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root/OpenMD/trunk/src/brains/ForceManager.cpp

Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1925 by gezelter, Wed Aug 7 15:24:16 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"
52	–	#include "UseTheForce/doForces_interface.h"
53		#define __OPENMD_C
54	–	#include "UseTheForce/DarkSide/fInteractionMap.h"
54		#include "utils/simError.h"
55		#include "primitives/Bond.hpp"
56		#include "primitives/Bend.hpp"
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), 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	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
78	>	ForceManager::~ForceManager() {
79	>	perturbations_.clear();
80
81	<	if (!info_->isFortranInitialized()) {
82	<	info_->update();
83	<	}
81	>	delete switcher_;
82	>	delete interactionMan_;
83	>	delete fDecomp_;
84	>	delete thermo;
85	>	}
86	>
87	>	/**
88	>	* setupCutoffs
89	>	*
90	>	* Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
91	>	* and cutoffPolicy
92	>	*
93	>	* cutoffRadius : realType
94	>	*  If the cutoffRadius was explicitly set, use that value.
95	>	*  If the cutoffRadius was not explicitly set:
96	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
97	>	*      No electrostatic atoms?  Poll the atom types present in the
98	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
99	>	*      Use the maximum suggested value that was found.
100	>	*
101	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, TAYLOR_SHIFTED,
102	>	*                        SHIFTED_POTENTIAL, or EWALD_FULL)
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	<	preCalculation();
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	<	calcShortRangeInteraction();
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	<	calcLongRangeInteraction(needPotential, needStress);
134	>	set<AtomType*>::iterator i;
135	>	set<AtomType*> atomTypes_;
136	>	atomTypes_ = info_->getSimulatedAtomTypes();
137
138	<	postCalculation(needStress);
138	>	if (simParams_->haveCutoffRadius()) {
139	>	rCut_ = simParams_->getCutoffRadius();
140	>	} else {
141	>	if (info_->usesElectrostaticAtoms()) {
142	>	sprintf(painCave.errMsg,
143	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
144	>	"\tOpenMD will use a default value of 12.0 angstroms"
145	>	"\tfor the cutoffRadius.\n");
146	>	painCave.isFatal = 0;
147	>	painCave.severity = OPENMD_INFO;
148	>	simError();
149	>	rCut_ = 12.0;
150	>	} else {
151	>	RealType thisCut;
152	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
153	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
154	>	rCut_ = max(thisCut, rCut_);
155	>	}
156	>	sprintf(painCave.errMsg,
157	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
158	>	"\tOpenMD will use %lf angstroms.\n",
159	>	rCut_);
160	>	painCave.isFatal = 0;
161	>	painCave.severity = OPENMD_INFO;
162	>	simError();
163	>	}
164	>	}
165	>
166	>	fDecomp_->setUserCutoff(rCut_);
167	>	interactionMan_->setCutoffRadius(rCut_);
168	>
169	>	map<string, CutoffMethod> stringToCutoffMethod;
170	>	stringToCutoffMethod["HARD"] = HARD;
171	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
172	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
173	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
174	>	stringToCutoffMethod["TAYLOR_SHIFTED"] = TAYLOR_SHIFTED;
175	>	stringToCutoffMethod["EWALD_FULL"] = EWALD_FULL;
176	>
177	>	if (simParams_->haveCutoffMethod()) {
178	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
179	>	map<string, CutoffMethod>::iterator i;
180	>	i = stringToCutoffMethod.find(cutMeth);
181	>	if (i == stringToCutoffMethod.end()) {
182	>	sprintf(painCave.errMsg,
183	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
184	>	"\tShould be one of: "
185	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, TAYLOR_SHIFTED,\n"
186	>	"\tSHIFTED_FORCE, or EWALD_FULL\n",
187	>	cutMeth.c_str());
188	>	painCave.isFatal = 1;
189	>	painCave.severity = OPENMD_ERROR;
190	>	simError();
191	>	} else {
192	>	cutoffMethod_ = i->second;
193	>	}
194	>	} else {
195	>	if (mdFileVersion > 1) {
196	>	sprintf(painCave.errMsg,
197	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
198	>	"\tOpenMD will use SHIFTED_FORCE.\n");
199	>	painCave.isFatal = 0;
200	>	painCave.severity = OPENMD_INFO;
201	>	simError();
202	>	cutoffMethod_ = SHIFTED_FORCE;
203	>	} else {
204	>	// handle the case where the old file version was in play
205	>	// (there should be no cutoffMethod, so we have to deduce it
206	>	// from other data).
207	>
208	>	sprintf(painCave.errMsg,
209	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
210	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
211	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
212	>	"\tbehavior of the older (version 1) code.  To remove this\n"
213	>	"\twarning, add an explicit cutoffMethod and change the top\n"
214	>	"\tof the file so that it begins with <OpenMD version=2>\n");
215	>	painCave.isFatal = 0;
216	>	painCave.severity = OPENMD_WARNING;
217	>	simError();
218	>
219	>	// The old file version tethered the shifting behavior to the
220	>	// electrostaticSummationMethod keyword.
221	>
222	>	if (simParams_->haveElectrostaticSummationMethod()) {
223	>	string myMethod = simParams_->getElectrostaticSummationMethod();
224	>	toUpper(myMethod);
225	>
226	>	if (myMethod == "SHIFTED_POTENTIAL") {
227	>	cutoffMethod_ = SHIFTED_POTENTIAL;
228	>	} else if (myMethod == "SHIFTED_FORCE") {
229	>	cutoffMethod_ = SHIFTED_FORCE;
230	>	} else if (myMethod == "TAYLOR_SHIFTED") {
231	>	cutoffMethod_ = TAYLOR_SHIFTED;
232	>	} else if (myMethod == "EWALD_FULL") {
233	>	cutoffMethod_ = EWALD_FULL;
234	>	}
235	>
236	>	if (simParams_->haveSwitchingRadius())
237	>	rSwitch_ = simParams_->getSwitchingRadius();
238	>
239	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE" ||
240	>	myMethod == "TAYLOR_SHIFTED" || myMethod == "EWALD_FULL") {
241	>	if (simParams_->haveSwitchingRadius()){
242	>	sprintf(painCave.errMsg,
243	>	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
244	>	"\tA value was set for the switchingRadius\n"
245	>	"\teven though the electrostaticSummationMethod was\n"
246	>	"\tset to %s\n", myMethod.c_str());
247	>	painCave.severity = OPENMD_WARNING;
248	>	painCave.isFatal = 1;
249	>	simError();
250	>	}
251	>	}
252	>	if (abs(rCut_ - rSwitch_) < 0.0001) {
253	>	if (cutoffMethod_ == SHIFTED_FORCE) {
254	>	sprintf(painCave.errMsg,
255	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
256	>	"\tcutoffRadius and switchingRadius are set to the\n"
257	>	"\tsame value.  OpenMD will use shifted force\n"
258	>	"\tpotentials instead of switching functions.\n");
259	>	painCave.isFatal = 0;
260	>	painCave.severity = OPENMD_WARNING;
261	>	simError();
262	>	} else {
263	>	cutoffMethod_ = SHIFTED_POTENTIAL;
264	>	sprintf(painCave.errMsg,
265	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
266	>	"\tcutoffRadius and switchingRadius are set to the\n"
267	>	"\tsame value.  OpenMD will use shifted potentials\n"
268	>	"\tinstead of switching functions.\n");
269	>	painCave.isFatal = 0;
270	>	painCave.severity = OPENMD_WARNING;
271	>	simError();
272	>	}
273	>	}
274	>	}
275	>	}
276	>	}
277	>
278	>	map<string, CutoffPolicy> stringToCutoffPolicy;
279	>	stringToCutoffPolicy["MIX"] = MIX;
280	>	stringToCutoffPolicy["MAX"] = MAX;
281	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
282	>
283	>	string cutPolicy;
284	>	if (forceFieldOptions_.haveCutoffPolicy()){
285	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
286	>	}else if (simParams_->haveCutoffPolicy()) {
287	>	cutPolicy = simParams_->getCutoffPolicy();
288	>	}
289	>
290	>	if (!cutPolicy.empty()){
291	>	toUpper(cutPolicy);
292	>	map<string, CutoffPolicy>::iterator i;
293	>	i = stringToCutoffPolicy.find(cutPolicy);
294	>
295	>	if (i == stringToCutoffPolicy.end()) {
296	>	sprintf(painCave.errMsg,
297	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
298	>	"\tShould be one of: "
299	>	"MIX, MAX, or TRADITIONAL\n",
300	>	cutPolicy.c_str());
301	>	painCave.isFatal = 1;
302	>	painCave.severity = OPENMD_ERROR;
303	>	simError();
304	>	} else {
305	>	cutoffPolicy_ = i->second;
306	>	}
307	>	} else {
308	>	sprintf(painCave.errMsg,
309	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
310	>	"\tOpenMD will use TRADITIONAL.\n");
311	>	painCave.isFatal = 0;
312	>	painCave.severity = OPENMD_INFO;
313	>	simError();
314	>	cutoffPolicy_ = TRADITIONAL;
315	>	}
316	>
317	>	fDecomp_->setCutoffPolicy(cutoffPolicy_);
318	>
319	>	// create the switching function object:
320	>
321	>	switcher_ = new SwitchingFunction();
322	>
323	>	if (cutoffMethod_ == SWITCHED) {
324	>	if (simParams_->haveSwitchingRadius()) {
325	>	rSwitch_ = simParams_->getSwitchingRadius();
326	>	if (rSwitch_ > rCut_) {
327	>	sprintf(painCave.errMsg,
328	>	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
329	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
330	>	painCave.isFatal = 1;
331	>	painCave.severity = OPENMD_ERROR;
332	>	simError();
333	>	}
334	>	} else {
335	>	rSwitch_ = 0.85 * rCut_;
336	>	sprintf(painCave.errMsg,
337	>	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
338	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
339	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
340	>	painCave.isFatal = 0;
341	>	painCave.severity = OPENMD_WARNING;
342	>	simError();
343	>	}
344	>	} else {
345	>	if (mdFileVersion > 1) {
346	>	// throw an error if we define a switching radius and don't need one.
347	>	// older file versions should not do this.
348	>	if (simParams_->haveSwitchingRadius()) {
349	>	map<string, CutoffMethod>::const_iterator it;
350	>	string theMeth;
351	>	for (it = stringToCutoffMethod.begin();
352	>	it != stringToCutoffMethod.end(); ++it) {
353	>	if (it->second == cutoffMethod_) {
354	>	theMeth = it->first;
355	>	break;
356	>	}
357	>	}
358	>	sprintf(painCave.errMsg,
359	>	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
360	>	"\tis not set to SWITCHED, so switchingRadius value\n"
361	>	"\twill be ignored for this simulation\n", theMeth.c_str());
362	>	painCave.isFatal = 0;
363	>	painCave.severity = OPENMD_WARNING;
364	>	simError();
365	>	}
366	>	}
367	>	rSwitch_ = rCut_;
368	>	}
369
370	+	// Default to cubic switching function.
371	+	sft_ = cubic;
372	+	if (simParams_->haveSwitchingFunctionType()) {
373	+	string funcType = simParams_->getSwitchingFunctionType();
374	+	toUpper(funcType);
375	+	if (funcType == "CUBIC") {
376	+	sft_ = cubic;
377	+	} else {
378	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
379	+	sft_ = fifth_order_poly;
380	+	} else {
381	+	// throw error
382	+	sprintf( painCave.errMsg,
383	+	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
384	+	"\tswitchingFunctionType must be one of: "
385	+	"\"cubic\" or \"fifth_order_polynomial\".",
386	+	funcType.c_str() );
387	+	painCave.isFatal = 1;
388	+	painCave.severity = OPENMD_ERROR;
389	+	simError();
390	+	}
391	+	}
392	+	}
393	+	switcher_->setSwitchType(sft_);
394	+	switcher_->setSwitch(rSwitch_, rCut_);
395		}
396	+
397	+
398	+
399
400	+	void ForceManager::initialize() {
401	+
402	+	if (!info_->isTopologyDone()) {
403	+
404	+	info_->update();
405	+	interactionMan_->setSimInfo(info_);
406	+	interactionMan_->initialize();
407	+
408	+	// We want to delay the cutoffs until after the interaction
409	+	// manager has set up the atom-atom interactions so that we can
410	+	// query them for suggested cutoff values
411	+	setupCutoffs();
412	+
413	+	info_->prepareTopology();
414	+
415	+	doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
416	+	doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
417	+	if (doHeatFlux_) doParticlePot_ = true;
418	+
419	+	doElectricField_ = info_->getSimParams()->getOutputElectricField();
420	+
421	+	}
422	+
423	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
424	+
425	+	// Force fields can set options on how to scale van der Waals and
426	+	// electrostatic interactions for atoms connected via bonds, bends
427	+	// and torsions in this case the topological distance between
428	+	// atoms is:
429	+	// 0 = topologically unconnected
430	+	// 1 = bonded together
431	+	// 2 = connected via a bend
432	+	// 3 = connected via a torsion
433	+
434	+	vdwScale_.reserve(4);
435	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
436	+
437	+	electrostaticScale_.reserve(4);
438	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
439	+
440	+	vdwScale_[0] = 1.0;
441	+	vdwScale_[1] = fopts.getvdw12scale();
442	+	vdwScale_[2] = fopts.getvdw13scale();
443	+	vdwScale_[3] = fopts.getvdw14scale();
444	+
445	+	electrostaticScale_[0] = 1.0;
446	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
447	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
448	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
449	+
450	+	if (info_->getSimParams()->haveElectricField()) {
451	+	ElectricField* eField = new ElectricField(info_);
452	+	perturbations_.push_back(eField);
453	+	}
454	+
455	+	usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
456	+
457	+	fDecomp_->distributeInitialData();
458	+
459	+	initialized_ = true;
460	+
461	+	}
462	+
463	+	void ForceManager::calcForces() {
464	+
465	+	if (!initialized_) initialize();
466	+
467	+	preCalculation();
468	+	shortRangeInteractions();
469	+	longRangeInteractions();
470	+	postCalculation();
471	+	}
472	+
473		void ForceManager::preCalculation() {
474		SimInfo::MoleculeIterator mi;
475		Molecule* mol;
#	Line 82 | Line 477 | namespace OpenMD {
477		Atom* atom;
478		Molecule::RigidBodyIterator rbIter;
479		RigidBody* rb;
480	+	Molecule::CutoffGroupIterator ci;
481	+	CutoffGroup* cg;
482
483	<	// forces are zeroed here, before any are accumulated.
484	<	// NOTE: do not rezero the forces in Fortran.
483	>	// forces and potentials are zeroed here, before any are
484	>	// accumulated.
485
486	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
487	+
488	+	snap->setBondPotential(0.0);
489	+	snap->setBendPotential(0.0);
490	+	snap->setTorsionPotential(0.0);
491	+	snap->setInversionPotential(0.0);
492	+
493	+	potVec zeroPot(0.0);
494	+	snap->setLongRangePotential(zeroPot);
495	+	snap->setExcludedPotentials(zeroPot);
496	+
497	+	snap->setRestraintPotential(0.0);
498	+	snap->setRawPotential(0.0);
499	+
500		for (mol = info_->beginMolecule(mi); mol != NULL;
501		mol = info_->nextMolecule(mi)) {
502	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
502	>	for(atom = mol->beginAtom(ai); atom != NULL;
503	>	atom = mol->nextAtom(ai)) {
504		atom->zeroForcesAndTorques();
505		}
506	<
506	>
507		//change the positions of atoms which belong to the rigidbodies
508		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
509		rb = mol->nextRigidBody(rbIter)) {
510		rb->zeroForcesAndTorques();
511		}
512	<
512	>
513	>	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
514	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
515	>	cg = mol->nextCutoffGroup(ci)) {
516	>	//calculate the center of mass of cutoff group
517	>	cg->updateCOM();
518	>	}
519	>	}
520		}
521
522		// Zero out the stress tensor
523	<	tau *= 0.0;
524	<
523	>	stressTensor *= 0.0;
524	>	// Zero out the heatFlux
525	>	fDecomp_->setHeatFlux( Vector3d(0.0) );
526		}
527
528	<	void ForceManager::calcShortRangeInteraction() {
528	>	void ForceManager::shortRangeInteractions() {
529		Molecule* mol;
530		RigidBody* rb;
531		Bond* bond;
#	Line 135 | Line 555 | namespace OpenMD {
555
556		for (bond = mol->beginBond(bondIter); bond != NULL;
557		bond = mol->nextBond(bondIter)) {
558	<	bond->calcForce();
558	>	bond->calcForce(doParticlePot_);
559		bondPotential += bond->getPotential();
560		}
561
#	Line 143 | Line 563 | namespace OpenMD {
563		bend = mol->nextBend(bendIter)) {
564
565		RealType angle;
566	<	bend->calcForce(angle);
566	>	bend->calcForce(angle, doParticlePot_);
567		RealType currBendPot = bend->getPotential();
568	+
569		bendPotential += bend->getPotential();
570	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
570	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
571		if (i == bendDataSets.end()) {
572		BendDataSet dataSet;
573		dataSet.prev.angle = dataSet.curr.angle = angle;
574		dataSet.prev.potential = dataSet.curr.potential = currBendPot;
575		dataSet.deltaV = 0.0;
576	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
576	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
577	>	dataSet));
578		}else {
579		i->second.prev.angle = i->second.curr.angle;
580		i->second.prev.potential = i->second.curr.potential;
#	Line 166 | Line 588 | namespace OpenMD {
588		for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
589		torsion = mol->nextTorsion(torsionIter)) {
590		RealType angle;
591	<	torsion->calcForce(angle);
591	>	torsion->calcForce(angle, doParticlePot_);
592		RealType currTorsionPot = torsion->getPotential();
593		torsionPotential += torsion->getPotential();
594	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
594	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
595		if (i == torsionDataSets.end()) {
596		TorsionDataSet dataSet;
597		dataSet.prev.angle = dataSet.curr.angle = angle;
598		dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
599		dataSet.deltaV = 0.0;
600	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
600	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
601		}else {
602		i->second.prev.angle = i->second.curr.angle;
603		i->second.prev.potential = i->second.curr.potential;
#	Line 185 | Line 607 | namespace OpenMD {
607		i->second.prev.potential);
608		}
609		}
610	<
610	>
611		for (inversion = mol->beginInversion(inversionIter);
612		inversion != NULL;
613		inversion = mol->nextInversion(inversionIter)) {
614		RealType angle;
615	<	inversion->calcForce(angle);
615	>	inversion->calcForce(angle, doParticlePot_);
616		RealType currInversionPot = inversion->getPotential();
617		inversionPotential += inversion->getPotential();
618	<	std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
618	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
619		if (i == inversionDataSets.end()) {
620		InversionDataSet dataSet;
621		dataSet.prev.angle = dataSet.curr.angle = angle;
622		dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
623		dataSet.deltaV = 0.0;
624	<	inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
624	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
625		}else {
626		i->second.prev.angle = i->second.curr.angle;
627		i->second.prev.potential = i->second.curr.potential;
#	Line 210 | Line 632 | namespace OpenMD {
632		}
633		}
634		}
635	<
636	<	RealType  shortRangePotential = bondPotential + bendPotential +
637	<	torsionPotential +  inversionPotential;
635	>
636	>	#ifdef IS_MPI
637	>	// Collect from all nodes.  This should eventually be moved into a
638	>	// SystemDecomposition, but this is a better place than in
639	>	// Thermo to do the collection.
640	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
641	>	MPI::SUM);
642	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
643	>	MPI::SUM);
644	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
645	>	MPI::REALTYPE, MPI::SUM);
646	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
647	>	MPI::REALTYPE, MPI::SUM);
648	>	#endif
649	>
650		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
651	<	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
652	<	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
653	<	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
654	<	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
655	<	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
651	>
652	>	curSnapshot->setBondPotential(bondPotential);
653	>	curSnapshot->setBendPotential(bendPotential);
654	>	curSnapshot->setTorsionPotential(torsionPotential);
655	>	curSnapshot->setInversionPotential(inversionPotential);
656
657	+	// RealType shortRangePotential = bondPotential + bendPotential +
658	+	//   torsionPotential +  inversionPotential;
659	+
660	+	// curSnapshot->setShortRangePotential(shortRangePotential);
661		}
662
663	<	void ForceManager::calcLongRangeInteraction(bool needPotential,
226	<	bool needStress) {
227	<	Snapshot* curSnapshot;
228	<	DataStorage* config;
229	<	RealType* frc;
230	<	RealType* pos;
231	<	RealType* trq;
232	<	RealType* A;
233	<	RealType* electroFrame;
234	<	RealType* rc;
235	<	RealType* particlePot;
236	<
237	<	//get current snapshot from SimInfo
238	<	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
239	<
240	<	//get array pointers
241	<	config = &(curSnapshot->atomData);
242	<	frc = config->getArrayPointer(DataStorage::dslForce);
243	<	pos = config->getArrayPointer(DataStorage::dslPosition);
244	<	trq = config->getArrayPointer(DataStorage::dslTorque);
245	<	A   = config->getArrayPointer(DataStorage::dslAmat);
246	<	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
247	<	particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
663	>	void ForceManager::longRangeInteractions() {
664
665	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
666	+	DataStorage* config = &(curSnapshot->atomData);
667	+	DataStorage* cgConfig = &(curSnapshot->cgData);
668	+
669	+
670		//calculate the center of mass of cutoff group
671	+
672		SimInfo::MoleculeIterator mi;
673		Molecule* mol;
674		Molecule::CutoffGroupIterator ci;
675		CutoffGroup* cg;
676	<	Vector3d com;
677	<	std::vector<Vector3d> rcGroup;
256	<
257	<	if(info_->getNCutoffGroups() > 0){
258	<
676	>
677	>	if(info_->getNCutoffGroups() > 0){
678		for (mol = info_->beginMolecule(mi); mol != NULL;
679		mol = info_->nextMolecule(mi)) {
680		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
681		cg = mol->nextCutoffGroup(ci)) {
682	<	cg->getCOM(com);
264	<	rcGroup.push_back(com);
682	>	cg->updateCOM();
683		}
684	<	}// end for (mol)
267	<
268	<	rc = rcGroup[0].getArrayPointer();
684	>	}
685		} else {
686		// center of mass of the group is the same as position of the atom
687		// if cutoff group does not exist
688	<	rc = pos;
688	>	cgConfig->position = config->position;
689	>	cgConfig->velocity = config->velocity;
690		}
691	+
692	+	fDecomp_->zeroWorkArrays();
693	+	fDecomp_->distributeData();
694
695	<	//initialize data before passing to fortran
696	<	RealType longRangePotential[LR_POT_TYPES];
697	<	RealType lrPot = 0.0;
698	<	Vector3d totalDipole;
699	<	short int passedCalcPot = needPotential;
700	<	short int passedCalcStress = needStress;
701	<	int isError = 0;
695	>	int cg1, cg2, atom1, atom2, topoDist;
696	>	Vector3d d_grp, dag, d, gvel2, vel2;
697	>	RealType rgrpsq, rgrp, r2, r;
698	>	RealType electroMult, vdwMult;
699	>	RealType vij;
700	>	Vector3d fij, fg, f1;
701	>	tuple3<RealType, RealType, RealType> cuts;
702	>	RealType rCut, rCutSq, rListSq;
703	>	bool in_switching_region;
704	>	RealType sw, dswdr, swderiv;
705	>	vector<int> atomListColumn, atomListRow;
706	>	InteractionData idat;
707	>	SelfData sdat;
708	>	RealType mf;
709	>	RealType vpair;
710	>	RealType dVdFQ1(0.0);
711	>	RealType dVdFQ2(0.0);
712	>	potVec longRangePotential(0.0);
713	>	RealType reciprocalPotential(0.0);
714	>	potVec workPot(0.0);
715	>	potVec exPot(0.0);
716	>	Vector3d eField1(0.0);
717	>	Vector3d eField2(0.0);
718	>	vector<int>::iterator ia, jb;
719
720	<	for (int i=0; i<LR_POT_TYPES;i++){
284	<	longRangePotential[i]=0.0; //Initialize array
285	<	}
720	>	int loopStart, loopEnd;
721
722	<	doForceLoop(pos,
723	<	rc,
724	<	A,
725	<	electroFrame,
726	<	frc,
727	<	trq,
728	<	tau.getArrayPointer(),
729	<	longRangePotential,
730	<	particlePot,
731	<	&passedCalcPot,
732	<	&passedCalcStress,
733	<	&isError );
722	>	idat.rcut = &rCut;
723	>	idat.vdwMult = &vdwMult;
724	>	idat.electroMult = &electroMult;
725	>	idat.pot = &workPot;
726	>	idat.excludedPot = &exPot;
727	>	sdat.pot = fDecomp_->getEmbeddingPotential();
728	>	sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
729	>	idat.vpair = &vpair;
730	>	idat.dVdFQ1 = &dVdFQ1;
731	>	idat.dVdFQ2 = &dVdFQ2;
732	>	idat.eField1 = &eField1;
733	>	idat.eField2 = &eField2;
734	>	idat.f1 = &f1;
735	>	idat.sw = &sw;
736	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
737	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE || cutoffMethod_ == TAYLOR_SHIFTED) ? true : false;
738	>	idat.doParticlePot = doParticlePot_;
739	>	idat.doElectricField = doElectricField_;
740	>	sdat.doParticlePot = doParticlePot_;
741
742	<	if( isError ){
743	<	sprintf( painCave.errMsg,
744	<	"Error returned from the fortran force calculation.\n" );
745	<	painCave.isFatal = 1;
746	<	simError();
742	>	loopEnd = PAIR_LOOP;
743	>	if (info_->requiresPrepair() ) {
744	>	loopStart = PREPAIR_LOOP;
745	>	} else {
746	>	loopStart = PAIR_LOOP;
747		}
748	<	for (int i=0; i<LR_POT_TYPES;i++){
307	<	lrPot += longRangePotential[i]; //Quick hack
308	<	}
748	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
749
750	<	// grab the simulation box dipole moment if specified
751	<	if (info_->getCalcBoxDipole()){
752	<	getAccumulatedBoxDipole(totalDipole.getArrayPointer());
753	<
754	<	curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
755	<	curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
756	<	curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
750	>	if (iLoop == loopStart) {
751	>	bool update_nlist = fDecomp_->checkNeighborList();
752	>	if (update_nlist) {
753	>	if (!usePeriodicBoundaryConditions_)
754	>	Mat3x3d bbox = thermo->getBoundingBox();
755	>	fDecomp_->buildNeighborList(neighborList_);
756	>	}
757	>	}
758	>
759	>	for (vector<pair<int, int> >::iterator it = neighborList_.begin();
760	>	it != neighborList_.end(); ++it) {
761	>
762	>	cg1 = (*it).first;
763	>	cg2 = (*it).second;
764	>
765	>	fDecomp_->getGroupCutoffs(cg1, cg2, rCut, rCutSq, rListSq);
766	>
767	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
768	>
769	>	// already wrapped in the getIntergroupVector call:
770	>	// curSnapshot->wrapVector(d_grp);
771	>	rgrpsq = d_grp.lengthSquare();
772	>
773	>	if (rgrpsq < rCutSq) {
774	>	if (iLoop == PAIR_LOOP) {
775	>	vij = 0.0;
776	>	fij.zero();
777	>	eField1.zero();
778	>	eField2.zero();
779	>	}
780	>
781	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
782	>	rgrp);
783	>
784	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
785	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
786	>
787	>	if (doHeatFlux_)
788	>	gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
789	>
790	>	for (ia = atomListRow.begin();
791	>	ia != atomListRow.end(); ++ia) {
792	>	atom1 = (*ia);
793	>
794	>	for (jb = atomListColumn.begin();
795	>	jb != atomListColumn.end(); ++jb) {
796	>	atom2 = (*jb);
797	>
798	>	if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
799	>
800	>	vpair = 0.0;
801	>	workPot = 0.0;
802	>	exPot = 0.0;
803	>	f1.zero();
804	>	dVdFQ1 = 0.0;
805	>	dVdFQ2 = 0.0;
806	>
807	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
808	>
809	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
810	>	vdwMult = vdwScale_[topoDist];
811	>	electroMult = electrostaticScale_[topoDist];
812	>
813	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
814	>	idat.d = &d_grp;
815	>	idat.r2 = &rgrpsq;
816	>	if (doHeatFlux_)
817	>	vel2 = gvel2;
818	>	} else {
819	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
820	>	curSnapshot->wrapVector( d );
821	>	r2 = d.lengthSquare();
822	>	idat.d = &d;
823	>	idat.r2 = &r2;
824	>	if (doHeatFlux_)
825	>	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
826	>	}
827	>
828	>	r = sqrt( *(idat.r2) );
829	>	idat.rij = &r;
830	>
831	>	if (iLoop == PREPAIR_LOOP) {
832	>	interactionMan_->doPrePair(idat);
833	>	} else {
834	>	interactionMan_->doPair(idat);
835	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
836	>	vij += vpair;
837	>	fij += f1;
838	>	stressTensor -= outProduct( *(idat.d), f1);
839	>	if (doHeatFlux_)
840	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
841	>	}
842	>	}
843	>	}
844	>	}
845	>
846	>	if (iLoop == PAIR_LOOP) {
847	>	if (in_switching_region) {
848	>	swderiv = vij * dswdr / rgrp;
849	>	fg = swderiv * d_grp;
850	>	fij += fg;
851	>
852	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
853	>	if (!fDecomp_->skipAtomPair(atomListRow[0],
854	>	atomListColumn[0],
855	>	cg1, cg2)) {
856	>	stressTensor -= outProduct( *(idat.d), fg);
857	>	if (doHeatFlux_)
858	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
859	>	}
860	>	}
861	>
862	>	for (ia = atomListRow.begin();
863	>	ia != atomListRow.end(); ++ia) {
864	>	atom1 = (*ia);
865	>	mf = fDecomp_->getMassFactorRow(atom1);
866	>	// fg is the force on atom ia due to cutoff group's
867	>	// presence in switching region
868	>	fg = swderiv * d_grp * mf;
869	>	fDecomp_->addForceToAtomRow(atom1, fg);
870	>	if (atomListRow.size() > 1) {
871	>	if (info_->usesAtomicVirial()) {
872	>	// find the distance between the atom
873	>	// and the center of the cutoff group:
874	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
875	>	stressTensor -= outProduct(dag, fg);
876	>	if (doHeatFlux_)
877	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
878	>	}
879	>	}
880	>	}
881	>	for (jb = atomListColumn.begin();
882	>	jb != atomListColumn.end(); ++jb) {
883	>	atom2 = (*jb);
884	>	mf = fDecomp_->getMassFactorColumn(atom2);
885	>	// fg is the force on atom jb due to cutoff group's
886	>	// presence in switching region
887	>	fg = -swderiv * d_grp * mf;
888	>	fDecomp_->addForceToAtomColumn(atom2, fg);
889	>
890	>	if (atomListColumn.size() > 1) {
891	>	if (info_->usesAtomicVirial()) {
892	>	// find the distance between the atom
893	>	// and the center of the cutoff group:
894	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
895	>	stressTensor -= outProduct(dag, fg);
896	>	if (doHeatFlux_)
897	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
898	>	}
899	>	}
900	>	}
901	>	}
902	>	//if (!info_->usesAtomicVirial()) {
903	>	//  stressTensor -= outProduct(d_grp, fij);
904	>	//  if (doHeatFlux_)
905	>	//     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
906	>	//}
907	>	}
908	>	}
909	>	}
910	>
911	>	if (iLoop == PREPAIR_LOOP) {
912	>	if (info_->requiresPrepair()) {
913	>
914	>	fDecomp_->collectIntermediateData();
915	>
916	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
917	>	fDecomp_->fillSelfData(sdat, atom1);
918	>	interactionMan_->doPreForce(sdat);
919	>	}
920	>
921	>	fDecomp_->distributeIntermediateData();
922	>
923	>	}
924	>	}
925		}
926
927	<	//store the tau and long range potential
928	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
929	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
930	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
927	>	// collects pairwise information
928	>	fDecomp_->collectData();
929	>	if (cutoffMethod_ == EWALD_FULL) {
930	>	interactionMan_->doReciprocalSpaceSum(reciprocalPotential);
931	>
932	>	curSnapshot->setReciprocalPotential(reciprocalPotential);
933	>	}
934	>
935	>	if (info_->requiresSelfCorrection()) {
936	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
937	>	fDecomp_->fillSelfData(sdat, atom1);
938	>	interactionMan_->doSelfCorrection(sdat);
939	>	}
940	>	}
941	>
942	>	// collects single-atom information
943	>	fDecomp_->collectSelfData();
944	>
945	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
946	>	*(fDecomp_->getPairwisePotential());
947	>
948	>	curSnapshot->setLongRangePotential(longRangePotential);
949	>
950	>	curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
951	>	*(fDecomp_->getExcludedPotential()));
952	>
953		}
954
955	<
956	<	void ForceManager::postCalculation(bool needStress) {
955	>	void ForceManager::postCalculation() {
956	>
957	>	vector<Perturbation*>::iterator pi;
958	>	for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
959	>	(*pi)->applyPerturbation();
960	>	}
961	>
962		SimInfo::MoleculeIterator mi;
963		Molecule* mol;
964		Molecule::RigidBodyIterator rbIter;
965		RigidBody* rb;
966		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
967	<
967	>
968		// collect the atomic forces onto rigid bodies
969
970		for (mol = info_->beginMolecule(mi); mol != NULL;
971		mol = info_->nextMolecule(mi)) {
972		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
973		rb = mol->nextRigidBody(rbIter)) {
974	<	if (needStress) {
975	<	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
341	<	tau += rbTau;
342	<	} else{
343	<	rb->calcForcesAndTorques();
344	<	}
974	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
975	>	stressTensor += rbTau;
976		}
977		}
978	<
348	<	if (needStress) {
978	>
979		#ifdef IS_MPI
980	<	Mat3x3d tmpTau(tau);
981	<	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
352	<	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
980	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
981	>	MPI::REALTYPE, MPI::SUM);
982		#endif
983	<	curSnapshot->statData.setTau(tau);
984	<	}
985	<	}
983	>	curSnapshot->setStressTensor(stressTensor);
984	>
985	>	if (info_->getSimParams()->getUseLongRangeCorrections()) {
986	>	/*
987	>	RealType vol = curSnapshot->getVolume();
988	>	RealType Elrc(0.0);
989	>	RealType Wlrc(0.0);
990
991	<	} //end namespace OpenMD
991	>	set<AtomType*>::iterator i;
992	>	set<AtomType*>::iterator j;
993	>
994	>	RealType n_i, n_j;
995	>	RealType rho_i, rho_j;
996	>	pair<RealType, RealType> LRI;
997	>
998	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
999	>	n_i = RealType(info_->getGlobalCountOfType(*i));
1000	>	rho_i = n_i /  vol;
1001	>	for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
1002	>	n_j = RealType(info_->getGlobalCountOfType(*j));
1003	>	rho_j = n_j / vol;
1004	>
1005	>	LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
1006	>
1007	>	Elrc += n_i   * rho_j * LRI.first;
1008	>	Wlrc -= rho_i * rho_j * LRI.second;
1009	>	}
1010	>	}
1011	>	Elrc *= 2.0 * NumericConstant::PI;
1012	>	Wlrc *= 2.0 * NumericConstant::PI;
1013	>
1014	>	RealType lrp = curSnapshot->getLongRangePotential();
1015	>	curSnapshot->setLongRangePotential(lrp + Elrc);
1016	>	stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
1017	>	curSnapshot->setStressTensor(stressTensor);
1018	>	*/
1019	>
1020	>	}
1021	>	}
1022	>	}

Comparing trunk/src/brains/ForceManager.cpp (property svn:keywords):
Revision 1390 by gezelter, Wed Nov 25 20:02:06 2009 UTC vs.
Revision 1925 by gezelter, Wed Aug 7 15:24:16 2013 UTC

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