| 40 |
|
*/ |
| 41 |
|
|
| 42 |
|
#include "nonbonded/InteractionManager.hpp" |
| 43 |
– |
#include "UseTheForce/doForces_interface.h" |
| 43 |
|
|
| 44 |
|
namespace OpenMD { |
| 45 |
|
|
| 46 |
< |
InteractionManager* InteractionManager::_instance = NULL; |
| 48 |
< |
SimInfo* InteractionManager::info_ = NULL; |
| 49 |
< |
bool InteractionManager::initialized_ = false; |
| 46 |
> |
InteractionManager::InteractionManager() { |
| 47 |
|
|
| 48 |
< |
RealType InteractionManager::rCut_ = 0.0; |
| 49 |
< |
RealType InteractionManager::rSwitch_ = 0.0; |
| 50 |
< |
RealType InteractionManager::skinThickness_ = 0.0; |
| 51 |
< |
RealType InteractionManager::listRadius_ = 0.0; |
| 52 |
< |
CutoffMethod InteractionManager::cutoffMethod_ = SHIFTED_FORCE; |
| 53 |
< |
SwitchingFunctionType InteractionManager::sft_ = cubic; |
| 54 |
< |
RealType InteractionManager::vdwScale_[4] = {1.0, 0.0, 0.0, 0.0}; |
| 55 |
< |
RealType InteractionManager::electrostaticScale_[4] = {1.0, 0.0, 0.0, 0.0}; |
| 56 |
< |
|
| 57 |
< |
map<int, AtomType*> InteractionManager::typeMap_; |
| 61 |
< |
map<pair<AtomType*, AtomType*>, set<NonBondedInteraction*> > InteractionManager::interactions_; |
| 62 |
< |
|
| 63 |
< |
LJ* InteractionManager::lj_ = new LJ(); |
| 64 |
< |
GB* InteractionManager::gb_ = new GB(); |
| 65 |
< |
Sticky* InteractionManager::sticky_ = new Sticky(); |
| 66 |
< |
Morse* InteractionManager::morse_ = new Morse(); |
| 67 |
< |
EAM* InteractionManager::eam_ = new EAM(); |
| 68 |
< |
SC* InteractionManager::sc_ = new SC(); |
| 69 |
< |
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; |
| 48 |
> |
initialized_ = false; |
| 49 |
> |
|
| 50 |
> |
lj_ = new LJ(); |
| 51 |
> |
gb_ = new GB(); |
| 52 |
> |
sticky_ = new Sticky(); |
| 53 |
> |
morse_ = new Morse(); |
| 54 |
> |
eam_ = new EAM(); |
| 55 |
> |
sc_ = new SC(); |
| 56 |
> |
electrostatic_ = new Electrostatic(); |
| 57 |
> |
maw_ = new MAW(); |
| 58 |
|
} |
| 59 |
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|
| 60 |
|
void InteractionManager::initialize() { |
| 67 |
|
eam_->setForceField(forceField_); |
| 68 |
|
sc_->setForceField(forceField_); |
| 69 |
|
morse_->setForceField(forceField_); |
| 70 |
+ |
electrostatic_->setSimInfo(info_); |
| 71 |
|
electrostatic_->setForceField(forceField_); |
| 72 |
|
maw_->setForceField(forceField_); |
| 73 |
|
|
| 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 = topologically unconnected |
| 99 |
– |
// 1 = bonded together |
| 100 |
– |
// 2 = connected via a bend |
| 101 |
– |
// 3 = connected via a torsion |
| 102 |
– |
|
| 103 |
– |
vdwScale_[0] = 1.0; |
| 104 |
– |
vdwScale_[1] = fopts.getvdw12scale(); |
| 105 |
– |
vdwScale_[2] = fopts.getvdw13scale(); |
| 106 |
– |
vdwScale_[3] = fopts.getvdw14scale(); |
| 107 |
– |
|
| 108 |
– |
electrostaticScale_[0] = 1.0; |
| 109 |
– |
electrostaticScale_[1] = fopts.getelectrostatic12scale(); |
| 110 |
– |
electrostaticScale_[2] = fopts.getelectrostatic13scale(); |
| 111 |
– |
electrostaticScale_[3] = fopts.getelectrostatic14scale(); |
| 112 |
– |
|
| 74 |
|
ForceField::AtomTypeContainer* atomTypes = forceField_->getAtomTypes(); |
| 75 |
|
ForceField::AtomTypeContainer::MapTypeIterator i1, i2; |
| 76 |
|
AtomType* atype1; |
| 242 |
|
} |
| 243 |
|
|
| 244 |
|
|
| 245 |
< |
// make sure every pair of atom types in this simulation has a |
| 246 |
< |
// non-bonded interaction: |
| 245 |
> |
// Make sure every pair of atom types in this simulation has a |
| 246 |
> |
// non-bonded interaction. If not, just inform the user. |
| 247 |
|
|
| 248 |
|
set<AtomType*> simTypes = info_->getSimulatedAtomTypes(); |
| 249 |
|
set<AtomType*>::iterator it, jt; |
| 250 |
+ |
|
| 251 |
|
for (it = simTypes.begin(); it != simTypes.end(); ++it) { |
| 252 |
|
atype1 = (*it); |
| 253 |
< |
for (jt = simTypes.begin(); jt != simTypes.end(); ++jt) { |
| 253 |
> |
for (jt = it; jt != simTypes.end(); ++jt) { |
| 254 |
|
atype2 = (*jt); |
| 255 |
|
key = make_pair(atype1, atype2); |
| 256 |
|
|
| 257 |
|
if (interactions_[key].size() == 0) { |
| 258 |
|
sprintf( painCave.errMsg, |
| 259 |
< |
"InteractionManager unable to find an appropriate non-bonded\n" |
| 260 |
< |
"\tinteraction for atom types %s - %s\n", |
| 259 |
> |
"InteractionManager could not find a matching non-bonded\n" |
| 260 |
> |
"\tinteraction for atom types %s - %s\n" |
| 261 |
> |
"\tProceeding without this interaction.\n", |
| 262 |
|
atype1->getName().c_str(), atype2->getName().c_str()); |
| 263 |
|
painCave.severity = OPENMD_INFO; |
| 264 |
< |
painCave.isFatal = 1; |
| 264 |
> |
painCave.isFatal = 0; |
| 265 |
|
simError(); |
| 266 |
|
} |
| 267 |
|
} |
| 268 |
|
} |
| 269 |
|
|
| 307 |
– |
setupCutoffs(); |
| 308 |
– |
setupSwitching(); |
| 309 |
– |
setupNeighborlists(); |
| 310 |
– |
|
| 311 |
– |
//int ljsp = cutoffMethod_ == SHIFTED_POTENTIAL ? 1 : 0; |
| 312 |
– |
//int ljsf = cutoffMethod_ == SHIFTED_FORCE ? 1 : 0; |
| 313 |
– |
//notifyFortranCutoffs(&rCut_, &rSwitch_, &ljsp, &ljsf); |
| 314 |
– |
//notifyFortranSkinThickness(&skinThickness_); |
| 315 |
– |
|
| 270 |
|
initialized_ = true; |
| 271 |
|
} |
| 318 |
– |
|
| 319 |
– |
/** |
| 320 |
– |
* setupCutoffs |
| 321 |
– |
* |
| 322 |
– |
* Sets the values of cutoffRadius and cutoffMethod |
| 323 |
– |
* |
| 324 |
– |
* cutoffRadius : realType |
| 325 |
– |
* If the cutoffRadius was explicitly set, use that value. |
| 326 |
– |
* If the cutoffRadius was not explicitly set: |
| 327 |
– |
* Are there electrostatic atoms? Use 12.0 Angstroms. |
| 328 |
– |
* No electrostatic atoms? Poll the atom types present in the |
| 329 |
– |
* simulation for suggested cutoff values (e.g. 2.5 * sigma). |
| 330 |
– |
* Use the maximum suggested value that was found. |
| 331 |
– |
* |
| 332 |
– |
* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL) |
| 333 |
– |
* If cutoffMethod was explicitly set, use that choice. |
| 334 |
– |
* If cutoffMethod was not explicitly set, use SHIFTED_FORCE |
| 335 |
– |
*/ |
| 336 |
– |
void InteractionManager::setupCutoffs() { |
| 337 |
– |
|
| 338 |
– |
Globals* simParams_ = info_->getSimParams(); |
| 339 |
– |
|
| 340 |
– |
if (simParams_->haveCutoffRadius()) { |
| 341 |
– |
rCut_ = simParams_->getCutoffRadius(); |
| 342 |
– |
} else { |
| 343 |
– |
if (info_->usesElectrostaticAtoms()) { |
| 344 |
– |
sprintf(painCave.errMsg, |
| 345 |
– |
"InteractionManager::setupCutoffs: No value was set for the cutoffRadius.\n" |
| 346 |
– |
"\tOpenMD will use a default value of 12.0 angstroms" |
| 347 |
– |
"\tfor the cutoffRadius.\n"); |
| 348 |
– |
painCave.isFatal = 0; |
| 349 |
– |
painCave.severity = OPENMD_INFO; |
| 350 |
– |
simError(); |
| 351 |
– |
rCut_ = 12.0; |
| 352 |
– |
} else { |
| 353 |
– |
RealType thisCut; |
| 354 |
– |
set<AtomType*>::iterator i; |
| 355 |
– |
set<AtomType*> atomTypes; |
| 356 |
– |
atomTypes = info_->getSimulatedAtomTypes(); |
| 357 |
– |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
| 358 |
– |
thisCut = getSuggestedCutoffRadius((*i)); |
| 359 |
– |
rCut_ = max(thisCut, rCut_); |
| 360 |
– |
} |
| 361 |
– |
sprintf(painCave.errMsg, |
| 362 |
– |
"InteractionManager::setupCutoffs: No value was set for the cutoffRadius.\n" |
| 363 |
– |
"\tOpenMD will use %lf angstroms.\n", |
| 364 |
– |
rCut_); |
| 365 |
– |
painCave.isFatal = 0; |
| 366 |
– |
painCave.severity = OPENMD_INFO; |
| 367 |
– |
simError(); |
| 368 |
– |
} |
| 369 |
– |
} |
| 272 |
|
|
| 273 |
< |
map<string, CutoffMethod> stringToCutoffMethod; |
| 274 |
< |
stringToCutoffMethod["HARD"] = HARD; |
| 275 |
< |
stringToCutoffMethod["SWITCHED"] = SWITCHED; |
| 374 |
< |
stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL; |
| 375 |
< |
stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE; |
| 376 |
< |
|
| 377 |
< |
if (simParams_->haveCutoffMethod()) { |
| 378 |
< |
string cutMeth = toUpperCopy(simParams_->getCutoffMethod()); |
| 379 |
< |
map<string, CutoffMethod>::iterator i; |
| 380 |
< |
i = stringToCutoffMethod.find(cutMeth); |
| 381 |
< |
if (i == stringToCutoffMethod.end()) { |
| 382 |
< |
sprintf(painCave.errMsg, |
| 383 |
< |
"InteractionManager::setupCutoffs: Could not find chosen cutoffMethod %s\n" |
| 384 |
< |
"\tShould be one of: " |
| 385 |
< |
"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n", |
| 386 |
< |
cutMeth.c_str()); |
| 387 |
< |
painCave.isFatal = 1; |
| 388 |
< |
painCave.severity = OPENMD_ERROR; |
| 389 |
< |
simError(); |
| 390 |
< |
} else { |
| 391 |
< |
cutoffMethod_ = i->second; |
| 392 |
< |
} |
| 393 |
< |
} else { |
| 394 |
< |
sprintf(painCave.errMsg, |
| 395 |
< |
"InteractionManager::setupCutoffs: No value was set for the cutoffMethod.\n" |
| 396 |
< |
"\tOpenMD will use SHIFTED_FORCE.\n"); |
| 397 |
< |
painCave.isFatal = 0; |
| 398 |
< |
painCave.severity = OPENMD_INFO; |
| 399 |
< |
simError(); |
| 400 |
< |
cutoffMethod_ = SHIFTED_FORCE; |
| 401 |
< |
} |
| 273 |
> |
void InteractionManager::setCutoffRadius(RealType rcut) { |
| 274 |
> |
electrostatic_->setCutoffRadius(rcut); |
| 275 |
> |
eam_->setCutoffRadius(rcut); |
| 276 |
|
} |
| 277 |
|
|
| 278 |
< |
|
| 279 |
< |
/** |
| 406 |
< |
* setupSwitching |
| 407 |
< |
* |
| 408 |
< |
* Sets the values of switchingRadius and |
| 409 |
< |
* If the switchingRadius was explicitly set, use that value (but check it) |
| 410 |
< |
* If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_ |
| 411 |
< |
*/ |
| 412 |
< |
void InteractionManager::setupSwitching() { |
| 413 |
< |
Globals* simParams_ = info_->getSimParams(); |
| 414 |
< |
|
| 415 |
< |
if (simParams_->haveSwitchingRadius()) { |
| 416 |
< |
rSwitch_ = simParams_->getSwitchingRadius(); |
| 417 |
< |
if (rSwitch_ > rCut_) { |
| 418 |
< |
sprintf(painCave.errMsg, |
| 419 |
< |
"InteractionManager::setupSwitching: switchingRadius (%f) is larger than cutoffRadius(%f)\n", |
| 420 |
< |
rSwitch_, rCut_); |
| 421 |
< |
painCave.isFatal = 1; |
| 422 |
< |
painCave.severity = OPENMD_ERROR; |
| 423 |
< |
simError(); |
| 424 |
< |
} |
| 425 |
< |
} else { |
| 426 |
< |
rSwitch_ = 0.85 * rCut_; |
| 427 |
< |
sprintf(painCave.errMsg, |
| 428 |
< |
"InteractionManager::setupSwitching: No value was set for the switchingRadius.\n" |
| 429 |
< |
"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n" |
| 430 |
< |
"\tswitchingRadius = %f. for this simulation\n", rSwitch_); |
| 431 |
< |
painCave.isFatal = 0; |
| 432 |
< |
painCave.severity = OPENMD_WARNING; |
| 433 |
< |
simError(); |
| 434 |
< |
} |
| 435 |
< |
|
| 436 |
< |
if (simParams_->haveSwitchingFunctionType()) { |
| 437 |
< |
string funcType = simParams_->getSwitchingFunctionType(); |
| 438 |
< |
toUpper(funcType); |
| 439 |
< |
if (funcType == "CUBIC") { |
| 440 |
< |
sft_ = cubic; |
| 441 |
< |
} else { |
| 442 |
< |
if (funcType == "FIFTH_ORDER_POLYNOMIAL") { |
| 443 |
< |
sft_ = fifth_order_poly; |
| 444 |
< |
} else { |
| 445 |
< |
// throw error |
| 446 |
< |
sprintf( painCave.errMsg, |
| 447 |
< |
"InteractionManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n" |
| 448 |
< |
"\tswitchingFunctionType must be one of: " |
| 449 |
< |
"\"cubic\" or \"fifth_order_polynomial\".", |
| 450 |
< |
funcType.c_str() ); |
| 451 |
< |
painCave.isFatal = 1; |
| 452 |
< |
painCave.severity = OPENMD_ERROR; |
| 453 |
< |
simError(); |
| 454 |
< |
} |
| 455 |
< |
} |
| 456 |
< |
} |
| 457 |
< |
|
| 458 |
< |
switcher_->setSwitchType(sft_); |
| 459 |
< |
switcher_->setSwitch(rSwitch_, rCut_); |
| 278 |
> |
void InteractionManager::setSwitchingRadius(RealType rswitch) { |
| 279 |
> |
electrostatic_->setSwitchingRadius(rswitch); |
| 280 |
|
} |
| 461 |
– |
|
| 462 |
– |
/** |
| 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(); |
| 281 |
|
|
| 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 |
– |
|
| 282 |
|
void InteractionManager::doPrePair(InteractionData idat){ |
| 283 |
|
|
| 284 |
|
if (!initialized_) initialize(); |
| 285 |
|
|
| 286 |
|
set<NonBondedInteraction*>::iterator it; |
| 287 |
|
|
| 288 |
< |
for (it = interactions_[idat.atypes].begin(); |
| 289 |
< |
it != interactions_[idat.atypes].end(); ++it){ |
| 288 |
> |
for (it = interactions_[ idat.atypes ].begin(); |
| 289 |
> |
it != interactions_[ idat.atypes ].end(); ++it){ |
| 290 |
|
if ((*it)->getFamily() == METALLIC_FAMILY) { |
| 291 |
|
dynamic_cast<MetallicInteraction*>(*it)->calcDensity(idat); |
| 292 |
|
} |
| 317 |
|
|
| 318 |
|
set<NonBondedInteraction*>::iterator it; |
| 319 |
|
|
| 320 |
< |
for (it = interactions_[idat.atypes].begin(); |
| 321 |
< |
it != interactions_[idat.atypes].end(); ++it) |
| 320 |
> |
for (it = interactions_[ idat.atypes ].begin(); |
| 321 |
> |
it != interactions_[ idat.atypes ].end(); ++it) |
| 322 |
|
(*it)->calcForce(idat); |
| 323 |
|
|
| 324 |
|
return; |
| 327 |
|
void InteractionManager::doSkipCorrection(InteractionData idat){ |
| 328 |
|
|
| 329 |
|
if (!initialized_) initialize(); |
| 330 |
< |
|
| 330 |
> |
|
| 331 |
|
set<NonBondedInteraction*>::iterator it; |
| 332 |
|
|
| 333 |
< |
for (it = interactions_[idat.atypes].begin(); |
| 334 |
< |
it != interactions_[idat.atypes].end(); ++it){ |
| 333 |
> |
for (it = interactions_[ idat.atypes ].begin(); |
| 334 |
> |
it != interactions_[ idat.atypes ].end(); ++it){ |
| 335 |
|
if ((*it)->getFamily() == ELECTROSTATIC_FAMILY) { |
| 336 |
|
dynamic_cast<ElectrostaticInteraction*>(*it)->calcSkipCorrection(idat); |
| 337 |
|
} |
