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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 466 by gezelter, Mon Apr 7 14:30:36 2003 UTC vs.
Revision 689 by tim, Tue Aug 12 19:56:49 2003 UTC

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

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