Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2013-2023 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 "Colvar.h"
      23             : #include "core/ActionRegister.h"
      24             : 
      25             : namespace PLMD {
      26             : namespace colvar {
      27             : 
      28             : //+PLUMEDOC COLVAR CELL
      29             : /*
      30             : Calculate the components of the simulation cell
      31             : 
      32             : \par Examples
      33             : 
      34             : The following input tells plumed to print the squared modulo of each of the three lattice vectors
      35             : \plumedfile
      36             : cell: CELL
      37             : aaa:    COMBINE ARG=cell.ax,cell.ay,cell.az POWERS=2,2,2 PERIODIC=NO
      38             : bbb:    COMBINE ARG=cell.bx,cell.by,cell.bz POWERS=2,2,2 PERIODIC=NO
      39             : ccc:    COMBINE ARG=cell.cx,cell.cy,cell.cz POWERS=2,2,2 PERIODIC=NO
      40             : PRINT ARG=aaa,bbb,ccc
      41             : \endplumedfile
      42             : 
      43             : */
      44             : //+ENDPLUMEDOC
      45             : 
      46             : 
      47             : class Cell : public Colvar {
      48             :   Value* components[3][3];
      49             : 
      50             : public:
      51             :   explicit Cell(const ActionOptions&);
      52             : // active methods:
      53             :   void calculate() override;
      54             : /// Register all the keywords for this action
      55             :   static void registerKeywords( Keywords& keys );
      56             : };
      57             : 
      58             : PLUMED_REGISTER_ACTION(Cell,"CELL")
      59             : 
      60          10 : Cell::Cell(const ActionOptions&ao):
      61          10 :   PLUMED_COLVAR_INIT(ao) {
      62             :   std::vector<AtomNumber> atoms;
      63          10 :   checkRead();
      64             : 
      65          20 :   addComponentWithDerivatives("ax");
      66          10 :   componentIsNotPeriodic("ax");
      67          10 :   components[0][0]=getPntrToComponent("ax");
      68          20 :   addComponentWithDerivatives("ay");
      69          10 :   componentIsNotPeriodic("ay");
      70          10 :   components[0][1]=getPntrToComponent("ay");
      71          20 :   addComponentWithDerivatives("az");
      72          10 :   componentIsNotPeriodic("az");
      73          10 :   components[0][2]=getPntrToComponent("az");
      74          20 :   addComponentWithDerivatives("bx");
      75          10 :   componentIsNotPeriodic("bx");
      76          10 :   components[1][0]=getPntrToComponent("bx");
      77          20 :   addComponentWithDerivatives("by");
      78          10 :   componentIsNotPeriodic("by");
      79          10 :   components[1][1]=getPntrToComponent("by");
      80          20 :   addComponentWithDerivatives("bz");
      81          10 :   componentIsNotPeriodic("bz");
      82          10 :   components[1][2]=getPntrToComponent("bz");
      83          20 :   addComponentWithDerivatives("cx");
      84          10 :   componentIsNotPeriodic("cx");
      85          10 :   components[2][0]=getPntrToComponent("cx");
      86          20 :   addComponentWithDerivatives("cy");
      87          10 :   componentIsNotPeriodic("cy");
      88          10 :   components[2][1]=getPntrToComponent("cy");
      89          20 :   addComponentWithDerivatives("cz");
      90          10 :   componentIsNotPeriodic("cz");
      91          10 :   components[2][2]=getPntrToComponent("cz");
      92          10 :   requestAtoms(atoms);
      93          10 : }
      94             : 
      95          12 : void Cell::registerKeywords( Keywords& keys ) {
      96          12 :   Action::registerKeywords( keys );
      97          12 :   ActionWithValue::registerKeywords( keys );
      98          12 :   ActionAtomistic::registerKeywords( keys );
      99          24 :   keys.addOutputComponent("ax","default","the ax component of the cell matrix");
     100          24 :   keys.addOutputComponent("ay","default","the ay component of the cell matrix");
     101          24 :   keys.addOutputComponent("az","default","the az component of the cell matrix");
     102          24 :   keys.addOutputComponent("bx","default","the bx component of the cell matrix");
     103          24 :   keys.addOutputComponent("by","default","the by component of the cell matrix");
     104          24 :   keys.addOutputComponent("bz","default","the bz component of the cell matrix");
     105          24 :   keys.addOutputComponent("cx","default","the cx component of the cell matrix");
     106          24 :   keys.addOutputComponent("cy","default","the cy component of the cell matrix");
     107          24 :   keys.addOutputComponent("cz","default","the cz component of the cell matrix");
     108          12 : }
     109             : 
     110             : 
     111             : // calculator
     112         151 : void Cell::calculate() {
     113             : 
     114         604 :   for(int i=0; i<3; i++)
     115        1812 :     for(int j=0; j<3; j++) {
     116        1359 :       components[i][j]->set(getBox()[i][j]);
     117             :     }
     118         604 :   for(int l=0; l<3; l++)
     119        1812 :     for(int m=0; m<3; m++) {
     120        1359 :       Tensor der;
     121        5436 :       for(int i=0; i<3; i++) {
     122        4077 :         der[i][m]=getBox()[l][i];
     123             :       }
     124        1359 :       setBoxDerivatives(components[l][m],-der);
     125             :     }
     126         151 : }
     127             : 
     128             : }
     129             : }
     130             : 
     131             : 
     132             :