127 lines
5.0 KiB
Groff
127 lines
5.0 KiB
Groff
LAMMPS (7 Feb 2024 - Development - patch_7Feb2024_update1-182-g93942f2013-modified)
|
|
OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (src/comm.cpp:98)
|
|
using 1 OpenMP thread(s) per MPI task
|
|
# Test of MEAM potential for HGa
|
|
|
|
# ------------------------ INITIALIZATION ----------------------------
|
|
units metal
|
|
dimension 3
|
|
boundary p p p
|
|
atom_style atomic
|
|
variable latparam equal 4.646
|
|
variable ncell equal 3
|
|
|
|
# ----------------------- ATOM DEFINITION ----------------------------
|
|
region box block -4 4 -4 4 -4 4
|
|
create_box 2 box
|
|
Created orthogonal box = (-4 -4 -4) to (4 4 4)
|
|
1 by 2 by 2 MPI processor grid
|
|
|
|
#
|
|
|
|
include potential.mod
|
|
# NOTE: This script can be modified for different pair styles
|
|
# See in.elastic for more info.
|
|
|
|
variable Pu string H
|
|
print "potential chosen ${Pu}"
|
|
potential chosen H
|
|
# Choose potential
|
|
pair_style meam/ms
|
|
print "we just executed"
|
|
we just executed
|
|
|
|
pair_coeff * * library.msmeam ${Pu} Ga4 HGa.msmeam ${Pu} Ga4
|
|
pair_coeff * * library.msmeam H Ga4 HGa.msmeam ${Pu} Ga4
|
|
pair_coeff * * library.msmeam H Ga4 HGa.msmeam H Ga4
|
|
Reading MEAM library file library.msmeam with DATE: 2018-09-22
|
|
# Setup neighbor style
|
|
neighbor 1.0 bin
|
|
neigh_modify once no every 1 delay 0 check yes
|
|
|
|
# Setup minimization style
|
|
variable dmax equal 1.0e-2
|
|
min_style cg
|
|
min_modify dmax ${dmax} line quadratic
|
|
min_modify dmax 0.01 line quadratic
|
|
compute eng all pe/atom
|
|
compute eatoms all reduce sum c_eng
|
|
|
|
# Setup output
|
|
thermo 100
|
|
thermo_style custom step temp etotal press pxx pyy pzz pxy pxz pyz lx ly lz vol c_eatoms
|
|
thermo_modify norm yes
|
|
create_atoms 1 single 0 0 0 units box
|
|
Created 1 atoms
|
|
using box units in orthogonal box = (-4 -4 -4) to (4 4 4)
|
|
create_atoms CPU = 0.000 seconds
|
|
create_atoms 2 single 2.2 0 0 units box
|
|
Created 1 atoms
|
|
using box units in orthogonal box = (-4 -4 -4) to (4 4 4)
|
|
create_atoms CPU = 0.000 seconds
|
|
create_atoms 2 single 0.3 2.3 0 units box
|
|
Created 1 atoms
|
|
using box units in orthogonal box = (-4 -4 -4) to (4 4 4)
|
|
create_atoms CPU = 0.000 seconds
|
|
# ---------- Define Settings ---------------------
|
|
variable teng equal "c_eatoms"
|
|
compute pot_energy all pe/atom
|
|
compute stress all stress/atom NULL
|
|
# dump 1 all custom 1 dump.msmeam id x y z fx fy fz c_pot_energy c_stress[1] c_stress[2] c_stress[3] c_stress[4] c_stress[5] c_stress[6]
|
|
run 1
|
|
WARNING: No fixes with time integration, atoms won't move (src/verlet.cpp:60)
|
|
Neighbor list info ...
|
|
update: every = 1 steps, delay = 0 steps, check = yes
|
|
max neighbors/atom: 2000, page size: 100000
|
|
master list distance cutoff = 6.9
|
|
ghost atom cutoff = 6.9
|
|
binsize = 3.45, bins = 3 3 3
|
|
2 neighbor lists, perpetual/occasional/extra = 2 0 0
|
|
(1) pair meam/ms, perpetual
|
|
attributes: full, newton on
|
|
pair build: full/bin/atomonly
|
|
stencil: full/bin/3d
|
|
bin: standard
|
|
(2) pair meam/ms, perpetual, half/full from (1)
|
|
attributes: half, newton on
|
|
pair build: halffull/newton
|
|
stencil: none
|
|
bin: none
|
|
Per MPI rank memory allocation (min/avg/max) = 7.965 | 8.123 | 8.594 Mbytes
|
|
Step Temp TotEng Press Pxx Pyy Pzz Pxy Pxz Pyz Lx Ly Lz Volume c_eatoms
|
|
0 0 15.433079 491354.7 838670.96 635393.15 0 80195.797 0 0 8 8 8 512 15.433079
|
|
1 0 15.433079 491354.7 838670.96 635393.15 0 80195.797 0 0 8 8 8 512 15.433079
|
|
Loop time of 8.70645e-05 on 4 procs for 1 steps with 3 atoms
|
|
|
|
Performance: 992.368 ns/day, 0.024 hours/ns, 11485.738 timesteps/s, 34.457 katom-step/s
|
|
29.0% CPU use with 4 MPI tasks x 1 OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 4.3957e-05 | 4.67e-05 | 5.1056e-05 | 0.0 | 53.64
|
|
Neigh | 0 | 0 | 0 | 0.0 | 0.00
|
|
Comm | 1.105e-05 | 1.3822e-05 | 1.7033e-05 | 0.0 | 15.88
|
|
Output | 1.5765e-05 | 1.9045e-05 | 2.5216e-05 | 0.0 | 21.87
|
|
Modify | 2.58e-07 | 3.465e-07 | 3.81e-07 | 0.0 | 0.40
|
|
Other | | 7.151e-06 | | | 8.21
|
|
|
|
Nlocal: 0.75 ave 3 max 0 min
|
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
|
Nghost: 38.25 ave 42 max 36 min
|
|
Histogram: 2 0 0 0 0 1 0 0 0 1
|
|
Neighs: 1.75 ave 7 max 0 min
|
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
|
FullNghs: 3.5 ave 14 max 0 min
|
|
Histogram: 3 0 0 0 0 0 0 0 0 1
|
|
|
|
Total # of neighbors = 14
|
|
Ave neighs/atom = 4.6666667
|
|
Neighbor list builds = 0
|
|
Dangerous builds = 0
|
|
#write_data data.msmeam
|
|
|
|
print "All done!"
|
|
All done!
|
|
Total wall time: 0:00:00
|