160 lines
7.7 KiB
Groff
160 lines
7.7 KiB
Groff
LAMMPS (19 Nov 2024 - Development - patch_19Nov2024-1172-g920337963b-modified)
|
|
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 0 0) to (13.624 17.114915 15.182639) with tilt (-5.7531563 -6.325466 7.4257288)
|
|
WARNING: Triclinic box skew is large. LAMMPS will run inefficiently. (src/domain.cpp:221)
|
|
1 by 2 by 2 MPI processor grid
|
|
reading atoms ...
|
|
384 atoms
|
|
read_data CPU = 0.001 seconds
|
|
|
|
pair_style reaxff control.reax_c.tatb
|
|
WARNING: Ignoring inactive control parameter: simulation_name (src/REAXFF/reaxff_control.cpp:99)
|
|
WARNING: Ignoring inactive control parameter: energy_update_freq (src/REAXFF/reaxff_control.cpp:99)
|
|
WARNING: Support for writing native trajectories has been removed after LAMMPS version 8 April 2021 (src/REAXFF/reaxff_control.cpp:114)
|
|
WARNING: Ignoring inactive control parameter: traj_title (src/REAXFF/reaxff_control.cpp:99)
|
|
WARNING: Ignoring inactive control parameter: atom_info (src/REAXFF/reaxff_control.cpp:99)
|
|
WARNING: Ignoring inactive control parameter: atom_forces (src/REAXFF/reaxff_control.cpp:99)
|
|
WARNING: Ignoring inactive control parameter: atom_velocities (src/REAXFF/reaxff_control.cpp:99)
|
|
WARNING: Ignoring inactive control parameter: bond_info (src/REAXFF/reaxff_control.cpp:99)
|
|
WARNING: Ignoring inactive control parameter: angle_info (src/REAXFF/reaxff_control.cpp:99)
|
|
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
|
|
compute bonds all reaxff/atom bonds yes
|
|
variable nqeq equal f_2
|
|
|
|
# dumps out the local bond information
|
|
dump 1 all local 5 bonds_local.reaxff c_bonds[1] c_bonds[2] c_bonds[3]
|
|
|
|
# dumps out the peratom bond information
|
|
dump 2 all custom 5 bonds_atom.reaxff id type q c_bonds[*]
|
|
|
|
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: doi:10.1016/j.parco.2011.08.005
|
|
|
|
@Article{Aktulga12,
|
|
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
|
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
|
journal = {Parallel Computing},
|
|
year = 2012,
|
|
volume = 38,
|
|
number = {4--5},
|
|
pages = {245--259}
|
|
}
|
|
|
|
- fix qeq/reaxff command: doi:10.1016/j.parco.2011.08.005
|
|
|
|
@Article{Aktulga12,
|
|
author = {H. M. Aktulga and J. C. Fogarty and S. A. Pandit and A. Y. Grama},
|
|
title = {Parallel Reactive Molecular Dynamics: {N}umerical Methods and Algorithmic Techniques},
|
|
journal = {Parallel Computing},
|
|
year = 2012,
|
|
volume = 38,
|
|
pages = {245--259}
|
|
}
|
|
|
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
|
|
|
Neighbor list info ...
|
|
update: every = 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/ghost/newtoff
|
|
stencil: full/ghost/bin/3d
|
|
bin: standard
|
|
(2) fix qeq/reaxff, perpetual, copy from (1)
|
|
attributes: half, newton off
|
|
pair build: copy
|
|
stencil: none
|
|
bin: none
|
|
Per MPI rank memory allocation (min/avg/max) = 99.8 | 99.8 | 99.8 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 -8740.6398 0 6391.0277 31
|
|
5 0.61603968 -44761.698 -44760.994 8934.6335 -61118.769 486.81263 4.7234094 0 1573.9241 20.768834 -278.24084 -1557.6713 252.64377 -655.74435 18859.379 -8738.1906 0 6388.6666 8.5
|
|
10 2.352554 -44763.227 -44760.541 12288.582 -61113.174 487.82738 4.7226863 0 1573.411 20.705939 -274.50357 -1560.7569 252.85309 -655.44063 18850.391 -8730.9762 0 6381.7139 10
|
|
15 4.9013231 -44766.36 -44760.764 17716.979 -61103.434 489.14722 4.7213644 0 1572.6349 20.593139 -268.56847 -1566.3829 252.95174 -654.96611 18835.777 -8719.2473 0 6370.4136 7
|
|
20 7.8294566 -44769.686 -44760.747 25205.638 -61089.006 490.21314 4.7193021 0 1571.7022 20.420943 -260.85565 -1573.7378 253.3539 -654.31623 18816.07 -8703.4803 0 6355.2315 8.5
|
|
25 10.6979 -44772.904 -44760.691 34232.844 -61069.308 490.25888 4.7163736 0 1570.7397 20.181346 -251.91378 -1582.3261 253.82253 -653.53184 18791.975 -8684.3433 0 6336.8241 9.5
|
|
Loop time of 0.771261 on 4 procs for 25 steps with 384 atoms
|
|
|
|
Performance: 0.175 ns/day, 137.113 hours/ns, 32.414 timesteps/s, 12.447 katom-step/s
|
|
99.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.56965 | 0.57597 | 0.58104 | 0.5 | 74.68
|
|
Neigh | 0.097254 | 0.097483 | 0.097832 | 0.1 | 12.64
|
|
Comm | 0.003347 | 0.0083916 | 0.014749 | 4.5 | 1.09
|
|
Output | 0.00131 | 0.0022935 | 0.0026708 | 1.2 | 0.30
|
|
Modify | 0.086284 | 0.086988 | 0.088382 | 0.3 | 11.28
|
|
Other | | 0.0001324 | | | 0.02
|
|
|
|
Nlocal: 96 ave 96 max 96 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Nghost: 5118 ave 5118 max 5118 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
Neighs: 79754 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: 0:00:00
|