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Comparing trunk/OOPSE-4/src/types/AtomType.cpp (file contents):
Revision 1670 by gezelter, Thu Oct 28 16:56:20 2004 UTC vs.
Revision 3172 by gezelter, Fri Jul 13 17:37:25 2007 UTC

# Line 1 | Line 1
1 + /*
2 + * Copyright (c) 2005 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. 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
19 + *    notice, this list of conditions and the following disclaimer.
20 + *
21 + * 3. Redistributions in binary form must reproduce the above copyright
22 + *    notice, this list of conditions and the following disclaimer in the
23 + *    documentation and/or other materials provided with the
24 + *    distribution.
25 + *
26 + * This software is provided "AS IS," without a warranty of any
27 + * kind. All express or implied conditions, representations and
28 + * warranties, including any implied warranty of merchantability,
29 + * fitness for a particular purpose or non-infringement, are hereby
30 + * excluded.  The University of Notre Dame and its licensors shall not
31 + * be liable for any damages suffered by licensee as a result of
32 + * using, modifying or distributing the software or its
33 + * derivatives. In no event will the University of Notre Dame or its
34 + * licensors be liable for any lost revenue, profit or data, or for
35 + * direct, indirect, special, consequential, incidental or punitive
36 + * damages, however caused and regardless of the theory of liability,
37 + * arising out of the use of or inability to use software, even if the
38 + * University of Notre Dame has been advised of the possibility of
39 + * such damages.
40 + */
41 +
42   #include <stdlib.h>
43   #include <stdio.h>
44   #include <string.h>
# Line 7 | Line 48
48   #include "utils/simError.h"
49   #define __C
50   #include "UseTheForce/DarkSide/atype_interface.h"
51 <
51 > #include "UseTheForce/DarkSide/lj_interface.h"
52 > #include "UseTheForce/DarkSide/eam_interface.h"
53 > #include "UseTheForce/DarkSide/electrostatic_interface.h"
54 > #include "UseTheForce/DarkSide/suttonchen_interface.h"
55   namespace oopse {
56    AtomType::AtomType(){
57      
58      // initialize to an error:
59      atp.ident = -1;
16 –
17 –    // and massless:
18 –    mass = 0.0;
60      
61 +    // and mass_less:
62 +    mass_ = 0.0;
63 +    
64      // atom type is a Tabula Rasa:
65      atp.is_Directional = 0;
66      atp.is_LennardJones = 0;
23 –    atp.is_Electrostatic = 0;
67      atp.is_Charge = 0;
68      atp.is_Dipole = 0;
69 +    atp.is_SplitDipole = 0;
70 +    atp.is_Quadrupole = 0;
71      atp.is_Sticky = 0;
72 +    atp.is_StickyPower = 0;
73      atp.is_GayBerne = 0;
74      atp.is_EAM = 0;
75      atp.is_Shape = 0;
76      atp.is_FLARB = 0;  
77 +    atp.is_SC = 0;
78    }
79 +  
80 +  void AtomType::makeFortranAtomType() {
81      
33 –  void AtomType::complete() {
34 –    
82      int status;
83 <
84 <    if (name.empty()) {
83 >    
84 >    if (name_.empty()) {
85        sprintf( painCave.errMsg,
86                 "Attempting to complete an AtomType without giving "
87 <               "it a name!\n");
87 >               "it a name_!\n");
88        painCave.severity = OOPSE_ERROR;
89        painCave.isFatal = 1;
90        simError();
# Line 46 | Line 93 | namespace oopse {
93      if (atp.ident == -1) {
94        sprintf( painCave.errMsg,
95                 "Attempting to complete AtomType %s without setting the"
96 <               " ident!/n", name.c_str());
96 >               " ident!/n", name_.c_str());
97        painCave.severity = OOPSE_ERROR;
98        painCave.isFatal = 1;
99        simError();          
100      }
101 <
101 >    
102      status = 0;
103 <
103 >    
104      makeAtype(&atp, &status);  
105      
106      if (status != 0) {
107        sprintf( painCave.errMsg,
108 <               "Fortran rejected AtomType %s!\n", name.c_str());
108 >               "Fortran rejected AtomType %s!\n", name_.c_str());
109        painCave.severity = OOPSE_ERROR;
110        painCave.isFatal = 1;
111        simError();          
112      }
113    }
114 +  
115 +  
116 +  void AtomType::complete() {
117 +    int isError;
118 +    GenericData* data;
119 +    
120 +    //notify a new LJtype atom type is created
121 +    if (isLennardJones()) {
122 +      data = getPropertyByName("LennardJones");
123 +      if (data != NULL) {
124 +        LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
125 +        
126 +        if (ljData != NULL) {
127 +          LJParam ljParam = ljData->getData();
128 +          
129 +          newLJtype(&atp.ident, &ljParam.sigma, &ljParam.epsilon,
130 +                    &ljParam.soft_pot, &isError);
131 +          
132 +          if (isError != 0) {
133 +            sprintf( painCave.errMsg,
134 +                     "Fortran rejected newLJtype\n");
135 +            painCave.severity = OOPSE_ERROR;
136 +            painCave.isFatal = 1;
137 +            simError();          
138 +          }
139 +          
140 +        } else {
141 +          sprintf( painCave.errMsg,
142 +                   "Can not cast GenericData to LJParam\n");
143 +          painCave.severity = OOPSE_ERROR;
144 +          painCave.isFatal = 1;
145 +          simError();          
146 +        }            
147 +      } else {
148 +        sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
149 +        painCave.severity = OOPSE_ERROR;
150 +        painCave.isFatal = 1;
151 +        simError();          
152 +      }
153 +    }
154 +    
155 +    if (isElectrostatic()) {
156 +      newElectrostaticType(&atp, &isError);
157 +      if (isError != 0) {
158 +        sprintf( painCave.errMsg,
159 +                 "Fortran rejected newElectrostaticType\n");
160 +        painCave.severity = OOPSE_ERROR;
161 +        painCave.isFatal = 1;
162 +        simError();          
163 +      }
164 +    }
165 +    
166 +    if (isCharge()) {
167 +      data = getPropertyByName("Charge");
168 +      if (data != NULL) {
169 +        DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
170 +        
171 +        if (doubleData != NULL) {
172 +          RealType charge = doubleData->getData();
173 +          setCharge(&atp.ident, &charge, &isError);
174 +          
175 +          if (isError != 0) {
176 +            sprintf( painCave.errMsg,
177 +                     "Fortran rejected setCharge\n");
178 +            painCave.severity = OOPSE_ERROR;
179 +            painCave.isFatal = 1;
180 +            simError();          
181 +          }
182 +        } else {
183 +          sprintf( painCave.errMsg,
184 +                   "Can not cast GenericData to DoubleGenericData\n");
185 +          painCave.severity = OOPSE_ERROR;
186 +          painCave.isFatal = 1;
187 +          simError();          
188 +        }
189 +      } else {
190 +        sprintf( painCave.errMsg, "Can not find Charge Parameters\n");
191 +        painCave.severity = OOPSE_ERROR;
192 +        painCave.isFatal = 1;
193 +        simError();          
194 +      }
195 +    }
196 +    
197 +    if (isEAM()) {
198 +      data = getPropertyByName("EAM");
199 +      if (data != NULL) {
200 +        EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
201 +        
202 +        if (eamData != NULL) {
203 +          
204 +          EAMParam eamParam = eamData->getData();
205 +          
206 +          
207 +          newEAMtype(&eamParam.latticeConstant, &eamParam.nrho,
208 +                     &eamParam.drho,  &eamParam.nr, &eamParam.dr,
209 +                     &eamParam.rcut, &eamParam.rvals[0], &eamParam.rhovals[0],
210 +                     &eamParam.Frhovals[0], &atp.ident, &isError );
211 +          
212 +          if (isError != 0) {
213 +            sprintf( painCave.errMsg,
214 +                     "Fortran rejected newEAMtype\n");
215 +            painCave.severity = OOPSE_ERROR;
216 +            painCave.isFatal = 1;
217 +            simError();          
218 +          }
219 +        } else {
220 +          sprintf( painCave.errMsg,
221 +                   "Can not cast GenericData to EAMParam\n");
222 +          painCave.severity = OOPSE_ERROR;
223 +          painCave.isFatal = 1;
224 +          simError();          
225 +        }
226 +      } else {
227 +        sprintf( painCave.errMsg, "Can not find EAM Parameters\n");
228 +        painCave.severity = OOPSE_ERROR;
229 +        painCave.isFatal = 1;
230 +        simError();          
231 +      }
232 +    }
233 +    
234 +    
235 +    if (isSC()) {
236 +      data = getPropertyByName("SC");
237 +      if (data != NULL) {
238 +        SCParamGenericData* SCData = dynamic_cast<SCParamGenericData*>(data);
239 +        
240 +        if (SCData != NULL) {
241 +          
242 +          SCParam scParam = SCData->getData();
243 +                    
244 +          newSCtype(&atp.ident, &scParam.c, &scParam.m,  
245 +                    &scParam.n, &scParam.alpha, &scParam.epsilon,
246 +                    &isError );
247 +          
248 +          if (isError != 0) {
249 +            sprintf( painCave.errMsg,
250 +                     "Fortran rejected newSCtype\n");
251 +            painCave.severity = OOPSE_ERROR;
252 +            painCave.isFatal = 1;
253 +            simError();          
254 +          }
255 +        } else {
256 +          sprintf( painCave.errMsg,
257 +                   "Can not cast GenericData to SCParam\n");
258 +          painCave.severity = OOPSE_ERROR;
259 +          painCave.isFatal = 1;
260 +          simError();          
261 +        }
262 +      } else {
263 +        sprintf( painCave.errMsg, "Can not find SC Parameters\n");
264 +        painCave.severity = OOPSE_ERROR;
265 +        painCave.isFatal = 1;
266 +        simError();          
267 +      }
268 +    }
269 +  }
270 +
271 +  void AtomType::addProperty(GenericData* genData) {
272 +    properties_.addProperty(genData);  
273 +  }
274 +  
275 +  void AtomType::removeProperty(const std::string& propName) {
276 +    properties_.removeProperty(propName);  
277 +  }
278 +  
279 +  void AtomType::clearProperties() {
280 +    properties_.clearProperties();
281 +  }
282 +  
283 +  std::vector<std::string> AtomType::getPropertyNames() {
284 +    return properties_.getPropertyNames();  
285 +  }
286 +  
287 +  std::vector<GenericData*> AtomType::getProperties() {
288 +    return properties_.getProperties();
289 +  }
290 +  
291 +  GenericData* AtomType::getPropertyByName(const std::string& propName) {
292 +    return properties_.getPropertyByName(propName);
293 +  }  
294   }

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