Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2017-2023 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             : Calculate the weights for configurations using the weighted histogram analysis method.
      29             : 
      30             : Suppose that you have run multiple \f$N\f$ trajectories each of which was computed by integrating a different biased Hamiltonian. We can calculate the probability of observing
      31             : the set of configurations during the \f$N\f$ trajectories that we ran using the product of multinomial distributions shown below:
      32             : \f[
      33             : P( \vec{T} ) \propto \prod_{j=1}^M \prod_{k=1}^N (c_k w_{kj} p_j)^{t_{kj}}
      34             : \label{eqn:wham1}
      35             : \f]
      36             : In this expression the second product runs over the biases that were used when calculating the \f$N\f$ trajectories.  The first product then runs over the
      37             : \f$M\f$ bins in our histogram.  The \f$p_j\f$ variable that is inside this product is the quantity we wish to extract; namely, the unbiased probability of
      38             : having a set of CV values that lie within the range for the \f$j\f$th bin.
      39             : 
      40             : The quantity that we can easily extract from our simulations, \f$t_{kj}\f$, however, measures the number of frames from trajectory \f$k\f$ that are inside the \f$j\f$th bin.
      41             : To interpret this quantity we must consider the bias that acts on each of the replicas so the \f$w_{kj}\f$ term is introduced.  This quantity is calculated as:
      42             : \f[
      43             : w_{kj} =
      44             : \f]
      45             : and is essentially the factor that we have to multiply the unbiased probability of being in the bin by in order to get the probability that we would be inside this same bin in
      46             : the \f$k\f$th of our biased simulations.  Obviously, these \f$w_{kj}\f$ values depend on the value that the CVs take and also on the particular trajectory that we are investigating
      47             : all of which, remember, have different simulation biases.  Finally, \f$c_k\f$ is a free parameter that ensures that, for each \f$k\f$, the biased probability is normalized.
      48             : 
      49             : We can use the equation for the probability that was given above to find a set of values for \f$p_j\f$ that maximizes the likelihood of observing the trajectory.
      50             : This constrained optimization must be performed using a set of Lagrange multipliers, \f$\lambda_k\f$, that ensure that each of the biased probability distributions
      51             : are normalized, that is \f$\sum_j c_kw_{kj}p_j=1\f$.  Furthermore, as the problem is made easier if the quantity in the equation above is replaced by its logarithm
      52             : we actually chose to minimize
      53             : \f[
      54             : \mathcal{L}= \sum_{j=1}^M \sum_{k=1}^N t_{kj} \ln c_k  w_{kj} p_j + \sum_k\lambda_k \left( \sum_{j=1}^N c_k w_{kj} p_j - 1 \right)
      55             : \f]
      56             : After some manipulations the following (WHAM) equations emerge:
      57             : \f[
      58             : \begin{aligned}
      59             : p_j & \propto \frac{\sum_{k=1}^N t_{kj}}{\sum_k c_k w_{kj}} \\
      60             : c_k & =\frac{1}{\sum_{j=1}^M w_{kj} p_j}
      61             : \end{aligned}
      62             : \f]
      63             : which can be solved by computing the \f$p_j\f$ values using the first of the two equations above with an initial guess for the \f$c_k\f$ values and by then refining
      64             : these \f$p_j\f$ values using the \f$c_k\f$ values that are obtained by inserting the \f$p_j\f$ values obtained into the second of the two equations above.
      65             : 
      66             : Notice that only \f$\sum_k t_{kj}\f$, which is the total number of configurations from all the replicas that enter the \f$j\f$th bin, enters the WHAM equations above.
      67             : There is thus no need to record which replica generated each of the frames.  One can thus simply gather the trajectories from all the replicas together at the outset.
      68             : This observation is important as it is the basis of the binless formulation of WHAM that is implemented within PLUMED.
      69             : 
      70             : \par Examples
      71             : 
      72             : */
      73             : //+ENDPLUMEDOC
      74             : 
      75             : namespace PLMD {
      76             : namespace bias {
      77             : 
      78             : class ReweightWham : public ReweightBase {
      79             : private:
      80             :   double thresh;
      81             :   unsigned nreplicas;
      82             :   unsigned maxiter;
      83             :   bool weightsCalculated;
      84             :   std::vector<double> stored_biases;
      85             :   std::vector<double> final_weights;
      86             : public:
      87             :   static void registerKeywords(Keywords&);
      88             :   explicit ReweightWham(const ActionOptions&ao);
      89          12 :   bool buildsWeightStore() const override { return true; }
      90             :   void calculateWeights( const unsigned& nframes ) override;
      91             :   void clearData() override;
      92             :   double getLogWeight() override;
      93             :   double getWeight( const unsigned& iweight ) const override;
      94             : };
      95             : 
      96       10443 : PLUMED_REGISTER_ACTION(ReweightWham,"REWEIGHT_WHAM")
      97             : 
      98          13 : void ReweightWham::registerKeywords(Keywords& keys ) {
      99          13 :   ReweightBase::registerKeywords( keys ); keys.remove("ARG");
     100          26 :   keys.add("compulsory","ARG","*.bias","the biases that must be taken into account when reweighting");
     101          26 :   keys.add("compulsory","MAXITER","1000","maximum number of iterations for WHAM algorithm");
     102          26 :   keys.add("compulsory","WHAMTOL","1e-10","threshold for convergence of WHAM algorithm");
     103          13 : }
     104             : 
     105          12 : ReweightWham::ReweightWham(const ActionOptions&ao):
     106             :   Action(ao),
     107             :   ReweightBase(ao),
     108          12 :   weightsCalculated(false)
     109             : {
     110          24 :   parse("MAXITER",maxiter); parse("WHAMTOL",thresh);
     111          12 :   if(comm.Get_rank()==0) nreplicas=multi_sim_comm.Get_size();
     112          12 :   comm.Bcast(nreplicas,0);
     113          12 : }
     114             : 
     115        4224 : double ReweightWham::getLogWeight() {
     116        4224 :   if( getStep()==0 ) return 1.0;  // This is here as first step is ignored in all analyses
     117        4212 :   weightsCalculated=false;
     118        8424 :   double bias=0.0; for(unsigned i=0; i<getNumberOfArguments(); ++i) bias+=getArgument(i);
     119             : 
     120        4212 :   std::vector<double> biases(nreplicas,0.0);
     121        4212 :   if(comm.Get_rank()==0) multi_sim_comm.Allgather(bias,biases);
     122        4212 :   comm.Bcast(biases,0);
     123       29484 :   for(unsigned i=0; i<biases.size(); i++) stored_biases.push_back( biases[i] );
     124             :   return 1.0;
     125             : }
     126             : 
     127           0 : void ReweightWham::clearData() {
     128           0 :   stored_biases.resize(0);
     129           0 : }
     130             : 
     131        2457 : double ReweightWham::getWeight( const unsigned& iweight ) const {
     132             :   plumed_dbg_assert( weightsCalculated && iweight<final_weights.size() );
     133        2457 :   return final_weights[iweight];
     134             : }
     135             : 
     136           7 : void ReweightWham::calculateWeights( const unsigned& nframes ) {
     137           7 :   if( stored_biases.size()!=nreplicas*nframes ) error("wrong number of weights stored");
     138             :   // Get the minimum value of the bias
     139           7 :   double minv = *min_element(std::begin(stored_biases), std::end(stored_biases));
     140             :   // Resize final weights array
     141           7 :   plumed_assert( stored_biases.size()%nreplicas==0 );
     142           7 :   final_weights.resize( stored_biases.size() / nreplicas, 1.0 );
     143             :   // Offset and exponential of the bias
     144           7 :   std::vector<double> expv( stored_biases.size() );
     145       14749 :   for(unsigned i=0; i<expv.size(); ++i) expv[i] = std::exp( (-stored_biases[i]+minv) / simtemp );
     146             :   // Initialize Z
     147           7 :   std::vector<double> Z( nreplicas, 1.0 ), oldZ( nreplicas );
     148             :   // Now the iterative loop to calculate the WHAM weights
     149        2674 :   for(unsigned iter=0; iter<maxiter; ++iter) {
     150             :     // Store Z
     151       18718 :     for(unsigned j=0; j<Z.size(); ++j) oldZ[j]=Z[j];
     152             :     // Recompute weights
     153             :     double norm=0;
     154      941248 :     for(unsigned j=0; j<final_weights.size(); ++j) {
     155             :       double ew=0;
     156     6570018 :       for(unsigned k=0; k<Z.size(); ++k) ew += expv[j*Z.size()+k]  / Z[k];
     157      938574 :       final_weights[j] = 1.0 / ew; norm += final_weights[j];
     158             :     }
     159             :     // Normalize weights
     160      941248 :     for(unsigned j=0; j<final_weights.size(); ++j) final_weights[j] /= norm;
     161             :     // Recompute Z
     162       18718 :     for(unsigned j=0; j<Z.size(); ++j) Z[j] = 0.0;
     163      941248 :     for(unsigned j=0; j<final_weights.size(); ++j) {
     164     6570018 :       for(unsigned k=0; k<Z.size(); ++k) Z[k] += final_weights[j]*expv[j*Z.size()+k];
     165             :     }
     166             :     // Normalize Z and compute change in Z
     167       18718 :     double change=0; norm=0; for(unsigned k=0; k<Z.size(); ++k) norm+=Z[k];
     168       18718 :     for(unsigned k=0; k<Z.size(); ++k) {
     169       16044 :       Z[k] /= norm; double d = std::log( Z[k] / oldZ[k] ); change += d*d;
     170             :     }
     171        2681 :     if( change<thresh ) { weightsCalculated=true; return; }
     172             :   }
     173           0 :   error("Too many iterations in WHAM" );
     174             : }
     175             : 
     176             : }
     177             : }