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

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trunk/src/brains/ForceManager.cpp (file contents), Revision 749 by tim, Wed Nov 16 23:10:02 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1581 by gezelter, Mon Jun 13 22:13:12 2011 UTC

#	Line 6 | Line 6
6		* redistribute this software in source and binary code form, provided
7		* that the following conditions are met:
8		*
9	<	* 1. Acknowledgement of the program authors must be made in any
10	<	*    publication of scientific results based in part on use of the
11	<	*    program.  An acceptable form of acknowledgement is citation of
12	<	*    the article in which the program was described (Matthew
13	<	*    A. Meineke, Charles F. Vardeman II, Teng Lin, Christopher
14	<	*    J. Fennell and J. Daniel Gezelter, "OOPSE: An Object-Oriented
15	<	*    Parallel Simulation Engine for Molecular Dynamics,"
16	<	*    J. Comput. Chem. 26, pp. 252-271 (2005))
17	<	*
18	<	* 2. Redistributions of source code must retain the above copyright
9	>	* 1. Redistributions of source code must retain the above copyright
10		*    notice, this list of conditions and the following disclaimer.
11		*
12	<	* 3. Redistributions in binary form must reproduce the above copyright
12	>	* 2. Redistributions in binary form must reproduce the above copyright
13		*    notice, this list of conditions and the following disclaimer in the
14		*    documentation and/or other materials provided with the
15		*    distribution.
#	Line 37 | Line 28
28		* arising out of the use of or inability to use software, even if the
29		* University of Notre Dame has been advised of the possibility of
30		* such damages.
31	+	*
32	+	* SUPPORT OPEN SCIENCE!  If you use OpenMD or its source code in your
33	+	* research, please cite the appropriate papers when you publish your
34	+	* work.  Good starting points are:
35	+	*
36	+	* [1]  Meineke, et al., J. Comp. Chem. 26, 252-271 (2005).
37	+	* [2]  Fennell & Gezelter, J. Chem. Phys. 124, 234104 (2006).
38	+	* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39	+	* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41
42		/**
#	Line 47 | Line 47
47		* @version 1.0
48		*/
49
50	+
51		#include "brains/ForceManager.hpp"
52		#include "primitives/Molecule.hpp"
53	<	#include "UseTheForce/doForces_interface.h"
53	<	#define __C
54	<	#include "UseTheForce/DarkSide/fInteractionMap.h"
53	>	#define __OPENMD_C
54		#include "utils/simError.h"
55	+	#include "primitives/Bond.hpp"
56		#include "primitives/Bend.hpp"
57	<	#include "primitives/Bend.hpp"
58	<	namespace oopse {
57	>	#include "primitives/Torsion.hpp"
58	>	#include "primitives/Inversion.hpp"
59	>	#include "nonbonded/NonBondedInteraction.hpp"
60	>	#include "parallel/ForceMatrixDecomposition.hpp"
61
62	<	struct BendOrderStruct {
63	<	Bend* bend;
64	<	BendDataSet dataSet;
65	<	};
66	<	struct TorsionOrderStruct {
67	<	Torsion* torsion;
68	<	TorsionDataSet dataSet;
67	<	};
68	<
69	<	bool  BendSortFunctor(const BendOrderStruct& b1, const BendOrderStruct& b2) {
70	<	return b1.dataSet.deltaV < b2.dataSet.deltaV;
62	>	using namespace std;
63	>	namespace OpenMD {
64	>
65	>	ForceManager::ForceManager(SimInfo * info) : info_(info) {
66	>	forceField_ = info_->getForceField();
67	>	interactionMan_ = new InteractionManager();
68	>	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
69		}
70
71	<	bool  TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
72	<	return t1.dataSet.deltaV < t2.dataSet.deltaV;
73	<	}
74	<
75	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
71	>	/**
72	>	* setupCutoffs
73	>	*
74	>	* Sets the values of cutoffRadius, cutoffMethod, and cutoffPolicy
75	>	*
76	>	* cutoffRadius : realType
77	>	*  If the cutoffRadius was explicitly set, use that value.
78	>	*  If the cutoffRadius was not explicitly set:
79	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
80	>	*      No electrostatic atoms?  Poll the atom types present in the
81	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
82	>	*      Use the maximum suggested value that was found.
83	>	*
84	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
85	>	*      If cutoffMethod was explicitly set, use that choice.
86	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
87	>	*
88	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
89	>	*      If cutoffPolicy was explicitly set, use that choice.
90	>	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
91	>	*/
92	>	void ForceManager::setupCutoffs() {
93	>
94	>	Globals* simParams_ = info_->getSimParams();
95	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
96	>
97	>	if (simParams_->haveCutoffRadius()) {
98	>	rCut_ = simParams_->getCutoffRadius();
99	>	} else {
100	>	if (info_->usesElectrostaticAtoms()) {
101	>	sprintf(painCave.errMsg,
102	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
103	>	"\tOpenMD will use a default value of 12.0 angstroms"
104	>	"\tfor the cutoffRadius.\n");
105	>	painCave.isFatal = 0;
106	>	painCave.severity = OPENMD_INFO;
107	>	simError();
108	>	rCut_ = 12.0;
109	>	} else {
110	>	RealType thisCut;
111	>	set<AtomType*>::iterator i;
112	>	set<AtomType*> atomTypes;
113	>	atomTypes = info_->getSimulatedAtomTypes();
114	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
115	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
116	>	rCut_ = max(thisCut, rCut_);
117	>	}
118	>	sprintf(painCave.errMsg,
119	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
120	>	"\tOpenMD will use %lf angstroms.\n",
121	>	rCut_);
122	>	painCave.isFatal = 0;
123	>	painCave.severity = OPENMD_INFO;
124	>	simError();
125	>	}
126	>	fDecomp_->setUserCutoff(rCut_);
127	>	}
128
129	<	if (!info_->isFortranInitialized()) {
130	<	info_->update();
129	>	map<string, CutoffMethod> stringToCutoffMethod;
130	>	stringToCutoffMethod["HARD"] = HARD;
131	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
132	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
133	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
134	>
135	>	if (simParams_->haveCutoffMethod()) {
136	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
137	>	map<string, CutoffMethod>::iterator i;
138	>	i = stringToCutoffMethod.find(cutMeth);
139	>	if (i == stringToCutoffMethod.end()) {
140	>	sprintf(painCave.errMsg,
141	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
142	>	"\tShould be one of: "
143	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
144	>	cutMeth.c_str());
145	>	painCave.isFatal = 1;
146	>	painCave.severity = OPENMD_ERROR;
147	>	simError();
148	>	} else {
149	>	cutoffMethod_ = i->second;
150	>	}
151	>	} else {
152	>	sprintf(painCave.errMsg,
153	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
154	>	"\tOpenMD will use SHIFTED_FORCE.\n");
155	>	painCave.isFatal = 0;
156	>	painCave.severity = OPENMD_INFO;
157	>	simError();
158	>	cutoffMethod_ = SHIFTED_FORCE;
159		}
160
161	<	preCalculation();
162	<
163	<	calcShortRangeInteraction();
161	>	map<string, CutoffPolicy> stringToCutoffPolicy;
162	>	stringToCutoffPolicy["MIX"] = MIX;
163	>	stringToCutoffPolicy["MAX"] = MAX;
164	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
165
166	<	calcLongRangeInteraction(needPotential, needStress);
166	>	std::string cutPolicy;
167	>	if (forceFieldOptions_.haveCutoffPolicy()){
168	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
169	>	}else if (simParams_->haveCutoffPolicy()) {
170	>	cutPolicy = simParams_->getCutoffPolicy();
171	>	}
172
173	<	postCalculation();
173	>	if (!cutPolicy.empty()){
174	>	toUpper(cutPolicy);
175	>	map<string, CutoffPolicy>::iterator i;
176	>	i = stringToCutoffPolicy.find(cutPolicy);
177
178	<	std::vector<BendOrderStruct> bendOrderStruct;
179	<	for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
180	<	BendOrderStruct tmp;
181	<	tmp.bend= const_cast<Bend*>(i->first);
182	<	tmp.dataSet = i->second;
183	<	bendOrderStruct.push_back(tmp);
178	>	if (i == stringToCutoffPolicy.end()) {
179	>	sprintf(painCave.errMsg,
180	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
181	>	"\tShould be one of: "
182	>	"MIX, MAX, or TRADITIONAL\n",
183	>	cutPolicy.c_str());
184	>	painCave.isFatal = 1;
185	>	painCave.severity = OPENMD_ERROR;
186	>	simError();
187	>	} else {
188	>	cutoffPolicy_ = i->second;
189	>	}
190	>	} else {
191	>	sprintf(painCave.errMsg,
192	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
193	>	"\tOpenMD will use TRADITIONAL.\n");
194	>	painCave.isFatal = 0;
195	>	painCave.severity = OPENMD_INFO;
196	>	simError();
197	>	cutoffPolicy_ = TRADITIONAL;
198		}
199	+	fDecomp_->setCutoffPolicy(cutoffPolicy_);
200	+	}
201
202	<	std::vector<TorsionOrderStruct> torsionOrderStruct;
203	<	for(std::map<Torsion*, TorsionDataSet>::iterator j = torsionDataSets.begin(); j != torsionDataSets.end(); ++j) {
204	<	TorsionOrderStruct tmp;
205	<	tmp.torsion = const_cast<Torsion*>(j->first);
206	<	tmp.dataSet = j->second;
207	<	torsionOrderStruct.push_back(tmp);
208	<	}
209	<
210	<	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
211	<	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
212	<	std::cout << "bend" << std::endl;
213	<	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
214	<	Bend* bend = k->bend;
215	<	std::cout << "atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
216	<	std::cout << "deltaV=" << k->dataSet.deltaV << ",p_theta=" << k->dataSet.prev.angle <<",p_pot=" << k->dataSet.prev.potential<< ",c_theta=" << k->dataSet.curr.angle << ", c_pot = " << k->dataSet.curr.potential <<std::endl;
202	>	/**
203	>	* setupSwitching
204	>	*
205	>	* Sets the values of switchingRadius and
206	>	*  If the switchingRadius was explicitly set, use that value (but check it)
207	>	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
208	>	*/
209	>	void ForceManager::setupSwitching() {
210	>	Globals* simParams_ = info_->getSimParams();
211	>
212	>	// create the switching function object:
213	>	switcher_ = new SwitchingFunction();
214	>
215	>	if (simParams_->haveSwitchingRadius()) {
216	>	rSwitch_ = simParams_->getSwitchingRadius();
217	>	if (rSwitch_ > rCut_) {
218	>	sprintf(painCave.errMsg,
219	>	"ForceManager::setupSwitching: switchingRadius (%f) is larger "
220	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
221	>	painCave.isFatal = 1;
222	>	painCave.severity = OPENMD_ERROR;
223	>	simError();
224	>	}
225	>	} else {
226	>	rSwitch_ = 0.85 * rCut_;
227	>	sprintf(painCave.errMsg,
228	>	"ForceManager::setupSwitching: No value was set for the switchingRadius.\n"
229	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
230	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
231	>	painCave.isFatal = 0;
232	>	painCave.severity = OPENMD_WARNING;
233	>	simError();
234	>	}
235	>
236	>	// Default to cubic switching function.
237	>	sft_ = cubic;
238	>	if (simParams_->haveSwitchingFunctionType()) {
239	>	string funcType = simParams_->getSwitchingFunctionType();
240	>	toUpper(funcType);
241	>	if (funcType == "CUBIC") {
242	>	sft_ = cubic;
243	>	} else {
244	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
245	>	sft_ = fifth_order_poly;
246	>	} else {
247	>	// throw error
248	>	sprintf( painCave.errMsg,
249	>	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
250	>	"\tswitchingFunctionType must be one of: "
251	>	"\"cubic\" or \"fifth_order_polynomial\".",
252	>	funcType.c_str() );
253	>	painCave.isFatal = 1;
254	>	painCave.severity = OPENMD_ERROR;
255	>	simError();
256	>	}
257	>	}
258		}
259	<	std::cout << "torsio" << std::endl;
260	<	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
261	<	Torsion* torsion = l->torsion;
262	<	std::cout << "atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
263	<	std::cout << "deltaV=" << l->dataSet.deltaV << ",p_theta=" << l->dataSet.prev.angle <<",p_pot=" << l->dataSet.prev.potential<< ",c_theta=" << l->dataSet.curr.angle << ", c_pot = " << l->dataSet.curr.potential <<std::endl;
259	>	switcher_->setSwitchType(sft_);
260	>	switcher_->setSwitch(rSwitch_, rCut_);
261	>	}
262	>
263	>	void ForceManager::initialize() {
264	>
265	>	if (!info_->isTopologyDone()) {
266	>	info_->update();
267	>	interactionMan_->setSimInfo(info_);
268	>	interactionMan_->initialize();
269	>
270	>	// We want to delay the cutoffs until after the interaction
271	>	// manager has set up the atom-atom interactions so that we can
272	>	// query them for suggested cutoff values
273	>
274	>	setupCutoffs();
275	>	setupSwitching();
276	>
277	>	info_->prepareTopology();
278		}
279	+
280	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
281
282	+	// Force fields can set options on how to scale van der Waals and electrostatic
283	+	// interactions for atoms connected via bonds, bends and torsions
284	+	// in this case the topological distance between atoms is:
285	+	// 0 = topologically unconnected
286	+	// 1 = bonded together
287	+	// 2 = connected via a bend
288	+	// 3 = connected via a torsion
289	+
290	+	vdwScale_.reserve(4);
291	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
292	+
293	+	electrostaticScale_.reserve(4);
294	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
295	+
296	+	vdwScale_[0] = 1.0;
297	+	vdwScale_[1] = fopts.getvdw12scale();
298	+	vdwScale_[2] = fopts.getvdw13scale();
299	+	vdwScale_[3] = fopts.getvdw14scale();
300	+
301	+	electrostaticScale_[0] = 1.0;
302	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
303	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
304	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
305	+
306	+	fDecomp_->distributeInitialData();
307	+
308	+	initialized_ = true;
309	+
310		}
311
312	+	void ForceManager::calcForces() {
313	+
314	+	if (!initialized_) initialize();
315	+
316	+	preCalculation();
317	+	shortRangeInteractions();
318	+	longRangeInteractions();
319	+	postCalculation();
320	+	}
321	+
322		void ForceManager::preCalculation() {
323		SimInfo::MoleculeIterator mi;
324		Molecule* mol;
#	Line 128 | Line 326 | namespace oopse {
326		Atom* atom;
327		Molecule::RigidBodyIterator rbIter;
328		RigidBody* rb;
329	+	Molecule::CutoffGroupIterator ci;
330	+	CutoffGroup* cg;
331
332		// forces are zeroed here, before any are accumulated.
333	<	// NOTE: do not rezero the forces in Fortran.
334	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
333	>
334	>	for (mol = info_->beginMolecule(mi); mol != NULL;
335	>	mol = info_->nextMolecule(mi)) {
336		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
337		atom->zeroForcesAndTorques();
338		}
339	<
339	>
340		//change the positions of atoms which belong to the rigidbodies
341	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
341	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
342	>	rb = mol->nextRigidBody(rbIter)) {
343		rb->zeroForcesAndTorques();
344		}
345	+
346	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
347	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
348	+	cg = mol->nextCutoffGroup(ci)) {
349	+	//calculate the center of mass of cutoff group
350	+	cg->updateCOM();
351	+	}
352	+	}
353		}
354	+
355	+	// Zero out the stress tensor
356	+	tau *= 0.0;
357
358		}
359	<
360	<	void ForceManager::calcShortRangeInteraction() {
359	>
360	>	void ForceManager::shortRangeInteractions() {
361		Molecule* mol;
362		RigidBody* rb;
363		Bond* bond;
364		Bend* bend;
365		Torsion* torsion;
366	+	Inversion* inversion;
367		SimInfo::MoleculeIterator mi;
368		Molecule::RigidBodyIterator rbIter;
369		Molecule::BondIterator bondIter;;
370		Molecule::BendIterator  bendIter;
371		Molecule::TorsionIterator  torsionIter;
372	<	double bondPotential = 0.0;
373	<	double bendPotential = 0.0;
374	<	double torsionPotential = 0.0;
372	>	Molecule::InversionIterator  inversionIter;
373	>	RealType bondPotential = 0.0;
374	>	RealType bendPotential = 0.0;
375	>	RealType torsionPotential = 0.0;
376	>	RealType inversionPotential = 0.0;
377
378		//calculate short range interactions
379	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
379	>	for (mol = info_->beginMolecule(mi); mol != NULL;
380	>	mol = info_->nextMolecule(mi)) {
381
382		//change the positions of atoms which belong to the rigidbodies
383	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
384	<	rb->updateAtoms();
383	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
384	>	rb = mol->nextRigidBody(rbIter)) {
385	>	rb->updateAtoms();
386		}
387
388	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
388	>	for (bond = mol->beginBond(bondIter); bond != NULL;
389	>	bond = mol->nextBond(bondIter)) {
390		bond->calcForce();
391		bondPotential += bond->getPotential();
392		}
393
394	<	//int i =0;
395	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
396	<	//std::cout << i++ << "\t";
397	<	double angle;
398	<	bend->calcForce(angle);
399	<	double currBendPot = bend->getPotential();
400	<	bendPotential += bend->getPotential();
401	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
402	<	if (i == bendDataSets.end()) {
403	<	BendDataSet dataSet;
404	<	dataSet.prev.angle = dataSet.curr.angle = angle;
405	<	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
406	<	dataSet.deltaV = 0.0;
407	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
408	<	}else {
409	<	i->second.prev.angle = i->second.curr.angle;
410	<	i->second.prev.potential = i->second.curr.potential;
411	<	i->second.curr.angle = angle;
412	<	i->second.curr.potential = currBendPot;
413	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
414	<	}
394	>	for (bend = mol->beginBend(bendIter); bend != NULL;
395	>	bend = mol->nextBend(bendIter)) {
396	>
397	>	RealType angle;
398	>	bend->calcForce(angle);
399	>	RealType currBendPot = bend->getPotential();
400	>
401	>	bendPotential += bend->getPotential();
402	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
403	>	if (i == bendDataSets.end()) {
404	>	BendDataSet dataSet;
405	>	dataSet.prev.angle = dataSet.curr.angle = angle;
406	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
407	>	dataSet.deltaV = 0.0;
408	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
409	>	}else {
410	>	i->second.prev.angle = i->second.curr.angle;
411	>	i->second.prev.potential = i->second.curr.potential;
412	>	i->second.curr.angle = angle;
413	>	i->second.curr.potential = currBendPot;
414	>	i->second.deltaV =  fabs(i->second.curr.potential -
415	>	i->second.prev.potential);
416	>	}
417		}
418	<
419	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
420	<	double angle;
421	<	torsion->calcForce(angle);
422	<	double currTorsionPot = torsion->getPotential();
423	<	torsionPotential += torsion->getPotential();
424	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
425	<	if (i == torsionDataSets.end()) {
426	<	TorsionDataSet dataSet;
427	<	dataSet.prev.angle = dataSet.curr.angle = angle;
428	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
429	<	dataSet.deltaV = 0.0;
430	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
431	<	}else {
432	<	i->second.prev.angle = i->second.curr.angle;
433	<	i->second.prev.potential = i->second.curr.potential;
434	<	i->second.curr.angle = angle;
435	<	i->second.curr.potential = currTorsionPot;
436	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
437	<	}
438	<	}
439	<
418	>
419	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
420	>	torsion = mol->nextTorsion(torsionIter)) {
421	>	RealType angle;
422	>	torsion->calcForce(angle);
423	>	RealType currTorsionPot = torsion->getPotential();
424	>	torsionPotential += torsion->getPotential();
425	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
426	>	if (i == torsionDataSets.end()) {
427	>	TorsionDataSet dataSet;
428	>	dataSet.prev.angle = dataSet.curr.angle = angle;
429	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
430	>	dataSet.deltaV = 0.0;
431	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
432	>	}else {
433	>	i->second.prev.angle = i->second.curr.angle;
434	>	i->second.prev.potential = i->second.curr.potential;
435	>	i->second.curr.angle = angle;
436	>	i->second.curr.potential = currTorsionPot;
437	>	i->second.deltaV =  fabs(i->second.curr.potential -
438	>	i->second.prev.potential);
439	>	}
440	>	}
441	>
442	>	for (inversion = mol->beginInversion(inversionIter);
443	>	inversion != NULL;
444	>	inversion = mol->nextInversion(inversionIter)) {
445	>	RealType angle;
446	>	inversion->calcForce(angle);
447	>	RealType currInversionPot = inversion->getPotential();
448	>	inversionPotential += inversion->getPotential();
449	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
450	>	if (i == inversionDataSets.end()) {
451	>	InversionDataSet dataSet;
452	>	dataSet.prev.angle = dataSet.curr.angle = angle;
453	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
454	>	dataSet.deltaV = 0.0;
455	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
456	>	}else {
457	>	i->second.prev.angle = i->second.curr.angle;
458	>	i->second.prev.potential = i->second.curr.potential;
459	>	i->second.curr.angle = angle;
460	>	i->second.curr.potential = currInversionPot;
461	>	i->second.deltaV =  fabs(i->second.curr.potential -
462	>	i->second.prev.potential);
463	>	}
464	>	}
465		}
466
467	<	double  shortRangePotential = bondPotential + bendPotential + torsionPotential;
467	>	RealType  shortRangePotential = bondPotential + bendPotential +
468	>	torsionPotential +  inversionPotential;
469		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
470		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
471		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
472		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
473		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
474	<
474	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
475		}
476	+
477	+	void ForceManager::longRangeInteractions() {
478
479	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
480	<	Snapshot* curSnapshot;
481	<	DataStorage* config;
233	<	double* frc;
234	<	double* pos;
235	<	double* trq;
236	<	double* A;
237	<	double* electroFrame;
238	<	double* rc;
239	<
240	<	//get current snapshot from SimInfo
241	<	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
479	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
480	>	DataStorage* config = &(curSnapshot->atomData);
481	>	DataStorage* cgConfig = &(curSnapshot->cgData);
482
243	–	//get array pointers
244	–	config = &(curSnapshot->atomData);
245	–	frc = config->getArrayPointer(DataStorage::dslForce);
246	–	pos = config->getArrayPointer(DataStorage::dslPosition);
247	–	trq = config->getArrayPointer(DataStorage::dslTorque);
248	–	A   = config->getArrayPointer(DataStorage::dslAmat);
249	–	electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
250	–
483		//calculate the center of mass of cutoff group
484	+
485		SimInfo::MoleculeIterator mi;
486		Molecule* mol;
487		Molecule::CutoffGroupIterator ci;
488		CutoffGroup* cg;
256	–	Vector3d com;
257	–	std::vector<Vector3d> rcGroup;
489
490	<	if(info_->getNCutoffGroups() > 0){
491	<
492	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
493	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
494	<	cg->getCOM(com);
495	<	rcGroup.push_back(com);
490	>	if(info_->getNCutoffGroups() > 0){
491	>	for (mol = info_->beginMolecule(mi); mol != NULL;
492	>	mol = info_->nextMolecule(mi)) {
493	>	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
494	>	cg = mol->nextCutoffGroup(ci)) {
495	>	cg->updateCOM();
496		}
497	<	}// end for (mol)
267	<
268	<	rc = rcGroup[0].getArrayPointer();
497	>	}
498		} else {
499	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
500	<	rc = pos;
499	>	// center of mass of the group is the same as position of the atom
500	>	// if cutoff group does not exist
501	>	cgConfig->position = config->position;
502		}
503	<
504	<	//initialize data before passing to fortran
505	<	double longRangePotential[LR_POT_TYPES];
276	<	double lrPot = 0.0;
503	>
504	>	fDecomp_->zeroWorkArrays();
505	>	fDecomp_->distributeData();
506
507	<	Mat3x3d tau;
508	<	short int passedCalcPot = needPotential;
509	<	short int passedCalcStress = needStress;
510	<	int isError = 0;
507	>	int cg1, cg2, atom1, atom2, topoDist;
508	>	Vector3d d_grp, dag, d;
509	>	RealType rgrpsq, rgrp, r2, r;
510	>	RealType electroMult, vdwMult;
511	>	RealType vij;
512	>	Vector3d fij, fg, f1;
513	>	tuple3<RealType, RealType, RealType> cuts;
514	>	RealType rCutSq;
515	>	bool in_switching_region;
516	>	RealType sw, dswdr, swderiv;
517	>	vector<int> atomListColumn, atomListRow, atomListLocal;
518	>	InteractionData idat;
519	>	SelfData sdat;
520	>	RealType mf;
521	>	potVec pot(0.0);
522	>	potVec longRangePotential(0.0);
523	>	RealType lrPot;
524	>	RealType vpair;
525
526	<	for (int i=0; i<LR_POT_TYPES;i++){
527	<	longRangePotential[i]=0.0; //Initialize array
526	>	int loopStart, loopEnd;
527	>
528	>	idat.vdwMult = &vdwMult;
529	>	idat.electroMult = &electroMult;
530	>	idat.pot = &pot;
531	>	idat.vpair = &vpair;
532	>	idat.f1 = &f1;
533	>	idat.sw = &sw;
534	>
535	>	loopEnd = PAIR_LOOP;
536	>	if (info_->requiresPrepair() ) {
537	>	loopStart = PREPAIR_LOOP;
538	>	} else {
539	>	loopStart = PAIR_LOOP;
540		}
541	+
542	+	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
543	+
544	+	if (iLoop == loopStart) {
545	+	bool update_nlist = fDecomp_->checkNeighborList();
546	+	if (update_nlist)
547	+	neighborList = fDecomp_->buildNeighborList();
548	+	}
549	+
550	+	for (vector<pair<int, int> >::iterator it = neighborList.begin();
551	+	it != neighborList.end(); ++it) {
552	+
553	+	cg1 = (*it).first;
554	+	cg2 = (*it).second;
555	+
556	+	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
557
558	<	doForceLoop( pos,
559	<	rc,
560	<	A,
290	<	electroFrame,
291	<	frc,
292	<	trq,
293	<	tau.getArrayPointer(),
294	<	longRangePotential,
295	<	&passedCalcPot,
296	<	&passedCalcStress,
297	<	&isError );
558	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
559	>	curSnapshot->wrapVector(d_grp);
560	>	rgrpsq = d_grp.lengthSquare();
561
562	<	if( isError ){
563	<	sprintf( painCave.errMsg,
564	<	"Error returned from the fortran force calculation.\n" );
565	<	painCave.isFatal = 1;
566	<	simError();
562	>	rCutSq = cuts.second;
563	>
564	>	if (rgrpsq < rCutSq) {
565	>	idat.rcut = &cuts.first;
566	>	if (iLoop == PAIR_LOOP) {
567	>	vij *= 0.0;
568	>	fij = V3Zero;
569	>	}
570	>
571	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
572	>	rgrp);
573	>
574	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
575	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
576	>
577	>	for (vector<int>::iterator ia = atomListRow.begin();
578	>	ia != atomListRow.end(); ++ia) {
579	>	atom1 = (*ia);
580	>
581	>	for (vector<int>::iterator jb = atomListColumn.begin();
582	>	jb != atomListColumn.end(); ++jb) {
583	>	atom2 = (*jb);
584	>
585	>	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
586	>
587	>	vpair = 0.0;
588	>	f1 = V3Zero;
589	>
590	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
591	>
592	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
593	>	vdwMult = vdwScale_[topoDist];
594	>	electroMult = electrostaticScale_[topoDist];
595	>
596	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
597	>	idat.d = &d_grp;
598	>	idat.r2 = &rgrpsq;
599	>	} else {
600	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
601	>	curSnapshot->wrapVector( d );
602	>	r2 = d.lengthSquare();
603	>	idat.d = &d;
604	>	idat.r2 = &r2;
605	>	}
606	>
607	>	r = sqrt( *(idat.r2) );
608	>	idat.rij = &r;
609	>
610	>	if (iLoop == PREPAIR_LOOP) {
611	>	interactionMan_->doPrePair(idat);
612	>	} else {
613	>	interactionMan_->doPair(idat);
614	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
615	>	vij += vpair;
616	>	fij += f1;
617	>	tau -= outProduct( *(idat.d), f1);
618	>	}
619	>	}
620	>	}
621	>	}
622	>
623	>	if (iLoop == PAIR_LOOP) {
624	>	if (in_switching_region) {
625	>	swderiv = vij * dswdr / rgrp;
626	>	fg = swderiv * d_grp;
627	>
628	>	fij += fg;
629	>
630	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
631	>	tau -= outProduct( *(idat.d), fg);
632	>	}
633	>
634	>	for (vector<int>::iterator ia = atomListRow.begin();
635	>	ia != atomListRow.end(); ++ia) {
636	>	atom1 = (*ia);
637	>	mf = fDecomp_->getMassFactorRow(atom1);
638	>	// fg is the force on atom ia due to cutoff group's
639	>	// presence in switching region
640	>	fg = swderiv * d_grp * mf;
641	>	fDecomp_->addForceToAtomRow(atom1, fg);
642	>
643	>	if (atomListRow.size() > 1) {
644	>	if (info_->usesAtomicVirial()) {
645	>	// find the distance between the atom
646	>	// and the center of the cutoff group:
647	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
648	>	tau -= outProduct(dag, fg);
649	>	}
650	>	}
651	>	}
652	>	for (vector<int>::iterator jb = atomListColumn.begin();
653	>	jb != atomListColumn.end(); ++jb) {
654	>	atom2 = (*jb);
655	>	mf = fDecomp_->getMassFactorColumn(atom2);
656	>	// fg is the force on atom jb due to cutoff group's
657	>	// presence in switching region
658	>	fg = -swderiv * d_grp * mf;
659	>	fDecomp_->addForceToAtomColumn(atom2, fg);
660	>
661	>	if (atomListColumn.size() > 1) {
662	>	if (info_->usesAtomicVirial()) {
663	>	// find the distance between the atom
664	>	// and the center of the cutoff group:
665	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
666	>	tau -= outProduct(dag, fg);
667	>	}
668	>	}
669	>	}
670	>	}
671	>	//if (!SIM_uses_AtomicVirial) {
672	>	//  tau -= outProduct(d_grp, fij);
673	>	//}
674	>	}
675	>	}
676	>	}
677	>
678	>	if (iLoop == PREPAIR_LOOP) {
679	>	if (info_->requiresPrepair()) {
680	>	fDecomp_->collectIntermediateData();
681	>
682	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
683	>	fDecomp_->fillSelfData(sdat, atom1);
684	>	interactionMan_->doPreForce(sdat);
685	>	}
686	>
687	>	fDecomp_->distributeIntermediateData();
688	>	}
689	>	}
690	>
691		}
692	<	for (int i=0; i<LR_POT_TYPES;i++){
693	<	lrPot += longRangePotential[i]; //Quick hack
692	>
693	>	fDecomp_->collectData();
694	>
695	>	if ( info_->requiresSkipCorrection() ) {
696	>
697	>	for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
698	>
699	>	vector<int> skipList = fDecomp_->getSkipsForAtom( atom1 );
700	>
701	>	for (vector<int>::iterator jb = skipList.begin();
702	>	jb != skipList.end(); ++jb) {
703	>
704	>	atom2 = (*jb);
705	>	fDecomp_->fillSkipData(idat, atom1, atom2);
706	>	interactionMan_->doSkipCorrection(idat);
707	>
708	>	}
709	>	}
710		}
711	+
712	+	if (info_->requiresSelfCorrection()) {
713
714	+	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
715	+	fDecomp_->fillSelfData(sdat, atom1);
716	+	interactionMan_->doSelfCorrection(sdat);
717	+	}
718	+
719	+	}
720	+
721	+	longRangePotential = fDecomp_->getLongRangePotential();
722	+	lrPot = longRangePotential.sum();
723	+
724		//store the tau and long range potential
725		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
726	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
727	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
313	<
314	<	curSnapshot->statData.setTau(tau);
726	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
727	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
728		}
729
730	<
730	>
731		void ForceManager::postCalculation() {
732		SimInfo::MoleculeIterator mi;
733		Molecule* mol;
734		Molecule::RigidBodyIterator rbIter;
735		RigidBody* rb;
736	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
737
738		// collect the atomic forces onto rigid bodies
739	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
740	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
741	<	rb->calcForcesAndTorques();
739	>
740	>	for (mol = info_->beginMolecule(mi); mol != NULL;
741	>	mol = info_->nextMolecule(mi)) {
742	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
743	>	rb = mol->nextRigidBody(rbIter)) {
744	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
745	>	tau += rbTau;
746		}
747		}
748	<
748	>
749	>	#ifdef IS_MPI
750	>	Mat3x3d tmpTau(tau);
751	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
752	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
753	>	#endif
754	>	curSnapshot->statData.setTau(tau);
755		}
756
757	<	} //end namespace oopse
757	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 749 by tim, Wed Nov 16 23:10:02 2005 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1581 by gezelter, Mon Jun 13 22:13:12 2011 UTC

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