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> |
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(); |
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 |
+ |
RealType 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 |
|
} |