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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 1540 by gezelter, Mon Jan 17 21:34:36 2011 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;
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)) {
100	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
101	<	atom->zeroForcesAndTorques();
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	>
106	>	//change the positions of atoms which belong to the rigidbodies
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	<
87	<	//change the positions of atoms which belong to the rigidbodies
88	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
89	<	rb->zeroForcesAndTorques();
90	<	}
119	>	}
120		}
121	+
122	+	// Zero out the stress tensor
123	+	tau *= 0.0;
124
125	<	}
126	<
127	<	void ForceManager::calcShortRangeInteraction() {
125	>	}
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();
152	<	}
149	>	//change the positions of atoms which belong to the rigidbodies
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();
157	<	}
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	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
186	<	torsion->calcForce();
187	<	}
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 (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	<	double  shortRangePotential = 0.0;
235	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
131	<	shortRangePotential += mol->getPotential();
132	<	}
133	<
234	>	RealType  shortRangePotential = bondPotential + bendPotential +
235	>	torsionPotential +  inversionPotential;
236		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
237		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
238	<	}
239	<
240	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
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() {
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;
162	<	Molecule::CutoffGroupIterator ci;
163	<	CutoffGroup* cg;
164	<	Vector3d com;
165	<	std::vector<Vector3d> rcGroup;
166	<
167	<	if(info_->getNCutoffGroups() > 0){
168	<
169	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
170	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
171	<	cg->getCOM(com);
172	<	rcGroup.push_back(com);
173	<	}
174	<	}// end for (mol)
175	<
176	<	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
275	<	rc = pos;
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		}
278	<
278	>
279		//initialize data before passing to fortran
280	<	double longRangePotential = 0.0;
281	<	Mat3x3d tau;
185	<	short int passedCalcPot = needPotential;
186	<	short int passedCalcStress = needStress;
280	>	RealType longRangePotential[LR_POT_TYPES];
281	>	RealType lrPot = 0.0;
282		int isError = 0;
283
284	<	doForceLoop( pos,
285	<	rc,
286	<	A,
287	<	electroFrame,
288	<	frc,
289	<	trq,
290	<	tau.getArrayPointer(),
291	<	&longRangePotential,
292	<	&passedCalcPot,
293	<	&passedCalcStress,
294	<	&isError );
295	<
284	>	for (int i=0; i<LR_POT_TYPES;i++){
285	>	longRangePotential[i]=0.0; //Initialize array
286	>	}
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" );
302	<	painCave.isFatal = 1;
303	<	simError();
300	>	sprintf( painCave.errMsg,
301	>	"Error returned from the fortran force calculation.\n" );
302	>	painCave.isFatal = 1;
303	>	simError();
304		}
305	<
305	>	for (int i=0; i<LR_POT_TYPES;i++){
306	>	lrPot += longRangePotential[i]; //Quick hack
307	>	}
308	>
309		//store the tau and long range potential
310	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
311	<	curSnapshot->statData.setTau(tau);
312	<	}
310	>	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
311	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
312	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
313	>	}
314
315	<
316	<	void ForceManager::postCalculation() {
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();
327	<	}
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	+
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	<	}
228	<
229	<	} //end namespace oopse
342	>	} //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 1540 by gezelter, Mon Jan 17 21:34:36 2011 UTC

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