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         189 : void AnalysisBase::registerKeywords( Keywords& keys ) {
      31         189 :   Action::registerKeywords( keys );
      32         189 :   ActionPilot::registerKeywords( keys );
      33         189 :   ActionWithValue::registerKeywords( keys );
      34         189 :   ActionAtomistic::registerKeywords( keys );
      35         189 :   ActionWithArguments::registerKeywords( keys );
      36         189 :   keys.remove("NUMERICAL_DERIVATIVES");
      37         189 :   ActionWithVessel::registerKeywords( keys );
      38         189 :   keys.remove("TOL");
      39         378 :   keys.reset_style("TIMINGS","hidden");
      40             :   keys.isAnalysis();
      41         378 :   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");
      42         189 : }
      43             : 
      44         109 : AnalysisBase::AnalysisBase(const ActionOptions&ao):
      45             :   Action(ao),
      46             :   ActionPilot(ao),
      47             :   ActionWithValue(ao),
      48             :   ActionAtomistic(ao),
      49             :   ActionWithArguments(ao),
      50             :   ActionWithVessel(ao),
      51         109 :   my_input_data(NULL) {
      52             :   // We have an if statement here so that this doesn't break with READ_DISSIMILARITIES
      53         218 :   if( keywords.exists("USE_OUTPUT_DATA_FROM") ) {
      54             :     std::string datastr;
      55          78 :     parse("USE_OUTPUT_DATA_FROM",datastr);
      56         156 :     if( keywords.style("USE_OUTPUT_DATA_FROM","atoms") && datastr.length()==0 ) {
      57           0 :       error("input analysis action was not specified use USE_OUTPUT_DATA_FROM");
      58             :     }
      59          78 :     if( datastr.length()>0 ) {
      60          77 :       my_input_data=plumed.getActionSet().selectWithLabel<AnalysisBase*>( datastr );
      61          77 :       log.printf("  performing analysis on output from %s \n",datastr.c_str() );
      62          77 :       if( !my_input_data ) {
      63           0 :         error("could not find analysis action named " + datastr );
      64             :       }
      65          77 :       addDependency( my_input_data );
      66             :     }
      67             :   }
      68         109 : }
      69             : 
      70          50 : std::vector<std::string> AnalysisBase::getArgumentNames() {
      71          50 :   std::vector<Value*> arg_p( getArgumentList() );
      72          50 :   std::vector<std::string> argn( arg_p.size() );
      73         124 :   for(unsigned i=0; i<arg_p.size(); ++i) {
      74          74 :     plumed_assert( i<argn.size() && i<arg_p.size() );
      75          74 :     argn[i]=arg_p[i]->getName();
      76             :   }
      77          50 :   return argn;
      78           0 : }
      79             : 
      80          39 : void AnalysisBase::update() {
      81          39 :   if( getStep()==0 || ( getStride()>0 && !onStep() ) ) {
      82           9 :     return;
      83             :   }
      84             :   // And do the analysis
      85          30 :   performAnalysis();
      86             : }
      87             : 
      88         107 : void AnalysisBase::runFinalJobs() {
      89         107 :   if( getStride()>0 ) {
      90             :     return;
      91             :   }
      92          69 :   performAnalysis();
      93             : }
      94             : 
      95             : }
      96             : }