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root/OpenMD/branches/development/src/brains/ForceManager.cpp

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trunk/src/brains/ForceManager.cpp (file contents), Revision 1292 by chuckv, Fri Sep 12 20:51:22 2008 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 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, 24107 (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/ElectricField.hpp"
61	>	#include "parallel/ForceMatrixDecomposition.hpp"
62
63	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
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	>	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	<	if (!info_->isFortranInitialized()) {
111	<	info_->update();
112	<	}
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	<	preCalculation();
116	<
117	<	calcShortRangeInteraction();
115	>	if (simParams_->haveMDfileVersion())
116	>	mdFileVersion = simParams_->getMDfileVersion();
117	>	else
118	>	mdFileVersion = 0;
119	>
120	>	if (simParams_->haveCutoffRadius()) {
121	>	rCut_ = simParams_->getCutoffRadius();
122	>	} else {
123	>	if (info_->usesElectrostaticAtoms()) {
124	>	sprintf(painCave.errMsg,
125	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
126	>	"\tOpenMD will use a default value of 12.0 angstroms"
127	>	"\tfor the cutoffRadius.\n");
128	>	painCave.isFatal = 0;
129	>	painCave.severity = OPENMD_INFO;
130	>	simError();
131	>	rCut_ = 12.0;
132	>	} else {
133	>	RealType thisCut;
134	>	set<AtomType*>::iterator i;
135	>	set<AtomType*> atomTypes;
136	>	atomTypes = info_->getSimulatedAtomTypes();
137	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
138	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
139	>	rCut_ = max(thisCut, rCut_);
140	>	}
141	>	sprintf(painCave.errMsg,
142	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
143	>	"\tOpenMD will use %lf angstroms.\n",
144	>	rCut_);
145	>	painCave.isFatal = 0;
146	>	painCave.severity = OPENMD_INFO;
147	>	simError();
148	>	}
149	>	}
150
151	<	calcLongRangeInteraction(needPotential, needStress);
151	>	fDecomp_->setUserCutoff(rCut_);
152	>	interactionMan_->setCutoffRadius(rCut_);
153
154	<	postCalculation(needStress);
154	>	map<string, CutoffMethod> stringToCutoffMethod;
155	>	stringToCutoffMethod["HARD"] = HARD;
156	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
157	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
158	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
159	>
160	>	if (simParams_->haveCutoffMethod()) {
161	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
162	>	map<string, CutoffMethod>::iterator i;
163	>	i = stringToCutoffMethod.find(cutMeth);
164	>	if (i == stringToCutoffMethod.end()) {
165	>	sprintf(painCave.errMsg,
166	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
167	>	"\tShould be one of: "
168	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
169	>	cutMeth.c_str());
170	>	painCave.isFatal = 1;
171	>	painCave.severity = OPENMD_ERROR;
172	>	simError();
173	>	} else {
174	>	cutoffMethod_ = i->second;
175	>	}
176	>	} else {
177	>	if (mdFileVersion > 1) {
178	>	sprintf(painCave.errMsg,
179	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
180	>	"\tOpenMD will use SHIFTED_FORCE.\n");
181	>	painCave.isFatal = 0;
182	>	painCave.severity = OPENMD_INFO;
183	>	simError();
184	>	cutoffMethod_ = SHIFTED_FORCE;
185	>	} else {
186	>	// handle the case where the old file version was in play
187	>	// (there should be no cutoffMethod, so we have to deduce it
188	>	// from other data).
189	>
190	>	sprintf(painCave.errMsg,
191	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
192	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
193	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
194	>	"\tbehavior of the older (version 1) code.  To remove this\n"
195	>	"\twarning, add an explicit cutoffMethod and change the top\n"
196	>	"\tof the file so that it begins with <OpenMD version=2>\n");
197	>	painCave.isFatal = 0;
198	>	painCave.severity = OPENMD_WARNING;
199	>	simError();
200	>
201	>	// The old file version tethered the shifting behavior to the
202	>	// electrostaticSummationMethod keyword.
203	>
204	>	if (simParams_->haveElectrostaticSummationMethod()) {
205	>	string myMethod = simParams_->getElectrostaticSummationMethod();
206	>	toUpper(myMethod);
207	>
208	>	if (myMethod == "SHIFTED_POTENTIAL") {
209	>	cutoffMethod_ = SHIFTED_POTENTIAL;
210	>	} else if (myMethod == "SHIFTED_FORCE") {
211	>	cutoffMethod_ = SHIFTED_FORCE;
212	>	}
213	>
214	>	if (simParams_->haveSwitchingRadius())
215	>	rSwitch_ = simParams_->getSwitchingRadius();
216	>
217	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
218	>	if (simParams_->haveSwitchingRadius()){
219	>	sprintf(painCave.errMsg,
220	>	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
221	>	"\tA value was set for the switchingRadius\n"
222	>	"\teven though the electrostaticSummationMethod was\n"
223	>	"\tset to %s\n", myMethod.c_str());
224	>	painCave.severity = OPENMD_WARNING;
225	>	painCave.isFatal = 1;
226	>	simError();
227	>	}
228	>	}
229	>	if (abs(rCut_ - rSwitch_) < 0.0001) {
230	>	if (cutoffMethod_ == SHIFTED_FORCE) {
231	>	sprintf(painCave.errMsg,
232	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
233	>	"\tcutoffRadius and switchingRadius are set to the\n"
234	>	"\tsame value.  OpenMD will use shifted force\n"
235	>	"\tpotentials instead of switching functions.\n");
236	>	painCave.isFatal = 0;
237	>	painCave.severity = OPENMD_WARNING;
238	>	simError();
239	>	} else {
240	>	cutoffMethod_ = SHIFTED_POTENTIAL;
241	>	sprintf(painCave.errMsg,
242	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
243	>	"\tcutoffRadius and switchingRadius are set to the\n"
244	>	"\tsame value.  OpenMD will use shifted potentials\n"
245	>	"\tinstead of switching functions.\n");
246	>	painCave.isFatal = 0;
247	>	painCave.severity = OPENMD_WARNING;
248	>	simError();
249	>	}
250	>	}
251	>	}
252	>	}
253	>	}
254	>
255	>	map<string, CutoffPolicy> stringToCutoffPolicy;
256	>	stringToCutoffPolicy["MIX"] = MIX;
257	>	stringToCutoffPolicy["MAX"] = MAX;
258	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
259	>
260	>	string cutPolicy;
261	>	if (forceFieldOptions_.haveCutoffPolicy()){
262	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
263	>	}else if (simParams_->haveCutoffPolicy()) {
264	>	cutPolicy = simParams_->getCutoffPolicy();
265	>	}
266	>
267	>	if (!cutPolicy.empty()){
268	>	toUpper(cutPolicy);
269	>	map<string, CutoffPolicy>::iterator i;
270	>	i = stringToCutoffPolicy.find(cutPolicy);
271	>
272	>	if (i == stringToCutoffPolicy.end()) {
273	>	sprintf(painCave.errMsg,
274	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
275	>	"\tShould be one of: "
276	>	"MIX, MAX, or TRADITIONAL\n",
277	>	cutPolicy.c_str());
278	>	painCave.isFatal = 1;
279	>	painCave.severity = OPENMD_ERROR;
280	>	simError();
281	>	} else {
282	>	cutoffPolicy_ = i->second;
283	>	}
284	>	} else {
285	>	sprintf(painCave.errMsg,
286	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
287	>	"\tOpenMD will use TRADITIONAL.\n");
288	>	painCave.isFatal = 0;
289	>	painCave.severity = OPENMD_INFO;
290	>	simError();
291	>	cutoffPolicy_ = TRADITIONAL;
292	>	}
293	>
294	>	fDecomp_->setCutoffPolicy(cutoffPolicy_);
295	>
296	>	// create the switching function object:
297	>
298	>	switcher_ = new SwitchingFunction();
299	>
300	>	if (cutoffMethod_ == SWITCHED) {
301	>	if (simParams_->haveSwitchingRadius()) {
302	>	rSwitch_ = simParams_->getSwitchingRadius();
303	>	if (rSwitch_ > rCut_) {
304	>	sprintf(painCave.errMsg,
305	>	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
306	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
307	>	painCave.isFatal = 1;
308	>	painCave.severity = OPENMD_ERROR;
309	>	simError();
310	>	}
311	>	} else {
312	>	rSwitch_ = 0.85 * rCut_;
313	>	sprintf(painCave.errMsg,
314	>	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
315	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
316	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
317	>	painCave.isFatal = 0;
318	>	painCave.severity = OPENMD_WARNING;
319	>	simError();
320	>	}
321	>	} else {
322	>	if (mdFileVersion > 1) {
323	>	// throw an error if we define a switching radius and don't need one.
324	>	// older file versions should not do this.
325	>	if (simParams_->haveSwitchingRadius()) {
326	>	map<string, CutoffMethod>::const_iterator it;
327	>	string theMeth;
328	>	for (it = stringToCutoffMethod.begin();
329	>	it != stringToCutoffMethod.end(); ++it) {
330	>	if (it->second == cutoffMethod_) {
331	>	theMeth = it->first;
332	>	break;
333	>	}
334	>	}
335	>	sprintf(painCave.errMsg,
336	>	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
337	>	"\tis not set to SWITCHED, so switchingRadius value\n"
338	>	"\twill be ignored for this simulation\n", theMeth.c_str());
339	>	painCave.isFatal = 0;
340	>	painCave.severity = OPENMD_WARNING;
341	>	simError();
342	>	}
343	>	}
344	>	rSwitch_ = rCut_;
345	>	}
346
347	+	// Default to cubic switching function.
348	+	sft_ = cubic;
349	+	if (simParams_->haveSwitchingFunctionType()) {
350	+	string funcType = simParams_->getSwitchingFunctionType();
351	+	toUpper(funcType);
352	+	if (funcType == "CUBIC") {
353	+	sft_ = cubic;
354	+	} else {
355	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
356	+	sft_ = fifth_order_poly;
357	+	} else {
358	+	// throw error
359	+	sprintf( painCave.errMsg,
360	+	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
361	+	"\tswitchingFunctionType must be one of: "
362	+	"\"cubic\" or \"fifth_order_polynomial\".",
363	+	funcType.c_str() );
364	+	painCave.isFatal = 1;
365	+	painCave.severity = OPENMD_ERROR;
366	+	simError();
367	+	}
368	+	}
369	+	}
370	+	switcher_->setSwitchType(sft_);
371	+	switcher_->setSwitch(rSwitch_, rCut_);
372		}
373	+
374	+
375	+
376
377	+	void ForceManager::initialize() {
378	+
379	+	if (!info_->isTopologyDone()) {
380	+
381	+	info_->update();
382	+	interactionMan_->setSimInfo(info_);
383	+	interactionMan_->initialize();
384	+
385	+	// We want to delay the cutoffs until after the interaction
386	+	// manager has set up the atom-atom interactions so that we can
387	+	// query them for suggested cutoff values
388	+	setupCutoffs();
389	+
390	+	info_->prepareTopology();
391	+
392	+	doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
393	+	doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
394	+	if (doHeatFlux_) doParticlePot_ = true;
395	+
396	+	doElectricField_ = info_->getSimParams()->getOutputElectricField();
397	+
398	+	}
399	+
400	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
401	+
402	+	// Force fields can set options on how to scale van der Waals and
403	+	// electrostatic interactions for atoms connected via bonds, bends
404	+	// and torsions in this case the topological distance between
405	+	// atoms is:
406	+	// 0 = topologically unconnected
407	+	// 1 = bonded together
408	+	// 2 = connected via a bend
409	+	// 3 = connected via a torsion
410	+
411	+	vdwScale_.reserve(4);
412	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
413	+
414	+	electrostaticScale_.reserve(4);
415	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
416	+
417	+	vdwScale_[0] = 1.0;
418	+	vdwScale_[1] = fopts.getvdw12scale();
419	+	vdwScale_[2] = fopts.getvdw13scale();
420	+	vdwScale_[3] = fopts.getvdw14scale();
421	+
422	+	electrostaticScale_[0] = 1.0;
423	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
424	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
425	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
426	+
427	+	if (info_->getSimParams()->haveElectricField()) {
428	+	ElectricField* eField = new ElectricField(info_);
429	+	perturbations_.push_back(eField);
430	+	}
431	+
432	+	fDecomp_->distributeInitialData();
433	+
434	+	initialized_ = true;
435	+
436	+	}
437	+
438	+	void ForceManager::calcForces() {
439	+
440	+	if (!initialized_) initialize();
441	+
442	+	preCalculation();
443	+	shortRangeInteractions();
444	+	longRangeInteractions();
445	+	postCalculation();
446	+	}
447	+
448		void ForceManager::preCalculation() {
449		SimInfo::MoleculeIterator mi;
450		Molecule* mol;
#	Line 82 | Line 452 | namespace oopse {
452		Atom* atom;
453		Molecule::RigidBodyIterator rbIter;
454		RigidBody* rb;
455	+	Molecule::CutoffGroupIterator ci;
456	+	CutoffGroup* cg;
457
458	<	// forces are zeroed here, before any are accumulated.
459	<	// NOTE: do not rezero the forces in Fortran.
458	>	// forces and potentials are zeroed here, before any are
459	>	// accumulated.
460
461	+	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
462	+
463	+	snap->setBondPotential(0.0);
464	+	snap->setBendPotential(0.0);
465	+	snap->setTorsionPotential(0.0);
466	+	snap->setInversionPotential(0.0);
467	+
468	+	potVec zeroPot(0.0);
469	+	snap->setLongRangePotential(zeroPot);
470	+	snap->setExcludedPotentials(zeroPot);
471	+
472	+	snap->setRestraintPotential(0.0);
473	+	snap->setRawPotential(0.0);
474	+
475		for (mol = info_->beginMolecule(mi); mol != NULL;
476		mol = info_->nextMolecule(mi)) {
477	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
477	>	for(atom = mol->beginAtom(ai); atom != NULL;
478	>	atom = mol->nextAtom(ai)) {
479		atom->zeroForcesAndTorques();
480		}
481	<
481	>
482		//change the positions of atoms which belong to the rigidbodies
483		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
484		rb = mol->nextRigidBody(rbIter)) {
485		rb->zeroForcesAndTorques();
486		}
487	<
487	>
488	>	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
489	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
490	>	cg = mol->nextCutoffGroup(ci)) {
491	>	//calculate the center of mass of cutoff group
492	>	cg->updateCOM();
493	>	}
494	>	}
495		}
496
497		// Zero out the stress tensor
498	<	tau *= 0.0;
499	<
498	>	stressTensor *= 0.0;
499	>	// Zero out the heatFlux
500	>	fDecomp_->setHeatFlux( Vector3d(0.0) );
501		}
502
503	<	void ForceManager::calcShortRangeInteraction() {
503	>	void ForceManager::shortRangeInteractions() {
504		Molecule* mol;
505		RigidBody* rb;
506		Bond* bond;
#	Line 135 | Line 530 | namespace oopse {
530
531		for (bond = mol->beginBond(bondIter); bond != NULL;
532		bond = mol->nextBond(bondIter)) {
533	<	bond->calcForce();
533	>	bond->calcForce(doParticlePot_);
534		bondPotential += bond->getPotential();
535		}
536
#	Line 143 | Line 538 | namespace oopse {
538		bend = mol->nextBend(bendIter)) {
539
540		RealType angle;
541	<	bend->calcForce(angle);
541	>	bend->calcForce(angle, doParticlePot_);
542		RealType currBendPot = bend->getPotential();
543	+
544		bendPotential += bend->getPotential();
545	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
545	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
546		if (i == bendDataSets.end()) {
547		BendDataSet dataSet;
548		dataSet.prev.angle = dataSet.curr.angle = angle;
549		dataSet.prev.potential = dataSet.curr.potential = currBendPot;
550		dataSet.deltaV = 0.0;
551	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
551	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
552	>	dataSet));
553		}else {
554		i->second.prev.angle = i->second.curr.angle;
555		i->second.prev.potential = i->second.curr.potential;
#	Line 166 | Line 563 | namespace oopse {
563		for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
564		torsion = mol->nextTorsion(torsionIter)) {
565		RealType angle;
566	<	torsion->calcForce(angle);
566	>	torsion->calcForce(angle, doParticlePot_);
567		RealType currTorsionPot = torsion->getPotential();
568		torsionPotential += torsion->getPotential();
569	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
569	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
570		if (i == torsionDataSets.end()) {
571		TorsionDataSet dataSet;
572		dataSet.prev.angle = dataSet.curr.angle = angle;
573		dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
574		dataSet.deltaV = 0.0;
575	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
575	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
576		}else {
577		i->second.prev.angle = i->second.curr.angle;
578		i->second.prev.potential = i->second.curr.potential;
#	Line 185 | Line 582 | namespace oopse {
582		i->second.prev.potential);
583		}
584		}
585	<
585	>
586		for (inversion = mol->beginInversion(inversionIter);
587		inversion != NULL;
588		inversion = mol->nextInversion(inversionIter)) {
589		RealType angle;
590	<	inversion->calcForce(angle);
590	>	inversion->calcForce(angle, doParticlePot_);
591		RealType currInversionPot = inversion->getPotential();
592		inversionPotential += inversion->getPotential();
593	<	std::map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
593	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
594		if (i == inversionDataSets.end()) {
595		InversionDataSet dataSet;
596		dataSet.prev.angle = dataSet.curr.angle = angle;
597		dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
598		dataSet.deltaV = 0.0;
599	<	inversionDataSets.insert(std::map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
599	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
600		}else {
601		i->second.prev.angle = i->second.curr.angle;
602		i->second.prev.potential = i->second.curr.potential;
#	Line 210 | Line 607 | namespace oopse {
607		}
608		}
609		}
610	<
611	<	RealType  shortRangePotential = bondPotential + bendPotential +
612	<	torsionPotential +  inversionPotential;
610	>
611	>	#ifdef IS_MPI
612	>	// Collect from all nodes.  This should eventually be moved into a
613	>	// SystemDecomposition, but this is a better place than in
614	>	// Thermo to do the collection.
615	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
616	>	MPI::SUM);
617	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
618	>	MPI::SUM);
619	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
620	>	MPI::REALTYPE, MPI::SUM);
621	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
622	>	MPI::REALTYPE, MPI::SUM);
623	>	#endif
624	>
625		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
626	<	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
627	<	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
628	<	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
629	<	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
630	<	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
626	>
627	>	curSnapshot->setBondPotential(bondPotential);
628	>	curSnapshot->setBendPotential(bendPotential);
629	>	curSnapshot->setTorsionPotential(torsionPotential);
630	>	curSnapshot->setInversionPotential(inversionPotential);
631
632	+	// RealType shortRangePotential = bondPotential + bendPotential +
633	+	//   torsionPotential +  inversionPotential;
634	+
635	+	// curSnapshot->setShortRangePotential(shortRangePotential);
636		}
637
638	<	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);
638	>	void ForceManager::longRangeInteractions() {
639
640	+
641	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
642	+	DataStorage* config = &(curSnapshot->atomData);
643	+	DataStorage* cgConfig = &(curSnapshot->cgData);
644	+
645		//calculate the center of mass of cutoff group
646	+
647		SimInfo::MoleculeIterator mi;
648		Molecule* mol;
649		Molecule::CutoffGroupIterator ci;
650		CutoffGroup* cg;
651	<	Vector3d com;
652	<	std::vector<Vector3d> rcGroup;
256	<
257	<	if(info_->getNCutoffGroups() > 0){
258	<
651	>
652	>	if(info_->getNCutoffGroups() > 0){
653		for (mol = info_->beginMolecule(mi); mol != NULL;
654		mol = info_->nextMolecule(mi)) {
655		for(cg = mol->beginCutoffGroup(ci); cg != NULL;
656		cg = mol->nextCutoffGroup(ci)) {
657	<	cg->getCOM(com);
264	<	rcGroup.push_back(com);
657	>	cg->updateCOM();
658		}
659	<	}// end for (mol)
267	<
268	<	rc = rcGroup[0].getArrayPointer();
659	>	}
660		} else {
661		// center of mass of the group is the same as position of the atom
662		// if cutoff group does not exist
663	<	rc = pos;
663	>	cgConfig->position = config->position;
664	>	cgConfig->velocity = config->velocity;
665		}
666	+
667	+	fDecomp_->zeroWorkArrays();
668	+	fDecomp_->distributeData();
669
670	<	//initialize data before passing to fortran
671	<	RealType longRangePotential[LR_POT_TYPES];
672	<	RealType lrPot = 0.0;
673	<	Vector3d totalDipole;
674	<	short int passedCalcPot = needPotential;
675	<	short int passedCalcStress = needStress;
676	<	int isError = 0;
670	>	int cg1, cg2, atom1, atom2, topoDist;
671	>	Vector3d d_grp, dag, d, gvel2, vel2;
672	>	RealType rgrpsq, rgrp, r2, r;
673	>	RealType electroMult, vdwMult;
674	>	RealType vij;
675	>	Vector3d fij, fg, f1;
676	>	tuple3<RealType, RealType, RealType> cuts;
677	>	RealType rCutSq;
678	>	bool in_switching_region;
679	>	RealType sw, dswdr, swderiv;
680	>	vector<int> atomListColumn, atomListRow, atomListLocal;
681	>	InteractionData idat;
682	>	SelfData sdat;
683	>	RealType mf;
684	>	RealType vpair;
685	>	RealType dVdFQ1(0.0);
686	>	RealType dVdFQ2(0.0);
687	>	potVec longRangePotential(0.0);
688	>	potVec workPot(0.0);
689	>	potVec exPot(0.0);
690	>	Vector3d eField1(0.0);
691	>	Vector3d eField2(0.0);
692	>	vector<int>::iterator ia, jb;
693
694	<	for (int i=0; i<LR_POT_TYPES;i++){
695	<	longRangePotential[i]=0.0; //Initialize array
696	<	}
694	>	int loopStart, loopEnd;
695	>
696	>	idat.vdwMult = &vdwMult;
697	>	idat.electroMult = &electroMult;
698	>	idat.pot = &workPot;
699	>	idat.excludedPot = &exPot;
700	>	sdat.pot = fDecomp_->getEmbeddingPotential();
701	>	sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
702	>	idat.vpair = &vpair;
703	>	idat.dVdFQ1 = &dVdFQ1;
704	>	idat.dVdFQ2 = &dVdFQ2;
705	>	idat.eField1 = &eField1;
706	>	idat.eField2 = &eField2;
707	>	idat.f1 = &f1;
708	>	idat.sw = &sw;
709	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
710	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
711	>	idat.doParticlePot = doParticlePot_;
712	>	idat.doElectricField = doElectricField_;
713	>	sdat.doParticlePot = doParticlePot_;
714
715	<	doForceLoop(pos,
716	<	rc,
717	<	A,
718	<	electroFrame,
719	<	frc,
292	<	trq,
293	<	tau.getArrayPointer(),
294	<	longRangePotential,
295	<	particlePot,
296	<	&passedCalcPot,
297	<	&passedCalcStress,
298	<	&isError );
299	<
300	<	if( isError ){
301	<	sprintf( painCave.errMsg,
302	<	"Error returned from the fortran force calculation.\n" );
303	<	painCave.isFatal = 1;
304	<	simError();
715	>	loopEnd = PAIR_LOOP;
716	>	if (info_->requiresPrepair() ) {
717	>	loopStart = PREPAIR_LOOP;
718	>	} else {
719	>	loopStart = PAIR_LOOP;
720		}
721	<	for (int i=0; i<LR_POT_TYPES;i++){
722	<	lrPot += longRangePotential[i]; //Quick hack
721	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
722	>
723	>	if (iLoop == loopStart) {
724	>	bool update_nlist = fDecomp_->checkNeighborList();
725	>	if (update_nlist)
726	>	neighborList = fDecomp_->buildNeighborList();
727	>	}
728	>
729	>	for (vector<pair<int, int> >::iterator it = neighborList.begin();
730	>	it != neighborList.end(); ++it) {
731	>
732	>	cg1 = (*it).first;
733	>	cg2 = (*it).second;
734	>
735	>	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
736	>
737	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
738	>
739	>	curSnapshot->wrapVector(d_grp);
740	>	rgrpsq = d_grp.lengthSquare();
741	>	rCutSq = cuts.second;
742	>
743	>	if (rgrpsq < rCutSq) {
744	>	idat.rcut = &cuts.first;
745	>	if (iLoop == PAIR_LOOP) {
746	>	vij = 0.0;
747	>	fij = V3Zero;
748	>	}
749	>
750	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
751	>	rgrp);
752	>
753	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
754	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
755	>
756	>	if (doHeatFlux_)
757	>	gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
758	>
759	>	for (ia = atomListRow.begin();
760	>	ia != atomListRow.end(); ++ia) {
761	>	atom1 = (*ia);
762	>
763	>	for (jb = atomListColumn.begin();
764	>	jb != atomListColumn.end(); ++jb) {
765	>	atom2 = (*jb);
766	>
767	>	if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
768	>
769	>	vpair = 0.0;
770	>	workPot = 0.0;
771	>	exPot = 0.0;
772	>	f1 = V3Zero;
773	>	dVdFQ1 = 0.0;
774	>	dVdFQ2 = 0.0;
775	>
776	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
777	>
778	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
779	>	vdwMult = vdwScale_[topoDist];
780	>	electroMult = electrostaticScale_[topoDist];
781	>
782	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
783	>	idat.d = &d_grp;
784	>	idat.r2 = &rgrpsq;
785	>	if (doHeatFlux_)
786	>	vel2 = gvel2;
787	>	} else {
788	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
789	>	curSnapshot->wrapVector( d );
790	>	r2 = d.lengthSquare();
791	>	idat.d = &d;
792	>	idat.r2 = &r2;
793	>	if (doHeatFlux_)
794	>	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
795	>	}
796	>
797	>	r = sqrt( *(idat.r2) );
798	>	idat.rij = &r;
799	>
800	>	if (iLoop == PREPAIR_LOOP) {
801	>	interactionMan_->doPrePair(idat);
802	>	} else {
803	>	interactionMan_->doPair(idat);
804	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
805	>	vij += vpair;
806	>	fij += f1;
807	>	stressTensor -= outProduct( *(idat.d), f1);
808	>	if (doHeatFlux_)
809	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
810	>	}
811	>	}
812	>	}
813	>	}
814	>
815	>	if (iLoop == PAIR_LOOP) {
816	>	if (in_switching_region) {
817	>	swderiv = vij * dswdr / rgrp;
818	>	fg = swderiv * d_grp;
819	>	fij += fg;
820	>
821	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
822	>	stressTensor -= outProduct( *(idat.d), fg);
823	>	if (doHeatFlux_)
824	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
825	>
826	>	}
827	>
828	>	for (ia = atomListRow.begin();
829	>	ia != atomListRow.end(); ++ia) {
830	>	atom1 = (*ia);
831	>	mf = fDecomp_->getMassFactorRow(atom1);
832	>	// fg is the force on atom ia due to cutoff group's
833	>	// presence in switching region
834	>	fg = swderiv * d_grp * mf;
835	>	fDecomp_->addForceToAtomRow(atom1, fg);
836	>	if (atomListRow.size() > 1) {
837	>	if (info_->usesAtomicVirial()) {
838	>	// find the distance between the atom
839	>	// and the center of the cutoff group:
840	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
841	>	stressTensor -= outProduct(dag, fg);
842	>	if (doHeatFlux_)
843	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
844	>	}
845	>	}
846	>	}
847	>	for (jb = atomListColumn.begin();
848	>	jb != atomListColumn.end(); ++jb) {
849	>	atom2 = (*jb);
850	>	mf = fDecomp_->getMassFactorColumn(atom2);
851	>	// fg is the force on atom jb due to cutoff group's
852	>	// presence in switching region
853	>	fg = -swderiv * d_grp * mf;
854	>	fDecomp_->addForceToAtomColumn(atom2, fg);
855	>
856	>	if (atomListColumn.size() > 1) {
857	>	if (info_->usesAtomicVirial()) {
858	>	// find the distance between the atom
859	>	// and the center of the cutoff group:
860	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
861	>	stressTensor -= outProduct(dag, fg);
862	>	if (doHeatFlux_)
863	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
864	>	}
865	>	}
866	>	}
867	>	}
868	>	//if (!info_->usesAtomicVirial()) {
869	>	//  stressTensor -= outProduct(d_grp, fij);
870	>	//  if (doHeatFlux_)
871	>	//     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
872	>	//}
873	>	}
874	>	}
875	>	}
876	>
877	>	if (iLoop == PREPAIR_LOOP) {
878	>	if (info_->requiresPrepair()) {
879	>
880	>	fDecomp_->collectIntermediateData();
881	>
882	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
883	>	fDecomp_->fillSelfData(sdat, atom1);
884	>	interactionMan_->doPreForce(sdat);
885	>	}
886	>
887	>	fDecomp_->distributeIntermediateData();
888	>
889	>	}
890	>	}
891		}
892
893	<	// grab the simulation box dipole moment if specified
894	<	if (info_->getCalcBoxDipole()){
895	<	getAccumulatedBoxDipole(totalDipole.getArrayPointer());
896	<
897	<	curSnapshot->statData[Stats::BOX_DIPOLE_X] = totalDipole(0);
898	<	curSnapshot->statData[Stats::BOX_DIPOLE_Y] = totalDipole(1);
899	<	curSnapshot->statData[Stats::BOX_DIPOLE_Z] = totalDipole(2);
893	>	// collects pairwise information
894	>	fDecomp_->collectData();
895	>
896	>	if (info_->requiresSelfCorrection()) {
897	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
898	>	fDecomp_->fillSelfData(sdat, atom1);
899	>	interactionMan_->doSelfCorrection(sdat);
900	>	}
901		}
902	+
903	+	// collects single-atom information
904	+	fDecomp_->collectSelfData();
905	+
906	+	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
907	+	*(fDecomp_->getPairwisePotential());
908	+
909	+	curSnapshot->setLongRangePotential(longRangePotential);
910	+
911	+	// collects single-atom information
912	+	fDecomp_->collectSelfData();
913	+
914	+	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
915	+	*(fDecomp_->getPairwisePotential());
916	+
917	+	curSnapshot->setLongRangePotential(longRangePotential);
918
919	<	//store the tau and long range potential
920	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
921	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
322	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
919	>	curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
920	>	*(fDecomp_->getExcludedPotential()));
921	>
922		}
923
924
925	<	void ForceManager::postCalculation(bool needStress) {
925	>	void ForceManager::postCalculation() {
926	>
927	>	vector<Perturbation*>::iterator pi;
928	>	for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
929	>	(*pi)->applyPerturbation();
930	>	}
931	>
932		SimInfo::MoleculeIterator mi;
933		Molecule* mol;
934		Molecule::RigidBodyIterator rbIter;
935		RigidBody* rb;
936		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
937	<
937	>
938		// collect the atomic forces onto rigid bodies
939
940		for (mol = info_->beginMolecule(mi); mol != NULL;
941		mol = info_->nextMolecule(mi)) {
942		for (rb = mol->beginRigidBody(rbIter); rb != NULL;
943		rb = mol->nextRigidBody(rbIter)) {
944	<	if (needStress) {
945	<	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
341	<	tau += rbTau;
342	<	} else{
343	<	rb->calcForcesAndTorques();
344	<	}
944	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
945	>	stressTensor += rbTau;
946		}
947		}
948	<
348	<	if (needStress) {
948	>
949		#ifdef IS_MPI
950	<	Mat3x3d tmpTau(tau);
951	<	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
352	<	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
950	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
951	>	MPI::REALTYPE, MPI::SUM);
952		#endif
953	<	curSnapshot->statData.setTau(tau);
954	<	}
953	>	curSnapshot->setStressTensor(stressTensor);
954	>
955		}
956	<
358	<	} //end namespace oopse
956	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 1292 by chuckv, Fri Sep 12 20:51:22 2008 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1808 by gezelter, Mon Oct 22 20:42:10 2012 UTC

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