Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2012-2017 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 "core/ActionWithValue.h"
      23             : #include "core/ActionWithArguments.h"
      24             : #include "core/ActionRegister.h"
      25             : #include "tools/Communicator.h"
      26             : 
      27             : //+PLUMEDOC ANALYSIS GATHER_REPLICAS
      28             : /*
      29             : Create a vector that contains the copies of the input quantities from all replicas
      30             : 
      31             : There are three ways that you can generate indistinguishable replicas of a system for calculating
      32             : ensemble averages:
      33             : 
      34             : - You can take a time average.
      35             : - You can run a multiple replica simulation and average over the replicas.
      36             : - You can do a spatial average and assume that there are multiple replicas of the system in the same simulation box and average over them.
      37             : 
      38             : Many actions within PLUMED will perform average over more than one of these type of replica.  However, since v2.10
      39             : we have tried to separate out these three ways of generating multiple replicas for averaging.  There are thus many actions
      40             : where you take time averages by using [ACCUMULATE](ACCUMULATE.md) or [COLLECT](COLLECT.md).  You take spatial averages by passing
      41             : working the vectors of values.  You then use this action to average over replicas.  The way this works in practise is illustrated by the simple
      42             : example shown below.
      43             : 
      44             : ```plumed
      45             : #SETTINGS NREPLICAS=2
      46             : # Calculate distance between atoms 1 and 2 on for all 2 replicas
      47             : d: DISTANCE ATOMS=1,2
      48             : # Now gather the values of this distance on all the replicas:
      49             : g: GATHER_REPLICAS ARG=d
      50             : # Now average the two distances on the two replicas
      51             : s: COMBINE ARG=g.rep-1,g.rep-2 COEFFICIENTS=0.5,0.5 PERIODIC=NO
      52             : # And print the instantaneous average for the distance on the two replicas
      53             : PRINT ARG=s FILE=colvar
      54             : ```
      55             : 
      56             : Now suppose that we wanted to calculate a time average of the distance and an average over the replicas.  We could use an input like this:
      57             : 
      58             : ```plumed
      59             : #SETTINGS NREPLICAS=2
      60             : d: DISTANCE ATOMS=1,2
      61             : g: GATHER_REPLICAS ARG=d
      62             : s: COMBINE ARG=g.rep-1,g.rep-2 COEFFICIENTS=0.5,0.5 PERIODIC=NO
      63             : # This does the time averaging
      64             : a: AVERAGE ARG=s
      65             : # And output the final average
      66             : PRINT ARG=a FILE=colvar
      67             : ```
      68             : 
      69             : */
      70             : //+ENDPLUMEDOC
      71             : 
      72             : namespace PLMD {
      73             : namespace generic {
      74             : 
      75             : class GatherReplicas :
      76             :   public ActionWithValue,
      77             :   public ActionWithArguments {
      78             : private:
      79             :   unsigned nreplicas;
      80             : public:
      81             :   static void registerKeywords( Keywords& keys );
      82             :   explicit GatherReplicas( const ActionOptions& );
      83             :   unsigned getNumberOfDerivatives();
      84             :   void calculate();
      85             :   void apply();
      86             : };
      87             : 
      88             : PLUMED_REGISTER_ACTION(GatherReplicas,"GATHER_REPLICAS")
      89             : 
      90          35 : void GatherReplicas::registerKeywords( Keywords& keys ) {
      91          35 :   Action::registerKeywords( keys );
      92          35 :   ActionWithValue::registerKeywords( keys );
      93          35 :   ActionWithArguments::registerKeywords( keys );
      94          70 :   keys.addInputKeyword("compulsory","ARG","scalar/vector/matrix/grid","the argument from the various replicas that you would like to gather");
      95          70 :   keys.addOutputComponent("rep","default","scalar/vector/matrix/grid","the input arguments for each of the replicas");
      96          35 :   keys.remove("NUMERICAL_DERIVATIVES");
      97          35 : }
      98             : 
      99          17 : GatherReplicas::GatherReplicas( const ActionOptions& ao ):
     100             :   Action(ao),
     101             :   ActionWithValue(ao),
     102          17 :   ActionWithArguments(ao) {
     103          17 :   if( getNumberOfArguments()!=1 ) {
     104           0 :     error("you can only gather one argument at a time with GatherReplicas");
     105             :   }
     106             : 
     107          17 :   std::vector<std::size_t> shape( getPntrToArgument(0)->getShape() );
     108             :   std::string min, max;
     109          17 :   nreplicas=getNumberOfReplicas();
     110             :   bool periodic=false;
     111          17 :   if( getPntrToArgument(0)->isPeriodic() ) {
     112             :     periodic=true;
     113           0 :     getPntrToArgument(0)->getDomain( min, max );
     114             :   }
     115             : 
     116          98 :   for(unsigned i=0; i<nreplicas; ++i) {
     117             :     std::string num;
     118          81 :     Tools::convert( i+1, num);
     119          81 :     if( getPntrToArgument(0)->hasDerivatives() ) {
     120         162 :       addComponentWithDerivatives( "rep-" + num, shape );
     121             :     } else {
     122           0 :       addComponent( "rep-" + num, shape );
     123             :     }
     124          81 :     if( periodic ) {
     125           0 :       componentIsPeriodic( "rep-" + num, min, max );
     126             :     } else {
     127         162 :       componentIsNotPeriodic( "rep-" + num );
     128             :     }
     129             :   }
     130          17 : }
     131             : 
     132           0 : unsigned GatherReplicas::getNumberOfDerivatives() {
     133           0 :   return getPntrToArgument(0)->getNumberOfDerivatives();
     134             : }
     135             : 
     136        4236 : void GatherReplicas::calculate() {
     137             :   Value* myarg = getPntrToArgument(0);
     138        4236 :   std::size_t nvals = myarg->getNumberOfValues(), nder = myarg->getNumberOfDerivatives();
     139        4236 :   std::vector<double> dval( nvals*(1+nder) ), datap(nreplicas*nvals*(1+nder) );
     140        8472 :   for(unsigned i=0; i<nvals; ++i) {
     141        4236 :     dval[i*(1+nder)] = myarg->get(i);
     142        4236 :     if( myarg->getRank()==0 ) {
     143        8640 :       for(unsigned j=0; j<nder; ++j) {
     144        4404 :         dval[i*(1+nder)+1+j] = myarg->getDerivative(j);
     145             :       }
     146           0 :     } else if( myarg->hasDerivatives() ) {
     147           0 :       for(unsigned j=0; j<nder; ++j) {
     148           0 :         dval[i*(1+nder)+1+j] = myarg->getGridDerivative( i, j );
     149             :       }
     150             :     }
     151             :   }
     152        4236 :   if(comm.Get_rank()==0) {
     153        4230 :     multi_sim_comm.Allgather(dval,datap);
     154             :   }
     155             :   // Only rank 0 of each replica takes part in the gather; share the result with
     156             :   // the other ranks of the replica, which would otherwise keep a zero-filled datap.
     157        4236 :   comm.Bcast(datap,0);
     158             : 
     159       29604 :   for(unsigned k=0; k<nreplicas; k++) {
     160       25368 :     Value* myout = getPntrToComponent(k);
     161       25368 :     if( myout->getNumberOfDerivatives()!=myarg->getNumberOfDerivatives() ) {
     162          80 :       myout->resizeDerivatives( myarg->getNumberOfDerivatives() );
     163             :     }
     164       25368 :     unsigned sstart=k*nvals*(1+nder);
     165       50736 :     for(unsigned i=0; i<nvals; ++i) {
     166       25368 :       myout->set( i, datap[sstart+i*(1+nder)] );
     167       25368 :       if( myarg->getRank()==0 ) {
     168       51072 :         for(unsigned j=0; j<nder; ++j) {
     169       25704 :           myout->setDerivative( j, dval[i*(1+nder)+1+j] );
     170             :         }
     171           0 :       } else if( myarg->hasDerivatives() ) {
     172             :         // the derivatives of a grid are part of the data gathered from replica k
     173           0 :         for(unsigned j=0; j<nder; ++j) {
     174           0 :           myout->addGridDerivatives( i, j, datap[sstart+i*(1+nder)+1+j] );
     175             :         }
     176             :       }
     177             :     }
     178             :   }
     179        4236 : }
     180             : 
     181        4236 : void GatherReplicas::apply() {
     182        4236 :   if( doNotCalculateDerivatives() ) {
     183        4236 :     return;
     184             :   }
     185           0 :   error("apply has not been implemented for GatherReplicas");
     186             : }
     187             : 
     188             : }
     189             : }