Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2023 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 "Colvar.h"
      23             : #include "ActionRegister.h"
      24             : #include "tools/Angle.h"
      25             : 
      26             : namespace PLMD {
      27             : namespace colvar {
      28             : 
      29             : //+PLUMEDOC COLVAR ANGLE
      30             : /*
      31             : Calculate an angle.
      32             : 
      33             : This command can be used to compute the angle between three atoms. Alternatively
      34             : if four atoms appear in the atom
      35             : specification it calculates the angle between
      36             : two vectors identified by two pairs of atoms.
      37             : 
      38             : If _three_ atoms are given, the angle is defined as:
      39             : \f[
      40             : \theta=\arccos\left(\frac{ {\bf r}_{21}\cdot {\bf r}_{23}}{
      41             : |{\bf r}_{21}| |{\bf r}_{23}|}\right)
      42             : \f]
      43             : Here \f$ {\bf r}_{ij}\f$ is the distance vector among the
      44             : \f$i\f$th and the \f$j\f$th listed atom.
      45             : 
      46             : If _four_ atoms are given, the angle is defined as:
      47             : \f[
      48             : \theta=\arccos\left(\frac{ {\bf r}_{21}\cdot {\bf r}_{34}}{
      49             : |{\bf r}_{21}| |{\bf r}_{34}|}\right)
      50             : \f]
      51             : 
      52             : Notice that angles defined in this way are non-periodic variables and
      53             : their value is limited by definition between 0 and \f$\pi\f$.
      54             : 
      55             : The vectors \f$ {\bf r}_{ij}\f$ are by default evaluated taking
      56             : periodic boundary conditions into account.
      57             : This behavior can be changed with the NOPBC flag.
      58             : 
      59             : \par Examples
      60             : 
      61             : This command tells plumed to calculate the angle between the vector connecting atom 1 to atom 2 and
      62             : the vector connecting atom 2 to atom 3 and to print it on file COLVAR1. At the same time,
      63             : the angle between vector connecting atom 1 to atom 2 and the vector connecting atom 3 to atom 4 is printed
      64             : on file COLVAR2.
      65             : \plumedfile
      66             : 
      67             : a: ANGLE ATOMS=1,2,3
      68             : # equivalently one could state:
      69             : # a: ANGLE ATOMS=1,2,2,3
      70             : 
      71             : b: ANGLE ATOMS=1,2,3,4
      72             : 
      73             : PRINT ARG=a FILE=COLVAR1
      74             : PRINT ARG=b FILE=COLVAR2
      75             : \endplumedfile
      76             : 
      77             : 
      78             : */
      79             : //+ENDPLUMEDOC
      80             : 
      81             : class Angle : public Colvar {
      82             :   bool pbc;
      83             : 
      84             : public:
      85             :   explicit Angle(const ActionOptions&);
      86             : // active methods:
      87             :   void calculate() override;
      88             :   static void registerKeywords( Keywords& keys );
      89             : };
      90             : 
      91       10454 : PLUMED_REGISTER_ACTION(Angle,"ANGLE")
      92             : 
      93          19 : void Angle::registerKeywords( Keywords& keys ) {
      94          19 :   Colvar::registerKeywords(keys);
      95          38 :   keys.add("atoms","ATOMS","the list of atoms involved in this collective variable (either 3 or 4 atoms)");
      96          19 : }
      97             : 
      98          18 : Angle::Angle(const ActionOptions&ao):
      99             :   PLUMED_COLVAR_INIT(ao),
     100          18 :   pbc(true)
     101             : {
     102             :   std::vector<AtomNumber> atoms;
     103          18 :   parseAtomList("ATOMS",atoms);
     104          18 :   bool nopbc=!pbc;
     105          18 :   parseFlag("NOPBC",nopbc);
     106          18 :   pbc=!nopbc;
     107             : 
     108          18 :   if(atoms.size()==3) {
     109          12 :     log.printf("  between atoms %d %d %d\n",atoms[0].serial(),atoms[1].serial(),atoms[2].serial());
     110          12 :     atoms.resize(4);
     111          12 :     atoms[3]=atoms[2];
     112          12 :     atoms[2]=atoms[1];
     113           6 :   } else if(atoms.size()==4) {
     114           5 :     log.printf("  between lines %d-%d and %d-%d\n",atoms[0].serial(),atoms[1].serial(),atoms[2].serial(),atoms[3].serial());
     115           2 :   } else error("Number of specified atoms should be either 3 or 4");
     116             : 
     117          17 :   if(pbc) log.printf("  using periodic boundary conditions\n");
     118           0 :   else    log.printf("  without periodic boundary conditions\n");
     119             : 
     120          17 :   addValueWithDerivatives(); setNotPeriodic();
     121          17 :   requestAtoms(atoms);
     122          17 :   checkRead();
     123          19 : }
     124             : 
     125             : // calculator
     126         304 : void Angle::calculate() {
     127             : 
     128         304 :   if(pbc) makeWhole();
     129             : 
     130         304 :   Vector dij,dik;
     131         304 :   dij=delta(getPosition(2),getPosition(3));
     132         304 :   dik=delta(getPosition(1),getPosition(0));
     133         304 :   Vector ddij,ddik;
     134             :   PLMD::Angle a;
     135         304 :   double angle=a.compute(dij,dik,ddij,ddik);
     136         304 :   setAtomsDerivatives(0,ddik);
     137         304 :   setAtomsDerivatives(1,-ddik);
     138         304 :   setAtomsDerivatives(2,-ddij);
     139         304 :   setAtomsDerivatives(3,ddij);
     140         304 :   setValue           (angle);
     141         304 :   setBoxDerivativesNoPbc();
     142         304 : }
     143             : 
     144             : }
     145             : }
     146             : 
     147             : 
     148             :