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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 580 by gezelter, Wed Jul 9 13:56:36 2003 UTC vs.
Revision 670 by mmeineke, Thu Aug 7 21:47:18 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
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	>	#define NVEZCONS_ENS   6
26	>	#define NVTZCONS_ENS   7
27	>	#define NPTiZCONS_ENS  8
28	>	#define NPTfZCONS_ENS  9
29	>	#define NPTimZCONS_ENS 10
30	>	#define NPTfmZCONS_ENS 11
31
32		#define FF_DUFF 0
33		#define FF_LJ   1
34	+	#define FF_EAM  2
35
36	+	using namespace std;
37
38		SimSetup::SimSetup(){
39	+
40	+	isInfoArray = 0;
41	+	nInfo = 1;
42	+
43		stamps = new MakeStamps();
44		globals = new Globals();
45
46	+
47		#ifdef IS_MPI
48		strcpy( checkPointMsg, "SimSetup creation successful" );
49		MPIcheckPoint();
#	Line 38 | Line 55 | void SimSetup::parseFile( char* fileName ){
55		delete globals;
56		}
57
58	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
59	+	info = the_info;
60	+	nInfo = theNinfo;
61	+	isInfoArray = 1;
62	+	}
63	+
64	+
65		void SimSetup::parseFile( char* fileName ){
66
67		#ifdef IS_MPI
#	Line 73 | Line 97 | void SimSetup::createSim( void ){
97
98		#endif // is_mpi
99
100	<	void SimSetup::createSim( void ){
100	>	void SimSetup::createSim(void){
101
78	–	MakeStamps *the_stamps;
79	–	Globals* the_globals;
102		int i, j, k, globalAtomIndex;
103
104	<	int ensembleCase;
83	<	int ffCase;
104	>	// gather all of the information from the Bass file
105
106	<	ensembleCase = -1;
86	<	ffCase = -1;
106	>	gatherInfo();
107
108	<	// get the stamps and globals;
89	<	the_stamps = stamps;
90	<	the_globals = globals;
108	>	// creation of complex system objects
109
110	<	// set the easy ones first
93	<	simnfo->target_temp = the_globals->getTargetTemp();
94	<	simnfo->dt = the_globals->getDt();
95	<	simnfo->run_time = the_globals->getRunTime();
110	>	sysObjectsCreation();
111
112	<	// get the ones we know are there, yet still may need some work.
113	<	n_components = the_globals->getNComponents();
114	<	strcpy( force_field, the_globals->getForceField() );
112	>	// check on the post processing info
113	>
114	>	finalInfoCheck();
115	>
116	>	// initialize the system coordinates
117	>
118	>	if( !isInfoArray ) initSystemCoords();
119	>
120	>	// make the output filenames
121	>
122	>	makeOutNames();
123	>
124	>	// make the integrator
125	>
126	>	makeIntegrator();
127	>
128	>	#ifdef IS_MPI
129	>	mpiSim->mpiRefresh();
130	>	#endif
131	>
132	>	// initialize the Fortran
133	>
134	>	initFortran();
135	>
136	>
137	>
138	>	}
139	>
140	>
141	>	void SimSetup::makeMolecules( void ){
142	>
143	>	int k,l;
144	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
145	>	molInit molInfo;
146	>	DirectionalAtom* dAtom;
147	>	LinkedAssign* extras;
148	>	LinkedAssign* current_extra;
149	>	AtomStamp* currentAtom;
150	>	BondStamp* currentBond;
151	>	BendStamp* currentBend;
152	>	TorsionStamp* currentTorsion;
153	>
154	>	bond_pair* theBonds;
155	>	bend_set* theBends;
156	>	torsion_set* theTorsions;
157	>
158	>
159	>	//init the forceField paramters
160	>
161	>	the_ff->readParams();
162	>
163	>
164	>	// init the atoms
165	>
166	>	double ux, uy, uz, u, uSqr;
167	>
168	>	for(k=0; k<nInfo; k++){
169	>
170	>	the_ff->setSimInfo( &(info[k]) );
171	>
172	>	atomOffset = 0;
173	>	excludeOffset = 0;
174	>	for(i=0; i<info[k].n_mol; i++){
175	>
176	>	stampID = info[k].molecules[i].getStampID();
177	>
178	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
179	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
180	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
181	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
182	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
183	>
184	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
185	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
186	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
187	>	molInfo.myBends = new Bend*[molInfo.nBends];
188	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
189	>
190	>	theBonds = new bond_pair[molInfo.nBonds];
191	>	theBends = new bend_set[molInfo.nBends];
192	>	theTorsions = new torsion_set[molInfo.nTorsions];
193	>
194	>	// make the Atoms
195	>
196	>	for(j=0; j<molInfo.nAtoms; j++){
197	>
198	>	currentAtom = comp_stamps[stampID]->getAtom( j );
199	>	if( currentAtom->haveOrientation() ){
200	>
201	>	dAtom = new DirectionalAtom( (j + atomOffset),
202	>	info[k].getConfiguration() );
203	>	info[k].n_oriented++;
204	>	molInfo.myAtoms[j] = dAtom;
205	>
206	>	ux = currentAtom->getOrntX();
207	>	uy = currentAtom->getOrntY();
208	>	uz = currentAtom->getOrntZ();
209	>
210	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
211	>
212	>	u = sqrt( uSqr );
213	>	ux = ux / u;
214	>	uy = uy / u;
215	>	uz = uz / u;
216	>
217	>	dAtom->setSUx( ux );
218	>	dAtom->setSUy( uy );
219	>	dAtom->setSUz( uz );
220	>	}
221	>	else{
222	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
223	>	info[k].getConfiguration() );
224	>	}
225	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
226	>
227	>	#ifdef IS_MPI
228	>
229	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
230	>
231	>	#endif // is_mpi
232	>	}
233	>
234	>	// make the bonds
235	>	for(j=0; j<molInfo.nBonds; j++){
236	>
237	>	currentBond = comp_stamps[stampID]->getBond( j );
238	>	theBonds[j].a = currentBond->getA() + atomOffset;
239	>	theBonds[j].b = currentBond->getB() + atomOffset;
240	>
241	>	exI = theBonds[j].a;
242	>	exJ = theBonds[j].b;
243	>
244	>	// exclude_I must always be the smaller of the pair
245	>	if( exI > exJ ){
246	>	tempEx = exI;
247	>	exI = exJ;
248	>	exJ = tempEx;
249	>	}
250	>	#ifdef IS_MPI
251	>	tempEx = exI;
252	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
253	>	tempEx = exJ;
254	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
255	>
256	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
257	>	#else  // isn't MPI
258	>
259	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
260	>	#endif  //is_mpi
261	>	}
262	>	excludeOffset += molInfo.nBonds;
263	>
264	>	//make the bends
265	>	for(j=0; j<molInfo.nBends; j++){
266	>
267	>	currentBend = comp_stamps[stampID]->getBend( j );
268	>	theBends[j].a = currentBend->getA() + atomOffset;
269	>	theBends[j].b = currentBend->getB() + atomOffset;
270	>	theBends[j].c = currentBend->getC() + atomOffset;
271	>
272	>	if( currentBend->haveExtras() ){
273	>
274	>	extras = currentBend->getExtras();
275	>	current_extra = extras;
276	>
277	>	while( current_extra != NULL ){
278	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
279	>
280	>	switch( current_extra->getType() ){
281	>
282	>	case 0:
283	>	theBends[j].ghost =
284	>	current_extra->getInt() + atomOffset;
285	>	theBends[j].isGhost = 1;
286	>	break;
287	>
288	>	case 1:
289	>	theBends[j].ghost =
290	>	(int)current_extra->getDouble() + atomOffset;
291	>	theBends[j].isGhost = 1;
292	>	break;
293	>
294	>	default:
295	>	sprintf( painCave.errMsg,
296	>	"SimSetup Error: ghostVectorSource was neither a "
297	>	"double nor an int.\n"
298	>	"-->Bend[%d] in %s\n",
299	>	j, comp_stamps[stampID]->getID() );
300	>	painCave.isFatal = 1;
301	>	simError();
302	>	}
303	>	}
304	>
305	>	else{
306	>
307	>	sprintf( painCave.errMsg,
308	>	"SimSetup Error: unhandled bend assignment:\n"
309	>	"    -->%s in Bend[%d] in %s\n",
310	>	current_extra->getlhs(),
311	>	j, comp_stamps[stampID]->getID() );
312	>	painCave.isFatal = 1;
313	>	simError();
314	>	}
315	>
316	>	current_extra = current_extra->getNext();
317	>	}
318	>	}
319	>
320	>	if( !theBends[j].isGhost ){
321	>
322	>	exI = theBends[j].a;
323	>	exJ = theBends[j].c;
324	>	}
325	>	else{
326	>
327	>	exI = theBends[j].a;
328	>	exJ = theBends[j].b;
329	>	}
330	>
331	>	// exclude_I must always be the smaller of the pair
332	>	if( exI > exJ ){
333	>	tempEx = exI;
334	>	exI = exJ;
335	>	exJ = tempEx;
336	>	}
337	>	#ifdef IS_MPI
338	>	tempEx = exI;
339	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
340	>	tempEx = exJ;
341	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
342	>
343	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
344	>	#else  // isn't MPI
345	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
346	>	#endif  //is_mpi
347	>	}
348	>	excludeOffset += molInfo.nBends;
349	>
350	>	for(j=0; j<molInfo.nTorsions; j++){
351	>
352	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
353	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
354	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
355	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
356	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
357	>
358	>	exI = theTorsions[j].a;
359	>	exJ = theTorsions[j].d;
360	>
361	>	// exclude_I must always be the smaller of the pair
362	>	if( exI > exJ ){
363	>	tempEx = exI;
364	>	exI = exJ;
365	>	exJ = tempEx;
366	>	}
367	>	#ifdef IS_MPI
368	>	tempEx = exI;
369	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
370	>	tempEx = exJ;
371	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
372	>
373	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
374	>	#else  // isn't MPI
375	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
376	>	#endif  //is_mpi
377	>	}
378	>	excludeOffset += molInfo.nTorsions;
379	>
380	>
381	>	// send the arrays off to the forceField for init.
382	>
383	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
384	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
385	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
386	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
387	>
388	>
389	>	info[k].molecules[i].initialize( molInfo );
390
391	+
392	+	atomOffset += molInfo.nAtoms;
393	+	delete[] theBonds;
394	+	delete[] theBends;
395	+	delete[] theTorsions;
396	+	}
397	+	}
398	+
399	+	#ifdef IS_MPI
400	+	sprintf( checkPointMsg, "all molecules initialized succesfully" );
401	+	MPIcheckPoint();
402	+	#endif // is_mpi
403	+
404	+	// clean up the forcefield
405	+
406	+	the_ff->calcRcut();
407	+	the_ff->cleanMe();
408	+
409	+	}
410	+
411	+	void SimSetup::initFromBass( void ){
412	+
413	+	int i, j, k;
414	+	int n_cells;
415	+	double cellx, celly, cellz;
416	+	double temp1, temp2, temp3;
417	+	int n_per_extra;
418	+	int n_extra;
419	+	int have_extra, done;
420	+
421	+	double vel[3];
422	+	vel[0] = 0.0;
423	+	vel[1] = 0.0;
424	+	vel[2] = 0.0;
425	+
426	+	temp1 = (double)tot_nmol / 4.0;
427	+	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
428	+	temp3 = ceil( temp2 );
429	+
430	+	have_extra =0;
431	+	if( temp2 < temp3 ){ // we have a non-complete lattice
432	+	have_extra =1;
433	+
434	+	n_cells = (int)temp3 - 1;
435	+	cellx = info[0].boxL[0] / temp3;
436	+	celly = info[0].boxL[1] / temp3;
437	+	cellz = info[0].boxL[2] / temp3;
438	+	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
439	+	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
440	+	n_per_extra = (int)ceil( temp1 );
441	+
442	+	if( n_per_extra > 4){
443	+	sprintf( painCave.errMsg,
444	+	"SimSetup error. There has been an error in constructing"
445	+	" the non-complete lattice.\n" );
446	+	painCave.isFatal = 1;
447	+	simError();
448	+	}
449	+	}
450	+	else{
451	+	n_cells = (int)temp3;
452	+	cellx = info[0].boxL[0] / temp3;
453	+	celly = info[0].boxL[1] / temp3;
454	+	cellz = info[0].boxL[2] / temp3;
455	+	}
456	+
457	+	current_mol = 0;
458	+	current_comp_mol = 0;
459	+	current_comp = 0;
460	+	current_atom_ndx = 0;
461	+
462	+	for( i=0; i < n_cells ; i++ ){
463	+	for( j=0; j < n_cells; j++ ){
464	+	for( k=0; k < n_cells; k++ ){
465	+
466	+	makeElement( i * cellx,
467	+	j * celly,
468	+	k * cellz );
469	+
470	+	makeElement( i * cellx + 0.5 * cellx,
471	+	j * celly + 0.5 * celly,
472	+	k * cellz );
473	+
474	+	makeElement( i * cellx,
475	+	j * celly + 0.5 * celly,
476	+	k * cellz + 0.5 * cellz );
477	+
478	+	makeElement( i * cellx + 0.5 * cellx,
479	+	j * celly,
480	+	k * cellz + 0.5 * cellz );
481	+	}
482	+	}
483	+	}
484	+
485	+	if( have_extra ){
486	+	done = 0;
487	+
488	+	int start_ndx;
489	+	for( i=0; i < (n_cells+1) && !done; i++ ){
490	+	for( j=0; j < (n_cells+1) && !done; j++ ){
491	+
492	+	if( i < n_cells ){
493	+
494	+	if( j < n_cells ){
495	+	start_ndx = n_cells;
496	+	}
497	+	else start_ndx = 0;
498	+	}
499	+	else start_ndx = 0;
500	+
501	+	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
502	+
503	+	makeElement( i * cellx,
504	+	j * celly,
505	+	k * cellz );
506	+	done = ( current_mol >= tot_nmol );
507	+
508	+	if( !done && n_per_extra > 1 ){
509	+	makeElement( i * cellx + 0.5 * cellx,
510	+	j * celly + 0.5 * celly,
511	+	k * cellz );
512	+	done = ( current_mol >= tot_nmol );
513	+	}
514	+
515	+	if( !done && n_per_extra > 2){
516	+	makeElement( i * cellx,
517	+	j * celly + 0.5 * celly,
518	+	k * cellz + 0.5 * cellz );
519	+	done = ( current_mol >= tot_nmol );
520	+	}
521	+
522	+	if( !done && n_per_extra > 3){
523	+	makeElement( i * cellx + 0.5 * cellx,
524	+	j * celly,
525	+	k * cellz + 0.5 * cellz );
526	+	done = ( current_mol >= tot_nmol );
527	+	}
528	+	}
529	+	}
530	+	}
531	+	}
532	+
533	+	for( i=0; i<info[0].n_atoms; i++ ){
534	+	info[0].atoms[i]->setVel( vel );
535	+	}
536	+	}
537	+
538	+	void SimSetup::makeElement( double x, double y, double z ){
539	+
540	+	int k;
541	+	AtomStamp* current_atom;
542	+	DirectionalAtom* dAtom;
543	+	double rotMat[3][3];
544	+	double pos[3];
545	+
546	+	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
547	+
548	+	current_atom = comp_stamps[current_comp]->getAtom( k );
549	+	if( !current_atom->havePosition() ){
550	+	sprintf( painCave.errMsg,
551	+	"SimSetup:initFromBass error.\n"
552	+	"\tComponent %s, atom %s does not have a position specified.\n"
553	+	"\tThe initialization routine is unable to give a start"
554	+	" position.\n",
555	+	comp_stamps[current_comp]->getID(),
556	+	current_atom->getType() );
557	+	painCave.isFatal = 1;
558	+	simError();
559	+	}
560	+
561	+	pos[0] = x + current_atom->getPosX();
562	+	pos[1] = y + current_atom->getPosY();
563	+	pos[2] = z + current_atom->getPosZ();
564	+
565	+	info[0].atoms[current_atom_ndx]->setPos( pos );
566	+
567	+	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
568	+
569	+	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
570	+
571	+	rotMat[0][0] = 1.0;
572	+	rotMat[0][1] = 0.0;
573	+	rotMat[0][2] = 0.0;
574	+
575	+	rotMat[1][0] = 0.0;
576	+	rotMat[1][1] = 1.0;
577	+	rotMat[1][2] = 0.0;
578	+
579	+	rotMat[2][0] = 0.0;
580	+	rotMat[2][1] = 0.0;
581	+	rotMat[2][2] = 1.0;
582	+
583	+	dAtom->setA( rotMat );
584	+	}
585	+
586	+	current_atom_ndx++;
587	+	}
588	+
589	+	current_mol++;
590	+	current_comp_mol++;
591	+
592	+	if( current_comp_mol >= components_nmol[current_comp] ){
593	+
594	+	current_comp_mol = 0;
595	+	current_comp++;
596	+	}
597	+	}
598	+
599	+
600	+	void SimSetup::gatherInfo( void ){
601	+	int i,j,k;
602	+
603	+	ensembleCase = -1;
604	+	ffCase = -1;
605	+
606	+	// set the easy ones first
607	+
608	+	for( i=0; i<nInfo; i++){
609	+	info[i].target_temp = globals->getTargetTemp();
610	+	info[i].dt = globals->getDt();
611	+	info[i].run_time = globals->getRunTime();
612	+	}
613	+	n_components = globals->getNComponents();
614	+
615	+
616	+	// get the forceField
617	+
618	+	strcpy( force_field, globals->getForceField() );
619	+
620		if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
621		else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
622	+	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
623		else{
624		sprintf( painCave.errMsg,
625		"SimSetup Error. Unrecognized force field -> %s\n",
#	Line 108 | Line 628 | void SimSetup::createSim( void ){
628		simError();
629		}
630
631	<	// get the ensemble:
112	<	strcpy( ensemble, the_globals->getEnsemble() );
631	>	// get the ensemble
632
633	+	strcpy( ensemble, globals->getEnsemble() );
634	+
635		if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
636		else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
637		else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
638		ensembleCase = NPTi_ENS;
639		else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
640	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
641	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
642	+
643	+	else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS;
644	+	else if( !strcasecmp( ensemble, "NVTZCONS"))  ensembleCase = NVTZCONS_ENS;
645	+	else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPTZCONS"))
646	+	ensembleCase = NPTiZCONS_ENS;
647	+	else if( !strcasecmp( ensemble, "NPTfZCONS"))  ensembleCase = NPTfZCONS_ENS;
648	+	else if( !strcasecmp( ensemble, "NPTimZCONS"))  ensembleCase = NPTimZCONS_ENS;
649	+	else if( !strcasecmp( ensemble, "NPTfmZCONS"))  ensembleCase = NPTfmZCONS_ENS;
650	+
651		else{
652		sprintf( painCave.errMsg,
653		"SimSetup Warning. Unrecognized Ensemble -> %s, "
#	Line 126 | Line 658 | void SimSetup::createSim( void ){
658		strcpy( ensemble, "NVE" );
659		ensembleCase = NVE_ENS;
660		}
661	<	strcpy( simnfo->ensemble, ensemble );
661	>
662	>	for(i=0; i<nInfo; i++){
663	>
664	>	strcpy( info[i].ensemble, ensemble );
665
666	+	// get the mixing rule
667
668	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
669	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
134	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
135	<	//     if (the_globals->haveTargetPressure())
136	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
137	<	//     else {
138	<	//       sprintf( painCave.errMsg,
139	<	//                "SimSetup error: If you use the constant pressure\n"
140	<	//                "    ensemble, you must set targetPressure.\n"
141	<	//                "    This was found in the BASS file.\n");
142	<	//       painCave.isFatal = 1;
143	<	//       simError();
144	<	//     }
145	<
146	<	//     if (the_globals->haveTauThermostat())
147	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
148	<	//     else if (the_globals->haveQmass())
149	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
150	<	//     else {
151	<	//       sprintf( painCave.errMsg,
152	<	//                "SimSetup error: If you use one of the constant temperature\n"
153	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
154	<	//                "    Neither of these was found in the BASS file.\n");
155	<	//       painCave.isFatal = 1;
156	<	//       simError();
157	<	//     }
158	<
159	<	//     if (the_globals->haveTauBarostat())
160	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
161	<	//     else {
162	<	//       sprintf( painCave.errMsg,
163	<	//                "SimSetup error: If you use the constant pressure\n"
164	<	//                "    ensemble, you must set tauBarostat.\n"
165	<	//                "    This was found in the BASS file.\n");
166	<	//       painCave.isFatal = 1;
167	<	//       simError();
168	<	//     }
169	<
170	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
171	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
172	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
173	<
174	<	//     if (the_globals->haveTauThermostat())
175	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
176	<	//     else if (the_globals->haveQmass())
177	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
178	<	//     else {
179	<	//       sprintf( painCave.errMsg,
180	<	//                "SimSetup error: If you use one of the constant temperature\n"
181	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
182	<	//                "    Neither of these was found in the BASS file.\n");
183	<	//       painCave.isFatal = 1;
184	<	//       simError();
185	<	//     }
186	<
187	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
188	<	simnfo->usePBC = the_globals->getPBC();
189	<
190	<	int usesDipoles = 0;
191	<	switch( ffCase ){
192	<
193	<	case FF_DUFF:
194	<	the_ff = new DUFF();
195	<	usesDipoles = 1;
196	<	break;
197	<
198	<	case FF_LJ:
199	<	the_ff = new LJFF();
200	<	break;
201	<
202	<	default:
203	<	sprintf( painCave.errMsg,
204	<	"SimSetup Error. Unrecognized force field in case statement.\n");
205	<	painCave.isFatal = 1;
206	<	simError();
668	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
669	>	info[i].usePBC = globals->getPBC();
670		}
671	<
209	<	#ifdef IS_MPI
210	<	strcpy( checkPointMsg, "ForceField creation successful" );
211	<	MPIcheckPoint();
212	<	#endif // is_mpi
213	<
671	>
672		// get the components and calculate the tot_nMol and indvidual n_mol
673	<	the_components = the_globals->getComponents();
673	>
674	>	the_components = globals->getComponents();
675		components_nmol = new int[n_components];
217	–	comp_stamps = new MoleculeStamp*[n_components];
676
677	<	if( !the_globals->haveNMol() ){
677	>
678	>	if( !globals->haveNMol() ){
679		// we don't have the total number of molecules, so we assume it is
680		// given in each component
681
#	Line 245 | Line 704 | void SimSetup::createSim( void ){
704		" Please give nMol in the components.\n" );
705		painCave.isFatal = 1;
706		simError();
248	–
249	–
250	–	//     tot_nmol = the_globals->getNMol();
251	–
252	–	//   //we have the total number of molecules, now we check for molfractions
253	–	//     for( i=0; i<n_components; i++ ){
254	–
255	–	//       if( !the_components[i]->haveMolFraction() ){
256	–
257	–	//  if( !the_components[i]->haveNMol() ){
258	–	//    //we have a problem
259	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
260	–	//              << " nMol was given in component
261	–
707		}
708
709	<	#ifdef IS_MPI
265	<	strcpy( checkPointMsg, "Have the number of components" );
266	<	MPIcheckPoint();
267	<	#endif // is_mpi
268	<
269	<	// make an array of molecule stamps that match the components used.
270	<	// also extract the used stamps out into a separate linked list
271	<
272	<	simnfo->nComponents = n_components;
273	<	simnfo->componentsNmol = components_nmol;
274	<	simnfo->compStamps = comp_stamps;
275	<	simnfo->headStamp = new LinkedMolStamp();
709	>	// set the status, sample, and thermal kick times
710
711	<	char* id;
278	<	LinkedMolStamp* headStamp = simnfo->headStamp;
279	<	LinkedMolStamp* currentStamp = NULL;
280	<	for( i=0; i<n_components; i++ ){
711	>	for(i=0; i<nInfo; i++){
712
713	<	id = the_components[i]->getType();
714	<	comp_stamps[i] = NULL;
713	>	if( globals->haveSampleTime() ){
714	>	info[i].sampleTime = globals->getSampleTime();
715	>	info[i].statusTime = info[i].sampleTime;
716	>	info[i].thermalTime = info[i].sampleTime;
717	>	}
718	>	else{
719	>	info[i].sampleTime = globals->getRunTime();
720	>	info[i].statusTime = info[i].sampleTime;
721	>	info[i].thermalTime = info[i].sampleTime;
722	>	}
723
724	<	// check to make sure the component isn't already in the list
724	>	if( globals->haveStatusTime() ){
725	>	info[i].statusTime = globals->getStatusTime();
726	>	}
727	>
728	>	if( globals->haveThermalTime() ){
729	>	info[i].thermalTime = globals->getThermalTime();
730	>	}
731
732	<	comp_stamps[i] = headStamp->match( id );
733	<	if( comp_stamps[i] == NULL ){
732	>	// check for the temperature set flag
733	>
734	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
735	>
736	>	// get some of the tricky things that may still be in the globals
737	>
738	>	double boxVector[3];
739	>	if( globals->haveBox() ){
740	>	boxVector[0] = globals->getBox();
741	>	boxVector[1] = globals->getBox();
742	>	boxVector[2] = globals->getBox();
743
744	<	// extract the component from the list;
744	>	info[i].setBox( boxVector );
745	>	}
746	>	else if( globals->haveDensity() ){
747
748	<	currentStamp = the_stamps->extractMolStamp( id );
749	<	if( currentStamp == NULL ){
748	>	double vol;
749	>	vol = (double)tot_nmol / globals->getDensity();
750	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
751	>	boxVector[1] = boxVector[0];
752	>	boxVector[2] = boxVector[0];
753	>
754	>	info[i].setBox( boxVector );
755	>	}
756	>	else{
757	>	if( !globals->haveBoxX() ){
758		sprintf( painCave.errMsg,
759	<	"SimSetup error: Component \"%s\" was not found in the "
296	<	"list of declared molecules\n",
297	<	id );
759	>	"SimSetup error, no periodic BoxX size given.\n" );
760		painCave.isFatal = 1;
761		simError();
762		}
763	+	boxVector[0] = globals->getBoxX();
764
765	<	headStamp->add( currentStamp );
766	<	comp_stamps[i] = headStamp->match( id );
765	>	if( !globals->haveBoxY() ){
766	>	sprintf( painCave.errMsg,
767	>	"SimSetup error, no periodic BoxY size given.\n" );
768	>	painCave.isFatal = 1;
769	>	simError();
770	>	}
771	>	boxVector[1] = globals->getBoxY();
772	>
773	>	if( !globals->haveBoxZ() ){
774	>	sprintf( painCave.errMsg,
775	>	"SimSetup error, no periodic BoxZ size given.\n" );
776	>	painCave.isFatal = 1;
777	>	simError();
778	>	}
779	>	boxVector[2] = globals->getBoxZ();
780	>
781	>	info[i].setBox( boxVector );
782		}
305	–	}
783
784	+	}
785	+
786		#ifdef IS_MPI
787	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
787	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
788		MPIcheckPoint();
789		#endif // is_mpi
311	–
790
791	+	}
792
793
794	<	// caclulate the number of atoms, bonds, bends and torsions
794	>	void SimSetup::finalInfoCheck( void ){
795	>	int index;
796	>	int usesDipoles;
797	>	int i;
798
799	<	tot_atoms = 0;
800	<	tot_bonds = 0;
319	<	tot_bends = 0;
320	<	tot_torsions = 0;
321	<	for( i=0; i<n_components; i++ ){
799	>	for(i=0; i<nInfo; i++){
800	>	// check electrostatic parameters
801
802	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
803	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
804	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
805	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
802	>	index = 0;
803	>	usesDipoles = 0;
804	>	while( (index < info[i].n_atoms) && !usesDipoles ){
805	>	usesDipoles = (info[i].atoms[index])->hasDipole();
806	>	index++;
807	>	}
808	>
809	>	#ifdef IS_MPI
810	>	int myUse = usesDipoles;
811	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
812	>	#endif //is_mpi
813	>
814	>	double theEcr, theEst;
815	>
816	>	if (globals->getUseRF() ) {
817	>	info[i].useReactionField = 1;
818	>
819	>	if( !globals->haveECR() ){
820	>	sprintf( painCave.errMsg,
821	>	"SimSetup Warning: using default value of 1/2 the smallest "
822	>	"box length for the electrostaticCutoffRadius.\n"
823	>	"I hope you have a very fast processor!\n");
824	>	painCave.isFatal = 0;
825	>	simError();
826	>	double smallest;
827	>	smallest = info[i].boxL[0];
828	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
829	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
830	>	theEcr = 0.5 * smallest;
831	>	} else {
832	>	theEcr = globals->getECR();
833	>	}
834	>
835	>	if( !globals->haveEST() ){
836	>	sprintf( painCave.errMsg,
837	>	"SimSetup Warning: using default value of 0.05 * the "
838	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
839	>	);
840	>	painCave.isFatal = 0;
841	>	simError();
842	>	theEst = 0.05 * theEcr;
843	>	} else {
844	>	theEst= globals->getEST();
845	>	}
846	>
847	>	info[i].setEcr( theEcr, theEst );
848	>
849	>	if(!globals->haveDielectric() ){
850	>	sprintf( painCave.errMsg,
851	>	"SimSetup Error: You are trying to use Reaction Field without"
852	>	"setting a dielectric constant!\n"
853	>	);
854	>	painCave.isFatal = 1;
855	>	simError();
856	>	}
857	>	info[i].dielectric = globals->getDielectric();
858	>	}
859	>	else {
860	>	if (usesDipoles) {
861	>
862	>	if( !globals->haveECR() ){
863	>	sprintf( painCave.errMsg,
864	>	"SimSetup Warning: using default value of 1/2 the smallest "
865	>	"box length for the electrostaticCutoffRadius.\n"
866	>	"I hope you have a very fast processor!\n");
867	>	painCave.isFatal = 0;
868	>	simError();
869	>	double smallest;
870	>	smallest = info[i].boxL[0];
871	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
872	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
873	>	theEcr = 0.5 * smallest;
874	>	} else {
875	>	theEcr = globals->getECR();
876	>	}
877	>
878	>	if( !globals->haveEST() ){
879	>	sprintf( painCave.errMsg,
880	>	"SimSetup Warning: using default value of 0.05 * the "
881	>	"electrostaticCutoffRadius for the "
882	>	"electrostaticSkinThickness\n"
883	>	);
884	>	painCave.isFatal = 0;
885	>	simError();
886	>	theEst = 0.05 * theEcr;
887	>	} else {
888	>	theEst= globals->getEST();
889	>	}
890	>
891	>	info[i].setEcr( theEcr, theEst );
892	>	}
893	>	}
894		}
895
329	–	tot_SRI = tot_bonds + tot_bends + tot_torsions;
330	–
331	–	simnfo->n_atoms = tot_atoms;
332	–	simnfo->n_bonds = tot_bonds;
333	–	simnfo->n_bends = tot_bends;
334	–	simnfo->n_torsions = tot_torsions;
335	–	simnfo->n_SRI = tot_SRI;
336	–	simnfo->n_mol = tot_nmol;
337	–
338	–	simnfo->molMembershipArray = new int[tot_atoms];
339	–
896		#ifdef IS_MPI
897	+	strcpy( checkPointMsg, "post processing checks out" );
898	+	MPIcheckPoint();
899	+	#endif // is_mpi
900
901	<	// divide the molecules among processors here.
343	<
344	<	mpiSim = new mpiSimulation( simnfo );
345	<
346	<	globalIndex = mpiSim->divideLabor();
901	>	}
902
903	<	// set up the local variables
903	>	void SimSetup::initSystemCoords( void ){
904	>	int i;
905
906	<	int localMol, allMol;
351	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
906	>	std::cerr << "Setting atom Coords\n";
907
908	<	int* mol2proc = mpiSim->getMolToProcMap();
354	<	int* molCompType = mpiSim->getMolComponentType();
908	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
909
910	<	allMol = 0;
357	<	localMol = 0;
358	<	local_atoms = 0;
359	<	local_bonds = 0;
360	<	local_bends = 0;
361	<	local_torsions = 0;
362	<	globalAtomIndex = 0;
363	<
364	<
365	<	for( i=0; i<n_components; i++ ){
366	<
367	<	for( j=0; j<components_nmol[i]; j++ ){
368	<
369	<	if( mol2proc[allMol] == worldRank ){
370	<
371	<	local_atoms +=    comp_stamps[i]->getNAtoms();
372	<	local_bonds +=    comp_stamps[i]->getNBonds();
373	<	local_bends +=    comp_stamps[i]->getNBends();
374	<	local_torsions += comp_stamps[i]->getNTorsions();
375	<	localMol++;
376	<	}
377	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
378	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
379	<	globalAtomIndex++;
380	<	}
381	<
382	<	allMol++;
383	<	}
384	<	}
385	<	local_SRI = local_bonds + local_bends + local_torsions;
910	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
911
912	<	simnfo->n_atoms = mpiSim->getMyNlocal();
913	<
914	<	if( local_atoms != simnfo->n_atoms ){
912	>	if( globals->haveInitialConfig() ){
913	>
914	>	InitializeFromFile* fileInit;
915	>	#ifdef IS_MPI // is_mpi
916	>	if( worldRank == 0 ){
917	>	#endif //is_mpi
918	>	fileInit = new InitializeFromFile( globals->getInitialConfig() );
919	>	#ifdef IS_MPI
920	>	}else fileInit = new InitializeFromFile( NULL );
921	>	#endif
922	>	fileInit->readInit( info ); // default velocities on
923	>
924	>	delete fileInit;
925	>	}
926	>	else{
927	>
928	>	#ifdef IS_MPI
929	>
930	>	// no init from bass
931	>
932		sprintf( painCave.errMsg,
933	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
934	<	" localAtom (%d) are not equal.\n",
393	<	simnfo->n_atoms,
394	<	local_atoms );
395	<	painCave.isFatal = 1;
933	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
934	>	painCave.isFatal;
935		simError();
936	+
937	+	#else
938	+
939	+	initFromBass();
940	+
941	+
942	+	#endif
943		}
398	–
399	–	simnfo->n_bonds = local_bonds;
400	–	simnfo->n_bends = local_bends;
401	–	simnfo->n_torsions = local_torsions;
402	–	simnfo->n_SRI = local_SRI;
403	–	simnfo->n_mol = localMol;
404	–
405	–	strcpy( checkPointMsg, "Passed nlocal consistency check." );
406	–	MPIcheckPoint();
944
945	<
945	>	#ifdef IS_MPI
946	>	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
947	>	MPIcheckPoint();
948		#endif // is_mpi
949
950	+	}
951
412	–	// create the atom and short range interaction arrays
952
953	<	Atom::createArrays(simnfo->n_atoms);
415	<	the_atoms = new Atom*[simnfo->n_atoms];
416	<	the_molecules = new Molecule[simnfo->n_mol];
417	<	int molIndex;
418	<
419	<	// initialize the molecule's stampID's
420	<
421	<	#ifdef IS_MPI
953	>	void SimSetup::makeOutNames( void ){
954
955	+	int k;
956
424	–	molIndex = 0;
425	–	for(i=0; i<mpiSim->getTotNmol(); i++){
426	–
427	–	if(mol2proc[i] == worldRank ){
428	–	the_molecules[molIndex].setStampID( molCompType[i] );
429	–	the_molecules[molIndex].setMyIndex( molIndex );
430	–	the_molecules[molIndex].setGlobalIndex( i );
431	–	molIndex++;
432	–	}
433	–	}
434	–
435	–	#else // is_mpi
957
958	<	molIndex = 0;
959	<	globalAtomIndex = 0;
960	<	for(i=0; i<n_components; i++){
961	<	for(j=0; j<components_nmol[i]; j++ ){
962	<	the_molecules[molIndex].setStampID( i );
963	<	the_molecules[molIndex].setMyIndex( molIndex );
964	<	the_molecules[molIndex].setGlobalIndex( molIndex );
965	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
445	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
446	<	globalAtomIndex++;
958	>	for(k=0; k<nInfo; k++){
959	>
960	>	#ifdef IS_MPI
961	>	if( worldRank == 0 ){
962	>	#endif // is_mpi
963	>
964	>	if( globals->haveFinalConfig() ){
965	>	strcpy( info[k].finalName, globals->getFinalConfig() );
966		}
967	<	molIndex++;
967	>	else{
968	>	strcpy( info[k].finalName, inFileName );
969	>	char* endTest;
970	>	int nameLength = strlen( info[k].finalName );
971	>	endTest = &(info[k].finalName[nameLength - 5]);
972	>	if( !strcmp( endTest, ".bass" ) ){
973	>	strcpy( endTest, ".eor" );
974	>	}
975	>	else if( !strcmp( endTest, ".BASS" ) ){
976	>	strcpy( endTest, ".eor" );
977	>	}
978	>	else{
979	>	endTest = &(info[k].finalName[nameLength - 4]);
980	>	if( !strcmp( endTest, ".bss" ) ){
981	>	strcpy( endTest, ".eor" );
982	>	}
983	>	else if( !strcmp( endTest, ".mdl" ) ){
984	>	strcpy( endTest, ".eor" );
985	>	}
986	>	else{
987	>	strcat( info[k].finalName, ".eor" );
988	>	}
989	>	}
990	>	}
991	>
992	>	// make the sample and status out names
993	>
994	>	strcpy( info[k].sampleName, inFileName );
995	>	char* endTest;
996	>	int nameLength = strlen( info[k].sampleName );
997	>	endTest = &(info[k].sampleName[nameLength - 5]);
998	>	if( !strcmp( endTest, ".bass" ) ){
999	>	strcpy( endTest, ".dump" );
1000	>	}
1001	>	else if( !strcmp( endTest, ".BASS" ) ){
1002	>	strcpy( endTest, ".dump" );
1003	>	}
1004	>	else{
1005	>	endTest = &(info[k].sampleName[nameLength - 4]);
1006	>	if( !strcmp( endTest, ".bss" ) ){
1007	>	strcpy( endTest, ".dump" );
1008	>	}
1009	>	else if( !strcmp( endTest, ".mdl" ) ){
1010	>	strcpy( endTest, ".dump" );
1011	>	}
1012	>	else{
1013	>	strcat( info[k].sampleName, ".dump" );
1014	>	}
1015	>	}
1016	>
1017	>	strcpy( info[k].statusName, inFileName );
1018	>	nameLength = strlen( info[k].statusName );
1019	>	endTest = &(info[k].statusName[nameLength - 5]);
1020	>	if( !strcmp( endTest, ".bass" ) ){
1021	>	strcpy( endTest, ".stat" );
1022	>	}
1023	>	else if( !strcmp( endTest, ".BASS" ) ){
1024	>	strcpy( endTest, ".stat" );
1025	>	}
1026	>	else{
1027	>	endTest = &(info[k].statusName[nameLength - 4]);
1028	>	if( !strcmp( endTest, ".bss" ) ){
1029	>	strcpy( endTest, ".stat" );
1030	>	}
1031	>	else if( !strcmp( endTest, ".mdl" ) ){
1032	>	strcpy( endTest, ".stat" );
1033	>	}
1034	>	else{
1035	>	strcat( info[k].statusName, ".stat" );
1036	>	}
1037	>	}
1038	>
1039	>	#ifdef IS_MPI
1040		}
1041	+	#endif // is_mpi
1042		}
1043	<
1043	>	}
1044
453	–	#endif // is_mpi
1045
1046	+	void SimSetup::sysObjectsCreation( void ){
1047	+
1048	+	int i,k;
1049	+
1050	+	// create the forceField
1051	+
1052	+	createFF();
1053
1054	<	if( simnfo->n_SRI ){
457	<
458	<	Exclude::createArray(simnfo->n_SRI);
459	<	the_excludes = new Exclude*[simnfo->n_SRI];
460	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
461	<	simnfo->globalExcludes = new int;
462	<	simnfo->n_exclude = simnfo->n_SRI;
463	<	}
464	<	else{
465	<
466	<	Exclude::createArray( 1 );
467	<	the_excludes = new Exclude*;
468	<	the_excludes[0] = new Exclude(0);
469	<	the_excludes[0]->setPair( 0,0 );
470	<	simnfo->globalExcludes = new int;
471	<	simnfo->globalExcludes[0] = 0;
472	<	simnfo->n_exclude = 0;
473	<	}
1054	>	// extract componentList
1055
1056	<	// set the arrays into the SimInfo object
1056	>	compList();
1057
1058	<	simnfo->atoms = the_atoms;
478	<	simnfo->molecules = the_molecules;
479	<	simnfo->nGlobalExcludes = 0;
480	<	simnfo->excludes = the_excludes;
1058	>	// calc the number of atoms, bond, bends, and torsions
1059
1060	+	calcSysValues();
1061
1062	<	// get some of the tricky things that may still be in the globals
1062	>	#ifdef IS_MPI
1063	>	// divide the molecules among the processors
1064	>
1065	>	mpiMolDivide();
1066	>	#endif //is_mpi
1067	>
1068	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1069	>
1070	>	makeSysArrays();
1071
1072	<	double boxVector[3];
1073	<	if( the_globals->haveBox() ){
1074	<	boxVector[0] = the_globals->getBox();
1075	<	boxVector[1] = the_globals->getBox();
1076	<	boxVector[2] = the_globals->getBox();
1077	<
1078	<	simnfo->setBox( boxVector );
1072	>	// make and initialize the molecules (all but atomic coordinates)
1073	>
1074	>	makeMolecules();
1075	>
1076	>	for(k=0; k<nInfo; k++){
1077	>	info[k].identArray = new int[info[k].n_atoms];
1078	>	for(i=0; i<info[k].n_atoms; i++){
1079	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1080	>	}
1081		}
1082	<	else if( the_globals->haveDensity() ){
1082	>	}
1083
495	–	double vol;
496	–	vol = (double)tot_nmol / the_globals->getDensity();
497	–	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
498	–	boxVector[1] = boxVector[0];
499	–	boxVector[2] = boxVector[0];
1084
1085	<	simnfo->setBox( boxVector );
502	<	}
503	<	else{
504	<	if( !the_globals->haveBoxX() ){
505	<	sprintf( painCave.errMsg,
506	<	"SimSetup error, no periodic BoxX size given.\n" );
507	<	painCave.isFatal = 1;
508	<	simError();
509	<	}
510	<	boxVector[0] = the_globals->getBoxX();
1085	>	void SimSetup::createFF( void ){
1086
1087	<	if( !the_globals->haveBoxY() ){
513	<	sprintf( painCave.errMsg,
514	<	"SimSetup error, no periodic BoxY size given.\n" );
515	<	painCave.isFatal = 1;
516	<	simError();
517	<	}
518	<	boxVector[1] = the_globals->getBoxY();
1087	>	switch( ffCase ){
1088
1089	<	if( !the_globals->haveBoxZ() ){
1090	<	sprintf( painCave.errMsg,
1091	<	"SimSetup error, no periodic BoxZ size given.\n" );
523	<	painCave.isFatal = 1;
524	<	simError();
525	<	}
526	<	boxVector[2] = the_globals->getBoxZ();
1089	>	case FF_DUFF:
1090	>	the_ff = new DUFF();
1091	>	break;
1092
1093	<	simnfo->setBox( boxVector );
1093	>	case FF_LJ:
1094	>	the_ff = new LJFF();
1095	>	break;
1096	>
1097	>	case FF_EAM:
1098	>	the_ff = new EAM_FF();
1099	>	break;
1100	>
1101	>	default:
1102	>	sprintf( painCave.errMsg,
1103	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1104	>	painCave.isFatal = 1;
1105	>	simError();
1106		}
1107
1108		#ifdef IS_MPI
1109	<	strcpy( checkPointMsg, "Box size set up" );
1109	>	strcpy( checkPointMsg, "ForceField creation successful" );
1110		MPIcheckPoint();
1111		#endif // is_mpi
1112
1113	+	}
1114
537	–	// initialize the arrays
1115
1116	<	the_ff->setSimInfo( simnfo );
1116	>	void SimSetup::compList( void ){
1117
1118	<	makeMolecules();
1119	<	simnfo->identArray = new int[simnfo->n_atoms];
1120	<	for(i=0; i<simnfo->n_atoms; i++){
1121	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
1122	<	}
1118	>	int i;
1119	>	char* id;
1120	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1121	>	LinkedMolStamp* currentStamp = NULL;
1122	>	comp_stamps = new MoleculeStamp*[n_components];
1123
1124	<	if (the_globals->getUseRF() ) {
1125	<	simnfo->useReactionField = 1;
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	<	if( !the_globals->haveECR() ){
1128	<	sprintf( painCave.errMsg,
1129	<	"SimSetup Warning: using default value of 1/2 the smallest "
1130	<	"box length for the electrostaticCutoffRadius.\n"
1131	<	"I hope you have a very fast processor!\n");
1132	<	painCave.isFatal = 0;
1133	<	simError();
557	<	double smallest;
558	<	smallest = simnfo->boxLx;
559	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
560	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
561	<	simnfo->ecr = 0.5 * smallest;
562	<	} else {
563	<	simnfo->ecr        = the_globals->getECR();
564	<	}
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	>	}
1133	>
1134
1135	<	if( !the_globals->haveEST() ){
1136	<	sprintf( painCave.errMsg,
1137	<	"SimSetup Warning: using default value of 0.05 * the "
1138	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
570	<	);
571	<	painCave.isFatal = 0;
572	<	simError();
573	<	simnfo->est = 0.05 * simnfo->ecr;
574	<	} else {
575	<	simnfo->est        = the_globals->getEST();
576	<	}
1135	>	for( i=0; i<n_components; i++ ){
1136	>
1137	>	id = the_components[i]->getType();
1138	>	comp_stamps[i] = NULL;
1139
1140	<	if(!the_globals->haveDielectric() ){
1141	<	sprintf( painCave.errMsg,
1142	<	"SimSetup Error: You are trying to use Reaction Field without"
1143	<	"setting a dielectric constant!\n"
582	<	);
583	<	painCave.isFatal = 1;
584	<	simError();
585	<	}
586	<	simnfo->dielectric = the_globals->getDielectric();
587	<	} else {
588	<	if (usesDipoles) {
1140	>	// check to make sure the component isn't already in the list
1141	>
1142	>	comp_stamps[i] = headStamp->match( id );
1143	>	if( comp_stamps[i] == NULL ){
1144
1145	<	if( !the_globals->haveECR() ){
591	<	sprintf( painCave.errMsg,
592	<	"SimSetup Warning: using default value of 1/2 the smallest "
593	<	"box length for the electrostaticCutoffRadius.\n"
594	<	"I hope you have a very fast processor!\n");
595	<	painCave.isFatal = 0;
596	<	simError();
597	<	double smallest;
598	<	smallest = simnfo->boxLx;
599	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
600	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
601	<	simnfo->ecr = 0.5 * smallest;
602	<	} else {
603	<	simnfo->ecr        = the_globals->getECR();
604	<	}
1145	>	// extract the component from the list;
1146
1147	<	if( !the_globals->haveEST() ){
1148	<	sprintf( painCave.errMsg,
1149	<	"SimSetup Warning: using default value of 5%% of the "
1150	<	"electrostaticCutoffRadius for the "
1151	<	"electrostaticSkinThickness\n"
1152	<	);
1153	<	painCave.isFatal = 0;
1154	<	simError();
614	<	simnfo->est = 0.05 * simnfo->ecr;
615	<	} else {
616	<	simnfo->est        = the_globals->getEST();
1147	>	currentStamp = stamps->extractMolStamp( id );
1148	>	if( currentStamp == NULL ){
1149	>	sprintf( painCave.errMsg,
1150	>	"SimSetup error: Component \"%s\" was not found in the "
1151	>	"list of declared molecules\n",
1152	>	id );
1153	>	painCave.isFatal = 1;
1154	>	simError();
1155		}
1156	+
1157	+	headStamp->add( currentStamp );
1158	+	comp_stamps[i] = headStamp->match( id );
1159		}
1160	<	}
1160	>	}
1161
1162		#ifdef IS_MPI
1163	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
1163	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1164		MPIcheckPoint();
1165		#endif // is_mpi
1166
626	–	if( the_globals->haveInitialConfig() ){
627	–
628	–	InitializeFromFile* fileInit;
629	–	#ifdef IS_MPI // is_mpi
630	–	if( worldRank == 0 ){
631	–	#endif //is_mpi
632	–	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
633	–	#ifdef IS_MPI
634	–	}else fileInit = new InitializeFromFile( NULL );
635	–	#endif
636	–	fileInit->read_xyz( simnfo ); // default velocities on
1167
1168	<	delete fileInit;
639	<	}
640	<	else{
1168	>	}
1169
1170	<	#ifdef IS_MPI
1171	<
644	<	// no init from bass
1170	>	void SimSetup::calcSysValues( void ){
1171	>	int i, j, k;
1172
1173	<	sprintf( painCave.errMsg,
647	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
648	<	painCave.isFatal;
649	<	simError();
1173	>	int *molMembershipArray;
1174
1175	<	#else
1175	>	tot_atoms = 0;
1176	>	tot_bonds = 0;
1177	>	tot_bends = 0;
1178	>	tot_torsions = 0;
1179	>	for( i=0; i<n_components; i++ ){
1180	>
1181	>	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1182	>	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1183	>	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1184	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1185	>	}
1186	>
1187	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1188	>	molMembershipArray = new int[tot_atoms];
1189	>
1190	>	for(i=0; i<nInfo; i++){
1191	>	info[i].n_atoms = tot_atoms;
1192	>	info[i].n_bonds = tot_bonds;
1193	>	info[i].n_bends = tot_bends;
1194	>	info[i].n_torsions = tot_torsions;
1195	>	info[i].n_SRI = tot_SRI;
1196	>	info[i].n_mol = tot_nmol;
1197	>
1198	>	info[i].molMembershipArray = molMembershipArray;
1199	>	}
1200	>	}
1201
1202	<	initFromBass();
1202	>	#ifdef IS_MPI
1203
1204	+	void SimSetup::mpiMolDivide( void ){
1205	+
1206	+	int i, j, k;
1207	+	int localMol, allMol;
1208	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1209
1210	<	#endif
1211	<	}
1210	>	mpiSim = new mpiSimulation( info );
1211	>
1212	>	globalIndex = mpiSim->divideLabor();
1213
1214	<	#ifdef IS_MPI
1215	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1214	>	// set up the local variables
1215	>
1216	>	mol2proc = mpiSim->getMolToProcMap();
1217	>	molCompType = mpiSim->getMolComponentType();
1218	>
1219	>	allMol = 0;
1220	>	localMol = 0;
1221	>	local_atoms = 0;
1222	>	local_bonds = 0;
1223	>	local_bends = 0;
1224	>	local_torsions = 0;
1225	>	globalAtomIndex = 0;
1226	>
1227	>
1228	>	for( i=0; i<n_components; i++ ){
1229	>
1230	>	for( j=0; j<components_nmol[i]; j++ ){
1231	>
1232	>	if( mol2proc[allMol] == worldRank ){
1233	>
1234	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1235	>	local_bonds +=    comp_stamps[i]->getNBonds();
1236	>	local_bends +=    comp_stamps[i]->getNBends();
1237	>	local_torsions += comp_stamps[i]->getNTorsions();
1238	>	localMol++;
1239	>	}
1240	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1241	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1242	>	globalAtomIndex++;
1243	>	}
1244	>
1245	>	allMol++;
1246	>	}
1247	>	}
1248	>	local_SRI = local_bonds + local_bends + local_torsions;
1249	>
1250	>	info[0].n_atoms = mpiSim->getMyNlocal();
1251	>
1252	>	if( local_atoms != info[0].n_atoms ){
1253	>	sprintf( painCave.errMsg,
1254	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1255	>	" localAtom (%d) are not equal.\n",
1256	>	info[0].n_atoms,
1257	>	local_atoms );
1258	>	painCave.isFatal = 1;
1259	>	simError();
1260	>	}
1261	>
1262	>	info[0].n_bonds = local_bonds;
1263	>	info[0].n_bends = local_bends;
1264	>	info[0].n_torsions = local_torsions;
1265	>	info[0].n_SRI = local_SRI;
1266	>	info[0].n_mol = localMol;
1267	>
1268	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1269		MPIcheckPoint();
1270	+	}
1271	+
1272		#endif // is_mpi
1273
1274
1275	<
1276	<
667	<
1275	>	void SimSetup::makeSysArrays( void ){
1276	>	int i, j, k, l;
1277
1278	+	Atom** the_atoms;
1279	+	Molecule* the_molecules;
1280	+	Exclude** the_excludes;
1281	+
1282
1283	+	for(l=0; l<nInfo; l++){
1284	+
1285	+	// create the atom and short range interaction arrays
1286	+
1287	+	the_atoms = new Atom*[info[l].n_atoms];
1288	+	the_molecules = new Molecule[info[l].n_mol];
1289	+	int molIndex;
1290	+
1291	+	// initialize the molecule's stampID's
1292	+
1293		#ifdef IS_MPI
671	–	if( worldRank == 0 ){
672	–	#endif // is_mpi
1294
674	–	if( the_globals->haveFinalConfig() ){
675	–	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
676	–	}
677	–	else{
678	–	strcpy( simnfo->finalName, inFileName );
679	–	char* endTest;
680	–	int nameLength = strlen( simnfo->finalName );
681	–	endTest = &(simnfo->finalName[nameLength - 5]);
682	–	if( !strcmp( endTest, ".bass" ) ){
683	–	strcpy( endTest, ".eor" );
684	–	}
685	–	else if( !strcmp( endTest, ".BASS" ) ){
686	–	strcpy( endTest, ".eor" );
687	–	}
688	–	else{
689	–	endTest = &(simnfo->finalName[nameLength - 4]);
690	–	if( !strcmp( endTest, ".bss" ) ){
691	–	strcpy( endTest, ".eor" );
692	–	}
693	–	else if( !strcmp( endTest, ".mdl" ) ){
694	–	strcpy( endTest, ".eor" );
695	–	}
696	–	else{
697	–	strcat( simnfo->finalName, ".eor" );
698	–	}
699	–	}
700	–	}
1295
1296	<	// make the sample and status out names
1296	>	molIndex = 0;
1297	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1298
1299	<	strcpy( simnfo->sampleName, inFileName );
1300	<	char* endTest;
1301	<	int nameLength = strlen( simnfo->sampleName );
1302	<	endTest = &(simnfo->sampleName[nameLength - 5]);
1303	<	if( !strcmp( endTest, ".bass" ) ){
709	<	strcpy( endTest, ".dump" );
710	<	}
711	<	else if( !strcmp( endTest, ".BASS" ) ){
712	<	strcpy( endTest, ".dump" );
713	<	}
714	<	else{
715	<	endTest = &(simnfo->sampleName[nameLength - 4]);
716	<	if( !strcmp( endTest, ".bss" ) ){
717	<	strcpy( endTest, ".dump" );
1299	>	if(mol2proc[i] == worldRank ){
1300	>	the_molecules[molIndex].setStampID( molCompType[i] );
1301	>	the_molecules[molIndex].setMyIndex( molIndex );
1302	>	the_molecules[molIndex].setGlobalIndex( i );
1303	>	molIndex++;
1304		}
719	–	else if( !strcmp( endTest, ".mdl" ) ){
720	–	strcpy( endTest, ".dump" );
721	–	}
722	–	else{
723	–	strcat( simnfo->sampleName, ".dump" );
724	–	}
1305		}
1306
1307	<	strcpy( simnfo->statusName, inFileName );
1308	<	nameLength = strlen( simnfo->statusName );
1309	<	endTest = &(simnfo->statusName[nameLength - 5]);
1310	<	if( !strcmp( endTest, ".bass" ) ){
1311	<	strcpy( endTest, ".stat" );
1312	<	}
1313	<	else if( !strcmp( endTest, ".BASS" ) ){
1314	<	strcpy( endTest, ".stat" );
1315	<	}
1316	<	else{
1317	<	endTest = &(simnfo->statusName[nameLength - 4]);
1318	<	if( !strcmp( endTest, ".bss" ) ){
1319	<	strcpy( endTest, ".stat" );
1307	>	#else // is_mpi
1308	>
1309	>	molIndex = 0;
1310	>	globalAtomIndex = 0;
1311	>	for(i=0; i<n_components; i++){
1312	>	for(j=0; j<components_nmol[i]; j++ ){
1313	>	the_molecules[molIndex].setStampID( i );
1314	>	the_molecules[molIndex].setMyIndex( molIndex );
1315	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1316	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1317	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1318	>	globalAtomIndex++;
1319	>	}
1320	>	molIndex++;
1321		}
741	–	else if( !strcmp( endTest, ".mdl" ) ){
742	–	strcpy( endTest, ".stat" );
743	–	}
744	–	else{
745	–	strcat( simnfo->statusName, ".stat" );
746	–	}
1322		}
1323
1324	<	#ifdef IS_MPI
750	<	}
1324	>
1325		#endif // is_mpi
752	–
753	–	// set the status, sample, and themal kick times
754	–
755	–	if( the_globals->haveSampleTime() ){
756	–	simnfo->sampleTime = the_globals->getSampleTime();
757	–	simnfo->statusTime = simnfo->sampleTime;
758	–	simnfo->thermalTime = simnfo->sampleTime;
759	–	}
760	–	else{
761	–	simnfo->sampleTime = the_globals->getRunTime();
762	–	simnfo->statusTime = simnfo->sampleTime;
763	–	simnfo->thermalTime = simnfo->sampleTime;
764	–	}
1326
766	–	if( the_globals->haveStatusTime() ){
767	–	simnfo->statusTime = the_globals->getStatusTime();
768	–	}
1327
1328	<	if( the_globals->haveThermalTime() ){
1329	<	simnfo->thermalTime = the_globals->getThermalTime();
1330	<	}
1328	>	if( info[l].n_SRI ){
1329	>
1330	>	Exclude::createArray(info[l].n_SRI);
1331	>	the_excludes = new Exclude*[info[l].n_SRI];
1332	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1333	>	the_excludes[ex] = new Exclude(ex);
1334	>	}
1335	>	info[l].globalExcludes = new int;
1336	>	info[l].n_exclude = info[l].n_SRI;
1337	>	}
1338	>	else{
1339	>
1340	>	Exclude::createArray( 1 );
1341	>	the_excludes = new Exclude*;
1342	>	the_excludes[0] = new Exclude(0);
1343	>	the_excludes[0]->setPair( 0,0 );
1344	>	info[l].globalExcludes = new int;
1345	>	info[l].globalExcludes[0] = 0;
1346	>	info[l].n_exclude = 0;
1347	>	}
1348
1349	<	// check for the temperature set flag
1349	>	// set the arrays into the SimInfo object
1350
1351	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
1351	>	info[l].atoms = the_atoms;
1352	>	info[l].molecules = the_molecules;
1353	>	info[l].nGlobalExcludes = 0;
1354	>	info[l].excludes = the_excludes;
1355
1356	+	the_ff->setSimInfo( info );
1357	+
1358	+	}
1359	+	}
1360
1361	<	// make the integrator
780	<
781	<
782	<	NVT* myNVT = NULL;
783	<	switch( ensembleCase ){
1361	>	void SimSetup::makeIntegrator( void ){
1362
1363	<	case NVE_ENS:
786	<	new NVE( simnfo, the_ff );
787	<	break;
1363	>	int k;
1364
1365	<	case NVT_ENS:
1366	<	myNVT = new NVT( simnfo, the_ff );
1367	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
1368	<
1369	<	if (the_globals->haveTauThermostat())
1370	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
1371	<	//     else if (the_globals->haveQmass())
1372	<	//       myNVT->setQmass(the_globals->getQmass());
1373	<	else {
1365	>	NVT<RealIntegrator>*  myNVT = NULL;
1366	>	NPTi<RealIntegrator>* myNPTi = NULL;
1367	>	NPTf<RealIntegrator>* myNPTf = NULL;
1368	>	NPTim<RealIntegrator>* myNPTim = NULL;
1369	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1370	>	ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1371	>	ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL;
1372	>	ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL;
1373	>	ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL;
1374	>	ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL;
1375	>	ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL;
1376	>
1377	>	for(k=0; k<nInfo; k++){
1378	>
1379	>	switch( ensembleCase ){
1380	>
1381	>	case NVE_ENS:
1382	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1383	>	break;
1384	>
1385	>	case NVT_ENS:
1386	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1387	>	myNVT->setTargetTemp(globals->getTargetTemp());
1388	>
1389	>	if (globals->haveTauThermostat())
1390	>	myNVT->setTauThermostat(globals->getTauThermostat());
1391	>
1392	>	else {
1393	>	sprintf( painCave.errMsg,
1394	>	"SimSetup error: If you use the NVT\n"
1395	>	"    ensemble, you must set tauThermostat.\n");
1396	>	painCave.isFatal = 1;
1397	>	simError();
1398	>	}
1399	>	break;
1400	>
1401	>	case NPTi_ENS:
1402	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1403	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1404	>
1405	>	if (globals->haveTargetPressure())
1406	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1407	>	else {
1408	>	sprintf( painCave.errMsg,
1409	>	"SimSetup error: If you use a constant pressure\n"
1410	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1411	>	painCave.isFatal = 1;
1412	>	simError();
1413	>	}
1414	>
1415	>	if( globals->haveTauThermostat() )
1416	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1417	>	else{
1418	>	sprintf( painCave.errMsg,
1419	>	"SimSetup error: If you use an NPT\n"
1420	>	"    ensemble, you must set tauThermostat.\n");
1421	>	painCave.isFatal = 1;
1422	>	simError();
1423	>	}
1424	>
1425	>	if( globals->haveTauBarostat() )
1426	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1427	>	else{
1428	>	sprintf( painCave.errMsg,
1429	>	"SimSetup error: If you use an NPT\n"
1430	>	"    ensemble, you must set tauBarostat.\n");
1431	>	painCave.isFatal = 1;
1432	>	simError();
1433	>	}
1434	>	break;
1435	>
1436	>	case NPTf_ENS:
1437	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1438	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1439	>
1440	>	if (globals->haveTargetPressure())
1441	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1442	>	else {
1443	>	sprintf( painCave.errMsg,
1444	>	"SimSetup error: If you use a constant pressure\n"
1445	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1446	>	painCave.isFatal = 1;
1447	>	simError();
1448	>	}
1449	>
1450	>	if( globals->haveTauThermostat() )
1451	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1452	>	else{
1453	>	sprintf( painCave.errMsg,
1454	>	"SimSetup error: If you use an NPT\n"
1455	>	"    ensemble, you must set tauThermostat.\n");
1456	>	painCave.isFatal = 1;
1457	>	simError();
1458	>	}
1459	>
1460	>	if( globals->haveTauBarostat() )
1461	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1462	>	else{
1463	>	sprintf( painCave.errMsg,
1464	>	"SimSetup error: If you use an NPT\n"
1465	>	"    ensemble, you must set tauBarostat.\n");
1466	>	painCave.isFatal = 1;
1467	>	simError();
1468	>	}
1469	>	break;
1470	>
1471	>	case NPTim_ENS:
1472	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1473	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1474	>
1475	>	if (globals->haveTargetPressure())
1476	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1477	>	else {
1478	>	sprintf( painCave.errMsg,
1479	>	"SimSetup error: If you use a constant pressure\n"
1480	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1481	>	painCave.isFatal = 1;
1482	>	simError();
1483	>	}
1484	>
1485	>	if( globals->haveTauThermostat() )
1486	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1487	>	else{
1488	>	sprintf( painCave.errMsg,
1489	>	"SimSetup error: If you use an NPT\n"
1490	>	"    ensemble, you must set tauThermostat.\n");
1491	>	painCave.isFatal = 1;
1492	>	simError();
1493	>	}
1494	>
1495	>	if( globals->haveTauBarostat() )
1496	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1497	>	else{
1498		sprintf( painCave.errMsg,
1499	<	"SimSetup error: If you use the NVT\n"
1500	<	"    ensemble, you must set either tauThermostat or qMass.\n"
801	<	"    Neither of these was found in the BASS file.\n");
1499	>	"SimSetup error: If you use an NPT\n"
1500	>	"    ensemble, you must set tauBarostat.\n");
1501		painCave.isFatal = 1;
1502		simError();
1503	+	}
1504	+	break;
1505	+
1506	+	case NPTfm_ENS:
1507	+	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1508	+	myNPTfm->setTargetTemp( globals->getTargetTemp());
1509	+
1510	+	if (globals->haveTargetPressure())
1511	+	myNPTfm->setTargetPressure(globals->getTargetPressure());
1512	+	else {
1513	+	sprintf( painCave.errMsg,
1514	+	"SimSetup error: If you use a constant pressure\n"
1515	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1516	+	painCave.isFatal = 1;
1517	+	simError();
1518	+	}
1519	+
1520	+	if( globals->haveTauThermostat() )
1521	+	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1522	+	else{
1523	+	sprintf( painCave.errMsg,
1524	+	"SimSetup error: If you use an NPT\n"
1525	+	"    ensemble, you must set tauThermostat.\n");
1526	+	painCave.isFatal = 1;
1527	+	simError();
1528	+	}
1529	+
1530	+	if( globals->haveTauBarostat() )
1531	+	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1532	+	else{
1533	+	sprintf( painCave.errMsg,
1534	+	"SimSetup error: If you use an NPT\n"
1535	+	"    ensemble, you must set tauBarostat.\n");
1536	+	painCave.isFatal = 1;
1537	+	simError();
1538	+	}
1539	+	break;
1540	+
1541	+	case NVEZCONS_ENS:
1542	+
1543	+
1544	+	//setup index of z-constraint molecules, z-constraint sampel time
1545	+	//and z-constraint force output name. These parameter should be known
1546	+	//before constructing the z-constraint integrator
1547	+	setupZConstraint();
1548	+
1549	+	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1550	+
1551	+	break;
1552	+
1553	+
1554	+	case NVTZCONS_ENS:
1555	+
1556	+	setupZConstraint();
1557	+
1558	+	myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1559	+	myNVTZCons->setTargetTemp(globals->getTargetTemp());
1560	+
1561	+	if (globals->haveTauThermostat())
1562	+	myNVTZCons->setTauThermostat(globals->getTauThermostat());
1563	+
1564	+	else {
1565	+	sprintf( painCave.errMsg,
1566	+	"SimSetup error: If you use the NVT\n"
1567	+	"    ensemble, you must set tauThermostat.\n");
1568	+	painCave.isFatal = 1;
1569	+	simError();
1570	+	}
1571	+	break;
1572	+
1573	+	case NPTiZCONS_ENS:
1574	+
1575	+	setupZConstraint();
1576	+
1577	+	myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1578	+	myNPTiZCons->setTargetTemp( globals->getTargetTemp() );
1579	+
1580	+	if (globals->haveTargetPressure())
1581	+	myNPTiZCons->setTargetPressure(globals->getTargetPressure());
1582	+	else {
1583	+	sprintf( painCave.errMsg,
1584	+	"SimSetup error: If you use a constant pressure\n"
1585	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1586	+	painCave.isFatal = 1;
1587	+	simError();
1588	+	}
1589	+
1590	+	if( globals->haveTauThermostat() )
1591	+	myNPTiZCons->setTauThermostat( globals->getTauThermostat() );
1592	+	else{
1593	+	sprintf( painCave.errMsg,
1594	+	"SimSetup error: If you use an NPT\n"
1595	+	"    ensemble, you must set tauThermostat.\n");
1596	+	painCave.isFatal = 1;
1597	+	simError();
1598	+	}
1599	+
1600	+	if( globals->haveTauBarostat() )
1601	+	myNPTiZCons->setTauBarostat( globals->getTauBarostat() );
1602	+	else{
1603	+	sprintf( painCave.errMsg,
1604	+	"SimSetup error: If you use an NPT\n"
1605	+	"    ensemble, you must set tauBarostat.\n");
1606	+	painCave.isFatal = 1;
1607	+	simError();
1608	+	}
1609	+
1610	+	break;
1611	+
1612	+	case NPTfZCONS_ENS:
1613	+
1614	+	setupZConstraint();
1615	+
1616	+	myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1617	+	myNPTfZCons->setTargetTemp( globals->getTargetTemp());
1618	+
1619	+	if (globals->haveTargetPressure())
1620	+	myNPTfZCons->setTargetPressure(globals->getTargetPressure());
1621	+	else {
1622	+	sprintf( painCave.errMsg,
1623	+	"SimSetup error: If you use a constant pressure\n"
1624	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1625	+	painCave.isFatal = 1;
1626	+	simError();
1627	+	}
1628	+
1629	+	if( globals->haveTauThermostat() )
1630	+	myNPTfZCons->setTauThermostat( globals->getTauThermostat() );
1631	+	else{
1632	+	sprintf( painCave.errMsg,
1633	+	"SimSetup error: If you use an NPT\n"
1634	+	"    ensemble, you must set tauThermostat.\n");
1635	+	painCave.isFatal = 1;
1636	+	simError();
1637	+	}
1638	+
1639	+	if( globals->haveTauBarostat() )
1640	+	myNPTfZCons->setTauBarostat( globals->getTauBarostat() );
1641	+	else{
1642	+	sprintf( painCave.errMsg,
1643	+	"SimSetup error: If you use an NPT\n"
1644	+	"    ensemble, you must set tauBarostat.\n");
1645	+	painCave.isFatal = 1;
1646	+	simError();
1647	+	}
1648	+
1649	+	break;
1650	+
1651	+	case NPTimZCONS_ENS:
1652	+
1653	+	setupZConstraint();
1654	+
1655	+	myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1656	+	myNPTimZCons->setTargetTemp( globals->getTargetTemp());
1657	+
1658	+	if (globals->haveTargetPressure())
1659	+	myNPTimZCons->setTargetPressure(globals->getTargetPressure());
1660	+	else {
1661	+	sprintf( painCave.errMsg,
1662	+	"SimSetup error: If you use a constant pressure\n"
1663	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1664	+	painCave.isFatal = 1;
1665	+	simError();
1666	+	}
1667	+
1668	+	if( globals->haveTauThermostat() )
1669	+	myNPTimZCons->setTauThermostat( globals->getTauThermostat() );
1670	+	else{
1671	+	sprintf( painCave.errMsg,
1672	+	"SimSetup error: If you use an NPT\n"
1673	+	"    ensemble, you must set tauThermostat.\n");
1674	+	painCave.isFatal = 1;
1675	+	simError();
1676	+	}
1677	+
1678	+	if( globals->haveTauBarostat() )
1679	+	myNPTimZCons->setTauBarostat( globals->getTauBarostat() );
1680	+	else{
1681	+	sprintf( painCave.errMsg,
1682	+	"SimSetup error: If you use an NPT\n"
1683	+	"    ensemble, you must set tauBarostat.\n");
1684	+	painCave.isFatal = 1;
1685	+	simError();
1686	+	}
1687	+
1688	+	break;
1689	+
1690	+	case NPTfmZCONS_ENS:
1691	+
1692	+	setupZConstraint();
1693	+
1694	+	myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1695	+	myNPTfmZCons->setTargetTemp( globals->getTargetTemp());
1696	+
1697	+	if (globals->haveTargetPressure())
1698	+	myNPTfmZCons->setTargetPressure(globals->getTargetPressure());
1699	+	else {
1700	+	sprintf( painCave.errMsg,
1701	+	"SimSetup error: If you use a constant pressure\n"
1702	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1703	+	painCave.isFatal = 1;
1704	+	simError();
1705	+	}
1706	+
1707	+	if( globals->haveTauThermostat() )
1708	+	myNPTfmZCons->setTauThermostat( globals->getTauThermostat() );
1709	+	else{
1710	+	sprintf( painCave.errMsg,
1711	+	"SimSetup error: If you use an NPT\n"
1712	+	"    ensemble, you must set tauThermostat.\n");
1713	+	painCave.isFatal = 1;
1714	+	simError();
1715	+	}
1716	+
1717	+	if( globals->haveTauBarostat() )
1718	+	myNPTfmZCons->setTauBarostat( globals->getTauBarostat() );
1719	+	else{
1720	+	sprintf( painCave.errMsg,
1721	+	"SimSetup error: If you use an NPT\n"
1722	+	"    ensemble, you must set tauBarostat.\n");
1723	+	painCave.isFatal = 1;
1724	+	simError();
1725	+	}
1726	+	break;
1727	+
1728	+
1729	+
1730	+	default:
1731	+	sprintf( painCave.errMsg,
1732	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1733	+	painCave.isFatal = 1;
1734	+	simError();
1735		}
805	–	break;
806	–
807	–	default:
808	–	sprintf( painCave.errMsg,
809	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
810	–	painCave.isFatal = 1;
811	–	simError();
1736		}
1737	+	}
1738
1739	+	void SimSetup::initFortran( void ){
1740
1741	<	#ifdef IS_MPI
816	<	mpiSim->mpiRefresh();
817	<	#endif
818	<
819	<	// initialize the Fortran
820	<
821	<
822	<	simnfo->refreshSim();
1741	>	info[0].refreshSim();
1742
1743	<	if( !strcmp( simnfo->mixingRule, "standard") ){
1743	>	if( !strcmp( info[0].mixingRule, "standard") ){
1744		the_ff->initForceField( LB_MIXING_RULE );
1745		}
1746	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
1746	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1747		the_ff->initForceField( EXPLICIT_MIXING_RULE );
1748		}
1749		else{
1750		sprintf( painCave.errMsg,
1751		"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1752	<	simnfo->mixingRule );
1752	>	info[0].mixingRule );
1753		painCave.isFatal = 1;
1754		simError();
1755		}
#	Line 841 | Line 1760 | void SimSetup::createSim( void ){
1760		"Successfully intialized the mixingRule for Fortran." );
1761		MPIcheckPoint();
1762		#endif // is_mpi
1763	+
1764		}
1765
1766	+	void SimSetup::setupZConstraint()
1767	+	{
1768	+	int k;
1769
1770	<	void SimSetup::makeMolecules( void ){
848	<
849	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
850	<	molInit info;
851	<	DirectionalAtom* dAtom;
852	<	LinkedAssign* extras;
853	<	LinkedAssign* current_extra;
854	<	AtomStamp* currentAtom;
855	<	BondStamp* currentBond;
856	<	BendStamp* currentBend;
857	<	TorsionStamp* currentTorsion;
858	<
859	<	bond_pair* theBonds;
860	<	bend_set* theBends;
861	<	torsion_set* theTorsions;
862	<
863	<
864	<	//init the forceField paramters
865	<
866	<	the_ff->readParams();
867	<
868	<
869	<	// init the atoms
870	<
871	<	double ux, uy, uz, u, uSqr;
872	<
873	<	atomOffset = 0;
874	<	excludeOffset = 0;
875	<	for(i=0; i<simnfo->n_mol; i++){
1770	>	for(k=0; k<nInfo; k++){
1771
1772	<	stampID = the_molecules[i].getStampID();
878	<
879	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
880	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
881	<	info.nBends    = comp_stamps[stampID]->getNBends();
882	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
883	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
884	<
885	<	info.myAtoms = &the_atoms[atomOffset];
886	<	info.myExcludes = &the_excludes[excludeOffset];
887	<	info.myBonds = new Bond*[info.nBonds];
888	<	info.myBends = new Bend*[info.nBends];
889	<	info.myTorsions = new Torsion*[info.nTorsions];
890	<
891	<	theBonds = new bond_pair[info.nBonds];
892	<	theBends = new bend_set[info.nBends];
893	<	theTorsions = new torsion_set[info.nTorsions];
894	<
895	<	// make the Atoms
896	<
897	<	for(j=0; j<info.nAtoms; j++){
1772	>	if(globals->haveZConsTime()){
1773
1774	<	currentAtom = comp_stamps[stampID]->getAtom( j );
1775	<	if( currentAtom->haveOrientation() ){
1776	<
1777	<	dAtom = new DirectionalAtom(j + atomOffset);
1778	<	simnfo->n_oriented++;
1779	<	info.myAtoms[j] = dAtom;
1780	<
1781	<	ux = currentAtom->getOrntX();
1782	<	uy = currentAtom->getOrntY();
1783	<	uz = currentAtom->getOrntZ();
1784	<
1785	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
1786	<
912	<	u = sqrt( uSqr );
913	<	ux = ux / u;
914	<	uy = uy / u;
915	<	uz = uz / u;
916	<
917	<	dAtom->setSUx( ux );
918	<	dAtom->setSUy( uy );
919	<	dAtom->setSUz( uz );
920	<	}
921	<	else{
922	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
923	<	}
924	<	info.myAtoms[j]->setType( currentAtom->getType() );
1774	>	//add sample time of z-constraint  into SimInfo's property list
1775	>	DoubleData* zconsTimeProp = new DoubleData();
1776	>	zconsTimeProp->setID("zconstime");
1777	>	zconsTimeProp->setData(globals->getZConsTime());
1778	>	info[k].addProperty(zconsTimeProp);
1779	>	}
1780	>	else{
1781	>	sprintf( painCave.errMsg,
1782	>	"ZConstraint error: If you use an ZConstraint\n"
1783	>	" , you must set sample time.\n");
1784	>	painCave.isFatal = 1;
1785	>	simError();
1786	>	}
1787
1788	<	#ifdef IS_MPI
1788	>	if(globals->haveIndexOfAllZConsMols()){
1789	>
1790	>	//add index of z-constraint molecules into SimInfo's property list
1791	>	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1792
1793	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
1793	>	//sort the index
1794	>	sort(tempIndex.begin(), tempIndex.end());
1795
1796	<	#endif // is_mpi
1797	<	}
1798	<
1799	<	// make the bonds
1800	<	for(j=0; j<info.nBonds; j++){
1796	>	IndexData* zconsIndex = new IndexData();
1797	>	zconsIndex->setID("zconsindex");
1798	>	zconsIndex->setIndexData(tempIndex);
1799	>	info[k].addProperty(zconsIndex);
1800	>	}
1801	>	else{
1802	>	sprintf( painCave.errMsg,
1803	>	"SimSetup error: If you use an ZConstraint\n"
1804	>	" , you must set index of z-constraint molecules.\n");
1805	>	painCave.isFatal = 1;
1806	>	simError();
1807
936	–	currentBond = comp_stamps[stampID]->getBond( j );
937	–	theBonds[j].a = currentBond->getA() + atomOffset;
938	–	theBonds[j].b = currentBond->getB() + atomOffset;
939	–
940	–	exI = theBonds[j].a;
941	–	exJ = theBonds[j].b;
942	–
943	–	// exclude_I must always be the smaller of the pair
944	–	if( exI > exJ ){
945	–	tempEx = exI;
946	–	exI = exJ;
947	–	exJ = tempEx;
948	–	}
949	–	#ifdef IS_MPI
950	–	tempEx = exI;
951	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
952	–	tempEx = exJ;
953	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
954	–
955	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
956	–	#else  // isn't MPI
957	–
958	–	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
959	–	#endif  //is_mpi
1808		}
961	–	excludeOffset += info.nBonds;
962	–
963	–	//make the bends
964	–	for(j=0; j<info.nBends; j++){
965	–
966	–	currentBend = comp_stamps[stampID]->getBend( j );
967	–	theBends[j].a = currentBend->getA() + atomOffset;
968	–	theBends[j].b = currentBend->getB() + atomOffset;
969	–	theBends[j].c = currentBend->getC() + atomOffset;
970	–
971	–	if( currentBend->haveExtras() ){
972	–
973	–	extras = currentBend->getExtras();
974	–	current_extra = extras;
975	–
976	–	while( current_extra != NULL ){
977	–	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
978	–
979	–	switch( current_extra->getType() ){
980	–
981	–	case 0:
982	–	theBends[j].ghost =
983	–	current_extra->getInt() + atomOffset;
984	–	theBends[j].isGhost = 1;
985	–	break;
986	–
987	–	case 1:
988	–	theBends[j].ghost =
989	–	(int)current_extra->getDouble() + atomOffset;
990	–	theBends[j].isGhost = 1;
991	–	break;
992	–
993	–	default:
994	–	sprintf( painCave.errMsg,
995	–	"SimSetup Error: ghostVectorSource was neither a "
996	–	"double nor an int.\n"
997	–	"-->Bend[%d] in %s\n",
998	–	j, comp_stamps[stampID]->getID() );
999	–	painCave.isFatal = 1;
1000	–	simError();
1001	–	}
1002	–	}
1003	–
1004	–	else{
1005	–
1006	–	sprintf( painCave.errMsg,
1007	–	"SimSetup Error: unhandled bend assignment:\n"
1008	–	"    -->%s in Bend[%d] in %s\n",
1009	–	current_extra->getlhs(),
1010	–	j, comp_stamps[stampID]->getID() );
1011	–	painCave.isFatal = 1;
1012	–	simError();
1013	–	}
1014	–
1015	–	current_extra = current_extra->getNext();
1016	–	}
1017	–	}
1018	–
1019	–	if( !theBends[j].isGhost ){
1020	–
1021	–	exI = theBends[j].a;
1022	–	exJ = theBends[j].c;
1023	–	}
1024	–	else{
1025	–
1026	–	exI = theBends[j].a;
1027	–	exJ = theBends[j].b;
1028	–	}
1029	–
1030	–	// exclude_I must always be the smaller of the pair
1031	–	if( exI > exJ ){
1032	–	tempEx = exI;
1033	–	exI = exJ;
1034	–	exJ = tempEx;
1035	–	}
1036	–	#ifdef IS_MPI
1037	–	tempEx = exI;
1038	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1039	–	tempEx = exJ;
1040	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1041	–
1042	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1043	–	#else  // isn't MPI
1044	–	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1045	–	#endif  //is_mpi
1046	–	}
1047	–	excludeOffset += info.nBends;
1048	–
1049	–	for(j=0; j<info.nTorsions; j++){
1050	–
1051	–	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1052	–	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1053	–	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1054	–	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1055	–	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1056	–
1057	–	exI = theTorsions[j].a;
1058	–	exJ = theTorsions[j].d;
1059	–
1060	–	// exclude_I must always be the smaller of the pair
1061	–	if( exI > exJ ){
1062	–	tempEx = exI;
1063	–	exI = exJ;
1064	–	exJ = tempEx;
1065	–	}
1066	–	#ifdef IS_MPI
1067	–	tempEx = exI;
1068	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1069	–	tempEx = exJ;
1070	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1071	–
1072	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1073	–	#else  // isn't MPI
1074	–	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1075	–	#endif  //is_mpi
1076	–	}
1077	–	excludeOffset += info.nTorsions;
1078	–
1809
1810	<	// send the arrays off to the forceField for init.
1811	<
1812	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1813	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1814	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1815	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1816	<
1817	<
1818	<	the_molecules[i].initialize( info );
1819	<
1820	<
1821	<	atomOffset += info.nAtoms;
1822	<	delete[] theBonds;
1093	<	delete[] theBends;
1094	<	delete[] theTorsions;
1810	>	//Determine the name of ouput file and add it into SimInfo's property list
1811	>	//Be careful, do not use inFileName, since it is a pointer which
1812	>	//point to a string at master node, and slave nodes do not contain that string
1813	>
1814	>	string zconsOutput(info[k].finalName);
1815	>
1816	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1817	>
1818	>	StringData* zconsFilename = new StringData();
1819	>	zconsFilename->setID("zconsfilename");
1820	>	zconsFilename->setData(zconsOutput);
1821	>
1822	>	info[k].addProperty(zconsFilename);
1823		}
1096	–
1097	–	#ifdef IS_MPI
1098	–	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1099	–	MPIcheckPoint();
1100	–	#endif // is_mpi
1101	–
1102	–	// clean up the forcefield
1103	–	the_ff->calcRcut();
1104	–	the_ff->cleanMe();
1105	–
1824		}
1107	–
1108	–	void SimSetup::initFromBass( void ){
1109	–
1110	–	int i, j, k;
1111	–	int n_cells;
1112	–	double cellx, celly, cellz;
1113	–	double temp1, temp2, temp3;
1114	–	int n_per_extra;
1115	–	int n_extra;
1116	–	int have_extra, done;
1117	–
1118	–	temp1 = (double)tot_nmol / 4.0;
1119	–	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1120	–	temp3 = ceil( temp2 );
1121	–
1122	–	have_extra =0;
1123	–	if( temp2 < temp3 ){ // we have a non-complete lattice
1124	–	have_extra =1;
1125	–
1126	–	n_cells = (int)temp3 - 1;
1127	–	cellx = simnfo->boxLx / temp3;
1128	–	celly = simnfo->boxLy / temp3;
1129	–	cellz = simnfo->boxLz / temp3;
1130	–	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1131	–	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1132	–	n_per_extra = (int)ceil( temp1 );
1133	–
1134	–	if( n_per_extra > 4){
1135	–	sprintf( painCave.errMsg,
1136	–	"SimSetup error. There has been an error in constructing"
1137	–	" the non-complete lattice.\n" );
1138	–	painCave.isFatal = 1;
1139	–	simError();
1140	–	}
1141	–	}
1142	–	else{
1143	–	n_cells = (int)temp3;
1144	–	cellx = simnfo->boxLx / temp3;
1145	–	celly = simnfo->boxLy / temp3;
1146	–	cellz = simnfo->boxLz / temp3;
1147	–	}
1148	–
1149	–	current_mol = 0;
1150	–	current_comp_mol = 0;
1151	–	current_comp = 0;
1152	–	current_atom_ndx = 0;
1153	–
1154	–	for( i=0; i < n_cells ; i++ ){
1155	–	for( j=0; j < n_cells; j++ ){
1156	–	for( k=0; k < n_cells; k++ ){
1157	–
1158	–	makeElement( i * cellx,
1159	–	j * celly,
1160	–	k * cellz );
1161	–
1162	–	makeElement( i * cellx + 0.5 * cellx,
1163	–	j * celly + 0.5 * celly,
1164	–	k * cellz );
1165	–
1166	–	makeElement( i * cellx,
1167	–	j * celly + 0.5 * celly,
1168	–	k * cellz + 0.5 * cellz );
1169	–
1170	–	makeElement( i * cellx + 0.5 * cellx,
1171	–	j * celly,
1172	–	k * cellz + 0.5 * cellz );
1173	–	}
1174	–	}
1175	–	}
1176	–
1177	–	if( have_extra ){
1178	–	done = 0;
1179	–
1180	–	int start_ndx;
1181	–	for( i=0; i < (n_cells+1) && !done; i++ ){
1182	–	for( j=0; j < (n_cells+1) && !done; j++ ){
1183	–
1184	–	if( i < n_cells ){
1185	–
1186	–	if( j < n_cells ){
1187	–	start_ndx = n_cells;
1188	–	}
1189	–	else start_ndx = 0;
1190	–	}
1191	–	else start_ndx = 0;
1192	–
1193	–	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1194	–
1195	–	makeElement( i * cellx,
1196	–	j * celly,
1197	–	k * cellz );
1198	–	done = ( current_mol >= tot_nmol );
1199	–
1200	–	if( !done && n_per_extra > 1 ){
1201	–	makeElement( i * cellx + 0.5 * cellx,
1202	–	j * celly + 0.5 * celly,
1203	–	k * cellz );
1204	–	done = ( current_mol >= tot_nmol );
1205	–	}
1206	–
1207	–	if( !done && n_per_extra > 2){
1208	–	makeElement( i * cellx,
1209	–	j * celly + 0.5 * celly,
1210	–	k * cellz + 0.5 * cellz );
1211	–	done = ( current_mol >= tot_nmol );
1212	–	}
1213	–
1214	–	if( !done && n_per_extra > 3){
1215	–	makeElement( i * cellx + 0.5 * cellx,
1216	–	j * celly,
1217	–	k * cellz + 0.5 * cellz );
1218	–	done = ( current_mol >= tot_nmol );
1219	–	}
1220	–	}
1221	–	}
1222	–	}
1223	–	}
1224	–
1225	–
1226	–	for( i=0; i<simnfo->n_atoms; i++ ){
1227	–	simnfo->atoms[i]->set_vx( 0.0 );
1228	–	simnfo->atoms[i]->set_vy( 0.0 );
1229	–	simnfo->atoms[i]->set_vz( 0.0 );
1230	–	}
1231	–	}
1232	–
1233	–	void SimSetup::makeElement( double x, double y, double z ){
1234	–
1235	–	int k;
1236	–	AtomStamp* current_atom;
1237	–	DirectionalAtom* dAtom;
1238	–	double rotMat[3][3];
1239	–
1240	–	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1241	–
1242	–	current_atom = comp_stamps[current_comp]->getAtom( k );
1243	–	if( !current_atom->havePosition() ){
1244	–	sprintf( painCave.errMsg,
1245	–	"SimSetup:initFromBass error.\n"
1246	–	"\tComponent %s, atom %s does not have a position specified.\n"
1247	–	"\tThe initialization routine is unable to give a start"
1248	–	" position.\n",
1249	–	comp_stamps[current_comp]->getID(),
1250	–	current_atom->getType() );
1251	–	painCave.isFatal = 1;
1252	–	simError();
1253	–	}
1254	–
1255	–	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1256	–	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1257	–	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1258	–
1259	–	if( the_atoms[current_atom_ndx]->isDirectional() ){
1260	–
1261	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1262	–
1263	–	rotMat[0][0] = 1.0;
1264	–	rotMat[0][1] = 0.0;
1265	–	rotMat[0][2] = 0.0;
1266	–
1267	–	rotMat[1][0] = 0.0;
1268	–	rotMat[1][1] = 1.0;
1269	–	rotMat[1][2] = 0.0;
1270	–
1271	–	rotMat[2][0] = 0.0;
1272	–	rotMat[2][1] = 0.0;
1273	–	rotMat[2][2] = 1.0;
1274	–
1275	–	dAtom->setA( rotMat );
1276	–	}
1277	–
1278	–	current_atom_ndx++;
1279	–	}
1280	–
1281	–	current_mol++;
1282	–	current_comp_mol++;
1283	–
1284	–	if( current_comp_mol >= components_nmol[current_comp] ){
1285	–
1286	–	current_comp_mol = 0;
1287	–	current_comp++;
1288	–	}
1289	–	}

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