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Comparing trunk/OOPSE-2.0/src/types/AtomType.cpp (file contents):
Revision 1637 by chrisfen, Fri Oct 22 22:54:15 2004 UTC vs.
Revision 1930 by gezelter, Wed Jan 12 22:41:40 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/charge_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_Quadrupole = 0;
69      atp.is_Sticky = 0;
70      atp.is_GayBerne = 0;
71      atp.is_EAM = 0;
# Line 30 | Line 73 | namespace oopse {
73      atp.is_FLARB = 0;  
74    }
75      
76 <  AtomType::~AtomType() {
34 <    if ( name != NULL ) free(name);
35 <  }
36 <
37 <  void AtomType::complete() {
76 >  void AtomType::makeFortranAtomType() {
77      
78      int status;
79  
80 <    if (name == NULL) {
80 >    if (name_.empty()) {
81        sprintf( painCave.errMsg,
82                 "Attempting to complete an AtomType without giving "
83 <               "it a name!\n");
83 >               "it a name_!\n");
84        painCave.severity = OOPSE_ERROR;
85        painCave.isFatal = 1;
86        simError();
# Line 50 | Line 89 | namespace oopse {
89      if (atp.ident == -1) {
90        sprintf( painCave.errMsg,
91                 "Attempting to complete AtomType %s without setting the"
92 <               " ident!/n", name);
92 >               " ident!/n", name_.c_str());
93        painCave.severity = OOPSE_ERROR;
94        painCave.isFatal = 1;
95        simError();          
# Line 58 | Line 97 | namespace oopse {
97  
98      status = 0;
99  
100 <    makeAtype(atp, &status);  
100 >    makeAtype(&atp, &status);  
101      
102      if (status != 0) {
103        sprintf( painCave.errMsg,
104 <               "Fortran rejected AtomType %s!\n", name);
104 >               "Fortran rejected AtomType %s!\n", name_.c_str());
105        painCave.severity = OOPSE_ERROR;
106        painCave.isFatal = 1;
107        simError();          
108      }
109    }
110 +
111 +
112 + void AtomType::complete() {
113 +    int isError;
114 +    GenericData* data;
115 +    
116 +    //notify a new LJtype atom type is created
117 +    if (isLennardJones()) {
118 +        data = getPropertyByName("LennardJones");
119 +        if (data != NULL) {
120 +            LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data);
121 +
122 +            if (ljData != NULL) {
123 +                LJParam ljParam = ljData->getData();
124 +                
125 +                newLJtype(&atp.ident, &ljParam.sigma, &ljParam.epsilon, &isError);
126 +
127 +                if (isError != 0) {
128 +                    sprintf( painCave.errMsg,
129 +                           "Fortran rejected newLJtype\n");
130 +                    painCave.severity = OOPSE_ERROR;
131 +                    painCave.isFatal = 1;
132 +                    simError();          
133 +                }
134 +                
135 +            } else {
136 +                    sprintf( painCave.errMsg,
137 +                           "Can not cast GenericData to LJParam\n");
138 +                    painCave.severity = OOPSE_ERROR;
139 +                    painCave.isFatal = 1;
140 +                    simError();          
141 +            }            
142 +        } else {
143 +            sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n");
144 +            painCave.severity = OOPSE_ERROR;
145 +            painCave.isFatal = 1;
146 +            simError();          
147 +        }
148 +    }
149 +
150 +    if (isCharge()) {
151 +        data = getPropertyByName("Charge");
152 +        if (data != NULL) {
153 +            DoubleGenericData* doubleData= dynamic_cast<DoubleGenericData*>(data);
154 +
155 +            if (doubleData != NULL) {
156 +                double charge = doubleData->getData();
157 +                newChargeType(&atp.ident, &charge, &isError);
158 +
159 +                if (isError != 0) {
160 +                    sprintf( painCave.errMsg,
161 +                           "Fortran rejected newChargeType\n");
162 +                    painCave.severity = OOPSE_ERROR;
163 +                    painCave.isFatal = 1;
164 +                    simError();          
165 +                }
166 +            } else {
167 +                    sprintf( painCave.errMsg,
168 +                           "Can not cast GenericData to DoubleGenericData\n");
169 +                    painCave.severity = OOPSE_ERROR;
170 +                    painCave.isFatal = 1;
171 +                    simError();          
172 +            }
173 +        } else {
174 +            sprintf( painCave.errMsg, "Can not find Charge Parameters\n");
175 +            painCave.severity = OOPSE_ERROR;
176 +            painCave.isFatal = 1;
177 +            simError();          
178 +        }
179 +    }
180 +
181 +    if (isEAM()) {
182 +        data = getPropertyByName("EAM");
183 +        if (data != NULL) {
184 +            EAMParamGenericData* eamData = dynamic_cast<EAMParamGenericData*>(data);
185 +
186 +            if (eamData != NULL) {
187 +
188 +                EAMParam eamParam = eamData->getData();
189 +                
190 +
191 +                newEAMtype(&eamParam.latticeConstant, &eamParam.nrho, &eamParam.drho,  &eamParam.nr, &eamParam.dr, &eamParam.rcut,
192 +                                &eamParam.rvals[0], &eamParam.rhovals[0], &eamParam.Frhovals[0], &atp.ident, &isError );
193 +
194 +                if (isError != 0) {
195 +                    sprintf( painCave.errMsg,
196 +                           "Fortran rejected newEAMtype\n");
197 +                    painCave.severity = OOPSE_ERROR;
198 +                    painCave.isFatal = 1;
199 +                    simError();          
200 +                }
201 +            } else {
202 +                    sprintf( painCave.errMsg,
203 +                           "Can not cast GenericData to EAMParam\n");
204 +                    painCave.severity = OOPSE_ERROR;
205 +                    painCave.isFatal = 1;
206 +                    simError();          
207 +            }
208 +        } else {
209 +            sprintf( painCave.errMsg, "Can not find EAM Parameters\n");
210 +            painCave.severity = OOPSE_ERROR;
211 +            painCave.isFatal = 1;
212 +            simError();          
213 +        }
214 +    }
215 +
216 +    
217   }
218 +
219 + void AtomType::addProperty(GenericData* genData) {
220 +    properties_.addProperty(genData);  
221 + }
222 +
223 + void AtomType::removeProperty(const std::string& propName) {
224 +    properties_.removeProperty(propName);  
225 + }
226 +
227 + void AtomType::clearProperties() {
228 +    properties_.clearProperties();
229 + }
230 +
231 + std::vector<std::string> AtomType::getPropertyNames() {
232 +    return properties_.getPropertyNames();  
233 + }
234 +      
235 + std::vector<GenericData*> AtomType::getProperties() {
236 +    return properties_.getProperties();
237 + }
238 +
239 + GenericData* AtomType::getPropertyByName(const std::string& propName) {
240 +    return properties_.getPropertyByName(propName);
241 + }  
242 + }

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