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 "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:	1665
Committed:	Tue Nov 22 20:38:56 2011 UTC (13 years, 5 months ago) by gezelter
File size:	7149 byte(s)
Log Message:	updated copyright notices
#	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	1501	#include "UseTheForce/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	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