[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 1868 by gezelter, Tue Apr 30 15:56:54 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	>	forceField_ = info_->getForceField();
72	>	interactionMan_ = new InteractionManager();
73	>	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
74	>	thermo = new Thermo(info_);
75	>	}
76
77	<	#ifdef IS_MPI
78	<	fDecomp_ = new ForceMatrixDecomposition(info_);
79	<	#else
80	<	// fDecomp_ = new ForceSerialDecomposition(info);
81	<	#endif
77	>	ForceManager::~ForceManager() {
78	>	perturbations_.clear();
79	>
80	>	delete switcher_;
81	>	delete interactionMan_;
82	>	delete fDecomp_;
83	>	delete thermo;
84		}
85
86	<	void ForceManager::calcForces() {
86	>	/**
87	>	* setupCutoffs
88	>	*
89	>	* Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
90	>	* and cutoffPolicy
91	>	*
92	>	* cutoffRadius : realType
93	>	* If the cutoffRadius was explicitly set, use that value.
94	>	* If the cutoffRadius was not explicitly set:
95	>	* Are there electrostatic atoms? Use 12.0 Angstroms.
96	>	* No electrostatic atoms? Poll the atom types present in the
97	>	* simulation for suggested cutoff values (e.g. 2.5 * sigma).
98	>	* Use the maximum suggested value that was found.
99	>	*
100	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
101	>	* or SHIFTED_POTENTIAL)
102	>	* If cutoffMethod was explicitly set, use that choice.
103	>	* If cutoffMethod was not explicitly set, use SHIFTED_FORCE
104	>	*
105	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
106	>	* If cutoffPolicy was explicitly set, use that choice.
107	>	* If cutoffPolicy was not explicitly set, use TRADITIONAL
108	>	*
109	>	* switchingRadius : realType
110	>	* If the cutoffMethod was set to SWITCHED:
111	>	* If the switchingRadius was explicitly set, use that value
112	>	* (but do a sanity check first).
113	>	* If the switchingRadius was not explicitly set: use 0.85 *
114	>	* cutoffRadius_
115	>	* If the cutoffMethod was not set to SWITCHED:
116	>	* Set switchingRadius equal to cutoffRadius for safety.
117	>	*/
118	>	void ForceManager::setupCutoffs() {
119	>
120	>	Globals* simParams_ = info_->getSimParams();
121	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
122	>	int mdFileVersion;
123	>	rCut_ = 0.0; //Needs a value for a later max() call;
124	>
125	>	if (simParams_->haveMDfileVersion())
126	>	mdFileVersion = simParams_->getMDfileVersion();
127	>	else
128	>	mdFileVersion = 0;
129	>
130	>	// We need the list of simulated atom types to figure out cutoffs
131	>	// as well as long range corrections.
132	>
133	>	set<AtomType*>::iterator i;
134	>	set<AtomType*> atomTypes_;
135	>	atomTypes_ = info_->getSimulatedAtomTypes();
136	>
137	>	if (simParams_->haveCutoffRadius()) {
138	>	rCut_ = simParams_->getCutoffRadius();
139	>	} else {
140	>	if (info_->usesElectrostaticAtoms()) {
141	>	sprintf(painCave.errMsg,
142	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
143	>	"\tOpenMD will use a default value of 12.0 angstroms"
144	>	"\tfor the cutoffRadius.\n");
145	>	painCave.isFatal = 0;
146	>	painCave.severity = OPENMD_INFO;
147	>	simError();
148	>	rCut_ = 12.0;
149	>	} else {
150	>	RealType thisCut;
151	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
152	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
153	>	rCut_ = max(thisCut, rCut_);
154	>	}
155	>	sprintf(painCave.errMsg,
156	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
157	>	"\tOpenMD will use %lf angstroms.\n",
158	>	rCut_);
159	>	painCave.isFatal = 0;
160	>	painCave.severity = OPENMD_INFO;
161	>	simError();
162	>	}
163	>	}
164	>
165	>	fDecomp_->setUserCutoff(rCut_);
166	>	interactionMan_->setCutoffRadius(rCut_);
167	>
168	>	map<string, CutoffMethod> stringToCutoffMethod;
169	>	stringToCutoffMethod["HARD"] = HARD;
170	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
171	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
172	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
173	>
174	>	if (simParams_->haveCutoffMethod()) {
175	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
176	>	map<string, CutoffMethod>::iterator i;
177	>	i = stringToCutoffMethod.find(cutMeth);
178	>	if (i == stringToCutoffMethod.end()) {
179	>	sprintf(painCave.errMsg,
180	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
181	>	"\tShould be one of: "
182	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
183	>	cutMeth.c_str());
184	>	painCave.isFatal = 1;
185	>	painCave.severity = OPENMD_ERROR;
186	>	simError();
187	>	} else {
188	>	cutoffMethod_ = i->second;
189	>	}
190	>	} else {
191	>	if (mdFileVersion > 1) {
192	>	sprintf(painCave.errMsg,
193	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
194	>	"\tOpenMD will use SHIFTED_FORCE.\n");
195	>	painCave.isFatal = 0;
196	>	painCave.severity = OPENMD_INFO;
197	>	simError();
198	>	cutoffMethod_ = SHIFTED_FORCE;
199	>	} else {
200	>	// handle the case where the old file version was in play
201	>	// (there should be no cutoffMethod, so we have to deduce it
202	>	// from other data).
203	>
204	>	sprintf(painCave.errMsg,
205	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
206	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
207	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
208	>	"\tbehavior of the older (version 1) code. To remove this\n"
209	>	"\twarning, add an explicit cutoffMethod and change the top\n"
210	>	"\tof the file so that it begins with <OpenMD version=2>\n");
211	>	painCave.isFatal = 0;
212	>	painCave.severity = OPENMD_WARNING;
213	>	simError();
214	>
215	>	// The old file version tethered the shifting behavior to the
216	>	// electrostaticSummationMethod keyword.
217	>
218	>	if (simParams_->haveElectrostaticSummationMethod()) {
219	>	string myMethod = simParams_->getElectrostaticSummationMethod();
220	>	toUpper(myMethod);
221	>
222	>	if (myMethod == "SHIFTED_POTENTIAL") {
223	>	cutoffMethod_ = SHIFTED_POTENTIAL;
224	>	} else if (myMethod == "SHIFTED_FORCE") {
225	>	cutoffMethod_ = SHIFTED_FORCE;
226	>	}
227	>
228	>	if (simParams_->haveSwitchingRadius())
229	>	rSwitch_ = simParams_->getSwitchingRadius();
230	>
231	>	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
232	>	if (simParams_->haveSwitchingRadius()){
233	>	sprintf(painCave.errMsg,
234	>	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
235	>	"\tA value was set for the switchingRadius\n"
236	>	"\teven though the electrostaticSummationMethod was\n"
237	>	"\tset to %s\n", myMethod.c_str());
238	>	painCave.severity = OPENMD_WARNING;
239	>	painCave.isFatal = 1;
240	>	simError();
241	>	}
242	>	}
243	>	if (abs(rCut_ - rSwitch_) < 0.0001) {
244	>	if (cutoffMethod_ == SHIFTED_FORCE) {
245	>	sprintf(painCave.errMsg,
246	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
247	>	"\tcutoffRadius and switchingRadius are set to the\n"
248	>	"\tsame value. OpenMD will use shifted force\n"
249	>	"\tpotentials instead of switching functions.\n");
250	>	painCave.isFatal = 0;
251	>	painCave.severity = OPENMD_WARNING;
252	>	simError();
253	>	} else {
254	>	cutoffMethod_ = SHIFTED_POTENTIAL;
255	>	sprintf(painCave.errMsg,
256	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
257	>	"\tcutoffRadius and switchingRadius are set to the\n"
258	>	"\tsame value. OpenMD will use shifted potentials\n"
259	>	"\tinstead of switching functions.\n");
260	>	painCave.isFatal = 0;
261	>	painCave.severity = OPENMD_WARNING;
262	>	simError();
263	>	}
264	>	}
265	>	}
266	>	}
267	>	}
268	>
269	>	map<string, CutoffPolicy> stringToCutoffPolicy;
270	>	stringToCutoffPolicy["MIX"] = MIX;
271	>	stringToCutoffPolicy["MAX"] = MAX;
272	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
273	>
274	>	string cutPolicy;
275	>	if (forceFieldOptions_.haveCutoffPolicy()){
276	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
277	>	}else if (simParams_->haveCutoffPolicy()) {
278	>	cutPolicy = simParams_->getCutoffPolicy();
279	>	}
280	>
281	>	if (!cutPolicy.empty()){
282	>	toUpper(cutPolicy);
283	>	map<string, CutoffPolicy>::iterator i;
284	>	i = stringToCutoffPolicy.find(cutPolicy);
285	>
286	>	if (i == stringToCutoffPolicy.end()) {
287	>	sprintf(painCave.errMsg,
288	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
289	>	"\tShould be one of: "
290	>	"MIX, MAX, or TRADITIONAL\n",
291	>	cutPolicy.c_str());
292	>	painCave.isFatal = 1;
293	>	painCave.severity = OPENMD_ERROR;
294	>	simError();
295	>	} else {
296	>	cutoffPolicy_ = i->second;
297	>	}
298	>	} else {
299	>	sprintf(painCave.errMsg,
300	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
301	>	"\tOpenMD will use TRADITIONAL.\n");
302	>	painCave.isFatal = 0;
303	>	painCave.severity = OPENMD_INFO;
304	>	simError();
305	>	cutoffPolicy_ = TRADITIONAL;
306	>	}
307	>
308	>	fDecomp_->setCutoffPolicy(cutoffPolicy_);
309	>
310	>	// create the switching function object:
311	>
312	>	switcher_ = new SwitchingFunction();
313	>
314	>	if (cutoffMethod_ == SWITCHED) {
315	>	if (simParams_->haveSwitchingRadius()) {
316	>	rSwitch_ = simParams_->getSwitchingRadius();
317	>	if (rSwitch_ > rCut_) {
318	>	sprintf(painCave.errMsg,
319	>	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
320	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
321	>	painCave.isFatal = 1;
322	>	painCave.severity = OPENMD_ERROR;
323	>	simError();
324	>	}
325	>	} else {
326	>	rSwitch_ = 0.85 * rCut_;
327	>	sprintf(painCave.errMsg,
328	>	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
329	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
330	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
331	>	painCave.isFatal = 0;
332	>	painCave.severity = OPENMD_WARNING;
333	>	simError();
334	>	}
335	>	} else {
336	>	if (mdFileVersion > 1) {
337	>	// throw an error if we define a switching radius and don't need one.
338	>	// older file versions should not do this.
339	>	if (simParams_->haveSwitchingRadius()) {
340	>	map<string, CutoffMethod>::const_iterator it;
341	>	string theMeth;
342	>	for (it = stringToCutoffMethod.begin();
343	>	it != stringToCutoffMethod.end(); ++it) {
344	>	if (it->second == cutoffMethod_) {
345	>	theMeth = it->first;
346	>	break;
347	>	}
348	>	}
349	>	sprintf(painCave.errMsg,
350	>	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
351	>	"\tis not set to SWITCHED, so switchingRadius value\n"
352	>	"\twill be ignored for this simulation\n", theMeth.c_str());
353	>	painCave.isFatal = 0;
354	>	painCave.severity = OPENMD_WARNING;
355	>	simError();
356	>	}
357	>	}
358	>	rSwitch_ = rCut_;
359	>	}
360
361	+	// Default to cubic switching function.
362	+	sft_ = cubic;
363	+	if (simParams_->haveSwitchingFunctionType()) {
364	+	string funcType = simParams_->getSwitchingFunctionType();
365	+	toUpper(funcType);
366	+	if (funcType == "CUBIC") {
367	+	sft_ = cubic;
368	+	} else {
369	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
370	+	sft_ = fifth_order_poly;
371	+	} else {
372	+	// throw error
373	+	sprintf( painCave.errMsg,
374	+	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
375	+	"\tswitchingFunctionType must be one of: "
376	+	"\"cubic\" or \"fifth_order_polynomial\".",
377	+	funcType.c_str() );
378	+	painCave.isFatal = 1;
379	+	painCave.severity = OPENMD_ERROR;
380	+	simError();
381	+	}
382	+	}
383	+	}
384	+	switcher_->setSwitchType(sft_);
385	+	switcher_->setSwitch(rSwitch_, rCut_);
386	+	}
387	+
388	+
389	+
390	+
391	+	void ForceManager::initialize() {
392	+
393		if (!info_->isTopologyDone()) {
394	+
395		info_->update();
396		interactionMan_->setSimInfo(info_);
397		interactionMan_->initialize();
398	<	swfun_ = interactionMan_->getSwitchingFunction();
399	<	fDecomp_->distributeInitialData();
400	<	info_->prepareTopology();
398	>
399	>	// We want to delay the cutoffs until after the interaction
400	>	// manager has set up the atom-atom interactions so that we can
401	>	// query them for suggested cutoff values
402	>	setupCutoffs();
403	>
404	>	info_->prepareTopology();
405	>
406	>	doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
407	>	doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
408	>	if (doHeatFlux_) doParticlePot_ = true;
409	>
410	>	doElectricField_ = info_->getSimParams()->getOutputElectricField();
411	>
412		}
413	+
414	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
415
416	+	// Force fields can set options on how to scale van der Waals and
417	+	// electrostatic interactions for atoms connected via bonds, bends
418	+	// and torsions in this case the topological distance between
419	+	// atoms is:
420	+	// 0 = topologically unconnected
421	+	// 1 = bonded together
422	+	// 2 = connected via a bend
423	+	// 3 = connected via a torsion
424	+
425	+	vdwScale_.reserve(4);
426	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
427	+
428	+	electrostaticScale_.reserve(4);
429	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
430	+
431	+	vdwScale_[0] = 1.0;
432	+	vdwScale_[1] = fopts.getvdw12scale();
433	+	vdwScale_[2] = fopts.getvdw13scale();
434	+	vdwScale_[3] = fopts.getvdw14scale();
435	+
436	+	electrostaticScale_[0] = 1.0;
437	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
438	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
439	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
440	+
441	+	if (info_->getSimParams()->haveElectricField()) {
442	+	ElectricField* eField = new ElectricField(info_);
443	+	perturbations_.push_back(eField);
444	+	}
445	+
446	+	usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
447	+
448	+	fDecomp_->distributeInitialData();
449	+
450	+	initialized_ = true;
451	+
452	+	}
453	+
454	+	void ForceManager::calcForces() {
455	+
456	+	if (!initialized_) initialize();
457	+
458		preCalculation();
459		shortRangeInteractions();
460		longRangeInteractions();
461	<	postCalculation();
88	<
461	>	postCalculation();
462		}
463
464		void ForceManager::preCalculation() {
#	Line 98 \| Line 471 \| namespace OpenMD {
471		Molecule::CutoffGroupIterator ci;
472		CutoffGroup* cg;
473
474	<	// forces are zeroed here, before any are accumulated.
474	>	// forces and potentials are zeroed here, before any are
475	>	// accumulated.
476
477	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
478	+
479	+	snap->setBondPotential(0.0);
480	+	snap->setBendPotential(0.0);
481	+	snap->setTorsionPotential(0.0);
482	+	snap->setInversionPotential(0.0);
483	+
484	+	potVec zeroPot(0.0);
485	+	snap->setLongRangePotential(zeroPot);
486	+	snap->setExcludedPotentials(zeroPot);
487	+
488	+	snap->setRestraintPotential(0.0);
489	+	snap->setRawPotential(0.0);
490	+
491		for (mol = info_->beginMolecule(mi); mol != NULL;
492		mol = info_->nextMolecule(mi)) {
493	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
493	>	for(atom = mol->beginAtom(ai); atom != NULL;
494	>	atom = mol->nextAtom(ai)) {
495		atom->zeroForcesAndTorques();
496		}
497	<
497	>
498		//change the positions of atoms which belong to the rigidbodies
499		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
500		rb = mol->nextRigidBody(rbIter)) {
501		rb->zeroForcesAndTorques();
502		}
503	<
503	>
504		if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
505		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
506		cg = mol->nextCutoffGroup(ci)) {
#	Line 120 \| Line 509 \| namespace OpenMD {
509		}
510		}
511		}
123	–
124	–	// Zero out the stress tensor
125	–	tau *= 0.0;
512
513	+	// Zero out the stress tensor
514	+	stressTensor *= 0.0;
515	+	// Zero out the heatFlux
516	+	fDecomp_->setHeatFlux( Vector3d(0.0) );
517		}
518
519		void ForceManager::shortRangeInteractions() {
#	Line 156 \| Line 546 \| namespace OpenMD {
546
547		for (bond = mol->beginBond(bondIter); bond != NULL;
548		bond = mol->nextBond(bondIter)) {
549	<	bond->calcForce();
549	>	bond->calcForce(doParticlePot_);
550		bondPotential += bond->getPotential();
551		}
552
#	Line 164 \| Line 554 \| namespace OpenMD {
554		bend = mol->nextBend(bendIter)) {
555
556		RealType angle;
557	<	bend->calcForce(angle);
557	>	bend->calcForce(angle, doParticlePot_);
558		RealType currBendPot = bend->getPotential();
559
560		bendPotential += bend->getPotential();
#	Line 174 \| Line 564 \| namespace OpenMD {
564		dataSet.prev.angle = dataSet.curr.angle = angle;
565		dataSet.prev.potential = dataSet.curr.potential = currBendPot;
566		dataSet.deltaV = 0.0;
567	<	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
567	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
568	>	dataSet));
569		}else {
570		i->second.prev.angle = i->second.curr.angle;
571		i->second.prev.potential = i->second.curr.potential;
#	Line 188 \| Line 579 \| namespace OpenMD {
579		for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
580		torsion = mol->nextTorsion(torsionIter)) {
581		RealType angle;
582	<	torsion->calcForce(angle);
582	>	torsion->calcForce(angle, doParticlePot_);
583		RealType currTorsionPot = torsion->getPotential();
584		torsionPotential += torsion->getPotential();
585		map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
#	Line 212 \| Line 603 \| namespace OpenMD {
603		inversion != NULL;
604		inversion = mol->nextInversion(inversionIter)) {
605		RealType angle;
606	<	inversion->calcForce(angle);
606	>	inversion->calcForce(angle, doParticlePot_);
607		RealType currInversionPot = inversion->getPotential();
608		inversionPotential += inversion->getPotential();
609		map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
#	Line 232 \| Line 623 \| namespace OpenMD {
623		}
624		}
625		}
626	<
627	<	RealType shortRangePotential = bondPotential + bendPotential +
628	<	torsionPotential + inversionPotential;
626	>
627	>	#ifdef IS_MPI
628	>	// Collect from all nodes. This should eventually be moved into a
629	>	// SystemDecomposition, but this is a better place than in
630	>	// Thermo to do the collection.
631	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
632	>	MPI::SUM);
633	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
634	>	MPI::SUM);
635	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
636	>	MPI::REALTYPE, MPI::SUM);
637	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
638	>	MPI::REALTYPE, MPI::SUM);
639	>	#endif
640	>
641		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
642	<	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
643	<	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
644	<	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
645	<	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
646	<	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
642	>
643	>	curSnapshot->setBondPotential(bondPotential);
644	>	curSnapshot->setBendPotential(bendPotential);
645	>	curSnapshot->setTorsionPotential(torsionPotential);
646	>	curSnapshot->setInversionPotential(inversionPotential);
647	>
648	>	// RealType shortRangePotential = bondPotential + bendPotential +
649	>	// torsionPotential + inversionPotential;
650	>
651	>	// curSnapshot->setShortRangePotential(shortRangePotential);
652		}
653
654		void ForceManager::longRangeInteractions() {
655
656	<	// some of this initial stuff will go away:
656	>
657		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
658		DataStorage* config = &(curSnapshot->atomData);
659		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;
660
661	<	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
662	<	rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
661	>	//calculate the center of mass of cutoff group
662	>
663	>	SimInfo::MoleculeIterator mi;
664	>	Molecule* mol;
665	>	Molecule::CutoffGroupIterator ci;
666	>	CutoffGroup* cg;
667	>
668	>	if(info_->getNCutoffGroups() > 0){
669	>	for (mol = info_->beginMolecule(mi); mol != NULL;
670	>	mol = info_->nextMolecule(mi)) {
671	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
672	>	cg = mol->nextCutoffGroup(ci)) {
673	>	cg->updateCOM();
674	>	}
675	>	}
676		} else {
677		// center of mass of the group is the same as position of the atom
678		// if cutoff group does not exist
679	<	rc = pos;
680	<	}
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
679	>	cgConfig->position = config->position;
680	>	cgConfig->velocity = config->velocity;
681		}
682
683	<	// new stuff starts here:
279	<
683	>	fDecomp_->zeroWorkArrays();
684		fDecomp_->distributeData();
685	<
686	<	int cg1, cg2, atom1, atom2;
687	<	Vector3d d_grp, dag;
688	<	RealType rgrpsq, rgrp;
685	>
686	>	int cg1, cg2, atom1, atom2, topoDist;
687	>	Vector3d d_grp, dag, d, gvel2, vel2;
688	>	RealType rgrpsq, rgrp, r2, r;
689	>	RealType electroMult, vdwMult;
690		RealType vij;
691	<	Vector3d fij, fg;
692	<	pair<int, int> gtypes;
691	>	Vector3d fij, fg, f1;
692	>	tuple3<RealType, RealType, RealType> cuts;
693		RealType rCutSq;
694		bool in_switching_region;
695		RealType sw, dswdr, swderiv;
#	Line 292 \| Line 697 \| namespace OpenMD {
697		InteractionData idat;
698		SelfData sdat;
699		RealType mf;
700	+	RealType vpair;
701	+	RealType dVdFQ1(0.0);
702	+	RealType dVdFQ2(0.0);
703	+	potVec longRangePotential(0.0);
704	+	potVec workPot(0.0);
705	+	potVec exPot(0.0);
706	+	Vector3d eField1(0.0);
707	+	Vector3d eField2(0.0);
708	+	vector<int>::iterator ia, jb;
709
710		int loopStart, loopEnd;
711
712	+	idat.vdwMult = &vdwMult;
713	+	idat.electroMult = &electroMult;
714	+	idat.pot = &workPot;
715	+	idat.excludedPot = &exPot;
716	+	sdat.pot = fDecomp_->getEmbeddingPotential();
717	+	sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
718	+	idat.vpair = &vpair;
719	+	idat.dVdFQ1 = &dVdFQ1;
720	+	idat.dVdFQ2 = &dVdFQ2;
721	+	idat.eField1 = &eField1;
722	+	idat.eField2 = &eField2;
723	+	idat.f1 = &f1;
724	+	idat.sw = &sw;
725	+	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
726	+	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
727	+	idat.doParticlePot = doParticlePot_;
728	+	idat.doElectricField = doElectricField_;
729	+	sdat.doParticlePot = doParticlePot_;
730	+
731		loopEnd = PAIR_LOOP;
732		if (info_->requiresPrepair() ) {
733		loopStart = PREPAIR_LOOP;
734		} else {
735		loopStart = PAIR_LOOP;
736		}
737	<
738	<	for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
306	<
737	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
738	>
739		if (iLoop == loopStart) {
740		bool update_nlist = fDecomp_->checkNeighborList();
741	<	if (update_nlist)
741	>	if (update_nlist) {
742	>	if (!usePeriodicBoundaryConditions_)
743	>	Mat3x3d bbox = thermo->getBoundingBox();
744		neighborList = fDecomp_->buildNeighborList();
745	+	}
746		}
747
748		for (vector<pair<int, int> >::iterator it = neighborList.begin();
749		it != neighborList.end(); ++it) {
750	<
750	>
751		cg1 = (*it).first;
752		cg2 = (*it).second;
753	+
754	+	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
755
319	–	gtypes = fDecomp_->getGroupTypes(cg1, cg2);
756		d_grp = fDecomp_->getIntergroupVector(cg1, cg2);
757	+
758		curSnapshot->wrapVector(d_grp);
759		rgrpsq = d_grp.lengthSquare();
760	<	rCutSq = groupCutoffMap[gtypes].first;
760	>	rCutSq = cuts.second;
761
762		if (rgrpsq < rCutSq) {
763	<	*(idat.rcut) = groupCutoffMap[gtypes].second;
763	>	idat.rcut = &cuts.first;
764		if (iLoop == PAIR_LOOP) {
765	<	vij *= 0.0;
765	>	vij = 0.0;
766		fij = V3Zero;
767	+	eField1 = V3Zero;
768	+	eField2 = V3Zero;
769		}
770
771	<	in_switching_region = swfun_->getSwitch(rgrpsq, *(idat.sw), dswdr,
772	<	rgrp);
771	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
772	>	rgrp);
773	>
774		atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
775		atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
776
777	<	for (vector<int>::iterator ia = atomListRow.begin();
777	>	if (doHeatFlux_)
778	>	gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
779	>
780	>	for (ia = atomListRow.begin();
781		ia != atomListRow.end(); ++ia) {
782		atom1 = (*ia);
783	<
784	<	for (vector<int>::iterator jb = atomListColumn.begin();
783	>
784	>	for (jb = atomListColumn.begin();
785		jb != atomListColumn.end(); ++jb) {
786		atom2 = (*jb);
787	<
788	<	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
346	<
347	<	idat = fDecomp_->fillInteractionData(atom1, atom2);
787	>
788	>	if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
789
790	+	vpair = 0.0;
791	+	workPot = 0.0;
792	+	exPot = 0.0;
793	+	f1 = V3Zero;
794	+	dVdFQ1 = 0.0;
795	+	dVdFQ2 = 0.0;
796	+
797	+	fDecomp_->fillInteractionData(idat, atom1, atom2);
798	+
799	+	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
800	+	vdwMult = vdwScale_[topoDist];
801	+	electroMult = electrostaticScale_[topoDist];
802	+
803		if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
804	<	*(idat.d) = d_grp;
805	<	*(idat.r2) = rgrpsq;
804	>	idat.d = &d_grp;
805	>	idat.r2 = &rgrpsq;
806	>	if (doHeatFlux_)
807	>	vel2 = gvel2;
808		} else {
809	<	*(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2);
810	<	curSnapshot->wrapVector( *(idat.d) );
811	<	*(idat.r2) = idat.d->lengthSquare();
809	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
810	>	curSnapshot->wrapVector( d );
811	>	r2 = d.lengthSquare();
812	>	idat.d = &d;
813	>	idat.r2 = &r2;
814	>	if (doHeatFlux_)
815	>	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
816		}
357	–
358	–	(idat.rij) = sqrt( (idat.r2) );
817
818	+	r = sqrt( *(idat.r2) );
819	+	idat.rij = &r;
820	+
821		if (iLoop == PREPAIR_LOOP) {
822		interactionMan_->doPrePair(idat);
823		} else {
824		interactionMan_->doPair(idat);
825	<	vij += *(idat.vpair);
826	<	fij += *(idat.f1);
827	<	tau -= outProduct( (idat.d), (idat.f1));
825	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
826	>	vij += vpair;
827	>	fij += f1;
828	>	stressTensor -= outProduct( *(idat.d), f1);
829	>	if (doHeatFlux_)
830	>	fDecomp_->addToHeatFlux((idat.d) dot(f1, vel2));
831		}
832		}
833		}
#	Line 373 \| Line 837 \| namespace OpenMD {
837		if (in_switching_region) {
838		swderiv = vij * dswdr / rgrp;
839		fg = swderiv * d_grp;
376	–
840		fij += fg;
841
842		if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
843	<	tau -= outProduct( *(idat.d), fg);
843	>	if (!fDecomp_->skipAtomPair(atomListRow[0],
844	>	atomListColumn[0],
845	>	cg1, cg2)) {
846	>	stressTensor -= outProduct( *(idat.d), fg);
847	>	if (doHeatFlux_)
848	>	fDecomp_->addToHeatFlux((idat.d) dot(fg, vel2));
849	>	}
850		}
851
852	<	for (vector<int>::iterator ia = atomListRow.begin();
852	>	for (ia = atomListRow.begin();
853		ia != atomListRow.end(); ++ia) {
854		atom1 = (*ia);
855		mf = fDecomp_->getMassFactorRow(atom1);
#	Line 388 \| Line 857 \| namespace OpenMD {
857		// presence in switching region
858		fg = swderiv * d_grp * mf;
859		fDecomp_->addForceToAtomRow(atom1, fg);
391	–
860		if (atomListRow.size() > 1) {
861		if (info_->usesAtomicVirial()) {
862		// find the distance between the atom
863		// and the center of the cutoff group:
864		dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
865	<	tau -= outProduct(dag, fg);
865	>	stressTensor -= outProduct(dag, fg);
866	>	if (doHeatFlux_)
867	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
868		}
869		}
870		}
871	<	for (vector<int>::iterator jb = atomListColumn.begin();
871	>	for (jb = atomListColumn.begin();
872		jb != atomListColumn.end(); ++jb) {
873		atom2 = (*jb);
874		mf = fDecomp_->getMassFactorColumn(atom2);
#	Line 412 \| Line 882 \| namespace OpenMD {
882		// find the distance between the atom
883		// and the center of the cutoff group:
884		dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
885	<	tau -= outProduct(dag, fg);
885	>	stressTensor -= outProduct(dag, fg);
886	>	if (doHeatFlux_)
887	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
888		}
889		}
890		}
891		}
892	<	//if (!SIM_uses_AtomicVirial) {
893	<	// tau -= outProduct(d_grp, fij);
892	>	//if (!info_->usesAtomicVirial()) {
893	>	// stressTensor -= outProduct(d_grp, fij);
894	>	// if (doHeatFlux_)
895	>	// fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
896		//}
897		}
898		}
899		}
900
901		if (iLoop == PREPAIR_LOOP) {
902	<	if (info_->requiresPrepair()) {
902	>	if (info_->requiresPrepair()) {
903	>
904		fDecomp_->collectIntermediateData();
905
906	<	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
907	<	sdat = fDecomp_->fillSelfData(atom1);
906	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
907	>	fDecomp_->fillSelfData(sdat, atom1);
908		interactionMan_->doPreForce(sdat);
909		}
910
911	<	fDecomp_->distributeIntermediateData();
911	>	fDecomp_->distributeIntermediateData();
912	>
913		}
914		}
439	–
915		}
916
917	+	// collects pairwise information
918		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 );
919
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	–
920		if (info_->requiresSelfCorrection()) {
921	<
922	<	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
464	<	sdat = fDecomp_->fillSelfData(atom1);
921	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
922	>	fDecomp_->fillSelfData(sdat, atom1);
923		interactionMan_->doSelfCorrection(sdat);
924		}
467	–
925		}
926
927	<	// dangerous to iterate over enums, but we'll live on the edge:
928	<	for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
929	<	lrPot += longRangePotential[i]; //Quick hack
930	<	}
931	<
932	<	//store the tau and long range potential
933	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
934	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
935	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
927	>	// collects single-atom information
928	>	fDecomp_->collectSelfData();
929	>
930	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
931	>	*(fDecomp_->getPairwisePotential());
932	>
933	>	curSnapshot->setLongRangePotential(longRangePotential);
934	>
935	>	curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
936	>	*(fDecomp_->getExcludedPotential()));
937	>
938		}
939
940
941		void ForceManager::postCalculation() {
942	+
943	+	vector<Perturbation*>::iterator pi;
944	+	for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
945	+	(*pi)->applyPerturbation();
946	+	}
947	+
948		SimInfo::MoleculeIterator mi;
949		Molecule* mol;
950		Molecule::RigidBodyIterator rbIter;
951		RigidBody* rb;
952		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
953	<
953	>
954		// collect the atomic forces onto rigid bodies
955
956		for (mol = info_->beginMolecule(mi); mol != NULL;
#	Line 493 \| Line 958 \| namespace OpenMD {
958		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
959		rb = mol->nextRigidBody(rbIter)) {
960		Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
961	<	tau += rbTau;
961	>	stressTensor += rbTau;
962		}
963		}
964
965		#ifdef IS_MPI
966	<	Mat3x3d tmpTau(tau);
967	<	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
503	<	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
966	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
967	>	MPI::REALTYPE, MPI::SUM);
968		#endif
969	<	curSnapshot->statData.setTau(tau);
970	<	}
969	>	curSnapshot->setStressTensor(stressTensor);
970	>
971	>	if (info_->getSimParams()->getUseLongRangeCorrections()) {
972	>	/*
973	>	RealType vol = curSnapshot->getVolume();
974	>	RealType Elrc(0.0);
975	>	RealType Wlrc(0.0);
976
977	<	} //end namespace OpenMD
977	>	set<AtomType*>::iterator i;
978	>	set<AtomType*>::iterator j;
979	>
980	>	RealType n_i, n_j;
981	>	RealType rho_i, rho_j;
982	>	pair<RealType, RealType> LRI;
983	>
984	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
985	>	n_i = RealType(info_->getGlobalCountOfType(*i));
986	>	rho_i = n_i / vol;
987	>	for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
988	>	n_j = RealType(info_->getGlobalCountOfType(*j));
989	>	rho_j = n_j / vol;
990	>
991	>	LRI = interactionMan_->getLongRangeIntegrals( (i), (j) );
992	>
993	>	Elrc += n_i * rho_j * LRI.first;
994	>	Wlrc -= rho_i * rho_j * LRI.second;
995	>	}
996	>	}
997	>	Elrc = 2.0 NumericConstant::PI;
998	>	Wlrc = 2.0 NumericConstant::PI;
999	>
1000	>	RealType lrp = curSnapshot->getLongRangePotential();
1001	>	curSnapshot->setLongRangePotential(lrp + Elrc);
1002	>	stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
1003	>	curSnapshot->setStressTensor(stressTensor);
1004	>	*/
1005	>
1006	>	}
1007	>	}
1008	>	}

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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 1868 by gezelter, Tue Apr 30 15:56:54 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 1868 by gezelter, Tue Apr 30 15:56:54 2013 UTC