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

Comparing:
trunk/src/brains/ForceManager.cpp (file contents), Revision 1215 by xsun, Wed Jan 23 21:22:37 2008 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1469 by gezelter, Mon Jul 19 14:07:59 2010 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	<	namespace oopse {
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	>	std::cerr << __PRETTY_FUNCTION__ << "\n";
66	>	lj_ = new LJ(info_->getForceField());
67	>	}
68	>
69	>	void ForceManager::calcForces() {
70
71	+	std::cerr << __PRETTY_FUNCTION__ << "\n";
72		if (!info_->isFortranInitialized()) {
73		info_->update();
74		}
75
76	+	if (!NBforcesInitialized_) {
77	+	lj_->initialize();
78	+	}
79	+
80		preCalculation();
81
82		calcShortRangeInteraction();
83
84	<	calcLongRangeInteraction(needPotential, needStress);
84	>	calcLongRangeInteraction();
85
86	<	postCalculation(needStress);
86	>	postCalculation();
87
88		}
89
#	Line 83 | Line 97 | namespace oopse {
97
98		// forces are zeroed here, before any are accumulated.
99		// NOTE: do not rezero the forces in Fortran.
100	<
100	>
101		for (mol = info_->beginMolecule(mi); mol != NULL;
102		mol = info_->nextMolecule(mi)) {
103		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
104		atom->zeroForcesAndTorques();
105		}
106	<
106	>
107		//change the positions of atoms which belong to the rigidbodies
108		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
109		rb = mol->nextRigidBody(rbIter)) {
110		rb->zeroForcesAndTorques();
111		}
112	+
113		}
114
115		// Zero out the stress tensor
#	Line 108 | Line 123 | namespace oopse {
123		Bond* bond;
124		Bend* bend;
125		Torsion* torsion;
126	+	Inversion* inversion;
127		SimInfo::MoleculeIterator mi;
128		Molecule::RigidBodyIterator rbIter;
129		Molecule::BondIterator bondIter;;
130		Molecule::BendIterator  bendIter;
131		Molecule::TorsionIterator  torsionIter;
132	+	Molecule::InversionIterator  inversionIter;
133		RealType bondPotential = 0.0;
134		RealType bendPotential = 0.0;
135		RealType torsionPotential = 0.0;
136	+	RealType inversionPotential = 0.0;
137
138		//calculate short range interactions
139		for (mol = info_->beginMolecule(mi); mol != NULL;
#	Line 139 | Line 157 | namespace oopse {
157		RealType angle;
158		bend->calcForce(angle);
159		RealType currBendPot = bend->getPotential();
160	+
161		bendPotential += bend->getPotential();
162		std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
163		if (i == bendDataSets.end()) {
#	Line 175 | Line 194 | namespace oopse {
194		i->second.prev.potential = i->second.curr.potential;
195		i->second.curr.angle = angle;
196		i->second.curr.potential = currTorsionPot;
197	+	i->second.deltaV =  fabs(i->second.curr.potential -
198	+	i->second.prev.potential);
199	+	}
200	+	}
201	+
202	+	for (inversion = mol->beginInversion(inversionIter);
203	+	inversion != NULL;
204	+	inversion = mol->nextInversion(inversionIter)) {
205	+	RealType angle;
206	+	inversion->calcForce(angle);
207	+	RealType currInversionPot = inversion->getPotential();
208	+	inversionPotential += inversion->getPotential();
209	+	std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
210	+	if (i == inversionDataSets.end()) {
211	+	InversionDataSet dataSet;
212	+	dataSet.prev.angle = dataSet.curr.angle = angle;
213	+	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
214	+	dataSet.deltaV = 0.0;
215	+	inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
216	+	}else {
217	+	i->second.prev.angle = i->second.curr.angle;
218	+	i->second.prev.potential = i->second.curr.potential;
219	+	i->second.curr.angle = angle;
220	+	i->second.curr.potential = currInversionPot;
221		i->second.deltaV =  fabs(i->second.curr.potential -
222		i->second.prev.potential);
223		}
#	Line 182 | Line 225 | namespace oopse {
225		}
226
227		RealType  shortRangePotential = bondPotential + bendPotential +
228	<	torsionPotential;
228	>	torsionPotential +  inversionPotential;
229		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
230		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
231		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
232		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
233		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
234	+	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
235
236		}
237
238	<	void ForceManager::calcLongRangeInteraction(bool needPotential,
195	<	bool needStress) {
238	>	void ForceManager::calcLongRangeInteraction() {
239		Snapshot* curSnapshot;
240		DataStorage* config;
241		RealType* frc;
#	Line 201 | Line 244 | namespace oopse {
244		RealType* A;
245		RealType* electroFrame;
246		RealType* rc;
247	+	RealType* particlePot;
248
249		//get current snapshot from SimInfo
250		curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
#	Line 212 | Line 256 | namespace oopse {
256		trq = config->getArrayPointer(DataStorage::dslTorque);
257		A   = config->getArrayPointer(DataStorage::dslAmat);
258		electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
259	+	particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
260
261		//calculate the center of mass of cutoff group
262		SimInfo::MoleculeIterator mi;
#	Line 243 | Line 288 | namespace oopse {
288		RealType longRangePotential[LR_POT_TYPES];
289		RealType lrPot = 0.0;
290		Vector3d totalDipole;
246	–	short int passedCalcPot = needPotential;
247	–	short int passedCalcStress = needStress;
291		int isError = 0;
292
293		for (int i=0; i<LR_POT_TYPES;i++){
#	Line 259 | Line 302 | namespace oopse {
302		trq,
303		tau.getArrayPointer(),
304		longRangePotential,
305	<	&passedCalcPot,
263	<	&passedCalcStress,
305	>	particlePot,
306		&isError );
307
308		if( isError ){
#	Line 289 | Line 331 | namespace oopse {
331		}
332
333
334	<	void ForceManager::postCalculation(bool needStress) {
334	>	void ForceManager::postCalculation() {
335		SimInfo::MoleculeIterator mi;
336		Molecule* mol;
337		Molecule::RigidBodyIterator rbIter;
#	Line 302 | Line 344 | namespace oopse {
344		mol = info_->nextMolecule(mi)) {
345		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
346		rb = mol->nextRigidBody(rbIter)) {
347	<	if (needStress) {
348	<	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
307	<	tau += rbTau;
308	<	} else{
309	<	rb->calcForcesAndTorques();
310	<	}
347	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
348	>	tau += rbTau;
349		}
350		}
351	<
314	<	if (needStress) {
351	>
352		#ifdef IS_MPI
353	<	Mat3x3d tmpTau(tau);
354	<	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
355	<	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
353	>	Mat3x3d tmpTau(tau);
354	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
355	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
356		#endif
357	<	curSnapshot->statData.setTau(tau);
321	<	}
357	>	curSnapshot->statData.setTau(tau);
358		}
359
360	<	} //end namespace oopse
360	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 1215 by xsun, Wed Jan 23 21:22:37 2008 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1469 by gezelter, Mon Jul 19 14:07:59 2010 UTC

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