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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 407 by mmeineke, Wed Mar 26 20:22:02 2003 UTC vs.
Revision 693 by tim, Wed Aug 13 19:21:53 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 12 | Line 15 | SimSetup::SimSetup(){
15		#include "mpiSimulation.hpp"
16		#endif
17
18	+	// some defines for ensemble and Forcefield  cases
19	+
20	+	#define NVE_ENS        0
21	+	#define NVT_ENS        1
22	+	#define NPTi_ENS       2
23	+	#define NPTf_ENS       3
24	+	#define NPTim_ENS      4
25	+	#define NPTfm_ENS      5
26	+
27	+	#define FF_DUFF 0
28	+	#define FF_LJ   1
29	+	#define FF_EAM  2
30	+
31	+	using namespace std;
32	+
33		SimSetup::SimSetup(){
34	+
35	+	isInfoArray = 0;
36	+	nInfo = 1;
37	+
38		stamps = new MakeStamps();
39		globals = new Globals();
40
41	+
42		#ifdef IS_MPI
43		strcpy( checkPointMsg, "SimSetup creation successful" );
44		MPIcheckPoint();
#	Line 27 | Line 50 | void SimSetup::parseFile( char* fileName ){
50		delete globals;
51		}
52
53	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
54	+	info = the_info;
55	+	nInfo = theNinfo;
56	+	isInfoArray = 1;
57	+	}
58	+
59	+
60		void SimSetup::parseFile( char* fileName ){
61
62		#ifdef IS_MPI
#	Line 62 | Line 92 | void SimSetup::createSim( void ){
92
93		#endif // is_mpi
94
95	<	void SimSetup::createSim( void ){
95	>	void SimSetup::createSim(void){
96
97	<	MakeStamps *the_stamps;
98	<	Globals* the_globals;
99	<	int i, j;
97	>	int i, j, k, globalAtomIndex;
98	>
99	>	// gather all of the information from the Bass file
100
101	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
101	>	gatherInfo();
102
103	<	// 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();
103	>	// creation of complex system objects
104
105	<	// 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 );
105	>	sysObjectsCreation();
106
107	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
107	>	// check on the post processing info
108
109	+	finalInfoCheck();
110
111	<	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	<	}
111	>	// initialize the system coordinates
112
113	<	#ifdef IS_MPI
104	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
113	>	if( !isInfoArray ) initSystemCoords();
114
115	+	// make the output filenames
116	+
117	+	makeOutNames();
118	+
119	+	// make the integrator
120
121	+	makeIntegrator();
122	+
123	+	#ifdef IS_MPI
124	+	mpiSim->mpiRefresh();
125	+	#endif
126
127	<	// 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];
127	>	// initialize the Fortran
128
129	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
129	>	initFortran();
130
119	–	tot_nmol = 0;
120	–	for( i=0; i<n_components; i++ ){
131
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	–	}
132
133	<	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	<	}
133	>	}
134
160	–	#ifdef IS_MPI
161	–	strcpy( checkPointMsg, "Have the number of components" );
162	–	MPIcheckPoint();
163	–	#endif // is_mpi
135
136	<	// make an array of molecule stamps that match the components used.
166	<	// also extract the used stamps out into a separate linked list
136	>	void SimSetup::makeMolecules( void ){
137
138	<	simnfo->nComponents = n_components;
139	<	simnfo->componentsNmol = components_nmol;
140	<	simnfo->compStamps = comp_stamps;
141	<	simnfo->headStamp = new LinkedMolStamp();
142	<
143	<	char* id;
144	<	LinkedMolStamp* headStamp = simnfo->headStamp;
145	<	LinkedMolStamp* currentStamp = NULL;
146	<	for( i=0; i<n_components; i++ ){
138	>	int k,l;
139	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140	>	molInit molInfo;
141	>	DirectionalAtom* dAtom;
142	>	LinkedAssign* extras;
143	>	LinkedAssign* current_extra;
144	>	AtomStamp* currentAtom;
145	>	BondStamp* currentBond;
146	>	BendStamp* currentBend;
147	>	TorsionStamp* currentTorsion;
148
149	<	id = the_components[i]->getType();
150	<	comp_stamps[i] = NULL;
151	<
181	<	// check to make sure the component isn't already in the list
149	>	bond_pair* theBonds;
150	>	bend_set* theBends;
151	>	torsion_set* theTorsions;
152
183	–	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	–	}
202	–
203	–	#ifdef IS_MPI
204	–	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
205	–	MPIcheckPoint();
206	–	#endif // is_mpi
153
154	+	//init the forceField paramters
155
156	+	the_ff->readParams();
157
210	–
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	–
158
159	<	#ifdef IS_MPI
159	>	// init the atoms
160
161	<	// divide the molecules among processors here.
161	>	double ux, uy, uz, u, uSqr;
162
163	<	mpiSim = new mpiSimulation( simnfo );
164	<
165	<
163	>	for(k=0; k<nInfo; k++){
164	>
165	>	the_ff->setSimInfo( &(info[k]) );
166
167	<	globalIndex = mpiSim->divideLabor();
167	>	atomOffset = 0;
168	>	excludeOffset = 0;
169	>	for(i=0; i<info[k].n_mol; i++){
170	>
171	>	stampID = info[k].molecules[i].getStampID();
172
173	<
174	<
175	<	// set up the local variables
176	<
177	<	int localMol, allMol;
250	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
251	<
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++ ){
173	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
174	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
175	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
176	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
177	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
178
179	<	if( mpiSim->getMyMolStart() <= allMol &&
180	<	allMol <= mpiSim->getMyMolEnd() ){
179	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
180	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
181	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
182	>	molInfo.myBends = new Bend*[molInfo.nBends];
183	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
184	>
185	>	theBonds = new bond_pair[molInfo.nBonds];
186	>	theBends = new bend_set[molInfo.nBends];
187	>	theTorsions = new torsion_set[molInfo.nTorsions];
188	>
189	>	// make the Atoms
190	>
191	>	for(j=0; j<molInfo.nAtoms; j++){
192
193	<	local_atoms +=    comp_stamps[i]->getNAtoms();
194	<	local_bonds +=    comp_stamps[i]->getNBonds();
195	<	local_bends +=    comp_stamps[i]->getNBends();
196	<	local_torsions += comp_stamps[i]->getNTorsions();
197	<	localMol++;
198	<	}
199	<	allMol++;
193	>	currentAtom = comp_stamps[stampID]->getAtom( j );
194	>	if( currentAtom->haveOrientation() ){
195	>
196	>	dAtom = new DirectionalAtom( (j + atomOffset),
197	>	info[k].getConfiguration() );
198	>	info[k].n_oriented++;
199	>	molInfo.myAtoms[j] = dAtom;
200	>
201	>	ux = currentAtom->getOrntX();
202	>	uy = currentAtom->getOrntY();
203	>	uz = currentAtom->getOrntZ();
204	>
205	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
206	>
207	>	u = sqrt( uSqr );
208	>	ux = ux / u;
209	>	uy = uy / u;
210	>	uz = uz / u;
211	>
212	>	dAtom->setSUx( ux );
213	>	dAtom->setSUy( uy );
214	>	dAtom->setSUz( uz );
215	>	}
216	>	else{
217	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
218	>	info[k].getConfiguration() );
219	>	}
220	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221	>
222	>	#ifdef IS_MPI
223	>
224	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
225	>
226	>	#endif // is_mpi
227	>	}
228	>
229	>	// make the bonds
230	>	for(j=0; j<molInfo.nBonds; j++){
231	>
232	>	currentBond = comp_stamps[stampID]->getBond( j );
233	>	theBonds[j].a = currentBond->getA() + atomOffset;
234	>	theBonds[j].b = currentBond->getB() + atomOffset;
235	>
236	>	exI = theBonds[j].a;
237	>	exJ = theBonds[j].b;
238	>
239	>	// exclude_I must always be the smaller of the pair
240	>	if( exI > exJ ){
241	>	tempEx = exI;
242	>	exI = exJ;
243	>	exJ = tempEx;
244	>	}
245	>	#ifdef IS_MPI
246	>	tempEx = exI;
247	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
248	>	tempEx = exJ;
249	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
250	>
251	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
252	>	#else  // isn't MPI
253	>
254	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
255	>	#endif  //is_mpi
256	>	}
257	>	excludeOffset += molInfo.nBonds;
258	>
259	>	//make the bends
260	>	for(j=0; j<molInfo.nBends; j++){
261	>
262	>	currentBend = comp_stamps[stampID]->getBend( j );
263	>	theBends[j].a = currentBend->getA() + atomOffset;
264	>	theBends[j].b = currentBend->getB() + atomOffset;
265	>	theBends[j].c = currentBend->getC() + atomOffset;
266	>
267	>	if( currentBend->haveExtras() ){
268	>
269	>	extras = currentBend->getExtras();
270	>	current_extra = extras;
271	>
272	>	while( current_extra != NULL ){
273	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
274	>
275	>	switch( current_extra->getType() ){
276	>
277	>	case 0:
278	>	theBends[j].ghost =
279	>	current_extra->getInt() + atomOffset;
280	>	theBends[j].isGhost = 1;
281	>	break;
282	>
283	>	case 1:
284	>	theBends[j].ghost =
285	>	(int)current_extra->getDouble() + atomOffset;
286	>	theBends[j].isGhost = 1;
287	>	break;
288	>
289	>	default:
290	>	sprintf( painCave.errMsg,
291	>	"SimSetup Error: ghostVectorSource was neither a "
292	>	"double nor an int.\n"
293	>	"-->Bend[%d] in %s\n",
294	>	j, comp_stamps[stampID]->getID() );
295	>	painCave.isFatal = 1;
296	>	simError();
297	>	}
298	>	}
299	>
300	>	else{
301	>
302	>	sprintf( painCave.errMsg,
303	>	"SimSetup Error: unhandled bend assignment:\n"
304	>	"    -->%s in Bend[%d] in %s\n",
305	>	current_extra->getlhs(),
306	>	j, comp_stamps[stampID]->getID() );
307	>	painCave.isFatal = 1;
308	>	simError();
309	>	}
310	>
311	>	current_extra = current_extra->getNext();
312	>	}
313	>	}
314	>
315	>	if( !theBends[j].isGhost ){
316	>
317	>	exI = theBends[j].a;
318	>	exJ = theBends[j].c;
319	>	}
320	>	else{
321	>
322	>	exI = theBends[j].a;
323	>	exJ = theBends[j].b;
324	>	}
325	>
326	>	// exclude_I must always be the smaller of the pair
327	>	if( exI > exJ ){
328	>	tempEx = exI;
329	>	exI = exJ;
330	>	exJ = tempEx;
331	>	}
332	>	#ifdef IS_MPI
333	>	tempEx = exI;
334	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
335	>	tempEx = exJ;
336	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
337	>
338	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
339	>	#else  // isn't MPI
340	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
341	>	#endif  //is_mpi
342	>	}
343	>	excludeOffset += molInfo.nBends;
344	>
345	>	for(j=0; j<molInfo.nTorsions; j++){
346	>
347	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
348	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
349	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
350	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
351	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
352	>
353	>	exI = theTorsions[j].a;
354	>	exJ = theTorsions[j].d;
355	>
356	>	// exclude_I must always be the smaller of the pair
357	>	if( exI > exJ ){
358	>	tempEx = exI;
359	>	exI = exJ;
360	>	exJ = tempEx;
361	>	}
362	>	#ifdef IS_MPI
363	>	tempEx = exI;
364	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
365	>	tempEx = exJ;
366	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
367	>
368	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
369	>	#else  // isn't MPI
370	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
371	>	#endif  //is_mpi
372	>	}
373	>	excludeOffset += molInfo.nTorsions;
374	>
375	>
376	>	// send the arrays off to the forceField for init.
377	>
378	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
379	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
380	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
381	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
382	>
383	>
384	>	info[k].molecules[i].initialize( molInfo );
385	>
386	>
387	>	atomOffset += molInfo.nAtoms;
388	>	delete[] theBonds;
389	>	delete[] theBends;
390	>	delete[] theTorsions;
391		}
392		}
274	–	local_SRI = local_bonds + local_bends + local_torsions;
393
394	+	#ifdef IS_MPI
395	+	sprintf( checkPointMsg, "all molecules initialized succesfully" );
396	+	MPIcheckPoint();
397	+	#endif // is_mpi
398	+
399	+	// clean up the forcefield
400
401	<	simnfo->n_atoms = mpiSim->getMyNlocal();
401	>	the_ff->calcRcut();
402	>	the_ff->cleanMe();
403
404	<	if( local_atoms != simnfo->n_atoms ){
405	<	sprintf( painCave.errMsg,
406	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
407	<	" localAtom (%d) are note equal.\n",
408	<	simnfo->n_atoms,
409	<	local_atoms );
410	<	painCave.isFatal = 1;
411	<	simError();
404	>	}
405	>
406	>	void SimSetup::initFromBass( void ){
407	>
408	>	int i, j, k;
409	>	int n_cells;
410	>	double cellx, celly, cellz;
411	>	double temp1, temp2, temp3;
412	>	int n_per_extra;
413	>	int n_extra;
414	>	int have_extra, done;
415	>
416	>	double vel[3];
417	>	vel[0] = 0.0;
418	>	vel[1] = 0.0;
419	>	vel[2] = 0.0;
420	>
421	>	temp1 = (double)tot_nmol / 4.0;
422	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
423	>	temp3 = ceil( temp2 );
424	>
425	>	have_extra =0;
426	>	if( temp2 < temp3 ){ // we have a non-complete lattice
427	>	have_extra =1;
428	>
429	>	n_cells = (int)temp3 - 1;
430	>	cellx = info[0].boxL[0] / temp3;
431	>	celly = info[0].boxL[1] / temp3;
432	>	cellz = info[0].boxL[2] / temp3;
433	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
434	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
435	>	n_per_extra = (int)ceil( temp1 );
436	>
437	>	if( n_per_extra > 4){
438	>	sprintf( painCave.errMsg,
439	>	"SimSetup error. There has been an error in constructing"
440	>	" the non-complete lattice.\n" );
441	>	painCave.isFatal = 1;
442	>	simError();
443	>	}
444		}
445	+	else{
446	+	n_cells = (int)temp3;
447	+	cellx = info[0].boxL[0] / temp3;
448	+	celly = info[0].boxL[1] / temp3;
449	+	cellz = info[0].boxL[2] / temp3;
450	+	}
451
452	<	simnfo->n_bonds = local_bonds;
453	<	simnfo->n_bends = local_bends;
454	<	simnfo->n_torsions = local_torsions;
455	<	simnfo->n_SRI = local_SRI;
293	<	simnfo->n_mol = localMol;
452	>	current_mol = 0;
453	>	current_comp_mol = 0;
454	>	current_comp = 0;
455	>	current_atom_ndx = 0;
456
457	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
458	<	MPIcheckPoint();
459	<
298	<
299	<	#endif // is_mpi
300	<
457	>	for( i=0; i < n_cells ; i++ ){
458	>	for( j=0; j < n_cells; j++ ){
459	>	for( k=0; k < n_cells; k++ ){
460
461	<	// create the atom and short range interaction arrays
461	>	makeElement( i * cellx,
462	>	j * celly,
463	>	k * cellz );
464
465	<	Atom::createArrays(simnfo->n_atoms);
466	<	the_atoms = new Atom*[simnfo->n_atoms];
467	<	the_molecules = new Molecule[simnfo->n_mol];
465	>	makeElement( i * cellx + 0.5 * cellx,
466	>	j * celly + 0.5 * celly,
467	>	k * cellz );
468
469	+	makeElement( i * cellx,
470	+	j * celly + 0.5 * celly,
471	+	k * cellz + 0.5 * cellz );
472
473	<	if( simnfo->n_SRI ){
474	<	the_sris = new SRI*[simnfo->n_SRI];
475	<	the_excludes = new int[2 * simnfo->n_SRI];
476	<	simnfo->globalExcludes = new int;
477	<	simnfo->n_exclude = tot_SRI;
314	<	}
315	<	else{
316	<
317	<	the_excludes = new int[2];
318	<	the_excludes[0] = 0;
319	<	the_excludes[1] = 0;
320	<	simnfo->globalExcludes = new int;
321	<	simnfo->globalExcludes[0] = 0;
322	<
323	<	simnfo->n_exclude = 1;
473	>	makeElement( i * cellx + 0.5 * cellx,
474	>	j * celly,
475	>	k * cellz + 0.5 * cellz );
476	>	}
477	>	}
478		}
479
480	<	// set the arrays into the SimInfo object
480	>	if( have_extra ){
481	>	done = 0;
482
483	<	simnfo->atoms = the_atoms;
484	<	simnfo->sr_interactions = the_sris;
485	<	simnfo->nGlobalExcludes = 0;
331	<	simnfo->excludes = the_excludes;
483	>	int start_ndx;
484	>	for( i=0; i < (n_cells+1) && !done; i++ ){
485	>	for( j=0; j < (n_cells+1) && !done; j++ ){
486
487	+	if( i < n_cells ){
488
489	<	// get some of the tricky things that may still be in the globals
489	>	if( j < n_cells ){
490	>	start_ndx = n_cells;
491	>	}
492	>	else start_ndx = 0;
493	>	}
494	>	else start_ndx = 0;
495
496	<
497	<	if( the_globals->haveBox() ){
498	<	simnfo->box_x = the_globals->getBox();
499	<	simnfo->box_y = the_globals->getBox();
500	<	simnfo->box_z = the_globals->getBox();
496	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
497	>
498	>	makeElement( i * cellx,
499	>	j * celly,
500	>	k * cellz );
501	>	done = ( current_mol >= tot_nmol );
502	>
503	>	if( !done && n_per_extra > 1 ){
504	>	makeElement( i * cellx + 0.5 * cellx,
505	>	j * celly + 0.5 * celly,
506	>	k * cellz );
507	>	done = ( current_mol >= tot_nmol );
508	>	}
509	>
510	>	if( !done && n_per_extra > 2){
511	>	makeElement( i * cellx,
512	>	j * celly + 0.5 * celly,
513	>	k * cellz + 0.5 * cellz );
514	>	done = ( current_mol >= tot_nmol );
515	>	}
516	>
517	>	if( !done && n_per_extra > 3){
518	>	makeElement( i * cellx + 0.5 * cellx,
519	>	j * celly,
520	>	k * cellz + 0.5 * cellz );
521	>	done = ( current_mol >= tot_nmol );
522	>	}
523	>	}
524	>	}
525	>	}
526		}
342	–	else if( the_globals->haveDensity() ){
527
528	<	double vol;
529	<	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;
528	>	for( i=0; i<info[0].n_atoms; i++ ){
529	>	info[0].atoms[i]->setVel( vel );
530		}
531	<	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();
531	>	}
532
533	<	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();
533	>	void SimSetup::makeElement( double x, double y, double z ){
534
535	<	if( !the_globals->haveBoxZ() ){
535	>	int k;
536	>	AtomStamp* current_atom;
537	>	DirectionalAtom* dAtom;
538	>	double rotMat[3][3];
539	>	double pos[3];
540	>
541	>	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
542	>
543	>	current_atom = comp_stamps[current_comp]->getAtom( k );
544	>	if( !current_atom->havePosition() ){
545		sprintf( painCave.errMsg,
546	<	"SimSetup error, no periodic BoxZ size given.\n" );
546	>	"SimSetup:initFromBass error.\n"
547	>	"\tComponent %s, atom %s does not have a position specified.\n"
548	>	"\tThe initialization routine is unable to give a start"
549	>	" position.\n",
550	>	comp_stamps[current_comp]->getID(),
551	>	current_atom->getType() );
552		painCave.isFatal = 1;
553		simError();
554		}
555	<	simnfo->box_z = the_globals->getBoxZ();
556	<	}
555	>
556	>	pos[0] = x + current_atom->getPosX();
557	>	pos[1] = y + current_atom->getPosY();
558	>	pos[2] = z + current_atom->getPosZ();
559	>
560	>	info[0].atoms[current_atom_ndx]->setPos( pos );
561
562	<	#ifdef IS_MPI
377	<	strcpy( checkPointMsg, "Box size set up" );
378	<	MPIcheckPoint();
379	<	#endif // is_mpi
562	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
563
564	+	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
565
566	<	// initialize the arrays
566	>	rotMat[0][0] = 1.0;
567	>	rotMat[0][1] = 0.0;
568	>	rotMat[0][2] = 0.0;
569
570	<	the_ff->setSimInfo( simnfo );
570	>	rotMat[1][0] = 0.0;
571	>	rotMat[1][1] = 1.0;
572	>	rotMat[1][2] = 0.0;
573
574	<	makeAtoms();
575	<	simnfo->identArray = new int[simnfo->n_atoms];
576	<	for(i=0; i<simnfo->n_atoms; i++){
577	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
574	>	rotMat[2][0] = 0.0;
575	>	rotMat[2][1] = 0.0;
576	>	rotMat[2][2] = 1.0;
577	>
578	>	dAtom->setA( rotMat );
579	>	}
580	>
581	>	current_atom_ndx++;
582		}
583	<
584	<	if( tot_bonds ){
585	<	makeBonds();
583	>
584	>	current_mol++;
585	>	current_comp_mol++;
586	>
587	>	if( current_comp_mol >= components_nmol[current_comp] ){
588	>
589	>	current_comp_mol = 0;
590	>	current_comp++;
591		}
592	+	}
593
594	<	if( tot_bends ){
595	<	makeBends();
594	>
595	>	void SimSetup::gatherInfo( void ){
596	>	int i,j,k;
597	>
598	>	ensembleCase = -1;
599	>	ffCase = -1;
600	>
601	>	// set the easy ones first
602	>
603	>	for( i=0; i<nInfo; i++){
604	>	info[i].target_temp = globals->getTargetTemp();
605	>	info[i].dt = globals->getDt();
606	>	info[i].run_time = globals->getRunTime();
607		}
608	+	n_components = globals->getNComponents();
609
610	<	if( tot_torsions ){
611	<	makeTorsions();
610	>
611	>	// get the forceField
612	>
613	>	strcpy( force_field, globals->getForceField() );
614	>
615	>	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
616	>	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
617	>	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
618	>	else{
619	>	sprintf( painCave.errMsg,
620	>	"SimSetup Error. Unrecognized force field -> %s\n",
621	>	force_field );
622	>	painCave.isFatal = 1;
623	>	simError();
624		}
625
626	+	// get the ensemble
627
628	<	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	<	}
628	>	strcpy( ensemble, globals->getEnsemble() );
629
630	<	if( !the_globals->haveEST() ){
631	<	sprintf( painCave.errMsg,
632	<	"SimSetup Warning: using default value of 0.05 * the "
633	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
634	<	);
635	<	painCave.isFatal = 0;
636	<	simError();
637	<	simnfo->est = 0.05 * simnfo->ecr;
638	<	} else {
639	<	simnfo->est        = the_globals->getEST();
640	<	}
630	>	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
631	>	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
632	>	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
633	>	ensembleCase = NPTi_ENS;
634	>	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
635	>	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
636	>	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
637	>	else{
638	>	sprintf( painCave.errMsg,
639	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
640	>	"reverting to NVE for this simulation.\n",
641	>	ensemble );
642	>	painCave.isFatal = 0;
643	>	simError();
644	>	strcpy( ensemble, "NVE" );
645	>	ensembleCase = NVE_ENS;
646	>	}
647	>
648	>	for(i=0; i<nInfo; i++){
649
650	<	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	<	}
650	>	strcpy( info[i].ensemble, ensemble );
651
652	<	#ifdef IS_MPI
480	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
481	<	MPIcheckPoint();
482	<	#endif // is_mpi
652	>	// get the mixing rule
653
654	<	if( the_globals->haveInitialConfig() ){
654	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
655	>	info[i].usePBC = globals->getPBC();
656	>	}
657	>
658	>	// get the components and calculate the tot_nMol and indvidual n_mol
659
660	<	InitializeFromFile* fileInit;
661	<	#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 );
493	<	#endif
494	<	fileInit->read_xyz( simnfo ); // default velocities on
660	>	the_components = globals->getComponents();
661	>	components_nmol = new int[n_components];
662
496	–	delete fileInit;
497	–	}
498	–	else{
663
664	<	#ifdef IS_MPI
664	>	if( !globals->haveNMol() ){
665	>	// we don't have the total number of molecules, so we assume it is
666	>	// given in each component
667
668	<	// no init from bass
669	<
504	<	sprintf( painCave.errMsg,
505	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
506	<	painCave.isFatal;
507	<	simError();
508	<
509	<	#else
668	>	tot_nmol = 0;
669	>	for( i=0; i<n_components; i++ ){
670
671	<	initFromBass();
671	>	if( !the_components[i]->haveNMol() ){
672	>	// we have a problem
673	>	sprintf( painCave.errMsg,
674	>	"SimSetup Error. No global NMol or component NMol"
675	>	" given. Cannot calculate the number of atoms.\n" );
676	>	painCave.isFatal = 1;
677	>	simError();
678	>	}
679
680	+	tot_nmol += the_components[i]->getNMol();
681	+	components_nmol[i] = the_components[i]->getNMol();
682	+	}
683	+	}
684	+	else{
685	+	sprintf( painCave.errMsg,
686	+	"SimSetup error.\n"
687	+	"\tSorry, the ability to specify total"
688	+	" nMols and then give molfractions in the components\n"
689	+	"\tis not currently supported."
690	+	" Please give nMol in the components.\n" );
691	+	painCave.isFatal = 1;
692	+	simError();
693	+	}
694
695	<	#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	<
695	>	// set the status, sample, and thermal kick times
696
697	+	for(i=0; i<nInfo; i++){
698
699	<
700	<	#ifdef IS_MPI
701	<	if( worldRank == 0 ){
702	<	#endif // is_mpi
531	<
532	<	if( the_globals->haveFinalConfig() ){
533	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
699	>	if( globals->haveSampleTime() ){
700	>	info[i].sampleTime = globals->getSampleTime();
701	>	info[i].statusTime = info[i].sampleTime;
702	>	info[i].thermalTime = info[i].sampleTime;
703		}
704		else{
705	<	strcpy( simnfo->finalName, inFileName );
706	<	char* endTest;
707	<	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	<	}
705	>	info[i].sampleTime = globals->getRunTime();
706	>	info[i].statusTime = info[i].sampleTime;
707	>	info[i].thermalTime = info[i].sampleTime;
708		}
709
710	<	// make the sample and status out names
710	>	if( globals->haveStatusTime() ){
711	>	info[i].statusTime = globals->getStatusTime();
712	>	}
713
714	<	strcpy( simnfo->sampleName, inFileName );
715	<	char* endTest;
564	<	int nameLength = strlen( simnfo->sampleName );
565	<	endTest = &(simnfo->sampleName[nameLength - 5]);
566	<	if( !strcmp( endTest, ".bass" ) ){
567	<	strcpy( endTest, ".dump" );
714	>	if( globals->haveThermalTime() ){
715	>	info[i].thermalTime = globals->getThermalTime();
716		}
717	<	else if( !strcmp( endTest, ".BASS" ) ){
718	<	strcpy( endTest, ".dump" );
717	>
718	>	// check for the temperature set flag
719	>
720	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
721	>
722	>	// get some of the tricky things that may still be in the globals
723	>
724	>	double boxVector[3];
725	>	if( globals->haveBox() ){
726	>	boxVector[0] = globals->getBox();
727	>	boxVector[1] = globals->getBox();
728	>	boxVector[2] = globals->getBox();
729	>
730	>	info[i].setBox( boxVector );
731		}
732	+	else if( globals->haveDensity() ){
733	+
734	+	double vol;
735	+	vol = (double)tot_nmol / globals->getDensity();
736	+	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
737	+	boxVector[1] = boxVector[0];
738	+	boxVector[2] = boxVector[0];
739	+
740	+	info[i].setBox( boxVector );
741	+	}
742		else{
743	<	endTest = &(simnfo->sampleName[nameLength - 4]);
744	<	if( !strcmp( endTest, ".bss" ) ){
745	<	strcpy( endTest, ".dump" );
743	>	if( !globals->haveBoxX() ){
744	>	sprintf( painCave.errMsg,
745	>	"SimSetup error, no periodic BoxX size given.\n" );
746	>	painCave.isFatal = 1;
747	>	simError();
748		}
749	<	else if( !strcmp( endTest, ".mdl" ) ){
750	<	strcpy( endTest, ".dump" );
749	>	boxVector[0] = globals->getBoxX();
750	>
751	>	if( !globals->haveBoxY() ){
752	>	sprintf( painCave.errMsg,
753	>	"SimSetup error, no periodic BoxY size given.\n" );
754	>	painCave.isFatal = 1;
755	>	simError();
756		}
757	<	else{
758	<	strcat( simnfo->sampleName, ".dump" );
757	>	boxVector[1] = globals->getBoxY();
758	>
759	>	if( !globals->haveBoxZ() ){
760	>	sprintf( painCave.errMsg,
761	>	"SimSetup error, no periodic BoxZ size given.\n" );
762	>	painCave.isFatal = 1;
763	>	simError();
764		}
765	+	boxVector[2] = globals->getBoxZ();
766	+
767	+	info[i].setBox( boxVector );
768		}
769	+
770	+	}
771
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	–
772		#ifdef IS_MPI
773	<	}
773	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
774	>	MPIcheckPoint();
775		#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	–	}
776
777	<	if( the_globals->haveStatusTime() ){
625	<	simnfo->statusTime = the_globals->getStatusTime();
626	<	}
777	>	}
778
628	–	if( the_globals->haveThermalTime() ){
629	–	simnfo->thermalTime = the_globals->getThermalTime();
630	–	}
779
780	<	// check for the temperature set flag
780	>	void SimSetup::finalInfoCheck( void ){
781	>	int index;
782	>	int usesDipoles;
783	>	int i;
784
785	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
785	>	for(i=0; i<nInfo; i++){
786	>	// check electrostatic parameters
787	>
788	>	index = 0;
789	>	usesDipoles = 0;
790	>	while( (index < info[i].n_atoms) && !usesDipoles ){
791	>	usesDipoles = (info[i].atoms[index])->hasDipole();
792	>	index++;
793	>	}
794	>
795	>	#ifdef IS_MPI
796	>	int myUse = usesDipoles;
797	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
798	>	#endif //is_mpi
799	>
800	>	double theEcr, theEst;
801	>
802	>	if (globals->getUseRF() ) {
803	>	info[i].useReactionField = 1;
804	>
805	>	if( !globals->haveECR() ){
806	>	sprintf( painCave.errMsg,
807	>	"SimSetup Warning: using default value of 1/2 the smallest "
808	>	"box length for the electrostaticCutoffRadius.\n"
809	>	"I hope you have a very fast processor!\n");
810	>	painCave.isFatal = 0;
811	>	simError();
812	>	double smallest;
813	>	smallest = info[i].boxL[0];
814	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
815	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
816	>	theEcr = 0.5 * smallest;
817	>	} else {
818	>	theEcr = globals->getECR();
819	>	}
820	>
821	>	if( !globals->haveEST() ){
822	>	sprintf( painCave.errMsg,
823	>	"SimSetup Warning: using default value of 0.05 * the "
824	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
825	>	);
826	>	painCave.isFatal = 0;
827	>	simError();
828	>	theEst = 0.05 * theEcr;
829	>	} else {
830	>	theEst= globals->getEST();
831	>	}
832	>
833	>	info[i].setEcr( theEcr, theEst );
834	>
835	>	if(!globals->haveDielectric() ){
836	>	sprintf( painCave.errMsg,
837	>	"SimSetup Error: You are trying to use Reaction Field without"
838	>	"setting a dielectric constant!\n"
839	>	);
840	>	painCave.isFatal = 1;
841	>	simError();
842	>	}
843	>	info[i].dielectric = globals->getDielectric();
844	>	}
845	>	else {
846	>	if (usesDipoles) {
847	>
848	>	if( !globals->haveECR() ){
849	>	sprintf( painCave.errMsg,
850	>	"SimSetup Warning: using default value of 1/2 the smallest "
851	>	"box length for the electrostaticCutoffRadius.\n"
852	>	"I hope you have a very fast processor!\n");
853	>	painCave.isFatal = 0;
854	>	simError();
855	>	double smallest;
856	>	smallest = info[i].boxL[0];
857	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
858	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
859	>	theEcr = 0.5 * smallest;
860	>	} else {
861	>	theEcr = globals->getECR();
862	>	}
863	>
864	>	if( !globals->haveEST() ){
865	>	sprintf( painCave.errMsg,
866	>	"SimSetup Warning: using default value of 0.05 * the "
867	>	"electrostaticCutoffRadius for the "
868	>	"electrostaticSkinThickness\n"
869	>	);
870	>	painCave.isFatal = 0;
871	>	simError();
872	>	theEst = 0.05 * theEcr;
873	>	} else {
874	>	theEst= globals->getEST();
875	>	}
876	>
877	>	info[i].setEcr( theEcr, theEst );
878	>	}
879	>	}
880	>	}
881
882	+	#ifdef IS_MPI
883	+	strcpy( checkPointMsg, "post processing checks out" );
884	+	MPIcheckPoint();
885	+	#endif // is_mpi
886
887	<	//   // make the longe range forces and the integrator
887	>	}
888
889	<	//   new AllLong( simnfo );
889	>	void SimSetup::initSystemCoords( void ){
890	>	int i;
891	>
892	>	char* inName;
893
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 );
894
895	<
647	<
648	<	// initialize the Fortran
895	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
896
897	<	simnfo->refreshSim();
897	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
898
899	<	if( !strcmp( simnfo->mixingRule, "standard") ){
900	<	the_ff->initForceField( LB_MIXING_RULE );
899	>	if( globals->haveInitialConfig() ){
900	>
901	>	InitializeFromFile* fileInit;
902	>	#ifdef IS_MPI // is_mpi
903	>	if( worldRank == 0 ){
904	>	#endif //is_mpi
905	>	inName = globals->getInitialConfig();
906	>	double* tempDouble = new double[1000000];
907	>	fileInit = new InitializeFromFile( inName );
908	>	#ifdef IS_MPI
909	>	}else fileInit = new InitializeFromFile( NULL );
910	>	#endif
911	>	fileInit->readInit( info ); // default velocities on
912	>
913	>	delete fileInit;
914		}
655	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
656	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
657	–	}
915		else{
916	+
917	+	#ifdef IS_MPI
918	+
919	+	// no init from bass
920	+
921		sprintf( painCave.errMsg,
922	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
923	<	simnfo->mixingRule );
662	<	painCave.isFatal = 1;
922	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
923	>	painCave.isFatal;
924		simError();
925	+
926	+	#else
927	+
928	+	initFromBass();
929	+
930	+
931	+	#endif
932		}
933	<
666	<
933	>
934		#ifdef IS_MPI
935	<	strcpy( checkPointMsg,
669	<	"Successfully intialized the mixingRule for Fortran." );
935	>	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
936		MPIcheckPoint();
937		#endif // is_mpi
938	+
939		}
940
941
942	<	void SimSetup::makeMolecules( void ){
676	<
677	<	int i, j, exI, exJ, tempEx, stampID, atomOffset;
678	<	molInit info;
679	<	DirectionalAtom* dAtom;
680	<	AtomStamp* currentAtom;
681	<	BondStamp* currentBond;
682	<	BendStamp* currentBend;
683	<	TorsionStamp* currentTorsion;
942	>	void SimSetup::makeOutNames( void ){
943
944	<	//init the forceField paramters
944	>	int k;
945
687	–	the_ff->readParams();
688	–
946
947	<	// init the molecules
947	>	for(k=0; k<nInfo; k++){
948
949	<	atomOffset = 0;
950	<	for(i=0; i<simnfo->n_mol; i++){
951	<
695	<	stampID = the_molecules[i].getStampID();
696	<
697	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
698	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
699	<	info.nBends    = comp_stamps[stampID]->getNBends();
700	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
701	<
702	<	info.myAtoms = &the_atoms[atomOffset];
703	<	info.myBonds = new Bond*[info.nBonds];
704	<	info.myBends = new Bend*[info.nBends];
705	<	info.myTorsions = new Torsions*[info.nTorsions];
706	<
707	<	theBonds = new bond_pair[info.nBonds];
708	<	theBends = new bend_set[info.nBends];
709	<	theTorsions = new torsion_set[info.nTorsions];
710	<
711	<	// make the Atoms
712	<
713	<	for(j=0; j<info.nAtoms; j++){
949	>	#ifdef IS_MPI
950	>	if( worldRank == 0 ){
951	>	#endif // is_mpi
952
953	<	currentAtom = theComponents[stampID]->getAtom( j );
954	<	if( currentAtom->haveOrientation() ){
717	<
718	<	dAtom = new DirectionalAtom(j + atomOffset);
719	<	simnfo->n_oriented++;
720	<	info.myAtoms[j] = dAtom;
721	<
722	<	ux = currentAtom->getOrntX();
723	<	uy = currentAtom->getOrntY();
724	<	uz = currentAtom->getOrntZ();
725	<
726	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
727	<
728	<	u = sqrt( uSqr );
729	<	ux = ux / u;
730	<	uy = uy / u;
731	<	uz = uz / u;
732	<
733	<	dAtom->setSUx( ux );
734	<	dAtom->setSUy( uy );
735	<	dAtom->setSUz( uz );
953	>	if( globals->haveFinalConfig() ){
954	>	strcpy( info[k].finalName, globals->getFinalConfig() );
955		}
956		else{
957	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
957	>	strcpy( info[k].finalName, inFileName );
958	>	char* endTest;
959	>	int nameLength = strlen( info[k].finalName );
960	>	endTest = &(info[k].finalName[nameLength - 5]);
961	>	if( !strcmp( endTest, ".bass" ) ){
962	>	strcpy( endTest, ".eor" );
963	>	}
964	>	else if( !strcmp( endTest, ".BASS" ) ){
965	>	strcpy( endTest, ".eor" );
966	>	}
967	>	else{
968	>	endTest = &(info[k].finalName[nameLength - 4]);
969	>	if( !strcmp( endTest, ".bss" ) ){
970	>	strcpy( endTest, ".eor" );
971	>	}
972	>	else if( !strcmp( endTest, ".mdl" ) ){
973	>	strcpy( endTest, ".eor" );
974	>	}
975	>	else{
976	>	strcat( info[k].finalName, ".eor" );
977	>	}
978	>	}
979		}
740	–	info.myAtoms[j]->setType( currentAtom->getType() );
741	–
742	–	#ifdef IS_MPI
980
981	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
981	>	// make the sample and status out names
982
983	<	#endif // is_mpi
984	<	}
985	<
986	<	// make the bonds
987	<	for(j=0; j<nBonds; j++){
983	>	strcpy( info[k].sampleName, inFileName );
984	>	char* endTest;
985	>	int nameLength = strlen( info[k].sampleName );
986	>	endTest = &(info[k].sampleName[nameLength - 5]);
987	>	if( !strcmp( endTest, ".bass" ) ){
988	>	strcpy( endTest, ".dump" );
989	>	}
990	>	else if( !strcmp( endTest, ".BASS" ) ){
991	>	strcpy( endTest, ".dump" );
992	>	}
993	>	else{
994	>	endTest = &(info[k].sampleName[nameLength - 4]);
995	>	if( !strcmp( endTest, ".bss" ) ){
996	>	strcpy( endTest, ".dump" );
997	>	}
998	>	else if( !strcmp( endTest, ".mdl" ) ){
999	>	strcpy( endTest, ".dump" );
1000	>	}
1001	>	else{
1002	>	strcat( info[k].sampleName, ".dump" );
1003	>	}
1004	>	}
1005
1006	<	currentBond = comp_stamps[stampID]->getBond( j );
1007	<	theBonds[j].a = currentBond->getA() + atomOffset;
1008	<	theBonds[j].b = currentBond->getB() + atomOffset;
1009	<
1010	<	exI = theBonds[i].a;
757	<	exJ = theBonds[i].b;
758	<
759	<	// exclude_I must always be the smaller of the pair
760	<	if( exI > exJ ){
761	<	tempEx = exI;
762	<	exI = exJ;
763	<	exJ = tempEx;
1006	>	strcpy( info[k].statusName, inFileName );
1007	>	nameLength = strlen( info[k].statusName );
1008	>	endTest = &(info[k].statusName[nameLength - 5]);
1009	>	if( !strcmp( endTest, ".bass" ) ){
1010	>	strcpy( endTest, ".stat" );
1011		}
1012	<	#ifdef IS_MPI
1012	>	else if( !strcmp( endTest, ".BASS" ) ){
1013	>	strcpy( endTest, ".stat" );
1014	>	}
1015	>	else{
1016	>	endTest = &(info[k].statusName[nameLength - 4]);
1017	>	if( !strcmp( endTest, ".bss" ) ){
1018	>	strcpy( endTest, ".stat" );
1019	>	}
1020	>	else if( !strcmp( endTest, ".mdl" ) ){
1021	>	strcpy( endTest, ".stat" );
1022	>	}
1023	>	else{
1024	>	strcat( info[k].statusName, ".stat" );
1025	>	}
1026	>	}
1027
1028	<	the_excludes[index*2] =
1029	<	the_atoms[exI]->getGlobalIndex() + 1;
1030	<	the_excludes[index*2 + 1] =
770	<	the_atoms[exJ]->getGlobalIndex() + 1;
771	<
772	<	#else  // isn't MPI
773	<
774	<	the_excludes[index*2] =     exI + 1;
775	<	the_excludes[index*2 + 1] = exJ + 1;
776	<	// fortran index from 1 (hence the +1 in the indexing)
777	<
778	<	#endif  //is_mpi
779	<
1028	>	#ifdef IS_MPI
1029	>	}
1030	>	#endif // is_mpi
1031		}
1032	+	}
1033	+
1034	+
1035	+	void SimSetup::sysObjectsCreation( void ){
1036	+
1037	+	int i,k;
1038	+
1039	+	// create the forceField
1040
1041	+	createFF();
1042
1043	+	// extract componentList
1044
1045	+	compList();
1046
1047	+	// calc the number of atoms, bond, bends, and torsions
1048
1049	+	calcSysValues();
1050
1051	+	#ifdef IS_MPI
1052	+	// divide the molecules among the processors
1053	+
1054	+	mpiMolDivide();
1055	+	#endif //is_mpi
1056	+
1057	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1058	+
1059	+	makeSysArrays();
1060
1061	+	// make and initialize the molecules (all but atomic coordinates)
1062	+
1063	+	makeMolecules();
1064	+
1065	+	for(k=0; k<nInfo; k++){
1066	+	info[k].identArray = new int[info[k].n_atoms];
1067	+	for(i=0; i<info[k].n_atoms; i++){
1068	+	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1069	+	}
1070	+	}
1071	+	}
1072
1073
1074	+	void SimSetup::createFF( void ){
1075
1076	+	switch( ffCase ){
1077
1078	+	case FF_DUFF:
1079	+	the_ff = new DUFF();
1080	+	break;
1081
1082	+	case FF_LJ:
1083	+	the_ff = new LJFF();
1084	+	break;
1085
1086	+	case FF_EAM:
1087	+	the_ff = new EAM_FF();
1088	+	break;
1089
1090	+	default:
1091	+	sprintf( painCave.errMsg,
1092	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1093	+	painCave.isFatal = 1;
1094	+	simError();
1095	+	}
1096
1097	<	void SimSetup::makeAtoms( void ){
1097	>	#ifdef IS_MPI
1098	>	strcpy( checkPointMsg, "ForceField creation successful" );
1099	>	MPIcheckPoint();
1100	>	#endif // is_mpi
1101
1102	<	int i, j, k, index;
799	<	double ux, uy, uz, uSqr, u;
800	<	AtomStamp* current_atom;
1102	>	}
1103
802	–	DirectionalAtom* dAtom;
803	–	int molIndex, molStart, molEnd, nMemb, lMolIndex;
1104
1105	<	lMolIndex = 0;
806	<	molIndex = 0;
807	<	index = 0;
808	<	for( i=0; i<n_components; i++ ){
1105	>	void SimSetup::compList( void ){
1106
1107	<	for( j=0; j<components_nmol[i]; j++ ){
1107	>	int i;
1108	>	char* id;
1109	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1110	>	LinkedMolStamp* currentStamp = NULL;
1111	>	comp_stamps = new MoleculeStamp*[n_components];
1112	>
1113	>	// make an array of molecule stamps that match the components used.
1114	>	// also extract the used stamps out into a separate linked list
1115	>
1116	>	for(i=0; i<nInfo; i++){
1117	>	info[i].nComponents = n_components;
1118	>	info[i].componentsNmol = components_nmol;
1119	>	info[i].compStamps = comp_stamps;
1120	>	info[i].headStamp = headStamp;
1121	>	}
1122	>
1123
1124	<	#ifdef IS_MPI
813	<	if( mpiSim->getMyMolStart() <= molIndex &&
814	<	molIndex <= mpiSim->getMyMolEnd() ){
815	<	#endif // is_mpi
1124	>	for( i=0; i<n_components; i++ ){
1125
1126	<	molStart = index;
1127	<	nMemb = comp_stamps[i]->getNAtoms();
1128	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
1129	<
821	<	current_atom = comp_stamps[i]->getAtom( k );
822	<	if( current_atom->haveOrientation() ){
823	<
824	<	dAtom = new DirectionalAtom(index);
825	<	simnfo->n_oriented++;
826	<	the_atoms[index] = dAtom;
827	<
828	<	ux = current_atom->getOrntX();
829	<	uy = current_atom->getOrntY();
830	<	uz = current_atom->getOrntZ();
831	<
832	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
833	<
834	<	u = sqrt( uSqr );
835	<	ux = ux / u;
836	<	uy = uy / u;
837	<	uz = uz / u;
838	<
839	<	dAtom->setSUx( ux );
840	<	dAtom->setSUy( uy );
841	<	dAtom->setSUz( uz );
842	<	}
843	<	else{
844	<	the_atoms[index] = new GeneralAtom(index);
845	<	}
846	<	the_atoms[index]->setType( current_atom->getType() );
847	<	the_atoms[index]->setIndex( index );
848	<
849	<	// increment the index and repeat;
850	<	index++;
851	<	}
852	<
853	<	molEnd = index -1;
854	<	the_molecules[lMolIndex].setNMembers( nMemb );
855	<	the_molecules[lMolIndex].setStartAtom( molStart );
856	<	the_molecules[lMolIndex].setEndAtom( molEnd );
857	<	the_molecules[lMolIndex].setStampID( i );
858	<	lMolIndex++;
1126	>	id = the_components[i]->getType();
1127	>	comp_stamps[i] = NULL;
1128	>
1129	>	// check to make sure the component isn't already in the list
1130
1131	<	#ifdef IS_MPI
1131	>	comp_stamps[i] = headStamp->match( id );
1132	>	if( comp_stamps[i] == NULL ){
1133	>
1134	>	// extract the component from the list;
1135	>
1136	>	currentStamp = stamps->extractMolStamp( id );
1137	>	if( currentStamp == NULL ){
1138	>	sprintf( painCave.errMsg,
1139	>	"SimSetup error: Component \"%s\" was not found in the "
1140	>	"list of declared molecules\n",
1141	>	id );
1142	>	painCave.isFatal = 1;
1143	>	simError();
1144		}
862	–	#endif //is_mpi
1145
1146	<	molIndex++;
1146	>	headStamp->add( currentStamp );
1147	>	comp_stamps[i] = headStamp->match( id );
1148		}
1149		}
1150
1151		#ifdef IS_MPI
1152	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
1153	<
1154	<	delete[] globalIndex;
1152	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1153	>	MPIcheckPoint();
1154	>	#endif // is_mpi
1155
1156	<	mpiSim->mpiRefresh();
874	<	#endif //IS_MPI
875	<
876	<	the_ff->initializeAtoms();
1156	>
1157		}
1158
1159	<	void SimSetup::makeBonds( void ){
1160	<
1161	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1162	<	bond_pair* the_bonds;
1163	<	BondStamp* current_bond;
1164	<
1165	<	the_bonds = new bond_pair[tot_bonds];
1166	<	index = 0;
1167	<	offset = 0;
888	<	molIndex = 0;
889	<
1159	>	void SimSetup::calcSysValues( void ){
1160	>	int i, j, k;
1161	>
1162	>	int *molMembershipArray;
1163	>
1164	>	tot_atoms = 0;
1165	>	tot_bonds = 0;
1166	>	tot_bends = 0;
1167	>	tot_torsions = 0;
1168		for( i=0; i<n_components; i++ ){
1169	+
1170	+	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1171	+	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1172	+	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1173	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1174	+	}
1175	+
1176	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1177	+	molMembershipArray = new int[tot_atoms];
1178	+
1179	+	for(i=0; i<nInfo; i++){
1180	+	info[i].n_atoms = tot_atoms;
1181	+	info[i].n_bonds = tot_bonds;
1182	+	info[i].n_bends = tot_bends;
1183	+	info[i].n_torsions = tot_torsions;
1184	+	info[i].n_SRI = tot_SRI;
1185	+	info[i].n_mol = tot_nmol;
1186	+
1187	+	info[i].molMembershipArray = molMembershipArray;
1188	+	}
1189	+	}
1190
892	–	for( j=0; j<components_nmol[i]; j++ ){
893	–
1191		#ifdef IS_MPI
895	–	if( mpiSim->getMyMolStart() <= molIndex &&
896	–	molIndex <= mpiSim->getMyMolEnd() ){
897	–	#endif // is_mpi
898	–
899	–	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
900	–
901	–	current_bond = comp_stamps[i]->getBond( k );
902	–	the_bonds[index].a = current_bond->getA() + offset;
903	–	the_bonds[index].b = current_bond->getB() + offset;
1192
1193	<	exI = the_bonds[index].a;
1194	<	exJ = the_bonds[index].b;
1193	>	void SimSetup::mpiMolDivide( void ){
1194	>
1195	>	int i, j, k;
1196	>	int localMol, allMol;
1197	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1198
1199	<	// exclude_I must always be the smaller of the pair
1200	<	if( exI > exJ ){
1201	<	tempEx = exI;
911	<	exI = exJ;
912	<	exJ = tempEx;
913	<	}
1199	>	mpiSim = new mpiSimulation( info );
1200	>
1201	>	globalIndex = mpiSim->divideLabor();
1202
1203	<
1204	<	#ifdef IS_MPI
1203	>	// set up the local variables
1204	>
1205	>	mol2proc = mpiSim->getMolToProcMap();
1206	>	molCompType = mpiSim->getMolComponentType();
1207	>
1208	>	allMol = 0;
1209	>	localMol = 0;
1210	>	local_atoms = 0;
1211	>	local_bonds = 0;
1212	>	local_bends = 0;
1213	>	local_torsions = 0;
1214	>	globalAtomIndex = 0;
1215
918	–	the_excludes[index*2] =
919	–	the_atoms[exI]->getGlobalIndex() + 1;
920	–	the_excludes[index*2 + 1] =
921	–	the_atoms[exJ]->getGlobalIndex() + 1;
1216
1217	<	#else  // isn't MPI
1218	<
1219	<	the_excludes[index*2] =     exI + 1;
1220	<	the_excludes[index*2 + 1] = exJ + 1;
1221	<	// fortran index from 1 (hence the +1 in the indexing)
928	<	#endif  //is_mpi
929	<
930	<	// increment the index and repeat;
931	<	index++;
932	<	}
933	<	offset += comp_stamps[i]->getNAtoms();
1217	>	for( i=0; i<n_components; i++ ){
1218	>
1219	>	for( j=0; j<components_nmol[i]; j++ ){
1220	>
1221	>	if( mol2proc[allMol] == worldRank ){
1222
1223	<	#ifdef IS_MPI
1223	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1224	>	local_bonds +=    comp_stamps[i]->getNBonds();
1225	>	local_bends +=    comp_stamps[i]->getNBends();
1226	>	local_torsions += comp_stamps[i]->getNTorsions();
1227	>	localMol++;
1228	>	}
1229	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1230	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1231	>	globalAtomIndex++;
1232		}
937	–	#endif //is_mpi
938	–
939	–	molIndex++;
940	–	}
941	–	}
1233
1234	<	the_ff->initializeBonds( the_bonds );
1235	<	}
1236	<
1237	<	void SimSetup::makeBends( void ){
947	<
948	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
949	<	bend_set* the_bends;
950	<	BendStamp* current_bend;
951	<	LinkedAssign* extras;
952	<	LinkedAssign* current_extra;
1234	>	allMol++;
1235	>	}
1236	>	}
1237	>	local_SRI = local_bonds + local_bends + local_torsions;
1238
1239	+	info[0].n_atoms = mpiSim->getMyNlocal();
1240	+
1241	+	if( local_atoms != info[0].n_atoms ){
1242	+	sprintf( painCave.errMsg,
1243	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1244	+	" localAtom (%d) are not equal.\n",
1245	+	info[0].n_atoms,
1246	+	local_atoms );
1247	+	painCave.isFatal = 1;
1248	+	simError();
1249	+	}
1250
1251	<	the_bends = new bend_set[tot_bends];
1252	<	index = 0;
1253	<	offset = 0;
1254	<	molIndex = 0;
1255	<	for( i=0; i<n_components; i++ ){
1251	>	info[0].n_bonds = local_bonds;
1252	>	info[0].n_bends = local_bends;
1253	>	info[0].n_torsions = local_torsions;
1254	>	info[0].n_SRI = local_SRI;
1255	>	info[0].n_mol = localMol;
1256
1257	<	for( j=0; j<components_nmol[i]; j++ ){
1257	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1258	>	MPIcheckPoint();
1259	>	}
1260	>
1261	>	#endif // is_mpi
1262
963	–	#ifdef IS_MPI
964	–	if( mpiSim->getMyMolStart() <= molIndex &&
965	–	molIndex <= mpiSim->getMyMolEnd() ){
966	–	#endif // is_mpi
1263
1264	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
1265	<
970	<	current_bend = comp_stamps[i]->getBend( k );
971	<	the_bends[index].a = current_bend->getA() + offset;
972	<	the_bends[index].b = current_bend->getB() + offset;
973	<	the_bends[index].c = current_bend->getC() + offset;
974	<
975	<	if( current_bend->haveExtras() ){
976	<
977	<	extras = current_bend->getExtras();
978	<	current_extra = extras;
979	<
980	<	while( current_extra != NULL ){
981	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
982	<
983	<	switch( current_extra->getType() ){
984	<
985	<	case 0:
986	<	the_bends[index].ghost =
987	<	current_extra->getInt() + offset;
988	<	the_bends[index].isGhost = 1;
989	<	break;
990	<
991	<	case 1:
992	<	the_bends[index].ghost =
993	<	(int)current_extra->getDouble() + offset;
994	<	the_bends[index].isGhost = 1;
995	<	break;
996	<
997	<	default:
998	<	sprintf( painCave.errMsg,
999	<	"SimSetup Error: ghostVectorSource was neiter a "
1000	<	"double nor an int.\n"
1001	<	"-->Bend[%d] in %s\n",
1002	<	k, comp_stamps[i]->getID() );
1003	<	painCave.isFatal = 1;
1004	<	simError();
1005	<	}
1006	<	}
1007	<
1008	<	else{
1009	<
1010	<	sprintf( painCave.errMsg,
1011	<	"SimSetup Error: unhandled bend assignment:\n"
1012	<	"    -->%s in Bend[%d] in %s\n",
1013	<	current_extra->getlhs(),
1014	<	k, comp_stamps[i]->getID() );
1015	<	painCave.isFatal = 1;
1016	<	simError();
1017	<	}
1018	<
1019	<	current_extra = current_extra->getNext();
1020	<	}
1021	<	}
1022	<
1023	<	if( !the_bends[index].isGhost ){
1024	<
1025	<	exI = the_bends[index].a;
1026	<	exJ = the_bends[index].c;
1027	<	}
1028	<	else{
1029	<
1030	<	exI = the_bends[index].a;
1031	<	exJ = the_bends[index].b;
1032	<	}
1033	<
1034	<	// exclude_I must always be the smaller of the pair
1035	<	if( exI > exJ ){
1036	<	tempEx = exI;
1037	<	exI = exJ;
1038	<	exJ = tempEx;
1039	<	}
1264	>	void SimSetup::makeSysArrays( void ){
1265	>	int i, j, k, l;
1266
1267	+	Atom** the_atoms;
1268	+	Molecule* the_molecules;
1269	+	Exclude** the_excludes;
1270
1271	<	#ifdef IS_MPI
1271	>
1272	>	for(l=0; l<nInfo; l++){
1273	>
1274	>	// create the atom and short range interaction arrays
1275	>
1276	>	the_atoms = new Atom*[info[l].n_atoms];
1277	>	the_molecules = new Molecule[info[l].n_mol];
1278	>	int molIndex;
1279
1280	<	the_excludes[(index + tot_bonds)*2] =
1281	<	the_atoms[exI]->getGlobalIndex() + 1;
1046	<	the_excludes[(index + tot_bonds)*2 + 1] =
1047	<	the_atoms[exJ]->getGlobalIndex() + 1;
1048	<
1049	<	#else  // isn't MPI
1050	<
1051	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
1052	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1053	<	// fortran index from 1 (hence the +1 in the indexing)
1054	<	#endif  //is_mpi
1055	<
1056	<
1057	<	// increment the index and repeat;
1058	<	index++;
1059	<	}
1060	<	offset += comp_stamps[i]->getNAtoms();
1061	<
1280	>	// initialize the molecule's stampID's
1281	>
1282		#ifdef IS_MPI
1283	+
1284	+
1285	+	molIndex = 0;
1286	+	for(i=0; i<mpiSim->getTotNmol(); i++){
1287	+
1288	+	if(mol2proc[i] == worldRank ){
1289	+	the_molecules[molIndex].setStampID( molCompType[i] );
1290	+	the_molecules[molIndex].setMyIndex( molIndex );
1291	+	the_molecules[molIndex].setGlobalIndex( i );
1292	+	molIndex++;
1293		}
1064	–	#endif //is_mpi
1065	–
1066	–	molIndex++;
1294		}
1295	<	}
1296	<
1297	<	#ifdef IS_MPI
1298	<	sprintf( checkPointMsg,
1299	<	"Successfully created the bends list.\n" );
1300	<	MPIcheckPoint();
1295	>
1296	>	#else // is_mpi
1297	>
1298	>	molIndex = 0;
1299	>	globalAtomIndex = 0;
1300	>	for(i=0; i<n_components; i++){
1301	>	for(j=0; j<components_nmol[i]; j++ ){
1302	>	the_molecules[molIndex].setStampID( i );
1303	>	the_molecules[molIndex].setMyIndex( molIndex );
1304	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1305	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1306	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1307	>	globalAtomIndex++;
1308	>	}
1309	>	molIndex++;
1310	>	}
1311	>	}
1312	>
1313	>
1314		#endif // is_mpi
1075	–
1315
1077	–	the_ff->initializeBends( the_bends );
1078	–	}
1316
1317	<	void SimSetup::makeTorsions( void ){
1317	>	if( info[l].n_SRI ){
1318	>
1319	>	Exclude::createArray(info[l].n_SRI);
1320	>	the_excludes = new Exclude*[info[l].n_SRI];
1321	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1322	>	the_excludes[ex] = new Exclude(ex);
1323	>	}
1324	>	info[l].globalExcludes = new int;
1325	>	info[l].n_exclude = info[l].n_SRI;
1326	>	}
1327	>	else{
1328	>
1329	>	Exclude::createArray( 1 );
1330	>	the_excludes = new Exclude*;
1331	>	the_excludes[0] = new Exclude(0);
1332	>	the_excludes[0]->setPair( 0,0 );
1333	>	info[l].globalExcludes = new int;
1334	>	info[l].globalExcludes[0] = 0;
1335	>	info[l].n_exclude = 0;
1336	>	}
1337
1338	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1083	<	torsion_set* the_torsions;
1084	<	TorsionStamp* current_torsion;
1338	>	// set the arrays into the SimInfo object
1339
1340	<	the_torsions = new torsion_set[tot_torsions];
1341	<	index = 0;
1342	<	offset = 0;
1343	<	molIndex = 0;
1090	<	for( i=0; i<n_components; i++ ){
1340	>	info[l].atoms = the_atoms;
1341	>	info[l].molecules = the_molecules;
1342	>	info[l].nGlobalExcludes = 0;
1343	>	info[l].excludes = the_excludes;
1344
1345	<	for( j=0; j<components_nmol[i]; j++ ){
1345	>	the_ff->setSimInfo( info );
1346	>
1347	>	}
1348	>	}
1349
1350	<	#ifdef IS_MPI
1095	<	if( mpiSim->getMyMolStart() <= molIndex &&
1096	<	molIndex <= mpiSim->getMyMolEnd() ){
1097	<	#endif // is_mpi
1350	>	void SimSetup::makeIntegrator( void ){
1351
1352	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1352	>	int k;
1353
1354	<	current_torsion = comp_stamps[i]->getTorsion( k );
1355	<	the_torsions[index].a = current_torsion->getA() + offset;
1356	<	the_torsions[index].b = current_torsion->getB() + offset;
1357	<	the_torsions[index].c = current_torsion->getC() + offset;
1358	<	the_torsions[index].d = current_torsion->getD() + offset;
1354	>	NVT<RealIntegrator>*  myNVT = NULL;
1355	>	NPTi<RealIntegrator>* myNPTi = NULL;
1356	>	NPTf<RealIntegrator>* myNPTf = NULL;
1357	>	NPTim<RealIntegrator>* myNPTim = NULL;
1358	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1359	>
1360	>	for(k=0; k<nInfo; k++){
1361	>
1362	>	switch( ensembleCase ){
1363	>
1364	>	case NVE_ENS:
1365	>	if (globals->haveZconstraints()){
1366	>	setupZConstraint(info[k]);
1367	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1368	>	}
1369
1370	<	exI = the_torsions[index].a;
1371	<	exJ = the_torsions[index].d;
1370	>	else
1371	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1372	>	break;
1373	>
1374	>	case NVT_ENS:
1375	>	if (globals->haveZconstraints()){
1376	>	setupZConstraint(info[k]);
1377	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1378	>	}
1379	>	else
1380	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1381
1382	<
1383	<	// exclude_I must always be the smaller of the pair
1384	<	if( exI > exJ ){
1385	<	tempEx = exI;
1386	<	exI = exJ;
1387	<	exJ = tempEx;
1382	>	myNVT->setTargetTemp(globals->getTargetTemp());
1383	>
1384	>	if (globals->haveTauThermostat())
1385	>	myNVT->setTauThermostat(globals->getTauThermostat());
1386	>
1387	>	else {
1388	>	sprintf( painCave.errMsg,
1389	>	"SimSetup error: If you use the NVT\n"
1390	>	"    ensemble, you must set tauThermostat.\n");
1391	>	painCave.isFatal = 1;
1392	>	simError();
1393	>	}
1394	>	break;
1395	>
1396	>	case NPTi_ENS:
1397	>	if (globals->haveZconstraints()){
1398	>	setupZConstraint(info[k]);
1399	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1400		}
1401	+	else
1402	+	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1403
1404	+	myNPTi->setTargetTemp( globals->getTargetTemp() );
1405	+
1406	+	if (globals->haveTargetPressure())
1407	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1408	+	else {
1409	+	sprintf( painCave.errMsg,
1410	+	"SimSetup error: If you use a constant pressure\n"
1411	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1412	+	painCave.isFatal = 1;
1413	+	simError();
1414	+	}
1415	+
1416	+	if( globals->haveTauThermostat() )
1417	+	myNPTi->setTauThermostat( globals->getTauThermostat() );
1418	+	else{
1419	+	sprintf( painCave.errMsg,
1420	+	"SimSetup error: If you use an NPT\n"
1421	+	"    ensemble, you must set tauThermostat.\n");
1422	+	painCave.isFatal = 1;
1423	+	simError();
1424	+	}
1425	+
1426	+	if( globals->haveTauBarostat() )
1427	+	myNPTi->setTauBarostat( globals->getTauBarostat() );
1428	+	else{
1429	+	sprintf( painCave.errMsg,
1430	+	"SimSetup error: If you use an NPT\n"
1431	+	"    ensemble, you must set tauBarostat.\n");
1432	+	painCave.isFatal = 1;
1433	+	simError();
1434	+	}
1435	+	break;
1436	+
1437	+	case NPTf_ENS:
1438	+	if (globals->haveZconstraints()){
1439	+	setupZConstraint(info[k]);
1440	+	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1441	+	}
1442	+	else
1443	+	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1444
1445	<	#ifdef IS_MPI
1446	<
1447	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
1448	<	the_atoms[exI]->getGlobalIndex() + 1;
1449	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1450	<	the_atoms[exJ]->getGlobalIndex() + 1;
1451	<
1452	<	#else  // isn't MPI
1453	<
1454	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1455	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1456	<	// fortran indexes from 1 (hence the +1 in the indexing)
1457	<	#endif  //is_mpi
1458	<
1459	<
1460	<	// increment the index and repeat;
1461	<	index++;
1445	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1446	>
1447	>	if (globals->haveTargetPressure())
1448	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1449	>	else {
1450	>	sprintf( painCave.errMsg,
1451	>	"SimSetup error: If you use a constant pressure\n"
1452	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1453	>	painCave.isFatal = 1;
1454	>	simError();
1455	>	}
1456	>
1457	>	if( globals->haveTauThermostat() )
1458	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1459	>	else{
1460	>	sprintf( painCave.errMsg,
1461	>	"SimSetup error: If you use an NPT\n"
1462	>	"    ensemble, you must set tauThermostat.\n");
1463	>	painCave.isFatal = 1;
1464	>	simError();
1465		}
1466	<	offset += comp_stamps[i]->getNAtoms();
1466	>
1467	>	if( globals->haveTauBarostat() )
1468	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1469	>	else{
1470	>	sprintf( painCave.errMsg,
1471	>	"SimSetup error: If you use an NPT\n"
1472	>	"    ensemble, you must set tauBarostat.\n");
1473	>	painCave.isFatal = 1;
1474	>	simError();
1475	>	}
1476	>	break;
1477	>
1478	>	case NPTim_ENS:
1479	>	if (globals->haveZconstraints()){
1480	>	setupZConstraint(info[k]);
1481	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1482	>	}
1483	>	else
1484	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1485
1486	<	#ifdef IS_MPI
1486	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1487	>
1488	>	if (globals->haveTargetPressure())
1489	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1490	>	else {
1491	>	sprintf( painCave.errMsg,
1492	>	"SimSetup error: If you use a constant pressure\n"
1493	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1494	>	painCave.isFatal = 1;
1495	>	simError();
1496		}
1497	<	#endif //is_mpi
1498	<
1499	<	molIndex++;
1500	<	}
1501	<	}
1502	<
1503	<	the_ff->initializeTorsions( the_torsions );
1504	<	}
1505	<
1506	<	void SimSetup::initFromBass( void ){
1507	<
1508	<	int i, j, k;
1509	<	int n_cells;
1510	<	double cellx, celly, cellz;
1155	<	double temp1, temp2, temp3;
1156	<	int n_per_extra;
1157	<	int n_extra;
1158	<	int have_extra, done;
1159	<
1160	<	temp1 = (double)tot_nmol / 4.0;
1161	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1162	<	temp3 = ceil( temp2 );
1163	<
1164	<	have_extra =0;
1165	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1166	<	have_extra =1;
1167	<
1168	<	n_cells = (int)temp3 - 1;
1169	<	cellx = simnfo->box_x / temp3;
1170	<	celly = simnfo->box_y / temp3;
1171	<	cellz = simnfo->box_z / temp3;
1172	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1173	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1174	<	n_per_extra = (int)ceil( temp1 );
1175	<
1176	<	if( n_per_extra > 4){
1497	>
1498	>	if( globals->haveTauThermostat() )
1499	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1500	>	else{
1501	>	sprintf( painCave.errMsg,
1502	>	"SimSetup error: If you use an NPT\n"
1503	>	"    ensemble, you must set tauThermostat.\n");
1504	>	painCave.isFatal = 1;
1505	>	simError();
1506	>	}
1507	>
1508	>	if( globals->haveTauBarostat() )
1509	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1510	>	else{
1511		sprintf( painCave.errMsg,
1512	<	"SimSetup error. There has been an error in constructing"
1513	<	" the non-complete lattice.\n" );
1512	>	"SimSetup error: If you use an NPT\n"
1513	>	"    ensemble, you must set tauBarostat.\n");
1514		painCave.isFatal = 1;
1515		simError();
1182	–	}
1183	–	}
1184	–	else{
1185	–	n_cells = (int)temp3;
1186	–	cellx = simnfo->box_x / temp3;
1187	–	celly = simnfo->box_y / temp3;
1188	–	cellz = simnfo->box_z / temp3;
1189	–	}
1190	–
1191	–	current_mol = 0;
1192	–	current_comp_mol = 0;
1193	–	current_comp = 0;
1194	–	current_atom_ndx = 0;
1195	–
1196	–	for( i=0; i < n_cells ; i++ ){
1197	–	for( j=0; j < n_cells; j++ ){
1198	–	for( k=0; k < n_cells; k++ ){
1199	–
1200	–	makeElement( i * cellx,
1201	–	j * celly,
1202	–	k * cellz );
1203	–
1204	–	makeElement( i * cellx + 0.5 * cellx,
1205	–	j * celly + 0.5 * celly,
1206	–	k * cellz );
1207	–
1208	–	makeElement( i * cellx,
1209	–	j * celly + 0.5 * celly,
1210	–	k * cellz + 0.5 * cellz );
1211	–
1212	–	makeElement( i * cellx + 0.5 * cellx,
1213	–	j * celly,
1214	–	k * cellz + 0.5 * cellz );
1516		}
1517	<	}
1518	<	}
1519	<
1520	<	if( have_extra ){
1521	<	done = 0;
1522	<
1222	<	int start_ndx;
1223	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1224	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1225	<
1226	<	if( i < n_cells ){
1227	<
1228	<	if( j < n_cells ){
1229	<	start_ndx = n_cells;
1230	<	}
1231	<	else start_ndx = 0;
1517	>	break;
1518	>
1519	>	case NPTfm_ENS:
1520	>	if (globals->haveZconstraints()){
1521	>	setupZConstraint(info[k]);
1522	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1523		}
1524	<	else start_ndx = 0;
1524	>	else
1525	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1526
1527	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1528	<
1529	<	makeElement( i * cellx,
1530	<	j * celly,
1531	<	k * cellz );
1532	<	done = ( current_mol >= tot_nmol );
1533	<
1534	<	if( !done && n_per_extra > 1 ){
1535	<	makeElement( i * cellx + 0.5 * cellx,
1536	<	j * celly + 0.5 * celly,
1245	<	k * cellz );
1246	<	done = ( current_mol >= tot_nmol );
1247	<	}
1248	<
1249	<	if( !done && n_per_extra > 2){
1250	<	makeElement( i * cellx,
1251	<	j * celly + 0.5 * celly,
1252	<	k * cellz + 0.5 * cellz );
1253	<	done = ( current_mol >= tot_nmol );
1254	<	}
1255	<
1256	<	if( !done && n_per_extra > 3){
1257	<	makeElement( i * cellx + 0.5 * cellx,
1258	<	j * celly,
1259	<	k * cellz + 0.5 * cellz );
1260	<	done = ( current_mol >= tot_nmol );
1261	<	}
1262	<	}
1527	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1528	>
1529	>	if (globals->haveTargetPressure())
1530	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1531	>	else {
1532	>	sprintf( painCave.errMsg,
1533	>	"SimSetup error: If you use a constant pressure\n"
1534	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1535	>	painCave.isFatal = 1;
1536	>	simError();
1537		}
1538	+
1539	+	if( globals->haveTauThermostat() )
1540	+	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1541	+	else{
1542	+	sprintf( painCave.errMsg,
1543	+	"SimSetup error: If you use an NPT\n"
1544	+	"    ensemble, you must set tauThermostat.\n");
1545	+	painCave.isFatal = 1;
1546	+	simError();
1547	+	}
1548	+
1549	+	if( globals->haveTauBarostat() )
1550	+	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1551	+	else{
1552	+	sprintf( painCave.errMsg,
1553	+	"SimSetup error: If you use an NPT\n"
1554	+	"    ensemble, you must set tauBarostat.\n");
1555	+	painCave.isFatal = 1;
1556	+	simError();
1557	+	}
1558	+	break;
1559	+
1560	+	default:
1561	+	sprintf( painCave.errMsg,
1562	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1563	+	painCave.isFatal = 1;
1564	+	simError();
1565		}
1566		}
1567	+	}
1568
1569	+	void SimSetup::initFortran( void ){
1570
1571	<	for( i=0; i<simnfo->n_atoms; i++ ){
1572	<	simnfo->atoms[i]->set_vx( 0.0 );
1573	<	simnfo->atoms[i]->set_vy( 0.0 );
1574	<	simnfo->atoms[i]->set_vz( 0.0 );
1571	>	info[0].refreshSim();
1572	>
1573	>	if( !strcmp( info[0].mixingRule, "standard") ){
1574	>	the_ff->initForceField( LB_MIXING_RULE );
1575		}
1576	<	}
1576	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1577	>	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1578	>	}
1579	>	else{
1580	>	sprintf( painCave.errMsg,
1581	>	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1582	>	info[0].mixingRule );
1583	>	painCave.isFatal = 1;
1584	>	simError();
1585	>	}
1586
1275	–	void SimSetup::makeElement( double x, double y, double z ){
1587
1588	<	int k;
1589	<	AtomStamp* current_atom;
1590	<	DirectionalAtom* dAtom;
1591	<	double rotMat[3][3];
1588	>	#ifdef IS_MPI
1589	>	strcpy( checkPointMsg,
1590	>	"Successfully intialized the mixingRule for Fortran." );
1591	>	MPIcheckPoint();
1592	>	#endif // is_mpi
1593
1594	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1594	>	}
1595
1596	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1597	<	if( !current_atom->havePosition() ){
1596	>	void SimSetup::setupZConstraint(SimInfo& theInfo)
1597	>	{
1598	>	int nZConstraints;
1599	>	ZconStamp** zconStamp;
1600	>
1601	>	if(globals->haveZconstraintTime()){
1602	>
1603	>	//add sample time of z-constraint  into SimInfo's property list
1604	>	DoubleData* zconsTimeProp = new DoubleData();
1605	>	zconsTimeProp->setID(ZCONSTIME_ID);
1606	>	zconsTimeProp->setData(globals->getZconsTime());
1607	>	theInfo.addProperty(zconsTimeProp);
1608	>	}
1609	>	else{
1610		sprintf( painCave.errMsg,
1611	<	"SimSetup:initFromBass error.\n"
1612	<	"\tComponent %s, atom %s does not have a position specified.\n"
1289	<	"\tThe initialization routine is unable to give a start"
1290	<	" position.\n",
1291	<	comp_stamps[current_comp]->getID(),
1292	<	current_atom->getType() );
1611	>	"ZConstraint error: If you use an ZConstraint\n"
1612	>	" , you must set sample time.\n");
1613		painCave.isFatal = 1;
1614	<	simError();
1614	>	simError();
1615		}
1616
1617	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1618	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1619	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1617	>	//
1618	>	nZConstraints = globals->getNzConstraints();
1619	>	theInfo.nZconstraints = nZConstraints;
1620	>
1621	>	zconStamp = globals->getZconStamp();
1622	>	ZConsParaItem tempParaItem;
1623
1624	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1624	>	ZConsParaData* zconsParaData = new ZConsParaData();
1625	>	zconsParaData->setID(ZCONSPARADATA_ID);
1626	>
1627	>	for(int i = 0; i < nZConstraints; i++){
1628	>	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1629	>	tempParaItem.zPos = zconStamp[i]->getZpos();
1630	>	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1631	>	tempParaItem.kRatio = zconStamp[i]->getKratio();
1632
1633	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1633	>	zconsParaData->addItem(tempParaItem);
1634	>	}
1635
1636	<	rotMat[0][0] = 1.0;
1637	<	rotMat[0][1] = 0.0;
1638	<	rotMat[0][2] = 0.0;
1636	>	//sort the parameters by index of molecules
1637	>	zconsParaData->sortByIndex();
1638	>
1639	>	//push data into siminfo, therefore, we can retrieve later
1640	>	theInfo.addProperty(zconsParaData);
1641
1642	<	rotMat[1][0] = 0.0;
1643	<	rotMat[1][1] = 1.0;
1644	<	rotMat[1][2] = 0.0;
1645	<
1646	<	rotMat[2][0] = 0.0;
1647	<	rotMat[2][1] = 0.0;
1315	<	rotMat[2][2] = 1.0;
1316	<
1317	<	dAtom->setA( rotMat );
1642	>	//push zconsTol into siminfo, if user does not specify
1643	>	//value for zconsTol, a default value will be used
1644	>	DoubleData* zconsTol = new DoubleData();
1645	>	zconsTol->setID(ZCONSTOL_ID);
1646	>	if(globals->haveZconsTol()){
1647	>	zconsTol->setData(globals->getZconsTol());
1648		}
1649	+	else{
1650	+	double defaultZConsTol = 1E-6;
1651	+	sprintf( painCave.errMsg,
1652	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1653	+	" , default value %f is used.\n", defaultZConsTol);
1654	+	painCave.isFatal = 0;
1655	+	simError();
1656
1657	<	current_atom_ndx++;
1658	<	}
1659	<
1660	<	current_mol++;
1661	<	current_comp_mol++;
1662	<
1663	<	if( current_comp_mol >= components_nmol[current_comp] ){
1664	<
1665	<	current_comp_mol = 0;
1666	<	current_comp++;
1667	<	}
1657	>	zconsTol->setData(defaultZConsTol);
1658	>	}
1659	>	theInfo.addProperty(zconsTol);
1660	>
1661	>	//Determine the name of ouput file and add it into SimInfo's property list
1662	>	//Be careful, do not use inFileName, since it is a pointer which
1663	>	//point to a string at master node, and slave nodes do not contain that string
1664	>
1665	>	string zconsOutput(theInfo.finalName);
1666	>
1667	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1668	>
1669	>	StringData* zconsFilename = new StringData();
1670	>	zconsFilename->setID(ZCONSFILENAME_ID);
1671	>	zconsFilename->setData(zconsOutput);
1672	>
1673	>	theInfo.addProperty(zconsFilename);
1674		}

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