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

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trunk/src/brains/ForceManager.cpp (file contents), Revision 681 by tim, Mon Oct 17 23:13:44 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1618 by gezelter, Mon Sep 12 17:09:26 2011 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]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 47 | Line 47
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 __C
54	<	#include "UseTheForce/DarkSide/fInteractionMap.h"
53	>	#define __OPENMD_C
54		#include "utils/simError.h"
55	<	namespace oopse {
55	>	#include "primitives/Bond.hpp"
56	>	#include "primitives/Bend.hpp"
57	>	#include "primitives/Torsion.hpp"
58	>	#include "primitives/Inversion.hpp"
59	>	#include "nonbonded/NonBondedInteraction.hpp"
60	>	#include "parallel/ForceMatrixDecomposition.hpp"
61
62	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
62	>	#include <cstdio>
63	>	#include <iostream>
64	>	#include <iomanip>
65
66	<	if (!info_->isFortranInitialized()) {
67	<	info_->update();
68	<	}
66	>	using namespace std;
67	>	namespace OpenMD {
68	>
69	>	ForceManager::ForceManager(SimInfo * info) : info_(info) {
70	>	forceField_ = info_->getForceField();
71	>	interactionMan_ = new InteractionManager();
72	>	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
73	>	}
74
75	<	preCalculation();
75	>	/**
76	>	* setupCutoffs
77	>	*
78	>	* Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
79	>	* and cutoffPolicy
80	>	*
81	>	* cutoffRadius : realType
82	>	*  If the cutoffRadius was explicitly set, use that value.
83	>	*  If the cutoffRadius was not explicitly set:
84	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
85	>	*      No electrostatic atoms?  Poll the atom types present in the
86	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
87	>	*      Use the maximum suggested value that was found.
88	>	*
89	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
90	>	*                        or SHIFTED_POTENTIAL)
91	>	*      If cutoffMethod was explicitly set, use that choice.
92	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
93	>	*
94	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
95	>	*      If cutoffPolicy was explicitly set, use that choice.
96	>	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
97	>	*
98	>	* switchingRadius : realType
99	>	*  If the cutoffMethod was set to SWITCHED:
100	>	*      If the switchingRadius was explicitly set, use that value
101	>	*          (but do a sanity check first).
102	>	*      If the switchingRadius was not explicitly set: use 0.85 *
103	>	*      cutoffRadius_
104	>	*  If the cutoffMethod was not set to SWITCHED:
105	>	*      Set switchingRadius equal to cutoffRadius for safety.
106	>	*/
107	>	void ForceManager::setupCutoffs() {
108
109	<	calcShortRangeInteraction();
109	>	Globals* simParams_ = info_->getSimParams();
110	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
111	>	int mdFileVersion;
112	>
113	>	if (simParams_->haveMDfileVersion())
114	>	mdFileVersion = simParams_->getMDfileVersion();
115	>	else
116	>	mdFileVersion = 0;
117	>
118	>	if (simParams_->haveCutoffRadius()) {
119	>	rCut_ = simParams_->getCutoffRadius();
120	>	} else {
121	>	if (info_->usesElectrostaticAtoms()) {
122	>	sprintf(painCave.errMsg,
123	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
124	>	"\tOpenMD will use a default value of 12.0 angstroms"
125	>	"\tfor the cutoffRadius.\n");
126	>	painCave.isFatal = 0;
127	>	painCave.severity = OPENMD_INFO;
128	>	simError();
129	>	rCut_ = 12.0;
130	>	} else {
131	>	RealType thisCut;
132	>	set<AtomType*>::iterator i;
133	>	set<AtomType*> atomTypes;
134	>	atomTypes = info_->getSimulatedAtomTypes();
135	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
136	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
137	>	rCut_ = max(thisCut, rCut_);
138	>	}
139	>	sprintf(painCave.errMsg,
140	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
141	>	"\tOpenMD will use %lf angstroms.\n",
142	>	rCut_);
143	>	painCave.isFatal = 0;
144	>	painCave.severity = OPENMD_INFO;
145	>	simError();
146	>	}
147	>	}
148
149	<	calcLongRangeInteraction(needPotential, needStress);
149	>	fDecomp_->setUserCutoff(rCut_);
150	>	interactionMan_->setCutoffRadius(rCut_);
151
152	<	postCalculation();
152	>	map<string, CutoffMethod> stringToCutoffMethod;
153	>	stringToCutoffMethod["HARD"] = HARD;
154	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
155	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
156	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
157	>
158	>	if (simParams_->haveCutoffMethod()) {
159	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
160	>	map<string, CutoffMethod>::iterator i;
161	>	i = stringToCutoffMethod.find(cutMeth);
162	>	if (i == stringToCutoffMethod.end()) {
163	>	sprintf(painCave.errMsg,
164	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
165	>	"\tShould be one of: "
166	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
167	>	cutMeth.c_str());
168	>	painCave.isFatal = 1;
169	>	painCave.severity = OPENMD_ERROR;
170	>	simError();
171	>	} else {
172	>	cutoffMethod_ = i->second;
173	>	}
174	>	} else {
175	>	if (mdFileVersion > 1) {
176	>	sprintf(painCave.errMsg,
177	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
178	>	"\tOpenMD will use SHIFTED_FORCE.\n");
179	>	painCave.isFatal = 0;
180	>	painCave.severity = OPENMD_INFO;
181	>	simError();
182	>	cutoffMethod_ = SHIFTED_FORCE;
183	>	} else {
184	>	// handle the case where the old file version was in play
185	>	// (there should be no cutoffMethod, so we have to deduce it
186	>	// from other data).
187	>
188	>	sprintf(painCave.errMsg,
189	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
190	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
191	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
192	>	"\tbehavior of the older (version 1) code.  To remove this\n"
193	>	"\twarning, add an explicit cutoffMethod and change the top\n"
194	>	"\tof the file so that it begins with <OpenMD version=2>\n");
195	>	painCave.isFatal = 0;
196	>	painCave.severity = OPENMD_WARNING;
197	>	simError();
198	>
199	>	// The old file version tethered the shifting behavior to the
200	>	// electrostaticSummationMethod keyword.
201	>
202	>	if (simParams_->haveElectrostaticSummationMethod()) {
203	>	std::string myMethod = simParams_->getElectrostaticSummationMethod();
204	>	toUpper(myMethod);
205	>
206	>	if (myMethod == "SHIFTED_POTENTIAL") {
207	>	cutoffMethod_ = SHIFTED_POTENTIAL;
208	>	} else if (myMethod == "SHIFTED_FORCE") {
209	>	cutoffMethod_ = SHIFTED_FORCE;
210	>	}
211	>
212	>	if (simParams_->haveSwitchingRadius())
213	>	rSwitch_ = simParams_->getSwitchingRadius();
214	>
215	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
216	>	if (simParams_->haveSwitchingRadius()){
217	>	sprintf(painCave.errMsg,
218	>	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
219	>	"\tA value was set for the switchingRadius\n"
220	>	"\teven though the electrostaticSummationMethod was\n"
221	>	"\tset to %s\n", myMethod.c_str());
222	>	painCave.severity = OPENMD_WARNING;
223	>	painCave.isFatal = 1;
224	>	simError();
225	>	}
226	>	}
227	>	if (abs(rCut_ - rSwitch_) < 0.0001) {
228	>	if (cutoffMethod_ == SHIFTED_FORCE) {
229	>	sprintf(painCave.errMsg,
230	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
231	>	"\tcutoffRadius and switchingRadius are set to the\n"
232	>	"\tsame value.  OpenMD will use shifted force\n"
233	>	"\tpotentials instead of switching functions.\n");
234	>	painCave.isFatal = 0;
235	>	painCave.severity = OPENMD_WARNING;
236	>	simError();
237	>	} else {
238	>	cutoffMethod_ = SHIFTED_POTENTIAL;
239	>	sprintf(painCave.errMsg,
240	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
241	>	"\tcutoffRadius and switchingRadius are set to the\n"
242	>	"\tsame value.  OpenMD will use shifted potentials\n"
243	>	"\tinstead of switching functions.\n");
244	>	painCave.isFatal = 0;
245	>	painCave.severity = OPENMD_WARNING;
246	>	simError();
247	>	}
248	>	}
249	>	}
250	>	}
251	>	}
252	>
253	>	map<string, CutoffPolicy> stringToCutoffPolicy;
254	>	stringToCutoffPolicy["MIX"] = MIX;
255	>	stringToCutoffPolicy["MAX"] = MAX;
256	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
257	>
258	>	std::string cutPolicy;
259	>	if (forceFieldOptions_.haveCutoffPolicy()){
260	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
261	>	}else if (simParams_->haveCutoffPolicy()) {
262	>	cutPolicy = simParams_->getCutoffPolicy();
263	>	}
264	>
265	>	if (!cutPolicy.empty()){
266	>	toUpper(cutPolicy);
267	>	map<string, CutoffPolicy>::iterator i;
268	>	i = stringToCutoffPolicy.find(cutPolicy);
269	>
270	>	if (i == stringToCutoffPolicy.end()) {
271	>	sprintf(painCave.errMsg,
272	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
273	>	"\tShould be one of: "
274	>	"MIX, MAX, or TRADITIONAL\n",
275	>	cutPolicy.c_str());
276	>	painCave.isFatal = 1;
277	>	painCave.severity = OPENMD_ERROR;
278	>	simError();
279	>	} else {
280	>	cutoffPolicy_ = i->second;
281	>	}
282	>	} else {
283	>	sprintf(painCave.errMsg,
284	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
285	>	"\tOpenMD will use TRADITIONAL.\n");
286	>	painCave.isFatal = 0;
287	>	painCave.severity = OPENMD_INFO;
288	>	simError();
289	>	cutoffPolicy_ = TRADITIONAL;
290	>	}
291	>
292	>	fDecomp_->setCutoffPolicy(cutoffPolicy_);
293
294	+	// create the switching function object:
295	+
296	+	switcher_ = new SwitchingFunction();
297	+
298	+	if (cutoffMethod_ == SWITCHED) {
299	+	if (simParams_->haveSwitchingRadius()) {
300	+	rSwitch_ = simParams_->getSwitchingRadius();
301	+	if (rSwitch_ > rCut_) {
302	+	sprintf(painCave.errMsg,
303	+	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
304	+	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
305	+	painCave.isFatal = 1;
306	+	painCave.severity = OPENMD_ERROR;
307	+	simError();
308	+	}
309	+	} else {
310	+	rSwitch_ = 0.85 * rCut_;
311	+	sprintf(painCave.errMsg,
312	+	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
313	+	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
314	+	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
315	+	painCave.isFatal = 0;
316	+	painCave.severity = OPENMD_WARNING;
317	+	simError();
318	+	}
319	+	} else {
320	+	if (mdFileVersion > 1) {
321	+	// throw an error if we define a switching radius and don't need one.
322	+	// older file versions should not do this.
323	+	if (simParams_->haveSwitchingRadius()) {
324	+	map<string, CutoffMethod>::const_iterator it;
325	+	string theMeth;
326	+	for (it = stringToCutoffMethod.begin();
327	+	it != stringToCutoffMethod.end(); ++it) {
328	+	if (it->second == cutoffMethod_) {
329	+	theMeth = it->first;
330	+	break;
331	+	}
332	+	}
333	+	sprintf(painCave.errMsg,
334	+	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
335	+	"\tis not set to SWITCHED, so switchingRadius value\n"
336	+	"\twill be ignored for this simulation\n", theMeth.c_str());
337	+	painCave.isFatal = 0;
338	+	painCave.severity = OPENMD_WARNING;
339	+	simError();
340	+	}
341	+	}
342	+	rSwitch_ = rCut_;
343	+	}
344	+
345	+	// Default to cubic switching function.
346	+	sft_ = cubic;
347	+	if (simParams_->haveSwitchingFunctionType()) {
348	+	string funcType = simParams_->getSwitchingFunctionType();
349	+	toUpper(funcType);
350	+	if (funcType == "CUBIC") {
351	+	sft_ = cubic;
352	+	} else {
353	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
354	+	sft_ = fifth_order_poly;
355	+	} else {
356	+	// throw error
357	+	sprintf( painCave.errMsg,
358	+	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
359	+	"\tswitchingFunctionType must be one of: "
360	+	"\"cubic\" or \"fifth_order_polynomial\".",
361	+	funcType.c_str() );
362	+	painCave.isFatal = 1;
363	+	painCave.severity = OPENMD_ERROR;
364	+	simError();
365	+	}
366	+	}
367	+	}
368	+	switcher_->setSwitchType(sft_);
369	+	switcher_->setSwitch(rSwitch_, rCut_);
370	+	interactionMan_->setSwitchingRadius(rSwitch_);
371		}
372
373	+
374	+
375	+
376	+	void ForceManager::initialize() {
377	+
378	+	if (!info_->isTopologyDone()) {
379	+
380	+	info_->update();
381	+	interactionMan_->setSimInfo(info_);
382	+	interactionMan_->initialize();
383	+
384	+	// We want to delay the cutoffs until after the interaction
385	+	// manager has set up the atom-atom interactions so that we can
386	+	// query them for suggested cutoff values
387	+	setupCutoffs();
388	+
389	+	info_->prepareTopology();
390	+	}
391	+
392	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
393	+
394	+	// Force fields can set options on how to scale van der Waals and
395	+	// electrostatic interactions for atoms connected via bonds, bends
396	+	// and torsions in this case the topological distance between
397	+	// atoms is:
398	+	// 0 = topologically unconnected
399	+	// 1 = bonded together
400	+	// 2 = connected via a bend
401	+	// 3 = connected via a torsion
402	+
403	+	vdwScale_.reserve(4);
404	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
405	+
406	+	electrostaticScale_.reserve(4);
407	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
408	+
409	+	vdwScale_[0] = 1.0;
410	+	vdwScale_[1] = fopts.getvdw12scale();
411	+	vdwScale_[2] = fopts.getvdw13scale();
412	+	vdwScale_[3] = fopts.getvdw14scale();
413	+
414	+	electrostaticScale_[0] = 1.0;
415	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
416	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
417	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
418	+
419	+	fDecomp_->distributeInitialData();
420	+
421	+	initialized_ = true;
422	+
423	+	}
424	+
425	+	void ForceManager::calcForces() {
426	+
427	+	if (!initialized_) initialize();
428	+
429	+	preCalculation();
430	+	shortRangeInteractions();
431	+	longRangeInteractions();
432	+	postCalculation();
433	+	}
434	+
435		void ForceManager::preCalculation() {
436		SimInfo::MoleculeIterator mi;
437		Molecule* mol;
#	Line 78 | Line 439 | namespace oopse {
439		Atom* atom;
440		Molecule::RigidBodyIterator rbIter;
441		RigidBody* rb;
442	+	Molecule::CutoffGroupIterator ci;
443	+	CutoffGroup* cg;
444
445		// forces are zeroed here, before any are accumulated.
446	<	// NOTE: do not rezero the forces in Fortran.
447	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
448	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
446	>
447	>	for (mol = info_->beginMolecule(mi); mol != NULL;
448	>	mol = info_->nextMolecule(mi)) {
449	>	for(atom = mol->beginAtom(ai); atom != NULL;
450	>	atom = mol->nextAtom(ai)) {
451		atom->zeroForcesAndTorques();
452		}
453	<
453	>
454		//change the positions of atoms which belong to the rigidbodies
455	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
455	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
456	>	rb = mol->nextRigidBody(rbIter)) {
457		rb->zeroForcesAndTorques();
458		}
459	+
460	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
461	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
462	+	cg = mol->nextCutoffGroup(ci)) {
463	+	//calculate the center of mass of cutoff group
464	+	cg->updateCOM();
465	+	}
466	+	}
467		}
468
469	+	// Zero out the stress tensor
470	+	tau *= 0.0;
471	+
472		}
473	<
474	<	void ForceManager::calcShortRangeInteraction() {
473	>
474	>	void ForceManager::shortRangeInteractions() {
475		Molecule* mol;
476		RigidBody* rb;
477		Bond* bond;
478		Bend* bend;
479		Torsion* torsion;
480	+	Inversion* inversion;
481		SimInfo::MoleculeIterator mi;
482		Molecule::RigidBodyIterator rbIter;
483		Molecule::BondIterator bondIter;;
484		Molecule::BendIterator  bendIter;
485		Molecule::TorsionIterator  torsionIter;
486	+	Molecule::InversionIterator  inversionIter;
487	+	RealType bondPotential = 0.0;
488	+	RealType bendPotential = 0.0;
489	+	RealType torsionPotential = 0.0;
490	+	RealType inversionPotential = 0.0;
491
492		//calculate short range interactions
493	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
493	>	for (mol = info_->beginMolecule(mi); mol != NULL;
494	>	mol = info_->nextMolecule(mi)) {
495
496		//change the positions of atoms which belong to the rigidbodies
497	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
498	<	rb->updateAtoms();
497	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
498	>	rb = mol->nextRigidBody(rbIter)) {
499	>	rb->updateAtoms();
500		}
501
502	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
503	<	bond->calcForce();
502	>	for (bond = mol->beginBond(bondIter); bond != NULL;
503	>	bond = mol->nextBond(bondIter)) {
504	>	bond->calcForce();
505	>	bondPotential += bond->getPotential();
506		}
507
508	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
509	<	bend->calcForce();
508	>	for (bend = mol->beginBend(bendIter); bend != NULL;
509	>	bend = mol->nextBend(bendIter)) {
510	>
511	>	RealType angle;
512	>	bend->calcForce(angle);
513	>	RealType currBendPot = bend->getPotential();
514	>
515	>	bendPotential += bend->getPotential();
516	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
517	>	if (i == bendDataSets.end()) {
518	>	BendDataSet dataSet;
519	>	dataSet.prev.angle = dataSet.curr.angle = angle;
520	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
521	>	dataSet.deltaV = 0.0;
522	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
523	>	dataSet));
524	>	}else {
525	>	i->second.prev.angle = i->second.curr.angle;
526	>	i->second.prev.potential = i->second.curr.potential;
527	>	i->second.curr.angle = angle;
528	>	i->second.curr.potential = currBendPot;
529	>	i->second.deltaV =  fabs(i->second.curr.potential -
530	>	i->second.prev.potential);
531	>	}
532		}
533	<
534	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
535	<	torsion->calcForce();
536	<	}
537	<
533	>
534	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
535	>	torsion = mol->nextTorsion(torsionIter)) {
536	>	RealType angle;
537	>	torsion->calcForce(angle);
538	>	RealType currTorsionPot = torsion->getPotential();
539	>	torsionPotential += torsion->getPotential();
540	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
541	>	if (i == torsionDataSets.end()) {
542	>	TorsionDataSet dataSet;
543	>	dataSet.prev.angle = dataSet.curr.angle = angle;
544	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
545	>	dataSet.deltaV = 0.0;
546	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
547	>	}else {
548	>	i->second.prev.angle = i->second.curr.angle;
549	>	i->second.prev.potential = i->second.curr.potential;
550	>	i->second.curr.angle = angle;
551	>	i->second.curr.potential = currTorsionPot;
552	>	i->second.deltaV =  fabs(i->second.curr.potential -
553	>	i->second.prev.potential);
554	>	}
555	>	}
556	>
557	>	for (inversion = mol->beginInversion(inversionIter);
558	>	inversion != NULL;
559	>	inversion = mol->nextInversion(inversionIter)) {
560	>	RealType angle;
561	>	inversion->calcForce(angle);
562	>	RealType currInversionPot = inversion->getPotential();
563	>	inversionPotential += inversion->getPotential();
564	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
565	>	if (i == inversionDataSets.end()) {
566	>	InversionDataSet dataSet;
567	>	dataSet.prev.angle = dataSet.curr.angle = angle;
568	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
569	>	dataSet.deltaV = 0.0;
570	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
571	>	}else {
572	>	i->second.prev.angle = i->second.curr.angle;
573	>	i->second.prev.potential = i->second.curr.potential;
574	>	i->second.curr.angle = angle;
575	>	i->second.curr.potential = currInversionPot;
576	>	i->second.deltaV =  fabs(i->second.curr.potential -
577	>	i->second.prev.potential);
578	>	}
579	>	}
580		}
581
582	<
583	<	double bondPotential = 0.0;
133	<	double bendPotential = 0.0;
134	<	double torsionPotential = 0.0;
135	<
136	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
137	<
138	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
139	<	bondPotential += bond->getPotential();
140	<	}
141	<
142	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
143	<	bendPotential += bend->getPotential();
144	<	}
145	<
146	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
147	<	torsionPotential += torsion->getPotential();
148	<	}
149	<
150	<	}
151	<
152	<	double  shortRangePotential = bondPotential + bendPotential + torsionPotential;
582	>	RealType  shortRangePotential = bondPotential + bendPotential +
583	>	torsionPotential +  inversionPotential;
584		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
585		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
586		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
587		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
588		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
589	<
589	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
590		}
591	+
592	+	void ForceManager::longRangeInteractions() {
593
594	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
595	<	Snapshot* curSnapshot;
596	<	DataStorage* config;
164	<	double* frc;
165	<	double* pos;
166	<	double* trq;
167	<	double* A;
168	<	double* electroFrame;
169	<	double* rc;
170	<
171	<	//get current snapshot from SimInfo
172	<	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
594	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
595	>	DataStorage* config = &(curSnapshot->atomData);
596	>	DataStorage* cgConfig = &(curSnapshot->cgData);
597
174	–	//get array pointers
175	–	config = &(curSnapshot->atomData);
176	–	frc = config->getArrayPointer(DataStorage::dslForce);
177	–	pos = config->getArrayPointer(DataStorage::dslPosition);
178	–	trq = config->getArrayPointer(DataStorage::dslTorque);
179	–	A   = config->getArrayPointer(DataStorage::dslAmat);
180	–	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
181	–
598		//calculate the center of mass of cutoff group
599	+
600		SimInfo::MoleculeIterator mi;
601		Molecule* mol;
602		Molecule::CutoffGroupIterator ci;
603		CutoffGroup* cg;
187	–	Vector3d com;
188	–	std::vector<Vector3d> rcGroup;
604
605	<	if(info_->getNCutoffGroups() > 0){
606	<
607	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
608	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
609	<	cg->getCOM(com);
610	<	rcGroup.push_back(com);
605	>	if(info_->getNCutoffGroups() > 0){
606	>	for (mol = info_->beginMolecule(mi); mol != NULL;
607	>	mol = info_->nextMolecule(mi)) {
608	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
609	>	cg = mol->nextCutoffGroup(ci)) {
610	>	cg->updateCOM();
611		}
612	<	}// end for (mol)
198	<
199	<	rc = rcGroup[0].getArrayPointer();
612	>	}
613		} else {
614	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
615	<	rc = pos;
614	>	// center of mass of the group is the same as position of the atom
615	>	// if cutoff group does not exist
616	>	cgConfig->position = config->position;
617		}
618	<
619	<	//initialize data before passing to fortran
620	<	double longRangePotential[LR_POT_TYPES];
207	<	double lrPot = 0.0;
618	>
619	>	fDecomp_->zeroWorkArrays();
620	>	fDecomp_->distributeData();
621
622	<	Mat3x3d tau;
623	<	short int passedCalcPot = needPotential;
624	<	short int passedCalcStress = needStress;
625	<	int isError = 0;
622	>	int cg1, cg2, atom1, atom2, topoDist;
623	>	Vector3d d_grp, dag, d;
624	>	RealType rgrpsq, rgrp, r2, r;
625	>	RealType electroMult, vdwMult;
626	>	RealType vij;
627	>	Vector3d fij, fg, f1;
628	>	tuple3<RealType, RealType, RealType> cuts;
629	>	RealType rCutSq;
630	>	bool in_switching_region;
631	>	RealType sw, dswdr, swderiv;
632	>	vector<int> atomListColumn, atomListRow, atomListLocal;
633	>	InteractionData idat;
634	>	SelfData sdat;
635	>	RealType mf;
636	>	RealType lrPot;
637	>	RealType vpair;
638	>	potVec longRangePotential(0.0);
639	>	potVec workPot(0.0);
640
641	<	for (int i=0; i<LR_POT_TYPES;i++){
642	<	longRangePotential[i]=0.0; //Initialize array
641	>	int loopStart, loopEnd;
642	>
643	>	idat.vdwMult = &vdwMult;
644	>	idat.electroMult = &electroMult;
645	>	idat.pot = &workPot;
646	>	sdat.pot = fDecomp_->getEmbeddingPotential();
647	>	idat.vpair = &vpair;
648	>	idat.f1 = &f1;
649	>	idat.sw = &sw;
650	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
651	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
652	>
653	>	loopEnd = PAIR_LOOP;
654	>	if (info_->requiresPrepair() ) {
655	>	loopStart = PREPAIR_LOOP;
656	>	} else {
657	>	loopStart = PAIR_LOOP;
658		}
659	+
660	+	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
661	+
662	+	if (iLoop == loopStart) {
663	+	bool update_nlist = fDecomp_->checkNeighborList();
664	+	if (update_nlist)
665	+	neighborList = fDecomp_->buildNeighborList();
666	+	}
667
668	+	for (vector<pair<int, int> >::iterator it = neighborList.begin();
669	+	it != neighborList.end(); ++it) {
670	+
671	+	cg1 = (*it).first;
672	+	cg2 = (*it).second;
673	+
674	+	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
675
676	+	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
677
678	<	doForceLoop( pos,
679	<	rc,
680	<	A,
223	<	electroFrame,
224	<	frc,
225	<	trq,
226	<	tau.getArrayPointer(),
227	<	longRangePotential,
228	<	&passedCalcPot,
229	<	&passedCalcStress,
230	<	&isError );
678	>	curSnapshot->wrapVector(d_grp);
679	>	rgrpsq = d_grp.lengthSquare();
680	>	rCutSq = cuts.second;
681
682	<	if( isError ){
683	<	sprintf( painCave.errMsg,
684	<	"Error returned from the fortran force calculation.\n" );
685	<	painCave.isFatal = 1;
686	<	simError();
682	>	if (rgrpsq < rCutSq) {
683	>	idat.rcut = &cuts.first;
684	>	if (iLoop == PAIR_LOOP) {
685	>	vij = 0.0;
686	>	fij = V3Zero;
687	>	}
688	>
689	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
690	>	rgrp);
691	>
692	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
693	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
694	>
695	>	for (vector<int>::iterator ia = atomListRow.begin();
696	>	ia != atomListRow.end(); ++ia) {
697	>	atom1 = (*ia);
698	>
699	>	for (vector<int>::iterator jb = atomListColumn.begin();
700	>	jb != atomListColumn.end(); ++jb) {
701	>	atom2 = (*jb);
702	>
703	>	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
704	>	vpair = 0.0;
705	>	workPot = 0.0;
706	>	f1 = V3Zero;
707	>
708	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
709	>
710	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
711	>	vdwMult = vdwScale_[topoDist];
712	>	electroMult = electrostaticScale_[topoDist];
713	>
714	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
715	>	idat.d = &d_grp;
716	>	idat.r2 = &rgrpsq;
717	>	} else {
718	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
719	>	curSnapshot->wrapVector( d );
720	>	r2 = d.lengthSquare();
721	>	idat.d = &d;
722	>	idat.r2 = &r2;
723	>	}
724	>
725	>	r = sqrt( *(idat.r2) );
726	>	idat.rij = &r;
727	>
728	>	if (iLoop == PREPAIR_LOOP) {
729	>	interactionMan_->doPrePair(idat);
730	>	} else {
731	>	interactionMan_->doPair(idat);
732	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
733	>	vij += vpair;
734	>	fij += f1;
735	>	tau -= outProduct( *(idat.d), f1);
736	>	}
737	>	}
738	>	}
739	>	}
740	>
741	>	if (iLoop == PAIR_LOOP) {
742	>	if (in_switching_region) {
743	>	swderiv = vij * dswdr / rgrp;
744	>	fg = swderiv * d_grp;
745	>	fij += fg;
746	>
747	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
748	>	tau -= outProduct( *(idat.d), fg);
749	>	}
750	>
751	>	for (vector<int>::iterator ia = atomListRow.begin();
752	>	ia != atomListRow.end(); ++ia) {
753	>	atom1 = (*ia);
754	>	mf = fDecomp_->getMassFactorRow(atom1);
755	>	// fg is the force on atom ia due to cutoff group's
756	>	// presence in switching region
757	>	fg = swderiv * d_grp * mf;
758	>	fDecomp_->addForceToAtomRow(atom1, fg);
759	>	if (atomListRow.size() > 1) {
760	>	if (info_->usesAtomicVirial()) {
761	>	// find the distance between the atom
762	>	// and the center of the cutoff group:
763	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
764	>	tau -= outProduct(dag, fg);
765	>	}
766	>	}
767	>	}
768	>	for (vector<int>::iterator jb = atomListColumn.begin();
769	>	jb != atomListColumn.end(); ++jb) {
770	>	atom2 = (*jb);
771	>	mf = fDecomp_->getMassFactorColumn(atom2);
772	>	// fg is the force on atom jb due to cutoff group's
773	>	// presence in switching region
774	>	fg = -swderiv * d_grp * mf;
775	>	fDecomp_->addForceToAtomColumn(atom2, fg);
776	>
777	>	if (atomListColumn.size() > 1) {
778	>	if (info_->usesAtomicVirial()) {
779	>	// find the distance between the atom
780	>	// and the center of the cutoff group:
781	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
782	>	tau -= outProduct(dag, fg);
783	>	}
784	>	}
785	>	}
786	>	}
787	>	//if (!info_->usesAtomicVirial()) {
788	>	//  tau -= outProduct(d_grp, fij);
789	>	//}
790	>	}
791	>	}
792	>	}
793	>
794	>	if (iLoop == PREPAIR_LOOP) {
795	>	if (info_->requiresPrepair()) {
796	>
797	>	fDecomp_->collectIntermediateData();
798	>
799	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
800	>	fDecomp_->fillSelfData(sdat, atom1);
801	>	interactionMan_->doPreForce(sdat);
802	>	}
803	>
804	>	fDecomp_->distributeIntermediateData();
805	>
806	>	}
807	>	}
808		}
809	<	for (int i=0; i<LR_POT_TYPES;i++){
810	<	lrPot += longRangePotential[i]; //Quick hack
809	>
810	>	fDecomp_->collectData();
811	>
812	>	if (info_->requiresSelfCorrection()) {
813	>
814	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
815	>	fDecomp_->fillSelfData(sdat, atom1);
816	>	interactionMan_->doSelfCorrection(sdat);
817	>	}
818	>
819		}
820
821	+	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
822	+	*(fDecomp_->getPairwisePotential());
823	+
824	+	lrPot = longRangePotential.sum();
825	+
826		//store the tau and long range potential
827		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
828	<	//  curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
829	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
246	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
247	<
248	<	curSnapshot->statData.setTau(tau);
828	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
829	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
830		}
831
832	<
832	>
833		void ForceManager::postCalculation() {
834		SimInfo::MoleculeIterator mi;
835		Molecule* mol;
836		Molecule::RigidBodyIterator rbIter;
837		RigidBody* rb;
838	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
839
840		// collect the atomic forces onto rigid bodies
841	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
842	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
843	<	rb->calcForcesAndTorques();
841	>
842	>	for (mol = info_->beginMolecule(mi); mol != NULL;
843	>	mol = info_->nextMolecule(mi)) {
844	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
845	>	rb = mol->nextRigidBody(rbIter)) {
846	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
847	>	tau += rbTau;
848		}
849		}
850	<
850	>
851	>	#ifdef IS_MPI
852	>	Mat3x3d tmpTau(tau);
853	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
854	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
855	>	#endif
856	>	curSnapshot->statData.setTau(tau);
857		}
858
859	<	} //end namespace oopse
859	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 681 by tim, Mon Oct 17 23:13:44 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1618 by gezelter, Mon Sep 12 17:09:26 2011 UTC

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