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          63 :   keys.needsAction("DISPLACEMENT"); keys.needsAction("CUSTOM"); keys.needsAction("OUTER_PRODUCT");
      57          63 :   keys.needsAction("TRANSPOSE"); keys.needsAction("MATRIX_PRODUCT_DIAGONAL"); keys.needsAction("CONSTANT");
      58          63 :   keys.needsAction("MATRIX_VECTOR_PRODUCT"); keys.needsAction("MATRIX_PRODUCT"); keys.needsAction("COMBINE");
      59          21 : }
      60             : 
      61          12 : MahalanobisDistance::MahalanobisDistance( const ActionOptions& ao):
      62             :   Action(ao),
      63          12 :   ActionShortcut(ao)
      64             : {
      65          36 :   std::string arg1, arg2, metstr; parse("ARG1",arg1); parse("ARG2",arg2); parse("METRIC",metstr);
      66             :   // Check on input metric
      67          12 :   ActionWithValue* mav=plumed.getActionSet().selectWithLabel<ActionWithValue*>( metstr );
      68          12 :   if( !mav ) error("could not find action named " + metstr + " to use for metric");
      69          12 :   if( mav->copyOutput(0)->getRank()!=2 ) error("metric has incorrect rank");
      70             : 
      71          24 :   readInputLine( getShortcutLabel() + "_diff: DISPLACEMENT ARG1=" + arg1 + " ARG2=" + arg2 );
      72          24 :   readInputLine( getShortcutLabel() + "_diffT: TRANSPOSE ARG=" + getShortcutLabel() + "_diff");
      73          24 :   bool von_miss, squared; parseFlag("VON_MISSES",von_miss); parseFlag("SQUARED",squared);
      74          12 :   if( von_miss ) {
      75           7 :     unsigned nrows = mav->copyOutput(0)->getShape()[0];
      76           7 :     if( mav->copyOutput(0)->getShape()[1]!=nrows ) error("metric is not symmetric");
      77             :     // Create a matrix that can be used to compute the off diagonal elements
      78             :     std::string valstr, nrstr;
      79           7 :     Tools::convert( mav->copyOutput(0)->get(0), valstr ); Tools::convert( nrows, nrstr );
      80           7 :     std::string diagmet = getShortcutLabel() + "_diagmet: CONSTANT VALUES=" + valstr;
      81          14 :     std::string offdiagmet = getShortcutLabel() + "_offdiagmet: CONSTANT NROWS=" + nrstr + " NCOLS=" + nrstr + " VALUES=0";
      82          21 :     for(unsigned i=0; i<nrows; ++i) {
      83          42 :       for(unsigned j=0; j<nrows; ++j) {
      84          28 :         Tools::convert( mav->copyOutput(0)->get(i*nrows+j), valstr );
      85          42 :         if( i==j && i>0 ) { offdiagmet += ",0"; diagmet += "," + valstr; }
      86          35 :         else if( i!=j ) { offdiagmet += "," + valstr; }
      87             :       }
      88             :     }
      89           7 :     readInputLine( diagmet ); readInputLine( offdiagmet );
      90             :     // Compute distances scaled by periods
      91          14 :     ActionWithValue* av=plumed.getActionSet().selectWithLabel<ActionWithValue*>( getShortcutLabel() + "_diff" ); plumed_assert( av );
      92           7 :     if( !av->copyOutput(0)->isPeriodic() ) error("VON_MISSES only works with periodic variables");
      93           7 :     std::string min, max; av->copyOutput(0)->getDomain(min,max);
      94          14 :     readInputLine( getShortcutLabel() + "_scaled: CUSTOM ARG=" + getShortcutLabel() + "_diffT FUNC=2*pi*x/(" + max +"-" + min + ") PERIODIC=NO");
      95             :     // We start calculating off-diagonal elements by computing the sines of the scaled differences (this is a column vector)
      96          14 :     readInputLine( getShortcutLabel() + "_sinediffT: CUSTOM ARG=" + getShortcutLabel() + "_scaled FUNC=sin(x) PERIODIC=NO");
      97             :     // Transpose sines to get a row vector
      98          14 :     readInputLine( getShortcutLabel() + "_sinediff: TRANSPOSE ARG=" + getShortcutLabel() + "_sinediffT");
      99             :     // Compute the off diagonal elements
     100          14 :     readInputLine( getShortcutLabel() + "_matvec: MATRIX_PRODUCT ARG=" + getShortcutLabel() + "_offdiagmet," + getShortcutLabel() +"_sinediffT");
     101          14 :     readInputLine( getShortcutLabel() + "_offdiag: MATRIX_PRODUCT_DIAGONAL ARG=" + getShortcutLabel() + "_sinediff," + getShortcutLabel() +"_matvec");
     102             :     // Sort out the metric for the diagonal elements
     103           7 :     std::string metstr2 = getShortcutLabel() + "_diagmet";
     104             :     // If this is a matrix we need create a matrix to multiply by
     105           7 :     if( av->copyOutput(0)->getShape()[0]>1 ) {
     106             :       // Create some ones
     107          21 :       std::string ones=" VALUES=1"; for(unsigned i=1; i<av->copyOutput(0)->getShape()[0]; ++i ) ones += ",1";
     108          14 :       readInputLine( getShortcutLabel() + "_ones: CONSTANT " + ones );
     109             :       // Now do some multiplication to create a matrix that can be multiplied by our "inverse variance" vector
     110          14 :       readInputLine( getShortcutLabel() + "_" + metstr + ": OUTER_PRODUCT ARG=" + metstr2 + "," + getShortcutLabel() + "_ones");
     111          14 :       metstr2 = getShortcutLabel() + "_" + metstr;
     112             :     }
     113             :     // Compute the diagonal elements
     114          14 :     readInputLine( getShortcutLabel() + "_prod: CUSTOM ARG=" + getShortcutLabel() + "_scaled," + metstr2 + " FUNC=2*(1-cos(x))*y PERIODIC=NO");
     115           7 :     std::string ncstr; Tools::convert( nrows, ncstr ); Tools::convert( av->copyOutput(0)->getShape()[0], nrstr );
     116          42 :     std::string ones=" VALUES=1"; for(unsigned i=1; i<av->copyOutput(0)->getNumberOfValues(); ++i) ones += ",1";
     117          14 :     readInputLine( getShortcutLabel() + "_matones: CONSTANT NROWS=" + nrstr + " NCOLS=" + ncstr + ones );
     118          14 :     readInputLine( getShortcutLabel() + "_diag: MATRIX_PRODUCT_DIAGONAL ARG=" + getShortcutLabel() + "_matones," + getShortcutLabel() + "_prod");
     119             :     // Sum everything
     120           7 :     if( !squared ) readInputLine( getShortcutLabel() + "_2: COMBINE ARG=" + getShortcutLabel() + "_offdiag," + getShortcutLabel() + "_diag PERIODIC=NO");
     121          14 :     else readInputLine( getShortcutLabel() + ": COMBINE ARG=" + getShortcutLabel() + "_offdiag," + getShortcutLabel() + "_diag PERIODIC=NO");
     122             :   } else {
     123          10 :     ActionWithValue* av=plumed.getActionSet().selectWithLabel<ActionWithValue*>( getShortcutLabel() + "_diffT" ); plumed_assert( av && av->getNumberOfComponents()==1 );
     124           9 :     if( (av->copyOutput(0))->getRank()==1 ) readInputLine( getShortcutLabel() + "_matvec: MATRIX_VECTOR_PRODUCT ARG=" + metstr + "," + getShortcutLabel() +"_diffT");
     125           2 :     else readInputLine( getShortcutLabel() + "_matvec: MATRIX_PRODUCT ARG=" + metstr + "," + getShortcutLabel() +"_diffT");
     126           5 :     std::string olab = getShortcutLabel(); if( !squared ) olab += "_2";
     127          10 :     readInputLine( olab + ": MATRIX_PRODUCT_DIAGONAL ARG=" + getShortcutLabel() + "_diff," + getShortcutLabel() +"_matvec");
     128             :   }
     129          17 :   if( !squared ) readInputLine( getShortcutLabel() + ": CUSTOM ARG=" + getShortcutLabel() + "_2 FUNC=sqrt(x) PERIODIC=NO");
     130          12 : }
     131             : 
     132             : }
     133             : }