Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2015-2023 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 "MultiColvarBase.h"
      23             : #include "AtomValuePack.h"
      24             : #include "core/ActionRegister.h"
      25             : 
      26             : #include <string>
      27             : #include <cmath>
      28             : 
      29             : namespace PLMD {
      30             : namespace multicolvar {
      31             : 
      32             : //+PLUMEDOC MCOLVAR XYDISTANCES
      33             : /*
      34             : Calculate distance between a pair of atoms neglecting the z-component.
      35             : 
      36             : You can then calculate functions of the distribution of values such as the minimum, the number less than a certain quantity and so on.
      37             : 
      38             : \par Examples
      39             : 
      40             : The following input tells plumed to calculate the projection of the length of the vector connecting atom 3
      41             : to atom 5 projected in the xy-plane and the projection of the length of the vector
      42             : the vector connecting atom 1 to atom 2 in the xy-plane.  The minimum of these two quantities is then
      43             : printed
      44             : \plumedfile
      45             : d1: XYDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
      46             : PRINT ARG=d1.min
      47             : \endplumedfile
      48             : (See also \ref PRINT).
      49             : 
      50             : */
      51             : //+ENDPLUMEDOC
      52             : 
      53             : //+PLUMEDOC MCOLVAR XZDISTANCES
      54             : /*
      55             : Calculate distance between a pair of atoms neglecting the y-component.
      56             : 
      57             : You can then calculate functions of the distribution of
      58             : values such as the minimum, the number less than a certain quantity and so on.
      59             : 
      60             : \par Examples
      61             : 
      62             : The following input tells plumed to calculate the projection of the length of the vector connecting atom 3
      63             : to atom 5 projected in the xz-plane and the projection of the length of the vector
      64             : the vector connecting atom 1 to atom 2 in the xz-plane.  The minimum of these two quantities is then
      65             : printed
      66             : \plumedfile
      67             : d1: XZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
      68             : PRINT ARG=d1.min
      69             : \endplumedfile
      70             : (See also \ref PRINT).
      71             : 
      72             : */
      73             : //+ENDPLUMEDOC
      74             : 
      75             : //+PLUMEDOC MCOLVAR YZDISTANCES
      76             : /*
      77             : Calculate distance between a pair of atoms neglecting the x-component.
      78             : 
      79             : You can then calculate functions of the distribution of
      80             : values such as the minimum, the number less than a certain quantity and so on.
      81             : 
      82             : \par Examples
      83             : 
      84             : The following input tells plumed to calculate the projection of the length of the vector connecting atom 3
      85             : to atom 5 in the yz-plane and the projection of the length of the vector
      86             : the vector connecting atom 1 to atom 2 in the yz-plane.  The minimum of these two quantities is then
      87             : printed
      88             : \plumedfile
      89             : d1: YZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
      90             : PRINT ARG=d1.min
      91             : \endplumedfile
      92             : (See also \ref PRINT).
      93             : 
      94             : */
      95             : //+ENDPLUMEDOC
      96             : 
      97             : 
      98             : class XYDistances : public MultiColvarBase {
      99             : private:
     100             :   unsigned myc1, myc2;
     101             : public:
     102             :   static void registerKeywords( Keywords& keys );
     103             :   explicit XYDistances(const ActionOptions&);
     104             : // active methods:
     105             :   double compute( const unsigned& tindex, AtomValuePack& myatoms ) const override;
     106             : /// Returns the number of coordinates of the field
     107           0 :   bool isPeriodic() override {
     108           0 :     return false;
     109             :   }
     110             : };
     111             : 
     112       13785 : PLUMED_REGISTER_ACTION(XYDistances,"XYDISTANCES")
     113       13785 : PLUMED_REGISTER_ACTION(XYDistances,"XZDISTANCES")
     114       13785 : PLUMED_REGISTER_ACTION(XYDistances,"YZDISTANCES")
     115             : 
     116          12 : void XYDistances::registerKeywords( Keywords& keys ) {
     117          12 :   MultiColvarBase::registerKeywords( keys );
     118          12 :   keys.use("MAX");
     119          12 :   keys.use("ALT_MIN");
     120          12 :   keys.use("MEAN");
     121          12 :   keys.use("MIN");
     122          12 :   keys.use("LESS_THAN");
     123          12 :   keys.use("LOWEST");
     124          12 :   keys.use("HIGHEST");
     125          12 :   keys.use("MORE_THAN");
     126          12 :   keys.use("BETWEEN");
     127          12 :   keys.use("HISTOGRAM");
     128          12 :   keys.use("MOMENTS");
     129          24 :   keys.add("numbered","ATOMS","the atoms involved in each of the distances you wish to calculate. "
     130             :            "Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one distance will be "
     131             :            "calculated for each ATOM keyword you specify (all ATOM keywords should "
     132             :            "specify the indices of two atoms).  The eventual number of quantities calculated by this "
     133             :            "action will depend on what functions of the distribution you choose to calculate.");
     134          24 :   keys.reset_style("ATOMS","atoms");
     135          24 :   keys.add("atoms-1","GROUP","Calculate the distance between each distinct pair of atoms in the group");
     136          24 :   keys.add("atoms-2","GROUPA","Calculate the distances between all the atoms in GROUPA and all "
     137             :            "the atoms in GROUPB. This must be used in conjunction with GROUPB.");
     138          24 :   keys.add("atoms-2","GROUPB","Calculate the distances between all the atoms in GROUPA and all the atoms "
     139             :            "in GROUPB. This must be used in conjunction with GROUPA.");
     140          12 : }
     141             : 
     142           0 : XYDistances::XYDistances(const ActionOptions&ao):
     143             :   Action(ao),
     144           0 :   MultiColvarBase(ao) {
     145           0 :   if( getName().find("XY")!=std::string::npos) {
     146           0 :     myc1=0;
     147           0 :     myc2=1;
     148           0 :   } else if( getName().find("XZ")!=std::string::npos) {
     149           0 :     myc1=0;
     150           0 :     myc2=2;
     151           0 :   } else if( getName().find("YZ")!=std::string::npos) {
     152           0 :     myc1=1;
     153           0 :     myc2=2;
     154             :   } else {
     155           0 :     plumed_error();
     156             :   }
     157             : 
     158             :   // Read in the atoms
     159             :   std::vector<AtomNumber> all_atoms;
     160           0 :   readTwoGroups( "GROUP", "GROUPA", "GROUPB", all_atoms );
     161           0 :   if( atom_lab.size()==0 ) {
     162           0 :     readAtomsLikeKeyword( "ATOMS", 2, all_atoms );
     163             :   }
     164           0 :   setupMultiColvarBase( all_atoms );
     165             :   // And check everything has been read in correctly
     166           0 :   checkRead();
     167           0 : }
     168             : 
     169           0 : double XYDistances::compute( const unsigned& tindex, AtomValuePack& myatoms ) const {
     170           0 :   Vector distance;
     171           0 :   distance=getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );
     172           0 :   const double value=std::sqrt(distance[myc1]*distance[myc1] + distance[myc2]*distance[myc2] );
     173           0 :   const double invvalue=1.0/value;
     174             : 
     175           0 :   Vector myvec;
     176           0 :   myvec.zero();
     177             :   // And finish the calculation
     178           0 :   myvec[myc1]=+invvalue*distance[myc1];
     179           0 :   myvec[myc2]=+invvalue*distance[myc2];
     180           0 :   addAtomDerivatives( 1, 1, myvec, myatoms  );
     181           0 :   myvec[myc1]=-invvalue*distance[myc1];
     182           0 :   myvec[myc2]=-invvalue*distance[myc2];
     183           0 :   addAtomDerivatives( 1, 0, myvec, myatoms );
     184           0 :   myatoms.addBoxDerivatives( 1, Tensor(distance,myvec) );
     185           0 :   return value;
     186             : }
     187             : 
     188             : }
     189             : }
     190             :