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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 1551 by gezelter, Thu Apr 28 18:38:21 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"
53	<	#define __C
54	<	#include "UseTheForce/DarkSide/fInteractionMap.h"
52	>	#define __OPENMD_C
53		#include "utils/simError.h"
54	+	#include "primitives/Bond.hpp"
55		#include "primitives/Bend.hpp"
56	<	#include "primitives/Bend.hpp"
57	<	namespace oopse {
56	>	#include "primitives/Torsion.hpp"
57	>	#include "primitives/Inversion.hpp"
58	>	#include "nonbonded/NonBondedInteraction.hpp"
59	>	#include "parallel/ForceMatrixDecomposition.hpp"
60
61	<	/*
62	<	struct BendOrderStruct {
63	<	Bend* bend;
64	<	BendDataSet dataSet;
64	<	};
65	<	struct TorsionOrderStruct {
66	<	Torsion* torsion;
67	<	TorsionDataSet dataSet;
68	<	};
61	>	using namespace std;
62	>	namespace OpenMD {
63	>
64	>	ForceManager::ForceManager(SimInfo * info) : info_(info) {
65
66	<	bool  BendSortFunctor(const BendOrderStruct& b1, const BendOrderStruct& b2) {
67	<	return b1.dataSet.deltaV < b2.dataSet.deltaV;
66	>	#ifdef IS_MPI
67	>	fDecomp_ = new ForceMatrixDecomposition(info_);
68	>	#else
69	>	// fDecomp_ = new ForceSerialDecomposition(info);
70	>	#endif
71		}
72	<
73	<	bool  TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
74	<	return t1.dataSet.deltaV < t2.dataSet.deltaV;
76	<	}
77	<	*/
78	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
79	<
72	>
73	>	void ForceManager::calcForces() {
74	>
75		if (!info_->isFortranInitialized()) {
76		info_->update();
77	+	interactionMan_->setSimInfo(info_);
78	+	interactionMan_->initialize();
79	+	swfun_ = interactionMan_->getSwitchingFunction();
80	+	fDecomp_->distributeInitialData();
81	+	info_->setupFortran();
82		}
83	–
84	–	preCalculation();
83
84	<	calcShortRangeInteraction();
85	<
86	<	calcLongRangeInteraction(needPotential, needStress);
89	<
84	>	preCalculation();
85	>	shortRangeInteractions();
86	>	longRangeInteractions();
87		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	–	}
88
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	–	*/
89		}
90	<
90	>
91		void ForceManager::preCalculation() {
92		SimInfo::MoleculeIterator mi;
93		Molecule* mol;
#	Line 128 | Line 95 | namespace oopse {
95		Atom* atom;
96		Molecule::RigidBodyIterator rbIter;
97		RigidBody* rb;
98	+	Molecule::CutoffGroupIterator ci;
99	+	CutoffGroup* cg;
100
101		// forces are zeroed here, before any are accumulated.
102	<	// NOTE: do not rezero the forces in Fortran.
103	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
102	>
103	>	for (mol = info_->beginMolecule(mi); mol != NULL;
104	>	mol = info_->nextMolecule(mi)) {
105		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
106		atom->zeroForcesAndTorques();
107		}
108	<
108	>
109		//change the positions of atoms which belong to the rigidbodies
110	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
110	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
111	>	rb = mol->nextRigidBody(rbIter)) {
112		rb->zeroForcesAndTorques();
113		}
114	+
115	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
116	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
117	+	cg = mol->nextCutoffGroup(ci)) {
118	+	//calculate the center of mass of cutoff group
119	+	cg->updateCOM();
120	+	}
121	+	}
122		}
123	+
124	+	// Zero out the stress tensor
125	+	tau *= 0.0;
126
127		}
128	<
129	<	void ForceManager::calcShortRangeInteraction() {
128	>
129	>	void ForceManager::shortRangeInteractions() {
130		Molecule* mol;
131		RigidBody* rb;
132		Bond* bond;
133		Bend* bend;
134		Torsion* torsion;
135	+	Inversion* inversion;
136		SimInfo::MoleculeIterator mi;
137		Molecule::RigidBodyIterator rbIter;
138		Molecule::BondIterator bondIter;;
139		Molecule::BendIterator  bendIter;
140		Molecule::TorsionIterator  torsionIter;
141	+	Molecule::InversionIterator  inversionIter;
142		RealType bondPotential = 0.0;
143		RealType bendPotential = 0.0;
144		RealType torsionPotential = 0.0;
145	+	RealType inversionPotential = 0.0;
146
147		//calculate short range interactions
148	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
148	>	for (mol = info_->beginMolecule(mi); mol != NULL;
149	>	mol = info_->nextMolecule(mi)) {
150
151		//change the positions of atoms which belong to the rigidbodies
152	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
153	<	rb->updateAtoms();
152	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
153	>	rb = mol->nextRigidBody(rbIter)) {
154	>	rb->updateAtoms();
155		}
156
157	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
157	>	for (bond = mol->beginBond(bondIter); bond != NULL;
158	>	bond = mol->nextBond(bondIter)) {
159		bond->calcForce();
160		bondPotential += bond->getPotential();
161		}
162
163	<
164	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
165	<
166	<	RealType angle;
167	<	bend->calcForce(angle);
168	<	RealType currBendPot = bend->getPotential();
169	<	bendPotential += bend->getPotential();
170	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
171	<	if (i == bendDataSets.end()) {
172	<	BendDataSet dataSet;
173	<	dataSet.prev.angle = dataSet.curr.angle = angle;
174	<	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
175	<	dataSet.deltaV = 0.0;
176	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
177	<	}else {
178	<	i->second.prev.angle = i->second.curr.angle;
179	<	i->second.prev.potential = i->second.curr.potential;
180	<	i->second.curr.angle = angle;
181	<	i->second.curr.potential = currBendPot;
182	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
183	<	}
163	>	for (bend = mol->beginBend(bendIter); bend != NULL;
164	>	bend = mol->nextBend(bendIter)) {
165	>
166	>	RealType angle;
167	>	bend->calcForce(angle);
168	>	RealType currBendPot = bend->getPotential();
169	>
170	>	bendPotential += bend->getPotential();
171	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
172	>	if (i == bendDataSets.end()) {
173	>	BendDataSet dataSet;
174	>	dataSet.prev.angle = dataSet.curr.angle = angle;
175	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
176	>	dataSet.deltaV = 0.0;
177	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
178	>	}else {
179	>	i->second.prev.angle = i->second.curr.angle;
180	>	i->second.prev.potential = i->second.curr.potential;
181	>	i->second.curr.angle = angle;
182	>	i->second.curr.potential = currBendPot;
183	>	i->second.deltaV =  fabs(i->second.curr.potential -
184	>	i->second.prev.potential);
185	>	}
186		}
187	<
188	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
187	>
188	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
189	>	torsion = mol->nextTorsion(torsionIter)) {
190		RealType angle;
191	<	torsion->calcForce(angle);
191	>	torsion->calcForce(angle);
192		RealType currTorsionPot = torsion->getPotential();
193	<	torsionPotential += torsion->getPotential();
194	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
195	<	if (i == torsionDataSets.end()) {
196	<	TorsionDataSet dataSet;
197	<	dataSet.prev.angle = dataSet.curr.angle = angle;
198	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
199	<	dataSet.deltaV = 0.0;
200	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
201	<	}else {
202	<	i->second.prev.angle = i->second.curr.angle;
203	<	i->second.prev.potential = i->second.curr.potential;
204	<	i->second.curr.angle = angle;
205	<	i->second.curr.potential = currTorsionPot;
206	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
207	<	}
208	<	}
209	<
193	>	torsionPotential += torsion->getPotential();
194	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
195	>	if (i == torsionDataSets.end()) {
196	>	TorsionDataSet dataSet;
197	>	dataSet.prev.angle = dataSet.curr.angle = angle;
198	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
199	>	dataSet.deltaV = 0.0;
200	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
201	>	}else {
202	>	i->second.prev.angle = i->second.curr.angle;
203	>	i->second.prev.potential = i->second.curr.potential;
204	>	i->second.curr.angle = angle;
205	>	i->second.curr.potential = currTorsionPot;
206	>	i->second.deltaV =  fabs(i->second.curr.potential -
207	>	i->second.prev.potential);
208	>	}
209	>	}
210	>
211	>	for (inversion = mol->beginInversion(inversionIter);
212	>	inversion != NULL;
213	>	inversion = mol->nextInversion(inversionIter)) {
214	>	RealType angle;
215	>	inversion->calcForce(angle);
216	>	RealType currInversionPot = inversion->getPotential();
217	>	inversionPotential += inversion->getPotential();
218	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
219	>	if (i == inversionDataSets.end()) {
220	>	InversionDataSet dataSet;
221	>	dataSet.prev.angle = dataSet.curr.angle = angle;
222	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
223	>	dataSet.deltaV = 0.0;
224	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
225	>	}else {
226	>	i->second.prev.angle = i->second.curr.angle;
227	>	i->second.prev.potential = i->second.curr.potential;
228	>	i->second.curr.angle = angle;
229	>	i->second.curr.potential = currInversionPot;
230	>	i->second.deltaV =  fabs(i->second.curr.potential -
231	>	i->second.prev.potential);
232	>	}
233	>	}
234		}
235
236	<	RealType  shortRangePotential = bondPotential + bendPotential + torsionPotential;
236	>	RealType  shortRangePotential = bondPotential + bendPotential +
237	>	torsionPotential +  inversionPotential;
238		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
239		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
240		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
241		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
242		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
243	<
243	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
244		}
245	+
246	+	void ForceManager::longRangeInteractions() {
247
248	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
249	<	Snapshot* curSnapshot;
250	<	DataStorage* config;
251	<	RealType* frc;
252	<	RealType* pos;
253	<	RealType* trq;
254	<	RealType* A;
255	<	RealType* electroFrame;
256	<	RealType* rc;
257	<
258	<	//get current snapshot from SimInfo
241	<	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
242	<
243	<	//get array pointers
244	<	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);
248	>	// some of this initial stuff will go away:
249	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
250	>	DataStorage* config = &(curSnapshot->atomData);
251	>	DataStorage* cgConfig = &(curSnapshot->cgData);
252	>	RealType* frc = config->getArrayPointer(DataStorage::dslForce);
253	>	RealType* pos = config->getArrayPointer(DataStorage::dslPosition);
254	>	RealType* trq = config->getArrayPointer(DataStorage::dslTorque);
255	>	RealType* A = config->getArrayPointer(DataStorage::dslAmat);
256	>	RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
257	>	RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
258	>	RealType* rc;
259
260	<	//calculate the center of mass of cutoff group
261	<	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();
260	>	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
261	>	rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
262		} else {
263	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
263	>	// center of mass of the group is the same as position of the atom
264	>	// if cutoff group does not exist
265		rc = pos;
266		}
267	<
267	>
268		//initialize data before passing to fortran
269	<	RealType longRangePotential[LR_POT_TYPES];
269	>	RealType longRangePotential[N_INTERACTION_FAMILIES];
270		RealType lrPot = 0.0;
277	–
278	–	Mat3x3d tau;
279	–	short int passedCalcPot = needPotential;
280	–	short int passedCalcStress = needStress;
271		int isError = 0;
272
273	<	for (int i=0; i<LR_POT_TYPES;i++){
273	>	// dangerous to iterate over enums, but we'll live on the edge:
274	>	for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
275		longRangePotential[i]=0.0; //Initialize array
276		}
277
278	<	doForceLoop( pos,
288	<	rc,
289	<	A,
290	<	electroFrame,
291	<	frc,
292	<	trq,
293	<	tau.getArrayPointer(),
294	<	longRangePotential,
295	<	&passedCalcPot,
296	<	&passedCalcStress,
297	<	&isError );
278	>	// new stuff starts here:
279
280	<	if( isError ){
281	<	sprintf( painCave.errMsg,
282	<	"Error returned from the fortran force calculation.\n" );
283	<	painCave.isFatal = 1;
284	<	simError();
280	>	fDecomp_->distributeData();
281	>
282	>	int cg1, cg2, atom1, atom2;
283	>	Vector3d d_grp, dag;
284	>	RealType rgrpsq, rgrp;
285	>	RealType vij;
286	>	Vector3d fij, fg;
287	>	pair<int, int> gtypes;
288	>	RealType rCutSq;
289	>	bool in_switching_region;
290	>	RealType sw, dswdr, swderiv;
291	>	vector<int> atomListColumn, atomListRow, atomListLocal;
292	>	InteractionData idat;
293	>	SelfData sdat;
294	>	RealType mf;
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	<	for (int i=0; i<LR_POT_TYPES;i++){
305	<	lrPot += longRangePotential[i]; //Quick hack
304	>
305	>	for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
306	>
307	>	if (iLoop == loopStart) {
308	>	bool update_nlist = fDecomp_->checkNeighborList();
309	>	if (update_nlist)
310	>	neighborList = fDecomp_->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	>	gtypes = fDecomp_->getGroupTypes(cg1, cg2);
320	>	d_grp  = fDecomp_->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, dswdr, rgrp);
333	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
334	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
335	>
336	>	for (vector<int>::iterator ia = atomListRow.begin();
337	>	ia != atomListRow.end(); ++ia) {
338	>	atom1 = (*ia);
339	>
340	>	for (vector<int>::iterator jb = atomListColumn.begin();
341	>	jb != atomListColumn.end(); ++jb) {
342	>	atom2 = (*jb);
343	>
344	>	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
345	>
346	>	idat = fDecomp_->fillInteractionData(atom1, atom2);
347	>
348	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
349	>	idat.d = d_grp;
350	>	idat.r2 = rgrpsq;
351	>	} else {
352	>	idat.d = fDecomp_->getInteratomicVector(atom1, atom2);
353	>	curSnapshot->wrapVector(idat.d);
354	>	idat.r2 = idat.d.lengthSquare();
355	>	}
356	>
357	>	idat.rij = sqrt(idat.r2);
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.f1);
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 (atomListRow.size() == 1 && atomListColumn.size() == 1) {
379	>	tau -= outProduct(idat.d, fg);
380	>	}
381	>
382	>	for (vector<int>::iterator ia = atomListRow.begin();
383	>	ia != atomListRow.end(); ++ia) {
384	>	atom1 = (*ia);
385	>	mf = fDecomp_->getMfactRow(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	>	fDecomp_->addForceToAtomRow(atom1, fg);
390	>
391	>	if (atomListRow.size() > 1) {
392	>	if (info_->usesAtomicVirial()) {
393	>	// find the distance between the atom
394	>	// and the center of the cutoff group:
395	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
396	>	tau -= outProduct(dag, fg);
397	>	}
398	>	}
399	>	}
400	>	for (vector<int>::iterator jb = atomListColumn.begin();
401	>	jb != atomListColumn.end(); ++jb) {
402	>	atom2 = (*jb);
403	>	mf = fDecomp_->getMfactColumn(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	>	fDecomp_->addForceToAtomColumn(atom2, fg);
408	>
409	>	if (atomListColumn.size() > 1) {
410	>	if (info_->usesAtomicVirial()) {
411	>	// find the distance between the atom
412	>	// and the center of the cutoff group:
413	>	dag = fDecomp_->getAtomToGroupVectorColumn(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	>	fDecomp_->collectIntermediateData();
429	>	atomListLocal = fDecomp_->getAtomList();
430	>	for (vector<int>::iterator ia = atomListLocal.begin();
431	>	ia != atomListLocal.end(); ++ia) {
432	>	atom1 = (*ia);
433	>	sdat = fDecomp_->fillSelfData(atom1);
434	>	interactionMan_->doPreForce(sdat);
435	>	}
436	>	fDecomp_->distributeIntermediateData();
437	>	}
438	>	}
439	>
440		}
441	+
442	+	fDecomp_->collectData();
443	+
444	+	if (info_->requiresSkipCorrection() || info_->requiresSelfCorrection()) {
445	+	atomListLocal = fDecomp_->getAtomList();
446	+	for (vector<int>::iterator ia = atomListLocal.begin();
447	+	ia != atomListLocal.end(); ++ia) {
448	+	atom1 = (*ia);
449
450	+	if (info_->requiresSkipCorrection()) {
451	+	vector<int> skipList = fDecomp_->getSkipsForAtom(atom1);
452	+	for (vector<int>::iterator jb = skipList.begin();
453	+	jb != skipList.end(); ++jb) {
454	+	atom2 = (*jb);
455	+	idat = fDecomp_->fillSkipData(atom1, atom2);
456	+	interactionMan_->doSkipCorrection(idat);
457	+	}
458	+	}
459	+
460	+	if (info_->requiresSelfCorrection()) {
461	+	sdat = fDecomp_->fillSelfData(atom1);
462	+	interactionMan_->doSelfCorrection(sdat);
463	+	}
464	+	}
465	+	}
466	+
467	+	// dangerous to iterate over enums, but we'll live on the edge:
468	+	for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++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];
313	<
314	<	curSnapshot->statData.setTau(tau);
474	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
475	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
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 1551 by gezelter, Thu Apr 28 18:38:21 2011 UTC

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