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

Comparing:
trunk/src/brains/ForceManager.cpp (file contents), Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1480 by gezelter, Mon Jul 26 19:50:53 2010 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;
65	<	};
66	<	struct TorsionOrderStruct {
66	<	Torsion* torsion;
67	<	TorsionDataSet dataSet;
68	<	};
61	>	namespace OpenMD {
62	>
63	>	ForceManager::ForceManager(SimInfo * info) : info_(info),
64	>	NBforcesInitialized_(false) {
65	>	lj_ = LJ::Instance();
66	>	lj_->setForceField(info_->getForceField());
67
68	<	bool  BendSortFunctor(const BendOrderStruct& b1, const BendOrderStruct& b2) {
69	<	return b1.dataSet.deltaV < b2.dataSet.deltaV;
68	>	eam_ = EAM::Instance();
69	>	eam_->setForceField(info_->getForceField());
70		}
71	<
72	<	bool  TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
73	<	return t1.dataSet.deltaV < t2.dataSet.deltaV;
76	<	}
77	<	*/
78	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
79	<
71	>
72	>	void ForceManager::calcForces() {
73	>
74		if (!info_->isFortranInitialized()) {
75		info_->update();
76		}
77	<
77	>
78		preCalculation();
79
80		calcShortRangeInteraction();
81
82	<	calcLongRangeInteraction(needPotential, needStress);
82	>	calcLongRangeInteraction();
83
84		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	–	}
85
109	–	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
110	–	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
111	–	std::cout << "bend" << std::endl;
112	–	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
113	–	Bend* bend = k->bend;
114	–	std::cout << "atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
115	–	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;
116	–	}
117	–	std::cout << "torsio" << std::endl;
118	–	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
119	–	Torsion* torsion = l->torsion;
120	–	std::cout << "atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
121	–	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;
122	–	}
123	–	*/
86		}
87	<
87	>
88		void ForceManager::preCalculation() {
89		SimInfo::MoleculeIterator mi;
90		Molecule* mol;
#	Line 133 | Line 95 | namespace oopse {
95
96		// forces are zeroed here, before any are accumulated.
97		// NOTE: do not rezero the forces in Fortran.
98	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
98	>
99	>	for (mol = info_->beginMolecule(mi); mol != NULL;
100	>	mol = info_->nextMolecule(mi)) {
101		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
102		atom->zeroForcesAndTorques();
103		}
104	<
104	>
105		//change the positions of atoms which belong to the rigidbodies
106	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
106	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
107	>	rb = mol->nextRigidBody(rbIter)) {
108		rb->zeroForcesAndTorques();
109		}
110	+
111		}
112
113	+	// Zero out the stress tensor
114	+	tau *= 0.0;
115	+
116		}
117	<
117	>
118		void ForceManager::calcShortRangeInteraction() {
119		Molecule* mol;
120		RigidBody* rb;
121		Bond* bond;
122		Bend* bend;
123		Torsion* torsion;
124	+	Inversion* inversion;
125		SimInfo::MoleculeIterator mi;
126		Molecule::RigidBodyIterator rbIter;
127		Molecule::BondIterator bondIter;;
128		Molecule::BendIterator  bendIter;
129		Molecule::TorsionIterator  torsionIter;
130	<	double bondPotential = 0.0;
131	<	double bendPotential = 0.0;
132	<	double torsionPotential = 0.0;
130	>	Molecule::InversionIterator  inversionIter;
131	>	RealType bondPotential = 0.0;
132	>	RealType bendPotential = 0.0;
133	>	RealType torsionPotential = 0.0;
134	>	RealType inversionPotential = 0.0;
135
136		//calculate short range interactions
137	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
137	>	for (mol = info_->beginMolecule(mi); mol != NULL;
138	>	mol = info_->nextMolecule(mi)) {
139
140		//change the positions of atoms which belong to the rigidbodies
141	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
142	<	rb->updateAtoms();
141	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
142	>	rb = mol->nextRigidBody(rbIter)) {
143	>	rb->updateAtoms();
144		}
145
146	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
146	>	for (bond = mol->beginBond(bondIter); bond != NULL;
147	>	bond = mol->nextBond(bondIter)) {
148		bond->calcForce();
149		bondPotential += bond->getPotential();
150		}
151
152	<
153	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
154	<
155	<	double angle;
156	<	bend->calcForce(angle);
157	<	double currBendPot = bend->getPotential();
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 -  i->second.prev.potential);
172	<	}
173	<	}
174	<
200	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
201	<	double angle;
202	<	torsion->calcForce(angle);
203	<	double currTorsionPot = torsion->getPotential();
204	<	torsionPotential += torsion->getPotential();
205	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
206	<	if (i == torsionDataSets.end()) {
207	<	TorsionDataSet dataSet;
208	<	dataSet.prev.angle = dataSet.curr.angle = angle;
209	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
210	<	dataSet.deltaV = 0.0;
211	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
212	<	}else {
213	<	i->second.prev.angle = i->second.curr.angle;
214	<	i->second.prev.potential = i->second.curr.potential;
215	<	i->second.curr.angle = angle;
216	<	i->second.curr.potential = currTorsionPot;
217	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
218	<	}
152	>	for (bend = mol->beginBend(bendIter); bend != NULL;
153	>	bend = mol->nextBend(bendIter)) {
154	>
155	>	RealType angle;
156	>	bend->calcForce(angle);
157	>	RealType currBendPot = bend->getPotential();
158	>
159	>	bendPotential += bend->getPotential();
160	>	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
161	>	if (i == bendDataSets.end()) {
162	>	BendDataSet dataSet;
163	>	dataSet.prev.angle = dataSet.curr.angle = angle;
164	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
165	>	dataSet.deltaV = 0.0;
166	>	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
167	>	}else {
168	>	i->second.prev.angle = i->second.curr.angle;
169	>	i->second.prev.potential = i->second.curr.potential;
170	>	i->second.curr.angle = angle;
171	>	i->second.curr.potential = currBendPot;
172	>	i->second.deltaV =  fabs(i->second.curr.potential -
173	>	i->second.prev.potential);
174	>	}
175		}
176	+
177	+	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
178	+	torsion = mol->nextTorsion(torsionIter)) {
179	+	RealType angle;
180	+	torsion->calcForce(angle);
181	+	RealType currTorsionPot = torsion->getPotential();
182	+	torsionPotential += torsion->getPotential();
183	+	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
184	+	if (i == torsionDataSets.end()) {
185	+	TorsionDataSet dataSet;
186	+	dataSet.prev.angle = dataSet.curr.angle = angle;
187	+	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
188	+	dataSet.deltaV = 0.0;
189	+	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
190	+	}else {
191	+	i->second.prev.angle = i->second.curr.angle;
192	+	i->second.prev.potential = i->second.curr.potential;
193	+	i->second.curr.angle = angle;
194	+	i->second.curr.potential = currTorsionPot;
195	+	i->second.deltaV =  fabs(i->second.curr.potential -
196	+	i->second.prev.potential);
197	+	}
198	+	}
199
200	+	for (inversion = mol->beginInversion(inversionIter);
201	+	inversion != NULL;
202	+	inversion = mol->nextInversion(inversionIter)) {
203	+	RealType angle;
204	+	inversion->calcForce(angle);
205	+	RealType currInversionPot = inversion->getPotential();
206	+	inversionPotential += inversion->getPotential();
207	+	std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
208	+	if (i == inversionDataSets.end()) {
209	+	InversionDataSet dataSet;
210	+	dataSet.prev.angle = dataSet.curr.angle = angle;
211	+	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
212	+	dataSet.deltaV = 0.0;
213	+	inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
214	+	}else {
215	+	i->second.prev.angle = i->second.curr.angle;
216	+	i->second.prev.potential = i->second.curr.potential;
217	+	i->second.curr.angle = angle;
218	+	i->second.curr.potential = currInversionPot;
219	+	i->second.deltaV =  fabs(i->second.curr.potential -
220	+	i->second.prev.potential);
221	+	}
222	+	}
223		}
224
225	<	double  shortRangePotential = bondPotential + bendPotential + torsionPotential;
225	>	RealType  shortRangePotential = bondPotential + bendPotential +
226	>	torsionPotential +  inversionPotential;
227		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
228		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
229		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
230		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
231		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
232	+	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
233
234		}
235	<
236	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
235	>
236	>	void ForceManager::calcLongRangeInteraction() {
237		Snapshot* curSnapshot;
238		DataStorage* config;
239	<	double* frc;
240	<	double* pos;
241	<	double* trq;
242	<	double* A;
243	<	double* electroFrame;
244	<	double* rc;
239	>	RealType* frc;
240	>	RealType* pos;
241	>	RealType* trq;
242	>	RealType* A;
243	>	RealType* electroFrame;
244	>	RealType* rc;
245	>	RealType* particlePot;
246
247		//get current snapshot from SimInfo
248		curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
249	<
249	>
250		//get array pointers
251		config = &(curSnapshot->atomData);
252		frc = config->getArrayPointer(DataStorage::dslForce);
#	Line 249 | Line 254 | namespace oopse {
254		trq = config->getArrayPointer(DataStorage::dslTorque);
255		A   = config->getArrayPointer(DataStorage::dslAmat);
256		electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
257	+	particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
258
259		//calculate the center of mass of cutoff group
260		SimInfo::MoleculeIterator mi;
#	Line 257 | Line 263 | namespace oopse {
263		CutoffGroup* cg;
264		Vector3d com;
265		std::vector<Vector3d> rcGroup;
266	<
266	>
267		if(info_->getNCutoffGroups() > 0){
268	<
269	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
270	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
268	>
269	>	for (mol = info_->beginMolecule(mi); mol != NULL;
270	>	mol = info_->nextMolecule(mi)) {
271	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
272	>	cg = mol->nextCutoffGroup(ci)) {
273		cg->getCOM(com);
274		rcGroup.push_back(com);
275		}
#	Line 269 | Line 277 | namespace oopse {
277
278		rc = rcGroup[0].getArrayPointer();
279		} else {
280	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
280	>	// center of mass of the group is the same as position of the atom
281	>	// if cutoff group does not exist
282		rc = pos;
283		}
275	–
276	–	//initialize data before passing to fortran
277	–	double longRangePotential[LR_POT_TYPES];
278	–	double lrPot = 0.0;
284
285	<	Mat3x3d tau;
286	<	short int passedCalcPot = needPotential;
287	<	short int passedCalcStress = needStress;
285	>	//initialize data before passing to fortran
286	>	RealType longRangePotential[LR_POT_TYPES];
287	>	RealType lrPot = 0.0;
288	>	Vector3d totalDipole;
289		int isError = 0;
290
291		for (int i=0; i<LR_POT_TYPES;i++){
292		longRangePotential[i]=0.0; //Initialize array
293		}
294	<
295	<	doForceLoop( pos,
296	<	rc,
297	<	A,
298	<	electroFrame,
299	<	frc,
300	<	trq,
301	<	tau.getArrayPointer(),
302	<	longRangePotential,
303	<	&passedCalcPot,
304	<	&passedCalcStress,
305	<	&isError );
300	<
294	>
295	>	doForceLoop(pos,
296	>	rc,
297	>	A,
298	>	electroFrame,
299	>	frc,
300	>	trq,
301	>	tau.getArrayPointer(),
302	>	longRangePotential,
303	>	particlePot,
304	>	&isError );
305	>
306		if( isError ){
307		sprintf( painCave.errMsg,
308		"Error returned from the fortran force calculation.\n" );
#	Line 307 | Line 312 | namespace oopse {
312		for (int i=0; i<LR_POT_TYPES;i++){
313		lrPot += longRangePotential[i]; //Quick hack
314		}
315	<
315	>
316	>	// grab the simulation box dipole moment if specified
317	>	if (info_->getCalcBoxDipole()){
318	>	getAccumulatedBoxDipole(totalDipole.getArrayPointer());
319	>
320	>	curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
321	>	curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
322	>	curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
323	>	}
324	>
325		//store the tau and long range potential
326		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
327		curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
328		curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
315	–
316	–	curSnapshot->statData.setTau(tau);
329		}
330
331	<
331	>
332		void ForceManager::postCalculation() {
333		SimInfo::MoleculeIterator mi;
334		Molecule* mol;
335		Molecule::RigidBodyIterator rbIter;
336		RigidBody* rb;
337	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
338
339		// collect the atomic forces onto rigid bodies
340	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
341	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
342	<	rb->calcForcesAndTorques();
340	>
341	>	for (mol = info_->beginMolecule(mi); mol != NULL;
342	>	mol = info_->nextMolecule(mi)) {
343	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
344	>	rb = mol->nextRigidBody(rbIter)) {
345	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
346	>	tau += rbTau;
347		}
348		}
349	<
349	>
350	>	#ifdef IS_MPI
351	>	Mat3x3d tmpTau(tau);
352	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
353	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
354	>	#endif
355	>	curSnapshot->statData.setTau(tau);
356		}
357
358	<	} //end namespace oopse
358	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 770 by tim, Fri Dec 2 15:38:03 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1480 by gezelter, Mon Jul 26 19:50:53 2010 UTC

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