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root/group/trunk/OOPSE-4/src/types/AtomType.cpp
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Comparing trunk/OOPSE-4/src/types/AtomType.cpp (file contents):
Revision 1632 by gezelter, Fri Oct 22 20:21:36 2004 UTC vs.
Revision 2427 by chuckv, Mon Nov 14 21:29:36 2005 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;
60 <    // make the type empty:
61 <    name = NULL;
62 <    // and massless:
19 <    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_Directional = 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 +    atp.is_MEAM = 0;
79    }
80      
81 <  AtomType::~AtomType() {
34 <    if ( name != NULL ) delete name;
35 <  }
36 <
37 <  void AtomType::complete() {
81 >  void AtomType::makeFortranAtomType() {
82      
83      int status;
84  
85 <    if (name == NULL) {
85 >    if (name_.empty()) {
86        sprintf( painCave.errMsg,
87                 "Attempting to complete an AtomType without giving "
88 <               "it a name!\n");
88 >               "it a name_!\n");
89        painCave.severity = OOPSE_ERROR;
90        painCave.isFatal = 1;
91        simError();
# Line 50 | Line 94 | namespace oopse {
94      if (atp.ident == -1) {
95        sprintf( painCave.errMsg,
96                 "Attempting to complete AtomType %s without setting the"
97 <               " ident!/n", name);
97 >               " ident!/n", name_.c_str());
98        painCave.severity = OOPSE_ERROR;
99        painCave.isFatal = 1;
100        simError();          
101      }
102  
103      status = 0;
60 –
61 –    makeAtype(atp, &status);  
104      
105 +    makeAtype(&atp, &status);  
106 +    
107      if (status != 0) {
108        sprintf( painCave.errMsg,
109 <               "Fortran rejected AtomType %s!\n", name);
109 >               "Fortran rejected AtomType %s!\n", name_.c_str());
110        painCave.severity = OOPSE_ERROR;
111        painCave.isFatal = 1;
112        simError();          
113      }
114    }
115 +
116 +
117 +  void AtomType::complete() {
118 +    int isError;
119 +    GenericData* data;
120 +    
121 +    //notify a new LJtype atom type is created
122 +    if (isLennardJones()) {
123 +      data = getPropertyByName("LennardJones");
124 +      if (data != NULL) {
125 +        LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
126 +
127 +        if (ljData != NULL) {
128 +          LJParam ljParam = ljData->getData();
129 +                
130 +          newLJtype(&atp.ident, &ljParam.sigma, &ljParam.epsilon, &ljParam.soft_pot,
131 +              &isError);
132 +
133 +          if (isError != 0) {
134 +            sprintf( painCave.errMsg,
135 +                     "Fortran rejected newLJtype\n");
136 +            painCave.severity = OOPSE_ERROR;
137 +            painCave.isFatal = 1;
138 +            simError();          
139 +          }
140 +                
141 +        } else {
142 +          sprintf( painCave.errMsg,
143 +                   "Can not cast GenericData to LJParam\n");
144 +          painCave.severity = OOPSE_ERROR;
145 +          painCave.isFatal = 1;
146 +          simError();          
147 +        }            
148 +      } else {
149 +        sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
150 +        painCave.severity = OOPSE_ERROR;
151 +        painCave.isFatal = 1;
152 +        simError();          
153 +      }
154 +    }
155 +
156 +    if (isElectrostatic()) {
157 +      newElectrostaticType(&atp, &isError);
158 +      if (isError != 0) {
159 +        sprintf( painCave.errMsg,
160 +                 "Fortran rejected newElectrostaticType\n");
161 +        painCave.severity = OOPSE_ERROR;
162 +        painCave.isFatal = 1;
163 +        simError();          
164 +      }
165 +    }
166 +      
167 +    if (isCharge()) {
168 +      data = getPropertyByName("Charge");
169 +      if (data != NULL) {
170 +        DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
171 +
172 +        if (doubleData != NULL) {
173 +          double charge = doubleData->getData();
174 +          setCharge(&atp.ident, &charge, &isError);
175 +                
176 +          if (isError != 0) {
177 +            sprintf( painCave.errMsg,
178 +                     "Fortran rejected setCharge\n");
179 +            painCave.severity = OOPSE_ERROR;
180 +            painCave.isFatal = 1;
181 +            simError();          
182 +          }
183 +        } else {
184 +          sprintf( painCave.errMsg,
185 +                   "Can not cast GenericData to DoubleGenericData\n");
186 +          painCave.severity = OOPSE_ERROR;
187 +          painCave.isFatal = 1;
188 +          simError();          
189 +        }
190 +      } else {
191 +        sprintf( painCave.errMsg, "Can not find Charge Parameters\n");
192 +        painCave.severity = OOPSE_ERROR;
193 +        painCave.isFatal = 1;
194 +        simError();          
195 +      }
196 +    }
197 +
198 +    if (isEAM()) {
199 +      data = getPropertyByName("EAM");
200 +      if (data != NULL) {
201 +        EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
202 +
203 +        if (eamData != NULL) {
204 +
205 +          EAMParam eamParam = eamData->getData();
206 +                
207 +
208 +          newEAMtype(&eamParam.latticeConstant, &eamParam.nrho, &eamParam.drho,  
209 +               &eamParam.nr, &eamParam.dr, &eamParam.rcut, &eamParam.rvals[0],
210 +               &eamParam.rhovals[0], &eamParam.Frhovals[0], &atp.ident,
211 +               &isError );
212 +
213 +          if (isError != 0) {
214 +            sprintf( painCave.errMsg,
215 +                     "Fortran rejected newEAMtype\n");
216 +            painCave.severity = OOPSE_ERROR;
217 +            painCave.isFatal = 1;
218 +            simError();          
219 +          }
220 +        } else {
221 +          sprintf( painCave.errMsg,
222 +                   "Can not cast GenericData to EAMParam\n");
223 +          painCave.severity = OOPSE_ERROR;
224 +          painCave.isFatal = 1;
225 +          simError();          
226 +        }
227 +      } else {
228 +        sprintf( painCave.errMsg, "Can not find EAM Parameters\n");
229 +        painCave.severity = OOPSE_ERROR;
230 +        painCave.isFatal = 1;
231 +        simError();          
232 +      }
233 +    }
234 +
235 +    
236 +    if (isSC()) {
237 +      data = getPropertyByName("SC");
238 +      if (data != NULL) {
239 +        SCParamGenericData* SCData = dynamic_cast<SCParamGenericData*>(data);
240 +        
241 +        if (SCData != NULL) {
242 +          
243 +          SCParam scParam = SCData->getData();
244 +          
245 +          
246 +          newSCtype(&atp.ident, &scParam.c, &scParam.m,  
247 +                     &scParam.n, &scParam.alpha, &scParam.epsilon,
248 +                     &isError );
249 +          
250 +          if (isError != 0) {
251 +            sprintf( painCave.errMsg,
252 +                     "Fortran rejected newSCtype\n");
253 +            painCave.severity = OOPSE_ERROR;
254 +            painCave.isFatal = 1;
255 +            simError();          
256 +          }
257 +        } else {
258 +          sprintf( painCave.errMsg,
259 +                   "Can not cast GenericData to SCParam\n");
260 +          painCave.severity = OOPSE_ERROR;
261 +          painCave.isFatal = 1;
262 +          simError();          
263 +        }
264 +      } else {
265 +        sprintf( painCave.errMsg, "Can not find SC Parameters\n");
266 +        painCave.severity = OOPSE_ERROR;
267 +        painCave.isFatal = 1;
268 +        simError();          
269 +      }
270 +    }
271 +    
272 +      
273 +    
274 +  }
275 +
276 +  void AtomType::addProperty(GenericData* genData) {
277 +    properties_.addProperty(genData);  
278 +  }
279 +
280 +  void AtomType::removeProperty(const std::string& propName) {
281 +    properties_.removeProperty(propName);  
282 +  }
283 +
284 +  void AtomType::clearProperties() {
285 +    properties_.clearProperties();
286 +  }
287 +
288 +  std::vector<std::string> AtomType::getPropertyNames() {
289 +    return properties_.getPropertyNames();  
290 +  }
291 +      
292 +  std::vector<GenericData*> AtomType::getProperties() {
293 +    return properties_.getProperties();
294 +  }
295 +
296 +  GenericData* AtomType::getPropertyByName(const std::string& propName) {
297 +    return properties_.getPropertyByName(propName);
298 +  }  
299   }

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