| 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). |
| 38 |
> |
* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008). |
| 39 |
> |
* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010). |
| 40 |
> |
* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011). |
| 41 |
|
*/ |
| 42 |
|
|
| 43 |
|
#include "nonbonded/InteractionManager.hpp" |
| 43 |
– |
#include "UseTheForce/doForces_interface.h" |
| 44 |
|
|
| 45 |
|
namespace OpenMD { |
| 46 |
|
|
| 47 |
< |
InteractionManager* InteractionManager::_instance = NULL; |
| 48 |
< |
SimInfo* InteractionManager::info_ = NULL; |
| 49 |
< |
bool InteractionManager::initialized_ = false; |
| 47 |
> |
InteractionManager::InteractionManager() { |
| 48 |
|
|
| 49 |
< |
RealType InteractionManager::rCut_ = 0.0; |
| 50 |
< |
RealType InteractionManager::rSwitch_ = 0.0; |
| 51 |
< |
RealType InteractionManager::skinThickness_ = 0.0; |
| 52 |
< |
RealType InteractionManager::listRadius_ = 0.0; |
| 53 |
< |
CutoffMethod InteractionManager::cutoffMethod_ = SHIFTED_FORCE; |
| 54 |
< |
SwitchingFunctionType InteractionManager::sft_ = cubic; |
| 55 |
< |
RealType InteractionManager::vdwScale_[4] = {0.0, 0.0, 0.0, 0.0}; |
| 56 |
< |
RealType InteractionManager::electrostaticScale_[4] = {0.0, 0.0, 0.0, 0.0}; |
| 49 |
> |
initialized_ = false; |
| 50 |
> |
|
| 51 |
> |
lj_ = new LJ(); |
| 52 |
> |
gb_ = new GB(); |
| 53 |
> |
sticky_ = new Sticky(); |
| 54 |
> |
morse_ = new Morse(); |
| 55 |
> |
repulsivePower_ = new RepulsivePower(); |
| 56 |
> |
eam_ = new EAM(); |
| 57 |
> |
sc_ = new SC(); |
| 58 |
> |
electrostatic_ = new Electrostatic(); |
| 59 |
> |
maw_ = new MAW(); |
| 60 |
> |
} |
| 61 |
|
|
| 62 |
< |
map<int, AtomType*> InteractionManager::typeMap_; |
| 63 |
< |
map<pair<AtomType*, AtomType*>, set<NonBondedInteraction*> > InteractionManager::interactions_; |
| 64 |
< |
|
| 65 |
< |
LJ* InteractionManager::lj_ = new LJ(); |
| 66 |
< |
GB* InteractionManager::gb_ = new GB(); |
| 67 |
< |
Sticky* InteractionManager::sticky_ = new Sticky(); |
| 68 |
< |
Morse* InteractionManager::morse_ = new Morse(); |
| 69 |
< |
EAM* InteractionManager::eam_ = new EAM(); |
| 70 |
< |
SC* InteractionManager::sc_ = new SC(); |
| 71 |
< |
Electrostatic* InteractionManager::electrostatic_ = new Electrostatic(); |
| 70 |
< |
MAW* InteractionManager::maw_ = new MAW(); |
| 71 |
< |
SwitchingFunction* InteractionManager::switcher_ = new SwitchingFunction(); |
| 72 |
< |
|
| 73 |
< |
InteractionManager* InteractionManager::Instance() { |
| 74 |
< |
if (!_instance) { |
| 75 |
< |
_instance = new InteractionManager(); |
| 76 |
< |
} |
| 77 |
< |
return _instance; |
| 62 |
> |
InteractionManager::~InteractionManager() { |
| 63 |
> |
delete lj_; |
| 64 |
> |
delete gb_; |
| 65 |
> |
delete sticky_; |
| 66 |
> |
delete morse_; |
| 67 |
> |
delete repulsivePower_; |
| 68 |
> |
delete eam_; |
| 69 |
> |
delete sc_; |
| 70 |
> |
delete electrostatic_; |
| 71 |
> |
delete maw_; |
| 72 |
|
} |
| 73 |
|
|
| 74 |
|
void InteractionManager::initialize() { |
| 75 |
< |
|
| 75 |
> |
|
| 76 |
> |
if (initialized_) return; |
| 77 |
> |
|
| 78 |
|
ForceField* forceField_ = info_->getForceField(); |
| 79 |
|
|
| 80 |
|
lj_->setForceField(forceField_); |
| 83 |
|
eam_->setForceField(forceField_); |
| 84 |
|
sc_->setForceField(forceField_); |
| 85 |
|
morse_->setForceField(forceField_); |
| 86 |
+ |
electrostatic_->setSimInfo(info_); |
| 87 |
|
electrostatic_->setForceField(forceField_); |
| 88 |
|
maw_->setForceField(forceField_); |
| 89 |
< |
|
| 93 |
< |
ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 94 |
< |
|
| 95 |
< |
// Force fields can set options on how to scale van der Waals and electrostatic |
| 96 |
< |
// interactions for atoms connected via bonds, bends and torsions |
| 97 |
< |
// in this case the topological distance between atoms is: |
| 98 |
< |
// 0 = the atom itself |
| 99 |
< |
// 1 = bonded together |
| 100 |
< |
// 2 = connected via a bend |
| 101 |
< |
// 3 = connected via a torsion |
| 89 |
> |
repulsivePower_->setForceField(forceField_); |
| 90 |
|
|
| 103 |
– |
vdwScale_[0] = 0.0; |
| 104 |
– |
vdwScale_[1] = fopts.getvdw12scale(); |
| 105 |
– |
vdwScale_[2] = fopts.getvdw13scale(); |
| 106 |
– |
vdwScale_[3] = fopts.getvdw14scale(); |
| 107 |
– |
|
| 108 |
– |
electrostaticScale_[0] = 0.0; |
| 109 |
– |
electrostaticScale_[1] = fopts.getelectrostatic12scale(); |
| 110 |
– |
electrostaticScale_[2] = fopts.getelectrostatic13scale(); |
| 111 |
– |
electrostaticScale_[3] = fopts.getelectrostatic14scale(); |
| 112 |
– |
|
| 91 |
|
ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); |
| 92 |
|
ForceField::AtomTypeContainer::MapTypeIterator i1, i2; |
| 93 |
|
AtomType* atype1; |
| 94 |
|
AtomType* atype2; |
| 95 |
|
pair<AtomType*, AtomType*> key; |
| 118 |
– |
pair<set<NonBondedInteraction*>::iterator, bool> ret; |
| 96 |
|
|
| 97 |
|
for (atype1 = atomTypes->beginType(i1); atype1 != NULL; |
| 98 |
|
atype1 = atomTypes->nextType(i1)) { |
| 99 |
|
|
| 100 |
|
// add it to the map: |
| 124 |
– |
AtomTypeProperties atp = atype1->getATP(); |
| 101 |
|
|
| 102 |
|
pair<map<int,AtomType*>::iterator,bool> ret; |
| 103 |
< |
ret = typeMap_.insert( pair<int, AtomType*>(atp.ident, atype1) ); |
| 103 |
> |
ret = typeMap_.insert( pair<int, AtomType*>(atype1->getIdent(), atype1) ); |
| 104 |
|
if (ret.second == false) { |
| 105 |
|
sprintf( painCave.errMsg, |
| 106 |
|
"InteractionManager already had a previous entry with ident %d\n", |
| 107 |
< |
atp.ident); |
| 107 |
> |
atype1->getIdent()); |
| 108 |
|
painCave.severity = OPENMD_INFO; |
| 109 |
|
painCave.isFatal = 0; |
| 110 |
|
simError(); |
| 119 |
|
|
| 120 |
|
for( it2 = typeMap_.begin(); it2 != typeMap_.end(); ++it2) { |
| 121 |
|
atype2 = (*it2).second; |
| 122 |
< |
|
| 147 |
< |
bool vdwExplicit = false; |
| 148 |
< |
bool metExplicit = false; |
| 149 |
< |
bool hbExplicit = false; |
| 150 |
< |
|
| 122 |
> |
|
| 123 |
|
key = make_pair(atype1, atype2); |
| 124 |
|
|
| 125 |
|
if (atype1->isLennardJones() && atype2->isLennardJones()) { |
| 154 |
|
|
| 155 |
|
if (nbiType != NULL) { |
| 156 |
|
|
| 157 |
+ |
bool vdwExplicit = false; |
| 158 |
+ |
bool metExplicit = false; |
| 159 |
+ |
// bool hbExplicit = false; |
| 160 |
+ |
|
| 161 |
|
if (nbiType->isLennardJones()) { |
| 162 |
|
// We found an explicit Lennard-Jones interaction. |
| 163 |
|
// override all other vdw entries for this pair of atom types: |
| 193 |
|
interactions_[key].insert(morse_); |
| 194 |
|
vdwExplicit = true; |
| 195 |
|
} |
| 196 |
+ |
|
| 197 |
+ |
if (nbiType->isRepulsivePower()) { |
| 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 RepulsivePower 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(repulsivePower_); |
| 217 |
+ |
vdwExplicit = true; |
| 218 |
+ |
} |
| 219 |
|
|
| 220 |
+ |
|
| 221 |
|
if (nbiType->isEAM()) { |
| 222 |
|
// We found an explicit EAM interaction. |
| 223 |
|
// override all other metallic entries for this pair of atom types: |
| 281 |
|
} |
| 282 |
|
|
| 283 |
|
|
| 284 |
< |
// make sure every pair of atom types in this simulation has a |
| 285 |
< |
// non-bonded interaction: |
| 284 |
> |
// Make sure every pair of atom types in this simulation has a |
| 285 |
> |
// non-bonded interaction. If not, just inform the user. |
| 286 |
|
|
| 287 |
|
set<AtomType*> simTypes = info_->getSimulatedAtomTypes(); |
| 288 |
|
set<AtomType*>::iterator it, jt; |
| 289 |
+ |
|
| 290 |
|
for (it = simTypes.begin(); it != simTypes.end(); ++it) { |
| 291 |
|
atype1 = (*it); |
| 292 |
< |
for (jt = simTypes.begin(); jt != simTypes.end(); ++jt) { |
| 292 |
> |
for (jt = it; jt != simTypes.end(); ++jt) { |
| 293 |
|
atype2 = (*jt); |
| 294 |
|
key = make_pair(atype1, atype2); |
| 295 |
|
|
| 296 |
|
if (interactions_[key].size() == 0) { |
| 297 |
|
sprintf( painCave.errMsg, |
| 298 |
< |
"InteractionManager unable to find an appropriate non-bonded\n" |
| 299 |
< |
"\tinteraction for atom types %s - %s\n", |
| 298 |
> |
"InteractionManager could not find a matching non-bonded\n" |
| 299 |
> |
"\tinteraction for atom types %s - %s\n" |
| 300 |
> |
"\tProceeding without this interaction.\n", |
| 301 |
|
atype1->getName().c_str(), atype2->getName().c_str()); |
| 302 |
|
painCave.severity = OPENMD_INFO; |
| 303 |
< |
painCave.isFatal = 1; |
| 303 |
> |
painCave.isFatal = 0; |
| 304 |
|
simError(); |
| 305 |
|
} |
| 306 |
|
} |
| 307 |
|
} |
| 308 |
|
|
| 307 |
– |
setupCutoffs(); |
| 308 |
– |
setupSwitching(); |
| 309 |
– |
setupNeighborlists(); |
| 310 |
– |
notifyFortranSkinThickness(&skinThickness_); |
| 311 |
– |
|
| 312 |
– |
int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0; |
| 313 |
– |
int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0; |
| 314 |
– |
notifyFortranCutoffs(&rCut_, &rSwitch_, &ljsp, &ljsf); |
| 315 |
– |
|
| 316 |
– |
int isError; |
| 317 |
– |
initFortranFF(&isError); |
| 318 |
– |
|
| 309 |
|
initialized_ = true; |
| 310 |
|
} |
| 321 |
– |
|
| 322 |
– |
/** |
| 323 |
– |
* setupCutoffs |
| 324 |
– |
* |
| 325 |
– |
* Sets the values of cutoffRadius and cutoffMethod |
| 326 |
– |
* |
| 327 |
– |
* cutoffRadius : realType |
| 328 |
– |
* If the cutoffRadius was explicitly set, use that value. |
| 329 |
– |
* If the cutoffRadius was not explicitly set: |
| 330 |
– |
* Are there electrostatic atoms? Use 12.0 Angstroms. |
| 331 |
– |
* No electrostatic atoms? Poll the atom types present in the |
| 332 |
– |
* simulation for suggested cutoff values (e.g. 2.5 * sigma). |
| 333 |
– |
* Use the maximum suggested value that was found. |
| 334 |
– |
* |
| 335 |
– |
* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL) |
| 336 |
– |
* If cutoffMethod was explicitly set, use that choice. |
| 337 |
– |
* If cutoffMethod was not explicitly set, use SHIFTED_FORCE |
| 338 |
– |
*/ |
| 339 |
– |
void InteractionManager::setupCutoffs() { |
| 340 |
– |
|
| 341 |
– |
Globals* simParams_ = info_->getSimParams(); |
| 342 |
– |
|
| 343 |
– |
if (simParams_->haveCutoffRadius()) { |
| 344 |
– |
rCut_ = simParams_->getCutoffRadius(); |
| 345 |
– |
} else { |
| 346 |
– |
if (info_->usesElectrostaticAtoms()) { |
| 347 |
– |
sprintf(painCave.errMsg, |
| 348 |
– |
"InteractionManager::setupCutoffs: No value was set for the cutoffRadius.\n" |
| 349 |
– |
"\tOpenMD will use a default value of 12.0 angstroms" |
| 350 |
– |
"\tfor the cutoffRadius.\n"); |
| 351 |
– |
painCave.isFatal = 0; |
| 352 |
– |
painCave.severity = OPENMD_INFO; |
| 353 |
– |
simError(); |
| 354 |
– |
rCut_ = 12.0; |
| 355 |
– |
} else { |
| 356 |
– |
RealType thisCut; |
| 357 |
– |
set<AtomType*>::iterator i; |
| 358 |
– |
set<AtomType*> atomTypes; |
| 359 |
– |
atomTypes = info_->getSimulatedAtomTypes(); |
| 360 |
– |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
| 361 |
– |
thisCut = getSuggestedCutoffRadius((*i)); |
| 362 |
– |
rCut_ = max(thisCut, rCut_); |
| 363 |
– |
} |
| 364 |
– |
sprintf(painCave.errMsg, |
| 365 |
– |
"InteractionManager::setupCutoffs: No value was set for the cutoffRadius.\n" |
| 366 |
– |
"\tOpenMD will use %lf angstroms.\n", |
| 367 |
– |
rCut_); |
| 368 |
– |
painCave.isFatal = 0; |
| 369 |
– |
painCave.severity = OPENMD_INFO; |
| 370 |
– |
simError(); |
| 371 |
– |
} |
| 372 |
– |
} |
| 311 |
|
|
| 312 |
< |
map<string, CutoffMethod> stringToCutoffMethod; |
| 375 |
< |
stringToCutoffMethod["HARD"] = HARD; |
| 376 |
< |
stringToCutoffMethod["SWITCHED"] = SWITCHED; |
| 377 |
< |
stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL; |
| 378 |
< |
stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE; |
| 379 |
< |
|
| 380 |
< |
if (simParams_->haveCutoffMethod()) { |
| 381 |
< |
string cutMeth = toUpperCopy(simParams_->getCutoffMethod()); |
| 382 |
< |
map<string, CutoffMethod>::iterator i; |
| 383 |
< |
i = stringToCutoffMethod.find(cutMeth); |
| 384 |
< |
if (i == stringToCutoffMethod.end()) { |
| 385 |
< |
sprintf(painCave.errMsg, |
| 386 |
< |
"InteractionManager::setupCutoffs: Could not find chosen cutoffMethod %s\n" |
| 387 |
< |
"\tShould be one of: " |
| 388 |
< |
"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n", |
| 389 |
< |
cutMeth.c_str()); |
| 390 |
< |
painCave.isFatal = 1; |
| 391 |
< |
painCave.severity = OPENMD_ERROR; |
| 392 |
< |
simError(); |
| 393 |
< |
} else { |
| 394 |
< |
cutoffMethod_ = i->second; |
| 395 |
< |
} |
| 396 |
< |
} else { |
| 397 |
< |
sprintf(painCave.errMsg, |
| 398 |
< |
"InteractionManager::setupCutoffs: No value was set for the cutoffMethod.\n" |
| 399 |
< |
"\tOpenMD will use SHIFTED_FORCE.\n"); |
| 400 |
< |
painCave.isFatal = 0; |
| 401 |
< |
painCave.severity = OPENMD_INFO; |
| 402 |
< |
simError(); |
| 403 |
< |
cutoffMethod_ = SHIFTED_FORCE; |
| 404 |
< |
} |
| 405 |
< |
} |
| 406 |
< |
|
| 407 |
< |
|
| 408 |
< |
/** |
| 409 |
< |
* setupSwitching |
| 410 |
< |
* |
| 411 |
< |
* Sets the values of switchingRadius and |
| 412 |
< |
* If the switchingRadius was explicitly set, use that value (but check it) |
| 413 |
< |
* If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_ |
| 414 |
< |
*/ |
| 415 |
< |
void InteractionManager::setupSwitching() { |
| 416 |
< |
Globals* simParams_ = info_->getSimParams(); |
| 417 |
< |
|
| 418 |
< |
if (simParams_->haveSwitchingRadius()) { |
| 419 |
< |
rSwitch_ = simParams_->getSwitchingRadius(); |
| 420 |
< |
if (rSwitch_ > rCut_) { |
| 421 |
< |
sprintf(painCave.errMsg, |
| 422 |
< |
"InteractionManager::setupSwitching: switchingRadius (%f) is larger than cutoffRadius(%f)\n", |
| 423 |
< |
rSwitch_, rCut_); |
| 424 |
< |
painCave.isFatal = 1; |
| 425 |
< |
painCave.severity = OPENMD_ERROR; |
| 426 |
< |
simError(); |
| 427 |
< |
} |
| 428 |
< |
} else { |
| 429 |
< |
rSwitch_ = 0.85 * rCut_; |
| 430 |
< |
sprintf(painCave.errMsg, |
| 431 |
< |
"InteractionManager::setupSwitching: No value was set for the switchingRadius.\n" |
| 432 |
< |
"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n" |
| 433 |
< |
"\tswitchingRadius = %f. for this simulation\n", rSwitch_); |
| 434 |
< |
painCave.isFatal = 0; |
| 435 |
< |
painCave.severity = OPENMD_WARNING; |
| 436 |
< |
simError(); |
| 437 |
< |
} |
| 312 |
> |
void InteractionManager::setCutoffRadius(RealType rcut) { |
| 313 |
|
|
| 314 |
< |
if (simParams_->haveSwitchingFunctionType()) { |
| 315 |
< |
string funcType = simParams_->getSwitchingFunctionType(); |
| 441 |
< |
toUpper(funcType); |
| 442 |
< |
if (funcType == "CUBIC") { |
| 443 |
< |
sft_ = cubic; |
| 444 |
< |
} else { |
| 445 |
< |
if (funcType == "FIFTH_ORDER_POLYNOMIAL") { |
| 446 |
< |
sft_ = fifth_order_poly; |
| 447 |
< |
} else { |
| 448 |
< |
// throw error |
| 449 |
< |
sprintf( painCave.errMsg, |
| 450 |
< |
"InteractionManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n" |
| 451 |
< |
"\tswitchingFunctionType must be one of: " |
| 452 |
< |
"\"cubic\" or \"fifth_order_polynomial\".", |
| 453 |
< |
funcType.c_str() ); |
| 454 |
< |
painCave.isFatal = 1; |
| 455 |
< |
painCave.severity = OPENMD_ERROR; |
| 456 |
< |
simError(); |
| 457 |
< |
} |
| 458 |
< |
} |
| 459 |
< |
} |
| 314 |
> |
electrostatic_->setCutoffRadius(rcut); |
| 315 |
> |
eam_->setCutoffRadius(rcut); |
| 316 |
|
} |
| 317 |
|
|
| 318 |
< |
/** |
| 463 |
< |
* setupNeighborlists |
| 464 |
< |
* |
| 465 |
< |
* If the skinThickness was explicitly set, use that value (but check it) |
| 466 |
< |
* If the skinThickness was not explicitly set: use 1.0 angstroms |
| 467 |
< |
*/ |
| 468 |
< |
void InteractionManager::setupNeighborlists() { |
| 469 |
< |
|
| 470 |
< |
Globals* simParams_ = info_->getSimParams(); |
| 471 |
< |
|
| 472 |
< |
if (simParams_->haveSkinThickness()) { |
| 473 |
< |
skinThickness_ = simParams_->getSkinThickness(); |
| 474 |
< |
} else { |
| 475 |
< |
skinThickness_ = 1.0; |
| 476 |
< |
sprintf(painCave.errMsg, |
| 477 |
< |
"InteractionManager::setupNeighborlists: No value was set for the skinThickness.\n" |
| 478 |
< |
"\tOpenMD will use a default value of %f Angstroms\n" |
| 479 |
< |
"\tfor this simulation\n", skinThickness_); |
| 480 |
< |
painCave.severity = OPENMD_INFO; |
| 481 |
< |
painCave.isFatal = 0; |
| 482 |
< |
simError(); |
| 483 |
< |
} |
| 484 |
< |
|
| 485 |
< |
listRadius_ = rCut_ + skinThickness_; |
| 486 |
< |
|
| 487 |
< |
} |
| 488 |
< |
|
| 489 |
< |
|
| 490 |
< |
void InteractionManager::doPrePair(int *atid1, int *atid2, RealType *rij, RealType *rho_i_at_j, RealType *rho_j_at_i){ |
| 318 |
> |
void InteractionManager::doPrePair(InteractionData idat){ |
| 319 |
|
|
| 320 |
|
if (!initialized_) initialize(); |
| 321 |
< |
|
| 322 |
< |
DensityData ddat; |
| 321 |
> |
|
| 322 |
> |
// excluded interaction, so just return |
| 323 |
> |
if (idat.excluded) return; |
| 324 |
|
|
| 496 |
– |
ddat.atype1 = typeMap_[*atid1]; |
| 497 |
– |
ddat.atype2 = typeMap_[*atid2]; |
| 498 |
– |
ddat.rij = *rij; |
| 499 |
– |
ddat.rho_i_at_j = *rho_i_at_j; |
| 500 |
– |
ddat.rho_j_at_i = *rho_j_at_i; |
| 501 |
– |
|
| 502 |
– |
pair<AtomType*, AtomType*> key = make_pair(ddat.atype1, ddat.atype2); |
| 325 |
|
set<NonBondedInteraction*>::iterator it; |
| 326 |
|
|
| 327 |
< |
for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){ |
| 327 |
> |
for (it = interactions_[ idat.atypes ].begin(); |
| 328 |
> |
it != interactions_[ idat.atypes ].end(); ++it){ |
| 329 |
|
if ((*it)->getFamily() == METALLIC_FAMILY) { |
| 330 |
< |
dynamic_cast<MetallicInteraction*>(*it)->calcDensity(ddat); |
| 330 |
> |
dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat); |
| 331 |
|
} |
| 332 |
|
} |
| 333 |
|
|
| 334 |
|
return; |
| 335 |
|
} |
| 336 |
|
|
| 337 |
< |
void InteractionManager::doPreForce(int *atid, RealType *rho, RealType *frho, RealType *dfrhodrho){ |
| 337 |
> |
void InteractionManager::doPreForce(SelfData sdat){ |
| 338 |
|
|
| 339 |
|
if (!initialized_) initialize(); |
| 340 |
< |
|
| 341 |
< |
FunctionalData fdat; |
| 519 |
< |
|
| 520 |
< |
fdat.atype = typeMap_[*atid]; |
| 521 |
< |
fdat.rho = *rho; |
| 522 |
< |
fdat.frho = *frho; |
| 523 |
< |
fdat.dfrhodrho = *dfrhodrho; |
| 524 |
< |
|
| 525 |
< |
pair<AtomType*, AtomType*> key = make_pair(fdat.atype, fdat.atype); |
| 340 |
> |
|
| 341 |
> |
pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype); |
| 342 |
|
set<NonBondedInteraction*>::iterator it; |
| 343 |
|
|
| 344 |
|
for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){ |
| 345 |
|
if ((*it)->getFamily() == METALLIC_FAMILY) { |
| 346 |
< |
dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(fdat); |
| 346 |
> |
dynamic_cast<MetallicInteraction*>(*it)->calcFunctional(sdat); |
| 347 |
|
} |
| 348 |
|
} |
| 349 |
|
|
| 350 |
|
return; |
| 351 |
|
} |
| 352 |
|
|
| 353 |
< |
void InteractionManager::doPair(int *atid1, int *atid2, RealType *d, RealType *r, RealType *r2, RealType *rcut, RealType *sw, int *topoDist, 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){ |
| 353 |
> |
void InteractionManager::doPair(InteractionData idat){ |
| 354 |
|
|
| 355 |
|
if (!initialized_) initialize(); |
| 540 |
– |
|
| 541 |
– |
InteractionData idat; |
| 542 |
– |
|
| 543 |
– |
idat.atype1 = typeMap_[*atid1]; |
| 544 |
– |
idat.atype2 = typeMap_[*atid2]; |
| 545 |
– |
idat.d = Vector3d(d); |
| 546 |
– |
idat.rij = *r; |
| 547 |
– |
idat.r2 = *r2; |
| 548 |
– |
idat.rcut = *rcut; |
| 549 |
– |
idat.sw = *sw; |
| 550 |
– |
idat.vdwMult = vdwScale_[*topoDist]; |
| 551 |
– |
idat.electroMult = electrostaticScale_[*topoDist]; |
| 552 |
– |
idat.pot = *pot; |
| 553 |
– |
idat.vpair = *vpair; |
| 554 |
– |
idat.f1 = Vector3d(f1); |
| 555 |
– |
idat.eFrame1 = Mat3x3d(eFrame1); |
| 556 |
– |
idat.eFrame2 = Mat3x3d(eFrame2); |
| 557 |
– |
idat.A1 = RotMat3x3d(A1); |
| 558 |
– |
idat.A2 = RotMat3x3d(A2); |
| 559 |
– |
idat.t1 = Vector3d(t1); |
| 560 |
– |
idat.t2 = Vector3d(t2); |
| 561 |
– |
idat.rho1 = *rho1; |
| 562 |
– |
idat.rho2 = *rho2; |
| 563 |
– |
idat.dfrho1 = *dfrho1; |
| 564 |
– |
idat.dfrho2 = *dfrho2; |
| 565 |
– |
idat.fshift1 = *fshift1; |
| 566 |
– |
idat.fshift2 = *fshift2; |
| 356 |
|
|
| 568 |
– |
pair<AtomType*, AtomType*> key = make_pair(idat.atype1, idat.atype2); |
| 357 |
|
set<NonBondedInteraction*>::iterator it; |
| 358 |
|
|
| 359 |
< |
for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) |
| 360 |
< |
(*it)->calcForce(idat); |
| 573 |
< |
|
| 574 |
< |
f1[0] = idat.f1.x(); |
| 575 |
< |
f1[1] = idat.f1.y(); |
| 576 |
< |
f1[2] = idat.f1.z(); |
| 577 |
< |
|
| 578 |
< |
t1[0] = idat.t1.x(); |
| 579 |
< |
t1[1] = idat.t1.y(); |
| 580 |
< |
t1[2] = idat.t1.z(); |
| 581 |
< |
|
| 582 |
< |
t2[0] = idat.t2.x(); |
| 583 |
< |
t2[1] = idat.t2.y(); |
| 584 |
< |
t2[2] = idat.t2.z(); |
| 359 |
> |
for (it = interactions_[ idat.atypes ].begin(); |
| 360 |
> |
it != interactions_[ idat.atypes ].end(); ++it) { |
| 361 |
|
|
| 362 |
< |
return; |
| 363 |
< |
} |
| 362 |
> |
// electrostatics still has to worry about indirect |
| 363 |
> |
// contributions from excluded pairs of atoms: |
| 364 |
|
|
| 365 |
< |
void InteractionManager::doSkipCorrection(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){ |
| 366 |
< |
|
| 591 |
< |
if (!initialized_) initialize(); |
| 592 |
< |
|
| 593 |
< |
SkipCorrectionData skdat; |
| 594 |
< |
|
| 595 |
< |
skdat.atype1 = typeMap_[*atid1]; |
| 596 |
< |
skdat.atype2 = typeMap_[*atid2]; |
| 597 |
< |
skdat.d = Vector3d(d); |
| 598 |
< |
skdat.rij = *r; |
| 599 |
< |
skdat.skippedCharge1 = *skippedCharge1; |
| 600 |
< |
skdat.skippedCharge2 = *skippedCharge2; |
| 601 |
< |
skdat.sw = *sw; |
| 602 |
< |
skdat.electroMult = *electroMult; |
| 603 |
< |
skdat.pot = *pot; |
| 604 |
< |
skdat.vpair = *vpair; |
| 605 |
< |
skdat.f1 = Vector3d(f1); |
| 606 |
< |
skdat.eFrame1 = Mat3x3d(eFrame1); |
| 607 |
< |
skdat.eFrame2 = Mat3x3d(eFrame2); |
| 608 |
< |
skdat.t1 = Vector3d(t1); |
| 609 |
< |
skdat.t2 = Vector3d(t2); |
| 610 |
< |
|
| 611 |
< |
pair<AtomType*, AtomType*> key = make_pair(skdat.atype1, skdat.atype2); |
| 612 |
< |
set<NonBondedInteraction*>::iterator it; |
| 613 |
< |
|
| 614 |
< |
for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){ |
| 615 |
< |
if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) { |
| 616 |
< |
dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(skdat); |
| 365 |
> |
if (!idat.excluded || (*it)->getFamily() == ELECTROSTATIC_FAMILY) { |
| 366 |
> |
(*it)->calcForce(idat); |
| 367 |
|
} |
| 368 |
|
} |
| 369 |
|
|
| 620 |
– |
f1[0] = skdat.f1.x(); |
| 621 |
– |
f1[1] = skdat.f1.y(); |
| 622 |
– |
f1[2] = skdat.f1.z(); |
| 623 |
– |
|
| 624 |
– |
t1[0] = skdat.t1.x(); |
| 625 |
– |
t1[1] = skdat.t1.y(); |
| 626 |
– |
t1[2] = skdat.t1.z(); |
| 627 |
– |
|
| 628 |
– |
t2[0] = skdat.t2.x(); |
| 629 |
– |
t2[1] = skdat.t2.y(); |
| 630 |
– |
t2[2] = skdat.t2.z(); |
| 631 |
– |
|
| 370 |
|
return; |
| 371 |
|
} |
| 372 |
|
|
| 373 |
< |
void InteractionManager::doSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge, RealType *pot, RealType *t){ |
| 373 |
> |
void InteractionManager::doSelfCorrection(SelfData sdat){ |
| 374 |
|
|
| 375 |
|
if (!initialized_) initialize(); |
| 376 |
|
|
| 377 |
< |
SelfCorrectionData scdat; |
| 640 |
< |
|
| 641 |
< |
scdat.atype = typeMap_[*atid]; |
| 642 |
< |
scdat.eFrame = Mat3x3d(eFrame); |
| 643 |
< |
scdat.skippedCharge = *skippedCharge; |
| 644 |
< |
scdat.pot = *pot; |
| 645 |
< |
scdat.t = Vector3d(t); |
| 646 |
< |
|
| 647 |
< |
pair<AtomType*, AtomType*> key = make_pair(scdat.atype, scdat.atype); |
| 377 |
> |
pair<AtomType*, AtomType*> key = make_pair(sdat.atype, sdat.atype); |
| 378 |
|
set<NonBondedInteraction*>::iterator it; |
| 379 |
|
|
| 380 |
|
for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it){ |
| 381 |
|
if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) { |
| 382 |
< |
dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(scdat); |
| 382 |
> |
dynamic_cast<ElectrostaticInteraction*>(*it)->calcSelfCorrection(sdat); |
| 383 |
|
} |
| 384 |
|
} |
| 385 |
< |
|
| 656 |
< |
t[0] = scdat.t.x(); |
| 657 |
< |
t[1] = scdat.t.y(); |
| 658 |
< |
t[2] = scdat.t.z(); |
| 659 |
< |
|
| 385 |
> |
|
| 386 |
|
return; |
| 387 |
|
} |
| 388 |
|
|
| 663 |
– |
|
| 389 |
|
RealType InteractionManager::getSuggestedCutoffRadius(int *atid) { |
| 390 |
|
if (!initialized_) initialize(); |
| 391 |
< |
|
| 391 |
> |
|
| 392 |
|
AtomType* atype = typeMap_[*atid]; |
| 393 |
|
|
| 394 |
|
pair<AtomType*, AtomType*> key = make_pair(atype, atype); |
| 396 |
|
RealType cutoff = 0.0; |
| 397 |
|
|
| 398 |
|
for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) |
| 399 |
< |
cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype)); |
| 399 |
> |
cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key)); |
| 400 |
|
return cutoff; |
| 401 |
|
} |
| 402 |
|
|
| 408 |
|
RealType cutoff = 0.0; |
| 409 |
|
|
| 410 |
|
for (it = interactions_[key].begin(); it != interactions_[key].end(); ++it) |
| 411 |
< |
cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(atype, atype)); |
| 411 |
> |
cutoff = max(cutoff, (*it)->getSuggestedCutoffRadius(key)); |
| 412 |
|
return cutoff; |
| 413 |
|
} |
| 689 |
– |
|
| 690 |
– |
|
| 691 |
– |
void InteractionManager::setSwitch(RealType *rIn, RealType *rOut) { |
| 692 |
– |
switcher_->setSwitch(*rIn, *rOut); |
| 693 |
– |
} |
| 694 |
– |
|
| 695 |
– |
void InteractionManager::getSwitch(RealType *r2, RealType *sw, RealType *dswdr, RealType *r, |
| 696 |
– |
int *in_switching_region) { |
| 697 |
– |
bool isr = switcher_->getSwitch(*r2, *sw, *dswdr, *r); |
| 698 |
– |
*in_switching_region = (int)isr; |
| 699 |
– |
} |
| 700 |
– |
|
| 414 |
|
} //end namespace OpenMD |
| 702 |
– |
|
| 703 |
– |
extern "C" { |
| 704 |
– |
|
| 705 |
– |
#define fortranDoPrePair FC_FUNC(do_prepair, DO_PREPAIR) |
| 706 |
– |
#define fortranDoPreForce FC_FUNC(do_preforce, DO_PREFORCE) |
| 707 |
– |
#define fortranDoPair FC_FUNC(do_pair, DO_PAIR) |
| 708 |
– |
#define fortranDoSkipCorrection FC_FUNC(do_skip_correction, DO_SKIP_CORRECTION) |
| 709 |
– |
#define fortranDoSelfCorrection FC_FUNC(do_self_correction, DO_SELF_CORRECTION) |
| 710 |
– |
#define fortranGetCutoff FC_FUNC(get_cutoff, GET_CUTOFF) |
| 711 |
– |
#define fortranSetSwitch FC_FUNC(set_switch, SET_SWITCH) |
| 712 |
– |
#define fortranGetSwitch FC_FUNC(get_switch, GET_SWITCH) |
| 713 |
– |
|
| 714 |
– |
void fortranDoPrePair(int *atid1, int *atid2, RealType *rij, |
| 715 |
– |
RealType *rho_i_at_j, RealType *rho_j_at_i) { |
| 716 |
– |
|
| 717 |
– |
return OpenMD::InteractionManager::Instance()->doPrePair(atid1, atid2, rij, |
| 718 |
– |
rho_i_at_j, |
| 719 |
– |
rho_j_at_i); |
| 720 |
– |
} |
| 721 |
– |
void fortranDoPreForce(int *atid, RealType *rho, RealType *frho, |
| 722 |
– |
RealType *dfrhodrho) { |
| 723 |
– |
|
| 724 |
– |
return OpenMD::InteractionManager::Instance()->doPreForce(atid, rho, frho, |
| 725 |
– |
dfrhodrho); |
| 726 |
– |
} |
| 727 |
– |
|
| 728 |
– |
void fortranDoPair(int *atid1, int *atid2, RealType *d, RealType *r, |
| 729 |
– |
RealType *r2, RealType *rcut, RealType *sw, int *topoDist, |
| 730 |
– |
RealType *pot, RealType *vpair, RealType *f1, RealType *eFrame1, |
| 731 |
– |
RealType *eFrame2, RealType *A1, RealType *A2, |
| 732 |
– |
RealType *t1, RealType *t2, RealType *rho1, RealType *rho2, |
| 733 |
– |
RealType *dfrho1, RealType *dfrho2, RealType *fshift1, |
| 734 |
– |
RealType *fshift2){ |
| 735 |
– |
|
| 736 |
– |
return OpenMD::InteractionManager::Instance()->doPair(atid1, atid2, d, r, |
| 737 |
– |
r2, rcut, sw, topoDist, |
| 738 |
– |
pot, vpair, f1, |
| 739 |
– |
eFrame1, eFrame2, |
| 740 |
– |
A1, A2, t1, t2, rho1, |
| 741 |
– |
rho2, dfrho1, dfrho2, |
| 742 |
– |
fshift1, fshift2); |
| 743 |
– |
} |
| 744 |
– |
|
| 745 |
– |
void fortranDoSkipCorrection(int *atid1, int *atid2, RealType *d, |
| 746 |
– |
RealType *r, RealType *skippedCharge1, |
| 747 |
– |
RealType *skippedCharge2, RealType *sw, |
| 748 |
– |
RealType *electroMult, RealType *pot, |
| 749 |
– |
RealType *vpair, RealType *f1, |
| 750 |
– |
RealType *eFrame1, RealType *eFrame2, |
| 751 |
– |
RealType *t1, RealType *t2){ |
| 752 |
– |
|
| 753 |
– |
return OpenMD::InteractionManager::Instance()->doSkipCorrection(atid1, |
| 754 |
– |
atid2, d, |
| 755 |
– |
r, |
| 756 |
– |
skippedCharge1, |
| 757 |
– |
skippedCharge2, |
| 758 |
– |
sw, electroMult, pot, |
| 759 |
– |
vpair, f1, eFrame1, |
| 760 |
– |
eFrame2, t1, t2); |
| 761 |
– |
} |
| 762 |
– |
|
| 763 |
– |
void fortranDoSelfCorrection(int *atid, RealType *eFrame, RealType *skippedCharge, |
| 764 |
– |
RealType *pot, RealType *t) { |
| 765 |
– |
|
| 766 |
– |
return OpenMD::InteractionManager::Instance()->doSelfCorrection(atid, |
| 767 |
– |
eFrame, |
| 768 |
– |
skippedCharge, |
| 769 |
– |
pot, t); |
| 770 |
– |
} |
| 771 |
– |
RealType fortranGetCutoff(int *atid) { |
| 772 |
– |
return OpenMD::InteractionManager::Instance()->getSuggestedCutoffRadius(atid); |
| 773 |
– |
} |
| 774 |
– |
|
| 775 |
– |
void fortranGetSwitch(RealType *r2, RealType *sw, RealType *dswdr, RealType *r, |
| 776 |
– |
int *in_switching_region) { |
| 777 |
– |
|
| 778 |
– |
return OpenMD::InteractionManager::Instance()->getSwitch(r2, sw, dswdr, r, |
| 779 |
– |
in_switching_region); |
| 780 |
– |
} |
| 781 |
– |
|
| 782 |
– |
void fortranSetSwitch(RealType *rIn, RealType *rOut) { |
| 783 |
– |
return OpenMD::InteractionManager::Instance()->setSwitch(rIn, rOut); |
| 784 |
– |
} |
| 785 |
– |
|
| 786 |
– |
} |
