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root/OpenMD/trunk/src/brains/ForceManager.cpp

Comparing trunk/src/brains/ForceManager.cpp (file contents):
Revision 665 by tim, Thu Oct 13 22:26:47 2005 UTC vs.
Revision 1788 by gezelter, Wed Aug 29 20:17:07 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	+	interactionMan_->setSwitchingRadius(rSwitch_);
374		}
375
376	+
377	+
378	+
379	+	void ForceManager::initialize() {
380	+
381	+	if (!info_->isTopologyDone()) {
382	+
383	+	info_->update();
384	+	interactionMan_->setSimInfo(info_);
385	+	interactionMan_->initialize();
386	+
387	+	// We want to delay the cutoffs until after the interaction
388	+	// manager has set up the atom-atom interactions so that we can
389	+	// query them for suggested cutoff values
390	+	setupCutoffs();
391	+
392	+	info_->prepareTopology();
393	+
394	+	doParticlePot_ = info_->getSimParams()->getOutputParticlePotential();
395	+	doHeatFlux_ = info_->getSimParams()->getPrintHeatFlux();
396	+	if (doHeatFlux_) doParticlePot_ = true;
397	+
398	+	}
399	+
400	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
401	+
402	+	// Force fields can set options on how to scale van der Waals and
403	+	// electrostatic interactions for atoms connected via bonds, bends
404	+	// and torsions in this case the topological distance between
405	+	// atoms is:
406	+	// 0 = topologically unconnected
407	+	// 1 = bonded together
408	+	// 2 = connected via a bend
409	+	// 3 = connected via a torsion
410	+
411	+	vdwScale_.reserve(4);
412	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
413	+
414	+	electrostaticScale_.reserve(4);
415	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
416	+
417	+	vdwScale_[0] = 1.0;
418	+	vdwScale_[1] = fopts.getvdw12scale();
419	+	vdwScale_[2] = fopts.getvdw13scale();
420	+	vdwScale_[3] = fopts.getvdw14scale();
421	+
422	+	electrostaticScale_[0] = 1.0;
423	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
424	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
425	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
426	+
427	+	if (info_->getSimParams()->haveElectricField()) {
428	+	ElectricField* eField = new ElectricField(info_);
429	+	perturbations_.push_back(eField);
430	+	}
431	+
432	+	fDecomp_->distributeInitialData();
433	+
434	+	initialized_ = true;
435	+
436	+	}
437	+
438	+	void ForceManager::calcForces() {
439	+
440	+	if (!initialized_) initialize();
441	+
442	+	preCalculation();
443	+	shortRangeInteractions();
444	+	longRangeInteractions();
445	+	postCalculation();
446	+	}
447	+
448		void ForceManager::preCalculation() {
449		SimInfo::MoleculeIterator mi;
450		Molecule* mol;
#	Line 78 | Line 452 | namespace oopse {
452		Atom* atom;
453		Molecule::RigidBodyIterator rbIter;
454		RigidBody* rb;
455	+	Molecule::CutoffGroupIterator ci;
456	+	CutoffGroup* cg;
457
458	<	// forces are zeroed here, before any are accumulated.
459	<	// NOTE: do not rezero the forces in Fortran.
460	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
461	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
458	>	// forces and potentials are zeroed here, before any are
459	>	// accumulated.
460	>
461	>	Snapshot* snap = info_->getSnapshotManager()->getCurrentSnapshot();
462	>
463	>	snap->setBondPotential(0.0);
464	>	snap->setBendPotential(0.0);
465	>	snap->setTorsionPotential(0.0);
466	>	snap->setInversionPotential(0.0);
467	>
468	>	potVec zeroPot(0.0);
469	>	snap->setLongRangePotential(zeroPot);
470	>	snap->setExcludedPotentials(zeroPot);
471	>
472	>	snap->setRestraintPotential(0.0);
473	>	snap->setRawPotential(0.0);
474	>
475	>	for (mol = info_->beginMolecule(mi); mol != NULL;
476	>	mol = info_->nextMolecule(mi)) {
477	>	for(atom = mol->beginAtom(ai); atom != NULL;
478	>	atom = mol->nextAtom(ai)) {
479		atom->zeroForcesAndTorques();
480		}
481	<
481	>
482		//change the positions of atoms which belong to the rigidbodies
483	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
483	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
484	>	rb = mol->nextRigidBody(rbIter)) {
485		rb->zeroForcesAndTorques();
486		}
487	+
488	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
489	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
490	+	cg = mol->nextCutoffGroup(ci)) {
491	+	//calculate the center of mass of cutoff group
492	+	cg->updateCOM();
493	+	}
494	+	}
495		}
496
497	+	// Zero out the stress tensor
498	+	stressTensor *= 0.0;
499	+	// Zero out the heatFlux
500	+	fDecomp_->setHeatFlux( Vector3d(0.0) );
501		}
502	<
503	<	void ForceManager::calcShortRangeInteraction() {
502	>
503	>	void ForceManager::shortRangeInteractions() {
504		Molecule* mol;
505		RigidBody* rb;
506		Bond* bond;
507		Bend* bend;
508		Torsion* torsion;
509	+	Inversion* inversion;
510		SimInfo::MoleculeIterator mi;
511		Molecule::RigidBodyIterator rbIter;
512		Molecule::BondIterator bondIter;;
513		Molecule::BendIterator  bendIter;
514		Molecule::TorsionIterator  torsionIter;
515	+	Molecule::InversionIterator  inversionIter;
516	+	RealType bondPotential = 0.0;
517	+	RealType bendPotential = 0.0;
518	+	RealType torsionPotential = 0.0;
519	+	RealType inversionPotential = 0.0;
520
521		//calculate short range interactions
522	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
522	>	for (mol = info_->beginMolecule(mi); mol != NULL;
523	>	mol = info_->nextMolecule(mi)) {
524
525		//change the positions of atoms which belong to the rigidbodies
526	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
527	<	rb->updateAtoms();
526	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
527	>	rb = mol->nextRigidBody(rbIter)) {
528	>	rb->updateAtoms();
529		}
530
531	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
532	<	bond->calcForce();
531	>	for (bond = mol->beginBond(bondIter); bond != NULL;
532	>	bond = mol->nextBond(bondIter)) {
533	>	bond->calcForce(doParticlePot_);
534	>	bondPotential += bond->getPotential();
535		}
536
537	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
538	<	bend->calcForce();
539	<	}
540	<
541	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
542	<	torsion->calcForce();
537	>	for (bend = mol->beginBend(bendIter); bend != NULL;
538	>	bend = mol->nextBend(bendIter)) {
539	>
540	>	RealType angle;
541	>	bend->calcForce(angle, doParticlePot_);
542	>	RealType currBendPot = bend->getPotential();
543	>
544	>	bendPotential += bend->getPotential();
545	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
546	>	if (i == bendDataSets.end()) {
547	>	BendDataSet dataSet;
548	>	dataSet.prev.angle = dataSet.curr.angle = angle;
549	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
550	>	dataSet.deltaV = 0.0;
551	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend,
552	>	dataSet));
553	>	}else {
554	>	i->second.prev.angle = i->second.curr.angle;
555	>	i->second.prev.potential = i->second.curr.potential;
556	>	i->second.curr.angle = angle;
557	>	i->second.curr.potential = currBendPot;
558	>	i->second.deltaV =  fabs(i->second.curr.potential -
559	>	i->second.prev.potential);
560	>	}
561		}
562	<
562	>
563	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
564	>	torsion = mol->nextTorsion(torsionIter)) {
565	>	RealType angle;
566	>	torsion->calcForce(angle, doParticlePot_);
567	>	RealType currTorsionPot = torsion->getPotential();
568	>	torsionPotential += torsion->getPotential();
569	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
570	>	if (i == torsionDataSets.end()) {
571	>	TorsionDataSet dataSet;
572	>	dataSet.prev.angle = dataSet.curr.angle = angle;
573	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
574	>	dataSet.deltaV = 0.0;
575	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
576	>	}else {
577	>	i->second.prev.angle = i->second.curr.angle;
578	>	i->second.prev.potential = i->second.curr.potential;
579	>	i->second.curr.angle = angle;
580	>	i->second.curr.potential = currTorsionPot;
581	>	i->second.deltaV =  fabs(i->second.curr.potential -
582	>	i->second.prev.potential);
583	>	}
584	>	}
585	>
586	>	for (inversion = mol->beginInversion(inversionIter);
587	>	inversion != NULL;
588	>	inversion = mol->nextInversion(inversionIter)) {
589	>	RealType angle;
590	>	inversion->calcForce(angle, doParticlePot_);
591	>	RealType currInversionPot = inversion->getPotential();
592	>	inversionPotential += inversion->getPotential();
593	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
594	>	if (i == inversionDataSets.end()) {
595	>	InversionDataSet dataSet;
596	>	dataSet.prev.angle = dataSet.curr.angle = angle;
597	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
598	>	dataSet.deltaV = 0.0;
599	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
600	>	}else {
601	>	i->second.prev.angle = i->second.curr.angle;
602	>	i->second.prev.potential = i->second.curr.potential;
603	>	i->second.curr.angle = angle;
604	>	i->second.curr.potential = currInversionPot;
605	>	i->second.deltaV =  fabs(i->second.curr.potential -
606	>	i->second.prev.potential);
607	>	}
608	>	}
609		}
130	–
610
611	<	double bondPotential = 0.0;
612	<	double bendPotential = 0.0;
613	<	double torsionPotential = 0.0;
611	>	#ifdef IS_MPI
612	>	// Collect from all nodes.  This should eventually be moved into a
613	>	// SystemDecomposition, but this is a better place than in
614	>	// Thermo to do the collection.
615	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bondPotential, 1, MPI::REALTYPE,
616	>	MPI::SUM);
617	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &bendPotential, 1, MPI::REALTYPE,
618	>	MPI::SUM);
619	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &torsionPotential, 1,
620	>	MPI::REALTYPE, MPI::SUM);
621	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, &inversionPotential, 1,
622	>	MPI::REALTYPE, MPI::SUM);
623	>	#endif
624
625	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
625	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
626
627	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
628	<	bondPotential += bond->getPotential();
629	<	}
627	>	curSnapshot->setBondPotential(bondPotential);
628	>	curSnapshot->setBendPotential(bendPotential);
629	>	curSnapshot->setTorsionPotential(torsionPotential);
630	>	curSnapshot->setInversionPotential(inversionPotential);
631	>
632	>	// RealType shortRangePotential = bondPotential + bendPotential +
633	>	//   torsionPotential +  inversionPotential;
634
635	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
636	<	bendPotential += bend->getPotential();
637	<	}
635	>	// curSnapshot->setShortRangePotential(shortRangePotential);
636	>	}
637	>
638	>	void ForceManager::longRangeInteractions() {
639
146	–	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
147	–	torsionPotential += torsion->getPotential();
148	–	}
640
150	–	}
151	–
152	–	double  shortRangePotential = bondPotential + bendPotential + torsionPotential;
641		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
642	<	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
643	<	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
156	<	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
157	<	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
158	<
159	<	}
642	>	DataStorage* config = &(curSnapshot->atomData);
643	>	DataStorage* cgConfig = &(curSnapshot->cgData);
644
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	–
645		//calculate the center of mass of cutoff group
646	+
647		SimInfo::MoleculeIterator mi;
648		Molecule* mol;
649		Molecule::CutoffGroupIterator ci;
650		CutoffGroup* cg;
187	–	Vector3d com;
188	–	std::vector<Vector3d> rcGroup;
651
652	<	if(info_->getNCutoffGroups() > 0){
653	<
654	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
655	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
656	<	cg->getCOM(com);
657	<	rcGroup.push_back(com);
652	>	if(info_->getNCutoffGroups() > 0){
653	>	for (mol = info_->beginMolecule(mi); mol != NULL;
654	>	mol = info_->nextMolecule(mi)) {
655	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
656	>	cg = mol->nextCutoffGroup(ci)) {
657	>	cg->updateCOM();
658		}
659	<	}// end for (mol)
198	<
199	<	rc = rcGroup[0].getArrayPointer();
659	>	}
660		} else {
661	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
662	<	rc = pos;
661	>	// center of mass of the group is the same as position of the atom
662	>	// if cutoff group does not exist
663	>	cgConfig->position = config->position;
664	>	cgConfig->velocity = config->velocity;
665		}
666	<
667	<	//initialize data before passing to fortran
668	<	double longRangePotential[LR_POT_TYPES];
207	<	double lrPot = 0.0;
666	>
667	>	fDecomp_->zeroWorkArrays();
668	>	fDecomp_->distributeData();
669
670	<	Mat3x3d tau;
671	<	short int passedCalcPot = needPotential;
672	<	short int passedCalcStress = needStress;
673	<	int isError = 0;
670	>	int cg1, cg2, atom1, atom2, topoDist;
671	>	Vector3d d_grp, dag, d, gvel2, vel2;
672	>	RealType rgrpsq, rgrp, r2, r;
673	>	RealType electroMult, vdwMult;
674	>	RealType vij;
675	>	Vector3d fij, fg, f1;
676	>	tuple3<RealType, RealType, RealType> cuts;
677	>	RealType rCutSq;
678	>	bool in_switching_region;
679	>	RealType sw, dswdr, swderiv;
680	>	vector<int> atomListColumn, atomListRow, atomListLocal;
681	>	InteractionData idat;
682	>	SelfData sdat;
683	>	RealType mf;
684	>	RealType vpair;
685	>	RealType dVdFQ1(0.0);
686	>	RealType dVdFQ2(0.0);
687	>	Vector3d eField1(0.0);
688	>	Vector3d eField2(0.0);
689	>	potVec longRangePotential(0.0);
690	>	potVec workPot(0.0);
691	>	potVec exPot(0.0);
692	>	vector<int>::iterator ia, jb;
693
694	<	for (int i=0; i<LR_POT_TYPES;i++){
215	<	longRangePotential[i]=0.0; //Initialize array
216	<	}
694	>	int loopStart, loopEnd;
695
696	<
697	<
698	<	doForceLoop( pos,
699	<	rc,
700	<	A,
701	<	electroFrame,
702	<	frc,
703	<	trq,
704	<	tau.getArrayPointer(),
705	<	longRangePotential,
706	<	&passedCalcPot,
707	<	&passedCalcStress,
708	<	&isError );
709	<
710	<	if( isError ){
711	<	sprintf( painCave.errMsg,
712	<	"Error returned from the fortran force calculation.\n" );
713	<	painCave.isFatal = 1;
714	<	simError();
715	<	}
716	<	for (int i=0; i<LR_POT_TYPES;i++){
717	<	lrPot += longRangePotential[i]; //Quick hack
696	>	idat.vdwMult = &vdwMult;
697	>	idat.electroMult = &electroMult;
698	>	idat.pot = &workPot;
699	>	idat.excludedPot = &exPot;
700	>	sdat.pot = fDecomp_->getEmbeddingPotential();
701	>	sdat.excludedPot = fDecomp_->getExcludedSelfPotential();
702	>	idat.vpair = &vpair;
703	>	idat.dVdFQ1 = &dVdFQ1;
704	>	idat.dVdFQ2 = &dVdFQ2;
705	>	idat.eField1 = &eField1;
706	>	idat.eField2 = &eField2;
707	>	idat.f1 = &f1;
708	>	idat.sw = &sw;
709	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
710	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
711	>	idat.doParticlePot = doParticlePot_;
712	>	sdat.doParticlePot = doParticlePot_;
713	>
714	>	loopEnd = PAIR_LOOP;
715	>	if (info_->requiresPrepair() ) {
716	>	loopStart = PREPAIR_LOOP;
717	>	} else {
718	>	loopStart = PAIR_LOOP;
719		}
720	+	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
721	+
722	+	if (iLoop == loopStart) {
723	+	bool update_nlist = fDecomp_->checkNeighborList();
724	+	if (update_nlist)
725	+	neighborList = fDecomp_->buildNeighborList();
726	+	}
727
728	<	//store the tau and long range potential
729	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
730	<	//  curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = longRangePotential;
731	<	curSnapshot->statData.setTau(tau);
732	<	}
728	>	for (vector<pair<int, int> >::iterator it = neighborList.begin();
729	>	it != neighborList.end(); ++it) {
730	>
731	>	cg1 = (*it).first;
732	>	cg2 = (*it).second;
733	>
734	>	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
735
736	+	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
737
738	+	curSnapshot->wrapVector(d_grp);
739	+	rgrpsq = d_grp.lengthSquare();
740	+	rCutSq = cuts.second;
741	+
742	+	if (rgrpsq < rCutSq) {
743	+	idat.rcut = &cuts.first;
744	+	if (iLoop == PAIR_LOOP) {
745	+	vij = 0.0;
746	+	fij = V3Zero;
747	+	}
748	+
749	+	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
750	+	rgrp);
751	+
752	+	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
753	+	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
754	+
755	+	if (doHeatFlux_)
756	+	gvel2 = fDecomp_->getGroupVelocityColumn(cg2);
757	+
758	+	for (ia = atomListRow.begin();
759	+	ia != atomListRow.end(); ++ia) {
760	+	atom1 = (*ia);
761	+
762	+	for (jb = atomListColumn.begin();
763	+	jb != atomListColumn.end(); ++jb) {
764	+	atom2 = (*jb);
765	+
766	+	if (!fDecomp_->skipAtomPair(atom1, atom2, cg1, cg2)) {
767	+
768	+	vpair = 0.0;
769	+	workPot = 0.0;
770	+	exPot = 0.0;
771	+	f1 = V3Zero;
772	+	dVdFQ1 = 0.0;
773	+	dVdFQ2 = 0.0;
774	+
775	+	fDecomp_->fillInteractionData(idat, atom1, atom2);
776	+
777	+	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
778	+	vdwMult = vdwScale_[topoDist];
779	+	electroMult = electrostaticScale_[topoDist];
780	+
781	+	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
782	+	idat.d = &d_grp;
783	+	idat.r2 = &rgrpsq;
784	+	if (doHeatFlux_)
785	+	vel2 = gvel2;
786	+	} else {
787	+	d = fDecomp_->getInteratomicVector(atom1, atom2);
788	+	curSnapshot->wrapVector( d );
789	+	r2 = d.lengthSquare();
790	+	idat.d = &d;
791	+	idat.r2 = &r2;
792	+	if (doHeatFlux_)
793	+	vel2 = fDecomp_->getAtomVelocityColumn(atom2);
794	+	}
795	+
796	+	r = sqrt( *(idat.r2) );
797	+	idat.rij = &r;
798	+
799	+	if (iLoop == PREPAIR_LOOP) {
800	+	interactionMan_->doPrePair(idat);
801	+	} else {
802	+	interactionMan_->doPair(idat);
803	+	fDecomp_->unpackInteractionData(idat, atom1, atom2);
804	+	vij += vpair;
805	+	fij += f1;
806	+	stressTensor -= outProduct( *(idat.d), f1);
807	+	if (doHeatFlux_)
808	+	fDecomp_->addToHeatFlux(*(idat.d) * dot(f1, vel2));
809	+	}
810	+	}
811	+	}
812	+	}
813	+
814	+	if (iLoop == PAIR_LOOP) {
815	+	if (in_switching_region) {
816	+	swderiv = vij * dswdr / rgrp;
817	+	fg = swderiv * d_grp;
818	+	fij += fg;
819	+
820	+	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
821	+	stressTensor -= outProduct( *(idat.d), fg);
822	+	if (doHeatFlux_)
823	+	fDecomp_->addToHeatFlux(*(idat.d) * dot(fg, vel2));
824	+
825	+	}
826	+
827	+	for (ia = atomListRow.begin();
828	+	ia != atomListRow.end(); ++ia) {
829	+	atom1 = (*ia);
830	+	mf = fDecomp_->getMassFactorRow(atom1);
831	+	// fg is the force on atom ia due to cutoff group's
832	+	// presence in switching region
833	+	fg = swderiv * d_grp * mf;
834	+	fDecomp_->addForceToAtomRow(atom1, fg);
835	+	if (atomListRow.size() > 1) {
836	+	if (info_->usesAtomicVirial()) {
837	+	// find the distance between the atom
838	+	// and the center of the cutoff group:
839	+	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
840	+	stressTensor -= outProduct(dag, fg);
841	+	if (doHeatFlux_)
842	+	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
843	+	}
844	+	}
845	+	}
846	+	for (jb = atomListColumn.begin();
847	+	jb != atomListColumn.end(); ++jb) {
848	+	atom2 = (*jb);
849	+	mf = fDecomp_->getMassFactorColumn(atom2);
850	+	// fg is the force on atom jb due to cutoff group's
851	+	// presence in switching region
852	+	fg = -swderiv * d_grp * mf;
853	+	fDecomp_->addForceToAtomColumn(atom2, fg);
854	+
855	+	if (atomListColumn.size() > 1) {
856	+	if (info_->usesAtomicVirial()) {
857	+	// find the distance between the atom
858	+	// and the center of the cutoff group:
859	+	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
860	+	stressTensor -= outProduct(dag, fg);
861	+	if (doHeatFlux_)
862	+	fDecomp_->addToHeatFlux( dag * dot(fg, vel2));
863	+	}
864	+	}
865	+	}
866	+	}
867	+	//if (!info_->usesAtomicVirial()) {
868	+	//  stressTensor -= outProduct(d_grp, fij);
869	+	//  if (doHeatFlux_)
870	+	//     fDecomp_->addToHeatFlux( d_grp * dot(fij, vel2));
871	+	//}
872	+	}
873	+	}
874	+	}
875	+
876	+	if (iLoop == PREPAIR_LOOP) {
877	+	if (info_->requiresPrepair()) {
878	+
879	+	fDecomp_->collectIntermediateData();
880	+
881	+	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
882	+	fDecomp_->fillSelfData(sdat, atom1);
883	+	interactionMan_->doPreForce(sdat);
884	+	}
885	+
886	+	fDecomp_->distributeIntermediateData();
887	+
888	+	}
889	+	}
890	+	}
891	+
892	+	// collects pairwise information
893	+	fDecomp_->collectData();
894	+
895	+	if (info_->requiresSelfCorrection()) {
896	+	for (unsigned int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
897	+	fDecomp_->fillSelfData(sdat, atom1);
898	+	interactionMan_->doSelfCorrection(sdat);
899	+	}
900	+	}
901	+
902	+	// collects single-atom information
903	+	fDecomp_->collectSelfData();
904	+
905	+	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
906	+	*(fDecomp_->getPairwisePotential());
907	+
908	+	curSnapshot->setLongRangePotential(longRangePotential);
909	+
910	+	curSnapshot->setExcludedPotentials(*(fDecomp_->getExcludedSelfPotential()) +
911	+	*(fDecomp_->getExcludedPotential()));
912	+
913	+	}
914	+
915	+
916		void ForceManager::postCalculation() {
917	+
918	+	vector<Perturbation*>::iterator pi;
919	+	for (pi = perturbations_.begin(); pi != perturbations_.end(); ++pi) {
920	+	(*pi)->applyPerturbation();
921	+	}
922	+
923		SimInfo::MoleculeIterator mi;
924		Molecule* mol;
925		Molecule::RigidBodyIterator rbIter;
926		RigidBody* rb;
927	<
927	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
928	>
929		// collect the atomic forces onto rigid bodies
930	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
931	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
932	<	rb->calcForcesAndTorques();
930	>
931	>	for (mol = info_->beginMolecule(mi); mol != NULL;
932	>	mol = info_->nextMolecule(mi)) {
933	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
934	>	rb = mol->nextRigidBody(rbIter)) {
935	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
936	>	stressTensor += rbTau;
937		}
938		}
939	<
939	>
940	>	#ifdef IS_MPI
941	>	MPI::COMM_WORLD.Allreduce(MPI::IN_PLACE, stressTensor.getArrayPointer(), 9,
942	>	MPI::REALTYPE, MPI::SUM);
943	>	#endif
944	>	curSnapshot->setStressTensor(stressTensor);
945	>
946		}
947	<
264	<	} //end namespace oopse
947	>	} //end namespace OpenMD

Comparing trunk/src/brains/ForceManager.cpp (property svn:keywords):
Revision 665 by tim, Thu Oct 13 22:26:47 2005 UTC vs.
Revision 1788 by gezelter, Wed Aug 29 20:17:07 2012 UTC

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