Loading doc/lammps.1 +1 −1 Original line number Diff line number Diff line .TH LAMMPS "7 August 2019" "2019-08-07" .TH LAMMPS "19 September 2019" "2019-09-19" .SH NAME .B LAMMPS \- Molecular Dynamics Simulator. Loading doc/src/Manual.txt +2 −2 Original line number Diff line number Diff line <!-- HTML_ONLY --> <HEAD> <TITLE>LAMMPS Users Manual</TITLE> <META NAME="docnumber" CONTENT="7 Aug 2019 version"> <META NAME="docnumber" CONTENT="19 Sep 2019 version"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> </HEAD> Loading @@ -21,7 +21,7 @@ :line LAMMPS Documentation :c,h1 7 Aug 2019 version :c,h2 19 Sep 2019 version :c,h2 "What is a LAMMPS version?"_Manual_version.html Loading doc/src/fix_bond_react.txt +31 −23 Original line number Diff line number Diff line Loading @@ -186,20 +186,25 @@ reacting atoms. Some atoms in the pre-reacted template that are not reacting may have missing topology with respect to the simulation. For example, the pre-reacted template may contain an atom that would connect to the rest of a long polymer chain. These are referred to as edge atoms, and are also specified in the map file. When the pre-reaction template contains edge atoms, not all atoms, bonds, charges, etc. specified in the reaction templates will be updated. Specifically, topology that involves only atoms that are 'too near' to template edges will not be updated. The definition of 'too near the edge' depends on which interactions are defined in the simulation. If the simulation has defined dihedrals, atoms within two bonds of edge atoms are considered 'too near the edge.' If the simulation defines angles, but not dihedrals, atoms within one bond of edge atoms are considered 'too near the edge.' If just bonds are defined, only edge atoms are pre-reacted template may contain an atom that, in the simulation, is currently connected to the rest of a long polymer chain. These are referred to as edge atoms, and are also specified in the map file. All pre-reaction template atoms should be linked to a bonding atom, via at least one path that does not involve edge atoms. When the pre-reaction template contains edge atoms, not all atoms, bonds, charges, etc. specified in the reaction templates will be updated. Specifically, topology that involves only atoms that are 'too near' to template edges will not be updated. The definition of 'too near the edge' depends on which interactions are defined in the simulation. If the simulation has defined dihedrals, atoms within two bonds of edge atoms are considered 'too near the edge.' If the simulation defines angles, but not dihedrals, atoms within one bond of edge atoms are considered 'too near the edge.' If just bonds are defined, only edge atoms are considered 'too near the edge.' NOTE: Small molecules, i.e. ones that have all their atoms contained within the reaction templates, never have edge atoms. Note that some care must be taken when a building a molecule template for a given simulation. All atom types in the pre-reacted template must be the same as those of a potential reaction site in the Loading Loading @@ -392,10 +397,11 @@ local command. [Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html, aside from internally-created per-atom properties. None of the "fix_modify"_fix_modify.html options are relevant to this fix. Cumulative reaction counts for each reaction are written to "binary restart files"_restart.html. These values are associated with the reaction name (react-ID). Additionally, internally-created per-atom properties are stored to allow for smooth restarts. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes one statistic for each {react} argument that it stores in a global vector, of length 'number of react arguments', that Loading @@ -406,8 +412,8 @@ These is 1 quantity for each react argument: (1) cumulative # of reactions occurred :ul No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. When fix bond/react is 'unfixed,' all internally-created groups are Loading @@ -417,18 +423,20 @@ all other fixes that use any group created by fix bond/react. [Restrictions:] This fix is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the "Build package"_Build_package.html doc page for more info. LAMMPS was built with that package. See the "Build package"_Build_package.html doc page for more info. [Related commands:] "fix bond/create"_fix_bond_create.html, "fix bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html, "fix bond/create"_fix_bond_create.html, "fix bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html, "dump local"_dump.html, "special_bonds"_special_bonds.html [Default:] The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60, update_edges = none The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60, update_edges = none :line Loading examples/README +2 −3 Original line number Diff line number Diff line Loading @@ -99,12 +99,11 @@ 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 qeq: use of QEQ package for charge equilibration reax: RDX and TATB models using the ReaxFF reax: RDX and TATB and several other models using ReaxFF rigid: rigid bodies modeled as independent or coupled shear: sideways shear applied to 2d solid, with and without a void snap: use of SNAP potential for Ta snap: examples for using several bundled SNAP potentials srd: stochastic rotation dynamics (SRD) particles as solvent snap: NVE dynamics for BCC tantalum crystal using SNAP potential steinhardt: Steinhardt-Nelson Q_l and W_l parameters usng orientorder/atom streitz: Streitz-Mintmire potential for Al2O3 tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si Loading examples/snap/WBe_Wood_PRB2019.snap 0 → 120000 +1 −0 Original line number Diff line number Diff line ../../potentials/WBe_Wood_PRB2019.snap No newline at end of file Loading
doc/lammps.1 +1 −1 Original line number Diff line number Diff line .TH LAMMPS "7 August 2019" "2019-08-07" .TH LAMMPS "19 September 2019" "2019-09-19" .SH NAME .B LAMMPS \- Molecular Dynamics Simulator. Loading
doc/src/Manual.txt +2 −2 Original line number Diff line number Diff line <!-- HTML_ONLY --> <HEAD> <TITLE>LAMMPS Users Manual</TITLE> <META NAME="docnumber" CONTENT="7 Aug 2019 version"> <META NAME="docnumber" CONTENT="19 Sep 2019 version"> <META NAME="author" CONTENT="http://lammps.sandia.gov - Sandia National Laboratories"> <META NAME="copyright" CONTENT="Copyright (2003) Sandia Corporation. This software and manual is distributed under the GNU General Public License."> </HEAD> Loading @@ -21,7 +21,7 @@ :line LAMMPS Documentation :c,h1 7 Aug 2019 version :c,h2 19 Sep 2019 version :c,h2 "What is a LAMMPS version?"_Manual_version.html Loading
doc/src/fix_bond_react.txt +31 −23 Original line number Diff line number Diff line Loading @@ -186,20 +186,25 @@ reacting atoms. Some atoms in the pre-reacted template that are not reacting may have missing topology with respect to the simulation. For example, the pre-reacted template may contain an atom that would connect to the rest of a long polymer chain. These are referred to as edge atoms, and are also specified in the map file. When the pre-reaction template contains edge atoms, not all atoms, bonds, charges, etc. specified in the reaction templates will be updated. Specifically, topology that involves only atoms that are 'too near' to template edges will not be updated. The definition of 'too near the edge' depends on which interactions are defined in the simulation. If the simulation has defined dihedrals, atoms within two bonds of edge atoms are considered 'too near the edge.' If the simulation defines angles, but not dihedrals, atoms within one bond of edge atoms are considered 'too near the edge.' If just bonds are defined, only edge atoms are pre-reacted template may contain an atom that, in the simulation, is currently connected to the rest of a long polymer chain. These are referred to as edge atoms, and are also specified in the map file. All pre-reaction template atoms should be linked to a bonding atom, via at least one path that does not involve edge atoms. When the pre-reaction template contains edge atoms, not all atoms, bonds, charges, etc. specified in the reaction templates will be updated. Specifically, topology that involves only atoms that are 'too near' to template edges will not be updated. The definition of 'too near the edge' depends on which interactions are defined in the simulation. If the simulation has defined dihedrals, atoms within two bonds of edge atoms are considered 'too near the edge.' If the simulation defines angles, but not dihedrals, atoms within one bond of edge atoms are considered 'too near the edge.' If just bonds are defined, only edge atoms are considered 'too near the edge.' NOTE: Small molecules, i.e. ones that have all their atoms contained within the reaction templates, never have edge atoms. Note that some care must be taken when a building a molecule template for a given simulation. All atom types in the pre-reacted template must be the same as those of a potential reaction site in the Loading Loading @@ -392,10 +397,11 @@ local command. [Restart, fix_modify, output, run start/stop, minimize info:] No information about this fix is written to "binary restart files"_restart.html, aside from internally-created per-atom properties. None of the "fix_modify"_fix_modify.html options are relevant to this fix. Cumulative reaction counts for each reaction are written to "binary restart files"_restart.html. These values are associated with the reaction name (react-ID). Additionally, internally-created per-atom properties are stored to allow for smooth restarts. None of the "fix_modify"_fix_modify.html options are relevant to this fix. This fix computes one statistic for each {react} argument that it stores in a global vector, of length 'number of react arguments', that Loading @@ -406,8 +412,8 @@ These is 1 quantity for each react argument: (1) cumulative # of reactions occurred :ul No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy No parameter of this fix can be used with the {start/stop} keywords of the "run"_run.html command. This fix is not invoked during "energy minimization"_minimize.html. When fix bond/react is 'unfixed,' all internally-created groups are Loading @@ -417,18 +423,20 @@ all other fixes that use any group created by fix bond/react. [Restrictions:] This fix is part of the USER-MISC package. It is only enabled if LAMMPS was built with that package. See the "Build package"_Build_package.html doc page for more info. LAMMPS was built with that package. See the "Build package"_Build_package.html doc page for more info. [Related commands:] "fix bond/create"_fix_bond_create.html, "fix bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html, "fix bond/create"_fix_bond_create.html, "fix bond/break"_fix_bond_break.html, "fix bond/swap"_fix_bond_swap.html, "dump local"_dump.html, "special_bonds"_special_bonds.html [Default:] The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60, update_edges = none The option defaults are stabilization = no, prob = 1.0, stabilize_steps = 60, update_edges = none :line Loading
examples/README +2 −3 Original line number Diff line number Diff line Loading @@ -99,12 +99,11 @@ 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 qeq: use of QEQ package for charge equilibration reax: RDX and TATB models using the ReaxFF reax: RDX and TATB and several other models using ReaxFF rigid: rigid bodies modeled as independent or coupled shear: sideways shear applied to 2d solid, with and without a void snap: use of SNAP potential for Ta snap: examples for using several bundled SNAP potentials srd: stochastic rotation dynamics (SRD) particles as solvent snap: NVE dynamics for BCC tantalum crystal using SNAP potential steinhardt: Steinhardt-Nelson Q_l and W_l parameters usng orientorder/atom streitz: Streitz-Mintmire potential for Al2O3 tad: temperature-accelerated dynamics of vacancy diffusion in bulk Si Loading
examples/snap/WBe_Wood_PRB2019.snap 0 → 120000 +1 −0 Original line number Diff line number Diff line ../../potentials/WBe_Wood_PRB2019.snap No newline at end of file
