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

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trunk/src/brains/ForceManager.cpp (file contents), Revision 1275 by cli2, Fri Jul 4 20:54:29 2008 UTC vs.
branches/devel_omp/src/brains/ForceManager.cpp (file contents), Revision 1595 by chuckv, Tue Jul 19 18:50:04 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 47 | Line 47
47		* @version 1.0
48		*/
49
50	+
51		#include "brains/ForceManager.hpp"
52		#include "primitives/Molecule.hpp"
53	<	#include "UseTheForce/doForces_interface.h"
53	<	#define __C
54	<	#include "UseTheForce/DarkSide/fInteractionMap.h"
53	>	#define __OPENMD_C
54		#include "utils/simError.h"
55		#include "primitives/Bond.hpp"
56		#include "primitives/Bend.hpp"
57		#include "primitives/Torsion.hpp"
58		#include "primitives/Inversion.hpp"
59	<	namespace oopse {
59	>	#include "nonbonded/NonBondedInteraction.hpp"
60	>	#include "parallel/ForceMatrixDecomposition.hpp"
61
62	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
62	>	#include <cstdio>
63	>	#include <iostream>
64	>	#include <iomanip>
65	>
66	>	using namespace std;
67	>	namespace OpenMD {
68	>
69	>	ForceManager::ForceManager(SimInfo * info) : info_(info) {
70	>	forceField_ = info_->getForceField();
71	>	interactionMan_ = new InteractionManager();
72	>	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
73	>	}
74	>
75	>	/**
76	>	* setupCutoffs
77	>	*
78	>	* Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
79	>	* and cutoffPolicy
80	>	*
81	>	* cutoffRadius : realType
82	>	*  If the cutoffRadius was explicitly set, use that value.
83	>	*  If the cutoffRadius was not explicitly set:
84	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
85	>	*      No electrostatic atoms?  Poll the atom types present in the
86	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
87	>	*      Use the maximum suggested value that was found.
88	>	*
89	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
90	>	*                        or SHIFTED_POTENTIAL)
91	>	*      If cutoffMethod was explicitly set, use that choice.
92	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
93	>	*
94	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
95	>	*      If cutoffPolicy was explicitly set, use that choice.
96	>	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
97	>	*
98	>	* switchingRadius : realType
99	>	*  If the cutoffMethod was set to SWITCHED:
100	>	*      If the switchingRadius was explicitly set, use that value
101	>	*          (but do a sanity check first).
102	>	*      If the switchingRadius was not explicitly set: use 0.85 *
103	>	*      cutoffRadius_
104	>	*  If the cutoffMethod was not set to SWITCHED:
105	>	*      Set switchingRadius equal to cutoffRadius for safety.
106	>	*/
107	>	void ForceManager::setupCutoffs() {
108
109	<	if (!info_->isFortranInitialized()) {
110	<	info_->update();
66	<	}
109	>	Globals* simParams_ = info_->getSimParams();
110	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
111
112	<	preCalculation();
113	<
114	<	calcShortRangeInteraction();
112	>	if (simParams_->haveCutoffRadius()) {
113	>	rCut_ = simParams_->getCutoffRadius();
114	>	} else {
115	>	if (info_->usesElectrostaticAtoms()) {
116	>	sprintf(painCave.errMsg,
117	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
118	>	"\tOpenMD will use a default value of 12.0 angstroms"
119	>	"\tfor the cutoffRadius.\n");
120	>	painCave.isFatal = 0;
121	>	painCave.severity = OPENMD_INFO;
122	>	simError();
123	>	rCut_ = 12.0;
124	>	} else {
125	>	RealType thisCut;
126	>	set<AtomType*>::iterator i;
127	>	set<AtomType*> atomTypes;
128	>	atomTypes = info_->getSimulatedAtomTypes();
129	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
130	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
131	>	rCut_ = max(thisCut, rCut_);
132	>	}
133	>	sprintf(painCave.errMsg,
134	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
135	>	"\tOpenMD will use %lf angstroms.\n",
136	>	rCut_);
137	>	painCave.isFatal = 0;
138	>	painCave.severity = OPENMD_INFO;
139	>	simError();
140	>	}
141	>	}
142
143	<	calcLongRangeInteraction(needPotential, needStress);
143	>	fDecomp_->setUserCutoff(rCut_);
144	>	interactionMan_->setCutoffRadius(rCut_);
145
146	<	postCalculation(needStress);
146	>	map<string, CutoffMethod> stringToCutoffMethod;
147	>	stringToCutoffMethod["HARD"] = HARD;
148	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
149	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
150	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
151	>
152	>	if (simParams_->haveCutoffMethod()) {
153	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
154	>	map<string, CutoffMethod>::iterator i;
155	>	i = stringToCutoffMethod.find(cutMeth);
156	>	if (i == stringToCutoffMethod.end()) {
157	>	sprintf(painCave.errMsg,
158	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
159	>	"\tShould be one of: "
160	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
161	>	cutMeth.c_str());
162	>	painCave.isFatal = 1;
163	>	painCave.severity = OPENMD_ERROR;
164	>	simError();
165	>	} else {
166	>	cutoffMethod_ = i->second;
167	>	}
168	>	} else {
169	>	sprintf(painCave.errMsg,
170	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
171	>	"\tOpenMD will use SHIFTED_FORCE.\n");
172	>	painCave.isFatal = 0;
173	>	painCave.severity = OPENMD_INFO;
174	>	simError();
175	>	cutoffMethod_ = SHIFTED_FORCE;
176	>	}
177	>
178	>	map<string, CutoffPolicy> stringToCutoffPolicy;
179	>	stringToCutoffPolicy["MIX"] = MIX;
180	>	stringToCutoffPolicy["MAX"] = MAX;
181	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
182	>
183	>	std::string cutPolicy;
184	>	if (forceFieldOptions_.haveCutoffPolicy()){
185	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
186	>	}else if (simParams_->haveCutoffPolicy()) {
187	>	cutPolicy = simParams_->getCutoffPolicy();
188	>	}
189	>
190	>	if (!cutPolicy.empty()){
191	>	toUpper(cutPolicy);
192	>	map<string, CutoffPolicy>::iterator i;
193	>	i = stringToCutoffPolicy.find(cutPolicy);
194	>
195	>	if (i == stringToCutoffPolicy.end()) {
196	>	sprintf(painCave.errMsg,
197	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
198	>	"\tShould be one of: "
199	>	"MIX, MAX, or TRADITIONAL\n",
200	>	cutPolicy.c_str());
201	>	painCave.isFatal = 1;
202	>	painCave.severity = OPENMD_ERROR;
203	>	simError();
204	>	} else {
205	>	cutoffPolicy_ = i->second;
206	>	}
207	>	} else {
208	>	sprintf(painCave.errMsg,
209	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
210	>	"\tOpenMD will use TRADITIONAL.\n");
211	>	painCave.isFatal = 0;
212	>	painCave.severity = OPENMD_INFO;
213	>	simError();
214	>	cutoffPolicy_ = TRADITIONAL;
215	>	}
216	>
217	>	fDecomp_->setCutoffPolicy(cutoffPolicy_);
218	>
219	>	// create the switching function object:
220	>
221	>	switcher_ = new SwitchingFunction();
222	>
223	>	if (cutoffMethod_ == SWITCHED) {
224	>	if (simParams_->haveSwitchingRadius()) {
225	>	rSwitch_ = simParams_->getSwitchingRadius();
226	>	if (rSwitch_ > rCut_) {
227	>	sprintf(painCave.errMsg,
228	>	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
229	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
230	>	painCave.isFatal = 1;
231	>	painCave.severity = OPENMD_ERROR;
232	>	simError();
233	>	}
234	>	} else {
235	>	rSwitch_ = 0.85 * rCut_;
236	>	sprintf(painCave.errMsg,
237	>	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
238	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
239	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
240	>	painCave.isFatal = 0;
241	>	painCave.severity = OPENMD_WARNING;
242	>	simError();
243	>	}
244	>	} else {
245	>	if (simParams_->haveSwitchingRadius()) {
246	>	map<string, CutoffMethod>::const_iterator it;
247	>	string theMeth;
248	>	for (it = stringToCutoffMethod.begin();
249	>	it != stringToCutoffMethod.end(); ++it) {
250	>	if (it->second == cutoffMethod_) {
251	>	theMeth = it->first;
252	>	break;
253	>	}
254	>	}
255	>	sprintf(painCave.errMsg,
256	>	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
257	>	"\tis not set to SWITCHED, so switchingRadius value\n"
258	>	"\twill be ignored for this simulation\n", theMeth.c_str());
259	>	painCave.isFatal = 0;
260	>	painCave.severity = OPENMD_WARNING;
261	>	simError();
262	>	}
263	>
264	>	rSwitch_ = rCut_;
265	>	}
266	>
267	>	// Default to cubic switching function.
268	>	sft_ = cubic;
269	>	if (simParams_->haveSwitchingFunctionType()) {
270	>	string funcType = simParams_->getSwitchingFunctionType();
271	>	toUpper(funcType);
272	>	if (funcType == "CUBIC") {
273	>	sft_ = cubic;
274	>	} else {
275	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
276	>	sft_ = fifth_order_poly;
277	>	} else {
278	>	// throw error
279	>	sprintf( painCave.errMsg,
280	>	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
281	>	"\tswitchingFunctionType must be one of: "
282	>	"\"cubic\" or \"fifth_order_polynomial\".",
283	>	funcType.c_str() );
284	>	painCave.isFatal = 1;
285	>	painCave.severity = OPENMD_ERROR;
286	>	simError();
287	>	}
288	>	}
289	>	}
290	>	switcher_->setSwitchType(sft_);
291	>	switcher_->setSwitch(rSwitch_, rCut_);
292	>	interactionMan_->setSwitchingRadius(rSwitch_);
293	>	}
294	>
295	>	void ForceManager::initialize() {
296	>
297	>	if (!info_->isTopologyDone()) {
298	>
299	>	info_->update();
300	>	interactionMan_->setSimInfo(info_);
301	>	interactionMan_->initialize();
302	>
303	>	// We want to delay the cutoffs until after the interaction
304	>	// manager has set up the atom-atom interactions so that we can
305	>	// query them for suggested cutoff values
306	>	setupCutoffs();
307	>
308	>	info_->prepareTopology();
309	>	}
310	>
311	>	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
312
313	+	// Force fields can set options on how to scale van der Waals and
314	+	// electrostatic interactions for atoms connected via bonds, bends
315	+	// and torsions in this case the topological distance between
316	+	// atoms is:
317	+	// 0 = topologically unconnected
318	+	// 1 = bonded together
319	+	// 2 = connected via a bend
320	+	// 3 = connected via a torsion
321	+
322	+	vdwScale_.reserve(4);
323	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
324	+
325	+	electrostaticScale_.reserve(4);
326	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
327	+
328	+	vdwScale_[0] = 1.0;
329	+	vdwScale_[1] = fopts.getvdw12scale();
330	+	vdwScale_[2] = fopts.getvdw13scale();
331	+	vdwScale_[3] = fopts.getvdw14scale();
332	+
333	+	electrostaticScale_[0] = 1.0;
334	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
335	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
336	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
337	+
338	+	fDecomp_->distributeInitialData();
339	+
340	+	initialized_ = true;
341	+
342		}
343	+
344	+	void ForceManager::calcForces() {
345	+
346	+	if (!initialized_) initialize();
347	+
348	+	preCalculation();
349	+	shortRangeInteractions();
350	+	//    longRangeInteractions();
351	+	longRangeInteractionsRapaport();
352	+	postCalculation();
353	+	}
354
355		void ForceManager::preCalculation() {
356		SimInfo::MoleculeIterator mi;
#	Line 82 | Line 359 | namespace oopse {
359		Atom* atom;
360		Molecule::RigidBodyIterator rbIter;
361		RigidBody* rb;
362	+	Molecule::CutoffGroupIterator ci;
363	+	CutoffGroup* cg;
364
365		// forces are zeroed here, before any are accumulated.
87	–	// NOTE: do not rezero the forces in Fortran.
366
367		for (mol = info_->beginMolecule(mi); mol != NULL;
368		mol = info_->nextMolecule(mi)) {
369	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
369	>	for(atom = mol->beginAtom(ai); atom != NULL;
370	>	atom = mol->nextAtom(ai)) {
371		atom->zeroForcesAndTorques();
372		}
373	<
373	>
374		//change the positions of atoms which belong to the rigidbodies
375		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
376		rb = mol->nextRigidBody(rbIter)) {
377		rb->zeroForcesAndTorques();
378		}
379	<
379	>
380	>	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
381	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
382	>	cg = mol->nextCutoffGroup(ci)) {
383	>	//calculate the center of mass of cutoff group
384	>	cg->updateCOM();
385	>	}
386	>	}
387		}
388
389		// Zero out the stress tensor
#	Line 105 | Line 391 | namespace oopse {
391
392		}
393
394	<	void ForceManager::calcShortRangeInteraction() {
394	>	void ForceManager::shortRangeInteractions() {
395		Molecule* mol;
396		RigidBody* rb;
397		Bond* bond;
#	Line 145 | Line 431 | namespace oopse {
431		RealType angle;
432		bend->calcForce(angle);
433		RealType currBendPot = bend->getPotential();
434	+
435		bendPotential += bend->getPotential();
436	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
436	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
437		if (i == bendDataSets.end()) {
438		BendDataSet dataSet;
439		dataSet.prev.angle = dataSet.curr.angle = angle;
440		dataSet.prev.potential = dataSet.curr.potential = currBendPot;
441		dataSet.deltaV = 0.0;
442	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
442	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
443	>	dataSet));
444		}else {
445		i->second.prev.angle = i->second.curr.angle;
446		i->second.prev.potential = i->second.curr.potential;
#	Line 169 | Line 457 | namespace oopse {
457		torsion->calcForce(angle);
458		RealType currTorsionPot = torsion->getPotential();
459		torsionPotential += torsion->getPotential();
460	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
460	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
461		if (i == torsionDataSets.end()) {
462		TorsionDataSet dataSet;
463		dataSet.prev.angle = dataSet.curr.angle = angle;
464		dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
465		dataSet.deltaV = 0.0;
466	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
466	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
467		}else {
468		i->second.prev.angle = i->second.curr.angle;
469		i->second.prev.potential = i->second.curr.potential;
#	Line 185 | Line 473 | namespace oopse {
473		i->second.prev.potential);
474		}
475		}
476	<
476	>
477		for (inversion = mol->beginInversion(inversionIter);
478		inversion != NULL;
479		inversion = mol->nextInversion(inversionIter)) {
#	Line 193 | Line 481 | namespace oopse {
481		inversion->calcForce(angle);
482		RealType currInversionPot = inversion->getPotential();
483		inversionPotential += inversion->getPotential();
484	<	std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
484	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
485		if (i == inversionDataSets.end()) {
486		InversionDataSet dataSet;
487		dataSet.prev.angle = dataSet.curr.angle = angle;
488		dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
489		dataSet.deltaV = 0.0;
490	<	inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
490	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
491		}else {
492		i->second.prev.angle = i->second.curr.angle;
493		i->second.prev.potential = i->second.curr.potential;
#	Line 218 | Line 506 | namespace oopse {
506		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
507		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
508		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
509	<	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
222	<
509	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
510		}
511
512	<	void ForceManager::calcLongRangeInteraction(bool needPotential,
226	<	bool needStress) {
227	<	Snapshot* curSnapshot;
228	<	DataStorage* config;
229	<	RealType* frc;
230	<	RealType* pos;
231	<	RealType* trq;
232	<	RealType* A;
233	<	RealType* electroFrame;
234	<	RealType* rc;
235	<	RealType* particlePot;
236	<
237	<	//get current snapshot from SimInfo
238	<	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
239	<
240	<	//get array pointers
241	<	config = &(curSnapshot->atomData);
242	<	frc = config->getArrayPointer(DataStorage::dslForce);
243	<	pos = config->getArrayPointer(DataStorage::dslPosition);
244	<	trq = config->getArrayPointer(DataStorage::dslTorque);
245	<	A   = config->getArrayPointer(DataStorage::dslAmat);
246	<	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
247	<	particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
512	>	void ForceManager::longRangeInteractionsRapaport() {
513
514	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
515	+	DataStorage* config = &(curSnapshot->atomData);
516	+	DataStorage* cgConfig = &(curSnapshot->cgData);
517	+
518		//calculate the center of mass of cutoff group
519	+
520		SimInfo::MoleculeIterator mi;
521		Molecule* mol;
522		Molecule::CutoffGroupIterator ci;
523		CutoffGroup* cg;
524	<	Vector3d com;
255	<	std::vector<Vector3d> rcGroup;
256	<
524	>
525		if(info_->getNCutoffGroups() > 0){
526	<
259	<	for (mol = info_->beginMolecule(mi); mol != NULL;
526	>	for (mol = info_->beginMolecule(mi); mol != NULL;
527		mol = info_->nextMolecule(mi)) {
528	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
528	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
529		cg = mol->nextCutoffGroup(ci)) {
530	<	cg->getCOM(com);
531	<	rcGroup.push_back(com);
530	>	cerr << "branch1\n";
531	>	cerr << "globind = " << cg->getGlobalIndex() << "\n";
532	>	cg->updateCOM();
533		}
534	<	}// end for (mol)
267	<
268	<	rc = rcGroup[0].getArrayPointer();
534	>	}
535		} else {
536	<	// center of mass of the group is the same as position of the atom
536	>	// center of mass of the group is the same as position of the atom
537		// if cutoff group does not exist
538	<	rc = pos;
538	>	cerr << "branch2\n";
539	>	cgConfig->position = config->position;
540		}
274	–
275	–	//initialize data before passing to fortran
276	–	RealType longRangePotential[LR_POT_TYPES];
277	–	RealType lrPot = 0.0;
278	–	Vector3d totalDipole;
279	–	short int passedCalcPot = needPotential;
280	–	short int passedCalcStress = needStress;
281	–	int isError = 0;
541
542	<	for (int i=0; i<LR_POT_TYPES;i++){
543	<	longRangePotential[i]=0.0; //Initialize array
544	<	}
545	<
546	<	doForceLoop(pos,
547	<	rc,
548	<	A,
549	<	electroFrame,
550	<	frc,
551	<	trq,
552	<	tau.getArrayPointer(),
553	<	longRangePotential,
554	<	particlePot,
555	<	&passedCalcPot,
556	<	&passedCalcStress,
557	<	&isError );
558	<
559	<	if( isError ){
560	<	sprintf( painCave.errMsg,
561	<	"Error returned from the fortran force calculation.\n" );
562	<	painCave.isFatal = 1;
563	<	simError();
564	<	}
565	<	for (int i=0; i<LR_POT_TYPES;i++){
566	<	lrPot += longRangePotential[i]; //Quick hack
567	<	}
568	<
569	<	// grab the simulation box dipole moment if specified
570	<	if (info_->getCalcBoxDipole()){
571	<	getAccumulatedBoxDipole(totalDipole.getArrayPointer());
572	<
573	<	curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
574	<	curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
575	<	curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
542	>	fDecomp_->zeroWorkArrays();
543	>	fDecomp_->distributeData();
544	>
545	>	int cg1, cg2, atom1, atom2, topoDist;
546	>	Vector3d d_grp, dag, d;
547	>	RealType rgrpsq, rgrp, r2, r;
548	>	RealType electroMult, vdwMult;
549	>	RealType vij;
550	>	Vector3d fij, fg, f1;
551	>	tuple3<RealType, RealType, RealType> cuts;
552	>	RealType rCutSq;
553	>	bool in_switching_region;
554	>	RealType sw, dswdr, swderiv;
555	>	vector<int> atomListColumn, atomListRow, atomListLocal;
556	>	InteractionData idat;
557	>	SelfData sdat;
558	>	RealType mf;
559	>	RealType lrPot;
560	>	RealType vpair;
561	>	potVec longRangePotential(0.0);
562	>	potVec workPot(0.0);
563	>
564	>	int loopStart, loopEnd;
565	>
566	>	idat.vdwMult = &vdwMult;
567	>	idat.electroMult = &electroMult;
568	>	idat.pot = &workPot;
569	>	sdat.pot = fDecomp_->getEmbeddingPotential();
570	>	idat.vpair = &vpair;
571	>	idat.f1 = &f1;
572	>	idat.sw = &sw;
573	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
574	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
575	>
576	>	loopEnd = PAIR_LOOP;
577	>	if (info_->requiresPrepair() ) {
578	>	loopStart = PREPAIR_LOOP;
579	>	} else {
580	>	loopStart = PAIR_LOOP;
581		}
582	+
583	+	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
584	+
585	+	if (iLoop == loopStart) {
586	+	bool update_nlist = fDecomp_->checkNeighborList();
587	+	if (update_nlist)
588	+	neighborMatW = fDecomp_->buildLayerBasedNeighborList();
589	+	}
590	+
591	+	int i;
592	+	#pragma omp parallel for num_threads(2) private(i)
593	+	for(i = 0; i < neighborMatW.size(); ++i)
594	+	for(vector<int>::iterator j = neighborMatW[i].begin(); j != neighborMatW[i].end(); ++j)
595	+	{
596	+	cg1 = i;
597	+	cg2 = *j;
598	+
599	+	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
600	+
601	+	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
602	+	curSnapshot->wrapVector(d_grp);
603	+	rgrpsq = d_grp.lengthSquare();
604	+
605	+	rCutSq = cuts.second;
606	+
607	+	if (rgrpsq < rCutSq) {
608	+	idat.rcut = &cuts.first;
609	+	if (iLoop == PAIR_LOOP) {
610	+	vij = 0.0;
611	+	fij = V3Zero;
612	+	}
613	+
614	+	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
615	+	rgrp);
616	+
617	+	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
618	+	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
619	+
620	+	for (vector<int>::iterator ia = atomListRow.begin();
621	+	ia != atomListRow.end(); ++ia) {
622	+	atom1 = (*ia);
623	+
624	+	for (vector<int>::iterator jb = atomListColumn.begin();
625	+	jb != atomListColumn.end(); ++jb) {
626	+	atom2 = (*jb);
627	+
628	+	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
629	+	vpair = 0.0;
630	+	workPot = 0.0;
631	+	f1 = V3Zero;
632	+
633	+	fDecomp_->fillInteractionData(idat, atom1, atom2);
634	+
635	+	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
636	+	vdwMult = vdwScale_[topoDist];
637	+	electroMult = electrostaticScale_[topoDist];
638	+
639	+	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
640	+	idat.d = &d_grp;
641	+	idat.r2 = &rgrpsq;
642	+	cerr << "dgrp = " << d_grp << "\n";
643	+	} else {
644	+	d = fDecomp_->getInteratomicVector(atom1, atom2);
645	+	curSnapshot->wrapVector( d );
646	+	r2 = d.lengthSquare();
647	+	cerr << "datm = " << d<< "\n";
648	+	idat.d = &d;
649	+	idat.r2 = &r2;
650	+	}
651	+
652	+	cerr << "idat.d = " << *(idat.d) << "\n";
653	+	r = sqrt( *(idat.r2) );
654	+	idat.rij = &r;
655	+
656	+	if (iLoop == PREPAIR_LOOP) {
657	+	interactionMan_->doPrePair(idat);
658	+	} else {
659	+	interactionMan_->doPair(idat);
660	+	fDecomp_->unpackInteractionData(idat, atom1, atom2);
661	+
662	+	cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << "\n";
663	+	vij += vpair;
664	+	fij += f1;
665	+	tau -= outProduct( *(idat.d), f1);
666	+	}
667	+	}
668	+	}
669	+	}
670	+
671	+	if (iLoop == PAIR_LOOP) {
672	+	if (in_switching_region) {
673	+	swderiv = vij * dswdr / rgrp;
674	+	fg = swderiv * d_grp;
675	+	fij += fg;
676	+
677	+	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
678	+	tau -= outProduct( *(idat.d), fg);
679	+	}
680	+
681	+	for (vector<int>::iterator ia = atomListRow.begin();
682	+	ia != atomListRow.end(); ++ia) {
683	+	atom1 = (*ia);
684	+	mf = fDecomp_->getMassFactorRow(atom1);
685	+	// fg is the force on atom ia due to cutoff group's
686	+	// presence in switching region
687	+	fg = swderiv * d_grp * mf;
688	+	fDecomp_->addForceToAtomRow(atom1, fg);
689	+
690	+	if (atomListRow.size() > 1) {
691	+	if (info_->usesAtomicVirial()) {
692	+	// find the distance between the atom
693	+	// and the center of the cutoff group:
694	+	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
695	+	tau -= outProduct(dag, fg);
696	+	}
697	+	}
698	+	}
699	+	for (vector<int>::iterator jb = atomListColumn.begin();
700	+	jb != atomListColumn.end(); ++jb) {
701	+	atom2 = (*jb);
702	+	mf = fDecomp_->getMassFactorColumn(atom2);
703	+	// fg is the force on atom jb due to cutoff group's
704	+	// presence in switching region
705	+	fg = -swderiv * d_grp * mf;
706	+	fDecomp_->addForceToAtomColumn(atom2, fg);
707	+
708	+	if (atomListColumn.size() > 1) {
709	+	if (info_->usesAtomicVirial()) {
710	+	// find the distance between the atom
711	+	// and the center of the cutoff group:
712	+	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
713	+	tau -= outProduct(dag, fg);
714	+	}
715	+	}
716	+	}
717	+	}
718	+	//if (!SIM_uses_AtomicVirial) {
719	+	//  tau -= outProduct(d_grp, fij);
720	+	//}
721	+	}
722	+	}
723	+	}
724	+
725	+	if (iLoop == PREPAIR_LOOP) {
726	+	if (info_->requiresPrepair()) {
727	+
728	+	fDecomp_->collectIntermediateData();
729	+
730	+	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
731	+	fDecomp_->fillSelfData(sdat, atom1);
732	+	interactionMan_->doPreForce(sdat);
733	+	}
734	+
735	+	fDecomp_->distributeIntermediateData();
736	+
737	+	}
738	+	}
739	+
740	+	}
741	+
742	+	fDecomp_->collectData();
743	+
744	+	if (info_->requiresSelfCorrection()) {
745	+
746	+	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
747	+	fDecomp_->fillSelfData(sdat, atom1);
748	+	interactionMan_->doSelfCorrection(sdat);
749	+	}
750	+
751	+	}
752	+
753	+	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
754	+	*(fDecomp_->getPairwisePotential());
755	+
756	+	lrPot = longRangePotential.sum();
757	+
758	+	//store the tau and long range potential
759	+	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
760	+	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
761	+	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
762	+	}
763	+
764	+	void ForceManager::longRangeInteractions() {
765	+
766	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
767	+	DataStorage* config = &(curSnapshot->atomData);
768	+	DataStorage* cgConfig = &(curSnapshot->cgData);
769	+
770	+	//calculate the center of mass of cutoff group
771	+
772	+	SimInfo::MoleculeIterator mi;
773	+	Molecule* mol;
774	+	Molecule::CutoffGroupIterator ci;
775	+	CutoffGroup* cg;
776	+
777	+	if(info_->getNCutoffGroups() > 0){
778	+	for (mol = info_->beginMolecule(mi); mol != NULL;
779	+	mol = info_->nextMolecule(mi)) {
780	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
781	+	cg = mol->nextCutoffGroup(ci)) {
782	+	cerr << "branch1\n";
783	+	cerr << "globind = " << cg->getGlobalIndex() << "\n";
784	+	cg->updateCOM();
785	+	}
786	+	}
787	+	} else {
788	+	// center of mass of the group is the same as position of the atom
789	+	// if cutoff group does not exist
790	+	cerr << "branch2\n";
791	+	cgConfig->position = config->position;
792	+	}
793	+
794	+	fDecomp_->zeroWorkArrays();
795	+	fDecomp_->distributeData();
796
797	+	int cg1, cg2, atom1, atom2, topoDist;
798	+	Vector3d d_grp, dag, d;
799	+	RealType rgrpsq, rgrp, r2, r;
800	+	RealType electroMult, vdwMult;
801	+	RealType vij;
802	+	Vector3d fij, fg, f1;
803	+	tuple3<RealType, RealType, RealType> cuts;
804	+	RealType rCutSq;
805	+	bool in_switching_region;
806	+	RealType sw, dswdr, swderiv;
807	+	vector<int> atomListColumn, atomListRow, atomListLocal;
808	+	InteractionData idat;
809	+	SelfData sdat;
810	+	RealType mf;
811	+	RealType lrPot;
812	+	RealType vpair;
813	+	potVec longRangePotential(0.0);
814	+	potVec workPot(0.0);
815	+
816	+	int loopStart, loopEnd;
817	+
818	+	idat.vdwMult = &vdwMult;
819	+	idat.electroMult = &electroMult;
820	+	idat.pot = &workPot;
821	+	sdat.pot = fDecomp_->getEmbeddingPotential();
822	+	idat.vpair = &vpair;
823	+	idat.f1 = &f1;
824	+	idat.sw = &sw;
825	+	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
826	+	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
827	+
828	+	loopEnd = PAIR_LOOP;
829	+	if (info_->requiresPrepair() ) {
830	+	loopStart = PREPAIR_LOOP;
831	+	} else {
832	+	loopStart = PAIR_LOOP;
833	+	}
834	+
835	+	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
836	+
837	+	if (iLoop == loopStart) {
838	+	bool update_nlist = fDecomp_->checkNeighborList();
839	+	if (update_nlist)
840	+	neighborList = fDecomp_->buildNeighborList();
841	+
842	+	}
843	+
844	+	for (vector<pair<int, int> >::iterator it = neighborList.begin();
845	+	it != neighborList.end(); ++it)
846	+	{
847	+	cg1 = (*it).first;
848	+	cg2 = (*it).second;
849	+
850	+	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
851	+
852	+	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
853	+	curSnapshot->wrapVector(d_grp);
854	+	rgrpsq = d_grp.lengthSquare();
855	+
856	+	rCutSq = cuts.second;
857	+
858	+	if (rgrpsq < rCutSq) {
859	+	idat.rcut = &cuts.first;
860	+	if (iLoop == PAIR_LOOP) {
861	+	vij = 0.0;
862	+	fij = V3Zero;
863	+	}
864	+
865	+	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
866	+	rgrp);
867	+
868	+	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
869	+	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
870	+
871	+	for (vector<int>::iterator ia = atomListRow.begin();
872	+	ia != atomListRow.end(); ++ia) {
873	+	atom1 = (*ia);
874	+
875	+	for (vector<int>::iterator jb = atomListColumn.begin();
876	+	jb != atomListColumn.end(); ++jb) {
877	+	atom2 = (*jb);
878	+
879	+	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
880	+	vpair = 0.0;
881	+	workPot = 0.0;
882	+	f1 = V3Zero;
883	+
884	+	fDecomp_->fillInteractionData(idat, atom1, atom2);
885	+
886	+	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
887	+	vdwMult = vdwScale_[topoDist];
888	+	electroMult = electrostaticScale_[topoDist];
889	+
890	+	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
891	+	idat.d = &d_grp;
892	+	idat.r2 = &rgrpsq;
893	+	cerr << "dgrp = " << d_grp << "\n";
894	+	} else {
895	+	d = fDecomp_->getInteratomicVector(atom1, atom2);
896	+	curSnapshot->wrapVector( d );
897	+	r2 = d.lengthSquare();
898	+	cerr << "datm = " << d<< "\n";
899	+	idat.d = &d;
900	+	idat.r2 = &r2;
901	+	}
902	+
903	+	cerr << "idat.d = " << *(idat.d) << "\n";
904	+	r = sqrt( *(idat.r2) );
905	+	idat.rij = &r;
906	+
907	+	if (iLoop == PREPAIR_LOOP) {
908	+	interactionMan_->doPrePair(idat);
909	+	} else {
910	+	interactionMan_->doPair(idat);
911	+	fDecomp_->unpackInteractionData(idat, atom1, atom2);
912	+
913	+	cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << "\n";
914	+	vij += vpair;
915	+	fij += f1;
916	+	tau -= outProduct( *(idat.d), f1);
917	+	}
918	+	}
919	+	}
920	+	}
921	+
922	+	if (iLoop == PAIR_LOOP) {
923	+	if (in_switching_region) {
924	+	swderiv = vij * dswdr / rgrp;
925	+	fg = swderiv * d_grp;
926	+	fij += fg;
927	+
928	+	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
929	+	tau -= outProduct( *(idat.d), fg);
930	+	}
931	+
932	+	for (vector<int>::iterator ia = atomListRow.begin();
933	+	ia != atomListRow.end(); ++ia) {
934	+	atom1 = (*ia);
935	+	mf = fDecomp_->getMassFactorRow(atom1);
936	+	// fg is the force on atom ia due to cutoff group's
937	+	// presence in switching region
938	+	fg = swderiv * d_grp * mf;
939	+	fDecomp_->addForceToAtomRow(atom1, fg);
940	+
941	+	if (atomListRow.size() > 1) {
942	+	if (info_->usesAtomicVirial()) {
943	+	// find the distance between the atom
944	+	// and the center of the cutoff group:
945	+	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
946	+	tau -= outProduct(dag, fg);
947	+	}
948	+	}
949	+	}
950	+	for (vector<int>::iterator jb = atomListColumn.begin();
951	+	jb != atomListColumn.end(); ++jb) {
952	+	atom2 = (*jb);
953	+	mf = fDecomp_->getMassFactorColumn(atom2);
954	+	// fg is the force on atom jb due to cutoff group's
955	+	// presence in switching region
956	+	fg = -swderiv * d_grp * mf;
957	+	fDecomp_->addForceToAtomColumn(atom2, fg);
958	+
959	+	if (atomListColumn.size() > 1) {
960	+	if (info_->usesAtomicVirial()) {
961	+	// find the distance between the atom
962	+	// and the center of the cutoff group:
963	+	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
964	+	tau -= outProduct(dag, fg);
965	+	}
966	+	}
967	+	}
968	+	}
969	+	//if (!SIM_uses_AtomicVirial) {
970	+	//  tau -= outProduct(d_grp, fij);
971	+	//}
972	+	}
973	+	}
974	+	}
975	+
976	+	if (iLoop == PREPAIR_LOOP) {
977	+	if (info_->requiresPrepair()) {
978	+
979	+	fDecomp_->collectIntermediateData();
980	+
981	+	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
982	+	fDecomp_->fillSelfData(sdat, atom1);
983	+	interactionMan_->doPreForce(sdat);
984	+	}
985	+
986	+	fDecomp_->distributeIntermediateData();
987	+
988	+	}
989	+	}
990	+
991	+	}
992	+
993	+	fDecomp_->collectData();
994	+
995	+	if (info_->requiresSelfCorrection()) {
996	+
997	+	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
998	+	fDecomp_->fillSelfData(sdat, atom1);
999	+	interactionMan_->doSelfCorrection(sdat);
1000	+	}
1001	+
1002	+	}
1003	+
1004	+	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
1005	+	*(fDecomp_->getPairwisePotential());
1006	+
1007	+	lrPot = longRangePotential.sum();
1008	+
1009		//store the tau and long range potential
1010		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
1011	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
1012	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
1011	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
1012	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
1013		}
1014
1015
1016	<	void ForceManager::postCalculation(bool needStress) {
1016	>	void ForceManager::postCalculation() {
1017		SimInfo::MoleculeIterator mi;
1018		Molecule* mol;
1019		Molecule::RigidBodyIterator rbIter;
#	Line 336 | Line 1026 | namespace oopse {
1026		mol = info_->nextMolecule(mi)) {
1027		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
1028		rb = mol->nextRigidBody(rbIter)) {
1029	<	if (needStress) {
1030	<	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
341	<	tau += rbTau;
342	<	} else{
343	<	rb->calcForcesAndTorques();
344	<	}
1029	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
1030	>	tau += rbTau;
1031		}
1032		}
1033	<
348	<	if (needStress) {
1033	>
1034		#ifdef IS_MPI
1035	<	Mat3x3d tmpTau(tau);
1036	<	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
1037	<	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1035	>	Mat3x3d tmpTau(tau);
1036	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
1037	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1038		#endif
1039	<	curSnapshot->statData.setTau(tau);
355	<	}
1039	>	curSnapshot->statData.setTau(tau);
1040		}
1041
1042	<	} //end namespace oopse
1042	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 1275 by cli2, Fri Jul 4 20:54:29 2008 UTC vs.
branches/devel_omp/src/brains/ForceManager.cpp (property svn:keywords), Revision 1595 by chuckv, Tue Jul 19 18:50:04 2011 UTC

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