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"
#include "utils/CaseConversion.hpp"

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();
            toLower(token);
            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();
            toLower(token);
            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();
            toLower(token);
            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:	2223
Committed:	Wed May 11 23:15:05 2005 UTC (19 years, 2 months ago) by chuckv
File size:	11643 byte(s)
Log Message:	Fixed build issues under ifc7.
#	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	chuckv	2223	#include "utils/CaseConversion.hpp"
52	chrisfen	2209
53			namespace oopse {
54
55	chrisfen	2211	ShapeAtomTypesSectionParser::ShapeAtomTypesSectionParser() {
56			setSectionName("ShapeAtomTypes");
57	chrisfen	2209	}
58
59			void ShapeAtomTypesSectionParser::parseLine(ForceField& ff,
60			const std::string& line,
61			int lineNo){
62			StringTokenizer tokenizer(line);
63	chrisfen	2211
64	chrisfen	2209	if (tokenizer.countTokens() >= 2) {
65			std::string shapeTypeName = tokenizer.nextToken();
66			std::string shapeFile = tokenizer.nextToken();
67	chrisfen	2211
68	chrisfen	2209	AtomType* atomType = ff.getAtomType(shapeTypeName);
69	chrisfen	2211	ShapeAtomType* sAtomType;
70			if (atomType == NULL){
71			sAtomType = new ShapeAtomType();
72			int ident = ff.getNAtomType() + 1;
73			sAtomType->setIdent(ident);
74			sAtomType->setName(shapeTypeName);
75			ff.addAtomType(shapeTypeName, sAtomType);
76			} else {
77			sAtomType = dynamic_cast<ShapeAtomType*>(atomType);
78			if (sAtomType == NULL) {
79			sprintf(painCave.errMsg,
80			"ShapeAtomTypesSectionParser:: Can't cast to ShapeAtomType");
81	chrisfen	2209	painCave.severity = OOPSE_ERROR;
82			painCave.isFatal = 1;
83	chrisfen	2211	simError();
84	chrisfen	2209	}
85			}
86	chrisfen	2211
87			sAtomType->setShape();
88			parseShapeFile(ff, shapeFile, sAtomType);
89
90	chrisfen	2209	} else {
91			sprintf(painCave.errMsg,
92			"ShapesAtomTypesSectionParser Error: "
93			"Not enough tokens at line %d\n",
94			lineNo);
95			painCave.severity = OOPSE_ERROR;
96			painCave.isFatal = 1;
97			simError();
98			}
99			}
100
101			void ShapeAtomTypesSectionParser::parseShapeFile(ForceField& ff,
102	chrisfen	2211	std::string& shapeFileName,
103	chrisfen	2209	ShapeAtomType* st) {
104
105			const int bufferSize = 65535;
106			char buffer[bufferSize];
107	chrisfen	2211	std::string token;
108	chrisfen	2209	std::string line;
109			int junk;
110			Mat3x3d momInert;
111			RealSphericalHarmonic* rsh;
112			std::vector<RealSphericalHarmonic*> functionVector;
113	chrisfen	2211	ifstrstream shapeStream;
114			std::string tempString;
115			std::string ffPath;
116			char* tempPath;
117	chrisfen	2209
118	chrisfen	2211	tempPath = getenv("FORCE_PARAM_PATH");
119
120			if (tempPath == NULL) {
121			//convert a macro from compiler to a string in c++
122			STR_DEFINE(ffPath, FRC_PATH );
123			} else {
124			ffPath = tempPath;
125			}
126
127			shapeStream.open( shapeFileName.c_str() );
128
129			if( shapeStream == NULL ){
130
131			tempString = ffPath;
132			tempString += "/";
133			tempString += shapeFileName;
134			shapeFileName = tempString;
135
136			shapeStream.open( shapeFileName.c_str() );
137
138			if( shapeStream == NULL ){
139
140			sprintf( painCave.errMsg,
141			"Error opening the shape file:\n"
142			"\t%s\n"
143			"\tHave you tried setting the FORCE_PARAM_PATH environment "
144			"variable?\n",
145			shapeFileName.c_str() );
146			painCave.severity = OOPSE_ERROR;
147			painCave.isFatal = 1;
148			simError();
149			}
150			}
151
152
153	chrisfen	2209	// first parse the info. in the ShapeInfo section
154			findBegin( shapeStream, "ShapeInfo");
155	chrisfen	2211	shapeStream.getline(buffer, bufferSize);
156	chrisfen	2209
157			// loop over the interior of the ShapeInfo section
158			while( !shapeStream.eof() ) {
159			// toss comment lines
160			if( buffer[0] != '!' && buffer[0] != '#' ){
161			// end marks section completion
162			if (isEndLine(buffer)) break;
163			StringTokenizer tokenInfo(buffer);
164			// blank lines are ignored
165			if (tokenInfo.countTokens() != 0) {
166			if (tokenInfo.countTokens() < 5) {
167			sprintf(painCave.errMsg,
168			"ShapesAtomTypesSectionParser Error: Not enough "
169			"information on a ShapeInfo line in file: %s\n",
170			shapeFileName.c_str() );
171			painCave.severity = OOPSE_ERROR;
172			painCave.isFatal = 1;
173			simError();
174			} else {
175			junk = tokenInfo.nextTokenAsInt();
176			st->setMass( tokenInfo.nextTokenAsDouble() );
177			momInert(0,0) = tokenInfo.nextTokenAsDouble();
178	chrisfen	2211	momInert(1,1) = tokenInfo.nextTokenAsDouble();
179			momInert(2,2) = tokenInfo.nextTokenAsDouble();
180	chrisfen	2209	st->setI(momInert);
181			}
182			}
183			}
184	chrisfen	2211	shapeStream.getline(buffer, bufferSize);
185	chrisfen	2209	}
186
187			// now grab the contact functions
188			findBegin(shapeStream, "ContactFunctions");
189			functionVector.clear();
190
191	chrisfen	2211	shapeStream.getline(buffer, bufferSize);
192	chrisfen	2209	while( !shapeStream.eof() ) {
193			// toss comment lines
194			if( buffer[0] != '!' && buffer[0] != '#' ){
195			// end marks section completion
196			if (isEndLine(buffer)) break;
197			StringTokenizer tokenInfo1(buffer);
198			// blank lines are ignored
199			if (tokenInfo1.countTokens() != 0) {
200			if (tokenInfo1.countTokens() < 4) {
201			sprintf( painCave.errMsg,
202			"ShapesAtomTypesSectionParser Error: Not enough "
203			"information on a ContactFunctions line in file: %s\n",
204			shapeFileName.c_str() );
205			painCave.severity = OOPSE_ERROR;
206			painCave.isFatal = 1;
207			simError();
208			} else {
209			// read in a spherical harmonic function
210			rsh = new RealSphericalHarmonic();
211			rsh->setL( tokenInfo1.nextTokenAsInt() );
212			rsh->setM( tokenInfo1.nextTokenAsInt() );
213	chrisfen	2211	token = tokenInfo1.nextToken();
214	chuckv	2223	toLower(token);
215	chrisfen	2211	if (token == "sin")
216	chrisfen	2209	rsh->makeSinFunction();
217			else
218			rsh->makeCosFunction();
219			rsh->setCoefficient( tokenInfo1.nextTokenAsDouble() );
220
221			functionVector.push_back(rsh);
222			}
223			}
224			}
225			shapeStream.getline(buffer, bufferSize);
226			}
227
228			// pass contact functions to ShapeType
229			st->setContactFuncs(functionVector);
230
231			// now grab the range functions
232			findBegin(shapeStream, "RangeFunctions");
233			functionVector.clear();
234
235	chrisfen	2211	shapeStream.getline(buffer, bufferSize);
236	chrisfen	2209	while( !shapeStream.eof() ) {
237			// toss comment lines
238			if( buffer[0] != '!' && buffer[0] != '#' ){
239			// end marks section completion
240			if (isEndLine(buffer)) break;
241			StringTokenizer tokenInfo2(buffer);
242			// blank lines are ignored
243			if (tokenInfo2.countTokens() != 0) {
244			if (tokenInfo2.countTokens() < 4) {
245			sprintf( painCave.errMsg,
246			"ShapesAtomTypesSectionParser Error: Not enough "
247			"information on a RangeFunctions line in file: %s\n",
248			shapeFileName.c_str() );
249			painCave.severity = OOPSE_ERROR;
250			painCave.isFatal = 1;
251			simError();
252			} else {
253			// read in a spherical harmonic function
254			rsh = new RealSphericalHarmonic();
255			rsh->setL( tokenInfo2.nextTokenAsInt() );
256			rsh->setM( tokenInfo2.nextTokenAsInt() );
257	chrisfen	2211	token = tokenInfo2.nextToken();
258	chuckv	2223	toLower(token);
259	chrisfen	2211	if (token == "sin")
260	chrisfen	2209	rsh->makeSinFunction();
261			else
262			rsh->makeCosFunction();
263			rsh->setCoefficient( tokenInfo2.nextTokenAsDouble() );
264
265			functionVector.push_back(rsh);
266			}
267			}
268			}
269			shapeStream.getline(buffer, bufferSize);
270			}
271
272			// pass range functions to ShapeType
273			st->setRangeFuncs(functionVector);
274
275			// finally grab the strength functions
276			findBegin(shapeStream, "StrengthFunctions");
277			functionVector.clear();
278
279	chrisfen	2211	shapeStream.getline(buffer, bufferSize);
280	chrisfen	2209	while( !shapeStream.eof() ) {
281			// toss comment lines
282			if( buffer[0] != '!' && buffer[0] != '#' ){
283			// end marks section completion
284			if (isEndLine(buffer)) break;
285			StringTokenizer tokenInfo3(buffer);
286			// blank lines are ignored
287			if (tokenInfo3.countTokens() != 0) {
288			if (tokenInfo3.countTokens() < 4) {
289			sprintf( painCave.errMsg,
290			"ShapesAtomTypesSectionParser Error: Not enough "
291			"information on a StrengthFunctions line in file: %s\n",
292			shapeFileName.c_str() );
293			painCave.severity = OOPSE_ERROR;
294			painCave.isFatal = 1;
295			simError();
296			} else {
297			// read in a spherical harmonic function
298			rsh = new RealSphericalHarmonic();
299			rsh->setL( tokenInfo3.nextTokenAsInt() );
300			rsh->setM( tokenInfo3.nextTokenAsInt() );
301	chrisfen	2211	token = tokenInfo3.nextToken();
302	chuckv	2223	toLower(token);
303	chrisfen	2211	if (token == "sin")
304	chrisfen	2209	rsh->makeSinFunction();
305			else
306			rsh->makeCosFunction();
307			rsh->setCoefficient( tokenInfo3.nextTokenAsDouble() );
308
309			functionVector.push_back(rsh);
310			}
311			}
312			}
313			shapeStream.getline(buffer, bufferSize);
314			}
315
316			// pass strength functions to ShapeType
317			st->setStrengthFuncs(functionVector);
318
319	chrisfen	2211	// delete shapeStream;
320	chrisfen	2209	}
321			} //end namespace oopse
322