diff --git a/doc/src/fix_bond_react.rst b/doc/src/fix_bond_react.rst old mode 100755 new mode 100644 index 25502c52d4..8d54ce755b --- a/doc/src/fix_bond_react.rst +++ b/doc/src/fix_bond_react.rst @@ -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 -` 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 ` 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 diff --git a/src/USER-REACTION/fix_bond_react.cpp b/src/USER-REACTION/fix_bond_react.cpp index c5efb8c5a7..0b0e41581d 100644 --- a/src/USER-REACTION/fix_bond_react.cpp +++ b/src/USER-REACTION/fix_bond_react.cpp @@ -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]);