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

Comparing:
trunk/src/brains/ForceManager.cpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1540 by gezelter, Mon Jan 17 21:34:36 2011 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 __C
53	>	#define __OPENMD_C
54		#include "UseTheForce/DarkSide/fInteractionMap.h"
55		#include "utils/simError.h"
56	+	#include "primitives/Bond.hpp"
57		#include "primitives/Bend.hpp"
58	<	#include "primitives/Bend.hpp"
59	<	namespace oopse {
58	>	#include "primitives/Torsion.hpp"
59	>	#include "primitives/Inversion.hpp"
60
61	<	/*
62	<	struct BendOrderStruct {
63	<	Bend* bend;
64	<	BendDataSet dataSet;
64	<	};
65	<	struct TorsionOrderStruct {
66	<	Torsion* torsion;
67	<	TorsionDataSet dataSet;
68	<	};
69	<
70	<	bool  BendSortFunctor(const BendOrderStruct& b1, const BendOrderStruct& b2) {
71	<	return b1.dataSet.deltaV < b2.dataSet.deltaV;
61	>	namespace OpenMD {
62	>
63	>	ForceManager::ForceManager(SimInfo * info) : info_(info),
64	>	NBforcesInitialized_(false) {
65		}
66	+
67	+	void ForceManager::calcForces() {
68	+
69
74	–	bool  TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
75	–	return t1.dataSet.deltaV < t2.dataSet.deltaV;
76	–	}
77	–	*/
78	–	void ForceManager::calcForces(bool needPotential, bool needStress) {
79	–
70		if (!info_->isFortranInitialized()) {
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();
91	–
92	–	/*
93	–	std::vector<BendOrderStruct> bendOrderStruct;
94	–	for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
95	–	BendOrderStruct tmp;
96	–	tmp.bend= const_cast<Bend*>(i->first);
97	–	tmp.dataSet = i->second;
98	–	bendOrderStruct.push_back(tmp);
99	–	}
100	–
101	–	std::vector<TorsionOrderStruct> torsionOrderStruct;
102	–	for(std::map<Torsion*, TorsionDataSet>::iterator j = torsionDataSets.begin(); j != torsionDataSets.end(); ++j) {
103	–	TorsionOrderStruct tmp;
104	–	tmp.torsion = const_cast<Torsion*>(j->first);
105	–	tmp.dataSet = j->second;
106	–	torsionOrderStruct.push_back(tmp);
107	–	}
84
109	–	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
110	–	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
111	–	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
112	–	Bend* bend = k->bend;
113	–	std::cout << "Bend: atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
114	–	std::cout << "deltaV=" << k->dataSet.deltaV << ",p_theta=" << k->dataSet.prev.angle <<",p_pot=" << k->dataSet.prev.potential<< ",c_theta=" << k->dataSet.curr.angle << ", c_pot = " << k->dataSet.curr.potential <<std::endl;
115	–	}
116	–	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
117	–	Torsion* torsion = l->torsion;
118	–	std::cout << "Torsion: atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
119	–	std::cout << "deltaV=" << l->dataSet.deltaV << ",p_theta=" << l->dataSet.prev.angle <<",p_pot=" << l->dataSet.prev.potential<< ",c_theta=" << l->dataSet.curr.angle << ", c_pot = " << l->dataSet.curr.potential <<std::endl;
120	–	}
121	–	*/
85		}
86	<
86	>
87		void ForceManager::preCalculation() {
88		SimInfo::MoleculeIterator mi;
89		Molecule* mol;
#	Line 128 | Line 91 | namespace oopse {
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)) {
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	<
105	>
106		//change the positions of atoms which belong to the rigidbodies
107	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
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	+	}
120		}
121	+
122	+	// Zero out the stress tensor
123	+	tau *= 0.0;
124
125		}
126	<
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();
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)) {
155	>	for (bond = mol->beginBond(bondIter); bond != NULL;
156	>	bond = mol->nextBond(bondIter)) {
157		bond->calcForce();
158		bondPotential += bond->getPotential();
159		}
160
161	<
162	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
163	<
178	<	RealType angle;
179	<	bend->calcForce(angle);
180	<	RealType currBendPot = bend->getPotential();
181	<	bendPotential += bend->getPotential();
182	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
183	<	if (i == bendDataSets.end()) {
184	<	BendDataSet dataSet;
185	<	dataSet.prev.angle = dataSet.curr.angle = angle;
186	<	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
187	<	dataSet.deltaV = 0.0;
188	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, 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 = currBendPot;
194	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
195	<	}
196	<	}
197	<
198	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
161	>	for (bend = mol->beginBend(bendIter); bend != NULL;
162	>	bend = mol->nextBend(bendIter)) {
163	>
164		RealType angle;
165	<	torsion->calcForce(angle);
166	<	RealType currTorsionPot = torsion->getPotential();
167	<	torsionPotential += torsion->getPotential();
168	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
169	<	if (i == torsionDataSets.end()) {
170	<	TorsionDataSet dataSet;
171	<	dataSet.prev.angle = dataSet.curr.angle = angle;
172	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
173	<	dataSet.deltaV = 0.0;
174	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
175	<	}else {
176	<	i->second.prev.angle = i->second.curr.angle;
177	<	i->second.prev.potential = i->second.curr.potential;
178	<	i->second.curr.angle = angle;
179	<	i->second.curr.potential = currTorsionPot;
180	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
181	<	}
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	+
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	<	RealType  shortRangePotential = bondPotential + bendPotential + torsionPotential;
234	>	RealType  shortRangePotential = bondPotential + bendPotential +
235	>	torsionPotential +  inversionPotential;
236		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
237		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
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(bool needPotential, bool needStress) {
244	>
245	>	void ForceManager::calcLongRangeInteraction() {
246		Snapshot* curSnapshot;
247		DataStorage* config;
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;
254	<	Molecule::CutoffGroupIterator ci;
255	<	CutoffGroup* cg;
256	<	Vector3d com;
257	<	std::vector<Vector3d> rcGroup;
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);
265	<	}
266	<	}// end for (mol)
267	<
268	<	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
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		RealType longRangePotential[LR_POT_TYPES];
281		RealType lrPot = 0.0;
277	–
278	–	Mat3x3d tau;
279	–	short int passedCalcPot = needPotential;
280	–	short int passedCalcStress = needStress;
282		int isError = 0;
283
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	<	&passedCalcPot,
297	<	&passedCalcStress,
298	<	&isError );
298	<
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" );
#	Line 305 | Line 305 | namespace oopse {
305		for (int i=0; i<LR_POT_TYPES;i++){
306		lrPot += longRangePotential[i]; //Quick hack
307		}
308	<
308	>
309		//store the tau and long range potential
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	–	curSnapshot->statData.setTau(tau);
313		}
314
315	<
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();
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	<
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	<	} //end namespace oopse
342	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 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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