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Comparing trunk/src/io/MetalNonMetalInteractionsSectionParser.cpp (file contents):
Revision 1229 by chuckv, Mon Mar 3 17:14:37 2008 UTC vs.
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC

# Line 6 | Line 6
6   * redistribute this software in source and binary code form, provided
7   * that the following conditions are met:
8   *
9 < * 1. Acknowledgement of the program authors must be made in any
10 < *    publication of scientific results based in part on use of the
11 < *    program.  An acceptable form of acknowledgement is citation of
12 < *    the article in which the program was described (Matthew
13 < *    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14 < *    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15 < *    Parallel Simulation Engine for Molecular Dynamics,"
16 < *    J. Comput. Chem. 26, pp. 252-271 (2005))
17 < *
18 < * 2. Redistributions of source code must retain the above copyright
9 > * 1. Redistributions of source code must retain the above copyright
10   *    notice, this list of conditions and the following disclaimer.
11   *
12 < * 3. Redistributions in binary form must reproduce the above copyright
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.
# Line 37 | Line 28
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/MetalNonMetalInteractionsSectionParser.hpp"
# Line 47 | Line 47
47   #include "types/RepulsiveMorseInteractionType.hpp"
48   #include "UseTheForce/ForceField.hpp"
49   #include "utils/simError.h"
50 < namespace oopse {
50 > namespace OpenMD {
51  
52    MetalNonMetalInteractionsSectionParser::MetalNonMetalInteractionsSectionParser(ForceFieldOptions& options) : options_(options){
53      setSectionName("MetalNonMetalInteractions");
# Line 75 | Line 75 | namespace oopse {
75      std::string at2 = tokenizer.nextToken();
76      std::string itype = tokenizer.nextToken();
77  
78 <        MetalNonMetalInteractionTypeEnum nbit = getMetalNonMetalInteractionTypeEnum(itype);
78 >    MetalNonMetalInteractionTypeEnum nbit = getMetalNonMetalInteractionTypeEnum(itype);
79      nTokens -= 3;
80 <                NonBondedInteractionType* interactionType;
80 >    NonBondedInteractionType* interactionType;
81          
82      //switch is a nightmare to maintain
83      switch(nbit) {
84      case MAW :
85 <                if (nTokens < 4) {
86 <                        sprintf(painCave.errMsg, "MetalNonMetalInteractionsSectionParser Error: Not enough tokens at line %d\n",
87 <                                lineNo);
88 <                        painCave.isFatal = 1;
89 <                        simError();
90 <                } else {
91 <                        RealType r_e = tokenizer.nextTokenAsDouble();
92 <                        RealType D_e = tokenizer.nextTokenAsDouble();
93 <                        RealType beta = tokenizer.nextTokenAsDouble();
94 <                        RealType alpha = tokenizer.nextTokenAsDouble();                
95 <      interactionType = new MAWInteractionType(D_e, beta, r_e, alpha);
96 <                }
97 <                break;
98 <            
85 >      if (nTokens < 5) {
86 >        sprintf(painCave.errMsg, "MetalNonMetalInteractionsSectionParser Error: Not enough tokens at line %d\n",
87 >                lineNo);
88 >        painCave.isFatal = 1;
89 >        simError();
90 >      } else {
91 >        RealType r_e = tokenizer.nextTokenAsDouble();
92 >        RealType D_e = tokenizer.nextTokenAsDouble();
93 >        RealType beta = tokenizer.nextTokenAsDouble();
94 >        RealType ca1 = tokenizer.nextTokenAsDouble();
95 >        RealType cb1 = tokenizer.nextTokenAsDouble();
96 >        interactionType = new MAWInteractionType(D_e, beta, r_e, ca1, cb1);
97 >      }
98 >      break;
99 >      
100      case ShiftedMorse :
101 <                if (nTokens < 3) {
102 <                        sprintf(painCave.errMsg, "MetalNonMetalInteractionsSectionParser Error: Not enough tokens at line %d\n",
103 <                                lineNo);
104 <                        painCave.isFatal = 1;
105 <                        simError();
106 <                } else {
107 <                        RealType r0 = tokenizer.nextTokenAsDouble();
108 <                        RealType D0 = tokenizer.nextTokenAsDouble();
109 <                        RealType beta0 = tokenizer.nextTokenAsDouble();
110 <      interactionType = new ShiftedMorseInteractionType(D0, beta0, r0);
111 <                }
112 <                break;
101 >      if (nTokens < 3) {
102 >        sprintf(painCave.errMsg, "MetalNonMetalInteractionsSectionParser Error: Not enough tokens at line %d\n",
103 >                lineNo);
104 >        painCave.isFatal = 1;
105 >        simError();
106 >      } else {
107 >        RealType r0 = tokenizer.nextTokenAsDouble();
108 >        RealType D0 = tokenizer.nextTokenAsDouble();
109 >        RealType beta0 = tokenizer.nextTokenAsDouble();
110 >        interactionType = new ShiftedMorseInteractionType(D0, beta0, r0);
111 >      }
112 >      break;
113  
114 <                 case RepulsiveMorse :
115 <                        if (nTokens < 3) {
116 <                                sprintf(painCave.errMsg, "MetalNonMetalInteractionsSectionParser Error: Not enough tokens at line %d\n",
117 <                                        lineNo);
118 <                                painCave.isFatal = 1;
119 <                                simError();
120 <                        } else {
121 <                                RealType r0 = tokenizer.nextTokenAsDouble();
122 <                                RealType D0 = tokenizer.nextTokenAsDouble();
123 <                                RealType beta0 = tokenizer.nextTokenAsDouble();
124 <              interactionType = new RepulsiveMorseInteractionType(D0, beta0, r0);
125 <                        }
126 <                        break;
114 >    case RepulsiveMorse :
115 >      if (nTokens < 3) {
116 >        sprintf(painCave.errMsg, "MetalNonMetalInteractionsSectionParser Error: Not enough tokens at line %d\n",
117 >                lineNo);
118 >        painCave.isFatal = 1;
119 >        simError();
120 >      } else {
121 >        RealType r0 = tokenizer.nextTokenAsDouble();
122 >        RealType D0 = tokenizer.nextTokenAsDouble();
123 >        RealType beta0 = tokenizer.nextTokenAsDouble();
124 >        interactionType = new RepulsiveMorseInteractionType(D0, beta0, r0);
125 >      }
126 >      break;
127  
128      case LennardJones :
129 <                if (nTokens < 2) {
130 <                        sprintf(painCave.errMsg, "MetalNonMetalInteractionsSectionParser Error: Not enough tokens at line %d\n",
131 <                                lineNo);
132 <                        painCave.isFatal = 1;
133 <                        simError();
134 <                } else {
135 <                        RealType sigma = tokenizer.nextTokenAsDouble();
136 <                        RealType epsilon = tokenizer.nextTokenAsDouble();
137 <      interactionType = new LennardJonesInteractionType(sigma, epsilon);
138 <                }
139 <                break;
129 >      if (nTokens < 2) {
130 >        sprintf(painCave.errMsg, "MetalNonMetalInteractionsSectionParser Error: Not enough tokens at line %d\n",
131 >                lineNo);
132 >        painCave.isFatal = 1;
133 >        simError();
134 >      } else {
135 >        RealType sigma = tokenizer.nextTokenAsDouble();
136 >        RealType epsilon = tokenizer.nextTokenAsDouble();
137 >        interactionType = new LennardJonesInteractionType(sigma, epsilon);
138 >      }
139 >      break;
140  
141      case Unknown :
142      default:
# Line 161 | Line 162 | namespace oopse {
162      return i == stringToEnumMap_.end() ? Unknown : i->second;
163    }
164  
165 < } //end namespace oopse
165 > } //end namespace OpenMD
166  

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