Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2013-2023 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 "core/ActionShortcut.h"
      23             : #include "core/ActionRegister.h"
      24             : #include "MultiColvarShortcuts.h"
      25             : 
      26             : #include <string>
      27             : #include <cmath>
      28             : 
      29             : namespace PLMD {
      30             : namespace multicolvar {
      31             : 
      32             : //+PLUMEDOC COLVAR ANGLES
      33             : /*
      34             : Calculate an angle.
      35             : 
      36             : This command can be used to compute the angle between three atoms. Alternatively
      37             : if four atoms appear in the atom
      38             : specification it calculates the angle between
      39             : two vectors identified by two pairs of atoms.
      40             : 
      41             : If _three_ atoms are given, the angle is defined as:
      42             : \f[
      43             : \theta=\arccos\left(\frac{ {\bf r}_{21}\cdot {\bf r}_{23}}{
      44             : |{\bf r}_{21}| |{\bf r}_{23}|}\right)
      45             : \f]
      46             : Here \f$ {\bf r}_{ij}\f$ is the distance vector among the
      47             : i-th and the j-th listed atom.
      48             : 
      49             : If _four_ atoms are given, the angle is defined as:
      50             : \f[
      51             : \theta=\arccos\left(\frac{ {\bf r}_{21}\cdot {\bf r}_{34}}{
      52             : |{\bf r}_{21}| |{\bf r}_{34}|}\right)
      53             : \f]
      54             : 
      55             : Notice that angles defined in this way are non-periodic variables and
      56             : their value is limited by definition between 0 and \f$\pi\f$.
      57             : 
      58             : The vectors \f$ {\bf r}_{ij}\f$ are by default evaluated taking
      59             : periodic boundary conditions into account.
      60             : This behavior can be changed with the NOPBC flag.
      61             : 
      62             : \par Examples
      63             : 
      64             : This command tells plumed to calculate the angle between the vector connecting atom 1 to atom 2 and
      65             : the vector connecting atom 2 to atom 3 and to print it on file COLVAR1. At the same time,
      66             : the angle between vector connecting atom 1 to atom 2 and the vector connecting atom 3 to atom 4 is printed
      67             : on file COLVAR2.
      68             : \plumedfile
      69             : 
      70             : a: ANGLE ATOMS=1,2,3
      71             : # equivalently one could state:
      72             : # a: ANGLE ATOMS=1,2,2,3
      73             : 
      74             : b: ANGLE ATOMS=1,2,3,4
      75             : 
      76             : PRINT ARG=a FILE=COLVAR1
      77             : PRINT ARG=b FILE=COLVAR2
      78             : \endplumedfile
      79             : 
      80             : This final example instructs plumed to calculate all the angles in the first coordination
      81             : spheres of the atoms. The bins for a normalized histogram of the distribution is then output
      82             : 
      83             : \plumedfile
      84             : ANGLES GROUP=1-38 HISTOGRAM={GAUSSIAN LOWER=0.0 UPPER=pi NBINS=20} SWITCH={GAUSSIAN R_0=1.0} LABEL=a1
      85             : PRINT ARG=a1.* FILE=colvar
      86             : \endplumedfile
      87             : 
      88             : 
      89             : */
      90             : //+ENDPLUMEDOC
      91             : 
      92             : class Angles : public ActionShortcut {
      93             : public:
      94             :   explicit Angles(const ActionOptions&);
      95             :   static void registerKeywords( Keywords& keys );
      96             : };
      97             : 
      98             : PLUMED_REGISTER_ACTION(Angles,"ANGLES")
      99             : 
     100           4 : void Angles::registerKeywords( Keywords& keys ) {
     101           4 :   ActionShortcut::registerKeywords( keys );
     102           8 :   keys.add("atoms-1","GROUP","Calculate angles for each distinct set of three atoms in the group");
     103           8 :   keys.add("atoms-2","GROUPA","A group of central atoms about which angles should be calculated");
     104           8 :   keys.add("atoms-2","GROUPB","When used in conjunction with GROUPA this keyword instructs plumed "
     105             :            "to calculate all distinct angles involving one atom from GROUPA "
     106             :            "and two atoms from GROUPB. The atom from GROUPA is the central atom.");
     107           8 :   keys.add("atoms-3","GROUPC","This must be used in conjunction with GROUPA and GROUPB.  All angles "
     108             :            "involving one atom from GROUPA, one atom from GROUPB and one atom from "
     109             :            "GROUPC are calculated. The GROUPA atoms are assumed to be the central "
     110             :            "atoms");
     111           8 :   keys.add("optional","SWITCH","the switching function specifies that only those bonds that have a length that is less than a certain threshold are considered");
     112           8 :   MultiColvarShortcuts::shortcutKeywords( keys ); keys.needsAction("ANGLE"); keys.needsAction("COORD_ANGLES");
     113           4 : }
     114             : 
     115           1 : Angles::Angles(const ActionOptions&ao):
     116             :   Action(ao),
     117           1 :   ActionShortcut(ao)
     118             : {
     119           2 :   std::string swit; parse("SWITCH",swit);
     120           1 :   if( swit.length()>0 ) {
     121           0 :     std::string cat, grp; parse("GROUPA",cat); parse("GROUPB",grp);
     122           0 :     if( cat.length()==0 || grp.length()==0 ) error("must use GROUPA/GROUPB when using SWITCH");
     123           0 :     readInputLine( getShortcutLabel() + ": COORD_ANGLES SWITCH={" +  swit + "} CATOMS=" + cat + " GROUP=" + grp + " " + convertInputLineToString() );
     124             :     return;
     125             :   }
     126           2 :   std::vector<std::string> group; parseVector("GROUP",group);
     127           2 :   std::vector<std::string> groupa; parseVector("GROUPA",groupa);
     128           2 :   std::vector<std::string> groupb; parseVector("GROUPB",groupb);
     129           2 :   std::vector<std::string> groupc; parseVector("GROUPC",groupc);
     130           1 :   if( group.size()>0 ) {
     131           0 :     if( groupa.size()>0 || groupb.size()>0 || groupc.size()>0 ) error("should only be GROUP keyword in input not GROUPA/GROUPB/GROUPC");
     132           0 :     Tools::interpretRanges( group ); std::string ainput = getShortcutLabel() + ": ANGLE"; unsigned n=1;
     133             :     // Not sure if this triple sum makes any sense
     134           0 :     for(unsigned i=2; i<group.size(); ++i ) {
     135           0 :       for(unsigned j=1; j<i; ++j ) {
     136           0 :         for(unsigned k=0; k<j; ++k) {
     137           0 :           std::string str_n; Tools::convert( n, str_n );
     138           0 :           ainput += " ATOMS" + str_n + "=" + group[i] + "," + group[j] + "," + group[k]; n++;
     139             :         }
     140             :       }
     141             :     }
     142           0 :     readInputLine( ainput );
     143           1 :   } else if( groupc.size()>0 ) {
     144           0 :     Tools::interpretRanges( groupa ); Tools::interpretRanges( groupb ); Tools::interpretRanges( groupc );
     145           0 :     unsigned n=1; std::string ainput = getShortcutLabel() + ": ANGLE";
     146           0 :     for(unsigned i=0; i<groupa.size(); ++i ) {
     147           0 :       for(unsigned j=0; j<groupb.size(); ++j ) {
     148           0 :         for(unsigned k=0; k<groupc.size(); ++k) {
     149           0 :           std::string str_n; Tools::convert( n, str_n );
     150           0 :           ainput += " ATOMS" + str_n + "=" + groupb[j] + "," + groupa[i] + "," + groupc[k]; n++;
     151             :         }
     152             :       }
     153             :     }
     154           0 :     readInputLine( ainput );
     155           1 :   } else if( groupa.size()>0 ) {
     156           1 :     Tools::interpretRanges( groupa ); Tools::interpretRanges( groupb );
     157           1 :     unsigned n=1; std::string ainput; ainput = getShortcutLabel() + ": ANGLE";
     158           2 :     for(unsigned i=0; i<groupa.size(); ++i ) {
     159           9 :       for(unsigned j=1; j<groupb.size(); ++j ) {
     160          44 :         for(unsigned k=0; k<j; ++k) {
     161          36 :           std::string str_n; Tools::convert( n, str_n );
     162          72 :           ainput += " ATOMS" + str_n + "=" + groupb[j] + "," + groupa[i] + "," + groupb[k]; n++;
     163             :         }
     164             :       }
     165             :     }
     166           1 :     readInputLine( ainput );
     167             :   }
     168           1 :   MultiColvarShortcuts::expandFunctions( getShortcutLabel(), getShortcutLabel(), "", this );
     169           1 : }
     170             : 
     171             : }
     172             : }
     173             : 
     174             : 
     175             :