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add minimal example and a unit test input

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Axel Kohlmeyer
2021-09-14 16:40:42 -04:00
parent 19bc606a20
commit b4acacf5cb
4 changed files with 535 additions and 0 deletions
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53
examples/reaxff/in.reaxff.rdx-acks2 Normal file
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# ReaxFF potential for RDX system
units real
atom_style charge
read_data data.rdx
pair_style reaxff control.reax_c.rdx
pair_coeff * * ffield.reax C H O N
compute reax all pair reaxff
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff
variable nqeq equal f_2
thermo 10
thermo_style custom step temp epair etotal press &
v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa &
v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxff.rdx
#dump 2 all image 25 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type &
# axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100

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examples/reaxff/log.31Aug21.reaxff.rdx-acks2.g++.1 Normal file
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LAMMPS (31 Aug 2021)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
units real
atom_style charge
read_data data.rdx
Reading data file ...
orthogonal box = (35.000000 35.000000 35.000000) to (48.000000 48.000000 48.000000)
1 by 1 by 1 MPI processor grid
reading atoms ...
21 atoms
read_data CPU = 0.000 seconds
pair_style reaxff control.reax_c.rdx
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113)
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97)
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reaxff
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff
variable nqeq equal f_2
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxff.rdx
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
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:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix acks2/reaxff command:
@Article{O'Hearn2020,
author = {K. A. O'Hearn, A. Alperen, and H. M. Aktulga},
title = {Fast Solvers for Charge Distribution Models on Shared Memory Platforms},
journal = {SIAM J. Sci. Comput.},
year = 2020,
volume = 42,
pages = {1--22}
}
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 = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 3
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 acks2/reaxff, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 15.42 | 15.42 | 15.42 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
0 0 -1808.3917 -1808.3917 28736.41 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -2.8201336e-06 0 0.00098778735 13
10 1304.7509 -1914.0924 -1836.3081 -21153.752 -2726.219 -17.446777 0.19121437 0 58.532415 2.5619735 -77.337316 0 14.042901 -5.8126196 837.38787 -6.2534642e-06 0 0.0069050076 8
20 427.93813 -1859.4968 -1833.9848 -23712.924 -2777.9198 1.1772924 0.029117162 0 88.192077 0.1543307 -53.152357 0 28.462512 -9.6520395 863.2094 -1.1899783e-06 0 0.0027021013 9.5
30 600.85197 -1867.8807 -1832.0602 -15720.955 -2765.2737 1.4937773 0.06185725 0 80.013841 0.090367845 -47.085245 0 16.406666 -11.121903 857.53144 2.0736158e-06 0 0.0022173663 11
40 1108.9095 -1898.9259 -1832.817 -38935.482 -2778.2032 2.0997015 0.14353694 0 78.798725 0.26421692 -58.91856 0 14.943876 -10.029332 851.97505 4.5556609e-07 0 1.3535608e-05 13.5
50 1155.316 -1890.9414 -1822.0658 7674.2712 -2804.003 8.5334231 0.15421192 0 78.75008 2.2698852 -77.319055 0 31.922369 -8.9637444 877.71732 6.9388694e-05 0 -0.0028728853 10
60 1237.1418 -1895.0813 -1821.3276 854.31642 -2722.5859 -14.2286 0.22149986 0 44.37587 9.5571735 -73.477237 0 18.566827 -4.8577223 847.34568 1.6885606e-05 0 0.0011149828 12
70 1025.7868 -1882.2967 -1821.1431 25212.869 -2890.8508 54.451033 0.29038763 0 112.30176 2.4666006 -64.1052 0 19.268525 -11.520433 895.4047 5.9278993e-06 0 -0.0032206344 9.5
80 619.97124 -1857.6805 -1820.7202 -12086.828 -2740.4855 -5.2006679 0.12319993 0 99.775674 2.7800075 -77.812022 0 25.298145 -7.562536 845.40484 3.766017e-05 0 -0.0017469014 9.5
90 1169.6095 -1893.5597 -1823.832 -6196.2424 -2816.571 34.143182 0.24873152 0 91.015691 0.81251232 -69.865835 0 17.93908 -10.502528 859.2142 1.3276274e-05 0 0.006324974 9.5
100 1032.79 -1882.6603 -1821.0893 6839.1293 -2811.285 8.1859322 0.22109056 0 69.13601 8.7302413 -74.363952 0 22.220038 -7.7705968 902.27101 6.5173803e-05 0 -0.005154992 7.5
Loop time of 0.118719 on 1 procs for 100 steps with 21 atoms
Performance: 72.777 ns/day, 0.330 hours/ns, 842.328 timesteps/s
99.8% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.09767 | 0.09767 | 0.09767 | 0.0 | 82.27
Neigh | 0.0055032 | 0.0055032 | 0.0055032 | 0.0 | 4.64
Comm | 0.00021768 | 0.00021768 | 0.00021768 | 0.0 | 0.18
Output | 0.00023556 | 0.00023556 | 0.00023556 | 0.0 | 0.20
Modify | 0.014979 | 0.014979 | 0.014979 | 0.0 | 12.62
Other | | 0.0001125 | | | 0.09
Nlocal: 21.0000 ave 21 max 21 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 546.000 ave 546 max 546 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 1102.00 ave 1102 max 1102 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1102
Ave neighs/atom = 52.476190
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:00

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LAMMPS (31 Aug 2021)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
units real
atom_style charge
read_data data.rdx
Reading data file ...
orthogonal box = (35.000000 35.000000 35.000000) to (48.000000 48.000000 48.000000)
1 by 2 by 2 MPI processor grid
reading atoms ...
21 atoms
read_data CPU = 0.000 seconds
pair_style reaxff control.reax_c.rdx
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:97)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:113)
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97)
pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reaxff
variable eb equal c_reax[1]
variable ea equal c_reax[2]
variable elp equal c_reax[3]
variable emol equal c_reax[4]
variable ev equal c_reax[5]
variable epen equal c_reax[6]
variable ecoa equal c_reax[7]
variable ehb equal c_reax[8]
variable et equal c_reax[9]
variable eco equal c_reax[10]
variable ew equal c_reax[11]
variable ep equal c_reax[12]
variable efi equal c_reax[13]
variable eqeq equal c_reax[14]
neighbor 2.5 bin
neigh_modify every 10 delay 0 check no
fix 1 all nve
fix 2 all acks2/reaxff 1 0.0 10.0 1.0e-6 reaxff
variable nqeq equal f_2
thermo 10
thermo_style custom step temp epair etotal press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
timestep 1.0
#dump 1 all atom 10 dump.reaxff.rdx
#dump 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 25 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
run 100
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:
@Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
title = {Parallel reactive molecular dynamics: Numerical methods and algorithmic techniques},
journal = {Parallel Computing},
year = 2012,
volume = 38,
pages = {245--259}
}
- fix acks2/reaxff command:
@Article{O'Hearn2020,
author = {K. A. O'Hearn, A. Alperen, and H. M. Aktulga},
title = {Fast Solvers for Charge Distribution Models on Shared Memory Platforms},
journal = {SIAM J. Sci. Comput.},
year = 2020,
volume = 42,
pages = {1--22}
}
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 = 12.5
ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 3
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 acks2/reaxff, perpetual, copy from (1)
attributes: half, newton off, ghost
pair build: copy
stencil: none
bin: none
Per MPI rank memory allocation (min/avg/max) = 11.41 | 12.58 | 13.79 Mbytes
Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_et v_eco v_ew v_ep v_efi v_eqeq v_nqeq
0 0 -1808.3956 -1808.3956 28736.41 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -5.6770858e-06 0 -0.0028392419 14
10 1304.7509 -1914.1049 -1836.3206 -21153.752 -2726.219 -17.446777 0.19121437 0 58.532415 2.5619735 -77.337316 0 14.042901 -5.8126196 837.38787 5.0978181e-06 0 -0.005556783 10
20 427.93812 -1859.4876 -1833.9756 -23712.923 -2777.9198 1.1772926 0.029117161 0 88.192077 0.1543307 -53.152357 0 28.462513 -9.6520395 863.2094 2.1862491e-05 0 0.011844766 6
30 600.85195 -1867.8815 -1832.061 -15720.949 -2765.2737 1.4937783 0.061857248 0 80.013842 0.090367838 -47.085244 0 16.406666 -11.121903 857.53144 -1.2004549e-06 0 0.0014350102 11
40 1108.9094 -1898.8905 -1832.7815 -38935.484 -2778.2032 2.0996992 0.14353693 0 78.798728 0.26421691 -58.91856 0 14.943875 -10.029332 851.97505 4.1455385e-06 0 0.03548355 8
50 1155.3161 -1890.9404 -1822.0649 7674.2794 -2804.0031 8.5334252 0.15421192 0 78.75008 2.2698849 -77.319055 0 31.92237 -8.9637447 877.71732 3.7570219e-05 0 -0.0018876928 7
60 1237.1418 -1895.0785 -1821.3248 854.31669 -2722.5859 -14.228606 0.22149986 0 44.375869 9.5571747 -73.477236 0 18.566825 -4.8577216 847.34567 -6.0652199e-06 0 0.0039746806 9
70 1025.7867 -1882.2715 -1821.118 25212.883 -2890.8508 54.451049 0.29038764 0 112.30178 2.4666008 -64.105192 0 19.268524 -11.520433 895.40472 7.5942987e-05 0 0.021807003 5.5
80 619.97151 -1857.6791 -1820.7188 -12086.851 -2740.4854 -5.2006737 0.12319996 0 99.775675 2.7800093 -77.812024 0 25.29814 -7.5625349 845.40485 -3.2701271e-06 0 -0.00028718671 11
90 1169.6099 -1893.5491 -1823.8214 -6196.2462 -2816.571 34.143181 0.24873153 0 91.015695 0.81251269 -69.865839 0 17.939079 -10.502527 859.2142 2.297465e-05 0 0.016894027 6.5
100 1032.7901 -1882.6521 -1821.081 6839.0982 -2811.2849 8.1859195 0.22109056 0 69.136035 8.730243 -74.363951 0 22.220028 -7.7705949 902.27102 6.4245187e-06 0 0.0030953783 10
Loop time of 0.140636 on 4 procs for 100 steps with 21 atoms
Performance: 61.435 ns/day, 0.391 hours/ns, 711.054 timesteps/s
95.2% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.042596 | 0.057261 | 0.073915 | 4.7 | 40.72
Neigh | 0.0024769 | 0.003423 | 0.0044286 | 1.2 | 2.43
Comm | 0.0078962 | 0.025491 | 0.040466 | 7.3 | 18.13
Output | 0.00030279 | 0.00066626 | 0.0017195 | 0.0 | 0.47
Modify | 0.05257 | 0.0536 | 0.054564 | 0.3 | 38.11
Other | | 0.0001949 | | | 0.14
Nlocal: 5.25000 ave 14 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 355.500 ave 433 max 282 min
Histogram: 1 0 0 0 2 0 0 0 0 1
Neighs: 303.000 ave 784 max 0 min
Histogram: 1 0 1 1 0 0 0 0 0 1
Total # of neighbors = 1212
Ave neighs/atom = 57.714286
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:00