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]  Vardeman & Gezelter, in progress (2009).                        
 */
 
#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 "UseTheForce/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:	1664
Committed:	Tue Nov 22 14:37:41 2011 UTC (13 years, 5 months ago) by gezelter
File size:	7083 byte(s)
Log Message:	Modified some of the nonbonded interactions and types
#	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] Vardeman & Gezelter, in progress (2009).
40	*/
41
42	#include "io/NonBondedInteractionsSectionParser.hpp"
43	#include "types/AtomType.hpp"
44	#include "types/MorseInteractionType.hpp"
45	#include "types/MAWInteractionType.hpp"
46	#include "types/LennardJonesInteractionType.hpp"
47	#include "types/RepulsivePowerInteractionType.hpp"
48	#include "UseTheForce/ForceField.hpp"
49	#include "utils/simError.h"
50	namespace OpenMD {
51
52	NonBondedInteractionsSectionParser::NonBondedInteractionsSectionParser(ForceFieldOptions& options) : options_(options){
53	setSectionName("NonBondedInteractions");
54
55	stringToEnumMap_["MAW"] = MAW;
56	stringToEnumMap_["ShiftedMorse"] = ShiftedMorse;
57	stringToEnumMap_["LennardJones"] = LennardJones;
58	stringToEnumMap_["RepulsiveMorse"] = RepulsiveMorse;
59	stringToEnumMap_["RepulsivePower"] = RepulsivePower;
60
61	}
62
63	void NonBondedInteractionsSectionParser::parseLine(ForceField& ff,const std::string& line, int lineNo){
64	StringTokenizer tokenizer(line);
65	NonBondedInteractionType* nbiType = NULL;
66	int nTokens = tokenizer.countTokens();
67
68	if (nTokens < 3) {
69	sprintf(painCave.errMsg, "NonBondedInteractionsSectionParser Error: Not enough tokens at line %d\n",
70	lineNo);
71	painCave.isFatal = 1;
72	simError();
73	}
74
75	std::string at1 = tokenizer.nextToken();
76	std::string at2 = tokenizer.nextToken();
77	std::string itype = tokenizer.nextToken();
78
79	NonBondedInteractionTypeEnum nbit = getNonBondedInteractionTypeEnum(itype);
80	nTokens -= 3;
81	NonBondedInteractionType* interactionType;
82
83	//switch is a nightmare to maintain
84	switch(nbit) {
85	case MAW :
86	if (nTokens < 5) {
87	sprintf(painCave.errMsg, "NonBondedInteractionsSectionParser Error: Not enough tokens at line %d\n",
88	lineNo);
89	painCave.isFatal = 1;
90	simError();
91	} else {
92	RealType r_e = tokenizer.nextTokenAsDouble();
93	RealType D_e = tokenizer.nextTokenAsDouble();
94	RealType beta = tokenizer.nextTokenAsDouble();
95	RealType ca1 = tokenizer.nextTokenAsDouble();
96	RealType cb1 = tokenizer.nextTokenAsDouble();
97	interactionType = new MAWInteractionType(D_e, beta, r_e, ca1, cb1);
98	}
99	break;
100
101	case ShiftedMorse :
102	if (nTokens < 3) {
103	sprintf(painCave.errMsg, "NonBondedInteractionsSectionParser Error: Not enough tokens at line %d\n",
104	lineNo);
105	painCave.isFatal = 1;
106	simError();
107	} else {
108	RealType r0 = tokenizer.nextTokenAsDouble();
109	RealType D0 = tokenizer.nextTokenAsDouble();
110	RealType beta0 = tokenizer.nextTokenAsDouble();
111	interactionType = new MorseInteractionType(D0, beta0, r0, mtShifted);
112	}
113	break;
114
115	case RepulsiveMorse :
116	if (nTokens < 3) {
117	sprintf(painCave.errMsg, "NonBondedInteractionsSectionParser Error: Not enough tokens at line %d\n",
118	lineNo);
119	painCave.isFatal = 1;
120	simError();
121	} else {
122	RealType r0 = tokenizer.nextTokenAsDouble();
123	RealType D0 = tokenizer.nextTokenAsDouble();
124	RealType beta0 = tokenizer.nextTokenAsDouble();
125	interactionType = new MorseInteractionType(D0, beta0, r0, mtRepulsive);
126	}
127	break;
128
129	case LennardJones :
130	if (nTokens < 2) {
131	sprintf(painCave.errMsg, "NonBondedInteractionsSectionParser Error: Not enough tokens at line %d\n",
132	lineNo);
133	painCave.isFatal = 1;
134	simError();
135	} else {
136	RealType sigma = tokenizer.nextTokenAsDouble();
137	RealType epsilon = tokenizer.nextTokenAsDouble();
138	interactionType = new LennardJonesInteractionType(sigma, epsilon);
139	}
140	break;
141
142	case RepulsivePower :
143	if (nTokens < 3) {
144	sprintf(painCave.errMsg, "NonBondedInteractionsSectionParser Error: Not enough tokens at line %d\n",
145	lineNo);
146	painCave.isFatal = 1;
147	simError();
148	} else {
149	RealType sigma = tokenizer.nextTokenAsDouble();
150	RealType epsilon = tokenizer.nextTokenAsDouble();
151	int nRep = tokenizer.nextTokenAsInt();
152	interactionType = new RepulsivePowerInteractionType(sigma, epsilon, nRep);
153	}
154	break;
155
156	case Unknown :
157	default:
158	sprintf(painCave.errMsg, "NonBondedInteractionsSectionParser Error: Unknown Interaction Type at line %d\n",
159	lineNo);
160	painCave.isFatal = 1;
161	simError();
162
163	break;
164
165	}
166
167	if (interactionType != NULL) {
168	ff.addNonBondedInteractionType(at1, at2, interactionType);
169	}
170
171	}
172
173	NonBondedInteractionsSectionParser::NonBondedInteractionTypeEnum NonBondedInteractionsSectionParser::getNonBondedInteractionTypeEnum(const std::string& str) {
174	std::map<std::string, NonBondedInteractionTypeEnum>::iterator i;
175	i = stringToEnumMap_.find(str);
176
177	return i == stringToEnumMap_.end() ? Unknown : i->second;
178	}
179
180	} //end namespace OpenMD
181