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

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trunk/src/brains/ForceManager.cpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1549 by gezelter, Wed Apr 27 18:38:15 2011 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 50 | Line 50
50		#include "brains/ForceManager.hpp"
51		#include "primitives/Molecule.hpp"
52		#include "UseTheForce/doForces_interface.h"
53	<	#define __C
53	>	#define __OPENMD_C
54		#include "UseTheForce/DarkSide/fInteractionMap.h"
55		#include "utils/simError.h"
56	+	#include "primitives/Bond.hpp"
57		#include "primitives/Bend.hpp"
58	<	#include "primitives/Bend.hpp"
59	<	namespace oopse {
58	>	#include "primitives/Torsion.hpp"
59	>	#include "primitives/Inversion.hpp"
60	>	#include "parallel/ForceMatrixDecomposition.hpp"
61	>	//#include "parallel/ForceSerialDecomposition.hpp"
62
63	<	/*
64	<	struct BendOrderStruct {
65	<	Bend* bend;
66	<	BendDataSet dataSet;
64	<	};
65	<	struct TorsionOrderStruct {
66	<	Torsion* torsion;
67	<	TorsionDataSet dataSet;
68	<	};
63	>	using namespace std;
64	>	namespace OpenMD {
65	>
66	>	ForceManager::ForceManager(SimInfo * info) : info_(info) {
67
68	<	bool  BendSortFunctor(const BendOrderStruct& b1, const BendOrderStruct& b2) {
69	<	return b1.dataSet.deltaV < b2.dataSet.deltaV;
68	>	#ifdef IS_MPI
69	>	fDecomp_ = new ForceMatrixDecomposition(info_);
70	>	#else
71	>	// fDecomp_ = new ForceSerialDecomposition(info);
72	>	#endif
73		}
74	<
75	<	bool  TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
76	<	return t1.dataSet.deltaV < t2.dataSet.deltaV;
76	<	}
77	<	*/
78	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
79	<
74	>
75	>	void ForceManager::calcForces() {
76	>
77		if (!info_->isFortranInitialized()) {
78		info_->update();
79	+	interactionMan_->setSimInfo(info_);
80	+	interactionMan_->initialize();
81	+	swfun_ = interactionMan_->getSwitchingFunction();
82	+	fDecomp_->distributeInitialData();
83	+	info_->setupFortran();
84		}
83	–
84	–	preCalculation();
85
86	<	calcShortRangeInteraction();
87	<
88	<	calcLongRangeInteraction(needPotential, needStress);
89	<
86	>	preCalculation();
87	>	shortRangeInteractions();
88	>	longRangeInteractions();
89		postCalculation();
91	–
92	–	/*
93	–	std::vector<BendOrderStruct> bendOrderStruct;
94	–	for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
95	–	BendOrderStruct tmp;
96	–	tmp.bend= const_cast<Bend*>(i->first);
97	–	tmp.dataSet = i->second;
98	–	bendOrderStruct.push_back(tmp);
99	–	}
100	–
101	–	std::vector<TorsionOrderStruct> torsionOrderStruct;
102	–	for(std::map<Torsion*, TorsionDataSet>::iterator j = torsionDataSets.begin(); j != torsionDataSets.end(); ++j) {
103	–	TorsionOrderStruct tmp;
104	–	tmp.torsion = const_cast<Torsion*>(j->first);
105	–	tmp.dataSet = j->second;
106	–	torsionOrderStruct.push_back(tmp);
107	–	}
90
109	–	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
110	–	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
111	–	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
112	–	Bend* bend = k->bend;
113	–	std::cout << "Bend: atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
114	–	std::cout << "deltaV=" << k->dataSet.deltaV << ",p_theta=" << k->dataSet.prev.angle <<",p_pot=" << k->dataSet.prev.potential<< ",c_theta=" << k->dataSet.curr.angle << ", c_pot = " << k->dataSet.curr.potential <<std::endl;
115	–	}
116	–	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
117	–	Torsion* torsion = l->torsion;
118	–	std::cout << "Torsion: atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
119	–	std::cout << "deltaV=" << l->dataSet.deltaV << ",p_theta=" << l->dataSet.prev.angle <<",p_pot=" << l->dataSet.prev.potential<< ",c_theta=" << l->dataSet.curr.angle << ", c_pot = " << l->dataSet.curr.potential <<std::endl;
120	–	}
121	–	*/
91		}
92	<
92	>
93		void ForceManager::preCalculation() {
94		SimInfo::MoleculeIterator mi;
95		Molecule* mol;
#	Line 128 | Line 97 | namespace oopse {
97		Atom* atom;
98		Molecule::RigidBodyIterator rbIter;
99		RigidBody* rb;
100	+	Molecule::CutoffGroupIterator ci;
101	+	CutoffGroup* cg;
102
103		// forces are zeroed here, before any are accumulated.
104	<	// NOTE: do not rezero the forces in Fortran.
105	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
104	>
105	>	for (mol = info_->beginMolecule(mi); mol != NULL;
106	>	mol = info_->nextMolecule(mi)) {
107		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
108		atom->zeroForcesAndTorques();
109		}
110	<
110	>
111		//change the positions of atoms which belong to the rigidbodies
112	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
112	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
113	>	rb = mol->nextRigidBody(rbIter)) {
114		rb->zeroForcesAndTorques();
115		}
116	+
117	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
118	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
119	+	cg = mol->nextCutoffGroup(ci)) {
120	+	//calculate the center of mass of cutoff group
121	+	cg->updateCOM();
122	+	}
123	+	}
124		}
125	+
126	+	// Zero out the stress tensor
127	+	tau *= 0.0;
128
129		}
130	<
131	<	void ForceManager::calcShortRangeInteraction() {
130	>
131	>	void ForceManager::shortRangeInteractions() {
132		Molecule* mol;
133		RigidBody* rb;
134		Bond* bond;
135		Bend* bend;
136		Torsion* torsion;
137	+	Inversion* inversion;
138		SimInfo::MoleculeIterator mi;
139		Molecule::RigidBodyIterator rbIter;
140		Molecule::BondIterator bondIter;;
141		Molecule::BendIterator  bendIter;
142		Molecule::TorsionIterator  torsionIter;
143	+	Molecule::InversionIterator  inversionIter;
144		RealType bondPotential = 0.0;
145		RealType bendPotential = 0.0;
146		RealType torsionPotential = 0.0;
147	+	RealType inversionPotential = 0.0;
148
149		//calculate short range interactions
150	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
150	>	for (mol = info_->beginMolecule(mi); mol != NULL;
151	>	mol = info_->nextMolecule(mi)) {
152
153		//change the positions of atoms which belong to the rigidbodies
154	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
155	<	rb->updateAtoms();
154	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
155	>	rb = mol->nextRigidBody(rbIter)) {
156	>	rb->updateAtoms();
157		}
158
159	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
159	>	for (bond = mol->beginBond(bondIter); bond != NULL;
160	>	bond = mol->nextBond(bondIter)) {
161		bond->calcForce();
162		bondPotential += bond->getPotential();
163		}
164
165	<
166	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
167	<
168	<	RealType angle;
169	<	bend->calcForce(angle);
170	<	RealType currBendPot = bend->getPotential();
171	<	bendPotential += bend->getPotential();
172	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
173	<	if (i == bendDataSets.end()) {
174	<	BendDataSet dataSet;
175	<	dataSet.prev.angle = dataSet.curr.angle = angle;
176	<	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
177	<	dataSet.deltaV = 0.0;
178	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
179	<	}else {
180	<	i->second.prev.angle = i->second.curr.angle;
181	<	i->second.prev.potential = i->second.curr.potential;
182	<	i->second.curr.angle = angle;
183	<	i->second.curr.potential = currBendPot;
184	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
185	<	}
165	>	for (bend = mol->beginBend(bendIter); bend != NULL;
166	>	bend = mol->nextBend(bendIter)) {
167	>
168	>	RealType angle;
169	>	bend->calcForce(angle);
170	>	RealType currBendPot = bend->getPotential();
171	>
172	>	bendPotential += bend->getPotential();
173	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
174	>	if (i == bendDataSets.end()) {
175	>	BendDataSet dataSet;
176	>	dataSet.prev.angle = dataSet.curr.angle = angle;
177	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
178	>	dataSet.deltaV = 0.0;
179	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
180	>	}else {
181	>	i->second.prev.angle = i->second.curr.angle;
182	>	i->second.prev.potential = i->second.curr.potential;
183	>	i->second.curr.angle = angle;
184	>	i->second.curr.potential = currBendPot;
185	>	i->second.deltaV =  fabs(i->second.curr.potential -
186	>	i->second.prev.potential);
187	>	}
188		}
189	<
190	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
189	>
190	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
191	>	torsion = mol->nextTorsion(torsionIter)) {
192		RealType angle;
193	<	torsion->calcForce(angle);
193	>	torsion->calcForce(angle);
194		RealType currTorsionPot = torsion->getPotential();
195	<	torsionPotential += torsion->getPotential();
196	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
197	<	if (i == torsionDataSets.end()) {
198	<	TorsionDataSet dataSet;
199	<	dataSet.prev.angle = dataSet.curr.angle = angle;
200	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
201	<	dataSet.deltaV = 0.0;
202	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
203	<	}else {
204	<	i->second.prev.angle = i->second.curr.angle;
205	<	i->second.prev.potential = i->second.curr.potential;
206	<	i->second.curr.angle = angle;
207	<	i->second.curr.potential = currTorsionPot;
208	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
209	<	}
210	<	}
211	<
195	>	torsionPotential += torsion->getPotential();
196	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
197	>	if (i == torsionDataSets.end()) {
198	>	TorsionDataSet dataSet;
199	>	dataSet.prev.angle = dataSet.curr.angle = angle;
200	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
201	>	dataSet.deltaV = 0.0;
202	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
203	>	}else {
204	>	i->second.prev.angle = i->second.curr.angle;
205	>	i->second.prev.potential = i->second.curr.potential;
206	>	i->second.curr.angle = angle;
207	>	i->second.curr.potential = currTorsionPot;
208	>	i->second.deltaV =  fabs(i->second.curr.potential -
209	>	i->second.prev.potential);
210	>	}
211	>	}
212	>
213	>	for (inversion = mol->beginInversion(inversionIter);
214	>	inversion != NULL;
215	>	inversion = mol->nextInversion(inversionIter)) {
216	>	RealType angle;
217	>	inversion->calcForce(angle);
218	>	RealType currInversionPot = inversion->getPotential();
219	>	inversionPotential += inversion->getPotential();
220	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
221	>	if (i == inversionDataSets.end()) {
222	>	InversionDataSet dataSet;
223	>	dataSet.prev.angle = dataSet.curr.angle = angle;
224	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
225	>	dataSet.deltaV = 0.0;
226	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
227	>	}else {
228	>	i->second.prev.angle = i->second.curr.angle;
229	>	i->second.prev.potential = i->second.curr.potential;
230	>	i->second.curr.angle = angle;
231	>	i->second.curr.potential = currInversionPot;
232	>	i->second.deltaV =  fabs(i->second.curr.potential -
233	>	i->second.prev.potential);
234	>	}
235	>	}
236		}
237
238	<	RealType  shortRangePotential = bondPotential + bendPotential + torsionPotential;
238	>	RealType  shortRangePotential = bondPotential + bendPotential +
239	>	torsionPotential +  inversionPotential;
240		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
241		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
242		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
243		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
244		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
245	<
245	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
246		}
247	+
248	+	void ForceManager::longRangeInteractions() {
249
250	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
251	<	Snapshot* curSnapshot;
252	<	DataStorage* config;
253	<	RealType* frc;
254	<	RealType* pos;
255	<	RealType* trq;
256	<	RealType* A;
257	<	RealType* electroFrame;
258	<	RealType* rc;
259	<
260	<	//get current snapshot from SimInfo
241	<	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
250	>	// some of this initial stuff will go away:
251	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
252	>	DataStorage* config = &(curSnapshot->atomData);
253	>	DataStorage* cgConfig = &(curSnapshot->cgData);
254	>	RealType* frc = config->getArrayPointer(DataStorage::dslForce);
255	>	RealType* pos = config->getArrayPointer(DataStorage::dslPosition);
256	>	RealType* trq = config->getArrayPointer(DataStorage::dslTorque);
257	>	RealType* A = config->getArrayPointer(DataStorage::dslAmat);
258	>	RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
259	>	RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
260	>	RealType* rc;
261
262	<	//get array pointers
263	<	config = &(curSnapshot->atomData);
245	<	frc = config->getArrayPointer(DataStorage::dslForce);
246	<	pos = config->getArrayPointer(DataStorage::dslPosition);
247	<	trq = config->getArrayPointer(DataStorage::dslTorque);
248	<	A   = config->getArrayPointer(DataStorage::dslAmat);
249	<	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
250	<
251	<	//calculate the center of mass of cutoff group
252	<	SimInfo::MoleculeIterator mi;
253	<	Molecule* mol;
254	<	Molecule::CutoffGroupIterator ci;
255	<	CutoffGroup* cg;
256	<	Vector3d com;
257	<	std::vector<Vector3d> rcGroup;
258	<
259	<	if(info_->getNCutoffGroups() > 0){
260	<
261	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
262	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
263	<	cg->getCOM(com);
264	<	rcGroup.push_back(com);
265	<	}
266	<	}// end for (mol)
267	<
268	<	rc = rcGroup[0].getArrayPointer();
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  if cutoff group does not exist
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	<
269	>
270		//initialize data before passing to fortran
271		RealType longRangePotential[LR_POT_TYPES];
272		RealType lrPot = 0.0;
277	–
278	–	Mat3x3d tau;
279	–	short int passedCalcPot = needPotential;
280	–	short int passedCalcStress = needStress;
273		int isError = 0;
274
275		for (int i=0; i<LR_POT_TYPES;i++){
276		longRangePotential[i]=0.0; //Initialize array
277		}
278
279	<	doForceLoop( pos,
288	<	rc,
289	<	A,
290	<	electroFrame,
291	<	frc,
292	<	trq,
293	<	tau.getArrayPointer(),
294	<	longRangePotential,
295	<	&passedCalcPot,
296	<	&passedCalcStress,
297	<	&isError );
279	>	// new stuff starts here:
280
281	<	if( isError ){
282	<	sprintf( painCave.errMsg,
283	<	"Error returned from the fortran force calculation.\n" );
284	<	painCave.isFatal = 1;
285	<	simError();
281	>	fDecomp_->distributeData();
282	>
283	>	int cg1, cg2, atom1, atom2;
284	>	Vector3d d_grp, dag;
285	>	RealType rgrpsq, rgrp;
286	>	RealType vij;
287	>	Vector3d fij, fg;
288	>	pair<int, int> gtypes;
289	>	RealType rCutSq;
290	>	bool in_switching_region;
291	>	RealType sw, dswdr, swderiv;
292	>	vector<int> atomListColumn, atomListRow, atomListLocal;
293	>	InteractionData idat;
294	>	SelfData sdat;
295	>	RealType mf;
296	>
297	>	int loopStart, loopEnd;
298	>
299	>	loopEnd = PAIR_LOOP;
300	>	if (info_->requiresPrepair() ) {
301	>	loopStart = PREPAIR_LOOP;
302	>	} else {
303	>	loopStart = PAIR_LOOP;
304		}
305	+
306	+	for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
307	+
308	+	if (iLoop == loopStart) {
309	+	bool update_nlist = fDecomp_->checkNeighborList();
310	+	if (update_nlist)
311	+	neighborList = fDecomp_->buildNeighborList();
312	+	}
313	+
314	+	for (vector<pair<int, int> >::iterator it = neighborList.begin();
315	+	it != neighborList.end(); ++it) {
316	+
317	+	cg1 = (*it).first;
318	+	cg2 = (*it).second;
319	+
320	+	gtypes = fDecomp_->getGroupTypes(cg1, cg2);
321	+	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
322	+	curSnapshot->wrapVector(d_grp);
323	+	rgrpsq = d_grp.lengthSquare();
324	+	rCutSq = groupCutoffMap[gtypes].first;
325	+
326	+	if (rgrpsq < rCutSq) {
327	+	idat.rcut = groupCutoffMap[gtypes].second;
328	+	if (iLoop == PAIR_LOOP) {
329	+	vij *= 0.0;
330	+	fij = V3Zero;
331	+	}
332	+
333	+	in_switching_region = swfun_->getSwitch(rgrpsq, idat.sw, dswdr, rgrp);
334	+	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
335	+	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
336	+
337	+	for (vector<int>::iterator ia = atomListRow.begin();
338	+	ia != atomListRow.end(); ++ia) {
339	+	atom1 = (*ia);
340	+
341	+	for (vector<int>::iterator jb = atomListColumn.begin();
342	+	jb != atomListColumn.end(); ++jb) {
343	+	atom2 = (*jb);
344	+
345	+	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
346	+
347	+	idat = fDecomp_->fillInteractionData(atom1, atom2);
348	+
349	+	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
350	+	idat.d = d_grp;
351	+	idat.r2 = rgrpsq;
352	+	} else {
353	+	idat.d = fDecomp_->getInteratomicVector(atom1, atom2);
354	+	curSnapshot->wrapVector(idat.d);
355	+	idat.r2 = idat.d.lengthSquare();
356	+	}
357	+
358	+	idat.rij = sqrt(idat.r2);
359	+
360	+	if (iLoop == PREPAIR_LOOP) {
361	+	interactionMan_->doPrePair(idat);
362	+	} else {
363	+	interactionMan_->doPair(idat);
364	+	vij += idat.vpair;
365	+	fij += idat.f1;
366	+	tau -= outProduct(idat.d, idat.f1);
367	+	}
368	+	}
369	+	}
370	+	}
371	+
372	+	if (iLoop == PAIR_LOOP) {
373	+	if (in_switching_region) {
374	+	swderiv = vij * dswdr / rgrp;
375	+	fg = swderiv * d_grp;
376	+
377	+	fij += fg;
378	+
379	+	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
380	+	tau -= outProduct(idat.d, fg);
381	+	}
382	+
383	+	for (vector<int>::iterator ia = atomListRow.begin();
384	+	ia != atomListRow.end(); ++ia) {
385	+	atom1 = (*ia);
386	+	mf = fDecomp_->getMfactRow(atom1);
387	+	// fg is the force on atom ia due to cutoff group's
388	+	// presence in switching region
389	+	fg = swderiv * d_grp * mf;
390	+	fDecomp_->addForceToAtomRow(atom1, fg);
391	+
392	+	if (atomListRow.size() > 1) {
393	+	if (info_->usesAtomicVirial()) {
394	+	// find the distance between the atom
395	+	// and the center of the cutoff group:
396	+	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
397	+	tau -= outProduct(dag, fg);
398	+	}
399	+	}
400	+	}
401	+	for (vector<int>::iterator jb = atomListColumn.begin();
402	+	jb != atomListColumn.end(); ++jb) {
403	+	atom2 = (*jb);
404	+	mf = fDecomp_->getMfactColumn(atom2);
405	+	// fg is the force on atom jb due to cutoff group's
406	+	// presence in switching region
407	+	fg = -swderiv * d_grp * mf;
408	+	fDecomp_->addForceToAtomColumn(atom2, fg);
409	+
410	+	if (atomListColumn.size() > 1) {
411	+	if (info_->usesAtomicVirial()) {
412	+	// find the distance between the atom
413	+	// and the center of the cutoff group:
414	+	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
415	+	tau -= outProduct(dag, fg);
416	+	}
417	+	}
418	+	}
419	+	}
420	+	//if (!SIM_uses_AtomicVirial) {
421	+	//  tau -= outProduct(d_grp, fij);
422	+	//}
423	+	}
424	+	}
425	+	}
426	+
427	+	if (iLoop == PREPAIR_LOOP) {
428	+	if (info_->requiresPrepair()) {
429	+	fDecomp_->collectIntermediateData();
430	+	atomListLocal = fDecomp_->getAtomList();
431	+	for (vector<int>::iterator ia = atomListLocal.begin();
432	+	ia != atomListLocal.end(); ++ia) {
433	+	atom1 = (*ia);
434	+	sdat = fDecomp_->fillSelfData(atom1);
435	+	interactionMan_->doPreForce(sdat);
436	+	}
437	+	fDecomp_->distributeIntermediateData();
438	+	}
439	+	}
440	+
441	+	}
442	+
443	+	fDecomp_->collectData();
444	+
445	+	if (info_->requiresSkipCorrection() || info_->requiresSelfCorrection()) {
446	+	atomListLocal = fDecomp_->getAtomList();
447	+	for (vector<int>::iterator ia = atomListLocal.begin();
448	+	ia != atomListLocal.end(); ++ia) {
449	+	atom1 = (*ia);
450	+
451	+	if (info_->requiresSkipCorrection()) {
452	+	vector<int> skipList = fDecomp_->getSkipsForAtom(atom1);
453	+	for (vector<int>::iterator jb = skipList.begin();
454	+	jb != skipList.end(); ++jb) {
455	+	atom2 = (*jb);
456	+	idat = fDecomp_->fillSkipData(atom1, atom2);
457	+	interactionMan_->doSkipCorrection(idat);
458	+	}
459	+	}
460	+
461	+	if (info_->requiresSelfCorrection()) {
462	+	sdat = fDecomp_->fillSelfData(atom1);
463	+	interactionMan_->doSelfCorrection(sdat);
464	+	}
465	+	}
466	+	}
467	+
468		for (int i=0; i<LR_POT_TYPES;i++){
469		lrPot += longRangePotential[i]; //Quick hack
470		}
471	<
471	>
472		//store the tau and long range potential
473		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
474		curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
475		curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
313	–
314	–	curSnapshot->statData.setTau(tau);
476		}
477
478	<
478	>
479		void ForceManager::postCalculation() {
480		SimInfo::MoleculeIterator mi;
481		Molecule* mol;
482		Molecule::RigidBodyIterator rbIter;
483		RigidBody* rb;
484	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
485
486		// collect the atomic forces onto rigid bodies
487	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
488	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
489	<	rb->calcForcesAndTorques();
487	>
488	>	for (mol = info_->beginMolecule(mi); mol != NULL;
489	>	mol = info_->nextMolecule(mi)) {
490	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
491	>	rb = mol->nextRigidBody(rbIter)) {
492	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
493	>	tau += rbTau;
494		}
495		}
496	<
496	>
497	>	#ifdef IS_MPI
498	>	Mat3x3d tmpTau(tau);
499	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
500	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
501	>	#endif
502	>	curSnapshot->statData.setTau(tau);
503		}
504
505	<	} //end namespace oopse
505	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1549 by gezelter, Wed Apr 27 18:38:15 2011 UTC

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