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           3 :   keys.needsAction("ONES");
      58           3 :   keys.needsAction("MATRIX_VECTOR_PRODUCT");
      59           3 :   keys.needsAction("COMBINE");
      60           3 :   keys.needsAction("CUSTOM");
      61           3 : }
      62             : 
      63           1 : LocalCrystallinity::LocalCrystallinity( const ActionOptions& ao):
      64             :   Action(ao),
      65           1 :   ActionShortcut(ao) {
      66             :   // This builds an adjacency matrix
      67             :   std::string sp_str, specA, specB;
      68           1 :   parse("SPECIES",sp_str);
      69           1 :   parse("SPECIESA",specA);
      70           1 :   parse("SPECIESB",specB);
      71           1 :   CoordinationNumbers::expandMatrix( true, getShortcutLabel(), sp_str, specA, specB, this );
      72             :   // Input for denominator (coord)
      73           1 :   ActionWithValue* av = plumed.getActionSet().selectWithLabel<ActionWithValue*>( getShortcutLabel() + "_mat");
      74           1 :   plumed_assert( av && av->getNumberOfComponents()>0 && (av->copyOutput(0))->getRank()==2 );
      75             :   std::string size;
      76           1 :   Tools::convert( (av->copyOutput(0))->getShape()[1], size );
      77           2 :   readInputLine( getShortcutLabel() + "_ones: ONES SIZE=" + size );
      78           2 :   readInputLine( getShortcutLabel() + "_denom: MATRIX_VECTOR_PRODUCT ARG=" + getShortcutLabel() + "_mat.w," + getShortcutLabel() + "_ones");
      79             :   // Input for numerator
      80           1 :   std::string finput = "";
      81           1 :   for(unsigned i=1;; ++i) {
      82             :     std::vector<std::string> gvec;
      83             :     std::string istr;
      84           4 :     Tools::convert( i, istr );
      85           8 :     if( !parseNumberedVector("GVECTOR",i,gvec) ) {
      86             :       break;
      87             :     }
      88           3 :     if( gvec.size()!=3 ) {
      89           0 :       error("gvectors should have size 3");
      90             :     }
      91             :     // This is the dot product between the input gvector and the bond vector
      92           9 :     readInputLine( getShortcutLabel() + "_dot" + istr + ": COMBINE ARG=" + getShortcutLabel() + "_mat.x," + getShortcutLabel() + "_mat.y," + getShortcutLabel() + "_mat.z "
      93           6 :                    "PERIODIC=NO COEFFICIENTS=" + gvec[0] + "," + gvec[1] + "," + gvec[2] );
      94             :     // Now calculate the sine and cosine of the dot product
      95           6 :     readInputLine( getShortcutLabel() + "_cos" + istr + ": CUSTOM ARG=" + getShortcutLabel() +"_mat.w," + getShortcutLabel() + "_dot" + istr + " FUNC=x*cos(y) PERIODIC=NO");
      96           6 :     readInputLine( getShortcutLabel() + "_sin" + istr + ": CUSTOM ARG=" + getShortcutLabel() +"_mat.w," + getShortcutLabel() + "_dot" + istr + " FUNC=x*sin(y) PERIODIC=NO");
      97             :     // And sum up the sine and cosine over the coordination spheres
      98           6 :     readInputLine( getShortcutLabel() + "_cossum" + istr + ": MATRIX_VECTOR_PRODUCT ARG=" + getShortcutLabel() + "_cos" + istr + "," + getShortcutLabel() + "_ones");
      99           6 :     readInputLine( getShortcutLabel() + "_sinsum" + istr + ": MATRIX_VECTOR_PRODUCT ARG=" + getShortcutLabel() + "_sin" + istr + "," + getShortcutLabel() + "_ones");
     100             :     // And average the sine and cosine over the number of bonds
     101           6 :     readInputLine( getShortcutLabel() + "_cosmean" + istr + ": CUSTOM FUNC=x/y PERIODIC=NO ARG=" + getShortcutLabel() + "_cossum" + istr + "," + getShortcutLabel() + "_denom");
     102           6 :     readInputLine( getShortcutLabel() + "_sinmean" + istr + ": CUSTOM FUNC=x/y PERIODIC=NO ARG=" + getShortcutLabel() + "_sinsum" + istr + "," + getShortcutLabel() + "_denom");
     103             :     // And work out the square modulus of this complex number
     104           6 :     readInputLine( getShortcutLabel() + "_" + istr + ": CUSTOM FUNC=x*x+y*y PERIODIC=NO ARG=" + getShortcutLabel() + "_cosmean" + istr + "," + getShortcutLabel() + "_sinmean" + istr);
     105             :     // These are all the kvectors that we are adding together in the final combine for the final CV
     106           3 :     if( i>1 ) {
     107             :       finput += ",";
     108             :     }
     109           6 :     finput += getShortcutLabel() + "_" + istr;
     110           4 :   }
     111             :   // This computes the final CV
     112           2 :   readInputLine( getShortcutLabel() + ": COMBINE NORMALIZE PERIODIC=NO ARG=" + finput );
     113             :   // Now calculate the total length of the vector
     114           2 :   multicolvar::MultiColvarShortcuts::expandFunctions( getShortcutLabel(), getShortcutLabel(), "", this );
     115           1 : }
     116             : 
     117             : }
     118             : }
     119             :