ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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 1544 by gezelter, Fri Mar 18 19:31:52 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	>	#include "parallel/ForceDecomposition.hpp"
61	>	//#include "parallel/SerialDecomposition.hpp"
62
63	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
63	>	namespace OpenMD {
64	>
65	>	ForceManager::ForceManager(SimInfo * info) : info_(info),
66	>	NBforcesInitialized_(false) {
67	>	#ifdef IS_MPI
68	>	decomp_ = new ForceDecomposition(info_);
69	>	#else
70	>	//  decomp_ = new SerialDecomposition(info);
71	>	#endif
72	>	}
73	>
74	>	void ForceManager::calcForces() {
75	>
76
77		if (!info_->isFortranInitialized()) {
78	<	info_->update();
78	>	info_->update();
79	>	nbiMan_->setSimInfo(info_);
80	>	nbiMan_->initialize();
81	>	decomp_->distributeInitialData();
82	>	info_->setupFortran();
83		}
61	–
62	–	preCalculation();
84
85	+	preCalculation();
86		calcShortRangeInteraction();
87	<
66	<	calcLongRangeInteraction(needPotential, needStress);
67	<
87	>	calcLongRangeInteraction();
88		postCalculation();
89	<
90	<	}
91	<
92	<	void ForceManager::preCalculation() {
89	>
90	>	}
91	>
92	>	void ForceManager::preCalculation() {
93		SimInfo::MoleculeIterator mi;
94		Molecule* mol;
95		Molecule::AtomIterator ai;
96		Atom* atom;
97		Molecule::RigidBodyIterator rbIter;
98		RigidBody* rb;
99	+	Molecule::CutoffGroupIterator ci;
100	+	CutoffGroup* cg;
101
102		// forces are zeroed here, before any are accumulated.
103		// NOTE: do not rezero the forces in Fortran.
104	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
105	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
106	<	atom->zeroForcesAndTorques();
104	>
105	>	for (mol = info_->beginMolecule(mi); mol != NULL;
106	>	mol = info_->nextMolecule(mi)) {
107	>	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
108	>	atom->zeroForcesAndTorques();
109	>	}
110	>
111	>	//change the positions of atoms which belong to the rigidbodies
112	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
113	>	rb = mol->nextRigidBody(rbIter)) {
114	>	rb->zeroForcesAndTorques();
115	>	}
116	>
117	>	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
118	>	std::cerr << "should not see me \n";
119	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
120	>	cg = mol->nextCutoffGroup(ci)) {
121	>	//calculate the center of mass of cutoff group
122	>	cg->updateCOM();
123		}
124	<
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	<	}
124	>	}
125		}
126	+
127	+	// Zero out the stress tensor
128	+	tau *= 0.0;
129
130	<	}
131	<
132	<	void ForceManager::calcShortRangeInteraction() {
130	>	}
131	>
132	>	void ForceManager::calcShortRangeInteraction() {
133		Molecule* mol;
134		RigidBody* rb;
135		Bond* bond;
136		Bend* bend;
137		Torsion* torsion;
138	+	Inversion* inversion;
139		SimInfo::MoleculeIterator mi;
140		Molecule::RigidBodyIterator rbIter;
141		Molecule::BondIterator bondIter;;
142		Molecule::BendIterator  bendIter;
143		Molecule::TorsionIterator  torsionIter;
144	+	Molecule::InversionIterator  inversionIter;
145	+	RealType bondPotential = 0.0;
146	+	RealType bendPotential = 0.0;
147	+	RealType torsionPotential = 0.0;
148	+	RealType inversionPotential = 0.0;
149
150		//calculate short range interactions
151	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
151	>	for (mol = info_->beginMolecule(mi); mol != NULL;
152	>	mol = info_->nextMolecule(mi)) {
153
154	<	//change the positions of atoms which belong to the rigidbodies
155	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
156	<	rb->updateAtoms();
157	<	}
154	>	//change the positions of atoms which belong to the rigidbodies
155	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
156	>	rb = mol->nextRigidBody(rbIter)) {
157	>	rb->updateAtoms();
158	>	}
159
160	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
161	<	bond->calcForce();
162	<	}
160	>	for (bond = mol->beginBond(bondIter); bond != NULL;
161	>	bond = mol->nextBond(bondIter)) {
162	>	bond->calcForce();
163	>	bondPotential += bond->getPotential();
164	>	}
165
166	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
167	<	bend->calcForce();
166	>	for (bend = mol->beginBend(bendIter); bend != NULL;
167	>	bend = mol->nextBend(bendIter)) {
168	>
169	>	RealType angle;
170	>	bend->calcForce(angle);
171	>	RealType currBendPot = bend->getPotential();
172	>
173	>	bendPotential += bend->getPotential();
174	>	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
175	>	if (i == bendDataSets.end()) {
176	>	BendDataSet dataSet;
177	>	dataSet.prev.angle = dataSet.curr.angle = angle;
178	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
179	>	dataSet.deltaV = 0.0;
180	>	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
181	>	}else {
182	>	i->second.prev.angle = i->second.curr.angle;
183	>	i->second.prev.potential = i->second.curr.potential;
184	>	i->second.curr.angle = angle;
185	>	i->second.curr.potential = currBendPot;
186	>	i->second.deltaV =  fabs(i->second.curr.potential -
187	>	i->second.prev.potential);
188		}
189	<
190	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
191	<	torsion->calcForce();
192	<	}
189	>	}
190	>
191	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
192	>	torsion = mol->nextTorsion(torsionIter)) {
193	>	RealType angle;
194	>	torsion->calcForce(angle);
195	>	RealType currTorsionPot = torsion->getPotential();
196	>	torsionPotential += torsion->getPotential();
197	>	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
198	>	if (i == torsionDataSets.end()) {
199	>	TorsionDataSet dataSet;
200	>	dataSet.prev.angle = dataSet.curr.angle = angle;
201	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
202	>	dataSet.deltaV = 0.0;
203	>	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, 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 = currTorsionPot;
209	>	i->second.deltaV =  fabs(i->second.curr.potential -
210	>	i->second.prev.potential);
211	>	}
212	>	}
213
214	+	for (inversion = mol->beginInversion(inversionIter);
215	+	inversion != NULL;
216	+	inversion = mol->nextInversion(inversionIter)) {
217	+	RealType angle;
218	+	inversion->calcForce(angle);
219	+	RealType currInversionPot = inversion->getPotential();
220	+	inversionPotential += inversion->getPotential();
221	+	std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
222	+	if (i == inversionDataSets.end()) {
223	+	InversionDataSet dataSet;
224	+	dataSet.prev.angle = dataSet.curr.angle = angle;
225	+	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
226	+	dataSet.deltaV = 0.0;
227	+	inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
228	+	}else {
229	+	i->second.prev.angle = i->second.curr.angle;
230	+	i->second.prev.potential = i->second.curr.potential;
231	+	i->second.curr.angle = angle;
232	+	i->second.curr.potential = currInversionPot;
233	+	i->second.deltaV =  fabs(i->second.curr.potential -
234	+	i->second.prev.potential);
235	+	}
236	+	}
237		}
238
239	<	double  shortRangePotential = 0.0;
240	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
131	<	shortRangePotential += mol->getPotential();
132	<	}
133	<
239	>	RealType  shortRangePotential = bondPotential + bendPotential +
240	>	torsionPotential +  inversionPotential;
241		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
242		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
243	<	}
244	<
245	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
243	>	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
244	>	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
245	>	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
246	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
247	>
248	>	}
249	>
250	>	void ForceManager::calcLongRangeInteraction() {
251		Snapshot* curSnapshot;
252		DataStorage* config;
253	<	double* frc;
254	<	double* pos;
255	<	double* trq;
256	<	double* A;
257	<	double* electroFrame;
258	<	double* rc;
253	>	DataStorage* cgConfig;
254	>	RealType* frc;
255	>	RealType* pos;
256	>	RealType* trq;
257	>	RealType* A;
258	>	RealType* electroFrame;
259	>	RealType* rc;
260	>	RealType* particlePot;
261
262		//get current snapshot from SimInfo
263		curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
264	<
264	>
265		//get array pointers
266		config = &(curSnapshot->atomData);
267	+	cgConfig = &(curSnapshot->cgData);
268		frc = config->getArrayPointer(DataStorage::dslForce);
269		pos = config->getArrayPointer(DataStorage::dslPosition);
270		trq = config->getArrayPointer(DataStorage::dslTorque);
271		A   = config->getArrayPointer(DataStorage::dslAmat);
272		electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
273	+	particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
274
275	<	//calculate the center of mass of cutoff group
276	<	SimInfo::MoleculeIterator mi;
277	<	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();
275	>	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
276	>	std::cerr << "should not see me \n";
277	>	rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
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,
194	<	trq,
195	<	tau.getArrayPointer(),
196	<	&longRangePotential,
197	<	&passedCalcPot,
198	<	&passedCalcStress,
199	<	&isError );
289	>	for (int i=0; i<LR_POT_TYPES;i++){
290	>	longRangePotential[i]=0.0; //Initialize array
291	>	}
292	>
293	>	decomp_->distributeData();
294
295	<	if( isError ){
296	<	sprintf( painCave.errMsg,
297	<	"Error returned from the fortran force calculation.\n" );
298	<	painCave.isFatal = 1;
299	<	simError();
295	>	int nLoops = 1;
296	>	for (int iLoop = 0; iLoop < nLoops; iLoop++) {
297	>	doForceLoop(pos,
298	>	rc,
299	>	A,
300	>	electroFrame,
301	>	frc,
302	>	trq,
303	>	tau.getArrayPointer(),
304	>	longRangePotential,
305	>	particlePot,
306	>	&isError );
307	>
308	>	if (nLoops > 1) {
309	>	decomp_->collectIntermediateData();
310	>	decomp_->distributeIntermediateData();
311	>	}
312		}
313	+
314	+	decomp_->collectData();
315
316	+	if( isError ){
317	+	sprintf( painCave.errMsg,
318	+	"Error returned from the fortran force calculation.\n" );
319	+	painCave.isFatal = 1;
320	+	simError();
321	+	}
322	+	for (int i=0; i<LR_POT_TYPES;i++){
323	+	lrPot += longRangePotential[i]; //Quick hack
324	+	}
325	+
326		//store the tau and long range potential
327	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
328	<	curSnapshot->statData.setTau(tau);
329	<	}
327	>	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
328	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
329	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
330	>	}
331
332	<
333	<	void ForceManager::postCalculation() {
332	>
333	>	void ForceManager::postCalculation() {
334		SimInfo::MoleculeIterator mi;
335		Molecule* mol;
336		Molecule::RigidBodyIterator rbIter;
337		RigidBody* rb;
338	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
339
340		// collect the atomic forces onto rigid bodies
341	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
342	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
343	<	rb->calcForcesAndTorques();
344	<	}
341	>
342	>	for (mol = info_->beginMolecule(mi); mol != NULL;
343	>	mol = info_->nextMolecule(mi)) {
344	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
345	>	rb = mol->nextRigidBody(rbIter)) {
346	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
347	>	tau += rbTau;
348	>	}
349		}
350	+
351	+	#ifdef IS_MPI
352	+	Mat3x3d tmpTau(tau);
353	+	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
354	+	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
355	+	#endif
356	+	curSnapshot->statData.setTau(tau);
357	+	}
358
359	<	}
228	<
229	<	} //end namespace oopse
359	>	} //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 1544 by gezelter, Fri Mar 18 19:31:52 2011 UTC

#	Line 0 | Line 1
1	+	Author Id Revision Date

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines