211 lines
7.7 KiB
Groff
211 lines
7.7 KiB
Groff
LAMMPS (10 Feb 2021)
|
|
# 3d Lennard-Jones melt
|
|
#
|
|
# This example requires that the KIM Portable Model (PM)
|
|
# `SW_StillingerWeber_1985_Si__MO_405512056662_005`
|
|
# is installed. This can be done with the command
|
|
# kim-api-collections-management install user SW_StillingerWeber_1985_Si__MO_405512056662_005
|
|
# If this command does not work, you may need to setup your PATH to find the utility.
|
|
# If you installed the kim-api using the LAMMPS CMake build, you can do the following
|
|
# (where the current working directory is assumed to be the LAMMPS build directory)
|
|
# source ./kim_build-prefix/bin/kim-api-activate
|
|
# If you installed the kim-api using the LAMMPS Make build, you can do the following
|
|
# (where the current working directory is assumed to be the LAMMPS src directory)
|
|
# source ../lib/kim/installed-kim-api-X.Y.Z/bin/kim-api-activate
|
|
# (where you should relplace X.Y.Z with the appropriate kim-api version number).
|
|
#
|
|
# Or, see `https://openkim.org/doc/obtaining-models` for alternative options.
|
|
#
|
|
|
|
variable x index 1
|
|
variable y index 1
|
|
variable z index 1
|
|
|
|
variable xx equal 20*$x
|
|
variable xx equal 20*1
|
|
variable yy equal 20*$y
|
|
variable yy equal 20*1
|
|
variable zz equal 20*$z
|
|
variable zz equal 20*1
|
|
|
|
kim init SW_StillingerWeber_1985_Si__MO_405512056662_005 real
|
|
#=== BEGIN kim init ==========================================
|
|
units real
|
|
neighbor 2.0 bin # Angstroms
|
|
timestep 1.0 # femtoseconds
|
|
|
|
This model has 9 mutable parameters.
|
|
No. | Parameter name | data type | extent
|
|
-----------------------------------------------------
|
|
1 | A | "Double" | 1
|
|
2 | B | "Double" | 1
|
|
3 | p | "Double" | 1
|
|
4 | q | "Double" | 1
|
|
5 | sigma | "Double" | 1
|
|
6 | gamma | "Double" | 1
|
|
7 | cutoff | "Double" | 1
|
|
8 | lambda | "Double" | 1
|
|
9 | costheta0 | "Double" | 1
|
|
#=== END kim init ============================================
|
|
|
|
kim query a0 get_lattice_constant_cubic crystal=["fcc"] species=["Si"] units=["angstrom"]
|
|
#=== BEGIN kim-query =========================================
|
|
variable a0 string "4.146581932902336"
|
|
#=== END kim-query ===========================================
|
|
|
|
|
|
lattice fcc ${a0}
|
|
lattice fcc 4.146581932902336
|
|
Lattice spacing in x,y,z = 4.1465819 4.1465819 4.1465819
|
|
region box block 0 ${xx} 0 ${yy} 0 ${zz}
|
|
region box block 0 20 0 ${yy} 0 ${zz}
|
|
region box block 0 20 0 20 0 ${zz}
|
|
region box block 0 20 0 20 0 20
|
|
create_box 1 box
|
|
Created orthogonal box = (0.0000000 0.0000000 0.0000000) to (82.931639 82.931639 82.931639)
|
|
1 by 2 by 2 MPI processor grid
|
|
create_atoms 1 box
|
|
Created 32000 atoms
|
|
create_atoms CPU = 0.001 seconds
|
|
|
|
kim interactions Si
|
|
#=== BEGIN kim interactions ==================================
|
|
pair_style kim SW_StillingerWeber_1985_Si__MO_405512056662_005
|
|
pair_coeff * * Si
|
|
#=== END kim interactions ====================================
|
|
|
|
|
|
mass 1 39.95
|
|
velocity all create 200.0 232345 loop geom
|
|
|
|
neighbor 0.3 bin
|
|
neigh_modify delay 0 every 1 check yes
|
|
|
|
fix 1 all nve
|
|
#fix 1 all npt temp 1.0 1.0 1.0 iso 1.0 1.0 3.0
|
|
|
|
run 100
|
|
|
|
CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE-CITE
|
|
|
|
Your simulation uses code contributions which should be cited:
|
|
|
|
- @Comment
|
|
{
|
|
\documentclass{article}
|
|
\usepackage{url}
|
|
\begin{document}
|
|
This Model originally published in \cite{MO_405512056662_005a, MO_405512056662_005b} is archived in OpenKIM~\cite{MO_405512056662_005, MD_335816936951_004, tadmor:elliott:2011, elliott:tadmor:2011}.
|
|
\bibliographystyle{vancouver}
|
|
\bibliography{kimcite-MO_405512056662_005.bib}
|
|
\end{document}
|
|
}
|
|
|
|
@Misc{MO_405512056662_005,
|
|
author = {Amit K Singh},
|
|
title = {{S}tillinger-{W}eber potential for {S}i due to {S}tillinger and {W}eber (1985) v005},
|
|
doi = {10.25950/c74b293f},
|
|
howpublished = {OpenKIM, \url{https://doi.org/10.25950/c74b293f}},
|
|
keywords = {OpenKIM, Model, MO_405512056662_005},
|
|
publisher = {OpenKIM},
|
|
year = 2018,
|
|
}
|
|
|
|
@Misc{MD_335816936951_004,
|
|
author = {Mingjian Wen},
|
|
title = {{S}tillinger-{W}eber ({SW}) {M}odel {D}river v004},
|
|
doi = {10.25950/f3abd2d6},
|
|
howpublished = {OpenKIM, \url{https://doi.org/10.25950/c74b293f}},
|
|
keywords = {OpenKIM, Model Driver, MD_335816936951_004},
|
|
publisher = {OpenKIM},
|
|
year = 2018,
|
|
}
|
|
|
|
@Article{tadmor:elliott:2011,
|
|
author = {E. B. Tadmor and R. S. Elliott and J. P. Sethna and R. E. Miller and C. A. Becker},
|
|
title = {The potential of atomistic simulations and the {K}nowledgebase of {I}nteratomic {M}odels},
|
|
journal = {{JOM}},
|
|
year = {2011},
|
|
volume = {63},
|
|
number = {7},
|
|
pages = {17},
|
|
doi = {10.1007/s11837-011-0102-6},
|
|
}
|
|
|
|
@Misc{elliott:tadmor:2011,
|
|
author = {Ryan S. Elliott and Ellad B. Tadmor},
|
|
title = {{K}nowledgebase of {I}nteratomic {M}odels ({KIM}) Application Programming Interface ({API})},
|
|
howpublished = {\url{https://openkim.org/kim-api}},
|
|
publisher = {OpenKIM},
|
|
year = 2011,
|
|
doi = {10.25950/ff8f563a},
|
|
}
|
|
|
|
@Article{MO_405512056662_005a,
|
|
author = {Stillinger, Frank H. and Weber, Thomas A.},
|
|
doi = {10.1103/PhysRevB.31.5262},
|
|
issue = {8},
|
|
journal = {Physical Review B},
|
|
month = {Apr},
|
|
pages = {5262--5271},
|
|
publisher = {American Physical Society},
|
|
title = {Computer simulation of local order in condensed phases of silicon},
|
|
volume = {31},
|
|
year = {1985},
|
|
}
|
|
|
|
@Book{MO_405512056662_005b,
|
|
author = {Tadmor, Ellad B. and Miller, Ronald E.},
|
|
doi = {10.1017/CBO9781139003582},
|
|
publisher = {Cambridge University Press},
|
|
title = {Modeling Materials: {C}ontinuum, Atomistic and Multiscale Techniques},
|
|
year = {2011},
|
|
}
|
|
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 = 4.07118
|
|
ghost atom cutoff = 4.07118
|
|
binsize = 2.03559, bins = 41 41 41
|
|
1 neighbor lists, perpetual/occasional/extra = 1 0 0
|
|
(1) pair kim, perpetual
|
|
attributes: full, newton off, cut 4.07118
|
|
pair build: full/bin/atomonly
|
|
stencil: full/bin/3d
|
|
bin: standard
|
|
Per MPI rank memory allocation (min/avg/max) = 3.489 | 3.489 | 3.489 Mbytes
|
|
Step Temp E_pair E_mol TotEng Press
|
|
0 200 -126084.25 0 -107007.66 1528.8768
|
|
100 94.450495 -116016.03 0 -107007.07 2282.2685
|
|
Loop time of 5.00432 on 4 procs for 100 steps with 32000 atoms
|
|
|
|
Performance: 1.727 ns/day, 13.901 hours/ns, 19.983 timesteps/s
|
|
99.7% CPU use with 4 MPI tasks x no OpenMP threads
|
|
|
|
MPI task timing breakdown:
|
|
Section | min time | avg time | max time |%varavg| %total
|
|
---------------------------------------------------------------
|
|
Pair | 4.9281 | 4.9366 | 4.9447 | 0.3 | 98.65
|
|
Neigh | 0.02399 | 0.024135 | 0.024318 | 0.1 | 0.48
|
|
Comm | 0.020646 | 0.029014 | 0.037515 | 4.3 | 0.58
|
|
Output | 2.9e-05 | 3.325e-05 | 4.2e-05 | 0.0 | 0.00
|
|
Modify | 0.008808 | 0.0088445 | 0.00888 | 0.0 | 0.18
|
|
Other | | 0.005691 | | | 0.11
|
|
|
|
Nlocal: 8000.00 ave 8029 max 7968 min
|
|
Histogram: 1 1 0 0 0 0 0 0 0 2
|
|
Nghost: 4259.00 ave 4303 max 4202 min
|
|
Histogram: 1 0 0 0 0 0 2 0 0 1
|
|
Neighs: 0.00000 ave 0 max 0 min
|
|
Histogram: 4 0 0 0 0 0 0 0 0 0
|
|
FullNghs: 112548.0 ave 113091 max 111995 min
|
|
Histogram: 1 0 0 1 0 0 0 1 0 1
|
|
|
|
Total # of neighbors = 450192
|
|
Ave neighs/atom = 14.068500
|
|
Neighbor list builds = 3
|
|
Dangerous builds = 0
|
|
Total wall time: 0:00:07
|