From 4e9bdc2995a5b40e609bfe86228f67963745d1f5 Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Mon, 28 Mar 2016 18:49:14 +0100
Subject: [PATCH] Improved documentation for CenterOfMultiColvar
---
src/multicolvar/CenterOfMultiColvar.cpp | 13 +++++++++++++
1 file changed, 13 insertions(+)
diff --git a/src/multicolvar/CenterOfMultiColvar.cpp b/src/multicolvar/CenterOfMultiColvar.cpp
index 2c3604752..5cfcbf059 100644
--- a/src/multicolvar/CenterOfMultiColvar.cpp
+++ b/src/multicolvar/CenterOfMultiColvar.cpp
@@ -64,6 +64,19 @@ The first line here calclates the coordination numbers of all the atoms in the s
of the coordination numbers calculated by the action labelled c1 when it calculates the Berry Phase average described above.
(N.B. the \f$w_i\f$ in the above expression are all set equal to 1 in this case)
+The above input is fine we can, however, refine this somewhat by making use of a multicolvar transform action as shown below:
+
+\verbatim
+c1: COORDINATIONNUMBER SPECIES=1-512 SWITCH={EXP D_0=4.0 R_0=0.5}
+cf: MTRANSFORM_MORE DATA=c1 SWITCH={RATIONAL D_0=2.0 R_0=0.1} LOWMEM
+cc: CENTER_OF_MULTICOLVAR DATA=cf
+\endverbatim
+
+This input once again calculates the coordination numbers of all the atoms in the system. The middle line then transforms these
+coordinations numbers to numbers between 0 and 1. Essentially any atom with a coordination number larger than 2.0 is given a weight
+of one and below this value the transformed value decays to zero. It is these transformed coordination numbers that are used to calculate
+the Berry phase average described in the previous section.
+
*/
//+ENDPLUMEDOC
--
GitLab