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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 394 by gezelter, Mon Mar 24 21:55:34 2003 UTC vs.
Revision 661 by tim, Fri Aug 1 16:18:13 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	+	#define NVTZCONS_ENS   7
27	+	#define NPTiZCONS_ENS  8
28	+	#define NPTfZCONS_ENS  9
29	+	#define NPTimZCONS_ENS 10
30	+	#define NPTfmZCONS_ENS 11
31	+
32	+	#define FF_DUFF 0
33	+	#define FF_LJ   1
34	+	#define FF_EAM  2
35	+
36	+	using namespace std;
37	+
38		SimSetup::SimSetup(){
39	+
40	+	isInfoArray = 0;
41	+	nInfo = 1;
42	+
43		stamps = new MakeStamps();
44		globals = new Globals();
45
46	+
47		#ifdef IS_MPI
48		strcpy( checkPointMsg, "SimSetup creation successful" );
49		MPIcheckPoint();
#	Line 27 | Line 55 | void SimSetup::parseFile( char* fileName ){
55		delete globals;
56		}
57
58	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
59	+	info = the_info;
60	+	nInfo = theNinfo;
61	+	isInfoArray = 1;
62	+	}
63	+
64	+
65		void SimSetup::parseFile( char* fileName ){
66
67		#ifdef IS_MPI
#	Line 64 | Line 99 | void SimSetup::createSim( void ){
99
100		void SimSetup::createSim( void ){
101
102	<	MakeStamps *the_stamps;
103	<	Globals* the_globals;
104	<	int i, j;
102	>	int i, j, k, globalAtomIndex;
103	>
104	>	// gather all of the information from the Bass file
105	>
106	>	gatherInfo();
107
108	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
108	>	// creation of complex system objects
109
110	<	// 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();
110	>	sysObjectsCreation();
111
112	<	// get the ones we know are there, yet still may need some work.
113	<	n_components = the_globals->getNComponents();
114	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
112	>	// check on the post processing info
113	>
114	>	finalInfoCheck();
115
116	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
116	>	// initialize the system coordinates
117
118	+	initSystemCoords();
119	+
120
121	<	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	<	}
121	>	// make the output filenames
122
123	+	makeOutNames();
124	+
125	+	// make the integrator
126	+
127	+	makeIntegrator();
128	+
129		#ifdef IS_MPI
130	<	strcpy( checkPointMsg, "ForceField creation successful" );
131	<	MPIcheckPoint();
106	<	#endif // is_mpi
130	>	mpiSim->mpiRefresh();
131	>	#endif
132
133	<
133	>	// initialize the Fortran
134
135	<	// 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];
135	>	initFortran();
136
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
137
119	–	tot_nmol = 0;
120	–	for( i=0; i<n_components; i++ ){
138
139	<	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	<	}
139	>	}
140
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	–	}
141
142	<	#ifdef IS_MPI
161	<	strcpy( checkPointMsg, "Have the number of components" );
162	<	MPIcheckPoint();
163	<	#endif // is_mpi
142	>	void SimSetup::makeMolecules( void ){
143
144	<	// make an array of molecule stamps that match the components used.
145	<	// also extract the used stamps out into a separate linked list
144	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
145	>	molInit molInfo;
146	>	DirectionalAtom* dAtom;
147	>	LinkedAssign* extras;
148	>	LinkedAssign* current_extra;
149	>	AtomStamp* currentAtom;
150	>	BondStamp* currentBond;
151	>	BendStamp* currentBend;
152	>	TorsionStamp* currentTorsion;
153
154	<	simnfo->nComponents = n_components;
155	<	simnfo->componentsNmol = components_nmol;
156	<	simnfo->compStamps = comp_stamps;
157	<	simnfo->headStamp = new LinkedMolStamp();
154	>	bond_pair* theBonds;
155	>	bend_set* theBends;
156	>	torsion_set* theTorsions;
157	>
158
159	<	char* id;
174	<	LinkedMolStamp* headStamp = simnfo->headStamp;
175	<	LinkedMolStamp* currentStamp = NULL;
176	<	for( i=0; i<n_components; i++ ){
159	>	//init the forceField paramters
160
161	<	id = the_components[i]->getType();
162	<	comp_stamps[i] = NULL;
161	>	the_ff->readParams();
162	>
163	>
164	>	// init the atoms
165	>
166	>	double ux, uy, uz, u, uSqr;
167	>
168	>	atomOffset = 0;
169	>	excludeOffset = 0;
170	>	for(i=0; i<info->n_mol; i++){
171
172	<	// check to make sure the component isn't already in the list
172	>	stampID = the_molecules[i].getStampID();
173
174	<	comp_stamps[i] = headStamp->match( id );
175	<	if( comp_stamps[i] == NULL ){
174	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
175	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
176	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
177	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
178	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
179	>
180	>	molInfo.myAtoms = &the_atoms[atomOffset];
181	>	molInfo.myExcludes = &the_excludes[excludeOffset];
182	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
183	>	molInfo.myBends = new Bend*[molInfo.nBends];
184	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
185	>
186	>	theBonds = new bond_pair[molInfo.nBonds];
187	>	theBends = new bend_set[molInfo.nBends];
188	>	theTorsions = new torsion_set[molInfo.nTorsions];
189	>
190	>	// make the Atoms
191	>
192	>	for(j=0; j<molInfo.nAtoms; j++){
193
194	<	// extract the component from the list;
195	<
196	<	currentStamp = the_stamps->extractMolStamp( id );
197	<	if( currentStamp == NULL ){
198	<	sprintf( painCave.errMsg,
199	<	"SimSetup error: Component \"%s\" was not found in the "
200	<	"list of declared molecules\n",
201	<	id );
202	<	painCave.isFatal = 1;
203	<	simError();
194	>	currentAtom = comp_stamps[stampID]->getAtom( j );
195	>	if( currentAtom->haveOrientation() ){
196	>
197	>	dAtom = new DirectionalAtom(j + atomOffset);
198	>	info->n_oriented++;
199	>	molInfo.myAtoms[j] = dAtom;
200	>
201	>	ux = currentAtom->getOrntX();
202	>	uy = currentAtom->getOrntY();
203	>	uz = currentAtom->getOrntZ();
204	>
205	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
206	>
207	>	u = sqrt( uSqr );
208	>	ux = ux / u;
209	>	uy = uy / u;
210	>	uz = uz / u;
211	>
212	>	dAtom->setSUx( ux );
213	>	dAtom->setSUy( uy );
214	>	dAtom->setSUz( uz );
215		}
216	<
217	<	headStamp->add( currentStamp );
218	<	comp_stamps[i] = headStamp->match( id );
219	<	}
220	<	}
202	<
216	>	else{
217	>	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
218	>	}
219	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
220	>
221		#ifdef IS_MPI
222	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
223	<	MPIcheckPoint();
222	>
223	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
224	>
225		#endif // is_mpi
226	<
226	>	}
227	>
228	>	// make the bonds
229	>	for(j=0; j<molInfo.nBonds; j++){
230	>
231	>	currentBond = comp_stamps[stampID]->getBond( j );
232	>	theBonds[j].a = currentBond->getA() + atomOffset;
233	>	theBonds[j].b = currentBond->getB() + atomOffset;
234
235	+	exI = theBonds[j].a;
236	+	exJ = theBonds[j].b;
237
238	+	// exclude_I must always be the smaller of the pair
239	+	if( exI > exJ ){
240	+	tempEx = exI;
241	+	exI = exJ;
242	+	exJ = tempEx;
243	+	}
244	+	#ifdef IS_MPI
245	+	tempEx = exI;
246	+	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
247	+	tempEx = exJ;
248	+	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
249	+
250	+	the_excludes[j+excludeOffset]->setPair( exI, exJ );
251	+	#else  // isn't MPI
252
253	<	// caclulate the number of atoms, bonds, bends and torsions
253	>	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
254	>	#endif  //is_mpi
255	>	}
256	>	excludeOffset += molInfo.nBonds;
257
258	<	tot_atoms = 0;
259	<	tot_bonds = 0;
260	<	tot_bends = 0;
261	<	tot_torsions = 0;
262	<	for( i=0; i<n_components; i++ ){
258	>	//make the bends
259	>	for(j=0; j<molInfo.nBends; j++){
260	>
261	>	currentBend = comp_stamps[stampID]->getBend( j );
262	>	theBends[j].a = currentBend->getA() + atomOffset;
263	>	theBends[j].b = currentBend->getB() + atomOffset;
264	>	theBends[j].c = currentBend->getC() + atomOffset;
265	>
266	>	if( currentBend->haveExtras() ){
267	>
268	>	extras = currentBend->getExtras();
269	>	current_extra = extras;
270	>
271	>	while( current_extra != NULL ){
272	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
273	>
274	>	switch( current_extra->getType() ){
275	>
276	>	case 0:
277	>	theBends[j].ghost =
278	>	current_extra->getInt() + atomOffset;
279	>	theBends[j].isGhost = 1;
280	>	break;
281	>
282	>	case 1:
283	>	theBends[j].ghost =
284	>	(int)current_extra->getDouble() + atomOffset;
285	>	theBends[j].isGhost = 1;
286	>	break;
287	>
288	>	default:
289	>	sprintf( painCave.errMsg,
290	>	"SimSetup Error: ghostVectorSource was neither a "
291	>	"double nor an int.\n"
292	>	"-->Bend[%d] in %s\n",
293	>	j, comp_stamps[stampID]->getID() );
294	>	painCave.isFatal = 1;
295	>	simError();
296	>	}
297	>	}
298	>
299	>	else{
300	>
301	>	sprintf( painCave.errMsg,
302	>	"SimSetup Error: unhandled bend assignment:\n"
303	>	"    -->%s in Bend[%d] in %s\n",
304	>	current_extra->getlhs(),
305	>	j, comp_stamps[stampID]->getID() );
306	>	painCave.isFatal = 1;
307	>	simError();
308	>	}
309	>
310	>	current_extra = current_extra->getNext();
311	>	}
312	>	}
313	>
314	>	if( !theBends[j].isGhost ){
315	>
316	>	exI = theBends[j].a;
317	>	exJ = theBends[j].c;
318	>	}
319	>	else{
320	>
321	>	exI = theBends[j].a;
322	>	exJ = theBends[j].b;
323	>	}
324	>
325	>	// exclude_I must always be the smaller of the pair
326	>	if( exI > exJ ){
327	>	tempEx = exI;
328	>	exI = exJ;
329	>	exJ = tempEx;
330	>	}
331	>	#ifdef IS_MPI
332	>	tempEx = exI;
333	>	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
334	>	tempEx = exJ;
335	>	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
336	>
337	>	the_excludes[j+excludeOffset]->setPair( exI, exJ );
338	>	#else  // isn't MPI
339	>	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
340	>	#endif  //is_mpi
341	>	}
342	>	excludeOffset += molInfo.nBends;
343	>
344	>	for(j=0; j<molInfo.nTorsions; j++){
345	>
346	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
347	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
348	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
349	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
350	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
351	>
352	>	exI = theTorsions[j].a;
353	>	exJ = theTorsions[j].d;
354	>
355	>	// exclude_I must always be the smaller of the pair
356	>	if( exI > exJ ){
357	>	tempEx = exI;
358	>	exI = exJ;
359	>	exJ = tempEx;
360	>	}
361	>	#ifdef IS_MPI
362	>	tempEx = exI;
363	>	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
364	>	tempEx = exJ;
365	>	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
366	>
367	>	the_excludes[j+excludeOffset]->setPair( exI, exJ );
368	>	#else  // isn't MPI
369	>	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
370	>	#endif  //is_mpi
371	>	}
372	>	excludeOffset += molInfo.nTorsions;
373	>
374
375	<	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	<	}
375	>	// send the arrays off to the forceField for init.
376
377	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
377	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
378	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
379	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
380	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
381
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;
382
383	<
383	>	the_molecules[i].initialize( molInfo );
384	>
385	>
386	>	atomOffset += molInfo.nAtoms;
387	>	delete[] theBonds;
388	>	delete[] theBends;
389	>	delete[] theTorsions;
390	>	}
391	>
392		#ifdef IS_MPI
393	+	sprintf( checkPointMsg, "all molecules initialized succesfully" );
394	+	MPIcheckPoint();
395	+	#endif // is_mpi
396
397	<	// divide the molecules among processors here.
398	<
399	<	mpiSim = new mpiSimulation( simnfo );
240	<
241	<
397	>	// clean up the forcefield
398	>	the_ff->calcRcut();
399	>	the_ff->cleanMe();
400
401	<	globalIndex = mpiSim->divideLabor();
401	>	}
402
403	+	void SimSetup::initFromBass( void ){
404
405	+	int i, j, k;
406	+	int n_cells;
407	+	double cellx, celly, cellz;
408	+	double temp1, temp2, temp3;
409	+	int n_per_extra;
410	+	int n_extra;
411	+	int have_extra, done;
412
413	<	// set up the local variables
414	<
415	<	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++ ){
413	>	temp1 = (double)tot_nmol / 4.0;
414	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
415	>	temp3 = ceil( temp2 );
416
417	<	for( j=0; j<components_nmol[i]; j++ ){
418	<
419	<	if( mpiSim->getMyMolStart() <= allMol &&
420	<	allMol <= mpiSim->getMyMolEnd() ){
421	<
422	<	local_atoms +=    comp_stamps[i]->getNAtoms();
423	<	local_bonds +=    comp_stamps[i]->getNBonds();
424	<	local_bends +=    comp_stamps[i]->getNBends();
425	<	local_torsions += comp_stamps[i]->getNTorsions();
426	<	localMol++;
427	<	}
428	<	allMol++;
417	>	have_extra =0;
418	>	if( temp2 < temp3 ){ // we have a non-complete lattice
419	>	have_extra =1;
420	>
421	>	n_cells = (int)temp3 - 1;
422	>	cellx = info->boxL[0] / temp3;
423	>	celly = info->boxL[1] / temp3;
424	>	cellz = info->boxL[2] / temp3;
425	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
426	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
427	>	n_per_extra = (int)ceil( temp1 );
428	>
429	>	if( n_per_extra > 4){
430	>	sprintf( painCave.errMsg,
431	>	"SimSetup error. There has been an error in constructing"
432	>	" the non-complete lattice.\n" );
433	>	painCave.isFatal = 1;
434	>	simError();
435		}
436		}
437	<	local_SRI = local_bonds + local_bends + local_torsions;
438	<
437	>	else{
438	>	n_cells = (int)temp3;
439	>	cellx = info->boxL[0] / temp3;
440	>	celly = info->boxL[1] / temp3;
441	>	cellz = info->boxL[2] / temp3;
442	>	}
443
444	<	simnfo->n_atoms = mpiSim->getMyNlocal();
445	<
446	<	if( local_atoms != simnfo->n_atoms ){
447	<	sprintf( painCave.errMsg,
448	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
449	<	" localAtom (%d) are note equal.\n",
450	<	simnfo->n_atoms,
451	<	local_atoms );
452	<	painCave.isFatal = 1;
453	<	simError();
444	>	current_mol = 0;
445	>	current_comp_mol = 0;
446	>	current_comp = 0;
447	>	current_atom_ndx = 0;
448	>
449	>	for( i=0; i < n_cells ; i++ ){
450	>	for( j=0; j < n_cells; j++ ){
451	>	for( k=0; k < n_cells; k++ ){
452	>
453	>	makeElement( i * cellx,
454	>	j * celly,
455	>	k * cellz );
456	>
457	>	makeElement( i * cellx + 0.5 * cellx,
458	>	j * celly + 0.5 * celly,
459	>	k * cellz );
460	>
461	>	makeElement( i * cellx,
462	>	j * celly + 0.5 * celly,
463	>	k * cellz + 0.5 * cellz );
464	>
465	>	makeElement( i * cellx + 0.5 * cellx,
466	>	j * celly,
467	>	k * cellz + 0.5 * cellz );
468	>	}
469	>	}
470		}
471
472	<	simnfo->n_bonds = local_bonds;
473	<	simnfo->n_bends = local_bends;
291	<	simnfo->n_torsions = local_torsions;
292	<	simnfo->n_SRI = local_SRI;
293	<	simnfo->n_mol = localMol;
472	>	if( have_extra ){
473	>	done = 0;
474
475	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
476	<	MPIcheckPoint();
477	<
298	<
299	<	#endif // is_mpi
300	<
475	>	int start_ndx;
476	>	for( i=0; i < (n_cells+1) && !done; i++ ){
477	>	for( j=0; j < (n_cells+1) && !done; j++ ){
478
479	<	// create the atom and short range interaction arrays
479	>	if( i < n_cells ){
480
481	<	Atom::createArrays(simnfo->n_atoms);
482	<	the_atoms = new Atom*[simnfo->n_atoms];
483	<	the_molecules = new Molecule[simnfo->n_mol];
481	>	if( j < n_cells ){
482	>	start_ndx = n_cells;
483	>	}
484	>	else start_ndx = 0;
485	>	}
486	>	else start_ndx = 0;
487
488	+	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
489	+
490	+	makeElement( i * cellx,
491	+	j * celly,
492	+	k * cellz );
493	+	done = ( current_mol >= tot_nmol );
494
495	<	if( simnfo->n_SRI ){
496	<	the_sris = new SRI*[simnfo->n_SRI];
497	<	the_excludes = new int[2 * simnfo->n_SRI];
498	<	simnfo->globalExcludes = new int;
499	<	simnfo->n_exclude = tot_SRI;
495	>	if( !done && n_per_extra > 1 ){
496	>	makeElement( i * cellx + 0.5 * cellx,
497	>	j * celly + 0.5 * celly,
498	>	k * cellz );
499	>	done = ( current_mol >= tot_nmol );
500	>	}
501	>
502	>	if( !done && n_per_extra > 2){
503	>	makeElement( i * cellx,
504	>	j * celly + 0.5 * celly,
505	>	k * cellz + 0.5 * cellz );
506	>	done = ( current_mol >= tot_nmol );
507	>	}
508	>
509	>	if( !done && n_per_extra > 3){
510	>	makeElement( i * cellx + 0.5 * cellx,
511	>	j * celly,
512	>	k * cellz + 0.5 * cellz );
513	>	done = ( current_mol >= tot_nmol );
514	>	}
515	>	}
516	>	}
517	>	}
518		}
519	+
520	+
521	+	for( i=0; i<info->n_atoms; i++ ){
522	+	info->atoms[i]->set_vx( 0.0 );
523	+	info->atoms[i]->set_vy( 0.0 );
524	+	info->atoms[i]->set_vz( 0.0 );
525	+	}
526	+	}
527	+
528	+	void SimSetup::makeElement( double x, double y, double z ){
529	+
530	+	int k;
531	+	AtomStamp* current_atom;
532	+	DirectionalAtom* dAtom;
533	+	double rotMat[3][3];
534	+
535	+	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
536	+
537	+	current_atom = comp_stamps[current_comp]->getAtom( k );
538	+	if( !current_atom->havePosition() ){
539	+	sprintf( painCave.errMsg,
540	+	"SimSetup:initFromBass error.\n"
541	+	"\tComponent %s, atom %s does not have a position specified.\n"
542	+	"\tThe initialization routine is unable to give a start"
543	+	" position.\n",
544	+	comp_stamps[current_comp]->getID(),
545	+	current_atom->getType() );
546	+	painCave.isFatal = 1;
547	+	simError();
548	+	}
549	+
550	+	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
551	+	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
552	+	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
553	+
554	+	if( the_atoms[current_atom_ndx]->isDirectional() ){
555	+
556	+	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
557	+
558	+	rotMat[0][0] = 1.0;
559	+	rotMat[0][1] = 0.0;
560	+	rotMat[0][2] = 0.0;
561	+
562	+	rotMat[1][0] = 0.0;
563	+	rotMat[1][1] = 1.0;
564	+	rotMat[1][2] = 0.0;
565	+
566	+	rotMat[2][0] = 0.0;
567	+	rotMat[2][1] = 0.0;
568	+	rotMat[2][2] = 1.0;
569	+
570	+	dAtom->setA( rotMat );
571	+	}
572	+
573	+	current_atom_ndx++;
574	+	}
575	+
576	+	current_mol++;
577	+	current_comp_mol++;
578	+
579	+	if( current_comp_mol >= components_nmol[current_comp] ){
580	+
581	+	current_comp_mol = 0;
582	+	current_comp++;
583	+	}
584	+	}
585	+
586	+
587	+	void SimSetup::gatherInfo( void ){
588	+	int i,j,k;
589	+
590	+	ensembleCase = -1;
591	+	ffCase = -1;
592	+
593	+	// get the stamps and globals;
594	+	stamps = stamps;
595	+	globals = globals;
596	+
597	+	// set the easy ones first
598	+	info->target_temp = globals->getTargetTemp();
599	+	info->dt = globals->getDt();
600	+	info->run_time = globals->getRunTime();
601	+	n_components = globals->getNComponents();
602	+
603	+
604	+	// get the forceField
605	+
606	+	strcpy( force_field, globals->getForceField() );
607	+
608	+	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
609	+	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
610	+	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
611		else{
612	<
613	<	the_excludes = new int[2];
614	<	the_excludes[0] = 0;
615	<	the_excludes[1] = 0;
616	<	simnfo->globalExcludes = new int;
617	<	simnfo->globalExcludes[0] = 0;
612	>	sprintf( painCave.errMsg,
613	>	"SimSetup Error. Unrecognized force field -> %s\n",
614	>	force_field );
615	>	painCave.isFatal = 1;
616	>	simError();
617	>	}
618
619	<	simnfo->n_exclude = 1;
619	>	// get the ensemble
620	>
621	>	strcpy( ensemble, globals->getEnsemble() );
622	>
623	>	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
624	>	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
625	>	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
626	>	ensembleCase = NPTi_ENS;
627	>	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
628	>	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
629	>	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
630	>
631	>	else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS;
632	>	else if( !strcasecmp( ensemble, "NVTZCONS"))  ensembleCase = NVTZCONS_ENS;
633	>	else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPTZCONS"))
634	>	ensembleCase = NPTiZCONS_ENS;
635	>	else if( !strcasecmp( ensemble, "NPTfZCONS"))  ensembleCase = NPTfZCONS_ENS;
636	>	else if( !strcasecmp( ensemble, "NPTimZCONS"))  ensembleCase = NPTimZCONS_ENS;
637	>	else if( !strcasecmp( ensemble, "NPTfmZCONS"))  ensembleCase = NPTfmZCONS_ENS;
638	>
639	>	else{
640	>	sprintf( painCave.errMsg,
641	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
642	>	"reverting to NVE for this simulation.\n",
643	>	ensemble );
644	>	painCave.isFatal = 0;
645	>	simError();
646	>	strcpy( ensemble, "NVE" );
647	>	ensembleCase = NVE_ENS;
648	>	}
649	>	strcpy( info->ensemble, ensemble );
650	>
651	>	// get the mixing rule
652	>
653	>	strcpy( info->mixingRule, globals->getMixingRule() );
654	>	info->usePBC = globals->getPBC();
655	>
656	>
657	>	// get the components and calculate the tot_nMol and indvidual n_mol
658	>
659	>	the_components = globals->getComponents();
660	>	components_nmol = new int[n_components];
661	>
662	>
663	>	if( !globals->haveNMol() ){
664	>	// we don't have the total number of molecules, so we assume it is
665	>	// given in each component
666	>
667	>	tot_nmol = 0;
668	>	for( i=0; i<n_components; i++ ){
669	>
670	>	if( !the_components[i]->haveNMol() ){
671	>	// we have a problem
672	>	sprintf( painCave.errMsg,
673	>	"SimSetup Error. No global NMol or component NMol"
674	>	" given. Cannot calculate the number of atoms.\n" );
675	>	painCave.isFatal = 1;
676	>	simError();
677	>	}
678	>
679	>	tot_nmol += the_components[i]->getNMol();
680	>	components_nmol[i] = the_components[i]->getNMol();
681	>	}
682		}
683	+	else{
684	+	sprintf( painCave.errMsg,
685	+	"SimSetup error.\n"
686	+	"\tSorry, the ability to specify total"
687	+	" nMols and then give molfractions in the components\n"
688	+	"\tis not currently supported."
689	+	" Please give nMol in the components.\n" );
690	+	painCave.isFatal = 1;
691	+	simError();
692	+	}
693
694	<	// set the arrays into the SimInfo object
694	>	// set the status, sample, and thermal kick times
695	>
696	>	if( globals->haveSampleTime() ){
697	>	info->sampleTime = globals->getSampleTime();
698	>	info->statusTime = info->sampleTime;
699	>	info->thermalTime = info->sampleTime;
700	>	}
701	>	else{
702	>	info->sampleTime = globals->getRunTime();
703	>	info->statusTime = info->sampleTime;
704	>	info->thermalTime = info->sampleTime;
705	>	}
706
707	<	simnfo->atoms = the_atoms;
708	<	simnfo->sr_interactions = the_sris;
709	<	simnfo->nGlobalExcludes = 0;
331	<	simnfo->excludes = the_excludes;
707	>	if( globals->haveStatusTime() ){
708	>	info->statusTime = globals->getStatusTime();
709	>	}
710
711	+	if( globals->haveThermalTime() ){
712	+	info->thermalTime = globals->getThermalTime();
713	+	}
714
715	+	// check for the temperature set flag
716	+
717	+	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
718	+
719		// get some of the tricky things that may still be in the globals
720
721	<
722	<	if( the_globals->haveBox() ){
723	<	simnfo->box_x = the_globals->getBox();
724	<	simnfo->box_y = the_globals->getBox();
725	<	simnfo->box_z = the_globals->getBox();
721	>	double boxVector[3];
722	>	if( globals->haveBox() ){
723	>	boxVector[0] = globals->getBox();
724	>	boxVector[1] = globals->getBox();
725	>	boxVector[2] = globals->getBox();
726	>
727	>	info->setBox( boxVector );
728		}
729	<	else if( the_globals->haveDensity() ){
729	>	else if( globals->haveDensity() ){
730
731		double vol;
732	<	vol = (double)tot_nmol / the_globals->getDensity();
733	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
734	<	simnfo->box_y = simnfo->box_x;
735	<	simnfo->box_z = simnfo->box_x;
732	>	vol = (double)tot_nmol / globals->getDensity();
733	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
734	>	boxVector[1] = boxVector[0];
735	>	boxVector[2] = boxVector[0];
736	>
737	>	info->setBox( boxVector );
738		}
739		else{
740	<	if( !the_globals->haveBoxX() ){
740	>	if( !globals->haveBoxX() ){
741		sprintf( painCave.errMsg,
742		"SimSetup error, no periodic BoxX size given.\n" );
743		painCave.isFatal = 1;
744		simError();
745		}
746	<	simnfo->box_x = the_globals->getBoxX();
746	>	boxVector[0] = globals->getBoxX();
747
748	<	if( !the_globals->haveBoxY() ){
748	>	if( !globals->haveBoxY() ){
749		sprintf( painCave.errMsg,
750		"SimSetup error, no periodic BoxY size given.\n" );
751		painCave.isFatal = 1;
752		simError();
753		}
754	<	simnfo->box_y = the_globals->getBoxY();
754	>	boxVector[1] = globals->getBoxY();
755
756	<	if( !the_globals->haveBoxZ() ){
756	>	if( !globals->haveBoxZ() ){
757		sprintf( painCave.errMsg,
758		"SimSetup error, no periodic BoxZ size given.\n" );
759		painCave.isFatal = 1;
760		simError();
761		}
762	<	simnfo->box_z = the_globals->getBoxZ();
762	>	boxVector[2] = globals->getBoxZ();
763	>
764	>	info->setBox( boxVector );
765		}
766
767	+
768	+
769		#ifdef IS_MPI
770	<	strcpy( checkPointMsg, "Box size set up" );
770	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
771		MPIcheckPoint();
772		#endif // is_mpi
773
774	+	}
775
382	–	// initialize the arrays
776
777	<	the_ff->setSimInfo( simnfo );
777	>	void SimSetup::finalInfoCheck( void ){
778	>	int index;
779	>	int usesDipoles;
780	>
781
782	<	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	<	}
782	>	// check electrostatic parameters
783
784	<	if( tot_bonds ){
785	<	makeBonds();
784	>	index = 0;
785	>	usesDipoles = 0;
786	>	while( (index < info->n_atoms) && !usesDipoles ){
787	>	usesDipoles = ((info->atoms)[index])->hasDipole();
788	>	index++;
789		}
790	+
791	+	#ifdef IS_MPI
792	+	int myUse = usesDipoles;
793	+	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
794	+	#endif //is_mpi
795
796	<	if( tot_bends ){
397	<	makeBends();
398	<	}
796	>	double theEcr, theEst;
797
798	<	if( tot_torsions ){
799	<	makeTorsions();
800	<	}
801	<
404	<
405	<	if (the_globals->getUseRF() ) {
406	<	simnfo->useReactionField = 1;
407	<
408	<	if( !the_globals->haveECR() ){
798	>	if (globals->getUseRF() ) {
799	>	info->useReactionField = 1;
800	>
801	>	if( !globals->haveECR() ){
802		sprintf( painCave.errMsg,
803		"SimSetup Warning: using default value of 1/2 the smallest "
804		"box length for the electrostaticCutoffRadius.\n"
#	Line 413 | Line 806 | void SimSetup::createSim( void ){
806		painCave.isFatal = 0;
807		simError();
808		double smallest;
809	<	smallest = simnfo->box_x;
810	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
811	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
812	<	simnfo->ecr = 0.5 * smallest;
809	>	smallest = info->boxL[0];
810	>	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
811	>	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
812	>	theEcr = 0.5 * smallest;
813		} else {
814	<	simnfo->ecr        = the_globals->getECR();
814	>	theEcr = globals->getECR();
815		}
816
817	<	if( !the_globals->haveEST() ){
817	>	if( !globals->haveEST() ){
818		sprintf( painCave.errMsg,
819		"SimSetup Warning: using default value of 0.05 * the "
820		"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
821		);
822		painCave.isFatal = 0;
823		simError();
824	<	simnfo->est = 0.05 * simnfo->ecr;
824	>	theEst = 0.05 * theEcr;
825		} else {
826	<	simnfo->est        = the_globals->getEST();
826	>	theEst= globals->getEST();
827		}
828	+
829	+	info->setEcr( theEcr, theEst );
830
831	<	if(!the_globals->haveDielectric() ){
831	>	if(!globals->haveDielectric() ){
832		sprintf( painCave.errMsg,
833		"SimSetup Error: You are trying to use Reaction Field without"
834		"setting a dielectric constant!\n"
#	Line 441 | Line 836 | void SimSetup::createSim( void ){
836		painCave.isFatal = 1;
837		simError();
838		}
839	<	simnfo->dielectric = the_globals->getDielectric();
840	<	} else {
841	<	if (simnfo->n_dipoles) {
839	>	info->dielectric = globals->getDielectric();
840	>	}
841	>	else {
842	>	if (usesDipoles) {
843
844	<	if( !the_globals->haveECR() ){
845	<	sprintf( painCave.errMsg,
846	<	"SimSetup Warning: using default value of 1/2 the smallest"
847	<	"box length for the electrostaticCutoffRadius.\n"
848	<	"I hope you have a very fast processor!\n");
849	<	painCave.isFatal = 0;
850	<	simError();
851	<	double smallest;
852	<	smallest = simnfo->box_x;
853	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
854	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
855	<	simnfo->ecr = 0.5 * smallest;
844	>	if( !globals->haveECR() ){
845	>	sprintf( painCave.errMsg,
846	>	"SimSetup Warning: using default value of 1/2 the smallest "
847	>	"box length for the electrostaticCutoffRadius.\n"
848	>	"I hope you have a very fast processor!\n");
849	>	painCave.isFatal = 0;
850	>	simError();
851	>	double smallest;
852	>	smallest = info->boxL[0];
853	>	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
854	>	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
855	>	theEcr = 0.5 * smallest;
856		} else {
857	<	simnfo->ecr        = the_globals->getECR();
857	>	theEcr = globals->getECR();
858		}
859
860	<	if( !the_globals->haveEST() ){
861	<	sprintf( painCave.errMsg,
862	<	"SimSetup Warning: using default value of 5% of the"
863	<	"electrostaticCutoffRadius for the "
864	<	"electrostaticSkinThickness\n"
865	<	);
866	<	painCave.isFatal = 0;
867	<	simError();
868	<	simnfo->est = 0.05 * simnfo->ecr;
869	<	} else {
870	<	simnfo->est        = the_globals->getEST();
860	>	if( !globals->haveEST() ){
861	>	sprintf( painCave.errMsg,
862	>	"SimSetup Warning: using default value of 0.05 * the "
863	>	"electrostaticCutoffRadius for the "
864	>	"electrostaticSkinThickness\n"
865	>	);
866	>	painCave.isFatal = 0;
867	>	simError();
868	>	theEst = 0.05 * theEcr;
869	>	} else {
870	>	theEst= globals->getEST();
871		}
872	+
873	+	info->setEcr( theEcr, theEst );
874		}
875		}
876
877		#ifdef IS_MPI
878	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
878	>	strcpy( checkPointMsg, "post processing checks out" );
879		MPIcheckPoint();
880		#endif // is_mpi
881
882	<	if( the_globals->haveInitialConfig() ){
882	>	}
883	>
884	>	void SimSetup::initSystemCoords( void ){
885	>
886	>	if( globals->haveInitialConfig() ){
887
888		InitializeFromFile* fileInit;
889		#ifdef IS_MPI // is_mpi
890		if( worldRank == 0 ){
891		#endif //is_mpi
892	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
892	>	fileInit = new InitializeFromFile( globals->getInitialConfig() );
893		#ifdef IS_MPI
894		}else fileInit = new InitializeFromFile( NULL );
895		#endif
896	<	fileInit->read_xyz( simnfo ); // default velocities on
896	>	fileInit->readInit( info ); // default velocities on
897
898		delete fileInit;
899		}
#	Line 519 | Line 921 | void SimSetup::createSim( void ){
921		MPIcheckPoint();
922		#endif // is_mpi
923
924	+	}
925
523	–
524	–
525	–
926
927	<
927	>	void SimSetup::makeOutNames( void ){
928	>
929		#ifdef IS_MPI
930		if( worldRank == 0 ){
931		#endif // is_mpi
932
933	<	if( the_globals->haveFinalConfig() ){
934	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
933	>	if( globals->haveFinalConfig() ){
934	>	strcpy( info->finalName, globals->getFinalConfig() );
935		}
936		else{
937	<	strcpy( simnfo->finalName, inFileName );
937	>	strcpy( info->finalName, inFileName );
938		char* endTest;
939	<	int nameLength = strlen( simnfo->finalName );
940	<	endTest = &(simnfo->finalName[nameLength - 5]);
939	>	int nameLength = strlen( info->finalName );
940	>	endTest = &(info->finalName[nameLength - 5]);
941		if( !strcmp( endTest, ".bass" ) ){
942		strcpy( endTest, ".eor" );
943		}
#	Line 544 | Line 945 | void SimSetup::createSim( void ){
945		strcpy( endTest, ".eor" );
946		}
947		else{
948	<	endTest = &(simnfo->finalName[nameLength - 4]);
948	>	endTest = &(info->finalName[nameLength - 4]);
949		if( !strcmp( endTest, ".bss" ) ){
950		strcpy( endTest, ".eor" );
951		}
#	Line 552 | Line 953 | void SimSetup::createSim( void ){
953		strcpy( endTest, ".eor" );
954		}
955		else{
956	<	strcat( simnfo->finalName, ".eor" );
956	>	strcat( info->finalName, ".eor" );
957		}
958		}
959		}
960
961		// make the sample and status out names
962
963	<	strcpy( simnfo->sampleName, inFileName );
963	>	strcpy( info->sampleName, inFileName );
964		char* endTest;
965	<	int nameLength = strlen( simnfo->sampleName );
966	<	endTest = &(simnfo->sampleName[nameLength - 5]);
965	>	int nameLength = strlen( info->sampleName );
966	>	endTest = &(info->sampleName[nameLength - 5]);
967		if( !strcmp( endTest, ".bass" ) ){
968		strcpy( endTest, ".dump" );
969		}
#	Line 570 | Line 971 | void SimSetup::createSim( void ){
971		strcpy( endTest, ".dump" );
972		}
973		else{
974	<	endTest = &(simnfo->sampleName[nameLength - 4]);
974	>	endTest = &(info->sampleName[nameLength - 4]);
975		if( !strcmp( endTest, ".bss" ) ){
976		strcpy( endTest, ".dump" );
977		}
#	Line 578 | Line 979 | void SimSetup::createSim( void ){
979		strcpy( endTest, ".dump" );
980		}
981		else{
982	<	strcat( simnfo->sampleName, ".dump" );
982	>	strcat( info->sampleName, ".dump" );
983		}
984		}
985
986	<	strcpy( simnfo->statusName, inFileName );
987	<	nameLength = strlen( simnfo->statusName );
988	<	endTest = &(simnfo->statusName[nameLength - 5]);
986	>	strcpy( info->statusName, inFileName );
987	>	nameLength = strlen( info->statusName );
988	>	endTest = &(info->statusName[nameLength - 5]);
989		if( !strcmp( endTest, ".bass" ) ){
990		strcpy( endTest, ".stat" );
991		}
#	Line 592 | Line 993 | void SimSetup::createSim( void ){
993		strcpy( endTest, ".stat" );
994		}
995		else{
996	<	endTest = &(simnfo->statusName[nameLength - 4]);
996	>	endTest = &(info->statusName[nameLength - 4]);
997		if( !strcmp( endTest, ".bss" ) ){
998		strcpy( endTest, ".stat" );
999		}
#	Line 600 | Line 1001 | void SimSetup::createSim( void ){
1001		strcpy( endTest, ".stat" );
1002		}
1003		else{
1004	<	strcat( simnfo->statusName, ".stat" );
1004	>	strcat( info->statusName, ".stat" );
1005		}
1006		}
1007
1008		#ifdef IS_MPI
1009		}
1010		#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	–	}
1011
1012	<	if( the_globals->haveStatusTime() ){
625	<	simnfo->statusTime = the_globals->getStatusTime();
626	<	}
1012	>	}
1013
628	–	if( the_globals->haveThermalTime() ){
629	–	simnfo->thermalTime = the_globals->getThermalTime();
630	–	}
1014
1015	<	// check for the temperature set flag
1015	>	void SimSetup::sysObjectsCreation( void ){
1016
1017	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
1017	>	int i;
1018
1019	+	// create the forceField
1020
1021	<	//   // make the longe range forces and the integrator
1021	>	createFF();
1022
1023	<	//   new AllLong( simnfo );
1023	>	// extract componentList
1024
1025	<	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 );
1025	>	compList();
1026
1027	+	// calc the number of atoms, bond, bends, and torsions
1028
1029	+	calcSysValues();
1030
1031	<	// initialize the Fortran
1031	>	#ifdef IS_MPI
1032	>	// divide the molecules among the processors
1033
1034	<	simnfo->refreshSim();
1034	>	mpiMolDivide();
1035	>	#endif //is_mpi
1036
1037	<	if( !strcmp( simnfo->mixingRule, "standard") ){
1038	<	the_ff->initForceField( LB_MIXING_RULE );
1037	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1038	>
1039	>	makeSysArrays();
1040	>
1041	>	// make and initialize the molecules (all but atomic coordinates)
1042	>
1043	>	makeMolecules();
1044	>	info->identArray = new int[info->n_atoms];
1045	>	for(i=0; i<info->n_atoms; i++){
1046	>	info->identArray[i] = the_atoms[i]->getIdent();
1047		}
1048	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
1049	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1050	<	}
1051	<	else{
1048	>
1049	>
1050	>
1051	>	}
1052	>
1053	>
1054	>	void SimSetup::createFF( void ){
1055	>
1056	>	switch( ffCase ){
1057	>
1058	>	case FF_DUFF:
1059	>	the_ff = new DUFF();
1060	>	break;
1061	>
1062	>	case FF_LJ:
1063	>	the_ff = new LJFF();
1064	>	break;
1065	>
1066	>	case FF_EAM:
1067	>	the_ff = new EAM_FF();
1068	>	break;
1069	>
1070	>	default:
1071		sprintf( painCave.errMsg,
1072	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
661	<	simnfo->mixingRule );
1072	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1073		painCave.isFatal = 1;
1074		simError();
1075		}
1076
666	–
1077		#ifdef IS_MPI
1078	<	strcpy( checkPointMsg,
669	<	"Successfully intialized the mixingRule for Fortran." );
1078	>	strcpy( checkPointMsg, "ForceField creation successful" );
1079		MPIcheckPoint();
1080		#endif // is_mpi
1081	+
1082		}
1083
674	–	void SimSetup::makeAtoms( void ){
1084
1085	<	int i, j, k, index;
677	<	double ux, uy, uz, uSqr, u;
678	<	AtomStamp* current_atom;
1085	>	void SimSetup::compList( void ){
1086
1087	<	DirectionalAtom* dAtom;
681	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
1087	>	int i;
1088
1089	<	lMolIndex = 0;
684	<	molIndex = 0;
685	<	index = 0;
686	<	for( i=0; i<n_components; i++ ){
1089	>	comp_stamps = new MoleculeStamp*[n_components];
1090
1091	<	for( j=0; j<components_nmol[i]; j++ ){
1091	>	// make an array of molecule stamps that match the components used.
1092	>	// also extract the used stamps out into a separate linked list
1093
1094	<	#ifdef IS_MPI
1095	<	if( mpiSim->getMyMolStart() <= molIndex &&
1096	<	molIndex <= mpiSim->getMyMolEnd() ){
1097	<	#endif // is_mpi
1094	>	info->nComponents = n_components;
1095	>	info->componentsNmol = components_nmol;
1096	>	info->compStamps = comp_stamps;
1097	>	info->headStamp = new LinkedMolStamp();
1098	>
1099	>	char* id;
1100	>	LinkedMolStamp* headStamp = info->headStamp;
1101	>	LinkedMolStamp* currentStamp = NULL;
1102	>	for( i=0; i<n_components; i++ ){
1103
1104	<	molStart = index;
1105	<	nMemb = comp_stamps[i]->getNAtoms();
1106	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
1107	<
699	<	current_atom = comp_stamps[i]->getAtom( k );
700	<	if( current_atom->haveOrientation() ){
701	<
702	<	dAtom = new DirectionalAtom(index);
703	<	simnfo->n_oriented++;
704	<	the_atoms[index] = dAtom;
705	<
706	<	ux = current_atom->getOrntX();
707	<	uy = current_atom->getOrntY();
708	<	uz = current_atom->getOrntZ();
709	<
710	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
711	<
712	<	u = sqrt( uSqr );
713	<	ux = ux / u;
714	<	uy = uy / u;
715	<	uz = uz / u;
716	<
717	<	dAtom->setSUx( ux );
718	<	dAtom->setSUy( uy );
719	<	dAtom->setSUz( uz );
720	<	}
721	<	else{
722	<	the_atoms[index] = new GeneralAtom(index);
723	<	}
724	<	the_atoms[index]->setType( current_atom->getType() );
725	<	the_atoms[index]->setIndex( index );
726	<
727	<	// increment the index and repeat;
728	<	index++;
729	<	}
730	<
731	<	molEnd = index -1;
732	<	the_molecules[lMolIndex].setNMembers( nMemb );
733	<	the_molecules[lMolIndex].setStartAtom( molStart );
734	<	the_molecules[lMolIndex].setEndAtom( molEnd );
735	<	the_molecules[lMolIndex].setStampID( i );
736	<	lMolIndex++;
1104	>	id = the_components[i]->getType();
1105	>	comp_stamps[i] = NULL;
1106	>
1107	>	// check to make sure the component isn't already in the list
1108
1109	<	#ifdef IS_MPI
1109	>	comp_stamps[i] = headStamp->match( id );
1110	>	if( comp_stamps[i] == NULL ){
1111	>
1112	>	// extract the component from the list;
1113	>
1114	>	currentStamp = stamps->extractMolStamp( id );
1115	>	if( currentStamp == NULL ){
1116	>	sprintf( painCave.errMsg,
1117	>	"SimSetup error: Component \"%s\" was not found in the "
1118	>	"list of declared molecules\n",
1119	>	id );
1120	>	painCave.isFatal = 1;
1121	>	simError();
1122		}
740	–	#endif //is_mpi
1123
1124	<	molIndex++;
1124	>	headStamp->add( currentStamp );
1125	>	comp_stamps[i] = headStamp->match( id );
1126		}
1127		}
1128
1129		#ifdef IS_MPI
1130	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
1131	<
1132	<	delete[] globalIndex;
1130	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1131	>	MPIcheckPoint();
1132	>	#endif // is_mpi
1133
1134	<	mpiSim->mpiRefresh();
752	<	#endif //IS_MPI
753	<
754	<	the_ff->initializeAtoms();
1134	>
1135		}
1136
1137	<	void SimSetup::makeBonds( void ){
1137	>	void SimSetup::calcSysValues( void ){
1138	>	int i, j, k;
1139
759	–	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
760	–	bond_pair* the_bonds;
761	–	BondStamp* current_bond;
1140
1141	<	the_bonds = new bond_pair[tot_bonds];
1142	<	index = 0;
1143	<	offset = 0;
1144	<	molIndex = 0;
767	<
1141	>	tot_atoms = 0;
1142	>	tot_bonds = 0;
1143	>	tot_bends = 0;
1144	>	tot_torsions = 0;
1145		for( i=0; i<n_components; i++ ){
1146	+
1147	+	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1148	+	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1149	+	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1150	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1151	+	}
1152
1153	<	for( j=0; j<components_nmol[i]; j++ ){
1153	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1154
1155	+	info->n_atoms = tot_atoms;
1156	+	info->n_bonds = tot_bonds;
1157	+	info->n_bends = tot_bends;
1158	+	info->n_torsions = tot_torsions;
1159	+	info->n_SRI = tot_SRI;
1160	+	info->n_mol = tot_nmol;
1161	+
1162	+	info->molMembershipArray = new int[tot_atoms];
1163	+	}
1164	+
1165	+
1166		#ifdef IS_MPI
773	–	if( mpiSim->getMyMolStart() <= molIndex &&
774	–	molIndex <= mpiSim->getMyMolEnd() ){
775	–	#endif // is_mpi
776	–
777	–	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
778	–
779	–	current_bond = comp_stamps[i]->getBond( k );
780	–	the_bonds[index].a = current_bond->getA() + offset;
781	–	the_bonds[index].b = current_bond->getB() + offset;
1167
1168	<	exI = the_bonds[index].a;
1169	<	exJ = the_bonds[index].b;
1168	>	void SimSetup::mpiMolDivide( void ){
1169	>
1170	>	int i, j, k;
1171	>	int localMol, allMol;
1172	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1173
1174	<	// exclude_I must always be the smaller of the pair
1175	<	if( exI > exJ ){
1176	<	tempEx = exI;
789	<	exI = exJ;
790	<	exJ = tempEx;
791	<	}
1174	>	mpiSim = new mpiSimulation( info );
1175	>
1176	>	globalIndex = mpiSim->divideLabor();
1177
1178	<
1179	<	#ifdef IS_MPI
1178	>	// set up the local variables
1179	>
1180	>	mol2proc = mpiSim->getMolToProcMap();
1181	>	molCompType = mpiSim->getMolComponentType();
1182	>
1183	>	allMol = 0;
1184	>	localMol = 0;
1185	>	local_atoms = 0;
1186	>	local_bonds = 0;
1187	>	local_bends = 0;
1188	>	local_torsions = 0;
1189	>	globalAtomIndex = 0;
1190
796	–	the_excludes[index*2] =
797	–	the_atoms[exI]->getGlobalIndex() + 1;
798	–	the_excludes[index*2 + 1] =
799	–	the_atoms[exJ]->getGlobalIndex() + 1;
1191
1192	<	#else  // isn't MPI
1193	<
1194	<	the_excludes[index*2] =     exI + 1;
1195	<	the_excludes[index*2 + 1] = exJ + 1;
1196	<	// fortran index from 1 (hence the +1 in the indexing)
806	<	#endif  //is_mpi
807	<
808	<	// increment the index and repeat;
809	<	index++;
810	<	}
811	<	offset += comp_stamps[i]->getNAtoms();
1192	>	for( i=0; i<n_components; i++ ){
1193	>
1194	>	for( j=0; j<components_nmol[i]; j++ ){
1195	>
1196	>	if( mol2proc[allMol] == worldRank ){
1197
1198	<	#ifdef IS_MPI
1198	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1199	>	local_bonds +=    comp_stamps[i]->getNBonds();
1200	>	local_bends +=    comp_stamps[i]->getNBends();
1201	>	local_torsions += comp_stamps[i]->getNTorsions();
1202	>	localMol++;
1203	>	}
1204	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1205	>	info->molMembershipArray[globalAtomIndex] = allMol;
1206	>	globalAtomIndex++;
1207		}
1208	<	#endif //is_mpi
1209	<
1210	<	molIndex++;
818	<	}
1208	>
1209	>	allMol++;
1210	>	}
1211		}
1212	+	local_SRI = local_bonds + local_bends + local_torsions;
1213	+
1214	+	info->n_atoms = mpiSim->getMyNlocal();
1215	+
1216	+	if( local_atoms != info->n_atoms ){
1217	+	sprintf( painCave.errMsg,
1218	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1219	+	" localAtom (%d) are not equal.\n",
1220	+	info->n_atoms,
1221	+	local_atoms );
1222	+	painCave.isFatal = 1;
1223	+	simError();
1224	+	}
1225
1226	<	the_ff->initializeBonds( the_bonds );
1226	>	info->n_bonds = local_bonds;
1227	>	info->n_bends = local_bends;
1228	>	info->n_torsions = local_torsions;
1229	>	info->n_SRI = local_SRI;
1230	>	info->n_mol = localMol;
1231	>
1232	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1233	>	MPIcheckPoint();
1234		}
1235	+
1236	+	#endif // is_mpi
1237
824	–	void SimSetup::makeBends( void ){
1238
1239	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1240	<	bend_set* the_bends;
828	<	BendStamp* current_bend;
829	<	LinkedAssign* extras;
830	<	LinkedAssign* current_extra;
831	<
1239	>	void SimSetup::makeSysArrays( void ){
1240	>	int i, j, k;
1241
833	–	the_bends = new bend_set[tot_bends];
834	–	index = 0;
835	–	offset = 0;
836	–	molIndex = 0;
837	–	for( i=0; i<n_components; i++ ){
1242
1243	<	for( j=0; j<components_nmol[i]; j++ ){
1243	>	// create the atom and short range interaction arrays
1244
1245	<	#ifdef IS_MPI
1246	<	if( mpiSim->getMyMolStart() <= molIndex &&
1247	<	molIndex <= mpiSim->getMyMolEnd() ){
1248	<	#endif // is_mpi
1245	>	Atom::createArrays(info->n_atoms);
1246	>	the_atoms = new Atom*[info->n_atoms];
1247	>	the_molecules = new Molecule[info->n_mol];
1248	>	int molIndex;
1249
1250	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
847	<
848	<	current_bend = comp_stamps[i]->getBend( k );
849	<	the_bends[index].a = current_bend->getA() + offset;
850	<	the_bends[index].b = current_bend->getB() + offset;
851	<	the_bends[index].c = current_bend->getC() + offset;
852	<
853	<	if( current_bend->haveExtras() ){
854	<
855	<	extras = current_bend->getExtras();
856	<	current_extra = extras;
857	<
858	<	while( current_extra != NULL ){
859	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
860	<
861	<	switch( current_extra->getType() ){
862	<
863	<	case 0:
864	<	the_bends[index].ghost =
865	<	current_extra->getInt() + offset;
866	<	the_bends[index].isGhost = 1;
867	<	break;
868	<
869	<	case 1:
870	<	the_bends[index].ghost =
871	<	(int)current_extra->getDouble() + offset;
872	<	the_bends[index].isGhost = 1;
873	<	break;
874	<
875	<	default:
876	<	sprintf( painCave.errMsg,
877	<	"SimSetup Error: ghostVectorSource was neiter a "
878	<	"double nor an int.\n"
879	<	"-->Bend[%d] in %s\n",
880	<	k, comp_stamps[i]->getID() );
881	<	painCave.isFatal = 1;
882	<	simError();
883	<	}
884	<	}
885	<
886	<	else{
887	<
888	<	sprintf( painCave.errMsg,
889	<	"SimSetup Error: unhandled bend assignment:\n"
890	<	"    -->%s in Bend[%d] in %s\n",
891	<	current_extra->getlhs(),
892	<	k, comp_stamps[i]->getID() );
893	<	painCave.isFatal = 1;
894	<	simError();
895	<	}
896	<
897	<	current_extra = current_extra->getNext();
898	<	}
899	<	}
900	<
901	<	if( !the_bends[index].isGhost ){
902	<
903	<	exI = the_bends[index].a;
904	<	exJ = the_bends[index].c;
905	<	}
906	<	else{
907	<
908	<	exI = the_bends[index].a;
909	<	exJ = the_bends[index].b;
910	<	}
911	<
912	<	// exclude_I must always be the smaller of the pair
913	<	if( exI > exJ ){
914	<	tempEx = exI;
915	<	exI = exJ;
916	<	exJ = tempEx;
917	<	}
1250	>	// initialize the molecule's stampID's
1251
919	–
1252		#ifdef IS_MPI
1253	+
1254
1255	<	the_excludes[(index + tot_bonds)*2] =
1256	<	the_atoms[exI]->getGlobalIndex() + 1;
1257	<	the_excludes[(index + tot_bonds)*2 + 1] =
1258	<	the_atoms[exJ]->getGlobalIndex() + 1;
1259	<
1260	<	#else  // isn't MPI
1261	<
1262	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
1263	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1264	<	// fortran index from 1 (hence the +1 in the indexing)
932	<	#endif  //is_mpi
933	<
934	<
935	<	// increment the index and repeat;
936	<	index++;
937	<	}
938	<	offset += comp_stamps[i]->getNAtoms();
939	<
940	<	#ifdef IS_MPI
941	<	}
942	<	#endif //is_mpi
1255	>	molIndex = 0;
1256	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1257	>
1258	>	if(mol2proc[i] == worldRank ){
1259	>	the_molecules[molIndex].setStampID( molCompType[i] );
1260	>	the_molecules[molIndex].setMyIndex( molIndex );
1261	>	the_molecules[molIndex].setGlobalIndex( i );
1262	>	molIndex++;
1263	>	}
1264	>	}
1265
1266	+	#else // is_mpi
1267	+
1268	+	molIndex = 0;
1269	+	globalAtomIndex = 0;
1270	+	for(i=0; i<n_components; i++){
1271	+	for(j=0; j<components_nmol[i]; j++ ){
1272	+	the_molecules[molIndex].setStampID( i );
1273	+	the_molecules[molIndex].setMyIndex( molIndex );
1274	+	the_molecules[molIndex].setGlobalIndex( molIndex );
1275	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1276	+	info->molMembershipArray[globalAtomIndex] = molIndex;
1277	+	globalAtomIndex++;
1278	+	}
1279		molIndex++;
1280		}
1281		}
1282	+
1283
948	–	#ifdef IS_MPI
949	–	sprintf( checkPointMsg,
950	–	"Successfully created the bends list.\n" );
951	–	MPIcheckPoint();
1284		#endif // is_mpi
953	–
1285
955	–	the_ff->initializeBends( the_bends );
956	–	}
1286
1287	<	void SimSetup::makeTorsions( void ){
1287	>	if( info->n_SRI ){
1288	>
1289	>	Exclude::createArray(info->n_SRI);
1290	>	the_excludes = new Exclude*[info->n_SRI];
1291	>	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1292	>	info->globalExcludes = new int;
1293	>	info->n_exclude = info->n_SRI;
1294	>	}
1295	>	else{
1296	>
1297	>	Exclude::createArray( 1 );
1298	>	the_excludes = new Exclude*;
1299	>	the_excludes[0] = new Exclude(0);
1300	>	the_excludes[0]->setPair( 0,0 );
1301	>	info->globalExcludes = new int;
1302	>	info->globalExcludes[0] = 0;
1303	>	info->n_exclude = 0;
1304	>	}
1305
1306	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
961	<	torsion_set* the_torsions;
962	<	TorsionStamp* current_torsion;
1306	>	// set the arrays into the SimInfo object
1307
1308	<	the_torsions = new torsion_set[tot_torsions];
1309	<	index = 0;
1310	<	offset = 0;
1311	<	molIndex = 0;
968	<	for( i=0; i<n_components; i++ ){
1308	>	info->atoms = the_atoms;
1309	>	info->molecules = the_molecules;
1310	>	info->nGlobalExcludes = 0;
1311	>	info->excludes = the_excludes;
1312
1313	<	for( j=0; j<components_nmol[i]; j++ ){
1313	>	the_ff->setSimInfo( info );
1314
1315	<	#ifdef IS_MPI
973	<	if( mpiSim->getMyMolStart() <= molIndex &&
974	<	molIndex <= mpiSim->getMyMolEnd() ){
975	<	#endif // is_mpi
1315	>	}
1316
1317	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1317	>	void SimSetup::makeIntegrator( void ){
1318
1319	<	current_torsion = comp_stamps[i]->getTorsion( k );
1320	<	the_torsions[index].a = current_torsion->getA() + offset;
1321	<	the_torsions[index].b = current_torsion->getB() + offset;
1322	<	the_torsions[index].c = current_torsion->getC() + offset;
1323	<	the_torsions[index].d = current_torsion->getD() + offset;
1319	>	NVT<RealIntegrator>*  myNVT = NULL;
1320	>	NPTi<RealIntegrator>* myNPTi = NULL;
1321	>	NPTf<RealIntegrator>* myNPTf = NULL;
1322	>	NPTim<RealIntegrator>* myNPTim = NULL;
1323	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1324	>	ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1325	>	ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL;
1326	>	ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL;
1327	>	ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL;
1328	>	ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL;
1329	>	ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL;
1330	>
1331	>	switch( ensembleCase ){
1332
1333	<	exI = the_torsions[index].a;
1334	<	exJ = the_torsions[index].d;
1333	>	case NVE_ENS:
1334	>	new NVE<RealIntegrator>( info, the_ff );
1335	>	break;
1336
1337	<
1338	<	// exclude_I must always be the smaller of the pair
1339	<	if( exI > exJ ){
991	<	tempEx = exI;
992	<	exI = exJ;
993	<	exJ = tempEx;
994	<	}
1337	>	case NVT_ENS:
1338	>	myNVT = new NVT<RealIntegrator>( info, the_ff );
1339	>	myNVT->setTargetTemp(globals->getTargetTemp());
1340
1341	+	if (globals->haveTauThermostat())
1342	+	myNVT->setTauThermostat(globals->getTauThermostat());
1343
1344	<	#ifdef IS_MPI
1345	<
1346	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
1347	<	the_atoms[exI]->getGlobalIndex() + 1;
1348	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1349	<	the_atoms[exJ]->getGlobalIndex() + 1;
1350	<
1351	<	#else  // isn't MPI
1005	<
1006	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1007	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1008	<	// fortran indexes from 1 (hence the +1 in the indexing)
1009	<	#endif  //is_mpi
1010	<
1344	>	else {
1345	>	sprintf( painCave.errMsg,
1346	>	"SimSetup error: If you use the NVT\n"
1347	>	"    ensemble, you must set tauThermostat.\n");
1348	>	painCave.isFatal = 1;
1349	>	simError();
1350	>	}
1351	>	break;
1352
1353	<	// increment the index and repeat;
1354	<	index++;
1355	<	}
1015	<	offset += comp_stamps[i]->getNAtoms();
1353	>	case NPTi_ENS:
1354	>	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1355	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1356
1357	<	#ifdef IS_MPI
1358	<	}
1359	<	#endif //is_mpi
1360	<
1361	<	molIndex++;
1357	>	if (globals->haveTargetPressure())
1358	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1359	>	else {
1360	>	sprintf( painCave.errMsg,
1361	>	"SimSetup error: If you use a constant pressure\n"
1362	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1363	>	painCave.isFatal = 1;
1364	>	simError();
1365	>	}
1366	>
1367	>	if( globals->haveTauThermostat() )
1368	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1369	>	else{
1370	>	sprintf( painCave.errMsg,
1371	>	"SimSetup error: If you use an NPT\n"
1372	>	"    ensemble, you must set tauThermostat.\n");
1373	>	painCave.isFatal = 1;
1374	>	simError();
1375		}
1023	–	}
1376
1377	<	the_ff->initializeTorsions( the_torsions );
1378	<	}
1377	>	if( globals->haveTauBarostat() )
1378	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1379	>	else{
1380	>	sprintf( painCave.errMsg,
1381	>	"SimSetup error: If you use an NPT\n"
1382	>	"    ensemble, you must set tauBarostat.\n");
1383	>	painCave.isFatal = 1;
1384	>	simError();
1385	>	}
1386	>	break;
1387
1388	<	void SimSetup::initFromBass( void ){
1388	>	case NPTf_ENS:
1389	>	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1390	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1391
1392	<	int i, j, k;
1393	<	int n_cells;
1394	<	double cellx, celly, cellz;
1395	<	double temp1, temp2, temp3;
1396	<	int n_per_extra;
1397	<	int n_extra;
1398	<	int have_extra, done;
1392	>	if (globals->haveTargetPressure())
1393	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1394	>	else {
1395	>	sprintf( painCave.errMsg,
1396	>	"SimSetup error: If you use a constant pressure\n"
1397	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1398	>	painCave.isFatal = 1;
1399	>	simError();
1400	>	}
1401
1402	<	temp1 = (double)tot_nmol / 4.0;
1403	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1404	<	temp3 = ceil( temp2 );
1402	>	if( globals->haveTauThermostat() )
1403	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1404	>	else{
1405	>	sprintf( painCave.errMsg,
1406	>	"SimSetup error: If you use an NPT\n"
1407	>	"    ensemble, you must set tauThermostat.\n");
1408	>	painCave.isFatal = 1;
1409	>	simError();
1410	>	}
1411
1412	<	have_extra =0;
1413	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1414	<	have_extra =1;
1412	>	if( globals->haveTauBarostat() )
1413	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1414	>	else{
1415	>	sprintf( painCave.errMsg,
1416	>	"SimSetup error: If you use an NPT\n"
1417	>	"    ensemble, you must set tauBarostat.\n");
1418	>	painCave.isFatal = 1;
1419	>	simError();
1420	>	}
1421	>	break;
1422	>
1423	>	case NPTim_ENS:
1424	>	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1425	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1426
1427	<	n_cells = (int)temp3 - 1;
1428	<	cellx = simnfo->box_x / temp3;
1429	<	celly = simnfo->box_y / temp3;
1049	<	cellz = simnfo->box_z / temp3;
1050	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1051	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1052	<	n_per_extra = (int)ceil( temp1 );
1053	<
1054	<	if( n_per_extra > 4){
1427	>	if (globals->haveTargetPressure())
1428	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1429	>	else {
1430		sprintf( painCave.errMsg,
1431	<	"SimSetup error. There has been an error in constructing"
1432	<	" the non-complete lattice.\n" );
1431	>	"SimSetup error: If you use a constant pressure\n"
1432	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1433		painCave.isFatal = 1;
1434		simError();
1435		}
1436	<	}
1437	<	else{
1438	<	n_cells = (int)temp3;
1439	<	cellx = simnfo->box_x / temp3;
1440	<	celly = simnfo->box_y / temp3;
1441	<	cellz = simnfo->box_z / temp3;
1442	<	}
1436	>
1437	>	if( globals->haveTauThermostat() )
1438	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1439	>	else{
1440	>	sprintf( painCave.errMsg,
1441	>	"SimSetup error: If you use an NPT\n"
1442	>	"    ensemble, you must set tauThermostat.\n");
1443	>	painCave.isFatal = 1;
1444	>	simError();
1445	>	}
1446
1447	<	current_mol = 0;
1448	<	current_comp_mol = 0;
1449	<	current_comp = 0;
1450	<	current_atom_ndx = 0;
1451	<
1452	<	for( i=0; i < n_cells ; i++ ){
1453	<	for( j=0; j < n_cells; j++ ){
1454	<	for( k=0; k < n_cells; k++ ){
1077	<
1078	<	makeElement( i * cellx,
1079	<	j * celly,
1080	<	k * cellz );
1081	<
1082	<	makeElement( i * cellx + 0.5 * cellx,
1083	<	j * celly + 0.5 * celly,
1084	<	k * cellz );
1085	<
1086	<	makeElement( i * cellx,
1087	<	j * celly + 0.5 * celly,
1088	<	k * cellz + 0.5 * cellz );
1089	<
1090	<	makeElement( i * cellx + 0.5 * cellx,
1091	<	j * celly,
1092	<	k * cellz + 0.5 * cellz );
1093	<	}
1447	>	if( globals->haveTauBarostat() )
1448	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1449	>	else{
1450	>	sprintf( painCave.errMsg,
1451	>	"SimSetup error: If you use an NPT\n"
1452	>	"    ensemble, you must set tauBarostat.\n");
1453	>	painCave.isFatal = 1;
1454	>	simError();
1455		}
1456	<	}
1456	>	break;
1457
1458	<	if( have_extra ){
1459	<	done = 0;
1458	>	case NPTfm_ENS:
1459	>	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1460	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1461
1462	<	int start_ndx;
1463	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1464	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1465	<
1466	<	if( i < n_cells ){
1467	<
1468	<	if( j < n_cells ){
1469	<	start_ndx = n_cells;
1108	<	}
1109	<	else start_ndx = 0;
1110	<	}
1111	<	else start_ndx = 0;
1112	<
1113	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1114	<
1115	<	makeElement( i * cellx,
1116	<	j * celly,
1117	<	k * cellz );
1118	<	done = ( current_mol >= tot_nmol );
1119	<
1120	<	if( !done && n_per_extra > 1 ){
1121	<	makeElement( i * cellx + 0.5 * cellx,
1122	<	j * celly + 0.5 * celly,
1123	<	k * cellz );
1124	<	done = ( current_mol >= tot_nmol );
1125	<	}
1126	<
1127	<	if( !done && n_per_extra > 2){
1128	<	makeElement( i * cellx,
1129	<	j * celly + 0.5 * celly,
1130	<	k * cellz + 0.5 * cellz );
1131	<	done = ( current_mol >= tot_nmol );
1132	<	}
1133	<
1134	<	if( !done && n_per_extra > 3){
1135	<	makeElement( i * cellx + 0.5 * cellx,
1136	<	j * celly,
1137	<	k * cellz + 0.5 * cellz );
1138	<	done = ( current_mol >= tot_nmol );
1139	<	}
1140	<	}
1141	<	}
1462	>	if (globals->haveTargetPressure())
1463	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1464	>	else {
1465	>	sprintf( painCave.errMsg,
1466	>	"SimSetup error: If you use a constant pressure\n"
1467	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1468	>	painCave.isFatal = 1;
1469	>	simError();
1470		}
1471	<	}
1471	>
1472	>	if( globals->haveTauThermostat() )
1473	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1474	>	else{
1475	>	sprintf( painCave.errMsg,
1476	>	"SimSetup error: If you use an NPT\n"
1477	>	"    ensemble, you must set tauThermostat.\n");
1478	>	painCave.isFatal = 1;
1479	>	simError();
1480	>	}
1481
1482	<
1483	<	for( i=0; i<simnfo->n_atoms; i++ ){
1484	<	simnfo->atoms[i]->set_vx( 0.0 );
1148	<	simnfo->atoms[i]->set_vy( 0.0 );
1149	<	simnfo->atoms[i]->set_vz( 0.0 );
1150	<	}
1151	<	}
1152	<
1153	<	void SimSetup::makeElement( double x, double y, double z ){
1154	<
1155	<	int k;
1156	<	AtomStamp* current_atom;
1157	<	DirectionalAtom* dAtom;
1158	<	double rotMat[3][3];
1159	<
1160	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1161	<
1162	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1163	<	if( !current_atom->havePosition() ){
1482	>	if( globals->haveTauBarostat() )
1483	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1484	>	else{
1485		sprintf( painCave.errMsg,
1486	<	"SimSetup:initFromBass error.\n"
1487	<	"\tComponent %s, atom %s does not have a position specified.\n"
1167	<	"\tThe initialization routine is unable to give a start"
1168	<	" position.\n",
1169	<	comp_stamps[current_comp]->getID(),
1170	<	current_atom->getType() );
1486	>	"SimSetup error: If you use an NPT\n"
1487	>	"    ensemble, you must set tauBarostat.\n");
1488		painCave.isFatal = 1;
1489		simError();
1490		}
1491	+	break;
1492	+
1493	+	case NVEZCONS_ENS:
1494
1175	–	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1176	–	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1177	–	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1495
1496	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1496	>	//setup index of z-constraint molecules, z-constraint sampel time
1497	>	//and z-constraint force output name. These parameter should be known
1498	>	//before constructing the z-constraint integrator
1499	>	setupZConstraint();
1500	>
1501	>	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff );
1502	>
1503	>	break;
1504	>
1505	>
1506	>	case NVTZCONS_ENS:
1507	>
1508	>	setupZConstraint();
1509	>
1510	>	myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( info, the_ff );
1511	>	myNVTZCons->setTargetTemp(globals->getTargetTemp());
1512
1513	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1513	>	if (globals->haveTauThermostat())
1514	>	myNVTZCons->setTauThermostat(globals->getTauThermostat());
1515
1516	<	rotMat[0][0] = 1.0;
1517	<	rotMat[0][1] = 0.0;
1518	<	rotMat[0][2] = 0.0;
1519	<
1520	<	rotMat[1][0] = 0.0;
1521	<	rotMat[1][1] = 1.0;
1522	<	rotMat[1][2] = 0.0;
1516	>	else {
1517	>	sprintf( painCave.errMsg,
1518	>	"SimSetup error: If you use the NVT\n"
1519	>	"    ensemble, you must set tauThermostat.\n");
1520	>	painCave.isFatal = 1;
1521	>	simError();
1522	>	}
1523	>	break;
1524	>
1525	>	case NPTiZCONS_ENS:
1526	>
1527	>	setupZConstraint();
1528	>
1529	>	myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( info, the_ff );
1530	>	myNPTiZCons->setTargetTemp( globals->getTargetTemp() );
1531
1532	<	rotMat[2][0] = 0.0;
1533	<	rotMat[2][1] = 0.0;
1534	<	rotMat[2][2] = 1.0;
1532	>	if (globals->haveTargetPressure())
1533	>	myNPTiZCons->setTargetPressure(globals->getTargetPressure());
1534	>	else {
1535	>	sprintf( painCave.errMsg,
1536	>	"SimSetup error: If you use a constant pressure\n"
1537	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1538	>	painCave.isFatal = 1;
1539	>	simError();
1540	>	}
1541	>
1542	>	if( globals->haveTauThermostat() )
1543	>	myNPTiZCons->setTauThermostat( globals->getTauThermostat() );
1544	>	else{
1545	>	sprintf( painCave.errMsg,
1546	>	"SimSetup error: If you use an NPT\n"
1547	>	"    ensemble, you must set tauThermostat.\n");
1548	>	painCave.isFatal = 1;
1549	>	simError();
1550	>	}
1551
1552	<	dAtom->setA( rotMat );
1552	>	if( globals->haveTauBarostat() )
1553	>	myNPTiZCons->setTauBarostat( globals->getTauBarostat() );
1554	>	else{
1555	>	sprintf( painCave.errMsg,
1556	>	"SimSetup error: If you use an NPT\n"
1557	>	"    ensemble, you must set tauBarostat.\n");
1558	>	painCave.isFatal = 1;
1559	>	simError();
1560	>	}
1561	>
1562	>	break;
1563	>
1564	>	case NPTfZCONS_ENS:
1565	>
1566	>	setupZConstraint();
1567	>
1568	>	myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( info, the_ff );
1569	>	myNPTfZCons->setTargetTemp( globals->getTargetTemp());
1570	>
1571	>	if (globals->haveTargetPressure())
1572	>	myNPTfZCons->setTargetPressure(globals->getTargetPressure());
1573	>	else {
1574	>	sprintf( painCave.errMsg,
1575	>	"SimSetup error: If you use a constant pressure\n"
1576	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1577	>	painCave.isFatal = 1;
1578	>	simError();
1579	>	}
1580	>
1581	>	if( globals->haveTauThermostat() )
1582	>	myNPTfZCons->setTauThermostat( globals->getTauThermostat() );
1583	>	else{
1584	>	sprintf( painCave.errMsg,
1585	>	"SimSetup error: If you use an NPT\n"
1586	>	"    ensemble, you must set tauThermostat.\n");
1587	>	painCave.isFatal = 1;
1588	>	simError();
1589		}
1590
1591	<	current_atom_ndx++;
1591	>	if( globals->haveTauBarostat() )
1592	>	myNPTfZCons->setTauBarostat( globals->getTauBarostat() );
1593	>	else{
1594	>	sprintf( painCave.errMsg,
1595	>	"SimSetup error: If you use an NPT\n"
1596	>	"    ensemble, you must set tauBarostat.\n");
1597	>	painCave.isFatal = 1;
1598	>	simError();
1599	>	}
1600	>
1601	>	break;
1602	>
1603	>	case NPTimZCONS_ENS:
1604	>
1605	>	setupZConstraint();
1606	>
1607	>	myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( info, the_ff );
1608	>	myNPTimZCons->setTargetTemp( globals->getTargetTemp());
1609	>
1610	>	if (globals->haveTargetPressure())
1611	>	myNPTimZCons->setTargetPressure(globals->getTargetPressure());
1612	>	else {
1613	>	sprintf( painCave.errMsg,
1614	>	"SimSetup error: If you use a constant pressure\n"
1615	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1616	>	painCave.isFatal = 1;
1617	>	simError();
1618	>	}
1619	>
1620	>	if( globals->haveTauThermostat() )
1621	>	myNPTimZCons->setTauThermostat( globals->getTauThermostat() );
1622	>	else{
1623	>	sprintf( painCave.errMsg,
1624	>	"SimSetup error: If you use an NPT\n"
1625	>	"    ensemble, you must set tauThermostat.\n");
1626	>	painCave.isFatal = 1;
1627	>	simError();
1628	>	}
1629	>
1630	>	if( globals->haveTauBarostat() )
1631	>	myNPTimZCons->setTauBarostat( globals->getTauBarostat() );
1632	>	else{
1633	>	sprintf( painCave.errMsg,
1634	>	"SimSetup error: If you use an NPT\n"
1635	>	"    ensemble, you must set tauBarostat.\n");
1636	>	painCave.isFatal = 1;
1637	>	simError();
1638	>	}
1639	>
1640	>	break;
1641	>
1642	>	case NPTfmZCONS_ENS:
1643	>
1644	>	setupZConstraint();
1645	>
1646	>	myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( info, the_ff );
1647	>	myNPTfmZCons->setTargetTemp( globals->getTargetTemp());
1648	>
1649	>	if (globals->haveTargetPressure())
1650	>	myNPTfmZCons->setTargetPressure(globals->getTargetPressure());
1651	>	else {
1652	>	sprintf( painCave.errMsg,
1653	>	"SimSetup error: If you use a constant pressure\n"
1654	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1655	>	painCave.isFatal = 1;
1656	>	simError();
1657	>	}
1658	>
1659	>	if( globals->haveTauThermostat() )
1660	>	myNPTfmZCons->setTauThermostat( globals->getTauThermostat() );
1661	>	else{
1662	>	sprintf( painCave.errMsg,
1663	>	"SimSetup error: If you use an NPT\n"
1664	>	"    ensemble, you must set tauThermostat.\n");
1665	>	painCave.isFatal = 1;
1666	>	simError();
1667	>	}
1668	>
1669	>	if( globals->haveTauBarostat() )
1670	>	myNPTfmZCons->setTauBarostat( globals->getTauBarostat() );
1671	>	else{
1672	>	sprintf( painCave.errMsg,
1673	>	"SimSetup error: If you use an NPT\n"
1674	>	"    ensemble, you must set tauBarostat.\n");
1675	>	painCave.isFatal = 1;
1676	>	simError();
1677	>	}
1678	>	break;
1679	>
1680	>
1681	>
1682	>	default:
1683	>	sprintf( painCave.errMsg,
1684	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1685	>	painCave.isFatal = 1;
1686	>	simError();
1687		}
1688
1689	<	current_mol++;
1202	<	current_comp_mol++;
1689	>	}
1690
1691	<	if( current_comp_mol >= components_nmol[current_comp] ){
1691	>	void SimSetup::initFortran( void ){
1692
1693	<	current_comp_mol = 0;
1694	<	current_comp++;
1693	>	info->refreshSim();
1694	>
1695	>	if( !strcmp( info->mixingRule, "standard") ){
1696	>	the_ff->initForceField( LB_MIXING_RULE );
1697		}
1698	+	else if( !strcmp( info->mixingRule, "explicit") ){
1699	+	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1700	+	}
1701	+	else{
1702	+	sprintf( painCave.errMsg,
1703	+	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1704	+	info->mixingRule );
1705	+	painCave.isFatal = 1;
1706	+	simError();
1707	+	}
1708	+
1709	+
1710	+	#ifdef IS_MPI
1711	+	strcpy( checkPointMsg,
1712	+	"Successfully intialized the mixingRule for Fortran." );
1713	+	MPIcheckPoint();
1714	+	#endif // is_mpi
1715	+
1716		}
1717	+
1718	+	void SimSetup::setupZConstraint()
1719	+	{
1720	+	if(globals->haveZConsTime()){
1721	+
1722	+	//add sample time of z-constraint  into SimInfo's property list
1723	+	DoubleData* zconsTimeProp = new DoubleData();
1724	+	zconsTimeProp->setID("zconstime");
1725	+	zconsTimeProp->setData(globals->getZConsTime());
1726	+	info->addProperty(zconsTimeProp);
1727	+	}
1728	+	else{
1729	+	sprintf( painCave.errMsg,
1730	+	"ZConstraint error: If you use an ZConstraint\n"
1731	+	" , you must set sample time.\n");
1732	+	painCave.isFatal = 1;
1733	+	simError();
1734	+	}
1735	+
1736	+	if(globals->haveIndexOfAllZConsMols()){
1737	+
1738	+	//add index of z-constraint molecules into SimInfo's property list
1739	+	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1740	+
1741	+	//sort the index
1742	+	sort(tempIndex.begin(), tempIndex.end());
1743	+
1744	+	IndexData* zconsIndex = new IndexData();
1745	+	zconsIndex->setID("zconsindex");
1746	+	zconsIndex->setIndexData(tempIndex);
1747	+	info->addProperty(zconsIndex);
1748	+	}
1749	+	else{
1750	+	sprintf( painCave.errMsg,
1751	+	"SimSetup error: If you use an ZConstraint\n"
1752	+	" , you must set index of z-constraint molecules.\n");
1753	+	painCave.isFatal = 1;
1754	+	simError();
1755	+
1756	+	}
1757	+
1758	+	//Determine the name of ouput file and add it into SimInfo's property list
1759	+	//Be careful, do not use inFileName, since it is a pointer which
1760	+	//point to a string at master node, and slave nodes do not contain that string
1761	+
1762	+	string zconsOutput(info->finalName);
1763	+
1764	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1765	+
1766	+	StringData* zconsFilename = new StringData();
1767	+	zconsFilename->setID("zconsfilename");
1768	+	zconsFilename->setData(zconsOutput);
1769	+
1770	+	info->addProperty(zconsFilename);
1771	+
1772	+	}

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