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

Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1569 by gezelter, Thu May 26 13:55:04 2011 UTC vs.
Revision 1874 by gezelter, Wed May 15 15:09:35 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,
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	>
175	>	if (simParams_->haveCutoffMethod()) {
176	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
177	>	map<string, CutoffMethod>::iterator i;
178	>	i = stringToCutoffMethod.find(cutMeth);
179	>	if (i == stringToCutoffMethod.end()) {
180	>	sprintf(painCave.errMsg,
181	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
182	>	"\tShould be one of: "
183	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
184	>	cutMeth.c_str());
185	>	painCave.isFatal = 1;
186	>	painCave.severity = OPENMD_ERROR;
187	>	simError();
188	>	} else {
189	>	cutoffMethod_ = i->second;
190	>	}
191	>	} else {
192	>	if (mdFileVersion > 1) {
193	>	sprintf(painCave.errMsg,
194	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
195	>	"\tOpenMD will use SHIFTED_FORCE.\n");
196	>	painCave.isFatal = 0;
197	>	painCave.severity = OPENMD_INFO;
198	>	simError();
199	>	cutoffMethod_ = SHIFTED_FORCE;
200	>	} else {
201	>	// handle the case where the old file version was in play
202	>	// (there should be no cutoffMethod, so we have to deduce it
203	>	// from other data).
204	>
205	>	sprintf(painCave.errMsg,
206	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
207	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
208	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
209	>	"\tbehavior of the older (version 1) code. To remove this\n"
210	>	"\twarning, add an explicit cutoffMethod and change the top\n"
211	>	"\tof the file so that it begins with <OpenMD version=2>\n");
212	>	painCave.isFatal = 0;
213	>	painCave.severity = OPENMD_WARNING;
214	>	simError();
215	>
216	>	// The old file version tethered the shifting behavior to the
217	>	// electrostaticSummationMethod keyword.
218	>
219	>	if (simParams_->haveElectrostaticSummationMethod()) {
220	>	string myMethod = simParams_->getElectrostaticSummationMethod();
221	>	toUpper(myMethod);
222	>
223	>	if (myMethod == "SHIFTED_POTENTIAL") {
224	>	cutoffMethod_ = SHIFTED_POTENTIAL;
225	>	} else if (myMethod == "SHIFTED_FORCE") {
226	>	cutoffMethod_ = SHIFTED_FORCE;
227	>	}
228	>
229	>	if (simParams_->haveSwitchingRadius())
230	>	rSwitch_ = simParams_->getSwitchingRadius();
231	>
232	>	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
233	>	if (simParams_->haveSwitchingRadius()){
234	>	sprintf(painCave.errMsg,
235	>	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
236	>	"\tA value was set for the switchingRadius\n"
237	>	"\teven though the electrostaticSummationMethod was\n"
238	>	"\tset to %s\n", myMethod.c_str());
239	>	painCave.severity = OPENMD_WARNING;
240	>	painCave.isFatal = 1;
241	>	simError();
242	>	}
243	>	}
244	>	if (abs(rCut_ - rSwitch_) < 0.0001) {
245	>	if (cutoffMethod_ == SHIFTED_FORCE) {
246	>	sprintf(painCave.errMsg,
247	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
248	>	"\tcutoffRadius and switchingRadius are set to the\n"
249	>	"\tsame value. OpenMD will use shifted force\n"
250	>	"\tpotentials instead of switching functions.\n");
251	>	painCave.isFatal = 0;
252	>	painCave.severity = OPENMD_WARNING;
253	>	simError();
254	>	} else {
255	>	cutoffMethod_ = SHIFTED_POTENTIAL;
256	>	sprintf(painCave.errMsg,
257	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
258	>	"\tcutoffRadius and switchingRadius are set to the\n"
259	>	"\tsame value. OpenMD will use shifted potentials\n"
260	>	"\tinstead of switching functions.\n");
261	>	painCave.isFatal = 0;
262	>	painCave.severity = OPENMD_WARNING;
263	>	simError();
264	>	}
265	>	}
266	>	}
267	>	}
268	>	}
269	>
270	>	map<string, CutoffPolicy> stringToCutoffPolicy;
271	>	stringToCutoffPolicy["MIX"] = MIX;
272	>	stringToCutoffPolicy["MAX"] = MAX;
273	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
274	>
275	>	string cutPolicy;
276	>	if (forceFieldOptions_.haveCutoffPolicy()){
277	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
278	>	}else if (simParams_->haveCutoffPolicy()) {
279	>	cutPolicy = simParams_->getCutoffPolicy();
280	>	}
281	>
282	>	if (!cutPolicy.empty()){
283	>	toUpper(cutPolicy);
284	>	map<string, CutoffPolicy>::iterator i;
285	>	i = stringToCutoffPolicy.find(cutPolicy);
286	>
287	>	if (i == stringToCutoffPolicy.end()) {
288	>	sprintf(painCave.errMsg,
289	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
290	>	"\tShould be one of: "
291	>	"MIX, MAX, or TRADITIONAL\n",
292	>	cutPolicy.c_str());
293	>	painCave.isFatal = 1;
294	>	painCave.severity = OPENMD_ERROR;
295	>	simError();
296	>	} else {
297	>	cutoffPolicy_ = i->second;
298	>	}
299	>	} else {
300	>	sprintf(painCave.errMsg,
301	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
302	>	"\tOpenMD will use TRADITIONAL.\n");
303	>	painCave.isFatal = 0;
304	>	painCave.severity = OPENMD_INFO;
305	>	simError();
306	>	cutoffPolicy_ = TRADITIONAL;
307	>	}
308	>
309	>	fDecomp_->setCutoffPolicy(cutoffPolicy_);
310	>
311	>	// create the switching function object:
312	>
313	>	switcher_ = new SwitchingFunction();
314	>
315	>	if (cutoffMethod_ == SWITCHED) {
316	>	if (simParams_->haveSwitchingRadius()) {
317	>	rSwitch_ = simParams_->getSwitchingRadius();
318	>	if (rSwitch_ > rCut_) {
319	>	sprintf(painCave.errMsg,
320	>	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
321	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
322	>	painCave.isFatal = 1;
323	>	painCave.severity = OPENMD_ERROR;
324	>	simError();
325	>	}
326	>	} else {
327	>	rSwitch_ = 0.85 * rCut_;
328	>	sprintf(painCave.errMsg,
329	>	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
330	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
331	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
332	>	painCave.isFatal = 0;
333	>	painCave.severity = OPENMD_WARNING;
334	>	simError();
335	>	}
336	>	} else {
337	>	if (mdFileVersion > 1) {
338	>	// throw an error if we define a switching radius and don't need one.
339	>	// older file versions should not do this.
340	>	if (simParams_->haveSwitchingRadius()) {
341	>	map<string, CutoffMethod>::const_iterator it;
342	>	string theMeth;
343	>	for (it = stringToCutoffMethod.begin();
344	>	it != stringToCutoffMethod.end(); ++it) {
345	>	if (it->second == cutoffMethod_) {
346	>	theMeth = it->first;
347	>	break;
348	>	}
349	>	}
350	>	sprintf(painCave.errMsg,
351	>	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
352	>	"\tis not set to SWITCHED, so switchingRadius value\n"
353	>	"\twill be ignored for this simulation\n", theMeth.c_str());
354	>	painCave.isFatal = 0;
355	>	painCave.severity = OPENMD_WARNING;
356	>	simError();
357	>	}
358	>	}
359	>	rSwitch_ = rCut_;
360	>	}
361
362	+	// Default to cubic switching function.
363	+	sft_ = cubic;
364	+	if (simParams_->haveSwitchingFunctionType()) {
365	+	string funcType = simParams_->getSwitchingFunctionType();
366	+	toUpper(funcType);
367	+	if (funcType == "CUBIC") {
368	+	sft_ = cubic;
369	+	} else {
370	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
371	+	sft_ = fifth_order_poly;
372	+	} else {
373	+	// throw error
374	+	sprintf( painCave.errMsg,
375	+	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
376	+	"\tswitchingFunctionType must be one of: "
377	+	"\"cubic\" or \"fifth_order_polynomial\".",
378	+	funcType.c_str() );
379	+	painCave.isFatal = 1;
380	+	painCave.severity = OPENMD_ERROR;
381	+	simError();
382	+	}
383	+	}
384	+	}
385	+	switcher_->setSwitchType(sft_);
386	+	switcher_->setSwitch(rSwitch_, rCut_);
387	+	}
388	+
389	+
390	+
391	+
392	+	void ForceManager::initialize() {
393	+
394		if (!info_->isTopologyDone()) {
395	+
396		info_->update();
397		interactionMan_->setSimInfo(info_);
398		interactionMan_->initialize();
399	<	swfun_ = interactionMan_->getSwitchingFunction();
400	<	fDecomp_->distributeInitialData();
401	<	info_->prepareTopology();
399	>
400	>	// We want to delay the cutoffs until after the interaction
401	>	// manager has set up the atom-atom interactions so that we can
402	>	// query them for suggested cutoff values
403	>	setupCutoffs();
404	>
405	>	info_->prepareTopology();
406	>
407	>	doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
408	>	doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
409	>	if (doHeatFlux_) doParticlePot_ = true;
410	>
411	>	doElectricField_ = info_->getSimParams()->getOutputElectricField();
412	>
413		}
414	+
415	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
416
417	+	// Force fields can set options on how to scale van der Waals and
418	+	// electrostatic interactions for atoms connected via bonds, bends
419	+	// and torsions in this case the topological distance between
420	+	// atoms is:
421	+	// 0 = topologically unconnected
422	+	// 1 = bonded together
423	+	// 2 = connected via a bend
424	+	// 3 = connected via a torsion
425	+
426	+	vdwScale_.reserve(4);
427	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
428	+
429	+	electrostaticScale_.reserve(4);
430	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
431	+
432	+	vdwScale_[0] = 1.0;
433	+	vdwScale_[1] = fopts.getvdw12scale();
434	+	vdwScale_[2] = fopts.getvdw13scale();
435	+	vdwScale_[3] = fopts.getvdw14scale();
436	+
437	+	electrostaticScale_[0] = 1.0;
438	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
439	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
440	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
441	+
442	+	if (info_->getSimParams()->haveElectricField()) {
443	+	ElectricField* eField = new ElectricField(info_);
444	+	perturbations_.push_back(eField);
445	+	}
446	+
447	+	usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
448	+
449	+	fDecomp_->distributeInitialData();
450	+
451	+	initialized_ = true;
452	+
453	+	}
454	+
455	+	void ForceManager::calcForces() {
456	+
457	+	if (!initialized_) initialize();
458	+
459		preCalculation();
460		shortRangeInteractions();
461		longRangeInteractions();
462	<	postCalculation();
88	<
462	>	postCalculation();
463		}
464
465		void ForceManager::preCalculation() {
#	Line 98 \| Line 472 \| namespace OpenMD {
472		Molecule::CutoffGroupIterator ci;
473		CutoffGroup* cg;
474
475	<	// forces are zeroed here, before any are accumulated.
475	>	// forces and potentials are zeroed here, before any are
476	>	// accumulated.
477
478	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
479	+
480	+	snap->setBondPotential(0.0);
481	+	snap->setBendPotential(0.0);
482	+	snap->setTorsionPotential(0.0);
483	+	snap->setInversionPotential(0.0);
484	+
485	+	potVec zeroPot(0.0);
486	+	snap->setLongRangePotential(zeroPot);
487	+	snap->setExcludedPotentials(zeroPot);
488	+
489	+	snap->setRestraintPotential(0.0);
490	+	snap->setRawPotential(0.0);
491	+
492		for (mol = info_->beginMolecule(mi); mol != NULL;
493		mol = info_->nextMolecule(mi)) {
494	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
494	>	for(atom = mol->beginAtom(ai); atom != NULL;
495	>	atom = mol->nextAtom(ai)) {
496		atom->zeroForcesAndTorques();
497		}
498	<
498	>
499		//change the positions of atoms which belong to the rigidbodies
500		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
501		rb = mol->nextRigidBody(rbIter)) {
502		rb->zeroForcesAndTorques();
503		}
504	<
504	>
505		if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
506		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
507		cg = mol->nextCutoffGroup(ci)) {
#	Line 120 \| Line 510 \| namespace OpenMD {
510		}
511		}
512		}
123	–
124	–	// Zero out the stress tensor
125	–	tau *= 0.0;
513
514	+	// Zero out the stress tensor
515	+	stressTensor *= 0.0;
516	+	// Zero out the heatFlux
517	+	fDecomp_->setHeatFlux( Vector3d(0.0) );
518		}
519
520		void ForceManager::shortRangeInteractions() {
#	Line 156 \| Line 547 \| namespace OpenMD {
547
548		for (bond = mol->beginBond(bondIter); bond != NULL;
549		bond = mol->nextBond(bondIter)) {
550	<	bond->calcForce();
550	>	bond->calcForce(doParticlePot_);
551		bondPotential += bond->getPotential();
552		}
553
#	Line 164 \| Line 555 \| namespace OpenMD {
555		bend = mol->nextBend(bendIter)) {
556
557		RealType angle;
558	<	bend->calcForce(angle);
558	>	bend->calcForce(angle, doParticlePot_);
559		RealType currBendPot = bend->getPotential();
560
561		bendPotential += bend->getPotential();
#	Line 174 \| Line 565 \| namespace OpenMD {
565		dataSet.prev.angle = dataSet.curr.angle = angle;
566		dataSet.prev.potential = dataSet.curr.potential = currBendPot;
567		dataSet.deltaV = 0.0;
568	<	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
568	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
569	>	dataSet));
570		}else {
571		i->second.prev.angle = i->second.curr.angle;
572		i->second.prev.potential = i->second.curr.potential;
#	Line 188 \| Line 580 \| namespace OpenMD {
580		for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
581		torsion = mol->nextTorsion(torsionIter)) {
582		RealType angle;
583	<	torsion->calcForce(angle);
583	>	torsion->calcForce(angle, doParticlePot_);
584		RealType currTorsionPot = torsion->getPotential();
585		torsionPotential += torsion->getPotential();
586		map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
#	Line 212 \| Line 604 \| namespace OpenMD {
604		inversion != NULL;
605		inversion = mol->nextInversion(inversionIter)) {
606		RealType angle;
607	<	inversion->calcForce(angle);
607	>	inversion->calcForce(angle, doParticlePot_);
608		RealType currInversionPot = inversion->getPotential();
609		inversionPotential += inversion->getPotential();
610		map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
#	Line 232 \| Line 624 \| namespace OpenMD {
624		}
625		}
626		}
627	<
628	<	RealType shortRangePotential = bondPotential + bendPotential +
629	<	torsionPotential + inversionPotential;
627	>
628	>	#ifdef IS_MPI
629	>	// Collect from all nodes. This should eventually be moved into a
630	>	// SystemDecomposition, but this is a better place than in
631	>	// Thermo to do the collection.
632	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
633	>	MPI::SUM);
634	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
635	>	MPI::SUM);
636	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
637	>	MPI::REALTYPE, MPI::SUM);
638	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
639	>	MPI::REALTYPE, MPI::SUM);
640	>	#endif
641	>
642		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
643	<	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
644	<	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
645	<	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
646	<	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
647	<	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
643	>
644	>	curSnapshot->setBondPotential(bondPotential);
645	>	curSnapshot->setBendPotential(bendPotential);
646	>	curSnapshot->setTorsionPotential(torsionPotential);
647	>	curSnapshot->setInversionPotential(inversionPotential);
648	>
649	>	// RealType shortRangePotential = bondPotential + bendPotential +
650	>	// torsionPotential + inversionPotential;
651	>
652	>	// curSnapshot->setShortRangePotential(shortRangePotential);
653		}
654
655		void ForceManager::longRangeInteractions() {
656
657	<	// some of this initial stuff will go away:
657	>
658		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
659		DataStorage* config = &(curSnapshot->atomData);
660		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;
661
662	<	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
663	<	rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
662	>	//calculate the center of mass of cutoff group
663	>
664	>	SimInfo::MoleculeIterator mi;
665	>	Molecule* mol;
666	>	Molecule::CutoffGroupIterator ci;
667	>	CutoffGroup* cg;
668	>
669	>	if(info_->getNCutoffGroups() > 0){
670	>	for (mol = info_->beginMolecule(mi); mol != NULL;
671	>	mol = info_->nextMolecule(mi)) {
672	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
673	>	cg = mol->nextCutoffGroup(ci)) {
674	>	cg->updateCOM();
675	>	}
676	>	}
677		} else {
678		// center of mass of the group is the same as position of the atom
679		// if cutoff group does not exist
680	<	rc = pos;
680	>	cgConfig->position = config->position;
681	>	cgConfig->velocity = config->velocity;
682		}
267	–
268	–	//initialize data before passing to fortran
269	–	RealType longRangePotential[N_INTERACTION_FAMILIES];
270	–	RealType lrPot = 0.0;
271	–	int isError = 0;
683
684	<	// 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
276	<	}
277	<
278	<	// new stuff starts here:
279	<
684	>	fDecomp_->zeroWorkArrays();
685		fDecomp_->distributeData();
686	<
687	<	int cg1, cg2, atom1, atom2;
688	<	Vector3d d_grp, dag;
689	<	RealType rgrpsq, rgrp;
686	>
687	>	int cg1, cg2, atom1, atom2, topoDist;
688	>	Vector3d d_grp, dag, d, gvel2, vel2;
689	>	RealType rgrpsq, rgrp, r2, r;
690	>	RealType electroMult, vdwMult;
691		RealType vij;
692	<	Vector3d fij, fg;
693	<	pair<int, int> gtypes;
692	>	Vector3d fij, fg, f1;
693	>	tuple3<RealType, RealType, RealType> cuts;
694		RealType rCutSq;
695		bool in_switching_region;
696		RealType sw, dswdr, swderiv;
697	<	vector<int> atomListColumn, atomListRow, atomListLocal;
697	>	vector<int> atomListColumn, atomListRow;
698		InteractionData idat;
699		SelfData sdat;
700		RealType mf;
701	+	RealType vpair;
702	+	RealType dVdFQ1(0.0);
703	+	RealType dVdFQ2(0.0);
704	+	potVec longRangePotential(0.0);
705	+	potVec workPot(0.0);
706	+	potVec exPot(0.0);
707	+	Vector3d eField1(0.0);
708	+	Vector3d eField2(0.0);
709	+	vector<int>::iterator ia, jb;
710
711		int loopStart, loopEnd;
712
713	+	idat.vdwMult = &vdwMult;
714	+	idat.electroMult = &electroMult;
715	+	idat.pot = &workPot;
716	+	idat.excludedPot = &exPot;
717	+	sdat.pot = fDecomp_->getEmbeddingPotential();
718	+	sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
719	+	idat.vpair = &vpair;
720	+	idat.dVdFQ1 = &dVdFQ1;
721	+	idat.dVdFQ2 = &dVdFQ2;
722	+	idat.eField1 = &eField1;
723	+	idat.eField2 = &eField2;
724	+	idat.f1 = &f1;
725	+	idat.sw = &sw;
726	+	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
727	+	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
728	+	idat.doParticlePot = doParticlePot_;
729	+	idat.doElectricField = doElectricField_;
730	+	sdat.doParticlePot = doParticlePot_;
731	+
732		loopEnd = PAIR_LOOP;
733		if (info_->requiresPrepair() ) {
734		loopStart = PREPAIR_LOOP;
735		} else {
736		loopStart = PAIR_LOOP;
737		}
738	<
739	<	for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
306	<
738	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
739	>
740		if (iLoop == loopStart) {
741		bool update_nlist = fDecomp_->checkNeighborList();
742	<	if (update_nlist)
742	>	if (update_nlist) {
743	>	if (!usePeriodicBoundaryConditions_)
744	>	Mat3x3d bbox = thermo->getBoundingBox();
745		neighborList = fDecomp_->buildNeighborList();
746	+	}
747		}
748
749		for (vector<pair<int, int> >::iterator it = neighborList.begin();
750		it != neighborList.end(); ++it) {
751	<
751	>
752		cg1 = (*it).first;
753		cg2 = (*it).second;
754	+
755	+	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
756
319	–	gtypes = fDecomp_->getGroupTypes(cg1, cg2);
757		d_grp = fDecomp_->getIntergroupVector(cg1, cg2);
758	+
759		curSnapshot->wrapVector(d_grp);
760		rgrpsq = d_grp.lengthSquare();
761	<	rCutSq = groupCutoffMap[gtypes].first;
761	>	rCutSq = cuts.second;
762
763		if (rgrpsq < rCutSq) {
764	<	*(idat.rcut) = groupCutoffMap[gtypes].second;
764	>	idat.rcut = &cuts.first;
765		if (iLoop == PAIR_LOOP) {
766	<	vij *= 0.0;
766	>	vij = 0.0;
767		fij = V3Zero;
768	+	eField1 = V3Zero;
769	+	eField2 = V3Zero;
770		}
771
772	<	in_switching_region = swfun_->getSwitch(rgrpsq, *(idat.sw), dswdr,
773	<	rgrp);
772	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
773	>	rgrp);
774	>
775		atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
776		atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
777
778	<	for (vector<int>::iterator ia = atomListRow.begin();
778	>	if (doHeatFlux_)
779	>	gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
780	>
781	>	for (ia = atomListRow.begin();
782		ia != atomListRow.end(); ++ia) {
783		atom1 = (*ia);
784	<
785	<	for (vector<int>::iterator jb = atomListColumn.begin();
784	>
785	>	for (jb = atomListColumn.begin();
786		jb != atomListColumn.end(); ++jb) {
787		atom2 = (*jb);
344	–
345	–	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
346	–
347	–	idat = fDecomp_->fillInteractionData(atom1, atom2);
788
789	<	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
790	<	*(idat.d) = d_grp;
791	<	*(idat.r2) = rgrpsq;
789	>	if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
790	>
791	>	vpair = 0.0;
792	>	workPot = 0.0;
793	>	exPot = 0.0;
794	>	f1 = V3Zero;
795	>	dVdFQ1 = 0.0;
796	>	dVdFQ2 = 0.0;
797	>
798	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
799	>
800	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
801	>	vdwMult = vdwScale_[topoDist];
802	>	electroMult = electrostaticScale_[topoDist];
803	>
804	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
805	>	idat.d = &d_grp;
806	>	idat.r2 = &rgrpsq;
807	>	if (doHeatFlux_)
808	>	vel2 = gvel2;
809		} else {
810	<	*(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2);
811	<	curSnapshot->wrapVector( *(idat.d) );
812	<	*(idat.r2) = idat.d->lengthSquare();
810	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
811	>	curSnapshot->wrapVector( d );
812	>	r2 = d.lengthSquare();
813	>	idat.d = &d;
814	>	idat.r2 = &r2;
815	>	if (doHeatFlux_)
816	>	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
817		}
357	–
358	–	(idat.rij) = sqrt( (idat.r2) );
818
819	+	r = sqrt( *(idat.r2) );
820	+	idat.rij = &r;
821	+
822		if (iLoop == PREPAIR_LOOP) {
823		interactionMan_->doPrePair(idat);
824		} else {
825		interactionMan_->doPair(idat);
826	<	vij += *(idat.vpair);
827	<	fij += *(idat.f1);
828	<	tau -= outProduct( (idat.d), (idat.f1));
826	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
827	>	vij += vpair;
828	>	fij += f1;
829	>	stressTensor -= outProduct( *(idat.d), f1);
830	>	if (doHeatFlux_)
831	>	fDecomp_->addToHeatFlux((idat.d) dot(f1, vel2));
832		}
833		}
834		}
#	Line 373 \| Line 838 \| namespace OpenMD {
838		if (in_switching_region) {
839		swderiv = vij * dswdr / rgrp;
840		fg = swderiv * d_grp;
376	–
841		fij += fg;
842
843		if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
844	<	tau -= outProduct( *(idat.d), fg);
844	>	if (!fDecomp_->skipAtomPair(atomListRow[0],
845	>	atomListColumn[0],
846	>	cg1, cg2)) {
847	>	stressTensor -= outProduct( *(idat.d), fg);
848	>	if (doHeatFlux_)
849	>	fDecomp_->addToHeatFlux((idat.d) dot(fg, vel2));
850	>	}
851		}
852
853	<	for (vector<int>::iterator ia = atomListRow.begin();
853	>	for (ia = atomListRow.begin();
854		ia != atomListRow.end(); ++ia) {
855		atom1 = (*ia);
856		mf = fDecomp_->getMassFactorRow(atom1);
#	Line 388 \| Line 858 \| namespace OpenMD {
858		// presence in switching region
859		fg = swderiv * d_grp * mf;
860		fDecomp_->addForceToAtomRow(atom1, fg);
391	–
861		if (atomListRow.size() > 1) {
862		if (info_->usesAtomicVirial()) {
863		// find the distance between the atom
864		// and the center of the cutoff group:
865		dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
866	<	tau -= outProduct(dag, fg);
866	>	stressTensor -= outProduct(dag, fg);
867	>	if (doHeatFlux_)
868	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
869		}
870		}
871		}
872	<	for (vector<int>::iterator jb = atomListColumn.begin();
872	>	for (jb = atomListColumn.begin();
873		jb != atomListColumn.end(); ++jb) {
874		atom2 = (*jb);
875		mf = fDecomp_->getMassFactorColumn(atom2);
#	Line 412 \| Line 883 \| namespace OpenMD {
883		// find the distance between the atom
884		// and the center of the cutoff group:
885		dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
886	<	tau -= outProduct(dag, fg);
886	>	stressTensor -= outProduct(dag, fg);
887	>	if (doHeatFlux_)
888	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
889		}
890		}
891		}
892		}
893	<	//if (!SIM_uses_AtomicVirial) {
894	<	// tau -= outProduct(d_grp, fij);
893	>	//if (!info_->usesAtomicVirial()) {
894	>	// stressTensor -= outProduct(d_grp, fij);
895	>	// if (doHeatFlux_)
896	>	// fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
897		//}
898		}
899		}
900		}
901
902		if (iLoop == PREPAIR_LOOP) {
903	<	if (info_->requiresPrepair()) {
903	>	if (info_->requiresPrepair()) {
904	>
905		fDecomp_->collectIntermediateData();
906	<	atomListLocal = fDecomp_->getAtomList();
907	<	for (vector<int>::iterator ia = atomListLocal.begin();
908	<	ia != atomListLocal.end(); ++ia) {
433	<	atom1 = (*ia);
434	<	sdat = fDecomp_->fillSelfData(atom1);
906	>
907	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
908	>	fDecomp_->fillSelfData(sdat, atom1);
909		interactionMan_->doPreForce(sdat);
910		}
911	<	fDecomp_->distributeIntermediateData();
911	>
912	>	fDecomp_->distributeIntermediateData();
913	>
914		}
915		}
440	–
916		}
917
918	+	// collects pairwise information
919		fDecomp_->collectData();
920	<
921	<	if (info_->requiresSkipCorrection() \|\| info_->requiresSelfCorrection()) {
922	<	atomListLocal = fDecomp_->getAtomList();
923	<	for (vector<int>::iterator ia = atomListLocal.begin();
924	<	ia != atomListLocal.end(); ++ia) {
449	<	atom1 = (*ia);
450	<
451	<	if (info_->requiresSkipCorrection()) {
452	<	vector<int> skipList = fDecomp_->getSkipsForAtom(atom1);
453	<	for (vector<int>::iterator jb = skipList.begin();
454	<	jb != skipList.end(); ++jb) {
455	<	atom2 = (*jb);
456	<	idat = fDecomp_->fillSkipData(atom1, atom2);
457	<	interactionMan_->doSkipCorrection(idat);
458	<	}
459	<	}
460	<
461	<	if (info_->requiresSelfCorrection()) {
462	<	sdat = fDecomp_->fillSelfData(atom1);
463	<	interactionMan_->doSelfCorrection(sdat);
464	<	}
920	>
921	>	if (info_->requiresSelfCorrection()) {
922	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
923	>	fDecomp_->fillSelfData(sdat, atom1);
924	>	interactionMan_->doSelfCorrection(sdat);
925		}
926		}
927
928	<	// dangerous to iterate over enums, but we'll live on the edge:
929	<	for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
930	<	lrPot += longRangePotential[i]; //Quick hack
931	<	}
932	<
933	<	//store the tau and long range potential
934	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
935	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
936	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
928	>	// collects single-atom information
929	>	fDecomp_->collectSelfData();
930	>
931	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
932	>	*(fDecomp_->getPairwisePotential());
933	>
934	>	curSnapshot->setLongRangePotential(longRangePotential);
935	>
936	>	curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
937	>	*(fDecomp_->getExcludedPotential()));
938	>
939		}
940
941
942		void ForceManager::postCalculation() {
943	+
944	+	vector<Perturbation*>::iterator pi;
945	+	for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
946	+	(*pi)->applyPerturbation();
947	+	}
948	+
949		SimInfo::MoleculeIterator mi;
950		Molecule* mol;
951		Molecule::RigidBodyIterator rbIter;
952		RigidBody* rb;
953		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
954	<
954	>
955		// collect the atomic forces onto rigid bodies
956
957		for (mol = info_->beginMolecule(mi); mol != NULL;
#	Line 491 \| Line 959 \| namespace OpenMD {
959		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
960		rb = mol->nextRigidBody(rbIter)) {
961		Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
962	<	tau += rbTau;
962	>	stressTensor += rbTau;
963		}
964		}
965
966		#ifdef IS_MPI
967	<	Mat3x3d tmpTau(tau);
968	<	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
501	<	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
967	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
968	>	MPI::REALTYPE, MPI::SUM);
969		#endif
970	<	curSnapshot->statData.setTau(tau);
971	<	}
970	>	curSnapshot->setStressTensor(stressTensor);
971	>
972	>	if (info_->getSimParams()->getUseLongRangeCorrections()) {
973	>	/*
974	>	RealType vol = curSnapshot->getVolume();
975	>	RealType Elrc(0.0);
976	>	RealType Wlrc(0.0);
977
978	<	} //end namespace OpenMD
978	>	set<AtomType*>::iterator i;
979	>	set<AtomType*>::iterator j;
980	>
981	>	RealType n_i, n_j;
982	>	RealType rho_i, rho_j;
983	>	pair<RealType, RealType> LRI;
984	>
985	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
986	>	n_i = RealType(info_->getGlobalCountOfType(*i));
987	>	rho_i = n_i / vol;
988	>	for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
989	>	n_j = RealType(info_->getGlobalCountOfType(*j));
990	>	rho_j = n_j / vol;
991	>
992	>	LRI = interactionMan_->getLongRangeIntegrals( (i), (j) );
993	>
994	>	Elrc += n_i * rho_j * LRI.first;
995	>	Wlrc -= rho_i * rho_j * LRI.second;
996	>	}
997	>	}
998	>	Elrc = 2.0 NumericConstant::PI;
999	>	Wlrc = 2.0 NumericConstant::PI;
1000	>
1001	>	RealType lrp = curSnapshot->getLongRangePotential();
1002	>	curSnapshot->setLongRangePotential(lrp + Elrc);
1003	>	stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
1004	>	curSnapshot->setStressTensor(stressTensor);
1005	>	*/
1006	>
1007	>	}
1008	>	}
1009	>	}

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Comparing branches/development/src/brains/ForceManager.cpp (file contents): Revision 1569 by gezelter, Thu May 26 13:55:04 2011 UTC vs. Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC

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Comparing branches/development/src/brains/ForceManager.cpp (file contents):
Revision 1569 by gezelter, Thu May 26 13:55:04 2011 UTC vs.
Revision 1874 by gezelter, Wed May 15 15:09:35 2013 UTC