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/* |
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/* |
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* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved. |
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* |
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* The University of Notre Dame grants you ("Licensee") a |
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* such damages. |
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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 <cmath> |
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#include <iostream> |
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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 "utils/StringUtils.hpp" |
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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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#include "types/ShapeAtomType.hpp" |
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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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|
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using namespace oopse; |
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|
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Shapes_FF::~Shapes_FF(){ |
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|
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destroyShapeTypes(); |
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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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#include "UseTheForce/DarkSide/lj_interface.h" |
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#include "UseTheForce/DarkSide/sticky_interface.h" |
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#include "UseTheForce/ForceFieldFactory.hpp" |
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#include "io/DirectionalAtomTypesSectionParser.hpp" |
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#include "io/AtomTypesSectionParser.hpp" |
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#include "io/LennardJonesAtomTypesSectionParser.hpp" |
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#include "io/ChargeAtomTypesSectionParser.hpp" |
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#include "io/MultipoleAtomTypesSectionParser.hpp" |
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#include "io/ShapeAtomTypesSectionParser.hpp" |
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#include "io/StickyAtomTypesSectionParser.hpp" |
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#include "io/BondTypesSectionParser.hpp" |
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#include "io/BendTypesSectionParser.hpp" |
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#include "io/TorsionTypesSectionParser.hpp" |
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#include "UseTheForce/ForceFieldCreator.hpp" |
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#include "utils/simError.h" |
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namespace oopse { |
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|
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forceFile.close(); |
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SHAPES_FF::SHAPES_FF(){ |
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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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//set default force field filename |
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setForceFieldFileName("EAM.frc"); |
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|
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//The order of adding section parsers are important |
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//DirectionalAtomTypesSectionParser should be added before |
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//AtomTypesSectionParser since these two section parsers will actually |
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//create "real" AtomTypes (AtomTypesSectionParser will create AtomType |
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//and DirectionalAtomTypesSectionParser will creat DirectionalAtomType |
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//which is a subclass of AtomType, therefore it should come first). Other |
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//AtomTypes Section Parser will not create the "real" AtomType, they only |
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//add and set some attribute of the AtomType. Thus their order are not |
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//important. AtomTypesSectionParser should be added before other atom |
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//type section parsers. Make sure they are added after |
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//DirectionalAtomTypesSectionParser and AtomTypesSectionParser. The order |
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//of BondTypesSectionParser, BendTypesSectionParser and |
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//TorsionTypesSectionParser are not important. |
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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 = bigContact; |
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MPI_Allreduce( &tempShapesRcut, &shapesRcut, 1, MPI_DOUBLE, MPI_MAX, |
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MPI_COMM_WORLD); |
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#else |
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shapesRcut = bigContact; |
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#endif //is_mpi |
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entry_plug->setDefaultRcut(shapesRcut); |
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spMan_.push_back(new ShapeAtomTypesSectionParser()); |
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spMan_.push_back(new DirectionalAtomTypesSectionParser()); |
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spMan_.push_back(new AtomTypesSectionParser()); |
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spMan_.push_back(new LennardJonesAtomTypesSectionParser()); |
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spMan_.push_back(new ChargeAtomTypesSectionParser()); |
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spMan_.push_back(new MultipoleAtomTypesSectionParser()); |
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spMan_.push_back(new StickyAtomTypesSectionParser()); |
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spMan_.push_back(new BondTypesSectionParser()); |
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spMan_.push_back(new BendTypesSectionParser()); |
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spMan_.push_back(new TorsionTypesSectionParser()); |
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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::readParams( void ){ |
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|
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char readLine[1024]; |
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|
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std::string fileName; |
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std::string shapeFileName; |
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std::string tempString; |
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|
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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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int isError; |
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std::string nameString; |
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AtomType* at; |
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DirectionalAtomType* dat; |
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ShapeAtomType* st; |
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|
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std::map<string, AtomType*>::iterator iter; |
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|
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// vectors for shape transfer to fortran |
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std::vector<RealSphericalHarmonic*> tempSHVector; |
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std::vector<int> contactL; |
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std::vector<int> contactM; |
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std::vector<int> contactFunc; |
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std::vector<double> contactCoeff; |
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std::vector<int> rangeL; |
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std::vector<int> rangeM; |
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std::vector<int> rangeFunc; |
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std::vector<double> rangeCoeff; |
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std::vector<int> strengthL; |
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std::vector<int> strengthM; |
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std::vector<int> strengthFunc; |
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std::vector<double> strengthCoeff; |
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|
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// generate the force file name |
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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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forceFile.open( fileName.c_str() ); |
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|
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if( forceFile == NULL ){ |
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|
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tempString = ffPath; |
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tempString += "/"; |
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tempString += fileName; |
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fileName = tempString; |
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|
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forceFile.open( fileName.c_str() ); |
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|
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if( forceFile == 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.c_str() ); |
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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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SHAPES_FF::~SHAPES_FF(){ |
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// We need to clean up the fortran side so we don't have bad things happen if |
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// we try to create a second EAM force field. |
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destroyEAMTypes(); |
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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( forceFile, "ShapeTypes" ); |
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|
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while( !forceFile.eof() ){ |
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forceFile.getline( readLine, sizeof(readLine) ); |
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} //end namespace oopse |
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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 = countTokens(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.c_str() ); |
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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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void SHAPES_FF::parse(const std::string& filename) { |
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ifstrstream* ffStream; |
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ffStream = openForceFieldFile(filename); |
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|
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// strings are not char arrays! |
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nameString = nameToken; |
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spMan_.parse(*ffStream, *this); |
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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 ShapeAtomType(); |
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ForceField::AtomTypeContainer::MapTypeIterator i; |
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AtomType* at; |
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|
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st->setName(nameString); |
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myATID = atomTypeMap.size() + 1; |
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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 std::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 = (ShapeAtomType*)(iter->second); |
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parseShapeFile(shapeFileName, st); |
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} |
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} |
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for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) { |
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at->makeFortranAtomType(); |
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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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|
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makeShape( &nContact, &contactL[0], &contactM[0], &contactFunc[0], |
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&contactCoeff[0], |
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&nRange, &rangeL[0], &rangeM[0], &rangeFunc[0], |
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&rangeCoeff[0], |
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&nStrength, &strengthL[0], &strengthM[0], |
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&strengthFunc[0], &strengthCoeff[0], |
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&myATID, |
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&isError); |
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|
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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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(iter->first).c_str() ); |
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painCave.isFatal = 1; |
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simError(); |
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} |
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} |
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for (at = atomTypeCont_.beginType(i); at != NULL; at = atomTypeCont_.nextType(i)) { |
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at->complete(); |
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} |
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} |
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|
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isError = 0; |
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completeShapeFF(&isError); |
318 |
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if( isError ){ |
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sprintf( painCave.errMsg, |
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"Error completing Shape FF in fortran\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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#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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|
333 |
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void Shapes_FF::cleanMe( void ){ |
334 |
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|
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} |
336 |
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|
337 |
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void Shapes_FF::initializeAtoms( int nAtoms, Atom** the_atoms ){ |
338 |
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|
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int i,j,k; |
340 |
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std::map<string, AtomType*>::iterator iter; |
341 |
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|
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// initialize the atoms |
343 |
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DirectionalAtom* dAtom; |
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AtomType* at; |
345 |
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DirectionalAtomType* dat; |
346 |
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ShapeAtomType* sat; |
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double longCutoff; |
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double ji[3]; |
349 |
< |
double inertialMat[3][3]; |
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Mat3x3d momInt; |
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std::string myTypeString; |
352 |
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|
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bigContact = 0.0; |
354 |
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|
355 |
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for( i=0; i<nAtoms; i++ ){ |
356 |
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|
357 |
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myTypeString = the_atoms[i]->getType().c_str(); |
358 |
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iter = atomTypeMap.find(myTypeString); |
359 |
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|
360 |
< |
if (iter == atomTypeMap.end()) { |
361 |
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sprintf( painCave.errMsg, |
362 |
< |
"AtomType error, %s not found in force file.\n", |
363 |
< |
the_atoms[i]->getType().c_str() ); |
364 |
< |
painCave.isFatal = 1; |
365 |
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simError(); |
366 |
< |
} else { |
367 |
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|
368 |
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at = (AtomType*)(iter->second); |
369 |
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|
370 |
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the_atoms[i]->setMass( at->getMass() ); |
371 |
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the_atoms[i]->setIdent( at->getIdent() ); |
372 |
< |
|
373 |
< |
if ( at->isShape() ) { |
374 |
< |
|
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sat = (ShapeAtomType*)at; |
376 |
< |
longCutoff = findCutoffDistance(sat); |
377 |
< |
if (longCutoff > bigContact) bigContact = longCutoff; |
378 |
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cout << bigContact << " is the cutoff value\n"; |
379 |
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|
380 |
< |
entry_plug->useShapes = 1; |
381 |
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} |
382 |
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|
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the_atoms[i]->setHasCharge(at->isCharge()); |
384 |
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|
385 |
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if( at->isDirectional() ){ |
386 |
< |
|
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< |
dat = (DirectionalAtomType*)at; |
388 |
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dAtom = (DirectionalAtom *) the_atoms[i]; |
389 |
< |
|
390 |
< |
momInt = dat->getI(); |
391 |
< |
|
392 |
< |
// zero out the moments of inertia matrix |
393 |
< |
for( j=0; j<3; j++ ) |
394 |
< |
for( k=0; k<3; k++ ) |
395 |
< |
inertialMat[j][k] = momInt(j,k); |
396 |
< |
dAtom->setI( inertialMat ); |
397 |
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|
398 |
< |
ji[0] = 0.0; |
399 |
< |
ji[1] = 0.0; |
400 |
< |
ji[2] = 0.0; |
401 |
< |
dAtom->setJ( ji ); |
402 |
< |
|
403 |
< |
if (dat->isDipole()) { |
404 |
< |
dAtom->setHasDipole( dat->isDipole() ); |
405 |
< |
entry_plug->n_dipoles++; |
406 |
< |
} |
407 |
< |
} |
408 |
< |
} |
409 |
< |
} |
116 |
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delete ffStream; |
117 |
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} |
118 |
|
|
412 |
– |
void Shapes_FF::initializeBonds( int nBonds, Bond** BondArray, |
413 |
– |
bond_pair* the_bonds ){ |
414 |
– |
|
415 |
– |
if( nBonds ){ |
416 |
– |
sprintf( painCave.errMsg, |
417 |
– |
"Shapes_FF does not support bonds.\n" ); |
418 |
– |
painCave.isFatal = 1; |
419 |
– |
simError(); |
420 |
– |
} |
421 |
– |
} |
119 |
|
|
120 |
< |
void Shapes_FF::initializeBends( int nBends, Bend** bendArray, |
424 |
< |
bend_set* the_bends ){ |
425 |
< |
|
426 |
< |
if( nBends ){ |
427 |
< |
sprintf( painCave.errMsg, |
428 |
< |
"Shapes_FF does not support bends.\n" ); |
429 |
< |
painCave.isFatal = 1; |
430 |
< |
simError(); |
431 |
< |
} |
432 |
< |
} |
120 |
> |
double SHAPES_FF::getRcutFromAtomType(AtomType* at){ |
121 |
|
|
434 |
– |
void Shapes_FF::initializeTorsions( int nTorsions, Torsion** torsionArray, |
435 |
– |
torsion_set* the_torsions ){ |
436 |
– |
|
437 |
– |
if( nTorsions ){ |
438 |
– |
sprintf( painCave.errMsg, |
439 |
– |
"Shapes_FF does not support torsions.\n" ); |
440 |
– |
painCave.isFatal = 1; |
441 |
– |
simError(); |
442 |
– |
} |
122 |
|
} |
123 |
|
|
445 |
– |
void Shapes_FF::parseShapeFile(string shapeFileName, ShapeAtomType* st){ |
446 |
– |
const int MAXLEN = 1024; |
447 |
– |
char inLine[MAXLEN]; |
448 |
– |
char *token; |
449 |
– |
char *delim = " ,;\t\n"; |
450 |
– |
int nTokens; |
451 |
– |
Mat3x3d momInert; |
452 |
– |
RealSphericalHarmonic* rsh; |
453 |
– |
std::vector<RealSphericalHarmonic*> functionVector; |
454 |
– |
ifstrstream shapeFile; |
455 |
– |
std::string tempString; |
124 |
|
|
457 |
– |
shapeFile.open( shapeFileName.c_str() ); |
458 |
– |
|
459 |
– |
if( shapeFile == NULL ){ |
460 |
– |
|
461 |
– |
tempString = ffPath; |
462 |
– |
tempString += "/"; |
463 |
– |
tempString += shapeFileName; |
464 |
– |
shapeFileName = tempString; |
465 |
– |
|
466 |
– |
shapeFile.open( shapeFileName.c_str() ); |
467 |
– |
|
468 |
– |
if( shapeFile == NULL ){ |
469 |
– |
|
470 |
– |
sprintf( painCave.errMsg, |
471 |
– |
"Error opening the shape file:\n" |
472 |
– |
"\t%s\n" |
473 |
– |
"\tHave you tried setting the FORCE_PARAM_PATH environment " |
474 |
– |
"variable?\n", |
475 |
– |
shapeFileName.c_str() ); |
476 |
– |
painCave.severity = OOPSE_ERROR; |
477 |
– |
painCave.isFatal = 1; |
478 |
– |
simError(); |
479 |
– |
} |
480 |
– |
} |
481 |
– |
|
482 |
– |
// read in the shape types. |
483 |
– |
|
484 |
– |
// first grab the values in the ShapeInfo section |
485 |
– |
findBegin( shapeFile, "ShapeInfo"); |
486 |
– |
|
487 |
– |
shapeFile.getline(inLine, MAXLEN); |
488 |
– |
while( !shapeFile.eof() ) { |
489 |
– |
// toss comment lines |
490 |
– |
if( inLine[0] != '!' && inLine[0] != '#' ){ |
491 |
– |
// end marks section completion |
492 |
– |
if (isEndLine(inLine)) break; |
493 |
– |
|
494 |
– |
nTokens = countTokens(inLine, delim); |
495 |
– |
if (nTokens != 0) { |
496 |
– |
if (nTokens < 5) { |
497 |
– |
sprintf( painCave.errMsg, |
498 |
– |
"Not enough data on a ShapeInfo line in file: %s\n", |
499 |
– |
shapeFileName.c_str() ); |
500 |
– |
painCave.severity = OOPSE_ERROR; |
501 |
– |
painCave.isFatal = 1; |
502 |
– |
simError(); |
503 |
– |
} else { |
504 |
– |
token = strtok(inLine, delim); |
505 |
– |
token = strtok(NULL, delim); |
506 |
– |
st->setMass(atof(token)); |
507 |
– |
token = strtok(NULL, delim); |
508 |
– |
momInert(0,0) = atof(token); |
509 |
– |
token = strtok(NULL, delim); |
510 |
– |
momInert(1,1) = atof(token); |
511 |
– |
token = strtok(NULL, delim); |
512 |
– |
momInert(2,2) = atof(token); |
513 |
– |
st->setI(momInert); |
514 |
– |
} |
515 |
– |
} |
516 |
– |
} |
517 |
– |
shapeFile.getline(inLine, MAXLEN); |
518 |
– |
} |
519 |
– |
|
520 |
– |
// now grab the contact functions |
521 |
– |
findBegin(shapeFile, "ContactFunctions"); |
522 |
– |
functionVector.clear(); |
523 |
– |
|
524 |
– |
shapeFile.getline(inLine, MAXLEN); |
525 |
– |
while( !shapeFile.eof() ) { |
526 |
– |
// toss comment lines |
527 |
– |
if( inLine[0] != '!' && inLine[0] != '#' ){ |
528 |
– |
// end marks section completion |
529 |
– |
if (isEndLine(inLine)) break; |
530 |
– |
nTokens = countTokens(inLine, delim); |
531 |
– |
if (nTokens != 0) { |
532 |
– |
if (nTokens < 4) { |
533 |
– |
sprintf( painCave.errMsg, |
534 |
– |
"Not enough data on a ContactFunctions line in file: %s\n", |
535 |
– |
shapeFileName.c_str() ); |
536 |
– |
painCave.severity = OOPSE_ERROR; |
537 |
– |
painCave.isFatal = 1; |
538 |
– |
simError(); |
539 |
– |
} else { |
540 |
– |
// read in a spherical harmonic function |
541 |
– |
token = strtok(inLine, delim); |
542 |
– |
rsh = new RealSphericalHarmonic(); |
543 |
– |
rsh->setL(atoi(token)); |
544 |
– |
token = strtok(NULL, delim); |
545 |
– |
rsh->setM(atoi(token)); |
546 |
– |
token = strtok(NULL, delim); |
547 |
– |
if (!strcasecmp("sin",token)) |
548 |
– |
rsh->makeSinFunction(); |
549 |
– |
else |
550 |
– |
rsh->makeCosFunction(); |
551 |
– |
token = strtok(NULL, delim); |
552 |
– |
rsh->setCoefficient(atof(token)); |
553 |
– |
|
554 |
– |
functionVector.push_back(rsh); |
555 |
– |
} |
556 |
– |
} |
557 |
– |
} |
558 |
– |
shapeFile.getline(inLine, MAXLEN); |
559 |
– |
} |
560 |
– |
|
561 |
– |
// pass contact functions to ShapeType |
562 |
– |
|
563 |
– |
st->setContactFuncs(functionVector); |
564 |
– |
|
565 |
– |
// now grab the range functions |
566 |
– |
findBegin(shapeFile, "RangeFunctions"); |
567 |
– |
functionVector.clear(); |
568 |
– |
|
569 |
– |
shapeFile.getline(inLine, MAXLEN); |
570 |
– |
while( !shapeFile.eof() ) { |
571 |
– |
// toss comment lines |
572 |
– |
if( inLine[0] != '!' && inLine[0] != '#' ){ |
573 |
– |
// end marks section completion |
574 |
– |
if (isEndLine(inLine)) break; |
575 |
– |
|
576 |
– |
nTokens = countTokens(inLine, delim); |
577 |
– |
if (nTokens != 0) { |
578 |
– |
if (nTokens < 4) { |
579 |
– |
sprintf( painCave.errMsg, |
580 |
– |
"Not enough data on a RangeFunctions line in file: %s\n", |
581 |
– |
shapeFileName.c_str() ); |
582 |
– |
painCave.severity = OOPSE_ERROR; |
583 |
– |
painCave.isFatal = 1; |
584 |
– |
simError(); |
585 |
– |
} else { |
586 |
– |
|
587 |
– |
// read in a spherical harmonic function |
588 |
– |
token = strtok(inLine, delim); |
589 |
– |
|
590 |
– |
rsh = new RealSphericalHarmonic(); |
591 |
– |
rsh->setL(atoi(token)); |
592 |
– |
token = strtok(NULL, delim); |
593 |
– |
rsh->setM(atoi(token)); |
594 |
– |
token = strtok(NULL, delim); |
595 |
– |
if (!strcasecmp("sin",token)) |
596 |
– |
rsh->makeSinFunction(); |
597 |
– |
else |
598 |
– |
rsh->makeCosFunction(); |
599 |
– |
token = strtok(NULL, delim); |
600 |
– |
rsh->setCoefficient(atof(token)); |
601 |
– |
|
602 |
– |
functionVector.push_back(rsh); |
603 |
– |
} |
604 |
– |
} |
605 |
– |
} |
606 |
– |
shapeFile.getline(inLine, MAXLEN); |
607 |
– |
} |
608 |
– |
|
609 |
– |
// pass range functions to ShapeType |
610 |
– |
st->setRangeFuncs(functionVector); |
611 |
– |
|
612 |
– |
// finally grab the strength functions |
613 |
– |
findBegin(shapeFile, "StrengthFunctions"); |
614 |
– |
functionVector.clear(); |
615 |
– |
|
616 |
– |
shapeFile.getline(inLine, MAXLEN); |
617 |
– |
while( !shapeFile.eof() ) { |
618 |
– |
// toss comment lines |
619 |
– |
if( inLine[0] != '!' && inLine[0] != '#' ){ |
620 |
– |
// end marks section completion |
621 |
– |
if (isEndLine(inLine)) break; |
622 |
– |
|
623 |
– |
nTokens = countTokens(inLine, delim); |
624 |
– |
if (nTokens != 0) { |
625 |
– |
if (nTokens < 4) { |
626 |
– |
sprintf( painCave.errMsg, |
627 |
– |
"Not enough data on a StrengthFunctions line in file: %s\n", |
628 |
– |
shapeFileName.c_str() ); |
629 |
– |
painCave.severity = OOPSE_ERROR; |
630 |
– |
painCave.isFatal = 1; |
631 |
– |
simError(); |
632 |
– |
} else { |
633 |
– |
|
634 |
– |
// read in a spherical harmonic function |
635 |
– |
token = strtok(inLine, delim); |
636 |
– |
rsh = new RealSphericalHarmonic(); |
637 |
– |
rsh->setL(atoi(token)); |
638 |
– |
token = strtok(NULL, delim); |
639 |
– |
rsh->setM(atoi(token)); |
640 |
– |
token = strtok(NULL, delim); |
641 |
– |
if (!strcasecmp("sin",token)) |
642 |
– |
rsh->makeSinFunction(); |
643 |
– |
else |
644 |
– |
rsh->makeCosFunction(); |
645 |
– |
token = strtok(NULL, delim); |
646 |
– |
rsh->setCoefficient(atof(token)); |
647 |
– |
|
648 |
– |
functionVector.push_back(rsh); |
649 |
– |
} |
650 |
– |
} |
651 |
– |
} |
652 |
– |
shapeFile.getline(inLine, MAXLEN); |
653 |
– |
} |
654 |
– |
|
655 |
– |
// pass strength functions to ShapeType |
656 |
– |
st->setStrengthFuncs(functionVector); |
657 |
– |
|
658 |
– |
// we're done reading from this file |
659 |
– |
shapeFile.close(); |
660 |
– |
} |
661 |
– |
|
662 |
– |
double Shapes_FF::findLargestContactDistance(ShapeAtomType* st) { |
663 |
– |
int i, j, nSteps; |
664 |
– |
double theta, thetaStep, thetaMin, costheta; |
665 |
– |
double phi, phiStep; |
666 |
– |
double sigma, bs; |
667 |
– |
|
668 |
– |
nSteps = 16; |
669 |
– |
|
670 |
– |
thetaStep = M_PI / nSteps; |
671 |
– |
thetaMin = thetaStep / 2.0; |
672 |
– |
phiStep = thetaStep * 2.0; |
673 |
– |
bs = 0.0; |
674 |
– |
|
675 |
– |
for (i = 0; i < nSteps; i++) { |
676 |
– |
|
677 |
– |
theta = thetaMin + i * thetaStep; |
678 |
– |
costheta = cos(theta); |
679 |
– |
|
680 |
– |
for (j = 0; j < nSteps; j++) { |
681 |
– |
|
682 |
– |
phi = j*phiStep; |
683 |
– |
|
684 |
– |
sigma = st->getContactValueAt(costheta, phi); |
685 |
– |
|
686 |
– |
if (sigma > bs) bs = sigma; |
687 |
– |
} |
688 |
– |
} |
689 |
– |
|
690 |
– |
return bs; |
691 |
– |
} |
692 |
– |
|
693 |
– |
|
694 |
– |
double Shapes_FF::findCutoffDistance(ShapeAtomType* st) { |
695 |
– |
int i, j, nSteps; |
696 |
– |
double theta, thetaStep, thetaMin, costheta; |
697 |
– |
double phi, phiStep; |
698 |
– |
double sigma, range; |
699 |
– |
double bigCut, tempCut; |
700 |
– |
|
701 |
– |
nSteps = 16; |
702 |
– |
|
703 |
– |
thetaStep = M_PI / nSteps; |
704 |
– |
thetaMin = thetaStep / 2.0; |
705 |
– |
phiStep = thetaStep * 2.0; |
706 |
– |
bigCut = 0.0; |
707 |
– |
|
708 |
– |
for (i = 0; i < nSteps; i++) { |
709 |
– |
|
710 |
– |
theta = thetaMin + i * thetaStep; |
711 |
– |
costheta = cos(theta); |
712 |
– |
|
713 |
– |
for (j = 0; j < nSteps; j++) { |
714 |
– |
|
715 |
– |
phi = j*phiStep; |
716 |
– |
|
717 |
– |
sigma = st->getContactValueAt(costheta, phi); |
718 |
– |
range = st->getRangeValueAt(costheta, phi); |
719 |
– |
|
720 |
– |
// cutoff for a shape is taken to be (1.5*rangeVal + contactVal) |
721 |
– |
tempCut = 1.5*range + sigma; |
722 |
– |
|
723 |
– |
if (tempCut > bigCut) bigCut = tempCut; |
724 |
– |
} |
725 |
– |
} |
726 |
– |
|
727 |
– |
return bigCut; |
728 |
– |
} |