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