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Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 1215 by xsun, Wed Jan 23 21:22:37 2008 UTC vs.
Revision 1610 by gezelter, Fri Aug 12 14:37:25 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	<	namespace oopse {
58	>	#include "primitives/Torsion.hpp"
59	>	#include "primitives/Inversion.hpp"
60	>	namespace OpenMD {
61
62	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
62	>	void ForceManager::calcForces() {
63
64		if (!info_->isFortranInitialized()) {
65		info_->update();
#	Line 67 | Line 69 | namespace oopse {
69
70		calcShortRangeInteraction();
71
72	<	calcLongRangeInteraction(needPotential, needStress);
72	>	calcLongRangeInteraction();
73
74	<	postCalculation(needStress);
74	>	postCalculation();
75
76		}
77
#	Line 83 | Line 85 | namespace oopse {
85
86		// forces are zeroed here, before any are accumulated.
87		// NOTE: do not rezero the forces in Fortran.
88	<
88	>
89		for (mol = info_->beginMolecule(mi); mol != NULL;
90		mol = info_->nextMolecule(mi)) {
91		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
92		atom->zeroForcesAndTorques();
93		}
94	<
94	>
95		//change the positions of atoms which belong to the rigidbodies
96		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
97		rb = mol->nextRigidBody(rbIter)) {
98		rb->zeroForcesAndTorques();
99		}
100	+
101		}
102
103		// Zero out the stress tensor
#	Line 108 | Line 111 | namespace oopse {
111		Bond* bond;
112		Bend* bend;
113		Torsion* torsion;
114	+	Inversion* inversion;
115		SimInfo::MoleculeIterator mi;
116		Molecule::RigidBodyIterator rbIter;
117		Molecule::BondIterator bondIter;;
118		Molecule::BendIterator  bendIter;
119		Molecule::TorsionIterator  torsionIter;
120	+	Molecule::InversionIterator  inversionIter;
121		RealType bondPotential = 0.0;
122		RealType bendPotential = 0.0;
123		RealType torsionPotential = 0.0;
124	+	RealType inversionPotential = 0.0;
125
126		//calculate short range interactions
127		for (mol = info_->beginMolecule(mi); mol != NULL;
#	Line 139 | Line 145 | namespace oopse {
145		RealType angle;
146		bend->calcForce(angle);
147		RealType currBendPot = bend->getPotential();
148	+
149		bendPotential += bend->getPotential();
150		std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
151		if (i == bendDataSets.end()) {
#	Line 175 | Line 182 | namespace oopse {
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 -
186	+	i->second.prev.potential);
187	+	}
188	+	}
189	+
190	+	for (inversion = mol->beginInversion(inversionIter);
191	+	inversion != NULL;
192	+	inversion = mol->nextInversion(inversionIter)) {
193	+	RealType angle;
194	+	inversion->calcForce(angle);
195	+	RealType currInversionPot = inversion->getPotential();
196	+	inversionPotential += inversion->getPotential();
197	+	std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
198	+	if (i == inversionDataSets.end()) {
199	+	InversionDataSet dataSet;
200	+	dataSet.prev.angle = dataSet.curr.angle = angle;
201	+	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
202	+	dataSet.deltaV = 0.0;
203	+	inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, 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 = currInversionPot;
209		i->second.deltaV =  fabs(i->second.curr.potential -
210		i->second.prev.potential);
211		}
#	Line 182 | Line 213 | namespace oopse {
213		}
214
215		RealType  shortRangePotential = bondPotential + bendPotential +
216	<	torsionPotential;
216	>	torsionPotential +  inversionPotential;
217		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
218		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
219		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
220		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
221		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
222	+	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
223
224		}
225
226	<	void ForceManager::calcLongRangeInteraction(bool needPotential,
195	<	bool needStress) {
226	>	void ForceManager::calcLongRangeInteraction() {
227		Snapshot* curSnapshot;
228		DataStorage* config;
229		RealType* frc;
#	Line 201 | Line 232 | namespace oopse {
232		RealType* A;
233		RealType* electroFrame;
234		RealType* rc;
235	+	RealType* particlePot;
236
237		//get current snapshot from SimInfo
238		curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
#	Line 212 | Line 244 | namespace oopse {
244		trq = config->getArrayPointer(DataStorage::dslTorque);
245		A   = config->getArrayPointer(DataStorage::dslAmat);
246		electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
247	+	particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
248
249		//calculate the center of mass of cutoff group
250		SimInfo::MoleculeIterator mi;
#	Line 243 | Line 276 | namespace oopse {
276		RealType longRangePotential[LR_POT_TYPES];
277		RealType lrPot = 0.0;
278		Vector3d totalDipole;
246	–	short int passedCalcPot = needPotential;
247	–	short int passedCalcStress = needStress;
279		int isError = 0;
280
281		for (int i=0; i<LR_POT_TYPES;i++){
#	Line 259 | Line 290 | namespace oopse {
290		trq,
291		tau.getArrayPointer(),
292		longRangePotential,
293	<	&passedCalcPot,
263	<	&passedCalcStress,
293	>	particlePot,
294		&isError );
295
296		if( isError ){
#	Line 272 | Line 302 | namespace oopse {
302		for (int i=0; i<LR_POT_TYPES;i++){
303		lrPot += longRangePotential[i]; //Quick hack
304		}
305	<
305	>
306		// grab the simulation box dipole moment if specified
307		if (info_->getCalcBoxDipole()){
308		getAccumulatedBoxDipole(totalDipole.getArrayPointer());
#	Line 289 | Line 319 | namespace oopse {
319		}
320
321
322	<	void ForceManager::postCalculation(bool needStress) {
322	>	void ForceManager::postCalculation() {
323		SimInfo::MoleculeIterator mi;
324		Molecule* mol;
325		Molecule::RigidBodyIterator rbIter;
#	Line 302 | Line 332 | namespace oopse {
332		mol = info_->nextMolecule(mi)) {
333		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
334		rb = mol->nextRigidBody(rbIter)) {
335	<	if (needStress) {
336	<	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
307	<	tau += rbTau;
308	<	} else{
309	<	rb->calcForcesAndTorques();
310	<	}
335	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
336	>	tau += rbTau;
337		}
338		}
339	<
314	<	if (needStress) {
339	>
340		#ifdef IS_MPI
341	<	Mat3x3d tmpTau(tau);
342	<	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
343	<	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
341	>	Mat3x3d tmpTau(tau);
342	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
343	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
344		#endif
345	<	curSnapshot->statData.setTau(tau);
321	<	}
345	>	curSnapshot->statData.setTau(tau);
346		}
347
348	<	} //end namespace oopse
348	>	} //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.
Revision 1610 by gezelter, Fri Aug 12 14:37:25 2011 UTC

#	Line 0 | Line 1
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