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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 466 by gezelter, Mon Apr 7 14:30:36 2003 UTC vs.
Revision 676 by tim, Mon Aug 11 19:40:06 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6
7		#include "SimSetup.hpp"
8		#include "parse_me.h"
#	Line 12 | Line 14 | SimSetup::SimSetup(){
14		#include "mpiSimulation.hpp"
15		#endif
16
17	+	// some defines for ensemble and Forcefield  cases
18	+
19	+	#define NVE_ENS        0
20	+	#define NVT_ENS        1
21	+	#define NPTi_ENS       2
22	+	#define NPTf_ENS       3
23	+	#define NPTim_ENS      4
24	+	#define NPTfm_ENS      5
25	+
26	+	#define FF_DUFF 0
27	+	#define FF_LJ   1
28	+	#define FF_EAM  2
29	+
30	+	using namespace std;
31	+
32		SimSetup::SimSetup(){
33	+
34	+	isInfoArray = 0;
35	+	nInfo = 1;
36	+
37		stamps = new MakeStamps();
38		globals = new Globals();
39
40	+
41		#ifdef IS_MPI
42		strcpy( checkPointMsg, "SimSetup creation successful" );
43		MPIcheckPoint();
#	Line 27 | Line 49 | void SimSetup::parseFile( char* fileName ){
49		delete globals;
50		}
51
52	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
53	+	info = the_info;
54	+	nInfo = theNinfo;
55	+	isInfoArray = 1;
56	+	}
57	+
58	+
59		void SimSetup::parseFile( char* fileName ){
60
61		#ifdef IS_MPI
#	Line 62 | Line 91 | void SimSetup::createSim( void ){
91
92		#endif // is_mpi
93
94	<	void SimSetup::createSim( void ){
94	>	void SimSetup::createSim(void){
95
96	<	MakeStamps *the_stamps;
97	<	Globals* the_globals;
98	<	ExtendedSystem* the_extendedsystem;
99	<	int i, j;
96	>	int i, j, k, globalAtomIndex;
97	>
98	>	// gather all of the information from the Bass file
99	>
100	>	gatherInfo();
101
102	<	// get the stamps and globals;
73	<	the_stamps = stamps;
74	<	the_globals = globals;
102	>	// creation of complex system objects
103
104	<	// set the easy ones first
77	<	simnfo->target_temp = the_globals->getTargetTemp();
78	<	simnfo->dt = the_globals->getDt();
79	<	simnfo->run_time = the_globals->getRunTime();
104	>	sysObjectsCreation();
105
106	<	// get the ones we know are there, yet still may need some work.
107	<	n_components = the_globals->getNComponents();
108	<	strcpy( force_field, the_globals->getForceField() );
106	>	// check on the post processing info
107	>
108	>	finalInfoCheck();
109
110	<	// get the ensemble and set up an extended system if we need it:
86	<	strcpy( ensemble, the_globals->getEnsemble() );
87	<	if( !strcasecmp( ensemble, "NPT" ) ) {
88	<	the_extendedsystem = new ExtendedSystem( simnfo );
89	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
90	<	the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
91	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
92	<	the_extendedsystem = new ExtendedSystem( simnfo );
93	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
94	<	} else if ( !strcasecmp( ensemble, "NVE") ) {
95	<	} else {
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
98	<	"reverting to NVE for this simulation.\n",
99	<	ensemble );
100	<	painCave.isFatal = 0;
101	<	simError();
102	<	strcpy( ensemble, "NVE" );
103	<	}
104	<	strcpy( simnfo->ensemble, ensemble );
110	>	// initialize the system coordinates
111
112	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
107	<	simnfo->usePBC = the_globals->getPBC();
108	<
109	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
110	<	else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
111	<	else{
112	<	sprintf( painCave.errMsg,
113	<	"SimSetup Error. Unrecognized force field -> %s\n",
114	<	force_field );
115	<	painCave.isFatal = 1;
116	<	simError();
117	<	}
112	>	if( !isInfoArray ) initSystemCoords();
113
114	<	#ifdef IS_MPI
120	<	strcpy( checkPointMsg, "ForceField creation successful" );
121	<	MPIcheckPoint();
122	<	#endif // is_mpi
114	>	// make the output filenames
115
116	+	makeOutNames();
117	+
118	+	// make the integrator
119
120	+	makeIntegrator();
121	+
122	+	#ifdef IS_MPI
123	+	mpiSim->mpiRefresh();
124	+	#endif
125
126	<	// get the components and calculate the tot_nMol and indvidual n_mol
127	<	the_components = the_globals->getComponents();
128	<	components_nmol = new int[n_components];
129	<	comp_stamps = new MoleculeStamp*[n_components];
126	>	// initialize the Fortran
127
128	<	if( !the_globals->haveNMol() ){
132	<	// we don't have the total number of molecules, so we assume it is
133	<	// given in each component
128	>	initFortran();
129
135	–	tot_nmol = 0;
136	–	for( i=0; i<n_components; i++ ){
130
138	–	if( !the_components[i]->haveNMol() ){
139	–	// we have a problem
140	–	sprintf( painCave.errMsg,
141	–	"SimSetup Error. No global NMol or component NMol"
142	–	" given. Cannot calculate the number of atoms.\n" );
143	–	painCave.isFatal = 1;
144	–	simError();
145	–	}
131
132	<	tot_nmol += the_components[i]->getNMol();
133	<	components_nmol[i] = the_components[i]->getNMol();
134	<	}
135	<	}
136	<	else{
137	<	sprintf( painCave.errMsg,
138	<	"SimSetup error.\n"
139	<	"\tSorry, the ability to specify total"
140	<	" nMols and then give molfractions in the components\n"
141	<	"\tis not currently supported."
142	<	" Please give nMol in the components.\n" );
143	<	painCave.isFatal = 1;
144	<	simError();
132	>	}
133	>
134	>
135	>	void SimSetup::makeMolecules( void ){
136	>
137	>	int k,l;
138	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
139	>	molInit molInfo;
140	>	DirectionalAtom* dAtom;
141	>	LinkedAssign* extras;
142	>	LinkedAssign* current_extra;
143	>	AtomStamp* currentAtom;
144	>	BondStamp* currentBond;
145	>	BendStamp* currentBend;
146	>	TorsionStamp* currentTorsion;
147	>
148	>	bond_pair* theBonds;
149	>	bend_set* theBends;
150	>	torsion_set* theTorsions;
151	>
152	>
153	>	//init the forceField paramters
154	>
155	>	the_ff->readParams();
156	>
157	>
158	>	// init the atoms
159	>
160	>	double ux, uy, uz, u, uSqr;
161	>
162	>	for(k=0; k<nInfo; k++){
163
164	+	the_ff->setSimInfo( &(info[k]) );
165	+
166	+	atomOffset = 0;
167	+	excludeOffset = 0;
168	+	for(i=0; i<info[k].n_mol; i++){
169
170	<	//     tot_nmol = the_globals->getNMol();
170	>	stampID = info[k].molecules[i].getStampID();
171	>
172	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
173	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
174	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
175	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
176	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
177	>
178	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
179	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
180	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
181	>	molInfo.myBends = new Bend*[molInfo.nBends];
182	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
183	>
184	>	theBonds = new bond_pair[molInfo.nBonds];
185	>	theBends = new bend_set[molInfo.nBends];
186	>	theTorsions = new torsion_set[molInfo.nTorsions];
187
188	<	//   //we have the total number of molecules, now we check for molfractions
165	<	//     for( i=0; i<n_components; i++ ){
188	>	// make the Atoms
189
190	<	//       if( !the_components[i]->haveMolFraction() ){
190	>	for(j=0; j<molInfo.nAtoms; j++){
191	>
192	>	currentAtom = comp_stamps[stampID]->getAtom( j );
193	>	if( currentAtom->haveOrientation() ){
194	>
195	>	dAtom = new DirectionalAtom( (j + atomOffset),
196	>	info[k].getConfiguration() );
197	>	info[k].n_oriented++;
198	>	molInfo.myAtoms[j] = dAtom;
199	>
200	>	ux = currentAtom->getOrntX();
201	>	uy = currentAtom->getOrntY();
202	>	uz = currentAtom->getOrntZ();
203	>
204	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
205	>
206	>	u = sqrt( uSqr );
207	>	ux = ux / u;
208	>	uy = uy / u;
209	>	uz = uz / u;
210	>
211	>	dAtom->setSUx( ux );
212	>	dAtom->setSUy( uy );
213	>	dAtom->setSUz( uz );
214	>	}
215	>	else{
216	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
217	>	info[k].getConfiguration() );
218	>	}
219	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
220
169	–	//  if( !the_components[i]->haveNMol() ){
170	–	//    //we have a problem
171	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
172	–	//              << " nMol was given in component
173	–
174	–	}
175	–
221		#ifdef IS_MPI
222	<	strcpy( checkPointMsg, "Have the number of components" );
223	<	MPIcheckPoint();
222	>
223	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
224	>
225		#endif // is_mpi
226	<
181	<	// make an array of molecule stamps that match the components used.
182	<	// also extract the used stamps out into a separate linked list
183	<
184	<	simnfo->nComponents = n_components;
185	<	simnfo->componentsNmol = components_nmol;
186	<	simnfo->compStamps = comp_stamps;
187	<	simnfo->headStamp = new LinkedMolStamp();
188	<
189	<	char* id;
190	<	LinkedMolStamp* headStamp = simnfo->headStamp;
191	<	LinkedMolStamp* currentStamp = NULL;
192	<	for( i=0; i<n_components; i++ ){
193	<
194	<	id = the_components[i]->getType();
195	<	comp_stamps[i] = NULL;
226	>	}
227
228	<	// check to make sure the component isn't already in the list
229	<
199	<	comp_stamps[i] = headStamp->match( id );
200	<	if( comp_stamps[i] == NULL ){
228	>	// make the bonds
229	>	for(j=0; j<molInfo.nBonds; j++){
230
231	<	// extract the component from the list;
231	>	currentBond = comp_stamps[stampID]->getBond( j );
232	>	theBonds[j].a = currentBond->getA() + atomOffset;
233	>	theBonds[j].b = currentBond->getB() + atomOffset;
234	>
235	>	exI = theBonds[j].a;
236	>	exJ = theBonds[j].b;
237	>
238	>	// exclude_I must always be the smaller of the pair
239	>	if( exI > exJ ){
240	>	tempEx = exI;
241	>	exI = exJ;
242	>	exJ = tempEx;
243	>	}
244	>	#ifdef IS_MPI
245	>	tempEx = exI;
246	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
247	>	tempEx = exJ;
248	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
249	>
250	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
251	>	#else  // isn't MPI
252	>
253	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
254	>	#endif  //is_mpi
255	>	}
256	>	excludeOffset += molInfo.nBonds;
257
258	<	currentStamp = the_stamps->extractMolStamp( id );
259	<	if( currentStamp == NULL ){
260	<	sprintf( painCave.errMsg,
261	<	"SimSetup error: Component \"%s\" was not found in the "
262	<	"list of declared molecules\n",
263	<	id );
264	<	painCave.isFatal = 1;
265	<	simError();
258	>	//make the bends
259	>	for(j=0; j<molInfo.nBends; j++){
260	>
261	>	currentBend = comp_stamps[stampID]->getBend( j );
262	>	theBends[j].a = currentBend->getA() + atomOffset;
263	>	theBends[j].b = currentBend->getB() + atomOffset;
264	>	theBends[j].c = currentBend->getC() + atomOffset;
265	>
266	>	if( currentBend->haveExtras() ){
267	>
268	>	extras = currentBend->getExtras();
269	>	current_extra = extras;
270	>
271	>	while( current_extra != NULL ){
272	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
273	>
274	>	switch( current_extra->getType() ){
275	>
276	>	case 0:
277	>	theBends[j].ghost =
278	>	current_extra->getInt() + atomOffset;
279	>	theBends[j].isGhost = 1;
280	>	break;
281	>
282	>	case 1:
283	>	theBends[j].ghost =
284	>	(int)current_extra->getDouble() + atomOffset;
285	>	theBends[j].isGhost = 1;
286	>	break;
287	>
288	>	default:
289	>	sprintf( painCave.errMsg,
290	>	"SimSetup Error: ghostVectorSource was neither a "
291	>	"double nor an int.\n"
292	>	"-->Bend[%d] in %s\n",
293	>	j, comp_stamps[stampID]->getID() );
294	>	painCave.isFatal = 1;
295	>	simError();
296	>	}
297	>	}
298	>
299	>	else{
300	>
301	>	sprintf( painCave.errMsg,
302	>	"SimSetup Error: unhandled bend assignment:\n"
303	>	"    -->%s in Bend[%d] in %s\n",
304	>	current_extra->getlhs(),
305	>	j, comp_stamps[stampID]->getID() );
306	>	painCave.isFatal = 1;
307	>	simError();
308	>	}
309	>
310	>	current_extra = current_extra->getNext();
311	>	}
312	>	}
313	>
314	>	if( !theBends[j].isGhost ){
315	>
316	>	exI = theBends[j].a;
317	>	exJ = theBends[j].c;
318	>	}
319	>	else{
320	>
321	>	exI = theBends[j].a;
322	>	exJ = theBends[j].b;
323	>	}
324	>
325	>	// exclude_I must always be the smaller of the pair
326	>	if( exI > exJ ){
327	>	tempEx = exI;
328	>	exI = exJ;
329	>	exJ = tempEx;
330	>	}
331	>	#ifdef IS_MPI
332	>	tempEx = exI;
333	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
334	>	tempEx = exJ;
335	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
336	>
337	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
338	>	#else  // isn't MPI
339	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
340	>	#endif  //is_mpi
341		}
342	+	excludeOffset += molInfo.nBends;
343
344	<	headStamp->add( currentStamp );
345	<	comp_stamps[i] = headStamp->match( id );
344	>	for(j=0; j<molInfo.nTorsions; j++){
345	>
346	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
347	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
348	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
349	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
350	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
351	>
352	>	exI = theTorsions[j].a;
353	>	exJ = theTorsions[j].d;
354	>
355	>	// exclude_I must always be the smaller of the pair
356	>	if( exI > exJ ){
357	>	tempEx = exI;
358	>	exI = exJ;
359	>	exJ = tempEx;
360	>	}
361	>	#ifdef IS_MPI
362	>	tempEx = exI;
363	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
364	>	tempEx = exJ;
365	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
366	>
367	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
368	>	#else  // isn't MPI
369	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
370	>	#endif  //is_mpi
371	>	}
372	>	excludeOffset += molInfo.nTorsions;
373	>
374	>
375	>	// send the arrays off to the forceField for init.
376	>
377	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
378	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
379	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
380	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
381	>
382	>
383	>	info[k].molecules[i].initialize( molInfo );
384	>
385	>
386	>	atomOffset += molInfo.nAtoms;
387	>	delete[] theBonds;
388	>	delete[] theBends;
389	>	delete[] theTorsions;
390		}
391		}
392	<
392	>
393		#ifdef IS_MPI
394	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
394	>	sprintf( checkPointMsg, "all molecules initialized succesfully" );
395		MPIcheckPoint();
396		#endif // is_mpi
397
398	+	// clean up the forcefield
399
400	+	the_ff->calcRcut();
401	+	the_ff->cleanMe();
402	+
403	+	}
404
405	+	void SimSetup::initFromBass( void ){
406
407	<	// caclulate the number of atoms, bonds, bends and torsions
407	>	int i, j, k;
408	>	int n_cells;
409	>	double cellx, celly, cellz;
410	>	double temp1, temp2, temp3;
411	>	int n_per_extra;
412	>	int n_extra;
413	>	int have_extra, done;
414
415	<	tot_atoms = 0;
416	<	tot_bonds = 0;
417	<	tot_bends = 0;
418	<	tot_torsions = 0;
233	<	for( i=0; i<n_components; i++ ){
234	<
235	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
236	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
237	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
238	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
239	<	}
415	>	double vel[3];
416	>	vel[0] = 0.0;
417	>	vel[1] = 0.0;
418	>	vel[2] = 0.0;
419
420	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
420	>	temp1 = (double)tot_nmol / 4.0;
421	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
422	>	temp3 = ceil( temp2 );
423
424	<	simnfo->n_atoms = tot_atoms;
425	<	simnfo->n_bonds = tot_bonds;
426	<	simnfo->n_bends = tot_bends;
246	<	simnfo->n_torsions = tot_torsions;
247	<	simnfo->n_SRI = tot_SRI;
248	<	simnfo->n_mol = tot_nmol;
424	>	have_extra =0;
425	>	if( temp2 < temp3 ){ // we have a non-complete lattice
426	>	have_extra =1;
427
428	<
429	<	#ifdef IS_MPI
428	>	n_cells = (int)temp3 - 1;
429	>	cellx = info[0].boxL[0] / temp3;
430	>	celly = info[0].boxL[1] / temp3;
431	>	cellz = info[0].boxL[2] / temp3;
432	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
433	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
434	>	n_per_extra = (int)ceil( temp1 );
435
436	<	// divide the molecules among processors here.
437	<
438	<	mpiSim = new mpiSimulation( simnfo );
439	<
440	<
436	>	if( n_per_extra > 4){
437	>	sprintf( painCave.errMsg,
438	>	"SimSetup error. There has been an error in constructing"
439	>	" the non-complete lattice.\n" );
440	>	painCave.isFatal = 1;
441	>	simError();
442	>	}
443	>	}
444	>	else{
445	>	n_cells = (int)temp3;
446	>	cellx = info[0].boxL[0] / temp3;
447	>	celly = info[0].boxL[1] / temp3;
448	>	cellz = info[0].boxL[2] / temp3;
449	>	}
450
451	<	globalIndex = mpiSim->divideLabor();
451	>	current_mol = 0;
452	>	current_comp_mol = 0;
453	>	current_comp = 0;
454	>	current_atom_ndx = 0;
455
456	<	// set up the local variables
457	<
458	<	int localMol, allMol;
264	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
456	>	for( i=0; i < n_cells ; i++ ){
457	>	for( j=0; j < n_cells; j++ ){
458	>	for( k=0; k < n_cells; k++ ){
459
460	<	int* mol2proc = mpiSim->getMolToProcMap();
461	<	int* molCompType = mpiSim->getMolComponentType();
462	<
269	<	allMol = 0;
270	<	localMol = 0;
271	<	local_atoms = 0;
272	<	local_bonds = 0;
273	<	local_bends = 0;
274	<	local_torsions = 0;
275	<	for( i=0; i<n_components; i++ ){
460	>	makeElement( i * cellx,
461	>	j * celly,
462	>	k * cellz );
463
464	<	for( j=0; j<components_nmol[i]; j++ ){
465	<
466	<	if( mol2proc[j] == worldRank ){
280	<
281	<	local_atoms +=    comp_stamps[i]->getNAtoms();
282	<	local_bonds +=    comp_stamps[i]->getNBonds();
283	<	local_bends +=    comp_stamps[i]->getNBends();
284	<	local_torsions += comp_stamps[i]->getNTorsions();
285	<	localMol++;
286	<	}
287	<	allMol++;
288	<	}
289	<	}
290	<	local_SRI = local_bonds + local_bends + local_torsions;
291	<
464	>	makeElement( i * cellx + 0.5 * cellx,
465	>	j * celly + 0.5 * celly,
466	>	k * cellz );
467
468	<	simnfo->n_atoms = mpiSim->getMyNlocal();
469	<
470	<	if( local_atoms != simnfo->n_atoms ){
471	<	sprintf( painCave.errMsg,
472	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
473	<	" localAtom (%d) are not equal.\n",
474	<	simnfo->n_atoms,
475	<	local_atoms );
476	<	painCave.isFatal = 1;
302	<	simError();
468	>	makeElement( i * cellx,
469	>	j * celly + 0.5 * celly,
470	>	k * cellz + 0.5 * cellz );
471	>
472	>	makeElement( i * cellx + 0.5 * cellx,
473	>	j * celly,
474	>	k * cellz + 0.5 * cellz );
475	>	}
476	>	}
477		}
478
479	<	simnfo->n_bonds = local_bonds;
480	<	simnfo->n_bends = local_bends;
307	<	simnfo->n_torsions = local_torsions;
308	<	simnfo->n_SRI = local_SRI;
309	<	simnfo->n_mol = localMol;
479	>	if( have_extra ){
480	>	done = 0;
481
482	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
483	<	MPIcheckPoint();
484	<
314	<
315	<	#endif // is_mpi
316	<
482	>	int start_ndx;
483	>	for( i=0; i < (n_cells+1) && !done; i++ ){
484	>	for( j=0; j < (n_cells+1) && !done; j++ ){
485
486	<	// create the atom and short range interaction arrays
486	>	if( i < n_cells ){
487
488	<	Atom::createArrays(simnfo->n_atoms);
489	<	the_atoms = new Atom*[simnfo->n_atoms];
490	<	the_molecules = new Molecule[simnfo->n_mol];
491	<	int molIndex;
488	>	if( j < n_cells ){
489	>	start_ndx = n_cells;
490	>	}
491	>	else start_ndx = 0;
492	>	}
493	>	else start_ndx = 0;
494
495	<	// initialize the molecule's stampID's
495	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
496
497	<	#ifdef IS_MPI
498	<
497	>	makeElement( i * cellx,
498	>	j * celly,
499	>	k * cellz );
500	>	done = ( current_mol >= tot_nmol );
501
502	<	molIndex = 0;
503	<	for(i=0; i<mpiSim->getTotNmol(); i++){
504	<
505	<	if(mol2proc[i] == worldRank ){
506	<	the_molecules[molIndex].setStampID( molCompType[i] );
507	<	the_molecules[molIndex].setMyIndex( molIndex );
508	<	molIndex++;
502	>	if( !done && n_per_extra > 1 ){
503	>	makeElement( i * cellx + 0.5 * cellx,
504	>	j * celly + 0.5 * celly,
505	>	k * cellz );
506	>	done = ( current_mol >= tot_nmol );
507	>	}
508	>
509	>	if( !done && n_per_extra > 2){
510	>	makeElement( i * cellx,
511	>	j * celly + 0.5 * celly,
512	>	k * cellz + 0.5 * cellz );
513	>	done = ( current_mol >= tot_nmol );
514	>	}
515	>
516	>	if( !done && n_per_extra > 3){
517	>	makeElement( i * cellx + 0.5 * cellx,
518	>	j * celly,
519	>	k * cellz + 0.5 * cellz );
520	>	done = ( current_mol >= tot_nmol );
521	>	}
522	>	}
523	>	}
524		}
525		}
526
527	<	#else // is_mpi
528	<
342	<	molIndex = 0;
343	<	for(i=0; i<n_components; i++){
344	<	for(j=0; j<components_nmol[i]; j++ ){
345	<	the_molecules[molIndex].setStampID( i );
346	<	the_molecules[molIndex].setMyIndex( molIndex );
347	<	molIndex++;
348	<	}
527	>	for( i=0; i<info[0].n_atoms; i++ ){
528	>	info[0].atoms[i]->setVel( vel );
529		}
530	<
530	>	}
531
532	<	#endif // is_mpi
532	>	void SimSetup::makeElement( double x, double y, double z ){
533
534	+	int k;
535	+	AtomStamp* current_atom;
536	+	DirectionalAtom* dAtom;
537	+	double rotMat[3][3];
538	+	double pos[3];
539
540	<	if( simnfo->n_SRI ){
540	>	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
541	>
542	>	current_atom = comp_stamps[current_comp]->getAtom( k );
543	>	if( !current_atom->havePosition() ){
544	>	sprintf( painCave.errMsg,
545	>	"SimSetup:initFromBass error.\n"
546	>	"\tComponent %s, atom %s does not have a position specified.\n"
547	>	"\tThe initialization routine is unable to give a start"
548	>	" position.\n",
549	>	comp_stamps[current_comp]->getID(),
550	>	current_atom->getType() );
551	>	painCave.isFatal = 1;
552	>	simError();
553	>	}
554
555	<	Exclude::createArray(simnfo->n_SRI);
556	<	the_excludes = new Exclude*[simnfo->n_SRI];
557	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
360	<	simnfo->globalExcludes = new int;
361	<	simnfo->n_exclude = simnfo->n_SRI;
362	<	}
363	<	else{
555	>	pos[0] = x + current_atom->getPosX();
556	>	pos[1] = y + current_atom->getPosY();
557	>	pos[2] = z + current_atom->getPosZ();
558
559	<	Exclude::createArray( 1 );
366	<	the_excludes = new Exclude*;
367	<	the_excludes[0] = new Exclude(0);
368	<	the_excludes[0]->setPair( 0,0 );
369	<	simnfo->globalExcludes = new int;
370	<	simnfo->globalExcludes[0] = 0;
371	<	simnfo->n_exclude = 0;
372	<	}
559	>	info[0].atoms[current_atom_ndx]->setPos( pos );
560
561	<	// set the arrays into the SimInfo object
561	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
562
563	<	simnfo->atoms = the_atoms;
377	<	simnfo->molecules = the_molecules;
378	<	simnfo->nGlobalExcludes = 0;
379	<	simnfo->excludes = the_excludes;
563	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
564
565	+	rotMat[0][0] = 1.0;
566	+	rotMat[0][1] = 0.0;
567	+	rotMat[0][2] = 0.0;
568
569	<	// get some of the tricky things that may still be in the globals
569	>	rotMat[1][0] = 0.0;
570	>	rotMat[1][1] = 1.0;
571	>	rotMat[1][2] = 0.0;
572
573	<
574	<	if( the_globals->haveBox() ){
575	<	simnfo->box_x = the_globals->getBox();
387	<	simnfo->box_y = the_globals->getBox();
388	<	simnfo->box_z = the_globals->getBox();
389	<	}
390	<	else if( the_globals->haveDensity() ){
573	>	rotMat[2][0] = 0.0;
574	>	rotMat[2][1] = 0.0;
575	>	rotMat[2][2] = 1.0;
576
577	<	double vol;
393	<	vol = (double)tot_nmol / the_globals->getDensity();
394	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
395	<	simnfo->box_y = simnfo->box_x;
396	<	simnfo->box_z = simnfo->box_x;
397	<	}
398	<	else{
399	<	if( !the_globals->haveBoxX() ){
400	<	sprintf( painCave.errMsg,
401	<	"SimSetup error, no periodic BoxX size given.\n" );
402	<	painCave.isFatal = 1;
403	<	simError();
577	>	dAtom->setA( rotMat );
578		}
405	–	simnfo->box_x = the_globals->getBoxX();
579
580	<	if( !the_globals->haveBoxY() ){
581	<	sprintf( painCave.errMsg,
409	<	"SimSetup error, no periodic BoxY size given.\n" );
410	<	painCave.isFatal = 1;
411	<	simError();
412	<	}
413	<	simnfo->box_y = the_globals->getBoxY();
580	>	current_atom_ndx++;
581	>	}
582
583	<	if( !the_globals->haveBoxZ() ){
584	<	sprintf( painCave.errMsg,
585	<	"SimSetup error, no periodic BoxZ size given.\n" );
586	<	painCave.isFatal = 1;
587	<	simError();
588	<	}
589	<	simnfo->box_z = the_globals->getBoxZ();
583	>	current_mol++;
584	>	current_comp_mol++;
585	>
586	>	if( current_comp_mol >= components_nmol[current_comp] ){
587	>
588	>	current_comp_mol = 0;
589	>	current_comp++;
590		}
591	+	}
592
424	–	#ifdef IS_MPI
425	–	strcpy( checkPointMsg, "Box size set up" );
426	–	MPIcheckPoint();
427	–	#endif // is_mpi
593
594	+	void SimSetup::gatherInfo( void ){
595	+	int i,j,k;
596
597	<	// initialize the arrays
597	>	ensembleCase = -1;
598	>	ffCase = -1;
599
600	<	the_ff->setSimInfo( simnfo );
600	>	// set the easy ones first
601
602	<	makeMolecules();
603	<	simnfo->identArray = new int[simnfo->n_atoms];
604	<	for(i=0; i<simnfo->n_atoms; i++){
605	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
602	>	for( i=0; i<nInfo; i++){
603	>	info[i].target_temp = globals->getTargetTemp();
604	>	info[i].dt = globals->getDt();
605	>	info[i].run_time = globals->getRunTime();
606		}
607	<
440	<	if (the_globals->getUseRF() ) {
441	<	simnfo->useReactionField = 1;
442	<
443	<	if( !the_globals->haveECR() ){
444	<	sprintf( painCave.errMsg,
445	<	"SimSetup Warning: using default value of 1/2 the smallest "
446	<	"box length for the electrostaticCutoffRadius.\n"
447	<	"I hope you have a very fast processor!\n");
448	<	painCave.isFatal = 0;
449	<	simError();
450	<	double smallest;
451	<	smallest = simnfo->box_x;
452	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
453	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
454	<	simnfo->ecr = 0.5 * smallest;
455	<	} else {
456	<	simnfo->ecr        = the_globals->getECR();
457	<	}
607	>	n_components = globals->getNComponents();
608
609	<	if( !the_globals->haveEST() ){
610	<	sprintf( painCave.errMsg,
611	<	"SimSetup Warning: using default value of 0.05 * the "
612	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
613	<	);
614	<	painCave.isFatal = 0;
615	<	simError();
616	<	simnfo->est = 0.05 * simnfo->ecr;
617	<	} else {
618	<	simnfo->est        = the_globals->getEST();
619	<	}
620	<
621	<	if(!the_globals->haveDielectric() ){
622	<	sprintf( painCave.errMsg,
623	<	"SimSetup Error: You are trying to use Reaction Field without"
624	<	"setting a dielectric constant!\n"
625	<	);
626	<	painCave.isFatal = 1;
627	<	simError();
628	<	}
629	<	simnfo->dielectric = the_globals->getDielectric();
630	<	} else {
631	<	if (simnfo->n_dipoles) {
632	<
633	<	if( !the_globals->haveECR() ){
634	<	sprintf( painCave.errMsg,
635	<	"SimSetup Warning: using default value of 1/2 the smallest"
636	<	"box length for the electrostaticCutoffRadius.\n"
637	<	"I hope you have a very fast processor!\n");
638	<	painCave.isFatal = 0;
639	<	simError();
640	<	double smallest;
641	<	smallest = simnfo->box_x;
642	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
643	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
644	<	simnfo->ecr = 0.5 * smallest;
495	<	} else {
496	<	simnfo->ecr        = the_globals->getECR();
497	<	}
498	<
499	<	if( !the_globals->haveEST() ){
500	<	sprintf( painCave.errMsg,
501	<	"SimSetup Warning: using default value of 5% of the"
502	<	"electrostaticCutoffRadius for the "
503	<	"electrostaticSkinThickness\n"
504	<	);
505	<	painCave.isFatal = 0;
506	<	simError();
507	<	simnfo->est = 0.05 * simnfo->ecr;
508	<	} else {
509	<	simnfo->est        = the_globals->getEST();
510	<	}
511	<	}
609	>
610	>	// get the forceField
611	>
612	>	strcpy( force_field, globals->getForceField() );
613	>
614	>	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
615	>	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
616	>	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
617	>	else{
618	>	sprintf( painCave.errMsg,
619	>	"SimSetup Error. Unrecognized force field -> %s\n",
620	>	force_field );
621	>	painCave.isFatal = 1;
622	>	simError();
623	>	}
624	>
625	>	// get the ensemble
626	>
627	>	strcpy( ensemble, globals->getEnsemble() );
628	>
629	>	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
630	>	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
631	>	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
632	>	ensembleCase = NPTi_ENS;
633	>	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
634	>	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
635	>	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
636	>	else{
637	>	sprintf( painCave.errMsg,
638	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
639	>	"reverting to NVE for this simulation.\n",
640	>	ensemble );
641	>	painCave.isFatal = 0;
642	>	simError();
643	>	strcpy( ensemble, "NVE" );
644	>	ensembleCase = NVE_ENS;
645		}
646	+
647	+	for(i=0; i<nInfo; i++){
648	+
649	+	strcpy( info[i].ensemble, ensemble );
650
651	<	#ifdef IS_MPI
515	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
516	<	MPIcheckPoint();
517	<	#endif // is_mpi
651	>	// get the mixing rule
652
653	<	if( the_globals->haveInitialConfig() ){
653	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
654	>	info[i].usePBC = globals->getPBC();
655	>	}
656	>
657	>	// get the components and calculate the tot_nMol and indvidual n_mol
658
659	<	InitializeFromFile* fileInit;
660	<	#ifdef IS_MPI // is_mpi
523	<	if( worldRank == 0 ){
524	<	#endif //is_mpi
525	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
526	<	#ifdef IS_MPI
527	<	}else fileInit = new InitializeFromFile( NULL );
528	<	#endif
529	<	fileInit->read_xyz( simnfo ); // default velocities on
659	>	the_components = globals->getComponents();
660	>	components_nmol = new int[n_components];
661
531	–	delete fileInit;
532	–	}
533	–	else{
662
663	<	#ifdef IS_MPI
663	>	if( !globals->haveNMol() ){
664	>	// we don't have the total number of molecules, so we assume it is
665	>	// given in each component
666
667	<	// no init from bass
668	<
539	<	sprintf( painCave.errMsg,
540	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
541	<	painCave.isFatal;
542	<	simError();
543	<
544	<	#else
667	>	tot_nmol = 0;
668	>	for( i=0; i<n_components; i++ ){
669
670	<	initFromBass();
670	>	if( !the_components[i]->haveNMol() ){
671	>	// we have a problem
672	>	sprintf( painCave.errMsg,
673	>	"SimSetup Error. No global NMol or component NMol"
674	>	" given. Cannot calculate the number of atoms.\n" );
675	>	painCave.isFatal = 1;
676	>	simError();
677	>	}
678
679	+	tot_nmol += the_components[i]->getNMol();
680	+	components_nmol[i] = the_components[i]->getNMol();
681	+	}
682	+	}
683	+	else{
684	+	sprintf( painCave.errMsg,
685	+	"SimSetup error.\n"
686	+	"\tSorry, the ability to specify total"
687	+	" nMols and then give molfractions in the components\n"
688	+	"\tis not currently supported."
689	+	" Please give nMol in the components.\n" );
690	+	painCave.isFatal = 1;
691	+	simError();
692	+	}
693
694	<	#endif
550	<	}
551	<
552	<	#ifdef IS_MPI
553	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
554	<	MPIcheckPoint();
555	<	#endif // is_mpi
556	<
557	<
558	<
559	<
694	>	// set the status, sample, and thermal kick times
695
696	+	for(i=0; i<nInfo; i++){
697
698	<
699	<	#ifdef IS_MPI
700	<	if( worldRank == 0 ){
701	<	#endif // is_mpi
566	<
567	<	if( the_globals->haveFinalConfig() ){
568	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
698	>	if( globals->haveSampleTime() ){
699	>	info[i].sampleTime = globals->getSampleTime();
700	>	info[i].statusTime = info[i].sampleTime;
701	>	info[i].thermalTime = info[i].sampleTime;
702		}
703		else{
704	<	strcpy( simnfo->finalName, inFileName );
705	<	char* endTest;
706	<	int nameLength = strlen( simnfo->finalName );
574	<	endTest = &(simnfo->finalName[nameLength - 5]);
575	<	if( !strcmp( endTest, ".bass" ) ){
576	<	strcpy( endTest, ".eor" );
577	<	}
578	<	else if( !strcmp( endTest, ".BASS" ) ){
579	<	strcpy( endTest, ".eor" );
580	<	}
581	<	else{
582	<	endTest = &(simnfo->finalName[nameLength - 4]);
583	<	if( !strcmp( endTest, ".bss" ) ){
584	<	strcpy( endTest, ".eor" );
585	<	}
586	<	else if( !strcmp( endTest, ".mdl" ) ){
587	<	strcpy( endTest, ".eor" );
588	<	}
589	<	else{
590	<	strcat( simnfo->finalName, ".eor" );
591	<	}
592	<	}
704	>	info[i].sampleTime = globals->getRunTime();
705	>	info[i].statusTime = info[i].sampleTime;
706	>	info[i].thermalTime = info[i].sampleTime;
707		}
708
709	<	// make the sample and status out names
709	>	if( globals->haveStatusTime() ){
710	>	info[i].statusTime = globals->getStatusTime();
711	>	}
712
713	<	strcpy( simnfo->sampleName, inFileName );
714	<	char* endTest;
599	<	int nameLength = strlen( simnfo->sampleName );
600	<	endTest = &(simnfo->sampleName[nameLength - 5]);
601	<	if( !strcmp( endTest, ".bass" ) ){
602	<	strcpy( endTest, ".dump" );
713	>	if( globals->haveThermalTime() ){
714	>	info[i].thermalTime = globals->getThermalTime();
715		}
716	<	else if( !strcmp( endTest, ".BASS" ) ){
717	<	strcpy( endTest, ".dump" );
716	>
717	>	// check for the temperature set flag
718	>
719	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
720	>
721	>	// get some of the tricky things that may still be in the globals
722	>
723	>	double boxVector[3];
724	>	if( globals->haveBox() ){
725	>	boxVector[0] = globals->getBox();
726	>	boxVector[1] = globals->getBox();
727	>	boxVector[2] = globals->getBox();
728	>
729	>	info[i].setBox( boxVector );
730		}
731	+	else if( globals->haveDensity() ){
732	+
733	+	double vol;
734	+	vol = (double)tot_nmol / globals->getDensity();
735	+	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
736	+	boxVector[1] = boxVector[0];
737	+	boxVector[2] = boxVector[0];
738	+
739	+	info[i].setBox( boxVector );
740	+	}
741		else{
742	<	endTest = &(simnfo->sampleName[nameLength - 4]);
743	<	if( !strcmp( endTest, ".bss" ) ){
744	<	strcpy( endTest, ".dump" );
742	>	if( !globals->haveBoxX() ){
743	>	sprintf( painCave.errMsg,
744	>	"SimSetup error, no periodic BoxX size given.\n" );
745	>	painCave.isFatal = 1;
746	>	simError();
747		}
748	<	else if( !strcmp( endTest, ".mdl" ) ){
749	<	strcpy( endTest, ".dump" );
750	<	}
751	<	else{
752	<	strcat( simnfo->sampleName, ".dump" );
748	>	boxVector[0] = globals->getBoxX();
749	>
750	>	if( !globals->haveBoxY() ){
751	>	sprintf( painCave.errMsg,
752	>	"SimSetup error, no periodic BoxY size given.\n" );
753	>	painCave.isFatal = 1;
754	>	simError();
755		}
756	<	}
757	<
758	<	strcpy( simnfo->statusName, inFileName );
759	<	nameLength = strlen( simnfo->statusName );
760	<	endTest = &(simnfo->statusName[nameLength - 5]);
761	<	if( !strcmp( endTest, ".bass" ) ){
762	<	strcpy( endTest, ".stat" );
625	<	}
626	<	else if( !strcmp( endTest, ".BASS" ) ){
627	<	strcpy( endTest, ".stat" );
628	<	}
629	<	else{
630	<	endTest = &(simnfo->statusName[nameLength - 4]);
631	<	if( !strcmp( endTest, ".bss" ) ){
632	<	strcpy( endTest, ".stat" );
756	>	boxVector[1] = globals->getBoxY();
757	>
758	>	if( !globals->haveBoxZ() ){
759	>	sprintf( painCave.errMsg,
760	>	"SimSetup error, no periodic BoxZ size given.\n" );
761	>	painCave.isFatal = 1;
762	>	simError();
763		}
764	<	else if( !strcmp( endTest, ".mdl" ) ){
765	<	strcpy( endTest, ".stat" );
766	<	}
637	<	else{
638	<	strcat( simnfo->statusName, ".stat" );
639	<	}
764	>	boxVector[2] = globals->getBoxZ();
765	>
766	>	info[i].setBox( boxVector );
767		}
768	+
769	+	}
770
771		#ifdef IS_MPI
772	<	}
772	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
773	>	MPIcheckPoint();
774		#endif // is_mpi
645	–
646	–	// set the status, sample, and themal kick times
647	–
648	–	if( the_globals->haveSampleTime() ){
649	–	simnfo->sampleTime = the_globals->getSampleTime();
650	–	simnfo->statusTime = simnfo->sampleTime;
651	–	simnfo->thermalTime = simnfo->sampleTime;
652	–	}
653	–	else{
654	–	simnfo->sampleTime = the_globals->getRunTime();
655	–	simnfo->statusTime = simnfo->sampleTime;
656	–	simnfo->thermalTime = simnfo->sampleTime;
657	–	}
775
776	<	if( the_globals->haveStatusTime() ){
660	<	simnfo->statusTime = the_globals->getStatusTime();
661	<	}
776	>	}
777
663	–	if( the_globals->haveThermalTime() ){
664	–	simnfo->thermalTime = the_globals->getThermalTime();
665	–	}
778
779	<	// check for the temperature set flag
779	>	void SimSetup::finalInfoCheck( void ){
780	>	int index;
781	>	int usesDipoles;
782	>	int i;
783
784	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
784	>	for(i=0; i<nInfo; i++){
785	>	// check electrostatic parameters
786	>
787	>	index = 0;
788	>	usesDipoles = 0;
789	>	while( (index < info[i].n_atoms) && !usesDipoles ){
790	>	usesDipoles = (info[i].atoms[index])->hasDipole();
791	>	index++;
792	>	}
793	>
794	>	#ifdef IS_MPI
795	>	int myUse = usesDipoles;
796	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
797	>	#endif //is_mpi
798	>
799	>	double theEcr, theEst;
800	>
801	>	if (globals->getUseRF() ) {
802	>	info[i].useReactionField = 1;
803	>
804	>	if( !globals->haveECR() ){
805	>	sprintf( painCave.errMsg,
806	>	"SimSetup Warning: using default value of 1/2 the smallest "
807	>	"box length for the electrostaticCutoffRadius.\n"
808	>	"I hope you have a very fast processor!\n");
809	>	painCave.isFatal = 0;
810	>	simError();
811	>	double smallest;
812	>	smallest = info[i].boxL[0];
813	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
814	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
815	>	theEcr = 0.5 * smallest;
816	>	} else {
817	>	theEcr = globals->getECR();
818	>	}
819	>
820	>	if( !globals->haveEST() ){
821	>	sprintf( painCave.errMsg,
822	>	"SimSetup Warning: using default value of 0.05 * the "
823	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
824	>	);
825	>	painCave.isFatal = 0;
826	>	simError();
827	>	theEst = 0.05 * theEcr;
828	>	} else {
829	>	theEst= globals->getEST();
830	>	}
831	>
832	>	info[i].setEcr( theEcr, theEst );
833	>
834	>	if(!globals->haveDielectric() ){
835	>	sprintf( painCave.errMsg,
836	>	"SimSetup Error: You are trying to use Reaction Field without"
837	>	"setting a dielectric constant!\n"
838	>	);
839	>	painCave.isFatal = 1;
840	>	simError();
841	>	}
842	>	info[i].dielectric = globals->getDielectric();
843	>	}
844	>	else {
845	>	if (usesDipoles) {
846	>
847	>	if( !globals->haveECR() ){
848	>	sprintf( painCave.errMsg,
849	>	"SimSetup Warning: using default value of 1/2 the smallest "
850	>	"box length for the electrostaticCutoffRadius.\n"
851	>	"I hope you have a very fast processor!\n");
852	>	painCave.isFatal = 0;
853	>	simError();
854	>	double smallest;
855	>	smallest = info[i].boxL[0];
856	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
857	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
858	>	theEcr = 0.5 * smallest;
859	>	} else {
860	>	theEcr = globals->getECR();
861	>	}
862	>
863	>	if( !globals->haveEST() ){
864	>	sprintf( painCave.errMsg,
865	>	"SimSetup Warning: using default value of 0.05 * the "
866	>	"electrostaticCutoffRadius for the "
867	>	"electrostaticSkinThickness\n"
868	>	);
869	>	painCave.isFatal = 0;
870	>	simError();
871	>	theEst = 0.05 * theEcr;
872	>	} else {
873	>	theEst= globals->getEST();
874	>	}
875	>
876	>	info[i].setEcr( theEcr, theEst );
877	>	}
878	>	}
879	>	}
880
671	–
672	–	//   // make the longe range forces and the integrator
673	–
674	–	//   new AllLong( simnfo );
675	–
676	–	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic(simnfo,
677	–	the_ff,
678	–	the_extendedsystem);
679	–	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo,
680	–	the_ff,
681	–	the_extendedsystem );
682	–
881		#ifdef IS_MPI
882	<	mpiSim->mpiRefresh();
883	<	#endif
882	>	strcpy( checkPointMsg, "post processing checks out" );
883	>	MPIcheckPoint();
884	>	#endif // is_mpi
885
886	<	// initialize the Fortran
886	>	}
887
888	+	void SimSetup::initSystemCoords( void ){
889	+	int i;
890	+
891	+	std::cerr << "Setting atom Coords\n";
892
893	<	simnfo->refreshSim();
893	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
894
895	<	if( !strcmp( simnfo->mixingRule, "standard") ){
896	<	the_ff->initForceField( LB_MIXING_RULE );
895	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
896	>
897	>	if( globals->haveInitialConfig() ){
898	>
899	>	InitializeFromFile* fileInit;
900	>	#ifdef IS_MPI // is_mpi
901	>	if( worldRank == 0 ){
902	>	#endif //is_mpi
903	>	fileInit = new InitializeFromFile( globals->getInitialConfig() );
904	>	#ifdef IS_MPI
905	>	}else fileInit = new InitializeFromFile( NULL );
906	>	#endif
907	>	fileInit->readInit( info ); // default velocities on
908	>
909	>	delete fileInit;
910		}
695	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
696	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
697	–	}
911		else{
912	+
913	+	#ifdef IS_MPI
914	+
915	+	// no init from bass
916	+
917		sprintf( painCave.errMsg,
918	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
919	<	simnfo->mixingRule );
702	<	painCave.isFatal = 1;
918	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
919	>	painCave.isFatal;
920		simError();
921	+
922	+	#else
923	+
924	+	initFromBass();
925	+
926	+
927	+	#endif
928		}
929	<
706	<
929	>
930		#ifdef IS_MPI
931	<	strcpy( checkPointMsg,
709	<	"Successfully intialized the mixingRule for Fortran." );
931	>	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
932		MPIcheckPoint();
933		#endif // is_mpi
934	+
935		}
936
937
938	<	void SimSetup::makeMolecules( void ){
716	<
717	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
718	<	molInit info;
719	<	DirectionalAtom* dAtom;
720	<	LinkedAssign* extras;
721	<	LinkedAssign* current_extra;
722	<	AtomStamp* currentAtom;
723	<	BondStamp* currentBond;
724	<	BendStamp* currentBend;
725	<	TorsionStamp* currentTorsion;
726	<
727	<	bond_pair* theBonds;
728	<	bend_set* theBends;
729	<	torsion_set* theTorsions;
730	<
938	>	void SimSetup::makeOutNames( void ){
939
940	<	//init the forceField paramters
940	>	int k;
941
734	–	the_ff->readParams();
735	–
942
943	<	// init the atoms
943	>	for(k=0; k<nInfo; k++){
944
739	–	double ux, uy, uz, u, uSqr;
740	–
741	–	atomOffset = 0;
742	–	excludeOffset = 0;
743	–	for(i=0; i<simnfo->n_mol; i++){
744	–
745	–	stampID = the_molecules[i].getStampID();
746	–
747	–	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
748	–	info.nBonds    = comp_stamps[stampID]->getNBonds();
749	–	info.nBends    = comp_stamps[stampID]->getNBends();
750	–	info.nTorsions = comp_stamps[stampID]->getNTorsions();
751	–	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
752	–
753	–	info.myAtoms = &the_atoms[atomOffset];
754	–	info.myExcludes = &the_excludes[excludeOffset];
755	–	info.myBonds = new Bond*[info.nBonds];
756	–	info.myBends = new Bend*[info.nBends];
757	–	info.myTorsions = new Torsion*[info.nTorsions];
758	–
759	–	theBonds = new bond_pair[info.nBonds];
760	–	theBends = new bend_set[info.nBends];
761	–	theTorsions = new torsion_set[info.nTorsions];
762	–
763	–	// make the Atoms
764	–
765	–	for(j=0; j<info.nAtoms; j++){
766	–
767	–	currentAtom = comp_stamps[stampID]->getAtom( j );
768	–	if( currentAtom->haveOrientation() ){
769	–
770	–	dAtom = new DirectionalAtom(j + atomOffset);
771	–	simnfo->n_oriented++;
772	–	info.myAtoms[j] = dAtom;
773	–
774	–	ux = currentAtom->getOrntX();
775	–	uy = currentAtom->getOrntY();
776	–	uz = currentAtom->getOrntZ();
777	–
778	–	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
779	–
780	–	u = sqrt( uSqr );
781	–	ux = ux / u;
782	–	uy = uy / u;
783	–	uz = uz / u;
784	–
785	–	dAtom->setSUx( ux );
786	–	dAtom->setSUy( uy );
787	–	dAtom->setSUz( uz );
788	–	}
789	–	else{
790	–	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
791	–	}
792	–	info.myAtoms[j]->setType( currentAtom->getType() );
793	–
945		#ifdef IS_MPI
946	<
796	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
797	<
946	>	if( worldRank == 0 ){
947		#endif // is_mpi
799	–	}
800	–
801	–	// make the bonds
802	–	for(j=0; j<info.nBonds; j++){
948
949	<	currentBond = comp_stamps[stampID]->getBond( j );
950	<	theBonds[j].a = currentBond->getA() + atomOffset;
806	<	theBonds[j].b = currentBond->getB() + atomOffset;
807	<
808	<	exI = theBonds[j].a;
809	<	exJ = theBonds[j].b;
810	<
811	<	// exclude_I must always be the smaller of the pair
812	<	if( exI > exJ ){
813	<	tempEx = exI;
814	<	exI = exJ;
815	<	exJ = tempEx;
949	>	if( globals->haveFinalConfig() ){
950	>	strcpy( info[k].finalName, globals->getFinalConfig() );
951		}
952	<	#ifdef IS_MPI
953	<	tempEx = exI;
954	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
955	<	tempEx = exJ;
956	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
957	<
958	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
959	<	#else  // isn't MPI
960	<
961	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
962	<	#endif  //is_mpi
963	<	}
964	<	excludeOffset += info.nBonds;
965	<
966	<	//make the bends
832	<	for(j=0; j<info.nBends; j++){
833	<
834	<	currentBend = comp_stamps[stampID]->getBend( j );
835	<	theBends[j].a = currentBend->getA() + atomOffset;
836	<	theBends[j].b = currentBend->getB() + atomOffset;
837	<	theBends[j].c = currentBend->getC() + atomOffset;
838	<
839	<	if( currentBend->haveExtras() ){
840	<
841	<	extras = currentBend->getExtras();
842	<	current_extra = extras;
843	<
844	<	while( current_extra != NULL ){
845	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
846	<
847	<	switch( current_extra->getType() ){
848	<
849	<	case 0:
850	<	theBends[j].ghost =
851	<	current_extra->getInt() + atomOffset;
852	<	theBends[j].isGhost = 1;
853	<	break;
854	<
855	<	case 1:
856	<	theBends[j].ghost =
857	<	(int)current_extra->getDouble() + atomOffset;
858	<	theBends[j].isGhost = 1;
859	<	break;
860	<
861	<	default:
862	<	sprintf( painCave.errMsg,
863	<	"SimSetup Error: ghostVectorSource was neither a "
864	<	"double nor an int.\n"
865	<	"-->Bend[%d] in %s\n",
866	<	j, comp_stamps[stampID]->getID() );
867	<	painCave.isFatal = 1;
868	<	simError();
869	<	}
952	>	else{
953	>	strcpy( info[k].finalName, inFileName );
954	>	char* endTest;
955	>	int nameLength = strlen( info[k].finalName );
956	>	endTest = &(info[k].finalName[nameLength - 5]);
957	>	if( !strcmp( endTest, ".bass" ) ){
958	>	strcpy( endTest, ".eor" );
959	>	}
960	>	else if( !strcmp( endTest, ".BASS" ) ){
961	>	strcpy( endTest, ".eor" );
962	>	}
963	>	else{
964	>	endTest = &(info[k].finalName[nameLength - 4]);
965	>	if( !strcmp( endTest, ".bss" ) ){
966	>	strcpy( endTest, ".eor" );
967		}
968	<
968	>	else if( !strcmp( endTest, ".mdl" ) ){
969	>	strcpy( endTest, ".eor" );
970	>	}
971		else{
972	<
874	<	sprintf( painCave.errMsg,
875	<	"SimSetup Error: unhandled bend assignment:\n"
876	<	"    -->%s in Bend[%d] in %s\n",
877	<	current_extra->getlhs(),
878	<	j, comp_stamps[stampID]->getID() );
879	<	painCave.isFatal = 1;
880	<	simError();
972	>	strcat( info[k].finalName, ".eor" );
973		}
882	–
883	–	current_extra = current_extra->getNext();
974		}
975		}
976	<
977	<	if( !theBends[j].isGhost ){
978	<
979	<	exI = theBends[j].a;
980	<	exJ = theBends[j].c;
976	>
977	>	// make the sample and status out names
978	>
979	>	strcpy( info[k].sampleName, inFileName );
980	>	char* endTest;
981	>	int nameLength = strlen( info[k].sampleName );
982	>	endTest = &(info[k].sampleName[nameLength - 5]);
983	>	if( !strcmp( endTest, ".bass" ) ){
984	>	strcpy( endTest, ".dump" );
985		}
986	+	else if( !strcmp( endTest, ".BASS" ) ){
987	+	strcpy( endTest, ".dump" );
988	+	}
989		else{
990	<
991	<	exI = theBends[j].a;
992	<	exJ = theBends[j].b;
990	>	endTest = &(info[k].sampleName[nameLength - 4]);
991	>	if( !strcmp( endTest, ".bss" ) ){
992	>	strcpy( endTest, ".dump" );
993	>	}
994	>	else if( !strcmp( endTest, ".mdl" ) ){
995	>	strcpy( endTest, ".dump" );
996	>	}
997	>	else{
998	>	strcat( info[k].sampleName, ".dump" );
999	>	}
1000		}
1001
1002	<	// exclude_I must always be the smaller of the pair
1003	<	if( exI > exJ ){
1004	<	tempEx = exI;
1005	<	exI = exJ;
1006	<	exJ = tempEx;
1002	>	strcpy( info[k].statusName, inFileName );
1003	>	nameLength = strlen( info[k].statusName );
1004	>	endTest = &(info[k].statusName[nameLength - 5]);
1005	>	if( !strcmp( endTest, ".bass" ) ){
1006	>	strcpy( endTest, ".stat" );
1007		}
1008	<	#ifdef IS_MPI
1009	<	tempEx = exI;
906	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
907	<	tempEx = exJ;
908	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
909	<
910	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
911	<	#else  // isn't MPI
912	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
913	<	#endif  //is_mpi
914	<	}
915	<	excludeOffset += info.nBends;
916	<
917	<	for(j=0; j<info.nTorsions; j++){
918	<
919	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
920	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
921	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
922	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
923	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
924	<
925	<	exI = theTorsions[j].a;
926	<	exJ = theTorsions[j].d;
927	<
928	<	// exclude_I must always be the smaller of the pair
929	<	if( exI > exJ ){
930	<	tempEx = exI;
931	<	exI = exJ;
932	<	exJ = tempEx;
1008	>	else if( !strcmp( endTest, ".BASS" ) ){
1009	>	strcpy( endTest, ".stat" );
1010		}
1011	<	#ifdef IS_MPI
1012	<	tempEx = exI;
1013	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1014	<	tempEx = exJ;
1015	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1011	>	else{
1012	>	endTest = &(info[k].statusName[nameLength - 4]);
1013	>	if( !strcmp( endTest, ".bss" ) ){
1014	>	strcpy( endTest, ".stat" );
1015	>	}
1016	>	else if( !strcmp( endTest, ".mdl" ) ){
1017	>	strcpy( endTest, ".stat" );
1018	>	}
1019	>	else{
1020	>	strcat( info[k].statusName, ".stat" );
1021	>	}
1022	>	}
1023
1024	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
941	<	#else  // isn't MPI
942	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
943	<	#endif  //is_mpi
1024	>	#ifdef IS_MPI
1025		}
1026	<	excludeOffset += info.nTorsions;
1026	>	#endif // is_mpi
1027	>	}
1028	>	}
1029
947	–
948	–	// send the arrays off to the forceField for init.
1030
1031	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1032	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1033	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1034	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1031	>	void SimSetup::sysObjectsCreation( void ){
1032	>
1033	>	int i,k;
1034	>
1035	>	// create the forceField
1036	>
1037	>	createFF();
1038
1039	+	// extract componentList
1040
1041	<	the_molecules[i].initialize( info );
1041	>	compList();
1042
1043	+	// calc the number of atoms, bond, bends, and torsions
1044
1045	<	atomOffset += info.nAtoms;
960	<	delete[] theBonds;
961	<	delete[] theBends;
962	<	delete[] theTorsions;
963	<	}
1045	>	calcSysValues();
1046
1047		#ifdef IS_MPI
1048	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1049	<	MPIcheckPoint();
1050	<	#endif // is_mpi
1048	>	// divide the molecules among the processors
1049	>
1050	>	mpiMolDivide();
1051	>	#endif //is_mpi
1052	>
1053	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1054	>
1055	>	makeSysArrays();
1056
1057	<	// clean up the forcefield
1058	<	the_ff->calcRcut();
1059	<	the_ff->cleanMe();
1060	<
1057	>	// make and initialize the molecules (all but atomic coordinates)
1058	>
1059	>	makeMolecules();
1060	>
1061	>	for(k=0; k<nInfo; k++){
1062	>	info[k].identArray = new int[info[k].n_atoms];
1063	>	for(i=0; i<info[k].n_atoms; i++){
1064	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1065	>	}
1066	>	}
1067		}
1068
976	–	void SimSetup::initFromBass( void ){
1069
1070	<	int i, j, k;
979	<	int n_cells;
980	<	double cellx, celly, cellz;
981	<	double temp1, temp2, temp3;
982	<	int n_per_extra;
983	<	int n_extra;
984	<	int have_extra, done;
1070	>	void SimSetup::createFF( void ){
1071
1072	<	temp1 = (double)tot_nmol / 4.0;
987	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
988	<	temp3 = ceil( temp2 );
1072	>	switch( ffCase ){
1073
1074	<	have_extra =0;
1075	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1076	<	have_extra =1;
1074	>	case FF_DUFF:
1075	>	the_ff = new DUFF();
1076	>	break;
1077
1078	<	n_cells = (int)temp3 - 1;
1079	<	cellx = simnfo->box_x / temp3;
1080	<	celly = simnfo->box_y / temp3;
997	<	cellz = simnfo->box_z / temp3;
998	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
999	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1000	<	n_per_extra = (int)ceil( temp1 );
1078	>	case FF_LJ:
1079	>	the_ff = new LJFF();
1080	>	break;
1081
1082	<	if( n_per_extra > 4){
1083	<	sprintf( painCave.errMsg,
1084	<	"SimSetup error. There has been an error in constructing"
1085	<	" the non-complete lattice.\n" );
1086	<	painCave.isFatal = 1;
1087	<	simError();
1088	<	}
1082	>	case FF_EAM:
1083	>	the_ff = new EAM_FF();
1084	>	break;
1085	>
1086	>	default:
1087	>	sprintf( painCave.errMsg,
1088	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1089	>	painCave.isFatal = 1;
1090	>	simError();
1091		}
1010	–	else{
1011	–	n_cells = (int)temp3;
1012	–	cellx = simnfo->box_x / temp3;
1013	–	celly = simnfo->box_y / temp3;
1014	–	cellz = simnfo->box_z / temp3;
1015	–	}
1092
1093	<	current_mol = 0;
1094	<	current_comp_mol = 0;
1095	<	current_comp = 0;
1096	<	current_atom_ndx = 0;
1093	>	#ifdef IS_MPI
1094	>	strcpy( checkPointMsg, "ForceField creation successful" );
1095	>	MPIcheckPoint();
1096	>	#endif // is_mpi
1097
1098	<	for( i=0; i < n_cells ; i++ ){
1023	<	for( j=0; j < n_cells; j++ ){
1024	<	for( k=0; k < n_cells; k++ ){
1098	>	}
1099
1026	–	makeElement( i * cellx,
1027	–	j * celly,
1028	–	k * cellz );
1100
1101	<	makeElement( i * cellx + 0.5 * cellx,
1031	<	j * celly + 0.5 * celly,
1032	<	k * cellz );
1101	>	void SimSetup::compList( void ){
1102
1103	<	makeElement( i * cellx,
1104	<	j * celly + 0.5 * celly,
1105	<	k * cellz + 0.5 * cellz );
1103	>	int i;
1104	>	char* id;
1105	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1106	>	LinkedMolStamp* currentStamp = NULL;
1107	>	comp_stamps = new MoleculeStamp*[n_components];
1108	>
1109	>	// make an array of molecule stamps that match the components used.
1110	>	// also extract the used stamps out into a separate linked list
1111	>
1112	>	for(i=0; i<nInfo; i++){
1113	>	info[i].nComponents = n_components;
1114	>	info[i].componentsNmol = components_nmol;
1115	>	info[i].compStamps = comp_stamps;
1116	>	info[i].headStamp = headStamp;
1117	>	}
1118	>
1119
1120	<	makeElement( i * cellx + 0.5 * cellx,
1121	<	j * celly,
1122	<	k * cellz + 0.5 * cellz );
1120	>	for( i=0; i<n_components; i++ ){
1121	>
1122	>	id = the_components[i]->getType();
1123	>	comp_stamps[i] = NULL;
1124	>
1125	>	// check to make sure the component isn't already in the list
1126	>
1127	>	comp_stamps[i] = headStamp->match( id );
1128	>	if( comp_stamps[i] == NULL ){
1129	>
1130	>	// extract the component from the list;
1131	>
1132	>	currentStamp = stamps->extractMolStamp( id );
1133	>	if( currentStamp == NULL ){
1134	>	sprintf( painCave.errMsg,
1135	>	"SimSetup error: Component \"%s\" was not found in the "
1136	>	"list of declared molecules\n",
1137	>	id );
1138	>	painCave.isFatal = 1;
1139	>	simError();
1140		}
1141	+
1142	+	headStamp->add( currentStamp );
1143	+	comp_stamps[i] = headStamp->match( id );
1144		}
1145		}
1146
1147	<	if( have_extra ){
1148	<	done = 0;
1147	>	#ifdef IS_MPI
1148	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1149	>	MPIcheckPoint();
1150	>	#endif // is_mpi
1151
1048	–	int start_ndx;
1049	–	for( i=0; i < (n_cells+1) && !done; i++ ){
1050	–	for( j=0; j < (n_cells+1) && !done; j++ ){
1152
1153	<	if( i < n_cells ){
1153	>	}
1154
1155	<	if( j < n_cells ){
1156	<	start_ndx = n_cells;
1157	<	}
1158	<	else start_ndx = 0;
1159	<	}
1160	<	else start_ndx = 0;
1155	>	void SimSetup::calcSysValues( void ){
1156	>	int i, j, k;
1157	>
1158	>	int *molMembershipArray;
1159	>
1160	>	tot_atoms = 0;
1161	>	tot_bonds = 0;
1162	>	tot_bends = 0;
1163	>	tot_torsions = 0;
1164	>	for( i=0; i<n_components; i++ ){
1165	>
1166	>	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1167	>	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1168	>	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1169	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1170	>	}
1171	>
1172	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1173	>	molMembershipArray = new int[tot_atoms];
1174	>
1175	>	for(i=0; i<nInfo; i++){
1176	>	info[i].n_atoms = tot_atoms;
1177	>	info[i].n_bonds = tot_bonds;
1178	>	info[i].n_bends = tot_bends;
1179	>	info[i].n_torsions = tot_torsions;
1180	>	info[i].n_SRI = tot_SRI;
1181	>	info[i].n_mol = tot_nmol;
1182	>
1183	>	info[i].molMembershipArray = molMembershipArray;
1184	>	}
1185	>	}
1186
1187	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1187	>	#ifdef IS_MPI
1188
1189	<	makeElement( i * cellx,
1190	<	j * celly,
1191	<	k * cellz );
1192	<	done = ( current_mol >= tot_nmol );
1189	>	void SimSetup::mpiMolDivide( void ){
1190	>
1191	>	int i, j, k;
1192	>	int localMol, allMol;
1193	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1194
1195	<	if( !done && n_per_extra > 1 ){
1196	<	makeElement( i * cellx + 0.5 * cellx,
1197	<	j * celly + 0.5 * celly,
1071	<	k * cellz );
1072	<	done = ( current_mol >= tot_nmol );
1073	<	}
1195	>	mpiSim = new mpiSimulation( info );
1196	>
1197	>	globalIndex = mpiSim->divideLabor();
1198
1199	<	if( !done && n_per_extra > 2){
1200	<	makeElement( i * cellx,
1201	<	j * celly + 0.5 * celly,
1202	<	k * cellz + 0.5 * cellz );
1203	<	done = ( current_mol >= tot_nmol );
1204	<	}
1199	>	// set up the local variables
1200	>
1201	>	mol2proc = mpiSim->getMolToProcMap();
1202	>	molCompType = mpiSim->getMolComponentType();
1203	>
1204	>	allMol = 0;
1205	>	localMol = 0;
1206	>	local_atoms = 0;
1207	>	local_bonds = 0;
1208	>	local_bends = 0;
1209	>	local_torsions = 0;
1210	>	globalAtomIndex = 0;
1211
1212	<	if( !done && n_per_extra > 3){
1213	<	makeElement( i * cellx + 0.5 * cellx,
1214	<	j * celly,
1215	<	k * cellz + 0.5 * cellz );
1216	<	done = ( current_mol >= tot_nmol );
1217	<	}
1218	<	}
1212	>
1213	>	for( i=0; i<n_components; i++ ){
1214	>
1215	>	for( j=0; j<components_nmol[i]; j++ ){
1216	>
1217	>	if( mol2proc[allMol] == worldRank ){
1218	>
1219	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1220	>	local_bonds +=    comp_stamps[i]->getNBonds();
1221	>	local_bends +=    comp_stamps[i]->getNBends();
1222	>	local_torsions += comp_stamps[i]->getNTorsions();
1223	>	localMol++;
1224	>	}
1225	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1226	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1227	>	globalAtomIndex++;
1228		}
1229	+
1230	+	allMol++;
1231		}
1232		}
1233	+	local_SRI = local_bonds + local_bends + local_torsions;
1234	+
1235	+	info[0].n_atoms = mpiSim->getMyNlocal();
1236	+
1237	+	if( local_atoms != info[0].n_atoms ){
1238	+	sprintf( painCave.errMsg,
1239	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1240	+	" localAtom (%d) are not equal.\n",
1241	+	info[0].n_atoms,
1242	+	local_atoms );
1243	+	painCave.isFatal = 1;
1244	+	simError();
1245	+	}
1246
1247	+	info[0].n_bonds = local_bonds;
1248	+	info[0].n_bends = local_bends;
1249	+	info[0].n_torsions = local_torsions;
1250	+	info[0].n_SRI = local_SRI;
1251	+	info[0].n_mol = localMol;
1252
1253	<	for( i=0; i<simnfo->n_atoms; i++ ){
1254	<	simnfo->atoms[i]->set_vx( 0.0 );
1096	<	simnfo->atoms[i]->set_vy( 0.0 );
1097	<	simnfo->atoms[i]->set_vz( 0.0 );
1098	<	}
1253	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1254	>	MPIcheckPoint();
1255		}
1256	+
1257	+	#endif // is_mpi
1258
1101	–	void SimSetup::makeElement( double x, double y, double z ){
1259
1260	<	int k;
1261	<	AtomStamp* current_atom;
1105	<	DirectionalAtom* dAtom;
1106	<	double rotMat[3][3];
1260	>	void SimSetup::makeSysArrays( void ){
1261	>	int i, j, k, l;
1262
1263	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1263	>	Atom** the_atoms;
1264	>	Molecule* the_molecules;
1265	>	Exclude** the_excludes;
1266
1267	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1268	<	if( !current_atom->havePosition() ){
1269	<	sprintf( painCave.errMsg,
1270	<	"SimSetup:initFromBass error.\n"
1271	<	"\tComponent %s, atom %s does not have a position specified.\n"
1272	<	"\tThe initialization routine is unable to give a start"
1273	<	" position.\n",
1274	<	comp_stamps[current_comp]->getID(),
1275	<	current_atom->getType() );
1276	<	painCave.isFatal = 1;
1277	<	simError();
1267	>
1268	>	for(l=0; l<nInfo; l++){
1269	>
1270	>	// create the atom and short range interaction arrays
1271	>
1272	>	the_atoms = new Atom*[info[l].n_atoms];
1273	>	the_molecules = new Molecule[info[l].n_mol];
1274	>	int molIndex;
1275	>
1276	>	// initialize the molecule's stampID's
1277	>
1278	>	#ifdef IS_MPI
1279	>
1280	>
1281	>	molIndex = 0;
1282	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1283	>
1284	>	if(mol2proc[i] == worldRank ){
1285	>	the_molecules[molIndex].setStampID( molCompType[i] );
1286	>	the_molecules[molIndex].setMyIndex( molIndex );
1287	>	the_molecules[molIndex].setGlobalIndex( i );
1288	>	molIndex++;
1289	>	}
1290		}
1291	+
1292	+	#else // is_mpi
1293	+
1294	+	molIndex = 0;
1295	+	globalAtomIndex = 0;
1296	+	for(i=0; i<n_components; i++){
1297	+	for(j=0; j<components_nmol[i]; j++ ){
1298	+	the_molecules[molIndex].setStampID( i );
1299	+	the_molecules[molIndex].setMyIndex( molIndex );
1300	+	the_molecules[molIndex].setGlobalIndex( molIndex );
1301	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1302	+	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1303	+	globalAtomIndex++;
1304	+	}
1305	+	molIndex++;
1306	+	}
1307	+	}
1308	+
1309	+
1310	+	#endif // is_mpi
1311
1123	–	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1124	–	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1125	–	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1312
1313	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1313	>	if( info[l].n_SRI ){
1314	>
1315	>	Exclude::createArray(info[l].n_SRI);
1316	>	the_excludes = new Exclude*[info[l].n_SRI];
1317	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1318	>	the_excludes[ex] = new Exclude(ex);
1319	>	}
1320	>	info[l].globalExcludes = new int;
1321	>	info[l].n_exclude = info[l].n_SRI;
1322	>	}
1323	>	else{
1324	>
1325	>	Exclude::createArray( 1 );
1326	>	the_excludes = new Exclude*;
1327	>	the_excludes[0] = new Exclude(0);
1328	>	the_excludes[0]->setPair( 0,0 );
1329	>	info[l].globalExcludes = new int;
1330	>	info[l].globalExcludes[0] = 0;
1331	>	info[l].n_exclude = 0;
1332	>	}
1333
1334	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1334	>	// set the arrays into the SimInfo object
1335
1336	<	rotMat[0][0] = 1.0;
1337	<	rotMat[0][1] = 0.0;
1338	<	rotMat[0][2] = 0.0;
1336	>	info[l].atoms = the_atoms;
1337	>	info[l].molecules = the_molecules;
1338	>	info[l].nGlobalExcludes = 0;
1339	>	info[l].excludes = the_excludes;
1340
1341	<	rotMat[1][0] = 0.0;
1342	<	rotMat[1][1] = 1.0;
1343	<	rotMat[1][2] = 0.0;
1341	>	the_ff->setSimInfo( info );
1342	>
1343	>	}
1344	>	}
1345
1346	<	rotMat[2][0] = 0.0;
1140	<	rotMat[2][1] = 0.0;
1141	<	rotMat[2][2] = 1.0;
1346	>	void SimSetup::makeIntegrator( void ){
1347
1348	<	dAtom->setA( rotMat );
1348	>	int k;
1349	>
1350	>	NVT<RealIntegrator>*  myNVT = NULL;
1351	>	NPTi<RealIntegrator>* myNPTi = NULL;
1352	>	NPTf<RealIntegrator>* myNPTf = NULL;
1353	>	NPTim<RealIntegrator>* myNPTim = NULL;
1354	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1355	>
1356	>	for(k=0; k<nInfo; k++){
1357	>
1358	>	switch( ensembleCase ){
1359	>
1360	>	case NVE_ENS:
1361	>	if (haveZConstraint){
1362	>	setupZConstraint();
1363	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1364	>	}
1365	>
1366	>	else
1367	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1368	>	break;
1369	>
1370	>	case NVT_ENS:
1371	>	if (haveZConstraint){
1372	>	setupZConstraint();
1373	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1374	>	}
1375	>	else
1376	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1377	>
1378	>	myNVT->setTargetTemp(globals->getTargetTemp());
1379	>
1380	>	if (globals->haveTauThermostat())
1381	>	myNVT->setTauThermostat(globals->getTauThermostat());
1382	>
1383	>	else {
1384	>	sprintf( painCave.errMsg,
1385	>	"SimSetup error: If you use the NVT\n"
1386	>	"    ensemble, you must set tauThermostat.\n");
1387	>	painCave.isFatal = 1;
1388	>	simError();
1389	>	}
1390	>	break;
1391	>
1392	>	case NPTi_ENS:
1393	>	if (haveZConstraint){
1394	>	setupZConstraint();
1395	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1396	>	}
1397	>	else
1398	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1399	>
1400	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1401	>
1402	>	if (globals->haveTargetPressure())
1403	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1404	>	else {
1405	>	sprintf( painCave.errMsg,
1406	>	"SimSetup error: If you use a constant pressure\n"
1407	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1408	>	painCave.isFatal = 1;
1409	>	simError();
1410	>	}
1411	>
1412	>	if( globals->haveTauThermostat() )
1413	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1414	>	else{
1415	>	sprintf( painCave.errMsg,
1416	>	"SimSetup error: If you use an NPT\n"
1417	>	"    ensemble, you must set tauThermostat.\n");
1418	>	painCave.isFatal = 1;
1419	>	simError();
1420	>	}
1421	>
1422	>	if( globals->haveTauBarostat() )
1423	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1424	>	else{
1425	>	sprintf( painCave.errMsg,
1426	>	"SimSetup error: If you use an NPT\n"
1427	>	"    ensemble, you must set tauBarostat.\n");
1428	>	painCave.isFatal = 1;
1429	>	simError();
1430	>	}
1431	>	break;
1432	>
1433	>	case NPTf_ENS:
1434	>	if (haveZConstraint){
1435	>	setupZConstraint();
1436	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1437	>	}
1438	>	else
1439	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1440	>
1441	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1442	>
1443	>	if (globals->haveTargetPressure())
1444	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1445	>	else {
1446	>	sprintf( painCave.errMsg,
1447	>	"SimSetup error: If you use a constant pressure\n"
1448	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1449	>	painCave.isFatal = 1;
1450	>	simError();
1451	>	}
1452	>
1453	>	if( globals->haveTauThermostat() )
1454	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1455	>	else{
1456	>	sprintf( painCave.errMsg,
1457	>	"SimSetup error: If you use an NPT\n"
1458	>	"    ensemble, you must set tauThermostat.\n");
1459	>	painCave.isFatal = 1;
1460	>	simError();
1461	>	}
1462	>
1463	>	if( globals->haveTauBarostat() )
1464	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1465	>	else{
1466	>	sprintf( painCave.errMsg,
1467	>	"SimSetup error: If you use an NPT\n"
1468	>	"    ensemble, you must set tauBarostat.\n");
1469	>	painCave.isFatal = 1;
1470	>	simError();
1471	>	}
1472	>	break;
1473	>
1474	>	case NPTim_ENS:
1475	>	if (haveZConstraint){
1476	>	setupZConstraint();
1477	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1478	>	}
1479	>	else
1480	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1481	>
1482	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1483	>
1484	>	if (globals->haveTargetPressure())
1485	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1486	>	else {
1487	>	sprintf( painCave.errMsg,
1488	>	"SimSetup error: If you use a constant pressure\n"
1489	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1490	>	painCave.isFatal = 1;
1491	>	simError();
1492	>	}
1493	>
1494	>	if( globals->haveTauThermostat() )
1495	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1496	>	else{
1497	>	sprintf( painCave.errMsg,
1498	>	"SimSetup error: If you use an NPT\n"
1499	>	"    ensemble, you must set tauThermostat.\n");
1500	>	painCave.isFatal = 1;
1501	>	simError();
1502	>	}
1503	>
1504	>	if( globals->haveTauBarostat() )
1505	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1506	>	else{
1507	>	sprintf( painCave.errMsg,
1508	>	"SimSetup error: If you use an NPT\n"
1509	>	"    ensemble, you must set tauBarostat.\n");
1510	>	painCave.isFatal = 1;
1511	>	simError();
1512	>	}
1513	>	break;
1514	>
1515	>	case NPTfm_ENS:
1516	>	if (haveZConstraint){
1517	>	setupZConstraint();
1518	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1519	>	}
1520	>	else
1521	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1522	>
1523	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1524	>
1525	>	if (globals->haveTargetPressure())
1526	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1527	>	else {
1528	>	sprintf( painCave.errMsg,
1529	>	"SimSetup error: If you use a constant pressure\n"
1530	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1531	>	painCave.isFatal = 1;
1532	>	simError();
1533	>	}
1534	>
1535	>	if( globals->haveTauThermostat() )
1536	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1537	>	else{
1538	>	sprintf( painCave.errMsg,
1539	>	"SimSetup error: If you use an NPT\n"
1540	>	"    ensemble, you must set tauThermostat.\n");
1541	>	painCave.isFatal = 1;
1542	>	simError();
1543	>	}
1544	>
1545	>	if( globals->haveTauBarostat() )
1546	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1547	>	else{
1548	>	sprintf( painCave.errMsg,
1549	>	"SimSetup error: If you use an NPT\n"
1550	>	"    ensemble, you must set tauBarostat.\n");
1551	>	painCave.isFatal = 1;
1552	>	simError();
1553	>	}
1554	>	break;
1555	>
1556	>	default:
1557	>	sprintf( painCave.errMsg,
1558	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1559	>	painCave.isFatal = 1;
1560	>	simError();
1561		}
1562	+	}
1563	+	}
1564
1565	<	current_atom_ndx++;
1565	>	void SimSetup::initFortran( void ){
1566	>
1567	>	info[0].refreshSim();
1568	>
1569	>	if( !strcmp( info[0].mixingRule, "standard") ){
1570	>	the_ff->initForceField( LB_MIXING_RULE );
1571		}
1572	+	else if( !strcmp( info[0].mixingRule, "explicit") ){
1573	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1574	+	}
1575	+	else{
1576	+	sprintf( painCave.errMsg,
1577	+	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1578	+	info[0].mixingRule );
1579	+	painCave.isFatal = 1;
1580	+	simError();
1581	+	}
1582
1149	–	current_mol++;
1150	–	current_comp_mol++;
1583
1584	<	if( current_comp_mol >= components_nmol[current_comp] ){
1584	>	#ifdef IS_MPI
1585	>	strcpy( checkPointMsg,
1586	>	"Successfully intialized the mixingRule for Fortran." );
1587	>	MPIcheckPoint();
1588	>	#endif // is_mpi
1589
1590	<	current_comp_mol = 0;
1591	<	current_comp++;
1590	>	}
1591	>
1592	>	void SimSetup::setupZConstraint()
1593	>	{
1594	>	int k;
1595	>
1596	>	for(k=0; k<nInfo; k++){
1597	>
1598	>	if(globals->haveZConsTime()){
1599	>
1600	>	//add sample time of z-constraint  into SimInfo's property list
1601	>	DoubleData* zconsTimeProp = new DoubleData();
1602	>	zconsTimeProp->setID("zconstime");
1603	>	zconsTimeProp->setData(globals->getZConsTime());
1604	>	info[k].addProperty(zconsTimeProp);
1605	>	}
1606	>	else{
1607	>	sprintf( painCave.errMsg,
1608	>	"ZConstraint error: If you use an ZConstraint\n"
1609	>	" , you must set sample time.\n");
1610	>	painCave.isFatal = 1;
1611	>	simError();
1612	>	}
1613	>
1614	>	if(globals->haveIndexOfAllZConsMols()){
1615	>
1616	>	//add index of z-constraint molecules into SimInfo's property list
1617	>	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1618	>
1619	>	//sort the index
1620	>	sort(tempIndex.begin(), tempIndex.end());
1621	>
1622	>	IndexData* zconsIndex = new IndexData();
1623	>	zconsIndex->setID("zconsindex");
1624	>	zconsIndex->setIndexData(tempIndex);
1625	>	info[k].addProperty(zconsIndex);
1626	>	}
1627	>	else{
1628	>	sprintf( painCave.errMsg,
1629	>	"SimSetup error: If you use an ZConstraint\n"
1630	>	" , you must set index of z-constraint molecules.\n");
1631	>	painCave.isFatal = 1;
1632	>	simError();
1633	>
1634	>	}
1635	>
1636	>	//Determine the name of ouput file and add it into SimInfo's property list
1637	>	//Be careful, do not use inFileName, since it is a pointer which
1638	>	//point to a string at master node, and slave nodes do not contain that string
1639	>
1640	>	string zconsOutput(info[k].finalName);
1641	>
1642	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1643	>
1644	>	StringData* zconsFilename = new StringData();
1645	>	zconsFilename->setID("zconsfilename");
1646	>	zconsFilename->setData(zconsOutput);
1647	>
1648	>	info[k].addProperty(zconsFilename);
1649		}
1650		}

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