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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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* non-exclusive, royalty free, license to use, modify and |
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* redistribute this software in source and binary code form, provided |
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* that the following conditions are met: |
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* |
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* 1. Acknowledgement of the program authors must be made in any |
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* publication of scientific results based in part on use of the |
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* program. An acceptable form of acknowledgement is citation of |
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* the article in which the program was described (Matthew |
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* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher |
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* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented |
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* Parallel Simulation Engine for Molecular Dynamics," |
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* J. Comput. Chem. 26, pp. 252-271 (2005)) |
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* |
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* 2. Redistributions of source code must retain the above copyright |
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* notice, this list of conditions and the following disclaimer. |
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* |
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* 3. Redistributions in binary form must reproduce the above copyright |
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* notice, this list of conditions and the following disclaimer in the |
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* documentation and/or other materials provided with the |
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* distribution. |
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* |
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* This software is provided "AS IS," without a warranty of any |
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* kind. All express or implied conditions, representations and |
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* warranties, including any implied warranty of merchantability, |
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* fitness for a particular purpose or non-infringement, are hereby |
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* excluded. The University of Notre Dame and its licensors shall not |
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* be liable for any damages suffered by licensee as a result of |
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* using, modifying or distributing the software or its |
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* derivatives. In no event will the University of Notre Dame or its |
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* licensors be liable for any lost revenue, profit or data, or for |
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* direct, indirect, special, consequential, incidental or punitive |
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* damages, however caused and regardless of the theory of liability, |
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* arising out of the use of or inability to use software, even if the |
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* University of Notre Dame has been advised of the possibility of |
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* such damages. |
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*/ |
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|
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#include "UseTheForce/ForceField.hpp" |
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#include "io/ShapeAtomTypesSectionParser.hpp" |
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#include "math/RealSphericalHarmonic.hpp" |
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#include "math/SquareMatrix3.hpp" |
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#include "types/AtomType.hpp" |
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#include "types/DirectionalAtomType.hpp" |
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#include "types/ShapeAtomType.hpp" |
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#include "utils/StringUtils.hpp" |
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#include "utils/simError.h" |
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|
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namespace oopse { |
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|
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ShapeAtomTypesSectionParser::ShapeAtomTypesSectionParser() { |
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setSectionName("ShapeAtomTypes"); |
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} |
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|
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void ShapeAtomTypesSectionParser::parseLine(ForceField& ff, |
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const std::string& line, |
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int lineNo){ |
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StringTokenizer tokenizer(line); |
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|
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if (tokenizer.countTokens() >= 2) { |
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std::string shapeTypeName = tokenizer.nextToken(); |
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std::string shapeFile = tokenizer.nextToken(); |
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|
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AtomType* atomType = ff.getAtomType(shapeTypeName); |
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ShapeAtomType* sAtomType; |
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if (atomType == NULL){ |
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sAtomType = new ShapeAtomType(); |
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int ident = ff.getNAtomType() + 1; |
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sAtomType->setIdent(ident); |
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sAtomType->setName(shapeTypeName); |
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ff.addAtomType(shapeTypeName, sAtomType); |
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} else { |
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sAtomType = dynamic_cast<ShapeAtomType*>(atomType); |
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if (sAtomType == NULL) { |
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sprintf(painCave.errMsg, |
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"ShapeAtomTypesSectionParser:: Can't cast to ShapeAtomType"); |
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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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sAtomType->setShape(); |
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parseShapeFile(ff, shapeFile, sAtomType); |
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|
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} else { |
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sprintf(painCave.errMsg, |
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"ShapesAtomTypesSectionParser Error: " |
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"Not enough tokens at line %d\n", |
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lineNo); |
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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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void ShapeAtomTypesSectionParser::parseShapeFile(ForceField& ff, |
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std::string& shapeFileName, |
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ShapeAtomType* st) { |
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|
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const int bufferSize = 65535; |
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char buffer[bufferSize]; |
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std::string token; |
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std::string line; |
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int junk; |
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Mat3x3d momInert; |
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RealSphericalHarmonic* rsh; |
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std::vector<RealSphericalHarmonic*> functionVector; |
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ifstrstream shapeStream; |
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std::string tempString; |
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std::string ffPath; |
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char* tempPath; |
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|
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tempPath = getenv("FORCE_PARAM_PATH"); |
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|
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if (tempPath == NULL) { |
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//convert a macro from compiler to a string in c++ |
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STR_DEFINE(ffPath, FRC_PATH ); |
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} else { |
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ffPath = tempPath; |
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} |
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|
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shapeStream.open( shapeFileName.c_str() ); |
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|
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if( shapeStream == NULL ){ |
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|
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tempString = ffPath; |
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tempString += "/"; |
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tempString += shapeFileName; |
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shapeFileName = tempString; |
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|
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shapeStream.open( shapeFileName.c_str() ); |
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|
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if( shapeStream == NULL ){ |
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|
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sprintf( painCave.errMsg, |
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"Error opening the shape 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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shapeFileName.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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|
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|
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// first parse the info. in the ShapeInfo section |
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findBegin( shapeStream, "ShapeInfo"); |
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shapeStream.getline(buffer, bufferSize); |
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|
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// loop over the interior of the ShapeInfo section |
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while( !shapeStream.eof() ) { |
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// toss comment lines |
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if( buffer[0] != '!' && buffer[0] != '#' ){ |
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// end marks section completion |
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if (isEndLine(buffer)) break; |
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StringTokenizer tokenInfo(buffer); |
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// blank lines are ignored |
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if (tokenInfo.countTokens() != 0) { |
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if (tokenInfo.countTokens() < 5) { |
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sprintf(painCave.errMsg, |
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"ShapesAtomTypesSectionParser Error: Not enough " |
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"information on a ShapeInfo line in file: %s\n", |
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shapeFileName.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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} else { |
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junk = tokenInfo.nextTokenAsInt(); |
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st->setMass( tokenInfo.nextTokenAsDouble() ); |
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momInert(0,0) = tokenInfo.nextTokenAsDouble(); |
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momInert(1,1) = tokenInfo.nextTokenAsDouble(); |
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momInert(2,2) = tokenInfo.nextTokenAsDouble(); |
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st->setI(momInert); |
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} |
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} |
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} |
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shapeStream.getline(buffer, bufferSize); |
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} |
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|
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// now grab the contact functions |
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findBegin(shapeStream, "ContactFunctions"); |
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functionVector.clear(); |
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|
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shapeStream.getline(buffer, bufferSize); |
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while( !shapeStream.eof() ) { |
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// toss comment lines |
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if( buffer[0] != '!' && buffer[0] != '#' ){ |
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// end marks section completion |
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if (isEndLine(buffer)) break; |
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StringTokenizer tokenInfo1(buffer); |
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// blank lines are ignored |
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if (tokenInfo1.countTokens() != 0) { |
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if (tokenInfo1.countTokens() < 4) { |
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sprintf( painCave.errMsg, |
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"ShapesAtomTypesSectionParser Error: Not enough " |
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"information on a ContactFunctions line in file: %s\n", |
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shapeFileName.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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} else { |
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// read in a spherical harmonic function |
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rsh = new RealSphericalHarmonic(); |
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rsh->setL( tokenInfo1.nextTokenAsInt() ); |
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rsh->setM( tokenInfo1.nextTokenAsInt() ); |
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token = tokenInfo1.nextToken(); |
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transform(token.begin(), token.end(), token.begin(), tolower); |
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if (token == "sin") |
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rsh->makeSinFunction(); |
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else |
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rsh->makeCosFunction(); |
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rsh->setCoefficient( tokenInfo1.nextTokenAsDouble() ); |
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|
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functionVector.push_back(rsh); |
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} |
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} |
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} |
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shapeStream.getline(buffer, bufferSize); |
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} |
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|
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// pass contact functions to ShapeType |
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st->setContactFuncs(functionVector); |
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|
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// now grab the range functions |
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findBegin(shapeStream, "RangeFunctions"); |
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functionVector.clear(); |
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|
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shapeStream.getline(buffer, bufferSize); |
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while( !shapeStream.eof() ) { |
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// toss comment lines |
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if( buffer[0] != '!' && buffer[0] != '#' ){ |
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// end marks section completion |
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if (isEndLine(buffer)) break; |
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StringTokenizer tokenInfo2(buffer); |
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// blank lines are ignored |
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if (tokenInfo2.countTokens() != 0) { |
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if (tokenInfo2.countTokens() < 4) { |
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sprintf( painCave.errMsg, |
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"ShapesAtomTypesSectionParser Error: Not enough " |
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"information on a RangeFunctions line in file: %s\n", |
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shapeFileName.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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} else { |
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// read in a spherical harmonic function |
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rsh = new RealSphericalHarmonic(); |
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rsh->setL( tokenInfo2.nextTokenAsInt() ); |
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rsh->setM( tokenInfo2.nextTokenAsInt() ); |
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token = tokenInfo2.nextToken(); |
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transform(token.begin(), token.end(), token.begin(), tolower); |
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if (token == "sin") |
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rsh->makeSinFunction(); |
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else |
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rsh->makeCosFunction(); |
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rsh->setCoefficient( tokenInfo2.nextTokenAsDouble() ); |
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|
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functionVector.push_back(rsh); |
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} |
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} |
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} |
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shapeStream.getline(buffer, bufferSize); |
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} |
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|
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// pass range functions to ShapeType |
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st->setRangeFuncs(functionVector); |
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|
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// finally grab the strength functions |
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findBegin(shapeStream, "StrengthFunctions"); |
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functionVector.clear(); |
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|
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shapeStream.getline(buffer, bufferSize); |
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while( !shapeStream.eof() ) { |
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// toss comment lines |
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if( buffer[0] != '!' && buffer[0] != '#' ){ |
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// end marks section completion |
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if (isEndLine(buffer)) break; |
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StringTokenizer tokenInfo3(buffer); |
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// blank lines are ignored |
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if (tokenInfo3.countTokens() != 0) { |
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if (tokenInfo3.countTokens() < 4) { |
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sprintf( painCave.errMsg, |
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"ShapesAtomTypesSectionParser Error: Not enough " |
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"information on a StrengthFunctions line in file: %s\n", |
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shapeFileName.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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} else { |
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// read in a spherical harmonic function |
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rsh = new RealSphericalHarmonic(); |
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rsh->setL( tokenInfo3.nextTokenAsInt() ); |
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rsh->setM( tokenInfo3.nextTokenAsInt() ); |
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token = tokenInfo3.nextToken(); |
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transform(token.begin(), token.end(), token.begin(), tolower); |
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if (token == "sin") |
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rsh->makeSinFunction(); |
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else |
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rsh->makeCosFunction(); |
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rsh->setCoefficient( tokenInfo3.nextTokenAsDouble() ); |
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|
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functionVector.push_back(rsh); |
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} |
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} |
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} |
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shapeStream.getline(buffer, bufferSize); |
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} |
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|
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// pass strength functions to ShapeType |
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st->setStrengthFuncs(functionVector); |
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|
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// delete shapeStream; |
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} |
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} //end namespace oopse |
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|
