src/io/DirectionalAtomTypesSectionParser.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 "io/DirectionalAtomTypesSectionParser.hpp"
#include "UseTheForce/ForceField.hpp"
#include "types/DirectionalAtomType.hpp"
#include "utils/simError.h"
namespace oopse {

  DirectionalAtomTypesSectionParser::DirectionalAtomTypesSectionParser() {
    setSectionName("DirectionalAtomTypes");
  }

  void DirectionalAtomTypesSectionParser::parseLine(ForceField& ff, 
                                                    const std::string& line, 
                                                    int lineNo){
    StringTokenizer tokenizer(line);
    int nTokens = tokenizer.countTokens();    

    //in AtomTypeSection, a line at least contains 2 tokens
    //atomTypeName and mass
    if (nTokens < 4)  {
      sprintf(painCave.errMsg, 
              "DirectionalAtomTypesSectionParser Error: Not enough tokens at line %d\n",
              lineNo);
      painCave.isFatal = 1;
      simError();
                   
    } else {

      std::string atomTypeName = tokenizer.nextToken();    
      AtomType* atomType = ff.getAtomType(atomTypeName);
      DirectionalAtomType* dAtomType;
      if (atomType == NULL) {
        dAtomType = new DirectionalAtomType();
        int ident = ff.getNAtomType() + 1;
        dAtomType->setIdent(ident); 
        dAtomType->setName(atomTypeName);
        ff.addAtomType(atomTypeName, dAtomType);
      } else {
        dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
        if (dAtomType == NULL) {
          sprintf(painCave.errMsg,
                  "DirectionalAtomTypesSectionParser:: Can not cast to DirectionalAtomType");
          painCave.isFatal = 1;
          simError();
        }
      }
      
      double Ixx = tokenizer.nextTokenAsDouble();
      double Iyy = tokenizer.nextTokenAsDouble();
      double Izz = tokenizer.nextTokenAsDouble();            
      Mat3x3d inertialMat;
      inertialMat(0, 0) = Ixx;
      inertialMat(1, 1) = Iyy;
      inertialMat(2, 2) = Izz;        
      dAtomType->setI(inertialMat);            
                       
    }    

  }

} //end namespace oopse
Revision:	2209
Committed:	Mon Apr 18 03:50:23 2005 UTC (19 years, 2 months ago) by chrisfen
File size:	4138 byte(s)
Log Message:	Working on the shapes parser...
#	User	Rev	Content
1	gezelter	2204	/*
2	gezelter	1930	* 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 "io/DirectionalAtomTypesSectionParser.hpp"
43			#include "UseTheForce/ForceField.hpp"
44			#include "types/DirectionalAtomType.hpp"
45	tim	1957	#include "utils/simError.h"
46	gezelter	1930	namespace oopse {
47
48	gezelter	2204	DirectionalAtomTypesSectionParser::DirectionalAtomTypesSectionParser() {
49	gezelter	1930	setSectionName("DirectionalAtomTypes");
50	gezelter	2204	}
51	gezelter	1930
52	chrisfen	2209	void DirectionalAtomTypesSectionParser::parseLine(ForceField& ff,
53			const std::string& line,
54			int lineNo){
55	gezelter	1930	StringTokenizer tokenizer(line);
56			int nTokens = tokenizer.countTokens();
57
58			//in AtomTypeSection, a line at least contains 2 tokens
59			//atomTypeName and mass
60			if (nTokens < 4) {
61	chrisfen	2209	sprintf(painCave.errMsg,
62			"DirectionalAtomTypesSectionParser Error: Not enough tokens at line %d\n",
63			lineNo);
64	gezelter	2204	painCave.isFatal = 1;
65			simError();
66	tim	1957
67	gezelter	1930	} else {
68
69	gezelter	2204	std::string atomTypeName = tokenizer.nextToken();
70			AtomType* atomType = ff.getAtomType(atomTypeName);
71			DirectionalAtomType* dAtomType;
72			if (atomType == NULL) {
73	chrisfen	2209	dAtomType = new DirectionalAtomType();
74			int ident = ff.getNAtomType() + 1;
75			dAtomType->setIdent(ident);
76			dAtomType->setName(atomTypeName);
77			ff.addAtomType(atomTypeName, dAtomType);
78	gezelter	2204	} else {
79	chrisfen	2209	dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
80			if (dAtomType == NULL) {
81			sprintf(painCave.errMsg,
82			"DirectionalAtomTypesSectionParser:: Can not cast to DirectionalAtomType");
83			painCave.isFatal = 1;
84			simError();
85			}
86	gezelter	2204	}
87	chrisfen	2209
88	gezelter	2204	double Ixx = tokenizer.nextTokenAsDouble();
89			double Iyy = tokenizer.nextTokenAsDouble();
90			double Izz = tokenizer.nextTokenAsDouble();
91			Mat3x3d inertialMat;
92			inertialMat(0, 0) = Ixx;
93			inertialMat(1, 1) = Iyy;
94			inertialMat(2, 2) = Izz;
95			dAtomType->setI(inertialMat);
96	gezelter	1930
97			}
98
99	gezelter	2204	}
100	gezelter	1930
101			} //end namespace oopse