Loading doc/src/Examples.txt +9 −1 Original line number Diff line number Diff line Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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=:) Loading Loading @@ -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=:) Loading examples/HEAT/README +1 −1 Original line number Diff line number Diff line 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, Loading examples/README +13 −14 Original line number Diff line number Diff line Loading @@ -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 Loading @@ -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 Loading Loading
doc/src/Examples.txt +9 −1 Original line number Diff line number Diff line Loading @@ -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 Loading @@ -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 Loading @@ -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 Loading @@ -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=:) Loading Loading @@ -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=:) Loading
examples/HEAT/README +1 −1 Original line number Diff line number Diff line 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, Loading
examples/README +13 −14 Original line number Diff line number Diff line Loading @@ -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 Loading @@ -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 Loading
