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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 604 by gezelter, Tue Jul 15 03:08:00 2003 UTC vs.
Revision 676 by tim, Mon Aug 11 19:40:06 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6
7		#include "SimSetup.hpp"
8		#include "parse_me.h"
#	Line 14 | Line 16
16
17		// some defines for ensemble and Forcefield  cases
18
19	<	#define NVE_ENS   0
20	<	#define NVT_ENS   1
21	<	#define NPTi_ENS  2
22	<	#define NPTf_ENS  3
23	<	#define NPTim_ENS 4
24	<	#define NPTfm_ENS 5
19	>	#define NVE_ENS        0
20	>	#define NVT_ENS        1
21	>	#define NPTi_ENS       2
22	>	#define NPTf_ENS       3
23	>	#define NPTim_ENS      4
24	>	#define NPTfm_ENS      5
25
24	–
26		#define FF_DUFF 0
27		#define FF_LJ   1
28	+	#define FF_EAM  2
29
30	+	using namespace std;
31
32		SimSetup::SimSetup(){
33	+
34	+	isInfoArray = 0;
35	+	nInfo = 1;
36	+
37		stamps = new MakeStamps();
38		globals = new Globals();
39
40	+
41		#ifdef IS_MPI
42		strcpy( checkPointMsg, "SimSetup creation successful" );
43		MPIcheckPoint();
#	Line 41 | Line 49 | void SimSetup::parseFile( char* fileName ){
49		delete globals;
50		}
51
52	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
53	+	info = the_info;
54	+	nInfo = theNinfo;
55	+	isInfoArray = 1;
56	+	}
57	+
58	+
59		void SimSetup::parseFile( char* fileName ){
60
61		#ifdef IS_MPI
#	Line 76 | Line 91 | void SimSetup::createSim( void ){
91
92		#endif // is_mpi
93
94	<	void SimSetup::createSim( void ){
94	>	void SimSetup::createSim(void){
95
81	–	MakeStamps *the_stamps;
82	–	Globals* the_globals;
96		int i, j, k, globalAtomIndex;
97
98	<	int ensembleCase;
86	<	int ffCase;
98	>	// gather all of the information from the Bass file
99
100	<	ensembleCase = -1;
89	<	ffCase = -1;
100	>	gatherInfo();
101
102	<	// get the stamps and globals;
92	<	the_stamps = stamps;
93	<	the_globals = globals;
102	>	// creation of complex system objects
103
104	<	// set the easy ones first
96	<	simnfo->target_temp = the_globals->getTargetTemp();
97	<	simnfo->dt = the_globals->getDt();
98	<	simnfo->run_time = the_globals->getRunTime();
104	>	sysObjectsCreation();
105
106	<	// get the ones we know are there, yet still may need some work.
107	<	n_components = the_globals->getNComponents();
108	<	strcpy( force_field, the_globals->getForceField() );
106	>	// check on the post processing info
107	>
108	>	finalInfoCheck();
109	>
110	>	// initialize the system coordinates
111	>
112	>	if( !isInfoArray ) initSystemCoords();
113	>
114	>	// make the output filenames
115	>
116	>	makeOutNames();
117	>
118	>	// make the integrator
119	>
120	>	makeIntegrator();
121	>
122	>	#ifdef IS_MPI
123	>	mpiSim->mpiRefresh();
124	>	#endif
125	>
126	>	// initialize the Fortran
127	>
128	>	initFortran();
129	>
130	>
131	>
132	>	}
133	>
134	>
135	>	void SimSetup::makeMolecules( void ){
136	>
137	>	int k,l;
138	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
139	>	molInit molInfo;
140	>	DirectionalAtom* dAtom;
141	>	LinkedAssign* extras;
142	>	LinkedAssign* current_extra;
143	>	AtomStamp* currentAtom;
144	>	BondStamp* currentBond;
145	>	BendStamp* currentBend;
146	>	TorsionStamp* currentTorsion;
147	>
148	>	bond_pair* theBonds;
149	>	bend_set* theBends;
150	>	torsion_set* theTorsions;
151	>
152	>
153	>	//init the forceField paramters
154	>
155	>	the_ff->readParams();
156	>
157	>
158	>	// init the atoms
159	>
160	>	double ux, uy, uz, u, uSqr;
161	>
162	>	for(k=0; k<nInfo; k++){
163	>
164	>	the_ff->setSimInfo( &(info[k]) );
165	>
166	>	atomOffset = 0;
167	>	excludeOffset = 0;
168	>	for(i=0; i<info[k].n_mol; i++){
169	>
170	>	stampID = info[k].molecules[i].getStampID();
171	>
172	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
173	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
174	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
175	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
176	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
177	>
178	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
179	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
180	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
181	>	molInfo.myBends = new Bend*[molInfo.nBends];
182	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
183	>
184	>	theBonds = new bond_pair[molInfo.nBonds];
185	>	theBends = new bend_set[molInfo.nBends];
186	>	theTorsions = new torsion_set[molInfo.nTorsions];
187	>
188	>	// make the Atoms
189	>
190	>	for(j=0; j<molInfo.nAtoms; j++){
191	>
192	>	currentAtom = comp_stamps[stampID]->getAtom( j );
193	>	if( currentAtom->haveOrientation() ){
194	>
195	>	dAtom = new DirectionalAtom( (j + atomOffset),
196	>	info[k].getConfiguration() );
197	>	info[k].n_oriented++;
198	>	molInfo.myAtoms[j] = dAtom;
199	>
200	>	ux = currentAtom->getOrntX();
201	>	uy = currentAtom->getOrntY();
202	>	uz = currentAtom->getOrntZ();
203	>
204	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
205	>
206	>	u = sqrt( uSqr );
207	>	ux = ux / u;
208	>	uy = uy / u;
209	>	uz = uz / u;
210	>
211	>	dAtom->setSUx( ux );
212	>	dAtom->setSUy( uy );
213	>	dAtom->setSUz( uz );
214	>	}
215	>	else{
216	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
217	>	info[k].getConfiguration() );
218	>	}
219	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
220	>
221	>	#ifdef IS_MPI
222	>
223	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
224	>
225	>	#endif // is_mpi
226	>	}
227	>
228	>	// make the bonds
229	>	for(j=0; j<molInfo.nBonds; j++){
230	>
231	>	currentBond = comp_stamps[stampID]->getBond( j );
232	>	theBonds[j].a = currentBond->getA() + atomOffset;
233	>	theBonds[j].b = currentBond->getB() + atomOffset;
234	>
235	>	exI = theBonds[j].a;
236	>	exJ = theBonds[j].b;
237	>
238	>	// exclude_I must always be the smaller of the pair
239	>	if( exI > exJ ){
240	>	tempEx = exI;
241	>	exI = exJ;
242	>	exJ = tempEx;
243	>	}
244	>	#ifdef IS_MPI
245	>	tempEx = exI;
246	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
247	>	tempEx = exJ;
248	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
249	>
250	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
251	>	#else  // isn't MPI
252	>
253	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
254	>	#endif  //is_mpi
255	>	}
256	>	excludeOffset += molInfo.nBonds;
257	>
258	>	//make the bends
259	>	for(j=0; j<molInfo.nBends; j++){
260	>
261	>	currentBend = comp_stamps[stampID]->getBend( j );
262	>	theBends[j].a = currentBend->getA() + atomOffset;
263	>	theBends[j].b = currentBend->getB() + atomOffset;
264	>	theBends[j].c = currentBend->getC() + atomOffset;
265	>
266	>	if( currentBend->haveExtras() ){
267	>
268	>	extras = currentBend->getExtras();
269	>	current_extra = extras;
270	>
271	>	while( current_extra != NULL ){
272	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
273	>
274	>	switch( current_extra->getType() ){
275	>
276	>	case 0:
277	>	theBends[j].ghost =
278	>	current_extra->getInt() + atomOffset;
279	>	theBends[j].isGhost = 1;
280	>	break;
281	>
282	>	case 1:
283	>	theBends[j].ghost =
284	>	(int)current_extra->getDouble() + atomOffset;
285	>	theBends[j].isGhost = 1;
286	>	break;
287	>
288	>	default:
289	>	sprintf( painCave.errMsg,
290	>	"SimSetup Error: ghostVectorSource was neither a "
291	>	"double nor an int.\n"
292	>	"-->Bend[%d] in %s\n",
293	>	j, comp_stamps[stampID]->getID() );
294	>	painCave.isFatal = 1;
295	>	simError();
296	>	}
297	>	}
298	>
299	>	else{
300	>
301	>	sprintf( painCave.errMsg,
302	>	"SimSetup Error: unhandled bend assignment:\n"
303	>	"    -->%s in Bend[%d] in %s\n",
304	>	current_extra->getlhs(),
305	>	j, comp_stamps[stampID]->getID() );
306	>	painCave.isFatal = 1;
307	>	simError();
308	>	}
309	>
310	>	current_extra = current_extra->getNext();
311	>	}
312	>	}
313	>
314	>	if( !theBends[j].isGhost ){
315	>
316	>	exI = theBends[j].a;
317	>	exJ = theBends[j].c;
318	>	}
319	>	else{
320	>
321	>	exI = theBends[j].a;
322	>	exJ = theBends[j].b;
323	>	}
324	>
325	>	// exclude_I must always be the smaller of the pair
326	>	if( exI > exJ ){
327	>	tempEx = exI;
328	>	exI = exJ;
329	>	exJ = tempEx;
330	>	}
331	>	#ifdef IS_MPI
332	>	tempEx = exI;
333	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
334	>	tempEx = exJ;
335	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
336	>
337	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
338	>	#else  // isn't MPI
339	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
340	>	#endif  //is_mpi
341	>	}
342	>	excludeOffset += molInfo.nBends;
343	>
344	>	for(j=0; j<molInfo.nTorsions; j++){
345	>
346	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
347	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
348	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
349	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
350	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
351	>
352	>	exI = theTorsions[j].a;
353	>	exJ = theTorsions[j].d;
354	>
355	>	// exclude_I must always be the smaller of the pair
356	>	if( exI > exJ ){
357	>	tempEx = exI;
358	>	exI = exJ;
359	>	exJ = tempEx;
360	>	}
361	>	#ifdef IS_MPI
362	>	tempEx = exI;
363	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
364	>	tempEx = exJ;
365	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
366	>
367	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
368	>	#else  // isn't MPI
369	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
370	>	#endif  //is_mpi
371	>	}
372	>	excludeOffset += molInfo.nTorsions;
373	>
374	>
375	>	// send the arrays off to the forceField for init.
376	>
377	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
378	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
379	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
380	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
381	>
382	>
383	>	info[k].molecules[i].initialize( molInfo );
384
385	+
386	+	atomOffset += molInfo.nAtoms;
387	+	delete[] theBonds;
388	+	delete[] theBends;
389	+	delete[] theTorsions;
390	+	}
391	+	}
392	+
393	+	#ifdef IS_MPI
394	+	sprintf( checkPointMsg, "all molecules initialized succesfully" );
395	+	MPIcheckPoint();
396	+	#endif // is_mpi
397	+
398	+	// clean up the forcefield
399	+
400	+	the_ff->calcRcut();
401	+	the_ff->cleanMe();
402	+
403	+	}
404	+
405	+	void SimSetup::initFromBass( void ){
406	+
407	+	int i, j, k;
408	+	int n_cells;
409	+	double cellx, celly, cellz;
410	+	double temp1, temp2, temp3;
411	+	int n_per_extra;
412	+	int n_extra;
413	+	int have_extra, done;
414	+
415	+	double vel[3];
416	+	vel[0] = 0.0;
417	+	vel[1] = 0.0;
418	+	vel[2] = 0.0;
419	+
420	+	temp1 = (double)tot_nmol / 4.0;
421	+	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
422	+	temp3 = ceil( temp2 );
423	+
424	+	have_extra =0;
425	+	if( temp2 < temp3 ){ // we have a non-complete lattice
426	+	have_extra =1;
427	+
428	+	n_cells = (int)temp3 - 1;
429	+	cellx = info[0].boxL[0] / temp3;
430	+	celly = info[0].boxL[1] / temp3;
431	+	cellz = info[0].boxL[2] / temp3;
432	+	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
433	+	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
434	+	n_per_extra = (int)ceil( temp1 );
435	+
436	+	if( n_per_extra > 4){
437	+	sprintf( painCave.errMsg,
438	+	"SimSetup error. There has been an error in constructing"
439	+	" the non-complete lattice.\n" );
440	+	painCave.isFatal = 1;
441	+	simError();
442	+	}
443	+	}
444	+	else{
445	+	n_cells = (int)temp3;
446	+	cellx = info[0].boxL[0] / temp3;
447	+	celly = info[0].boxL[1] / temp3;
448	+	cellz = info[0].boxL[2] / temp3;
449	+	}
450	+
451	+	current_mol = 0;
452	+	current_comp_mol = 0;
453	+	current_comp = 0;
454	+	current_atom_ndx = 0;
455	+
456	+	for( i=0; i < n_cells ; i++ ){
457	+	for( j=0; j < n_cells; j++ ){
458	+	for( k=0; k < n_cells; k++ ){
459	+
460	+	makeElement( i * cellx,
461	+	j * celly,
462	+	k * cellz );
463	+
464	+	makeElement( i * cellx + 0.5 * cellx,
465	+	j * celly + 0.5 * celly,
466	+	k * cellz );
467	+
468	+	makeElement( i * cellx,
469	+	j * celly + 0.5 * celly,
470	+	k * cellz + 0.5 * cellz );
471	+
472	+	makeElement( i * cellx + 0.5 * cellx,
473	+	j * celly,
474	+	k * cellz + 0.5 * cellz );
475	+	}
476	+	}
477	+	}
478	+
479	+	if( have_extra ){
480	+	done = 0;
481	+
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	+
486	+	if( i < n_cells ){
487	+
488	+	if( j < n_cells ){
489	+	start_ndx = n_cells;
490	+	}
491	+	else start_ndx = 0;
492	+	}
493	+	else start_ndx = 0;
494	+
495	+	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
496	+
497	+	makeElement( i * cellx,
498	+	j * celly,
499	+	k * cellz );
500	+	done = ( current_mol >= tot_nmol );
501	+
502	+	if( !done && n_per_extra > 1 ){
503	+	makeElement( i * cellx + 0.5 * cellx,
504	+	j * celly + 0.5 * celly,
505	+	k * cellz );
506	+	done = ( current_mol >= tot_nmol );
507	+	}
508	+
509	+	if( !done && n_per_extra > 2){
510	+	makeElement( i * cellx,
511	+	j * celly + 0.5 * celly,
512	+	k * cellz + 0.5 * cellz );
513	+	done = ( current_mol >= tot_nmol );
514	+	}
515	+
516	+	if( !done && n_per_extra > 3){
517	+	makeElement( i * cellx + 0.5 * cellx,
518	+	j * celly,
519	+	k * cellz + 0.5 * cellz );
520	+	done = ( current_mol >= tot_nmol );
521	+	}
522	+	}
523	+	}
524	+	}
525	+	}
526	+
527	+	for( i=0; i<info[0].n_atoms; i++ ){
528	+	info[0].atoms[i]->setVel( vel );
529	+	}
530	+	}
531	+
532	+	void SimSetup::makeElement( double x, double y, double z ){
533	+
534	+	int k;
535	+	AtomStamp* current_atom;
536	+	DirectionalAtom* dAtom;
537	+	double rotMat[3][3];
538	+	double pos[3];
539	+
540	+	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
541	+
542	+	current_atom = comp_stamps[current_comp]->getAtom( k );
543	+	if( !current_atom->havePosition() ){
544	+	sprintf( painCave.errMsg,
545	+	"SimSetup:initFromBass error.\n"
546	+	"\tComponent %s, atom %s does not have a position specified.\n"
547	+	"\tThe initialization routine is unable to give a start"
548	+	" position.\n",
549	+	comp_stamps[current_comp]->getID(),
550	+	current_atom->getType() );
551	+	painCave.isFatal = 1;
552	+	simError();
553	+	}
554	+
555	+	pos[0] = x + current_atom->getPosX();
556	+	pos[1] = y + current_atom->getPosY();
557	+	pos[2] = z + current_atom->getPosZ();
558	+
559	+	info[0].atoms[current_atom_ndx]->setPos( pos );
560	+
561	+	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
562	+
563	+	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
564	+
565	+	rotMat[0][0] = 1.0;
566	+	rotMat[0][1] = 0.0;
567	+	rotMat[0][2] = 0.0;
568	+
569	+	rotMat[1][0] = 0.0;
570	+	rotMat[1][1] = 1.0;
571	+	rotMat[1][2] = 0.0;
572	+
573	+	rotMat[2][0] = 0.0;
574	+	rotMat[2][1] = 0.0;
575	+	rotMat[2][2] = 1.0;
576	+
577	+	dAtom->setA( rotMat );
578	+	}
579	+
580	+	current_atom_ndx++;
581	+	}
582	+
583	+	current_mol++;
584	+	current_comp_mol++;
585	+
586	+	if( current_comp_mol >= components_nmol[current_comp] ){
587	+
588	+	current_comp_mol = 0;
589	+	current_comp++;
590	+	}
591	+	}
592	+
593	+
594	+	void SimSetup::gatherInfo( void ){
595	+	int i,j,k;
596	+
597	+	ensembleCase = -1;
598	+	ffCase = -1;
599	+
600	+	// set the easy ones first
601	+
602	+	for( i=0; i<nInfo; i++){
603	+	info[i].target_temp = globals->getTargetTemp();
604	+	info[i].dt = globals->getDt();
605	+	info[i].run_time = globals->getRunTime();
606	+	}
607	+	n_components = globals->getNComponents();
608	+
609	+
610	+	// get the forceField
611	+
612	+	strcpy( force_field, globals->getForceField() );
613	+
614		if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
615		else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
616	+	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
617		else{
618		sprintf( painCave.errMsg,
619		"SimSetup Error. Unrecognized force field -> %s\n",
#	Line 111 | Line 622 | void SimSetup::createSim( void ){
622		simError();
623		}
624
625	<	// get the ensemble:
115	<	strcpy( ensemble, the_globals->getEnsemble() );
625	>	// get the ensemble
626
627	+	strcpy( ensemble, globals->getEnsemble() );
628	+
629		if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
630		else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
631		else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
#	Line 131 | Line 643 | void SimSetup::createSim( void ){
643		strcpy( ensemble, "NVE" );
644		ensembleCase = NVE_ENS;
645		}
646	<	strcpy( simnfo->ensemble, ensemble );
646	>
647	>	for(i=0; i<nInfo; i++){
648	>
649	>	strcpy( info[i].ensemble, ensemble );
650
651	+	// get the mixing rule
652
653	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
654	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
139	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
140	<	//     if (the_globals->haveTargetPressure())
141	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
142	<	//     else {
143	<	//       sprintf( painCave.errMsg,
144	<	//                "SimSetup error: If you use the constant pressure\n"
145	<	//                "    ensemble, you must set targetPressure.\n"
146	<	//                "    This was found in the BASS file.\n");
147	<	//       painCave.isFatal = 1;
148	<	//       simError();
149	<	//     }
150	<
151	<	//     if (the_globals->haveTauThermostat())
152	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
153	<	//     else if (the_globals->haveQmass())
154	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
155	<	//     else {
156	<	//       sprintf( painCave.errMsg,
157	<	//                "SimSetup error: If you use one of the constant temperature\n"
158	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
159	<	//                "    Neither of these was found in the BASS file.\n");
160	<	//       painCave.isFatal = 1;
161	<	//       simError();
162	<	//     }
163	<
164	<	//     if (the_globals->haveTauBarostat())
165	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
166	<	//     else {
167	<	//       sprintf( painCave.errMsg,
168	<	//                "SimSetup error: If you use the constant pressure\n"
169	<	//                "    ensemble, you must set tauBarostat.\n"
170	<	//                "    This was found in the BASS file.\n");
171	<	//       painCave.isFatal = 1;
172	<	//       simError();
173	<	//     }
174	<
175	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
176	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
177	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
178	<
179	<	//     if (the_globals->haveTauThermostat())
180	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
181	<	//     else if (the_globals->haveQmass())
182	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
183	<	//     else {
184	<	//       sprintf( painCave.errMsg,
185	<	//                "SimSetup error: If you use one of the constant temperature\n"
186	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
187	<	//                "    Neither of these was found in the BASS file.\n");
188	<	//       painCave.isFatal = 1;
189	<	//       simError();
190	<	//     }
191	<
192	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
193	<	simnfo->usePBC = the_globals->getPBC();
194	<
195	<	int usesDipoles = 0;
196	<	switch( ffCase ){
197	<
198	<	case FF_DUFF:
199	<	the_ff = new DUFF();
200	<	usesDipoles = 1;
201	<	break;
202	<
203	<	case FF_LJ:
204	<	the_ff = new LJFF();
205	<	break;
206	<
207	<	default:
208	<	sprintf( painCave.errMsg,
209	<	"SimSetup Error. Unrecognized force field in case statement.\n");
210	<	painCave.isFatal = 1;
211	<	simError();
653	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
654	>	info[i].usePBC = globals->getPBC();
655		}
656	<
214	<	#ifdef IS_MPI
215	<	strcpy( checkPointMsg, "ForceField creation successful" );
216	<	MPIcheckPoint();
217	<	#endif // is_mpi
218	<
656	>
657		// get the components and calculate the tot_nMol and indvidual n_mol
658	<	the_components = the_globals->getComponents();
658	>
659	>	the_components = globals->getComponents();
660		components_nmol = new int[n_components];
222	–	comp_stamps = new MoleculeStamp*[n_components];
661
662	<	if( !the_globals->haveNMol() ){
662	>
663	>	if( !globals->haveNMol() ){
664		// we don't have the total number of molecules, so we assume it is
665		// given in each component
666
#	Line 250 | Line 689 | void SimSetup::createSim( void ){
689		" Please give nMol in the components.\n" );
690		painCave.isFatal = 1;
691		simError();
253	–
254	–
255	–	//     tot_nmol = the_globals->getNMol();
256	–
257	–	//   //we have the total number of molecules, now we check for molfractions
258	–	//     for( i=0; i<n_components; i++ ){
259	–
260	–	//       if( !the_components[i]->haveMolFraction() ){
261	–
262	–	//  if( !the_components[i]->haveNMol() ){
263	–	//    //we have a problem
264	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
265	–	//              << " nMol was given in component
266	–
692		}
693
694	<	#ifdef IS_MPI
270	<	strcpy( checkPointMsg, "Have the number of components" );
271	<	MPIcheckPoint();
272	<	#endif // is_mpi
273	<
274	<	// make an array of molecule stamps that match the components used.
275	<	// also extract the used stamps out into a separate linked list
276	<
277	<	simnfo->nComponents = n_components;
278	<	simnfo->componentsNmol = components_nmol;
279	<	simnfo->compStamps = comp_stamps;
280	<	simnfo->headStamp = new LinkedMolStamp();
694	>	// set the status, sample, and thermal kick times
695
696	<	char* id;
283	<	LinkedMolStamp* headStamp = simnfo->headStamp;
284	<	LinkedMolStamp* currentStamp = NULL;
285	<	for( i=0; i<n_components; i++ ){
696	>	for(i=0; i<nInfo; i++){
697
698	<	id = the_components[i]->getType();
699	<	comp_stamps[i] = NULL;
698	>	if( globals->haveSampleTime() ){
699	>	info[i].sampleTime = globals->getSampleTime();
700	>	info[i].statusTime = info[i].sampleTime;
701	>	info[i].thermalTime = info[i].sampleTime;
702	>	}
703	>	else{
704	>	info[i].sampleTime = globals->getRunTime();
705	>	info[i].statusTime = info[i].sampleTime;
706	>	info[i].thermalTime = info[i].sampleTime;
707	>	}
708
709	<	// check to make sure the component isn't already in the list
709	>	if( globals->haveStatusTime() ){
710	>	info[i].statusTime = globals->getStatusTime();
711	>	}
712	>
713	>	if( globals->haveThermalTime() ){
714	>	info[i].thermalTime = globals->getThermalTime();
715	>	}
716
717	<	comp_stamps[i] = headStamp->match( id );
718	<	if( comp_stamps[i] == NULL ){
717	>	// check for the temperature set flag
718	>
719	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
720	>
721	>	// get some of the tricky things that may still be in the globals
722	>
723	>	double boxVector[3];
724	>	if( globals->haveBox() ){
725	>	boxVector[0] = globals->getBox();
726	>	boxVector[1] = globals->getBox();
727	>	boxVector[2] = globals->getBox();
728
729	<	// extract the component from the list;
729	>	info[i].setBox( boxVector );
730	>	}
731	>	else if( globals->haveDensity() ){
732
733	<	currentStamp = the_stamps->extractMolStamp( id );
734	<	if( currentStamp == NULL ){
733	>	double vol;
734	>	vol = (double)tot_nmol / globals->getDensity();
735	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
736	>	boxVector[1] = boxVector[0];
737	>	boxVector[2] = boxVector[0];
738	>
739	>	info[i].setBox( boxVector );
740	>	}
741	>	else{
742	>	if( !globals->haveBoxX() ){
743		sprintf( painCave.errMsg,
744	<	"SimSetup error: Component \"%s\" was not found in the "
301	<	"list of declared molecules\n",
302	<	id );
744	>	"SimSetup error, no periodic BoxX size given.\n" );
745		painCave.isFatal = 1;
746		simError();
747		}
748	+	boxVector[0] = globals->getBoxX();
749
750	<	headStamp->add( currentStamp );
751	<	comp_stamps[i] = headStamp->match( id );
750	>	if( !globals->haveBoxY() ){
751	>	sprintf( painCave.errMsg,
752	>	"SimSetup error, no periodic BoxY size given.\n" );
753	>	painCave.isFatal = 1;
754	>	simError();
755	>	}
756	>	boxVector[1] = globals->getBoxY();
757	>
758	>	if( !globals->haveBoxZ() ){
759	>	sprintf( painCave.errMsg,
760	>	"SimSetup error, no periodic BoxZ size given.\n" );
761	>	painCave.isFatal = 1;
762	>	simError();
763	>	}
764	>	boxVector[2] = globals->getBoxZ();
765	>
766	>	info[i].setBox( boxVector );
767		}
310	–	}
768
769	+	}
770	+
771		#ifdef IS_MPI
772	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
772	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
773		MPIcheckPoint();
774		#endif // is_mpi
316	–
775
776	+	}
777
778
779	<	// caclulate the number of atoms, bonds, bends and torsions
779	>	void SimSetup::finalInfoCheck( void ){
780	>	int index;
781	>	int usesDipoles;
782	>	int i;
783
784	<	tot_atoms = 0;
785	<	tot_bonds = 0;
324	<	tot_bends = 0;
325	<	tot_torsions = 0;
326	<	for( i=0; i<n_components; i++ ){
784	>	for(i=0; i<nInfo; i++){
785	>	// check electrostatic parameters
786
787	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
788	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
789	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
790	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
791	<	}
792	<
793	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
794	<
795	<	simnfo->n_atoms = tot_atoms;
796	<	simnfo->n_bonds = tot_bonds;
797	<	simnfo->n_bends = tot_bends;
798	<	simnfo->n_torsions = tot_torsions;
799	<	simnfo->n_SRI = tot_SRI;
341	<	simnfo->n_mol = tot_nmol;
787	>	index = 0;
788	>	usesDipoles = 0;
789	>	while( (index < info[i].n_atoms) && !usesDipoles ){
790	>	usesDipoles = (info[i].atoms[index])->hasDipole();
791	>	index++;
792	>	}
793	>
794	>	#ifdef IS_MPI
795	>	int myUse = usesDipoles;
796	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
797	>	#endif //is_mpi
798	>
799	>	double theEcr, theEst;
800
801	<	simnfo->molMembershipArray = new int[tot_atoms];
801	>	if (globals->getUseRF() ) {
802	>	info[i].useReactionField = 1;
803	>
804	>	if( !globals->haveECR() ){
805	>	sprintf( painCave.errMsg,
806	>	"SimSetup Warning: using default value of 1/2 the smallest "
807	>	"box length for the electrostaticCutoffRadius.\n"
808	>	"I hope you have a very fast processor!\n");
809	>	painCave.isFatal = 0;
810	>	simError();
811	>	double smallest;
812	>	smallest = info[i].boxL[0];
813	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
814	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
815	>	theEcr = 0.5 * smallest;
816	>	} else {
817	>	theEcr = globals->getECR();
818	>	}
819	>
820	>	if( !globals->haveEST() ){
821	>	sprintf( painCave.errMsg,
822	>	"SimSetup Warning: using default value of 0.05 * the "
823	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
824	>	);
825	>	painCave.isFatal = 0;
826	>	simError();
827	>	theEst = 0.05 * theEcr;
828	>	} else {
829	>	theEst= globals->getEST();
830	>	}
831	>
832	>	info[i].setEcr( theEcr, theEst );
833	>
834	>	if(!globals->haveDielectric() ){
835	>	sprintf( painCave.errMsg,
836	>	"SimSetup Error: You are trying to use Reaction Field without"
837	>	"setting a dielectric constant!\n"
838	>	);
839	>	painCave.isFatal = 1;
840	>	simError();
841	>	}
842	>	info[i].dielectric = globals->getDielectric();
843	>	}
844	>	else {
845	>	if (usesDipoles) {
846	>
847	>	if( !globals->haveECR() ){
848	>	sprintf( painCave.errMsg,
849	>	"SimSetup Warning: using default value of 1/2 the smallest "
850	>	"box length for the electrostaticCutoffRadius.\n"
851	>	"I hope you have a very fast processor!\n");
852	>	painCave.isFatal = 0;
853	>	simError();
854	>	double smallest;
855	>	smallest = info[i].boxL[0];
856	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
857	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
858	>	theEcr = 0.5 * smallest;
859	>	} else {
860	>	theEcr = globals->getECR();
861	>	}
862	>
863	>	if( !globals->haveEST() ){
864	>	sprintf( painCave.errMsg,
865	>	"SimSetup Warning: using default value of 0.05 * the "
866	>	"electrostaticCutoffRadius for the "
867	>	"electrostaticSkinThickness\n"
868	>	);
869	>	painCave.isFatal = 0;
870	>	simError();
871	>	theEst = 0.05 * theEcr;
872	>	} else {
873	>	theEst= globals->getEST();
874	>	}
875	>
876	>	info[i].setEcr( theEcr, theEst );
877	>	}
878	>	}
879	>	}
880
881		#ifdef IS_MPI
882	+	strcpy( checkPointMsg, "post processing checks out" );
883	+	MPIcheckPoint();
884	+	#endif // is_mpi
885
886	<	// divide the molecules among processors here.
348	<
349	<	mpiSim = new mpiSimulation( simnfo );
350	<
351	<	globalIndex = mpiSim->divideLabor();
886	>	}
887
888	<	// set up the local variables
888	>	void SimSetup::initSystemCoords( void ){
889	>	int i;
890
891	<	int localMol, allMol;
356	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
891	>	std::cerr << "Setting atom Coords\n";
892
893	<	int* mol2proc = mpiSim->getMolToProcMap();
359	<	int* molCompType = mpiSim->getMolComponentType();
893	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
894
895	<	allMol = 0;
362	<	localMol = 0;
363	<	local_atoms = 0;
364	<	local_bonds = 0;
365	<	local_bends = 0;
366	<	local_torsions = 0;
367	<	globalAtomIndex = 0;
368	<
369	<
370	<	for( i=0; i<n_components; i++ ){
371	<
372	<	for( j=0; j<components_nmol[i]; j++ ){
373	<
374	<	if( mol2proc[allMol] == worldRank ){
375	<
376	<	local_atoms +=    comp_stamps[i]->getNAtoms();
377	<	local_bonds +=    comp_stamps[i]->getNBonds();
378	<	local_bends +=    comp_stamps[i]->getNBends();
379	<	local_torsions += comp_stamps[i]->getNTorsions();
380	<	localMol++;
381	<	}
382	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
383	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
384	<	globalAtomIndex++;
385	<	}
386	<
387	<	allMol++;
388	<	}
389	<	}
390	<	local_SRI = local_bonds + local_bends + local_torsions;
895	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
896
897	<	simnfo->n_atoms = mpiSim->getMyNlocal();
898	<
899	<	if( local_atoms != simnfo->n_atoms ){
897	>	if( globals->haveInitialConfig() ){
898	>
899	>	InitializeFromFile* fileInit;
900	>	#ifdef IS_MPI // is_mpi
901	>	if( worldRank == 0 ){
902	>	#endif //is_mpi
903	>	fileInit = new InitializeFromFile( globals->getInitialConfig() );
904	>	#ifdef IS_MPI
905	>	}else fileInit = new InitializeFromFile( NULL );
906	>	#endif
907	>	fileInit->readInit( info ); // default velocities on
908	>
909	>	delete fileInit;
910	>	}
911	>	else{
912	>
913	>	#ifdef IS_MPI
914	>
915	>	// no init from bass
916	>
917		sprintf( painCave.errMsg,
918	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
919	<	" localAtom (%d) are not equal.\n",
398	<	simnfo->n_atoms,
399	<	local_atoms );
400	<	painCave.isFatal = 1;
918	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
919	>	painCave.isFatal;
920		simError();
921	+
922	+	#else
923	+
924	+	initFromBass();
925	+
926	+
927	+	#endif
928		}
403	–
404	–	simnfo->n_bonds = local_bonds;
405	–	simnfo->n_bends = local_bends;
406	–	simnfo->n_torsions = local_torsions;
407	–	simnfo->n_SRI = local_SRI;
408	–	simnfo->n_mol = localMol;
409	–
410	–	strcpy( checkPointMsg, "Passed nlocal consistency check." );
411	–	MPIcheckPoint();
929
930	<
930	>	#ifdef IS_MPI
931	>	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
932	>	MPIcheckPoint();
933		#endif // is_mpi
934
935	+	}
936
417	–	// create the atom and short range interaction arrays
937
938	<	Atom::createArrays(simnfo->n_atoms);
420	<	the_atoms = new Atom*[simnfo->n_atoms];
421	<	the_molecules = new Molecule[simnfo->n_mol];
422	<	int molIndex;
423	<
424	<	// initialize the molecule's stampID's
425	<
426	<	#ifdef IS_MPI
938	>	void SimSetup::makeOutNames( void ){
939
940	+	int k;
941
429	–	molIndex = 0;
430	–	for(i=0; i<mpiSim->getTotNmol(); i++){
431	–
432	–	if(mol2proc[i] == worldRank ){
433	–	the_molecules[molIndex].setStampID( molCompType[i] );
434	–	the_molecules[molIndex].setMyIndex( molIndex );
435	–	the_molecules[molIndex].setGlobalIndex( i );
436	–	molIndex++;
437	–	}
438	–	}
439	–
440	–	#else // is_mpi
942
943	<	molIndex = 0;
443	<	globalAtomIndex = 0;
444	<	for(i=0; i<n_components; i++){
445	<	for(j=0; j<components_nmol[i]; j++ ){
446	<	the_molecules[molIndex].setStampID( i );
447	<	the_molecules[molIndex].setMyIndex( molIndex );
448	<	the_molecules[molIndex].setGlobalIndex( molIndex );
449	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
450	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
451	<	globalAtomIndex++;
452	<	}
453	<	molIndex++;
454	<	}
455	<	}
456	<
943	>	for(k=0; k<nInfo; k++){
944
945	+	#ifdef IS_MPI
946	+	if( worldRank == 0 ){
947		#endif // is_mpi
948	+
949	+	if( globals->haveFinalConfig() ){
950	+	strcpy( info[k].finalName, globals->getFinalConfig() );
951	+	}
952	+	else{
953	+	strcpy( info[k].finalName, inFileName );
954	+	char* endTest;
955	+	int nameLength = strlen( info[k].finalName );
956	+	endTest = &(info[k].finalName[nameLength - 5]);
957	+	if( !strcmp( endTest, ".bass" ) ){
958	+	strcpy( endTest, ".eor" );
959	+	}
960	+	else if( !strcmp( endTest, ".BASS" ) ){
961	+	strcpy( endTest, ".eor" );
962	+	}
963	+	else{
964	+	endTest = &(info[k].finalName[nameLength - 4]);
965	+	if( !strcmp( endTest, ".bss" ) ){
966	+	strcpy( endTest, ".eor" );
967	+	}
968	+	else if( !strcmp( endTest, ".mdl" ) ){
969	+	strcpy( endTest, ".eor" );
970	+	}
971	+	else{
972	+	strcat( info[k].finalName, ".eor" );
973	+	}
974	+	}
975	+	}
976	+
977	+	// make the sample and status out names
978	+
979	+	strcpy( info[k].sampleName, inFileName );
980	+	char* endTest;
981	+	int nameLength = strlen( info[k].sampleName );
982	+	endTest = &(info[k].sampleName[nameLength - 5]);
983	+	if( !strcmp( endTest, ".bass" ) ){
984	+	strcpy( endTest, ".dump" );
985	+	}
986	+	else if( !strcmp( endTest, ".BASS" ) ){
987	+	strcpy( endTest, ".dump" );
988	+	}
989	+	else{
990	+	endTest = &(info[k].sampleName[nameLength - 4]);
991	+	if( !strcmp( endTest, ".bss" ) ){
992	+	strcpy( endTest, ".dump" );
993	+	}
994	+	else if( !strcmp( endTest, ".mdl" ) ){
995	+	strcpy( endTest, ".dump" );
996	+	}
997	+	else{
998	+	strcat( info[k].sampleName, ".dump" );
999	+	}
1000	+	}
1001	+
1002	+	strcpy( info[k].statusName, inFileName );
1003	+	nameLength = strlen( info[k].statusName );
1004	+	endTest = &(info[k].statusName[nameLength - 5]);
1005	+	if( !strcmp( endTest, ".bass" ) ){
1006	+	strcpy( endTest, ".stat" );
1007	+	}
1008	+	else if( !strcmp( endTest, ".BASS" ) ){
1009	+	strcpy( endTest, ".stat" );
1010	+	}
1011	+	else{
1012	+	endTest = &(info[k].statusName[nameLength - 4]);
1013	+	if( !strcmp( endTest, ".bss" ) ){
1014	+	strcpy( endTest, ".stat" );
1015	+	}
1016	+	else if( !strcmp( endTest, ".mdl" ) ){
1017	+	strcpy( endTest, ".stat" );
1018	+	}
1019	+	else{
1020	+	strcat( info[k].statusName, ".stat" );
1021	+	}
1022	+	}
1023	+
1024	+	#ifdef IS_MPI
1025	+	}
1026	+	#endif // is_mpi
1027	+	}
1028	+	}
1029
1030
1031	<	if( simnfo->n_SRI ){
1032	<
1033	<	Exclude::createArray(simnfo->n_SRI);
1034	<	the_excludes = new Exclude*[simnfo->n_SRI];
1035	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1036	<	simnfo->globalExcludes = new int;
1037	<	simnfo->n_exclude = simnfo->n_SRI;
468	<	}
469	<	else{
470	<
471	<	Exclude::createArray( 1 );
472	<	the_excludes = new Exclude*;
473	<	the_excludes[0] = new Exclude(0);
474	<	the_excludes[0]->setPair( 0,0 );
475	<	simnfo->globalExcludes = new int;
476	<	simnfo->globalExcludes[0] = 0;
477	<	simnfo->n_exclude = 0;
478	<	}
1031	>	void SimSetup::sysObjectsCreation( void ){
1032	>
1033	>	int i,k;
1034	>
1035	>	// create the forceField
1036	>
1037	>	createFF();
1038
1039	<	// set the arrays into the SimInfo object
1039	>	// extract componentList
1040
1041	<	simnfo->atoms = the_atoms;
483	<	simnfo->molecules = the_molecules;
484	<	simnfo->nGlobalExcludes = 0;
485	<	simnfo->excludes = the_excludes;
1041	>	compList();
1042
1043	+	// calc the number of atoms, bond, bends, and torsions
1044
1045	<	// get some of the tricky things that may still be in the globals
1045	>	calcSysValues();
1046
1047	<	double boxVector[3];
1048	<	if( the_globals->haveBox() ){
1049	<	boxVector[0] = the_globals->getBox();
1050	<	boxVector[1] = the_globals->getBox();
1051	<	boxVector[2] = the_globals->getBox();
1052	<
1053	<	simnfo->setBox( boxVector );
1047	>	#ifdef IS_MPI
1048	>	// divide the molecules among the processors
1049	>
1050	>	mpiMolDivide();
1051	>	#endif //is_mpi
1052	>
1053	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1054	>
1055	>	makeSysArrays();
1056	>
1057	>	// make and initialize the molecules (all but atomic coordinates)
1058	>
1059	>	makeMolecules();
1060	>
1061	>	for(k=0; k<nInfo; k++){
1062	>	info[k].identArray = new int[info[k].n_atoms];
1063	>	for(i=0; i<info[k].n_atoms; i++){
1064	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1065	>	}
1066		}
1067	<	else if( the_globals->haveDensity() ){
1067	>	}
1068
500	–	double vol;
501	–	vol = (double)tot_nmol / the_globals->getDensity();
502	–	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
503	–	boxVector[1] = boxVector[0];
504	–	boxVector[2] = boxVector[0];
1069
1070	<	simnfo->setBox( boxVector );
507	<	}
508	<	else{
509	<	if( !the_globals->haveBoxX() ){
510	<	sprintf( painCave.errMsg,
511	<	"SimSetup error, no periodic BoxX size given.\n" );
512	<	painCave.isFatal = 1;
513	<	simError();
514	<	}
515	<	boxVector[0] = the_globals->getBoxX();
1070	>	void SimSetup::createFF( void ){
1071
1072	<	if( !the_globals->haveBoxY() ){
518	<	sprintf( painCave.errMsg,
519	<	"SimSetup error, no periodic BoxY size given.\n" );
520	<	painCave.isFatal = 1;
521	<	simError();
522	<	}
523	<	boxVector[1] = the_globals->getBoxY();
1072	>	switch( ffCase ){
1073
1074	<	if( !the_globals->haveBoxZ() ){
1075	<	sprintf( painCave.errMsg,
1076	<	"SimSetup error, no periodic BoxZ size given.\n" );
528	<	painCave.isFatal = 1;
529	<	simError();
530	<	}
531	<	boxVector[2] = the_globals->getBoxZ();
1074	>	case FF_DUFF:
1075	>	the_ff = new DUFF();
1076	>	break;
1077
1078	<	simnfo->setBox( boxVector );
1078	>	case FF_LJ:
1079	>	the_ff = new LJFF();
1080	>	break;
1081	>
1082	>	case FF_EAM:
1083	>	the_ff = new EAM_FF();
1084	>	break;
1085	>
1086	>	default:
1087	>	sprintf( painCave.errMsg,
1088	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1089	>	painCave.isFatal = 1;
1090	>	simError();
1091		}
1092
1093		#ifdef IS_MPI
1094	<	strcpy( checkPointMsg, "Box size set up" );
1094	>	strcpy( checkPointMsg, "ForceField creation successful" );
1095		MPIcheckPoint();
1096		#endif // is_mpi
1097
1098	+	}
1099
542	–	// initialize the arrays
1100
1101	<	the_ff->setSimInfo( simnfo );
1101	>	void SimSetup::compList( void ){
1102
1103	<	makeMolecules();
1104	<	simnfo->identArray = new int[simnfo->n_atoms];
1105	<	for(i=0; i<simnfo->n_atoms; i++){
1106	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
1107	<	}
1103	>	int i;
1104	>	char* id;
1105	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1106	>	LinkedMolStamp* currentStamp = NULL;
1107	>	comp_stamps = new MoleculeStamp*[n_components];
1108
1109	<	if (the_globals->getUseRF() ) {
1110	<	simnfo->useReactionField = 1;
1109	>	// make an array of molecule stamps that match the components used.
1110	>	// also extract the used stamps out into a separate linked list
1111
1112	<	if( !the_globals->haveECR() ){
1113	<	sprintf( painCave.errMsg,
1114	<	"SimSetup Warning: using default value of 1/2 the smallest "
1115	<	"box length for the electrostaticCutoffRadius.\n"
1116	<	"I hope you have a very fast processor!\n");
1117	<	painCave.isFatal = 0;
1118	<	simError();
562	<	double smallest;
563	<	smallest = simnfo->boxLx;
564	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
565	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
566	<	simnfo->ecr = 0.5 * smallest;
567	<	} else {
568	<	simnfo->ecr        = the_globals->getECR();
569	<	}
1112	>	for(i=0; i<nInfo; i++){
1113	>	info[i].nComponents = n_components;
1114	>	info[i].componentsNmol = components_nmol;
1115	>	info[i].compStamps = comp_stamps;
1116	>	info[i].headStamp = headStamp;
1117	>	}
1118	>
1119
1120	<	if( !the_globals->haveEST() ){
1121	<	sprintf( painCave.errMsg,
1122	<	"SimSetup Warning: using default value of 0.05 * the "
1123	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
575	<	);
576	<	painCave.isFatal = 0;
577	<	simError();
578	<	simnfo->est = 0.05 * simnfo->ecr;
579	<	} else {
580	<	simnfo->est        = the_globals->getEST();
581	<	}
1120	>	for( i=0; i<n_components; i++ ){
1121	>
1122	>	id = the_components[i]->getType();
1123	>	comp_stamps[i] = NULL;
1124
1125	<	if(!the_globals->haveDielectric() ){
1126	<	sprintf( painCave.errMsg,
1127	<	"SimSetup Error: You are trying to use Reaction Field without"
1128	<	"setting a dielectric constant!\n"
587	<	);
588	<	painCave.isFatal = 1;
589	<	simError();
590	<	}
591	<	simnfo->dielectric = the_globals->getDielectric();
592	<	} else {
593	<	if (usesDipoles) {
1125	>	// check to make sure the component isn't already in the list
1126	>
1127	>	comp_stamps[i] = headStamp->match( id );
1128	>	if( comp_stamps[i] == NULL ){
1129
1130	<	if( !the_globals->haveECR() ){
596	<	sprintf( painCave.errMsg,
597	<	"SimSetup Warning: using default value of 1/2 the smallest "
598	<	"box length for the electrostaticCutoffRadius.\n"
599	<	"I hope you have a very fast processor!\n");
600	<	painCave.isFatal = 0;
601	<	simError();
602	<	double smallest;
603	<	smallest = simnfo->boxLx;
604	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
605	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
606	<	simnfo->ecr = 0.5 * smallest;
607	<	} else {
608	<	simnfo->ecr        = the_globals->getECR();
609	<	}
1130	>	// extract the component from the list;
1131
1132	<	if( !the_globals->haveEST() ){
1133	<	sprintf( painCave.errMsg,
1134	<	"SimSetup Warning: using default value of 5%% of the "
1135	<	"electrostaticCutoffRadius for the "
1136	<	"electrostaticSkinThickness\n"
1137	<	);
1138	<	painCave.isFatal = 0;
1139	<	simError();
619	<	simnfo->est = 0.05 * simnfo->ecr;
620	<	} else {
621	<	simnfo->est        = the_globals->getEST();
1132	>	currentStamp = stamps->extractMolStamp( id );
1133	>	if( currentStamp == NULL ){
1134	>	sprintf( painCave.errMsg,
1135	>	"SimSetup error: Component \"%s\" was not found in the "
1136	>	"list of declared molecules\n",
1137	>	id );
1138	>	painCave.isFatal = 1;
1139	>	simError();
1140		}
1141	+
1142	+	headStamp->add( currentStamp );
1143	+	comp_stamps[i] = headStamp->match( id );
1144		}
1145	<	}
1145	>	}
1146
1147		#ifdef IS_MPI
1148	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
1148	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1149		MPIcheckPoint();
1150		#endif // is_mpi
1151
631	–	if( the_globals->haveInitialConfig() ){
632	–
633	–	InitializeFromFile* fileInit;
634	–	#ifdef IS_MPI // is_mpi
635	–	if( worldRank == 0 ){
636	–	#endif //is_mpi
637	–	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
638	–	#ifdef IS_MPI
639	–	}else fileInit = new InitializeFromFile( NULL );
640	–	#endif
641	–	fileInit->read_xyz( simnfo ); // default velocities on
1152
1153	<	delete fileInit;
644	<	}
645	<	else{
1153	>	}
1154
1155	<	#ifdef IS_MPI
1156	<
649	<	// no init from bass
1155	>	void SimSetup::calcSysValues( void ){
1156	>	int i, j, k;
1157
1158	<	sprintf( painCave.errMsg,
652	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
653	<	painCave.isFatal;
654	<	simError();
1158	>	int *molMembershipArray;
1159
1160	<	#else
1160	>	tot_atoms = 0;
1161	>	tot_bonds = 0;
1162	>	tot_bends = 0;
1163	>	tot_torsions = 0;
1164	>	for( i=0; i<n_components; i++ ){
1165	>
1166	>	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1167	>	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1168	>	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1169	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1170	>	}
1171	>
1172	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1173	>	molMembershipArray = new int[tot_atoms];
1174	>
1175	>	for(i=0; i<nInfo; i++){
1176	>	info[i].n_atoms = tot_atoms;
1177	>	info[i].n_bonds = tot_bonds;
1178	>	info[i].n_bends = tot_bends;
1179	>	info[i].n_torsions = tot_torsions;
1180	>	info[i].n_SRI = tot_SRI;
1181	>	info[i].n_mol = tot_nmol;
1182	>
1183	>	info[i].molMembershipArray = molMembershipArray;
1184	>	}
1185	>	}
1186
658	–	initFromBass();
659	–
660	–
661	–	#endif
662	–	}
663	–
1187		#ifdef IS_MPI
1188	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1188	>
1189	>	void SimSetup::mpiMolDivide( void ){
1190	>
1191	>	int i, j, k;
1192	>	int localMol, allMol;
1193	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1194	>
1195	>	mpiSim = new mpiSimulation( info );
1196	>
1197	>	globalIndex = mpiSim->divideLabor();
1198	>
1199	>	// set up the local variables
1200	>
1201	>	mol2proc = mpiSim->getMolToProcMap();
1202	>	molCompType = mpiSim->getMolComponentType();
1203	>
1204	>	allMol = 0;
1205	>	localMol = 0;
1206	>	local_atoms = 0;
1207	>	local_bonds = 0;
1208	>	local_bends = 0;
1209	>	local_torsions = 0;
1210	>	globalAtomIndex = 0;
1211	>
1212	>
1213	>	for( i=0; i<n_components; i++ ){
1214	>
1215	>	for( j=0; j<components_nmol[i]; j++ ){
1216	>
1217	>	if( mol2proc[allMol] == worldRank ){
1218	>
1219	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1220	>	local_bonds +=    comp_stamps[i]->getNBonds();
1221	>	local_bends +=    comp_stamps[i]->getNBends();
1222	>	local_torsions += comp_stamps[i]->getNTorsions();
1223	>	localMol++;
1224	>	}
1225	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1226	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1227	>	globalAtomIndex++;
1228	>	}
1229	>
1230	>	allMol++;
1231	>	}
1232	>	}
1233	>	local_SRI = local_bonds + local_bends + local_torsions;
1234	>
1235	>	info[0].n_atoms = mpiSim->getMyNlocal();
1236	>
1237	>	if( local_atoms != info[0].n_atoms ){
1238	>	sprintf( painCave.errMsg,
1239	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1240	>	" localAtom (%d) are not equal.\n",
1241	>	info[0].n_atoms,
1242	>	local_atoms );
1243	>	painCave.isFatal = 1;
1244	>	simError();
1245	>	}
1246	>
1247	>	info[0].n_bonds = local_bonds;
1248	>	info[0].n_bends = local_bends;
1249	>	info[0].n_torsions = local_torsions;
1250	>	info[0].n_SRI = local_SRI;
1251	>	info[0].n_mol = localMol;
1252	>
1253	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1254		MPIcheckPoint();
1255	+	}
1256	+
1257		#endif // is_mpi
1258
1259
1260	<
1261	<
672	<
1260	>	void SimSetup::makeSysArrays( void ){
1261	>	int i, j, k, l;
1262
1263	+	Atom** the_atoms;
1264	+	Molecule* the_molecules;
1265	+	Exclude** the_excludes;
1266	+
1267
1268	+	for(l=0; l<nInfo; l++){
1269	+
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
676	–	if( worldRank == 0 ){
677	–	#endif // is_mpi
1279
679	–	if( the_globals->haveFinalConfig() ){
680	–	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
681	–	}
682	–	else{
683	–	strcpy( simnfo->finalName, inFileName );
684	–	char* endTest;
685	–	int nameLength = strlen( simnfo->finalName );
686	–	endTest = &(simnfo->finalName[nameLength - 5]);
687	–	if( !strcmp( endTest, ".bass" ) ){
688	–	strcpy( endTest, ".eor" );
689	–	}
690	–	else if( !strcmp( endTest, ".BASS" ) ){
691	–	strcpy( endTest, ".eor" );
692	–	}
693	–	else{
694	–	endTest = &(simnfo->finalName[nameLength - 4]);
695	–	if( !strcmp( endTest, ".bss" ) ){
696	–	strcpy( endTest, ".eor" );
697	–	}
698	–	else if( !strcmp( endTest, ".mdl" ) ){
699	–	strcpy( endTest, ".eor" );
700	–	}
701	–	else{
702	–	strcat( simnfo->finalName, ".eor" );
703	–	}
704	–	}
705	–	}
1280
1281	<	// make the sample and status out names
1281	>	molIndex = 0;
1282	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1283
1284	<	strcpy( simnfo->sampleName, inFileName );
1285	<	char* endTest;
1286	<	int nameLength = strlen( simnfo->sampleName );
1287	<	endTest = &(simnfo->sampleName[nameLength - 5]);
1288	<	if( !strcmp( endTest, ".bass" ) ){
714	<	strcpy( endTest, ".dump" );
715	<	}
716	<	else if( !strcmp( endTest, ".BASS" ) ){
717	<	strcpy( endTest, ".dump" );
718	<	}
719	<	else{
720	<	endTest = &(simnfo->sampleName[nameLength - 4]);
721	<	if( !strcmp( endTest, ".bss" ) ){
722	<	strcpy( endTest, ".dump" );
1284	>	if(mol2proc[i] == worldRank ){
1285	>	the_molecules[molIndex].setStampID( molCompType[i] );
1286	>	the_molecules[molIndex].setMyIndex( molIndex );
1287	>	the_molecules[molIndex].setGlobalIndex( i );
1288	>	molIndex++;
1289		}
724	–	else if( !strcmp( endTest, ".mdl" ) ){
725	–	strcpy( endTest, ".dump" );
726	–	}
727	–	else{
728	–	strcat( simnfo->sampleName, ".dump" );
729	–	}
1290		}
1291
1292	<	strcpy( simnfo->statusName, inFileName );
1293	<	nameLength = strlen( simnfo->statusName );
1294	<	endTest = &(simnfo->statusName[nameLength - 5]);
1295	<	if( !strcmp( endTest, ".bass" ) ){
1296	<	strcpy( endTest, ".stat" );
1297	<	}
1298	<	else if( !strcmp( endTest, ".BASS" ) ){
1299	<	strcpy( endTest, ".stat" );
1300	<	}
1301	<	else{
1302	<	endTest = &(simnfo->statusName[nameLength - 4]);
1303	<	if( !strcmp( endTest, ".bss" ) ){
1304	<	strcpy( endTest, ".stat" );
1292	>	#else // is_mpi
1293	>
1294	>	molIndex = 0;
1295	>	globalAtomIndex = 0;
1296	>	for(i=0; i<n_components; i++){
1297	>	for(j=0; j<components_nmol[i]; j++ ){
1298	>	the_molecules[molIndex].setStampID( i );
1299	>	the_molecules[molIndex].setMyIndex( molIndex );
1300	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1301	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1302	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1303	>	globalAtomIndex++;
1304	>	}
1305	>	molIndex++;
1306		}
746	–	else if( !strcmp( endTest, ".mdl" ) ){
747	–	strcpy( endTest, ".stat" );
748	–	}
749	–	else{
750	–	strcat( simnfo->statusName, ".stat" );
751	–	}
1307		}
1308
1309	<	#ifdef IS_MPI
755	<	}
1309	>
1310		#endif // is_mpi
757	–
758	–	// set the status, sample, and themal kick times
759	–
760	–	if( the_globals->haveSampleTime() ){
761	–	simnfo->sampleTime = the_globals->getSampleTime();
762	–	simnfo->statusTime = simnfo->sampleTime;
763	–	simnfo->thermalTime = simnfo->sampleTime;
764	–	}
765	–	else{
766	–	simnfo->sampleTime = the_globals->getRunTime();
767	–	simnfo->statusTime = simnfo->sampleTime;
768	–	simnfo->thermalTime = simnfo->sampleTime;
769	–	}
1311
771	–	if( the_globals->haveStatusTime() ){
772	–	simnfo->statusTime = the_globals->getStatusTime();
773	–	}
1312
1313	<	if( the_globals->haveThermalTime() ){
1314	<	simnfo->thermalTime = the_globals->getThermalTime();
1315	<	}
1313	>	if( info[l].n_SRI ){
1314	>
1315	>	Exclude::createArray(info[l].n_SRI);
1316	>	the_excludes = new Exclude*[info[l].n_SRI];
1317	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1318	>	the_excludes[ex] = new Exclude(ex);
1319	>	}
1320	>	info[l].globalExcludes = new int;
1321	>	info[l].n_exclude = info[l].n_SRI;
1322	>	}
1323	>	else{
1324	>
1325	>	Exclude::createArray( 1 );
1326	>	the_excludes = new Exclude*;
1327	>	the_excludes[0] = new Exclude(0);
1328	>	the_excludes[0]->setPair( 0,0 );
1329	>	info[l].globalExcludes = new int;
1330	>	info[l].globalExcludes[0] = 0;
1331	>	info[l].n_exclude = 0;
1332	>	}
1333
1334	<	// check for the temperature set flag
1334	>	// set the arrays into the SimInfo object
1335
1336	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
1336	>	info[l].atoms = the_atoms;
1337	>	info[l].molecules = the_molecules;
1338	>	info[l].nGlobalExcludes = 0;
1339	>	info[l].excludes = the_excludes;
1340
1341	+	the_ff->setSimInfo( info );
1342	+
1343	+	}
1344	+	}
1345
1346	<	// make the integrator
785	<
786	<
787	<	NVT*  myNVT = NULL;
788	<	NPTi* myNPTi = NULL;
789	<	NPTf* myNPTf = NULL;
790	<	NPTim* myNPTim = NULL;
1346	>	void SimSetup::makeIntegrator( void ){
1347
1348	<	switch( ensembleCase ){
1348	>	int k;
1349
1350	<	case NVE_ENS:
1351	<	new NVE( simnfo, the_ff );
1352	<	break;
1353	<
1354	<	case NVT_ENS:
1355	<	myNVT = new NVT( simnfo, the_ff );
1356	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
801	<
802	<	if (the_globals->haveTauThermostat())
803	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
804	<
805	<	else {
806	<	sprintf( painCave.errMsg,
807	<	"SimSetup error: If you use the NVT\n"
808	<	"    ensemble, you must set tauThermostat.\n");
809	<	painCave.isFatal = 1;
810	<	simError();
811	<	}
812	<	break;
813	<
814	<	case NPTi_ENS:
815	<	myNPTi = new NPTi( simnfo, the_ff );
816	<	myNPTi->setTargetTemp( the_globals->getTargetTemp());
817	<
818	<	if (the_globals->haveTargetPressure())
819	<	myNPTi->setTargetPressure(the_globals->getTargetPressure());
820	<	else {
821	<	sprintf( painCave.errMsg,
822	<	"SimSetup error: If you use a constant pressure\n"
823	<	"    ensemble, you must set targetPressure in the BASS file.\n");
824	<	painCave.isFatal = 1;
825	<	simError();
826	<	}
1350	>	NVT<RealIntegrator>*  myNVT = NULL;
1351	>	NPTi<RealIntegrator>* myNPTi = NULL;
1352	>	NPTf<RealIntegrator>* myNPTf = NULL;
1353	>	NPTim<RealIntegrator>* myNPTim = NULL;
1354	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1355	>
1356	>	for(k=0; k<nInfo; k++){
1357
1358	<	if( the_globals->haveTauThermostat() )
1359	<	myNPTi->setTauThermostat( the_globals->getTauThermostat() );
1360	<	else{
1361	<	sprintf( painCave.errMsg,
1362	<	"SimSetup error: If you use an NPT\n"
1363	<	"    ensemble, you must set tauThermostat.\n");
1364	<	painCave.isFatal = 1;
835	<	simError();
836	<	}
1358	>	switch( ensembleCase ){
1359	>
1360	>	case NVE_ENS:
1361	>	if (haveZConstraint){
1362	>	setupZConstraint();
1363	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1364	>	}
1365
1366	<	if( the_globals->haveTauBarostat() )
1367	<	myNPTi->setTauBarostat( the_globals->getTauBarostat() );
1368	<	else{
1369	<	sprintf( painCave.errMsg,
1370	<	"SimSetup error: If you use an NPT\n"
1371	<	"    ensemble, you must set tauBarostat.\n");
1372	<	painCave.isFatal = 1;
1373	<	simError();
1374	<	}
1375	<	break;
1366	>	else
1367	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1368	>	break;
1369	>
1370	>	case NVT_ENS:
1371	>	if (haveZConstraint){
1372	>	setupZConstraint();
1373	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1374	>	}
1375	>	else
1376	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1377
1378	<	case NPTf_ENS:
1379	<	myNPTf = new NPTf( simnfo, the_ff );
1380	<	myNPTf->setTargetTemp( the_globals->getTargetTemp());
1378	>	myNVT->setTargetTemp(globals->getTargetTemp());
1379	>
1380	>	if (globals->haveTauThermostat())
1381	>	myNVT->setTauThermostat(globals->getTauThermostat());
1382	>
1383	>	else {
1384	>	sprintf( painCave.errMsg,
1385	>	"SimSetup error: If you use the NVT\n"
1386	>	"    ensemble, you must set tauThermostat.\n");
1387	>	painCave.isFatal = 1;
1388	>	simError();
1389	>	}
1390	>	break;
1391	>
1392	>	case NPTi_ENS:
1393	>	if (haveZConstraint){
1394	>	setupZConstraint();
1395	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1396	>	}
1397	>	else
1398	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1399
1400	<	if (the_globals->haveTargetPressure())
1401	<	myNPTf->setTargetPressure(the_globals->getTargetPressure());
1402	<	else {
1403	<	sprintf( painCave.errMsg,
1404	<	"SimSetup error: If you use a constant pressure\n"
1405	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1406	<	painCave.isFatal = 1;
1407	<	simError();
1408	<	}
1409	<
1410	<	if( the_globals->haveTauThermostat() )
1411	<	myNPTf->setTauThermostat( the_globals->getTauThermostat() );
1412	<	else{
1413	<	sprintf( painCave.errMsg,
1414	<	"SimSetup error: If you use an NPT\n"
1400	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1401	>
1402	>	if (globals->haveTargetPressure())
1403	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1404	>	else {
1405	>	sprintf( painCave.errMsg,
1406	>	"SimSetup error: If you use a constant pressure\n"
1407	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1408	>	painCave.isFatal = 1;
1409	>	simError();
1410	>	}
1411	>
1412	>	if( globals->haveTauThermostat() )
1413	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1414	>	else{
1415	>	sprintf( painCave.errMsg,
1416	>	"SimSetup error: If you use an NPT\n"
1417	>	"    ensemble, you must set tauThermostat.\n");
1418	>	painCave.isFatal = 1;
1419	>	simError();
1420	>	}
1421	>
1422	>	if( globals->haveTauBarostat() )
1423	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1424	>	else{
1425	>	sprintf( painCave.errMsg,
1426	>	"SimSetup error: If you use an NPT\n"
1427	>	"    ensemble, you must set tauBarostat.\n");
1428	>	painCave.isFatal = 1;
1429	>	simError();
1430	>	}
1431	>	break;
1432	>
1433	>	case NPTf_ENS:
1434	>	if (haveZConstraint){
1435	>	setupZConstraint();
1436	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1437	>	}
1438	>	else
1439	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1440	>
1441	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1442	>
1443	>	if (globals->haveTargetPressure())
1444	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1445	>	else {
1446	>	sprintf( painCave.errMsg,
1447	>	"SimSetup error: If you use a constant pressure\n"
1448	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1449	>	painCave.isFatal = 1;
1450	>	simError();
1451	>	}
1452	>
1453	>	if( globals->haveTauThermostat() )
1454	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1455	>	else{
1456	>	sprintf( painCave.errMsg,
1457	>	"SimSetup error: If you use an NPT\n"
1458		"    ensemble, you must set tauThermostat.\n");
1459	<	painCave.isFatal = 1;
1460	<	simError();
1461	<	}
1459	>	painCave.isFatal = 1;
1460	>	simError();
1461	>	}
1462	>
1463	>	if( globals->haveTauBarostat() )
1464	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
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	>	break;
1473	>
1474	>	case NPTim_ENS:
1475	>	if (haveZConstraint){
1476	>	setupZConstraint();
1477	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1478	>	}
1479	>	else
1480	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1481
1482	<	if( the_globals->haveTauBarostat() )
1483	<	myNPTf->setTauBarostat( the_globals->getTauBarostat() );
1484	<	else{
1482	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1483	>
1484	>	if (globals->haveTargetPressure())
1485	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1486	>	else {
1487	>	sprintf( painCave.errMsg,
1488	>	"SimSetup error: If you use a constant pressure\n"
1489	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1490	>	painCave.isFatal = 1;
1491	>	simError();
1492	>	}
1493	>
1494	>	if( globals->haveTauThermostat() )
1495	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1496	>	else{
1497	>	sprintf( painCave.errMsg,
1498	>	"SimSetup error: If you use an NPT\n"
1499	>	"    ensemble, you must set tauThermostat.\n");
1500	>	painCave.isFatal = 1;
1501	>	simError();
1502	>	}
1503	>
1504	>	if( globals->haveTauBarostat() )
1505	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1506	>	else{
1507		sprintf( painCave.errMsg,
1508		"SimSetup error: If you use an NPT\n"
1509		"    ensemble, you must set tauBarostat.\n");
1510		painCave.isFatal = 1;
1511		simError();
1512	<	}
1513	<	break;
1514	<
1515	<	case NPTim_ENS:
1516	<	myNPTim = new NPTim( simnfo, the_ff );
1517	<	myNPTim->setTargetTemp( the_globals->getTargetTemp());
1512	>	}
1513	>	break;
1514	>
1515	>	case NPTfm_ENS:
1516	>	if (haveZConstraint){
1517	>	setupZConstraint();
1518	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1519	>	}
1520	>	else
1521	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1522
1523	<	if (the_globals->haveTargetPressure())
1524	<	myNPTim->setTargetPressure(the_globals->getTargetPressure());
1525	<	else {
1523	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1524	>
1525	>	if (globals->haveTargetPressure())
1526	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1527	>	else {
1528	>	sprintf( painCave.errMsg,
1529	>	"SimSetup error: If you use a constant pressure\n"
1530	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1531	>	painCave.isFatal = 1;
1532	>	simError();
1533	>	}
1534	>
1535	>	if( globals->haveTauThermostat() )
1536	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1537	>	else{
1538	>	sprintf( painCave.errMsg,
1539	>	"SimSetup error: If you use an NPT\n"
1540	>	"    ensemble, you must set tauThermostat.\n");
1541	>	painCave.isFatal = 1;
1542	>	simError();
1543	>	}
1544	>
1545	>	if( globals->haveTauBarostat() )
1546	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1547	>	else{
1548	>	sprintf( painCave.errMsg,
1549	>	"SimSetup error: If you use an NPT\n"
1550	>	"    ensemble, you must set tauBarostat.\n");
1551	>	painCave.isFatal = 1;
1552	>	simError();
1553	>	}
1554	>	break;
1555	>
1556	>	default:
1557		sprintf( painCave.errMsg,
1558	<	"SimSetup error: If you use a constant pressure\n"
893	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1558	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1559		painCave.isFatal = 1;
1560		simError();
1561		}
897	–
898	–	if( the_globals->haveTauThermostat() )
899	–	myNPTim->setTauThermostat( the_globals->getTauThermostat() );
900	–	else{
901	–	sprintf( painCave.errMsg,
902	–	"SimSetup error: If you use an NPT\n"
903	–	"    ensemble, you must set tauThermostat.\n");
904	–	painCave.isFatal = 1;
905	–	simError();
906	–	}
907	–
908	–	if( the_globals->haveTauBarostat() )
909	–	myNPTim->setTauBarostat( the_globals->getTauBarostat() );
910	–	else{
911	–	sprintf( painCave.errMsg,
912	–	"SimSetup error: If you use an NPT\n"
913	–	"    ensemble, you must set tauBarostat.\n");
914	–	painCave.isFatal = 1;
915	–	simError();
916	–	}
917	–	break;
918	–
919	–
920	–
921	–	default:
922	–	sprintf( painCave.errMsg,
923	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
924	–	painCave.isFatal = 1;
925	–	simError();
1562		}
1563	+	}
1564
1565	+	void SimSetup::initFortran( void ){
1566
1567	<	#ifdef IS_MPI
930	<	mpiSim->mpiRefresh();
931	<	#endif
932	<
933	<	// initialize the Fortran
934	<
935	<
936	<	simnfo->refreshSim();
1567	>	info[0].refreshSim();
1568
1569	<	if( !strcmp( simnfo->mixingRule, "standard") ){
1569	>	if( !strcmp( info[0].mixingRule, "standard") ){
1570		the_ff->initForceField( LB_MIXING_RULE );
1571		}
1572	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
1572	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1573		the_ff->initForceField( EXPLICIT_MIXING_RULE );
1574		}
1575		else{
1576		sprintf( painCave.errMsg,
1577		"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1578	<	simnfo->mixingRule );
1578	>	info[0].mixingRule );
1579		painCave.isFatal = 1;
1580		simError();
1581		}
#	Line 955 | Line 1586 | void SimSetup::createSim( void ){
1586		"Successfully intialized the mixingRule for Fortran." );
1587		MPIcheckPoint();
1588		#endif // is_mpi
1589	+
1590		}
1591
1592	+	void SimSetup::setupZConstraint()
1593	+	{
1594	+	int k;
1595
1596	<	void SimSetup::makeMolecules( void ){
962	<
963	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
964	<	molInit info;
965	<	DirectionalAtom* dAtom;
966	<	LinkedAssign* extras;
967	<	LinkedAssign* current_extra;
968	<	AtomStamp* currentAtom;
969	<	BondStamp* currentBond;
970	<	BendStamp* currentBend;
971	<	TorsionStamp* currentTorsion;
972	<
973	<	bond_pair* theBonds;
974	<	bend_set* theBends;
975	<	torsion_set* theTorsions;
976	<
977	<
978	<	//init the forceField paramters
979	<
980	<	the_ff->readParams();
981	<
982	<
983	<	// init the atoms
984	<
985	<	double ux, uy, uz, u, uSqr;
986	<
987	<	atomOffset = 0;
988	<	excludeOffset = 0;
989	<	for(i=0; i<simnfo->n_mol; i++){
1596	>	for(k=0; k<nInfo; k++){
1597
1598	<	stampID = the_molecules[i].getStampID();
992	<
993	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
994	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
995	<	info.nBends    = comp_stamps[stampID]->getNBends();
996	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
997	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
998	<
999	<	info.myAtoms = &the_atoms[atomOffset];
1000	<	info.myExcludes = &the_excludes[excludeOffset];
1001	<	info.myBonds = new Bond*[info.nBonds];
1002	<	info.myBends = new Bend*[info.nBends];
1003	<	info.myTorsions = new Torsion*[info.nTorsions];
1004	<
1005	<	theBonds = new bond_pair[info.nBonds];
1006	<	theBends = new bend_set[info.nBends];
1007	<	theTorsions = new torsion_set[info.nTorsions];
1008	<
1009	<	// make the Atoms
1010	<
1011	<	for(j=0; j<info.nAtoms; j++){
1598	>	if(globals->haveZConsTime()){
1599
1600	<	currentAtom = comp_stamps[stampID]->getAtom( j );
1601	<	if( currentAtom->haveOrientation() ){
1602	<
1603	<	dAtom = new DirectionalAtom(j + atomOffset);
1604	<	simnfo->n_oriented++;
1605	<	info.myAtoms[j] = dAtom;
1606	<
1607	<	ux = currentAtom->getOrntX();
1608	<	uy = currentAtom->getOrntY();
1609	<	uz = currentAtom->getOrntZ();
1610	<
1611	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
1612	<
1026	<	u = sqrt( uSqr );
1027	<	ux = ux / u;
1028	<	uy = uy / u;
1029	<	uz = uz / u;
1030	<
1031	<	dAtom->setSUx( ux );
1032	<	dAtom->setSUy( uy );
1033	<	dAtom->setSUz( uz );
1034	<	}
1035	<	else{
1036	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
1037	<	}
1038	<	info.myAtoms[j]->setType( currentAtom->getType() );
1600	>	//add sample time of z-constraint  into SimInfo's property list
1601	>	DoubleData* zconsTimeProp = new DoubleData();
1602	>	zconsTimeProp->setID("zconstime");
1603	>	zconsTimeProp->setData(globals->getZConsTime());
1604	>	info[k].addProperty(zconsTimeProp);
1605	>	}
1606	>	else{
1607	>	sprintf( painCave.errMsg,
1608	>	"ZConstraint error: If you use an ZConstraint\n"
1609	>	" , you must set sample time.\n");
1610	>	painCave.isFatal = 1;
1611	>	simError();
1612	>	}
1613
1614	<	#ifdef IS_MPI
1614	>	if(globals->haveIndexOfAllZConsMols()){
1615	>
1616	>	//add index of z-constraint molecules into SimInfo's property list
1617	>	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1618
1619	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
1619	>	//sort the index
1620	>	sort(tempIndex.begin(), tempIndex.end());
1621
1622	<	#endif // is_mpi
1623	<	}
1624	<
1625	<	// make the bonds
1626	<	for(j=0; j<info.nBonds; j++){
1622	>	IndexData* zconsIndex = new IndexData();
1623	>	zconsIndex->setID("zconsindex");
1624	>	zconsIndex->setIndexData(tempIndex);
1625	>	info[k].addProperty(zconsIndex);
1626	>	}
1627	>	else{
1628	>	sprintf( painCave.errMsg,
1629	>	"SimSetup error: If you use an ZConstraint\n"
1630	>	" , you must set index of z-constraint molecules.\n");
1631	>	painCave.isFatal = 1;
1632	>	simError();
1633
1050	–	currentBond = comp_stamps[stampID]->getBond( j );
1051	–	theBonds[j].a = currentBond->getA() + atomOffset;
1052	–	theBonds[j].b = currentBond->getB() + atomOffset;
1053	–
1054	–	exI = theBonds[j].a;
1055	–	exJ = theBonds[j].b;
1056	–
1057	–	// exclude_I must always be the smaller of the pair
1058	–	if( exI > exJ ){
1059	–	tempEx = exI;
1060	–	exI = exJ;
1061	–	exJ = tempEx;
1062	–	}
1063	–	#ifdef IS_MPI
1064	–	tempEx = exI;
1065	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1066	–	tempEx = exJ;
1067	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1068	–
1069	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1070	–	#else  // isn't MPI
1071	–
1072	–	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1073	–	#endif  //is_mpi
1634		}
1075	–	excludeOffset += info.nBonds;
1076	–
1077	–	//make the bends
1078	–	for(j=0; j<info.nBends; j++){
1079	–
1080	–	currentBend = comp_stamps[stampID]->getBend( j );
1081	–	theBends[j].a = currentBend->getA() + atomOffset;
1082	–	theBends[j].b = currentBend->getB() + atomOffset;
1083	–	theBends[j].c = currentBend->getC() + atomOffset;
1084	–
1085	–	if( currentBend->haveExtras() ){
1086	–
1087	–	extras = currentBend->getExtras();
1088	–	current_extra = extras;
1089	–
1090	–	while( current_extra != NULL ){
1091	–	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1092	–
1093	–	switch( current_extra->getType() ){
1094	–
1095	–	case 0:
1096	–	theBends[j].ghost =
1097	–	current_extra->getInt() + atomOffset;
1098	–	theBends[j].isGhost = 1;
1099	–	break;
1100	–
1101	–	case 1:
1102	–	theBends[j].ghost =
1103	–	(int)current_extra->getDouble() + atomOffset;
1104	–	theBends[j].isGhost = 1;
1105	–	break;
1106	–
1107	–	default:
1108	–	sprintf( painCave.errMsg,
1109	–	"SimSetup Error: ghostVectorSource was neither a "
1110	–	"double nor an int.\n"
1111	–	"-->Bend[%d] in %s\n",
1112	–	j, comp_stamps[stampID]->getID() );
1113	–	painCave.isFatal = 1;
1114	–	simError();
1115	–	}
1116	–	}
1117	–
1118	–	else{
1119	–
1120	–	sprintf( painCave.errMsg,
1121	–	"SimSetup Error: unhandled bend assignment:\n"
1122	–	"    -->%s in Bend[%d] in %s\n",
1123	–	current_extra->getlhs(),
1124	–	j, comp_stamps[stampID]->getID() );
1125	–	painCave.isFatal = 1;
1126	–	simError();
1127	–	}
1128	–
1129	–	current_extra = current_extra->getNext();
1130	–	}
1131	–	}
1132	–
1133	–	if( !theBends[j].isGhost ){
1134	–
1135	–	exI = theBends[j].a;
1136	–	exJ = theBends[j].c;
1137	–	}
1138	–	else{
1139	–
1140	–	exI = theBends[j].a;
1141	–	exJ = theBends[j].b;
1142	–	}
1143	–
1144	–	// exclude_I must always be the smaller of the pair
1145	–	if( exI > exJ ){
1146	–	tempEx = exI;
1147	–	exI = exJ;
1148	–	exJ = tempEx;
1149	–	}
1150	–	#ifdef IS_MPI
1151	–	tempEx = exI;
1152	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1153	–	tempEx = exJ;
1154	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1155	–
1156	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1157	–	#else  // isn't MPI
1158	–	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1159	–	#endif  //is_mpi
1160	–	}
1161	–	excludeOffset += info.nBends;
1162	–
1163	–	for(j=0; j<info.nTorsions; j++){
1164	–
1165	–	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1166	–	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1167	–	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1168	–	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1169	–	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1170	–
1171	–	exI = theTorsions[j].a;
1172	–	exJ = theTorsions[j].d;
1173	–
1174	–	// exclude_I must always be the smaller of the pair
1175	–	if( exI > exJ ){
1176	–	tempEx = exI;
1177	–	exI = exJ;
1178	–	exJ = tempEx;
1179	–	}
1180	–	#ifdef IS_MPI
1181	–	tempEx = exI;
1182	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1183	–	tempEx = exJ;
1184	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1185	–
1186	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1187	–	#else  // isn't MPI
1188	–	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1189	–	#endif  //is_mpi
1190	–	}
1191	–	excludeOffset += info.nTorsions;
1192	–
1635
1636	<	// send the arrays off to the forceField for init.
1637	<
1638	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1639	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1640	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1641	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1642	<
1643	<
1644	<	the_molecules[i].initialize( info );
1645	<
1646	<
1647	<	atomOffset += info.nAtoms;
1648	<	delete[] theBonds;
1207	<	delete[] theBends;
1208	<	delete[] theTorsions;
1636	>	//Determine the name of ouput file and add it into SimInfo's property list
1637	>	//Be careful, do not use inFileName, since it is a pointer which
1638	>	//point to a string at master node, and slave nodes do not contain that string
1639	>
1640	>	string zconsOutput(info[k].finalName);
1641	>
1642	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1643	>
1644	>	StringData* zconsFilename = new StringData();
1645	>	zconsFilename->setID("zconsfilename");
1646	>	zconsFilename->setData(zconsOutput);
1647	>
1648	>	info[k].addProperty(zconsFilename);
1649		}
1210	–
1211	–	#ifdef IS_MPI
1212	–	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1213	–	MPIcheckPoint();
1214	–	#endif // is_mpi
1215	–
1216	–	// clean up the forcefield
1217	–	the_ff->calcRcut();
1218	–	the_ff->cleanMe();
1219	–
1650		}
1221	–
1222	–	void SimSetup::initFromBass( void ){
1223	–
1224	–	int i, j, k;
1225	–	int n_cells;
1226	–	double cellx, celly, cellz;
1227	–	double temp1, temp2, temp3;
1228	–	int n_per_extra;
1229	–	int n_extra;
1230	–	int have_extra, done;
1231	–
1232	–	temp1 = (double)tot_nmol / 4.0;
1233	–	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1234	–	temp3 = ceil( temp2 );
1235	–
1236	–	have_extra =0;
1237	–	if( temp2 < temp3 ){ // we have a non-complete lattice
1238	–	have_extra =1;
1239	–
1240	–	n_cells = (int)temp3 - 1;
1241	–	cellx = simnfo->boxLx / temp3;
1242	–	celly = simnfo->boxLy / temp3;
1243	–	cellz = simnfo->boxLz / temp3;
1244	–	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1245	–	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1246	–	n_per_extra = (int)ceil( temp1 );
1247	–
1248	–	if( n_per_extra > 4){
1249	–	sprintf( painCave.errMsg,
1250	–	"SimSetup error. There has been an error in constructing"
1251	–	" the non-complete lattice.\n" );
1252	–	painCave.isFatal = 1;
1253	–	simError();
1254	–	}
1255	–	}
1256	–	else{
1257	–	n_cells = (int)temp3;
1258	–	cellx = simnfo->boxLx / temp3;
1259	–	celly = simnfo->boxLy / temp3;
1260	–	cellz = simnfo->boxLz / temp3;
1261	–	}
1262	–
1263	–	current_mol = 0;
1264	–	current_comp_mol = 0;
1265	–	current_comp = 0;
1266	–	current_atom_ndx = 0;
1267	–
1268	–	for( i=0; i < n_cells ; i++ ){
1269	–	for( j=0; j < n_cells; j++ ){
1270	–	for( k=0; k < n_cells; k++ ){
1271	–
1272	–	makeElement( i * cellx,
1273	–	j * celly,
1274	–	k * cellz );
1275	–
1276	–	makeElement( i * cellx + 0.5 * cellx,
1277	–	j * celly + 0.5 * celly,
1278	–	k * cellz );
1279	–
1280	–	makeElement( i * cellx,
1281	–	j * celly + 0.5 * celly,
1282	–	k * cellz + 0.5 * cellz );
1283	–
1284	–	makeElement( i * cellx + 0.5 * cellx,
1285	–	j * celly,
1286	–	k * cellz + 0.5 * cellz );
1287	–	}
1288	–	}
1289	–	}
1290	–
1291	–	if( have_extra ){
1292	–	done = 0;
1293	–
1294	–	int start_ndx;
1295	–	for( i=0; i < (n_cells+1) && !done; i++ ){
1296	–	for( j=0; j < (n_cells+1) && !done; j++ ){
1297	–
1298	–	if( i < n_cells ){
1299	–
1300	–	if( j < n_cells ){
1301	–	start_ndx = n_cells;
1302	–	}
1303	–	else start_ndx = 0;
1304	–	}
1305	–	else start_ndx = 0;
1306	–
1307	–	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1308	–
1309	–	makeElement( i * cellx,
1310	–	j * celly,
1311	–	k * cellz );
1312	–	done = ( current_mol >= tot_nmol );
1313	–
1314	–	if( !done && n_per_extra > 1 ){
1315	–	makeElement( i * cellx + 0.5 * cellx,
1316	–	j * celly + 0.5 * celly,
1317	–	k * cellz );
1318	–	done = ( current_mol >= tot_nmol );
1319	–	}
1320	–
1321	–	if( !done && n_per_extra > 2){
1322	–	makeElement( i * cellx,
1323	–	j * celly + 0.5 * celly,
1324	–	k * cellz + 0.5 * cellz );
1325	–	done = ( current_mol >= tot_nmol );
1326	–	}
1327	–
1328	–	if( !done && n_per_extra > 3){
1329	–	makeElement( i * cellx + 0.5 * cellx,
1330	–	j * celly,
1331	–	k * cellz + 0.5 * cellz );
1332	–	done = ( current_mol >= tot_nmol );
1333	–	}
1334	–	}
1335	–	}
1336	–	}
1337	–	}
1338	–
1339	–
1340	–	for( i=0; i<simnfo->n_atoms; i++ ){
1341	–	simnfo->atoms[i]->set_vx( 0.0 );
1342	–	simnfo->atoms[i]->set_vy( 0.0 );
1343	–	simnfo->atoms[i]->set_vz( 0.0 );
1344	–	}
1345	–	}
1346	–
1347	–	void SimSetup::makeElement( double x, double y, double z ){
1348	–
1349	–	int k;
1350	–	AtomStamp* current_atom;
1351	–	DirectionalAtom* dAtom;
1352	–	double rotMat[3][3];
1353	–
1354	–	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1355	–
1356	–	current_atom = comp_stamps[current_comp]->getAtom( k );
1357	–	if( !current_atom->havePosition() ){
1358	–	sprintf( painCave.errMsg,
1359	–	"SimSetup:initFromBass error.\n"
1360	–	"\tComponent %s, atom %s does not have a position specified.\n"
1361	–	"\tThe initialization routine is unable to give a start"
1362	–	" position.\n",
1363	–	comp_stamps[current_comp]->getID(),
1364	–	current_atom->getType() );
1365	–	painCave.isFatal = 1;
1366	–	simError();
1367	–	}
1368	–
1369	–	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1370	–	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1371	–	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1372	–
1373	–	if( the_atoms[current_atom_ndx]->isDirectional() ){
1374	–
1375	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1376	–
1377	–	rotMat[0][0] = 1.0;
1378	–	rotMat[0][1] = 0.0;
1379	–	rotMat[0][2] = 0.0;
1380	–
1381	–	rotMat[1][0] = 0.0;
1382	–	rotMat[1][1] = 1.0;
1383	–	rotMat[1][2] = 0.0;
1384	–
1385	–	rotMat[2][0] = 0.0;
1386	–	rotMat[2][1] = 0.0;
1387	–	rotMat[2][2] = 1.0;
1388	–
1389	–	dAtom->setA( rotMat );
1390	–	}
1391	–
1392	–	current_atom_ndx++;
1393	–	}
1394	–
1395	–	current_mol++;
1396	–	current_comp_mol++;
1397	–
1398	–	if( current_comp_mol >= components_nmol[current_comp] ){
1399	–
1400	–	current_comp_mol = 0;
1401	–	current_comp++;
1402	–	}
1403	–	}

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