Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2014-2019 The plumed team
       3             :    (see the PEOPLE file at the root of the distribution for a list of names)
       4             : 
       5             :    See http://www.plumed.org for more information.
       6             : 
       7             :    This file is part of plumed, version 2.
       8             : 
       9             :    plumed is free software: you can redistribute it and/or modify
      10             :    it under the terms of the GNU Lesser General Public License as published by
      11             :    the Free Software Foundation, either version 3 of the License, or
      12             :    (at your option) any later version.
      13             : 
      14             :    plumed is distributed in the hope that it will be useful,
      15             :    but WITHOUT ANY WARRANTY; without even the implied warranty of
      16             :    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
      17             :    GNU Lesser General Public License for more details.
      18             : 
      19             :    You should have received a copy of the GNU Lesser General Public License
      20             :    along with plumed.  If not, see <http://www.gnu.org/licenses/>.
      21             : +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++ */
      22             : #ifndef __PLUMED_multicolvar_VolumeGradientBase_h
      23             : #define __PLUMED_multicolvar_VolumeGradientBase_h
      24             : 
      25             : #include "BridgedMultiColvarFunction.h"
      26             : 
      27             : namespace PLMD {
      28             : namespace multicolvar {
      29             : 
      30          60 : class VolumeGradientBase : public BridgedMultiColvarFunction {
      31             :   friend class MultiColvarBase;
      32             : private:
      33             : /// This is used to store forces temporarily in apply
      34             :   std::vector<double> tmpforces;
      35             : protected:
      36             : /// Get the cell box
      37             :   const Tensor & getBox() const;
      38             : /// Get reference to Pbc
      39             :   const Pbc & getPbc() const;
      40             : /// Calculate distance between two points
      41             :   Vector pbcDistance( const Vector& v1, const Vector& v2) const;
      42             : /// Get position of atom
      43             :   Vector getPosition( int iatom ) const ;
      44             : /// Request the atoms
      45             :   void requestAtoms( const std::vector<AtomNumber>& atoms );
      46             : /// Set the number in the volume
      47             :   void setNumberInVolume( const unsigned&, const unsigned&, const double&, const Vector&, const Tensor&, const std::vector<Vector>&, MultiValue& ) const ;
      48             : public:
      49             :   static void registerKeywords( Keywords& keys );
      50             :   explicit VolumeGradientBase(const ActionOptions&);
      51             : /// Do jobs required before tasks are undertaken
      52             :   void doJobsRequiredBeforeTaskList();
      53             : /// Actually do what we are asked
      54             :   void completeTask( const unsigned& curr, MultiValue& invals, MultiValue& outvals ) const ;
      55             : /// Calculate what is in the volumes
      56             :   virtual void calculateAllVolumes( const unsigned& curr, MultiValue& outvals ) const=0;
      57             : /// Setup the regions that this is based on
      58             :   virtual void setupRegions()=0;
      59             : /// Forces here are applied through the bridge
      60             :   void addBridgeForces( const std::vector<double>& bb );
      61             : };
      62             : 
      63             : inline
      64             : const Tensor & VolumeGradientBase::getBox()const {
      65             :   return getPntrToMultiColvar()->getBox();
      66             : }
      67             : 
      68             : inline
      69             : const Pbc & VolumeGradientBase::getPbc() const {
      70             :   return getPntrToMultiColvar()->getPbc();
      71             : }
      72             : 
      73             : inline
      74             : Vector VolumeGradientBase::pbcDistance( const Vector& v1, const Vector& v2) const {
      75      233947 :   return getPntrToMultiColvar()->pbcDistance(v1,v2);
      76             : }
      77             : 
      78             : inline
      79      240427 : Vector VolumeGradientBase::getPosition( int iatom ) const {
      80      468374 :   if( !checkNumericalDerivatives() ) return ActionAtomistic::getPosition(iatom);
      81             : // This is for numerical derivatives of quantity wrt to the local atoms
      82       12480 :   Vector tmp_p = ActionAtomistic::getPosition(iatom);
      83       24960 :   if( bridgeVariable<3*getNumberOfAtoms() ) {
      84        5760 :     if( bridgeVariable>=3*iatom && bridgeVariable<(iatom+1)*3 ) tmp_p[bridgeVariable%3]+=sqrt(epsilon);
      85             :   }
      86             : // This makes sure that numerical derivatives of virial are calculated correctly
      87       12480 :   tmp_p = ActionAtomistic::getPbc().realToScaled( tmp_p );
      88       12480 :   tmp_p = getPbc().scaledToReal( tmp_p );
      89       12480 :   return tmp_p;
      90             : }
      91             : 
      92             : }
      93             : }
      94             : #endif