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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 1575 by gezelter, Fri Jun 3 21:39:49 2011 UTC

#	Line 49 | Line 49
49
50		#include "brains/ForceManager.hpp"
51		#include "primitives/Molecule.hpp"
52	–	#include "UseTheForce/doForces_interface.h"
52		#define __OPENMD_C
54	–	#include "UseTheForce/DarkSide/fInteractionMap.h"
53		#include "utils/simError.h"
54		#include "primitives/Bond.hpp"
55		#include "primitives/Bend.hpp"
56		#include "primitives/Torsion.hpp"
57		#include "primitives/Inversion.hpp"
58	+	#include "nonbonded/NonBondedInteraction.hpp"
59	+	#include "parallel/ForceMatrixDecomposition.hpp"
60	+
61	+	using namespace std;
62		namespace OpenMD {
63	+
64	+	ForceManager::ForceManager(SimInfo * info) : info_(info) {
65
66	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
66	>	fDecomp_ = new ForceMatrixDecomposition(info_);
67	>	}
68	>
69	>	void ForceManager::calcForces() {
70
71	<	if (!info_->isFortranInitialized()) {
71	>	if (!info_->isTopologyDone()) {
72		info_->update();
73	+	interactionMan_->setSimInfo(info_);
74	+	interactionMan_->initialize();
75	+	swfun_ = interactionMan_->getSwitchingFunction();
76	+	info_->prepareTopology();
77	+	fDecomp_->distributeInitialData();
78		}
79
80	<	preCalculation();
80	>	preCalculation();
81	>	shortRangeInteractions();
82	>	longRangeInteractions();
83	>	postCalculation();
84
70	–	calcShortRangeInteraction();
71	–
72	–	calcLongRangeInteraction(needPotential, needStress);
73	–
74	–	postCalculation(needStress);
75	–
85		}
86
87		void ForceManager::preCalculation() {
#	Line 82 | Line 91 | namespace OpenMD {
91		Atom* atom;
92		Molecule::RigidBodyIterator rbIter;
93		RigidBody* rb;
94	+	Molecule::CutoffGroupIterator ci;
95	+	CutoffGroup* cg;
96
97		// forces are zeroed here, before any are accumulated.
87	–	// NOTE: do not rezero the forces in Fortran.
98
99		for (mol = info_->beginMolecule(mi); mol != NULL;
100		mol = info_->nextMolecule(mi)) {
#	Line 97 | Line 107 | namespace OpenMD {
107		rb = mol->nextRigidBody(rbIter)) {
108		rb->zeroForcesAndTorques();
109		}
110	<
110	>
111	>	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
112	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
113	>	cg = mol->nextCutoffGroup(ci)) {
114	>	//calculate the center of mass of cutoff group
115	>	cg->updateCOM();
116	>	}
117	>	}
118		}
119	<
119	>
120		// Zero out the stress tensor
121		tau *= 0.0;
122
123		}
124
125	<	void ForceManager::calcShortRangeInteraction() {
125	>	void ForceManager::shortRangeInteractions() {
126		Molecule* mol;
127		RigidBody* rb;
128		Bond* bond;
#	Line 145 | Line 162 | namespace OpenMD {
162		RealType angle;
163		bend->calcForce(angle);
164		RealType currBendPot = bend->getPotential();
165	+
166		bendPotential += bend->getPotential();
167	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
167	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
168		if (i == bendDataSets.end()) {
169		BendDataSet dataSet;
170		dataSet.prev.angle = dataSet.curr.angle = angle;
171		dataSet.prev.potential = dataSet.curr.potential = currBendPot;
172		dataSet.deltaV = 0.0;
173	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
173	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
174		}else {
175		i->second.prev.angle = i->second.curr.angle;
176		i->second.prev.potential = i->second.curr.potential;
#	Line 169 | Line 187 | namespace OpenMD {
187		torsion->calcForce(angle);
188		RealType currTorsionPot = torsion->getPotential();
189		torsionPotential += torsion->getPotential();
190	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
190	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
191		if (i == torsionDataSets.end()) {
192		TorsionDataSet dataSet;
193		dataSet.prev.angle = dataSet.curr.angle = angle;
194		dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
195		dataSet.deltaV = 0.0;
196	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
196	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
197		}else {
198		i->second.prev.angle = i->second.curr.angle;
199		i->second.prev.potential = i->second.curr.potential;
#	Line 185 | Line 203 | namespace OpenMD {
203		i->second.prev.potential);
204		}
205		}
206	<
206	>
207		for (inversion = mol->beginInversion(inversionIter);
208		inversion != NULL;
209		inversion = mol->nextInversion(inversionIter)) {
#	Line 193 | Line 211 | namespace OpenMD {
211		inversion->calcForce(angle);
212		RealType currInversionPot = inversion->getPotential();
213		inversionPotential += inversion->getPotential();
214	<	std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
214	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
215		if (i == inversionDataSets.end()) {
216		InversionDataSet dataSet;
217		dataSet.prev.angle = dataSet.curr.angle = angle;
218		dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
219		dataSet.deltaV = 0.0;
220	<	inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
220	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
221		}else {
222		i->second.prev.angle = i->second.curr.angle;
223		i->second.prev.potential = i->second.curr.potential;
#	Line 218 | Line 236 | namespace OpenMD {
236		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
237		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
238		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
239	<	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
222	<
239	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
240		}
241
242	<	void ForceManager::calcLongRangeInteraction(bool needPotential,
226	<	bool needStress) {
227	<	Snapshot* curSnapshot;
228	<	DataStorage* config;
229	<	RealType* frc;
230	<	RealType* pos;
231	<	RealType* trq;
232	<	RealType* A;
233	<	RealType* electroFrame;
234	<	RealType* rc;
235	<	RealType* particlePot;
236	<
237	<	//get current snapshot from SimInfo
238	<	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
239	<
240	<	//get array pointers
241	<	config = &(curSnapshot->atomData);
242	<	frc = config->getArrayPointer(DataStorage::dslForce);
243	<	pos = config->getArrayPointer(DataStorage::dslPosition);
244	<	trq = config->getArrayPointer(DataStorage::dslTorque);
245	<	A   = config->getArrayPointer(DataStorage::dslAmat);
246	<	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
247	<	particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
242	>	void ForceManager::longRangeInteractions() {
243
244	<	//calculate the center of mass of cutoff group
245	<	SimInfo::MoleculeIterator mi;
246	<	Molecule* mol;
247	<	Molecule::CutoffGroupIterator ci;
248	<	CutoffGroup* cg;
249	<	Vector3d com;
250	<	std::vector<Vector3d> rcGroup;
251	<
252	<	if(info_->getNCutoffGroups() > 0){
253	<
254	<	for (mol = info_->beginMolecule(mi); mol != NULL;
255	<	mol = info_->nextMolecule(mi)) {
256	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
257	<	cg = mol->nextCutoffGroup(ci)) {
263	<	cg->getCOM(com);
264	<	rcGroup.push_back(com);
265	<	}
266	<	}// end for (mol)
267	<
268	<	rc = rcGroup[0].getArrayPointer();
244	>	// some of this initial stuff will go away:
245	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
246	>	DataStorage* config = &(curSnapshot->atomData);
247	>	DataStorage* cgConfig = &(curSnapshot->cgData);
248	>	RealType* frc = config->getArrayPointer(DataStorage::dslForce);
249	>	RealType* pos = config->getArrayPointer(DataStorage::dslPosition);
250	>	RealType* trq = config->getArrayPointer(DataStorage::dslTorque);
251	>	RealType* A = config->getArrayPointer(DataStorage::dslAmat);
252	>	RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
253	>	RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
254	>	RealType* rc;
255	>
256	>	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
257	>	rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
258		} else {
259		// center of mass of the group is the same as position of the atom
260		// if cutoff group does not exist
261		rc = pos;
262		}
263
264	<	//initialize data before passing to fortran
265	<	RealType longRangePotential[LR_POT_TYPES];
266	<	RealType lrPot = 0.0;
267	<	Vector3d totalDipole;
268	<	short int passedCalcPot = needPotential;
269	<	short int passedCalcStress = needStress;
270	<	int isError = 0;
264	>	// new stuff starts here:
265	>	fDecomp_->zeroWorkArrays();
266	>	fDecomp_->distributeData();
267	>
268	>	int cg1, cg2, atom1, atom2;
269	>	Vector3d d_grp, dag;
270	>	RealType rgrpsq, rgrp;
271	>	RealType vij;
272	>	Vector3d fij, fg;
273	>	pair<int, int> gtypes;
274	>	RealType rCutSq;
275	>	bool in_switching_region;
276	>	RealType sw, dswdr, swderiv;
277	>	vector<int> atomListColumn, atomListRow, atomListLocal;
278	>	InteractionData idat;
279	>	SelfData sdat;
280	>	RealType mf;
281	>	potVec pot(0.0);
282	>	potVec longRangePotential(0.0);
283	>	RealType lrPot;
284
285	<	for (int i=0; i<LR_POT_TYPES;i++){
286	<	longRangePotential[i]=0.0; //Initialize array
285	>	int loopStart, loopEnd;
286	>
287	>	loopEnd = PAIR_LOOP;
288	>	if (info_->requiresPrepair() ) {
289	>	loopStart = PREPAIR_LOOP;
290	>	} else {
291	>	loopStart = PAIR_LOOP;
292		}
293	<
294	<	doForceLoop(pos,
288	<	rc,
289	<	A,
290	<	electroFrame,
291	<	frc,
292	<	trq,
293	<	tau.getArrayPointer(),
294	<	longRangePotential,
295	<	particlePot,
296	<	&passedCalcPot,
297	<	&passedCalcStress,
298	<	&isError );
299	<
300	<	if( isError ){
301	<	sprintf( painCave.errMsg,
302	<	"Error returned from the fortran force calculation.\n" );
303	<	painCave.isFatal = 1;
304	<	simError();
305	<	}
306	<	for (int i=0; i<LR_POT_TYPES;i++){
307	<	lrPot += longRangePotential[i]; //Quick hack
308	<	}
309	<
310	<	// grab the simulation box dipole moment if specified
311	<	if (info_->getCalcBoxDipole()){
312	<	getAccumulatedBoxDipole(totalDipole.getArrayPointer());
293	>
294	>	for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
295
296	<	curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
297	<	curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
298	<	curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
296	>	if (iLoop == loopStart) {
297	>	bool update_nlist = fDecomp_->checkNeighborList();
298	>	if (update_nlist)
299	>	neighborList = fDecomp_->buildNeighborList();
300	>	}
301	>
302	>	for (vector<pair<int, int> >::iterator it = neighborList.begin();
303	>	it != neighborList.end(); ++it) {
304	>
305	>	cg1 = (*it).first;
306	>	cg2 = (*it).second;
307	>
308	>	gtypes = fDecomp_->getGroupTypes(cg1, cg2);
309	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
310	>	curSnapshot->wrapVector(d_grp);
311	>	rgrpsq = d_grp.lengthSquare();
312	>	rCutSq = groupCutoffMap[gtypes].first;
313	>
314	>	if (rgrpsq < rCutSq) {
315	>	*(idat.rcut) = groupCutoffMap[gtypes].second;
316	>	if (iLoop == PAIR_LOOP) {
317	>	vij *= 0.0;
318	>	fij = V3Zero;
319	>	}
320	>
321	>	in_switching_region = swfun_->getSwitch(rgrpsq, *(idat.sw), dswdr,
322	>	rgrp);
323	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
324	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
325	>
326	>	for (vector<int>::iterator ia = atomListRow.begin();
327	>	ia != atomListRow.end(); ++ia) {
328	>	atom1 = (*ia);
329	>
330	>	for (vector<int>::iterator jb = atomListColumn.begin();
331	>	jb != atomListColumn.end(); ++jb) {
332	>	atom2 = (*jb);
333	>
334	>	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
335	>
336	>	pot *= 0.0;
337	>
338	>	idat = fDecomp_->fillInteractionData(atom1, atom2);
339	>	*(idat.pot) = pot;
340	>
341	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
342	>	*(idat.d) = d_grp;
343	>	*(idat.r2) = rgrpsq;
344	>	} else {
345	>	*(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2);
346	>	curSnapshot->wrapVector( *(idat.d) );
347	>	*(idat.r2) = idat.d->lengthSquare();
348	>	}
349	>
350	>	*(idat.rij) = sqrt( *(idat.r2) );
351	>
352	>	if (iLoop == PREPAIR_LOOP) {
353	>	interactionMan_->doPrePair(idat);
354	>	} else {
355	>	interactionMan_->doPair(idat);
356	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
357	>	vij += *(idat.vpair);
358	>	fij += *(idat.f1);
359	>	tau -= outProduct( *(idat.d), *(idat.f1));
360	>	}
361	>	}
362	>	}
363	>	}
364	>
365	>	if (iLoop == PAIR_LOOP) {
366	>	if (in_switching_region) {
367	>	swderiv = vij * dswdr / rgrp;
368	>	fg = swderiv * d_grp;
369	>
370	>	fij += fg;
371	>
372	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
373	>	tau -= outProduct( *(idat.d), fg);
374	>	}
375	>
376	>	for (vector<int>::iterator ia = atomListRow.begin();
377	>	ia != atomListRow.end(); ++ia) {
378	>	atom1 = (*ia);
379	>	mf = fDecomp_->getMassFactorRow(atom1);
380	>	// fg is the force on atom ia due to cutoff group's
381	>	// presence in switching region
382	>	fg = swderiv * d_grp * mf;
383	>	fDecomp_->addForceToAtomRow(atom1, fg);
384	>
385	>	if (atomListRow.size() > 1) {
386	>	if (info_->usesAtomicVirial()) {
387	>	// find the distance between the atom
388	>	// and the center of the cutoff group:
389	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
390	>	tau -= outProduct(dag, fg);
391	>	}
392	>	}
393	>	}
394	>	for (vector<int>::iterator jb = atomListColumn.begin();
395	>	jb != atomListColumn.end(); ++jb) {
396	>	atom2 = (*jb);
397	>	mf = fDecomp_->getMassFactorColumn(atom2);
398	>	// fg is the force on atom jb due to cutoff group's
399	>	// presence in switching region
400	>	fg = -swderiv * d_grp * mf;
401	>	fDecomp_->addForceToAtomColumn(atom2, fg);
402	>
403	>	if (atomListColumn.size() > 1) {
404	>	if (info_->usesAtomicVirial()) {
405	>	// find the distance between the atom
406	>	// and the center of the cutoff group:
407	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
408	>	tau -= outProduct(dag, fg);
409	>	}
410	>	}
411	>	}
412	>	}
413	>	//if (!SIM_uses_AtomicVirial) {
414	>	//  tau -= outProduct(d_grp, fij);
415	>	//}
416	>	}
417	>	}
418	>	}
419	>
420	>	if (iLoop == PREPAIR_LOOP) {
421	>	if (info_->requiresPrepair()) {
422	>	fDecomp_->collectIntermediateData();
423	>
424	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
425	>	sdat = fDecomp_->fillSelfData(atom1);
426	>	interactionMan_->doPreForce(sdat);
427	>	}
428	>
429	>	fDecomp_->distributeIntermediateData();
430	>	}
431	>	}
432	>
433		}
434
435	+	fDecomp_->collectData();
436	+
437	+	if ( info_->requiresSkipCorrection() ) {
438	+
439	+	for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
440	+
441	+	vector<int> skipList = fDecomp_->getSkipsForRowAtom( atom1 );
442	+
443	+	for (vector<int>::iterator jb = skipList.begin();
444	+	jb != skipList.end(); ++jb) {
445	+
446	+	atom2 = (*jb);
447	+	idat = fDecomp_->fillSkipData(atom1, atom2);
448	+	interactionMan_->doSkipCorrection(idat);
449	+
450	+	}
451	+	}
452	+	}
453	+
454	+	if (info_->requiresSelfCorrection()) {
455	+
456	+	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
457	+	sdat = fDecomp_->fillSelfData(atom1);
458	+	interactionMan_->doSelfCorrection(sdat);
459	+	}
460	+
461	+	}
462	+
463	+	longRangePotential = fDecomp_->getLongRangePotential();
464	+	lrPot = longRangePotential.sum();
465	+
466		//store the tau and long range potential
467		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
468	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
469	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
468	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
469	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
470		}
471
472
473	<	void ForceManager::postCalculation(bool needStress) {
473	>	void ForceManager::postCalculation() {
474		SimInfo::MoleculeIterator mi;
475		Molecule* mol;
476		Molecule::RigidBodyIterator rbIter;
#	Line 336 | Line 483 | namespace OpenMD {
483		mol = info_->nextMolecule(mi)) {
484		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
485		rb = mol->nextRigidBody(rbIter)) {
486	<	if (needStress) {
487	<	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
341	<	tau += rbTau;
342	<	} else{
343	<	rb->calcForcesAndTorques();
344	<	}
486	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
487	>	tau += rbTau;
488		}
489		}
490	<
348	<	if (needStress) {
490	>
491		#ifdef IS_MPI
492	<	Mat3x3d tmpTau(tau);
493	<	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
494	<	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
492	>	Mat3x3d tmpTau(tau);
493	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
494	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
495		#endif
496	<	curSnapshot->statData.setTau(tau);
355	<	}
496	>	curSnapshot->statData.setTau(tau);
497		}
498
499		} //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 1575 by gezelter, Fri Jun 3 21:39:49 2011 UTC

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