[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 1850 by gezelter, Wed Feb 20 15:39:39 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_);
68	<	#else
69	<	// fDecomp_ = new ForceSerialDecomposition(info);
70	<	#endif
71	>	forceField_ = info_->getForceField();
72	>	interactionMan_ = new InteractionManager();
73	>	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
74		}
75	+
76	+	/**
77	+	* setupCutoffs
78	+	*
79	+	* Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
80	+	* and cutoffPolicy
81	+	*
82	+	* cutoffRadius : realType
83	+	* If the cutoffRadius was explicitly set, use that value.
84	+	* If the cutoffRadius was not explicitly set:
85	+	* Are there electrostatic atoms? Use 12.0 Angstroms.
86	+	* No electrostatic atoms? Poll the atom types present in the
87	+	* simulation for suggested cutoff values (e.g. 2.5 * sigma).
88	+	* Use the maximum suggested value that was found.
89	+	*
90	+	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
91	+	* or SHIFTED_POTENTIAL)
92	+	* If cutoffMethod was explicitly set, use that choice.
93	+	* If cutoffMethod was not explicitly set, use SHIFTED_FORCE
94	+	*
95	+	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
96	+	* If cutoffPolicy was explicitly set, use that choice.
97	+	* If cutoffPolicy was not explicitly set, use TRADITIONAL
98	+	*
99	+	* switchingRadius : realType
100	+	* If the cutoffMethod was set to SWITCHED:
101	+	* If the switchingRadius was explicitly set, use that value
102	+	* (but do a sanity check first).
103	+	* If the switchingRadius was not explicitly set: use 0.85 *
104	+	* cutoffRadius_
105	+	* If the cutoffMethod was not set to SWITCHED:
106	+	* Set switchingRadius equal to cutoffRadius for safety.
107	+	*/
108	+	void ForceManager::setupCutoffs() {
109	+
110	+	Globals* simParams_ = info_->getSimParams();
111	+	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
112	+	int mdFileVersion;
113	+	rCut_ = 0.0; //Needs a value for a later max() call;
114	+
115	+	if (simParams_->haveMDfileVersion())
116	+	mdFileVersion = simParams_->getMDfileVersion();
117	+	else
118	+	mdFileVersion = 0;
119	+
120	+	// We need the list of simulated atom types to figure out cutoffs
121	+	// as well as long range corrections.
122	+
123	+	set<AtomType*>::iterator i;
124	+	set<AtomType*> atomTypes_;
125	+	atomTypes_ = info_->getSimulatedAtomTypes();
126	+
127	+	if (simParams_->haveCutoffRadius()) {
128	+	rCut_ = simParams_->getCutoffRadius();
129	+	} else {
130	+	if (info_->usesElectrostaticAtoms()) {
131	+	sprintf(painCave.errMsg,
132	+	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
133	+	"\tOpenMD will use a default value of 12.0 angstroms"
134	+	"\tfor the cutoffRadius.\n");
135	+	painCave.isFatal = 0;
136	+	painCave.severity = OPENMD_INFO;
137	+	simError();
138	+	rCut_ = 12.0;
139	+	} else {
140	+	RealType thisCut;
141	+	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
142	+	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
143	+	rCut_ = max(thisCut, rCut_);
144	+	}
145	+	sprintf(painCave.errMsg,
146	+	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
147	+	"\tOpenMD will use %lf angstroms.\n",
148	+	rCut_);
149	+	painCave.isFatal = 0;
150	+	painCave.severity = OPENMD_INFO;
151	+	simError();
152	+	}
153	+	}
154	+
155	+	fDecomp_->setUserCutoff(rCut_);
156	+	interactionMan_->setCutoffRadius(rCut_);
157	+
158	+	map<string, CutoffMethod> stringToCutoffMethod;
159	+	stringToCutoffMethod["HARD"] = HARD;
160	+	stringToCutoffMethod["SWITCHED"] = SWITCHED;
161	+	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
162	+	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
163
164	<	void ForceManager::calcForces() {
164	>	if (simParams_->haveCutoffMethod()) {
165	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
166	>	map<string, CutoffMethod>::iterator i;
167	>	i = stringToCutoffMethod.find(cutMeth);
168	>	if (i == stringToCutoffMethod.end()) {
169	>	sprintf(painCave.errMsg,
170	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
171	>	"\tShould be one of: "
172	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
173	>	cutMeth.c_str());
174	>	painCave.isFatal = 1;
175	>	painCave.severity = OPENMD_ERROR;
176	>	simError();
177	>	} else {
178	>	cutoffMethod_ = i->second;
179	>	}
180	>	} else {
181	>	if (mdFileVersion > 1) {
182	>	sprintf(painCave.errMsg,
183	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
184	>	"\tOpenMD will use SHIFTED_FORCE.\n");
185	>	painCave.isFatal = 0;
186	>	painCave.severity = OPENMD_INFO;
187	>	simError();
188	>	cutoffMethod_ = SHIFTED_FORCE;
189	>	} else {
190	>	// handle the case where the old file version was in play
191	>	// (there should be no cutoffMethod, so we have to deduce it
192	>	// from other data).
193	>
194	>	sprintf(painCave.errMsg,
195	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
196	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
197	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
198	>	"\tbehavior of the older (version 1) code. To remove this\n"
199	>	"\twarning, add an explicit cutoffMethod and change the top\n"
200	>	"\tof the file so that it begins with <OpenMD version=2>\n");
201	>	painCave.isFatal = 0;
202	>	painCave.severity = OPENMD_WARNING;
203	>	simError();
204	>
205	>	// The old file version tethered the shifting behavior to the
206	>	// electrostaticSummationMethod keyword.
207	>
208	>	if (simParams_->haveElectrostaticSummationMethod()) {
209	>	string myMethod = simParams_->getElectrostaticSummationMethod();
210	>	toUpper(myMethod);
211	>
212	>	if (myMethod == "SHIFTED_POTENTIAL") {
213	>	cutoffMethod_ = SHIFTED_POTENTIAL;
214	>	} else if (myMethod == "SHIFTED_FORCE") {
215	>	cutoffMethod_ = SHIFTED_FORCE;
216	>	}
217	>
218	>	if (simParams_->haveSwitchingRadius())
219	>	rSwitch_ = simParams_->getSwitchingRadius();
220	>
221	>	if (myMethod == "SHIFTED_POTENTIAL" \|\| myMethod == "SHIFTED_FORCE") {
222	>	if (simParams_->haveSwitchingRadius()){
223	>	sprintf(painCave.errMsg,
224	>	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
225	>	"\tA value was set for the switchingRadius\n"
226	>	"\teven though the electrostaticSummationMethod was\n"
227	>	"\tset to %s\n", myMethod.c_str());
228	>	painCave.severity = OPENMD_WARNING;
229	>	painCave.isFatal = 1;
230	>	simError();
231	>	}
232	>	}
233	>	if (abs(rCut_ - rSwitch_) < 0.0001) {
234	>	if (cutoffMethod_ == SHIFTED_FORCE) {
235	>	sprintf(painCave.errMsg,
236	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
237	>	"\tcutoffRadius and switchingRadius are set to the\n"
238	>	"\tsame value. OpenMD will use shifted force\n"
239	>	"\tpotentials instead of switching functions.\n");
240	>	painCave.isFatal = 0;
241	>	painCave.severity = OPENMD_WARNING;
242	>	simError();
243	>	} else {
244	>	cutoffMethod_ = SHIFTED_POTENTIAL;
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 potentials\n"
249	>	"\tinstead of switching functions.\n");
250	>	painCave.isFatal = 0;
251	>	painCave.severity = OPENMD_WARNING;
252	>	simError();
253	>	}
254	>	}
255	>	}
256	>	}
257	>	}
258	>
259	>	map<string, CutoffPolicy> stringToCutoffPolicy;
260	>	stringToCutoffPolicy["MIX"] = MIX;
261	>	stringToCutoffPolicy["MAX"] = MAX;
262	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
263	>
264	>	string cutPolicy;
265	>	if (forceFieldOptions_.haveCutoffPolicy()){
266	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
267	>	}else if (simParams_->haveCutoffPolicy()) {
268	>	cutPolicy = simParams_->getCutoffPolicy();
269	>	}
270	>
271	>	if (!cutPolicy.empty()){
272	>	toUpper(cutPolicy);
273	>	map<string, CutoffPolicy>::iterator i;
274	>	i = stringToCutoffPolicy.find(cutPolicy);
275	>
276	>	if (i == stringToCutoffPolicy.end()) {
277	>	sprintf(painCave.errMsg,
278	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
279	>	"\tShould be one of: "
280	>	"MIX, MAX, or TRADITIONAL\n",
281	>	cutPolicy.c_str());
282	>	painCave.isFatal = 1;
283	>	painCave.severity = OPENMD_ERROR;
284	>	simError();
285	>	} else {
286	>	cutoffPolicy_ = i->second;
287	>	}
288	>	} else {
289	>	sprintf(painCave.errMsg,
290	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
291	>	"\tOpenMD will use TRADITIONAL.\n");
292	>	painCave.isFatal = 0;
293	>	painCave.severity = OPENMD_INFO;
294	>	simError();
295	>	cutoffPolicy_ = TRADITIONAL;
296	>	}
297	>
298	>	fDecomp_->setCutoffPolicy(cutoffPolicy_);
299	>
300	>	// create the switching function object:
301	>
302	>	switcher_ = new SwitchingFunction();
303	>
304	>	if (cutoffMethod_ == SWITCHED) {
305	>	if (simParams_->haveSwitchingRadius()) {
306	>	rSwitch_ = simParams_->getSwitchingRadius();
307	>	if (rSwitch_ > rCut_) {
308	>	sprintf(painCave.errMsg,
309	>	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
310	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
311	>	painCave.isFatal = 1;
312	>	painCave.severity = OPENMD_ERROR;
313	>	simError();
314	>	}
315	>	} else {
316	>	rSwitch_ = 0.85 * rCut_;
317	>	sprintf(painCave.errMsg,
318	>	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
319	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
320	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
321	>	painCave.isFatal = 0;
322	>	painCave.severity = OPENMD_WARNING;
323	>	simError();
324	>	}
325	>	} else {
326	>	if (mdFileVersion > 1) {
327	>	// throw an error if we define a switching radius and don't need one.
328	>	// older file versions should not do this.
329	>	if (simParams_->haveSwitchingRadius()) {
330	>	map<string, CutoffMethod>::const_iterator it;
331	>	string theMeth;
332	>	for (it = stringToCutoffMethod.begin();
333	>	it != stringToCutoffMethod.end(); ++it) {
334	>	if (it->second == cutoffMethod_) {
335	>	theMeth = it->first;
336	>	break;
337	>	}
338	>	}
339	>	sprintf(painCave.errMsg,
340	>	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
341	>	"\tis not set to SWITCHED, so switchingRadius value\n"
342	>	"\twill be ignored for this simulation\n", theMeth.c_str());
343	>	painCave.isFatal = 0;
344	>	painCave.severity = OPENMD_WARNING;
345	>	simError();
346	>	}
347	>	}
348	>	rSwitch_ = rCut_;
349	>	}
350
351	+	// Default to cubic switching function.
352	+	sft_ = cubic;
353	+	if (simParams_->haveSwitchingFunctionType()) {
354	+	string funcType = simParams_->getSwitchingFunctionType();
355	+	toUpper(funcType);
356	+	if (funcType == "CUBIC") {
357	+	sft_ = cubic;
358	+	} else {
359	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
360	+	sft_ = fifth_order_poly;
361	+	} else {
362	+	// throw error
363	+	sprintf( painCave.errMsg,
364	+	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
365	+	"\tswitchingFunctionType must be one of: "
366	+	"\"cubic\" or \"fifth_order_polynomial\".",
367	+	funcType.c_str() );
368	+	painCave.isFatal = 1;
369	+	painCave.severity = OPENMD_ERROR;
370	+	simError();
371	+	}
372	+	}
373	+	}
374	+	switcher_->setSwitchType(sft_);
375	+	switcher_->setSwitch(rSwitch_, rCut_);
376	+	}
377	+
378	+
379	+
380	+
381	+	void ForceManager::initialize() {
382	+
383		if (!info_->isTopologyDone()) {
384	+
385		info_->update();
386		interactionMan_->setSimInfo(info_);
387		interactionMan_->initialize();
388	<	swfun_ = interactionMan_->getSwitchingFunction();
389	<	fDecomp_->distributeInitialData();
390	<	info_->prepareTopology();
388	>
389	>	// We want to delay the cutoffs until after the interaction
390	>	// manager has set up the atom-atom interactions so that we can
391	>	// query them for suggested cutoff values
392	>	setupCutoffs();
393	>
394	>	info_->prepareTopology();
395	>
396	>	doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
397	>	doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
398	>	if (doHeatFlux_) doParticlePot_ = true;
399	>
400	>	doElectricField_ = info_->getSimParams()->getOutputElectricField();
401	>
402		}
403	+
404	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
405
406	+	// Force fields can set options on how to scale van der Waals and
407	+	// electrostatic interactions for atoms connected via bonds, bends
408	+	// and torsions in this case the topological distance between
409	+	// atoms is:
410	+	// 0 = topologically unconnected
411	+	// 1 = bonded together
412	+	// 2 = connected via a bend
413	+	// 3 = connected via a torsion
414	+
415	+	vdwScale_.reserve(4);
416	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
417	+
418	+	electrostaticScale_.reserve(4);
419	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
420	+
421	+	vdwScale_[0] = 1.0;
422	+	vdwScale_[1] = fopts.getvdw12scale();
423	+	vdwScale_[2] = fopts.getvdw13scale();
424	+	vdwScale_[3] = fopts.getvdw14scale();
425	+
426	+	electrostaticScale_[0] = 1.0;
427	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
428	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
429	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
430	+
431	+	if (info_->getSimParams()->haveElectricField()) {
432	+	ElectricField* eField = new ElectricField(info_);
433	+	perturbations_.push_back(eField);
434	+	}
435	+
436	+	fDecomp_->distributeInitialData();
437	+
438	+	initialized_ = true;
439	+
440	+	}
441	+
442	+	void ForceManager::calcForces() {
443	+
444	+	if (!initialized_) initialize();
445	+
446		preCalculation();
447		shortRangeInteractions();
448		longRangeInteractions();
449	<	postCalculation();
88	<
449	>	postCalculation();
450		}
451
452		void ForceManager::preCalculation() {
#	Line 98 \| Line 459 \| namespace OpenMD {
459		Molecule::CutoffGroupIterator ci;
460		CutoffGroup* cg;
461
462	<	// forces are zeroed here, before any are accumulated.
462	>	// forces and potentials are zeroed here, before any are
463	>	// accumulated.
464
465	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
466	+
467	+	snap->setBondPotential(0.0);
468	+	snap->setBendPotential(0.0);
469	+	snap->setTorsionPotential(0.0);
470	+	snap->setInversionPotential(0.0);
471	+
472	+	potVec zeroPot(0.0);
473	+	snap->setLongRangePotential(zeroPot);
474	+	snap->setExcludedPotentials(zeroPot);
475	+
476	+	snap->setRestraintPotential(0.0);
477	+	snap->setRawPotential(0.0);
478	+
479		for (mol = info_->beginMolecule(mi); mol != NULL;
480		mol = info_->nextMolecule(mi)) {
481	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
481	>	for(atom = mol->beginAtom(ai); atom != NULL;
482	>	atom = mol->nextAtom(ai)) {
483		atom->zeroForcesAndTorques();
484		}
485	<
485	>
486		//change the positions of atoms which belong to the rigidbodies
487		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
488		rb = mol->nextRigidBody(rbIter)) {
489		rb->zeroForcesAndTorques();
490		}
491	<
491	>
492		if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
493		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
494		cg = mol->nextCutoffGroup(ci)) {
#	Line 120 \| Line 497 \| namespace OpenMD {
497		}
498		}
499		}
123	–
124	–	// Zero out the stress tensor
125	–	tau *= 0.0;
500
501	+	// Zero out the stress tensor
502	+	stressTensor *= 0.0;
503	+	// Zero out the heatFlux
504	+	fDecomp_->setHeatFlux( Vector3d(0.0) );
505		}
506
507		void ForceManager::shortRangeInteractions() {
#	Line 156 \| Line 534 \| namespace OpenMD {
534
535		for (bond = mol->beginBond(bondIter); bond != NULL;
536		bond = mol->nextBond(bondIter)) {
537	<	bond->calcForce();
537	>	bond->calcForce(doParticlePot_);
538		bondPotential += bond->getPotential();
539		}
540
#	Line 164 \| Line 542 \| namespace OpenMD {
542		bend = mol->nextBend(bendIter)) {
543
544		RealType angle;
545	<	bend->calcForce(angle);
545	>	bend->calcForce(angle, doParticlePot_);
546		RealType currBendPot = bend->getPotential();
547
548		bendPotential += bend->getPotential();
#	Line 174 \| Line 552 \| namespace OpenMD {
552		dataSet.prev.angle = dataSet.curr.angle = angle;
553		dataSet.prev.potential = dataSet.curr.potential = currBendPot;
554		dataSet.deltaV = 0.0;
555	<	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
555	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
556	>	dataSet));
557		}else {
558		i->second.prev.angle = i->second.curr.angle;
559		i->second.prev.potential = i->second.curr.potential;
#	Line 188 \| Line 567 \| namespace OpenMD {
567		for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
568		torsion = mol->nextTorsion(torsionIter)) {
569		RealType angle;
570	<	torsion->calcForce(angle);
570	>	torsion->calcForce(angle, doParticlePot_);
571		RealType currTorsionPot = torsion->getPotential();
572		torsionPotential += torsion->getPotential();
573		map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
#	Line 212 \| Line 591 \| namespace OpenMD {
591		inversion != NULL;
592		inversion = mol->nextInversion(inversionIter)) {
593		RealType angle;
594	<	inversion->calcForce(angle);
594	>	inversion->calcForce(angle, doParticlePot_);
595		RealType currInversionPot = inversion->getPotential();
596		inversionPotential += inversion->getPotential();
597		map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
#	Line 232 \| Line 611 \| namespace OpenMD {
611		}
612		}
613		}
614	<
615	<	RealType shortRangePotential = bondPotential + bendPotential +
616	<	torsionPotential + inversionPotential;
614	>
615	>	#ifdef IS_MPI
616	>	// Collect from all nodes. This should eventually be moved into a
617	>	// SystemDecomposition, but this is a better place than in
618	>	// Thermo to do the collection.
619	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
620	>	MPI::SUM);
621	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
622	>	MPI::SUM);
623	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
624	>	MPI::REALTYPE, MPI::SUM);
625	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
626	>	MPI::REALTYPE, MPI::SUM);
627	>	#endif
628	>
629		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
630	<	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
631	<	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
632	<	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
633	<	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
634	<	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
630	>
631	>	curSnapshot->setBondPotential(bondPotential);
632	>	curSnapshot->setBendPotential(bendPotential);
633	>	curSnapshot->setTorsionPotential(torsionPotential);
634	>	curSnapshot->setInversionPotential(inversionPotential);
635	>
636	>	// RealType shortRangePotential = bondPotential + bendPotential +
637	>	// torsionPotential + inversionPotential;
638	>
639	>	// curSnapshot->setShortRangePotential(shortRangePotential);
640		}
641
642		void ForceManager::longRangeInteractions() {
643
644	<	// some of this initial stuff will go away:
644	>
645		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
646		DataStorage* config = &(curSnapshot->atomData);
647		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;
648
649	<	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
650	<	rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
649	>	//calculate the center of mass of cutoff group
650	>
651	>	SimInfo::MoleculeIterator mi;
652	>	Molecule* mol;
653	>	Molecule::CutoffGroupIterator ci;
654	>	CutoffGroup* cg;
655	>
656	>	if(info_->getNCutoffGroups() > 0){
657	>	for (mol = info_->beginMolecule(mi); mol != NULL;
658	>	mol = info_->nextMolecule(mi)) {
659	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
660	>	cg = mol->nextCutoffGroup(ci)) {
661	>	cg->updateCOM();
662	>	}
663	>	}
664		} else {
665		// center of mass of the group is the same as position of the atom
666		// if cutoff group does not exist
667	<	rc = pos;
668	<	}
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
667	>	cgConfig->position = config->position;
668	>	cgConfig->velocity = config->velocity;
669		}
670
671	<	// new stuff starts here:
279	<
671	>	fDecomp_->zeroWorkArrays();
672		fDecomp_->distributeData();
673	<
674	<	int cg1, cg2, atom1, atom2;
675	<	Vector3d d_grp, dag;
676	<	RealType rgrpsq, rgrp;
673	>
674	>	int cg1, cg2, atom1, atom2, topoDist;
675	>	Vector3d d_grp, dag, d, gvel2, vel2;
676	>	RealType rgrpsq, rgrp, r2, r;
677	>	RealType electroMult, vdwMult;
678		RealType vij;
679	<	Vector3d fij, fg;
680	<	pair<int, int> gtypes;
679	>	Vector3d fij, fg, f1;
680	>	tuple3<RealType, RealType, RealType> cuts;
681		RealType rCutSq;
682		bool in_switching_region;
683		RealType sw, dswdr, swderiv;
#	Line 292 \| Line 685 \| namespace OpenMD {
685		InteractionData idat;
686		SelfData sdat;
687		RealType mf;
688	+	RealType vpair;
689	+	RealType dVdFQ1(0.0);
690	+	RealType dVdFQ2(0.0);
691	+	potVec longRangePotential(0.0);
692	+	potVec workPot(0.0);
693	+	potVec exPot(0.0);
694	+	Vector3d eField1(0.0);
695	+	Vector3d eField2(0.0);
696	+	vector<int>::iterator ia, jb;
697
698		int loopStart, loopEnd;
699
700	+	idat.vdwMult = &vdwMult;
701	+	idat.electroMult = &electroMult;
702	+	idat.pot = &workPot;
703	+	idat.excludedPot = &exPot;
704	+	sdat.pot = fDecomp_->getEmbeddingPotential();
705	+	sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
706	+	idat.vpair = &vpair;
707	+	idat.dVdFQ1 = &dVdFQ1;
708	+	idat.dVdFQ2 = &dVdFQ2;
709	+	idat.eField1 = &eField1;
710	+	idat.eField2 = &eField2;
711	+	idat.f1 = &f1;
712	+	idat.sw = &sw;
713	+	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
714	+	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
715	+	idat.doParticlePot = doParticlePot_;
716	+	idat.doElectricField = doElectricField_;
717	+	sdat.doParticlePot = doParticlePot_;
718	+
719		loopEnd = PAIR_LOOP;
720		if (info_->requiresPrepair() ) {
721		loopStart = PREPAIR_LOOP;
722		} else {
723		loopStart = PAIR_LOOP;
724		}
725	<
726	<	for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
306	<
725	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
726	>
727		if (iLoop == loopStart) {
728		bool update_nlist = fDecomp_->checkNeighborList();
729		if (update_nlist)
730		neighborList = fDecomp_->buildNeighborList();
731	<	}
731	>	}
732
733		for (vector<pair<int, int> >::iterator it = neighborList.begin();
734		it != neighborList.end(); ++it) {
735	<
735	>
736		cg1 = (*it).first;
737		cg2 = (*it).second;
738	+
739	+	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
740
319	–	gtypes = fDecomp_->getGroupTypes(cg1, cg2);
741		d_grp = fDecomp_->getIntergroupVector(cg1, cg2);
742	+
743		curSnapshot->wrapVector(d_grp);
744		rgrpsq = d_grp.lengthSquare();
745	<	rCutSq = groupCutoffMap[gtypes].first;
745	>	rCutSq = cuts.second;
746
747		if (rgrpsq < rCutSq) {
748	<	*(idat.rcut) = groupCutoffMap[gtypes].second;
748	>	idat.rcut = &cuts.first;
749		if (iLoop == PAIR_LOOP) {
750	<	vij *= 0.0;
750	>	vij = 0.0;
751		fij = V3Zero;
752	+	eField1 = V3Zero;
753	+	eField2 = V3Zero;
754		}
755
756	<	in_switching_region = swfun_->getSwitch(rgrpsq, *(idat.sw), dswdr,
757	<	rgrp);
756	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
757	>	rgrp);
758	>
759		atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
760		atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
761
762	<	for (vector<int>::iterator ia = atomListRow.begin();
762	>	if (doHeatFlux_)
763	>	gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
764	>
765	>	for (ia = atomListRow.begin();
766		ia != atomListRow.end(); ++ia) {
767		atom1 = (*ia);
768	<
769	<	for (vector<int>::iterator jb = atomListColumn.begin();
768	>
769	>	for (jb = atomListColumn.begin();
770		jb != atomListColumn.end(); ++jb) {
771		atom2 = (*jb);
344	–
345	–	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
346	–
347	–	idat = fDecomp_->fillInteractionData(atom1, atom2);
772
773	<	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
774	<	*(idat.d) = d_grp;
775	<	*(idat.r2) = rgrpsq;
773	>	if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
774	>
775	>	vpair = 0.0;
776	>	workPot = 0.0;
777	>	exPot = 0.0;
778	>	f1 = V3Zero;
779	>	dVdFQ1 = 0.0;
780	>	dVdFQ2 = 0.0;
781	>
782	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
783	>
784	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
785	>	vdwMult = vdwScale_[topoDist];
786	>	electroMult = electrostaticScale_[topoDist];
787	>
788	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
789	>	idat.d = &d_grp;
790	>	idat.r2 = &rgrpsq;
791	>	if (doHeatFlux_)
792	>	vel2 = gvel2;
793		} else {
794	<	*(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2);
795	<	curSnapshot->wrapVector( *(idat.d) );
796	<	*(idat.r2) = idat.d->lengthSquare();
794	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
795	>	curSnapshot->wrapVector( d );
796	>	r2 = d.lengthSquare();
797	>	idat.d = &d;
798	>	idat.r2 = &r2;
799	>	if (doHeatFlux_)
800	>	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
801		}
357	–
358	–	(idat.rij) = sqrt( (idat.r2) );
802
803	+	r = sqrt( *(idat.r2) );
804	+	idat.rij = &r;
805	+
806		if (iLoop == PREPAIR_LOOP) {
807		interactionMan_->doPrePair(idat);
808		} else {
809		interactionMan_->doPair(idat);
810	<	vij += *(idat.vpair);
811	<	fij += *(idat.f1);
812	<	tau -= outProduct( (idat.d), (idat.f1));
810	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
811	>	vij += vpair;
812	>	fij += f1;
813	>	stressTensor -= outProduct( *(idat.d), f1);
814	>	if (doHeatFlux_)
815	>	fDecomp_->addToHeatFlux((idat.d) dot(f1, vel2));
816		}
817		}
818		}
#	Line 373 \| Line 822 \| namespace OpenMD {
822		if (in_switching_region) {
823		swderiv = vij * dswdr / rgrp;
824		fg = swderiv * d_grp;
376	–
825		fij += fg;
826
827		if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
828	<	tau -= outProduct( *(idat.d), fg);
828	>	if (!fDecomp_->skipAtomPair(atomListRow[0],
829	>	atomListColumn[0],
830	>	cg1, cg2)) {
831	>	stressTensor -= outProduct( *(idat.d), fg);
832	>	if (doHeatFlux_)
833	>	fDecomp_->addToHeatFlux((idat.d) dot(fg, vel2));
834	>	}
835		}
836
837	<	for (vector<int>::iterator ia = atomListRow.begin();
837	>	for (ia = atomListRow.begin();
838		ia != atomListRow.end(); ++ia) {
839		atom1 = (*ia);
840		mf = fDecomp_->getMassFactorRow(atom1);
#	Line 388 \| Line 842 \| namespace OpenMD {
842		// presence in switching region
843		fg = swderiv * d_grp * mf;
844		fDecomp_->addForceToAtomRow(atom1, fg);
391	–
845		if (atomListRow.size() > 1) {
846		if (info_->usesAtomicVirial()) {
847		// find the distance between the atom
848		// and the center of the cutoff group:
849		dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
850	<	tau -= outProduct(dag, fg);
850	>	stressTensor -= outProduct(dag, fg);
851	>	if (doHeatFlux_)
852	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
853		}
854		}
855		}
856	<	for (vector<int>::iterator jb = atomListColumn.begin();
856	>	for (jb = atomListColumn.begin();
857		jb != atomListColumn.end(); ++jb) {
858		atom2 = (*jb);
859		mf = fDecomp_->getMassFactorColumn(atom2);
#	Line 412 \| Line 867 \| namespace OpenMD {
867		// find the distance between the atom
868		// and the center of the cutoff group:
869		dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
870	<	tau -= outProduct(dag, fg);
870	>	stressTensor -= outProduct(dag, fg);
871	>	if (doHeatFlux_)
872	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
873		}
874		}
875		}
876		}
877	<	//if (!SIM_uses_AtomicVirial) {
878	<	// tau -= outProduct(d_grp, fij);
877	>	//if (!info_->usesAtomicVirial()) {
878	>	// stressTensor -= outProduct(d_grp, fij);
879	>	// if (doHeatFlux_)
880	>	// fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
881		//}
882		}
883		}
884		}
885
886		if (iLoop == PREPAIR_LOOP) {
887	<	if (info_->requiresPrepair()) {
887	>	if (info_->requiresPrepair()) {
888	>
889		fDecomp_->collectIntermediateData();
890
891	<	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
892	<	sdat = fDecomp_->fillSelfData(atom1);
891	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
892	>	fDecomp_->fillSelfData(sdat, atom1);
893		interactionMan_->doPreForce(sdat);
894		}
895
896	<	fDecomp_->distributeIntermediateData();
896	>	fDecomp_->distributeIntermediateData();
897	>
898		}
899		}
439	–
900		}
901
902	+	// collects pairwise information
903		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 );
904
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	–
905		if (info_->requiresSelfCorrection()) {
906	<
907	<	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
464	<	sdat = fDecomp_->fillSelfData(atom1);
906	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
907	>	fDecomp_->fillSelfData(sdat, atom1);
908		interactionMan_->doSelfCorrection(sdat);
909		}
467	–
910		}
911
912	<	// dangerous to iterate over enums, but we'll live on the edge:
913	<	for (int i = NO_FAMILY; i != N_INTERACTION_FAMILIES; ++i){
914	<	lrPot += longRangePotential[i]; //Quick hack
915	<	}
916	<
917	<	//store the tau and long range potential
918	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
919	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
920	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
912	>	// collects single-atom information
913	>	fDecomp_->collectSelfData();
914	>
915	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
916	>	*(fDecomp_->getPairwisePotential());
917	>
918	>	curSnapshot->setLongRangePotential(longRangePotential);
919	>
920	>	curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
921	>	*(fDecomp_->getExcludedPotential()));
922	>
923		}
924
925
926		void ForceManager::postCalculation() {
927	+
928	+	vector<Perturbation*>::iterator pi;
929	+	for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
930	+	(*pi)->applyPerturbation();
931	+	}
932	+
933		SimInfo::MoleculeIterator mi;
934		Molecule* mol;
935		Molecule::RigidBodyIterator rbIter;
936		RigidBody* rb;
937		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
938	<
938	>
939		// collect the atomic forces onto rigid bodies
940
941		for (mol = info_->beginMolecule(mi); mol != NULL;
#	Line 493 \| Line 943 \| namespace OpenMD {
943		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
944		rb = mol->nextRigidBody(rbIter)) {
945		Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
946	<	tau += rbTau;
946	>	stressTensor += rbTau;
947		}
948		}
949
950		#ifdef IS_MPI
951	<	Mat3x3d tmpTau(tau);
952	<	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
503	<	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
951	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
952	>	MPI::REALTYPE, MPI::SUM);
953		#endif
954	<	curSnapshot->statData.setTau(tau);
955	<	}
954	>	curSnapshot->setStressTensor(stressTensor);
955	>
956	>	if (info_->getSimParams()->getUseLongRangeCorrections()) {
957	>	/*
958	>	RealType vol = curSnapshot->getVolume();
959	>	RealType Elrc(0.0);
960	>	RealType Wlrc(0.0);
961
962	<	} //end namespace OpenMD
962	>	set<AtomType*>::iterator i;
963	>	set<AtomType*>::iterator j;
964	>
965	>	RealType n_i, n_j;
966	>	RealType rho_i, rho_j;
967	>	pair<RealType, RealType> LRI;
968	>
969	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
970	>	n_i = RealType(info_->getGlobalCountOfType(*i));
971	>	rho_i = n_i / vol;
972	>	for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
973	>	n_j = RealType(info_->getGlobalCountOfType(*j));
974	>	rho_j = n_j / vol;
975	>
976	>	LRI = interactionMan_->getLongRangeIntegrals( (i), (j) );
977	>
978	>	Elrc += n_i * rho_j * LRI.first;
979	>	Wlrc -= rho_i * rho_j * LRI.second;
980	>	}
981	>	}
982	>	Elrc = 2.0 NumericConstant::PI;
983	>	Wlrc = 2.0 NumericConstant::PI;
984	>
985	>	RealType lrp = curSnapshot->getLongRangePotential();
986	>	curSnapshot->setLongRangePotential(lrp + Elrc);
987	>	stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
988	>	curSnapshot->setStressTensor(stressTensor);
989	>	*/
990	>
991	>	}
992	>	}
993	>	}

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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 1850 by gezelter, Wed Feb 20 15:39:39 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 1850 by gezelter, Wed Feb 20 15:39:39 2013 UTC