GlobalMasterSymmetry Class Reference

#include <GlobalMasterSymmetry.h>

Inheritance diagram for GlobalMasterSymmetry:

GlobalMaster List of all members.

Public Member Functions

 GlobalMasterSymmetry ()
 ~GlobalMasterSymmetry ()

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 16 of file GlobalMasterSymmetry.h.


Constructor & Destructor Documentation

GlobalMasterSymmetry::GlobalMasterSymmetry (  ) 

Definition at line 57 of file GlobalMasterSymmetry.C.

References Node::configList, StringList::data, DebugM, ConfigList::find(), SimParameters::firstTimestep, if(), Node::molecule, NAMD_die(), StringList::next, Molecule::numAtoms, Node::Object(), Node::simParameters, SimParameters::symmetryFirstFullStep, SimParameters::symmetryFirstStep, SimParameters::symmetryk, SimParameters::symmetryLastFullStep, SimParameters::symmetryLastStep, and SimParameters::symmetryScaleForces.

00057                                            {
00058   DebugM(3,"initialize called\n");
00059   SimParameters *params = Node::Object()->simParameters;
00060   currentStep = params->firstTimestep;
00061   firstStep = params->symmetryFirstStep;
00062   lastStep = params->symmetryLastStep;
00063   firstFullStep = params->symmetryFirstFullStep;
00064   lastFullStep = params->symmetryLastFullStep;
00065   K = params->symmetryk;
00066 
00067   StringList *klist = Node::Object()->configList->find("symmetrykfile");
00068   if (!K){
00069     //if (!params->symmetrykfile){NAMD_die("A pdb file containing per-atom force constants must be specified if symmetryk is not in configuration file!");}
00070     if (!klist){NAMD_die("A pdb file containing per-atom force constants must be specified if symmetryk is not in configuration file!");}
00071     //symmetrykfile = params->symmetrykfile;
00072   }
00073   scaleForces = params->symmetryScaleForces;
00074   if (scaleForces && lastStep == -1){
00075     NAMD_die("symmetryLastStep must be specified if symmetryScaleForces is enabled!");
00076   }
00077   StringList *matrixList = Node::Object()->configList->find("symmetryMatrixFile");
00078   StringList *symmetryList = Node::Object()->configList->find("symmetryFile");
00079   int symfileindex = 0;
00080   if (!K) {symmetrykfile = klist->data;}
00081   for (; symmetryList; symmetryList = symmetryList->next) {  
00082     parseAtoms(symmetryList->data, Node::Object()->molecule->numAtoms, symfileindex);
00083     if(!K){
00084       klist = klist->next;
00085      if (klist){ symmetrykfile = klist->data;}
00086     }
00087   }
00088 
00089   map<int, vector<int> >::iterator it = simmap.begin();
00090   if (!matrixList) {initialTransform();}
00091   for (; matrixList; matrixList = matrixList->next, ++it){
00092       parseMatrix(it->first, matrixList->data);
00093   }
00094 
00095   DebugM(1,"done with initialize\n");
00096 }

GlobalMasterSymmetry::~GlobalMasterSymmetry (  ) 

Definition at line 395 of file GlobalMasterSymmetry.C.

00395                                             { 
00396   map <int, BigReal *>::iterator pit = posmap.begin();
00397   for (; pit != posmap.end(); ++pit){delete pit->second;}
00398 }


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