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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 676 by tim, Mon Aug 11 19:40:06 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6
7		#include "SimSetup.hpp"
8		#include "parse_me.h"
#	Line 12 | Line 14 | SimSetup::SimSetup(){
14		#include "mpiSimulation.hpp"
15		#endif
16
17	+	// some defines for ensemble and Forcefield  cases
18	+
19	+	#define NVE_ENS        0
20	+	#define NVT_ENS        1
21	+	#define NPTi_ENS       2
22	+	#define NPTf_ENS       3
23	+	#define NPTim_ENS      4
24	+	#define NPTfm_ENS      5
25	+
26	+	#define FF_DUFF 0
27	+	#define FF_LJ   1
28	+	#define FF_EAM  2
29	+
30	+	using namespace std;
31	+
32		SimSetup::SimSetup(){
33	+
34	+	isInfoArray = 0;
35	+	nInfo = 1;
36	+
37		stamps = new MakeStamps();
38		globals = new Globals();
39
40	+
41		#ifdef IS_MPI
42		strcpy( checkPointMsg, "SimSetup creation successful" );
43		MPIcheckPoint();
#	Line 27 | Line 49 | void SimSetup::parseFile( char* fileName ){
49		delete globals;
50		}
51
52	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
53	+	info = the_info;
54	+	nInfo = theNinfo;
55	+	isInfoArray = 1;
56	+	}
57	+
58	+
59		void SimSetup::parseFile( char* fileName ){
60
61		#ifdef IS_MPI
#	Line 62 | Line 91 | void SimSetup::createSim( void ){
91
92		#endif // is_mpi
93
94	<	void SimSetup::createSim( void ){
94	>	void SimSetup::createSim(void){
95
67	–	MakeStamps *the_stamps;
68	–	Globals* the_globals;
69	–	ExtendedSystem* the_extendedsystem;
96		int i, j, k, globalAtomIndex;
97	+
98	+	// gather all of the information from the Bass file
99	+
100	+	gatherInfo();
101
102	<	// get the stamps and globals;
73	<	the_stamps = stamps;
74	<	the_globals = globals;
102	>	// creation of complex system objects
103
104	<	// 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();
104	>	sysObjectsCreation();
105
106	<	// get the ones we know are there, yet still may need some work.
107	<	n_components = the_globals->getNComponents();
108	<	strcpy( force_field, the_globals->getForceField() );
106	>	// check on the post processing info
107	>
108	>	finalInfoCheck();
109
110	<	// 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	<	}
110	>	// initialize the system coordinates
111
112	<	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	<	}
112	>	if( !isInfoArray ) initSystemCoords();
113
114	<	if (the_globals->haveTauBarostat())
115	<	the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
116	<	else {
114	>	// make the output filenames
115	>
116	>	makeOutNames();
117	>
118	>	// make the integrator
119	>
120	>	makeIntegrator();
121	>
122	>	#ifdef IS_MPI
123	>	mpiSim->mpiRefresh();
124	>	#endif
125	>
126	>	// initialize the Fortran
127	>
128	>	initFortran();
129	>
130	>
131	>
132	>	}
133	>
134	>
135	>	void SimSetup::makeMolecules( void ){
136	>
137	>	int k,l;
138	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
139	>	molInit molInfo;
140	>	DirectionalAtom* dAtom;
141	>	LinkedAssign* extras;
142	>	LinkedAssign* current_extra;
143	>	AtomStamp* currentAtom;
144	>	BondStamp* currentBond;
145	>	BendStamp* currentBend;
146	>	TorsionStamp* currentTorsion;
147	>
148	>	bond_pair* theBonds;
149	>	bend_set* theBends;
150	>	torsion_set* theTorsions;
151	>
152	>
153	>	//init the forceField paramters
154	>
155	>	the_ff->readParams();
156	>
157	>
158	>	// init the atoms
159	>
160	>	double ux, uy, uz, u, uSqr;
161	>
162	>	for(k=0; k<nInfo; k++){
163	>
164	>	the_ff->setSimInfo( &(info[k]) );
165	>
166	>	atomOffset = 0;
167	>	excludeOffset = 0;
168	>	for(i=0; i<info[k].n_mol; i++){
169	>
170	>	stampID = info[k].molecules[i].getStampID();
171	>
172	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
173	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
174	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
175	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
176	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
177	>
178	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
179	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
180	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
181	>	molInfo.myBends = new Bend*[molInfo.nBends];
182	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
183	>
184	>	theBonds = new bond_pair[molInfo.nBonds];
185	>	theBends = new bend_set[molInfo.nBends];
186	>	theTorsions = new torsion_set[molInfo.nTorsions];
187	>
188	>	// make the Atoms
189	>
190	>	for(j=0; j<molInfo.nAtoms; j++){
191	>
192	>	currentAtom = comp_stamps[stampID]->getAtom( j );
193	>	if( currentAtom->haveOrientation() ){
194	>
195	>	dAtom = new DirectionalAtom( (j + atomOffset),
196	>	info[k].getConfiguration() );
197	>	info[k].n_oriented++;
198	>	molInfo.myAtoms[j] = dAtom;
199	>
200	>	ux = currentAtom->getOrntX();
201	>	uy = currentAtom->getOrntY();
202	>	uz = currentAtom->getOrntZ();
203	>
204	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
205	>
206	>	u = sqrt( uSqr );
207	>	ux = ux / u;
208	>	uy = uy / u;
209	>	uz = uz / u;
210	>
211	>	dAtom->setSUx( ux );
212	>	dAtom->setSUy( uy );
213	>	dAtom->setSUz( uz );
214	>	}
215	>	else{
216	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
217	>	info[k].getConfiguration() );
218	>	}
219	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
220	>
221	>	#ifdef IS_MPI
222	>
223	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
224	>
225	>	#endif // is_mpi
226	>	}
227	>
228	>	// make the bonds
229	>	for(j=0; j<molInfo.nBonds; j++){
230	>
231	>	currentBond = comp_stamps[stampID]->getBond( j );
232	>	theBonds[j].a = currentBond->getA() + atomOffset;
233	>	theBonds[j].b = currentBond->getB() + atomOffset;
234	>
235	>	exI = theBonds[j].a;
236	>	exJ = theBonds[j].b;
237	>
238	>	// exclude_I must always be the smaller of the pair
239	>	if( exI > exJ ){
240	>	tempEx = exI;
241	>	exI = exJ;
242	>	exJ = tempEx;
243	>	}
244	>	#ifdef IS_MPI
245	>	tempEx = exI;
246	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
247	>	tempEx = exJ;
248	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
249	>
250	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
251	>	#else  // isn't MPI
252	>
253	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
254	>	#endif  //is_mpi
255	>	}
256	>	excludeOffset += molInfo.nBonds;
257	>
258	>	//make the bends
259	>	for(j=0; j<molInfo.nBends; j++){
260	>
261	>	currentBend = comp_stamps[stampID]->getBend( j );
262	>	theBends[j].a = currentBend->getA() + atomOffset;
263	>	theBends[j].b = currentBend->getB() + atomOffset;
264	>	theBends[j].c = currentBend->getC() + atomOffset;
265	>
266	>	if( currentBend->haveExtras() ){
267	>
268	>	extras = currentBend->getExtras();
269	>	current_extra = extras;
270	>
271	>	while( current_extra != NULL ){
272	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
273	>
274	>	switch( current_extra->getType() ){
275	>
276	>	case 0:
277	>	theBends[j].ghost =
278	>	current_extra->getInt() + atomOffset;
279	>	theBends[j].isGhost = 1;
280	>	break;
281	>
282	>	case 1:
283	>	theBends[j].ghost =
284	>	(int)current_extra->getDouble() + atomOffset;
285	>	theBends[j].isGhost = 1;
286	>	break;
287	>
288	>	default:
289	>	sprintf( painCave.errMsg,
290	>	"SimSetup Error: ghostVectorSource was neither a "
291	>	"double nor an int.\n"
292	>	"-->Bend[%d] in %s\n",
293	>	j, comp_stamps[stampID]->getID() );
294	>	painCave.isFatal = 1;
295	>	simError();
296	>	}
297	>	}
298	>
299	>	else{
300	>
301	>	sprintf( painCave.errMsg,
302	>	"SimSetup Error: unhandled bend assignment:\n"
303	>	"    -->%s in Bend[%d] in %s\n",
304	>	current_extra->getlhs(),
305	>	j, comp_stamps[stampID]->getID() );
306	>	painCave.isFatal = 1;
307	>	simError();
308	>	}
309	>
310	>	current_extra = current_extra->getNext();
311	>	}
312	>	}
313	>
314	>	if( !theBends[j].isGhost ){
315	>
316	>	exI = theBends[j].a;
317	>	exJ = theBends[j].c;
318	>	}
319	>	else{
320	>
321	>	exI = theBends[j].a;
322	>	exJ = theBends[j].b;
323	>	}
324	>
325	>	// exclude_I must always be the smaller of the pair
326	>	if( exI > exJ ){
327	>	tempEx = exI;
328	>	exI = exJ;
329	>	exJ = tempEx;
330	>	}
331	>	#ifdef IS_MPI
332	>	tempEx = exI;
333	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
334	>	tempEx = exJ;
335	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
336	>
337	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
338	>	#else  // isn't MPI
339	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
340	>	#endif  //is_mpi
341	>	}
342	>	excludeOffset += molInfo.nBends;
343	>
344	>	for(j=0; j<molInfo.nTorsions; j++){
345	>
346	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
347	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
348	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
349	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
350	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
351	>
352	>	exI = theTorsions[j].a;
353	>	exJ = theTorsions[j].d;
354	>
355	>	// exclude_I must always be the smaller of the pair
356	>	if( exI > exJ ){
357	>	tempEx = exI;
358	>	exI = exJ;
359	>	exJ = tempEx;
360	>	}
361	>	#ifdef IS_MPI
362	>	tempEx = exI;
363	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
364	>	tempEx = exJ;
365	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
366	>
367	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
368	>	#else  // isn't MPI
369	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
370	>	#endif  //is_mpi
371	>	}
372	>	excludeOffset += molInfo.nTorsions;
373	>
374	>
375	>	// send the arrays off to the forceField for init.
376	>
377	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
378	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
379	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
380	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
381	>
382	>
383	>	info[k].molecules[i].initialize( molInfo );
384	>
385	>
386	>	atomOffset += molInfo.nAtoms;
387	>	delete[] theBonds;
388	>	delete[] theBends;
389	>	delete[] theTorsions;
390	>	}
391	>	}
392	>
393	>	#ifdef IS_MPI
394	>	sprintf( checkPointMsg, "all molecules initialized succesfully" );
395	>	MPIcheckPoint();
396	>	#endif // is_mpi
397	>
398	>	// clean up the forcefield
399	>
400	>	the_ff->calcRcut();
401	>	the_ff->cleanMe();
402	>
403	>	}
404	>
405	>	void SimSetup::initFromBass( void ){
406	>
407	>	int i, j, k;
408	>	int n_cells;
409	>	double cellx, celly, cellz;
410	>	double temp1, temp2, temp3;
411	>	int n_per_extra;
412	>	int n_extra;
413	>	int have_extra, done;
414	>
415	>	double vel[3];
416	>	vel[0] = 0.0;
417	>	vel[1] = 0.0;
418	>	vel[2] = 0.0;
419	>
420	>	temp1 = (double)tot_nmol / 4.0;
421	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
422	>	temp3 = ceil( temp2 );
423	>
424	>	have_extra =0;
425	>	if( temp2 < temp3 ){ // we have a non-complete lattice
426	>	have_extra =1;
427	>
428	>	n_cells = (int)temp3 - 1;
429	>	cellx = info[0].boxL[0] / temp3;
430	>	celly = info[0].boxL[1] / temp3;
431	>	cellz = info[0].boxL[2] / temp3;
432	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
433	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
434	>	n_per_extra = (int)ceil( temp1 );
435	>
436	>	if( n_per_extra > 4){
437		sprintf( painCave.errMsg,
438	<	"SimSetup error: If you use the constant pressure\n"
439	<	"    ensemble, you must set tauBarostat.\n"
120	<	"    This was found in the BASS file.\n");
438	>	"SimSetup error. There has been an error in constructing"
439	>	" the non-complete lattice.\n" );
440		painCave.isFatal = 1;
441		simError();
442		}
443	+	}
444	+	else{
445	+	n_cells = (int)temp3;
446	+	cellx = info[0].boxL[0] / temp3;
447	+	celly = info[0].boxL[1] / temp3;
448	+	cellz = info[0].boxL[2] / temp3;
449	+	}
450
451	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
452	<	the_extendedsystem = new ExtendedSystem( simnfo );
453	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
451	>	current_mol = 0;
452	>	current_comp_mol = 0;
453	>	current_comp = 0;
454	>	current_atom_ndx = 0;
455
456	<	if (the_globals->haveTauThermostat())
457	<	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
458	<	else if (the_globals->haveQmass())
459	<	the_extendedsystem->setQmass(the_globals->getQmass());
460	<	else {
456	>	for( i=0; i < n_cells ; i++ ){
457	>	for( j=0; j < n_cells; j++ ){
458	>	for( k=0; k < n_cells; k++ ){
459	>
460	>	makeElement( i * cellx,
461	>	j * celly,
462	>	k * cellz );
463	>
464	>	makeElement( i * cellx + 0.5 * cellx,
465	>	j * celly + 0.5 * celly,
466	>	k * cellz );
467	>
468	>	makeElement( i * cellx,
469	>	j * celly + 0.5 * celly,
470	>	k * cellz + 0.5 * cellz );
471	>
472	>	makeElement( i * cellx + 0.5 * cellx,
473	>	j * celly,
474	>	k * cellz + 0.5 * cellz );
475	>	}
476	>	}
477	>	}
478	>
479	>	if( have_extra ){
480	>	done = 0;
481	>
482	>	int start_ndx;
483	>	for( i=0; i < (n_cells+1) && !done; i++ ){
484	>	for( j=0; j < (n_cells+1) && !done; j++ ){
485	>
486	>	if( i < n_cells ){
487	>
488	>	if( j < n_cells ){
489	>	start_ndx = n_cells;
490	>	}
491	>	else start_ndx = 0;
492	>	}
493	>	else start_ndx = 0;
494	>
495	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
496	>
497	>	makeElement( i * cellx,
498	>	j * celly,
499	>	k * cellz );
500	>	done = ( current_mol >= tot_nmol );
501	>
502	>	if( !done && n_per_extra > 1 ){
503	>	makeElement( i * cellx + 0.5 * cellx,
504	>	j * celly + 0.5 * celly,
505	>	k * cellz );
506	>	done = ( current_mol >= tot_nmol );
507	>	}
508	>
509	>	if( !done && n_per_extra > 2){
510	>	makeElement( i * cellx,
511	>	j * celly + 0.5 * celly,
512	>	k * cellz + 0.5 * cellz );
513	>	done = ( current_mol >= tot_nmol );
514	>	}
515	>
516	>	if( !done && n_per_extra > 3){
517	>	makeElement( i * cellx + 0.5 * cellx,
518	>	j * celly,
519	>	k * cellz + 0.5 * cellz );
520	>	done = ( current_mol >= tot_nmol );
521	>	}
522	>	}
523	>	}
524	>	}
525	>	}
526	>
527	>	for( i=0; i<info[0].n_atoms; i++ ){
528	>	info[0].atoms[i]->setVel( vel );
529	>	}
530	>	}
531	>
532	>	void SimSetup::makeElement( double x, double y, double z ){
533	>
534	>	int k;
535	>	AtomStamp* current_atom;
536	>	DirectionalAtom* dAtom;
537	>	double rotMat[3][3];
538	>	double pos[3];
539	>
540	>	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
541	>
542	>	current_atom = comp_stamps[current_comp]->getAtom( k );
543	>	if( !current_atom->havePosition() ){
544		sprintf( painCave.errMsg,
545	<	"SimSetup error: If you use one of the constant temperature\n"
546	<	"    ensembles, you must set either tauThermostat or qMass.\n"
547	<	"    Neither of these was found in the BASS file.\n");
545	>	"SimSetup:initFromBass error.\n"
546	>	"\tComponent %s, atom %s does not have a position specified.\n"
547	>	"\tThe initialization routine is unable to give a start"
548	>	" position.\n",
549	>	comp_stamps[current_comp]->getID(),
550	>	current_atom->getType() );
551		painCave.isFatal = 1;
552		simError();
553		}
554	<
555	<	} else if ( !strcasecmp( ensemble, "NVE") ) {
556	<	} else {
557	<	sprintf( painCave.errMsg,
558	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
559	<	"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 );
554	>
555	>	pos[0] = x + current_atom->getPosX();
556	>	pos[1] = y + current_atom->getPosY();
557	>	pos[2] = z + current_atom->getPosZ();
558	>
559	>	info[0].atoms[current_atom_ndx]->setPos( pos );
560
561	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
562	<	simnfo->usePBC = the_globals->getPBC();
563	<
564	<	int usesDipoles = 0;
565	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
566	<	the_ff = new TraPPE_ExFF();
567	<	usesDipoles = 1;
561	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
562	>
563	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
564	>
565	>	rotMat[0][0] = 1.0;
566	>	rotMat[0][1] = 0.0;
567	>	rotMat[0][2] = 0.0;
568	>
569	>	rotMat[1][0] = 0.0;
570	>	rotMat[1][1] = 1.0;
571	>	rotMat[1][2] = 0.0;
572	>
573	>	rotMat[2][0] = 0.0;
574	>	rotMat[2][1] = 0.0;
575	>	rotMat[2][2] = 1.0;
576	>
577	>	dAtom->setA( rotMat );
578	>	}
579	>
580	>	current_atom_ndx++;
581		}
582	<	else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
582	>
583	>	current_mol++;
584	>	current_comp_mol++;
585	>
586	>	if( current_comp_mol >= components_nmol[current_comp] ){
587	>
588	>	current_comp_mol = 0;
589	>	current_comp++;
590	>	}
591	>	}
592	>
593	>
594	>	void SimSetup::gatherInfo( void ){
595	>	int i,j,k;
596	>
597	>	ensembleCase = -1;
598	>	ffCase = -1;
599	>
600	>	// set the easy ones first
601	>
602	>	for( i=0; i<nInfo; i++){
603	>	info[i].target_temp = globals->getTargetTemp();
604	>	info[i].dt = globals->getDt();
605	>	info[i].run_time = globals->getRunTime();
606	>	}
607	>	n_components = globals->getNComponents();
608	>
609	>
610	>	// get the forceField
611	>
612	>	strcpy( force_field, globals->getForceField() );
613	>
614	>	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
615	>	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
616	>	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
617		else{
618		sprintf( painCave.errMsg,
619		"SimSetup Error. Unrecognized force field -> %s\n",
#	Line 168 | Line 622 | void SimSetup::createSim( void ){
622		simError();
623		}
624
625	<	#ifdef IS_MPI
172	<	strcpy( checkPointMsg, "ForceField creation successful" );
173	<	MPIcheckPoint();
174	<	#endif // is_mpi
625	>	// get the ensemble
626
627	+	strcpy( ensemble, globals->getEnsemble() );
628	+
629	+	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
630	+	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
631	+	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
632	+	ensembleCase = NPTi_ENS;
633	+	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
634	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
635	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
636	+	else{
637	+	sprintf( painCave.errMsg,
638	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
639	+	"reverting to NVE for this simulation.\n",
640	+	ensemble );
641	+	painCave.isFatal = 0;
642	+	simError();
643	+	strcpy( ensemble, "NVE" );
644	+	ensembleCase = NVE_ENS;
645	+	}
646
647	+	for(i=0; i<nInfo; i++){
648	+
649	+	strcpy( info[i].ensemble, ensemble );
650
651	+	// get the mixing rule
652	+
653	+	strcpy( info[i].mixingRule, globals->getMixingRule() );
654	+	info[i].usePBC = globals->getPBC();
655	+	}
656	+
657		// get the components and calculate the tot_nMol and indvidual n_mol
658	<	the_components = the_globals->getComponents();
658	>
659	>	the_components = globals->getComponents();
660		components_nmol = new int[n_components];
181	–	comp_stamps = new MoleculeStamp*[n_components];
661
662	<	if( !the_globals->haveNMol() ){
662	>
663	>	if( !globals->haveNMol() ){
664		// we don't have the total number of molecules, so we assume it is
665		// given in each component
666
#	Line 209 | Line 689 | void SimSetup::createSim( void ){
689		" Please give nMol in the components.\n" );
690		painCave.isFatal = 1;
691		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	–
692		}
693
694	<	#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();
694	>	// set the status, sample, and thermal kick times
695
696	<	char* id;
242	<	LinkedMolStamp* headStamp = simnfo->headStamp;
243	<	LinkedMolStamp* currentStamp = NULL;
244	<	for( i=0; i<n_components; i++ ){
696	>	for(i=0; i<nInfo; i++){
697
698	<	id = the_components[i]->getType();
699	<	comp_stamps[i] = NULL;
698	>	if( globals->haveSampleTime() ){
699	>	info[i].sampleTime = globals->getSampleTime();
700	>	info[i].statusTime = info[i].sampleTime;
701	>	info[i].thermalTime = info[i].sampleTime;
702	>	}
703	>	else{
704	>	info[i].sampleTime = globals->getRunTime();
705	>	info[i].statusTime = info[i].sampleTime;
706	>	info[i].thermalTime = info[i].sampleTime;
707	>	}
708
709	<	// check to make sure the component isn't already in the list
709	>	if( globals->haveStatusTime() ){
710	>	info[i].statusTime = globals->getStatusTime();
711	>	}
712	>
713	>	if( globals->haveThermalTime() ){
714	>	info[i].thermalTime = globals->getThermalTime();
715	>	}
716
717	<	comp_stamps[i] = headStamp->match( id );
718	<	if( comp_stamps[i] == NULL ){
717	>	// check for the temperature set flag
718	>
719	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
720	>
721	>	// get some of the tricky things that may still be in the globals
722	>
723	>	double boxVector[3];
724	>	if( globals->haveBox() ){
725	>	boxVector[0] = globals->getBox();
726	>	boxVector[1] = globals->getBox();
727	>	boxVector[2] = globals->getBox();
728
729	<	// extract the component from the list;
729	>	info[i].setBox( boxVector );
730	>	}
731	>	else if( globals->haveDensity() ){
732
733	<	currentStamp = the_stamps->extractMolStamp( id );
734	<	if( currentStamp == NULL ){
733	>	double vol;
734	>	vol = (double)tot_nmol / globals->getDensity();
735	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
736	>	boxVector[1] = boxVector[0];
737	>	boxVector[2] = boxVector[0];
738	>
739	>	info[i].setBox( boxVector );
740	>	}
741	>	else{
742	>	if( !globals->haveBoxX() ){
743		sprintf( painCave.errMsg,
744	<	"SimSetup error: Component \"%s\" was not found in the "
260	<	"list of declared molecules\n",
261	<	id );
744	>	"SimSetup error, no periodic BoxX size given.\n" );
745		painCave.isFatal = 1;
746		simError();
747		}
748	+	boxVector[0] = globals->getBoxX();
749
750	<	headStamp->add( currentStamp );
751	<	comp_stamps[i] = headStamp->match( id );
750	>	if( !globals->haveBoxY() ){
751	>	sprintf( painCave.errMsg,
752	>	"SimSetup error, no periodic BoxY size given.\n" );
753	>	painCave.isFatal = 1;
754	>	simError();
755	>	}
756	>	boxVector[1] = globals->getBoxY();
757	>
758	>	if( !globals->haveBoxZ() ){
759	>	sprintf( painCave.errMsg,
760	>	"SimSetup error, no periodic BoxZ size given.\n" );
761	>	painCave.isFatal = 1;
762	>	simError();
763	>	}
764	>	boxVector[2] = globals->getBoxZ();
765	>
766	>	info[i].setBox( boxVector );
767		}
269	–	}
768
769	+	}
770	+
771		#ifdef IS_MPI
772	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
772	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
773		MPIcheckPoint();
774		#endif // is_mpi
275	–
775
776	+	}
777
778
779	<	// caclulate the number of atoms, bonds, bends and torsions
779	>	void SimSetup::finalInfoCheck( void ){
780	>	int index;
781	>	int usesDipoles;
782	>	int i;
783
784	<	tot_atoms = 0;
785	<	tot_bonds = 0;
283	<	tot_bends = 0;
284	<	tot_torsions = 0;
285	<	for( i=0; i<n_components; i++ ){
784	>	for(i=0; i<nInfo; i++){
785	>	// check electrostatic parameters
786
787	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
788	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
789	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
790	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
791	<	}
792	<
793	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
794	<
795	<	simnfo->n_atoms = tot_atoms;
796	<	simnfo->n_bonds = tot_bonds;
797	<	simnfo->n_bends = tot_bends;
798	<	simnfo->n_torsions = tot_torsions;
799	<	simnfo->n_SRI = tot_SRI;
800	<	simnfo->n_mol = tot_nmol;
801	<
802	<	simnfo->molMembershipArray = new int[tot_atoms];
787	>	index = 0;
788	>	usesDipoles = 0;
789	>	while( (index < info[i].n_atoms) && !usesDipoles ){
790	>	usesDipoles = (info[i].atoms[index])->hasDipole();
791	>	index++;
792	>	}
793	>
794	>	#ifdef IS_MPI
795	>	int myUse = usesDipoles;
796	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
797	>	#endif //is_mpi
798	>
799	>	double theEcr, theEst;
800	>
801	>	if (globals->getUseRF() ) {
802	>	info[i].useReactionField = 1;
803	>
804	>	if( !globals->haveECR() ){
805	>	sprintf( painCave.errMsg,
806	>	"SimSetup Warning: using default value of 1/2 the smallest "
807	>	"box length for the electrostaticCutoffRadius.\n"
808	>	"I hope you have a very fast processor!\n");
809	>	painCave.isFatal = 0;
810	>	simError();
811	>	double smallest;
812	>	smallest = info[i].boxL[0];
813	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
814	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
815	>	theEcr = 0.5 * smallest;
816	>	} else {
817	>	theEcr = globals->getECR();
818	>	}
819	>
820	>	if( !globals->haveEST() ){
821	>	sprintf( painCave.errMsg,
822	>	"SimSetup Warning: using default value of 0.05 * the "
823	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
824	>	);
825	>	painCave.isFatal = 0;
826	>	simError();
827	>	theEst = 0.05 * theEcr;
828	>	} else {
829	>	theEst= globals->getEST();
830	>	}
831	>
832	>	info[i].setEcr( theEcr, theEst );
833	>
834	>	if(!globals->haveDielectric() ){
835	>	sprintf( painCave.errMsg,
836	>	"SimSetup Error: You are trying to use Reaction Field without"
837	>	"setting a dielectric constant!\n"
838	>	);
839	>	painCave.isFatal = 1;
840	>	simError();
841	>	}
842	>	info[i].dielectric = globals->getDielectric();
843	>	}
844	>	else {
845	>	if (usesDipoles) {
846	>
847	>	if( !globals->haveECR() ){
848	>	sprintf( painCave.errMsg,
849	>	"SimSetup Warning: using default value of 1/2 the smallest "
850	>	"box length for the electrostaticCutoffRadius.\n"
851	>	"I hope you have a very fast processor!\n");
852	>	painCave.isFatal = 0;
853	>	simError();
854	>	double smallest;
855	>	smallest = info[i].boxL[0];
856	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
857	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
858	>	theEcr = 0.5 * smallest;
859	>	} else {
860	>	theEcr = globals->getECR();
861	>	}
862	>
863	>	if( !globals->haveEST() ){
864	>	sprintf( painCave.errMsg,
865	>	"SimSetup Warning: using default value of 0.05 * the "
866	>	"electrostaticCutoffRadius for the "
867	>	"electrostaticSkinThickness\n"
868	>	);
869	>	painCave.isFatal = 0;
870	>	simError();
871	>	theEst = 0.05 * theEcr;
872	>	} else {
873	>	theEst= globals->getEST();
874	>	}
875	>
876	>	info[i].setEcr( theEcr, theEst );
877	>	}
878	>	}
879	>	}
880
881		#ifdef IS_MPI
882	+	strcpy( checkPointMsg, "post processing checks out" );
883	+	MPIcheckPoint();
884	+	#endif // is_mpi
885
886	<	// divide the molecules among processors here.
307	<
308	<	mpiSim = new mpiSimulation( simnfo );
309	<
310	<	globalIndex = mpiSim->divideLabor();
886	>	}
887
888	<	// set up the local variables
888	>	void SimSetup::initSystemCoords( void ){
889	>	int i;
890
891	<	int localMol, allMol;
315	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
891	>	std::cerr << "Setting atom Coords\n";
892
893	<	int* mol2proc = mpiSim->getMolToProcMap();
318	<	int* molCompType = mpiSim->getMolComponentType();
893	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
894
895	<	allMol = 0;
321	<	localMol = 0;
322	<	local_atoms = 0;
323	<	local_bonds = 0;
324	<	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	<	}
348	<	}
349	<	local_SRI = local_bonds + local_bends + local_torsions;
895	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
896
897	<	simnfo->n_atoms = mpiSim->getMyNlocal();
898	<
899	<	if( local_atoms != simnfo->n_atoms ){
897	>	if( globals->haveInitialConfig() ){
898	>
899	>	InitializeFromFile* fileInit;
900	>	#ifdef IS_MPI // is_mpi
901	>	if( worldRank == 0 ){
902	>	#endif //is_mpi
903	>	fileInit = new InitializeFromFile( globals->getInitialConfig() );
904	>	#ifdef IS_MPI
905	>	}else fileInit = new InitializeFromFile( NULL );
906	>	#endif
907	>	fileInit->readInit( info ); // default velocities on
908	>
909	>	delete fileInit;
910	>	}
911	>	else{
912	>
913	>	#ifdef IS_MPI
914	>
915	>	// no init from bass
916	>
917		sprintf( painCave.errMsg,
918	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
919	<	" localAtom (%d) are not equal.\n",
357	<	simnfo->n_atoms,
358	<	local_atoms );
359	<	painCave.isFatal = 1;
918	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
919	>	painCave.isFatal;
920		simError();
921	+
922	+	#else
923	+
924	+	initFromBass();
925	+
926	+
927	+	#endif
928		}
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();
929
930	<
930	>	#ifdef IS_MPI
931	>	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
932	>	MPIcheckPoint();
933		#endif // is_mpi
934
935	+	}
936
376	–	// create the atom and short range interaction arrays
937
938	<	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
938	>	void SimSetup::makeOutNames( void ){
939
940	+	int k;
941
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
942
943	<	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	<
943	>	for(k=0; k<nInfo; k++){
944
945	+	#ifdef IS_MPI
946	+	if( worldRank == 0 ){
947		#endif // is_mpi
948	<
949	<
950	<	if( simnfo->n_SRI ){
951	<
952	<	Exclude::createArray(simnfo->n_SRI);
953	<	the_excludes = new Exclude*[simnfo->n_SRI];
954	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
955	<	simnfo->globalExcludes = new int;
956	<	simnfo->n_exclude = simnfo->n_SRI;
948	>
949	>	if( globals->haveFinalConfig() ){
950	>	strcpy( info[k].finalName, globals->getFinalConfig() );
951	>	}
952	>	else{
953	>	strcpy( info[k].finalName, inFileName );
954	>	char* endTest;
955	>	int nameLength = strlen( info[k].finalName );
956	>	endTest = &(info[k].finalName[nameLength - 5]);
957	>	if( !strcmp( endTest, ".bass" ) ){
958	>	strcpy( endTest, ".eor" );
959	>	}
960	>	else if( !strcmp( endTest, ".BASS" ) ){
961	>	strcpy( endTest, ".eor" );
962	>	}
963	>	else{
964	>	endTest = &(info[k].finalName[nameLength - 4]);
965	>	if( !strcmp( endTest, ".bss" ) ){
966	>	strcpy( endTest, ".eor" );
967	>	}
968	>	else if( !strcmp( endTest, ".mdl" ) ){
969	>	strcpy( endTest, ".eor" );
970	>	}
971	>	else{
972	>	strcat( info[k].finalName, ".eor" );
973	>	}
974	>	}
975	>	}
976	>
977	>	// make the sample and status out names
978	>
979	>	strcpy( info[k].sampleName, inFileName );
980	>	char* endTest;
981	>	int nameLength = strlen( info[k].sampleName );
982	>	endTest = &(info[k].sampleName[nameLength - 5]);
983	>	if( !strcmp( endTest, ".bass" ) ){
984	>	strcpy( endTest, ".dump" );
985	>	}
986	>	else if( !strcmp( endTest, ".BASS" ) ){
987	>	strcpy( endTest, ".dump" );
988	>	}
989	>	else{
990	>	endTest = &(info[k].sampleName[nameLength - 4]);
991	>	if( !strcmp( endTest, ".bss" ) ){
992	>	strcpy( endTest, ".dump" );
993	>	}
994	>	else if( !strcmp( endTest, ".mdl" ) ){
995	>	strcpy( endTest, ".dump" );
996	>	}
997	>	else{
998	>	strcat( info[k].sampleName, ".dump" );
999	>	}
1000	>	}
1001	>
1002	>	strcpy( info[k].statusName, inFileName );
1003	>	nameLength = strlen( info[k].statusName );
1004	>	endTest = &(info[k].statusName[nameLength - 5]);
1005	>	if( !strcmp( endTest, ".bass" ) ){
1006	>	strcpy( endTest, ".stat" );
1007	>	}
1008	>	else if( !strcmp( endTest, ".BASS" ) ){
1009	>	strcpy( endTest, ".stat" );
1010	>	}
1011	>	else{
1012	>	endTest = &(info[k].statusName[nameLength - 4]);
1013	>	if( !strcmp( endTest, ".bss" ) ){
1014	>	strcpy( endTest, ".stat" );
1015	>	}
1016	>	else if( !strcmp( endTest, ".mdl" ) ){
1017	>	strcpy( endTest, ".stat" );
1018	>	}
1019	>	else{
1020	>	strcat( info[k].statusName, ".stat" );
1021	>	}
1022	>	}
1023	>
1024	>	#ifdef IS_MPI
1025	>	}
1026	>	#endif // is_mpi
1027		}
1028	<	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	<	}
1028	>	}
1029
439	–	// set the arrays into the SimInfo object
1030
1031	<	simnfo->atoms = the_atoms;
1032	<	simnfo->molecules = the_molecules;
1033	<	simnfo->nGlobalExcludes = 0;
1034	<	simnfo->excludes = the_excludes;
1031	>	void SimSetup::sysObjectsCreation( void ){
1032	>
1033	>	int i,k;
1034	>
1035	>	// create the forceField
1036	>
1037	>	createFF();
1038
1039	+	// extract componentList
1040
1041	<	// get some of the tricky things that may still be in the globals
1041	>	compList();
1042
1043	+	// calc the number of atoms, bond, bends, and torsions
1044	+
1045	+	calcSysValues();
1046	+
1047	+	#ifdef IS_MPI
1048	+	// divide the molecules among the processors
1049
1050	<	if( the_globals->haveBox() ){
1051	<	simnfo->box_x = the_globals->getBox();
1052	<	simnfo->box_y = the_globals->getBox();
1053	<	simnfo->box_z = the_globals->getBox();
1054	<	}
1055	<	else if( the_globals->haveDensity() ){
1050	>	mpiMolDivide();
1051	>	#endif //is_mpi
1052	>
1053	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1054	>
1055	>	makeSysArrays();
1056
1057	<	double vol;
1058	<	vol = (double)tot_nmol / the_globals->getDensity();
1059	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
1060	<	simnfo->box_y = simnfo->box_x;
1061	<	simnfo->box_z = simnfo->box_x;
1062	<	}
1063	<	else{
1064	<	if( !the_globals->haveBoxX() ){
465	<	sprintf( painCave.errMsg,
466	<	"SimSetup error, no periodic BoxX size given.\n" );
467	<	painCave.isFatal = 1;
468	<	simError();
1057	>	// make and initialize the molecules (all but atomic coordinates)
1058	>
1059	>	makeMolecules();
1060	>
1061	>	for(k=0; k<nInfo; k++){
1062	>	info[k].identArray = new int[info[k].n_atoms];
1063	>	for(i=0; i<info[k].n_atoms; i++){
1064	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1065		}
1066	<	simnfo->box_x = the_globals->getBoxX();
1066	>	}
1067	>	}
1068
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();
1069
1070	<	if( !the_globals->haveBoxZ() ){
1071	<	sprintf( painCave.errMsg,
1072	<	"SimSetup error, no periodic BoxZ size given.\n" );
1073	<	painCave.isFatal = 1;
1074	<	simError();
1075	<	}
1076	<	simnfo->box_z = the_globals->getBoxZ();
1070	>	void SimSetup::createFF( void ){
1071	>
1072	>	switch( ffCase ){
1073	>
1074	>	case FF_DUFF:
1075	>	the_ff = new DUFF();
1076	>	break;
1077	>
1078	>	case FF_LJ:
1079	>	the_ff = new LJFF();
1080	>	break;
1081	>
1082	>	case FF_EAM:
1083	>	the_ff = new EAM_FF();
1084	>	break;
1085	>
1086	>	default:
1087	>	sprintf( painCave.errMsg,
1088	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1089	>	painCave.isFatal = 1;
1090	>	simError();
1091		}
1092
1093		#ifdef IS_MPI
1094	<	strcpy( checkPointMsg, "Box size set up" );
1094	>	strcpy( checkPointMsg, "ForceField creation successful" );
1095		MPIcheckPoint();
1096		#endif // is_mpi
1097
1098	+	}
1099
495	–	// initialize the arrays
1100
1101	<	the_ff->setSimInfo( simnfo );
1101	>	void SimSetup::compList( void ){
1102
1103	<	makeMolecules();
1104	<	simnfo->identArray = new int[simnfo->n_atoms];
1105	<	for(i=0; i<simnfo->n_atoms; i++){
1106	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
1107	<	}
1103	>	int i;
1104	>	char* id;
1105	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1106	>	LinkedMolStamp* currentStamp = NULL;
1107	>	comp_stamps = new MoleculeStamp*[n_components];
1108
1109	<	if (the_globals->getUseRF() ) {
1110	<	simnfo->useReactionField = 1;
1109	>	// make an array of molecule stamps that match the components used.
1110	>	// also extract the used stamps out into a separate linked list
1111
1112	<	if( !the_globals->haveECR() ){
1113	<	sprintf( painCave.errMsg,
1114	<	"SimSetup Warning: using default value of 1/2 the smallest "
1115	<	"box length for the electrostaticCutoffRadius.\n"
1116	<	"I hope you have a very fast processor!\n");
1117	<	painCave.isFatal = 0;
1118	<	simError();
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	<	}
1112	>	for(i=0; i<nInfo; i++){
1113	>	info[i].nComponents = n_components;
1114	>	info[i].componentsNmol = components_nmol;
1115	>	info[i].compStamps = comp_stamps;
1116	>	info[i].headStamp = headStamp;
1117	>	}
1118	>
1119
1120	<	if( !the_globals->haveEST() ){
1121	<	sprintf( painCave.errMsg,
1122	<	"SimSetup Warning: using default value of 0.05 * the "
1123	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
528	<	);
529	<	painCave.isFatal = 0;
530	<	simError();
531	<	simnfo->est = 0.05 * simnfo->ecr;
532	<	} else {
533	<	simnfo->est        = the_globals->getEST();
534	<	}
1120	>	for( i=0; i<n_components; i++ ){
1121	>
1122	>	id = the_components[i]->getType();
1123	>	comp_stamps[i] = NULL;
1124
1125	<	if(!the_globals->haveDielectric() ){
1126	<	sprintf( painCave.errMsg,
1127	<	"SimSetup Error: You are trying to use Reaction Field without"
1128	<	"setting a dielectric constant!\n"
540	<	);
541	<	painCave.isFatal = 1;
542	<	simError();
543	<	}
544	<	simnfo->dielectric = the_globals->getDielectric();
545	<	} else {
546	<	if (usesDipoles) {
1125	>	// check to make sure the component isn't already in the list
1126	>
1127	>	comp_stamps[i] = headStamp->match( id );
1128	>	if( comp_stamps[i] == NULL ){
1129
1130	<	if( !the_globals->haveECR() ){
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	<	}
1130	>	// extract the component from the list;
1131
1132	<	if( !the_globals->haveEST() ){
1133	<	sprintf( painCave.errMsg,
1134	<	"SimSetup Warning: using default value of 5%% of the "
1135	<	"electrostaticCutoffRadius for the "
1136	<	"electrostaticSkinThickness\n"
1137	<	);
1138	<	painCave.isFatal = 0;
1139	<	simError();
572	<	simnfo->est = 0.05 * simnfo->ecr;
573	<	} else {
574	<	simnfo->est        = the_globals->getEST();
1132	>	currentStamp = stamps->extractMolStamp( id );
1133	>	if( currentStamp == NULL ){
1134	>	sprintf( painCave.errMsg,
1135	>	"SimSetup error: Component \"%s\" was not found in the "
1136	>	"list of declared molecules\n",
1137	>	id );
1138	>	painCave.isFatal = 1;
1139	>	simError();
1140		}
1141	+
1142	+	headStamp->add( currentStamp );
1143	+	comp_stamps[i] = headStamp->match( id );
1144		}
1145	<	}
1145	>	}
1146
1147		#ifdef IS_MPI
1148	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
1148	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1149		MPIcheckPoint();
1150		#endif // is_mpi
1151
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
1152
1153	<	delete fileInit;
597	<	}
598	<	else{
1153	>	}
1154
1155	<	#ifdef IS_MPI
1156	<
602	<	// no init from bass
1155	>	void SimSetup::calcSysValues( void ){
1156	>	int i, j, k;
1157
1158	<	sprintf( painCave.errMsg,
605	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
606	<	painCave.isFatal;
607	<	simError();
1158	>	int *molMembershipArray;
1159
1160	<	#else
1161	<
1162	<	initFromBass();
1163	<
1164	<
1165	<	#endif
1166	<	}
1160	>	tot_atoms = 0;
1161	>	tot_bonds = 0;
1162	>	tot_bends = 0;
1163	>	tot_torsions = 0;
1164	>	for( i=0; i<n_components; i++ ){
1165	>
1166	>	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1167	>	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1168	>	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1169	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1170	>	}
1171	>
1172	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1173	>	molMembershipArray = new int[tot_atoms];
1174	>
1175	>	for(i=0; i<nInfo; i++){
1176	>	info[i].n_atoms = tot_atoms;
1177	>	info[i].n_bonds = tot_bonds;
1178	>	info[i].n_bends = tot_bends;
1179	>	info[i].n_torsions = tot_torsions;
1180	>	info[i].n_SRI = tot_SRI;
1181	>	info[i].n_mol = tot_nmol;
1182	>
1183	>	info[i].molMembershipArray = molMembershipArray;
1184	>	}
1185	>	}
1186
1187		#ifdef IS_MPI
1188	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
1188	>
1189	>	void SimSetup::mpiMolDivide( void ){
1190	>
1191	>	int i, j, k;
1192	>	int localMol, allMol;
1193	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1194	>
1195	>	mpiSim = new mpiSimulation( info );
1196	>
1197	>	globalIndex = mpiSim->divideLabor();
1198	>
1199	>	// set up the local variables
1200	>
1201	>	mol2proc = mpiSim->getMolToProcMap();
1202	>	molCompType = mpiSim->getMolComponentType();
1203	>
1204	>	allMol = 0;
1205	>	localMol = 0;
1206	>	local_atoms = 0;
1207	>	local_bonds = 0;
1208	>	local_bends = 0;
1209	>	local_torsions = 0;
1210	>	globalAtomIndex = 0;
1211	>
1212	>
1213	>	for( i=0; i<n_components; i++ ){
1214	>
1215	>	for( j=0; j<components_nmol[i]; j++ ){
1216	>
1217	>	if( mol2proc[allMol] == worldRank ){
1218	>
1219	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1220	>	local_bonds +=    comp_stamps[i]->getNBonds();
1221	>	local_bends +=    comp_stamps[i]->getNBends();
1222	>	local_torsions += comp_stamps[i]->getNTorsions();
1223	>	localMol++;
1224	>	}
1225	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1226	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1227	>	globalAtomIndex++;
1228	>	}
1229	>
1230	>	allMol++;
1231	>	}
1232	>	}
1233	>	local_SRI = local_bonds + local_bends + local_torsions;
1234	>
1235	>	info[0].n_atoms = mpiSim->getMyNlocal();
1236	>
1237	>	if( local_atoms != info[0].n_atoms ){
1238	>	sprintf( painCave.errMsg,
1239	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1240	>	" localAtom (%d) are not equal.\n",
1241	>	info[0].n_atoms,
1242	>	local_atoms );
1243	>	painCave.isFatal = 1;
1244	>	simError();
1245	>	}
1246	>
1247	>	info[0].n_bonds = local_bonds;
1248	>	info[0].n_bends = local_bends;
1249	>	info[0].n_torsions = local_torsions;
1250	>	info[0].n_SRI = local_SRI;
1251	>	info[0].n_mol = localMol;
1252	>
1253	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1254		MPIcheckPoint();
1255	+	}
1256	+
1257		#endif // is_mpi
1258
1259
1260	<
1261	<
625	<
1260	>	void SimSetup::makeSysArrays( void ){
1261	>	int i, j, k, l;
1262
1263	+	Atom** the_atoms;
1264	+	Molecule* the_molecules;
1265	+	Exclude** the_excludes;
1266	+
1267
1268	+	for(l=0; l<nInfo; l++){
1269	+
1270	+	// create the atom and short range interaction arrays
1271	+
1272	+	the_atoms = new Atom*[info[l].n_atoms];
1273	+	the_molecules = new Molecule[info[l].n_mol];
1274	+	int molIndex;
1275	+
1276	+	// initialize the molecule's stampID's
1277	+
1278		#ifdef IS_MPI
629	–	if( worldRank == 0 ){
630	–	#endif // is_mpi
1279
632	–	if( the_globals->haveFinalConfig() ){
633	–	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
634	–	}
635	–	else{
636	–	strcpy( simnfo->finalName, inFileName );
637	–	char* endTest;
638	–	int nameLength = strlen( simnfo->finalName );
639	–	endTest = &(simnfo->finalName[nameLength - 5]);
640	–	if( !strcmp( endTest, ".bass" ) ){
641	–	strcpy( endTest, ".eor" );
642	–	}
643	–	else if( !strcmp( endTest, ".BASS" ) ){
644	–	strcpy( endTest, ".eor" );
645	–	}
646	–	else{
647	–	endTest = &(simnfo->finalName[nameLength - 4]);
648	–	if( !strcmp( endTest, ".bss" ) ){
649	–	strcpy( endTest, ".eor" );
650	–	}
651	–	else if( !strcmp( endTest, ".mdl" ) ){
652	–	strcpy( endTest, ".eor" );
653	–	}
654	–	else{
655	–	strcat( simnfo->finalName, ".eor" );
656	–	}
657	–	}
658	–	}
1280
1281	<	// make the sample and status out names
1281	>	molIndex = 0;
1282	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1283
1284	<	strcpy( simnfo->sampleName, inFileName );
1285	<	char* endTest;
1286	<	int nameLength = strlen( simnfo->sampleName );
1287	<	endTest = &(simnfo->sampleName[nameLength - 5]);
1288	<	if( !strcmp( endTest, ".bass" ) ){
667	<	strcpy( endTest, ".dump" );
668	<	}
669	<	else if( !strcmp( endTest, ".BASS" ) ){
670	<	strcpy( endTest, ".dump" );
671	<	}
672	<	else{
673	<	endTest = &(simnfo->sampleName[nameLength - 4]);
674	<	if( !strcmp( endTest, ".bss" ) ){
675	<	strcpy( endTest, ".dump" );
1284	>	if(mol2proc[i] == worldRank ){
1285	>	the_molecules[molIndex].setStampID( molCompType[i] );
1286	>	the_molecules[molIndex].setMyIndex( molIndex );
1287	>	the_molecules[molIndex].setGlobalIndex( i );
1288	>	molIndex++;
1289		}
677	–	else if( !strcmp( endTest, ".mdl" ) ){
678	–	strcpy( endTest, ".dump" );
679	–	}
680	–	else{
681	–	strcat( simnfo->sampleName, ".dump" );
682	–	}
1290		}
1291
1292	<	strcpy( simnfo->statusName, inFileName );
1293	<	nameLength = strlen( simnfo->statusName );
1294	<	endTest = &(simnfo->statusName[nameLength - 5]);
1295	<	if( !strcmp( endTest, ".bass" ) ){
1296	<	strcpy( endTest, ".stat" );
1297	<	}
1298	<	else if( !strcmp( endTest, ".BASS" ) ){
1299	<	strcpy( endTest, ".stat" );
1300	<	}
1301	<	else{
1302	<	endTest = &(simnfo->statusName[nameLength - 4]);
1303	<	if( !strcmp( endTest, ".bss" ) ){
1304	<	strcpy( endTest, ".stat" );
1292	>	#else // is_mpi
1293	>
1294	>	molIndex = 0;
1295	>	globalAtomIndex = 0;
1296	>	for(i=0; i<n_components; i++){
1297	>	for(j=0; j<components_nmol[i]; j++ ){
1298	>	the_molecules[molIndex].setStampID( i );
1299	>	the_molecules[molIndex].setMyIndex( molIndex );
1300	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1301	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1302	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1303	>	globalAtomIndex++;
1304	>	}
1305	>	molIndex++;
1306		}
699	–	else if( !strcmp( endTest, ".mdl" ) ){
700	–	strcpy( endTest, ".stat" );
701	–	}
702	–	else{
703	–	strcat( simnfo->statusName, ".stat" );
704	–	}
1307		}
1308
1309	<	#ifdef IS_MPI
708	<	}
1309	>
1310		#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	–	}
1311
724	–	if( the_globals->haveStatusTime() ){
725	–	simnfo->statusTime = the_globals->getStatusTime();
726	–	}
1312
1313	<	if( the_globals->haveThermalTime() ){
1314	<	simnfo->thermalTime = the_globals->getThermalTime();
1315	<	}
1313	>	if( info[l].n_SRI ){
1314	>
1315	>	Exclude::createArray(info[l].n_SRI);
1316	>	the_excludes = new Exclude*[info[l].n_SRI];
1317	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1318	>	the_excludes[ex] = new Exclude(ex);
1319	>	}
1320	>	info[l].globalExcludes = new int;
1321	>	info[l].n_exclude = info[l].n_SRI;
1322	>	}
1323	>	else{
1324	>
1325	>	Exclude::createArray( 1 );
1326	>	the_excludes = new Exclude*;
1327	>	the_excludes[0] = new Exclude(0);
1328	>	the_excludes[0]->setPair( 0,0 );
1329	>	info[l].globalExcludes = new int;
1330	>	info[l].globalExcludes[0] = 0;
1331	>	info[l].n_exclude = 0;
1332	>	}
1333
1334	<	// check for the temperature set flag
1334	>	// set the arrays into the SimInfo object
1335
1336	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
1336	>	info[l].atoms = the_atoms;
1337	>	info[l].molecules = the_molecules;
1338	>	info[l].nGlobalExcludes = 0;
1339	>	info[l].excludes = the_excludes;
1340
1341	+	the_ff->setSimInfo( info );
1342	+
1343	+	}
1344	+	}
1345
1346	<	//   // make the longe range forces and the integrator
1346	>	void SimSetup::makeIntegrator( void ){
1347
1348	<	//   new AllLong( simnfo );
1348	>	int k;
1349
1350	+	NVT<RealIntegrator>*  myNVT = NULL;
1351	+	NPTi<RealIntegrator>* myNPTi = NULL;
1352	+	NPTf<RealIntegrator>* myNPTf = NULL;
1353	+	NPTim<RealIntegrator>* myNPTim = NULL;
1354	+	NPTfm<RealIntegrator>* myNPTfm = NULL;
1355	+
1356	+	for(k=0; k<nInfo; k++){
1357	+
1358	+	switch( ensembleCase ){
1359	+
1360	+	case NVE_ENS:
1361	+	if (haveZConstraint){
1362	+	setupZConstraint();
1363	+	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1364	+	}
1365
1366	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
1367	<	new Symplectic(simnfo, the_ff, the_extendedsystem);
1368	<	}
1369	<	else if( !strcmp( force_field, "LJ" ) ){
1370	<	new Verlet( *simnfo, the_ff, the_extendedsystem );
1371	<	}
1366	>	else
1367	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1368	>	break;
1369	>
1370	>	case NVT_ENS:
1371	>	if (haveZConstraint){
1372	>	setupZConstraint();
1373	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1374	>	}
1375	>	else
1376	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1377
1378	<	#ifdef IS_MPI
1379	<	mpiSim->mpiRefresh();
1380	<	#endif
1378	>	myNVT->setTargetTemp(globals->getTargetTemp());
1379	>
1380	>	if (globals->haveTauThermostat())
1381	>	myNVT->setTauThermostat(globals->getTauThermostat());
1382	>
1383	>	else {
1384	>	sprintf( painCave.errMsg,
1385	>	"SimSetup error: If you use the NVT\n"
1386	>	"    ensemble, you must set tauThermostat.\n");
1387	>	painCave.isFatal = 1;
1388	>	simError();
1389	>	}
1390	>	break;
1391	>
1392	>	case NPTi_ENS:
1393	>	if (haveZConstraint){
1394	>	setupZConstraint();
1395	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1396	>	}
1397	>	else
1398	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1399
1400	<	// initialize the Fortran
1400	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1401	>
1402	>	if (globals->haveTargetPressure())
1403	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1404	>	else {
1405	>	sprintf( painCave.errMsg,
1406	>	"SimSetup error: If you use a constant pressure\n"
1407	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1408	>	painCave.isFatal = 1;
1409	>	simError();
1410	>	}
1411	>
1412	>	if( globals->haveTauThermostat() )
1413	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1414	>	else{
1415	>	sprintf( painCave.errMsg,
1416	>	"SimSetup error: If you use an NPT\n"
1417	>	"    ensemble, you must set tauThermostat.\n");
1418	>	painCave.isFatal = 1;
1419	>	simError();
1420	>	}
1421	>
1422	>	if( globals->haveTauBarostat() )
1423	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1424	>	else{
1425	>	sprintf( painCave.errMsg,
1426	>	"SimSetup error: If you use an NPT\n"
1427	>	"    ensemble, you must set tauBarostat.\n");
1428	>	painCave.isFatal = 1;
1429	>	simError();
1430	>	}
1431	>	break;
1432	>
1433	>	case NPTf_ENS:
1434	>	if (haveZConstraint){
1435	>	setupZConstraint();
1436	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1437	>	}
1438	>	else
1439	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1440
1441	+	myNPTf->setTargetTemp( globals->getTargetTemp());
1442	+
1443	+	if (globals->haveTargetPressure())
1444	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1445	+	else {
1446	+	sprintf( painCave.errMsg,
1447	+	"SimSetup error: If you use a constant pressure\n"
1448	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1449	+	painCave.isFatal = 1;
1450	+	simError();
1451	+	}
1452	+
1453	+	if( globals->haveTauThermostat() )
1454	+	myNPTf->setTauThermostat( globals->getTauThermostat() );
1455	+	else{
1456	+	sprintf( painCave.errMsg,
1457	+	"SimSetup error: If you use an NPT\n"
1458	+	"    ensemble, you must set tauThermostat.\n");
1459	+	painCave.isFatal = 1;
1460	+	simError();
1461	+	}
1462	+
1463	+	if( globals->haveTauBarostat() )
1464	+	myNPTf->setTauBarostat( globals->getTauBarostat() );
1465	+	else{
1466	+	sprintf( painCave.errMsg,
1467	+	"SimSetup error: If you use an NPT\n"
1468	+	"    ensemble, you must set tauBarostat.\n");
1469	+	painCave.isFatal = 1;
1470	+	simError();
1471	+	}
1472	+	break;
1473	+
1474	+	case NPTim_ENS:
1475	+	if (haveZConstraint){
1476	+	setupZConstraint();
1477	+	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1478	+	}
1479	+	else
1480	+	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1481
1482	<	simnfo->refreshSim();
1482	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1483	>
1484	>	if (globals->haveTargetPressure())
1485	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1486	>	else {
1487	>	sprintf( painCave.errMsg,
1488	>	"SimSetup error: If you use a constant pressure\n"
1489	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1490	>	painCave.isFatal = 1;
1491	>	simError();
1492	>	}
1493	>
1494	>	if( globals->haveTauThermostat() )
1495	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1496	>	else{
1497	>	sprintf( painCave.errMsg,
1498	>	"SimSetup error: If you use an NPT\n"
1499	>	"    ensemble, you must set tauThermostat.\n");
1500	>	painCave.isFatal = 1;
1501	>	simError();
1502	>	}
1503	>
1504	>	if( globals->haveTauBarostat() )
1505	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1506	>	else{
1507	>	sprintf( painCave.errMsg,
1508	>	"SimSetup error: If you use an NPT\n"
1509	>	"    ensemble, you must set tauBarostat.\n");
1510	>	painCave.isFatal = 1;
1511	>	simError();
1512	>	}
1513	>	break;
1514	>
1515	>	case NPTfm_ENS:
1516	>	if (haveZConstraint){
1517	>	setupZConstraint();
1518	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1519	>	}
1520	>	else
1521	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1522	>
1523	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1524	>
1525	>	if (globals->haveTargetPressure())
1526	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1527	>	else {
1528	>	sprintf( painCave.errMsg,
1529	>	"SimSetup error: If you use a constant pressure\n"
1530	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1531	>	painCave.isFatal = 1;
1532	>	simError();
1533	>	}
1534	>
1535	>	if( globals->haveTauThermostat() )
1536	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1537	>	else{
1538	>	sprintf( painCave.errMsg,
1539	>	"SimSetup error: If you use an NPT\n"
1540	>	"    ensemble, you must set tauThermostat.\n");
1541	>	painCave.isFatal = 1;
1542	>	simError();
1543	>	}
1544	>
1545	>	if( globals->haveTauBarostat() )
1546	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1547	>	else{
1548	>	sprintf( painCave.errMsg,
1549	>	"SimSetup error: If you use an NPT\n"
1550	>	"    ensemble, you must set tauBarostat.\n");
1551	>	painCave.isFatal = 1;
1552	>	simError();
1553	>	}
1554	>	break;
1555	>
1556	>	default:
1557	>	sprintf( painCave.errMsg,
1558	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1559	>	painCave.isFatal = 1;
1560	>	simError();
1561	>	}
1562	>	}
1563	>	}
1564	>
1565	>	void SimSetup::initFortran( void ){
1566	>
1567	>	info[0].refreshSim();
1568
1569	<	if( !strcmp( simnfo->mixingRule, "standard") ){
1569	>	if( !strcmp( info[0].mixingRule, "standard") ){
1570		the_ff->initForceField( LB_MIXING_RULE );
1571		}
1572	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
1572	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1573		the_ff->initForceField( EXPLICIT_MIXING_RULE );
1574		}
1575		else{
1576		sprintf( painCave.errMsg,
1577		"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1578	<	simnfo->mixingRule );
1578	>	info[0].mixingRule );
1579		painCave.isFatal = 1;
1580		simError();
1581		}
#	Line 775 | Line 1586 | void SimSetup::createSim( void ){
1586		"Successfully intialized the mixingRule for Fortran." );
1587		MPIcheckPoint();
1588		#endif // is_mpi
1589	+
1590		}
1591
1592	+	void SimSetup::setupZConstraint()
1593	+	{
1594	+	int k;
1595
1596	<	void SimSetup::makeMolecules( void ){
782	<
783	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
784	<	molInit info;
785	<	DirectionalAtom* dAtom;
786	<	LinkedAssign* extras;
787	<	LinkedAssign* current_extra;
788	<	AtomStamp* currentAtom;
789	<	BondStamp* currentBond;
790	<	BendStamp* currentBend;
791	<	TorsionStamp* currentTorsion;
792	<
793	<	bond_pair* theBonds;
794	<	bend_set* theBends;
795	<	torsion_set* theTorsions;
796	<
797	<
798	<	//init the forceField paramters
799	<
800	<	the_ff->readParams();
801	<
802	<
803	<	// init the atoms
804	<
805	<	double ux, uy, uz, u, uSqr;
806	<
807	<	atomOffset = 0;
808	<	excludeOffset = 0;
809	<	for(i=0; i<simnfo->n_mol; i++){
1596	>	for(k=0; k<nInfo; k++){
1597
1598	<	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];
828	<
829	<	// make the Atoms
830	<
831	<	for(j=0; j<info.nAtoms; j++){
1598	>	if(globals->haveZConsTime()){
1599
1600	<	currentAtom = comp_stamps[stampID]->getAtom( j );
1601	<	if( currentAtom->haveOrientation() ){
1602	<
1603	<	dAtom = new DirectionalAtom(j + atomOffset);
1604	<	simnfo->n_oriented++;
1605	<	info.myAtoms[j] = dAtom;
1606	<
1607	<	ux = currentAtom->getOrntX();
1608	<	uy = currentAtom->getOrntY();
1609	<	uz = currentAtom->getOrntZ();
1610	<
1611	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
1612	<
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() );
1600	>	//add sample time of z-constraint  into SimInfo's property list
1601	>	DoubleData* zconsTimeProp = new DoubleData();
1602	>	zconsTimeProp->setID("zconstime");
1603	>	zconsTimeProp->setData(globals->getZConsTime());
1604	>	info[k].addProperty(zconsTimeProp);
1605	>	}
1606	>	else{
1607	>	sprintf( painCave.errMsg,
1608	>	"ZConstraint error: If you use an ZConstraint\n"
1609	>	" , you must set sample time.\n");
1610	>	painCave.isFatal = 1;
1611	>	simError();
1612	>	}
1613
1614	<	#ifdef IS_MPI
1614	>	if(globals->haveIndexOfAllZConsMols()){
1615	>
1616	>	//add index of z-constraint molecules into SimInfo's property list
1617	>	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1618
1619	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
1619	>	//sort the index
1620	>	sort(tempIndex.begin(), tempIndex.end());
1621
1622	<	#endif // is_mpi
1623	<	}
1624	<
1625	<	// make the bonds
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;
873	<
874	<	exI = theBonds[j].a;
875	<	exJ = theBonds[j].b;
876	<
877	<	// 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
1622	>	IndexData* zconsIndex = new IndexData();
1623	>	zconsIndex->setID("zconsindex");
1624	>	zconsIndex->setIndexData(tempIndex);
1625	>	info[k].addProperty(zconsIndex);
1626		}
1627	<	excludeOffset += info.nBonds;
1628	<
1629	<	//make the bends
1630	<	for(j=0; j<info.nBends; j++){
1631	<
1632	<	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{
959	<
960	<	exI = theBends[j].a;
961	<	exJ = theBends[j].b;
962	<	}
1627	>	else{
1628	>	sprintf( painCave.errMsg,
1629	>	"SimSetup error: If you use an ZConstraint\n"
1630	>	" , you must set index of z-constraint molecules.\n");
1631	>	painCave.isFatal = 1;
1632	>	simError();
1633
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
1634		}
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	–
1635
1636	<	// send the arrays off to the forceField for init.
1637	<
1638	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1639	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1640	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1641	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1642	<
1643	<
1644	<	the_molecules[i].initialize( info );
1645	<
1646	<
1647	<	atomOffset += info.nAtoms;
1648	<	delete[] theBonds;
1027	<	delete[] theBends;
1028	<	delete[] theTorsions;
1636	>	//Determine the name of ouput file and add it into SimInfo's property list
1637	>	//Be careful, do not use inFileName, since it is a pointer which
1638	>	//point to a string at master node, and slave nodes do not contain that string
1639	>
1640	>	string zconsOutput(info[k].finalName);
1641	>
1642	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1643	>
1644	>	StringData* zconsFilename = new StringData();
1645	>	zconsFilename->setID("zconsfilename");
1646	>	zconsFilename->setData(zconsOutput);
1647	>
1648	>	info[k].addProperty(zconsFilename);
1649		}
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	–
1650		}
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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