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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 504 by mmeineke, Thu Apr 17 21:54:18 2003 UTC vs.
Revision 699 by tim, Fri Aug 15 19:24:13 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 "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 12 | Line 15
15		#include "mpiSimulation.hpp"
16		#endif
17
18	+	// some defines for ensemble and Forcefield  cases
19	+
20	+	#define NVE_ENS        0
21	+	#define NVT_ENS        1
22	+	#define NPTi_ENS       2
23	+	#define NPTf_ENS       3
24	+	#define NPTim_ENS      4
25	+	#define NPTfm_ENS      5
26	+
27	+	#define FF_DUFF 0
28	+	#define FF_LJ   1
29	+	#define FF_EAM  2
30	+
31	+	using namespace std;
32	+
33		SimSetup::SimSetup(){
34	+
35	+	isInfoArray = 0;
36	+	nInfo = 1;
37	+
38		stamps = new MakeStamps();
39		globals = new Globals();
40
41	+
42		#ifdef IS_MPI
43		strcpy( checkPointMsg, "SimSetup creation successful" );
44		MPIcheckPoint();
#	Line 27 | Line 50 | SimSetup::~SimSetup(){
50		delete globals;
51		}
52
53	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
54	+	info = the_info;
55	+	nInfo = theNinfo;
56	+	isInfoArray = 1;
57	+	}
58	+
59	+
60		void SimSetup::parseFile( char* fileName ){
61
62		#ifdef IS_MPI
#	Line 62 | Line 92 | void SimSetup::receiveParse(void){
92
93		#endif // is_mpi
94
95	<	void SimSetup::createSim( void ){
95	>	void SimSetup::createSim(void){
96
67	–	MakeStamps *the_stamps;
68	–	Globals* the_globals;
69	–	ExtendedSystem* the_extendedsystem;
97		int i, j, k, globalAtomIndex;
98	+
99	+	// gather all of the information from the Bass file
100
101	<	// get the stamps and globals;
73	<	the_stamps = stamps;
74	<	the_globals = globals;
101	>	gatherInfo();
102
103	<	// set the easy ones first
77	<	simnfo->target_temp = the_globals->getTargetTemp();
78	<	simnfo->dt = the_globals->getDt();
79	<	simnfo->run_time = the_globals->getRunTime();
103	>	// creation of complex system objects
104
105	<	// get the ones we know are there, yet still may need some work.
82	<	n_components = the_globals->getNComponents();
83	<	strcpy( force_field, the_globals->getForceField() );
105	>	sysObjectsCreation();
106
107	<	// get the ensemble and set up an extended system if we need it:
86	<	strcpy( ensemble, the_globals->getEnsemble() );
87	<	if( !strcasecmp( ensemble, "NPT" ) ) {
88	<	the_extendedsystem = new ExtendedSystem( simnfo );
89	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
90	<	if (the_globals->haveTargetPressure())
91	<	the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
92	<	else {
93	<	sprintf( painCave.errMsg,
94	<	"SimSetup error: If you use the constant pressure\n"
95	<	"    ensemble, you must set targetPressure.\n"
96	<	"    This was found in the BASS file.\n");
97	<	painCave.isFatal = 1;
98	<	simError();
99	<	}
107	>	// check on the post processing info
108
109	<	if (the_globals->haveTauThermostat())
102	<	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
103	<	else if (the_globals->haveQmass())
104	<	the_extendedsystem->setQmass(the_globals->getQmass());
105	<	else {
106	<	sprintf( painCave.errMsg,
107	<	"SimSetup error: If you use one of the constant temperature\n"
108	<	"    ensembles, you must set either tauThermostat or qMass.\n"
109	<	"    Neither of these was found in the BASS file.\n");
110	<	painCave.isFatal = 1;
111	<	simError();
112	<	}
109	>	finalInfoCheck();
110
111	<	if (the_globals->haveTauBarostat())
112	<	the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
113	<	else {
111	>	// initialize the system coordinates
112	>
113	>	if( !isInfoArray ) initSystemCoords();
114	>
115	>	// make the output filenames
116	>
117	>	makeOutNames();
118	>
119	>	// make the integrator
120	>
121	>	makeIntegrator();
122	>
123	>	#ifdef IS_MPI
124	>	mpiSim->mpiRefresh();
125	>	#endif
126	>
127	>	// initialize the Fortran
128	>
129	>	initFortran();
130	>
131	>
132	>
133	>	}
134	>
135	>
136	>	void SimSetup::makeMolecules( void ){
137	>
138	>	int k,l;
139	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140	>	molInit molInfo;
141	>	DirectionalAtom* dAtom;
142	>	LinkedAssign* extras;
143	>	LinkedAssign* current_extra;
144	>	AtomStamp* currentAtom;
145	>	BondStamp* currentBond;
146	>	BendStamp* currentBend;
147	>	TorsionStamp* currentTorsion;
148	>
149	>	bond_pair* theBonds;
150	>	bend_set* theBends;
151	>	torsion_set* theTorsions;
152	>
153	>
154	>	//init the forceField paramters
155	>
156	>	the_ff->readParams();
157	>
158	>
159	>	// init the atoms
160	>
161	>	double ux, uy, uz, u, uSqr;
162	>
163	>	for(k=0; k<nInfo; k++){
164	>
165	>	the_ff->setSimInfo( &(info[k]) );
166	>
167	>	atomOffset = 0;
168	>	excludeOffset = 0;
169	>	for(i=0; i<info[k].n_mol; i++){
170	>
171	>	stampID = info[k].molecules[i].getStampID();
172	>
173	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
174	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
175	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
176	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
177	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
178	>
179	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
180	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
181	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
182	>	molInfo.myBends = new Bend*[molInfo.nBends];
183	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
184	>
185	>	theBonds = new bond_pair[molInfo.nBonds];
186	>	theBends = new bend_set[molInfo.nBends];
187	>	theTorsions = new torsion_set[molInfo.nTorsions];
188	>
189	>	// make the Atoms
190	>
191	>	for(j=0; j<molInfo.nAtoms; j++){
192	>
193	>	currentAtom = comp_stamps[stampID]->getAtom( j );
194	>	if( currentAtom->haveOrientation() ){
195	>
196	>	dAtom = new DirectionalAtom( (j + atomOffset),
197	>	info[k].getConfiguration() );
198	>	info[k].n_oriented++;
199	>	molInfo.myAtoms[j] = dAtom;
200	>
201	>	ux = currentAtom->getOrntX();
202	>	uy = currentAtom->getOrntY();
203	>	uz = currentAtom->getOrntZ();
204	>
205	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
206	>
207	>	u = sqrt( uSqr );
208	>	ux = ux / u;
209	>	uy = uy / u;
210	>	uz = uz / u;
211	>
212	>	dAtom->setSUx( ux );
213	>	dAtom->setSUy( uy );
214	>	dAtom->setSUz( uz );
215	>	}
216	>	else{
217	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
218	>	info[k].getConfiguration() );
219	>	}
220	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221	>
222	>	#ifdef IS_MPI
223	>
224	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
225	>
226	>	#endif // is_mpi
227	>	}
228	>
229	>	// make the bonds
230	>	for(j=0; j<molInfo.nBonds; j++){
231	>
232	>	currentBond = comp_stamps[stampID]->getBond( j );
233	>	theBonds[j].a = currentBond->getA() + atomOffset;
234	>	theBonds[j].b = currentBond->getB() + atomOffset;
235	>
236	>	exI = theBonds[j].a;
237	>	exJ = theBonds[j].b;
238	>
239	>	// exclude_I must always be the smaller of the pair
240	>	if( exI > exJ ){
241	>	tempEx = exI;
242	>	exI = exJ;
243	>	exJ = tempEx;
244	>	}
245	>	#ifdef IS_MPI
246	>	tempEx = exI;
247	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
248	>	tempEx = exJ;
249	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
250	>
251	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
252	>	#else  // isn't MPI
253	>
254	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
255	>	#endif  //is_mpi
256	>	}
257	>	excludeOffset += molInfo.nBonds;
258	>
259	>	//make the bends
260	>	for(j=0; j<molInfo.nBends; j++){
261	>
262	>	currentBend = comp_stamps[stampID]->getBend( j );
263	>	theBends[j].a = currentBend->getA() + atomOffset;
264	>	theBends[j].b = currentBend->getB() + atomOffset;
265	>	theBends[j].c = currentBend->getC() + atomOffset;
266	>
267	>	if( currentBend->haveExtras() ){
268	>
269	>	extras = currentBend->getExtras();
270	>	current_extra = extras;
271	>
272	>	while( current_extra != NULL ){
273	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
274	>
275	>	switch( current_extra->getType() ){
276	>
277	>	case 0:
278	>	theBends[j].ghost =
279	>	current_extra->getInt() + atomOffset;
280	>	theBends[j].isGhost = 1;
281	>	break;
282	>
283	>	case 1:
284	>	theBends[j].ghost =
285	>	(int)current_extra->getDouble() + atomOffset;
286	>	theBends[j].isGhost = 1;
287	>	break;
288	>
289	>	default:
290	>	sprintf( painCave.errMsg,
291	>	"SimSetup Error: ghostVectorSource was neither a "
292	>	"double nor an int.\n"
293	>	"-->Bend[%d] in %s\n",
294	>	j, comp_stamps[stampID]->getID() );
295	>	painCave.isFatal = 1;
296	>	simError();
297	>	}
298	>	}
299	>
300	>	else{
301	>
302	>	sprintf( painCave.errMsg,
303	>	"SimSetup Error: unhandled bend assignment:\n"
304	>	"    -->%s in Bend[%d] in %s\n",
305	>	current_extra->getlhs(),
306	>	j, comp_stamps[stampID]->getID() );
307	>	painCave.isFatal = 1;
308	>	simError();
309	>	}
310	>
311	>	current_extra = current_extra->getNext();
312	>	}
313	>	}
314	>
315	>	if( !theBends[j].isGhost ){
316	>
317	>	exI = theBends[j].a;
318	>	exJ = theBends[j].c;
319	>	}
320	>	else{
321	>
322	>	exI = theBends[j].a;
323	>	exJ = theBends[j].b;
324	>	}
325	>
326	>	// exclude_I must always be the smaller of the pair
327	>	if( exI > exJ ){
328	>	tempEx = exI;
329	>	exI = exJ;
330	>	exJ = tempEx;
331	>	}
332	>	#ifdef IS_MPI
333	>	tempEx = exI;
334	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
335	>	tempEx = exJ;
336	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
337	>
338	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
339	>	#else  // isn't MPI
340	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
341	>	#endif  //is_mpi
342	>	}
343	>	excludeOffset += molInfo.nBends;
344	>
345	>	for(j=0; j<molInfo.nTorsions; j++){
346	>
347	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
348	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
349	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
350	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
351	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
352	>
353	>	exI = theTorsions[j].a;
354	>	exJ = theTorsions[j].d;
355	>
356	>	// exclude_I must always be the smaller of the pair
357	>	if( exI > exJ ){
358	>	tempEx = exI;
359	>	exI = exJ;
360	>	exJ = tempEx;
361	>	}
362	>	#ifdef IS_MPI
363	>	tempEx = exI;
364	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
365	>	tempEx = exJ;
366	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
367	>
368	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
369	>	#else  // isn't MPI
370	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
371	>	#endif  //is_mpi
372	>	}
373	>	excludeOffset += molInfo.nTorsions;
374	>
375	>
376	>	// send the arrays off to the forceField for init.
377	>
378	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
379	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
380	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
381	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
382	>
383	>
384	>	info[k].molecules[i].initialize( molInfo );
385	>
386	>
387	>	atomOffset += molInfo.nAtoms;
388	>	delete[] theBonds;
389	>	delete[] theBends;
390	>	delete[] theTorsions;
391	>	}
392	>	}
393	>
394	>	#ifdef IS_MPI
395	>	sprintf( checkPointMsg, "all molecules initialized succesfully" );
396	>	MPIcheckPoint();
397	>	#endif // is_mpi
398	>
399	>	// clean up the forcefield
400	>
401	>	the_ff->calcRcut();
402	>	the_ff->cleanMe();
403	>
404	>	}
405	>
406	>	void SimSetup::initFromBass( void ){
407	>
408	>	int i, j, k;
409	>	int n_cells;
410	>	double cellx, celly, cellz;
411	>	double temp1, temp2, temp3;
412	>	int n_per_extra;
413	>	int n_extra;
414	>	int have_extra, done;
415	>
416	>	double vel[3];
417	>	vel[0] = 0.0;
418	>	vel[1] = 0.0;
419	>	vel[2] = 0.0;
420	>
421	>	temp1 = (double)tot_nmol / 4.0;
422	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
423	>	temp3 = ceil( temp2 );
424	>
425	>	have_extra =0;
426	>	if( temp2 < temp3 ){ // we have a non-complete lattice
427	>	have_extra =1;
428	>
429	>	n_cells = (int)temp3 - 1;
430	>	cellx = info[0].boxL[0] / temp3;
431	>	celly = info[0].boxL[1] / temp3;
432	>	cellz = info[0].boxL[2] / temp3;
433	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
434	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
435	>	n_per_extra = (int)ceil( temp1 );
436	>
437	>	if( n_per_extra > 4){
438		sprintf( painCave.errMsg,
439	<	"SimSetup error: If you use the constant pressure\n"
440	<	"    ensemble, you must set tauBarostat.\n"
120	<	"    This was found in the BASS file.\n");
439	>	"SimSetup error. There has been an error in constructing"
440	>	" the non-complete lattice.\n" );
441		painCave.isFatal = 1;
442		simError();
443		}
444	+	}
445	+	else{
446	+	n_cells = (int)temp3;
447	+	cellx = info[0].boxL[0] / temp3;
448	+	celly = info[0].boxL[1] / temp3;
449	+	cellz = info[0].boxL[2] / temp3;
450	+	}
451
452	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
453	<	the_extendedsystem = new ExtendedSystem( simnfo );
454	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
452	>	current_mol = 0;
453	>	current_comp_mol = 0;
454	>	current_comp = 0;
455	>	current_atom_ndx = 0;
456
457	<	if (the_globals->haveTauThermostat())
458	<	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
459	<	else if (the_globals->haveQmass())
460	<	the_extendedsystem->setQmass(the_globals->getQmass());
461	<	else {
457	>	for( i=0; i < n_cells ; i++ ){
458	>	for( j=0; j < n_cells; j++ ){
459	>	for( k=0; k < n_cells; k++ ){
460	>
461	>	makeElement( i * cellx,
462	>	j * celly,
463	>	k * cellz );
464	>
465	>	makeElement( i * cellx + 0.5 * cellx,
466	>	j * celly + 0.5 * celly,
467	>	k * cellz );
468	>
469	>	makeElement( i * cellx,
470	>	j * celly + 0.5 * celly,
471	>	k * cellz + 0.5 * cellz );
472	>
473	>	makeElement( i * cellx + 0.5 * cellx,
474	>	j * celly,
475	>	k * cellz + 0.5 * cellz );
476	>	}
477	>	}
478	>	}
479	>
480	>	if( have_extra ){
481	>	done = 0;
482	>
483	>	int start_ndx;
484	>	for( i=0; i < (n_cells+1) && !done; i++ ){
485	>	for( j=0; j < (n_cells+1) && !done; j++ ){
486	>
487	>	if( i < n_cells ){
488	>
489	>	if( j < n_cells ){
490	>	start_ndx = n_cells;
491	>	}
492	>	else start_ndx = 0;
493	>	}
494	>	else start_ndx = 0;
495	>
496	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
497	>
498	>	makeElement( i * cellx,
499	>	j * celly,
500	>	k * cellz );
501	>	done = ( current_mol >= tot_nmol );
502	>
503	>	if( !done && n_per_extra > 1 ){
504	>	makeElement( i * cellx + 0.5 * cellx,
505	>	j * celly + 0.5 * celly,
506	>	k * cellz );
507	>	done = ( current_mol >= tot_nmol );
508	>	}
509	>
510	>	if( !done && n_per_extra > 2){
511	>	makeElement( i * cellx,
512	>	j * celly + 0.5 * celly,
513	>	k * cellz + 0.5 * cellz );
514	>	done = ( current_mol >= tot_nmol );
515	>	}
516	>
517	>	if( !done && n_per_extra > 3){
518	>	makeElement( i * cellx + 0.5 * cellx,
519	>	j * celly,
520	>	k * cellz + 0.5 * cellz );
521	>	done = ( current_mol >= tot_nmol );
522	>	}
523	>	}
524	>	}
525	>	}
526	>	}
527	>
528	>	for( i=0; i<info[0].n_atoms; i++ ){
529	>	info[0].atoms[i]->setVel( vel );
530	>	}
531	>	}
532	>
533	>	void SimSetup::makeElement( double x, double y, double z ){
534	>
535	>	int k;
536	>	AtomStamp* current_atom;
537	>	DirectionalAtom* dAtom;
538	>	double rotMat[3][3];
539	>	double pos[3];
540	>
541	>	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
542	>
543	>	current_atom = comp_stamps[current_comp]->getAtom( k );
544	>	if( !current_atom->havePosition() ){
545		sprintf( painCave.errMsg,
546	<	"SimSetup error: If you use one of the constant temperature\n"
547	<	"    ensembles, you must set either tauThermostat or qMass.\n"
548	<	"    Neither of these was found in the BASS file.\n");
546	>	"SimSetup:initFromBass error.\n"
547	>	"\tComponent %s, atom %s does not have a position specified.\n"
548	>	"\tThe initialization routine is unable to give a start"
549	>	" position.\n",
550	>	comp_stamps[current_comp]->getID(),
551	>	current_atom->getType() );
552		painCave.isFatal = 1;
553		simError();
554		}
555	<
556	<	} else if ( !strcasecmp( ensemble, "NVE") ) {
557	<	} else {
558	<	sprintf( painCave.errMsg,
559	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
560	<	"reverting to NVE for this simulation.\n",
147	<	ensemble );
148	<	painCave.isFatal = 0;
149	<	simError();
150	<	strcpy( ensemble, "NVE" );
151	<	}
152	<	strcpy( simnfo->ensemble, ensemble );
555	>
556	>	pos[0] = x + current_atom->getPosX();
557	>	pos[1] = y + current_atom->getPosY();
558	>	pos[2] = z + current_atom->getPosZ();
559	>
560	>	info[0].atoms[current_atom_ndx]->setPos( pos );
561
562	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
563	<	simnfo->usePBC = the_globals->getPBC();
564	<
565	<	int usesDipoles = 0;
566	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
567	<	the_ff = new TraPPE_ExFF();
568	<	usesDipoles = 1;
562	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
563	>
564	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
565	>
566	>	rotMat[0][0] = 1.0;
567	>	rotMat[0][1] = 0.0;
568	>	rotMat[0][2] = 0.0;
569	>
570	>	rotMat[1][0] = 0.0;
571	>	rotMat[1][1] = 1.0;
572	>	rotMat[1][2] = 0.0;
573	>
574	>	rotMat[2][0] = 0.0;
575	>	rotMat[2][1] = 0.0;
576	>	rotMat[2][2] = 1.0;
577	>
578	>	dAtom->setA( rotMat );
579	>	}
580	>
581	>	current_atom_ndx++;
582		}
583	<	else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
583	>
584	>	current_mol++;
585	>	current_comp_mol++;
586	>
587	>	if( current_comp_mol >= components_nmol[current_comp] ){
588	>
589	>	current_comp_mol = 0;
590	>	current_comp++;
591	>	}
592	>	}
593	>
594	>
595	>	void SimSetup::gatherInfo( void ){
596	>	int i,j,k;
597	>
598	>	ensembleCase = -1;
599	>	ffCase = -1;
600	>
601	>	// set the easy ones first
602	>
603	>	for( i=0; i<nInfo; i++){
604	>	info[i].target_temp = globals->getTargetTemp();
605	>	info[i].dt = globals->getDt();
606	>	info[i].run_time = globals->getRunTime();
607	>	}
608	>	n_components = globals->getNComponents();
609	>
610	>
611	>	// get the forceField
612	>
613	>	strcpy( force_field, globals->getForceField() );
614	>
615	>	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
616	>	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
617	>	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
618		else{
619		sprintf( painCave.errMsg,
620		"SimSetup Error. Unrecognized force field -> %s\n",
#	Line 168 | Line 623 | void SimSetup::createSim( void ){
623		simError();
624		}
625
626	<	#ifdef IS_MPI
172	<	strcpy( checkPointMsg, "ForceField creation successful" );
173	<	MPIcheckPoint();
174	<	#endif // is_mpi
626	>	// get the ensemble
627
628	+	strcpy( ensemble, globals->getEnsemble() );
629	+
630	+	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
631	+	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
632	+	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
633	+	ensembleCase = NPTi_ENS;
634	+	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
635	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
636	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
637	+	else{
638	+	sprintf( painCave.errMsg,
639	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
640	+	"reverting to NVE for this simulation.\n",
641	+	ensemble );
642	+	painCave.isFatal = 0;
643	+	simError();
644	+	strcpy( ensemble, "NVE" );
645	+	ensembleCase = NVE_ENS;
646	+	}
647
648	+	for(i=0; i<nInfo; i++){
649	+
650	+	strcpy( info[i].ensemble, ensemble );
651
652	+	// get the mixing rule
653	+
654	+	strcpy( info[i].mixingRule, globals->getMixingRule() );
655	+	info[i].usePBC = globals->getPBC();
656	+	}
657	+
658		// get the components and calculate the tot_nMol and indvidual n_mol
659	<	the_components = the_globals->getComponents();
659	>
660	>	the_components = globals->getComponents();
661		components_nmol = new int[n_components];
181	–	comp_stamps = new MoleculeStamp*[n_components];
662
663	<	if( !the_globals->haveNMol() ){
663	>
664	>	if( !globals->haveNMol() ){
665		// we don't have the total number of molecules, so we assume it is
666		// given in each component
667
#	Line 209 | Line 690 | void SimSetup::createSim( void ){
690		" Please give nMol in the components.\n" );
691		painCave.isFatal = 1;
692		simError();
693	+	}
694	+
695	+	// set the status, sample, and thermal kick times
696	+
697	+	for(i=0; i<nInfo; i++){
698	+
699	+	if( globals->haveSampleTime() ){
700	+	info[i].sampleTime = globals->getSampleTime();
701	+	info[i].statusTime = info[i].sampleTime;
702	+	info[i].thermalTime = info[i].sampleTime;
703	+	}
704	+	else{
705	+	info[i].sampleTime = globals->getRunTime();
706	+	info[i].statusTime = info[i].sampleTime;
707	+	info[i].thermalTime = info[i].sampleTime;
708	+	}
709
710	+	if( globals->haveStatusTime() ){
711	+	info[i].statusTime = globals->getStatusTime();
712	+	}
713
714	<	//     tot_nmol = the_globals->getNMol();
714	>	if( globals->haveThermalTime() ){
715	>	info[i].thermalTime = globals->getThermalTime();
716	>	}
717	>
718	>	// check for the temperature set flag
719	>
720	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
721
722	<	//   //we have the total number of molecules, now we check for molfractions
217	<	//     for( i=0; i<n_components; i++ ){
722	>	// get some of the tricky things that may still be in the globals
723
724	<	//       if( !the_components[i]->haveMolFraction() ){
725	<
726	<	//  if( !the_components[i]->haveNMol() ){
727	<	//    //we have a problem
728	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
729	<	//              << " nMol was given in component
730	<
724	>	double boxVector[3];
725	>	if( globals->haveBox() ){
726	>	boxVector[0] = globals->getBox();
727	>	boxVector[1] = globals->getBox();
728	>	boxVector[2] = globals->getBox();
729	>
730	>	info[i].setBox( boxVector );
731	>	}
732	>	else if( globals->haveDensity() ){
733	>
734	>	double vol;
735	>	vol = (double)tot_nmol / globals->getDensity();
736	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
737	>	boxVector[1] = boxVector[0];
738	>	boxVector[2] = boxVector[0];
739	>
740	>	info[i].setBox( boxVector );
741		}
742	+	else{
743	+	if( !globals->haveBoxX() ){
744	+	sprintf( painCave.errMsg,
745	+	"SimSetup error, no periodic BoxX size given.\n" );
746	+	painCave.isFatal = 1;
747	+	simError();
748	+	}
749	+	boxVector[0] = globals->getBoxX();
750	+
751	+	if( !globals->haveBoxY() ){
752	+	sprintf( painCave.errMsg,
753	+	"SimSetup error, no periodic BoxY size given.\n" );
754	+	painCave.isFatal = 1;
755	+	simError();
756	+	}
757	+	boxVector[1] = globals->getBoxY();
758	+
759	+	if( !globals->haveBoxZ() ){
760	+	sprintf( painCave.errMsg,
761	+	"SimSetup error, no periodic BoxZ size given.\n" );
762	+	painCave.isFatal = 1;
763	+	simError();
764	+	}
765	+	boxVector[2] = globals->getBoxZ();
766	+
767	+	info[i].setBox( boxVector );
768	+	}
769
770	+	}
771	+
772		#ifdef IS_MPI
773	<	strcpy( checkPointMsg, "Have the number of components" );
773	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
774		MPIcheckPoint();
775		#endif // is_mpi
776
777	<	// make an array of molecule stamps that match the components used.
234	<	// also extract the used stamps out into a separate linked list
777	>	}
778
236	–	simnfo->nComponents = n_components;
237	–	simnfo->componentsNmol = components_nmol;
238	–	simnfo->compStamps = comp_stamps;
239	–	simnfo->headStamp = new LinkedMolStamp();
240	–
241	–	char* id;
242	–	LinkedMolStamp* headStamp = simnfo->headStamp;
243	–	LinkedMolStamp* currentStamp = NULL;
244	–	for( i=0; i<n_components; i++ ){
779
780	<	id = the_components[i]->getType();
781	<	comp_stamps[i] = NULL;
782	<
783	<	// check to make sure the component isn't already in the list
780	>	void SimSetup::finalInfoCheck( void ){
781	>	int index;
782	>	int usesDipoles;
783	>	int i;
784
785	<	comp_stamps[i] = headStamp->match( id );
786	<	if( comp_stamps[i] == NULL ){
785	>	for(i=0; i<nInfo; i++){
786	>	// check electrostatic parameters
787	>
788	>	index = 0;
789	>	usesDipoles = 0;
790	>	while( (index < info[i].n_atoms) && !usesDipoles ){
791	>	usesDipoles = (info[i].atoms[index])->hasDipole();
792	>	index++;
793	>	}
794	>
795	>	#ifdef IS_MPI
796	>	int myUse = usesDipoles;
797	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
798	>	#endif //is_mpi
799	>
800	>	double theEcr, theEst;
801	>
802	>	if (globals->getUseRF() ) {
803	>	info[i].useReactionField = 1;
804
805	<	// extract the component from the list;
805	>	if( !globals->haveECR() ){
806	>	sprintf( painCave.errMsg,
807	>	"SimSetup Warning: using default value of 1/2 the smallest "
808	>	"box length for the electrostaticCutoffRadius.\n"
809	>	"I hope you have a very fast processor!\n");
810	>	painCave.isFatal = 0;
811	>	simError();
812	>	double smallest;
813	>	smallest = info[i].boxL[0];
814	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
815	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
816	>	theEcr = 0.5 * smallest;
817	>	} else {
818	>	theEcr = globals->getECR();
819	>	}
820
821	<	currentStamp = the_stamps->extractMolStamp( id );
257	<	if( currentStamp == NULL ){
821	>	if( !globals->haveEST() ){
822		sprintf( painCave.errMsg,
823	<	"SimSetup error: Component \"%s\" was not found in the "
824	<	"list of declared molecules\n",
825	<	id );
826	<	painCave.isFatal = 1;
823	>	"SimSetup Warning: using default value of 0.05 * the "
824	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
825	>	);
826	>	painCave.isFatal = 0;
827		simError();
828	+	theEst = 0.05 * theEcr;
829	+	} else {
830	+	theEst= globals->getEST();
831		}
832
833	<	headStamp->add( currentStamp );
834	<	comp_stamps[i] = headStamp->match( id );
835	<	}
833	>	info[i].setEcr( theEcr, theEst );
834	>
835	>	if(!globals->haveDielectric() ){
836	>	sprintf( painCave.errMsg,
837	>	"SimSetup Error: You are trying to use Reaction Field without"
838	>	"setting a dielectric constant!\n"
839	>	);
840	>	painCave.isFatal = 1;
841	>	simError();
842	>	}
843	>	info[i].dielectric = globals->getDielectric();
844	>	}
845	>	else {
846	>	if (usesDipoles) {
847	>
848	>	if( !globals->haveECR() ){
849	>	sprintf( painCave.errMsg,
850	>	"SimSetup Warning: using default value of 1/2 the smallest "
851	>	"box length for the electrostaticCutoffRadius.\n"
852	>	"I hope you have a very fast processor!\n");
853	>	painCave.isFatal = 0;
854	>	simError();
855	>	double smallest;
856	>	smallest = info[i].boxL[0];
857	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
858	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
859	>	theEcr = 0.5 * smallest;
860	>	} else {
861	>	theEcr = globals->getECR();
862	>	}
863	>
864	>	if( !globals->haveEST() ){
865	>	sprintf( painCave.errMsg,
866	>	"SimSetup Warning: using default value of 0.05 * the "
867	>	"electrostaticCutoffRadius for the "
868	>	"electrostaticSkinThickness\n"
869	>	);
870	>	painCave.isFatal = 0;
871	>	simError();
872	>	theEst = 0.05 * theEcr;
873	>	} else {
874	>	theEst= globals->getEST();
875	>	}
876	>
877	>	info[i].setEcr( theEcr, theEst );
878	>	}
879	>	}
880		}
881
882		#ifdef IS_MPI
883	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
883	>	strcpy( checkPointMsg, "post processing checks out" );
884		MPIcheckPoint();
885		#endif // is_mpi
275	–
886
887	+	}
888
889	<
890	<	// caclulate the number of atoms, bonds, bends and torsions
280	<
281	<	tot_atoms = 0;
282	<	tot_bonds = 0;
283	<	tot_bends = 0;
284	<	tot_torsions = 0;
285	<	for( i=0; i<n_components; i++ ){
286	<
287	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
288	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
289	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
290	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
291	<	}
292	<
293	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
294	<
295	<	simnfo->n_atoms = tot_atoms;
296	<	simnfo->n_bonds = tot_bonds;
297	<	simnfo->n_bends = tot_bends;
298	<	simnfo->n_torsions = tot_torsions;
299	<	simnfo->n_SRI = tot_SRI;
300	<	simnfo->n_mol = tot_nmol;
889	>	void SimSetup::initSystemCoords( void ){
890	>	int i;
891
892	<	simnfo->molMembershipArray = new int[tot_atoms];
892	>	char* inName;
893
304	–	#ifdef IS_MPI
894
895	<	// divide the molecules among processors here.
895	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
896
897	<	mpiSim = new mpiSimulation( simnfo );
897	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
898
899	<	globalIndex = mpiSim->divideLabor();
900	<
901	<	// set up the local variables
902	<
903	<	int localMol, allMol;
904	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
905	<
906	<	int* mol2proc = mpiSim->getMolToProcMap();
907	<	int* molCompType = mpiSim->getMolComponentType();
908	<
909	<	allMol = 0;
910	<	localMol = 0;
911	<	local_atoms = 0;
912	<	local_bonds = 0;
913	<	local_bends = 0;
325	<	local_torsions = 0;
326	<	globalAtomIndex = 0;
327	<
328	<
329	<	for( i=0; i<n_components; i++ ){
330	<
331	<	for( j=0; j<components_nmol[i]; j++ ){
332	<
333	<	if( mol2proc[allMol] == worldRank ){
334	<
335	<	local_atoms +=    comp_stamps[i]->getNAtoms();
336	<	local_bonds +=    comp_stamps[i]->getNBonds();
337	<	local_bends +=    comp_stamps[i]->getNBends();
338	<	local_torsions += comp_stamps[i]->getNTorsions();
339	<	localMol++;
340	<	}
341	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
342	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
343	<	globalAtomIndex++;
344	<	}
345	<
346	<	allMol++;
347	<	}
899	>	if( globals->haveInitialConfig() ){
900	>
901	>	InitializeFromFile* fileInit;
902	>	#ifdef IS_MPI // is_mpi
903	>	if( worldRank == 0 ){
904	>	#endif //is_mpi
905	>	inName = globals->getInitialConfig();
906	>	double* tempDouble = new double[1000000];
907	>	fileInit = new InitializeFromFile( inName );
908	>	#ifdef IS_MPI
909	>	}else fileInit = new InitializeFromFile( NULL );
910	>	#endif
911	>	fileInit->readInit( info ); // default velocities on
912	>
913	>	delete fileInit;
914		}
915	<	local_SRI = local_bonds + local_bends + local_torsions;
916	<
917	<	simnfo->n_atoms = mpiSim->getMyNlocal();
918	<
919	<	if( local_atoms != simnfo->n_atoms ){
915	>	else{
916	>
917	>	#ifdef IS_MPI
918	>
919	>	// no init from bass
920	>
921		sprintf( painCave.errMsg,
922	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
923	<	" localAtom (%d) are not equal.\n",
357	<	simnfo->n_atoms,
358	<	local_atoms );
359	<	painCave.isFatal = 1;
922	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
923	>	painCave.isFatal;
924		simError();
925	+
926	+	#else
927	+
928	+	initFromBass();
929	+
930	+
931	+	#endif
932		}
362	–
363	–	simnfo->n_bonds = local_bonds;
364	–	simnfo->n_bends = local_bends;
365	–	simnfo->n_torsions = local_torsions;
366	–	simnfo->n_SRI = local_SRI;
367	–	simnfo->n_mol = localMol;
368	–
369	–	strcpy( checkPointMsg, "Passed nlocal consistency check." );
370	–	MPIcheckPoint();
933
934	<
934	>	#ifdef IS_MPI
935	>	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
936	>	MPIcheckPoint();
937		#endif // is_mpi
938
939	+	}
940
376	–	// create the atom and short range interaction arrays
941
942	<	Atom::createArrays(simnfo->n_atoms);
379	<	the_atoms = new Atom*[simnfo->n_atoms];
380	<	the_molecules = new Molecule[simnfo->n_mol];
381	<	int molIndex;
382	<
383	<	// initialize the molecule's stampID's
384	<
385	<	#ifdef IS_MPI
942	>	void SimSetup::makeOutNames( void ){
943
944	+	int k;
945
388	–	molIndex = 0;
389	–	for(i=0; i<mpiSim->getTotNmol(); i++){
390	–
391	–	if(mol2proc[i] == worldRank ){
392	–	the_molecules[molIndex].setStampID( molCompType[i] );
393	–	the_molecules[molIndex].setMyIndex( molIndex );
394	–	the_molecules[molIndex].setGlobalIndex( i );
395	–	molIndex++;
396	–	}
397	–	}
398	–
399	–	#else // is_mpi
946
947	<	molIndex = 0;
402	<	globalAtomIndex = 0;
403	<	for(i=0; i<n_components; i++){
404	<	for(j=0; j<components_nmol[i]; j++ ){
405	<	the_molecules[molIndex].setStampID( i );
406	<	the_molecules[molIndex].setMyIndex( molIndex );
407	<	the_molecules[molIndex].setGlobalIndex( molIndex );
408	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
409	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
410	<	globalAtomIndex++;
411	<	}
412	<	molIndex++;
413	<	}
414	<	}
415	<
947	>	for(k=0; k<nInfo; k++){
948
949	+	#ifdef IS_MPI
950	+	if( worldRank == 0 ){
951		#endif // is_mpi
952	<
953	<
954	<	if( simnfo->n_SRI ){
955	<
956	<	Exclude::createArray(simnfo->n_SRI);
957	<	the_excludes = new Exclude*[simnfo->n_SRI];
958	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
959	<	simnfo->globalExcludes = new int;
960	<	simnfo->n_exclude = simnfo->n_SRI;
952	>
953	>	if( globals->haveFinalConfig() ){
954	>	strcpy( info[k].finalName, globals->getFinalConfig() );
955	>	}
956	>	else{
957	>	strcpy( info[k].finalName, inFileName );
958	>	char* endTest;
959	>	int nameLength = strlen( info[k].finalName );
960	>	endTest = &(info[k].finalName[nameLength - 5]);
961	>	if( !strcmp( endTest, ".bass" ) ){
962	>	strcpy( endTest, ".eor" );
963	>	}
964	>	else if( !strcmp( endTest, ".BASS" ) ){
965	>	strcpy( endTest, ".eor" );
966	>	}
967	>	else{
968	>	endTest = &(info[k].finalName[nameLength - 4]);
969	>	if( !strcmp( endTest, ".bss" ) ){
970	>	strcpy( endTest, ".eor" );
971	>	}
972	>	else if( !strcmp( endTest, ".mdl" ) ){
973	>	strcpy( endTest, ".eor" );
974	>	}
975	>	else{
976	>	strcat( info[k].finalName, ".eor" );
977	>	}
978	>	}
979	>	}
980	>
981	>	// make the sample and status out names
982	>
983	>	strcpy( info[k].sampleName, inFileName );
984	>	char* endTest;
985	>	int nameLength = strlen( info[k].sampleName );
986	>	endTest = &(info[k].sampleName[nameLength - 5]);
987	>	if( !strcmp( endTest, ".bass" ) ){
988	>	strcpy( endTest, ".dump" );
989	>	}
990	>	else if( !strcmp( endTest, ".BASS" ) ){
991	>	strcpy( endTest, ".dump" );
992	>	}
993	>	else{
994	>	endTest = &(info[k].sampleName[nameLength - 4]);
995	>	if( !strcmp( endTest, ".bss" ) ){
996	>	strcpy( endTest, ".dump" );
997	>	}
998	>	else if( !strcmp( endTest, ".mdl" ) ){
999	>	strcpy( endTest, ".dump" );
1000	>	}
1001	>	else{
1002	>	strcat( info[k].sampleName, ".dump" );
1003	>	}
1004	>	}
1005	>
1006	>	strcpy( info[k].statusName, inFileName );
1007	>	nameLength = strlen( info[k].statusName );
1008	>	endTest = &(info[k].statusName[nameLength - 5]);
1009	>	if( !strcmp( endTest, ".bass" ) ){
1010	>	strcpy( endTest, ".stat" );
1011	>	}
1012	>	else if( !strcmp( endTest, ".BASS" ) ){
1013	>	strcpy( endTest, ".stat" );
1014	>	}
1015	>	else{
1016	>	endTest = &(info[k].statusName[nameLength - 4]);
1017	>	if( !strcmp( endTest, ".bss" ) ){
1018	>	strcpy( endTest, ".stat" );
1019	>	}
1020	>	else if( !strcmp( endTest, ".mdl" ) ){
1021	>	strcpy( endTest, ".stat" );
1022	>	}
1023	>	else{
1024	>	strcat( info[k].statusName, ".stat" );
1025	>	}
1026	>	}
1027	>
1028	>	#ifdef IS_MPI
1029	>	}
1030	>	#endif // is_mpi
1031		}
1032	<	else{
429	<
430	<	Exclude::createArray( 1 );
431	<	the_excludes = new Exclude*;
432	<	the_excludes[0] = new Exclude(0);
433	<	the_excludes[0]->setPair( 0,0 );
434	<	simnfo->globalExcludes = new int;
435	<	simnfo->globalExcludes[0] = 0;
436	<	simnfo->n_exclude = 0;
437	<	}
1032	>	}
1033
439	–	// set the arrays into the SimInfo object
1034
1035	<	simnfo->atoms = the_atoms;
1036	<	simnfo->molecules = the_molecules;
1037	<	simnfo->nGlobalExcludes = 0;
1038	<	simnfo->excludes = the_excludes;
1035	>	void SimSetup::sysObjectsCreation( void ){
1036	>
1037	>	int i,k;
1038	>
1039	>	// create the forceField
1040
1041	+	createFF();
1042
1043	<	// get some of the tricky things that may still be in the globals
1043	>	// extract componentList
1044
1045	+	compList();
1046	+
1047	+	// calc the number of atoms, bond, bends, and torsions
1048	+
1049	+	calcSysValues();
1050	+
1051	+	#ifdef IS_MPI
1052	+	// divide the molecules among the processors
1053
1054	<	if( the_globals->haveBox() ){
1055	<	simnfo->box_x = the_globals->getBox();
1056	<	simnfo->box_y = the_globals->getBox();
1057	<	simnfo->box_z = the_globals->getBox();
1058	<	}
1059	<	else if( the_globals->haveDensity() ){
1054	>	mpiMolDivide();
1055	>	#endif //is_mpi
1056	>
1057	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1058	>
1059	>	makeSysArrays();
1060
1061	<	double vol;
1062	<	vol = (double)tot_nmol / the_globals->getDensity();
1063	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
1064	<	simnfo->box_y = simnfo->box_x;
1065	<	simnfo->box_z = simnfo->box_x;
1066	<	}
1067	<	else{
1068	<	if( !the_globals->haveBoxX() ){
465	<	sprintf( painCave.errMsg,
466	<	"SimSetup error, no periodic BoxX size given.\n" );
467	<	painCave.isFatal = 1;
468	<	simError();
1061	>	// make and initialize the molecules (all but atomic coordinates)
1062	>
1063	>	makeMolecules();
1064	>
1065	>	for(k=0; k<nInfo; k++){
1066	>	info[k].identArray = new int[info[k].n_atoms];
1067	>	for(i=0; i<info[k].n_atoms; i++){
1068	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1069		}
1070	<	simnfo->box_x = the_globals->getBoxX();
1070	>	}
1071	>	}
1072
472	–	if( !the_globals->haveBoxY() ){
473	–	sprintf( painCave.errMsg,
474	–	"SimSetup error, no periodic BoxY size given.\n" );
475	–	painCave.isFatal = 1;
476	–	simError();
477	–	}
478	–	simnfo->box_y = the_globals->getBoxY();
1073
1074	<	if( !the_globals->haveBoxZ() ){
1075	<	sprintf( painCave.errMsg,
1076	<	"SimSetup error, no periodic BoxZ size given.\n" );
1077	<	painCave.isFatal = 1;
1078	<	simError();
1079	<	}
1080	<	simnfo->box_z = the_globals->getBoxZ();
1074	>	void SimSetup::createFF( void ){
1075	>
1076	>	switch( ffCase ){
1077	>
1078	>	case FF_DUFF:
1079	>	the_ff = new DUFF();
1080	>	break;
1081	>
1082	>	case FF_LJ:
1083	>	the_ff = new LJFF();
1084	>	break;
1085	>
1086	>	case FF_EAM:
1087	>	the_ff = new EAM_FF();
1088	>	break;
1089	>
1090	>	default:
1091	>	sprintf( painCave.errMsg,
1092	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1093	>	painCave.isFatal = 1;
1094	>	simError();
1095		}
1096
1097		#ifdef IS_MPI
1098	<	strcpy( checkPointMsg, "Box size set up" );
1098	>	strcpy( checkPointMsg, "ForceField creation successful" );
1099		MPIcheckPoint();
1100		#endif // is_mpi
1101
1102	+	}
1103
495	–	// initialize the arrays
1104
1105	<	the_ff->setSimInfo( simnfo );
1105	>	void SimSetup::compList( void ){
1106
1107	<	makeMolecules();
1108	<	simnfo->identArray = new int[simnfo->n_atoms];
1109	<	for(i=0; i<simnfo->n_atoms; i++){
1110	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
1111	<	}
1107	>	int i;
1108	>	char* id;
1109	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1110	>	LinkedMolStamp* currentStamp = NULL;
1111	>	comp_stamps = new MoleculeStamp*[n_components];
1112
1113	<	if (the_globals->getUseRF() ) {
1114	<	simnfo->useReactionField = 1;
1113	>	// make an array of molecule stamps that match the components used.
1114	>	// also extract the used stamps out into a separate linked list
1115
1116	<	if( !the_globals->haveECR() ){
1117	<	sprintf( painCave.errMsg,
1118	<	"SimSetup Warning: using default value of 1/2 the smallest "
1119	<	"box length for the electrostaticCutoffRadius.\n"
1120	<	"I hope you have a very fast processor!\n");
1121	<	painCave.isFatal = 0;
1122	<	simError();
515	<	double smallest;
516	<	smallest = simnfo->box_x;
517	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
518	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
519	<	simnfo->ecr = 0.5 * smallest;
520	<	} else {
521	<	simnfo->ecr        = the_globals->getECR();
522	<	}
1116	>	for(i=0; i<nInfo; i++){
1117	>	info[i].nComponents = n_components;
1118	>	info[i].componentsNmol = components_nmol;
1119	>	info[i].compStamps = comp_stamps;
1120	>	info[i].headStamp = headStamp;
1121	>	}
1122	>
1123
1124	<	if( !the_globals->haveEST() ){
1125	<	sprintf( painCave.errMsg,
1126	<	"SimSetup Warning: using default value of 0.05 * the "
1127	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
528	<	);
529	<	painCave.isFatal = 0;
530	<	simError();
531	<	simnfo->est = 0.05 * simnfo->ecr;
532	<	} else {
533	<	simnfo->est        = the_globals->getEST();
534	<	}
1124	>	for( i=0; i<n_components; i++ ){
1125	>
1126	>	id = the_components[i]->getType();
1127	>	comp_stamps[i] = NULL;
1128
1129	<	if(!the_globals->haveDielectric() ){
1130	<	sprintf( painCave.errMsg,
1131	<	"SimSetup Error: You are trying to use Reaction Field without"
1132	<	"setting a dielectric constant!\n"
540	<	);
541	<	painCave.isFatal = 1;
542	<	simError();
543	<	}
544	<	simnfo->dielectric = the_globals->getDielectric();
545	<	} else {
546	<	if (usesDipoles) {
1129	>	// check to make sure the component isn't already in the list
1130	>
1131	>	comp_stamps[i] = headStamp->match( id );
1132	>	if( comp_stamps[i] == NULL ){
1133
1134	<	if( !the_globals->haveECR() ){
549	<	sprintf( painCave.errMsg,
550	<	"SimSetup Warning: using default value of 1/2 the smallest "
551	<	"box length for the electrostaticCutoffRadius.\n"
552	<	"I hope you have a very fast processor!\n");
553	<	painCave.isFatal = 0;
554	<	simError();
555	<	double smallest;
556	<	smallest = simnfo->box_x;
557	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
558	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
559	<	simnfo->ecr = 0.5 * smallest;
560	<	} else {
561	<	simnfo->ecr        = the_globals->getECR();
562	<	}
1134	>	// extract the component from the list;
1135
1136	<	if( !the_globals->haveEST() ){
1137	<	sprintf( painCave.errMsg,
1138	<	"SimSetup Warning: using default value of 5%% of the "
1139	<	"electrostaticCutoffRadius for the "
1140	<	"electrostaticSkinThickness\n"
1141	<	);
1142	<	painCave.isFatal = 0;
1143	<	simError();
572	<	simnfo->est = 0.05 * simnfo->ecr;
573	<	} else {
574	<	simnfo->est        = the_globals->getEST();
1136	>	currentStamp = stamps->extractMolStamp( id );
1137	>	if( currentStamp == NULL ){
1138	>	sprintf( painCave.errMsg,
1139	>	"SimSetup error: Component \"%s\" was not found in the "
1140	>	"list of declared molecules\n",
1141	>	id );
1142	>	painCave.isFatal = 1;
1143	>	simError();
1144		}
1145	+
1146	+	headStamp->add( currentStamp );
1147	+	comp_stamps[i] = headStamp->match( id );
1148		}
1149	<	}
1149	>	}
1150
1151		#ifdef IS_MPI
1152	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
1152	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1153		MPIcheckPoint();
1154		#endif // is_mpi
1155
584	–	if( the_globals->haveInitialConfig() ){
585	–
586	–	InitializeFromFile* fileInit;
587	–	#ifdef IS_MPI // is_mpi
588	–	if( worldRank == 0 ){
589	–	#endif //is_mpi
590	–	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
591	–	#ifdef IS_MPI
592	–	}else fileInit = new InitializeFromFile( NULL );
593	–	#endif
594	–	fileInit->read_xyz( simnfo ); // default velocities on
1156
1157	<	delete fileInit;
597	<	}
598	<	else{
1157	>	}
1158
1159	<	#ifdef IS_MPI
1160	<
602	<	// no init from bass
1159	>	void SimSetup::calcSysValues( void ){
1160	>	int i, j, k;
1161
1162	<	sprintf( painCave.errMsg,
605	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
606	<	painCave.isFatal;
607	<	simError();
1162	>	int *molMembershipArray;
1163
1164	<	#else
1164	>	tot_atoms = 0;
1165	>	tot_bonds = 0;
1166	>	tot_bends = 0;
1167	>	tot_torsions = 0;
1168	>	for( i=0; i<n_components; i++ ){
1169	>
1170	>	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1171	>	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1172	>	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1173	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1174	>	}
1175	>
1176	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1177	>	molMembershipArray = new int[tot_atoms];
1178	>
1179	>	for(i=0; i<nInfo; i++){
1180	>	info[i].n_atoms = tot_atoms;
1181	>	info[i].n_bonds = tot_bonds;
1182	>	info[i].n_bends = tot_bends;
1183	>	info[i].n_torsions = tot_torsions;
1184	>	info[i].n_SRI = tot_SRI;
1185	>	info[i].n_mol = tot_nmol;
1186	>
1187	>	info[i].molMembershipArray = molMembershipArray;
1188	>	}
1189	>	}
1190
1191	<	initFromBass();
1191	>	#ifdef IS_MPI
1192
1193	+	void SimSetup::mpiMolDivide( void ){
1194	+
1195	+	int i, j, k;
1196	+	int localMol, allMol;
1197	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1198
1199	<	#endif
1200	<	}
1199	>	mpiSim = new mpiSimulation( info );
1200	>
1201	>	globalIndex = mpiSim->divideLabor();
1202
1203	<	#ifdef IS_MPI
1204	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1203	>	// set up the local variables
1204	>
1205	>	mol2proc = mpiSim->getMolToProcMap();
1206	>	molCompType = mpiSim->getMolComponentType();
1207	>
1208	>	allMol = 0;
1209	>	localMol = 0;
1210	>	local_atoms = 0;
1211	>	local_bonds = 0;
1212	>	local_bends = 0;
1213	>	local_torsions = 0;
1214	>	globalAtomIndex = 0;
1215	>
1216	>
1217	>	for( i=0; i<n_components; i++ ){
1218	>
1219	>	for( j=0; j<components_nmol[i]; j++ ){
1220	>
1221	>	if( mol2proc[allMol] == worldRank ){
1222	>
1223	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1224	>	local_bonds +=    comp_stamps[i]->getNBonds();
1225	>	local_bends +=    comp_stamps[i]->getNBends();
1226	>	local_torsions += comp_stamps[i]->getNTorsions();
1227	>	localMol++;
1228	>	}
1229	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1230	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1231	>	globalAtomIndex++;
1232	>	}
1233	>
1234	>	allMol++;
1235	>	}
1236	>	}
1237	>	local_SRI = local_bonds + local_bends + local_torsions;
1238	>
1239	>	info[0].n_atoms = mpiSim->getMyNlocal();
1240	>
1241	>	if( local_atoms != info[0].n_atoms ){
1242	>	sprintf( painCave.errMsg,
1243	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1244	>	" localAtom (%d) are not equal.\n",
1245	>	info[0].n_atoms,
1246	>	local_atoms );
1247	>	painCave.isFatal = 1;
1248	>	simError();
1249	>	}
1250	>
1251	>	info[0].n_bonds = local_bonds;
1252	>	info[0].n_bends = local_bends;
1253	>	info[0].n_torsions = local_torsions;
1254	>	info[0].n_SRI = local_SRI;
1255	>	info[0].n_mol = localMol;
1256	>
1257	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1258		MPIcheckPoint();
1259	+	}
1260	+
1261		#endif // is_mpi
1262
1263
1264	<
1265	<
625	<
1264	>	void SimSetup::makeSysArrays( void ){
1265	>	int i, j, k, l;
1266
1267	+	Atom** the_atoms;
1268	+	Molecule* the_molecules;
1269	+	Exclude** the_excludes;
1270	+
1271
1272	+	for(l=0; l<nInfo; l++){
1273	+
1274	+	// create the atom and short range interaction arrays
1275	+
1276	+	the_atoms = new Atom*[info[l].n_atoms];
1277	+	the_molecules = new Molecule[info[l].n_mol];
1278	+	int molIndex;
1279	+
1280	+	// initialize the molecule's stampID's
1281	+
1282		#ifdef IS_MPI
629	–	if( worldRank == 0 ){
630	–	#endif // is_mpi
1283
1284	<	if( the_globals->haveFinalConfig() ){
1285	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
1286	<	}
1287	<	else{
1288	<	strcpy( simnfo->finalName, inFileName );
1289	<	char* endTest;
1290	<	int nameLength = strlen( simnfo->finalName );
1291	<	endTest = &(simnfo->finalName[nameLength - 5]);
1292	<	if( !strcmp( endTest, ".bass" ) ){
641	<	strcpy( endTest, ".eor" );
1284	>
1285	>	molIndex = 0;
1286	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1287	>
1288	>	if(mol2proc[i] == worldRank ){
1289	>	the_molecules[molIndex].setStampID( molCompType[i] );
1290	>	the_molecules[molIndex].setMyIndex( molIndex );
1291	>	the_molecules[molIndex].setGlobalIndex( i );
1292	>	molIndex++;
1293		}
1294	<	else if( !strcmp( endTest, ".BASS" ) ){
1295	<	strcpy( endTest, ".eor" );
1296	<	}
1297	<	else{
1298	<	endTest = &(simnfo->finalName[nameLength - 4]);
1299	<	if( !strcmp( endTest, ".bss" ) ){
1300	<	strcpy( endTest, ".eor" );
1294	>	}
1295	>
1296	>	#else // is_mpi
1297	>
1298	>	molIndex = 0;
1299	>	globalAtomIndex = 0;
1300	>	for(i=0; i<n_components; i++){
1301	>	for(j=0; j<components_nmol[i]; j++ ){
1302	>	the_molecules[molIndex].setStampID( i );
1303	>	the_molecules[molIndex].setMyIndex( molIndex );
1304	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1305	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1306	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1307	>	globalAtomIndex++;
1308		}
1309	<	else if( !strcmp( endTest, ".mdl" ) ){
652	<	strcpy( endTest, ".eor" );
653	<	}
654	<	else{
655	<	strcat( simnfo->finalName, ".eor" );
656	<	}
1309	>	molIndex++;
1310		}
1311		}
1312
660	–	// make the sample and status out names
1313
1314	<	strcpy( simnfo->sampleName, inFileName );
1315	<	char* endTest;
1316	<	int nameLength = strlen( simnfo->sampleName );
1317	<	endTest = &(simnfo->sampleName[nameLength - 5]);
1318	<	if( !strcmp( endTest, ".bass" ) ){
1319	<	strcpy( endTest, ".dump" );
1320	<	}
1321	<	else if( !strcmp( endTest, ".BASS" ) ){
1322	<	strcpy( endTest, ".dump" );
671	<	}
672	<	else{
673	<	endTest = &(simnfo->sampleName[nameLength - 4]);
674	<	if( !strcmp( endTest, ".bss" ) ){
675	<	strcpy( endTest, ".dump" );
1314	>	#endif // is_mpi
1315	>
1316	>
1317	>	if( info[l].n_SRI ){
1318	>
1319	>	Exclude::createArray(info[l].n_SRI);
1320	>	the_excludes = new Exclude*[info[l].n_SRI];
1321	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1322	>	the_excludes[ex] = new Exclude(ex);
1323		}
1324	<	else if( !strcmp( endTest, ".mdl" ) ){
1325	<	strcpy( endTest, ".dump" );
679	<	}
680	<	else{
681	<	strcat( simnfo->sampleName, ".dump" );
682	<	}
1324	>	info[l].globalExcludes = new int;
1325	>	info[l].n_exclude = info[l].n_SRI;
1326		}
1327	+	else{
1328
1329	<	strcpy( simnfo->statusName, inFileName );
1330	<	nameLength = strlen( simnfo->statusName );
1331	<	endTest = &(simnfo->statusName[nameLength - 5]);
1332	<	if( !strcmp( endTest, ".bass" ) ){
1333	<	strcpy( endTest, ".stat" );
1329	>	Exclude::createArray( 1 );
1330	>	the_excludes = new Exclude*;
1331	>	the_excludes[0] = new Exclude(0);
1332	>	the_excludes[0]->setPair( 0,0 );
1333	>	info[l].globalExcludes = new int;
1334	>	info[l].globalExcludes[0] = 0;
1335	>	info[l].n_exclude = 0;
1336		}
1337	<	else if( !strcmp( endTest, ".BASS" ) ){
1338	<	strcpy( endTest, ".stat" );
1339	<	}
1340	<	else{
1341	<	endTest = &(simnfo->statusName[nameLength - 4]);
1342	<	if( !strcmp( endTest, ".bss" ) ){
1343	<	strcpy( endTest, ".stat" );
1344	<	}
1345	<	else if( !strcmp( endTest, ".mdl" ) ){
700	<	strcpy( endTest, ".stat" );
701	<	}
702	<	else{
703	<	strcat( simnfo->statusName, ".stat" );
704	<	}
705	<	}
1337	>
1338	>	// set the arrays into the SimInfo object
1339	>
1340	>	info[l].atoms = the_atoms;
1341	>	info[l].molecules = the_molecules;
1342	>	info[l].nGlobalExcludes = 0;
1343	>	info[l].excludes = the_excludes;
1344	>
1345	>	the_ff->setSimInfo( info );
1346
707	–	#ifdef IS_MPI
1347		}
1348	<	#endif // is_mpi
710	<
711	<	// set the status, sample, and themal kick times
712	<
713	<	if( the_globals->haveSampleTime() ){
714	<	simnfo->sampleTime = the_globals->getSampleTime();
715	<	simnfo->statusTime = simnfo->sampleTime;
716	<	simnfo->thermalTime = simnfo->sampleTime;
717	<	}
718	<	else{
719	<	simnfo->sampleTime = the_globals->getRunTime();
720	<	simnfo->statusTime = simnfo->sampleTime;
721	<	simnfo->thermalTime = simnfo->sampleTime;
722	<	}
1348	>	}
1349
1350	<	if( the_globals->haveStatusTime() ){
725	<	simnfo->statusTime = the_globals->getStatusTime();
726	<	}
1350	>	void SimSetup::makeIntegrator( void ){
1351
1352	<	if( the_globals->haveThermalTime() ){
729	<	simnfo->thermalTime = the_globals->getThermalTime();
730	<	}
1352	>	int k;
1353
1354	<	// check for the temperature set flag
1354	>	NVT<RealIntegrator>*  myNVT = NULL;
1355	>	NPTi<RealIntegrator>* myNPTi = NULL;
1356	>	NPTf<RealIntegrator>* myNPTf = NULL;
1357	>	NPTim<RealIntegrator>* myNPTim = NULL;
1358	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1359	>
1360	>	for(k=0; k<nInfo; k++){
1361	>
1362	>	switch( ensembleCase ){
1363	>
1364	>	case NVE_ENS:
1365	>	if (globals->haveZconstraints()){
1366	>	setupZConstraint(info[k]);
1367	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1368	>	}
1369
1370	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
1370	>	else
1371	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1372	>	break;
1373	>
1374	>	case NVT_ENS:
1375	>	if (globals->haveZconstraints()){
1376	>	setupZConstraint(info[k]);
1377	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1378	>	}
1379	>	else
1380	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1381
1382	+	myNVT->setTargetTemp(globals->getTargetTemp());
1383	+
1384	+	if (globals->haveTauThermostat())
1385	+	myNVT->setTauThermostat(globals->getTauThermostat());
1386	+
1387	+	else {
1388	+	sprintf( painCave.errMsg,
1389	+	"SimSetup error: If you use the NVT\n"
1390	+	"    ensemble, you must set tauThermostat.\n");
1391	+	painCave.isFatal = 1;
1392	+	simError();
1393	+	}
1394	+	break;
1395	+
1396	+	case NPTi_ENS:
1397	+	if (globals->haveZconstraints()){
1398	+	setupZConstraint(info[k]);
1399	+	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1400	+	}
1401	+	else
1402	+	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1403
1404	<	//   // make the longe range forces and the integrator
1404	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1405	>
1406	>	if (globals->haveTargetPressure())
1407	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1408	>	else {
1409	>	sprintf( painCave.errMsg,
1410	>	"SimSetup error: If you use a constant pressure\n"
1411	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1412	>	painCave.isFatal = 1;
1413	>	simError();
1414	>	}
1415	>
1416	>	if( globals->haveTauThermostat() )
1417	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1418	>	else{
1419	>	sprintf( painCave.errMsg,
1420	>	"SimSetup error: If you use an NPT\n"
1421	>	"    ensemble, you must set tauThermostat.\n");
1422	>	painCave.isFatal = 1;
1423	>	simError();
1424	>	}
1425	>
1426	>	if( globals->haveTauBarostat() )
1427	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1428	>	else{
1429	>	sprintf( painCave.errMsg,
1430	>	"SimSetup error: If you use an NPT\n"
1431	>	"    ensemble, you must set tauBarostat.\n");
1432	>	painCave.isFatal = 1;
1433	>	simError();
1434	>	}
1435	>	break;
1436	>
1437	>	case NPTf_ENS:
1438	>	if (globals->haveZconstraints()){
1439	>	setupZConstraint(info[k]);
1440	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1441	>	}
1442	>	else
1443	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1444
1445	<	//   new AllLong( simnfo );
1445	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1446	>
1447	>	if (globals->haveTargetPressure())
1448	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1449	>	else {
1450	>	sprintf( painCave.errMsg,
1451	>	"SimSetup error: If you use a constant pressure\n"
1452	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1453	>	painCave.isFatal = 1;
1454	>	simError();
1455	>	}
1456	>
1457	>	if( globals->haveTauThermostat() )
1458	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1459	>	else{
1460	>	sprintf( painCave.errMsg,
1461	>	"SimSetup error: If you use an NPT\n"
1462	>	"    ensemble, you must set tauThermostat.\n");
1463	>	painCave.isFatal = 1;
1464	>	simError();
1465	>	}
1466	>
1467	>	if( globals->haveTauBarostat() )
1468	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1469	>	else{
1470	>	sprintf( painCave.errMsg,
1471	>	"SimSetup error: If you use an NPT\n"
1472	>	"    ensemble, you must set tauBarostat.\n");
1473	>	painCave.isFatal = 1;
1474	>	simError();
1475	>	}
1476	>	break;
1477	>
1478	>	case NPTim_ENS:
1479	>	if (globals->haveZconstraints()){
1480	>	setupZConstraint(info[k]);
1481	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1482	>	}
1483	>	else
1484	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1485
1486	+	myNPTim->setTargetTemp( globals->getTargetTemp());
1487	+
1488	+	if (globals->haveTargetPressure())
1489	+	myNPTim->setTargetPressure(globals->getTargetPressure());
1490	+	else {
1491	+	sprintf( painCave.errMsg,
1492	+	"SimSetup error: If you use a constant pressure\n"
1493	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1494	+	painCave.isFatal = 1;
1495	+	simError();
1496	+	}
1497	+
1498	+	if( globals->haveTauThermostat() )
1499	+	myNPTim->setTauThermostat( globals->getTauThermostat() );
1500	+	else{
1501	+	sprintf( painCave.errMsg,
1502	+	"SimSetup error: If you use an NPT\n"
1503	+	"    ensemble, you must set tauThermostat.\n");
1504	+	painCave.isFatal = 1;
1505	+	simError();
1506	+	}
1507	+
1508	+	if( globals->haveTauBarostat() )
1509	+	myNPTim->setTauBarostat( globals->getTauBarostat() );
1510	+	else{
1511	+	sprintf( painCave.errMsg,
1512	+	"SimSetup error: If you use an NPT\n"
1513	+	"    ensemble, you must set tauBarostat.\n");
1514	+	painCave.isFatal = 1;
1515	+	simError();
1516	+	}
1517	+	break;
1518	+
1519	+	case NPTfm_ENS:
1520	+	if (globals->haveZconstraints()){
1521	+	setupZConstraint(info[k]);
1522	+	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1523	+	}
1524	+	else
1525	+	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1526
1527	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
1528	<	new Symplectic(simnfo, the_ff, the_extendedsystem);
1527	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1528	>
1529	>	if (globals->haveTargetPressure())
1530	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1531	>	else {
1532	>	sprintf( painCave.errMsg,
1533	>	"SimSetup error: If you use a constant pressure\n"
1534	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1535	>	painCave.isFatal = 1;
1536	>	simError();
1537	>	}
1538	>
1539	>	if( globals->haveTauThermostat() )
1540	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1541	>	else{
1542	>	sprintf( painCave.errMsg,
1543	>	"SimSetup error: If you use an NPT\n"
1544	>	"    ensemble, you must set tauThermostat.\n");
1545	>	painCave.isFatal = 1;
1546	>	simError();
1547	>	}
1548	>
1549	>	if( globals->haveTauBarostat() )
1550	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1551	>	else{
1552	>	sprintf( painCave.errMsg,
1553	>	"SimSetup error: If you use an NPT\n"
1554	>	"    ensemble, you must set tauBarostat.\n");
1555	>	painCave.isFatal = 1;
1556	>	simError();
1557	>	}
1558	>	break;
1559	>
1560	>	default:
1561	>	sprintf( painCave.errMsg,
1562	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1563	>	painCave.isFatal = 1;
1564	>	simError();
1565	>	}
1566		}
1567	<	else if( !strcmp( force_field, "LJ" ) ){
746	<	new Verlet( *simnfo, the_ff, the_extendedsystem );
747	<	}
1567	>	}
1568
1569	<	#ifdef IS_MPI
750	<	mpiSim->mpiRefresh();
751	<	#endif
1569	>	void SimSetup::initFortran( void ){
1570
1571	<	// initialize the Fortran
754	<
755	<
756	<	simnfo->refreshSim();
1571	>	info[0].refreshSim();
1572
1573	<	if( !strcmp( simnfo->mixingRule, "standard") ){
1573	>	if( !strcmp( info[0].mixingRule, "standard") ){
1574		the_ff->initForceField( LB_MIXING_RULE );
1575		}
1576	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
1576	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1577		the_ff->initForceField( EXPLICIT_MIXING_RULE );
1578		}
1579		else{
1580		sprintf( painCave.errMsg,
1581		"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1582	<	simnfo->mixingRule );
1582	>	info[0].mixingRule );
1583		painCave.isFatal = 1;
1584		simError();
1585		}
#	Line 775 | Line 1590 | void SimSetup::createSim( void ){
1590		"Successfully intialized the mixingRule for Fortran." );
1591		MPIcheckPoint();
1592		#endif // is_mpi
1593	+
1594		}
1595
1596	+	void SimSetup::setupZConstraint(SimInfo& theInfo)
1597	+	{
1598	+	int nZConstraints;
1599	+	ZconStamp** zconStamp;
1600	+
1601	+	if(globals->haveZconstraintTime()){
1602	+
1603	+	//add sample time of z-constraint  into SimInfo's property list
1604	+	DoubleData* zconsTimeProp = new DoubleData();
1605	+	zconsTimeProp->setID(ZCONSTIME_ID);
1606	+	zconsTimeProp->setData(globals->getZconsTime());
1607	+	theInfo.addProperty(zconsTimeProp);
1608	+	}
1609	+	else{
1610	+	sprintf( painCave.errMsg,
1611	+	"ZConstraint error: If you use an ZConstraint\n"
1612	+	" , you must set sample time.\n");
1613	+	painCave.isFatal = 1;
1614	+	simError();
1615	+	}
1616
1617	<	void SimSetup::makeMolecules( void ){
1617	>	//push zconsTol into siminfo, if user does not specify
1618	>	//value for zconsTol, a default value will be used
1619	>	DoubleData* zconsTol = new DoubleData();
1620	>	zconsTol->setID(ZCONSTOL_ID);
1621	>	if(globals->haveZconsTol()){
1622	>	zconsTol->setData(globals->getZconsTol());
1623	>	}
1624	>	else{
1625	>	double defaultZConsTol = 0.01;
1626	>	sprintf( painCave.errMsg,
1627	>	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1628	>	" , default value %f is used.\n", defaultZConsTol);
1629	>	painCave.isFatal = 0;
1630	>	simError();
1631
1632	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
1633	<	molInit info;
1634	<	DirectionalAtom* dAtom;
786	<	LinkedAssign* extras;
787	<	LinkedAssign* current_extra;
788	<	AtomStamp* currentAtom;
789	<	BondStamp* currentBond;
790	<	BendStamp* currentBend;
791	<	TorsionStamp* currentTorsion;
1632	>	zconsTol->setData(defaultZConsTol);
1633	>	}
1634	>	theInfo.addProperty(zconsTol);
1635
1636	<	bond_pair* theBonds;
1637	<	bend_set* theBends;
1638	<	torsion_set* theTorsions;
1639	<
1640	<
1641	<	//init the forceField paramters
1642	<
1643	<	the_ff->readParams();
1644	<
1645	<
1646	<	// init the atoms
1647	<
1648	<	double ux, uy, uz, u, uSqr;
1649	<
1650	<	atomOffset = 0;
1651	<	excludeOffset = 0;
1652	<	for(i=0; i<simnfo->n_mol; i++){
1636	>	//set Force Substraction Policy
1637	>	StringData* zconsForcePolicy =  new StringData();
1638	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1639	>
1640	>	if(globals->haveZconsForcePolicy()){
1641	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1642	>	}
1643	>	else{
1644	>	sprintf( painCave.errMsg,
1645	>	"ZConstraint Warning: User does not set force substraction policy, "
1646	>	"average force substraction policy is used\n");
1647	>	painCave.isFatal = 0;
1648	>	simError();
1649	>	zconsForcePolicy->setData("BYNUMBER");
1650	>	}
1651	>
1652	>	theInfo.addProperty(zconsForcePolicy);
1653	>
1654	>	//Determine the name of ouput file and add it into SimInfo's property list
1655	>	//Be careful, do not use inFileName, since it is a pointer which
1656	>	//point to a string at master node, and slave nodes do not contain that string
1657
1658	<	stampID = the_molecules[i].getStampID();
812	<
813	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
814	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
815	<	info.nBends    = comp_stamps[stampID]->getNBends();
816	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
817	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
818	<
819	<	info.myAtoms = &the_atoms[atomOffset];
820	<	info.myExcludes = &the_excludes[excludeOffset];
821	<	info.myBonds = new Bond*[info.nBonds];
822	<	info.myBends = new Bend*[info.nBends];
823	<	info.myTorsions = new Torsion*[info.nTorsions];
824	<
825	<	theBonds = new bond_pair[info.nBonds];
826	<	theBends = new bend_set[info.nBends];
827	<	theTorsions = new torsion_set[info.nTorsions];
1658	>	string zconsOutput(theInfo.finalName);
1659
1660	<	// make the Atoms
1660	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1661
1662	<	for(j=0; j<info.nAtoms; j++){
1663	<
1664	<	currentAtom = comp_stamps[stampID]->getAtom( j );
834	<	if( currentAtom->haveOrientation() ){
835	<
836	<	dAtom = new DirectionalAtom(j + atomOffset);
837	<	simnfo->n_oriented++;
838	<	info.myAtoms[j] = dAtom;
839	<
840	<	ux = currentAtom->getOrntX();
841	<	uy = currentAtom->getOrntY();
842	<	uz = currentAtom->getOrntZ();
843	<
844	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
845	<
846	<	u = sqrt( uSqr );
847	<	ux = ux / u;
848	<	uy = uy / u;
849	<	uz = uz / u;
850	<
851	<	dAtom->setSUx( ux );
852	<	dAtom->setSUy( uy );
853	<	dAtom->setSUz( uz );
854	<	}
855	<	else{
856	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
857	<	}
858	<	info.myAtoms[j]->setType( currentAtom->getType() );
1662	>	StringData* zconsFilename = new StringData();
1663	>	zconsFilename->setID(ZCONSFILENAME_ID);
1664	>	zconsFilename->setData(zconsOutput);
1665
1666	<	#ifdef IS_MPI
1667	<
1668	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
1669	<
1670	<	#endif // is_mpi
1671	<	}
1672	<
1673	<	// make the bonds
868	<	for(j=0; j<info.nBonds; j++){
869	<
870	<	currentBond = comp_stamps[stampID]->getBond( j );
871	<	theBonds[j].a = currentBond->getA() + atomOffset;
872	<	theBonds[j].b = currentBond->getB() + atomOffset;
1666	>	theInfo.addProperty(zconsFilename);
1667	>
1668	>	//setup index, pos and other parameters of z-constraint molecules
1669	>	nZConstraints = globals->getNzConstraints();
1670	>	theInfo.nZconstraints = nZConstraints;
1671	>
1672	>	zconStamp = globals->getZconStamp();
1673	>	ZConsParaItem tempParaItem;
1674
1675	<	exI = theBonds[j].a;
1676	<	exJ = theBonds[j].b;
1675	>	ZConsParaData* zconsParaData = new ZConsParaData();
1676	>	zconsParaData->setID(ZCONSPARADATA_ID);
1677	>
1678	>	for(int i = 0; i < nZConstraints; i++){
1679	>	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1680	>	tempParaItem.zPos = zconStamp[i]->getZpos();
1681	>	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1682	>	tempParaItem.kRatio = zconStamp[i]->getKratio();
1683
1684	<	// exclude_I must always be the smaller of the pair
878	<	if( exI > exJ ){
879	<	tempEx = exI;
880	<	exI = exJ;
881	<	exJ = tempEx;
882	<	}
883	<	#ifdef IS_MPI
884	<	tempEx = exI;
885	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
886	<	tempEx = exJ;
887	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
888	<
889	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
890	<	#else  // isn't MPI
891	<
892	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
893	<	#endif  //is_mpi
1684	>	zconsParaData->addItem(tempParaItem);
1685		}
895	–	excludeOffset += info.nBonds;
1686
1687	<	//make the bends
1688	<	for(j=0; j<info.nBends; j++){
899	<
900	<	currentBend = comp_stamps[stampID]->getBend( j );
901	<	theBends[j].a = currentBend->getA() + atomOffset;
902	<	theBends[j].b = currentBend->getB() + atomOffset;
903	<	theBends[j].c = currentBend->getC() + atomOffset;
904	<
905	<	if( currentBend->haveExtras() ){
906	<
907	<	extras = currentBend->getExtras();
908	<	current_extra = extras;
909	<
910	<	while( current_extra != NULL ){
911	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
912	<
913	<	switch( current_extra->getType() ){
914	<
915	<	case 0:
916	<	theBends[j].ghost =
917	<	current_extra->getInt() + atomOffset;
918	<	theBends[j].isGhost = 1;
919	<	break;
920	<
921	<	case 1:
922	<	theBends[j].ghost =
923	<	(int)current_extra->getDouble() + atomOffset;
924	<	theBends[j].isGhost = 1;
925	<	break;
926	<
927	<	default:
928	<	sprintf( painCave.errMsg,
929	<	"SimSetup Error: ghostVectorSource was neither a "
930	<	"double nor an int.\n"
931	<	"-->Bend[%d] in %s\n",
932	<	j, comp_stamps[stampID]->getID() );
933	<	painCave.isFatal = 1;
934	<	simError();
935	<	}
936	<	}
937	<
938	<	else{
939	<
940	<	sprintf( painCave.errMsg,
941	<	"SimSetup Error: unhandled bend assignment:\n"
942	<	"    -->%s in Bend[%d] in %s\n",
943	<	current_extra->getlhs(),
944	<	j, comp_stamps[stampID]->getID() );
945	<	painCave.isFatal = 1;
946	<	simError();
947	<	}
948	<
949	<	current_extra = current_extra->getNext();
950	<	}
951	<	}
952	<
953	<	if( !theBends[j].isGhost ){
954	<
955	<	exI = theBends[j].a;
956	<	exJ = theBends[j].c;
957	<	}
958	<	else{
1687	>	//sort the parameters by index of molecules
1688	>	zconsParaData->sortByIndex();
1689
1690	<	exI = theBends[j].a;
1691	<	exJ = theBends[j].b;
962	<	}
1690	>	//push data into siminfo, therefore, we can retrieve later
1691	>	theInfo.addProperty(zconsParaData);
1692
964	–	// exclude_I must always be the smaller of the pair
965	–	if( exI > exJ ){
966	–	tempEx = exI;
967	–	exI = exJ;
968	–	exJ = tempEx;
969	–	}
970	–	#ifdef IS_MPI
971	–	tempEx = exI;
972	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
973	–	tempEx = exJ;
974	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
975	–
976	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
977	–	#else  // isn't MPI
978	–	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
979	–	#endif  //is_mpi
980	–	}
981	–	excludeOffset += info.nBends;
982	–
983	–	for(j=0; j<info.nTorsions; j++){
984	–
985	–	currentTorsion = comp_stamps[stampID]->getTorsion( j );
986	–	theTorsions[j].a = currentTorsion->getA() + atomOffset;
987	–	theTorsions[j].b = currentTorsion->getB() + atomOffset;
988	–	theTorsions[j].c = currentTorsion->getC() + atomOffset;
989	–	theTorsions[j].d = currentTorsion->getD() + atomOffset;
990	–
991	–	exI = theTorsions[j].a;
992	–	exJ = theTorsions[j].d;
993	–
994	–	// exclude_I must always be the smaller of the pair
995	–	if( exI > exJ ){
996	–	tempEx = exI;
997	–	exI = exJ;
998	–	exJ = tempEx;
999	–	}
1000	–	#ifdef IS_MPI
1001	–	tempEx = exI;
1002	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1003	–	tempEx = exJ;
1004	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1005	–
1006	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1007	–	#else  // isn't MPI
1008	–	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1009	–	#endif  //is_mpi
1010	–	}
1011	–	excludeOffset += info.nTorsions;
1012	–
1013	–
1014	–	// send the arrays off to the forceField for init.
1015	–
1016	–	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1017	–	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1018	–	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1019	–	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1020	–
1021	–
1022	–	the_molecules[i].initialize( info );
1023	–
1024	–
1025	–	atomOffset += info.nAtoms;
1026	–	delete[] theBonds;
1027	–	delete[] theBends;
1028	–	delete[] theTorsions;
1029	–	}
1030	–
1031	–	#ifdef IS_MPI
1032	–	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1033	–	MPIcheckPoint();
1034	–	#endif // is_mpi
1035	–
1036	–	// clean up the forcefield
1037	–	the_ff->calcRcut();
1038	–	the_ff->cleanMe();
1039	–
1693		}
1041	–
1042	–	void SimSetup::initFromBass( void ){
1043	–
1044	–	int i, j, k;
1045	–	int n_cells;
1046	–	double cellx, celly, cellz;
1047	–	double temp1, temp2, temp3;
1048	–	int n_per_extra;
1049	–	int n_extra;
1050	–	int have_extra, done;
1051	–
1052	–	temp1 = (double)tot_nmol / 4.0;
1053	–	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1054	–	temp3 = ceil( temp2 );
1055	–
1056	–	have_extra =0;
1057	–	if( temp2 < temp3 ){ // we have a non-complete lattice
1058	–	have_extra =1;
1059	–
1060	–	n_cells = (int)temp3 - 1;
1061	–	cellx = simnfo->box_x / temp3;
1062	–	celly = simnfo->box_y / temp3;
1063	–	cellz = simnfo->box_z / temp3;
1064	–	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1065	–	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1066	–	n_per_extra = (int)ceil( temp1 );
1067	–
1068	–	if( n_per_extra > 4){
1069	–	sprintf( painCave.errMsg,
1070	–	"SimSetup error. There has been an error in constructing"
1071	–	" the non-complete lattice.\n" );
1072	–	painCave.isFatal = 1;
1073	–	simError();
1074	–	}
1075	–	}
1076	–	else{
1077	–	n_cells = (int)temp3;
1078	–	cellx = simnfo->box_x / temp3;
1079	–	celly = simnfo->box_y / temp3;
1080	–	cellz = simnfo->box_z / temp3;
1081	–	}
1082	–
1083	–	current_mol = 0;
1084	–	current_comp_mol = 0;
1085	–	current_comp = 0;
1086	–	current_atom_ndx = 0;
1087	–
1088	–	for( i=0; i < n_cells ; i++ ){
1089	–	for( j=0; j < n_cells; j++ ){
1090	–	for( k=0; k < n_cells; k++ ){
1091	–
1092	–	makeElement( i * cellx,
1093	–	j * celly,
1094	–	k * cellz );
1095	–
1096	–	makeElement( i * cellx + 0.5 * cellx,
1097	–	j * celly + 0.5 * celly,
1098	–	k * cellz );
1099	–
1100	–	makeElement( i * cellx,
1101	–	j * celly + 0.5 * celly,
1102	–	k * cellz + 0.5 * cellz );
1103	–
1104	–	makeElement( i * cellx + 0.5 * cellx,
1105	–	j * celly,
1106	–	k * cellz + 0.5 * cellz );
1107	–	}
1108	–	}
1109	–	}
1110	–
1111	–	if( have_extra ){
1112	–	done = 0;
1113	–
1114	–	int start_ndx;
1115	–	for( i=0; i < (n_cells+1) && !done; i++ ){
1116	–	for( j=0; j < (n_cells+1) && !done; j++ ){
1117	–
1118	–	if( i < n_cells ){
1119	–
1120	–	if( j < n_cells ){
1121	–	start_ndx = n_cells;
1122	–	}
1123	–	else start_ndx = 0;
1124	–	}
1125	–	else start_ndx = 0;
1126	–
1127	–	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1128	–
1129	–	makeElement( i * cellx,
1130	–	j * celly,
1131	–	k * cellz );
1132	–	done = ( current_mol >= tot_nmol );
1133	–
1134	–	if( !done && n_per_extra > 1 ){
1135	–	makeElement( i * cellx + 0.5 * cellx,
1136	–	j * celly + 0.5 * celly,
1137	–	k * cellz );
1138	–	done = ( current_mol >= tot_nmol );
1139	–	}
1140	–
1141	–	if( !done && n_per_extra > 2){
1142	–	makeElement( i * cellx,
1143	–	j * celly + 0.5 * celly,
1144	–	k * cellz + 0.5 * cellz );
1145	–	done = ( current_mol >= tot_nmol );
1146	–	}
1147	–
1148	–	if( !done && n_per_extra > 3){
1149	–	makeElement( i * cellx + 0.5 * cellx,
1150	–	j * celly,
1151	–	k * cellz + 0.5 * cellz );
1152	–	done = ( current_mol >= tot_nmol );
1153	–	}
1154	–	}
1155	–	}
1156	–	}
1157	–	}
1158	–
1159	–
1160	–	for( i=0; i<simnfo->n_atoms; i++ ){
1161	–	simnfo->atoms[i]->set_vx( 0.0 );
1162	–	simnfo->atoms[i]->set_vy( 0.0 );
1163	–	simnfo->atoms[i]->set_vz( 0.0 );
1164	–	}
1165	–	}
1166	–
1167	–	void SimSetup::makeElement( double x, double y, double z ){
1168	–
1169	–	int k;
1170	–	AtomStamp* current_atom;
1171	–	DirectionalAtom* dAtom;
1172	–	double rotMat[3][3];
1173	–
1174	–	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1175	–
1176	–	current_atom = comp_stamps[current_comp]->getAtom( k );
1177	–	if( !current_atom->havePosition() ){
1178	–	sprintf( painCave.errMsg,
1179	–	"SimSetup:initFromBass error.\n"
1180	–	"\tComponent %s, atom %s does not have a position specified.\n"
1181	–	"\tThe initialization routine is unable to give a start"
1182	–	" position.\n",
1183	–	comp_stamps[current_comp]->getID(),
1184	–	current_atom->getType() );
1185	–	painCave.isFatal = 1;
1186	–	simError();
1187	–	}
1188	–
1189	–	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1190	–	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1191	–	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1192	–
1193	–	if( the_atoms[current_atom_ndx]->isDirectional() ){
1194	–
1195	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1196	–
1197	–	rotMat[0][0] = 1.0;
1198	–	rotMat[0][1] = 0.0;
1199	–	rotMat[0][2] = 0.0;
1200	–
1201	–	rotMat[1][0] = 0.0;
1202	–	rotMat[1][1] = 1.0;
1203	–	rotMat[1][2] = 0.0;
1204	–
1205	–	rotMat[2][0] = 0.0;
1206	–	rotMat[2][1] = 0.0;
1207	–	rotMat[2][2] = 1.0;
1208	–
1209	–	dAtom->setA( rotMat );
1210	–	}
1211	–
1212	–	current_atom_ndx++;
1213	–	}
1214	–
1215	–	current_mol++;
1216	–	current_comp_mol++;
1217	–
1218	–	if( current_comp_mol >= components_nmol[current_comp] ){
1219	–
1220	–	current_comp_mol = 0;
1221	–	current_comp++;
1222	–	}
1223	–	}

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