff
bin: standard
(2) fix qeq/reax, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 12.14 | 13.04 | 13.9 Mbytes
Step Temp E_pair E_mol TotEng Press
0 0 -10197.932 0 -10197.932 38.347492
3000 509.89257 -10091.36 0 -9933.2916 1406.1215
Loop time of 10.8858 on 4 procs for 3000 steps with 105 atoms
Performance: 5.953 ns/day, 4.032 hours/ns, 275.588 timesteps/s
98.1% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 9.3081 | 9.4054 | 9.4994 | 2.6 | 86.40
Neigh | 0.15541 | 0.18258 | 0.2099 | 4.7 | 1.68
Comm | 0.070516 | 0.16621 | 0.26541 | 19.7 | 1.53
Output | 2.2173e-05 | 2.5153e-05 | 3.3855e-05 | 0.0 | 0.00
Modify | 1.0979 | 1.1272 | 1.1568 | 2.1 | 10.35
Other | | 0.004379 | | | 0.04
Nlocal: 26.25 ave 46 max 8 min
Histogram: 1 0 0 1 0 1 0 0 0 1
Nghost: 399.5 ave 512 max 288 min
Histogram: 1 0 0 1 0 0 1 0 0 1
Neighs: 1011.25 ave 1819 max 420 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 4045
Ave neighs/atom = 38.5238
Neighbor list builds = 300
Dangerous builds not checked
Please see the log.cite file for references relevant to this simulation
Total wall time: 0:00:11