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

Comparing:
trunk/src/brains/ForceManager.cpp (file contents), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1483 by gezelter, Tue Jul 27 21:17:31 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 __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	>	lj_ = LJ::Instance();
66	>	lj_->setForceField(info_->getForceField());
67
68	+	gb_ = GB::Instance();
69	+	gb_->setForceField(info_->getForceField());
70	+
71	+	eam_ = EAM::Instance();
72	+	eam_->setForceField(info_->getForceField());
73	+	}
74	+
75	+	void ForceManager::calcForces() {
76	+
77		if (!info_->isFortranInitialized()) {
78		info_->update();
79		}
80	<
80	>
81		preCalculation();
82
83		calcShortRangeInteraction();
84
85	<	calcLongRangeInteraction(needPotential, needStress);
85	>	calcLongRangeInteraction();
86
87		postCalculation();
88	<
88	>
89		}
90	<
90	>
91		void ForceManager::preCalculation() {
92		SimInfo::MoleculeIterator mi;
93		Molecule* mol;
#	Line 79 | Line 98 | namespace oopse {
98
99		// forces are zeroed here, before any are accumulated.
100		// NOTE: do not rezero the forces in Fortran.
101	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
101	>
102	>	for (mol = info_->beginMolecule(mi); mol != NULL;
103	>	mol = info_->nextMolecule(mi)) {
104		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
105		atom->zeroForcesAndTorques();
106		}
107	<
107	>
108		//change the positions of atoms which belong to the rigidbodies
109	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
109	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
110	>	rb = mol->nextRigidBody(rbIter)) {
111		rb->zeroForcesAndTorques();
112		}
113	+
114		}
115
116	+	// Zero out the stress tensor
117	+	tau *= 0.0;
118	+
119		}
120	<
120	>
121		void ForceManager::calcShortRangeInteraction() {
122		Molecule* mol;
123		RigidBody* rb;
124		Bond* bond;
125		Bend* bend;
126		Torsion* torsion;
127	+	Inversion* inversion;
128		SimInfo::MoleculeIterator mi;
129		Molecule::RigidBodyIterator rbIter;
130		Molecule::BondIterator bondIter;;
131		Molecule::BendIterator  bendIter;
132		Molecule::TorsionIterator  torsionIter;
133	+	Molecule::InversionIterator  inversionIter;
134	+	RealType bondPotential = 0.0;
135	+	RealType bendPotential = 0.0;
136	+	RealType torsionPotential = 0.0;
137	+	RealType inversionPotential = 0.0;
138
139		//calculate short range interactions
140	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
140	>	for (mol = info_->beginMolecule(mi); mol != NULL;
141	>	mol = info_->nextMolecule(mi)) {
142
143		//change the positions of atoms which belong to the rigidbodies
144	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
145	<	rb->updateAtoms();
144	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
145	>	rb = mol->nextRigidBody(rbIter)) {
146	>	rb->updateAtoms();
147		}
148
149	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
150	<	bond->calcForce();
149	>	for (bond = mol->beginBond(bondIter); bond != NULL;
150	>	bond = mol->nextBond(bondIter)) {
151	>	bond->calcForce();
152	>	bondPotential += bond->getPotential();
153		}
154
155	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
156	<	bend->calcForce();
155	>	for (bend = mol->beginBend(bendIter); bend != NULL;
156	>	bend = mol->nextBend(bendIter)) {
157	>
158	>	RealType angle;
159	>	bend->calcForce(angle);
160	>	RealType currBendPot = bend->getPotential();
161	>
162	>	bendPotential += bend->getPotential();
163	>	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
164	>	if (i == bendDataSets.end()) {
165	>	BendDataSet dataSet;
166	>	dataSet.prev.angle = dataSet.curr.angle = angle;
167	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
168	>	dataSet.deltaV = 0.0;
169	>	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
170	>	}else {
171	>	i->second.prev.angle = i->second.curr.angle;
172	>	i->second.prev.potential = i->second.curr.potential;
173	>	i->second.curr.angle = angle;
174	>	i->second.curr.potential = currBendPot;
175	>	i->second.deltaV =  fabs(i->second.curr.potential -
176	>	i->second.prev.potential);
177	>	}
178		}
179	+
180	+	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
181	+	torsion = mol->nextTorsion(torsionIter)) {
182	+	RealType angle;
183	+	torsion->calcForce(angle);
184	+	RealType currTorsionPot = torsion->getPotential();
185	+	torsionPotential += torsion->getPotential();
186	+	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
187	+	if (i == torsionDataSets.end()) {
188	+	TorsionDataSet dataSet;
189	+	dataSet.prev.angle = dataSet.curr.angle = angle;
190	+	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
191	+	dataSet.deltaV = 0.0;
192	+	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
193	+	}else {
194	+	i->second.prev.angle = i->second.curr.angle;
195	+	i->second.prev.potential = i->second.curr.potential;
196	+	i->second.curr.angle = angle;
197	+	i->second.curr.potential = currTorsionPot;
198	+	i->second.deltaV =  fabs(i->second.curr.potential -
199	+	i->second.prev.potential);
200	+	}
201	+	}
202
203	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
204	<	torsion->calcForce();
205	<	}
206	<
203	>	for (inversion = mol->beginInversion(inversionIter);
204	>	inversion != NULL;
205	>	inversion = mol->nextInversion(inversionIter)) {
206	>	RealType angle;
207	>	inversion->calcForce(angle);
208	>	RealType currInversionPot = inversion->getPotential();
209	>	inversionPotential += inversion->getPotential();
210	>	std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
211	>	if (i == inversionDataSets.end()) {
212	>	InversionDataSet dataSet;
213	>	dataSet.prev.angle = dataSet.curr.angle = angle;
214	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
215	>	dataSet.deltaV = 0.0;
216	>	inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
217	>	}else {
218	>	i->second.prev.angle = i->second.curr.angle;
219	>	i->second.prev.potential = i->second.curr.potential;
220	>	i->second.curr.angle = angle;
221	>	i->second.curr.potential = currInversionPot;
222	>	i->second.deltaV =  fabs(i->second.curr.potential -
223	>	i->second.prev.potential);
224	>	}
225	>	}
226		}
227
228	<	double  shortRangePotential = 0.0;
229	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
131	<	shortRangePotential += mol->getPotential();
132	<	}
133	<
228	>	RealType  shortRangePotential = bondPotential + bendPotential +
229	>	torsionPotential +  inversionPotential;
230		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
231		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
232	+	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
233	+	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
234	+	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
235	+	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
236	+
237		}
238	<
239	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
238	>
239	>	void ForceManager::calcLongRangeInteraction() {
240		Snapshot* curSnapshot;
241		DataStorage* config;
242	<	double* frc;
243	<	double* pos;
244	<	double* trq;
245	<	double* A;
246	<	double* electroFrame;
247	<	double* rc;
242	>	RealType* frc;
243	>	RealType* pos;
244	>	RealType* trq;
245	>	RealType* A;
246	>	RealType* electroFrame;
247	>	RealType* rc;
248	>	RealType* particlePot;
249
250		//get current snapshot from SimInfo
251		curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
252	<
252	>
253		//get array pointers
254		config = &(curSnapshot->atomData);
255		frc = config->getArrayPointer(DataStorage::dslForce);
#	Line 155 | Line 257 | namespace oopse {
257		trq = config->getArrayPointer(DataStorage::dslTorque);
258		A   = config->getArrayPointer(DataStorage::dslAmat);
259		electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
260	+	particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
261
262		//calculate the center of mass of cutoff group
263		SimInfo::MoleculeIterator mi;
#	Line 165 | Line 268 | namespace oopse {
268		std::vector<Vector3d> rcGroup;
269
270		if(info_->getNCutoffGroups() > 0){
271	<
272	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
273	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
271	>
272	>	for (mol = info_->beginMolecule(mi); mol != NULL;
273	>	mol = info_->nextMolecule(mi)) {
274	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
275	>	cg = mol->nextCutoffGroup(ci)) {
276		cg->getCOM(com);
277		rcGroup.push_back(com);
278		}
#	Line 175 | Line 280 | namespace oopse {
280
281		rc = rcGroup[0].getArrayPointer();
282		} else {
283	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
283	>	// center of mass of the group is the same as position of the atom
284	>	// if cutoff group does not exist
285		rc = pos;
286		}
287	<
287	>
288		//initialize data before passing to fortran
289	<	double longRangePotential = 0.0;
290	<	Mat3x3d tau;
291	<	short int passedCalcPot = needPotential;
186	<	short int passedCalcStress = needStress;
289	>	RealType longRangePotential[LR_POT_TYPES];
290	>	RealType lrPot = 0.0;
291	>	Vector3d totalDipole;
292		int isError = 0;
293
294	<	doForceLoop( pos,
295	<	rc,
296	<	A,
297	<	electroFrame,
298	<	frc,
299	<	trq,
300	<	tau.getArrayPointer(),
301	<	&longRangePotential,
302	<	&passedCalcPot,
303	<	&passedCalcStress,
304	<	&isError );
305	<
294	>	for (int i=0; i<LR_POT_TYPES;i++){
295	>	longRangePotential[i]=0.0; //Initialize array
296	>	}
297	>
298	>	doForceLoop(pos,
299	>	rc,
300	>	A,
301	>	electroFrame,
302	>	frc,
303	>	trq,
304	>	tau.getArrayPointer(),
305	>	longRangePotential,
306	>	particlePot,
307	>	&isError );
308	>
309		if( isError ){
310		sprintf( painCave.errMsg,
311		"Error returned from the fortran force calculation.\n" );
312		painCave.isFatal = 1;
313		simError();
314		}
315	<
315	>	for (int i=0; i<LR_POT_TYPES;i++){
316	>	lrPot += longRangePotential[i]; //Quick hack
317	>	}
318	>
319	>	// grab the simulation box dipole moment if specified
320	>	if (info_->getCalcBoxDipole()){
321	>	getAccumulatedBoxDipole(totalDipole.getArrayPointer());
322	>
323	>	curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
324	>	curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
325	>	curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
326	>	}
327	>
328		//store the tau and long range potential
329	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
330	<	curSnapshot->statData.setTau(tau);
329	>	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
330	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
331	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
332		}
333
334	<
334	>
335		void ForceManager::postCalculation() {
336		SimInfo::MoleculeIterator mi;
337		Molecule* mol;
338		Molecule::RigidBodyIterator rbIter;
339		RigidBody* rb;
340	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
341
342		// collect the atomic forces onto rigid bodies
343	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
344	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
345	<	rb->calcForcesAndTorques();
343	>
344	>	for (mol = info_->beginMolecule(mi); mol != NULL;
345	>	mol = info_->nextMolecule(mi)) {
346	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
347	>	rb = mol->nextRigidBody(rbIter)) {
348	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
349	>	tau += rbTau;
350		}
351		}
352	<
352	>
353	>	#ifdef IS_MPI
354	>	Mat3x3d tmpTau(tau);
355	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
356	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
357	>	#endif
358	>	curSnapshot->statData.setTau(tau);
359		}
360
361	<	} //end namespace oopse
361	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 507 by gezelter, Fri Apr 15 22:04:00 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1483 by gezelter, Tue Jul 27 21:17:31 2010 UTC

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