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

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trunk/src/brains/ForceManager.cpp (file contents), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1571 by gezelter, Fri May 27 16:45:44 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 49 | Line 49
49
50		#include "brains/ForceManager.hpp"
51		#include "primitives/Molecule.hpp"
52	<	#include "UseTheForce/doForces_interface.h"
52	>	#define __OPENMD_C
53		#include "utils/simError.h"
54	<	namespace oopse {
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	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
61	>	using namespace std;
62	>	namespace OpenMD {
63	>
64	>	ForceManager::ForceManager(SimInfo * info) : info_(info) {
65
66	<	if (!info_->isFortranInitialized()) {
66	>	fDecomp_ = new ForceMatrixDecomposition(info_);
67	>	}
68	>
69	>	void ForceManager::calcForces() {
70	>
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		}
61	–
62	–	preCalculation();
79
80	<	calcShortRangeInteraction();
81	<
82	<	calcLongRangeInteraction(needPotential, needStress);
67	<
80	>	preCalculation();
81	>	shortRangeInteractions();
82	>	longRangeInteractions();
83		postCalculation();
84	<
84	>
85		}
86	<
86	>
87		void ForceManager::preCalculation() {
88		SimInfo::MoleculeIterator mi;
89		Molecule* mol;
#	Line 76 | Line 91 | namespace oopse {
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.
98	<	// NOTE: do not rezero the forces in Fortran.
99	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
98	>
99	>	for (mol = info_->beginMolecule(mi); mol != NULL;
100	>	mol = info_->nextMolecule(mi)) {
101		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
102		atom->zeroForcesAndTorques();
103		}
104	<
104	>
105		//change the positions of atoms which belong to the rigidbodies
106	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
106	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
107	>	rb = mol->nextRigidBody(rbIter)) {
108		rb->zeroForcesAndTorques();
109		}
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	+
120	+	// Zero out the stress tensor
121	+	tau *= 0.0;
122
123		}
124	<
125	<	void ForceManager::calcShortRangeInteraction() {
124	>
125	>	void ForceManager::shortRangeInteractions() {
126		Molecule* mol;
127		RigidBody* rb;
128		Bond* bond;
129		Bend* bend;
130		Torsion* torsion;
131	+	Inversion* inversion;
132		SimInfo::MoleculeIterator mi;
133		Molecule::RigidBodyIterator rbIter;
134		Molecule::BondIterator bondIter;;
135		Molecule::BendIterator  bendIter;
136		Molecule::TorsionIterator  torsionIter;
137	+	Molecule::InversionIterator  inversionIter;
138	+	RealType bondPotential = 0.0;
139	+	RealType bendPotential = 0.0;
140	+	RealType torsionPotential = 0.0;
141	+	RealType inversionPotential = 0.0;
142
143		//calculate short range interactions
144	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
144	>	for (mol = info_->beginMolecule(mi); mol != NULL;
145	>	mol = info_->nextMolecule(mi)) {
146
147		//change the positions of atoms which belong to the rigidbodies
148	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
149	<	rb->updateAtoms();
148	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
149	>	rb = mol->nextRigidBody(rbIter)) {
150	>	rb->updateAtoms();
151		}
152
153	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
154	<	bond->calcForce();
153	>	for (bond = mol->beginBond(bondIter); bond != NULL;
154	>	bond = mol->nextBond(bondIter)) {
155	>	bond->calcForce();
156	>	bondPotential += bond->getPotential();
157		}
158
159	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
160	<	bend->calcForce();
159	>	for (bend = mol->beginBend(bendIter); bend != NULL;
160	>	bend = mol->nextBend(bendIter)) {
161	>
162	>	RealType angle;
163	>	bend->calcForce(angle);
164	>	RealType currBendPot = bend->getPotential();
165	>
166	>	bendPotential += bend->getPotential();
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(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;
177	>	i->second.curr.angle = angle;
178	>	i->second.curr.potential = currBendPot;
179	>	i->second.deltaV =  fabs(i->second.curr.potential -
180	>	i->second.prev.potential);
181	>	}
182		}
183	<
184	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
185	<	torsion->calcForce();
186	<	}
187	<
183	>
184	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
185	>	torsion = mol->nextTorsion(torsionIter)) {
186	>	RealType angle;
187	>	torsion->calcForce(angle);
188	>	RealType currTorsionPot = torsion->getPotential();
189	>	torsionPotential += torsion->getPotential();
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(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;
200	>	i->second.curr.angle = angle;
201	>	i->second.curr.potential = currTorsionPot;
202	>	i->second.deltaV =  fabs(i->second.curr.potential -
203	>	i->second.prev.potential);
204	>	}
205	>	}
206	>
207	>	for (inversion = mol->beginInversion(inversionIter);
208	>	inversion != NULL;
209	>	inversion = mol->nextInversion(inversionIter)) {
210	>	RealType angle;
211	>	inversion->calcForce(angle);
212	>	RealType currInversionPot = inversion->getPotential();
213	>	inversionPotential += inversion->getPotential();
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(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;
224	>	i->second.curr.angle = angle;
225	>	i->second.curr.potential = currInversionPot;
226	>	i->second.deltaV =  fabs(i->second.curr.potential -
227	>	i->second.prev.potential);
228	>	}
229	>	}
230		}
231
232	<	double  shortRangePotential = 0.0;
233	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
131	<	shortRangePotential += mol->getPotential();
132	<	}
133	<
232	>	RealType  shortRangePotential = bondPotential + bendPotential +
233	>	torsionPotential +  inversionPotential;
234		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
235		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
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;
240		}
241	+
242	+	void ForceManager::longRangeInteractions() {
243
244	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
245	<	Snapshot* curSnapshot;
246	<	DataStorage* config;
247	<	double* frc;
248	<	double* pos;
249	<	double* trq;
250	<	double* A;
251	<	double* electroFrame;
252	<	double* rc;
253	<
254	<	//get current snapshot from SimInfo
149	<	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
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	<	//get array pointers
257	<	config = &(curSnapshot->atomData);
153	<	frc = config->getArrayPointer(DataStorage::dslForce);
154	<	pos = config->getArrayPointer(DataStorage::dslPosition);
155	<	trq = config->getArrayPointer(DataStorage::dslTorque);
156	<	A   = config->getArrayPointer(DataStorage::dslAmat);
157	<	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
158	<
159	<	//calculate the center of mass of cutoff group
160	<	SimInfo::MoleculeIterator mi;
161	<	Molecule* mol;
162	<	Molecule::CutoffGroupIterator ci;
163	<	CutoffGroup* cg;
164	<	Vector3d com;
165	<	std::vector<Vector3d> rcGroup;
166	<
167	<	if(info_->getNCutoffGroups() > 0){
168	<
169	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
170	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
171	<	cg->getCOM(com);
172	<	rcGroup.push_back(com);
173	<	}
174	<	}// end for (mol)
175	<
176	<	rc = rcGroup[0].getArrayPointer();
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  if cutoff group does not exist
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	<
263	>
264		//initialize data before passing to fortran
265	<	double longRangePotential = 0.0;
266	<	Mat3x3d tau;
185	<	short int passedCalcPot = needPotential;
186	<	short int passedCalcStress = needStress;
265	>	RealType longRangePotential[N_INTERACTION_FAMILIES];
266	>	RealType lrPot = 0.0;
267		int isError = 0;
268
269	<	doForceLoop( pos,
270	<	rc,
271	<	A,
272	<	electroFrame,
193	<	frc,
194	<	trq,
195	<	tau.getArrayPointer(),
196	<	&longRangePotential,
197	<	&passedCalcPot,
198	<	&passedCalcStress,
199	<	&isError );
269	>	// dangerous to iterate over enums, but we'll live on the edge:
270	>	for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
271	>	longRangePotential[i]=0.0; //Initialize array
272	>	}
273
274	<	if( isError ){
275	<	sprintf( painCave.errMsg,
276	<	"Error returned from the fortran force calculation.\n" );
277	<	painCave.isFatal = 1;
278	<	simError();
274	>	// new stuff starts here:
275	>
276	>	fDecomp_->distributeData();
277	>
278	>	int cg1, cg2, atom1, atom2;
279	>	Vector3d d_grp, dag;
280	>	RealType rgrpsq, rgrp;
281	>	RealType vij;
282	>	Vector3d fij, fg;
283	>	pair<int, int> gtypes;
284	>	RealType rCutSq;
285	>	bool in_switching_region;
286	>	RealType sw, dswdr, swderiv;
287	>	vector<int> atomListColumn, atomListRow, atomListLocal;
288	>	InteractionData idat;
289	>	SelfData sdat;
290	>	RealType mf;
291	>
292	>	int loopStart, loopEnd;
293	>
294	>	loopEnd = PAIR_LOOP;
295	>	if (info_->requiresPrepair() ) {
296	>	loopStart = PREPAIR_LOOP;
297	>	} else {
298	>	loopStart = PAIR_LOOP;
299		}
300
301	+	for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
302	+
303	+	if (iLoop == loopStart) {
304	+	bool update_nlist = fDecomp_->checkNeighborList();
305	+	if (update_nlist)
306	+	neighborList = fDecomp_->buildNeighborList();
307	+	}
308	+
309	+	for (vector<pair<int, int> >::iterator it = neighborList.begin();
310	+	it != neighborList.end(); ++it) {
311	+
312	+	cg1 = (*it).first;
313	+	cg2 = (*it).second;
314	+
315	+	gtypes = fDecomp_->getGroupTypes(cg1, cg2);
316	+	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
317	+	curSnapshot->wrapVector(d_grp);
318	+	rgrpsq = d_grp.lengthSquare();
319	+	rCutSq = groupCutoffMap[gtypes].first;
320	+
321	+	if (rgrpsq < rCutSq) {
322	+	*(idat.rcut) = groupCutoffMap[gtypes].second;
323	+	if (iLoop == PAIR_LOOP) {
324	+	vij *= 0.0;
325	+	fij = V3Zero;
326	+	}
327	+
328	+	in_switching_region = swfun_->getSwitch(rgrpsq, *(idat.sw), dswdr,
329	+	rgrp);
330	+	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
331	+	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
332	+
333	+	for (vector<int>::iterator ia = atomListRow.begin();
334	+	ia != atomListRow.end(); ++ia) {
335	+	atom1 = (*ia);
336	+
337	+	for (vector<int>::iterator jb = atomListColumn.begin();
338	+	jb != atomListColumn.end(); ++jb) {
339	+	atom2 = (*jb);
340	+
341	+	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
342	+
343	+	idat = fDecomp_->fillInteractionData(atom1, atom2);
344	+
345	+	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
346	+	*(idat.d) = d_grp;
347	+	*(idat.r2) = rgrpsq;
348	+	} else {
349	+	*(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2);
350	+	curSnapshot->wrapVector( *(idat.d) );
351	+	*(idat.r2) = idat.d->lengthSquare();
352	+	}
353	+
354	+	*(idat.rij) = sqrt( *(idat.r2) );
355	+
356	+	if (iLoop == PREPAIR_LOOP) {
357	+	interactionMan_->doPrePair(idat);
358	+	} else {
359	+	interactionMan_->doPair(idat);
360	+	vij += *(idat.vpair);
361	+	fij += *(idat.f1);
362	+	tau -= outProduct( *(idat.d), *(idat.f1));
363	+	}
364	+	}
365	+	}
366	+	}
367	+
368	+	if (iLoop == PAIR_LOOP) {
369	+	if (in_switching_region) {
370	+	swderiv = vij * dswdr / rgrp;
371	+	fg = swderiv * d_grp;
372	+
373	+	fij += fg;
374	+
375	+	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
376	+	tau -= outProduct( *(idat.d), fg);
377	+	}
378	+
379	+	for (vector<int>::iterator ia = atomListRow.begin();
380	+	ia != atomListRow.end(); ++ia) {
381	+	atom1 = (*ia);
382	+	mf = fDecomp_->getMassFactorRow(atom1);
383	+	// fg is the force on atom ia due to cutoff group's
384	+	// presence in switching region
385	+	fg = swderiv * d_grp * mf;
386	+	fDecomp_->addForceToAtomRow(atom1, fg);
387	+
388	+	if (atomListRow.size() > 1) {
389	+	if (info_->usesAtomicVirial()) {
390	+	// find the distance between the atom
391	+	// and the center of the cutoff group:
392	+	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
393	+	tau -= outProduct(dag, fg);
394	+	}
395	+	}
396	+	}
397	+	for (vector<int>::iterator jb = atomListColumn.begin();
398	+	jb != atomListColumn.end(); ++jb) {
399	+	atom2 = (*jb);
400	+	mf = fDecomp_->getMassFactorColumn(atom2);
401	+	// fg is the force on atom jb due to cutoff group's
402	+	// presence in switching region
403	+	fg = -swderiv * d_grp * mf;
404	+	fDecomp_->addForceToAtomColumn(atom2, fg);
405	+
406	+	if (atomListColumn.size() > 1) {
407	+	if (info_->usesAtomicVirial()) {
408	+	// find the distance between the atom
409	+	// and the center of the cutoff group:
410	+	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
411	+	tau -= outProduct(dag, fg);
412	+	}
413	+	}
414	+	}
415	+	}
416	+	//if (!SIM_uses_AtomicVirial) {
417	+	//  tau -= outProduct(d_grp, fij);
418	+	//}
419	+	}
420	+	}
421	+	}
422	+
423	+	if (iLoop == PREPAIR_LOOP) {
424	+	if (info_->requiresPrepair()) {
425	+	fDecomp_->collectIntermediateData();
426	+
427	+	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
428	+	sdat = fDecomp_->fillSelfData(atom1);
429	+	interactionMan_->doPreForce(sdat);
430	+	}
431	+
432	+	fDecomp_->distributeIntermediateData();
433	+	}
434	+	}
435	+
436	+	}
437	+
438	+	fDecomp_->collectData();
439	+
440	+	if ( info_->requiresSkipCorrection() ) {
441	+
442	+	for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
443	+
444	+	vector<int> skipList = fDecomp_->getSkipsForRowAtom( atom1 );
445	+
446	+	for (vector<int>::iterator jb = skipList.begin();
447	+	jb != skipList.end(); ++jb) {
448	+
449	+	atom2 = (*jb);
450	+	idat = fDecomp_->fillSkipData(atom1, atom2);
451	+	interactionMan_->doSkipCorrection(idat);
452	+
453	+	}
454	+	}
455	+	}
456	+
457	+	if (info_->requiresSelfCorrection()) {
458	+
459	+	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
460	+	sdat = fDecomp_->fillSelfData(atom1);
461	+	interactionMan_->doSelfCorrection(sdat);
462	+	}
463	+
464	+	}
465	+
466	+	// dangerous to iterate over enums, but we'll live on the edge:
467	+	for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
468	+	lrPot += longRangePotential[i]; //Quick hack
469	+	}
470	+
471		//store the tau and long range potential
472	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
473	<	curSnapshot->statData.setTau(tau);
472	>	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
473	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
474	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
475		}
476
477	<
477	>
478		void ForceManager::postCalculation() {
479		SimInfo::MoleculeIterator mi;
480		Molecule* mol;
481		Molecule::RigidBodyIterator rbIter;
482		RigidBody* rb;
483	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
484
485		// collect the atomic forces onto rigid bodies
486	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
487	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
488	<	rb->calcForcesAndTorques();
486	>
487	>	for (mol = info_->beginMolecule(mi); mol != NULL;
488	>	mol = info_->nextMolecule(mi)) {
489	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
490	>	rb = mol->nextRigidBody(rbIter)) {
491	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
492	>	tau += rbTau;
493		}
494		}
495	<
495	>
496	>	#ifdef IS_MPI
497	>	Mat3x3d tmpTau(tau);
498	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
499	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
500	>	#endif
501	>	curSnapshot->statData.setTau(tau);
502		}
503
504	<	} //end namespace oopse
504	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1571 by gezelter, Fri May 27 16:45:44 2011 UTC

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