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

Comparing:
branches/development/src/brains/ForceManager.cpp (file contents), Revision 1587 by gezelter, Fri Jul 8 20:25:32 2011 UTC vs.
branches/devel_omp/src/brains/ForceManager.cpp (file contents), Revision 1608 by mciznick, Tue Aug 9 01:58:56 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	+
67		using namespace std;
68		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	–	}
69
70	<	/**
71	<	* setupCutoffs
72	<	*
73	<	* Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
74	<	* and cutoffPolicy
75	<	*
81	<	* cutoffRadius : realType
82	<	*  If the cutoffRadius was explicitly set, use that value.
83	<	*  If the cutoffRadius was not explicitly set:
84	<	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
85	<	*      No electrostatic atoms?  Poll the atom types present in the
86	<	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
87	<	*      Use the maximum suggested value that was found.
88	<	*
89	<	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE, SHIFTED_POTENTIAL)
90	<	*      If cutoffMethod was explicitly set, use that choice.
91	<	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
92	<	*
93	<	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
94	<	*      If cutoffPolicy was explicitly set, use that choice.
95	<	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
96	<	*
97	<	* switchingRadius : realType
98	<	*  If the cutoffMethod was set to SWITCHED:
99	<	*      If the switchingRadius was explicitly set, use that value
100	<	*          (but do a sanity check first).
101	<	*      If the switchingRadius was not explicitly set: use 0.85 *
102	<	*      cutoffRadius_
103	<	*  If the cutoffMethod was not set to SWITCHED:
104	<	*      Set switchingRadius equal to cutoffRadius for safety.
105	<	*/
106	<	void ForceManager::setupCutoffs() {
107	<
108	<	Globals* simParams_ = info_->getSimParams();
109	<	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
110	<
111	<	if (simParams_->haveCutoffRadius()) {
112	<	rCut_ = simParams_->getCutoffRadius();
113	<	} else {
114	<	if (info_->usesElectrostaticAtoms()) {
115	<	sprintf(painCave.errMsg,
116	<	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
117	<	"\tOpenMD will use a default value of 12.0 angstroms"
118	<	"\tfor the cutoffRadius.\n");
119	<	painCave.isFatal = 0;
120	<	painCave.severity = OPENMD_INFO;
121	<	simError();
122	<	rCut_ = 12.0;
123	<	} else {
124	<	RealType thisCut;
125	<	set<AtomType*>::iterator i;
126	<	set<AtomType*> atomTypes;
127	<	atomTypes = info_->getSimulatedAtomTypes();
128	<	for (i = atomTypes.begin(); i != atomTypes.end(); ++i) {
129	<	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
130	<	rCut_ = max(thisCut, rCut_);
131	<	}
132	<	sprintf(painCave.errMsg,
133	<	"ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
134	<	"\tOpenMD will use %lf angstroms.\n",
135	<	rCut_);
136	<	painCave.isFatal = 0;
137	<	painCave.severity = OPENMD_INFO;
138	<	simError();
139	<	}
140	<	}
70	>	ForceManager::ForceManager(SimInfo * info) :
71	>	info_(info) {
72	>	forceField_ = info_->getForceField();
73	>	interactionMan_ = new InteractionManager();
74	>	fDecomp_ = new ForceMatrixDecomposition(info_, interactionMan_);
75	>	}
76
77	<	fDecomp_->setUserCutoff(rCut_);
78	<	interactionMan_->setCutoffRadius(rCut_);
77	>	/**
78	>	* setupCutoffs
79	>	*
80	>	* Sets the values of cutoffRadius, switchingRadius, cutoffMethod,
81	>	* and cutoffPolicy
82	>	*
83	>	* cutoffRadius : realType
84	>	*  If the cutoffRadius was explicitly set, use that value.
85	>	*  If the cutoffRadius was not explicitly set:
86	>	*      Are there electrostatic atoms?  Use 12.0 Angstroms.
87	>	*      No electrostatic atoms?  Poll the atom types present in the
88	>	*      simulation for suggested cutoff values (e.g. 2.5 * sigma).
89	>	*      Use the maximum suggested value that was found.
90	>	*
91	>	* cutoffMethod : (one of HARD, SWITCHED, SHIFTED_FORCE,
92	>	*                        or SHIFTED_POTENTIAL)
93	>	*      If cutoffMethod was explicitly set, use that choice.
94	>	*      If cutoffMethod was not explicitly set, use SHIFTED_FORCE
95	>	*
96	>	* cutoffPolicy : (one of MIX, MAX, TRADITIONAL)
97	>	*      If cutoffPolicy was explicitly set, use that choice.
98	>	*      If cutoffPolicy was not explicitly set, use TRADITIONAL
99	>	*
100	>	* switchingRadius : realType
101	>	*  If the cutoffMethod was set to SWITCHED:
102	>	*      If the switchingRadius was explicitly set, use that value
103	>	*          (but do a sanity check first).
104	>	*      If the switchingRadius was not explicitly set: use 0.85 *
105	>	*      cutoffRadius_
106	>	*  If the cutoffMethod was not set to SWITCHED:
107	>	*      Set switchingRadius equal to cutoffRadius for safety.
108	>	*/
109	>	void ForceManager::setupCutoffs() {
110
111	<	map<string, CutoffMethod> stringToCutoffMethod;
112	<	stringToCutoffMethod["HARD"] = HARD;
147	<	stringToCutoffMethod["SWITCHED"] = SWITCHED;
148	<	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
149	<	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
150	<
151	<	if (simParams_->haveCutoffMethod()) {
152	<	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
153	<	map<string, CutoffMethod>::iterator i;
154	<	i = stringToCutoffMethod.find(cutMeth);
155	<	if (i == stringToCutoffMethod.end()) {
156	<	sprintf(painCave.errMsg,
157	<	"ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
158	<	"\tShould be one of: "
159	<	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n",
160	<	cutMeth.c_str());
161	<	painCave.isFatal = 1;
162	<	painCave.severity = OPENMD_ERROR;
163	<	simError();
164	<	} else {
165	<	cutoffMethod_ = i->second;
166	<	}
167	<	} else {
168	<	sprintf(painCave.errMsg,
169	<	"ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
170	<	"\tOpenMD will use SHIFTED_FORCE.\n");
171	<	painCave.isFatal = 0;
172	<	painCave.severity = OPENMD_INFO;
173	<	simError();
174	<	cutoffMethod_ = SHIFTED_FORCE;
175	<	}
111	>	Globals* simParams_ = info_->getSimParams();
112	>	ForceFieldOptions& forceFieldOptions_ = forceField_->getForceFieldOptions();
113
114	<	map<string, CutoffPolicy> stringToCutoffPolicy;
115	<	stringToCutoffPolicy["MIX"] = MIX;
116	<	stringToCutoffPolicy["MAX"] = MAX;
117	<	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
114	>	if (simParams_->haveCutoffRadius())
115	>	{
116	>	rCut_ = simParams_->getCutoffRadius();
117	>	} else
118	>	{
119	>	if (info_->usesElectrostaticAtoms())
120	>	{
121	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
122	>	"\tOpenMD will use a default value of 12.0 angstroms"
123	>	"\tfor the cutoffRadius.\n");
124	>	painCave.isFatal = 0;
125	>	painCave.severity = OPENMD_INFO;
126	>	simError();
127	>	rCut_ = 12.0;
128	>	} else
129	>	{
130	>	RealType thisCut;
131	>	set<AtomType*>::iterator i;
132	>	set<AtomType*> atomTypes;
133	>	atomTypes = info_->getSimulatedAtomTypes();
134	>	for (i = atomTypes.begin(); i != atomTypes.end(); ++i)
135	>	{
136	>	thisCut = interactionMan_->getSuggestedCutoffRadius((*i));
137	>	rCut_ = max(thisCut, rCut_);
138	>	}
139	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: No value was set for the cutoffRadius.\n"
140	>	"\tOpenMD will use %lf angstroms.\n", rCut_);
141	>	painCave.isFatal = 0;
142	>	painCave.severity = OPENMD_INFO;
143	>	simError();
144	>	}
145	>	}
146
147	<	std::string cutPolicy;
148	<	if (forceFieldOptions_.haveCutoffPolicy()){
184	<	cutPolicy = forceFieldOptions_.getCutoffPolicy();
185	<	}else if (simParams_->haveCutoffPolicy()) {
186	<	cutPolicy = simParams_->getCutoffPolicy();
187	<	}
147	>	fDecomp_->setUserCutoff(rCut_);
148	>	interactionMan_->setCutoffRadius(rCut_);
149
150	<	if (!cutPolicy.empty()){
151	<	toUpper(cutPolicy);
152	<	map<string, CutoffPolicy>::iterator i;
153	<	i = stringToCutoffPolicy.find(cutPolicy);
150	>	map<string, CutoffMethod> stringToCutoffMethod;
151	>	stringToCutoffMethod["HARD"] = HARD;
152	>	stringToCutoffMethod["SWITCHED"] = SWITCHED;
153	>	stringToCutoffMethod["SHIFTED_POTENTIAL"] = SHIFTED_POTENTIAL;
154	>	stringToCutoffMethod["SHIFTED_FORCE"] = SHIFTED_FORCE;
155
156	<	if (i == stringToCutoffPolicy.end()) {
157	<	sprintf(painCave.errMsg,
158	<	"ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
159	<	"\tShould be one of: "
160	<	"MIX, MAX, or TRADITIONAL\n",
161	<	cutPolicy.c_str());
162	<	painCave.isFatal = 1;
163	<	painCave.severity = OPENMD_ERROR;
164	<	simError();
165	<	} else {
166	<	cutoffPolicy_ = i->second;
167	<	}
168	<	} else {
169	<	sprintf(painCave.errMsg,
170	<	"ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
171	<	"\tOpenMD will use TRADITIONAL.\n");
172	<	painCave.isFatal = 0;
173	<	painCave.severity = OPENMD_INFO;
174	<	simError();
175	<	cutoffPolicy_ = TRADITIONAL;
176	<	}
156	>	if (simParams_->haveCutoffMethod())
157	>	{
158	>	string cutMeth = toUpperCopy(simParams_->getCutoffMethod());
159	>	map<string, CutoffMethod>::iterator i;
160	>	i = stringToCutoffMethod.find(cutMeth);
161	>	if (i == stringToCutoffMethod.end())
162	>	{
163	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: Could not find chosen cutoffMethod %s\n"
164	>	"\tShould be one of: "
165	>	"HARD, SWITCHED, SHIFTED_POTENTIAL, or SHIFTED_FORCE\n", cutMeth.c_str());
166	>	painCave.isFatal = 1;
167	>	painCave.severity = OPENMD_ERROR;
168	>	simError();
169	>	} else
170	>	{
171	>	cutoffMethod_ = i->second;
172	>	}
173	>	} else
174	>	{
175	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: No value was set for the cutoffMethod.\n"
176	>	"\tOpenMD will use SHIFTED_FORCE.\n");
177	>	painCave.isFatal = 0;
178	>	painCave.severity = OPENMD_INFO;
179	>	simError();
180	>	cutoffMethod_ = SHIFTED_FORCE;
181	>	}
182
183	<	fDecomp_->setCutoffPolicy(cutoffPolicy_);
184	<
185	<	// create the switching function object:
183	>	map<string, CutoffPolicy> stringToCutoffPolicy;
184	>	stringToCutoffPolicy["MIX"] = MIX;
185	>	stringToCutoffPolicy["MAX"] = MAX;
186	>	stringToCutoffPolicy["TRADITIONAL"] = TRADITIONAL;
187
188	<	switcher_ = new SwitchingFunction();
189	<
190	<	if (cutoffMethod_ == SWITCHED) {
191	<	if (simParams_->haveSwitchingRadius()) {
192	<	rSwitch_ = simParams_->getSwitchingRadius();
193	<	if (rSwitch_ > rCut_) {
194	<	sprintf(painCave.errMsg,
195	<	"ForceManager::setupCutoffs: switchingRadius (%f) is larger "
228	<	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
229	<	painCave.isFatal = 1;
230	<	painCave.severity = OPENMD_ERROR;
231	<	simError();
232	<	}
233	<	} else {
234	<	rSwitch_ = 0.85 * rCut_;
235	<	sprintf(painCave.errMsg,
236	<	"ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
237	<	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
238	<	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
239	<	painCave.isFatal = 0;
240	<	painCave.severity = OPENMD_WARNING;
241	<	simError();
242	<	}
243	<	} else {
244	<	if (simParams_->haveSwitchingRadius()) {
245	<	map<string, CutoffMethod>::const_iterator it;
246	<	string theMeth;
247	<	for (it = stringToCutoffMethod.begin();
248	<	it != stringToCutoffMethod.end(); ++it) {
249	<	if (it->second == cutoffMethod_) {
250	<	theMeth = it->first;
251	<	break;
252	<	}
253	<	}
254	<	sprintf(painCave.errMsg,
255	<	"ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
256	<	"\tis not set to SWITCHED, so switchingRadius value\n"
257	<	"\twill be ignored for this simulation\n", theMeth.c_str());
258	<	painCave.isFatal = 0;
259	<	painCave.severity = OPENMD_WARNING;
260	<	simError();
261	<	}
188	>	std::string cutPolicy;
189	>	if (forceFieldOptions_.haveCutoffPolicy())
190	>	{
191	>	cutPolicy = forceFieldOptions_.getCutoffPolicy();
192	>	} else if (simParams_->haveCutoffPolicy())
193	>	{
194	>	cutPolicy = simParams_->getCutoffPolicy();
195	>	}
196
197	<	rSwitch_ = rCut_;
198	<	}
199	<
200	<	// Default to cubic switching function.
201	<	sft_ = cubic;
268	<	if (simParams_->haveSwitchingFunctionType()) {
269	<	string funcType = simParams_->getSwitchingFunctionType();
270	<	toUpper(funcType);
271	<	if (funcType == "CUBIC") {
272	<	sft_ = cubic;
273	<	} else {
274	<	if (funcType == "FIFTH_ORDER_POLYNOMIAL") {
275	<	sft_ = fifth_order_poly;
276	<	} else {
277	<	// throw error
278	<	sprintf( painCave.errMsg,
279	<	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
280	<	"\tswitchingFunctionType must be one of: "
281	<	"\"cubic\" or \"fifth_order_polynomial\".",
282	<	funcType.c_str() );
283	<	painCave.isFatal = 1;
284	<	painCave.severity = OPENMD_ERROR;
285	<	simError();
286	<	}
287	<	}
288	<	}
289	<	switcher_->setSwitchType(sft_);
290	<	switcher_->setSwitch(rSwitch_, rCut_);
291	<	interactionMan_->setSwitchingRadius(rSwitch_);
292	<	}
293	<
294	<	void ForceManager::initialize() {
197	>	if (!cutPolicy.empty())
198	>	{
199	>	toUpper(cutPolicy);
200	>	map<string, CutoffPolicy>::iterator i;
201	>	i = stringToCutoffPolicy.find(cutPolicy);
202
203	<	if (!info_->isTopologyDone()) {
204	<	info_->update();
205	<	interactionMan_->setSimInfo(info_);
206	<	interactionMan_->initialize();
203	>	if (i == stringToCutoffPolicy.end())
204	>	{
205	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: Could not find chosen cutoffPolicy %s\n"
206	>	"\tShould be one of: "
207	>	"MIX, MAX, or TRADITIONAL\n", cutPolicy.c_str());
208	>	painCave.isFatal = 1;
209	>	painCave.severity = OPENMD_ERROR;
210	>	simError();
211	>	} else
212	>	{
213	>	cutoffPolicy_ = i->second;
214	>	}
215	>	} else
216	>	{
217	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: No value was set for the cutoffPolicy.\n"
218	>	"\tOpenMD will use TRADITIONAL.\n");
219	>	painCave.isFatal = 0;
220	>	painCave.severity = OPENMD_INFO;
221	>	simError();
222	>	cutoffPolicy_ = TRADITIONAL;
223	>	}
224
225	<	// We want to delay the cutoffs until after the interaction
302	<	// manager has set up the atom-atom interactions so that we can
303	<	// query them for suggested cutoff values
225	>	fDecomp_->setCutoffPolicy(cutoffPolicy_);
226
227	<	setupCutoffs();
227	>	// create the switching function object:
228
229	<	info_->prepareTopology();
308	<	}
229	>	switcher_ = new SwitchingFunction();
230
231	<	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
232	<
233	<	// Force fields can set options on how to scale van der Waals and electrostatic
234	<	// interactions for atoms connected via bonds, bends and torsions
235	<	// in this case the topological distance between atoms is:
236	<	// 0 = topologically unconnected
237	<	// 1 = bonded together
238	<	// 2 = connected via a bend
239	<	// 3 = connected via a torsion
240	<
241	<	vdwScale_.reserve(4);
242	<	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
231	>	if (cutoffMethod_ == SWITCHED)
232	>	{
233	>	if (simParams_->haveSwitchingRadius())
234	>	{
235	>	rSwitch_ = simParams_->getSwitchingRadius();
236	>	if (rSwitch_ > rCut_)
237	>	{
238	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: switchingRadius (%f) is larger "
239	>	"than the cutoffRadius(%f)\n", rSwitch_, rCut_);
240	>	painCave.isFatal = 1;
241	>	painCave.severity = OPENMD_ERROR;
242	>	simError();
243	>	}
244	>	} else
245	>	{
246	>	rSwitch_ = 0.85 * rCut_;
247	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: No value was set for the switchingRadius.\n"
248	>	"\tOpenMD will use a default value of 85 percent of the cutoffRadius.\n"
249	>	"\tswitchingRadius = %f. for this simulation\n", rSwitch_);
250	>	painCave.isFatal = 0;
251	>	painCave.severity = OPENMD_WARNING;
252	>	simError();
253	>	}
254	>	} else
255	>	{
256	>	if (simParams_->haveSwitchingRadius())
257	>	{
258	>	map<string, CutoffMethod>::const_iterator it;
259	>	string theMeth;
260	>	for (it = stringToCutoffMethod.begin(); it != stringToCutoffMethod.end(); ++it)
261	>	{
262	>	if (it->second == cutoffMethod_)
263	>	{
264	>	theMeth = it->first;
265	>	break;
266	>	}
267	>	}
268	>	sprintf(painCave.errMsg, "ForceManager::setupCutoffs: the cutoffMethod (%s)\n"
269	>	"\tis not set to SWITCHED, so switchingRadius value\n"
270	>	"\twill be ignored for this simulation\n", theMeth.c_str());
271	>	painCave.isFatal = 0;
272	>	painCave.severity = OPENMD_WARNING;
273	>	simError();
274	>	}
275
276	<	electrostaticScale_.reserve(4);
277	<	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
276	>	rSwitch_ = rCut_;
277	>	}
278
279	<	vdwScale_[0] = 1.0;
280	<	vdwScale_[1] = fopts.getvdw12scale();
281	<	vdwScale_[2] = fopts.getvdw13scale();
282	<	vdwScale_[3] = fopts.getvdw14scale();
283	<
284	<	electrostaticScale_[0] = 1.0;
285	<	electrostaticScale_[1] = fopts.getelectrostatic12scale();
286	<	electrostaticScale_[2] = fopts.getelectrostatic13scale();
287	<	electrostaticScale_[3] = fopts.getelectrostatic14scale();
288	<
289	<	fDecomp_->distributeInitialData();
290	<
291	<	initialized_ = true;
279	>	// Default to cubic switching function.
280	>	sft_ = cubic;
281	>	if (simParams_->haveSwitchingFunctionType())
282	>	{
283	>	string funcType = simParams_->getSwitchingFunctionType();
284	>	toUpper(funcType);
285	>	if (funcType == "CUBIC")
286	>	{
287	>	sft_ = cubic;
288	>	} else
289	>	{
290	>	if (funcType == "FIFTH_ORDER_POLYNOMIAL")
291	>	{
292	>	sft_ = fifth_order_poly;
293	>	} else
294	>	{
295	>	// throw error
296	>	sprintf(painCave.errMsg,
297	>	"ForceManager::setupSwitching : Unknown switchingFunctionType. (Input file specified %s .)\n"
298	>	"\tswitchingFunctionType must be one of: "
299	>	"\"cubic\" or \"fifth_order_polynomial\".", funcType.c_str());
300	>	painCave.isFatal = 1;
301	>	painCave.severity = OPENMD_ERROR;
302	>	simError();
303	>	}
304	>	}
305	>	}
306	>	switcher_->setSwitchType(sft_);
307	>	switcher_->setSwitch(rSwitch_, rCut_);
308	>	interactionMan_->setSwitchingRadius(rSwitch_);
309	>	}
310
311	<	}
311	>	void ForceManager::initialize() {
312
313	<	void ForceManager::calcForces() {
314	<
344	<	if (!initialized_) initialize();
313	>	if (!info_->isTopologyDone())
314	>	{
315
316	<	preCalculation();
317	<	shortRangeInteractions();
318	<	longRangeInteractions();
349	<	postCalculation();
350	<	}
351	<
352	<	void ForceManager::preCalculation() {
353	<	SimInfo::MoleculeIterator mi;
354	<	Molecule* mol;
355	<	Molecule::AtomIterator ai;
356	<	Atom* atom;
357	<	Molecule::RigidBodyIterator rbIter;
358	<	RigidBody* rb;
359	<	Molecule::CutoffGroupIterator ci;
360	<	CutoffGroup* cg;
361	<
362	<	// forces are zeroed here, before any are accumulated.
363	<
364	<	for (mol = info_->beginMolecule(mi); mol != NULL;
365	<	mol = info_->nextMolecule(mi)) {
366	<	for(atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai)) {
367	<	atom->zeroForcesAndTorques();
368	<	}
369	<
370	<	//change the positions of atoms which belong to the rigidbodies
371	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
372	<	rb = mol->nextRigidBody(rbIter)) {
373	<	rb->zeroForcesAndTorques();
374	<	}
316	>	info_->update();
317	>	interactionMan_->setSimInfo(info_);
318	>	interactionMan_->initialize();
319
320	<	if(info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms()){
321	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
322	<	cg = mol->nextCutoffGroup(ci)) {
323	<	//calculate the center of mass of cutoff group
380	<	cg->updateCOM();
381	<	}
382	<	}
383	<	}
384	<
385	<	// Zero out the stress tensor
386	<	tau *= 0.0;
387	<
388	<	}
389	<
390	<	void ForceManager::shortRangeInteractions() {
391	<	Molecule* mol;
392	<	RigidBody* rb;
393	<	Bond* bond;
394	<	Bend* bend;
395	<	Torsion* torsion;
396	<	Inversion* inversion;
397	<	SimInfo::MoleculeIterator mi;
398	<	Molecule::RigidBodyIterator rbIter;
399	<	Molecule::BondIterator bondIter;;
400	<	Molecule::BendIterator  bendIter;
401	<	Molecule::TorsionIterator  torsionIter;
402	<	Molecule::InversionIterator  inversionIter;
403	<	RealType bondPotential = 0.0;
404	<	RealType bendPotential = 0.0;
405	<	RealType torsionPotential = 0.0;
406	<	RealType inversionPotential = 0.0;
320	>	// We want to delay the cutoffs until after the interaction
321	>	// manager has set up the atom-atom interactions so that we can
322	>	// query them for suggested cutoff values
323	>	setupCutoffs();
324
325	<	//calculate short range interactions
326	<	for (mol = info_->beginMolecule(mi); mol != NULL;
410	<	mol = info_->nextMolecule(mi)) {
325	>	info_->prepareTopology();
326	>	}
327
328	<	//change the positions of atoms which belong to the rigidbodies
413	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
414	<	rb = mol->nextRigidBody(rbIter)) {
415	<	rb->updateAtoms();
416	<	}
328	>	ForceFieldOptions& fopts = forceField_->getForceFieldOptions();
329
330	<	for (bond = mol->beginBond(bondIter); bond != NULL;
331	<	bond = mol->nextBond(bondIter)) {
332	<	bond->calcForce();
333	<	bondPotential += bond->getPotential();
334	<	}
330	>	// Force fields can set options on how to scale van der Waals and
331	>	// electrostatic interactions for atoms connected via bonds, bends
332	>	// and torsions in this case the topological distance between
333	>	// atoms is:
334	>	// 0 = topologically unconnected
335	>	// 1 = bonded together
336	>	// 2 = connected via a bend
337	>	// 3 = connected via a torsion
338
339	<	for (bend = mol->beginBend(bendIter); bend != NULL;
340	<	bend = mol->nextBend(bendIter)) {
426	<
427	<	RealType angle;
428	<	bend->calcForce(angle);
429	<	RealType currBendPot = bend->getPotential();
430	<
431	<	bendPotential += bend->getPotential();
432	<	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
433	<	if (i == bendDataSets.end()) {
434	<	BendDataSet dataSet;
435	<	dataSet.prev.angle = dataSet.curr.angle = angle;
436	<	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
437	<	dataSet.deltaV = 0.0;
438	<	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
439	<	}else {
440	<	i->second.prev.angle = i->second.curr.angle;
441	<	i->second.prev.potential = i->second.curr.potential;
442	<	i->second.curr.angle = angle;
443	<	i->second.curr.potential = currBendPot;
444	<	i->second.deltaV =  fabs(i->second.curr.potential -
445	<	i->second.prev.potential);
446	<	}
447	<	}
448	<
449	<	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL;
450	<	torsion = mol->nextTorsion(torsionIter)) {
451	<	RealType angle;
452	<	torsion->calcForce(angle);
453	<	RealType currTorsionPot = torsion->getPotential();
454	<	torsionPotential += torsion->getPotential();
455	<	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
456	<	if (i == torsionDataSets.end()) {
457	<	TorsionDataSet dataSet;
458	<	dataSet.prev.angle = dataSet.curr.angle = angle;
459	<	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
460	<	dataSet.deltaV = 0.0;
461	<	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
462	<	}else {
463	<	i->second.prev.angle = i->second.curr.angle;
464	<	i->second.prev.potential = i->second.curr.potential;
465	<	i->second.curr.angle = angle;
466	<	i->second.curr.potential = currTorsionPot;
467	<	i->second.deltaV =  fabs(i->second.curr.potential -
468	<	i->second.prev.potential);
469	<	}
470	<	}
471	<
472	<	for (inversion = mol->beginInversion(inversionIter);
473	<	inversion != NULL;
474	<	inversion = mol->nextInversion(inversionIter)) {
475	<	RealType angle;
476	<	inversion->calcForce(angle);
477	<	RealType currInversionPot = inversion->getPotential();
478	<	inversionPotential += inversion->getPotential();
479	<	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
480	<	if (i == inversionDataSets.end()) {
481	<	InversionDataSet dataSet;
482	<	dataSet.prev.angle = dataSet.curr.angle = angle;
483	<	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
484	<	dataSet.deltaV = 0.0;
485	<	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
486	<	}else {
487	<	i->second.prev.angle = i->second.curr.angle;
488	<	i->second.prev.potential = i->second.curr.potential;
489	<	i->second.curr.angle = angle;
490	<	i->second.curr.potential = currInversionPot;
491	<	i->second.deltaV =  fabs(i->second.curr.potential -
492	<	i->second.prev.potential);
493	<	}
494	<	}
495	<	}
496	<
497	<	RealType  shortRangePotential = bondPotential + bendPotential +
498	<	torsionPotential +  inversionPotential;
499	<	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
500	<	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
501	<	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
502	<	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
503	<	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
504	<	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
505	<	}
506	<
507	<	void ForceManager::longRangeInteractions() {
339	>	vdwScale_.reserve(4);
340	>	fill(vdwScale_.begin(), vdwScale_.end(), 0.0);
341
342	<	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
343	<	DataStorage* config = &(curSnapshot->atomData);
511	<	DataStorage* cgConfig = &(curSnapshot->cgData);
342	>	electrostaticScale_.reserve(4);
343	>	fill(electrostaticScale_.begin(), electrostaticScale_.end(), 0.0);
344
345	<	//calculate the center of mass of cutoff group
345	>	vdwScale_[0] = 1.0;
346	>	vdwScale_[1] = fopts.getvdw12scale();
347	>	vdwScale_[2] = fopts.getvdw13scale();
348	>	vdwScale_[3] = fopts.getvdw14scale();
349
350	<	SimInfo::MoleculeIterator mi;
351	<	Molecule* mol;
352	<	Molecule::CutoffGroupIterator ci;
353	<	CutoffGroup* cg;
350	>	electrostaticScale_[0] = 1.0;
351	>	electrostaticScale_[1] = fopts.getelectrostatic12scale();
352	>	electrostaticScale_[2] = fopts.getelectrostatic13scale();
353	>	electrostaticScale_[3] = fopts.getelectrostatic14scale();
354
355	<	if(info_->getNCutoffGroups() > 0){
521	<	for (mol = info_->beginMolecule(mi); mol != NULL;
522	<	mol = info_->nextMolecule(mi)) {
523	<	for(cg = mol->beginCutoffGroup(ci); cg != NULL;
524	<	cg = mol->nextCutoffGroup(ci)) {
525	<	cg->updateCOM();
526	<	}
527	<	}
528	<	} else {
529	<	// center of mass of the group is the same as position of the atom
530	<	// if cutoff group does not exist
531	<	cgConfig->position = config->position;
532	<	}
355	>	fDecomp_->distributeInitialData();
356
357	<	fDecomp_->zeroWorkArrays();
535	<	fDecomp_->distributeData();
536	<
537	<	int cg1, cg2, atom1, atom2, topoDist;
538	<	Vector3d d_grp, dag, d;
539	<	RealType rgrpsq, rgrp, r2, r;
540	<	RealType electroMult, vdwMult;
541	<	RealType vij;
542	<	Vector3d fij, fg, f1;
543	<	tuple3<RealType, RealType, RealType> cuts;
544	<	RealType rCutSq;
545	<	bool in_switching_region;
546	<	RealType sw, dswdr, swderiv;
547	<	vector<int> atomListColumn, atomListRow, atomListLocal;
548	<	InteractionData idat;
549	<	SelfData sdat;
550	<	RealType mf;
551	<	RealType lrPot;
552	<	RealType vpair;
553	<	potVec longRangePotential(0.0);
554	<	potVec workPot(0.0);
357	>	initialized_ = true;
358
359	<	int loopStart, loopEnd;
359	>	}
360
361	<	idat.vdwMult = &vdwMult;
559	<	idat.electroMult = &electroMult;
560	<	idat.pot = &workPot;
561	<	sdat.pot = fDecomp_->getEmbeddingPotential();
562	<	idat.vpair = &vpair;
563	<	idat.f1 = &f1;
564	<	idat.sw = &sw;
565	<	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
566	<	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
567	<
568	<	loopEnd = PAIR_LOOP;
569	<	if (info_->requiresPrepair() ) {
570	<	loopStart = PREPAIR_LOOP;
571	<	} else {
572	<	loopStart = PAIR_LOOP;
573	<	}
574	<
575	<	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++) {
576	<
577	<	if (iLoop == loopStart) {
578	<	bool update_nlist = fDecomp_->checkNeighborList();
579	<	if (update_nlist)
580	<	neighborList = fDecomp_->buildNeighborList();
581	<	}
582	<
583	<	for (vector<pair<int, int> >::iterator it = neighborList.begin();
584	<	it != neighborList.end(); ++it) {
585	<
586	<	cg1 = (*it).first;
587	<	cg2 = (*it).second;
588	<
589	<	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
361	>	void ForceManager::calcForces() {
362
363	<	d_grp  = fDecomp_->getIntergroupVector(cg1, cg2);
364	<	curSnapshot->wrapVector(d_grp);
593	<	rgrpsq = d_grp.lengthSquare();
363	>	if (!initialized_)
364	>	initialize();
365
366	<	rCutSq = cuts.second;
366	>	preCalculation();
367	>	shortRangeInteractions();
368	>	//    longRangeInteractions();
369	>	//      longRangeInteractionsRapaport();
370	>	longRangeInteractionsParallel();
371	>	postCalculation();
372	>	}
373
374	<	if (rgrpsq < rCutSq) {
375	<	idat.rcut = &cuts.first;
376	<	if (iLoop == PAIR_LOOP) {
377	<	vij = 0.0;
378	<	fij = V3Zero;
379	<	}
380	<
381	<	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr,
382	<	rgrp);
606	<
607	<	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
608	<	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
374	>	void ForceManager::preCalculation() {
375	>	SimInfo::MoleculeIterator mi;
376	>	Molecule* mol;
377	>	Molecule::AtomIterator ai;
378	>	Atom* atom;
379	>	Molecule::RigidBodyIterator rbIter;
380	>	RigidBody* rb;
381	>	Molecule::CutoffGroupIterator ci;
382	>	CutoffGroup* cg;
383
384	<	for (vector<int>::iterator ia = atomListRow.begin();
611	<	ia != atomListRow.end(); ++ia) {
612	<	atom1 = (*ia);
613	<
614	<	for (vector<int>::iterator jb = atomListColumn.begin();
615	<	jb != atomListColumn.end(); ++jb) {
616	<	atom2 = (*jb);
617	<
618	<	if (!fDecomp_->skipAtomPair(atom1, atom2)) {
619	<	vpair = 0.0;
620	<	workPot = 0.0;
621	<	f1 = V3Zero;
384	>	// forces are zeroed here, before any are accumulated.
385
386	<	fDecomp_->fillInteractionData(idat, atom1, atom2);
387	<
388	<	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
389	<	vdwMult = vdwScale_[topoDist];
390	<	electroMult = electrostaticScale_[topoDist];
386	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
387	>	{
388	>	for (atom = mol->beginAtom(ai); atom != NULL; atom = mol->nextAtom(ai))
389	>	{
390	>	atom->zeroForcesAndTorques();
391	>	}
392
393	<	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
394	<	idat.d = &d_grp;
395	<	idat.r2 = &rgrpsq;
396	<	} else {
397	<	d = fDecomp_->getInteratomicVector(atom1, atom2);
634	<	curSnapshot->wrapVector( d );
635	<	r2 = d.lengthSquare();
636	<	idat.d = &d;
637	<	idat.r2 = &r2;
638	<	}
639	<
640	<	r = sqrt( *(idat.r2) );
641	<	idat.rij = &r;
642	<
643	<	if (iLoop == PREPAIR_LOOP) {
644	<	interactionMan_->doPrePair(idat);
645	<	} else {
646	<	interactionMan_->doPair(idat);
647	<	fDecomp_->unpackInteractionData(idat, atom1, atom2);
648	<	vij += vpair;
649	<	fij += f1;
650	<	tau -= outProduct( *(idat.d), f1);
651	<	}
652	<	}
653	<	}
654	<	}
393	>	//change the positions of atoms which belong to the rigidbodies
394	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter))
395	>	{
396	>	rb->zeroForcesAndTorques();
397	>	}
398
399	<	if (iLoop == PAIR_LOOP) {
400	<	if (in_switching_region) {
401	<	swderiv = vij * dswdr / rgrp;
402	<	fg = swderiv * d_grp;
403	<	fij += fg;
399	>	if (info_->getNGlobalCutoffGroups() != info_->getNGlobalAtoms())
400	>	{
401	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
402	>	{
403	>	//calculate the center of mass of cutoff group
404	>	cg->updateCOM();
405	>	}
406	>	}
407	>	}
408
409	<	if (atomListRow.size() == 1 && atomListColumn.size() == 1) {
410	<	tau -= outProduct( *(idat.d), fg);
664	<	}
665	<
666	<	for (vector<int>::iterator ia = atomListRow.begin();
667	<	ia != atomListRow.end(); ++ia) {
668	<	atom1 = (*ia);
669	<	mf = fDecomp_->getMassFactorRow(atom1);
670	<	// fg is the force on atom ia due to cutoff group's
671	<	// presence in switching region
672	<	fg = swderiv * d_grp * mf;
673	<	fDecomp_->addForceToAtomRow(atom1, fg);
409	>	// Zero out the stress tensor
410	>	tau *= 0.0;
411
412	<	if (atomListRow.size() > 1) {
676	<	if (info_->usesAtomicVirial()) {
677	<	// find the distance between the atom
678	<	// and the center of the cutoff group:
679	<	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
680	<	tau -= outProduct(dag, fg);
681	<	}
682	<	}
683	<	}
684	<	for (vector<int>::iterator jb = atomListColumn.begin();
685	<	jb != atomListColumn.end(); ++jb) {
686	<	atom2 = (*jb);
687	<	mf = fDecomp_->getMassFactorColumn(atom2);
688	<	// fg is the force on atom jb due to cutoff group's
689	<	// presence in switching region
690	<	fg = -swderiv * d_grp * mf;
691	<	fDecomp_->addForceToAtomColumn(atom2, fg);
412	>	}
413
414	<	if (atomListColumn.size() > 1) {
415	<	if (info_->usesAtomicVirial()) {
416	<	// find the distance between the atom
417	<	// and the center of the cutoff group:
418	<	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
419	<	tau -= outProduct(dag, fg);
420	<	}
421	<	}
422	<	}
423	<	}
424	<	//if (!SIM_uses_AtomicVirial) {
425	<	//  tau -= outProduct(d_grp, fij);
426	<	//}
427	<	}
428	<	}
429	<	}
414	>	void ForceManager::shortRangeInteractions() {
415	>	Molecule* mol;
416	>	RigidBody* rb;
417	>	Bond* bond;
418	>	Bend* bend;
419	>	Torsion* torsion;
420	>	Inversion* inversion;
421	>	SimInfo::MoleculeIterator mi;
422	>	Molecule::RigidBodyIterator rbIter;
423	>	Molecule::BondIterator bondIter;
424	>	;
425	>	Molecule::BendIterator bendIter;
426	>	Molecule::TorsionIterator torsionIter;
427	>	Molecule::InversionIterator inversionIter;
428	>	RealType bondPotential = 0.0;
429	>	RealType bendPotential = 0.0;
430	>	RealType torsionPotential = 0.0;
431	>	RealType inversionPotential = 0.0;
432
433	<	if (iLoop == PREPAIR_LOOP) {
434	<	if (info_->requiresPrepair()) {
435	<	fDecomp_->collectIntermediateData();
433	>	//calculate short range interactions
434	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
435	>	{
436
437	<	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
438	<	fDecomp_->fillSelfData(sdat, atom1);
439	<	interactionMan_->doPreForce(sdat);
440	<	}
441	<
719	<
720	<	fDecomp_->distributeIntermediateData();
721	<	}
722	<	}
437	>	//change the positions of atoms which belong to the rigidbodies
438	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter))
439	>	{
440	>	rb->updateAtoms();
441	>	}
442
443	<	}
444	<
445	<	fDecomp_->collectData();
446	<
447	<	if (info_->requiresSelfCorrection()) {
443	>	for (bond = mol->beginBond(bondIter); bond != NULL; bond = mol->nextBond(bondIter))
444	>	{
445	>	bond->calcForce();
446	>	bondPotential += bond->getPotential();
447	>	}
448
449	<	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++) {
450	<	fDecomp_->fillSelfData(sdat, atom1);
732	<	interactionMan_->doSelfCorrection(sdat);
733	<	}
449	>	for (bend = mol->beginBend(bendIter); bend != NULL; bend = mol->nextBend(bendIter))
450	>	{
451
452	<	}
452	>	RealType angle;
453	>	bend->calcForce(angle);
454	>	RealType currBendPot = bend->getPotential();
455
456	<	longRangePotential = *(fDecomp_->getEmbeddingPotential()) +
457	<	*(fDecomp_->getPairwisePotential());
456	>	bendPotential += bend->getPotential();
457	>	map<Bend*, BendDataSet>::iterator i = bendDataSets.find(bend);
458	>	if (i == bendDataSets.end())
459	>	{
460	>	BendDataSet dataSet;
461	>	dataSet.prev.angle = dataSet.curr.angle = angle;
462	>	dataSet.prev.potential = dataSet.curr.potential = currBendPot;
463	>	dataSet.deltaV = 0.0;
464	>	bendDataSets.insert(map<Bend*, BendDataSet>::value_type(bend, dataSet));
465	>	} else
466	>	{
467	>	i->second.prev.angle = i->second.curr.angle;
468	>	i->second.prev.potential = i->second.curr.potential;
469	>	i->second.curr.angle = angle;
470	>	i->second.curr.potential = currBendPot;
471	>	i->second.deltaV = fabs(i->second.curr.potential - i->second.prev.potential);
472	>	}
473	>	}
474
475	<	lrPot = longRangePotential.sum();
476	<
477	<	//store the tau and long range potential
478	<	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
479	<	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
480	<	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
481	<	}
475	>	for (torsion = mol->beginTorsion(torsionIter); torsion != NULL; torsion = mol->nextTorsion(torsionIter))
476	>	{
477	>	RealType angle;
478	>	torsion->calcForce(angle);
479	>	RealType currTorsionPot = torsion->getPotential();
480	>	torsionPotential += torsion->getPotential();
481	>	map<Torsion*, TorsionDataSet>::iterator i = torsionDataSets.find(torsion);
482	>	if (i == torsionDataSets.end())
483	>	{
484	>	TorsionDataSet dataSet;
485	>	dataSet.prev.angle = dataSet.curr.angle = angle;
486	>	dataSet.prev.potential = dataSet.curr.potential = currTorsionPot;
487	>	dataSet.deltaV = 0.0;
488	>	torsionDataSets.insert(map<Torsion*, TorsionDataSet>::value_type(torsion, dataSet));
489	>	} else
490	>	{
491	>	i->second.prev.angle = i->second.curr.angle;
492	>	i->second.prev.potential = i->second.curr.potential;
493	>	i->second.curr.angle = angle;
494	>	i->second.curr.potential = currTorsionPot;
495	>	i->second.deltaV = fabs(i->second.curr.potential - i->second.prev.potential);
496	>	}
497	>	}
498
499	<
500	<	void ForceManager::postCalculation() {
501	<	SimInfo::MoleculeIterator mi;
502	<	Molecule* mol;
503	<	Molecule::RigidBodyIterator rbIter;
504	<	RigidBody* rb;
505	<	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
506	<
507	<	// collect the atomic forces onto rigid bodies
508	<
509	<	for (mol = info_->beginMolecule(mi); mol != NULL;
510	<	mol = info_->nextMolecule(mi)) {
511	<	for (rb = mol->beginRigidBody(rbIter); rb != NULL;
512	<	rb = mol->nextRigidBody(rbIter)) {
513	<	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
514	<	tau += rbTau;
515	<	}
516	<	}
517	<
518	<	#ifdef IS_MPI
519	<	Mat3x3d tmpTau(tau);
520	<	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
521	<	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
499	>	for (inversion = mol->beginInversion(inversionIter); inversion != NULL; inversion = mol->nextInversion(
500	>	inversionIter))
501	>	{
502	>	RealType angle;
503	>	inversion->calcForce(angle);
504	>	RealType currInversionPot = inversion->getPotential();
505	>	inversionPotential += inversion->getPotential();
506	>	map<Inversion*, InversionDataSet>::iterator i = inversionDataSets.find(inversion);
507	>	if (i == inversionDataSets.end())
508	>	{
509	>	InversionDataSet dataSet;
510	>	dataSet.prev.angle = dataSet.curr.angle = angle;
511	>	dataSet.prev.potential = dataSet.curr.potential = currInversionPot;
512	>	dataSet.deltaV = 0.0;
513	>	inversionDataSets.insert(map<Inversion*, InversionDataSet>::value_type(inversion, dataSet));
514	>	} else
515	>	{
516	>	i->second.prev.angle = i->second.curr.angle;
517	>	i->second.prev.potential = i->second.curr.potential;
518	>	i->second.curr.angle = angle;
519	>	i->second.curr.potential = currInversionPot;
520	>	i->second.deltaV = fabs(i->second.curr.potential - i->second.prev.potential);
521	>	}
522	>	}
523	>	}
524	>
525	>	RealType shortRangePotential = bondPotential + bendPotential + torsionPotential + inversionPotential;
526	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
527	>	curSnapshot->statData[Stats::SHORT_RANGE_POTENTIAL] = shortRangePotential;
528	>	curSnapshot->statData[Stats::BOND_POTENTIAL] = bondPotential;
529	>	curSnapshot->statData[Stats::BEND_POTENTIAL] = bendPotential;
530	>	curSnapshot->statData[Stats::DIHEDRAL_POTENTIAL] = torsionPotential;
531	>	curSnapshot->statData[Stats::INVERSION_POTENTIAL] = inversionPotential;
532	>	}
533	>
534	>	void ForceManager::longRangeInteractionsParallel() {
535	>
536	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
537	>	DataStorage* config = &(curSnapshot->atomData);
538	>	DataStorage* cgConfig = &(curSnapshot->cgData);
539	>
540	>	//calculate the center of mass of cutoff group
541	>
542	>	SimInfo::MoleculeIterator mi;
543	>	Molecule* mol;
544	>	Molecule::CutoffGroupIterator ci;
545	>	CutoffGroup* cg;
546	>
547	>	if (info_->getNCutoffGroups() > 0)
548	>	{
549	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
550	>	{
551	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
552	>	{
553	>	//                              cerr << "branch1\n";
554	>	//                              cerr << "globind = " << cg->getGlobalIndex() << ":" << __LINE__ << "\n";
555	>	cg->updateCOM();
556	>
557	>	//                              cerr << "gbI: " << cg->getGlobalIndex() << " locI: " << cg->getLocalIndex() << " x: "
558	>	//                                              << cgConfig->position[cg->getLocalIndex()].x() << " y: " << cgConfig->position[cg->getLocalIndex()].y()
559	>	//                                              << " z: " << cgConfig->position[cg->getLocalIndex()].z() << "\n";
560	>	}
561	>	}
562	>	} else
563	>	{
564	>	// center of mass of the group is the same as position of the atom
565	>	// if cutoff group does not exist
566	>	//              cerr << ":" << __LINE__ << "branch2\n";
567	>	cgConfig->position = config->position;
568	>	}
569	>
570	>	fDecomp_->zeroWorkArrays();
571	>	fDecomp_->distributeData();
572	>
573	>	int atom1, atom2, topoDist;
574	>	Vector3d d_grp, dag, d;
575	>	RealType rgrpsq, rgrp, r2, r;
576	>	RealType electroMult, vdwMult;
577	>	RealType vij;
578	>	Vector3d fij, fg, f1;
579	>	tuple3<RealType, RealType, RealType> cuts;
580	>	RealType rCutSq;
581	>	bool in_switching_region;
582	>	RealType sw, dswdr, swderiv;
583	>	vector<int> atomListColumn, atomListRow, atomListLocal;
584	>
585	>	InteractionDataPrv idatPrv;
586	>
587	>	SelfData sdat;
588	>	RealType mf;
589	>	RealType lrPot;
590	>	RealType vpair;
591	>	potVec longRangePotential(0.0);
592	>	potVec workPot(0.0);
593	>
594	>	int loopStart, loopEnd;
595	>	sdat.pot = fDecomp_->getEmbeddingPotential();
596	>
597	>	vector<CutoffGroup *> cgs;
598	>
599	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
600	>	{
601	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
602	>	{
603	>	cgs.push_back(cg);
604	>	}
605	>	}
606	>
607	>	loopEnd = PAIR_LOOP;
608	>	if (info_->requiresPrepair())
609	>	{
610	>	loopStart = PREPAIR_LOOP;
611	>	} else
612	>	{
613	>	loopStart = PAIR_LOOP;
614	>	}
615	>
616	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++)
617	>	{
618	>
619	>	if (iLoop == loopStart)
620	>	{
621	>	bool update_nlist = fDecomp_->checkNeighborList();
622	>	if (update_nlist)
623	>	neighborMatW = fDecomp_->buildLayerBasedNeighborList();
624	>	}
625	>
626	>	vector<CutoffGroup *>::iterator cg1;
627	>	vector<CutoffGroup *>::iterator cg2;
628	>
629	>	//              int nThreads = 2;
630	>	int chunkSize = cgs.size() / (omp_get_num_threads() * 20);
631	>
632	>	//              printf("before omp loop\n");
633	>	#pragma omp parallel /*num_threads(nThreads)*/ default(none) shared(curSnapshot, iLoop, cgs, chunkSize) \
634	>	private(cg1, cg2, cuts, d_grp, rgrpsq, rCutSq, idatPrv, vij, fij, in_switching_region, dswdr, rgrp, \
635	>	atomListRow, atomListColumn, atom1, atom2, topoDist, d, r2, swderiv, fg, mf, dag)
636	>	{
637	>	idatPrv.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
638	>	idatPrv.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
639	>
640	>	//                      printf("Thread %d\n", omp_get_thread_num());
641	>	#pragma omp for schedule(dynamic, chunkSize)
642	>	for (cg1 = cgs.begin(); cg1 < cgs.end(); ++cg1)
643	>	{
644	>	for (cg2 = neighborMatW[(*cg1)->getGlobalIndex()].begin(); cg2 < neighborMatW[(*cg1)->getGlobalIndex()].end(); ++cg2)
645	>	{
646	>
647	>	cuts = fDecomp_->getGroupCutoffs((*cg1)->getGlobalIndex(), (*cg2)->getGlobalIndex());
648	>
649	>	d_grp = fDecomp_->getIntergroupVector((*cg1), (*cg2));
650	>	curSnapshot->wrapVector(d_grp);
651	>	rgrpsq = d_grp.lengthSquare();
652	>
653	>	rCutSq = cuts.second;
654	>
655	>	//                                      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);
656	>
657	>	if (rgrpsq < rCutSq)
658	>	{
659	>	idatPrv.rcut = cuts.first;
660	>	if (iLoop == PAIR_LOOP)
661	>	{
662	>	vij = 0.0;
663	>	fij = V3Zero;
664	>	}
665	>
666	>	in_switching_region = switcher_->getSwitch(rgrpsq, /*sw*/idatPrv.sw, dswdr, rgrp);
667	>
668	>	//                                              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);
669	>
670	>	atomListRow = fDecomp_->getAtomsInGroupRow((*cg1)->getGlobalIndex());
671	>	atomListColumn = fDecomp_->getAtomsInGroupColumn((*cg2)->getGlobalIndex());
672	>
673	>	for (vector<int>::iterator ia = atomListRow.begin(); ia != atomListRow.end(); ++ia)
674	>	{
675	>	atom1 = (*ia);
676	>
677	>	for (vector<int>::iterator jb = atomListColumn.begin(); jb != atomListColumn.end(); ++jb)
678	>	{
679	>	atom2 = (*jb);
680	>
681	>	//                                                              printf("atom1:%d atom2:%d\n", atom1, atom2);
682	>	if (!fDecomp_->skipAtomPair(atom1, atom2))
683	>	{
684	>	idatPrv.vpair = 0.0;
685	>	idatPrv.pot = 0.0;
686	>	idatPrv.f1 = V3Zero;
687	>
688	>	fDecomp_->fillInteractionDataOMP(idatPrv, atom1, atom2);
689	>
690	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
691	>	idatPrv.vdwMult = vdwScale_[topoDist];
692	>	idatPrv.electroMult = electrostaticScale_[topoDist];
693	>
694	>	//                                                                      printf("topoDist:%d\tidatPrv.vdwMult:%f\tidatPrv.electroMult:%f\n", topoDist, idatPrv.vdwMult, idatPrv.electroMult);
695	>
696	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1)
697	>	{
698	>	idatPrv.d = d_grp;
699	>	idatPrv.r2 = rgrpsq;
700	>	//                                                                              cerr << "dgrp = " << d_grp << ":" << __LINE__ << "\n";
701	>	} else
702	>	{
703	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
704	>	curSnapshot->wrapVector(d);
705	>	r2 = d.lengthSquare();
706	>	//                                                                              cerr << "datm = " << d << ":" << __LINE__ << "\n";
707	>	idatPrv.d = d;
708	>	idatPrv.r2 = r2;
709	>	}
710	>
711	>	//                                                                      printf("idatPrv.d x:%f\ty:%f\tz:%f\tidatPrv.r2:%f\n", (idatPrv.d).x(), (idatPrv.d).y(), (idatPrv.d).z(), idatPrv.r2);
712	>
713	>	//                                                                      cerr << "idat.d = " << *(idat.d) << ":" << __LINE__ << "\n";
714	>	idatPrv.rij = sqrt((idatPrv.r2));
715	>	//                                                                      cerr << "idat.rij = " << *(idat.rij) << "\n";
716	>
717	>	#pragma omp critical
718	>	{
719	>	interactionMan_->initializeOMP();
720	>	}
721	>
722	>	if (iLoop == PREPAIR_LOOP)
723	>	{
724	>	interactionMan_->doPrePairOMP(idatPrv);
725	>	} else
726	>	{
727	>	interactionMan_->doPairOMP(idatPrv);
728	>	fDecomp_->unpackInteractionDataOMP(idatPrv, atom1, atom2);
729	>
730	>	//                                                                              cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << ":" << __LINE__ << "\n";
731	>	//                                                                              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());
732	>	#pragma omp critical
733	>	{
734	>	vij += idatPrv.vpair;
735	>	fij += idatPrv.f1;
736	>	tau -= outProduct(idatPrv.d, idatPrv.f1);
737	>
738	>	//                                                                                      printf("vij:%f fij x:%f y:%f z:%f\n", vij, fij.x(), fij.y(), fij.z());
739	>	}
740	>	}
741	>	}
742	>	}
743	>	}
744	>
745	>	if (iLoop == PAIR_LOOP)
746	>	{
747	>	if (in_switching_region)
748	>	{
749	>	swderiv = vij * dswdr / rgrp;
750	>	fg = swderiv * d_grp;
751	>	fij += fg;
752	>
753	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1)
754	>	{
755	>	#pragma omp critical
756	>	{
757	>	tau -= outProduct(idatPrv.d, fg);
758	>	}
759	>	}
760	>
761	>	for (vector<int>::iterator ia = atomListRow.begin(); ia != atomListRow.end(); ++ia)
762	>	{
763	>	atom1 = (*ia);
764	>	mf = fDecomp_->getMassFactorRow(atom1);
765	>	// fg is the force on atom ia due to cutoff group's
766	>	// presence in switching region
767	>	fg = swderiv * d_grp * mf;
768	>	fDecomp_->addForceToAtomRowOMP(atom1, fg);
769	>
770	>	if (atomListRow.size() > 1)
771	>	{
772	>	if (info_->usesAtomicVirial())
773	>	{
774	>	// find the distance between the atom
775	>	// and the center of the cutoff group:
776	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, (*cg1)->getGlobalIndex());
777	>	#pragma omp critical
778	>	{
779	>	tau -= outProduct(dag, fg);
780	>	}
781	>	}
782	>	}
783	>	}
784	>	for (vector<int>::iterator jb = atomListColumn.begin(); jb != atomListColumn.end(); ++jb)
785	>	{
786	>	atom2 = (*jb);
787	>	mf = fDecomp_->getMassFactorColumn(atom2);
788	>	// fg is the force on atom jb due to cutoff group's
789	>	// presence in switching region
790	>	fg = -swderiv * d_grp * mf;
791	>	fDecomp_->addForceToAtomColumn(atom2, fg);
792	>
793	>	if (atomListColumn.size() > 1)
794	>	{
795	>	if (info_->usesAtomicVirial())
796	>	{
797	>	// find the distance between the atom
798	>	// and the center of the cutoff group:
799	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, (*cg2)->getGlobalIndex());
800	>	#pragma omp critical
801	>	{
802	>	tau -= outProduct(dag, fg);
803	>	}
804	>	}
805	>	}
806	>	}
807	>	}
808	>	//if (!SIM_uses_AtomicVirial) {
809	>	//  tau -= outProduct(d_grp, fij);
810	>	//}
811	>	}
812	>	}
813	>	}
814	>	}// END: omp for loop
815	>	//              printf("after omp loop\n");
816	>	}
817	>
818	>	if (iLoop == PREPAIR_LOOP)
819	>	{
820	>	if (info_->requiresPrepair())
821	>	{
822	>
823	>	fDecomp_->collectIntermediateData();
824	>
825	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++)
826	>	{
827	>	fDecomp_->fillSelfData(sdat, atom1);
828	>	interactionMan_->doPreForce(sdat);
829	>	}
830	>
831	>	fDecomp_->distributeIntermediateData();
832	>
833	>	}
834	>	}
835	>	}
836	>
837	>	fDecomp_->collectData();
838	>
839	>	if (info_->requiresSelfCorrection())
840	>	{
841	>
842	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++)
843	>	{
844	>	fDecomp_->fillSelfData(sdat, atom1);
845	>	interactionMan_->doSelfCorrection(sdat);
846	>	}
847	>
848	>	}
849	>
850	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) + *(fDecomp_->getPairwisePotential());
851	>
852	>	lrPot = longRangePotential.sum();
853	>
854	>	//store the tau and long range potential
855	>	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
856	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
857	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
858	>	}
859	>
860	>	void ForceManager::longRangeInteractionsRapaport() {
861	>
862	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
863	>	DataStorage* config = &(curSnapshot->atomData);
864	>	DataStorage* cgConfig = &(curSnapshot->cgData);
865	>
866	>	//calculate the center of mass of cutoff group
867	>
868	>	SimInfo::MoleculeIterator mi;
869	>	Molecule* mol;
870	>	Molecule::CutoffGroupIterator ci;
871	>	CutoffGroup* cg;
872	>
873	>	if (info_->getNCutoffGroups() > 0)
874	>	{
875	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
876	>	{
877	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
878	>	{
879	>	//                              cerr << "branch1\n";
880	>	//                              cerr << "globind = " << cg->getGlobalIndex() << ":" << __LINE__ << "\n";
881	>	cg->updateCOM();
882	>
883	>	//                              cerr << "gbI: " << cg->getGlobalIndex() << " locI: " << cg->getLocalIndex() << " x: "
884	>	//                                              << cgConfig->position[cg->getLocalIndex()].x() << " y: " << cgConfig->position[cg->getLocalIndex()].y()
885	>	//                                              << " z: " << cgConfig->position[cg->getLocalIndex()].z() << "\n";
886	>	}
887	>	}
888	>	} else
889	>	{
890	>	// center of mass of the group is the same as position of the atom
891	>	// if cutoff group does not exist
892	>	//              cerr << ":" << __LINE__ << "branch2\n";
893	>	cgConfig->position = config->position;
894	>	}
895	>
896	>	fDecomp_->zeroWorkArrays();
897	>	fDecomp_->distributeData();
898	>
899	>	int atom1, atom2, topoDist;
900	>	CutoffGroup *cg1;
901	>	Vector3d d_grp, dag, d;
902	>	RealType rgrpsq, rgrp, r2, r;
903	>	RealType electroMult, vdwMult;
904	>	RealType vij;
905	>	Vector3d fij, fg, f1;
906	>	tuple3<RealType, RealType, RealType> cuts;
907	>	RealType rCutSq;
908	>	bool in_switching_region;
909	>	RealType sw, dswdr, swderiv;
910	>	vector<int> atomListColumn, atomListRow, atomListLocal;
911	>	InteractionData idat;
912	>	SelfData sdat;
913	>	RealType mf;
914	>	RealType lrPot;
915	>	RealType vpair;
916	>	potVec longRangePotential(0.0);
917	>	potVec workPot(0.0);
918	>
919	>	int loopStart, loopEnd;
920	>
921	>	idat.vdwMult = &vdwMult;
922	>	idat.electroMult = &electroMult;
923	>	idat.pot = &workPot;
924	>	sdat.pot = fDecomp_->getEmbeddingPotential();
925	>	idat.vpair = &vpair;
926	>	idat.f1 = &f1;
927	>	idat.sw = &sw;
928	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
929	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
930	>
931	>	loopEnd = PAIR_LOOP;
932	>	if (info_->requiresPrepair())
933	>	{
934	>	loopStart = PREPAIR_LOOP;
935	>	} else
936	>	{
937	>	loopStart = PAIR_LOOP;
938	>	}
939	>
940	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++)
941	>	{
942	>
943	>	if (iLoop == loopStart)
944	>	{
945	>	bool update_nlist = fDecomp_->checkNeighborList();
946	>	if (update_nlist)
947	>	neighborMatW = fDecomp_->buildLayerBasedNeighborList();
948	>	}
949	>
950	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
951	>	{
952	>	for (cg1 = mol->beginCutoffGroup(ci); cg1 != NULL; cg1 = mol->nextCutoffGroup(ci))
953	>	{
954	>	//                      printf("Thread %d executes loop iteration %d\n", omp_get_thread_num(), i);
955	>	for (vector<CutoffGroup *>::iterator cg2 = neighborMatW[cg1->getGlobalIndex()].begin(); cg2
956	>	!= neighborMatW[cg1->getGlobalIndex()].end(); ++cg2)
957	>	{
958	>
959	>	cuts = fDecomp_->getGroupCutoffs(cg1->getGlobalIndex(), (*cg2)->getGlobalIndex());
960	>
961	>	d_grp = fDecomp_->getIntergroupVector(cg1, (*cg2));
962	>	curSnapshot->wrapVector(d_grp);
963	>	rgrpsq = d_grp.lengthSquare();
964	>
965	>	rCutSq = cuts.second;
966	>
967	>	if (rgrpsq < rCutSq)
968	>	{
969	>	idat.rcut = &cuts.first;
970	>	if (iLoop == PAIR_LOOP)
971	>	{
972	>	vij = 0.0;
973	>	fij = V3Zero;
974	>	}
975	>
976	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, rgrp);
977	>
978	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1->getGlobalIndex());
979	>	atomListColumn = fDecomp_->getAtomsInGroupColumn((*cg2)->getGlobalIndex());
980	>
981	>	for (vector<int>::iterator ia = atomListRow.begin(); ia != atomListRow.end(); ++ia)
982	>	{
983	>	atom1 = (*ia);
984	>
985	>	for (vector<int>::iterator jb = atomListColumn.begin(); jb != atomListColumn.end(); ++jb)
986	>	{
987	>	atom2 = (*jb);
988	>
989	>	if (!fDecomp_->skipAtomPair(atom1, atom2))
990	>	{
991	>	vpair = 0.0;
992	>	workPot = 0.0;
993	>	f1 = V3Zero;
994	>
995	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
996	>
997	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
998	>	vdwMult = vdwScale_[topoDist];
999	>	electroMult = electrostaticScale_[topoDist];
1000	>
1001	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1)
1002	>	{
1003	>	idat.d = &d_grp;
1004	>	idat.r2 = &rgrpsq;
1005	>	//                                                                              cerr << "dgrp = " << d_grp << ":" << __LINE__ << "\n";
1006	>	} else
1007	>	{
1008	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
1009	>	curSnapshot->wrapVector(d);
1010	>	r2 = d.lengthSquare();
1011	>	//                                                                              cerr << "datm = " << d << ":" << __LINE__ << "\n";
1012	>	idat.d = &d;
1013	>	idat.r2 = &r2;
1014	>	}
1015	>
1016	>	//                                                                      cerr << "idat.d = " << *(idat.d) << ":" << __LINE__ << "\n";
1017	>	r = sqrt(*(idat.r2));
1018	>	idat.rij = &r;
1019	>	//                                                                      cerr << "idat.rij = " << *(idat.rij) << "\n";
1020	>
1021	>	if (iLoop == PREPAIR_LOOP)
1022	>	{
1023	>	interactionMan_->doPrePair(idat);
1024	>	} else
1025	>	{
1026	>	interactionMan_->doPair(idat);
1027	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
1028	>
1029	>	//                                                                              cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << ":" << __LINE__ << "\n";
1030	>	vij += vpair;
1031	>	fij += f1;
1032	>	tau -= outProduct(*(idat.d), f1);
1033	>	}
1034	>	}
1035	>	}
1036	>	}
1037	>
1038	>	if (iLoop == PAIR_LOOP)
1039	>	{
1040	>	if (in_switching_region)
1041	>	{
1042	>	swderiv = vij * dswdr / rgrp;
1043	>	fg = swderiv * d_grp;
1044	>	fij += fg;
1045	>
1046	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1)
1047	>	{
1048	>	tau -= outProduct(*(idat.d), fg);
1049	>	}
1050	>
1051	>	for (vector<int>::iterator ia = atomListRow.begin(); ia != atomListRow.end(); ++ia)
1052	>	{
1053	>	atom1 = (*ia);
1054	>	mf = fDecomp_->getMassFactorRow(atom1);
1055	>	// fg is the force on atom ia due to cutoff group's
1056	>	// presence in switching region
1057	>	fg = swderiv * d_grp * mf;
1058	>	fDecomp_->addForceToAtomRow(atom1, fg);
1059	>
1060	>	if (atomListRow.size() > 1)
1061	>	{
1062	>	if (info_->usesAtomicVirial())
1063	>	{
1064	>	// find the distance between the atom
1065	>	// and the center of the cutoff group:
1066	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1->getGlobalIndex());
1067	>	tau -= outProduct(dag, fg);
1068	>	}
1069	>	}
1070	>	}
1071	>	for (vector<int>::iterator jb = atomListColumn.begin(); jb != atomListColumn.end(); ++jb)
1072	>	{
1073	>	atom2 = (*jb);
1074	>	mf = fDecomp_->getMassFactorColumn(atom2);
1075	>	// fg is the force on atom jb due to cutoff group's
1076	>	// presence in switching region
1077	>	fg = -swderiv * d_grp * mf;
1078	>	fDecomp_->addForceToAtomColumn(atom2, fg);
1079	>
1080	>	if (atomListColumn.size() > 1)
1081	>	{
1082	>	if (info_->usesAtomicVirial())
1083	>	{
1084	>	// find the distance between the atom
1085	>	// and the center of the cutoff group:
1086	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, (*cg2)->getGlobalIndex());
1087	>	tau -= outProduct(dag, fg);
1088	>	}
1089	>	}
1090	>	}
1091	>	}
1092	>	//if (!SIM_uses_AtomicVirial) {
1093	>	//  tau -= outProduct(d_grp, fij);
1094	>	//}
1095	>	}
1096	>	}
1097	>	}
1098	>	}
1099	>	}
1100	>
1101	>	if (iLoop == PREPAIR_LOOP)
1102	>	{
1103	>	if (info_->requiresPrepair())
1104	>	{
1105	>
1106	>	fDecomp_->collectIntermediateData();
1107	>
1108	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++)
1109	>	{
1110	>	fDecomp_->fillSelfData(sdat, atom1);
1111	>	interactionMan_->doPreForce(sdat);
1112	>	}
1113	>
1114	>	fDecomp_->distributeIntermediateData();
1115	>
1116	>	}
1117	>	}
1118	>	}
1119	>
1120	>	fDecomp_->collectData();
1121	>
1122	>	if (info_->requiresSelfCorrection())
1123	>	{
1124	>
1125	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++)
1126	>	{
1127	>	fDecomp_->fillSelfData(sdat, atom1);
1128	>	interactionMan_->doSelfCorrection(sdat);
1129	>	}
1130	>
1131	>	}
1132	>
1133	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) + *(fDecomp_->getPairwisePotential());
1134	>
1135	>	lrPot = longRangePotential.sum();
1136	>
1137	>	//store the tau and long range potential
1138	>	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
1139	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
1140	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
1141	>	}
1142	>
1143	>	void ForceManager::longRangeInteractions() {
1144	>
1145	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
1146	>	DataStorage* config = &(curSnapshot->atomData);
1147	>	DataStorage* cgConfig = &(curSnapshot->cgData);
1148	>
1149	>	//calculate the center of mass of cutoff group
1150	>
1151	>	SimInfo::MoleculeIterator mi;
1152	>	Molecule* mol;
1153	>	Molecule::CutoffGroupIterator ci;
1154	>	CutoffGroup* cg;
1155	>
1156	>	if (info_->getNCutoffGroups() > 0)
1157	>	{
1158	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1159	>	{
1160	>	for (cg = mol->beginCutoffGroup(ci); cg != NULL; cg = mol->nextCutoffGroup(ci))
1161	>	{
1162	>	cerr << "branch1\n";
1163	>	cerr << "globind = " << cg->getGlobalIndex() << "\n";
1164	>	cg->updateCOM();
1165	>	}
1166	>	}
1167	>	} else
1168	>	{
1169	>	// center of mass of the group is the same as position of the atom
1170	>	// if cutoff group does not exist
1171	>	cerr << "branch2\n";
1172	>	cgConfig->position = config->position;
1173	>	}
1174	>
1175	>	fDecomp_->zeroWorkArrays();
1176	>	fDecomp_->distributeData();
1177	>
1178	>	int cg1, cg2, atom1, atom2, topoDist;
1179	>	Vector3d d_grp, dag, d;
1180	>	RealType rgrpsq, rgrp, r2, r;
1181	>	RealType electroMult, vdwMult;
1182	>	RealType vij;
1183	>	Vector3d fij, fg, f1;
1184	>	tuple3<RealType, RealType, RealType> cuts;
1185	>	RealType rCutSq;
1186	>	bool in_switching_region;
1187	>	RealType sw, dswdr, swderiv;
1188	>	vector<int> atomListColumn, atomListRow, atomListLocal;
1189	>	InteractionData idat;
1190	>	SelfData sdat;
1191	>	RealType mf;
1192	>	RealType lrPot;
1193	>	RealType vpair;
1194	>	potVec longRangePotential(0.0);
1195	>	potVec workPot(0.0);
1196	>
1197	>	int loopStart, loopEnd;
1198	>
1199	>	idat.vdwMult = &vdwMult;
1200	>	idat.electroMult = &electroMult;
1201	>	idat.pot = &workPot;
1202	>	sdat.pot = fDecomp_->getEmbeddingPotential();
1203	>	idat.vpair = &vpair;
1204	>	idat.f1 = &f1;
1205	>	idat.sw = &sw;
1206	>	idat.shiftedPot = (cutoffMethod_ == SHIFTED_POTENTIAL) ? true : false;
1207	>	idat.shiftedForce = (cutoffMethod_ == SHIFTED_FORCE) ? true : false;
1208	>
1209	>	loopEnd = PAIR_LOOP;
1210	>	if (info_->requiresPrepair())
1211	>	{
1212	>	loopStart = PREPAIR_LOOP;
1213	>	} else
1214	>	{
1215	>	loopStart = PAIR_LOOP;
1216	>	}
1217	>
1218	>	for (int iLoop = loopStart; iLoop <= loopEnd; iLoop++)
1219	>	{
1220	>
1221	>	if (iLoop == loopStart)
1222	>	{
1223	>	bool update_nlist = fDecomp_->checkNeighborList();
1224	>	if (update_nlist)
1225	>	neighborList = fDecomp_->buildNeighborList();
1226	>
1227	>	}
1228	>
1229	>	for (vector<pair<int, int> >::iterator it = neighborList.begin(); it != neighborList.end(); ++it)
1230	>	{
1231	>	cg1 = (*it).first;
1232	>	cg2 = (*it).second;
1233	>
1234	>	cuts = fDecomp_->getGroupCutoffs(cg1, cg2);
1235	>
1236	>	d_grp = fDecomp_->getIntergroupVector(cg1, cg2);
1237	>	curSnapshot->wrapVector(d_grp);
1238	>	rgrpsq = d_grp.lengthSquare();
1239	>
1240	>	rCutSq = cuts.second;
1241	>
1242	>	if (rgrpsq < rCutSq)
1243	>	{
1244	>	idat.rcut = &cuts.first;
1245	>	if (iLoop == PAIR_LOOP)
1246	>	{
1247	>	vij = 0.0;
1248	>	fij = V3Zero;
1249	>	}
1250	>
1251	>	in_switching_region = switcher_->getSwitch(rgrpsq, sw, dswdr, rgrp);
1252	>
1253	>	atomListRow = fDecomp_->getAtomsInGroupRow(cg1);
1254	>	atomListColumn = fDecomp_->getAtomsInGroupColumn(cg2);
1255	>
1256	>	for (vector<int>::iterator ia = atomListRow.begin(); ia != atomListRow.end(); ++ia)
1257	>	{
1258	>	atom1 = (*ia);
1259	>
1260	>	for (vector<int>::iterator jb = atomListColumn.begin(); jb != atomListColumn.end(); ++jb)
1261	>	{
1262	>	atom2 = (*jb);
1263	>
1264	>	if (!fDecomp_->skipAtomPair(atom1, atom2))
1265	>	{
1266	>	vpair = 0.0;
1267	>	workPot = 0.0;
1268	>	f1 = V3Zero;
1269	>
1270	>	fDecomp_->fillInteractionData(idat, atom1, atom2);
1271	>
1272	>	topoDist = fDecomp_->getTopologicalDistance(atom1, atom2);
1273	>	vdwMult = vdwScale_[topoDist];
1274	>	electroMult = electrostaticScale_[topoDist];
1275	>
1276	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1)
1277	>	{
1278	>	idat.d = &d_grp;
1279	>	idat.r2 = &rgrpsq;
1280	>	cerr << "dgrp = " << d_grp << "\n";
1281	>	} else
1282	>	{
1283	>	d = fDecomp_->getInteratomicVector(atom1, atom2);
1284	>	curSnapshot->wrapVector(d);
1285	>	r2 = d.lengthSquare();
1286	>	cerr << "datm = " << d << "\n";
1287	>	idat.d = &d;
1288	>	idat.r2 = &r2;
1289	>	}
1290	>
1291	>	cerr << "idat.d = " << *(idat.d) << "\n";
1292	>	r = sqrt(*(idat.r2));
1293	>	idat.rij = &r;
1294	>
1295	>	if (iLoop == PREPAIR_LOOP)
1296	>	{
1297	>	interactionMan_->doPrePair(idat);
1298	>	} else
1299	>	{
1300	>	interactionMan_->doPair(idat);
1301	>	fDecomp_->unpackInteractionData(idat, atom1, atom2);
1302	>
1303	>	cerr << "d = " << *(idat.d) << "\tv=" << vpair << "\tf=" << f1 << "\n";
1304	>	vij += vpair;
1305	>	fij += f1;
1306	>	tau -= outProduct(*(idat.d), f1);
1307	>	}
1308	>	}
1309	>	}
1310	>	}
1311	>
1312	>	if (iLoop == PAIR_LOOP)
1313	>	{
1314	>	if (in_switching_region)
1315	>	{
1316	>	swderiv = vij * dswdr / rgrp;
1317	>	fg = swderiv * d_grp;
1318	>	fij += fg;
1319	>
1320	>	if (atomListRow.size() == 1 && atomListColumn.size() == 1)
1321	>	{
1322	>	tau -= outProduct(*(idat.d), fg);
1323	>	}
1324	>
1325	>	for (vector<int>::iterator ia = atomListRow.begin(); ia != atomListRow.end(); ++ia)
1326	>	{
1327	>	atom1 = (*ia);
1328	>	mf = fDecomp_->getMassFactorRow(atom1);
1329	>	// fg is the force on atom ia due to cutoff group's
1330	>	// presence in switching region
1331	>	fg = swderiv * d_grp * mf;
1332	>	fDecomp_->addForceToAtomRow(atom1, fg);
1333	>
1334	>	if (atomListRow.size() > 1)
1335	>	{
1336	>	if (info_->usesAtomicVirial())
1337	>	{
1338	>	// find the distance between the atom
1339	>	// and the center of the cutoff group:
1340	>	dag = fDecomp_->getAtomToGroupVectorRow(atom1, cg1);
1341	>	tau -= outProduct(dag, fg);
1342	>	}
1343	>	}
1344	>	}
1345	>	for (vector<int>::iterator jb = atomListColumn.begin(); jb != atomListColumn.end(); ++jb)
1346	>	{
1347	>	atom2 = (*jb);
1348	>	mf = fDecomp_->getMassFactorColumn(atom2);
1349	>	// fg is the force on atom jb due to cutoff group's
1350	>	// presence in switching region
1351	>	fg = -swderiv * d_grp * mf;
1352	>	fDecomp_->addForceToAtomColumn(atom2, fg);
1353	>
1354	>	if (atomListColumn.size() > 1)
1355	>	{
1356	>	if (info_->usesAtomicVirial())
1357	>	{
1358	>	// find the distance between the atom
1359	>	// and the center of the cutoff group:
1360	>	dag = fDecomp_->getAtomToGroupVectorColumn(atom2, cg2);
1361	>	tau -= outProduct(dag, fg);
1362	>	}
1363	>	}
1364	>	}
1365	>	}
1366	>	//if (!SIM_uses_AtomicVirial) {
1367	>	//  tau -= outProduct(d_grp, fij);
1368	>	//}
1369	>	}
1370	>	}
1371	>	}
1372	>
1373	>	if (iLoop == PREPAIR_LOOP)
1374	>	{
1375	>	if (info_->requiresPrepair())
1376	>	{
1377	>
1378	>	fDecomp_->collectIntermediateData();
1379	>
1380	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++)
1381	>	{
1382	>	fDecomp_->fillSelfData(sdat, atom1);
1383	>	interactionMan_->doPreForce(sdat);
1384	>	}
1385	>
1386	>	fDecomp_->distributeIntermediateData();
1387	>
1388	>	}
1389	>	}
1390	>
1391	>	}
1392	>
1393	>	fDecomp_->collectData();
1394	>
1395	>	if (info_->requiresSelfCorrection())
1396	>	{
1397	>
1398	>	for (int atom1 = 0; atom1 < info_->getNAtoms(); atom1++)
1399	>	{
1400	>	fDecomp_->fillSelfData(sdat, atom1);
1401	>	interactionMan_->doSelfCorrection(sdat);
1402	>	}
1403	>
1404	>	}
1405	>
1406	>	longRangePotential = *(fDecomp_->getEmbeddingPotential()) + *(fDecomp_->getPairwisePotential());
1407	>
1408	>	lrPot = longRangePotential.sum();
1409	>
1410	>	//store the tau and long range potential
1411	>	curSnapshot->statData[Stats::LONG_RANGE_POTENTIAL] = lrPot;
1412	>	curSnapshot->statData[Stats::VANDERWAALS_POTENTIAL] = longRangePotential[VANDERWAALS_FAMILY];
1413	>	curSnapshot->statData[Stats::ELECTROSTATIC_POTENTIAL] = longRangePotential[ELECTROSTATIC_FAMILY];
1414	>	}
1415	>
1416	>	void ForceManager::postCalculation() {
1417	>	SimInfo::MoleculeIterator mi;
1418	>	Molecule* mol;
1419	>	Molecule::RigidBodyIterator rbIter;
1420	>	RigidBody* rb;
1421	>	Snapshot* curSnapshot = info_->getSnapshotManager()->getCurrentSnapshot();
1422	>
1423	>	// collect the atomic forces onto rigid bodies
1424	>
1425	>	for (mol = info_->beginMolecule(mi); mol != NULL; mol = info_->nextMolecule(mi))
1426	>	{
1427	>	for (rb = mol->beginRigidBody(rbIter); rb != NULL; rb = mol->nextRigidBody(rbIter))
1428	>	{
1429	>	Mat3x3d rbTau = rb->calcForcesAndTorquesAndVirial();
1430	>	tau += rbTau;
1431	>	}
1432	>	}
1433	>
1434	>	#ifdef IS_MPI
1435	>	Mat3x3d tmpTau(tau);
1436	>	MPI_Allreduce(tmpTau.getArrayPointer(), tau.getArrayPointer(),
1437	>	9, MPI_REALTYPE, MPI_SUM, MPI_COMM_WORLD);
1438		#endif
1439	<	curSnapshot->statData.setTau(tau);
1440	<	}
1439	>	curSnapshot->statData.setTau(tau);
1440	>	}
1441
1442		} //end namespace OpenMD

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