Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2012-2020 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 "PathMSDBase.h"
      23             : #include "core/PlumedMain.h"
      24             : 
      25             : using namespace std;
      26             : 
      27             : namespace PLMD {
      28             : namespace colvar {
      29             : 
      30             : //+PLUMEDOC COLVAR PROPERTYMAP
      31             : /*
      32             : Calculate generic property maps.
      33             : 
      34             : This Colvar calculates the property maps according to the work of Spiwok \cite Spiwok:2011ce.
      35             : 
      36             : 
      37             : Basically it calculates
      38             : \f{eqnarray*}{
      39             : X=\frac{\sum_i X_i*\exp(-\lambda D_i(x))}{\sum_i  \exp(-\lambda D_i(x))} \\
      40             : Y=\frac{\sum_i Y_i*\exp(-\lambda D_i(x))}{\sum_i  \exp(-\lambda D_i(x))} \\
      41             : \cdots\\
      42             : zzz=-\frac{1}{\lambda}\log(\sum_i  \exp(-\lambda D_i(x)))
      43             : \f}
      44             : 
      45             : where the parameters \f$X_i\f$  and  \f$Y_i\f$ are provided in the input pdb (allv.pdb in this case) and
      46             :  \f$D_i(x)\f$  is the mean squared displacement after optimal alignment calculated on the pdb frames you input (see Kearsley).
      47             : 
      48             : 
      49             : When running with periodic boundary conditions, the atoms should be
      50             : in the proper periodic image. This is done automatically since PLUMED 2.5,
      51             : by considering the ordered list of atoms and rebuilding molecules using a procedure
      52             : that is equivalent to that done in \ref WHOLEMOLECULES . Notice that
      53             : rebuilding is local to this action. This is different from \ref WHOLEMOLECULES
      54             : which actually modifies the coordinates stored in PLUMED.
      55             : 
      56             : In case you want to recover the old behavior you should use the NOPBC flag.
      57             : In that case you need to take care that atoms are in the correct
      58             : periodic image.
      59             : 
      60             : \par Examples
      61             : 
      62             : \plumedfile
      63             : p3: PROPERTYMAP REFERENCE=allv.pdb PROPERTY=X,Y LAMBDA=69087 NEIGH_SIZE=8 NEIGH_STRIDE=4
      64             : PRINT ARG=p3.X,p3.Y,p3.zzz STRIDE=1 FILE=colvar FMT=%8.4f
      65             : \endplumedfile
      66             : 
      67             : note that NEIGH_STRIDE=4 NEIGH_SIZE=8 control the neighbor list parameter (optional but
      68             : recommended for performance) and states that the neighbor list will be calculated every 4
      69             : steps and consider only the closest 8 member to the actual md snapshots.
      70             : 
      71             : In this case the input line instructs plumed to look for two properties X and Y with attached values in the REMARK
      72             : line of the reference pdb (Note: No spaces from X and = and 1 !!!!).
      73             : e.g.
      74             : 
      75             : \auxfile{allv.pdb}
      76             : REMARK X=1 Y=2
      77             : ATOM      1  CL  ALA     1      -3.171   0.295   2.045  1.00  1.00
      78             : ATOM      5  CLP ALA     1      -1.819  -0.143   1.679  1.00  1.00
      79             : END
      80             : REMARK X=2 Y=3
      81             : ATOM      1  CL  ALA     1      -3.175   0.365   2.024  1.00  1.00
      82             : ATOM      5  CLP ALA     1      -1.814  -0.106   1.685  1.00  1.00
      83             : END
      84             : \endauxfile
      85             : 
      86             : \note
      87             : The implementation of this collective variable and of \ref PATHMSD
      88             : is shared, as well as most input options.
      89             : 
      90             : */
      91             : //+ENDPLUMEDOC
      92             : 
      93          22 : class PropertyMap : public PathMSDBase {
      94             : public:
      95             :   explicit PropertyMap(const ActionOptions&);
      96             :   static void registerKeywords(Keywords& keys);
      97             : };
      98             : 
      99        7378 : PLUMED_REGISTER_ACTION(PropertyMap,"PROPERTYMAP")
     100             : 
     101          12 : void PropertyMap::registerKeywords(Keywords& keys) {
     102          12 :   PathMSDBase::registerKeywords(keys);
     103          48 :   keys.add("compulsory","PROPERTY","the property to be used in the indexing: this goes in the REMARK field of the reference");
     104          12 :   ActionWithValue::useCustomisableComponents(keys);
     105          48 :   keys.addOutputComponent("zzz","default","the minimum distance from the reference points");
     106          12 : }
     107             : 
     108          11 : PropertyMap::PropertyMap(const ActionOptions&ao):
     109             :   Action(ao),
     110          11 :   PathMSDBase(ao)
     111             : {
     112             :   // this is the only additional keyword needed
     113          22 :   parseVector("PROPERTY",labels);
     114          11 :   checkRead();
     115          11 :   log<<"  Bibliography "
     116          33 :      <<plumed.cite("Spiwok V, Kralova B  J. Chem. Phys. 135,  224504 (2011)")
     117          22 :      <<"\n";
     118          11 :   if(labels.size()==0) {
     119             :     char buf[500];
     120             :     sprintf(buf,"Need to specify PROPERTY with this action\n");
     121           0 :     plumed_merror(buf);
     122             :   } else {
     123          88 :     for(unsigned i=0; i<labels.size(); i++) {
     124          44 :       log<<" found custom propety to be found in the REMARK line: "<<labels[i].c_str()<<"\n";
     125          66 :       addComponentWithDerivatives(labels[i]); componentIsNotPeriodic(labels[i]);
     126             :     }
     127             :     // add distance anyhow
     128          33 :     addComponentWithDerivatives("zzz"); componentIsNotPeriodic("zzz");
     129             :     //reparse the REMARK field and pick the index
     130        1408 :     for(unsigned i=0; i<pdbv.size(); i++) {
     131             :       // now look for X=1.34555 Y=5.6677
     132             :       vector<double> labelvals;
     133        3696 :       for(unsigned j=0; j<labels.size(); j++) {
     134             :         double val;
     135         924 :         if( pdbv[i].getArgumentValue(labels[j],val) ) {labelvals.push_back(val);}
     136             :         else {
     137             :           char buf[500];
     138             :           sprintf(buf,"PROPERTY LABEL \" %s \" NOT FOUND IN REMARK FOR FRAME %u \n",labels[j].c_str(),i);
     139           0 :           plumed_merror(buf);
     140             :         };
     141             :       }
     142         462 :       indexvec.push_back(labelvals);
     143             :     }
     144             :   }
     145          11 :   requestAtoms(pdbv[0].getAtomNumbers());
     146             : 
     147          11 : }
     148             : 
     149             : }
     150        5517 : }
     151             : 
     152             :