Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2015-2019 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 "PammObject.h"
      23             : #include "tools/IFile.h"
      24             : #include <memory>
      25             : 
      26             : namespace PLMD {
      27             : namespace pamm {
      28             : 
      29           6 : PammObject::PammObject():
      30           6 :   regulariser(0.001)
      31             : {
      32           6 : }
      33             : 
      34      274915 : PammObject::PammObject( const PammObject& in ):
      35             :   regulariser(in.regulariser),
      36             :   pbc(in.pbc),
      37             :   min(in.min),
      38      274915 :   max(in.max)
      39             : {
      40     6579785 :   for(unsigned i=0; i<in.kernels.size(); ++i) kernels.emplace_back( new KernelFunctions( in.kernels[i].get() ) );
      41      274918 : }
      42             : 
      43           6 : void PammObject::setup( const std::string& filename, const double& reg, const std::vector<std::string>& valnames,
      44             :                         const std::vector<bool>& pbcin, const std::vector<std::string>& imin, const std::vector<std::string>& imax,
      45             :                         std::string& errorstr ) {
      46           6 :   IFile ifile; regulariser=reg;
      47           6 :   if( !ifile.FileExist(filename) ) {
      48           0 :     errorstr = "could not find file named " + filename;
      49           6 :     return;
      50             :   }
      51             : 
      52           6 :   std::vector<std::unique_ptr<Value>> pos;
      53           6 :   pbc.resize( valnames.size() );
      54           6 :   min.resize( valnames.size() );
      55           6 :   max.resize( valnames.size() );
      56          36 :   for(unsigned i=0; i<valnames.size(); ++i) {
      57             :     pbc[i]=pbcin[i]; min[i]=imin[i]; max[i]=imax[i];
      58          15 :     pos.emplace_back( new Value() );
      59          28 :     if( !pbc[i] ) pos[i]->setNotPeriodic();
      60           2 :     else pos[i]->setDomain( min[i], max[i] );
      61             :   }
      62             : 
      63           6 :   ifile.open(filename); ifile.allowIgnoredFields(); kernels.resize(0);
      64             :   for(unsigned k=0;; ++k) {
      65          59 :     std::unique_ptr<KernelFunctions> kk = KernelFunctions::read( &ifile, false, valnames );
      66          59 :     if( !kk ) break ;
      67         159 :     kk->normalize( Tools::unique2raw( pos ) );
      68          53 :     kernels.emplace_back( std::move(kk) );
      69          53 :     ifile.scanField();
      70          53 :   }
      71          12 :   ifile.close();
      72             : }
      73             : 
      74      784471 : void PammObject::evaluate( const std::vector<double>& invar, std::vector<double>& outvals, std::vector<std::vector<double> >& der ) const {
      75             :   std::vector<std::unique_ptr<Value>> pos;
      76     6290688 :   for(unsigned i=0; i<pbc.size(); ++i) {
      77     2358300 :     pos.emplace_back( new Value() );
      78     4721684 :     if( !pbc[i] ) pos[i]->setNotPeriodic();
      79          36 :     else pos[i]->setDomain( min[i], max[i] );
      80             :     // And set the value
      81     2360905 :     pos[i]->set( invar[i] );
      82             :   }
      83             : 
      84             :   // convert pointers once
      85      787044 :   auto pos_ptr=Tools::unique2raw(pos);
      86             : 
      87             :   // Evaluate the set of kernels
      88     1574086 :   double denom=regulariser; std::vector<double> dderiv( der[0].size(), 0 );
      89    18884696 :   for(unsigned i=0; i<kernels.size(); ++i) {
      90    17312466 :     outvals[i]=kernels[i]->evaluate( pos_ptr, der[i] ); denom+=outvals[i];
      91    95210321 :     for(unsigned j=0; j<der[i].size(); ++j) dderiv[j] += der[i][j];
      92             :   }
      93             :   // Evaluate the set of derivatives
      94    18041249 :   for(unsigned i=0; i<kernels.size(); ++i) {
      95     8627142 :     outvals[i]/=denom;
      96   120174868 :     for(unsigned j=0; j<der[i].size(); ++j) der[i][j]=der[i][j]/denom - outvals[i]*dderiv[j]/denom;
      97      786852 :   }
      98             : 
      99      786902 : }
     100             : 
     101             : 
     102             : }
     103             : }