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update standard examples for new style names

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This commit is contained in:
Axel Kohlmeyer
2021-07-21 22:52:43 -04:00
parent 9cf50eb4db
commit c78d4eab36
19 changed files with 1078 additions and 1132 deletions
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9
examples/reaxff/in.reaxc.rdx → examples/reaxff/in.reaxff.rdx
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@ -1,15 +1,14 @@
# ReaxFF potential for RDX system # ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real units real
atom_style charge atom_style charge
read_data data.rdx read_data data.rdx
pair_style reax/c control.reax_c.rdx pair_style reaxff control.reax_c.rdx
pair_coeff * * ffield.reax C H O N pair_coeff * * ffield.reax C H O N
compute reax all pair reax/c compute reax all pair reaxff
variable eb equal c_reax[1] variable eb equal c_reax[1]
variable ea equal c_reax[2] variable ea equal c_reax[2]
@ -30,7 +29,7 @@ neighbor 2.5 bin
neigh_modify every 10 delay 0 check no 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 1.0e-6 reax/c fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
variable nqeq equal f_2 variable nqeq equal f_2
@ -41,7 +40,7 @@ thermo_style custom step temp epair etotal press &
timestep 1.0 timestep 1.0
#dump 1 all atom 10 dump.reaxc.rdx #dump 1 all atom 10 dump.reaxff.rdx
#dump 2 all image 25 image.*.jpg type type & #dump 2 all image 25 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30 # axes yes 0.8 0.02 view 60 -30

9
examples/reaxff/in.reaxc.rdx-shielded → examples/reaxff/in.reaxff.rdx-shielded
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@ -1,15 +1,14 @@
# ReaxFF potential for RDX system # ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real units real
atom_style charge atom_style charge
read_data data.rdx read_data data.rdx
pair_style reax/c control.reax_c.rdx pair_style reaxff control.reax_c.rdx
pair_coeff * * ffield.reax C H O N pair_coeff * * ffield.reax C H O N
compute reax all pair reax/c compute reax all pair reaxff
variable eb equal c_reax[1] variable eb equal c_reax[1]
variable ea equal c_reax[2] variable ea equal c_reax[2]
@ -30,7 +29,7 @@ neighbor 2.5 bin
neigh_modify every 10 delay 0 check no neigh_modify every 10 delay 0 check no
fix 1 all nve fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff
variable nqeq equal f_2 variable nqeq equal f_2
thermo 10 thermo 10
@ -40,7 +39,7 @@ thermo_style custom step temp epair etotal press &
timestep 1.0 timestep 1.0
#dump 1 all atom 10 dump.reaxc.rdx #dump 1 all atom 10 dump.reaxff.rdx
#dump 2 all image 25 image.*.jpg type type & #dump 2 all image 25 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30 # axes yes 0.8 0.02 view 60 -30

13
examples/reaxff/in.reaxc.tatb → examples/reaxff/in.reaxff.tatb
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@ -1,15 +1,14 @@
# ReaxFF potential for TATB system # ReaxFF potential for TATB system
# this run is equivalent to reax/in.reax.tatb,
units real units real
atom_style charge atom_style charge
read_data data.tatb read_data data.tatb
pair_style reax/c control.reax_c.tatb pair_style reaxff control.reax_c.tatb
pair_coeff * * ffield.reax C H O N pair_coeff * * ffield.reax C H O N
compute reax all pair reax/c compute reax all pair reaxff
variable eb equal c_reax[1] variable eb equal c_reax[1]
variable ea equal c_reax[2] variable ea equal c_reax[2]
@ -30,8 +29,8 @@ neighbor 2.5 bin
neigh_modify delay 0 every 5 check no neigh_modify delay 0 every 5 check no
fix 1 all nve fix 1 all nve
fix 2 all qeq/reax 1 0.0 10.0 1.0e-6 reax/c fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
fix 4 all reax/c/bonds 5 bonds.reaxc fix 4 all reaxff/bonds 5 bonds.reaxff
variable nqeq equal f_2 variable nqeq equal f_2
thermo 5 thermo 5
@ -41,7 +40,7 @@ thermo_style custom step temp epair etotal press &
timestep 0.0625 timestep 0.0625
#dump 1 all custom 100 dump.reaxc.tatb id type q x y z #dump 1 all custom 100 dump.reaxff.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type & #dump 2 all image 5 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30 # axes yes 0.8 0.02 view 60 -30
@ -51,6 +50,6 @@ timestep 0.0625
# axes yes 0.8 0.02 view 60 -30 # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3 #dump_modify 3 pad 3
fix 3 all reax/c/species 1 5 5 species.tatb fix 3 all reaxff/species 1 5 5 species.tatb
run 25 run 25

13
examples/reaxff/in.reaxc.tatb-shielded → examples/reaxff/in.reaxff.tatb-shielded
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@ -1,15 +1,14 @@
# ReaxFF potential for TATB system # ReaxFF potential for TATB system
# this run is equivalent to reax/in.reax.tatb,
units real units real
atom_style charge atom_style charge
read_data data.tatb read_data data.tatb
pair_style reax/c control.reax_c.tatb pair_style reaxff control.reax_c.tatb
pair_coeff * * ffield.reax C H O N pair_coeff * * ffield.reax C H O N
compute reax all pair reax/c compute reax all pair reaxff
variable eb equal c_reax[1] variable eb equal c_reax[1]
variable ea equal c_reax[2] variable ea equal c_reax[2]
@ -30,8 +29,8 @@ neighbor 2.5 bin
neigh_modify delay 0 every 5 check no neigh_modify delay 0 every 5 check no
fix 1 all nve fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reax/c fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff
fix 4 all reax/c/bonds 5 bonds.reaxc fix 4 all reaxff/bonds 5 bonds.reaxff
variable nqeq equal f_2 variable nqeq equal f_2
thermo 5 thermo 5
@ -41,7 +40,7 @@ thermo_style custom step temp epair etotal press &
timestep 0.0625 timestep 0.0625
#dump 1 all custom 100 dump.reaxc.tatb id type q x y z #dump 1 all custom 100 dump.reaxff.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type & #dump 2 all image 5 image.*.jpg type type &
# axes yes 0.8 0.02 view 60 -30 # axes yes 0.8 0.02 view 60 -30
@ -51,6 +50,6 @@ timestep 0.0625
# axes yes 0.8 0.02 view 60 -30 # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3 #dump_modify 3 pad 3
fix 3 all reax/c/species 1 5 5 species.tatb fix 3 all reaxff/species 1 5 5 species.tatb
run 25 run 25

154
examples/reaxff/log.21Apr21.reaxc.rdx-shielded.g++.4
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@ -1,154 +0,0 @@
LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
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 = 0.001 seconds
pair_style reax/c control.reax_c.rdx
WARNING: Ignoring inactive control parameter: simulation_name (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/USER-REAXC/reaxc_control.cpp:113)
WARNING: Ignoring inactive control parameter: traj_title (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_info (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_forces (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_velocities (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: bond_info (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: angle_info (src/USER-REAXC/reaxc_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 reax/c
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 qeq/reax 1 0.0 10.0 1.0e-6 reax/c
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.reaxc.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 reax/c 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 qeq/reax 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}
}
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 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) = 13.36 | 13.36 | 13.36 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 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79931 0 168.88396 12.5
10 1288.6116 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.607221 0.2017796 0 54.629557 3.125229 -77.7067 0 14.933901 -5.8108541 843.92073 -180.43321 0 107.75935 8
20 538.95819 -1942.7037 -1910.5731 -10725.639 -2803.7394 7.9078269 0.07792668 0 81.610053 0.22951941 -57.557107 0 30.331207 -10.178049 878.99009 -159.68914 0 89.313379 7
30 463.09535 -1933.5765 -1905.9686 -33255.546 -2749.859 -8.0154745 0.02762893 0 81.627395 0.11972413 -50.262293 0 20.820303 -9.6327015 851.88715 -149.49499 0 79.205727 8
40 885.49171 -1958.9125 -1906.1229 -4814.6856 -2795.644 9.150669 0.13747498 0 70.947982 0.24360485 -57.862663 0 19.076496 -11.141218 873.73893 -159.99393 0 92.434096 11
50 861.16578 -1954.4599 -1903.1205 -1896.7713 -2784.845 3.8270515 0.15793266 0 79.851823 3.3492142 -78.06613 0 32.629016 -7.956541 872.81838 -190.98567 0 114.75995 10
60 1167.7852 -1971.8429 -1902.224 -3482.7305 -2705.863 -17.12171 0.22749077 0 44.507654 7.8560745 -74.788955 0 16.256483 -4.6046431 835.8304 -188.33691 0 114.19413 10
70 1439.9966 -1989.3024 -1903.4553 23845.651 -2890.7895 31.958845 0.26671721 0 85.758695 3.1803544 -71.002903 0 24.357134 -10.31131 905.86775 -175.38471 0 106.79648 10
80 502.39438 -1930.7544 -1900.8035 -20356.316 -2703.8115 -18.662467 0.11286011 0 99.804201 2.0329024 -76.171317 0 19.237028 -6.2786907 826.47451 -166.03125 0 92.539398 9
90 749.08499 -1946.9838 -1902.3262 17798.51 -2863.7576 42.068716 0.2433807 0 96.181613 0.96184888 -69.955448 0 24.615302 -11.582765 903.68818 -190.13843 0 120.69141 11
100 1109.6968 -1968.5874 -1902.4315 -4490.1018 -2755.8965 -7.1231014 0.21757699 0 61.806018 7.0827673 -75.645345 0 20.114997 -6.2371964 863.5635 -198.56976 0 122.09961 10.5
Loop time of 0.617778 on 1 procs for 100 steps with 21 atoms
Performance: 13.986 ns/day, 1.716 hours/ns, 161.871 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 | 0.52159 | 0.52159 | 0.52159 | 0.0 | 84.43
Neigh | 0.03479 | 0.03479 | 0.03479 | 0.0 | 5.63
Comm | 0.0017166 | 0.0017166 | 0.0017166 | 0.0 | 0.28
Output | 0.00061226 | 0.00061226 | 0.00061226 | 0.0 | 0.10
Modify | 0.058924 | 0.058924 | 0.058924 | 0.0 | 9.54
Other | | 0.0001466 | | | 0.02
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: 1096.00 ave 1096 max 1096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1096
Ave neighs/atom = 52.190476
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:00

154
examples/reaxff/log.21Apr21.reaxc.rdx.g++.1
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@ -1,154 +0,0 @@
LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
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 = 0.001 seconds
pair_style reax/c control.reax_c.rdx
WARNING: Ignoring inactive control parameter: simulation_name (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/USER-REAXC/reaxc_control.cpp:113)
WARNING: Ignoring inactive control parameter: traj_title (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_info (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_forces (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_velocities (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: bond_info (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: angle_info (src/USER-REAXC/reaxc_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 reax/c
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 qeq/reax 1 0.0 10.0 1.0e-6 reax/c
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.reaxc.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 reax/c 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 qeq/reax 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}
}
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 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) = 13.36 | 13.36 | 13.36 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 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79931 0 168.88396 12.5
10 1288.6116 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.607221 0.2017796 0 54.629557 3.125229 -77.7067 0 14.933901 -5.8108541 843.92073 -180.43321 0 107.75935 8
20 538.95819 -1942.7037 -1910.5731 -10725.639 -2803.7394 7.9078269 0.07792668 0 81.610053 0.22951941 -57.557107 0 30.331207 -10.178049 878.99009 -159.68914 0 89.313379 7
30 463.09535 -1933.5765 -1905.9686 -33255.546 -2749.859 -8.0154745 0.02762893 0 81.627395 0.11972413 -50.262293 0 20.820303 -9.6327015 851.88715 -149.49499 0 79.205727 8
40 885.49171 -1958.9125 -1906.1229 -4814.6856 -2795.644 9.150669 0.13747498 0 70.947982 0.24360485 -57.862663 0 19.076496 -11.141218 873.73893 -159.99393 0 92.434096 11
50 861.16578 -1954.4599 -1903.1205 -1896.7713 -2784.845 3.8270515 0.15793266 0 79.851823 3.3492142 -78.06613 0 32.629016 -7.956541 872.81838 -190.98567 0 114.75995 10
60 1167.7852 -1971.8429 -1902.224 -3482.7305 -2705.863 -17.12171 0.22749077 0 44.507654 7.8560745 -74.788955 0 16.256483 -4.6046431 835.8304 -188.33691 0 114.19413 10
70 1439.9966 -1989.3024 -1903.4553 23845.651 -2890.7895 31.958845 0.26671721 0 85.758695 3.1803544 -71.002903 0 24.357134 -10.31131 905.86775 -175.38471 0 106.79648 10
80 502.39438 -1930.7544 -1900.8035 -20356.316 -2703.8115 -18.662467 0.11286011 0 99.804201 2.0329024 -76.171317 0 19.237028 -6.2786907 826.47451 -166.03125 0 92.539398 9
90 749.08499 -1946.9838 -1902.3262 17798.51 -2863.7576 42.068716 0.2433807 0 96.181613 0.96184888 -69.955448 0 24.615302 -11.582765 903.68818 -190.13843 0 120.69141 11
100 1109.6968 -1968.5874 -1902.4315 -4490.1018 -2755.8965 -7.1231014 0.21757699 0 61.806018 7.0827673 -75.645345 0 20.114997 -6.2371964 863.5635 -198.56976 0 122.09961 10.5
Loop time of 0.618477 on 1 procs for 100 steps with 21 atoms
Performance: 13.970 ns/day, 1.718 hours/ns, 161.687 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.52329 | 0.52329 | 0.52329 | 0.0 | 84.61
Neigh | 0.03397 | 0.03397 | 0.03397 | 0.0 | 5.49
Comm | 0.0017006 | 0.0017006 | 0.0017006 | 0.0 | 0.27
Output | 0.00060892 | 0.00060892 | 0.00060892 | 0.0 | 0.10
Modify | 0.058764 | 0.058764 | 0.058764 | 0.0 | 9.50
Other | | 0.0001407 | | | 0.02
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: 1096.00 ave 1096 max 1096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1096
Ave neighs/atom = 52.190476
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:00

154
examples/reaxff/log.21Apr21.reaxc.rdx.g++.4
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@ -1,154 +0,0 @@
LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
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 = 0.001 seconds
pair_style reax/c control.reax_c.rdx
WARNING: Ignoring inactive control parameter: simulation_name (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/USER-REAXC/reaxc_control.cpp:113)
WARNING: Ignoring inactive control parameter: traj_title (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_info (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_forces (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_velocities (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: bond_info (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: angle_info (src/USER-REAXC/reaxc_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 reax/c
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 qeq/reax 1 0.0 10.0 1.0e-6 reax/c
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.reaxc.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 reax/c 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 qeq/reax 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}
}
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 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) = 13.36 | 13.36 | 13.36 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 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79931 0 168.88396 12.5
10 1288.6116 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.607221 0.2017796 0 54.629557 3.125229 -77.7067 0 14.933901 -5.8108541 843.92073 -180.43321 0 107.75935 8
20 538.95819 -1942.7037 -1910.5731 -10725.639 -2803.7394 7.9078269 0.07792668 0 81.610053 0.22951941 -57.557107 0 30.331207 -10.178049 878.99009 -159.68914 0 89.313379 7
30 463.09535 -1933.5765 -1905.9686 -33255.546 -2749.859 -8.0154745 0.02762893 0 81.627395 0.11972413 -50.262293 0 20.820303 -9.6327015 851.88715 -149.49499 0 79.205727 8
40 885.49171 -1958.9125 -1906.1229 -4814.6856 -2795.644 9.150669 0.13747498 0 70.947982 0.24360485 -57.862663 0 19.076496 -11.141218 873.73893 -159.99393 0 92.434096 11
50 861.16578 -1954.4599 -1903.1205 -1896.7713 -2784.845 3.8270515 0.15793266 0 79.851823 3.3492142 -78.06613 0 32.629016 -7.956541 872.81838 -190.98567 0 114.75995 10
60 1167.7852 -1971.8429 -1902.224 -3482.7305 -2705.863 -17.12171 0.22749077 0 44.507654 7.8560745 -74.788955 0 16.256483 -4.6046431 835.8304 -188.33691 0 114.19413 10
70 1439.9966 -1989.3024 -1903.4553 23845.651 -2890.7895 31.958845 0.26671721 0 85.758695 3.1803544 -71.002903 0 24.357134 -10.31131 905.86775 -175.38471 0 106.79648 10
80 502.39438 -1930.7544 -1900.8035 -20356.316 -2703.8115 -18.662467 0.11286011 0 99.804201 2.0329024 -76.171317 0 19.237028 -6.2786907 826.47451 -166.03125 0 92.539398 9
90 749.08499 -1946.9838 -1902.3262 17798.51 -2863.7576 42.068716 0.2433807 0 96.181613 0.96184888 -69.955448 0 24.615302 -11.582765 903.68818 -190.13843 0 120.69141 11
100 1109.6968 -1968.5874 -1902.4315 -4490.1018 -2755.8965 -7.1231014 0.21757699 0 61.806018 7.0827673 -75.645345 0 20.114997 -6.2371964 863.5635 -198.56976 0 122.09961 10.5
Loop time of 0.618479 on 1 procs for 100 steps with 21 atoms
Performance: 13.970 ns/day, 1.718 hours/ns, 161.687 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 | 0.52299 | 0.52299 | 0.52299 | 0.0 | 84.56
Neigh | 0.034338 | 0.034338 | 0.034338 | 0.0 | 5.55
Comm | 0.0017166 | 0.0017166 | 0.0017166 | 0.0 | 0.28
Output | 0.00060272 | 0.00060272 | 0.00060272 | 0.0 | 0.10
Modify | 0.058692 | 0.058692 | 0.058692 | 0.0 | 9.49
Other | | 0.0001385 | | | 0.02
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: 1096.00 ave 1096 max 1096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1096
Ave neighs/atom = 52.190476
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:00

154
examples/reaxff/log.21Apr21.reaxc.tatb-shielded.g++.1
View File

@ -1,154 +0,0 @@
LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
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 = 0.001 seconds
pair_style reax/c control.reax_c.rdx
WARNING: Ignoring inactive control parameter: simulation_name (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/USER-REAXC/reaxc_control.cpp:113)
WARNING: Ignoring inactive control parameter: traj_title (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_info (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_forces (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_velocities (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: bond_info (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: angle_info (src/USER-REAXC/reaxc_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 reax/c
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 qeq/reax 1 0.0 10.0 1.0e-6 reax/c
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.reaxc.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 reax/c 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 qeq/reax 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}
}
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 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) = 13.36 | 13.36 | 13.36 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 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79931 0 168.88396 12.5
10 1288.6116 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.607221 0.2017796 0 54.629557 3.125229 -77.7067 0 14.933901 -5.8108541 843.92073 -180.43321 0 107.75935 8
20 538.95819 -1942.7037 -1910.5731 -10725.639 -2803.7394 7.9078269 0.07792668 0 81.610053 0.22951941 -57.557107 0 30.331207 -10.178049 878.99009 -159.68914 0 89.313379 7
30 463.09535 -1933.5765 -1905.9686 -33255.546 -2749.859 -8.0154745 0.02762893 0 81.627395 0.11972413 -50.262293 0 20.820303 -9.6327015 851.88715 -149.49499 0 79.205727 8
40 885.49171 -1958.9125 -1906.1229 -4814.6856 -2795.644 9.150669 0.13747498 0 70.947982 0.24360485 -57.862663 0 19.076496 -11.141218 873.73893 -159.99393 0 92.434096 11
50 861.16578 -1954.4599 -1903.1205 -1896.7713 -2784.845 3.8270515 0.15793266 0 79.851823 3.3492142 -78.06613 0 32.629016 -7.956541 872.81838 -190.98567 0 114.75995 10
60 1167.7852 -1971.8429 -1902.224 -3482.7305 -2705.863 -17.12171 0.22749077 0 44.507654 7.8560745 -74.788955 0 16.256483 -4.6046431 835.8304 -188.33691 0 114.19413 10
70 1439.9966 -1989.3024 -1903.4553 23845.651 -2890.7895 31.958845 0.26671721 0 85.758695 3.1803544 -71.002903 0 24.357134 -10.31131 905.86775 -175.38471 0 106.79648 10
80 502.39438 -1930.7544 -1900.8035 -20356.316 -2703.8115 -18.662467 0.11286011 0 99.804201 2.0329024 -76.171317 0 19.237028 -6.2786907 826.47451 -166.03125 0 92.539398 9
90 749.08499 -1946.9838 -1902.3262 17798.51 -2863.7576 42.068716 0.2433807 0 96.181613 0.96184888 -69.955448 0 24.615302 -11.582765 903.68818 -190.13843 0 120.69141 11
100 1109.6968 -1968.5874 -1902.4315 -4490.1018 -2755.8965 -7.1231014 0.21757699 0 61.806018 7.0827673 -75.645345 0 20.114997 -6.2371964 863.5635 -198.56976 0 122.09961 10.5
Loop time of 0.618214 on 1 procs for 100 steps with 21 atoms
Performance: 13.976 ns/day, 1.717 hours/ns, 161.756 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.52298 | 0.52298 | 0.52298 | 0.0 | 84.60
Neigh | 0.033964 | 0.033964 | 0.033964 | 0.0 | 5.49
Comm | 0.001708 | 0.001708 | 0.001708 | 0.0 | 0.28
Output | 0.00060844 | 0.00060844 | 0.00060844 | 0.0 | 0.10
Modify | 0.058812 | 0.058812 | 0.058812 | 0.0 | 9.51
Other | | 0.0001411 | | | 0.02
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: 1096.00 ave 1096 max 1096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1096
Ave neighs/atom = 52.190476
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:00

154
examples/reaxff/log.21Apr21.reaxc.tatb-shielded.g++.4
View File

@ -1,154 +0,0 @@
LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
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 = 0.001 seconds
pair_style reax/c control.reax_c.rdx
WARNING: Ignoring inactive control parameter: simulation_name (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/USER-REAXC/reaxc_control.cpp:113)
WARNING: Ignoring inactive control parameter: traj_title (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_info (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_forces (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_velocities (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: bond_info (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: angle_info (src/USER-REAXC/reaxc_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 reax/c
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 qeq/reax 1 0.0 10.0 1.0e-6 reax/c
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.reaxc.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 reax/c 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 qeq/reax 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}
}
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 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) = 13.36 | 13.36 | 13.36 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 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79931 0 168.88396 12.5
10 1288.6116 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.607221 0.2017796 0 54.629557 3.125229 -77.7067 0 14.933901 -5.8108541 843.92073 -180.43321 0 107.75935 8
20 538.95819 -1942.7037 -1910.5731 -10725.639 -2803.7394 7.9078269 0.07792668 0 81.610053 0.22951941 -57.557107 0 30.331207 -10.178049 878.99009 -159.68914 0 89.313379 7
30 463.09535 -1933.5765 -1905.9686 -33255.546 -2749.859 -8.0154745 0.02762893 0 81.627395 0.11972413 -50.262293 0 20.820303 -9.6327015 851.88715 -149.49499 0 79.205727 8
40 885.49171 -1958.9125 -1906.1229 -4814.6856 -2795.644 9.150669 0.13747498 0 70.947982 0.24360485 -57.862663 0 19.076496 -11.141218 873.73893 -159.99393 0 92.434096 11
50 861.16578 -1954.4599 -1903.1205 -1896.7713 -2784.845 3.8270515 0.15793266 0 79.851823 3.3492142 -78.06613 0 32.629016 -7.956541 872.81838 -190.98567 0 114.75995 10
60 1167.7852 -1971.8429 -1902.224 -3482.7305 -2705.863 -17.12171 0.22749077 0 44.507654 7.8560745 -74.788955 0 16.256483 -4.6046431 835.8304 -188.33691 0 114.19413 10
70 1439.9966 -1989.3024 -1903.4553 23845.651 -2890.7895 31.958845 0.26671721 0 85.758695 3.1803544 -71.002903 0 24.357134 -10.31131 905.86775 -175.38471 0 106.79648 10
80 502.39438 -1930.7544 -1900.8035 -20356.316 -2703.8115 -18.662467 0.11286011 0 99.804201 2.0329024 -76.171317 0 19.237028 -6.2786907 826.47451 -166.03125 0 92.539398 9
90 749.08499 -1946.9838 -1902.3262 17798.51 -2863.7576 42.068716 0.2433807 0 96.181613 0.96184888 -69.955448 0 24.615302 -11.582765 903.68818 -190.13843 0 120.69141 11
100 1109.6968 -1968.5874 -1902.4315 -4490.1018 -2755.8965 -7.1231014 0.21757699 0 61.806018 7.0827673 -75.645345 0 20.114997 -6.2371964 863.5635 -198.56976 0 122.09961 10.5
Loop time of 0.617311 on 1 procs for 100 steps with 21 atoms
Performance: 13.996 ns/day, 1.715 hours/ns, 161.993 timesteps/s
99.9% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.52226 | 0.52226 | 0.52226 | 0.0 | 84.60
Neigh | 0.033952 | 0.033952 | 0.033952 | 0.0 | 5.50
Comm | 0.0017183 | 0.0017183 | 0.0017183 | 0.0 | 0.28
Output | 0.00060129 | 0.00060129 | 0.00060129 | 0.0 | 0.10
Modify | 0.058648 | 0.058648 | 0.058648 | 0.0 | 9.50
Other | | 0.0001364 | | | 0.02
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: 1096.00 ave 1096 max 1096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1096
Ave neighs/atom = 52.190476
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:00

154
examples/reaxff/log.21Apr21.reaxc.tatb.g++.1
View File

@ -1,154 +0,0 @@
LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
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 = 0.001 seconds
pair_style reax/c control.reax_c.rdx
WARNING: Ignoring inactive control parameter: simulation_name (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/USER-REAXC/reaxc_control.cpp:113)
WARNING: Ignoring inactive control parameter: traj_title (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_info (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_forces (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_velocities (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: bond_info (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: angle_info (src/USER-REAXC/reaxc_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 reax/c
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 qeq/reax 1 0.0 10.0 1.0e-6 reax/c
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.reaxc.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 reax/c 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 qeq/reax 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}
}
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 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) = 13.36 | 13.36 | 13.36 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 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79931 0 168.88396 12.5
10 1288.6116 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.607221 0.2017796 0 54.629557 3.125229 -77.7067 0 14.933901 -5.8108541 843.92073 -180.43321 0 107.75935 8
20 538.95819 -1942.7037 -1910.5731 -10725.639 -2803.7394 7.9078269 0.07792668 0 81.610053 0.22951941 -57.557107 0 30.331207 -10.178049 878.99009 -159.68914 0 89.313379 7
30 463.09535 -1933.5765 -1905.9686 -33255.546 -2749.859 -8.0154745 0.02762893 0 81.627395 0.11972413 -50.262293 0 20.820303 -9.6327015 851.88715 -149.49499 0 79.205727 8
40 885.49171 -1958.9125 -1906.1229 -4814.6856 -2795.644 9.150669 0.13747498 0 70.947982 0.24360485 -57.862663 0 19.076496 -11.141218 873.73893 -159.99393 0 92.434096 11
50 861.16578 -1954.4599 -1903.1205 -1896.7713 -2784.845 3.8270515 0.15793266 0 79.851823 3.3492142 -78.06613 0 32.629016 -7.956541 872.81838 -190.98567 0 114.75995 10
60 1167.7852 -1971.8429 -1902.224 -3482.7305 -2705.863 -17.12171 0.22749077 0 44.507654 7.8560745 -74.788955 0 16.256483 -4.6046431 835.8304 -188.33691 0 114.19413 10
70 1439.9966 -1989.3024 -1903.4553 23845.651 -2890.7895 31.958845 0.26671721 0 85.758695 3.1803544 -71.002903 0 24.357134 -10.31131 905.86775 -175.38471 0 106.79648 10
80 502.39438 -1930.7544 -1900.8035 -20356.316 -2703.8115 -18.662467 0.11286011 0 99.804201 2.0329024 -76.171317 0 19.237028 -6.2786907 826.47451 -166.03125 0 92.539398 9
90 749.08499 -1946.9838 -1902.3262 17798.51 -2863.7576 42.068716 0.2433807 0 96.181613 0.96184888 -69.955448 0 24.615302 -11.582765 903.68818 -190.13843 0 120.69141 11
100 1109.6968 -1968.5874 -1902.4315 -4490.1018 -2755.8965 -7.1231014 0.21757699 0 61.806018 7.0827673 -75.645345 0 20.114997 -6.2371964 863.5635 -198.56976 0 122.09961 10.5
Loop time of 0.617401 on 1 procs for 100 steps with 21 atoms
Performance: 13.994 ns/day, 1.715 hours/ns, 161.969 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 | 0.52185 | 0.52185 | 0.52185 | 0.0 | 84.52
Neigh | 0.034507 | 0.034507 | 0.034507 | 0.0 | 5.59
Comm | 0.0017211 | 0.0017211 | 0.0017211 | 0.0 | 0.28
Output | 0.00060844 | 0.00060844 | 0.00060844 | 0.0 | 0.10
Modify | 0.058573 | 0.058573 | 0.058573 | 0.0 | 9.49
Other | | 0.0001466 | | | 0.02
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: 1096.00 ave 1096 max 1096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1096
Ave neighs/atom = 52.190476
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:00

154
examples/reaxff/log.21Apr21.reaxc.tatb.g++.4
View File

@ -1,154 +0,0 @@
LAMMPS (8 Apr 2021)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
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 = 0.001 seconds
pair_style reax/c control.reax_c.rdx
WARNING: Ignoring inactive control parameter: simulation_name (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/USER-REAXC/reaxc_control.cpp:113)
WARNING: Ignoring inactive control parameter: traj_title (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_info (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_forces (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_velocities (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: bond_info (src/USER-REAXC/reaxc_control.cpp:97)
WARNING: Ignoring inactive control parameter: angle_info (src/USER-REAXC/reaxc_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 reax/c
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 qeq/reax 1 0.0 10.0 1.0e-6 reax/c
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.reaxc.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 reax/c 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 qeq/reax 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}
}
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 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) = 13.36 | 13.36 | 13.36 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 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79931 0 168.88396 12.5
10 1288.6116 -1989.6644 -1912.8422 -19456.353 -2734.6769 -15.607221 0.2017796 0 54.629557 3.125229 -77.7067 0 14.933901 -5.8108541 843.92073 -180.43321 0 107.75935 8
20 538.95819 -1942.7037 -1910.5731 -10725.639 -2803.7394 7.9078269 0.07792668 0 81.610053 0.22951941 -57.557107 0 30.331207 -10.178049 878.99009 -159.68914 0 89.313379 7
30 463.09535 -1933.5765 -1905.9686 -33255.546 -2749.859 -8.0154745 0.02762893 0 81.627395 0.11972413 -50.262293 0 20.820303 -9.6327015 851.88715 -149.49499 0 79.205727 8
40 885.49171 -1958.9125 -1906.1229 -4814.6856 -2795.644 9.150669 0.13747498 0 70.947982 0.24360485 -57.862663 0 19.076496 -11.141218 873.73893 -159.99393 0 92.434096 11
50 861.16578 -1954.4599 -1903.1205 -1896.7713 -2784.845 3.8270515 0.15793266 0 79.851823 3.3492142 -78.06613 0 32.629016 -7.956541 872.81838 -190.98567 0 114.75995 10
60 1167.7852 -1971.8429 -1902.224 -3482.7305 -2705.863 -17.12171 0.22749077 0 44.507654 7.8560745 -74.788955 0 16.256483 -4.6046431 835.8304 -188.33691 0 114.19413 10
70 1439.9966 -1989.3024 -1903.4553 23845.651 -2890.7895 31.958845 0.26671721 0 85.758695 3.1803544 -71.002903 0 24.357134 -10.31131 905.86775 -175.38471 0 106.79648 10
80 502.39438 -1930.7544 -1900.8035 -20356.316 -2703.8115 -18.662467 0.11286011 0 99.804201 2.0329024 -76.171317 0 19.237028 -6.2786907 826.47451 -166.03125 0 92.539398 9
90 749.08499 -1946.9838 -1902.3262 17798.51 -2863.7576 42.068716 0.2433807 0 96.181613 0.96184888 -69.955448 0 24.615302 -11.582765 903.68818 -190.13843 0 120.69141 11
100 1109.6968 -1968.5874 -1902.4315 -4490.1018 -2755.8965 -7.1231014 0.21757699 0 61.806018 7.0827673 -75.645345 0 20.114997 -6.2371964 863.5635 -198.56976 0 122.09961 10.5
Loop time of 0.617397 on 1 procs for 100 steps with 21 atoms
Performance: 13.994 ns/day, 1.715 hours/ns, 161.970 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 | 0.52183 | 0.52183 | 0.52183 | 0.0 | 84.52
Neigh | 0.034217 | 0.034217 | 0.034217 | 0.0 | 5.54
Comm | 0.0017104 | 0.0017104 | 0.0017104 | 0.0 | 0.28
Output | 0.00059891 | 0.00059891 | 0.00059891 | 0.0 | 0.10
Modify | 0.0589 | 0.0589 | 0.0589 | 0.0 | 9.54
Other | | 0.0001419 | | | 0.02
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: 1096.00 ave 1096 max 1096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1096
Ave neighs/atom = 52.190476
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:00

144
examples/reaxff/log.21Jul21.reaxff.rdx-shielded.g++.1 Normal file
View File

@ -0,0 +1,144 @@
LAMMPS (2 Jul 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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 = 0.001 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 qeq/shielded 1 10.0 1.0e-6 100 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}
}
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 qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 13.86 | 13.86 | 13.86 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 -1884.3081 -1884.3081 27186.181 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79932 0 168.88397 12
10 1288.6114 -1989.6644 -1912.8422 -19456.349 -2734.6769 -15.607218 0.20177961 0 54.629555 3.1252297 -77.7067 0 14.933901 -5.810854 843.92074 -180.43322 0 107.75935 8
20 538.95852 -1942.7037 -1910.5731 -10725.667 -2803.7395 7.9078343 0.077926704 0 81.610044 0.22951937 -57.557105 0 30.331203 -10.178049 878.99016 -159.69263 0 89.316862 7
30 463.09515 -1933.5765 -1905.9685 -33255.499 -2749.8591 -8.0154635 0.02762867 0 81.627413 0.1197239 -50.262272 0 20.82032 -9.632703 851.88721 -149.49497 0 79.205707 8
40 885.49689 -1958.9125 -1906.1226 -4814.6325 -2795.644 9.1505916 0.13747481 0 70.948074 0.24360544 -57.862695 0 19.076518 -11.14121 873.73893 -159.9939 0 92.434061 11
50 861.16008 -1954.4602 -1903.1211 -1896.648 -2784.8451 3.8269988 0.1579331 0 79.851597 3.349208 -78.066133 0 32.628942 -7.9565363 872.8186 -190.98572 0 114.76001 10
60 1167.7831 -1971.8435 -1902.2247 -3482.927 -2705.8639 -17.121541 0.22749081 0 44.507721 7.8559737 -74.789039 0 16.2565 -4.6046718 835.8307 -188.33687 0 114.19412 10
70 1439.9897 -1989.3024 -1903.4557 23845.83 -2890.7894 31.958658 0.26671716 0 85.758318 3.1804201 -71.002959 0 24.35723 -10.31128 905.86819 -175.38505 0 106.79678 10
80 502.39931 -1930.7551 -1900.804 -20356.375 -2703.8109 -18.66274 0.1128617 0 99.80351 2.0329611 -76.171312 0 19.236815 -6.2786426 826.47424 -166.03148 0 92.539616 9
90 749.08601 -1946.984 -1902.3264 17798.716 -2863.7585 42.068606 0.24338046 0 96.181674 0.96183581 -69.955564 0 24.615514 -11.582742 903.68878 -190.13822 0 120.69121 11
100 1109.6946 -1968.588 -1902.4322 -4490.4001 -2755.899 -7.1224954 0.21757676 0 61.805955 7.0825894 -75.645488 0 20.115437 -6.2372635 863.56481 -198.56946 0 122.09935 10
Loop time of 0.23792 on 1 procs for 100 steps with 21 atoms
Performance: 36.315 ns/day, 0.661 hours/ns, 420.310 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 | 0.21046 | 0.21046 | 0.21046 | 0.0 | 88.46
Neigh | 0.010947 | 0.010947 | 0.010947 | 0.0 | 4.60
Comm | 0.00060345 | 0.00060345 | 0.00060345 | 0.0 | 0.25
Output | 0.00071705 | 0.00071705 | 0.00071705 | 0.0 | 0.30
Modify | 0.014873 | 0.014873 | 0.014873 | 0.0 | 6.25
Other | | 0.0003213 | | | 0.14
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: 1096.00 ave 1096 max 1096 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 1306.00 ave 1306 max 1306 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 1306
Ave neighs/atom = 62.190476
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:00

144
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@ -0,0 +1,144 @@
LAMMPS (2 Jul 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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 = 0.003 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 qeq/shielded 1 10.0 1.0e-6 100 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}
}
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 qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 9.856 | 11.02 | 12.23 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 -1884.3081 -1884.3081 27186.179 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79963 0 168.88428 12
10 1288.6115 -1989.6644 -1912.8422 -19456.352 -2734.6769 -15.607219 0.20177961 0 54.629556 3.1252291 -77.7067 0 14.933901 -5.8108542 843.92074 -180.43321 0 107.75934 8
20 538.95831 -1942.7037 -1910.5731 -10725.628 -2803.7395 7.9078316 0.077926725 0 81.610046 0.22951948 -57.55711 0 30.331206 -10.178049 878.99011 -159.68964 0 89.313879 6
30 463.09528 -1933.5765 -1905.9685 -33255.523 -2749.859 -8.015479 0.027628772 0 81.627413 0.11972402 -50.262283 0 20.82031 -9.6327014 851.88714 -149.49498 0 79.205717 8
40 885.49492 -1958.9125 -1906.1227 -4814.6646 -2795.6439 9.1506063 0.13747482 0 70.948055 0.2436053 -57.862686 0 19.076515 -11.141211 873.73888 -159.99391 0 92.434067 11
50 861.15982 -1954.4602 -1903.1212 -1896.7209 -2784.845 3.8269674 0.15793308 0 79.851587 3.3492059 -78.06613 0 32.628933 -7.9565341 872.81849 -190.9857 0 114.75999 10
60 1167.7827 -1971.8436 -1902.2248 -3482.8501 -2705.8641 -17.121497 0.22749093 0 44.507698 7.8559911 -74.78902 0 16.256511 -4.6046743 835.83081 -188.33692 0 114.19416 10
70 1439.9904 -1989.3026 -1903.4558 23846.02 -2890.7894 31.95863 0.26671716 0 85.758232 3.1804311 -71.002978 0 24.357223 -10.311272 905.86809 -175.38506 0 106.79678 10
80 502.39774 -1930.7552 -1900.8041 -20356.27 -2703.8119 -18.66246 0.11286127 0 99.803504 2.0329528 -76.171312 0 19.236983 -6.278675 826.47474 -166.03143 0 92.539573 9
90 749.07673 -1946.984 -1902.3269 17798.497 -2863.7581 42.06868 0.24338043 0 96.181508 0.9618341 -69.955454 0 24.615416 -11.582759 903.68853 -190.13817 0 120.69116 11
100 1109.6909 -1968.5881 -1902.4325 -4490.3603 -2755.8994 -7.1223998 0.21757662 0 61.805909 7.0826145 -75.645472 0 20.115466 -6.2372802 863.565 -198.56948 0 122.09938 10
Loop time of 0.427646 on 4 procs for 100 steps with 21 atoms
Performance: 20.204 ns/day, 1.188 hours/ns, 233.838 timesteps/s
88.6% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.1373 | 0.20047 | 0.27938 | 11.8 | 46.88
Neigh | 0.0067 | 0.009334 | 0.01249 | 2.1 | 2.18
Comm | 0.057132 | 0.13685 | 0.19972 | 14.4 | 32.00
Output | 0.00078935 | 0.0013884 | 0.0031266 | 2.7 | 0.32
Modify | 0.075213 | 0.079164 | 0.082556 | 0.9 | 18.51
Other | | 0.0004359 | | | 0.10
Nlocal: 5.25000 ave 15 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 355.500 ave 432 max 282 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 298.750 ave 822 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
FullNghs: 326.500 ave 927 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 1306
Ave neighs/atom = 62.190476
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:00

60
examples/reaxff/log.21Apr21.reaxc.rdx-shielded.g++.1 → examples/reaxff/log.21Jul21.reaxff.rdx.g++.1
View File

@ -1,7 +1,7 @@
LAMMPS (8 Apr 2021) LAMMPS (2 Jul 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for RDX system # ReaxFF potential for RDX system
# this run is equivalent to reax/in.reax.rdx
units real units real
@ -14,20 +14,20 @@ Reading data file ...
21 atoms 21 atoms
read_data CPU = 0.001 seconds read_data CPU = 0.001 seconds
pair_style reax/c control.reax_c.rdx pair_style reaxff control.reax_c.rdx
WARNING: Ignoring inactive control parameter: simulation_name (src/USER-REAXC/reaxc_control.cpp:97) WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: energy_update_freq (src/USER-REAXC/reaxc_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/USER-REAXC/reaxc_control.cpp:113) 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/USER-REAXC/reaxc_control.cpp:97) WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_info (src/USER-REAXC/reaxc_control.cpp:97) WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_forces (src/USER-REAXC/reaxc_control.cpp:97) WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: atom_velocities (src/USER-REAXC/reaxc_control.cpp:97) WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: bond_info (src/USER-REAXC/reaxc_control.cpp:97) WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:97)
WARNING: Ignoring inactive control parameter: angle_info (src/USER-REAXC/reaxc_control.cpp:97) WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:97)
pair_coeff * * ffield.reax C H O N pair_coeff * * ffield.reax C H O N
Reading potential file ffield.reax with DATE: 2010-02-19 Reading potential file ffield.reax with DATE: 2010-02-19
compute reax all pair reax/c compute reax all pair reaxff
variable eb equal c_reax[1] variable eb equal c_reax[1]
variable ea equal c_reax[2] variable ea equal c_reax[2]
@ -48,7 +48,7 @@ neighbor 2.5 bin
neigh_modify every 10 delay 0 check no 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 1.0e-6 reax/c fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
variable nqeq equal f_2 variable nqeq equal f_2
@ -57,7 +57,7 @@ thermo_style custom step temp epair etotal press v_eb v_ea v_
timestep 1.0 timestep 1.0
#dump 1 all atom 10 dump.reaxc.rdx #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 2 all image 25 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3 #dump_modify 2 pad 3
@ -71,7 +71,7 @@ CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Your simulation uses code contributions which should be cited: Your simulation uses code contributions which should be cited:
- pair reax/c command: - pair reaxff command:
@Article{Aktulga12, @Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama}, author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
@ -82,7 +82,7 @@ Your simulation uses code contributions which should be cited:
pages = {245--259} pages = {245--259}
} }
- fix qeq/reax command: - fix qeq/reaxff command:
@Article{Aktulga12, @Article{Aktulga12,
author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama}, author = {H. M. Aktulga, J. C. Fogarty, S. A. Pandit, A. Y. Grama},
@ -102,12 +102,12 @@ Neighbor list info ...
ghost atom cutoff = 12.5 ghost atom cutoff = 12.5
binsize = 6.25, bins = 3 3 3 binsize = 6.25, bins = 3 3 3
2 neighbor lists, perpetual/occasional/extra = 2 0 0 2 neighbor lists, perpetual/occasional/extra = 2 0 0
(1) pair reax/c, perpetual (1) pair reaxff, perpetual
attributes: half, newton off, ghost attributes: half, newton off, ghost
pair build: half/bin/newtoff/ghost pair build: half/bin/newtoff/ghost
stencil: half/ghost/bin/3d/newtoff stencil: full/ghost/bin/3d
bin: standard bin: standard
(2) fix qeq/reax, perpetual, copy from (1) (2) fix qeq/reaxff, perpetual, copy from (1)
attributes: half, newton off, ghost attributes: half, newton off, ghost
pair build: copy pair build: copy
stencil: none stencil: none
@ -123,22 +123,22 @@ Step Temp E_pair TotEng Press v_eb v_ea v_elp v_emol v_ev v_epen v_ecoa v_ehb v_
60 1167.7852 -1971.8429 -1902.224 -3482.7305 -2705.863 -17.12171 0.22749077 0 44.507654 7.8560745 -74.788955 0 16.256483 -4.6046431 835.8304 -188.33691 0 114.19413 10 60 1167.7852 -1971.8429 -1902.224 -3482.7305 -2705.863 -17.12171 0.22749077 0 44.507654 7.8560745 -74.788955 0 16.256483 -4.6046431 835.8304 -188.33691 0 114.19413 10
70 1439.9966 -1989.3024 -1903.4553 23845.651 -2890.7895 31.958845 0.26671721 0 85.758695 3.1803544 -71.002903 0 24.357134 -10.31131 905.86775 -175.38471 0 106.79648 10 70 1439.9966 -1989.3024 -1903.4553 23845.651 -2890.7895 31.958845 0.26671721 0 85.758695 3.1803544 -71.002903 0 24.357134 -10.31131 905.86775 -175.38471 0 106.79648 10
80 502.39438 -1930.7544 -1900.8035 -20356.316 -2703.8115 -18.662467 0.11286011 0 99.804201 2.0329024 -76.171317 0 19.237028 -6.2786907 826.47451 -166.03125 0 92.539398 9 80 502.39438 -1930.7544 -1900.8035 -20356.316 -2703.8115 -18.662467 0.11286011 0 99.804201 2.0329024 -76.171317 0 19.237028 -6.2786907 826.47451 -166.03125 0 92.539398 9
90 749.08499 -1946.9838 -1902.3262 17798.51 -2863.7576 42.068716 0.2433807 0 96.181613 0.96184888 -69.955448 0 24.615302 -11.582765 903.68818 -190.13843 0 120.69141 11 90 749.08499 -1946.9838 -1902.3262 17798.51 -2863.7576 42.068717 0.2433807 0 96.181613 0.96184887 -69.955448 0 24.615302 -11.582765 903.68818 -190.13843 0 120.69141 11
100 1109.6968 -1968.5874 -1902.4315 -4490.1018 -2755.8965 -7.1231014 0.21757699 0 61.806018 7.0827673 -75.645345 0 20.114997 -6.2371964 863.5635 -198.56976 0 122.09961 10.5 100 1109.6968 -1968.5874 -1902.4315 -4490.1018 -2755.8965 -7.1231014 0.21757699 0 61.806018 7.0827673 -75.645345 0 20.114997 -6.2371964 863.5635 -198.56976 0 122.09961 10.5
Loop time of 0.617026 on 1 procs for 100 steps with 21 atoms Loop time of 0.231802 on 1 procs for 100 steps with 21 atoms
Performance: 14.003 ns/day, 1.714 hours/ns, 162.068 timesteps/s Performance: 37.273 ns/day, 0.644 hours/ns, 431.402 timesteps/s
99.7% CPU use with 1 MPI tasks x 1 OpenMP threads 99.2% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown: MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total Section | min time | avg time | max time |%varavg| %total
--------------------------------------------------------------- ---------------------------------------------------------------
Pair | 0.52176 | 0.52176 | 0.52176 | 0.0 | 84.56 Pair | 0.20857 | 0.20857 | 0.20857 | 0.0 | 89.98
Neigh | 0.033948 | 0.033948 | 0.033948 | 0.0 | 5.50 Neigh | 0.010489 | 0.010489 | 0.010489 | 0.0 | 4.52
Comm | 0.0017188 | 0.0017188 | 0.0017188 | 0.0 | 0.28 Comm | 0.00059632 | 0.00059632 | 0.00059632 | 0.0 | 0.26
Output | 0.00059319 | 0.00059319 | 0.00059319 | 0.0 | 0.10 Output | 0.00067498 | 0.00067498 | 0.00067498 | 0.0 | 0.29
Modify | 0.05887 | 0.05887 | 0.05887 | 0.0 | 9.54 Modify | 0.011161 | 0.011161 | 0.011161 | 0.0 | 4.82
Other | | 0.0001347 | | | 0.02 Other | | 0.000307 | | | 0.13
Nlocal: 21.0000 ave 21 max 21 min Nlocal: 21.0000 ave 21 max 21 min
Histogram: 1 0 0 0 0 0 0 0 0 0 Histogram: 1 0 0 0 0 0 0 0 0 0

154
examples/reaxff/log.21Jul21.reaxff.rdx.g++.4 Normal file
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@ -0,0 +1,154 @@
LAMMPS (2 Jul 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
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 = 0.001 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 qeq/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 qeq/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}
}
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 qeq/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) = 9.353 | 10.52 | 11.73 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 -1884.3081 -1884.3081 27186.18 -2958.4712 79.527715 0.31082031 0 98.589783 25.846176 -0.18034154 0 16.709078 -9.1620736 938.43732 -244.79953 0 168.88418 12
10 1288.6115 -1989.6644 -1912.8422 -19456.352 -2734.6769 -15.607219 0.20177961 0 54.629556 3.1252292 -77.7067 0 14.933901 -5.8108542 843.92074 -180.43321 0 107.75934 8
20 538.95847 -1942.7037 -1910.5731 -10725.668 -2803.7395 7.9078328 0.077926688 0 81.610045 0.22951933 -57.557103 0 30.331203 -10.178049 878.99015 -159.69262 0 89.316856 7
30 463.09521 -1933.5765 -1905.9685 -33255.503 -2749.8591 -8.0154614 0.027628708 0 81.627408 0.11972393 -50.262275 0 20.820319 -9.6327031 851.88721 -149.49497 0 79.205707 8
40 885.49559 -1958.9126 -1906.1227 -4814.661 -2795.644 9.1506103 0.13747486 0 70.948058 0.24360549 -57.862693 0 19.076514 -11.141211 873.73894 -159.9939 0 92.434063 11
50 861.16222 -1954.4601 -1903.1209 -1896.7328 -2784.8449 3.8269573 0.15793301 0 79.851661 3.3492101 -78.066131 0 32.628939 -7.9565311 872.81847 -190.9857 0 114.75999 10
60 1167.7838 -1971.8434 -1902.2246 -3482.8253 -2705.8639 -17.121553 0.22749078 0 44.507707 7.8560156 -74.789002 0 16.256509 -4.6046674 835.83076 -188.33689 0 114.19413 10
70 1439.9922 -1989.3024 -1903.4556 23845.682 -2890.7894 31.958742 0.26671722 0 85.758402 3.1803955 -71.002937 0 24.357176 -10.311293 905.86805 -175.38494 0 106.79668 10
80 502.39847 -1930.7549 -1900.8038 -20356.357 -2703.8111 -18.662668 0.11286141 0 99.803668 2.0329484 -76.17132 0 19.236866 -6.2786536 826.47435 -166.03145 0 92.539587 9
90 749.0857 -1946.984 -1902.3263 17798.657 -2863.7584 42.068704 0.24338054 0 96.181666 0.96183837 -69.955527 0 24.615445 -11.58275 903.68864 -190.13828 0 120.69127 11
100 1109.695 -1968.5879 -1902.4321 -4490.3441 -2755.8984 -7.1226574 0.21757683 0 61.806014 7.0826278 -75.645456 0 20.115306 -6.2372466 863.56451 -198.56953 0 122.09941 10.5
Loop time of 0.371707 on 4 procs for 100 steps with 21 atoms
Performance: 23.244 ns/day, 1.033 hours/ns, 269.029 timesteps/s
91.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 0.13518 | 0.19123 | 0.24947 | 9.7 | 51.45
Neigh | 0.0073075 | 0.0096968 | 0.012228 | 1.8 | 2.61
Comm | 0.034511 | 0.093329 | 0.14912 | 14.0 | 25.11
Output | 0.00081416 | 0.0011345 | 0.0019655 | 1.4 | 0.31
Modify | 0.073177 | 0.075449 | 0.078618 | 0.7 | 20.30
Other | | 0.0008711 | | | 0.23
Nlocal: 5.25000 ave 15 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Nghost: 355.500 ave 432 max 282 min
Histogram: 1 0 0 0 1 1 0 0 0 1
Neighs: 298.750 ave 822 max 0 min
Histogram: 1 0 2 0 0 0 0 0 0 1
Total # of neighbors = 1195
Ave neighs/atom = 56.904762
Neighbor list builds = 10
Dangerous builds not checked
Total wall time: 0:00:00

142
examples/reaxff/log.21Jul21.reaxff.tatb-shielded.g++.1 Normal file
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@ -0,0 +1,142 @@
LAMMPS (2 Jul 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system
units real
atom_style charge
read_data data.tatb
Reading data file ...
triclinic box = (0.0000000 0.0000000 0.0000000) to (13.624000 17.114915 15.182639) with tilt (-5.7531563 -6.3254660 7.4257288)
1 by 1 by 1 MPI processor grid
reading atoms ...
384 atoms
read_data CPU = 0.002 seconds
pair_style reaxff control.reax_c.tatb
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 delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff
fix 4 all reaxff/bonds 5 bonds.reaxff
variable nqeq equal f_2
thermo 5
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 0.0625
#dump 1 all custom 100 dump.reaxff.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reaxff/species 1 5 5 species.tatb
run 25
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}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 5 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 = 5 4 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 qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 141.3 | 141.3 | 141.3 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 -44760.998 -44760.998 7827.7874 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6395 0 6391.0275 31
5 0.61603968 -44761.698 -44760.994 8934.6339 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1905 0 6388.6665 8
10 2.3525543 -44763.227 -44760.541 12288.589 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9762 0 6381.714 10
15 4.9013256 -44766.36 -44760.764 17716.957 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2536 0 6370.4198 9
20 7.8294699 -44769.686 -44760.747 25205.552 -61089.006 490.21314 4.7193021 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.5055 0 6355.2567 8
25 10.697916 -44772.904 -44760.691 34232.955 -61069.308 490.25886 4.7163736 0 1570.7397 20.181347 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.308 0 6336.7889 7
Loop time of 3.31728 on 1 procs for 25 steps with 384 atoms
Performance: 0.041 ns/day, 589.738 hours/ns, 7.536 timesteps/s
99.4% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9321 | 1.9321 | 1.9321 | 0.0 | 58.24
Neigh | 0.6452 | 0.6452 | 0.6452 | 0.0 | 19.45
Comm | 0.0020122 | 0.0020122 | 0.0020122 | 0.0 | 0.06
Output | 0.00030173 | 0.00030173 | 0.00030173 | 0.0 | 0.01
Modify | 0.73726 | 0.73726 | 0.73726 | 0.0 | 22.22
Other | | 0.0003829 | | | 0.01
Nlocal: 384.000 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7559.00 ave 7559 max 7559 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 286828.0 ave 286828 max 286828 min
Histogram: 1 0 0 0 0 0 0 0 0 0
FullNghs: 336304.0 ave 336304 max 336304 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 336304
Ave neighs/atom = 875.79167
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:03

142
examples/reaxff/log.21Jul21.reaxff.tatb-shielded.g++.4 Normal file
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@ -0,0 +1,142 @@
LAMMPS (2 Jul 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system
units real
atom_style charge
read_data data.tatb
Reading data file ...
triclinic box = (0.0000000 0.0000000 0.0000000) to (13.624000 17.114915 15.182639) with tilt (-5.7531563 -6.3254660 7.4257288)
1 by 2 by 2 MPI processor grid
reading atoms ...
384 atoms
read_data CPU = 0.004 seconds
pair_style reaxff control.reax_c.tatb
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 delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/shielded 1 10.0 1.0e-6 100 reaxff
fix 4 all reaxff/bonds 5 bonds.reaxff
variable nqeq equal f_2
thermo 5
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 0.0625
#dump 1 all custom 100 dump.reaxff.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reaxff/species 1 5 5 species.tatb
run 25
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}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 5 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 = 5 4 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 qeq/shielded, perpetual
attributes: full, newton on
pair build: full/bin/atomonly
stencil: full/bin/3d
bin: standard
Per MPI rank memory allocation (min/avg/max) = 94.50 | 94.50 | 94.50 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 -44760.998 -44760.998 7827.7865 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6398 0 6391.0278 31
5 0.61603964 -44761.698 -44760.994 8934.6344 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1911 0 6388.6671 9
10 2.3525559 -44763.227 -44760.541 12288.611 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9712 0 6381.7089 11
15 4.9013319 -44766.36 -44760.764 17716.965 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2514 0 6370.4176 9
20 7.8294706 -44769.686 -44760.747 25205.511 -61089.006 490.21313 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.5196 0 6355.2708 7
25 10.69792 -44772.904 -44760.691 34232.831 -61069.308 490.25885 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.353 0 6336.8339 11
Loop time of 2.66226 on 4 procs for 25 steps with 384 atoms
Performance: 0.051 ns/day, 473.290 hours/ns, 9.391 timesteps/s
96.9% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.7311 | 1.7619 | 1.794 | 2.0 | 66.18
Neigh | 0.46483 | 0.46901 | 0.47348 | 0.5 | 17.62
Comm | 0.039253 | 0.073989 | 0.10705 | 10.7 | 2.78
Output | 0.0012206 | 0.0080282 | 0.010299 | 4.4 | 0.30
Modify | 0.34359 | 0.3488 | 0.36264 | 1.4 | 13.10
Other | | 0.0005529 | | | 0.02
Nlocal: 96.0000 ave 96 max 96 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5118.00 ave 5118 max 5118 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 79754.0 ave 79754 max 79754 min
Histogram: 4 0 0 0 0 0 0 0 0 0
FullNghs: 84076.0 ave 84076 max 84076 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 336304
Ave neighs/atom = 875.79167
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:03

151
examples/reaxff/log.21Jul21.reaxff.tatb.g++.1 Normal file
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@ -0,0 +1,151 @@
LAMMPS (2 Jul 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system
units real
atom_style charge
read_data data.tatb
Reading data file ...
triclinic box = (0.0000000 0.0000000 0.0000000) to (13.624000 17.114915 15.182639) with tilt (-5.7531563 -6.3254660 7.4257288)
1 by 1 by 1 MPI processor grid
reading atoms ...
384 atoms
read_data CPU = 0.008 seconds
pair_style reaxff control.reax_c.tatb
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 delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
fix 4 all reaxff/bonds 5 bonds.reaxff
variable nqeq equal f_2
thermo 5
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 0.0625
#dump 1 all custom 100 dump.reaxff.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reaxff/species 1 5 5 species.tatb
run 25
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 qeq/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}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 5 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 = 5 4 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 qeq/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) = 148.1 | 148.1 | 148.1 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 -44760.998 -44760.998 7827.7878 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6394 0 6391.0274 31.5
5 0.61603968 -44761.698 -44760.994 8934.6346 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1911 0 6388.6671 9
10 2.3525552 -44763.227 -44760.541 12288.581 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9765 0 6381.7142 10.5
15 4.9013309 -44766.36 -44760.764 17716.918 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2622 0 6370.4284 9.5
20 7.829469 -44769.686 -44760.747 25205.568 -61089.006 490.21314 4.719302 0 1571.7022 20.420943 -260.85564 -1573.7378 253.3539 -654.31623 18816.07 -8703.5126 0 6355.2639 8
25 10.697899 -44772.904 -44760.691 34232.788 -61069.308 490.25886 4.7163736 0 1570.7397 20.181346 -251.91377 -1582.3261 253.82253 -653.53184 18791.975 -8684.3619 0 6336.8427 11
Loop time of 2.91659 on 1 procs for 25 steps with 384 atoms
Performance: 0.046 ns/day, 518.504 hours/ns, 8.572 timesteps/s
99.6% CPU use with 1 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.9139 | 1.9139 | 1.9139 | 0.0 | 65.62
Neigh | 0.5948 | 0.5948 | 0.5948 | 0.0 | 20.39
Comm | 0.0020205 | 0.0020205 | 0.0020205 | 0.0 | 0.07
Output | 0.00031287 | 0.00031287 | 0.00031287 | 0.0 | 0.01
Modify | 0.40513 | 0.40513 | 0.40513 | 0.0 | 13.89
Other | | 0.0003856 | | | 0.01
Nlocal: 384.000 ave 384 max 384 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Nghost: 7559.00 ave 7559 max 7559 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Neighs: 286828.0 ave 286828 max 286828 min
Histogram: 1 0 0 0 0 0 0 0 0 0
Total # of neighbors = 286828
Ave neighs/atom = 746.94792
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:03

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LAMMPS (2 Jul 2021)
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
using 1 OpenMP thread(s) per MPI task
# ReaxFF potential for TATB system
units real
atom_style charge
read_data data.tatb
Reading data file ...
triclinic box = (0.0000000 0.0000000 0.0000000) to (13.624000 17.114915 15.182639) with tilt (-5.7531563 -6.3254660 7.4257288)
1 by 2 by 2 MPI processor grid
reading atoms ...
384 atoms
read_data CPU = 0.002 seconds
pair_style reaxff control.reax_c.tatb
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 delay 0 every 5 check no
fix 1 all nve
fix 2 all qeq/reaxff 1 0.0 10.0 1.0e-6 reaxff
fix 4 all reaxff/bonds 5 bonds.reaxff
variable nqeq equal f_2
thermo 5
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 0.0625
#dump 1 all custom 100 dump.reaxff.tatb id type q x y z
#dump 2 all image 5 image.*.jpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 2 pad 3
#dump 3 all movie 5 movie.mpg type type # axes yes 0.8 0.02 view 60 -30
#dump_modify 3 pad 3
fix 3 all reaxff/species 1 5 5 species.tatb
run 25
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 qeq/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}
}
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
Neighbor list info ...
update every 5 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 = 5 4 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 qeq/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) = 99.27 | 99.27 | 99.27 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 -44760.998 -44760.998 7827.7866 -61120.591 486.4378 4.7236377 0 1574.1033 20.788929 -279.51642 -1556.4696 252.57147 -655.84699 18862.412 -8740.6397 0 6391.0277 31
5 0.61603941 -44761.698 -44760.994 8934.6279 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.193 0 6388.6691 10
10 2.352555 -44763.227 -44760.541 12288.61 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50358 -1560.7569 252.85309 -655.44063 18850.391 -8730.9686 0 6381.7064 9
15 4.9013339 -44766.36 -44760.764 17716.995 -61103.434 489.14721 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2413 0 6370.4076 10.5
20 7.8294636 -44769.686 -44760.747 25205.611 -61089.006 490.21313 4.719302 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.4966 0 6355.2478 10
25 10.6979 -44772.904 -44760.691 34232.798 -61069.308 490.25886 4.7163736 0 1570.7397 20.181346 -251.91378 -1582.3261 253.82253 -653.53184 18791.975 -8684.3574 0 6336.8382 10.5
Loop time of 2.53633 on 4 procs for 25 steps with 384 atoms
Performance: 0.053 ns/day, 450.902 hours/ns, 9.857 timesteps/s
97.8% CPU use with 4 MPI tasks x 1 OpenMP threads
MPI task timing breakdown:
Section | min time | avg time | max time |%varavg| %total
---------------------------------------------------------------
Pair | 1.7343 | 1.7637 | 1.815 | 2.4 | 69.54
Neigh | 0.44441 | 0.44869 | 0.45403 | 0.6 | 17.69
Comm | 0.025287 | 0.074702 | 0.10592 | 11.9 | 2.95
Output | 0.0016916 | 0.0080527 | 0.010178 | 4.1 | 0.32
Modify | 0.23126 | 0.24065 | 0.25706 | 2.1 | 9.49
Other | | 0.000566 | | | 0.02
Nlocal: 96.0000 ave 96 max 96 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Nghost: 5118.00 ave 5118 max 5118 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Neighs: 79754.0 ave 79754 max 79754 min
Histogram: 4 0 0 0 0 0 0 0 0 0
Total # of neighbors = 319016
Ave neighs/atom = 830.77083
Neighbor list builds = 5
Dangerous builds not checked
Total wall time: 0:00:02