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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 394 by gezelter, Mon Mar 24 21:55:34 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	<	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;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
102	>	// creation of complex system objects
103
104	<	// 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();
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() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
106	>	// check on the post processing info
107	>
108	>	finalInfoCheck();
109
110	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
110	>	// initialize the system coordinates
111
112	+	if( !isInfoArray ) initSystemCoords();
113
114	<	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	<	}
114	>	// make the output filenames
115
116	+	makeOutNames();
117	+
118	+	// make the integrator
119	+
120	+	makeIntegrator();
121	+
122		#ifdef IS_MPI
123	<	strcpy( checkPointMsg, "ForceField creation successful" );
124	<	MPIcheckPoint();
106	<	#endif // is_mpi
123	>	mpiSim->mpiRefresh();
124	>	#endif
125
126	<
126	>	// initialize the Fortran
127
128	<	// 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];
128	>	initFortran();
129
115	–	if( !the_globals->haveNMol() ){
116	–	// we don't have the total number of molecules, so we assume it is
117	–	// given in each component
130
119	–	tot_nmol = 0;
120	–	for( i=0; i<n_components; i++ ){
131
132	<	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
131	–	tot_nmol += the_components[i]->getNMol();
132	–	components_nmol[i] = the_components[i]->getNMol();
133	–	}
134	–	}
135	–	else{
136	–	sprintf( painCave.errMsg,
137	–	"SimSetup error.\n"
138	–	"\tSorry, the ability to specify total"
139	–	" nMols and then give molfractions in the components\n"
140	–	"\tis not currently supported."
141	–	" Please give nMol in the components.\n" );
142	–	painCave.isFatal = 1;
143	–	simError();
144	–
145	–
146	–	//     tot_nmol = the_globals->getNMol();
147	–
148	–	//   //we have the total number of molecules, now we check for molfractions
149	–	//     for( i=0; i<n_components; i++ ){
150	–
151	–	//       if( !the_components[i]->haveMolFraction() ){
152	–
153	–	//  if( !the_components[i]->haveNMol() ){
154	–	//    //we have a problem
155	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
156	–	//              << " nMol was given in component
157	–
158	–	}
134
135	<	#ifdef IS_MPI
161	<	strcpy( checkPointMsg, "Have the number of components" );
162	<	MPIcheckPoint();
163	<	#endif // is_mpi
135	>	void SimSetup::makeMolecules( void ){
136
137	<	// make an array of molecule stamps that match the components used.
138	<	// also extract the used stamps out into a separate linked list
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	<	simnfo->nComponents = n_components;
149	<	simnfo->componentsNmol = components_nmol;
150	<	simnfo->compStamps = comp_stamps;
171	<	simnfo->headStamp = new LinkedMolStamp();
172	<
173	<	char* id;
174	<	LinkedMolStamp* headStamp = simnfo->headStamp;
175	<	LinkedMolStamp* currentStamp = NULL;
176	<	for( i=0; i<n_components; i++ ){
148	>	bond_pair* theBonds;
149	>	bend_set* theBends;
150	>	torsion_set* theTorsions;
151
178	–	id = the_components[i]->getType();
179	–	comp_stamps[i] = NULL;
180	–
181	–	// check to make sure the component isn't already in the list
182	–
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
152
153	+	//init the forceField paramters
154
155	+	the_ff->readParams();
156
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	–
157
158	<	#ifdef IS_MPI
158	>	// init the atoms
159
160	<	// divide the molecules among processors here.
160	>	double ux, uy, uz, u, uSqr;
161
162	<	mpiSim = new mpiSimulation( simnfo );
163	<
164	<
162	>	for(k=0; k<nInfo; k++){
163	>
164	>	the_ff->setSimInfo( &(info[k]) );
165
166	<	globalIndex = mpiSim->divideLabor();
166	>	atomOffset = 0;
167	>	excludeOffset = 0;
168	>	for(i=0; i<info[k].n_mol; i++){
169	>
170	>	stampID = info[k].molecules[i].getStampID();
171
172	<
173	<
174	<	// set up the local variables
175	<
176	<	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++ ){
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	<	if( mpiSim->getMyMolStart() <= allMol &&
179	<	allMol <= mpiSim->getMyMolEnd() ){
178	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
179	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
180	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
181	>	molInfo.myBends = new Bend*[molInfo.nBends];
182	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
183	>
184	>	theBonds = new bond_pair[molInfo.nBonds];
185	>	theBends = new bend_set[molInfo.nBends];
186	>	theTorsions = new torsion_set[molInfo.nTorsions];
187	>
188	>	// make the Atoms
189	>
190	>	for(j=0; j<molInfo.nAtoms; j++){
191
192	<	local_atoms +=    comp_stamps[i]->getNAtoms();
193	<	local_bonds +=    comp_stamps[i]->getNBonds();
194	<	local_bends +=    comp_stamps[i]->getNBends();
195	<	local_torsions += comp_stamps[i]->getNTorsions();
196	<	localMol++;
197	<	}
198	<	allMol++;
192	>	currentAtom = comp_stamps[stampID]->getAtom( j );
193	>	if( currentAtom->haveOrientation() ){
194	>
195	>	dAtom = new DirectionalAtom( (j + atomOffset),
196	>	info[k].getConfiguration() );
197	>	info[k].n_oriented++;
198	>	molInfo.myAtoms[j] = dAtom;
199	>
200	>	ux = currentAtom->getOrntX();
201	>	uy = currentAtom->getOrntY();
202	>	uz = currentAtom->getOrntZ();
203	>
204	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
205	>
206	>	u = sqrt( uSqr );
207	>	ux = ux / u;
208	>	uy = uy / u;
209	>	uz = uz / u;
210	>
211	>	dAtom->setSUx( ux );
212	>	dAtom->setSUy( uy );
213	>	dAtom->setSUz( uz );
214	>	}
215	>	else{
216	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
217	>	info[k].getConfiguration() );
218	>	}
219	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
220	>
221	>	#ifdef IS_MPI
222	>
223	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
224	>
225	>	#endif // is_mpi
226	>	}
227	>
228	>	// make the bonds
229	>	for(j=0; j<molInfo.nBonds; j++){
230	>
231	>	currentBond = comp_stamps[stampID]->getBond( j );
232	>	theBonds[j].a = currentBond->getA() + atomOffset;
233	>	theBonds[j].b = currentBond->getB() + atomOffset;
234	>
235	>	exI = theBonds[j].a;
236	>	exJ = theBonds[j].b;
237	>
238	>	// exclude_I must always be the smaller of the pair
239	>	if( exI > exJ ){
240	>	tempEx = exI;
241	>	exI = exJ;
242	>	exJ = tempEx;
243	>	}
244	>	#ifdef IS_MPI
245	>	tempEx = exI;
246	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
247	>	tempEx = exJ;
248	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
249	>
250	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
251	>	#else  // isn't MPI
252	>
253	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
254	>	#endif  //is_mpi
255	>	}
256	>	excludeOffset += molInfo.nBonds;
257	>
258	>	//make the bends
259	>	for(j=0; j<molInfo.nBends; j++){
260	>
261	>	currentBend = comp_stamps[stampID]->getBend( j );
262	>	theBends[j].a = currentBend->getA() + atomOffset;
263	>	theBends[j].b = currentBend->getB() + atomOffset;
264	>	theBends[j].c = currentBend->getC() + atomOffset;
265	>
266	>	if( currentBend->haveExtras() ){
267	>
268	>	extras = currentBend->getExtras();
269	>	current_extra = extras;
270	>
271	>	while( current_extra != NULL ){
272	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
273	>
274	>	switch( current_extra->getType() ){
275	>
276	>	case 0:
277	>	theBends[j].ghost =
278	>	current_extra->getInt() + atomOffset;
279	>	theBends[j].isGhost = 1;
280	>	break;
281	>
282	>	case 1:
283	>	theBends[j].ghost =
284	>	(int)current_extra->getDouble() + atomOffset;
285	>	theBends[j].isGhost = 1;
286	>	break;
287	>
288	>	default:
289	>	sprintf( painCave.errMsg,
290	>	"SimSetup Error: ghostVectorSource was neither a "
291	>	"double nor an int.\n"
292	>	"-->Bend[%d] in %s\n",
293	>	j, comp_stamps[stampID]->getID() );
294	>	painCave.isFatal = 1;
295	>	simError();
296	>	}
297	>	}
298	>
299	>	else{
300	>
301	>	sprintf( painCave.errMsg,
302	>	"SimSetup Error: unhandled bend assignment:\n"
303	>	"    -->%s in Bend[%d] in %s\n",
304	>	current_extra->getlhs(),
305	>	j, comp_stamps[stampID]->getID() );
306	>	painCave.isFatal = 1;
307	>	simError();
308	>	}
309	>
310	>	current_extra = current_extra->getNext();
311	>	}
312	>	}
313	>
314	>	if( !theBends[j].isGhost ){
315	>
316	>	exI = theBends[j].a;
317	>	exJ = theBends[j].c;
318	>	}
319	>	else{
320	>
321	>	exI = theBends[j].a;
322	>	exJ = theBends[j].b;
323	>	}
324	>
325	>	// exclude_I must always be the smaller of the pair
326	>	if( exI > exJ ){
327	>	tempEx = exI;
328	>	exI = exJ;
329	>	exJ = tempEx;
330	>	}
331	>	#ifdef IS_MPI
332	>	tempEx = exI;
333	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
334	>	tempEx = exJ;
335	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
336	>
337	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
338	>	#else  // isn't MPI
339	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
340	>	#endif  //is_mpi
341	>	}
342	>	excludeOffset += molInfo.nBends;
343	>
344	>	for(j=0; j<molInfo.nTorsions; j++){
345	>
346	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
347	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
348	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
349	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
350	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
351	>
352	>	exI = theTorsions[j].a;
353	>	exJ = theTorsions[j].d;
354	>
355	>	// exclude_I must always be the smaller of the pair
356	>	if( exI > exJ ){
357	>	tempEx = exI;
358	>	exI = exJ;
359	>	exJ = tempEx;
360	>	}
361	>	#ifdef IS_MPI
362	>	tempEx = exI;
363	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
364	>	tempEx = exJ;
365	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
366	>
367	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
368	>	#else  // isn't MPI
369	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
370	>	#endif  //is_mpi
371	>	}
372	>	excludeOffset += molInfo.nTorsions;
373	>
374	>
375	>	// send the arrays off to the forceField for init.
376	>
377	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
378	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
379	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
380	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
381	>
382	>
383	>	info[k].molecules[i].initialize( molInfo );
384	>
385	>
386	>	atomOffset += molInfo.nAtoms;
387	>	delete[] theBonds;
388	>	delete[] theBends;
389	>	delete[] theTorsions;
390		}
391		}
274	–	local_SRI = local_bonds + local_bends + local_torsions;
392
393	+	#ifdef IS_MPI
394	+	sprintf( checkPointMsg, "all molecules initialized succesfully" );
395	+	MPIcheckPoint();
396	+	#endif // is_mpi
397	+
398	+	// clean up the forcefield
399
400	<	simnfo->n_atoms = mpiSim->getMyNlocal();
400	>	the_ff->calcRcut();
401	>	the_ff->cleanMe();
402
403	<	if( local_atoms != simnfo->n_atoms ){
280	<	sprintf( painCave.errMsg,
281	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282	<	" localAtom (%d) are note equal.\n",
283	<	simnfo->n_atoms,
284	<	local_atoms );
285	<	painCave.isFatal = 1;
286	<	simError();
287	<	}
403	>	}
404
405	<	simnfo->n_bonds = local_bonds;
290	<	simnfo->n_bends = local_bends;
291	<	simnfo->n_torsions = local_torsions;
292	<	simnfo->n_SRI = local_SRI;
293	<	simnfo->n_mol = localMol;
405	>	void SimSetup::initFromBass( void ){
406
407	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
408	<	MPIcheckPoint();
409	<
410	<
411	<	#endif // is_mpi
412	<
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	<	// create the atom and short range interaction arrays
415	>	double vel[3];
416	>	vel[0] = 0.0;
417	>	vel[1] = 0.0;
418	>	vel[2] = 0.0;
419
420	<	Atom::createArrays(simnfo->n_atoms);
421	<	the_atoms = new Atom*[simnfo->n_atoms];
422	<	the_molecules = new Molecule[simnfo->n_mol];
420	>	temp1 = (double)tot_nmol / 4.0;
421	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
422	>	temp3 = ceil( temp2 );
423
424	+	have_extra =0;
425	+	if( temp2 < temp3 ){ // we have a non-complete lattice
426	+	have_extra =1;
427
428	<	if( simnfo->n_SRI ){
429	<	the_sris = new SRI*[simnfo->n_SRI];
430	<	the_excludes = new int[2 * simnfo->n_SRI];
431	<	simnfo->globalExcludes = new int;
432	<	simnfo->n_exclude = tot_SRI;
428	>	n_cells = (int)temp3 - 1;
429	>	cellx = info[0].boxL[0] / temp3;
430	>	celly = info[0].boxL[1] / temp3;
431	>	cellz = info[0].boxL[2] / temp3;
432	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
433	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
434	>	n_per_extra = (int)ceil( temp1 );
435	>
436	>	if( n_per_extra > 4){
437	>	sprintf( painCave.errMsg,
438	>	"SimSetup error. There has been an error in constructing"
439	>	" the non-complete lattice.\n" );
440	>	painCave.isFatal = 1;
441	>	simError();
442	>	}
443		}
444	<	else{
445	<
446	<	the_excludes = new int[2];
447	<	the_excludes[0] = 0;
448	<	the_excludes[1] = 0;
449	<	simnfo->globalExcludes = new int;
450	<	simnfo->globalExcludes[0] = 0;
451	<
452	<	simnfo->n_exclude = 1;
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	>	current_mol = 0;
452	>	current_comp_mol = 0;
453	>	current_comp = 0;
454	>	current_atom_ndx = 0;
455	>
456	>	for( i=0; i < n_cells ; i++ ){
457	>	for( j=0; j < n_cells; j++ ){
458	>	for( k=0; k < n_cells; k++ ){
459	>
460	>	makeElement( i * cellx,
461	>	j * celly,
462	>	k * cellz );
463	>
464	>	makeElement( i * cellx + 0.5 * cellx,
465	>	j * celly + 0.5 * celly,
466	>	k * cellz );
467	>
468	>	makeElement( i * cellx,
469	>	j * celly + 0.5 * celly,
470	>	k * cellz + 0.5 * cellz );
471	>
472	>	makeElement( i * cellx + 0.5 * cellx,
473	>	j * celly,
474	>	k * cellz + 0.5 * cellz );
475	>	}
476	>	}
477		}
478
479	<	// set the arrays into the SimInfo object
479	>	if( have_extra ){
480	>	done = 0;
481
482	<	simnfo->atoms = the_atoms;
483	<	simnfo->sr_interactions = the_sris;
484	<	simnfo->nGlobalExcludes = 0;
331	<	simnfo->excludes = the_excludes;
482	>	int start_ndx;
483	>	for( i=0; i < (n_cells+1) && !done; i++ ){
484	>	for( j=0; j < (n_cells+1) && !done; j++ ){
485
486	+	if( i < n_cells ){
487
488	<	// get some of the tricky things that may still be in the globals
488	>	if( j < n_cells ){
489	>	start_ndx = n_cells;
490	>	}
491	>	else start_ndx = 0;
492	>	}
493	>	else start_ndx = 0;
494
495	<
496	<	if( the_globals->haveBox() ){
497	<	simnfo->box_x = the_globals->getBox();
498	<	simnfo->box_y = the_globals->getBox();
499	<	simnfo->box_z = the_globals->getBox();
495	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
496	>
497	>	makeElement( i * cellx,
498	>	j * celly,
499	>	k * cellz );
500	>	done = ( current_mol >= tot_nmol );
501	>
502	>	if( !done && n_per_extra > 1 ){
503	>	makeElement( i * cellx + 0.5 * cellx,
504	>	j * celly + 0.5 * celly,
505	>	k * cellz );
506	>	done = ( current_mol >= tot_nmol );
507	>	}
508	>
509	>	if( !done && n_per_extra > 2){
510	>	makeElement( i * cellx,
511	>	j * celly + 0.5 * celly,
512	>	k * cellz + 0.5 * cellz );
513	>	done = ( current_mol >= tot_nmol );
514	>	}
515	>
516	>	if( !done && n_per_extra > 3){
517	>	makeElement( i * cellx + 0.5 * cellx,
518	>	j * celly,
519	>	k * cellz + 0.5 * cellz );
520	>	done = ( current_mol >= tot_nmol );
521	>	}
522	>	}
523	>	}
524	>	}
525		}
342	–	else if( the_globals->haveDensity() ){
526
527	<	double vol;
528	<	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;
527	>	for( i=0; i<info[0].n_atoms; i++ ){
528	>	info[0].atoms[i]->setVel( vel );
529		}
530	<	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();
530	>	}
531
532	<	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();
532	>	void SimSetup::makeElement( double x, double y, double z ){
533
534	<	if( !the_globals->haveBoxZ() ){
534	>	int k;
535	>	AtomStamp* current_atom;
536	>	DirectionalAtom* dAtom;
537	>	double rotMat[3][3];
538	>	double pos[3];
539	>
540	>	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
541	>
542	>	current_atom = comp_stamps[current_comp]->getAtom( k );
543	>	if( !current_atom->havePosition() ){
544		sprintf( painCave.errMsg,
545	<	"SimSetup error, no periodic BoxZ size given.\n" );
545	>	"SimSetup:initFromBass error.\n"
546	>	"\tComponent %s, atom %s does not have a position specified.\n"
547	>	"\tThe initialization routine is unable to give a start"
548	>	" position.\n",
549	>	comp_stamps[current_comp]->getID(),
550	>	current_atom->getType() );
551		painCave.isFatal = 1;
552		simError();
553		}
554	<	simnfo->box_z = the_globals->getBoxZ();
555	<	}
554	>
555	>	pos[0] = x + current_atom->getPosX();
556	>	pos[1] = y + current_atom->getPosY();
557	>	pos[2] = z + current_atom->getPosZ();
558	>
559	>	info[0].atoms[current_atom_ndx]->setPos( pos );
560
561	<	#ifdef IS_MPI
377	<	strcpy( checkPointMsg, "Box size set up" );
378	<	MPIcheckPoint();
379	<	#endif // is_mpi
561	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
562
563	+	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
564
565	<	// initialize the arrays
565	>	rotMat[0][0] = 1.0;
566	>	rotMat[0][1] = 0.0;
567	>	rotMat[0][2] = 0.0;
568
569	<	the_ff->setSimInfo( simnfo );
569	>	rotMat[1][0] = 0.0;
570	>	rotMat[1][1] = 1.0;
571	>	rotMat[1][2] = 0.0;
572
573	<	makeAtoms();
574	<	simnfo->identArray = new int[simnfo->n_atoms];
575	<	for(i=0; i<simnfo->n_atoms; i++){
389	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
390	<	}
391	<
392	<	if( tot_bonds ){
393	<	makeBonds();
394	<	}
573	>	rotMat[2][0] = 0.0;
574	>	rotMat[2][1] = 0.0;
575	>	rotMat[2][2] = 1.0;
576
577	<	if( tot_bends ){
578	<	makeBends();
398	<	}
577	>	dAtom->setA( rotMat );
578	>	}
579
580	<	if( tot_torsions ){
401	<	makeTorsions();
580	>	current_atom_ndx++;
581		}
582
583	+	current_mol++;
584	+	current_comp_mol++;
585
586	<	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	<	}
586	>	if( current_comp_mol >= components_nmol[current_comp] ){
587
588	<	if( !the_globals->haveEST() ){
589	<	sprintf( painCave.errMsg,
590	<	"SimSetup Warning: using default value of 0.05 * the "
591	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
428	<	);
429	<	painCave.isFatal = 0;
430	<	simError();
431	<	simnfo->est = 0.05 * simnfo->ecr;
432	<	} else {
433	<	simnfo->est        = the_globals->getEST();
434	<	}
435	<
436	<	if(!the_globals->haveDielectric() ){
437	<	sprintf( painCave.errMsg,
438	<	"SimSetup Error: You are trying to use Reaction Field without"
439	<	"setting a dielectric constant!\n"
440	<	);
441	<	painCave.isFatal = 1;
442	<	simError();
443	<	}
444	<	simnfo->dielectric = the_globals->getDielectric();
445	<	} else {
446	<	if (simnfo->n_dipoles) {
447	<
448	<	if( !the_globals->haveECR() ){
449	<	sprintf( painCave.errMsg,
450	<	"SimSetup Warning: using default value of 1/2 the smallest"
451	<	"box length for the electrostaticCutoffRadius.\n"
452	<	"I hope you have a very fast processor!\n");
453	<	painCave.isFatal = 0;
454	<	simError();
455	<	double smallest;
456	<	smallest = simnfo->box_x;
457	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
458	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
459	<	simnfo->ecr = 0.5 * smallest;
460	<	} else {
461	<	simnfo->ecr        = the_globals->getECR();
462	<	}
463	<
464	<	if( !the_globals->haveEST() ){
465	<	sprintf( painCave.errMsg,
466	<	"SimSetup Warning: using default value of 5% of the"
467	<	"electrostaticCutoffRadius for the "
468	<	"electrostaticSkinThickness\n"
469	<	);
470	<	painCave.isFatal = 0;
471	<	simError();
472	<	simnfo->est = 0.05 * simnfo->ecr;
473	<	} else {
474	<	simnfo->est        = the_globals->getEST();
475	<	}
476	<	}
477	<	}
588	>	current_comp_mol = 0;
589	>	current_comp++;
590	>	}
591	>	}
592
479	–	#ifdef IS_MPI
480	–	strcpy( checkPointMsg, "electrostatic parameters check out" );
481	–	MPIcheckPoint();
482	–	#endif // is_mpi
593
594	<	if( the_globals->haveInitialConfig() ){
595	<
486	<	InitializeFromFile* fileInit;
487	<	#ifdef IS_MPI // is_mpi
488	<	if( worldRank == 0 ){
489	<	#endif //is_mpi
490	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
491	<	#ifdef IS_MPI
492	<	}else fileInit = new InitializeFromFile( NULL );
493	<	#endif
494	<	fileInit->read_xyz( simnfo ); // default velocities on
594	>	void SimSetup::gatherInfo( void ){
595	>	int i,j,k;
596
597	<	delete fileInit;
598	<	}
498	<	else{
597	>	ensembleCase = -1;
598	>	ffCase = -1;
599
600	<	#ifdef IS_MPI
600	>	// set the easy ones first
601
602	<	// no init from bass
602	>	for( i=0; i<nInfo; i++){
603	>	info[i].target_temp = globals->getTargetTemp();
604	>	info[i].dt = globals->getDt();
605	>	info[i].run_time = globals->getRunTime();
606	>	}
607	>	n_components = globals->getNComponents();
608	>
609	>
610	>	// get the forceField
611	>
612	>	strcpy( force_field, globals->getForceField() );
613	>
614	>	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
615	>	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
616	>	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
617	>	else{
618	>	sprintf( painCave.errMsg,
619	>	"SimSetup Error. Unrecognized force field -> %s\n",
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	<	sprintf( painCave.errMsg,
648	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
649	<	painCave.isFatal;
650	<	simError();
647	>	for(i=0; i<nInfo; i++){
648	>
649	>	strcpy( info[i].ensemble, ensemble );
650	>
651	>	// get the mixing rule
652	>
653	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
654	>	info[i].usePBC = globals->getPBC();
655	>	}
656
657	<	#else
657	>	// get the components and calculate the tot_nMol and indvidual n_mol
658	>
659	>	the_components = globals->getComponents();
660	>	components_nmol = new int[n_components];
661
511	–	initFromBass();
662
663	+	if( !globals->haveNMol() ){
664	+	// we don't have the total number of molecules, so we assume it is
665	+	// given in each component
666
667	<	#endif
668	<	}
667	>	tot_nmol = 0;
668	>	for( i=0; i<n_components; i++ ){
669
670	<	#ifdef IS_MPI
671	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
672	<	MPIcheckPoint();
673	<	#endif // is_mpi
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	<
524	<
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
531	<
532	<	if( the_globals->haveFinalConfig() ){
533	<	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 );
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	<	}
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;
564	<	int nameLength = strlen( simnfo->sampleName );
565	<	endTest = &(simnfo->sampleName[nameLength - 5]);
566	<	if( !strcmp( endTest, ".bass" ) ){
567	<	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" );
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	<	else{
757	<	strcat( simnfo->sampleName, ".dump" );
756	>	boxVector[1] = globals->getBoxY();
757	>
758	>	if( !globals->haveBoxZ() ){
759	>	sprintf( painCave.errMsg,
760	>	"SimSetup error, no periodic BoxZ size given.\n" );
761	>	painCave.isFatal = 1;
762	>	simError();
763		}
764	+	boxVector[2] = globals->getBoxZ();
765	+
766	+	info[i].setBox( boxVector );
767		}
768	+
769	+	}
770
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	–
771		#ifdef IS_MPI
772	<	}
772	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
773	>	MPIcheckPoint();
774		#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	–	}
775
776	<	if( the_globals->haveStatusTime() ){
625	<	simnfo->statusTime = the_globals->getStatusTime();
626	<	}
776	>	}
777
628	–	if( the_globals->haveThermalTime() ){
629	–	simnfo->thermalTime = the_globals->getThermalTime();
630	–	}
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
881	+	#ifdef IS_MPI
882	+	strcpy( checkPointMsg, "post processing checks out" );
883	+	MPIcheckPoint();
884	+	#endif // is_mpi
885
886	<	//   // make the longe range forces and the integrator
886	>	}
887
888	<	//   new AllLong( simnfo );
888	>	void SimSetup::initSystemCoords( void ){
889	>	int i;
890	>
891	>	std::cerr << "Setting atom Coords\n";
892
893	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
642	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
643	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
644	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
645	<
646	<
647	<
648	<	// initialize the Fortran
893	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
894
895	<	simnfo->refreshSim();
895	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
896
897	<	if( !strcmp( simnfo->mixingRule, "standard") ){
898	<	the_ff->initForceField( LB_MIXING_RULE );
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		}
655	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
656	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
657	–	}
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 );
662	<	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	<
666	<
929	>
930		#ifdef IS_MPI
931	<	strcpy( checkPointMsg,
669	<	"Successfully intialized the mixingRule for Fortran." );
931	>	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
932		MPIcheckPoint();
933		#endif // is_mpi
934	+
935		}
936
674	–	void SimSetup::makeAtoms( void ){
937
938	<	int i, j, k, index;
939	<	double ux, uy, uz, uSqr, u;
940	<	AtomStamp* current_atom;
938	>	void SimSetup::makeOutNames( void ){
939	>
940	>	int k;
941
942	<	DirectionalAtom* dAtom;
943	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
942	>
943	>	for(k=0; k<nInfo; k++){
944
683	–	lMolIndex = 0;
684	–	molIndex = 0;
685	–	index = 0;
686	–	for( i=0; i<n_components; i++ ){
687	–
688	–	for( j=0; j<components_nmol[i]; j++ ){
689	–
945		#ifdef IS_MPI
946	<	if( mpiSim->getMyMolStart() <= molIndex &&
947	<	molIndex <= mpiSim->getMyMolEnd() ){
948	<	#endif // is_mpi
949	<
950	<	molStart = index;
951	<	nMemb = comp_stamps[i]->getNAtoms();
952	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
953	<
954	<	current_atom = comp_stamps[i]->getAtom( k );
955	<	if( current_atom->haveOrientation() ){
956	<
957	<	dAtom = new DirectionalAtom(index);
958	<	simnfo->n_oriented++;
959	<	the_atoms[index] = dAtom;
960	<
961	<	ux = current_atom->getOrntX();
962	<	uy = current_atom->getOrntY();
963	<	uz = current_atom->getOrntZ();
964	<
965	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
966	<
712	<	u = sqrt( uSqr );
713	<	ux = ux / u;
714	<	uy = uy / u;
715	<	uz = uz / u;
716	<
717	<	dAtom->setSUx( ux );
718	<	dAtom->setSUy( uy );
719	<	dAtom->setSUz( uz );
946	>	if( worldRank == 0 ){
947	>	#endif // is_mpi
948	>
949	>	if( globals->haveFinalConfig() ){
950	>	strcpy( info[k].finalName, globals->getFinalConfig() );
951	>	}
952	>	else{
953	>	strcpy( info[k].finalName, inFileName );
954	>	char* endTest;
955	>	int nameLength = strlen( info[k].finalName );
956	>	endTest = &(info[k].finalName[nameLength - 5]);
957	>	if( !strcmp( endTest, ".bass" ) ){
958	>	strcpy( endTest, ".eor" );
959	>	}
960	>	else if( !strcmp( endTest, ".BASS" ) ){
961	>	strcpy( endTest, ".eor" );
962	>	}
963	>	else{
964	>	endTest = &(info[k].finalName[nameLength - 4]);
965	>	if( !strcmp( endTest, ".bss" ) ){
966	>	strcpy( endTest, ".eor" );
967		}
968	+	else if( !strcmp( endTest, ".mdl" ) ){
969	+	strcpy( endTest, ".eor" );
970	+	}
971		else{
972	<	the_atoms[index] = new GeneralAtom(index);
972	>	strcat( info[k].finalName, ".eor" );
973		}
724	–	the_atoms[index]->setType( current_atom->getType() );
725	–	the_atoms[index]->setIndex( index );
726	–
727	–	// increment the index and repeat;
728	–	index++;
974		}
730	–
731	–	molEnd = index -1;
732	–	the_molecules[lMolIndex].setNMembers( nMemb );
733	–	the_molecules[lMolIndex].setStartAtom( molStart );
734	–	the_molecules[lMolIndex].setEndAtom( molEnd );
735	–	the_molecules[lMolIndex].setStampID( i );
736	–	lMolIndex++;
737	–
738	–	#ifdef IS_MPI
975		}
740	–	#endif //is_mpi
976
977	<	molIndex++;
977	>	// make the sample and status out names
978	>
979	>	strcpy( info[k].sampleName, inFileName );
980	>	char* endTest;
981	>	int nameLength = strlen( info[k].sampleName );
982	>	endTest = &(info[k].sampleName[nameLength - 5]);
983	>	if( !strcmp( endTest, ".bass" ) ){
984	>	strcpy( endTest, ".dump" );
985	>	}
986	>	else if( !strcmp( endTest, ".BASS" ) ){
987	>	strcpy( endTest, ".dump" );
988	>	}
989	>	else{
990	>	endTest = &(info[k].sampleName[nameLength - 4]);
991	>	if( !strcmp( endTest, ".bss" ) ){
992	>	strcpy( endTest, ".dump" );
993	>	}
994	>	else if( !strcmp( endTest, ".mdl" ) ){
995	>	strcpy( endTest, ".dump" );
996	>	}
997	>	else{
998	>	strcat( info[k].sampleName, ".dump" );
999	>	}
1000	>	}
1001	>
1002	>	strcpy( info[k].statusName, inFileName );
1003	>	nameLength = strlen( info[k].statusName );
1004	>	endTest = &(info[k].statusName[nameLength - 5]);
1005	>	if( !strcmp( endTest, ".bass" ) ){
1006	>	strcpy( endTest, ".stat" );
1007	>	}
1008	>	else if( !strcmp( endTest, ".BASS" ) ){
1009	>	strcpy( endTest, ".stat" );
1010	>	}
1011	>	else{
1012	>	endTest = &(info[k].statusName[nameLength - 4]);
1013	>	if( !strcmp( endTest, ".bss" ) ){
1014	>	strcpy( endTest, ".stat" );
1015	>	}
1016	>	else if( !strcmp( endTest, ".mdl" ) ){
1017	>	strcpy( endTest, ".stat" );
1018	>	}
1019	>	else{
1020	>	strcat( info[k].statusName, ".stat" );
1021	>	}
1022	>	}
1023	>
1024	>	#ifdef IS_MPI
1025		}
1026	+	#endif // is_mpi
1027		}
745	–
746	–	#ifdef IS_MPI
747	–	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
748	–
749	–	delete[] globalIndex;
750	–
751	–	mpiSim->mpiRefresh();
752	–	#endif //IS_MPI
753	–
754	–	the_ff->initializeAtoms();
1028		}
1029
757	–	void SimSetup::makeBonds( void ){
1030
1031	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1032	<	bond_pair* the_bonds;
1033	<	BondStamp* current_bond;
1031	>	void SimSetup::sysObjectsCreation( void ){
1032	>
1033	>	int i,k;
1034	>
1035	>	// create the forceField
1036	>
1037	>	createFF();
1038
1039	<	the_bonds = new bond_pair[tot_bonds];
764	<	index = 0;
765	<	offset = 0;
766	<	molIndex = 0;
1039	>	// extract componentList
1040
1041	<	for( i=0; i<n_components; i++ ){
1041	>	compList();
1042
1043	<	for( j=0; j<components_nmol[i]; j++ ){
1043	>	// calc the number of atoms, bond, bends, and torsions
1044
1045	<	#ifdef IS_MPI
773	<	if( mpiSim->getMyMolStart() <= molIndex &&
774	<	molIndex <= mpiSim->getMyMolEnd() ){
775	<	#endif // is_mpi
776	<
777	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
778	<
779	<	current_bond = comp_stamps[i]->getBond( k );
780	<	the_bonds[index].a = current_bond->getA() + offset;
781	<	the_bonds[index].b = current_bond->getB() + offset;
1045	>	calcSysValues();
1046
783	–	exI = the_bonds[index].a;
784	–	exJ = the_bonds[index].b;
785	–
786	–	// exclude_I must always be the smaller of the pair
787	–	if( exI > exJ ){
788	–	tempEx = exI;
789	–	exI = exJ;
790	–	exJ = tempEx;
791	–	}
792	–
793	–
1047		#ifdef IS_MPI
1048	<
1049	<	the_excludes[index*2] =
1050	<	the_atoms[exI]->getGlobalIndex() + 1;
798	<	the_excludes[index*2 + 1] =
799	<	the_atoms[exJ]->getGlobalIndex() + 1;
800	<
801	<	#else  // isn't MPI
802	<
803	<	the_excludes[index*2] =     exI + 1;
804	<	the_excludes[index*2 + 1] = exJ + 1;
805	<	// fortran index from 1 (hence the +1 in the indexing)
806	<	#endif  //is_mpi
807	<
808	<	// increment the index and repeat;
809	<	index++;
810	<	}
811	<	offset += comp_stamps[i]->getNAtoms();
812	<
813	<	#ifdef IS_MPI
814	<	}
1048	>	// divide the molecules among the processors
1049	>
1050	>	mpiMolDivide();
1051		#endif //is_mpi
1052	<
1053	<	molIndex++;
1054	<	}
1055	<	}
1052	>
1053	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1054	>
1055	>	makeSysArrays();
1056
1057	<	the_ff->initializeBonds( the_bonds );
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
824	–	void SimSetup::makeBends( void ){
1069
1070	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
827	<	bend_set* the_bends;
828	<	BendStamp* current_bend;
829	<	LinkedAssign* extras;
830	<	LinkedAssign* current_extra;
831	<
1070	>	void SimSetup::createFF( void ){
1071
1072	<	the_bends = new bend_set[tot_bends];
834	<	index = 0;
835	<	offset = 0;
836	<	molIndex = 0;
837	<	for( i=0; i<n_components; i++ ){
1072	>	switch( ffCase ){
1073
1074	<	for( j=0; j<components_nmol[i]; j++ ){
1074	>	case FF_DUFF:
1075	>	the_ff = new DUFF();
1076	>	break;
1077
1078	<	#ifdef IS_MPI
1079	<	if( mpiSim->getMyMolStart() <= molIndex &&
1080	<	molIndex <= mpiSim->getMyMolEnd() ){
844	<	#endif // is_mpi
1078	>	case FF_LJ:
1079	>	the_ff = new LJFF();
1080	>	break;
1081
1082	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
1083	<
1084	<	current_bend = comp_stamps[i]->getBend( k );
849	<	the_bends[index].a = current_bend->getA() + offset;
850	<	the_bends[index].b = current_bend->getB() + offset;
851	<	the_bends[index].c = current_bend->getC() + offset;
852	<
853	<	if( current_bend->haveExtras() ){
854	<
855	<	extras = current_bend->getExtras();
856	<	current_extra = extras;
857	<
858	<	while( current_extra != NULL ){
859	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
860	<
861	<	switch( current_extra->getType() ){
862	<
863	<	case 0:
864	<	the_bends[index].ghost =
865	<	current_extra->getInt() + offset;
866	<	the_bends[index].isGhost = 1;
867	<	break;
868	<
869	<	case 1:
870	<	the_bends[index].ghost =
871	<	(int)current_extra->getDouble() + offset;
872	<	the_bends[index].isGhost = 1;
873	<	break;
874	<
875	<	default:
876	<	sprintf( painCave.errMsg,
877	<	"SimSetup Error: ghostVectorSource was neiter a "
878	<	"double nor an int.\n"
879	<	"-->Bend[%d] in %s\n",
880	<	k, comp_stamps[i]->getID() );
881	<	painCave.isFatal = 1;
882	<	simError();
883	<	}
884	<	}
885	<
886	<	else{
887	<
888	<	sprintf( painCave.errMsg,
889	<	"SimSetup Error: unhandled bend assignment:\n"
890	<	"    -->%s in Bend[%d] in %s\n",
891	<	current_extra->getlhs(),
892	<	k, comp_stamps[i]->getID() );
893	<	painCave.isFatal = 1;
894	<	simError();
895	<	}
896	<
897	<	current_extra = current_extra->getNext();
898	<	}
899	<	}
900	<
901	<	if( !the_bends[index].isGhost ){
902	<
903	<	exI = the_bends[index].a;
904	<	exJ = the_bends[index].c;
905	<	}
906	<	else{
907	<
908	<	exI = the_bends[index].a;
909	<	exJ = the_bends[index].b;
910	<	}
911	<
912	<	// exclude_I must always be the smaller of the pair
913	<	if( exI > exJ ){
914	<	tempEx = exI;
915	<	exI = exJ;
916	<	exJ = tempEx;
917	<	}
1082	>	case FF_EAM:
1083	>	the_ff = new EAM_FF();
1084	>	break;
1085
1086	<
1087	<	#ifdef IS_MPI
1088	<
1089	<	the_excludes[(index + tot_bonds)*2] =
1090	<	the_atoms[exI]->getGlobalIndex() + 1;
924	<	the_excludes[(index + tot_bonds)*2 + 1] =
925	<	the_atoms[exJ]->getGlobalIndex() + 1;
926	<
927	<	#else  // isn't MPI
928	<
929	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
930	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
931	<	// fortran index from 1 (hence the +1 in the indexing)
932	<	#endif  //is_mpi
933	<
934	<
935	<	// increment the index and repeat;
936	<	index++;
937	<	}
938	<	offset += comp_stamps[i]->getNAtoms();
939	<
940	<	#ifdef IS_MPI
941	<	}
942	<	#endif //is_mpi
943	<
944	<	molIndex++;
945	<	}
1086	>	default:
1087	>	sprintf( painCave.errMsg,
1088	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1089	>	painCave.isFatal = 1;
1090	>	simError();
1091		}
1092
1093		#ifdef IS_MPI
1094	<	sprintf( checkPointMsg,
950	<	"Successfully created the bends list.\n" );
1094	>	strcpy( checkPointMsg, "ForceField creation successful" );
1095		MPIcheckPoint();
1096		#endif // is_mpi
953	–
1097
955	–	the_ff->initializeBends( the_bends );
1098		}
1099
958	–	void SimSetup::makeTorsions( void ){
1100
1101	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
961	<	torsion_set* the_torsions;
962	<	TorsionStamp* current_torsion;
1101	>	void SimSetup::compList( void ){
1102
1103	<	the_torsions = new torsion_set[tot_torsions];
1104	<	index = 0;
1105	<	offset = 0;
1106	<	molIndex = 0;
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		for( i=0; i<n_components; i++ ){
1121
1122	<	for( j=0; j<components_nmol[i]; j++ ){
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		#ifdef IS_MPI
1148	<	if( mpiSim->getMyMolStart() <= molIndex &&
1149	<	molIndex <= mpiSim->getMyMolEnd() ){
1150	<	#endif // is_mpi
1148	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1149	>	MPIcheckPoint();
1150	>	#endif // is_mpi
1151
977	–	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1152
1153	<	current_torsion = comp_stamps[i]->getTorsion( k );
980	<	the_torsions[index].a = current_torsion->getA() + offset;
981	<	the_torsions[index].b = current_torsion->getB() + offset;
982	<	the_torsions[index].c = current_torsion->getC() + offset;
983	<	the_torsions[index].d = current_torsion->getD() + offset;
984	<
985	<	exI = the_torsions[index].a;
986	<	exJ = the_torsions[index].d;
987	<
988	<
989	<	// exclude_I must always be the smaller of the pair
990	<	if( exI > exJ ){
991	<	tempEx = exI;
992	<	exI = exJ;
993	<	exJ = tempEx;
994	<	}
995	<
996	<
997	<	#ifdef IS_MPI
998	<
999	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
1000	<	the_atoms[exI]->getGlobalIndex() + 1;
1001	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1002	<	the_atoms[exJ]->getGlobalIndex() + 1;
1003	<
1004	<	#else  // isn't MPI
1005	<
1006	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1007	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1008	<	// fortran indexes from 1 (hence the +1 in the indexing)
1009	<	#endif  //is_mpi
1010	<
1153	>	}
1154
1155	<	// increment the index and repeat;
1156	<	index++;
1157	<	}
1158	<	offset += comp_stamps[i]->getNAtoms();
1159	<
1160	<	#ifdef IS_MPI
1161	<	}
1162	<	#endif //is_mpi
1163	<
1164	<	molIndex++;
1165	<	}
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	<	the_ff->initializeTorsions( the_torsions );
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	<	void SimSetup::initFromBass( void ){
1187	>	#ifdef IS_MPI
1188
1189	+	void SimSetup::mpiMolDivide( void ){
1190	+
1191		int i, j, k;
1192	<	int n_cells;
1193	<	double cellx, celly, cellz;
1033	<	double temp1, temp2, temp3;
1034	<	int n_per_extra;
1035	<	int n_extra;
1036	<	int have_extra, done;
1192	>	int localMol, allMol;
1193	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1194
1195	<	temp1 = (double)tot_nmol / 4.0;
1196	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1197	<	temp3 = ceil( temp2 );
1195	>	mpiSim = new mpiSimulation( info );
1196	>
1197	>	globalIndex = mpiSim->divideLabor();
1198
1199	<	have_extra =0;
1200	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1201	<	have_extra =1;
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
1046	–	n_cells = (int)temp3 - 1;
1047	–	cellx = simnfo->box_x / temp3;
1048	–	celly = simnfo->box_y / temp3;
1049	–	cellz = simnfo->box_z / temp3;
1050	–	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1051	–	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1052	–	n_per_extra = (int)ceil( temp1 );
1212
1213	<	if( n_per_extra > 4){
1214	<	sprintf( painCave.errMsg,
1215	<	"SimSetup error. There has been an error in constructing"
1216	<	" the non-complete lattice.\n" );
1217	<	painCave.isFatal = 1;
1218	<	simError();
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	<	else{
1234	<	n_cells = (int)temp3;
1235	<	cellx = simnfo->box_x / temp3;
1236	<	celly = simnfo->box_y / temp3;
1237	<	cellz = simnfo->box_z / temp3;
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	<	current_mol = 0;
1248	<	current_comp_mol = 0;
1249	<	current_comp = 0;
1250	<	current_atom_ndx = 0;
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 < n_cells ; i++ ){
1254	<	for( j=0; j < n_cells; j++ ){
1255	<	for( k=0; k < n_cells; k++ ){
1253	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1254	>	MPIcheckPoint();
1255	>	}
1256	>
1257	>	#endif // is_mpi
1258
1078	–	makeElement( i * cellx,
1079	–	j * celly,
1080	–	k * cellz );
1259
1260	<	makeElement( i * cellx + 0.5 * cellx,
1261	<	j * celly + 0.5 * celly,
1084	<	k * cellz );
1260	>	void SimSetup::makeSysArrays( void ){
1261	>	int i, j, k, l;
1262
1263	<	makeElement( i * cellx,
1264	<	j * celly + 0.5 * celly,
1265	<	k * cellz + 0.5 * cellz );
1263	>	Atom** the_atoms;
1264	>	Molecule* the_molecules;
1265	>	Exclude** the_excludes;
1266
1267	<	makeElement( i * cellx + 0.5 * cellx,
1268	<	j * celly,
1269	<	k * cellz + 0.5 * cellz );
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	<
1293	<	if( have_extra ){
1294	<	done = 0;
1295	<
1296	<	int start_ndx;
1297	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1298	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1299	<
1300	<	if( i < n_cells ){
1301	<
1302	<	if( j < n_cells ){
1303	<	start_ndx = n_cells;
1108	<	}
1109	<	else start_ndx = 0;
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	<	else start_ndx = 0;
1305	>	molIndex++;
1306	>	}
1307	>	}
1308	>
1309	>
1310	>	#endif // is_mpi
1311
1113	–	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1312
1313	<	makeElement( i * cellx,
1314	<	j * celly,
1315	<	k * cellz );
1316	<	done = ( current_mol >= tot_nmol );
1317	<
1318	<	if( !done && n_per_extra > 1 ){
1121	<	makeElement( i * cellx + 0.5 * cellx,
1122	<	j * celly + 0.5 * celly,
1123	<	k * cellz );
1124	<	done = ( current_mol >= tot_nmol );
1125	<	}
1126	<
1127	<	if( !done && n_per_extra > 2){
1128	<	makeElement( i * cellx,
1129	<	j * celly + 0.5 * celly,
1130	<	k * cellz + 0.5 * cellz );
1131	<	done = ( current_mol >= tot_nmol );
1132	<	}
1133	<
1134	<	if( !done && n_per_extra > 3){
1135	<	makeElement( i * cellx + 0.5 * cellx,
1136	<	j * celly,
1137	<	k * cellz + 0.5 * cellz );
1138	<	done = ( current_mol >= tot_nmol );
1139	<	}
1140	<	}
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	<	}
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	+	// set the arrays into the SimInfo object
1335
1336	<	for( i=0; i<simnfo->n_atoms; i++ ){
1337	<	simnfo->atoms[i]->set_vx( 0.0 );
1338	<	simnfo->atoms[i]->set_vy( 0.0 );
1339	<	simnfo->atoms[i]->set_vz( 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	>	the_ff->setSimInfo( info );
1342	>
1343		}
1344		}
1345
1346	<	void SimSetup::makeElement( double x, double y, double z ){
1346	>	void SimSetup::makeIntegrator( void ){
1347
1348		int k;
1156	–	AtomStamp* current_atom;
1157	–	DirectionalAtom* dAtom;
1158	–	double rotMat[3][3];
1349
1350	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
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	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1367	<	if( !current_atom->havePosition() ){
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:initFromBass error.\n"
1509	<	"\tComponent %s, atom %s does not have a position specified.\n"
1167	<	"\tThe initialization routine is unable to give a start"
1168	<	" position.\n",
1169	<	comp_stamps[current_comp]->getID(),
1170	<	current_atom->getType() );
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	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1176	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1177	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1565	>	void SimSetup::initFortran( void ){
1566
1567	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
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
1181	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1583
1584	<	rotMat[0][0] = 1.0;
1585	<	rotMat[0][1] = 0.0;
1586	<	rotMat[0][2] = 0.0;
1584	>	#ifdef IS_MPI
1585	>	strcpy( checkPointMsg,
1586	>	"Successfully intialized the mixingRule for Fortran." );
1587	>	MPIcheckPoint();
1588	>	#endif // is_mpi
1589
1590	<	rotMat[1][0] = 0.0;
1188	<	rotMat[1][1] = 1.0;
1189	<	rotMat[1][2] = 0.0;
1590	>	}
1591
1592	<	rotMat[2][0] = 0.0;
1593	<	rotMat[2][1] = 0.0;
1594	<	rotMat[2][2] = 1.0;
1592	>	void SimSetup::setupZConstraint()
1593	>	{
1594	>	int k;
1595
1596	<	dAtom->setA( rotMat );
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	<
1607	<	current_atom_ndx++;
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		}
1200	–
1201	–	current_mol++;
1202	–	current_comp_mol++;
1203	–
1204	–	if( current_comp_mol >= components_nmol[current_comp] ){
1205	–
1206	–	current_comp_mol = 0;
1207	–	current_comp++;
1208	–	}
1650		}

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