From 888f4f7c5a8e59c8a14cdfe5d1896e3100f84783 Mon Sep 17 00:00:00 2001
From: Giovanni Bussi <giovanni.bussi@gmail.com>
Date: Mon, 28 May 2018 17:06:54 +0200
Subject: [PATCH] Fixed problem with mapping/virtual atoms
backport of 4a96057e4fef8ca9c02cfcfa7a58707dce008f9b
---
src/mapping/Mapping.cpp | 26 ++++----------------------
src/mapping/Mapping.h | 2 --
2 files changed, 4 insertions(+), 24 deletions(-)
diff --git a/src/mapping/Mapping.cpp b/src/mapping/Mapping.cpp
index df771be10..0e83e3407 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 );
@@ -128,26 +130,6 @@ Mapping::~Mapping() {
delete mymap;
}
-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
- forcesToApply.resize( 3*getNumberOfAtoms() + 9 + 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 83b7eec99..02670d7a5 100644
--- a/src/mapping/Mapping.h
+++ b/src/mapping/Mapping.h
@@ -90,8 +90,6 @@ 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();
};
--
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