Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2013-2020 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 "core/ActionShortcut.h"
      23             : #include "core/ActionRegister.h"
      24             : #include "core/ActionWithValue.h"
      25             : #include "core/PlumedMain.h"
      26             : #include "core/ActionSet.h"
      27             : 
      28             : //+PLUMEDOC MATRIXF SPRINT
      29             : /*
      30             : Calculate SPRINT topological variables from an adjacency matrix.
      31             : 
      32             : The SPRINT topological variables are calculated from the largest eigenvalue, \f$\lambda\f$ of
      33             : an \f$n\times n\f$ adjacency matrix and its corresponding eigenvector, \f$\mathbf{V}\f$, using:
      34             : 
      35             : \f[
      36             : s_i = \sqrt{n} \lambda v_i
      37             : \f]
      38             : 
      39             : You can use different quantities to measure whether or not two given atoms/molecules are
      40             : adjacent or not in the adjacency matrix.  The simplest measure of adjacency is is whether
      41             : two atoms/molecules are within some cutoff of each other.  Further complexity can be added by
      42             : insisting that two molecules are adjacent if they are within a certain distance of each
      43             : other and if they have similar orientations.
      44             : 
      45             : \par Examples
      46             : 
      47             : This example input calculates the 7 SPRINT coordinates for a 7 atom cluster of Lennard-Jones
      48             : atoms and prints their values to a file.  In this input the SPRINT coordinates are calculated
      49             : in the manner described in ?? so two atoms are adjacent if they are within a cutoff:
      50             : 
      51             : \plumedfile
      52             : DENSITY SPECIES=1-7 LABEL=d1
      53             : CONTACT_MATRIX ATOMS=d1 SWITCH={RATIONAL R_0=0.1} LABEL=mat
      54             : SPRINT MATRIX=mat LABEL=ss
      55             : PRINT ARG=ss.* FILE=colvar
      56             : \endplumedfile
      57             : 
      58             : This example input calculates the 14 SPRINT coordinates for a molecule composed of 7 hydrogen and
      59             : 7 carbon atoms.  Once again two atoms are adjacent if they are within a cutoff:
      60             : 
      61             : \plumedfile
      62             : DENSITY SPECIES=1-7 LABEL=c
      63             : DENSITY SPECIES=8-14 LABEL=h
      64             : 
      65             : CONTACT_MATRIX ...
      66             :   ATOMS=c,h
      67             :   SWITCH11={RATIONAL R_0=2.6 NN=6 MM=12}
      68             :   SWITCH12={RATIONAL R_0=2.2 NN=6 MM=12}
      69             :   SWITCH22={RATIONAL R_0=2.2 NN=6 MM=12}
      70             :   LABEL=mat
      71             : ... CONTACT_MATRIX
      72             : 
      73             : SPRINT MATRIX=mat LABEL=ss
      74             : 
      75             : PRINT ARG=ss.* FILE=colvar
      76             : \endplumedfile
      77             : 
      78             : */
      79             : //+ENDPLUMEDOC
      80             : 
      81             : namespace PLMD {
      82             : namespace sprint {
      83             : 
      84             : class Sprint : public ActionShortcut {
      85             : public:
      86             :   static void registerKeywords(Keywords& keys);
      87             :   explicit Sprint(const ActionOptions&);
      88             : };
      89             : 
      90             : PLUMED_REGISTER_ACTION(Sprint,"SPRINT")
      91             : 
      92           3 : void Sprint::registerKeywords(Keywords& keys) {
      93           3 :   ActionShortcut::registerKeywords( keys );
      94           6 :   keys.add("optional","MATRIX","the matrix that you would like to perform SPRINT on");
      95           6 :   keys.add("numbered","GROUP","specifies the list of atoms that should be assumed indistinguishable");
      96           6 :   keys.add("numbered","SWITCH","specify the switching function to use between two sets of indistinguishable atoms");
      97           9 :   keys.needsAction("CONTACT_MATRIX"); keys.needsAction("DIAGONALIZE"); keys.needsAction("CUSTOM");
      98           9 :   keys.needsAction("SELECT_COMPONENTS"); keys.needsAction("SORT"); keys.needsAction("COMBINE");
      99           6 :   keys.addOutputComponent("coord","default","scalar","the sprint coordinates");
     100           3 : }
     101             : 
     102           1 : Sprint::Sprint(const ActionOptions& ao):
     103             :   Action(ao),
     104           1 :   ActionShortcut(ao)
     105             : {
     106           2 :   std::string matinp; parse("MATRIX",matinp);
     107           1 :   if( matinp.length()==0 ) {
     108           2 :     readInputLine( getShortcutLabel() + "_jmat: CONTACT_MATRIX " + convertInputLineToString() );
     109           2 :     matinp = getShortcutLabel() + "_jmat";
     110             :   }
     111           1 :   std::vector<unsigned> nin_group; unsigned ntot_atoms=0;
     112           1 :   for(unsigned i=1;; ++i) {
     113           3 :     std::string inum; Tools::convert( i, inum );
     114           6 :     ActionWithValue* av = plumed.getActionSet().selectWithLabel<ActionWithValue*>( matinp + inum + inum );
     115           3 :     if( !av ) break ;
     116           2 :     unsigned natoms = (av->copyOutput(0))->getShape()[0]; nin_group.push_back( natoms ); ntot_atoms += natoms;
     117           2 :   }
     118             : 
     119             :   // Diagonalization
     120           2 :   readInputLine( getShortcutLabel() + "_diag: DIAGONALIZE ARG=" + matinp + " VECTORS=1");
     121             :   // Compute sprint coordinates as product of eigenvalue and eigenvector times square root of number of atoms in all groups
     122           1 :   std::string str_natoms; Tools::convert( ntot_atoms, str_natoms );
     123           3 :   readInputLine( getShortcutLabel() + "_sp: CUSTOM ARG=" + getShortcutLabel() + "_diag.vals-1," + getShortcutLabel() +
     124           2 :                  "_diag.vecs-1 FUNC=sqrt(" + str_natoms + ")*x*y PERIODIC=NO");
     125             :   // Sort sprint coordinates for each group of atoms
     126           1 :   unsigned k=0, kk=0;
     127           3 :   for(unsigned j=0; j<nin_group.size(); ++j) {
     128           2 :     std::string jnum, knum; Tools::convert( j+1, jnum ); Tools::convert(k+1, knum); k++;
     129           4 :     std::string sort_act = getShortcutLabel() + "_selection" + jnum + ": SELECT_COMPONENTS ARG=" + getShortcutLabel() + "_sp COMPONENTS=" + knum;
     130          14 :     for(unsigned n=1; n<nin_group[j]; ++n) {
     131          24 :       Tools::convert( k+1, knum ); sort_act += ","+ knum; k++;
     132             :     }
     133           2 :     readInputLine( sort_act );
     134           4 :     readInputLine( getShortcutLabel() + jnum + ": SORT ARG=" + getShortcutLabel() + "_selection" + jnum );
     135          16 :     for(unsigned n=0; n<nin_group[j]; ++n) {
     136          14 :       std::string knum, nnum; Tools::convert( kk, knum ); Tools::convert( n+1, nnum ); kk++;
     137          28 :       readInputLine( getShortcutLabel() + "_coord-" + knum + ": COMBINE ARG=" + getShortcutLabel() + jnum + "." + nnum + " PERIODIC=NO" );
     138             :     }
     139             :   }
     140           1 : }
     141             : 
     142             : }
     143             : }