ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing:
trunk/src/brains/ForceManager.cpp (file contents), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1545 by gezelter, Fri Apr 8 21:25:19 2011 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	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	<	/**
43	<	* @file ForceManager.cpp
44	<	* @author tlin
45	<	* @date 11/09/2004
46	<	* @time 10:39am
47	<	* @version 1.0
48	<	*/
42	>	/**
43	>	* @file ForceManager.cpp
44	>	* @author tlin
45	>	* @date 11/09/2004
46	>	* @time 10:39am
47	>	* @version 1.0
48	>	*/
49
50		#include "brains/ForceManager.hpp"
51		#include "primitives/Molecule.hpp"
52		#include "UseTheForce/doForces_interface.h"
53	+	#define __OPENMD_C
54	+	#include "UseTheForce/DarkSide/fInteractionMap.h"
55		#include "utils/simError.h"
56	<	namespace oopse {
56	>	#include "primitives/Bond.hpp"
57	>	#include "primitives/Bend.hpp"
58	>	#include "primitives/Torsion.hpp"
59	>	#include "primitives/Inversion.hpp"
60	>	#include "parallel/ForceDecomposition.hpp"
61	>	//#include "parallel/SerialDecomposition.hpp"
62
63	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
63	>	using namespace std;
64	>	namespace OpenMD {
65	>
66	>	ForceManager::ForceManager(SimInfo * info) : info_(info) {
67
68	+	#ifdef IS_MPI
69	+	decomp_ = new ForceDecomposition(info_);
70	+	#else
71	+	// decomp_ = new SerialDecomposition(info);
72	+	#endif
73	+	}
74	+
75	+	void ForceManager::calcForces() {
76	+
77		if (!info_->isFortranInitialized()) {
78	<	info_->update();
78	>	info_->update();
79	>	nbiMan_->setSimInfo(info_);
80	>	nbiMan_->initialize();
81	>	swfun_ = nbiMan_->getSwitchingFunction();
82	>	decomp_->distributeInitialData();
83	>	info_->setupFortran();
84		}
61	–
62	–	preCalculation();
85
86	+	preCalculation();
87		calcShortRangeInteraction();
88	<
66	<	calcLongRangeInteraction(needPotential, needStress);
67	<
88	>	calcLongRangeInteraction();
89		postCalculation();
90	<
91	<	}
92	<
93	<	void ForceManager::preCalculation() {
90	>
91	>	}
92	>
93	>	void ForceManager::preCalculation() {
94		SimInfo::MoleculeIterator mi;
95		Molecule* mol;
96		Molecule::AtomIterator ai;
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)) {
106	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
107	<	atom->zeroForcesAndTorques();
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	>
111	>	//change the positions of atoms which belong to the rigidbodies
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	<
87	<	//change the positions of atoms which belong to the rigidbodies
88	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
89	<	rb->zeroForcesAndTorques();
90	<	}
123	>	}
124		}
125	+
126	+	// Zero out the stress tensor
127	+	tau *= 0.0;
128
129	<	}
130	<
131	<	void ForceManager::calcShortRangeInteraction() {
129	>	}
130	>
131	>	void ForceManager::calcShortRangeInteraction() {
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();
156	<	}
153	>	//change the positions of atoms which belong to the rigidbodies
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)) {
160	<	bond->calcForce();
161	<	}
159	>	for (bond = mol->beginBond(bondIter); bond != NULL;
160	>	bond = mol->nextBond(bondIter)) {
161	>	bond->calcForce();
162	>	bondPotential += bond->getPotential();
163	>	}
164
165	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
166	<	bend->calcForce();
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	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
190	<	torsion->calcForce();
191	<	}
192	<
188	>	}
189	>
190	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
191	>	torsion = mol->nextTorsion(torsionIter)) {
192	>	RealType angle;
193	>	torsion->calcForce(angle);
194	>	RealType currTorsionPot = torsion->getPotential();
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	<	double  shortRangePotential = 0.0;
239	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
131	<	shortRangePotential += mol->getPotential();
132	<	}
133	<
238	>	RealType  shortRangePotential = bondPotential + bendPotential +
239	>	torsionPotential +  inversionPotential;
240		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
241		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
242	<	}
242	>	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
243	>	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
244	>	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
245	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
246	>	}
247	>
248	>	void ForceManager::calcLongRangeInteraction() {
249
250	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
251	<	Snapshot* curSnapshot;
252	<	DataStorage* config;
253	<	double* frc;
254	<	double* pos;
255	<	double* trq;
256	<	double* A;
257	<	double* electroFrame;
258	<	double* rc;
259	<
260	<	//get current snapshot from SimInfo
149	<	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);
264	<	frc = config->getArrayPointer(DataStorage::dslForce);
265	<	pos = config->getArrayPointer(DataStorage::dslPosition);
266	<	trq = config->getArrayPointer(DataStorage::dslTorque);
267	<	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();
177	<	} else {
178	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
179	<	rc = pos;
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	<
269	>
270		//initialize data before passing to fortran
271	<	double longRangePotential = 0.0;
272	<	Mat3x3d tau;
185	<	short int passedCalcPot = needPotential;
186	<	short int passedCalcStress = needStress;
271	>	RealType longRangePotential[LR_POT_TYPES];
272	>	RealType lrPot = 0.0;
273		int isError = 0;
274
275	<	doForceLoop( pos,
276	<	rc,
277	<	A,
192	<	electroFrame,
193	<	frc,
194	<	trq,
195	<	tau.getArrayPointer(),
196	<	&longRangePotential,
197	<	&passedCalcPot,
198	<	&passedCalcStress,
199	<	&isError );
275	>	for (int i=0; i<LR_POT_TYPES;i++){
276	>	longRangePotential[i]=0.0; //Initialize array
277	>	}
278
279	<	if( isError ){
280	<	sprintf( painCave.errMsg,
281	<	"Error returned from the fortran force calculation.\n" );
282	<	painCave.isFatal = 1;
283	<	simError();
279	>	// new stuff starts here:
280	>
281	>	decomp_->distributeData();
282	>
283	>	int cg1, cg2;
284	>	Vector3d d_grp;
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> atomListI;
293	>	vector<int> atomListJ;
294	>	InteractionData idat;
295	>
296	>	int loopStart, loopEnd;
297	>
298	>	loopEnd = PAIR_LOOP;
299	>	if (info_->requiresPrepair_) {
300	>	loopStart = PREPAIR_LOOP;
301	>	} else {
302	>	loopStart = PAIR_LOOP;
303		}
304
305	<	//store the tau and long range potential
306	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
307	<	curSnapshot->statData.setTau(tau);
308	<	}
305	>	for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
306	>
307	>	if (iLoop == loopStart) {
308	>	bool update_nlist = decomp_->checkNeighborList();
309	>	if (update_nlist)
310	>	neighborList = decomp_->buildNeighborList();
311	>	}
312
313	+	for (vector<pair<int, int> >::iterator it = neighborList.begin();
314	+	it != neighborList.end(); ++it) {
315	+
316	+	cg1 = (*it).first;
317	+	cg2 = (*it).second;
318
319	<	void ForceManager::postCalculation() {
319	>	gtypes = decomp_->getGroupTypes(cg1, cg2);
320	>	d_grp  = decomp_->getIntergroupVector(cg1, cg2);
321	>	curSnapshot->wrapVector(d_grp);
322	>	rgrpsq = d_grp.lengthSquare();
323	>	rCutSq = groupCutoffMap(gtypes).first;
324	>
325	>	if (rgrpsq < rCutSq) {
326	>	idat.rcut = groupCutoffMap(gtypes).second;
327	>	if (iLoop == PAIR_LOOP) {
328	>	vij = 0.0;
329	>	fij = V3Zero;
330	>	}
331	>
332	>	in_switching_region = swfun_->getSwitch(rgrpsq, idat.sw, idat.dswdr, rgrp);
333	>
334	>	atomListI = decomp_->getAtomsInGroupI(cg1);
335	>	atomListJ = decomp_->getAtomsInGroupJ(cg2);
336	>
337	>	for (vector<int>::iterator ia = atomListI.begin();
338	>	ia != atomListI.end(); ++ia) {
339	>	atom1 = (*ia);
340	>
341	>	for (vector<int>::iterator jb = atomListJ.begin();
342	>	jb != atomListJ.end(); ++jb) {
343	>	atom2 = (*jb);
344	>
345	>	if (!decomp_->skipAtomPair(atom1, atom2)) {
346	>
347	>	if (atomListI.size() == 1 && atomListJ.size() == 1) {
348	>	idat.d = d_grp;
349	>	idat.r2 = rgrpsq;
350	>	} else {
351	>	idat.d = decomp_->getInteratomicVector(atom1, atom2);
352	>	curSnapshot->wrapVector(idat.d);
353	>	idat.r2 = idat.d.lengthSquare();
354	>	}
355	>
356	>	idat.r = sqrt(idat.r2);
357	>	decomp_->fillInteractionData(atom1, atom2, idat);
358	>
359	>	if (iLoop == PREPAIR_LOOP) {
360	>	interactionMan_->doPrePair(idat);
361	>	} else {
362	>	interactionMan_->doPair(idat);
363	>	vij += idat.vpair;
364	>	fij += idat.f1;
365	>	tau -= outProduct(idat.d, idat.f);
366	>	}
367	>	}
368	>	}
369	>	}
370	>
371	>	if (iLoop == PAIR_LOOP) {
372	>	if (in_switching_region) {
373	>	swderiv = vij * dswdr / rgrp;
374	>	fg = swderiv * d_grp;
375	>
376	>	fij += fg;
377	>
378	>	if (atomListI.size() == 1 && atomListJ.size() == 1) {
379	>	tau -= outProduct(idat.d, fg);
380	>	}
381	>
382	>	for (vector<int>::iterator ia = atomListI.begin();
383	>	ia != atomListI.end(); ++ia) {
384	>	atom1 = (*ia);
385	>	mf = decomp_->getMfactI(atom1);
386	>	// fg is the force on atom ia due to cutoff group's
387	>	// presence in switching region
388	>	fg = swderiv * d_grp * mf;
389	>	decomp_->addForceToAtomI(atom1, fg);
390	>
391	>	if (atomListI.size() > 1) {
392	>	if (info_->usesAtomicVirial_) {
393	>	// find the distance between the atom
394	>	// and the center of the cutoff group:
395	>	dag = decomp_->getAtomToGroupVectorI(atom1, cg1);
396	>	tau -= outProduct(dag, fg);
397	>	}
398	>	}
399	>	}
400	>	for (vector<int>::iterator jb = atomListJ.begin();
401	>	jb != atomListJ.end(); ++jb) {
402	>	atom2 = (*jb);
403	>	mf = decomp_->getMfactJ(atom2);
404	>	// fg is the force on atom jb due to cutoff group's
405	>	// presence in switching region
406	>	fg = -swderiv * d_grp * mf;
407	>	decomp_->addForceToAtomJ(atom2, fg);
408	>
409	>	if (atomListJ.size() > 1) {
410	>	if (info_->usesAtomicVirial_) {
411	>	// find the distance between the atom
412	>	// and the center of the cutoff group:
413	>	dag = decomp_->getAtomToGroupVectorJ(atom2, cg2);
414	>	tau -= outProduct(dag, fg);
415	>	}
416	>	}
417	>	}
418	>	}
419	>	//if (!SIM_uses_AtomicVirial) {
420	>	//  tau -= outProduct(d_grp, fij);
421	>	//}
422	>	}
423	>	}
424	>	}
425	>
426	>	if (iLoop == PREPAIR_LOOP) {
427	>	if (info_->requiresPrepair_) {
428	>	decomp_->collectIntermediateData();
429	>	atomList = decomp_->getAtomList();
430	>	for (vector<int>::iterator ia = atomList.begin();
431	>	ia != atomList.end(); ++ia) {
432	>	atom1 = (*ia);
433	>	decomp_->populateSelfData(atom1, SelfData sdat);
434	>	interactionMan_->doPreForce(sdat);
435	>	}
436	>	decomp_->distributeIntermediateData();
437	>	}
438	>	}
439	>
440	>	}
441	>
442	>	decomp_->collectData();
443	>
444	>	if (info_->requiresSkipCorrection_ || info_->requiresSelfCorrection_) {
445	>	atomList = decomp_->getAtomList();
446	>	for (vector<int>::iterator ia = atomList.begin();
447	>	ia != atomList.end(); ++ia) {
448	>	atom1 = (*ia);
449	>
450	>	if (info_->requiresSkipCorrection_) {
451	>	vector<int> skipList = decomp_->getSkipsForAtom(atom1);
452	>	for (vector<int>::iterator jb = skipList.begin();
453	>	jb != skipList.end(); ++jb) {
454	>	atom2 = (*jb);
455	>	decomp_->populateSkipData(atom1, atom2, InteractionData idat);
456	>	interactionMan_->doSkipCorrection(idat);
457	>	}
458	>	}
459	>
460	>	if (info_->requiresSelfCorrection_) {
461	>	decomp_->populateSelfData(atom1, SelfData sdat);
462	>	interactionMan_->doSelfCorrection(sdat);
463	>	}
464	>
465	>
466	>	}
467	>
468	>	for (int i=0; i<LR_POT_TYPES;i++){
469	>	lrPot += longRangePotential[i]; //Quick hack
470	>	}
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];
476	>	}
477	>
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();
490	<	}
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	+
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	<	}
228	<
229	<	} //end namespace oopse
505	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1545 by gezelter, Fri Apr 8 21:25:19 2011 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines