| 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 |
|
/** |
| 44 |
|
* @file ForceManager.cpp |
| 45 |
|
* @author tlin |
| 46 |
|
* @date 11/09/2004 |
| 46 |
– |
* @time 10:39am |
| 47 |
|
* @version 1.0 |
| 48 |
|
*/ |
| 49 |
|
|
| 57 |
|
#include "primitives/Torsion.hpp" |
| 58 |
|
#include "primitives/Inversion.hpp" |
| 59 |
|
#include "nonbonded/NonBondedInteraction.hpp" |
| 60 |
+ |
#include "perturbations/ElectricField.hpp" |
| 61 |
|
#include "parallel/ForceMatrixDecomposition.hpp" |
| 62 |
|
|
| 63 |
+ |
#include <cstdio> |
| 64 |
+ |
#include <iostream> |
| 65 |
+ |
#include <iomanip> |
| 66 |
+ |
|
| 67 |
|
using namespace std; |
| 68 |
|
namespace OpenMD { |
| 69 |
|
|
| 70 |
< |
ForceManager::ForceManager(SimInfo * info) : info_(info) { |
| 70 |
> |
ForceManager::ForceManager(SimInfo * info) : info_(info), switcher_(NULL), |
| 71 |
> |
initialized_(false) { |
| 72 |
|
forceField_ = info_->getForceField(); |
| 73 |
|
interactionMan_ = new InteractionManager(); |
| 74 |
|
fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_); |
| 75 |
+ |
thermo = new Thermo(info_); |
| 76 |
|
} |
| 77 |
|
|
| 78 |
+ |
ForceManager::~ForceManager() { |
| 79 |
+ |
perturbations_.clear(); |
| 80 |
+ |
|
| 81 |
+ |
delete switcher_; |
| 82 |
+ |
delete interactionMan_; |
| 83 |
+ |
delete fDecomp_; |
| 84 |
+ |
delete thermo; |
| 85 |
+ |
} |
| 86 |
+ |
|
| 87 |
|
/** |
| 88 |
|
* setupCutoffs |
| 89 |
|
* |
| 90 |
< |
* Sets the values of cutoffRadius, cutoffMethod, and cutoffPolicy |
| 90 |
> |
* Sets the values of cutoffRadius, switchingRadius, cutoffMethod, |
| 91 |
> |
* and cutoffPolicy |
| 92 |
|
* |
| 93 |
|
* cutoffRadius : realType |
| 94 |
|
* If the cutoffRadius was explicitly set, use that value. |
| 98 |
|
* simulation for suggested cutoff values (e.g. 2.5 * sigma). |
| 99 |
|
* Use the maximum suggested value that was found. |
| 100 |
|
* |
| 101 |
< |
* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL) |
| 101 |
> |
* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, |
| 102 |
> |
* or SHIFTED_POTENTIAL) |
| 103 |
|
* If cutoffMethod was explicitly set, use that choice. |
| 104 |
|
* If cutoffMethod was not explicitly set, use SHIFTED_FORCE |
| 105 |
|
* |
| 106 |
|
* cutoffPolicy : (one of MIX, MAX, TRADITIONAL) |
| 107 |
|
* If cutoffPolicy was explicitly set, use that choice. |
| 108 |
|
* If cutoffPolicy was not explicitly set, use TRADITIONAL |
| 109 |
+ |
* |
| 110 |
+ |
* switchingRadius : realType |
| 111 |
+ |
* If the cutoffMethod was set to SWITCHED: |
| 112 |
+ |
* If the switchingRadius was explicitly set, use that value |
| 113 |
+ |
* (but do a sanity check first). |
| 114 |
+ |
* If the switchingRadius was not explicitly set: use 0.85 * |
| 115 |
+ |
* cutoffRadius_ |
| 116 |
+ |
* If the cutoffMethod was not set to SWITCHED: |
| 117 |
+ |
* Set switchingRadius equal to cutoffRadius for safety. |
| 118 |
|
*/ |
| 119 |
|
void ForceManager::setupCutoffs() { |
| 120 |
|
|
| 121 |
|
Globals* simParams_ = info_->getSimParams(); |
| 122 |
|
ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions(); |
| 123 |
+ |
int mdFileVersion; |
| 124 |
+ |
rCut_ = 0.0; //Needs a value for a later max() call; |
| 125 |
|
|
| 126 |
+ |
if (simParams_->haveMDfileVersion()) |
| 127 |
+ |
mdFileVersion = simParams_->getMDfileVersion(); |
| 128 |
+ |
else |
| 129 |
+ |
mdFileVersion = 0; |
| 130 |
+ |
|
| 131 |
+ |
// We need the list of simulated atom types to figure out cutoffs |
| 132 |
+ |
// as well as long range corrections. |
| 133 |
+ |
|
| 134 |
+ |
set<AtomType*>::iterator i; |
| 135 |
+ |
set<AtomType*> atomTypes_; |
| 136 |
+ |
atomTypes_ = info_->getSimulatedAtomTypes(); |
| 137 |
+ |
|
| 138 |
|
if (simParams_->haveCutoffRadius()) { |
| 139 |
|
rCut_ = simParams_->getCutoffRadius(); |
| 140 |
|
} else { |
| 149 |
|
rCut_ = 12.0; |
| 150 |
|
} else { |
| 151 |
|
RealType thisCut; |
| 152 |
< |
set<AtomType*>::iterator i; |
| 112 |
< |
set<AtomType*> atomTypes; |
| 113 |
< |
atomTypes = info_->getSimulatedAtomTypes(); |
| 114 |
< |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
| 152 |
> |
for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) { |
| 153 |
|
thisCut = interactionMan_->getSuggestedCutoffRadius((*i)); |
| 154 |
|
rCut_ = max(thisCut, rCut_); |
| 155 |
|
} |
| 161 |
|
painCave.severity = OPENMD_INFO; |
| 162 |
|
simError(); |
| 163 |
|
} |
| 126 |
– |
fDecomp_->setUserCutoff(rCut_); |
| 164 |
|
} |
| 165 |
|
|
| 166 |
+ |
fDecomp_->setUserCutoff(rCut_); |
| 167 |
+ |
interactionMan_->setCutoffRadius(rCut_); |
| 168 |
+ |
|
| 169 |
|
map<string, CutoffMethod> stringToCutoffMethod; |
| 170 |
|
stringToCutoffMethod["HARD"] = HARD; |
| 171 |
|
stringToCutoffMethod["SWITCHED"] = SWITCHED; |
| 189 |
|
cutoffMethod_ = i->second; |
| 190 |
|
} |
| 191 |
|
} else { |
| 192 |
< |
sprintf(painCave.errMsg, |
| 193 |
< |
"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n" |
| 194 |
< |
"\tOpenMD will use SHIFTED_FORCE.\n"); |
| 195 |
< |
painCave.isFatal = 0; |
| 196 |
< |
painCave.severity = OPENMD_INFO; |
| 197 |
< |
simError(); |
| 198 |
< |
cutoffMethod_ = SHIFTED_FORCE; |
| 192 |
> |
if (mdFileVersion > 1) { |
| 193 |
> |
sprintf(painCave.errMsg, |
| 194 |
> |
"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n" |
| 195 |
> |
"\tOpenMD will use SHIFTED_FORCE.\n"); |
| 196 |
> |
painCave.isFatal = 0; |
| 197 |
> |
painCave.severity = OPENMD_INFO; |
| 198 |
> |
simError(); |
| 199 |
> |
cutoffMethod_ = SHIFTED_FORCE; |
| 200 |
> |
} else { |
| 201 |
> |
// handle the case where the old file version was in play |
| 202 |
> |
// (there should be no cutoffMethod, so we have to deduce it |
| 203 |
> |
// from other data). |
| 204 |
> |
|
| 205 |
> |
sprintf(painCave.errMsg, |
| 206 |
> |
"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n" |
| 207 |
> |
"\tOpenMD found a file which does not set a cutoffMethod.\n" |
| 208 |
> |
"\tOpenMD will attempt to deduce a cutoffMethod using the\n" |
| 209 |
> |
"\tbehavior of the older (version 1) code. To remove this\n" |
| 210 |
> |
"\twarning, add an explicit cutoffMethod and change the top\n" |
| 211 |
> |
"\tof the file so that it begins with <OpenMD version=2>\n"); |
| 212 |
> |
painCave.isFatal = 0; |
| 213 |
> |
painCave.severity = OPENMD_WARNING; |
| 214 |
> |
simError(); |
| 215 |
> |
|
| 216 |
> |
// The old file version tethered the shifting behavior to the |
| 217 |
> |
// electrostaticSummationMethod keyword. |
| 218 |
> |
|
| 219 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
| 220 |
> |
string myMethod = simParams_->getElectrostaticSummationMethod(); |
| 221 |
> |
toUpper(myMethod); |
| 222 |
> |
|
| 223 |
> |
if (myMethod == "SHIFTED_POTENTIAL") { |
| 224 |
> |
cutoffMethod_ = SHIFTED_POTENTIAL; |
| 225 |
> |
} else if (myMethod == "SHIFTED_FORCE") { |
| 226 |
> |
cutoffMethod_ = SHIFTED_FORCE; |
| 227 |
> |
} |
| 228 |
> |
|
| 229 |
> |
if (simParams_->haveSwitchingRadius()) |
| 230 |
> |
rSwitch_ = simParams_->getSwitchingRadius(); |
| 231 |
> |
|
| 232 |
> |
if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") { |
| 233 |
> |
if (simParams_->haveSwitchingRadius()){ |
| 234 |
> |
sprintf(painCave.errMsg, |
| 235 |
> |
"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n" |
| 236 |
> |
"\tA value was set for the switchingRadius\n" |
| 237 |
> |
"\teven though the electrostaticSummationMethod was\n" |
| 238 |
> |
"\tset to %s\n", myMethod.c_str()); |
| 239 |
> |
painCave.severity = OPENMD_WARNING; |
| 240 |
> |
painCave.isFatal = 1; |
| 241 |
> |
simError(); |
| 242 |
> |
} |
| 243 |
> |
} |
| 244 |
> |
if (abs(rCut_ - rSwitch_) < 0.0001) { |
| 245 |
> |
if (cutoffMethod_ == SHIFTED_FORCE) { |
| 246 |
> |
sprintf(painCave.errMsg, |
| 247 |
> |
"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n" |
| 248 |
> |
"\tcutoffRadius and switchingRadius are set to the\n" |
| 249 |
> |
"\tsame value. OpenMD will use shifted force\n" |
| 250 |
> |
"\tpotentials instead of switching functions.\n"); |
| 251 |
> |
painCave.isFatal = 0; |
| 252 |
> |
painCave.severity = OPENMD_WARNING; |
| 253 |
> |
simError(); |
| 254 |
> |
} else { |
| 255 |
> |
cutoffMethod_ = SHIFTED_POTENTIAL; |
| 256 |
> |
sprintf(painCave.errMsg, |
| 257 |
> |
"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n" |
| 258 |
> |
"\tcutoffRadius and switchingRadius are set to the\n" |
| 259 |
> |
"\tsame value. OpenMD will use shifted potentials\n" |
| 260 |
> |
"\tinstead of switching functions.\n"); |
| 261 |
> |
painCave.isFatal = 0; |
| 262 |
> |
painCave.severity = OPENMD_WARNING; |
| 263 |
> |
simError(); |
| 264 |
> |
} |
| 265 |
> |
} |
| 266 |
> |
} |
| 267 |
> |
} |
| 268 |
|
} |
| 269 |
|
|
| 270 |
|
map<string, CutoffPolicy> stringToCutoffPolicy; |
| 272 |
|
stringToCutoffPolicy["MAX"] = MAX; |
| 273 |
|
stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL; |
| 274 |
|
|
| 275 |
< |
std::string cutPolicy; |
| 275 |
> |
string cutPolicy; |
| 276 |
|
if (forceFieldOptions_.haveCutoffPolicy()){ |
| 277 |
|
cutPolicy = forceFieldOptions_.getCutoffPolicy(); |
| 278 |
|
}else if (simParams_->haveCutoffPolicy()) { |
| 305 |
|
simError(); |
| 306 |
|
cutoffPolicy_ = TRADITIONAL; |
| 307 |
|
} |
| 199 |
– |
fDecomp_->setCutoffPolicy(cutoffPolicy_); |
| 200 |
– |
} |
| 308 |
|
|
| 309 |
< |
/** |
| 310 |
< |
* setupSwitching |
| 204 |
< |
* |
| 205 |
< |
* Sets the values of switchingRadius and |
| 206 |
< |
* If the switchingRadius was explicitly set, use that value (but check it) |
| 207 |
< |
* If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_ |
| 208 |
< |
*/ |
| 209 |
< |
void ForceManager::setupSwitching() { |
| 210 |
< |
Globals* simParams_ = info_->getSimParams(); |
| 211 |
< |
|
| 309 |
> |
fDecomp_->setCutoffPolicy(cutoffPolicy_); |
| 310 |
> |
|
| 311 |
|
// create the switching function object: |
| 312 |
+ |
|
| 313 |
|
switcher_ = new SwitchingFunction(); |
| 314 |
< |
|
| 315 |
< |
if (simParams_->haveSwitchingRadius()) { |
| 316 |
< |
rSwitch_ = simParams_->getSwitchingRadius(); |
| 317 |
< |
if (rSwitch_ > rCut_) { |
| 314 |
> |
|
| 315 |
> |
if (cutoffMethod_ == SWITCHED) { |
| 316 |
> |
if (simParams_->haveSwitchingRadius()) { |
| 317 |
> |
rSwitch_ = simParams_->getSwitchingRadius(); |
| 318 |
> |
if (rSwitch_ > rCut_) { |
| 319 |
> |
sprintf(painCave.errMsg, |
| 320 |
> |
"ForceManager::setupCutoffs: switchingRadius (%f) is larger " |
| 321 |
> |
"than the cutoffRadius(%f)\n", rSwitch_, rCut_); |
| 322 |
> |
painCave.isFatal = 1; |
| 323 |
> |
painCave.severity = OPENMD_ERROR; |
| 324 |
> |
simError(); |
| 325 |
> |
} |
| 326 |
> |
} else { |
| 327 |
> |
rSwitch_ = 0.85 * rCut_; |
| 328 |
|
sprintf(painCave.errMsg, |
| 329 |
< |
"ForceManager::setupSwitching: switchingRadius (%f) is larger " |
| 330 |
< |
"than the cutoffRadius(%f)\n", rSwitch_, rCut_); |
| 331 |
< |
painCave.isFatal = 1; |
| 332 |
< |
painCave.severity = OPENMD_ERROR; |
| 329 |
> |
"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n" |
| 330 |
> |
"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n" |
| 331 |
> |
"\tswitchingRadius = %f. for this simulation\n", rSwitch_); |
| 332 |
> |
painCave.isFatal = 0; |
| 333 |
> |
painCave.severity = OPENMD_WARNING; |
| 334 |
|
simError(); |
| 335 |
|
} |
| 336 |
< |
} else { |
| 337 |
< |
rSwitch_ = 0.85 * rCut_; |
| 338 |
< |
sprintf(painCave.errMsg, |
| 339 |
< |
"ForceManager::setupSwitching: No value was set for the switchingRadius.\n" |
| 340 |
< |
"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n" |
| 341 |
< |
"\tswitchingRadius = %f. for this simulation\n", rSwitch_); |
| 342 |
< |
painCave.isFatal = 0; |
| 343 |
< |
painCave.severity = OPENMD_WARNING; |
| 344 |
< |
simError(); |
| 345 |
< |
} |
| 336 |
> |
} else { |
| 337 |
> |
if (mdFileVersion > 1) { |
| 338 |
> |
// throw an error if we define a switching radius and don't need one. |
| 339 |
> |
// older file versions should not do this. |
| 340 |
> |
if (simParams_->haveSwitchingRadius()) { |
| 341 |
> |
map<string, CutoffMethod>::const_iterator it; |
| 342 |
> |
string theMeth; |
| 343 |
> |
for (it = stringToCutoffMethod.begin(); |
| 344 |
> |
it != stringToCutoffMethod.end(); ++it) { |
| 345 |
> |
if (it->second == cutoffMethod_) { |
| 346 |
> |
theMeth = it->first; |
| 347 |
> |
break; |
| 348 |
> |
} |
| 349 |
> |
} |
| 350 |
> |
sprintf(painCave.errMsg, |
| 351 |
> |
"ForceManager::setupCutoffs: the cutoffMethod (%s)\n" |
| 352 |
> |
"\tis not set to SWITCHED, so switchingRadius value\n" |
| 353 |
> |
"\twill be ignored for this simulation\n", theMeth.c_str()); |
| 354 |
> |
painCave.isFatal = 0; |
| 355 |
> |
painCave.severity = OPENMD_WARNING; |
| 356 |
> |
simError(); |
| 357 |
> |
} |
| 358 |
> |
} |
| 359 |
> |
rSwitch_ = rCut_; |
| 360 |
> |
} |
| 361 |
|
|
| 362 |
|
// Default to cubic switching function. |
| 363 |
|
sft_ = cubic; |
| 385 |
|
switcher_->setSwitchType(sft_); |
| 386 |
|
switcher_->setSwitch(rSwitch_, rCut_); |
| 387 |
|
} |
| 388 |
+ |
|
| 389 |
+ |
|
| 390 |
+ |
|
| 391 |
|
|
| 392 |
|
void ForceManager::initialize() { |
| 393 |
|
|
| 394 |
|
if (!info_->isTopologyDone()) { |
| 395 |
+ |
|
| 396 |
|
info_->update(); |
| 397 |
|
interactionMan_->setSimInfo(info_); |
| 398 |
|
interactionMan_->initialize(); |
| 400 |
|
// We want to delay the cutoffs until after the interaction |
| 401 |
|
// manager has set up the atom-atom interactions so that we can |
| 402 |
|
// query them for suggested cutoff values |
| 273 |
– |
|
| 403 |
|
setupCutoffs(); |
| 275 |
– |
setupSwitching(); |
| 404 |
|
|
| 405 |
|
info_->prepareTopology(); |
| 406 |
+ |
|
| 407 |
+ |
doParticlePot_ = info_->getSimParams()->getOutputParticlePotential(); |
| 408 |
+ |
doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux(); |
| 409 |
+ |
if (doHeatFlux_) doParticlePot_ = true; |
| 410 |
+ |
|
| 411 |
+ |
doElectricField_ = info_->getSimParams()->getOutputElectricField(); |
| 412 |
+ |
|
| 413 |
|
} |
| 414 |
|
|
| 415 |
|
ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 416 |
|
|
| 417 |
< |
// Force fields can set options on how to scale van der Waals and electrostatic |
| 418 |
< |
// interactions for atoms connected via bonds, bends and torsions |
| 419 |
< |
// in this case the topological distance between atoms is: |
| 417 |
> |
// Force fields can set options on how to scale van der Waals and |
| 418 |
> |
// electrostatic interactions for atoms connected via bonds, bends |
| 419 |
> |
// and torsions in this case the topological distance between |
| 420 |
> |
// atoms is: |
| 421 |
|
// 0 = topologically unconnected |
| 422 |
|
// 1 = bonded together |
| 423 |
|
// 2 = connected via a bend |
| 439 |
|
electrostaticScale_[2] = fopts.getelectrostatic13scale(); |
| 440 |
|
electrostaticScale_[3] = fopts.getelectrostatic14scale(); |
| 441 |
|
|
| 442 |
+ |
if (info_->getSimParams()->haveElectricField()) { |
| 443 |
+ |
ElectricField* eField = new ElectricField(info_); |
| 444 |
+ |
perturbations_.push_back(eField); |
| 445 |
+ |
} |
| 446 |
+ |
|
| 447 |
+ |
usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions(); |
| 448 |
+ |
|
| 449 |
|
fDecomp_->distributeInitialData(); |
| 450 |
< |
|
| 450 |
> |
|
| 451 |
|
initialized_ = true; |
| 452 |
< |
|
| 452 |
> |
|
| 453 |
|
} |
| 454 |
< |
|
| 454 |
> |
|
| 455 |
|
void ForceManager::calcForces() { |
| 456 |
|
|
| 457 |
|
if (!initialized_) initialize(); |
| 458 |
< |
|
| 458 |
> |
|
| 459 |
|
preCalculation(); |
| 460 |
|
shortRangeInteractions(); |
| 461 |
|
longRangeInteractions(); |
| 472 |
|
Molecule::CutoffGroupIterator ci; |
| 473 |
|
CutoffGroup* cg; |
| 474 |
|
|
| 475 |
< |
// forces are zeroed here, before any are accumulated. |
| 475 |
> |
// forces and potentials are zeroed here, before any are |
| 476 |
> |
// accumulated. |
| 477 |
|
|
| 478 |
+ |
Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 479 |
+ |
|
| 480 |
+ |
snap->setBondPotential(0.0); |
| 481 |
+ |
snap->setBendPotential(0.0); |
| 482 |
+ |
snap->setTorsionPotential(0.0); |
| 483 |
+ |
snap->setInversionPotential(0.0); |
| 484 |
+ |
|
| 485 |
+ |
potVec zeroPot(0.0); |
| 486 |
+ |
snap->setLongRangePotential(zeroPot); |
| 487 |
+ |
snap->setExcludedPotentials(zeroPot); |
| 488 |
+ |
|
| 489 |
+ |
snap->setRestraintPotential(0.0); |
| 490 |
+ |
snap->setRawPotential(0.0); |
| 491 |
+ |
|
| 492 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 493 |
|
mol = info_->nextMolecule(mi)) { |
| 494 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 494 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; |
| 495 |
> |
atom = mol->nextAtom(ai)) { |
| 496 |
|
atom->zeroForcesAndTorques(); |
| 497 |
|
} |
| 498 |
< |
|
| 498 |
> |
|
| 499 |
|
//change the positions of atoms which belong to the rigidbodies |
| 500 |
|
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 501 |
|
rb = mol->nextRigidBody(rbIter)) { |
| 502 |
|
rb->zeroForcesAndTorques(); |
| 503 |
|
} |
| 504 |
< |
|
| 504 |
> |
|
| 505 |
|
if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){ |
| 506 |
|
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 507 |
|
cg = mol->nextCutoffGroup(ci)) { |
| 510 |
|
} |
| 511 |
|
} |
| 512 |
|
} |
| 354 |
– |
|
| 355 |
– |
// Zero out the stress tensor |
| 356 |
– |
tau *= 0.0; |
| 513 |
|
|
| 514 |
+ |
// Zero out the stress tensor |
| 515 |
+ |
stressTensor *= 0.0; |
| 516 |
+ |
// Zero out the heatFlux |
| 517 |
+ |
fDecomp_->setHeatFlux( Vector3d(0.0) ); |
| 518 |
|
} |
| 519 |
|
|
| 520 |
|
void ForceManager::shortRangeInteractions() { |
| 547 |
|
|
| 548 |
|
for (bond = mol->beginBond(bondIter); bond != NULL; |
| 549 |
|
bond = mol->nextBond(bondIter)) { |
| 550 |
< |
bond->calcForce(); |
| 550 |
> |
bond->calcForce(doParticlePot_); |
| 551 |
|
bondPotential += bond->getPotential(); |
| 552 |
|
} |
| 553 |
|
|
| 555 |
|
bend = mol->nextBend(bendIter)) { |
| 556 |
|
|
| 557 |
|
RealType angle; |
| 558 |
< |
bend->calcForce(angle); |
| 558 |
> |
bend->calcForce(angle, doParticlePot_); |
| 559 |
|
RealType currBendPot = bend->getPotential(); |
| 560 |
|
|
| 561 |
|
bendPotential += bend->getPotential(); |
| 565 |
|
dataSet.prev.angle = dataSet.curr.angle = angle; |
| 566 |
|
dataSet.prev.potential = dataSet.curr.potential = currBendPot; |
| 567 |
|
dataSet.deltaV = 0.0; |
| 568 |
< |
bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet)); |
| 568 |
> |
bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, |
| 569 |
> |
dataSet)); |
| 570 |
|
}else { |
| 571 |
|
i->second.prev.angle = i->second.curr.angle; |
| 572 |
|
i->second.prev.potential = i->second.curr.potential; |
| 580 |
|
for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; |
| 581 |
|
torsion = mol->nextTorsion(torsionIter)) { |
| 582 |
|
RealType angle; |
| 583 |
< |
torsion->calcForce(angle); |
| 583 |
> |
torsion->calcForce(angle, doParticlePot_); |
| 584 |
|
RealType currTorsionPot = torsion->getPotential(); |
| 585 |
|
torsionPotential += torsion->getPotential(); |
| 586 |
|
map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion); |
| 604 |
|
inversion != NULL; |
| 605 |
|
inversion = mol->nextInversion(inversionIter)) { |
| 606 |
|
RealType angle; |
| 607 |
< |
inversion->calcForce(angle); |
| 607 |
> |
inversion->calcForce(angle, doParticlePot_); |
| 608 |
|
RealType currInversionPot = inversion->getPotential(); |
| 609 |
|
inversionPotential += inversion->getPotential(); |
| 610 |
|
map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion); |
| 624 |
|
} |
| 625 |
|
} |
| 626 |
|
} |
| 627 |
< |
|
| 628 |
< |
RealType shortRangePotential = bondPotential + bendPotential + |
| 629 |
< |
torsionPotential + inversionPotential; |
| 627 |
> |
|
| 628 |
> |
#ifdef IS_MPI |
| 629 |
> |
// Collect from all nodes. This should eventually be moved into a |
| 630 |
> |
// SystemDecomposition, but this is a better place than in |
| 631 |
> |
// Thermo to do the collection. |
| 632 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE, |
| 633 |
> |
MPI::SUM); |
| 634 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE, |
| 635 |
> |
MPI::SUM); |
| 636 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1, |
| 637 |
> |
MPI::REALTYPE, MPI::SUM); |
| 638 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1, |
| 639 |
> |
MPI::REALTYPE, MPI::SUM); |
| 640 |
> |
#endif |
| 641 |
> |
|
| 642 |
|
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 643 |
< |
curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential; |
| 644 |
< |
curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential; |
| 645 |
< |
curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential; |
| 646 |
< |
curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential; |
| 647 |
< |
curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential; |
| 643 |
> |
|
| 644 |
> |
curSnapshot->setBondPotential(bondPotential); |
| 645 |
> |
curSnapshot->setBendPotential(bendPotential); |
| 646 |
> |
curSnapshot->setTorsionPotential(torsionPotential); |
| 647 |
> |
curSnapshot->setInversionPotential(inversionPotential); |
| 648 |
> |
|
| 649 |
> |
// RealType shortRangePotential = bondPotential + bendPotential + |
| 650 |
> |
// torsionPotential + inversionPotential; |
| 651 |
> |
|
| 652 |
> |
// curSnapshot->setShortRangePotential(shortRangePotential); |
| 653 |
|
} |
| 654 |
|
|
| 655 |
|
void ForceManager::longRangeInteractions() { |
| 656 |
< |
// some of this initial stuff will go away: |
| 656 |
> |
|
| 657 |
> |
|
| 658 |
|
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 659 |
|
DataStorage* config = &(curSnapshot->atomData); |
| 660 |
|
DataStorage* cgConfig = &(curSnapshot->cgData); |
| 482 |
– |
RealType* frc = config->getArrayPointer(DataStorage::dslForce); |
| 483 |
– |
RealType* pos = config->getArrayPointer(DataStorage::dslPosition); |
| 484 |
– |
RealType* trq = config->getArrayPointer(DataStorage::dslTorque); |
| 485 |
– |
RealType* A = config->getArrayPointer(DataStorage::dslAmat); |
| 486 |
– |
RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame); |
| 487 |
– |
RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot); |
| 661 |
|
|
| 662 |
< |
// new stuff starts here: |
| 663 |
< |
|
| 662 |
> |
//calculate the center of mass of cutoff group |
| 663 |
> |
|
| 664 |
> |
SimInfo::MoleculeIterator mi; |
| 665 |
> |
Molecule* mol; |
| 666 |
> |
Molecule::CutoffGroupIterator ci; |
| 667 |
> |
CutoffGroup* cg; |
| 668 |
> |
|
| 669 |
> |
if(info_->getNCutoffGroups() > 0){ |
| 670 |
> |
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 671 |
> |
mol = info_->nextMolecule(mi)) { |
| 672 |
> |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 673 |
> |
cg = mol->nextCutoffGroup(ci)) { |
| 674 |
> |
cg->updateCOM(); |
| 675 |
> |
} |
| 676 |
> |
} |
| 677 |
> |
} else { |
| 678 |
> |
// center of mass of the group is the same as position of the atom |
| 679 |
> |
// if cutoff group does not exist |
| 680 |
> |
cgConfig->position = config->position; |
| 681 |
> |
cgConfig->velocity = config->velocity; |
| 682 |
> |
} |
| 683 |
> |
|
| 684 |
|
fDecomp_->zeroWorkArrays(); |
| 685 |
|
fDecomp_->distributeData(); |
| 686 |
|
|
| 687 |
|
int cg1, cg2, atom1, atom2, topoDist; |
| 688 |
< |
Vector3d d_grp, dag, d; |
| 688 |
> |
Vector3d d_grp, dag, d, gvel2, vel2; |
| 689 |
|
RealType rgrpsq, rgrp, r2, r; |
| 690 |
|
RealType electroMult, vdwMult; |
| 691 |
|
RealType vij; |
| 692 |
< |
Vector3d fij, fg; |
| 692 |
> |
Vector3d fij, fg, f1; |
| 693 |
|
tuple3<RealType, RealType, RealType> cuts; |
| 694 |
|
RealType rCutSq; |
| 695 |
|
bool in_switching_region; |
| 696 |
|
RealType sw, dswdr, swderiv; |
| 697 |
< |
vector<int> atomListColumn, atomListRow, atomListLocal; |
| 697 |
> |
vector<int> atomListColumn, atomListRow; |
| 698 |
|
InteractionData idat; |
| 699 |
|
SelfData sdat; |
| 700 |
|
RealType mf; |
| 508 |
– |
potVec pot(0.0); |
| 509 |
– |
potVec longRangePotential(0.0); |
| 510 |
– |
RealType lrPot; |
| 701 |
|
RealType vpair; |
| 702 |
+ |
RealType dVdFQ1(0.0); |
| 703 |
+ |
RealType dVdFQ2(0.0); |
| 704 |
+ |
potVec longRangePotential(0.0); |
| 705 |
+ |
potVec workPot(0.0); |
| 706 |
+ |
potVec exPot(0.0); |
| 707 |
+ |
Vector3d eField1(0.0); |
| 708 |
+ |
Vector3d eField2(0.0); |
| 709 |
+ |
vector<int>::iterator ia, jb; |
| 710 |
|
|
| 711 |
|
int loopStart, loopEnd; |
| 712 |
|
|
| 713 |
+ |
idat.vdwMult = &vdwMult; |
| 714 |
+ |
idat.electroMult = &electroMult; |
| 715 |
+ |
idat.pot = &workPot; |
| 716 |
+ |
idat.excludedPot = &exPot; |
| 717 |
+ |
sdat.pot = fDecomp_->getEmbeddingPotential(); |
| 718 |
+ |
sdat.excludedPot = fDecomp_->getExcludedSelfPotential(); |
| 719 |
+ |
idat.vpair = &vpair; |
| 720 |
+ |
idat.dVdFQ1 = &dVdFQ1; |
| 721 |
+ |
idat.dVdFQ2 = &dVdFQ2; |
| 722 |
+ |
idat.eField1 = &eField1; |
| 723 |
+ |
idat.eField2 = &eField2; |
| 724 |
+ |
idat.f1 = &f1; |
| 725 |
+ |
idat.sw = &sw; |
| 726 |
+ |
idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false; |
| 727 |
+ |
idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false; |
| 728 |
+ |
idat.doParticlePot = doParticlePot_; |
| 729 |
+ |
idat.doElectricField = doElectricField_; |
| 730 |
+ |
sdat.doParticlePot = doParticlePot_; |
| 731 |
+ |
|
| 732 |
|
loopEnd = PAIR_LOOP; |
| 733 |
|
if (info_->requiresPrepair() ) { |
| 734 |
|
loopStart = PREPAIR_LOOP; |
| 735 |
|
} else { |
| 736 |
|
loopStart = PAIR_LOOP; |
| 737 |
|
} |
| 521 |
– |
|
| 522 |
– |
|
| 738 |
|
for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) { |
| 739 |
|
|
| 740 |
|
if (iLoop == loopStart) { |
| 741 |
|
bool update_nlist = fDecomp_->checkNeighborList(); |
| 742 |
< |
if (update_nlist) |
| 742 |
> |
if (update_nlist) { |
| 743 |
> |
if (!usePeriodicBoundaryConditions_) |
| 744 |
> |
Mat3x3d bbox = thermo->getBoundingBox(); |
| 745 |
|
neighborList = fDecomp_->buildNeighborList(); |
| 746 |
< |
} |
| 747 |
< |
|
| 746 |
> |
} |
| 747 |
> |
} |
| 748 |
> |
|
| 749 |
|
for (vector<pair<int, int> >::iterator it = neighborList.begin(); |
| 750 |
|
it != neighborList.end(); ++it) { |
| 751 |
|
|
| 755 |
|
cuts = fDecomp_->getGroupCutoffs(cg1, cg2); |
| 756 |
|
|
| 757 |
|
d_grp = fDecomp_->getIntergroupVector(cg1, cg2); |
| 758 |
+ |
|
| 759 |
|
curSnapshot->wrapVector(d_grp); |
| 760 |
|
rgrpsq = d_grp.lengthSquare(); |
| 542 |
– |
|
| 761 |
|
rCutSq = cuts.second; |
| 762 |
|
|
| 763 |
|
if (rgrpsq < rCutSq) { |
| 764 |
|
idat.rcut = &cuts.first; |
| 765 |
|
if (iLoop == PAIR_LOOP) { |
| 766 |
< |
vij *= 0.0; |
| 766 |
> |
vij = 0.0; |
| 767 |
|
fij = V3Zero; |
| 768 |
+ |
eField1 = V3Zero; |
| 769 |
+ |
eField2 = V3Zero; |
| 770 |
|
} |
| 771 |
|
|
| 772 |
|
in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, |
| 773 |
|
rgrp); |
| 774 |
|
|
| 555 |
– |
idat.sw = &sw; |
| 556 |
– |
|
| 775 |
|
atomListRow = fDecomp_->getAtomsInGroupRow(cg1); |
| 776 |
|
atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2); |
| 777 |
|
|
| 778 |
< |
for (vector<int>::iterator ia = atomListRow.begin(); |
| 778 |
> |
if (doHeatFlux_) |
| 779 |
> |
gvel2 = fDecomp_->getGroupVelocityColumn(cg2); |
| 780 |
> |
|
| 781 |
> |
for (ia = atomListRow.begin(); |
| 782 |
|
ia != atomListRow.end(); ++ia) { |
| 783 |
|
atom1 = (*ia); |
| 784 |
< |
|
| 785 |
< |
for (vector<int>::iterator jb = atomListColumn.begin(); |
| 784 |
> |
|
| 785 |
> |
for (jb = atomListColumn.begin(); |
| 786 |
|
jb != atomListColumn.end(); ++jb) { |
| 787 |
|
atom2 = (*jb); |
| 788 |
< |
|
| 789 |
< |
cerr << "doing atoms " << atom1 << " " << atom2 << "\n"; |
| 790 |
< |
if (!fDecomp_->skipAtomPair(atom1, atom2)) { |
| 570 |
< |
|
| 788 |
> |
|
| 789 |
> |
if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) { |
| 790 |
> |
|
| 791 |
|
vpair = 0.0; |
| 792 |
+ |
workPot = 0.0; |
| 793 |
+ |
exPot = 0.0; |
| 794 |
+ |
f1 = V3Zero; |
| 795 |
+ |
dVdFQ1 = 0.0; |
| 796 |
+ |
dVdFQ2 = 0.0; |
| 797 |
|
|
| 798 |
< |
cerr << "filling idat atoms " << atom1 << " " << atom2 << "\n"; |
| 799 |
< |
idat = fDecomp_->fillInteractionData(atom1, atom2); |
| 575 |
< |
cerr << "done with idat\n"; |
| 576 |
< |
|
| 798 |
> |
fDecomp_->fillInteractionData(idat, atom1, atom2); |
| 799 |
> |
|
| 800 |
|
topoDist = fDecomp_->getTopologicalDistance(atom1, atom2); |
| 801 |
|
vdwMult = vdwScale_[topoDist]; |
| 802 |
|
electroMult = electrostaticScale_[topoDist]; |
| 803 |
|
|
| 581 |
– |
idat.vdwMult = &vdwMult; |
| 582 |
– |
idat.electroMult = &electroMult; |
| 583 |
– |
idat.pot = &pot; |
| 584 |
– |
idat.vpair = &vpair; |
| 585 |
– |
|
| 804 |
|
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 805 |
|
idat.d = &d_grp; |
| 806 |
|
idat.r2 = &rgrpsq; |
| 807 |
+ |
if (doHeatFlux_) |
| 808 |
+ |
vel2 = gvel2; |
| 809 |
|
} else { |
| 810 |
|
d = fDecomp_->getInteratomicVector(atom1, atom2); |
| 811 |
|
curSnapshot->wrapVector( d ); |
| 812 |
|
r2 = d.lengthSquare(); |
| 813 |
|
idat.d = &d; |
| 814 |
|
idat.r2 = &r2; |
| 815 |
+ |
if (doHeatFlux_) |
| 816 |
+ |
vel2 = fDecomp_->getAtomVelocityColumn(atom2); |
| 817 |
|
} |
| 818 |
< |
|
| 819 |
< |
cerr << "d = " << d << "\n"; |
| 598 |
< |
cerr << "r2 = " << r2 << "\n"; |
| 599 |
< |
r = sqrt( r2 ); |
| 818 |
> |
|
| 819 |
> |
r = sqrt( *(idat.r2) ); |
| 820 |
|
idat.rij = &r; |
| 821 |
|
|
| 822 |
|
if (iLoop == PREPAIR_LOOP) { |
| 823 |
|
interactionMan_->doPrePair(idat); |
| 824 |
|
} else { |
| 605 |
– |
cerr << "doing doPair " << atom1 << " " << atom2 << " " << r << "\n"; |
| 825 |
|
interactionMan_->doPair(idat); |
| 826 |
|
fDecomp_->unpackInteractionData(idat, atom1, atom2); |
| 827 |
< |
vij += *(idat.vpair); |
| 828 |
< |
fij += *(idat.f1); |
| 829 |
< |
tau -= outProduct( *(idat.d), *(idat.f1)); |
| 827 |
> |
vij += vpair; |
| 828 |
> |
fij += f1; |
| 829 |
> |
stressTensor -= outProduct( *(idat.d), f1); |
| 830 |
> |
if (doHeatFlux_) |
| 831 |
> |
fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2)); |
| 832 |
|
} |
| 833 |
|
} |
| 834 |
|
} |
| 838 |
|
if (in_switching_region) { |
| 839 |
|
swderiv = vij * dswdr / rgrp; |
| 840 |
|
fg = swderiv * d_grp; |
| 620 |
– |
|
| 841 |
|
fij += fg; |
| 842 |
|
|
| 843 |
|
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 844 |
< |
tau -= outProduct( *(idat.d), fg); |
| 844 |
> |
if (!fDecomp_->skipAtomPair(atomListRow[0], |
| 845 |
> |
atomListColumn[0], |
| 846 |
> |
cg1, cg2)) { |
| 847 |
> |
stressTensor -= outProduct( *(idat.d), fg); |
| 848 |
> |
if (doHeatFlux_) |
| 849 |
> |
fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2)); |
| 850 |
> |
} |
| 851 |
|
} |
| 852 |
|
|
| 853 |
< |
for (vector<int>::iterator ia = atomListRow.begin(); |
| 853 |
> |
for (ia = atomListRow.begin(); |
| 854 |
|
ia != atomListRow.end(); ++ia) { |
| 855 |
|
atom1 = (*ia); |
| 856 |
|
mf = fDecomp_->getMassFactorRow(atom1); |
| 858 |
|
// presence in switching region |
| 859 |
|
fg = swderiv * d_grp * mf; |
| 860 |
|
fDecomp_->addForceToAtomRow(atom1, fg); |
| 635 |
– |
|
| 861 |
|
if (atomListRow.size() > 1) { |
| 862 |
|
if (info_->usesAtomicVirial()) { |
| 863 |
|
// find the distance between the atom |
| 864 |
|
// and the center of the cutoff group: |
| 865 |
|
dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1); |
| 866 |
< |
tau -= outProduct(dag, fg); |
| 866 |
> |
stressTensor -= outProduct(dag, fg); |
| 867 |
> |
if (doHeatFlux_) |
| 868 |
> |
fDecomp_->addToHeatFlux( dag * dot(fg, vel2)); |
| 869 |
|
} |
| 870 |
|
} |
| 871 |
|
} |
| 872 |
< |
for (vector<int>::iterator jb = atomListColumn.begin(); |
| 872 |
> |
for (jb = atomListColumn.begin(); |
| 873 |
|
jb != atomListColumn.end(); ++jb) { |
| 874 |
|
atom2 = (*jb); |
| 875 |
|
mf = fDecomp_->getMassFactorColumn(atom2); |
| 883 |
|
// find the distance between the atom |
| 884 |
|
// and the center of the cutoff group: |
| 885 |
|
dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2); |
| 886 |
< |
tau -= outProduct(dag, fg); |
| 886 |
> |
stressTensor -= outProduct(dag, fg); |
| 887 |
> |
if (doHeatFlux_) |
| 888 |
> |
fDecomp_->addToHeatFlux( dag * dot(fg, vel2)); |
| 889 |
|
} |
| 890 |
|
} |
| 891 |
|
} |
| 892 |
|
} |
| 893 |
< |
//if (!SIM_uses_AtomicVirial) { |
| 894 |
< |
// tau -= outProduct(d_grp, fij); |
| 893 |
> |
//if (!info_->usesAtomicVirial()) { |
| 894 |
> |
// stressTensor -= outProduct(d_grp, fij); |
| 895 |
> |
// if (doHeatFlux_) |
| 896 |
> |
// fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2)); |
| 897 |
|
//} |
| 898 |
|
} |
| 899 |
|
} |
| 900 |
|
} |
| 901 |
|
|
| 902 |
|
if (iLoop == PREPAIR_LOOP) { |
| 903 |
< |
if (info_->requiresPrepair()) { |
| 903 |
> |
if (info_->requiresPrepair()) { |
| 904 |
> |
|
| 905 |
|
fDecomp_->collectIntermediateData(); |
| 906 |
|
|
| 907 |
< |
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 908 |
< |
sdat = fDecomp_->fillSelfData(atom1); |
| 907 |
> |
for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 908 |
> |
fDecomp_->fillSelfData(sdat, atom1); |
| 909 |
|
interactionMan_->doPreForce(sdat); |
| 910 |
|
} |
| 911 |
|
|
| 912 |
< |
fDecomp_->distributeIntermediateData(); |
| 912 |
> |
fDecomp_->distributeIntermediateData(); |
| 913 |
> |
|
| 914 |
|
} |
| 915 |
|
} |
| 683 |
– |
|
| 916 |
|
} |
| 917 |
|
|
| 918 |
+ |
// collects pairwise information |
| 919 |
|
fDecomp_->collectData(); |
| 687 |
– |
|
| 688 |
– |
if ( info_->requiresSkipCorrection() ) { |
| 689 |
– |
|
| 690 |
– |
for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) { |
| 691 |
– |
|
| 692 |
– |
vector<int> skipList = fDecomp_->getSkipsForAtom( atom1 ); |
| 920 |
|
|
| 694 |
– |
for (vector<int>::iterator jb = skipList.begin(); |
| 695 |
– |
jb != skipList.end(); ++jb) { |
| 696 |
– |
|
| 697 |
– |
atom2 = (*jb); |
| 698 |
– |
idat = fDecomp_->fillSkipData(atom1, atom2); |
| 699 |
– |
interactionMan_->doSkipCorrection(idat); |
| 700 |
– |
|
| 701 |
– |
} |
| 702 |
– |
} |
| 703 |
– |
} |
| 704 |
– |
|
| 921 |
|
if (info_->requiresSelfCorrection()) { |
| 922 |
< |
|
| 923 |
< |
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 708 |
< |
sdat = fDecomp_->fillSelfData(atom1); |
| 922 |
> |
for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 923 |
> |
fDecomp_->fillSelfData(sdat, atom1); |
| 924 |
|
interactionMan_->doSelfCorrection(sdat); |
| 925 |
|
} |
| 711 |
– |
|
| 926 |
|
} |
| 927 |
|
|
| 928 |
< |
longRangePotential = fDecomp_->getLongRangePotential(); |
| 929 |
< |
lrPot = longRangePotential.sum(); |
| 928 |
> |
// collects single-atom information |
| 929 |
> |
fDecomp_->collectSelfData(); |
| 930 |
|
|
| 931 |
< |
//store the tau and long range potential |
| 932 |
< |
curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot; |
| 933 |
< |
curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY]; |
| 934 |
< |
curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY]; |
| 931 |
> |
longRangePotential = *(fDecomp_->getEmbeddingPotential()) + |
| 932 |
> |
*(fDecomp_->getPairwisePotential()); |
| 933 |
> |
|
| 934 |
> |
curSnapshot->setLongRangePotential(longRangePotential); |
| 935 |
> |
|
| 936 |
> |
curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) + |
| 937 |
> |
*(fDecomp_->getExcludedPotential())); |
| 938 |
> |
|
| 939 |
|
} |
| 940 |
|
|
| 941 |
|
|
| 942 |
|
void ForceManager::postCalculation() { |
| 943 |
+ |
|
| 944 |
+ |
vector<Perturbation*>::iterator pi; |
| 945 |
+ |
for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) { |
| 946 |
+ |
(*pi)->applyPerturbation(); |
| 947 |
+ |
} |
| 948 |
+ |
|
| 949 |
|
SimInfo::MoleculeIterator mi; |
| 950 |
|
Molecule* mol; |
| 951 |
|
Molecule::RigidBodyIterator rbIter; |
| 952 |
|
RigidBody* rb; |
| 953 |
|
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 954 |
< |
|
| 954 |
> |
|
| 955 |
|
// collect the atomic forces onto rigid bodies |
| 956 |
|
|
| 957 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 959 |
|
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 960 |
|
rb = mol->nextRigidBody(rbIter)) { |
| 961 |
|
Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial(); |
| 962 |
< |
tau += rbTau; |
| 962 |
> |
stressTensor += rbTau; |
| 963 |
|
} |
| 964 |
|
} |
| 965 |
|
|
| 966 |
|
#ifdef IS_MPI |
| 967 |
< |
Mat3x3d tmpTau(tau); |
| 968 |
< |
MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(), |
| 745 |
< |
9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD); |
| 967 |
> |
MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9, |
| 968 |
> |
MPI::REALTYPE, MPI::SUM); |
| 969 |
|
#endif |
| 970 |
< |
curSnapshot->statData.setTau(tau); |
| 971 |
< |
} |
| 970 |
> |
curSnapshot->setStressTensor(stressTensor); |
| 971 |
> |
|
| 972 |
> |
if (info_->getSimParams()->getUseLongRangeCorrections()) { |
| 973 |
> |
/* |
| 974 |
> |
RealType vol = curSnapshot->getVolume(); |
| 975 |
> |
RealType Elrc(0.0); |
| 976 |
> |
RealType Wlrc(0.0); |
| 977 |
|
|
| 978 |
< |
} //end namespace OpenMD |
| 978 |
> |
set<AtomType*>::iterator i; |
| 979 |
> |
set<AtomType*>::iterator j; |
| 980 |
> |
|
| 981 |
> |
RealType n_i, n_j; |
| 982 |
> |
RealType rho_i, rho_j; |
| 983 |
> |
pair<RealType, RealType> LRI; |
| 984 |
> |
|
| 985 |
> |
for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) { |
| 986 |
> |
n_i = RealType(info_->getGlobalCountOfType(*i)); |
| 987 |
> |
rho_i = n_i / vol; |
| 988 |
> |
for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) { |
| 989 |
> |
n_j = RealType(info_->getGlobalCountOfType(*j)); |
| 990 |
> |
rho_j = n_j / vol; |
| 991 |
> |
|
| 992 |
> |
LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) ); |
| 993 |
> |
|
| 994 |
> |
Elrc += n_i * rho_j * LRI.first; |
| 995 |
> |
Wlrc -= rho_i * rho_j * LRI.second; |
| 996 |
> |
} |
| 997 |
> |
} |
| 998 |
> |
Elrc *= 2.0 * NumericConstant::PI; |
| 999 |
> |
Wlrc *= 2.0 * NumericConstant::PI; |
| 1000 |
> |
|
| 1001 |
> |
RealType lrp = curSnapshot->getLongRangePotential(); |
| 1002 |
> |
curSnapshot->setLongRangePotential(lrp + Elrc); |
| 1003 |
> |
stressTensor += Wlrc * SquareMatrix3<RealType>::identity(); |
| 1004 |
> |
curSnapshot->setStressTensor(stressTensor); |
| 1005 |
> |
*/ |
| 1006 |
> |
|
| 1007 |
> |
} |
| 1008 |
> |
} |
| 1009 |
> |
} |
