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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 431 by mmeineke, Thu Mar 27 22:16:27 2003 UTC vs.
Revision 701 by tim, Wed Aug 20 14:34:04 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 12 | Line 15 | SimSetup::SimSetup(){
15		#include "mpiSimulation.hpp"
16		#endif
17
18	+	// some defines for ensemble and Forcefield  cases
19	+
20	+	#define NVE_ENS        0
21	+	#define NVT_ENS        1
22	+	#define NPTi_ENS       2
23	+	#define NPTf_ENS       3
24	+	#define NPTim_ENS      4
25	+	#define NPTfm_ENS      5
26	+
27	+	#define FF_DUFF 0
28	+	#define FF_LJ   1
29	+	#define FF_EAM  2
30	+
31	+	using namespace std;
32	+
33		SimSetup::SimSetup(){
34	+
35	+	isInfoArray = 0;
36	+	nInfo = 1;
37	+
38		stamps = new MakeStamps();
39		globals = new Globals();
40
41	+
42		#ifdef IS_MPI
43		strcpy( checkPointMsg, "SimSetup creation successful" );
44		MPIcheckPoint();
#	Line 27 | Line 50 | void SimSetup::parseFile( char* fileName ){
50		delete globals;
51		}
52
53	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
54	+	info = the_info;
55	+	nInfo = theNinfo;
56	+	isInfoArray = 1;
57	+	}
58	+
59	+
60		void SimSetup::parseFile( char* fileName ){
61
62		#ifdef IS_MPI
#	Line 62 | Line 92 | void SimSetup::createSim( void ){
92
93		#endif // is_mpi
94
95	<	void SimSetup::createSim( void ){
95	>	void SimSetup::createSim(void){
96
97	<	MakeStamps *the_stamps;
98	<	Globals* the_globals;
99	<	int i, j;
97	>	int i, j, k, globalAtomIndex;
98	>
99	>	// gather all of the information from the Bass file
100
101	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
101	>	gatherInfo();
102
103	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	simnfo->run_time = the_globals->getRunTime();
103	>	// creation of complex system objects
104
105	<	// get the ones we know are there, yet still may need some work.
81	<	n_components = the_globals->getNComponents();
82	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
105	>	sysObjectsCreation();
106
107	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
107	>	// check on the post processing info
108
109	+	finalInfoCheck();
110
111	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
92	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
93	<	else{
94	<	sprintf( painCave.errMsg,
95	<	"SimSetup Error. Unrecognized force field -> %s\n",
96	<	force_field );
97	<	painCave.isFatal = 1;
98	<	simError();
99	<	}
111	>	// initialize the system coordinates
112
113	<	#ifdef IS_MPI
102	<	strcpy( checkPointMsg, "ForceField creation successful" );
103	<	MPIcheckPoint();
104	<	#endif // is_mpi
113	>	if( !isInfoArray ) initSystemCoords();
114
115	<
115	>	// make the output filenames
116
117	<	// get the components and calculate the tot_nMol and indvidual n_mol
118	<	the_components = the_globals->getComponents();
119	<	components_nmol = new int[n_components];
120	<	comp_stamps = new MoleculeStamp*[n_components];
121	<
122	<	if( !the_globals->haveNMol() ){
114	<	// we don't have the total number of molecules, so we assume it is
115	<	// given in each component
116	<
117	<	tot_nmol = 0;
118	<	for( i=0; i<n_components; i++ ){
119	<
120	<	if( !the_components[i]->haveNMol() ){
121	<	// we have a problem
122	<	sprintf( painCave.errMsg,
123	<	"SimSetup Error. No global NMol or component NMol"
124	<	" given. Cannot calculate the number of atoms.\n" );
125	<	painCave.isFatal = 1;
126	<	simError();
127	<	}
128	<
129	<	tot_nmol += the_components[i]->getNMol();
130	<	components_nmol[i] = the_components[i]->getNMol();
131	<	}
132	<	}
133	<	else{
134	<	sprintf( painCave.errMsg,
135	<	"SimSetup error.\n"
136	<	"\tSorry, the ability to specify total"
137	<	" nMols and then give molfractions in the components\n"
138	<	"\tis not currently supported."
139	<	" Please give nMol in the components.\n" );
140	<	painCave.isFatal = 1;
141	<	simError();
142	<
143	<
144	<	//     tot_nmol = the_globals->getNMol();
145	<
146	<	//   //we have the total number of molecules, now we check for molfractions
147	<	//     for( i=0; i<n_components; i++ ){
148	<
149	<	//       if( !the_components[i]->haveMolFraction() ){
150	<
151	<	//  if( !the_components[i]->haveNMol() ){
152	<	//    //we have a problem
153	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
154	<	//              << " nMol was given in component
155	<
156	<	}
157	<
117	>	makeOutNames();
118	>
119	>	// make the integrator
120	>
121	>	makeIntegrator();
122	>
123		#ifdef IS_MPI
124	<	strcpy( checkPointMsg, "Have the number of components" );
125	<	MPIcheckPoint();
161	<	#endif // is_mpi
124	>	mpiSim->mpiRefresh();
125	>	#endif
126
127	<	// make an array of molecule stamps that match the components used.
164	<	// also extract the used stamps out into a separate linked list
127	>	// initialize the Fortran
128
129	<	simnfo->nComponents = n_components;
167	<	simnfo->componentsNmol = components_nmol;
168	<	simnfo->compStamps = comp_stamps;
169	<	simnfo->headStamp = new LinkedMolStamp();
170	<
171	<	char* id;
172	<	LinkedMolStamp* headStamp = simnfo->headStamp;
173	<	LinkedMolStamp* currentStamp = NULL;
174	<	for( i=0; i<n_components; i++ ){
129	>	initFortran();
130
176	–	id = the_components[i]->getType();
177	–	comp_stamps[i] = NULL;
178	–
179	–	// check to make sure the component isn't already in the list
131
181	–	comp_stamps[i] = headStamp->match( id );
182	–	if( comp_stamps[i] == NULL ){
183	–
184	–	// extract the component from the list;
185	–
186	–	currentStamp = the_stamps->extractMolStamp( id );
187	–	if( currentStamp == NULL ){
188	–	sprintf( painCave.errMsg,
189	–	"SimSetup error: Component \"%s\" was not found in the "
190	–	"list of declared molecules\n",
191	–	id );
192	–	painCave.isFatal = 1;
193	–	simError();
194	–	}
195	–
196	–	headStamp->add( currentStamp );
197	–	comp_stamps[i] = headStamp->match( id );
198	–	}
199	–	}
132
133	<	#ifdef IS_MPI
202	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
203	<	MPIcheckPoint();
204	<	#endif // is_mpi
205	<
133	>	}
134
135
136	+	void SimSetup::makeMolecules( void ){
137
138	<	// caclulate the number of atoms, bonds, bends and torsions
138	>	int k,l;
139	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140	>	molInit molInfo;
141	>	DirectionalAtom* dAtom;
142	>	LinkedAssign* extras;
143	>	LinkedAssign* current_extra;
144	>	AtomStamp* currentAtom;
145	>	BondStamp* currentBond;
146	>	BendStamp* currentBend;
147	>	TorsionStamp* currentTorsion;
148
149	<	tot_atoms = 0;
150	<	tot_bonds = 0;
151	<	tot_bends = 0;
214	<	tot_torsions = 0;
215	<	for( i=0; i<n_components; i++ ){
216	<
217	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
218	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
219	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
220	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
221	<	}
149	>	bond_pair* theBonds;
150	>	bend_set* theBends;
151	>	torsion_set* theTorsions;
152
223	–	tot_SRI = tot_bonds + tot_bends + tot_torsions;
224	–
225	–	simnfo->n_atoms = tot_atoms;
226	–	simnfo->n_bonds = tot_bonds;
227	–	simnfo->n_bends = tot_bends;
228	–	simnfo->n_torsions = tot_torsions;
229	–	simnfo->n_SRI = tot_SRI;
230	–	simnfo->n_mol = tot_nmol;
231	–
153
154	<	#ifdef IS_MPI
154	>	//init the forceField paramters
155
156	<	// divide the molecules among processors here.
236	<
237	<	mpiSim = new mpiSimulation( simnfo );
238	<
239	<
156	>	the_ff->readParams();
157
241	–	globalIndex = mpiSim->divideLabor();
242	–
243	–
244	–
245	–	// set up the local variables
158
159	<	int localMol, allMol;
248	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
159	>	// init the atoms
160
161	<	int* mol2proc = mpiSim->getMolToProcMap();
251	<	int* molCompType = mpiSim->getMolComponentType();
161	>	double ux, uy, uz, u, uSqr;
162
163	<	allMol = 0;
164	<	localMol = 0;
165	<	local_atoms = 0;
256	<	local_bonds = 0;
257	<	local_bends = 0;
258	<	local_torsions = 0;
259	<	for( i=0; i<n_components; i++ ){
163	>	for(k=0; k<nInfo; k++){
164	>
165	>	the_ff->setSimInfo( &(info[k]) );
166
167	<	for( j=0; j<components_nmol[i]; j++ ){
167	>	atomOffset = 0;
168	>	excludeOffset = 0;
169	>	for(i=0; i<info[k].n_mol; i++){
170	>
171	>	stampID = info[k].molecules[i].getStampID();
172	>
173	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
174	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
175	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
176	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
177	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
178
179	<	if( mol2proc[j] == worldRank ){
180	<
181	<	local_atoms +=    comp_stamps[i]->getNAtoms();
182	<	local_bonds +=    comp_stamps[i]->getNBonds();
183	<	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	<
179	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
180	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
181	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
182	>	molInfo.myBends = new Bend*[molInfo.nBends];
183	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
184
185	<	simnfo->n_atoms = mpiSim->getMyNlocal();
185	>	theBonds = new bond_pair[molInfo.nBonds];
186	>	theBends = new bend_set[molInfo.nBends];
187	>	theTorsions = new torsion_set[molInfo.nTorsions];
188	>
189	>	// make the Atoms
190	>
191	>	for(j=0; j<molInfo.nAtoms; j++){
192
193	<	if( local_atoms != simnfo->n_atoms ){
193	>	currentAtom = comp_stamps[stampID]->getAtom( j );
194	>	if( currentAtom->haveOrientation() ){
195	>
196	>	dAtom = new DirectionalAtom( (j + atomOffset),
197	>	info[k].getConfiguration() );
198	>	info[k].n_oriented++;
199	>	molInfo.myAtoms[j] = dAtom;
200	>
201	>	ux = currentAtom->getOrntX();
202	>	uy = currentAtom->getOrntY();
203	>	uz = currentAtom->getOrntZ();
204	>
205	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
206	>
207	>	u = sqrt( uSqr );
208	>	ux = ux / u;
209	>	uy = uy / u;
210	>	uz = uz / u;
211	>
212	>	dAtom->setSUx( ux );
213	>	dAtom->setSUy( uy );
214	>	dAtom->setSUz( uz );
215	>	}
216	>	else{
217	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
218	>	info[k].getConfiguration() );
219	>	}
220	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221	>
222	>	#ifdef IS_MPI
223	>
224	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
225	>
226	>	#endif // is_mpi
227	>	}
228	>
229	>	// make the bonds
230	>	for(j=0; j<molInfo.nBonds; j++){
231	>
232	>	currentBond = comp_stamps[stampID]->getBond( j );
233	>	theBonds[j].a = currentBond->getA() + atomOffset;
234	>	theBonds[j].b = currentBond->getB() + atomOffset;
235	>
236	>	exI = theBonds[j].a;
237	>	exJ = theBonds[j].b;
238	>
239	>	// exclude_I must always be the smaller of the pair
240	>	if( exI > exJ ){
241	>	tempEx = exI;
242	>	exI = exJ;
243	>	exJ = tempEx;
244	>	}
245	>	#ifdef IS_MPI
246	>	tempEx = exI;
247	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
248	>	tempEx = exJ;
249	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
250	>
251	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
252	>	#else  // isn't MPI
253	>
254	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
255	>	#endif  //is_mpi
256	>	}
257	>	excludeOffset += molInfo.nBonds;
258	>
259	>	//make the bends
260	>	for(j=0; j<molInfo.nBends; j++){
261	>
262	>	currentBend = comp_stamps[stampID]->getBend( j );
263	>	theBends[j].a = currentBend->getA() + atomOffset;
264	>	theBends[j].b = currentBend->getB() + atomOffset;
265	>	theBends[j].c = currentBend->getC() + atomOffset;
266	>
267	>	if( currentBend->haveExtras() ){
268	>
269	>	extras = currentBend->getExtras();
270	>	current_extra = extras;
271	>
272	>	while( current_extra != NULL ){
273	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
274	>
275	>	switch( current_extra->getType() ){
276	>
277	>	case 0:
278	>	theBends[j].ghost =
279	>	current_extra->getInt() + atomOffset;
280	>	theBends[j].isGhost = 1;
281	>	break;
282	>
283	>	case 1:
284	>	theBends[j].ghost =
285	>	(int)current_extra->getDouble() + atomOffset;
286	>	theBends[j].isGhost = 1;
287	>	break;
288	>
289	>	default:
290		sprintf( painCave.errMsg,
291	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
292	<	" localAtom (%d) are not equal.\n",
293	<	simnfo->n_atoms,
294	<	local_atoms );
291	>	"SimSetup Error: ghostVectorSource was neither a "
292	>	"double nor an int.\n"
293	>	"-->Bend[%d] in %s\n",
294	>	j, comp_stamps[stampID]->getID() );
295		painCave.isFatal = 1;
296		simError();
297	+	}
298	+	}
299	+
300	+	else{
301	+
302	+	sprintf( painCave.errMsg,
303	+	"SimSetup Error: unhandled bend assignment:\n"
304	+	"    -->%s in Bend[%d] in %s\n",
305	+	current_extra->getlhs(),
306	+	j, comp_stamps[stampID]->getID() );
307	+	painCave.isFatal = 1;
308	+	simError();
309	+	}
310	+
311	+	current_extra = current_extra->getNext();
312	+	}
313		}
288	–
289	–	simnfo->n_bonds = local_bonds;
290	–	simnfo->n_bends = local_bends;
291	–	simnfo->n_torsions = local_torsions;
292	–	simnfo->n_SRI = local_SRI;
293	–	simnfo->n_mol = localMol;
294	–
295	–	strcpy( checkPointMsg, "Passed nlocal consistency check." );
296	–	MPIcheckPoint();
314
315	+	if( !theBends[j].isGhost ){
316	+
317	+	exI = theBends[j].a;
318	+	exJ = theBends[j].c;
319	+	}
320	+	else{
321	+
322	+	exI = theBends[j].a;
323	+	exJ = theBends[j].b;
324	+	}
325
326	<	#endif // is_mpi
326	>	// exclude_I must always be the smaller of the pair
327	>	if( exI > exJ ){
328	>	tempEx = exI;
329	>	exI = exJ;
330	>	exJ = tempEx;
331	>	}
332	>	#ifdef IS_MPI
333	>	tempEx = exI;
334	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
335	>	tempEx = exJ;
336	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
337	>
338	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
339	>	#else  // isn't MPI
340	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
341	>	#endif  //is_mpi
342	>	}
343	>	excludeOffset += molInfo.nBends;
344	>
345	>	for(j=0; j<molInfo.nTorsions; j++){
346
347	<
348	<	// create the atom and short range interaction arrays
349	<
350	<	Atom::createArrays(simnfo->n_atoms);
351	<	the_atoms = new Atom*[simnfo->n_atoms];
352	<	the_molecules = new Molecule[simnfo->n_mol];
353	<	int molIndex;
354	<
355	<	// initialize the molecule's stampID's
356	<
347	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
348	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
349	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
350	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
351	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
352	>
353	>	exI = theTorsions[j].a;
354	>	exJ = theTorsions[j].d;
355	>
356	>	// exclude_I must always be the smaller of the pair
357	>	if( exI > exJ ){
358	>	tempEx = exI;
359	>	exI = exJ;
360	>	exJ = tempEx;
361	>	}
362		#ifdef IS_MPI
363	+	tempEx = exI;
364	+	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
365	+	tempEx = exJ;
366	+	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
367
368	+	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
369	+	#else  // isn't MPI
370	+	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
371	+	#endif  //is_mpi
372	+	}
373	+	excludeOffset += molInfo.nTorsions;
374	+
375	+
376	+	// send the arrays off to the forceField for init.
377	+
378	+	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
379	+	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
380	+	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
381	+	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
382	+
383	+
384	+	info[k].molecules[i].initialize( molInfo );
385
386	<	molIndex = 0;
387	<	for(i=0; i<mpiSim->getTotNmol(); i++){
388	<
389	<	if(mol2proc[i] == worldRank ){
390	<	the_molecules[molIndex].setStampID( molCompType[i] );
319	<	molIndex++;
386	>
387	>	atomOffset += molInfo.nAtoms;
388	>	delete[] theBonds;
389	>	delete[] theBends;
390	>	delete[] theTorsions;
391		}
392		}
393	+
394	+	#ifdef IS_MPI
395	+	sprintf( checkPointMsg, "all molecules initialized succesfully" );
396	+	MPIcheckPoint();
397	+	#endif // is_mpi
398	+
399	+	// clean up the forcefield
400
401	<	#else // is_mpi
401	>	the_ff->calcRcut();
402	>	the_ff->cleanMe();
403
404	<	molIndex = 0;
405	<	for(i=0; i<n_components; i++){
406	<	for(j=0; j<components_nmol[i]; j++ ){
407	<	the_molecules[molIndex].setStampID( i );
408	<	molIndex++;
404	>	}
405	>
406	>	void SimSetup::initFromBass( void ){
407	>
408	>	int i, j, k;
409	>	int n_cells;
410	>	double cellx, celly, cellz;
411	>	double temp1, temp2, temp3;
412	>	int n_per_extra;
413	>	int n_extra;
414	>	int have_extra, done;
415	>
416	>	double vel[3];
417	>	vel[0] = 0.0;
418	>	vel[1] = 0.0;
419	>	vel[2] = 0.0;
420	>
421	>	temp1 = (double)tot_nmol / 4.0;
422	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
423	>	temp3 = ceil( temp2 );
424	>
425	>	have_extra =0;
426	>	if( temp2 < temp3 ){ // we have a non-complete lattice
427	>	have_extra =1;
428	>
429	>	n_cells = (int)temp3 - 1;
430	>	cellx = info[0].boxL[0] / temp3;
431	>	celly = info[0].boxL[1] / temp3;
432	>	cellz = info[0].boxL[2] / temp3;
433	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
434	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
435	>	n_per_extra = (int)ceil( temp1 );
436	>
437	>	if( n_per_extra > 4){
438	>	sprintf( painCave.errMsg,
439	>	"SimSetup error. There has been an error in constructing"
440	>	" the non-complete lattice.\n" );
441	>	painCave.isFatal = 1;
442	>	simError();
443		}
444		}
445	<
445	>	else{
446	>	n_cells = (int)temp3;
447	>	cellx = info[0].boxL[0] / temp3;
448	>	celly = info[0].boxL[1] / temp3;
449	>	cellz = info[0].boxL[2] / temp3;
450	>	}
451
452	<	#endif // is_mpi
452	>	current_mol = 0;
453	>	current_comp_mol = 0;
454	>	current_comp = 0;
455	>	current_atom_ndx = 0;
456
457	+	for( i=0; i < n_cells ; i++ ){
458	+	for( j=0; j < n_cells; j++ ){
459	+	for( k=0; k < n_cells; k++ ){
460
461	<	if( simnfo->n_SRI ){
462	<
463	<	std::cerr << "n_SRI = " << simnfo->n_SRI << "\n";
340	<
341	<	Exclude::createArray(simnfo->n_SRI);
342	<	the_excludes = new Exclude*[simnfo->n_SRI];
343	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
344	<	simnfo->globalExcludes = new int;
345	<	simnfo->n_exclude = tot_SRI;
346	<	}
347	<	else{
348	<
349	<	Exclude::createArray( 1 );
350	<	the_excludes = new Exclude*;
351	<	the_excludes[0] = new Exclude(0);
352	<	the_excludes[0]->setPair( 0,0 );
353	<	simnfo->globalExcludes = new int;
354	<	simnfo->globalExcludes[0] = 0;
355	<	simnfo->n_exclude = 0;
356	<	}
461	>	makeElement( i * cellx,
462	>	j * celly,
463	>	k * cellz );
464
465	<	// set the arrays into the SimInfo object
465	>	makeElement( i * cellx + 0.5 * cellx,
466	>	j * celly + 0.5 * celly,
467	>	k * cellz );
468
469	<	simnfo->atoms = the_atoms;
470	<	simnfo->molecules = the_molecules;
471	<	simnfo->nGlobalExcludes = 0;
363	<	simnfo->excludes = the_excludes;
469	>	makeElement( i * cellx,
470	>	j * celly + 0.5 * celly,
471	>	k * cellz + 0.5 * cellz );
472
473	+	makeElement( i * cellx + 0.5 * cellx,
474	+	j * celly,
475	+	k * cellz + 0.5 * cellz );
476	+	}
477	+	}
478	+	}
479
480	<	// get some of the tricky things that may still be in the globals
480	>	if( have_extra ){
481	>	done = 0;
482
483	<
484	<	if( the_globals->haveBox() ){
485	<	simnfo->box_x = the_globals->getBox();
371	<	simnfo->box_y = the_globals->getBox();
372	<	simnfo->box_z = the_globals->getBox();
373	<	}
374	<	else if( the_globals->haveDensity() ){
483	>	int start_ndx;
484	>	for( i=0; i < (n_cells+1) && !done; i++ ){
485	>	for( j=0; j < (n_cells+1) && !done; j++ ){
486
487	<	double vol;
488	<	vol = (double)tot_nmol / the_globals->getDensity();
489	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
490	<	simnfo->box_y = simnfo->box_x;
491	<	simnfo->box_z = simnfo->box_x;
487	>	if( i < n_cells ){
488	>
489	>	if( j < n_cells ){
490	>	start_ndx = n_cells;
491	>	}
492	>	else start_ndx = 0;
493		}
494	<	else{
495	<	if( !the_globals->haveBoxX() ){
496	<	sprintf( painCave.errMsg,
497	<	"SimSetup error, no periodic BoxX size given.\n" );
498	<	painCave.isFatal = 1;
499	<	simError();
494	>	else start_ndx = 0;
495	>
496	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
497	>
498	>	makeElement( i * cellx,
499	>	j * celly,
500	>	k * cellz );
501	>	done = ( current_mol >= tot_nmol );
502	>
503	>	if( !done && n_per_extra > 1 ){
504	>	makeElement( i * cellx + 0.5 * cellx,
505	>	j * celly + 0.5 * celly,
506	>	k * cellz );
507	>	done = ( current_mol >= tot_nmol );
508		}
389	–	simnfo->box_x = the_globals->getBoxX();
509
510	<	if( !the_globals->haveBoxY() ){
511	<	sprintf( painCave.errMsg,
512	<	"SimSetup error, no periodic BoxY size given.\n" );
513	<	painCave.isFatal = 1;
514	<	simError();
510	>	if( !done && n_per_extra > 2){
511	>	makeElement( i * cellx,
512	>	j * celly + 0.5 * celly,
513	>	k * cellz + 0.5 * cellz );
514	>	done = ( current_mol >= tot_nmol );
515		}
397	–	simnfo->box_y = the_globals->getBoxY();
516
517	<	if( !the_globals->haveBoxZ() ){
518	<	sprintf( painCave.errMsg,
519	<	"SimSetup error, no periodic BoxZ size given.\n" );
520	<	painCave.isFatal = 1;
521	<	simError();
517	>	if( !done && n_per_extra > 3){
518	>	makeElement( i * cellx + 0.5 * cellx,
519	>	j * celly,
520	>	k * cellz + 0.5 * cellz );
521	>	done = ( current_mol >= tot_nmol );
522		}
405	–	simnfo->box_z = the_globals->getBoxZ();
523		}
524	+	}
525	+	}
526	+	}
527
528	<	#ifdef IS_MPI
529	<	strcpy( checkPointMsg, "Box size set up" );
530	<	MPIcheckPoint();
531	<	#endif // is_mpi
528	>	for( i=0; i<info[0].n_atoms; i++ ){
529	>	info[0].atoms[i]->setVel( vel );
530	>	}
531	>	}
532
533	+	void SimSetup::makeElement( double x, double y, double z ){
534
535	<	// initialize the arrays
535	>	int k;
536	>	AtomStamp* current_atom;
537	>	DirectionalAtom* dAtom;
538	>	double rotMat[3][3];
539	>	double pos[3];
540
541	<	the_ff->setSimInfo( simnfo );
541	>	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
542
543	<	makeMolecules();
544	<	simnfo->identArray = new int[simnfo->n_atoms];
420	<	for(i=0; i<simnfo->n_atoms; i++){
421	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
422	<	}
423	<
424	<	if (the_globals->getUseRF() ) {
425	<	simnfo->useReactionField = 1;
426	<
427	<	if( !the_globals->haveECR() ){
543	>	current_atom = comp_stamps[current_comp]->getAtom( k );
544	>	if( !current_atom->havePosition() ){
545		sprintf( painCave.errMsg,
546	<	"SimSetup Warning: using default value of 1/2 the smallest "
547	<	"box length for the electrostaticCutoffRadius.\n"
548	<	"I hope you have a very fast processor!\n");
549	<	painCave.isFatal = 0;
550	<	simError();
551	<	double smallest;
435	<	smallest = simnfo->box_x;
436	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
437	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
438	<	simnfo->ecr = 0.5 * smallest;
439	<	} else {
440	<	simnfo->ecr        = the_globals->getECR();
441	<	}
442	<
443	<	if( !the_globals->haveEST() ){
444	<	sprintf( painCave.errMsg,
445	<	"SimSetup Warning: using default value of 0.05 * the "
446	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
447	<	);
448	<	painCave.isFatal = 0;
449	<	simError();
450	<	simnfo->est = 0.05 * simnfo->ecr;
451	<	} else {
452	<	simnfo->est        = the_globals->getEST();
453	<	}
454	<
455	<	if(!the_globals->haveDielectric() ){
456	<	sprintf( painCave.errMsg,
457	<	"SimSetup Error: You are trying to use Reaction Field without"
458	<	"setting a dielectric constant!\n"
459	<	);
546	>	"SimSetup:initFromBass error.\n"
547	>	"\tComponent %s, atom %s does not have a position specified.\n"
548	>	"\tThe initialization routine is unable to give a start"
549	>	" position.\n",
550	>	comp_stamps[current_comp]->getID(),
551	>	current_atom->getType() );
552		painCave.isFatal = 1;
553		simError();
554		}
555	<	simnfo->dielectric = the_globals->getDielectric();
556	<	} else {
557	<	if (simnfo->n_dipoles) {
558	<
559	<	if( !the_globals->haveECR() ){
560	<	sprintf( painCave.errMsg,
469	<	"SimSetup Warning: using default value of 1/2 the smallest"
470	<	"box length for the electrostaticCutoffRadius.\n"
471	<	"I hope you have a very fast processor!\n");
472	<	painCave.isFatal = 0;
473	<	simError();
474	<	double smallest;
475	<	smallest = simnfo->box_x;
476	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
477	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
478	<	simnfo->ecr = 0.5 * smallest;
479	<	} else {
480	<	simnfo->ecr        = the_globals->getECR();
481	<	}
482	<
483	<	if( !the_globals->haveEST() ){
484	<	sprintf( painCave.errMsg,
485	<	"SimSetup Warning: using default value of 5% of the"
486	<	"electrostaticCutoffRadius for the "
487	<	"electrostaticSkinThickness\n"
488	<	);
489	<	painCave.isFatal = 0;
490	<	simError();
491	<	simnfo->est = 0.05 * simnfo->ecr;
492	<	} else {
493	<	simnfo->est        = the_globals->getEST();
494	<	}
495	<	}
496	<	}
555	>
556	>	pos[0] = x + current_atom->getPosX();
557	>	pos[1] = y + current_atom->getPosY();
558	>	pos[2] = z + current_atom->getPosZ();
559	>
560	>	info[0].atoms[current_atom_ndx]->setPos( pos );
561
562	<	#ifdef IS_MPI
499	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
500	<	MPIcheckPoint();
501	<	#endif // is_mpi
562	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
563
564	<	if( the_globals->haveInitialConfig() ){
504	<
505	<	InitializeFromFile* fileInit;
506	<	#ifdef IS_MPI // is_mpi
507	<	if( worldRank == 0 ){
508	<	#endif //is_mpi
509	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
510	<	#ifdef IS_MPI
511	<	}else fileInit = new InitializeFromFile( NULL );
512	<	#endif
513	<	fileInit->read_xyz( simnfo ); // default velocities on
564	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
565
566	<	delete fileInit;
567	<	}
568	<	else{
566	>	rotMat[0][0] = 1.0;
567	>	rotMat[0][1] = 0.0;
568	>	rotMat[0][2] = 0.0;
569
570	<	#ifdef IS_MPI
570	>	rotMat[1][0] = 0.0;
571	>	rotMat[1][1] = 1.0;
572	>	rotMat[1][2] = 0.0;
573
574	<	// no init from bass
575	<
576	<	sprintf( painCave.errMsg,
524	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
525	<	painCave.isFatal;
526	<	simError();
527	<
528	<	#else
574	>	rotMat[2][0] = 0.0;
575	>	rotMat[2][1] = 0.0;
576	>	rotMat[2][2] = 1.0;
577
578	<	initFromBass();
578	>	dAtom->setA( rotMat );
579	>	}
580
581	+	current_atom_ndx++;
582	+	}
583
584	<	#endif
585	<	}
584	>	current_mol++;
585	>	current_comp_mol++;
586
587	<	#ifdef IS_MPI
537	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
538	<	MPIcheckPoint();
539	<	#endif // is_mpi
587	>	if( current_comp_mol >= components_nmol[current_comp] ){
588
589	<
590	<
543	<
544	<
545	<
546	<
547	<	#ifdef IS_MPI
548	<	if( worldRank == 0 ){
549	<	#endif // is_mpi
550	<
551	<	if( the_globals->haveFinalConfig() ){
552	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
553	<	}
554	<	else{
555	<	strcpy( simnfo->finalName, inFileName );
556	<	char* endTest;
557	<	int nameLength = strlen( simnfo->finalName );
558	<	endTest = &(simnfo->finalName[nameLength - 5]);
559	<	if( !strcmp( endTest, ".bass" ) ){
560	<	strcpy( endTest, ".eor" );
561	<	}
562	<	else if( !strcmp( endTest, ".BASS" ) ){
563	<	strcpy( endTest, ".eor" );
564	<	}
565	<	else{
566	<	endTest = &(simnfo->finalName[nameLength - 4]);
567	<	if( !strcmp( endTest, ".bss" ) ){
568	<	strcpy( endTest, ".eor" );
569	<	}
570	<	else if( !strcmp( endTest, ".mdl" ) ){
571	<	strcpy( endTest, ".eor" );
572	<	}
573	<	else{
574	<	strcat( simnfo->finalName, ".eor" );
575	<	}
576	<	}
577	<	}
578	<
579	<	// make the sample and status out names
580	<
581	<	strcpy( simnfo->sampleName, inFileName );
582	<	char* endTest;
583	<	int nameLength = strlen( simnfo->sampleName );
584	<	endTest = &(simnfo->sampleName[nameLength - 5]);
585	<	if( !strcmp( endTest, ".bass" ) ){
586	<	strcpy( endTest, ".dump" );
587	<	}
588	<	else if( !strcmp( endTest, ".BASS" ) ){
589	<	strcpy( endTest, ".dump" );
590	<	}
591	<	else{
592	<	endTest = &(simnfo->sampleName[nameLength - 4]);
593	<	if( !strcmp( endTest, ".bss" ) ){
594	<	strcpy( endTest, ".dump" );
595	<	}
596	<	else if( !strcmp( endTest, ".mdl" ) ){
597	<	strcpy( endTest, ".dump" );
598	<	}
599	<	else{
600	<	strcat( simnfo->sampleName, ".dump" );
601	<	}
602	<	}
603	<
604	<	strcpy( simnfo->statusName, inFileName );
605	<	nameLength = strlen( simnfo->statusName );
606	<	endTest = &(simnfo->statusName[nameLength - 5]);
607	<	if( !strcmp( endTest, ".bass" ) ){
608	<	strcpy( endTest, ".stat" );
609	<	}
610	<	else if( !strcmp( endTest, ".BASS" ) ){
611	<	strcpy( endTest, ".stat" );
612	<	}
613	<	else{
614	<	endTest = &(simnfo->statusName[nameLength - 4]);
615	<	if( !strcmp( endTest, ".bss" ) ){
616	<	strcpy( endTest, ".stat" );
617	<	}
618	<	else if( !strcmp( endTest, ".mdl" ) ){
619	<	strcpy( endTest, ".stat" );
620	<	}
621	<	else{
622	<	strcat( simnfo->statusName, ".stat" );
623	<	}
624	<	}
625	<
626	<	#ifdef IS_MPI
589	>	current_comp_mol = 0;
590	>	current_comp++;
591		}
592	<	#endif // is_mpi
629	<
630	<	// set the status, sample, and themal kick times
631	<
632	<	if( the_globals->haveSampleTime() ){
633	<	simnfo->sampleTime = the_globals->getSampleTime();
634	<	simnfo->statusTime = simnfo->sampleTime;
635	<	simnfo->thermalTime = simnfo->sampleTime;
636	<	}
637	<	else{
638	<	simnfo->sampleTime = the_globals->getRunTime();
639	<	simnfo->statusTime = simnfo->sampleTime;
640	<	simnfo->thermalTime = simnfo->sampleTime;
641	<	}
592	>	}
593
643	–	if( the_globals->haveStatusTime() ){
644	–	simnfo->statusTime = the_globals->getStatusTime();
645	–	}
594
595	<	if( the_globals->haveThermalTime() ){
596	<	simnfo->thermalTime = the_globals->getThermalTime();
649	<	}
595	>	void SimSetup::gatherInfo( void ){
596	>	int i,j,k;
597
598	<	// check for the temperature set flag
598	>	ensembleCase = -1;
599	>	ffCase = -1;
600
601	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
601	>	// set the easy ones first
602
603	+	for( i=0; i<nInfo; i++){
604	+	info[i].target_temp = globals->getTargetTemp();
605	+	info[i].dt = globals->getDt();
606	+	info[i].run_time = globals->getRunTime();
607	+	}
608	+	n_components = globals->getNComponents();
609
656	–	//   // make the longe range forces and the integrator
610
611	<	//   new AllLong( simnfo );
611	>	// get the forceField
612
613	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
661	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
613	>	strcpy( force_field, globals->getForceField() );
614
615	<
616	<
617	<	// initialize the Fortran
666	<
667	<	simnfo->refreshSim();
668	<
669	<	if( !strcmp( simnfo->mixingRule, "standard") ){
670	<	the_ff->initForceField( LB_MIXING_RULE );
671	<	}
672	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
673	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
674	<	}
615	>	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
616	>	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
617	>	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
618		else{
619		sprintf( painCave.errMsg,
620	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
621	<	simnfo->mixingRule );
620	>	"SimSetup Error. Unrecognized force field -> %s\n",
621	>	force_field );
622		painCave.isFatal = 1;
623		simError();
624		}
625
626	+	// get the ensemble
627
628	<	#ifdef IS_MPI
685	<	strcpy( checkPointMsg,
686	<	"Successfully intialized the mixingRule for Fortran." );
687	<	MPIcheckPoint();
688	<	#endif // is_mpi
689	<	}
628	>	strcpy( ensemble, globals->getEnsemble() );
629
630	+	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
631	+	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
632	+	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
633	+	ensembleCase = NPTi_ENS;
634	+	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
635	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
636	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
637	+	else{
638	+	sprintf( painCave.errMsg,
639	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
640	+	"reverting to NVE for this simulation.\n",
641	+	ensemble );
642	+	painCave.isFatal = 0;
643	+	simError();
644	+	strcpy( ensemble, "NVE" );
645	+	ensembleCase = NVE_ENS;
646	+	}
647	+
648	+	for(i=0; i<nInfo; i++){
649	+
650	+	strcpy( info[i].ensemble, ensemble );
651
652	<	void SimSetup::makeMolecules( void ){
652	>	// get the mixing rule
653
654	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
655	<	molInit info;
656	<	DirectionalAtom* dAtom;
697	<	LinkedAssign* extras;
698	<	LinkedAssign* current_extra;
699	<	AtomStamp* currentAtom;
700	<	BondStamp* currentBond;
701	<	BendStamp* currentBend;
702	<	TorsionStamp* currentTorsion;
703	<
704	<	bond_pair* theBonds;
705	<	bend_set* theBends;
706	<	torsion_set* theTorsions;
707	<
654	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
655	>	info[i].usePBC = globals->getPBC();
656	>	}
657
658	<	//init the forceField paramters
658	>	// get the components and calculate the tot_nMol and indvidual n_mol
659	>
660	>	the_components = globals->getComponents();
661	>	components_nmol = new int[n_components];
662
711	–	the_ff->readParams();
663
664	<
665	<	// init the atoms
664	>	if( !globals->haveNMol() ){
665	>	// we don't have the total number of molecules, so we assume it is
666	>	// given in each component
667
668	<	double ux, uy, uz, u, uSqr;
669	<
718	<	atomOffset = 0;
719	<	excludeOffset = 0;
720	<	for(i=0; i<simnfo->n_mol; i++){
721	<
722	<	stampID = the_molecules[i].getStampID();
668	>	tot_nmol = 0;
669	>	for( i=0; i<n_components; i++ ){
670
671	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
672	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
673	<	info.nBends    = comp_stamps[stampID]->getNBends();
674	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
675	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
671	>	if( !the_components[i]->haveNMol() ){
672	>	// we have a problem
673	>	sprintf( painCave.errMsg,
674	>	"SimSetup Error. No global NMol or component NMol"
675	>	" given. Cannot calculate the number of atoms.\n" );
676	>	painCave.isFatal = 1;
677	>	simError();
678	>	}
679
680	<	info.myAtoms = &the_atoms[atomOffset];
681	<	info.myExcludes = &the_excludes[excludeOffset];
682	<	info.myBonds = new Bond*[info.nBonds];
683	<	info.myBends = new Bend*[info.nBends];
684	<	info.myTorsions = new Torsion*[info.nTorsions];
680	>	tot_nmol += the_components[i]->getNMol();
681	>	components_nmol[i] = the_components[i]->getNMol();
682	>	}
683	>	}
684	>	else{
685	>	sprintf( painCave.errMsg,
686	>	"SimSetup error.\n"
687	>	"\tSorry, the ability to specify total"
688	>	" nMols and then give molfractions in the components\n"
689	>	"\tis not currently supported."
690	>	" Please give nMol in the components.\n" );
691	>	painCave.isFatal = 1;
692	>	simError();
693	>	}
694
695	<	theBonds = new bond_pair[info.nBonds];
696	<	theBends = new bend_set[info.nBends];
697	<	theTorsions = new torsion_set[info.nTorsions];
695	>	// set the status, sample, and thermal kick times
696	>
697	>	for(i=0; i<nInfo; i++){
698	>
699	>	if( globals->haveSampleTime() ){
700	>	info[i].sampleTime = globals->getSampleTime();
701	>	info[i].statusTime = info[i].sampleTime;
702	>	info[i].thermalTime = info[i].sampleTime;
703	>	}
704	>	else{
705	>	info[i].sampleTime = globals->getRunTime();
706	>	info[i].statusTime = info[i].sampleTime;
707	>	info[i].thermalTime = info[i].sampleTime;
708	>	}
709
710	<	// make the Atoms
710	>	if( globals->haveStatusTime() ){
711	>	info[i].statusTime = globals->getStatusTime();
712	>	}
713
714	<	for(j=0; j<info.nAtoms; j++){
715	<
716	<	currentAtom = comp_stamps[stampID]->getAtom( j );
717	<	if( currentAtom->haveOrientation() ){
718	<
719	<	dAtom = new DirectionalAtom(j + atomOffset);
720	<	simnfo->n_oriented++;
749	<	info.myAtoms[j] = dAtom;
750	<
751	<	ux = currentAtom->getOrntX();
752	<	uy = currentAtom->getOrntY();
753	<	uz = currentAtom->getOrntZ();
754	<
755	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
756	<
757	<	u = sqrt( uSqr );
758	<	ux = ux / u;
759	<	uy = uy / u;
760	<	uz = uz / u;
761	<
762	<	dAtom->setSUx( ux );
763	<	dAtom->setSUy( uy );
764	<	dAtom->setSUz( uz );
765	<	}
766	<	else{
767	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
768	<	}
769	<	info.myAtoms[j]->setType( currentAtom->getType() );
714	>	if( globals->haveThermalTime() ){
715	>	info[i].thermalTime = globals->getThermalTime();
716	>	}
717	>
718	>	// check for the temperature set flag
719	>
720	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
721
722	<	#ifdef IS_MPI
772	<
773	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
774	<
775	<	#endif // is_mpi
776	<	}
722	>	// get some of the tricky things that may still be in the globals
723
724	<	// make the bonds
725	<	for(j=0; j<info.nBonds; j++){
724	>	double boxVector[3];
725	>	if( globals->haveBox() ){
726	>	boxVector[0] = globals->getBox();
727	>	boxVector[1] = globals->getBox();
728	>	boxVector[2] = globals->getBox();
729
730	<	currentBond = comp_stamps[stampID]->getBond( j );
782	<	theBonds[j].a = currentBond->getA() + atomOffset;
783	<	theBonds[j].b = currentBond->getB() + atomOffset;
784	<
785	<	exI = theBonds[i].a;
786	<	exJ = theBonds[i].b;
787	<
788	<	// exclude_I must always be the smaller of the pair
789	<	if( exI > exJ ){
790	<	tempEx = exI;
791	<	exI = exJ;
792	<	exJ = tempEx;
793	<	}
794	<	#ifdef IS_MPI
795	<	tempEx = exI;
796	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
797	<	tempEx = exJ;
798	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
799	<
800	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
801	<	#else  // isn't MPI
802	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
803	<	#endif  //is_mpi
730	>	info[i].setBox( boxVector );
731		}
732	<	excludeOffset += info.nBonds;
806	<
807	<	//make the bends
808	<	for(j=0; j<info.nBends; j++){
732	>	else if( globals->haveDensity() ){
733
734	<	currentBend = comp_stamps[stampID]->getBend( j );
735	<	theBends[j].a = currentBend->getA() + atomOffset;
736	<	theBends[j].b = currentBend->getB() + atomOffset;
737	<	theBends[j].c = currentBend->getC() + atomOffset;
738	<
739	<	if( currentBend->haveExtras() ){
740	<
741	<	extras = currentBend->getExtras();
742	<	current_extra = extras;
743	<
744	<	while( current_extra != NULL ){
745	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
746	<
747	<	switch( current_extra->getType() ){
824	<
825	<	case 0:
826	<	theBends[j].ghost =
827	<	current_extra->getInt() + atomOffset;
828	<	theBends[j].isGhost = 1;
829	<	break;
830	<
831	<	case 1:
832	<	theBends[j].ghost =
833	<	(int)current_extra->getDouble() + atomOffset;
834	<	theBends[j].isGhost = 1;
835	<	break;
836	<
837	<	default:
838	<	sprintf( painCave.errMsg,
839	<	"SimSetup Error: ghostVectorSource was neiter a "
840	<	"double nor an int.\n"
841	<	"-->Bend[%d] in %s\n",
842	<	j, comp_stamps[stampID]->getID() );
843	<	painCave.isFatal = 1;
844	<	simError();
845	<	}
846	<	}
847	<
848	<	else{
849	<
850	<	sprintf( painCave.errMsg,
851	<	"SimSetup Error: unhandled bend assignment:\n"
852	<	"    -->%s in Bend[%d] in %s\n",
853	<	current_extra->getlhs(),
854	<	j, comp_stamps[stampID]->getID() );
855	<	painCave.isFatal = 1;
856	<	simError();
857	<	}
858	<
859	<	current_extra = current_extra->getNext();
860	<	}
734	>	double vol;
735	>	vol = (double)tot_nmol / globals->getDensity();
736	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
737	>	boxVector[1] = boxVector[0];
738	>	boxVector[2] = boxVector[0];
739	>
740	>	info[i].setBox( boxVector );
741	>	}
742	>	else{
743	>	if( !globals->haveBoxX() ){
744	>	sprintf( painCave.errMsg,
745	>	"SimSetup error, no periodic BoxX size given.\n" );
746	>	painCave.isFatal = 1;
747	>	simError();
748		}
749	<
863	<	if( !theBends[j].isGhost ){
864	<
865	<	exI = theBends[j].a;
866	<	exJ = theBends[j].c;
867	<	}
868	<	else{
869	<
870	<	exI = theBends[j].a;
871	<	exJ = theBends[j].b;
872	<	}
749	>	boxVector[0] = globals->getBoxX();
750
751	<	// exclude_I must always be the smaller of the pair
752	<	if( exI > exJ ){
753	<	tempEx = exI;
754	<	exI = exJ;
755	<	exJ = tempEx;
751	>	if( !globals->haveBoxY() ){
752	>	sprintf( painCave.errMsg,
753	>	"SimSetup error, no periodic BoxY size given.\n" );
754	>	painCave.isFatal = 1;
755	>	simError();
756		}
757	<	#ifdef IS_MPI
881	<	tempEx = exI;
882	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
883	<	tempEx = exJ;
884	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
757	>	boxVector[1] = globals->getBoxY();
758
759	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
760	<	#else  // isn't MPI
761	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
762	<	#endif  //is_mpi
763	<	}
891	<	excludeOffset += info.nBends;
892	<
893	<	for(j=0; j<info.nTorsions; j++){
894	<
895	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
896	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
897	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
898	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
899	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
900	<
901	<	exI = theTorsions[j].a;
902	<	exJ = theTorsions[j].d;
903	<
904	<	// exclude_I must always be the smaller of the pair
905	<	if( exI > exJ ){
906	<	tempEx = exI;
907	<	exI = exJ;
908	<	exJ = tempEx;
759	>	if( !globals->haveBoxZ() ){
760	>	sprintf( painCave.errMsg,
761	>	"SimSetup error, no periodic BoxZ size given.\n" );
762	>	painCave.isFatal = 1;
763	>	simError();
764		}
765	<	#ifdef IS_MPI
911	<	tempEx = exI;
912	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
913	<	tempEx = exJ;
914	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
765	>	boxVector[2] = globals->getBoxZ();
766
767	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
917	<	#else  // isn't MPI
918	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
919	<	#endif  //is_mpi
767	>	info[i].setBox( boxVector );
768		}
921	–	excludeOffset += info.nTorsions;
769
770	+	}
771
772	<	// send the arrays off to the forceField for init.
772	>	#ifdef IS_MPI
773	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
774	>	MPIcheckPoint();
775	>	#endif // is_mpi
776
926	–	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
927	–	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
928	–	the_ff->initializeBends( info.nBends, info.myBends, theBends );
929	–	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
930	–
931	–
932	–	the_molecules[i].initialize( info );
933	–	atomOffset += info.nAtoms;
934	–	delete[] theBonds;
935	–	delete[] theBends;
936	–	delete[] theTorsions;
937	–	}
938	–
939	–	// clean up the forcefield
940	–	the_ff->calcRcut();
941	–	the_ff->cleanMe();
777		}
778
944	–	void SimSetup::initFromBass( void ){
779
780	<	int i, j, k;
781	<	int n_cells;
782	<	double cellx, celly, cellz;
783	<	double temp1, temp2, temp3;
950	<	int n_per_extra;
951	<	int n_extra;
952	<	int have_extra, done;
780	>	void SimSetup::finalInfoCheck( void ){
781	>	int index;
782	>	int usesDipoles;
783	>	int i;
784
785	<	temp1 = (double)tot_nmol / 4.0;
786	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
787	<	temp3 = ceil( temp2 );
788	<
789	<	have_extra =0;
790	<	if( temp2 < temp3 ){ // we have a non-complete lattice
791	<	have_extra =1;
792	<
962	<	n_cells = (int)temp3 - 1;
963	<	cellx = simnfo->box_x / temp3;
964	<	celly = simnfo->box_y / temp3;
965	<	cellz = simnfo->box_z / temp3;
966	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
967	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
968	<	n_per_extra = (int)ceil( temp1 );
969	<
970	<	if( n_per_extra > 4){
971	<	sprintf( painCave.errMsg,
972	<	"SimSetup error. There has been an error in constructing"
973	<	" the non-complete lattice.\n" );
974	<	painCave.isFatal = 1;
975	<	simError();
785	>	for(i=0; i<nInfo; i++){
786	>	// check electrostatic parameters
787	>
788	>	index = 0;
789	>	usesDipoles = 0;
790	>	while( (index < info[i].n_atoms) && !usesDipoles ){
791	>	usesDipoles = (info[i].atoms[index])->hasDipole();
792	>	index++;
793		}
794	+
795	+	#ifdef IS_MPI
796	+	int myUse = usesDipoles;
797	+	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
798	+	#endif //is_mpi
799	+
800	+	double theEcr, theEst;
801	+
802	+	if (globals->getUseRF() ) {
803	+	info[i].useReactionField = 1;
804	+
805	+	if( !globals->haveECR() ){
806	+	sprintf( painCave.errMsg,
807	+	"SimSetup Warning: using default value of 1/2 the smallest "
808	+	"box length for the electrostaticCutoffRadius.\n"
809	+	"I hope you have a very fast processor!\n");
810	+	painCave.isFatal = 0;
811	+	simError();
812	+	double smallest;
813	+	smallest = info[i].boxL[0];
814	+	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
815	+	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
816	+	theEcr = 0.5 * smallest;
817	+	} else {
818	+	theEcr = globals->getECR();
819	+	}
820	+
821	+	if( !globals->haveEST() ){
822	+	sprintf( painCave.errMsg,
823	+	"SimSetup Warning: using default value of 0.05 * the "
824	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
825	+	);
826	+	painCave.isFatal = 0;
827	+	simError();
828	+	theEst = 0.05 * theEcr;
829	+	} else {
830	+	theEst= globals->getEST();
831	+	}
832	+
833	+	info[i].setEcr( theEcr, theEst );
834	+
835	+	if(!globals->haveDielectric() ){
836	+	sprintf( painCave.errMsg,
837	+	"SimSetup Error: You are trying to use Reaction Field without"
838	+	"setting a dielectric constant!\n"
839	+	);
840	+	painCave.isFatal = 1;
841	+	simError();
842	+	}
843	+	info[i].dielectric = globals->getDielectric();
844	+	}
845	+	else {
846	+	if (usesDipoles) {
847	+
848	+	if( !globals->haveECR() ){
849	+	sprintf( painCave.errMsg,
850	+	"SimSetup Warning: using default value of 1/2 the smallest "
851	+	"box length for the electrostaticCutoffRadius.\n"
852	+	"I hope you have a very fast processor!\n");
853	+	painCave.isFatal = 0;
854	+	simError();
855	+	double smallest;
856	+	smallest = info[i].boxL[0];
857	+	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
858	+	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
859	+	theEcr = 0.5 * smallest;
860	+	} else {
861	+	theEcr = globals->getECR();
862		}
863	<	else{
864	<	n_cells = (int)temp3;
865	<	cellx = simnfo->box_x / temp3;
866	<	celly = simnfo->box_y / temp3;
867	<	cellz = simnfo->box_z / temp3;
863	>
864	>	if( !globals->haveEST() ){
865	>	sprintf( painCave.errMsg,
866	>	"SimSetup Warning: using default value of 0.05 * the "
867	>	"electrostaticCutoffRadius for the "
868	>	"electrostaticSkinThickness\n"
869	>	);
870	>	painCave.isFatal = 0;
871	>	simError();
872	>	theEst = 0.05 * theEcr;
873	>	} else {
874	>	theEst= globals->getEST();
875		}
876	+
877	+	info[i].setEcr( theEcr, theEst );
878	+	}
879	+	}
880	+	}
881
882	<	current_mol = 0;
883	<	current_comp_mol = 0;
884	<	current_comp = 0;
885	<	current_atom_ndx = 0;
882	>	#ifdef IS_MPI
883	>	strcpy( checkPointMsg, "post processing checks out" );
884	>	MPIcheckPoint();
885	>	#endif // is_mpi
886
887	<	for( i=0; i < n_cells ; i++ ){
991	<	for( j=0; j < n_cells; j++ ){
992	<	for( k=0; k < n_cells; k++ ){
887	>	}
888
889	<	makeElement( i * cellx,
890	<	j * celly,
891	<	k * cellz );
889	>	void SimSetup::initSystemCoords( void ){
890	>	int i;
891	>
892	>	char* inName;
893
998	–	makeElement( i * cellx + 0.5 * cellx,
999	–	j * celly + 0.5 * celly,
1000	–	k * cellz );
894
895	<	makeElement( i * cellx,
896	<	j * celly + 0.5 * celly,
897	<	k * cellz + 0.5 * cellz );
895	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
896	>
897	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
898	>
899	>	if( globals->haveInitialConfig() ){
900	>
901	>	InitializeFromFile* fileInit;
902	>	#ifdef IS_MPI // is_mpi
903	>	if( worldRank == 0 ){
904	>	#endif //is_mpi
905	>	inName = globals->getInitialConfig();
906	>	double* tempDouble = new double[1000000];
907	>	fileInit = new InitializeFromFile( inName );
908	>	#ifdef IS_MPI
909	>	}else fileInit = new InitializeFromFile( NULL );
910	>	#endif
911	>	fileInit->readInit( info ); // default velocities on
912	>
913	>	delete fileInit;
914	>	}
915	>	else{
916	>
917	>	#ifdef IS_MPI
918	>
919	>	// no init from bass
920	>
921	>	sprintf( painCave.errMsg,
922	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
923	>	painCave.isFatal;
924	>	simError();
925	>
926	>	#else
927	>
928	>	initFromBass();
929	>
930	>
931	>	#endif
932	>	}
933	>
934	>	#ifdef IS_MPI
935	>	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
936	>	MPIcheckPoint();
937	>	#endif // is_mpi
938	>
939	>	}
940
941	<	makeElement( i * cellx + 0.5 * cellx,
942	<	j * celly,
943	<	k * cellz + 0.5 * cellz );
941	>
942	>	void SimSetup::makeOutNames( void ){
943	>
944	>	int k;
945	>
946	>
947	>	for(k=0; k<nInfo; k++){
948	>
949	>	#ifdef IS_MPI
950	>	if( worldRank == 0 ){
951	>	#endif // is_mpi
952	>
953	>	if( globals->haveFinalConfig() ){
954	>	strcpy( info[k].finalName, globals->getFinalConfig() );
955		}
956	+	else{
957	+	strcpy( info[k].finalName, inFileName );
958	+	char* endTest;
959	+	int nameLength = strlen( info[k].finalName );
960	+	endTest = &(info[k].finalName[nameLength - 5]);
961	+	if( !strcmp( endTest, ".bass" ) ){
962	+	strcpy( endTest, ".eor" );
963	+	}
964	+	else if( !strcmp( endTest, ".BASS" ) ){
965	+	strcpy( endTest, ".eor" );
966	+	}
967	+	else{
968	+	endTest = &(info[k].finalName[nameLength - 4]);
969	+	if( !strcmp( endTest, ".bss" ) ){
970	+	strcpy( endTest, ".eor" );
971		}
972	+	else if( !strcmp( endTest, ".mdl" ) ){
973	+	strcpy( endTest, ".eor" );
974	+	}
975	+	else{
976	+	strcat( info[k].finalName, ".eor" );
977	+	}
978		}
979	+	}
980	+
981	+	// make the sample and status out names
982	+
983	+	strcpy( info[k].sampleName, inFileName );
984	+	char* endTest;
985	+	int nameLength = strlen( info[k].sampleName );
986	+	endTest = &(info[k].sampleName[nameLength - 5]);
987	+	if( !strcmp( endTest, ".bass" ) ){
988	+	strcpy( endTest, ".dump" );
989	+	}
990	+	else if( !strcmp( endTest, ".BASS" ) ){
991	+	strcpy( endTest, ".dump" );
992	+	}
993	+	else{
994	+	endTest = &(info[k].sampleName[nameLength - 4]);
995	+	if( !strcmp( endTest, ".bss" ) ){
996	+	strcpy( endTest, ".dump" );
997	+	}
998	+	else if( !strcmp( endTest, ".mdl" ) ){
999	+	strcpy( endTest, ".dump" );
1000	+	}
1001	+	else{
1002	+	strcat( info[k].sampleName, ".dump" );
1003	+	}
1004	+	}
1005	+
1006	+	strcpy( info[k].statusName, inFileName );
1007	+	nameLength = strlen( info[k].statusName );
1008	+	endTest = &(info[k].statusName[nameLength - 5]);
1009	+	if( !strcmp( endTest, ".bass" ) ){
1010	+	strcpy( endTest, ".stat" );
1011	+	}
1012	+	else if( !strcmp( endTest, ".BASS" ) ){
1013	+	strcpy( endTest, ".stat" );
1014	+	}
1015	+	else{
1016	+	endTest = &(info[k].statusName[nameLength - 4]);
1017	+	if( !strcmp( endTest, ".bss" ) ){
1018	+	strcpy( endTest, ".stat" );
1019	+	}
1020	+	else if( !strcmp( endTest, ".mdl" ) ){
1021	+	strcpy( endTest, ".stat" );
1022	+	}
1023	+	else{
1024	+	strcat( info[k].statusName, ".stat" );
1025	+	}
1026	+	}
1027	+
1028	+	#ifdef IS_MPI
1029	+	}
1030	+	#endif // is_mpi
1031	+	}
1032	+	}
1033
1013	–	if( have_extra ){
1014	–	done = 0;
1034
1035	<	int start_ndx;
1036	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1037	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1035	>	void SimSetup::sysObjectsCreation( void ){
1036	>
1037	>	int i,k;
1038	>
1039	>	// create the forceField
1040
1041	<	if( i < n_cells ){
1041	>	createFF();
1042
1043	<	if( j < n_cells ){
1023	<	start_ndx = n_cells;
1024	<	}
1025	<	else start_ndx = 0;
1026	<	}
1027	<	else start_ndx = 0;
1043	>	// extract componentList
1044
1045	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1045	>	compList();
1046
1047	<	makeElement( i * cellx,
1048	<	j * celly,
1049	<	k * cellz );
1050	<	done = ( current_mol >= tot_nmol );
1047	>	// calc the number of atoms, bond, bends, and torsions
1048	>
1049	>	calcSysValues();
1050	>
1051	>	#ifdef IS_MPI
1052	>	// divide the molecules among the processors
1053	>
1054	>	mpiMolDivide();
1055	>	#endif //is_mpi
1056	>
1057	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1058	>
1059	>	makeSysArrays();
1060	>
1061	>	// make and initialize the molecules (all but atomic coordinates)
1062	>
1063	>	makeMolecules();
1064	>
1065	>	for(k=0; k<nInfo; k++){
1066	>	info[k].identArray = new int[info[k].n_atoms];
1067	>	for(i=0; i<info[k].n_atoms; i++){
1068	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1069	>	}
1070	>	}
1071	>	}
1072	>
1073	>
1074	>	void SimSetup::createFF( void ){
1075	>
1076	>	switch( ffCase ){
1077	>
1078	>	case FF_DUFF:
1079	>	the_ff = new DUFF();
1080	>	break;
1081	>
1082	>	case FF_LJ:
1083	>	the_ff = new LJFF();
1084	>	break;
1085	>
1086	>	case FF_EAM:
1087	>	the_ff = new EAM_FF();
1088	>	break;
1089	>
1090	>	default:
1091	>	sprintf( painCave.errMsg,
1092	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1093	>	painCave.isFatal = 1;
1094	>	simError();
1095	>	}
1096	>
1097	>	#ifdef IS_MPI
1098	>	strcpy( checkPointMsg, "ForceField creation successful" );
1099	>	MPIcheckPoint();
1100	>	#endif // is_mpi
1101	>
1102	>	}
1103	>
1104	>
1105	>	void SimSetup::compList( void ){
1106	>
1107	>	int i;
1108	>	char* id;
1109	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1110	>	LinkedMolStamp* currentStamp = NULL;
1111	>	comp_stamps = new MoleculeStamp*[n_components];
1112	>
1113	>	// make an array of molecule stamps that match the components used.
1114	>	// also extract the used stamps out into a separate linked list
1115	>
1116	>	for(i=0; i<nInfo; i++){
1117	>	info[i].nComponents = n_components;
1118	>	info[i].componentsNmol = components_nmol;
1119	>	info[i].compStamps = comp_stamps;
1120	>	info[i].headStamp = headStamp;
1121	>	}
1122	>
1123
1124	<	if( !done && n_per_extra > 1 ){
1037	<	makeElement( i * cellx + 0.5 * cellx,
1038	<	j * celly + 0.5 * celly,
1039	<	k * cellz );
1040	<	done = ( current_mol >= tot_nmol );
1041	<	}
1124	>	for( i=0; i<n_components; i++ ){
1125
1126	<	if( !done && n_per_extra > 2){
1127	<	makeElement( i * cellx,
1128	<	j * celly + 0.5 * celly,
1129	<	k * cellz + 0.5 * cellz );
1047	<	done = ( current_mol >= tot_nmol );
1048	<	}
1126	>	id = the_components[i]->getType();
1127	>	comp_stamps[i] = NULL;
1128	>
1129	>	// check to make sure the component isn't already in the list
1130
1131	<	if( !done && n_per_extra > 3){
1132	<	makeElement( i * cellx + 0.5 * cellx,
1133	<	j * celly,
1134	<	k * cellz + 0.5 * cellz );
1135	<	done = ( current_mol >= tot_nmol );
1136	<	}
1137	<	}
1131	>	comp_stamps[i] = headStamp->match( id );
1132	>	if( comp_stamps[i] == NULL ){
1133	>
1134	>	// extract the component from the list;
1135	>
1136	>	currentStamp = stamps->extractMolStamp( id );
1137	>	if( currentStamp == NULL ){
1138	>	sprintf( painCave.errMsg,
1139	>	"SimSetup error: Component \"%s\" was not found in the "
1140	>	"list of declared molecules\n",
1141	>	id );
1142	>	painCave.isFatal = 1;
1143	>	simError();
1144		}
1145	+
1146	+	headStamp->add( currentStamp );
1147	+	comp_stamps[i] = headStamp->match( id );
1148		}
1149		}
1150
1151	+	#ifdef IS_MPI
1152	+	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1153	+	MPIcheckPoint();
1154	+	#endif // is_mpi
1155
1156	<	for( i=0; i<simnfo->n_atoms; i++ ){
1157	<	simnfo->atoms[i]->set_vx( 0.0 );
1158	<	simnfo->atoms[i]->set_vy( 0.0 );
1159	<	simnfo->atoms[i]->set_vz( 0.0 );
1156	>
1157	>	}
1158	>
1159	>	void SimSetup::calcSysValues( void ){
1160	>	int i, j, k;
1161	>
1162	>	int *molMembershipArray;
1163	>
1164	>	tot_atoms = 0;
1165	>	tot_bonds = 0;
1166	>	tot_bends = 0;
1167	>	tot_torsions = 0;
1168	>	for( i=0; i<n_components; i++ ){
1169	>
1170	>	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1171	>	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1172	>	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1173	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1174		}
1175	+
1176	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1177	+	molMembershipArray = new int[tot_atoms];
1178	+
1179	+	for(i=0; i<nInfo; i++){
1180	+	info[i].n_atoms = tot_atoms;
1181	+	info[i].n_bonds = tot_bonds;
1182	+	info[i].n_bends = tot_bends;
1183	+	info[i].n_torsions = tot_torsions;
1184	+	info[i].n_SRI = tot_SRI;
1185	+	info[i].n_mol = tot_nmol;
1186	+
1187	+	info[i].molMembershipArray = molMembershipArray;
1188	+	}
1189		}
1190
1191	<	void SimSetup::makeElement( double x, double y, double z ){
1191	>	#ifdef IS_MPI
1192
1193	<	int k;
1194	<	AtomStamp* current_atom;
1195	<	DirectionalAtom* dAtom;
1196	<	double rotMat[3][3];
1193	>	void SimSetup::mpiMolDivide( void ){
1194	>
1195	>	int i, j, k;
1196	>	int localMol, allMol;
1197	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1198
1199	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1199	>	mpiSim = new mpiSimulation( info );
1200	>
1201	>	globalIndex = mpiSim->divideLabor();
1202
1203	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1204	<	if( !current_atom->havePosition() ){
1205	<	sprintf( painCave.errMsg,
1206	<	"SimSetup:initFromBass error.\n"
1207	<	"\tComponent %s, atom %s does not have a position specified.\n"
1208	<	"\tThe initialization routine is unable to give a start"
1209	<	" position.\n",
1210	<	comp_stamps[current_comp]->getID(),
1211	<	current_atom->getType() );
1212	<	painCave.isFatal = 1;
1213	<	simError();
1203	>	// set up the local variables
1204	>
1205	>	mol2proc = mpiSim->getMolToProcMap();
1206	>	molCompType = mpiSim->getMolComponentType();
1207	>
1208	>	allMol = 0;
1209	>	localMol = 0;
1210	>	local_atoms = 0;
1211	>	local_bonds = 0;
1212	>	local_bends = 0;
1213	>	local_torsions = 0;
1214	>	globalAtomIndex = 0;
1215	>
1216	>
1217	>	for( i=0; i<n_components; i++ ){
1218	>
1219	>	for( j=0; j<components_nmol[i]; j++ ){
1220	>
1221	>	if( mol2proc[allMol] == worldRank ){
1222	>
1223	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1224	>	local_bonds +=    comp_stamps[i]->getNBonds();
1225	>	local_bends +=    comp_stamps[i]->getNBends();
1226	>	local_torsions += comp_stamps[i]->getNTorsions();
1227	>	localMol++;
1228	>	}
1229	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1230	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1231	>	globalAtomIndex++;
1232	>	}
1233	>
1234	>	allMol++;
1235		}
1236	+	}
1237	+	local_SRI = local_bonds + local_bends + local_torsions;
1238	+
1239	+	info[0].n_atoms = mpiSim->getMyNlocal();
1240	+
1241	+	if( local_atoms != info[0].n_atoms ){
1242	+	sprintf( painCave.errMsg,
1243	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1244	+	" localAtom (%d) are not equal.\n",
1245	+	info[0].n_atoms,
1246	+	local_atoms );
1247	+	painCave.isFatal = 1;
1248	+	simError();
1249	+	}
1250
1251	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1252	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1253	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1251	>	info[0].n_bonds = local_bonds;
1252	>	info[0].n_bends = local_bends;
1253	>	info[0].n_torsions = local_torsions;
1254	>	info[0].n_SRI = local_SRI;
1255	>	info[0].n_mol = localMol;
1256
1257	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1257	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1258	>	MPIcheckPoint();
1259	>	}
1260	>
1261	>	#endif // is_mpi
1262
1097	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1263
1264	<	rotMat[0][0] = 1.0;
1265	<	rotMat[0][1] = 0.0;
1101	<	rotMat[0][2] = 0.0;
1264	>	void SimSetup::makeSysArrays( void ){
1265	>	int i, j, k, l;
1266
1267	<	rotMat[1][0] = 0.0;
1268	<	rotMat[1][1] = 1.0;
1269	<	rotMat[1][2] = 0.0;
1267	>	Atom** the_atoms;
1268	>	Molecule* the_molecules;
1269	>	Exclude** the_excludes;
1270
1271	<	rotMat[2][0] = 0.0;
1272	<	rotMat[2][1] = 0.0;
1273	<	rotMat[2][2] = 1.0;
1271	>
1272	>	for(l=0; l<nInfo; l++){
1273	>
1274	>	// create the atom and short range interaction arrays
1275	>
1276	>	the_atoms = new Atom*[info[l].n_atoms];
1277	>	the_molecules = new Molecule[info[l].n_mol];
1278	>	int molIndex;
1279
1280	<	dAtom->setA( rotMat );
1280	>	// initialize the molecule's stampID's
1281	>
1282	>	#ifdef IS_MPI
1283	>
1284	>
1285	>	molIndex = 0;
1286	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1287	>
1288	>	if(mol2proc[i] == worldRank ){
1289	>	the_molecules[molIndex].setStampID( molCompType[i] );
1290	>	the_molecules[molIndex].setMyIndex( molIndex );
1291	>	the_molecules[molIndex].setGlobalIndex( i );
1292	>	molIndex++;
1293	>	}
1294		}
1295	+
1296	+	#else // is_mpi
1297	+
1298	+	molIndex = 0;
1299	+	globalAtomIndex = 0;
1300	+	for(i=0; i<n_components; i++){
1301	+	for(j=0; j<components_nmol[i]; j++ ){
1302	+	the_molecules[molIndex].setStampID( i );
1303	+	the_molecules[molIndex].setMyIndex( molIndex );
1304	+	the_molecules[molIndex].setGlobalIndex( molIndex );
1305	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1306	+	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1307	+	globalAtomIndex++;
1308	+	}
1309	+	molIndex++;
1310	+	}
1311	+	}
1312	+
1313	+
1314	+	#endif // is_mpi
1315
1316	<	current_atom_ndx++;
1316	>
1317	>	if( info[l].n_SRI ){
1318	>
1319	>	Exclude::createArray(info[l].n_SRI);
1320	>	the_excludes = new Exclude*[info[l].n_SRI];
1321	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1322	>	the_excludes[ex] = new Exclude(ex);
1323	>	}
1324	>	info[l].globalExcludes = new int;
1325	>	info[l].n_exclude = info[l].n_SRI;
1326	>	}
1327	>	else{
1328	>
1329	>	Exclude::createArray( 1 );
1330	>	the_excludes = new Exclude*;
1331	>	the_excludes[0] = new Exclude(0);
1332	>	the_excludes[0]->setPair( 0,0 );
1333	>	info[l].globalExcludes = new int;
1334	>	info[l].globalExcludes[0] = 0;
1335	>	info[l].n_exclude = 0;
1336	>	}
1337	>
1338	>	// set the arrays into the SimInfo object
1339	>
1340	>	info[l].atoms = the_atoms;
1341	>	info[l].molecules = the_molecules;
1342	>	info[l].nGlobalExcludes = 0;
1343	>	info[l].excludes = the_excludes;
1344	>
1345	>	the_ff->setSimInfo( info );
1346	>
1347		}
1348	+	}
1349
1350	<	current_mol++;
1118	<	current_comp_mol++;
1350	>	void SimSetup::makeIntegrator( void ){
1351
1352	<	if( current_comp_mol >= components_nmol[current_comp] ){
1352	>	int k;
1353
1354	<	current_comp_mol = 0;
1355	<	current_comp++;
1354	>	NVT<RealIntegrator>*  myNVT = NULL;
1355	>	NPTi<RealIntegrator>* myNPTi = NULL;
1356	>	NPTf<RealIntegrator>* myNPTf = NULL;
1357	>	NPTim<RealIntegrator>* myNPTim = NULL;
1358	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1359	>
1360	>	for(k=0; k<nInfo; k++){
1361	>
1362	>	switch( ensembleCase ){
1363	>
1364	>	case NVE_ENS:
1365	>	if (globals->haveZconstraints()){
1366	>	setupZConstraint(info[k]);
1367	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1368	>	}
1369	>
1370	>	else
1371	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1372	>	break;
1373	>
1374	>	case NVT_ENS:
1375	>	if (globals->haveZconstraints()){
1376	>	setupZConstraint(info[k]);
1377	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1378	>	}
1379	>	else
1380	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1381	>
1382	>	myNVT->setTargetTemp(globals->getTargetTemp());
1383	>
1384	>	if (globals->haveTauThermostat())
1385	>	myNVT->setTauThermostat(globals->getTauThermostat());
1386	>
1387	>	else {
1388	>	sprintf( painCave.errMsg,
1389	>	"SimSetup error: If you use the NVT\n"
1390	>	"    ensemble, you must set tauThermostat.\n");
1391	>	painCave.isFatal = 1;
1392	>	simError();
1393	>	}
1394	>	break;
1395	>
1396	>	case NPTi_ENS:
1397	>	if (globals->haveZconstraints()){
1398	>	setupZConstraint(info[k]);
1399	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1400	>	}
1401	>	else
1402	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1403	>
1404	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1405	>
1406	>	if (globals->haveTargetPressure())
1407	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1408	>	else {
1409	>	sprintf( painCave.errMsg,
1410	>	"SimSetup error: If you use a constant pressure\n"
1411	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1412	>	painCave.isFatal = 1;
1413	>	simError();
1414	>	}
1415	>
1416	>	if( globals->haveTauThermostat() )
1417	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1418	>	else{
1419	>	sprintf( painCave.errMsg,
1420	>	"SimSetup error: If you use an NPT\n"
1421	>	"    ensemble, you must set tauThermostat.\n");
1422	>	painCave.isFatal = 1;
1423	>	simError();
1424	>	}
1425	>
1426	>	if( globals->haveTauBarostat() )
1427	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1428	>	else{
1429	>	sprintf( painCave.errMsg,
1430	>	"SimSetup error: If you use an NPT\n"
1431	>	"    ensemble, you must set tauBarostat.\n");
1432	>	painCave.isFatal = 1;
1433	>	simError();
1434	>	}
1435	>	break;
1436	>
1437	>	case NPTf_ENS:
1438	>	if (globals->haveZconstraints()){
1439	>	setupZConstraint(info[k]);
1440	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1441	>	}
1442	>	else
1443	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1444	>
1445	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1446	>
1447	>	if (globals->haveTargetPressure())
1448	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1449	>	else {
1450	>	sprintf( painCave.errMsg,
1451	>	"SimSetup error: If you use a constant pressure\n"
1452	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1453	>	painCave.isFatal = 1;
1454	>	simError();
1455	>	}
1456	>
1457	>	if( globals->haveTauThermostat() )
1458	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1459	>	else{
1460	>	sprintf( painCave.errMsg,
1461	>	"SimSetup error: If you use an NPT\n"
1462	>	"    ensemble, you must set tauThermostat.\n");
1463	>	painCave.isFatal = 1;
1464	>	simError();
1465	>	}
1466	>
1467	>	if( globals->haveTauBarostat() )
1468	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1469	>	else{
1470	>	sprintf( painCave.errMsg,
1471	>	"SimSetup error: If you use an NPT\n"
1472	>	"    ensemble, you must set tauBarostat.\n");
1473	>	painCave.isFatal = 1;
1474	>	simError();
1475	>	}
1476	>	break;
1477	>
1478	>	case NPTim_ENS:
1479	>	if (globals->haveZconstraints()){
1480	>	setupZConstraint(info[k]);
1481	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1482	>	}
1483	>	else
1484	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1485	>
1486	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1487	>
1488	>	if (globals->haveTargetPressure())
1489	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1490	>	else {
1491	>	sprintf( painCave.errMsg,
1492	>	"SimSetup error: If you use a constant pressure\n"
1493	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1494	>	painCave.isFatal = 1;
1495	>	simError();
1496	>	}
1497	>
1498	>	if( globals->haveTauThermostat() )
1499	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1500	>	else{
1501	>	sprintf( painCave.errMsg,
1502	>	"SimSetup error: If you use an NPT\n"
1503	>	"    ensemble, you must set tauThermostat.\n");
1504	>	painCave.isFatal = 1;
1505	>	simError();
1506	>	}
1507	>
1508	>	if( globals->haveTauBarostat() )
1509	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1510	>	else{
1511	>	sprintf( painCave.errMsg,
1512	>	"SimSetup error: If you use an NPT\n"
1513	>	"    ensemble, you must set tauBarostat.\n");
1514	>	painCave.isFatal = 1;
1515	>	simError();
1516	>	}
1517	>	break;
1518	>
1519	>	case NPTfm_ENS:
1520	>	if (globals->haveZconstraints()){
1521	>	setupZConstraint(info[k]);
1522	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1523	>	}
1524	>	else
1525	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1526	>
1527	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1528	>
1529	>	if (globals->haveTargetPressure())
1530	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1531	>	else {
1532	>	sprintf( painCave.errMsg,
1533	>	"SimSetup error: If you use a constant pressure\n"
1534	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1535	>	painCave.isFatal = 1;
1536	>	simError();
1537	>	}
1538	>
1539	>	if( globals->haveTauThermostat() )
1540	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1541	>	else{
1542	>	sprintf( painCave.errMsg,
1543	>	"SimSetup error: If you use an NPT\n"
1544	>	"    ensemble, you must set tauThermostat.\n");
1545	>	painCave.isFatal = 1;
1546	>	simError();
1547	>	}
1548	>
1549	>	if( globals->haveTauBarostat() )
1550	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1551	>	else{
1552	>	sprintf( painCave.errMsg,
1553	>	"SimSetup error: If you use an NPT\n"
1554	>	"    ensemble, you must set tauBarostat.\n");
1555	>	painCave.isFatal = 1;
1556	>	simError();
1557	>	}
1558	>	break;
1559	>
1560	>	default:
1561	>	sprintf( painCave.errMsg,
1562	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1563	>	painCave.isFatal = 1;
1564	>	simError();
1565	>	}
1566		}
1567		}
1568	+
1569	+	void SimSetup::initFortran( void ){
1570	+
1571	+	info[0].refreshSim();
1572	+
1573	+	if( !strcmp( info[0].mixingRule, "standard") ){
1574	+	the_ff->initForceField( LB_MIXING_RULE );
1575	+	}
1576	+	else if( !strcmp( info[0].mixingRule, "explicit") ){
1577	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1578	+	}
1579	+	else{
1580	+	sprintf( painCave.errMsg,
1581	+	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1582	+	info[0].mixingRule );
1583	+	painCave.isFatal = 1;
1584	+	simError();
1585	+	}
1586	+
1587	+
1588	+	#ifdef IS_MPI
1589	+	strcpy( checkPointMsg,
1590	+	"Successfully intialized the mixingRule for Fortran." );
1591	+	MPIcheckPoint();
1592	+	#endif // is_mpi
1593	+
1594	+	}
1595	+
1596	+	void SimSetup::setupZConstraint(SimInfo& theInfo)
1597	+	{
1598	+	int nZConstraints;
1599	+	ZconStamp** zconStamp;
1600	+
1601	+	if(globals->haveZconstraintTime()){
1602	+
1603	+	//add sample time of z-constraint  into SimInfo's property list
1604	+	DoubleData* zconsTimeProp = new DoubleData();
1605	+	zconsTimeProp->setID(ZCONSTIME_ID);
1606	+	zconsTimeProp->setData(globals->getZconsTime());
1607	+	theInfo.addProperty(zconsTimeProp);
1608	+	}
1609	+	else{
1610	+	sprintf( painCave.errMsg,
1611	+	"ZConstraint error: If you use an ZConstraint\n"
1612	+	" , you must set sample time.\n");
1613	+	painCave.isFatal = 1;
1614	+	simError();
1615	+	}
1616	+
1617	+	//push zconsTol into siminfo, if user does not specify
1618	+	//value for zconsTol, a default value will be used
1619	+	DoubleData* zconsTol = new DoubleData();
1620	+	zconsTol->setID(ZCONSTOL_ID);
1621	+	if(globals->haveZconsTol()){
1622	+	zconsTol->setData(globals->getZconsTol());
1623	+	}
1624	+	else{
1625	+	double defaultZConsTol = 0.01;
1626	+	sprintf( painCave.errMsg,
1627	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1628	+	" , default value %f is used.\n", defaultZConsTol);
1629	+	painCave.isFatal = 0;
1630	+	simError();
1631	+
1632	+	zconsTol->setData(defaultZConsTol);
1633	+	}
1634	+	theInfo.addProperty(zconsTol);
1635	+
1636	+	//set Force Substraction Policy
1637	+	StringData* zconsForcePolicy =  new StringData();
1638	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1639	+
1640	+	if(globals->haveZconsForcePolicy()){
1641	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1642	+	}
1643	+	else{
1644	+	sprintf( painCave.errMsg,
1645	+	"ZConstraint Warning: User does not set force substraction policy, "
1646	+	"average force substraction policy is used\n");
1647	+	painCave.isFatal = 0;
1648	+	simError();
1649	+	zconsForcePolicy->setData("BYNUMBER");
1650	+	}
1651	+
1652	+	theInfo.addProperty(zconsForcePolicy);
1653	+
1654	+	//Determine the name of ouput file and add it into SimInfo's property list
1655	+	//Be careful, do not use inFileName, since it is a pointer which
1656	+	//point to a string at master node, and slave nodes do not contain that string
1657	+
1658	+	string zconsOutput(theInfo.finalName);
1659	+
1660	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1661	+
1662	+	StringData* zconsFilename = new StringData();
1663	+	zconsFilename->setID(ZCONSFILENAME_ID);
1664	+	zconsFilename->setData(zconsOutput);
1665	+
1666	+	theInfo.addProperty(zconsFilename);
1667	+
1668	+	//setup index, pos and other parameters of z-constraint molecules
1669	+	nZConstraints = globals->getNzConstraints();
1670	+	theInfo.nZconstraints = nZConstraints;
1671	+
1672	+	zconStamp = globals->getZconStamp();
1673	+	ZConsParaItem tempParaItem;
1674	+
1675	+	ZConsParaData* zconsParaData = new ZConsParaData();
1676	+	zconsParaData->setID(ZCONSPARADATA_ID);
1677	+
1678	+	for(int i = 0; i < nZConstraints; i++){
1679	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1680	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1681	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1682	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1683	+
1684	+	zconsParaData->addItem(tempParaItem);
1685	+	}
1686	+
1687	+	//sort the parameters by index of molecules
1688	+	zconsParaData->sortByIndex();
1689	+
1690	+	//push data into siminfo, therefore, we can retrieve later
1691	+	theInfo.addProperty(zconsParaData);
1692	+
1693	+	}

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