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update docs

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Jacob Gissinger
2020-11-17 22:46:42 -05:00
parent 1931cfa56a
commit 337d47ca6c
1 changed files with 24 additions and 11 deletions
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doc/src/fix_bond_react.rst
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@ -41,7 +41,7 @@ Syntax
* template-ID(post-reacted) = ID of a molecule template containing post-reaction topology
* map_file = name of file specifying corresponding atom-IDs in the pre- and post-reacted templates
* zero or more individual keyword/value pairs may be appended to each react argument
* individual_keyword = *prob* or *max_rxn* or *stabilize_steps* or *custom_charges*
* individual_keyword = *prob* or *max_rxn* or *stabilize_steps* or *custom_charges* or *modify_create*
.. parsed-literal::
@ -55,9 +55,12 @@ Syntax
*custom_charges* value = *no* or *fragmentID*
no = update all atomic charges (default)
fragmentID = ID of molecule fragment whose charges are updated
*modify_create* value = *no* or *fragmentID*
no = use all eligible atoms for create-atoms fit (default)
fragmentID = ID of molecule fragment used for create-atoms fit
*modify_create* keyword values
*fit* value = *all* or *fragmentID*
all = use all eligible atoms for create-atoms fit (default)
fragmentID = ID of molecule fragment used for create-atoms fit
*near* value = R
R = only insert atom/molecule if further than R from existing particles (distance units)
Examples
""""""""
@ -362,13 +365,23 @@ pre-reaction template. The inserted positions of created atoms are
determined by the coordinates of the post-reaction template, after
optimal translation and rotation of the post-reaction template to the
reaction site (using a fit with atoms that are neither created nor
deleted). Or, the *modify_create* keyword can be used to specify which
post-reaction atoms are used for this fit. The *fragmentID* value must
be the name of a molecule fragment defined in the post-reaction
:doc:`molecule <molecule>` template, and only atoms in this fragment
are used for the fit. The velocity of each created atom is initialized
in a random direction with a magnitude calculated from the
instantaneous temperature of the reaction site.
deleted). The *modify_create* keyword can be used to modify the
default behavior when creating atoms. The *modify_create* keyword has
two sub-keywords, *fit* and *near*. One or more of the sub-keywords
may be used after the *modify_create* keyword. The *fit* sub-keyword
can be used to specify which post-reaction atoms are used for the
optimal translation and rotation of the post-reaction template. The
*fragmentID* value of the *fit* sub-keyword must be the name of a
molecule fragment defined in the post-reaction :doc:`molecule
<molecule>` template, and only atoms in this fragment are used for the
fit. Atoms are created only if no current atom in the simulation is
within a distance R of any created atom, including the effect of
periodic boundary conditions if applicable. R is defined by the *near*
sub-keyword. Note that the default value for R is 0.0, which will
allow atoms to strongly overlap if you are inserting where other atoms
are present. The velocity of each created atom is initialized in a
random direction with a magnitude calculated from the instantaneous
temperature of the reaction site.
The handedness of atoms that are chiral centers can be enforced by
listing their IDs in the ChiralIDs section. A chiral atom must be