ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing:
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1583 by gezelter, Thu Jun 16 22:00:08 2011 UTC vs.
branches/devel_omp/src/brains/ForceManager.cpp (file contents), Revision 1614 by mciznick, Tue Aug 23 20:55:51 2011 UTC

#	Line 38 | Line 38
38		* [3]  Sun, Lin & Gezelter, J. Chem. Phys. 128, 24107 (2008).
39		* [4]  Vardeman & Gezelter, in progress (2009).
40		*/
41	<
41	>
42		/**
43		* @file ForceManager.cpp
44		* @author tlin
#	Line 47 | Line 47
47		* @version 1.0
48		*/
49
50	–
50		#include "brains/ForceManager.hpp"
51		#include "primitives/Molecule.hpp"
52		#define __OPENMD_C
#	Line 63 | Line 62
62		#include <iostream>
63		#include <iomanip>
64
65	+	#include <omp.h>
66	+	//#include <time.h>
67	+	#include <sys/time.h>
68	+
69		using namespace std;
70		namespace OpenMD {
68	–
69	–	ForceManager::ForceManager(SimInfo * info) : info_(info) {
70	–	forceField_ = info_->getForceField();
71	–	interactionMan_ = new InteractionManager();
72	–	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
73	–	}
71
72	<	/**
76	<	* setupCutoffs
77	<	*
78	<	* Sets the values of cutoffRadius, cutoffMethod, and cutoffPolicy
79	<	*
80	<	* cutoffRadius : realType
81	<	*  If the cutoffRadius was explicitly set, use that value.
82	<	*  If the cutoffRadius was not explicitly set:
83	<	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
84	<	*      No electrostatic atoms?  Poll the atom types present in the
85	<	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
86	<	*      Use the maximum suggested value that was found.
87	<	*
88	<	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
89	<	*      If cutoffMethod was explicitly set, use that choice.
90	<	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
91	<	*
92	<	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
93	<	*      If cutoffPolicy was explicitly set, use that choice.
94	<	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
95	<	*/
96	<	void ForceManager::setupCutoffs() {
97	<
98	<	Globals* simParams_ = info_->getSimParams();
99	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
100	<
101	<	if (simParams_->haveCutoffRadius()) {
102	<	rCut_ = simParams_->getCutoffRadius();
103	<	} else {
104	<	if (info_->usesElectrostaticAtoms()) {
105	<	sprintf(painCave.errMsg,
106	<	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
107	<	"\tOpenMD will use a default value of 12.0 angstroms"
108	<	"\tfor the cutoffRadius.\n");
109	<	painCave.isFatal = 0;
110	<	painCave.severity = OPENMD_INFO;
111	<	simError();
112	<	rCut_ = 12.0;
113	<	} else {
114	<	RealType thisCut;
115	<	set<AtomType*>::iterator i;
116	<	set<AtomType*> atomTypes;
117	<	atomTypes = info_->getSimulatedAtomTypes();
118	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
119	<	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
120	<	rCut_ = max(thisCut, rCut_);
121	<	}
122	<	sprintf(painCave.errMsg,
123	<	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
124	<	"\tOpenMD will use %lf angstroms.\n",
125	<	rCut_);
126	<	painCave.isFatal = 0;
127	<	painCave.severity = OPENMD_INFO;
128	<	simError();
129	<	}
130	<	}
72	>	//long int elapsedTime = 0;
73
74	<	fDecomp_->setUserCutoff(rCut_);
74	>	ForceManager::ForceManager(SimInfo * info) :
75	>	info_(info) {
76	>	forceField_ = info_->getForceField();
77	>	interactionMan_ = new InteractionManager();
78	>	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
79	>	}
80
81	<	map<string, CutoffMethod> stringToCutoffMethod;
82	<	stringToCutoffMethod["HARD"] = HARD;
83	<	stringToCutoffMethod["SWITCHED"] = SWITCHED;
84	<	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
85	<	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
86	<
87	<	if (simParams_->haveCutoffMethod()) {
88	<	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
89	<	map<string, CutoffMethod>::iterator i;
90	<	i = stringToCutoffMethod.find(cutMeth);
91	<	if (i == stringToCutoffMethod.end()) {
92	<	sprintf(painCave.errMsg,
93	<	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
94	<	"\tShould be one of: "
95	<	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
96	<	cutMeth.c_str());
97	<	painCave.isFatal = 1;
98	<	painCave.severity = OPENMD_ERROR;
99	<	simError();
100	<	} else {
101	<	cutoffMethod_ = i->second;
102	<	}
103	<	} else {
104	<	sprintf(painCave.errMsg,
105	<	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
106	<	"\tOpenMD will use SHIFTED_FORCE.\n");
107	<	painCave.isFatal = 0;
108	<	painCave.severity = OPENMD_INFO;
109	<	simError();
110	<	cutoffMethod_ = SHIFTED_FORCE;
111	<	}
81	>	/**
82	>	* setupCutoffs
83	>	*
84	>	* Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
85	>	* and cutoffPolicy
86	>	*
87	>	* cutoffRadius : realType
88	>	*  If the cutoffRadius was explicitly set, use that value.
89	>	*  If the cutoffRadius was not explicitly set:
90	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
91	>	*      No electrostatic atoms?  Poll the atom types present in the
92	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
93	>	*      Use the maximum suggested value that was found.
94	>	*
95	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
96	>	*                        or SHIFTED_POTENTIAL)
97	>	*      If cutoffMethod was explicitly set, use that choice.
98	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
99	>	*
100	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
101	>	*      If cutoffPolicy was explicitly set, use that choice.
102	>	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
103	>	*
104	>	* switchingRadius : realType
105	>	*  If the cutoffMethod was set to SWITCHED:
106	>	*      If the switchingRadius was explicitly set, use that value
107	>	*          (but do a sanity check first).
108	>	*      If the switchingRadius was not explicitly set: use 0.85 *
109	>	*      cutoffRadius_
110	>	*  If the cutoffMethod was not set to SWITCHED:
111	>	*      Set switchingRadius equal to cutoffRadius for safety.
112	>	*/
113	>	void ForceManager::setupCutoffs() {
114
115	<	map<string, CutoffPolicy> stringToCutoffPolicy;
116	<	stringToCutoffPolicy["MIX"] = MIX;
168	<	stringToCutoffPolicy["MAX"] = MAX;
169	<	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
115	>	Globals* simParams_ = info_->getSimParams();
116	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
117
118	<	std::string cutPolicy;
119	<	if (forceFieldOptions_.haveCutoffPolicy()){
120	<	cutPolicy = forceFieldOptions_.getCutoffPolicy();
121	<	}else if (simParams_->haveCutoffPolicy()) {
122	<	cutPolicy = simParams_->getCutoffPolicy();
123	<	}
118	>	if (simParams_->haveCutoffRadius())
119	>	{
120	>	rCut_ = simParams_->getCutoffRadius();
121	>	} else
122	>	{
123	>	if (info_->usesElectrostaticAtoms())
124	>	{
125	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
126	>	"\tOpenMD will use a default value of 12.0 angstroms"
127	>	"\tfor the cutoffRadius.\n");
128	>	painCave.isFatal = 0;
129	>	painCave.severity = OPENMD_INFO;
130	>	simError();
131	>	rCut_ = 12.0;
132	>	} else
133	>	{
134	>	RealType thisCut;
135	>	set<AtomType*>::iterator i;
136	>	set<AtomType*> atomTypes;
137	>	atomTypes = info_->getSimulatedAtomTypes();
138	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
139	>	{
140	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
141	>	rCut_ = max(thisCut, rCut_);
142	>	}
143	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
144	>	"\tOpenMD will use %lf angstroms.\n", rCut_);
145	>	painCave.isFatal = 0;
146	>	painCave.severity = OPENMD_INFO;
147	>	simError();
148	>	}
149	>	}
150
151	<	if (!cutPolicy.empty()){
152	<	toUpper(cutPolicy);
180	<	map<string, CutoffPolicy>::iterator i;
181	<	i = stringToCutoffPolicy.find(cutPolicy);
151	>	fDecomp_->setUserCutoff(rCut_);
152	>	interactionMan_->setCutoffRadius(rCut_);
153
154	<	if (i == stringToCutoffPolicy.end()) {
155	<	sprintf(painCave.errMsg,
156	<	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
157	<	"\tShould be one of: "
158	<	"MIX, MAX, or TRADITIONAL\n",
188	<	cutPolicy.c_str());
189	<	painCave.isFatal = 1;
190	<	painCave.severity = OPENMD_ERROR;
191	<	simError();
192	<	} else {
193	<	cutoffPolicy_ = i->second;
194	<	}
195	<	} else {
196	<	sprintf(painCave.errMsg,
197	<	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
198	<	"\tOpenMD will use TRADITIONAL.\n");
199	<	painCave.isFatal = 0;
200	<	painCave.severity = OPENMD_INFO;
201	<	simError();
202	<	cutoffPolicy_ = TRADITIONAL;
203	<	}
204	<	fDecomp_->setCutoffPolicy(cutoffPolicy_);
205	<	}
154	>	map<string, CutoffMethod> stringToCutoffMethod;
155	>	stringToCutoffMethod["HARD"] = HARD;
156	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
157	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
158	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
159
160	<	/**
161	<	* setupSwitching
162	<	*
163	<	* Sets the values of switchingRadius and
164	<	*  If the switchingRadius was explicitly set, use that value (but check it)
165	<	*  If the switchingRadius was not explicitly set: use 0.85 * cutoffRadius_
166	<	*/
167	<	void ForceManager::setupSwitching() {
168	<	Globals* simParams_ = info_->getSimParams();
160	>	if (simParams_->haveCutoffMethod())
161	>	{
162	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
163	>	map<string, CutoffMethod>::iterator i;
164	>	i = stringToCutoffMethod.find(cutMeth);
165	>	if (i == stringToCutoffMethod.end())
166	>	{
167	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
168	>	"\tShould be one of: "
169	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n", cutMeth.c_str());
170	>	painCave.isFatal = 1;
171	>	painCave.severity = OPENMD_ERROR;
172	>	simError();
173	>	} else
174	>	{
175	>	cutoffMethod_ = i->second;
176	>	}
177	>	} else
178	>	{
179	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
180	>	"\tOpenMD will use SHIFTED_FORCE.\n");
181	>	painCave.isFatal = 0;
182	>	painCave.severity = OPENMD_INFO;
183	>	simError();
184	>	cutoffMethod_ = SHIFTED_FORCE;
185	>	}
186
187	<	// create the switching function object:
188	<	switcher_ = new SwitchingFunction();
189	<
190	<	if (simParams_->haveSwitchingRadius()) {
221	<	rSwitch_ = simParams_->getSwitchingRadius();
222	<	if (rSwitch_ > rCut_) {
223	<	sprintf(painCave.errMsg,
224	<	"ForceManager::setupSwitching: switchingRadius (%f) is larger "
225	<	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
226	<	painCave.isFatal = 1;
227	<	painCave.severity = OPENMD_ERROR;
228	<	simError();
229	<	}
230	<	} else {
231	<	rSwitch_ = 0.85 * rCut_;
232	<	sprintf(painCave.errMsg,
233	<	"ForceManager::setupSwitching: No value was set for the switchingRadius.\n"
234	<	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
235	<	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
236	<	painCave.isFatal = 0;
237	<	painCave.severity = OPENMD_WARNING;
238	<	simError();
239	<	}
240	<
241	<	// Default to cubic switching function.
242	<	sft_ = cubic;
243	<	if (simParams_->haveSwitchingFunctionType()) {
244	<	string funcType = simParams_->getSwitchingFunctionType();
245	<	toUpper(funcType);
246	<	if (funcType == "CUBIC") {
247	<	sft_ = cubic;
248	<	} else {
249	<	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
250	<	sft_ = fifth_order_poly;
251	<	} else {
252	<	// throw error
253	<	sprintf( painCave.errMsg,
254	<	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
255	<	"\tswitchingFunctionType must be one of: "
256	<	"\"cubic\" or \"fifth_order_polynomial\".",
257	<	funcType.c_str() );
258	<	painCave.isFatal = 1;
259	<	painCave.severity = OPENMD_ERROR;
260	<	simError();
261	<	}
262	<	}
263	<	}
264	<	switcher_->setSwitchType(sft_);
265	<	switcher_->setSwitch(rSwitch_, rCut_);
266	<	}
267	<
268	<	void ForceManager::initialize() {
187	>	map<string, CutoffPolicy> stringToCutoffPolicy;
188	>	stringToCutoffPolicy["MIX"] = MIX;
189	>	stringToCutoffPolicy["MAX"] = MAX;
190	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
191
192	<	if (!info_->isTopologyDone()) {
193	<	info_->update();
194	<	interactionMan_->setSimInfo(info_);
195	<	interactionMan_->initialize();
192	>	std::string cutPolicy;
193	>	if (forceFieldOptions_.haveCutoffPolicy())
194	>	{
195	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
196	>	} else if (simParams_->haveCutoffPolicy())
197	>	{
198	>	cutPolicy = simParams_->getCutoffPolicy();
199	>	}
200
201	<	// We want to delay the cutoffs until after the interaction
202	<	// manager has set up the atom-atom interactions so that we can
203	<	// query them for suggested cutoff values
201	>	if (!cutPolicy.empty())
202	>	{
203	>	toUpper(cutPolicy);
204	>	map<string, CutoffPolicy>::iterator i;
205	>	i = stringToCutoffPolicy.find(cutPolicy);
206
207	<	setupCutoffs();
208	<	setupSwitching();
207	>	if (i == stringToCutoffPolicy.end())
208	>	{
209	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
210	>	"\tShould be one of: "
211	>	"MIX, MAX, or TRADITIONAL\n", cutPolicy.c_str());
212	>	painCave.isFatal = 1;
213	>	painCave.severity = OPENMD_ERROR;
214	>	simError();
215	>	} else
216	>	{
217	>	cutoffPolicy_ = i->second;
218	>	}
219	>	} else
220	>	{
221	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
222	>	"\tOpenMD will use TRADITIONAL.\n");
223	>	painCave.isFatal = 0;
224	>	painCave.severity = OPENMD_INFO;
225	>	simError();
226	>	cutoffPolicy_ = TRADITIONAL;
227	>	}
228
229	<	info_->prepareTopology();
283	<	}
229	>	fDecomp_->setCutoffPolicy(cutoffPolicy_);
230
231	<	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
286	<
287	<	// Force fields can set options on how to scale van der Waals and electrostatic
288	<	// interactions for atoms connected via bonds, bends and torsions
289	<	// in this case the topological distance between atoms is:
290	<	// 0 = topologically unconnected
291	<	// 1 = bonded together
292	<	// 2 = connected via a bend
293	<	// 3 = connected via a torsion
294	<
295	<	vdwScale_.reserve(4);
296	<	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
231	>	// create the switching function object:
232
233	<	electrostaticScale_.reserve(4);
299	<	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
233	>	switcher_ = new SwitchingFunction();
234
235	<	vdwScale_[0] = 1.0;
236	<	vdwScale_[1] = fopts.getvdw12scale();
237	<	vdwScale_[2] = fopts.getvdw13scale();
238	<	vdwScale_[3] = fopts.getvdw14scale();
239	<
240	<	electrostaticScale_[0] = 1.0;
241	<	electrostaticScale_[1] = fopts.getelectrostatic12scale();
242	<	electrostaticScale_[2] = fopts.getelectrostatic13scale();
243	<	electrostaticScale_[3] = fopts.getelectrostatic14scale();
244	<
245	<	fDecomp_->distributeInitialData();
246	<
247	<	initialized_ = true;
235	>	if (cutoffMethod_ == SWITCHED)
236	>	{
237	>	if (simParams_->haveSwitchingRadius())
238	>	{
239	>	rSwitch_ = simParams_->getSwitchingRadius();
240	>	if (rSwitch_ > rCut_)
241	>	{
242	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: switchingRadius (%f) is larger "
243	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
244	>	painCave.isFatal = 1;
245	>	painCave.severity = OPENMD_ERROR;
246	>	simError();
247	>	}
248	>	} else
249	>	{
250	>	rSwitch_ = 0.85 * rCut_;
251	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
252	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
253	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
254	>	painCave.isFatal = 0;
255	>	painCave.severity = OPENMD_WARNING;
256	>	simError();
257	>	}
258	>	} else
259	>	{
260	>	if (simParams_->haveSwitchingRadius())
261	>	{
262	>	map<string, CutoffMethod>::const_iterator it;
263	>	string theMeth;
264	>	for (it = stringToCutoffMethod.begin(); it != stringToCutoffMethod.end(); ++it)
265	>	{
266	>	if (it->second == cutoffMethod_)
267	>	{
268	>	theMeth = it->first;
269	>	break;
270	>	}
271	>	}
272	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
273	>	"\tis not set to SWITCHED, so switchingRadius value\n"
274	>	"\twill be ignored for this simulation\n", theMeth.c_str());
275	>	painCave.isFatal = 0;
276	>	painCave.severity = OPENMD_WARNING;
277	>	simError();
278	>	}
279
280	<	}
280	>	rSwitch_ = rCut_;
281	>	}
282
283	<	void ForceManager::calcForces() {
284	<
285	<	if (!initialized_) initialize();
283	>	// Default to cubic switching function.
284	>	sft_ = cubic;
285	>	if (simParams_->haveSwitchingFunctionType())
286	>	{
287	>	string funcType = simParams_->getSwitchingFunctionType();
288	>	toUpper(funcType);
289	>	if (funcType == "CUBIC")
290	>	{
291	>	sft_ = cubic;
292	>	} else
293	>	{
294	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL")
295	>	{
296	>	sft_ = fifth_order_poly;
297	>	} else
298	>	{
299	>	// throw error
300	>	sprintf(painCave.errMsg,
301	>	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
302	>	"\tswitchingFunctionType must be one of: "
303	>	"\"cubic\" or \"fifth_order_polynomial\".", funcType.c_str());
304	>	painCave.isFatal = 1;
305	>	painCave.severity = OPENMD_ERROR;
306	>	simError();
307	>	}
308	>	}
309	>	}
310	>	switcher_->setSwitchType(sft_);
311	>	switcher_->setSwitch(rSwitch_, rCut_);
312	>	interactionMan_->setSwitchingRadius(rSwitch_);
313	>	}
314
315	<	preCalculation();
322	<	shortRangeInteractions();
323	<	longRangeInteractions();
324	<	postCalculation();
325	<	}
326	<
327	<	void ForceManager::preCalculation() {
328	<	SimInfo::MoleculeIterator mi;
329	<	Molecule* mol;
330	<	Molecule::AtomIterator ai;
331	<	Atom* atom;
332	<	Molecule::RigidBodyIterator rbIter;
333	<	RigidBody* rb;
334	<	Molecule::CutoffGroupIterator ci;
335	<	CutoffGroup* cg;
336	<
337	<	// forces are zeroed here, before any are accumulated.
338	<
339	<	for (mol = info_->beginMolecule(mi); mol != NULL;
340	<	mol = info_->nextMolecule(mi)) {
341	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
342	<	atom->zeroForcesAndTorques();
343	<	}
344	<
345	<	//change the positions of atoms which belong to the rigidbodies
346	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
347	<	rb = mol->nextRigidBody(rbIter)) {
348	<	rb->zeroForcesAndTorques();
349	<	}
315	>	void ForceManager::initialize() {
316
317	<	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
318	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
353	<	cg = mol->nextCutoffGroup(ci)) {
354	<	//calculate the center of mass of cutoff group
355	<	cg->updateCOM();
356	<	}
357	<	}
358	<	}
359	<
360	<	// Zero out the stress tensor
361	<	tau *= 0.0;
362	<
363	<	}
364	<
365	<	void ForceManager::shortRangeInteractions() {
366	<	Molecule* mol;
367	<	RigidBody* rb;
368	<	Bond* bond;
369	<	Bend* bend;
370	<	Torsion* torsion;
371	<	Inversion* inversion;
372	<	SimInfo::MoleculeIterator mi;
373	<	Molecule::RigidBodyIterator rbIter;
374	<	Molecule::BondIterator bondIter;;
375	<	Molecule::BendIterator  bendIter;
376	<	Molecule::TorsionIterator  torsionIter;
377	<	Molecule::InversionIterator  inversionIter;
378	<	RealType bondPotential = 0.0;
379	<	RealType bendPotential = 0.0;
380	<	RealType torsionPotential = 0.0;
381	<	RealType inversionPotential = 0.0;
317	>	if (!info_->isTopologyDone())
318	>	{
319
320	<	//calculate short range interactions
321	<	for (mol = info_->beginMolecule(mi); mol != NULL;
322	<	mol = info_->nextMolecule(mi)) {
320	>	info_->update();
321	>	interactionMan_->setSimInfo(info_);
322	>	interactionMan_->initialize();
323
324	<	//change the positions of atoms which belong to the rigidbodies
325	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
326	<	rb = mol->nextRigidBody(rbIter)) {
327	<	rb->updateAtoms();
391	<	}
324	>	// We want to delay the cutoffs until after the interaction
325	>	// manager has set up the atom-atom interactions so that we can
326	>	// query them for suggested cutoff values
327	>	setupCutoffs();
328
329	<	for (bond = mol->beginBond(bondIter); bond != NULL;
330	<	bond = mol->nextBond(bondIter)) {
395	<	bond->calcForce();
396	<	bondPotential += bond->getPotential();
397	<	}
329	>	info_->prepareTopology();
330	>	}
331
332	<	for (bend = mol->beginBend(bendIter); bend != NULL;
400	<	bend = mol->nextBend(bendIter)) {
401	<
402	<	RealType angle;
403	<	bend->calcForce(angle);
404	<	RealType currBendPot = bend->getPotential();
405	<
406	<	bendPotential += bend->getPotential();
407	<	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
408	<	if (i == bendDataSets.end()) {
409	<	BendDataSet dataSet;
410	<	dataSet.prev.angle = dataSet.curr.angle = angle;
411	<	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
412	<	dataSet.deltaV = 0.0;
413	<	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
414	<	}else {
415	<	i->second.prev.angle = i->second.curr.angle;
416	<	i->second.prev.potential = i->second.curr.potential;
417	<	i->second.curr.angle = angle;
418	<	i->second.curr.potential = currBendPot;
419	<	i->second.deltaV =  fabs(i->second.curr.potential -
420	<	i->second.prev.potential);
421	<	}
422	<	}
423	<
424	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
425	<	torsion = mol->nextTorsion(torsionIter)) {
426	<	RealType angle;
427	<	torsion->calcForce(angle);
428	<	RealType currTorsionPot = torsion->getPotential();
429	<	torsionPotential += torsion->getPotential();
430	<	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
431	<	if (i == torsionDataSets.end()) {
432	<	TorsionDataSet dataSet;
433	<	dataSet.prev.angle = dataSet.curr.angle = angle;
434	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
435	<	dataSet.deltaV = 0.0;
436	<	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
437	<	}else {
438	<	i->second.prev.angle = i->second.curr.angle;
439	<	i->second.prev.potential = i->second.curr.potential;
440	<	i->second.curr.angle = angle;
441	<	i->second.curr.potential = currTorsionPot;
442	<	i->second.deltaV =  fabs(i->second.curr.potential -
443	<	i->second.prev.potential);
444	<	}
445	<	}
446	<
447	<	for (inversion = mol->beginInversion(inversionIter);
448	<	inversion != NULL;
449	<	inversion = mol->nextInversion(inversionIter)) {
450	<	RealType angle;
451	<	inversion->calcForce(angle);
452	<	RealType currInversionPot = inversion->getPotential();
453	<	inversionPotential += inversion->getPotential();
454	<	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
455	<	if (i == inversionDataSets.end()) {
456	<	InversionDataSet dataSet;
457	<	dataSet.prev.angle = dataSet.curr.angle = angle;
458	<	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
459	<	dataSet.deltaV = 0.0;
460	<	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
461	<	}else {
462	<	i->second.prev.angle = i->second.curr.angle;
463	<	i->second.prev.potential = i->second.curr.potential;
464	<	i->second.curr.angle = angle;
465	<	i->second.curr.potential = currInversionPot;
466	<	i->second.deltaV =  fabs(i->second.curr.potential -
467	<	i->second.prev.potential);
468	<	}
469	<	}
470	<	}
471	<
472	<	RealType  shortRangePotential = bondPotential + bendPotential +
473	<	torsionPotential +  inversionPotential;
474	<	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
475	<	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
476	<	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
477	<	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
478	<	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
479	<	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
480	<	}
481	<
482	<	void ForceManager::longRangeInteractions() {
332	>	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
333
334	<	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
335	<	DataStorage* config = &(curSnapshot->atomData);
336	<	DataStorage* cgConfig = &(curSnapshot->cgData);
334	>	// Force fields can set options on how to scale van der Waals and
335	>	// electrostatic interactions for atoms connected via bonds, bends
336	>	// and torsions in this case the topological distance between
337	>	// atoms is:
338	>	// 0 = topologically unconnected
339	>	// 1 = bonded together
340	>	// 2 = connected via a bend
341	>	// 3 = connected via a torsion
342
343	<	//calculate the center of mass of cutoff group
343	>	vdwScale_.reserve(4);
344	>	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
345
346	<	SimInfo::MoleculeIterator mi;
347	<	Molecule* mol;
492	<	Molecule::CutoffGroupIterator ci;
493	<	CutoffGroup* cg;
346	>	electrostaticScale_.reserve(4);
347	>	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
348
349	<	if(info_->getNCutoffGroups() > 0){
350	<	for (mol = info_->beginMolecule(mi); mol != NULL;
351	<	mol = info_->nextMolecule(mi)) {
352	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
499	<	cg = mol->nextCutoffGroup(ci)) {
500	<	cg->updateCOM();
501	<	}
502	<	}
503	<	} else {
504	<	// center of mass of the group is the same as position of the atom
505	<	// if cutoff group does not exist
506	<	cgConfig->position = config->position;
507	<	}
349	>	vdwScale_[0] = 1.0;
350	>	vdwScale_[1] = fopts.getvdw12scale();
351	>	vdwScale_[2] = fopts.getvdw13scale();
352	>	vdwScale_[3] = fopts.getvdw14scale();
353
354	<	fDecomp_->zeroWorkArrays();
355	<	fDecomp_->distributeData();
356	<
357	<	int cg1, cg2, atom1, atom2, topoDist;
513	<	Vector3d d_grp, dag, d;
514	<	RealType rgrpsq, rgrp, r2, r;
515	<	RealType electroMult, vdwMult;
516	<	RealType vij;
517	<	Vector3d fij, fg, f1;
518	<	tuple3<RealType, RealType, RealType> cuts;
519	<	RealType rCutSq;
520	<	bool in_switching_region;
521	<	RealType sw, dswdr, swderiv;
522	<	vector<int> atomListColumn, atomListRow, atomListLocal;
523	<	InteractionData idat;
524	<	SelfData sdat;
525	<	RealType mf;
526	<	RealType lrPot;
527	<	RealType vpair;
528	<	potVec longRangePotential(0.0);
529	<	potVec workPot(0.0);
354	>	electrostaticScale_[0] = 1.0;
355	>	electrostaticScale_[1] = fopts.getelectrostatic12scale();
356	>	electrostaticScale_[2] = fopts.getelectrostatic13scale();
357	>	electrostaticScale_[3] = fopts.getelectrostatic14scale();
358
359	<	int loopStart, loopEnd;
359	>	fDecomp_->distributeInitialData();
360
361	<	idat.vdwMult = &vdwMult;
534	<	idat.electroMult = &electroMult;
535	<	idat.pot = &workPot;
536	<	sdat.pot = fDecomp_->getEmbeddingPotential();
537	<	idat.vpair = &vpair;
538	<	idat.f1 = &f1;
539	<	idat.sw = &sw;
540	<	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
541	<	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
542	<
543	<	loopEnd = PAIR_LOOP;
544	<	if (info_->requiresPrepair() ) {
545	<	loopStart = PREPAIR_LOOP;
546	<	} else {
547	<	loopStart = PAIR_LOOP;
548	<	}
549	<
550	<	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
551	<
552	<	if (iLoop == loopStart) {
553	<	bool update_nlist = fDecomp_->checkNeighborList();
554	<	if (update_nlist)
555	<	neighborList = fDecomp_->buildNeighborList();
556	<	}
557	<
558	<	for (vector<pair<int, int> >::iterator it = neighborList.begin();
559	<	it != neighborList.end(); ++it) {
560	<
561	<	cg1 = (*it).first;
562	<	cg2 = (*it).second;
563	<
564	<	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
361	>	initialized_ = true;
362
363	<	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
567	<	curSnapshot->wrapVector(d_grp);
568	<	rgrpsq = d_grp.lengthSquare();
363	>	}
364
365	<	rCutSq = cuts.second;
365	>	void ForceManager::calcForces() {
366
367	<	if (rgrpsq < rCutSq) {
368	<	idat.rcut = &cuts.first;
574	<	if (iLoop == PAIR_LOOP) {
575	<	vij *= 0.0;
576	<	fij = V3Zero;
577	<	}
578	<
579	<	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
580	<	rgrp);
581	<
582	<	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
583	<	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
367	>	if (!initialized_)
368	>	initialize();
369
370	<	for (vector<int>::iterator ia = atomListRow.begin();
371	<	ia != atomListRow.end(); ++ia) {
372	<	atom1 = (*ia);
373	<
374	<	for (vector<int>::iterator jb = atomListColumn.begin();
375	<	jb != atomListColumn.end(); ++jb) {
376	<	atom2 = (*jb);
592	<
593	<	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
594	<	vpair = 0.0;
595	<	workPot = 0.0;
596	<	f1 = V3Zero;
370	>	preCalculation();
371	>	shortRangeInteractions();
372	>	//    longRangeInteractions();
373	>	//      longRangeInteractionsRapaport();
374	>	longRangeInteractionsParallel();
375	>	postCalculation();
376	>	}
377
378	<	fDecomp_->fillInteractionData(idat, atom1, atom2);
379	<
380	<	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
381	<	vdwMult = vdwScale_[topoDist];
382	<	electroMult = electrostaticScale_[topoDist];
378	>	void ForceManager::preCalculation() {
379	>	SimInfo::MoleculeIterator mi;
380	>	Molecule* mol;
381	>	Molecule::AtomIterator ai;
382	>	Atom* atom;
383	>	Molecule::RigidBodyIterator rbIter;
384	>	RigidBody* rb;
385	>	Molecule::CutoffGroupIterator ci;
386	>	CutoffGroup* cg;
387
388	<	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
605	<	idat.d = &d_grp;
606	<	idat.r2 = &rgrpsq;
607	<	} else {
608	<	d = fDecomp_->getInteratomicVector(atom1, atom2);
609	<	curSnapshot->wrapVector( d );
610	<	r2 = d.lengthSquare();
611	<	idat.d = &d;
612	<	idat.r2 = &r2;
613	<	}
614	<
615	<	r = sqrt( *(idat.r2) );
616	<	idat.rij = &r;
617	<
618	<	if (iLoop == PREPAIR_LOOP) {
619	<	interactionMan_->doPrePair(idat);
620	<	} else {
621	<	interactionMan_->doPair(idat);
622	<	fDecomp_->unpackInteractionData(idat, atom1, atom2);
623	<	vij += vpair;
624	<	fij += f1;
625	<	tau -= outProduct( *(idat.d), f1);
626	<	}
627	<	}
628	<	}
629	<	}
388	>	// forces are zeroed here, before any are accumulated.
389
390	<	if (iLoop == PAIR_LOOP) {
391	<	if (in_switching_region) {
392	<	swderiv = vij * dswdr / rgrp;
393	<	fg = swderiv * d_grp;
390	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
391	>	{
392	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai))
393	>	{
394	>	atom->zeroForcesAndTorques();
395	>	}
396
397	<	fij += fg;
397	>	//change the positions of atoms which belong to the rigidbodies
398	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter))
399	>	{
400	>	rb->zeroForcesAndTorques();
401	>	}
402
403	<	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
404	<	tau -= outProduct( *(idat.d), fg);
405	<	}
406	<
407	<	for (vector<int>::iterator ia = atomListRow.begin();
408	<	ia != atomListRow.end(); ++ia) {
409	<	atom1 = (*ia);
410	<	mf = fDecomp_->getMassFactorRow(atom1);
411	<	// fg is the force on atom ia due to cutoff group's
647	<	// presence in switching region
648	<	fg = swderiv * d_grp * mf;
649	<	fDecomp_->addForceToAtomRow(atom1, fg);
403	>	if (info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms())
404	>	{
405	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
406	>	{
407	>	//calculate the center of mass of cutoff group
408	>	cg->updateCOM();
409	>	}
410	>	}
411	>	}
412
413	<	if (atomListRow.size() > 1) {
414	<	if (info_->usesAtomicVirial()) {
653	<	// find the distance between the atom
654	<	// and the center of the cutoff group:
655	<	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
656	<	tau -= outProduct(dag, fg);
657	<	}
658	<	}
659	<	}
660	<	for (vector<int>::iterator jb = atomListColumn.begin();
661	<	jb != atomListColumn.end(); ++jb) {
662	<	atom2 = (*jb);
663	<	mf = fDecomp_->getMassFactorColumn(atom2);
664	<	// fg is the force on atom jb due to cutoff group's
665	<	// presence in switching region
666	<	fg = -swderiv * d_grp * mf;
667	<	fDecomp_->addForceToAtomColumn(atom2, fg);
413	>	// Zero out the stress tensor
414	>	tau *= 0.0;
415
416	<	if (atomListColumn.size() > 1) {
670	<	if (info_->usesAtomicVirial()) {
671	<	// find the distance between the atom
672	<	// and the center of the cutoff group:
673	<	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
674	<	tau -= outProduct(dag, fg);
675	<	}
676	<	}
677	<	}
678	<	}
679	<	//if (!SIM_uses_AtomicVirial) {
680	<	//  tau -= outProduct(d_grp, fij);
681	<	//}
682	<	}
683	<	}
684	<	}
416	>	}
417
418	<	if (iLoop == PREPAIR_LOOP) {
419	<	if (info_->requiresPrepair()) {
420	<	fDecomp_->collectIntermediateData();
418	>	void ForceManager::shortRangeInteractions() {
419	>	Molecule* mol;
420	>	RigidBody* rb;
421	>	Bond* bond;
422	>	Bend* bend;
423	>	Torsion* torsion;
424	>	Inversion* inversion;
425	>	SimInfo::MoleculeIterator mi;
426	>	Molecule::RigidBodyIterator rbIter;
427	>	Molecule::BondIterator bondIter;
428	>	;
429	>	Molecule::BendIterator bendIter;
430	>	Molecule::TorsionIterator torsionIter;
431	>	Molecule::InversionIterator inversionIter;
432	>	RealType bondPotential = 0.0;
433	>	RealType bendPotential = 0.0;
434	>	RealType torsionPotential = 0.0;
435	>	RealType inversionPotential = 0.0;
436
437	<	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
438	<	fDecomp_->fillSelfData(sdat, atom1);
439	<	interactionMan_->doPreForce(sdat);
693	<	}
694	<
695	<
696	<	fDecomp_->distributeIntermediateData();
697	<	}
698	<	}
437	>	//calculate short range interactions
438	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
439	>	{
440
441	<	}
442	<
443	<	fDecomp_->collectData();
444	<
445	<	if ( info_->requiresSkipCorrection() ) {
705	<
706	<	for (int atom1 = 0; atom1 < fDecomp_->getNAtomsInRow(); atom1++) {
441	>	//change the positions of atoms which belong to the rigidbodies
442	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter))
443	>	{
444	>	rb->updateAtoms();
445	>	}
446
447	<	vector<int> skipList = fDecomp_->getSkipsForAtom( atom1 );
448	<
449	<	for (vector<int>::iterator jb = skipList.begin();
450	<	jb != skipList.end(); ++jb) {
451	<
713	<	atom2 = (*jb);
714	<	fDecomp_->fillSkipData(idat, atom1, atom2);
715	<	interactionMan_->doSkipCorrection(idat);
716	<	fDecomp_->unpackSkipData(idat, atom1, atom2);
447	>	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter))
448	>	{
449	>	bond->calcForce();
450	>	bondPotential += bond->getPotential();
451	>	}
452
453	<	}
454	<	}
720	<	}
721	<
722	<	if (info_->requiresSelfCorrection()) {
453	>	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter))
454	>	{
455
456	<	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
457	<	fDecomp_->fillSelfData(sdat, atom1);
458	<	interactionMan_->doSelfCorrection(sdat);
727	<	}
456	>	RealType angle;
457	>	bend->calcForce(angle);
458	>	RealType currBendPot = bend->getPotential();
459
460	<	}
460	>	bendPotential += bend->getPotential();
461	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
462	>	if (i == bendDataSets.end())
463	>	{
464	>	BendDataSet dataSet;
465	>	dataSet.prev.angle = dataSet.curr.angle = angle;
466	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
467	>	dataSet.deltaV = 0.0;
468	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
469	>	} else
470	>	{
471	>	i->second.prev.angle = i->second.curr.angle;
472	>	i->second.prev.potential = i->second.curr.potential;
473	>	i->second.curr.angle = angle;
474	>	i->second.curr.potential = currBendPot;
475	>	i->second.deltaV = fabs(i->second.curr.potential - i->second.prev.potential);
476	>	}
477	>	}
478
479	<	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
480	<	*(fDecomp_->getPairwisePotential());
479	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter))
480	>	{
481	>	RealType angle;
482	>	torsion->calcForce(angle);
483	>	RealType currTorsionPot = torsion->getPotential();
484	>	torsionPotential += torsion->getPotential();
485	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
486	>	if (i == torsionDataSets.end())
487	>	{
488	>	TorsionDataSet dataSet;
489	>	dataSet.prev.angle = dataSet.curr.angle = angle;
490	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
491	>	dataSet.deltaV = 0.0;
492	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
493	>	} else
494	>	{
495	>	i->second.prev.angle = i->second.curr.angle;
496	>	i->second.prev.potential = i->second.curr.potential;
497	>	i->second.curr.angle = angle;
498	>	i->second.curr.potential = currTorsionPot;
499	>	i->second.deltaV = fabs(i->second.curr.potential - i->second.prev.potential);
500	>	}
501	>	}
502
503	<	lrPot = longRangePotential.sum();
503	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL; inversion = mol->nextInversion(
504	>	inversionIter))
505	>	{
506	>	RealType angle;
507	>	inversion->calcForce(angle);
508	>	RealType currInversionPot = inversion->getPotential();
509	>	inversionPotential += inversion->getPotential();
510	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
511	>	if (i == inversionDataSets.end())
512	>	{
513	>	InversionDataSet dataSet;
514	>	dataSet.prev.angle = dataSet.curr.angle = angle;
515	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
516	>	dataSet.deltaV = 0.0;
517	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
518	>	} else
519	>	{
520	>	i->second.prev.angle = i->second.curr.angle;
521	>	i->second.prev.potential = i->second.curr.potential;
522	>	i->second.curr.angle = angle;
523	>	i->second.curr.potential = currInversionPot;
524	>	i->second.deltaV = fabs(i->second.curr.potential - i->second.prev.potential);
525	>	}
526	>	}
527	>	}
528
529	<	//store the tau and long range potential
530	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
531	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
532	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
533	<	}
529	>	RealType shortRangePotential = bondPotential + bendPotential + torsionPotential + inversionPotential;
530	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
531	>	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
532	>	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
533	>	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
534	>	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
535	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
536	>	}
537
538	<
539	<	void ForceManager::postCalculation() {
540	<	SimInfo::MoleculeIterator mi;
541	<	Molecule* mol;
542	<	Molecule::RigidBodyIterator rbIter;
543	<	RigidBody* rb;
544	<	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
545	<
546	<	// collect the atomic forces onto rigid bodies
547	<
548	<	for (mol = info_->beginMolecule(mi); mol != NULL;
549	<	mol = info_->nextMolecule(mi)) {
550	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
551	<	rb = mol->nextRigidBody(rbIter)) {
552	<	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
553	<	tau += rbTau;
554	<	}
555	<	}
556	<
557	<	#ifdef IS_MPI
558	<	Mat3x3d tmpTau(tau);
559	<	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
560	<	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
538	>	void ForceManager::longRangeInteractionsParallel() {
539	>
540	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
541	>	DataStorage* config = &(curSnapshot->atomData);
542	>	DataStorage* cgConfig = &(curSnapshot->cgData);
543	>
544	>	//calculate the center of mass of cutoff group
545	>
546	>	SimInfo::MoleculeIterator mi;
547	>	Molecule* mol;
548	>	Molecule::CutoffGroupIterator ci;
549	>	CutoffGroup* cg;
550	>
551	>	if (info_->getNCutoffGroups() > 0)
552	>	{
553	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
554	>	{
555	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
556	>	{
557	>	//                              cerr << "branch1\n";
558	>	//                              cerr << "globind = " << cg->getGlobalIndex() << ":" << __LINE__ << "\n";
559	>	cg->updateCOM();
560	>
561	>	//                              cerr << "gbI: " << cg->getGlobalIndex() << " locI: " << cg->getLocalIndex() << " x: "
562	>	//                                              << cgConfig->position[cg->getLocalIndex()].x() << " y: " << cgConfig->position[cg->getLocalIndex()].y()
563	>	//                                              << " z: " << cgConfig->position[cg->getLocalIndex()].z() << "\n";
564	>	}
565	>	}
566	>	} else
567	>	{
568	>	// center of mass of the group is the same as position of the atom
569	>	// if cutoff group does not exist
570	>	//              cerr << ":" << __LINE__ << "branch2\n";
571	>	cgConfig->position = config->position;
572	>	}
573	>
574	>	fDecomp_->zeroWorkArrays();
575	>	fDecomp_->distributeData();
576	>
577	>	int atom1, atom2, topoDist;
578	>	Vector3d d_grp, dag, d;
579	>	RealType rgrpsq, rgrp, r2, r;
580	>	RealType electroMult, vdwMult;
581	>	RealType vij;
582	>	Vector3d fij, fg, f1;
583	>	tuple3<RealType, RealType, RealType> cuts;
584	>	RealType rCutSq;
585	>	bool in_switching_region;
586	>	RealType sw, dswdr, swderiv;
587	>	vector<int> atomListColumn, atomListRow, atomListLocal;
588	>
589	>	/* Defines local interaction data to each thread */
590	>	InteractionDataPrv idatPrv;
591	>
592	>	SelfData sdat;
593	>	RealType mf;
594	>	RealType lrPot;
595	>	RealType vpair;
596	>	potVec longRangePotential(0.0);
597	>	potVec workPot(0.0);
598	>
599	>	int loopStart, loopEnd;
600	>	sdat.pot = fDecomp_->getEmbeddingPotential();
601	>
602	>	vector<CutoffGroup *> cgs;
603	>
604	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
605	>	{
606	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
607	>	{
608	>	cgs.push_back(cg);
609	>	}
610	>	}
611	>
612	>	loopEnd = PAIR_LOOP;
613	>	if (info_->requiresPrepair())
614	>	{
615	>	loopStart = PREPAIR_LOOP;
616	>	} else
617	>	{
618	>	loopStart = PAIR_LOOP;
619	>	}
620	>
621	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++)
622	>	{
623	>
624	>	if (iLoop == loopStart)
625	>	{
626	>	bool update_nlist = fDecomp_->checkNeighborList();
627	>	if (update_nlist)
628	>	neighborMatW = fDecomp_->buildLayerBasedNeighborList();
629	>	}
630	>
631	>	/* Eager initialization */
632	>	/* Initializes InteractionManager before force calculations */
633	>	interactionMan_->initializeOMP();
634	>	/* Initializes forces used in simulation before force calculations */
635	>	interactionMan_->initNonbondedForces();
636	>
637	>	vector<CutoffGroup *>::iterator cg1;
638	>	vector<CutoffGroup *>::iterator cg2;
639	>
640	>	/* Defines local accumulators for each thread */
641	>	vector<Vector3d> forceLcl;
642	>	Vector3d fatom1Lcl;
643	>	Mat3x3d tauLcl;
644	>	potVec potLcl;
645	>
646	>	/* Defines the size of chunks into which the loop iterations will be split */
647	>	int chunkSize = cgs.size() / (omp_get_max_threads() * 5);
648	>
649	>	/*struct timeval tv, tv2;
650	>
651	>	gettimeofday(&tv, NULL);*/
652	>
653	>	/* Defines the parallel region and the list of variables that should be shared and private to each thread */
654	>	#pragma omp parallel default(none) shared(curSnapshot, iLoop, cgs, chunkSize, config) \
655	>	private(cg1, cg2, cuts, d_grp, rgrpsq, rCutSq, idatPrv, vij, fij, in_switching_region, \
656	>	dswdr, rgrp, atomListRow, atomListColumn, atom1, atom2, topoDist, d, r2, swderiv, fg, mf, \
657	>	dag, tauLcl, forceLcl, fatom1Lcl, potLcl)
658	>	{
659	>	idatPrv.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
660	>	idatPrv.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
661	>	forceLcl = vector<Vector3d>(config->force.size());
662	>	tauLcl *= 0;
663	>
664	>	/* Spreads force calculations between threads. Each thread receives chunkSize portion of the CutoffGroups. */
665	>	#pragma omp for schedule(dynamic, chunkSize)
666	>	for (cg1 = cgs.begin(); cg1 < cgs.end(); ++cg1)
667	>	{
668	>	/* Iterates between neighbors of the CutoffGroup */
669	>	for (cg2 = neighborMatW[(*cg1)->getGlobalIndex()].begin(); cg2 < neighborMatW[(*cg1)->getGlobalIndex()].end(); ++cg2)
670	>	{
671	>
672	>	cuts = fDecomp_->getGroupCutoffs((*cg1)->getGlobalIndex(), (*cg2)->getGlobalIndex());
673	>
674	>	d_grp = fDecomp_->getIntergroupVector((*cg1), (*cg2));
675	>	curSnapshot->wrapVector(d_grp);
676	>	rgrpsq = d_grp.lengthSquare();
677	>
678	>	rCutSq = cuts.second;
679	>
680	>	//                                      printf("Thread %d\tcg1:%d\tcg2:%d d_grp\tx:%f\ty:%f\tz:%f\trgrpsq:%f\n", omp_get_thread_num(), (*cg1)->getGlobalIndex(), (*cg2)->getGlobalIndex(), d_grp.x(), d_grp.y(), d_grp.z(), rgrpsq);
681	>
682	>	if (rgrpsq < rCutSq)
683	>	{
684	>	idatPrv.rcut = cuts.first;
685	>	if (iLoop == PAIR_LOOP)
686	>	{
687	>	vij = 0.0;
688	>	fij = V3Zero;
689	>	}
690	>
691	>	in_switching_region = switcher_->getSwitch(rgrpsq, idatPrv.sw, dswdr, rgrp);
692	>
693	>	//                                              printf("in_switching_region:%d\trgrpsq:%f\t*idatPrv.sw:%f\tdswdr:%f\trgrp:%f\n", (in_switching_region == false ? 0 : 1), rgrpsq, idatPrv.sw, dswdr, rgrp);
694	>
695	>	atomListRow = fDecomp_->getAtomsInGroupRow((*cg1)->getGlobalIndex());
696	>	atomListColumn = fDecomp_->getAtomsInGroupColumn((*cg2)->getGlobalIndex());
697	>
698	>	for (vector<int>::iterator ia = atomListRow.begin(); ia != atomListRow.end(); ++ia)
699	>	{
700	>	atom1 = (*ia);
701	>	fatom1Lcl = V3Zero;
702	>
703	>	for (vector<int>::iterator jb = atomListColumn.begin(); jb != atomListColumn.end(); ++jb)
704	>	{
705	>	atom2 = (*jb);
706	>
707	>	if (!fDecomp_->skipAtomPair(atom1, atom2))
708	>	{
709	>	idatPrv.vpair = 0.0;
710	>	idatPrv.pot = 0.0;
711	>	idatPrv.f1 = V3Zero;
712	>
713	>	fDecomp_->fillInteractionDataOMP(idatPrv, atom1, atom2);
714	>
715	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
716	>	idatPrv.vdwMult = vdwScale_[topoDist];
717	>	idatPrv.electroMult = electrostaticScale_[topoDist];
718	>
719	>	//                                                                      printf("topoDist:%d\tidatPrv.vdwMult:%f\tidatPrv.electroMult:%f\n", topoDist, idatPrv.vdwMult, idatPrv.electroMult);
720	>
721	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1)
722	>	{
723	>	idatPrv.d = d_grp;
724	>	idatPrv.r2 = rgrpsq;
725	>	//cerr << "dgrp = " << d_grp << ":" << __LINE__ << "\n";
726	>	} else
727	>	{
728	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
729	>	curSnapshot->wrapVector(d);
730	>	r2 = d.lengthSquare();
731	>	//cerr << "datm = " << d << ":" << __LINE__ << "\n";
732	>	idatPrv.d = d;
733	>	idatPrv.r2 = r2;
734	>	}
735	>
736	>	//printf("idatPrv.d x:%f\ty:%f\tz:%f\tidatPrv.r2:%f\n", (idatPrv.d).x(), (idatPrv.d).y(), (idatPrv.d).z(), idatPrv.r2);
737	>	//cerr << "idat.d = " << *(idat.d) << ":" << __LINE__ << "\n";
738	>	idatPrv.rij = sqrt((idatPrv.r2));
739	>	//cerr << "idat.rij = " << *(idat.rij) << "\n";
740	>
741	>	if (iLoop == PREPAIR_LOOP)
742	>	{
743	>	interactionMan_->doPrePairOMP(idatPrv);
744	>	} else
745	>	{
746	>	interactionMan_->doPairOMP(idatPrv);
747	>
748	>	/* Accumulates potential and forces in local arrays */
749	>	potLcl += idatPrv.pot;
750	>	fatom1Lcl += idatPrv.f1;
751	>	forceLcl[atom2] -= idatPrv.f1;
752	>	//cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << ":" << __LINE__ << "\n";
753	>	//printf("d x:%f y:%f z:%f vpair:%f f1 x:%f y:%f z:%f\n", idatPrv.d.x(), idatPrv.d.y(), idatPrv.d.z(), idatPrv.vpair, idatPrv.f1.x(), idatPrv.f1.y(), idatPrv.f1.z());
754	>	vij += idatPrv.vpair;
755	>	fij += idatPrv.f1;
756	>	tauLcl -= outProduct(idatPrv.d, idatPrv.f1);
757	>	//printf("vij:%f fij x:%f y:%f z:%f\n", vij, fij.x(), fij.y(), fij.z());
758	>	}
759	>	}
760	>	}
761	>	/* We can accumulate force for current CutoffGroup in shared memory without worring about read after write bugs*/
762	>	config->force[atom1] += fatom1Lcl;
763	>	}
764	>
765	>	if (iLoop == PAIR_LOOP)
766	>	{
767	>	if (in_switching_region)
768	>	{
769	>	swderiv = vij * dswdr / rgrp;
770	>	fg = swderiv * d_grp;
771	>	fij += fg;
772	>
773	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1)
774	>	{
775	>	tauLcl -= outProduct(idatPrv.d, fg);
776	>	}
777	>
778	>	for (vector<int>::iterator ia = atomListRow.begin(); ia != atomListRow.end(); ++ia)
779	>	{
780	>	atom1 = (*ia);
781	>	mf = fDecomp_->getMassFactorRow(atom1);
782	>	// fg is the force on atom ia due to cutoff group's
783	>	// presence in switching region
784	>	fg = swderiv * d_grp * mf;
785	>	#pragma omp critical (forceLck)
786	>	{
787	>	fDecomp_->addForceToAtomRow(atom1, fg);
788	>	}
789	>
790	>	if (atomListRow.size() > 1)
791	>	{
792	>	if (info_->usesAtomicVirial())
793	>	{
794	>	// find the distance between the atom
795	>	// and the center of the cutoff group:
796	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, (*cg1)->getGlobalIndex());
797	>	tauLcl -= outProduct(dag, fg);
798	>	}
799	>	}
800	>	}
801	>	for (vector<int>::iterator jb = atomListColumn.begin(); jb != atomListColumn.end(); ++jb)
802	>	{
803	>	atom2 = (*jb);
804	>	mf = fDecomp_->getMassFactorColumn(atom2);
805	>	// fg is the force on atom jb due to cutoff group's
806	>	// presence in switching region
807	>	fg = -swderiv * d_grp * mf;
808	>	#pragma omp critical (forceLck)
809	>	{
810	>	fDecomp_->addForceToAtomColumn(atom2, fg);
811	>	}
812	>
813	>	if (atomListColumn.size() > 1)
814	>	{
815	>	if (info_->usesAtomicVirial())
816	>	{
817	>	// find the distance between the atom
818	>	// and the center of the cutoff group:
819	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, (*cg2)->getGlobalIndex());
820	>	tauLcl -= outProduct(dag, fg);
821	>	}
822	>	}
823	>	}
824	>	}
825	>	//if (!SIM_uses_AtomicVirial) {
826	>	//  tau -= outProduct(d_grp, fij);
827	>	//}
828	>	}
829	>	}
830	>	}
831	>	}// END: omp for loop
832	>	/* Critical region which accumulates forces from local to shared arrays  */
833	>	#pragma omp critical (forceAdd)
834	>	{
835	>	for (int currAtom = 0; currAtom < config->force.size(); ++currAtom)
836	>	{
837	>	config->force[currAtom] += forceLcl[currAtom];
838	>	}
839	>
840	>	tau -= tauLcl;
841	>	*(fDecomp_->getPairwisePotential()) += potLcl;
842	>	}
843	>	}// END: omp parallel region
844	>
845	>	/*gettimeofday(&tv2, NULL);
846	>
847	>	elapsedTime += 1000000 * (tv2.tv_sec - tv.tv_sec)
848	>	+ (tv2.tv_usec - tv.tv_usec);
849	>
850	>	Globals *simParams_ = info_->getSimParams();
851	>
852	>	if(curSnapshot->getTime() >= simParams_->getRunTime() - 1)
853	>	{
854	>	printf("Force calculation time: %ld [us]\n", elapsedTime);
855	>	}*/
856	>
857	>	if (iLoop == PREPAIR_LOOP)
858	>	{
859	>	if (info_->requiresPrepair())
860	>	{
861	>
862	>	fDecomp_->collectIntermediateData();
863	>
864	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++)
865	>	{
866	>	fDecomp_->fillSelfData(sdat, atom1);
867	>	interactionMan_->doPreForce(sdat);
868	>	}
869	>
870	>	fDecomp_->distributeIntermediateData();
871	>
872	>	}
873	>	}
874	>	}
875	>
876	>	fDecomp_->collectData();
877	>
878	>	if (info_->requiresSelfCorrection())
879	>	{
880	>
881	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++)
882	>	{
883	>	fDecomp_->fillSelfData(sdat, atom1);
884	>	interactionMan_->doSelfCorrection(sdat);
885	>	}
886	>
887	>	}
888	>
889	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) + *(fDecomp_->getPairwisePotential());
890	>
891	>	lrPot = longRangePotential.sum();
892	>
893	>	//store the tau and long range potential
894	>	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
895	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
896	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
897	>	}
898	>
899	>	void ForceManager::longRangeInteractionsRapaport() {
900	>
901	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
902	>	DataStorage* config = &(curSnapshot->atomData);
903	>	DataStorage* cgConfig = &(curSnapshot->cgData);
904	>
905	>	//calculate the center of mass of cutoff group
906	>
907	>	SimInfo::MoleculeIterator mi;
908	>	Molecule* mol;
909	>	Molecule::CutoffGroupIterator ci;
910	>	CutoffGroup* cg;
911	>
912	>	if (info_->getNCutoffGroups() > 0)
913	>	{
914	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
915	>	{
916	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
917	>	{
918	>	//                              cerr << "branch1\n";
919	>	//                              cerr << "globind = " << cg->getGlobalIndex() << ":" << __LINE__ << "\n";
920	>	cg->updateCOM();
921	>
922	>	//                              cerr << "gbI: " << cg->getGlobalIndex() << " locI: " << cg->getLocalIndex() << " x: "
923	>	//                                              << cgConfig->position[cg->getLocalIndex()].x() << " y: " << cgConfig->position[cg->getLocalIndex()].y()
924	>	//                                              << " z: " << cgConfig->position[cg->getLocalIndex()].z() << "\n";
925	>	}
926	>	}
927	>	} else
928	>	{
929	>	// center of mass of the group is the same as position of the atom
930	>	// if cutoff group does not exist
931	>	//              cerr << ":" << __LINE__ << "branch2\n";
932	>	cgConfig->position = config->position;
933	>	}
934	>
935	>	fDecomp_->zeroWorkArrays();
936	>	fDecomp_->distributeData();
937	>
938	>	int atom1, atom2, topoDist;
939	>	CutoffGroup *cg1;
940	>	Vector3d d_grp, dag, d;
941	>	RealType rgrpsq, rgrp, r2, r;
942	>	RealType electroMult, vdwMult;
943	>	RealType vij;
944	>	Vector3d fij, fg, f1;
945	>	tuple3<RealType, RealType, RealType> cuts;
946	>	RealType rCutSq;
947	>	bool in_switching_region;
948	>	RealType sw, dswdr, swderiv;
949	>	vector<int> atomListColumn, atomListRow, atomListLocal;
950	>	InteractionData idat;
951	>	SelfData sdat;
952	>	RealType mf;
953	>	RealType lrPot;
954	>	RealType vpair;
955	>	potVec longRangePotential(0.0);
956	>	potVec workPot(0.0);
957	>
958	>	int loopStart, loopEnd;
959	>
960	>	idat.vdwMult = &vdwMult;
961	>	idat.electroMult = &electroMult;
962	>	idat.pot = &workPot;
963	>	sdat.pot = fDecomp_->getEmbeddingPotential();
964	>	idat.vpair = &vpair;
965	>	idat.f1 = &f1;
966	>	idat.sw = &sw;
967	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
968	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
969	>
970	>	loopEnd = PAIR_LOOP;
971	>	if (info_->requiresPrepair())
972	>	{
973	>	loopStart = PREPAIR_LOOP;
974	>	} else
975	>	{
976	>	loopStart = PAIR_LOOP;
977	>	}
978	>
979	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++)
980	>	{
981	>
982	>	if (iLoop == loopStart)
983	>	{
984	>	bool update_nlist = fDecomp_->checkNeighborList();
985	>	if (update_nlist)
986	>	neighborMatW = fDecomp_->buildLayerBasedNeighborList();
987	>	}
988	>
989	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
990	>	{
991	>	for (cg1 = mol->beginCutoffGroup(ci); cg1 != NULL; cg1 = mol->nextCutoffGroup(ci))
992	>	{
993	>	//                      printf("Thread %d executes loop iteration %d\n", omp_get_thread_num(), i);
994	>	for (vector<CutoffGroup *>::iterator cg2 = neighborMatW[cg1->getGlobalIndex()].begin(); cg2
995	>	!= neighborMatW[cg1->getGlobalIndex()].end(); ++cg2)
996	>	{
997	>
998	>	cuts = fDecomp_->getGroupCutoffs(cg1->getGlobalIndex(), (*cg2)->getGlobalIndex());
999	>
1000	>	d_grp = fDecomp_->getIntergroupVector(cg1, (*cg2));
1001	>	curSnapshot->wrapVector(d_grp);
1002	>	rgrpsq = d_grp.lengthSquare();
1003	>
1004	>	rCutSq = cuts.second;
1005	>
1006	>	if (rgrpsq < rCutSq)
1007	>	{
1008	>	idat.rcut = &cuts.first;
1009	>	if (iLoop == PAIR_LOOP)
1010	>	{
1011	>	vij = 0.0;
1012	>	fij = V3Zero;
1013	>	}
1014	>
1015	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, rgrp);
1016	>
1017	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1->getGlobalIndex());
1018	>	atomListColumn = fDecomp_->getAtomsInGroupColumn((*cg2)->getGlobalIndex());
1019	>
1020	>	for (vector<int>::iterator ia = atomListRow.begin(); ia != atomListRow.end(); ++ia)
1021	>	{
1022	>	atom1 = (*ia);
1023	>
1024	>	for (vector<int>::iterator jb = atomListColumn.begin(); jb != atomListColumn.end(); ++jb)
1025	>	{
1026	>	atom2 = (*jb);
1027	>
1028	>	if (!fDecomp_->skipAtomPair(atom1, atom2))
1029	>	{
1030	>	vpair = 0.0;
1031	>	workPot = 0.0;
1032	>	f1 = V3Zero;
1033	>
1034	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
1035	>
1036	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
1037	>	vdwMult = vdwScale_[topoDist];
1038	>	electroMult = electrostaticScale_[topoDist];
1039	>
1040	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1)
1041	>	{
1042	>	idat.d = &d_grp;
1043	>	idat.r2 = &rgrpsq;
1044	>	//                                                                              cerr << "dgrp = " << d_grp << ":" << __LINE__ << "\n";
1045	>	} else
1046	>	{
1047	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
1048	>	curSnapshot->wrapVector(d);
1049	>	r2 = d.lengthSquare();
1050	>	//                                                                              cerr << "datm = " << d << ":" << __LINE__ << "\n";
1051	>	idat.d = &d;
1052	>	idat.r2 = &r2;
1053	>	}
1054	>
1055	>	//                                                                      cerr << "idat.d = " << *(idat.d) << ":" << __LINE__ << "\n";
1056	>	r = sqrt(*(idat.r2));
1057	>	idat.rij = &r;
1058	>	//                                                                      cerr << "idat.rij = " << *(idat.rij) << "\n";
1059	>
1060	>	if (iLoop == PREPAIR_LOOP)
1061	>	{
1062	>	interactionMan_->doPrePair(idat);
1063	>	} else
1064	>	{
1065	>	interactionMan_->doPair(idat);
1066	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
1067	>
1068	>	//                                                                              cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << ":" << __LINE__ << "\n";
1069	>	vij += vpair;
1070	>	fij += f1;
1071	>	tau -= outProduct(*(idat.d), f1);
1072	>	}
1073	>	}
1074	>	}
1075	>	}
1076	>
1077	>	if (iLoop == PAIR_LOOP)
1078	>	{
1079	>	if (in_switching_region)
1080	>	{
1081	>	swderiv = vij * dswdr / rgrp;
1082	>	fg = swderiv * d_grp;
1083	>	fij += fg;
1084	>
1085	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1)
1086	>	{
1087	>	tau -= outProduct(*(idat.d), fg);
1088	>	}
1089	>
1090	>	for (vector<int>::iterator ia = atomListRow.begin(); ia != atomListRow.end(); ++ia)
1091	>	{
1092	>	atom1 = (*ia);
1093	>	mf = fDecomp_->getMassFactorRow(atom1);
1094	>	// fg is the force on atom ia due to cutoff group's
1095	>	// presence in switching region
1096	>	fg = swderiv * d_grp * mf;
1097	>	fDecomp_->addForceToAtomRow(atom1, fg);
1098	>
1099	>	if (atomListRow.size() > 1)
1100	>	{
1101	>	if (info_->usesAtomicVirial())
1102	>	{
1103	>	// find the distance between the atom
1104	>	// and the center of the cutoff group:
1105	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1->getGlobalIndex());
1106	>	tau -= outProduct(dag, fg);
1107	>	}
1108	>	}
1109	>	}
1110	>	for (vector<int>::iterator jb = atomListColumn.begin(); jb != atomListColumn.end(); ++jb)
1111	>	{
1112	>	atom2 = (*jb);
1113	>	mf = fDecomp_->getMassFactorColumn(atom2);
1114	>	// fg is the force on atom jb due to cutoff group's
1115	>	// presence in switching region
1116	>	fg = -swderiv * d_grp * mf;
1117	>	fDecomp_->addForceToAtomColumn(atom2, fg);
1118	>
1119	>	if (atomListColumn.size() > 1)
1120	>	{
1121	>	if (info_->usesAtomicVirial())
1122	>	{
1123	>	// find the distance between the atom
1124	>	// and the center of the cutoff group:
1125	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, (*cg2)->getGlobalIndex());
1126	>	tau -= outProduct(dag, fg);
1127	>	}
1128	>	}
1129	>	}
1130	>	}
1131	>	//if (!SIM_uses_AtomicVirial) {
1132	>	//  tau -= outProduct(d_grp, fij);
1133	>	//}
1134	>	}
1135	>	}
1136	>	}
1137	>	}
1138	>	}
1139	>
1140	>	if (iLoop == PREPAIR_LOOP)
1141	>	{
1142	>	if (info_->requiresPrepair())
1143	>	{
1144	>
1145	>	fDecomp_->collectIntermediateData();
1146	>
1147	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++)
1148	>	{
1149	>	fDecomp_->fillSelfData(sdat, atom1);
1150	>	interactionMan_->doPreForce(sdat);
1151	>	}
1152	>
1153	>	fDecomp_->distributeIntermediateData();
1154	>
1155	>	}
1156	>	}
1157	>	}
1158	>
1159	>	fDecomp_->collectData();
1160	>
1161	>	if (info_->requiresSelfCorrection())
1162	>	{
1163	>
1164	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++)
1165	>	{
1166	>	fDecomp_->fillSelfData(sdat, atom1);
1167	>	interactionMan_->doSelfCorrection(sdat);
1168	>	}
1169	>
1170	>	}
1171	>
1172	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) + *(fDecomp_->getPairwisePotential());
1173	>
1174	>	lrPot = longRangePotential.sum();
1175	>
1176	>	//store the tau and long range potential
1177	>	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
1178	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
1179	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
1180	>	}
1181	>
1182	>	void ForceManager::longRangeInteractions() {
1183	>
1184	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
1185	>	DataStorage* config = &(curSnapshot->atomData);
1186	>	DataStorage* cgConfig = &(curSnapshot->cgData);
1187	>
1188	>	//calculate the center of mass of cutoff group
1189	>
1190	>	SimInfo::MoleculeIterator mi;
1191	>	Molecule* mol;
1192	>	Molecule::CutoffGroupIterator ci;
1193	>	CutoffGroup* cg;
1194	>
1195	>	if (info_->getNCutoffGroups() > 0)
1196	>	{
1197	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1198	>	{
1199	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
1200	>	{
1201	>	cerr << "branch1\n";
1202	>	cerr << "globind = " << cg->getGlobalIndex() << "\n";
1203	>	cg->updateCOM();
1204	>	}
1205	>	}
1206	>	} else
1207	>	{
1208	>	// center of mass of the group is the same as position of the atom
1209	>	// if cutoff group does not exist
1210	>	cerr << "branch2\n";
1211	>	cgConfig->position = config->position;
1212	>	}
1213	>
1214	>	fDecomp_->zeroWorkArrays();
1215	>	fDecomp_->distributeData();
1216	>
1217	>	int cg1, cg2, atom1, atom2, topoDist;
1218	>	Vector3d d_grp, dag, d;
1219	>	RealType rgrpsq, rgrp, r2, r;
1220	>	RealType electroMult, vdwMult;
1221	>	RealType vij;
1222	>	Vector3d fij, fg, f1;
1223	>	tuple3<RealType, RealType, RealType> cuts;
1224	>	RealType rCutSq;
1225	>	bool in_switching_region;
1226	>	RealType sw, dswdr, swderiv;
1227	>	vector<int> atomListColumn, atomListRow, atomListLocal;
1228	>	InteractionData idat;
1229	>	SelfData sdat;
1230	>	RealType mf;
1231	>	RealType lrPot;
1232	>	RealType vpair;
1233	>	potVec longRangePotential(0.0);
1234	>	potVec workPot(0.0);
1235	>
1236	>	int loopStart, loopEnd;
1237	>
1238	>	idat.vdwMult = &vdwMult;
1239	>	idat.electroMult = &electroMult;
1240	>	idat.pot = &workPot;
1241	>	sdat.pot = fDecomp_->getEmbeddingPotential();
1242	>	idat.vpair = &vpair;
1243	>	idat.f1 = &f1;
1244	>	idat.sw = &sw;
1245	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
1246	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
1247	>
1248	>	loopEnd = PAIR_LOOP;
1249	>	if (info_->requiresPrepair())
1250	>	{
1251	>	loopStart = PREPAIR_LOOP;
1252	>	} else
1253	>	{
1254	>	loopStart = PAIR_LOOP;
1255	>	}
1256	>
1257	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++)
1258	>	{
1259	>
1260	>	if (iLoop == loopStart)
1261	>	{
1262	>	bool update_nlist = fDecomp_->checkNeighborList();
1263	>	if (update_nlist)
1264	>	neighborList = fDecomp_->buildNeighborList();
1265	>
1266	>	}
1267	>
1268	>	for (vector<pair<int, int> >::iterator it = neighborList.begin(); it != neighborList.end(); ++it)
1269	>	{
1270	>	cg1 = (*it).first;
1271	>	cg2 = (*it).second;
1272	>
1273	>	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
1274	>
1275	>	d_grp = fDecomp_->getIntergroupVector(cg1, cg2);
1276	>	curSnapshot->wrapVector(d_grp);
1277	>	rgrpsq = d_grp.lengthSquare();
1278	>
1279	>	rCutSq = cuts.second;
1280	>
1281	>	if (rgrpsq < rCutSq)
1282	>	{
1283	>	idat.rcut = &cuts.first;
1284	>	if (iLoop == PAIR_LOOP)
1285	>	{
1286	>	vij = 0.0;
1287	>	fij = V3Zero;
1288	>	}
1289	>
1290	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, rgrp);
1291	>
1292	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
1293	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
1294	>
1295	>	for (vector<int>::iterator ia = atomListRow.begin(); ia != atomListRow.end(); ++ia)
1296	>	{
1297	>	atom1 = (*ia);
1298	>
1299	>	for (vector<int>::iterator jb = atomListColumn.begin(); jb != atomListColumn.end(); ++jb)
1300	>	{
1301	>	atom2 = (*jb);
1302	>
1303	>	if (!fDecomp_->skipAtomPair(atom1, atom2))
1304	>	{
1305	>	vpair = 0.0;
1306	>	workPot = 0.0;
1307	>	f1 = V3Zero;
1308	>
1309	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
1310	>
1311	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
1312	>	vdwMult = vdwScale_[topoDist];
1313	>	electroMult = electrostaticScale_[topoDist];
1314	>
1315	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1)
1316	>	{
1317	>	idat.d = &d_grp;
1318	>	idat.r2 = &rgrpsq;
1319	>	cerr << "dgrp = " << d_grp << "\n";
1320	>	} else
1321	>	{
1322	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
1323	>	curSnapshot->wrapVector(d);
1324	>	r2 = d.lengthSquare();
1325	>	cerr << "datm = " << d << "\n";
1326	>	idat.d = &d;
1327	>	idat.r2 = &r2;
1328	>	}
1329	>
1330	>	cerr << "idat.d = " << *(idat.d) << "\n";
1331	>	r = sqrt(*(idat.r2));
1332	>	idat.rij = &r;
1333	>
1334	>	if (iLoop == PREPAIR_LOOP)
1335	>	{
1336	>	interactionMan_->doPrePair(idat);
1337	>	} else
1338	>	{
1339	>	interactionMan_->doPair(idat);
1340	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
1341	>
1342	>	cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << "\n";
1343	>	vij += vpair;
1344	>	fij += f1;
1345	>	tau -= outProduct(*(idat.d), f1);
1346	>	}
1347	>	}
1348	>	}
1349	>	}
1350	>
1351	>	if (iLoop == PAIR_LOOP)
1352	>	{
1353	>	if (in_switching_region)
1354	>	{
1355	>	swderiv = vij * dswdr / rgrp;
1356	>	fg = swderiv * d_grp;
1357	>	fij += fg;
1358	>
1359	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1)
1360	>	{
1361	>	tau -= outProduct(*(idat.d), fg);
1362	>	}
1363	>
1364	>	for (vector<int>::iterator ia = atomListRow.begin(); ia != atomListRow.end(); ++ia)
1365	>	{
1366	>	atom1 = (*ia);
1367	>	mf = fDecomp_->getMassFactorRow(atom1);
1368	>	// fg is the force on atom ia due to cutoff group's
1369	>	// presence in switching region
1370	>	fg = swderiv * d_grp * mf;
1371	>	fDecomp_->addForceToAtomRow(atom1, fg);
1372	>
1373	>	if (atomListRow.size() > 1)
1374	>	{
1375	>	if (info_->usesAtomicVirial())
1376	>	{
1377	>	// find the distance between the atom
1378	>	// and the center of the cutoff group:
1379	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
1380	>	tau -= outProduct(dag, fg);
1381	>	}
1382	>	}
1383	>	}
1384	>	for (vector<int>::iterator jb = atomListColumn.begin(); jb != atomListColumn.end(); ++jb)
1385	>	{
1386	>	atom2 = (*jb);
1387	>	mf = fDecomp_->getMassFactorColumn(atom2);
1388	>	// fg is the force on atom jb due to cutoff group's
1389	>	// presence in switching region
1390	>	fg = -swderiv * d_grp * mf;
1391	>	fDecomp_->addForceToAtomColumn(atom2, fg);
1392	>
1393	>	if (atomListColumn.size() > 1)
1394	>	{
1395	>	if (info_->usesAtomicVirial())
1396	>	{
1397	>	// find the distance between the atom
1398	>	// and the center of the cutoff group:
1399	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
1400	>	tau -= outProduct(dag, fg);
1401	>	}
1402	>	}
1403	>	}
1404	>	}
1405	>	//if (!SIM_uses_AtomicVirial) {
1406	>	//  tau -= outProduct(d_grp, fij);
1407	>	//}
1408	>	}
1409	>	}
1410	>	}
1411	>
1412	>	if (iLoop == PREPAIR_LOOP)
1413	>	{
1414	>	if (info_->requiresPrepair())
1415	>	{
1416	>
1417	>	fDecomp_->collectIntermediateData();
1418	>
1419	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++)
1420	>	{
1421	>	fDecomp_->fillSelfData(sdat, atom1);
1422	>	interactionMan_->doPreForce(sdat);
1423	>	}
1424	>
1425	>	fDecomp_->distributeIntermediateData();
1426	>
1427	>	}
1428	>	}
1429	>
1430	>	}
1431	>
1432	>	fDecomp_->collectData();
1433	>
1434	>	if (info_->requiresSelfCorrection())
1435	>	{
1436	>
1437	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++)
1438	>	{
1439	>	fDecomp_->fillSelfData(sdat, atom1);
1440	>	interactionMan_->doSelfCorrection(sdat);
1441	>	}
1442	>
1443	>	}
1444	>
1445	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) + *(fDecomp_->getPairwisePotential());
1446	>
1447	>	lrPot = longRangePotential.sum();
1448	>
1449	>	//store the tau and long range potential
1450	>	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
1451	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
1452	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
1453	>	}
1454	>
1455	>	void ForceManager::postCalculation() {
1456	>	SimInfo::MoleculeIterator mi;
1457	>	Molecule* mol;
1458	>	Molecule::RigidBodyIterator rbIter;
1459	>	RigidBody* rb;
1460	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
1461	>
1462	>	// collect the atomic forces onto rigid bodies
1463	>
1464	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1465	>	{
1466	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter))
1467	>	{
1468	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
1469	>	tau += rbTau;
1470	>	}
1471	>	}
1472	>
1473	>	#ifdef IS_MPI
1474	>	Mat3x3d tmpTau(tau);
1475	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
1476	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1477		#endif
1478	<	curSnapshot->statData.setTau(tau);
1479	<	}
1478	>	curSnapshot->statData.setTau(tau);
1479	>	}
1480
1481		} //end namespace OpenMD

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines