From 032ccd57214c5489755383588a5d4a3e0edd7a6e Mon Sep 17 00:00:00 2001
From: Marco <mark.nava@gmail.com>
Date: Thu, 9 Mar 2017 14:02:29 +0100
Subject: [PATCH] Applied suggested modifications: citation and virial.
* Citation fixed as suggested
* Added PBC-friendly virial contributions: compared with the numerical derivatives
for a configuration and the same with a dimer shifted by the lattice vector on one of its components.
---
src/colvar/Dimer.cpp | 14 ++++++++++++--
1 file changed, 12 insertions(+), 2 deletions(-)
diff --git a/src/colvar/Dimer.cpp b/src/colvar/Dimer.cpp
index 9bc3c7781..758e06f66 100644
--- a/src/colvar/Dimer.cpp
+++ b/src/colvar/Dimer.cpp
@@ -23,6 +23,8 @@
#include "Colvar.h"
#include "ActionRegister.h"
+#include "core/PlumedMain.h"
+
#include <string>
#include <cmath>
#include <cassert>
@@ -165,7 +167,7 @@ Dimer::Dimer(const ActionOptions& ao):
PLUMED_COLVAR_INIT(ao)
{
- log<<" Please cite J. Chem. Theory Comput. 13, 425(2017)";
+ log<<" Bibliography "<<plumed.cite("M Nava, F. Palazzesi, C. Perego and M. Parrinello, J. Chem. Theory Comput. 13, 425(2017)")<<"\n";
parseVector("DSIGMA",dsigmas);
parse("Q",qexp);
parse("TEMP",temperature);
@@ -245,6 +247,7 @@ Dimer::Dimer(const ActionOptions& ao):
void Dimer::calculate()
{
double cv_val=0;
+ Tensor virial;
vector<Vector> derivatives;
vector<Vector> my_pos=getPositions();
int atms = my_pos.size();
@@ -272,6 +275,13 @@ void Dimer::calculate()
}
derivatives.push_back(der_val);
der_b2.push_back(mder_val);
+
+ // virial part: each dimer contributes -x_{ij}*ds/dx_{ij} (s is the CV)
+ double dfunc = fac1qm1/(beta*dsigquad);
+ Vector dd(dfunc*dist);
+ Tensor vv(dd,dist);
+ virial -= vv;
+
}
derivatives.insert(derivatives.end(), der_b2.begin(), der_b2.end());
@@ -279,8 +289,8 @@ void Dimer::calculate()
for(unsigned int i=0;i<derivatives.size();i++)
setAtomsDerivatives(i,derivatives[i]);
- setBoxDerivativesNoPbc();
setValue(cv_val);
+ setBoxDerivatives(virial);
}
--
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