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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 412 by mmeineke, Wed Mar 26 21:50:33 2003 UTC vs.
Revision 658 by tim, Thu Jul 31 15:35:07 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6
7		#include "SimSetup.hpp"
8		#include "parse_me.h"
#	Line 12 | Line 14 | SimSetup::SimSetup(){
14		#include "mpiSimulation.hpp"
15		#endif
16
17	+	// some defines for ensemble and Forcefield  cases
18	+
19	+	#define NVE_ENS   0
20	+	#define NVT_ENS   1
21	+	#define NPTi_ENS  2
22	+	#define NPTf_ENS  3
23	+	#define NPTim_ENS 4
24	+	#define NPTfm_ENS 5
25	+	#define NVEZCONS_ENS 6
26	+
27	+
28	+	#define FF_DUFF 0
29	+	#define FF_LJ   1
30	+	#define FF_EAM  2
31	+
32	+	using namespace std;
33	+
34		SimSetup::SimSetup(){
35	+
36	+	isInfoArray = 0;
37	+	nInfo = 1;
38	+
39		stamps = new MakeStamps();
40		globals = new Globals();
41
42	+
43		#ifdef IS_MPI
44		strcpy( checkPointMsg, "SimSetup creation successful" );
45		MPIcheckPoint();
#	Line 27 | Line 51 | void SimSetup::parseFile( char* fileName ){
51		delete globals;
52		}
53
54	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
55	+	info = the_info;
56	+	nInfo = theNinfo;
57	+	isInfoArray = 1;
58	+	}
59	+
60	+
61		void SimSetup::parseFile( char* fileName ){
62
63		#ifdef IS_MPI
#	Line 64 | Line 95 | void SimSetup::createSim( void ){
95
96		void SimSetup::createSim( void ){
97
98	<	MakeStamps *the_stamps;
99	<	Globals* the_globals;
100	<	int i, j;
98	>	int i, j, k, globalAtomIndex;
99	>
100	>	// gather all of the information from the Bass file
101	>
102	>	gatherInfo();
103
104	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
104	>	// creation of complex system objects
105
106	<	// 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();
106	>	sysObjectsCreation();
107
108	<	// get the ones we know are there, yet still may need some work.
109	<	n_components = the_globals->getNComponents();
110	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
108	>	// check on the post processing info
109	>
110	>	finalInfoCheck();
111
112	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
112	>	// initialize the system coordinates
113
114	+	initSystemCoords();
115	+
116
117	<	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	<	}
117	>	// make the output filenames
118
119	+	makeOutNames();
120	+
121	+	// make the integrator
122	+
123	+	makeIntegrator();
124	+
125		#ifdef IS_MPI
126	<	strcpy( checkPointMsg, "ForceField creation successful" );
127	<	MPIcheckPoint();
106	<	#endif // is_mpi
126	>	mpiSim->mpiRefresh();
127	>	#endif
128
129	<
129	>	// initialize the Fortran
130
131	<	// 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];
131	>	initFortran();
132
115	–	if( !the_globals->haveNMol() ){
116	–	// we don't have the total number of molecules, so we assume it is
117	–	// given in each component
133
119	–	tot_nmol = 0;
120	–	for( i=0; i<n_components; i++ ){
134
135	<	if( !the_components[i]->haveNMol() ){
123	<	// we have a problem
124	<	sprintf( painCave.errMsg,
125	<	"SimSetup Error. No global NMol or component NMol"
126	<	" given. Cannot calculate the number of atoms.\n" );
127	<	painCave.isFatal = 1;
128	<	simError();
129	<	}
135	>	}
136
131	–	tot_nmol += the_components[i]->getNMol();
132	–	components_nmol[i] = the_components[i]->getNMol();
133	–	}
134	–	}
135	–	else{
136	–	sprintf( painCave.errMsg,
137	–	"SimSetup error.\n"
138	–	"\tSorry, the ability to specify total"
139	–	" nMols and then give molfractions in the components\n"
140	–	"\tis not currently supported."
141	–	" Please give nMol in the components.\n" );
142	–	painCave.isFatal = 1;
143	–	simError();
144	–
145	–
146	–	//     tot_nmol = the_globals->getNMol();
147	–
148	–	//   //we have the total number of molecules, now we check for molfractions
149	–	//     for( i=0; i<n_components; i++ ){
150	–
151	–	//       if( !the_components[i]->haveMolFraction() ){
152	–
153	–	//  if( !the_components[i]->haveNMol() ){
154	–	//    //we have a problem
155	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
156	–	//              << " nMol was given in component
157	–
158	–	}
137
138	<	#ifdef IS_MPI
161	<	strcpy( checkPointMsg, "Have the number of components" );
162	<	MPIcheckPoint();
163	<	#endif // is_mpi
138	>	void SimSetup::makeMolecules( void ){
139
140	<	// make an array of molecule stamps that match the components used.
141	<	// also extract the used stamps out into a separate linked list
140	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
141	>	molInit molInfo;
142	>	DirectionalAtom* dAtom;
143	>	LinkedAssign* extras;
144	>	LinkedAssign* current_extra;
145	>	AtomStamp* currentAtom;
146	>	BondStamp* currentBond;
147	>	BendStamp* currentBend;
148	>	TorsionStamp* currentTorsion;
149
150	<	simnfo->nComponents = n_components;
151	<	simnfo->componentsNmol = components_nmol;
152	<	simnfo->compStamps = comp_stamps;
153	<	simnfo->headStamp = new LinkedMolStamp();
150	>	bond_pair* theBonds;
151	>	bend_set* theBends;
152	>	torsion_set* theTorsions;
153	>
154
155	<	char* id;
174	<	LinkedMolStamp* headStamp = simnfo->headStamp;
175	<	LinkedMolStamp* currentStamp = NULL;
176	<	for( i=0; i<n_components; i++ ){
155	>	//init the forceField paramters
156
157	<	id = the_components[i]->getType();
158	<	comp_stamps[i] = NULL;
157	>	the_ff->readParams();
158	>
159	>
160	>	// init the atoms
161	>
162	>	double ux, uy, uz, u, uSqr;
163	>
164	>	atomOffset = 0;
165	>	excludeOffset = 0;
166	>	for(i=0; i<info->n_mol; i++){
167
168	<	// check to make sure the component isn't already in the list
168	>	stampID = the_molecules[i].getStampID();
169
170	<	comp_stamps[i] = headStamp->match( id );
171	<	if( comp_stamps[i] == NULL ){
170	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
171	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
172	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
173	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
174	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
175	>
176	>	molInfo.myAtoms = &the_atoms[atomOffset];
177	>	molInfo.myExcludes = &the_excludes[excludeOffset];
178	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
179	>	molInfo.myBends = new Bend*[molInfo.nBends];
180	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
181	>
182	>	theBonds = new bond_pair[molInfo.nBonds];
183	>	theBends = new bend_set[molInfo.nBends];
184	>	theTorsions = new torsion_set[molInfo.nTorsions];
185	>
186	>	// make the Atoms
187	>
188	>	for(j=0; j<molInfo.nAtoms; j++){
189
190	<	// extract the component from the list;
191	<
192	<	currentStamp = the_stamps->extractMolStamp( id );
193	<	if( currentStamp == NULL ){
194	<	sprintf( painCave.errMsg,
195	<	"SimSetup error: Component \"%s\" was not found in the "
196	<	"list of declared molecules\n",
197	<	id );
198	<	painCave.isFatal = 1;
199	<	simError();
190	>	currentAtom = comp_stamps[stampID]->getAtom( j );
191	>	if( currentAtom->haveOrientation() ){
192	>
193	>	dAtom = new DirectionalAtom(j + atomOffset);
194	>	info->n_oriented++;
195	>	molInfo.myAtoms[j] = dAtom;
196	>
197	>	ux = currentAtom->getOrntX();
198	>	uy = currentAtom->getOrntY();
199	>	uz = currentAtom->getOrntZ();
200	>
201	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
202	>
203	>	u = sqrt( uSqr );
204	>	ux = ux / u;
205	>	uy = uy / u;
206	>	uz = uz / u;
207	>
208	>	dAtom->setSUx( ux );
209	>	dAtom->setSUy( uy );
210	>	dAtom->setSUz( uz );
211		}
212	<
213	<	headStamp->add( currentStamp );
214	<	comp_stamps[i] = headStamp->match( id );
215	<	}
216	<	}
202	<
212	>	else{
213	>	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
214	>	}
215	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
216	>
217		#ifdef IS_MPI
218	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
219	<	MPIcheckPoint();
218	>
219	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
220	>
221		#endif // is_mpi
222	<
222	>	}
223	>
224	>	// make the bonds
225	>	for(j=0; j<molInfo.nBonds; j++){
226	>
227	>	currentBond = comp_stamps[stampID]->getBond( j );
228	>	theBonds[j].a = currentBond->getA() + atomOffset;
229	>	theBonds[j].b = currentBond->getB() + atomOffset;
230
231	+	exI = theBonds[j].a;
232	+	exJ = theBonds[j].b;
233
234	+	// exclude_I must always be the smaller of the pair
235	+	if( exI > exJ ){
236	+	tempEx = exI;
237	+	exI = exJ;
238	+	exJ = tempEx;
239	+	}
240	+	#ifdef IS_MPI
241	+	tempEx = exI;
242	+	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
243	+	tempEx = exJ;
244	+	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
245	+
246	+	the_excludes[j+excludeOffset]->setPair( exI, exJ );
247	+	#else  // isn't MPI
248
249	<	// caclulate the number of atoms, bonds, bends and torsions
249	>	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
250	>	#endif  //is_mpi
251	>	}
252	>	excludeOffset += molInfo.nBonds;
253
254	<	tot_atoms = 0;
255	<	tot_bonds = 0;
256	<	tot_bends = 0;
257	<	tot_torsions = 0;
258	<	for( i=0; i<n_components; i++ ){
254	>	//make the bends
255	>	for(j=0; j<molInfo.nBends; j++){
256	>
257	>	currentBend = comp_stamps[stampID]->getBend( j );
258	>	theBends[j].a = currentBend->getA() + atomOffset;
259	>	theBends[j].b = currentBend->getB() + atomOffset;
260	>	theBends[j].c = currentBend->getC() + atomOffset;
261	>
262	>	if( currentBend->haveExtras() ){
263	>
264	>	extras = currentBend->getExtras();
265	>	current_extra = extras;
266	>
267	>	while( current_extra != NULL ){
268	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
269	>
270	>	switch( current_extra->getType() ){
271	>
272	>	case 0:
273	>	theBends[j].ghost =
274	>	current_extra->getInt() + atomOffset;
275	>	theBends[j].isGhost = 1;
276	>	break;
277	>
278	>	case 1:
279	>	theBends[j].ghost =
280	>	(int)current_extra->getDouble() + atomOffset;
281	>	theBends[j].isGhost = 1;
282	>	break;
283	>
284	>	default:
285	>	sprintf( painCave.errMsg,
286	>	"SimSetup Error: ghostVectorSource was neither a "
287	>	"double nor an int.\n"
288	>	"-->Bend[%d] in %s\n",
289	>	j, comp_stamps[stampID]->getID() );
290	>	painCave.isFatal = 1;
291	>	simError();
292	>	}
293	>	}
294	>
295	>	else{
296	>
297	>	sprintf( painCave.errMsg,
298	>	"SimSetup Error: unhandled bend assignment:\n"
299	>	"    -->%s in Bend[%d] in %s\n",
300	>	current_extra->getlhs(),
301	>	j, comp_stamps[stampID]->getID() );
302	>	painCave.isFatal = 1;
303	>	simError();
304	>	}
305	>
306	>	current_extra = current_extra->getNext();
307	>	}
308	>	}
309	>
310	>	if( !theBends[j].isGhost ){
311	>
312	>	exI = theBends[j].a;
313	>	exJ = theBends[j].c;
314	>	}
315	>	else{
316	>
317	>	exI = theBends[j].a;
318	>	exJ = theBends[j].b;
319	>	}
320	>
321	>	// exclude_I must always be the smaller of the pair
322	>	if( exI > exJ ){
323	>	tempEx = exI;
324	>	exI = exJ;
325	>	exJ = tempEx;
326	>	}
327	>	#ifdef IS_MPI
328	>	tempEx = exI;
329	>	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
330	>	tempEx = exJ;
331	>	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
332	>
333	>	the_excludes[j+excludeOffset]->setPair( exI, exJ );
334	>	#else  // isn't MPI
335	>	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
336	>	#endif  //is_mpi
337	>	}
338	>	excludeOffset += molInfo.nBends;
339	>
340	>	for(j=0; j<molInfo.nTorsions; j++){
341	>
342	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
343	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
344	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
345	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
346	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
347	>
348	>	exI = theTorsions[j].a;
349	>	exJ = theTorsions[j].d;
350	>
351	>	// exclude_I must always be the smaller of the pair
352	>	if( exI > exJ ){
353	>	tempEx = exI;
354	>	exI = exJ;
355	>	exJ = tempEx;
356	>	}
357	>	#ifdef IS_MPI
358	>	tempEx = exI;
359	>	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
360	>	tempEx = exJ;
361	>	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
362	>
363	>	the_excludes[j+excludeOffset]->setPair( exI, exJ );
364	>	#else  // isn't MPI
365	>	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
366	>	#endif  //is_mpi
367	>	}
368	>	excludeOffset += molInfo.nTorsions;
369	>
370
371	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
220	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
221	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
222	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
223	<	}
371	>	// send the arrays off to the forceField for init.
372
373	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
373	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
374	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
375	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
376	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
377
227	–	simnfo->n_atoms = tot_atoms;
228	–	simnfo->n_bonds = tot_bonds;
229	–	simnfo->n_bends = tot_bends;
230	–	simnfo->n_torsions = tot_torsions;
231	–	simnfo->n_SRI = tot_SRI;
232	–	simnfo->n_mol = tot_nmol;
378
379	<
379	>	the_molecules[i].initialize( molInfo );
380	>
381	>
382	>	atomOffset += molInfo.nAtoms;
383	>	delete[] theBonds;
384	>	delete[] theBends;
385	>	delete[] theTorsions;
386	>	}
387	>
388		#ifdef IS_MPI
389	+	sprintf( checkPointMsg, "all molecules initialized succesfully" );
390	+	MPIcheckPoint();
391	+	#endif // is_mpi
392
393	<	// divide the molecules among processors here.
394	<
395	<	mpiSim = new mpiSimulation( simnfo );
240	<
241	<
393	>	// clean up the forcefield
394	>	the_ff->calcRcut();
395	>	the_ff->cleanMe();
396
397	<	globalIndex = mpiSim->divideLabor();
397	>	}
398
399	+	void SimSetup::initFromBass( void ){
400
401	+	int i, j, k;
402	+	int n_cells;
403	+	double cellx, celly, cellz;
404	+	double temp1, temp2, temp3;
405	+	int n_per_extra;
406	+	int n_extra;
407	+	int have_extra, done;
408
409	<	// set up the local variables
410	<
411	<	int localMol, allMol;
250	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
251	<
252	<	allMol = 0;
253	<	localMol = 0;
254	<	local_atoms = 0;
255	<	local_bonds = 0;
256	<	local_bends = 0;
257	<	local_torsions = 0;
258	<	for( i=0; i<n_components; i++ ){
409	>	temp1 = (double)tot_nmol / 4.0;
410	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
411	>	temp3 = ceil( temp2 );
412
413	<	for( j=0; j<components_nmol[i]; j++ ){
414	<
415	<	if( mpiSim->getMyMolStart() <= allMol &&
416	<	allMol <= mpiSim->getMyMolEnd() ){
417	<
418	<	local_atoms +=    comp_stamps[i]->getNAtoms();
419	<	local_bonds +=    comp_stamps[i]->getNBonds();
420	<	local_bends +=    comp_stamps[i]->getNBends();
421	<	local_torsions += comp_stamps[i]->getNTorsions();
422	<	localMol++;
423	<	}
424	<	allMol++;
413	>	have_extra =0;
414	>	if( temp2 < temp3 ){ // we have a non-complete lattice
415	>	have_extra =1;
416	>
417	>	n_cells = (int)temp3 - 1;
418	>	cellx = info->boxL[0] / temp3;
419	>	celly = info->boxL[1] / temp3;
420	>	cellz = info->boxL[2] / temp3;
421	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
422	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
423	>	n_per_extra = (int)ceil( temp1 );
424	>
425	>	if( n_per_extra > 4){
426	>	sprintf( painCave.errMsg,
427	>	"SimSetup error. There has been an error in constructing"
428	>	" the non-complete lattice.\n" );
429	>	painCave.isFatal = 1;
430	>	simError();
431		}
432		}
433	<	local_SRI = local_bonds + local_bends + local_torsions;
434	<
433	>	else{
434	>	n_cells = (int)temp3;
435	>	cellx = info->boxL[0] / temp3;
436	>	celly = info->boxL[1] / temp3;
437	>	cellz = info->boxL[2] / temp3;
438	>	}
439
440	<	simnfo->n_atoms = mpiSim->getMyNlocal();
441	<
442	<	if( local_atoms != simnfo->n_atoms ){
443	<	sprintf( painCave.errMsg,
444	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
445	<	" localAtom (%d) are note equal.\n",
446	<	simnfo->n_atoms,
447	<	local_atoms );
448	<	painCave.isFatal = 1;
449	<	simError();
440	>	current_mol = 0;
441	>	current_comp_mol = 0;
442	>	current_comp = 0;
443	>	current_atom_ndx = 0;
444	>
445	>	for( i=0; i < n_cells ; i++ ){
446	>	for( j=0; j < n_cells; j++ ){
447	>	for( k=0; k < n_cells; k++ ){
448	>
449	>	makeElement( i * cellx,
450	>	j * celly,
451	>	k * cellz );
452	>
453	>	makeElement( i * cellx + 0.5 * cellx,
454	>	j * celly + 0.5 * celly,
455	>	k * cellz );
456	>
457	>	makeElement( i * cellx,
458	>	j * celly + 0.5 * celly,
459	>	k * cellz + 0.5 * cellz );
460	>
461	>	makeElement( i * cellx + 0.5 * cellx,
462	>	j * celly,
463	>	k * cellz + 0.5 * cellz );
464	>	}
465	>	}
466		}
467
468	<	simnfo->n_bonds = local_bonds;
469	<	simnfo->n_bends = local_bends;
291	<	simnfo->n_torsions = local_torsions;
292	<	simnfo->n_SRI = local_SRI;
293	<	simnfo->n_mol = localMol;
468	>	if( have_extra ){
469	>	done = 0;
470
471	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
472	<	MPIcheckPoint();
473	<
298	<
299	<	#endif // is_mpi
300	<
471	>	int start_ndx;
472	>	for( i=0; i < (n_cells+1) && !done; i++ ){
473	>	for( j=0; j < (n_cells+1) && !done; j++ ){
474
475	<	// create the atom and short range interaction arrays
475	>	if( i < n_cells ){
476
477	<	Atom::createArrays(simnfo->n_atoms);
478	<	the_atoms = new Atom*[simnfo->n_atoms];
479	<	the_molecules = new Molecule[simnfo->n_mol];
477	>	if( j < n_cells ){
478	>	start_ndx = n_cells;
479	>	}
480	>	else start_ndx = 0;
481	>	}
482	>	else start_ndx = 0;
483
484	+	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
485	+
486	+	makeElement( i * cellx,
487	+	j * celly,
488	+	k * cellz );
489	+	done = ( current_mol >= tot_nmol );
490
491	<	if( simnfo->n_SRI ){
492	<	Exclude::createArray(simnfo->n_SRI);
493	<	the_excludes = new Exclude*[simnfo->n_SRI];
494	<	simnfo->globalExcludes = new int;
495	<	simnfo->n_exclude = tot_SRI;
491	>	if( !done && n_per_extra > 1 ){
492	>	makeElement( i * cellx + 0.5 * cellx,
493	>	j * celly + 0.5 * celly,
494	>	k * cellz );
495	>	done = ( current_mol >= tot_nmol );
496	>	}
497	>
498	>	if( !done && n_per_extra > 2){
499	>	makeElement( i * cellx,
500	>	j * celly + 0.5 * celly,
501	>	k * cellz + 0.5 * cellz );
502	>	done = ( current_mol >= tot_nmol );
503	>	}
504	>
505	>	if( !done && n_per_extra > 3){
506	>	makeElement( i * cellx + 0.5 * cellx,
507	>	j * celly,
508	>	k * cellz + 0.5 * cellz );
509	>	done = ( current_mol >= tot_nmol );
510	>	}
511	>	}
512	>	}
513	>	}
514		}
515	+
516	+
517	+	for( i=0; i<info->n_atoms; i++ ){
518	+	info->atoms[i]->set_vx( 0.0 );
519	+	info->atoms[i]->set_vy( 0.0 );
520	+	info->atoms[i]->set_vz( 0.0 );
521	+	}
522	+	}
523	+
524	+	void SimSetup::makeElement( double x, double y, double z ){
525	+
526	+	int k;
527	+	AtomStamp* current_atom;
528	+	DirectionalAtom* dAtom;
529	+	double rotMat[3][3];
530	+
531	+	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
532	+
533	+	current_atom = comp_stamps[current_comp]->getAtom( k );
534	+	if( !current_atom->havePosition() ){
535	+	sprintf( painCave.errMsg,
536	+	"SimSetup:initFromBass error.\n"
537	+	"\tComponent %s, atom %s does not have a position specified.\n"
538	+	"\tThe initialization routine is unable to give a start"
539	+	" position.\n",
540	+	comp_stamps[current_comp]->getID(),
541	+	current_atom->getType() );
542	+	painCave.isFatal = 1;
543	+	simError();
544	+	}
545	+
546	+	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
547	+	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
548	+	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
549	+
550	+	if( the_atoms[current_atom_ndx]->isDirectional() ){
551	+
552	+	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
553	+
554	+	rotMat[0][0] = 1.0;
555	+	rotMat[0][1] = 0.0;
556	+	rotMat[0][2] = 0.0;
557	+
558	+	rotMat[1][0] = 0.0;
559	+	rotMat[1][1] = 1.0;
560	+	rotMat[1][2] = 0.0;
561	+
562	+	rotMat[2][0] = 0.0;
563	+	rotMat[2][1] = 0.0;
564	+	rotMat[2][2] = 1.0;
565	+
566	+	dAtom->setA( rotMat );
567	+	}
568	+
569	+	current_atom_ndx++;
570	+	}
571	+
572	+	current_mol++;
573	+	current_comp_mol++;
574	+
575	+	if( current_comp_mol >= components_nmol[current_comp] ){
576	+
577	+	current_comp_mol = 0;
578	+	current_comp++;
579	+	}
580	+	}
581	+
582	+
583	+	void SimSetup::gatherInfo( void ){
584	+	int i,j,k;
585	+
586	+	ensembleCase = -1;
587	+	ffCase = -1;
588	+
589	+	// get the stamps and globals;
590	+	stamps = stamps;
591	+	globals = globals;
592	+
593	+	// set the easy ones first
594	+	info->target_temp = globals->getTargetTemp();
595	+	info->dt = globals->getDt();
596	+	info->run_time = globals->getRunTime();
597	+	n_components = globals->getNComponents();
598	+
599	+
600	+	// get the forceField
601	+
602	+	strcpy( force_field, globals->getForceField() );
603	+
604	+	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
605	+	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
606	+	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
607		else{
608	<
609	<	Exclude::createArray( 1 );
610	<	the_excludes = new Exclude*;
611	<	the_excludes[0] = new Exclude(0);
612	<	the_excludes[0]->setPair( 0,0 );
321	<	simnfo->globalExcludes = new int;
322	<	simnfo->globalExcludes[0] = 0;
323	<	simnfo->n_exclude = 0;
608	>	sprintf( painCave.errMsg,
609	>	"SimSetup Error. Unrecognized force field -> %s\n",
610	>	force_field );
611	>	painCave.isFatal = 1;
612	>	simError();
613		}
614
615	<	// set the arrays into the SimInfo object
615	>	// get the ensemble
616
617	<	simnfo->atoms = the_atoms;
329	<	simnfo->sr_interactions = the_sris;
330	<	simnfo->nGlobalExcludes = 0;
331	<	simnfo->excludes = the_excludes;
617	>	strcpy( ensemble, globals->getEnsemble() );
618
619	+	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
620	+	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
621	+	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
622	+	ensembleCase = NPTi_ENS;
623	+	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
624	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
625	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
626	+	else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS;
627	+	else{
628	+	sprintf( painCave.errMsg,
629	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
630	+	"reverting to NVE for this simulation.\n",
631	+	ensemble );
632	+	painCave.isFatal = 0;
633	+	simError();
634	+	strcpy( ensemble, "NVE" );
635	+	ensembleCase = NVE_ENS;
636	+	}
637	+	strcpy( info->ensemble, ensemble );
638
639	<	// get some of the tricky things that may still be in the globals
639	>	// get the mixing rule
640
641	+	strcpy( info->mixingRule, globals->getMixingRule() );
642	+	info->usePBC = globals->getPBC();
643	+
644
645	<	if( the_globals->haveBox() ){
646	<	simnfo->box_x = the_globals->getBox();
647	<	simnfo->box_y = the_globals->getBox();
648	<	simnfo->box_z = the_globals->getBox();
645	>	// get the components and calculate the tot_nMol and indvidual n_mol
646	>
647	>	the_components = globals->getComponents();
648	>	components_nmol = new int[n_components];
649	>
650	>
651	>	if( !globals->haveNMol() ){
652	>	// we don't have the total number of molecules, so we assume it is
653	>	// given in each component
654	>
655	>	tot_nmol = 0;
656	>	for( i=0; i<n_components; i++ ){
657	>
658	>	if( !the_components[i]->haveNMol() ){
659	>	// we have a problem
660	>	sprintf( painCave.errMsg,
661	>	"SimSetup Error. No global NMol or component NMol"
662	>	" given. Cannot calculate the number of atoms.\n" );
663	>	painCave.isFatal = 1;
664	>	simError();
665	>	}
666	>
667	>	tot_nmol += the_components[i]->getNMol();
668	>	components_nmol[i] = the_components[i]->getNMol();
669	>	}
670		}
671	<	else if( the_globals->haveDensity() ){
671	>	else{
672	>	sprintf( painCave.errMsg,
673	>	"SimSetup error.\n"
674	>	"\tSorry, the ability to specify total"
675	>	" nMols and then give molfractions in the components\n"
676	>	"\tis not currently supported."
677	>	" Please give nMol in the components.\n" );
678	>	painCave.isFatal = 1;
679	>	simError();
680	>	}
681
682	+	// set the status, sample, and thermal kick times
683	+
684	+	if( globals->haveSampleTime() ){
685	+	info->sampleTime = globals->getSampleTime();
686	+	info->statusTime = info->sampleTime;
687	+	info->thermalTime = info->sampleTime;
688	+	}
689	+	else{
690	+	info->sampleTime = globals->getRunTime();
691	+	info->statusTime = info->sampleTime;
692	+	info->thermalTime = info->sampleTime;
693	+	}
694	+
695	+	if( globals->haveStatusTime() ){
696	+	info->statusTime = globals->getStatusTime();
697	+	}
698	+
699	+	if( globals->haveThermalTime() ){
700	+	info->thermalTime = globals->getThermalTime();
701	+	}
702	+
703	+	// check for the temperature set flag
704	+
705	+	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
706	+
707	+	// get some of the tricky things that may still be in the globals
708	+
709	+	double boxVector[3];
710	+	if( globals->haveBox() ){
711	+	boxVector[0] = globals->getBox();
712	+	boxVector[1] = globals->getBox();
713	+	boxVector[2] = globals->getBox();
714	+
715	+	info->setBox( boxVector );
716	+	}
717	+	else if( globals->haveDensity() ){
718	+
719		double vol;
720	<	vol = (double)tot_nmol / the_globals->getDensity();
721	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
722	<	simnfo->box_y = simnfo->box_x;
723	<	simnfo->box_z = simnfo->box_x;
720	>	vol = (double)tot_nmol / globals->getDensity();
721	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
722	>	boxVector[1] = boxVector[0];
723	>	boxVector[2] = boxVector[0];
724	>
725	>	info->setBox( boxVector );
726		}
727		else{
728	<	if( !the_globals->haveBoxX() ){
728	>	if( !globals->haveBoxX() ){
729		sprintf( painCave.errMsg,
730		"SimSetup error, no periodic BoxX size given.\n" );
731		painCave.isFatal = 1;
732		simError();
733		}
734	<	simnfo->box_x = the_globals->getBoxX();
734	>	boxVector[0] = globals->getBoxX();
735
736	<	if( !the_globals->haveBoxY() ){
736	>	if( !globals->haveBoxY() ){
737		sprintf( painCave.errMsg,
738		"SimSetup error, no periodic BoxY size given.\n" );
739		painCave.isFatal = 1;
740		simError();
741		}
742	<	simnfo->box_y = the_globals->getBoxY();
742	>	boxVector[1] = globals->getBoxY();
743
744	<	if( !the_globals->haveBoxZ() ){
744	>	if( !globals->haveBoxZ() ){
745		sprintf( painCave.errMsg,
746		"SimSetup error, no periodic BoxZ size given.\n" );
747		painCave.isFatal = 1;
748		simError();
749		}
750	<	simnfo->box_z = the_globals->getBoxZ();
750	>	boxVector[2] = globals->getBoxZ();
751	>
752	>	info->setBox( boxVector );
753		}
754
755	+
756	+
757		#ifdef IS_MPI
758	<	strcpy( checkPointMsg, "Box size set up" );
758	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
759		MPIcheckPoint();
760		#endif // is_mpi
761
762	+	}
763
382	–	// initialize the arrays
764
765	<	the_ff->setSimInfo( simnfo );
765	>	void SimSetup::finalInfoCheck( void ){
766	>	int index;
767	>	int usesDipoles;
768	>
769
770	<	makeAtoms();
387	<	simnfo->identArray = new int[simnfo->n_atoms];
388	<	for(i=0; i<simnfo->n_atoms; i++){
389	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
390	<	}
770	>	// check electrostatic parameters
771
772	<	if( tot_bonds ){
773	<	makeBonds();
772	>	index = 0;
773	>	usesDipoles = 0;
774	>	while( (index < info->n_atoms) && !usesDipoles ){
775	>	usesDipoles = ((info->atoms)[index])->hasDipole();
776	>	index++;
777		}
778	+
779	+	#ifdef IS_MPI
780	+	int myUse = usesDipoles;
781	+	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
782	+	#endif //is_mpi
783
784	<	if( tot_bends ){
397	<	makeBends();
398	<	}
784	>	double theEcr, theEst;
785
786	<	if( tot_torsions ){
787	<	makeTorsions();
788	<	}
789	<
404	<
405	<	if (the_globals->getUseRF() ) {
406	<	simnfo->useReactionField = 1;
407	<
408	<	if( !the_globals->haveECR() ){
786	>	if (globals->getUseRF() ) {
787	>	info->useReactionField = 1;
788	>
789	>	if( !globals->haveECR() ){
790		sprintf( painCave.errMsg,
791		"SimSetup Warning: using default value of 1/2 the smallest "
792		"box length for the electrostaticCutoffRadius.\n"
#	Line 413 | Line 794 | void SimSetup::createSim( void ){
794		painCave.isFatal = 0;
795		simError();
796		double smallest;
797	<	smallest = simnfo->box_x;
798	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
799	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
800	<	simnfo->ecr = 0.5 * smallest;
797	>	smallest = info->boxL[0];
798	>	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
799	>	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
800	>	theEcr = 0.5 * smallest;
801		} else {
802	<	simnfo->ecr        = the_globals->getECR();
802	>	theEcr = globals->getECR();
803		}
804
805	<	if( !the_globals->haveEST() ){
805	>	if( !globals->haveEST() ){
806		sprintf( painCave.errMsg,
807		"SimSetup Warning: using default value of 0.05 * the "
808		"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
809		);
810		painCave.isFatal = 0;
811		simError();
812	<	simnfo->est = 0.05 * simnfo->ecr;
812	>	theEst = 0.05 * theEcr;
813		} else {
814	<	simnfo->est        = the_globals->getEST();
814	>	theEst= globals->getEST();
815		}
816	+
817	+	info->setEcr( theEcr, theEst );
818
819	<	if(!the_globals->haveDielectric() ){
819	>	if(!globals->haveDielectric() ){
820		sprintf( painCave.errMsg,
821		"SimSetup Error: You are trying to use Reaction Field without"
822		"setting a dielectric constant!\n"
#	Line 441 | Line 824 | void SimSetup::createSim( void ){
824		painCave.isFatal = 1;
825		simError();
826		}
827	<	simnfo->dielectric = the_globals->getDielectric();
828	<	} else {
829	<	if (simnfo->n_dipoles) {
827	>	info->dielectric = globals->getDielectric();
828	>	}
829	>	else {
830	>	if (usesDipoles) {
831
832	<	if( !the_globals->haveECR() ){
833	<	sprintf( painCave.errMsg,
834	<	"SimSetup Warning: using default value of 1/2 the smallest"
835	<	"box length for the electrostaticCutoffRadius.\n"
836	<	"I hope you have a very fast processor!\n");
837	<	painCave.isFatal = 0;
838	<	simError();
839	<	double smallest;
840	<	smallest = simnfo->box_x;
841	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
842	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
843	<	simnfo->ecr = 0.5 * smallest;
832	>	if( !globals->haveECR() ){
833	>	sprintf( painCave.errMsg,
834	>	"SimSetup Warning: using default value of 1/2 the smallest "
835	>	"box length for the electrostaticCutoffRadius.\n"
836	>	"I hope you have a very fast processor!\n");
837	>	painCave.isFatal = 0;
838	>	simError();
839	>	double smallest;
840	>	smallest = info->boxL[0];
841	>	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
842	>	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
843	>	theEcr = 0.5 * smallest;
844		} else {
845	<	simnfo->ecr        = the_globals->getECR();
845	>	theEcr = globals->getECR();
846		}
847
848	<	if( !the_globals->haveEST() ){
849	<	sprintf( painCave.errMsg,
850	<	"SimSetup Warning: using default value of 5% of the"
851	<	"electrostaticCutoffRadius for the "
852	<	"electrostaticSkinThickness\n"
853	<	);
854	<	painCave.isFatal = 0;
855	<	simError();
856	<	simnfo->est = 0.05 * simnfo->ecr;
848	>	if( !globals->haveEST() ){
849	>	sprintf( painCave.errMsg,
850	>	"SimSetup Warning: using default value of 0.05 * the "
851	>	"electrostaticCutoffRadius for the "
852	>	"electrostaticSkinThickness\n"
853	>	);
854	>	painCave.isFatal = 0;
855	>	simError();
856	>	theEst = 0.05 * theEcr;
857		} else {
858	<	simnfo->est        = the_globals->getEST();
858	>	theEst= globals->getEST();
859		}
860	+
861	+	info->setEcr( theEcr, theEst );
862		}
863		}
864
865		#ifdef IS_MPI
866	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
866	>	strcpy( checkPointMsg, "post processing checks out" );
867		MPIcheckPoint();
868		#endif // is_mpi
869
870	<	if( the_globals->haveInitialConfig() ){
870	>	}
871	>
872	>	void SimSetup::initSystemCoords( void ){
873	>
874	>	if( globals->haveInitialConfig() ){
875
876		InitializeFromFile* fileInit;
877		#ifdef IS_MPI // is_mpi
878		if( worldRank == 0 ){
879		#endif //is_mpi
880	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
880	>	fileInit = new InitializeFromFile( globals->getInitialConfig() );
881		#ifdef IS_MPI
882		}else fileInit = new InitializeFromFile( NULL );
883		#endif
884	<	fileInit->read_xyz( simnfo ); // default velocities on
884	>	fileInit->readInit( info ); // default velocities on
885
886		delete fileInit;
887		}
#	Line 519 | Line 909 | void SimSetup::createSim( void ){
909		MPIcheckPoint();
910		#endif // is_mpi
911
912	+	}
913
523	–
524	–
525	–
914
915	<
915	>	void SimSetup::makeOutNames( void ){
916	>
917		#ifdef IS_MPI
918		if( worldRank == 0 ){
919		#endif // is_mpi
920
921	<	if( the_globals->haveFinalConfig() ){
922	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
921	>	if( globals->haveFinalConfig() ){
922	>	strcpy( info->finalName, globals->getFinalConfig() );
923		}
924		else{
925	<	strcpy( simnfo->finalName, inFileName );
925	>	strcpy( info->finalName, inFileName );
926		char* endTest;
927	<	int nameLength = strlen( simnfo->finalName );
928	<	endTest = &(simnfo->finalName[nameLength - 5]);
927	>	int nameLength = strlen( info->finalName );
928	>	endTest = &(info->finalName[nameLength - 5]);
929		if( !strcmp( endTest, ".bass" ) ){
930		strcpy( endTest, ".eor" );
931		}
#	Line 544 | Line 933 | void SimSetup::createSim( void ){
933		strcpy( endTest, ".eor" );
934		}
935		else{
936	<	endTest = &(simnfo->finalName[nameLength - 4]);
936	>	endTest = &(info->finalName[nameLength - 4]);
937		if( !strcmp( endTest, ".bss" ) ){
938		strcpy( endTest, ".eor" );
939		}
#	Line 552 | Line 941 | void SimSetup::createSim( void ){
941		strcpy( endTest, ".eor" );
942		}
943		else{
944	<	strcat( simnfo->finalName, ".eor" );
944	>	strcat( info->finalName, ".eor" );
945		}
946		}
947		}
948
949		// make the sample and status out names
950
951	<	strcpy( simnfo->sampleName, inFileName );
951	>	strcpy( info->sampleName, inFileName );
952		char* endTest;
953	<	int nameLength = strlen( simnfo->sampleName );
954	<	endTest = &(simnfo->sampleName[nameLength - 5]);
953	>	int nameLength = strlen( info->sampleName );
954	>	endTest = &(info->sampleName[nameLength - 5]);
955		if( !strcmp( endTest, ".bass" ) ){
956		strcpy( endTest, ".dump" );
957		}
#	Line 570 | Line 959 | void SimSetup::createSim( void ){
959		strcpy( endTest, ".dump" );
960		}
961		else{
962	<	endTest = &(simnfo->sampleName[nameLength - 4]);
962	>	endTest = &(info->sampleName[nameLength - 4]);
963		if( !strcmp( endTest, ".bss" ) ){
964		strcpy( endTest, ".dump" );
965		}
#	Line 578 | Line 967 | void SimSetup::createSim( void ){
967		strcpy( endTest, ".dump" );
968		}
969		else{
970	<	strcat( simnfo->sampleName, ".dump" );
970	>	strcat( info->sampleName, ".dump" );
971		}
972		}
973
974	<	strcpy( simnfo->statusName, inFileName );
975	<	nameLength = strlen( simnfo->statusName );
976	<	endTest = &(simnfo->statusName[nameLength - 5]);
974	>	strcpy( info->statusName, inFileName );
975	>	nameLength = strlen( info->statusName );
976	>	endTest = &(info->statusName[nameLength - 5]);
977		if( !strcmp( endTest, ".bass" ) ){
978		strcpy( endTest, ".stat" );
979		}
#	Line 592 | Line 981 | void SimSetup::createSim( void ){
981		strcpy( endTest, ".stat" );
982		}
983		else{
984	<	endTest = &(simnfo->statusName[nameLength - 4]);
984	>	endTest = &(info->statusName[nameLength - 4]);
985		if( !strcmp( endTest, ".bss" ) ){
986		strcpy( endTest, ".stat" );
987		}
#	Line 600 | Line 989 | void SimSetup::createSim( void ){
989		strcpy( endTest, ".stat" );
990		}
991		else{
992	<	strcat( simnfo->statusName, ".stat" );
992	>	strcat( info->statusName, ".stat" );
993		}
994		}
995
996		#ifdef IS_MPI
997		}
998		#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	–	}
999
1000	<	if( the_globals->haveStatusTime() ){
625	<	simnfo->statusTime = the_globals->getStatusTime();
626	<	}
1000	>	}
1001
628	–	if( the_globals->haveThermalTime() ){
629	–	simnfo->thermalTime = the_globals->getThermalTime();
630	–	}
1002
1003	<	// check for the temperature set flag
1003	>	void SimSetup::sysObjectsCreation( void ){
1004
1005	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
1005	>	int i;
1006
1007	+	// create the forceField
1008
1009	<	//   // make the longe range forces and the integrator
1009	>	createFF();
1010
1011	<	//   new AllLong( simnfo );
1011	>	// extract componentList
1012
1013	<	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 );
1013	>	compList();
1014
1015	+	// calc the number of atoms, bond, bends, and torsions
1016
1017	+	calcSysValues();
1018
1019	<	// initialize the Fortran
1019	>	#ifdef IS_MPI
1020	>	// divide the molecules among the processors
1021
1022	<	simnfo->refreshSim();
1022	>	mpiMolDivide();
1023	>	#endif //is_mpi
1024
1025	<	if( !strcmp( simnfo->mixingRule, "standard") ){
1026	<	the_ff->initForceField( LB_MIXING_RULE );
1025	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1026	>
1027	>	makeSysArrays();
1028	>
1029	>	// make and initialize the molecules (all but atomic coordinates)
1030	>
1031	>	makeMolecules();
1032	>	info->identArray = new int[info->n_atoms];
1033	>	for(i=0; i<info->n_atoms; i++){
1034	>	info->identArray[i] = the_atoms[i]->getIdent();
1035		}
1036	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
1037	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1038	<	}
1039	<	else{
1036	>
1037	>
1038	>
1039	>	}
1040	>
1041	>
1042	>	void SimSetup::createFF( void ){
1043	>
1044	>	switch( ffCase ){
1045	>
1046	>	case FF_DUFF:
1047	>	the_ff = new DUFF();
1048	>	break;
1049	>
1050	>	case FF_LJ:
1051	>	the_ff = new LJFF();
1052	>	break;
1053	>
1054	>	case FF_EAM:
1055	>	the_ff = new EAM_FF();
1056	>	break;
1057	>
1058	>	default:
1059		sprintf( painCave.errMsg,
1060	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
661	<	simnfo->mixingRule );
1060	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1061		painCave.isFatal = 1;
1062		simError();
1063		}
1064
666	–
1065		#ifdef IS_MPI
1066	<	strcpy( checkPointMsg,
669	<	"Successfully intialized the mixingRule for Fortran." );
1066	>	strcpy( checkPointMsg, "ForceField creation successful" );
1067		MPIcheckPoint();
1068		#endif // is_mpi
1069	+
1070		}
1071
1072
1073	<	void SimSetup::makeMolecules( void ){
1073	>	void SimSetup::compList( void ){
1074
1075	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
678	<	molInit info;
679	<	DirectionalAtom* dAtom;
680	<	LinkedAssign* extras;
681	<	LinkedAssign* current_extra;
682	<	AtomStamp* currentAtom;
683	<	BondStamp* currentBond;
684	<	BendStamp* currentBend;
685	<	TorsionStamp* currentTorsion;
686	<
687	<	//init the forceField paramters
1075	>	int i;
1076
1077	<	the_ff->readParams();
1077	>	comp_stamps = new MoleculeStamp*[n_components];
1078
1079	+	// make an array of molecule stamps that match the components used.
1080	+	// also extract the used stamps out into a separate linked list
1081	+
1082	+	info->nComponents = n_components;
1083	+	info->componentsNmol = components_nmol;
1084	+	info->compStamps = comp_stamps;
1085	+	info->headStamp = new LinkedMolStamp();
1086
1087	<	// init the molecules
1087	>	char* id;
1088	>	LinkedMolStamp* headStamp = info->headStamp;
1089	>	LinkedMolStamp* currentStamp = NULL;
1090	>	for( i=0; i<n_components; i++ ){
1091
1092	<	atomOffset = 0;
1093	<	excludeOffset = 0;
696	<	for(i=0; i<simnfo->n_mol; i++){
1092	>	id = the_components[i]->getType();
1093	>	comp_stamps[i] = NULL;
1094
1095	<	stampID = the_molecules[i].getStampID();
1095	>	// check to make sure the component isn't already in the list
1096
1097	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
1098	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
702	<	info.nBends    = comp_stamps[stampID]->getNBends();
703	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
704	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
705	<
706	<	info.myAtoms = &the_atoms[atomOffset];
707	<	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];
711	<
712	<	theBonds = new bond_pair[info.nBonds];
713	<	theBends = new bend_set[info.nBends];
714	<	theTorsions = new torsion_set[info.nTorsions];
715	<
716	<	// make the Atoms
717	<
718	<	for(j=0; j<info.nAtoms; j++){
1097	>	comp_stamps[i] = headStamp->match( id );
1098	>	if( comp_stamps[i] == NULL ){
1099
1100	<	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 );
741	<	}
742	<	else{
743	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
744	<	}
745	<	info.myAtoms[j]->setType( currentAtom->getType() );
746	<
747	<	#ifdef IS_MPI
1100	>	// extract the component from the list;
1101
1102	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
1103	<
1104	<	#endif // is_mpi
1105	<	}
1106	<
1107	<	// make the bonds
1108	<	for(j=0; j<info.nBonds; j++){
1109	<
757	<	currentBond = comp_stamps[stampID]->getBond( j );
758	<	theBonds[j].a = currentBond->getA() + atomOffset;
759	<	theBonds[j].b = currentBond->getB() + atomOffset;
760	<
761	<	exI = theBonds[i].a;
762	<	exJ = theBonds[i].b;
763	<
764	<	// exclude_I must always be the smaller of the pair
765	<	if( exI > exJ ){
766	<	tempEx = exI;
767	<	exI = exJ;
768	<	exJ = tempEx;
1102	>	currentStamp = stamps->extractMolStamp( id );
1103	>	if( currentStamp == NULL ){
1104	>	sprintf( painCave.errMsg,
1105	>	"SimSetup error: Component \"%s\" was not found in the "
1106	>	"list of declared molecules\n",
1107	>	id );
1108	>	painCave.isFatal = 1;
1109	>	simError();
1110		}
770	–	#ifdef IS_MPI
771	–	tempEx = exI;
772	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
773	–	tempEx = exJ;
774	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1111
1112	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1113	<	#else  // isn't MPI
778	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
779	<	#endif  //is_mpi
1112	>	headStamp->add( currentStamp );
1113	>	comp_stamps[i] = headStamp->match( id );
1114		}
1115	<	excludeOffset += info.nBonds;
1115	>	}
1116
783	–	//make the bends
784	–	for(j=0; j<info.nBends; j++){
785	–
786	–	currentBend = comp_stamps[stampID]->getBend( j );
787	–	theBends[j].a = currentBend->getA() + atomOffset;
788	–	theBends[j].b = currentBend->getB() + atomOffset;
789	–	theBends[j].c = currentBend->getC() + atomOffset;
790	–
791	–	if( currentBend->haveExtras() ){
792	–
793	–	extras = current_bend->getExtras();
794	–	current_extra = extras;
795	–
796	–	while( current_extra != NULL ){
797	–	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
798	–
799	–	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	–	}
837	–	}
838	–
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	–	}
849	–
850	–	// exclude_I must always be the smaller of the pair
851	–	if( exI > exJ ){
852	–	tempEx = exI;
853	–	exI = exJ;
854	–	exJ = tempEx;
855	–	}
1117		#ifdef IS_MPI
1118	<	tempEx = exI;
1119	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1120	<	tempEx = exJ;
860	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
861	<
862	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
863	<	#else  // isn't MPI
864	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
865	<	#endif  //is_mpi
866	<	}
867	<	excludeOffset += info.nBends;
1118	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1119	>	MPIcheckPoint();
1120	>	#endif // is_mpi
1121
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;
1122
1123	<	// exclude_I must always be the smaller of the pair
881	<	if( exI > exJ ){
882	<	tempEx = exI;
883	<	exI = exJ;
884	<	exJ = tempEx;
885	<	}
886	<	#ifdef IS_MPI
887	<	tempEx = exI;
888	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
889	<	tempEx = exJ;
890	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
891	<
892	<	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
896	<	}
897	<	excludeOffset += info.nTorsions;
1123	>	}
1124
1125	+	void SimSetup::calcSysValues( void ){
1126	+	int i, j, k;
1127	+
1128	+
1129	+	tot_atoms = 0;
1130	+	tot_bonds = 0;
1131	+	tot_bends = 0;
1132	+	tot_torsions = 0;
1133	+	for( i=0; i<n_components; i++ ){
1134
1135	+	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1136	+	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1137	+	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1138	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1139	+	}
1140
1141	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1142
1143	+	info->n_atoms = tot_atoms;
1144	+	info->n_bonds = tot_bonds;
1145	+	info->n_bends = tot_bends;
1146	+	info->n_torsions = tot_torsions;
1147	+	info->n_SRI = tot_SRI;
1148	+	info->n_mol = tot_nmol;
1149	+
1150	+	info->molMembershipArray = new int[tot_atoms];
1151	+	}
1152
1153
1154	+	#ifdef IS_MPI
1155
1156	+	void SimSetup::mpiMolDivide( void ){
1157	+
1158	+	int i, j, k;
1159	+	int localMol, allMol;
1160	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1161
1162	<	void SimSetup::makeAtoms( void ){
1162	>	mpiSim = new mpiSimulation( info );
1163	>
1164	>	globalIndex = mpiSim->divideLabor();
1165
1166	<	int i, j, k, index;
1167	<	double ux, uy, uz, uSqr, u;
1168	<	AtomStamp* current_atom;
1166	>	// set up the local variables
1167	>
1168	>	mol2proc = mpiSim->getMolToProcMap();
1169	>	molCompType = mpiSim->getMolComponentType();
1170	>
1171	>	allMol = 0;
1172	>	localMol = 0;
1173	>	local_atoms = 0;
1174	>	local_bonds = 0;
1175	>	local_bends = 0;
1176	>	local_torsions = 0;
1177	>	globalAtomIndex = 0;
1178
912	–	DirectionalAtom* dAtom;
913	–	int molIndex, molStart, molEnd, nMemb, lMolIndex;
1179
915	–	lMolIndex = 0;
916	–	molIndex = 0;
917	–	index = 0;
1180		for( i=0; i<n_components; i++ ){
1181
1182		for( j=0; j<components_nmol[i]; j++ ){
1183	<
1184	<	#ifdef IS_MPI
923	<	if( mpiSim->getMyMolStart() <= molIndex &&
924	<	molIndex <= mpiSim->getMyMolEnd() ){
925	<	#endif // is_mpi
926	<
927	<	molStart = index;
928	<	nMemb = comp_stamps[i]->getNAtoms();
929	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
930	<
931	<	current_atom = comp_stamps[i]->getAtom( k );
932	<	if( current_atom->haveOrientation() ){
933	<
934	<	dAtom = new DirectionalAtom(index);
935	<	simnfo->n_oriented++;
936	<	the_atoms[index] = dAtom;
937	<
938	<	ux = current_atom->getOrntX();
939	<	uy = current_atom->getOrntY();
940	<	uz = current_atom->getOrntZ();
941	<
942	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
943	<
944	<	u = sqrt( uSqr );
945	<	ux = ux / u;
946	<	uy = uy / u;
947	<	uz = uz / u;
948	<
949	<	dAtom->setSUx( ux );
950	<	dAtom->setSUy( uy );
951	<	dAtom->setSUz( uz );
952	<	}
953	<	else{
954	<	the_atoms[index] = new GeneralAtom(index);
955	<	}
956	<	the_atoms[index]->setType( current_atom->getType() );
957	<	the_atoms[index]->setIndex( index );
958	<
959	<	// increment the index and repeat;
960	<	index++;
961	<	}
1183	>
1184	>	if( mol2proc[allMol] == worldRank ){
1185
1186	<	molEnd = index -1;
1187	<	the_molecules[lMolIndex].setNMembers( nMemb );
1188	<	the_molecules[lMolIndex].setStartAtom( molStart );
1189	<	the_molecules[lMolIndex].setEndAtom( molEnd );
1190	<	the_molecules[lMolIndex].setStampID( i );
1191	<	lMolIndex++;
1192	<
1193	<	#ifdef IS_MPI
1186	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1187	>	local_bonds +=    comp_stamps[i]->getNBonds();
1188	>	local_bends +=    comp_stamps[i]->getNBends();
1189	>	local_torsions += comp_stamps[i]->getNTorsions();
1190	>	localMol++;
1191	>	}
1192	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1193	>	info->molMembershipArray[globalAtomIndex] = allMol;
1194	>	globalAtomIndex++;
1195		}
1196	<	#endif //is_mpi
1197	<
974	<	molIndex++;
1196	>
1197	>	allMol++;
1198		}
1199		}
1200	+	local_SRI = local_bonds + local_bends + local_torsions;
1201	+
1202	+	info->n_atoms = mpiSim->getMyNlocal();
1203	+
1204	+	if( local_atoms != info->n_atoms ){
1205	+	sprintf( painCave.errMsg,
1206	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1207	+	" localAtom (%d) are not equal.\n",
1208	+	info->n_atoms,
1209	+	local_atoms );
1210	+	painCave.isFatal = 1;
1211	+	simError();
1212	+	}
1213
1214	<	#ifdef IS_MPI
1215	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
1216	<
1217	<	delete[] globalIndex;
1214	>	info->n_bonds = local_bonds;
1215	>	info->n_bends = local_bends;
1216	>	info->n_torsions = local_torsions;
1217	>	info->n_SRI = local_SRI;
1218	>	info->n_mol = localMol;
1219
1220	<	mpiSim->mpiRefresh();
1221	<	#endif //IS_MPI
985	<
986	<	the_ff->initializeAtoms();
1220	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1221	>	MPIcheckPoint();
1222		}
1223	+
1224	+	#endif // is_mpi
1225
989	–	void SimSetup::makeBonds( void ){
1226
1227	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1228	<	bond_pair* the_bonds;
993	<	BondStamp* current_bond;
1227	>	void SimSetup::makeSysArrays( void ){
1228	>	int i, j, k;
1229
995	–	the_bonds = new bond_pair[tot_bonds];
996	–	index = 0;
997	–	offset = 0;
998	–	molIndex = 0;
1230
1231	<	for( i=0; i<n_components; i++ ){
1231	>	// create the atom and short range interaction arrays
1232
1233	<	for( j=0; j<components_nmol[i]; j++ ){
1233	>	Atom::createArrays(info->n_atoms);
1234	>	the_atoms = new Atom*[info->n_atoms];
1235	>	the_molecules = new Molecule[info->n_mol];
1236	>	int molIndex;
1237
1238	<	#ifdef IS_MPI
1005	<	if( mpiSim->getMyMolStart() <= molIndex &&
1006	<	molIndex <= mpiSim->getMyMolEnd() ){
1007	<	#endif // is_mpi
1008	<
1009	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
1010	<
1011	<	current_bond = comp_stamps[i]->getBond( k );
1012	<	the_bonds[index].a = current_bond->getA() + offset;
1013	<	the_bonds[index].b = current_bond->getB() + offset;
1238	>	// initialize the molecule's stampID's
1239
1015	–	exI = the_bonds[index].a;
1016	–	exJ = the_bonds[index].b;
1017	–
1018	–	// exclude_I must always be the smaller of the pair
1019	–	if( exI > exJ ){
1020	–	tempEx = exI;
1021	–	exI = exJ;
1022	–	exJ = tempEx;
1023	–	}
1024	–
1025	–
1240		#ifdef IS_MPI
1241	+
1242
1243	<	the_excludes[index*2] =
1244	<	the_atoms[exI]->getGlobalIndex() + 1;
1245	<	the_excludes[index*2 + 1] =
1246	<	the_atoms[exJ]->getGlobalIndex() + 1;
1247	<
1248	<	#else  // isn't MPI
1249	<
1035	<	the_excludes[index*2] =     exI + 1;
1036	<	the_excludes[index*2 + 1] = exJ + 1;
1037	<	// fortran index from 1 (hence the +1 in the indexing)
1038	<	#endif  //is_mpi
1039	<
1040	<	// increment the index and repeat;
1041	<	index++;
1042	<	}
1043	<	offset += comp_stamps[i]->getNAtoms();
1044	<
1045	<	#ifdef IS_MPI
1046	<	}
1047	<	#endif //is_mpi
1048	<
1243	>	molIndex = 0;
1244	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1245	>
1246	>	if(mol2proc[i] == worldRank ){
1247	>	the_molecules[molIndex].setStampID( molCompType[i] );
1248	>	the_molecules[molIndex].setMyIndex( molIndex );
1249	>	the_molecules[molIndex].setGlobalIndex( i );
1250		molIndex++;
1251	<	}
1251	>	}
1252		}
1253
1254	<	the_ff->initializeBonds( the_bonds );
1054	<	}
1055	<
1056	<	void SimSetup::makeBends( void ){
1057	<
1058	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1059	<	bend_set* the_bends;
1060	<	BendStamp* current_bend;
1061	<	LinkedAssign* extras;
1062	<	LinkedAssign* current_extra;
1254	>	#else // is_mpi
1255
1064	–
1065	–	the_bends = new bend_set[tot_bends];
1066	–	index = 0;
1067	–	offset = 0;
1256		molIndex = 0;
1257	<	for( i=0; i<n_components; i++ ){
1258	<
1259	<	for( j=0; j<components_nmol[i]; j++ ){
1260	<
1261	<	#ifdef IS_MPI
1262	<	if( mpiSim->getMyMolStart() <= molIndex &&
1263	<	molIndex <= mpiSim->getMyMolEnd() ){
1264	<	#endif // is_mpi
1265	<
1078	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
1079	<
1080	<	current_bend = comp_stamps[i]->getBend( k );
1081	<	the_bends[index].a = current_bend->getA() + offset;
1082	<	the_bends[index].b = current_bend->getB() + offset;
1083	<	the_bends[index].c = current_bend->getC() + offset;
1084	<
1085	<	if( current_bend->haveExtras() ){
1086	<
1087	<	extras = current_bend->getExtras();
1088	<	current_extra = extras;
1089	<
1090	<	while( current_extra != NULL ){
1091	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1092	<
1093	<	switch( current_extra->getType() ){
1094	<
1095	<	case 0:
1096	<	the_bends[index].ghost =
1097	<	current_extra->getInt() + offset;
1098	<	the_bends[index].isGhost = 1;
1099	<	break;
1100	<
1101	<	case 1:
1102	<	the_bends[index].ghost =
1103	<	(int)current_extra->getDouble() + offset;
1104	<	the_bends[index].isGhost = 1;
1105	<	break;
1106	<
1107	<	default:
1108	<	sprintf( painCave.errMsg,
1109	<	"SimSetup Error: ghostVectorSource was neiter a "
1110	<	"double nor an int.\n"
1111	<	"-->Bend[%d] in %s\n",
1112	<	k, comp_stamps[i]->getID() );
1113	<	painCave.isFatal = 1;
1114	<	simError();
1115	<	}
1116	<	}
1117	<
1118	<	else{
1119	<
1120	<	sprintf( painCave.errMsg,
1121	<	"SimSetup Error: unhandled bend assignment:\n"
1122	<	"    -->%s in Bend[%d] in %s\n",
1123	<	current_extra->getlhs(),
1124	<	k, comp_stamps[i]->getID() );
1125	<	painCave.isFatal = 1;
1126	<	simError();
1127	<	}
1128	<
1129	<	current_extra = current_extra->getNext();
1130	<	}
1131	<	}
1132	<
1133	<	if( !the_bends[index].isGhost ){
1134	<
1135	<	exI = the_bends[index].a;
1136	<	exJ = the_bends[index].c;
1137	<	}
1138	<	else{
1139	<
1140	<	exI = the_bends[index].a;
1141	<	exJ = the_bends[index].b;
1142	<	}
1143	<
1144	<	// exclude_I must always be the smaller of the pair
1145	<	if( exI > exJ ){
1146	<	tempEx = exI;
1147	<	exI = exJ;
1148	<	exJ = tempEx;
1149	<	}
1150	<
1151	<
1152	<	#ifdef IS_MPI
1153	<
1154	<	the_excludes[(index + tot_bonds)*2] =
1155	<	the_atoms[exI]->getGlobalIndex() + 1;
1156	<	the_excludes[(index + tot_bonds)*2 + 1] =
1157	<	the_atoms[exJ]->getGlobalIndex() + 1;
1158	<
1159	<	#else  // isn't MPI
1160	<
1161	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
1162	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1163	<	// fortran index from 1 (hence the +1 in the indexing)
1164	<	#endif  //is_mpi
1165	<
1166	<
1167	<	// increment the index and repeat;
1168	<	index++;
1169	<	}
1170	<	offset += comp_stamps[i]->getNAtoms();
1171	<
1172	<	#ifdef IS_MPI
1257	>	globalAtomIndex = 0;
1258	>	for(i=0; i<n_components; i++){
1259	>	for(j=0; j<components_nmol[i]; j++ ){
1260	>	the_molecules[molIndex].setStampID( i );
1261	>	the_molecules[molIndex].setMyIndex( molIndex );
1262	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1263	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1264	>	info->molMembershipArray[globalAtomIndex] = molIndex;
1265	>	globalAtomIndex++;
1266		}
1174	–	#endif //is_mpi
1175	–
1267		molIndex++;
1268		}
1269		}
1270	+
1271
1180	–	#ifdef IS_MPI
1181	–	sprintf( checkPointMsg,
1182	–	"Successfully created the bends list.\n" );
1183	–	MPIcheckPoint();
1272		#endif // is_mpi
1185	–
1273
1187	–	the_ff->initializeBends( the_bends );
1188	–	}
1274
1275	<	void SimSetup::makeTorsions( void ){
1275	>	if( info->n_SRI ){
1276	>
1277	>	Exclude::createArray(info->n_SRI);
1278	>	the_excludes = new Exclude*[info->n_SRI];
1279	>	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1280	>	info->globalExcludes = new int;
1281	>	info->n_exclude = info->n_SRI;
1282	>	}
1283	>	else{
1284	>
1285	>	Exclude::createArray( 1 );
1286	>	the_excludes = new Exclude*;
1287	>	the_excludes[0] = new Exclude(0);
1288	>	the_excludes[0]->setPair( 0,0 );
1289	>	info->globalExcludes = new int;
1290	>	info->globalExcludes[0] = 0;
1291	>	info->n_exclude = 0;
1292	>	}
1293
1294	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1193	<	torsion_set* the_torsions;
1194	<	TorsionStamp* current_torsion;
1294	>	// set the arrays into the SimInfo object
1295
1296	<	the_torsions = new torsion_set[tot_torsions];
1297	<	index = 0;
1298	<	offset = 0;
1299	<	molIndex = 0;
1200	<	for( i=0; i<n_components; i++ ){
1296	>	info->atoms = the_atoms;
1297	>	info->molecules = the_molecules;
1298	>	info->nGlobalExcludes = 0;
1299	>	info->excludes = the_excludes;
1300
1301	<	for( j=0; j<components_nmol[i]; j++ ){
1301	>	the_ff->setSimInfo( info );
1302
1303	<	#ifdef IS_MPI
1205	<	if( mpiSim->getMyMolStart() <= molIndex &&
1206	<	molIndex <= mpiSim->getMyMolEnd() ){
1207	<	#endif // is_mpi
1303	>	}
1304
1305	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1305	>	void SimSetup::makeIntegrator( void ){
1306
1307	<	current_torsion = comp_stamps[i]->getTorsion( k );
1308	<	the_torsions[index].a = current_torsion->getA() + offset;
1309	<	the_torsions[index].b = current_torsion->getB() + offset;
1310	<	the_torsions[index].c = current_torsion->getC() + offset;
1311	<	the_torsions[index].d = current_torsion->getD() + offset;
1307	>	NVT<RealIntegrator>*  myNVT = NULL;
1308	>	NPTi<RealIntegrator>* myNPTi = NULL;
1309	>	NPTf<RealIntegrator>* myNPTf = NULL;
1310	>	NPTim<RealIntegrator>* myNPTim = NULL;
1311	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1312	>	ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1313	>
1314	>	cerr << "setting integrator" <<endl;
1315	>
1316	>	switch( ensembleCase ){
1317
1318	<	exI = the_torsions[index].a;
1319	<	exJ = the_torsions[index].d;
1318	>	case NVE_ENS:
1319	>	new NVE<RealIntegrator>( info, the_ff );
1320	>	break;
1321
1322	<
1323	<	// exclude_I must always be the smaller of the pair
1324	<	if( exI > exJ ){
1223	<	tempEx = exI;
1224	<	exI = exJ;
1225	<	exJ = tempEx;
1226	<	}
1322	>	case NVT_ENS:
1323	>	myNVT = new NVT<RealIntegrator>( info, the_ff );
1324	>	myNVT->setTargetTemp(globals->getTargetTemp());
1325
1326	+	if (globals->haveTauThermostat())
1327	+	myNVT->setTauThermostat(globals->getTauThermostat());
1328
1329	<	#ifdef IS_MPI
1330	<
1331	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
1332	<	the_atoms[exI]->getGlobalIndex() + 1;
1333	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1334	<	the_atoms[exJ]->getGlobalIndex() + 1;
1235	<
1236	<	#else  // isn't MPI
1237	<
1238	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1239	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1240	<	// fortran indexes from 1 (hence the +1 in the indexing)
1241	<	#endif  //is_mpi
1242	<
1243	<
1244	<	// increment the index and repeat;
1245	<	index++;
1246	<	}
1247	<	offset += comp_stamps[i]->getNAtoms();
1248	<
1249	<	#ifdef IS_MPI
1250	<	}
1251	<	#endif //is_mpi
1252	<
1253	<	molIndex++;
1329	>	else {
1330	>	sprintf( painCave.errMsg,
1331	>	"SimSetup error: If you use the NVT\n"
1332	>	"    ensemble, you must set tauThermostat.\n");
1333	>	painCave.isFatal = 1;
1334	>	simError();
1335		}
1336	<	}
1336	>	break;
1337
1338	<	the_ff->initializeTorsions( the_torsions );
1339	<	}
1338	>	case NPTi_ENS:
1339	>	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1340	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1341
1342	<	void SimSetup::initFromBass( void ){
1343	<
1344	<	int i, j, k;
1263	<	int n_cells;
1264	<	double cellx, celly, cellz;
1265	<	double temp1, temp2, temp3;
1266	<	int n_per_extra;
1267	<	int n_extra;
1268	<	int have_extra, done;
1269	<
1270	<	temp1 = (double)tot_nmol / 4.0;
1271	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1272	<	temp3 = ceil( temp2 );
1273	<
1274	<	have_extra =0;
1275	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1276	<	have_extra =1;
1277	<
1278	<	n_cells = (int)temp3 - 1;
1279	<	cellx = simnfo->box_x / temp3;
1280	<	celly = simnfo->box_y / temp3;
1281	<	cellz = simnfo->box_z / temp3;
1282	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1283	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1284	<	n_per_extra = (int)ceil( temp1 );
1285	<
1286	<	if( n_per_extra > 4){
1342	>	if (globals->haveTargetPressure())
1343	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1344	>	else {
1345		sprintf( painCave.errMsg,
1346	<	"SimSetup error. There has been an error in constructing"
1347	<	" the non-complete lattice.\n" );
1346	>	"SimSetup error: If you use a constant pressure\n"
1347	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1348		painCave.isFatal = 1;
1349		simError();
1350		}
1351	<	}
1352	<	else{
1353	<	n_cells = (int)temp3;
1354	<	cellx = simnfo->box_x / temp3;
1355	<	celly = simnfo->box_y / temp3;
1356	<	cellz = simnfo->box_z / temp3;
1357	<	}
1351	>
1352	>	if( globals->haveTauThermostat() )
1353	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1354	>	else{
1355	>	sprintf( painCave.errMsg,
1356	>	"SimSetup error: If you use an NPT\n"
1357	>	"    ensemble, you must set tauThermostat.\n");
1358	>	painCave.isFatal = 1;
1359	>	simError();
1360	>	}
1361
1362	<	current_mol = 0;
1363	<	current_comp_mol = 0;
1364	<	current_comp = 0;
1365	<	current_atom_ndx = 0;
1366	<
1367	<	for( i=0; i < n_cells ; i++ ){
1368	<	for( j=0; j < n_cells; j++ ){
1369	<	for( k=0; k < n_cells; k++ ){
1309	<
1310	<	makeElement( i * cellx,
1311	<	j * celly,
1312	<	k * cellz );
1313	<
1314	<	makeElement( i * cellx + 0.5 * cellx,
1315	<	j * celly + 0.5 * celly,
1316	<	k * cellz );
1317	<
1318	<	makeElement( i * cellx,
1319	<	j * celly + 0.5 * celly,
1320	<	k * cellz + 0.5 * cellz );
1321	<
1322	<	makeElement( i * cellx + 0.5 * cellx,
1323	<	j * celly,
1324	<	k * cellz + 0.5 * cellz );
1325	<	}
1362	>	if( globals->haveTauBarostat() )
1363	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1364	>	else{
1365	>	sprintf( painCave.errMsg,
1366	>	"SimSetup error: If you use an NPT\n"
1367	>	"    ensemble, you must set tauBarostat.\n");
1368	>	painCave.isFatal = 1;
1369	>	simError();
1370		}
1371	<	}
1371	>	break;
1372
1373	<	if( have_extra ){
1374	<	done = 0;
1373	>	case NPTf_ENS:
1374	>	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1375	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1376
1377	<	int start_ndx;
1378	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1379	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1380	<
1381	<	if( i < n_cells ){
1377	>	if (globals->haveTargetPressure())
1378	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1379	>	else {
1380	>	sprintf( painCave.errMsg,
1381	>	"SimSetup error: If you use a constant pressure\n"
1382	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1383	>	painCave.isFatal = 1;
1384	>	simError();
1385	>	}
1386
1387	<	if( j < n_cells ){
1388	<	start_ndx = n_cells;
1389	<	}
1390	<	else start_ndx = 0;
1391	<	}
1392	<	else start_ndx = 0;
1387	>	if( globals->haveTauThermostat() )
1388	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1389	>	else{
1390	>	sprintf( painCave.errMsg,
1391	>	"SimSetup error: If you use an NPT\n"
1392	>	"    ensemble, you must set tauThermostat.\n");
1393	>	painCave.isFatal = 1;
1394	>	simError();
1395	>	}
1396
1397	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1397	>	if( globals->haveTauBarostat() )
1398	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1399	>	else{
1400	>	sprintf( painCave.errMsg,
1401	>	"SimSetup error: If you use an NPT\n"
1402	>	"    ensemble, you must set tauBarostat.\n");
1403	>	painCave.isFatal = 1;
1404	>	simError();
1405	>	}
1406	>	break;
1407	>
1408	>	case NPTim_ENS:
1409	>	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1410	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1411
1412	<	makeElement( i * cellx,
1413	<	j * celly,
1414	<	k * cellz );
1415	<	done = ( current_mol >= tot_nmol );
1412	>	if (globals->haveTargetPressure())
1413	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1414	>	else {
1415	>	sprintf( painCave.errMsg,
1416	>	"SimSetup error: If you use a constant pressure\n"
1417	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1418	>	painCave.isFatal = 1;
1419	>	simError();
1420	>	}
1421	>
1422	>	if( globals->haveTauThermostat() )
1423	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1424	>	else{
1425	>	sprintf( painCave.errMsg,
1426	>	"SimSetup error: If you use an NPT\n"
1427	>	"    ensemble, you must set tauThermostat.\n");
1428	>	painCave.isFatal = 1;
1429	>	simError();
1430	>	}
1431
1432	<	if( !done && n_per_extra > 1 ){
1433	<	makeElement( i * cellx + 0.5 * cellx,
1434	<	j * celly + 0.5 * celly,
1435	<	k * cellz );
1436	<	done = ( current_mol >= tot_nmol );
1437	<	}
1432	>	if( globals->haveTauBarostat() )
1433	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1434	>	else{
1435	>	sprintf( painCave.errMsg,
1436	>	"SimSetup error: If you use an NPT\n"
1437	>	"    ensemble, you must set tauBarostat.\n");
1438	>	painCave.isFatal = 1;
1439	>	simError();
1440	>	}
1441	>	break;
1442
1443	<	if( !done && n_per_extra > 2){
1444	<	makeElement( i * cellx,
1445	<	j * celly + 0.5 * celly,
1362	<	k * cellz + 0.5 * cellz );
1363	<	done = ( current_mol >= tot_nmol );
1364	<	}
1443	>	case NPTfm_ENS:
1444	>	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1445	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1446
1447	<	if( !done && n_per_extra > 3){
1448	<	makeElement( i * cellx + 0.5 * cellx,
1449	<	j * celly,
1450	<	k * cellz + 0.5 * cellz );
1451	<	done = ( current_mol >= tot_nmol );
1452	<	}
1453	<	}
1454	<	}
1447	>	if (globals->haveTargetPressure())
1448	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1449	>	else {
1450	>	sprintf( painCave.errMsg,
1451	>	"SimSetup error: If you use a constant pressure\n"
1452	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1453	>	painCave.isFatal = 1;
1454	>	simError();
1455		}
1456	<	}
1456	>
1457	>	if( globals->haveTauThermostat() )
1458	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1459	>	else{
1460	>	sprintf( painCave.errMsg,
1461	>	"SimSetup error: If you use an NPT\n"
1462	>	"    ensemble, you must set tauThermostat.\n");
1463	>	painCave.isFatal = 1;
1464	>	simError();
1465	>	}
1466
1467	<
1468	<	for( i=0; i<simnfo->n_atoms; i++ ){
1469	<	simnfo->atoms[i]->set_vx( 0.0 );
1380	<	simnfo->atoms[i]->set_vy( 0.0 );
1381	<	simnfo->atoms[i]->set_vz( 0.0 );
1382	<	}
1383	<	}
1384	<
1385	<	void SimSetup::makeElement( double x, double y, double z ){
1386	<
1387	<	int k;
1388	<	AtomStamp* current_atom;
1389	<	DirectionalAtom* dAtom;
1390	<	double rotMat[3][3];
1391	<
1392	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1393	<
1394	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1395	<	if( !current_atom->havePosition() ){
1467	>	if( globals->haveTauBarostat() )
1468	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1469	>	else{
1470		sprintf( painCave.errMsg,
1471	<	"SimSetup:initFromBass error.\n"
1472	<	"\tComponent %s, atom %s does not have a position specified.\n"
1399	<	"\tThe initialization routine is unable to give a start"
1400	<	" position.\n",
1401	<	comp_stamps[current_comp]->getID(),
1402	<	current_atom->getType() );
1471	>	"SimSetup error: If you use an NPT\n"
1472	>	"    ensemble, you must set tauBarostat.\n");
1473		painCave.isFatal = 1;
1474		simError();
1475		}
1476	+	break;
1477	+
1478	+	case NVEZCONS_ENS:
1479	+	{
1480
1481	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1482	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1483	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1481	>	if(globals->haveZConsTime()){
1482	>
1483	>	//add sample time of z-constraint  into SimInfo's property list
1484	>	DoubleData* zconsTimeProp = new DoubleData();
1485	>	zconsTimeProp->setID("zconstime");
1486	>	zconsTimeProp->setData(globals->getZConsTime());
1487	>	info->addProperty(zconsTimeProp);
1488	>	}
1489	>	else{
1490	>	sprintf( painCave.errMsg,
1491	>	"ZConstraint error: If you use an ZConstraint\n"
1492	>	" , you must set sample time.\n");
1493	>	painCave.isFatal = 1;
1494	>	simError();
1495	>	}
1496	>
1497	>	if(globals->haveIndexOfAllZConsMols()){
1498	>
1499	>	//add index of z-constraint molecules into SimInfo's property list
1500	>	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1501	>	sort(tempIndex.begin(), tempIndex.end());
1502	>
1503	>	IndexData* zconsIndex = new IndexData();
1504	>	zconsIndex->setID("zconsindex");
1505	>	zconsIndex->setIndexData(tempIndex);
1506	>	info->addProperty(zconsIndex);
1507	>	}
1508	>	else{
1509	>	sprintf( painCave.errMsg,
1510	>	"SimSetup error: If you use an ZConstraint\n"
1511	>	" , you must set index of z-constraint molecules.\n");
1512	>	painCave.isFatal = 1;
1513	>	simError();
1514	>
1515	>	}
1516
1517	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1517	>	//Determine the name of ouput file and add it into SimInfo's property list
1518	>	//Be careful, do not use inFileName, since it is a pointer which
1519	>	//point to a string at master node, and slave nodes do not contain that string
1520	>
1521	>	string zconsOutput(info->finalName);
1522	>
1523	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1524	>
1525	>	StringData* zconsFilename = new StringData();
1526	>	zconsFilename->setID("zconsfilename");
1527	>	zconsFilename->setData(zconsOutput);
1528
1529	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1529	>	info->addProperty(zconsFilename);
1530	>
1531	>	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff );
1532	>
1533	>	break;
1534	>	}
1535	>
1536	>	default:
1537	>	sprintf( painCave.errMsg,
1538	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1539	>	painCave.isFatal = 1;
1540	>	simError();
1541	>	}
1542
1543	<	rotMat[0][0] = 1.0;
1416	<	rotMat[0][1] = 0.0;
1417	<	rotMat[0][2] = 0.0;
1543	>	}
1544
1545	<	rotMat[1][0] = 0.0;
1420	<	rotMat[1][1] = 1.0;
1421	<	rotMat[1][2] = 0.0;
1545	>	void SimSetup::initFortran( void ){
1546
1547	<	rotMat[2][0] = 0.0;
1548	<	rotMat[2][1] = 0.0;
1549	<	rotMat[2][2] = 1.0;
1550	<
1427	<	dAtom->setA( rotMat );
1428	<	}
1429	<
1430	<	current_atom_ndx++;
1547	>	info->refreshSim();
1548	>
1549	>	if( !strcmp( info->mixingRule, "standard") ){
1550	>	the_ff->initForceField( LB_MIXING_RULE );
1551		}
1552	+	else if( !strcmp( info->mixingRule, "explicit") ){
1553	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1554	+	}
1555	+	else{
1556	+	sprintf( painCave.errMsg,
1557	+	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1558	+	info->mixingRule );
1559	+	painCave.isFatal = 1;
1560	+	simError();
1561	+	}
1562
1433	–	current_mol++;
1434	–	current_comp_mol++;
1563
1564	<	if( current_comp_mol >= components_nmol[current_comp] ){
1564	>	#ifdef IS_MPI
1565	>	strcpy( checkPointMsg,
1566	>	"Successfully intialized the mixingRule for Fortran." );
1567	>	MPIcheckPoint();
1568	>	#endif // is_mpi
1569
1438	–	current_comp_mol = 0;
1439	–	current_comp++;
1440	–	}
1570		}

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