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update/correct list of example folders

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Axel Kohlmeyer
2019-05-20 15:08:33 -04:00
parent 55116db8fb
commit 0349e9fee9
3 changed files with 23 additions and 16 deletions
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10
doc/src/Examples.txt
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@ -52,13 +52,14 @@ Lowercase directories :h4
accelerate: run with various acceleration options (OpenMP, GPU, Phi) accelerate: run with various acceleration options (OpenMP, GPU, Phi)
airebo: polyethylene with AIREBO potential airebo: polyethylene with AIREBO potential
atm: Axilrod-Teller-Muto potential example
balance: dynamic load balancing, 2d system balance: dynamic load balancing, 2d system
body: body particles, 2d system body: body particles, 2d system
cmap: CMAP 5-body contributions to CHARMM force field cmap: CMAP 5-body contributions to CHARMM force field
colloid: big colloid particles in a small particle solvent, 2d system colloid: big colloid particles in a small particle solvent, 2d system
comb: models using the COMB potential comb: models using the COMB potential
coreshell: core/shell model using CORESHELL package
controller: use of fix controller as a thermostat controller: use of fix controller as a thermostat
coreshell: core/shell model using CORESHELL package
crack: crack propagation in a 2d solid crack: crack propagation in a 2d solid
deposit: deposit atoms and molecules on a surface deposit: deposit atoms and molecules on a surface
dipole: point dipolar particles, 2d system dipole: point dipolar particles, 2d system
@ -70,10 +71,13 @@ friction: frictional contact of spherical asperities between 2d surfaces
gcmc: Grand Canonical Monte Carlo (GCMC) via the fix gcmc command gcmc: Grand Canonical Monte Carlo (GCMC) via the fix gcmc command
granregion: use of fix wall/region/gran as boundary on granular particles granregion: use of fix wall/region/gran as boundary on granular particles
hugoniostat: Hugoniostat shock dynamics hugoniostat: Hugoniostat shock dynamics
hyper: global and local hyperdynamics of diffusion on Pt surface
indent: spherical indenter into a 2d solid indent: spherical indenter into a 2d solid
kim: use of potentials in Knowledge Base for Interatomic Models (KIM) kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
latte: examples for using fix latte for DFTB via the LATTE library
meam: MEAM test for SiC and shear (same as shear examples) meam: MEAM test for SiC and shear (same as shear examples)
melt: rapid melt of 3d LJ system melt: rapid melt of 3d LJ system
message: demos for LAMMPS client/server coupling with the MESSAGE package
micelle: self-assembly of small lipid-like molecules into 2d bilayers micelle: self-assembly of small lipid-like molecules into 2d bilayers
min: energy minimization of 2d LJ melt min: energy minimization of 2d LJ melt
mscg: parameterize a multi-scale coarse-graining (MSCG) model mscg: parameterize a multi-scale coarse-graining (MSCG) model
@ -88,6 +92,7 @@ pour: pouring of granular particles into a 3d box, then chute flow
prd: parallel replica dynamics of vacancy diffusion in bulk Si prd: parallel replica dynamics of vacancy diffusion in bulk Si
python: using embedded Python in a LAMMPS input script python: using embedded Python in a LAMMPS input script
qeq: use of the QEQ package for charge equilibration qeq: use of the QEQ package for charge equilibration
rdf-adf: computing radial and angle distribution functions for water
reax: RDX and TATB models using the ReaxFF reax: RDX and TATB models using the ReaxFF
rigid: rigid bodies modeled as independent or coupled rigid: rigid bodies modeled as independent or coupled
shear: sideways shear applied to 2d solid, with and without a void shear: sideways shear applied to 2d solid, with and without a void
@ -95,6 +100,7 @@ snap: NVE dynamics for BCC tantalum crystal using SNAP potential
srd: stochastic rotation dynamics (SRD) particles as solvent srd: stochastic rotation dynamics (SRD) particles as solvent
streitz: use of Streitz/Mintmire potential with charge equilibration streitz: use of Streitz/Mintmire potential with charge equilibration
tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
threebody: regression test input for a variety of manybody potentials
vashishta: use of the Vashishta potential vashishta: use of the Vashishta potential
voronoi: Voronoi tesselation via compute voronoi/atom command :tb(s=:) voronoi: Voronoi tesselation via compute voronoi/atom command :tb(s=:)
@ -131,8 +137,10 @@ COUPLE: examples of how to use LAMMPS as a library
DIFFUSE: compute diffusion coefficients via several methods DIFFUSE: compute diffusion coefficients via several methods
ELASTIC: compute elastic constants at zero temperature ELASTIC: compute elastic constants at zero temperature
ELASTIC_T: compute elastic constants at finite temperature ELASTIC_T: compute elastic constants at finite temperature
HEAT: compute thermal conductivity for LJ and water via fix ehex
KAPPA: compute thermal conductivity via several methods KAPPA: compute thermal conductivity via several methods
MC: using LAMMPS in a Monte Carlo mode to relax the energy of a system MC: using LAMMPS in a Monte Carlo mode to relax the energy of a system
SPIN: examples for features of the SPIN package
USER: examples for USER packages and USER-contributed commands USER: examples for USER packages and USER-contributed commands
VISCOSITY: compute viscosity via several methods :tb(s=:) VISCOSITY: compute viscosity via several methods :tb(s=:)

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examples/HEAT/README
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@ -1,6 +1,6 @@
This directory contains 4 input scripts for carrying out NEMD This directory contains 4 input scripts for carrying out NEMD
simulations of thermal gradients for a Lennard-Jones fluid and SPC/E simulations of thermal gradients for a Lennard-Jones fluid and SPC/E
water using the HEX/a (fix heat) and eHEX/a (fix ehex) algorithms. water using the HEX/a (fix ehex w/ hex option) and eHEX/a (fix ehex) algorithms.
All input scripts are part of the supplementary (open access) material All input scripts are part of the supplementary (open access) material
supporting the publication of Wirnsberger et al. [J. Chem. Phys. 143, supporting the publication of Wirnsberger et al. [J. Chem. Phys. 143,

27
examples/README
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@ -64,37 +64,37 @@ balance: dynamic load balancing, 2d system
body: body particles, 2d system body: body particles, 2d system
cmap: CMAP 5-body contributions to CHARMM force field cmap: CMAP 5-body contributions to CHARMM force field
colloid: big colloid particles in a small particle solvent, 2d system colloid: big colloid particles in a small particle solvent, 2d system
comb: models using the COMB potential comb: models using the COMB potential
coreshell: adiabatic core/shell model coreshell: adiabatic core/shell model
controller: use of fix controller as a thermostat controller: use of fix controller as a thermostat
crack: crack propagation in a 2d solid crack: crack propagation in a 2d solid
deposit: deposition of atoms and molecules onto a 3d substrate deposit: deposition of atoms and molecules onto a 3d substrate
dipole: point dipolar particles, 2d system dipole: point dipolar particles, 2d system
dreiding: methanol via Dreiding FF dreiding: methanol via Dreiding FF
eim: NaCl using the EIM potential eim: NaCl using the EIM potential
ellipse: ellipsoidal particles in spherical solvent, 2d system ellipse: ellipsoidal particles in spherical solvent, 2d system
flow: Couette and Poiseuille flow in a 2d channel flow: Couette and Poiseuille flow in a 2d channel
friction: frictional contact of spherical asperities between 2d surfaces friction: frictional contact of spherical asperities between 2d surfaces
gcmc: Grand Canonical Monte Carlo (GCMC) via the fix gcmc command gcmc: Grand Canonical Monte Carlo (GCMC) via the fix gcmc command
granregion: use of fix wall/region/gran as boundary on granular particles granregion: use of fix wall/region/gran as boundary on granular particles
hugoniostat: Hugoniostat shock dynamics hugoniostat: Hugoniostat shock dynamics
hyper: global and local hyperdynamics of diffusion on Pt surface hyper: global and local hyperdynamics of diffusion on Pt surface
indent: spherical indenter into a 2d solid indent: spherical indenter into a 2d solid
kim: use of potentials in Knowledge Base for Interatomic Models (KIM) kim: use of potentials in Knowledge Base for Interatomic Models (KIM)
latte: use of LATTE density-functional tight-binding quantum code latte: use of LATTE density-functional tight-binding quantum code
meam: MEAM test for SiC and shear (same as shear examples) meam: MEAM test for SiC and shear (same as shear examples)
melt: rapid melt of 3d LJ system melt: rapid melt of 3d LJ system
message: client/server coupling of 2 codes message: client/server coupling of 2 codes
micelle: self-assembly of small lipid-like molecules into 2d bilayers micelle: self-assembly of small lipid-like molecules into 2d bilayers
min: energy minimization of 2d LJ melt min: energy minimization of 2d LJ melt
mscg: parameterize a multi-scale coarse-graining (MSCG) model mscg: parameterize a multi-scale coarse-graining (MSCG) model
msst: MSST shock dynamics msst: MSST shock dynamics
nb3b: use of nonbonded 3-body harmonic pair style nb3b: use of nonbonded 3-body harmonic pair style
neb: nudged elastic band (NEB) calculation for barrier finding neb: nudged elastic band (NEB) calculation for barrier finding
nemd: non-equilibrium MD of 2d sheared system nemd: non-equilibrium MD of 2d sheared system
obstacle: flow around two voids in a 2d channel obstacle: flow around two voids in a 2d channel
peptide: dynamics of a small solvated peptide chain (5-mer) peptide: dynamics of a small solvated peptide chain (5-mer)
peri: Peridynamic model of cylinder impacted by indenter peri: Peridynamic model of cylinder impacted by indenter
pour: pouring of granular particles into a 3d box, then chute flow pour: pouring of granular particles into a 3d box, then chute flow
prd: parallel replica dynamics of vacancy diffusion in bulk Si prd: parallel replica dynamics of vacancy diffusion in bulk Si
python: use of PYTHON package to invoke Python code from input script python: use of PYTHON package to invoke Python code from input script
@ -107,6 +107,7 @@ srd: stochastic rotation dynamics (SRD) particles as solvent
snap: NVE dynamics for BCC tantalum crystal using SNAP potential snap: NVE dynamics for BCC tantalum crystal using SNAP potential
streitz: Streitz-Mintmire potential for Al2O3 streitz: Streitz-Mintmire potential for Al2O3
tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si
threebody: regression test input for a variety of manybody potentials
vashishta: models using the Vashishta potential vashishta: models using the Vashishta potential
voronoi: Voronoi tesselation via compute voronoi/atom command voronoi: Voronoi tesselation via compute voronoi/atom command
@ -117,9 +118,7 @@ cp ../../src/lmp_mpi . # copy LAMMPS executable to this dir
lmp_mpi -in in.indent # run the problem lmp_mpi -in in.indent # run the problem
Running the simulation produces the files {dump.indent} and Running the simulation produces the files {dump.indent} and
{log.lammps}. You can visualize the dump file as follows: {log.lammps}.
../../tools/xmovie/xmovie -scale dump.indent
If you uncomment the dump image line(s) in the input script a series If you uncomment the dump image line(s) in the input script a series
of JPG images will be produced by the run. These can be viewed of JPG images will be produced by the run. These can be viewed