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update/correct list of example folders

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Axel Kohlmeyer 2019-05-20 15:08:33 -04:00
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3 changed files with 23 additions and 16 deletions
doc/src
Examples.txt
examples
HEAT
README
README

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doc/src/Examples.txt
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@ -52,13 +52,14 @@ Lowercase directories :h4
accelerate: run with various acceleration options (OpenMP, GPU, Phi)
airebo: polyethylene with AIREBO potential
atm: Axilrod-Teller-Muto potential example
balance: dynamic load balancing, 2d system
body: body particles, 2d system
cmap: CMAP 5-body contributions to CHARMM force field
colloid: big colloid particles in a small particle solvent, 2d system
comb: models using the COMB potential
coreshell: core/shell model using CORESHELL package
controller: use of fix controller as a thermostat
coreshell: core/shell model using CORESHELL package
crack: crack propagation in a 2d solid
deposit: deposit atoms and molecules on a surface
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
granregion: use of fix wall/region/gran as boundary on granular particles
hugoniostat: Hugoniostat shock dynamics
hyper: global and local hyperdynamics of diffusion on Pt surface
indent: spherical indenter into a 2d solid
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)
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
min: energy minimization of 2d LJ melt
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
python: using embedded Python in a LAMMPS input script
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
rigid: rigid bodies modeled as independent or coupled
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
streitz: use of Streitz/Mintmire potential with charge equilibration
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
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
ELASTIC: compute elastic constants at zero 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
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
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
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
supporting the publication of Wirnsberger et al. [J. Chem. Phys. 143,

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examples/README
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@ -64,37 +64,37 @@ balance: dynamic load balancing, 2d system
body: body particles, 2d system
cmap: CMAP 5-body contributions to CHARMM force field
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
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
dipole: point dipolar particles, 2d system
dreiding: methanol via Dreiding FF
eim: NaCl using the EIM potential
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
gcmc: Grand Canonical Monte Carlo (GCMC) via the fix gcmc command
granregion: use of fix wall/region/gran as boundary on granular particles
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)
latte: use of LATTE density-functional tight-binding quantum code
meam: MEAM test for SiC and shear (same as shear examples)
melt: rapid melt of 3d LJ system
meam: MEAM test for SiC and shear (same as shear examples)
melt: rapid melt of 3d LJ system
message: client/server coupling of 2 codes
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
msst: MSST shock dynamics
msst: MSST shock dynamics
nb3b: use of nonbonded 3-body harmonic pair style
neb: nudged elastic band (NEB) calculation for barrier finding
nemd: non-equilibrium MD of 2d sheared system
neb: nudged elastic band (NEB) calculation for barrier finding
nemd: non-equilibrium MD of 2d sheared system
obstacle: flow around two voids in a 2d channel
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
prd: parallel replica dynamics of vacancy diffusion in bulk Si
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
streitz: Streitz-Mintmire potential for Al2O3
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
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
Running the simulation produces the files {dump.indent} and
{log.lammps}. You can visualize the dump file as follows:
../../tools/xmovie/xmovie -scale dump.indent
{log.lammps}.
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