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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 708 by tim, Wed Aug 20 22:23:34 2003 UTC vs.
Revision 812 by mmeineke, Wed Oct 22 21:17:32 2003 UTC

#	Line 3 | Line 3
3		#include <iostream>
4		#include <cmath>
5		#include <string>
6	<	#include <sys/time.h>
6	>	#include <sprng.h>
7
8		#include "SimSetup.hpp"
9		#include "ReadWrite.hpp"
#	Line 22 | Line 22
22		#define NVT_ENS        1
23		#define NPTi_ENS       2
24		#define NPTf_ENS       3
25	<	#define NPTim_ENS      4
26	<	#define NPTfm_ENS      5
25	>	#define NPTxyz_ENS     4
26
27	+
28		#define FF_DUFF 0
29		#define FF_LJ   1
30		#define FF_EAM  2
#	Line 32 | Line 32 | SimSetup::SimSetup(){
32		using namespace std;
33
34		SimSetup::SimSetup(){
35	–
35		isInfoArray = 0;
36		nInfo = 1;
37	<
37	>
38		stamps = new MakeStamps();
39		globals = new Globals();
40	<
41	<
40	>
41	>
42		#ifdef IS_MPI
43	<	strcpy( checkPointMsg, "SimSetup creation successful" );
43	>	strcpy(checkPointMsg, "SimSetup creation successful");
44		MPIcheckPoint();
45		#endif // IS_MPI
46		}
#	Line 51 | Line 50 | void SimSetup::setSimInfo( SimInfo* the_info, int theN
50		delete globals;
51		}
52
53	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
54	<	info = the_info;
55	<	nInfo = theNinfo;
56	<	isInfoArray = 1;
53	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
54	>	info = the_info;
55	>	nInfo = theNinfo;
56	>	isInfoArray = 1;
57		}
58
59
60	<	void SimSetup::parseFile( char* fileName ){
62	<
60	>	void SimSetup::parseFile(char* fileName){
61		#ifdef IS_MPI
62	<	if( worldRank == 0 ){
62	>	if (worldRank == 0){
63		#endif // is_mpi
64	<
64	>
65		inFileName = fileName;
66	<	set_interface_stamps( stamps, globals );
67	<
66	>	set_interface_stamps(stamps, globals);
67	>
68		#ifdef IS_MPI
69		mpiEventInit();
70		#endif
71
72	<	yacc_BASS( fileName );
72	>	yacc_BASS(fileName);
73
74		#ifdef IS_MPI
75		throwMPIEvent(NULL);
76		}
77	<	else receiveParse();
77	>	else{
78	>	receiveParse();
79	>	}
80		#endif
81
82		}
83
84		#ifdef IS_MPI
85		void SimSetup::receiveParse(void){
86	<
87	<	set_interface_stamps( stamps, globals );
88	<	mpiEventInit();
89	<	MPIcheckPoint();
90	<	mpiEventLoop();
91	<
86	>	set_interface_stamps(stamps, globals);
87	>	mpiEventInit();
88	>	MPIcheckPoint();
89	>	mpiEventLoop();
90		}
91
92		#endif // is_mpi
93
94		void SimSetup::createSim(void){
95
98	–	int i, j, k, globalAtomIndex;
99	–
96		// gather all of the information from the Bass file
97
98		gatherInfo();
#	Line 111 | Line 107 | void SimSetup::createSim(void){
107
108		// initialize the system coordinates
109
110	<	if( !isInfoArray ) initSystemCoords();
110	>	if (!isInfoArray){
111	>	initSystemCoords();
112
113	+	if( !(globals->getUseInitTime()) )
114	+	info[0].currentTime = 0.0;
115	+	}
116	+
117		// make the output filenames
118
119		makeOutNames();
120	<
120	>
121		// make the integrator
122	<
122	>
123		makeIntegrator();
124	<
124	>
125		#ifdef IS_MPI
126		mpiSim->mpiRefresh();
127		#endif
#	Line 128 | Line 129 | void SimSetup::createSim(void){
129		// initialize the Fortran
130
131		initFortran();
131	–
132	–
133	–
132		}
133
134
135	<	void SimSetup::makeMolecules( void ){
136	<
139	<	int k,l;
135	>	void SimSetup::makeMolecules(void){
136	>	int k;
137		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
138		molInit molInfo;
139		DirectionalAtom* dAtom;
#	Line 151 | Line 148 | void SimSetup::makeMolecules( void ){
148		bend_set* theBends;
149		torsion_set* theTorsions;
150
151	<
151	>
152		//init the forceField paramters
153
154		the_ff->readParams();
155
156	<
156	>
157		// init the atoms
158
159		double ux, uy, uz, u, uSqr;
163	–
164	–	for(k=0; k<nInfo; k++){
165	–
166	–	the_ff->setSimInfo( &(info[k]) );
160
161	+	for (k = 0; k < nInfo; k++){
162	+	the_ff->setSimInfo(&(info[k]));
163	+
164		atomOffset = 0;
165		excludeOffset = 0;
166	<	for(i=0; i<info[k].n_mol; i++){
171	<
166	>	for (i = 0; i < info[k].n_mol; i++){
167		stampID = info[k].molecules[i].getStampID();
168
169	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
170	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
171	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
169	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
170	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
171	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
172		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
173		molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
174	<
174	>
175		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
176		molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
177	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
178	<	molInfo.myBends = new Bend*[molInfo.nBends];
179	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
177	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
178	>	molInfo.myBends = new Bend * [molInfo.nBends];
179	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
180
181		theBonds = new bond_pair[molInfo.nBonds];
182		theBends = new bend_set[molInfo.nBends];
183		theTorsions = new torsion_set[molInfo.nTorsions];
184	<
184	>
185		// make the Atoms
186	<
187	<	for(j=0; j<molInfo.nAtoms; j++){
188	<
189	<	currentAtom = comp_stamps[stampID]->getAtom( j );
190	<	if( currentAtom->haveOrientation() ){
191	<
192	<	dAtom = new DirectionalAtom( (j + atomOffset),
193	<	info[k].getConfiguration() );
194	<	info[k].n_oriented++;
195	<	molInfo.myAtoms[j] = dAtom;
196	<
197	<	ux = currentAtom->getOrntX();
198	<	uy = currentAtom->getOrntY();
199	<	uz = currentAtom->getOrntZ();
200	<
201	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
202	<
203	<	u = sqrt( uSqr );
204	<	ux = ux / u;
205	<	uy = uy / u;
206	<	uz = uz / u;
207	<
208	<	dAtom->setSUx( ux );
209	<	dAtom->setSUy( uy );
210	<	dAtom->setSUz( uz );
211	<	}
212	<	else{
213	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
214	<	info[k].getConfiguration() );
215	<	}
221	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
222	<
186	>
187	>	for (j = 0; j < molInfo.nAtoms; j++){
188	>	currentAtom = comp_stamps[stampID]->getAtom(j);
189	>	if (currentAtom->haveOrientation()){
190	>	dAtom = new DirectionalAtom((j + atomOffset),
191	>	info[k].getConfiguration());
192	>	info[k].n_oriented++;
193	>	molInfo.myAtoms[j] = dAtom;
194	>
195	>	ux = currentAtom->getOrntX();
196	>	uy = currentAtom->getOrntY();
197	>	uz = currentAtom->getOrntZ();
198	>
199	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
200	>
201	>	u = sqrt(uSqr);
202	>	ux = ux / u;
203	>	uy = uy / u;
204	>	uz = uz / u;
205	>
206	>	dAtom->setSUx(ux);
207	>	dAtom->setSUy(uy);
208	>	dAtom->setSUz(uz);
209	>	}
210	>	else{
211	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
212	>	info[k].getConfiguration());
213	>	}
214	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
215	>
216		#ifdef IS_MPI
217	<
218	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
219	<
217	>
218	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
219	>
220		#endif // is_mpi
221		}
222	<
223	<	// make the bonds
224	<	for(j=0; j<molInfo.nBonds; j++){
225	<
226	<	currentBond = comp_stamps[stampID]->getBond( j );
227	<	theBonds[j].a = currentBond->getA() + atomOffset;
228	<	theBonds[j].b = currentBond->getB() + atomOffset;
229	<
230	<	exI = theBonds[j].a;
231	<	exJ = theBonds[j].b;
232	<
233	<	// exclude_I must always be the smaller of the pair
234	<	if( exI > exJ ){
235	<	tempEx = exI;
236	<	exI = exJ;
237	<	exJ = tempEx;
245	<	}
222	>
223	>	// make the bonds
224	>	for (j = 0; j < molInfo.nBonds; j++){
225	>	currentBond = comp_stamps[stampID]->getBond(j);
226	>	theBonds[j].a = currentBond->getA() + atomOffset;
227	>	theBonds[j].b = currentBond->getB() + atomOffset;
228	>
229	>	exI = theBonds[j].a;
230	>	exJ = theBonds[j].b;
231	>
232	>	// exclude_I must always be the smaller of the pair
233	>	if (exI > exJ){
234	>	tempEx = exI;
235	>	exI = exJ;
236	>	exJ = tempEx;
237	>	}
238		#ifdef IS_MPI
239	<	tempEx = exI;
240	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
241	<	tempEx = exJ;
242	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
243	<
244	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
239	>	tempEx = exI;
240	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
241	>	tempEx = exJ;
242	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
243	>
244	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
245		#else  // isn't MPI
246	<
247	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
246	>
247	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
248		#endif  //is_mpi
249		}
250		excludeOffset += molInfo.nBonds;
251	<
251	>
252		//make the bends
253	<	for(j=0; j<molInfo.nBends; j++){
254	<
255	<	currentBend = comp_stamps[stampID]->getBend( j );
256	<	theBends[j].a = currentBend->getA() + atomOffset;
257	<	theBends[j].b = currentBend->getB() + atomOffset;
258	<	theBends[j].c = currentBend->getC() + atomOffset;
259	<
260	<	if( currentBend->haveExtras() ){
261	<
262	<	extras = currentBend->getExtras();
263	<	current_extra = extras;
264	<
265	<	while( current_extra != NULL ){
266	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
267	<
268	<	switch( current_extra->getType() ){
269	<
270	<	case 0:
271	<	theBends[j].ghost =
272	<	current_extra->getInt() + atomOffset;
273	<	theBends[j].isGhost = 1;
274	<	break;
275	<
276	<	case 1:
277	<	theBends[j].ghost =
278	<	(int)current_extra->getDouble() + atomOffset;
279	<	theBends[j].isGhost = 1;
280	<	break;
281	<
282	<	default:
283	<	sprintf( painCave.errMsg,
284	<	"SimSetup Error: ghostVectorSource was neither a "
285	<	"double nor an int.\n"
286	<	"-->Bend[%d] in %s\n",
287	<	j, comp_stamps[stampID]->getID() );
288	<	painCave.isFatal = 1;
289	<	simError();
253	>	for (j = 0; j < molInfo.nBends; j++){
254	>	currentBend = comp_stamps[stampID]->getBend(j);
255	>	theBends[j].a = currentBend->getA() + atomOffset;
256	>	theBends[j].b = currentBend->getB() + atomOffset;
257	>	theBends[j].c = currentBend->getC() + atomOffset;
258	>
259	>	if (currentBend->haveExtras()){
260	>	extras = currentBend->getExtras();
261	>	current_extra = extras;
262	>
263	>	while (current_extra != NULL){
264	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
265	>	switch (current_extra->getType()){
266	>	case 0:
267	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
268	>	theBends[j].isGhost = 1;
269	>	break;
270	>
271	>	case 1:
272	>	theBends[j].ghost = (int) current_extra->getDouble() +
273	>	atomOffset;
274	>	theBends[j].isGhost = 1;
275	>	break;
276	>
277	>	default:
278	>	sprintf(painCave.errMsg,
279	>	"SimSetup Error: ghostVectorSource was neither a "
280	>	"double nor an int.\n"
281	>	"-->Bend[%d] in %s\n",
282	>	j, comp_stamps[stampID]->getID());
283	>	painCave.isFatal = 1;
284	>	simError();
285	>	}
286	>	}
287	>	else{
288	>	sprintf(painCave.errMsg,
289	>	"SimSetup Error: unhandled bend assignment:\n"
290	>	"    -->%s in Bend[%d] in %s\n",
291	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
292	>	painCave.isFatal = 1;
293	>	simError();
294	>	}
295	>
296	>	current_extra = current_extra->getNext();
297	>	}
298		}
299	<	}
300	<
301	<	else{
302	<
303	<	sprintf( painCave.errMsg,
304	<	"SimSetup Error: unhandled bend assignment:\n"
305	<	"    -->%s in Bend[%d] in %s\n",
306	<	current_extra->getlhs(),
307	<	j, comp_stamps[stampID]->getID() );
308	<	painCave.isFatal = 1;
309	<	simError();
310	<	}
311	<
312	<	current_extra = current_extra->getNext();
313	<	}
314	<	}
315	<
316	<	if( !theBends[j].isGhost ){
317	<
318	<	exI = theBends[j].a;
319	<	exJ = theBends[j].c;
320	<	}
321	<	else{
322	<
323	<	exI = theBends[j].a;
324	<	exJ = theBends[j].b;
325	<	}
326	<
327	<	// exclude_I must always be the smaller of the pair
328	<	if( exI > exJ ){
329	<	tempEx = exI;
330	<	exI = exJ;
331	<	exJ = tempEx;
332	<	}
299	>
300	>	if (!theBends[j].isGhost){
301	>	exI = theBends[j].a;
302	>	exJ = theBends[j].c;
303	>	}
304	>	else{
305	>	exI = theBends[j].a;
306	>	exJ = theBends[j].b;
307	>	}
308	>
309	>	// exclude_I must always be the smaller of the pair
310	>	if (exI > exJ){
311	>	tempEx = exI;
312	>	exI = exJ;
313	>	exJ = tempEx;
314	>	}
315		#ifdef IS_MPI
316	<	tempEx = exI;
317	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
318	<	tempEx = exJ;
319	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
320	<
321	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
316	>	tempEx = exI;
317	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
318	>	tempEx = exJ;
319	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
320	>
321	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
322		#else  // isn't MPI
323	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
323	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
324		#endif  //is_mpi
325		}
326		excludeOffset += molInfo.nBends;
327	<
328	<	for(j=0; j<molInfo.nTorsions; j++){
329	<
330	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
331	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
332	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
333	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
334	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
335	<
336	<	exI = theTorsions[j].a;
337	<	exJ = theTorsions[j].d;
338	<
339	<	// exclude_I must always be the smaller of the pair
340	<	if( exI > exJ ){
341	<	tempEx = exI;
342	<	exI = exJ;
343	<	exJ = tempEx;
362	<	}
327	>
328	>	for (j = 0; j < molInfo.nTorsions; j++){
329	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
330	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
331	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
332	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
333	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
334	>
335	>	exI = theTorsions[j].a;
336	>	exJ = theTorsions[j].d;
337	>
338	>	// exclude_I must always be the smaller of the pair
339	>	if (exI > exJ){
340	>	tempEx = exI;
341	>	exI = exJ;
342	>	exJ = tempEx;
343	>	}
344		#ifdef IS_MPI
345	<	tempEx = exI;
346	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
347	<	tempEx = exJ;
348	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
349	<
350	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
345	>	tempEx = exI;
346	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
347	>	tempEx = exJ;
348	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
349	>
350	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
351		#else  // isn't MPI
352	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
352	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
353		#endif  //is_mpi
354		}
355		excludeOffset += molInfo.nTorsions;
356	<
357	<
356	>
357	>
358		// send the arrays off to the forceField for init.
378	–
379	–	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
380	–	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
381	–	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
382	–	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
383	–
384	–
385	–	info[k].molecules[i].initialize( molInfo );
359
360	<
360	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
361	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
362	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
363	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
364	>	theTorsions);
365	>
366	>
367	>	info[k].molecules[i].initialize(molInfo);
368	>
369	>
370		atomOffset += molInfo.nAtoms;
371		delete[] theBonds;
372		delete[] theBends;
373		delete[] theTorsions;
374		}
375		}
376	<
376	>
377		#ifdef IS_MPI
378	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
378	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
379		MPIcheckPoint();
380		#endif // is_mpi
381	<
381	>
382		// clean up the forcefield
383
384		the_ff->calcRcut();
385		the_ff->cleanMe();
404	–
386		}
387
388	<	void SimSetup::initFromBass( void ){
408	<
388	>	void SimSetup::initFromBass(void){
389		int i, j, k;
390		int n_cells;
391		double cellx, celly, cellz;
#	Line 419 | Line 399 | void SimSetup::initFromBass( void ){
399		vel[1] = 0.0;
400		vel[2] = 0.0;
401
402	<	temp1 = (double)tot_nmol / 4.0;
403	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
404	<	temp3 = ceil( temp2 );
402	>	temp1 = (double) tot_nmol / 4.0;
403	>	temp2 = pow(temp1, (1.0 / 3.0));
404	>	temp3 = ceil(temp2);
405
406	<	have_extra =0;
407	<	if( temp2 < temp3 ){ // we have a non-complete lattice
408	<	have_extra =1;
406	>	have_extra = 0;
407	>	if (temp2 < temp3){
408	>	// we have a non-complete lattice
409	>	have_extra = 1;
410
411	<	n_cells = (int)temp3 - 1;
411	>	n_cells = (int) temp3 - 1;
412		cellx = info[0].boxL[0] / temp3;
413		celly = info[0].boxL[1] / temp3;
414		cellz = info[0].boxL[2] / temp3;
415	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
416	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
417	<	n_per_extra = (int)ceil( temp1 );
415	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
416	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
417	>	n_per_extra = (int) ceil(temp1);
418
419	<	if( n_per_extra > 4){
420	<	sprintf( painCave.errMsg,
421	<	"SimSetup error. There has been an error in constructing"
422	<	" the non-complete lattice.\n" );
419	>	if (n_per_extra > 4){
420	>	sprintf(painCave.errMsg,
421	>	"SimSetup error. There has been an error in constructing"
422	>	" the non-complete lattice.\n");
423		painCave.isFatal = 1;
424		simError();
425		}
426		}
427		else{
428	<	n_cells = (int)temp3;
428	>	n_cells = (int) temp3;
429		cellx = info[0].boxL[0] / temp3;
430		celly = info[0].boxL[1] / temp3;
431		cellz = info[0].boxL[2] / temp3;
#	Line 455 | Line 436 | void SimSetup::initFromBass( void ){
436		current_comp = 0;
437		current_atom_ndx = 0;
438
439	<	for( i=0; i < n_cells ; i++ ){
440	<	for( j=0; j < n_cells; j++ ){
441	<	for( k=0; k < n_cells; k++ ){
439	>	for (i = 0; i < n_cells ; i++){
440	>	for (j = 0; j < n_cells; j++){
441	>	for (k = 0; k < n_cells; k++){
442	>	makeElement(i * cellx, j * celly, k * cellz);
443
444	<	makeElement( i * cellx,
463	<	j * celly,
464	<	k * cellz );
444	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
445
446	<	makeElement( i * cellx + 0.5 * cellx,
467	<	j * celly + 0.5 * celly,
468	<	k * cellz );
446	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
447
448	<	makeElement( i * cellx,
471	<	j * celly + 0.5 * celly,
472	<	k * cellz + 0.5 * cellz );
473	<
474	<	makeElement( i * cellx + 0.5 * cellx,
475	<	j * celly,
476	<	k * cellz + 0.5 * cellz );
448	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
449		}
450		}
451		}
452
453	<	if( have_extra ){
453	>	if (have_extra){
454		done = 0;
455
456		int start_ndx;
457	<	for( i=0; i < (n_cells+1) && !done; i++ ){
458	<	for( j=0; j < (n_cells+1) && !done; j++ ){
457	>	for (i = 0; i < (n_cells + 1) && !done; i++){
458	>	for (j = 0; j < (n_cells + 1) && !done; j++){
459	>	if (i < n_cells){
460	>	if (j < n_cells){
461	>	start_ndx = n_cells;
462	>	}
463	>	else
464	>	start_ndx = 0;
465	>	}
466	>	else
467	>	start_ndx = 0;
468
469	<	if( i < n_cells ){
469	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
470	>	makeElement(i * cellx, j * celly, k * cellz);
471	>	done = (current_mol >= tot_nmol);
472
473	<	if( j < n_cells ){
474	<	start_ndx = n_cells;
475	<	}
476	<	else start_ndx = 0;
477	<	}
495	<	else start_ndx = 0;
473	>	if (!done && n_per_extra > 1){
474	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
475	>	k * cellz);
476	>	done = (current_mol >= tot_nmol);
477	>	}
478
479	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
479	>	if (!done && n_per_extra > 2){
480	>	makeElement(i * cellx, j * celly + 0.5 * celly,
481	>	k * cellz + 0.5 * cellz);
482	>	done = (current_mol >= tot_nmol);
483	>	}
484
485	<	makeElement( i * cellx,
486	<	j * celly,
487	<	k * cellz );
488	<	done = ( current_mol >= tot_nmol );
489	<
490	<	if( !done && n_per_extra > 1 ){
505	<	makeElement( i * cellx + 0.5 * cellx,
506	<	j * celly + 0.5 * celly,
507	<	k * cellz );
508	<	done = ( current_mol >= tot_nmol );
509	<	}
510	<
511	<	if( !done && n_per_extra > 2){
512	<	makeElement( i * cellx,
513	<	j * celly + 0.5 * celly,
514	<	k * cellz + 0.5 * cellz );
515	<	done = ( current_mol >= tot_nmol );
516	<	}
517	<
518	<	if( !done && n_per_extra > 3){
519	<	makeElement( i * cellx + 0.5 * cellx,
520	<	j * celly,
521	<	k * cellz + 0.5 * cellz );
522	<	done = ( current_mol >= tot_nmol );
523	<	}
524	<	}
485	>	if (!done && n_per_extra > 3){
486	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
487	>	k * cellz + 0.5 * cellz);
488	>	done = (current_mol >= tot_nmol);
489	>	}
490	>	}
491		}
492		}
493		}
494
495	<	for( i=0; i<info[0].n_atoms; i++ ){
496	<	info[0].atoms[i]->setVel( vel );
495	>	for (i = 0; i < info[0].n_atoms; i++){
496	>	info[0].atoms[i]->setVel(vel);
497		}
498		}
499
500	<	void SimSetup::makeElement( double x, double y, double z ){
535	<
500	>	void SimSetup::makeElement(double x, double y, double z){
501		int k;
502		AtomStamp* current_atom;
503		DirectionalAtom* dAtom;
504		double rotMat[3][3];
505		double pos[3];
506
507	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
508	<
509	<	current_atom = comp_stamps[current_comp]->getAtom( k );
510	<	if( !current_atom->havePosition() ){
511	<	sprintf( painCave.errMsg,
512	<	"SimSetup:initFromBass error.\n"
513	<	"\tComponent %s, atom %s does not have a position specified.\n"
514	<	"\tThe initialization routine is unable to give a start"
515	<	" position.\n",
551	<	comp_stamps[current_comp]->getID(),
552	<	current_atom->getType() );
507	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
508	>	current_atom = comp_stamps[current_comp]->getAtom(k);
509	>	if (!current_atom->havePosition()){
510	>	sprintf(painCave.errMsg,
511	>	"SimSetup:initFromBass error.\n"
512	>	"\tComponent %s, atom %s does not have a position specified.\n"
513	>	"\tThe initialization routine is unable to give a start"
514	>	" position.\n",
515	>	comp_stamps[current_comp]->getID(), current_atom->getType());
516		painCave.isFatal = 1;
517		simError();
518		}
519	<
519	>
520		pos[0] = x + current_atom->getPosX();
521		pos[1] = y + current_atom->getPosY();
522		pos[2] = z + current_atom->getPosZ();
560	–
561	–	info[0].atoms[current_atom_ndx]->setPos( pos );
523
524	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
524	>	info[0].atoms[current_atom_ndx]->setPos(pos);
525
526	<	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
526	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
527	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
528
529		rotMat[0][0] = 1.0;
530		rotMat[0][1] = 0.0;
#	Line 576 | Line 538 | void SimSetup::makeElement( double x, double y, double
538		rotMat[2][1] = 0.0;
539		rotMat[2][2] = 1.0;
540
541	<	dAtom->setA( rotMat );
541	>	dAtom->setA(rotMat);
542		}
543
544		current_atom_ndx++;
#	Line 585 | Line 547 | void SimSetup::makeElement( double x, double y, double
547		current_mol++;
548		current_comp_mol++;
549
550	<	if( current_comp_mol >= components_nmol[current_comp] ){
589	<
550	>	if (current_comp_mol >= components_nmol[current_comp]){
551		current_comp_mol = 0;
552		current_comp++;
553		}
554		}
555
556
557	<	void SimSetup::gatherInfo( void ){
558	<	int i,j,k;
557	>	void SimSetup::gatherInfo(void){
558	>	int i;
559
560		ensembleCase = -1;
561		ffCase = -1;
562
563		// set the easy ones first
564
565	<	for( i=0; i<nInfo; i++){
565	>	for (i = 0; i < nInfo; i++){
566		info[i].target_temp = globals->getTargetTemp();
567		info[i].dt = globals->getDt();
568		info[i].run_time = globals->getRunTime();
#	Line 611 | Line 572 | void SimSetup::gatherInfo( void ){
572
573		// get the forceField
574
575	<	strcpy( force_field, globals->getForceField() );
575	>	strcpy(force_field, globals->getForceField());
576
577	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
578	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
579	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
577	>	if (!strcasecmp(force_field, "DUFF")){
578	>	ffCase = FF_DUFF;
579	>	}
580	>	else if (!strcasecmp(force_field, "LJ")){
581	>	ffCase = FF_LJ;
582	>	}
583	>	else if (!strcasecmp(force_field, "EAM")){
584	>	ffCase = FF_EAM;
585	>	}
586		else{
587	<	sprintf( painCave.errMsg,
588	<	"SimSetup Error. Unrecognized force field -> %s\n",
589	<	force_field );
590	<	painCave.isFatal = 1;
624	<	simError();
587	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
588	>	force_field);
589	>	painCave.isFatal = 1;
590	>	simError();
591		}
592
593	<	// get the ensemble
593	>	// get the ensemble
594
595	<	strcpy( ensemble, globals->getEnsemble() );
595	>	strcpy(ensemble, globals->getEnsemble());
596
597	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
598	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
599	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
597	>	if (!strcasecmp(ensemble, "NVE")){
598	>	ensembleCase = NVE_ENS;
599	>	}
600	>	else if (!strcasecmp(ensemble, "NVT")){
601	>	ensembleCase = NVT_ENS;
602	>	}
603	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
604		ensembleCase = NPTi_ENS;
605	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
606	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
607	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
605	>	}
606	>	else if (!strcasecmp(ensemble, "NPTf")){
607	>	ensembleCase = NPTf_ENS;
608	>	}
609	>	else if (!strcasecmp(ensemble, "NPTxyz")){
610	>	ensembleCase = NPTxyz_ENS;
611	>	}
612		else{
613	<	sprintf( painCave.errMsg,
614	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
615	<	"reverting to NVE for this simulation.\n",
616	<	ensemble );
617	<	painCave.isFatal = 0;
618	<	simError();
619	<	strcpy( ensemble, "NVE" );
620	<	ensembleCase = NVE_ENS;
613	>	sprintf(painCave.errMsg,
614	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
615	>	"reverting to NVE for this simulation.\n",
616	>	ensemble);
617	>	painCave.isFatal = 0;
618	>	simError();
619	>	strcpy(ensemble, "NVE");
620	>	ensembleCase = NVE_ENS;
621		}
648	–
649	–	for(i=0; i<nInfo; i++){
650	–
651	–	strcpy( info[i].ensemble, ensemble );
622
623	+	for (i = 0; i < nInfo; i++){
624	+	strcpy(info[i].ensemble, ensemble);
625	+
626		// get the mixing rule
627
628	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
628	>	strcpy(info[i].mixingRule, globals->getMixingRule());
629		info[i].usePBC = globals->getPBC();
630		}
631	<
631	>
632		// get the components and calculate the tot_nMol and indvidual n_mol
633	<
633	>
634		the_components = globals->getComponents();
635		components_nmol = new int[n_components];
636
637
638	<	if( !globals->haveNMol() ){
638	>	if (!globals->haveNMol()){
639		// we don't have the total number of molecules, so we assume it is
640		// given in each component
641
642		tot_nmol = 0;
643	<	for( i=0; i<n_components; i++ ){
644	<
645	<	if( !the_components[i]->haveNMol() ){
646	<	// we have a problem
647	<	sprintf( painCave.errMsg,
648	<	"SimSetup Error. No global NMol or component NMol"
649	<	" given. Cannot calculate the number of atoms.\n" );
650	<	painCave.isFatal = 1;
678	<	simError();
643	>	for (i = 0; i < n_components; i++){
644	>	if (!the_components[i]->haveNMol()){
645	>	// we have a problem
646	>	sprintf(painCave.errMsg,
647	>	"SimSetup Error. No global NMol or component NMol"
648	>	" given. Cannot calculate the number of atoms.\n");
649	>	painCave.isFatal = 1;
650	>	simError();
651		}
652
653		tot_nmol += the_components[i]->getNMol();
#	Line 683 | Line 655 | void SimSetup::gatherInfo( void ){
655		}
656		}
657		else{
658	<	sprintf( painCave.errMsg,
659	<	"SimSetup error.\n"
660	<	"\tSorry, the ability to specify total"
661	<	" nMols and then give molfractions in the components\n"
662	<	"\tis not currently supported."
663	<	" Please give nMol in the components.\n" );
658	>	sprintf(painCave.errMsg,
659	>	"SimSetup error.\n"
660	>	"\tSorry, the ability to specify total"
661	>	" nMols and then give molfractions in the components\n"
662	>	"\tis not currently supported."
663	>	" Please give nMol in the components.\n");
664		painCave.isFatal = 1;
665		simError();
666		}
667
668		// set the status, sample, and thermal kick times
697	–
698	–	for(i=0; i<nInfo; i++){
669
670	<	if( globals->haveSampleTime() ){
670	>	for (i = 0; i < nInfo; i++){
671	>	if (globals->haveSampleTime()){
672		info[i].sampleTime = globals->getSampleTime();
673		info[i].statusTime = info[i].sampleTime;
674		info[i].thermalTime = info[i].sampleTime;
#	Line 707 | Line 678 | void SimSetup::gatherInfo( void ){
678		info[i].statusTime = info[i].sampleTime;
679		info[i].thermalTime = info[i].sampleTime;
680		}
681	<
682	<	if( globals->haveStatusTime() ){
681	>
682	>	if (globals->haveStatusTime()){
683		info[i].statusTime = globals->getStatusTime();
684		}
685	<
686	<	if( globals->haveThermalTime() ){
685	>
686	>	if (globals->haveThermalTime()){
687		info[i].thermalTime = globals->getThermalTime();
688		}
689
690	+	info[i].resetIntegrator = 0;
691	+	if( globals->haveResetTime() ){
692	+	info[i].resetTime = globals->getResetTime();
693	+	info[i].resetIntegrator = 1;
694	+	}
695	+
696		// check for the temperature set flag
697
698	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
699	<
698	>	if (globals->haveTempSet())
699	>	info[i].setTemp = globals->getTempSet();
700	>
701		// get some of the tricky things that may still be in the globals
702	<
702	>
703		double boxVector[3];
704	<	if( globals->haveBox() ){
704	>	if (globals->haveBox()){
705		boxVector[0] = globals->getBox();
706		boxVector[1] = globals->getBox();
707		boxVector[2] = globals->getBox();
708	<
709	<	info[i].setBox( boxVector );
708	>
709	>	info[i].setBox(boxVector);
710		}
711	<	else if( globals->haveDensity() ){
734	<
711	>	else if (globals->haveDensity()){
712		double vol;
713	<	vol = (double)tot_nmol / globals->getDensity();
714	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
713	>	vol = (double) tot_nmol / globals->getDensity();
714	>	boxVector[0] = pow(vol, (1.0 / 3.0));
715		boxVector[1] = boxVector[0];
716		boxVector[2] = boxVector[0];
717	<
718	<	info[i].setBox( boxVector );
719	<	}
717	>
718	>	info[i].setBox(boxVector);
719	>	}
720		else{
721	<	if( !globals->haveBoxX() ){
722	<	sprintf( painCave.errMsg,
723	<	"SimSetup error, no periodic BoxX size given.\n" );
724	<	painCave.isFatal = 1;
725	<	simError();
721	>	if (!globals->haveBoxX()){
722	>	sprintf(painCave.errMsg,
723	>	"SimSetup error, no periodic BoxX size given.\n");
724	>	painCave.isFatal = 1;
725	>	simError();
726		}
727		boxVector[0] = globals->getBoxX();
728	<
729	<	if( !globals->haveBoxY() ){
730	<	sprintf( painCave.errMsg,
731	<	"SimSetup error, no periodic BoxY size given.\n" );
732	<	painCave.isFatal = 1;
733	<	simError();
728	>
729	>	if (!globals->haveBoxY()){
730	>	sprintf(painCave.errMsg,
731	>	"SimSetup error, no periodic BoxY size given.\n");
732	>	painCave.isFatal = 1;
733	>	simError();
734		}
735		boxVector[1] = globals->getBoxY();
736	<
737	<	if( !globals->haveBoxZ() ){
738	<	sprintf( painCave.errMsg,
739	<	"SimSetup error, no periodic BoxZ size given.\n" );
740	<	painCave.isFatal = 1;
741	<	simError();
736	>
737	>	if (!globals->haveBoxZ()){
738	>	sprintf(painCave.errMsg,
739	>	"SimSetup error, no periodic BoxZ size given.\n");
740	>	painCave.isFatal = 1;
741	>	simError();
742		}
743		boxVector[2] = globals->getBoxZ();
744	<
745	<	info[i].setBox( boxVector );
744	>
745	>	info[i].setBox(boxVector);
746		}
747		}
748
749	+	//setup seed for random number generator
750		int seedValue;
773	–	struct timeval now_time_val;
774	–	struct timezone time_zone;
751
752	<	if(globals->haveSeed()){
752	>	if (globals->haveSeed()){
753		seedValue = globals->getSeed();
754	<	}
754	>
755	>	if(seedValue / 1E9 == 0){
756	>	sprintf(painCave.errMsg,
757	>	"Seed for sprng library should contain at least 9 digits\n"
758	>	"OOPSE will generate a seed for user\n");
759	>	painCave.isFatal = 0;
760	>	simError();
761	>
762	>	//using seed generated by system instead of invalid seed set by user
763	>	#ifndef IS_MPI
764	>	seedValue = make_sprng_seed();
765	>	#else
766	>	if (worldRank == 0){
767	>	seedValue = make_sprng_seed();
768	>	}
769	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
770	>	#endif
771	>	}
772	>	}//end of if branch of globals->haveSeed()
773		else{
774	+
775		#ifndef IS_MPI
776	<	gettimeofday(&now_time_val, &time_zone);  // get the time now
782	<	seedValue = (int) now_time_val.tv_sec;      //  convert to epoch time
776	>	seedValue = make_sprng_seed();
777		#else
778	<	if(worldRank == 0){
779	<	gettimeofday(&now_time_val, &time_zone);  // get the time now
786	<	seedValue = (int) now_time_val.tv_sec;      //  convert to epoch time
778	>	if (worldRank == 0){
779	>	seedValue = make_sprng_seed();
780		}
781	<	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
781	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
782		#endif
783	<	}
783	>	}//end of globals->haveSeed()
784
785	<	for(int i = 0; i < nInfo; i++){
785	>	for (int i = 0; i < nInfo; i++){
786		info[i].setSeed(seedValue);
787		}
788
789		#ifdef IS_MPI
790	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
790	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
791		MPIcheckPoint();
792		#endif // is_mpi
800	–
793		}
794
795
796	<	void SimSetup::finalInfoCheck( void ){
796	>	void SimSetup::finalInfoCheck(void){
797		int index;
798		int usesDipoles;
799		int i;
800
801	<	for(i=0; i<nInfo; i++){
801	>	for (i = 0; i < nInfo; i++){
802		// check electrostatic parameters
803	<
803	>
804		index = 0;
805		usesDipoles = 0;
806	<	while( (index < info[i].n_atoms) && !usesDipoles ){
806	>	while ((index < info[i].n_atoms) && !usesDipoles){
807		usesDipoles = (info[i].atoms[index])->hasDipole();
808		index++;
809		}
810	<
810	>
811		#ifdef IS_MPI
812		int myUse = usesDipoles;
813	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
813	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814		#endif //is_mpi
815	<
815	>
816		double theEcr, theEst;
817	<
818	<	if (globals->getUseRF() ) {
817	>
818	>	if (globals->getUseRF()){
819		info[i].useReactionField = 1;
820	<
821	<	if( !globals->haveECR() ){
822	<	sprintf( painCave.errMsg,
823	<	"SimSetup Warning: using default value of 1/2 the smallest "
824	<	"box length for the electrostaticCutoffRadius.\n"
825	<	"I hope you have a very fast processor!\n");
826	<	painCave.isFatal = 0;
827	<	simError();
828	<	double smallest;
829	<	smallest = info[i].boxL[0];
830	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
831	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
832	<	theEcr = 0.5 * smallest;
833	<	} else {
834	<	theEcr = globals->getECR();
820	>
821	>	if (!globals->haveECR()){
822	>	sprintf(painCave.errMsg,
823	>	"SimSetup Warning: using default value of 1/2 the smallest "
824	>	"box length for the electrostaticCutoffRadius.\n"
825	>	"I hope you have a very fast processor!\n");
826	>	painCave.isFatal = 0;
827	>	simError();
828	>	double smallest;
829	>	smallest = info[i].boxL[0];
830	>	if (info[i].boxL[1] <= smallest)
831	>	smallest = info[i].boxL[1];
832	>	if (info[i].boxL[2] <= smallest)
833	>	smallest = info[i].boxL[2];
834	>	theEcr = 0.5 * smallest;
835		}
836	<
837	<	if( !globals->haveEST() ){
846	<	sprintf( painCave.errMsg,
847	<	"SimSetup Warning: using default value of 0.05 * the "
848	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
849	<	);
850	<	painCave.isFatal = 0;
851	<	simError();
852	<	theEst = 0.05 * theEcr;
853	<	} else {
854	<	theEst= globals->getEST();
836	>	else{
837	>	theEcr = globals->getECR();
838		}
839	<
840	<	info[i].setEcr( theEcr, theEst );
841	<
842	<	if(!globals->haveDielectric() ){
843	<	sprintf( painCave.errMsg,
844	<	"SimSetup Error: You are trying to use Reaction Field without"
845	<	"setting a dielectric constant!\n"
846	<	);
864	<	painCave.isFatal = 1;
865	<	simError();
839	>
840	>	if (!globals->haveEST()){
841	>	sprintf(painCave.errMsg,
842	>	"SimSetup Warning: using default value of 0.05 * the "
843	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
844	>	painCave.isFatal = 0;
845	>	simError();
846	>	theEst = 0.05 * theEcr;
847		}
848	<	info[i].dielectric = globals->getDielectric();
849	<	}
869	<	else {
870	<	if (usesDipoles) {
871	<
872	<	if( !globals->haveECR() ){
873	<	sprintf( painCave.errMsg,
874	<	"SimSetup Warning: using default value of 1/2 the smallest "
875	<	"box length for the electrostaticCutoffRadius.\n"
876	<	"I hope you have a very fast processor!\n");
877	<	painCave.isFatal = 0;
878	<	simError();
879	<	double smallest;
880	<	smallest = info[i].boxL[0];
881	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
882	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
883	<	theEcr = 0.5 * smallest;
884	<	} else {
885	<	theEcr = globals->getECR();
886	<	}
887	<
888	<	if( !globals->haveEST() ){
889	<	sprintf( painCave.errMsg,
890	<	"SimSetup Warning: using default value of 0.05 * the "
891	<	"electrostaticCutoffRadius for the "
892	<	"electrostaticSkinThickness\n"
893	<	);
894	<	painCave.isFatal = 0;
895	<	simError();
896	<	theEst = 0.05 * theEcr;
897	<	} else {
898	<	theEst= globals->getEST();
899	<	}
900	<
901	<	info[i].setEcr( theEcr, theEst );
848	>	else{
849	>	theEst = globals->getEST();
850		}
851	<	}
851	>
852	>	info[i].setEcr(theEcr, theEst);
853	>
854	>	if (!globals->haveDielectric()){
855	>	sprintf(painCave.errMsg,
856	>	"SimSetup Error: You are trying to use Reaction Field without"
857	>	"setting a dielectric constant!\n");
858	>	painCave.isFatal = 1;
859	>	simError();
860	>	}
861	>	info[i].dielectric = globals->getDielectric();
862	>	}
863	>	else{
864	>	if (usesDipoles){
865	>	if (!globals->haveECR()){
866	>	sprintf(painCave.errMsg,
867	>	"SimSetup Warning: using default value of 1/2 the smallest "
868	>	"box length for the electrostaticCutoffRadius.\n"
869	>	"I hope you have a very fast processor!\n");
870	>	painCave.isFatal = 0;
871	>	simError();
872	>	double smallest;
873	>	smallest = info[i].boxL[0];
874	>	if (info[i].boxL[1] <= smallest)
875	>	smallest = info[i].boxL[1];
876	>	if (info[i].boxL[2] <= smallest)
877	>	smallest = info[i].boxL[2];
878	>	theEcr = 0.5 * smallest;
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].setEcr(theEcr, theEst);
898	>	}
899	>	}
900		}
901
902		#ifdef IS_MPI
903	<	strcpy( checkPointMsg, "post processing checks out" );
903	>	strcpy(checkPointMsg, "post processing checks out");
904		MPIcheckPoint();
905		#endif // is_mpi
910	–
906		}
907
908	<	void SimSetup::initSystemCoords( void ){
908	>	void SimSetup::initSystemCoords(void){
909		int i;
910	<
910	>
911		char* inName;
912
913	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
913	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
914
915	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
916	<
917	<	if( globals->haveInitialConfig() ){
918	<
915	>	for (i = 0; i < info[0].n_atoms; i++)
916	>	info[0].atoms[i]->setCoords();
917	>
918	>	if (globals->haveInitialConfig()){
919		InitializeFromFile* fileInit;
920		#ifdef IS_MPI // is_mpi
921	<	if( worldRank == 0 ){
921	>	if (worldRank == 0){
922		#endif //is_mpi
923		inName = globals->getInitialConfig();
924	<	double* tempDouble = new double[1000000];
930	<	fileInit = new InitializeFromFile( inName );
924	>	fileInit = new InitializeFromFile(inName);
925		#ifdef IS_MPI
926	<	}else fileInit = new InitializeFromFile( NULL );
926	>	}
927	>	else
928	>	fileInit = new InitializeFromFile(NULL);
929		#endif
930	<	fileInit->readInit( info ); // default velocities on
931	<
930	>	fileInit->readInit(info); // default velocities on
931	>
932		delete fileInit;
933		}
934		else{
939	–
935		#ifdef IS_MPI
936	<
936	>
937		// no init from bass
938	<
939	<	sprintf( painCave.errMsg,
940	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
941	<	painCave.isFatal;
938	>
939	>	sprintf(painCave.errMsg,
940	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
941	>	painCave.isFatal = 1;;
942		simError();
943	<
943	>
944		#else
945	<
945	>
946		initFromBass();
947	<
948	<
947	>
948	>
949		#endif
950		}
951	<
951	>
952		#ifdef IS_MPI
953	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
953	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
954		MPIcheckPoint();
955		#endif // is_mpi
961	–
956		}
957
958
959	<	void SimSetup::makeOutNames( void ){
966	<
959	>	void SimSetup::makeOutNames(void){
960		int k;
961
969	–
970	–	for(k=0; k<nInfo; k++){
962
963	+	for (k = 0; k < nInfo; k++){
964		#ifdef IS_MPI
965	<	if( worldRank == 0 ){
965	>	if (worldRank == 0){
966		#endif // is_mpi
967	<
968	<	if( globals->haveFinalConfig() ){
969	<	strcpy( info[k].finalName, globals->getFinalConfig() );
967	>
968	>	if (globals->haveFinalConfig()){
969	>	strcpy(info[k].finalName, globals->getFinalConfig());
970		}
971		else{
972	<	strcpy( info[k].finalName, inFileName );
973	<	char* endTest;
974	<	int nameLength = strlen( info[k].finalName );
975	<	endTest = &(info[k].finalName[nameLength - 5]);
976	<	if( !strcmp( endTest, ".bass" ) ){
977	<	strcpy( endTest, ".eor" );
978	<	}
979	<	else if( !strcmp( endTest, ".BASS" ) ){
980	<	strcpy( endTest, ".eor" );
981	<	}
982	<	else{
983	<	endTest = &(info[k].finalName[nameLength - 4]);
984	<	if( !strcmp( endTest, ".bss" ) ){
985	<	strcpy( endTest, ".eor" );
986	<	}
987	<	else if( !strcmp( endTest, ".mdl" ) ){
988	<	strcpy( endTest, ".eor" );
989	<	}
990	<	else{
991	<	strcat( info[k].finalName, ".eor" );
992	<	}
993	<	}
972	>	strcpy(info[k].finalName, inFileName);
973	>	char* endTest;
974	>	int nameLength = strlen(info[k].finalName);
975	>	endTest = &(info[k].finalName[nameLength - 5]);
976	>	if (!strcmp(endTest, ".bass")){
977	>	strcpy(endTest, ".eor");
978	>	}
979	>	else if (!strcmp(endTest, ".BASS")){
980	>	strcpy(endTest, ".eor");
981	>	}
982	>	else{
983	>	endTest = &(info[k].finalName[nameLength - 4]);
984	>	if (!strcmp(endTest, ".bss")){
985	>	strcpy(endTest, ".eor");
986	>	}
987	>	else if (!strcmp(endTest, ".mdl")){
988	>	strcpy(endTest, ".eor");
989	>	}
990	>	else{
991	>	strcat(info[k].finalName, ".eor");
992	>	}
993	>	}
994		}
995	<
995	>
996		// make the sample and status out names
997	<
998	<	strcpy( info[k].sampleName, inFileName );
997	>
998	>	strcpy(info[k].sampleName, inFileName);
999		char* endTest;
1000	<	int nameLength = strlen( info[k].sampleName );
1000	>	int nameLength = strlen(info[k].sampleName);
1001		endTest = &(info[k].sampleName[nameLength - 5]);
1002	<	if( !strcmp( endTest, ".bass" ) ){
1003	<	strcpy( endTest, ".dump" );
1002	>	if (!strcmp(endTest, ".bass")){
1003	>	strcpy(endTest, ".dump");
1004		}
1005	<	else if( !strcmp( endTest, ".BASS" ) ){
1006	<	strcpy( endTest, ".dump" );
1005	>	else if (!strcmp(endTest, ".BASS")){
1006	>	strcpy(endTest, ".dump");
1007		}
1008		else{
1009	<	endTest = &(info[k].sampleName[nameLength - 4]);
1010	<	if( !strcmp( endTest, ".bss" ) ){
1011	<	strcpy( endTest, ".dump" );
1012	<	}
1013	<	else if( !strcmp( endTest, ".mdl" ) ){
1014	<	strcpy( endTest, ".dump" );
1015	<	}
1016	<	else{
1017	<	strcat( info[k].sampleName, ".dump" );
1018	<	}
1009	>	endTest = &(info[k].sampleName[nameLength - 4]);
1010	>	if (!strcmp(endTest, ".bss")){
1011	>	strcpy(endTest, ".dump");
1012	>	}
1013	>	else if (!strcmp(endTest, ".mdl")){
1014	>	strcpy(endTest, ".dump");
1015	>	}
1016	>	else{
1017	>	strcat(info[k].sampleName, ".dump");
1018	>	}
1019		}
1020	<
1021	<	strcpy( info[k].statusName, inFileName );
1022	<	nameLength = strlen( info[k].statusName );
1020	>
1021	>	strcpy(info[k].statusName, inFileName);
1022	>	nameLength = strlen(info[k].statusName);
1023		endTest = &(info[k].statusName[nameLength - 5]);
1024	<	if( !strcmp( endTest, ".bass" ) ){
1025	<	strcpy( endTest, ".stat" );
1024	>	if (!strcmp(endTest, ".bass")){
1025	>	strcpy(endTest, ".stat");
1026		}
1027	<	else if( !strcmp( endTest, ".BASS" ) ){
1028	<	strcpy( endTest, ".stat" );
1027	>	else if (!strcmp(endTest, ".BASS")){
1028	>	strcpy(endTest, ".stat");
1029		}
1030		else{
1031	<	endTest = &(info[k].statusName[nameLength - 4]);
1032	<	if( !strcmp( endTest, ".bss" ) ){
1033	<	strcpy( endTest, ".stat" );
1034	<	}
1035	<	else if( !strcmp( endTest, ".mdl" ) ){
1036	<	strcpy( endTest, ".stat" );
1037	<	}
1038	<	else{
1039	<	strcat( info[k].statusName, ".stat" );
1040	<	}
1031	>	endTest = &(info[k].statusName[nameLength - 4]);
1032	>	if (!strcmp(endTest, ".bss")){
1033	>	strcpy(endTest, ".stat");
1034	>	}
1035	>	else if (!strcmp(endTest, ".mdl")){
1036	>	strcpy(endTest, ".stat");
1037	>	}
1038	>	else{
1039	>	strcat(info[k].statusName, ".stat");
1040	>	}
1041		}
1042	<
1042	>
1043		#ifdef IS_MPI
1044	+
1045		}
1046		#endif // is_mpi
1047		}
1048		}
1049
1050
1051	<	void SimSetup::sysObjectsCreation( void ){
1052	<
1053	<	int i,k;
1061	<
1051	>	void SimSetup::sysObjectsCreation(void){
1052	>	int i, k;
1053	>
1054		// create the forceField
1055
1056		createFF();
#	Line 1073 | Line 1065 | void SimSetup::sysObjectsCreation( void ){
1065
1066		#ifdef IS_MPI
1067		// divide the molecules among the processors
1068	<
1068	>
1069		mpiMolDivide();
1070		#endif //is_mpi
1071	<
1071	>
1072		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1073	<
1073	>
1074		makeSysArrays();
1075
1076		// make and initialize the molecules (all but atomic coordinates)
1077	<
1077	>
1078		makeMolecules();
1079	<
1080	<	for(k=0; k<nInfo; k++){
1079	>
1080	>	for (k = 0; k < nInfo; k++){
1081		info[k].identArray = new int[info[k].n_atoms];
1082	<	for(i=0; i<info[k].n_atoms; i++){
1082	>	for (i = 0; i < info[k].n_atoms; i++){
1083		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1084		}
1085		}
1086		}
1087
1088
1089	<	void SimSetup::createFF( void ){
1089	>	void SimSetup::createFF(void){
1090	>	switch (ffCase){
1091	>	case FF_DUFF:
1092	>	the_ff = new DUFF();
1093	>	break;
1094
1095	<	switch( ffCase ){
1095	>	case FF_LJ:
1096	>	the_ff = new LJFF();
1097	>	break;
1098
1099	<	case FF_DUFF:
1100	<	the_ff = new DUFF();
1101	<	break;
1099	>	case FF_EAM:
1100	>	the_ff = new EAM_FF();
1101	>	break;
1102
1103	<	case FF_LJ:
1104	<	the_ff = new LJFF();
1105	<	break;
1106	<
1107	<	case FF_EAM:
1110	<	the_ff = new EAM_FF();
1111	<	break;
1112	<
1113	<	default:
1114	<	sprintf( painCave.errMsg,
1115	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1116	<	painCave.isFatal = 1;
1117	<	simError();
1103	>	default:
1104	>	sprintf(painCave.errMsg,
1105	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1106	>	painCave.isFatal = 1;
1107	>	simError();
1108		}
1109
1110		#ifdef IS_MPI
1111	<	strcpy( checkPointMsg, "ForceField creation successful" );
1111	>	strcpy(checkPointMsg, "ForceField creation successful");
1112		MPIcheckPoint();
1113		#endif // is_mpi
1124	–
1114		}
1115
1116
1117	<	void SimSetup::compList( void ){
1129	<
1117	>	void SimSetup::compList(void){
1118		int i;
1119		char* id;
1120		LinkedMolStamp* headStamp = new LinkedMolStamp();
1121		LinkedMolStamp* currentStamp = NULL;
1122	<	comp_stamps = new MoleculeStamp*[n_components];
1123	<
1122	>	comp_stamps = new MoleculeStamp * [n_components];
1123	>
1124		// make an array of molecule stamps that match the components used.
1125		// also extract the used stamps out into a separate linked list
1126	<
1127	<	for(i=0; i<nInfo; i++){
1126	>
1127	>	for (i = 0; i < nInfo; i++){
1128		info[i].nComponents = n_components;
1129		info[i].componentsNmol = components_nmol;
1130		info[i].compStamps = comp_stamps;
1131		info[i].headStamp = headStamp;
1132		}
1145	–
1133
1147	–	for( i=0; i<n_components; i++ ){
1134
1135	+	for (i = 0; i < n_components; i++){
1136		id = the_components[i]->getType();
1137		comp_stamps[i] = NULL;
1138	<
1138	>
1139		// check to make sure the component isn't already in the list
1140
1141	<	comp_stamps[i] = headStamp->match( id );
1142	<	if( comp_stamps[i] == NULL ){
1156	<
1141	>	comp_stamps[i] = headStamp->match(id);
1142	>	if (comp_stamps[i] == NULL){
1143		// extract the component from the list;
1144	<
1145	<	currentStamp = stamps->extractMolStamp( id );
1146	<	if( currentStamp == NULL ){
1147	<	sprintf( painCave.errMsg,
1148	<	"SimSetup error: Component \"%s\" was not found in the "
1149	<	"list of declared molecules\n",
1150	<	id );
1151	<	painCave.isFatal = 1;
1152	<	simError();
1144	>
1145	>	currentStamp = stamps->extractMolStamp(id);
1146	>	if (currentStamp == NULL){
1147	>	sprintf(painCave.errMsg,
1148	>	"SimSetup error: Component \"%s\" was not found in the "
1149	>	"list of declared molecules\n",
1150	>	id);
1151	>	painCave.isFatal = 1;
1152	>	simError();
1153		}
1154	<
1155	<	headStamp->add( currentStamp );
1156	<	comp_stamps[i] = headStamp->match( id );
1154	>
1155	>	headStamp->add(currentStamp);
1156	>	comp_stamps[i] = headStamp->match(id);
1157		}
1158		}
1159
1160		#ifdef IS_MPI
1161	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1161	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1162		MPIcheckPoint();
1163		#endif // is_mpi
1164	+	}
1165
1166	+	void SimSetup::calcSysValues(void){
1167	+	int i;
1168
1169	<	}
1169	>	int* molMembershipArray;
1170
1182	–	void SimSetup::calcSysValues( void ){
1183	–	int i, j, k;
1184	–
1185	–	int *molMembershipArray;
1186	–
1171		tot_atoms = 0;
1172		tot_bonds = 0;
1173		tot_bends = 0;
1174		tot_torsions = 0;
1175	<	for( i=0; i<n_components; i++ ){
1176	<
1177	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1178	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1195	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1175	>	for (i = 0; i < n_components; i++){
1176	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1177	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1178	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1179		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1180		}
1181	<
1181	>
1182		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1183		molMembershipArray = new int[tot_atoms];
1184	<
1185	<	for(i=0; i<nInfo; i++){
1184	>
1185	>	for (i = 0; i < nInfo; i++){
1186		info[i].n_atoms = tot_atoms;
1187		info[i].n_bonds = tot_bonds;
1188		info[i].n_bends = tot_bends;
1189		info[i].n_torsions = tot_torsions;
1190		info[i].n_SRI = tot_SRI;
1191		info[i].n_mol = tot_nmol;
1192	<
1192	>
1193		info[i].molMembershipArray = molMembershipArray;
1194	<	}
1194	>	}
1195		}
1196
1197		#ifdef IS_MPI
1198
1199	<	void SimSetup::mpiMolDivide( void ){
1217	<
1199	>	void SimSetup::mpiMolDivide(void){
1200		int i, j, k;
1201		int localMol, allMol;
1202		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1203
1204	<	mpiSim = new mpiSimulation( info );
1205	<
1204	>	mpiSim = new mpiSimulation(info);
1205	>
1206		globalIndex = mpiSim->divideLabor();
1207
1208		// set up the local variables
1209	<
1209	>
1210		mol2proc = mpiSim->getMolToProcMap();
1211		molCompType = mpiSim->getMolComponentType();
1212	<
1212	>
1213		allMol = 0;
1214		localMol = 0;
1215		local_atoms = 0;
#	Line 1237 | Line 1219 | void SimSetup::mpiMolDivide( void ){
1219		globalAtomIndex = 0;
1220
1221
1222	<	for( i=0; i<n_components; i++ ){
1223	<
1224	<	for( j=0; j<components_nmol[i]; j++ ){
1225	<
1226	<	if( mol2proc[allMol] == worldRank ){
1227	<
1228	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1229	<	local_bonds +=    comp_stamps[i]->getNBonds();
1248	<	local_bends +=    comp_stamps[i]->getNBends();
1249	<	local_torsions += comp_stamps[i]->getNTorsions();
1250	<	localMol++;
1222	>	for (i = 0; i < n_components; i++){
1223	>	for (j = 0; j < components_nmol[i]; j++){
1224	>	if (mol2proc[allMol] == worldRank){
1225	>	local_atoms += comp_stamps[i]->getNAtoms();
1226	>	local_bonds += comp_stamps[i]->getNBonds();
1227	>	local_bends += comp_stamps[i]->getNBends();
1228	>	local_torsions += comp_stamps[i]->getNTorsions();
1229	>	localMol++;
1230		}
1231	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1231	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1232		info[0].molMembershipArray[globalAtomIndex] = allMol;
1233		globalAtomIndex++;
1234		}
1235
1236	<	allMol++;
1236	>	allMol++;
1237		}
1238		}
1239		local_SRI = local_bonds + local_bends + local_torsions;
1240	<
1240	>
1241		info[0].n_atoms = mpiSim->getMyNlocal();
1242	<
1243	<	if( local_atoms != info[0].n_atoms ){
1244	<	sprintf( painCave.errMsg,
1245	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1246	<	" localAtom (%d) are not equal.\n",
1247	<	info[0].n_atoms,
1269	<	local_atoms );
1242	>
1243	>	if (local_atoms != info[0].n_atoms){
1244	>	sprintf(painCave.errMsg,
1245	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1246	>	" localAtom (%d) are not equal.\n",
1247	>	info[0].n_atoms, local_atoms);
1248		painCave.isFatal = 1;
1249		simError();
1250		}
#	Line 1277 | Line 1255 | void SimSetup::mpiMolDivide( void ){
1255		info[0].n_SRI = local_SRI;
1256		info[0].n_mol = localMol;
1257
1258	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1258	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1259		MPIcheckPoint();
1260		}
1261	<
1261	>
1262		#endif // is_mpi
1263
1264
1265	<	void SimSetup::makeSysArrays( void ){
1266	<	int i, j, k, l;
1265	>	void SimSetup::makeSysArrays(void){
1266	>
1267	>	#ifndef IS_MPI
1268	>	int k, j;
1269	>	#endif // is_mpi
1270	>	int i, l;
1271
1272		Atom** the_atoms;
1273		Molecule* the_molecules;
1274		Exclude** the_excludes;
1275
1276	<
1277	<	for(l=0; l<nInfo; l++){
1296	<
1276	>
1277	>	for (l = 0; l < nInfo; l++){
1278		// create the atom and short range interaction arrays
1279	<
1280	<	the_atoms = new Atom*[info[l].n_atoms];
1279	>
1280	>	the_atoms = new Atom * [info[l].n_atoms];
1281		the_molecules = new Molecule[info[l].n_mol];
1282		int molIndex;
1283
1284		// initialize the molecule's stampID's
1285	<
1285	>
1286		#ifdef IS_MPI
1287	<
1288	<
1287	>
1288	>
1289		molIndex = 0;
1290	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1291	<
1292	<	if(mol2proc[i] == worldRank ){
1293	<	the_molecules[molIndex].setStampID( molCompType[i] );
1294	<	the_molecules[molIndex].setMyIndex( molIndex );
1295	<	the_molecules[molIndex].setGlobalIndex( i );
1315	<	molIndex++;
1290	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1291	>	if (mol2proc[i] == worldRank){
1292	>	the_molecules[molIndex].setStampID(molCompType[i]);
1293	>	the_molecules[molIndex].setMyIndex(molIndex);
1294	>	the_molecules[molIndex].setGlobalIndex(i);
1295	>	molIndex++;
1296		}
1297		}
1298	<
1298	>
1299		#else // is_mpi
1300	<
1300	>
1301		molIndex = 0;
1302		globalAtomIndex = 0;
1303	<	for(i=0; i<n_components; i++){
1304	<	for(j=0; j<components_nmol[i]; j++ ){
1305	<	the_molecules[molIndex].setStampID( i );
1306	<	the_molecules[molIndex].setMyIndex( molIndex );
1307	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1308	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1309	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1310	<	globalAtomIndex++;
1311	<	}
1312	<	molIndex++;
1303	>	for (i = 0; i < n_components; i++){
1304	>	for (j = 0; j < components_nmol[i]; j++){
1305	>	the_molecules[molIndex].setStampID(i);
1306	>	the_molecules[molIndex].setMyIndex(molIndex);
1307	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1308	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1309	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1310	>	globalAtomIndex++;
1311	>	}
1312	>	molIndex++;
1313		}
1314		}
1315	<
1316	<
1315	>
1316	>
1317		#endif // is_mpi
1318
1319
1320	<	if( info[l].n_SRI ){
1341	<
1320	>	if (info[l].n_SRI){
1321		Exclude::createArray(info[l].n_SRI);
1322	<	the_excludes = new Exclude*[info[l].n_SRI];
1323	<	for( int ex=0; ex<info[l].n_SRI; ex++){
1324	<	the_excludes[ex] = new Exclude(ex);
1322	>	the_excludes = new Exclude * [info[l].n_SRI];
1323	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1324	>	the_excludes[ex] = new Exclude(ex);
1325		}
1326		info[l].globalExcludes = new int;
1327		info[l].n_exclude = info[l].n_SRI;
1328		}
1329		else{
1330	<
1331	<	Exclude::createArray( 1 );
1353	<	the_excludes = new Exclude*;
1330	>	Exclude::createArray(1);
1331	>	the_excludes = new Exclude * ;
1332		the_excludes[0] = new Exclude(0);
1333	<	the_excludes[0]->setPair( 0,0 );
1333	>	the_excludes[0]->setPair(0, 0);
1334		info[l].globalExcludes = new int;
1335		info[l].globalExcludes[0] = 0;
1336		info[l].n_exclude = 0;
#	Line 1365 | Line 1343 | void SimSetup::makeSysArrays( void ){
1343		info[l].nGlobalExcludes = 0;
1344		info[l].excludes = the_excludes;
1345
1346	<	the_ff->setSimInfo( info );
1369	<
1346	>	the_ff->setSimInfo(info);
1347		}
1348		}
1349
1350	<	void SimSetup::makeIntegrator( void ){
1374	<
1350	>	void SimSetup::makeIntegrator(void){
1351		int k;
1352
1353	<	NVT<RealIntegrator>*  myNVT = NULL;
1354	<	NPTi<RealIntegrator>* myNPTi = NULL;
1355	<	NPTf<RealIntegrator>* myNPTf = NULL;
1356	<	NPTim<RealIntegrator>* myNPTim = NULL;
1357	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1358	<
1359	<	for(k=0; k<nInfo; k++){
1360	<
1361	<	switch( ensembleCase ){
1362	<
1363	<	case NVE_ENS:
1364	<	if (globals->haveZconstraints()){
1365	<	setupZConstraint(info[k]);
1366	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1367	<	}
1353	>	NVE<RealIntegrator>* myNVE = NULL;
1354	>	NVT<RealIntegrator>* myNVT = NULL;
1355	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1356	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1357	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1358	>
1359	>	for (k = 0; k < nInfo; k++){
1360	>	switch (ensembleCase){
1361	>	case NVE_ENS:
1362	>	if (globals->haveZconstraints()){
1363	>	setupZConstraint(info[k]);
1364	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1365	>	}
1366	>	else{
1367	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1368	>	}
1369	>
1370	>	info->the_integrator = myNVE;
1371	>	break;
1372
1373	<	else
1374	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1375	<	break;
1376	<
1377	<	case NVT_ENS:
1378	<	if (globals->haveZconstraints()){
1379	<	setupZConstraint(info[k]);
1400	<	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1401	<	}
1402	<	else
1403	<	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1373	>	case NVT_ENS:
1374	>	if (globals->haveZconstraints()){
1375	>	setupZConstraint(info[k]);
1376	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1377	>	}
1378	>	else
1379	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1380
1381		myNVT->setTargetTemp(globals->getTargetTemp());
1382	<
1383	<	if (globals->haveTauThermostat())
1382	>
1383	>	if (globals->haveTauThermostat())
1384		myNVT->setTauThermostat(globals->getTauThermostat());
1385	<
1386	<	else {
1387	<	sprintf( painCave.errMsg,
1388	<	"SimSetup error: If you use the NVT\n"
1413	<	"    ensemble, you must set tauThermostat.\n");
1385	>	else{
1386	>	sprintf(painCave.errMsg,
1387	>	"SimSetup error: If you use the NVT\n"
1388	>	"    ensemble, you must set tauThermostat.\n");
1389		painCave.isFatal = 1;
1390		simError();
1391		}
1392	+
1393	+	info->the_integrator = myNVT;
1394		break;
1418	–
1419	–	case NPTi_ENS:
1420	–	if (globals->haveZconstraints()){
1421	–	setupZConstraint(info[k]);
1422	–	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1423	–	}
1424	–	else
1425	–	myNPTi = new NPTi<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"
1434	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1435	<	painCave.isFatal = 1;
1436	<	simError();
1437	<	}
1438	<
1439	<	if( globals->haveTauThermostat() )
1440	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1441	<	else{
1442	<	sprintf( painCave.errMsg,
1443	<	"SimSetup error: If you use an NPT\n"
1444	<	"    ensemble, you must set tauThermostat.\n");
1445	<	painCave.isFatal = 1;
1446	<	simError();
1447	<	}
1448	<
1449	<	if( globals->haveTauBarostat() )
1450	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1451	<	else{
1452	<	sprintf( painCave.errMsg,
1453	<	"SimSetup error: If you use an NPT\n"
1454	<	"    ensemble, you must set tauBarostat.\n");
1455	<	painCave.isFatal = 1;
1456	<	simError();
1457	<	}
1458	<	break;
1459	<
1460	<	case NPTf_ENS:
1461	<	if (globals->haveZconstraints()){
1462	<	setupZConstraint(info[k]);
1463	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1464	<	}
1465	<	else
1466	<	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1396	>	case NPTi_ENS:
1397	>	if (globals->haveZconstraints()){
1398	>	setupZConstraint(info[k]);
1399	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1400	>	}
1401	>	else
1402	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1403
1404	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1469	<
1470	<	if (globals->haveTargetPressure())
1471	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1472	<	else {
1473	<	sprintf( painCave.errMsg,
1474	<	"SimSetup error: If you use a constant pressure\n"
1475	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1476	<	painCave.isFatal = 1;
1477	<	simError();
1478	<	}
1479	<
1480	<	if( globals->haveTauThermostat() )
1481	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1482	<	else{
1483	<	sprintf( painCave.errMsg,
1484	<	"SimSetup error: If you use an NPT\n"
1485	<	"    ensemble, you must set tauThermostat.\n");
1486	<	painCave.isFatal = 1;
1487	<	simError();
1488	<	}
1489	<
1490	<	if( globals->haveTauBarostat() )
1491	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1492	<	else{
1493	<	sprintf( painCave.errMsg,
1494	<	"SimSetup error: If you use an NPT\n"
1495	<	"    ensemble, you must set tauBarostat.\n");
1496	<	painCave.isFatal = 1;
1497	<	simError();
1498	<	}
1499	<	break;
1500	<
1501	<	case NPTim_ENS:
1502	<	if (globals->haveZconstraints()){
1503	<	setupZConstraint(info[k]);
1504	<	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1505	<	}
1506	<	else
1507	<	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1404	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1405
1406	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1407	<
1408	<	if (globals->haveTargetPressure())
1409	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1513	<	else {
1514	<	sprintf( painCave.errMsg,
1406	>	if (globals->haveTargetPressure())
1407	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1408	>	else{
1409	>	sprintf(painCave.errMsg,
1410		"SimSetup error: If you use a constant pressure\n"
1411		"    ensemble, you must set targetPressure in the BASS file.\n");
1412	<	painCave.isFatal = 1;
1413	<	simError();
1414	<	}
1415	<
1416	<	if( globals->haveTauThermostat() )
1417	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1418	<	else{
1419	<	sprintf( painCave.errMsg,
1412	>	painCave.isFatal = 1;
1413	>	simError();
1414	>	}
1415	>
1416	>	if (globals->haveTauThermostat())
1417	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1418	>	else{
1419	>	sprintf(painCave.errMsg,
1420		"SimSetup error: If you use an NPT\n"
1421		"    ensemble, you must set tauThermostat.\n");
1422	<	painCave.isFatal = 1;
1423	<	simError();
1424	<	}
1530	<
1531	<	if( globals->haveTauBarostat() )
1532	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1533	<	else{
1534	<	sprintf( painCave.errMsg,
1535	<	"SimSetup error: If you use an NPT\n"
1536	<	"    ensemble, you must set tauBarostat.\n");
1537	<	painCave.isFatal = 1;
1538	<	simError();
1539	<	}
1540	<	break;
1541	<
1542	<	case NPTfm_ENS:
1543	<	if (globals->haveZconstraints()){
1544	<	setupZConstraint(info[k]);
1545	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1546	<	}
1547	<	else
1548	<	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1422	>	painCave.isFatal = 1;
1423	>	simError();
1424	>	}
1425
1426	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1427	<
1428	<	if (globals->haveTargetPressure())
1429	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1554	<	else {
1555	<	sprintf( painCave.errMsg,
1556	<	"SimSetup error: If you use a constant pressure\n"
1557	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1558	<	painCave.isFatal = 1;
1559	<	simError();
1560	<	}
1561	<
1562	<	if( globals->haveTauThermostat() )
1563	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1564	<	else{
1565	<	sprintf( painCave.errMsg,
1426	>	if (globals->haveTauBarostat())
1427	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1428	>	else{
1429	>	sprintf(painCave.errMsg,
1430		"SimSetup error: If you use an NPT\n"
1431	<	"    ensemble, you must set tauThermostat.\n");
1432	<	painCave.isFatal = 1;
1433	<	simError();
1434	<	}
1431	>	"    ensemble, you must set tauBarostat.\n");
1432	>	painCave.isFatal = 1;
1433	>	simError();
1434	>	}
1435
1436	<	if( globals->haveTauBarostat() )
1437	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1438	<	else{
1439	<	sprintf( painCave.errMsg,
1436	>	info->the_integrator = myNPTi;
1437	>	break;
1438	>
1439	>	case NPTf_ENS:
1440	>	if (globals->haveZconstraints()){
1441	>	setupZConstraint(info[k]);
1442	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1443	>	}
1444	>	else
1445	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1446	>
1447	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1448	>
1449	>	if (globals->haveTargetPressure())
1450	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1451	>	else{
1452	>	sprintf(painCave.errMsg,
1453	>	"SimSetup error: If you use a constant pressure\n"
1454	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1455	>	painCave.isFatal = 1;
1456	>	simError();
1457	>	}
1458	>
1459	>	if (globals->haveTauThermostat())
1460	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1461	>	else{
1462	>	sprintf(painCave.errMsg,
1463		"SimSetup error: If you use an NPT\n"
1464	+	"    ensemble, you must set tauThermostat.\n");
1465	+	painCave.isFatal = 1;
1466	+	simError();
1467	+	}
1468	+
1469	+	if (globals->haveTauBarostat())
1470	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1471	+	else{
1472	+	sprintf(painCave.errMsg,
1473	+	"SimSetup error: If you use an NPT\n"
1474		"    ensemble, you must set tauBarostat.\n");
1475	+	painCave.isFatal = 1;
1476	+	simError();
1477	+	}
1478	+
1479	+	info->the_integrator = myNPTf;
1480	+	break;
1481	+
1482	+	case NPTxyz_ENS:
1483	+	if (globals->haveZconstraints()){
1484	+	setupZConstraint(info[k]);
1485	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1486	+	}
1487	+	else
1488	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1489	+
1490	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1491	+
1492	+	if (globals->haveTargetPressure())
1493	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1494	+	else{
1495	+	sprintf(painCave.errMsg,
1496	+	"SimSetup error: If you use a constant pressure\n"
1497	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1498	+	painCave.isFatal = 1;
1499	+	simError();
1500	+	}
1501	+
1502	+	if (globals->haveTauThermostat())
1503	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1504	+	else{
1505	+	sprintf(painCave.errMsg,
1506	+	"SimSetup error: If you use an NPT\n"
1507	+	"    ensemble, you must set tauThermostat.\n");
1508	+	painCave.isFatal = 1;
1509	+	simError();
1510	+	}
1511	+
1512	+	if (globals->haveTauBarostat())
1513	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1514	+	else{
1515	+	sprintf(painCave.errMsg,
1516	+	"SimSetup error: If you use an NPT\n"
1517	+	"    ensemble, you must set tauBarostat.\n");
1518	+	painCave.isFatal = 1;
1519	+	simError();
1520	+	}
1521	+
1522	+	info->the_integrator = myNPTxyz;
1523	+	break;
1524	+
1525	+	default:
1526	+	sprintf(painCave.errMsg,
1527	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1528		painCave.isFatal = 1;
1529		simError();
1580	–	}
1581	–	break;
1582	–
1583	–	default:
1584	–	sprintf( painCave.errMsg,
1585	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1586	–	painCave.isFatal = 1;
1587	–	simError();
1530		}
1531		}
1532		}
1533
1534	<	void SimSetup::initFortran( void ){
1593	<
1534	>	void SimSetup::initFortran(void){
1535		info[0].refreshSim();
1536	<
1537	<	if( !strcmp( info[0].mixingRule, "standard") ){
1538	<	the_ff->initForceField( LB_MIXING_RULE );
1536	>
1537	>	if (!strcmp(info[0].mixingRule, "standard")){
1538	>	the_ff->initForceField(LB_MIXING_RULE);
1539		}
1540	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1541	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1540	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1541	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1542		}
1543		else{
1544	<	sprintf( painCave.errMsg,
1545	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1605	<	info[0].mixingRule );
1544	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1545	>	info[0].mixingRule);
1546		painCave.isFatal = 1;
1547		simError();
1548		}
1549
1550
1551		#ifdef IS_MPI
1552	<	strcpy( checkPointMsg,
1613	<	"Successfully intialized the mixingRule for Fortran." );
1552	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1553		MPIcheckPoint();
1554		#endif // is_mpi
1616	–
1555		}
1556
1557	<	void SimSetup::setupZConstraint(SimInfo& theInfo)
1620	<	{
1557	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1558		int nZConstraints;
1559		ZconStamp** zconStamp;
1560
1561	<	if(globals->haveZconstraintTime()){
1625	<
1561	>	if (globals->haveZconstraintTime()){
1562		//add sample time of z-constraint  into SimInfo's property list
1563		DoubleData* zconsTimeProp = new DoubleData();
1564		zconsTimeProp->setID(ZCONSTIME_ID);
#	Line 1630 | Line 1566 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1566		theInfo.addProperty(zconsTimeProp);
1567		}
1568		else{
1569	<	sprintf( painCave.errMsg,
1570	<	"ZConstraint error: If you use an ZConstraint\n"
1571	<	" , you must set sample time.\n");
1569	>	sprintf(painCave.errMsg,
1570	>	"ZConstraint error: If you use an ZConstraint\n"
1571	>	" , you must set sample time.\n");
1572		painCave.isFatal = 1;
1573	<	simError();
1573	>	simError();
1574		}
1575
1576		//push zconsTol into siminfo, if user does not specify
1577		//value for zconsTol, a default value will be used
1578		DoubleData* zconsTol = new DoubleData();
1579		zconsTol->setID(ZCONSTOL_ID);
1580	<	if(globals->haveZconsTol()){
1580	>	if (globals->haveZconsTol()){
1581		zconsTol->setData(globals->getZconsTol());
1582		}
1583		else{
1584	<	double defaultZConsTol = 0.01;
1585	<	sprintf( painCave.errMsg,
1586	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1587	<	" , default value %f is used.\n", defaultZConsTol);
1584	>	double defaultZConsTol = 0.01;
1585	>	sprintf(painCave.errMsg,
1586	>	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1587	>	" , default value %f is used.\n",
1588	>	defaultZConsTol);
1589		painCave.isFatal = 0;
1590		simError();
1591
#	Line 1656 | Line 1593 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1593		}
1594		theInfo.addProperty(zconsTol);
1595
1596	<	//set Force Substraction Policy
1597	<	StringData* zconsForcePolicy =  new StringData();
1596	>	//set Force Subtraction Policy
1597	>	StringData* zconsForcePolicy = new StringData();
1598		zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1599	<
1600	<	if(globals->haveZconsForcePolicy()){
1599	>
1600	>	if (globals->haveZconsForcePolicy()){
1601		zconsForcePolicy->setData(globals->getZconsForcePolicy());
1602	<	}
1602	>	}
1603		else{
1604	<	sprintf( painCave.errMsg,
1605	<	"ZConstraint Warning: User does not set force substraction policy, "
1606	<	"average force substraction policy is used\n");
1607	<	painCave.isFatal = 0;
1608	<	simError();
1609	<	zconsForcePolicy->setData("BYNUMBER");
1604	>	sprintf(painCave.errMsg,
1605	>	"ZConstraint Warning: User does not set force Subtraction policy, "
1606	>	"PolicyByMass is used\n");
1607	>	painCave.isFatal = 0;
1608	>	simError();
1609	>	zconsForcePolicy->setData("BYMASS");
1610		}
1611	<
1612	<	theInfo.addProperty(zconsForcePolicy);
1613	<
1611	>
1612	>	theInfo.addProperty(zconsForcePolicy);
1613	>
1614		//Determine the name of ouput file and add it into SimInfo's property list
1615		//Be careful, do not use inFileName, since it is a pointer which
1616		//point to a string at master node, and slave nodes do not contain that string
1617	<
1617	>
1618		string zconsOutput(theInfo.finalName);
1619	<
1619	>
1620		zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1621	<
1621	>
1622		StringData* zconsFilename = new StringData();
1623		zconsFilename->setID(ZCONSFILENAME_ID);
1624		zconsFilename->setData(zconsOutput);
1625	<
1625	>
1626		theInfo.addProperty(zconsFilename);
1627	<
1627	>
1628		//setup index, pos and other parameters of z-constraint molecules
1629		nZConstraints = globals->getNzConstraints();
1630		theInfo.nZconstraints = nZConstraints;
#	Line 1697 | Line 1634 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1634
1635		ZConsParaData* zconsParaData = new ZConsParaData();
1636		zconsParaData->setID(ZCONSPARADATA_ID);
1637	<
1638	<	for(int i = 0; i < nZConstraints; i++){
1637	>
1638	>	for (int i = 0; i < nZConstraints; i++){
1639		tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1640		tempParaItem.zPos = zconStamp[i]->getZpos();
1641		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
#	Line 1707 | Line 1644 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1644		zconsParaData->addItem(tempParaItem);
1645		}
1646
1647	+	//check the uniqueness of index
1648	+	if(!zconsParaData->isIndexUnique()){
1649	+	sprintf(painCave.errMsg,
1650	+	"ZConstraint Error: molIndex is not unique\n");
1651	+	painCave.isFatal = 1;
1652	+	simError();
1653	+	}
1654	+
1655		//sort the parameters by index of molecules
1656		zconsParaData->sortByIndex();
1657
1658		//push data into siminfo, therefore, we can retrieve later
1659		theInfo.addProperty(zconsParaData);
1715	–
1660		}

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