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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 2406 by chuckv, Tue Nov 1 23:32:25 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   namespace oopse {
55    AtomType::AtomType(){
56      
57      // initialize to an error:
58      atp.ident = -1;
59 <    // make the type empty:
60 <    name = NULL;
61 <    // and massless:
19 <    mass = 0.0;
59 >
60 >    // and mass_less:
61 >    mass_ = 0.0;
62      
63      // atom type is a Tabula Rasa:
64 +    atp.is_Directional = 0;
65      atp.is_LennardJones = 0;
23 –    atp.is_Electrostatic = 0;
66      atp.is_Charge = 0;
67 <    atp.is_Directional = 0;
67 >    atp.is_Dipole = 0;
68 >    atp.is_SplitDipole = 0;
69 >    atp.is_Quadrupole = 0;
70      atp.is_Sticky = 0;
71 +    atp.is_StickyPower = 0;
72      atp.is_GayBerne = 0;
73      atp.is_EAM = 0;
74      atp.is_Shape = 0;
75      atp.is_FLARB = 0;  
76 +    atp.is_SuttonChen = 0;
77 +    atp.is_MEAM = 0;
78    }
79      
80 <  AtomType::~AtomType() {
34 <    if ( name != NULL ) delete name;
35 <  }
36 <
37 <  void AtomType::complete() {
80 >  void AtomType::makeFortranAtomType() {
81      
82      int status;
83  
84 <    if (name == NULL) {
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 50 | 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);
96 >               " ident!/n", name_.c_str());
97        painCave.severity = OOPSE_ERROR;
98        painCave.isFatal = 1;
99        simError();          
100      }
101  
102      status = 0;
60 –
61 –    makeAtype(atp, &status);  
103      
104 +    makeAtype(&atp, &status);  
105 +    
106      if (status != 0) {
107        sprintf( painCave.errMsg,
108 <               "Fortran rejected AtomType %s!\n", name);
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, &ljParam.soft_pot,
130 +              &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 +          double 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, &eamParam.drho,  
208 +               &eamParam.nr, &eamParam.dr, &eamParam.rcut, &eamParam.rvals[0],
209 +               &eamParam.rhovals[0], &eamParam.Frhovals[0], &atp.ident,
210 +               &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 +  }
236 +
237 +  void AtomType::addProperty(GenericData* genData) {
238 +    properties_.addProperty(genData);  
239 +  }
240 +
241 +  void AtomType::removeProperty(const std::string& propName) {
242 +    properties_.removeProperty(propName);  
243 +  }
244 +
245 +  void AtomType::clearProperties() {
246 +    properties_.clearProperties();
247 +  }
248 +
249 +  std::vector<std::string> AtomType::getPropertyNames() {
250 +    return properties_.getPropertyNames();  
251 +  }
252 +      
253 +  std::vector<GenericData*> AtomType::getProperties() {
254 +    return properties_.getProperties();
255 +  }
256 +
257 +  GenericData* AtomType::getPropertyByName(const std::string& propName) {
258 +    return properties_.getPropertyByName(propName);
259 +  }  
260   }

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