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

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trunk/src/brains/ForceManager.cpp (file contents), Revision 681 by tim, Mon Oct 17 23:13:44 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1584 by gezelter, Fri Jun 17 20:16:35 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	<	namespace oopse {
55	>	#include "primitives/Bond.hpp"
56	>	#include "primitives/Bend.hpp"
57	>	#include "primitives/Torsion.hpp"
58	>	#include "primitives/Inversion.hpp"
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	<	if (!info_->isFortranInitialized()) {
67	<	info_->update();
68	<	}
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	<	preCalculation();
75	>	/**
76	>	* setupCutoffs
77	>	*
78	>	* Sets the values of cutoffRadius, cutoffMethod, and cutoffPolicy
79	>	*
80	>	* cutoffRadius : realType
81	>	*  If the cutoffRadius was explicitly set, use that value.
82	>	*  If the cutoffRadius was not explicitly set:
83	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
84	>	*      No electrostatic atoms?  Poll the atom types present in the
85	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
86	>	*      Use the maximum suggested value that was found.
87	>	*
88	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
89	>	*      If cutoffMethod was explicitly set, use that choice.
90	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
91	>	*
92	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
93	>	*      If cutoffPolicy was explicitly set, use that choice.
94	>	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
95	>	*/
96	>	void ForceManager::setupCutoffs() {
97
98	<	calcShortRangeInteraction();
98	>	Globals* simParams_ = info_->getSimParams();
99	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
100	>
101	>	if (simParams_->haveCutoffRadius()) {
102	>	rCut_ = simParams_->getCutoffRadius();
103	>	} else {
104	>	if (info_->usesElectrostaticAtoms()) {
105	>	sprintf(painCave.errMsg,
106	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
107	>	"\tOpenMD will use a default value of 12.0 angstroms"
108	>	"\tfor the cutoffRadius.\n");
109	>	painCave.isFatal = 0;
110	>	painCave.severity = OPENMD_INFO;
111	>	simError();
112	>	rCut_ = 12.0;
113	>	} else {
114	>	RealType thisCut;
115	>	set<AtomType*>::iterator i;
116	>	set<AtomType*> atomTypes;
117	>	atomTypes = info_->getSimulatedAtomTypes();
118	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
119	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
120	>	rCut_ = max(thisCut, rCut_);
121	>	}
122	>	sprintf(painCave.errMsg,
123	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
124	>	"\tOpenMD will use %lf angstroms.\n",
125	>	rCut_);
126	>	painCave.isFatal = 0;
127	>	painCave.severity = OPENMD_INFO;
128	>	simError();
129	>	}
130	>	}
131
132	<	calcLongRangeInteraction(needPotential, needStress);
132	>	fDecomp_->setUserCutoff(rCut_);
133	>	interactionMan_->setCutoffRadius(rCut_);
134
135	<	postCalculation();
136	<
135	>	map<string, CutoffMethod> stringToCutoffMethod;
136	>	stringToCutoffMethod["HARD"] = HARD;
137	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
138	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
139	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
140	>
141	>	if (simParams_->haveCutoffMethod()) {
142	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
143	>	map<string, CutoffMethod>::iterator i;
144	>	i = stringToCutoffMethod.find(cutMeth);
145	>	if (i == stringToCutoffMethod.end()) {
146	>	sprintf(painCave.errMsg,
147	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
148	>	"\tShould be one of: "
149	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
150	>	cutMeth.c_str());
151	>	painCave.isFatal = 1;
152	>	painCave.severity = OPENMD_ERROR;
153	>	simError();
154	>	} else {
155	>	cutoffMethod_ = i->second;
156	>	}
157	>	} else {
158	>	sprintf(painCave.errMsg,
159	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
160	>	"\tOpenMD will use SHIFTED_FORCE.\n");
161	>	painCave.isFatal = 0;
162	>	painCave.severity = OPENMD_INFO;
163	>	simError();
164	>	cutoffMethod_ = SHIFTED_FORCE;
165	>	}
166	>
167	>	map<string, CutoffPolicy> stringToCutoffPolicy;
168	>	stringToCutoffPolicy["MIX"] = MIX;
169	>	stringToCutoffPolicy["MAX"] = MAX;
170	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
171	>
172	>	std::string cutPolicy;
173	>	if (forceFieldOptions_.haveCutoffPolicy()){
174	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
175	>	}else if (simParams_->haveCutoffPolicy()) {
176	>	cutPolicy = simParams_->getCutoffPolicy();
177	>	}
178	>
179	>	if (!cutPolicy.empty()){
180	>	toUpper(cutPolicy);
181	>	map<string, CutoffPolicy>::iterator i;
182	>	i = stringToCutoffPolicy.find(cutPolicy);
183	>
184	>	if (i == stringToCutoffPolicy.end()) {
185	>	sprintf(painCave.errMsg,
186	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
187	>	"\tShould be one of: "
188	>	"MIX, MAX, or TRADITIONAL\n",
189	>	cutPolicy.c_str());
190	>	painCave.isFatal = 1;
191	>	painCave.severity = OPENMD_ERROR;
192	>	simError();
193	>	} else {
194	>	cutoffPolicy_ = i->second;
195	>	}
196	>	} else {
197	>	sprintf(painCave.errMsg,
198	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
199	>	"\tOpenMD will use TRADITIONAL.\n");
200	>	painCave.isFatal = 0;
201	>	painCave.severity = OPENMD_INFO;
202	>	simError();
203	>	cutoffPolicy_ = TRADITIONAL;
204	>	}
205	>	fDecomp_->setCutoffPolicy(cutoffPolicy_);
206		}
207
208	+	/**
209	+	* setupSwitching
210	+	*
211	+	* Sets the values of switchingRadius and
212	+	*  If the switchingRadius was explicitly set, use that value (but check it)
213	+	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
214	+	*/
215	+	void ForceManager::setupSwitching() {
216	+	Globals* simParams_ = info_->getSimParams();
217	+
218	+	// create the switching function object:
219	+	switcher_ = new SwitchingFunction();
220	+
221	+	if (simParams_->haveSwitchingRadius()) {
222	+	rSwitch_ = simParams_->getSwitchingRadius();
223	+	if (rSwitch_ > rCut_) {
224	+	sprintf(painCave.errMsg,
225	+	"ForceManager::setupSwitching: switchingRadius (%f) is larger "
226	+	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
227	+	painCave.isFatal = 1;
228	+	painCave.severity = OPENMD_ERROR;
229	+	simError();
230	+	}
231	+	} else {
232	+	rSwitch_ = 0.85 * rCut_;
233	+	sprintf(painCave.errMsg,
234	+	"ForceManager::setupSwitching: No value was set for the switchingRadius.\n"
235	+	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
236	+	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
237	+	painCave.isFatal = 0;
238	+	painCave.severity = OPENMD_WARNING;
239	+	simError();
240	+	}
241	+
242	+	// Default to cubic switching function.
243	+	sft_ = cubic;
244	+	if (simParams_->haveSwitchingFunctionType()) {
245	+	string funcType = simParams_->getSwitchingFunctionType();
246	+	toUpper(funcType);
247	+	if (funcType == "CUBIC") {
248	+	sft_ = cubic;
249	+	} else {
250	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
251	+	sft_ = fifth_order_poly;
252	+	} else {
253	+	// throw error
254	+	sprintf( painCave.errMsg,
255	+	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
256	+	"\tswitchingFunctionType must be one of: "
257	+	"\"cubic\" or \"fifth_order_polynomial\".",
258	+	funcType.c_str() );
259	+	painCave.isFatal = 1;
260	+	painCave.severity = OPENMD_ERROR;
261	+	simError();
262	+	}
263	+	}
264	+	}
265	+	switcher_->setSwitchType(sft_);
266	+	switcher_->setSwitch(rSwitch_, rCut_);
267	+	interactionMan_->setSwitchingRadius(rSwitch_);
268	+	}
269	+
270	+	void ForceManager::initialize() {
271	+
272	+	if (!info_->isTopologyDone()) {
273	+	info_->update();
274	+	interactionMan_->setSimInfo(info_);
275	+	interactionMan_->initialize();
276	+
277	+	// We want to delay the cutoffs until after the interaction
278	+	// manager has set up the atom-atom interactions so that we can
279	+	// query them for suggested cutoff values
280	+
281	+	setupCutoffs();
282	+	setupSwitching();
283	+
284	+	info_->prepareTopology();
285	+	}
286	+
287	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
288	+
289	+	// Force fields can set options on how to scale van der Waals and electrostatic
290	+	// interactions for atoms connected via bonds, bends and torsions
291	+	// in this case the topological distance between atoms is:
292	+	// 0 = topologically unconnected
293	+	// 1 = bonded together
294	+	// 2 = connected via a bend
295	+	// 3 = connected via a torsion
296	+
297	+	vdwScale_.reserve(4);
298	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
299	+
300	+	electrostaticScale_.reserve(4);
301	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
302	+
303	+	vdwScale_[0] = 1.0;
304	+	vdwScale_[1] = fopts.getvdw12scale();
305	+	vdwScale_[2] = fopts.getvdw13scale();
306	+	vdwScale_[3] = fopts.getvdw14scale();
307	+
308	+	electrostaticScale_[0] = 1.0;
309	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
310	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
311	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
312	+
313	+	fDecomp_->distributeInitialData();
314	+
315	+	initialized_ = true;
316	+
317	+	}
318	+
319	+	void ForceManager::calcForces() {
320	+
321	+	if (!initialized_) initialize();
322	+
323	+	preCalculation();
324	+	shortRangeInteractions();
325	+	longRangeInteractions();
326	+	postCalculation();
327	+	}
328	+
329		void ForceManager::preCalculation() {
330		SimInfo::MoleculeIterator mi;
331		Molecule* mol;
#	Line 78 | Line 333 | namespace oopse {
333		Atom* atom;
334		Molecule::RigidBodyIterator rbIter;
335		RigidBody* rb;
336	+	Molecule::CutoffGroupIterator ci;
337	+	CutoffGroup* cg;
338
339		// forces are zeroed here, before any are accumulated.
340	<	// NOTE: do not rezero the forces in Fortran.
341	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
340	>
341	>	for (mol = info_->beginMolecule(mi); mol != NULL;
342	>	mol = info_->nextMolecule(mi)) {
343		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
344		atom->zeroForcesAndTorques();
345		}
346	<
346	>
347		//change the positions of atoms which belong to the rigidbodies
348	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
348	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
349	>	rb = mol->nextRigidBody(rbIter)) {
350		rb->zeroForcesAndTorques();
351		}
352	+
353	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
354	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
355	+	cg = mol->nextCutoffGroup(ci)) {
356	+	//calculate the center of mass of cutoff group
357	+	cg->updateCOM();
358	+	}
359	+	}
360		}
361	+
362	+	// Zero out the stress tensor
363	+	tau *= 0.0;
364
365		}
366	<
367	<	void ForceManager::calcShortRangeInteraction() {
366	>
367	>	void ForceManager::shortRangeInteractions() {
368		Molecule* mol;
369		RigidBody* rb;
370		Bond* bond;
371		Bend* bend;
372		Torsion* torsion;
373	+	Inversion* inversion;
374		SimInfo::MoleculeIterator mi;
375		Molecule::RigidBodyIterator rbIter;
376		Molecule::BondIterator bondIter;;
377		Molecule::BendIterator  bendIter;
378		Molecule::TorsionIterator  torsionIter;
379	+	Molecule::InversionIterator  inversionIter;
380	+	RealType bondPotential = 0.0;
381	+	RealType bendPotential = 0.0;
382	+	RealType torsionPotential = 0.0;
383	+	RealType inversionPotential = 0.0;
384
385		//calculate short range interactions
386	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
386	>	for (mol = info_->beginMolecule(mi); mol != NULL;
387	>	mol = info_->nextMolecule(mi)) {
388
389		//change the positions of atoms which belong to the rigidbodies
390	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
391	<	rb->updateAtoms();
390	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
391	>	rb = mol->nextRigidBody(rbIter)) {
392	>	rb->updateAtoms();
393		}
394
395	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
396	<	bond->calcForce();
395	>	for (bond = mol->beginBond(bondIter); bond != NULL;
396	>	bond = mol->nextBond(bondIter)) {
397	>	bond->calcForce();
398	>	bondPotential += bond->getPotential();
399		}
400
401	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
402	<	bend->calcForce();
401	>	for (bend = mol->beginBend(bendIter); bend != NULL;
402	>	bend = mol->nextBend(bendIter)) {
403	>
404	>	RealType angle;
405	>	bend->calcForce(angle);
406	>	RealType currBendPot = bend->getPotential();
407	>
408	>	bendPotential += bend->getPotential();
409	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
410	>	if (i == bendDataSets.end()) {
411	>	BendDataSet dataSet;
412	>	dataSet.prev.angle = dataSet.curr.angle = angle;
413	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
414	>	dataSet.deltaV = 0.0;
415	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
416	>	}else {
417	>	i->second.prev.angle = i->second.curr.angle;
418	>	i->second.prev.potential = i->second.curr.potential;
419	>	i->second.curr.angle = angle;
420	>	i->second.curr.potential = currBendPot;
421	>	i->second.deltaV =  fabs(i->second.curr.potential -
422	>	i->second.prev.potential);
423	>	}
424		}
425	<
426	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
427	<	torsion->calcForce();
428	<	}
429	<
425	>
426	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
427	>	torsion = mol->nextTorsion(torsionIter)) {
428	>	RealType angle;
429	>	torsion->calcForce(angle);
430	>	RealType currTorsionPot = torsion->getPotential();
431	>	torsionPotential += torsion->getPotential();
432	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
433	>	if (i == torsionDataSets.end()) {
434	>	TorsionDataSet dataSet;
435	>	dataSet.prev.angle = dataSet.curr.angle = angle;
436	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
437	>	dataSet.deltaV = 0.0;
438	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
439	>	}else {
440	>	i->second.prev.angle = i->second.curr.angle;
441	>	i->second.prev.potential = i->second.curr.potential;
442	>	i->second.curr.angle = angle;
443	>	i->second.curr.potential = currTorsionPot;
444	>	i->second.deltaV =  fabs(i->second.curr.potential -
445	>	i->second.prev.potential);
446	>	}
447	>	}
448	>
449	>	for (inversion = mol->beginInversion(inversionIter);
450	>	inversion != NULL;
451	>	inversion = mol->nextInversion(inversionIter)) {
452	>	RealType angle;
453	>	inversion->calcForce(angle);
454	>	RealType currInversionPot = inversion->getPotential();
455	>	inversionPotential += inversion->getPotential();
456	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
457	>	if (i == inversionDataSets.end()) {
458	>	InversionDataSet dataSet;
459	>	dataSet.prev.angle = dataSet.curr.angle = angle;
460	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
461	>	dataSet.deltaV = 0.0;
462	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
463	>	}else {
464	>	i->second.prev.angle = i->second.curr.angle;
465	>	i->second.prev.potential = i->second.curr.potential;
466	>	i->second.curr.angle = angle;
467	>	i->second.curr.potential = currInversionPot;
468	>	i->second.deltaV =  fabs(i->second.curr.potential -
469	>	i->second.prev.potential);
470	>	}
471	>	}
472		}
473
474	<
475	<	double bondPotential = 0.0;
133	<	double bendPotential = 0.0;
134	<	double torsionPotential = 0.0;
135	<
136	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
137	<
138	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
139	<	bondPotential += bond->getPotential();
140	<	}
141	<
142	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
143	<	bendPotential += bend->getPotential();
144	<	}
145	<
146	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
147	<	torsionPotential += torsion->getPotential();
148	<	}
149	<
150	<	}
151	<
152	<	double  shortRangePotential = bondPotential + bendPotential + torsionPotential;
474	>	RealType  shortRangePotential = bondPotential + bendPotential +
475	>	torsionPotential +  inversionPotential;
476		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
477		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
478		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
479		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
480		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
481	<
481	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
482		}
483	+
484	+	void ForceManager::longRangeInteractions() {
485
486	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
487	<	Snapshot* curSnapshot;
488	<	DataStorage* config;
164	<	double* frc;
165	<	double* pos;
166	<	double* trq;
167	<	double* A;
168	<	double* electroFrame;
169	<	double* rc;
170	<
171	<	//get current snapshot from SimInfo
172	<	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
486	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
487	>	DataStorage* config = &(curSnapshot->atomData);
488	>	DataStorage* cgConfig = &(curSnapshot->cgData);
489
174	–	//get array pointers
175	–	config = &(curSnapshot->atomData);
176	–	frc = config->getArrayPointer(DataStorage::dslForce);
177	–	pos = config->getArrayPointer(DataStorage::dslPosition);
178	–	trq = config->getArrayPointer(DataStorage::dslTorque);
179	–	A   = config->getArrayPointer(DataStorage::dslAmat);
180	–	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
181	–
490		//calculate the center of mass of cutoff group
491	+
492		SimInfo::MoleculeIterator mi;
493		Molecule* mol;
494		Molecule::CutoffGroupIterator ci;
495		CutoffGroup* cg;
187	–	Vector3d com;
188	–	std::vector<Vector3d> rcGroup;
496
497	<	if(info_->getNCutoffGroups() > 0){
498	<
499	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
500	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
501	<	cg->getCOM(com);
502	<	rcGroup.push_back(com);
497	>	if(info_->getNCutoffGroups() > 0){
498	>	for (mol = info_->beginMolecule(mi); mol != NULL;
499	>	mol = info_->nextMolecule(mi)) {
500	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
501	>	cg = mol->nextCutoffGroup(ci)) {
502	>	cg->updateCOM();
503		}
504	<	}// end for (mol)
198	<
199	<	rc = rcGroup[0].getArrayPointer();
504	>	}
505		} else {
506	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
507	<	rc = pos;
506	>	// center of mass of the group is the same as position of the atom
507	>	// if cutoff group does not exist
508	>	cgConfig->position = config->position;
509		}
510	<
511	<	//initialize data before passing to fortran
512	<	double longRangePotential[LR_POT_TYPES];
207	<	double lrPot = 0.0;
510	>
511	>	fDecomp_->zeroWorkArrays();
512	>	fDecomp_->distributeData();
513
514	<	Mat3x3d tau;
515	<	short int passedCalcPot = needPotential;
516	<	short int passedCalcStress = needStress;
517	<	int isError = 0;
514	>	int cg1, cg2, atom1, atom2, topoDist;
515	>	Vector3d d_grp, dag, d;
516	>	RealType rgrpsq, rgrp, r2, r;
517	>	RealType electroMult, vdwMult;
518	>	RealType vij;
519	>	Vector3d fij, fg, f1;
520	>	tuple3<RealType, RealType, RealType> cuts;
521	>	RealType rCutSq;
522	>	bool in_switching_region;
523	>	RealType sw, dswdr, swderiv;
524	>	vector<int> atomListColumn, atomListRow, atomListLocal;
525	>	InteractionData idat;
526	>	SelfData sdat;
527	>	RealType mf;
528	>	RealType lrPot;
529	>	RealType vpair;
530	>	potVec longRangePotential(0.0);
531	>	potVec workPot(0.0);
532
533	<	for (int i=0; i<LR_POT_TYPES;i++){
534	<	longRangePotential[i]=0.0; //Initialize array
533	>	int loopStart, loopEnd;
534	>
535	>	idat.vdwMult = &vdwMult;
536	>	idat.electroMult = &electroMult;
537	>	idat.pot = &workPot;
538	>	sdat.pot = fDecomp_->getEmbeddingPotential();
539	>	idat.vpair = &vpair;
540	>	idat.f1 = &f1;
541	>	idat.sw = &sw;
542	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
543	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
544	>
545	>	loopEnd = PAIR_LOOP;
546	>	if (info_->requiresPrepair() ) {
547	>	loopStart = PREPAIR_LOOP;
548	>	} else {
549	>	loopStart = PAIR_LOOP;
550		}
551	+
552	+	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
553	+
554	+	if (iLoop == loopStart) {
555	+	bool update_nlist = fDecomp_->checkNeighborList();
556	+	if (update_nlist)
557	+	neighborList = fDecomp_->buildNeighborList();
558	+	}
559	+
560	+	for (vector<pair<int, int> >::iterator it = neighborList.begin();
561	+	it != neighborList.end(); ++it) {
562	+
563	+	cg1 = (*it).first;
564	+	cg2 = (*it).second;
565	+
566	+	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
567
568	+	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
569	+	curSnapshot->wrapVector(d_grp);
570	+	rgrpsq = d_grp.lengthSquare();
571
572	+	rCutSq = cuts.second;
573
574	<	doForceLoop( pos,
575	<	rc,
576	<	A,
577	<	electroFrame,
578	<	frc,
579	<	trq,
580	<	tau.getArrayPointer(),
581	<	longRangePotential,
582	<	&passedCalcPot,
583	<	&passedCalcStress,
584	<	&isError );
574	>	if (rgrpsq < rCutSq) {
575	>	idat.rcut = &cuts.first;
576	>	if (iLoop == PAIR_LOOP) {
577	>	vij *= 0.0;
578	>	fij = V3Zero;
579	>	}
580	>
581	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
582	>	rgrp);
583	>
584	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
585	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
586
587	<	if( isError ){
588	<	sprintf( painCave.errMsg,
589	<	"Error returned from the fortran force calculation.\n" );
590	<	painCave.isFatal = 1;
591	<	simError();
587	>	for (vector<int>::iterator ia = atomListRow.begin();
588	>	ia != atomListRow.end(); ++ia) {
589	>	atom1 = (*ia);
590	>
591	>	for (vector<int>::iterator jb = atomListColumn.begin();
592	>	jb != atomListColumn.end(); ++jb) {
593	>	atom2 = (*jb);
594	>
595	>	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
596	>	vpair = 0.0;
597	>	workPot = 0.0;
598	>	f1 = V3Zero;
599	>
600	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
601	>
602	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
603	>	vdwMult = vdwScale_[topoDist];
604	>	electroMult = electrostaticScale_[topoDist];
605	>
606	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
607	>	idat.d = &d_grp;
608	>	idat.r2 = &rgrpsq;
609	>	} else {
610	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
611	>	curSnapshot->wrapVector( d );
612	>	r2 = d.lengthSquare();
613	>	idat.d = &d;
614	>	idat.r2 = &r2;
615	>	}
616	>
617	>	r = sqrt( *(idat.r2) );
618	>	idat.rij = &r;
619	>
620	>	if (iLoop == PREPAIR_LOOP) {
621	>	interactionMan_->doPrePair(idat);
622	>	} else {
623	>	interactionMan_->doPair(idat);
624	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
625	>	vij += vpair;
626	>	fij += f1;
627	>	tau -= outProduct( *(idat.d), f1);
628	>	}
629	>	}
630	>	}
631	>	}
632	>
633	>	if (iLoop == PAIR_LOOP) {
634	>	if (in_switching_region) {
635	>	swderiv = vij * dswdr / rgrp;
636	>	fg = swderiv * d_grp;
637	>
638	>	fij += fg;
639	>
640	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
641	>	tau -= outProduct( *(idat.d), fg);
642	>	}
643	>
644	>	for (vector<int>::iterator ia = atomListRow.begin();
645	>	ia != atomListRow.end(); ++ia) {
646	>	atom1 = (*ia);
647	>	mf = fDecomp_->getMassFactorRow(atom1);
648	>	// fg is the force on atom ia due to cutoff group's
649	>	// presence in switching region
650	>	fg = swderiv * d_grp * mf;
651	>	fDecomp_->addForceToAtomRow(atom1, fg);
652	>
653	>	if (atomListRow.size() > 1) {
654	>	if (info_->usesAtomicVirial()) {
655	>	// find the distance between the atom
656	>	// and the center of the cutoff group:
657	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
658	>	tau -= outProduct(dag, fg);
659	>	}
660	>	}
661	>	}
662	>	for (vector<int>::iterator jb = atomListColumn.begin();
663	>	jb != atomListColumn.end(); ++jb) {
664	>	atom2 = (*jb);
665	>	mf = fDecomp_->getMassFactorColumn(atom2);
666	>	// fg is the force on atom jb due to cutoff group's
667	>	// presence in switching region
668	>	fg = -swderiv * d_grp * mf;
669	>	fDecomp_->addForceToAtomColumn(atom2, fg);
670	>
671	>	if (atomListColumn.size() > 1) {
672	>	if (info_->usesAtomicVirial()) {
673	>	// find the distance between the atom
674	>	// and the center of the cutoff group:
675	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
676	>	tau -= outProduct(dag, fg);
677	>	}
678	>	}
679	>	}
680	>	}
681	>	//if (!SIM_uses_AtomicVirial) {
682	>	//  tau -= outProduct(d_grp, fij);
683	>	//}
684	>	}
685	>	}
686	>	}
687	>
688	>	if (iLoop == PREPAIR_LOOP) {
689	>	if (info_->requiresPrepair()) {
690	>	fDecomp_->collectIntermediateData();
691	>
692	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
693	>	fDecomp_->fillSelfData(sdat, atom1);
694	>	interactionMan_->doPreForce(sdat);
695	>	}
696	>
697	>
698	>	fDecomp_->distributeIntermediateData();
699	>	}
700	>	}
701	>
702		}
703	<	for (int i=0; i<LR_POT_TYPES;i++){
704	<	lrPot += longRangePotential[i]; //Quick hack
703	>
704	>	fDecomp_->collectData();
705	>
706	>	if ( info_->requiresSkipCorrection() ) {
707	>
708	>	for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
709	>
710	>	vector<int> skipList = fDecomp_->getSkipsForAtom( atom1 );
711	>
712	>	for (vector<int>::iterator jb = skipList.begin();
713	>	jb != skipList.end(); ++jb) {
714	>
715	>	atom2 = (*jb);
716	>	fDecomp_->fillSkipData(idat, atom1, atom2);
717	>	interactionMan_->doSkipCorrection(idat);
718	>	fDecomp_->unpackSkipData(idat, atom1, atom2);
719	>
720	>	}
721	>	}
722		}
723	+
724	+	if (info_->requiresSelfCorrection()) {
725
726	+	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
727	+	fDecomp_->fillSelfData(sdat, atom1);
728	+	interactionMan_->doSelfCorrection(sdat);
729	+	}
730	+
731	+	}
732	+
733	+	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
734	+	*(fDecomp_->getPairwisePotential());
735	+
736	+	lrPot = longRangePotential.sum();
737	+
738		//store the tau and long range potential
739		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
740	<	//  curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
741	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
246	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
247	<
248	<	curSnapshot->statData.setTau(tau);
740	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
741	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
742		}
743
744	<
744	>
745		void ForceManager::postCalculation() {
746		SimInfo::MoleculeIterator mi;
747		Molecule* mol;
748		Molecule::RigidBodyIterator rbIter;
749		RigidBody* rb;
750	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
751
752		// collect the atomic forces onto rigid bodies
753	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
754	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
755	<	rb->calcForcesAndTorques();
753	>
754	>	for (mol = info_->beginMolecule(mi); mol != NULL;
755	>	mol = info_->nextMolecule(mi)) {
756	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
757	>	rb = mol->nextRigidBody(rbIter)) {
758	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
759	>	tau += rbTau;
760		}
761		}
762	<
762	>
763	>	#ifdef IS_MPI
764	>	Mat3x3d tmpTau(tau);
765	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
766	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
767	>	#endif
768	>	curSnapshot->statData.setTau(tau);
769		}
770
771	<	} //end namespace oopse
771	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 681 by tim, Mon Oct 17 23:13:44 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1584 by gezelter, Fri Jun 17 20:16:35 2011 UTC

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