From 375fb4b3145717734b708bfae99843d04c722acb Mon Sep 17 00:00:00 2001 From: Jacob Gissinger Date: Sat, 23 May 2020 23:32:49 -0600 Subject: [PATCH] bond/react: change 'general name' for method and update contact info --- doc/src/Packages_details.rst | 2 +- doc/utils/sphinx-config/false_positives.txt | 2 +- src/USER-REACTION/README | 8 ++++---- 3 files changed, 6 insertions(+), 6 deletions(-) diff --git a/doc/src/Packages_details.rst b/doc/src/Packages_details.rst index 8251c5301e..2353df777f 100644 --- a/doc/src/Packages_details.rst +++ b/doc/src/Packages_details.rst @@ -2064,7 +2064,7 @@ molecules, and chiral-sensitive reactions. * examples/USER/reaction * `2017 LAMMPS Workshop `_ * `2019 LAMMPS Workshop `_ -* disarmmd.org +* reacter.org ---------- diff --git a/doc/utils/sphinx-config/false_positives.txt b/doc/utils/sphinx-config/false_positives.txt index 3d9f3ddcc9..25dc652321 100644 --- a/doc/utils/sphinx-config/false_positives.txt +++ b/doc/utils/sphinx-config/false_positives.txt @@ -629,7 +629,6 @@ dipolar dir Direc dirname -disarmmd discoverable discretization discretized @@ -2456,6 +2455,7 @@ rdc rdf RDideal rdx +reacter README realtime reamin diff --git a/src/USER-REACTION/README b/src/USER-REACTION/README index f099ace103..ed2e760e64 100644 --- a/src/USER-REACTION/README +++ b/src/USER-REACTION/README @@ -1,4 +1,4 @@ -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 @@ -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 @@ -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.