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        2185 : void PbcAction::registerKeywords( Keywords& keys ) {
      65        2185 :   Action::registerKeywords( keys );
      66        2185 :   keys.add("hidden","NO_ACTION_LOG","suppresses printing from action on the log");
      67        4370 :   keys.setValueDescription("matrix","a matrix containing the cell vectors that were passed from the MD code");
      68        2185 : }
      69             : 
      70        2176 : PbcAction::PbcAction(const ActionOptions&ao):
      71             :   Action(ao),
      72             :   ActionToPutData(ao),
      73        2176 :   interface(NULL) {
      74        2176 :   std::vector<std::size_t> shape(2);
      75        2176 :   shape[0]=shape[1]=3;
      76        2176 :   addValue( shape );
      77        2176 :   setNotPeriodic();
      78        4352 :   setUnit( "length", "energy" );
      79        2176 :   getPntrToValue()->reshapeMatrixStore(3);
      80        2176 : }
      81             : 
      82             : 
      83      160048 : void PbcAction::setPbc() {
      84      160048 :   if( !interface ) {
      85        1811 :     std::vector<DomainDecomposition*> allput=plumed.getActionSet().select<DomainDecomposition*>();
      86        1811 :     if( allput.size()>1 ) {
      87           0 :       warning("found more than one interface so don't know how to broadcast cell");
      88             :     }
      89        1811 :     if( !allput.empty() ) {
      90        1811 :       interface = allput[0];
      91             :     }
      92             :   }
      93      160048 :   Tensor box;
      94      160048 :   if( interface ) {
      95      160048 :     interface->broadcastToDomains( getPntrToValue() );
      96             :   }
      97      640192 :   for(unsigned i=0; i<3; ++i)
      98     1920576 :     for(unsigned j=0; j<3; ++j) {
      99     1440432 :       box(i,j) = getPntrToValue()->get(3*i+j);
     100             :     }
     101      160048 :   pbc.setBox(box);
     102      160048 : }
     103             : 
     104      159922 : void PbcAction::wait() {
     105      159922 :   ActionToPutData::wait();
     106      159922 :   setPbc();
     107      159922 : }
     108             : 
     109         126 : void PbcAction::readBinary(std::istream&i) {
     110         126 :   ActionToPutData::readBinary(i);
     111         126 :   setPbc();
     112         126 : }
     113             : 
     114             : }
     115             : 
     116             : 
     117             :