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

Comparing:
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 1544 by gezelter, Fri Mar 18 19:31:52 2011 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 50 | Line 50
50		#include "brains/ForceManager.hpp"
51		#include "primitives/Molecule.hpp"
52		#include "UseTheForce/doForces_interface.h"
53	<	#define __C
53	>	#define __OPENMD_C
54		#include "UseTheForce/DarkSide/fInteractionMap.h"
55		#include "utils/simError.h"
56	+	#include "primitives/Bond.hpp"
57		#include "primitives/Bend.hpp"
58	<	#include "primitives/Bend.hpp"
59	<	namespace oopse {
58	>	#include "primitives/Torsion.hpp"
59	>	#include "primitives/Inversion.hpp"
60	>	#include "parallel/ForceDecomposition.hpp"
61	>	//#include "parallel/SerialDecomposition.hpp"
62
63	<	/*
64	<	struct BendOrderStruct {
65	<	Bend* bend;
66	<	BendDataSet dataSet;
67	<	};
68	<	struct TorsionOrderStruct {
69	<	Torsion* torsion;
70	<	TorsionDataSet dataSet;
71	<	};
69	<
70	<	bool  BendSortFunctor(const BendOrderStruct& b1, const BendOrderStruct& b2) {
71	<	return b1.dataSet.deltaV < b2.dataSet.deltaV;
63	>	namespace OpenMD {
64	>
65	>	ForceManager::ForceManager(SimInfo * info) : info_(info),
66	>	NBforcesInitialized_(false) {
67	>	#ifdef IS_MPI
68	>	decomp_ = new ForceDecomposition(info_);
69	>	#else
70	>	//  decomp_ = new SerialDecomposition(info);
71	>	#endif
72		}
73	+
74	+	void ForceManager::calcForces() {
75	+
76
74	–	bool  TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
75	–	return t1.dataSet.deltaV < t2.dataSet.deltaV;
76	–	}
77	–	*/
78	–	void ForceManager::calcForces(bool needPotential, bool needStress) {
79	–
77		if (!info_->isFortranInitialized()) {
78		info_->update();
79	+	nbiMan_->setSimInfo(info_);
80	+	nbiMan_->initialize();
81	+	decomp_->distributeInitialData();
82	+	info_->setupFortran();
83		}
83	–
84	–	preCalculation();
84
85	+	preCalculation();
86		calcShortRangeInteraction();
87	<
88	<	calcLongRangeInteraction(needPotential, needStress);
89	<
87	>	calcLongRangeInteraction();
88		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	–	}
89
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	–	*/
90		}
91	<
91	>
92		void ForceManager::preCalculation() {
93		SimInfo::MoleculeIterator mi;
94		Molecule* mol;
#	Line 128 | Line 96 | namespace oopse {
96		Atom* atom;
97		Molecule::RigidBodyIterator rbIter;
98		RigidBody* rb;
99	+	Molecule::CutoffGroupIterator ci;
100	+	CutoffGroup* cg;
101
102		// forces are zeroed here, before any are accumulated.
103		// NOTE: do not rezero the forces in Fortran.
104	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
104	>
105	>	for (mol = info_->beginMolecule(mi); mol != NULL;
106	>	mol = info_->nextMolecule(mi)) {
107		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
108		atom->zeroForcesAndTorques();
109		}
110	<
110	>
111		//change the positions of atoms which belong to the rigidbodies
112	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
112	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
113	>	rb = mol->nextRigidBody(rbIter)) {
114		rb->zeroForcesAndTorques();
115		}
116	+
117	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
118	+	std::cerr << "should not see me \n";
119	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
120	+	cg = mol->nextCutoffGroup(ci)) {
121	+	//calculate the center of mass of cutoff group
122	+	cg->updateCOM();
123	+	}
124	+	}
125		}
126	+
127	+	// Zero out the stress tensor
128	+	tau *= 0.0;
129
130		}
131	<
131	>
132		void ForceManager::calcShortRangeInteraction() {
133		Molecule* mol;
134		RigidBody* rb;
135		Bond* bond;
136		Bend* bend;
137		Torsion* torsion;
138	+	Inversion* inversion;
139		SimInfo::MoleculeIterator mi;
140		Molecule::RigidBodyIterator rbIter;
141		Molecule::BondIterator bondIter;;
142		Molecule::BendIterator  bendIter;
143		Molecule::TorsionIterator  torsionIter;
144	+	Molecule::InversionIterator  inversionIter;
145		RealType bondPotential = 0.0;
146		RealType bendPotential = 0.0;
147		RealType torsionPotential = 0.0;
148	+	RealType inversionPotential = 0.0;
149
150		//calculate short range interactions
151	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
151	>	for (mol = info_->beginMolecule(mi); mol != NULL;
152	>	mol = info_->nextMolecule(mi)) {
153
154		//change the positions of atoms which belong to the rigidbodies
155	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
156	<	rb->updateAtoms();
155	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
156	>	rb = mol->nextRigidBody(rbIter)) {
157	>	rb->updateAtoms();
158		}
159
160	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
160	>	for (bond = mol->beginBond(bondIter); bond != NULL;
161	>	bond = mol->nextBond(bondIter)) {
162		bond->calcForce();
163		bondPotential += bond->getPotential();
164		}
165
166	<
167	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
168	<
178	<	RealType angle;
179	<	bend->calcForce(angle);
180	<	RealType currBendPot = bend->getPotential();
181	<	bendPotential += bend->getPotential();
182	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
183	<	if (i == bendDataSets.end()) {
184	<	BendDataSet dataSet;
185	<	dataSet.prev.angle = dataSet.curr.angle = angle;
186	<	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
187	<	dataSet.deltaV = 0.0;
188	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
189	<	}else {
190	<	i->second.prev.angle = i->second.curr.angle;
191	<	i->second.prev.potential = i->second.curr.potential;
192	<	i->second.curr.angle = angle;
193	<	i->second.curr.potential = currBendPot;
194	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
195	<	}
196	<	}
197	<
198	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
166	>	for (bend = mol->beginBend(bendIter); bend != NULL;
167	>	bend = mol->nextBend(bendIter)) {
168	>
169		RealType angle;
170	<	torsion->calcForce(angle);
171	<	RealType currTorsionPot = torsion->getPotential();
172	<	torsionPotential += torsion->getPotential();
173	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
174	<	if (i == torsionDataSets.end()) {
175	<	TorsionDataSet dataSet;
176	<	dataSet.prev.angle = dataSet.curr.angle = angle;
177	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
178	<	dataSet.deltaV = 0.0;
179	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, 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 = currTorsionPot;
185	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
186	<	}
170	>	bend->calcForce(angle);
171	>	RealType currBendPot = bend->getPotential();
172	>
173	>	bendPotential += bend->getPotential();
174	>	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
175	>	if (i == bendDataSets.end()) {
176	>	BendDataSet dataSet;
177	>	dataSet.prev.angle = dataSet.curr.angle = angle;
178	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
179	>	dataSet.deltaV = 0.0;
180	>	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
181	>	}else {
182	>	i->second.prev.angle = i->second.curr.angle;
183	>	i->second.prev.potential = i->second.curr.potential;
184	>	i->second.curr.angle = angle;
185	>	i->second.curr.potential = currBendPot;
186	>	i->second.deltaV =  fabs(i->second.curr.potential -
187	>	i->second.prev.potential);
188	>	}
189		}
190	+
191	+	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
192	+	torsion = mol->nextTorsion(torsionIter)) {
193	+	RealType angle;
194	+	torsion->calcForce(angle);
195	+	RealType currTorsionPot = torsion->getPotential();
196	+	torsionPotential += torsion->getPotential();
197	+	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
198	+	if (i == torsionDataSets.end()) {
199	+	TorsionDataSet dataSet;
200	+	dataSet.prev.angle = dataSet.curr.angle = angle;
201	+	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
202	+	dataSet.deltaV = 0.0;
203	+	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
204	+	}else {
205	+	i->second.prev.angle = i->second.curr.angle;
206	+	i->second.prev.potential = i->second.curr.potential;
207	+	i->second.curr.angle = angle;
208	+	i->second.curr.potential = currTorsionPot;
209	+	i->second.deltaV =  fabs(i->second.curr.potential -
210	+	i->second.prev.potential);
211	+	}
212	+	}
213
214	+	for (inversion = mol->beginInversion(inversionIter);
215	+	inversion != NULL;
216	+	inversion = mol->nextInversion(inversionIter)) {
217	+	RealType angle;
218	+	inversion->calcForce(angle);
219	+	RealType currInversionPot = inversion->getPotential();
220	+	inversionPotential += inversion->getPotential();
221	+	std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
222	+	if (i == inversionDataSets.end()) {
223	+	InversionDataSet dataSet;
224	+	dataSet.prev.angle = dataSet.curr.angle = angle;
225	+	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
226	+	dataSet.deltaV = 0.0;
227	+	inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
228	+	}else {
229	+	i->second.prev.angle = i->second.curr.angle;
230	+	i->second.prev.potential = i->second.curr.potential;
231	+	i->second.curr.angle = angle;
232	+	i->second.curr.potential = currInversionPot;
233	+	i->second.deltaV =  fabs(i->second.curr.potential -
234	+	i->second.prev.potential);
235	+	}
236	+	}
237		}
238
239	<	RealType  shortRangePotential = bondPotential + bendPotential + torsionPotential;
239	>	RealType  shortRangePotential = bondPotential + bendPotential +
240	>	torsionPotential +  inversionPotential;
241		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
242		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
243		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
244		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
245		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
246	+	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
247
248		}
249	<
250	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
249	>
250	>	void ForceManager::calcLongRangeInteraction() {
251		Snapshot* curSnapshot;
252		DataStorage* config;
253	+	DataStorage* cgConfig;
254		RealType* frc;
255		RealType* pos;
256		RealType* trq;
257		RealType* A;
258		RealType* electroFrame;
259		RealType* rc;
260	+	RealType* particlePot;
261
262		//get current snapshot from SimInfo
263		curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
264	<
264	>
265		//get array pointers
266		config = &(curSnapshot->atomData);
267	+	cgConfig = &(curSnapshot->cgData);
268		frc = config->getArrayPointer(DataStorage::dslForce);
269		pos = config->getArrayPointer(DataStorage::dslPosition);
270		trq = config->getArrayPointer(DataStorage::dslTorque);
271		A   = config->getArrayPointer(DataStorage::dslAmat);
272		electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
273	+	particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
274
275	<	//calculate the center of mass of cutoff group
276	<	SimInfo::MoleculeIterator mi;
277	<	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();
275	>	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
276	>	std::cerr << "should not see me \n";
277	>	rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
278		} else {
279	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
279	>	// center of mass of the group is the same as position of the atom
280	>	// if cutoff group does not exist
281		rc = pos;
282		}
283	<
283	>
284		//initialize data before passing to fortran
285		RealType longRangePotential[LR_POT_TYPES];
286		RealType lrPot = 0.0;
277	–
278	–	Mat3x3d tau;
279	–	short int passedCalcPot = needPotential;
280	–	short int passedCalcStress = needStress;
287		int isError = 0;
288
289		for (int i=0; i<LR_POT_TYPES;i++){
290		longRangePotential[i]=0.0; //Initialize array
291		}
292	+
293	+	decomp_->distributeData();
294
295	<	doForceLoop( pos,
296	<	rc,
297	<	A,
298	<	electroFrame,
299	<	frc,
300	<	trq,
301	<	tau.getArrayPointer(),
302	<	longRangePotential,
303	<	&passedCalcPot,
304	<	&passedCalcStress,
305	<	&isError );
295	>	int nLoops = 1;
296	>	for (int iLoop = 0; iLoop < nLoops; iLoop++) {
297	>	doForceLoop(pos,
298	>	rc,
299	>	A,
300	>	electroFrame,
301	>	frc,
302	>	trq,
303	>	tau.getArrayPointer(),
304	>	longRangePotential,
305	>	particlePot,
306	>	&isError );
307
308	+	if (nLoops > 1) {
309	+	decomp_->collectIntermediateData();
310	+	decomp_->distributeIntermediateData();
311	+	}
312	+	}
313	+
314	+	decomp_->collectData();
315	+
316		if( isError ){
317		sprintf( painCave.errMsg,
318		"Error returned from the fortran force calculation.\n" );
#	Line 305 | Line 322 | namespace oopse {
322		for (int i=0; i<LR_POT_TYPES;i++){
323		lrPot += longRangePotential[i]; //Quick hack
324		}
325	<
325	>
326		//store the tau and long range potential
327		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
328		curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
329		curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
313	–
314	–	curSnapshot->statData.setTau(tau);
330		}
331
332	<
332	>
333		void ForceManager::postCalculation() {
334		SimInfo::MoleculeIterator mi;
335		Molecule* mol;
336		Molecule::RigidBodyIterator rbIter;
337		RigidBody* rb;
338	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
339
340		// collect the atomic forces onto rigid bodies
341	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
342	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
343	<	rb->calcForcesAndTorques();
341	>
342	>	for (mol = info_->beginMolecule(mi); mol != NULL;
343	>	mol = info_->nextMolecule(mi)) {
344	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
345	>	rb = mol->nextRigidBody(rbIter)) {
346	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
347	>	tau += rbTau;
348		}
349		}
350	<
350	>
351	>	#ifdef IS_MPI
352	>	Mat3x3d tmpTau(tau);
353	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
354	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
355	>	#endif
356	>	curSnapshot->statData.setTau(tau);
357		}
358
359	<	} //end namespace oopse
359	>	} //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 1544 by gezelter, Fri Mar 18 19:31:52 2011 UTC

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