GlobalMasterTMD Class Reference

#include <GlobalMasterTMD.h>

Inheritance diagram for GlobalMasterTMD:

GlobalMaster List of all members.

Public Member Functions

 GlobalMasterTMD ()
 ~GlobalMasterTMD ()

Detailed Description

Copyright (c) 1995, 1996, 1997, 1998, 1999, 2000 by The Board of Trustees of the University of Illinois. All rights reserved.

Definition at line 17 of file GlobalMasterTMD.h.


Constructor & Destructor Documentation

GlobalMasterTMD::GlobalMasterTMD (  ) 

Definition at line 81 of file GlobalMasterTMD.C.

References DebugM, endi(), SimParameters::firstTimestep, if(), iINFO(), iout, Node::molecule, Molecule::numAtoms, Node::Object(), Node::simParameters, SimParameters::TMDDiffRMSD, SimParameters::TMDFile, SimParameters::TMDFile2, SimParameters::TMDFinalRMSD, SimParameters::TMDFirstStep, SimParameters::TMDInitialRMSD, SimParameters::TMDk, SimParameters::TMDLastStep, and SimParameters::TMDOutputFreq.

00081                                  {
00082   DebugM(3,"initialize called\n");
00083   SimParameters *params = Node::Object()->simParameters;
00084   outputFreq = params->TMDOutputFreq;
00085   K = params->TMDk;
00086 /*  if (params->TMDInitialRMSD < 0){
00087     initialRMS = -1; // get from first coordinates
00088   }
00089   else */
00090     initialRMS = params->TMDInitialRMSD;
00091   finalRMS = params->TMDFinalRMSD;
00092   
00093   currentStep = params->firstTimestep;
00094   firstStep = params->TMDFirstStep;
00095   lastStep = params->TMDLastStep;
00096   qDiffRMSD=params->TMDDiffRMSD;
00097   altloc = 0;
00098   target = 0;
00099   target2 = 0;
00100   weight = 0;
00101   if (qDiffRMSD) parseAtoms(params->TMDFile2,Node::Object()->molecule->numAtoms, 1);
00102   parseAtoms(params->TMDFile,Node::Object()->molecule->numAtoms, 0);
00103 
00104   //iterate through all domains to see if altloc is used
00105   map <int, vector<int> >::iterator it;
00106   for (it = dmap.begin(); it != dmap.end(); ++it){  
00107     int refcount = 0;
00108     int biascount = 0;
00109     for(int i = 0; i<it->second.size(); i++){
00110       char aloc = altloc[it->second[i]];
00111       if ( aloc & 1 ) ++biascount;
00112       if ( aloc & 2 ) ++refcount;
00113     }
00114     altlocmap[it->first] = ( refcount ? 1 : 0 );
00115     if ( ! refcount ) refcount = it->second.size();
00116     iout << iINFO << "TMD domain " << it->first <<
00117       " has " << it->second.size() << " atoms " <<
00118       refcount << " fitted " << biascount << " biased\n" << endi;
00119   }
00120 
00121  // k /= numTMDatoms;
00122   iout << iINFO << numTMDatoms << " TMD ATOMS\n" << endi;
00123   DebugM(1,"done with initialize\n");
00124 }

GlobalMasterTMD::~GlobalMasterTMD (  ) 

Definition at line 227 of file GlobalMasterTMD.C.

00227                                   { 
00228   delete [] target;
00229  // delete [] target_aid;
00230 //  delete [] aidmap;
00231   delete [] atompos;
00232   delete [] atompos2;
00233   delete [] altloc;
00234   delete [] target2;
00235 }


The documentation for this class was generated from the following files:
Generated on Sat Sep 23 01:17:19 2017 for NAMD by  doxygen 1.4.7