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, 234107 (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);
    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:	1879
Committed:	Sun Jun 16 15:15:42 2013 UTC (12 years, 4 months ago) by gezelter
File size:	7099 byte(s)
Log Message:	MERGE OpenMD development 1783:1878 into trunk
#	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	gezelter	1879	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (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			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	gezelter	1664	interactionType = new MorseInteractionType(D0, beta0, r0, mtShifted);
112	gezelter	1501	}
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	gezelter	1664	interactionType = new MorseInteractionType(D0, beta0, r0, mtRepulsive);
126	gezelter	1501	}
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	gezelter	1624
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	gezelter	1501
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