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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 1576 by gezelter, Wed Jun 8 16:05:07 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;
66	<	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	>	fDecomp_ = new ForceMatrixDecomposition(info_);
68		}
69
70	<	bool  TorsionSortFunctor(const TorsionOrderStruct& t1, const TorsionOrderStruct& t2) {
71	<	return t1.dataSet.deltaV < t2.dataSet.deltaV;
72	<	}
73	<
74	<	void ForceManager::calcForces(bool needPotential, bool needStress) {
70	>	/**
71	>	* setupCutoffs
72	>	*
73	>	* Sets the values of cutoffRadius, cutoffMethod, and cutoffPolicy
74	>	*
75	>	* cutoffRadius : realType
76	>	*  If the cutoffRadius was explicitly set, use that value.
77	>	*  If the cutoffRadius was not explicitly set:
78	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
79	>	*      No electrostatic atoms?  Poll the atom types present in the
80	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
81	>	*      Use the maximum suggested value that was found.
82	>	*
83	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
84	>	*      If cutoffMethod was explicitly set, use that choice.
85	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
86	>	*
87	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
88	>	*      If cutoffPolicy was explicitly set, use that choice.
89	>	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
90	>	*/
91	>	void ForceManager::setupCutoffs() {
92	>
93	>	Globals* simParams_ = info_->getSimParams();
94	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
95	>
96	>	if (simParams_->haveCutoffRadius()) {
97	>	rCut_ = simParams_->getCutoffRadius();
98	>	} else {
99	>	if (info_->usesElectrostaticAtoms()) {
100	>	sprintf(painCave.errMsg,
101	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
102	>	"\tOpenMD will use a default value of 12.0 angstroms"
103	>	"\tfor the cutoffRadius.\n");
104	>	painCave.isFatal = 0;
105	>	painCave.severity = OPENMD_INFO;
106	>	simError();
107	>	rCut_ = 12.0;
108	>	} else {
109	>	RealType thisCut;
110	>	set<AtomType*>::iterator i;
111	>	set<AtomType*> atomTypes;
112	>	atomTypes = info_->getSimulatedAtomTypes();
113	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
114	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
115	>	rCut_ = max(thisCut, rCut_);
116	>	}
117	>	sprintf(painCave.errMsg,
118	>	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
119	>	"\tOpenMD will use %lf angstroms.\n",
120	>	rCut_);
121	>	painCave.isFatal = 0;
122	>	painCave.severity = OPENMD_INFO;
123	>	simError();
124	>	}
125	>	}
126
127	<	if (!info_->isFortranInitialized()) {
128	<	info_->update();
127	>	map<string, CutoffMethod> stringToCutoffMethod;
128	>	stringToCutoffMethod["HARD"] = HARD;
129	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
130	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
131	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
132	>
133	>	if (simParams_->haveCutoffMethod()) {
134	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
135	>	map<string, CutoffMethod>::iterator i;
136	>	i = stringToCutoffMethod.find(cutMeth);
137	>	if (i == stringToCutoffMethod.end()) {
138	>	sprintf(painCave.errMsg,
139	>	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
140	>	"\tShould be one of: "
141	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
142	>	cutMeth.c_str());
143	>	painCave.isFatal = 1;
144	>	painCave.severity = OPENMD_ERROR;
145	>	simError();
146	>	} else {
147	>	cutoffMethod_ = i->second;
148	>	}
149	>	} else {
150	>	sprintf(painCave.errMsg,
151	>	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
152	>	"\tOpenMD will use SHIFTED_FORCE.\n");
153	>	painCave.isFatal = 0;
154	>	painCave.severity = OPENMD_INFO;
155	>	simError();
156	>	cutoffMethod_ = SHIFTED_FORCE;
157		}
158
159	<	preCalculation();
160	<
161	<	calcShortRangeInteraction();
159	>	map<string, CutoffPolicy> stringToCutoffPolicy;
160	>	stringToCutoffPolicy["MIX"] = MIX;
161	>	stringToCutoffPolicy["MAX"] = MAX;
162	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
163
164	<	calcLongRangeInteraction(needPotential, needStress);
164	>	std::string cutPolicy;
165	>	if (forceFieldOptions_.haveCutoffPolicy()){
166	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
167	>	}else if (simParams_->haveCutoffPolicy()) {
168	>	cutPolicy = simParams_->getCutoffPolicy();
169	>	}
170
171	<	postCalculation();
171	>	if (!cutPolicy.empty()){
172	>	toUpper(cutPolicy);
173	>	map<string, CutoffPolicy>::iterator i;
174	>	i = stringToCutoffPolicy.find(cutPolicy);
175
176	<	std::vector<BendOrderStruct> bendOrderStruct;
177	<	for(std::map<Bend*, BendDataSet>::iterator i = bendDataSets.begin(); i != bendDataSets.end(); ++i) {
178	<	BendOrderStruct tmp;
179	<	tmp.bend= const_cast<Bend*>(i->first);
180	<	tmp.dataSet = i->second;
181	<	bendOrderStruct.push_back(tmp);
176	>	if (i == stringToCutoffPolicy.end()) {
177	>	sprintf(painCave.errMsg,
178	>	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
179	>	"\tShould be one of: "
180	>	"MIX, MAX, or TRADITIONAL\n",
181	>	cutPolicy.c_str());
182	>	painCave.isFatal = 1;
183	>	painCave.severity = OPENMD_ERROR;
184	>	simError();
185	>	} else {
186	>	cutoffPolicy_ = i->second;
187	>	}
188	>	} else {
189	>	sprintf(painCave.errMsg,
190	>	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
191	>	"\tOpenMD will use TRADITIONAL.\n");
192	>	painCave.isFatal = 0;
193	>	painCave.severity = OPENMD_INFO;
194	>	simError();
195	>	cutoffPolicy_ = TRADITIONAL;
196		}
197	+	}
198
199	<	std::vector<TorsionOrderStruct> torsionOrderStruct;
200	<	for(std::map<Torsion*, TorsionDataSet>::iterator j = torsionDataSets.begin(); j != torsionDataSets.end(); ++j) {
201	<	TorsionOrderStruct tmp;
202	<	tmp.torsion = const_cast<Torsion*>(j->first);
203	<	tmp.dataSet = j->second;
204	<	torsionOrderStruct.push_back(tmp);
205	<	}
206	<
207	<	std::sort(bendOrderStruct.begin(), bendOrderStruct.end(), std::ptr_fun(BendSortFunctor));
208	<	std::sort(torsionOrderStruct.begin(), torsionOrderStruct.end(), std::ptr_fun(TorsionSortFunctor));
209	<	std::cout << "bend" << std::endl;
210	<	for (std::vector<BendOrderStruct>::iterator k = bendOrderStruct.begin(); k != bendOrderStruct.end(); ++k) {
211	<	Bend* bend = k->bend;
212	<	std::cout << "atom1=" <<bend->getAtomA()->getGlobalIndex() << ",atom2 = "<< bend->getAtomB()->getGlobalIndex() << ",atom3="<<bend->getAtomC()->getGlobalIndex() << " ";
213	<	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;
199	>	/**
200	>	* setupSwitching
201	>	*
202	>	* Sets the values of switchingRadius and
203	>	*  If the switchingRadius was explicitly set, use that value (but check it)
204	>	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
205	>	*/
206	>	void ForceManager::setupSwitching() {
207	>	Globals* simParams_ = info_->getSimParams();
208	>
209	>	if (simParams_->haveSwitchingRadius()) {
210	>	rSwitch_ = simParams_->getSwitchingRadius();
211	>	if (rSwitch_ > rCut_) {
212	>	sprintf(painCave.errMsg,
213	>	"ForceManager::setupSwitching: switchingRadius (%f) is larger than cutoffRadius(%f)\n",
214	>	rSwitch_, rCut_);
215	>	painCave.isFatal = 1;
216	>	painCave.severity = OPENMD_ERROR;
217	>	simError();
218	>	}
219	>	} else {
220	>	rSwitch_ = 0.85 * rCut_;
221	>	sprintf(painCave.errMsg,
222	>	"ForceManager::setupSwitching: No value was set for the switchingRadius.\n"
223	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
224	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
225	>	painCave.isFatal = 0;
226	>	painCave.severity = OPENMD_WARNING;
227	>	simError();
228	>	}
229	>
230	>	if (simParams_->haveSwitchingFunctionType()) {
231	>	string funcType = simParams_->getSwitchingFunctionType();
232	>	toUpper(funcType);
233	>	if (funcType == "CUBIC") {
234	>	sft_ = cubic;
235	>	} else {
236	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
237	>	sft_ = fifth_order_poly;
238	>	} else {
239	>	// throw error
240	>	sprintf( painCave.errMsg,
241	>	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
242	>	"\tswitchingFunctionType must be one of: "
243	>	"\"cubic\" or \"fifth_order_polynomial\".",
244	>	funcType.c_str() );
245	>	painCave.isFatal = 1;
246	>	painCave.severity = OPENMD_ERROR;
247	>	simError();
248	>	}
249	>	}
250		}
251	<	std::cout << "torsio" << std::endl;
252	<	for (std::vector<TorsionOrderStruct>::iterator l = torsionOrderStruct.begin(); l != torsionOrderStruct.end(); ++l) {
253	<	Torsion* torsion = l->torsion;
254	<	std::cout << "atom1=" <<torsion->getAtomA()->getGlobalIndex() << ",atom2 = "<< torsion->getAtomB()->getGlobalIndex() << ",atom3="<<torsion->getAtomC()->getGlobalIndex() << ",atom4="<<torsion->getAtomD()->getGlobalIndex()<< " ";
255	<	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;
251	>	switcher_->setSwitchType(sft_);
252	>	switcher_->setSwitch(rSwitch_, rCut_);
253	>	}
254	>
255	>	void ForceManager::initialize() {
256	>
257	>	if (!info_->isTopologyDone()) {
258	>	info_->update();
259	>	interactionMan_->setSimInfo(info_);
260	>	interactionMan_->initialize();
261	>
262	>	// We want to delay the cutoffs until after the interaction
263	>	// manager has set up the atom-atom interactions so that we can
264	>	// query them for suggested cutoff values
265	>
266	>	setupCutoffs();
267	>	setupSwitching();
268	>
269	>	info_->prepareTopology();
270		}
271	+
272	+	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
273
274	+	// Force fields can set options on how to scale van der Waals and electrostatic
275	+	// interactions for atoms connected via bonds, bends and torsions
276	+	// in this case the topological distance between atoms is:
277	+	// 0 = topologically unconnected
278	+	// 1 = bonded together
279	+	// 2 = connected via a bend
280	+	// 3 = connected via a torsion
281	+
282	+	vdwScale_.reserve(4);
283	+	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
284	+
285	+	electrostaticScale_.reserve(4);
286	+	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
287	+
288	+	vdwScale_[0] = 1.0;
289	+	vdwScale_[1] = fopts.getvdw12scale();
290	+	vdwScale_[2] = fopts.getvdw13scale();
291	+	vdwScale_[3] = fopts.getvdw14scale();
292	+
293	+	electrostaticScale_[0] = 1.0;
294	+	electrostaticScale_[1] = fopts.getelectrostatic12scale();
295	+	electrostaticScale_[2] = fopts.getelectrostatic13scale();
296	+	electrostaticScale_[3] = fopts.getelectrostatic14scale();
297	+
298	+	fDecomp_->distributeInitialData();
299	+
300	+	initialized_ = true;
301	+
302		}
303
304	+	void ForceManager::calcForces() {
305	+
306	+	if (!initialized_) initialize();
307	+
308	+	preCalculation();
309	+	shortRangeInteractions();
310	+	longRangeInteractions();
311	+	postCalculation();
312	+	}
313	+
314		void ForceManager::preCalculation() {
315		SimInfo::MoleculeIterator mi;
316		Molecule* mol;
#	Line 128 | Line 318 | namespace oopse {
318		Atom* atom;
319		Molecule::RigidBodyIterator rbIter;
320		RigidBody* rb;
321	+	Molecule::CutoffGroupIterator ci;
322	+	CutoffGroup* cg;
323
324		// forces are zeroed here, before any are accumulated.
325	<	// NOTE: do not rezero the forces in Fortran.
326	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
325	>
326	>	for (mol = info_->beginMolecule(mi); mol != NULL;
327	>	mol = info_->nextMolecule(mi)) {
328		for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
329		atom->zeroForcesAndTorques();
330		}
331	<
331	>
332		//change the positions of atoms which belong to the rigidbodies
333	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
333	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
334	>	rb = mol->nextRigidBody(rbIter)) {
335		rb->zeroForcesAndTorques();
336		}
337	+
338	+	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
339	+	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
340	+	cg = mol->nextCutoffGroup(ci)) {
341	+	//calculate the center of mass of cutoff group
342	+	cg->updateCOM();
343	+	}
344	+	}
345		}
346	+
347	+	// Zero out the stress tensor
348	+	tau *= 0.0;
349
350		}
351	<
352	<	void ForceManager::calcShortRangeInteraction() {
351	>
352	>	void ForceManager::shortRangeInteractions() {
353		Molecule* mol;
354		RigidBody* rb;
355		Bond* bond;
356		Bend* bend;
357		Torsion* torsion;
358	+	Inversion* inversion;
359		SimInfo::MoleculeIterator mi;
360		Molecule::RigidBodyIterator rbIter;
361		Molecule::BondIterator bondIter;;
362		Molecule::BendIterator  bendIter;
363		Molecule::TorsionIterator  torsionIter;
364	<	double bondPotential = 0.0;
365	<	double bendPotential = 0.0;
366	<	double torsionPotential = 0.0;
364	>	Molecule::InversionIterator  inversionIter;
365	>	RealType bondPotential = 0.0;
366	>	RealType bendPotential = 0.0;
367	>	RealType torsionPotential = 0.0;
368	>	RealType inversionPotential = 0.0;
369
370		//calculate short range interactions
371	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
371	>	for (mol = info_->beginMolecule(mi); mol != NULL;
372	>	mol = info_->nextMolecule(mi)) {
373
374		//change the positions of atoms which belong to the rigidbodies
375	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
376	<	rb->updateAtoms();
375	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
376	>	rb = mol->nextRigidBody(rbIter)) {
377	>	rb->updateAtoms();
378		}
379
380	<	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter)) {
380	>	for (bond = mol->beginBond(bondIter); bond != NULL;
381	>	bond = mol->nextBond(bondIter)) {
382		bond->calcForce();
383		bondPotential += bond->getPotential();
384		}
385
386	<	//int i =0;
387	<	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter)) {
388	<	//std::cout << i++ << "\t";
389	<	double angle;
390	<	bend->calcForce(angle);
391	<	double currBendPot = bend->getPotential();
392	<	bendPotential += bend->getPotential();
393	<	std::map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
394	<	if (i == bendDataSets.end()) {
395	<	BendDataSet dataSet;
396	<	dataSet.prev.angle = dataSet.curr.angle = angle;
397	<	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
398	<	dataSet.deltaV = 0.0;
399	<	bendDataSets.insert(std::map<Bend*, BendDataSet>::value_type(bend, dataSet));
400	<	}else {
401	<	i->second.prev.angle = i->second.curr.angle;
402	<	i->second.prev.potential = i->second.curr.potential;
403	<	i->second.curr.angle = angle;
404	<	i->second.curr.potential = currBendPot;
405	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
406	<	}
386	>	for (bend = mol->beginBend(bendIter); bend != NULL;
387	>	bend = mol->nextBend(bendIter)) {
388	>
389	>	RealType angle;
390	>	bend->calcForce(angle);
391	>	RealType currBendPot = bend->getPotential();
392	>
393	>	bendPotential += bend->getPotential();
394	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
395	>	if (i == bendDataSets.end()) {
396	>	BendDataSet dataSet;
397	>	dataSet.prev.angle = dataSet.curr.angle = angle;
398	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
399	>	dataSet.deltaV = 0.0;
400	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
401	>	}else {
402	>	i->second.prev.angle = i->second.curr.angle;
403	>	i->second.prev.potential = i->second.curr.potential;
404	>	i->second.curr.angle = angle;
405	>	i->second.curr.potential = currBendPot;
406	>	i->second.deltaV =  fabs(i->second.curr.potential -
407	>	i->second.prev.potential);
408	>	}
409		}
410	<
411	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter)) {
412	<	double angle;
413	<	torsion->calcForce(angle);
414	<	double currTorsionPot = torsion->getPotential();
415	<	torsionPotential += torsion->getPotential();
416	<	std::map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
417	<	if (i == torsionDataSets.end()) {
418	<	TorsionDataSet dataSet;
419	<	dataSet.prev.angle = dataSet.curr.angle = angle;
420	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
421	<	dataSet.deltaV = 0.0;
422	<	torsionDataSets.insert(std::map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
423	<	}else {
424	<	i->second.prev.angle = i->second.curr.angle;
425	<	i->second.prev.potential = i->second.curr.potential;
426	<	i->second.curr.angle = angle;
427	<	i->second.curr.potential = currTorsionPot;
428	<	i->second.deltaV =  fabs(i->second.curr.potential -  i->second.prev.potential);
429	<	}
430	<	}
431	<
410	>
411	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
412	>	torsion = mol->nextTorsion(torsionIter)) {
413	>	RealType angle;
414	>	torsion->calcForce(angle);
415	>	RealType currTorsionPot = torsion->getPotential();
416	>	torsionPotential += torsion->getPotential();
417	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
418	>	if (i == torsionDataSets.end()) {
419	>	TorsionDataSet dataSet;
420	>	dataSet.prev.angle = dataSet.curr.angle = angle;
421	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
422	>	dataSet.deltaV = 0.0;
423	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
424	>	}else {
425	>	i->second.prev.angle = i->second.curr.angle;
426	>	i->second.prev.potential = i->second.curr.potential;
427	>	i->second.curr.angle = angle;
428	>	i->second.curr.potential = currTorsionPot;
429	>	i->second.deltaV =  fabs(i->second.curr.potential -
430	>	i->second.prev.potential);
431	>	}
432	>	}
433	>
434	>	for (inversion = mol->beginInversion(inversionIter);
435	>	inversion != NULL;
436	>	inversion = mol->nextInversion(inversionIter)) {
437	>	RealType angle;
438	>	inversion->calcForce(angle);
439	>	RealType currInversionPot = inversion->getPotential();
440	>	inversionPotential += inversion->getPotential();
441	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
442	>	if (i == inversionDataSets.end()) {
443	>	InversionDataSet dataSet;
444	>	dataSet.prev.angle = dataSet.curr.angle = angle;
445	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
446	>	dataSet.deltaV = 0.0;
447	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
448	>	}else {
449	>	i->second.prev.angle = i->second.curr.angle;
450	>	i->second.prev.potential = i->second.curr.potential;
451	>	i->second.curr.angle = angle;
452	>	i->second.curr.potential = currInversionPot;
453	>	i->second.deltaV =  fabs(i->second.curr.potential -
454	>	i->second.prev.potential);
455	>	}
456	>	}
457		}
458
459	<	double  shortRangePotential = bondPotential + bendPotential + torsionPotential;
459	>	RealType  shortRangePotential = bondPotential + bendPotential +
460	>	torsionPotential +  inversionPotential;
461		Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
462		curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
463		curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
464		curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
465		curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
466	<
466	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
467		}
468	+
469	+	void ForceManager::longRangeInteractions() {
470
471	<	void ForceManager::calcLongRangeInteraction(bool needPotential, bool needStress) {
472	<	Snapshot* curSnapshot;
473	<	DataStorage* config;
474	<	double* frc;
475	<	double* pos;
476	<	double* trq;
477	<	double* A;
478	<	double* electroFrame;
479	<	double* rc;
471	>	// some of this initial stuff will go away:
472	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
473	>	DataStorage* config = &(curSnapshot->atomData);
474	>	DataStorage* cgConfig = &(curSnapshot->cgData);
475	>	RealType* frc = config->getArrayPointer(DataStorage::dslForce);
476	>	RealType* pos = config->getArrayPointer(DataStorage::dslPosition);
477	>	RealType* trq = config->getArrayPointer(DataStorage::dslTorque);
478	>	RealType* A = config->getArrayPointer(DataStorage::dslAmat);
479	>	RealType* electroFrame = config->getArrayPointer(DataStorage::dslElectroFrame);
480	>	RealType* particlePot = config->getArrayPointer(DataStorage::dslParticlePot);
481	>	RealType* rc;
482	>
483	>	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
484	>	rc = cgConfig->getArrayPointer(DataStorage::dslPosition);
485	>	} else {
486	>	// center of mass of the group is the same as position of the atom
487	>	// if cutoff group does not exist
488	>	rc = pos;
489	>	}
490
491	<	//get current snapshot from SimInfo
492	<	curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
491	>	// new stuff starts here:
492	>	fDecomp_->zeroWorkArrays();
493	>	fDecomp_->distributeData();
494	>
495	>	int cg1, cg2, atom1, atom2;
496	>	Vector3d d_grp, dag;
497	>	RealType rgrpsq, rgrp;
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
512	<	//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);
512	>	int loopStart, loopEnd;
513
514	<	//calculate the center of mass of cutoff group
515	<	SimInfo::MoleculeIterator mi;
516	<	Molecule* mol;
517	<	Molecule::CutoffGroupIterator ci;
518	<	CutoffGroup* cg;
519	<	Vector3d com;
257	<	std::vector<Vector3d> rcGroup;
514	>	loopEnd = PAIR_LOOP;
515	>	if (info_->requiresPrepair() ) {
516	>	loopStart = PREPAIR_LOOP;
517	>	} else {
518	>	loopStart = PAIR_LOOP;
519	>	}
520
521	<	if(info_->getNCutoffGroups() > 0){
522	<
523	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
524	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci)) {
525	<	cg->getCOM(com);
526	<	rcGroup.push_back(com);
521	>	for (int iLoop = loopStart; iLoop < loopEnd; iLoop++) {
522	>
523	>	if (iLoop == loopStart) {
524	>	bool update_nlist = fDecomp_->checkNeighborList();
525	>	if (update_nlist)
526	>	neighborList = fDecomp_->buildNeighborList();
527	>	}
528	>
529	>	for (vector<pair<int, int> >::iterator it = neighborList.begin();
530	>	it != neighborList.end(); ++it) {
531	>
532	>	cg1 = (*it).first;
533	>	cg2 = (*it).second;
534	>
535	>	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
536	>
537	>	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
538	>	curSnapshot->wrapVector(d_grp);
539	>	rgrpsq = d_grp.lengthSquare();
540	>
541	>	rCutSq = cuts.second;
542	>
543	>	if (rgrpsq < rCutSq) {
544	>	*(idat.rcut) = cuts.first;
545	>	if (iLoop == PAIR_LOOP) {
546	>	vij *= 0.0;
547	>	fij = V3Zero;
548	>	}
549	>
550	>	in_switching_region = switcher_->getSwitch(rgrpsq, *(idat.sw), dswdr,
551	>	rgrp);
552	>
553	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
554	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
555	>
556	>	for (vector<int>::iterator ia = atomListRow.begin();
557	>	ia != atomListRow.end(); ++ia) {
558	>	atom1 = (*ia);
559	>
560	>	for (vector<int>::iterator jb = atomListColumn.begin();
561	>	jb != atomListColumn.end(); ++jb) {
562	>	atom2 = (*jb);
563	>
564	>	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
565	>
566	>	pot *= 0.0;
567	>
568	>	idat = fDecomp_->fillInteractionData(atom1, atom2);
569	>	*(idat.pot) = pot;
570	>
571	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
572	>	*(idat.d) = d_grp;
573	>	*(idat.r2) = rgrpsq;
574	>	} else {
575	>	*(idat.d) = fDecomp_->getInteratomicVector(atom1, atom2);
576	>	curSnapshot->wrapVector( *(idat.d) );
577	>	*(idat.r2) = idat.d->lengthSquare();
578	>	}
579	>
580	>	*(idat.rij) = sqrt( *(idat.r2) );
581	>
582	>	if (iLoop == PREPAIR_LOOP) {
583	>	interactionMan_->doPrePair(idat);
584	>	} else {
585	>	interactionMan_->doPair(idat);
586	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
587	>	vij += *(idat.vpair);
588	>	fij += *(idat.f1);
589	>	tau -= outProduct( *(idat.d), *(idat.f1));
590	>	}
591	>	}
592	>	}
593	>	}
594	>
595	>	if (iLoop == PAIR_LOOP) {
596	>	if (in_switching_region) {
597	>	swderiv = vij * dswdr / rgrp;
598	>	fg = swderiv * d_grp;
599	>
600	>	fij += fg;
601	>
602	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
603	>	tau -= outProduct( *(idat.d), fg);
604	>	}
605	>
606	>	for (vector<int>::iterator ia = atomListRow.begin();
607	>	ia != atomListRow.end(); ++ia) {
608	>	atom1 = (*ia);
609	>	mf = fDecomp_->getMassFactorRow(atom1);
610	>	// fg is the force on atom ia due to cutoff group's
611	>	// presence in switching region
612	>	fg = swderiv * d_grp * mf;
613	>	fDecomp_->addForceToAtomRow(atom1, fg);
614	>
615	>	if (atomListRow.size() > 1) {
616	>	if (info_->usesAtomicVirial()) {
617	>	// find the distance between the atom
618	>	// and the center of the cutoff group:
619	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
620	>	tau -= outProduct(dag, fg);
621	>	}
622	>	}
623	>	}
624	>	for (vector<int>::iterator jb = atomListColumn.begin();
625	>	jb != atomListColumn.end(); ++jb) {
626	>	atom2 = (*jb);
627	>	mf = fDecomp_->getMassFactorColumn(atom2);
628	>	// fg is the force on atom jb due to cutoff group's
629	>	// presence in switching region
630	>	fg = -swderiv * d_grp * mf;
631	>	fDecomp_->addForceToAtomColumn(atom2, fg);
632	>
633	>	if (atomListColumn.size() > 1) {
634	>	if (info_->usesAtomicVirial()) {
635	>	// find the distance between the atom
636	>	// and the center of the cutoff group:
637	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
638	>	tau -= outProduct(dag, fg);
639	>	}
640	>	}
641	>	}
642	>	}
643	>	//if (!SIM_uses_AtomicVirial) {
644	>	//  tau -= outProduct(d_grp, fij);
645	>	//}
646	>	}
647		}
648	<	}// end for (mol)
649	<
650	<	rc = rcGroup[0].getArrayPointer();
651	<	} else {
652	<	// center of mass of the group is the same as position of the atom  if cutoff group does not exist
653	<	rc = pos;
648	>	}
649	>
650	>	if (iLoop == PREPAIR_LOOP) {
651	>	if (info_->requiresPrepair()) {
652	>	fDecomp_->collectIntermediateData();
653	>
654	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
655	>	sdat = fDecomp_->fillSelfData(atom1);
656	>	interactionMan_->doPreForce(sdat);
657	>	}
658	>
659	>	fDecomp_->distributeIntermediateData();
660	>	}
661	>	}
662	>
663		}
273	–
274	–	//initialize data before passing to fortran
275	–	double longRangePotential[LR_POT_TYPES];
276	–	double lrPot = 0.0;
664
665	<	Mat3x3d tau;
666	<	short int passedCalcPot = needPotential;
667	<	short int passedCalcStress = needStress;
668	<	int isError = 0;
665	>	fDecomp_->collectData();
666	>
667	>	if ( info_->requiresSkipCorrection() ) {
668	>
669	>	for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
670
671	<	for (int i=0; i<LR_POT_TYPES;i++){
672	<	longRangePotential[i]=0.0; //Initialize array
671	>	vector<int> skipList = fDecomp_->getSkipsForRowAtom( atom1 );
672	>
673	>	for (vector<int>::iterator jb = skipList.begin();
674	>	jb != skipList.end(); ++jb) {
675	>
676	>	atom2 = (*jb);
677	>	idat = fDecomp_->fillSkipData(atom1, atom2);
678	>	interactionMan_->doSkipCorrection(idat);
679	>
680	>	}
681	>	}
682		}
683	+
684	+	if (info_->requiresSelfCorrection()) {
685
686	<	doForceLoop( pos,
687	<	rc,
688	<	A,
689	<	electroFrame,
291	<	frc,
292	<	trq,
293	<	tau.getArrayPointer(),
294	<	longRangePotential,
295	<	&passedCalcPot,
296	<	&passedCalcStress,
297	<	&isError );
686	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
687	>	sdat = fDecomp_->fillSelfData(atom1);
688	>	interactionMan_->doSelfCorrection(sdat);
689	>	}
690
299	–	if( isError ){
300	–	sprintf( painCave.errMsg,
301	–	"Error returned from the fortran force calculation.\n" );
302	–	painCave.isFatal = 1;
303	–	simError();
691		}
305	–	for (int i=0; i<LR_POT_TYPES;i++){
306	–	lrPot += longRangePotential[i]; //Quick hack
307	–	}
692
693	+	longRangePotential = fDecomp_->getLongRangePotential();
694	+	lrPot = longRangePotential.sum();
695	+
696		//store the tau and long range potential
697		curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
698	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VDW_POT];
699	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_POT];
313	<
314	<	curSnapshot->statData.setTau(tau);
698	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
699	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
700		}
701
702	<
702	>
703		void ForceManager::postCalculation() {
704		SimInfo::MoleculeIterator mi;
705		Molecule* mol;
706		Molecule::RigidBodyIterator rbIter;
707		RigidBody* rb;
708	+	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
709
710		// collect the atomic forces onto rigid bodies
711	<	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi)) {
712	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter)) {
713	<	rb->calcForcesAndTorques();
711	>
712	>	for (mol = info_->beginMolecule(mi); mol != NULL;
713	>	mol = info_->nextMolecule(mi)) {
714	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
715	>	rb = mol->nextRigidBody(rbIter)) {
716	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
717	>	tau += rbTau;
718		}
719		}
720	<
720	>
721	>	#ifdef IS_MPI
722	>	Mat3x3d tmpTau(tau);
723	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
724	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
725	>	#endif
726	>	curSnapshot->statData.setTau(tau);
727		}
728
729	<	} //end namespace oopse
729	>	} //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 1576 by gezelter, Wed Jun 8 16:05:07 2011 UTC

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