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

Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 1292 by chuckv, Fri Sep 12 20:51:22 2008 UTC vs.
Revision 2067 by gezelter, Thu Mar 5 15:35:37 2015 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
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, 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	<	#include "UseTheForce/doForces_interface.h"
53	<	#define __OOPSE_C
54	<	#include "UseTheForce/DarkSide/fInteractionMap.h"
53	>	#define __OPENMD_C
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	<	namespace oopse {
59	>	#include "nonbonded/NonBondedInteraction.hpp"
60	>	#include "perturbations/UniformField.hpp"
61	>	#include "perturbations/UniformGradient.hpp"
62	>	#include "parallel/ForceMatrixDecomposition.hpp"
63
64	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
64	>	#include <cstdio>
65	>	#include <iostream>
66	>	#include <iomanip>
67	>
68	>	using namespace std;
69	>	namespace OpenMD {
70	>
71	>	ForceManager::ForceManager(SimInfo * info) : initialized_(false), info_(info),
72	>	switcher_(NULL) {
73	>	forceField_ = info_->getForceField();
74	>	interactionMan_ = new InteractionManager();
75	>	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
76	>	thermo = new Thermo(info_);
77	>	}
78	>
79	>	ForceManager::~ForceManager() {
80	>	perturbations_.clear();
81
82	<	if (!info_->isFortranInitialized()) {
83	<	info_->update();
84	<	}
82	>	delete switcher_;
83	>	delete interactionMan_;
84	>	delete fDecomp_;
85	>	delete thermo;
86	>	}
87	>
88	>	/**
89	>	* setupCutoffs
90	>	*
91	>	* Sets the values of cutoffRadius, switchingRadius, and cutoffMethod
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	>	* switchingRadius : realType
107	>	*  If the cutoffMethod was set to SWITCHED:
108	>	*      If the switchingRadius was explicitly set, use that value
109	>	*          (but do a sanity check first).
110	>	*      If the switchingRadius was not explicitly set: use 0.85 *
111	>	*      cutoffRadius_
112	>	*  If the cutoffMethod was not set to SWITCHED:
113	>	*      Set switchingRadius equal to cutoffRadius for safety.
114	>	*/
115	>	void ForceManager::setupCutoffs() {
116
117	<	preCalculation();
117	>	Globals* simParams_ = info_->getSimParams();
118	>	int mdFileVersion;
119	>	rCut_ = 0.0; //Needs a value for a later max() call;
120
121	<	calcShortRangeInteraction();
121	>	if (simParams_->haveMDfileVersion())
122	>	mdFileVersion = simParams_->getMDfileVersion();
123	>	else
124	>	mdFileVersion = 0;
125	>
126	>	// We need the list of simulated atom types to figure out cutoffs
127	>	// as well as long range corrections.
128
129	<	calcLongRangeInteraction(needPotential, needStress);
129	>	set<AtomType*>::iterator i;
130	>	set<AtomType*> atomTypes_;
131	>	atomTypes_ = info_->getSimulatedAtomTypes();
132
133	<	postCalculation(needStress);
133	>	if (simParams_->haveCutoffRadius()) {
134	>	rCut_ = simParams_->getCutoffRadius();
135	>	} else {
136	>	if (info_->usesElectrostaticAtoms()) {
137	>	sprintf(painCave.errMsg,
138	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
139	>	"\tOpenMD will use a default value of 12.0 angstroms"
140	>	"\tfor the cutoffRadius.\n");
141	>	painCave.isFatal = 0;
142	>	painCave.severity = OPENMD_INFO;
143	>	simError();
144	>	rCut_ = 12.0;
145	>	} else {
146	>	RealType thisCut;
147	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
148	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
149	>	rCut_ = max(thisCut, rCut_);
150	>	}
151	>	sprintf(painCave.errMsg,
152	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
153	>	"\tOpenMD will use %lf angstroms.\n",
154	>	rCut_);
155	>	painCave.isFatal = 0;
156	>	painCave.severity = OPENMD_INFO;
157	>	simError();
158	>	}
159	>	}
160	>
161	>	fDecomp_->setCutoffRadius(rCut_);
162	>	interactionMan_->setCutoffRadius(rCut_);
163	>	rCutSq_ = rCut_ * rCut_;
164	>
165	>	map<string, CutoffMethod> stringToCutoffMethod;
166	>	stringToCutoffMethod["HARD"] = HARD;
167	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
168	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
169	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
170	>	stringToCutoffMethod["TAYLOR_SHIFTED"] = TAYLOR_SHIFTED;
171	>	stringToCutoffMethod["EWALD_FULL"] = EWALD_FULL;
172	>
173	>	if (simParams_->haveCutoffMethod()) {
174	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
175	>	map<string, CutoffMethod>::iterator i;
176	>	i = stringToCutoffMethod.find(cutMeth);
177	>	if (i == stringToCutoffMethod.end()) {
178	>	sprintf(painCave.errMsg,
179	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
180	>	"\tShould be one of: "
181	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, TAYLOR_SHIFTED,\n"
182	>	"\tSHIFTED_FORCE, or EWALD_FULL\n",
183	>	cutMeth.c_str());
184	>	painCave.isFatal = 1;
185	>	painCave.severity = OPENMD_ERROR;
186	>	simError();
187	>	} else {
188	>	cutoffMethod_ = i->second;
189	>	}
190	>	} else {
191	>	if (mdFileVersion > 1) {
192	>	sprintf(painCave.errMsg,
193	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
194	>	"\tOpenMD will use SHIFTED_FORCE.\n");
195	>	painCave.isFatal = 0;
196	>	painCave.severity = OPENMD_INFO;
197	>	simError();
198	>	cutoffMethod_ = SHIFTED_FORCE;
199	>	} else {
200	>	// handle the case where the old file version was in play
201	>	// (there should be no cutoffMethod, so we have to deduce it
202	>	// from other data).
203	>
204	>	sprintf(painCave.errMsg,
205	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
206	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
207	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
208	>	"\tbehavior of the older (version 1) code.  To remove this\n"
209	>	"\twarning, add an explicit cutoffMethod and change the top\n"
210	>	"\tof the file so that it begins with <OpenMD version=2>\n");
211	>	painCave.isFatal = 0;
212	>	painCave.severity = OPENMD_WARNING;
213	>	simError();
214	>
215	>	// The old file version tethered the shifting behavior to the
216	>	// electrostaticSummationMethod keyword.
217	>
218	>	if (simParams_->haveElectrostaticSummationMethod()) {
219	>	string myMethod = simParams_->getElectrostaticSummationMethod();
220	>	toUpper(myMethod);
221	>
222	>	if (myMethod == "SHIFTED_POTENTIAL") {
223	>	cutoffMethod_ = SHIFTED_POTENTIAL;
224	>	} else if (myMethod == "SHIFTED_FORCE") {
225	>	cutoffMethod_ = SHIFTED_FORCE;
226	>	} else if (myMethod == "TAYLOR_SHIFTED") {
227	>	cutoffMethod_ = TAYLOR_SHIFTED;
228	>	} else if (myMethod == "EWALD_FULL") {
229	>	cutoffMethod_ = EWALD_FULL;
230	>	}
231	>
232	>	if (simParams_->haveSwitchingRadius())
233	>	rSwitch_ = simParams_->getSwitchingRadius();
234	>
235	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE" ||
236	>	myMethod == "TAYLOR_SHIFTED" || myMethod == "EWALD_FULL") {
237	>	if (simParams_->haveSwitchingRadius()){
238	>	sprintf(painCave.errMsg,
239	>	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
240	>	"\tA value was set for the switchingRadius\n"
241	>	"\teven though the electrostaticSummationMethod was\n"
242	>	"\tset to %s\n", myMethod.c_str());
243	>	painCave.severity = OPENMD_WARNING;
244	>	painCave.isFatal = 1;
245	>	simError();
246	>	}
247	>	}
248	>	if (abs(rCut_ - rSwitch_) < 0.0001) {
249	>	if (cutoffMethod_ == SHIFTED_FORCE) {
250	>	sprintf(painCave.errMsg,
251	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
252	>	"\tcutoffRadius and switchingRadius are set to the\n"
253	>	"\tsame value.  OpenMD will use shifted force\n"
254	>	"\tpotentials instead of switching functions.\n");
255	>	painCave.isFatal = 0;
256	>	painCave.severity = OPENMD_WARNING;
257	>	simError();
258	>	} else {
259	>	cutoffMethod_ = SHIFTED_POTENTIAL;
260	>	sprintf(painCave.errMsg,
261	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
262	>	"\tcutoffRadius and switchingRadius are set to the\n"
263	>	"\tsame value.  OpenMD will use shifted potentials\n"
264	>	"\tinstead of switching functions.\n");
265	>	painCave.isFatal = 0;
266	>	painCave.severity = OPENMD_WARNING;
267	>	simError();
268	>	}
269	>	}
270	>	}
271	>	}
272	>	}
273	>
274	>	// create the switching function object:
275	>
276	>	switcher_ = new SwitchingFunction();
277	>
278	>	if (cutoffMethod_ == SWITCHED) {
279	>	if (simParams_->haveSwitchingRadius()) {
280	>	rSwitch_ = simParams_->getSwitchingRadius();
281	>	if (rSwitch_ > rCut_) {
282	>	sprintf(painCave.errMsg,
283	>	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
284	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
285	>	painCave.isFatal = 1;
286	>	painCave.severity = OPENMD_ERROR;
287	>	simError();
288	>	}
289	>	} else {
290	>	rSwitch_ = 0.85 * rCut_;
291	>	sprintf(painCave.errMsg,
292	>	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
293	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
294	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
295	>	painCave.isFatal = 0;
296	>	painCave.severity = OPENMD_WARNING;
297	>	simError();
298	>	}
299	>	} else {
300	>	if (mdFileVersion > 1) {
301	>	// throw an error if we define a switching radius and don't need one.
302	>	// older file versions should not do this.
303	>	if (simParams_->haveSwitchingRadius()) {
304	>	map<string, CutoffMethod>::const_iterator it;
305	>	string theMeth;
306	>	for (it = stringToCutoffMethod.begin();
307	>	it != stringToCutoffMethod.end(); ++it) {
308	>	if (it->second == cutoffMethod_) {
309	>	theMeth = it->first;
310	>	break;
311	>	}
312	>	}
313	>	sprintf(painCave.errMsg,
314	>	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
315	>	"\tis not set to SWITCHED, so switchingRadius value\n"
316	>	"\twill be ignored for this simulation\n", theMeth.c_str());
317	>	painCave.isFatal = 0;
318	>	painCave.severity = OPENMD_WARNING;
319	>	simError();
320	>	}
321	>	}
322	>	rSwitch_ = rCut_;
323	>	}
324
325	+	// Default to cubic switching function.
326	+	sft_ = cubic;
327	+	if (simParams_->haveSwitchingFunctionType()) {
328	+	string funcType = simParams_->getSwitchingFunctionType();
329	+	toUpper(funcType);
330	+	if (funcType == "CUBIC") {
331	+	sft_ = cubic;
332	+	} else {
333	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
334	+	sft_ = fifth_order_poly;
335	+	} else {
336	+	// throw error
337	+	sprintf( painCave.errMsg,
338	+	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
339	+	"\tswitchingFunctionType must be one of: "
340	+	"\"cubic\" or \"fifth_order_polynomial\".",
341	+	funcType.c_str() );
342	+	painCave.isFatal = 1;
343	+	painCave.severity = OPENMD_ERROR;
344	+	simError();
345	+	}
346	+	}
347	+	}
348	+	switcher_->setSwitchType(sft_);
349	+	switcher_->setSwitch(rSwitch_, rCut_);
350		}
351	+
352	+	void ForceManager::initialize() {
353	+
354	+	if (!info_->isTopologyDone()) {
355	+
356	+	info_->update();
357	+	interactionMan_->setSimInfo(info_);
358	+	interactionMan_->initialize();
359	+
360	+	//! We want to delay the cutoffs until after the interaction
361	+	//! manager has set up the atom-atom interactions so that we can
362	+	//! query them for suggested cutoff values
363	+	setupCutoffs();
364	+
365	+	info_->prepareTopology();
366	+
367	+	doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
368	+	doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
369	+	if (doHeatFlux_) doParticlePot_ = true;
370	+
371	+	doElectricField_ = info_->getSimParams()->getOutputElectricField();
372	+	doSitePotential_ = info_->getSimParams()->getOutputSitePotential();
373	+
374	+	}
375	+
376	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
377	+
378	+	//! Force fields can set options on how to scale van der Waals and
379	+	//! electrostatic interactions for atoms connected via bonds, bends
380	+	//! and torsions in this case the topological distance between
381	+	//! atoms is:
382	+	//! 0 = topologically unconnected
383	+	//! 1 = bonded together
384	+	//! 2 = connected via a bend
385	+	//! 3 = connected via a torsion
386	+
387	+	vdwScale_.reserve(4);
388	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
389	+
390	+	electrostaticScale_.reserve(4);
391	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
392	+
393	+	vdwScale_[0] = 1.0;
394	+	vdwScale_[1] = fopts.getvdw12scale();
395	+	vdwScale_[2] = fopts.getvdw13scale();
396	+	vdwScale_[3] = fopts.getvdw14scale();
397	+
398	+	electrostaticScale_[0] = 1.0;
399	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
400	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
401	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
402	+
403	+	if (info_->getSimParams()->haveUniformField()) {
404	+	UniformField* eField = new UniformField(info_);
405	+	perturbations_.push_back(eField);
406	+	}
407	+	if (info_->getSimParams()->haveUniformGradientStrength() ||
408	+	info_->getSimParams()->haveUniformGradientDirection1() ||
409	+	info_->getSimParams()->haveUniformGradientDirection2() ) {
410	+	UniformGradient* eGrad = new UniformGradient(info_);
411	+	perturbations_.push_back(eGrad);
412	+	}
413	+
414	+	usePeriodicBoundaryConditions_ = info_->getSimParams()->getUsePeriodicBoundaryConditions();
415	+
416	+	fDecomp_->distributeInitialData();
417	+
418	+	initialized_ = true;
419	+
420	+	}
421
422	+	void ForceManager::calcForces() {
423	+
424	+	if (!initialized_) initialize();
425	+
426	+	preCalculation();
427	+	shortRangeInteractions();
428	+	longRangeInteractions();
429	+	postCalculation();
430	+	}
431	+
432		void ForceManager::preCalculation() {
433		SimInfo::MoleculeIterator mi;
434		Molecule* mol;
#	Line 82 | Line 436 | namespace oopse {
436		Atom* atom;
437		Molecule::RigidBodyIterator rbIter;
438		RigidBody* rb;
439	+	Molecule::CutoffGroupIterator ci;
440	+	CutoffGroup* cg;
441
442	<	// forces are zeroed here, before any are accumulated.
443	<	// NOTE: do not rezero the forces in Fortran.
442	>	// forces and potentials are zeroed here, before any are
443	>	// accumulated.
444
445	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
446	+
447	+	snap->setBondPotential(0.0);
448	+	snap->setBendPotential(0.0);
449	+	snap->setTorsionPotential(0.0);
450	+	snap->setInversionPotential(0.0);
451	+
452	+	potVec zeroPot(0.0);
453	+	snap->setLongRangePotential(zeroPot);
454	+	snap->setExcludedPotentials(zeroPot);
455	+
456	+	snap->setRestraintPotential(0.0);
457	+	snap->setRawPotential(0.0);
458	+
459		for (mol = info_->beginMolecule(mi); mol != NULL;
460		mol = info_->nextMolecule(mi)) {
461	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
461	>	for(atom = mol->beginAtom(ai); atom != NULL;
462	>	atom = mol->nextAtom(ai)) {
463		atom->zeroForcesAndTorques();
464		}
465	<
465	>
466		//change the positions of atoms which belong to the rigidbodies
467		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
468		rb = mol->nextRigidBody(rbIter)) {
469		rb->zeroForcesAndTorques();
470		}
471	<
471	>
472	>	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
473	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
474	>	cg = mol->nextCutoffGroup(ci)) {
475	>	//calculate the center of mass of cutoff group
476	>	cg->updateCOM();
477	>	}
478	>	}
479		}
480
481		// Zero out the stress tensor
482	<	tau *= 0.0;
483	<
482	>	stressTensor *= 0.0;
483	>	// Zero out the heatFlux
484	>	fDecomp_->setHeatFlux( Vector3d(0.0) );
485		}
486
487	<	void ForceManager::calcShortRangeInteraction() {
487	>	void ForceManager::shortRangeInteractions() {
488		Molecule* mol;
489		RigidBody* rb;
490		Bond* bond;
#	Line 135 | Line 514 | namespace oopse {
514
515		for (bond = mol->beginBond(bondIter); bond != NULL;
516		bond = mol->nextBond(bondIter)) {
517	<	bond->calcForce();
517	>	bond->calcForce(doParticlePot_);
518		bondPotential += bond->getPotential();
519		}
520
#	Line 143 | Line 522 | namespace oopse {
522		bend = mol->nextBend(bendIter)) {
523
524		RealType angle;
525	<	bend->calcForce(angle);
525	>	bend->calcForce(angle, doParticlePot_);
526		RealType currBendPot = bend->getPotential();
527	+
528		bendPotential += bend->getPotential();
529	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
529	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
530		if (i == bendDataSets.end()) {
531		BendDataSet dataSet;
532		dataSet.prev.angle = dataSet.curr.angle = angle;
533		dataSet.prev.potential = dataSet.curr.potential = currBendPot;
534		dataSet.deltaV = 0.0;
535	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
535	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
536	>	dataSet));
537		}else {
538		i->second.prev.angle = i->second.curr.angle;
539		i->second.prev.potential = i->second.curr.potential;
#	Line 166 | Line 547 | namespace oopse {
547		for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
548		torsion = mol->nextTorsion(torsionIter)) {
549		RealType angle;
550	<	torsion->calcForce(angle);
550	>	torsion->calcForce(angle, doParticlePot_);
551		RealType currTorsionPot = torsion->getPotential();
552		torsionPotential += torsion->getPotential();
553	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
553	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
554		if (i == torsionDataSets.end()) {
555		TorsionDataSet dataSet;
556		dataSet.prev.angle = dataSet.curr.angle = angle;
557		dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
558		dataSet.deltaV = 0.0;
559	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
559	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
560		}else {
561		i->second.prev.angle = i->second.curr.angle;
562		i->second.prev.potential = i->second.curr.potential;
#	Line 185 | Line 566 | namespace oopse {
566		i->second.prev.potential);
567		}
568		}
569	<
569	>
570		for (inversion = mol->beginInversion(inversionIter);
571		inversion != NULL;
572		inversion = mol->nextInversion(inversionIter)) {
573		RealType angle;
574	<	inversion->calcForce(angle);
574	>	inversion->calcForce(angle, doParticlePot_);
575		RealType currInversionPot = inversion->getPotential();
576		inversionPotential += inversion->getPotential();
577	<	std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
577	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
578		if (i == inversionDataSets.end()) {
579		InversionDataSet dataSet;
580		dataSet.prev.angle = dataSet.curr.angle = angle;
581		dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
582		dataSet.deltaV = 0.0;
583	<	inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
583	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
584		}else {
585		i->second.prev.angle = i->second.curr.angle;
586		i->second.prev.potential = i->second.curr.potential;
#	Line 210 | Line 591 | namespace oopse {
591		}
592		}
593		}
594	<
595	<	RealType  shortRangePotential = bondPotential + bendPotential +
596	<	torsionPotential +  inversionPotential;
594	>
595	>	#ifdef IS_MPI
596	>	// Collect from all nodes.  This should eventually be moved into a
597	>	// SystemDecomposition, but this is a better place than in
598	>	// Thermo to do the collection.
599	>
600	>	MPI_Allreduce(MPI_IN_PLACE, &bondPotential, 1, MPI_REALTYPE,
601	>	MPI_SUM, MPI_COMM_WORLD);
602	>	MPI_Allreduce(MPI_IN_PLACE, &bendPotential, 1, MPI_REALTYPE,
603	>	MPI_SUM, MPI_COMM_WORLD);
604	>	MPI_Allreduce(MPI_IN_PLACE, &torsionPotential, 1,
605	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
606	>	MPI_Allreduce(MPI_IN_PLACE, &inversionPotential, 1,
607	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
608	>	#endif
609	>
610		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
611	<	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
612	<	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
613	<	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
614	<	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
615	<	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
611	>
612	>	curSnapshot->setBondPotential(bondPotential);
613	>	curSnapshot->setBendPotential(bendPotential);
614	>	curSnapshot->setTorsionPotential(torsionPotential);
615	>	curSnapshot->setInversionPotential(inversionPotential);
616
617	+	// RealType shortRangePotential = bondPotential + bendPotential +
618	+	//   torsionPotential +  inversionPotential;
619	+
620	+	// curSnapshot->setShortRangePotential(shortRangePotential);
621		}
622
623	<	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);
623	>	void ForceManager::longRangeInteractions() {
624
625	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
626	+	DataStorage* config = &(curSnapshot->atomData);
627	+	DataStorage* cgConfig = &(curSnapshot->cgData);
628	+
629		//calculate the center of mass of cutoff group
630	+
631		SimInfo::MoleculeIterator mi;
632		Molecule* mol;
633		Molecule::CutoffGroupIterator ci;
634		CutoffGroup* cg;
254	–	Vector3d com;
255	–	std::vector<Vector3d> rcGroup;
635
636	<	if(info_->getNCutoffGroups() > 0){
258	<
636	>	if(info_->getNCutoffGroups() != info_->getNAtoms()){
637		for (mol = info_->beginMolecule(mi); mol != NULL;
638		mol = info_->nextMolecule(mi)) {
639		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
640		cg = mol->nextCutoffGroup(ci)) {
641	<	cg->getCOM(com);
264	<	rcGroup.push_back(com);
641	>	cg->updateCOM();
642		}
643	<	}// end for (mol)
267	<
268	<	rc = rcGroup[0].getArrayPointer();
643	>	}
644		} else {
645		// center of mass of the group is the same as position of the atom
646		// if cutoff group does not exist
647	<	rc = pos;
647	>	cgConfig->position = config->position;
648	>	cgConfig->velocity = config->velocity;
649		}
650	+
651	+	fDecomp_->zeroWorkArrays();
652	+	fDecomp_->distributeData();
653
654	<	//initialize data before passing to fortran
655	<	RealType longRangePotential[LR_POT_TYPES];
656	<	RealType lrPot = 0.0;
657	<	Vector3d totalDipole;
658	<	short int passedCalcPot = needPotential;
659	<	short int passedCalcStress = needStress;
660	<	int isError = 0;
654	>	int cg1, cg2, atom1, atom2, topoDist;
655	>	Vector3d d_grp, dag, d, gvel2, vel2;
656	>	RealType rgrpsq, rgrp, r2, r;
657	>	RealType electroMult, vdwMult;
658	>	RealType vij;
659	>	Vector3d fij, fg, f1;
660	>	bool in_switching_region;
661	>	RealType sw, dswdr, swderiv;
662	>	vector<int> atomListColumn, atomListRow;
663	>	InteractionData idat;
664	>	SelfData sdat;
665	>	RealType mf;
666	>	RealType vpair;
667	>	RealType dVdFQ1(0.0);
668	>	RealType dVdFQ2(0.0);
669	>	potVec longRangePotential(0.0);
670	>	RealType reciprocalPotential(0.0);
671	>	potVec workPot(0.0);
672	>	potVec exPot(0.0);
673	>	Vector3d eField1(0.0);
674	>	Vector3d eField2(0.0);
675	>	RealType sPot1(0.0);
676	>	RealType sPot2(0.0);
677	>	bool newAtom1;
678	>
679	>	vector<int>::iterator ia, jb;
680
681	<	for (int i=0; i<LR_POT_TYPES;i++){
284	<	longRangePotential[i]=0.0; //Initialize array
285	<	}
681	>	int loopStart, loopEnd;
682
683	<	doForceLoop(pos,
684	<	rc,
685	<	A,
686	<	electroFrame,
687	<	frc,
688	<	trq,
689	<	tau.getArrayPointer(),
690	<	longRangePotential,
691	<	particlePot,
692	<	&passedCalcPot,
693	<	&passedCalcStress,
694	<	&isError );
683	>	idat.rcut = &rCut_;
684	>	idat.vdwMult = &vdwMult;
685	>	idat.electroMult = &electroMult;
686	>	idat.pot = &workPot;
687	>	idat.excludedPot = &exPot;
688	>	sdat.pot = fDecomp_->getEmbeddingPotential();
689	>	sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
690	>	idat.vpair = &vpair;
691	>	idat.dVdFQ1 = &dVdFQ1;
692	>	idat.dVdFQ2 = &dVdFQ2;
693	>	idat.eField1 = &eField1;
694	>	idat.eField2 = &eField2;
695	>	idat.sPot1 = &sPot1;
696	>	idat.sPot2 = &sPot2;
697	>	idat.f1 = &f1;
698	>	idat.sw = &sw;
699	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
700	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE ||
701	>	cutoffMethod_ == TAYLOR_SHIFTED) ? true : false;
702	>	idat.doParticlePot = doParticlePot_;
703	>	idat.doElectricField = doElectricField_;
704	>	idat.doSitePotential = doSitePotential_;
705	>	sdat.doParticlePot = doParticlePot_;
706
707	<	if( isError ){
708	<	sprintf( painCave.errMsg,
709	<	"Error returned from the fortran force calculation.\n" );
710	<	painCave.isFatal = 1;
711	<	simError();
707	>	loopEnd = PAIR_LOOP;
708	>	if (info_->requiresPrepair() ) {
709	>	loopStart = PREPAIR_LOOP;
710	>	} else {
711	>	loopStart = PAIR_LOOP;
712		}
713	<	for (int i=0; i<LR_POT_TYPES;i++){
307	<	lrPot += longRangePotential[i]; //Quick hack
308	<	}
713	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
714
715	<	// grab the simulation box dipole moment if specified
716	<	if (info_->getCalcBoxDipole()){
717	<	getAccumulatedBoxDipole(totalDipole.getArrayPointer());
718	<
719	<	curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
720	<	curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
721	<	curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
715	>	if (iLoop == loopStart) {
716	>	bool update_nlist = fDecomp_->checkNeighborList();
717	>	if (update_nlist) {
718	>	if (!usePeriodicBoundaryConditions_)
719	>	Mat3x3d bbox = thermo->getBoundingBox();
720	>	fDecomp_->buildNeighborList(neighborList_, point_);
721	>	}
722	>	}
723	>
724	>	for (cg1 = 0; cg1 < int(point_.size()) - 1; cg1++) {
725	>
726	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
727	>	newAtom1 = true;
728	>
729	>	for (int m2 = point_[cg1]; m2 < point_[cg1+1]; m2++) {
730	>
731	>	cg2 = neighborList_[m2];
732	>
733	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
734	>
735	>	// already wrapped in the getIntergroupVector call:
736	>	// curSnapshot->wrapVector(d_grp);
737	>	rgrpsq = d_grp.lengthSquare();
738	>
739	>	if (rgrpsq < rCutSq_) {
740	>	if (iLoop == PAIR_LOOP) {
741	>	vij = 0.0;
742	>	fij.zero();
743	>	eField1.zero();
744	>	eField2.zero();
745	>	sPot1 = 0.0;
746	>	sPot2 = 0.0;
747	>	}
748	>
749	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
750	>	rgrp);
751	>
752	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
753	>
754	>	if (doHeatFlux_)
755	>	gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
756	>
757	>	for (ia = atomListRow.begin();
758	>	ia != atomListRow.end(); ++ia) {
759	>	atom1 = (*ia);
760	>
761	>	for (jb = atomListColumn.begin();
762	>	jb != atomListColumn.end(); ++jb) {
763	>	atom2 = (*jb);
764	>
765	>	if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
766	>
767	>	vpair = 0.0;
768	>	workPot = 0.0;
769	>	exPot = 0.0;
770	>	f1.zero();
771	>	dVdFQ1 = 0.0;
772	>	dVdFQ2 = 0.0;
773	>
774	>	fDecomp_->fillInteractionData(idat, atom1, atom2, newAtom1);
775	>
776	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
777	>	vdwMult = vdwScale_[topoDist];
778	>	electroMult = electrostaticScale_[topoDist];
779	>
780	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
781	>	idat.d = &d_grp;
782	>	idat.r2 = &rgrpsq;
783	>	if (doHeatFlux_)
784	>	vel2 = gvel2;
785	>	} else {
786	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
787	>	curSnapshot->wrapVector( d );
788	>	r2 = d.lengthSquare();
789	>	idat.d = &d;
790	>	idat.r2 = &r2;
791	>	if (doHeatFlux_)
792	>	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
793	>	}
794	>
795	>	r = sqrt( *(idat.r2) );
796	>	idat.rij = &r;
797	>
798	>	if (iLoop == PREPAIR_LOOP) {
799	>	interactionMan_->doPrePair(idat);
800	>	} else {
801	>	interactionMan_->doPair(idat);
802	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
803	>	vij += vpair;
804	>	fij += f1;
805	>	stressTensor -= outProduct( *(idat.d), f1);
806	>	if (doHeatFlux_)
807	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
808	>	}
809	>	}
810	>	}
811	>	}
812	>
813	>	if (iLoop == PAIR_LOOP) {
814	>	if (in_switching_region) {
815	>	swderiv = vij * dswdr / rgrp;
816	>	fg = swderiv * d_grp;
817	>	fij += fg;
818	>
819	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
820	>	if (!fDecomp_->skipAtomPair(atomListRow[0],
821	>	atomListColumn[0],
822	>	cg1, cg2)) {
823	>	stressTensor -= outProduct( *(idat.d), fg);
824	>	if (doHeatFlux_)
825	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
826	>	}
827	>	}
828	>
829	>	for (ia = atomListRow.begin();
830	>	ia != atomListRow.end(); ++ia) {
831	>	atom1 = (*ia);
832	>	mf = fDecomp_->getMassFactorRow(atom1);
833	>	// fg is the force on atom ia due to cutoff group's
834	>	// presence in switching region
835	>	fg = swderiv * d_grp * mf;
836	>	fDecomp_->addForceToAtomRow(atom1, fg);
837	>	if (atomListRow.size() > 1) {
838	>	if (info_->usesAtomicVirial()) {
839	>	// find the distance between the atom
840	>	// and the center of the cutoff group:
841	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
842	>	stressTensor -= outProduct(dag, fg);
843	>	if (doHeatFlux_)
844	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
845	>	}
846	>	}
847	>	}
848	>	for (jb = atomListColumn.begin();
849	>	jb != atomListColumn.end(); ++jb) {
850	>	atom2 = (*jb);
851	>	mf = fDecomp_->getMassFactorColumn(atom2);
852	>	// fg is the force on atom jb due to cutoff group's
853	>	// presence in switching region
854	>	fg = -swderiv * d_grp * mf;
855	>	fDecomp_->addForceToAtomColumn(atom2, fg);
856	>
857	>	if (atomListColumn.size() > 1) {
858	>	if (info_->usesAtomicVirial()) {
859	>	// find the distance between the atom
860	>	// and the center of the cutoff group:
861	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
862	>	stressTensor -= outProduct(dag, fg);
863	>	if (doHeatFlux_)
864	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
865	>	}
866	>	}
867	>	}
868	>	}
869	>	//if (!info_->usesAtomicVirial()) {
870	>	//  stressTensor -= outProduct(d_grp, fij);
871	>	//  if (doHeatFlux_)
872	>	//     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
873	>	//}
874	>	}
875	>	}
876	>	}
877	>	newAtom1 = false;
878	>	}
879	>
880	>	if (iLoop == PREPAIR_LOOP) {
881	>	if (info_->requiresPrepair()) {
882	>
883	>	fDecomp_->collectIntermediateData();
884	>
885	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
886	>	fDecomp_->fillSelfData(sdat, atom1);
887	>	interactionMan_->doPreForce(sdat);
888	>	}
889	>
890	>	fDecomp_->distributeIntermediateData();
891	>
892	>	}
893	>	}
894		}
895
896	<	//store the tau and long range potential
897	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
898	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
899	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
896	>	// collects pairwise information
897	>	fDecomp_->collectData();
898	>	if (cutoffMethod_ == EWALD_FULL) {
899	>	interactionMan_->doReciprocalSpaceSum(reciprocalPotential);
900	>
901	>	curSnapshot->setReciprocalPotential(reciprocalPotential);
902	>	}
903	>
904	>	if (info_->requiresSelfCorrection()) {
905	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
906	>	fDecomp_->fillSelfData(sdat, atom1);
907	>	interactionMan_->doSelfCorrection(sdat);
908	>	}
909	>	}
910	>
911	>	// collects single-atom information
912	>	fDecomp_->collectSelfData();
913	>
914	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
915	>	*(fDecomp_->getPairwisePotential());
916	>
917	>	curSnapshot->setLongRangePotential(longRangePotential);
918	>
919	>	curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
920	>	*(fDecomp_->getExcludedPotential()));
921	>
922		}
923
924	<
925	<	void ForceManager::postCalculation(bool needStress) {
924	>	void ForceManager::postCalculation() {
925	>
926	>	vector<Perturbation*>::iterator pi;
927	>	for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
928	>	(*pi)->applyPerturbation();
929	>	}
930	>
931		SimInfo::MoleculeIterator mi;
932		Molecule* mol;
933		Molecule::RigidBodyIterator rbIter;
934		RigidBody* rb;
935		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
936	<
936	>
937		// collect the atomic forces onto rigid bodies
938
939		for (mol = info_->beginMolecule(mi); mol != NULL;
940		mol = info_->nextMolecule(mi)) {
941		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
942		rb = mol->nextRigidBody(rbIter)) {
943	<	if (needStress) {
944	<	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
341	<	tau += rbTau;
342	<	} else{
343	<	rb->calcForcesAndTorques();
344	<	}
943	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
944	>	stressTensor += rbTau;
945		}
946		}
947	<
348	<	if (needStress) {
947	>
948		#ifdef IS_MPI
949	<	Mat3x3d tmpTau(tau);
950	<	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
352	<	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
949	>	MPI_Allreduce(MPI_IN_PLACE, stressTensor.getArrayPointer(), 9,
950	>	MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
951		#endif
952	<	curSnapshot->statData.setTau(tau);
953	<	}
954	<	}
952	>	curSnapshot->setStressTensor(stressTensor);
953	>
954	>	if (info_->getSimParams()->getUseLongRangeCorrections()) {
955	>	/*
956	>	RealType vol = curSnapshot->getVolume();
957	>	RealType Elrc(0.0);
958	>	RealType Wlrc(0.0);
959
960	<	} //end namespace oopse
960	>	set<AtomType*>::iterator i;
961	>	set<AtomType*>::iterator j;
962	>
963	>	RealType n_i, n_j;
964	>	RealType rho_i, rho_j;
965	>	pair<RealType, RealType> LRI;
966	>
967	>	for (i = atomTypes_.begin(); i != atomTypes_.end(); ++i) {
968	>	n_i = RealType(info_->getGlobalCountOfType(*i));
969	>	rho_i = n_i /  vol;
970	>	for (j = atomTypes_.begin(); j != atomTypes_.end(); ++j) {
971	>	n_j = RealType(info_->getGlobalCountOfType(*j));
972	>	rho_j = n_j / vol;
973	>
974	>	LRI = interactionMan_->getLongRangeIntegrals( (*i), (*j) );
975	>
976	>	Elrc += n_i   * rho_j * LRI.first;
977	>	Wlrc -= rho_i * rho_j * LRI.second;
978	>	}
979	>	}
980	>	Elrc *= 2.0 * NumericConstant::PI;
981	>	Wlrc *= 2.0 * NumericConstant::PI;
982	>
983	>	RealType lrp = curSnapshot->getLongRangePotential();
984	>	curSnapshot->setLongRangePotential(lrp + Elrc);
985	>	stressTensor += Wlrc * SquareMatrix3<RealType>::identity();
986	>	curSnapshot->setStressTensor(stressTensor);
987	>	*/
988	>
989	>	}
990	>	}
991	>	}

Comparing trunk/src/brains/ForceManager.cpp (property svn:keywords):
Revision 1292 by chuckv, Fri Sep 12 20:51:22 2008 UTC vs.
Revision 2067 by gezelter, Thu Mar 5 15:35:37 2015 UTC

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