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

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trunk/src/brains/ForceManager.cpp (file contents), Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1575 by gezelter, Fri Jun 3 21:39:49 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) {
71	<	return b1.dataSet.deltaV < b2.dataSet.deltaV;
66	>	fDecomp_ = new ForceMatrixDecomposition(info_);
67		}
68	<
69	<	bool  TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
70	<	return t1.dataSet.deltaV < t2.dataSet.deltaV;
71	<	}
77	<	*/
78	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
79	<
80	<	if (!info_->isFortranInitialized()) {
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		}
83	–
84	–	preCalculation();
79
80	<	calcShortRangeInteraction();
81	<
82	<	calcLongRangeInteraction(needPotential, needStress);
89	<
80	>	preCalculation();
81	>	shortRangeInteractions();
82	>	longRangeInteractions();
83		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	–	}
84
109	–	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
110	–	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
111	–	std::cout << "bend" << std::endl;
112	–	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
113	–	Bend* bend = k->bend;
114	–	std::cout << "atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
115	–	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;
116	–	}
117	–	std::cout << "torsio" << std::endl;
118	–	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
119	–	Torsion* torsion = l->torsion;
120	–	std::cout << "atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
121	–	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;
122	–	}
123	–	*/
85		}
86	<
86	>
87		void ForceManager::preCalculation() {
88		SimInfo::MoleculeIterator mi;
89		Molecule* mol;
#	Line 130 | 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	<	double bondPotential = 0.0;
138	<	double bendPotential = 0.0;
139	<	double torsionPotential = 0.0;
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)) {
153	>	for (bond = mol->beginBond(bondIter); bond != NULL;
154	>	bond = mol->nextBond(bondIter)) {
155		bond->calcForce();
156		bondPotential += bond->getPotential();
157		}
158
159	<
160	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
161	<
162	<	double angle;
163	<	bend->calcForce(angle);
164	<	double currBendPot = bend->getPotential();
165	<	bendPotential += bend->getPotential();
166	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
167	<	if (i == bendDataSets.end()) {
168	<	BendDataSet dataSet;
169	<	dataSet.prev.angle = dataSet.curr.angle = angle;
170	<	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
171	<	dataSet.deltaV = 0.0;
172	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
173	<	}else {
174	<	i->second.prev.angle = i->second.curr.angle;
175	<	i->second.prev.potential = i->second.curr.potential;
176	<	i->second.curr.angle = angle;
177	<	i->second.curr.potential = currBendPot;
178	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
179	<	}
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	<	double angle;
186	<	torsion->calcForce(angle);
187	<	double currTorsionPot = torsion->getPotential();
188	<	torsionPotential += torsion->getPotential();
189	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
190	<	if (i == torsionDataSets.end()) {
191	<	TorsionDataSet dataSet;
192	<	dataSet.prev.angle = dataSet.curr.angle = angle;
193	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
194	<	dataSet.deltaV = 0.0;
195	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
196	<	}else {
197	<	i->second.prev.angle = i->second.curr.angle;
198	<	i->second.prev.potential = i->second.curr.potential;
199	<	i->second.curr.angle = angle;
200	<	i->second.curr.potential = currTorsionPot;
201	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
202	<	}
203	<	}
204	<
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 = bondPotential + bendPotential + torsionPotential;
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	<
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
243	<	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
244	<
245	<	//get array pointers
246	<	config = &(curSnapshot->atomData);
247	<	frc = config->getArrayPointer(DataStorage::dslForce);
248	<	pos = config->getArrayPointer(DataStorage::dslPosition);
249	<	trq = config->getArrayPointer(DataStorage::dslTorque);
250	<	A   = config->getArrayPointer(DataStorage::dslAmat);
251	<	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
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	<	//calculate the center of mass of cutoff group
257	<	SimInfo::MoleculeIterator mi;
255	<	Molecule* mol;
256	<	Molecule::CutoffGroupIterator ci;
257	<	CutoffGroup* cg;
258	<	Vector3d com;
259	<	std::vector<Vector3d> rcGroup;
260	<
261	<	if(info_->getNCutoffGroups() > 0){
262	<
263	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
264	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
265	<	cg->getCOM(com);
266	<	rcGroup.push_back(com);
267	<	}
268	<	}// end for (mol)
269	<
270	<	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		}
275	–
276	–	//initialize data before passing to fortran
277	–	double longRangePotential[LR_POT_TYPES];
278	–	double lrPot = 0.0;
263
264	<	Mat3x3d tau;
265	<	short int passedCalcPot = needPotential;
266	<	short int passedCalcStress = needStress;
267	<	int isError = 0;
264	>	// new stuff starts here:
265	>	fDecomp_->zeroWorkArrays();
266	>	fDecomp_->distributeData();
267	>
268	>	int cg1, cg2, atom1, atom2;
269	>	Vector3d d_grp, dag;
270	>	RealType rgrpsq, rgrp;
271	>	RealType vij;
272	>	Vector3d fij, fg;
273	>	pair<int, int> gtypes;
274	>	RealType rCutSq;
275	>	bool in_switching_region;
276	>	RealType sw, dswdr, swderiv;
277	>	vector<int> atomListColumn, atomListRow, atomListLocal;
278	>	InteractionData idat;
279	>	SelfData sdat;
280	>	RealType mf;
281	>	potVec pot(0.0);
282	>	potVec longRangePotential(0.0);
283	>	RealType lrPot;
284
285	<	for (int i=0; i<LR_POT_TYPES;i++){
286	<	longRangePotential[i]=0.0; //Initialize array
285	>	int loopStart, loopEnd;
286	>
287	>	loopEnd = PAIR_LOOP;
288	>	if (info_->requiresPrepair() ) {
289	>	loopStart = PREPAIR_LOOP;
290	>	} else {
291	>	loopStart = PAIR_LOOP;
292		}
293
294	<	doForceLoop( pos,
295	<	rc,
296	<	A,
297	<	electroFrame,
298	<	frc,
299	<	trq,
300	<	tau.getArrayPointer(),
296	<	longRangePotential,
297	<	&passedCalcPot,
298	<	&passedCalcStress,
299	<	&isError );
294	>	for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
295	>
296	>	if (iLoop == loopStart) {
297	>	bool update_nlist = fDecomp_->checkNeighborList();
298	>	if (update_nlist)
299	>	neighborList = fDecomp_->buildNeighborList();
300	>	}
301
302	<	if( isError ){
303	<	sprintf( painCave.errMsg,
304	<	"Error returned from the fortran force calculation.\n" );
305	<	painCave.isFatal = 1;
306	<	simError();
302	>	for (vector<pair<int, int> >::iterator it = neighborList.begin();
303	>	it != neighborList.end(); ++it) {
304	>
305	>	cg1 = (*it).first;
306	>	cg2 = (*it).second;
307	>
308	>	gtypes = fDecomp_->getGroupTypes(cg1, cg2);
309	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
310	>	curSnapshot->wrapVector(d_grp);
311	>	rgrpsq = d_grp.lengthSquare();
312	>	rCutSq = groupCutoffMap[gtypes].first;
313	>
314	>	if (rgrpsq < rCutSq) {
315	>	*(idat.rcut) = groupCutoffMap[gtypes].second;
316	>	if (iLoop == PAIR_LOOP) {
317	>	vij *= 0.0;
318	>	fij = V3Zero;
319	>	}
320	>
321	>	in_switching_region = swfun_->getSwitch(rgrpsq, *(idat.sw), dswdr,
322	>	rgrp);
323	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
324	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
325	>
326	>	for (vector<int>::iterator ia = atomListRow.begin();
327	>	ia != atomListRow.end(); ++ia) {
328	>	atom1 = (*ia);
329	>
330	>	for (vector<int>::iterator jb = atomListColumn.begin();
331	>	jb != atomListColumn.end(); ++jb) {
332	>	atom2 = (*jb);
333	>
334	>	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
335	>
336	>	pot *= 0.0;
337	>
338	>	idat = fDecomp_->fillInteractionData(atom1, atom2);
339	>	*(idat.pot) = pot;
340	>
341	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
342	>	*(idat.d) = d_grp;
343	>	*(idat.r2) = rgrpsq;
344	>	} else {
345	>	*(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2);
346	>	curSnapshot->wrapVector( *(idat.d) );
347	>	*(idat.r2) = idat.d->lengthSquare();
348	>	}
349	>
350	>	*(idat.rij) = sqrt( *(idat.r2) );
351	>
352	>	if (iLoop == PREPAIR_LOOP) {
353	>	interactionMan_->doPrePair(idat);
354	>	} else {
355	>	interactionMan_->doPair(idat);
356	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
357	>	vij += *(idat.vpair);
358	>	fij += *(idat.f1);
359	>	tau -= outProduct( *(idat.d), *(idat.f1));
360	>	}
361	>	}
362	>	}
363	>	}
364	>
365	>	if (iLoop == PAIR_LOOP) {
366	>	if (in_switching_region) {
367	>	swderiv = vij * dswdr / rgrp;
368	>	fg = swderiv * d_grp;
369	>
370	>	fij += fg;
371	>
372	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
373	>	tau -= outProduct( *(idat.d), fg);
374	>	}
375	>
376	>	for (vector<int>::iterator ia = atomListRow.begin();
377	>	ia != atomListRow.end(); ++ia) {
378	>	atom1 = (*ia);
379	>	mf = fDecomp_->getMassFactorRow(atom1);
380	>	// fg is the force on atom ia due to cutoff group's
381	>	// presence in switching region
382	>	fg = swderiv * d_grp * mf;
383	>	fDecomp_->addForceToAtomRow(atom1, fg);
384	>
385	>	if (atomListRow.size() > 1) {
386	>	if (info_->usesAtomicVirial()) {
387	>	// find the distance between the atom
388	>	// and the center of the cutoff group:
389	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
390	>	tau -= outProduct(dag, fg);
391	>	}
392	>	}
393	>	}
394	>	for (vector<int>::iterator jb = atomListColumn.begin();
395	>	jb != atomListColumn.end(); ++jb) {
396	>	atom2 = (*jb);
397	>	mf = fDecomp_->getMassFactorColumn(atom2);
398	>	// fg is the force on atom jb due to cutoff group's
399	>	// presence in switching region
400	>	fg = -swderiv * d_grp * mf;
401	>	fDecomp_->addForceToAtomColumn(atom2, fg);
402	>
403	>	if (atomListColumn.size() > 1) {
404	>	if (info_->usesAtomicVirial()) {
405	>	// find the distance between the atom
406	>	// and the center of the cutoff group:
407	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
408	>	tau -= outProduct(dag, fg);
409	>	}
410	>	}
411	>	}
412	>	}
413	>	//if (!SIM_uses_AtomicVirial) {
414	>	//  tau -= outProduct(d_grp, fij);
415	>	//}
416	>	}
417	>	}
418	>	}
419	>
420	>	if (iLoop == PREPAIR_LOOP) {
421	>	if (info_->requiresPrepair()) {
422	>	fDecomp_->collectIntermediateData();
423	>
424	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
425	>	sdat = fDecomp_->fillSelfData(atom1);
426	>	interactionMan_->doPreForce(sdat);
427	>	}
428	>
429	>	fDecomp_->distributeIntermediateData();
430	>	}
431	>	}
432	>
433		}
434	<	for (int i=0; i<LR_POT_TYPES;i++){
435	<	lrPot += longRangePotential[i]; //Quick hack
434	>
435	>	fDecomp_->collectData();
436	>
437	>	if ( info_->requiresSkipCorrection() ) {
438	>
439	>	for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
440	>
441	>	vector<int> skipList = fDecomp_->getSkipsForRowAtom( atom1 );
442	>
443	>	for (vector<int>::iterator jb = skipList.begin();
444	>	jb != skipList.end(); ++jb) {
445	>
446	>	atom2 = (*jb);
447	>	idat = fDecomp_->fillSkipData(atom1, atom2);
448	>	interactionMan_->doSkipCorrection(idat);
449	>
450	>	}
451	>	}
452		}
453	+
454	+	if (info_->requiresSelfCorrection()) {
455
456	+	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
457	+	sdat = fDecomp_->fillSelfData(atom1);
458	+	interactionMan_->doSelfCorrection(sdat);
459	+	}
460	+
461	+	}
462	+
463	+	longRangePotential = fDecomp_->getLongRangePotential();
464	+	lrPot = longRangePotential.sum();
465	+
466		//store the tau and long range potential
467		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
468	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
469	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
315	<
316	<	curSnapshot->statData.setTau(tau);
468	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
469	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
470		}
471
472	<
472	>
473		void ForceManager::postCalculation() {
474		SimInfo::MoleculeIterator mi;
475		Molecule* mol;
476		Molecule::RigidBodyIterator rbIter;
477		RigidBody* rb;
478	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
479
480		// collect the atomic forces onto rigid bodies
481	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
482	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
483	<	rb->calcForcesAndTorques();
481	>
482	>	for (mol = info_->beginMolecule(mi); mol != NULL;
483	>	mol = info_->nextMolecule(mi)) {
484	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
485	>	rb = mol->nextRigidBody(rbIter)) {
486	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
487	>	tau += rbTau;
488		}
489		}
490	<
490	>
491	>	#ifdef IS_MPI
492	>	Mat3x3d tmpTau(tau);
493	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
494	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
495	>	#endif
496	>	curSnapshot->statData.setTau(tau);
497		}
498
499	<	} //end namespace oopse
499	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1575 by gezelter, Fri Jun 3 21:39:49 2011 UTC

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