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root/OpenMD/branches/heatflux/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/heatflux/src/brains/ForceManager.cpp (file contents), Revision 1671 by chuckv, Mon Jan 30 21:31:09 2012 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	–	*/
41
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	>	namespace OpenMD {
61
62	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
62	>	void ForceManager::calcForces() {
63
64		if (!info_->isFortranInitialized()) {
65	<	info_->update();
65	>	info_->update();
66		}
67
68		preCalculation();
69	<
69	>
70		calcShortRangeInteraction();
71
72	<	calcLongRangeInteraction(needPotential, needStress);
72	>	calcLongRangeInteraction();
73
74		postCalculation();
69	–
70	–	}
75
76	<	void ForceManager::preCalculation() {
76	>	}
77	>
78	>	void ForceManager::preCalculation() {
79		SimInfo::MoleculeIterator mi;
80		Molecule* mol;
81		Molecule::AtomIterator ai;
82		Atom* atom;
83		Molecule::RigidBodyIterator rbIter;
84		RigidBody* rb;
85	<
85	>
86		// forces are zeroed here, before any are accumulated.
87		// NOTE: do not rezero the forces in Fortran.
88	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
89	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
90	<	atom->zeroForcesAndTorques();
91	<	}
92	<
93	<	//change the positions of atoms which belong to the rigidbodies
94	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
95	<	rb->zeroForcesAndTorques();
96	<	}
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	>
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		}
92	–
93	–	}
102
103	<	void ForceManager::calcShortRangeInteraction() {
103	>	// Zero out the stress tensor
104	>	tau *= 0.0;
105	>
106	>	}
107	>
108	>	void ForceManager::calcShortRangeInteraction() {
109		Molecule* mol;
110		RigidBody* rb;
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; mol = info_->nextMolecule(mi)) {
126	>	//calculate short range interactions
127	>	for (mol = info_->beginMolecule(mi); mol != NULL;
128	>	mol = info_->nextMolecule(mi)) {
129
130	<	//change the positions of atoms which belong to the rigidbodies
131	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
132	<	rb->updateAtoms();
133	<	}
130	>	//change the positions of atoms which belong to the rigidbodies
131	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
132	>	rb = mol->nextRigidBody(rbIter)) {
133	>	rb->updateAtoms();
134	>	}
135
136	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
137	<	bond->calcForce();
138	<	}
136	>	for (bond = mol->beginBond(bondIter); bond != NULL;
137	>	bond = mol->nextBond(bondIter)) {
138	>	bond->calcForce();
139	>	bondPotential += bond->getPotential();
140	>	}
141
142	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
143	<	bend->calcForce();
142	>	for (bend = mol->beginBend(bendIter); bend != NULL;
143	>	bend = mol->nextBend(bendIter)) {
144	>
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()) {
152	>	BendDataSet dataSet;
153	>	dataSet.prev.angle = dataSet.curr.angle = angle;
154	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
155	>	dataSet.deltaV = 0.0;
156	>	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
157	>	}else {
158	>	i->second.prev.angle = i->second.curr.angle;
159	>	i->second.prev.potential = i->second.curr.potential;
160	>	i->second.curr.angle = angle;
161	>	i->second.curr.potential = currBendPot;
162	>	i->second.deltaV =  fabs(i->second.curr.potential -
163	>	i->second.prev.potential);
164		}
165	+	}
166
167	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
168	<	torsion->calcForce();
167	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
168	>	torsion = mol->nextTorsion(torsionIter)) {
169	>	RealType angle;
170	>	torsion->calcForce(angle);
171	>	RealType currTorsionPot = torsion->getPotential();
172	>	torsionPotential += torsion->getPotential();
173	>	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
174	>	if (i == torsionDataSets.end()) {
175	>	TorsionDataSet dataSet;
176	>	dataSet.prev.angle = dataSet.curr.angle = angle;
177	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
178	>	dataSet.deltaV = 0.0;
179	>	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
180	>	}else {
181	>	i->second.prev.angle = i->second.curr.angle;
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	<	}
191	<
192	<	double  shortRangePotential = 0.0;
193	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
194	<	shortRangePotential += mol->getPotential();
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	>	}
212	>	}
213		}
214
215	+	RealType  shortRangePotential = bondPotential + bendPotential +
216	+	torsionPotential +  inversionPotential;
217		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
218		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
219	<	}
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	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
224	>	}
225	>
226	>	void ForceManager::calcLongRangeInteraction() {
227		Snapshot* curSnapshot;
228		DataStorage* config;
229	<	double* frc;
230	<	double* pos;
231	<	double* trq;
232	<	double* A;
233	<	double* electroFrame;
234	<	double* rc;
235	<
229	>	RealType* frc;
230	>	RealType* pos;
231	>	RealType* vel;
232	>	RealType* trq;
233	>	RealType* A;
234	>	RealType* electroFrame;
235	>	RealType* rc;
236	>	RealType* particlePot;
237	>
238		//get current snapshot from SimInfo
239		curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
240
#	Line 152 | Line 242 | void ForceManager::calcLongRangeInteraction(bool needP
242		config = &(curSnapshot->atomData);
243		frc = config->getArrayPointer(DataStorage::dslForce);
244		pos = config->getArrayPointer(DataStorage::dslPosition);
245	+	vel = config->getArrayPointer(DataStorage::dslVelocity);
246		trq = config->getArrayPointer(DataStorage::dslTorque);
247		A   = config->getArrayPointer(DataStorage::dslAmat);
248		electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
249	+	particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
250
251		//calculate the center of mass of cutoff group
252		SimInfo::MoleculeIterator mi;
#	Line 163 | Line 255 | void ForceManager::calcLongRangeInteraction(bool needP
255		CutoffGroup* cg;
256		Vector3d com;
257		std::vector<Vector3d> rcGroup;
258	<
258	>
259		if(info_->getNCutoffGroups() > 0){
260
261	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
262	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
263	<	cg->getCOM(com);
264	<	rcGroup.push_back(com);
261	>	for (mol = info_->beginMolecule(mi); mol != NULL;
262	>	mol = info_->nextMolecule(mi)) {
263	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
264	>	cg = mol->nextCutoffGroup(ci)) {
265	>	cg->getCOM(com);
266	>	rcGroup.push_back(com);
267		}
268	<	}// end for (mol)
269	<
270	<	rc = rcGroup[0].getArrayPointer();
268	>	}// end for (mol)
269	>
270	>	rc = rcGroup[0].getArrayPointer();
271		} else {
272	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
273	<	rc = pos;
272	>	// center of mass of the group is the same as position of the atom
273	>	// if cutoff group does not exist
274	>	rc = pos;
275		}
276	<
276	>
277		//initialize data before passing to fortran
278	<	double longRangePotential = 0.0;
279	<	Mat3x3d tau;
280	<	short int passedCalcPot = needPotential;
281	<	short int passedCalcStress = needStress;
278	>	RealType longRangePotential[LR_POT_TYPES];
279	>	RealType lrPot = 0.0;
280	>	Vector3d totalDipole;
281	>
282	>
283	>
284		int isError = 0;
285
286	<	doForceLoop( pos,
287	<	rc,
288	<	A,
192	<	electroFrame,
193	<	frc,
194	<	trq,
195	<	tau.getArrayPointer(),
196	<	&longRangePotential,
197	<	&passedCalcPot,
198	<	&passedCalcStress,
199	<	&isError );
286	>	for (int i=0; i<LR_POT_TYPES;i++){
287	>	longRangePotential[i]=0.0; //Initialize array
288	>	}
289
290	+	doForceLoop(pos,
291	+	vel,
292	+	rc,
293	+	A,
294	+	electroFrame,
295	+	frc,
296	+	trq,
297	+	tau.getArrayPointer(),
298	+	Jv_.getArrayPointer(),
299	+	longRangePotential,
300	+	particlePot,
301	+	&isError );
302	+
303		if( isError ){
304	<	sprintf( painCave.errMsg,
305	<	"Error returned from the fortran force calculation.\n" );
306	<	painCave.isFatal = 1;
307	<	simError();
304	>	sprintf( painCave.errMsg,
305	>	"Error returned from the fortran force calculation.\n" );
306	>	painCave.isFatal = 1;
307	>	simError();
308		}
309	+	for (int i=0; i<LR_POT_TYPES;i++){
310	+	lrPot += longRangePotential[i]; //Quick hack
311	+	}
312
313	<	//store the tau and long range potential
314	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
315	<	curSnapshot->statData.setTau(tau);
211	<	}
313	>	// grab the simulation box dipole moment if specified
314	>	if (info_->getCalcBoxDipole()){
315	>	getAccumulatedBoxDipole(totalDipole.getArrayPointer());
316
317	+	curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
318	+	curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
319	+	curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
320	+	}
321
322	<	void ForceManager::postCalculation() {
322	>	//store the tau and long range potential
323	>	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
324	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
325	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
326	>	}
327	>
328	>
329	>	void ForceManager::postCalculation() {
330		SimInfo::MoleculeIterator mi;
331		Molecule* mol;
332		Molecule::RigidBodyIterator rbIter;
333		RigidBody* rb;
334	<
334	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
335	>
336		// collect the atomic forces onto rigid bodies
337	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
338	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
339	<	rb->calcForcesAndTorques();
340	<	}
337	>
338	>	for (mol = info_->beginMolecule(mi); mol != NULL;
339	>	mol = info_->nextMolecule(mi)) {
340	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
341	>	rb = mol->nextRigidBody(rbIter)) {
342	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
343	>	tau += rbTau;
344	>	}
345		}
346
347	<	}
347	>	#ifdef IS_MPI
348	>	Mat3x3d tmpTau(tau);
349	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
350	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
351	>	#endif
352	>	curSnapshot->statData.setTau(tau);
353	>
354	>	curSnapshot->statData.setJv(Jv_);
355	>	}
356
357	<	} //end namespace oopse
357	>	} //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/heatflux/src/brains/ForceManager.cpp (property svn:keywords), Revision 1671 by chuckv, Mon Jan 30 21:31:09 2012 UTC

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