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root/OpenMD/branches/development/src/brains/ForceManager.cpp

Comparing:
trunk/src/brains/ForceManager.cpp (file contents), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1544 by gezelter, Fri Mar 18 19:31:52 2011 UTC

#	Line 57 | Line 57
57		#include "primitives/Bend.hpp"
58		#include "primitives/Torsion.hpp"
59		#include "primitives/Inversion.hpp"
60	<	namespace OpenMD {
60	>	#include "parallel/ForceDecomposition.hpp"
61	>	//#include "parallel/SerialDecomposition.hpp"
62
63	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
63	>	namespace OpenMD {
64	>
65	>	ForceManager::ForceManager(SimInfo * info) : info_(info),
66	>	NBforcesInitialized_(false) {
67	>	#ifdef IS_MPI
68	>	decomp_ = new ForceDecomposition(info_);
69	>	#else
70	>	//  decomp_ = new SerialDecomposition(info);
71	>	#endif
72	>	}
73	>
74	>	void ForceManager::calcForces() {
75
76	+
77		if (!info_->isFortranInitialized()) {
78		info_->update();
79	+	nbiMan_->setSimInfo(info_);
80	+	nbiMan_->initialize();
81	+	decomp_->distributeInitialData();
82	+	info_->setupFortran();
83		}
84
85	<	preCalculation();
69	<
85	>	preCalculation();
86		calcShortRangeInteraction();
87	<
88	<	calcLongRangeInteraction(needPotential, needStress);
73	<
74	<	postCalculation(needStress);
87	>	calcLongRangeInteraction();
88	>	postCalculation();
89
90		}
91
#	Line 82 | Line 96 | namespace OpenMD {
96		Atom* atom;
97		Molecule::RigidBodyIterator rbIter;
98		RigidBody* rb;
99	+	Molecule::CutoffGroupIterator ci;
100	+	CutoffGroup* cg;
101
102		// forces are zeroed here, before any are accumulated.
103		// NOTE: do not rezero the forces in Fortran.
#	Line 97 | Line 113 | namespace OpenMD {
113		rb = mol->nextRigidBody(rbIter)) {
114		rb->zeroForcesAndTorques();
115		}
116	<
116	>
117	>	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
118	>	std::cerr << "should not see me \n";
119	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
120	>	cg = mol->nextCutoffGroup(ci)) {
121	>	//calculate the center of mass of cutoff group
122	>	cg->updateCOM();
123	>	}
124	>	}
125		}
126	<
126	>
127		// Zero out the stress tensor
128		tau *= 0.0;
129
#	Line 145 | Line 169 | namespace OpenMD {
169		RealType angle;
170		bend->calcForce(angle);
171		RealType currBendPot = bend->getPotential();
172	+
173		bendPotential += bend->getPotential();
174		std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
175		if (i == bendDataSets.end()) {
#	Line 222 | Line 247 | namespace OpenMD {
247
248		}
249
250	<	void ForceManager::calcLongRangeInteraction(bool needPotential,
226	<	bool needStress) {
250	>	void ForceManager::calcLongRangeInteraction() {
251		Snapshot* curSnapshot;
252		DataStorage* config;
253	+	DataStorage* cgConfig;
254		RealType* frc;
255		RealType* pos;
256		RealType* trq;
#	Line 239 | Line 264 | namespace OpenMD {
264
265		//get array pointers
266		config = &(curSnapshot->atomData);
267	+	cgConfig = &(curSnapshot->cgData);
268		frc = config->getArrayPointer(DataStorage::dslForce);
269		pos = config->getArrayPointer(DataStorage::dslPosition);
270		trq = config->getArrayPointer(DataStorage::dslTorque);
#	Line 246 | Line 272 | namespace OpenMD {
272		electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
273		particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
274
275	<	//calculate the center of mass of cutoff group
276	<	SimInfo::MoleculeIterator mi;
277	<	Molecule* mol;
252	<	Molecule::CutoffGroupIterator ci;
253	<	CutoffGroup* cg;
254	<	Vector3d com;
255	<	std::vector<Vector3d> rcGroup;
256	<
257	<	if(info_->getNCutoffGroups() > 0){
258	<
259	<	for (mol = info_->beginMolecule(mi); mol != NULL;
260	<	mol = info_->nextMolecule(mi)) {
261	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
262	<	cg = mol->nextCutoffGroup(ci)) {
263	<	cg->getCOM(com);
264	<	rcGroup.push_back(com);
265	<	}
266	<	}// end for (mol)
267	<
268	<	rc = rcGroup[0].getArrayPointer();
275	>	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
276	>	std::cerr << "should not see me \n";
277	>	rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
278		} else {
279		// center of mass of the group is the same as position of the atom
280		// if cutoff group does not exist
#	Line 275 | Line 284 | namespace OpenMD {
284		//initialize data before passing to fortran
285		RealType longRangePotential[LR_POT_TYPES];
286		RealType lrPot = 0.0;
278	–	Vector3d totalDipole;
279	–	short int passedCalcPot = needPotential;
280	–	short int passedCalcStress = needStress;
287		int isError = 0;
288
289		for (int i=0; i<LR_POT_TYPES;i++){
290		longRangePotential[i]=0.0; //Initialize array
291		}
292
293	<	doForceLoop(pos,
294	<	rc,
295	<	A,
296	<	electroFrame,
297	<	frc,
298	<	trq,
299	<	tau.getArrayPointer(),
300	<	longRangePotential,
301	<	particlePot,
302	<	&passedCalcPot,
303	<	&passedCalcStress,
304	<	&isError );
305	<
293	>	decomp_->distributeData();
294	>
295	>	int nLoops = 1;
296	>	for (int iLoop = 0; iLoop < nLoops; iLoop++) {
297	>	doForceLoop(pos,
298	>	rc,
299	>	A,
300	>	electroFrame,
301	>	frc,
302	>	trq,
303	>	tau.getArrayPointer(),
304	>	longRangePotential,
305	>	particlePot,
306	>	&isError );
307	>
308	>	if (nLoops > 1) {
309	>	decomp_->collectIntermediateData();
310	>	decomp_->distributeIntermediateData();
311	>	}
312	>	}
313	>
314	>	decomp_->collectData();
315	>
316		if( isError ){
317		sprintf( painCave.errMsg,
318		"Error returned from the fortran force calculation.\n" );
#	Line 306 | Line 322 | namespace OpenMD {
322		for (int i=0; i<LR_POT_TYPES;i++){
323		lrPot += longRangePotential[i]; //Quick hack
324		}
325	<
310	<	// grab the simulation box dipole moment if specified
311	<	if (info_->getCalcBoxDipole()){
312	<	getAccumulatedBoxDipole(totalDipole.getArrayPointer());
313	<
314	<	curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
315	<	curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
316	<	curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
317	<	}
318	<
325	>
326		//store the tau and long range potential
327		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
328		curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
#	Line 323 | Line 330 | namespace OpenMD {
330		}
331
332
333	<	void ForceManager::postCalculation(bool needStress) {
333	>	void ForceManager::postCalculation() {
334		SimInfo::MoleculeIterator mi;
335		Molecule* mol;
336		Molecule::RigidBodyIterator rbIter;
#	Line 336 | Line 343 | namespace OpenMD {
343		mol = info_->nextMolecule(mi)) {
344		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
345		rb = mol->nextRigidBody(rbIter)) {
346	<	if (needStress) {
347	<	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
341	<	tau += rbTau;
342	<	} else{
343	<	rb->calcForcesAndTorques();
344	<	}
346	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
347	>	tau += rbTau;
348		}
349		}
350	<
348	<	if (needStress) {
350	>
351		#ifdef IS_MPI
352	<	Mat3x3d tmpTau(tau);
353	<	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
354	<	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
352	>	Mat3x3d tmpTau(tau);
353	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
354	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
355		#endif
356	<	curSnapshot->statData.setTau(tau);
355	<	}
356	>	curSnapshot->statData.setTau(tau);
357		}
358
359		} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1544 by gezelter, Fri Mar 18 19:31:52 2011 UTC

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