Loading doc/lammps.1 +1 −1 Original line number Diff line number Diff line .TH LAMMPS "5 May 2020" "2020-05-5" .TH LAMMPS "2 June 2020" "2020-06-02" .SH NAME .B LAMMPS \- Molecular Dynamics Simulator. Loading doc/src/Packages_details.rst +1 −1 Original line number Diff line number Diff line Loading @@ -2064,7 +2064,7 @@ molecules, and chiral-sensitive reactions. * examples/USER/reaction * `2017 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug17/pdf/gissinger.pdf>`_ * `2019 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug19/talk_gissinger.pdf>`_ * disarmmd.org * reacter.org ---------- Loading doc/src/fix_bond_react.rst +27 −17 Original line number Diff line number Diff line Loading @@ -300,7 +300,8 @@ either 'none' or 'charges.' Further details are provided in the discussion of the 'update_edges' keyword. The fifth optional section begins with the keyword 'Constraints' and lists additional criteria that must be satisfied in order for the reaction to occur. Currently, there are four types of constraints available, as discussed below. there are four types of constraints available, as discussed below: 'distance', 'angle', 'dihedral', and 'arrhenius'. A sample map file is given below: Loading Loading @@ -353,8 +354,9 @@ has syntax as follows: distance *ID1* *ID2* *rmin* *rmax* where 'distance' is the required keyword, *ID1* and *ID2* are pre-reaction atom IDs, and these two atoms must be separated by a distance between *rmin* and *rmax* for the reaction to occur. pre-reaction atom IDs (or molecule-fragment IDs, see below), and these two atoms must be separated by a distance between *rmin* and *rmax* for the reaction to occur. The constraint of type 'angle' has the following syntax: Loading @@ -363,11 +365,11 @@ The constraint of type 'angle' has the following syntax: angle *ID1* *ID2* *ID3* *amin* *amax* where 'angle' is the required keyword, *ID1*\ , *ID2* and *ID3* are pre-reaction atom IDs, and these three atoms must form an angle between *amin* and *amax* for the reaction to occur (where *ID2* is the central atom). Angles must be specified in degrees. This constraint can be used to enforce a certain orientation between reacting molecules. pre-reaction atom IDs (or molecule-fragment IDs, see below), and these three atoms must form an angle between *amin* and *amax* for the reaction to occur (where *ID2* is the central atom). Angles must be specified in degrees. This constraint can be used to enforce a certain orientation between reacting molecules. The constraint of type 'dihedral' has the following syntax: Loading @@ -376,15 +378,23 @@ The constraint of type 'dihedral' has the following syntax: dihedral *ID1* *ID2* *ID3* *ID4* *amin* *amax* *amin2* *amax2* where 'dihedral' is the required keyword, and *ID1*\ , *ID2*\ , *ID3* and *ID4* are pre-reaction atom IDs. Dihedral angles are calculated in the interval (-180,180]. Refer to the :doc:`dihedral style <dihedral_style>` documentation for further details on convention. If *amin* is less than *amax*, these four atoms must form a dihedral angle greater than *amin* **and** less than *amax* for the reaction to occur. If *amin* is greater than *amax*, these four atoms must form a dihedral angle greater than *amin* **or** less than *amax* for the reaction to occur. Angles must be specified in degrees. Optionally, a second range of permissible angles *amin2*-*amax2* can be specified. and *ID4* are pre-reaction atom IDs (or molecule-fragment IDs, see below). Dihedral angles are calculated in the interval (-180,180]. Refer to the :doc:`dihedral style <dihedral_style>` documentation for further details on convention. If *amin* is less than *amax*, these four atoms must form a dihedral angle greater than *amin* **and** less than *amax* for the reaction to occur. If *amin* is greater than *amax*, these four atoms must form a dihedral angle greater than *amin* **or** less than *amax* for the reaction to occur. Angles must be specified in degrees. Optionally, a second range of permissible angles *amin2*-*amax2* can be specified. For the 'distance', 'angle', and 'dihedral' constraints (explained above), atom IDs can be replaced by pre-reaction molecule-fragment IDs. The molecule-fragment ID must begin with a letter. The location of the ID is the geometric center of all atom positions in the fragment. The molecule fragment must have been defined in the :doc:`molecule <molecule>` command for the pre-reaction template. The constraint of type 'arrhenius' imposes an additional reaction probability according to the temperature-dependent Arrhenius equation: Loading doc/utils/sphinx-config/false_positives.txt +1 −1 Original line number Diff line number Diff line Loading @@ -629,7 +629,6 @@ dipolar dir Direc dirname disarmmd discoverable discretization discretized Loading Loading @@ -2457,6 +2456,7 @@ rdc rdf RDideal rdx reacter README realtime reamin Loading src/USER-REACTION/README +4 −4 Original line number Diff line number Diff line This package implements the DisARMMD protocol (disarmmd.org) as This package implements the REACTER protocol (reacter.org) as "fix bond/react." This fix allows for complex topology changes during a running MD simulation, when using classical force fields. Topology changes are defined in pre- and post-reaction molecule Loading @@ -6,7 +6,7 @@ templates and can include creation and deletion of bonds, angles, dihedrals, impropers, atom types, bond types, angle types, dihedral types, improper types, and/or atomic charges. The DisARMMD protocol is a method for modeling chemical reactions in The REACTER protocol is a method for modeling chemical reactions in classical molecular dynamics simulations. It was developed to build physically-realistic initial configurations for amorphous or crosslinked materials. Any number of competing or reversible reaction Loading @@ -15,9 +15,9 @@ advanced options currently available include reaction constraints (e.g. angle and Arrhenius constraints), deletion of reaction byproducts or other small molecules, and chiral-sensitive reactions. The DisARMMD methodology is detailed in: The REACTER methodology is detailed in: Gissinger et al., Polymer 128, 211-217 (2017) https://doi.org/10.1016/j.polymer.2017.09.038 This package was created by Jacob Gissinger (info@disarmmd.org), This package was created by Jacob Gissinger (jrgiss05@gmail.com), while at the NASA Langley Research Center. Loading
doc/lammps.1 +1 −1 Original line number Diff line number Diff line .TH LAMMPS "5 May 2020" "2020-05-5" .TH LAMMPS "2 June 2020" "2020-06-02" .SH NAME .B LAMMPS \- Molecular Dynamics Simulator. Loading
doc/src/Packages_details.rst +1 −1 Original line number Diff line number Diff line Loading @@ -2064,7 +2064,7 @@ molecules, and chiral-sensitive reactions. * examples/USER/reaction * `2017 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug17/pdf/gissinger.pdf>`_ * `2019 LAMMPS Workshop <https://lammps.sandia.gov/workshops/Aug19/talk_gissinger.pdf>`_ * disarmmd.org * reacter.org ---------- Loading
doc/src/fix_bond_react.rst +27 −17 Original line number Diff line number Diff line Loading @@ -300,7 +300,8 @@ either 'none' or 'charges.' Further details are provided in the discussion of the 'update_edges' keyword. The fifth optional section begins with the keyword 'Constraints' and lists additional criteria that must be satisfied in order for the reaction to occur. Currently, there are four types of constraints available, as discussed below. there are four types of constraints available, as discussed below: 'distance', 'angle', 'dihedral', and 'arrhenius'. A sample map file is given below: Loading Loading @@ -353,8 +354,9 @@ has syntax as follows: distance *ID1* *ID2* *rmin* *rmax* where 'distance' is the required keyword, *ID1* and *ID2* are pre-reaction atom IDs, and these two atoms must be separated by a distance between *rmin* and *rmax* for the reaction to occur. pre-reaction atom IDs (or molecule-fragment IDs, see below), and these two atoms must be separated by a distance between *rmin* and *rmax* for the reaction to occur. The constraint of type 'angle' has the following syntax: Loading @@ -363,11 +365,11 @@ The constraint of type 'angle' has the following syntax: angle *ID1* *ID2* *ID3* *amin* *amax* where 'angle' is the required keyword, *ID1*\ , *ID2* and *ID3* are pre-reaction atom IDs, and these three atoms must form an angle between *amin* and *amax* for the reaction to occur (where *ID2* is the central atom). Angles must be specified in degrees. This constraint can be used to enforce a certain orientation between reacting molecules. pre-reaction atom IDs (or molecule-fragment IDs, see below), and these three atoms must form an angle between *amin* and *amax* for the reaction to occur (where *ID2* is the central atom). Angles must be specified in degrees. This constraint can be used to enforce a certain orientation between reacting molecules. The constraint of type 'dihedral' has the following syntax: Loading @@ -376,15 +378,23 @@ The constraint of type 'dihedral' has the following syntax: dihedral *ID1* *ID2* *ID3* *ID4* *amin* *amax* *amin2* *amax2* where 'dihedral' is the required keyword, and *ID1*\ , *ID2*\ , *ID3* and *ID4* are pre-reaction atom IDs. Dihedral angles are calculated in the interval (-180,180]. Refer to the :doc:`dihedral style <dihedral_style>` documentation for further details on convention. If *amin* is less than *amax*, these four atoms must form a dihedral angle greater than *amin* **and** less than *amax* for the reaction to occur. If *amin* is greater than *amax*, these four atoms must form a dihedral angle greater than *amin* **or** less than *amax* for the reaction to occur. Angles must be specified in degrees. Optionally, a second range of permissible angles *amin2*-*amax2* can be specified. and *ID4* are pre-reaction atom IDs (or molecule-fragment IDs, see below). Dihedral angles are calculated in the interval (-180,180]. Refer to the :doc:`dihedral style <dihedral_style>` documentation for further details on convention. If *amin* is less than *amax*, these four atoms must form a dihedral angle greater than *amin* **and** less than *amax* for the reaction to occur. If *amin* is greater than *amax*, these four atoms must form a dihedral angle greater than *amin* **or** less than *amax* for the reaction to occur. Angles must be specified in degrees. Optionally, a second range of permissible angles *amin2*-*amax2* can be specified. For the 'distance', 'angle', and 'dihedral' constraints (explained above), atom IDs can be replaced by pre-reaction molecule-fragment IDs. The molecule-fragment ID must begin with a letter. The location of the ID is the geometric center of all atom positions in the fragment. The molecule fragment must have been defined in the :doc:`molecule <molecule>` command for the pre-reaction template. The constraint of type 'arrhenius' imposes an additional reaction probability according to the temperature-dependent Arrhenius equation: Loading
doc/utils/sphinx-config/false_positives.txt +1 −1 Original line number Diff line number Diff line Loading @@ -629,7 +629,6 @@ dipolar dir Direc dirname disarmmd discoverable discretization discretized Loading Loading @@ -2457,6 +2456,7 @@ rdc rdf RDideal rdx reacter README realtime reamin Loading
src/USER-REACTION/README +4 −4 Original line number Diff line number Diff line This package implements the DisARMMD protocol (disarmmd.org) as This package implements the REACTER protocol (reacter.org) as "fix bond/react." This fix allows for complex topology changes during a running MD simulation, when using classical force fields. Topology changes are defined in pre- and post-reaction molecule Loading @@ -6,7 +6,7 @@ templates and can include creation and deletion of bonds, angles, dihedrals, impropers, atom types, bond types, angle types, dihedral types, improper types, and/or atomic charges. The DisARMMD protocol is a method for modeling chemical reactions in The REACTER protocol is a method for modeling chemical reactions in classical molecular dynamics simulations. It was developed to build physically-realistic initial configurations for amorphous or crosslinked materials. Any number of competing or reversible reaction Loading @@ -15,9 +15,9 @@ advanced options currently available include reaction constraints (e.g. angle and Arrhenius constraints), deletion of reaction byproducts or other small molecules, and chiral-sensitive reactions. The DisARMMD methodology is detailed in: The REACTER methodology is detailed in: Gissinger et al., Polymer 128, 211-217 (2017) https://doi.org/10.1016/j.polymer.2017.09.038 This package was created by Jacob Gissinger (info@disarmmd.org), This package was created by Jacob Gissinger (jrgiss05@gmail.com), while at the NASA Langley Research Center.
