| 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" |
| 59 |
< |
#include "parallel/ForceDecomposition.hpp" |
| 60 |
< |
//#include "parallel/SerialDecomposition.hpp" |
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> |
#include "nonbonded/NonBondedInteraction.hpp" |
| 60 |
> |
#include "parallel/ForceMatrixDecomposition.hpp" |
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|
| 62 |
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using namespace std; |
| 63 |
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namespace OpenMD { |
| 64 |
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|
| 65 |
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ForceManager::ForceManager(SimInfo * info) : info_(info) { |
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+ |
forceField_ = info_->getForceField(); |
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+ |
interactionMan_ = new InteractionManager(); |
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+ |
fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_); |
| 69 |
+ |
} |
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|
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< |
#ifdef IS_MPI |
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< |
decomp_ = new ForceDecomposition(info_); |
| 73 |
< |
#else |
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< |
// decomp_ = new SerialDecomposition(info); |
| 75 |
< |
#endif |
| 71 |
> |
/** |
| 72 |
> |
* setupCutoffs |
| 73 |
> |
* |
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> |
* Sets the values of cutoffRadius, cutoffMethod, and cutoffPolicy |
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> |
* |
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> |
* cutoffRadius : realType |
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> |
* If the cutoffRadius was explicitly set, use that value. |
| 78 |
> |
* If the cutoffRadius was not explicitly set: |
| 79 |
> |
* Are there electrostatic atoms? Use 12.0 Angstroms. |
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> |
* No electrostatic atoms? Poll the atom types present in the |
| 81 |
> |
* simulation for suggested cutoff values (e.g. 2.5 * sigma). |
| 82 |
> |
* Use the maximum suggested value that was found. |
| 83 |
> |
* |
| 84 |
> |
* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL) |
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> |
* If cutoffMethod was explicitly set, use that choice. |
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> |
* If cutoffMethod was not explicitly set, use SHIFTED_FORCE |
| 87 |
> |
* |
| 88 |
> |
* cutoffPolicy : (one of MIX, MAX, TRADITIONAL) |
| 89 |
> |
* If cutoffPolicy was explicitly set, use that choice. |
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> |
* If cutoffPolicy was not explicitly set, use TRADITIONAL |
| 91 |
> |
*/ |
| 92 |
> |
void ForceManager::setupCutoffs() { |
| 93 |
> |
|
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> |
Globals* simParams_ = info_->getSimParams(); |
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> |
ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions(); |
| 96 |
> |
|
| 97 |
> |
if (simParams_->haveCutoffRadius()) { |
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> |
rCut_ = simParams_->getCutoffRadius(); |
| 99 |
> |
} else { |
| 100 |
> |
if (info_->usesElectrostaticAtoms()) { |
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> |
sprintf(painCave.errMsg, |
| 102 |
> |
"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n" |
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> |
"\tOpenMD will use a default value of 12.0 angstroms" |
| 104 |
> |
"\tfor the cutoffRadius.\n"); |
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> |
painCave.isFatal = 0; |
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> |
painCave.severity = OPENMD_INFO; |
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> |
simError(); |
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> |
rCut_ = 12.0; |
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> |
} else { |
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> |
RealType thisCut; |
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> |
set<AtomType*>::iterator i; |
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> |
set<AtomType*> atomTypes; |
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> |
atomTypes = info_->getSimulatedAtomTypes(); |
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> |
for (i = atomTypes.begin(); i != atomTypes.end(); ++i) { |
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> |
thisCut = interactionMan_->getSuggestedCutoffRadius((*i)); |
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> |
rCut_ = max(thisCut, rCut_); |
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> |
} |
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> |
sprintf(painCave.errMsg, |
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> |
"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n" |
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> |
"\tOpenMD will use %lf angstroms.\n", |
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> |
rCut_); |
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> |
painCave.isFatal = 0; |
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> |
painCave.severity = OPENMD_INFO; |
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> |
simError(); |
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> |
} |
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> |
fDecomp_->setUserCutoff(rCut_); |
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> |
} |
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> |
|
| 129 |
> |
map<string, CutoffMethod> stringToCutoffMethod; |
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> |
stringToCutoffMethod["HARD"] = HARD; |
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> |
stringToCutoffMethod["SWITCHED"] = SWITCHED; |
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> |
stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL; |
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> |
stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE; |
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> |
|
| 135 |
> |
if (simParams_->haveCutoffMethod()) { |
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> |
string cutMeth = toUpperCopy(simParams_->getCutoffMethod()); |
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> |
map<string, CutoffMethod>::iterator i; |
| 138 |
> |
i = stringToCutoffMethod.find(cutMeth); |
| 139 |
> |
if (i == stringToCutoffMethod.end()) { |
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> |
sprintf(painCave.errMsg, |
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> |
"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n" |
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> |
"\tShould be one of: " |
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> |
"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n", |
| 144 |
> |
cutMeth.c_str()); |
| 145 |
> |
painCave.isFatal = 1; |
| 146 |
> |
painCave.severity = OPENMD_ERROR; |
| 147 |
> |
simError(); |
| 148 |
> |
} else { |
| 149 |
> |
cutoffMethod_ = i->second; |
| 150 |
> |
} |
| 151 |
> |
} else { |
| 152 |
> |
sprintf(painCave.errMsg, |
| 153 |
> |
"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n" |
| 154 |
> |
"\tOpenMD will use SHIFTED_FORCE.\n"); |
| 155 |
> |
painCave.isFatal = 0; |
| 156 |
> |
painCave.severity = OPENMD_INFO; |
| 157 |
> |
simError(); |
| 158 |
> |
cutoffMethod_ = SHIFTED_FORCE; |
| 159 |
> |
} |
| 160 |
> |
|
| 161 |
> |
map<string, CutoffPolicy> stringToCutoffPolicy; |
| 162 |
> |
stringToCutoffPolicy["MIX"] = MIX; |
| 163 |
> |
stringToCutoffPolicy["MAX"] = MAX; |
| 164 |
> |
stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL; |
| 165 |
> |
|
| 166 |
> |
std::string cutPolicy; |
| 167 |
> |
if (forceFieldOptions_.haveCutoffPolicy()){ |
| 168 |
> |
cutPolicy = forceFieldOptions_.getCutoffPolicy(); |
| 169 |
> |
}else if (simParams_->haveCutoffPolicy()) { |
| 170 |
> |
cutPolicy = simParams_->getCutoffPolicy(); |
| 171 |
> |
} |
| 172 |
> |
|
| 173 |
> |
if (!cutPolicy.empty()){ |
| 174 |
> |
toUpper(cutPolicy); |
| 175 |
> |
map<string, CutoffPolicy>::iterator i; |
| 176 |
> |
i = stringToCutoffPolicy.find(cutPolicy); |
| 177 |
> |
|
| 178 |
> |
if (i == stringToCutoffPolicy.end()) { |
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> |
sprintf(painCave.errMsg, |
| 180 |
> |
"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n" |
| 181 |
> |
"\tShould be one of: " |
| 182 |
> |
"MIX, MAX, or TRADITIONAL\n", |
| 183 |
> |
cutPolicy.c_str()); |
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> |
painCave.isFatal = 1; |
| 185 |
> |
painCave.severity = OPENMD_ERROR; |
| 186 |
> |
simError(); |
| 187 |
> |
} else { |
| 188 |
> |
cutoffPolicy_ = i->second; |
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> |
} |
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> |
} else { |
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> |
sprintf(painCave.errMsg, |
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> |
"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n" |
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> |
"\tOpenMD will use TRADITIONAL.\n"); |
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> |
painCave.isFatal = 0; |
| 195 |
> |
painCave.severity = OPENMD_INFO; |
| 196 |
> |
simError(); |
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> |
cutoffPolicy_ = TRADITIONAL; |
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> |
} |
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> |
fDecomp_->setCutoffPolicy(cutoffPolicy_); |
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} |
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< |
|
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< |
void ForceManager::calcForces() { |
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> |
|
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> |
/** |
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> |
* setupSwitching |
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> |
* |
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> |
* Sets the values of switchingRadius and |
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> |
* If the switchingRadius was explicitly set, use that value (but check it) |
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> |
* If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_ |
| 208 |
> |
*/ |
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> |
void ForceManager::setupSwitching() { |
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> |
Globals* simParams_ = info_->getSimParams(); |
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> |
|
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> |
// create the switching function object: |
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> |
switcher_ = new SwitchingFunction(); |
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|
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< |
if (!info_->isFortranInitialized()) { |
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> |
if (simParams_->haveSwitchingRadius()) { |
| 216 |
> |
rSwitch_ = simParams_->getSwitchingRadius(); |
| 217 |
> |
if (rSwitch_ > rCut_) { |
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> |
sprintf(painCave.errMsg, |
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> |
"ForceManager::setupSwitching: switchingRadius (%f) is larger " |
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> |
"than the cutoffRadius(%f)\n", rSwitch_, rCut_); |
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> |
painCave.isFatal = 1; |
| 222 |
> |
painCave.severity = OPENMD_ERROR; |
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> |
simError(); |
| 224 |
> |
} |
| 225 |
> |
} else { |
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> |
rSwitch_ = 0.85 * rCut_; |
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> |
sprintf(painCave.errMsg, |
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> |
"ForceManager::setupSwitching: No value was set for the switchingRadius.\n" |
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> |
"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n" |
| 230 |
> |
"\tswitchingRadius = %f. for this simulation\n", rSwitch_); |
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> |
painCave.isFatal = 0; |
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> |
painCave.severity = OPENMD_WARNING; |
| 233 |
> |
simError(); |
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> |
} |
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> |
|
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> |
// Default to cubic switching function. |
| 237 |
> |
sft_ = cubic; |
| 238 |
> |
if (simParams_->haveSwitchingFunctionType()) { |
| 239 |
> |
string funcType = simParams_->getSwitchingFunctionType(); |
| 240 |
> |
toUpper(funcType); |
| 241 |
> |
if (funcType == "CUBIC") { |
| 242 |
> |
sft_ = cubic; |
| 243 |
> |
} else { |
| 244 |
> |
if (funcType == "FIFTH_ORDER_POLYNOMIAL") { |
| 245 |
> |
sft_ = fifth_order_poly; |
| 246 |
> |
} else { |
| 247 |
> |
// throw error |
| 248 |
> |
sprintf( painCave.errMsg, |
| 249 |
> |
"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n" |
| 250 |
> |
"\tswitchingFunctionType must be one of: " |
| 251 |
> |
"\"cubic\" or \"fifth_order_polynomial\".", |
| 252 |
> |
funcType.c_str() ); |
| 253 |
> |
painCave.isFatal = 1; |
| 254 |
> |
painCave.severity = OPENMD_ERROR; |
| 255 |
> |
simError(); |
| 256 |
> |
} |
| 257 |
> |
} |
| 258 |
> |
} |
| 259 |
> |
switcher_->setSwitchType(sft_); |
| 260 |
> |
switcher_->setSwitch(rSwitch_, rCut_); |
| 261 |
> |
} |
| 262 |
> |
|
| 263 |
> |
void ForceManager::initialize() { |
| 264 |
> |
|
| 265 |
> |
if (!info_->isTopologyDone()) { |
| 266 |
|
info_->update(); |
| 267 |
< |
nbiMan_->setSimInfo(info_); |
| 268 |
< |
nbiMan_->initialize(); |
| 269 |
< |
swfun_ = nbiMan_->getSwitchingFunction(); |
| 270 |
< |
decomp_->distributeInitialData(); |
| 271 |
< |
info_->setupFortran(); |
| 267 |
> |
interactionMan_->setSimInfo(info_); |
| 268 |
> |
interactionMan_->initialize(); |
| 269 |
> |
|
| 270 |
> |
// We want to delay the cutoffs until after the interaction |
| 271 |
> |
// manager has set up the atom-atom interactions so that we can |
| 272 |
> |
// query them for suggested cutoff values |
| 273 |
> |
|
| 274 |
> |
setupCutoffs(); |
| 275 |
> |
setupSwitching(); |
| 276 |
> |
|
| 277 |
> |
info_->prepareTopology(); |
| 278 |
|
} |
| 279 |
+ |
|
| 280 |
+ |
ForceFieldOptions& fopts = forceField_->getForceFieldOptions(); |
| 281 |
|
|
| 282 |
< |
preCalculation(); |
| 283 |
< |
calcShortRangeInteraction(); |
| 284 |
< |
calcLongRangeInteraction(); |
| 285 |
< |
postCalculation(); |
| 282 |
> |
// Force fields can set options on how to scale van der Waals and electrostatic |
| 283 |
> |
// interactions for atoms connected via bonds, bends and torsions |
| 284 |
> |
// in this case the topological distance between atoms is: |
| 285 |
> |
// 0 = topologically unconnected |
| 286 |
> |
// 1 = bonded together |
| 287 |
> |
// 2 = connected via a bend |
| 288 |
> |
// 3 = connected via a torsion |
| 289 |
|
|
| 290 |
+ |
vdwScale_.reserve(4); |
| 291 |
+ |
fill(vdwScale_.begin(), vdwScale_.end(), 0.0); |
| 292 |
+ |
|
| 293 |
+ |
electrostaticScale_.reserve(4); |
| 294 |
+ |
fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0); |
| 295 |
+ |
|
| 296 |
+ |
vdwScale_[0] = 1.0; |
| 297 |
+ |
vdwScale_[1] = fopts.getvdw12scale(); |
| 298 |
+ |
vdwScale_[2] = fopts.getvdw13scale(); |
| 299 |
+ |
vdwScale_[3] = fopts.getvdw14scale(); |
| 300 |
+ |
|
| 301 |
+ |
electrostaticScale_[0] = 1.0; |
| 302 |
+ |
electrostaticScale_[1] = fopts.getelectrostatic12scale(); |
| 303 |
+ |
electrostaticScale_[2] = fopts.getelectrostatic13scale(); |
| 304 |
+ |
electrostaticScale_[3] = fopts.getelectrostatic14scale(); |
| 305 |
+ |
|
| 306 |
+ |
fDecomp_->distributeInitialData(); |
| 307 |
+ |
|
| 308 |
+ |
initialized_ = true; |
| 309 |
+ |
|
| 310 |
|
} |
| 311 |
+ |
|
| 312 |
+ |
void ForceManager::calcForces() { |
| 313 |
+ |
|
| 314 |
+ |
if (!initialized_) initialize(); |
| 315 |
+ |
|
| 316 |
+ |
preCalculation(); |
| 317 |
+ |
shortRangeInteractions(); |
| 318 |
+ |
longRangeInteractions(); |
| 319 |
+ |
postCalculation(); |
| 320 |
+ |
} |
| 321 |
|
|
| 322 |
|
void ForceManager::preCalculation() { |
| 323 |
|
SimInfo::MoleculeIterator mi; |
| 357 |
|
|
| 358 |
|
} |
| 359 |
|
|
| 360 |
< |
void ForceManager::calcShortRangeInteraction() { |
| 360 |
> |
void ForceManager::shortRangeInteractions() { |
| 361 |
|
Molecule* mol; |
| 362 |
|
RigidBody* rb; |
| 363 |
|
Bond* bond; |
| 474 |
|
curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential; |
| 475 |
|
} |
| 476 |
|
|
| 477 |
< |
void ForceManager::calcLongRangeInteraction() { |
| 249 |
< |
|
| 477 |
> |
void ForceManager::longRangeInteractions() { |
| 478 |
|
// some of this initial stuff will go away: |
| 479 |
|
Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot(); |
| 480 |
|
DataStorage* config = &(curSnapshot->atomData); |
| 485 |
|
RealType* A = config->getArrayPointer(DataStorage::dslAmat); |
| 486 |
|
RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame); |
| 487 |
|
RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot); |
| 260 |
– |
RealType* rc; |
| 488 |
|
|
| 262 |
– |
if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){ |
| 263 |
– |
rc = cgConfig->getArrayPointer(DataStorage::dslPosition); |
| 264 |
– |
} else { |
| 265 |
– |
// center of mass of the group is the same as position of the atom |
| 266 |
– |
// if cutoff group does not exist |
| 267 |
– |
rc = pos; |
| 268 |
– |
} |
| 269 |
– |
|
| 270 |
– |
//initialize data before passing to fortran |
| 271 |
– |
RealType longRangePotential[LR_POT_TYPES]; |
| 272 |
– |
RealType lrPot = 0.0; |
| 273 |
– |
int isError = 0; |
| 274 |
– |
|
| 275 |
– |
for (int i=0; i<LR_POT_TYPES;i++){ |
| 276 |
– |
longRangePotential[i]=0.0; //Initialize array |
| 277 |
– |
} |
| 278 |
– |
|
| 489 |
|
// new stuff starts here: |
| 490 |
< |
|
| 491 |
< |
decomp_->distributeData(); |
| 492 |
< |
|
| 493 |
< |
int cg1, cg2; |
| 494 |
< |
Vector3d d_grp; |
| 495 |
< |
RealType rgrpsq, rgrp; |
| 490 |
> |
|
| 491 |
> |
fDecomp_->zeroWorkArrays(); |
| 492 |
> |
fDecomp_->distributeData(); |
| 493 |
> |
|
| 494 |
> |
int cg1, cg2, atom1, atom2, topoDist; |
| 495 |
> |
Vector3d d_grp, dag, d; |
| 496 |
> |
RealType rgrpsq, rgrp, r2, r; |
| 497 |
> |
RealType electroMult, vdwMult; |
| 498 |
|
RealType vij; |
| 499 |
|
Vector3d fij, fg; |
| 500 |
< |
pair<int, int> gtypes; |
| 500 |
> |
tuple3<RealType, RealType, RealType> cuts; |
| 501 |
|
RealType rCutSq; |
| 502 |
|
bool in_switching_region; |
| 503 |
|
RealType sw, dswdr, swderiv; |
| 504 |
< |
vector<int> atomListI; |
| 293 |
< |
vector<int> atomListJ; |
| 504 |
> |
vector<int> atomListColumn, atomListRow, atomListLocal; |
| 505 |
|
InteractionData idat; |
| 506 |
+ |
SelfData sdat; |
| 507 |
+ |
RealType mf; |
| 508 |
+ |
potVec pot(0.0); |
| 509 |
+ |
potVec longRangePotential(0.0); |
| 510 |
+ |
RealType lrPot; |
| 511 |
+ |
RealType vpair; |
| 512 |
|
|
| 513 |
|
int loopStart, loopEnd; |
| 514 |
|
|
| 515 |
|
loopEnd = PAIR_LOOP; |
| 516 |
< |
if (info_->requiresPrepair_) { |
| 516 |
> |
if (info_->requiresPrepair() ) { |
| 517 |
|
loopStart = PREPAIR_LOOP; |
| 518 |
|
} else { |
| 519 |
|
loopStart = PAIR_LOOP; |
| 520 |
|
} |
| 521 |
+ |
|
| 522 |
|
|
| 523 |
< |
for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) { |
| 524 |
< |
|
| 523 |
> |
for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) { |
| 524 |
> |
|
| 525 |
|
if (iLoop == loopStart) { |
| 526 |
< |
bool update_nlist = decomp_->checkNeighborList(); |
| 526 |
> |
bool update_nlist = fDecomp_->checkNeighborList(); |
| 527 |
|
if (update_nlist) |
| 528 |
< |
neighborList = decomp_->buildNeighborList(); |
| 529 |
< |
} |
| 530 |
< |
|
| 528 |
> |
neighborList = fDecomp_->buildNeighborList(); |
| 529 |
> |
} |
| 530 |
> |
|
| 531 |
|
for (vector<pair<int, int> >::iterator it = neighborList.begin(); |
| 532 |
|
it != neighborList.end(); ++it) { |
| 533 |
< |
|
| 533 |
> |
|
| 534 |
|
cg1 = (*it).first; |
| 535 |
|
cg2 = (*it).second; |
| 536 |
+ |
|
| 537 |
+ |
cuts = fDecomp_->getGroupCutoffs(cg1, cg2); |
| 538 |
|
|
| 539 |
< |
gtypes = decomp_->getGroupTypes(cg1, cg2); |
| 320 |
< |
d_grp = decomp_->getIntergroupVector(cg1, cg2); |
| 539 |
> |
d_grp = fDecomp_->getIntergroupVector(cg1, cg2); |
| 540 |
|
curSnapshot->wrapVector(d_grp); |
| 541 |
|
rgrpsq = d_grp.lengthSquare(); |
| 323 |
– |
rCutSq = groupCutoffMap(gtypes).first; |
| 542 |
|
|
| 543 |
+ |
rCutSq = cuts.second; |
| 544 |
+ |
|
| 545 |
|
if (rgrpsq < rCutSq) { |
| 546 |
< |
idat.rcut = groupCutoffMap(gtypes).second; |
| 546 |
> |
idat.rcut = &cuts.first; |
| 547 |
|
if (iLoop == PAIR_LOOP) { |
| 548 |
< |
vij = 0.0; |
| 548 |
> |
vij *= 0.0; |
| 549 |
|
fij = V3Zero; |
| 550 |
|
} |
| 551 |
|
|
| 552 |
< |
in_switching_region = swfun_->getSwitch(rgrpsq, idat.sw, idat.dswdr, rgrp); |
| 553 |
< |
|
| 334 |
< |
atomListI = decomp_->getAtomsInGroupI(cg1); |
| 335 |
< |
atomListJ = decomp_->getAtomsInGroupJ(cg2); |
| 552 |
> |
in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, |
| 553 |
> |
rgrp); |
| 554 |
|
|
| 555 |
< |
for (vector<int>::iterator ia = atomListI.begin(); |
| 556 |
< |
ia != atomListI.end(); ++ia) { |
| 555 |
> |
idat.sw = &sw; |
| 556 |
> |
|
| 557 |
> |
atomListRow = fDecomp_->getAtomsInGroupRow(cg1); |
| 558 |
> |
atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2); |
| 559 |
> |
|
| 560 |
> |
for (vector<int>::iterator ia = atomListRow.begin(); |
| 561 |
> |
ia != atomListRow.end(); ++ia) { |
| 562 |
|
atom1 = (*ia); |
| 563 |
|
|
| 564 |
< |
for (vector<int>::iterator jb = atomListJ.begin(); |
| 565 |
< |
jb != atomListJ.end(); ++jb) { |
| 564 |
> |
for (vector<int>::iterator jb = atomListColumn.begin(); |
| 565 |
> |
jb != atomListColumn.end(); ++jb) { |
| 566 |
|
atom2 = (*jb); |
| 567 |
|
|
| 568 |
< |
if (!decomp_->skipAtomPair(atom1, atom2)) { |
| 568 |
> |
cerr << "doing atoms " << atom1 << " " << atom2 << "\n"; |
| 569 |
> |
if (!fDecomp_->skipAtomPair(atom1, atom2)) { |
| 570 |
|
|
| 571 |
< |
if (atomListI.size() == 1 && atomListJ.size() == 1) { |
| 572 |
< |
idat.d = d_grp; |
| 573 |
< |
idat.r2 = rgrpsq; |
| 571 |
> |
vpair = 0.0; |
| 572 |
> |
|
| 573 |
> |
cerr << "filling idat atoms " << atom1 << " " << atom2 << "\n"; |
| 574 |
> |
idat = fDecomp_->fillInteractionData(atom1, atom2); |
| 575 |
> |
cerr << "done with idat\n"; |
| 576 |
> |
|
| 577 |
> |
topoDist = fDecomp_->getTopologicalDistance(atom1, atom2); |
| 578 |
> |
vdwMult = vdwScale_[topoDist]; |
| 579 |
> |
electroMult = electrostaticScale_[topoDist]; |
| 580 |
> |
|
| 581 |
> |
idat.vdwMult = &vdwMult; |
| 582 |
> |
idat.electroMult = &electroMult; |
| 583 |
> |
idat.pot = &pot; |
| 584 |
> |
idat.vpair = &vpair; |
| 585 |
> |
|
| 586 |
> |
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 587 |
> |
idat.d = &d_grp; |
| 588 |
> |
idat.r2 = &rgrpsq; |
| 589 |
|
} else { |
| 590 |
< |
idat.d = decomp_->getInteratomicVector(atom1, atom2); |
| 591 |
< |
curSnapshot->wrapVector(idat.d); |
| 592 |
< |
idat.r2 = idat.d.lengthSquare(); |
| 590 |
> |
d = fDecomp_->getInteratomicVector(atom1, atom2); |
| 591 |
> |
curSnapshot->wrapVector( d ); |
| 592 |
> |
r2 = d.lengthSquare(); |
| 593 |
> |
idat.d = &d; |
| 594 |
> |
idat.r2 = &r2; |
| 595 |
|
} |
| 596 |
|
|
| 597 |
< |
idat.r = sqrt(idat.r2); |
| 598 |
< |
decomp_->fillInteractionData(atom1, atom2, idat); |
| 599 |
< |
|
| 597 |
> |
cerr << "d = " << d << "\n"; |
| 598 |
> |
cerr << "r2 = " << r2 << "\n"; |
| 599 |
> |
r = sqrt( r2 ); |
| 600 |
> |
idat.rij = &r; |
| 601 |
> |
|
| 602 |
|
if (iLoop == PREPAIR_LOOP) { |
| 603 |
|
interactionMan_->doPrePair(idat); |
| 604 |
|
} else { |
| 605 |
+ |
cerr << "doing doPair " << atom1 << " " << atom2 << " " << r << "\n"; |
| 606 |
|
interactionMan_->doPair(idat); |
| 607 |
< |
vij += idat.vpair; |
| 608 |
< |
fij += idat.f1; |
| 609 |
< |
tau -= outProduct(idat.d, idat.f); |
| 607 |
> |
fDecomp_->unpackInteractionData(idat, atom1, atom2); |
| 608 |
> |
vij += *(idat.vpair); |
| 609 |
> |
fij += *(idat.f1); |
| 610 |
> |
tau -= outProduct( *(idat.d), *(idat.f1)); |
| 611 |
|
} |
| 612 |
|
} |
| 613 |
|
} |
| 620 |
|
|
| 621 |
|
fij += fg; |
| 622 |
|
|
| 623 |
< |
if (atomListI.size() == 1 && atomListJ.size() == 1) { |
| 624 |
< |
tau -= outProduct(idat.d, fg); |
| 623 |
> |
if (atomListRow.size() == 1 && atomListColumn.size() == 1) { |
| 624 |
> |
tau -= outProduct( *(idat.d), fg); |
| 625 |
|
} |
| 626 |
|
|
| 627 |
< |
for (vector<int>::iterator ia = atomListI.begin(); |
| 628 |
< |
ia != atomListI.end(); ++ia) { |
| 627 |
> |
for (vector<int>::iterator ia = atomListRow.begin(); |
| 628 |
> |
ia != atomListRow.end(); ++ia) { |
| 629 |
|
atom1 = (*ia); |
| 630 |
< |
mf = decomp_->getMfactI(atom1); |
| 630 |
> |
mf = fDecomp_->getMassFactorRow(atom1); |
| 631 |
|
// fg is the force on atom ia due to cutoff group's |
| 632 |
|
// presence in switching region |
| 633 |
|
fg = swderiv * d_grp * mf; |
| 634 |
< |
decomp_->addForceToAtomI(atom1, fg); |
| 634 |
> |
fDecomp_->addForceToAtomRow(atom1, fg); |
| 635 |
|
|
| 636 |
< |
if (atomListI.size() > 1) { |
| 637 |
< |
if (info_->usesAtomicVirial_) { |
| 636 |
> |
if (atomListRow.size() > 1) { |
| 637 |
> |
if (info_->usesAtomicVirial()) { |
| 638 |
|
// find the distance between the atom |
| 639 |
|
// and the center of the cutoff group: |
| 640 |
< |
dag = decomp_->getAtomToGroupVectorI(atom1, cg1); |
| 640 |
> |
dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1); |
| 641 |
|
tau -= outProduct(dag, fg); |
| 642 |
|
} |
| 643 |
|
} |
| 644 |
|
} |
| 645 |
< |
for (vector<int>::iterator jb = atomListJ.begin(); |
| 646 |
< |
jb != atomListJ.end(); ++jb) { |
| 645 |
> |
for (vector<int>::iterator jb = atomListColumn.begin(); |
| 646 |
> |
jb != atomListColumn.end(); ++jb) { |
| 647 |
|
atom2 = (*jb); |
| 648 |
< |
mf = decomp_->getMfactJ(atom2); |
| 648 |
> |
mf = fDecomp_->getMassFactorColumn(atom2); |
| 649 |
|
// fg is the force on atom jb due to cutoff group's |
| 650 |
|
// presence in switching region |
| 651 |
|
fg = -swderiv * d_grp * mf; |
| 652 |
< |
decomp_->addForceToAtomJ(atom2, fg); |
| 652 |
> |
fDecomp_->addForceToAtomColumn(atom2, fg); |
| 653 |
|
|
| 654 |
< |
if (atomListJ.size() > 1) { |
| 655 |
< |
if (info_->usesAtomicVirial_) { |
| 654 |
> |
if (atomListColumn.size() > 1) { |
| 655 |
> |
if (info_->usesAtomicVirial()) { |
| 656 |
|
// find the distance between the atom |
| 657 |
|
// and the center of the cutoff group: |
| 658 |
< |
dag = decomp_->getAtomToGroupVectorJ(atom2, cg2); |
| 658 |
> |
dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2); |
| 659 |
|
tau -= outProduct(dag, fg); |
| 660 |
|
} |
| 661 |
|
} |
| 669 |
|
} |
| 670 |
|
|
| 671 |
|
if (iLoop == PREPAIR_LOOP) { |
| 672 |
< |
if (info_->requiresPrepair_) { |
| 673 |
< |
decomp_->collectIntermediateData(); |
| 674 |
< |
atomList = decomp_->getAtomList(); |
| 675 |
< |
for (vector<int>::iterator ia = atomList.begin(); |
| 676 |
< |
ia != atomList.end(); ++ia) { |
| 432 |
< |
atom1 = (*ia); |
| 433 |
< |
decomp_->populateSelfData(atom1, SelfData sdat); |
| 672 |
> |
if (info_->requiresPrepair()) { |
| 673 |
> |
fDecomp_->collectIntermediateData(); |
| 674 |
> |
|
| 675 |
> |
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 676 |
> |
sdat = fDecomp_->fillSelfData(atom1); |
| 677 |
|
interactionMan_->doPreForce(sdat); |
| 678 |
|
} |
| 679 |
< |
decomp_->distributeIntermediateData(); |
| 679 |
> |
|
| 680 |
> |
fDecomp_->distributeIntermediateData(); |
| 681 |
|
} |
| 682 |
|
} |
| 683 |
|
|
| 684 |
|
} |
| 685 |
|
|
| 686 |
< |
decomp_->collectData(); |
| 686 |
> |
fDecomp_->collectData(); |
| 687 |
|
|
| 688 |
< |
if (info_->requiresSkipCorrection_ || info_->requiresSelfCorrection_) { |
| 689 |
< |
atomList = decomp_->getAtomList(); |
| 690 |
< |
for (vector<int>::iterator ia = atomList.begin(); |
| 447 |
< |
ia != atomList.end(); ++ia) { |
| 448 |
< |
atom1 = (*ia); |
| 688 |
> |
if ( info_->requiresSkipCorrection() ) { |
| 689 |
> |
|
| 690 |
> |
for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) { |
| 691 |
|
|
| 692 |
< |
if (info_->requiresSkipCorrection_) { |
| 693 |
< |
vector<int> skipList = decomp_->getSkipsForAtom(atom1); |
| 694 |
< |
for (vector<int>::iterator jb = skipList.begin(); |
| 695 |
< |
jb != skipList.end(); ++jb) { |
| 696 |
< |
atom2 = (*jb); |
| 697 |
< |
decomp_->populateSkipData(atom1, atom2, InteractionData idat); |
| 698 |
< |
interactionMan_->doSkipCorrection(idat); |
| 699 |
< |
} |
| 692 |
> |
vector<int> skipList = fDecomp_->getSkipsForAtom( atom1 ); |
| 693 |
> |
|
| 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 |
|
} |
| 459 |
– |
|
| 460 |
– |
if (info_->requiresSelfCorrection_) { |
| 461 |
– |
decomp_->populateSelfData(atom1, SelfData sdat); |
| 462 |
– |
interactionMan_->doSelfCorrection(sdat); |
| 702 |
|
} |
| 464 |
– |
|
| 465 |
– |
|
| 703 |
|
} |
| 704 |
+ |
|
| 705 |
+ |
if (info_->requiresSelfCorrection()) { |
| 706 |
|
|
| 707 |
< |
for (int i=0; i<LR_POT_TYPES;i++){ |
| 708 |
< |
lrPot += longRangePotential[i]; //Quick hack |
| 707 |
> |
for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) { |
| 708 |
> |
sdat = fDecomp_->fillSelfData(atom1); |
| 709 |
> |
interactionMan_->doSelfCorrection(sdat); |
| 710 |
> |
} |
| 711 |
> |
|
| 712 |
|
} |
| 713 |
< |
|
| 713 |
> |
|
| 714 |
> |
longRangePotential = fDecomp_->getLongRangePotential(); |
| 715 |
> |
lrPot = longRangePotential.sum(); |
| 716 |
> |
|
| 717 |
|
//store the tau and long range potential |
| 718 |
|
curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot; |
| 719 |
< |
curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT]; |
| 720 |
< |
curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT]; |
| 719 |
> |
curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY]; |
| 720 |
> |
curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY]; |
| 721 |
|
} |
| 722 |
|
|
| 723 |
|
|
