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

Comparing:
branches/mmeineke/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/libmdtools/SimSetup.cpp (file contents), 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	<	the_sris = new SRI*[simnfo->n_SRI];
418	<	the_excludes = new int[2 * simnfo->n_SRI];
419	<	simnfo->globalExcludes = new int;
313	<	simnfo->n_exclude = tot_SRI;
314	<	}
315	<	else{
316	<
317	<	the_excludes = new int[2];
318	<	the_excludes[0] = 0;
319	<	the_excludes[1] = 0;
320	<	simnfo->globalExcludes = new int;
321	<	simnfo->globalExcludes[0] = 0;
416	>	double vel[3];
417	>	vel[0] = 0.0;
418	>	vel[1] = 0.0;
419	>	vel[2] = 0.0;
420
421	<	simnfo->n_exclude = 1;
422	<	}
421	>	temp1 = (double)tot_nmol / 4.0;
422	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
423	>	temp3 = ceil( temp2 );
424
425	<	// set the arrays into the SimInfo object
425	>	have_extra =0;
426	>	if( temp2 < temp3 ){ // we have a non-complete lattice
427	>	have_extra =1;
428
429	<	simnfo->atoms = the_atoms;
430	<	simnfo->sr_interactions = the_sris;
431	<	simnfo->nGlobalExcludes = 0;
432	<	simnfo->excludes = the_excludes;
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	<
334	<	// get some of the tricky things that may still be in the globals
335	<
336	<	if( simnfo->n_dipoles ){
337	<
338	<	if( !the_globals->haveRRF() ){
437	>	if( n_per_extra > 4){
438		sprintf( painCave.errMsg,
439	<	"SimSetup Error, system has dipoles, but no rRF was set.\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	<	if( !the_globals->haveDielectric() ){
445	<	sprintf( painCave.errMsg,
446	<	"SimSetup Error, system has dipoles, but no"
447	<	" dielectric was set.\n" );
448	<	painCave.isFatal = 1;
449	<	simError();
350	<	}
351	<
352	<	simnfo->rRF        = the_globals->getRRF();
353	<	simnfo->dielectric = the_globals->getDielectric();
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	<	#ifdef IS_MPI
453	<	strcpy( checkPointMsg, "rRf and dielectric check out" );
454	<	MPIcheckPoint();
455	<	#endif // is_mpi
360	<
361	<	if( the_globals->haveBox() ){
362	<	simnfo->box_x = the_globals->getBox();
363	<	simnfo->box_y = the_globals->getBox();
364	<	simnfo->box_z = the_globals->getBox();
365	<	}
366	<	else if( the_globals->haveDensity() ){
452	>	current_mol = 0;
453	>	current_comp_mol = 0;
454	>	current_comp = 0;
455	>	current_atom_ndx = 0;
456
457	<	double vol;
458	<	vol = (double)tot_nmol / the_globals->getDensity();
459	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
371	<	simnfo->box_y = simnfo->box_x;
372	<	simnfo->box_z = simnfo->box_x;
373	<	}
374	<	else{
375	<	if( !the_globals->haveBoxX() ){
376	<	sprintf( painCave.errMsg,
377	<	"SimSetup error, no periodic BoxX size given.\n" );
378	<	painCave.isFatal = 1;
379	<	simError();
380	<	}
381	<	simnfo->box_x = the_globals->getBoxX();
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( !the_globals->haveBoxY() ){
462	<	sprintf( painCave.errMsg,
463	<	"SimSetup error, no periodic BoxY size given.\n" );
464	<	painCave.isFatal = 1;
465	<	simError();
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
401	<	strcpy( checkPointMsg, "Box size set up" );
402	<	MPIcheckPoint();
403	<	#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 ){
417	<	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 ){
425	<	makeTorsions();
426	<	}
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	+	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
542
543	+	current_atom = comp_stamps[current_comp]->getAtom( k );
544	+	if( !current_atom->havePosition() ){
545	+	sprintf( painCave.errMsg,
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	+
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	+	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
563
564	+	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
565
566	<	if( the_globals->haveInitialConfig() ){
567	<
568	<	InitializeFromFile* fileInit;
436	<	#ifdef IS_MPI // is_mpi
437	<	if( worldRank == 0 ){
438	<	#endif //is_mpi
439	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
440	<	#ifdef IS_MPI
441	<	}else fileInit = new InitializeFromFile( NULL );
442	<	#endif
443	<	fileInit->read_xyz( simnfo ); // default velocities on
566	>	rotMat[0][0] = 1.0;
567	>	rotMat[0][1] = 0.0;
568	>	rotMat[0][2] = 0.0;
569
570	<	delete fileInit;
571	<	}
572	<	else{
570	>	rotMat[1][0] = 0.0;
571	>	rotMat[1][1] = 1.0;
572	>	rotMat[1][2] = 0.0;
573
574	<	#ifdef IS_MPI
574	>	rotMat[2][0] = 0.0;
575	>	rotMat[2][1] = 0.0;
576	>	rotMat[2][2] = 1.0;
577
578	<	// no init from bass
579	<
453	<	sprintf( painCave.errMsg,
454	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
455	<	painCave.isFatal;
456	<	simError();
457	<
458	<	#else
578	>	dAtom->setA( rotMat );
579	>	}
580
581	<	initFromBass();
581	>	current_atom_ndx++;
582	>	}
583
584	+	current_mol++;
585	+	current_comp_mol++;
586
587	<	#endif
464	<	}
587	>	if( current_comp_mol >= components_nmol[current_comp] ){
588
589	<	#ifdef IS_MPI
590	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
591	<	MPIcheckPoint();
592	<	#endif // is_mpi
589	>	current_comp_mol = 0;
590	>	current_comp++;
591	>	}
592	>	}
593
594
595	<
596	<
474	<
595	>	void SimSetup::gatherInfo( void ){
596	>	int i,j,k;
597
598	<
599	<	#ifdef IS_MPI
478	<	if( worldRank == 0 ){
479	<	#endif // is_mpi
480	<
481	<	if( the_globals->haveFinalConfig() ){
482	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
483	<	}
484	<	else{
485	<	strcpy( simnfo->finalName, inFileName );
486	<	char* endTest;
487	<	int nameLength = strlen( simnfo->finalName );
488	<	endTest = &(simnfo->finalName[nameLength - 5]);
489	<	if( !strcmp( endTest, ".bass" ) ){
490	<	strcpy( endTest, ".eor" );
491	<	}
492	<	else if( !strcmp( endTest, ".BASS" ) ){
493	<	strcpy( endTest, ".eor" );
494	<	}
495	<	else{
496	<	endTest = &(simnfo->finalName[nameLength - 4]);
497	<	if( !strcmp( endTest, ".bss" ) ){
498	<	strcpy( endTest, ".eor" );
499	<	}
500	<	else if( !strcmp( endTest, ".mdl" ) ){
501	<	strcpy( endTest, ".eor" );
502	<	}
503	<	else{
504	<	strcat( simnfo->finalName, ".eor" );
505	<	}
506	<	}
507	<	}
508	<
509	<	// make the sample and status out names
510	<
511	<	strcpy( simnfo->sampleName, inFileName );
512	<	char* endTest;
513	<	int nameLength = strlen( simnfo->sampleName );
514	<	endTest = &(simnfo->sampleName[nameLength - 5]);
515	<	if( !strcmp( endTest, ".bass" ) ){
516	<	strcpy( endTest, ".dump" );
517	<	}
518	<	else if( !strcmp( endTest, ".BASS" ) ){
519	<	strcpy( endTest, ".dump" );
520	<	}
521	<	else{
522	<	endTest = &(simnfo->sampleName[nameLength - 4]);
523	<	if( !strcmp( endTest, ".bss" ) ){
524	<	strcpy( endTest, ".dump" );
525	<	}
526	<	else if( !strcmp( endTest, ".mdl" ) ){
527	<	strcpy( endTest, ".dump" );
528	<	}
529	<	else{
530	<	strcat( simnfo->sampleName, ".dump" );
531	<	}
532	<	}
533	<
534	<	strcpy( simnfo->statusName, inFileName );
535	<	nameLength = strlen( simnfo->statusName );
536	<	endTest = &(simnfo->statusName[nameLength - 5]);
537	<	if( !strcmp( endTest, ".bass" ) ){
538	<	strcpy( endTest, ".stat" );
539	<	}
540	<	else if( !strcmp( endTest, ".BASS" ) ){
541	<	strcpy( endTest, ".stat" );
542	<	}
543	<	else{
544	<	endTest = &(simnfo->statusName[nameLength - 4]);
545	<	if( !strcmp( endTest, ".bss" ) ){
546	<	strcpy( endTest, ".stat" );
547	<	}
548	<	else if( !strcmp( endTest, ".mdl" ) ){
549	<	strcpy( endTest, ".stat" );
550	<	}
551	<	else{
552	<	strcat( simnfo->statusName, ".stat" );
553	<	}
554	<	}
555	<
556	<	#ifdef IS_MPI
557	<	}
558	<	#endif // is_mpi
559	<
560	<	// set the status, sample, and themal kick times
561	<
562	<	if( the_globals->haveSampleTime() ){
563	<	simnfo->sampleTime = the_globals->getSampleTime();
564	<	simnfo->statusTime = simnfo->sampleTime;
565	<	simnfo->thermalTime = simnfo->sampleTime;
566	<	}
567	<	else{
568	<	simnfo->sampleTime = the_globals->getRunTime();
569	<	simnfo->statusTime = simnfo->sampleTime;
570	<	simnfo->thermalTime = simnfo->sampleTime;
571	<	}
598	>	ensembleCase = -1;
599	>	ffCase = -1;
600
601	<	if( the_globals->haveStatusTime() ){
574	<	simnfo->statusTime = the_globals->getStatusTime();
575	<	}
601	>	// set the easy ones first
602
603	<	if( the_globals->haveThermalTime() ){
604	<	simnfo->thermalTime = the_globals->getThermalTime();
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
581	–	// check for the temperature set flag
610
611	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
611	>	// get the forceField
612
613	+	strcpy( force_field, globals->getForceField() );
614
615	<	//   // make the longe range forces and the integrator
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. Unrecognized force field -> %s\n",
621	>	force_field );
622	>	painCave.isFatal = 1;
623	>	simError();
624	>	}
625
626	<	//   new AllLong( simnfo );
626	>	// get the ensemble
627
628	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
591	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
592	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
593	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
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	+	// get the mixing rule
653
654	<	// initialize the Fortran
654	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
655	>	info[i].usePBC = globals->getPBC();
656	>	}
657
658	<	simnfo->refreshSim();
659	<
660	<	if( !strcmp( simnfo->mixingRule, "standard") ){
661	<	the_ff->initForceField( LB_MIXING_RULE );
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	>
663	>
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	>	tot_nmol = 0;
669	>	for( i=0; i<n_components; i++ ){
670	>
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	>	tot_nmol += the_components[i]->getNMol();
681	>	components_nmol[i] = the_components[i]->getNMol();
682	>	}
683		}
604	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
605	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
606	–	}
684		else{
685		sprintf( painCave.errMsg,
686	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
687	<	simnfo->mixingRule );
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	+	if( globals->haveStatusTime() ){
711	+	info[i].statusTime = globals->getStatusTime();
712	+	}
713	+
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	+	// 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	+	info[i].setBox( boxVector );
731	+	}
732	+	else if( globals->haveDensity() ){
733	+
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	+	boxVector[0] = globals->getBoxX();
750	+
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	+	boxVector[1] = globals->getBoxY();
758	+
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	+	boxVector[2] = globals->getBoxZ();
766	+
767	+	info[i].setBox( boxVector );
768	+	}
769	+
770	+	}
771	+
772		#ifdef IS_MPI
773	<	strcpy( checkPointMsg,
618	<	"Successfully intialized the mixingRule for Fortran." );
773	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
774		MPIcheckPoint();
775		#endif // is_mpi
776	+
777		}
778
623	–	void SimSetup::makeAtoms( void ){
779
780	<	int i, j, k, index;
781	<	double ux, uy, uz, uSqr, u;
782	<	AtomStamp* current_atom;
780	>	void SimSetup::finalInfoCheck( void ){
781	>	int index;
782	>	int usesDipoles;
783	>	int i;
784
785	<	DirectionalAtom* dAtom;
786	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
787	<
788	<	lMolIndex = 0;
789	<	molIndex = 0;
790	<	index = 0;
791	<	for( i=0; i<n_components; i++ ){
792	<
793	<	for( j=0; j<components_nmol[i]; j++ ){
794	<
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	<	if( mpiSim->getMyMolStart() <= molIndex &&
797	<	molIndex <= mpiSim->getMyMolEnd() ){
642	<	#endif // is_mpi
643	<
644	<	molStart = index;
645	<	nMemb = comp_stamps[i]->getNAtoms();
646	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
647	<
648	<	current_atom = comp_stamps[i]->getAtom( k );
649	<	if( current_atom->haveOrientation() ){
650	<
651	<	dAtom = new DirectionalAtom(index);
652	<	simnfo->n_oriented++;
653	<	the_atoms[index] = dAtom;
654	<
655	<	ux = current_atom->getOrntX();
656	<	uy = current_atom->getOrntY();
657	<	uz = current_atom->getOrntZ();
658	<
659	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
660	<
661	<	u = sqrt( uSqr );
662	<	ux = ux / u;
663	<	uy = uy / u;
664	<	uz = uz / u;
665	<
666	<	dAtom->setSUx( ux );
667	<	dAtom->setSUy( uy );
668	<	dAtom->setSUz( uz );
669	<	}
670	<	else{
671	<	the_atoms[index] = new GeneralAtom(index);
672	<	}
673	<	the_atoms[index]->setType( current_atom->getType() );
674	<	the_atoms[index]->setIndex( index );
675	<
676	<	// increment the index and repeat;
677	<	index++;
678	<	}
679	<
680	<	molEnd = index -1;
681	<	the_molecules[lMolIndex].setNMembers( nMemb );
682	<	the_molecules[lMolIndex].setStartAtom( molStart );
683	<	the_molecules[lMolIndex].setEndAtom( molEnd );
684	<	the_molecules[lMolIndex].setStampID( i );
685	<	lMolIndex++;
686	<
687	<	#ifdef IS_MPI
688	<	}
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	<	molIndex++;
806	<	}
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	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
884	<
885	<	delete[] globalIndex;
883	>	strcpy( checkPointMsg, "post processing checks out" );
884	>	MPIcheckPoint();
885	>	#endif // is_mpi
886
700	–	mpiSim->mpiRefresh();
701	–	#endif //IS_MPI
702	–
703	–	the_ff->initializeAtoms();
887		}
888
889	<	void SimSetup::makeBonds( void ){
889	>	void SimSetup::initSystemCoords( void ){
890	>	int i;
891	>
892	>	char* inName;
893
894	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
709	<	bond_pair* the_bonds;
710	<	BondStamp* current_bond;
894	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
895
896	<	the_bonds = new bond_pair[tot_bonds];
897	<	index = 0;
898	<	offset = 0;
899	<	molIndex = 0;
900	<
901	<	for( i=0; i<n_components; i++ ){
902	<
903	<	for( j=0; j<components_nmol[i]; j++ ){
904	<
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	<	if( mpiSim->getMyMolStart() <= molIndex &&
909	<	molIndex <= mpiSim->getMyMolEnd() ){
910	<	#endif // is_mpi
911	<
912	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
913	<
914	<	current_bond = comp_stamps[i]->getBond( k );
915	<	the_bonds[index].a = current_bond->getA() + offset;
916	<	the_bonds[index].b = current_bond->getB() + offset;
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
732	–	exI = the_bonds[index].a;
733	–	exJ = the_bonds[index].b;
940
941	<	// exclude_I must always be the smaller of the pair
942	<	if( exI > exJ ){
943	<	tempEx = exI;
738	<	exI = exJ;
739	<	exJ = tempEx;
740	<	}
941	>	void SimSetup::makeOutNames( void ){
942	>
943	>	int k;
944
945	<
946	<	#ifdef IS_MPI
945	>
946	>	for(k=0; k<nInfo; k++){
947
745	–	the_excludes[index*2] =
746	–	the_atoms[exI]->getGlobalIndex() + 1;
747	–	the_excludes[index*2 + 1] =
748	–	the_atoms[exJ]->getGlobalIndex() + 1;
749	–
750	–	#else  // isn't MPI
751	–
752	–	the_excludes[index*2] =     exI + 1;
753	–	the_excludes[index*2 + 1] = exJ + 1;
754	–	// fortran index from 1 (hence the +1 in the indexing)
755	–	#endif  //is_mpi
756	–
757	–	// increment the index and repeat;
758	–	index++;
759	–	}
760	–	offset += comp_stamps[i]->getNAtoms();
761	–
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	<	#endif //is_mpi
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	<	molIndex++;
981	<	}
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	<
998	<	the_ff->initializeBonds( the_bonds );
999	<	}
1000	<
1001	<	void SimSetup::makeBends( void ){
997	>	else if( !strcmp( endTest, ".mdl" ) ){
998	>	strcpy( endTest, ".dump" );
999	>	}
1000	>	else{
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
1033	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1034	<	bend_set* the_bends;
777	<	BendStamp* current_bend;
778	<	LinkedAssign* extras;
779	<	LinkedAssign* current_extra;
1033	>
1034	>	void SimSetup::sysObjectsCreation( void ){
1035
1036	+	int i,k;
1037	+
1038	+	// create the forceField
1039
1040	<	the_bends = new bend_set[tot_bends];
783	<	index = 0;
784	<	offset = 0;
785	<	molIndex = 0;
786	<	for( i=0; i<n_components; i++ ){
1040	>	createFF();
1041
1042	<	for( j=0; j<components_nmol[i]; j++ ){
1042	>	// extract componentList
1043
1044	<	#ifdef IS_MPI
791	<	if( mpiSim->getMyMolStart() <= molIndex &&
792	<	molIndex <= mpiSim->getMyMolEnd() ){
793	<	#endif // is_mpi
1044	>	compList();
1045
1046	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
796	<
797	<	current_bend = comp_stamps[i]->getBend( k );
798	<	the_bends[index].a = current_bend->getA() + offset;
799	<	the_bends[index].b = current_bend->getB() + offset;
800	<	the_bends[index].c = current_bend->getC() + offset;
801	<
802	<	if( current_bend->haveExtras() ){
803	<
804	<	extras = current_bend->getExtras();
805	<	current_extra = extras;
806	<
807	<	while( current_extra != NULL ){
808	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
809	<
810	<	switch( current_extra->getType() ){
811	<
812	<	case 0:
813	<	the_bends[index].ghost =
814	<	current_extra->getInt() + offset;
815	<	the_bends[index].isGhost = 1;
816	<	break;
817	<
818	<	case 1:
819	<	the_bends[index].ghost =
820	<	(int)current_extra->getDouble() + offset;
821	<	the_bends[index].isGhost = 1;
822	<	break;
823	<
824	<	default:
825	<	sprintf( painCave.errMsg,
826	<	"SimSetup Error: ghostVectorSource was neiter a "
827	<	"double nor an int.\n"
828	<	"-->Bend[%d] in %s\n",
829	<	k, comp_stamps[i]->getID() );
830	<	painCave.isFatal = 1;
831	<	simError();
832	<	}
833	<	}
834	<
835	<	else{
836	<
837	<	sprintf( painCave.errMsg,
838	<	"SimSetup Error: unhandled bend assignment:\n"
839	<	"    -->%s in Bend[%d] in %s\n",
840	<	current_extra->getlhs(),
841	<	k, comp_stamps[i]->getID() );
842	<	painCave.isFatal = 1;
843	<	simError();
844	<	}
845	<
846	<	current_extra = current_extra->getNext();
847	<	}
848	<	}
849	<
850	<	if( !the_bends[index].isGhost ){
851	<
852	<	exI = the_bends[index].a;
853	<	exJ = the_bends[index].c;
854	<	}
855	<	else{
856	<
857	<	exI = the_bends[index].a;
858	<	exJ = the_bends[index].b;
859	<	}
860	<
861	<	// exclude_I must always be the smaller of the pair
862	<	if( exI > exJ ){
863	<	tempEx = exI;
864	<	exI = exJ;
865	<	exJ = tempEx;
866	<	}
1046	>	// calc the number of atoms, bond, bends, and torsions
1047
1048	+	calcSysValues();
1049
1050		#ifdef IS_MPI
1051	<
1052	<	the_excludes[(index + tot_bonds)*2] =
1053	<	the_atoms[exI]->getGlobalIndex() + 1;
873	<	the_excludes[(index + tot_bonds)*2 + 1] =
874	<	the_atoms[exJ]->getGlobalIndex() + 1;
875	<
876	<	#else  // isn't MPI
877	<
878	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
879	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
880	<	// fortran index from 1 (hence the +1 in the indexing)
881	<	#endif  //is_mpi
882	<
883	<
884	<	// increment the index and repeat;
885	<	index++;
886	<	}
887	<	offset += comp_stamps[i]->getNAtoms();
888	<
889	<	#ifdef IS_MPI
890	<	}
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	<	molIndex++;
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
897	–	#ifdef IS_MPI
898	–	sprintf( checkPointMsg,
899	–	"Successfully created the bends list.\n" );
900	–	MPIcheckPoint();
901	–	#endif // is_mpi
902	–
1072
1073	<	the_ff->initializeBends( the_bends );
905	<	}
1073	>	void SimSetup::createFF( void ){
1074
1075	<	void SimSetup::makeTorsions( void ){
1075	>	switch( ffCase ){
1076
1077	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1078	<	torsion_set* the_torsions;
1079	<	TorsionStamp* current_torsion;
1077	>	case FF_DUFF:
1078	>	the_ff = new DUFF();
1079	>	break;
1080
1081	<	the_torsions = new torsion_set[tot_torsions];
1082	<	index = 0;
1083	<	offset = 0;
916	<	molIndex = 0;
917	<	for( i=0; i<n_components; i++ ){
1081	>	case FF_LJ:
1082	>	the_ff = new LJFF();
1083	>	break;
1084
1085	<	for( j=0; j<components_nmol[i]; j++ ){
1085	>	case FF_EAM:
1086	>	the_ff = new EAM_FF();
1087	>	break;
1088
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		#ifdef IS_MPI
1097	<	if( mpiSim->getMyMolStart() <= molIndex &&
1098	<	molIndex <= mpiSim->getMyMolEnd() ){
1099	<	#endif // is_mpi
1097	>	strcpy( checkPointMsg, "ForceField creation successful" );
1098	>	MPIcheckPoint();
1099	>	#endif // is_mpi
1100
1101	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1101	>	}
1102
928	–	current_torsion = comp_stamps[i]->getTorsion( k );
929	–	the_torsions[index].a = current_torsion->getA() + offset;
930	–	the_torsions[index].b = current_torsion->getB() + offset;
931	–	the_torsions[index].c = current_torsion->getC() + offset;
932	–	the_torsions[index].d = current_torsion->getD() + offset;
1103
1104	<	exI = the_torsions[index].a;
935	<	exJ = the_torsions[index].d;
1104	>	void SimSetup::compList( void ){
1105
1106	<
1107	<	// exclude_I must always be the smaller of the pair
1108	<	if( exI > exJ ){
1109	<	tempEx = exI;
1110	<	exI = exJ;
1111	<	exJ = tempEx;
1112	<	}
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	<	#ifdef IS_MPI
1126	<
1127	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
1128	<	the_atoms[exI]->getGlobalIndex() + 1;
950	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
951	<	the_atoms[exJ]->getGlobalIndex() + 1;
952	<
953	<	#else  // isn't MPI
954	<
955	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
956	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
957	<	// fortran indexes from 1 (hence the +1 in the indexing)
958	<	#endif  //is_mpi
959	<
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	<	// increment the index and repeat;
1131	<	index++;
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	<	offset += comp_stamps[i]->getNAtoms();
1144	>
1145	>	headStamp->add( currentStamp );
1146	>	comp_stamps[i] = headStamp->match( id );
1147	>	}
1148	>	}
1149
1150		#ifdef IS_MPI
1151	<	}
1152	<	#endif //is_mpi
1151	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1152	>	MPIcheckPoint();
1153	>	#endif // is_mpi
1154
970	–	molIndex++;
971	–	}
972	–	}
1155
974	–	the_ff->initializeTorsions( the_torsions );
1156		}
1157
1158	<	void SimSetup::initFromBass( void ){
978	<
1158	>	void SimSetup::calcSysValues( void ){
1159		int i, j, k;
1160	<	int n_cells;
1161	<	double cellx, celly, cellz;
1162	<	double temp1, temp2, temp3;
1163	<	int n_per_extra;
1164	<	int n_extra;
1165	<	int have_extra, done;
1166	<
1167	<	temp1 = (double)tot_nmol / 4.0;
1168	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1169	<	temp3 = ceil( temp2 );
1170	<
1171	<	have_extra =0;
1172	<	if( temp2 < temp3 ){ // we have a non-complete lattice
993	<	have_extra =1;
994	<
995	<	n_cells = (int)temp3 - 1;
996	<	cellx = simnfo->box_x / temp3;
997	<	celly = simnfo->box_y / temp3;
998	<	cellz = simnfo->box_z / temp3;
999	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1000	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1001	<	n_per_extra = (int)ceil( temp1 );
1002	<
1003	<	if( n_per_extra > 4){
1004	<	sprintf( painCave.errMsg,
1005	<	"SimSetup error. There has been an error in constructing"
1006	<	" the non-complete lattice.\n" );
1007	<	painCave.isFatal = 1;
1008	<	simError();
1009	<	}
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	<	else{
1175	<	n_cells = (int)temp3;
1176	<	cellx = simnfo->box_x / temp3;
1177	<	celly = simnfo->box_y / temp3;
1178	<	cellz = simnfo->box_z / temp3;
1179	<	}
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	<	current_mol = 0;
1019	<	current_comp_mol = 0;
1020	<	current_comp = 0;
1021	<	current_atom_ndx = 0;
1190	>	#ifdef IS_MPI
1191
1192	<	for( i=0; i < n_cells ; i++ ){
1193	<	for( j=0; j < n_cells; j++ ){
1194	<	for( k=0; k < n_cells; k++ ){
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	<	makeElement( i * cellx,
1199	<	j * celly,
1200	<	k * cellz );
1198	>	mpiSim = new mpiSimulation( info );
1199	>
1200	>	globalIndex = mpiSim->divideLabor();
1201
1202	<	makeElement( i * cellx + 0.5 * cellx,
1203	<	j * celly + 0.5 * celly,
1204	<	k * cellz );
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
1035	–	makeElement( i * cellx,
1036	–	j * celly + 0.5 * celly,
1037	–	k * cellz + 0.5 * cellz );
1215
1216	<	makeElement( i * cellx + 0.5 * cellx,
1217	<	j * celly,
1218	<	k * cellz + 0.5 * cellz );
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	<	if( have_extra ){
1251	<	done = 0;
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	<	int start_ndx;
1257	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1258	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1256	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1257	>	MPIcheckPoint();
1258	>	}
1259	>
1260	>	#endif // is_mpi
1261
1053	–	if( i < n_cells ){
1262
1263	<	if( j < n_cells ){
1264	<	start_ndx = n_cells;
1057	<	}
1058	<	else start_ndx = 0;
1059	<	}
1060	<	else start_ndx = 0;
1263	>	void SimSetup::makeSysArrays( void ){
1264	>	int i, j, k, l;
1265
1266	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1266	>	Atom** the_atoms;
1267	>	Molecule* the_molecules;
1268	>	Exclude** the_excludes;
1269
1270	<	makeElement( i * cellx,
1271	<	j * celly,
1272	<	k * cellz );
1273	<	done = ( current_mol >= tot_nmol );
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	<	if( !done && n_per_extra > 1 ){
1280	<	makeElement( i * cellx + 0.5 * cellx,
1281	<	j * celly + 0.5 * celly,
1282	<	k * cellz );
1283	<	done = ( current_mol >= tot_nmol );
1284	<	}
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
1076	–	if( !done && n_per_extra > 2){
1077	–	makeElement( i * cellx,
1078	–	j * celly + 0.5 * celly,
1079	–	k * cellz + 0.5 * cellz );
1080	–	done = ( current_mol >= tot_nmol );
1081	–	}
1315
1316	<	if( !done && n_per_extra > 3){
1317	<	makeElement( i * cellx + 0.5 * cellx,
1318	<	j * celly,
1319	<	k * cellz + 0.5 * cellz );
1320	<	done = ( current_mol >= tot_nmol );
1321	<	}
1089	<	}
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	<	}
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	<	for( i=0; i<simnfo->n_atoms; i++ ){
1340	<	simnfo->atoms[i]->set_vx( 0.0 );
1341	<	simnfo->atoms[i]->set_vy( 0.0 );
1342	<	simnfo->atoms[i]->set_vz( 0.0 );
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	<	void SimSetup::makeElement( double x, double y, double z ){
1349	>	void SimSetup::makeIntegrator( void ){
1350
1351		int k;
1105	–	AtomStamp* current_atom;
1106	–	DirectionalAtom* dAtom;
1107	–	double rotMat[3][3];
1352
1353	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
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	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1370	<	if( !current_atom->havePosition() ){
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:initFromBass error.\n"
1115	<	"\tComponent %s, atom %s does not have a position specified.\n"
1116	<	"\tThe initialization routine is unable to give a start"
1117	<	" position.\n",
1118	<	comp_stamps[current_comp]->getID(),
1119	<	current_atom->getType() );
1561	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1562		painCave.isFatal = 1;
1563		simError();
1564		}
1565	+	}
1566	+	}
1567
1568	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1125	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1126	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1568	>	void SimSetup::initFortran( void ){
1569
1570	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
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
1130	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1586
1587	<	rotMat[0][0] = 1.0;
1588	<	rotMat[0][1] = 0.0;
1589	<	rotMat[0][2] = 0.0;
1587	>	#ifdef IS_MPI
1588	>	strcpy( checkPointMsg,
1589	>	"Successfully intialized the mixingRule for Fortran." );
1590	>	MPIcheckPoint();
1591	>	#endif // is_mpi
1592
1593	<	rotMat[1][0] = 0.0;
1137	<	rotMat[1][1] = 1.0;
1138	<	rotMat[1][2] = 0.0;
1593	>	}
1594
1595	<	rotMat[2][0] = 0.0;
1596	<	rotMat[2][1] = 0.0;
1597	<	rotMat[2][2] = 1.0;
1595	>	void SimSetup::setupZConstraint(SimInfo& theInfo)
1596	>	{
1597	>	int nZConstraints;
1598	>	ZconStamp** zconStamp;
1599
1600	<	dAtom->setA( rotMat );
1601	<	}
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	<	current_atom_ndx++;
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	<	current_mol++;
1632	<	current_comp_mol++;
1631	>	zconsTol->setData(defaultZConsTol);
1632	>	}
1633	>	theInfo.addProperty(zconsTol);
1634
1635	<	if( current_comp_mol >= components_nmol[current_comp] ){
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	<	current_comp_mol = 0;
1672	<	current_comp++;
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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