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"

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)  {
        std::cerr << "DirectionalAtomTypesSectionParser:: Not enought Tokens" << std::endl;                       
    } 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) {
                std::cerr << "DirectionalAtomTypesSectionParser:: Can not cast to DirectionalAtomType" << std::endl;                       
            }
        }

        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:	1930
Committed:	Wed Jan 12 22:41:40 2005 UTC (19 years, 5 months ago) by gezelter
File size:	3913 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	User	Rev	Content
1	gezelter	1930	/*
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 "io/DirectionalAtomTypesSectionParser.hpp"
43			#include "UseTheForce/ForceField.hpp"
44			#include "types/DirectionalAtomType.hpp"
45
46			namespace oopse {
47
48			DirectionalAtomTypesSectionParser::DirectionalAtomTypesSectionParser() {
49			setSectionName("DirectionalAtomTypes");
50			}
51
52			void DirectionalAtomTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
53			StringTokenizer tokenizer(line);
54			int nTokens = tokenizer.countTokens();
55
56			//in AtomTypeSection, a line at least contains 2 tokens
57			//atomTypeName and mass
58			if (nTokens < 4) {
59			std::cerr << "DirectionalAtomTypesSectionParser:: Not enought Tokens" << std::endl;
60			} else {
61
62			std::string atomTypeName = tokenizer.nextToken();
63			AtomType* atomType = ff.getAtomType(atomTypeName);
64			DirectionalAtomType* dAtomType;
65			if (atomType == NULL) {
66			dAtomType = new DirectionalAtomType();
67			int ident = ff.getNAtomType() + 1;
68			dAtomType->setIdent(ident);
69			dAtomType->setName(atomTypeName);
70			ff.addAtomType(atomTypeName, dAtomType);
71			} else {
72			dAtomType = dynamic_cast<DirectionalAtomType*>(atomType);
73			if (dAtomType == NULL) {
74			std::cerr << "DirectionalAtomTypesSectionParser:: Can not cast to DirectionalAtomType" << std::endl;
75			}
76			}
77
78			double Ixx = tokenizer.nextTokenAsDouble();
79			double Iyy = tokenizer.nextTokenAsDouble();
80			double Izz = tokenizer.nextTokenAsDouble();
81			Mat3x3d inertialMat;
82			inertialMat(0, 0) = Ixx;
83			inertialMat(1, 1) = Iyy;
84			inertialMat(2, 2) = Izz;
85			dAtomType->setI(inertialMat);
86
87			}
88
89			}
90
91			} //end namespace oopse