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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 378 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
Revision 689 by tim, Tue Aug 12 19:56:49 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 12 | Line 15 | SimSetup::SimSetup(){
15		#include "mpiSimulation.hpp"
16		#endif
17
18	+	// some defines for ensemble and Forcefield  cases
19	+
20	+	#define NVE_ENS        0
21	+	#define NVT_ENS        1
22	+	#define NPTi_ENS       2
23	+	#define NPTf_ENS       3
24	+	#define NPTim_ENS      4
25	+	#define NPTfm_ENS      5
26	+
27	+	#define FF_DUFF 0
28	+	#define FF_LJ   1
29	+	#define FF_EAM  2
30	+
31	+	using namespace std;
32	+
33		SimSetup::SimSetup(){
34	+
35	+	isInfoArray = 0;
36	+	nInfo = 1;
37	+
38		stamps = new MakeStamps();
39		globals = new Globals();
40
41	+
42		#ifdef IS_MPI
43		strcpy( checkPointMsg, "SimSetup creation successful" );
44		MPIcheckPoint();
#	Line 27 | Line 50 | void SimSetup::parseFile( char* fileName ){
50		delete globals;
51		}
52
53	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
54	+	info = the_info;
55	+	nInfo = theNinfo;
56	+	isInfoArray = 1;
57	+	}
58	+
59	+
60		void SimSetup::parseFile( char* fileName ){
61
62		#ifdef IS_MPI
#	Line 62 | Line 92 | void SimSetup::createSim( void ){
92
93		#endif // is_mpi
94
95	<	void SimSetup::createSim( void ){
95	>	void SimSetup::createSim(void){
96
97	<	MakeStamps *the_stamps;
98	<	Globals* the_globals;
99	<	int i, j;
97	>	int i, j, k, globalAtomIndex;
98	>
99	>	// gather all of the information from the Bass file
100
101	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
101	>	std::cerr << "gathering info\n";
102
103	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	simnfo->run_time = the_globals->getRunTime();
103	>	gatherInfo();
104
105	<	// get the ones we know are there, yet still may need some work.
81	<	n_components = the_globals->getNComponents();
82	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
105	>	// creation of complex system objects
106
107	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
107	>	std::cerr << "creating system objects\n";
108
109	+	sysObjectsCreation();
110
111	<	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
92	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
93	<	else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
94	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
95	<	else{
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Error. Unrecognized force field -> %s\n",
98	<	force_field );
99	<	painCave.isFatal = 1;
100	<	simError();
101	<	}
102	<
103	<	#ifdef IS_MPI
104	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
107	<
111	>	// check on the post processing info
112
113	+	std::cerr << "performing final info check.\n";
114
115	<	// 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];
115	>	finalInfoCheck();
116
117	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
117	>	// initialize the system coordinates
118
119	<	tot_nmol = 0;
120	<	for( i=0; i<n_components; i++ ){
119	>	std::cerr << "about to init coords\n";
120
121	<	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	<	}
121	>	if( !isInfoArray ) initSystemCoords();
122
123	<	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	<	}
123	>	// make the output filenames
124
125	+	makeOutNames();
126	+
127	+	// make the integrator
128	+
129	+	makeIntegrator();
130	+
131		#ifdef IS_MPI
132	<	strcpy( checkPointMsg, "Have the number of components" );
133	<	MPIcheckPoint();
163	<	#endif // is_mpi
132	>	mpiSim->mpiRefresh();
133	>	#endif
134
135	<	// make an array of molecule stamps that match the components used.
166	<	// also extract the used stamps out into a separate linked list
135	>	// initialize the Fortran
136
137	<	simnfo->nComponents = n_components;
169	<	simnfo->componentsNmol = components_nmol;
170	<	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++ ){
137	>	initFortran();
138
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
139
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	–	}
140
141	<	#ifdef IS_MPI
204	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
205	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
141	>	}
142
143
144	+	void SimSetup::makeMolecules( void ){
145
146	<	// caclulate the number of atoms, bonds, bends and torsions
146	>	int k,l;
147	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
148	>	molInit molInfo;
149	>	DirectionalAtom* dAtom;
150	>	LinkedAssign* extras;
151	>	LinkedAssign* current_extra;
152	>	AtomStamp* currentAtom;
153	>	BondStamp* currentBond;
154	>	BendStamp* currentBend;
155	>	TorsionStamp* currentTorsion;
156
157	<	tot_atoms = 0;
158	<	tot_bonds = 0;
159	<	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	<	}
157	>	bond_pair* theBonds;
158	>	bend_set* theBends;
159	>	torsion_set* theTorsions;
160
161	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
161	>
162	>	//init the forceField paramters
163
164	<	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;
164	>	the_ff->readParams();
165
166
167	<	#ifdef IS_MPI
167	>	// init the atoms
168
169	<	// divide the molecules among processors here.
169	>	double ux, uy, uz, u, uSqr;
170
171	<	mpiSim = new mpiSimulation( simnfo );
172	<
173	<
171	>	for(k=0; k<nInfo; k++){
172	>
173	>	the_ff->setSimInfo( &(info[k]) );
174
175	<	globalIndex = mpiSim->divideLabor();
175	>	atomOffset = 0;
176	>	excludeOffset = 0;
177	>	for(i=0; i<info[k].n_mol; i++){
178	>
179	>	stampID = info[k].molecules[i].getStampID();
180
181	<
182	<
183	<	// set up the local variables
184	<
185	<	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++ ){
181	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
182	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
183	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
184	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
185	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
186
187	<	if( mpiSim->getMyMolStart() <= allMol &&
188	<	allMol <= mpiSim->getMyMolEnd() ){
189	<
190	<	local_atoms +=    comp_stamps[i]->getNAtoms();
191	<	local_bonds +=    comp_stamps[i]->getNBonds();
267	<	local_bends +=    comp_stamps[i]->getNBends();
268	<	local_torsions += comp_stamps[i]->getNTorsions();
269	<	localMol++;
270	<	}
271	<	allMol++;
272	<	}
273	<	}
274	<	local_SRI = local_bonds + local_bends + local_torsions;
275	<
187	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
188	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
189	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
190	>	molInfo.myBends = new Bend*[molInfo.nBends];
191	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
192
193	<	simnfo->n_atoms = mpiSim->getMyNlocal();
194	<
195	<	if( local_atoms != simnfo->n_atoms ){
196	<	sprintf( painCave.errMsg,
197	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
198	<	" localAtom (%d) are note equal.\n",
199	<	simnfo->n_atoms,
200	<	local_atoms );
201	<	painCave.isFatal = 1;
202	<	simError();
203	<	}
204	<
205	<	simnfo->n_bonds = local_bonds;
206	<	simnfo->n_bends = local_bends;
207	<	simnfo->n_torsions = local_torsions;
208	<	simnfo->n_SRI = local_SRI;
209	<	simnfo->n_mol = localMol;
193	>	theBonds = new bond_pair[molInfo.nBonds];
194	>	theBends = new bend_set[molInfo.nBends];
195	>	theTorsions = new torsion_set[molInfo.nTorsions];
196	>
197	>	// make the Atoms
198	>
199	>	for(j=0; j<molInfo.nAtoms; j++){
200	>
201	>	currentAtom = comp_stamps[stampID]->getAtom( j );
202	>	if( currentAtom->haveOrientation() ){
203	>
204	>	dAtom = new DirectionalAtom( (j + atomOffset),
205	>	info[k].getConfiguration() );
206	>	info[k].n_oriented++;
207	>	molInfo.myAtoms[j] = dAtom;
208	>
209	>	ux = currentAtom->getOrntX();
210	>	uy = currentAtom->getOrntY();
211	>	uz = currentAtom->getOrntZ();
212	>
213	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
214	>
215	>	u = sqrt( uSqr );
216	>	ux = ux / u;
217	>	uy = uy / u;
218	>	uz = uz / u;
219	>
220	>	dAtom->setSUx( ux );
221	>	dAtom->setSUy( uy );
222	>	dAtom->setSUz( uz );
223	>	}
224	>	else{
225	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
226	>	info[k].getConfiguration() );
227	>	}
228	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
229	>
230	>	#ifdef IS_MPI
231	>
232	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
233	>
234	>	#endif // is_mpi
235	>	}
236	>
237	>	// make the bonds
238	>	for(j=0; j<molInfo.nBonds; j++){
239	>
240	>	currentBond = comp_stamps[stampID]->getBond( j );
241	>	theBonds[j].a = currentBond->getA() + atomOffset;
242	>	theBonds[j].b = currentBond->getB() + atomOffset;
243	>
244	>	exI = theBonds[j].a;
245	>	exJ = theBonds[j].b;
246	>
247	>	// exclude_I must always be the smaller of the pair
248	>	if( exI > exJ ){
249	>	tempEx = exI;
250	>	exI = exJ;
251	>	exJ = tempEx;
252	>	}
253	>	#ifdef IS_MPI
254	>	tempEx = exI;
255	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
256	>	tempEx = exJ;
257	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
258	>
259	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
260	>	#else  // isn't MPI
261	>
262	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
263	>	#endif  //is_mpi
264	>	}
265	>	excludeOffset += molInfo.nBonds;
266	>
267	>	//make the bends
268	>	for(j=0; j<molInfo.nBends; j++){
269	>
270	>	currentBend = comp_stamps[stampID]->getBend( j );
271	>	theBends[j].a = currentBend->getA() + atomOffset;
272	>	theBends[j].b = currentBend->getB() + atomOffset;
273	>	theBends[j].c = currentBend->getC() + atomOffset;
274	>
275	>	if( currentBend->haveExtras() ){
276	>
277	>	extras = currentBend->getExtras();
278	>	current_extra = extras;
279	>
280	>	while( current_extra != NULL ){
281	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
282	>
283	>	switch( current_extra->getType() ){
284	>
285	>	case 0:
286	>	theBends[j].ghost =
287	>	current_extra->getInt() + atomOffset;
288	>	theBends[j].isGhost = 1;
289	>	break;
290	>
291	>	case 1:
292	>	theBends[j].ghost =
293	>	(int)current_extra->getDouble() + atomOffset;
294	>	theBends[j].isGhost = 1;
295	>	break;
296	>
297	>	default:
298	>	sprintf( painCave.errMsg,
299	>	"SimSetup Error: ghostVectorSource was neither a "
300	>	"double nor an int.\n"
301	>	"-->Bend[%d] in %s\n",
302	>	j, comp_stamps[stampID]->getID() );
303	>	painCave.isFatal = 1;
304	>	simError();
305	>	}
306	>	}
307	>
308	>	else{
309	>
310	>	sprintf( painCave.errMsg,
311	>	"SimSetup Error: unhandled bend assignment:\n"
312	>	"    -->%s in Bend[%d] in %s\n",
313	>	current_extra->getlhs(),
314	>	j, comp_stamps[stampID]->getID() );
315	>	painCave.isFatal = 1;
316	>	simError();
317	>	}
318	>
319	>	current_extra = current_extra->getNext();
320	>	}
321	>	}
322	>
323	>	if( !theBends[j].isGhost ){
324	>
325	>	exI = theBends[j].a;
326	>	exJ = theBends[j].c;
327	>	}
328	>	else{
329	>
330	>	exI = theBends[j].a;
331	>	exJ = theBends[j].b;
332	>	}
333	>
334	>	// exclude_I must always be the smaller of the pair
335	>	if( exI > exJ ){
336	>	tempEx = exI;
337	>	exI = exJ;
338	>	exJ = tempEx;
339	>	}
340	>	#ifdef IS_MPI
341	>	tempEx = exI;
342	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
343	>	tempEx = exJ;
344	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345	>
346	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
347	>	#else  // isn't MPI
348	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
349	>	#endif  //is_mpi
350	>	}
351	>	excludeOffset += molInfo.nBends;
352	>
353	>	for(j=0; j<molInfo.nTorsions; j++){
354	>
355	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
356	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
357	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
358	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
359	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
360	>
361	>	exI = theTorsions[j].a;
362	>	exJ = theTorsions[j].d;
363	>
364	>	// exclude_I must always be the smaller of the pair
365	>	if( exI > exJ ){
366	>	tempEx = exI;
367	>	exI = exJ;
368	>	exJ = tempEx;
369	>	}
370	>	#ifdef IS_MPI
371	>	tempEx = exI;
372	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
373	>	tempEx = exJ;
374	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
375	>
376	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
377	>	#else  // isn't MPI
378	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
379	>	#endif  //is_mpi
380	>	}
381	>	excludeOffset += molInfo.nTorsions;
382	>
383	>
384	>	// send the arrays off to the forceField for init.
385	>
386	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
387	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
388	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
389	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
390	>
391	>
392	>	info[k].molecules[i].initialize( molInfo );
393
394	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
395	<	MPIcheckPoint();
394	>
395	>	atomOffset += molInfo.nAtoms;
396	>	delete[] theBonds;
397	>	delete[] theBends;
398	>	delete[] theTorsions;
399	>	}
400	>	}
401
402	<
402	>	#ifdef IS_MPI
403	>	sprintf( checkPointMsg, "all molecules initialized succesfully" );
404	>	MPIcheckPoint();
405		#endif // is_mpi
406
407	+	// clean up the forcefield
408
409	<	// create the atom and short range interaction arrays
409	>	the_ff->calcRcut();
410	>	the_ff->cleanMe();
411	>
412	>	}
413
414	<	Atom::createArrays(simnfo->n_atoms);
305	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
414	>	void SimSetup::initFromBass( void ){
415
416	+	int i, j, k;
417	+	int n_cells;
418	+	double cellx, celly, cellz;
419	+	double temp1, temp2, temp3;
420	+	int n_per_extra;
421	+	int n_extra;
422	+	int have_extra, done;
423
424	<	if( simnfo->n_SRI ){
425	<	the_sris = new SRI*[simnfo->n_SRI];
426	<	the_excludes = new int[2 * simnfo->n_SRI];
427	<	simnfo->globalExcludes = new int;
313	<	simnfo->n_exclude = tot_SRI;
314	<	}
315	<	else{
316	<
317	<	the_excludes = new int[2];
318	<	the_excludes[0] = 0;
319	<	the_excludes[1] = 0;
320	<	simnfo->globalExcludes = new int;
321	<	simnfo->globalExcludes[0] = 0;
424	>	double vel[3];
425	>	vel[0] = 0.0;
426	>	vel[1] = 0.0;
427	>	vel[2] = 0.0;
428
429	<	simnfo->n_exclude = 1;
430	<	}
429	>	temp1 = (double)tot_nmol / 4.0;
430	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
431	>	temp3 = ceil( temp2 );
432
433	<	// set the arrays into the SimInfo object
433	>	have_extra =0;
434	>	if( temp2 < temp3 ){ // we have a non-complete lattice
435	>	have_extra =1;
436
437	<	simnfo->atoms = the_atoms;
438	<	simnfo->sr_interactions = the_sris;
439	<	simnfo->nGlobalExcludes = 0;
440	<	simnfo->excludes = the_excludes;
437	>	n_cells = (int)temp3 - 1;
438	>	cellx = info[0].boxL[0] / temp3;
439	>	celly = info[0].boxL[1] / temp3;
440	>	cellz = info[0].boxL[2] / temp3;
441	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
442	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
443	>	n_per_extra = (int)ceil( temp1 );
444
445	<
334	<	// get some of the tricky things that may still be in the globals
335	<
336	<	if( simnfo->n_dipoles ){
337	<
338	<	if( !the_globals->haveRRF() ){
445	>	if( n_per_extra > 4){
446		sprintf( painCave.errMsg,
447	<	"SimSetup Error, system has dipoles, but no rRF was set.\n");
447	>	"SimSetup error. There has been an error in constructing"
448	>	" the non-complete lattice.\n" );
449		painCave.isFatal = 1;
450		simError();
451		}
452	<	if( !the_globals->haveDielectric() ){
453	<	sprintf( painCave.errMsg,
454	<	"SimSetup Error, system has dipoles, but no"
455	<	" dielectric was set.\n" );
456	<	painCave.isFatal = 1;
457	<	simError();
458	<	}
452	>	}
453	>	else{
454	>	n_cells = (int)temp3;
455	>	cellx = info[0].boxL[0] / temp3;
456	>	celly = info[0].boxL[1] / temp3;
457	>	cellz = info[0].boxL[2] / temp3;
458	>	}
459
460	<	simnfo->rRF        = the_globals->getRRF();
461	<	simnfo->dielectric = the_globals->getDielectric();
460	>	current_mol = 0;
461	>	current_comp_mol = 0;
462	>	current_comp = 0;
463	>	current_atom_ndx = 0;
464	>
465	>	for( i=0; i < n_cells ; i++ ){
466	>	for( j=0; j < n_cells; j++ ){
467	>	for( k=0; k < n_cells; k++ ){
468	>
469	>	makeElement( i * cellx,
470	>	j * celly,
471	>	k * cellz );
472	>
473	>	makeElement( i * cellx + 0.5 * cellx,
474	>	j * celly + 0.5 * celly,
475	>	k * cellz );
476	>
477	>	makeElement( i * cellx,
478	>	j * celly + 0.5 * celly,
479	>	k * cellz + 0.5 * cellz );
480	>
481	>	makeElement( i * cellx + 0.5 * cellx,
482	>	j * celly,
483	>	k * cellz + 0.5 * cellz );
484	>	}
485	>	}
486		}
487
488	<	#ifdef IS_MPI
489	<	strcpy( checkPointMsg, "rRf and dielectric check out" );
490	<	MPIcheckPoint();
491	<	#endif // is_mpi
492	<
493	<	if( the_globals->haveBox() ){
494	<	simnfo->box_x = the_globals->getBox();
495	<	simnfo->box_y = the_globals->getBox();
496	<	simnfo->box_z = the_globals->getBox();
488	>	if( have_extra ){
489	>	done = 0;
490	>
491	>	int start_ndx;
492	>	for( i=0; i < (n_cells+1) && !done; i++ ){
493	>	for( j=0; j < (n_cells+1) && !done; j++ ){
494	>
495	>	if( i < n_cells ){
496	>
497	>	if( j < n_cells ){
498	>	start_ndx = n_cells;
499	>	}
500	>	else start_ndx = 0;
501	>	}
502	>	else start_ndx = 0;
503	>
504	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
505	>
506	>	makeElement( i * cellx,
507	>	j * celly,
508	>	k * cellz );
509	>	done = ( current_mol >= tot_nmol );
510	>
511	>	if( !done && n_per_extra > 1 ){
512	>	makeElement( i * cellx + 0.5 * cellx,
513	>	j * celly + 0.5 * celly,
514	>	k * cellz );
515	>	done = ( current_mol >= tot_nmol );
516	>	}
517	>
518	>	if( !done && n_per_extra > 2){
519	>	makeElement( i * cellx,
520	>	j * celly + 0.5 * celly,
521	>	k * cellz + 0.5 * cellz );
522	>	done = ( current_mol >= tot_nmol );
523	>	}
524	>
525	>	if( !done && n_per_extra > 3){
526	>	makeElement( i * cellx + 0.5 * cellx,
527	>	j * celly,
528	>	k * cellz + 0.5 * cellz );
529	>	done = ( current_mol >= tot_nmol );
530	>	}
531	>	}
532	>	}
533	>	}
534		}
366	–	else if( the_globals->haveDensity() ){
535
536	<	double vol;
537	<	vol = (double)tot_nmol / the_globals->getDensity();
370	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
371	<	simnfo->box_y = simnfo->box_x;
372	<	simnfo->box_z = simnfo->box_x;
536	>	for( i=0; i<info[0].n_atoms; i++ ){
537	>	info[0].atoms[i]->setVel( vel );
538		}
539	<	else{
375	<	if( !the_globals->haveBoxX() ){
376	<	sprintf( painCave.errMsg,
377	<	"SimSetup error, no periodic BoxX size given.\n" );
378	<	painCave.isFatal = 1;
379	<	simError();
380	<	}
381	<	simnfo->box_x = the_globals->getBoxX();
539	>	}
540
541	<	if( !the_globals->haveBoxY() ){
384	<	sprintf( painCave.errMsg,
385	<	"SimSetup error, no periodic BoxY size given.\n" );
386	<	painCave.isFatal = 1;
387	<	simError();
388	<	}
389	<	simnfo->box_y = the_globals->getBoxY();
541	>	void SimSetup::makeElement( double x, double y, double z ){
542
543	<	if( !the_globals->haveBoxZ() ){
543	>	int k;
544	>	AtomStamp* current_atom;
545	>	DirectionalAtom* dAtom;
546	>	double rotMat[3][3];
547	>	double pos[3];
548	>
549	>	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
550	>
551	>	current_atom = comp_stamps[current_comp]->getAtom( k );
552	>	if( !current_atom->havePosition() ){
553		sprintf( painCave.errMsg,
554	<	"SimSetup error, no periodic BoxZ size given.\n" );
554	>	"SimSetup:initFromBass error.\n"
555	>	"\tComponent %s, atom %s does not have a position specified.\n"
556	>	"\tThe initialization routine is unable to give a start"
557	>	" position.\n",
558	>	comp_stamps[current_comp]->getID(),
559	>	current_atom->getType() );
560		painCave.isFatal = 1;
561		simError();
562		}
563	<	simnfo->box_z = the_globals->getBoxZ();
564	<	}
563	>
564	>	pos[0] = x + current_atom->getPosX();
565	>	pos[1] = y + current_atom->getPosY();
566	>	pos[2] = z + current_atom->getPosZ();
567	>
568	>	info[0].atoms[current_atom_ndx]->setPos( pos );
569
570	<	#ifdef IS_MPI
401	<	strcpy( checkPointMsg, "Box size set up" );
402	<	MPIcheckPoint();
403	<	#endif // is_mpi
570	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
571
572	+	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
573
574	<	// initialize the arrays
574	>	rotMat[0][0] = 1.0;
575	>	rotMat[0][1] = 0.0;
576	>	rotMat[0][2] = 0.0;
577
578	<	the_ff->setSimInfo( simnfo );
578	>	rotMat[1][0] = 0.0;
579	>	rotMat[1][1] = 1.0;
580	>	rotMat[1][2] = 0.0;
581
582	<	makeAtoms();
583	<	simnfo->identArray = new int[simnfo->n_atoms];
584	<	for(i=0; i<simnfo->n_atoms; i++){
413	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
414	<	}
415	<
416	<	if( tot_bonds ){
417	<	makeBonds();
418	<	}
582	>	rotMat[2][0] = 0.0;
583	>	rotMat[2][1] = 0.0;
584	>	rotMat[2][2] = 1.0;
585
586	<	if( tot_bends ){
587	<	makeBends();
422	<	}
586	>	dAtom->setA( rotMat );
587	>	}
588
589	<	if( tot_torsions ){
425	<	makeTorsions();
589	>	current_atom_ndx++;
590		}
591
592	+	current_mol++;
593	+	current_comp_mol++;
594
595	+	if( current_comp_mol >= components_nmol[current_comp] ){
596
597	+	current_comp_mol = 0;
598	+	current_comp++;
599	+	}
600	+	}
601
602
603	+	void SimSetup::gatherInfo( void ){
604	+	int i,j,k;
605
606	<	if( the_globals->haveInitialConfig() ){
607	<
435	<	InitializeFromFile* fileInit;
436	<	#ifdef IS_MPI // is_mpi
437	<	if( worldRank == 0 ){
438	<	#endif //is_mpi
439	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
440	<	#ifdef IS_MPI
441	<	}else fileInit = new InitializeFromFile( NULL );
442	<	#endif
443	<	fileInit->read_xyz( simnfo ); // default velocities on
606	>	ensembleCase = -1;
607	>	ffCase = -1;
608
609	<	delete fileInit;
446	<	}
447	<	else{
609	>	// set the easy ones first
610
611	<	#ifdef IS_MPI
611	>	for( i=0; i<nInfo; i++){
612	>	info[i].target_temp = globals->getTargetTemp();
613	>	info[i].dt = globals->getDt();
614	>	info[i].run_time = globals->getRunTime();
615	>	}
616	>	n_components = globals->getNComponents();
617
451	–	// no init from bass
452	–
453	–	sprintf( painCave.errMsg,
454	–	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
455	–	painCave.isFatal;
456	–	simError();
457	–
458	–	#else
618
619	<	initFromBass();
619	>	// get the forceField
620
621	+	strcpy( force_field, globals->getForceField() );
622
623	<	#endif
624	<	}
623	>	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
624	>	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
625	>	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
626	>	else{
627	>	sprintf( painCave.errMsg,
628	>	"SimSetup Error. Unrecognized force field -> %s\n",
629	>	force_field );
630	>	painCave.isFatal = 1;
631	>	simError();
632	>	}
633
634	<	#ifdef IS_MPI
467	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
468	<	MPIcheckPoint();
469	<	#endif // is_mpi
634	>	// get the ensemble
635
636	+	strcpy( ensemble, globals->getEnsemble() );
637
638	<
639	<
638	>	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
639	>	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
640	>	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
641	>	ensembleCase = NPTi_ENS;
642	>	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
643	>	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
644	>	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
645	>	else{
646	>	sprintf( painCave.errMsg,
647	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
648	>	"reverting to NVE for this simulation.\n",
649	>	ensemble );
650	>	painCave.isFatal = 0;
651	>	simError();
652	>	strcpy( ensemble, "NVE" );
653	>	ensembleCase = NVE_ENS;
654	>	}
655
656	+	for(i=0; i<nInfo; i++){
657	+
658	+	strcpy( info[i].ensemble, ensemble );
659
660	+	// get the mixing rule
661	+
662	+	strcpy( info[i].mixingRule, globals->getMixingRule() );
663	+	info[i].usePBC = globals->getPBC();
664	+	}
665
666	<	#ifdef IS_MPI
667	<	if( worldRank == 0 ){
668	<	#endif // is_mpi
669	<
670	<	if( the_globals->haveFinalConfig() ){
671	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
672	<	}
673	<	else{
674	<	strcpy( simnfo->finalName, inFileName );
675	<	char* endTest;
676	<	int nameLength = strlen( simnfo->finalName );
677	<	endTest = &(simnfo->finalName[nameLength - 5]);
678	<	if( !strcmp( endTest, ".bass" ) ){
679	<	strcpy( endTest, ".eor" );
666	>	// get the components and calculate the tot_nMol and indvidual n_mol
667	>
668	>	the_components = globals->getComponents();
669	>	components_nmol = new int[n_components];
670	>
671	>
672	>	if( !globals->haveNMol() ){
673	>	// we don't have the total number of molecules, so we assume it is
674	>	// given in each component
675	>
676	>	tot_nmol = 0;
677	>	for( i=0; i<n_components; i++ ){
678	>
679	>	if( !the_components[i]->haveNMol() ){
680	>	// we have a problem
681	>	sprintf( painCave.errMsg,
682	>	"SimSetup Error. No global NMol or component NMol"
683	>	" given. Cannot calculate the number of atoms.\n" );
684	>	painCave.isFatal = 1;
685	>	simError();
686		}
687	<	else if( !strcmp( endTest, ".BASS" ) ){
688	<	strcpy( endTest, ".eor" );
689	<	}
495	<	else{
496	<	endTest = &(simnfo->finalName[nameLength - 4]);
497	<	if( !strcmp( endTest, ".bss" ) ){
498	<	strcpy( endTest, ".eor" );
499	<	}
500	<	else if( !strcmp( endTest, ".mdl" ) ){
501	<	strcpy( endTest, ".eor" );
502	<	}
503	<	else{
504	<	strcat( simnfo->finalName, ".eor" );
505	<	}
506	<	}
687	>
688	>	tot_nmol += the_components[i]->getNMol();
689	>	components_nmol[i] = the_components[i]->getNMol();
690		}
691	<
692	<	// make the sample and status out names
693	<
694	<	strcpy( simnfo->sampleName, inFileName );
695	<	char* endTest;
696	<	int nameLength = strlen( simnfo->sampleName );
697	<	endTest = &(simnfo->sampleName[nameLength - 5]);
698	<	if( !strcmp( endTest, ".bass" ) ){
699	<	strcpy( endTest, ".dump" );
691	>	}
692	>	else{
693	>	sprintf( painCave.errMsg,
694	>	"SimSetup error.\n"
695	>	"\tSorry, the ability to specify total"
696	>	" nMols and then give molfractions in the components\n"
697	>	"\tis not currently supported."
698	>	" Please give nMol in the components.\n" );
699	>	painCave.isFatal = 1;
700	>	simError();
701	>	}
702	>
703	>	// set the status, sample, and thermal kick times
704	>
705	>	for(i=0; i<nInfo; i++){
706	>
707	>	if( globals->haveSampleTime() ){
708	>	info[i].sampleTime = globals->getSampleTime();
709	>	info[i].statusTime = info[i].sampleTime;
710	>	info[i].thermalTime = info[i].sampleTime;
711		}
518	–	else if( !strcmp( endTest, ".BASS" ) ){
519	–	strcpy( endTest, ".dump" );
520	–	}
712		else{
713	<	endTest = &(simnfo->sampleName[nameLength - 4]);
714	<	if( !strcmp( endTest, ".bss" ) ){
715	<	strcpy( endTest, ".dump" );
525	<	}
526	<	else if( !strcmp( endTest, ".mdl" ) ){
527	<	strcpy( endTest, ".dump" );
528	<	}
529	<	else{
530	<	strcat( simnfo->sampleName, ".dump" );
531	<	}
713	>	info[i].sampleTime = globals->getRunTime();
714	>	info[i].statusTime = info[i].sampleTime;
715	>	info[i].thermalTime = info[i].sampleTime;
716		}
717
718	<	strcpy( simnfo->statusName, inFileName );
719	<	nameLength = strlen( simnfo->statusName );
536	<	endTest = &(simnfo->statusName[nameLength - 5]);
537	<	if( !strcmp( endTest, ".bass" ) ){
538	<	strcpy( endTest, ".stat" );
718	>	if( globals->haveStatusTime() ){
719	>	info[i].statusTime = globals->getStatusTime();
720		}
721	<	else if( !strcmp( endTest, ".BASS" ) ){
722	<	strcpy( endTest, ".stat" );
721	>
722	>	if( globals->haveThermalTime() ){
723	>	info[i].thermalTime = globals->getThermalTime();
724		}
725	+
726	+	// check for the temperature set flag
727	+
728	+	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
729	+
730	+	// get some of the tricky things that may still be in the globals
731	+
732	+	double boxVector[3];
733	+	if( globals->haveBox() ){
734	+	boxVector[0] = globals->getBox();
735	+	boxVector[1] = globals->getBox();
736	+	boxVector[2] = globals->getBox();
737	+
738	+	info[i].setBox( boxVector );
739	+	}
740	+	else if( globals->haveDensity() ){
741	+
742	+	double vol;
743	+	vol = (double)tot_nmol / globals->getDensity();
744	+	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
745	+	boxVector[1] = boxVector[0];
746	+	boxVector[2] = boxVector[0];
747	+
748	+	info[i].setBox( boxVector );
749	+	}
750		else{
751	<	endTest = &(simnfo->statusName[nameLength - 4]);
752	<	if( !strcmp( endTest, ".bss" ) ){
753	<	strcpy( endTest, ".stat" );
751	>	if( !globals->haveBoxX() ){
752	>	sprintf( painCave.errMsg,
753	>	"SimSetup error, no periodic BoxX size given.\n" );
754	>	painCave.isFatal = 1;
755	>	simError();
756		}
757	<	else if( !strcmp( endTest, ".mdl" ) ){
758	<	strcpy( endTest, ".stat" );
757	>	boxVector[0] = globals->getBoxX();
758	>
759	>	if( !globals->haveBoxY() ){
760	>	sprintf( painCave.errMsg,
761	>	"SimSetup error, no periodic BoxY size given.\n" );
762	>	painCave.isFatal = 1;
763	>	simError();
764		}
765	<	else{
766	<	strcat( simnfo->statusName, ".stat" );
765	>	boxVector[1] = globals->getBoxY();
766	>
767	>	if( !globals->haveBoxZ() ){
768	>	sprintf( painCave.errMsg,
769	>	"SimSetup error, no periodic BoxZ size given.\n" );
770	>	painCave.isFatal = 1;
771	>	simError();
772		}
773	+	boxVector[2] = globals->getBoxZ();
774	+
775	+	info[i].setBox( boxVector );
776		}
777	+
778	+	}
779
780		#ifdef IS_MPI
781	<	}
781	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
782	>	MPIcheckPoint();
783		#endif // is_mpi
559	–
560	–	// set the status, sample, and themal kick times
561	–
562	–	if( the_globals->haveSampleTime() ){
563	–	simnfo->sampleTime = the_globals->getSampleTime();
564	–	simnfo->statusTime = simnfo->sampleTime;
565	–	simnfo->thermalTime = simnfo->sampleTime;
566	–	}
567	–	else{
568	–	simnfo->sampleTime = the_globals->getRunTime();
569	–	simnfo->statusTime = simnfo->sampleTime;
570	–	simnfo->thermalTime = simnfo->sampleTime;
571	–	}
784
785	<	if( the_globals->haveStatusTime() ){
574	<	simnfo->statusTime = the_globals->getStatusTime();
575	<	}
785	>	}
786
577	–	if( the_globals->haveThermalTime() ){
578	–	simnfo->thermalTime = the_globals->getThermalTime();
579	–	}
787
788	<	// check for the temperature set flag
788	>	void SimSetup::finalInfoCheck( void ){
789	>	int index;
790	>	int usesDipoles;
791	>	int i;
792
793	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
794	<
795	<
796	<	//   // make the longe range forces and the integrator
797	<
798	<	//   new AllLong( simnfo );
799	<
800	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
801	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
802	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
803	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
804	<
805	<
806	<
807	<	// initialize the Fortran
808	<
599	<	simnfo->refreshSim();
793	>	for(i=0; i<nInfo; i++){
794	>	// check electrostatic parameters
795	>
796	>	index = 0;
797	>	usesDipoles = 0;
798	>	while( (index < info[i].n_atoms) && !usesDipoles ){
799	>	usesDipoles = (info[i].atoms[index])->hasDipole();
800	>	index++;
801	>	}
802	>
803	>	#ifdef IS_MPI
804	>	int myUse = usesDipoles;
805	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
806	>	#endif //is_mpi
807	>
808	>	double theEcr, theEst;
809
810	<	if( !strcmp( simnfo->mixingRule, "standard") ){
811	<	the_ff->initForceField( LB_MIXING_RULE );
810	>	if (globals->getUseRF() ) {
811	>	info[i].useReactionField = 1;
812	>
813	>	if( !globals->haveECR() ){
814	>	sprintf( painCave.errMsg,
815	>	"SimSetup Warning: using default value of 1/2 the smallest "
816	>	"box length for the electrostaticCutoffRadius.\n"
817	>	"I hope you have a very fast processor!\n");
818	>	painCave.isFatal = 0;
819	>	simError();
820	>	double smallest;
821	>	smallest = info[i].boxL[0];
822	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
823	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
824	>	theEcr = 0.5 * smallest;
825	>	} else {
826	>	theEcr = globals->getECR();
827	>	}
828	>
829	>	if( !globals->haveEST() ){
830	>	sprintf( painCave.errMsg,
831	>	"SimSetup Warning: using default value of 0.05 * the "
832	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
833	>	);
834	>	painCave.isFatal = 0;
835	>	simError();
836	>	theEst = 0.05 * theEcr;
837	>	} else {
838	>	theEst= globals->getEST();
839	>	}
840	>
841	>	info[i].setEcr( theEcr, theEst );
842	>
843	>	if(!globals->haveDielectric() ){
844	>	sprintf( painCave.errMsg,
845	>	"SimSetup Error: You are trying to use Reaction Field without"
846	>	"setting a dielectric constant!\n"
847	>	);
848	>	painCave.isFatal = 1;
849	>	simError();
850	>	}
851	>	info[i].dielectric = globals->getDielectric();
852	>	}
853	>	else {
854	>	if (usesDipoles) {
855	>
856	>	if( !globals->haveECR() ){
857	>	sprintf( painCave.errMsg,
858	>	"SimSetup Warning: using default value of 1/2 the smallest "
859	>	"box length for the electrostaticCutoffRadius.\n"
860	>	"I hope you have a very fast processor!\n");
861	>	painCave.isFatal = 0;
862	>	simError();
863	>	double smallest;
864	>	smallest = info[i].boxL[0];
865	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
866	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
867	>	theEcr = 0.5 * smallest;
868	>	} else {
869	>	theEcr = globals->getECR();
870	>	}
871	>
872	>	if( !globals->haveEST() ){
873	>	sprintf( painCave.errMsg,
874	>	"SimSetup Warning: using default value of 0.05 * the "
875	>	"electrostaticCutoffRadius for the "
876	>	"electrostaticSkinThickness\n"
877	>	);
878	>	painCave.isFatal = 0;
879	>	simError();
880	>	theEst = 0.05 * theEcr;
881	>	} else {
882	>	theEst= globals->getEST();
883	>	}
884	>
885	>	info[i].setEcr( theEcr, theEst );
886	>	}
887	>	}
888		}
889	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
890	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
889	>
890	>	#ifdef IS_MPI
891	>	strcpy( checkPointMsg, "post processing checks out" );
892	>	MPIcheckPoint();
893	>	#endif // is_mpi
894	>
895	>	}
896	>
897	>	void SimSetup::initSystemCoords( void ){
898	>	int i;
899	>
900	>	char* inName;
901	>
902	>	std::cerr << "Setting atom Coords\n";
903	>
904	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
905	>
906	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
907	>
908	>	if( globals->haveInitialConfig() ){
909	>
910	>	InitializeFromFile* fileInit;
911	>	#ifdef IS_MPI // is_mpi
912	>	if( worldRank == 0 ){
913	>	#endif //is_mpi
914	>	inName = globals->getInitialConfig();
915	>	fileInit = new InitializeFromFile( inName );
916	>	#ifdef IS_MPI
917	>	}else fileInit = new InitializeFromFile( NULL );
918	>	#endif
919	>	fileInit->readInit( info ); // default velocities on
920	>
921	>	delete fileInit;
922		}
923		else{
924	+
925	+	#ifdef IS_MPI
926	+
927	+	// no init from bass
928	+
929		sprintf( painCave.errMsg,
930	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
931	<	simnfo->mixingRule );
611	<	painCave.isFatal = 1;
930	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
931	>	painCave.isFatal;
932		simError();
933	+
934	+	#else
935	+
936	+	initFromBass();
937	+
938	+
939	+	#endif
940		}
941	<
615	<
941	>
942		#ifdef IS_MPI
943	<	strcpy( checkPointMsg,
618	<	"Successfully intialized the mixingRule for Fortran." );
943	>	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
944		MPIcheckPoint();
945		#endif // is_mpi
946	+
947		}
948
623	–	void SimSetup::makeAtoms( void ){
949
950	<	int i, j, k, index;
951	<	double ux, uy, uz, uSqr, u;
952	<	AtomStamp* current_atom;
950	>	void SimSetup::makeOutNames( void ){
951	>
952	>	int k;
953
954	<	DirectionalAtom* dAtom;
955	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
954	>
955	>	for(k=0; k<nInfo; k++){
956
632	–	lMolIndex = 0;
633	–	molIndex = 0;
634	–	index = 0;
635	–	for( i=0; i<n_components; i++ ){
636	–
637	–	for( j=0; j<components_nmol[i]; j++ ){
638	–
957		#ifdef IS_MPI
958	<	if( mpiSim->getMyMolStart() <= molIndex &&
959	<	molIndex <= mpiSim->getMyMolEnd() ){
960	<	#endif // is_mpi
961	<
962	<	molStart = index;
963	<	nMemb = comp_stamps[i]->getNAtoms();
964	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
965	<
966	<	current_atom = comp_stamps[i]->getAtom( k );
967	<	if( current_atom->haveOrientation() ){
968	<
969	<	dAtom = new DirectionalAtom(index);
970	<	simnfo->n_oriented++;
971	<	the_atoms[index] = dAtom;
972	<
973	<	ux = current_atom->getOrntX();
974	<	uy = current_atom->getOrntY();
975	<	uz = current_atom->getOrntZ();
976	<
977	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
978	<
661	<	u = sqrt( uSqr );
662	<	ux = ux / u;
663	<	uy = uy / u;
664	<	uz = uz / u;
665	<
666	<	dAtom->setSUx( ux );
667	<	dAtom->setSUy( uy );
668	<	dAtom->setSUz( uz );
958	>	if( worldRank == 0 ){
959	>	#endif // is_mpi
960	>
961	>	if( globals->haveFinalConfig() ){
962	>	strcpy( info[k].finalName, globals->getFinalConfig() );
963	>	}
964	>	else{
965	>	strcpy( info[k].finalName, inFileName );
966	>	char* endTest;
967	>	int nameLength = strlen( info[k].finalName );
968	>	endTest = &(info[k].finalName[nameLength - 5]);
969	>	if( !strcmp( endTest, ".bass" ) ){
970	>	strcpy( endTest, ".eor" );
971	>	}
972	>	else if( !strcmp( endTest, ".BASS" ) ){
973	>	strcpy( endTest, ".eor" );
974	>	}
975	>	else{
976	>	endTest = &(info[k].finalName[nameLength - 4]);
977	>	if( !strcmp( endTest, ".bss" ) ){
978	>	strcpy( endTest, ".eor" );
979		}
980	+	else if( !strcmp( endTest, ".mdl" ) ){
981	+	strcpy( endTest, ".eor" );
982	+	}
983		else{
984	<	the_atoms[index] = new GeneralAtom(index);
984	>	strcat( info[k].finalName, ".eor" );
985		}
673	–	the_atoms[index]->setType( current_atom->getType() );
674	–	the_atoms[index]->setIndex( index );
675	–
676	–	// increment the index and repeat;
677	–	index++;
986		}
679	–
680	–	molEnd = index -1;
681	–	the_molecules[lMolIndex].setNMembers( nMemb );
682	–	the_molecules[lMolIndex].setStartAtom( molStart );
683	–	the_molecules[lMolIndex].setEndAtom( molEnd );
684	–	the_molecules[lMolIndex].setStampID( i );
685	–	lMolIndex++;
686	–
687	–	#ifdef IS_MPI
987		}
689	–	#endif //is_mpi
988
989	<	molIndex++;
989	>	// make the sample and status out names
990	>
991	>	strcpy( info[k].sampleName, inFileName );
992	>	char* endTest;
993	>	int nameLength = strlen( info[k].sampleName );
994	>	endTest = &(info[k].sampleName[nameLength - 5]);
995	>	if( !strcmp( endTest, ".bass" ) ){
996	>	strcpy( endTest, ".dump" );
997	>	}
998	>	else if( !strcmp( endTest, ".BASS" ) ){
999	>	strcpy( endTest, ".dump" );
1000	>	}
1001	>	else{
1002	>	endTest = &(info[k].sampleName[nameLength - 4]);
1003	>	if( !strcmp( endTest, ".bss" ) ){
1004	>	strcpy( endTest, ".dump" );
1005	>	}
1006	>	else if( !strcmp( endTest, ".mdl" ) ){
1007	>	strcpy( endTest, ".dump" );
1008	>	}
1009	>	else{
1010	>	strcat( info[k].sampleName, ".dump" );
1011	>	}
1012	>	}
1013	>
1014	>	strcpy( info[k].statusName, inFileName );
1015	>	nameLength = strlen( info[k].statusName );
1016	>	endTest = &(info[k].statusName[nameLength - 5]);
1017	>	if( !strcmp( endTest, ".bass" ) ){
1018	>	strcpy( endTest, ".stat" );
1019	>	}
1020	>	else if( !strcmp( endTest, ".BASS" ) ){
1021	>	strcpy( endTest, ".stat" );
1022	>	}
1023	>	else{
1024	>	endTest = &(info[k].statusName[nameLength - 4]);
1025	>	if( !strcmp( endTest, ".bss" ) ){
1026	>	strcpy( endTest, ".stat" );
1027	>	}
1028	>	else if( !strcmp( endTest, ".mdl" ) ){
1029	>	strcpy( endTest, ".stat" );
1030	>	}
1031	>	else{
1032	>	strcat( info[k].statusName, ".stat" );
1033	>	}
1034	>	}
1035	>
1036	>	#ifdef IS_MPI
1037		}
1038	+	#endif // is_mpi
1039		}
1040	+	}
1041
695	–	#ifdef IS_MPI
696	–	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
697	–
698	–	delete[] globalIndex;
1042
1043	<	mpiSim->mpiRefresh();
1044	<	#endif //IS_MPI
1045	<
1046	<	the_ff->initializeAtoms();
1047	<	}
1043	>	void SimSetup::sysObjectsCreation( void ){
1044	>
1045	>	int i,k;
1046	>
1047	>	// create the forceField
1048
1049	<	void SimSetup::makeBonds( void ){
1049	>	createFF();
1050
1051	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
709	<	bond_pair* the_bonds;
710	<	BondStamp* current_bond;
1051	>	// extract componentList
1052
1053	<	the_bonds = new bond_pair[tot_bonds];
713	<	index = 0;
714	<	offset = 0;
715	<	molIndex = 0;
1053	>	compList();
1054
1055	<	for( i=0; i<n_components; i++ ){
1055	>	// calc the number of atoms, bond, bends, and torsions
1056
1057	<	for( j=0; j<components_nmol[i]; j++ ){
1057	>	calcSysValues();
1058
1059		#ifdef IS_MPI
1060	<	if( mpiSim->getMyMolStart() <= molIndex &&
1061	<	molIndex <= mpiSim->getMyMolEnd() ){
1062	<	#endif // is_mpi
1063	<
1064	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
1065	<
1066	<	current_bond = comp_stamps[i]->getBond( k );
1067	<	the_bonds[index].a = current_bond->getA() + offset;
730	<	the_bonds[index].b = current_bond->getB() + offset;
731	<
732	<	exI = the_bonds[index].a;
733	<	exJ = the_bonds[index].b;
1060	>	// divide the molecules among the processors
1061	>
1062	>	mpiMolDivide();
1063	>	#endif //is_mpi
1064	>
1065	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1066	>
1067	>	makeSysArrays();
1068
1069	<	// exclude_I must always be the smaller of the pair
1070	<	if( exI > exJ ){
1071	<	tempEx = exI;
1072	<	exI = exJ;
1073	<	exJ = tempEx;
1074	<	}
1069	>	// make and initialize the molecules (all but atomic coordinates)
1070	>
1071	>	makeMolecules();
1072	>
1073	>	for(k=0; k<nInfo; k++){
1074	>	info[k].identArray = new int[info[k].n_atoms];
1075	>	for(i=0; i<info[k].n_atoms; i++){
1076	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1077	>	}
1078	>	}
1079	>	}
1080
742	–
743	–	#ifdef IS_MPI
1081
1082	<	the_excludes[index*2] =
746	<	the_atoms[exI]->getGlobalIndex() + 1;
747	<	the_excludes[index*2 + 1] =
748	<	the_atoms[exJ]->getGlobalIndex() + 1;
1082	>	void SimSetup::createFF( void ){
1083
1084	<	#else  // isn't MPI
751	<
752	<	the_excludes[index*2] =     exI + 1;
753	<	the_excludes[index*2 + 1] = exJ + 1;
754	<	// fortran index from 1 (hence the +1 in the indexing)
755	<	#endif  //is_mpi
756	<
757	<	// increment the index and repeat;
758	<	index++;
759	<	}
760	<	offset += comp_stamps[i]->getNAtoms();
761	<
762	<	#ifdef IS_MPI
763	<	}
764	<	#endif //is_mpi
765	<
766	<	molIndex++;
767	<	}
768	<	}
1084	>	switch( ffCase ){
1085
1086	<	the_ff->initializeBonds( the_bonds );
1087	<	}
1086	>	case FF_DUFF:
1087	>	the_ff = new DUFF();
1088	>	break;
1089
1090	<	void SimSetup::makeBends( void ){
1090	>	case FF_LJ:
1091	>	the_ff = new LJFF();
1092	>	break;
1093
1094	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1095	<	bend_set* the_bends;
1096	<	BendStamp* current_bend;
778	<	LinkedAssign* extras;
779	<	LinkedAssign* current_extra;
780	<
1094	>	case FF_EAM:
1095	>	the_ff = new EAM_FF();
1096	>	break;
1097
1098	<	the_bends = new bend_set[tot_bends];
1099	<	index = 0;
1100	<	offset = 0;
1101	<	molIndex = 0;
1102	<	for( i=0; i<n_components; i++ ){
1098	>	default:
1099	>	sprintf( painCave.errMsg,
1100	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1101	>	painCave.isFatal = 1;
1102	>	simError();
1103	>	}
1104
788	–	for( j=0; j<components_nmol[i]; j++ ){
789	–
1105		#ifdef IS_MPI
1106	<	if( mpiSim->getMyMolStart() <= molIndex &&
1107	<	molIndex <= mpiSim->getMyMolEnd() ){
1108	<	#endif // is_mpi
1106	>	strcpy( checkPointMsg, "ForceField creation successful" );
1107	>	MPIcheckPoint();
1108	>	#endif // is_mpi
1109
1110	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
796	<
797	<	current_bend = comp_stamps[i]->getBend( k );
798	<	the_bends[index].a = current_bend->getA() + offset;
799	<	the_bends[index].b = current_bend->getB() + offset;
800	<	the_bends[index].c = current_bend->getC() + offset;
801	<
802	<	if( current_bend->haveExtras() ){
803	<
804	<	extras = current_bend->getExtras();
805	<	current_extra = extras;
806	<
807	<	while( current_extra != NULL ){
808	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
809	<
810	<	switch( current_extra->getType() ){
811	<
812	<	case 0:
813	<	the_bends[index].ghost =
814	<	current_extra->getInt() + offset;
815	<	the_bends[index].isGhost = 1;
816	<	break;
817	<
818	<	case 1:
819	<	the_bends[index].ghost =
820	<	(int)current_extra->getDouble() + offset;
821	<	the_bends[index].isGhost = 1;
822	<	break;
823	<
824	<	default:
825	<	sprintf( painCave.errMsg,
826	<	"SimSetup Error: ghostVectorSource was neiter a "
827	<	"double nor an int.\n"
828	<	"-->Bend[%d] in %s\n",
829	<	k, comp_stamps[i]->getID() );
830	<	painCave.isFatal = 1;
831	<	simError();
832	<	}
833	<	}
834	<
835	<	else{
836	<
837	<	sprintf( painCave.errMsg,
838	<	"SimSetup Error: unhandled bend assignment:\n"
839	<	"    -->%s in Bend[%d] in %s\n",
840	<	current_extra->getlhs(),
841	<	k, comp_stamps[i]->getID() );
842	<	painCave.isFatal = 1;
843	<	simError();
844	<	}
845	<
846	<	current_extra = current_extra->getNext();
847	<	}
848	<	}
849	<
850	<	if( !the_bends[index].isGhost ){
851	<
852	<	exI = the_bends[index].a;
853	<	exJ = the_bends[index].c;
854	<	}
855	<	else{
856	<
857	<	exI = the_bends[index].a;
858	<	exJ = the_bends[index].b;
859	<	}
860	<
861	<	// exclude_I must always be the smaller of the pair
862	<	if( exI > exJ ){
863	<	tempEx = exI;
864	<	exI = exJ;
865	<	exJ = tempEx;
866	<	}
1110	>	}
1111
1112
1113	<	#ifdef IS_MPI
1113	>	void SimSetup::compList( void ){
1114
1115	<	the_excludes[(index + tot_bonds)*2] =
1116	<	the_atoms[exI]->getGlobalIndex() + 1;
1117	<	the_excludes[(index + tot_bonds)*2 + 1] =
1118	<	the_atoms[exJ]->getGlobalIndex() + 1;
1119	<
1120	<	#else  // isn't MPI
1121	<
1122	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
1123	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1124	<	// fortran index from 1 (hence the +1 in the indexing)
1125	<	#endif  //is_mpi
1126	<
1127	<
1128	<	// increment the index and repeat;
1129	<	index++;
1130	<	}
887	<	offset += comp_stamps[i]->getNAtoms();
888	<
889	<	#ifdef IS_MPI
890	<	}
891	<	#endif //is_mpi
1115	>	int i;
1116	>	char* id;
1117	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1118	>	LinkedMolStamp* currentStamp = NULL;
1119	>	comp_stamps = new MoleculeStamp*[n_components];
1120	>
1121	>	// make an array of molecule stamps that match the components used.
1122	>	// also extract the used stamps out into a separate linked list
1123	>
1124	>	for(i=0; i<nInfo; i++){
1125	>	info[i].nComponents = n_components;
1126	>	info[i].componentsNmol = components_nmol;
1127	>	info[i].compStamps = comp_stamps;
1128	>	info[i].headStamp = headStamp;
1129	>	}
1130	>
1131
1132	<	molIndex++;
1132	>	for( i=0; i<n_components; i++ ){
1133	>
1134	>	id = the_components[i]->getType();
1135	>	comp_stamps[i] = NULL;
1136	>
1137	>	// check to make sure the component isn't already in the list
1138	>
1139	>	comp_stamps[i] = headStamp->match( id );
1140	>	if( comp_stamps[i] == NULL ){
1141	>
1142	>	// extract the component from the list;
1143	>
1144	>	currentStamp = stamps->extractMolStamp( id );
1145	>	if( currentStamp == NULL ){
1146	>	sprintf( painCave.errMsg,
1147	>	"SimSetup error: Component \"%s\" was not found in the "
1148	>	"list of declared molecules\n",
1149	>	id );
1150	>	painCave.isFatal = 1;
1151	>	simError();
1152	>	}
1153	>
1154	>	headStamp->add( currentStamp );
1155	>	comp_stamps[i] = headStamp->match( id );
1156		}
1157		}
1158
1159		#ifdef IS_MPI
1160	<	sprintf( checkPointMsg,
899	<	"Successfully created the bends list.\n" );
1160	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1161		MPIcheckPoint();
1162		#endif // is_mpi
902	–
1163
1164	<	the_ff->initializeBends( the_bends );
1164	>
1165		}
1166
1167	<	void SimSetup::makeTorsions( void ){
1168	<
1169	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1170	<	torsion_set* the_torsions;
1171	<	TorsionStamp* current_torsion;
1172	<
1173	<	the_torsions = new torsion_set[tot_torsions];
1174	<	index = 0;
1175	<	offset = 0;
916	<	molIndex = 0;
1167	>	void SimSetup::calcSysValues( void ){
1168	>	int i, j, k;
1169	>
1170	>	int *molMembershipArray;
1171	>
1172	>	tot_atoms = 0;
1173	>	tot_bonds = 0;
1174	>	tot_bends = 0;
1175	>	tot_torsions = 0;
1176		for( i=0; i<n_components; i++ ){
1177	+
1178	+	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1179	+	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1180	+	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1181	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1182	+	}
1183	+
1184	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1185	+	molMembershipArray = new int[tot_atoms];
1186	+
1187	+	for(i=0; i<nInfo; i++){
1188	+	info[i].n_atoms = tot_atoms;
1189	+	info[i].n_bonds = tot_bonds;
1190	+	info[i].n_bends = tot_bends;
1191	+	info[i].n_torsions = tot_torsions;
1192	+	info[i].n_SRI = tot_SRI;
1193	+	info[i].n_mol = tot_nmol;
1194	+
1195	+	info[i].molMembershipArray = molMembershipArray;
1196	+	}
1197	+	}
1198
919	–	for( j=0; j<components_nmol[i]; j++ ){
920	–
1199		#ifdef IS_MPI
922	–	if( mpiSim->getMyMolStart() <= molIndex &&
923	–	molIndex <= mpiSim->getMyMolEnd() ){
924	–	#endif // is_mpi
1200
1201	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1201	>	void SimSetup::mpiMolDivide( void ){
1202	>
1203	>	int i, j, k;
1204	>	int localMol, allMol;
1205	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1206
1207	<	current_torsion = comp_stamps[i]->getTorsion( k );
1208	<	the_torsions[index].a = current_torsion->getA() + offset;
1209	<	the_torsions[index].b = current_torsion->getB() + offset;
931	<	the_torsions[index].c = current_torsion->getC() + offset;
932	<	the_torsions[index].d = current_torsion->getD() + offset;
1207	>	mpiSim = new mpiSimulation( info );
1208	>
1209	>	globalIndex = mpiSim->divideLabor();
1210
1211	<	exI = the_torsions[index].a;
1212	<	exJ = the_torsions[index].d;
1213	<
1214	<
1215	<	// exclude_I must always be the smaller of the pair
1216	<	if( exI > exJ ){
1217	<	tempEx = exI;
1218	<	exI = exJ;
1219	<	exJ = tempEx;
1220	<	}
1211	>	// set up the local variables
1212	>
1213	>	mol2proc = mpiSim->getMolToProcMap();
1214	>	molCompType = mpiSim->getMolComponentType();
1215	>
1216	>	allMol = 0;
1217	>	localMol = 0;
1218	>	local_atoms = 0;
1219	>	local_bonds = 0;
1220	>	local_bends = 0;
1221	>	local_torsions = 0;
1222	>	globalAtomIndex = 0;
1223
1224
1225	<	#ifdef IS_MPI
947	<
948	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
949	<	the_atoms[exI]->getGlobalIndex() + 1;
950	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
951	<	the_atoms[exJ]->getGlobalIndex() + 1;
952	<
953	<	#else  // isn't MPI
954	<
955	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
956	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
957	<	// fortran indexes from 1 (hence the +1 in the indexing)
958	<	#endif  //is_mpi
959	<
1225	>	for( i=0; i<n_components; i++ ){
1226
1227	<	// increment the index and repeat;
1228	<	index++;
1227	>	for( j=0; j<components_nmol[i]; j++ ){
1228	>
1229	>	if( mol2proc[allMol] == worldRank ){
1230	>
1231	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1232	>	local_bonds +=    comp_stamps[i]->getNBonds();
1233	>	local_bends +=    comp_stamps[i]->getNBends();
1234	>	local_torsions += comp_stamps[i]->getNTorsions();
1235	>	localMol++;
1236	>	}
1237	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1238	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1239	>	globalAtomIndex++;
1240		}
964	–	offset += comp_stamps[i]->getNAtoms();
1241
1242	<	#ifdef IS_MPI
967	<	}
968	<	#endif //is_mpi
969	<
970	<	molIndex++;
1242	>	allMol++;
1243		}
1244		}
1245	+	local_SRI = local_bonds + local_bends + local_torsions;
1246	+
1247	+	info[0].n_atoms = mpiSim->getMyNlocal();
1248	+
1249	+	if( local_atoms != info[0].n_atoms ){
1250	+	sprintf( painCave.errMsg,
1251	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1252	+	" localAtom (%d) are not equal.\n",
1253	+	info[0].n_atoms,
1254	+	local_atoms );
1255	+	painCave.isFatal = 1;
1256	+	simError();
1257	+	}
1258
1259	<	the_ff->initializeTorsions( the_torsions );
1259	>	info[0].n_bonds = local_bonds;
1260	>	info[0].n_bends = local_bends;
1261	>	info[0].n_torsions = local_torsions;
1262	>	info[0].n_SRI = local_SRI;
1263	>	info[0].n_mol = localMol;
1264	>
1265	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1266	>	MPIcheckPoint();
1267		}
1268	+
1269	+	#endif // is_mpi
1270
977	–	void SimSetup::initFromBass( void ){
1271
1272	<	int i, j, k;
1273	<	int n_cells;
981	<	double cellx, celly, cellz;
982	<	double temp1, temp2, temp3;
983	<	int n_per_extra;
984	<	int n_extra;
985	<	int have_extra, done;
1272	>	void SimSetup::makeSysArrays( void ){
1273	>	int i, j, k, l;
1274
1275	<	temp1 = (double)tot_nmol / 4.0;
1276	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1277	<	temp3 = ceil( temp2 );
1275	>	Atom** the_atoms;
1276	>	Molecule* the_molecules;
1277	>	Exclude** the_excludes;
1278
1279	<	have_extra =0;
1280	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1281	<	have_extra =1;
1279	>
1280	>	for(l=0; l<nInfo; l++){
1281	>
1282	>	// create the atom and short range interaction arrays
1283	>
1284	>	the_atoms = new Atom*[info[l].n_atoms];
1285	>	the_molecules = new Molecule[info[l].n_mol];
1286	>	int molIndex;
1287
1288	<	n_cells = (int)temp3 - 1;
1289	<	cellx = simnfo->box_x / temp3;
1290	<	celly = simnfo->box_y / temp3;
1291	<	cellz = simnfo->box_z / temp3;
1292	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1293	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1294	<	n_per_extra = (int)ceil( temp1 );
1295	<
1296	<	if( n_per_extra > 4){
1297	<	sprintf( painCave.errMsg,
1298	<	"SimSetup error. There has been an error in constructing"
1299	<	" the non-complete lattice.\n" );
1300	<	painCave.isFatal = 1;
1301	<	simError();
1288	>	// initialize the molecule's stampID's
1289	>
1290	>	#ifdef IS_MPI
1291	>
1292	>
1293	>	molIndex = 0;
1294	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1295	>
1296	>	if(mol2proc[i] == worldRank ){
1297	>	the_molecules[molIndex].setStampID( molCompType[i] );
1298	>	the_molecules[molIndex].setMyIndex( molIndex );
1299	>	the_molecules[molIndex].setGlobalIndex( i );
1300	>	molIndex++;
1301	>	}
1302		}
1303	<	}
1304	<	else{
1305	<	n_cells = (int)temp3;
1306	<	cellx = simnfo->box_x / temp3;
1307	<	celly = simnfo->box_y / temp3;
1308	<	cellz = simnfo->box_z / temp3;
1309	<	}
1303	>
1304	>	#else // is_mpi
1305	>
1306	>	molIndex = 0;
1307	>	globalAtomIndex = 0;
1308	>	for(i=0; i<n_components; i++){
1309	>	for(j=0; j<components_nmol[i]; j++ ){
1310	>	the_molecules[molIndex].setStampID( i );
1311	>	the_molecules[molIndex].setMyIndex( molIndex );
1312	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1313	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1314	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1315	>	globalAtomIndex++;
1316	>	}
1317	>	molIndex++;
1318	>	}
1319	>	}
1320	>
1321	>
1322	>	#endif // is_mpi
1323
1018	–	current_mol = 0;
1019	–	current_comp_mol = 0;
1020	–	current_comp = 0;
1021	–	current_atom_ndx = 0;
1324
1325	<	for( i=0; i < n_cells ; i++ ){
1326	<	for( j=0; j < n_cells; j++ ){
1327	<	for( k=0; k < n_cells; k++ ){
1325	>	if( info[l].n_SRI ){
1326	>
1327	>	Exclude::createArray(info[l].n_SRI);
1328	>	the_excludes = new Exclude*[info[l].n_SRI];
1329	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1330	>	the_excludes[ex] = new Exclude(ex);
1331	>	}
1332	>	info[l].globalExcludes = new int;
1333	>	info[l].n_exclude = info[l].n_SRI;
1334	>	}
1335	>	else{
1336	>
1337	>	Exclude::createArray( 1 );
1338	>	the_excludes = new Exclude*;
1339	>	the_excludes[0] = new Exclude(0);
1340	>	the_excludes[0]->setPair( 0,0 );
1341	>	info[l].globalExcludes = new int;
1342	>	info[l].globalExcludes[0] = 0;
1343	>	info[l].n_exclude = 0;
1344	>	}
1345
1346	<	makeElement( i * cellx,
1028	<	j * celly,
1029	<	k * cellz );
1346	>	// set the arrays into the SimInfo object
1347
1348	<	makeElement( i * cellx + 0.5 * cellx,
1349	<	j * celly + 0.5 * celly,
1350	<	k * cellz );
1348	>	info[l].atoms = the_atoms;
1349	>	info[l].molecules = the_molecules;
1350	>	info[l].nGlobalExcludes = 0;
1351	>	info[l].excludes = the_excludes;
1352
1353	<	makeElement( i * cellx,
1354	<	j * celly + 0.5 * celly,
1037	<	k * cellz + 0.5 * cellz );
1038	<
1039	<	makeElement( i * cellx + 0.5 * cellx,
1040	<	j * celly,
1041	<	k * cellz + 0.5 * cellz );
1042	<	}
1043	<	}
1353	>	the_ff->setSimInfo( info );
1354	>
1355		}
1356	+	}
1357
1358	<	if( have_extra ){
1047	<	done = 0;
1358	>	void SimSetup::makeIntegrator( void ){
1359
1360	<	int start_ndx;
1050	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1051	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1360	>	int k;
1361
1362	<	if( i < n_cells ){
1362	>	NVT<RealIntegrator>*  myNVT = NULL;
1363	>	NPTi<RealIntegrator>* myNPTi = NULL;
1364	>	NPTf<RealIntegrator>* myNPTf = NULL;
1365	>	NPTim<RealIntegrator>* myNPTim = NULL;
1366	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1367	>
1368	>	for(k=0; k<nInfo; k++){
1369	>
1370	>	switch( ensembleCase ){
1371	>
1372	>	case NVE_ENS:
1373	>	if (globals->haveZconstraints()){
1374	>	setupZConstraint(info[k]);
1375	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1376	>	}
1377
1378	<	if( j < n_cells ){
1379	<	start_ndx = n_cells;
1380	<	}
1381	<	else start_ndx = 0;
1378	>	else
1379	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1380	>	break;
1381	>
1382	>	case NVT_ENS:
1383	>	if (globals->haveZconstraints()){
1384	>	setupZConstraint(info[k]);
1385	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1386		}
1387	<	else start_ndx = 0;
1387	>	else
1388	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1389
1390	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1390	>	myNVT->setTargetTemp(globals->getTargetTemp());
1391	>
1392	>	if (globals->haveTauThermostat())
1393	>	myNVT->setTauThermostat(globals->getTauThermostat());
1394	>
1395	>	else {
1396	>	sprintf( painCave.errMsg,
1397	>	"SimSetup error: If you use the NVT\n"
1398	>	"    ensemble, you must set tauThermostat.\n");
1399	>	painCave.isFatal = 1;
1400	>	simError();
1401	>	}
1402	>	break;
1403	>
1404	>	case NPTi_ENS:
1405	>	if (globals->haveZconstraints()){
1406	>	setupZConstraint(info[k]);
1407	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1408	>	}
1409	>	else
1410	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1411
1412	<	makeElement( i * cellx,
1413	<	j * celly,
1414	<	k * cellz );
1415	<	done = ( current_mol >= tot_nmol );
1416	<
1417	<	if( !done && n_per_extra > 1 ){
1418	<	makeElement( i * cellx + 0.5 * cellx,
1419	<	j * celly + 0.5 * celly,
1420	<	k * cellz );
1421	<	done = ( current_mol >= tot_nmol );
1422	<	}
1423	<
1424	<	if( !done && n_per_extra > 2){
1425	<	makeElement( i * cellx,
1426	<	j * celly + 0.5 * celly,
1427	<	k * cellz + 0.5 * cellz );
1428	<	done = ( current_mol >= tot_nmol );
1429	<	}
1430	<
1431	<	if( !done && n_per_extra > 3){
1432	<	makeElement( i * cellx + 0.5 * cellx,
1433	<	j * celly,
1434	<	k * cellz + 0.5 * cellz );
1435	<	done = ( current_mol >= tot_nmol );
1436	<	}
1412	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1413	>
1414	>	if (globals->haveTargetPressure())
1415	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1416	>	else {
1417	>	sprintf( painCave.errMsg,
1418	>	"SimSetup error: If you use a constant pressure\n"
1419	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1420	>	painCave.isFatal = 1;
1421	>	simError();
1422	>	}
1423	>
1424	>	if( globals->haveTauThermostat() )
1425	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1426	>	else{
1427	>	sprintf( painCave.errMsg,
1428	>	"SimSetup error: If you use an NPT\n"
1429	>	"    ensemble, you must set tauThermostat.\n");
1430	>	painCave.isFatal = 1;
1431	>	simError();
1432	>	}
1433	>
1434	>	if( globals->haveTauBarostat() )
1435	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1436	>	else{
1437	>	sprintf( painCave.errMsg,
1438	>	"SimSetup error: If you use an NPT\n"
1439	>	"    ensemble, you must set tauBarostat.\n");
1440	>	painCave.isFatal = 1;
1441	>	simError();
1442	>	}
1443	>	break;
1444	>
1445	>	case NPTf_ENS:
1446	>	if (globals->haveZconstraints()){
1447	>	setupZConstraint(info[k]);
1448	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1449		}
1450	+	else
1451	+	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1452	+
1453	+	myNPTf->setTargetTemp( globals->getTargetTemp());
1454	+
1455	+	if (globals->haveTargetPressure())
1456	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1457	+	else {
1458	+	sprintf( painCave.errMsg,
1459	+	"SimSetup error: If you use a constant pressure\n"
1460	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1461	+	painCave.isFatal = 1;
1462	+	simError();
1463	+	}
1464	+
1465	+	if( globals->haveTauThermostat() )
1466	+	myNPTf->setTauThermostat( globals->getTauThermostat() );
1467	+	else{
1468	+	sprintf( painCave.errMsg,
1469	+	"SimSetup error: If you use an NPT\n"
1470	+	"    ensemble, you must set tauThermostat.\n");
1471	+	painCave.isFatal = 1;
1472	+	simError();
1473		}
1474	+
1475	+	if( globals->haveTauBarostat() )
1476	+	myNPTf->setTauBarostat( globals->getTauBarostat() );
1477	+	else{
1478	+	sprintf( painCave.errMsg,
1479	+	"SimSetup error: If you use an NPT\n"
1480	+	"    ensemble, you must set tauBarostat.\n");
1481	+	painCave.isFatal = 1;
1482	+	simError();
1483	+	}
1484	+	break;
1485	+
1486	+	case NPTim_ENS:
1487	+	if (globals->haveZconstraints()){
1488	+	setupZConstraint(info[k]);
1489	+	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1490	+	}
1491	+	else
1492	+	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1493	+
1494	+	myNPTim->setTargetTemp( globals->getTargetTemp());
1495	+
1496	+	if (globals->haveTargetPressure())
1497	+	myNPTim->setTargetPressure(globals->getTargetPressure());
1498	+	else {
1499	+	sprintf( painCave.errMsg,
1500	+	"SimSetup error: If you use a constant pressure\n"
1501	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1502	+	painCave.isFatal = 1;
1503	+	simError();
1504	+	}
1505	+
1506	+	if( globals->haveTauThermostat() )
1507	+	myNPTim->setTauThermostat( globals->getTauThermostat() );
1508	+	else{
1509	+	sprintf( painCave.errMsg,
1510	+	"SimSetup error: If you use an NPT\n"
1511	+	"    ensemble, you must set tauThermostat.\n");
1512	+	painCave.isFatal = 1;
1513	+	simError();
1514	+	}
1515	+
1516	+	if( globals->haveTauBarostat() )
1517	+	myNPTim->setTauBarostat( globals->getTauBarostat() );
1518	+	else{
1519	+	sprintf( painCave.errMsg,
1520	+	"SimSetup error: If you use an NPT\n"
1521	+	"    ensemble, you must set tauBarostat.\n");
1522	+	painCave.isFatal = 1;
1523	+	simError();
1524	+	}
1525	+	break;
1526	+
1527	+	case NPTfm_ENS:
1528	+	if (globals->haveZconstraints()){
1529	+	setupZConstraint(info[k]);
1530	+	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1531	+	}
1532	+	else
1533	+	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1534	+
1535	+	myNPTfm->setTargetTemp( globals->getTargetTemp());
1536	+
1537	+	if (globals->haveTargetPressure())
1538	+	myNPTfm->setTargetPressure(globals->getTargetPressure());
1539	+	else {
1540	+	sprintf( painCave.errMsg,
1541	+	"SimSetup error: If you use a constant pressure\n"
1542	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1543	+	painCave.isFatal = 1;
1544	+	simError();
1545	+	}
1546	+
1547	+	if( globals->haveTauThermostat() )
1548	+	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1549	+	else{
1550	+	sprintf( painCave.errMsg,
1551	+	"SimSetup error: If you use an NPT\n"
1552	+	"    ensemble, you must set tauThermostat.\n");
1553	+	painCave.isFatal = 1;
1554	+	simError();
1555	+	}
1556	+
1557	+	if( globals->haveTauBarostat() )
1558	+	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1559	+	else{
1560	+	sprintf( painCave.errMsg,
1561	+	"SimSetup error: If you use an NPT\n"
1562	+	"    ensemble, you must set tauBarostat.\n");
1563	+	painCave.isFatal = 1;
1564	+	simError();
1565	+	}
1566	+	break;
1567	+
1568	+	default:
1569	+	sprintf( painCave.errMsg,
1570	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1571	+	painCave.isFatal = 1;
1572	+	simError();
1573		}
1574		}
1575	+	}
1576
1577	+	void SimSetup::initFortran( void ){
1578
1579	<	for( i=0; i<simnfo->n_atoms; i++ ){
1580	<	simnfo->atoms[i]->set_vx( 0.0 );
1581	<	simnfo->atoms[i]->set_vy( 0.0 );
1582	<	simnfo->atoms[i]->set_vz( 0.0 );
1579	>	info[0].refreshSim();
1580	>
1581	>	if( !strcmp( info[0].mixingRule, "standard") ){
1582	>	the_ff->initForceField( LB_MIXING_RULE );
1583		}
1584	<	}
1584	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1585	>	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1586	>	}
1587	>	else{
1588	>	sprintf( painCave.errMsg,
1589	>	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1590	>	info[0].mixingRule );
1591	>	painCave.isFatal = 1;
1592	>	simError();
1593	>	}
1594
1102	–	void SimSetup::makeElement( double x, double y, double z ){
1595
1596	<	int k;
1597	<	AtomStamp* current_atom;
1598	<	DirectionalAtom* dAtom;
1599	<	double rotMat[3][3];
1596	>	#ifdef IS_MPI
1597	>	strcpy( checkPointMsg,
1598	>	"Successfully intialized the mixingRule for Fortran." );
1599	>	MPIcheckPoint();
1600	>	#endif // is_mpi
1601
1602	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1602	>	}
1603
1604	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1605	<	if( !current_atom->havePosition() ){
1604	>	void SimSetup::setupZConstraint(SimInfo& theInfo)
1605	>	{
1606	>	int nZConstraints;
1607	>	ZconStamp** zconStamp;
1608	>
1609	>	if(globals->haveZconstraintTime()){
1610	>
1611	>	//add sample time of z-constraint  into SimInfo's property list
1612	>	DoubleData* zconsTimeProp = new DoubleData();
1613	>	zconsTimeProp->setID(ZCONSTIME_ID);
1614	>	zconsTimeProp->setData(globals->getZconsTime());
1615	>	theInfo.addProperty(zconsTimeProp);
1616	>	}
1617	>	else{
1618		sprintf( painCave.errMsg,
1619	<	"SimSetup:initFromBass error.\n"
1620	<	"\tComponent %s, atom %s does not have a position specified.\n"
1116	<	"\tThe initialization routine is unable to give a start"
1117	<	" position.\n",
1118	<	comp_stamps[current_comp]->getID(),
1119	<	current_atom->getType() );
1619	>	"ZConstraint error: If you use an ZConstraint\n"
1620	>	" , you must set sample time.\n");
1621		painCave.isFatal = 1;
1622	<	simError();
1622	>	simError();
1623		}
1624
1625	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1626	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1627	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1625	>	//
1626	>	nZConstraints = globals->getNzConstraints();
1627	>	zconStamp = globals->getZconStamp();
1628	>	ZConsParaItem tempParaItem;
1629
1630	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1630	>	ZConsParaData* zconsParaData = new ZConsParaData();
1631	>	zconsParaData->setID(ZCONSPARADATA_ID);
1632	>
1633	>	for(int i = 0; i < nZConstraints; i++){
1634	>	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1635	>	tempParaItem.zPos = zconStamp[i]->getZpos();
1636	>	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1637	>	tempParaItem.kRatio = zconStamp[i]->getKratio();
1638
1639	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1639	>	zconsParaData->addItem(tempParaItem);
1640	>	}
1641
1642	<	rotMat[0][0] = 1.0;
1643	<	rotMat[0][1] = 0.0;
1644	<	rotMat[0][2] = 0.0;
1642	>	//sort the parameters by index of molecules
1643	>	zconsParaData->sortByIndex();
1644	>
1645	>	//push data into siminfo, therefore, we can retrieve later
1646	>	theInfo.addProperty(zconsParaData);
1647
1648	<	rotMat[1][0] = 0.0;
1649	<	rotMat[1][1] = 1.0;
1650	<	rotMat[1][2] = 0.0;
1651	<
1652	<	rotMat[2][0] = 0.0;
1653	<	rotMat[2][1] = 0.0;
1142	<	rotMat[2][2] = 1.0;
1143	<
1144	<	dAtom->setA( rotMat );
1648	>	//push zconsTol into siminfo, if user does not specify
1649	>	//value for zconsTol, a default value will be used
1650	>	DoubleData* zconsTol = new DoubleData();
1651	>	zconsTol->setID(ZCONSTOL_ID);
1652	>	if(globals->haveZconsTol()){
1653	>	zconsTol->setData(globals->getZconsTol());
1654		}
1655	+	else{
1656	+	double defaultZConsTol = 1E-6;
1657	+	sprintf( painCave.errMsg,
1658	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1659	+	" , default value %f is used.\n", defaultZConsTol);
1660	+	painCave.isFatal = 0;
1661	+	simError();
1662
1663	<	current_atom_ndx++;
1664	<	}
1665	<
1666	<	current_mol++;
1667	<	current_comp_mol++;
1668	<
1669	<	if( current_comp_mol >= components_nmol[current_comp] ){
1670	<
1671	<	current_comp_mol = 0;
1672	<	current_comp++;
1673	<	}
1663	>	zconsTol->setData(defaultZConsTol);
1664	>	}
1665	>	theInfo.addProperty(zconsTol);
1666	>
1667	>	//Determine the name of ouput file and add it into SimInfo's property list
1668	>	//Be careful, do not use inFileName, since it is a pointer which
1669	>	//point to a string at master node, and slave nodes do not contain that string
1670	>
1671	>	string zconsOutput(theInfo.finalName);
1672	>
1673	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1674	>
1675	>	StringData* zconsFilename = new StringData();
1676	>	zconsFilename->setID(ZCONSFILENAME_ID);
1677	>	zconsFilename->setData(zconsOutput);
1678	>
1679	>	theInfo.addProperty(zconsFilename);
1680		}

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