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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 1787 by gezelter, Wed Aug 29 18:13:11 2012 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Kuang & Gezelter,  J. Chem. Phys. 133, 164101 (2010).
40	+	* [5]  Vardeman, Stocker & Gezelter, J. Chem. Theory Comput. 7, 834 (2011).
41		*/
42
43		/**
#	Line 47 | Line 48
48		* @version 1.0
49		*/
50
51	+
52		#include "brains/ForceManager.hpp"
53		#include "primitives/Molecule.hpp"
54	<	#include "UseTheForce/doForces_interface.h"
53	<	#define __C
54	<	#include "UseTheForce/DarkSide/fInteractionMap.h"
54	>	#define __OPENMD_C
55		#include "utils/simError.h"
56	<	namespace oopse {
56	>	#include "primitives/Bond.hpp"
57	>	#include "primitives/Bend.hpp"
58	>	#include "primitives/Torsion.hpp"
59	>	#include "primitives/Inversion.hpp"
60	>	#include "nonbonded/NonBondedInteraction.hpp"
61	>	#include "perturbations/ElectricField.hpp"
62	>	#include "parallel/ForceMatrixDecomposition.hpp"
63
64	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
64	>	#include <cstdio>
65	>	#include <iostream>
66	>	#include <iomanip>
67
68	<	if (!info_->isFortranInitialized()) {
69	<	info_->update();
70	<	}
68	>	using namespace std;
69	>	namespace OpenMD {
70	>
71	>	ForceManager::ForceManager(SimInfo * info) : info_(info) {
72	>	forceField_ = info_->getForceField();
73	>	interactionMan_ = new InteractionManager();
74	>	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
75	>	}
76
77	<	preCalculation();
77	>	/**
78	>	* setupCutoffs
79	>	*
80	>	* Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
81	>	* and cutoffPolicy
82	>	*
83	>	* cutoffRadius : realType
84	>	*  If the cutoffRadius was explicitly set, use that value.
85	>	*  If the cutoffRadius was not explicitly set:
86	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
87	>	*      No electrostatic atoms?  Poll the atom types present in the
88	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
89	>	*      Use the maximum suggested value that was found.
90	>	*
91	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
92	>	*                        or SHIFTED_POTENTIAL)
93	>	*      If cutoffMethod was explicitly set, use that choice.
94	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
95	>	*
96	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
97	>	*      If cutoffPolicy was explicitly set, use that choice.
98	>	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
99	>	*
100	>	* switchingRadius : realType
101	>	*  If the cutoffMethod was set to SWITCHED:
102	>	*      If the switchingRadius was explicitly set, use that value
103	>	*          (but do a sanity check first).
104	>	*      If the switchingRadius was not explicitly set: use 0.85 *
105	>	*      cutoffRadius_
106	>	*  If the cutoffMethod was not set to SWITCHED:
107	>	*      Set switchingRadius equal to cutoffRadius for safety.
108	>	*/
109	>	void ForceManager::setupCutoffs() {
110
111	<	calcShortRangeInteraction();
111	>	Globals* simParams_ = info_->getSimParams();
112	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
113	>	int mdFileVersion;
114	>	rCut_ = 0.0; //Needs a value for a later max() call;
115	>
116	>	if (simParams_->haveMDfileVersion())
117	>	mdFileVersion = simParams_->getMDfileVersion();
118	>	else
119	>	mdFileVersion = 0;
120	>
121	>	if (simParams_->haveCutoffRadius()) {
122	>	rCut_ = simParams_->getCutoffRadius();
123	>	} else {
124	>	if (info_->usesElectrostaticAtoms()) {
125	>	sprintf(painCave.errMsg,
126	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
127	>	"\tOpenMD will use a default value of 12.0 angstroms"
128	>	"\tfor the cutoffRadius.\n");
129	>	painCave.isFatal = 0;
130	>	painCave.severity = OPENMD_INFO;
131	>	simError();
132	>	rCut_ = 12.0;
133	>	} else {
134	>	RealType thisCut;
135	>	set<AtomType*>::iterator i;
136	>	set<AtomType*> atomTypes;
137	>	atomTypes = info_->getSimulatedAtomTypes();
138	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
139	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
140	>	rCut_ = max(thisCut, rCut_);
141	>	}
142	>	sprintf(painCave.errMsg,
143	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
144	>	"\tOpenMD will use %lf angstroms.\n",
145	>	rCut_);
146	>	painCave.isFatal = 0;
147	>	painCave.severity = OPENMD_INFO;
148	>	simError();
149	>	}
150	>	}
151
152	<	calcLongRangeInteraction(needPotential, needStress);
152	>	fDecomp_->setUserCutoff(rCut_);
153	>	interactionMan_->setCutoffRadius(rCut_);
154
155	<	postCalculation();
155	>	map<string, CutoffMethod> stringToCutoffMethod;
156	>	stringToCutoffMethod["HARD"] = HARD;
157	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
158	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
159	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
160	>
161	>	if (simParams_->haveCutoffMethod()) {
162	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
163	>	map<string, CutoffMethod>::iterator i;
164	>	i = stringToCutoffMethod.find(cutMeth);
165	>	if (i == stringToCutoffMethod.end()) {
166	>	sprintf(painCave.errMsg,
167	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
168	>	"\tShould be one of: "
169	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
170	>	cutMeth.c_str());
171	>	painCave.isFatal = 1;
172	>	painCave.severity = OPENMD_ERROR;
173	>	simError();
174	>	} else {
175	>	cutoffMethod_ = i->second;
176	>	}
177	>	} else {
178	>	if (mdFileVersion > 1) {
179	>	sprintf(painCave.errMsg,
180	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
181	>	"\tOpenMD will use SHIFTED_FORCE.\n");
182	>	painCave.isFatal = 0;
183	>	painCave.severity = OPENMD_INFO;
184	>	simError();
185	>	cutoffMethod_ = SHIFTED_FORCE;
186	>	} else {
187	>	// handle the case where the old file version was in play
188	>	// (there should be no cutoffMethod, so we have to deduce it
189	>	// from other data).
190	>
191	>	sprintf(painCave.errMsg,
192	>	"ForceManager::setupCutoffs : DEPRECATED FILE FORMAT!\n"
193	>	"\tOpenMD found a file which does not set a cutoffMethod.\n"
194	>	"\tOpenMD will attempt to deduce a cutoffMethod using the\n"
195	>	"\tbehavior of the older (version 1) code.  To remove this\n"
196	>	"\twarning, add an explicit cutoffMethod and change the top\n"
197	>	"\tof the file so that it begins with <OpenMD version=2>\n");
198	>	painCave.isFatal = 0;
199	>	painCave.severity = OPENMD_WARNING;
200	>	simError();
201	>
202	>	// The old file version tethered the shifting behavior to the
203	>	// electrostaticSummationMethod keyword.
204
205	+	if (simParams_->haveElectrostaticSummationMethod()) {
206	+	string myMethod = simParams_->getElectrostaticSummationMethod();
207	+	toUpper(myMethod);
208	+
209	+	if (myMethod == "SHIFTED_POTENTIAL") {
210	+	cutoffMethod_ = SHIFTED_POTENTIAL;
211	+	} else if (myMethod == "SHIFTED_FORCE") {
212	+	cutoffMethod_ = SHIFTED_FORCE;
213	+	}
214	+
215	+	if (simParams_->haveSwitchingRadius())
216	+	rSwitch_ = simParams_->getSwitchingRadius();
217	+
218	+	if (myMethod == "SHIFTED_POTENTIAL" || myMethod == "SHIFTED_FORCE") {
219	+	if (simParams_->haveSwitchingRadius()){
220	+	sprintf(painCave.errMsg,
221	+	"ForceManager::setupCutoffs : DEPRECATED ERROR MESSAGE\n"
222	+	"\tA value was set for the switchingRadius\n"
223	+	"\teven though the electrostaticSummationMethod was\n"
224	+	"\tset to %s\n", myMethod.c_str());
225	+	painCave.severity = OPENMD_WARNING;
226	+	painCave.isFatal = 1;
227	+	simError();
228	+	}
229	+	}
230	+	if (abs(rCut_ - rSwitch_) < 0.0001) {
231	+	if (cutoffMethod_ == SHIFTED_FORCE) {
232	+	sprintf(painCave.errMsg,
233	+	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
234	+	"\tcutoffRadius and switchingRadius are set to the\n"
235	+	"\tsame value.  OpenMD will use shifted force\n"
236	+	"\tpotentials instead of switching functions.\n");
237	+	painCave.isFatal = 0;
238	+	painCave.severity = OPENMD_WARNING;
239	+	simError();
240	+	} else {
241	+	cutoffMethod_ = SHIFTED_POTENTIAL;
242	+	sprintf(painCave.errMsg,
243	+	"ForceManager::setupCutoffs : DEPRECATED BEHAVIOR\n"
244	+	"\tcutoffRadius and switchingRadius are set to the\n"
245	+	"\tsame value.  OpenMD will use shifted potentials\n"
246	+	"\tinstead of switching functions.\n");
247	+	painCave.isFatal = 0;
248	+	painCave.severity = OPENMD_WARNING;
249	+	simError();
250	+	}
251	+	}
252	+	}
253	+	}
254	+	}
255	+
256	+	map<string, CutoffPolicy> stringToCutoffPolicy;
257	+	stringToCutoffPolicy["MIX"] = MIX;
258	+	stringToCutoffPolicy["MAX"] = MAX;
259	+	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
260	+
261	+	string cutPolicy;
262	+	if (forceFieldOptions_.haveCutoffPolicy()){
263	+	cutPolicy = forceFieldOptions_.getCutoffPolicy();
264	+	}else if (simParams_->haveCutoffPolicy()) {
265	+	cutPolicy = simParams_->getCutoffPolicy();
266	+	}
267	+
268	+	if (!cutPolicy.empty()){
269	+	toUpper(cutPolicy);
270	+	map<string, CutoffPolicy>::iterator i;
271	+	i = stringToCutoffPolicy.find(cutPolicy);
272	+
273	+	if (i == stringToCutoffPolicy.end()) {
274	+	sprintf(painCave.errMsg,
275	+	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
276	+	"\tShould be one of: "
277	+	"MIX, MAX, or TRADITIONAL\n",
278	+	cutPolicy.c_str());
279	+	painCave.isFatal = 1;
280	+	painCave.severity = OPENMD_ERROR;
281	+	simError();
282	+	} else {
283	+	cutoffPolicy_ = i->second;
284	+	}
285	+	} else {
286	+	sprintf(painCave.errMsg,
287	+	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
288	+	"\tOpenMD will use TRADITIONAL.\n");
289	+	painCave.isFatal = 0;
290	+	painCave.severity = OPENMD_INFO;
291	+	simError();
292	+	cutoffPolicy_ = TRADITIONAL;
293	+	}
294	+
295	+	fDecomp_->setCutoffPolicy(cutoffPolicy_);
296	+
297	+	// create the switching function object:
298	+
299	+	switcher_ = new SwitchingFunction();
300	+
301	+	if (cutoffMethod_ == SWITCHED) {
302	+	if (simParams_->haveSwitchingRadius()) {
303	+	rSwitch_ = simParams_->getSwitchingRadius();
304	+	if (rSwitch_ > rCut_) {
305	+	sprintf(painCave.errMsg,
306	+	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
307	+	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
308	+	painCave.isFatal = 1;
309	+	painCave.severity = OPENMD_ERROR;
310	+	simError();
311	+	}
312	+	} else {
313	+	rSwitch_ = 0.85 * rCut_;
314	+	sprintf(painCave.errMsg,
315	+	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
316	+	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
317	+	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
318	+	painCave.isFatal = 0;
319	+	painCave.severity = OPENMD_WARNING;
320	+	simError();
321	+	}
322	+	} else {
323	+	if (mdFileVersion > 1) {
324	+	// throw an error if we define a switching radius and don't need one.
325	+	// older file versions should not do this.
326	+	if (simParams_->haveSwitchingRadius()) {
327	+	map<string, CutoffMethod>::const_iterator it;
328	+	string theMeth;
329	+	for (it = stringToCutoffMethod.begin();
330	+	it != stringToCutoffMethod.end(); ++it) {
331	+	if (it->second == cutoffMethod_) {
332	+	theMeth = it->first;
333	+	break;
334	+	}
335	+	}
336	+	sprintf(painCave.errMsg,
337	+	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
338	+	"\tis not set to SWITCHED, so switchingRadius value\n"
339	+	"\twill be ignored for this simulation\n", theMeth.c_str());
340	+	painCave.isFatal = 0;
341	+	painCave.severity = OPENMD_WARNING;
342	+	simError();
343	+	}
344	+	}
345	+	rSwitch_ = rCut_;
346	+	}
347	+
348	+	// Default to cubic switching function.
349	+	sft_ = cubic;
350	+	if (simParams_->haveSwitchingFunctionType()) {
351	+	string funcType = simParams_->getSwitchingFunctionType();
352	+	toUpper(funcType);
353	+	if (funcType == "CUBIC") {
354	+	sft_ = cubic;
355	+	} else {
356	+	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
357	+	sft_ = fifth_order_poly;
358	+	} else {
359	+	// throw error
360	+	sprintf( painCave.errMsg,
361	+	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
362	+	"\tswitchingFunctionType must be one of: "
363	+	"\"cubic\" or \"fifth_order_polynomial\".",
364	+	funcType.c_str() );
365	+	painCave.isFatal = 1;
366	+	painCave.severity = OPENMD_ERROR;
367	+	simError();
368	+	}
369	+	}
370	+	}
371	+	switcher_->setSwitchType(sft_);
372	+	switcher_->setSwitch(rSwitch_, rCut_);
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	+	doElectricField_ = info_->getSimParams()->getOutputElectricField();
398	+
399	+	}
400	+
401	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
402	+
403	+	// Force fields can set options on how to scale van der Waals and
404	+	// electrostatic interactions for atoms connected via bonds, bends
405	+	// and torsions in this case the topological distance between
406	+	// atoms is:
407	+	// 0 = topologically unconnected
408	+	// 1 = bonded together
409	+	// 2 = connected via a bend
410	+	// 3 = connected via a torsion
411	+
412	+	vdwScale_.reserve(4);
413	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
414	+
415	+	electrostaticScale_.reserve(4);
416	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
417	+
418	+	vdwScale_[0] = 1.0;
419	+	vdwScale_[1] = fopts.getvdw12scale();
420	+	vdwScale_[2] = fopts.getvdw13scale();
421	+	vdwScale_[3] = fopts.getvdw14scale();
422	+
423	+	electrostaticScale_[0] = 1.0;
424	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
425	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
426	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
427	+
428	+	if (info_->getSimParams()->haveElectricField()) {
429	+	ElectricField* eField = new ElectricField(info_);
430	+	perturbations_.push_back(eField);
431	+	}
432	+
433	+	fDecomp_->distributeInitialData();
434	+
435	+	initialized_ = true;
436	+
437	+	}
438	+
439	+	void ForceManager::calcForces() {
440	+
441	+	if (!initialized_) initialize();
442	+
443	+	preCalculation();
444	+	shortRangeInteractions();
445	+	longRangeInteractions();
446	+	postCalculation();
447	+	}
448	+
449		void ForceManager::preCalculation() {
450		SimInfo::MoleculeIterator mi;
451		Molecule* mol;
#	Line 78 | Line 453 | namespace oopse {
453		Atom* atom;
454		Molecule::RigidBodyIterator rbIter;
455		RigidBody* rb;
456	+	Molecule::CutoffGroupIterator ci;
457	+	CutoffGroup* cg;
458
459	<	// forces are zeroed here, before any are accumulated.
460	<	// NOTE: do not rezero the forces in Fortran.
461	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
462	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
459	>	// forces and potentials are zeroed here, before any are
460	>	// accumulated.
461	>
462	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
463	>
464	>	snap->setBondPotential(0.0);
465	>	snap->setBendPotential(0.0);
466	>	snap->setTorsionPotential(0.0);
467	>	snap->setInversionPotential(0.0);
468	>
469	>	potVec zeroPot(0.0);
470	>	snap->setLongRangePotential(zeroPot);
471	>	snap->setExcludedPotentials(zeroPot);
472	>
473	>	snap->setRestraintPotential(0.0);
474	>	snap->setRawPotential(0.0);
475	>
476	>	for (mol = info_->beginMolecule(mi); mol != NULL;
477	>	mol = info_->nextMolecule(mi)) {
478	>	for(atom = mol->beginAtom(ai); atom != NULL;
479	>	atom = mol->nextAtom(ai)) {
480		atom->zeroForcesAndTorques();
481		}
482	<
482	>
483		//change the positions of atoms which belong to the rigidbodies
484	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
484	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
485	>	rb = mol->nextRigidBody(rbIter)) {
486		rb->zeroForcesAndTorques();
487		}
488	+
489	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
490	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
491	+	cg = mol->nextCutoffGroup(ci)) {
492	+	//calculate the center of mass of cutoff group
493	+	cg->updateCOM();
494	+	}
495	+	}
496		}
497
498	+	// Zero out the stress tensor
499	+	stressTensor *= 0.0;
500	+	// Zero out the heatFlux
501	+	fDecomp_->setHeatFlux( Vector3d(0.0) );
502		}
503	<
504	<	void ForceManager::calcShortRangeInteraction() {
503	>
504	>	void ForceManager::shortRangeInteractions() {
505		Molecule* mol;
506		RigidBody* rb;
507		Bond* bond;
508		Bend* bend;
509		Torsion* torsion;
510	+	Inversion* inversion;
511		SimInfo::MoleculeIterator mi;
512		Molecule::RigidBodyIterator rbIter;
513		Molecule::BondIterator bondIter;;
514		Molecule::BendIterator  bendIter;
515		Molecule::TorsionIterator  torsionIter;
516	+	Molecule::InversionIterator  inversionIter;
517	+	RealType bondPotential = 0.0;
518	+	RealType bendPotential = 0.0;
519	+	RealType torsionPotential = 0.0;
520	+	RealType inversionPotential = 0.0;
521
522		//calculate short range interactions
523	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
523	>	for (mol = info_->beginMolecule(mi); mol != NULL;
524	>	mol = info_->nextMolecule(mi)) {
525
526		//change the positions of atoms which belong to the rigidbodies
527	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
528	<	rb->updateAtoms();
527	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
528	>	rb = mol->nextRigidBody(rbIter)) {
529	>	rb->updateAtoms();
530		}
531
532	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
533	<	bond->calcForce();
532	>	for (bond = mol->beginBond(bondIter); bond != NULL;
533	>	bond = mol->nextBond(bondIter)) {
534	>	bond->calcForce(doParticlePot_);
535	>	bondPotential += bond->getPotential();
536		}
537
538	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
539	<	bend->calcForce();
540	<	}
541	<
542	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
543	<	torsion->calcForce();
538	>	for (bend = mol->beginBend(bendIter); bend != NULL;
539	>	bend = mol->nextBend(bendIter)) {
540	>
541	>	RealType angle;
542	>	bend->calcForce(angle, doParticlePot_);
543	>	RealType currBendPot = bend->getPotential();
544	>
545	>	bendPotential += bend->getPotential();
546	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
547	>	if (i == bendDataSets.end()) {
548	>	BendDataSet dataSet;
549	>	dataSet.prev.angle = dataSet.curr.angle = angle;
550	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
551	>	dataSet.deltaV = 0.0;
552	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
553	>	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 = currBendPot;
559	>	i->second.deltaV =  fabs(i->second.curr.potential -
560	>	i->second.prev.potential);
561	>	}
562		}
563	<
563	>
564	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
565	>	torsion = mol->nextTorsion(torsionIter)) {
566	>	RealType angle;
567	>	torsion->calcForce(angle, doParticlePot_);
568	>	RealType currTorsionPot = torsion->getPotential();
569	>	torsionPotential += torsion->getPotential();
570	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
571	>	if (i == torsionDataSets.end()) {
572	>	TorsionDataSet dataSet;
573	>	dataSet.prev.angle = dataSet.curr.angle = angle;
574	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
575	>	dataSet.deltaV = 0.0;
576	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
577	>	}else {
578	>	i->second.prev.angle = i->second.curr.angle;
579	>	i->second.prev.potential = i->second.curr.potential;
580	>	i->second.curr.angle = angle;
581	>	i->second.curr.potential = currTorsionPot;
582	>	i->second.deltaV =  fabs(i->second.curr.potential -
583	>	i->second.prev.potential);
584	>	}
585	>	}
586	>
587	>	for (inversion = mol->beginInversion(inversionIter);
588	>	inversion != NULL;
589	>	inversion = mol->nextInversion(inversionIter)) {
590	>	RealType angle;
591	>	inversion->calcForce(angle, doParticlePot_);
592	>	RealType currInversionPot = inversion->getPotential();
593	>	inversionPotential += inversion->getPotential();
594	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
595	>	if (i == inversionDataSets.end()) {
596	>	InversionDataSet dataSet;
597	>	dataSet.prev.angle = dataSet.curr.angle = angle;
598	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
599	>	dataSet.deltaV = 0.0;
600	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
601	>	}else {
602	>	i->second.prev.angle = i->second.curr.angle;
603	>	i->second.prev.potential = i->second.curr.potential;
604	>	i->second.curr.angle = angle;
605	>	i->second.curr.potential = currInversionPot;
606	>	i->second.deltaV =  fabs(i->second.curr.potential -
607	>	i->second.prev.potential);
608	>	}
609	>	}
610		}
130	–
611
612	<	double bondPotential = 0.0;
613	<	double bendPotential = 0.0;
614	<	double torsionPotential = 0.0;
612	>	#ifdef IS_MPI
613	>	// Collect from all nodes.  This should eventually be moved into a
614	>	// SystemDecomposition, but this is a better place than in
615	>	// Thermo to do the collection.
616	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
617	>	MPI::SUM);
618	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
619	>	MPI::SUM);
620	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
621	>	MPI::REALTYPE, MPI::SUM);
622	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
623	>	MPI::REALTYPE, MPI::SUM);
624	>	#endif
625
626	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
626	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
627
628	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
629	<	bondPotential += bond->getPotential();
630	<	}
628	>	curSnapshot->setBondPotential(bondPotential);
629	>	curSnapshot->setBendPotential(bendPotential);
630	>	curSnapshot->setTorsionPotential(torsionPotential);
631	>	curSnapshot->setInversionPotential(inversionPotential);
632	>
633	>	// RealType shortRangePotential = bondPotential + bendPotential +
634	>	//   torsionPotential +  inversionPotential;
635
636	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
637	<	bendPotential += bend->getPotential();
638	<	}
636	>	// curSnapshot->setShortRangePotential(shortRangePotential);
637	>	}
638	>
639	>	void ForceManager::longRangeInteractions() {
640
146	–	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
147	–	torsionPotential += torsion->getPotential();
148	–	}
641
150	–	}
151	–
152	–	double  shortRangePotential = bondPotential + bendPotential + torsionPotential;
642		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
643	<	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
644	<	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
156	<	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
157	<	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
158	<
159	<	}
643	>	DataStorage* config = &(curSnapshot->atomData);
644	>	DataStorage* cgConfig = &(curSnapshot->cgData);
645
161	–	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
162	–	Snapshot* curSnapshot;
163	–	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();
173	–
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	–
646		//calculate the center of mass of cutoff group
647	+
648		SimInfo::MoleculeIterator mi;
649		Molecule* mol;
650		Molecule::CutoffGroupIterator ci;
651		CutoffGroup* cg;
187	–	Vector3d com;
188	–	std::vector<Vector3d> rcGroup;
652
653	<	if(info_->getNCutoffGroups() > 0){
654	<
655	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
656	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
657	<	cg->getCOM(com);
658	<	rcGroup.push_back(com);
653	>	if(info_->getNCutoffGroups() > 0){
654	>	for (mol = info_->beginMolecule(mi); mol != NULL;
655	>	mol = info_->nextMolecule(mi)) {
656	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
657	>	cg = mol->nextCutoffGroup(ci)) {
658	>	cg->updateCOM();
659		}
660	<	}// end for (mol)
198	<
199	<	rc = rcGroup[0].getArrayPointer();
660	>	}
661		} else {
662	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
663	<	rc = pos;
662	>	// center of mass of the group is the same as position of the atom
663	>	// if cutoff group does not exist
664	>	cgConfig->position = config->position;
665	>	cgConfig->velocity = config->velocity;
666		}
667	<
668	<	//initialize data before passing to fortran
669	<	double longRangePotential[LR_POT_TYPES];
207	<	double lrPot = 0.0;
667	>
668	>	fDecomp_->zeroWorkArrays();
669	>	fDecomp_->distributeData();
670
671	<	Mat3x3d tau;
672	<	short int passedCalcPot = needPotential;
673	<	short int passedCalcStress = needStress;
674	<	int isError = 0;
671	>	int cg1, cg2, atom1, atom2, topoDist;
672	>	Vector3d d_grp, dag, d, gvel2, vel2;
673	>	RealType rgrpsq, rgrp, r2, r;
674	>	RealType electroMult, vdwMult;
675	>	RealType vij;
676	>	Vector3d fij, fg, f1;
677	>	tuple3<RealType, RealType, RealType> cuts;
678	>	RealType rCutSq;
679	>	bool in_switching_region;
680	>	RealType sw, dswdr, swderiv;
681	>	vector<int> atomListColumn, atomListRow, atomListLocal;
682	>	InteractionData idat;
683	>	SelfData sdat;
684	>	RealType mf;
685	>	RealType vpair;
686	>	RealType dVdFQ1(0.0);
687	>	RealType dVdFQ2(0.0);
688	>	potVec longRangePotential(0.0);
689	>	potVec workPot(0.0);
690	>	potVec exPot(0.0);
691	>	Vector3d eField1(0.0);
692	>	Vector3d eField2(0.0);
693	>	vector<int>::iterator ia, jb;
694
695	<	for (int i=0; i<LR_POT_TYPES;i++){
215	<	longRangePotential[i]=0.0; //Initialize array
216	<	}
695	>	int loopStart, loopEnd;
696
697	<
698	<
699	<	doForceLoop( pos,
700	<	rc,
701	<	A,
702	<	electroFrame,
703	<	frc,
704	<	trq,
705	<	tau.getArrayPointer(),
706	<	longRangePotential,
707	<	&passedCalcPot,
708	<	&passedCalcStress,
709	<	&isError );
710	<
711	<	if( isError ){
712	<	sprintf( painCave.errMsg,
713	<	"Error returned from the fortran force calculation.\n" );
714	<	painCave.isFatal = 1;
715	<	simError();
697	>	idat.vdwMult = &vdwMult;
698	>	idat.electroMult = &electroMult;
699	>	idat.pot = &workPot;
700	>	idat.excludedPot = &exPot;
701	>	sdat.pot = fDecomp_->getEmbeddingPotential();
702	>	sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
703	>	idat.vpair = &vpair;
704	>	idat.dVdFQ1 = &dVdFQ1;
705	>	idat.dVdFQ2 = &dVdFQ2;
706	>	idat.eField1 = &eField1;
707	>	idat.eField2 = &eField2;
708	>	idat.f1 = &f1;
709	>	idat.sw = &sw;
710	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
711	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
712	>	idat.doParticlePot = doParticlePot_;
713	>	idat.doElectricField = doElectricField_;
714	>	sdat.doParticlePot = doParticlePot_;
715	>
716	>	loopEnd = PAIR_LOOP;
717	>	if (info_->requiresPrepair() ) {
718	>	loopStart = PREPAIR_LOOP;
719	>	} else {
720	>	loopStart = PAIR_LOOP;
721		}
722	<	for (int i=0; i<LR_POT_TYPES;i++){
723	<	lrPot += longRangePotential[i]; //Quick hack
722	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
723	>
724	>	if (iLoop == loopStart) {
725	>	bool update_nlist = fDecomp_->checkNeighborList();
726	>	if (update_nlist)
727	>	neighborList = fDecomp_->buildNeighborList();
728	>	}
729	>
730	>	for (vector<pair<int, int> >::iterator it = neighborList.begin();
731	>	it != neighborList.end(); ++it) {
732	>
733	>	cg1 = (*it).first;
734	>	cg2 = (*it).second;
735	>
736	>	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
737	>
738	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
739	>
740	>	curSnapshot->wrapVector(d_grp);
741	>	rgrpsq = d_grp.lengthSquare();
742	>	rCutSq = cuts.second;
743	>
744	>	if (rgrpsq < rCutSq) {
745	>	idat.rcut = &cuts.first;
746	>	if (iLoop == PAIR_LOOP) {
747	>	vij = 0.0;
748	>	fij = V3Zero;
749	>	}
750	>
751	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
752	>	rgrp);
753	>
754	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
755	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
756	>
757	>	if (doHeatFlux_)
758	>	gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
759	>
760	>	for (ia = atomListRow.begin();
761	>	ia != atomListRow.end(); ++ia) {
762	>	atom1 = (*ia);
763	>
764	>	for (jb = atomListColumn.begin();
765	>	jb != atomListColumn.end(); ++jb) {
766	>	atom2 = (*jb);
767	>
768	>	if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
769	>
770	>	vpair = 0.0;
771	>	workPot = 0.0;
772	>	exPot = 0.0;
773	>	f1 = V3Zero;
774	>	dVdFQ1 = 0.0;
775	>	dVdFQ2 = 0.0;
776	>
777	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
778	>
779	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
780	>	vdwMult = vdwScale_[topoDist];
781	>	electroMult = electrostaticScale_[topoDist];
782	>
783	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
784	>	idat.d = &d_grp;
785	>	idat.r2 = &rgrpsq;
786	>	if (doHeatFlux_)
787	>	vel2 = gvel2;
788	>	} else {
789	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
790	>	curSnapshot->wrapVector( d );
791	>	r2 = d.lengthSquare();
792	>	idat.d = &d;
793	>	idat.r2 = &r2;
794	>	if (doHeatFlux_)
795	>	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
796	>	}
797	>
798	>	r = sqrt( *(idat.r2) );
799	>	idat.rij = &r;
800	>
801	>	if (iLoop == PREPAIR_LOOP) {
802	>	interactionMan_->doPrePair(idat);
803	>	} else {
804	>	interactionMan_->doPair(idat);
805	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
806	>	vij += vpair;
807	>	fij += f1;
808	>	stressTensor -= outProduct( *(idat.d), f1);
809	>	if (doHeatFlux_)
810	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
811	>	}
812	>	}
813	>	}
814	>	}
815	>
816	>	if (iLoop == PAIR_LOOP) {
817	>	if (in_switching_region) {
818	>	swderiv = vij * dswdr / rgrp;
819	>	fg = swderiv * d_grp;
820	>	fij += fg;
821	>
822	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
823	>	stressTensor -= outProduct( *(idat.d), fg);
824	>	if (doHeatFlux_)
825	>	fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
826	>
827	>	}
828	>
829	>	for (ia = atomListRow.begin();
830	>	ia != atomListRow.end(); ++ia) {
831	>	atom1 = (*ia);
832	>	mf = fDecomp_->getMassFactorRow(atom1);
833	>	// fg is the force on atom ia due to cutoff group's
834	>	// presence in switching region
835	>	fg = swderiv * d_grp * mf;
836	>	fDecomp_->addForceToAtomRow(atom1, fg);
837	>	if (atomListRow.size() > 1) {
838	>	if (info_->usesAtomicVirial()) {
839	>	// find the distance between the atom
840	>	// and the center of the cutoff group:
841	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
842	>	stressTensor -= outProduct(dag, fg);
843	>	if (doHeatFlux_)
844	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
845	>	}
846	>	}
847	>	}
848	>	for (jb = atomListColumn.begin();
849	>	jb != atomListColumn.end(); ++jb) {
850	>	atom2 = (*jb);
851	>	mf = fDecomp_->getMassFactorColumn(atom2);
852	>	// fg is the force on atom jb due to cutoff group's
853	>	// presence in switching region
854	>	fg = -swderiv * d_grp * mf;
855	>	fDecomp_->addForceToAtomColumn(atom2, fg);
856	>
857	>	if (atomListColumn.size() > 1) {
858	>	if (info_->usesAtomicVirial()) {
859	>	// find the distance between the atom
860	>	// and the center of the cutoff group:
861	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
862	>	stressTensor -= outProduct(dag, fg);
863	>	if (doHeatFlux_)
864	>	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
865	>	}
866	>	}
867	>	}
868	>	}
869	>	//if (!info_->usesAtomicVirial()) {
870	>	//  stressTensor -= outProduct(d_grp, fij);
871	>	//  if (doHeatFlux_)
872	>	//     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
873	>	//}
874	>	}
875	>	}
876	>	}
877	>
878	>	if (iLoop == PREPAIR_LOOP) {
879	>	if (info_->requiresPrepair()) {
880	>
881	>	fDecomp_->collectIntermediateData();
882	>
883	>	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
884	>	fDecomp_->fillSelfData(sdat, atom1);
885	>	interactionMan_->doPreForce(sdat);
886	>	}
887	>
888	>	fDecomp_->distributeIntermediateData();
889	>
890	>	}
891	>	}
892		}
893	+
894	+	// collects pairwise information
895	+	fDecomp_->collectData();
896	+
897	+	if (info_->requiresSelfCorrection()) {
898	+	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
899	+	fDecomp_->fillSelfData(sdat, atom1);
900	+	interactionMan_->doSelfCorrection(sdat);
901	+	}
902	+	}
903
904	<	//store the tau and long range potential
905	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
244	<	//  curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
245	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
246	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
904	>	// collects single-atom information
905	>	fDecomp_->collectSelfData();
906
907	<	curSnapshot->statData.setTau(tau);
908	<	}
907	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
908	>	*(fDecomp_->getPairwisePotential());
909
910	+	curSnapshot->setLongRangePotential(longRangePotential);
911	+
912	+	curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
913	+	*(fDecomp_->getExcludedPotential()));
914
915	+	}
916	+
917	+
918		void ForceManager::postCalculation() {
919	+
920	+	vector<Perturbation*>::iterator pi;
921	+	for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
922	+	(*pi)->applyPerturbation();
923	+	}
924	+
925		SimInfo::MoleculeIterator mi;
926		Molecule* mol;
927		Molecule::RigidBodyIterator rbIter;
928		RigidBody* rb;
929	<
929	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
930	>
931		// collect the atomic forces onto rigid bodies
932	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
933	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
934	<	rb->calcForcesAndTorques();
932	>
933	>	for (mol = info_->beginMolecule(mi); mol != NULL;
934	>	mol = info_->nextMolecule(mi)) {
935	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
936	>	rb = mol->nextRigidBody(rbIter)) {
937	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
938	>	stressTensor += rbTau;
939		}
940		}
941	<
941	>
942	>	#ifdef IS_MPI
943	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
944	>	MPI::REALTYPE, MPI::SUM);
945	>	#endif
946	>	curSnapshot->setStressTensor(stressTensor);
947	>
948		}
949	<
267	<	} //end namespace oopse
949	>	} //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 1787 by gezelter, Wed Aug 29 18:13:11 2012 UTC

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