147 lines
5.5 KiB
Groff
147 lines
5.5 KiB
Groff
LAMMPS (21 Nov 2023)
|
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# This example demonstrates the use of various fix qeq variants with pair reaxff
|
|
# You can comment in/out various versions below
|
|
#
|
|
# 1) Fix qeq/shielded generates the same results compared to fix qeq/reax when
|
|
# used with pair_style reaxff, provided that the QEq parameters are the same.
|
|
#
|
|
# 2) Fix qeq/point and fix qeq/dynamic generate comparable results provided that
|
|
# the QEq parameters are the same. These two styles can also be used with
|
|
# pair_style reaxff.
|
|
|
|
units real
|
|
atom_style charge
|
|
|
|
read_data data.CHO
|
|
Reading data file ...
|
|
orthogonal box = (0 0 0) to (25 25 25)
|
|
1 by 1 by 1 MPI processor grid
|
|
reading atoms ...
|
|
105 atoms
|
|
read_data CPU = 0.001 seconds
|
|
|
|
pair_style reaxff NULL checkqeq no
|
|
pair_coeff * * ffield.reax.cho H C O
|
|
Reading potential file ffield.reax.cho with DATE: 2011-02-18
|
|
|
|
neighbor 1 bin
|
|
neigh_modify every 1 delay 0 check yes
|
|
|
|
group type1 type 1
|
|
60 atoms in group type1
|
|
compute charge1 type1 property/atom q
|
|
compute q1 type1 reduce ave c_charge1
|
|
group type2 type 2
|
|
25 atoms in group type2
|
|
compute charge2 type2 property/atom q
|
|
compute q2 type2 reduce ave c_charge2
|
|
group type3 type 3
|
|
20 atoms in group type3
|
|
compute charge3 type3 property/atom q
|
|
compute q3 type3 reduce ave c_charge3
|
|
variable qtot equal count(type1)*c_q1+count(type2)*c_q2+count(type3)*c_q3
|
|
|
|
thermo_style custom step pe c_q1 c_q2 c_q3 v_qtot
|
|
thermo 1
|
|
|
|
velocity all create 300.0 1281937
|
|
fix 1 all nve
|
|
|
|
fix 2 all qeq/reax 1 0.0 10.0 1e-6 param.qeq.reax
|
|
#fix 2 all qeq/shielded 1 10.0 1e-6 400 param.qeq1
|
|
#fix 2 all qeq/point 1 10.0 1e-6 400 param.qeq1
|
|
#fix 2 all qeq/dynamic 1 10.0 1e-3 100 param.qeq1
|
|
|
|
timestep 0.25
|
|
|
|
run 10
|
|
|
|
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 = 1 steps, delay = 0 steps, check = yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 11
|
|
ghost atom cutoff = 11
|
|
binsize = 5.5, bins = 5 5 5
|
|
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
|
(1) pair reaxff, perpetual
|
|
attributes: half, newton off, ghost
|
|
pair build: half/bin/newtoff/ghost
|
|
stencil: full/ghost/bin/3d
|
|
bin: standard
|
|
(2) fix qeq/reax, perpetual, copy from (1)
|
|
attributes: half, newton off
|
|
pair build: copy
|
|
stencil: none
|
|
bin: none
|
|
Per MPI rank memory allocation (min/avg/max) = 14.54 | 14.54 | 14.54 Mbytes
|
|
Step PotEng c_q1 c_q2 c_q3 v_qtot
|
|
0 -10226.557 0.095633909 -0.15658753 -0.091167311 -2.8865799e-15
|
|
1 -10225.799 0.095650157 -0.15662321 -0.091171465 5.3290705e-15
|
|
2 -10223.656 0.095669727 -0.15666713 -0.091175264 -2.8865799e-15
|
|
3 -10220.276 0.095691262 -0.15671593 -0.09117887 4.6629367e-15
|
|
4 -10215.894 0.095714037 -0.15676816 -0.091181914 4.4408921e-16
|
|
5 -10210.804 0.095733939 -0.15681378 -0.091184589 -3.9968029e-15
|
|
6 -10205.342 0.09575102 -0.15685378 -0.091185835 -3.5527137e-15
|
|
7 -10199.848 0.095762356 -0.1568802 -0.091186815 2.220446e-15
|
|
8 -10194.646 0.095766731 -0.15689071 -0.091186805 -3.9968029e-15
|
|
9 -10190.016 0.095761083 -0.15687817 -0.091185537 -2.6645353e-15
|
|
10 -10186.168 0.095747444 -0.15684695 -0.091183644 -1.5543122e-15
|
|
Loop time of 0.013327 on 1 procs for 10 steps with 105 atoms
|
|
|
|
Performance: 16.208 ns/day, 1.481 hours/ns, 750.359 timesteps/s, 78.788 katom-step/s
|
|
97.3% CPU use with 1 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 0.010565 | 0.010565 | 0.010565 | 0.0 | 79.28
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
Comm | 2.3272e-05 | 2.3272e-05 | 2.3272e-05 | 0.0 | 0.17
|
|
Output | 0.00023198 | 0.00023198 | 0.00023198 | 0.0 | 1.74
|
|
Modify | 0.0024913 | 0.0024913 | 0.0024913 | 0.0 | 18.69
|
|
Other | | 1.529e-05 | | | 0.11
|
|
|
|
Nlocal: 105 ave 105 max 105 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Nghost: 512 ave 512 max 512 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
Neighs: 3417 ave 3417 max 3417 min
|
|
Histogram: 1 0 0 0 0 0 0 0 0 0
|
|
|
|
Total # of neighbors = 3417
|
|
Ave neighs/atom = 32.542857
|
|
Neighbor list builds = 0
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:00
|