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/* |
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* Shapes_FF.cpp |
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* oopse |
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* |
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* Created by Chris Fennell on 10/20/04. |
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* Copyright 2004 __MyCompanyName__. All rights reserved. |
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* |
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*/ |
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|
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#include <stdlib.h> |
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#include <stdio.h> |
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#include <string.h> |
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#include <map> |
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#include <iostream> |
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|
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using namespace std; |
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using namespace oopse; |
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|
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#ifdef IS_MPI |
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#include <mpi.h> |
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#endif //is_mpi |
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|
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#include "UseTheForce/ForceFields.hpp" |
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#include "primitives/SRI.hpp" |
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#include "utils/simError.h" |
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#include "io/basic_ifstrstream.hpp" |
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#include "math/RealSphericalHarmonic.hpp" |
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#include "math/SquareMatrix3.hpp" |
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|
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#include "UseTheForce/DarkSide/atype_interface.h" |
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#include "UseTheForce/DarkSide/shapes_interface.h" |
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|
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#ifdef IS_MPI |
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#include "UseTheForce/mpiForceField.h" |
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#endif // is_mpi |
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|
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Shapes_FF::Shapes_FF() { |
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Shapes_FF(""); |
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} |
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|
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Shapes_FF::Shapes_FF(char* the_variant){ |
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ffPath_env = "FORCE_PARAM_PATH"; |
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|
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} |
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|
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Shapes_FF::~Shapes_FF(){ |
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|
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#ifdef IS_MPI |
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if( worldRank == 0 ){ |
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#endif // is_mpi |
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|
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fclose( frcFile ); |
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|
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#ifdef IS_MPI |
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} |
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#endif // is_mpi |
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} |
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|
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|
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void Shapes_FF::calcRcut( void ){ |
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|
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#ifdef IS_MPI |
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double tempShapesRcut = shapesRcut; |
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MPI_Allreduce( &tempShapesRcut, &shapesRcut, 1, MPI_DOUBLE, MPI_MAX, |
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MPI_COMM_WORLD); |
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#endif //is_mpi |
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entry_plug->setDefaultRcut(shapesRcut); |
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} |
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|
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|
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void Shapes_FF::initForceField(){ |
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initFortran(0); |
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} |
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|
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|
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void Shapes_FF::readForceFile( void ){ |
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|
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char readLine[1024]; |
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char fileName[200]; |
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char temp[200]; |
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char* ffPath; |
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char *shapeFileName; |
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char *nameToken; |
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char *delim = " ,;\t\n"; |
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int nTokens, i; |
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int nContact = 0; |
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int nRange = 0; |
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int nStrength = 0; |
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int myATID; |
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string nameString; |
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ShapeType* st; |
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map<string, AtomType*> atomTypeMap; |
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map<string, AtomType*>::iterator iter; |
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|
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// vectors for shape transfer to fortran |
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vector<RealSphericalHarmonic> tempSHVector; |
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vector<int> contactL; |
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vector<int> contactM; |
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vector<int> contactFunc; |
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vector<double> contactCoeff; |
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vector<int> rangeL; |
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vector<int> rangeM; |
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vector<int> rangeFunc; |
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vector<double> rangeCoeff; |
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vector<int> strengthL; |
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vector<int> strengthM; |
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vector<int> strengthFunc; |
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vector<double> strengthCoeff; |
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|
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// build a basic file reader |
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ifstrsteam frcReader; |
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|
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// generate the force file name |
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strcpy( fileName, "Shapes.frc" ); |
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|
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// attempt to open the file in the current directory first. |
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frcReader.open( fileName ); |
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|
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if( frcReader == NULL ){ |
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|
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// next see if the force path enviorment variable is set |
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|
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ffPath = getenv( ffPath_env ); |
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if( ffPath == NULL ) { |
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STR_DEFINE(ffPath, FRC_PATH ); |
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} |
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|
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strcpy( temp, ffPath ); |
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strcat( temp, "/" ); |
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strcat( temp, fileName ); |
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strcpy( fileName, temp ); |
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|
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frcReader.open( fileName ); |
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|
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if( frcFile == NULL ){ |
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|
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sprintf( painCave.errMsg, |
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"Error opening the force field parameter file:\n" |
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"\t%s\n" |
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"\tHave you tried setting the FORCE_PARAM_PATH environment " |
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"variable?\n", |
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fileName ); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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// read in the shape types. |
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|
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findBegin( "ShapeTypes" ); |
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|
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while( !frcReader.eof() ){ |
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frcReader.getline( readLine, sizeof(readLine) ); |
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|
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// toss comment lines |
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if( readLine[0] != '!' && readLine[0] != '#' ){ |
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|
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if (isEndLine(readLine)) break; |
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|
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nTokens = count_tokens(readLine, " ,;\t"); |
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if (nTokens != 0) { |
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if (nTokens < 2) { |
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sprintf( painCave.errMsg, |
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"Not enough data on a ShapeTypes line in file: %s\n" |
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fileName ); |
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painCave.severity = OOPSE_ERROR; |
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painCave.isFatal = 1; |
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simError(); |
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} |
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|
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nameToken = strtok( readLine, delim ); |
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shapeFileName = strtok( NULL, delim ); |
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|
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// strings are not char arrays! |
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nameString = nameToken; |
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|
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// does this AtomType name already exist in the map? |
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iter = atomTypeMap.find(nameString); |
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if (iter == atomTypeMap.end()) { |
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// no, it doesn't, so we may proceed: |
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|
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st = new ShapeType(); |
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|
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st->setName(nameString); |
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myATID = atomTypeMap.size(); |
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st->setIdent(myATID); |
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parseShapeFile(shapeFileName, st); |
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st->complete(); |
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atomTypeMap.insert(make_pair(nameString, st)); |
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|
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} else { |
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// atomType map already contained this string (i.e. it was |
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// declared in a previous block, and we just need to add |
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// the shape-specific information for this AtomType: |
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|
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st = (ShapeType*)(iter->second); |
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parseShapeFile(shapeFileName, st); |
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} |
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} |
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} |
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} |
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|
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#ifdef IS_MPI |
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|
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// looks like all the processors have their ShapeType vectors ready... |
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sprintf( checkPointMsg, |
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"Shapes_FF shape objects read successfully." ); |
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MPIcheckPoint(); |
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|
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#endif // is_mpi |
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|
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// pack up and send the necessary info to fortran |
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for (iter = atomTypeMap.begin(); iter != atomTypeMap.end(); ++iter){ |
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|
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at = (AtomType*)(iter.second); |
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|
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if (at->isDirectional()) { |
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|
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dat = (DirectionalAtomType*)at; |
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|
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if (dat->isShape()) { |
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|
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st = (ShapeAtomType*)at; |
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|
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contactL.clear(); |
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contactM.clear(); |
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contactFunc.clear(); |
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contactCoeff.clear(); |
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|
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tempSHVector = st->getContactFuncs(); |
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|
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nContact = tempSHVector.size(); |
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for (i=0; i<nContact; i++){ |
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contactL.push_back(tempSHVector[i].getL()); |
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contactM.push_back(tempSHVector[i].getM()); |
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contactFunc.push_back(tempSHVector[i].getFunctionType()); |
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contactCoeff.push_back(tempSHVector[i].getCoefficient()); |
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} |
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|
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rangeL.clear(); |
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rangeM.clear(); |
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rangeFunc.clear(); |
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rangeCoeff.clear(); |
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|
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tempSHVector = st->getRangeFuncs(); |
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|
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nRange = tempSHVector.size(); |
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for (i=0; i<nRange; i++){ |
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rangeL.push_back(tempSHVector[i].getL()); |
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rangeM.push_back(tempSHVector[i].getM()); |
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rangeFunc.push_back(tempSHVector[i].getFunctionType()); |
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rangeCoeff.push_back(tempSHVector[i].getCoefficient()); |
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} |
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|
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strengthL.clear(); |
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strengthM.clear(); |
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strengthFunc.clear(); |
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strengthCoeff.clear(); |
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|
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tempSHVector = st->getStrengthFuncs(); |
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|
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nStrength = tempSHVector.size(); |
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for (i=0; i<nStrength; i++){ |
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strengthL.push_back(tempSHVector[i].getL()); |
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strengthM.push_back(tempSHVector[i].getM()); |
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strengthFunc.push_back(tempSHVector[i].getFunctionType()); |
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strengthCoeff.push_back(tempSHVector[i].getCoefficient()); |
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} |
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|
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isError = 0; |
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myATID = at->getIdent(); |
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makeShape( &nContact, &contactL, &contactM, &contactFunc, |
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&contactCoeff, |
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&nRange, &rangeL, &rangeM, &rangeFunc, &rangeCoeff, |
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&nStrength, &strengthL, &strengthM, |
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&strengthFunc, &strengthCoeff, |
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&myATID, |
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&isError); |
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if( isError ){ |
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sprintf( painCave.errMsg, |
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"Error initializing the \"%s\" shape in fortran\n", |
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marker->first ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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} |
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} |
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|
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#ifdef IS_MPI |
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sprintf( checkPointMsg, |
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"Shapes_FF atom structures successfully sent to fortran\n" ); |
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MPIcheckPoint(); |
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#endif // is_mpi |
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|
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} |
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|
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void SHAPES_FF::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
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|
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int i,j,k; |
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|
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// initialize the atoms |
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DirectionalAtom* dAtom; |
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AtomType* at; |
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DirectionalAtomType* dat; |
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double mySigma; |
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double ji[3]; |
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double inertialMat[3][3]; |
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Mat3x3d momInt; |
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string myTypeString; |
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|
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for( i=0; i<nAtoms; i++ ){ |
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|
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myTypeString = the_atoms[i]->getType(); |
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iter = atomTypeMap.find(myTypeString); |
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|
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if (iter == atomTypeMap.end()) { |
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sprintf( painCave.errMsg, |
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"AtomType error, %s not found in force file.\n", |
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the_atoms[i]->getType() ); |
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painCave.isFatal = 1; |
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simError(); |
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} else { |
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|
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at = (AtomType*)(iter->second); |
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|
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the_atoms[i]->setMass( at->getMass() ); |
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the_atoms[i]->setIdent( at->getIdent() ); |
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|
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if( at->isLennardJones() ) { |
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mySigma = at->properties->getPropertyByName("sigma"); |
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if( bigSigma < mySigma ) bigSigma = mySigma; |
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} |
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|
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the_atoms[i]->setHasCharge(at->isCharge()); |
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|
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if( at->isDirectional() ){ |
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|
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dat = (DirectionalAtomType*)at; |
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dAtom = (DirectionalAtom *) the_atoms[i]; |
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|
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momInt = dat->getI(); |
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|
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// zero out the moments of inertia matrix |
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for( j=0; j<3; j++ ) |
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for( k=0; k<3; k++ ) |
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inertialMat[j][k] = momInt(j,k); |
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dAtom->setI( inertialMat ); |
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|
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ji[0] = 0.0; |
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ji[1] = 0.0; |
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ji[2] = 0.0; |
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dAtom->setJ( ji ); |
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|
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if (dat->isDipole()) { |
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dAtom->setHasDipole( dat->isDipole() ); |
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entry_plug->n_dipoles++; |
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} |
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} |
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} |
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} |
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} |
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|
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void Shapes_FF::initializeBonds( int nBonds, Bond** BondArray, |
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bond_pair* the_bonds ){ |
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|
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if( nBonds ){ |
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sprintf( painCave.errMsg, |
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"Shapes_FF does not support bonds.\n" ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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void Shapes_FF::initializeBends( int nBends, Bend** bendArray, |
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bend_set* the_bends ){ |
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|
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if( nBends ){ |
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sprintf( painCave.errMsg, |
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"Shapes_FF does not support bends.\n" ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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void Shapes_FF::initializeTorsions( int nTorsions, Torsion** torsionArray, |
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torsion_set* the_torsions ){ |
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|
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if( nTorsions ){ |
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sprintf( painCave.errMsg, |
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"Shapes_FF does not support torsions.\n" ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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|
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int Shapes_FF::parseShapeFile(char *shapeFile, ShapeAtomType* st){ |
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const int MAXLEN = 1024; |
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char inLine[MAXLEN]; |
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char *token; |
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char *delim = " ,;\t\n"; |
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Mat3x3d momInert; |
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RealSphericalHarmonic tempHarmonic; |
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vector<RealSphericalHarmonic> functionVector; |
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|
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ifstrstream shapeFile; |
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|
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// first grab the values in the ShapeInfo section |
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findBegin(shapeFile, "ShapeInfo"); |
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|
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shapeFile.getline(inLine, MAXLEN); |
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while( !shapeFile.eof() ) { |
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// toss comment lines |
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if( inLine[0] != '!' && inLine[0] != '#' ){ |
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// end marks section completion |
417 |
if (isEndLine(inLine)) break; |
418 |
|
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nTokens = count_tokens(inLine, delim); |
420 |
if (nTokens != 0) { |
421 |
if (nTokens < 5) { |
422 |
sprintf( painCave.errMsg, |
423 |
"Not enough data on a ShapeInfo line in file: %s\n" |
424 |
fileName ); |
425 |
painCave.severity = OOPSE_ERROR; |
426 |
painCave.isFatal = 1; |
427 |
simError(); |
428 |
|
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token = strtok(inLine, delim); |
430 |
token = strtok(NULL, delim); |
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st->setMass(atof(token)); |
432 |
token = strtok(NULL, delim); |
433 |
momInert(0,0) = atof(token); |
434 |
token = strtok(NULL, delim); |
435 |
momInert(1,1) = atof(token); |
436 |
token = strtok(NULL, delim); |
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momInert(2,2) = atof(token); |
438 |
st->setI(momInert); |
439 |
} |
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} |
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} |
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} |
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|
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// now grab the contact functions |
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findBegin(shapeFile, "ContactFunctions"); |
446 |
functionVector.clear(); |
447 |
|
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shapeFile.getline(inLine, MAXLEN); |
449 |
while( !shapeFile.eof() ) { |
450 |
// toss comment lines |
451 |
if( inLine[0] != '!' && inLine[0] != '#' ){ |
452 |
// end marks section completion |
453 |
if (isEndLine(inLine)) break; |
454 |
|
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nTokens = count_tokens(inLine, delim); |
456 |
if (nTokens != 0) { |
457 |
if (nTokens < 4) { |
458 |
sprintf( painCave.errMsg, |
459 |
"Not enough data on a ContactFunctions line in file: %s\n" |
460 |
fileName ); |
461 |
painCave.severity = OOPSE_ERROR; |
462 |
painCave.isFatal = 1; |
463 |
simError(); |
464 |
|
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// read in a spherical harmonic function |
466 |
token = strtok(inLine, delim); |
467 |
tempHarmonic.setL(atoi(token)); |
468 |
token = strtok(NULL, delim); |
469 |
tempHarmonic.setM(atoi(token)); |
470 |
token = strtok(NULL, delim); |
471 |
if (!strcasecmp("sin",token)) |
472 |
tempHarmonic.makeSinFunction(); |
473 |
else |
474 |
tempHarmonic.makeCosFunction(); |
475 |
token = strtok(NULL, delim); |
476 |
tempHarmonic.setCoefficient(atof(token)); |
477 |
|
478 |
functionVector.push_back(tempHarmonic); |
479 |
} |
480 |
} |
481 |
} |
482 |
} |
483 |
|
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// pass contact functions to ShapeType |
485 |
st->setContactFuncs(functionVector); |
486 |
|
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// now grab the range functions |
488 |
findBegin(shapeFile, "RangeFunctions"); |
489 |
functionVector.clear(); |
490 |
|
491 |
shapeFile.getline(inLine, MAXLEN); |
492 |
while( !shapeFile.eof() ) { |
493 |
// toss comment lines |
494 |
if( inLine[0] != '!' && inLine[0] != '#' ){ |
495 |
// end marks section completion |
496 |
if (isEndLine(inLine)) break; |
497 |
|
498 |
nTokens = count_tokens(inLine, delim); |
499 |
if (nTokens != 0) { |
500 |
if (nTokens < 4) { |
501 |
sprintf( painCave.errMsg, |
502 |
"Not enough data on a RangeFunctions line in file: %s\n" |
503 |
fileName ); |
504 |
painCave.severity = OOPSE_ERROR; |
505 |
painCave.isFatal = 1; |
506 |
simError(); |
507 |
|
508 |
// read in a spherical harmonic function |
509 |
token = strtok(inLine, delim); |
510 |
tempHarmonic.setL(atoi(token)); |
511 |
token = strtok(NULL, delim); |
512 |
tempHarmonic.setM(atoi(token)); |
513 |
token = strtok(NULL, delim); |
514 |
if (!strcasecmp("sin",token)) |
515 |
tempHarmonic.makeSinFunction(); |
516 |
else |
517 |
tempHarmonic.makeCosFunction(); |
518 |
token = strtok(NULL, delim); |
519 |
tempHarmonic.setCoefficient(atof(token)); |
520 |
|
521 |
functionVector.push_back(tempHarmonic); |
522 |
} |
523 |
} |
524 |
} |
525 |
} |
526 |
|
527 |
// pass range functions to ShapeType |
528 |
st->setRangeFuncs(functionVector); |
529 |
|
530 |
// finally grab the strength functions |
531 |
findBegin(shapeFile, "StrengthFunctions"); |
532 |
functionVector.clear(); |
533 |
|
534 |
shapeFile.getline(inLine, MAXLEN); |
535 |
while( !shapeFile.eof() ) { |
536 |
// toss comment lines |
537 |
if( inLine[0] != '!' && inLine[0] != '#' ){ |
538 |
// end marks section completion |
539 |
if (isEndLine(inLine)) break; |
540 |
|
541 |
nTokens = count_tokens(inLine, delim); |
542 |
if (nTokens != 0) { |
543 |
if (nTokens < 4) { |
544 |
sprintf( painCave.errMsg, |
545 |
"Not enough data on a StrengthFunctions line in file: %s\n" |
546 |
fileName ); |
547 |
painCave.severity = OOPSE_ERROR; |
548 |
painCave.isFatal = 1; |
549 |
simError(); |
550 |
|
551 |
// read in a spherical harmonic function |
552 |
token = strtok(inLine, delim); |
553 |
tempHarmonic.setL(atoi(token)); |
554 |
token = strtok(NULL, delim); |
555 |
tempHarmonic.setM(atoi(token)); |
556 |
token = strtok(NULL, delim); |
557 |
if (!strcasecmp("sin",token)) |
558 |
tempHarmonic.makeSinFunction(); |
559 |
else |
560 |
tempHarmonic.makeCosFunction(); |
561 |
token = strtok(NULL, delim); |
562 |
tempHarmonic.setCoefficient(atof(token)); |
563 |
|
564 |
functionVector.push_back(tempHarmonic); |
565 |
} |
566 |
} |
567 |
} |
568 |
} |
569 |
|
570 |
// pass strength functions to ShapeType |
571 |
st->setStrengthFuncs(functionVector); |
572 |
|
573 |
// we're done reading from this file |
574 |
shapeFile.close(); |
575 |
return 0; |
576 |
} |
577 |
|