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             : In the example input below we measure adjacency between atoms using a [BRIDGE_MATRIX](BRIDGE_MATRIX.md) and then compute the SPRINT CVs
      73             : by diagonalizing this matrix.
      74             : 
      75             : ```plumed
      76             : b: BRIDGE_MATRIX GROUP=1-7 BRIDGING_ATOMS=8-100 SWITCH={RATIONAL R_0=0.2}
      77             : s: SPRINT MATRIX=b
      78             : PRINT ARG=s.* FILE=colvar
      79             : ```
      80             : 
      81             : */
      82             : //+ENDPLUMEDOC
      83             : 
      84             : namespace PLMD {
      85             : namespace sprint {
      86             : 
      87             : class Sprint : public ActionShortcut {
      88             : public:
      89             :   static void registerKeywords(Keywords& keys);
      90             :   explicit Sprint(const ActionOptions&);
      91             : };
      92             : 
      93             : PLUMED_REGISTER_ACTION(Sprint,"SPRINT")
      94             : 
      95          15 : void Sprint::registerKeywords(Keywords& keys) {
      96          15 :   ActionShortcut::registerKeywords( keys );
      97          15 :   keys.add("optional","MATRIX","the matrix that you would like to perform SPRINT on");
      98          15 :   keys.add("numbered","GROUP","specifies the list of atoms that should be assumed indistinguishable");
      99          15 :   keys.add("numbered","SWITCH","specify the switching function to use between two sets of indistinguishable atoms");
     100          15 :   keys.needsAction("CONTACT_MATRIX");
     101          15 :   keys.needsAction("DIAGONALIZE");
     102          15 :   keys.needsAction("CUSTOM");
     103          15 :   keys.needsAction("SELECT_COMPONENTS");
     104          15 :   keys.needsAction("SORT");
     105          15 :   keys.needsAction("COMBINE");
     106          30 :   keys.addOutputComponent("coord","default","scalar","the sprint coordinates");
     107          15 :   keys.addDOI("10.1103/PhysRevLett.107.085504");
     108          15 : }
     109             : 
     110           6 : Sprint::Sprint(const ActionOptions& ao):
     111             :   Action(ao),
     112           6 :   ActionShortcut(ao) {
     113             :   std::string matinp;
     114          12 :   parse("MATRIX",matinp);
     115           6 :   if( matinp.length()==0 ) {
     116           4 :     readInputLine( getShortcutLabel() + "_jmat: CONTACT_MATRIX " + convertInputLineToString() );
     117           4 :     matinp = getShortcutLabel() + "_jmat";
     118             :   }
     119           6 :   std::vector<unsigned> nin_group;
     120           6 :   unsigned ntot_atoms=0;
     121           6 :   for(unsigned i=1;; ++i) {
     122             :     std::string inum;
     123          10 :     Tools::convert( i, inum );
     124          10 :     ActionWithValue* av = plumed.getActionSet().selectWithLabel<ActionWithValue*>( matinp + inum + inum );
     125          10 :     if( !av ) {
     126             :       break ;
     127             :     }
     128           4 :     unsigned natoms = (av->copyOutput(0))->getShape()[0];
     129           4 :     nin_group.push_back( natoms );
     130           4 :     ntot_atoms += natoms;
     131           4 :   }
     132           6 :   if( nin_group.size()==0 ) {
     133           4 :     ActionWithValue* av = plumed.getActionSet().selectWithLabel<ActionWithValue*>( matinp );
     134           4 :     unsigned natoms = (av->copyOutput(0))->getShape()[0];
     135           4 :     nin_group.push_back( natoms );
     136           4 :     ntot_atoms = natoms;
     137             :   }
     138             : 
     139             :   // Diagonalization
     140          18 :   readInputLine( getShortcutLabel() + "_diag: DIAGONALIZE ARG=" + matinp + " VECTORS=1");
     141             :   // Compute sprint coordinates as product of eigenvalue and eigenvector times square root of number of atoms in all groups
     142             :   std::string str_natoms;
     143           6 :   Tools::convert( ntot_atoms, str_natoms );
     144          18 :   readInputLine( getShortcutLabel() + "_sp: CUSTOM ARG=" + getShortcutLabel() + "_diag.vecs-1," + getShortcutLabel() +
     145           6 :                  "_diag.vals-1 FUNC=sqrt(" + str_natoms + ")*x*y PERIODIC=NO");
     146             :   // Sort sprint coordinates for each group of atoms
     147           6 :   unsigned k=0, kk=0;
     148          14 :   for(unsigned j=0; j<nin_group.size(); ++j) {
     149             :     std::string jnum;
     150             :     std::string knum;
     151             :     std::string nnum;
     152           8 :     Tools::convert( j+1, jnum );
     153           8 :     Tools::convert(k+1, knum);
     154             :     k++;
     155          24 :     std::string sort_act = getShortcutLabel() + "_selection" + jnum + ": SELECT_COMPONENTS ARG=" + getShortcutLabel() + "_sp COMPONENTS=" + knum;
     156          84 :     for(unsigned n=1; n<nin_group[j]; ++n) {
     157          76 :       Tools::convert( k+1, knum );
     158          76 :       sort_act += ","+ knum;
     159             :       k++;
     160             :     }
     161           8 :     readInputLine( sort_act );
     162          24 :     readInputLine( getShortcutLabel() + jnum + ": SORT ARG=" + getShortcutLabel() + "_selection" + jnum );
     163          92 :     for(unsigned n=0; n<nin_group[j]; ++n) {
     164          84 :       Tools::convert( kk, knum );
     165          84 :       Tools::convert( n+1, nnum );
     166          84 :       kk++;
     167         420 :       readInputLine( getShortcutLabel() + "_coord-" + knum + ": COMBINE ARG=" + getShortcutLabel() + jnum + "." + nnum + " PERIODIC=NO" );
     168             :     }
     169             :   }
     170          88 : }
     171             : 
     172             : }
     173             : }