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

Comparing:
trunk/src/brains/ForceManager.cpp (file contents), Revision 664 by chuckv, Wed Oct 12 21:57:16 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1733 by jmichalk, Tue Jun 5 17:48:40 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		/**
#	Line 47 | Line 48
48		* @version 1.0
49		*/
50
51	+
52		#include "brains/ForceManager.hpp"
53		#include "primitives/Molecule.hpp"
54	<	#include "UseTheForce/doForces_interface.h"
53	<	#define __C
54	<	#include "UseTheForce/DarkSide/fInteractionMap.h"
54	>	#define __OPENMD_C
55		#include "utils/simError.h"
56	<	namespace oopse {
56	>	#include "primitives/Bond.hpp"
57	>	#include "primitives/Bend.hpp"
58	>	#include "primitives/Torsion.hpp"
59	>	#include "primitives/Inversion.hpp"
60	>	#include "nonbonded/NonBondedInteraction.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	<	if (!info_->isFortranInitialized()) {
68	<	info_->update();
69	<	}
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	<	preCalculation();
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	<	calcShortRangeInteraction();
110	>	Globals* simParams_ = info_->getSimParams();
111	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
112	>	int mdFileVersion;
113	>
114	>	if (simParams_->haveMDfileVersion())
115	>	mdFileVersion = simParams_->getMDfileVersion();
116	>	else
117	>	mdFileVersion = 0;
118	>
119	>	if (simParams_->haveCutoffRadius()) {
120	>	rCut_ = simParams_->getCutoffRadius();
121	>	} else {
122	>	if (info_->usesElectrostaticAtoms()) {
123	>	sprintf(painCave.errMsg,
124	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
125	>	"\tOpenMD will use a default value of 12.0 angstroms"
126	>	"\tfor the cutoffRadius.\n");
127	>	painCave.isFatal = 0;
128	>	painCave.severity = OPENMD_INFO;
129	>	simError();
130	>	rCut_ = 12.0;
131	>	} else {
132	>	RealType thisCut;
133	>	set<AtomType*>::iterator i;
134	>	set<AtomType*> atomTypes;
135	>	atomTypes = info_->getSimulatedAtomTypes();
136	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
137	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
138	>	rCut_ = max(thisCut, rCut_);
139	>	}
140	>	sprintf(painCave.errMsg,
141	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
142	>	"\tOpenMD will use %lf angstroms.\n",
143	>	rCut_);
144	>	painCave.isFatal = 0;
145	>	painCave.severity = OPENMD_INFO;
146	>	simError();
147	>	}
148	>	}
149
150	<	calcLongRangeInteraction(needPotential, needStress);
150	>	fDecomp_->setUserCutoff(rCut_);
151	>	interactionMan_->setCutoffRadius(rCut_);
152
153	<	postCalculation();
153	>	map<string, CutoffMethod> stringToCutoffMethod;
154	>	stringToCutoffMethod["HARD"] = HARD;
155	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
156	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
157	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
158	>
159	>	if (simParams_->haveCutoffMethod()) {
160	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
161	>	map<string, CutoffMethod>::iterator i;
162	>	i = stringToCutoffMethod.find(cutMeth);
163	>	if (i == stringToCutoffMethod.end()) {
164	>	sprintf(painCave.errMsg,
165	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
166	>	"\tShould be one of: "
167	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
168	>	cutMeth.c_str());
169	>	painCave.isFatal = 1;
170	>	painCave.severity = OPENMD_ERROR;
171	>	simError();
172	>	} else {
173	>	cutoffMethod_ = i->second;
174	>	}
175	>	} else {
176	>	if (mdFileVersion > 1) {
177	>	sprintf(painCave.errMsg,
178	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
179	>	"\tOpenMD will use SHIFTED_FORCE.\n");
180	>	painCave.isFatal = 0;
181	>	painCave.severity = OPENMD_INFO;
182	>	simError();
183	>	cutoffMethod_ = SHIFTED_FORCE;
184	>	} else {
185	>	// handle the case where the old file version was in play
186	>	// (there should be no cutoffMethod, so we have to deduce it
187	>	// from other data).
188	>
189	>	sprintf(painCave.errMsg,
190	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
191	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
192	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
193	>	"\tbehavior of the older (version 1) code.  To remove this\n"
194	>	"\twarning, add an explicit cutoffMethod and change the top\n"
195	>	"\tof the file so that it begins with <OpenMD version=2>\n");
196	>	painCave.isFatal = 0;
197	>	painCave.severity = OPENMD_WARNING;
198	>	simError();
199	>
200	>	// The old file version tethered the shifting behavior to the
201	>	// electrostaticSummationMethod keyword.
202	>
203	>	if (simParams_->haveElectrostaticSummationMethod()) {
204	>	string myMethod = simParams_->getElectrostaticSummationMethod();
205	>	toUpper(myMethod);
206	>
207	>	if (myMethod == "SHIFTED_POTENTIAL") {
208	>	cutoffMethod_ = SHIFTED_POTENTIAL;
209	>	} else if (myMethod == "SHIFTED_FORCE") {
210	>	cutoffMethod_ = SHIFTED_FORCE;
211	>	}
212	>
213	>	if (simParams_->haveSwitchingRadius())
214	>	rSwitch_ = simParams_->getSwitchingRadius();
215	>
216	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
217	>	if (simParams_->haveSwitchingRadius()){
218	>	sprintf(painCave.errMsg,
219	>	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
220	>	"\tA value was set for the switchingRadius\n"
221	>	"\teven though the electrostaticSummationMethod was\n"
222	>	"\tset to %s\n", myMethod.c_str());
223	>	painCave.severity = OPENMD_WARNING;
224	>	painCave.isFatal = 1;
225	>	simError();
226	>	}
227	>	}
228	>	if (abs(rCut_ - rSwitch_) < 0.0001) {
229	>	if (cutoffMethod_ == SHIFTED_FORCE) {
230	>	sprintf(painCave.errMsg,
231	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
232	>	"\tcutoffRadius and switchingRadius are set to the\n"
233	>	"\tsame value.  OpenMD will use shifted force\n"
234	>	"\tpotentials instead of switching functions.\n");
235	>	painCave.isFatal = 0;
236	>	painCave.severity = OPENMD_WARNING;
237	>	simError();
238	>	} else {
239	>	cutoffMethod_ = SHIFTED_POTENTIAL;
240	>	sprintf(painCave.errMsg,
241	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
242	>	"\tcutoffRadius and switchingRadius are set to the\n"
243	>	"\tsame value.  OpenMD will use shifted potentials\n"
244	>	"\tinstead of switching functions.\n");
245	>	painCave.isFatal = 0;
246	>	painCave.severity = OPENMD_WARNING;
247	>	simError();
248	>	}
249	>	}
250	>	}
251	>	}
252	>	}
253	>
254	>	map<string, CutoffPolicy> stringToCutoffPolicy;
255	>	stringToCutoffPolicy["MIX"] = MIX;
256	>	stringToCutoffPolicy["MAX"] = MAX;
257	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
258	>
259	>	string cutPolicy;
260	>	if (forceFieldOptions_.haveCutoffPolicy()){
261	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
262	>	}else if (simParams_->haveCutoffPolicy()) {
263	>	cutPolicy = simParams_->getCutoffPolicy();
264	>	}
265	>
266	>	if (!cutPolicy.empty()){
267	>	toUpper(cutPolicy);
268	>	map<string, CutoffPolicy>::iterator i;
269	>	i = stringToCutoffPolicy.find(cutPolicy);
270	>
271	>	if (i == stringToCutoffPolicy.end()) {
272	>	sprintf(painCave.errMsg,
273	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
274	>	"\tShould be one of: "
275	>	"MIX, MAX, or TRADITIONAL\n",
276	>	cutPolicy.c_str());
277	>	painCave.isFatal = 1;
278	>	painCave.severity = OPENMD_ERROR;
279	>	simError();
280	>	} else {
281	>	cutoffPolicy_ = i->second;
282	>	}
283	>	} else {
284	>	sprintf(painCave.errMsg,
285	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
286	>	"\tOpenMD will use TRADITIONAL.\n");
287	>	painCave.isFatal = 0;
288	>	painCave.severity = OPENMD_INFO;
289	>	simError();
290	>	cutoffPolicy_ = TRADITIONAL;
291	>	}
292	>
293	>	fDecomp_->setCutoffPolicy(cutoffPolicy_);
294
295	+	// create the switching function object:
296	+
297	+	switcher_ = new SwitchingFunction();
298	+
299	+	if (cutoffMethod_ == SWITCHED) {
300	+	if (simParams_->haveSwitchingRadius()) {
301	+	rSwitch_ = simParams_->getSwitchingRadius();
302	+	if (rSwitch_ > rCut_) {
303	+	sprintf(painCave.errMsg,
304	+	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
305	+	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
306	+	painCave.isFatal = 1;
307	+	painCave.severity = OPENMD_ERROR;
308	+	simError();
309	+	}
310	+	} else {
311	+	rSwitch_ = 0.85 * rCut_;
312	+	sprintf(painCave.errMsg,
313	+	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
314	+	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
315	+	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
316	+	painCave.isFatal = 0;
317	+	painCave.severity = OPENMD_WARNING;
318	+	simError();
319	+	}
320	+	} else {
321	+	if (mdFileVersion > 1) {
322	+	// throw an error if we define a switching radius and don't need one.
323	+	// older file versions should not do this.
324	+	if (simParams_->haveSwitchingRadius()) {
325	+	map<string, CutoffMethod>::const_iterator it;
326	+	string theMeth;
327	+	for (it = stringToCutoffMethod.begin();
328	+	it != stringToCutoffMethod.end(); ++it) {
329	+	if (it->second == cutoffMethod_) {
330	+	theMeth = it->first;
331	+	break;
332	+	}
333	+	}
334	+	sprintf(painCave.errMsg,
335	+	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
336	+	"\tis not set to SWITCHED, so switchingRadius value\n"
337	+	"\twill be ignored for this simulation\n", theMeth.c_str());
338	+	painCave.isFatal = 0;
339	+	painCave.severity = OPENMD_WARNING;
340	+	simError();
341	+	}
342	+	}
343	+	rSwitch_ = rCut_;
344	+	}
345	+
346	+	// Default to cubic switching function.
347	+	sft_ = cubic;
348	+	if (simParams_->haveSwitchingFunctionType()) {
349	+	string funcType = simParams_->getSwitchingFunctionType();
350	+	toUpper(funcType);
351	+	if (funcType == "CUBIC") {
352	+	sft_ = cubic;
353	+	} else {
354	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
355	+	sft_ = fifth_order_poly;
356	+	} else {
357	+	// throw error
358	+	sprintf( painCave.errMsg,
359	+	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
360	+	"\tswitchingFunctionType must be one of: "
361	+	"\"cubic\" or \"fifth_order_polynomial\".",
362	+	funcType.c_str() );
363	+	painCave.isFatal = 1;
364	+	painCave.severity = OPENMD_ERROR;
365	+	simError();
366	+	}
367	+	}
368	+	}
369	+	switcher_->setSwitchType(sft_);
370	+	switcher_->setSwitch(rSwitch_, rCut_);
371	+	interactionMan_->setSwitchingRadius(rSwitch_);
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	+	}
397	+
398	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
399	+
400	+	// Force fields can set options on how to scale van der Waals and
401	+	// electrostatic interactions for atoms connected via bonds, bends
402	+	// and torsions in this case the topological distance between
403	+	// atoms is:
404	+	// 0 = topologically unconnected
405	+	// 1 = bonded together
406	+	// 2 = connected via a bend
407	+	// 3 = connected via a torsion
408	+
409	+	vdwScale_.reserve(4);
410	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
411	+
412	+	electrostaticScale_.reserve(4);
413	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
414	+
415	+	vdwScale_[0] = 1.0;
416	+	vdwScale_[1] = fopts.getvdw12scale();
417	+	vdwScale_[2] = fopts.getvdw13scale();
418	+	vdwScale_[3] = fopts.getvdw14scale();
419	+
420	+	electrostaticScale_[0] = 1.0;
421	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
422	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
423	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
424	+
425	+	fDecomp_->distributeInitialData();
426	+
427	+	initialized_ = true;
428	+
429	+	}
430	+
431	+	void ForceManager::calcForces() {
432	+
433	+	if (!initialized_) initialize();
434	+
435	+	preCalculation();
436	+	shortRangeInteractions();
437	+	longRangeInteractions();
438	+	postCalculation();
439	+	}
440	+
441		void ForceManager::preCalculation() {
442		SimInfo::MoleculeIterator mi;
443		Molecule* mol;
#	Line 78 | Line 445 | namespace oopse {
445		Atom* atom;
446		Molecule::RigidBodyIterator rbIter;
447		RigidBody* rb;
448	+	Molecule::CutoffGroupIterator ci;
449	+	CutoffGroup* cg;
450
451		// forces are zeroed here, before any are accumulated.
452	<	// NOTE: do not rezero the forces in Fortran.
453	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
454	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
452	>
453	>	for (mol = info_->beginMolecule(mi); mol != NULL;
454	>	mol = info_->nextMolecule(mi)) {
455	>	for(atom = mol->beginAtom(ai); atom != NULL;
456	>	atom = mol->nextAtom(ai)) {
457		atom->zeroForcesAndTorques();
458		}
459	<
459	>
460		//change the positions of atoms which belong to the rigidbodies
461	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
461	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
462	>	rb = mol->nextRigidBody(rbIter)) {
463		rb->zeroForcesAndTorques();
464		}
465	+
466	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
467	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
468	+	cg = mol->nextCutoffGroup(ci)) {
469	+	//calculate the center of mass of cutoff group
470	+	cg->updateCOM();
471	+	}
472	+	}
473		}
474
475	+	// Zero out the stress tensor
476	+	stressTensor *= 0.0;
477	+	// Zero out the heatFlux
478	+	fDecomp_->setHeatFlux( V3Zero );
479		}
480	<
481	<	void ForceManager::calcShortRangeInteraction() {
480	>
481	>	void ForceManager::shortRangeInteractions() {
482		Molecule* mol;
483		RigidBody* rb;
484		Bond* bond;
485		Bend* bend;
486		Torsion* torsion;
487	+	Inversion* inversion;
488		SimInfo::MoleculeIterator mi;
489		Molecule::RigidBodyIterator rbIter;
490		Molecule::BondIterator bondIter;;
491		Molecule::BendIterator  bendIter;
492		Molecule::TorsionIterator  torsionIter;
493	+	Molecule::InversionIterator  inversionIter;
494	+	RealType bondPotential = 0.0;
495	+	RealType bendPotential = 0.0;
496	+	RealType torsionPotential = 0.0;
497	+	RealType inversionPotential = 0.0;
498
499		//calculate short range interactions
500	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
500	>	for (mol = info_->beginMolecule(mi); mol != NULL;
501	>	mol = info_->nextMolecule(mi)) {
502
503		//change the positions of atoms which belong to the rigidbodies
504	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
505	<	rb->updateAtoms();
504	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
505	>	rb = mol->nextRigidBody(rbIter)) {
506	>	rb->updateAtoms();
507		}
508
509	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
510	<	bond->calcForce();
509	>	for (bond = mol->beginBond(bondIter); bond != NULL;
510	>	bond = mol->nextBond(bondIter)) {
511	>	bond->calcForce(doParticlePot_);
512	>	bondPotential += bond->getPotential();
513		}
514
515	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
516	<	bend->calcForce();
515	>	for (bend = mol->beginBend(bendIter); bend != NULL;
516	>	bend = mol->nextBend(bendIter)) {
517	>
518	>	RealType angle;
519	>	bend->calcForce(angle, doParticlePot_);
520	>	RealType currBendPot = bend->getPotential();
521	>
522	>	bendPotential += bend->getPotential();
523	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
524	>	if (i == bendDataSets.end()) {
525	>	BendDataSet dataSet;
526	>	dataSet.prev.angle = dataSet.curr.angle = angle;
527	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
528	>	dataSet.deltaV = 0.0;
529	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
530	>	dataSet));
531	>	}else {
532	>	i->second.prev.angle = i->second.curr.angle;
533	>	i->second.prev.potential = i->second.curr.potential;
534	>	i->second.curr.angle = angle;
535	>	i->second.curr.potential = currBendPot;
536	>	i->second.deltaV =  fabs(i->second.curr.potential -
537	>	i->second.prev.potential);
538	>	}
539		}
540	<
541	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
542	<	torsion->calcForce();
543	<	}
544	<
540	>
541	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
542	>	torsion = mol->nextTorsion(torsionIter)) {
543	>	RealType angle;
544	>	torsion->calcForce(angle, doParticlePot_);
545	>	RealType currTorsionPot = torsion->getPotential();
546	>	torsionPotential += torsion->getPotential();
547	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
548	>	if (i == torsionDataSets.end()) {
549	>	TorsionDataSet dataSet;
550	>	dataSet.prev.angle = dataSet.curr.angle = angle;
551	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
552	>	dataSet.deltaV = 0.0;
553	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
554	>	}else {
555	>	i->second.prev.angle = i->second.curr.angle;
556	>	i->second.prev.potential = i->second.curr.potential;
557	>	i->second.curr.angle = angle;
558	>	i->second.curr.potential = currTorsionPot;
559	>	i->second.deltaV =  fabs(i->second.curr.potential -
560	>	i->second.prev.potential);
561	>	}
562	>	}
563	>
564	>	for (inversion = mol->beginInversion(inversionIter);
565	>	inversion != NULL;
566	>	inversion = mol->nextInversion(inversionIter)) {
567	>	RealType angle;
568	>	inversion->calcForce(angle, doParticlePot_);
569	>	RealType currInversionPot = inversion->getPotential();
570	>	inversionPotential += inversion->getPotential();
571	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
572	>	if (i == inversionDataSets.end()) {
573	>	InversionDataSet dataSet;
574	>	dataSet.prev.angle = dataSet.curr.angle = angle;
575	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
576	>	dataSet.deltaV = 0.0;
577	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
578	>	}else {
579	>	i->second.prev.angle = i->second.curr.angle;
580	>	i->second.prev.potential = i->second.curr.potential;
581	>	i->second.curr.angle = angle;
582	>	i->second.curr.potential = currInversionPot;
583	>	i->second.deltaV =  fabs(i->second.curr.potential -
584	>	i->second.prev.potential);
585	>	}
586	>	}
587		}
588
589	<	double  shortRangePotential = 0.0;
590	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
133	<	shortRangePotential += mol->getPotential();
134	<	}
135	<
589	>	RealType  shortRangePotential = bondPotential + bendPotential +
590	>	torsionPotential +  inversionPotential;
591		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
592		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
593	+	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
594	+	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
595	+	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
596	+	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
597		}
598	+
599	+	void ForceManager::longRangeInteractions() {
600
140	–	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
141	–	Snapshot* curSnapshot;
142	–	DataStorage* config;
143	–	double* frc;
144	–	double* pos;
145	–	double* trq;
146	–	double* A;
147	–	double* electroFrame;
148	–	double* rc;
149	–
150	–	//get current snapshot from SimInfo
151	–	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
601
602	<	//get array pointers
603	<	config = &(curSnapshot->atomData);
604	<	frc = config->getArrayPointer(DataStorage::dslForce);
156	<	pos = config->getArrayPointer(DataStorage::dslPosition);
157	<	trq = config->getArrayPointer(DataStorage::dslTorque);
158	<	A   = config->getArrayPointer(DataStorage::dslAmat);
159	<	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
602	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
603	>	DataStorage* config = &(curSnapshot->atomData);
604	>	DataStorage* cgConfig = &(curSnapshot->cgData);
605
606		//calculate the center of mass of cutoff group
607	+
608		SimInfo::MoleculeIterator mi;
609		Molecule* mol;
610		Molecule::CutoffGroupIterator ci;
611		CutoffGroup* cg;
166	–	Vector3d com;
167	–	std::vector<Vector3d> rcGroup;
612
613	<	if(info_->getNCutoffGroups() > 0){
614	<
615	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
616	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
617	<	cg->getCOM(com);
618	<	rcGroup.push_back(com);
613	>	if(info_->getNCutoffGroups() > 0){
614	>	for (mol = info_->beginMolecule(mi); mol != NULL;
615	>	mol = info_->nextMolecule(mi)) {
616	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
617	>	cg = mol->nextCutoffGroup(ci)) {
618	>	cg->updateCOM();
619		}
620	<	}// end for (mol)
177	<
178	<	rc = rcGroup[0].getArrayPointer();
620	>	}
621		} else {
622	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
623	<	rc = pos;
622	>	// center of mass of the group is the same as position of the atom
623	>	// if cutoff group does not exist
624	>	cgConfig->position = config->position;
625	>	cgConfig->velocity = config->velocity;
626		}
627	<
628	<	//initialize data before passing to fortran
629	<	double longRangePotential[LR_POT_TYPES];
186	<	double lrPot = 0.0;
627	>
628	>	fDecomp_->zeroWorkArrays();
629	>	fDecomp_->distributeData();
630
631	<	Mat3x3d tau;
632	<	short int passedCalcPot = needPotential;
633	<	short int passedCalcStress = needStress;
634	<	int isError = 0;
631	>	int cg1, cg2, atom1, atom2, topoDist;
632	>	Vector3d d_grp, dag, d, gvel2, vel2;
633	>	RealType rgrpsq, rgrp, r2, r;
634	>	RealType electroMult, vdwMult;
635	>	RealType vij;
636	>	Vector3d fij, fg, f1;
637	>	tuple3<RealType, RealType, RealType> cuts;
638	>	RealType rCutSq;
639	>	bool in_switching_region;
640	>	RealType sw, dswdr, swderiv;
641	>	vector<int> atomListColumn, atomListRow, atomListLocal;
642	>	InteractionData idat;
643	>	SelfData sdat;
644	>	RealType mf;
645	>	RealType lrPot;
646	>	RealType vpair;
647	>	RealType dVdFQ1(0.0);
648	>	RealType dVdFQ2(0.0);
649	>	potVec longRangePotential(0.0);
650	>	potVec workPot(0.0);
651	>	vector<int>::iterator ia, jb;
652
653	<	for (int i=0; i<LR_POT_TYPES;i++){
654	<	longRangePotential[i]=0.0; //Initialize array
653	>	int loopStart, loopEnd;
654	>
655	>	idat.vdwMult = &vdwMult;
656	>	idat.electroMult = &electroMult;
657	>	idat.pot = &workPot;
658	>	sdat.pot = fDecomp_->getEmbeddingPotential();
659	>	idat.vpair = &vpair;
660	>	idat.dVdFQ1 = &dVdFQ1;
661	>	idat.dVdFQ2 = &dVdFQ2;
662	>	idat.f1 = &f1;
663	>	idat.sw = &sw;
664	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
665	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
666	>	idat.doParticlePot = doParticlePot_;
667	>	sdat.doParticlePot = doParticlePot_;
668	>
669	>	loopEnd = PAIR_LOOP;
670	>	if (info_->requiresPrepair() ) {
671	>	loopStart = PREPAIR_LOOP;
672	>	} else {
673	>	loopStart = PAIR_LOOP;
674		}
675	+
676	+	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
677	+
678	+	if (iLoop == loopStart) {
679	+	bool update_nlist = fDecomp_->checkNeighborList();
680	+	if (update_nlist)
681	+	neighborList = fDecomp_->buildNeighborList();
682	+	}
683
684	+	for (vector<pair<int, int> >::iterator it = neighborList.begin();
685	+	it != neighborList.end(); ++it) {
686	+
687	+	cg1 = (*it).first;
688	+	cg2 = (*it).second;
689	+
690	+	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
691
692	+	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
693
694	<	doForceLoop( pos,
695	<	rc,
696	<	A,
202	<	electroFrame,
203	<	frc,
204	<	trq,
205	<	tau.getArrayPointer(),
206	<	longRangePotential,
207	<	&passedCalcPot,
208	<	&passedCalcStress,
209	<	&isError );
694	>	curSnapshot->wrapVector(d_grp);
695	>	rgrpsq = d_grp.lengthSquare();
696	>	rCutSq = cuts.second;
697
698	<	if( isError ){
699	<	sprintf( painCave.errMsg,
700	<	"Error returned from the fortran force calculation.\n" );
701	<	painCave.isFatal = 1;
702	<	simError();
698	>	if (rgrpsq < rCutSq) {
699	>	idat.rcut = &cuts.first;
700	>	if (iLoop == PAIR_LOOP) {
701	>	vij = 0.0;
702	>	fij = V3Zero;
703	>	}
704	>
705	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
706	>	rgrp);
707	>
708	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
709	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
710	>
711	>	if (doHeatFlux_)
712	>	gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
713	>
714	>	for (ia = atomListRow.begin();
715	>	ia != atomListRow.end(); ++ia) {
716	>	atom1 = (*ia);
717	>
718	>	for (jb = atomListColumn.begin();
719	>	jb != atomListColumn.end(); ++jb) {
720	>	atom2 = (*jb);
721	>
722	>	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
723	>	vpair = 0.0;
724	>	workPot = 0.0;
725	>	f1 = V3Zero;
726	>	dVdFQ1 = 0.0;
727	>	dVdFQ2 = 0.0;
728	>
729	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
730	>
731	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
732	>	vdwMult = vdwScale_[topoDist];
733	>	electroMult = electrostaticScale_[topoDist];
734	>
735	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
736	>	idat.d = &d_grp;
737	>	idat.r2 = &rgrpsq;
738	>	if (doHeatFlux_)
739	>	vel2 = gvel2;
740	>	} else {
741	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
742	>	curSnapshot->wrapVector( d );
743	>	r2 = d.lengthSquare();
744	>	idat.d = &d;
745	>	idat.r2 = &r2;
746	>	if (doHeatFlux_)
747	>	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
748	>	}
749	>
750	>	r = sqrt( *(idat.r2) );
751	>	idat.rij = &r;
752	>
753	>	if (iLoop == PREPAIR_LOOP) {
754	>	interactionMan_->doPrePair(idat);
755	>	} else {
756	>	interactionMan_->doPair(idat);
757	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
758	>	vij += vpair;
759	>	fij += f1;
760	>	stressTensor -= outProduct( *(idat.d), f1);
761	>	if (doHeatFlux_)
762	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
763	>	}
764	>	}
765	>	}
766	>	}
767	>
768	>	if (iLoop == PAIR_LOOP) {
769	>	if (in_switching_region) {
770	>	swderiv = vij * dswdr / rgrp;
771	>	fg = swderiv * d_grp;
772	>	fij += fg;
773	>
774	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
775	>	stressTensor -= outProduct( *(idat.d), fg);
776	>	if (doHeatFlux_)
777	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
778	>
779	>	}
780	>
781	>	for (ia = atomListRow.begin();
782	>	ia != atomListRow.end(); ++ia) {
783	>	atom1 = (*ia);
784	>	mf = fDecomp_->getMassFactorRow(atom1);
785	>	// fg is the force on atom ia due to cutoff group's
786	>	// presence in switching region
787	>	fg = swderiv * d_grp * mf;
788	>	fDecomp_->addForceToAtomRow(atom1, fg);
789	>	if (atomListRow.size() > 1) {
790	>	if (info_->usesAtomicVirial()) {
791	>	// find the distance between the atom
792	>	// and the center of the cutoff group:
793	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
794	>	stressTensor -= outProduct(dag, fg);
795	>	if (doHeatFlux_)
796	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
797	>	}
798	>	}
799	>	}
800	>	for (jb = atomListColumn.begin();
801	>	jb != atomListColumn.end(); ++jb) {
802	>	atom2 = (*jb);
803	>	mf = fDecomp_->getMassFactorColumn(atom2);
804	>	// fg is the force on atom jb due to cutoff group's
805	>	// presence in switching region
806	>	fg = -swderiv * d_grp * mf;
807	>	fDecomp_->addForceToAtomColumn(atom2, fg);
808	>
809	>	if (atomListColumn.size() > 1) {
810	>	if (info_->usesAtomicVirial()) {
811	>	// find the distance between the atom
812	>	// and the center of the cutoff group:
813	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
814	>	stressTensor -= outProduct(dag, fg);
815	>	if (doHeatFlux_)
816	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
817	>	}
818	>	}
819	>	}
820	>	}
821	>	//if (!info_->usesAtomicVirial()) {
822	>	//  stressTensor -= outProduct(d_grp, fij);
823	>	//  if (doHeatFlux_)
824	>	//     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
825	>	//}
826	>	}
827	>	}
828	>	}
829	>
830	>	if (iLoop == PREPAIR_LOOP) {
831	>	if (info_->requiresPrepair()) {
832	>
833	>	fDecomp_->collectIntermediateData();
834	>
835	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
836	>	fDecomp_->fillSelfData(sdat, atom1);
837	>	interactionMan_->doPreForce(sdat);
838	>	}
839	>
840	>	fDecomp_->distributeIntermediateData();
841	>
842	>	}
843	>	}
844		}
845	<	for (int i=0; i<LR_POT_TYPES;i++){
846	<	lrPot += longRangePotential[i]; //Quick hack
845	>
846	>	fDecomp_->collectData();
847	>
848	>	if (info_->requiresSelfCorrection()) {
849	>
850	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
851	>	fDecomp_->fillSelfData(sdat, atom1);
852	>	interactionMan_->doSelfCorrection(sdat);
853	>	}
854	>
855		}
856
857	<	//store the tau and long range potential
857	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
858	>	*(fDecomp_->getPairwisePotential());
859	>
860	>	lrPot = longRangePotential.sum();
861	>
862	>	//store the stressTensor and long range potential
863		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
864	<	//  curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
865	<	curSnapshot->statData.setTau(tau);
864	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
865	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
866		}
867
868	<
868	>
869		void ForceManager::postCalculation() {
870		SimInfo::MoleculeIterator mi;
871		Molecule* mol;
872		Molecule::RigidBodyIterator rbIter;
873		RigidBody* rb;
874	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
875
876		// collect the atomic forces onto rigid bodies
877	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
878	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
879	<	rb->calcForcesAndTorques();
877	>
878	>	for (mol = info_->beginMolecule(mi); mol != NULL;
879	>	mol = info_->nextMolecule(mi)) {
880	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
881	>	rb = mol->nextRigidBody(rbIter)) {
882	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
883	>	stressTensor += rbTau;
884		}
885		}
886	+
887	+	#ifdef IS_MPI
888
889	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
890	+	MPI::REALTYPE, MPI::SUM);
891	+	#endif
892	+	curSnapshot->setStressTensor(stressTensor);
893	+
894		}
895
896	<	} //end namespace oopse
896	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 664 by chuckv, Wed Oct 12 21:57:16 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1733 by jmichalk, Tue Jun 5 17:48:40 2012 UTC

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