[ViewVC] Diff of: OpenMD/branches/development/src/brains/ForceManager.cpp

Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1570 by gezelter, Thu May 26 21:56:04 2011 UTC vs.
Revision 1877 by gezelter, Thu Jun 6 15:43:35 2013 UTC

#	Line 35 \| Line 35
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).
38	>	* [3] Sun, Lin & Gezelter, J. Chem. Phys. 128, 234107 (2008).
39	>	* [4] Kuang & Gezelter, J. Chem. Phys. 133, 164101 (2010).
40	>	* [5] Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
44		* @file ForceManager.cpp
45		* @author tlin
46		* @date 11/09/2004
46	–	* @time 10:39am
47		* @version 1.0
48		*/
49
50	+
51		#include "brains/ForceManager.hpp"
52		#include "primitives/Molecule.hpp"
53		#define __OPENMD_C
#	Line 56 \| Line 57
57		#include "primitives/Torsion.hpp"
58		#include "primitives/Inversion.hpp"
59		#include "nonbonded/NonBondedInteraction.hpp"
60	+	#include "perturbations/ElectricField.hpp"
61		#include "parallel/ForceMatrixDecomposition.hpp"
62
63	+	#include <cstdio>
64	+	#include <iostream>
65	+	#include <iomanip>
66	+
67		using namespace std;
68		namespace OpenMD {
69
70	<	ForceManager::ForceManager(SimInfo * info) : info_(info) {
70	>	ForceManager::ForceManager(SimInfo * info) : info_(info), switcher_(NULL),
71	>	initialized_(false) {
72	>	forceField_ = info_->getForceField();
73	>	interactionMan_ = new InteractionManager();
74	>	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
75	>	thermo = new Thermo(info_);
76	>	}
77
78	<	#ifdef IS_MPI
79	<	fDecomp_ = new ForceMatrixDecomposition(info_);
80	<	#else
81	<	// fDecomp_ = new ForceSerialDecomposition(info);
82	<	#endif
78	>	ForceManager::~ForceManager() {
79	>	perturbations_.clear();
80	>
81	>	delete switcher_;
82	>	delete interactionMan_;
83	>	delete fDecomp_;
84	>	delete thermo;
85		}
86
87	<	void ForceManager::calcForces() {
87	>	/**
88	>	* setupCutoffs
89	>	*
90	>	* Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
91	>	* and cutoffPolicy
92	>	*
93	>	* cutoffRadius : realType
94	>	* If the cutoffRadius was explicitly set, use that value.
95	>	* If the cutoffRadius was not explicitly set:
96	>	* Are there electrostatic atoms? Use 12.0 Angstroms.
97	>	* No electrostatic atoms? Poll the atom types present in the
98	>	* simulation for suggested cutoff values (e.g. 2.5 * sigma).
99	>	* Use the maximum suggested value that was found.
100	>	*
101	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, TAYLOR_SHIFTED,
102	>	* or SHIFTED_POTENTIAL)
103	>	* If cutoffMethod was explicitly set, use that choice.
104	>	* If cutoffMethod was not explicitly set, use SHIFTED_FORCE
105	>	*
106	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
107	>	* If cutoffPolicy was explicitly set, use that choice.
108	>	* If cutoffPolicy was not explicitly set, use TRADITIONAL
109	>	*
110	>	* switchingRadius : realType
111	>	* If the cutoffMethod was set to SWITCHED:
112	>	* If the switchingRadius was explicitly set, use that value
113	>	* (but do a sanity check first).
114	>	* If the switchingRadius was not explicitly set: use 0.85 *
115	>	* cutoffRadius_
116	>	* If the cutoffMethod was not set to SWITCHED:
117	>	* Set switchingRadius equal to cutoffRadius for safety.
118	>	*/
119	>	void ForceManager::setupCutoffs() {
120
121	+	Globals* simParams_ = info_->getSimParams();
122	+	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
123	+	int mdFileVersion;
124	+	rCut_ = 0.0; //Needs a value for a later max() call;
125	+
126	+	if (simParams_->haveMDfileVersion())
127	+	mdFileVersion = simParams_->getMDfileVersion();
128	+	else
129	+	mdFileVersion = 0;
130	+
131	+	// We need the list of simulated atom types to figure out cutoffs
132	+	// as well as long range corrections.
133	+
134	+	set<AtomType*>::iterator i;
135	+	set<AtomType*> atomTypes_;
136	+	atomTypes_ = info_->getSimulatedAtomTypes();
137	+
138	+	if (simParams_->haveCutoffRadius()) {
139	+	rCut_ = simParams_->getCutoffRadius();
140	+	} else {
141	+	if (info_->usesElectrostaticAtoms()) {
142	+	sprintf(painCave.errMsg,
143	+	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
144	+	"\tOpenMD will use a default value of 12.0 angstroms"
145	+	"\tfor the cutoffRadius.\n");
146	+	painCave.isFatal = 0;
147	+	painCave.severity = OPENMD_INFO;
148	+	simError();
149	+	rCut_ = 12.0;
150	+	} else {
151	+	RealType thisCut;
152	+	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
153	+	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
154	+	rCut_ = max(thisCut, rCut_);
155	+	}
156	+	sprintf(painCave.errMsg,
157	+	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
158	+	"\tOpenMD will use %lf angstroms.\n",
159	+	rCut_);
160	+	painCave.isFatal = 0;
161	+	painCave.severity = OPENMD_INFO;
162	+	simError();
163	+	}
164	+	}
165	+
166	+	fDecomp_->setUserCutoff(rCut_);
167	+	interactionMan_->setCutoffRadius(rCut_);
168	+
169	+	map<string, CutoffMethod> stringToCutoffMethod;
170	+	stringToCutoffMethod["HARD"] = HARD;
171	+	stringToCutoffMethod["SWITCHED"] = SWITCHED;
172	+	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
173	+	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
174	+	stringToCutoffMethod["TAYLOR_SHIFTED"] = TAYLOR_SHIFTED;
175	+
176	+	if (simParams_->haveCutoffMethod()) {
177	+	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
178	+	map<string, CutoffMethod>::iterator i;
179	+	i = stringToCutoffMethod.find(cutMeth);
180	+	if (i == stringToCutoffMethod.end()) {
181	+	sprintf(painCave.errMsg,
182	+	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
183	+	"\tShould be one of: "
184	+	"HARD, SWITCHED, SHIFTED_POTENTIAL, TAYLOR_SHIFTED,\n"
185	+	"\tor SHIFTED_FORCE\n",
186	+	cutMeth.c_str());
187	+	painCave.isFatal = 1;
188	+	painCave.severity = OPENMD_ERROR;
189	+	simError();
190	+	} else {
191	+	cutoffMethod_ = i->second;
192	+	}
193	+	} else {
194	+	if (mdFileVersion > 1) {
195	+	sprintf(painCave.errMsg,
196	+	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
197	+	"\tOpenMD will use SHIFTED_FORCE.\n");
198	+	painCave.isFatal = 0;
199	+	painCave.severity = OPENMD_INFO;
200	+	simError();
201	+	cutoffMethod_ = SHIFTED_FORCE;
202	+	} else {
203	+	// handle the case where the old file version was in play
204	+	// (there should be no cutoffMethod, so we have to deduce it
205	+	// from other data).
206	+
207	+	sprintf(painCave.errMsg,
208	+	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
209	+	"\tOpenMD found a file which does not set a cutoffMethod.\n"
210	+	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
211	+	"\tbehavior of the older (version 1) code. To remove this\n"
212	+	"\twarning, add an explicit cutoffMethod and change the top\n"
213	+	"\tof the file so that it begins with <OpenMD version=2>\n");
214	+	painCave.isFatal = 0;
215	+	painCave.severity = OPENMD_WARNING;
216	+	simError();
217	+
218	+	// The old file version tethered the shifting behavior to the
219	+	// electrostaticSummationMethod keyword.
220	+
221	+	if (simParams_->haveElectrostaticSummationMethod()) {
222	+	string myMethod = simParams_->getElectrostaticSummationMethod();
223	+	toUpper(myMethod);
224	+
225	+	if (myMethod == "SHIFTED_POTENTIAL") {
226	+	cutoffMethod_ = SHIFTED_POTENTIAL;
227	+	} else if (myMethod == "SHIFTED_FORCE") {
228	+	cutoffMethod_ = SHIFTED_FORCE;
229	+	} else if (myMethod == "TAYLOR_SHIFTED") {
230	+	cutoffMethod_ = TAYLOR_SHIFTED;
231	+	}
232	+
233	+	if (simParams_->haveSwitchingRadius())
234	+	rSwitch_ = simParams_->getSwitchingRadius();
235	+
236	+	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE" \|\|
237	+	myMethod == "TAYLOR_SHIFTED") {
238	+	if (simParams_->haveSwitchingRadius()){
239	+	sprintf(painCave.errMsg,
240	+	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
241	+	"\tA value was set for the switchingRadius\n"
242	+	"\teven though the electrostaticSummationMethod was\n"
243	+	"\tset to %s\n", myMethod.c_str());
244	+	painCave.severity = OPENMD_WARNING;
245	+	painCave.isFatal = 1;
246	+	simError();
247	+	}
248	+	}
249	+	if (abs(rCut_ - rSwitch_) < 0.0001) {
250	+	if (cutoffMethod_ == SHIFTED_FORCE) {
251	+	sprintf(painCave.errMsg,
252	+	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
253	+	"\tcutoffRadius and switchingRadius are set to the\n"
254	+	"\tsame value. OpenMD will use shifted force\n"
255	+	"\tpotentials instead of switching functions.\n");
256	+	painCave.isFatal = 0;
257	+	painCave.severity = OPENMD_WARNING;
258	+	simError();
259	+	} else {
260	+	cutoffMethod_ = SHIFTED_POTENTIAL;
261	+	sprintf(painCave.errMsg,
262	+	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
263	+	"\tcutoffRadius and switchingRadius are set to the\n"
264	+	"\tsame value. OpenMD will use shifted potentials\n"
265	+	"\tinstead of switching functions.\n");
266	+	painCave.isFatal = 0;
267	+	painCave.severity = OPENMD_WARNING;
268	+	simError();
269	+	}
270	+	}
271	+	}
272	+	}
273	+	}
274	+
275	+	map<string, CutoffPolicy> stringToCutoffPolicy;
276	+	stringToCutoffPolicy["MIX"] = MIX;
277	+	stringToCutoffPolicy["MAX"] = MAX;
278	+	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
279	+
280	+	string cutPolicy;
281	+	if (forceFieldOptions_.haveCutoffPolicy()){
282	+	cutPolicy = forceFieldOptions_.getCutoffPolicy();
283	+	}else if (simParams_->haveCutoffPolicy()) {
284	+	cutPolicy = simParams_->getCutoffPolicy();
285	+	}
286	+
287	+	if (!cutPolicy.empty()){
288	+	toUpper(cutPolicy);
289	+	map<string, CutoffPolicy>::iterator i;
290	+	i = stringToCutoffPolicy.find(cutPolicy);
291	+
292	+	if (i == stringToCutoffPolicy.end()) {
293	+	sprintf(painCave.errMsg,
294	+	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
295	+	"\tShould be one of: "
296	+	"MIX, MAX, or TRADITIONAL\n",
297	+	cutPolicy.c_str());
298	+	painCave.isFatal = 1;
299	+	painCave.severity = OPENMD_ERROR;
300	+	simError();
301	+	} else {
302	+	cutoffPolicy_ = i->second;
303	+	}
304	+	} else {
305	+	sprintf(painCave.errMsg,
306	+	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
307	+	"\tOpenMD will use TRADITIONAL.\n");
308	+	painCave.isFatal = 0;
309	+	painCave.severity = OPENMD_INFO;
310	+	simError();
311	+	cutoffPolicy_ = TRADITIONAL;
312	+	}
313	+
314	+	fDecomp_->setCutoffPolicy(cutoffPolicy_);
315	+
316	+	// create the switching function object:
317	+
318	+	switcher_ = new SwitchingFunction();
319	+
320	+	if (cutoffMethod_ == SWITCHED) {
321	+	if (simParams_->haveSwitchingRadius()) {
322	+	rSwitch_ = simParams_->getSwitchingRadius();
323	+	if (rSwitch_ > rCut_) {
324	+	sprintf(painCave.errMsg,
325	+	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
326	+	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
327	+	painCave.isFatal = 1;
328	+	painCave.severity = OPENMD_ERROR;
329	+	simError();
330	+	}
331	+	} else {
332	+	rSwitch_ = 0.85 * rCut_;
333	+	sprintf(painCave.errMsg,
334	+	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
335	+	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
336	+	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
337	+	painCave.isFatal = 0;
338	+	painCave.severity = OPENMD_WARNING;
339	+	simError();
340	+	}
341	+	} else {
342	+	if (mdFileVersion > 1) {
343	+	// throw an error if we define a switching radius and don't need one.
344	+	// older file versions should not do this.
345	+	if (simParams_->haveSwitchingRadius()) {
346	+	map<string, CutoffMethod>::const_iterator it;
347	+	string theMeth;
348	+	for (it = stringToCutoffMethod.begin();
349	+	it != stringToCutoffMethod.end(); ++it) {
350	+	if (it->second == cutoffMethod_) {
351	+	theMeth = it->first;
352	+	break;
353	+	}
354	+	}
355	+	sprintf(painCave.errMsg,
356	+	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
357	+	"\tis not set to SWITCHED, so switchingRadius value\n"
358	+	"\twill be ignored for this simulation\n", theMeth.c_str());
359	+	painCave.isFatal = 0;
360	+	painCave.severity = OPENMD_WARNING;
361	+	simError();
362	+	}
363	+	}
364	+	rSwitch_ = rCut_;
365	+	}
366	+
367	+	// Default to cubic switching function.
368	+	sft_ = cubic;
369	+	if (simParams_->haveSwitchingFunctionType()) {
370	+	string funcType = simParams_->getSwitchingFunctionType();
371	+	toUpper(funcType);
372	+	if (funcType == "CUBIC") {
373	+	sft_ = cubic;
374	+	} else {
375	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
376	+	sft_ = fifth_order_poly;
377	+	} else {
378	+	// throw error
379	+	sprintf( painCave.errMsg,
380	+	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
381	+	"\tswitchingFunctionType must be one of: "
382	+	"\"cubic\" or \"fifth_order_polynomial\".",
383	+	funcType.c_str() );
384	+	painCave.isFatal = 1;
385	+	painCave.severity = OPENMD_ERROR;
386	+	simError();
387	+	}
388	+	}
389	+	}
390	+	switcher_->setSwitchType(sft_);
391	+	switcher_->setSwitch(rSwitch_, rCut_);
392	+	}
393	+
394	+
395	+
396	+
397	+	void ForceManager::initialize() {
398	+
399		if (!info_->isTopologyDone()) {
400	+
401		info_->update();
402		interactionMan_->setSimInfo(info_);
403		interactionMan_->initialize();
404	<	swfun_ = interactionMan_->getSwitchingFunction();
405	<	fDecomp_->distributeInitialData();
406	<	info_->prepareTopology();
404	>
405	>	// We want to delay the cutoffs until after the interaction
406	>	// manager has set up the atom-atom interactions so that we can
407	>	// query them for suggested cutoff values
408	>	setupCutoffs();
409	>
410	>	info_->prepareTopology();
411	>
412	>	doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
413	>	doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
414	>	if (doHeatFlux_) doParticlePot_ = true;
415	>
416	>	doElectricField_ = info_->getSimParams()->getOutputElectricField();
417	>
418		}
419	+
420	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
421
422	+	// Force fields can set options on how to scale van der Waals and
423	+	// electrostatic interactions for atoms connected via bonds, bends
424	+	// and torsions in this case the topological distance between
425	+	// atoms is:
426	+	// 0 = topologically unconnected
427	+	// 1 = bonded together
428	+	// 2 = connected via a bend
429	+	// 3 = connected via a torsion
430	+
431	+	vdwScale_.reserve(4);
432	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
433	+
434	+	electrostaticScale_.reserve(4);
435	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
436	+
437	+	vdwScale_[0] = 1.0;
438	+	vdwScale_[1] = fopts.getvdw12scale();
439	+	vdwScale_[2] = fopts.getvdw13scale();
440	+	vdwScale_[3] = fopts.getvdw14scale();
441	+
442	+	electrostaticScale_[0] = 1.0;
443	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
444	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
445	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
446	+
447	+	if (info_->getSimParams()->haveElectricField()) {
448	+	ElectricField* eField = new ElectricField(info_);
449	+	perturbations_.push_back(eField);
450	+	}
451	+
452	+	usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
453	+
454	+	fDecomp_->distributeInitialData();
455	+
456	+	initialized_ = true;
457	+
458	+	}
459	+
460	+	void ForceManager::calcForces() {
461	+
462	+	if (!initialized_) initialize();
463	+
464		preCalculation();
465		shortRangeInteractions();
466		longRangeInteractions();
467	<	postCalculation();
88	<
467	>	postCalculation();
468		}
469
470		void ForceManager::preCalculation() {
#	Line 98 \| Line 477 \| namespace OpenMD {
477		Molecule::CutoffGroupIterator ci;
478		CutoffGroup* cg;
479
480	<	// forces are zeroed here, before any are accumulated.
480	>	// forces and potentials are zeroed here, before any are
481	>	// accumulated.
482
483	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
484	+
485	+	snap->setBondPotential(0.0);
486	+	snap->setBendPotential(0.0);
487	+	snap->setTorsionPotential(0.0);
488	+	snap->setInversionPotential(0.0);
489	+
490	+	potVec zeroPot(0.0);
491	+	snap->setLongRangePotential(zeroPot);
492	+	snap->setExcludedPotentials(zeroPot);
493	+
494	+	snap->setRestraintPotential(0.0);
495	+	snap->setRawPotential(0.0);
496	+
497		for (mol = info_->beginMolecule(mi); mol != NULL;
498		mol = info_->nextMolecule(mi)) {
499	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
499	>	for(atom = mol->beginAtom(ai); atom != NULL;
500	>	atom = mol->nextAtom(ai)) {
501		atom->zeroForcesAndTorques();
502		}
503	<
503	>
504		//change the positions of atoms which belong to the rigidbodies
505		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
506		rb = mol->nextRigidBody(rbIter)) {
507		rb->zeroForcesAndTorques();
508		}
509	<
509	>
510		if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
511		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
512		cg = mol->nextCutoffGroup(ci)) {
#	Line 120 \| Line 515 \| namespace OpenMD {
515		}
516		}
517		}
123	–
124	–	// Zero out the stress tensor
125	–	tau *= 0.0;
518
519	+	// Zero out the stress tensor
520	+	stressTensor *= 0.0;
521	+	// Zero out the heatFlux
522	+	fDecomp_->setHeatFlux( Vector3d(0.0) );
523		}
524
525		void ForceManager::shortRangeInteractions() {
#	Line 156 \| Line 552 \| namespace OpenMD {
552
553		for (bond = mol->beginBond(bondIter); bond != NULL;
554		bond = mol->nextBond(bondIter)) {
555	<	bond->calcForce();
555	>	bond->calcForce(doParticlePot_);
556		bondPotential += bond->getPotential();
557		}
558
#	Line 164 \| Line 560 \| namespace OpenMD {
560		bend = mol->nextBend(bendIter)) {
561
562		RealType angle;
563	<	bend->calcForce(angle);
563	>	bend->calcForce(angle, doParticlePot_);
564		RealType currBendPot = bend->getPotential();
565
566		bendPotential += bend->getPotential();
#	Line 174 \| Line 570 \| namespace OpenMD {
570		dataSet.prev.angle = dataSet.curr.angle = angle;
571		dataSet.prev.potential = dataSet.curr.potential = currBendPot;
572		dataSet.deltaV = 0.0;
573	<	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
573	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
574	>	dataSet));
575		}else {
576		i->second.prev.angle = i->second.curr.angle;
577		i->second.prev.potential = i->second.curr.potential;
#	Line 188 \| Line 585 \| namespace OpenMD {
585		for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
586		torsion = mol->nextTorsion(torsionIter)) {
587		RealType angle;
588	<	torsion->calcForce(angle);
588	>	torsion->calcForce(angle, doParticlePot_);
589		RealType currTorsionPot = torsion->getPotential();
590		torsionPotential += torsion->getPotential();
591		map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
#	Line 212 \| Line 609 \| namespace OpenMD {
609		inversion != NULL;
610		inversion = mol->nextInversion(inversionIter)) {
611		RealType angle;
612	<	inversion->calcForce(angle);
612	>	inversion->calcForce(angle, doParticlePot_);
613		RealType currInversionPot = inversion->getPotential();
614		inversionPotential += inversion->getPotential();
615		map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
#	Line 232 \| Line 629 \| namespace OpenMD {
629		}
630		}
631		}
632	<
633	<	RealType shortRangePotential = bondPotential + bendPotential +
634	<	torsionPotential + inversionPotential;
632	>
633	>	#ifdef IS_MPI
634	>	// Collect from all nodes. This should eventually be moved into a
635	>	// SystemDecomposition, but this is a better place than in
636	>	// Thermo to do the collection.
637	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
638	>	MPI::SUM);
639	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
640	>	MPI::SUM);
641	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
642	>	MPI::REALTYPE, MPI::SUM);
643	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
644	>	MPI::REALTYPE, MPI::SUM);
645	>	#endif
646	>
647		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
648	<	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
649	<	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
650	<	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
651	<	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
652	<	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
648	>
649	>	curSnapshot->setBondPotential(bondPotential);
650	>	curSnapshot->setBendPotential(bendPotential);
651	>	curSnapshot->setTorsionPotential(torsionPotential);
652	>	curSnapshot->setInversionPotential(inversionPotential);
653	>
654	>	// RealType shortRangePotential = bondPotential + bendPotential +
655	>	// torsionPotential + inversionPotential;
656	>
657	>	// curSnapshot->setShortRangePotential(shortRangePotential);
658		}
659
660		void ForceManager::longRangeInteractions() {
661
248	–	// some of this initial stuff will go away:
662		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
663		DataStorage* config = &(curSnapshot->atomData);
664		DataStorage* cgConfig = &(curSnapshot->cgData);
252	–	RealType* frc = config->getArrayPointer(DataStorage::dslForce);
253	–	RealType* pos = config->getArrayPointer(DataStorage::dslPosition);
254	–	RealType* trq = config->getArrayPointer(DataStorage::dslTorque);
255	–	RealType* A = config->getArrayPointer(DataStorage::dslAmat);
256	–	RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
257	–	RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
258	–	RealType* rc;
665
666	<	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
667	<	rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
666	>	//calculate the center of mass of cutoff group
667	>
668	>	SimInfo::MoleculeIterator mi;
669	>	Molecule* mol;
670	>	Molecule::CutoffGroupIterator ci;
671	>	CutoffGroup* cg;
672	>
673	>	if(info_->getNCutoffGroups() > 0){
674	>	for (mol = info_->beginMolecule(mi); mol != NULL;
675	>	mol = info_->nextMolecule(mi)) {
676	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
677	>	cg = mol->nextCutoffGroup(ci)) {
678	>	cg->updateCOM();
679	>	}
680	>	}
681		} else {
682		// center of mass of the group is the same as position of the atom
683		// if cutoff group does not exist
684	<	rc = pos;
685	<	}
267	<
268	<	//initialize data before passing to fortran
269	<	RealType longRangePotential[N_INTERACTION_FAMILIES];
270	<	RealType lrPot = 0.0;
271	<	int isError = 0;
272	<
273	<	// dangerous to iterate over enums, but we'll live on the edge:
274	<	for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
275	<	longRangePotential[i]=0.0; //Initialize array
684	>	cgConfig->position = config->position;
685	>	cgConfig->velocity = config->velocity;
686		}
687
688	<	// new stuff starts here:
279	<
688	>	fDecomp_->zeroWorkArrays();
689		fDecomp_->distributeData();
690	<
691	<	int cg1, cg2, atom1, atom2;
692	<	Vector3d d_grp, dag;
693	<	RealType rgrpsq, rgrp;
690	>
691	>	int cg1, cg2, atom1, atom2, topoDist;
692	>	Vector3d d_grp, dag, d, gvel2, vel2;
693	>	RealType rgrpsq, rgrp, r2, r;
694	>	RealType electroMult, vdwMult;
695		RealType vij;
696	<	Vector3d fij, fg;
697	<	pair<int, int> gtypes;
696	>	Vector3d fij, fg, f1;
697	>	tuple3<RealType, RealType, RealType> cuts;
698		RealType rCutSq;
699		bool in_switching_region;
700		RealType sw, dswdr, swderiv;
701	<	vector<int> atomListColumn, atomListRow, atomListLocal;
701	>	vector<int> atomListColumn, atomListRow;
702		InteractionData idat;
703		SelfData sdat;
704		RealType mf;
705	+	RealType vpair;
706	+	RealType dVdFQ1(0.0);
707	+	RealType dVdFQ2(0.0);
708	+	potVec longRangePotential(0.0);
709	+	potVec workPot(0.0);
710	+	potVec exPot(0.0);
711	+	Vector3d eField1(0.0);
712	+	Vector3d eField2(0.0);
713	+	vector<int>::iterator ia, jb;
714
715		int loopStart, loopEnd;
716
717	+	idat.vdwMult = &vdwMult;
718	+	idat.electroMult = &electroMult;
719	+	idat.pot = &workPot;
720	+	idat.excludedPot = &exPot;
721	+	sdat.pot = fDecomp_->getEmbeddingPotential();
722	+	sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
723	+	idat.vpair = &vpair;
724	+	idat.dVdFQ1 = &dVdFQ1;
725	+	idat.dVdFQ2 = &dVdFQ2;
726	+	idat.eField1 = &eField1;
727	+	idat.eField2 = &eField2;
728	+	idat.f1 = &f1;
729	+	idat.sw = &sw;
730	+	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
731	+	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE \|\| cutoffMethod_ == TAYLOR_SHIFTED) ? true : false;
732	+	idat.doParticlePot = doParticlePot_;
733	+	idat.doElectricField = doElectricField_;
734	+	sdat.doParticlePot = doParticlePot_;
735	+
736		loopEnd = PAIR_LOOP;
737		if (info_->requiresPrepair() ) {
738		loopStart = PREPAIR_LOOP;
739		} else {
740		loopStart = PAIR_LOOP;
741		}
742	<
743	<	for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
306	<
742	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
743	>
744		if (iLoop == loopStart) {
745		bool update_nlist = fDecomp_->checkNeighborList();
746	<	if (update_nlist)
746	>	if (update_nlist) {
747	>	if (!usePeriodicBoundaryConditions_)
748	>	Mat3x3d bbox = thermo->getBoundingBox();
749		neighborList = fDecomp_->buildNeighborList();
750	+	}
751		}
752
753		for (vector<pair<int, int> >::iterator it = neighborList.begin();
754		it != neighborList.end(); ++it) {
755	<
755	>
756		cg1 = (*it).first;
757		cg2 = (*it).second;
758	+
759	+	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
760
319	–	gtypes = fDecomp_->getGroupTypes(cg1, cg2);
761		d_grp = fDecomp_->getIntergroupVector(cg1, cg2);
762	+
763		curSnapshot->wrapVector(d_grp);
764		rgrpsq = d_grp.lengthSquare();
765	<	rCutSq = groupCutoffMap[gtypes].first;
765	>	rCutSq = cuts.second;
766
767		if (rgrpsq < rCutSq) {
768	<	*(idat.rcut) = groupCutoffMap[gtypes].second;
768	>	idat.rcut = &cuts.first;
769		if (iLoop == PAIR_LOOP) {
770	<	vij *= 0.0;
771	<	fij = V3Zero;
770	>	vij = 0.0;
771	>	fij.zero();
772	>	eField1.zero();
773	>	eField2.zero();
774		}
775
776	<	in_switching_region = swfun_->getSwitch(rgrpsq, *(idat.sw), dswdr,
777	<	rgrp);
776	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
777	>	rgrp);
778	>
779		atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
780		atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
781
782	<	for (vector<int>::iterator ia = atomListRow.begin();
782	>	if (doHeatFlux_)
783	>	gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
784	>
785	>	for (ia = atomListRow.begin();
786		ia != atomListRow.end(); ++ia) {
787		atom1 = (*ia);
788	<
789	<	for (vector<int>::iterator jb = atomListColumn.begin();
788	>
789	>	for (jb = atomListColumn.begin();
790		jb != atomListColumn.end(); ++jb) {
791		atom2 = (*jb);
344	–
345	–	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
346	–
347	–	idat = fDecomp_->fillInteractionData(atom1, atom2);
792
793	+	if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
794	+
795	+	vpair = 0.0;
796	+	workPot = 0.0;
797	+	exPot = 0.0;
798	+	f1.zero();
799	+	dVdFQ1 = 0.0;
800	+	dVdFQ2 = 0.0;
801	+
802	+	fDecomp_->fillInteractionData(idat, atom1, atom2);
803	+
804	+	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
805	+	vdwMult = vdwScale_[topoDist];
806	+	electroMult = electrostaticScale_[topoDist];
807	+
808		if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
809	<	*(idat.d) = d_grp;
810	<	*(idat.r2) = rgrpsq;
809	>	idat.d = &d_grp;
810	>	idat.r2 = &rgrpsq;
811	>	if (doHeatFlux_)
812	>	vel2 = gvel2;
813		} else {
814	<	*(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2);
815	<	curSnapshot->wrapVector( *(idat.d) );
816	<	*(idat.r2) = idat.d->lengthSquare();
814	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
815	>	curSnapshot->wrapVector( d );
816	>	r2 = d.lengthSquare();
817	>	idat.d = &d;
818	>	idat.r2 = &r2;
819	>	if (doHeatFlux_)
820	>	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
821		}
357	–
358	–	(idat.rij) = sqrt( (idat.r2) );
822
823	+	r = sqrt( *(idat.r2) );
824	+	idat.rij = &r;
825	+
826		if (iLoop == PREPAIR_LOOP) {
827		interactionMan_->doPrePair(idat);
828		} else {
829		interactionMan_->doPair(idat);
830	<	vij += *(idat.vpair);
831	<	fij += *(idat.f1);
832	<	tau -= outProduct( (idat.d), (idat.f1));
830	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
831	>	vij += vpair;
832	>	fij += f1;
833	>	stressTensor -= outProduct( *(idat.d), f1);
834	>	if (doHeatFlux_)
835	>	fDecomp_->addToHeatFlux((idat.d) dot(f1, vel2));
836		}
837		}
838		}
#	Line 373 \| Line 842 \| namespace OpenMD {
842		if (in_switching_region) {
843		swderiv = vij * dswdr / rgrp;
844		fg = swderiv * d_grp;
376	–
845		fij += fg;
846
847		if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
848	<	tau -= outProduct( *(idat.d), fg);
848	>	if (!fDecomp_->skipAtomPair(atomListRow[0],
849	>	atomListColumn[0],
850	>	cg1, cg2)) {
851	>	stressTensor -= outProduct( *(idat.d), fg);
852	>	if (doHeatFlux_)
853	>	fDecomp_->addToHeatFlux((idat.d) dot(fg, vel2));
854	>	}
855		}
856
857	<	for (vector<int>::iterator ia = atomListRow.begin();
857	>	for (ia = atomListRow.begin();
858		ia != atomListRow.end(); ++ia) {
859		atom1 = (*ia);
860		mf = fDecomp_->getMassFactorRow(atom1);
#	Line 388 \| Line 862 \| namespace OpenMD {
862		// presence in switching region
863		fg = swderiv * d_grp * mf;
864		fDecomp_->addForceToAtomRow(atom1, fg);
391	–
865		if (atomListRow.size() > 1) {
866		if (info_->usesAtomicVirial()) {
867		// find the distance between the atom
868		// and the center of the cutoff group:
869		dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
870	<	tau -= outProduct(dag, fg);
870	>	stressTensor -= outProduct(dag, fg);
871	>	if (doHeatFlux_)
872	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
873		}
874		}
875		}
876	<	for (vector<int>::iterator jb = atomListColumn.begin();
876	>	for (jb = atomListColumn.begin();
877		jb != atomListColumn.end(); ++jb) {
878		atom2 = (*jb);
879		mf = fDecomp_->getMassFactorColumn(atom2);
#	Line 412 \| Line 887 \| namespace OpenMD {
887		// find the distance between the atom
888		// and the center of the cutoff group:
889		dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
890	<	tau -= outProduct(dag, fg);
890	>	stressTensor -= outProduct(dag, fg);
891	>	if (doHeatFlux_)
892	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
893		}
894		}
895		}
896		}
897	<	//if (!SIM_uses_AtomicVirial) {
898	<	// tau -= outProduct(d_grp, fij);
897	>	//if (!info_->usesAtomicVirial()) {
898	>	// stressTensor -= outProduct(d_grp, fij);
899	>	// if (doHeatFlux_)
900	>	// fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
901		//}
902		}
903		}
904		}
905
906		if (iLoop == PREPAIR_LOOP) {
907	<	if (info_->requiresPrepair()) {
907	>	if (info_->requiresPrepair()) {
908	>
909		fDecomp_->collectIntermediateData();
910
911	<	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
912	<	sdat = fDecomp_->fillSelfData(atom1);
911	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
912	>	fDecomp_->fillSelfData(sdat, atom1);
913		interactionMan_->doPreForce(sdat);
914		}
915
916	<	fDecomp_->distributeIntermediateData();
916	>	fDecomp_->distributeIntermediateData();
917	>
918		}
919		}
439	–
920		}
921
922	+	// collects pairwise information
923		fDecomp_->collectData();
443	–
444	–	if ( info_->requiresSkipCorrection() ) {
445	–
446	–	for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
447	–
448	–	vector<int> skipList = fDecomp_->getSkipsForRowAtom( atom1 );
924
450	–	for (vector<int>::iterator jb = skipList.begin();
451	–	jb != skipList.end(); ++jb) {
452	–
453	–	atom2 = (*jb);
454	–	idat = fDecomp_->fillSkipData(atom1, atom2);
455	–	interactionMan_->doSkipCorrection(idat);
456	–
457	–	}
458	–	}
459	–	}
460	–
925		if (info_->requiresSelfCorrection()) {
926	<
927	<	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
464	<	sdat = fDecomp_->fillSelfData(atom1);
926	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
927	>	fDecomp_->fillSelfData(sdat, atom1);
928		interactionMan_->doSelfCorrection(sdat);
929		}
467	–
930		}
931
932	<	// dangerous to iterate over enums, but we'll live on the edge:
933	<	for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
934	<	lrPot += longRangePotential[i]; //Quick hack
935	<	}
936	<
937	<	//store the tau and long range potential
938	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
939	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
940	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
932	>	// collects single-atom information
933	>	fDecomp_->collectSelfData();
934	>
935	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
936	>	*(fDecomp_->getPairwisePotential());
937	>
938	>	curSnapshot->setLongRangePotential(longRangePotential);
939	>
940	>	curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
941	>	*(fDecomp_->getExcludedPotential()));
942	>
943		}
944
945
946		void ForceManager::postCalculation() {
947	+
948	+	vector<Perturbation*>::iterator pi;
949	+	for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
950	+	(*pi)->applyPerturbation();
951	+	}
952	+
953		SimInfo::MoleculeIterator mi;
954		Molecule* mol;
955		Molecule::RigidBodyIterator rbIter;
956		RigidBody* rb;
957		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
958	<
958	>
959		// collect the atomic forces onto rigid bodies
960
961		for (mol = info_->beginMolecule(mi); mol != NULL;
#	Line 493 \| Line 963 \| namespace OpenMD {
963		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
964		rb = mol->nextRigidBody(rbIter)) {
965		Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
966	<	tau += rbTau;
966	>	stressTensor += rbTau;
967		}
968		}
969
970		#ifdef IS_MPI
971	<	Mat3x3d tmpTau(tau);
972	<	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
503	<	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
971	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
972	>	MPI::REALTYPE, MPI::SUM);
973		#endif
974	<	curSnapshot->statData.setTau(tau);
975	<	}
974	>	curSnapshot->setStressTensor(stressTensor);
975	>
976	>	if (info_->getSimParams()->getUseLongRangeCorrections()) {
977	>	/*
978	>	RealType vol = curSnapshot->getVolume();
979	>	RealType Elrc(0.0);
980	>	RealType Wlrc(0.0);
981
982	<	} //end namespace OpenMD
982	>	set<AtomType*>::iterator i;
983	>	set<AtomType*>::iterator j;
984	>
985	>	RealType n_i, n_j;
986	>	RealType rho_i, rho_j;
987	>	pair<RealType, RealType> LRI;
988	>
989	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
990	>	n_i = RealType(info_->getGlobalCountOfType(*i));
991	>	rho_i = n_i / vol;
992	>	for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
993	>	n_j = RealType(info_->getGlobalCountOfType(*j));
994	>	rho_j = n_j / vol;
995	>
996	>	LRI = interactionMan_->getLongRangeIntegrals( (i), (j) );
997	>
998	>	Elrc += n_i * rho_j * LRI.first;
999	>	Wlrc -= rho_i * rho_j * LRI.second;
1000	>	}
1001	>	}
1002	>	Elrc = 2.0 NumericConstant::PI;
1003	>	Wlrc = 2.0 NumericConstant::PI;
1004	>
1005	>	RealType lrp = curSnapshot->getLongRangePotential();
1006	>	curSnapshot->setLongRangePotential(lrp + Elrc);
1007	>	stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
1008	>	curSnapshot->setStressTensor(stressTensor);
1009	>	*/
1010	>
1011	>	}
1012	>	}
1013	>	}

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Comparing branches/development/src/brains/ForceManager.cpp (file contents): Revision 1570 by gezelter, Thu May 26 21:56:04 2011 UTC vs. Revision 1877 by gezelter, Thu Jun 6 15:43:35 2013 UTC

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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1570 by gezelter, Thu May 26 21:56:04 2011 UTC vs.
Revision 1877 by gezelter, Thu Jun 6 15:43:35 2013 UTC