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/ActionShortcut.h"
      24             : #include "core/PlumedMain.h"
      25             : #include "core/ActionSet.h"
      26             : #include "core/ActionWithValue.h"
      27             : 
      28             : //+PLUMEDOC MCOLVAR EUCLIDEAN_DISTANCE
      29             : /*
      30             : Calculate the euclidean distance between two vectors of arguments
      31             : 
      32             : \par Examples
      33             : 
      34             : */
      35             : //+ENDPLUMEDOC
      36             : 
      37             : namespace PLMD {
      38             : namespace refdist {
      39             : 
      40             : class EuclideanDistance : public ActionShortcut {
      41             : public:
      42             :   static void registerKeywords( Keywords& keys );
      43             :   explicit EuclideanDistance(const ActionOptions&ao);
      44             : };
      45             : 
      46             : PLUMED_REGISTER_ACTION(EuclideanDistance,"EUCLIDEAN_DISTANCE")
      47             : 
      48          35 : void EuclideanDistance::registerKeywords( Keywords& keys ) {
      49          35 :   ActionShortcut::registerKeywords(keys);
      50          70 :   keys.add("compulsory","ARG1","The poin that we are calculating the distance from");
      51          70 :   keys.add("compulsory","ARG2","The point that we are calculating the distance to");
      52          70 :   keys.addFlag("SQUARED",false,"The squared distance should be calculated");
      53          35 :   keys.setValueDescription("the euclidean distances between the input vectors");
      54          35 :   keys.needsAction("DISPLACEMENT");
      55          35 :   keys.needsAction("CUSTOM");
      56          35 :   keys.needsAction("TRANSPOSE");
      57          35 :   keys.needsAction("MATRIX_PRODUCT_DIAGONAL");
      58          35 : }
      59             : 
      60          28 : EuclideanDistance::EuclideanDistance( const ActionOptions& ao):
      61             :   Action(ao),
      62          28 :   ActionShortcut(ao) {
      63             :   std::string arg1, arg2;
      64          28 :   parse("ARG1",arg1);
      65          28 :   parse("ARG2",arg2);
      66             :   // Vectors are in rows here
      67          56 :   readInputLine( getShortcutLabel() + "_diff: DISPLACEMENT ARG1=" + arg1 + " ARG2=" + arg2 );
      68             :   // Get the action that computes the differences
      69          28 :   ActionWithValue* av = plumed.getActionSet().selectWithLabel<ActionWithValue*>( getShortcutLabel() + "_diff");
      70          28 :   plumed_assert( av );
      71             :   // Check if squared
      72             :   bool squared;
      73          28 :   parseFlag("SQUARED",squared);
      74          28 :   std::string olab = getShortcutLabel();
      75          28 :   if( !squared ) {
      76             :     olab += "_2";
      77             :   }
      78             :   // Deal with an annoying corner case when displacement has a single argument
      79          28 :   if( av->copyOutput(0)->getRank()==0 ) {
      80           0 :     readInputLine( olab + ": CUSTOM ARG=" + getShortcutLabel() + "_diff FUNC=x*x PERIODIC=NO");
      81             :   } else {
      82             :     // Notice that the vectors are in the columns here
      83          56 :     readInputLine( getShortcutLabel() + "_diffT: TRANSPOSE ARG=" + getShortcutLabel() + "_diff");
      84          56 :     readInputLine( olab + ": MATRIX_PRODUCT_DIAGONAL ARG=" + getShortcutLabel() + "_diff," + getShortcutLabel() + "_diffT");
      85             :   }
      86          28 :   if( !squared ) {
      87          46 :     readInputLine( getShortcutLabel() + ": CUSTOM ARG=" + getShortcutLabel() + "_2 FUNC=sqrt(x) PERIODIC=NO");
      88             :   }
      89          28 : }
      90             : 
      91             : }
      92             : }