src/io/TorsionTypesSectionParser.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/TorsionTypesSectionParser.hpp"
#include "types/TorsionType.hpp"
#include "types/CubicTorsionType.hpp"
#include "types/QuarticTorsionType.hpp"
#include "types/PolynomialTorsionType.hpp"
#include "types/CharmmTorsionType.hpp"
#include "UseTheForce/ForceField.hpp"

namespace oopse {

TorsionTypesSectionParser::TorsionTypesSectionParser() {
    setSectionName("TorsionTypes");


    stringToEnumMap_["Cubic"] = ttCubic;
    stringToEnumMap_["Quartic"] = ttQuartic;
    stringToEnumMap_["Polynomial"] = ttPolynomial;
    stringToEnumMap_["Charmm"] =  ttCharmm;

}

void TorsionTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
    StringTokenizer tokenizer(line);
    TorsionType* torsionType = NULL;

    int nTokens = tokenizer.countTokens();

    if (nTokens < 5) {

        return;
    }
    
    std::string at1 = tokenizer.nextToken();
    std::string at2 = tokenizer.nextToken();
    std::string at3 = tokenizer.nextToken();
    std::string at4 = tokenizer.nextToken();
    TorsionTypeEnum tt = getTorsionTypeEnum(tokenizer.nextToken());

    nTokens -= 5;

    switch(tt) {
            
        case TorsionTypesSectionParser::ttCubic :
            if (nTokens < 4) {

            } else {

                double k3 = tokenizer.nextTokenAsDouble();
                double k2 = tokenizer.nextTokenAsDouble();
                double k1 = tokenizer.nextTokenAsDouble();
                double k0 = tokenizer.nextTokenAsDouble();
                
                torsionType = new CubicTorsionType(k3, k2, k1, k0);
            }
            break;
            
        case TorsionTypesSectionParser::ttQuartic:
            if (nTokens < 5) {

            } else {

                double k4 = tokenizer.nextTokenAsDouble();
                double k3 = tokenizer.nextTokenAsDouble();
                double k2 = tokenizer.nextTokenAsDouble();
                double k1 = tokenizer.nextTokenAsDouble();
                double k0 = tokenizer.nextTokenAsDouble();
                
                torsionType = new QuarticTorsionType( k4, k3, k2, k1, k0);
            }
            break;

        
        case TorsionTypesSectionParser::ttPolynomial:
            if (nTokens < 2 || nTokens % 2 != 0) {

            } else {
                int nPairs = nTokens / 2;
                int power;
                double coefficient;
                PolynomialTorsionType* ptt = new PolynomialTorsionType();
                
                for (int i = 0; i < nPairs; ++i) {
                    power = tokenizer.nextTokenAsInt();
                    coefficient = tokenizer.nextTokenAsDouble();
                    ptt->setCoefficient(power, coefficient);
                }
            }
            
            break;
             
        case TorsionTypesSectionParser::ttCharmm:
            
            if (nTokens < 3 || nTokens % 3 != 0) {

            } else {
                int nSets = nTokens / 3;
  
                CharmmTorsionType* ctt = new CharmmTorsionType();
                
                for (int i = 0; i < nSets; ++i) {
                    double kchi = tokenizer.nextTokenAsDouble();
                    int n = tokenizer.nextTokenAsInt();
                    double delta = tokenizer.nextTokenAsDouble();
    
                    ctt->setCharmmTorsionParameter(kchi, n, delta);
                }
            }

            break;
            
        case TorsionTypesSectionParser::ttUnknown :
        default:

            break;
            
    }

    if (torsionType != NULL) {
        ff.addTorsionType(at1, at2, at3, at4, torsionType);
    }

}

TorsionTypesSectionParser::TorsionTypeEnum TorsionTypesSectionParser::getTorsionTypeEnum(const std::string& str) {
    std::map<std::string, TorsionTypeEnum>::iterator i;
    i = stringToEnumMap_.find(str);

    return i == stringToEnumMap_.end() ? TorsionTypesSectionParser::ttUnknown : i->second;
}

} //end namespace oopse


Revision:	1930
Committed:	Wed Jan 12 22:41:40 2005 UTC (19 years, 5 months ago) by gezelter
File size:	6032 byte(s)
Log Message:	merging new_design branch into OOPSE-2.0
#	Content
1	/*
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/TorsionTypesSectionParser.hpp"
43	#include "types/TorsionType.hpp"
44	#include "types/CubicTorsionType.hpp"
45	#include "types/QuarticTorsionType.hpp"
46	#include "types/PolynomialTorsionType.hpp"
47	#include "types/CharmmTorsionType.hpp"
48	#include "UseTheForce/ForceField.hpp"
49
50	namespace oopse {
51
52	TorsionTypesSectionParser::TorsionTypesSectionParser() {
53	setSectionName("TorsionTypes");
54
55
56	stringToEnumMap_["Cubic"] = ttCubic;
57	stringToEnumMap_["Quartic"] = ttQuartic;
58	stringToEnumMap_["Polynomial"] = ttPolynomial;
59	stringToEnumMap_["Charmm"] = ttCharmm;
60
61	}
62
63	void TorsionTypesSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
64	StringTokenizer tokenizer(line);
65	TorsionType* torsionType = NULL;
66
67	int nTokens = tokenizer.countTokens();
68
69	if (nTokens < 5) {
70
71	return;
72	}
73
74	std::string at1 = tokenizer.nextToken();
75	std::string at2 = tokenizer.nextToken();
76	std::string at3 = tokenizer.nextToken();
77	std::string at4 = tokenizer.nextToken();
78	TorsionTypeEnum tt = getTorsionTypeEnum(tokenizer.nextToken());
79
80	nTokens -= 5;
81
82	switch(tt) {
83
84	case TorsionTypesSectionParser::ttCubic :
85	if (nTokens < 4) {
86
87	} else {
88
89	double k3 = tokenizer.nextTokenAsDouble();
90	double k2 = tokenizer.nextTokenAsDouble();
91	double k1 = tokenizer.nextTokenAsDouble();
92	double k0 = tokenizer.nextTokenAsDouble();
93
94	torsionType = new CubicTorsionType(k3, k2, k1, k0);
95	}
96	break;
97
98	case TorsionTypesSectionParser::ttQuartic:
99	if (nTokens < 5) {
100
101	} else {
102
103	double k4 = tokenizer.nextTokenAsDouble();
104	double k3 = tokenizer.nextTokenAsDouble();
105	double k2 = tokenizer.nextTokenAsDouble();
106	double k1 = tokenizer.nextTokenAsDouble();
107	double k0 = tokenizer.nextTokenAsDouble();
108
109	torsionType = new QuarticTorsionType( k4, k3, k2, k1, k0);
110	}
111	break;
112
113
114	case TorsionTypesSectionParser::ttPolynomial:
115	if (nTokens < 2 \|\| nTokens % 2 != 0) {
116
117	} else {
118	int nPairs = nTokens / 2;
119	int power;
120	double coefficient;
121	PolynomialTorsionType* ptt = new PolynomialTorsionType();
122
123	for (int i = 0; i < nPairs; ++i) {
124	power = tokenizer.nextTokenAsInt();
125	coefficient = tokenizer.nextTokenAsDouble();
126	ptt->setCoefficient(power, coefficient);
127	}
128	}
129
130	break;
131
132	case TorsionTypesSectionParser::ttCharmm:
133
134	if (nTokens < 3 \|\| nTokens % 3 != 0) {
135
136	} else {
137	int nSets = nTokens / 3;
138
139	CharmmTorsionType* ctt = new CharmmTorsionType();
140
141	for (int i = 0; i < nSets; ++i) {
142	double kchi = tokenizer.nextTokenAsDouble();
143	int n = tokenizer.nextTokenAsInt();
144	double delta = tokenizer.nextTokenAsDouble();
145
146	ctt->setCharmmTorsionParameter(kchi, n, delta);
147	}
148	}
149
150	break;
151
152	case TorsionTypesSectionParser::ttUnknown :
153	default:
154
155	break;
156
157	}
158
159	if (torsionType != NULL) {
160	ff.addTorsionType(at1, at2, at3, at4, torsionType);
161	}
162
163	}
164
165	TorsionTypesSectionParser::TorsionTypeEnum TorsionTypesSectionParser::getTorsionTypeEnum(const std::string& str) {
166	std::map<std::string, TorsionTypeEnum>::iterator i;
167	i = stringToEnumMap_.find(str);
168
169	return i == stringToEnumMap_.end() ? TorsionTypesSectionParser::ttUnknown : i->second;
170	}
171
172	} //end namespace oopse
173
174
175