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.
#	User	Rev	Content
1	gezelter	1501	/*
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	gezelter	1665	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40			* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41	gezelter	1501	*/
42
43			#include "io/NonBondedInteractionsSectionParser.hpp"
44			#include "types/AtomType.hpp"
45	gezelter	1664	#include "types/MorseInteractionType.hpp"
46	gezelter	1501	#include "types/MAWInteractionType.hpp"
47			#include "types/LennardJonesInteractionType.hpp"
48	gezelter	1624	#include "types/RepulsivePowerInteractionType.hpp"
49	gezelter	1725	#include "brains/ForceField.hpp"
50	gezelter	1501	#include "utils/simError.h"
51			namespace OpenMD {
52
53			NonBondedInteractionsSectionParser::NonBondedInteractionsSectionParser(ForceFieldOptions& options) : options_(options){
54			setSectionName("NonBondedInteractions");
55
56			stringToEnumMap_["MAW"] = MAW;
57	gezelter	1624	stringToEnumMap_["ShiftedMorse"] = ShiftedMorse;
58	gezelter	1501	stringToEnumMap_["LennardJones"] = LennardJones;
59			stringToEnumMap_["RepulsiveMorse"] = RepulsiveMorse;
60	gezelter	1624	stringToEnumMap_["RepulsivePower"] = RepulsivePower;
61	gezelter	1501
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	gezelter	1664	interactionType = new MorseInteractionType(D0, beta0, r0, mtShifted);
113	gezelter	1501	}
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	gezelter	1664	interactionType = new MorseInteractionType(D0, beta0, r0, mtRepulsive);
127	gezelter	1501	}
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	gezelter	1624
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	gezelter	1501
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