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/ActionRegister.h"
      23             : #include "core/PlumedMain.h"
      24             : #include "core/ActionSet.h"
      25             : #include "core/ActionShortcut.h"
      26             : #include "core/ActionWithValue.h"
      27             : 
      28             : //+PLUMEDOC FUNCTION MAHALANOBIS_DISTANCE
      29             : /*
      30             : Calculate the mahalanobis distance between two points in CV space
      31             : 
      32             : \par Examples
      33             : 
      34             : */
      35             : //+ENDPLUMEDOC
      36             : 
      37             : namespace PLMD {
      38             : namespace refdist {
      39             : 
      40             : class MahalanobisDistance : public ActionShortcut {
      41             : public:
      42             :   static void registerKeywords( Keywords& keys );
      43             :   explicit MahalanobisDistance(const ActionOptions&ao);
      44             : };
      45             : 
      46             : PLUMED_REGISTER_ACTION(MahalanobisDistance,"MAHALANOBIS_DISTANCE")
      47             : 
      48          21 : void MahalanobisDistance::registerKeywords( Keywords& keys ) {
      49          21 :   ActionShortcut::registerKeywords(keys);
      50          42 :   keys.add("compulsory","ARG1","The point that we are calculating the distance from");
      51          42 :   keys.add("compulsory","ARG2","The point that we are calculating the distance to");
      52          42 :   keys.add("compulsory","METRIC","The inverse covariance matrix that should be used when calculating the distance");
      53          42 :   keys.addFlag("SQUARED",false,"The squared distance should be calculated");
      54          42 :   keys.addFlag("VON_MISSES",false,"Compute the mahalanobis distance in a way that is more sympathetic to the periodic boundary conditions");
      55          21 :   keys.setValueDescription("the Mahalanobis distances between the input vectors");
      56          21 :   keys.needsAction("DISPLACEMENT");
      57          21 :   keys.needsAction("CUSTOM");
      58          21 :   keys.needsAction("OUTER_PRODUCT");
      59          21 :   keys.needsAction("TRANSPOSE");
      60          21 :   keys.needsAction("MATRIX_PRODUCT_DIAGONAL");
      61          21 :   keys.needsAction("CONSTANT");
      62          21 :   keys.needsAction("MATRIX_VECTOR_PRODUCT");
      63          21 :   keys.needsAction("MATRIX_PRODUCT");
      64          21 :   keys.needsAction("COMBINE");
      65          21 : }
      66             : 
      67          12 : MahalanobisDistance::MahalanobisDistance( const ActionOptions& ao):
      68             :   Action(ao),
      69          12 :   ActionShortcut(ao) {
      70             :   std::string arg1, arg2, metstr;
      71          12 :   parse("ARG1",arg1);
      72          12 :   parse("ARG2",arg2);
      73          12 :   parse("METRIC",metstr);
      74             :   // Check on input metric
      75          12 :   ActionWithValue* mav=plumed.getActionSet().selectWithLabel<ActionWithValue*>( metstr );
      76          12 :   if( !mav ) {
      77           0 :     error("could not find action named " + metstr + " to use for metric");
      78             :   }
      79          12 :   if( mav->copyOutput(0)->getRank()!=2 ) {
      80           0 :     error("metric has incorrect rank");
      81             :   }
      82             : 
      83          24 :   readInputLine( getShortcutLabel() + "_diff: DISPLACEMENT ARG1=" + arg1 + " ARG2=" + arg2 );
      84          24 :   readInputLine( getShortcutLabel() + "_diffT: TRANSPOSE ARG=" + getShortcutLabel() + "_diff");
      85             :   bool von_miss, squared;
      86          12 :   parseFlag("VON_MISSES",von_miss);
      87          12 :   parseFlag("SQUARED",squared);
      88          12 :   if( von_miss ) {
      89           7 :     unsigned nrows = mav->copyOutput(0)->getShape()[0];
      90           7 :     if( mav->copyOutput(0)->getShape()[1]!=nrows ) {
      91           0 :       error("metric is not symmetric");
      92             :     }
      93             :     // Create a matrix that can be used to compute the off diagonal elements
      94             :     std::string valstr, nrstr;
      95           7 :     Tools::convert( mav->copyOutput(0)->get(0), valstr );
      96           7 :     Tools::convert( nrows, nrstr );
      97           7 :     std::string diagmet = getShortcutLabel() + "_diagmet: CONSTANT VALUES=" + valstr;
      98          14 :     std::string offdiagmet = getShortcutLabel() + "_offdiagmet: CONSTANT NROWS=" + nrstr + " NCOLS=" + nrstr + " VALUES=0";
      99          21 :     for(unsigned i=0; i<nrows; ++i) {
     100          42 :       for(unsigned j=0; j<nrows; ++j) {
     101          28 :         Tools::convert( mav->copyOutput(0)->get(i*nrows+j), valstr );
     102          28 :         if( i==j && i>0 ) {
     103             :           offdiagmet += ",0";
     104          14 :           diagmet += "," + valstr;
     105          21 :         } else if( i!=j ) {
     106          28 :           offdiagmet += "," + valstr;
     107             :         }
     108             :       }
     109             :     }
     110           7 :     readInputLine( diagmet );
     111           7 :     readInputLine( offdiagmet );
     112             :     // Compute distances scaled by periods
     113           7 :     ActionWithValue* av=plumed.getActionSet().selectWithLabel<ActionWithValue*>( getShortcutLabel() + "_diff" );
     114           7 :     plumed_assert( av );
     115           7 :     if( !av->copyOutput(0)->isPeriodic() ) {
     116           0 :       error("VON_MISSES only works with periodic variables");
     117             :     }
     118             :     std::string min, max;
     119           7 :     av->copyOutput(0)->getDomain(min,max);
     120          14 :     readInputLine( getShortcutLabel() + "_scaled: CUSTOM ARG=" + getShortcutLabel() + "_diffT FUNC=2*pi*x/(" + max +"-" + min + ") PERIODIC=NO");
     121             :     // We start calculating off-diagonal elements by computing the sines of the scaled differences (this is a column vector)
     122          14 :     readInputLine( getShortcutLabel() + "_sinediffT: CUSTOM ARG=" + getShortcutLabel() + "_scaled FUNC=sin(x) PERIODIC=NO");
     123             :     // Transpose sines to get a row vector
     124          14 :     readInputLine( getShortcutLabel() + "_sinediff: TRANSPOSE ARG=" + getShortcutLabel() + "_sinediffT");
     125             :     // Compute the off diagonal elements
     126          14 :     readInputLine( getShortcutLabel() + "_matvec: MATRIX_PRODUCT ARG=" + getShortcutLabel() + "_offdiagmet," + getShortcutLabel() +"_sinediffT");
     127          14 :     readInputLine( getShortcutLabel() + "_offdiag: MATRIX_PRODUCT_DIAGONAL ARG=" + getShortcutLabel() + "_sinediff," + getShortcutLabel() +"_matvec");
     128             :     // Sort out the metric for the diagonal elements
     129           7 :     std::string metstr2 = getShortcutLabel() + "_diagmet";
     130             :     // If this is a matrix we need create a matrix to multiply by
     131           7 :     if( av->copyOutput(0)->getShape()[0]>1 ) {
     132             :       // Create some ones
     133           7 :       std::string ones=" VALUES=1";
     134          21 :       for(unsigned i=1; i<av->copyOutput(0)->getShape()[0]; ++i ) {
     135             :         ones += ",1";
     136             :       }
     137          14 :       readInputLine( getShortcutLabel() + "_ones: CONSTANT " + ones );
     138             :       // Now do some multiplication to create a matrix that can be multiplied by our "inverse variance" vector
     139          14 :       readInputLine( getShortcutLabel() + "_" + metstr + ": OUTER_PRODUCT ARG=" + metstr2 + "," + getShortcutLabel() + "_ones");
     140          14 :       metstr2 = getShortcutLabel() + "_" + metstr;
     141             :     }
     142             :     // Compute the diagonal elements
     143          14 :     readInputLine( getShortcutLabel() + "_prod: CUSTOM ARG=" + getShortcutLabel() + "_scaled," + metstr2 + " FUNC=2*(1-cos(x))*y PERIODIC=NO");
     144             :     std::string ncstr;
     145           7 :     Tools::convert( nrows, ncstr );
     146           7 :     Tools::convert( av->copyOutput(0)->getShape()[0], nrstr );
     147           7 :     std::string ones=" VALUES=1";
     148          42 :     for(unsigned i=1; i<av->copyOutput(0)->getNumberOfValues(); ++i) {
     149             :       ones += ",1";
     150             :     }
     151          14 :     readInputLine( getShortcutLabel() + "_matones: CONSTANT NROWS=" + nrstr + " NCOLS=" + ncstr + ones );
     152          14 :     readInputLine( getShortcutLabel() + "_diag: MATRIX_PRODUCT_DIAGONAL ARG=" + getShortcutLabel() + "_matones," + getShortcutLabel() + "_prod");
     153             :     // Sum everything
     154           7 :     if( !squared ) {
     155           0 :       readInputLine( getShortcutLabel() + "_2: COMBINE ARG=" + getShortcutLabel() + "_offdiag," + getShortcutLabel() + "_diag PERIODIC=NO");
     156             :     } else {
     157          14 :       readInputLine( getShortcutLabel() + ": COMBINE ARG=" + getShortcutLabel() + "_offdiag," + getShortcutLabel() + "_diag PERIODIC=NO");
     158             :     }
     159             :   } else {
     160           5 :     ActionWithValue* av=plumed.getActionSet().selectWithLabel<ActionWithValue*>( getShortcutLabel() + "_diffT" );
     161           5 :     plumed_assert( av && av->getNumberOfComponents()==1 );
     162           5 :     if( (av->copyOutput(0))->getRank()==1 ) {
     163           8 :       readInputLine( getShortcutLabel() + "_matvec: MATRIX_VECTOR_PRODUCT ARG=" + metstr + "," + getShortcutLabel() +"_diffT");
     164             :     } else {
     165           2 :       readInputLine( getShortcutLabel() + "_matvec: MATRIX_PRODUCT ARG=" + metstr + "," + getShortcutLabel() +"_diffT");
     166             :     }
     167           5 :     std::string olab = getShortcutLabel();
     168           5 :     if( !squared ) {
     169             :       olab += "_2";
     170             :     }
     171          10 :     readInputLine( olab + ": MATRIX_PRODUCT_DIAGONAL ARG=" + getShortcutLabel() + "_diff," + getShortcutLabel() +"_matvec");
     172             :   }
     173          12 :   if( !squared ) {
     174          10 :     readInputLine( getShortcutLabel() + ": CUSTOM ARG=" + getShortcutLabel() + "_2 FUNC=sqrt(x) PERIODIC=NO");
     175             :   }
     176          12 : }
     177             : 
     178             : }
     179             : }