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root/group/trunk/OOPSE/libmdtools/SimSetup.cpp

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 378 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
Revision 962 by tim, Mon Jan 19 18:36:21 2004 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 12 | Line 15 | SimSetup::SimSetup(){
15		#include "mpiSimulation.hpp"
16		#endif
17
18	+	// some defines for ensemble and Forcefield  cases
19	+
20	+	#define NVE_ENS        0
21	+	#define NVT_ENS        1
22	+	#define NPTi_ENS       2
23	+	#define NPTf_ENS       3
24	+	#define NPTxyz_ENS     4
25	+
26	+
27	+	#define FF_DUFF 0
28	+	#define FF_LJ   1
29	+	#define FF_EAM  2
30	+
31	+	using namespace std;
32	+
33	+	/**
34	+	* Check whether dividend is divisble by divisor or not
35	+	*/
36	+	bool isDivisible(double dividend, double divisor){
37	+	double tolerance = 0.000001;
38	+	double quotient;
39	+	double diff;
40	+	int intQuotient;
41	+
42	+	quotient = dividend / divisor;
43	+
44	+	if (quotient < 0)
45	+	quotient = -quotient;
46	+
47	+	intQuotient = int (quotient + tolerance);
48	+
49	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
50	+
51	+	if (diff <= tolerance)
52	+	return true;
53	+	else
54	+	return false;
55	+	}
56	+
57		SimSetup::SimSetup(){
58	+
59	+	initSuspend = false;
60	+	isInfoArray = 0;
61	+	nInfo = 1;
62	+
63		stamps = new MakeStamps();
64		globals = new Globals();
65	<
65	>
66	>
67		#ifdef IS_MPI
68	<	strcpy( checkPointMsg, "SimSetup creation successful" );
68	>	strcpy(checkPointMsg, "SimSetup creation successful");
69		MPIcheckPoint();
70		#endif // IS_MPI
71		}
#	Line 27 | Line 75 | void SimSetup::parseFile( char* fileName ){
75		delete globals;
76		}
77
78	<	void SimSetup::parseFile( char* fileName ){
78	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
79	>	info = the_info;
80	>	nInfo = theNinfo;
81	>	isInfoArray = 1;
82	>	initSuspend = true;
83	>	}
84
85	+
86	+	void SimSetup::parseFile(char* fileName){
87		#ifdef IS_MPI
88	<	if( worldRank == 0 ){
88	>	if (worldRank == 0){
89		#endif // is_mpi
90	<
90	>
91		inFileName = fileName;
92	<	set_interface_stamps( stamps, globals );
93	<
92	>	set_interface_stamps(stamps, globals);
93	>
94		#ifdef IS_MPI
95		mpiEventInit();
96		#endif
97
98	<	yacc_BASS( fileName );
98	>	yacc_BASS(fileName);
99
100		#ifdef IS_MPI
101		throwMPIEvent(NULL);
102		}
103	<	else receiveParse();
103	>	else{
104	>	receiveParse();
105	>	}
106		#endif
107
108		}
109
110		#ifdef IS_MPI
111		void SimSetup::receiveParse(void){
112	<
113	<	set_interface_stamps( stamps, globals );
114	<	mpiEventInit();
115	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
112	>	set_interface_stamps(stamps, globals);
113	>	mpiEventInit();
114	>	MPIcheckPoint();
115	>	mpiEventLoop();
116		}
117
118		#endif // is_mpi
119
120	<	void SimSetup::createSim( void ){
120	>	void SimSetup::createSim(void){
121
122	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
122	>	// gather all of the information from the Bass file
123
124	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
124	>	gatherInfo();
125
126	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	simnfo->run_time = the_globals->getRunTime();
126	>	// creation of complex system objects
127
128	<	// get the ones we know are there, yet still may need some work.
81	<	n_components = the_globals->getNComponents();
82	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
128	>	sysObjectsCreation();
129
130	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
130	>	// check on the post processing info
131
132	+	finalInfoCheck();
133
134	<	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
92	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
93	<	else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
94	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
95	<	else{
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Error. Unrecognized force field -> %s\n",
98	<	force_field );
99	<	painCave.isFatal = 1;
100	<	simError();
101	<	}
134	>	// initialize the system coordinates
135
136	<	#ifdef IS_MPI
137	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
136	>	if ( !initSuspend ){
137	>	initSystemCoords();
138
139	<
139	>	if( !(globals->getUseInitTime()) )
140	>	info[0].currentTime = 0.0;
141	>	}
142
143	<	// get the components and calculate the tot_nMol and indvidual n_mol
111	<	the_components = the_globals->getComponents();
112	<	components_nmol = new int[n_components];
113	<	comp_stamps = new MoleculeStamp*[n_components];
143	>	// make the output filenames
144
145	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
145	>	makeOutNames();
146
147	<	tot_nmol = 0;
120	<	for( i=0; i<n_components; i++ ){
147	>	// make the integrator
148
149	<	if( !the_components[i]->haveNMol() ){
123	<	// we have a problem
124	<	sprintf( painCave.errMsg,
125	<	"SimSetup Error. No global NMol or component NMol"
126	<	" given. Cannot calculate the number of atoms.\n" );
127	<	painCave.isFatal = 1;
128	<	simError();
129	<	}
149	>	makeIntegrator();
150
131	–	tot_nmol += the_components[i]->getNMol();
132	–	components_nmol[i] = the_components[i]->getNMol();
133	–	}
134	–	}
135	–	else{
136	–	sprintf( painCave.errMsg,
137	–	"SimSetup error.\n"
138	–	"\tSorry, the ability to specify total"
139	–	" nMols and then give molfractions in the components\n"
140	–	"\tis not currently supported."
141	–	" Please give nMol in the components.\n" );
142	–	painCave.isFatal = 1;
143	–	simError();
144	–
145	–
146	–	//     tot_nmol = the_globals->getNMol();
147	–
148	–	//   //we have the total number of molecules, now we check for molfractions
149	–	//     for( i=0; i<n_components; i++ ){
150	–
151	–	//       if( !the_components[i]->haveMolFraction() ){
152	–
153	–	//  if( !the_components[i]->haveNMol() ){
154	–	//    //we have a problem
155	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
156	–	//              << " nMol was given in component
157	–
158	–	}
159	–
151		#ifdef IS_MPI
152	<	strcpy( checkPointMsg, "Have the number of components" );
153	<	MPIcheckPoint();
163	<	#endif // is_mpi
152	>	mpiSim->mpiRefresh();
153	>	#endif
154
155	<	// make an array of molecule stamps that match the components used.
166	<	// also extract the used stamps out into a separate linked list
155	>	// initialize the Fortran
156
157	<	simnfo->nComponents = n_components;
158	<	simnfo->componentsNmol = components_nmol;
170	<	simnfo->compStamps = comp_stamps;
171	<	simnfo->headStamp = new LinkedMolStamp();
172	<
173	<	char* id;
174	<	LinkedMolStamp* headStamp = simnfo->headStamp;
175	<	LinkedMolStamp* currentStamp = NULL;
176	<	for( i=0; i<n_components; i++ ){
157	>	initFortran();
158	>	}
159
178	–	id = the_components[i]->getType();
179	–	comp_stamps[i] = NULL;
180	–
181	–	// check to make sure the component isn't already in the list
160
161	<	comp_stamps[i] = headStamp->match( id );
162	<	if( comp_stamps[i] == NULL ){
163	<
164	<	// extract the component from the list;
165	<
166	<	currentStamp = the_stamps->extractMolStamp( id );
167	<	if( currentStamp == NULL ){
168	<	sprintf( painCave.errMsg,
169	<	"SimSetup error: Component \"%s\" was not found in the "
170	<	"list of declared molecules\n",
171	<	id );
194	<	painCave.isFatal = 1;
195	<	simError();
196	<	}
197	<
198	<	headStamp->add( currentStamp );
199	<	comp_stamps[i] = headStamp->match( id );
200	<	}
201	<	}
161	>	void SimSetup::makeMolecules(void){
162	>	int k;
163	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
164	>	molInit molInfo;
165	>	DirectionalAtom* dAtom;
166	>	LinkedAssign* extras;
167	>	LinkedAssign* current_extra;
168	>	AtomStamp* currentAtom;
169	>	BondStamp* currentBond;
170	>	BendStamp* currentBend;
171	>	TorsionStamp* currentTorsion;
172
173	<	#ifdef IS_MPI
174	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
175	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
173	>	bond_pair* theBonds;
174	>	bend_set* theBends;
175	>	torsion_set* theTorsions;
176
177
178	+	//init the forceField paramters
179
180	<	// caclulate the number of atoms, bonds, bends and torsions
180	>	the_ff->readParams();
181
213	–	tot_atoms = 0;
214	–	tot_bonds = 0;
215	–	tot_bends = 0;
216	–	tot_torsions = 0;
217	–	for( i=0; i<n_components; i++ ){
218	–
219	–	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
220	–	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
221	–	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
222	–	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
223	–	}
182
183	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
183	>	// init the atoms
184
185	<	simnfo->n_atoms = tot_atoms;
228	<	simnfo->n_bonds = tot_bonds;
229	<	simnfo->n_bends = tot_bends;
230	<	simnfo->n_torsions = tot_torsions;
231	<	simnfo->n_SRI = tot_SRI;
232	<	simnfo->n_mol = tot_nmol;
185	>	double ux, uy, uz, u, uSqr;
186
187	<
188	<	#ifdef IS_MPI
187	>	for (k = 0; k < nInfo; k++){
188	>	the_ff->setSimInfo(&(info[k]));
189
190	<	// divide the molecules among processors here.
191	<
192	<	mpiSim = new mpiSimulation( simnfo );
193	<
241	<
190	>	atomOffset = 0;
191	>	excludeOffset = 0;
192	>	for (i = 0; i < info[k].n_mol; i++){
193	>	stampID = info[k].molecules[i].getStampID();
194
195	<	globalIndex = mpiSim->divideLabor();
195	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
196	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
197	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
198	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
199	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
200	>
201	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
202	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
203	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
204	>	molInfo.myBends = new Bend * [molInfo.nBends];
205	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
206
207	+	theBonds = new bond_pair[molInfo.nBonds];
208	+	theBends = new bend_set[molInfo.nBends];
209	+	theTorsions = new torsion_set[molInfo.nTorsions];
210
211	+	// make the Atoms
212
213	<	// set up the local variables
214	<
215	<	int localMol, allMol;
216	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
217	<
218	<	allMol = 0;
219	<	localMol = 0;
254	<	local_atoms = 0;
255	<	local_bonds = 0;
256	<	local_bends = 0;
257	<	local_torsions = 0;
258	<	for( i=0; i<n_components; i++ ){
213	>	for (j = 0; j < molInfo.nAtoms; j++){
214	>	currentAtom = comp_stamps[stampID]->getAtom(j);
215	>	if (currentAtom->haveOrientation()){
216	>	dAtom = new DirectionalAtom((j + atomOffset),
217	>	info[k].getConfiguration());
218	>	info[k].n_oriented++;
219	>	molInfo.myAtoms[j] = dAtom;
220
221	<	for( j=0; j<components_nmol[i]; j++ ){
222	<
223	<	if( mpiSim->getMyMolStart() <= allMol &&
263	<	allMol <= mpiSim->getMyMolEnd() ){
264	<
265	<	local_atoms +=    comp_stamps[i]->getNAtoms();
266	<	local_bonds +=    comp_stamps[i]->getNBonds();
267	<	local_bends +=    comp_stamps[i]->getNBends();
268	<	local_torsions += comp_stamps[i]->getNTorsions();
269	<	localMol++;
270	<	}
271	<	allMol++;
272	<	}
273	<	}
274	<	local_SRI = local_bonds + local_bends + local_torsions;
275	<
221	>	ux = currentAtom->getOrntX();
222	>	uy = currentAtom->getOrntY();
223	>	uz = currentAtom->getOrntZ();
224
225	<	simnfo->n_atoms = mpiSim->getMyNlocal();
278	<
279	<	if( local_atoms != simnfo->n_atoms ){
280	<	sprintf( painCave.errMsg,
281	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282	<	" localAtom (%d) are note equal.\n",
283	<	simnfo->n_atoms,
284	<	local_atoms );
285	<	painCave.isFatal = 1;
286	<	simError();
287	<	}
225	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
226
227	<	simnfo->n_bonds = local_bonds;
228	<	simnfo->n_bends = local_bends;
229	<	simnfo->n_torsions = local_torsions;
230	<	simnfo->n_SRI = local_SRI;
293	<	simnfo->n_mol = localMol;
227	>	u = sqrt(uSqr);
228	>	ux = ux / u;
229	>	uy = uy / u;
230	>	uz = uz / u;
231
232	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
233	<	MPIcheckPoint();
234	<
235	<
236	<	#endif // is_mpi
237	<
232	>	dAtom->setSUx(ux);
233	>	dAtom->setSUy(uy);
234	>	dAtom->setSUz(uz);
235	>	}
236	>	else{
237	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
238	>	info[k].getConfiguration());
239	>	}
240	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
241
242	<	// create the atom and short range interaction arrays
242	>	#ifdef IS_MPI
243
244	<	Atom::createArrays(simnfo->n_atoms);
305	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
244	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
245
246	+	#endif // is_mpi
247	+	}
248
249	<	if( simnfo->n_SRI ){
250	<	the_sris = new SRI*[simnfo->n_SRI];
251	<	the_excludes = new int[2 * simnfo->n_SRI];
252	<	simnfo->globalExcludes = new int;
253	<	simnfo->n_exclude = tot_SRI;
314	<	}
315	<	else{
316	<
317	<	the_excludes = new int[2];
318	<	the_excludes[0] = 0;
319	<	the_excludes[1] = 0;
320	<	simnfo->globalExcludes = new int;
321	<	simnfo->globalExcludes[0] = 0;
249	>	// make the bonds
250	>	for (j = 0; j < molInfo.nBonds; j++){
251	>	currentBond = comp_stamps[stampID]->getBond(j);
252	>	theBonds[j].a = currentBond->getA() + atomOffset;
253	>	theBonds[j].b = currentBond->getB() + atomOffset;
254
255	<	simnfo->n_exclude = 1;
256	<	}
255	>	exI = theBonds[j].a;
256	>	exJ = theBonds[j].b;
257
258	<	// set the arrays into the SimInfo object
258	>	// exclude_I must always be the smaller of the pair
259	>	if (exI > exJ){
260	>	tempEx = exI;
261	>	exI = exJ;
262	>	exJ = tempEx;
263	>	}
264	>	#ifdef IS_MPI
265	>	tempEx = exI;
266	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
267	>	tempEx = exJ;
268	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
269
270	<	simnfo->atoms = the_atoms;
271	<	simnfo->sr_interactions = the_sris;
330	<	simnfo->nGlobalExcludes = 0;
331	<	simnfo->excludes = the_excludes;
270	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
271	>	#else  // isn't MPI
272
273	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
274	+	#endif  //is_mpi
275	+	}
276	+	excludeOffset += molInfo.nBonds;
277
278	<	// get some of the tricky things that may still be in the globals
278	>	//make the bends
279	>	for (j = 0; j < molInfo.nBends; j++){
280	>	currentBend = comp_stamps[stampID]->getBend(j);
281	>	theBends[j].a = currentBend->getA() + atomOffset;
282	>	theBends[j].b = currentBend->getB() + atomOffset;
283	>	theBends[j].c = currentBend->getC() + atomOffset;
284
285	<	if( simnfo->n_dipoles ){
285	>	if (currentBend->haveExtras()){
286	>	extras = currentBend->getExtras();
287	>	current_extra = extras;
288
289	<	if( !the_globals->haveRRF() ){
290	<	sprintf( painCave.errMsg,
291	<	"SimSetup Error, system has dipoles, but no rRF was set.\n");
292	<	painCave.isFatal = 1;
293	<	simError();
294	<	}
295	<	if( !the_globals->haveDielectric() ){
345	<	sprintf( painCave.errMsg,
346	<	"SimSetup Error, system has dipoles, but no"
347	<	" dielectric was set.\n" );
348	<	painCave.isFatal = 1;
349	<	simError();
350	<	}
289	>	while (current_extra != NULL){
290	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
291	>	switch (current_extra->getType()){
292	>	case 0:
293	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
294	>	theBends[j].isGhost = 1;
295	>	break;
296
297	<	simnfo->rRF        = the_globals->getRRF();
298	<	simnfo->dielectric = the_globals->getDielectric();
299	<	}
297	>	case 1:
298	>	theBends[j].ghost = (int) current_extra->getDouble() +
299	>	atomOffset;
300	>	theBends[j].isGhost = 1;
301	>	break;
302
303	<	#ifdef IS_MPI
304	<	strcpy( checkPointMsg, "rRf and dielectric check out" );
305	<	MPIcheckPoint();
306	<	#endif // is_mpi
307	<
308	<	if( the_globals->haveBox() ){
309	<	simnfo->box_x = the_globals->getBox();
310	<	simnfo->box_y = the_globals->getBox();
311	<	simnfo->box_z = the_globals->getBox();
312	<	}
313	<	else if( the_globals->haveDensity() ){
303	>	default:
304	>	sprintf(painCave.errMsg,
305	>	"SimSetup Error: ghostVectorSource was neither a "
306	>	"double nor an int.\n"
307	>	"-->Bend[%d] in %s\n",
308	>	j, comp_stamps[stampID]->getID());
309	>	painCave.isFatal = 1;
310	>	simError();
311	>	}
312	>	}
313	>	else{
314	>	sprintf(painCave.errMsg,
315	>	"SimSetup Error: unhandled bend assignment:\n"
316	>	"    -->%s in Bend[%d] in %s\n",
317	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
318	>	painCave.isFatal = 1;
319	>	simError();
320	>	}
321
322	<	double vol;
323	<	vol = (double)tot_nmol / the_globals->getDensity();
324	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
371	<	simnfo->box_y = simnfo->box_x;
372	<	simnfo->box_z = simnfo->box_x;
373	<	}
374	<	else{
375	<	if( !the_globals->haveBoxX() ){
376	<	sprintf( painCave.errMsg,
377	<	"SimSetup error, no periodic BoxX size given.\n" );
378	<	painCave.isFatal = 1;
379	<	simError();
380	<	}
381	<	simnfo->box_x = the_globals->getBoxX();
322	>	current_extra = current_extra->getNext();
323	>	}
324	>	}
325
326	<	if( !the_globals->haveBoxY() ){
327	<	sprintf( painCave.errMsg,
328	<	"SimSetup error, no periodic BoxY size given.\n" );
329	<	painCave.isFatal = 1;
330	<	simError();
331	<	}
332	<	simnfo->box_y = the_globals->getBoxY();
326	>	if (!theBends[j].isGhost){
327	>	exI = theBends[j].a;
328	>	exJ = theBends[j].c;
329	>	}
330	>	else{
331	>	exI = theBends[j].a;
332	>	exJ = theBends[j].b;
333	>	}
334
335	<	if( !the_globals->haveBoxZ() ){
336	<	sprintf( painCave.errMsg,
337	<	"SimSetup error, no periodic BoxZ size given.\n" );
338	<	painCave.isFatal = 1;
339	<	simError();
340	<	}
397	<	simnfo->box_z = the_globals->getBoxZ();
398	<	}
399	<
335	>	// exclude_I must always be the smaller of the pair
336	>	if (exI > exJ){
337	>	tempEx = exI;
338	>	exI = exJ;
339	>	exJ = tempEx;
340	>	}
341		#ifdef IS_MPI
342	<	strcpy( checkPointMsg, "Box size set up" );
343	<	MPIcheckPoint();
344	<	#endif // is_mpi
342	>	tempEx = exI;
343	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
344	>	tempEx = exJ;
345	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
346
347	<
348	<	// initialize the arrays
349	<
350	<	the_ff->setSimInfo( simnfo );
347	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
348	>	#else  // isn't MPI
349	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
350	>	#endif  //is_mpi
351	>	}
352	>	excludeOffset += molInfo.nBends;
353
354	<	makeAtoms();
355	<	simnfo->identArray = new int[simnfo->n_atoms];
356	<	for(i=0; i<simnfo->n_atoms; i++){
357	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
358	<	}
359	<
416	<	if( tot_bonds ){
417	<	makeBonds();
418	<	}
354	>	for (j = 0; j < molInfo.nTorsions; j++){
355	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
356	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
357	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
358	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
359	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
360
361	<	if( tot_bends ){
362	<	makeBends();
422	<	}
361	>	exI = theTorsions[j].a;
362	>	exJ = theTorsions[j].d;
363
364	<	if( tot_torsions ){
365	<	makeTorsions();
366	<	}
364	>	// exclude_I must always be the smaller of the pair
365	>	if (exI > exJ){
366	>	tempEx = exI;
367	>	exI = exJ;
368	>	exJ = tempEx;
369	>	}
370	>	#ifdef IS_MPI
371	>	tempEx = exI;
372	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
373	>	tempEx = exJ;
374	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
375
376	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
377	+	#else  // isn't MPI
378	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
379	+	#endif  //is_mpi
380	+	}
381	+	excludeOffset += molInfo.nTorsions;
382
383
384	+	// send the arrays off to the forceField for init.
385
386	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
387	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
388	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
389	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
390	+	theTorsions);
391
392
393	<	if( the_globals->haveInitialConfig() ){
434	<
435	<	InitializeFromFile* fileInit;
436	<	#ifdef IS_MPI // is_mpi
437	<	if( worldRank == 0 ){
438	<	#endif //is_mpi
439	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
440	<	#ifdef IS_MPI
441	<	}else fileInit = new InitializeFromFile( NULL );
442	<	#endif
443	<	fileInit->read_xyz( simnfo ); // default velocities on
393	>	info[k].molecules[i].initialize(molInfo);
394
445	–	delete fileInit;
446	–	}
447	–	else{
395
396	<	#ifdef IS_MPI
396	>	atomOffset += molInfo.nAtoms;
397	>	delete[] theBonds;
398	>	delete[] theBends;
399	>	delete[] theTorsions;
400	>	}
401	>	}
402
403	<	// no init from bass
404	<
405	<	sprintf( painCave.errMsg,
406	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
455	<	painCave.isFatal;
456	<	simError();
457	<
458	<	#else
403	>	#ifdef IS_MPI
404	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
405	>	MPIcheckPoint();
406	>	#endif // is_mpi
407
408	<	initFromBass();
408	>	// clean up the forcefield
409
410	+	the_ff->calcRcut();
411	+	the_ff->cleanMe();
412	+	}
413
414	<	#endif
415	<	}
414	>	void SimSetup::initFromBass(void){
415	>	int i, j, k;
416	>	int n_cells;
417	>	double cellx, celly, cellz;
418	>	double temp1, temp2, temp3;
419	>	int n_per_extra;
420	>	int n_extra;
421	>	int have_extra, done;
422
423	<	#ifdef IS_MPI
424	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
425	<	MPIcheckPoint();
426	<	#endif // is_mpi
423	>	double vel[3];
424	>	vel[0] = 0.0;
425	>	vel[1] = 0.0;
426	>	vel[2] = 0.0;
427
428	+	temp1 = (double) tot_nmol / 4.0;
429	+	temp2 = pow(temp1, (1.0 / 3.0));
430	+	temp3 = ceil(temp2);
431
432	<
433	<
434	<
432	>	have_extra = 0;
433	>	if (temp2 < temp3){
434	>	// we have a non-complete lattice
435	>	have_extra = 1;
436
437	<
438	<	#ifdef IS_MPI
439	<	if( worldRank == 0 ){
440	<	#endif // is_mpi
441	<
442	<	if( the_globals->haveFinalConfig() ){
443	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
437	>	n_cells = (int) temp3 - 1;
438	>	cellx = info[0].boxL[0] / temp3;
439	>	celly = info[0].boxL[1] / temp3;
440	>	cellz = info[0].boxL[2] / temp3;
441	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
442	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
443	>	n_per_extra = (int) ceil(temp1);
444	>
445	>	if (n_per_extra > 4){
446	>	sprintf(painCave.errMsg,
447	>	"SimSetup error. There has been an error in constructing"
448	>	" the non-complete lattice.\n");
449	>	painCave.isFatal = 1;
450	>	simError();
451		}
484	–	else{
485	–	strcpy( simnfo->finalName, inFileName );
486	–	char* endTest;
487	–	int nameLength = strlen( simnfo->finalName );
488	–	endTest = &(simnfo->finalName[nameLength - 5]);
489	–	if( !strcmp( endTest, ".bass" ) ){
490	–	strcpy( endTest, ".eor" );
491	–	}
492	–	else if( !strcmp( endTest, ".BASS" ) ){
493	–	strcpy( endTest, ".eor" );
494	–	}
495	–	else{
496	–	endTest = &(simnfo->finalName[nameLength - 4]);
497	–	if( !strcmp( endTest, ".bss" ) ){
498	–	strcpy( endTest, ".eor" );
499	–	}
500	–	else if( !strcmp( endTest, ".mdl" ) ){
501	–	strcpy( endTest, ".eor" );
502	–	}
503	–	else{
504	–	strcat( simnfo->finalName, ".eor" );
505	–	}
506	–	}
507	–	}
508	–
509	–	// make the sample and status out names
510	–
511	–	strcpy( simnfo->sampleName, inFileName );
512	–	char* endTest;
513	–	int nameLength = strlen( simnfo->sampleName );
514	–	endTest = &(simnfo->sampleName[nameLength - 5]);
515	–	if( !strcmp( endTest, ".bass" ) ){
516	–	strcpy( endTest, ".dump" );
517	–	}
518	–	else if( !strcmp( endTest, ".BASS" ) ){
519	–	strcpy( endTest, ".dump" );
520	–	}
521	–	else{
522	–	endTest = &(simnfo->sampleName[nameLength - 4]);
523	–	if( !strcmp( endTest, ".bss" ) ){
524	–	strcpy( endTest, ".dump" );
525	–	}
526	–	else if( !strcmp( endTest, ".mdl" ) ){
527	–	strcpy( endTest, ".dump" );
528	–	}
529	–	else{
530	–	strcat( simnfo->sampleName, ".dump" );
531	–	}
532	–	}
533	–
534	–	strcpy( simnfo->statusName, inFileName );
535	–	nameLength = strlen( simnfo->statusName );
536	–	endTest = &(simnfo->statusName[nameLength - 5]);
537	–	if( !strcmp( endTest, ".bass" ) ){
538	–	strcpy( endTest, ".stat" );
539	–	}
540	–	else if( !strcmp( endTest, ".BASS" ) ){
541	–	strcpy( endTest, ".stat" );
542	–	}
543	–	else{
544	–	endTest = &(simnfo->statusName[nameLength - 4]);
545	–	if( !strcmp( endTest, ".bss" ) ){
546	–	strcpy( endTest, ".stat" );
547	–	}
548	–	else if( !strcmp( endTest, ".mdl" ) ){
549	–	strcpy( endTest, ".stat" );
550	–	}
551	–	else{
552	–	strcat( simnfo->statusName, ".stat" );
553	–	}
554	–	}
555	–
556	–	#ifdef IS_MPI
452		}
558	–	#endif // is_mpi
559	–
560	–	// set the status, sample, and themal kick times
561	–
562	–	if( the_globals->haveSampleTime() ){
563	–	simnfo->sampleTime = the_globals->getSampleTime();
564	–	simnfo->statusTime = simnfo->sampleTime;
565	–	simnfo->thermalTime = simnfo->sampleTime;
566	–	}
453		else{
454	<	simnfo->sampleTime = the_globals->getRunTime();
455	<	simnfo->statusTime = simnfo->sampleTime;
456	<	simnfo->thermalTime = simnfo->sampleTime;
454	>	n_cells = (int) temp3;
455	>	cellx = info[0].boxL[0] / temp3;
456	>	celly = info[0].boxL[1] / temp3;
457	>	cellz = info[0].boxL[2] / temp3;
458		}
459
460	<	if( the_globals->haveStatusTime() ){
461	<	simnfo->statusTime = the_globals->getStatusTime();
462	<	}
460	>	current_mol = 0;
461	>	current_comp_mol = 0;
462	>	current_comp = 0;
463	>	current_atom_ndx = 0;
464
465	<	if( the_globals->haveThermalTime() ){
466	<	simnfo->thermalTime = the_globals->getThermalTime();
467	<	}
465	>	for (i = 0; i < n_cells ; i++){
466	>	for (j = 0; j < n_cells; j++){
467	>	for (k = 0; k < n_cells; k++){
468	>	makeElement(i * cellx, j * celly, k * cellz);
469
470	<	// check for the temperature set flag
470	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
471
472	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
472	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
473
474	+	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
475	+	}
476	+	}
477	+	}
478
479	<	//   // make the longe range forces and the integrator
479	>	if (have_extra){
480	>	done = 0;
481
482	<	//   new AllLong( simnfo );
483	<
484	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
485	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
486	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
487	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
482	>	int start_ndx;
483	>	for (i = 0; i < (n_cells + 1) && !done; i++){
484	>	for (j = 0; j < (n_cells + 1) && !done; j++){
485	>	if (i < n_cells){
486	>	if (j < n_cells){
487	>	start_ndx = n_cells;
488	>	}
489	>	else
490	>	start_ndx = 0;
491	>	}
492	>	else
493	>	start_ndx = 0;
494
495	+	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
496	+	makeElement(i * cellx, j * celly, k * cellz);
497	+	done = (current_mol >= tot_nmol);
498
499	+	if (!done && n_per_extra > 1){
500	+	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
501	+	k * cellz);
502	+	done = (current_mol >= tot_nmol);
503	+	}
504
505	<	// initialize the Fortran
506	<
507	<	simnfo->refreshSim();
508	<
509	<	if( !strcmp( simnfo->mixingRule, "standard") ){
510	<	the_ff->initForceField( LB_MIXING_RULE );
505	>	if (!done && n_per_extra > 2){
506	>	makeElement(i * cellx, j * celly + 0.5 * celly,
507	>	k * cellz + 0.5 * cellz);
508	>	done = (current_mol >= tot_nmol);
509	>	}
510	>
511	>	if (!done && n_per_extra > 3){
512	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
513	>	k * cellz + 0.5 * cellz);
514	>	done = (current_mol >= tot_nmol);
515	>	}
516	>	}
517	>	}
518	>	}
519		}
604	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
605	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
606	–	}
607	–	else{
608	–	sprintf( painCave.errMsg,
609	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
610	–	simnfo->mixingRule );
611	–	painCave.isFatal = 1;
612	–	simError();
613	–	}
520
521	<
522	<	#ifdef IS_MPI
523	<	strcpy( checkPointMsg,
618	<	"Successfully intialized the mixingRule for Fortran." );
619	<	MPIcheckPoint();
620	<	#endif // is_mpi
521	>	for (i = 0; i < info[0].n_atoms; i++){
522	>	info[0].atoms[i]->setVel(vel);
523	>	}
524		}
525
526	<	void SimSetup::makeAtoms( void ){
527	<
625	<	int i, j, k, index;
626	<	double ux, uy, uz, uSqr, u;
526	>	void SimSetup::makeElement(double x, double y, double z){
527	>	int k;
528		AtomStamp* current_atom;
628	–
529		DirectionalAtom* dAtom;
530	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
530	>	double rotMat[3][3];
531	>	double pos[3];
532
533	<	lMolIndex = 0;
534	<	molIndex = 0;
535	<	index = 0;
536	<	for( i=0; i<n_components; i++ ){
533	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
534	>	current_atom = comp_stamps[current_comp]->getAtom(k);
535	>	if (!current_atom->havePosition()){
536	>	sprintf(painCave.errMsg,
537	>	"SimSetup:initFromBass error.\n"
538	>	"\tComponent %s, atom %s does not have a position specified.\n"
539	>	"\tThe initialization routine is unable to give a start"
540	>	" position.\n",
541	>	comp_stamps[current_comp]->getID(), current_atom->getType());
542	>	painCave.isFatal = 1;
543	>	simError();
544	>	}
545
546	<	for( j=0; j<components_nmol[i]; j++ ){
546	>	pos[0] = x + current_atom->getPosX();
547	>	pos[1] = y + current_atom->getPosY();
548	>	pos[2] = z + current_atom->getPosZ();
549
550	<	#ifdef IS_MPI
640	<	if( mpiSim->getMyMolStart() <= molIndex &&
641	<	molIndex <= mpiSim->getMyMolEnd() ){
642	<	#endif // is_mpi
550	>	info[0].atoms[current_atom_ndx]->setPos(pos);
551
552	<	molStart = index;
553	<	nMemb = comp_stamps[i]->getNAtoms();
646	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
647	<
648	<	current_atom = comp_stamps[i]->getAtom( k );
649	<	if( current_atom->haveOrientation() ){
650	<
651	<	dAtom = new DirectionalAtom(index);
652	<	simnfo->n_oriented++;
653	<	the_atoms[index] = dAtom;
654	<
655	<	ux = current_atom->getOrntX();
656	<	uy = current_atom->getOrntY();
657	<	uz = current_atom->getOrntZ();
658	<
659	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
660	<
661	<	u = sqrt( uSqr );
662	<	ux = ux / u;
663	<	uy = uy / u;
664	<	uz = uz / u;
665	<
666	<	dAtom->setSUx( ux );
667	<	dAtom->setSUy( uy );
668	<	dAtom->setSUz( uz );
669	<	}
670	<	else{
671	<	the_atoms[index] = new GeneralAtom(index);
672	<	}
673	<	the_atoms[index]->setType( current_atom->getType() );
674	<	the_atoms[index]->setIndex( index );
675	<
676	<	// increment the index and repeat;
677	<	index++;
678	<	}
679	<
680	<	molEnd = index -1;
681	<	the_molecules[lMolIndex].setNMembers( nMemb );
682	<	the_molecules[lMolIndex].setStartAtom( molStart );
683	<	the_molecules[lMolIndex].setEndAtom( molEnd );
684	<	the_molecules[lMolIndex].setStampID( i );
685	<	lMolIndex++;
552	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
553	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
554
555	<	#ifdef IS_MPI
556	<	}
557	<	#endif //is_mpi
558	<
559	<	molIndex++;
555	>	rotMat[0][0] = 1.0;
556	>	rotMat[0][1] = 0.0;
557	>	rotMat[0][2] = 0.0;
558	>
559	>	rotMat[1][0] = 0.0;
560	>	rotMat[1][1] = 1.0;
561	>	rotMat[1][2] = 0.0;
562	>
563	>	rotMat[2][0] = 0.0;
564	>	rotMat[2][1] = 0.0;
565	>	rotMat[2][2] = 1.0;
566	>
567	>	dAtom->setA(rotMat);
568		}
569	+
570	+	current_atom_ndx++;
571		}
572
573	<	#ifdef IS_MPI
574	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
697	<
698	<	delete[] globalIndex;
573	>	current_mol++;
574	>	current_comp_mol++;
575
576	<	mpiSim->mpiRefresh();
577	<	#endif //IS_MPI
578	<
579	<	the_ff->initializeAtoms();
576	>	if (current_comp_mol >= components_nmol[current_comp]){
577	>	current_comp_mol = 0;
578	>	current_comp++;
579	>	}
580		}
581
706	–	void SimSetup::makeBonds( void ){
582
583	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
584	<	bond_pair* the_bonds;
710	<	BondStamp* current_bond;
583	>	void SimSetup::gatherInfo(void){
584	>	int i;
585
586	<	the_bonds = new bond_pair[tot_bonds];
587	<	index = 0;
714	<	offset = 0;
715	<	molIndex = 0;
586	>	ensembleCase = -1;
587	>	ffCase = -1;
588
589	<	for( i=0; i<n_components; i++ ){
589	>	// set the easy ones first
590
591	<	for( j=0; j<components_nmol[i]; j++ ){
591	>	for (i = 0; i < nInfo; i++){
592	>	info[i].target_temp = globals->getTargetTemp();
593	>	info[i].dt = globals->getDt();
594	>	info[i].run_time = globals->getRunTime();
595	>	}
596	>	n_components = globals->getNComponents();
597
721	–	#ifdef IS_MPI
722	–	if( mpiSim->getMyMolStart() <= molIndex &&
723	–	molIndex <= mpiSim->getMyMolEnd() ){
724	–	#endif // is_mpi
725	–
726	–	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
727	–
728	–	current_bond = comp_stamps[i]->getBond( k );
729	–	the_bonds[index].a = current_bond->getA() + offset;
730	–	the_bonds[index].b = current_bond->getB() + offset;
598
599	<	exI = the_bonds[index].a;
733	<	exJ = the_bonds[index].b;
599	>	// get the forceField
600
601	<	// exclude_I must always be the smaller of the pair
736	<	if( exI > exJ ){
737	<	tempEx = exI;
738	<	exI = exJ;
739	<	exJ = tempEx;
740	<	}
601	>	strcpy(force_field, globals->getForceField());
602
603	<
604	<	#ifdef IS_MPI
744	<
745	<	the_excludes[index*2] =
746	<	the_atoms[exI]->getGlobalIndex() + 1;
747	<	the_excludes[index*2 + 1] =
748	<	the_atoms[exJ]->getGlobalIndex() + 1;
749	<
750	<	#else  // isn't MPI
751	<
752	<	the_excludes[index*2] =     exI + 1;
753	<	the_excludes[index*2 + 1] = exJ + 1;
754	<	// fortran index from 1 (hence the +1 in the indexing)
755	<	#endif  //is_mpi
756	<
757	<	// increment the index and repeat;
758	<	index++;
759	<	}
760	<	offset += comp_stamps[i]->getNAtoms();
761	<
762	<	#ifdef IS_MPI
763	<	}
764	<	#endif //is_mpi
765	<
766	<	molIndex++;
767	<	}
603	>	if (!strcasecmp(force_field, "DUFF")){
604	>	ffCase = FF_DUFF;
605		}
606	+	else if (!strcasecmp(force_field, "LJ")){
607	+	ffCase = FF_LJ;
608	+	}
609	+	else if (!strcasecmp(force_field, "EAM")){
610	+	ffCase = FF_EAM;
611	+	}
612	+	else{
613	+	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
614	+	force_field);
615	+	painCave.isFatal = 1;
616	+	simError();
617	+	}
618
619	<	the_ff->initializeBonds( the_bonds );
771	<	}
619	>	// get the ensemble
620
621	<	void SimSetup::makeBends( void ){
621	>	strcpy(ensemble, globals->getEnsemble());
622
623	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
624	<	bend_set* the_bends;
625	<	BendStamp* current_bend;
626	<	LinkedAssign* extras;
627	<	LinkedAssign* current_extra;
628	<
623	>	if (!strcasecmp(ensemble, "NVE")){
624	>	ensembleCase = NVE_ENS;
625	>	}
626	>	else if (!strcasecmp(ensemble, "NVT")){
627	>	ensembleCase = NVT_ENS;
628	>	}
629	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
630	>	ensembleCase = NPTi_ENS;
631	>	}
632	>	else if (!strcasecmp(ensemble, "NPTf")){
633	>	ensembleCase = NPTf_ENS;
634	>	}
635	>	else if (!strcasecmp(ensemble, "NPTxyz")){
636	>	ensembleCase = NPTxyz_ENS;
637	>	}
638	>	else{
639	>	sprintf(painCave.errMsg,
640	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
641	>	"reverting to NVE for this simulation.\n",
642	>	ensemble);
643	>	painCave.isFatal = 0;
644	>	simError();
645	>	strcpy(ensemble, "NVE");
646	>	ensembleCase = NVE_ENS;
647	>	}
648
649	<	the_bends = new bend_set[tot_bends];
650	<	index = 0;
784	<	offset = 0;
785	<	molIndex = 0;
786	<	for( i=0; i<n_components; i++ ){
649	>	for (i = 0; i < nInfo; i++){
650	>	strcpy(info[i].ensemble, ensemble);
651
652	<	for( j=0; j<components_nmol[i]; j++ ){
652	>	// get the mixing rule
653
654	<	#ifdef IS_MPI
655	<	if( mpiSim->getMyMolStart() <= molIndex &&
656	<	molIndex <= mpiSim->getMyMolEnd() ){
793	<	#endif // is_mpi
654	>	strcpy(info[i].mixingRule, globals->getMixingRule());
655	>	info[i].usePBC = globals->getPBC();
656	>	}
657
658	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
796	<
797	<	current_bend = comp_stamps[i]->getBend( k );
798	<	the_bends[index].a = current_bend->getA() + offset;
799	<	the_bends[index].b = current_bend->getB() + offset;
800	<	the_bends[index].c = current_bend->getC() + offset;
801	<
802	<	if( current_bend->haveExtras() ){
803	<
804	<	extras = current_bend->getExtras();
805	<	current_extra = extras;
806	<
807	<	while( current_extra != NULL ){
808	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
809	<
810	<	switch( current_extra->getType() ){
811	<
812	<	case 0:
813	<	the_bends[index].ghost =
814	<	current_extra->getInt() + offset;
815	<	the_bends[index].isGhost = 1;
816	<	break;
817	<
818	<	case 1:
819	<	the_bends[index].ghost =
820	<	(int)current_extra->getDouble() + offset;
821	<	the_bends[index].isGhost = 1;
822	<	break;
823	<
824	<	default:
825	<	sprintf( painCave.errMsg,
826	<	"SimSetup Error: ghostVectorSource was neiter a "
827	<	"double nor an int.\n"
828	<	"-->Bend[%d] in %s\n",
829	<	k, comp_stamps[i]->getID() );
830	<	painCave.isFatal = 1;
831	<	simError();
832	<	}
833	<	}
834	<
835	<	else{
836	<
837	<	sprintf( painCave.errMsg,
838	<	"SimSetup Error: unhandled bend assignment:\n"
839	<	"    -->%s in Bend[%d] in %s\n",
840	<	current_extra->getlhs(),
841	<	k, comp_stamps[i]->getID() );
842	<	painCave.isFatal = 1;
843	<	simError();
844	<	}
845	<
846	<	current_extra = current_extra->getNext();
847	<	}
848	<	}
849	<
850	<	if( !the_bends[index].isGhost ){
851	<
852	<	exI = the_bends[index].a;
853	<	exJ = the_bends[index].c;
854	<	}
855	<	else{
856	<
857	<	exI = the_bends[index].a;
858	<	exJ = the_bends[index].b;
859	<	}
860	<
861	<	// exclude_I must always be the smaller of the pair
862	<	if( exI > exJ ){
863	<	tempEx = exI;
864	<	exI = exJ;
865	<	exJ = tempEx;
866	<	}
658	>	// get the components and calculate the tot_nMol and indvidual n_mol
659
660	+	the_components = globals->getComponents();
661	+	components_nmol = new int[n_components];
662
869	–	#ifdef IS_MPI
663
664	<	the_excludes[(index + tot_bonds)*2] =
665	<	the_atoms[exI]->getGlobalIndex() + 1;
666	<	the_excludes[(index + tot_bonds)*2 + 1] =
667	<	the_atoms[exJ]->getGlobalIndex() + 1;
668	<
669	<	#else  // isn't MPI
670	<
671	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
672	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
673	<	// fortran index from 1 (hence the +1 in the indexing)
674	<	#endif  //is_mpi
675	<
676	<
884	<	// increment the index and repeat;
885	<	index++;
886	<	}
887	<	offset += comp_stamps[i]->getNAtoms();
888	<
889	<	#ifdef IS_MPI
664	>	if (!globals->haveNMol()){
665	>	// we don't have the total number of molecules, so we assume it is
666	>	// given in each component
667	>
668	>	tot_nmol = 0;
669	>	for (i = 0; i < n_components; i++){
670	>	if (!the_components[i]->haveNMol()){
671	>	// we have a problem
672	>	sprintf(painCave.errMsg,
673	>	"SimSetup Error. No global NMol or component NMol"
674	>	" given. Cannot calculate the number of atoms.\n");
675	>	painCave.isFatal = 1;
676	>	simError();
677		}
891	–	#endif //is_mpi
678
679	<	molIndex++;
679	>	tot_nmol += the_components[i]->getNMol();
680	>	components_nmol[i] = the_components[i]->getNMol();
681		}
682		}
683	+	else{
684	+	sprintf(painCave.errMsg,
685	+	"SimSetup error.\n"
686	+	"\tSorry, the ability to specify total"
687	+	" nMols and then give molfractions in the components\n"
688	+	"\tis not currently supported."
689	+	" Please give nMol in the components.\n");
690	+	painCave.isFatal = 1;
691	+	simError();
692	+	}
693
694	<	#ifdef IS_MPI
695	<	sprintf( checkPointMsg,
696	<	"Successfully created the bends list.\n" );
697	<	MPIcheckPoint();
698	<	#endif // is_mpi
699	<
694	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
695	>	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
696	>	sprintf(painCave.errMsg,
697	>	"Sample time is not divisible by dt \n");
698	>	painCave.isFatal = 0;
699	>	simError();
700	>	}
701
702	<	the_ff->initializeBends( the_bends );
703	<	}
702	>	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
703	>	sprintf(painCave.errMsg,
704	>	"Status time is not divisible by dt\n");
705	>	painCave.isFatal = 0;
706	>	simError();
707	>	}
708
709	<	void SimSetup::makeTorsions( void ){
709	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
710	>	sprintf(painCave.errMsg,
711	>	"Thermal time is not divisible by dt\n");
712	>	painCave.isFatal = 0;
713	>	simError();
714	>	}
715
716	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
717	<	torsion_set* the_torsions;
718	<	TorsionStamp* current_torsion;
716	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
717	>	sprintf(painCave.errMsg,
718	>	"Reset time is not divisible by dt\n");
719	>	painCave.isFatal = 0;
720	>	simError();
721	>	}
722
723	<	the_torsions = new torsion_set[tot_torsions];
914	<	index = 0;
915	<	offset = 0;
916	<	molIndex = 0;
917	<	for( i=0; i<n_components; i++ ){
723	>	// set the status, sample, and thermal kick times
724
725	<	for( j=0; j<components_nmol[i]; j++ ){
725	>	for (i = 0; i < nInfo; i++){
726	>	if (globals->haveSampleTime()){
727	>	info[i].sampleTime = globals->getSampleTime();
728	>	info[i].statusTime = info[i].sampleTime;
729	>	info[i].thermalTime = info[i].sampleTime;
730	>	}
731	>	else{
732	>	info[i].sampleTime = globals->getRunTime();
733	>	info[i].statusTime = info[i].sampleTime;
734	>	info[i].thermalTime = info[i].sampleTime;
735	>	}
736
737	<	#ifdef IS_MPI
738	<	if( mpiSim->getMyMolStart() <= molIndex &&
739	<	molIndex <= mpiSim->getMyMolEnd() ){
924	<	#endif // is_mpi
737	>	if (globals->haveStatusTime()){
738	>	info[i].statusTime = globals->getStatusTime();
739	>	}
740
741	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
741	>	if (globals->haveThermalTime()){
742	>	info[i].thermalTime = globals->getThermalTime();
743	>	}
744
745	<	current_torsion = comp_stamps[i]->getTorsion( k );
746	<	the_torsions[index].a = current_torsion->getA() + offset;
747	<	the_torsions[index].b = current_torsion->getB() + offset;
748	<	the_torsions[index].c = current_torsion->getC() + offset;
749	<	the_torsions[index].d = current_torsion->getD() + offset;
745	>	info[i].resetIntegrator = 0;
746	>	if( globals->haveResetTime() ){
747	>	info[i].resetTime = globals->getResetTime();
748	>	info[i].resetIntegrator = 1;
749	>	}
750
751	<	exI = the_torsions[index].a;
752	<	exJ = the_torsions[index].d;
751	>	// check for the temperature set flag
752	>
753	>	if (globals->haveTempSet())
754	>	info[i].setTemp = globals->getTempSet();
755
756	<
938	<	// exclude_I must always be the smaller of the pair
939	<	if( exI > exJ ){
940	<	tempEx = exI;
941	<	exI = exJ;
942	<	exJ = tempEx;
943	<	}
756	>	// check for the extended State init
757
758	+	info[i].useInitXSstate = globals->getUseInitXSstate();
759	+	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
760	+
761	+	}
762	+
763	+	//setup seed for random number generator
764	+	int seedValue;
765
766	<	#ifdef IS_MPI
767	<
948	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
949	<	the_atoms[exI]->getGlobalIndex() + 1;
950	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
951	<	the_atoms[exJ]->getGlobalIndex() + 1;
952	<
953	<	#else  // isn't MPI
954	<
955	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
956	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
957	<	// fortran indexes from 1 (hence the +1 in the indexing)
958	<	#endif  //is_mpi
959	<
766	>	if (globals->haveSeed()){
767	>	seedValue = globals->getSeed();
768
769	<	// increment the index and repeat;
770	<	index++;
769	>	if(seedValue / 1E9 == 0){
770	>	sprintf(painCave.errMsg,
771	>	"Seed for sprng library should contain at least 9 digits\n"
772	>	"OOPSE will generate a seed for user\n");
773	>	painCave.isFatal = 0;
774	>	simError();
775	>
776	>	//using seed generated by system instead of invalid seed set by user
777	>	#ifndef IS_MPI
778	>	seedValue = make_sprng_seed();
779	>	#else
780	>	if (worldRank == 0){
781	>	seedValue = make_sprng_seed();
782		}
783	<	offset += comp_stamps[i]->getNAtoms();
783	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
784	>	#endif
785	>	}
786	>	}//end of if branch of globals->haveSeed()
787	>	else{
788	>
789	>	#ifndef IS_MPI
790	>	seedValue = make_sprng_seed();
791	>	#else
792	>	if (worldRank == 0){
793	>	seedValue = make_sprng_seed();
794	>	}
795	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
796	>	#endif
797	>	}//end of globals->haveSeed()
798
799	+	for (int i = 0; i < nInfo; i++){
800	+	info[i].setSeed(seedValue);
801	+	}
802	+
803		#ifdef IS_MPI
804	<	}
805	<	#endif //is_mpi
804	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
805	>	MPIcheckPoint();
806	>	#endif // is_mpi
807	>	}
808
809	<	molIndex++;
809	>
810	>	void SimSetup::finalInfoCheck(void){
811	>	int index;
812	>	int usesDipoles;
813	>	int i;
814	>
815	>	for (i = 0; i < nInfo; i++){
816	>	// check electrostatic parameters
817	>
818	>	index = 0;
819	>	usesDipoles = 0;
820	>	while ((index < info[i].n_atoms) && !usesDipoles){
821	>	usesDipoles = (info[i].atoms[index])->hasDipole();
822	>	index++;
823		}
972	–	}
824
825	<	the_ff->initializeTorsions( the_torsions );
826	<	}
825	>	#ifdef IS_MPI
826	>	int myUse = usesDipoles;
827	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
828	>	#endif //is_mpi
829
830	<	void SimSetup::initFromBass( void ){
830	>	double theEcr, theEst;
831
832	<	int i, j, k;
833	<	int n_cells;
981	<	double cellx, celly, cellz;
982	<	double temp1, temp2, temp3;
983	<	int n_per_extra;
984	<	int n_extra;
985	<	int have_extra, done;
832	>	if (globals->getUseRF()){
833	>	info[i].useReactionField = 1;
834
835	<	temp1 = (double)tot_nmol / 4.0;
836	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
837	<	temp3 = ceil( temp2 );
835	>	if (!globals->haveECR()){
836	>	sprintf(painCave.errMsg,
837	>	"SimSetup Warning: using default value of 15.0 angstroms"
838	>	"box length for the electrostaticCutoffRadius.\n");
839	>	painCave.isFatal = 0;
840	>	simError();
841	>	theEcr = 15.0;
842	>	}
843	>	else{
844	>	theEcr = globals->getECR();
845	>	}
846
847	<	have_extra =0;
848	<	if( temp2 < temp3 ){ // we have a non-complete lattice
849	<	have_extra =1;
847	>	if (!globals->haveEST()){
848	>	sprintf(painCave.errMsg,
849	>	"SimSetup Warning: using default value of 0.05 * the "
850	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
851	>	painCave.isFatal = 0;
852	>	simError();
853	>	theEst = 0.05 * theEcr;
854	>	}
855	>	else{
856	>	theEst = globals->getEST();
857	>	}
858
859	<	n_cells = (int)temp3 - 1;
996	<	cellx = simnfo->box_x / temp3;
997	<	celly = simnfo->box_y / temp3;
998	<	cellz = simnfo->box_z / temp3;
999	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1000	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1001	<	n_per_extra = (int)ceil( temp1 );
859	>	info[i].setDefaultEcr(theEcr, theEst);
860
861	<	if( n_per_extra > 4){
862	<	sprintf( painCave.errMsg,
863	<	"SimSetup error. There has been an error in constructing"
864	<	" the non-complete lattice.\n" );
865	<	painCave.isFatal = 1;
866	<	simError();
861	>	if (!globals->haveDielectric()){
862	>	sprintf(painCave.errMsg,
863	>	"SimSetup Error: You are trying to use Reaction Field without"
864	>	"setting a dielectric constant!\n");
865	>	painCave.isFatal = 1;
866	>	simError();
867	>	}
868	>	info[i].dielectric = globals->getDielectric();
869		}
870	+	else{
871	+	if (usesDipoles){
872	+	if (!globals->haveECR()){
873	+	sprintf(painCave.errMsg,
874	+	"SimSetup Warning: using default value of 15.0 angstroms"
875	+	"box length for the electrostaticCutoffRadius.\n");
876	+	painCave.isFatal = 0;
877	+	simError();
878	+	theEcr = 15.0;
879	+	}
880	+	else{
881	+	theEcr = globals->getECR();
882	+	}
883	+
884	+	if (!globals->haveEST()){
885	+	sprintf(painCave.errMsg,
886	+	"SimSetup Warning: using default value of 0.05 * the "
887	+	"electrostaticCutoffRadius for the "
888	+	"electrostaticSkinThickness\n");
889	+	painCave.isFatal = 0;
890	+	simError();
891	+	theEst = 0.05 * theEcr;
892	+	}
893	+	else{
894	+	theEst = globals->getEST();
895	+	}
896	+
897	+	info[i].setDefaultEcr(theEcr, theEst);
898	+	}
899	+	}
900		}
901	+	#ifdef IS_MPI
902	+	strcpy(checkPointMsg, "post processing checks out");
903	+	MPIcheckPoint();
904	+	#endif // is_mpi
905	+	}
906	+
907	+	void SimSetup::initSystemCoords(void){
908	+	int i;
909	+
910	+	char* inName;
911	+
912	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
913	+
914	+	for (i = 0; i < info[0].n_atoms; i++)
915	+	info[0].atoms[i]->setCoords();
916	+
917	+	if (globals->haveInitialConfig()){
918	+	InitializeFromFile* fileInit;
919	+	#ifdef IS_MPI // is_mpi
920	+	if (worldRank == 0){
921	+	#endif //is_mpi
922	+	inName = globals->getInitialConfig();
923	+	fileInit = new InitializeFromFile(inName);
924	+	#ifdef IS_MPI
925	+	}
926	+	else
927	+	fileInit = new InitializeFromFile(NULL);
928	+	#endif
929	+	fileInit->readInit(info); // default velocities on
930	+
931	+	delete fileInit;
932	+	}
933		else{
934	<	n_cells = (int)temp3;
935	<	cellx = simnfo->box_x / temp3;
936	<	celly = simnfo->box_y / temp3;
937	<	cellz = simnfo->box_z / temp3;
934	>
935	>	// no init from bass
936	>
937	>	sprintf(painCave.errMsg,
938	>	"Cannot intialize a simulation without an initial configuration file.\n");
939	>	painCave.isFatal = 1;;
940	>	simError();
941	>
942		}
943
944	<	current_mol = 0;
945	<	current_comp_mol = 0;
946	<	current_comp = 0;
947	<	current_atom_ndx = 0;
944	>	#ifdef IS_MPI
945	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
946	>	MPIcheckPoint();
947	>	#endif // is_mpi
948	>	}
949
1023	–	for( i=0; i < n_cells ; i++ ){
1024	–	for( j=0; j < n_cells; j++ ){
1025	–	for( k=0; k < n_cells; k++ ){
950
951	<	makeElement( i * cellx,
952	<	j * celly,
1029	<	k * cellz );
951	>	void SimSetup::makeOutNames(void){
952	>	int k;
953
1031	–	makeElement( i * cellx + 0.5 * cellx,
1032	–	j * celly + 0.5 * celly,
1033	–	k * cellz );
954
955	<	makeElement( i * cellx,
956	<	j * celly + 0.5 * celly,
957	<	k * cellz + 0.5 * cellz );
955	>	for (k = 0; k < nInfo; k++){
956	>	#ifdef IS_MPI
957	>	if (worldRank == 0){
958	>	#endif // is_mpi
959
960	<	makeElement( i * cellx + 0.5 * cellx,
961	<	j * celly,
1041	<	k * cellz + 0.5 * cellz );
960	>	if (globals->haveFinalConfig()){
961	>	strcpy(info[k].finalName, globals->getFinalConfig());
962		}
963	+	else{
964	+	strcpy(info[k].finalName, inFileName);
965	+	char* endTest;
966	+	int nameLength = strlen(info[k].finalName);
967	+	endTest = &(info[k].finalName[nameLength - 5]);
968	+	if (!strcmp(endTest, ".bass")){
969	+	strcpy(endTest, ".eor");
970	+	}
971	+	else if (!strcmp(endTest, ".BASS")){
972	+	strcpy(endTest, ".eor");
973	+	}
974	+	else{
975	+	endTest = &(info[k].finalName[nameLength - 4]);
976	+	if (!strcmp(endTest, ".bss")){
977	+	strcpy(endTest, ".eor");
978	+	}
979	+	else if (!strcmp(endTest, ".mdl")){
980	+	strcpy(endTest, ".eor");
981	+	}
982	+	else{
983	+	strcat(info[k].finalName, ".eor");
984	+	}
985	+	}
986	+	}
987	+
988	+	// make the sample and status out names
989	+
990	+	strcpy(info[k].sampleName, inFileName);
991	+	char* endTest;
992	+	int nameLength = strlen(info[k].sampleName);
993	+	endTest = &(info[k].sampleName[nameLength - 5]);
994	+	if (!strcmp(endTest, ".bass")){
995	+	strcpy(endTest, ".dump");
996	+	}
997	+	else if (!strcmp(endTest, ".BASS")){
998	+	strcpy(endTest, ".dump");
999	+	}
1000	+	else{
1001	+	endTest = &(info[k].sampleName[nameLength - 4]);
1002	+	if (!strcmp(endTest, ".bss")){
1003	+	strcpy(endTest, ".dump");
1004	+	}
1005	+	else if (!strcmp(endTest, ".mdl")){
1006	+	strcpy(endTest, ".dump");
1007	+	}
1008	+	else{
1009	+	strcat(info[k].sampleName, ".dump");
1010	+	}
1011	+	}
1012	+
1013	+	strcpy(info[k].statusName, inFileName);
1014	+	nameLength = strlen(info[k].statusName);
1015	+	endTest = &(info[k].statusName[nameLength - 5]);
1016	+	if (!strcmp(endTest, ".bass")){
1017	+	strcpy(endTest, ".stat");
1018	+	}
1019	+	else if (!strcmp(endTest, ".BASS")){
1020	+	strcpy(endTest, ".stat");
1021	+	}
1022	+	else{
1023	+	endTest = &(info[k].statusName[nameLength - 4]);
1024	+	if (!strcmp(endTest, ".bss")){
1025	+	strcpy(endTest, ".stat");
1026	+	}
1027	+	else if (!strcmp(endTest, ".mdl")){
1028	+	strcpy(endTest, ".stat");
1029	+	}
1030	+	else{
1031	+	strcat(info[k].statusName, ".stat");
1032	+	}
1033	+	}
1034	+
1035	+	#ifdef IS_MPI
1036	+
1037		}
1038	+	#endif // is_mpi
1039		}
1040	+	}
1041
1046	–	if( have_extra ){
1047	–	done = 0;
1042
1043	<	int start_ndx;
1044	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1051	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1043	>	void SimSetup::sysObjectsCreation(void){
1044	>	int i, k;
1045
1046	<	if( i < n_cells ){
1046	>	// create the forceField
1047
1048	<	if( j < n_cells ){
1056	<	start_ndx = n_cells;
1057	<	}
1058	<	else start_ndx = 0;
1059	<	}
1060	<	else start_ndx = 0;
1048	>	createFF();
1049
1050	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1050	>	// extract componentList
1051
1052	<	makeElement( i * cellx,
1065	<	j * celly,
1066	<	k * cellz );
1067	<	done = ( current_mol >= tot_nmol );
1052	>	compList();
1053
1054	<	if( !done && n_per_extra > 1 ){
1070	<	makeElement( i * cellx + 0.5 * cellx,
1071	<	j * celly + 0.5 * celly,
1072	<	k * cellz );
1073	<	done = ( current_mol >= tot_nmol );
1074	<	}
1054	>	// calc the number of atoms, bond, bends, and torsions
1055
1056	<	if( !done && n_per_extra > 2){
1077	<	makeElement( i * cellx,
1078	<	j * celly + 0.5 * celly,
1079	<	k * cellz + 0.5 * cellz );
1080	<	done = ( current_mol >= tot_nmol );
1081	<	}
1056	>	calcSysValues();
1057
1058	<	if( !done && n_per_extra > 3){
1059	<	makeElement( i * cellx + 0.5 * cellx,
1085	<	j * celly,
1086	<	k * cellz + 0.5 * cellz );
1087	<	done = ( current_mol >= tot_nmol );
1088	<	}
1089	<	}
1090	<	}
1091	<	}
1092	<	}
1058	>	#ifdef IS_MPI
1059	>	// divide the molecules among the processors
1060
1061	+	mpiMolDivide();
1062	+	#endif //is_mpi
1063
1064	<	for( i=0; i<simnfo->n_atoms; i++ ){
1065	<	simnfo->atoms[i]->set_vx( 0.0 );
1066	<	simnfo->atoms[i]->set_vy( 0.0 );
1067	<	simnfo->atoms[i]->set_vz( 0.0 );
1064	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1065	>
1066	>	makeSysArrays();
1067	>
1068	>	// make and initialize the molecules (all but atomic coordinates)
1069	>
1070	>	makeMolecules();
1071	>
1072	>	for (k = 0; k < nInfo; k++){
1073	>	info[k].identArray = new int[info[k].n_atoms];
1074	>	for (i = 0; i < info[k].n_atoms; i++){
1075	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1076	>	}
1077		}
1078		}
1079
1102	–	void SimSetup::makeElement( double x, double y, double z ){
1080
1081	<	int k;
1082	<	AtomStamp* current_atom;
1083	<	DirectionalAtom* dAtom;
1084	<	double rotMat[3][3];
1081	>	void SimSetup::createFF(void){
1082	>	switch (ffCase){
1083	>	case FF_DUFF:
1084	>	the_ff = new DUFF();
1085	>	break;
1086
1087	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1087	>	case FF_LJ:
1088	>	the_ff = new LJFF();
1089	>	break;
1090
1091	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1092	<	if( !current_atom->havePosition() ){
1093	<	sprintf( painCave.errMsg,
1094	<	"SimSetup:initFromBass error.\n"
1095	<	"\tComponent %s, atom %s does not have a position specified.\n"
1096	<	"\tThe initialization routine is unable to give a start"
1097	<	" position.\n",
1118	<	comp_stamps[current_comp]->getID(),
1119	<	current_atom->getType() );
1091	>	case FF_EAM:
1092	>	the_ff = new EAM_FF();
1093	>	break;
1094	>
1095	>	default:
1096	>	sprintf(painCave.errMsg,
1097	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1098		painCave.isFatal = 1;
1099		simError();
1100	+	}
1101	+
1102	+	#ifdef IS_MPI
1103	+	strcpy(checkPointMsg, "ForceField creation successful");
1104	+	MPIcheckPoint();
1105	+	#endif // is_mpi
1106	+	}
1107	+
1108	+
1109	+	void SimSetup::compList(void){
1110	+	int i;
1111	+	char* id;
1112	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1113	+	LinkedMolStamp* currentStamp = NULL;
1114	+	comp_stamps = new MoleculeStamp * [n_components];
1115	+
1116	+	// make an array of molecule stamps that match the components used.
1117	+	// also extract the used stamps out into a separate linked list
1118	+
1119	+	for (i = 0; i < nInfo; i++){
1120	+	info[i].nComponents = n_components;
1121	+	info[i].componentsNmol = components_nmol;
1122	+	info[i].compStamps = comp_stamps;
1123	+	info[i].headStamp = headStamp;
1124	+	}
1125	+
1126	+
1127	+	for (i = 0; i < n_components; i++){
1128	+	id = the_components[i]->getType();
1129	+	comp_stamps[i] = NULL;
1130	+
1131	+	// check to make sure the component isn't already in the list
1132	+
1133	+	comp_stamps[i] = headStamp->match(id);
1134	+	if (comp_stamps[i] == NULL){
1135	+	// extract the component from the list;
1136	+
1137	+	currentStamp = stamps->extractMolStamp(id);
1138	+	if (currentStamp == NULL){
1139	+	sprintf(painCave.errMsg,
1140	+	"SimSetup error: Component \"%s\" was not found in the "
1141	+	"list of declared molecules\n",
1142	+	id);
1143	+	painCave.isFatal = 1;
1144	+	simError();
1145	+	}
1146	+
1147	+	headStamp->add(currentStamp);
1148	+	comp_stamps[i] = headStamp->match(id);
1149		}
1150	+	}
1151
1152	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1153	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1154	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1152	>	#ifdef IS_MPI
1153	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1154	>	MPIcheckPoint();
1155	>	#endif // is_mpi
1156	>	}
1157
1158	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1158	>	void SimSetup::calcSysValues(void){
1159	>	int i;
1160
1161	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1161	>	int* molMembershipArray;
1162
1163	<	rotMat[0][0] = 1.0;
1164	<	rotMat[0][1] = 0.0;
1165	<	rotMat[0][2] = 0.0;
1163	>	tot_atoms = 0;
1164	>	tot_bonds = 0;
1165	>	tot_bends = 0;
1166	>	tot_torsions = 0;
1167	>	for (i = 0; i < n_components; i++){
1168	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1169	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1170	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1171	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1172	>	}
1173
1174	<	rotMat[1][0] = 0.0;
1175	<	rotMat[1][1] = 1.0;
1138	<	rotMat[1][2] = 0.0;
1174	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1175	>	molMembershipArray = new int[tot_atoms];
1176
1177	<	rotMat[2][0] = 0.0;
1178	<	rotMat[2][1] = 0.0;
1179	<	rotMat[2][2] = 1.0;
1177	>	for (i = 0; i < nInfo; i++){
1178	>	info[i].n_atoms = tot_atoms;
1179	>	info[i].n_bonds = tot_bonds;
1180	>	info[i].n_bends = tot_bends;
1181	>	info[i].n_torsions = tot_torsions;
1182	>	info[i].n_SRI = tot_SRI;
1183	>	info[i].n_mol = tot_nmol;
1184
1185	<	dAtom->setA( rotMat );
1185	>	info[i].molMembershipArray = molMembershipArray;
1186	>	}
1187	>	}
1188	>
1189	>	#ifdef IS_MPI
1190	>
1191	>	void SimSetup::mpiMolDivide(void){
1192	>	int i, j, k;
1193	>	int localMol, allMol;
1194	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1195	>
1196	>	mpiSim = new mpiSimulation(info);
1197	>
1198	>	globalIndex = mpiSim->divideLabor();
1199	>
1200	>	// set up the local variables
1201	>
1202	>	mol2proc = mpiSim->getMolToProcMap();
1203	>	molCompType = mpiSim->getMolComponentType();
1204	>
1205	>	allMol = 0;
1206	>	localMol = 0;
1207	>	local_atoms = 0;
1208	>	local_bonds = 0;
1209	>	local_bends = 0;
1210	>	local_torsions = 0;
1211	>	globalAtomIndex = 0;
1212	>
1213	>
1214	>	for (i = 0; i < n_components; i++){
1215	>	for (j = 0; j < components_nmol[i]; j++){
1216	>	if (mol2proc[allMol] == worldRank){
1217	>	local_atoms += comp_stamps[i]->getNAtoms();
1218	>	local_bonds += comp_stamps[i]->getNBonds();
1219	>	local_bends += comp_stamps[i]->getNBends();
1220	>	local_torsions += comp_stamps[i]->getNTorsions();
1221	>	localMol++;
1222	>	}
1223	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1224	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1225	>	globalAtomIndex++;
1226	>	}
1227	>
1228	>	allMol++;
1229		}
1230	+	}
1231	+	local_SRI = local_bonds + local_bends + local_torsions;
1232
1233	<	current_atom_ndx++;
1233	>	info[0].n_atoms = mpiSim->getMyNlocal();
1234	>
1235	>	if (local_atoms != info[0].n_atoms){
1236	>	sprintf(painCave.errMsg,
1237	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1238	>	" localAtom (%d) are not equal.\n",
1239	>	info[0].n_atoms, local_atoms);
1240	>	painCave.isFatal = 1;
1241	>	simError();
1242		}
1243
1244	<	current_mol++;
1245	<	current_comp_mol++;
1244	>	info[0].n_bonds = local_bonds;
1245	>	info[0].n_bends = local_bends;
1246	>	info[0].n_torsions = local_torsions;
1247	>	info[0].n_SRI = local_SRI;
1248	>	info[0].n_mol = localMol;
1249
1250	<	if( current_comp_mol >= components_nmol[current_comp] ){
1250	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1251	>	MPIcheckPoint();
1252	>	}
1253
1254	<	current_comp_mol = 0;
1255	<	current_comp++;
1254	>	#endif // is_mpi
1255	>
1256	>
1257	>	void SimSetup::makeSysArrays(void){
1258	>
1259	>	#ifndef IS_MPI
1260	>	int k, j;
1261	>	#endif // is_mpi
1262	>	int i, l;
1263	>
1264	>	Atom** the_atoms;
1265	>	Molecule* the_molecules;
1266	>	Exclude** the_excludes;
1267	>
1268	>
1269	>	for (l = 0; l < nInfo; l++){
1270	>	// create the atom and short range interaction arrays
1271	>
1272	>	the_atoms = new Atom * [info[l].n_atoms];
1273	>	the_molecules = new Molecule[info[l].n_mol];
1274	>	int molIndex;
1275	>
1276	>	// initialize the molecule's stampID's
1277	>
1278	>	#ifdef IS_MPI
1279	>
1280	>
1281	>	molIndex = 0;
1282	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1283	>	if (mol2proc[i] == worldRank){
1284	>	the_molecules[molIndex].setStampID(molCompType[i]);
1285	>	the_molecules[molIndex].setMyIndex(molIndex);
1286	>	the_molecules[molIndex].setGlobalIndex(i);
1287	>	molIndex++;
1288	>	}
1289	>	}
1290	>
1291	>	#else // is_mpi
1292	>
1293	>	molIndex = 0;
1294	>	globalAtomIndex = 0;
1295	>	for (i = 0; i < n_components; i++){
1296	>	for (j = 0; j < components_nmol[i]; j++){
1297	>	the_molecules[molIndex].setStampID(i);
1298	>	the_molecules[molIndex].setMyIndex(molIndex);
1299	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1300	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1301	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1302	>	globalAtomIndex++;
1303	>	}
1304	>	molIndex++;
1305	>	}
1306	>	}
1307	>
1308	>
1309	>	#endif // is_mpi
1310	>
1311	>
1312	>	if (info[l].n_SRI){
1313	>	Exclude::createArray(info[l].n_SRI);
1314	>	the_excludes = new Exclude * [info[l].n_SRI];
1315	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1316	>	the_excludes[ex] = new Exclude(ex);
1317	>	}
1318	>	info[l].globalExcludes = new int;
1319	>	info[l].n_exclude = info[l].n_SRI;
1320	>	}
1321	>	else{
1322	>	Exclude::createArray(1);
1323	>	the_excludes = new Exclude * ;
1324	>	the_excludes[0] = new Exclude(0);
1325	>	the_excludes[0]->setPair(0, 0);
1326	>	info[l].globalExcludes = new int;
1327	>	info[l].globalExcludes[0] = 0;
1328	>	info[l].n_exclude = 0;
1329	>	}
1330	>
1331	>	// set the arrays into the SimInfo object
1332	>
1333	>	info[l].atoms = the_atoms;
1334	>	info[l].molecules = the_molecules;
1335	>	info[l].nGlobalExcludes = 0;
1336	>	info[l].excludes = the_excludes;
1337	>
1338	>	the_ff->setSimInfo(info);
1339	>	}
1340	>	}
1341	>
1342	>	void SimSetup::makeIntegrator(void){
1343	>	int k;
1344	>
1345	>	NVE<RealIntegrator>* myNVE = NULL;
1346	>	NVT<RealIntegrator>* myNVT = NULL;
1347	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1348	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1349	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1350	>
1351	>	for (k = 0; k < nInfo; k++){
1352	>	switch (ensembleCase){
1353	>	case NVE_ENS:
1354	>	if (globals->haveZconstraints()){
1355	>	setupZConstraint(info[k]);
1356	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1357	>	}
1358	>	else{
1359	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1360	>	}
1361	>
1362	>	info->the_integrator = myNVE;
1363	>	break;
1364	>
1365	>	case NVT_ENS:
1366	>	if (globals->haveZconstraints()){
1367	>	setupZConstraint(info[k]);
1368	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1369	>	}
1370	>	else
1371	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1372	>
1373	>	myNVT->setTargetTemp(globals->getTargetTemp());
1374	>
1375	>	if (globals->haveTauThermostat())
1376	>	myNVT->setTauThermostat(globals->getTauThermostat());
1377	>	else{
1378	>	sprintf(painCave.errMsg,
1379	>	"SimSetup error: If you use the NVT\n"
1380	>	"    ensemble, you must set tauThermostat.\n");
1381	>	painCave.isFatal = 1;
1382	>	simError();
1383	>	}
1384	>
1385	>	info->the_integrator = myNVT;
1386	>	break;
1387	>
1388	>	case NPTi_ENS:
1389	>	if (globals->haveZconstraints()){
1390	>	setupZConstraint(info[k]);
1391	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1392	>	}
1393	>	else
1394	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1395	>
1396	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1397	>
1398	>	if (globals->haveTargetPressure())
1399	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1400	>	else{
1401	>	sprintf(painCave.errMsg,
1402	>	"SimSetup error: If you use a constant pressure\n"
1403	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1404	>	painCave.isFatal = 1;
1405	>	simError();
1406	>	}
1407	>
1408	>	if (globals->haveTauThermostat())
1409	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1410	>	else{
1411	>	sprintf(painCave.errMsg,
1412	>	"SimSetup error: If you use an NPT\n"
1413	>	"    ensemble, you must set tauThermostat.\n");
1414	>	painCave.isFatal = 1;
1415	>	simError();
1416	>	}
1417	>
1418	>	if (globals->haveTauBarostat())
1419	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1420	>	else{
1421	>	sprintf(painCave.errMsg,
1422	>	"SimSetup error: If you use an NPT\n"
1423	>	"    ensemble, you must set tauBarostat.\n");
1424	>	painCave.isFatal = 1;
1425	>	simError();
1426	>	}
1427	>
1428	>	info->the_integrator = myNPTi;
1429	>	break;
1430	>
1431	>	case NPTf_ENS:
1432	>	if (globals->haveZconstraints()){
1433	>	setupZConstraint(info[k]);
1434	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1435	>	}
1436	>	else
1437	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1438	>
1439	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1440	>
1441	>	if (globals->haveTargetPressure())
1442	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1443	>	else{
1444	>	sprintf(painCave.errMsg,
1445	>	"SimSetup error: If you use a constant pressure\n"
1446	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1447	>	painCave.isFatal = 1;
1448	>	simError();
1449	>	}
1450	>
1451	>	if (globals->haveTauThermostat())
1452	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1453	>
1454	>	else{
1455	>	sprintf(painCave.errMsg,
1456	>	"SimSetup error: If you use an NPT\n"
1457	>	"    ensemble, you must set tauThermostat.\n");
1458	>	painCave.isFatal = 1;
1459	>	simError();
1460	>	}
1461	>
1462	>	if (globals->haveTauBarostat())
1463	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1464	>
1465	>	else{
1466	>	sprintf(painCave.errMsg,
1467	>	"SimSetup error: If you use an NPT\n"
1468	>	"    ensemble, you must set tauBarostat.\n");
1469	>	painCave.isFatal = 1;
1470	>	simError();
1471	>	}
1472	>
1473	>	info->the_integrator = myNPTf;
1474	>	break;
1475	>
1476	>	case NPTxyz_ENS:
1477	>	if (globals->haveZconstraints()){
1478	>	setupZConstraint(info[k]);
1479	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1480	>	}
1481	>	else
1482	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1483	>
1484	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1485	>
1486	>	if (globals->haveTargetPressure())
1487	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1488	>	else{
1489	>	sprintf(painCave.errMsg,
1490	>	"SimSetup error: If you use a constant pressure\n"
1491	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1492	>	painCave.isFatal = 1;
1493	>	simError();
1494	>	}
1495	>
1496	>	if (globals->haveTauThermostat())
1497	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1498	>	else{
1499	>	sprintf(painCave.errMsg,
1500	>	"SimSetup error: If you use an NPT\n"
1501	>	"    ensemble, you must set tauThermostat.\n");
1502	>	painCave.isFatal = 1;
1503	>	simError();
1504	>	}
1505	>
1506	>	if (globals->haveTauBarostat())
1507	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1508	>	else{
1509	>	sprintf(painCave.errMsg,
1510	>	"SimSetup error: If you use an NPT\n"
1511	>	"    ensemble, you must set tauBarostat.\n");
1512	>	painCave.isFatal = 1;
1513	>	simError();
1514	>	}
1515	>
1516	>	info->the_integrator = myNPTxyz;
1517	>	break;
1518	>
1519	>	default:
1520	>	sprintf(painCave.errMsg,
1521	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1522	>	painCave.isFatal = 1;
1523	>	simError();
1524	>	}
1525		}
1526		}
1527	+
1528	+	void SimSetup::initFortran(void){
1529	+	info[0].refreshSim();
1530	+
1531	+	if (!strcmp(info[0].mixingRule, "standard")){
1532	+	the_ff->initForceField(LB_MIXING_RULE);
1533	+	}
1534	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1535	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1536	+	}
1537	+	else{
1538	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1539	+	info[0].mixingRule);
1540	+	painCave.isFatal = 1;
1541	+	simError();
1542	+	}
1543	+
1544	+
1545	+	#ifdef IS_MPI
1546	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1547	+	MPIcheckPoint();
1548	+	#endif // is_mpi
1549	+	}
1550	+
1551	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1552	+	int nZConstraints;
1553	+	ZconStamp** zconStamp;
1554	+
1555	+	if (globals->haveZconstraintTime()){
1556	+	//add sample time of z-constraint  into SimInfo's property list
1557	+	DoubleData* zconsTimeProp = new DoubleData();
1558	+	zconsTimeProp->setID(ZCONSTIME_ID);
1559	+	zconsTimeProp->setData(globals->getZconsTime());
1560	+	theInfo.addProperty(zconsTimeProp);
1561	+	}
1562	+	else{
1563	+	sprintf(painCave.errMsg,
1564	+	"ZConstraint error: If you use an ZConstraint\n"
1565	+	" , you must set sample time.\n");
1566	+	painCave.isFatal = 1;
1567	+	simError();
1568	+	}
1569	+
1570	+	//push zconsTol into siminfo, if user does not specify
1571	+	//value for zconsTol, a default value will be used
1572	+	DoubleData* zconsTol = new DoubleData();
1573	+	zconsTol->setID(ZCONSTOL_ID);
1574	+	if (globals->haveZconsTol()){
1575	+	zconsTol->setData(globals->getZconsTol());
1576	+	}
1577	+	else{
1578	+	double defaultZConsTol = 0.01;
1579	+	sprintf(painCave.errMsg,
1580	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1581	+	" , default value %f is used.\n",
1582	+	defaultZConsTol);
1583	+	painCave.isFatal = 0;
1584	+	simError();
1585	+
1586	+	zconsTol->setData(defaultZConsTol);
1587	+	}
1588	+	theInfo.addProperty(zconsTol);
1589	+
1590	+	//set Force Subtraction Policy
1591	+	StringData* zconsForcePolicy = new StringData();
1592	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1593	+
1594	+	if (globals->haveZconsForcePolicy()){
1595	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1596	+	}
1597	+	else{
1598	+	sprintf(painCave.errMsg,
1599	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1600	+	"PolicyByMass is used\n");
1601	+	painCave.isFatal = 0;
1602	+	simError();
1603	+	zconsForcePolicy->setData("BYMASS");
1604	+	}
1605	+
1606	+	theInfo.addProperty(zconsForcePolicy);
1607	+
1608	+	//Determine the name of ouput file and add it into SimInfo's property list
1609	+	//Be careful, do not use inFileName, since it is a pointer which
1610	+	//point to a string at master node, and slave nodes do not contain that string
1611	+
1612	+	string zconsOutput(theInfo.finalName);
1613	+
1614	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1615	+
1616	+	StringData* zconsFilename = new StringData();
1617	+	zconsFilename->setID(ZCONSFILENAME_ID);
1618	+	zconsFilename->setData(zconsOutput);
1619	+
1620	+	theInfo.addProperty(zconsFilename);
1621	+
1622	+	//setup index, pos and other parameters of z-constraint molecules
1623	+	nZConstraints = globals->getNzConstraints();
1624	+	theInfo.nZconstraints = nZConstraints;
1625	+
1626	+	zconStamp = globals->getZconStamp();
1627	+	ZConsParaItem tempParaItem;
1628	+
1629	+	ZConsParaData* zconsParaData = new ZConsParaData();
1630	+	zconsParaData->setID(ZCONSPARADATA_ID);
1631	+
1632	+	for (int i = 0; i < nZConstraints; i++){
1633	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1634	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1635	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1636	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1637	+
1638	+	zconsParaData->addItem(tempParaItem);
1639	+	}
1640	+
1641	+	//check the uniqueness of index
1642	+	if(!zconsParaData->isIndexUnique()){
1643	+	sprintf(painCave.errMsg,
1644	+	"ZConstraint Error: molIndex is not unique\n");
1645	+	painCave.isFatal = 1;
1646	+	simError();
1647	+	}
1648	+
1649	+	//sort the parameters by index of molecules
1650	+	zconsParaData->sortByIndex();
1651	+
1652	+	//push data into siminfo, therefore, we can retrieve later
1653	+	theInfo.addProperty(zconsParaData);
1654	+	}

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