| 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 |
| 9 |
> |
* 1. Redistributions of source code must retain the above copyright |
| 10 |
|
* notice, this list of conditions and the following disclaimer. |
| 11 |
|
* |
| 12 |
< |
* 3. Redistributions in binary form must reproduce the above copyright |
| 12 |
> |
* 2. Redistributions in binary form must reproduce the above copyright |
| 13 |
|
* notice, this list of conditions and the following disclaimer in the |
| 14 |
|
* documentation and/or other materials provided with the |
| 15 |
|
* distribution. |
| 28 |
|
* arising out of the use of or inability to use software, even if the |
| 29 |
|
* University of Notre Dame has been advised of the possibility of |
| 30 |
|
* such damages. |
| 31 |
+ |
* |
| 32 |
+ |
* SUPPORT OPEN SCIENCE! If you use OpenMD or its source code in your |
| 33 |
+ |
* research, please cite the appropriate papers when you publish your |
| 34 |
+ |
* work. Good starting points are: |
| 35 |
+ |
* |
| 36 |
+ |
* [1] Meineke, et al., J. Comp. Chem. 26, 252-271 (2005). |
| 37 |
+ |
* [2] Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006). |
| 38 |
+ |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008). |
| 39 |
+ |
* [4] Vardeman & Gezelter, in progress (2009). |
| 40 |
|
*/ |
| 41 |
|
|
| 42 |
|
/** |
| 47 |
|
* @version 1.0 |
| 48 |
|
*/ |
| 49 |
|
|
| 50 |
+ |
#include <algorithm> |
| 51 |
|
#include "UseTheForce/ForceField.hpp" |
| 52 |
|
#include "utils/simError.h" |
| 53 |
< |
#include "UseTheForce/DarkSide/atype_interface.h" |
| 54 |
< |
#include "UseTheForce/DarkSide/fForceOptions_interface.h" |
| 54 |
< |
#include "UseTheForce/DarkSide/switcheroo_interface.h" |
| 55 |
< |
namespace oopse { |
| 53 |
> |
#include "utils/Tuple.hpp" |
| 54 |
> |
namespace OpenMD { |
| 55 |
|
|
| 56 |
|
ForceField::ForceField() { |
| 57 |
+ |
|
| 58 |
|
char* tempPath; |
| 59 |
|
tempPath = getenv("FORCE_PARAM_PATH"); |
| 60 |
< |
|
| 60 |
> |
|
| 61 |
|
if (tempPath == NULL) { |
| 62 |
|
//convert a macro from compiler to a string in c++ |
| 63 |
|
STR_DEFINE(ffPath_, FRC_PATH ); |
| 66 |
|
} |
| 67 |
|
} |
| 68 |
|
|
| 69 |
< |
|
| 70 |
< |
ForceField::~ForceField() { |
| 71 |
< |
deleteAtypes(); |
| 72 |
< |
deleteSwitch(); |
| 73 |
< |
} |
| 74 |
< |
|
| 69 |
> |
/** |
| 70 |
> |
* getAtomType by string |
| 71 |
> |
* |
| 72 |
> |
* finds the requested atom type in this force field using the string |
| 73 |
> |
* name of the atom type. |
| 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, const std::string &at2) { |
| 81 |
> |
/** |
| 82 |
> |
* getAtomType by ident |
| 83 |
> |
* |
| 84 |
> |
* finds the requested atom type in this force field using the |
| 85 |
> |
* integer ident instead of the string name of the atom type. |
| 86 |
> |
*/ |
| 87 |
> |
AtomType* ForceField::getAtomType(int ident) { |
| 88 |
> |
std::string at = atypeIdentToName.find(ident)->second; |
| 89 |
> |
return getAtomType(at); |
| 90 |
> |
} |
| 91 |
> |
|
| 92 |
> |
BondType* ForceField::getBondType(const std::string &at1, |
| 93 |
> |
const std::string &at2) { |
| 94 |
|
std::vector<std::string> keys; |
| 95 |
|
keys.push_back(at1); |
| 96 |
|
keys.push_back(at2); |
| 100 |
|
if (bondType) { |
| 101 |
|
return bondType; |
| 102 |
|
} else { |
| 103 |
< |
//if no exact match found, try wild card match |
| 104 |
< |
return bondTypeCont_.find(keys, wildCardAtomTypeName_); |
| 105 |
< |
} |
| 103 |
> |
AtomType* atype1; |
| 104 |
> |
AtomType* atype2; |
| 105 |
> |
std::vector<std::string> at1key; |
| 106 |
> |
at1key.push_back(at1); |
| 107 |
> |
atype1 = atomTypeCont_.find(at1key); |
| 108 |
> |
|
| 109 |
> |
std::vector<std::string> at2key; |
| 110 |
> |
at2key.push_back(at2); |
| 111 |
> |
atype2 = atomTypeCont_.find(at2key); |
| 112 |
|
|
| 113 |
< |
} |
| 113 |
> |
// query atom types for their chains of responsibility |
| 114 |
> |
std::vector<AtomType*> at1Chain = atype1->allYourBase(); |
| 115 |
> |
std::vector<AtomType*> at2Chain = atype2->allYourBase(); |
| 116 |
|
|
| 117 |
< |
BendType* ForceField::getBendType(const std::string &at1, const std::string &at2, |
| 117 |
> |
std::vector<AtomType*>::iterator i; |
| 118 |
> |
std::vector<AtomType*>::iterator j; |
| 119 |
> |
|
| 120 |
> |
int ii = 0; |
| 121 |
> |
int jj = 0; |
| 122 |
> |
int bondTypeScore; |
| 123 |
> |
|
| 124 |
> |
std::vector<std::pair<int, std::vector<std::string> > > foundBonds; |
| 125 |
> |
|
| 126 |
> |
for (i = at1Chain.begin(); i != at1Chain.end(); i++) { |
| 127 |
> |
jj = 0; |
| 128 |
> |
for (j = at2Chain.begin(); j != at2Chain.end(); j++) { |
| 129 |
> |
|
| 130 |
> |
bondTypeScore = ii + jj; |
| 131 |
> |
|
| 132 |
> |
std::vector<std::string> myKeys; |
| 133 |
> |
myKeys.push_back((*i)->getName()); |
| 134 |
> |
myKeys.push_back((*j)->getName()); |
| 135 |
> |
|
| 136 |
> |
BondType* bondType = bondTypeCont_.find(myKeys); |
| 137 |
> |
if (bondType) { |
| 138 |
> |
foundBonds.push_back(std::make_pair(bondTypeScore, myKeys)); |
| 139 |
> |
} |
| 140 |
> |
jj++; |
| 141 |
> |
} |
| 142 |
> |
ii++; |
| 143 |
> |
} |
| 144 |
> |
|
| 145 |
> |
|
| 146 |
> |
if (foundBonds.size() > 0) { |
| 147 |
> |
// sort the foundBonds by the score: |
| 148 |
> |
std::sort(foundBonds.begin(), foundBonds.end()); |
| 149 |
> |
|
| 150 |
> |
int bestScore = foundBonds[0].first; |
| 151 |
> |
std::vector<std::string> theKeys = foundBonds[0].second; |
| 152 |
> |
|
| 153 |
> |
BondType* bestType = bondTypeCont_.find(theKeys); |
| 154 |
> |
|
| 155 |
> |
return bestType; |
| 156 |
> |
} else { |
| 157 |
> |
//if no exact match found, try wild card match |
| 158 |
> |
return bondTypeCont_.find(keys, wildCardAtomTypeName_); |
| 159 |
> |
} |
| 160 |
> |
} |
| 161 |
> |
} |
| 162 |
> |
|
| 163 |
> |
BendType* ForceField::getBendType(const std::string &at1, |
| 164 |
> |
const std::string &at2, |
| 165 |
|
const std::string &at3) { |
| 166 |
|
std::vector<std::string> keys; |
| 167 |
|
keys.push_back(at1); |
| 173 |
|
if (bendType) { |
| 174 |
|
return bendType; |
| 175 |
|
} else { |
| 176 |
< |
//if no exact match found, try wild card match |
| 177 |
< |
return bendTypeCont_.find(keys, wildCardAtomTypeName_); |
| 176 |
> |
|
| 177 |
> |
AtomType* atype1; |
| 178 |
> |
AtomType* atype2; |
| 179 |
> |
AtomType* atype3; |
| 180 |
> |
std::vector<std::string> at1key; |
| 181 |
> |
at1key.push_back(at1); |
| 182 |
> |
atype1 = atomTypeCont_.find(at1key); |
| 183 |
> |
|
| 184 |
> |
std::vector<std::string> at2key; |
| 185 |
> |
at2key.push_back(at2); |
| 186 |
> |
atype2 = atomTypeCont_.find(at2key); |
| 187 |
> |
|
| 188 |
> |
std::vector<std::string> at3key; |
| 189 |
> |
at3key.push_back(at3); |
| 190 |
> |
atype3 = atomTypeCont_.find(at3key); |
| 191 |
> |
|
| 192 |
> |
// query atom types for their chains of responsibility |
| 193 |
> |
std::vector<AtomType*> at1Chain = atype1->allYourBase(); |
| 194 |
> |
std::vector<AtomType*> at2Chain = atype2->allYourBase(); |
| 195 |
> |
std::vector<AtomType*> at3Chain = atype3->allYourBase(); |
| 196 |
> |
|
| 197 |
> |
std::vector<AtomType*>::iterator i; |
| 198 |
> |
std::vector<AtomType*>::iterator j; |
| 199 |
> |
std::vector<AtomType*>::iterator k; |
| 200 |
> |
|
| 201 |
> |
int ii = 0; |
| 202 |
> |
int jj = 0; |
| 203 |
> |
int kk = 0; |
| 204 |
> |
int IKscore; |
| 205 |
> |
|
| 206 |
> |
std::vector<tuple3<int, int, std::vector<std::string> > > foundBends; |
| 207 |
> |
|
| 208 |
> |
for (j = at2Chain.begin(); j != at2Chain.end(); j++) { |
| 209 |
> |
ii = 0; |
| 210 |
> |
for (i = at1Chain.begin(); i != at1Chain.end(); i++) { |
| 211 |
> |
kk = 0; |
| 212 |
> |
for (k = at3Chain.begin(); k != at3Chain.end(); k++) { |
| 213 |
> |
|
| 214 |
> |
IKscore = ii + kk; |
| 215 |
> |
|
| 216 |
> |
std::vector<std::string> myKeys; |
| 217 |
> |
myKeys.push_back((*i)->getName()); |
| 218 |
> |
myKeys.push_back((*j)->getName()); |
| 219 |
> |
myKeys.push_back((*k)->getName()); |
| 220 |
> |
|
| 221 |
> |
BendType* bendType = bendTypeCont_.find(myKeys); |
| 222 |
> |
if (bendType) { |
| 223 |
> |
foundBends.push_back( make_tuple3(jj, IKscore, myKeys) ); |
| 224 |
> |
} |
| 225 |
> |
kk++; |
| 226 |
> |
} |
| 227 |
> |
ii++; |
| 228 |
> |
} |
| 229 |
> |
jj++; |
| 230 |
> |
} |
| 231 |
> |
|
| 232 |
> |
if (foundBends.size() > 0) { |
| 233 |
> |
std::sort(foundBends.begin(), foundBends.end()); |
| 234 |
> |
int jscore = foundBends[0].first; |
| 235 |
> |
int ikscore = foundBends[0].second; |
| 236 |
> |
std::vector<std::string> theKeys = foundBends[0].third; |
| 237 |
> |
|
| 238 |
> |
BendType* bestType = bendTypeCont_.find(theKeys); |
| 239 |
> |
return bestType; |
| 240 |
> |
} else { |
| 241 |
> |
//if no exact match found, try wild card match |
| 242 |
> |
return bendTypeCont_.find(keys, wildCardAtomTypeName_); |
| 243 |
> |
} |
| 244 |
|
} |
| 245 |
|
} |
| 246 |
|
|
| 247 |
< |
TorsionType* ForceField::getTorsionType(const std::string &at1, const std::string &at2, |
| 248 |
< |
const std::string &at3, const std::string &at4) { |
| 247 |
> |
TorsionType* ForceField::getTorsionType(const std::string &at1, |
| 248 |
> |
const std::string &at2, |
| 249 |
> |
const std::string &at3, |
| 250 |
> |
const std::string &at4) { |
| 251 |
|
std::vector<std::string> keys; |
| 252 |
|
keys.push_back(at1); |
| 253 |
|
keys.push_back(at2); |
| 254 |
|
keys.push_back(at3); |
| 255 |
|
keys.push_back(at4); |
| 256 |
|
|
| 257 |
+ |
|
| 258 |
+ |
//try exact match first |
| 259 |
|
TorsionType* torsionType = torsionTypeCont_.find(keys); |
| 260 |
|
if (torsionType) { |
| 261 |
|
return torsionType; |
| 262 |
|
} else { |
| 126 |
– |
//if no exact match found, try wild card match |
| 127 |
– |
return torsionTypeCont_.find(keys, wildCardAtomTypeName_); |
| 128 |
– |
} |
| 129 |
– |
|
| 130 |
– |
return torsionTypeCont_.find(keys, wildCardAtomTypeName_); |
| 263 |
|
|
| 264 |
+ |
AtomType* atype1; |
| 265 |
+ |
AtomType* atype2; |
| 266 |
+ |
AtomType* atype3; |
| 267 |
+ |
AtomType* atype4; |
| 268 |
+ |
std::vector<std::string> at1key; |
| 269 |
+ |
at1key.push_back(at1); |
| 270 |
+ |
atype1 = atomTypeCont_.find(at1key); |
| 271 |
+ |
|
| 272 |
+ |
std::vector<std::string> at2key; |
| 273 |
+ |
at2key.push_back(at2); |
| 274 |
+ |
atype2 = atomTypeCont_.find(at2key); |
| 275 |
+ |
|
| 276 |
+ |
std::vector<std::string> at3key; |
| 277 |
+ |
at3key.push_back(at3); |
| 278 |
+ |
atype3 = atomTypeCont_.find(at3key); |
| 279 |
+ |
|
| 280 |
+ |
std::vector<std::string> at4key; |
| 281 |
+ |
at4key.push_back(at4); |
| 282 |
+ |
atype4 = atomTypeCont_.find(at4key); |
| 283 |
+ |
|
| 284 |
+ |
// query atom types for their chains of responsibility |
| 285 |
+ |
std::vector<AtomType*> at1Chain = atype1->allYourBase(); |
| 286 |
+ |
std::vector<AtomType*> at2Chain = atype2->allYourBase(); |
| 287 |
+ |
std::vector<AtomType*> at3Chain = atype3->allYourBase(); |
| 288 |
+ |
std::vector<AtomType*> at4Chain = atype4->allYourBase(); |
| 289 |
+ |
|
| 290 |
+ |
std::vector<AtomType*>::iterator i; |
| 291 |
+ |
std::vector<AtomType*>::iterator j; |
| 292 |
+ |
std::vector<AtomType*>::iterator k; |
| 293 |
+ |
std::vector<AtomType*>::iterator l; |
| 294 |
+ |
|
| 295 |
+ |
int ii = 0; |
| 296 |
+ |
int jj = 0; |
| 297 |
+ |
int kk = 0; |
| 298 |
+ |
int ll = 0; |
| 299 |
+ |
int ILscore; |
| 300 |
+ |
int JKscore; |
| 301 |
+ |
|
| 302 |
+ |
std::vector<tuple3<int, int, std::vector<std::string> > > foundTorsions; |
| 303 |
+ |
|
| 304 |
+ |
for (j = at2Chain.begin(); j != at2Chain.end(); j++) { |
| 305 |
+ |
kk = 0; |
| 306 |
+ |
for (k = at3Chain.begin(); k != at3Chain.end(); k++) { |
| 307 |
+ |
ii = 0; |
| 308 |
+ |
for (i = at1Chain.begin(); i != at1Chain.end(); i++) { |
| 309 |
+ |
ll = 0; |
| 310 |
+ |
for (l = at4Chain.begin(); l != at4Chain.end(); l++) { |
| 311 |
+ |
|
| 312 |
+ |
ILscore = ii + ll; |
| 313 |
+ |
JKscore = jj + kk; |
| 314 |
+ |
|
| 315 |
+ |
std::vector<std::string> myKeys; |
| 316 |
+ |
myKeys.push_back((*i)->getName()); |
| 317 |
+ |
myKeys.push_back((*j)->getName()); |
| 318 |
+ |
myKeys.push_back((*k)->getName()); |
| 319 |
+ |
myKeys.push_back((*l)->getName()); |
| 320 |
+ |
|
| 321 |
+ |
TorsionType* torsionType = torsionTypeCont_.find(myKeys); |
| 322 |
+ |
if (torsionType) { |
| 323 |
+ |
foundTorsions.push_back( make_tuple3(JKscore, ILscore, myKeys) ); |
| 324 |
+ |
} |
| 325 |
+ |
ll++; |
| 326 |
+ |
} |
| 327 |
+ |
ii++; |
| 328 |
+ |
} |
| 329 |
+ |
kk++; |
| 330 |
+ |
} |
| 331 |
+ |
jj++; |
| 332 |
+ |
} |
| 333 |
+ |
|
| 334 |
+ |
if (foundTorsions.size() > 0) { |
| 335 |
+ |
std::sort(foundTorsions.begin(), foundTorsions.end()); |
| 336 |
+ |
int jkscore = foundTorsions[0].first; |
| 337 |
+ |
int ilscore = foundTorsions[0].second; |
| 338 |
+ |
std::vector<std::string> theKeys = foundTorsions[0].third; |
| 339 |
+ |
|
| 340 |
+ |
TorsionType* bestType = torsionTypeCont_.find(theKeys); |
| 341 |
+ |
return bestType; |
| 342 |
+ |
} else { |
| 343 |
+ |
//if no exact match found, try wild card match |
| 344 |
+ |
return torsionTypeCont_.find(keys, wildCardAtomTypeName_); |
| 345 |
+ |
} |
| 346 |
+ |
} |
| 347 |
|
} |
| 348 |
|
|
| 349 |
< |
BondType* ForceField::getExactBondType(const std::string &at1, const std::string &at2){ |
| 349 |
> |
InversionType* ForceField::getInversionType(const std::string &at1, |
| 350 |
> |
const std::string &at2, |
| 351 |
> |
const std::string &at3, |
| 352 |
> |
const std::string &at4) { |
| 353 |
|
std::vector<std::string> keys; |
| 354 |
|
keys.push_back(at1); |
| 355 |
|
keys.push_back(at2); |
| 356 |
+ |
keys.push_back(at3); |
| 357 |
+ |
keys.push_back(at4); |
| 358 |
+ |
|
| 359 |
+ |
//try exact match first |
| 360 |
+ |
InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(keys); |
| 361 |
+ |
if (inversionType) { |
| 362 |
+ |
return inversionType; |
| 363 |
+ |
} else { |
| 364 |
+ |
|
| 365 |
+ |
AtomType* atype1; |
| 366 |
+ |
AtomType* atype2; |
| 367 |
+ |
AtomType* atype3; |
| 368 |
+ |
AtomType* atype4; |
| 369 |
+ |
std::vector<std::string> at1key; |
| 370 |
+ |
at1key.push_back(at1); |
| 371 |
+ |
atype1 = atomTypeCont_.find(at1key); |
| 372 |
+ |
|
| 373 |
+ |
std::vector<std::string> at2key; |
| 374 |
+ |
at2key.push_back(at2); |
| 375 |
+ |
atype2 = atomTypeCont_.find(at2key); |
| 376 |
+ |
|
| 377 |
+ |
std::vector<std::string> at3key; |
| 378 |
+ |
at3key.push_back(at3); |
| 379 |
+ |
atype3 = atomTypeCont_.find(at3key); |
| 380 |
+ |
|
| 381 |
+ |
std::vector<std::string> at4key; |
| 382 |
+ |
at4key.push_back(at4); |
| 383 |
+ |
atype4 = atomTypeCont_.find(at4key); |
| 384 |
+ |
|
| 385 |
+ |
// query atom types for their chains of responsibility |
| 386 |
+ |
std::vector<AtomType*> at1Chain = atype1->allYourBase(); |
| 387 |
+ |
std::vector<AtomType*> at2Chain = atype2->allYourBase(); |
| 388 |
+ |
std::vector<AtomType*> at3Chain = atype3->allYourBase(); |
| 389 |
+ |
std::vector<AtomType*> at4Chain = atype4->allYourBase(); |
| 390 |
+ |
|
| 391 |
+ |
std::vector<AtomType*>::iterator i; |
| 392 |
+ |
std::vector<AtomType*>::iterator j; |
| 393 |
+ |
std::vector<AtomType*>::iterator k; |
| 394 |
+ |
std::vector<AtomType*>::iterator l; |
| 395 |
+ |
|
| 396 |
+ |
int ii = 0; |
| 397 |
+ |
int jj = 0; |
| 398 |
+ |
int kk = 0; |
| 399 |
+ |
int ll = 0; |
| 400 |
+ |
int Iscore; |
| 401 |
+ |
int JKLscore; |
| 402 |
+ |
|
| 403 |
+ |
std::vector<tuple3<int, int, std::vector<std::string> > > foundInversions; |
| 404 |
+ |
|
| 405 |
+ |
for (j = at2Chain.begin(); j != at2Chain.end(); j++) { |
| 406 |
+ |
kk = 0; |
| 407 |
+ |
for (k = at3Chain.begin(); k != at3Chain.end(); k++) { |
| 408 |
+ |
ii = 0; |
| 409 |
+ |
for (i = at1Chain.begin(); i != at1Chain.end(); i++) { |
| 410 |
+ |
ll = 0; |
| 411 |
+ |
for (l = at4Chain.begin(); l != at4Chain.end(); l++) { |
| 412 |
+ |
|
| 413 |
+ |
Iscore = ii; |
| 414 |
+ |
JKLscore = jj + kk + ll; |
| 415 |
+ |
|
| 416 |
+ |
std::vector<std::string> myKeys; |
| 417 |
+ |
myKeys.push_back((*i)->getName()); |
| 418 |
+ |
myKeys.push_back((*j)->getName()); |
| 419 |
+ |
myKeys.push_back((*k)->getName()); |
| 420 |
+ |
myKeys.push_back((*l)->getName()); |
| 421 |
+ |
|
| 422 |
+ |
InversionType* inversionType = inversionTypeCont_.permutedFindSkippingFirstElement(myKeys); |
| 423 |
+ |
if (inversionType) { |
| 424 |
+ |
foundInversions.push_back( make_tuple3(Iscore, JKLscore, myKeys) ); |
| 425 |
+ |
} |
| 426 |
+ |
ll++; |
| 427 |
+ |
} |
| 428 |
+ |
ii++; |
| 429 |
+ |
} |
| 430 |
+ |
kk++; |
| 431 |
+ |
} |
| 432 |
+ |
jj++; |
| 433 |
+ |
} |
| 434 |
+ |
|
| 435 |
+ |
if (foundInversions.size() > 0) { |
| 436 |
+ |
std::sort(foundInversions.begin(), foundInversions.end()); |
| 437 |
+ |
int iscore = foundInversions[0].first; |
| 438 |
+ |
int jklscore = foundInversions[0].second; |
| 439 |
+ |
std::vector<std::string> theKeys = foundInversions[0].third; |
| 440 |
+ |
|
| 441 |
+ |
InversionType* bestType = inversionTypeCont_.permutedFindSkippingFirstElement(theKeys); |
| 442 |
+ |
return bestType; |
| 443 |
+ |
} else { |
| 444 |
+ |
//if no exact match found, try wild card match |
| 445 |
+ |
return inversionTypeCont_.find(keys, wildCardAtomTypeName_); |
| 446 |
+ |
} |
| 447 |
+ |
} |
| 448 |
+ |
} |
| 449 |
+ |
|
| 450 |
+ |
NonBondedInteractionType* ForceField::getNonBondedInteractionType(const std::string &at1, const std::string &at2) { |
| 451 |
+ |
std::vector<std::string> keys; |
| 452 |
+ |
keys.push_back(at1); |
| 453 |
+ |
keys.push_back(at2); |
| 454 |
+ |
|
| 455 |
+ |
//try exact match first |
| 456 |
+ |
NonBondedInteractionType* nbiType = nonBondedInteractionTypeCont_.find(keys); |
| 457 |
+ |
if (nbiType) { |
| 458 |
+ |
return nbiType; |
| 459 |
+ |
} else { |
| 460 |
+ |
//if no exact match found, try wild card match |
| 461 |
+ |
return nonBondedInteractionTypeCont_.find(keys, wildCardAtomTypeName_); |
| 462 |
+ |
} |
| 463 |
+ |
} |
| 464 |
+ |
|
| 465 |
+ |
BondType* ForceField::getExactBondType(const std::string &at1, |
| 466 |
+ |
const std::string &at2){ |
| 467 |
+ |
std::vector<std::string> keys; |
| 468 |
+ |
keys.push_back(at1); |
| 469 |
+ |
keys.push_back(at2); |
| 470 |
|
return bondTypeCont_.find(keys); |
| 471 |
|
} |
| 472 |
< |
|
| 473 |
< |
BendType* ForceField::getExactBendType(const std::string &at1, const std::string &at2, |
| 472 |
> |
|
| 473 |
> |
BendType* ForceField::getExactBendType(const std::string &at1, |
| 474 |
> |
const std::string &at2, |
| 475 |
|
const std::string &at3){ |
| 476 |
|
std::vector<std::string> keys; |
| 477 |
|
keys.push_back(at1); |
| 479 |
|
keys.push_back(at3); |
| 480 |
|
return bendTypeCont_.find(keys); |
| 481 |
|
} |
| 482 |
< |
|
| 483 |
< |
TorsionType* ForceField::getExactTorsionType(const std::string &at1, const std::string &at2, |
| 484 |
< |
const std::string &at3, const std::string &at4){ |
| 482 |
> |
|
| 483 |
> |
TorsionType* ForceField::getExactTorsionType(const std::string &at1, |
| 484 |
> |
const std::string &at2, |
| 485 |
> |
const std::string &at3, |
| 486 |
> |
const std::string &at4){ |
| 487 |
|
std::vector<std::string> keys; |
| 488 |
|
keys.push_back(at1); |
| 489 |
|
keys.push_back(at2); |
| 491 |
|
keys.push_back(at4); |
| 492 |
|
return torsionTypeCont_.find(keys); |
| 493 |
|
} |
| 494 |
+ |
|
| 495 |
+ |
InversionType* ForceField::getExactInversionType(const std::string &at1, |
| 496 |
+ |
const std::string &at2, |
| 497 |
+ |
const std::string &at3, |
| 498 |
+ |
const std::string &at4){ |
| 499 |
+ |
std::vector<std::string> keys; |
| 500 |
+ |
keys.push_back(at1); |
| 501 |
+ |
keys.push_back(at2); |
| 502 |
+ |
keys.push_back(at3); |
| 503 |
+ |
keys.push_back(at4); |
| 504 |
+ |
return inversionTypeCont_.find(keys); |
| 505 |
+ |
} |
| 506 |
+ |
|
| 507 |
+ |
NonBondedInteractionType* ForceField::getExactNonBondedInteractionType(const std::string &at1, const std::string &at2){ |
| 508 |
+ |
std::vector<std::string> keys; |
| 509 |
+ |
keys.push_back(at1); |
| 510 |
+ |
keys.push_back(at2); |
| 511 |
+ |
return nonBondedInteractionTypeCont_.find(keys); |
| 512 |
+ |
} |
| 513 |
+ |
|
| 514 |
+ |
|
| 515 |
|
bool ForceField::addAtomType(const std::string &at, AtomType* atomType) { |
| 516 |
|
std::vector<std::string> keys; |
| 517 |
|
keys.push_back(at); |
| 518 |
+ |
atypeIdentToName[atomType->getIdent()] = at; |
| 519 |
|
return atomTypeCont_.add(keys, atomType); |
| 520 |
|
} |
| 521 |
|
|
| 522 |
< |
bool ForceField::addBondType(const std::string &at1, const std::string &at2, BondType* bondType) { |
| 522 |
> |
bool ForceField::replaceAtomType(const std::string &at, AtomType* atomType) { |
| 523 |
|
std::vector<std::string> keys; |
| 524 |
+ |
keys.push_back(at); |
| 525 |
+ |
atypeIdentToName[atomType->getIdent()] = at; |
| 526 |
+ |
return atomTypeCont_.replace(keys, atomType); |
| 527 |
+ |
} |
| 528 |
+ |
|
| 529 |
+ |
bool ForceField::addBondType(const std::string &at1, const std::string &at2, |
| 530 |
+ |
BondType* bondType) { |
| 531 |
+ |
std::vector<std::string> keys; |
| 532 |
|
keys.push_back(at1); |
| 533 |
|
keys.push_back(at2); |
| 534 |
< |
return bondTypeCont_.add(keys, bondType); |
| 170 |
< |
|
| 534 |
> |
return bondTypeCont_.add(keys, bondType); |
| 535 |
|
} |
| 536 |
< |
|
| 536 |
> |
|
| 537 |
|
bool ForceField::addBendType(const std::string &at1, const std::string &at2, |
| 538 |
|
const std::string &at3, BendType* bendType) { |
| 539 |
|
std::vector<std::string> keys; |
| 542 |
|
keys.push_back(at3); |
| 543 |
|
return bendTypeCont_.add(keys, bendType); |
| 544 |
|
} |
| 545 |
< |
|
| 546 |
< |
bool ForceField::addTorsionType(const std::string &at1, const std::string &at2, |
| 547 |
< |
const std::string &at3, const std::string &at4, TorsionType* torsionType) { |
| 545 |
> |
|
| 546 |
> |
bool ForceField::addTorsionType(const std::string &at1, |
| 547 |
> |
const std::string &at2, |
| 548 |
> |
const std::string &at3, |
| 549 |
> |
const std::string &at4, |
| 550 |
> |
TorsionType* torsionType) { |
| 551 |
|
std::vector<std::string> keys; |
| 552 |
|
keys.push_back(at1); |
| 553 |
|
keys.push_back(at2); |
| 556 |
|
return torsionTypeCont_.add(keys, torsionType); |
| 557 |
|
} |
| 558 |
|
|
| 559 |
+ |
bool ForceField::addInversionType(const std::string &at1, |
| 560 |
+ |
const std::string &at2, |
| 561 |
+ |
const std::string &at3, |
| 562 |
+ |
const std::string &at4, |
| 563 |
+ |
InversionType* inversionType) { |
| 564 |
+ |
std::vector<std::string> keys; |
| 565 |
+ |
keys.push_back(at1); |
| 566 |
+ |
keys.push_back(at2); |
| 567 |
+ |
keys.push_back(at3); |
| 568 |
+ |
keys.push_back(at4); |
| 569 |
+ |
return inversionTypeCont_.add(keys, inversionType); |
| 570 |
+ |
} |
| 571 |
+ |
|
| 572 |
+ |
bool ForceField::addNonBondedInteractionType(const std::string &at1, |
| 573 |
+ |
const std::string &at2, |
| 574 |
+ |
NonBondedInteractionType* nbiType) { |
| 575 |
+ |
std::vector<std::string> keys; |
| 576 |
+ |
keys.push_back(at1); |
| 577 |
+ |
keys.push_back(at2); |
| 578 |
+ |
return nonBondedInteractionTypeCont_.add(keys, nbiType); |
| 579 |
+ |
} |
| 580 |
+ |
|
| 581 |
|
RealType ForceField::getRcutFromAtomType(AtomType* at) { |
| 582 |
|
/**@todo */ |
| 583 |
|
GenericData* data; |
| 584 |
|
RealType rcut = 0.0; |
| 585 |
< |
|
| 585 |
> |
|
| 586 |
|
if (at->isLennardJones()) { |
| 587 |
|
data = at->getPropertyByName("LennardJones"); |
| 588 |
|
if (data != NULL) { |
| 589 |
|
LJParamGenericData* ljData = dynamic_cast<LJParamGenericData*>(data); |
| 590 |
< |
|
| 590 |
> |
|
| 591 |
|
if (ljData != NULL) { |
| 592 |
|
LJParam ljParam = ljData->getData(); |
| 593 |
< |
|
| 593 |
> |
|
| 594 |
|
//by default use 2.5*sigma as cutoff radius |
| 595 |
|
rcut = 2.5 * ljParam.sigma; |
| 596 |
< |
|
| 596 |
> |
|
| 597 |
|
} else { |
| 598 |
|
sprintf( painCave.errMsg, |
| 599 |
|
"Can not cast GenericData to LJParam\n"); |
| 600 |
< |
painCave.severity = OOPSE_ERROR; |
| 600 |
> |
painCave.severity = OPENMD_ERROR; |
| 601 |
|
painCave.isFatal = 1; |
| 602 |
|
simError(); |
| 603 |
|
} |
| 604 |
|
} else { |
| 605 |
|
sprintf( painCave.errMsg, "Can not find Parameters for LennardJones\n"); |
| 606 |
< |
painCave.severity = OOPSE_ERROR; |
| 606 |
> |
painCave.severity = OPENMD_ERROR; |
| 607 |
|
painCave.isFatal = 1; |
| 608 |
|
simError(); |
| 609 |
|
} |
| 610 |
|
} |
| 222 |
– |
|
| 611 |
|
return rcut; |
| 612 |
|
} |
| 613 |
+ |
|
| 614 |
|
|
| 226 |
– |
|
| 615 |
|
ifstrstream* ForceField::openForceFieldFile(const std::string& filename) { |
| 616 |
|
std::string forceFieldFilename(filename); |
| 617 |
|
ifstrstream* ffStream = new ifstrstream(); |
| 633 |
|
"\tHave you tried setting the FORCE_PARAM_PATH environment " |
| 634 |
|
"variable?\n", |
| 635 |
|
forceFieldFilename.c_str() ); |
| 636 |
< |
painCave.severity = OOPSE_ERROR; |
| 636 |
> |
painCave.severity = OPENMD_ERROR; |
| 637 |
|
painCave.isFatal = 1; |
| 638 |
|
simError(); |
| 639 |
|
} |
| 640 |
|
} |
| 253 |
– |
|
| 641 |
|
return ffStream; |
| 255 |
– |
|
| 642 |
|
} |
| 643 |
|
|
| 644 |
< |
void ForceField::setFortranForceOptions(){ |
| 259 |
< |
ForceOptions theseFortranOptions; |
| 260 |
< |
forceFieldOptions_.makeFortranOptions(theseFortranOptions); |
| 261 |
< |
setfForceOptions(&theseFortranOptions); |
| 262 |
< |
} |
| 263 |
< |
} //end namespace oopse |
| 644 |
> |
} //end namespace OpenMD |
