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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 420 by mmeineke, Thu Mar 27 17:32:03 2003 UTC vs.
Revision 707 by mmeineke, Wed Aug 20 19:42:31 2003 UTC

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

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