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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 490 by gezelter, Fri Apr 11 15:16:59 2003 UTC vs.
Revision 689 by tim, Tue Aug 12 19:56:49 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 | SimSetup::SimSetup(){
15		#include "mpiSimulation.hpp"
16		#endif
17
18	+	// some defines for ensemble and Forcefield  cases
19	+
20	+	#define NVE_ENS        0
21	+	#define NVT_ENS        1
22	+	#define NPTi_ENS       2
23	+	#define NPTf_ENS       3
24	+	#define 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 | void SimSetup::parseFile( char* fileName ){
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::createSim( 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	>	std::cerr << "gathering info\n";
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	>	gatherInfo();
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	>	// creation of complex system objects
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	>	std::cerr << "creating system objects\n";
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	>	sysObjectsCreation();
110
111	<	if (the_globals->haveTauBarostat())
112	<	the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
113	<	else {
111	>	// check on the post processing info
112	>
113	>	std::cerr << "performing final info check.\n";
114	>
115	>	finalInfoCheck();
116	>
117	>	// initialize the system coordinates
118	>
119	>	std::cerr << "about to init coords\n";
120	>
121	>	if( !isInfoArray ) initSystemCoords();
122	>
123	>	// make the output filenames
124	>
125	>	makeOutNames();
126	>
127	>	// make the integrator
128	>
129	>	makeIntegrator();
130	>
131	>	#ifdef IS_MPI
132	>	mpiSim->mpiRefresh();
133	>	#endif
134	>
135	>	// initialize the Fortran
136	>
137	>	initFortran();
138	>
139	>
140	>
141	>	}
142	>
143	>
144	>	void SimSetup::makeMolecules( void ){
145	>
146	>	int k,l;
147	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
148	>	molInit molInfo;
149	>	DirectionalAtom* dAtom;
150	>	LinkedAssign* extras;
151	>	LinkedAssign* current_extra;
152	>	AtomStamp* currentAtom;
153	>	BondStamp* currentBond;
154	>	BendStamp* currentBend;
155	>	TorsionStamp* currentTorsion;
156	>
157	>	bond_pair* theBonds;
158	>	bend_set* theBends;
159	>	torsion_set* theTorsions;
160	>
161	>
162	>	//init the forceField paramters
163	>
164	>	the_ff->readParams();
165	>
166	>
167	>	// init the atoms
168	>
169	>	double ux, uy, uz, u, uSqr;
170	>
171	>	for(k=0; k<nInfo; k++){
172	>
173	>	the_ff->setSimInfo( &(info[k]) );
174	>
175	>	atomOffset = 0;
176	>	excludeOffset = 0;
177	>	for(i=0; i<info[k].n_mol; i++){
178	>
179	>	stampID = info[k].molecules[i].getStampID();
180	>
181	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
182	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
183	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
184	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
185	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
186	>
187	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
188	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
189	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
190	>	molInfo.myBends = new Bend*[molInfo.nBends];
191	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
192	>
193	>	theBonds = new bond_pair[molInfo.nBonds];
194	>	theBends = new bend_set[molInfo.nBends];
195	>	theTorsions = new torsion_set[molInfo.nTorsions];
196	>
197	>	// make the Atoms
198	>
199	>	for(j=0; j<molInfo.nAtoms; j++){
200	>
201	>	currentAtom = comp_stamps[stampID]->getAtom( j );
202	>	if( currentAtom->haveOrientation() ){
203	>
204	>	dAtom = new DirectionalAtom( (j + atomOffset),
205	>	info[k].getConfiguration() );
206	>	info[k].n_oriented++;
207	>	molInfo.myAtoms[j] = dAtom;
208	>
209	>	ux = currentAtom->getOrntX();
210	>	uy = currentAtom->getOrntY();
211	>	uz = currentAtom->getOrntZ();
212	>
213	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
214	>
215	>	u = sqrt( uSqr );
216	>	ux = ux / u;
217	>	uy = uy / u;
218	>	uz = uz / u;
219	>
220	>	dAtom->setSUx( ux );
221	>	dAtom->setSUy( uy );
222	>	dAtom->setSUz( uz );
223	>	}
224	>	else{
225	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
226	>	info[k].getConfiguration() );
227	>	}
228	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
229	>
230	>	#ifdef IS_MPI
231	>
232	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
233	>
234	>	#endif // is_mpi
235	>	}
236	>
237	>	// make the bonds
238	>	for(j=0; j<molInfo.nBonds; j++){
239	>
240	>	currentBond = comp_stamps[stampID]->getBond( j );
241	>	theBonds[j].a = currentBond->getA() + atomOffset;
242	>	theBonds[j].b = currentBond->getB() + atomOffset;
243	>
244	>	exI = theBonds[j].a;
245	>	exJ = theBonds[j].b;
246	>
247	>	// exclude_I must always be the smaller of the pair
248	>	if( exI > exJ ){
249	>	tempEx = exI;
250	>	exI = exJ;
251	>	exJ = tempEx;
252	>	}
253	>	#ifdef IS_MPI
254	>	tempEx = exI;
255	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
256	>	tempEx = exJ;
257	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
258	>
259	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
260	>	#else  // isn't MPI
261	>
262	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
263	>	#endif  //is_mpi
264	>	}
265	>	excludeOffset += molInfo.nBonds;
266	>
267	>	//make the bends
268	>	for(j=0; j<molInfo.nBends; j++){
269	>
270	>	currentBend = comp_stamps[stampID]->getBend( j );
271	>	theBends[j].a = currentBend->getA() + atomOffset;
272	>	theBends[j].b = currentBend->getB() + atomOffset;
273	>	theBends[j].c = currentBend->getC() + atomOffset;
274	>
275	>	if( currentBend->haveExtras() ){
276	>
277	>	extras = currentBend->getExtras();
278	>	current_extra = extras;
279	>
280	>	while( current_extra != NULL ){
281	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
282	>
283	>	switch( current_extra->getType() ){
284	>
285	>	case 0:
286	>	theBends[j].ghost =
287	>	current_extra->getInt() + atomOffset;
288	>	theBends[j].isGhost = 1;
289	>	break;
290	>
291	>	case 1:
292	>	theBends[j].ghost =
293	>	(int)current_extra->getDouble() + atomOffset;
294	>	theBends[j].isGhost = 1;
295	>	break;
296	>
297	>	default:
298	>	sprintf( painCave.errMsg,
299	>	"SimSetup Error: ghostVectorSource was neither a "
300	>	"double nor an int.\n"
301	>	"-->Bend[%d] in %s\n",
302	>	j, comp_stamps[stampID]->getID() );
303	>	painCave.isFatal = 1;
304	>	simError();
305	>	}
306	>	}
307	>
308	>	else{
309	>
310	>	sprintf( painCave.errMsg,
311	>	"SimSetup Error: unhandled bend assignment:\n"
312	>	"    -->%s in Bend[%d] in %s\n",
313	>	current_extra->getlhs(),
314	>	j, comp_stamps[stampID]->getID() );
315	>	painCave.isFatal = 1;
316	>	simError();
317	>	}
318	>
319	>	current_extra = current_extra->getNext();
320	>	}
321	>	}
322	>
323	>	if( !theBends[j].isGhost ){
324	>
325	>	exI = theBends[j].a;
326	>	exJ = theBends[j].c;
327	>	}
328	>	else{
329	>
330	>	exI = theBends[j].a;
331	>	exJ = theBends[j].b;
332	>	}
333	>
334	>	// exclude_I must always be the smaller of the pair
335	>	if( exI > exJ ){
336	>	tempEx = exI;
337	>	exI = exJ;
338	>	exJ = tempEx;
339	>	}
340	>	#ifdef IS_MPI
341	>	tempEx = exI;
342	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
343	>	tempEx = exJ;
344	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345	>
346	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
347	>	#else  // isn't MPI
348	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
349	>	#endif  //is_mpi
350	>	}
351	>	excludeOffset += molInfo.nBends;
352	>
353	>	for(j=0; j<molInfo.nTorsions; j++){
354	>
355	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
356	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
357	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
358	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
359	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
360	>
361	>	exI = theTorsions[j].a;
362	>	exJ = theTorsions[j].d;
363	>
364	>	// exclude_I must always be the smaller of the pair
365	>	if( exI > exJ ){
366	>	tempEx = exI;
367	>	exI = exJ;
368	>	exJ = tempEx;
369	>	}
370	>	#ifdef IS_MPI
371	>	tempEx = exI;
372	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
373	>	tempEx = exJ;
374	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
375	>
376	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
377	>	#else  // isn't MPI
378	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
379	>	#endif  //is_mpi
380	>	}
381	>	excludeOffset += molInfo.nTorsions;
382	>
383	>
384	>	// send the arrays off to the forceField for init.
385	>
386	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
387	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
388	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
389	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
390	>
391	>
392	>	info[k].molecules[i].initialize( molInfo );
393	>
394	>
395	>	atomOffset += molInfo.nAtoms;
396	>	delete[] theBonds;
397	>	delete[] theBends;
398	>	delete[] theTorsions;
399	>	}
400	>	}
401	>
402	>	#ifdef IS_MPI
403	>	sprintf( checkPointMsg, "all molecules initialized succesfully" );
404	>	MPIcheckPoint();
405	>	#endif // is_mpi
406	>
407	>	// clean up the forcefield
408	>
409	>	the_ff->calcRcut();
410	>	the_ff->cleanMe();
411	>
412	>	}
413	>
414	>	void SimSetup::initFromBass( void ){
415	>
416	>	int i, j, k;
417	>	int n_cells;
418	>	double cellx, celly, cellz;
419	>	double temp1, temp2, temp3;
420	>	int n_per_extra;
421	>	int n_extra;
422	>	int have_extra, done;
423	>
424	>	double vel[3];
425	>	vel[0] = 0.0;
426	>	vel[1] = 0.0;
427	>	vel[2] = 0.0;
428	>
429	>	temp1 = (double)tot_nmol / 4.0;
430	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
431	>	temp3 = ceil( temp2 );
432	>
433	>	have_extra =0;
434	>	if( temp2 < temp3 ){ // we have a non-complete lattice
435	>	have_extra =1;
436	>
437	>	n_cells = (int)temp3 - 1;
438	>	cellx = info[0].boxL[0] / temp3;
439	>	celly = info[0].boxL[1] / temp3;
440	>	cellz = info[0].boxL[2] / temp3;
441	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
442	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
443	>	n_per_extra = (int)ceil( temp1 );
444	>
445	>	if( n_per_extra > 4){
446		sprintf( painCave.errMsg,
447	<	"SimSetup error: If you use the constant pressure\n"
448	<	"    ensemble, you must set tauBarostat.\n"
120	<	"    This was found in the BASS file.\n");
447	>	"SimSetup error. There has been an error in constructing"
448	>	" the non-complete lattice.\n" );
449		painCave.isFatal = 1;
450		simError();
451		}
452	+	}
453	+	else{
454	+	n_cells = (int)temp3;
455	+	cellx = info[0].boxL[0] / temp3;
456	+	celly = info[0].boxL[1] / temp3;
457	+	cellz = info[0].boxL[2] / temp3;
458	+	}
459
460	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
461	<	the_extendedsystem = new ExtendedSystem( simnfo );
462	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
460	>	current_mol = 0;
461	>	current_comp_mol = 0;
462	>	current_comp = 0;
463	>	current_atom_ndx = 0;
464
465	<	if (the_globals->haveTauThermostat())
466	<	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
467	<	else if (the_globals->haveQmass())
468	<	the_extendedsystem->setQmass(the_globals->getQmass());
469	<	else {
465	>	for( i=0; i < n_cells ; i++ ){
466	>	for( j=0; j < n_cells; j++ ){
467	>	for( k=0; k < n_cells; k++ ){
468	>
469	>	makeElement( i * cellx,
470	>	j * celly,
471	>	k * cellz );
472	>
473	>	makeElement( i * cellx + 0.5 * cellx,
474	>	j * celly + 0.5 * celly,
475	>	k * cellz );
476	>
477	>	makeElement( i * cellx,
478	>	j * celly + 0.5 * celly,
479	>	k * cellz + 0.5 * cellz );
480	>
481	>	makeElement( i * cellx + 0.5 * cellx,
482	>	j * celly,
483	>	k * cellz + 0.5 * cellz );
484	>	}
485	>	}
486	>	}
487	>
488	>	if( have_extra ){
489	>	done = 0;
490	>
491	>	int start_ndx;
492	>	for( i=0; i < (n_cells+1) && !done; i++ ){
493	>	for( j=0; j < (n_cells+1) && !done; j++ ){
494	>
495	>	if( i < n_cells ){
496	>
497	>	if( j < n_cells ){
498	>	start_ndx = n_cells;
499	>	}
500	>	else start_ndx = 0;
501	>	}
502	>	else start_ndx = 0;
503	>
504	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
505	>
506	>	makeElement( i * cellx,
507	>	j * celly,
508	>	k * cellz );
509	>	done = ( current_mol >= tot_nmol );
510	>
511	>	if( !done && n_per_extra > 1 ){
512	>	makeElement( i * cellx + 0.5 * cellx,
513	>	j * celly + 0.5 * celly,
514	>	k * cellz );
515	>	done = ( current_mol >= tot_nmol );
516	>	}
517	>
518	>	if( !done && n_per_extra > 2){
519	>	makeElement( i * cellx,
520	>	j * celly + 0.5 * celly,
521	>	k * cellz + 0.5 * cellz );
522	>	done = ( current_mol >= tot_nmol );
523	>	}
524	>
525	>	if( !done && n_per_extra > 3){
526	>	makeElement( i * cellx + 0.5 * cellx,
527	>	j * celly,
528	>	k * cellz + 0.5 * cellz );
529	>	done = ( current_mol >= tot_nmol );
530	>	}
531	>	}
532	>	}
533	>	}
534	>	}
535	>
536	>	for( i=0; i<info[0].n_atoms; i++ ){
537	>	info[0].atoms[i]->setVel( vel );
538	>	}
539	>	}
540	>
541	>	void SimSetup::makeElement( double x, double y, double z ){
542	>
543	>	int k;
544	>	AtomStamp* current_atom;
545	>	DirectionalAtom* dAtom;
546	>	double rotMat[3][3];
547	>	double pos[3];
548	>
549	>	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
550	>
551	>	current_atom = comp_stamps[current_comp]->getAtom( k );
552	>	if( !current_atom->havePosition() ){
553		sprintf( painCave.errMsg,
554	<	"SimSetup error: If you use one of the constant temperature\n"
555	<	"    ensembles, you must set either tauThermostat or qMass.\n"
556	<	"    Neither of these was found in the BASS file.\n");
554	>	"SimSetup:initFromBass error.\n"
555	>	"\tComponent %s, atom %s does not have a position specified.\n"
556	>	"\tThe initialization routine is unable to give a start"
557	>	" position.\n",
558	>	comp_stamps[current_comp]->getID(),
559	>	current_atom->getType() );
560		painCave.isFatal = 1;
561		simError();
562		}
563	+
564	+	pos[0] = x + current_atom->getPosX();
565	+	pos[1] = y + current_atom->getPosY();
566	+	pos[2] = z + current_atom->getPosZ();
567	+
568	+	info[0].atoms[current_atom_ndx]->setPos( pos );
569
570	<	} else if ( !strcasecmp( ensemble, "NVE") ) {
143	<	} else {
144	<	sprintf( painCave.errMsg,
145	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
146	<	"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 );
570	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
571
572	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
573	<	simnfo->usePBC = the_globals->getPBC();
574	<
575	<	int usesDipoles = 0;
576	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
577	<	the_ff = new TraPPE_ExFF();
578	<	usesDipoles = 1;
572	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
573	>
574	>	rotMat[0][0] = 1.0;
575	>	rotMat[0][1] = 0.0;
576	>	rotMat[0][2] = 0.0;
577	>
578	>	rotMat[1][0] = 0.0;
579	>	rotMat[1][1] = 1.0;
580	>	rotMat[1][2] = 0.0;
581	>
582	>	rotMat[2][0] = 0.0;
583	>	rotMat[2][1] = 0.0;
584	>	rotMat[2][2] = 1.0;
585	>
586	>	dAtom->setA( rotMat );
587	>	}
588	>
589	>	current_atom_ndx++;
590		}
591	<	else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
591	>
592	>	current_mol++;
593	>	current_comp_mol++;
594	>
595	>	if( current_comp_mol >= components_nmol[current_comp] ){
596	>
597	>	current_comp_mol = 0;
598	>	current_comp++;
599	>	}
600	>	}
601	>
602	>
603	>	void SimSetup::gatherInfo( void ){
604	>	int i,j,k;
605	>
606	>	ensembleCase = -1;
607	>	ffCase = -1;
608	>
609	>	// set the easy ones first
610	>
611	>	for( i=0; i<nInfo; i++){
612	>	info[i].target_temp = globals->getTargetTemp();
613	>	info[i].dt = globals->getDt();
614	>	info[i].run_time = globals->getRunTime();
615	>	}
616	>	n_components = globals->getNComponents();
617	>
618	>
619	>	// get the forceField
620	>
621	>	strcpy( force_field, globals->getForceField() );
622	>
623	>	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
624	>	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
625	>	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
626		else{
627		sprintf( painCave.errMsg,
628		"SimSetup Error. Unrecognized force field -> %s\n",
#	Line 168 | Line 631 | void SimSetup::createSim( void ){
631		simError();
632		}
633
634	<	#ifdef IS_MPI
172	<	strcpy( checkPointMsg, "ForceField creation successful" );
173	<	MPIcheckPoint();
174	<	#endif // is_mpi
634	>	// get the ensemble
635
636	+	strcpy( ensemble, globals->getEnsemble() );
637	+
638	+	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
639	+	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
640	+	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
641	+	ensembleCase = NPTi_ENS;
642	+	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
643	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
644	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
645	+	else{
646	+	sprintf( painCave.errMsg,
647	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
648	+	"reverting to NVE for this simulation.\n",
649	+	ensemble );
650	+	painCave.isFatal = 0;
651	+	simError();
652	+	strcpy( ensemble, "NVE" );
653	+	ensembleCase = NVE_ENS;
654	+	}
655
656	+	for(i=0; i<nInfo; i++){
657	+
658	+	strcpy( info[i].ensemble, ensemble );
659
660	+	// get the mixing rule
661	+
662	+	strcpy( info[i].mixingRule, globals->getMixingRule() );
663	+	info[i].usePBC = globals->getPBC();
664	+	}
665	+
666		// get the components and calculate the tot_nMol and indvidual n_mol
667	<	the_components = the_globals->getComponents();
667	>
668	>	the_components = globals->getComponents();
669		components_nmol = new int[n_components];
181	–	comp_stamps = new MoleculeStamp*[n_components];
670
671	<	if( !the_globals->haveNMol() ){
671	>
672	>	if( !globals->haveNMol() ){
673		// we don't have the total number of molecules, so we assume it is
674		// given in each component
675
#	Line 209 | Line 698 | void SimSetup::createSim( void ){
698		" Please give nMol in the components.\n" );
699		painCave.isFatal = 1;
700		simError();
212	–
213	–
214	–	//     tot_nmol = the_globals->getNMol();
215	–
216	–	//   //we have the total number of molecules, now we check for molfractions
217	–	//     for( i=0; i<n_components; i++ ){
218	–
219	–	//       if( !the_components[i]->haveMolFraction() ){
220	–
221	–	//  if( !the_components[i]->haveNMol() ){
222	–	//    //we have a problem
223	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
224	–	//              << " nMol was given in component
225	–
701		}
702
703	<	#ifdef IS_MPI
229	<	strcpy( checkPointMsg, "Have the number of components" );
230	<	MPIcheckPoint();
231	<	#endif // is_mpi
232	<
233	<	// make an array of molecule stamps that match the components used.
234	<	// also extract the used stamps out into a separate linked list
235	<
236	<	simnfo->nComponents = n_components;
237	<	simnfo->componentsNmol = components_nmol;
238	<	simnfo->compStamps = comp_stamps;
239	<	simnfo->headStamp = new LinkedMolStamp();
703	>	// set the status, sample, and thermal kick times
704
705	<	char* id;
242	<	LinkedMolStamp* headStamp = simnfo->headStamp;
243	<	LinkedMolStamp* currentStamp = NULL;
244	<	for( i=0; i<n_components; i++ ){
705	>	for(i=0; i<nInfo; i++){
706
707	<	id = the_components[i]->getType();
708	<	comp_stamps[i] = NULL;
707	>	if( globals->haveSampleTime() ){
708	>	info[i].sampleTime = globals->getSampleTime();
709	>	info[i].statusTime = info[i].sampleTime;
710	>	info[i].thermalTime = info[i].sampleTime;
711	>	}
712	>	else{
713	>	info[i].sampleTime = globals->getRunTime();
714	>	info[i].statusTime = info[i].sampleTime;
715	>	info[i].thermalTime = info[i].sampleTime;
716	>	}
717
718	<	// check to make sure the component isn't already in the list
718	>	if( globals->haveStatusTime() ){
719	>	info[i].statusTime = globals->getStatusTime();
720	>	}
721	>
722	>	if( globals->haveThermalTime() ){
723	>	info[i].thermalTime = globals->getThermalTime();
724	>	}
725
726	<	comp_stamps[i] = headStamp->match( id );
727	<	if( comp_stamps[i] == NULL ){
726	>	// check for the temperature set flag
727	>
728	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
729	>
730	>	// get some of the tricky things that may still be in the globals
731	>
732	>	double boxVector[3];
733	>	if( globals->haveBox() ){
734	>	boxVector[0] = globals->getBox();
735	>	boxVector[1] = globals->getBox();
736	>	boxVector[2] = globals->getBox();
737
738	<	// extract the component from the list;
738	>	info[i].setBox( boxVector );
739	>	}
740	>	else if( globals->haveDensity() ){
741
742	<	currentStamp = the_stamps->extractMolStamp( id );
743	<	if( currentStamp == NULL ){
742	>	double vol;
743	>	vol = (double)tot_nmol / globals->getDensity();
744	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
745	>	boxVector[1] = boxVector[0];
746	>	boxVector[2] = boxVector[0];
747	>
748	>	info[i].setBox( boxVector );
749	>	}
750	>	else{
751	>	if( !globals->haveBoxX() ){
752		sprintf( painCave.errMsg,
753	<	"SimSetup error: Component \"%s\" was not found in the "
260	<	"list of declared molecules\n",
261	<	id );
753	>	"SimSetup error, no periodic BoxX size given.\n" );
754		painCave.isFatal = 1;
755		simError();
756		}
757	+	boxVector[0] = globals->getBoxX();
758
759	<	headStamp->add( currentStamp );
760	<	comp_stamps[i] = headStamp->match( id );
759	>	if( !globals->haveBoxY() ){
760	>	sprintf( painCave.errMsg,
761	>	"SimSetup error, no periodic BoxY size given.\n" );
762	>	painCave.isFatal = 1;
763	>	simError();
764	>	}
765	>	boxVector[1] = globals->getBoxY();
766	>
767	>	if( !globals->haveBoxZ() ){
768	>	sprintf( painCave.errMsg,
769	>	"SimSetup error, no periodic BoxZ size given.\n" );
770	>	painCave.isFatal = 1;
771	>	simError();
772	>	}
773	>	boxVector[2] = globals->getBoxZ();
774	>
775	>	info[i].setBox( boxVector );
776		}
269	–	}
777
778	+	}
779	+
780		#ifdef IS_MPI
781	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
781	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
782		MPIcheckPoint();
783		#endif // is_mpi
275	–
784
785	+	}
786
787
788	<	// caclulate the number of atoms, bonds, bends and torsions
788	>	void SimSetup::finalInfoCheck( void ){
789	>	int index;
790	>	int usesDipoles;
791	>	int i;
792
793	<	tot_atoms = 0;
794	<	tot_bonds = 0;
795	<	tot_bends = 0;
796	<	tot_torsions = 0;
797	<	for( i=0; i<n_components; i++ ){
798	<
799	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
800	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
801	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
802	<	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;
301	<	simnfo->molMembershipArray = new int[tot_atoms];
302	<
793	>	for(i=0; i<nInfo; i++){
794	>	// check electrostatic parameters
795	>
796	>	index = 0;
797	>	usesDipoles = 0;
798	>	while( (index < info[i].n_atoms) && !usesDipoles ){
799	>	usesDipoles = (info[i].atoms[index])->hasDipole();
800	>	index++;
801	>	}
802	>
803		#ifdef IS_MPI
804	<
805	<	// divide the molecules among processors here.
804	>	int myUse = usesDipoles;
805	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
806	>	#endif //is_mpi
807	>
808	>	double theEcr, theEst;
809
810	<	mpiSim = new mpiSimulation( simnfo );
811	<
309	<	globalIndex = mpiSim->divideLabor();
310	<
311	<	// set up the local variables
312	<
313	<	int localMol, allMol;
314	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
315	<
316	<	int* mol2proc = mpiSim->getMolToProcMap();
317	<	int* molCompType = mpiSim->getMolComponentType();
318	<
319	<	allMol = 0;
320	<	localMol = 0;
321	<	local_atoms = 0;
322	<	local_bonds = 0;
323	<	local_bends = 0;
324	<	local_torsions = 0;
325	<	globalAtomIndex = 0;
326	<
327	<
328	<	for( i=0; i<n_components; i++ ){
329	<
330	<	for( j=0; j<components_nmol[i]; j++ ){
810	>	if (globals->getUseRF() ) {
811	>	info[i].useReactionField = 1;
812
813	<	if( mol2proc[allMol] == worldRank ){
813	>	if( !globals->haveECR() ){
814	>	sprintf( painCave.errMsg,
815	>	"SimSetup Warning: using default value of 1/2 the smallest "
816	>	"box length for the electrostaticCutoffRadius.\n"
817	>	"I hope you have a very fast processor!\n");
818	>	painCave.isFatal = 0;
819	>	simError();
820	>	double smallest;
821	>	smallest = info[i].boxL[0];
822	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
823	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
824	>	theEcr = 0.5 * smallest;
825	>	} else {
826	>	theEcr = globals->getECR();
827	>	}
828	>
829	>	if( !globals->haveEST() ){
830	>	sprintf( painCave.errMsg,
831	>	"SimSetup Warning: using default value of 0.05 * the "
832	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
833	>	);
834	>	painCave.isFatal = 0;
835	>	simError();
836	>	theEst = 0.05 * theEcr;
837	>	} else {
838	>	theEst= globals->getEST();
839	>	}
840	>
841	>	info[i].setEcr( theEcr, theEst );
842	>
843	>	if(!globals->haveDielectric() ){
844	>	sprintf( painCave.errMsg,
845	>	"SimSetup Error: You are trying to use Reaction Field without"
846	>	"setting a dielectric constant!\n"
847	>	);
848	>	painCave.isFatal = 1;
849	>	simError();
850	>	}
851	>	info[i].dielectric = globals->getDielectric();
852	>	}
853	>	else {
854	>	if (usesDipoles) {
855
856	<	local_atoms +=    comp_stamps[i]->getNAtoms();
857	<	local_bonds +=    comp_stamps[i]->getNBonds();
858	<	local_bends +=    comp_stamps[i]->getNBends();
859	<	local_torsions += comp_stamps[i]->getNTorsions();
860	<	localMol++;
861	<	}
862	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
863	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
864	<	globalAtomIndex++;
856	>	if( !globals->haveECR() ){
857	>	sprintf( painCave.errMsg,
858	>	"SimSetup Warning: using default value of 1/2 the smallest "
859	>	"box length for the electrostaticCutoffRadius.\n"
860	>	"I hope you have a very fast processor!\n");
861	>	painCave.isFatal = 0;
862	>	simError();
863	>	double smallest;
864	>	smallest = info[i].boxL[0];
865	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
866	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
867	>	theEcr = 0.5 * smallest;
868	>	} else {
869	>	theEcr = globals->getECR();
870	>	}
871	>
872	>	if( !globals->haveEST() ){
873	>	sprintf( painCave.errMsg,
874	>	"SimSetup Warning: using default value of 0.05 * the "
875	>	"electrostaticCutoffRadius for the "
876	>	"electrostaticSkinThickness\n"
877	>	);
878	>	painCave.isFatal = 0;
879	>	simError();
880	>	theEst = 0.05 * theEcr;
881	>	} else {
882	>	theEst= globals->getEST();
883	>	}
884	>
885	>	info[i].setEcr( theEcr, theEst );
886		}
887	<
345	<	allMol++;
346	<	}
887	>	}
888		}
889	<	local_SRI = local_bonds + local_bends + local_torsions;
889	>
890	>	#ifdef IS_MPI
891	>	strcpy( checkPointMsg, "post processing checks out" );
892	>	MPIcheckPoint();
893	>	#endif // is_mpi
894	>
895	>	}
896	>
897	>	void SimSetup::initSystemCoords( void ){
898	>	int i;
899
900	<	if (worldRank != 0) {
351	<	for (i =0; i < tot_atoms; i++){
352	<	std::cerr << "i = " << i << " molMembershipArray[i] = " << simnfo->molMembershipArray[i] << "\n";
353	<	}
354	<	}
900	>	char* inName;
901
902	<	simnfo->n_atoms = mpiSim->getMyNlocal();
902	>	std::cerr << "Setting atom Coords\n";
903	>
904	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
905
906	<	if( local_atoms != simnfo->n_atoms ){
906	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
907	>
908	>	if( globals->haveInitialConfig() ){
909	>
910	>	InitializeFromFile* fileInit;
911	>	#ifdef IS_MPI // is_mpi
912	>	if( worldRank == 0 ){
913	>	#endif //is_mpi
914	>	inName = globals->getInitialConfig();
915	>	fileInit = new InitializeFromFile( inName );
916	>	#ifdef IS_MPI
917	>	}else fileInit = new InitializeFromFile( NULL );
918	>	#endif
919	>	fileInit->readInit( info ); // default velocities on
920	>
921	>	delete fileInit;
922	>	}
923	>	else{
924	>
925	>	#ifdef IS_MPI
926	>
927	>	// no init from bass
928	>
929		sprintf( painCave.errMsg,
930	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
931	<	" localAtom (%d) are not equal.\n",
362	<	simnfo->n_atoms,
363	<	local_atoms );
364	<	painCave.isFatal = 1;
930	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
931	>	painCave.isFatal;
932		simError();
933	+
934	+	#else
935	+
936	+	initFromBass();
937	+
938	+
939	+	#endif
940		}
367	–
368	–	simnfo->n_bonds = local_bonds;
369	–	simnfo->n_bends = local_bends;
370	–	simnfo->n_torsions = local_torsions;
371	–	simnfo->n_SRI = local_SRI;
372	–	simnfo->n_mol = localMol;
373	–
374	–	strcpy( checkPointMsg, "Passed nlocal consistency check." );
375	–	MPIcheckPoint();
941
942	<
942	>	#ifdef IS_MPI
943	>	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
944	>	MPIcheckPoint();
945		#endif // is_mpi
946
947	+	}
948
381	–	// create the atom and short range interaction arrays
949
950	<	Atom::createArrays(simnfo->n_atoms);
384	<	the_atoms = new Atom*[simnfo->n_atoms];
385	<	the_molecules = new Molecule[simnfo->n_mol];
386	<	int molIndex;
387	<
388	<	// initialize the molecule's stampID's
389	<
390	<	#ifdef IS_MPI
950	>	void SimSetup::makeOutNames( void ){
951
952	+	int k;
953
393	–	molIndex = 0;
394	–	for(i=0; i<mpiSim->getTotNmol(); i++){
395	–
396	–	if(mol2proc[i] == worldRank ){
397	–	the_molecules[molIndex].setStampID( molCompType[i] );
398	–	the_molecules[molIndex].setMyIndex( molIndex );
399	–	the_molecules[molIndex].setGlobalIndex( i );
400	–	molIndex++;
401	–	}
402	–	}
403	–
404	–	#else // is_mpi
954
955	<	molIndex = 0;
956	<	globalAtomIndex = 0;
957	<	for(i=0; i<n_components; i++){
958	<	for(j=0; j<components_nmol[i]; j++ ){
959	<	the_molecules[molIndex].setStampID( i );
960	<	the_molecules[molIndex].setMyIndex( molIndex );
961	<	the_molecules[molIndex].setGlobalIndex( molIndex );
962	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
963	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
964	<	globalAtomIndex++;
965	<	}
966	<	molIndex++;
955	>	for(k=0; k<nInfo; k++){
956	>
957	>	#ifdef IS_MPI
958	>	if( worldRank == 0 ){
959	>	#endif // is_mpi
960	>
961	>	if( globals->haveFinalConfig() ){
962	>	strcpy( info[k].finalName, globals->getFinalConfig() );
963	>	}
964	>	else{
965	>	strcpy( info[k].finalName, inFileName );
966	>	char* endTest;
967	>	int nameLength = strlen( info[k].finalName );
968	>	endTest = &(info[k].finalName[nameLength - 5]);
969	>	if( !strcmp( endTest, ".bass" ) ){
970	>	strcpy( endTest, ".eor" );
971	>	}
972	>	else if( !strcmp( endTest, ".BASS" ) ){
973	>	strcpy( endTest, ".eor" );
974	>	}
975	>	else{
976	>	endTest = &(info[k].finalName[nameLength - 4]);
977	>	if( !strcmp( endTest, ".bss" ) ){
978	>	strcpy( endTest, ".eor" );
979	>	}
980	>	else if( !strcmp( endTest, ".mdl" ) ){
981	>	strcpy( endTest, ".eor" );
982	>	}
983	>	else{
984	>	strcat( info[k].finalName, ".eor" );
985	>	}
986	>	}
987	>	}
988	>
989	>	// make the sample and status out names
990	>
991	>	strcpy( info[k].sampleName, inFileName );
992	>	char* endTest;
993	>	int nameLength = strlen( info[k].sampleName );
994	>	endTest = &(info[k].sampleName[nameLength - 5]);
995	>	if( !strcmp( endTest, ".bass" ) ){
996	>	strcpy( endTest, ".dump" );
997	>	}
998	>	else if( !strcmp( endTest, ".BASS" ) ){
999	>	strcpy( endTest, ".dump" );
1000	>	}
1001	>	else{
1002	>	endTest = &(info[k].sampleName[nameLength - 4]);
1003	>	if( !strcmp( endTest, ".bss" ) ){
1004	>	strcpy( endTest, ".dump" );
1005	>	}
1006	>	else if( !strcmp( endTest, ".mdl" ) ){
1007	>	strcpy( endTest, ".dump" );
1008	>	}
1009	>	else{
1010	>	strcat( info[k].sampleName, ".dump" );
1011	>	}
1012	>	}
1013	>
1014	>	strcpy( info[k].statusName, inFileName );
1015	>	nameLength = strlen( info[k].statusName );
1016	>	endTest = &(info[k].statusName[nameLength - 5]);
1017	>	if( !strcmp( endTest, ".bass" ) ){
1018	>	strcpy( endTest, ".stat" );
1019	>	}
1020	>	else if( !strcmp( endTest, ".BASS" ) ){
1021	>	strcpy( endTest, ".stat" );
1022	>	}
1023	>	else{
1024	>	endTest = &(info[k].statusName[nameLength - 4]);
1025	>	if( !strcmp( endTest, ".bss" ) ){
1026	>	strcpy( endTest, ".stat" );
1027	>	}
1028	>	else if( !strcmp( endTest, ".mdl" ) ){
1029	>	strcpy( endTest, ".stat" );
1030	>	}
1031	>	else{
1032	>	strcat( info[k].statusName, ".stat" );
1033	>	}
1034	>	}
1035	>
1036	>	#ifdef IS_MPI
1037		}
1038	+	#endif // is_mpi
1039		}
1040	<
1040	>	}
1041
422	–	#endif // is_mpi
1042
1043	+	void SimSetup::sysObjectsCreation( void ){
1044	+
1045	+	int i,k;
1046	+
1047	+	// create the forceField
1048
1049	<	if( simnfo->n_SRI ){
426	<
427	<	Exclude::createArray(simnfo->n_SRI);
428	<	the_excludes = new Exclude*[simnfo->n_SRI];
429	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
430	<	simnfo->globalExcludes = new int;
431	<	simnfo->n_exclude = simnfo->n_SRI;
432	<	}
433	<	else{
434	<
435	<	Exclude::createArray( 1 );
436	<	the_excludes = new Exclude*;
437	<	the_excludes[0] = new Exclude(0);
438	<	the_excludes[0]->setPair( 0,0 );
439	<	simnfo->globalExcludes = new int;
440	<	simnfo->globalExcludes[0] = 0;
441	<	simnfo->n_exclude = 0;
442	<	}
1049	>	createFF();
1050
1051	<	// set the arrays into the SimInfo object
1051	>	// extract componentList
1052
1053	<	simnfo->atoms = the_atoms;
447	<	simnfo->molecules = the_molecules;
448	<	simnfo->nGlobalExcludes = 0;
449	<	simnfo->excludes = the_excludes;
1053	>	compList();
1054
1055	+	// calc the number of atoms, bond, bends, and torsions
1056
1057	<	// get some of the tricky things that may still be in the globals
1057	>	calcSysValues();
1058
1059	+	#ifdef IS_MPI
1060	+	// divide the molecules among the processors
1061
1062	<	if( the_globals->haveBox() ){
1063	<	simnfo->box_x = the_globals->getBox();
1064	<	simnfo->box_y = the_globals->getBox();
1065	<	simnfo->box_z = the_globals->getBox();
1066	<	}
1067	<	else if( the_globals->haveDensity() ){
1062	>	mpiMolDivide();
1063	>	#endif //is_mpi
1064	>
1065	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1066	>
1067	>	makeSysArrays();
1068
1069	<	double vol;
1070	<	vol = (double)tot_nmol / the_globals->getDensity();
1071	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
1072	<	simnfo->box_y = simnfo->box_x;
1073	<	simnfo->box_z = simnfo->box_x;
1074	<	}
1075	<	else{
1076	<	if( !the_globals->haveBoxX() ){
470	<	sprintf( painCave.errMsg,
471	<	"SimSetup error, no periodic BoxX size given.\n" );
472	<	painCave.isFatal = 1;
473	<	simError();
1069	>	// make and initialize the molecules (all but atomic coordinates)
1070	>
1071	>	makeMolecules();
1072	>
1073	>	for(k=0; k<nInfo; k++){
1074	>	info[k].identArray = new int[info[k].n_atoms];
1075	>	for(i=0; i<info[k].n_atoms; i++){
1076	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1077		}
1078	<	simnfo->box_x = the_globals->getBoxX();
1078	>	}
1079	>	}
1080
477	–	if( !the_globals->haveBoxY() ){
478	–	sprintf( painCave.errMsg,
479	–	"SimSetup error, no periodic BoxY size given.\n" );
480	–	painCave.isFatal = 1;
481	–	simError();
482	–	}
483	–	simnfo->box_y = the_globals->getBoxY();
1081
1082	<	if( !the_globals->haveBoxZ() ){
1083	<	sprintf( painCave.errMsg,
1084	<	"SimSetup error, no periodic BoxZ size given.\n" );
1085	<	painCave.isFatal = 1;
1086	<	simError();
1087	<	}
1088	<	simnfo->box_z = the_globals->getBoxZ();
1082	>	void SimSetup::createFF( void ){
1083	>
1084	>	switch( ffCase ){
1085	>
1086	>	case FF_DUFF:
1087	>	the_ff = new DUFF();
1088	>	break;
1089	>
1090	>	case FF_LJ:
1091	>	the_ff = new LJFF();
1092	>	break;
1093	>
1094	>	case FF_EAM:
1095	>	the_ff = new EAM_FF();
1096	>	break;
1097	>
1098	>	default:
1099	>	sprintf( painCave.errMsg,
1100	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1101	>	painCave.isFatal = 1;
1102	>	simError();
1103		}
1104
1105		#ifdef IS_MPI
1106	<	strcpy( checkPointMsg, "Box size set up" );
1106	>	strcpy( checkPointMsg, "ForceField creation successful" );
1107		MPIcheckPoint();
1108		#endif // is_mpi
1109
1110	+	}
1111
500	–	// initialize the arrays
1112
1113	<	the_ff->setSimInfo( simnfo );
1113	>	void SimSetup::compList( void ){
1114
1115	<	makeMolecules();
1116	<	simnfo->identArray = new int[simnfo->n_atoms];
1117	<	for(i=0; i<simnfo->n_atoms; i++){
1118	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
1119	<	}
1115	>	int i;
1116	>	char* id;
1117	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1118	>	LinkedMolStamp* currentStamp = NULL;
1119	>	comp_stamps = new MoleculeStamp*[n_components];
1120
1121	<	if (the_globals->getUseRF() ) {
1122	<	simnfo->useReactionField = 1;
1121	>	// make an array of molecule stamps that match the components used.
1122	>	// also extract the used stamps out into a separate linked list
1123
1124	<	if( !the_globals->haveECR() ){
1125	<	sprintf( painCave.errMsg,
1126	<	"SimSetup Warning: using default value of 1/2 the smallest "
1127	<	"box length for the electrostaticCutoffRadius.\n"
1128	<	"I hope you have a very fast processor!\n");
1129	<	painCave.isFatal = 0;
1130	<	simError();
520	<	double smallest;
521	<	smallest = simnfo->box_x;
522	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
523	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
524	<	simnfo->ecr = 0.5 * smallest;
525	<	} else {
526	<	simnfo->ecr        = the_globals->getECR();
527	<	}
1124	>	for(i=0; i<nInfo; i++){
1125	>	info[i].nComponents = n_components;
1126	>	info[i].componentsNmol = components_nmol;
1127	>	info[i].compStamps = comp_stamps;
1128	>	info[i].headStamp = headStamp;
1129	>	}
1130	>
1131
1132	<	if( !the_globals->haveEST() ){
1133	<	sprintf( painCave.errMsg,
1134	<	"SimSetup Warning: using default value of 0.05 * the "
1135	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
533	<	);
534	<	painCave.isFatal = 0;
535	<	simError();
536	<	simnfo->est = 0.05 * simnfo->ecr;
537	<	} else {
538	<	simnfo->est        = the_globals->getEST();
539	<	}
1132	>	for( i=0; i<n_components; i++ ){
1133	>
1134	>	id = the_components[i]->getType();
1135	>	comp_stamps[i] = NULL;
1136
1137	<	if(!the_globals->haveDielectric() ){
1138	<	sprintf( painCave.errMsg,
1139	<	"SimSetup Error: You are trying to use Reaction Field without"
1140	<	"setting a dielectric constant!\n"
545	<	);
546	<	painCave.isFatal = 1;
547	<	simError();
548	<	}
549	<	simnfo->dielectric = the_globals->getDielectric();
550	<	} else {
551	<	if (usesDipoles) {
1137	>	// check to make sure the component isn't already in the list
1138	>
1139	>	comp_stamps[i] = headStamp->match( id );
1140	>	if( comp_stamps[i] == NULL ){
1141
1142	<	if( !the_globals->haveECR() ){
554	<	sprintf( painCave.errMsg,
555	<	"SimSetup Warning: using default value of 1/2 the smallest "
556	<	"box length for the electrostaticCutoffRadius.\n"
557	<	"I hope you have a very fast processor!\n");
558	<	painCave.isFatal = 0;
559	<	simError();
560	<	double smallest;
561	<	smallest = simnfo->box_x;
562	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
563	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
564	<	simnfo->ecr = 0.5 * smallest;
565	<	} else {
566	<	simnfo->ecr        = the_globals->getECR();
567	<	}
1142	>	// extract the component from the list;
1143
1144	<	if( !the_globals->haveEST() ){
1145	<	sprintf( painCave.errMsg,
1146	<	"SimSetup Warning: using default value of 5%% of the "
1147	<	"electrostaticCutoffRadius for the "
1148	<	"electrostaticSkinThickness\n"
1149	<	);
1150	<	painCave.isFatal = 0;
1151	<	simError();
577	<	simnfo->est = 0.05 * simnfo->ecr;
578	<	} else {
579	<	simnfo->est        = the_globals->getEST();
1144	>	currentStamp = stamps->extractMolStamp( id );
1145	>	if( currentStamp == NULL ){
1146	>	sprintf( painCave.errMsg,
1147	>	"SimSetup error: Component \"%s\" was not found in the "
1148	>	"list of declared molecules\n",
1149	>	id );
1150	>	painCave.isFatal = 1;
1151	>	simError();
1152		}
1153	+
1154	+	headStamp->add( currentStamp );
1155	+	comp_stamps[i] = headStamp->match( id );
1156		}
1157	<	}
1157	>	}
1158
1159		#ifdef IS_MPI
1160	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
1160	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1161		MPIcheckPoint();
1162		#endif // is_mpi
1163
589	–	if( the_globals->haveInitialConfig() ){
590	–
591	–	InitializeFromFile* fileInit;
592	–	#ifdef IS_MPI // is_mpi
593	–	if( worldRank == 0 ){
594	–	#endif //is_mpi
595	–	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
596	–	#ifdef IS_MPI
597	–	}else fileInit = new InitializeFromFile( NULL );
598	–	#endif
599	–	fileInit->read_xyz( simnfo ); // default velocities on
1164
1165	<	delete fileInit;
602	<	}
603	<	else{
1165	>	}
1166
1167	<	#ifdef IS_MPI
1168	<
607	<	// no init from bass
1167	>	void SimSetup::calcSysValues( void ){
1168	>	int i, j, k;
1169
1170	<	sprintf( painCave.errMsg,
610	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
611	<	painCave.isFatal;
612	<	simError();
1170	>	int *molMembershipArray;
1171
1172	<	#else
1173	<
1174	<	initFromBass();
1175	<
1176	<
1177	<	#endif
1178	<	}
1172	>	tot_atoms = 0;
1173	>	tot_bonds = 0;
1174	>	tot_bends = 0;
1175	>	tot_torsions = 0;
1176	>	for( i=0; i<n_components; i++ ){
1177	>
1178	>	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1179	>	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1180	>	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1181	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1182	>	}
1183	>
1184	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1185	>	molMembershipArray = new int[tot_atoms];
1186	>
1187	>	for(i=0; i<nInfo; i++){
1188	>	info[i].n_atoms = tot_atoms;
1189	>	info[i].n_bonds = tot_bonds;
1190	>	info[i].n_bends = tot_bends;
1191	>	info[i].n_torsions = tot_torsions;
1192	>	info[i].n_SRI = tot_SRI;
1193	>	info[i].n_mol = tot_nmol;
1194	>
1195	>	info[i].molMembershipArray = molMembershipArray;
1196	>	}
1197	>	}
1198
1199		#ifdef IS_MPI
1200	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1200	>
1201	>	void SimSetup::mpiMolDivide( void ){
1202	>
1203	>	int i, j, k;
1204	>	int localMol, allMol;
1205	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1206	>
1207	>	mpiSim = new mpiSimulation( info );
1208	>
1209	>	globalIndex = mpiSim->divideLabor();
1210	>
1211	>	// set up the local variables
1212	>
1213	>	mol2proc = mpiSim->getMolToProcMap();
1214	>	molCompType = mpiSim->getMolComponentType();
1215	>
1216	>	allMol = 0;
1217	>	localMol = 0;
1218	>	local_atoms = 0;
1219	>	local_bonds = 0;
1220	>	local_bends = 0;
1221	>	local_torsions = 0;
1222	>	globalAtomIndex = 0;
1223	>
1224	>
1225	>	for( i=0; i<n_components; i++ ){
1226	>
1227	>	for( j=0; j<components_nmol[i]; j++ ){
1228	>
1229	>	if( mol2proc[allMol] == worldRank ){
1230	>
1231	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1232	>	local_bonds +=    comp_stamps[i]->getNBonds();
1233	>	local_bends +=    comp_stamps[i]->getNBends();
1234	>	local_torsions += comp_stamps[i]->getNTorsions();
1235	>	localMol++;
1236	>	}
1237	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1238	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1239	>	globalAtomIndex++;
1240	>	}
1241	>
1242	>	allMol++;
1243	>	}
1244	>	}
1245	>	local_SRI = local_bonds + local_bends + local_torsions;
1246	>
1247	>	info[0].n_atoms = mpiSim->getMyNlocal();
1248	>
1249	>	if( local_atoms != info[0].n_atoms ){
1250	>	sprintf( painCave.errMsg,
1251	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1252	>	" localAtom (%d) are not equal.\n",
1253	>	info[0].n_atoms,
1254	>	local_atoms );
1255	>	painCave.isFatal = 1;
1256	>	simError();
1257	>	}
1258	>
1259	>	info[0].n_bonds = local_bonds;
1260	>	info[0].n_bends = local_bends;
1261	>	info[0].n_torsions = local_torsions;
1262	>	info[0].n_SRI = local_SRI;
1263	>	info[0].n_mol = localMol;
1264	>
1265	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1266		MPIcheckPoint();
1267	+	}
1268	+
1269		#endif // is_mpi
1270
1271
1272	<
1273	<
630	<
1272	>	void SimSetup::makeSysArrays( void ){
1273	>	int i, j, k, l;
1274
1275	+	Atom** the_atoms;
1276	+	Molecule* the_molecules;
1277	+	Exclude** the_excludes;
1278	+
1279
1280	+	for(l=0; l<nInfo; l++){
1281	+
1282	+	// create the atom and short range interaction arrays
1283	+
1284	+	the_atoms = new Atom*[info[l].n_atoms];
1285	+	the_molecules = new Molecule[info[l].n_mol];
1286	+	int molIndex;
1287	+
1288	+	// initialize the molecule's stampID's
1289	+
1290		#ifdef IS_MPI
634	–	if( worldRank == 0 ){
635	–	#endif // is_mpi
1291
637	–	if( the_globals->haveFinalConfig() ){
638	–	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
639	–	}
640	–	else{
641	–	strcpy( simnfo->finalName, inFileName );
642	–	char* endTest;
643	–	int nameLength = strlen( simnfo->finalName );
644	–	endTest = &(simnfo->finalName[nameLength - 5]);
645	–	if( !strcmp( endTest, ".bass" ) ){
646	–	strcpy( endTest, ".eor" );
647	–	}
648	–	else if( !strcmp( endTest, ".BASS" ) ){
649	–	strcpy( endTest, ".eor" );
650	–	}
651	–	else{
652	–	endTest = &(simnfo->finalName[nameLength - 4]);
653	–	if( !strcmp( endTest, ".bss" ) ){
654	–	strcpy( endTest, ".eor" );
655	–	}
656	–	else if( !strcmp( endTest, ".mdl" ) ){
657	–	strcpy( endTest, ".eor" );
658	–	}
659	–	else{
660	–	strcat( simnfo->finalName, ".eor" );
661	–	}
662	–	}
663	–	}
1292
1293	<	// make the sample and status out names
1293	>	molIndex = 0;
1294	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1295
1296	<	strcpy( simnfo->sampleName, inFileName );
1297	<	char* endTest;
1298	<	int nameLength = strlen( simnfo->sampleName );
1299	<	endTest = &(simnfo->sampleName[nameLength - 5]);
1300	<	if( !strcmp( endTest, ".bass" ) ){
672	<	strcpy( endTest, ".dump" );
673	<	}
674	<	else if( !strcmp( endTest, ".BASS" ) ){
675	<	strcpy( endTest, ".dump" );
676	<	}
677	<	else{
678	<	endTest = &(simnfo->sampleName[nameLength - 4]);
679	<	if( !strcmp( endTest, ".bss" ) ){
680	<	strcpy( endTest, ".dump" );
1296	>	if(mol2proc[i] == worldRank ){
1297	>	the_molecules[molIndex].setStampID( molCompType[i] );
1298	>	the_molecules[molIndex].setMyIndex( molIndex );
1299	>	the_molecules[molIndex].setGlobalIndex( i );
1300	>	molIndex++;
1301		}
682	–	else if( !strcmp( endTest, ".mdl" ) ){
683	–	strcpy( endTest, ".dump" );
684	–	}
685	–	else{
686	–	strcat( simnfo->sampleName, ".dump" );
687	–	}
1302		}
1303
1304	<	strcpy( simnfo->statusName, inFileName );
1305	<	nameLength = strlen( simnfo->statusName );
1306	<	endTest = &(simnfo->statusName[nameLength - 5]);
1307	<	if( !strcmp( endTest, ".bass" ) ){
1308	<	strcpy( endTest, ".stat" );
1309	<	}
1310	<	else if( !strcmp( endTest, ".BASS" ) ){
1311	<	strcpy( endTest, ".stat" );
1312	<	}
1313	<	else{
1314	<	endTest = &(simnfo->statusName[nameLength - 4]);
1315	<	if( !strcmp( endTest, ".bss" ) ){
1316	<	strcpy( endTest, ".stat" );
1304	>	#else // is_mpi
1305	>
1306	>	molIndex = 0;
1307	>	globalAtomIndex = 0;
1308	>	for(i=0; i<n_components; i++){
1309	>	for(j=0; j<components_nmol[i]; j++ ){
1310	>	the_molecules[molIndex].setStampID( i );
1311	>	the_molecules[molIndex].setMyIndex( molIndex );
1312	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1313	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1314	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1315	>	globalAtomIndex++;
1316	>	}
1317	>	molIndex++;
1318		}
704	–	else if( !strcmp( endTest, ".mdl" ) ){
705	–	strcpy( endTest, ".stat" );
706	–	}
707	–	else{
708	–	strcat( simnfo->statusName, ".stat" );
709	–	}
1319		}
1320
1321	<	#ifdef IS_MPI
713	<	}
1321	>
1322		#endif // is_mpi
715	–
716	–	// set the status, sample, and themal kick times
717	–
718	–	if( the_globals->haveSampleTime() ){
719	–	simnfo->sampleTime = the_globals->getSampleTime();
720	–	simnfo->statusTime = simnfo->sampleTime;
721	–	simnfo->thermalTime = simnfo->sampleTime;
722	–	}
723	–	else{
724	–	simnfo->sampleTime = the_globals->getRunTime();
725	–	simnfo->statusTime = simnfo->sampleTime;
726	–	simnfo->thermalTime = simnfo->sampleTime;
727	–	}
1323
729	–	if( the_globals->haveStatusTime() ){
730	–	simnfo->statusTime = the_globals->getStatusTime();
731	–	}
1324
1325	<	if( the_globals->haveThermalTime() ){
1326	<	simnfo->thermalTime = the_globals->getThermalTime();
1327	<	}
1325	>	if( info[l].n_SRI ){
1326	>
1327	>	Exclude::createArray(info[l].n_SRI);
1328	>	the_excludes = new Exclude*[info[l].n_SRI];
1329	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1330	>	the_excludes[ex] = new Exclude(ex);
1331	>	}
1332	>	info[l].globalExcludes = new int;
1333	>	info[l].n_exclude = info[l].n_SRI;
1334	>	}
1335	>	else{
1336	>
1337	>	Exclude::createArray( 1 );
1338	>	the_excludes = new Exclude*;
1339	>	the_excludes[0] = new Exclude(0);
1340	>	the_excludes[0]->setPair( 0,0 );
1341	>	info[l].globalExcludes = new int;
1342	>	info[l].globalExcludes[0] = 0;
1343	>	info[l].n_exclude = 0;
1344	>	}
1345
1346	<	// check for the temperature set flag
1346	>	// set the arrays into the SimInfo object
1347
1348	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
1348	>	info[l].atoms = the_atoms;
1349	>	info[l].molecules = the_molecules;
1350	>	info[l].nGlobalExcludes = 0;
1351	>	info[l].excludes = the_excludes;
1352
1353	+	the_ff->setSimInfo( info );
1354	+
1355	+	}
1356	+	}
1357
1358	<	//   // make the longe range forces and the integrator
1358	>	void SimSetup::makeIntegrator( void ){
1359
1360	<	//   new AllLong( simnfo );
1360	>	int k;
1361
1362	+	NVT<RealIntegrator>*  myNVT = NULL;
1363	+	NPTi<RealIntegrator>* myNPTi = NULL;
1364	+	NPTf<RealIntegrator>* myNPTf = NULL;
1365	+	NPTim<RealIntegrator>* myNPTim = NULL;
1366	+	NPTfm<RealIntegrator>* myNPTfm = NULL;
1367	+
1368	+	for(k=0; k<nInfo; k++){
1369	+
1370	+	switch( ensembleCase ){
1371	+
1372	+	case NVE_ENS:
1373	+	if (globals->haveZconstraints()){
1374	+	setupZConstraint(info[k]);
1375	+	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1376	+	}
1377
1378	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
1379	<	new Symplectic(simnfo, the_ff, the_extendedsystem);
1380	<	}
1381	<	else if( !strcmp( force_field, "LJ" ) ){
1382	<	new Verlet( *simnfo, the_ff, the_extendedsystem );
1383	<	}
1384	<	else {
1385	<	std::cerr << "I'm a bug.\n";
1386	<	fprintf( stderr, "Ima bug. stderr %s\n", force_field);
1387	<	}
1388	<	#ifdef IS_MPI
758	<	mpiSim->mpiRefresh();
759	<	#endif
1378	>	else
1379	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1380	>	break;
1381	>
1382	>	case NVT_ENS:
1383	>	if (globals->haveZconstraints()){
1384	>	setupZConstraint(info[k]);
1385	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1386	>	}
1387	>	else
1388	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1389
1390	<	// initialize the Fortran
1390	>	myNVT->setTargetTemp(globals->getTargetTemp());
1391	>
1392	>	if (globals->haveTauThermostat())
1393	>	myNVT->setTauThermostat(globals->getTauThermostat());
1394	>
1395	>	else {
1396	>	sprintf( painCave.errMsg,
1397	>	"SimSetup error: If you use the NVT\n"
1398	>	"    ensemble, you must set tauThermostat.\n");
1399	>	painCave.isFatal = 1;
1400	>	simError();
1401	>	}
1402	>	break;
1403	>
1404	>	case NPTi_ENS:
1405	>	if (globals->haveZconstraints()){
1406	>	setupZConstraint(info[k]);
1407	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1408	>	}
1409	>	else
1410	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1411
1412	<
1413	<	simnfo->refreshSim();
1412	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1413	>
1414	>	if (globals->haveTargetPressure())
1415	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1416	>	else {
1417	>	sprintf( painCave.errMsg,
1418	>	"SimSetup error: If you use a constant pressure\n"
1419	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1420	>	painCave.isFatal = 1;
1421	>	simError();
1422	>	}
1423	>
1424	>	if( globals->haveTauThermostat() )
1425	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1426	>	else{
1427	>	sprintf( painCave.errMsg,
1428	>	"SimSetup error: If you use an NPT\n"
1429	>	"    ensemble, you must set tauThermostat.\n");
1430	>	painCave.isFatal = 1;
1431	>	simError();
1432	>	}
1433	>
1434	>	if( globals->haveTauBarostat() )
1435	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1436	>	else{
1437	>	sprintf( painCave.errMsg,
1438	>	"SimSetup error: If you use an NPT\n"
1439	>	"    ensemble, you must set tauBarostat.\n");
1440	>	painCave.isFatal = 1;
1441	>	simError();
1442	>	}
1443	>	break;
1444	>
1445	>	case NPTf_ENS:
1446	>	if (globals->haveZconstraints()){
1447	>	setupZConstraint(info[k]);
1448	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1449	>	}
1450	>	else
1451	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1452	>
1453	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1454	>
1455	>	if (globals->haveTargetPressure())
1456	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1457	>	else {
1458	>	sprintf( painCave.errMsg,
1459	>	"SimSetup error: If you use a constant pressure\n"
1460	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1461	>	painCave.isFatal = 1;
1462	>	simError();
1463	>	}
1464	>
1465	>	if( globals->haveTauThermostat() )
1466	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1467	>	else{
1468	>	sprintf( painCave.errMsg,
1469	>	"SimSetup error: If you use an NPT\n"
1470	>	"    ensemble, you must set tauThermostat.\n");
1471	>	painCave.isFatal = 1;
1472	>	simError();
1473	>	}
1474	>
1475	>	if( globals->haveTauBarostat() )
1476	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1477	>	else{
1478	>	sprintf( painCave.errMsg,
1479	>	"SimSetup error: If you use an NPT\n"
1480	>	"    ensemble, you must set tauBarostat.\n");
1481	>	painCave.isFatal = 1;
1482	>	simError();
1483	>	}
1484	>	break;
1485	>
1486	>	case NPTim_ENS:
1487	>	if (globals->haveZconstraints()){
1488	>	setupZConstraint(info[k]);
1489	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1490	>	}
1491	>	else
1492	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1493	>
1494	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1495	>
1496	>	if (globals->haveTargetPressure())
1497	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1498	>	else {
1499	>	sprintf( painCave.errMsg,
1500	>	"SimSetup error: If you use a constant pressure\n"
1501	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1502	>	painCave.isFatal = 1;
1503	>	simError();
1504	>	}
1505	>
1506	>	if( globals->haveTauThermostat() )
1507	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1508	>	else{
1509	>	sprintf( painCave.errMsg,
1510	>	"SimSetup error: If you use an NPT\n"
1511	>	"    ensemble, you must set tauThermostat.\n");
1512	>	painCave.isFatal = 1;
1513	>	simError();
1514	>	}
1515	>
1516	>	if( globals->haveTauBarostat() )
1517	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1518	>	else{
1519	>	sprintf( painCave.errMsg,
1520	>	"SimSetup error: If you use an NPT\n"
1521	>	"    ensemble, you must set tauBarostat.\n");
1522	>	painCave.isFatal = 1;
1523	>	simError();
1524	>	}
1525	>	break;
1526	>
1527	>	case NPTfm_ENS:
1528	>	if (globals->haveZconstraints()){
1529	>	setupZConstraint(info[k]);
1530	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1531	>	}
1532	>	else
1533	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1534	>
1535	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1536	>
1537	>	if (globals->haveTargetPressure())
1538	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1539	>	else {
1540	>	sprintf( painCave.errMsg,
1541	>	"SimSetup error: If you use a constant pressure\n"
1542	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1543	>	painCave.isFatal = 1;
1544	>	simError();
1545	>	}
1546	>
1547	>	if( globals->haveTauThermostat() )
1548	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1549	>	else{
1550	>	sprintf( painCave.errMsg,
1551	>	"SimSetup error: If you use an NPT\n"
1552	>	"    ensemble, you must set tauThermostat.\n");
1553	>	painCave.isFatal = 1;
1554	>	simError();
1555	>	}
1556	>
1557	>	if( globals->haveTauBarostat() )
1558	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1559	>	else{
1560	>	sprintf( painCave.errMsg,
1561	>	"SimSetup error: If you use an NPT\n"
1562	>	"    ensemble, you must set tauBarostat.\n");
1563	>	painCave.isFatal = 1;
1564	>	simError();
1565	>	}
1566	>	break;
1567	>
1568	>	default:
1569	>	sprintf( painCave.errMsg,
1570	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1571	>	painCave.isFatal = 1;
1572	>	simError();
1573	>	}
1574	>	}
1575	>	}
1576	>
1577	>	void SimSetup::initFortran( void ){
1578	>
1579	>	info[0].refreshSim();
1580
1581	<	if( !strcmp( simnfo->mixingRule, "standard") ){
1581	>	if( !strcmp( info[0].mixingRule, "standard") ){
1582		the_ff->initForceField( LB_MIXING_RULE );
1583		}
1584	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
1584	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1585		the_ff->initForceField( EXPLICIT_MIXING_RULE );
1586		}
1587		else{
1588		sprintf( painCave.errMsg,
1589		"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1590	<	simnfo->mixingRule );
1590	>	info[0].mixingRule );
1591		painCave.isFatal = 1;
1592		simError();
1593		}
#	Line 783 | Line 1598 | void SimSetup::createSim( void ){
1598		"Successfully intialized the mixingRule for Fortran." );
1599		MPIcheckPoint();
1600		#endif // is_mpi
1601	+
1602		}
1603
1604	+	void SimSetup::setupZConstraint(SimInfo& theInfo)
1605	+	{
1606	+	int nZConstraints;
1607	+	ZconStamp** zconStamp;
1608	+
1609	+	if(globals->haveZconstraintTime()){
1610	+
1611	+	//add sample time of z-constraint  into SimInfo's property list
1612	+	DoubleData* zconsTimeProp = new DoubleData();
1613	+	zconsTimeProp->setID(ZCONSTIME_ID);
1614	+	zconsTimeProp->setData(globals->getZconsTime());
1615	+	theInfo.addProperty(zconsTimeProp);
1616	+	}
1617	+	else{
1618	+	sprintf( painCave.errMsg,
1619	+	"ZConstraint error: If you use an ZConstraint\n"
1620	+	" , you must set sample time.\n");
1621	+	painCave.isFatal = 1;
1622	+	simError();
1623	+	}
1624
1625	<	void SimSetup::makeMolecules( void ){
1625	>	//
1626	>	nZConstraints = globals->getNzConstraints();
1627	>	zconStamp = globals->getZconStamp();
1628	>	ZConsParaItem tempParaItem;
1629
1630	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
1631	<	molInit info;
1632	<	DirectionalAtom* dAtom;
1633	<	LinkedAssign* extras;
1634	<	LinkedAssign* current_extra;
1635	<	AtomStamp* currentAtom;
1636	<	BondStamp* currentBond;
1637	<	BendStamp* currentBend;
799	<	TorsionStamp* currentTorsion;
1630	>	ZConsParaData* zconsParaData = new ZConsParaData();
1631	>	zconsParaData->setID(ZCONSPARADATA_ID);
1632	>
1633	>	for(int i = 0; i < nZConstraints; i++){
1634	>	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1635	>	tempParaItem.zPos = zconStamp[i]->getZpos();
1636	>	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1637	>	tempParaItem.kRatio = zconStamp[i]->getKratio();
1638
1639	<	bond_pair* theBonds;
1640	<	bend_set* theBends;
803	<	torsion_set* theTorsions;
1639	>	zconsParaData->addItem(tempParaItem);
1640	>	}
1641
1642	<
1643	<	//init the forceField paramters
1642	>	//sort the parameters by index of molecules
1643	>	zconsParaData->sortByIndex();
1644	>
1645	>	//push data into siminfo, therefore, we can retrieve later
1646	>	theInfo.addProperty(zconsParaData);
1647
1648	<	the_ff->readParams();
1648	>	//push zconsTol into siminfo, if user does not specify
1649	>	//value for zconsTol, a default value will be used
1650	>	DoubleData* zconsTol = new DoubleData();
1651	>	zconsTol->setID(ZCONSTOL_ID);
1652	>	if(globals->haveZconsTol()){
1653	>	zconsTol->setData(globals->getZconsTol());
1654	>	}
1655	>	else{
1656	>	double defaultZConsTol = 1E-6;
1657	>	sprintf( painCave.errMsg,
1658	>	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1659	>	" , default value %f is used.\n", defaultZConsTol);
1660	>	painCave.isFatal = 0;
1661	>	simError();
1662
1663	<
1664	<	// init the atoms
1665	<
1666	<	double ux, uy, uz, u, uSqr;
1667	<
1668	<	atomOffset = 0;
1669	<	excludeOffset = 0;
817	<	for(i=0; i<simnfo->n_mol; i++){
1663	>	zconsTol->setData(defaultZConsTol);
1664	>	}
1665	>	theInfo.addProperty(zconsTol);
1666	>
1667	>	//Determine the name of ouput file and add it into SimInfo's property list
1668	>	//Be careful, do not use inFileName, since it is a pointer which
1669	>	//point to a string at master node, and slave nodes do not contain that string
1670
1671	<	stampID = the_molecules[i].getStampID();
820	<
821	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
822	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
823	<	info.nBends    = comp_stamps[stampID]->getNBends();
824	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
825	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
826	<
827	<	info.myAtoms = &the_atoms[atomOffset];
828	<	info.myExcludes = &the_excludes[excludeOffset];
829	<	info.myBonds = new Bond*[info.nBonds];
830	<	info.myBends = new Bend*[info.nBends];
831	<	info.myTorsions = new Torsion*[info.nTorsions];
832	<
833	<	theBonds = new bond_pair[info.nBonds];
834	<	theBends = new bend_set[info.nBends];
835	<	theTorsions = new torsion_set[info.nTorsions];
1671	>	string zconsOutput(theInfo.finalName);
1672
1673	<	// make the Atoms
1673	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1674
1675	<	for(j=0; j<info.nAtoms; j++){
1676	<
1677	<	currentAtom = comp_stamps[stampID]->getAtom( j );
842	<	if( currentAtom->haveOrientation() ){
843	<
844	<	dAtom = new DirectionalAtom(j + atomOffset);
845	<	simnfo->n_oriented++;
846	<	info.myAtoms[j] = dAtom;
847	<
848	<	ux = currentAtom->getOrntX();
849	<	uy = currentAtom->getOrntY();
850	<	uz = currentAtom->getOrntZ();
851	<
852	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
853	<
854	<	u = sqrt( uSqr );
855	<	ux = ux / u;
856	<	uy = uy / u;
857	<	uz = uz / u;
858	<
859	<	dAtom->setSUx( ux );
860	<	dAtom->setSUy( uy );
861	<	dAtom->setSUz( uz );
862	<	}
863	<	else{
864	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
865	<	}
866	<	info.myAtoms[j]->setType( currentAtom->getType() );
1675	>	StringData* zconsFilename = new StringData();
1676	>	zconsFilename->setID(ZCONSFILENAME_ID);
1677	>	zconsFilename->setData(zconsOutput);
1678
1679	<	#ifdef IS_MPI
869	<
870	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
871	<
872	<	#endif // is_mpi
873	<	}
874	<
875	<	// make the bonds
876	<	for(j=0; j<info.nBonds; j++){
877	<
878	<	currentBond = comp_stamps[stampID]->getBond( j );
879	<	theBonds[j].a = currentBond->getA() + atomOffset;
880	<	theBonds[j].b = currentBond->getB() + atomOffset;
881	<
882	<	exI = theBonds[j].a;
883	<	exJ = theBonds[j].b;
884	<
885	<	// exclude_I must always be the smaller of the pair
886	<	if( exI > exJ ){
887	<	tempEx = exI;
888	<	exI = exJ;
889	<	exJ = tempEx;
890	<	}
891	<	#ifdef IS_MPI
892	<	tempEx = exI;
893	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
894	<	tempEx = exJ;
895	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
896	<
897	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
898	<	#else  // isn't MPI
899	<
900	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
901	<	#endif  //is_mpi
902	<	}
903	<	excludeOffset += info.nBonds;
904	<
905	<	//make the bends
906	<	for(j=0; j<info.nBends; j++){
907	<
908	<	currentBend = comp_stamps[stampID]->getBend( j );
909	<	theBends[j].a = currentBend->getA() + atomOffset;
910	<	theBends[j].b = currentBend->getB() + atomOffset;
911	<	theBends[j].c = currentBend->getC() + atomOffset;
912	<
913	<	if( currentBend->haveExtras() ){
914	<
915	<	extras = currentBend->getExtras();
916	<	current_extra = extras;
917	<
918	<	while( current_extra != NULL ){
919	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
920	<
921	<	switch( current_extra->getType() ){
922	<
923	<	case 0:
924	<	theBends[j].ghost =
925	<	current_extra->getInt() + atomOffset;
926	<	theBends[j].isGhost = 1;
927	<	break;
928	<
929	<	case 1:
930	<	theBends[j].ghost =
931	<	(int)current_extra->getDouble() + atomOffset;
932	<	theBends[j].isGhost = 1;
933	<	break;
934	<
935	<	default:
936	<	sprintf( painCave.errMsg,
937	<	"SimSetup Error: ghostVectorSource was neither a "
938	<	"double nor an int.\n"
939	<	"-->Bend[%d] in %s\n",
940	<	j, comp_stamps[stampID]->getID() );
941	<	painCave.isFatal = 1;
942	<	simError();
943	<	}
944	<	}
945	<
946	<	else{
947	<
948	<	sprintf( painCave.errMsg,
949	<	"SimSetup Error: unhandled bend assignment:\n"
950	<	"    -->%s in Bend[%d] in %s\n",
951	<	current_extra->getlhs(),
952	<	j, comp_stamps[stampID]->getID() );
953	<	painCave.isFatal = 1;
954	<	simError();
955	<	}
956	<
957	<	current_extra = current_extra->getNext();
958	<	}
959	<	}
960	<
961	<	if( !theBends[j].isGhost ){
962	<
963	<	exI = theBends[j].a;
964	<	exJ = theBends[j].c;
965	<	}
966	<	else{
967	<
968	<	exI = theBends[j].a;
969	<	exJ = theBends[j].b;
970	<	}
971	<
972	<	// exclude_I must always be the smaller of the pair
973	<	if( exI > exJ ){
974	<	tempEx = exI;
975	<	exI = exJ;
976	<	exJ = tempEx;
977	<	}
978	<	#ifdef IS_MPI
979	<	tempEx = exI;
980	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
981	<	tempEx = exJ;
982	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
983	<
984	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
985	<	#else  // isn't MPI
986	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
987	<	#endif  //is_mpi
988	<	}
989	<	excludeOffset += info.nBends;
990	<
991	<	for(j=0; j<info.nTorsions; j++){
992	<
993	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
994	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
995	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
996	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
997	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
998	<
999	<	exI = theTorsions[j].a;
1000	<	exJ = theTorsions[j].d;
1001	<
1002	<	// exclude_I must always be the smaller of the pair
1003	<	if( exI > exJ ){
1004	<	tempEx = exI;
1005	<	exI = exJ;
1006	<	exJ = tempEx;
1007	<	}
1008	<	#ifdef IS_MPI
1009	<	tempEx = exI;
1010	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1011	<	tempEx = exJ;
1012	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1013	<
1014	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1015	<	#else  // isn't MPI
1016	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1017	<	#endif  //is_mpi
1018	<	}
1019	<	excludeOffset += info.nTorsions;
1020	<
1021	<
1022	<	// send the arrays off to the forceField for init.
1023	<
1024	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1025	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1026	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1027	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1028	<
1029	<
1030	<	the_molecules[i].initialize( info );
1031	<
1032	<
1033	<	atomOffset += info.nAtoms;
1034	<	delete[] theBonds;
1035	<	delete[] theBends;
1036	<	delete[] theTorsions;
1037	<	}
1038	<
1039	<	#ifdef IS_MPI
1040	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1041	<	MPIcheckPoint();
1042	<	#endif // is_mpi
1043	<
1044	<	// clean up the forcefield
1045	<	the_ff->calcRcut();
1046	<	the_ff->cleanMe();
1047	<
1679	>	theInfo.addProperty(zconsFilename);
1680		}
1049	–
1050	–	void SimSetup::initFromBass( void ){
1051	–
1052	–	int i, j, k;
1053	–	int n_cells;
1054	–	double cellx, celly, cellz;
1055	–	double temp1, temp2, temp3;
1056	–	int n_per_extra;
1057	–	int n_extra;
1058	–	int have_extra, done;
1059	–
1060	–	temp1 = (double)tot_nmol / 4.0;
1061	–	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1062	–	temp3 = ceil( temp2 );
1063	–
1064	–	have_extra =0;
1065	–	if( temp2 < temp3 ){ // we have a non-complete lattice
1066	–	have_extra =1;
1067	–
1068	–	n_cells = (int)temp3 - 1;
1069	–	cellx = simnfo->box_x / temp3;
1070	–	celly = simnfo->box_y / temp3;
1071	–	cellz = simnfo->box_z / temp3;
1072	–	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1073	–	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1074	–	n_per_extra = (int)ceil( temp1 );
1075	–
1076	–	if( n_per_extra > 4){
1077	–	sprintf( painCave.errMsg,
1078	–	"SimSetup error. There has been an error in constructing"
1079	–	" the non-complete lattice.\n" );
1080	–	painCave.isFatal = 1;
1081	–	simError();
1082	–	}
1083	–	}
1084	–	else{
1085	–	n_cells = (int)temp3;
1086	–	cellx = simnfo->box_x / temp3;
1087	–	celly = simnfo->box_y / temp3;
1088	–	cellz = simnfo->box_z / temp3;
1089	–	}
1090	–
1091	–	current_mol = 0;
1092	–	current_comp_mol = 0;
1093	–	current_comp = 0;
1094	–	current_atom_ndx = 0;
1095	–
1096	–	for( i=0; i < n_cells ; i++ ){
1097	–	for( j=0; j < n_cells; j++ ){
1098	–	for( k=0; k < n_cells; k++ ){
1099	–
1100	–	makeElement( i * cellx,
1101	–	j * celly,
1102	–	k * cellz );
1103	–
1104	–	makeElement( i * cellx + 0.5 * cellx,
1105	–	j * celly + 0.5 * celly,
1106	–	k * cellz );
1107	–
1108	–	makeElement( i * cellx,
1109	–	j * celly + 0.5 * celly,
1110	–	k * cellz + 0.5 * cellz );
1111	–
1112	–	makeElement( i * cellx + 0.5 * cellx,
1113	–	j * celly,
1114	–	k * cellz + 0.5 * cellz );
1115	–	}
1116	–	}
1117	–	}
1118	–
1119	–	if( have_extra ){
1120	–	done = 0;
1121	–
1122	–	int start_ndx;
1123	–	for( i=0; i < (n_cells+1) && !done; i++ ){
1124	–	for( j=0; j < (n_cells+1) && !done; j++ ){
1125	–
1126	–	if( i < n_cells ){
1127	–
1128	–	if( j < n_cells ){
1129	–	start_ndx = n_cells;
1130	–	}
1131	–	else start_ndx = 0;
1132	–	}
1133	–	else start_ndx = 0;
1134	–
1135	–	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1136	–
1137	–	makeElement( i * cellx,
1138	–	j * celly,
1139	–	k * cellz );
1140	–	done = ( current_mol >= tot_nmol );
1141	–
1142	–	if( !done && n_per_extra > 1 ){
1143	–	makeElement( i * cellx + 0.5 * cellx,
1144	–	j * celly + 0.5 * celly,
1145	–	k * cellz );
1146	–	done = ( current_mol >= tot_nmol );
1147	–	}
1148	–
1149	–	if( !done && n_per_extra > 2){
1150	–	makeElement( i * cellx,
1151	–	j * celly + 0.5 * celly,
1152	–	k * cellz + 0.5 * cellz );
1153	–	done = ( current_mol >= tot_nmol );
1154	–	}
1155	–
1156	–	if( !done && n_per_extra > 3){
1157	–	makeElement( i * cellx + 0.5 * cellx,
1158	–	j * celly,
1159	–	k * cellz + 0.5 * cellz );
1160	–	done = ( current_mol >= tot_nmol );
1161	–	}
1162	–	}
1163	–	}
1164	–	}
1165	–	}
1166	–
1167	–
1168	–	for( i=0; i<simnfo->n_atoms; i++ ){
1169	–	simnfo->atoms[i]->set_vx( 0.0 );
1170	–	simnfo->atoms[i]->set_vy( 0.0 );
1171	–	simnfo->atoms[i]->set_vz( 0.0 );
1172	–	}
1173	–	}
1174	–
1175	–	void SimSetup::makeElement( double x, double y, double z ){
1176	–
1177	–	int k;
1178	–	AtomStamp* current_atom;
1179	–	DirectionalAtom* dAtom;
1180	–	double rotMat[3][3];
1181	–
1182	–	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1183	–
1184	–	current_atom = comp_stamps[current_comp]->getAtom( k );
1185	–	if( !current_atom->havePosition() ){
1186	–	sprintf( painCave.errMsg,
1187	–	"SimSetup:initFromBass error.\n"
1188	–	"\tComponent %s, atom %s does not have a position specified.\n"
1189	–	"\tThe initialization routine is unable to give a start"
1190	–	" position.\n",
1191	–	comp_stamps[current_comp]->getID(),
1192	–	current_atom->getType() );
1193	–	painCave.isFatal = 1;
1194	–	simError();
1195	–	}
1196	–
1197	–	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1198	–	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1199	–	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1200	–
1201	–	if( the_atoms[current_atom_ndx]->isDirectional() ){
1202	–
1203	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1204	–
1205	–	rotMat[0][0] = 1.0;
1206	–	rotMat[0][1] = 0.0;
1207	–	rotMat[0][2] = 0.0;
1208	–
1209	–	rotMat[1][0] = 0.0;
1210	–	rotMat[1][1] = 1.0;
1211	–	rotMat[1][2] = 0.0;
1212	–
1213	–	rotMat[2][0] = 0.0;
1214	–	rotMat[2][1] = 0.0;
1215	–	rotMat[2][2] = 1.0;
1216	–
1217	–	dAtom->setA( rotMat );
1218	–	}
1219	–
1220	–	current_atom_ndx++;
1221	–	}
1222	–
1223	–	current_mol++;
1224	–	current_comp_mol++;
1225	–
1226	–	if( current_comp_mol >= components_nmol[current_comp] ){
1227	–
1228	–	current_comp_mol = 0;
1229	–	current_comp++;
1230	–	}
1231	–	}

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