Line data    Source code

       1             : /* +++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
       2             :    Copyright (c) 2015-2023 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 "AnalysisBase.h"
      23             : #include "ReadAnalysisFrames.h"
      24             : #include "core/PlumedMain.h"
      25             : #include "core/ActionSet.h"
      26             : 
      27             : namespace PLMD {
      28             : namespace analysis {
      29             : 
      30         129 : void AnalysisBase::registerKeywords( Keywords& keys ) {
      31         129 :   Action::registerKeywords( keys ); ActionPilot::registerKeywords( keys );
      32         129 :   ActionWithValue::registerKeywords( keys ); ActionAtomistic::registerKeywords( keys );
      33         129 :   ActionWithArguments::registerKeywords( keys ); keys.remove("NUMERICAL_DERIVATIVES");
      34         387 :   ActionWithVessel::registerKeywords( keys ); keys.remove("TOL"); keys.reset_style("TIMINGS","hidden"); keys.isAnalysis();
      35         387 :   keys.add("atoms-2","USE_OUTPUT_DATA_FROM","use the output of the analysis performed by this object as input to your new analysis object");
      36         129 : }
      37             : 
      38         109 : AnalysisBase::AnalysisBase(const ActionOptions&ao):
      39             :   Action(ao),
      40             :   ActionPilot(ao),
      41             :   ActionWithValue(ao),
      42             :   ActionAtomistic(ao),
      43             :   ActionWithArguments(ao),
      44             :   ActionWithVessel(ao),
      45         109 :   my_input_data(NULL)
      46             : {
      47             :   // We have an if statement here so that this doesn't break with READ_DISSIMILARITIES
      48         218 :   if( keywords.exists("USE_OUTPUT_DATA_FROM") ) {
      49          78 :     std::string datastr; parse("USE_OUTPUT_DATA_FROM",datastr);
      50         156 :     if( keywords.style("USE_OUTPUT_DATA_FROM","atoms") && datastr.length()==0 ) error("input analysis action was not specified use USE_OUTPUT_DATA_FROM");
      51          78 :     if( datastr.length()>0 ) {
      52          77 :       my_input_data=plumed.getActionSet().selectWithLabel<AnalysisBase*>( datastr );
      53          77 :       log.printf("  performing analysis on output from %s \n",datastr.c_str() );
      54          77 :       if( !my_input_data ) error("could not find analysis action named " + datastr );
      55          77 :       addDependency( my_input_data );
      56             :     }
      57             :   }
      58         109 : }
      59             : 
      60          50 : std::vector<std::string> AnalysisBase::getArgumentNames() {
      61          50 :   std::vector<Value*> arg_p( getArgumentList() );
      62          50 :   std::vector<std::string> argn( arg_p.size() );
      63         124 :   for(unsigned i=0; i<arg_p.size(); ++i) {
      64          74 :     plumed_assert( i<argn.size() && i<arg_p.size() );
      65          74 :     argn[i]=arg_p[i]->getName();
      66             :   }
      67          50 :   return argn;
      68           0 : }
      69             : 
      70          39 : void AnalysisBase::update() {
      71          39 :   if( getStep()==0 || ( getStride()>0 && !onStep() ) ) return;
      72             :   // And do the analysis
      73          30 :   performAnalysis();
      74             : }
      75             : 
      76         107 : void AnalysisBase::runFinalJobs() {
      77         107 :   if( getStride()>0 ) return;
      78          69 :   performAnalysis();
      79             : }
      80             : 
      81             : }
      82             : }