From 7fcf66b752500f228ed6863b7374ef33a96fdab6 Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Thu, 10 Mar 2016 22:55:10 +0000
Subject: [PATCH] Small fix to manual for HBOND_MATRIX
[makedoc]
---
src/adjmat/HbondMatrix.cpp | 7 ++++---
1 file changed, 4 insertions(+), 3 deletions(-)
diff --git a/src/adjmat/HbondMatrix.cpp b/src/adjmat/HbondMatrix.cpp
index c35f3969e..f2984afed 100644
--- a/src/adjmat/HbondMatrix.cpp
+++ b/src/adjmat/HbondMatrix.cpp
@@ -70,12 +70,15 @@ PLUMED_REGISTER_ACTION(HBondMatrix,"HBOND_MATRIX")
void HBondMatrix::registerKeywords( Keywords& keys ){
AdjacencyMatrixBase::registerKeywords( keys );
- keys.add("atoms-1","ATOMS","The list of atoms which can be part of a hydrogen bond. When this command is used the set of atoms that can donate a "
+ keys.add("atoms","ATOMS","The list of atoms which can be part of a hydrogen bond. When this command is used the set of atoms that can donate a "
"hydrogen bond is assumed to be the same as the set of atoms that can form hydrogen bonds. The atoms involved must be specified"
"as a list of labels of \\ref mcolv or labels of a \\ref multicolvarfunction actions. If you would just like to use "
"the atomic positions you can use a \\ref DENSITY command to specify a group of atoms. Specifying your atomic positions using labels of "
"other \\ref mcolv or \\ref multicolvarfunction commands is useful, however, as you can then exploit a much wider "
"variety of functions of the contact matrix as described in \\ref contactmatrix");
+ keys.add("atoms","HYDROGENS","The list of hydrogen atoms that can form part of a hydrogen bond. The atoms must be specified using a comma separated list, "
+ "an index range or by using a \\ref GROUP. A list of hydrogen atoms is always required even if you specify the other atoms using "
+ "DONORS and ACCEPTORS as described below.");
keys.add("atoms-2","DONORS","The list of atoms which can donate a hydrogen bond. The atoms involved must be specified "
"as a list of labels of \\ref mcolv or labels of a \\ref multicolvarfunction actions. If you would just like to use "
"the atomic positions you can use a \\ref DENSITY command to specify a group of atoms. Specifying your atomic positions using labels of "
@@ -86,8 +89,6 @@ void HBondMatrix::registerKeywords( Keywords& keys ){
"the atomic positions you can use a \\ref DENSITY command to specify a group of atoms. Specifying your atomic positions using labels of "
"other \\ref mcolv or \\ref multicolvarfunction commands is useful, however, as you can then exploit a much wider "
"variety of functions of the contact matrix as described in \\ref contactmatrix");
- keys.add("atoms","HYDROGENS","The list of hydrogen atoms that can form part of a hydrogen bond. The atoms must be specified using a comma separated list, "
- "an index range or by using a \\ref GROUP");
keys.add("numbered","SWITCH","The \\ref switchingfunction that specifies how close a pair of atoms must be together for there to be a hydrogen bond between them");
keys.add("numbered","HSWITCH","The \\ref switchingfunction that specifies how close the hydrogen must be to the donor atom of the hydrogen bond for it to be "
"considered a hydrogen bond");
--
GitLab