ICODE-ADC/lammps
4
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

Merge pull request #3569 from jrgissing/type-labels-bond/react-examples

Browse Source 
Type labels for bond/react examples
This commit is contained in:
Axel Kohlmeyer
2023-01-05 19:22:43 -05:00
committed by GitHub
parent 821b34de78 a235cd4719
commit 843cc98531
89 changed files with 13421 additions and 11678 deletions
Download Patch File Download Diff File Expand all files Collapse all files

24
doc/src/Packages_details.rst
View File

@ -2544,17 +2544,18 @@ REACTION package
**Contents:**
This package allows for complex bond topology changes (reactions)
during a running MD simulation, when using classical force fields.
Topology changes are defined in pre- and post-reaction molecule
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. Other options currently
available include reaction constraints (e.g. angle and Arrhenius
constraints), deletion of reaction byproducts or other small
molecules, and chiral-sensitive reactions.
This package implements the REACTER protocol, which allows for complex
bond topology changes (reactions) during a running MD simulation when
using classical force fields. Topology changes are defined in pre- and
post-reaction molecule 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. Other
options currently available include reaction constraints (e.g., angle
and Arrhenius constraints), deletion of reaction byproducts or other
small molecules, creation of new atoms or molecules bonded to existing
atoms, and using LAMMPS variables for input parameters.
**Author:** Jacob R. Gissinger (CU Boulder) while at NASA Langley Research Center.
**Author:** Jacob R. Gissinger (NASA Langley Research Center).
**Supporting info:**
@ -2564,7 +2565,8 @@ molecules, and chiral-sensitive reactions.
* examples/PACKAGES/reaction
* `2017 LAMMPS Workshop <https://www.lammps.org/workshops/Aug17/pdf/gissinger.pdf>`_
* `2019 LAMMPS Workshop <https://www.lammps.org/workshops/Aug19/talk_gissinger.pdf>`_
* reacter.org
* `2021 LAMMPS Workshop <https://www.lammps.org/workshops/Aug21/talk/jacob-gissinger/>`_
* `REACTER website (reacter.org) <https://www.reacter.org/>`_
----------

40
doc/src/fix_bond_react.rst
View File

@ -123,6 +123,17 @@ using this fix is
(4) create a map that relates the template-atom-IDs of each atom between pre- and post-reaction molecule templates
(5) fill a simulation box with molecules and run a simulation with fix bond/react.
.. note::
.. versionadded:: 15Sep2022
:doc:`Type labels <Howto_type_labels>` allow for molecule templates
and data files to use alphanumeric atom types that match those of
a force field. Input files that use type labels are inherently
compatible with each other and portable between different
simulations. Therefore, it is highly recommended to use type labels
to specify atom, bond, etc. types when using fix bond/react.
Only one 'fix bond/react' command can be used at a time. Multiple
reactions can be simultaneously applied by specifying multiple *react*
arguments to a single 'fix bond/react' command. This syntax is
@ -228,18 +239,18 @@ pairs are identified within the cutoff distance:
initiator partners, these two atoms are identified as the initiator atom
pair of the reaction site.
Note that it can be helpful to select
unique atom types for the initiator atoms: if an initiator atom pair
is identified, as described in the previous steps, but it does not
correspond to the same pair specified in the pre-reaction template, an
otherwise eligible reaction could be prevented from occurring. Once
this unique initiator atom pair is identified for each reaction, there
could be two or more reactions that involve the same atom on the same
time step. If this is the case, only one such reaction is permitted to
occur. This reaction is chosen randomly from all potential reactions
involving the overlapping atom. This capability allows, for example,
different reaction pathways to proceed from identical reaction sites
with user-specified probabilities.
Note that it can be helpful to select unique atom types for the
initiator atoms: if an initiator atom pair is identified, as described
in the previous steps, but it does not correspond to the same pair
specified in the pre-reaction template, an otherwise eligible reaction
could be prevented from occurring. Once this unique initiator atom
pair is identified for each reaction, there could be two or more
reactions that involve the same atom on the same time step. If this is
the case, only one such reaction is permitted to occur. This reaction
is chosen randomly from all potential reactions involving the
overlapping atom. This capability allows, for example, different
reaction pathways to proceed from identical reaction sites with
user-specified probabilities.
The pre-reacted molecule template is specified by a molecule command.
This molecule template file contains a sample reaction site and its
@ -280,7 +291,10 @@ 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
simulation. A detailed discussion of matching molecule template atom
types with the simulation is provided on the :doc:`molecule <molecule>`
command page.
command page. It is highly recommended to use :doc:`Type labels <Howto_type_labels>`
(added in version 15Sep2022) in both molecule templates and data
files, which automates the process of syncing atom types between
different input files.
The post-reacted molecule template contains a sample of the reaction
site and its surrounding topology after the reaction has occurred. It