src/io/NonBondedInteractionsSectionParser.cpp

/*
 * Copyright (c) 2007 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. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. 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.
 *
 * SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
 * research, please cite the appropriate papers when you publish your
 * work.  Good starting points are:
 *                                                                      
 * [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).             
 * [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).          
 * [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).          
 * [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
 * [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
 */
 
#include "io/NonBondedInteractionsSectionParser.hpp"
#include "types/AtomType.hpp"
#include "types/MorseInteractionType.hpp"
#include "types/MAWInteractionType.hpp"
#include "types/LennardJonesInteractionType.hpp"
#include "types/RepulsivePowerInteractionType.hpp"
#include "brains/ForceField.hpp"
#include "utils/simError.h"
namespace OpenMD {

  NonBondedInteractionsSectionParser::NonBondedInteractionsSectionParser(ForceFieldOptions& options) : options_(options){
    setSectionName("NonBondedInteractions");
    
    stringToEnumMap_["MAW"] =  MAW;                
    stringToEnumMap_["ShiftedMorse"] =  ShiftedMorse;
    stringToEnumMap_["LennardJones"] = LennardJones;
    stringToEnumMap_["RepulsiveMorse"] = RepulsiveMorse;
    stringToEnumMap_["RepulsivePower"] = RepulsivePower;
    
  }
  
  void NonBondedInteractionsSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
    StringTokenizer tokenizer(line);
    NonBondedInteractionType* nbiType = NULL;
    int nTokens = tokenizer.countTokens();
    
    if (nTokens < 3) {
      sprintf(painCave.errMsg, "NonBondedInteractionsSectionParser Error: Not enough tokens at line %d\n",
              lineNo);
      painCave.isFatal = 1;
      simError();
    }
    
    std::string at1 = tokenizer.nextToken();
    std::string at2 = tokenizer.nextToken();
    std::string itype = tokenizer.nextToken();
    
    NonBondedInteractionTypeEnum nbit = getNonBondedInteractionTypeEnum(itype);
    nTokens -= 3;
    NonBondedInteractionType* interactionType;
    
    //switch is a nightmare to maintain
    switch(nbit) {
    case MAW :
      if (nTokens < 5) {
        sprintf(painCave.errMsg, "NonBondedInteractionsSectionParser Error: Not enough tokens at line %d\n",
                lineNo);
        painCave.isFatal = 1;
        simError();
      } else {
        RealType r_e = tokenizer.nextTokenAsDouble();
        RealType D_e = tokenizer.nextTokenAsDouble();
        RealType beta = tokenizer.nextTokenAsDouble();
        RealType ca1 = tokenizer.nextTokenAsDouble();
        RealType cb1 = tokenizer.nextTokenAsDouble();
        interactionType = new MAWInteractionType(D_e, beta, r_e, ca1, cb1);
      }
      break;
      
    case ShiftedMorse :
      if (nTokens < 3) {
        sprintf(painCave.errMsg, "NonBondedInteractionsSectionParser Error: Not enough tokens at line %d\n",
                lineNo);
        painCave.isFatal = 1;
        simError();
      } else {
        RealType r0 = tokenizer.nextTokenAsDouble();
        RealType D0 = tokenizer.nextTokenAsDouble();
        RealType beta0 = tokenizer.nextTokenAsDouble();
        interactionType = new MorseInteractionType(D0, beta0, r0, mtShifted);
      }
      break;
      
    case RepulsiveMorse :
      if (nTokens < 3) {
        sprintf(painCave.errMsg, "NonBondedInteractionsSectionParser Error: Not enough tokens at line %d\n",
                lineNo);
        painCave.isFatal = 1;
        simError();
      } else {
        RealType r0 = tokenizer.nextTokenAsDouble();
        RealType D0 = tokenizer.nextTokenAsDouble();
        RealType beta0 = tokenizer.nextTokenAsDouble();
        interactionType = new MorseInteractionType(D0, beta0, r0, mtRepulsive);
      }
      break;
      
    case LennardJones :
      if (nTokens < 2) {
        sprintf(painCave.errMsg, "NonBondedInteractionsSectionParser Error: Not enough tokens at line %d\n",
                lineNo);
        painCave.isFatal = 1;
        simError();
      } else {
        RealType sigma = tokenizer.nextTokenAsDouble();
        RealType epsilon = tokenizer.nextTokenAsDouble();
        interactionType = new LennardJonesInteractionType(sigma, epsilon);
      }
      break;

    case RepulsivePower :
      if (nTokens < 3) {
        sprintf(painCave.errMsg, "NonBondedInteractionsSectionParser Error: Not enough tokens at line %d\n",
                lineNo);
        painCave.isFatal = 1;
        simError();
      } else {
        RealType sigma = tokenizer.nextTokenAsDouble();
        RealType epsilon = tokenizer.nextTokenAsDouble();
        int nRep = tokenizer.nextTokenAsInt();
        interactionType = new RepulsivePowerInteractionType(sigma, epsilon, nRep);
      }
      break;
      
    case Unknown :
    default:
      sprintf(painCave.errMsg, "NonBondedInteractionsSectionParser Error: Unknown Interaction Type at line %d\n",
              lineNo);
      painCave.isFatal = 1;
      simError();
      
      break;
            
    }
    
    if (interactionType != NULL) {
      ff.addNonBondedInteractionType(at1, at2, interactionType);
    }
    
  }
  
  NonBondedInteractionsSectionParser::NonBondedInteractionTypeEnum NonBondedInteractionsSectionParser::getNonBondedInteractionTypeEnum(const std::string& str) {
    std::map<std::string, NonBondedInteractionTypeEnum>::iterator i;
    i = stringToEnumMap_.find(str);
    
    return i == stringToEnumMap_.end() ? Unknown : i->second;
  }
  
} //end namespace OpenMD

Revision:	1725
Committed:	Sat May 26 18:13:43 2012 UTC (12 years, 11 months ago) by gezelter
File size:	7144 byte(s)
Log Message:	Individual ForceField classes have been removed (they were essentially all duplicates anyway). ForceField has moved to brains, and since only one force field is in play at any time, the ForceFieldFactory and Register methods have been removed.
#	Content
1	/*
2	* Copyright (c) 2007 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. Redistributions of source code must retain the above copyright
10	* notice, this list of conditions and the following disclaimer.
11	*
12	* 2. Redistributions in binary form must reproduce the above copyright
13	* notice, this list of conditions and the following disclaimer in the
14	* documentation and/or other materials provided with the
15	* distribution.
16	*
17	* This software is provided "AS IS," without a warranty of any
18	* kind. All express or implied conditions, representations and
19	* warranties, including any implied warranty of merchantability,
20	* fitness for a particular purpose or non-infringement, are hereby
21	* excluded. The University of Notre Dame and its licensors shall not
22	* be liable for any damages suffered by licensee as a result of
23	* using, modifying or distributing the software or its
24	* derivatives. In no event will the University of Notre Dame or its
25	* licensors be liable for any lost revenue, profit or data, or for
26	* direct, indirect, special, consequential, incidental or punitive
27	* damages, however caused and regardless of the theory of liability,
28	* arising out of the use of or inability to use software, even if the
29	* University of Notre Dame has been advised of the possibility of
30	* such damages.
31	*
32	* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your
33	* research, please cite the appropriate papers when you publish your
34	* work. Good starting points are:
35	*
36	* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	*/
42
43	#include "io/NonBondedInteractionsSectionParser.hpp"
44	#include "types/AtomType.hpp"
45	#include "types/MorseInteractionType.hpp"
46	#include "types/MAWInteractionType.hpp"
47	#include "types/LennardJonesInteractionType.hpp"
48	#include "types/RepulsivePowerInteractionType.hpp"
49	#include "brains/ForceField.hpp"
50	#include "utils/simError.h"
51	namespace OpenMD {
52
53	NonBondedInteractionsSectionParser::NonBondedInteractionsSectionParser(ForceFieldOptions& options) : options_(options){
54	setSectionName("NonBondedInteractions");
55
56	stringToEnumMap_["MAW"] = MAW;
57	stringToEnumMap_["ShiftedMorse"] = ShiftedMorse;
58	stringToEnumMap_["LennardJones"] = LennardJones;
59	stringToEnumMap_["RepulsiveMorse"] = RepulsiveMorse;
60	stringToEnumMap_["RepulsivePower"] = RepulsivePower;
61
62	}
63
64	void NonBondedInteractionsSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
65	StringTokenizer tokenizer(line);
66	NonBondedInteractionType* nbiType = NULL;
67	int nTokens = tokenizer.countTokens();
68
69	if (nTokens < 3) {
70	sprintf(painCave.errMsg, "NonBondedInteractionsSectionParser Error: Not enough tokens at line %d\n",
71	lineNo);
72	painCave.isFatal = 1;
73	simError();
74	}
75
76	std::string at1 = tokenizer.nextToken();
77	std::string at2 = tokenizer.nextToken();
78	std::string itype = tokenizer.nextToken();
79
80	NonBondedInteractionTypeEnum nbit = getNonBondedInteractionTypeEnum(itype);
81	nTokens -= 3;
82	NonBondedInteractionType* interactionType;
83
84	//switch is a nightmare to maintain
85	switch(nbit) {
86	case MAW :
87	if (nTokens < 5) {
88	sprintf(painCave.errMsg, "NonBondedInteractionsSectionParser Error: Not enough tokens at line %d\n",
89	lineNo);
90	painCave.isFatal = 1;
91	simError();
92	} else {
93	RealType r_e = tokenizer.nextTokenAsDouble();
94	RealType D_e = tokenizer.nextTokenAsDouble();
95	RealType beta = tokenizer.nextTokenAsDouble();
96	RealType ca1 = tokenizer.nextTokenAsDouble();
97	RealType cb1 = tokenizer.nextTokenAsDouble();
98	interactionType = new MAWInteractionType(D_e, beta, r_e, ca1, cb1);
99	}
100	break;
101
102	case ShiftedMorse :
103	if (nTokens < 3) {
104	sprintf(painCave.errMsg, "NonBondedInteractionsSectionParser Error: Not enough tokens at line %d\n",
105	lineNo);
106	painCave.isFatal = 1;
107	simError();
108	} else {
109	RealType r0 = tokenizer.nextTokenAsDouble();
110	RealType D0 = tokenizer.nextTokenAsDouble();
111	RealType beta0 = tokenizer.nextTokenAsDouble();
112	interactionType = new MorseInteractionType(D0, beta0, r0, mtShifted);
113	}
114	break;
115
116	case RepulsiveMorse :
117	if (nTokens < 3) {
118	sprintf(painCave.errMsg, "NonBondedInteractionsSectionParser Error: Not enough tokens at line %d\n",
119	lineNo);
120	painCave.isFatal = 1;
121	simError();
122	} else {
123	RealType r0 = tokenizer.nextTokenAsDouble();
124	RealType D0 = tokenizer.nextTokenAsDouble();
125	RealType beta0 = tokenizer.nextTokenAsDouble();
126	interactionType = new MorseInteractionType(D0, beta0, r0, mtRepulsive);
127	}
128	break;
129
130	case LennardJones :
131	if (nTokens < 2) {
132	sprintf(painCave.errMsg, "NonBondedInteractionsSectionParser Error: Not enough tokens at line %d\n",
133	lineNo);
134	painCave.isFatal = 1;
135	simError();
136	} else {
137	RealType sigma = tokenizer.nextTokenAsDouble();
138	RealType epsilon = tokenizer.nextTokenAsDouble();
139	interactionType = new LennardJonesInteractionType(sigma, epsilon);
140	}
141	break;
142
143	case RepulsivePower :
144	if (nTokens < 3) {
145	sprintf(painCave.errMsg, "NonBondedInteractionsSectionParser Error: Not enough tokens at line %d\n",
146	lineNo);
147	painCave.isFatal = 1;
148	simError();
149	} else {
150	RealType sigma = tokenizer.nextTokenAsDouble();
151	RealType epsilon = tokenizer.nextTokenAsDouble();
152	int nRep = tokenizer.nextTokenAsInt();
153	interactionType = new RepulsivePowerInteractionType(sigma, epsilon, nRep);
154	}
155	break;
156
157	case Unknown :
158	default:
159	sprintf(painCave.errMsg, "NonBondedInteractionsSectionParser Error: Unknown Interaction Type at line %d\n",
160	lineNo);
161	painCave.isFatal = 1;
162	simError();
163
164	break;
165
166	}
167
168	if (interactionType != NULL) {
169	ff.addNonBondedInteractionType(at1, at2, interactionType);
170	}
171
172	}
173
174	NonBondedInteractionsSectionParser::NonBondedInteractionTypeEnum NonBondedInteractionsSectionParser::getNonBondedInteractionTypeEnum(const std::string& str) {
175	std::map<std::string, NonBondedInteractionTypeEnum>::iterator i;
176	i = stringToEnumMap_.find(str);
177
178	return i == stringToEnumMap_.end() ? Unknown : i->second;
179	}
180
181	} //end namespace OpenMD
182