Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2016-2018 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/ActionRegister.h"
      23             : #include "core/ActionShortcut.h"
      24             : #include "CoordinationNumbers.h"
      25             : #include "multicolvar/MultiColvarShortcuts.h"
      26             : 
      27             : //+PLUMEDOC MCOLVAR TETRA_ANGULAR
      28             : /*
      29             : Calculate the angular tetra CV
      30             : 
      31             : This shortcut calculates a [symmetry function](https://www.plumed-tutorials.org/lessons/23/001/data/SymmetryFunction.html). The particular function that is being
      32             : evaluated for the coordination sphere here is as follows:
      33             : 
      34             : $$
      35             : s_i = 1 - \frac{3}{8}\sum_{j=2}^4 \sum_{k=1}^{j-1} \left( \cos(\theta_{jik} + \frac{1}{2} \right)^2
      36             : $$
      37             : 
      38             : In this expression the 4 atoms in the sums over $j$ and $k$ are the four atoms that are nearest to atom $i$.  $\theta_{jik}$ is the angle between the vectors connecting
      39             : atoms $i$ and $j$ and the vector connecting atoms $i$ and $k$.  The CV is large if the four atoms nearest atom $i$ are arranged on the vertices of a regular tetrahedron
      40             : and small otherwise.  The following example shows how you can use this action to measure the degree of tetrahedral order in a system.
      41             : 
      42             : ```plumed
      43             : # Calculate a vector that contains 64 values for the symmetry function.
      44             : # Sum the elements of the vector and calculate the mean value on the atoms from this sum.
      45             : acv: TETRA_ANGULAR SPECIES=1-64 SUM MEAN
      46             : # Print out the positions of the 64 atoms for which the symmetry function was calculated
      47             : # to an xyz file along with the values of the symmetry function
      48             : DUMPATOMS ATOMS=1-64 ARG=acv FILE=mcolv.xyz
      49             : # Print out the average value of the symmetry function and the sum of all the symmetry functions
      50             : PRINT ARG=acv_sum,acv_mean FILE=colvar
      51             : ```
      52             : 
      53             : */
      54             : //+ENDPLUMEDOC
      55             : 
      56             : namespace PLMD {
      57             : namespace symfunc {
      58             : 
      59             : class AngularTetra : public ActionShortcut {
      60             : public:
      61             :   static void registerKeywords( Keywords& keys );
      62             :   explicit AngularTetra(const ActionOptions&ao);
      63             : };
      64             : 
      65             : PLUMED_REGISTER_ACTION(AngularTetra,"TETRA_ANGULAR")
      66             : 
      67           3 : void AngularTetra::registerKeywords( Keywords& keys ) {
      68           3 :   CoordinationNumbers::shortcutKeywords( keys );
      69           3 :   keys.addFlag("NOPBC",false,"ignore the periodic boundary conditions when calculating distances");
      70           3 :   keys.add("compulsory","CUTOFF","-1","ignore distances that have a value larger than this cutoff");
      71           6 :   keys.setValueDescription("vector","the value of the angular tetehedrality parameter for each of the input atoms");
      72           3 :   keys.remove("NN");
      73           3 :   keys.remove("MM");
      74           3 :   keys.remove("D_0");
      75           3 :   keys.remove("R_0");
      76           3 :   keys.remove("SWITCH");
      77           3 :   keys.needsAction("DISTANCE_MATRIX");
      78           3 :   keys.needsAction("NEIGHBORS");
      79           3 :   keys.needsAction("GSYMFUNC_THREEBODY");
      80           3 :   keys.needsAction("CUSTOM");
      81           3 : }
      82             : 
      83           1 : AngularTetra::AngularTetra( const ActionOptions& ao):
      84             :   Action(ao),
      85           1 :   ActionShortcut(ao) {
      86             :   bool nopbc;
      87           1 :   parseFlag("NOPBC",nopbc);
      88           1 :   std::string pbcstr="";
      89           1 :   if( nopbc ) {
      90             :     pbcstr = " NOPBC";
      91             :   }
      92             :   // Read species input and create the matrix
      93             :   std::string sp_str, rcut;
      94           1 :   parse("SPECIES",sp_str);
      95           2 :   parse("CUTOFF",rcut);
      96           1 :   if( sp_str.length()>0 ) {
      97           2 :     readInputLine( getShortcutLabel() + "_mat: DISTANCE_MATRIX COMPONENTS GROUP=" + sp_str + " CUTOFF=" + rcut + pbcstr );
      98             :   } else {
      99             :     std::string specA, specB;
     100           0 :     parse("SPECIESA",specA);
     101           0 :     parse("SPECIESB",specB);
     102           0 :     if( specA.length()==0 ) {
     103           0 :       error("missing input atoms");
     104             :     }
     105           0 :     if( specB.length()==0 ) {
     106           0 :       error("missing SPECIESB keyword");
     107             :     }
     108           0 :     readInputLine( getShortcutLabel() + "_mat: DISTANCE_MATRIX COMPONENTS GROUPA=" + specA + " GROUPB=" + specB + " CUTOFF=" + rcut + pbcstr );
     109             :   }
     110             :   // Get the neighbors matrix
     111           2 :   readInputLine( getShortcutLabel() + "_neigh: NEIGHBORS ARG=" + getShortcutLabel() + "_mat.w NLOWEST=4");
     112             :   // Now construct the symmetry function (sum of cos(a) + 1/3)
     113           3 :   readInputLine( getShortcutLabel() + "_g8: GSYMFUNC_THREEBODY WEIGHT=" + getShortcutLabel() + "_neigh " +
     114           3 :                  "ARG=" + getShortcutLabel() + "_mat.x," + getShortcutLabel() + "_mat.y," + getShortcutLabel() + "_mat.z FUNCTION1={FUNC=(cos(ajik)+1/3)^2 LABEL=g8}");
     115             :   // Now evaluate the actual per atom CV
     116           2 :   readInputLine( getShortcutLabel() + ": CUSTOM ARG=" + getShortcutLabel() + "_g8.g8 FUNC=(1-(3*x/8)) PERIODIC=NO");
     117             :   // And get the things to do with the quantities we have computed
     118             :   std::map<std::string,std::string> keymap;
     119           1 :   multicolvar::MultiColvarShortcuts::readShortcutKeywords( keymap, this );
     120           2 :   multicolvar::MultiColvarShortcuts::expandFunctions( getShortcutLabel(), getShortcutLabel(), "", keymap, this );
     121           1 : }
     122             : 
     123             : }
     124             : }