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

Comparing:
trunk/src/brains/ForceManager.cpp (file contents), Revision 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1485 by gezelter, Wed Jul 28 19:52:00 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;
72	<	}
68	>	gb_ = GB::Instance();
69	>	gb_->setForceField(info_->getForceField());
70
71	<	bool  TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
72	<	return t1.dataSet.deltaV < t2.dataSet.deltaV;
76	<	}
77	<	*/
78	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
71	>	sticky_ = Sticky::Instance();
72	>	sticky_->setForceField(info_->getForceField());
73
74	+	eam_ = EAM::Instance();
75	+	eam_->setForceField(info_->getForceField());
76	+	}
77	+
78	+	void ForceManager::calcForces() {
79	+
80		if (!info_->isFortranInitialized()) {
81		info_->update();
82		}
83	<
83	>
84		preCalculation();
85
86		calcShortRangeInteraction();
87
88	<	calcLongRangeInteraction(needPotential, needStress);
88	>	calcLongRangeInteraction();
89
90		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	–	}
91
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	–	*/
92		}
93	<
93	>
94		void ForceManager::preCalculation() {
95		SimInfo::MoleculeIterator mi;
96		Molecule* mol;
#	Line 131 | Line 101 | namespace oopse {
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)) {
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	<
110	>
111		//change the positions of atoms which belong to the rigidbodies
112	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
112	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
113	>	rb = mol->nextRigidBody(rbIter)) {
114		rb->zeroForcesAndTorques();
115		}
116	+
117		}
118
119	+	// Zero out the stress tensor
120	+	tau *= 0.0;
121	+
122		}
123	<
123	>
124		void ForceManager::calcShortRangeInteraction() {
125		Molecule* mol;
126		RigidBody* rb;
127		Bond* bond;
128		Bend* bend;
129		Torsion* torsion;
130	+	Inversion* inversion;
131		SimInfo::MoleculeIterator mi;
132		Molecule::RigidBodyIterator rbIter;
133		Molecule::BondIterator bondIter;;
134		Molecule::BendIterator  bendIter;
135		Molecule::TorsionIterator  torsionIter;
136	+	Molecule::InversionIterator  inversionIter;
137		RealType bondPotential = 0.0;
138		RealType bendPotential = 0.0;
139		RealType torsionPotential = 0.0;
140	+	RealType inversionPotential = 0.0;
141
142		//calculate short range interactions
143	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
143	>	for (mol = info_->beginMolecule(mi); mol != NULL;
144	>	mol = info_->nextMolecule(mi)) {
145
146		//change the positions of atoms which belong to the rigidbodies
147	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
148	<	rb->updateAtoms();
147	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
148	>	rb = mol->nextRigidBody(rbIter)) {
149	>	rb->updateAtoms();
150		}
151
152	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
152	>	for (bond = mol->beginBond(bondIter); bond != NULL;
153	>	bond = mol->nextBond(bondIter)) {
154		bond->calcForce();
155		bondPotential += bond->getPotential();
156		}
157
158	<
159	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
160	<
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)) {
158	>	for (bend = mol->beginBend(bendIter); bend != NULL;
159	>	bend = mol->nextBend(bendIter)) {
160	>
161		RealType angle;
162	<	torsion->calcForce(angle);
163	<	RealType currTorsionPot = torsion->getPotential();
164	<	torsionPotential += torsion->getPotential();
165	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
166	<	if (i == torsionDataSets.end()) {
167	<	TorsionDataSet dataSet;
168	<	dataSet.prev.angle = dataSet.curr.angle = angle;
169	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
170	<	dataSet.deltaV = 0.0;
171	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
172	<	}else {
173	<	i->second.prev.angle = i->second.curr.angle;
174	<	i->second.prev.potential = i->second.curr.potential;
175	<	i->second.curr.angle = angle;
176	<	i->second.curr.potential = currTorsionPot;
177	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
178	<	}
162	>	bend->calcForce(angle);
163	>	RealType currBendPot = bend->getPotential();
164	>
165	>	bendPotential += bend->getPotential();
166	>	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
167	>	if (i == bendDataSets.end()) {
168	>	BendDataSet dataSet;
169	>	dataSet.prev.angle = dataSet.curr.angle = angle;
170	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
171	>	dataSet.deltaV = 0.0;
172	>	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
173	>	}else {
174	>	i->second.prev.angle = i->second.curr.angle;
175	>	i->second.prev.potential = i->second.curr.potential;
176	>	i->second.curr.angle = angle;
177	>	i->second.curr.potential = currBendPot;
178	>	i->second.deltaV =  fabs(i->second.curr.potential -
179	>	i->second.prev.potential);
180	>	}
181		}
182	+
183	+	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
184	+	torsion = mol->nextTorsion(torsionIter)) {
185	+	RealType angle;
186	+	torsion->calcForce(angle);
187	+	RealType currTorsionPot = torsion->getPotential();
188	+	torsionPotential += torsion->getPotential();
189	+	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
190	+	if (i == torsionDataSets.end()) {
191	+	TorsionDataSet dataSet;
192	+	dataSet.prev.angle = dataSet.curr.angle = angle;
193	+	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
194	+	dataSet.deltaV = 0.0;
195	+	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
196	+	}else {
197	+	i->second.prev.angle = i->second.curr.angle;
198	+	i->second.prev.potential = i->second.curr.potential;
199	+	i->second.curr.angle = angle;
200	+	i->second.curr.potential = currTorsionPot;
201	+	i->second.deltaV =  fabs(i->second.curr.potential -
202	+	i->second.prev.potential);
203	+	}
204	+	}
205
206	+	for (inversion = mol->beginInversion(inversionIter);
207	+	inversion != NULL;
208	+	inversion = mol->nextInversion(inversionIter)) {
209	+	RealType angle;
210	+	inversion->calcForce(angle);
211	+	RealType currInversionPot = inversion->getPotential();
212	+	inversionPotential += inversion->getPotential();
213	+	std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
214	+	if (i == inversionDataSets.end()) {
215	+	InversionDataSet dataSet;
216	+	dataSet.prev.angle = dataSet.curr.angle = angle;
217	+	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
218	+	dataSet.deltaV = 0.0;
219	+	inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
220	+	}else {
221	+	i->second.prev.angle = i->second.curr.angle;
222	+	i->second.prev.potential = i->second.curr.potential;
223	+	i->second.curr.angle = angle;
224	+	i->second.curr.potential = currInversionPot;
225	+	i->second.deltaV =  fabs(i->second.curr.potential -
226	+	i->second.prev.potential);
227	+	}
228	+	}
229		}
230
231	<	RealType  shortRangePotential = bondPotential + bendPotential + torsionPotential;
231	>	RealType  shortRangePotential = bondPotential + bendPotential +
232	>	torsionPotential +  inversionPotential;
233		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
234		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
235		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
236		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
237		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
238	+	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
239
240		}
241	<
242	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
241	>
242	>	void ForceManager::calcLongRangeInteraction() {
243		Snapshot* curSnapshot;
244		DataStorage* config;
245		RealType* frc;
#	Line 236 | Line 248 | namespace oopse {
248		RealType* A;
249		RealType* electroFrame;
250		RealType* rc;
251	+	RealType* particlePot;
252
253		//get current snapshot from SimInfo
254		curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
255	<
255	>
256		//get array pointers
257		config = &(curSnapshot->atomData);
258		frc = config->getArrayPointer(DataStorage::dslForce);
#	Line 247 | Line 260 | namespace oopse {
260		trq = config->getArrayPointer(DataStorage::dslTorque);
261		A   = config->getArrayPointer(DataStorage::dslAmat);
262		electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
263	+	particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
264
265		//calculate the center of mass of cutoff group
266		SimInfo::MoleculeIterator mi;
#	Line 255 | Line 269 | namespace oopse {
269		CutoffGroup* cg;
270		Vector3d com;
271		std::vector<Vector3d> rcGroup;
272	<
272	>
273		if(info_->getNCutoffGroups() > 0){
274	<
275	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
276	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
274	>
275	>	for (mol = info_->beginMolecule(mi); mol != NULL;
276	>	mol = info_->nextMolecule(mi)) {
277	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
278	>	cg = mol->nextCutoffGroup(ci)) {
279		cg->getCOM(com);
280		rcGroup.push_back(com);
281		}
#	Line 267 | Line 283 | namespace oopse {
283
284		rc = rcGroup[0].getArrayPointer();
285		} else {
286	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
286	>	// center of mass of the group is the same as position of the atom
287	>	// if cutoff group does not exist
288		rc = pos;
289		}
290	<
290	>
291		//initialize data before passing to fortran
292		RealType longRangePotential[LR_POT_TYPES];
293		RealType lrPot = 0.0;
294		Vector3d totalDipole;
278	–	Mat3x3d tau;
279	–	short int passedCalcPot = needPotential;
280	–	short int passedCalcStress = needStress;
295		int isError = 0;
296
297		for (int i=0; i<LR_POT_TYPES;i++){
298		longRangePotential[i]=0.0; //Initialize array
299		}
300	<
301	<	doForceLoop( pos,
302	<	rc,
303	<	A,
304	<	electroFrame,
305	<	frc,
306	<	trq,
307	<	tau.getArrayPointer(),
308	<	longRangePotential,
309	<	&passedCalcPot,
310	<	&passedCalcStress,
311	<	&isError );
298	<
300	>
301	>	doForceLoop(pos,
302	>	rc,
303	>	A,
304	>	electroFrame,
305	>	frc,
306	>	trq,
307	>	tau.getArrayPointer(),
308	>	longRangePotential,
309	>	particlePot,
310	>	&isError );
311	>
312		if( isError ){
313		sprintf( painCave.errMsg,
314		"Error returned from the fortran force calculation.\n" );
#	Line 305 | Line 318 | namespace oopse {
318		for (int i=0; i<LR_POT_TYPES;i++){
319		lrPot += longRangePotential[i]; //Quick hack
320		}
321	<
321	>
322		// grab the simulation box dipole moment if specified
323		if (info_->getCalcBoxDipole()){
324		getAccumulatedBoxDipole(totalDipole.getArrayPointer());
325	<
325	>
326		curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
327		curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
328		curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
329		}
330	<
330	>
331		//store the tau and long range potential
332		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
333		curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
334		curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
322	–
323	–	curSnapshot->statData.setTau(tau);
335		}
336
337	<
337	>
338		void ForceManager::postCalculation() {
339		SimInfo::MoleculeIterator mi;
340		Molecule* mol;
341		Molecule::RigidBodyIterator rbIter;
342		RigidBody* rb;
343	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
344
345		// collect the atomic forces onto rigid bodies
346	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
347	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
348	<	rb->calcForcesAndTorques();
346	>
347	>	for (mol = info_->beginMolecule(mi); mol != NULL;
348	>	mol = info_->nextMolecule(mi)) {
349	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
350	>	rb = mol->nextRigidBody(rbIter)) {
351	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
352	>	tau += rbTau;
353		}
354	<	}
355	<
354	>	}
355	>
356	>	#ifdef IS_MPI
357	>	Mat3x3d tmpTau(tau);
358	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
359	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
360	>	#endif
361	>	curSnapshot->statData.setTau(tau);
362		}
363
364	<	} //end namespace oopse
364	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 998 by chrisfen, Mon Jul 3 13:18:43 2006 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1485 by gezelter, Wed Jul 28 19:52:00 2010 UTC

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