ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 414 by mmeineke, Wed Mar 26 22:02:36 2003 UTC vs.
Revision 658 by tim, Thu Jul 31 15:35:07 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	+	#define NVEZCONS_ENS 6
26	+
27	+
28	+	#define FF_DUFF 0
29	+	#define FF_LJ   1
30	+	#define FF_EAM  2
31	+
32	+	using namespace std;
33	+
34		SimSetup::SimSetup(){
35	+
36	+	isInfoArray = 0;
37	+	nInfo = 1;
38	+
39		stamps = new MakeStamps();
40		globals = new Globals();
41
42	+
43		#ifdef IS_MPI
44		strcpy( checkPointMsg, "SimSetup creation successful" );
45		MPIcheckPoint();
#	Line 27 | Line 51 | void SimSetup::parseFile( char* fileName ){
51		delete globals;
52		}
53
54	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
55	+	info = the_info;
56	+	nInfo = theNinfo;
57	+	isInfoArray = 1;
58	+	}
59	+
60	+
61		void SimSetup::parseFile( char* fileName ){
62
63		#ifdef IS_MPI
#	Line 64 | Line 95 | void SimSetup::createSim( void ){
95
96		void SimSetup::createSim( void ){
97
98	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
70	<
71	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
74	<
75	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	simnfo->run_time = the_globals->getRunTime();
79	<
80	<	// get the ones we know are there, yet still may need some work.
81	<	n_components = the_globals->getNComponents();
82	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
85	<
86	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
89	<
90	<
91	<	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
92	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
93	<	else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
94	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
95	<	else{
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Error. Unrecognized force field -> %s\n",
98	<	force_field );
99	<	painCave.isFatal = 1;
100	<	simError();
101	<	}
102	<
103	<	#ifdef IS_MPI
104	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
107	<
98	>	int i, j, k, globalAtomIndex;
99
100	<
110	<	// get the components and calculate the tot_nMol and indvidual n_mol
111	<	the_components = the_globals->getComponents();
112	<	components_nmol = new int[n_components];
113	<	comp_stamps = new MoleculeStamp*[n_components];
114	<
115	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
118	<
119	<	tot_nmol = 0;
120	<	for( i=0; i<n_components; i++ ){
121	<
122	<	if( !the_components[i]->haveNMol() ){
123	<	// we have a problem
124	<	sprintf( painCave.errMsg,
125	<	"SimSetup Error. No global NMol or component NMol"
126	<	" given. Cannot calculate the number of atoms.\n" );
127	<	painCave.isFatal = 1;
128	<	simError();
129	<	}
130	<
131	<	tot_nmol += the_components[i]->getNMol();
132	<	components_nmol[i] = the_components[i]->getNMol();
133	<	}
134	<	}
135	<	else{
136	<	sprintf( painCave.errMsg,
137	<	"SimSetup error.\n"
138	<	"\tSorry, the ability to specify total"
139	<	" nMols and then give molfractions in the components\n"
140	<	"\tis not currently supported."
141	<	" Please give nMol in the components.\n" );
142	<	painCave.isFatal = 1;
143	<	simError();
144	<
145	<
146	<	//     tot_nmol = the_globals->getNMol();
147	<
148	<	//   //we have the total number of molecules, now we check for molfractions
149	<	//     for( i=0; i<n_components; i++ ){
150	<
151	<	//       if( !the_components[i]->haveMolFraction() ){
152	<
153	<	//  if( !the_components[i]->haveNMol() ){
154	<	//    //we have a problem
155	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
156	<	//              << " nMol was given in component
157	<
158	<	}
159	<
160	<	#ifdef IS_MPI
161	<	strcpy( checkPointMsg, "Have the number of components" );
162	<	MPIcheckPoint();
163	<	#endif // is_mpi
164	<
165	<	// make an array of molecule stamps that match the components used.
166	<	// also extract the used stamps out into a separate linked list
167	<
168	<	simnfo->nComponents = n_components;
169	<	simnfo->componentsNmol = components_nmol;
170	<	simnfo->compStamps = comp_stamps;
171	<	simnfo->headStamp = new LinkedMolStamp();
100	>	// gather all of the information from the Bass file
101
102	<	char* id;
174	<	LinkedMolStamp* headStamp = simnfo->headStamp;
175	<	LinkedMolStamp* currentStamp = NULL;
176	<	for( i=0; i<n_components; i++ ){
102	>	gatherInfo();
103
104	<	id = the_components[i]->getType();
179	<	comp_stamps[i] = NULL;
180	<
181	<	// check to make sure the component isn't already in the list
104	>	// creation of complex system objects
105
106	<	comp_stamps[i] = headStamp->match( id );
184	<	if( comp_stamps[i] == NULL ){
185	<
186	<	// extract the component from the list;
187	<
188	<	currentStamp = the_stamps->extractMolStamp( id );
189	<	if( currentStamp == NULL ){
190	<	sprintf( painCave.errMsg,
191	<	"SimSetup error: Component \"%s\" was not found in the "
192	<	"list of declared molecules\n",
193	<	id );
194	<	painCave.isFatal = 1;
195	<	simError();
196	<	}
197	<
198	<	headStamp->add( currentStamp );
199	<	comp_stamps[i] = headStamp->match( id );
200	<	}
201	<	}
106	>	sysObjectsCreation();
107
108	<	#ifdef IS_MPI
204	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
205	<	MPIcheckPoint();
206	<	#endif // is_mpi
108	>	// check on the post processing info
109
110	+	finalInfoCheck();
111
112	+	// initialize the system coordinates
113
114	<
211	<	// caclulate the number of atoms, bonds, bends and torsions
212	<
213	<	tot_atoms = 0;
214	<	tot_bonds = 0;
215	<	tot_bends = 0;
216	<	tot_torsions = 0;
217	<	for( i=0; i<n_components; i++ ){
218	<
219	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
220	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
221	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
222	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
223	<	}
224	<
225	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
226	<
227	<	simnfo->n_atoms = tot_atoms;
228	<	simnfo->n_bonds = tot_bonds;
229	<	simnfo->n_bends = tot_bends;
230	<	simnfo->n_torsions = tot_torsions;
231	<	simnfo->n_SRI = tot_SRI;
232	<	simnfo->n_mol = tot_nmol;
233	<
114	>	initSystemCoords();
115
235	–	#ifdef IS_MPI
116
117	<	// divide the molecules among processors here.
238	<
239	<	mpiSim = new mpiSimulation( simnfo );
240	<
241	<
117	>	// make the output filenames
118
119	<	globalIndex = mpiSim->divideLabor();
120	<
121	<
246	<
247	<	// set up the local variables
119	>	makeOutNames();
120	>
121	>	// make the integrator
122
123	<	int localMol, allMol;
250	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
123	>	makeIntegrator();
124
252	–	allMol = 0;
253	–	localMol = 0;
254	–	local_atoms = 0;
255	–	local_bonds = 0;
256	–	local_bends = 0;
257	–	local_torsions = 0;
258	–	for( i=0; i<n_components; i++ ){
259	–
260	–	for( j=0; j<components_nmol[i]; j++ ){
261	–
262	–	if( mpiSim->getMyMolStart() <= allMol &&
263	–	allMol <= mpiSim->getMyMolEnd() ){
264	–
265	–	local_atoms +=    comp_stamps[i]->getNAtoms();
266	–	local_bonds +=    comp_stamps[i]->getNBonds();
267	–	local_bends +=    comp_stamps[i]->getNBends();
268	–	local_torsions += comp_stamps[i]->getNTorsions();
269	–	localMol++;
270	–	}
271	–	allMol++;
272	–	}
273	–	}
274	–	local_SRI = local_bonds + local_bends + local_torsions;
275	–
276	–
277	–	simnfo->n_atoms = mpiSim->getMyNlocal();
278	–
279	–	if( local_atoms != simnfo->n_atoms ){
280	–	sprintf( painCave.errMsg,
281	–	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282	–	" localAtom (%d) are note equal.\n",
283	–	simnfo->n_atoms,
284	–	local_atoms );
285	–	painCave.isFatal = 1;
286	–	simError();
287	–	}
288	–
289	–	simnfo->n_bonds = local_bonds;
290	–	simnfo->n_bends = local_bends;
291	–	simnfo->n_torsions = local_torsions;
292	–	simnfo->n_SRI = local_SRI;
293	–	simnfo->n_mol = localMol;
294	–
295	–	strcpy( checkPointMsg, "Passed nlocal consistency check." );
296	–	MPIcheckPoint();
297	–
298	–
299	–	#endif // is_mpi
300	–
301	–
302	–	// create the atom and short range interaction arrays
303	–
304	–	Atom::createArrays(simnfo->n_atoms);
305	–	the_atoms = new Atom*[simnfo->n_atoms];
306	–	the_molecules = new Molecule[simnfo->n_mol];
307	–
308	–
309	–	if( simnfo->n_SRI ){
310	–	Exclude::createArray(simnfo->n_SRI);
311	–	the_excludes = new Exclude*[simnfo->n_SRI];
312	–	simnfo->globalExcludes = new int;
313	–	simnfo->n_exclude = tot_SRI;
314	–	}
315	–	else{
316	–
317	–	Exclude::createArray( 1 );
318	–	the_excludes = new Exclude*;
319	–	the_excludes[0] = new Exclude(0);
320	–	the_excludes[0]->setPair( 0,0 );
321	–	simnfo->globalExcludes = new int;
322	–	simnfo->globalExcludes[0] = 0;
323	–	simnfo->n_exclude = 0;
324	–	}
325	–
326	–	// set the arrays into the SimInfo object
327	–
328	–	simnfo->atoms = the_atoms;
329	–	simnfo->sr_interactions = the_sris;
330	–	simnfo->nGlobalExcludes = 0;
331	–	simnfo->excludes = the_excludes;
332	–
333	–
334	–	// get some of the tricky things that may still be in the globals
335	–
336	–
337	–	if( the_globals->haveBox() ){
338	–	simnfo->box_x = the_globals->getBox();
339	–	simnfo->box_y = the_globals->getBox();
340	–	simnfo->box_z = the_globals->getBox();
341	–	}
342	–	else if( the_globals->haveDensity() ){
343	–
344	–	double vol;
345	–	vol = (double)tot_nmol / the_globals->getDensity();
346	–	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
347	–	simnfo->box_y = simnfo->box_x;
348	–	simnfo->box_z = simnfo->box_x;
349	–	}
350	–	else{
351	–	if( !the_globals->haveBoxX() ){
352	–	sprintf( painCave.errMsg,
353	–	"SimSetup error, no periodic BoxX size given.\n" );
354	–	painCave.isFatal = 1;
355	–	simError();
356	–	}
357	–	simnfo->box_x = the_globals->getBoxX();
358	–
359	–	if( !the_globals->haveBoxY() ){
360	–	sprintf( painCave.errMsg,
361	–	"SimSetup error, no periodic BoxY size given.\n" );
362	–	painCave.isFatal = 1;
363	–	simError();
364	–	}
365	–	simnfo->box_y = the_globals->getBoxY();
366	–
367	–	if( !the_globals->haveBoxZ() ){
368	–	sprintf( painCave.errMsg,
369	–	"SimSetup error, no periodic BoxZ size given.\n" );
370	–	painCave.isFatal = 1;
371	–	simError();
372	–	}
373	–	simnfo->box_z = the_globals->getBoxZ();
374	–	}
375	–
125		#ifdef IS_MPI
126	<	strcpy( checkPointMsg, "Box size set up" );
378	<	MPIcheckPoint();
379	<	#endif // is_mpi
380	<
381	<
382	<	// initialize the arrays
383	<
384	<	the_ff->setSimInfo( simnfo );
385	<
386	<	makeAtoms();
387	<	simnfo->identArray = new int[simnfo->n_atoms];
388	<	for(i=0; i<simnfo->n_atoms; i++){
389	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
390	<	}
391	<
392	<	if( tot_bonds ){
393	<	makeBonds();
394	<	}
395	<
396	<	if( tot_bends ){
397	<	makeBends();
398	<	}
399	<
400	<	if( tot_torsions ){
401	<	makeTorsions();
402	<	}
403	<
404	<
405	<	if (the_globals->getUseRF() ) {
406	<	simnfo->useReactionField = 1;
407	<
408	<	if( !the_globals->haveECR() ){
409	<	sprintf( painCave.errMsg,
410	<	"SimSetup Warning: using default value of 1/2 the smallest "
411	<	"box length for the electrostaticCutoffRadius.\n"
412	<	"I hope you have a very fast processor!\n");
413	<	painCave.isFatal = 0;
414	<	simError();
415	<	double smallest;
416	<	smallest = simnfo->box_x;
417	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
418	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
419	<	simnfo->ecr = 0.5 * smallest;
420	<	} else {
421	<	simnfo->ecr        = the_globals->getECR();
422	<	}
423	<
424	<	if( !the_globals->haveEST() ){
425	<	sprintf( painCave.errMsg,
426	<	"SimSetup Warning: using default value of 0.05 * the "
427	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
428	<	);
429	<	painCave.isFatal = 0;
430	<	simError();
431	<	simnfo->est = 0.05 * simnfo->ecr;
432	<	} else {
433	<	simnfo->est        = the_globals->getEST();
434	<	}
435	<
436	<	if(!the_globals->haveDielectric() ){
437	<	sprintf( painCave.errMsg,
438	<	"SimSetup Error: You are trying to use Reaction Field without"
439	<	"setting a dielectric constant!\n"
440	<	);
441	<	painCave.isFatal = 1;
442	<	simError();
443	<	}
444	<	simnfo->dielectric = the_globals->getDielectric();
445	<	} else {
446	<	if (simnfo->n_dipoles) {
447	<
448	<	if( !the_globals->haveECR() ){
449	<	sprintf( painCave.errMsg,
450	<	"SimSetup Warning: using default value of 1/2 the smallest"
451	<	"box length for the electrostaticCutoffRadius.\n"
452	<	"I hope you have a very fast processor!\n");
453	<	painCave.isFatal = 0;
454	<	simError();
455	<	double smallest;
456	<	smallest = simnfo->box_x;
457	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
458	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
459	<	simnfo->ecr = 0.5 * smallest;
460	<	} else {
461	<	simnfo->ecr        = the_globals->getECR();
462	<	}
463	<
464	<	if( !the_globals->haveEST() ){
465	<	sprintf( painCave.errMsg,
466	<	"SimSetup Warning: using default value of 5% of the"
467	<	"electrostaticCutoffRadius for the "
468	<	"electrostaticSkinThickness\n"
469	<	);
470	<	painCave.isFatal = 0;
471	<	simError();
472	<	simnfo->est = 0.05 * simnfo->ecr;
473	<	} else {
474	<	simnfo->est        = the_globals->getEST();
475	<	}
476	<	}
477	<	}
478	<
479	<	#ifdef IS_MPI
480	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
481	<	MPIcheckPoint();
482	<	#endif // is_mpi
483	<
484	<	if( the_globals->haveInitialConfig() ){
485	<
486	<	InitializeFromFile* fileInit;
487	<	#ifdef IS_MPI // is_mpi
488	<	if( worldRank == 0 ){
489	<	#endif //is_mpi
490	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
491	<	#ifdef IS_MPI
492	<	}else fileInit = new InitializeFromFile( NULL );
126	>	mpiSim->mpiRefresh();
127		#endif
494	–	fileInit->read_xyz( simnfo ); // default velocities on
128
129	<	delete fileInit;
497	<	}
498	<	else{
129	>	// initialize the Fortran
130
131	<	#ifdef IS_MPI
501	<
502	<	// no init from bass
503	<
504	<	sprintf( painCave.errMsg,
505	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
506	<	painCave.isFatal;
507	<	simError();
508	<
509	<	#else
510	<
511	<	initFromBass();
512	<
513	<
514	<	#endif
515	<	}
516	<
517	<	#ifdef IS_MPI
518	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
519	<	MPIcheckPoint();
520	<	#endif // is_mpi
521	<
522	<
523	<
524	<
525	<
526	<
527	<
528	<	#ifdef IS_MPI
529	<	if( worldRank == 0 ){
530	<	#endif // is_mpi
531	<
532	<	if( the_globals->haveFinalConfig() ){
533	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
534	<	}
535	<	else{
536	<	strcpy( simnfo->finalName, inFileName );
537	<	char* endTest;
538	<	int nameLength = strlen( simnfo->finalName );
539	<	endTest = &(simnfo->finalName[nameLength - 5]);
540	<	if( !strcmp( endTest, ".bass" ) ){
541	<	strcpy( endTest, ".eor" );
542	<	}
543	<	else if( !strcmp( endTest, ".BASS" ) ){
544	<	strcpy( endTest, ".eor" );
545	<	}
546	<	else{
547	<	endTest = &(simnfo->finalName[nameLength - 4]);
548	<	if( !strcmp( endTest, ".bss" ) ){
549	<	strcpy( endTest, ".eor" );
550	<	}
551	<	else if( !strcmp( endTest, ".mdl" ) ){
552	<	strcpy( endTest, ".eor" );
553	<	}
554	<	else{
555	<	strcat( simnfo->finalName, ".eor" );
556	<	}
557	<	}
558	<	}
559	<
560	<	// make the sample and status out names
561	<
562	<	strcpy( simnfo->sampleName, inFileName );
563	<	char* endTest;
564	<	int nameLength = strlen( simnfo->sampleName );
565	<	endTest = &(simnfo->sampleName[nameLength - 5]);
566	<	if( !strcmp( endTest, ".bass" ) ){
567	<	strcpy( endTest, ".dump" );
568	<	}
569	<	else if( !strcmp( endTest, ".BASS" ) ){
570	<	strcpy( endTest, ".dump" );
571	<	}
572	<	else{
573	<	endTest = &(simnfo->sampleName[nameLength - 4]);
574	<	if( !strcmp( endTest, ".bss" ) ){
575	<	strcpy( endTest, ".dump" );
576	<	}
577	<	else if( !strcmp( endTest, ".mdl" ) ){
578	<	strcpy( endTest, ".dump" );
579	<	}
580	<	else{
581	<	strcat( simnfo->sampleName, ".dump" );
582	<	}
583	<	}
584	<
585	<	strcpy( simnfo->statusName, inFileName );
586	<	nameLength = strlen( simnfo->statusName );
587	<	endTest = &(simnfo->statusName[nameLength - 5]);
588	<	if( !strcmp( endTest, ".bass" ) ){
589	<	strcpy( endTest, ".stat" );
590	<	}
591	<	else if( !strcmp( endTest, ".BASS" ) ){
592	<	strcpy( endTest, ".stat" );
593	<	}
594	<	else{
595	<	endTest = &(simnfo->statusName[nameLength - 4]);
596	<	if( !strcmp( endTest, ".bss" ) ){
597	<	strcpy( endTest, ".stat" );
598	<	}
599	<	else if( !strcmp( endTest, ".mdl" ) ){
600	<	strcpy( endTest, ".stat" );
601	<	}
602	<	else{
603	<	strcat( simnfo->statusName, ".stat" );
604	<	}
605	<	}
606	<
607	<	#ifdef IS_MPI
608	<	}
609	<	#endif // is_mpi
610	<
611	<	// set the status, sample, and themal kick times
612	<
613	<	if( the_globals->haveSampleTime() ){
614	<	simnfo->sampleTime = the_globals->getSampleTime();
615	<	simnfo->statusTime = simnfo->sampleTime;
616	<	simnfo->thermalTime = simnfo->sampleTime;
617	<	}
618	<	else{
619	<	simnfo->sampleTime = the_globals->getRunTime();
620	<	simnfo->statusTime = simnfo->sampleTime;
621	<	simnfo->thermalTime = simnfo->sampleTime;
622	<	}
131	>	initFortran();
132
624	–	if( the_globals->haveStatusTime() ){
625	–	simnfo->statusTime = the_globals->getStatusTime();
626	–	}
133
628	–	if( the_globals->haveThermalTime() ){
629	–	simnfo->thermalTime = the_globals->getThermalTime();
630	–	}
134
632	–	// check for the temperature set flag
633	–
634	–	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
635	–
636	–
637	–	//   // make the longe range forces and the integrator
638	–
639	–	//   new AllLong( simnfo );
640	–
641	–	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
642	–	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
643	–	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
644	–	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
645	–
646	–
647	–
648	–	// initialize the Fortran
649	–
650	–	simnfo->refreshSim();
651	–
652	–	if( !strcmp( simnfo->mixingRule, "standard") ){
653	–	the_ff->initForceField( LB_MIXING_RULE );
654	–	}
655	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
656	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
657	–	}
658	–	else{
659	–	sprintf( painCave.errMsg,
660	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
661	–	simnfo->mixingRule );
662	–	painCave.isFatal = 1;
663	–	simError();
664	–	}
665	–
666	–
667	–	#ifdef IS_MPI
668	–	strcpy( checkPointMsg,
669	–	"Successfully intialized the mixingRule for Fortran." );
670	–	MPIcheckPoint();
671	–	#endif // is_mpi
135		}
136
137
138		void SimSetup::makeMolecules( void ){
139
140		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
141	<	molInit info;
141	>	molInit molInfo;
142		DirectionalAtom* dAtom;
143		LinkedAssign* extras;
144		LinkedAssign* current_extra;
#	Line 683 | Line 146 | void SimSetup::makeMolecules( void ){
146		BondStamp* currentBond;
147		BendStamp* currentBend;
148		TorsionStamp* currentTorsion;
149	+
150	+	bond_pair* theBonds;
151	+	bend_set* theBends;
152	+	torsion_set* theTorsions;
153	+
154
155		//init the forceField paramters
156
157		the_ff->readParams();
158
159
160	<	// init the molecules
160	>	// init the atoms
161
162	+	double ux, uy, uz, u, uSqr;
163	+
164		atomOffset = 0;
165		excludeOffset = 0;
166	<	for(i=0; i<simnfo->n_mol; i++){
166	>	for(i=0; i<info->n_mol; i++){
167
168		stampID = the_molecules[i].getStampID();
169
170	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
171	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
172	<	info.nBends    = comp_stamps[stampID]->getNBends();
173	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
174	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
170	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
171	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
172	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
173	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
174	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
175
176	<	info.myAtoms = &the_atoms[atomOffset];
177	<	info.myExcludes = &the_excludes[excludeOffset];
178	<	info.myBonds = new Bond*[info.nBonds];
179	<	info.myBends = new Bend*[info.nBends];
180	<	info.myTorsions = new Torsions*[info.nTorsions];
176	>	molInfo.myAtoms = &the_atoms[atomOffset];
177	>	molInfo.myExcludes = &the_excludes[excludeOffset];
178	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
179	>	molInfo.myBends = new Bend*[molInfo.nBends];
180	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
181
182	<	theBonds = new bond_pair[info.nBonds];
183	<	theBends = new bend_set[info.nBends];
184	<	theTorsions = new torsion_set[info.nTorsions];
182	>	theBonds = new bond_pair[molInfo.nBonds];
183	>	theBends = new bend_set[molInfo.nBends];
184	>	theTorsions = new torsion_set[molInfo.nTorsions];
185
186		// make the Atoms
187
188	<	for(j=0; j<info.nAtoms; j++){
188	>	for(j=0; j<molInfo.nAtoms; j++){
189
190	<	currentAtom = theComponents[stampID]->getAtom( j );
190	>	currentAtom = comp_stamps[stampID]->getAtom( j );
191		if( currentAtom->haveOrientation() ){
192
193		dAtom = new DirectionalAtom(j + atomOffset);
194	<	simnfo->n_oriented++;
195	<	info.myAtoms[j] = dAtom;
194	>	info->n_oriented++;
195	>	molInfo.myAtoms[j] = dAtom;
196
197		ux = currentAtom->getOrntX();
198		uy = currentAtom->getOrntY();
#	Line 740 | Line 210 | void SimSetup::makeMolecules( void ){
210		dAtom->setSUz( uz );
211		}
212		else{
213	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
213	>	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
214		}
215	<	info.myAtoms[j]->setType( currentAtom->getType() );
215	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
216
217		#ifdef IS_MPI
218
219	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
219	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
220
221		#endif // is_mpi
222		}
223
224		// make the bonds
225	<	for(j=0; j<info.nBonds; j++){
225	>	for(j=0; j<molInfo.nBonds; j++){
226
227		currentBond = comp_stamps[stampID]->getBond( j );
228		theBonds[j].a = currentBond->getA() + atomOffset;
229		theBonds[j].b = currentBond->getB() + atomOffset;
230
231	<	exI = theBonds[i].a;
232	<	exJ = theBonds[i].b;
231	>	exI = theBonds[j].a;
232	>	exJ = theBonds[j].b;
233
234		// exclude_I must always be the smaller of the pair
235		if( exI > exJ ){
#	Line 775 | Line 245 | void SimSetup::makeMolecules( void ){
245
246		the_excludes[j+excludeOffset]->setPair( exI, exJ );
247		#else  // isn't MPI
248	+
249		the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
250		#endif  //is_mpi
251		}
252	<	excludeOffset += info.nBonds;
252	>	excludeOffset += molInfo.nBonds;
253
254		//make the bends
255	<	for(j=0; j<info.nBends; j++){
255	>	for(j=0; j<molInfo.nBends; j++){
256
257		currentBend = comp_stamps[stampID]->getBend( j );
258		theBends[j].a = currentBend->getA() + atomOffset;
#	Line 790 | Line 261 | void SimSetup::makeMolecules( void ){
261
262		if( currentBend->haveExtras() ){
263
264	<	extras = current_bend->getExtras();
264	>	extras = currentBend->getExtras();
265		current_extra = extras;
266
267		while( current_extra != NULL ){
#	Line 812 | Line 283 | void SimSetup::makeMolecules( void ){
283
284		default:
285		sprintf( painCave.errMsg,
286	<	"SimSetup Error: ghostVectorSource was neiter a "
286	>	"SimSetup Error: ghostVectorSource was neither a "
287		"double nor an int.\n"
288		"-->Bend[%d] in %s\n",
289		j, comp_stamps[stampID]->getID() );
#	Line 864 | Line 335 | void SimSetup::makeMolecules( void ){
335		the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
336		#endif  //is_mpi
337		}
338	<	excludeOffset += info.nBends;
338	>	excludeOffset += molInfo.nBends;
339
340	<	for(j=0; j<info.nTorsions; j++){
340	>	for(j=0; j<molInfo.nTorsions; j++){
341
342		currentTorsion = comp_stamps[stampID]->getTorsion( j );
343		theTorsions[j].a = currentTorsion->getA() + atomOffset;
#	Line 894 | Line 365 | void SimSetup::makeMolecules( void ){
365		the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
366		#endif  //is_mpi
367		}
368	<	excludeOffset += info.nTorsions;
368	>	excludeOffset += molInfo.nTorsions;
369
370
371		// send the arrays off to the forceField for init.
372
373	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
374	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
375	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
376	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
373	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
374	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
375	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
376	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
377
378
379	<	the_molecules[i].initialize( info );
380	<	atomOffset += info.nAtoms;
379	>	the_molecules[i].initialize( molInfo );
380	>
381	>
382	>	atomOffset += molInfo.nAtoms;
383	>	delete[] theBonds;
384	>	delete[] theBends;
385	>	delete[] theTorsions;
386		}
387
388	<	// clean up the forcefield
388	>	#ifdef IS_MPI
389	>	sprintf( checkPointMsg, "all molecules initialized succesfully" );
390	>	MPIcheckPoint();
391	>	#endif // is_mpi
392
393	+	// clean up the forcefield
394	+	the_ff->calcRcut();
395		the_ff->cleanMe();
396	+
397		}
398
399	+	void SimSetup::initFromBass( void ){
400
401	+	int i, j, k;
402	+	int n_cells;
403	+	double cellx, celly, cellz;
404	+	double temp1, temp2, temp3;
405	+	int n_per_extra;
406	+	int n_extra;
407	+	int have_extra, done;
408
409	<	void SimSetup::makeAtoms( void ){
409	>	temp1 = (double)tot_nmol / 4.0;
410	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
411	>	temp3 = ceil( temp2 );
412
413	<	int i, j, k, index;
414	<	double ux, uy, uz, uSqr, u;
415	<	AtomStamp* current_atom;
413	>	have_extra =0;
414	>	if( temp2 < temp3 ){ // we have a non-complete lattice
415	>	have_extra =1;
416
417	<	DirectionalAtom* dAtom;
418	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
417	>	n_cells = (int)temp3 - 1;
418	>	cellx = info->boxL[0] / temp3;
419	>	celly = info->boxL[1] / temp3;
420	>	cellz = info->boxL[2] / temp3;
421	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
422	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
423	>	n_per_extra = (int)ceil( temp1 );
424
425	<	lMolIndex = 0;
426	<	molIndex = 0;
427	<	index = 0;
428	<	for( i=0; i<n_components; i++ ){
429	<
430	<	for( j=0; j<components_nmol[i]; j++ ){
934	<
935	<	#ifdef IS_MPI
936	<	if( mpiSim->getMyMolStart() <= molIndex &&
937	<	molIndex <= mpiSim->getMyMolEnd() ){
938	<	#endif // is_mpi
939	<
940	<	molStart = index;
941	<	nMemb = comp_stamps[i]->getNAtoms();
942	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
943	<
944	<	current_atom = comp_stamps[i]->getAtom( k );
945	<	if( current_atom->haveOrientation() ){
946	<
947	<	dAtom = new DirectionalAtom(index);
948	<	simnfo->n_oriented++;
949	<	the_atoms[index] = dAtom;
950	<
951	<	ux = current_atom->getOrntX();
952	<	uy = current_atom->getOrntY();
953	<	uz = current_atom->getOrntZ();
954	<
955	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
956	<
957	<	u = sqrt( uSqr );
958	<	ux = ux / u;
959	<	uy = uy / u;
960	<	uz = uz / u;
961	<
962	<	dAtom->setSUx( ux );
963	<	dAtom->setSUy( uy );
964	<	dAtom->setSUz( uz );
965	<	}
966	<	else{
967	<	the_atoms[index] = new GeneralAtom(index);
968	<	}
969	<	the_atoms[index]->setType( current_atom->getType() );
970	<	the_atoms[index]->setIndex( index );
971	<
972	<	// increment the index and repeat;
973	<	index++;
974	<	}
975	<
976	<	molEnd = index -1;
977	<	the_molecules[lMolIndex].setNMembers( nMemb );
978	<	the_molecules[lMolIndex].setStartAtom( molStart );
979	<	the_molecules[lMolIndex].setEndAtom( molEnd );
980	<	the_molecules[lMolIndex].setStampID( i );
981	<	lMolIndex++;
982	<
983	<	#ifdef IS_MPI
984	<	}
985	<	#endif //is_mpi
986	<
987	<	molIndex++;
425	>	if( n_per_extra > 4){
426	>	sprintf( painCave.errMsg,
427	>	"SimSetup error. There has been an error in constructing"
428	>	" the non-complete lattice.\n" );
429	>	painCave.isFatal = 1;
430	>	simError();
431		}
432		}
433	+	else{
434	+	n_cells = (int)temp3;
435	+	cellx = info->boxL[0] / temp3;
436	+	celly = info->boxL[1] / temp3;
437	+	cellz = info->boxL[2] / temp3;
438	+	}
439
440	<	#ifdef IS_MPI
441	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
442	<
443	<	delete[] globalIndex;
440	>	current_mol = 0;
441	>	current_comp_mol = 0;
442	>	current_comp = 0;
443	>	current_atom_ndx = 0;
444
445	<	mpiSim->mpiRefresh();
446	<	#endif //IS_MPI
447	<
999	<	the_ff->initializeAtoms();
1000	<	}
445	>	for( i=0; i < n_cells ; i++ ){
446	>	for( j=0; j < n_cells; j++ ){
447	>	for( k=0; k < n_cells; k++ ){
448
449	<	void SimSetup::makeBonds( void ){
449	>	makeElement( i * cellx,
450	>	j * celly,
451	>	k * cellz );
452
453	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
454	<	bond_pair* the_bonds;
455	<	BondStamp* current_bond;
453	>	makeElement( i * cellx + 0.5 * cellx,
454	>	j * celly + 0.5 * celly,
455	>	k * cellz );
456
457	<	the_bonds = new bond_pair[tot_bonds];
458	<	index = 0;
459	<	offset = 0;
1011	<	molIndex = 0;
457	>	makeElement( i * cellx,
458	>	j * celly + 0.5 * celly,
459	>	k * cellz + 0.5 * cellz );
460
461	<	for( i=0; i<n_components; i++ ){
461	>	makeElement( i * cellx + 0.5 * cellx,
462	>	j * celly,
463	>	k * cellz + 0.5 * cellz );
464	>	}
465	>	}
466	>	}
467
468	<	for( j=0; j<components_nmol[i]; j++ ){
468	>	if( have_extra ){
469	>	done = 0;
470
471	<	#ifdef IS_MPI
472	<	if( mpiSim->getMyMolStart() <= molIndex &&
473	<	molIndex <= mpiSim->getMyMolEnd() ){
1020	<	#endif // is_mpi
1021	<
1022	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
1023	<
1024	<	current_bond = comp_stamps[i]->getBond( k );
1025	<	the_bonds[index].a = current_bond->getA() + offset;
1026	<	the_bonds[index].b = current_bond->getB() + offset;
471	>	int start_ndx;
472	>	for( i=0; i < (n_cells+1) && !done; i++ ){
473	>	for( j=0; j < (n_cells+1) && !done; j++ ){
474
475	<	exI = the_bonds[index].a;
1029	<	exJ = the_bonds[index].b;
475	>	if( i < n_cells ){
476
477	<	// exclude_I must always be the smaller of the pair
478	<	if( exI > exJ ){
1033	<	tempEx = exI;
1034	<	exI = exJ;
1035	<	exJ = tempEx;
477	>	if( j < n_cells ){
478	>	start_ndx = n_cells;
479		}
480	+	else start_ndx = 0;
481	+	}
482	+	else start_ndx = 0;
483
484	<
1039	<	#ifdef IS_MPI
484	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
485
486	<	the_excludes[index*2] =
487	<	the_atoms[exI]->getGlobalIndex() + 1;
488	<	the_excludes[index*2 + 1] =
489	<	the_atoms[exJ]->getGlobalIndex() + 1;
486	>	makeElement( i * cellx,
487	>	j * celly,
488	>	k * cellz );
489	>	done = ( current_mol >= tot_nmol );
490
491	<	#else  // isn't MPI
492	<
493	<	the_excludes[index*2] =     exI + 1;
494	<	the_excludes[index*2 + 1] = exJ + 1;
495	<	// fortran index from 1 (hence the +1 in the indexing)
496	<	#endif  //is_mpi
497	<
498	<	// increment the index and repeat;
499	<	index++;
491	>	if( !done && n_per_extra > 1 ){
492	>	makeElement( i * cellx + 0.5 * cellx,
493	>	j * celly + 0.5 * celly,
494	>	k * cellz );
495	>	done = ( current_mol >= tot_nmol );
496	>	}
497	>
498	>	if( !done && n_per_extra > 2){
499	>	makeElement( i * cellx,
500	>	j * celly + 0.5 * celly,
501	>	k * cellz + 0.5 * cellz );
502	>	done = ( current_mol >= tot_nmol );
503	>	}
504	>
505	>	if( !done && n_per_extra > 3){
506	>	makeElement( i * cellx + 0.5 * cellx,
507	>	j * celly,
508	>	k * cellz + 0.5 * cellz );
509	>	done = ( current_mol >= tot_nmol );
510	>	}
511		}
1056	–	offset += comp_stamps[i]->getNAtoms();
1057	–
1058	–	#ifdef IS_MPI
512		}
513	<	#endif //is_mpi
1061	<
1062	<	molIndex++;
1063	<	}
513	>	}
514		}
515
516	<	the_ff->initializeBonds( the_bonds );
516	>
517	>	for( i=0; i<info->n_atoms; i++ ){
518	>	info->atoms[i]->set_vx( 0.0 );
519	>	info->atoms[i]->set_vy( 0.0 );
520	>	info->atoms[i]->set_vz( 0.0 );
521	>	}
522		}
523
524	<	void SimSetup::makeBends( void ){
524	>	void SimSetup::makeElement( double x, double y, double z ){
525
526	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
527	<	bend_set* the_bends;
528	<	BendStamp* current_bend;
529	<	LinkedAssign* extras;
1075	<	LinkedAssign* current_extra;
1076	<
526	>	int k;
527	>	AtomStamp* current_atom;
528	>	DirectionalAtom* dAtom;
529	>	double rotMat[3][3];
530
531	<	the_bends = new bend_set[tot_bends];
1079	<	index = 0;
1080	<	offset = 0;
1081	<	molIndex = 0;
1082	<	for( i=0; i<n_components; i++ ){
531	>	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
532
533	<	for( j=0; j<components_nmol[i]; j++ ){
533	>	current_atom = comp_stamps[current_comp]->getAtom( k );
534	>	if( !current_atom->havePosition() ){
535	>	sprintf( painCave.errMsg,
536	>	"SimSetup:initFromBass error.\n"
537	>	"\tComponent %s, atom %s does not have a position specified.\n"
538	>	"\tThe initialization routine is unable to give a start"
539	>	" position.\n",
540	>	comp_stamps[current_comp]->getID(),
541	>	current_atom->getType() );
542	>	painCave.isFatal = 1;
543	>	simError();
544	>	}
545
546	<	#ifdef IS_MPI
547	<	if( mpiSim->getMyMolStart() <= molIndex &&
548	<	molIndex <= mpiSim->getMyMolEnd() ){
1089	<	#endif // is_mpi
546	>	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
547	>	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
548	>	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
549
550	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
551	<
552	<	current_bend = comp_stamps[i]->getBend( k );
553	<	the_bends[index].a = current_bend->getA() + offset;
554	<	the_bends[index].b = current_bend->getB() + offset;
555	<	the_bends[index].c = current_bend->getC() + offset;
556	<
557	<	if( current_bend->haveExtras() ){
558	<
559	<	extras = current_bend->getExtras();
560	<	current_extra = extras;
561	<
562	<	while( current_extra != NULL ){
563	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
564	<
565	<	switch( current_extra->getType() ){
566	<
567	<	case 0:
568	<	the_bends[index].ghost =
569	<	current_extra->getInt() + offset;
570	<	the_bends[index].isGhost = 1;
571	<	break;
572	<
573	<	case 1:
574	<	the_bends[index].ghost =
575	<	(int)current_extra->getDouble() + offset;
576	<	the_bends[index].isGhost = 1;
577	<	break;
578	<
579	<	default:
580	<	sprintf( painCave.errMsg,
581	<	"SimSetup Error: ghostVectorSource was neiter a "
582	<	"double nor an int.\n"
583	<	"-->Bend[%d] in %s\n",
584	<	k, comp_stamps[i]->getID() );
585	<	painCave.isFatal = 1;
586	<	simError();
587	<	}
588	<	}
589	<
590	<	else{
591	<
1133	<	sprintf( painCave.errMsg,
1134	<	"SimSetup Error: unhandled bend assignment:\n"
1135	<	"    -->%s in Bend[%d] in %s\n",
1136	<	current_extra->getlhs(),
1137	<	k, comp_stamps[i]->getID() );
1138	<	painCave.isFatal = 1;
1139	<	simError();
1140	<	}
1141	<
1142	<	current_extra = current_extra->getNext();
1143	<	}
1144	<	}
1145	<
1146	<	if( !the_bends[index].isGhost ){
1147	<
1148	<	exI = the_bends[index].a;
1149	<	exJ = the_bends[index].c;
1150	<	}
1151	<	else{
1152	<
1153	<	exI = the_bends[index].a;
1154	<	exJ = the_bends[index].b;
1155	<	}
1156	<
1157	<	// exclude_I must always be the smaller of the pair
1158	<	if( exI > exJ ){
1159	<	tempEx = exI;
1160	<	exI = exJ;
1161	<	exJ = tempEx;
1162	<	}
550	>	if( the_atoms[current_atom_ndx]->isDirectional() ){
551	>
552	>	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
553	>
554	>	rotMat[0][0] = 1.0;
555	>	rotMat[0][1] = 0.0;
556	>	rotMat[0][2] = 0.0;
557	>
558	>	rotMat[1][0] = 0.0;
559	>	rotMat[1][1] = 1.0;
560	>	rotMat[1][2] = 0.0;
561	>
562	>	rotMat[2][0] = 0.0;
563	>	rotMat[2][1] = 0.0;
564	>	rotMat[2][2] = 1.0;
565	>
566	>	dAtom->setA( rotMat );
567	>	}
568	>
569	>	current_atom_ndx++;
570	>	}
571	>
572	>	current_mol++;
573	>	current_comp_mol++;
574	>
575	>	if( current_comp_mol >= components_nmol[current_comp] ){
576	>
577	>	current_comp_mol = 0;
578	>	current_comp++;
579	>	}
580	>	}
581	>
582	>
583	>	void SimSetup::gatherInfo( void ){
584	>	int i,j,k;
585	>
586	>	ensembleCase = -1;
587	>	ffCase = -1;
588	>
589	>	// get the stamps and globals;
590	>	stamps = stamps;
591	>	globals = globals;
592
593	+	// set the easy ones first
594	+	info->target_temp = globals->getTargetTemp();
595	+	info->dt = globals->getDt();
596	+	info->run_time = globals->getRunTime();
597	+	n_components = globals->getNComponents();
598
1165	–	#ifdef IS_MPI
599
600	<	the_excludes[(index + tot_bonds)*2] =
1168	<	the_atoms[exI]->getGlobalIndex() + 1;
1169	<	the_excludes[(index + tot_bonds)*2 + 1] =
1170	<	the_atoms[exJ]->getGlobalIndex() + 1;
1171	<
1172	<	#else  // isn't MPI
1173	<
1174	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
1175	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1176	<	// fortran index from 1 (hence the +1 in the indexing)
1177	<	#endif  //is_mpi
1178	<
1179	<
1180	<	// increment the index and repeat;
1181	<	index++;
1182	<	}
1183	<	offset += comp_stamps[i]->getNAtoms();
1184	<
1185	<	#ifdef IS_MPI
1186	<	}
1187	<	#endif //is_mpi
600	>	// get the forceField
601
602	<	molIndex++;
603	<	}
602	>	strcpy( force_field, globals->getForceField() );
603	>
604	>	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
605	>	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
606	>	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
607	>	else{
608	>	sprintf( painCave.errMsg,
609	>	"SimSetup Error. Unrecognized force field -> %s\n",
610	>	force_field );
611	>	painCave.isFatal = 1;
612	>	simError();
613		}
614
615	<	#ifdef IS_MPI
1194	<	sprintf( checkPointMsg,
1195	<	"Successfully created the bends list.\n" );
1196	<	MPIcheckPoint();
1197	<	#endif // is_mpi
1198	<
615	>	// get the ensemble
616
617	<	the_ff->initializeBends( the_bends );
1201	<	}
617	>	strcpy( ensemble, globals->getEnsemble() );
618
619	<	void SimSetup::makeTorsions( void ){
619	>	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
620	>	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
621	>	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
622	>	ensembleCase = NPTi_ENS;
623	>	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
624	>	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
625	>	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
626	>	else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS;
627	>	else{
628	>	sprintf( painCave.errMsg,
629	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
630	>	"reverting to NVE for this simulation.\n",
631	>	ensemble );
632	>	painCave.isFatal = 0;
633	>	simError();
634	>	strcpy( ensemble, "NVE" );
635	>	ensembleCase = NVE_ENS;
636	>	}
637	>	strcpy( info->ensemble, ensemble );
638
639	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1206	<	torsion_set* the_torsions;
1207	<	TorsionStamp* current_torsion;
639	>	// get the mixing rule
640
641	<	the_torsions = new torsion_set[tot_torsions];
642	<	index = 0;
1211	<	offset = 0;
1212	<	molIndex = 0;
1213	<	for( i=0; i<n_components; i++ ){
1214	<
1215	<	for( j=0; j<components_nmol[i]; j++ ){
1216	<
1217	<	#ifdef IS_MPI
1218	<	if( mpiSim->getMyMolStart() <= molIndex &&
1219	<	molIndex <= mpiSim->getMyMolEnd() ){
1220	<	#endif // is_mpi
1221	<
1222	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1223	<
1224	<	current_torsion = comp_stamps[i]->getTorsion( k );
1225	<	the_torsions[index].a = current_torsion->getA() + offset;
1226	<	the_torsions[index].b = current_torsion->getB() + offset;
1227	<	the_torsions[index].c = current_torsion->getC() + offset;
1228	<	the_torsions[index].d = current_torsion->getD() + offset;
1229	<
1230	<	exI = the_torsions[index].a;
1231	<	exJ = the_torsions[index].d;
1232	<
641	>	strcpy( info->mixingRule, globals->getMixingRule() );
642	>	info->usePBC = globals->getPBC();
643
644	<	// exclude_I must always be the smaller of the pair
645	<	if( exI > exJ ){
646	<	tempEx = exI;
647	<	exI = exJ;
648	<	exJ = tempEx;
1239	<	}
644	>
645	>	// get the components and calculate the tot_nMol and indvidual n_mol
646	>
647	>	the_components = globals->getComponents();
648	>	components_nmol = new int[n_components];
649
650
651	<	#ifdef IS_MPI
652	<
653	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
1245	<	the_atoms[exI]->getGlobalIndex() + 1;
1246	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1247	<	the_atoms[exJ]->getGlobalIndex() + 1;
1248	<
1249	<	#else  // isn't MPI
1250	<
1251	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1252	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1253	<	// fortran indexes from 1 (hence the +1 in the indexing)
1254	<	#endif  //is_mpi
1255	<
651	>	if( !globals->haveNMol() ){
652	>	// we don't have the total number of molecules, so we assume it is
653	>	// given in each component
654
655	<	// increment the index and repeat;
656	<	index++;
1259	<	}
1260	<	offset += comp_stamps[i]->getNAtoms();
655	>	tot_nmol = 0;
656	>	for( i=0; i<n_components; i++ ){
657
658	<	#ifdef IS_MPI
658	>	if( !the_components[i]->haveNMol() ){
659	>	// we have a problem
660	>	sprintf( painCave.errMsg,
661	>	"SimSetup Error. No global NMol or component NMol"
662	>	" given. Cannot calculate the number of atoms.\n" );
663	>	painCave.isFatal = 1;
664	>	simError();
665		}
1264	–	#endif //is_mpi
666
667	<	molIndex++;
667	>	tot_nmol += the_components[i]->getNMol();
668	>	components_nmol[i] = the_components[i]->getNMol();
669		}
670		}
671	+	else{
672	+	sprintf( painCave.errMsg,
673	+	"SimSetup error.\n"
674	+	"\tSorry, the ability to specify total"
675	+	" nMols and then give molfractions in the components\n"
676	+	"\tis not currently supported."
677	+	" Please give nMol in the components.\n" );
678	+	painCave.isFatal = 1;
679	+	simError();
680	+	}
681
682	<	the_ff->initializeTorsions( the_torsions );
683	<	}
682	>	// set the status, sample, and thermal kick times
683	>
684	>	if( globals->haveSampleTime() ){
685	>	info->sampleTime = globals->getSampleTime();
686	>	info->statusTime = info->sampleTime;
687	>	info->thermalTime = info->sampleTime;
688	>	}
689	>	else{
690	>	info->sampleTime = globals->getRunTime();
691	>	info->statusTime = info->sampleTime;
692	>	info->thermalTime = info->sampleTime;
693	>	}
694
695	<	void SimSetup::initFromBass( void ){
695	>	if( globals->haveStatusTime() ){
696	>	info->statusTime = globals->getStatusTime();
697	>	}
698
699	<	int i, j, k;
700	<	int n_cells;
701	<	double cellx, celly, cellz;
1278	<	double temp1, temp2, temp3;
1279	<	int n_per_extra;
1280	<	int n_extra;
1281	<	int have_extra, done;
699	>	if( globals->haveThermalTime() ){
700	>	info->thermalTime = globals->getThermalTime();
701	>	}
702
703	<	temp1 = (double)tot_nmol / 4.0;
1284	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1285	<	temp3 = ceil( temp2 );
703	>	// check for the temperature set flag
704
705	<	have_extra =0;
1288	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1289	<	have_extra =1;
705	>	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
706
707	<	n_cells = (int)temp3 - 1;
1292	<	cellx = simnfo->box_x / temp3;
1293	<	celly = simnfo->box_y / temp3;
1294	<	cellz = simnfo->box_z / temp3;
1295	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1296	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1297	<	n_per_extra = (int)ceil( temp1 );
707	>	// get some of the tricky things that may still be in the globals
708
709	<	if( n_per_extra > 4){
709	>	double boxVector[3];
710	>	if( globals->haveBox() ){
711	>	boxVector[0] = globals->getBox();
712	>	boxVector[1] = globals->getBox();
713	>	boxVector[2] = globals->getBox();
714	>
715	>	info->setBox( boxVector );
716	>	}
717	>	else if( globals->haveDensity() ){
718	>
719	>	double vol;
720	>	vol = (double)tot_nmol / globals->getDensity();
721	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
722	>	boxVector[1] = boxVector[0];
723	>	boxVector[2] = boxVector[0];
724	>
725	>	info->setBox( boxVector );
726	>	}
727	>	else{
728	>	if( !globals->haveBoxX() ){
729		sprintf( painCave.errMsg,
730	<	"SimSetup error. There has been an error in constructing"
1302	<	" the non-complete lattice.\n" );
730	>	"SimSetup error, no periodic BoxX size given.\n" );
731		painCave.isFatal = 1;
732		simError();
733		}
734	+	boxVector[0] = globals->getBoxX();
735	+
736	+	if( !globals->haveBoxY() ){
737	+	sprintf( painCave.errMsg,
738	+	"SimSetup error, no periodic BoxY size given.\n" );
739	+	painCave.isFatal = 1;
740	+	simError();
741	+	}
742	+	boxVector[1] = globals->getBoxY();
743	+
744	+	if( !globals->haveBoxZ() ){
745	+	sprintf( painCave.errMsg,
746	+	"SimSetup error, no periodic BoxZ size given.\n" );
747	+	painCave.isFatal = 1;
748	+	simError();
749	+	}
750	+	boxVector[2] = globals->getBoxZ();
751	+
752	+	info->setBox( boxVector );
753		}
1307	–	else{
1308	–	n_cells = (int)temp3;
1309	–	cellx = simnfo->box_x / temp3;
1310	–	celly = simnfo->box_y / temp3;
1311	–	cellz = simnfo->box_z / temp3;
1312	–	}
754
1314	–	current_mol = 0;
1315	–	current_comp_mol = 0;
1316	–	current_comp = 0;
1317	–	current_atom_ndx = 0;
755
756	<	for( i=0; i < n_cells ; i++ ){
757	<	for( j=0; j < n_cells; j++ ){
758	<	for( k=0; k < n_cells; k++ ){
756	>
757	>	#ifdef IS_MPI
758	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
759	>	MPIcheckPoint();
760	>	#endif // is_mpi
761
762	<	makeElement( i * cellx,
1324	<	j * celly,
1325	<	k * cellz );
762	>	}
763
1327	–	makeElement( i * cellx + 0.5 * cellx,
1328	–	j * celly + 0.5 * celly,
1329	–	k * cellz );
764
765	<	makeElement( i * cellx,
766	<	j * celly + 0.5 * celly,
767	<	k * cellz + 0.5 * cellz );
765	>	void SimSetup::finalInfoCheck( void ){
766	>	int index;
767	>	int usesDipoles;
768	>
769
770	<	makeElement( i * cellx + 0.5 * cellx,
771	<	j * celly,
772	<	k * cellz + 0.5 * cellz );
770	>	// check electrostatic parameters
771	>
772	>	index = 0;
773	>	usesDipoles = 0;
774	>	while( (index < info->n_atoms) && !usesDipoles ){
775	>	usesDipoles = ((info->atoms)[index])->hasDipole();
776	>	index++;
777	>	}
778	>
779	>	#ifdef IS_MPI
780	>	int myUse = usesDipoles;
781	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
782	>	#endif //is_mpi
783	>
784	>	double theEcr, theEst;
785	>
786	>	if (globals->getUseRF() ) {
787	>	info->useReactionField = 1;
788	>
789	>	if( !globals->haveECR() ){
790	>	sprintf( painCave.errMsg,
791	>	"SimSetup Warning: using default value of 1/2 the smallest "
792	>	"box length for the electrostaticCutoffRadius.\n"
793	>	"I hope you have a very fast processor!\n");
794	>	painCave.isFatal = 0;
795	>	simError();
796	>	double smallest;
797	>	smallest = info->boxL[0];
798	>	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
799	>	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
800	>	theEcr = 0.5 * smallest;
801	>	} else {
802	>	theEcr = globals->getECR();
803	>	}
804	>
805	>	if( !globals->haveEST() ){
806	>	sprintf( painCave.errMsg,
807	>	"SimSetup Warning: using default value of 0.05 * the "
808	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
809	>	);
810	>	painCave.isFatal = 0;
811	>	simError();
812	>	theEst = 0.05 * theEcr;
813	>	} else {
814	>	theEst= globals->getEST();
815	>	}
816	>
817	>	info->setEcr( theEcr, theEst );
818	>
819	>	if(!globals->haveDielectric() ){
820	>	sprintf( painCave.errMsg,
821	>	"SimSetup Error: You are trying to use Reaction Field without"
822	>	"setting a dielectric constant!\n"
823	>	);
824	>	painCave.isFatal = 1;
825	>	simError();
826	>	}
827	>	info->dielectric = globals->getDielectric();
828	>	}
829	>	else {
830	>	if (usesDipoles) {
831	>
832	>	if( !globals->haveECR() ){
833	>	sprintf( painCave.errMsg,
834	>	"SimSetup Warning: using default value of 1/2 the smallest "
835	>	"box length for the electrostaticCutoffRadius.\n"
836	>	"I hope you have a very fast processor!\n");
837	>	painCave.isFatal = 0;
838	>	simError();
839	>	double smallest;
840	>	smallest = info->boxL[0];
841	>	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
842	>	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
843	>	theEcr = 0.5 * smallest;
844	>	} else {
845	>	theEcr = globals->getECR();
846		}
847	+
848	+	if( !globals->haveEST() ){
849	+	sprintf( painCave.errMsg,
850	+	"SimSetup Warning: using default value of 0.05 * the "
851	+	"electrostaticCutoffRadius for the "
852	+	"electrostaticSkinThickness\n"
853	+	);
854	+	painCave.isFatal = 0;
855	+	simError();
856	+	theEst = 0.05 * theEcr;
857	+	} else {
858	+	theEst= globals->getEST();
859	+	}
860	+
861	+	info->setEcr( theEcr, theEst );
862		}
863	<	}
863	>	}
864
865	<	if( have_extra ){
866	<	done = 0;
865	>	#ifdef IS_MPI
866	>	strcpy( checkPointMsg, "post processing checks out" );
867	>	MPIcheckPoint();
868	>	#endif // is_mpi
869
870	<	int start_ndx;
1346	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1347	<	for( j=0; j < (n_cells+1) && !done; j++ ){
870	>	}
871
872	<	if( i < n_cells ){
872	>	void SimSetup::initSystemCoords( void ){
873
874	<	if( j < n_cells ){
875	<	start_ndx = n_cells;
876	<	}
877	<	else start_ndx = 0;
874	>	if( globals->haveInitialConfig() ){
875	>
876	>	InitializeFromFile* fileInit;
877	>	#ifdef IS_MPI // is_mpi
878	>	if( worldRank == 0 ){
879	>	#endif //is_mpi
880	>	fileInit = new InitializeFromFile( globals->getInitialConfig() );
881	>	#ifdef IS_MPI
882	>	}else fileInit = new InitializeFromFile( NULL );
883	>	#endif
884	>	fileInit->readInit( info ); // default velocities on
885	>
886	>	delete fileInit;
887	>	}
888	>	else{
889	>
890	>	#ifdef IS_MPI
891	>
892	>	// no init from bass
893	>
894	>	sprintf( painCave.errMsg,
895	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
896	>	painCave.isFatal;
897	>	simError();
898	>
899	>	#else
900	>
901	>	initFromBass();
902	>
903	>
904	>	#endif
905	>	}
906	>
907	>	#ifdef IS_MPI
908	>	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
909	>	MPIcheckPoint();
910	>	#endif // is_mpi
911	>
912	>	}
913	>
914	>
915	>	void SimSetup::makeOutNames( void ){
916	>
917	>	#ifdef IS_MPI
918	>	if( worldRank == 0 ){
919	>	#endif // is_mpi
920	>
921	>	if( globals->haveFinalConfig() ){
922	>	strcpy( info->finalName, globals->getFinalConfig() );
923	>	}
924	>	else{
925	>	strcpy( info->finalName, inFileName );
926	>	char* endTest;
927	>	int nameLength = strlen( info->finalName );
928	>	endTest = &(info->finalName[nameLength - 5]);
929	>	if( !strcmp( endTest, ".bass" ) ){
930	>	strcpy( endTest, ".eor" );
931	>	}
932	>	else if( !strcmp( endTest, ".BASS" ) ){
933	>	strcpy( endTest, ".eor" );
934	>	}
935	>	else{
936	>	endTest = &(info->finalName[nameLength - 4]);
937	>	if( !strcmp( endTest, ".bss" ) ){
938	>	strcpy( endTest, ".eor" );
939		}
940	<	else start_ndx = 0;
940	>	else if( !strcmp( endTest, ".mdl" ) ){
941	>	strcpy( endTest, ".eor" );
942	>	}
943	>	else{
944	>	strcat( info->finalName, ".eor" );
945	>	}
946	>	}
947	>	}
948	>
949	>	// make the sample and status out names
950	>
951	>	strcpy( info->sampleName, inFileName );
952	>	char* endTest;
953	>	int nameLength = strlen( info->sampleName );
954	>	endTest = &(info->sampleName[nameLength - 5]);
955	>	if( !strcmp( endTest, ".bass" ) ){
956	>	strcpy( endTest, ".dump" );
957	>	}
958	>	else if( !strcmp( endTest, ".BASS" ) ){
959	>	strcpy( endTest, ".dump" );
960	>	}
961	>	else{
962	>	endTest = &(info->sampleName[nameLength - 4]);
963	>	if( !strcmp( endTest, ".bss" ) ){
964	>	strcpy( endTest, ".dump" );
965	>	}
966	>	else if( !strcmp( endTest, ".mdl" ) ){
967	>	strcpy( endTest, ".dump" );
968	>	}
969	>	else{
970	>	strcat( info->sampleName, ".dump" );
971	>	}
972	>	}
973	>
974	>	strcpy( info->statusName, inFileName );
975	>	nameLength = strlen( info->statusName );
976	>	endTest = &(info->statusName[nameLength - 5]);
977	>	if( !strcmp( endTest, ".bass" ) ){
978	>	strcpy( endTest, ".stat" );
979	>	}
980	>	else if( !strcmp( endTest, ".BASS" ) ){
981	>	strcpy( endTest, ".stat" );
982	>	}
983	>	else{
984	>	endTest = &(info->statusName[nameLength - 4]);
985	>	if( !strcmp( endTest, ".bss" ) ){
986	>	strcpy( endTest, ".stat" );
987	>	}
988	>	else if( !strcmp( endTest, ".mdl" ) ){
989	>	strcpy( endTest, ".stat" );
990	>	}
991	>	else{
992	>	strcat( info->statusName, ".stat" );
993	>	}
994	>	}
995	>
996	>	#ifdef IS_MPI
997	>	}
998	>	#endif // is_mpi
999
1000	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1000	>	}
1001
1360	–	makeElement( i * cellx,
1361	–	j * celly,
1362	–	k * cellz );
1363	–	done = ( current_mol >= tot_nmol );
1002
1003	<	if( !done && n_per_extra > 1 ){
1366	<	makeElement( i * cellx + 0.5 * cellx,
1367	<	j * celly + 0.5 * celly,
1368	<	k * cellz );
1369	<	done = ( current_mol >= tot_nmol );
1370	<	}
1003	>	void SimSetup::sysObjectsCreation( void ){
1004
1005	<	if( !done && n_per_extra > 2){
1006	<	makeElement( i * cellx,
1007	<	j * celly + 0.5 * celly,
1008	<	k * cellz + 0.5 * cellz );
1009	<	done = ( current_mol >= tot_nmol );
1010	<	}
1005	>	int i;
1006	>
1007	>	// create the forceField
1008	>
1009	>	createFF();
1010	>
1011	>	// extract componentList
1012
1013	<	if( !done && n_per_extra > 3){
1014	<	makeElement( i * cellx + 0.5 * cellx,
1015	<	j * celly,
1016	<	k * cellz + 0.5 * cellz );
1017	<	done = ( current_mol >= tot_nmol );
1018	<	}
1019	<	}
1013	>	compList();
1014	>
1015	>	// calc the number of atoms, bond, bends, and torsions
1016	>
1017	>	calcSysValues();
1018	>
1019	>	#ifdef IS_MPI
1020	>	// divide the molecules among the processors
1021	>
1022	>	mpiMolDivide();
1023	>	#endif //is_mpi
1024	>
1025	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1026	>
1027	>	makeSysArrays();
1028	>
1029	>	// make and initialize the molecules (all but atomic coordinates)
1030	>
1031	>	makeMolecules();
1032	>	info->identArray = new int[info->n_atoms];
1033	>	for(i=0; i<info->n_atoms; i++){
1034	>	info->identArray[i] = the_atoms[i]->getIdent();
1035	>	}
1036	>
1037	>
1038	>
1039	>	}
1040	>
1041	>
1042	>	void SimSetup::createFF( void ){
1043	>
1044	>	switch( ffCase ){
1045	>
1046	>	case FF_DUFF:
1047	>	the_ff = new DUFF();
1048	>	break;
1049	>
1050	>	case FF_LJ:
1051	>	the_ff = new LJFF();
1052	>	break;
1053	>
1054	>	case FF_EAM:
1055	>	the_ff = new EAM_FF();
1056	>	break;
1057	>
1058	>	default:
1059	>	sprintf( painCave.errMsg,
1060	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1061	>	painCave.isFatal = 1;
1062	>	simError();
1063	>	}
1064	>
1065	>	#ifdef IS_MPI
1066	>	strcpy( checkPointMsg, "ForceField creation successful" );
1067	>	MPIcheckPoint();
1068	>	#endif // is_mpi
1069	>
1070	>	}
1071	>
1072	>
1073	>	void SimSetup::compList( void ){
1074	>
1075	>	int i;
1076	>
1077	>	comp_stamps = new MoleculeStamp*[n_components];
1078	>
1079	>	// make an array of molecule stamps that match the components used.
1080	>	// also extract the used stamps out into a separate linked list
1081	>
1082	>	info->nComponents = n_components;
1083	>	info->componentsNmol = components_nmol;
1084	>	info->compStamps = comp_stamps;
1085	>	info->headStamp = new LinkedMolStamp();
1086	>
1087	>	char* id;
1088	>	LinkedMolStamp* headStamp = info->headStamp;
1089	>	LinkedMolStamp* currentStamp = NULL;
1090	>	for( i=0; i<n_components; i++ ){
1091	>
1092	>	id = the_components[i]->getType();
1093	>	comp_stamps[i] = NULL;
1094	>
1095	>	// check to make sure the component isn't already in the list
1096	>
1097	>	comp_stamps[i] = headStamp->match( id );
1098	>	if( comp_stamps[i] == NULL ){
1099	>
1100	>	// extract the component from the list;
1101	>
1102	>	currentStamp = stamps->extractMolStamp( id );
1103	>	if( currentStamp == NULL ){
1104	>	sprintf( painCave.errMsg,
1105	>	"SimSetup error: Component \"%s\" was not found in the "
1106	>	"list of declared molecules\n",
1107	>	id );
1108	>	painCave.isFatal = 1;
1109	>	simError();
1110		}
1111	+
1112	+	headStamp->add( currentStamp );
1113	+	comp_stamps[i] = headStamp->match( id );
1114		}
1115		}
1116
1117	+	#ifdef IS_MPI
1118	+	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1119	+	MPIcheckPoint();
1120	+	#endif // is_mpi
1121
1122	<	for( i=0; i<simnfo->n_atoms; i++ ){
1123	<	simnfo->atoms[i]->set_vx( 0.0 );
1124	<	simnfo->atoms[i]->set_vy( 0.0 );
1125	<	simnfo->atoms[i]->set_vz( 0.0 );
1122	>
1123	>	}
1124	>
1125	>	void SimSetup::calcSysValues( void ){
1126	>	int i, j, k;
1127	>
1128	>
1129	>	tot_atoms = 0;
1130	>	tot_bonds = 0;
1131	>	tot_bends = 0;
1132	>	tot_torsions = 0;
1133	>	for( i=0; i<n_components; i++ ){
1134	>
1135	>	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1136	>	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1137	>	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1138	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1139		}
1140	+
1141	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1142	+
1143	+	info->n_atoms = tot_atoms;
1144	+	info->n_bonds = tot_bonds;
1145	+	info->n_bends = tot_bends;
1146	+	info->n_torsions = tot_torsions;
1147	+	info->n_SRI = tot_SRI;
1148	+	info->n_mol = tot_nmol;
1149	+
1150	+	info->molMembershipArray = new int[tot_atoms];
1151		}
1152
1398	–	void SimSetup::makeElement( double x, double y, double z ){
1153
1154	<	int k;
1401	<	AtomStamp* current_atom;
1402	<	DirectionalAtom* dAtom;
1403	<	double rotMat[3][3];
1154	>	#ifdef IS_MPI
1155
1156	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1156	>	void SimSetup::mpiMolDivide( void ){
1157	>
1158	>	int i, j, k;
1159	>	int localMol, allMol;
1160	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1161
1162	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1163	<	if( !current_atom->havePosition() ){
1164	<	sprintf( painCave.errMsg,
1165	<	"SimSetup:initFromBass error.\n"
1166	<	"\tComponent %s, atom %s does not have a position specified.\n"
1167	<	"\tThe initialization routine is unable to give a start"
1168	<	" position.\n",
1169	<	comp_stamps[current_comp]->getID(),
1170	<	current_atom->getType() );
1171	<	painCave.isFatal = 1;
1172	<	simError();
1162	>	mpiSim = new mpiSimulation( info );
1163	>
1164	>	globalIndex = mpiSim->divideLabor();
1165	>
1166	>	// set up the local variables
1167	>
1168	>	mol2proc = mpiSim->getMolToProcMap();
1169	>	molCompType = mpiSim->getMolComponentType();
1170	>
1171	>	allMol = 0;
1172	>	localMol = 0;
1173	>	local_atoms = 0;
1174	>	local_bonds = 0;
1175	>	local_bends = 0;
1176	>	local_torsions = 0;
1177	>	globalAtomIndex = 0;
1178	>
1179	>
1180	>	for( i=0; i<n_components; i++ ){
1181	>
1182	>	for( j=0; j<components_nmol[i]; j++ ){
1183	>
1184	>	if( mol2proc[allMol] == worldRank ){
1185	>
1186	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1187	>	local_bonds +=    comp_stamps[i]->getNBonds();
1188	>	local_bends +=    comp_stamps[i]->getNBends();
1189	>	local_torsions += comp_stamps[i]->getNTorsions();
1190	>	localMol++;
1191	>	}
1192	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1193	>	info->molMembershipArray[globalAtomIndex] = allMol;
1194	>	globalAtomIndex++;
1195	>	}
1196	>
1197	>	allMol++;
1198		}
1199	+	}
1200	+	local_SRI = local_bonds + local_bends + local_torsions;
1201	+
1202	+	info->n_atoms = mpiSim->getMyNlocal();
1203	+
1204	+	if( local_atoms != info->n_atoms ){
1205	+	sprintf( painCave.errMsg,
1206	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1207	+	" localAtom (%d) are not equal.\n",
1208	+	info->n_atoms,
1209	+	local_atoms );
1210	+	painCave.isFatal = 1;
1211	+	simError();
1212	+	}
1213
1214	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1215	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1216	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1214	>	info->n_bonds = local_bonds;
1215	>	info->n_bends = local_bends;
1216	>	info->n_torsions = local_torsions;
1217	>	info->n_SRI = local_SRI;
1218	>	info->n_mol = localMol;
1219
1220	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1220	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1221	>	MPIcheckPoint();
1222	>	}
1223	>
1224	>	#endif // is_mpi
1225
1426	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1226
1227	<	rotMat[0][0] = 1.0;
1228	<	rotMat[0][1] = 0.0;
1430	<	rotMat[0][2] = 0.0;
1227	>	void SimSetup::makeSysArrays( void ){
1228	>	int i, j, k;
1229
1432	–	rotMat[1][0] = 0.0;
1433	–	rotMat[1][1] = 1.0;
1434	–	rotMat[1][2] = 0.0;
1230
1231	<	rotMat[2][0] = 0.0;
1437	<	rotMat[2][1] = 0.0;
1438	<	rotMat[2][2] = 1.0;
1231	>	// create the atom and short range interaction arrays
1232
1233	<	dAtom->setA( rotMat );
1233	>	Atom::createArrays(info->n_atoms);
1234	>	the_atoms = new Atom*[info->n_atoms];
1235	>	the_molecules = new Molecule[info->n_mol];
1236	>	int molIndex;
1237	>
1238	>	// initialize the molecule's stampID's
1239	>
1240	>	#ifdef IS_MPI
1241	>
1242	>
1243	>	molIndex = 0;
1244	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1245	>
1246	>	if(mol2proc[i] == worldRank ){
1247	>	the_molecules[molIndex].setStampID( molCompType[i] );
1248	>	the_molecules[molIndex].setMyIndex( molIndex );
1249	>	the_molecules[molIndex].setGlobalIndex( i );
1250	>	molIndex++;
1251		}
1252	+	}
1253
1254	<	current_atom_ndx++;
1254	>	#else // is_mpi
1255	>
1256	>	molIndex = 0;
1257	>	globalAtomIndex = 0;
1258	>	for(i=0; i<n_components; i++){
1259	>	for(j=0; j<components_nmol[i]; j++ ){
1260	>	the_molecules[molIndex].setStampID( i );
1261	>	the_molecules[molIndex].setMyIndex( molIndex );
1262	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1263	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1264	>	info->molMembershipArray[globalAtomIndex] = molIndex;
1265	>	globalAtomIndex++;
1266	>	}
1267	>	molIndex++;
1268	>	}
1269		}
1270	+
1271
1272	<	current_mol++;
1447	<	current_comp_mol++;
1272	>	#endif // is_mpi
1273
1449	–	if( current_comp_mol >= components_nmol[current_comp] ){
1274
1275	<	current_comp_mol = 0;
1276	<	current_comp++;
1275	>	if( info->n_SRI ){
1276	>
1277	>	Exclude::createArray(info->n_SRI);
1278	>	the_excludes = new Exclude*[info->n_SRI];
1279	>	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1280	>	info->globalExcludes = new int;
1281	>	info->n_exclude = info->n_SRI;
1282		}
1283	+	else{
1284	+
1285	+	Exclude::createArray( 1 );
1286	+	the_excludes = new Exclude*;
1287	+	the_excludes[0] = new Exclude(0);
1288	+	the_excludes[0]->setPair( 0,0 );
1289	+	info->globalExcludes = new int;
1290	+	info->globalExcludes[0] = 0;
1291	+	info->n_exclude = 0;
1292	+	}
1293	+
1294	+	// set the arrays into the SimInfo object
1295	+
1296	+	info->atoms = the_atoms;
1297	+	info->molecules = the_molecules;
1298	+	info->nGlobalExcludes = 0;
1299	+	info->excludes = the_excludes;
1300	+
1301	+	the_ff->setSimInfo( info );
1302	+
1303		}
1304	+
1305	+	void SimSetup::makeIntegrator( void ){
1306	+
1307	+	NVT<RealIntegrator>*  myNVT = NULL;
1308	+	NPTi<RealIntegrator>* myNPTi = NULL;
1309	+	NPTf<RealIntegrator>* myNPTf = NULL;
1310	+	NPTim<RealIntegrator>* myNPTim = NULL;
1311	+	NPTfm<RealIntegrator>* myNPTfm = NULL;
1312	+	ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1313	+
1314	+	cerr << "setting integrator" <<endl;
1315	+
1316	+	switch( ensembleCase ){
1317	+
1318	+	case NVE_ENS:
1319	+	new NVE<RealIntegrator>( info, the_ff );
1320	+	break;
1321	+
1322	+	case NVT_ENS:
1323	+	myNVT = new NVT<RealIntegrator>( info, the_ff );
1324	+	myNVT->setTargetTemp(globals->getTargetTemp());
1325	+
1326	+	if (globals->haveTauThermostat())
1327	+	myNVT->setTauThermostat(globals->getTauThermostat());
1328	+
1329	+	else {
1330	+	sprintf( painCave.errMsg,
1331	+	"SimSetup error: If you use the NVT\n"
1332	+	"    ensemble, you must set tauThermostat.\n");
1333	+	painCave.isFatal = 1;
1334	+	simError();
1335	+	}
1336	+	break;
1337	+
1338	+	case NPTi_ENS:
1339	+	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1340	+	myNPTi->setTargetTemp( globals->getTargetTemp() );
1341	+
1342	+	if (globals->haveTargetPressure())
1343	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1344	+	else {
1345	+	sprintf( painCave.errMsg,
1346	+	"SimSetup error: If you use a constant pressure\n"
1347	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1348	+	painCave.isFatal = 1;
1349	+	simError();
1350	+	}
1351	+
1352	+	if( globals->haveTauThermostat() )
1353	+	myNPTi->setTauThermostat( globals->getTauThermostat() );
1354	+	else{
1355	+	sprintf( painCave.errMsg,
1356	+	"SimSetup error: If you use an NPT\n"
1357	+	"    ensemble, you must set tauThermostat.\n");
1358	+	painCave.isFatal = 1;
1359	+	simError();
1360	+	}
1361	+
1362	+	if( globals->haveTauBarostat() )
1363	+	myNPTi->setTauBarostat( globals->getTauBarostat() );
1364	+	else{
1365	+	sprintf( painCave.errMsg,
1366	+	"SimSetup error: If you use an NPT\n"
1367	+	"    ensemble, you must set tauBarostat.\n");
1368	+	painCave.isFatal = 1;
1369	+	simError();
1370	+	}
1371	+	break;
1372	+
1373	+	case NPTf_ENS:
1374	+	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1375	+	myNPTf->setTargetTemp( globals->getTargetTemp());
1376	+
1377	+	if (globals->haveTargetPressure())
1378	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1379	+	else {
1380	+	sprintf( painCave.errMsg,
1381	+	"SimSetup error: If you use a constant pressure\n"
1382	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1383	+	painCave.isFatal = 1;
1384	+	simError();
1385	+	}
1386	+
1387	+	if( globals->haveTauThermostat() )
1388	+	myNPTf->setTauThermostat( globals->getTauThermostat() );
1389	+	else{
1390	+	sprintf( painCave.errMsg,
1391	+	"SimSetup error: If you use an NPT\n"
1392	+	"    ensemble, you must set tauThermostat.\n");
1393	+	painCave.isFatal = 1;
1394	+	simError();
1395	+	}
1396	+
1397	+	if( globals->haveTauBarostat() )
1398	+	myNPTf->setTauBarostat( globals->getTauBarostat() );
1399	+	else{
1400	+	sprintf( painCave.errMsg,
1401	+	"SimSetup error: If you use an NPT\n"
1402	+	"    ensemble, you must set tauBarostat.\n");
1403	+	painCave.isFatal = 1;
1404	+	simError();
1405	+	}
1406	+	break;
1407	+
1408	+	case NPTim_ENS:
1409	+	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1410	+	myNPTim->setTargetTemp( globals->getTargetTemp());
1411	+
1412	+	if (globals->haveTargetPressure())
1413	+	myNPTim->setTargetPressure(globals->getTargetPressure());
1414	+	else {
1415	+	sprintf( painCave.errMsg,
1416	+	"SimSetup error: If you use a constant pressure\n"
1417	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1418	+	painCave.isFatal = 1;
1419	+	simError();
1420	+	}
1421	+
1422	+	if( globals->haveTauThermostat() )
1423	+	myNPTim->setTauThermostat( globals->getTauThermostat() );
1424	+	else{
1425	+	sprintf( painCave.errMsg,
1426	+	"SimSetup error: If you use an NPT\n"
1427	+	"    ensemble, you must set tauThermostat.\n");
1428	+	painCave.isFatal = 1;
1429	+	simError();
1430	+	}
1431	+
1432	+	if( globals->haveTauBarostat() )
1433	+	myNPTim->setTauBarostat( globals->getTauBarostat() );
1434	+	else{
1435	+	sprintf( painCave.errMsg,
1436	+	"SimSetup error: If you use an NPT\n"
1437	+	"    ensemble, you must set tauBarostat.\n");
1438	+	painCave.isFatal = 1;
1439	+	simError();
1440	+	}
1441	+	break;
1442	+
1443	+	case NPTfm_ENS:
1444	+	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1445	+	myNPTfm->setTargetTemp( globals->getTargetTemp());
1446	+
1447	+	if (globals->haveTargetPressure())
1448	+	myNPTfm->setTargetPressure(globals->getTargetPressure());
1449	+	else {
1450	+	sprintf( painCave.errMsg,
1451	+	"SimSetup error: If you use a constant pressure\n"
1452	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1453	+	painCave.isFatal = 1;
1454	+	simError();
1455	+	}
1456	+
1457	+	if( globals->haveTauThermostat() )
1458	+	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1459	+	else{
1460	+	sprintf( painCave.errMsg,
1461	+	"SimSetup error: If you use an NPT\n"
1462	+	"    ensemble, you must set tauThermostat.\n");
1463	+	painCave.isFatal = 1;
1464	+	simError();
1465	+	}
1466	+
1467	+	if( globals->haveTauBarostat() )
1468	+	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1469	+	else{
1470	+	sprintf( painCave.errMsg,
1471	+	"SimSetup error: If you use an NPT\n"
1472	+	"    ensemble, you must set tauBarostat.\n");
1473	+	painCave.isFatal = 1;
1474	+	simError();
1475	+	}
1476	+	break;
1477	+
1478	+	case NVEZCONS_ENS:
1479	+	{
1480	+
1481	+	if(globals->haveZConsTime()){
1482	+
1483	+	//add sample time of z-constraint  into SimInfo's property list
1484	+	DoubleData* zconsTimeProp = new DoubleData();
1485	+	zconsTimeProp->setID("zconstime");
1486	+	zconsTimeProp->setData(globals->getZConsTime());
1487	+	info->addProperty(zconsTimeProp);
1488	+	}
1489	+	else{
1490	+	sprintf( painCave.errMsg,
1491	+	"ZConstraint error: If you use an ZConstraint\n"
1492	+	" , you must set sample time.\n");
1493	+	painCave.isFatal = 1;
1494	+	simError();
1495	+	}
1496	+
1497	+	if(globals->haveIndexOfAllZConsMols()){
1498	+
1499	+	//add index of z-constraint molecules into SimInfo's property list
1500	+	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1501	+	sort(tempIndex.begin(), tempIndex.end());
1502	+
1503	+	IndexData* zconsIndex = new IndexData();
1504	+	zconsIndex->setID("zconsindex");
1505	+	zconsIndex->setIndexData(tempIndex);
1506	+	info->addProperty(zconsIndex);
1507	+	}
1508	+	else{
1509	+	sprintf( painCave.errMsg,
1510	+	"SimSetup error: If you use an ZConstraint\n"
1511	+	" , you must set index of z-constraint molecules.\n");
1512	+	painCave.isFatal = 1;
1513	+	simError();
1514	+
1515	+	}
1516	+
1517	+	//Determine the name of ouput file and add it into SimInfo's property list
1518	+	//Be careful, do not use inFileName, since it is a pointer which
1519	+	//point to a string at master node, and slave nodes do not contain that string
1520	+
1521	+	string zconsOutput(info->finalName);
1522	+
1523	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1524	+
1525	+	StringData* zconsFilename = new StringData();
1526	+	zconsFilename->setID("zconsfilename");
1527	+	zconsFilename->setData(zconsOutput);
1528	+
1529	+	info->addProperty(zconsFilename);
1530	+
1531	+	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff );
1532	+
1533	+	break;
1534	+	}
1535	+
1536	+	default:
1537	+	sprintf( painCave.errMsg,
1538	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1539	+	painCave.isFatal = 1;
1540	+	simError();
1541	+	}
1542	+
1543	+	}
1544	+
1545	+	void SimSetup::initFortran( void ){
1546	+
1547	+	info->refreshSim();
1548	+
1549	+	if( !strcmp( info->mixingRule, "standard") ){
1550	+	the_ff->initForceField( LB_MIXING_RULE );
1551	+	}
1552	+	else if( !strcmp( info->mixingRule, "explicit") ){
1553	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1554	+	}
1555	+	else{
1556	+	sprintf( painCave.errMsg,
1557	+	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1558	+	info->mixingRule );
1559	+	painCave.isFatal = 1;
1560	+	simError();
1561	+	}
1562	+
1563	+
1564	+	#ifdef IS_MPI
1565	+	strcpy( checkPointMsg,
1566	+	"Successfully intialized the mixingRule for Fortran." );
1567	+	MPIcheckPoint();
1568	+	#endif // is_mpi
1569	+
1570	+	}

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines