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

Comparing:
trunk/src/brains/ForceManager.cpp (file contents), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1535 by gezelter, Fri Dec 31 18:31:56 2010 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	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	<	/**
43	<	* @file ForceManager.cpp
44	<	* @author tlin
45	<	* @date 11/09/2004
46	<	* @time 10:39am
47	<	* @version 1.0
48	<	*/
42	>	/**
43	>	* @file ForceManager.cpp
44	>	* @author tlin
45	>	* @date 11/09/2004
46	>	* @time 10:39am
47	>	* @version 1.0
48	>	*/
49
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	>	}
66	>
67	>	void ForceManager::calcForces() {
68	>
69
70		if (!info_->isFortranInitialized()) {
71	<	info_->update();
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	<
85	<	}
86	<
87	<	void ForceManager::preCalculation() {
84	>
85	>	}
86	>
87	>	void ForceManager::preCalculation() {
88		SimInfo::MoleculeIterator mi;
89		Molecule* mol;
90		Molecule::AtomIterator ai;
#	Line 79 | Line 94 | void ForceManager::preCalculation() {
94
95		// forces are zeroed here, before any are accumulated.
96		// NOTE: do not rezero the forces in Fortran.
97	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
98	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
99	<	atom->zeroForcesAndTorques();
100	<	}
101	<
102	<	//change the positions of atoms which belong to the rigidbodies
103	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
104	<	rb->zeroForcesAndTorques();
105	<	}
97	>
98	>	for (mol = info_->beginMolecule(mi); mol != NULL;
99	>	mol = info_->nextMolecule(mi)) {
100	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
101	>	atom->zeroForcesAndTorques();
102	>	}
103	>
104	>	//change the positions of atoms which belong to the rigidbodies
105	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
106	>	rb = mol->nextRigidBody(rbIter)) {
107	>	rb->zeroForcesAndTorques();
108	>	}
109	>
110		}
111
112	<	}
113	<
114	<	void ForceManager::calcShortRangeInteraction() {
112	>	// Zero out the stress tensor
113	>	tau *= 0.0;
114	>
115	>	}
116	>
117	>	void ForceManager::calcShortRangeInteraction() {
118		Molecule* mol;
119		RigidBody* rb;
120		Bond* bond;
121		Bend* bend;
122		Torsion* torsion;
123	+	Inversion* inversion;
124		SimInfo::MoleculeIterator mi;
125		Molecule::RigidBodyIterator rbIter;
126		Molecule::BondIterator bondIter;;
127		Molecule::BendIterator  bendIter;
128		Molecule::TorsionIterator  torsionIter;
129	+	Molecule::InversionIterator  inversionIter;
130	+	RealType bondPotential = 0.0;
131	+	RealType bendPotential = 0.0;
132	+	RealType torsionPotential = 0.0;
133	+	RealType inversionPotential = 0.0;
134
135		//calculate short range interactions
136	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
136	>	for (mol = info_->beginMolecule(mi); mol != NULL;
137	>	mol = info_->nextMolecule(mi)) {
138
139	<	//change the positions of atoms which belong to the rigidbodies
140	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
141	<	rb->updateAtoms();
142	<	}
139	>	//change the positions of atoms which belong to the rigidbodies
140	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
141	>	rb = mol->nextRigidBody(rbIter)) {
142	>	rb->updateAtoms();
143	>	}
144
145	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
146	<	bond->calcForce();
147	<	}
145	>	for (bond = mol->beginBond(bondIter); bond != NULL;
146	>	bond = mol->nextBond(bondIter)) {
147	>	bond->calcForce();
148	>	bondPotential += bond->getPotential();
149	>	}
150
151	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
152	<	bend->calcForce();
151	>	for (bend = mol->beginBend(bendIter); bend != NULL;
152	>	bend = mol->nextBend(bendIter)) {
153	>
154	>	RealType angle;
155	>	bend->calcForce(angle);
156	>	RealType currBendPot = bend->getPotential();
157	>
158	>	bendPotential += bend->getPotential();
159	>	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
160	>	if (i == bendDataSets.end()) {
161	>	BendDataSet dataSet;
162	>	dataSet.prev.angle = dataSet.curr.angle = angle;
163	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
164	>	dataSet.deltaV = 0.0;
165	>	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
166	>	}else {
167	>	i->second.prev.angle = i->second.curr.angle;
168	>	i->second.prev.potential = i->second.curr.potential;
169	>	i->second.curr.angle = angle;
170	>	i->second.curr.potential = currBendPot;
171	>	i->second.deltaV =  fabs(i->second.curr.potential -
172	>	i->second.prev.potential);
173		}
174	<
175	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
176	<	torsion->calcForce();
177	<	}
174	>	}
175	>
176	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
177	>	torsion = mol->nextTorsion(torsionIter)) {
178	>	RealType angle;
179	>	torsion->calcForce(angle);
180	>	RealType currTorsionPot = torsion->getPotential();
181	>	torsionPotential += torsion->getPotential();
182	>	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
183	>	if (i == torsionDataSets.end()) {
184	>	TorsionDataSet dataSet;
185	>	dataSet.prev.angle = dataSet.curr.angle = angle;
186	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
187	>	dataSet.deltaV = 0.0;
188	>	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, 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 = currTorsionPot;
194	>	i->second.deltaV =  fabs(i->second.curr.potential -
195	>	i->second.prev.potential);
196	>	}
197	>	}
198
199	+	for (inversion = mol->beginInversion(inversionIter);
200	+	inversion != NULL;
201	+	inversion = mol->nextInversion(inversionIter)) {
202	+	RealType angle;
203	+	inversion->calcForce(angle);
204	+	RealType currInversionPot = inversion->getPotential();
205	+	inversionPotential += inversion->getPotential();
206	+	std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
207	+	if (i == inversionDataSets.end()) {
208	+	InversionDataSet dataSet;
209	+	dataSet.prev.angle = dataSet.curr.angle = angle;
210	+	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
211	+	dataSet.deltaV = 0.0;
212	+	inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
213	+	}else {
214	+	i->second.prev.angle = i->second.curr.angle;
215	+	i->second.prev.potential = i->second.curr.potential;
216	+	i->second.curr.angle = angle;
217	+	i->second.curr.potential = currInversionPot;
218	+	i->second.deltaV =  fabs(i->second.curr.potential -
219	+	i->second.prev.potential);
220	+	}
221	+	}
222		}
223
224	<	double  shortRangePotential = 0.0;
225	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
131	<	shortRangePotential += mol->getPotential();
132	<	}
133	<
224	>	RealType  shortRangePotential = bondPotential + bendPotential +
225	>	torsionPotential +  inversionPotential;
226		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
227		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
228	<	}
229	<
230	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
228	>	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
229	>	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
230	>	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
231	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
232	>
233	>	}
234	>
235	>	void ForceManager::calcLongRangeInteraction() {
236		Snapshot* curSnapshot;
237		DataStorage* config;
238	<	double* frc;
239	<	double* pos;
240	<	double* trq;
241	<	double* A;
242	<	double* electroFrame;
243	<	double* rc;
238	>	RealType* frc;
239	>	RealType* pos;
240	>	RealType* trq;
241	>	RealType* A;
242	>	RealType* electroFrame;
243	>	RealType* rc;
244	>	RealType* particlePot;
245
246		//get current snapshot from SimInfo
247		curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
248	<
248	>
249		//get array pointers
250		config = &(curSnapshot->atomData);
251		frc = config->getArrayPointer(DataStorage::dslForce);
#	Line 155 | Line 253 | void ForceManager::calcLongRangeInteraction(bool needP
253		trq = config->getArrayPointer(DataStorage::dslTorque);
254		A   = config->getArrayPointer(DataStorage::dslAmat);
255		electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
256	+	particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
257
258		//calculate the center of mass of cutoff group
259		SimInfo::MoleculeIterator mi;
#	Line 165 | Line 264 | void ForceManager::calcLongRangeInteraction(bool needP
264		std::vector<Vector3d> rcGroup;
265
266		if(info_->getNCutoffGroups() > 0){
267	<
268	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
269	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
270	<	cg->getCOM(com);
271	<	rcGroup.push_back(com);
267	>
268	>	for (mol = info_->beginMolecule(mi); mol != NULL;
269	>	mol = info_->nextMolecule(mi)) {
270	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
271	>	cg = mol->nextCutoffGroup(ci)) {
272	>	cg->getCOM(com);
273	>	rcGroup.push_back(com);
274		}
275	<	}// end for (mol)
275	>	}// end for (mol)
276
277	<	rc = rcGroup[0].getArrayPointer();
277	>	rc = rcGroup[0].getArrayPointer();
278		} else {
279	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
280	<	rc = pos;
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	<	double longRangePotential = 0.0;
286	<	Mat3x3d tau;
185	<	short int passedCalcPot = needPotential;
186	<	short int passedCalcStress = needStress;
285	>	RealType longRangePotential[LR_POT_TYPES];
286	>	RealType lrPot = 0.0;
287		int isError = 0;
288
289	<	doForceLoop( pos,
290	<	rc,
291	<	A,
292	<	electroFrame,
293	<	frc,
294	<	trq,
295	<	tau.getArrayPointer(),
296	<	&longRangePotential,
297	<	&passedCalcPot,
298	<	&passedCalcStress,
299	<	&isError );
300	<
289	>	for (int i=0; i<LR_POT_TYPES;i++){
290	>	longRangePotential[i]=0.0; //Initialize array
291	>	}
292	>
293	>	doForceLoop(pos,
294	>	rc,
295	>	A,
296	>	electroFrame,
297	>	frc,
298	>	trq,
299	>	tau.getArrayPointer(),
300	>	longRangePotential,
301	>	particlePot,
302	>	&isError );
303	>
304		if( isError ){
305	<	sprintf( painCave.errMsg,
306	<	"Error returned from the fortran force calculation.\n" );
307	<	painCave.isFatal = 1;
308	<	simError();
305	>	sprintf( painCave.errMsg,
306	>	"Error returned from the fortran force calculation.\n" );
307	>	painCave.isFatal = 1;
308	>	simError();
309		}
310	<
310	>	for (int i=0; i<LR_POT_TYPES;i++){
311	>	lrPot += longRangePotential[i]; //Quick hack
312	>	}
313	>
314		//store the tau and long range potential
315	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
316	<	curSnapshot->statData.setTau(tau);
317	<	}
315	>	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
316	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
317	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
318	>	}
319
320	<
321	<	void ForceManager::postCalculation() {
320	>
321	>	void ForceManager::postCalculation() {
322		SimInfo::MoleculeIterator mi;
323		Molecule* mol;
324		Molecule::RigidBodyIterator rbIter;
325		RigidBody* rb;
326	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
327
328		// collect the atomic forces onto rigid bodies
329	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
330	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
331	<	rb->calcForcesAndTorques();
332	<	}
329	>
330	>	for (mol = info_->beginMolecule(mi); mol != NULL;
331	>	mol = info_->nextMolecule(mi)) {
332	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
333	>	rb = mol->nextRigidBody(rbIter)) {
334	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
335	>	tau += rbTau;
336	>	}
337		}
338	+
339	+	#ifdef IS_MPI
340	+	Mat3x3d tmpTau(tau);
341	+	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
342	+	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
343	+	#endif
344	+	curSnapshot->statData.setTau(tau);
345	+	}
346
347	<	}
228	<
229	<	} //end namespace oopse
347	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1535 by gezelter, Fri Dec 31 18:31:56 2010 UTC

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