| 47 |
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* @version 1.0 |
| 48 |
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*/ |
| 49 |
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|
| 50 |
+ |
|
| 51 |
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#include "brains/ForceManager.hpp" |
| 52 |
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#include "primitives/Molecule.hpp" |
| 52 |
– |
#include "UseTheForce/doForces_interface.h" |
| 53 |
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#define __OPENMD_C |
| 54 |
– |
#include "UseTheForce/DarkSide/fInteractionMap.h" |
| 54 |
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#include "utils/simError.h" |
| 55 |
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#include "primitives/Bond.hpp" |
| 56 |
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#include "primitives/Bend.hpp" |
| 57 |
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#include "primitives/Torsion.hpp" |
| 58 |
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#include "primitives/Inversion.hpp" |
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+ |
#include "nonbonded/NonBondedInteraction.hpp" |
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+ |
#include "parallel/ForceMatrixDecomposition.hpp" |
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|
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+ |
#include <cstdio> |
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+ |
#include <iostream> |
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+ |
#include <iomanip> |
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+ |
|
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+ |
using namespace std; |
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namespace OpenMD { |
| 68 |
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|
| 69 |
< |
ForceManager::ForceManager(SimInfo * info) : info_(info), |
| 70 |
< |
NBforcesInitialized_(false) { |
| 71 |
< |
lj_ = LJ::Instance(); |
| 72 |
< |
lj_->setForceField(info_->getForceField()); |
| 69 |
> |
ForceManager::ForceManager(SimInfo * info) : info_(info) { |
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> |
forceField_ = info_->getForceField(); |
| 71 |
> |
interactionMan_ = new InteractionManager(); |
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> |
fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_); |
| 73 |
> |
} |
| 74 |
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|
| 75 |
< |
gb_ = GB::Instance(); |
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< |
gb_->setForceField(info_->getForceField()); |
| 75 |
> |
/** |
| 76 |
> |
* setupCutoffs |
| 77 |
> |
* |
| 78 |
> |
* Sets the values of cutoffRadius, switchingRadius, cutoffMethod, |
| 79 |
> |
* and cutoffPolicy |
| 80 |
> |
* |
| 81 |
> |
* cutoffRadius : realType |
| 82 |
> |
* If the cutoffRadius was explicitly set, use that value. |
| 83 |
> |
* If the cutoffRadius was not explicitly set: |
| 84 |
> |
* Are there electrostatic atoms? Use 12.0 Angstroms. |
| 85 |
> |
* No electrostatic atoms? Poll the atom types present in the |
| 86 |
> |
* simulation for suggested cutoff values (e.g. 2.5 * sigma). |
| 87 |
> |
* Use the maximum suggested value that was found. |
| 88 |
> |
* |
| 89 |
> |
* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, |
| 90 |
> |
* or SHIFTED_POTENTIAL) |
| 91 |
> |
* If cutoffMethod was explicitly set, use that choice. |
| 92 |
> |
* If cutoffMethod was not explicitly set, use SHIFTED_FORCE |
| 93 |
> |
* |
| 94 |
> |
* cutoffPolicy : (one of MIX, MAX, TRADITIONAL) |
| 95 |
> |
* If cutoffPolicy was explicitly set, use that choice. |
| 96 |
> |
* If cutoffPolicy was not explicitly set, use TRADITIONAL |
| 97 |
> |
* |
| 98 |
> |
* switchingRadius : realType |
| 99 |
> |
* If the cutoffMethod was set to SWITCHED: |
| 100 |
> |
* If the switchingRadius was explicitly set, use that value |
| 101 |
> |
* (but do a sanity check first). |
| 102 |
> |
* If the switchingRadius was not explicitly set: use 0.85 * |
| 103 |
> |
* cutoffRadius_ |
| 104 |
> |
* If the cutoffMethod was not set to SWITCHED: |
| 105 |
> |
* Set switchingRadius equal to cutoffRadius for safety. |
| 106 |
> |
*/ |
| 107 |
> |
void ForceManager::setupCutoffs() { |
| 108 |
> |
|
| 109 |
> |
Globals* simParams_ = info_->getSimParams(); |
| 110 |
> |
ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions(); |
| 111 |
> |
int mdFileVersion; |
| 112 |
> |
|
| 113 |
> |
if (simParams_->haveMDfileVersion()) |
| 114 |
> |
mdFileVersion = simParams_->getMDfileVersion(); |
| 115 |
> |
else |
| 116 |
> |
mdFileVersion = 0; |
| 117 |
> |
|
| 118 |
> |
if (simParams_->haveCutoffRadius()) { |
| 119 |
> |
rCut_ = simParams_->getCutoffRadius(); |
| 120 |
> |
} else { |
| 121 |
> |
if (info_->usesElectrostaticAtoms()) { |
| 122 |
> |
sprintf(painCave.errMsg, |
| 123 |
> |
"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n" |
| 124 |
> |
"\tOpenMD will use a default value of 12.0 angstroms" |
| 125 |
> |
"\tfor the cutoffRadius.\n"); |
| 126 |
> |
painCave.isFatal = 0; |
| 127 |
> |
painCave.severity = OPENMD_INFO; |
| 128 |
> |
simError(); |
| 129 |
> |
rCut_ = 12.0; |
| 130 |
> |
} else { |
| 131 |
> |
RealType thisCut; |
| 132 |
> |
set<AtomType*>::iterator i; |
| 133 |
> |
set<AtomType*> atomTypes; |
| 134 |
> |
atomTypes = info_->getSimulatedAtomTypes(); |
| 135 |
> |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
| 136 |
> |
thisCut = interactionMan_->getSuggestedCutoffRadius((*i)); |
| 137 |
> |
rCut_ = max(thisCut, rCut_); |
| 138 |
> |
} |
| 139 |
> |
sprintf(painCave.errMsg, |
| 140 |
> |
"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n" |
| 141 |
> |
"\tOpenMD will use %lf angstroms.\n", |
| 142 |
> |
rCut_); |
| 143 |
> |
painCave.isFatal = 0; |
| 144 |
> |
painCave.severity = OPENMD_INFO; |
| 145 |
> |
simError(); |
| 146 |
> |
} |
| 147 |
> |
} |
| 148 |
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|
| 149 |
< |
eam_ = EAM::Instance(); |
| 150 |
< |
eam_->setForceField(info_->getForceField()); |
| 151 |
< |
} |
| 152 |
< |
|
| 153 |
< |
void ForceManager::calcForces() { |
| 149 |
> |
fDecomp_->setUserCutoff(rCut_); |
| 150 |
> |
interactionMan_->setCutoffRadius(rCut_); |
| 151 |
> |
|
| 152 |
> |
map<string, CutoffMethod> stringToCutoffMethod; |
| 153 |
> |
stringToCutoffMethod["HARD"] = HARD; |
| 154 |
> |
stringToCutoffMethod["SWITCHED"] = SWITCHED; |
| 155 |
> |
stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL; |
| 156 |
> |
stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE; |
| 157 |
> |
|
| 158 |
> |
if (simParams_->haveCutoffMethod()) { |
| 159 |
> |
string cutMeth = toUpperCopy(simParams_->getCutoffMethod()); |
| 160 |
> |
map<string, CutoffMethod>::iterator i; |
| 161 |
> |
i = stringToCutoffMethod.find(cutMeth); |
| 162 |
> |
if (i == stringToCutoffMethod.end()) { |
| 163 |
> |
sprintf(painCave.errMsg, |
| 164 |
> |
"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n" |
| 165 |
> |
"\tShould be one of: " |
| 166 |
> |
"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n", |
| 167 |
> |
cutMeth.c_str()); |
| 168 |
> |
painCave.isFatal = 1; |
| 169 |
> |
painCave.severity = OPENMD_ERROR; |
| 170 |
> |
simError(); |
| 171 |
> |
} else { |
| 172 |
> |
cutoffMethod_ = i->second; |
| 173 |
> |
} |
| 174 |
> |
} else { |
| 175 |
> |
if (mdFileVersion > 1) { |
| 176 |
> |
sprintf(painCave.errMsg, |
| 177 |
> |
"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n" |
| 178 |
> |
"\tOpenMD will use SHIFTED_FORCE.\n"); |
| 179 |
> |
painCave.isFatal = 0; |
| 180 |
> |
painCave.severity = OPENMD_INFO; |
| 181 |
> |
simError(); |
| 182 |
> |
cutoffMethod_ = SHIFTED_FORCE; |
| 183 |
> |
} else { |
| 184 |
> |
// handle the case where the old file version was in play |
| 185 |
> |
// (there should be no cutoffMethod, so we have to deduce it |
| 186 |
> |
// from other data). |
| 187 |
> |
|
| 188 |
> |
sprintf(painCave.errMsg, |
| 189 |
> |
"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n" |
| 190 |
> |
"\tOpenMD found a file which does not set a cutoffMethod.\n" |
| 191 |
> |
"\tOpenMD will attempt to deduce a cutoffMethod using the\n" |
| 192 |
> |
"\tbehavior of the older (version 1) code. To remove this\n" |
| 193 |
> |
"\twarning, add an explicit cutoffMethod and change the top\n" |
| 194 |
> |
"\tof the file so that it begins with <OpenMD version=2>\n"); |
| 195 |
> |
painCave.isFatal = 0; |
| 196 |
> |
painCave.severity = OPENMD_WARNING; |
| 197 |
> |
simError(); |
| 198 |
> |
|
| 199 |
> |
// The old file version tethered the shifting behavior to the |
| 200 |
> |
// electrostaticSummationMethod keyword. |
| 201 |
> |
|
| 202 |
> |
if (simParams_->haveElectrostaticSummationMethod()) { |
| 203 |
> |
std::string myMethod = simParams_->getElectrostaticSummationMethod(); |
| 204 |
> |
toUpper(myMethod); |
| 205 |
> |
|
| 206 |
> |
if (myMethod == "SHIFTED_POTENTIAL") { |
| 207 |
> |
cutoffMethod_ = SHIFTED_POTENTIAL; |
| 208 |
> |
} else if (myMethod == "SHIFTED_FORCE") { |
| 209 |
> |
cutoffMethod_ = SHIFTED_FORCE; |
| 210 |
> |
} |
| 211 |
> |
|
| 212 |
> |
if (simParams_->haveSwitchingRadius()) |
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> |
rSwitch_ = simParams_->getSwitchingRadius(); |
| 214 |
> |
|
| 215 |
> |
if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") { |
| 216 |
> |
if (simParams_->haveSwitchingRadius()){ |
| 217 |
> |
sprintf(painCave.errMsg, |
| 218 |
> |
"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n" |
| 219 |
> |
"\tA value was set for the switchingRadius\n" |
| 220 |
> |
"\teven though the electrostaticSummationMethod was\n" |
| 221 |
> |
"\tset to %s\n", myMethod.c_str()); |
| 222 |
> |
painCave.severity = OPENMD_WARNING; |
| 223 |
> |
painCave.isFatal = 1; |
| 224 |
> |
simError(); |
| 225 |
> |
} |
| 226 |
> |
} |
| 227 |
> |
if (abs(rCut_ - rSwitch_) < 0.0001) { |
| 228 |
> |
if (cutoffMethod_ == SHIFTED_FORCE) { |
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> |
sprintf(painCave.errMsg, |
| 230 |
> |
"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n" |
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> |
"\tcutoffRadius and switchingRadius are set to the\n" |
| 232 |
> |
"\tsame value. OpenMD will use shifted force\n" |
| 233 |
> |
"\tpotentials instead of switching functions.\n"); |
| 234 |
> |
painCave.isFatal = 0; |
| 235 |
> |
painCave.severity = OPENMD_WARNING; |
| 236 |
> |
simError(); |
| 237 |
> |
} else { |
| 238 |
> |
cutoffMethod_ = SHIFTED_POTENTIAL; |
| 239 |
> |
sprintf(painCave.errMsg, |
| 240 |
> |
"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n" |
| 241 |
> |
"\tcutoffRadius and switchingRadius are set to the\n" |
| 242 |
> |
"\tsame value. OpenMD will use shifted potentials\n" |
| 243 |
> |
"\tinstead of switching functions.\n"); |
| 244 |
> |
painCave.isFatal = 0; |
| 245 |
> |
painCave.severity = OPENMD_WARNING; |
| 246 |
> |
simError(); |
| 247 |
> |
} |
| 248 |
> |
} |
| 249 |
> |
} |
| 250 |
> |
} |
| 251 |
> |
} |
| 252 |
> |
|
| 253 |
> |
map<string, CutoffPolicy> stringToCutoffPolicy; |
| 254 |
> |
stringToCutoffPolicy["MIX"] = MIX; |
| 255 |
> |
stringToCutoffPolicy["MAX"] = MAX; |
| 256 |
> |
stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL; |
| 257 |
> |
|
| 258 |
> |
std::string cutPolicy; |
| 259 |
> |
if (forceFieldOptions_.haveCutoffPolicy()){ |
| 260 |
> |
cutPolicy = forceFieldOptions_.getCutoffPolicy(); |
| 261 |
> |
}else if (simParams_->haveCutoffPolicy()) { |
| 262 |
> |
cutPolicy = simParams_->getCutoffPolicy(); |
| 263 |
> |
} |
| 264 |
> |
|
| 265 |
> |
if (!cutPolicy.empty()){ |
| 266 |
> |
toUpper(cutPolicy); |
| 267 |
> |
map<string, CutoffPolicy>::iterator i; |
| 268 |
> |
i = stringToCutoffPolicy.find(cutPolicy); |
| 269 |
> |
|
| 270 |
> |
if (i == stringToCutoffPolicy.end()) { |
| 271 |
> |
sprintf(painCave.errMsg, |
| 272 |
> |
"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n" |
| 273 |
> |
"\tShould be one of: " |
| 274 |
> |
"MIX, MAX, or TRADITIONAL\n", |
| 275 |
> |
cutPolicy.c_str()); |
| 276 |
> |
painCave.isFatal = 1; |
| 277 |
> |
painCave.severity = OPENMD_ERROR; |
| 278 |
> |
simError(); |
| 279 |
> |
} else { |
| 280 |
> |
cutoffPolicy_ = i->second; |
| 281 |
> |
} |
| 282 |
> |
} else { |
| 283 |
> |
sprintf(painCave.errMsg, |
| 284 |
> |
"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n" |
| 285 |
> |
"\tOpenMD will use TRADITIONAL.\n"); |
| 286 |
> |
painCave.isFatal = 0; |
| 287 |
> |
painCave.severity = OPENMD_INFO; |
| 288 |
> |
simError(); |
| 289 |
> |
cutoffPolicy_ = TRADITIONAL; |
| 290 |
> |
} |
| 291 |
> |
|
| 292 |
> |
fDecomp_->setCutoffPolicy(cutoffPolicy_); |
| 293 |
> |
|
| 294 |
> |
// create the switching function object: |
| 295 |
> |
|
| 296 |
> |
switcher_ = new SwitchingFunction(); |
| 297 |
> |
|
| 298 |
> |
if (cutoffMethod_ == SWITCHED) { |
| 299 |
> |
if (simParams_->haveSwitchingRadius()) { |
| 300 |
> |
rSwitch_ = simParams_->getSwitchingRadius(); |
| 301 |
> |
if (rSwitch_ > rCut_) { |
| 302 |
> |
sprintf(painCave.errMsg, |
| 303 |
> |
"ForceManager::setupCutoffs: switchingRadius (%f) is larger " |
| 304 |
> |
"than the cutoffRadius(%f)\n", rSwitch_, rCut_); |
| 305 |
> |
painCave.isFatal = 1; |
| 306 |
> |
painCave.severity = OPENMD_ERROR; |
| 307 |
> |
simError(); |
| 308 |
> |
} |
| 309 |
> |
} else { |
| 310 |
> |
rSwitch_ = 0.85 * rCut_; |
| 311 |
> |
sprintf(painCave.errMsg, |
| 312 |
> |
"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n" |
| 313 |
> |
"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n" |
| 314 |
> |
"\tswitchingRadius = %f. for this simulation\n", rSwitch_); |
| 315 |
> |
painCave.isFatal = 0; |
| 316 |
> |
painCave.severity = OPENMD_WARNING; |
| 317 |
> |
simError(); |
| 318 |
> |
} |
| 319 |
> |
} else { |
| 320 |
> |
if (mdFileVersion > 1) { |
| 321 |
> |
// throw an error if we define a switching radius and don't need one. |
| 322 |
> |
// older file versions should not do this. |
| 323 |
> |
if (simParams_->haveSwitchingRadius()) { |
| 324 |
> |
map<string, CutoffMethod>::const_iterator it; |
| 325 |
> |
string theMeth; |
| 326 |
> |
for (it = stringToCutoffMethod.begin(); |
| 327 |
> |
it != stringToCutoffMethod.end(); ++it) { |
| 328 |
> |
if (it->second == cutoffMethod_) { |
| 329 |
> |
theMeth = it->first; |
| 330 |
> |
break; |
| 331 |
> |
} |
| 332 |
> |
} |
| 333 |
> |
sprintf(painCave.errMsg, |
| 334 |
> |
"ForceManager::setupCutoffs: the cutoffMethod (%s)\n" |
| 335 |
> |
"\tis not set to SWITCHED, so switchingRadius value\n" |
| 336 |
> |
"\twill be ignored for this simulation\n", theMeth.c_str()); |
| 337 |
> |
painCave.isFatal = 0; |
| 338 |
> |
painCave.severity = OPENMD_WARNING; |
| 339 |
> |
simError(); |
| 340 |
> |
} |
| 341 |
> |
} |
| 342 |
> |
rSwitch_ = rCut_; |
| 343 |
> |
} |
| 344 |
|
|
| 345 |
< |
if (!info_->isFortranInitialized()) { |
| 345 |
> |
// Default to cubic switching function. |
| 346 |
> |
sft_ = cubic; |
| 347 |
> |
if (simParams_->haveSwitchingFunctionType()) { |
| 348 |
> |
string funcType = simParams_->getSwitchingFunctionType(); |
| 349 |
> |
toUpper(funcType); |
| 350 |
> |
if (funcType == "CUBIC") { |
| 351 |
> |
sft_ = cubic; |
| 352 |
> |
} else { |
| 353 |
> |
if (funcType == "FIFTH_ORDER_POLYNOMIAL") { |
| 354 |
> |
sft_ = fifth_order_poly; |
| 355 |
> |
} else { |
| 356 |
> |
// throw error |
| 357 |
> |
sprintf( painCave.errMsg, |
| 358 |
> |
"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n" |
| 359 |
> |
"\tswitchingFunctionType must be one of: " |
| 360 |
> |
"\"cubic\" or \"fifth_order_polynomial\".", |
| 361 |
> |
funcType.c_str() ); |
| 362 |
> |
painCave.isFatal = 1; |
| 363 |
> |
painCave.severity = OPENMD_ERROR; |
| 364 |
> |
simError(); |
| 365 |
> |
} |
| 366 |
> |
} |
| 367 |
> |
} |
| 368 |
> |
switcher_->setSwitchType(sft_); |
| 369 |
> |
switcher_->setSwitch(rSwitch_, rCut_); |
| 370 |
> |
interactionMan_->setSwitchingRadius(rSwitch_); |
| 371 |
> |
} |
| 372 |
> |
|
| 373 |
> |
|
| 374 |
> |
|
| 375 |
> |
|
| 376 |
> |
void ForceManager::initialize() { |
| 377 |
> |
|
| 378 |
> |
if (!info_->isTopologyDone()) { |
| 379 |
> |
|
| 380 |
|
info_->update(); |
| 381 |
+ |
interactionMan_->setSimInfo(info_); |
| 382 |
+ |
interactionMan_->initialize(); |
| 383 |
+ |
|
| 384 |
+ |
// We want to delay the cutoffs until after the interaction |
| 385 |
+ |
// manager has set up the atom-atom interactions so that we can |
| 386 |
+ |
// query them for suggested cutoff values |
| 387 |
+ |
setupCutoffs(); |
| 388 |
+ |
|
| 389 |
+ |
info_->prepareTopology(); |
| 390 |
|
} |
| 391 |
+ |
|
| 392 |
+ |
ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 393 |
|
|
| 394 |
< |
preCalculation(); |
| 394 |
> |
// Force fields can set options on how to scale van der Waals and |
| 395 |
> |
// electrostatic interactions for atoms connected via bonds, bends |
| 396 |
> |
// and torsions in this case the topological distance between |
| 397 |
> |
// atoms is: |
| 398 |
> |
// 0 = topologically unconnected |
| 399 |
> |
// 1 = bonded together |
| 400 |
> |
// 2 = connected via a bend |
| 401 |
> |
// 3 = connected via a torsion |
| 402 |
|
|
| 403 |
< |
calcShortRangeInteraction(); |
| 403 |
> |
vdwScale_.reserve(4); |
| 404 |
> |
fill(vdwScale_.begin(), vdwScale_.end(), 0.0); |
| 405 |
|
|
| 406 |
< |
calcLongRangeInteraction(); |
| 406 |
> |
electrostaticScale_.reserve(4); |
| 407 |
> |
fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0); |
| 408 |
|
|
| 409 |
< |
postCalculation(); |
| 409 |
> |
vdwScale_[0] = 1.0; |
| 410 |
> |
vdwScale_[1] = fopts.getvdw12scale(); |
| 411 |
> |
vdwScale_[2] = fopts.getvdw13scale(); |
| 412 |
> |
vdwScale_[3] = fopts.getvdw14scale(); |
| 413 |
|
|
| 414 |
+ |
electrostaticScale_[0] = 1.0; |
| 415 |
+ |
electrostaticScale_[1] = fopts.getelectrostatic12scale(); |
| 416 |
+ |
electrostaticScale_[2] = fopts.getelectrostatic13scale(); |
| 417 |
+ |
electrostaticScale_[3] = fopts.getelectrostatic14scale(); |
| 418 |
+ |
|
| 419 |
+ |
fDecomp_->distributeInitialData(); |
| 420 |
+ |
|
| 421 |
+ |
initialized_ = true; |
| 422 |
+ |
|
| 423 |
|
} |
| 424 |
+ |
|
| 425 |
+ |
void ForceManager::calcForces() { |
| 426 |
+ |
|
| 427 |
+ |
if (!initialized_) initialize(); |
| 428 |
+ |
|
| 429 |
+ |
preCalculation(); |
| 430 |
+ |
shortRangeInteractions(); |
| 431 |
+ |
longRangeInteractions(); |
| 432 |
+ |
postCalculation(); |
| 433 |
+ |
} |
| 434 |
|
|
| 435 |
|
void ForceManager::preCalculation() { |
| 436 |
|
SimInfo::MoleculeIterator mi; |
| 439 |
|
Atom* atom; |
| 440 |
|
Molecule::RigidBodyIterator rbIter; |
| 441 |
|
RigidBody* rb; |
| 442 |
+ |
Molecule::CutoffGroupIterator ci; |
| 443 |
+ |
CutoffGroup* cg; |
| 444 |
|
|
| 445 |
|
// forces are zeroed here, before any are accumulated. |
| 100 |
– |
// NOTE: do not rezero the forces in Fortran. |
| 446 |
|
|
| 447 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 448 |
|
mol = info_->nextMolecule(mi)) { |
| 449 |
< |
for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) { |
| 449 |
> |
for(atom = mol->beginAtom(ai); atom != NULL; |
| 450 |
> |
atom = mol->nextAtom(ai)) { |
| 451 |
|
atom->zeroForcesAndTorques(); |
| 452 |
|
} |
| 453 |
< |
|
| 453 |
> |
|
| 454 |
|
//change the positions of atoms which belong to the rigidbodies |
| 455 |
|
for (rb = mol->beginRigidBody(rbIter); rb != NULL; |
| 456 |
|
rb = mol->nextRigidBody(rbIter)) { |
| 457 |
|
rb->zeroForcesAndTorques(); |
| 458 |
|
} |
| 459 |
< |
|
| 459 |
> |
|
| 460 |
> |
if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){ |
| 461 |
> |
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 462 |
> |
cg = mol->nextCutoffGroup(ci)) { |
| 463 |
> |
//calculate the center of mass of cutoff group |
| 464 |
> |
cg->updateCOM(); |
| 465 |
> |
} |
| 466 |
> |
} |
| 467 |
|
} |
| 468 |
|
|
| 469 |
|
// Zero out the stress tensor |
| 471 |
|
|
| 472 |
|
} |
| 473 |
|
|
| 474 |
< |
void ForceManager::calcShortRangeInteraction() { |
| 474 |
> |
void ForceManager::shortRangeInteractions() { |
| 475 |
|
Molecule* mol; |
| 476 |
|
RigidBody* rb; |
| 477 |
|
Bond* bond; |
| 513 |
|
RealType currBendPot = bend->getPotential(); |
| 514 |
|
|
| 515 |
|
bendPotential += bend->getPotential(); |
| 516 |
< |
std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend); |
| 516 |
> |
map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend); |
| 517 |
|
if (i == bendDataSets.end()) { |
| 518 |
|
BendDataSet dataSet; |
| 519 |
|
dataSet.prev.angle = dataSet.curr.angle = angle; |
| 520 |
|
dataSet.prev.potential = dataSet.curr.potential = currBendPot; |
| 521 |
|
dataSet.deltaV = 0.0; |
| 522 |
< |
bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet)); |
| 522 |
> |
bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, |
| 523 |
> |
dataSet)); |
| 524 |
|
}else { |
| 525 |
|
i->second.prev.angle = i->second.curr.angle; |
| 526 |
|
i->second.prev.potential = i->second.curr.potential; |
| 537 |
|
torsion->calcForce(angle); |
| 538 |
|
RealType currTorsionPot = torsion->getPotential(); |
| 539 |
|
torsionPotential += torsion->getPotential(); |
| 540 |
< |
std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion); |
| 540 |
> |
map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion); |
| 541 |
|
if (i == torsionDataSets.end()) { |
| 542 |
|
TorsionDataSet dataSet; |
| 543 |
|
dataSet.prev.angle = dataSet.curr.angle = angle; |
| 544 |
|
dataSet.prev.potential = dataSet.curr.potential = currTorsionPot; |
| 545 |
|
dataSet.deltaV = 0.0; |
| 546 |
< |
torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet)); |
| 546 |
> |
torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet)); |
| 547 |
|
}else { |
| 548 |
|
i->second.prev.angle = i->second.curr.angle; |
| 549 |
|
i->second.prev.potential = i->second.curr.potential; |
| 553 |
|
i->second.prev.potential); |
| 554 |
|
} |
| 555 |
|
} |
| 556 |
< |
|
| 556 |
> |
|
| 557 |
|
for (inversion = mol->beginInversion(inversionIter); |
| 558 |
|
inversion != NULL; |
| 559 |
|
inversion = mol->nextInversion(inversionIter)) { |
| 561 |
|
inversion->calcForce(angle); |
| 562 |
|
RealType currInversionPot = inversion->getPotential(); |
| 563 |
|
inversionPotential += inversion->getPotential(); |
| 564 |
< |
std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion); |
| 564 |
> |
map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion); |
| 565 |
|
if (i == inversionDataSets.end()) { |
| 566 |
|
InversionDataSet dataSet; |
| 567 |
|
dataSet.prev.angle = dataSet.curr.angle = angle; |
| 568 |
|
dataSet.prev.potential = dataSet.curr.potential = currInversionPot; |
| 569 |
|
dataSet.deltaV = 0.0; |
| 570 |
< |
inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet)); |
| 570 |
> |
inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet)); |
| 571 |
|
}else { |
| 572 |
|
i->second.prev.angle = i->second.curr.angle; |
| 573 |
|
i->second.prev.potential = i->second.curr.potential; |
| 586 |
|
curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential; |
| 587 |
|
curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential; |
| 588 |
|
curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential; |
| 589 |
< |
curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential; |
| 236 |
< |
|
| 589 |
> |
curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential; |
| 590 |
|
} |
| 591 |
|
|
| 592 |
< |
void ForceManager::calcLongRangeInteraction() { |
| 240 |
< |
Snapshot* curSnapshot; |
| 241 |
< |
DataStorage* config; |
| 242 |
< |
RealType* frc; |
| 243 |
< |
RealType* pos; |
| 244 |
< |
RealType* trq; |
| 245 |
< |
RealType* A; |
| 246 |
< |
RealType* electroFrame; |
| 247 |
< |
RealType* rc; |
| 248 |
< |
RealType* particlePot; |
| 249 |
< |
|
| 250 |
< |
//get current snapshot from SimInfo |
| 251 |
< |
curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 252 |
< |
|
| 253 |
< |
//get array pointers |
| 254 |
< |
config = &(curSnapshot->atomData); |
| 255 |
< |
frc = config->getArrayPointer(DataStorage::dslForce); |
| 256 |
< |
pos = config->getArrayPointer(DataStorage::dslPosition); |
| 257 |
< |
trq = config->getArrayPointer(DataStorage::dslTorque); |
| 258 |
< |
A = config->getArrayPointer(DataStorage::dslAmat); |
| 259 |
< |
electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame); |
| 260 |
< |
particlePot = config->getArrayPointer(DataStorage::dslParticlePot); |
| 592 |
> |
void ForceManager::longRangeInteractions() { |
| 593 |
|
|
| 594 |
+ |
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 595 |
+ |
DataStorage* config = &(curSnapshot->atomData); |
| 596 |
+ |
DataStorage* cgConfig = &(curSnapshot->cgData); |
| 597 |
+ |
|
| 598 |
|
//calculate the center of mass of cutoff group |
| 599 |
+ |
|
| 600 |
|
SimInfo::MoleculeIterator mi; |
| 601 |
|
Molecule* mol; |
| 602 |
|
Molecule::CutoffGroupIterator ci; |
| 603 |
|
CutoffGroup* cg; |
| 604 |
< |
Vector3d com; |
| 605 |
< |
std::vector<Vector3d> rcGroup; |
| 269 |
< |
|
| 270 |
< |
if(info_->getNCutoffGroups() > 0){ |
| 271 |
< |
|
| 604 |
> |
|
| 605 |
> |
if(info_->getNCutoffGroups() > 0){ |
| 606 |
|
for (mol = info_->beginMolecule(mi); mol != NULL; |
| 607 |
|
mol = info_->nextMolecule(mi)) { |
| 608 |
|
for(cg = mol->beginCutoffGroup(ci); cg != NULL; |
| 609 |
|
cg = mol->nextCutoffGroup(ci)) { |
| 610 |
< |
cg->getCOM(com); |
| 277 |
< |
rcGroup.push_back(com); |
| 610 |
> |
cg->updateCOM(); |
| 611 |
|
} |
| 612 |
< |
}// end for (mol) |
| 280 |
< |
|
| 281 |
< |
rc = rcGroup[0].getArrayPointer(); |
| 612 |
> |
} |
| 613 |
|
} else { |
| 614 |
|
// center of mass of the group is the same as position of the atom |
| 615 |
|
// if cutoff group does not exist |
| 616 |
< |
rc = pos; |
| 616 |
> |
cgConfig->position = config->position; |
| 617 |
|
} |
| 618 |
+ |
|
| 619 |
+ |
fDecomp_->zeroWorkArrays(); |
| 620 |
+ |
fDecomp_->distributeData(); |
| 621 |
|
|
| 622 |
< |
//initialize data before passing to fortran |
| 623 |
< |
RealType longRangePotential[LR_POT_TYPES]; |
| 624 |
< |
RealType lrPot = 0.0; |
| 625 |
< |
Vector3d totalDipole; |
| 626 |
< |
int isError = 0; |
| 622 |
> |
int cg1, cg2, atom1, atom2, topoDist; |
| 623 |
> |
Vector3d d_grp, dag, d; |
| 624 |
> |
RealType rgrpsq, rgrp, r2, r; |
| 625 |
> |
RealType electroMult, vdwMult; |
| 626 |
> |
RealType vij; |
| 627 |
> |
Vector3d fij, fg, f1; |
| 628 |
> |
tuple3<RealType, RealType, RealType> cuts; |
| 629 |
> |
RealType rCutSq; |
| 630 |
> |
bool in_switching_region; |
| 631 |
> |
RealType sw, dswdr, swderiv; |
| 632 |
> |
vector<int> atomListColumn, atomListRow, atomListLocal; |
| 633 |
> |
InteractionData idat; |
| 634 |
> |
SelfData sdat; |
| 635 |
> |
RealType mf; |
| 636 |
> |
RealType lrPot; |
| 637 |
> |
RealType vpair; |
| 638 |
> |
potVec longRangePotential(0.0); |
| 639 |
> |
potVec workPot(0.0); |
| 640 |
|
|
| 641 |
< |
for (int i=0; i<LR_POT_TYPES;i++){ |
| 642 |
< |
longRangePotential[i]=0.0; //Initialize array |
| 643 |
< |
} |
| 641 |
> |
int loopStart, loopEnd; |
| 642 |
> |
|
| 643 |
> |
idat.vdwMult = &vdwMult; |
| 644 |
> |
idat.electroMult = &electroMult; |
| 645 |
> |
idat.pot = &workPot; |
| 646 |
> |
sdat.pot = fDecomp_->getEmbeddingPotential(); |
| 647 |
> |
idat.vpair = &vpair; |
| 648 |
> |
idat.f1 = &f1; |
| 649 |
> |
idat.sw = &sw; |
| 650 |
> |
idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false; |
| 651 |
> |
idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false; |
| 652 |
|
|
| 653 |
< |
doForceLoop(pos, |
| 654 |
< |
rc, |
| 655 |
< |
A, |
| 656 |
< |
electroFrame, |
| 657 |
< |
frc, |
| 303 |
< |
trq, |
| 304 |
< |
tau.getArrayPointer(), |
| 305 |
< |
longRangePotential, |
| 306 |
< |
particlePot, |
| 307 |
< |
&isError ); |
| 308 |
< |
|
| 309 |
< |
if( isError ){ |
| 310 |
< |
sprintf( painCave.errMsg, |
| 311 |
< |
"Error returned from the fortran force calculation.\n" ); |
| 312 |
< |
painCave.isFatal = 1; |
| 313 |
< |
simError(); |
| 653 |
> |
loopEnd = PAIR_LOOP; |
| 654 |
> |
if (info_->requiresPrepair() ) { |
| 655 |
> |
loopStart = PREPAIR_LOOP; |
| 656 |
> |
} else { |
| 657 |
> |
loopStart = PAIR_LOOP; |
| 658 |
|
} |
| 659 |
< |
for (int i=0; i<LR_POT_TYPES;i++){ |
| 660 |
< |
lrPot += longRangePotential[i]; //Quick hack |
| 659 |
> |
|
| 660 |
> |
for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) { |
| 661 |
> |
|
| 662 |
> |
if (iLoop == loopStart) { |
| 663 |
> |
bool update_nlist = fDecomp_->checkNeighborList(); |
| 664 |
> |
if (update_nlist) |
| 665 |
> |
neighborList = fDecomp_->buildNeighborList(); |
| 666 |
> |
} |
| 667 |
> |
|
| 668 |
> |
for (vector<pair<int, int> >::iterator it = neighborList.begin(); |
| 669 |
> |
it != neighborList.end(); ++it) { |
| 670 |
> |
|
| 671 |
> |
cg1 = (*it).first; |
| 672 |
> |
cg2 = (*it).second; |
| 673 |
> |
|
| 674 |
> |
cuts = fDecomp_->getGroupCutoffs(cg1, cg2); |
| 675 |
> |
|
| 676 |
> |
d_grp = fDecomp_->getIntergroupVector(cg1, cg2); |
| 677 |
> |
|
| 678 |
> |
curSnapshot->wrapVector(d_grp); |
| 679 |
> |
rgrpsq = d_grp.lengthSquare(); |
| 680 |
> |
rCutSq = cuts.second; |
| 681 |
> |
|
| 682 |
> |
if (rgrpsq < rCutSq) { |
| 683 |
> |
idat.rcut = &cuts.first; |
| 684 |
> |
if (iLoop == PAIR_LOOP) { |
| 685 |
> |
vij = 0.0; |
| 686 |
> |
fij = V3Zero; |
| 687 |
> |
} |
| 688 |
> |
|
| 689 |
> |
in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, |
| 690 |
> |
rgrp); |
| 691 |
> |
|
| 692 |
> |
atomListRow = fDecomp_->getAtomsInGroupRow(cg1); |
| 693 |
> |
atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2); |
| 694 |
> |
|
| 695 |
> |
for (vector<int>::iterator ia = atomListRow.begin(); |
| 696 |
> |
ia != atomListRow.end(); ++ia) { |
| 697 |
> |
atom1 = (*ia); |
| 698 |
> |
|
| 699 |
> |
for (vector<int>::iterator jb = atomListColumn.begin(); |
| 700 |
> |
jb != atomListColumn.end(); ++jb) { |
| 701 |
> |
atom2 = (*jb); |
| 702 |
> |
|
| 703 |
> |
if (!fDecomp_->skipAtomPair(atom1, atom2)) { |
| 704 |
> |
vpair = 0.0; |
| 705 |
> |
workPot = 0.0; |
| 706 |
> |
f1 = V3Zero; |
| 707 |
> |
|
| 708 |
> |
fDecomp_->fillInteractionData(idat, atom1, atom2); |
| 709 |
> |
|
| 710 |
> |
topoDist = fDecomp_->getTopologicalDistance(atom1, atom2); |
| 711 |
> |
vdwMult = vdwScale_[topoDist]; |
| 712 |
> |
electroMult = electrostaticScale_[topoDist]; |
| 713 |
> |
|
| 714 |
> |
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 715 |
> |
idat.d = &d_grp; |
| 716 |
> |
idat.r2 = &rgrpsq; |
| 717 |
> |
} else { |
| 718 |
> |
d = fDecomp_->getInteratomicVector(atom1, atom2); |
| 719 |
> |
curSnapshot->wrapVector( d ); |
| 720 |
> |
r2 = d.lengthSquare(); |
| 721 |
> |
idat.d = &d; |
| 722 |
> |
idat.r2 = &r2; |
| 723 |
> |
} |
| 724 |
> |
|
| 725 |
> |
r = sqrt( *(idat.r2) ); |
| 726 |
> |
idat.rij = &r; |
| 727 |
> |
|
| 728 |
> |
if (iLoop == PREPAIR_LOOP) { |
| 729 |
> |
interactionMan_->doPrePair(idat); |
| 730 |
> |
} else { |
| 731 |
> |
interactionMan_->doPair(idat); |
| 732 |
> |
fDecomp_->unpackInteractionData(idat, atom1, atom2); |
| 733 |
> |
vij += vpair; |
| 734 |
> |
fij += f1; |
| 735 |
> |
tau -= outProduct( *(idat.d), f1); |
| 736 |
> |
} |
| 737 |
> |
} |
| 738 |
> |
} |
| 739 |
> |
} |
| 740 |
> |
|
| 741 |
> |
if (iLoop == PAIR_LOOP) { |
| 742 |
> |
if (in_switching_region) { |
| 743 |
> |
swderiv = vij * dswdr / rgrp; |
| 744 |
> |
fg = swderiv * d_grp; |
| 745 |
> |
fij += fg; |
| 746 |
> |
|
| 747 |
> |
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 748 |
> |
tau -= outProduct( *(idat.d), fg); |
| 749 |
> |
} |
| 750 |
> |
|
| 751 |
> |
for (vector<int>::iterator ia = atomListRow.begin(); |
| 752 |
> |
ia != atomListRow.end(); ++ia) { |
| 753 |
> |
atom1 = (*ia); |
| 754 |
> |
mf = fDecomp_->getMassFactorRow(atom1); |
| 755 |
> |
// fg is the force on atom ia due to cutoff group's |
| 756 |
> |
// presence in switching region |
| 757 |
> |
fg = swderiv * d_grp * mf; |
| 758 |
> |
fDecomp_->addForceToAtomRow(atom1, fg); |
| 759 |
> |
if (atomListRow.size() > 1) { |
| 760 |
> |
if (info_->usesAtomicVirial()) { |
| 761 |
> |
// find the distance between the atom |
| 762 |
> |
// and the center of the cutoff group: |
| 763 |
> |
dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1); |
| 764 |
> |
tau -= outProduct(dag, fg); |
| 765 |
> |
} |
| 766 |
> |
} |
| 767 |
> |
} |
| 768 |
> |
for (vector<int>::iterator jb = atomListColumn.begin(); |
| 769 |
> |
jb != atomListColumn.end(); ++jb) { |
| 770 |
> |
atom2 = (*jb); |
| 771 |
> |
mf = fDecomp_->getMassFactorColumn(atom2); |
| 772 |
> |
// fg is the force on atom jb due to cutoff group's |
| 773 |
> |
// presence in switching region |
| 774 |
> |
fg = -swderiv * d_grp * mf; |
| 775 |
> |
fDecomp_->addForceToAtomColumn(atom2, fg); |
| 776 |
> |
|
| 777 |
> |
if (atomListColumn.size() > 1) { |
| 778 |
> |
if (info_->usesAtomicVirial()) { |
| 779 |
> |
// find the distance between the atom |
| 780 |
> |
// and the center of the cutoff group: |
| 781 |
> |
dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2); |
| 782 |
> |
tau -= outProduct(dag, fg); |
| 783 |
> |
} |
| 784 |
> |
} |
| 785 |
> |
} |
| 786 |
> |
} |
| 787 |
> |
//if (!info_->usesAtomicVirial()) { |
| 788 |
> |
// tau -= outProduct(d_grp, fij); |
| 789 |
> |
//} |
| 790 |
> |
} |
| 791 |
> |
} |
| 792 |
> |
} |
| 793 |
> |
|
| 794 |
> |
if (iLoop == PREPAIR_LOOP) { |
| 795 |
> |
if (info_->requiresPrepair()) { |
| 796 |
> |
|
| 797 |
> |
fDecomp_->collectIntermediateData(); |
| 798 |
> |
|
| 799 |
> |
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 800 |
> |
fDecomp_->fillSelfData(sdat, atom1); |
| 801 |
> |
interactionMan_->doPreForce(sdat); |
| 802 |
> |
} |
| 803 |
> |
|
| 804 |
> |
fDecomp_->distributeIntermediateData(); |
| 805 |
> |
|
| 806 |
> |
} |
| 807 |
> |
} |
| 808 |
|
} |
| 809 |
|
|
| 810 |
< |
// grab the simulation box dipole moment if specified |
| 811 |
< |
if (info_->getCalcBoxDipole()){ |
| 812 |
< |
getAccumulatedBoxDipole(totalDipole.getArrayPointer()); |
| 813 |
< |
|
| 814 |
< |
curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0); |
| 815 |
< |
curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1); |
| 816 |
< |
curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2); |
| 810 |
> |
fDecomp_->collectData(); |
| 811 |
> |
|
| 812 |
> |
if (info_->requiresSelfCorrection()) { |
| 813 |
> |
|
| 814 |
> |
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 815 |
> |
fDecomp_->fillSelfData(sdat, atom1); |
| 816 |
> |
interactionMan_->doSelfCorrection(sdat); |
| 817 |
> |
} |
| 818 |
> |
|
| 819 |
|
} |
| 820 |
< |
|
| 820 |
> |
|
| 821 |
> |
longRangePotential = *(fDecomp_->getEmbeddingPotential()) + |
| 822 |
> |
*(fDecomp_->getPairwisePotential()); |
| 823 |
> |
|
| 824 |
> |
lrPot = longRangePotential.sum(); |
| 825 |
> |
|
| 826 |
|
//store the tau and long range potential |
| 827 |
|
curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot; |
| 828 |
< |
curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT]; |
| 829 |
< |
curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT]; |
| 828 |
> |
curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY]; |
| 829 |
> |
curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY]; |
| 830 |
|
} |
| 831 |
|
|
| 832 |
|
|
