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 "multicolvar/MultiColvarShortcuts.h"
      24             : #include "core/PlumedMain.h"
      25             : #include "core/ActionSet.h"
      26             : #include "core/ActionRegister.h"
      27             : #include "core/ActionWithValue.h"
      28             : #include "CoordinationNumbers.h"
      29             : 
      30             : #include <complex>
      31             : 
      32             : namespace PLMD {
      33             : namespace symfunc {
      34             : 
      35             : //+PLUMEDOC MCOLVAR HEXACTIC_PARAMETER
      36             : /*
      37             : Calculate the hexatic order parameter
      38             : 
      39             : \bug Virial is not working currently
      40             : 
      41             : \par Examples
      42             : 
      43             : 
      44             : */
      45             : //+ENDPLUMEDOC
      46             : 
      47             : 
      48             : class HexacticParameter : public ActionShortcut {
      49             : private:
      50             :   void createVectorNormInput( const std::string& ilab, const std::string& olab, const std::string& vlab );
      51             : public:
      52             :   static void registerKeywords( Keywords& keys );
      53             :   explicit HexacticParameter(const ActionOptions&);
      54             : };
      55             : 
      56             : PLUMED_REGISTER_ACTION(HexacticParameter,"HEXACTIC_PARAMETER")
      57             : 
      58           5 : void HexacticParameter::registerKeywords( Keywords& keys ) {
      59           5 :   CoordinationNumbers::shortcutKeywords( keys );
      60          10 :   keys.add("compulsory","PLANE","the plane to use when calculating the value of the order parameter should be xy, xz or yz");
      61          10 :   keys.addFlag("VMEAN",false,"calculate the norm of the mean vector.");
      62          10 :   keys.addOutputComponent("_vmean","VMEAN","the norm of the mean vector");
      63          10 :   keys.addFlag("VSUM",false,"calculate the norm of the sum of all the vectors");
      64          10 :   keys.addOutputComponent("_vsum","VSUM","the norm of the mean vector");
      65           5 :   keys.needsAction("CYLINDRICAL_HARMONIC_MATRIX");
      66           5 :   keys.needsAction("ONES");
      67           5 :   keys.needsAction("MATRIX_VECTOR_PRODUCT");
      68           5 :   keys.needsAction("CUSTOM");
      69           5 :   keys.needsAction("MEAN");
      70           5 :   keys.needsAction("SUM");
      71           5 :   keys.needsAction("COMBINE");
      72           5 : }
      73             : 
      74           1 : HexacticParameter::HexacticParameter( const ActionOptions& ao):
      75             :   Action(ao),
      76           1 :   ActionShortcut(ao) {
      77             :   std::string sp_str, specA, specB;
      78           1 :   parse("SPECIES",sp_str);
      79           1 :   parse("SPECIESA",specA);
      80           1 :   parse("SPECIESB",specB);
      81           1 :   CoordinationNumbers::expandMatrix( true, getShortcutLabel(), sp_str, specA, specB, this );
      82             :   std::string myplane;
      83           2 :   parse("PLANE",myplane);
      84           1 :   if( myplane=="xy" ) {
      85           2 :     readInputLine( getShortcutLabel() + ": CYLINDRICAL_HARMONIC_MATRIX DEGREE=6 ARG=" + getShortcutLabel() + "_mat.x," + getShortcutLabel() + "_mat.y," + getShortcutLabel() + "_mat.w" );
      86           0 :   } else if( myplane=="xz" ) {
      87           0 :     readInputLine( getShortcutLabel() + ": CYLINDRICAL_HARMONIC_MATRIX DEGREE=6 ARG=" + getShortcutLabel() + "_mat.x," + getShortcutLabel() + "_mat.z," + getShortcutLabel() + "_mat.w" );
      88           0 :   } else if( myplane=="yz" ) {
      89           0 :     readInputLine( getShortcutLabel() + ": CYLINDRICAL_HARMONIC_MATRIX DEGREE=6 ARG=" + getShortcutLabel() + "_mat.y," + getShortcutLabel() + "_mat.z," + getShortcutLabel() + "_mat.w" );
      90             :   } else {
      91           0 :     error("invalid input for plane -- should be xy, xz or yz");
      92             :   }
      93             :   // And coordination number
      94           1 :   ActionWithValue* av = plumed.getActionSet().selectWithLabel<ActionWithValue*>( getShortcutLabel() + "_mat");
      95           1 :   plumed_assert( av && av->getNumberOfComponents()>0 && (av->copyOutput(0))->getRank()==2 );
      96             :   std::string size;
      97           1 :   Tools::convert( (av->copyOutput(0))->getShape()[1], size );
      98           2 :   readInputLine( getShortcutLabel() + "_ones: ONES SIZE=" + size );
      99           2 :   readInputLine( getShortcutLabel() + "_rm: MATRIX_VECTOR_PRODUCT ARG=" + getShortcutLabel() + ".rm," + getShortcutLabel() + "_ones");
     100           2 :   readInputLine( getShortcutLabel() + "_im: MATRIX_VECTOR_PRODUCT ARG=" + getShortcutLabel() + ".im," + getShortcutLabel() + "_ones");
     101             :   // Input for denominator (coord)
     102           2 :   readInputLine( getShortcutLabel() + "_denom: MATRIX_VECTOR_PRODUCT ARG=" + getShortcutLabel() + "_mat.w," + getShortcutLabel() + "_ones");
     103             :   // Divide real part by coordination numbers
     104           2 :   readInputLine( getShortcutLabel() + "_rmn: CUSTOM ARG=" + getShortcutLabel() + "_rm," + getShortcutLabel() + "_denom FUNC=x/y PERIODIC=NO");
     105             :   // Devide imaginary part by coordination number
     106           2 :   readInputLine( getShortcutLabel() + "_imn: CUSTOM ARG=" + getShortcutLabel() + "_im," + getShortcutLabel() + "_denom FUNC=x/y PERIODIC=NO");
     107             : 
     108             :   // If we are doing VMEAN determine sum of vector components
     109             :   bool do_vmean;
     110           1 :   parseFlag("VMEAN",do_vmean);
     111           1 :   if( do_vmean ) {
     112             :     // Real part
     113           0 :     readInputLine( getShortcutLabel() + "_rms: MEAN ARG=" + getShortcutLabel() + "_rmn PERIODIC=NO");
     114             :     // Imaginary part
     115           0 :     readInputLine( getShortcutLabel() + "_ims: MEAN ARG=" + getShortcutLabel() + "_imn PERIODIC=NO");
     116             :     // Now calculate the total length of the vector
     117           0 :     createVectorNormInput( getShortcutLabel(), getShortcutLabel() + "_vmean", "ms" );
     118             :   }
     119             :   bool do_vsum;
     120           1 :   parseFlag("VSUM",do_vsum);
     121           1 :   if( do_vsum ) {
     122             :     // Real part
     123           0 :     readInputLine( getShortcutLabel() + "_rmz: SUM ARG=" + getShortcutLabel() + "_rmn PERIODIC=NO");
     124             :     // Imaginary part
     125           0 :     readInputLine( getShortcutLabel() + "_imz: SUM ARG=" + getShortcutLabel() + "_imn PERIODIC=NO");
     126             :     // Now calculate the total length of the vector
     127           0 :     createVectorNormInput( getShortcutLabel(), getShortcutLabel() + "_vsum", "mz" );
     128             :   }
     129             : 
     130             :   // Now calculate the total length of the vector
     131           2 :   createVectorNormInput( getShortcutLabel(), getShortcutLabel() + "_norm", "mn" );
     132           2 :   multicolvar::MultiColvarShortcuts::expandFunctions( getShortcutLabel(), getShortcutLabel() + "_norm", "", this );
     133           1 : }
     134             : 
     135           1 : void HexacticParameter::createVectorNormInput( const std::string& ilab, const std::string& olab, const std::string& vlab ) {
     136           2 :   readInputLine( olab + "2: COMBINE PERIODIC=NO ARG=" + ilab + "_r" + vlab + "," + ilab + "_i" + vlab + " POWERS=2,2" );
     137           2 :   readInputLine( olab + ": CUSTOM ARG=" + olab + "2 FUNC=sqrt(x) PERIODIC=NO");
     138           1 : }
     139             : 
     140             : }
     141             : }
     142             :