Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2015-2020 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 "MultiColvarBase.h"
      23             : #include "AtomValuePack.h"
      24             : #include "core/ActionRegister.h"
      25             : 
      26             : #include <string>
      27             : #include <cmath>
      28             : 
      29             : using namespace std;
      30             : 
      31             : namespace PLMD {
      32             : namespace multicolvar {
      33             : 
      34             : //+PLUMEDOC MCOLVAR XYDISTANCES
      35             : /*
      36             : Calculate distance between a pair of atoms neglecting the z-component.
      37             : 
      38             : You can then calculate functions of the distribution of values such as the minimum, the number less than a certain quantity and so on.
      39             : 
      40             : \par Examples
      41             : 
      42             : The following input tells plumed to calculate the projection of the length of the vector connecting atom 3
      43             : to atom 5 projected in the xy-plane and the projection of the length of the vector
      44             : the vector connecting atom 1 to atom 2 in the xy-plane.  The minimum of these two quantities is then
      45             : printed
      46             : \plumedfile
      47             : d1: XYDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
      48             : PRINT ARG=d1.min
      49             : \endplumedfile
      50             : (See also \ref PRINT).
      51             : 
      52             : */
      53             : //+ENDPLUMEDOC
      54             : 
      55             : //+PLUMEDOC MCOLVAR XZDISTANCES
      56             : /*
      57             : Calculate distance between a pair of atoms neglecting the y-component.
      58             : 
      59             : You can then calculate functions of the distribution of
      60             : values such as the minimum, the number less than a certain quantity and so on.
      61             : 
      62             : \par Examples
      63             : 
      64             : The following input tells plumed to calculate the projection of the length of the vector connecting atom 3
      65             : to atom 5 projected in the xz-plane and the projection of the length of the vector
      66             : the vector connecting atom 1 to atom 2 in the xz-plane.  The minimum of these two quantities is then
      67             : printed
      68             : \plumedfile
      69             : d1: XZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
      70             : PRINT ARG=d1.min
      71             : \endplumedfile
      72             : (See also \ref PRINT).
      73             : 
      74             : */
      75             : //+ENDPLUMEDOC
      76             : 
      77             : //+PLUMEDOC MCOLVAR YZDISTANCES
      78             : /*
      79             : Calculate distance between a pair of atoms neglecting the x-component.
      80             : 
      81             : You can then calculate functions of the distribution of
      82             : values such as the minimum, the number less than a certain quantity and so on.
      83             : 
      84             : \par Examples
      85             : 
      86             : The following input tells plumed to calculate the projection of the length of the vector connecting atom 3
      87             : to atom 5 in the yz-plane and the projection of the length of the vector
      88             : the vector connecting atom 1 to atom 2 in the yz-plane.  The minimum of these two quantities is then
      89             : printed
      90             : \plumedfile
      91             : d1: YZDISTANCES ATOMS1=3,5 ATOMS2=1,2 MIN={BETA=0.1}
      92             : PRINT ARG=d1.min
      93             : \endplumedfile
      94             : (See also \ref PRINT).
      95             : 
      96             : */
      97             : //+ENDPLUMEDOC
      98             : 
      99             : 
     100           0 : class XYDistances : public MultiColvarBase {
     101             : private:
     102             :   unsigned myc1, myc2;
     103             : public:
     104             :   static void registerKeywords( Keywords& keys );
     105             :   explicit XYDistances(const ActionOptions&);
     106             : // active methods:
     107             :   virtual double compute( const unsigned& tindex, AtomValuePack& myatoms ) const ;
     108             : /// Returns the number of coordinates of the field
     109           0 :   bool isPeriodic() { return false; }
     110             : };
     111             : 
     112        7356 : PLUMED_REGISTER_ACTION(XYDistances,"XYDISTANCES")
     113        7356 : PLUMED_REGISTER_ACTION(XYDistances,"XZDISTANCES")
     114        7356 : PLUMED_REGISTER_ACTION(XYDistances,"YZDISTANCES")
     115             : 
     116           3 : void XYDistances::registerKeywords( Keywords& keys ) {
     117           3 :   MultiColvarBase::registerKeywords( keys );
     118           9 :   keys.use("MAX"); keys.use("ALT_MIN");
     119          18 :   keys.use("MEAN"); keys.use("MIN"); keys.use("LESS_THAN"); keys.use("LOWEST"); keys.use("HIGHEST");
     120          15 :   keys.use("MORE_THAN"); keys.use("BETWEEN"); keys.use("HISTOGRAM"); keys.use("MOMENTS");
     121          12 :   keys.add("numbered","ATOMS","the atoms involved in each of the distances you wish to calculate. "
     122             :            "Keywords like ATOMS1, ATOMS2, ATOMS3,... should be listed and one distance will be "
     123             :            "calculated for each ATOM keyword you specify (all ATOM keywords should "
     124             :            "specify the indices of two atoms).  The eventual number of quantities calculated by this "
     125             :            "action will depend on what functions of the distribution you choose to calculate.");
     126           9 :   keys.reset_style("ATOMS","atoms");
     127          12 :   keys.add("atoms-1","GROUP","Calculate the distance between each distinct pair of atoms in the group");
     128          12 :   keys.add("atoms-2","GROUPA","Calculate the distances between all the atoms in GROUPA and all "
     129             :            "the atoms in GROUPB. This must be used in conjunction with GROUPB.");
     130          12 :   keys.add("atoms-2","GROUPB","Calculate the distances between all the atoms in GROUPA and all the atoms "
     131             :            "in GROUPB. This must be used in conjunction with GROUPA.");
     132           3 : }
     133             : 
     134           0 : XYDistances::XYDistances(const ActionOptions&ao):
     135             :   Action(ao),
     136           0 :   MultiColvarBase(ao)
     137             : {
     138           0 :   if( getName().find("XY")!=std::string::npos) {
     139           0 :     myc1=0; myc2=1;
     140           0 :   } else if( getName().find("XZ")!=std::string::npos) {
     141           0 :     myc1=0; myc2=2;
     142           0 :   } else if( getName().find("YZ")!=std::string::npos) {
     143           0 :     myc1=1; myc2=2;
     144           0 :   } else plumed_error();
     145             : 
     146             :   // Read in the atoms
     147             :   std::vector<AtomNumber> all_atoms;
     148           0 :   readTwoGroups( "GROUP", "GROUPA", "GROUPB", all_atoms );
     149           0 :   if( atom_lab.size()==0 ) readAtomsLikeKeyword( "ATOMS", 2, all_atoms );
     150           0 :   setupMultiColvarBase( all_atoms );
     151             :   // And check everything has been read in correctly
     152           0 :   checkRead();
     153           0 : }
     154             : 
     155           0 : double XYDistances::compute( const unsigned& tindex, AtomValuePack& myatoms ) const {
     156           0 :   Vector distance;
     157           0 :   distance=getSeparation( myatoms.getPosition(0), myatoms.getPosition(1) );
     158           0 :   const double value=sqrt(distance[myc1]*distance[myc1] + distance[myc2]*distance[myc2] );
     159           0 :   const double invvalue=1.0/value;
     160             : 
     161           0 :   Vector myvec; myvec.zero();
     162             :   // And finish the calculation
     163           0 :   myvec[myc1]=+invvalue*distance[myc1]; myvec[myc2]=+invvalue*distance[myc2]; addAtomDerivatives( 1, 1, myvec, myatoms  );
     164           0 :   myvec[myc1]=-invvalue*distance[myc1]; myvec[myc2]=-invvalue*distance[myc2]; addAtomDerivatives( 1, 0, myvec, myatoms );
     165           0 :   myatoms.addBoxDerivatives( 1, Tensor(distance,myvec) );
     166           0 :   return value;
     167             : }
     168             : 
     169             : }
     170        5517 : }
     171             :