Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2014-2018 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             : #include "BridgedMultiColvarFunction.h"
      23             : #include "core/PlumedMain.h"
      24             : #include "core/ActionSet.h"
      25             : #include "CatomPack.h"
      26             : 
      27             : namespace PLMD {
      28             : namespace multicolvar {
      29             : 
      30          55 : void BridgedMultiColvarFunction::registerKeywords( Keywords& keys ) {
      31          55 :   MultiColvarBase::registerKeywords( keys );
      32          55 :   keys.add("compulsory","DATA","The multicolvar that calculates the set of base quantities that we are interested in");
      33          55 : }
      34             : 
      35          43 : BridgedMultiColvarFunction::BridgedMultiColvarFunction(const ActionOptions&ao):
      36             :   Action(ao),
      37          43 :   MultiColvarBase(ao)
      38             : {
      39          43 :   std::string mlab; parse("DATA",mlab);
      40          43 :   mycolv = plumed.getActionSet().selectWithLabel<MultiColvarBase*>(mlab);
      41          43 :   if(!mycolv) error("action labeled " + mlab + " does not exist or is not a multicolvar");
      42             : 
      43             :   // When using numerical derivatives here we must use numerical derivatives
      44             :   // in base multicolvar
      45          43 :   if( checkNumericalDerivatives() ) mycolv->useNumericalDerivatives();
      46             : 
      47          43 :   myBridgeVessel = mycolv->addBridgingVessel( this ); addDependency(mycolv);
      48          43 :   weightHasDerivatives=true; usespecies=mycolv->usespecies;
      49             :   // Number of tasks is the same as the number in the underlying MultiColvar
      50          43 :   for(unsigned i=0; i<mycolv->getFullNumberOfTasks(); ++i) addTaskToList( mycolv->getTaskCode(i) );
      51          43 : }
      52             : 
      53          43 : void BridgedMultiColvarFunction::turnOnDerivatives() {
      54          43 :   BridgedMultiColvarFunction* check = dynamic_cast<BridgedMultiColvarFunction*>( mycolv );
      55          43 :   if( check ) {
      56           0 :     if( check->getNumberOfAtoms()>0 ) error("cannot calculate required derivatives of this quantity");
      57             :   }
      58          43 :   MultiColvarBase::turnOnDerivatives();
      59          43 : }
      60             : 
      61      100553 : void BridgedMultiColvarFunction::transformBridgedDerivatives( const unsigned& current, MultiValue& invals, MultiValue& outvals ) const {
      62      100553 :   completeTask( current, invals, outvals );
      63             : 
      64             :   // Now update the outvals derivatives lists
      65      100578 :   if( derivativesAreRequired() ) {
      66       93668 :     outvals.emptyActiveMembers();
      67       93594 :     if( mycolv->isDensity() ) {
      68       43317 :       for(unsigned j=0; j<3; ++j) outvals.putIndexInActiveArray( 3*current+j );
      69       43408 :       for(unsigned j=invals.getNumberOfDerivatives()-9; j<invals.getNumberOfDerivatives(); ++j) outvals.putIndexInActiveArray(j);
      70             :     } else {
      71       50266 :       for(unsigned j=0; j<invals.getNumberActive(); ++j) outvals.putIndexInActiveArray( invals.getActiveIndex(j) );
      72             :     }
      73       93676 :     for(unsigned j=invals.getNumberOfDerivatives(); j<outvals.getNumberOfDerivatives(); ++j) outvals.putIndexInActiveArray( j );
      74       93680 :     outvals.completeUpdate();
      75             :   }
      76      100586 : }
      77             : 
      78       13042 : void BridgedMultiColvarFunction::performTask( const unsigned& taskIndex, const unsigned& current, MultiValue& myvals ) const {
      79       13042 :   MultiValue invals( mycolv->getNumberOfQuantities(), mycolv->getNumberOfDerivatives() );
      80       13042 :   invals.clearAll(); mycolv->performTask( taskIndex, current, invals );
      81       13042 :   transformBridgedDerivatives( taskIndex, invals, myvals );
      82       13042 : }
      83             : 
      84          60 : void BridgedMultiColvarFunction::calculateNumericalDerivatives( ActionWithValue* a ) {
      85          60 :   if(!a) {
      86          60 :     a=dynamic_cast<ActionWithValue*>(this);
      87          60 :     plumed_massert(a,"cannot compute numerical derivatives for an action without values");
      88             :   }
      89          60 :   if( myBridgeVessel ) {
      90          60 :     myBridgeVessel->completeNumericalDerivatives();
      91             :   } else {
      92           0 :     error("numerical derivatives are not implemented");
      93             :   }
      94          60 : }
      95             : 
      96           0 : void BridgedMultiColvarFunction::applyBridgeForces( const std::vector<double>& bb ) {
      97           0 :   if( getNumberOfAtoms()==0 ) return ;
      98             : 
      99           0 :   std::vector<Vector>& f( modifyForces() );
     100           0 :   for(unsigned i=0; i<getNumberOfAtoms(); ++i) {
     101           0 :     f[i][0]+=bb[3*i+0]; f[i][1]+=bb[3*i+1]; f[i][2]+=bb[3*i+2];
     102             :   }
     103             : }
     104             : 
     105          34 : bool BridgedMultiColvarFunction::isPeriodic() {
     106          34 :   return mycolv->isPeriodic();
     107             : }
     108             : 
     109           0 : void BridgedMultiColvarFunction::deactivate_task( const unsigned& taskno ) {
     110           0 :   plumed_merror("This should never be called");
     111             : }
     112             : 
     113       11582 : CatomPack BridgedMultiColvarFunction::getCentralAtomPack( const unsigned& basn, const unsigned& curr ) {
     114       11582 :   return mycolv->getCentralAtomPack( basn, curr );
     115             : }
     116             : 
     117             : }
     118        2523 : }