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

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trunk/src/brains/ForceManager.cpp (file contents), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC

#	Line 1 | Line 1
1	<	/*
1	>	/*
2		* Copyright (c) 2005 The University of Notre Dame. All Rights Reserved.
3		*
4		* The University of Notre Dame grants you ("Licensee") a
#	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
47	<	* @time 10:39am
48	<	* @version 1.0
49	<	*/
43	>	/**
44	>	* @file ForceManager.cpp
45	>	* @author tlin
46	>	* @date 11/09/2004
47	>	* @time 10:39am
48	>	* @version 1.0
49	>	*/
50
51	+
52		#include "brains/ForceManager.hpp"
53		#include "primitives/Molecule.hpp"
54	<	#include "UseTheForce/doForces_interface.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	<	}
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	<	void ForceManager::preCalculation() {
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;
444		Molecule::AtomIterator ai;
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)) {
455	<	atom->zeroForcesAndTorques();
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	>
460	>	//change the positions of atoms which belong to the rigidbodies
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	<
87	<	//change the positions of atoms which belong to the rigidbodies
88	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
89	<	rb->zeroForcesAndTorques();
90	<	}
472	>	}
473		}
474
475	<	}
476	<
477	<	void ForceManager::calcShortRangeInteraction() {
475	>	// Zero out the stress tensor
476	>	stressTensor *= 0.0;
477	>	// Zero out the heatFlux
478	>	fDecomp_->setHeatFlux( V3Zero );
479	>	}
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	<
494	<	//calculate short range interactions
495	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
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	<	//change the positions of atoms which belong to the rigidbodies
500	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
501	<	rb->updateAtoms();
113	<	}
499	>	//calculate short range interactions
500	>	for (mol = info_->beginMolecule(mi); mol != NULL;
501	>	mol = info_->nextMolecule(mi)) {
502
503	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
504	<	bond->calcForce();
505	<	}
503	>	//change the positions of atoms which belong to the rigidbodies
504	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
505	>	rb = mol->nextRigidBody(rbIter)) {
506	>	rb->updateAtoms();
507	>	}
508
509	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
510	<	bend->calcForce();
511	<	}
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 (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
516	<	torsion->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	<
539	>	}
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)) {
131	<	shortRangePotential += mol->getPotential();
132	<	}
133	<
589	>	RealType  shortRangePotential = bondPotential + bendPotential +
590	>	torsionPotential +  inversionPotential;
591		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
592		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
593	<	}
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
138	–	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
139	–	Snapshot* curSnapshot;
140	–	DataStorage* config;
141	–	double* frc;
142	–	double* pos;
143	–	double* trq;
144	–	double* A;
145	–	double* electroFrame;
146	–	double* rc;
147	–
148	–	//get current snapshot from SimInfo
149	–	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
601
602	<	//get array pointers
603	<	config = &(curSnapshot->atomData);
604	<	frc = config->getArrayPointer(DataStorage::dslForce);
154	<	pos = config->getArrayPointer(DataStorage::dslPosition);
155	<	trq = config->getArrayPointer(DataStorage::dslTorque);
156	<	A   = config->getArrayPointer(DataStorage::dslAmat);
157	<	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;
164	–	Vector3d com;
165	–	std::vector<Vector3d> rcGroup;
166	–
167	–	if(info_->getNCutoffGroups() > 0){
612
613	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
614	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
615	<	cg->getCOM(com);
616	<	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)
175	<
176	<	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		}
181	–
182	–	//initialize data before passing to fortran
183	–	double longRangePotential = 0.0;
184	–	Mat3x3d tau;
185	–	short int passedCalcPot = needPotential;
186	–	short int passedCalcStress = needStress;
187	–	int isError = 0;
627
628	<	doForceLoop( pos,
629	<	rc,
630	<	A,
631	<	electroFrame,
632	<	frc,
633	<	trq,
634	<	tau.getArrayPointer(),
635	<	&longRangePotential,
636	<	&passedCalcPot,
637	<	&passedCalcStress,
638	<	&isError );
628	>	fDecomp_->zeroWorkArrays();
629	>	fDecomp_->distributeData();
630	>
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	>	potVec longRangePotential(0.0);
648	>	potVec workPot(0.0);
649	>	vector<int>::iterator ia, jb;
650
651	<	if( isError ){
202	<	sprintf( painCave.errMsg,
203	<	"Error returned from the fortran force calculation.\n" );
204	<	painCave.isFatal = 1;
205	<	simError();
206	<	}
651	>	int loopStart, loopEnd;
652
653	<	//store the tau and long range potential
654	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
655	<	curSnapshot->statData.setTau(tau);
656	<	}
653	>	idat.vdwMult = &vdwMult;
654	>	idat.electroMult = &electroMult;
655	>	idat.pot = &workPot;
656	>	sdat.pot = fDecomp_->getEmbeddingPotential();
657	>	idat.vpair = &vpair;
658	>	idat.f1 = &f1;
659	>	idat.sw = &sw;
660	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
661	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
662	>	idat.doParticlePot = doParticlePot_;
663	>	sdat.doParticlePot = doParticlePot_;
664	>
665	>	loopEnd = PAIR_LOOP;
666	>	if (info_->requiresPrepair() ) {
667	>	loopStart = PREPAIR_LOOP;
668	>	} else {
669	>	loopStart = PAIR_LOOP;
670	>	}
671	>
672	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
673	>
674	>	if (iLoop == loopStart) {
675	>	bool update_nlist = fDecomp_->checkNeighborList();
676	>	if (update_nlist)
677	>	neighborList = fDecomp_->buildNeighborList();
678	>	}
679
680	+	for (vector<pair<int, int> >::iterator it = neighborList.begin();
681	+	it != neighborList.end(); ++it) {
682	+
683	+	cg1 = (*it).first;
684	+	cg2 = (*it).second;
685	+
686	+	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
687
688	<	void ForceManager::postCalculation() {
688	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
689	>
690	>	curSnapshot->wrapVector(d_grp);
691	>	rgrpsq = d_grp.lengthSquare();
692	>	rCutSq = cuts.second;
693	>
694	>	if (rgrpsq < rCutSq) {
695	>	idat.rcut = &cuts.first;
696	>	if (iLoop == PAIR_LOOP) {
697	>	vij = 0.0;
698	>	fij = V3Zero;
699	>	}
700	>
701	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
702	>	rgrp);
703	>
704	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
705	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
706	>
707	>	if (doHeatFlux_)
708	>	gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
709	>
710	>	for (ia = atomListRow.begin();
711	>	ia != atomListRow.end(); ++ia) {
712	>	atom1 = (*ia);
713	>
714	>	for (jb = atomListColumn.begin();
715	>	jb != atomListColumn.end(); ++jb) {
716	>	atom2 = (*jb);
717	>
718	>	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
719	>	vpair = 0.0;
720	>	workPot = 0.0;
721	>	f1 = V3Zero;
722	>
723	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
724	>
725	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
726	>	vdwMult = vdwScale_[topoDist];
727	>	electroMult = electrostaticScale_[topoDist];
728	>
729	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
730	>	idat.d = &d_grp;
731	>	idat.r2 = &rgrpsq;
732	>	if (doHeatFlux_)
733	>	vel2 = gvel2;
734	>	} else {
735	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
736	>	curSnapshot->wrapVector( d );
737	>	r2 = d.lengthSquare();
738	>	idat.d = &d;
739	>	idat.r2 = &r2;
740	>	if (doHeatFlux_)
741	>	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
742	>	}
743	>
744	>	r = sqrt( *(idat.r2) );
745	>	idat.rij = &r;
746	>
747	>	if (iLoop == PREPAIR_LOOP) {
748	>	interactionMan_->doPrePair(idat);
749	>	} else {
750	>	interactionMan_->doPair(idat);
751	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
752	>	vij += vpair;
753	>	fij += f1;
754	>	stressTensor -= outProduct( *(idat.d), f1);
755	>	if (doHeatFlux_)
756	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
757	>	}
758	>	}
759	>	}
760	>	}
761	>
762	>	if (iLoop == PAIR_LOOP) {
763	>	if (in_switching_region) {
764	>	swderiv = vij * dswdr / rgrp;
765	>	fg = swderiv * d_grp;
766	>	fij += fg;
767	>
768	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
769	>	stressTensor -= outProduct( *(idat.d), fg);
770	>	if (doHeatFlux_)
771	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
772	>
773	>	}
774	>
775	>	for (ia = atomListRow.begin();
776	>	ia != atomListRow.end(); ++ia) {
777	>	atom1 = (*ia);
778	>	mf = fDecomp_->getMassFactorRow(atom1);
779	>	// fg is the force on atom ia due to cutoff group's
780	>	// presence in switching region
781	>	fg = swderiv * d_grp * mf;
782	>	fDecomp_->addForceToAtomRow(atom1, fg);
783	>	if (atomListRow.size() > 1) {
784	>	if (info_->usesAtomicVirial()) {
785	>	// find the distance between the atom
786	>	// and the center of the cutoff group:
787	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
788	>	stressTensor -= outProduct(dag, fg);
789	>	if (doHeatFlux_)
790	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
791	>	}
792	>	}
793	>	}
794	>	for (jb = atomListColumn.begin();
795	>	jb != atomListColumn.end(); ++jb) {
796	>	atom2 = (*jb);
797	>	mf = fDecomp_->getMassFactorColumn(atom2);
798	>	// fg is the force on atom jb due to cutoff group's
799	>	// presence in switching region
800	>	fg = -swderiv * d_grp * mf;
801	>	fDecomp_->addForceToAtomColumn(atom2, fg);
802	>
803	>	if (atomListColumn.size() > 1) {
804	>	if (info_->usesAtomicVirial()) {
805	>	// find the distance between the atom
806	>	// and the center of the cutoff group:
807	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
808	>	stressTensor -= outProduct(dag, fg);
809	>	if (doHeatFlux_)
810	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
811	>	}
812	>	}
813	>	}
814	>	}
815	>	//if (!info_->usesAtomicVirial()) {
816	>	//  stressTensor -= outProduct(d_grp, fij);
817	>	//  if (doHeatFlux_)
818	>	//     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
819	>	//}
820	>	}
821	>	}
822	>	}
823	>
824	>	if (iLoop == PREPAIR_LOOP) {
825	>	if (info_->requiresPrepair()) {
826	>
827	>	fDecomp_->collectIntermediateData();
828	>
829	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
830	>	fDecomp_->fillSelfData(sdat, atom1);
831	>	interactionMan_->doPreForce(sdat);
832	>	}
833	>
834	>	fDecomp_->distributeIntermediateData();
835	>
836	>	}
837	>	}
838	>	}
839	>
840	>	fDecomp_->collectData();
841	>
842	>	if (info_->requiresSelfCorrection()) {
843	>
844	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
845	>	fDecomp_->fillSelfData(sdat, atom1);
846	>	interactionMan_->doSelfCorrection(sdat);
847	>	}
848	>
849	>	}
850	>
851	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
852	>	*(fDecomp_->getPairwisePotential());
853	>
854	>	lrPot = longRangePotential.sum();
855	>
856	>	//store the stressTensor and long range potential
857	>	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
858	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
859	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
860	>	}
861	>
862	>
863	>	void ForceManager::postCalculation() {
864		SimInfo::MoleculeIterator mi;
865		Molecule* mol;
866		Molecule::RigidBodyIterator rbIter;
867		RigidBody* rb;
868	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
869
870		// collect the atomic forces onto rigid bodies
871	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
872	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
873	<	rb->calcForcesAndTorques();
874	<	}
871	>
872	>	for (mol = info_->beginMolecule(mi); mol != NULL;
873	>	mol = info_->nextMolecule(mi)) {
874	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
875	>	rb = mol->nextRigidBody(rbIter)) {
876	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
877	>	stressTensor += rbTau;
878	>	}
879		}
880	+
881	+	#ifdef IS_MPI
882
883	<	}
883	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
884	>	MPI::REALTYPE, MPI::SUM);
885	>	#endif
886	>	curSnapshot->setStressTensor(stressTensor);
887	>
888	>	}
889
890	<	} //end namespace oopse
890	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 246 by gezelter, Wed Jan 12 22:41:40 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1723 by gezelter, Thu May 24 20:59:54 2012 UTC

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