From 4a96057e4fef8ca9c02cfcfa7a58707dce008f9b Mon Sep 17 00:00:00 2001
From: Gareth Tribello <gareth.tribello@gmail.com>
Date: Fri, 25 May 2018 16:45:04 +0100
Subject: [PATCH] Fixed a bug that can occur when using mappings with virtual
atoms
---
src/mapping/Mapping.cpp | 30 ++++--------------------------
src/mapping/Mapping.h | 2 --
2 files changed, 4 insertions(+), 28 deletions(-)
diff --git a/src/mapping/Mapping.cpp b/src/mapping/Mapping.cpp
index 8a05b6ee3..2b063ffb9 100644
--- a/src/mapping/Mapping.cpp
+++ b/src/mapping/Mapping.cpp
@@ -103,8 +103,10 @@ Mapping::Mapping(const ActionOptions&ao):
// Get the arguments and atoms that are required
std::vector<AtomNumber> atoms; std::vector<std::string> args;
mymap->getAtomAndArgumentRequirements( atoms, args );
- requestAtoms( atoms ); std::vector<Value*> req_args;
- interpretArgumentList( args, req_args ); requestArguments( req_args );
+ std::vector<Value*> req_args; interpretArgumentList( args, req_args );
+ if( req_args.size()>0 && atoms.size()>0 ) error("cannot mix atoms and arguments");
+ if( req_args.size()>0 ) requestArguments( req_args );
+ if( atoms.size()>0 ) requestAtoms( atoms );
// Duplicate all frames (duplicates are used by sketch-map)
// mymap->duplicateFrameList();
// fframes.resize( 2*nfram, 0.0 ); dfframes.resize( 2*nfram, 0.0 );
@@ -124,30 +126,6 @@ void Mapping::turnOnDerivatives() {
needsDerivatives();
}
-void Mapping::prepare() {
- if( mymap->mappingNeedsSetup() ) {
- // Get the arguments and atoms that are required
- std::vector<AtomNumber> atoms; std::vector<std::string> args;
- mymap->getAtomAndArgumentRequirements( atoms, args );
- requestAtoms( atoms ); std::vector<Value*> req_args;
- interpretArgumentList( args, req_args ); requestArguments( req_args );
- // Duplicate all frames (duplicates are used by sketch-map)
- //mymap->duplicateFrameList();
- // Get the number of frames in the path
- // unsigned nfram=getNumberOfReferencePoints();
- // fframes.resize( 2*nfram, 0.0 ); dfframes.resize( 2*nfram, 0.0 );
- // plumed_assert( !mymap->mappingNeedsSetup() );
- // Resize all derivative arrays
- // mymap->setNumberOfAtomsAndArguments( atoms.size(), args.size() );
- // Resize forces array
- if( getNumberOfAtoms()>0 ) {
- forcesToApply.resize( 3*getNumberOfAtoms() + 9 + getNumberOfArguments() );
- } else {
- forcesToApply.resize( getNumberOfArguments() );
- }
- }
-}
-
unsigned Mapping::getPropertyIndex( const std::string& name ) const {
return mymap->getPropertyIndex( name );
}
diff --git a/src/mapping/Mapping.h b/src/mapping/Mapping.h
index 91d14fcc6..33164ecc1 100644
--- a/src/mapping/Mapping.h
+++ b/src/mapping/Mapping.h
@@ -95,8 +95,6 @@ public:
std::string getArgumentName( unsigned& iarg );
/// Get the value of the ith property for the current frame
double getPropertyValue( const unsigned& current, const unsigned& iprop ) const ;
-/// Stuff to do before we do the calculation
- void prepare();
/// Apply the forces
void apply();
};
--
GitLab