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

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trunk/src/brains/ForceManager.cpp (file contents), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1579 by gezelter, Thu Jun 9 20:26:29 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	<	/*
63	<	struct BendOrderStruct {
64	<	Bend* bend;
65	<	BendDataSet dataSet;
66	<	};
67	<	struct TorsionOrderStruct {
68	<	Torsion* torsion;
67	<	TorsionDataSet dataSet;
68	<	};
69	<
70	<	bool  BendSortFunctor(const BendOrderStruct& b1, const BendOrderStruct& b2) {
71	<	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	<	/*
179	<	std::vector<BendOrderStruct> bendOrderStruct;
180	<	for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
181	<	BendOrderStruct tmp;
182	<	tmp.bend= const_cast<Bend*>(i->first);
183	<	tmp.dataSet = i->second;
184	<	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	<	}
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	<	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
216	<	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
217	<	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
218	<	Bend* bend = k->bend;
219	<	std::cout << "Bend: atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
220	<	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;
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	<	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
260	<	Torsion* torsion = l->torsion;
261	<	std::cout << "Torsion: atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
262	<	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	<	*/
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	+	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	<
395	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
396	<
178	<	RealType angle;
179	<	bend->calcForce(angle);
180	<	RealType currBendPot = bend->getPotential();
181	<	bendPotential += bend->getPotential();
182	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
183	<	if (i == bendDataSets.end()) {
184	<	BendDataSet dataSet;
185	<	dataSet.prev.angle = dataSet.curr.angle = angle;
186	<	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
187	<	dataSet.deltaV = 0.0;
188	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
189	<	}else {
190	<	i->second.prev.angle = i->second.curr.angle;
191	<	i->second.prev.potential = i->second.curr.potential;
192	<	i->second.curr.angle = angle;
193	<	i->second.curr.potential = currBendPot;
194	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
195	<	}
196	<	}
197	<
198	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
394	>	for (bend = mol->beginBend(bendIter); bend != NULL;
395	>	bend = mol->nextBend(bendIter)) {
396	>
397		RealType angle;
398	<	torsion->calcForce(angle);
399	<	RealType currTorsionPot = torsion->getPotential();
400	<	torsionPotential += torsion->getPotential();
401	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
402	<	if (i == torsionDataSets.end()) {
403	<	TorsionDataSet dataSet;
404	<	dataSet.prev.angle = dataSet.curr.angle = angle;
405	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
406	<	dataSet.deltaV = 0.0;
407	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, 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 = currTorsionPot;
413	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
414	<	}
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	<
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	<	RealType  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	+	// some of this initial stuff will go away:
479	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
480	+	DataStorage* config = &(curSnapshot->atomData);
481	+	DataStorage* cgConfig = &(curSnapshot->cgData);
482	+	RealType* frc = config->getArrayPointer(DataStorage::dslForce);
483	+	RealType* pos = config->getArrayPointer(DataStorage::dslPosition);
484	+	RealType* trq = config->getArrayPointer(DataStorage::dslTorque);
485	+	RealType* A = config->getArrayPointer(DataStorage::dslAmat);
486	+	RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
487	+	RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
488
489	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
231	<	Snapshot* curSnapshot;
232	<	DataStorage* config;
233	<	RealType* frc;
234	<	RealType* pos;
235	<	RealType* trq;
236	<	RealType* A;
237	<	RealType* electroFrame;
238	<	RealType* rc;
489	>	// new stuff starts here:
490
491	<	//get current snapshot from SimInfo
492	<	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
491	>	fDecomp_->zeroWorkArrays();
492	>	fDecomp_->distributeData();
493	>
494	>	int cg1, cg2, atom1, atom2, topoDist;
495	>	Vector3d d_grp, dag, d;
496	>	RealType rgrpsq, rgrp, r2, r;
497	>	RealType electroMult, vdwMult;
498	>	RealType vij;
499	>	Vector3d fij, fg;
500	>	tuple3<RealType, RealType, RealType> cuts;
501	>	RealType rCutSq;
502	>	bool in_switching_region;
503	>	RealType sw, dswdr, swderiv;
504	>	vector<int> atomListColumn, atomListRow, atomListLocal;
505	>	InteractionData idat;
506	>	SelfData sdat;
507	>	RealType mf;
508	>	potVec pot(0.0);
509	>	potVec longRangePotential(0.0);
510	>	RealType lrPot;
511	>	RealType vpair;
512
513	<	//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);
513	>	int loopStart, loopEnd;
514
515	<	//calculate the center of mass of cutoff group
516	<	SimInfo::MoleculeIterator mi;
517	<	Molecule* mol;
518	<	Molecule::CutoffGroupIterator ci;
519	<	CutoffGroup* cg;
520	<	Vector3d com;
521	<	std::vector<Vector3d> rcGroup;
515	>	loopEnd = PAIR_LOOP;
516	>	if (info_->requiresPrepair() ) {
517	>	loopStart = PREPAIR_LOOP;
518	>	} else {
519	>	loopStart = PAIR_LOOP;
520	>	}
521	>
522
523	<	if(info_->getNCutoffGroups() > 0){
524	<
525	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
526	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
527	<	cg->getCOM(com);
528	<	rcGroup.push_back(com);
523	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
524	>
525	>	if (iLoop == loopStart) {
526	>	bool update_nlist = fDecomp_->checkNeighborList();
527	>	if (update_nlist)
528	>	neighborList = fDecomp_->buildNeighborList();
529	>	}
530	>
531	>	for (vector<pair<int, int> >::iterator it = neighborList.begin();
532	>	it != neighborList.end(); ++it) {
533	>
534	>	cg1 = (*it).first;
535	>	cg2 = (*it).second;
536	>
537	>	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
538	>
539	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
540	>	curSnapshot->wrapVector(d_grp);
541	>	rgrpsq = d_grp.lengthSquare();
542	>
543	>	rCutSq = cuts.second;
544	>
545	>	if (rgrpsq < rCutSq) {
546	>	idat.rcut = &cuts.first;
547	>	if (iLoop == PAIR_LOOP) {
548	>	vij *= 0.0;
549	>	fij = V3Zero;
550	>	}
551	>
552	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
553	>	rgrp);
554	>
555	>	idat.sw = &sw;
556	>
557	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
558	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
559	>
560	>	for (vector<int>::iterator ia = atomListRow.begin();
561	>	ia != atomListRow.end(); ++ia) {
562	>	atom1 = (*ia);
563	>
564	>	for (vector<int>::iterator jb = atomListColumn.begin();
565	>	jb != atomListColumn.end(); ++jb) {
566	>	atom2 = (*jb);
567	>
568	>	cerr << "doing atoms " << atom1 << " " << atom2 << "\n";
569	>	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
570	>
571	>	vpair = 0.0;
572	>
573	>	cerr << "filling idat atoms " << atom1 << " " << atom2 << "\n";
574	>	idat = fDecomp_->fillInteractionData(atom1, atom2);
575	>	cerr << "done with idat\n";
576	>
577	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
578	>	vdwMult = vdwScale_[topoDist];
579	>	electroMult = electrostaticScale_[topoDist];
580	>
581	>	idat.vdwMult = &vdwMult;
582	>	idat.electroMult = &electroMult;
583	>	idat.pot = &pot;
584	>	idat.vpair = &vpair;
585	>
586	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
587	>	idat.d = &d_grp;
588	>	idat.r2 = &rgrpsq;
589	>	} else {
590	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
591	>	curSnapshot->wrapVector( d );
592	>	r2 = d.lengthSquare();
593	>	idat.d = &d;
594	>	idat.r2 = &r2;
595	>	}
596	>
597	>	cerr << "d = " << d << "\n";
598	>	cerr << "r2 = " << r2 << "\n";
599	>	r = sqrt( r2 );
600	>	idat.rij = &r;
601	>
602	>	if (iLoop == PREPAIR_LOOP) {
603	>	interactionMan_->doPrePair(idat);
604	>	} else {
605	>	cerr << "doing doPair " << atom1 << " " << atom2 << " " << r << "\n";
606	>	interactionMan_->doPair(idat);
607	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
608	>	vij += *(idat.vpair);
609	>	fij += *(idat.f1);
610	>	tau -= outProduct( *(idat.d), *(idat.f1));
611	>	}
612	>	}
613	>	}
614	>	}
615	>
616	>	if (iLoop == PAIR_LOOP) {
617	>	if (in_switching_region) {
618	>	swderiv = vij * dswdr / rgrp;
619	>	fg = swderiv * d_grp;
620	>
621	>	fij += fg;
622	>
623	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
624	>	tau -= outProduct( *(idat.d), fg);
625	>	}
626	>
627	>	for (vector<int>::iterator ia = atomListRow.begin();
628	>	ia != atomListRow.end(); ++ia) {
629	>	atom1 = (*ia);
630	>	mf = fDecomp_->getMassFactorRow(atom1);
631	>	// fg is the force on atom ia due to cutoff group's
632	>	// presence in switching region
633	>	fg = swderiv * d_grp * mf;
634	>	fDecomp_->addForceToAtomRow(atom1, fg);
635	>
636	>	if (atomListRow.size() > 1) {
637	>	if (info_->usesAtomicVirial()) {
638	>	// find the distance between the atom
639	>	// and the center of the cutoff group:
640	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
641	>	tau -= outProduct(dag, fg);
642	>	}
643	>	}
644	>	}
645	>	for (vector<int>::iterator jb = atomListColumn.begin();
646	>	jb != atomListColumn.end(); ++jb) {
647	>	atom2 = (*jb);
648	>	mf = fDecomp_->getMassFactorColumn(atom2);
649	>	// fg is the force on atom jb due to cutoff group's
650	>	// presence in switching region
651	>	fg = -swderiv * d_grp * mf;
652	>	fDecomp_->addForceToAtomColumn(atom2, fg);
653	>
654	>	if (atomListColumn.size() > 1) {
655	>	if (info_->usesAtomicVirial()) {
656	>	// find the distance between the atom
657	>	// and the center of the cutoff group:
658	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
659	>	tau -= outProduct(dag, fg);
660	>	}
661	>	}
662	>	}
663	>	}
664	>	//if (!SIM_uses_AtomicVirial) {
665	>	//  tau -= outProduct(d_grp, fij);
666	>	//}
667	>	}
668		}
669	<	}// end for (mol)
670	<
671	<	rc = rcGroup[0].getArrayPointer();
672	<	} else {
673	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
674	<	rc = pos;
669	>	}
670	>
671	>	if (iLoop == PREPAIR_LOOP) {
672	>	if (info_->requiresPrepair()) {
673	>	fDecomp_->collectIntermediateData();
674	>
675	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
676	>	sdat = fDecomp_->fillSelfData(atom1);
677	>	interactionMan_->doPreForce(sdat);
678	>	}
679	>
680	>	fDecomp_->distributeIntermediateData();
681	>	}
682	>	}
683	>
684		}
273	–
274	–	//initialize data before passing to fortran
275	–	RealType longRangePotential[LR_POT_TYPES];
276	–	RealType lrPot = 0.0;
685
686	<	Mat3x3d tau;
687	<	short int passedCalcPot = needPotential;
688	<	short int passedCalcStress = needStress;
689	<	int isError = 0;
686	>	fDecomp_->collectData();
687	>
688	>	if ( info_->requiresSkipCorrection() ) {
689	>
690	>	for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
691
692	<	for (int i=0; i<LR_POT_TYPES;i++){
693	<	longRangePotential[i]=0.0; //Initialize array
692	>	vector<int> skipList = fDecomp_->getSkipsForAtom( atom1 );
693	>
694	>	for (vector<int>::iterator jb = skipList.begin();
695	>	jb != skipList.end(); ++jb) {
696	>
697	>	atom2 = (*jb);
698	>	idat = fDecomp_->fillSkipData(atom1, atom2);
699	>	interactionMan_->doSkipCorrection(idat);
700	>
701	>	}
702	>	}
703		}
704	+
705	+	if (info_->requiresSelfCorrection()) {
706
707	<	doForceLoop( pos,
708	<	rc,
709	<	A,
710	<	electroFrame,
291	<	frc,
292	<	trq,
293	<	tau.getArrayPointer(),
294	<	longRangePotential,
295	<	&passedCalcPot,
296	<	&passedCalcStress,
297	<	&isError );
707	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
708	>	sdat = fDecomp_->fillSelfData(atom1);
709	>	interactionMan_->doSelfCorrection(sdat);
710	>	}
711
299	–	if( isError ){
300	–	sprintf( painCave.errMsg,
301	–	"Error returned from the fortran force calculation.\n" );
302	–	painCave.isFatal = 1;
303	–	simError();
712		}
305	–	for (int i=0; i<LR_POT_TYPES;i++){
306	–	lrPot += longRangePotential[i]; //Quick hack
307	–	}
713
714	+	longRangePotential = fDecomp_->getLongRangePotential();
715	+	lrPot = longRangePotential.sum();
716	+
717		//store the tau and long range potential
718		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
719	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
720	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
313	<
314	<	curSnapshot->statData.setTau(tau);
719	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
720	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
721		}
722
723	<
723	>
724		void ForceManager::postCalculation() {
725		SimInfo::MoleculeIterator mi;
726		Molecule* mol;
727		Molecule::RigidBodyIterator rbIter;
728		RigidBody* rb;
729	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
730
731		// collect the atomic forces onto rigid bodies
732	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
733	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
734	<	rb->calcForcesAndTorques();
732	>
733	>	for (mol = info_->beginMolecule(mi); mol != NULL;
734	>	mol = info_->nextMolecule(mi)) {
735	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
736	>	rb = mol->nextRigidBody(rbIter)) {
737	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
738	>	tau += rbTau;
739		}
740		}
741	<
741	>
742	>	#ifdef IS_MPI
743	>	Mat3x3d tmpTau(tau);
744	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
745	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
746	>	#endif
747	>	curSnapshot->statData.setTau(tau);
748		}
749
750	<	} //end namespace oopse
750	>	} //end namespace OpenMD

Comparing:
trunk/src/brains/ForceManager.cpp (property svn:keywords), Revision 963 by tim, Wed May 17 21:51:42 2006 UTC vs.
branches/development/src/brains/ForceManager.cpp (property svn:keywords), Revision 1579 by gezelter, Thu Jun 9 20:26:29 2011 UTC

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