src/io/ShapeAtomTypesSectionParser.cpp

 /*
 * Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
 *
 * The University of Notre Dame grants you ("Licensee") a
 * non-exclusive, royalty free, license to use, modify and
 * redistribute this software in source and binary code form, provided
 * that the following conditions are met:
 *
 * 1. Acknowledgement of the program authors must be made in any
 *    publication of scientific results based in part on use of the
 *    program.  An acceptable form of acknowledgement is citation of
 *    the article in which the program was described (Matthew
 *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
 *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
 *    Parallel Simulation Engine for Molecular Dynamics,"
 *    J. Comput. Chem. 26, pp. 252-271 (2005))
 *
 * 2. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 3. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * This software is provided "AS IS," without a warranty of any
 * kind. All express or implied conditions, representations and
 * warranties, including any implied warranty of merchantability,
 * fitness for a particular purpose or non-infringement, are hereby
 * excluded.  The University of Notre Dame and its licensors shall not
 * be liable for any damages suffered by licensee as a result of
 * using, modifying or distributing the software or its
 * derivatives. In no event will the University of Notre Dame or its
 * licensors be liable for any lost revenue, profit or data, or for
 * direct, indirect, special, consequential, incidental or punitive
 * damages, however caused and regardless of the theory of liability,
 * arising out of the use of or inability to use software, even if the
 * University of Notre Dame has been advised of the possibility of
 * such damages.
 */
 
#include "UseTheForce/ForceField.hpp"
#include "io/ShapeAtomTypesSectionParser.hpp"
#include "math/RealSphericalHarmonic.hpp"
#include "math/SquareMatrix3.hpp"
#include "types/AtomType.hpp"
#include "types/DirectionalAtomType.hpp"
#include "types/ShapeAtomType.hpp"
#include "utils/StringUtils.hpp"
#include "utils/simError.h"

namespace oopse {
  
  ShapeAtomTypesSectionParser::ShapeAtomTypesSectionParser() {
    setSectionName("ShapeAtomTypes");
  }
  
  void ShapeAtomTypesSectionParser::parseLine(ForceField& ff, 
                                              const std::string& line, 
                                              int lineNo){
    StringTokenizer tokenizer(line);
      
    if (tokenizer.countTokens() >= 2) {
      std::string shapeTypeName = tokenizer.nextToken();
      std::string shapeFile = tokenizer.nextToken();
       
      AtomType* atomType = ff.getAtomType(shapeTypeName);
      ShapeAtomType* sAtomType;
      if (atomType == NULL){
        sAtomType = new ShapeAtomType();
        int ident = ff.getNAtomType() + 1;
        sAtomType->setIdent(ident); 
        sAtomType->setName(shapeTypeName);
        ff.addAtomType(shapeTypeName, sAtomType);
      } else {
        sAtomType = dynamic_cast<ShapeAtomType*>(atomType);
        if (sAtomType == NULL) {
          sprintf(painCave.errMsg,
                  "ShapeAtomTypesSectionParser:: Can't cast to ShapeAtomType");
          painCave.severity = OOPSE_ERROR;
          painCave.isFatal = 1;
          simError();
        }
      }
      
      sAtomType->setShape();   
      parseShapeFile(ff, shapeFile, sAtomType);                                                    
  
    } else {
      sprintf(painCave.errMsg, 
              "ShapesAtomTypesSectionParser Error: "
              "Not enough tokens at line %d\n",
              lineNo);
      painCave.severity = OOPSE_ERROR;
      painCave.isFatal = 1;
      simError();    
    }
  }
  
  void ShapeAtomTypesSectionParser::parseShapeFile(ForceField& ff,
                                                   std::string& shapeFileName, 
                                                   ShapeAtomType* st) {
    
    const int bufferSize = 65535;
    char buffer[bufferSize];
    std::string token;
    std::string line;
    int junk;
    Mat3x3d momInert;
    RealSphericalHarmonic* rsh;
    std::vector<RealSphericalHarmonic*> functionVector;
    ifstrstream shapeStream;
    std::string tempString;
    std::string ffPath;
    char* tempPath; 
    
    tempPath = getenv("FORCE_PARAM_PATH");
    
    if (tempPath == NULL) {
      //convert a macro from compiler to a string in c++
      STR_DEFINE(ffPath, FRC_PATH );
    } else {
      ffPath = tempPath;
    }
    
    shapeStream.open( shapeFileName.c_str() );
    
    if( shapeStream == NULL ){
      
      tempString = ffPath;
      tempString += "/";
      tempString += shapeFileName;
      shapeFileName = tempString;
      
      shapeStream.open( shapeFileName.c_str() );
      
      if( shapeStream == NULL ){
        
        sprintf( painCave.errMsg,
                 "Error opening the shape file:\n"
                 "\t%s\n"
                 "\tHave you tried setting the FORCE_PARAM_PATH environment "
                 "variable?\n",
                 shapeFileName.c_str() );
        painCave.severity = OOPSE_ERROR;
        painCave.isFatal = 1;
        simError();
      }
    }
    
    
    // first parse the info. in the ShapeInfo section
    findBegin( shapeStream, "ShapeInfo");
    shapeStream.getline(buffer, bufferSize);
    
    // loop over the interior of the ShapeInfo section
    while( !shapeStream.eof() ) {
      // toss comment lines
      if( buffer[0] != '!' && buffer[0] != '#' ){
        // end marks section completion
        if (isEndLine(buffer)) break;
        StringTokenizer tokenInfo(buffer);
        // blank lines are ignored
        if (tokenInfo.countTokens() != 0) {
          if (tokenInfo.countTokens() < 5) {
            sprintf(painCave.errMsg, 
                    "ShapesAtomTypesSectionParser Error: Not enough "
                    "information on a ShapeInfo line in file: %s\n", 
                    shapeFileName.c_str() );
            painCave.severity = OOPSE_ERROR;
            painCave.isFatal = 1;
            simError();  
          } else {
            junk = tokenInfo.nextTokenAsInt();
            st->setMass( tokenInfo.nextTokenAsDouble() );
            momInert(0,0) = tokenInfo.nextTokenAsDouble();
            momInert(1,1) = tokenInfo.nextTokenAsDouble();
            momInert(2,2) = tokenInfo.nextTokenAsDouble();
            st->setI(momInert);
          }
        }
      }
      shapeStream.getline(buffer, bufferSize);
    }
    
    // now grab the contact functions
    findBegin(shapeStream, "ContactFunctions");
    functionVector.clear();
    
    shapeStream.getline(buffer, bufferSize);
    while( !shapeStream.eof() ) {
      // toss comment lines
      if( buffer[0] != '!' && buffer[0] != '#' ){
        // end marks section completion
        if (isEndLine(buffer)) break;
        StringTokenizer tokenInfo1(buffer);
        // blank lines are ignored
        if (tokenInfo1.countTokens() != 0) {
          if (tokenInfo1.countTokens() < 4) {
            sprintf( painCave.errMsg,
                     "ShapesAtomTypesSectionParser Error: Not enough "
                     "information on a ContactFunctions line in file: %s\n", 
                     shapeFileName.c_str() );
            painCave.severity = OOPSE_ERROR;
            painCave.isFatal = 1;
            simError();
          } else {
            // read in a spherical harmonic function
            rsh = new RealSphericalHarmonic();
            rsh->setL( tokenInfo1.nextTokenAsInt() );
            rsh->setM( tokenInfo1.nextTokenAsInt() );
            token = tokenInfo1.nextToken();
            transform(token.begin(), token.end(), token.begin(), tolower);
            if (token == "sin")
              rsh->makeSinFunction();
            else
              rsh->makeCosFunction();
            rsh->setCoefficient( tokenInfo1.nextTokenAsDouble() );
            
            functionVector.push_back(rsh);
          }
        }
      }
      shapeStream.getline(buffer, bufferSize);
    }
    
    // pass contact functions to ShapeType
    st->setContactFuncs(functionVector);
    
    // now grab the range functions
    findBegin(shapeStream, "RangeFunctions");
    functionVector.clear();
    
    shapeStream.getline(buffer, bufferSize);
    while( !shapeStream.eof() ) {
      // toss comment lines
      if( buffer[0] != '!' && buffer[0] != '#' ){
        // end marks section completion
        if (isEndLine(buffer)) break;
        StringTokenizer tokenInfo2(buffer);
        // blank lines are ignored
        if (tokenInfo2.countTokens() != 0) {
          if (tokenInfo2.countTokens() < 4) {
            sprintf( painCave.errMsg,
                     "ShapesAtomTypesSectionParser Error: Not enough "
                     "information on a RangeFunctions line in file: %s\n", 
                     shapeFileName.c_str() );
            painCave.severity = OOPSE_ERROR;
            painCave.isFatal = 1;
            simError();
          } else {
            // read in a spherical harmonic function
            rsh = new RealSphericalHarmonic();
            rsh->setL( tokenInfo2.nextTokenAsInt() );
            rsh->setM( tokenInfo2.nextTokenAsInt() );
            token = tokenInfo2.nextToken();
            transform(token.begin(), token.end(), token.begin(), tolower);
            if (token == "sin")
              rsh->makeSinFunction();
            else
              rsh->makeCosFunction();
            rsh->setCoefficient( tokenInfo2.nextTokenAsDouble() );
            
            functionVector.push_back(rsh);
          }
        }
      }
      shapeStream.getline(buffer, bufferSize);
    }
    
    // pass range functions to ShapeType
    st->setRangeFuncs(functionVector);
    
    // finally grab the strength functions
    findBegin(shapeStream, "StrengthFunctions");
    functionVector.clear();
    
    shapeStream.getline(buffer, bufferSize);
    while( !shapeStream.eof() ) {
      // toss comment lines
      if( buffer[0] != '!' && buffer[0] != '#' ){
        // end marks section completion
        if (isEndLine(buffer)) break;
        StringTokenizer tokenInfo3(buffer);
        // blank lines are ignored
        if (tokenInfo3.countTokens() != 0) {
          if (tokenInfo3.countTokens() < 4) {
            sprintf( painCave.errMsg,
                     "ShapesAtomTypesSectionParser Error: Not enough "
                     "information on a StrengthFunctions line in file: %s\n", 
                     shapeFileName.c_str() );
            painCave.severity = OOPSE_ERROR;
            painCave.isFatal = 1;
            simError();
          } else {
            // read in a spherical harmonic function
            rsh = new RealSphericalHarmonic();
            rsh->setL( tokenInfo3.nextTokenAsInt() );
            rsh->setM( tokenInfo3.nextTokenAsInt() );
            token = tokenInfo3.nextToken();
            transform(token.begin(), token.end(), token.begin(), tolower);
            if (token == "sin")
              rsh->makeSinFunction();
            else
              rsh->makeCosFunction();
            rsh->setCoefficient( tokenInfo3.nextTokenAsDouble() );
            
            functionVector.push_back(rsh);
          }
        }
      }
      shapeStream.getline(buffer, bufferSize);
    }
    
    // pass strength functions to ShapeType
    st->setStrengthFuncs(functionVector);
        
  //  delete shapeStream;
  }
} //end namespace oopse

Revision:	2211
Committed:	Thu Apr 21 14:12:19 2005 UTC (19 years, 2 months ago) by chrisfen
File size:	11748 byte(s)
Log Message:	Shapes is limping along with a array bounds overwrite (I think...). At least the parser loads the forcefield fine...
#	User	Rev	Content
1	chrisfen	2209	/*
2			* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3			*
4			* The University of Notre Dame grants you ("Licensee") a
5			* non-exclusive, royalty free, license to use, modify and
6			* redistribute this software in source and binary code form, provided
7			* that the following conditions are met:
8			*
9			* 1. Acknowledgement of the program authors must be made in any
10			* publication of scientific results based in part on use of the
11			* program. An acceptable form of acknowledgement is citation of
12			* the article in which the program was described (Matthew
13			* A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14			* J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15			* Parallel Simulation Engine for Molecular Dynamics,"
16			* J. Comput. Chem. 26, pp. 252-271 (2005))
17			*
18			* 2. Redistributions of source code must retain the above copyright
19			* notice, this list of conditions and the following disclaimer.
20			*
21			* 3. Redistributions in binary form must reproduce the above copyright
22			* notice, this list of conditions and the following disclaimer in the
23			* documentation and/or other materials provided with the
24			* distribution.
25			*
26			* This software is provided "AS IS," without a warranty of any
27			* kind. All express or implied conditions, representations and
28			* warranties, including any implied warranty of merchantability,
29			* fitness for a particular purpose or non-infringement, are hereby
30			* excluded. The University of Notre Dame and its licensors shall not
31			* be liable for any damages suffered by licensee as a result of
32			* using, modifying or distributing the software or its
33			* derivatives. In no event will the University of Notre Dame or its
34			* licensors be liable for any lost revenue, profit or data, or for
35			* direct, indirect, special, consequential, incidental or punitive
36			* damages, however caused and regardless of the theory of liability,
37			* arising out of the use of or inability to use software, even if the
38			* University of Notre Dame has been advised of the possibility of
39			* such damages.
40			*/
41
42			#include "UseTheForce/ForceField.hpp"
43			#include "io/ShapeAtomTypesSectionParser.hpp"
44			#include "math/RealSphericalHarmonic.hpp"
45			#include "math/SquareMatrix3.hpp"
46			#include "types/AtomType.hpp"
47			#include "types/DirectionalAtomType.hpp"
48			#include "types/ShapeAtomType.hpp"
49			#include "utils/StringUtils.hpp"
50			#include "utils/simError.h"
51
52			namespace oopse {
53
54	chrisfen	2211	ShapeAtomTypesSectionParser::ShapeAtomTypesSectionParser() {
55			setSectionName("ShapeAtomTypes");
56	chrisfen	2209	}
57
58			void ShapeAtomTypesSectionParser::parseLine(ForceField& ff,
59			const std::string& line,
60			int lineNo){
61			StringTokenizer tokenizer(line);
62	chrisfen	2211
63	chrisfen	2209	if (tokenizer.countTokens() >= 2) {
64			std::string shapeTypeName = tokenizer.nextToken();
65			std::string shapeFile = tokenizer.nextToken();
66	chrisfen	2211
67	chrisfen	2209	AtomType* atomType = ff.getAtomType(shapeTypeName);
68	chrisfen	2211	ShapeAtomType* sAtomType;
69			if (atomType == NULL){
70			sAtomType = new ShapeAtomType();
71			int ident = ff.getNAtomType() + 1;
72			sAtomType->setIdent(ident);
73			sAtomType->setName(shapeTypeName);
74			ff.addAtomType(shapeTypeName, sAtomType);
75			} else {
76			sAtomType = dynamic_cast<ShapeAtomType*>(atomType);
77			if (sAtomType == NULL) {
78			sprintf(painCave.errMsg,
79			"ShapeAtomTypesSectionParser:: Can't cast to ShapeAtomType");
80	chrisfen	2209	painCave.severity = OOPSE_ERROR;
81			painCave.isFatal = 1;
82	chrisfen	2211	simError();
83	chrisfen	2209	}
84			}
85	chrisfen	2211
86			sAtomType->setShape();
87			parseShapeFile(ff, shapeFile, sAtomType);
88
89	chrisfen	2209	} else {
90			sprintf(painCave.errMsg,
91			"ShapesAtomTypesSectionParser Error: "
92			"Not enough tokens at line %d\n",
93			lineNo);
94			painCave.severity = OOPSE_ERROR;
95			painCave.isFatal = 1;
96			simError();
97			}
98			}
99
100			void ShapeAtomTypesSectionParser::parseShapeFile(ForceField& ff,
101	chrisfen	2211	std::string& shapeFileName,
102	chrisfen	2209	ShapeAtomType* st) {
103
104			const int bufferSize = 65535;
105			char buffer[bufferSize];
106	chrisfen	2211	std::string token;
107	chrisfen	2209	std::string line;
108			int junk;
109			Mat3x3d momInert;
110			RealSphericalHarmonic* rsh;
111			std::vector<RealSphericalHarmonic*> functionVector;
112	chrisfen	2211	ifstrstream shapeStream;
113			std::string tempString;
114			std::string ffPath;
115			char* tempPath;
116	chrisfen	2209
117	chrisfen	2211	tempPath = getenv("FORCE_PARAM_PATH");
118
119			if (tempPath == NULL) {
120			//convert a macro from compiler to a string in c++
121			STR_DEFINE(ffPath, FRC_PATH );
122			} else {
123			ffPath = tempPath;
124			}
125
126			shapeStream.open( shapeFileName.c_str() );
127
128			if( shapeStream == NULL ){
129
130			tempString = ffPath;
131			tempString += "/";
132			tempString += shapeFileName;
133			shapeFileName = tempString;
134
135			shapeStream.open( shapeFileName.c_str() );
136
137			if( shapeStream == NULL ){
138
139			sprintf( painCave.errMsg,
140			"Error opening the shape file:\n"
141			"\t%s\n"
142			"\tHave you tried setting the FORCE_PARAM_PATH environment "
143			"variable?\n",
144			shapeFileName.c_str() );
145			painCave.severity = OOPSE_ERROR;
146			painCave.isFatal = 1;
147			simError();
148			}
149			}
150
151
152	chrisfen	2209	// first parse the info. in the ShapeInfo section
153			findBegin( shapeStream, "ShapeInfo");
154	chrisfen	2211	shapeStream.getline(buffer, bufferSize);
155	chrisfen	2209
156			// loop over the interior of the ShapeInfo section
157			while( !shapeStream.eof() ) {
158			// toss comment lines
159			if( buffer[0] != '!' && buffer[0] != '#' ){
160			// end marks section completion
161			if (isEndLine(buffer)) break;
162			StringTokenizer tokenInfo(buffer);
163			// blank lines are ignored
164			if (tokenInfo.countTokens() != 0) {
165			if (tokenInfo.countTokens() < 5) {
166			sprintf(painCave.errMsg,
167			"ShapesAtomTypesSectionParser Error: Not enough "
168			"information on a ShapeInfo line in file: %s\n",
169			shapeFileName.c_str() );
170			painCave.severity = OOPSE_ERROR;
171			painCave.isFatal = 1;
172			simError();
173			} else {
174			junk = tokenInfo.nextTokenAsInt();
175			st->setMass( tokenInfo.nextTokenAsDouble() );
176			momInert(0,0) = tokenInfo.nextTokenAsDouble();
177	chrisfen	2211	momInert(1,1) = tokenInfo.nextTokenAsDouble();
178			momInert(2,2) = tokenInfo.nextTokenAsDouble();
179	chrisfen	2209	st->setI(momInert);
180			}
181			}
182			}
183	chrisfen	2211	shapeStream.getline(buffer, bufferSize);
184	chrisfen	2209	}
185
186			// now grab the contact functions
187			findBegin(shapeStream, "ContactFunctions");
188			functionVector.clear();
189
190	chrisfen	2211	shapeStream.getline(buffer, bufferSize);
191	chrisfen	2209	while( !shapeStream.eof() ) {
192			// toss comment lines
193			if( buffer[0] != '!' && buffer[0] != '#' ){
194			// end marks section completion
195			if (isEndLine(buffer)) break;
196			StringTokenizer tokenInfo1(buffer);
197			// blank lines are ignored
198			if (tokenInfo1.countTokens() != 0) {
199			if (tokenInfo1.countTokens() < 4) {
200			sprintf( painCave.errMsg,
201			"ShapesAtomTypesSectionParser Error: Not enough "
202			"information on a ContactFunctions line in file: %s\n",
203			shapeFileName.c_str() );
204			painCave.severity = OOPSE_ERROR;
205			painCave.isFatal = 1;
206			simError();
207			} else {
208			// read in a spherical harmonic function
209			rsh = new RealSphericalHarmonic();
210			rsh->setL( tokenInfo1.nextTokenAsInt() );
211			rsh->setM( tokenInfo1.nextTokenAsInt() );
212	chrisfen	2211	token = tokenInfo1.nextToken();
213			transform(token.begin(), token.end(), token.begin(), tolower);
214			if (token == "sin")
215	chrisfen	2209	rsh->makeSinFunction();
216			else
217			rsh->makeCosFunction();
218			rsh->setCoefficient( tokenInfo1.nextTokenAsDouble() );
219
220			functionVector.push_back(rsh);
221			}
222			}
223			}
224			shapeStream.getline(buffer, bufferSize);
225			}
226
227			// pass contact functions to ShapeType
228			st->setContactFuncs(functionVector);
229
230			// now grab the range functions
231			findBegin(shapeStream, "RangeFunctions");
232			functionVector.clear();
233
234	chrisfen	2211	shapeStream.getline(buffer, bufferSize);
235	chrisfen	2209	while( !shapeStream.eof() ) {
236			// toss comment lines
237			if( buffer[0] != '!' && buffer[0] != '#' ){
238			// end marks section completion
239			if (isEndLine(buffer)) break;
240			StringTokenizer tokenInfo2(buffer);
241			// blank lines are ignored
242			if (tokenInfo2.countTokens() != 0) {
243			if (tokenInfo2.countTokens() < 4) {
244			sprintf( painCave.errMsg,
245			"ShapesAtomTypesSectionParser Error: Not enough "
246			"information on a RangeFunctions line in file: %s\n",
247			shapeFileName.c_str() );
248			painCave.severity = OOPSE_ERROR;
249			painCave.isFatal = 1;
250			simError();
251			} else {
252			// read in a spherical harmonic function
253			rsh = new RealSphericalHarmonic();
254			rsh->setL( tokenInfo2.nextTokenAsInt() );
255			rsh->setM( tokenInfo2.nextTokenAsInt() );
256	chrisfen	2211	token = tokenInfo2.nextToken();
257			transform(token.begin(), token.end(), token.begin(), tolower);
258			if (token == "sin")
259	chrisfen	2209	rsh->makeSinFunction();
260			else
261			rsh->makeCosFunction();
262			rsh->setCoefficient( tokenInfo2.nextTokenAsDouble() );
263
264			functionVector.push_back(rsh);
265			}
266			}
267			}
268			shapeStream.getline(buffer, bufferSize);
269			}
270
271			// pass range functions to ShapeType
272			st->setRangeFuncs(functionVector);
273
274			// finally grab the strength functions
275			findBegin(shapeStream, "StrengthFunctions");
276			functionVector.clear();
277
278	chrisfen	2211	shapeStream.getline(buffer, bufferSize);
279	chrisfen	2209	while( !shapeStream.eof() ) {
280			// toss comment lines
281			if( buffer[0] != '!' && buffer[0] != '#' ){
282			// end marks section completion
283			if (isEndLine(buffer)) break;
284			StringTokenizer tokenInfo3(buffer);
285			// blank lines are ignored
286			if (tokenInfo3.countTokens() != 0) {
287			if (tokenInfo3.countTokens() < 4) {
288			sprintf( painCave.errMsg,
289			"ShapesAtomTypesSectionParser Error: Not enough "
290			"information on a StrengthFunctions line in file: %s\n",
291			shapeFileName.c_str() );
292			painCave.severity = OOPSE_ERROR;
293			painCave.isFatal = 1;
294			simError();
295			} else {
296			// read in a spherical harmonic function
297			rsh = new RealSphericalHarmonic();
298			rsh->setL( tokenInfo3.nextTokenAsInt() );
299			rsh->setM( tokenInfo3.nextTokenAsInt() );
300	chrisfen	2211	token = tokenInfo3.nextToken();
301			transform(token.begin(), token.end(), token.begin(), tolower);
302			if (token == "sin")
303	chrisfen	2209	rsh->makeSinFunction();
304			else
305			rsh->makeCosFunction();
306			rsh->setCoefficient( tokenInfo3.nextTokenAsDouble() );
307
308			functionVector.push_back(rsh);
309			}
310			}
311			}
312			shapeStream.getline(buffer, bufferSize);
313			}
314
315			// pass strength functions to ShapeType
316			st->setStrengthFuncs(functionVector);
317
318	chrisfen	2211	// delete shapeStream;
319	chrisfen	2209	}
320			} //end namespace oopse
321