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

bond/react docs tweak: address a common mistake

Browse Source 
no atom of a small molecule should be specified as an edge atom
This commit is contained in:
jrgissing
2019-09-05 23:50:57 -06:00
parent 50af20d194
commit 49b5825e8d
1 changed files with 16 additions and 13 deletions
Download Patch File Download Diff File Expand all files Collapse all files

29
doc/src/fix_bond_react.txt
View File

@ -186,19 +186,22 @@ reacting atoms.
Some atoms in the pre-reacted template that are not reacting may have Some atoms in the pre-reacted template that are not reacting may have
missing topology with respect to the simulation. For example, the missing topology with respect to the simulation. For example, the
pre-reacted template may contain an atom that would connect to the pre-reacted template may contain an atom that, in the simulation, is
rest of a long polymer chain. These are referred to as edge atoms, and currently connected to the rest of a long polymer chain. These are
are also specified in the map file. When the pre-reaction template referred to as edge atoms, and are also specified in the map file.
contains edge atoms, not all atoms, bonds, charges, etc. specified in When the pre-reaction template contains edge atoms, not all atoms,
the reaction templates will be updated. Specifically, topology that bonds, charges, etc. specified in the reaction templates will be
involves only atoms that are 'too near' to template edges will not be updated. Specifically, topology that involves only atoms that are 'too
updated. The definition of 'too near the edge' depends on which near' to template edges will not be updated. The definition of 'too
interactions are defined in the simulation. If the simulation has near the edge' depends on which interactions are defined in the
defined dihedrals, atoms within two bonds of edge atoms are considered simulation. If the simulation has defined dihedrals, atoms within two
'too near the edge.' If the simulation defines angles, but not bonds of edge atoms are considered 'too near the edge.' If the
dihedrals, atoms within one bond of edge atoms are considered 'too simulation defines angles, but not dihedrals, atoms within one bond of
near the edge.' If just bonds are defined, only edge atoms are edge atoms are considered 'too near the edge.' If just bonds are
considered 'too near the edge.' defined, only edge atoms are considered 'too near the edge.'
NOTE: Small molecules, i.e. ones that have all their atoms contained
within the reaction templates, never have edge atoms.
Note that some care must be taken when a building a molecule template Note that some care must be taken when a building a molecule template
for a given simulation. All atom types in the pre-reacted template for a given simulation. All atom types in the pre-reacted template