Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2011-2023 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 "PbcAction.h"
      23             : #include "DomainDecomposition.h"
      24             : #include "tools/Pbc.h"
      25             : #include "PlumedMain.h"
      26             : #include "ActionSet.h"
      27             : #include "ActionRegister.h"
      28             : 
      29             : //+PLUMEDOC ANALYSIS PBC
      30             : /*
      31             : Pass the cell vectors into PLUMED.
      32             : 
      33             : This command is used to pass the cell vectors from an MD code to PLUMED. The command is a specialised
      34             : version of the [PUT](PUT.md) command that accepts a $3\times 3$ matrix.  The additional specialisation is
      35             : required because the cell vectors play a special role when you do calculations with PLUMED.
      36             : 
      37             : Notice that when you create a [DOMAIN_DECOMPOSITION](DOMAIN_DECOMPOSITION.md) action a PBC action is created
      38             : automatically.
      39             : 
      40             : You would only use the PBC command if you were calling PLUMED from python or an MD code. There is no reason for using this command in a conventional PLUMED
      41             : input file like this:
      42             : 
      43             : ```plumed
      44             : pbc: PBC
      45             : ```
      46             : 
      47             : Instead this command would be called from python like this:
      48             : 
      49             : ```python
      50             : import plumed
      51             : 
      52             : # Create a PLUMED object
      53             : p = plumed.Plumed()
      54             : p.cmd("readInputLine", "pbc: PBC")
      55             : ```
      56             : 
      57             : */
      58             : //+ENDPLUMEDOC
      59             : 
      60             : namespace PLMD {
      61             : 
      62             : PLUMED_REGISTER_ACTION(PbcAction,"PBC")
      63             : 
      64        1223 : void PbcAction::registerKeywords( Keywords& keys ) {
      65        1223 :   Action::registerKeywords( keys );
      66        1223 :   keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log");
      67        2446 :   keys.setValueDescription("matrix","a matrix containing the cell vectors that were passed from the MD code");
      68        1223 : }
      69             : 
      70        1216 : PbcAction::PbcAction(const ActionOptions&ao):
      71             :   Action(ao),
      72             :   ActionToPutData(ao),
      73        1216 :   interface(NULL) {
      74        1216 :   std::vector<unsigned> shape(2);
      75        1216 :   shape[0]=shape[1]=3;
      76        1216 :   addValue( shape );
      77        1216 :   setNotPeriodic();
      78        2432 :   setUnit( "length", "energy" );
      79        1216 :   getPntrToValue()->buildDataStore();
      80        1216 :   getPntrToValue()->reshapeMatrixStore(3);
      81        1216 : }
      82             : 
      83             : 
      84       68710 : void PbcAction::setPbc() {
      85       68710 :   if( !interface ) {
      86        1013 :     std::vector<DomainDecomposition*> allput=plumed.getActionSet().select<DomainDecomposition*>();
      87        1013 :     if( allput.size()>1 ) {
      88           0 :       warning("found more than one interface so don't know how to broadcast cell");
      89             :     }
      90        1013 :     interface = allput[0];
      91             :   }
      92       68710 :   Tensor box;
      93       68710 :   if( interface ) {
      94       68710 :     interface->broadcastToDomains( getPntrToValue() );
      95             :   }
      96      274840 :   for(unsigned i=0; i<3; ++i)
      97      824520 :     for(unsigned j=0; j<3; ++j) {
      98      618390 :       box(i,j) = getPntrToValue()->get(3*i+j);
      99             :     }
     100       68710 :   pbc.setBox(box);
     101       68710 : }
     102             : 
     103       68596 : void PbcAction::wait() {
     104       68596 :   ActionToPutData::wait();
     105       68596 :   setPbc();
     106       68596 : }
     107             : 
     108         114 : void PbcAction::readBinary(std::istream&i) {
     109         114 :   ActionToPutData::readBinary(i);
     110         114 :   setPbc();
     111         114 : }
     112             : 
     113             : }
     114             : 
     115             : 
     116             :