Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2012-2017 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/PlumedMain.h"
      25             : #include "core/ActionSet.h"
      26             : #include "core/ActionWithValue.h"
      27             : #include "CoordinationNumbers.h"
      28             : #include "multicolvar/MultiColvarShortcuts.h"
      29             : 
      30             : #include <complex>
      31             : 
      32             : namespace PLMD {
      33             : namespace symfunc {
      34             : 
      35             : //+PLUMEDOC MCOLVAR LOCAL_CRYSTALINITY
      36             : /*
      37             : Calculate the local crystalinity symmetry function
      38             : 
      39             : \par Examples
      40             : 
      41             : 
      42             : */
      43             : //+ENDPLUMEDOC
      44             : 
      45             : 
      46             : class LocalCrystallinity : public ActionShortcut {
      47             : public:
      48             :   static void registerKeywords( Keywords& keys );
      49             :   explicit LocalCrystallinity(const ActionOptions&);
      50             : };
      51             : 
      52             : PLUMED_REGISTER_ACTION(LocalCrystallinity,"LOCAL_CRYSTALINITY")
      53             : 
      54           3 : void LocalCrystallinity::registerKeywords( Keywords& keys ) {
      55           3 :   CoordinationNumbers::shortcutKeywords( keys );
      56           6 :   keys.add("numbered","GVECTOR","the coefficients of the linear combinations to compute for the CV");
      57           6 :   keys.setValueDescription("vector","the value of the local crystalinity for each of the input atoms");
      58           6 :   keys.needsAction("ONES"); keys.needsAction("MATRIX_VECTOR_PRODUCT");
      59           6 :   keys.needsAction("COMBINE"); keys.needsAction("CUSTOM");
      60           3 : }
      61             : 
      62           1 : LocalCrystallinity::LocalCrystallinity( const ActionOptions& ao):
      63             :   Action(ao),
      64           1 :   ActionShortcut(ao)
      65             : {
      66             :   // This builds an adjacency matrix
      67           3 :   std::string sp_str, specA, specB; parse("SPECIES",sp_str); parse("SPECIESA",specA); parse("SPECIESB",specB);
      68           1 :   CoordinationNumbers::expandMatrix( true, getShortcutLabel(), sp_str, specA, specB, this );
      69             :   // Input for denominator (coord)
      70           1 :   ActionWithValue* av = plumed.getActionSet().selectWithLabel<ActionWithValue*>( getShortcutLabel() + "_mat");
      71           1 :   plumed_assert( av && av->getNumberOfComponents()>0 && (av->copyOutput(0))->getRank()==2 );
      72           1 :   std::string size; Tools::convert( (av->copyOutput(0))->getShape()[1], size );
      73           2 :   readInputLine( getShortcutLabel() + "_ones: ONES SIZE=" + size );
      74           2 :   readInputLine( getShortcutLabel() + "_denom: MATRIX_VECTOR_PRODUCT ARG=" + getShortcutLabel() + "_mat.w," + getShortcutLabel() + "_ones");
      75             :   // Input for numerator
      76           1 :   std::string finput = "";
      77           1 :   for(unsigned i=1;; ++i) {
      78           4 :     std::vector<std::string> gvec; std::string istr; Tools::convert( i, istr );
      79           8 :     if( !parseNumberedVector("GVECTOR",i,gvec) ) { break; }
      80           3 :     if( gvec.size()!=3 ) error("gvectors should have size 3");
      81             :     // This is the dot product between the input gvector and the bond vector
      82           9 :     readInputLine( getShortcutLabel() + "_dot" + istr + ": COMBINE ARG=" + getShortcutLabel() + "_mat.x," + getShortcutLabel() + "_mat.y," + getShortcutLabel() + "_mat.z "
      83           6 :                    "PERIODIC=NO COEFFICIENTS=" + gvec[0] + "," + gvec[1] + "," + gvec[2] );
      84             :     // Now calculate the sine and cosine of the dot product
      85           6 :     readInputLine( getShortcutLabel() + "_cos" + istr + ": CUSTOM ARG=" + getShortcutLabel() +"_mat.w," + getShortcutLabel() + "_dot" + istr + " FUNC=x*cos(y) PERIODIC=NO");
      86           6 :     readInputLine( getShortcutLabel() + "_sin" + istr + ": CUSTOM ARG=" + getShortcutLabel() +"_mat.w," + getShortcutLabel() + "_dot" + istr + " FUNC=x*sin(y) PERIODIC=NO");
      87             :     // And sum up the sine and cosine over the coordination spheres
      88           6 :     readInputLine( getShortcutLabel() + "_cossum" + istr + ": MATRIX_VECTOR_PRODUCT ARG=" + getShortcutLabel() + "_cos" + istr + "," + getShortcutLabel() + "_ones");
      89           6 :     readInputLine( getShortcutLabel() + "_sinsum" + istr + ": MATRIX_VECTOR_PRODUCT ARG=" + getShortcutLabel() + "_sin" + istr + "," + getShortcutLabel() + "_ones");
      90             :     // And average the sine and cosine over the number of bonds
      91           6 :     readInputLine( getShortcutLabel() + "_cosmean" + istr + ": CUSTOM FUNC=x/y PERIODIC=NO ARG=" + getShortcutLabel() + "_cossum" + istr + "," + getShortcutLabel() + "_denom");
      92           6 :     readInputLine( getShortcutLabel() + "_sinmean" + istr + ": CUSTOM FUNC=x/y PERIODIC=NO ARG=" + getShortcutLabel() + "_sinsum" + istr + "," + getShortcutLabel() + "_denom");
      93             :     // And work out the square modulus of this complex number
      94           6 :     readInputLine( getShortcutLabel() + "_" + istr + ": CUSTOM FUNC=x*x+y*y PERIODIC=NO ARG=" + getShortcutLabel() + "_cosmean" + istr + "," + getShortcutLabel() + "_sinmean" + istr);
      95             :     // These are all the kvectors that we are adding together in the final combine for the final CV
      96           3 :     if( i>1 ) finput += ",";
      97           6 :     finput += getShortcutLabel() + "_" + istr;
      98           4 :   }
      99             :   // This computes the final CV
     100           2 :   readInputLine( getShortcutLabel() + ": COMBINE NORMALIZE PERIODIC=NO ARG=" + finput );
     101             :   // Now calculate the total length of the vector
     102           2 :   multicolvar::MultiColvarShortcuts::expandFunctions( getShortcutLabel(), getShortcutLabel(), "", this );
     103           1 : }
     104             : 
     105             : }
     106             : }
     107             :