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             : This shortcut provides an implementation of the local crystalinity order parameter that is described in the paper in the bibliography.
      40             : To use this CV you define a series of unit vectors, $g_k$, using multiple instances of the GVECTOR keyword.  This allows you to define a
      41             : [symmetry function](https://www.plumed-tutorials.org/lessons/23/001/data/SymmetryFunction.html) for the $i$th atom as:
      42             : 
      43             : $$
      44             : s_i = \sum_k \left| \frac{\sum_j \sigma(|r_{ij}|) e^{ig_k r_{ij}}}{\sum_j \sigma(|r_{ij}|) \right|^2
      45             : $$
      46             : 
      47             : In this expression $r_{ij}$ is the vector connecting atom $i$ to atom $j$ and $\sigma$ is a switching function that acts upon the magnidue of this vector, $|r_{ij}|$.
      48             : The following input is an example that shows how this symmetry function can be used in practice.
      49             : 
      50             : ```plumed
      51             : lc: LOCAL_CRYSTALINITY SPECIES=1-64 SWITCH={RATIONAL D_0=3.0 R_0=1.5} GVECTOR1=1,1,1 GVECTOR2=1,0.5,0.5 GVECTOR3=0.5,1.0,1.0 SUM
      52             : PRINT ARG=lc_sum FILE=colvar
      53             : ```
      54             : 
      55             : As you can see if you expand the shortcut in this input, the sum over $k$ in the above expression has three terms in this input as 3 GVECTORS are specified.
      56             : Sixty four values for the expression above are computed.  These sixty four numbers are then added together in order to give a global mesuare of the crystallinity
      57             : for the simulated system.
      58             : 
      59             : */
      60             : //+ENDPLUMEDOC
      61             : 
      62             : 
      63             : class LocalCrystallinity : public ActionShortcut {
      64             : public:
      65             :   static void registerKeywords( Keywords& keys );
      66             :   explicit LocalCrystallinity(const ActionOptions&);
      67             : };
      68             : 
      69             : PLUMED_REGISTER_ACTION(LocalCrystallinity,"LOCAL_CRYSTALINITY")
      70             : 
      71           3 : void LocalCrystallinity::registerKeywords( Keywords& keys ) {
      72           3 :   CoordinationNumbers::shortcutKeywords( keys );
      73           3 :   keys.add("numbered","GVECTOR","the coefficients of the linear combinations to compute for the CV");
      74           6 :   keys.setValueDescription("vector","the value of the local crystalinity for each of the input atoms");
      75           3 :   keys.needsAction("ONES");
      76           3 :   keys.needsAction("MATRIX_VECTOR_PRODUCT");
      77           3 :   keys.needsAction("COMBINE");
      78           3 :   keys.needsAction("CUSTOM");
      79           3 :   keys.addDOI("10.1063/1.4822877");
      80           3 : }
      81             : 
      82           1 : LocalCrystallinity::LocalCrystallinity( const ActionOptions& ao):
      83             :   Action(ao),
      84           1 :   ActionShortcut(ao) {
      85             :   // This builds an adjacency matrix
      86             :   std::string sp_str, specA, specB;
      87           1 :   parse("SPECIES",sp_str);
      88           1 :   parse("SPECIESA",specA);
      89           1 :   parse("SPECIESB",specB);
      90           1 :   CoordinationNumbers::expandMatrix( true, getShortcutLabel(), sp_str, specA, specB, this );
      91             :   // Input for denominator (coord)
      92           1 :   ActionWithValue* av = plumed.getActionSet().selectWithLabel<ActionWithValue*>( getShortcutLabel() + "_mat");
      93           1 :   plumed_assert( av && av->getNumberOfComponents()>0 && (av->copyOutput(0))->getRank()==2 );
      94             :   std::string size;
      95           1 :   Tools::convert( (av->copyOutput(0))->getShape()[1], size );
      96           2 :   readInputLine( getShortcutLabel() + "_ones: ONES SIZE=" + size );
      97           2 :   readInputLine( getShortcutLabel() + "_denom: MATRIX_VECTOR_PRODUCT ARG=" + getShortcutLabel() + "_mat.w," + getShortcutLabel() + "_ones");
      98             :   // Input for numerator
      99           1 :   std::string finput = "";
     100           1 :   for(unsigned i=1;; ++i) {
     101             :     std::vector<std::string> gvec;
     102             :     std::string istr;
     103           4 :     Tools::convert( i, istr );
     104           8 :     if( !parseNumberedVector("GVECTOR",i,gvec) ) {
     105             :       break;
     106             :     }
     107           3 :     if( gvec.size()!=3 ) {
     108           0 :       error("gvectors should have size 3");
     109             :     }
     110             :     // This is the dot product between the input gvector and the bond vector
     111           9 :     readInputLine( getShortcutLabel() + "_dot" + istr + ": COMBINE ARG=" + getShortcutLabel() + "_mat.x," + getShortcutLabel() + "_mat.y," + getShortcutLabel() + "_mat.z "
     112           6 :                    "PERIODIC=NO COEFFICIENTS=" + gvec[0] + "," + gvec[1] + "," + gvec[2] );
     113             :     // Now calculate the sine and cosine of the dot product
     114           6 :     readInputLine( getShortcutLabel() + "_cos" + istr + ": CUSTOM ARG=" + getShortcutLabel() +"_mat.w," + getShortcutLabel() + "_dot" + istr + " FUNC=x*cos(y) PERIODIC=NO");
     115           6 :     readInputLine( getShortcutLabel() + "_sin" + istr + ": CUSTOM ARG=" + getShortcutLabel() +"_mat.w," + getShortcutLabel() + "_dot" + istr + " FUNC=x*sin(y) PERIODIC=NO");
     116             :     // And sum up the sine and cosine over the coordination spheres
     117           6 :     readInputLine( getShortcutLabel() + "_cossum" + istr + ": MATRIX_VECTOR_PRODUCT ARG=" + getShortcutLabel() + "_cos" + istr + "," + getShortcutLabel() + "_ones");
     118           6 :     readInputLine( getShortcutLabel() + "_sinsum" + istr + ": MATRIX_VECTOR_PRODUCT ARG=" + getShortcutLabel() + "_sin" + istr + "," + getShortcutLabel() + "_ones");
     119             :     // And average the sine and cosine over the number of bonds
     120           6 :     readInputLine( getShortcutLabel() + "_cosmean" + istr + ": CUSTOM FUNC=x/y PERIODIC=NO ARG=" + getShortcutLabel() + "_cossum" + istr + "," + getShortcutLabel() + "_denom");
     121           6 :     readInputLine( getShortcutLabel() + "_sinmean" + istr + ": CUSTOM FUNC=x/y PERIODIC=NO ARG=" + getShortcutLabel() + "_sinsum" + istr + "," + getShortcutLabel() + "_denom");
     122             :     // And work out the square modulus of this complex number
     123           6 :     readInputLine( getShortcutLabel() + "_" + istr + ": CUSTOM FUNC=x*x+y*y PERIODIC=NO ARG=" + getShortcutLabel() + "_cosmean" + istr + "," + getShortcutLabel() + "_sinmean" + istr);
     124             :     // These are all the kvectors that we are adding together in the final combine for the final CV
     125           3 :     if( i>1 ) {
     126             :       finput += ",";
     127             :     }
     128           6 :     finput += getShortcutLabel() + "_" + istr;
     129           4 :   }
     130             :   // This computes the final CV
     131           2 :   readInputLine( getShortcutLabel() + ": COMBINE NORMALIZE PERIODIC=NO ARG=" + finput );
     132             :   // Now calculate the total length of the vector
     133           2 :   multicolvar::MultiColvarShortcuts::expandFunctions( getShortcutLabel(), getShortcutLabel(), "", this );
     134           1 : }
     135             : 
     136             : }
     137             : }
     138             :