From 14c45395f51141a931d28013c4308de384d174e7 Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Thu, 3 Aug 2017 17:05:19 +0200
Subject: [PATCH] Ran astyle and added description of changes
---
CHANGES/v2.5.md | 8 ++++++++
src/multicolvar/VolumeBetweenContours.cpp | 2 +-
src/pamm/PammObject.cpp | 25 +++++++++++++++--------
3 files changed, 25 insertions(+), 10 deletions(-)
diff --git a/CHANGES/v2.5.md b/CHANGES/v2.5.md
index dbbed1220..0dedfb37c 100644
--- a/CHANGES/v2.5.md
+++ b/CHANGES/v2.5.md
@@ -2,3 +2,11 @@
This page contains changes that will end up in 2.5
+Changes from version 2.4 which are relevant for users:
+- Changes leading to incompatible behavior:
+- New actions:
+ - \ref PAMM
+ - \ref HBPAMM_MATRIX
+ - \ref HBPAMM_SH
+
+Changes from version 2.4 which are relevant for developers:
diff --git a/src/multicolvar/VolumeBetweenContours.cpp b/src/multicolvar/VolumeBetweenContours.cpp
index afe7b0da2..737c77ffc 100644
--- a/src/multicolvar/VolumeBetweenContours.cpp
+++ b/src/multicolvar/VolumeBetweenContours.cpp
@@ -104,7 +104,7 @@ VolumeInEnvelope::VolumeInEnvelope(const ActionOptions& ao):
std::vector<double> pp(3,0.0), bandwidth(3); parseVector("BANDWIDTH",bandwidth);
log.printf(" using %s kernel with bandwidths %f %f %f \n",getKernelType().c_str(),bandwidth[0],bandwidth[1],bandwidth[2] );
- kernel = new KernelFunctions( pp, bandwidth, getKernelType(), "DIAGONAL", 1.0 );
+ kernel = new KernelFunctions( pp, bandwidth, getKernelType(), "DIAGONAL", 1.0 );
for(unsigned i=0; i<3; ++i) { pos.push_back(new Value()); pos[i]->setNotPeriodic(); }
std::vector<double> csupport( kernel->getContinuousSupport() );
double maxs = csupport[0];
diff --git a/src/pamm/PammObject.cpp b/src/pamm/PammObject.cpp
index e0528dba7..4147cadb1 100644
--- a/src/pamm/PammObject.cpp
+++ b/src/pamm/PammObject.cpp
@@ -34,7 +34,8 @@ PammObject::PammObject( const PammObject& in ):
regulariser(in.regulariser),
pbc(in.pbc),
min(in.min),
- max(in.max)
+ max(in.max),
+ kgroup_start(in.kgroup_start)
{
for(unsigned i=0; i<in.kernels.size(); ++i) kernels.push_back( new KernelFunctions( in.kernels[i] ) );
}
@@ -63,13 +64,15 @@ void PammObject::setup( const std::string& filename, const double& reg, const st
else pos[i]->setDomain( min[i], max[i] );
}
- ifile.open(filename); ifile.allowIgnoredFields(); kernels.resize(0);
+ ifile.open(filename); ifile.allowIgnoredFields();
+ kernels.resize(0); kgroup_start.resize(0); kgroup_start.push_back(0);
for(unsigned k=0;; ++k) {
KernelFunctions* kk = KernelFunctions::read( &ifile, false, valnames );
if( !kk ) break ;
kk->normalize( pos );
kernels.push_back( kk );
ifile.scanField();
+ kgroup_start.push_back( kernels.size() );
}
ifile.close();
for(unsigned i=0; i<valnames.size(); ++i) delete pos[i];
@@ -86,15 +89,19 @@ void PammObject::evaluate( const std::vector<double>& invar, std::vector<double>
}
// Evaluate the set of kernels
- double denom=regulariser;
- std::vector<double> dderiv( der[0].size(), 0 );
- for(unsigned i=0; i<kernels.size(); ++i) {
- outvals[i]=kernels[i]->evaluate( pos, der[i] );
- denom+=outvals[i];
- for(unsigned j=0; j<der[i].size(); ++j) dderiv[j] += der[i][j];
+ double denom=regulariser; unsigned ikernel=0;
+ std::vector<double> tmpder( der[0].size() ), dderiv( der[0].size(), 0 );
+ for(unsigned i=0; i<kgroup_start.size()-1; ++i) {
+ outvals[i]=0;
+ for(unsigned k=kgroup_start[i]; k<kgroup_start[i+1]; ++k) {
+ outvals[i] += kernels[ikernel]->evaluate( pos, tmpder );
+ denom+=outvals[i];
+ for(unsigned j=0; j<der[i].size(); ++j) { der[i][j] += tmpder[j]; dderiv[j] += tmpder[j]; }
+ ikernel++;
+ }
}
// Evaluate the set of derivatives
- for(unsigned i=0; i<kernels.size(); ++i) {
+ for(unsigned i=0; i<kgroup_start.size()-1; ++i) {
outvals[i]/=denom;
for(unsigned j=0; j<der[i].size(); ++j) der[i][j]=der[i][j]/denom - outvals[i]*dderiv[j]/denom;
}
--
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