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, $\lambda$ of
      33             : an $n\times n$ adjacency matrix and its corresponding eigenvector, $V$, using:
      34             : 
      35             : $$
      36             : s_i = \sqrt{n} \lambda v_i
      37             : $$
      38             : 
      39             : The example input below calculates the 7 SPRINT coordinates for a 7 atom cluster of Lennard-Jones
      40             : atoms and prints their values to a file.
      41             : 
      42             : ```plumed
      43             : ss: SPRINT GROUP=1-7 SWITCH={RATIONAL R_0=0.1}
      44             : PRINT ARG=ss.* FILE=colvar
      45             : ```
      46             : 
      47             : This example input calculates the 14 SPRINT coordinates for a molecule composed of 7 hydrogen and
      48             : 7 carbon atoms.
      49             : 
      50             : ```plumed
      51             : ss: SPRINT ...
      52             :   GROUP1=1-7 GROUP2=8-14
      53             :   SWITCH11={RATIONAL R_0=2.6 NN=6 MM=12}
      54             :   SWITCH12={RATIONAL R_0=2.2 NN=6 MM=12}
      55             :   SWITCH22={RATIONAL R_0=2.2 NN=6 MM=12}
      56             : ...
      57             : 
      58             : PRINT ARG=ss.* FILE=colvar
      59             : ```
      60             : 
      61             : If you explore the inputs above you can see that when PLUMED reads them it creates a more complicated input file
      62             : for calculating the SPRINT CVs. You can get a sense of how these CVs are calculated by looking at the
      63             : expanded versions of the shortcuts in the inputs above. The insight into these methods that you can obtain by looking
      64             : at these expanded input should hopefully give you ideas for developing new versions of these methods that use the same
      65             : body of theory.  For example, if you look at the inputs above you can see that one or more [CONTACT_MATRIX](CONTACT_MATRIX.md) actions are
      66             : used to calculate sprint.  These CONTACT_MATRIX determine whether atoms are adjacent or not.  However, you can
      67             : use different quantities to measure whether or not two given atoms/molecules are
      68             : adjacent or not and compute a different type of adjacency matrix. For example you can say that two molecules are
      69             : adjacent if they are within a certain distance of each other and if they have similar orientations or you can argue that
      70             : two molecules are adjacent if there is a hydrogen bond between them.
      71             : */
      72             : //+ENDPLUMEDOC
      73             : 
      74             : namespace PLMD {
      75             : namespace sprint {
      76             : 
      77             : class Sprint : public ActionShortcut {
      78             : public:
      79             :   static void registerKeywords(Keywords& keys);
      80             :   explicit Sprint(const ActionOptions&);
      81             : };
      82             : 
      83             : PLUMED_REGISTER_ACTION(Sprint,"SPRINT")
      84             : 
      85           3 : void Sprint::registerKeywords(Keywords& keys) {
      86           3 :   ActionShortcut::registerKeywords( keys );
      87           3 :   keys.add("optional","MATRIX","the matrix that you would like to perform SPRINT on");
      88           3 :   keys.add("numbered","GROUP","specifies the list of atoms that should be assumed indistinguishable");
      89           3 :   keys.add("numbered","SWITCH","specify the switching function to use between two sets of indistinguishable atoms");
      90           3 :   keys.needsAction("CONTACT_MATRIX");
      91           3 :   keys.needsAction("DIAGONALIZE");
      92           3 :   keys.needsAction("CUSTOM");
      93           3 :   keys.needsAction("SELECT_COMPONENTS");
      94           3 :   keys.needsAction("SORT");
      95           3 :   keys.needsAction("COMBINE");
      96           6 :   keys.addOutputComponent("coord","default","scalar","the sprint coordinates");
      97           3 :   keys.addDOI("10.1103/PhysRevLett.107.085504");
      98           3 : }
      99             : 
     100           1 : Sprint::Sprint(const ActionOptions& ao):
     101             :   Action(ao),
     102           1 :   ActionShortcut(ao) {
     103             :   std::string matinp;
     104           2 :   parse("MATRIX",matinp);
     105           1 :   if( matinp.length()==0 ) {
     106           2 :     readInputLine( getShortcutLabel() + "_jmat: CONTACT_MATRIX " + convertInputLineToString() );
     107           2 :     matinp = getShortcutLabel() + "_jmat";
     108             :   }
     109             :   std::vector<unsigned> nin_group;
     110           1 :   unsigned ntot_atoms=0;
     111           1 :   for(unsigned i=1;; ++i) {
     112             :     std::string inum;
     113           3 :     Tools::convert( i, inum );
     114           6 :     ActionWithValue* av = plumed.getActionSet().selectWithLabel<ActionWithValue*>( matinp + inum + inum );
     115           3 :     if( !av ) {
     116             :       break ;
     117             :     }
     118           2 :     unsigned natoms = (av->copyOutput(0))->getShape()[0];
     119           2 :     nin_group.push_back( natoms );
     120           2 :     ntot_atoms += natoms;
     121           2 :   }
     122           1 :   if( nin_group.size()==0 ) {
     123           0 :     ActionWithValue* av = plumed.getActionSet().selectWithLabel<ActionWithValue*>( matinp );
     124           0 :     unsigned natoms = (av->copyOutput(0))->getShape()[0];
     125           0 :     nin_group.push_back( natoms );
     126           0 :     ntot_atoms = natoms;
     127             :   }
     128             : 
     129             :   // Diagonalization
     130           2 :   readInputLine( getShortcutLabel() + "_diag: DIAGONALIZE ARG=" + matinp + " VECTORS=1");
     131             :   // Compute sprint coordinates as product of eigenvalue and eigenvector times square root of number of atoms in all groups
     132             :   std::string str_natoms;
     133           1 :   Tools::convert( ntot_atoms, str_natoms );
     134           3 :   readInputLine( getShortcutLabel() + "_sp: CUSTOM ARG=" + getShortcutLabel() + "_diag.vals-1," + getShortcutLabel() +
     135           2 :                  "_diag.vecs-1 FUNC=sqrt(" + str_natoms + ")*x*y PERIODIC=NO");
     136             :   // Sort sprint coordinates for each group of atoms
     137           1 :   unsigned k=0, kk=0;
     138           3 :   for(unsigned j=0; j<nin_group.size(); ++j) {
     139             :     std::string jnum, knum;
     140           2 :     Tools::convert( j+1, jnum );
     141           2 :     Tools::convert(k+1, knum);
     142             :     k++;
     143           4 :     std::string sort_act = getShortcutLabel() + "_selection" + jnum + ": SELECT_COMPONENTS ARG=" + getShortcutLabel() + "_sp COMPONENTS=" + knum;
     144          14 :     for(unsigned n=1; n<nin_group[j]; ++n) {
     145          12 :       Tools::convert( k+1, knum );
     146          24 :       sort_act += ","+ knum;
     147             :       k++;
     148             :     }
     149           2 :     readInputLine( sort_act );
     150           4 :     readInputLine( getShortcutLabel() + jnum + ": SORT ARG=" + getShortcutLabel() + "_selection" + jnum );
     151          16 :     for(unsigned n=0; n<nin_group[j]; ++n) {
     152             :       std::string knum, nnum;
     153          14 :       Tools::convert( kk, knum );
     154          14 :       Tools::convert( n+1, nnum );
     155          14 :       kk++;
     156          28 :       readInputLine( getShortcutLabel() + "_coord-" + knum + ": COMBINE ARG=" + getShortcutLabel() + jnum + "." + nnum + " PERIODIC=NO" );
     157             :     }
     158             :   }
     159           1 : }
     160             : 
     161             : }
     162             : }