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

bond/react: make rmsd constraint lowercase

Browse Source
This commit is contained in:
Jacob Gissinger
2020-08-28 11:06:27 -04:00
parent 2686df3760
commit ef50a67169
2 changed files with 15 additions and 15 deletions
Download Patch File Download Diff File Expand all files Collapse all files

28
doc/src/fix_bond_react.rst Executable file → Normal file
View File

@ -312,7 +312,7 @@ 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 five types of constraints available, as discussed below:
'distance', 'angle', 'dihedral', 'arrhenius', and 'RMSD'.
'distance', 'angle', 'dihedral', 'arrhenius', and 'rmsd'.
A sample map file is given below:
@ -432,24 +432,24 @@ temperature calculations. A uniform random number between 0 and 1 is
generated using *seed*\ ; if this number is less than the result of the
Arrhenius equation above, the reaction is permitted to occur.
The constraint of type 'RMSD' has the following syntax:
The constraint of type 'rmsd' has the following syntax:
.. parsed-literal::
RMSD *RMSDmax* *molfragment*
rmsd *RMSDmax* *molfragment*
where 'RMSD' is the required keyword, and *RMSDmax* is the maximum
where 'rmsd' is the required keyword, and *RMSDmax* is the maximum
root-mean-square deviation between atom positions of the pre-reaction
template and the local reaction site, after optimal translation and
rotation of the pre-reaction template. Optionally, the name of a
molecule fragment (of the pre-reaction template) can be specified by
*molfragment*\ . If a molecule fragment is specified, only atoms that
are part of this molecule fragment are used to determine the RMSD. A
molecule fragment must have been defined in the :doc:`molecule
<molecule>` command for the pre-reaction template. For example, the
molecule fragment could consist of only the backbone atoms of a
polymer chain. This constraint can be used to enforce a specific
relative position and orientation between reacting molecules.
template and the local reaction site (distance units), after optimal
translation and rotation of the pre-reaction template. Optionally, the
name of a molecule fragment (of the pre-reaction template) can be
specified by *molfragment*\ . If a molecule fragment is specified,
only atoms that are part of this molecule fragment are used to
determine the RMSD. A molecule fragment must have been defined in the
:doc:`molecule <molecule>` command for the pre-reaction template. For
example, the molecule fragment could consist of only the backbone
atoms of a polymer chain. This constraint can be used to enforce a
specific relative position and orientation between reacting molecules.
Once a reaction site has been successfully identified, data structures
within LAMMPS that store bond topology are updated to reflect the

2
src/USER-REACTION/fix_bond_react.cpp
View File

@ -3360,7 +3360,7 @@ void FixBondReact::Constraints(char *line, int myrxn)
constraints[nconstraints][4] = tmp[1];
constraints[nconstraints][5] = tmp[2];
constraints[nconstraints][6] = tmp[3];
} else if (strcmp(constraint_type,"RMSD") == 0) {
} else if (strcmp(constraint_type,"rmsd") == 0) {
constraints[nconstraints][1] = RMSD;
strcpy(strargs[0],"0");
sscanf(line,"%*s %lg %s",&tmp[0],strargs[0]);