[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 1866 by gezelter, Thu Apr 25 14:32:56 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) {
71	<
72	<	#ifdef IS_MPI
73	<	fDecomp_ = new ForceMatrixDecomposition(info_);
74	<	#else
69	<	// fDecomp_ = new ForceSerialDecomposition(info);
70	<	#endif
71	>	forceField_ = info_->getForceField();
72	>	interactionMan_ = new InteractionManager();
73	>	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
74	>	thermo = new Thermo(info_);
75		}
76	+
77	+	/**
78	+	* setupCutoffs
79	+	*
80	+	* Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
81	+	* and cutoffPolicy
82	+	*
83	+	* cutoffRadius : realType
84	+	* If the cutoffRadius was explicitly set, use that value.
85	+	* If the cutoffRadius was not explicitly set:
86	+	* Are there electrostatic atoms? Use 12.0 Angstroms.
87	+	* No electrostatic atoms? Poll the atom types present in the
88	+	* simulation for suggested cutoff values (e.g. 2.5 * sigma).
89	+	* Use the maximum suggested value that was found.
90	+	*
91	+	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
92	+	* or SHIFTED_POTENTIAL)
93	+	* If cutoffMethod was explicitly set, use that choice.
94	+	* If cutoffMethod was not explicitly set, use SHIFTED_FORCE
95	+	*
96	+	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
97	+	* If cutoffPolicy was explicitly set, use that choice.
98	+	* If cutoffPolicy was not explicitly set, use TRADITIONAL
99	+	*
100	+	* switchingRadius : realType
101	+	* If the cutoffMethod was set to SWITCHED:
102	+	* If the switchingRadius was explicitly set, use that value
103	+	* (but do a sanity check first).
104	+	* If the switchingRadius was not explicitly set: use 0.85 *
105	+	* cutoffRadius_
106	+	* If the cutoffMethod was not set to SWITCHED:
107	+	* Set switchingRadius equal to cutoffRadius for safety.
108	+	*/
109	+	void ForceManager::setupCutoffs() {
110	+
111	+	Globals* simParams_ = info_->getSimParams();
112	+	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
113	+	int mdFileVersion;
114	+	rCut_ = 0.0; //Needs a value for a later max() call;
115	+
116	+	if (simParams_->haveMDfileVersion())
117	+	mdFileVersion = simParams_->getMDfileVersion();
118	+	else
119	+	mdFileVersion = 0;
120	+
121	+	// We need the list of simulated atom types to figure out cutoffs
122	+	// as well as long range corrections.
123	+
124	+	set<AtomType*>::iterator i;
125	+	set<AtomType*> atomTypes_;
126	+	atomTypes_ = info_->getSimulatedAtomTypes();
127	+
128	+	if (simParams_->haveCutoffRadius()) {
129	+	rCut_ = simParams_->getCutoffRadius();
130	+	} else {
131	+	if (info_->usesElectrostaticAtoms()) {
132	+	sprintf(painCave.errMsg,
133	+	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
134	+	"\tOpenMD will use a default value of 12.0 angstroms"
135	+	"\tfor the cutoffRadius.\n");
136	+	painCave.isFatal = 0;
137	+	painCave.severity = OPENMD_INFO;
138	+	simError();
139	+	rCut_ = 12.0;
140	+	} else {
141	+	RealType thisCut;
142	+	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
143	+	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
144	+	rCut_ = max(thisCut, rCut_);
145	+	}
146	+	sprintf(painCave.errMsg,
147	+	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
148	+	"\tOpenMD will use %lf angstroms.\n",
149	+	rCut_);
150	+	painCave.isFatal = 0;
151	+	painCave.severity = OPENMD_INFO;
152	+	simError();
153	+	}
154	+	}
155	+
156	+	fDecomp_->setUserCutoff(rCut_);
157	+	interactionMan_->setCutoffRadius(rCut_);
158	+
159	+	map<string, CutoffMethod> stringToCutoffMethod;
160	+	stringToCutoffMethod["HARD"] = HARD;
161	+	stringToCutoffMethod["SWITCHED"] = SWITCHED;
162	+	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
163	+	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
164
165	<	void ForceManager::calcForces() {
165	>	if (simParams_->haveCutoffMethod()) {
166	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
167	>	map<string, CutoffMethod>::iterator i;
168	>	i = stringToCutoffMethod.find(cutMeth);
169	>	if (i == stringToCutoffMethod.end()) {
170	>	sprintf(painCave.errMsg,
171	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
172	>	"\tShould be one of: "
173	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
174	>	cutMeth.c_str());
175	>	painCave.isFatal = 1;
176	>	painCave.severity = OPENMD_ERROR;
177	>	simError();
178	>	} else {
179	>	cutoffMethod_ = i->second;
180	>	}
181	>	} else {
182	>	if (mdFileVersion > 1) {
183	>	sprintf(painCave.errMsg,
184	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
185	>	"\tOpenMD will use SHIFTED_FORCE.\n");
186	>	painCave.isFatal = 0;
187	>	painCave.severity = OPENMD_INFO;
188	>	simError();
189	>	cutoffMethod_ = SHIFTED_FORCE;
190	>	} else {
191	>	// handle the case where the old file version was in play
192	>	// (there should be no cutoffMethod, so we have to deduce it
193	>	// from other data).
194	>
195	>	sprintf(painCave.errMsg,
196	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
197	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
198	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
199	>	"\tbehavior of the older (version 1) code. To remove this\n"
200	>	"\twarning, add an explicit cutoffMethod and change the top\n"
201	>	"\tof the file so that it begins with <OpenMD version=2>\n");
202	>	painCave.isFatal = 0;
203	>	painCave.severity = OPENMD_WARNING;
204	>	simError();
205	>
206	>	// The old file version tethered the shifting behavior to the
207	>	// electrostaticSummationMethod keyword.
208	>
209	>	if (simParams_->haveElectrostaticSummationMethod()) {
210	>	string myMethod = simParams_->getElectrostaticSummationMethod();
211	>	toUpper(myMethod);
212	>
213	>	if (myMethod == "SHIFTED_POTENTIAL") {
214	>	cutoffMethod_ = SHIFTED_POTENTIAL;
215	>	} else if (myMethod == "SHIFTED_FORCE") {
216	>	cutoffMethod_ = SHIFTED_FORCE;
217	>	}
218	>
219	>	if (simParams_->haveSwitchingRadius())
220	>	rSwitch_ = simParams_->getSwitchingRadius();
221	>
222	>	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
223	>	if (simParams_->haveSwitchingRadius()){
224	>	sprintf(painCave.errMsg,
225	>	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
226	>	"\tA value was set for the switchingRadius\n"
227	>	"\teven though the electrostaticSummationMethod was\n"
228	>	"\tset to %s\n", myMethod.c_str());
229	>	painCave.severity = OPENMD_WARNING;
230	>	painCave.isFatal = 1;
231	>	simError();
232	>	}
233	>	}
234	>	if (abs(rCut_ - rSwitch_) < 0.0001) {
235	>	if (cutoffMethod_ == SHIFTED_FORCE) {
236	>	sprintf(painCave.errMsg,
237	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
238	>	"\tcutoffRadius and switchingRadius are set to the\n"
239	>	"\tsame value. OpenMD will use shifted force\n"
240	>	"\tpotentials instead of switching functions.\n");
241	>	painCave.isFatal = 0;
242	>	painCave.severity = OPENMD_WARNING;
243	>	simError();
244	>	} else {
245	>	cutoffMethod_ = SHIFTED_POTENTIAL;
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 potentials\n"
250	>	"\tinstead of switching functions.\n");
251	>	painCave.isFatal = 0;
252	>	painCave.severity = OPENMD_WARNING;
253	>	simError();
254	>	}
255	>	}
256	>	}
257	>	}
258	>	}
259	>
260	>	map<string, CutoffPolicy> stringToCutoffPolicy;
261	>	stringToCutoffPolicy["MIX"] = MIX;
262	>	stringToCutoffPolicy["MAX"] = MAX;
263	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
264	>
265	>	string cutPolicy;
266	>	if (forceFieldOptions_.haveCutoffPolicy()){
267	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
268	>	}else if (simParams_->haveCutoffPolicy()) {
269	>	cutPolicy = simParams_->getCutoffPolicy();
270	>	}
271	>
272	>	if (!cutPolicy.empty()){
273	>	toUpper(cutPolicy);
274	>	map<string, CutoffPolicy>::iterator i;
275	>	i = stringToCutoffPolicy.find(cutPolicy);
276	>
277	>	if (i == stringToCutoffPolicy.end()) {
278	>	sprintf(painCave.errMsg,
279	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
280	>	"\tShould be one of: "
281	>	"MIX, MAX, or TRADITIONAL\n",
282	>	cutPolicy.c_str());
283	>	painCave.isFatal = 1;
284	>	painCave.severity = OPENMD_ERROR;
285	>	simError();
286	>	} else {
287	>	cutoffPolicy_ = i->second;
288	>	}
289	>	} else {
290	>	sprintf(painCave.errMsg,
291	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
292	>	"\tOpenMD will use TRADITIONAL.\n");
293	>	painCave.isFatal = 0;
294	>	painCave.severity = OPENMD_INFO;
295	>	simError();
296	>	cutoffPolicy_ = TRADITIONAL;
297	>	}
298	>
299	>	fDecomp_->setCutoffPolicy(cutoffPolicy_);
300	>
301	>	// create the switching function object:
302	>
303	>	switcher_ = new SwitchingFunction();
304	>
305	>	if (cutoffMethod_ == SWITCHED) {
306	>	if (simParams_->haveSwitchingRadius()) {
307	>	rSwitch_ = simParams_->getSwitchingRadius();
308	>	if (rSwitch_ > rCut_) {
309	>	sprintf(painCave.errMsg,
310	>	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
311	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
312	>	painCave.isFatal = 1;
313	>	painCave.severity = OPENMD_ERROR;
314	>	simError();
315	>	}
316	>	} else {
317	>	rSwitch_ = 0.85 * rCut_;
318	>	sprintf(painCave.errMsg,
319	>	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
320	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
321	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
322	>	painCave.isFatal = 0;
323	>	painCave.severity = OPENMD_WARNING;
324	>	simError();
325	>	}
326	>	} else {
327	>	if (mdFileVersion > 1) {
328	>	// throw an error if we define a switching radius and don't need one.
329	>	// older file versions should not do this.
330	>	if (simParams_->haveSwitchingRadius()) {
331	>	map<string, CutoffMethod>::const_iterator it;
332	>	string theMeth;
333	>	for (it = stringToCutoffMethod.begin();
334	>	it != stringToCutoffMethod.end(); ++it) {
335	>	if (it->second == cutoffMethod_) {
336	>	theMeth = it->first;
337	>	break;
338	>	}
339	>	}
340	>	sprintf(painCave.errMsg,
341	>	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
342	>	"\tis not set to SWITCHED, so switchingRadius value\n"
343	>	"\twill be ignored for this simulation\n", theMeth.c_str());
344	>	painCave.isFatal = 0;
345	>	painCave.severity = OPENMD_WARNING;
346	>	simError();
347	>	}
348	>	}
349	>	rSwitch_ = rCut_;
350	>	}
351
352	+	// Default to cubic switching function.
353	+	sft_ = cubic;
354	+	if (simParams_->haveSwitchingFunctionType()) {
355	+	string funcType = simParams_->getSwitchingFunctionType();
356	+	toUpper(funcType);
357	+	if (funcType == "CUBIC") {
358	+	sft_ = cubic;
359	+	} else {
360	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
361	+	sft_ = fifth_order_poly;
362	+	} else {
363	+	// throw error
364	+	sprintf( painCave.errMsg,
365	+	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
366	+	"\tswitchingFunctionType must be one of: "
367	+	"\"cubic\" or \"fifth_order_polynomial\".",
368	+	funcType.c_str() );
369	+	painCave.isFatal = 1;
370	+	painCave.severity = OPENMD_ERROR;
371	+	simError();
372	+	}
373	+	}
374	+	}
375	+	switcher_->setSwitchType(sft_);
376	+	switcher_->setSwitch(rSwitch_, rCut_);
377	+	}
378	+
379	+
380	+
381	+
382	+	void ForceManager::initialize() {
383	+
384		if (!info_->isTopologyDone()) {
385	+
386		info_->update();
387		interactionMan_->setSimInfo(info_);
388		interactionMan_->initialize();
389	<	swfun_ = interactionMan_->getSwitchingFunction();
390	<	fDecomp_->distributeInitialData();
391	<	info_->prepareTopology();
389	>
390	>	// We want to delay the cutoffs until after the interaction
391	>	// manager has set up the atom-atom interactions so that we can
392	>	// query them for suggested cutoff values
393	>	setupCutoffs();
394	>
395	>	info_->prepareTopology();
396	>
397	>	doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
398	>	doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
399	>	if (doHeatFlux_) doParticlePot_ = true;
400	>
401	>	doElectricField_ = info_->getSimParams()->getOutputElectricField();
402	>
403		}
404	+
405	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
406
407	+	// Force fields can set options on how to scale van der Waals and
408	+	// electrostatic interactions for atoms connected via bonds, bends
409	+	// and torsions in this case the topological distance between
410	+	// atoms is:
411	+	// 0 = topologically unconnected
412	+	// 1 = bonded together
413	+	// 2 = connected via a bend
414	+	// 3 = connected via a torsion
415	+
416	+	vdwScale_.reserve(4);
417	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
418	+
419	+	electrostaticScale_.reserve(4);
420	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
421	+
422	+	vdwScale_[0] = 1.0;
423	+	vdwScale_[1] = fopts.getvdw12scale();
424	+	vdwScale_[2] = fopts.getvdw13scale();
425	+	vdwScale_[3] = fopts.getvdw14scale();
426	+
427	+	electrostaticScale_[0] = 1.0;
428	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
429	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
430	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
431	+
432	+	if (info_->getSimParams()->haveElectricField()) {
433	+	ElectricField* eField = new ElectricField(info_);
434	+	perturbations_.push_back(eField);
435	+	}
436	+
437	+	usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
438	+
439	+	fDecomp_->distributeInitialData();
440	+
441	+	initialized_ = true;
442	+
443	+	}
444	+
445	+	void ForceManager::calcForces() {
446	+
447	+	if (!initialized_) initialize();
448	+
449		preCalculation();
450		shortRangeInteractions();
451		longRangeInteractions();
452	<	postCalculation();
88	<
452	>	postCalculation();
453		}
454
455		void ForceManager::preCalculation() {
#	Line 98 \| Line 462 \| namespace OpenMD {
462		Molecule::CutoffGroupIterator ci;
463		CutoffGroup* cg;
464
465	<	// forces are zeroed here, before any are accumulated.
465	>	// forces and potentials are zeroed here, before any are
466	>	// accumulated.
467
468	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
469	+
470	+	snap->setBondPotential(0.0);
471	+	snap->setBendPotential(0.0);
472	+	snap->setTorsionPotential(0.0);
473	+	snap->setInversionPotential(0.0);
474	+
475	+	potVec zeroPot(0.0);
476	+	snap->setLongRangePotential(zeroPot);
477	+	snap->setExcludedPotentials(zeroPot);
478	+
479	+	snap->setRestraintPotential(0.0);
480	+	snap->setRawPotential(0.0);
481	+
482		for (mol = info_->beginMolecule(mi); mol != NULL;
483		mol = info_->nextMolecule(mi)) {
484	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
484	>	for(atom = mol->beginAtom(ai); atom != NULL;
485	>	atom = mol->nextAtom(ai)) {
486		atom->zeroForcesAndTorques();
487		}
488	<
488	>
489		//change the positions of atoms which belong to the rigidbodies
490		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
491		rb = mol->nextRigidBody(rbIter)) {
492		rb->zeroForcesAndTorques();
493		}
494	<
494	>
495		if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
496		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
497		cg = mol->nextCutoffGroup(ci)) {
#	Line 120 \| Line 500 \| namespace OpenMD {
500		}
501		}
502		}
123	–
124	–	// Zero out the stress tensor
125	–	tau *= 0.0;
503
504	+	// Zero out the stress tensor
505	+	stressTensor *= 0.0;
506	+	// Zero out the heatFlux
507	+	fDecomp_->setHeatFlux( Vector3d(0.0) );
508		}
509
510		void ForceManager::shortRangeInteractions() {
#	Line 156 \| Line 537 \| namespace OpenMD {
537
538		for (bond = mol->beginBond(bondIter); bond != NULL;
539		bond = mol->nextBond(bondIter)) {
540	<	bond->calcForce();
540	>	bond->calcForce(doParticlePot_);
541		bondPotential += bond->getPotential();
542		}
543
#	Line 164 \| Line 545 \| namespace OpenMD {
545		bend = mol->nextBend(bendIter)) {
546
547		RealType angle;
548	<	bend->calcForce(angle);
548	>	bend->calcForce(angle, doParticlePot_);
549		RealType currBendPot = bend->getPotential();
550
551		bendPotential += bend->getPotential();
#	Line 174 \| Line 555 \| namespace OpenMD {
555		dataSet.prev.angle = dataSet.curr.angle = angle;
556		dataSet.prev.potential = dataSet.curr.potential = currBendPot;
557		dataSet.deltaV = 0.0;
558	<	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
558	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
559	>	dataSet));
560		}else {
561		i->second.prev.angle = i->second.curr.angle;
562		i->second.prev.potential = i->second.curr.potential;
#	Line 188 \| Line 570 \| namespace OpenMD {
570		for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
571		torsion = mol->nextTorsion(torsionIter)) {
572		RealType angle;
573	<	torsion->calcForce(angle);
573	>	torsion->calcForce(angle, doParticlePot_);
574		RealType currTorsionPot = torsion->getPotential();
575		torsionPotential += torsion->getPotential();
576		map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
#	Line 212 \| Line 594 \| namespace OpenMD {
594		inversion != NULL;
595		inversion = mol->nextInversion(inversionIter)) {
596		RealType angle;
597	<	inversion->calcForce(angle);
597	>	inversion->calcForce(angle, doParticlePot_);
598		RealType currInversionPot = inversion->getPotential();
599		inversionPotential += inversion->getPotential();
600		map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
#	Line 232 \| Line 614 \| namespace OpenMD {
614		}
615		}
616		}
617	<
618	<	RealType shortRangePotential = bondPotential + bendPotential +
619	<	torsionPotential + inversionPotential;
617	>
618	>	#ifdef IS_MPI
619	>	// Collect from all nodes. This should eventually be moved into a
620	>	// SystemDecomposition, but this is a better place than in
621	>	// Thermo to do the collection.
622	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
623	>	MPI::SUM);
624	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
625	>	MPI::SUM);
626	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
627	>	MPI::REALTYPE, MPI::SUM);
628	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
629	>	MPI::REALTYPE, MPI::SUM);
630	>	#endif
631	>
632		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
633	<	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
634	<	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
635	<	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
636	<	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
637	<	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
633	>
634	>	curSnapshot->setBondPotential(bondPotential);
635	>	curSnapshot->setBendPotential(bendPotential);
636	>	curSnapshot->setTorsionPotential(torsionPotential);
637	>	curSnapshot->setInversionPotential(inversionPotential);
638	>
639	>	// RealType shortRangePotential = bondPotential + bendPotential +
640	>	// torsionPotential + inversionPotential;
641	>
642	>	// curSnapshot->setShortRangePotential(shortRangePotential);
643		}
644
645		void ForceManager::longRangeInteractions() {
646
647	<	// some of this initial stuff will go away:
647	>
648		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
649		DataStorage* config = &(curSnapshot->atomData);
650		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;
651
652	<	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
653	<	rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
652	>	//calculate the center of mass of cutoff group
653	>
654	>	SimInfo::MoleculeIterator mi;
655	>	Molecule* mol;
656	>	Molecule::CutoffGroupIterator ci;
657	>	CutoffGroup* cg;
658	>
659	>	if(info_->getNCutoffGroups() > 0){
660	>	for (mol = info_->beginMolecule(mi); mol != NULL;
661	>	mol = info_->nextMolecule(mi)) {
662	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
663	>	cg = mol->nextCutoffGroup(ci)) {
664	>	cg->updateCOM();
665	>	}
666	>	}
667		} else {
668		// center of mass of the group is the same as position of the atom
669		// if cutoff group does not exist
670	<	rc = pos;
671	<	}
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
670	>	cgConfig->position = config->position;
671	>	cgConfig->velocity = config->velocity;
672		}
673
674	<	// new stuff starts here:
279	<
674	>	fDecomp_->zeroWorkArrays();
675		fDecomp_->distributeData();
676	<
677	<	int cg1, cg2, atom1, atom2;
678	<	Vector3d d_grp, dag;
679	<	RealType rgrpsq, rgrp;
676	>
677	>	int cg1, cg2, atom1, atom2, topoDist;
678	>	Vector3d d_grp, dag, d, gvel2, vel2;
679	>	RealType rgrpsq, rgrp, r2, r;
680	>	RealType electroMult, vdwMult;
681		RealType vij;
682	<	Vector3d fij, fg;
683	<	pair<int, int> gtypes;
682	>	Vector3d fij, fg, f1;
683	>	tuple3<RealType, RealType, RealType> cuts;
684		RealType rCutSq;
685		bool in_switching_region;
686		RealType sw, dswdr, swderiv;
#	Line 292 \| Line 688 \| namespace OpenMD {
688		InteractionData idat;
689		SelfData sdat;
690		RealType mf;
691	+	RealType vpair;
692	+	RealType dVdFQ1(0.0);
693	+	RealType dVdFQ2(0.0);
694	+	potVec longRangePotential(0.0);
695	+	potVec workPot(0.0);
696	+	potVec exPot(0.0);
697	+	Vector3d eField1(0.0);
698	+	Vector3d eField2(0.0);
699	+	vector<int>::iterator ia, jb;
700
701		int loopStart, loopEnd;
702
703	+	idat.vdwMult = &vdwMult;
704	+	idat.electroMult = &electroMult;
705	+	idat.pot = &workPot;
706	+	idat.excludedPot = &exPot;
707	+	sdat.pot = fDecomp_->getEmbeddingPotential();
708	+	sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
709	+	idat.vpair = &vpair;
710	+	idat.dVdFQ1 = &dVdFQ1;
711	+	idat.dVdFQ2 = &dVdFQ2;
712	+	idat.eField1 = &eField1;
713	+	idat.eField2 = &eField2;
714	+	idat.f1 = &f1;
715	+	idat.sw = &sw;
716	+	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
717	+	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
718	+	idat.doParticlePot = doParticlePot_;
719	+	idat.doElectricField = doElectricField_;
720	+	sdat.doParticlePot = doParticlePot_;
721	+
722		loopEnd = PAIR_LOOP;
723		if (info_->requiresPrepair() ) {
724		loopStart = PREPAIR_LOOP;
725		} else {
726		loopStart = PAIR_LOOP;
727		}
728	<
729	<	for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
306	<
728	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
729	>
730		if (iLoop == loopStart) {
731		bool update_nlist = fDecomp_->checkNeighborList();
732	<	if (update_nlist)
732	>	if (update_nlist) {
733	>	if (!usePeriodicBoundaryConditions_)
734	>	Mat3x3d bbox = thermo->getBoundingBox();
735		neighborList = fDecomp_->buildNeighborList();
736	+	}
737		}
738
739		for (vector<pair<int, int> >::iterator it = neighborList.begin();
740		it != neighborList.end(); ++it) {
741	<
741	>
742		cg1 = (*it).first;
743		cg2 = (*it).second;
744	+
745	+	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
746
319	–	gtypes = fDecomp_->getGroupTypes(cg1, cg2);
747		d_grp = fDecomp_->getIntergroupVector(cg1, cg2);
748	+
749		curSnapshot->wrapVector(d_grp);
750		rgrpsq = d_grp.lengthSquare();
751	<	rCutSq = groupCutoffMap[gtypes].first;
751	>	rCutSq = cuts.second;
752
753		if (rgrpsq < rCutSq) {
754	<	*(idat.rcut) = groupCutoffMap[gtypes].second;
754	>	idat.rcut = &cuts.first;
755		if (iLoop == PAIR_LOOP) {
756	<	vij *= 0.0;
756	>	vij = 0.0;
757		fij = V3Zero;
758	+	eField1 = V3Zero;
759	+	eField2 = V3Zero;
760		}
761
762	<	in_switching_region = swfun_->getSwitch(rgrpsq, *(idat.sw), dswdr,
763	<	rgrp);
762	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
763	>	rgrp);
764	>
765		atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
766		atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
767
768	<	for (vector<int>::iterator ia = atomListRow.begin();
768	>	if (doHeatFlux_)
769	>	gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
770	>
771	>	for (ia = atomListRow.begin();
772		ia != atomListRow.end(); ++ia) {
773		atom1 = (*ia);
774	<
775	<	for (vector<int>::iterator jb = atomListColumn.begin();
774	>
775	>	for (jb = atomListColumn.begin();
776		jb != atomListColumn.end(); ++jb) {
777		atom2 = (*jb);
344	–
345	–	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
346	–
347	–	idat = fDecomp_->fillInteractionData(atom1, atom2);
778
779	+	if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
780	+
781	+	vpair = 0.0;
782	+	workPot = 0.0;
783	+	exPot = 0.0;
784	+	f1 = V3Zero;
785	+	dVdFQ1 = 0.0;
786	+	dVdFQ2 = 0.0;
787	+
788	+	fDecomp_->fillInteractionData(idat, atom1, atom2);
789	+
790	+	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
791	+	vdwMult = vdwScale_[topoDist];
792	+	electroMult = electrostaticScale_[topoDist];
793	+
794		if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
795	<	*(idat.d) = d_grp;
796	<	*(idat.r2) = rgrpsq;
795	>	idat.d = &d_grp;
796	>	idat.r2 = &rgrpsq;
797	>	if (doHeatFlux_)
798	>	vel2 = gvel2;
799		} else {
800	<	*(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2);
801	<	curSnapshot->wrapVector( *(idat.d) );
802	<	*(idat.r2) = idat.d->lengthSquare();
800	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
801	>	curSnapshot->wrapVector( d );
802	>	r2 = d.lengthSquare();
803	>	idat.d = &d;
804	>	idat.r2 = &r2;
805	>	if (doHeatFlux_)
806	>	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
807		}
357	–
358	–	(idat.rij) = sqrt( (idat.r2) );
808
809	+	r = sqrt( *(idat.r2) );
810	+	idat.rij = &r;
811	+
812		if (iLoop == PREPAIR_LOOP) {
813		interactionMan_->doPrePair(idat);
814		} else {
815		interactionMan_->doPair(idat);
816	<	vij += *(idat.vpair);
817	<	fij += *(idat.f1);
818	<	tau -= outProduct( (idat.d), (idat.f1));
816	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
817	>	vij += vpair;
818	>	fij += f1;
819	>	stressTensor -= outProduct( *(idat.d), f1);
820	>	if (doHeatFlux_)
821	>	fDecomp_->addToHeatFlux((idat.d) dot(f1, vel2));
822		}
823		}
824		}
#	Line 373 \| Line 828 \| namespace OpenMD {
828		if (in_switching_region) {
829		swderiv = vij * dswdr / rgrp;
830		fg = swderiv * d_grp;
376	–
831		fij += fg;
832
833		if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
834	<	tau -= outProduct( *(idat.d), fg);
834	>	if (!fDecomp_->skipAtomPair(atomListRow[0],
835	>	atomListColumn[0],
836	>	cg1, cg2)) {
837	>	stressTensor -= outProduct( *(idat.d), fg);
838	>	if (doHeatFlux_)
839	>	fDecomp_->addToHeatFlux((idat.d) dot(fg, vel2));
840	>	}
841		}
842
843	<	for (vector<int>::iterator ia = atomListRow.begin();
843	>	for (ia = atomListRow.begin();
844		ia != atomListRow.end(); ++ia) {
845		atom1 = (*ia);
846		mf = fDecomp_->getMassFactorRow(atom1);
#	Line 388 \| Line 848 \| namespace OpenMD {
848		// presence in switching region
849		fg = swderiv * d_grp * mf;
850		fDecomp_->addForceToAtomRow(atom1, fg);
391	–
851		if (atomListRow.size() > 1) {
852		if (info_->usesAtomicVirial()) {
853		// find the distance between the atom
854		// and the center of the cutoff group:
855		dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
856	<	tau -= outProduct(dag, fg);
856	>	stressTensor -= outProduct(dag, fg);
857	>	if (doHeatFlux_)
858	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
859		}
860		}
861		}
862	<	for (vector<int>::iterator jb = atomListColumn.begin();
862	>	for (jb = atomListColumn.begin();
863		jb != atomListColumn.end(); ++jb) {
864		atom2 = (*jb);
865		mf = fDecomp_->getMassFactorColumn(atom2);
#	Line 412 \| Line 873 \| namespace OpenMD {
873		// find the distance between the atom
874		// and the center of the cutoff group:
875		dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
876	<	tau -= outProduct(dag, fg);
876	>	stressTensor -= outProduct(dag, fg);
877	>	if (doHeatFlux_)
878	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
879		}
880		}
881		}
882		}
883	<	//if (!SIM_uses_AtomicVirial) {
884	<	// tau -= outProduct(d_grp, fij);
883	>	//if (!info_->usesAtomicVirial()) {
884	>	// stressTensor -= outProduct(d_grp, fij);
885	>	// if (doHeatFlux_)
886	>	// fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
887		//}
888		}
889		}
890		}
891
892		if (iLoop == PREPAIR_LOOP) {
893	<	if (info_->requiresPrepair()) {
893	>	if (info_->requiresPrepair()) {
894	>
895		fDecomp_->collectIntermediateData();
896
897	<	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
898	<	sdat = fDecomp_->fillSelfData(atom1);
897	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
898	>	fDecomp_->fillSelfData(sdat, atom1);
899		interactionMan_->doPreForce(sdat);
900		}
901
902	<	fDecomp_->distributeIntermediateData();
902	>	fDecomp_->distributeIntermediateData();
903	>
904		}
905		}
439	–
906		}
907
908	+	// collects pairwise information
909		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 );
910
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	–
911		if (info_->requiresSelfCorrection()) {
912	<
913	<	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
464	<	sdat = fDecomp_->fillSelfData(atom1);
912	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
913	>	fDecomp_->fillSelfData(sdat, atom1);
914		interactionMan_->doSelfCorrection(sdat);
915		}
467	–
916		}
917
918	<	// dangerous to iterate over enums, but we'll live on the edge:
919	<	for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
920	<	lrPot += longRangePotential[i]; //Quick hack
921	<	}
922	<
923	<	//store the tau and long range potential
924	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
925	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
926	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
918	>	// collects single-atom information
919	>	fDecomp_->collectSelfData();
920	>
921	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
922	>	*(fDecomp_->getPairwisePotential());
923	>
924	>	curSnapshot->setLongRangePotential(longRangePotential);
925	>
926	>	curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
927	>	*(fDecomp_->getExcludedPotential()));
928	>
929		}
930
931
932		void ForceManager::postCalculation() {
933	+
934	+	vector<Perturbation*>::iterator pi;
935	+	for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
936	+	(*pi)->applyPerturbation();
937	+	}
938	+
939		SimInfo::MoleculeIterator mi;
940		Molecule* mol;
941		Molecule::RigidBodyIterator rbIter;
942		RigidBody* rb;
943		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
944	<
944	>
945		// collect the atomic forces onto rigid bodies
946
947		for (mol = info_->beginMolecule(mi); mol != NULL;
#	Line 493 \| Line 949 \| namespace OpenMD {
949		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
950		rb = mol->nextRigidBody(rbIter)) {
951		Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
952	<	tau += rbTau;
952	>	stressTensor += rbTau;
953		}
954		}
955
956		#ifdef IS_MPI
957	<	Mat3x3d tmpTau(tau);
958	<	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
503	<	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
957	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
958	>	MPI::REALTYPE, MPI::SUM);
959		#endif
960	<	curSnapshot->statData.setTau(tau);
961	<	}
960	>	curSnapshot->setStressTensor(stressTensor);
961	>
962	>	if (info_->getSimParams()->getUseLongRangeCorrections()) {
963	>	/*
964	>	RealType vol = curSnapshot->getVolume();
965	>	RealType Elrc(0.0);
966	>	RealType Wlrc(0.0);
967
968	<	} //end namespace OpenMD
968	>	set<AtomType*>::iterator i;
969	>	set<AtomType*>::iterator j;
970	>
971	>	RealType n_i, n_j;
972	>	RealType rho_i, rho_j;
973	>	pair<RealType, RealType> LRI;
974	>
975	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
976	>	n_i = RealType(info_->getGlobalCountOfType(*i));
977	>	rho_i = n_i / vol;
978	>	for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
979	>	n_j = RealType(info_->getGlobalCountOfType(*j));
980	>	rho_j = n_j / vol;
981	>
982	>	LRI = interactionMan_->getLongRangeIntegrals( (i), (j) );
983	>
984	>	Elrc += n_i * rho_j * LRI.first;
985	>	Wlrc -= rho_i * rho_j * LRI.second;
986	>	}
987	>	}
988	>	Elrc = 2.0 NumericConstant::PI;
989	>	Wlrc = 2.0 NumericConstant::PI;
990	>
991	>	RealType lrp = curSnapshot->getLongRangePotential();
992	>	curSnapshot->setLongRangePotential(lrp + Elrc);
993	>	stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
994	>	curSnapshot->setStressTensor(stressTensor);
995	>	*/
996	>
997	>	}
998	>	}
999	>	}

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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 1866 by gezelter, Thu Apr 25 14:32:56 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 1866 by gezelter, Thu Apr 25 14:32:56 2013 UTC