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

Comparing:
trunk/src/brains/ForceManager.cpp (file contents), Revision 665 by tim, Thu Oct 13 22:26:47 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1540 by gezelter, Mon Jan 17 21:34:36 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	<	namespace oopse {
56	>	#include "primitives/Bond.hpp"
57	>	#include "primitives/Bend.hpp"
58	>	#include "primitives/Torsion.hpp"
59	>	#include "primitives/Inversion.hpp"
60
61	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
61	>	namespace OpenMD {
62	>
63	>	ForceManager::ForceManager(SimInfo * info) : info_(info),
64	>	NBforcesInitialized_(false) {
65	>	}
66	>
67	>	void ForceManager::calcForces() {
68	>
69
70		if (!info_->isFortranInitialized()) {
71		info_->update();
72	+	nbiMan_->setSimInfo(info_);
73	+	nbiMan_->initialize();
74	+	info_->setupFortran();
75		}
76	<
76	>
77		preCalculation();
78
79		calcShortRangeInteraction();
80
81	<	calcLongRangeInteraction(needPotential, needStress);
81	>	calcLongRangeInteraction();
82
83		postCalculation();
84	<
84	>
85		}
86	<
86	>
87		void ForceManager::preCalculation() {
88		SimInfo::MoleculeIterator mi;
89		Molecule* mol;
#	Line 78 | 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)) {
99	>
100	>	for (mol = info_->beginMolecule(mi); mol != NULL;
101	>	mol = info_->nextMolecule(mi)) {
102		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
103		atom->zeroForcesAndTorques();
104		}
105	<
105	>
106		//change the positions of atoms which belong to the rigidbodies
107	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
107	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
108	>	rb = mol->nextRigidBody(rbIter)) {
109		rb->zeroForcesAndTorques();
110		}
111	+
112	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
113	+	std::cerr << "should not see me \n";
114	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
115	+	cg = mol->nextCutoffGroup(ci)) {
116	+	//calculate the center of mass of cutoff group
117	+	cg->updateCOM();
118	+	}
119	+	}
120		}
121	+
122	+	// Zero out the stress tensor
123	+	tau *= 0.0;
124
125		}
126	<
126	>
127		void ForceManager::calcShortRangeInteraction() {
128		Molecule* mol;
129		RigidBody* rb;
130		Bond* bond;
131		Bend* bend;
132		Torsion* torsion;
133	+	Inversion* inversion;
134		SimInfo::MoleculeIterator mi;
135		Molecule::RigidBodyIterator rbIter;
136		Molecule::BondIterator bondIter;;
137		Molecule::BendIterator  bendIter;
138		Molecule::TorsionIterator  torsionIter;
139	+	Molecule::InversionIterator  inversionIter;
140	+	RealType bondPotential = 0.0;
141	+	RealType bendPotential = 0.0;
142	+	RealType torsionPotential = 0.0;
143	+	RealType inversionPotential = 0.0;
144
145		//calculate short range interactions
146	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
146	>	for (mol = info_->beginMolecule(mi); mol != NULL;
147	>	mol = info_->nextMolecule(mi)) {
148
149		//change the positions of atoms which belong to the rigidbodies
150	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
151	<	rb->updateAtoms();
150	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
151	>	rb = mol->nextRigidBody(rbIter)) {
152	>	rb->updateAtoms();
153		}
154
155	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
156	<	bond->calcForce();
155	>	for (bond = mol->beginBond(bondIter); bond != NULL;
156	>	bond = mol->nextBond(bondIter)) {
157	>	bond->calcForce();
158	>	bondPotential += bond->getPotential();
159		}
160
161	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
162	<	bend->calcForce();
161	>	for (bend = mol->beginBend(bendIter); bend != NULL;
162	>	bend = mol->nextBend(bendIter)) {
163	>
164	>	RealType angle;
165	>	bend->calcForce(angle);
166	>	RealType currBendPot = bend->getPotential();
167	>
168	>	bendPotential += bend->getPotential();
169	>	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
170	>	if (i == bendDataSets.end()) {
171	>	BendDataSet dataSet;
172	>	dataSet.prev.angle = dataSet.curr.angle = angle;
173	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
174	>	dataSet.deltaV = 0.0;
175	>	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
176	>	}else {
177	>	i->second.prev.angle = i->second.curr.angle;
178	>	i->second.prev.potential = i->second.curr.potential;
179	>	i->second.curr.angle = angle;
180	>	i->second.curr.potential = currBendPot;
181	>	i->second.deltaV =  fabs(i->second.curr.potential -
182	>	i->second.prev.potential);
183	>	}
184		}
185	+
186	+	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
187	+	torsion = mol->nextTorsion(torsionIter)) {
188	+	RealType angle;
189	+	torsion->calcForce(angle);
190	+	RealType currTorsionPot = torsion->getPotential();
191	+	torsionPotential += torsion->getPotential();
192	+	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
193	+	if (i == torsionDataSets.end()) {
194	+	TorsionDataSet dataSet;
195	+	dataSet.prev.angle = dataSet.curr.angle = angle;
196	+	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
197	+	dataSet.deltaV = 0.0;
198	+	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
199	+	}else {
200	+	i->second.prev.angle = i->second.curr.angle;
201	+	i->second.prev.potential = i->second.curr.potential;
202	+	i->second.curr.angle = angle;
203	+	i->second.curr.potential = currTorsionPot;
204	+	i->second.deltaV =  fabs(i->second.curr.potential -
205	+	i->second.prev.potential);
206	+	}
207	+	}
208
209	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
210	<	torsion->calcForce();
211	<	}
212	<
209	>	for (inversion = mol->beginInversion(inversionIter);
210	>	inversion != NULL;
211	>	inversion = mol->nextInversion(inversionIter)) {
212	>	RealType angle;
213	>	inversion->calcForce(angle);
214	>	RealType currInversionPot = inversion->getPotential();
215	>	inversionPotential += inversion->getPotential();
216	>	std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
217	>	if (i == inversionDataSets.end()) {
218	>	InversionDataSet dataSet;
219	>	dataSet.prev.angle = dataSet.curr.angle = angle;
220	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
221	>	dataSet.deltaV = 0.0;
222	>	inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
223	>	}else {
224	>	i->second.prev.angle = i->second.curr.angle;
225	>	i->second.prev.potential = i->second.curr.potential;
226	>	i->second.curr.angle = angle;
227	>	i->second.curr.potential = currInversionPot;
228	>	i->second.deltaV =  fabs(i->second.curr.potential -
229	>	i->second.prev.potential);
230	>	}
231	>	}
232		}
233
234	<
235	<	double bondPotential = 0.0;
133	<	double bendPotential = 0.0;
134	<	double torsionPotential = 0.0;
135	<
136	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
137	<
138	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
139	<	bondPotential += bond->getPotential();
140	<	}
141	<
142	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
143	<	bendPotential += bend->getPotential();
144	<	}
145	<
146	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
147	<	torsionPotential += torsion->getPotential();
148	<	}
149	<
150	<	}
151	<
152	<	double  shortRangePotential = bondPotential + bendPotential + torsionPotential;
234	>	RealType  shortRangePotential = bondPotential + bendPotential +
235	>	torsionPotential +  inversionPotential;
236		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
237		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
238		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
239		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
240		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
241	+	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
242
243		}
244	<
245	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
244	>
245	>	void ForceManager::calcLongRangeInteraction() {
246		Snapshot* curSnapshot;
247		DataStorage* config;
248	<	double* frc;
249	<	double* pos;
250	<	double* trq;
251	<	double* A;
252	<	double* electroFrame;
253	<	double* rc;
248	>	DataStorage* cgConfig;
249	>	RealType* frc;
250	>	RealType* pos;
251	>	RealType* trq;
252	>	RealType* A;
253	>	RealType* electroFrame;
254	>	RealType* rc;
255	>	RealType* particlePot;
256
257		//get current snapshot from SimInfo
258		curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
259	<
259	>
260		//get array pointers
261		config = &(curSnapshot->atomData);
262	+	cgConfig = &(curSnapshot->cgData);
263		frc = config->getArrayPointer(DataStorage::dslForce);
264		pos = config->getArrayPointer(DataStorage::dslPosition);
265		trq = config->getArrayPointer(DataStorage::dslTorque);
266		A   = config->getArrayPointer(DataStorage::dslAmat);
267		electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
268	+	particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
269
270	<	//calculate the center of mass of cutoff group
271	<	SimInfo::MoleculeIterator mi;
272	<	Molecule* mol;
185	<	Molecule::CutoffGroupIterator ci;
186	<	CutoffGroup* cg;
187	<	Vector3d com;
188	<	std::vector<Vector3d> rcGroup;
189	<
190	<	if(info_->getNCutoffGroups() > 0){
191	<
192	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
193	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
194	<	cg->getCOM(com);
195	<	rcGroup.push_back(com);
196	<	}
197	<	}// end for (mol)
198	<
199	<	rc = rcGroup[0].getArrayPointer();
270	>	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
271	>	std::cerr << "should not see me \n";
272	>	rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
273		} else {
274	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
274	>	// center of mass of the group is the same as position of the atom
275	>	// if cutoff group does not exist
276		rc = pos;
277		}
204	–
205	–	//initialize data before passing to fortran
206	–	double longRangePotential[LR_POT_TYPES];
207	–	double lrPot = 0.0;
278
279	<	Mat3x3d tau;
280	<	short int passedCalcPot = needPotential;
281	<	short int passedCalcStress = needStress;
279	>	//initialize data before passing to fortran
280	>	RealType longRangePotential[LR_POT_TYPES];
281	>	RealType lrPot = 0.0;
282		int isError = 0;
283
284		for (int i=0; i<LR_POT_TYPES;i++){
285		longRangePotential[i]=0.0; //Initialize array
286		}
287	<
288	<
289	<
290	<	doForceLoop( pos,
291	<	rc,
292	<	A,
293	<	electroFrame,
294	<	frc,
295	<	trq,
296	<	tau.getArrayPointer(),
297	<	longRangePotential,
298	<	&passedCalcPot,
229	<	&passedCalcStress,
230	<	&isError );
231	<
287	>
288	>	doForceLoop(pos,
289	>	rc,
290	>	A,
291	>	electroFrame,
292	>	frc,
293	>	trq,
294	>	tau.getArrayPointer(),
295	>	longRangePotential,
296	>	particlePot,
297	>	&isError );
298	>
299		if( isError ){
300		sprintf( painCave.errMsg,
301		"Error returned from the fortran force calculation.\n" );
#	Line 238 | Line 305 | namespace oopse {
305		for (int i=0; i<LR_POT_TYPES;i++){
306		lrPot += longRangePotential[i]; //Quick hack
307		}
308	<
308	>
309		//store the tau and long range potential
310		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
311	<	//  curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
312	<	curSnapshot->statData.setTau(tau);
311	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
312	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
313		}
314
315	<
315	>
316		void ForceManager::postCalculation() {
317		SimInfo::MoleculeIterator mi;
318		Molecule* mol;
319		Molecule::RigidBodyIterator rbIter;
320		RigidBody* rb;
321	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
322
323		// collect the atomic forces onto rigid bodies
324	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
325	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
326	<	rb->calcForcesAndTorques();
324	>
325	>	for (mol = info_->beginMolecule(mi); mol != NULL;
326	>	mol = info_->nextMolecule(mi)) {
327	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
328	>	rb = mol->nextRigidBody(rbIter)) {
329	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
330	>	tau += rbTau;
331		}
332		}
333	<
333	>
334	>	#ifdef IS_MPI
335	>	Mat3x3d tmpTau(tau);
336	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
337	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
338	>	#endif
339	>	curSnapshot->statData.setTau(tau);
340		}
341
342	<	} //end namespace oopse
342	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 665 by tim, Thu Oct 13 22:26:47 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1540 by gezelter, Mon Jan 17 21:34:36 2011 UTC

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