Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2016-2018 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 "core/ActionWithValue.h"
      23             : #include "core/ActionPilot.h"
      24             : #include "core/ActionWithArguments.h"
      25             : #include "core/ActionRegister.h"
      26             : #include "tools/Matrix.h"
      27             : #include "PathProjectionCalculator.h"
      28             : 
      29             : //+PLUMEDOC ANALYSIS AVERAGE_PATH_DISPLACEMENT
      30             : /*
      31             : Accumulate the distances between the reference frames in the paths and the configurations visited
      32             : 
      33             : \par Examples
      34             : 
      35             : */
      36             : //+ENDPLUMEDOC
      37             : 
      38             : namespace PLMD {
      39             : namespace mapping {
      40             : 
      41             : class PathDisplacements : public ActionWithValue, public ActionPilot, public ActionWithArguments {
      42             : private:
      43             :   bool clearnextstep;
      44             :   unsigned clearstride;
      45             :   double fadefact;
      46             :   std::vector<double> wsum, displace_v;
      47             :   Matrix<double> displacements;
      48             :   PathProjectionCalculator path_projector;
      49             : public:
      50             :   static void registerKeywords( Keywords& keys );
      51             :   explicit PathDisplacements(const ActionOptions&);
      52             :   unsigned getNumberOfDerivatives();
      53         573 :   void clearDerivatives( const bool& force=false ) {}
      54         573 :   void calculate() {}
      55         573 :   void apply() {}
      56             :   void update();
      57             : };
      58             : 
      59             : PLUMED_REGISTER_ACTION(PathDisplacements,"AVERAGE_PATH_DISPLACEMENT")
      60             : 
      61           6 : void PathDisplacements::registerKeywords( Keywords& keys ) {
      62           6 :   Action::registerKeywords( keys ); ActionWithValue::registerKeywords( keys ); ActionPilot::registerKeywords( keys );
      63           6 :   ActionWithArguments::registerKeywords( keys ); PathProjectionCalculator::registerKeywords( keys );
      64          12 :   keys.add("compulsory","STRIDE","1","the frequency with which the average displacements should be collected and added to the average displacements");
      65          12 :   keys.add("compulsory","HALFLIFE","-1","the number of MD steps after which a previously measured path distance weighs only 50 percent in the average. This option may increase convergence by allowing to forget the memory of a bad initial guess path. The default is to set this to infinity");
      66          12 :   keys.add("compulsory","CLEAR","0","the frequency with which to clear all the accumulated data.  The default value "
      67             :            "of 0 implies that all the data will be used and that the grid will never be cleared");
      68          12 :   keys.setValueDescription("matrix","matrix containing the average displacement between the trajectory and each of the landmarks that makes up the path");
      69           6 : }
      70             : 
      71           2 : PathDisplacements::PathDisplacements(const ActionOptions& ao):
      72             :   Action(ao),
      73             :   ActionWithValue(ao),
      74             :   ActionPilot(ao),
      75             :   ActionWithArguments(ao),
      76           2 :   clearnextstep(false),
      77           2 :   path_projector(this)
      78             : {
      79             :   // Read in clear instructions
      80           2 :   parse("CLEAR",clearstride);
      81           2 :   if( clearstride>0 ) {
      82           2 :     if( clearstride%getStride()!=0 ) error("CLEAR parameter must be a multiple of STRIDE");
      83           2 :     log.printf("  clearing average every %u steps \n",clearstride);
      84             :   }
      85           2 :   double halflife; parse("HALFLIFE",halflife);
      86           2 :   log.printf("  weight of contribution to frame halves every %f steps \n",halflife);
      87           2 :   if( halflife<0 ) fadefact=1.0;
      88           0 :   else fadefact = exp( -0.693147180559945 / static_cast<double>(halflife) );
      89             :   // Now create the weights vector and displacements matrix
      90           2 :   unsigned nrows = getPntrToArgument(0)->getShape()[0];
      91           2 :   unsigned ncols = getPntrToArgument(0)->getShape()[1];
      92           2 :   wsum.resize( nrows ); displacements.resize( nrows, ncols );
      93          64 :   for(unsigned i=0; i<nrows; ++i) {
      94        1740 :     wsum[i]=0; for(unsigned j=0; j<ncols; ++j) displacements(i,j)=0;
      95             :   }
      96             :   // Add bibliography
      97           4 :   log<<"  Bibliography "<<plumed.cite("Diaz Leines and Ensing, Phys. Rev. Lett. 109, 020601 (2012)")<<"\n";
      98             :   // And create a value to hold the displacements
      99           2 :   std::vector<unsigned> shape(2); shape[0]=nrows; shape[1]=ncols;
     100           2 :   addValue( shape ); setNotPeriodic();
     101           2 :   getPntrToComponent(0)->buildDataStore();
     102           2 :   getPntrToComponent(0)->reshapeMatrixStore( shape[1] );
     103           2 : }
     104             : 
     105           0 : unsigned PathDisplacements::getNumberOfDerivatives() {
     106           0 :   return 0;
     107             : }
     108             : 
     109         573 : void PathDisplacements::update() {
     110         573 :   unsigned nrows = getPntrToArgument(0)->getShape()[0];
     111         573 :   unsigned ncols = getPntrToArgument(0)->getShape()[1];
     112             : 
     113         573 :   if( clearnextstep ) {
     114             :     unsigned k=0;
     115        1010 :     for(unsigned i=0; i<nrows; ++i) {
     116       38700 :       for(unsigned j=0; j<ncols; ++j) { displacements(i,j)=0; getPntrToComponent(0)->set(k,0); k++; }
     117             :     }
     118          24 :     clearnextstep=false;
     119             :   }
     120             : 
     121             :   unsigned k=0, iclose1=0, iclose2=0; double v1v1=0, v3v3=0;
     122       22417 :   for(unsigned i=0; i<nrows; ++i) {
     123             :     double dist = 0;
     124      799020 :     for(unsigned j=0; j<ncols; ++j) {
     125      777176 :       double tmp = getPntrToArgument(0)->get(k);
     126      777176 :       dist += tmp*tmp; k++;
     127             :     }
     128       21844 :     if( i==0 ) { v1v1 = dist; iclose1 = 0; }
     129       21271 :     else if( dist<v1v1 ) { v3v3=v1v1; v1v1=dist; iclose2=iclose1; iclose1=i; }
     130       10991 :     else if( i==1 ) { v3v3=dist; iclose2=1; }
     131       10991 :     else if( dist<v3v3 ) { v3v3=dist; iclose2=i; }
     132             :   }
     133             :   // And find third closest point
     134         573 :   int isign = iclose1 - iclose2;
     135             :   if( isign>1 ) isign=1; else if( isign<-1 ) isign=-1;
     136         573 :   int iclose3 = iclose1 + isign;
     137         573 :   unsigned ifrom=iclose1, ito=iclose3; if( iclose3<0 || iclose3>=nrows ) { ifrom=iclose2; ito=iclose1; }
     138             : 
     139             :   // Calculate the dot product of v1 with v2
     140         573 :   path_projector.getDisplaceVector( ifrom, ito, displace_v );
     141         573 :   double v2v2=0, v1v2=0; unsigned kclose1 = iclose1*ncols;
     142       19183 :   for(unsigned i=0; i<displace_v.size(); ++i) { v2v2 += displace_v[i]*displace_v[i]; v1v2 += displace_v[i]*getPntrToArgument(0)->get(kclose1+i); }
     143             : 
     144         573 :   double root = sqrt( v1v2*v1v2 - v2v2 * ( v1v1 - v3v3) );
     145         573 :   double dx = 0.5 * ( (root + v1v2) / v2v2 - 1.);
     146         573 :   double weight2 = -1.* dx; double weight1 = 1.0 + dx;
     147         573 :   if( weight1>1.0 ) {
     148             :     weight1=1.0; weight2=0.0;
     149         573 :   } else if( weight2>1.0 ) {
     150             :     weight1=0.0; weight2=1.0;
     151             :   }
     152             : 
     153             :   // Accumulate displacements for path
     154       19183 :   for(unsigned i=0; i<ncols; ++i) {
     155       18610 :     double displace = getPntrToArgument(0)->get(kclose1+i) - dx*displace_v[i];
     156       18610 :     displacements(iclose1,i) += weight1 * displace; displacements(iclose2,i) += weight2 * displace;
     157             :   }
     158             : 
     159             :   // Update weight accumulators
     160         573 :   wsum[iclose1] *= fadefact; wsum[iclose2] *= fadefact;
     161         573 :   wsum[iclose1] += weight1; wsum[iclose2] += weight2;
     162             : 
     163             :   // Update numbers in values
     164         573 :   if( wsum[iclose1] > epsilon ) {
     165       19183 :     for(unsigned i=0; i<ncols; ++i) getPntrToComponent(0)->set( kclose1+i, displacements(iclose1,i) / wsum[iclose1] );
     166             :   }
     167         573 :   if( wsum[iclose2] > epsilon ) {
     168         573 :     unsigned kclose2 = iclose2*ncols;
     169       19183 :     for(unsigned i=0; i<ncols; ++i) getPntrToComponent(0)->set( kclose2+i, displacements(iclose2,i) / wsum[iclose2] );
     170             :   }
     171             : 
     172             :   // Clear if required
     173         573 :   if( (getStep()>0 && clearstride>0 && getStep()%clearstride==0) ) clearnextstep=true;
     174         573 : }
     175             : 
     176             : }
     177             : }