Loading doc/Makefile +1 −1 Original line number Diff line number Diff line Loading @@ -211,7 +211,7 @@ $(VENV): @( \ $(VIRTUALENV) -p $(PYTHON) $(VENV); \ . $(VENV)/bin/activate; \ pip install Sphinx==1.7.6; \ pip install Sphinx; \ deactivate;\ ) Loading doc/src/Build_extras.txt +0 −44 Original line number Diff line number Diff line Loading @@ -30,7 +30,6 @@ This is the list of packages that may require additional steps. "KIM"_#kim, "KOKKOS"_#kokkos, "LATTE"_#latte, "MEAM"_#meam, "MESSAGE"_#message, "MSCG"_#mscg, "OPT"_#opt, Loading Loading @@ -351,49 +350,6 @@ the compiler you use on your system to build LATTE. :line MEAM package :h4,link(meam) NOTE: the use of the MEAM package is discouraged, as it has been superseded by the USER-MEAMC package, which is a direct translation of the Fortran code in the MEAM library to C++. The code in USER-MEAMC should be functionally equivalent to the MEAM package, fully supports use of "pair_style hybrid"_pair_hybrid.html (the MEAM package does not), and has optimizations that make it significantly faster than the MEAM package. [CMake build]: No additional settings are needed besides "-D PKG_MEAM=yes". [Traditional make]: Before building LAMMPS, you must build the MEAM library in lib/meam. You can build the MEAM library manually if you prefer; follow the instructions in lib/meam/README. You can also do it in one step from the lammps/src dir, using a command like these, which simply invoke the lib/meam/Install.py script with the specified args: make lib-meam # print help message make lib-meam args="-m mpi" # build with default Fortran compiler compatible with your MPI library make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran) make lib-meam args="-m ifort" # build with Intel Fortran compiler using Makefile.ifort :pre NOTE: You should test building the MEAM library with both the Intel and GNU compilers to see if a simulation runs faster with one versus the other on your system. The build should produce two files: lib/meam/libmeam.a and lib/meam/Makefile.lammps. The latter is copied from an existing Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with Fortran (MEAM library). Typically the two compilers used for LAMMPS and the MEAM library need to be consistent (e.g. both Intel or both GNU compilers). If necessary, you can edit/create a new lib/meam/Makefile.machine file for your system, which should define an EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine file. :line MESSAGE package :h4,link(message) This package can optionally include support for messaging via sockets, Loading doc/src/Build_package.txt +0 −1 Original line number Diff line number Diff line Loading @@ -41,7 +41,6 @@ packages: "KIM"_Build_extras.html#kim, "KOKKOS"_Build_extras.html#kokkos, "LATTE"_Build_extras.html#latte, "MEAM"_Build_extras.html#meam, "MESSAGE"_Build_extras.html#message, "MSCG"_Build_extras.html#mscg, "OPT"_Build_extras.html#opt, Loading doc/src/Errors_messages.txt +10 −10 Original line number Diff line number Diff line Loading @@ -9990,25 +9990,25 @@ quote. :dd Self-explanatory. :dd {Unexpected end of AngleCoeffs section} :dt {Unexpected empty line in AngleCoeffs section} :dt Read a blank line. :dd Read a blank line where there should be coefficient data. :dd {Unexpected end of BondCoeffs section} :dt {Unexpected empty line in BondCoeffs section} :dt Read a blank line. :dd Read a blank line where there should be coefficient data. :dd {Unexpected end of DihedralCoeffs section} :dt {Unexpected empty line in DihedralCoeffs section} :dt Read a blank line. :dd Read a blank line where there should be coefficient data. :dd {Unexpected end of ImproperCoeffs section} :dt {Unexpected empty line in ImproperCoeffs section} :dt Read a blank line. :dd Read a blank line where there should be coefficient data. :dd {Unexpected end of PairCoeffs section} :dt {Unexpected empty line in PairCoeffs section} :dt Read a blank line. :dd Read a blank line where there should be coefficient data. :dd {Unexpected end of custom file} :dt 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 Loading
doc/Makefile +1 −1 Original line number Diff line number Diff line Loading @@ -211,7 +211,7 @@ $(VENV): @( \ $(VIRTUALENV) -p $(PYTHON) $(VENV); \ . $(VENV)/bin/activate; \ pip install Sphinx==1.7.6; \ pip install Sphinx; \ deactivate;\ ) Loading
doc/src/Build_extras.txt +0 −44 Original line number Diff line number Diff line Loading @@ -30,7 +30,6 @@ This is the list of packages that may require additional steps. "KIM"_#kim, "KOKKOS"_#kokkos, "LATTE"_#latte, "MEAM"_#meam, "MESSAGE"_#message, "MSCG"_#mscg, "OPT"_#opt, Loading Loading @@ -351,49 +350,6 @@ the compiler you use on your system to build LATTE. :line MEAM package :h4,link(meam) NOTE: the use of the MEAM package is discouraged, as it has been superseded by the USER-MEAMC package, which is a direct translation of the Fortran code in the MEAM library to C++. The code in USER-MEAMC should be functionally equivalent to the MEAM package, fully supports use of "pair_style hybrid"_pair_hybrid.html (the MEAM package does not), and has optimizations that make it significantly faster than the MEAM package. [CMake build]: No additional settings are needed besides "-D PKG_MEAM=yes". [Traditional make]: Before building LAMMPS, you must build the MEAM library in lib/meam. You can build the MEAM library manually if you prefer; follow the instructions in lib/meam/README. You can also do it in one step from the lammps/src dir, using a command like these, which simply invoke the lib/meam/Install.py script with the specified args: make lib-meam # print help message make lib-meam args="-m mpi" # build with default Fortran compiler compatible with your MPI library make lib-meam args="-m serial" # build with compiler compatible with "make serial" (GNU Fortran) make lib-meam args="-m ifort" # build with Intel Fortran compiler using Makefile.ifort :pre NOTE: You should test building the MEAM library with both the Intel and GNU compilers to see if a simulation runs faster with one versus the other on your system. The build should produce two files: lib/meam/libmeam.a and lib/meam/Makefile.lammps. The latter is copied from an existing Makefile.lammps.* and has settings needed to link C++ (LAMMPS) with Fortran (MEAM library). Typically the two compilers used for LAMMPS and the MEAM library need to be consistent (e.g. both Intel or both GNU compilers). If necessary, you can edit/create a new lib/meam/Makefile.machine file for your system, which should define an EXTRAMAKE variable to specify a corresponding Makefile.lammps.machine file. :line MESSAGE package :h4,link(message) This package can optionally include support for messaging via sockets, Loading
doc/src/Build_package.txt +0 −1 Original line number Diff line number Diff line Loading @@ -41,7 +41,6 @@ packages: "KIM"_Build_extras.html#kim, "KOKKOS"_Build_extras.html#kokkos, "LATTE"_Build_extras.html#latte, "MEAM"_Build_extras.html#meam, "MESSAGE"_Build_extras.html#message, "MSCG"_Build_extras.html#mscg, "OPT"_Build_extras.html#opt, Loading
doc/src/Errors_messages.txt +10 −10 Original line number Diff line number Diff line Loading @@ -9990,25 +9990,25 @@ quote. :dd Self-explanatory. :dd {Unexpected end of AngleCoeffs section} :dt {Unexpected empty line in AngleCoeffs section} :dt Read a blank line. :dd Read a blank line where there should be coefficient data. :dd {Unexpected end of BondCoeffs section} :dt {Unexpected empty line in BondCoeffs section} :dt Read a blank line. :dd Read a blank line where there should be coefficient data. :dd {Unexpected end of DihedralCoeffs section} :dt {Unexpected empty line in DihedralCoeffs section} :dt Read a blank line. :dd Read a blank line where there should be coefficient data. :dd {Unexpected end of ImproperCoeffs section} :dt {Unexpected empty line in ImproperCoeffs section} :dt Read a blank line. :dd Read a blank line where there should be coefficient data. :dd {Unexpected end of PairCoeffs section} :dt {Unexpected empty line in PairCoeffs section} :dt Read a blank line. :dd Read a blank line where there should be coefficient data. :dd {Unexpected end of custom file} :dt 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
