Loading examples/README +1 −0 Original line number Diff line number Diff line Loading @@ -88,6 +88,7 @@ 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 mliap: examples for using several bundled MLIAP potentials mscg: parameterize a multi-scale coarse-graining (MSCG) model msst: MSST shock dynamics nb3b: use of nonbonded 3-body harmonic pair style Loading tools/README +4 −0 Original line number Diff line number Diff line Loading @@ -17,6 +17,7 @@ binary2txt convert a LAMMPS dump file from binary to ASCII text ch2lmp convert CHARMM files to LAMMPS input chain create a data file of bead-spring chains cmake tools and scripts for use with CMake coding_standard python scripts to detect and fix some LAMMPS conventions colvars post-process output of the fix colvars command createatoms generate lattices of atoms within a geometry drude create Drude core/electron atom pairs in a data file Loading @@ -31,6 +32,7 @@ kate add-ons to Kate editor for editing LAMMPS input scripts lmp2arc convert LAMMPS output to Accelrys Insight format lmp2cfg convert LAMMPS output to CFG files for AtomEye viz matlab MatLab scripts for post-processing LAMMPS output mesont Tools for use with the USER-MESONT package micelle2d create a data file of small lipid chains in solvent moltemplate Instructions for installing the Moltemplate builder program msi2lmp use Accelrys Insight code to setup LAMMPS input Loading @@ -40,8 +42,10 @@ pymol_asphere convert LAMMPS output of ellipsoids to PyMol format python Python scripts for post-processing LAMMPS output reax Tools for analyzing output of ReaxFF simulations replica tool to reorder LAMMPS replica trajectories according to temperature singularity Singularity container descriptions suitable for LAMMPS development smd convert Smooth Mach Dynamics triangles to VTK spin perform a cubic polynomial interpolation of a GNEB MEP valgrind suppression files for use with valgrind's memcheck tool vim add-ons to VIM editor for editing LAMMPS input scripts xmgrace a collection of scripts to generate xmgrace plots Loading tools/coding_standard/README 0 → 100644 +5 −0 Original line number Diff line number Diff line These Python scripts help to detect whether files in the repository conform to LAMMPS coding conventions or not, and can fix those issues, too. permissions.py detects if sources have executable permissions and scripts have not whitespace.py (currently) detects trailing whitespace tools/valgrind/README 0 → 100644 +15 −0 Original line number Diff line number Diff line These files contain additional suppressions for LAMMPS when using valgrind's memcheck tool to search for memory access violations and memory leaks. These will suppress known false positives and thus help to focus finding and fixing real issues. When using CMake, these are automatically included when running "ctest -T memcheck". To manually add them to do a memory check on running LAMMPS, use a command line like following: valgrind --show-leak-kinds=all --track-origins=yes \ --suppressions=/path/to/lammps/tools/valgrind/OpenMP.supp \ --suppressions=/path/to/lammps/tools/valgrind/OpenMPI.supp \ --suppressions=/path/to/lammps/tools/valgrind/Python3.supp \ lmp -in in.melt Last update: 2020-06-24 Loading
examples/README +1 −0 Original line number Diff line number Diff line Loading @@ -88,6 +88,7 @@ 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 mliap: examples for using several bundled MLIAP potentials mscg: parameterize a multi-scale coarse-graining (MSCG) model msst: MSST shock dynamics nb3b: use of nonbonded 3-body harmonic pair style Loading
tools/README +4 −0 Original line number Diff line number Diff line Loading @@ -17,6 +17,7 @@ binary2txt convert a LAMMPS dump file from binary to ASCII text ch2lmp convert CHARMM files to LAMMPS input chain create a data file of bead-spring chains cmake tools and scripts for use with CMake coding_standard python scripts to detect and fix some LAMMPS conventions colvars post-process output of the fix colvars command createatoms generate lattices of atoms within a geometry drude create Drude core/electron atom pairs in a data file Loading @@ -31,6 +32,7 @@ kate add-ons to Kate editor for editing LAMMPS input scripts lmp2arc convert LAMMPS output to Accelrys Insight format lmp2cfg convert LAMMPS output to CFG files for AtomEye viz matlab MatLab scripts for post-processing LAMMPS output mesont Tools for use with the USER-MESONT package micelle2d create a data file of small lipid chains in solvent moltemplate Instructions for installing the Moltemplate builder program msi2lmp use Accelrys Insight code to setup LAMMPS input Loading @@ -40,8 +42,10 @@ pymol_asphere convert LAMMPS output of ellipsoids to PyMol format python Python scripts for post-processing LAMMPS output reax Tools for analyzing output of ReaxFF simulations replica tool to reorder LAMMPS replica trajectories according to temperature singularity Singularity container descriptions suitable for LAMMPS development smd convert Smooth Mach Dynamics triangles to VTK spin perform a cubic polynomial interpolation of a GNEB MEP valgrind suppression files for use with valgrind's memcheck tool vim add-ons to VIM editor for editing LAMMPS input scripts xmgrace a collection of scripts to generate xmgrace plots Loading
tools/coding_standard/README 0 → 100644 +5 −0 Original line number Diff line number Diff line These Python scripts help to detect whether files in the repository conform to LAMMPS coding conventions or not, and can fix those issues, too. permissions.py detects if sources have executable permissions and scripts have not whitespace.py (currently) detects trailing whitespace
tools/valgrind/README 0 → 100644 +15 −0 Original line number Diff line number Diff line These files contain additional suppressions for LAMMPS when using valgrind's memcheck tool to search for memory access violations and memory leaks. These will suppress known false positives and thus help to focus finding and fixing real issues. When using CMake, these are automatically included when running "ctest -T memcheck". To manually add them to do a memory check on running LAMMPS, use a command line like following: valgrind --show-leak-kinds=all --track-origins=yes \ --suppressions=/path/to/lammps/tools/valgrind/OpenMP.supp \ --suppressions=/path/to/lammps/tools/valgrind/OpenMPI.supp \ --suppressions=/path/to/lammps/tools/valgrind/Python3.supp \ lmp -in in.melt Last update: 2020-06-24
