| 42 |
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#include "nonbonded/InteractionManager.hpp" |
| 43 |
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|
| 44 |
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namespace OpenMD { |
| 45 |
< |
|
| 45 |
> |
|
| 46 |
> |
InteractionManager* InteractionManager::_instance = NULL; |
| 47 |
> |
SimInfo* InteractionManager::info_ = NULL; |
| 48 |
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bool InteractionManager::initialized_ = false; |
| 49 |
< |
ForceField* InteractionManager::forceField_ = NULL; |
| 50 |
< |
InteractionManager* InteractionManager::_instance = NULL; |
| 49 |
> |
|
| 50 |
> |
RealType InteractionManager::rCut_ = 0.0; |
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> |
RealType InteractionManager::rSwitch_ = 0.0; |
| 52 |
> |
RealType InteractionManager::skinThickness_ = 0.0; |
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> |
RealType InteractionManager::listRadius_ = 0.0; |
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> |
CutoffMethod InteractionManager::cutoffMethod_ = SHIFTED_FORCE; |
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> |
SwitchingFunctionType InteractionManager::sft_ = cubic; |
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> |
RealType InteractionManager::vdwScale_[4] = {1.0, 0.0, 0.0, 0.0}; |
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> |
RealType InteractionManager::electrostaticScale_[4] = {1.0, 0.0, 0.0, 0.0}; |
| 58 |
> |
|
| 59 |
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map<int, AtomType*> InteractionManager::typeMap_; |
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map<pair<AtomType*, AtomType*>, set<NonBondedInteraction*> > InteractionManager::interactions_; |
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+ |
|
| 62 |
+ |
LJ* InteractionManager::lj_ = new LJ(); |
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+ |
GB* InteractionManager::gb_ = new GB(); |
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+ |
Sticky* InteractionManager::sticky_ = new Sticky(); |
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+ |
Morse* InteractionManager::morse_ = new Morse(); |
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+ |
EAM* InteractionManager::eam_ = new EAM(); |
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+ |
SC* InteractionManager::sc_ = new SC(); |
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+ |
Electrostatic* InteractionManager::electrostatic_ = new Electrostatic(); |
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+ |
MAW* InteractionManager::maw_ = new MAW(); |
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+ |
SwitchingFunction* InteractionManager::switcher_ = new SwitchingFunction(); |
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|
| 72 |
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InteractionManager* InteractionManager::Instance() { |
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if (!_instance) { |
| 78 |
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|
| 79 |
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void InteractionManager::initialize() { |
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|
| 81 |
< |
lj_ = new LJ(); |
| 82 |
< |
gb_ = new GB(); |
| 63 |
< |
sticky_ = new Sticky(); |
| 64 |
< |
eam_ = new EAM(); |
| 65 |
< |
sc_ = new SC(); |
| 66 |
< |
morse_ = new Morse(); |
| 67 |
< |
electrostatic_ = new Electrostatic(); |
| 68 |
< |
|
| 81 |
> |
ForceField* forceField_ = info_->getForceField(); |
| 82 |
> |
|
| 83 |
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lj_->setForceField(forceField_); |
| 84 |
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gb_->setForceField(forceField_); |
| 85 |
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sticky_->setForceField(forceField_); |
| 87 |
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sc_->setForceField(forceField_); |
| 88 |
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morse_->setForceField(forceField_); |
| 89 |
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electrostatic_->setForceField(forceField_); |
| 90 |
+ |
maw_->setForceField(forceField_); |
| 91 |
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|
| 92 |
+ |
ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 93 |
+ |
|
| 94 |
+ |
// Force fields can set options on how to scale van der Waals and electrostatic |
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+ |
// interactions for atoms connected via bonds, bends and torsions |
| 96 |
+ |
// in this case the topological distance between atoms is: |
| 97 |
+ |
// 0 = topologically unconnected |
| 98 |
+ |
// 1 = bonded together |
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+ |
// 2 = connected via a bend |
| 100 |
+ |
// 3 = connected via a torsion |
| 101 |
+ |
|
| 102 |
+ |
vdwScale_[0] = 1.0; |
| 103 |
+ |
vdwScale_[1] = fopts.getvdw12scale(); |
| 104 |
+ |
vdwScale_[2] = fopts.getvdw13scale(); |
| 105 |
+ |
vdwScale_[3] = fopts.getvdw14scale(); |
| 106 |
+ |
|
| 107 |
+ |
electrostaticScale_[0] = 1.0; |
| 108 |
+ |
electrostaticScale_[1] = fopts.getelectrostatic12scale(); |
| 109 |
+ |
electrostaticScale_[2] = fopts.getelectrostatic13scale(); |
| 110 |
+ |
electrostaticScale_[3] = fopts.getelectrostatic14scale(); |
| 111 |
+ |
|
| 112 |
|
ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); |
| 113 |
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ForceField::AtomTypeContainer::MapTypeIterator i1, i2; |
| 114 |
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AtomType* atype1; |
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// look for an explicitly-set non-bonded interaction type using the |
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// two atom types. |
| 180 |
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NonBondedInteractionType* nbiType = forceField_->getNonBondedInteractionType(atype1->getName(), atype2->getName()); |
| 181 |
+ |
|
| 182 |
+ |
if (nbiType != NULL) { |
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|
| 184 |
< |
if (nbiType->isLennardJones()) { |
| 185 |
< |
// We found an explicit Lennard-Jones interaction. |
| 186 |
< |
// override all other vdw entries for this pair of atom types: |
| 187 |
< |
set<NonBondedInteraction*>::iterator it; |
| 188 |
< |
for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) { |
| 189 |
< |
InteractionFamily ifam = (*it)->getFamily(); |
| 190 |
< |
if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it); |
| 184 |
> |
if (nbiType->isLennardJones()) { |
| 185 |
> |
// We found an explicit Lennard-Jones interaction. |
| 186 |
> |
// override all other vdw entries for this pair of atom types: |
| 187 |
> |
set<NonBondedInteraction*>::iterator it; |
| 188 |
> |
for (it = interactions_[key].begin(); |
| 189 |
> |
it != interactions_[key].end(); ++it) { |
| 190 |
> |
InteractionFamily ifam = (*it)->getFamily(); |
| 191 |
> |
if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it); |
| 192 |
> |
} |
| 193 |
> |
interactions_[key].insert(lj_); |
| 194 |
> |
vdwExplicit = true; |
| 195 |
|
} |
| 196 |
< |
interactions_[key].insert(lj_); |
| 197 |
< |
vdwExplicit = true; |
| 198 |
< |
} |
| 199 |
< |
|
| 200 |
< |
if (nbiType->isMorse()) { |
| 201 |
< |
if (vdwExplicit) { |
| 202 |
< |
sprintf( painCave.errMsg, |
| 203 |
< |
"InteractionManager::initialize found more than one explicit\n" |
| 204 |
< |
"\tvan der Waals interaction for atom types %s - %s\n", |
| 205 |
< |
atype1->getName().c_str(), atype2->getName().c_str()); |
| 206 |
< |
painCave.severity = OPENMD_ERROR; |
| 207 |
< |
painCave.isFatal = 1; |
| 208 |
< |
simError(); |
| 196 |
> |
|
| 197 |
> |
if (nbiType->isMorse()) { |
| 198 |
> |
if (vdwExplicit) { |
| 199 |
> |
sprintf( painCave.errMsg, |
| 200 |
> |
"InteractionManager::initialize found more than one " |
| 201 |
> |
"explicit \n" |
| 202 |
> |
"\tvan der Waals interaction for atom types %s - %s\n", |
| 203 |
> |
atype1->getName().c_str(), atype2->getName().c_str()); |
| 204 |
> |
painCave.severity = OPENMD_ERROR; |
| 205 |
> |
painCave.isFatal = 1; |
| 206 |
> |
simError(); |
| 207 |
> |
} |
| 208 |
> |
// We found an explicit Morse interaction. |
| 209 |
> |
// override all other vdw entries for this pair of atom types: |
| 210 |
> |
set<NonBondedInteraction*>::iterator it; |
| 211 |
> |
for (it = interactions_[key].begin(); |
| 212 |
> |
it != interactions_[key].end(); ++it) { |
| 213 |
> |
InteractionFamily ifam = (*it)->getFamily(); |
| 214 |
> |
if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it); |
| 215 |
> |
} |
| 216 |
> |
interactions_[key].insert(morse_); |
| 217 |
> |
vdwExplicit = true; |
| 218 |
|
} |
| 219 |
< |
// We found an explicit Morse interaction. |
| 220 |
< |
// override all other vdw entries for this pair of atom types: |
| 221 |
< |
set<NonBondedInteraction*>::iterator it; |
| 222 |
< |
for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) { |
| 223 |
< |
InteractionFamily ifam = (*it)->getFamily(); |
| 224 |
< |
if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it); |
| 219 |
> |
|
| 220 |
> |
if (nbiType->isEAM()) { |
| 221 |
> |
// We found an explicit EAM interaction. |
| 222 |
> |
// override all other metallic entries for this pair of atom types: |
| 223 |
> |
set<NonBondedInteraction*>::iterator it; |
| 224 |
> |
for (it = interactions_[key].begin(); |
| 225 |
> |
it != interactions_[key].end(); ++it) { |
| 226 |
> |
InteractionFamily ifam = (*it)->getFamily(); |
| 227 |
> |
if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it); |
| 228 |
> |
} |
| 229 |
> |
interactions_[key].insert(eam_); |
| 230 |
> |
metExplicit = true; |
| 231 |
|
} |
| 232 |
< |
interactions_[key].insert(morse_); |
| 233 |
< |
vdwExplicit = true; |
| 234 |
< |
} |
| 235 |
< |
|
| 236 |
< |
if (nbiType->isEAM()) { |
| 237 |
< |
// We found an explicit EAM interaction. |
| 238 |
< |
// override all other metallic entries for this pair of atom types: |
| 239 |
< |
set<NonBondedInteraction*>::iterator it; |
| 240 |
< |
for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) { |
| 241 |
< |
InteractionFamily ifam = (*it)->getFamily(); |
| 242 |
< |
if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it); |
| 243 |
< |
} |
| 244 |
< |
interactions_[key].insert(eam_); |
| 245 |
< |
metExplicit = true; |
| 246 |
< |
} |
| 247 |
< |
|
| 248 |
< |
if (nbiType->isSC()) { |
| 249 |
< |
if (metExplicit) { |
| 250 |
< |
sprintf( painCave.errMsg, |
| 251 |
< |
"InteractionManager::initialize found more than one explicit\n" |
| 252 |
< |
"\tmetallic interaction for atom types %s - %s\n", |
| 253 |
< |
atype1->getName().c_str(), atype2->getName().c_str()); |
| 198 |
< |
painCave.severity = OPENMD_ERROR; |
| 199 |
< |
painCave.isFatal = 1; |
| 200 |
< |
simError(); |
| 201 |
< |
} |
| 202 |
< |
// We found an explicit Sutton-Chen interaction. |
| 203 |
< |
// override all other metallic entries for this pair of atom types: |
| 204 |
< |
set<NonBondedInteraction*>::iterator it; |
| 205 |
< |
for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) { |
| 206 |
< |
InteractionFamily ifam = (*it)->getFamily(); |
| 207 |
< |
if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it); |
| 232 |
> |
|
| 233 |
> |
if (nbiType->isSC()) { |
| 234 |
> |
if (metExplicit) { |
| 235 |
> |
sprintf( painCave.errMsg, |
| 236 |
> |
"InteractionManager::initialize found more than one " |
| 237 |
> |
"explicit\n" |
| 238 |
> |
"\tmetallic interaction for atom types %s - %s\n", |
| 239 |
> |
atype1->getName().c_str(), atype2->getName().c_str()); |
| 240 |
> |
painCave.severity = OPENMD_ERROR; |
| 241 |
> |
painCave.isFatal = 1; |
| 242 |
> |
simError(); |
| 243 |
> |
} |
| 244 |
> |
// We found an explicit Sutton-Chen interaction. |
| 245 |
> |
// override all other metallic entries for this pair of atom types: |
| 246 |
> |
set<NonBondedInteraction*>::iterator it; |
| 247 |
> |
for (it = interactions_[key].begin(); |
| 248 |
> |
it != interactions_[key].end(); ++it) { |
| 249 |
> |
InteractionFamily ifam = (*it)->getFamily(); |
| 250 |
> |
if (ifam == METALLIC_FAMILY) interactions_[key].erase(*it); |
| 251 |
> |
} |
| 252 |
> |
interactions_[key].insert(sc_); |
| 253 |
> |
metExplicit = true; |
| 254 |
|
} |
| 255 |
< |
interactions_[key].insert(sc_); |
| 256 |
< |
metExplicit = true; |
| 255 |
> |
|
| 256 |
> |
if (nbiType->isMAW()) { |
| 257 |
> |
if (vdwExplicit) { |
| 258 |
> |
sprintf( painCave.errMsg, |
| 259 |
> |
"InteractionManager::initialize found more than one " |
| 260 |
> |
"explicit\n" |
| 261 |
> |
"\tvan der Waals interaction for atom types %s - %s\n", |
| 262 |
> |
atype1->getName().c_str(), atype2->getName().c_str()); |
| 263 |
> |
painCave.severity = OPENMD_ERROR; |
| 264 |
> |
painCave.isFatal = 1; |
| 265 |
> |
simError(); |
| 266 |
> |
} |
| 267 |
> |
// We found an explicit MAW interaction. |
| 268 |
> |
// override all other vdw entries for this pair of atom types: |
| 269 |
> |
set<NonBondedInteraction*>::iterator it; |
| 270 |
> |
for (it = interactions_[key].begin(); |
| 271 |
> |
it != interactions_[key].end(); ++it) { |
| 272 |
> |
InteractionFamily ifam = (*it)->getFamily(); |
| 273 |
> |
if (ifam == VANDERWAALS_FAMILY) interactions_[key].erase(*it); |
| 274 |
> |
} |
| 275 |
> |
interactions_[key].insert(maw_); |
| 276 |
> |
vdwExplicit = true; |
| 277 |
> |
} |
| 278 |
|
} |
| 279 |
|
} |
| 280 |
|
} |
| 281 |
|
|
| 282 |
< |
// make sure every pair of atom types has a non-bonded interaction: |
| 283 |
< |
for (atype1 = atomTypes->beginType(i1); atype1 != NULL; |
| 284 |
< |
atype1 = atomTypes->nextType(i1)) { |
| 285 |
< |
for (atype2 = atomTypes->beginType(i2); atype2 != NULL; |
| 286 |
< |
atype2 = atomTypes->nextType(i2)) { |
| 282 |
> |
|
| 283 |
> |
// make sure every pair of atom types in this simulation has a |
| 284 |
> |
// non-bonded interaction: |
| 285 |
> |
|
| 286 |
> |
set<AtomType*> simTypes = info_->getSimulatedAtomTypes(); |
| 287 |
> |
set<AtomType*>::iterator it, jt; |
| 288 |
> |
for (it = simTypes.begin(); it != simTypes.end(); ++it) { |
| 289 |
> |
atype1 = (*it); |
| 290 |
> |
for (jt = simTypes.begin(); jt != simTypes.end(); ++jt) { |
| 291 |
> |
atype2 = (*jt); |
| 292 |
|
key = make_pair(atype1, atype2); |
| 293 |
|
|
| 294 |
|
if (interactions_[key].size() == 0) { |
| 302 |
|
} |
| 303 |
|
} |
| 304 |
|
} |
| 233 |
– |
} |
| 305 |
|
|
| 306 |
+ |
setupCutoffs(); |
| 307 |
+ |
setupSwitching(); |
| 308 |
+ |
setupNeighborlists(); |
| 309 |
|
|
| 310 |
< |
void InteractionManager::doPrePair(AtomType* atype1, |
| 311 |
< |
AtomType* atype2, |
| 312 |
< |
RealType rij, |
| 313 |
< |
RealType &rho_i_at_j, |
| 314 |
< |
RealType &rho_j_at_i) { |
| 310 |
> |
//int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0; |
| 311 |
> |
//int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0; |
| 312 |
> |
//notifyFortranCutoffs(&rCut_, &rSwitch_, &ljsp, &ljsf); |
| 313 |
> |
//notifyFortranSkinThickness(&skinThickness_); |
| 314 |
> |
|
| 315 |
> |
initialized_ = true; |
| 316 |
> |
} |
| 317 |
> |
|
| 318 |
> |
/** |
| 319 |
> |
* setupCutoffs |
| 320 |
> |
* |
| 321 |
> |
* Sets the values of cutoffRadius and cutoffMethod |
| 322 |
> |
* |
| 323 |
> |
* cutoffRadius : realType |
| 324 |
> |
* If the cutoffRadius was explicitly set, use that value. |
| 325 |
> |
* If the cutoffRadius was not explicitly set: |
| 326 |
> |
* Are there electrostatic atoms? Use 12.0 Angstroms. |
| 327 |
> |
* No electrostatic atoms? Poll the atom types present in the |
| 328 |
> |
* simulation for suggested cutoff values (e.g. 2.5 * sigma). |
| 329 |
> |
* Use the maximum suggested value that was found. |
| 330 |
> |
* |
| 331 |
> |
* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL) |
| 332 |
> |
* If cutoffMethod was explicitly set, use that choice. |
| 333 |
> |
* If cutoffMethod was not explicitly set, use SHIFTED_FORCE |
| 334 |
> |
*/ |
| 335 |
> |
void InteractionManager::setupCutoffs() { |
| 336 |
> |
|
| 337 |
> |
Globals* simParams_ = info_->getSimParams(); |
| 338 |
> |
|
| 339 |
> |
if (simParams_->haveCutoffRadius()) { |
| 340 |
> |
rCut_ = simParams_->getCutoffRadius(); |
| 341 |
> |
} else { |
| 342 |
> |
if (info_->usesElectrostaticAtoms()) { |
| 343 |
> |
sprintf(painCave.errMsg, |
| 344 |
> |
"InteractionManager::setupCutoffs: No value was set for the cutoffRadius.\n" |
| 345 |
> |
"\tOpenMD will use a default value of 12.0 angstroms" |
| 346 |
> |
"\tfor the cutoffRadius.\n"); |
| 347 |
> |
painCave.isFatal = 0; |
| 348 |
> |
painCave.severity = OPENMD_INFO; |
| 349 |
> |
simError(); |
| 350 |
> |
rCut_ = 12.0; |
| 351 |
> |
} else { |
| 352 |
> |
RealType thisCut; |
| 353 |
> |
set<AtomType*>::iterator i; |
| 354 |
> |
set<AtomType*> atomTypes; |
| 355 |
> |
atomTypes = info_->getSimulatedAtomTypes(); |
| 356 |
> |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
| 357 |
> |
thisCut = getSuggestedCutoffRadius((*i)); |
| 358 |
> |
rCut_ = max(thisCut, rCut_); |
| 359 |
> |
} |
| 360 |
> |
sprintf(painCave.errMsg, |
| 361 |
> |
"InteractionManager::setupCutoffs: No value was set for the cutoffRadius.\n" |
| 362 |
> |
"\tOpenMD will use %lf angstroms.\n", |
| 363 |
> |
rCut_); |
| 364 |
> |
painCave.isFatal = 0; |
| 365 |
> |
painCave.severity = OPENMD_INFO; |
| 366 |
> |
simError(); |
| 367 |
> |
} |
| 368 |
> |
} |
| 369 |
> |
|
| 370 |
> |
map<string, CutoffMethod> stringToCutoffMethod; |
| 371 |
> |
stringToCutoffMethod["HARD"] = HARD; |
| 372 |
> |
stringToCutoffMethod["SWITCHED"] = SWITCHED; |
| 373 |
> |
stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL; |
| 374 |
> |
stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE; |
| 375 |
> |
|
| 376 |
> |
if (simParams_->haveCutoffMethod()) { |
| 377 |
> |
string cutMeth = toUpperCopy(simParams_->getCutoffMethod()); |
| 378 |
> |
map<string, CutoffMethod>::iterator i; |
| 379 |
> |
i = stringToCutoffMethod.find(cutMeth); |
| 380 |
> |
if (i == stringToCutoffMethod.end()) { |
| 381 |
> |
sprintf(painCave.errMsg, |
| 382 |
> |
"InteractionManager::setupCutoffs: Could not find chosen cutoffMethod %s\n" |
| 383 |
> |
"\tShould be one of: " |
| 384 |
> |
"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n", |
| 385 |
> |
cutMeth.c_str()); |
| 386 |
> |
painCave.isFatal = 1; |
| 387 |
> |
painCave.severity = OPENMD_ERROR; |
| 388 |
> |
simError(); |
| 389 |
> |
} else { |
| 390 |
> |
cutoffMethod_ = i->second; |
| 391 |
> |
} |
| 392 |
> |
} else { |
| 393 |
> |
sprintf(painCave.errMsg, |
| 394 |
> |
"InteractionManager::setupCutoffs: No value was set for the cutoffMethod.\n" |
| 395 |
> |
"\tOpenMD will use SHIFTED_FORCE.\n"); |
| 396 |
> |
painCave.isFatal = 0; |
| 397 |
> |
painCave.severity = OPENMD_INFO; |
| 398 |
> |
simError(); |
| 399 |
> |
cutoffMethod_ = SHIFTED_FORCE; |
| 400 |
> |
} |
| 401 |
> |
} |
| 402 |
> |
|
| 403 |
> |
|
| 404 |
> |
/** |
| 405 |
> |
* setupSwitching |
| 406 |
> |
* |
| 407 |
> |
* Sets the values of switchingRadius and |
| 408 |
> |
* If the switchingRadius was explicitly set, use that value (but check it) |
| 409 |
> |
* If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_ |
| 410 |
> |
*/ |
| 411 |
> |
void InteractionManager::setupSwitching() { |
| 412 |
> |
Globals* simParams_ = info_->getSimParams(); |
| 413 |
> |
|
| 414 |
> |
if (simParams_->haveSwitchingRadius()) { |
| 415 |
> |
rSwitch_ = simParams_->getSwitchingRadius(); |
| 416 |
> |
if (rSwitch_ > rCut_) { |
| 417 |
> |
sprintf(painCave.errMsg, |
| 418 |
> |
"InteractionManager::setupSwitching: switchingRadius (%f) is larger than cutoffRadius(%f)\n", |
| 419 |
> |
rSwitch_, rCut_); |
| 420 |
> |
painCave.isFatal = 1; |
| 421 |
> |
painCave.severity = OPENMD_ERROR; |
| 422 |
> |
simError(); |
| 423 |
> |
} |
| 424 |
> |
} else { |
| 425 |
> |
rSwitch_ = 0.85 * rCut_; |
| 426 |
> |
sprintf(painCave.errMsg, |
| 427 |
> |
"InteractionManager::setupSwitching: No value was set for the switchingRadius.\n" |
| 428 |
> |
"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n" |
| 429 |
> |
"\tswitchingRadius = %f. for this simulation\n", rSwitch_); |
| 430 |
> |
painCave.isFatal = 0; |
| 431 |
> |
painCave.severity = OPENMD_WARNING; |
| 432 |
> |
simError(); |
| 433 |
> |
} |
| 434 |
|
|
| 435 |
+ |
if (simParams_->haveSwitchingFunctionType()) { |
| 436 |
+ |
string funcType = simParams_->getSwitchingFunctionType(); |
| 437 |
+ |
toUpper(funcType); |
| 438 |
+ |
if (funcType == "CUBIC") { |
| 439 |
+ |
sft_ = cubic; |
| 440 |
+ |
} else { |
| 441 |
+ |
if (funcType == "FIFTH_ORDER_POLYNOMIAL") { |
| 442 |
+ |
sft_ = fifth_order_poly; |
| 443 |
+ |
} else { |
| 444 |
+ |
// throw error |
| 445 |
+ |
sprintf( painCave.errMsg, |
| 446 |
+ |
"InteractionManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n" |
| 447 |
+ |
"\tswitchingFunctionType must be one of: " |
| 448 |
+ |
"\"cubic\" or \"fifth_order_polynomial\".", |
| 449 |
+ |
funcType.c_str() ); |
| 450 |
+ |
painCave.isFatal = 1; |
| 451 |
+ |
painCave.severity = OPENMD_ERROR; |
| 452 |
+ |
simError(); |
| 453 |
+ |
} |
| 454 |
+ |
} |
| 455 |
+ |
} |
| 456 |
+ |
|
| 457 |
+ |
switcher_->setSwitchType(sft_); |
| 458 |
+ |
switcher_->setSwitch(rSwitch_, rCut_); |
| 459 |
|
} |
| 460 |
+ |
|
| 461 |
+ |
/** |
| 462 |
+ |
* setupNeighborlists |
| 463 |
+ |
* |
| 464 |
+ |
* If the skinThickness was explicitly set, use that value (but check it) |
| 465 |
+ |
* If the skinThickness was not explicitly set: use 1.0 angstroms |
| 466 |
+ |
*/ |
| 467 |
+ |
void InteractionManager::setupNeighborlists() { |
| 468 |
+ |
|
| 469 |
+ |
Globals* simParams_ = info_->getSimParams(); |
| 470 |
|
|
| 471 |
< |
void InteractionManager::doPreForce(AtomType* atype, |
| 472 |
< |
RealType rho, |
| 473 |
< |
RealType &frho, |
| 474 |
< |
RealType &dfrhodrho) { |
| 475 |
< |
} |
| 471 |
> |
if (simParams_->haveSkinThickness()) { |
| 472 |
> |
skinThickness_ = simParams_->getSkinThickness(); |
| 473 |
> |
} else { |
| 474 |
> |
skinThickness_ = 1.0; |
| 475 |
> |
sprintf(painCave.errMsg, |
| 476 |
> |
"InteractionManager::setupNeighborlists: No value was set for the skinThickness.\n" |
| 477 |
> |
"\tOpenMD will use a default value of %f Angstroms\n" |
| 478 |
> |
"\tfor this simulation\n", skinThickness_); |
| 479 |
> |
painCave.severity = OPENMD_INFO; |
| 480 |
> |
painCave.isFatal = 0; |
| 481 |
> |
simError(); |
| 482 |
> |
} |
| 483 |
|
|
| 484 |
< |
void InteractionManager::doSkipCorrection(AtomType* atype1, |
| 251 |
< |
AtomType* atype2, |
| 252 |
< |
Vector3d d, |
| 253 |
< |
RealType rij, |
| 254 |
< |
RealType &skippedCharge1, |
| 255 |
< |
RealType &skippedCharge2, |
| 256 |
< |
RealType sw, |
| 257 |
< |
RealType electroMult, |
| 258 |
< |
RealType &pot, |
| 259 |
< |
RealType &vpair, |
| 260 |
< |
Vector3d &f1, |
| 261 |
< |
Mat3x3d eFrame1, |
| 262 |
< |
Mat3x3d eFrame2, |
| 263 |
< |
Vector3d &t1, |
| 264 |
< |
Vector3d &t2) { |
| 484 |
> |
listRadius_ = rCut_ + skinThickness_; |
| 485 |
|
} |
| 266 |
– |
|
| 267 |
– |
void InteractionManager::doSelfCorrection(AtomType* atype, |
| 268 |
– |
Mat3x3d eFrame, |
| 269 |
– |
RealType skippedCharge, |
| 270 |
– |
RealType &pot, |
| 271 |
– |
Vector3d &t) { |
| 272 |
– |
} |
| 486 |
|
|
| 487 |
< |
void InteractionManager::do_prepair(int *atid1, int *atid2, RealType *rij, RealType *rho_i_at_j, RealType *rho_j_at_i){ |
| 487 |
> |
|
| 488 |
> |
void InteractionManager::doPrePair(InteractionData idat){ |
| 489 |
|
|
| 490 |
|
if (!initialized_) initialize(); |
| 491 |
< |
AtomType* atype1 = typeMap_[*atid1]; |
| 492 |
< |
AtomType* atype2 = typeMap_[*atid2]; |
| 491 |
> |
|
| 492 |
> |
set<NonBondedInteraction*>::iterator it; |
| 493 |
> |
|
| 494 |
> |
for (it = interactions_[ *(idat.atypes) ].begin(); |
| 495 |
> |
it != interactions_[ *(idat.atypes) ].end(); ++it){ |
| 496 |
> |
if ((*it)->getFamily() == METALLIC_FAMILY) { |
| 497 |
> |
dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat); |
| 498 |
> |
} |
| 499 |
> |
} |
| 500 |
|
|
| 280 |
– |
doPrePair(atype1, atype2, *rij, *rho_i_at_j, *rho_j_at_i); |
| 281 |
– |
|
| 501 |
|
return; |
| 502 |
|
} |
| 503 |
+ |
|
| 504 |
+ |
void InteractionManager::doPreForce(SelfData sdat){ |
| 505 |
|
|
| 506 |
< |
void InteractionManager::do_preforce(int *atid, RealType *rho, RealType *frho, RealType *dfrhodrho){ |
| 286 |
< |
|
| 287 |
< |
if (!initialized_) initialize(); |
| 288 |
< |
AtomType* atype = typeMap_[*atid]; |
| 289 |
< |
|
| 290 |
< |
doPreForce(atype, *rho, *frho, *dfrhodrho); |
| 506 |
> |
if (!initialized_) initialize(); |
| 507 |
|
|
| 508 |
+ |
pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype); |
| 509 |
+ |
set<NonBondedInteraction*>::iterator it; |
| 510 |
+ |
|
| 511 |
+ |
for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){ |
| 512 |
+ |
if ((*it)->getFamily() == METALLIC_FAMILY) { |
| 513 |
+ |
dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat); |
| 514 |
+ |
} |
| 515 |
+ |
} |
| 516 |
+ |
|
| 517 |
|
return; |
| 518 |
|
} |
| 519 |
|
|
| 520 |
< |
void InteractionManager::do_pair(int *atid1, int *atid2, RealType *d, RealType *r, RealType *r2, RealType *rcut, RealType *sw, RealType *vdwMult,RealType *electroMult, RealType *pot, RealType *vpair, RealType *f1, RealType *eFrame1, RealType *eFrame2, RealType *A1, RealType *A2, RealType *t1, RealType *t2, RealType *rho1, RealType *rho2, RealType *dfrho1, RealType *dfrho2, RealType *fshift1, RealType *fshift2){ |
| 521 |
< |
|
| 520 |
> |
void InteractionManager::doPair(InteractionData idat){ |
| 521 |
> |
|
| 522 |
|
if (!initialized_) initialize(); |
| 523 |
< |
|
| 299 |
< |
InteractionData idat; |
| 300 |
< |
|
| 301 |
< |
idat.atype1 = typeMap_[*atid1]; |
| 302 |
< |
idat.atype2 = typeMap_[*atid2]; |
| 303 |
< |
idat.d = Vector3d(d); |
| 304 |
< |
idat.rij = *r; |
| 305 |
< |
idat.r2 = *r2; |
| 306 |
< |
idat.rcut = *rcut; |
| 307 |
< |
idat.sw = *sw; |
| 308 |
< |
idat.vdwMult = *vdwMult; |
| 309 |
< |
idat.electroMult = *electroMult; |
| 310 |
< |
idat.pot = *pot; |
| 311 |
< |
idat.vpair = *vpair; |
| 312 |
< |
idat.f1 = Vector3d(f1); |
| 313 |
< |
idat.eFrame1 = Mat3x3d(eFrame1); |
| 314 |
< |
idat.eFrame2 = Mat3x3d(eFrame2); |
| 315 |
< |
idat.A1 = RotMat3x3d(A1); |
| 316 |
< |
idat.A2 = RotMat3x3d(A2); |
| 317 |
< |
idat.t1 = Vector3d(t1); |
| 318 |
< |
idat.t2 = Vector3d(t2); |
| 319 |
< |
idat.rho1 = *rho1; |
| 320 |
< |
idat.rho2 = *rho2; |
| 321 |
< |
idat.dfrho1 = *dfrho1; |
| 322 |
< |
idat.dfrho2 = *dfrho2; |
| 323 |
< |
idat.fshift1 = *fshift1; |
| 324 |
< |
idat.fshift2 = *fshift2; |
| 325 |
< |
|
| 326 |
< |
pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2); |
| 523 |
> |
|
| 524 |
|
set<NonBondedInteraction*>::iterator it; |
| 525 |
|
|
| 526 |
< |
for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) |
| 526 |
> |
for (it = interactions_[ *(idat.atypes) ].begin(); |
| 527 |
> |
it != interactions_[ *(idat.atypes) ].end(); ++it) |
| 528 |
|
(*it)->calcForce(idat); |
| 529 |
|
|
| 332 |
– |
f1[0] = idat.f1.x(); |
| 333 |
– |
f1[1] = idat.f1.y(); |
| 334 |
– |
f1[2] = idat.f1.z(); |
| 335 |
– |
|
| 336 |
– |
t1[0] = idat.t1.x(); |
| 337 |
– |
t1[1] = idat.t1.y(); |
| 338 |
– |
t1[2] = idat.t1.z(); |
| 339 |
– |
|
| 340 |
– |
t2[0] = idat.t2.x(); |
| 341 |
– |
t2[1] = idat.t2.y(); |
| 342 |
– |
t2[2] = idat.t2.z(); |
| 343 |
– |
|
| 530 |
|
return; |
| 531 |
|
} |
| 532 |
|
|
| 533 |
< |
void InteractionManager::do_skip_correction(int *atid1, int *atid2, RealType *d, RealType *r, RealType *skippedCharge1, RealType *skippedCharge2, RealType *sw, RealType *electroMult, RealType *pot, RealType *vpair, RealType *f1, RealType *eFrame1, RealType *eFrame2, RealType *t1, RealType *t2){ |
| 533 |
> |
void InteractionManager::doSkipCorrection(InteractionData idat){ |
| 534 |
|
|
| 535 |
< |
if (!initialized_) initialize(); |
| 350 |
< |
|
| 351 |
< |
AtomType* atype1 = typeMap_[*atid1]; |
| 352 |
< |
AtomType* atype2 = typeMap_[*atid2]; |
| 353 |
< |
Vector3d disp(d); |
| 354 |
< |
Vector3d frc(f1); |
| 355 |
< |
Vector3d trq1(t1); |
| 356 |
< |
Vector3d trq2(t2); |
| 357 |
< |
Mat3x3d eFi(eFrame1); |
| 358 |
< |
Mat3x3d eFj(eFrame2); |
| 359 |
< |
|
| 360 |
< |
doSkipCorrection(atype1, atype2, disp, *r, *skippedCharge1, *skippedCharge2, *sw, |
| 361 |
< |
*electroMult, *pot, *vpair, frc, eFi, eFj, trq1, trq2); |
| 362 |
< |
|
| 363 |
< |
f1[0] = frc.x(); |
| 364 |
< |
f1[1] = frc.y(); |
| 365 |
< |
f1[2] = frc.z(); |
| 535 |
> |
if (!initialized_) initialize(); |
| 536 |
|
|
| 537 |
< |
t1[0] = trq1.x(); |
| 368 |
< |
t1[1] = trq1.y(); |
| 369 |
< |
t1[2] = trq1.z(); |
| 370 |
< |
|
| 371 |
< |
t2[0] = trq2.x(); |
| 372 |
< |
t2[1] = trq2.y(); |
| 373 |
< |
t2[2] = trq2.z(); |
| 537 |
> |
set<NonBondedInteraction*>::iterator it; |
| 538 |
|
|
| 539 |
< |
return; |
| 539 |
> |
for (it = interactions_[ *(idat.atypes) ].begin(); |
| 540 |
> |
it != interactions_[ *(idat.atypes) ].end(); ++it){ |
| 541 |
> |
if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) { |
| 542 |
> |
dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(idat); |
| 543 |
> |
} |
| 544 |
> |
} |
| 545 |
> |
|
| 546 |
> |
return; |
| 547 |
|
} |
| 548 |
|
|
| 549 |
< |
void InteractionManager::do_self_correction(int *atid, RealType *eFrame, RealType *skippedCharge, RealType *pot, RealType *t){ |
| 549 |
> |
void InteractionManager::doSelfCorrection(SelfData sdat){ |
| 550 |
|
|
| 551 |
|
if (!initialized_) initialize(); |
| 552 |
< |
|
| 553 |
< |
AtomType* atype = typeMap_[*atid]; |
| 554 |
< |
Mat3x3d eFi(eFrame); |
| 384 |
< |
Vector3d trq1(t); |
| 385 |
< |
|
| 386 |
< |
doSelfCorrection(atype, eFi, *skippedCharge, *pot, trq1); |
| 552 |
> |
|
| 553 |
> |
pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype); |
| 554 |
> |
set<NonBondedInteraction*>::iterator it; |
| 555 |
|
|
| 556 |
< |
t[0] = trq1.x(); |
| 557 |
< |
t[1] = trq1.y(); |
| 558 |
< |
t[2] = trq1.z(); |
| 559 |
< |
|
| 560 |
< |
return; |
| 556 |
> |
for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){ |
| 557 |
> |
if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) { |
| 558 |
> |
dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat); |
| 559 |
> |
} |
| 560 |
> |
} |
| 561 |
> |
|
| 562 |
> |
return; |
| 563 |
|
} |
| 564 |
|
|
| 565 |
< |
} //end namespace OpenMD |
| 566 |
< |
|
| 397 |
< |
extern "C" { |
| 398 |
< |
|
| 399 |
< |
#define fortranDoPrePair FC_FUNC(do_prepair, DO_PREPAIR) |
| 400 |
< |
#define fortranDoPreForce FC_FUNC(do_preforce, DO_PREFORCE) |
| 401 |
< |
#define fortranDoPair FC_FUNC(do_pair, DO_PAIR) |
| 402 |
< |
#define fortranDoSkipCorrection FC_FUNC(do_skip_correction, DO_SKIP_CORRECTION) |
| 403 |
< |
#define fortranDoSelfCorrection FC_FUNC(do_self_correction, DO_SELF_CORRECTION) |
| 404 |
< |
#define fortranGetCutoff FC_FUNC(get_cutoff, GET_CUTOFF) |
| 405 |
< |
|
| 406 |
< |
void fortranDoPrePair(int *atid1, int *atid2, RealType *rij, |
| 407 |
< |
RealType *rho_i_at_j, RealType *rho_j_at_i) { |
| 408 |
< |
|
| 409 |
< |
return OpenMD::InteractionManager::Instance()->do_prepair(atid1, atid2, rij, |
| 410 |
< |
rho_i_at_j, |
| 411 |
< |
rho_j_at_i); |
| 412 |
< |
} |
| 413 |
< |
void fortranDoPreforce(int *atid, RealType *rho, RealType *frho, |
| 414 |
< |
RealType *dfrhodrho) { |
| 565 |
> |
RealType InteractionManager::getSuggestedCutoffRadius(int *atid) { |
| 566 |
> |
if (!initialized_) initialize(); |
| 567 |
|
|
| 568 |
< |
return OpenMD::InteractionManager::Instance()->do_preforce(atid, rho, frho, |
| 417 |
< |
dfrhodrho); |
| 418 |
< |
} |
| 419 |
< |
|
| 420 |
< |
void fortranDoPair(int *atid1, int *atid2, RealType *d, RealType *r, |
| 421 |
< |
RealType *r2, RealType *rcut, RealType *sw, RealType *vdwMult, |
| 422 |
< |
RealType *electroMult, RealType *pot, RealType *vpair, RealType *f1, |
| 423 |
< |
RealType *eFrame1, RealType *eFrame2, RealType *A1, RealType *A2, |
| 424 |
< |
RealType *t1, RealType *t2, |
| 425 |
< |
RealType *rho1, RealType *rho2, RealType *dfrho1, RealType *dfrho2, |
| 426 |
< |
RealType *fshift1, RealType *fshift2){ |
| 427 |
< |
|
| 428 |
< |
return OpenMD::InteractionManager::Instance()->do_pair(atid1, atid2, d, r, r2, rcut, |
| 429 |
< |
sw, vdwMult, electroMult, pot, |
| 430 |
< |
vpair, f1, eFrame1, eFrame2, |
| 431 |
< |
A1, A2, t1, t2, rho1, rho2, |
| 432 |
< |
dfrho1, dfrho2, fshift1, fshift2); |
| 433 |
< |
} |
| 568 |
> |
AtomType* atype = typeMap_[*atid]; |
| 569 |
|
|
| 570 |
< |
void fortranDoSkipCorrection(int *atid1, int *atid2, RealType *d, RealType *r, |
| 571 |
< |
RealType *skippedCharge1, RealType *skippedCharge2, |
| 572 |
< |
RealType *sw, RealType *electroMult, RealType *pot, |
| 438 |
< |
RealType *vpair, RealType *f1, |
| 439 |
< |
RealType *eFrame1, RealType *eFrame2, |
| 440 |
< |
RealType *t1, RealType *t2){ |
| 570 |
> |
pair<AtomType*, AtomType*> key = make_pair(atype, atype); |
| 571 |
> |
set<NonBondedInteraction*>::iterator it; |
| 572 |
> |
RealType cutoff = 0.0; |
| 573 |
|
|
| 574 |
< |
return OpenMD::InteractionManager::Instance()->do_skip_correction(atid1, atid2, d, r, |
| 575 |
< |
skippedCharge1, |
| 576 |
< |
skippedCharge2, |
| 445 |
< |
sw, electroMult, pot, |
| 446 |
< |
vpair, f1, eFrame1, |
| 447 |
< |
eFrame2, t1, t2); |
| 574 |
> |
for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) |
| 575 |
> |
cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key)); |
| 576 |
> |
return cutoff; |
| 577 |
|
} |
| 578 |
|
|
| 579 |
< |
void fortranDoSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge, |
| 580 |
< |
RealType *pot, RealType *t) { |
| 579 |
> |
RealType InteractionManager::getSuggestedCutoffRadius(AtomType* atype) { |
| 580 |
> |
if (!initialized_) initialize(); |
| 581 |
|
|
| 582 |
< |
return OpenMD::InteractionManager::Instance()->do_self_correction(atid, eFrame, |
| 583 |
< |
skippedCharge, |
| 584 |
< |
pot, t); |
| 582 |
> |
pair<AtomType*, AtomType*> key = make_pair(atype, atype); |
| 583 |
> |
set<NonBondedInteraction*>::iterator it; |
| 584 |
> |
RealType cutoff = 0.0; |
| 585 |
> |
|
| 586 |
> |
for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) |
| 587 |
> |
cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key)); |
| 588 |
> |
return cutoff; |
| 589 |
|
} |
| 590 |
< |
RealType fortranGetCutoff() { |
| 458 |
< |
return OpenMD::InteractionManager::Instance()->getCutoff(); |
| 459 |
< |
} |
| 460 |
< |
} |
| 590 |
> |
} //end namespace OpenMD |
