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 |
/** |
43 |
* @file ForceField.cpp |
44 |
* @author tlin |
45 |
* @date 11/04/2004 |
46 |
* @time 22:51am |
47 |
* @version 1.0 |
48 |
*/ |
49 |
|
50 |
#include "UseTheForce/ForceField.hpp" |
51 |
#include "utils/simError.h" |
52 |
#include "UseTheForce/DarkSide/atype_interface.h" |
53 |
#include "UseTheForce/DarkSide/fForceOptions_interface.h" |
54 |
#include "UseTheForce/DarkSide/switcheroo_interface.h" |
55 |
namespace oopse { |
56 |
|
57 |
ForceField::ForceField() { |
58 |
char* tempPath; |
59 |
tempPath = getenv("FORCE_PARAM_PATH"); |
60 |
|
61 |
if (tempPath == NULL) { |
62 |
//convert a macro from compiler to a string in c++ |
63 |
STR_DEFINE(ffPath_, FRC_PATH ); |
64 |
} else { |
65 |
ffPath_ = tempPath; |
66 |
} |
67 |
} |
68 |
|
69 |
|
70 |
ForceField::~ForceField() { |
71 |
deleteAtypes(); |
72 |
deleteSwitch(); |
73 |
} |
74 |
|
75 |
AtomType* ForceField::getAtomType(const std::string &at) { |
76 |
std::vector<std::string> keys; |
77 |
keys.push_back(at); |
78 |
return atomTypeCont_.find(keys); |
79 |
} |
80 |
|
81 |
BondType* ForceField::getBondType(const std::string &at1, |
82 |
const std::string &at2) { |
83 |
std::vector<std::string> keys; |
84 |
keys.push_back(at1); |
85 |
keys.push_back(at2); |
86 |
|
87 |
//try exact match first |
88 |
BondType* bondType = bondTypeCont_.find(keys); |
89 |
if (bondType) { |
90 |
return bondType; |
91 |
} else { |
92 |
//if no exact match found, try wild card match |
93 |
return bondTypeCont_.find(keys, wildCardAtomTypeName_); |
94 |
} |
95 |
} |
96 |
|
97 |
BendType* ForceField::getBendType(const std::string &at1, |
98 |
const std::string &at2, |
99 |
const std::string &at3) { |
100 |
std::vector<std::string> keys; |
101 |
keys.push_back(at1); |
102 |
keys.push_back(at2); |
103 |
keys.push_back(at3); |
104 |
|
105 |
//try exact match first |
106 |
BendType* bendType = bendTypeCont_.find(keys); |
107 |
if (bendType) { |
108 |
return bendType; |
109 |
} else { |
110 |
//if no exact match found, try wild card match |
111 |
return bendTypeCont_.find(keys, wildCardAtomTypeName_); |
112 |
} |
113 |
} |
114 |
|
115 |
TorsionType* ForceField::getTorsionType(const std::string &at1, |
116 |
const std::string &at2, |
117 |
const std::string &at3, |
118 |
const std::string &at4) { |
119 |
std::vector<std::string> keys; |
120 |
keys.push_back(at1); |
121 |
keys.push_back(at2); |
122 |
keys.push_back(at3); |
123 |
keys.push_back(at4); |
124 |
|
125 |
TorsionType* torsionType = torsionTypeCont_.find(keys); |
126 |
if (torsionType) { |
127 |
return torsionType; |
128 |
} else { |
129 |
//if no exact match found, try wild card match |
130 |
return torsionTypeCont_.find(keys, wildCardAtomTypeName_); |
131 |
} |
132 |
|
133 |
return torsionTypeCont_.find(keys, wildCardAtomTypeName_); |
134 |
} |
135 |
|
136 |
NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) { |
137 |
std::vector<std::string> keys; |
138 |
keys.push_back(at1); |
139 |
keys.push_back(at2); |
140 |
|
141 |
//try exact match first |
142 |
NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys); |
143 |
if (nbiType) { |
144 |
return nbiType; |
145 |
} else { |
146 |
//if no exact match found, try wild card match |
147 |
return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_); |
148 |
} |
149 |
} |
150 |
|
151 |
BondType* ForceField::getExactBondType(const std::string &at1, |
152 |
const std::string &at2){ |
153 |
std::vector<std::string> keys; |
154 |
keys.push_back(at1); |
155 |
keys.push_back(at2); |
156 |
return bondTypeCont_.find(keys); |
157 |
} |
158 |
|
159 |
BendType* ForceField::getExactBendType(const std::string &at1, |
160 |
const std::string &at2, |
161 |
const std::string &at3){ |
162 |
std::vector<std::string> keys; |
163 |
keys.push_back(at1); |
164 |
keys.push_back(at2); |
165 |
keys.push_back(at3); |
166 |
return bendTypeCont_.find(keys); |
167 |
} |
168 |
|
169 |
TorsionType* ForceField::getExactTorsionType(const std::string &at1, |
170 |
const std::string &at2, |
171 |
const std::string &at3, |
172 |
const std::string &at4){ |
173 |
std::vector<std::string> keys; |
174 |
keys.push_back(at1); |
175 |
keys.push_back(at2); |
176 |
keys.push_back(at3); |
177 |
keys.push_back(at4); |
178 |
return torsionTypeCont_.find(keys); |
179 |
} |
180 |
|
181 |
NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){ |
182 |
std::vector<std::string> keys; |
183 |
keys.push_back(at1); |
184 |
keys.push_back(at2); |
185 |
return nonBondedInteractionTypeCont_.find(keys); |
186 |
} |
187 |
|
188 |
|
189 |
bool ForceField::addAtomType(const std::string &at, AtomType* atomType) { |
190 |
std::vector<std::string> keys; |
191 |
keys.push_back(at); |
192 |
return atomTypeCont_.add(keys, atomType); |
193 |
} |
194 |
|
195 |
bool ForceField::addBondType(const std::string &at1, const std::string &at2, |
196 |
BondType* bondType) { |
197 |
std::vector<std::string> keys; |
198 |
keys.push_back(at1); |
199 |
keys.push_back(at2); |
200 |
return bondTypeCont_.add(keys, bondType); |
201 |
} |
202 |
|
203 |
bool ForceField::addBendType(const std::string &at1, const std::string &at2, |
204 |
const std::string &at3, BendType* bendType) { |
205 |
std::vector<std::string> keys; |
206 |
keys.push_back(at1); |
207 |
keys.push_back(at2); |
208 |
keys.push_back(at3); |
209 |
return bendTypeCont_.add(keys, bendType); |
210 |
} |
211 |
|
212 |
bool ForceField::addTorsionType(const std::string &at1, |
213 |
const std::string &at2, |
214 |
const std::string &at3, |
215 |
const std::string &at4, |
216 |
TorsionType* torsionType) { |
217 |
std::vector<std::string> keys; |
218 |
keys.push_back(at1); |
219 |
keys.push_back(at2); |
220 |
keys.push_back(at3); |
221 |
keys.push_back(at4); |
222 |
return torsionTypeCont_.add(keys, torsionType); |
223 |
} |
224 |
|
225 |
bool ForceField::addNonBondedInteractionType(const std::string &at1, |
226 |
const std::string &at2, |
227 |
NonBondedInteractionType* nbiType) { |
228 |
std::vector<std::string> keys; |
229 |
keys.push_back(at1); |
230 |
keys.push_back(at2); |
231 |
return nonBondedInteractionTypeCont_.add(keys, nbiType); |
232 |
} |
233 |
|
234 |
RealType ForceField::getRcutFromAtomType(AtomType* at) { |
235 |
/**@todo */ |
236 |
GenericData* data; |
237 |
RealType rcut = 0.0; |
238 |
|
239 |
if (at->isLennardJones()) { |
240 |
data = at->getPropertyByName("LennardJones"); |
241 |
if (data != NULL) { |
242 |
LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
243 |
|
244 |
if (ljData != NULL) { |
245 |
LJParam ljParam = ljData->getData(); |
246 |
|
247 |
//by default use 2.5*sigma as cutoff radius |
248 |
rcut = 2.5 * ljParam.sigma; |
249 |
|
250 |
} else { |
251 |
sprintf( painCave.errMsg, |
252 |
"Can not cast GenericData to LJParam\n"); |
253 |
painCave.severity = OOPSE_ERROR; |
254 |
painCave.isFatal = 1; |
255 |
simError(); |
256 |
} |
257 |
} else { |
258 |
sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n"); |
259 |
painCave.severity = OOPSE_ERROR; |
260 |
painCave.isFatal = 1; |
261 |
simError(); |
262 |
} |
263 |
} |
264 |
return rcut; |
265 |
} |
266 |
|
267 |
|
268 |
ifstrstream* ForceField::openForceFieldFile(const std::string& filename) { |
269 |
std::string forceFieldFilename(filename); |
270 |
ifstrstream* ffStream = new ifstrstream(); |
271 |
|
272 |
//try to open the force filed file in current directory first |
273 |
ffStream->open(forceFieldFilename.c_str()); |
274 |
if(!ffStream->is_open()){ |
275 |
|
276 |
forceFieldFilename = ffPath_ + "/" + forceFieldFilename; |
277 |
ffStream->open( forceFieldFilename.c_str() ); |
278 |
|
279 |
//if current directory does not contain the force field file, |
280 |
//try to open it in the path |
281 |
if(!ffStream->is_open()){ |
282 |
|
283 |
sprintf( painCave.errMsg, |
284 |
"Error opening the force field parameter file:\n" |
285 |
"\t%s\n" |
286 |
"\tHave you tried setting the FORCE_PARAM_PATH environment " |
287 |
"variable?\n", |
288 |
forceFieldFilename.c_str() ); |
289 |
painCave.severity = OOPSE_ERROR; |
290 |
painCave.isFatal = 1; |
291 |
simError(); |
292 |
} |
293 |
} |
294 |
return ffStream; |
295 |
} |
296 |
|
297 |
void ForceField::setFortranForceOptions(){ |
298 |
ForceOptions theseFortranOptions; |
299 |
forceFieldOptions_.makeFortranOptions(theseFortranOptions); |
300 |
setfForceOptions(&theseFortranOptions); |
301 |
} |
302 |
} //end namespace oopse |