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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 1756 by gezelter, Mon Jun 18 18:23:20 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	>	rCut_ = 0.0; //Needs a value for a later max() call;
114	>
115	>	if (simParams_->haveMDfileVersion())
116	>	mdFileVersion = simParams_->getMDfileVersion();
117	>	else
118	>	mdFileVersion = 0;
119	>
120	>	if (simParams_->haveCutoffRadius()) {
121	>	rCut_ = simParams_->getCutoffRadius();
122	>	} else {
123	>	if (info_->usesElectrostaticAtoms()) {
124	>	sprintf(painCave.errMsg,
125	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
126	>	"\tOpenMD will use a default value of 12.0 angstroms"
127	>	"\tfor the cutoffRadius.\n");
128	>	painCave.isFatal = 0;
129	>	painCave.severity = OPENMD_INFO;
130	>	simError();
131	>	rCut_ = 12.0;
132	>	} else {
133	>	RealType thisCut;
134	>	set<AtomType*>::iterator i;
135	>	set<AtomType*> atomTypes;
136	>	atomTypes = info_->getSimulatedAtomTypes();
137	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
138	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
139	>	rCut_ = max(thisCut, rCut_);
140	>	}
141	>	sprintf(painCave.errMsg,
142	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
143	>	"\tOpenMD will use %lf angstroms.\n",
144	>	rCut_);
145	>	painCave.isFatal = 0;
146	>	painCave.severity = OPENMD_INFO;
147	>	simError();
148	>	}
149	>	}
150
151	<	calcLongRangeInteraction(needPotential, needStress);
151	>	fDecomp_->setUserCutoff(rCut_);
152	>	interactionMan_->setCutoffRadius(rCut_);
153
154	<	postCalculation();
154	>	map<string, CutoffMethod> stringToCutoffMethod;
155	>	stringToCutoffMethod["HARD"] = HARD;
156	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
157	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
158	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
159	>
160	>	if (simParams_->haveCutoffMethod()) {
161	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
162	>	map<string, CutoffMethod>::iterator i;
163	>	i = stringToCutoffMethod.find(cutMeth);
164	>	if (i == stringToCutoffMethod.end()) {
165	>	sprintf(painCave.errMsg,
166	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
167	>	"\tShould be one of: "
168	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
169	>	cutMeth.c_str());
170	>	painCave.isFatal = 1;
171	>	painCave.severity = OPENMD_ERROR;
172	>	simError();
173	>	} else {
174	>	cutoffMethod_ = i->second;
175	>	}
176	>	} else {
177	>	if (mdFileVersion > 1) {
178	>	sprintf(painCave.errMsg,
179	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
180	>	"\tOpenMD will use SHIFTED_FORCE.\n");
181	>	painCave.isFatal = 0;
182	>	painCave.severity = OPENMD_INFO;
183	>	simError();
184	>	cutoffMethod_ = SHIFTED_FORCE;
185	>	} else {
186	>	// handle the case where the old file version was in play
187	>	// (there should be no cutoffMethod, so we have to deduce it
188	>	// from other data).
189	>
190	>	sprintf(painCave.errMsg,
191	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
192	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
193	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
194	>	"\tbehavior of the older (version 1) code.  To remove this\n"
195	>	"\twarning, add an explicit cutoffMethod and change the top\n"
196	>	"\tof the file so that it begins with <OpenMD version=2>\n");
197	>	painCave.isFatal = 0;
198	>	painCave.severity = OPENMD_WARNING;
199	>	simError();
200	>
201	>	// The old file version tethered the shifting behavior to the
202	>	// electrostaticSummationMethod keyword.
203
204	<	}
204	>	if (simParams_->haveElectrostaticSummationMethod()) {
205	>	string myMethod = simParams_->getElectrostaticSummationMethod();
206	>	toUpper(myMethod);
207	>
208	>	if (myMethod == "SHIFTED_POTENTIAL") {
209	>	cutoffMethod_ = SHIFTED_POTENTIAL;
210	>	} else if (myMethod == "SHIFTED_FORCE") {
211	>	cutoffMethod_ = SHIFTED_FORCE;
212	>	}
213	>
214	>	if (simParams_->haveSwitchingRadius())
215	>	rSwitch_ = simParams_->getSwitchingRadius();
216
217	<	void ForceManager::preCalculation() {
217	>	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
218	>	if (simParams_->haveSwitchingRadius()){
219	>	sprintf(painCave.errMsg,
220	>	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
221	>	"\tA value was set for the switchingRadius\n"
222	>	"\teven though the electrostaticSummationMethod was\n"
223	>	"\tset to %s\n", myMethod.c_str());
224	>	painCave.severity = OPENMD_WARNING;
225	>	painCave.isFatal = 1;
226	>	simError();
227	>	}
228	>	}
229	>	if (abs(rCut_ - rSwitch_) < 0.0001) {
230	>	if (cutoffMethod_ == SHIFTED_FORCE) {
231	>	sprintf(painCave.errMsg,
232	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
233	>	"\tcutoffRadius and switchingRadius are set to the\n"
234	>	"\tsame value.  OpenMD will use shifted force\n"
235	>	"\tpotentials instead of switching functions.\n");
236	>	painCave.isFatal = 0;
237	>	painCave.severity = OPENMD_WARNING;
238	>	simError();
239	>	} else {
240	>	cutoffMethod_ = SHIFTED_POTENTIAL;
241	>	sprintf(painCave.errMsg,
242	>	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
243	>	"\tcutoffRadius and switchingRadius are set to the\n"
244	>	"\tsame value.  OpenMD will use shifted potentials\n"
245	>	"\tinstead of switching functions.\n");
246	>	painCave.isFatal = 0;
247	>	painCave.severity = OPENMD_WARNING;
248	>	simError();
249	>	}
250	>	}
251	>	}
252	>	}
253	>	}
254	>
255	>	map<string, CutoffPolicy> stringToCutoffPolicy;
256	>	stringToCutoffPolicy["MIX"] = MIX;
257	>	stringToCutoffPolicy["MAX"] = MAX;
258	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
259	>
260	>	string cutPolicy;
261	>	if (forceFieldOptions_.haveCutoffPolicy()){
262	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
263	>	}else if (simParams_->haveCutoffPolicy()) {
264	>	cutPolicy = simParams_->getCutoffPolicy();
265	>	}
266	>
267	>	if (!cutPolicy.empty()){
268	>	toUpper(cutPolicy);
269	>	map<string, CutoffPolicy>::iterator i;
270	>	i = stringToCutoffPolicy.find(cutPolicy);
271	>
272	>	if (i == stringToCutoffPolicy.end()) {
273	>	sprintf(painCave.errMsg,
274	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
275	>	"\tShould be one of: "
276	>	"MIX, MAX, or TRADITIONAL\n",
277	>	cutPolicy.c_str());
278	>	painCave.isFatal = 1;
279	>	painCave.severity = OPENMD_ERROR;
280	>	simError();
281	>	} else {
282	>	cutoffPolicy_ = i->second;
283	>	}
284	>	} else {
285	>	sprintf(painCave.errMsg,
286	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
287	>	"\tOpenMD will use TRADITIONAL.\n");
288	>	painCave.isFatal = 0;
289	>	painCave.severity = OPENMD_INFO;
290	>	simError();
291	>	cutoffPolicy_ = TRADITIONAL;
292	>	}
293	>
294	>	fDecomp_->setCutoffPolicy(cutoffPolicy_);
295	>
296	>	// create the switching function object:
297	>
298	>	switcher_ = new SwitchingFunction();
299	>
300	>	if (cutoffMethod_ == SWITCHED) {
301	>	if (simParams_->haveSwitchingRadius()) {
302	>	rSwitch_ = simParams_->getSwitchingRadius();
303	>	if (rSwitch_ > rCut_) {
304	>	sprintf(painCave.errMsg,
305	>	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
306	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
307	>	painCave.isFatal = 1;
308	>	painCave.severity = OPENMD_ERROR;
309	>	simError();
310	>	}
311	>	} else {
312	>	rSwitch_ = 0.85 * rCut_;
313	>	sprintf(painCave.errMsg,
314	>	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
315	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
316	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
317	>	painCave.isFatal = 0;
318	>	painCave.severity = OPENMD_WARNING;
319	>	simError();
320	>	}
321	>	} else {
322	>	if (mdFileVersion > 1) {
323	>	// throw an error if we define a switching radius and don't need one.
324	>	// older file versions should not do this.
325	>	if (simParams_->haveSwitchingRadius()) {
326	>	map<string, CutoffMethod>::const_iterator it;
327	>	string theMeth;
328	>	for (it = stringToCutoffMethod.begin();
329	>	it != stringToCutoffMethod.end(); ++it) {
330	>	if (it->second == cutoffMethod_) {
331	>	theMeth = it->first;
332	>	break;
333	>	}
334	>	}
335	>	sprintf(painCave.errMsg,
336	>	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
337	>	"\tis not set to SWITCHED, so switchingRadius value\n"
338	>	"\twill be ignored for this simulation\n", theMeth.c_str());
339	>	painCave.isFatal = 0;
340	>	painCave.severity = OPENMD_WARNING;
341	>	simError();
342	>	}
343	>	}
344	>	rSwitch_ = rCut_;
345	>	}
346	>
347	>	// Default to cubic switching function.
348	>	sft_ = cubic;
349	>	if (simParams_->haveSwitchingFunctionType()) {
350	>	string funcType = simParams_->getSwitchingFunctionType();
351	>	toUpper(funcType);
352	>	if (funcType == "CUBIC") {
353	>	sft_ = cubic;
354	>	} else {
355	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
356	>	sft_ = fifth_order_poly;
357	>	} else {
358	>	// throw error
359	>	sprintf( painCave.errMsg,
360	>	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
361	>	"\tswitchingFunctionType must be one of: "
362	>	"\"cubic\" or \"fifth_order_polynomial\".",
363	>	funcType.c_str() );
364	>	painCave.isFatal = 1;
365	>	painCave.severity = OPENMD_ERROR;
366	>	simError();
367	>	}
368	>	}
369	>	}
370	>	switcher_->setSwitchType(sft_);
371	>	switcher_->setSwitch(rSwitch_, rCut_);
372	>	interactionMan_->setSwitchingRadius(rSwitch_);
373	>	}
374	>
375	>
376	>
377	>
378	>	void ForceManager::initialize() {
379	>
380	>	if (!info_->isTopologyDone()) {
381	>
382	>	info_->update();
383	>	interactionMan_->setSimInfo(info_);
384	>	interactionMan_->initialize();
385	>
386	>	// We want to delay the cutoffs until after the interaction
387	>	// manager has set up the atom-atom interactions so that we can
388	>	// query them for suggested cutoff values
389	>	setupCutoffs();
390	>
391	>	info_->prepareTopology();
392	>
393	>	doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
394	>	doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
395	>	if (doHeatFlux_) doParticlePot_ = true;
396	>
397	>	}
398	>
399	>	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
400	>
401	>	// Force fields can set options on how to scale van der Waals and
402	>	// electrostatic interactions for atoms connected via bonds, bends
403	>	// and torsions in this case the topological distance between
404	>	// atoms is:
405	>	// 0 = topologically unconnected
406	>	// 1 = bonded together
407	>	// 2 = connected via a bend
408	>	// 3 = connected via a torsion
409	>
410	>	vdwScale_.reserve(4);
411	>	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
412	>
413	>	electrostaticScale_.reserve(4);
414	>	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
415	>
416	>	vdwScale_[0] = 1.0;
417	>	vdwScale_[1] = fopts.getvdw12scale();
418	>	vdwScale_[2] = fopts.getvdw13scale();
419	>	vdwScale_[3] = fopts.getvdw14scale();
420	>
421	>	electrostaticScale_[0] = 1.0;
422	>	electrostaticScale_[1] = fopts.getelectrostatic12scale();
423	>	electrostaticScale_[2] = fopts.getelectrostatic13scale();
424	>	electrostaticScale_[3] = fopts.getelectrostatic14scale();
425	>
426	>	fDecomp_->distributeInitialData();
427	>
428	>	initialized_ = true;
429	>
430	>	}
431	>
432	>	void ForceManager::calcForces() {
433	>
434	>	if (!initialized_) initialize();
435	>
436	>	preCalculation();
437	>	shortRangeInteractions();
438	>	longRangeInteractions();
439	>	postCalculation();
440	>	}
441	>
442	>	void ForceManager::preCalculation() {
443		SimInfo::MoleculeIterator mi;
444		Molecule* mol;
445		Molecule::AtomIterator ai;
446		Atom* atom;
447		Molecule::RigidBodyIterator rbIter;
448		RigidBody* rb;
449	+	Molecule::CutoffGroupIterator ci;
450	+	CutoffGroup* cg;
451
452		// forces are zeroed here, before any are accumulated.
453	<	// NOTE: do not rezero the forces in Fortran.
454	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
455	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
456	<	atom->zeroForcesAndTorques();
453	>
454	>	for (mol = info_->beginMolecule(mi); mol != NULL;
455	>	mol = info_->nextMolecule(mi)) {
456	>	for(atom = mol->beginAtom(ai); atom != NULL;
457	>	atom = mol->nextAtom(ai)) {
458	>	atom->zeroForcesAndTorques();
459	>	}
460	>
461	>	//change the positions of atoms which belong to the rigidbodies
462	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
463	>	rb = mol->nextRigidBody(rbIter)) {
464	>	rb->zeroForcesAndTorques();
465	>	}
466	>
467	>	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
468	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
469	>	cg = mol->nextCutoffGroup(ci)) {
470	>	//calculate the center of mass of cutoff group
471	>	cg->updateCOM();
472		}
473	<
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	<	}
473	>	}
474		}
475
476	<	}
477	<
478	<	void ForceManager::calcShortRangeInteraction() {
476	>	// Zero out the stress tensor
477	>	stressTensor *= 0.0;
478	>	// Zero out the heatFlux
479	>	fDecomp_->setHeatFlux( Vector3d(0.0) );
480	>	}
481	>
482	>	void ForceManager::shortRangeInteractions() {
483		Molecule* mol;
484		RigidBody* rb;
485		Bond* bond;
486		Bend* bend;
487		Torsion* torsion;
488	+	Inversion* inversion;
489		SimInfo::MoleculeIterator mi;
490		Molecule::RigidBodyIterator rbIter;
491		Molecule::BondIterator bondIter;;
492		Molecule::BendIterator  bendIter;
493		Molecule::TorsionIterator  torsionIter;
494	+	Molecule::InversionIterator  inversionIter;
495	+	RealType bondPotential = 0.0;
496	+	RealType bendPotential = 0.0;
497	+	RealType torsionPotential = 0.0;
498	+	RealType inversionPotential = 0.0;
499
500		//calculate short range interactions
501	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
501	>	for (mol = info_->beginMolecule(mi); mol != NULL;
502	>	mol = info_->nextMolecule(mi)) {
503
504	<	//change the positions of atoms which belong to the rigidbodies
505	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
506	<	rb->updateAtoms();
507	<	}
504	>	//change the positions of atoms which belong to the rigidbodies
505	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
506	>	rb = mol->nextRigidBody(rbIter)) {
507	>	rb->updateAtoms();
508	>	}
509
510	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
511	<	bond->calcForce();
512	<	}
510	>	for (bond = mol->beginBond(bondIter); bond != NULL;
511	>	bond = mol->nextBond(bondIter)) {
512	>	bond->calcForce(doParticlePot_);
513	>	bondPotential += bond->getPotential();
514	>	}
515
516	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
517	<	bend->calcForce();
516	>	for (bend = mol->beginBend(bendIter); bend != NULL;
517	>	bend = mol->nextBend(bendIter)) {
518	>
519	>	RealType angle;
520	>	bend->calcForce(angle, doParticlePot_);
521	>	RealType currBendPot = bend->getPotential();
522	>
523	>	bendPotential += bend->getPotential();
524	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
525	>	if (i == bendDataSets.end()) {
526	>	BendDataSet dataSet;
527	>	dataSet.prev.angle = dataSet.curr.angle = angle;
528	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
529	>	dataSet.deltaV = 0.0;
530	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
531	>	dataSet));
532	>	}else {
533	>	i->second.prev.angle = i->second.curr.angle;
534	>	i->second.prev.potential = i->second.curr.potential;
535	>	i->second.curr.angle = angle;
536	>	i->second.curr.potential = currBendPot;
537	>	i->second.deltaV =  fabs(i->second.curr.potential -
538	>	i->second.prev.potential);
539		}
540	<
541	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
542	<	torsion->calcForce();
543	<	}
544	<
540	>	}
541	>
542	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
543	>	torsion = mol->nextTorsion(torsionIter)) {
544	>	RealType angle;
545	>	torsion->calcForce(angle, doParticlePot_);
546	>	RealType currTorsionPot = torsion->getPotential();
547	>	torsionPotential += torsion->getPotential();
548	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
549	>	if (i == torsionDataSets.end()) {
550	>	TorsionDataSet dataSet;
551	>	dataSet.prev.angle = dataSet.curr.angle = angle;
552	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
553	>	dataSet.deltaV = 0.0;
554	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
555	>	}else {
556	>	i->second.prev.angle = i->second.curr.angle;
557	>	i->second.prev.potential = i->second.curr.potential;
558	>	i->second.curr.angle = angle;
559	>	i->second.curr.potential = currTorsionPot;
560	>	i->second.deltaV =  fabs(i->second.curr.potential -
561	>	i->second.prev.potential);
562	>	}
563	>	}
564	>
565	>	for (inversion = mol->beginInversion(inversionIter);
566	>	inversion != NULL;
567	>	inversion = mol->nextInversion(inversionIter)) {
568	>	RealType angle;
569	>	inversion->calcForce(angle, doParticlePot_);
570	>	RealType currInversionPot = inversion->getPotential();
571	>	inversionPotential += inversion->getPotential();
572	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
573	>	if (i == inversionDataSets.end()) {
574	>	InversionDataSet dataSet;
575	>	dataSet.prev.angle = dataSet.curr.angle = angle;
576	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
577	>	dataSet.deltaV = 0.0;
578	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
579	>	}else {
580	>	i->second.prev.angle = i->second.curr.angle;
581	>	i->second.prev.potential = i->second.curr.potential;
582	>	i->second.curr.angle = angle;
583	>	i->second.curr.potential = currInversionPot;
584	>	i->second.deltaV =  fabs(i->second.curr.potential -
585	>	i->second.prev.potential);
586	>	}
587	>	}
588		}
589
590	<	double  shortRangePotential = 0.0;
591	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
131	<	shortRangePotential += mol->getPotential();
132	<	}
133	<
590	>	RealType  shortRangePotential = bondPotential + bendPotential +
591	>	torsionPotential +  inversionPotential;
592		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
593		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
594	<	}
594	>	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
595	>	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
596	>	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
597	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
598	>	}
599	>
600	>	void ForceManager::longRangeInteractions() {
601
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();
602
603	<	//get array pointers
604	<	config = &(curSnapshot->atomData);
605	<	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);
603	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
604	>	DataStorage* config = &(curSnapshot->atomData);
605	>	DataStorage* cgConfig = &(curSnapshot->cgData);
606
607		//calculate the center of mass of cutoff group
608	+
609		SimInfo::MoleculeIterator mi;
610		Molecule* mol;
611		Molecule::CutoffGroupIterator ci;
612		CutoffGroup* cg;
164	–	Vector3d com;
165	–	std::vector<Vector3d> rcGroup;
166	–
167	–	if(info_->getNCutoffGroups() > 0){
613
614	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
615	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
616	<	cg->getCOM(com);
617	<	rcGroup.push_back(com);
614	>	if(info_->getNCutoffGroups() > 0){
615	>	for (mol = info_->beginMolecule(mi); mol != NULL;
616	>	mol = info_->nextMolecule(mi)) {
617	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
618	>	cg = mol->nextCutoffGroup(ci)) {
619	>	cg->updateCOM();
620		}
621	<	}// end for (mol)
175	<
176	<	rc = rcGroup[0].getArrayPointer();
621	>	}
622		} else {
623	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
624	<	rc = pos;
623	>	// center of mass of the group is the same as position of the atom
624	>	// if cutoff group does not exist
625	>	cgConfig->position = config->position;
626	>	cgConfig->velocity = config->velocity;
627		}
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;
628
629	<	doForceLoop( pos,
630	<	rc,
631	<	A,
632	<	electroFrame,
633	<	frc,
634	<	trq,
635	<	tau.getArrayPointer(),
636	<	&longRangePotential,
637	<	&passedCalcPot,
638	<	&passedCalcStress,
639	<	&isError );
629	>	fDecomp_->zeroWorkArrays();
630	>	fDecomp_->distributeData();
631	>
632	>	int cg1, cg2, atom1, atom2, topoDist;
633	>	Vector3d d_grp, dag, d, gvel2, vel2;
634	>	RealType rgrpsq, rgrp, r2, r;
635	>	RealType electroMult, vdwMult;
636	>	RealType vij;
637	>	Vector3d fij, fg, f1;
638	>	tuple3<RealType, RealType, RealType> cuts;
639	>	RealType rCutSq;
640	>	bool in_switching_region;
641	>	RealType sw, dswdr, swderiv;
642	>	vector<int> atomListColumn, atomListRow, atomListLocal;
643	>	InteractionData idat;
644	>	SelfData sdat;
645	>	RealType mf;
646	>	RealType lrPot;
647	>	RealType vpair;
648	>	RealType dVdFQ1(0.0);
649	>	RealType dVdFQ2(0.0);
650	>	potVec longRangePotential(0.0);
651	>	potVec workPot(0.0);
652	>	vector<int>::iterator ia, jb;
653
654	<	if( isError ){
202	<	sprintf( painCave.errMsg,
203	<	"Error returned from the fortran force calculation.\n" );
204	<	painCave.isFatal = 1;
205	<	simError();
206	<	}
654	>	int loopStart, loopEnd;
655
656	<	//store the tau and long range potential
657	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
658	<	curSnapshot->statData.setTau(tau);
659	<	}
656	>	idat.vdwMult = &vdwMult;
657	>	idat.electroMult = &electroMult;
658	>	idat.pot = &workPot;
659	>	sdat.pot = fDecomp_->getEmbeddingPotential();
660	>	idat.vpair = &vpair;
661	>	idat.dVdFQ1 = &dVdFQ1;
662	>	idat.dVdFQ2 = &dVdFQ2;
663	>	idat.f1 = &f1;
664	>	idat.sw = &sw;
665	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
666	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
667	>	idat.doParticlePot = doParticlePot_;
668	>	sdat.doParticlePot = doParticlePot_;
669	>
670	>	loopEnd = PAIR_LOOP;
671	>	if (info_->requiresPrepair() ) {
672	>	loopStart = PREPAIR_LOOP;
673	>	} else {
674	>	loopStart = PAIR_LOOP;
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	<	void ForceManager::postCalculation() {
692	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
693	>
694	>	curSnapshot->wrapVector(d_grp);
695	>	rgrpsq = d_grp.lengthSquare();
696	>	rCutSq = cuts.second;
697	>
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, cg1, cg2)) {
723	>
724	>	vpair = 0.0;
725	>	workPot = 0.0;
726	>	f1 = V3Zero;
727	>	dVdFQ1 = 0.0;
728	>	dVdFQ2 = 0.0;
729	>
730	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
731	>
732	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
733	>	vdwMult = vdwScale_[topoDist];
734	>	electroMult = electrostaticScale_[topoDist];
735	>
736	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
737	>	idat.d = &d_grp;
738	>	idat.r2 = &rgrpsq;
739	>	if (doHeatFlux_)
740	>	vel2 = gvel2;
741	>	} else {
742	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
743	>	curSnapshot->wrapVector( d );
744	>	r2 = d.lengthSquare();
745	>	idat.d = &d;
746	>	idat.r2 = &r2;
747	>	if (doHeatFlux_)
748	>	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
749	>	}
750	>
751	>	r = sqrt( *(idat.r2) );
752	>	idat.rij = &r;
753	>
754	>	if (iLoop == PREPAIR_LOOP) {
755	>	interactionMan_->doPrePair(idat);
756	>	} else {
757	>	interactionMan_->doPair(idat);
758	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
759	>	vij += vpair;
760	>	fij += f1;
761	>	stressTensor -= outProduct( *(idat.d), f1);
762	>	if (doHeatFlux_)
763	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
764	>	}
765	>	}
766	>	}
767	>	}
768	>
769	>	if (iLoop == PAIR_LOOP) {
770	>	if (in_switching_region) {
771	>	swderiv = vij * dswdr / rgrp;
772	>	fg = swderiv * d_grp;
773	>	fij += fg;
774	>
775	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
776	>	stressTensor -= outProduct( *(idat.d), fg);
777	>	if (doHeatFlux_)
778	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
779	>
780	>	}
781	>
782	>	for (ia = atomListRow.begin();
783	>	ia != atomListRow.end(); ++ia) {
784	>	atom1 = (*ia);
785	>	mf = fDecomp_->getMassFactorRow(atom1);
786	>	// fg is the force on atom ia due to cutoff group's
787	>	// presence in switching region
788	>	fg = swderiv * d_grp * mf;
789	>	fDecomp_->addForceToAtomRow(atom1, fg);
790	>	if (atomListRow.size() > 1) {
791	>	if (info_->usesAtomicVirial()) {
792	>	// find the distance between the atom
793	>	// and the center of the cutoff group:
794	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
795	>	stressTensor -= outProduct(dag, fg);
796	>	if (doHeatFlux_)
797	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
798	>	}
799	>	}
800	>	}
801	>	for (jb = atomListColumn.begin();
802	>	jb != atomListColumn.end(); ++jb) {
803	>	atom2 = (*jb);
804	>	mf = fDecomp_->getMassFactorColumn(atom2);
805	>	// fg is the force on atom jb due to cutoff group's
806	>	// presence in switching region
807	>	fg = -swderiv * d_grp * mf;
808	>	fDecomp_->addForceToAtomColumn(atom2, fg);
809	>
810	>	if (atomListColumn.size() > 1) {
811	>	if (info_->usesAtomicVirial()) {
812	>	// find the distance between the atom
813	>	// and the center of the cutoff group:
814	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
815	>	stressTensor -= outProduct(dag, fg);
816	>	if (doHeatFlux_)
817	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
818	>	}
819	>	}
820	>	}
821	>	}
822	>	//if (!info_->usesAtomicVirial()) {
823	>	//  stressTensor -= outProduct(d_grp, fij);
824	>	//  if (doHeatFlux_)
825	>	//     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
826	>	//}
827	>	}
828	>	}
829	>	}
830	>
831	>	if (iLoop == PREPAIR_LOOP) {
832	>	if (info_->requiresPrepair()) {
833	>
834	>	fDecomp_->collectIntermediateData();
835	>
836	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
837	>	fDecomp_->fillSelfData(sdat, atom1);
838	>	interactionMan_->doPreForce(sdat);
839	>	}
840	>
841	>	fDecomp_->distributeIntermediateData();
842	>
843	>	}
844	>	}
845	>	}
846	>
847	>	// collects pairwise information
848	>	fDecomp_->collectData();
849	>
850	>	if (info_->requiresSelfCorrection()) {
851	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
852	>	fDecomp_->fillSelfData(sdat, atom1);
853	>	interactionMan_->doSelfCorrection(sdat);
854	>	}
855	>	}
856	>
857	>	// collects single-atom information
858	>	fDecomp_->collectSelfData();
859	>
860	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
861	>	*(fDecomp_->getPairwisePotential());
862	>
863	>	lrPot = longRangePotential.sum();
864	>
865	>	//store the stressTensor and long range potential
866	>	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
867	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
868	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
869	>	}
870	>
871	>
872	>	void ForceManager::postCalculation() {
873		SimInfo::MoleculeIterator mi;
874		Molecule* mol;
875		Molecule::RigidBodyIterator rbIter;
876		RigidBody* rb;
877	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
878
879		// collect the atomic forces onto rigid bodies
880	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
881	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
882	<	rb->calcForcesAndTorques();
883	<	}
880	>
881	>	for (mol = info_->beginMolecule(mi); mol != NULL;
882	>	mol = info_->nextMolecule(mi)) {
883	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
884	>	rb = mol->nextRigidBody(rbIter)) {
885	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
886	>	stressTensor += rbTau;
887	>	}
888		}
889	+
890	+	#ifdef IS_MPI
891	+	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
892	+	MPI::REALTYPE, MPI::SUM);
893	+	#endif
894	+	curSnapshot->setStressTensor(stressTensor);
895	+
896	+	}
897
898	<	}
228	<
229	<	} //end namespace oopse
898	>	} //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 1756 by gezelter, Mon Jun 18 18:23:20 2012 UTC

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