Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2017-2019 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             : #include "ReweightBase.h"
      23             : #include "core/ActionRegister.h"
      24             : #include "tools/Communicator.h"
      25             : 
      26             : //+PLUMEDOC REWEIGHTING REWEIGHT_WHAM
      27             : /*
      28             : 
      29             : \par Examples
      30             : 
      31             : */
      32             : //+ENDPLUMEDOC
      33             : 
      34             : namespace PLMD {
      35             : namespace bias {
      36             : 
      37          36 : class ReweightWham : public ReweightBase {
      38             : private:
      39             :   double thresh;
      40             :   unsigned nreplicas;
      41             :   unsigned maxiter;
      42             :   bool weightsCalculated;
      43             :   std::vector<double> stored_biases;
      44             :   std::vector<double> final_weights;
      45             : public:
      46             :   static void registerKeywords(Keywords&);
      47             :   explicit ReweightWham(const ActionOptions&ao);
      48          12 :   bool buildsWeightStore() const override { return true; }
      49             :   void calculateWeights( const unsigned& nframes ) override;
      50             :   void clearData() override;
      51             :   double getLogWeight() override;
      52             :   double getWeight( const unsigned& iweight ) const override;
      53             : };
      54             : 
      55        7856 : PLUMED_REGISTER_ACTION(ReweightWham,"REWEIGHT_WHAM")
      56             : 
      57          13 : void ReweightWham::registerKeywords(Keywords& keys ) {
      58          26 :   ReweightBase::registerKeywords( keys ); keys.remove("ARG");
      59          65 :   keys.add("compulsory","ARG","*.bias","the biases that must be taken into account when reweighting");
      60          65 :   keys.add("compulsory","MAXITER","1000","maximum number of iterations for WHAM algorithm");
      61          65 :   keys.add("compulsory","WHAMTOL","1e-10","threshold for convergence of WHAM algorithm");
      62          13 : }
      63             : 
      64          12 : ReweightWham::ReweightWham(const ActionOptions&ao):
      65             :   Action(ao),
      66             :   ReweightBase(ao),
      67          12 :   weightsCalculated(false)
      68             : {
      69          36 :   parse("MAXITER",maxiter); parse("WHAMTOL",thresh);
      70          12 :   if(comm.Get_rank()==0) nreplicas=multi_sim_comm.Get_size();
      71          12 :   comm.Bcast(nreplicas,0);
      72          12 : }
      73             : 
      74        4224 : double ReweightWham::getLogWeight() {
      75        4224 :   if( getStep()==0 ) return 1.0;  // This is here as first step is ignored in all analyses
      76        4212 :   weightsCalculated=false;
      77        8424 :   double bias=0.0; for(unsigned i=0; i<getNumberOfArguments(); ++i) bias+=getArgument(i);
      78             : 
      79        4212 :   std::vector<double> biases(nreplicas,0.0);
      80        4212 :   if(comm.Get_rank()==0) multi_sim_comm.Allgather(bias,biases);
      81        4212 :   comm.Bcast(biases,0);
      82       54756 :   for(unsigned i=0; i<biases.size(); i++) stored_biases.push_back( biases[i] );
      83             :   return 1.0;
      84             : }
      85             : 
      86           0 : void ReweightWham::clearData() {
      87           0 :   stored_biases.resize(0);
      88           0 : }
      89             : 
      90        2457 : double ReweightWham::getWeight( const unsigned& iweight ) const {
      91             :   plumed_dbg_assert( weightsCalculated && iweight<final_weights.size() );
      92        4914 :   return final_weights[iweight];
      93             : }
      94             : 
      95           7 : void ReweightWham::calculateWeights( const unsigned& nframes ) {
      96           7 :   if( stored_biases.size()!=nreplicas*nframes ) error("wrong number of weights stored");
      97             :   // Get the minimum value of the bias
      98          14 :   double minv = *min_element(std::begin(stored_biases), std::end(stored_biases));
      99             :   // Resize final weights array
     100           7 :   plumed_assert( stored_biases.size()%nreplicas==0 );
     101           7 :   final_weights.resize( stored_biases.size() / nreplicas, 1.0 );
     102             :   // Offset and exponential of the bias
     103           7 :   std::vector<double> expv( stored_biases.size() );
     104       29498 :   for(unsigned i=0; i<expv.size(); ++i) expv[i] = exp( (-stored_biases[i]+minv) / simtemp );
     105             :   // Initialize Z
     106           7 :   std::vector<double> Z( nreplicas, 1.0 ), oldZ( nreplicas );
     107             :   // Now the iterative loop to calculate the WHAM weights
     108        2674 :   for(unsigned iter=0; iter<maxiter; ++iter) {
     109             :     // Store Z
     110       34762 :     for(unsigned j=0; j<Z.size(); ++j) oldZ[j]=Z[j];
     111             :     // Recompute weights
     112             :     double norm=0;
     113     1879822 :     for(unsigned j=0; j<final_weights.size(); ++j) {
     114             :       double ew=0;
     115    23464350 :       for(unsigned k=0; k<Z.size(); ++k) ew += expv[j*Z.size()+k]  / Z[k];
     116     1877148 :       final_weights[j] = 1.0 / ew; norm += final_weights[j];
     117             :     }
     118             :     // Normalize weights
     119     1879822 :     for(unsigned j=0; j<final_weights.size(); ++j) final_weights[j] /= norm;
     120             :     // Recompute Z
     121       34762 :     for(unsigned j=0; j<Z.size(); ++j) Z[j] = 0.0;
     122     1879822 :     for(unsigned j=0; j<final_weights.size(); ++j) {
     123    23464350 :       for(unsigned k=0; k<Z.size(); ++k) Z[k] += final_weights[j]*expv[j*Z.size()+k];
     124             :     }
     125             :     // Normalize Z and compute change in Z
     126       34762 :     double change=0; norm=0; for(unsigned k=0; k<Z.size(); ++k) norm+=Z[k];
     127       34762 :     for(unsigned k=0; k<Z.size(); ++k) {
     128       48132 :       Z[k] /= norm; double d = std::log( Z[k] / oldZ[k] ); change += d*d;
     129             :     }
     130        2681 :     if( change<thresh ) { weightsCalculated=true; return; }
     131             :   }
     132           0 :   error("Too many iterations in WHAM" );
     133             : }
     134             : 
     135             : }
     136        5874 : }