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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 435 by mmeineke, Fri Mar 28 19:33:37 2003 UTC vs.
Revision 707 by mmeineke, Wed Aug 20 19:42:31 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 12 | Line 15 | SimSetup::SimSetup(){
15		#include "mpiSimulation.hpp"
16		#endif
17
18	+	// some defines for ensemble and Forcefield  cases
19	+
20	+	#define NVE_ENS        0
21	+	#define NVT_ENS        1
22	+	#define NPTi_ENS       2
23	+	#define NPTf_ENS       3
24	+	#define NPTim_ENS      4
25	+	#define NPTfm_ENS      5
26	+
27	+	#define FF_DUFF 0
28	+	#define FF_LJ   1
29	+	#define FF_EAM  2
30	+
31	+	using namespace std;
32	+
33		SimSetup::SimSetup(){
34	+
35	+	isInfoArray = 0;
36	+	nInfo = 1;
37	+
38		stamps = new MakeStamps();
39		globals = new Globals();
40
41	+
42		#ifdef IS_MPI
43		strcpy( checkPointMsg, "SimSetup creation successful" );
44		MPIcheckPoint();
#	Line 27 | Line 50 | void SimSetup::parseFile( char* fileName ){
50		delete globals;
51		}
52
53	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
54	+	info = the_info;
55	+	nInfo = theNinfo;
56	+	isInfoArray = 1;
57	+	}
58	+
59	+
60		void SimSetup::parseFile( char* fileName ){
61
62		#ifdef IS_MPI
#	Line 62 | Line 92 | void SimSetup::createSim( void ){
92
93		#endif // is_mpi
94
95	<	void SimSetup::createSim( void ){
95	>	void SimSetup::createSim(void){
96
97	<	MakeStamps *the_stamps;
98	<	Globals* the_globals;
99	<	int i, j;
97	>	int i, j, k, globalAtomIndex;
98	>
99	>	// gather all of the information from the Bass file
100
101	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
101	>	gatherInfo();
102
103	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	simnfo->run_time = the_globals->getRunTime();
103	>	// creation of complex system objects
104
105	<	// get the ones we know are there, yet still may need some work.
81	<	n_components = the_globals->getNComponents();
82	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
105	>	sysObjectsCreation();
106
107	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
107	>	// check on the post processing info
108
109	+	finalInfoCheck();
110
111	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
92	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
93	<	else{
94	<	sprintf( painCave.errMsg,
95	<	"SimSetup Error. Unrecognized force field -> %s\n",
96	<	force_field );
97	<	painCave.isFatal = 1;
98	<	simError();
99	<	}
111	>	// initialize the system coordinates
112
113	<	#ifdef IS_MPI
102	<	strcpy( checkPointMsg, "ForceField creation successful" );
103	<	MPIcheckPoint();
104	<	#endif // is_mpi
113	>	if( !isInfoArray ) initSystemCoords();
114
115	<
115	>	// make the output filenames
116
117	<	// get the components and calculate the tot_nMol and indvidual n_mol
118	<	the_components = the_globals->getComponents();
119	<	components_nmol = new int[n_components];
120	<	comp_stamps = new MoleculeStamp*[n_components];
121	<
122	<	if( !the_globals->haveNMol() ){
114	<	// we don't have the total number of molecules, so we assume it is
115	<	// given in each component
116	<
117	<	tot_nmol = 0;
118	<	for( i=0; i<n_components; i++ ){
119	<
120	<	if( !the_components[i]->haveNMol() ){
121	<	// we have a problem
122	<	sprintf( painCave.errMsg,
123	<	"SimSetup Error. No global NMol or component NMol"
124	<	" given. Cannot calculate the number of atoms.\n" );
125	<	painCave.isFatal = 1;
126	<	simError();
127	<	}
128	<
129	<	tot_nmol += the_components[i]->getNMol();
130	<	components_nmol[i] = the_components[i]->getNMol();
131	<	}
132	<	}
133	<	else{
134	<	sprintf( painCave.errMsg,
135	<	"SimSetup error.\n"
136	<	"\tSorry, the ability to specify total"
137	<	" nMols and then give molfractions in the components\n"
138	<	"\tis not currently supported."
139	<	" Please give nMol in the components.\n" );
140	<	painCave.isFatal = 1;
141	<	simError();
142	<
143	<
144	<	//     tot_nmol = the_globals->getNMol();
145	<
146	<	//   //we have the total number of molecules, now we check for molfractions
147	<	//     for( i=0; i<n_components; i++ ){
148	<
149	<	//       if( !the_components[i]->haveMolFraction() ){
150	<
151	<	//  if( !the_components[i]->haveNMol() ){
152	<	//    //we have a problem
153	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
154	<	//              << " nMol was given in component
155	<
156	<	}
157	<
117	>	makeOutNames();
118	>
119	>	// make the integrator
120	>
121	>	makeIntegrator();
122	>
123		#ifdef IS_MPI
124	<	strcpy( checkPointMsg, "Have the number of components" );
125	<	MPIcheckPoint();
161	<	#endif // is_mpi
124	>	mpiSim->mpiRefresh();
125	>	#endif
126
127	<	// make an array of molecule stamps that match the components used.
164	<	// also extract the used stamps out into a separate linked list
127	>	// initialize the Fortran
128
129	<	simnfo->nComponents = n_components;
167	<	simnfo->componentsNmol = components_nmol;
168	<	simnfo->compStamps = comp_stamps;
169	<	simnfo->headStamp = new LinkedMolStamp();
170	<
171	<	char* id;
172	<	LinkedMolStamp* headStamp = simnfo->headStamp;
173	<	LinkedMolStamp* currentStamp = NULL;
174	<	for( i=0; i<n_components; i++ ){
129	>	initFortran();
130
176	–	id = the_components[i]->getType();
177	–	comp_stamps[i] = NULL;
178	–
179	–	// check to make sure the component isn't already in the list
131
181	–	comp_stamps[i] = headStamp->match( id );
182	–	if( comp_stamps[i] == NULL ){
183	–
184	–	// extract the component from the list;
185	–
186	–	currentStamp = the_stamps->extractMolStamp( id );
187	–	if( currentStamp == NULL ){
188	–	sprintf( painCave.errMsg,
189	–	"SimSetup error: Component \"%s\" was not found in the "
190	–	"list of declared molecules\n",
191	–	id );
192	–	painCave.isFatal = 1;
193	–	simError();
194	–	}
195	–
196	–	headStamp->add( currentStamp );
197	–	comp_stamps[i] = headStamp->match( id );
198	–	}
199	–	}
132
133	<	#ifdef IS_MPI
202	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
203	<	MPIcheckPoint();
204	<	#endif // is_mpi
205	<
133	>	}
134
135
136	+	void SimSetup::makeMolecules( void ){
137
138	<	// caclulate the number of atoms, bonds, bends and torsions
138	>	int k,l;
139	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140	>	molInit molInfo;
141	>	DirectionalAtom* dAtom;
142	>	LinkedAssign* extras;
143	>	LinkedAssign* current_extra;
144	>	AtomStamp* currentAtom;
145	>	BondStamp* currentBond;
146	>	BendStamp* currentBend;
147	>	TorsionStamp* currentTorsion;
148
149	<	tot_atoms = 0;
150	<	tot_bonds = 0;
151	<	tot_bends = 0;
214	<	tot_torsions = 0;
215	<	for( i=0; i<n_components; i++ ){
216	<
217	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
218	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
219	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
220	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
221	<	}
149	>	bond_pair* theBonds;
150	>	bend_set* theBends;
151	>	torsion_set* theTorsions;
152
223	–	tot_SRI = tot_bonds + tot_bends + tot_torsions;
224	–
225	–	simnfo->n_atoms = tot_atoms;
226	–	simnfo->n_bonds = tot_bonds;
227	–	simnfo->n_bends = tot_bends;
228	–	simnfo->n_torsions = tot_torsions;
229	–	simnfo->n_SRI = tot_SRI;
230	–	simnfo->n_mol = tot_nmol;
231	–
153
154	<	#ifdef IS_MPI
154	>	//init the forceField paramters
155
156	<	// divide the molecules among processors here.
236	<
237	<	mpiSim = new mpiSimulation( simnfo );
238	<
239	<
156	>	the_ff->readParams();
157
241	–	globalIndex = mpiSim->divideLabor();
242	–
243	–	// set up the local variables
158
159	<	int localMol, allMol;
246	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
159	>	// init the atoms
160
161	<	int* mol2proc = mpiSim->getMolToProcMap();
249	<	int* molCompType = mpiSim->getMolComponentType();
161	>	double ux, uy, uz, u, uSqr;
162
163	<	allMol = 0;
164	<	localMol = 0;
165	<	local_atoms = 0;
254	<	local_bonds = 0;
255	<	local_bends = 0;
256	<	local_torsions = 0;
257	<	for( i=0; i<n_components; i++ ){
163	>	for(k=0; k<nInfo; k++){
164	>
165	>	the_ff->setSimInfo( &(info[k]) );
166
167	<	for( j=0; j<components_nmol[i]; j++ ){
167	>	atomOffset = 0;
168	>	excludeOffset = 0;
169	>	for(i=0; i<info[k].n_mol; i++){
170	>
171	>	stampID = info[k].molecules[i].getStampID();
172	>
173	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
174	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
175	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
176	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
177	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
178
179	<	if( mol2proc[j] == worldRank ){
180	<
181	<	local_atoms +=    comp_stamps[i]->getNAtoms();
182	<	local_bonds +=    comp_stamps[i]->getNBonds();
183	<	local_bends +=    comp_stamps[i]->getNBends();
266	<	local_torsions += comp_stamps[i]->getNTorsions();
267	<	localMol++;
268	<	}
269	<	allMol++;
270	<	}
271	<	}
272	<	local_SRI = local_bonds + local_bends + local_torsions;
273	<
179	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
180	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
181	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
182	>	molInfo.myBends = new Bend*[molInfo.nBends];
183	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
184
185	<	simnfo->n_atoms = mpiSim->getMyNlocal();
185	>	theBonds = new bond_pair[molInfo.nBonds];
186	>	theBends = new bend_set[molInfo.nBends];
187	>	theTorsions = new torsion_set[molInfo.nTorsions];
188	>
189	>	// make the Atoms
190	>
191	>	for(j=0; j<molInfo.nAtoms; j++){
192
193	<	if( local_atoms != simnfo->n_atoms ){
193	>	currentAtom = comp_stamps[stampID]->getAtom( j );
194	>	if( currentAtom->haveOrientation() ){
195	>
196	>	dAtom = new DirectionalAtom( (j + atomOffset),
197	>	info[k].getConfiguration() );
198	>	info[k].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	>	else{
217	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
218	>	info[k].getConfiguration() );
219	>	}
220	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221	>
222	>	#ifdef IS_MPI
223	>
224	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
225	>
226	>	#endif // is_mpi
227	>	}
228	>
229	>	// make the bonds
230	>	for(j=0; j<molInfo.nBonds; j++){
231	>
232	>	currentBond = comp_stamps[stampID]->getBond( j );
233	>	theBonds[j].a = currentBond->getA() + atomOffset;
234	>	theBonds[j].b = currentBond->getB() + atomOffset;
235	>
236	>	exI = theBonds[j].a;
237	>	exJ = theBonds[j].b;
238	>
239	>	// exclude_I must always be the smaller of the pair
240	>	if( exI > exJ ){
241	>	tempEx = exI;
242	>	exI = exJ;
243	>	exJ = tempEx;
244	>	}
245	>	#ifdef IS_MPI
246	>	tempEx = exI;
247	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
248	>	tempEx = exJ;
249	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
250	>
251	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
252	>	#else  // isn't MPI
253	>
254	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
255	>	#endif  //is_mpi
256	>	}
257	>	excludeOffset += molInfo.nBonds;
258	>
259	>	//make the bends
260	>	for(j=0; j<molInfo.nBends; j++){
261	>
262	>	currentBend = comp_stamps[stampID]->getBend( j );
263	>	theBends[j].a = currentBend->getA() + atomOffset;
264	>	theBends[j].b = currentBend->getB() + atomOffset;
265	>	theBends[j].c = currentBend->getC() + atomOffset;
266	>
267	>	if( currentBend->haveExtras() ){
268	>
269	>	extras = currentBend->getExtras();
270	>	current_extra = extras;
271	>
272	>	while( current_extra != NULL ){
273	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
274	>
275	>	switch( current_extra->getType() ){
276	>
277	>	case 0:
278	>	theBends[j].ghost =
279	>	current_extra->getInt() + atomOffset;
280	>	theBends[j].isGhost = 1;
281	>	break;
282	>
283	>	case 1:
284	>	theBends[j].ghost =
285	>	(int)current_extra->getDouble() + atomOffset;
286	>	theBends[j].isGhost = 1;
287	>	break;
288	>
289	>	default:
290		sprintf( painCave.errMsg,
291	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
292	<	" localAtom (%d) are not equal.\n",
293	<	simnfo->n_atoms,
294	<	local_atoms );
291	>	"SimSetup Error: ghostVectorSource was neither a "
292	>	"double nor an int.\n"
293	>	"-->Bend[%d] in %s\n",
294	>	j, comp_stamps[stampID]->getID() );
295		painCave.isFatal = 1;
296		simError();
297	+	}
298	+	}
299	+
300	+	else{
301	+
302	+	sprintf( painCave.errMsg,
303	+	"SimSetup Error: unhandled bend assignment:\n"
304	+	"    -->%s in Bend[%d] in %s\n",
305	+	current_extra->getlhs(),
306	+	j, comp_stamps[stampID]->getID() );
307	+	painCave.isFatal = 1;
308	+	simError();
309	+	}
310	+
311	+	current_extra = current_extra->getNext();
312	+	}
313		}
286	–
287	–	simnfo->n_bonds = local_bonds;
288	–	simnfo->n_bends = local_bends;
289	–	simnfo->n_torsions = local_torsions;
290	–	simnfo->n_SRI = local_SRI;
291	–	simnfo->n_mol = localMol;
292	–
293	–	strcpy( checkPointMsg, "Passed nlocal consistency check." );
294	–	MPIcheckPoint();
314
315	+	if( !theBends[j].isGhost ){
316	+
317	+	exI = theBends[j].a;
318	+	exJ = theBends[j].c;
319	+	}
320	+	else{
321	+
322	+	exI = theBends[j].a;
323	+	exJ = theBends[j].b;
324	+	}
325
326	<	#endif // is_mpi
326	>	// exclude_I must always be the smaller of the pair
327	>	if( exI > exJ ){
328	>	tempEx = exI;
329	>	exI = exJ;
330	>	exJ = tempEx;
331	>	}
332	>	#ifdef IS_MPI
333	>	tempEx = exI;
334	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
335	>	tempEx = exJ;
336	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
337	>
338	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
339	>	#else  // isn't MPI
340	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
341	>	#endif  //is_mpi
342	>	}
343	>	excludeOffset += molInfo.nBends;
344	>
345	>	for(j=0; j<molInfo.nTorsions; j++){
346
347	<
348	<	// create the atom and short range interaction arrays
349	<
350	<	Atom::createArrays(simnfo->n_atoms);
351	<	the_atoms = new Atom*[simnfo->n_atoms];
352	<	the_molecules = new Molecule[simnfo->n_mol];
353	<	int molIndex;
354	<
355	<	// initialize the molecule's stampID's
356	<
347	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
348	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
349	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
350	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
351	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
352	>
353	>	exI = theTorsions[j].a;
354	>	exJ = theTorsions[j].d;
355	>
356	>	// exclude_I must always be the smaller of the pair
357	>	if( exI > exJ ){
358	>	tempEx = exI;
359	>	exI = exJ;
360	>	exJ = tempEx;
361	>	}
362		#ifdef IS_MPI
363	+	tempEx = exI;
364	+	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
365	+	tempEx = exJ;
366	+	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
367
368	+	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
369	+	#else  // isn't MPI
370	+	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
371	+	#endif  //is_mpi
372	+	}
373	+	excludeOffset += molInfo.nTorsions;
374	+
375	+
376	+	// send the arrays off to the forceField for init.
377	+
378	+	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
379	+	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
380	+	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
381	+	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
382	+
383	+
384	+	info[k].molecules[i].initialize( molInfo );
385
386	<	molIndex = 0;
387	<	for(i=0; i<mpiSim->getTotNmol(); i++){
388	<
389	<	if(mol2proc[i] == worldRank ){
390	<	the_molecules[molIndex].setStampID( molCompType[i] );
317	<	molIndex++;
386	>
387	>	atomOffset += molInfo.nAtoms;
388	>	delete[] theBonds;
389	>	delete[] theBends;
390	>	delete[] theTorsions;
391		}
392		}
393	+
394	+	#ifdef IS_MPI
395	+	sprintf( checkPointMsg, "all molecules initialized succesfully" );
396	+	MPIcheckPoint();
397	+	#endif // is_mpi
398	+
399	+	// clean up the forcefield
400
401	<	#else // is_mpi
401	>	the_ff->calcRcut();
402	>	the_ff->cleanMe();
403
404	<	molIndex = 0;
405	<	for(i=0; i<n_components; i++){
406	<	for(j=0; j<components_nmol[i]; j++ ){
407	<	the_molecules[molIndex].setStampID( i );
408	<	molIndex++;
404	>	}
405	>
406	>	void SimSetup::initFromBass( void ){
407	>
408	>	int i, j, k;
409	>	int n_cells;
410	>	double cellx, celly, cellz;
411	>	double temp1, temp2, temp3;
412	>	int n_per_extra;
413	>	int n_extra;
414	>	int have_extra, done;
415	>
416	>	double vel[3];
417	>	vel[0] = 0.0;
418	>	vel[1] = 0.0;
419	>	vel[2] = 0.0;
420	>
421	>	temp1 = (double)tot_nmol / 4.0;
422	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
423	>	temp3 = ceil( temp2 );
424	>
425	>	have_extra =0;
426	>	if( temp2 < temp3 ){ // we have a non-complete lattice
427	>	have_extra =1;
428	>
429	>	n_cells = (int)temp3 - 1;
430	>	cellx = info[0].boxL[0] / temp3;
431	>	celly = info[0].boxL[1] / temp3;
432	>	cellz = info[0].boxL[2] / temp3;
433	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
434	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
435	>	n_per_extra = (int)ceil( temp1 );
436	>
437	>	if( n_per_extra > 4){
438	>	sprintf( painCave.errMsg,
439	>	"SimSetup error. There has been an error in constructing"
440	>	" the non-complete lattice.\n" );
441	>	painCave.isFatal = 1;
442	>	simError();
443		}
444		}
445	<
445	>	else{
446	>	n_cells = (int)temp3;
447	>	cellx = info[0].boxL[0] / temp3;
448	>	celly = info[0].boxL[1] / temp3;
449	>	cellz = info[0].boxL[2] / temp3;
450	>	}
451
452	<	#endif // is_mpi
452	>	current_mol = 0;
453	>	current_comp_mol = 0;
454	>	current_comp = 0;
455	>	current_atom_ndx = 0;
456
457	+	for( i=0; i < n_cells ; i++ ){
458	+	for( j=0; j < n_cells; j++ ){
459	+	for( k=0; k < n_cells; k++ ){
460
461	<	if( simnfo->n_SRI ){
462	<
463	<	std::cerr << "n_SRI = " << simnfo->n_SRI << "\n";
338	<
339	<	Exclude::createArray(simnfo->n_SRI);
340	<	the_excludes = new Exclude*[simnfo->n_SRI];
341	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
342	<	simnfo->globalExcludes = new int;
343	<	simnfo->n_exclude = tot_SRI;
344	<	}
345	<	else{
346	<
347	<	Exclude::createArray( 1 );
348	<	the_excludes = new Exclude*;
349	<	the_excludes[0] = new Exclude(0);
350	<	the_excludes[0]->setPair( 0,0 );
351	<	simnfo->globalExcludes = new int;
352	<	simnfo->globalExcludes[0] = 0;
353	<	simnfo->n_exclude = 0;
354	<	}
461	>	makeElement( i * cellx,
462	>	j * celly,
463	>	k * cellz );
464
465	<	// set the arrays into the SimInfo object
465	>	makeElement( i * cellx + 0.5 * cellx,
466	>	j * celly + 0.5 * celly,
467	>	k * cellz );
468
469	<	simnfo->atoms = the_atoms;
470	<	simnfo->molecules = the_molecules;
471	<	simnfo->nGlobalExcludes = 0;
361	<	simnfo->excludes = the_excludes;
469	>	makeElement( i * cellx,
470	>	j * celly + 0.5 * celly,
471	>	k * cellz + 0.5 * cellz );
472
473	+	makeElement( i * cellx + 0.5 * cellx,
474	+	j * celly,
475	+	k * cellz + 0.5 * cellz );
476	+	}
477	+	}
478	+	}
479
480	<	// get some of the tricky things that may still be in the globals
480	>	if( have_extra ){
481	>	done = 0;
482
483	<
484	<	if( the_globals->haveBox() ){
485	<	simnfo->box_x = the_globals->getBox();
369	<	simnfo->box_y = the_globals->getBox();
370	<	simnfo->box_z = the_globals->getBox();
371	<	}
372	<	else if( the_globals->haveDensity() ){
483	>	int start_ndx;
484	>	for( i=0; i < (n_cells+1) && !done; i++ ){
485	>	for( j=0; j < (n_cells+1) && !done; j++ ){
486
487	<	double vol;
375	<	vol = (double)tot_nmol / the_globals->getDensity();
376	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
377	<	simnfo->box_y = simnfo->box_x;
378	<	simnfo->box_z = simnfo->box_x;
379	<	}
380	<	else{
381	<	if( !the_globals->haveBoxX() ){
382	<	sprintf( painCave.errMsg,
383	<	"SimSetup error, no periodic BoxX size given.\n" );
384	<	painCave.isFatal = 1;
385	<	simError();
386	<	}
387	<	simnfo->box_x = the_globals->getBoxX();
487	>	if( i < n_cells ){
488
489	<	if( !the_globals->haveBoxY() ){
490	<	sprintf( painCave.errMsg,
391	<	"SimSetup error, no periodic BoxY size given.\n" );
392	<	painCave.isFatal = 1;
393	<	simError();
489	>	if( j < n_cells ){
490	>	start_ndx = n_cells;
491		}
492	<	simnfo->box_y = the_globals->getBoxY();
396	<
397	<	if( !the_globals->haveBoxZ() ){
398	<	sprintf( painCave.errMsg,
399	<	"SimSetup error, no periodic BoxZ size given.\n" );
400	<	painCave.isFatal = 1;
401	<	simError();
402	<	}
403	<	simnfo->box_z = the_globals->getBoxZ();
492	>	else start_ndx = 0;
493		}
494	+	else start_ndx = 0;
495
496	<	#ifdef IS_MPI
407	<	strcpy( checkPointMsg, "Box size set up" );
408	<	MPIcheckPoint();
409	<	#endif // is_mpi
496	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
497
498	+	makeElement( i * cellx,
499	+	j * celly,
500	+	k * cellz );
501	+	done = ( current_mol >= tot_nmol );
502
503	<	// initialize the arrays
503	>	if( !done && n_per_extra > 1 ){
504	>	makeElement( i * cellx + 0.5 * cellx,
505	>	j * celly + 0.5 * celly,
506	>	k * cellz );
507	>	done = ( current_mol >= tot_nmol );
508	>	}
509
510	<	the_ff->setSimInfo( simnfo );
511	<
512	<	makeMolecules();
513	<	simnfo->identArray = new int[simnfo->n_atoms];
514	<	for(i=0; i<simnfo->n_atoms; i++){
419	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
420	<	}
421	<
422	<	if (the_globals->getUseRF() ) {
423	<	simnfo->useReactionField = 1;
424	<
425	<	if( !the_globals->haveECR() ){
426	<	sprintf( painCave.errMsg,
427	<	"SimSetup Warning: using default value of 1/2 the smallest "
428	<	"box length for the electrostaticCutoffRadius.\n"
429	<	"I hope you have a very fast processor!\n");
430	<	painCave.isFatal = 0;
431	<	simError();
432	<	double smallest;
433	<	smallest = simnfo->box_x;
434	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
435	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
436	<	simnfo->ecr = 0.5 * smallest;
437	<	} else {
438	<	simnfo->ecr        = the_globals->getECR();
510	>	if( !done && n_per_extra > 2){
511	>	makeElement( i * cellx,
512	>	j * celly + 0.5 * celly,
513	>	k * cellz + 0.5 * cellz );
514	>	done = ( current_mol >= tot_nmol );
515		}
516
517	<	if( !the_globals->haveEST() ){
518	<	sprintf( painCave.errMsg,
519	<	"SimSetup Warning: using default value of 0.05 * the "
520	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
521	<	);
446	<	painCave.isFatal = 0;
447	<	simError();
448	<	simnfo->est = 0.05 * simnfo->ecr;
449	<	} else {
450	<	simnfo->est        = the_globals->getEST();
517	>	if( !done && n_per_extra > 3){
518	>	makeElement( i * cellx + 0.5 * cellx,
519	>	j * celly,
520	>	k * cellz + 0.5 * cellz );
521	>	done = ( current_mol >= tot_nmol );
522		}
523	<
453	<	if(!the_globals->haveDielectric() ){
454	<	sprintf( painCave.errMsg,
455	<	"SimSetup Error: You are trying to use Reaction Field without"
456	<	"setting a dielectric constant!\n"
457	<	);
458	<	painCave.isFatal = 1;
459	<	simError();
460	<	}
461	<	simnfo->dielectric = the_globals->getDielectric();
462	<	} else {
463	<	if (simnfo->n_dipoles) {
464	<
465	<	if( !the_globals->haveECR() ){
466	<	sprintf( painCave.errMsg,
467	<	"SimSetup Warning: using default value of 1/2 the smallest"
468	<	"box length for the electrostaticCutoffRadius.\n"
469	<	"I hope you have a very fast processor!\n");
470	<	painCave.isFatal = 0;
471	<	simError();
472	<	double smallest;
473	<	smallest = simnfo->box_x;
474	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
475	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
476	<	simnfo->ecr = 0.5 * smallest;
477	<	} else {
478	<	simnfo->ecr        = the_globals->getECR();
523	>	}
524		}
480	–
481	–	if( !the_globals->haveEST() ){
482	–	sprintf( painCave.errMsg,
483	–	"SimSetup Warning: using default value of 5% of the"
484	–	"electrostaticCutoffRadius for the "
485	–	"electrostaticSkinThickness\n"
486	–	);
487	–	painCave.isFatal = 0;
488	–	simError();
489	–	simnfo->est = 0.05 * simnfo->ecr;
490	–	} else {
491	–	simnfo->est        = the_globals->getEST();
492	–	}
525		}
526	<	}
526	>	}
527
528	<	#ifdef IS_MPI
529	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
530	<	MPIcheckPoint();
531	<	#endif // is_mpi
528	>	for( i=0; i<info[0].n_atoms; i++ ){
529	>	info[0].atoms[i]->setVel( vel );
530	>	}
531	>	}
532
533	<	if( the_globals->haveInitialConfig() ){
502	<
503	<	InitializeFromFile* fileInit;
504	<	#ifdef IS_MPI // is_mpi
505	<	if( worldRank == 0 ){
506	<	#endif //is_mpi
507	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
508	<	#ifdef IS_MPI
509	<	}else fileInit = new InitializeFromFile( NULL );
510	<	#endif
511	<	fileInit->read_xyz( simnfo ); // default velocities on
533	>	void SimSetup::makeElement( double x, double y, double z ){
534
535	<	delete fileInit;
536	<	}
537	<	else{
535	>	int k;
536	>	AtomStamp* current_atom;
537	>	DirectionalAtom* dAtom;
538	>	double rotMat[3][3];
539	>	double pos[3];
540
541	<	#ifdef IS_MPI
541	>	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
542
543	<	// no init from bass
544	<
545	<	sprintf( painCave.errMsg,
546	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
547	<	painCave.isFatal;
548	<	simError();
549	<
550	<	#else
551	<
552	<	initFromBass();
553	<
530	<
531	<	#endif
532	<	}
533	<
534	<	#ifdef IS_MPI
535	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
536	<	MPIcheckPoint();
537	<	#endif // is_mpi
538	<
539	<
540	<
541	<
542	<
543	<
544	<
545	<	#ifdef IS_MPI
546	<	if( worldRank == 0 ){
547	<	#endif // is_mpi
548	<
549	<	if( the_globals->haveFinalConfig() ){
550	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
543	>	current_atom = comp_stamps[current_comp]->getAtom( k );
544	>	if( !current_atom->havePosition() ){
545	>	sprintf( painCave.errMsg,
546	>	"SimSetup:initFromBass error.\n"
547	>	"\tComponent %s, atom %s does not have a position specified.\n"
548	>	"\tThe initialization routine is unable to give a start"
549	>	" position.\n",
550	>	comp_stamps[current_comp]->getID(),
551	>	current_atom->getType() );
552	>	painCave.isFatal = 1;
553	>	simError();
554		}
552	–	else{
553	–	strcpy( simnfo->finalName, inFileName );
554	–	char* endTest;
555	–	int nameLength = strlen( simnfo->finalName );
556	–	endTest = &(simnfo->finalName[nameLength - 5]);
557	–	if( !strcmp( endTest, ".bass" ) ){
558	–	strcpy( endTest, ".eor" );
559	–	}
560	–	else if( !strcmp( endTest, ".BASS" ) ){
561	–	strcpy( endTest, ".eor" );
562	–	}
563	–	else{
564	–	endTest = &(simnfo->finalName[nameLength - 4]);
565	–	if( !strcmp( endTest, ".bss" ) ){
566	–	strcpy( endTest, ".eor" );
567	–	}
568	–	else if( !strcmp( endTest, ".mdl" ) ){
569	–	strcpy( endTest, ".eor" );
570	–	}
571	–	else{
572	–	strcat( simnfo->finalName, ".eor" );
573	–	}
574	–	}
575	–	}
555
556	<	// make the sample and status out names
556	>	pos[0] = x + current_atom->getPosX();
557	>	pos[1] = y + current_atom->getPosY();
558	>	pos[2] = z + current_atom->getPosZ();
559
560	<	strcpy( simnfo->sampleName, inFileName );
561	<	char* endTest;
562	<	int nameLength = strlen( simnfo->sampleName );
563	<	endTest = &(simnfo->sampleName[nameLength - 5]);
564	<	if( !strcmp( endTest, ".bass" ) ){
565	<	strcpy( endTest, ".dump" );
560	>	info[0].atoms[current_atom_ndx]->setPos( pos );
561	>
562	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
563	>
564	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
565	>
566	>	rotMat[0][0] = 1.0;
567	>	rotMat[0][1] = 0.0;
568	>	rotMat[0][2] = 0.0;
569	>
570	>	rotMat[1][0] = 0.0;
571	>	rotMat[1][1] = 1.0;
572	>	rotMat[1][2] = 0.0;
573	>
574	>	rotMat[2][0] = 0.0;
575	>	rotMat[2][1] = 0.0;
576	>	rotMat[2][2] = 1.0;
577	>
578	>	dAtom->setA( rotMat );
579		}
586	–	else if( !strcmp( endTest, ".BASS" ) ){
587	–	strcpy( endTest, ".dump" );
588	–	}
589	–	else{
590	–	endTest = &(simnfo->sampleName[nameLength - 4]);
591	–	if( !strcmp( endTest, ".bss" ) ){
592	–	strcpy( endTest, ".dump" );
593	–	}
594	–	else if( !strcmp( endTest, ".mdl" ) ){
595	–	strcpy( endTest, ".dump" );
596	–	}
597	–	else{
598	–	strcat( simnfo->sampleName, ".dump" );
599	–	}
600	–	}
601	–
602	–	strcpy( simnfo->statusName, inFileName );
603	–	nameLength = strlen( simnfo->statusName );
604	–	endTest = &(simnfo->statusName[nameLength - 5]);
605	–	if( !strcmp( endTest, ".bass" ) ){
606	–	strcpy( endTest, ".stat" );
607	–	}
608	–	else if( !strcmp( endTest, ".BASS" ) ){
609	–	strcpy( endTest, ".stat" );
610	–	}
611	–	else{
612	–	endTest = &(simnfo->statusName[nameLength - 4]);
613	–	if( !strcmp( endTest, ".bss" ) ){
614	–	strcpy( endTest, ".stat" );
615	–	}
616	–	else if( !strcmp( endTest, ".mdl" ) ){
617	–	strcpy( endTest, ".stat" );
618	–	}
619	–	else{
620	–	strcat( simnfo->statusName, ".stat" );
621	–	}
622	–	}
623	–
624	–	#ifdef IS_MPI
625	–	}
626	–	#endif // is_mpi
627	–
628	–	// set the status, sample, and themal kick times
629	–
630	–	if( the_globals->haveSampleTime() ){
631	–	simnfo->sampleTime = the_globals->getSampleTime();
632	–	simnfo->statusTime = simnfo->sampleTime;
633	–	simnfo->thermalTime = simnfo->sampleTime;
634	–	}
635	–	else{
636	–	simnfo->sampleTime = the_globals->getRunTime();
637	–	simnfo->statusTime = simnfo->sampleTime;
638	–	simnfo->thermalTime = simnfo->sampleTime;
639	–	}
580
581	<	if( the_globals->haveStatusTime() ){
642	<	simnfo->statusTime = the_globals->getStatusTime();
581	>	current_atom_ndx++;
582		}
583
584	<	if( the_globals->haveThermalTime() ){
585	<	simnfo->thermalTime = the_globals->getThermalTime();
647	<	}
584	>	current_mol++;
585	>	current_comp_mol++;
586
587	<	// check for the temperature set flag
587	>	if( current_comp_mol >= components_nmol[current_comp] ){
588
589	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
589	>	current_comp_mol = 0;
590	>	current_comp++;
591	>	}
592	>	}
593
594
595	<	//   // make the longe range forces and the integrator
595	>	void SimSetup::gatherInfo( void ){
596	>	int i,j,k;
597
598	<	//   new AllLong( simnfo );
598	>	ensembleCase = -1;
599	>	ffCase = -1;
600
601	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
659	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
601	>	// set the easy ones first
602
603	<	#ifdef IS_MPI
604	<	mpiSim->mpiRefresh();
605	<	#endif
603	>	for( i=0; i<nInfo; i++){
604	>	info[i].target_temp = globals->getTargetTemp();
605	>	info[i].dt = globals->getDt();
606	>	info[i].run_time = globals->getRunTime();
607	>	}
608	>	n_components = globals->getNComponents();
609
665	–	// initialize the Fortran
610
611	+	// get the forceField
612
613	<	simnfo->refreshSim();
614	<
615	<	if( !strcmp( simnfo->mixingRule, "standard") ){
616	<	the_ff->initForceField( LB_MIXING_RULE );
617	<	}
673	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
674	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
675	<	}
613	>	strcpy( force_field, globals->getForceField() );
614	>
615	>	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
616	>	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
617	>	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
618		else{
619		sprintf( painCave.errMsg,
620	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
621	<	simnfo->mixingRule );
620	>	"SimSetup Error. Unrecognized force field -> %s\n",
621	>	force_field );
622		painCave.isFatal = 1;
623		simError();
624		}
625
626	+	// get the ensemble
627
628	<	#ifdef IS_MPI
686	<	strcpy( checkPointMsg,
687	<	"Successfully intialized the mixingRule for Fortran." );
688	<	MPIcheckPoint();
689	<	#endif // is_mpi
690	<	}
628	>	strcpy( ensemble, globals->getEnsemble() );
629
630	<
631	<	void SimSetup::makeMolecules( void ){
632	<
633	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
634	<	molInit info;
635	<	DirectionalAtom* dAtom;
636	<	LinkedAssign* extras;
637	<	LinkedAssign* current_extra;
638	<	AtomStamp* currentAtom;
639	<	BondStamp* currentBond;
640	<	BendStamp* currentBend;
641	<	TorsionStamp* currentTorsion;
642	<
643	<	bond_pair* theBonds;
644	<	bend_set* theBends;
645	<	torsion_set* theTorsions;
646	<
630	>	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
631	>	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
632	>	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
633	>	ensembleCase = NPTi_ENS;
634	>	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
635	>	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
636	>	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
637	>	else{
638	>	sprintf( painCave.errMsg,
639	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
640	>	"reverting to NVE for this simulation.\n",
641	>	ensemble );
642	>	painCave.isFatal = 0;
643	>	simError();
644	>	strcpy( ensemble, "NVE" );
645	>	ensembleCase = NVE_ENS;
646	>	}
647
648	<	//init the forceField paramters
648	>	for(i=0; i<nInfo; i++){
649	>
650	>	strcpy( info[i].ensemble, ensemble );
651
652	<	the_ff->readParams();
652	>	// get the mixing rule
653
654	+	strcpy( info[i].mixingRule, globals->getMixingRule() );
655	+	info[i].usePBC = globals->getPBC();
656	+	}
657
658	<	// init the atoms
658	>	// get the components and calculate the tot_nMol and indvidual n_mol
659	>
660	>	the_components = globals->getComponents();
661	>	components_nmol = new int[n_components];
662
717	–	double ux, uy, uz, u, uSqr;
718	–
719	–	atomOffset = 0;
720	–	excludeOffset = 0;
721	–	for(i=0; i<simnfo->n_mol; i++){
722	–
723	–	stampID = the_molecules[i].getStampID();
663
664	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
665	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
666	<	info.nBends    = comp_stamps[stampID]->getNBends();
728	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
729	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
664	>	if( !globals->haveNMol() ){
665	>	// we don't have the total number of molecules, so we assume it is
666	>	// given in each component
667
668	<	info.myAtoms = &the_atoms[atomOffset];
669	<	info.myExcludes = &the_excludes[excludeOffset];
733	<	info.myBonds = new Bond*[info.nBonds];
734	<	info.myBends = new Bend*[info.nBends];
735	<	info.myTorsions = new Torsion*[info.nTorsions];
668	>	tot_nmol = 0;
669	>	for( i=0; i<n_components; i++ ){
670
671	<	theBonds = new bond_pair[info.nBonds];
672	<	theBends = new bend_set[info.nBends];
673	<	theTorsions = new torsion_set[info.nTorsions];
674	<
675	<	// make the Atoms
676	<
677	<	for(j=0; j<info.nAtoms; j++){
744	<
745	<	currentAtom = comp_stamps[stampID]->getAtom( j );
746	<	if( currentAtom->haveOrientation() ){
747	<
748	<	dAtom = new DirectionalAtom(j + atomOffset);
749	<	simnfo->n_oriented++;
750	<	info.myAtoms[j] = dAtom;
751	<
752	<	ux = currentAtom->getOrntX();
753	<	uy = currentAtom->getOrntY();
754	<	uz = currentAtom->getOrntZ();
755	<
756	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
757	<
758	<	u = sqrt( uSqr );
759	<	ux = ux / u;
760	<	uy = uy / u;
761	<	uz = uz / u;
762	<
763	<	dAtom->setSUx( ux );
764	<	dAtom->setSUy( uy );
765	<	dAtom->setSUz( uz );
671	>	if( !the_components[i]->haveNMol() ){
672	>	// we have a problem
673	>	sprintf( painCave.errMsg,
674	>	"SimSetup Error. No global NMol or component NMol"
675	>	" given. Cannot calculate the number of atoms.\n" );
676	>	painCave.isFatal = 1;
677	>	simError();
678		}
679	<	else{
680	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
681	<	}
682	<	info.myAtoms[j]->setType( currentAtom->getType() );
679	>
680	>	tot_nmol += the_components[i]->getNMol();
681	>	components_nmol[i] = the_components[i]->getNMol();
682	>	}
683	>	}
684	>	else{
685	>	sprintf( painCave.errMsg,
686	>	"SimSetup error.\n"
687	>	"\tSorry, the ability to specify total"
688	>	" nMols and then give molfractions in the components\n"
689	>	"\tis not currently supported."
690	>	" Please give nMol in the components.\n" );
691	>	painCave.isFatal = 1;
692	>	simError();
693	>	}
694	>
695	>	// set the status, sample, and thermal kick times
696	>
697	>	for(i=0; i<nInfo; i++){
698	>
699	>	if( globals->haveSampleTime() ){
700	>	info[i].sampleTime = globals->getSampleTime();
701	>	info[i].statusTime = info[i].sampleTime;
702	>	info[i].thermalTime = info[i].sampleTime;
703	>	}
704	>	else{
705	>	info[i].sampleTime = globals->getRunTime();
706	>	info[i].statusTime = info[i].sampleTime;
707	>	info[i].thermalTime = info[i].sampleTime;
708	>	}
709
710	<	#ifdef IS_MPI
711	<
712	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
775	<
776	<	#endif // is_mpi
777	<	}
710	>	if( globals->haveStatusTime() ){
711	>	info[i].statusTime = globals->getStatusTime();
712	>	}
713
714	<	// make the bonds
715	<	for(j=0; j<info.nBonds; j++){
716	<
782	<	currentBond = comp_stamps[stampID]->getBond( j );
783	<	theBonds[j].a = currentBond->getA() + atomOffset;
784	<	theBonds[j].b = currentBond->getB() + atomOffset;
714	>	if( globals->haveThermalTime() ){
715	>	info[i].thermalTime = globals->getThermalTime();
716	>	}
717
718	<	exI = theBonds[j].a;
787	<	exJ = theBonds[j].b;
718	>	// check for the temperature set flag
719
720	<	// exclude_I must always be the smaller of the pair
721	<	if( exI > exJ ){
722	<	tempEx = exI;
723	<	exI = exJ;
724	<	exJ = tempEx;
725	<	}
726	<	#ifdef IS_MPI
727	<	tempEx = exI;
728	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
798	<	tempEx = exJ;
799	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
720	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
721	>
722	>	// get some of the tricky things that may still be in the globals
723	>
724	>	double boxVector[3];
725	>	if( globals->haveBox() ){
726	>	boxVector[0] = globals->getBox();
727	>	boxVector[1] = globals->getBox();
728	>	boxVector[2] = globals->getBox();
729
730	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
802	<	#else  // isn't MPI
803	<
804	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
805	<	#endif  //is_mpi
730	>	info[i].setBox( boxVector );
731		}
732	<	excludeOffset += info.nBonds;
808	<
809	<	//make the bends
810	<	for(j=0; j<info.nBends; j++){
732	>	else if( globals->haveDensity() ){
733
734	<	currentBend = comp_stamps[stampID]->getBend( j );
735	<	theBends[j].a = currentBend->getA() + atomOffset;
736	<	theBends[j].b = currentBend->getB() + atomOffset;
737	<	theBends[j].c = currentBend->getC() + atomOffset;
738	<
739	<	if( currentBend->haveExtras() ){
740	<
741	<	extras = currentBend->getExtras();
742	<	current_extra = extras;
743	<
744	<	while( current_extra != NULL ){
745	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
746	<
747	<	switch( current_extra->getType() ){
826	<
827	<	case 0:
828	<	theBends[j].ghost =
829	<	current_extra->getInt() + atomOffset;
830	<	theBends[j].isGhost = 1;
831	<	break;
832	<
833	<	case 1:
834	<	theBends[j].ghost =
835	<	(int)current_extra->getDouble() + atomOffset;
836	<	theBends[j].isGhost = 1;
837	<	break;
838	<
839	<	default:
840	<	sprintf( painCave.errMsg,
841	<	"SimSetup Error: ghostVectorSource was neither a "
842	<	"double nor an int.\n"
843	<	"-->Bend[%d] in %s\n",
844	<	j, comp_stamps[stampID]->getID() );
845	<	painCave.isFatal = 1;
846	<	simError();
847	<	}
848	<	}
849	<
850	<	else{
851	<
852	<	sprintf( painCave.errMsg,
853	<	"SimSetup Error: unhandled bend assignment:\n"
854	<	"    -->%s in Bend[%d] in %s\n",
855	<	current_extra->getlhs(),
856	<	j, comp_stamps[stampID]->getID() );
857	<	painCave.isFatal = 1;
858	<	simError();
859	<	}
860	<
861	<	current_extra = current_extra->getNext();
862	<	}
734	>	double vol;
735	>	vol = (double)tot_nmol / globals->getDensity();
736	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
737	>	boxVector[1] = boxVector[0];
738	>	boxVector[2] = boxVector[0];
739	>
740	>	info[i].setBox( boxVector );
741	>	}
742	>	else{
743	>	if( !globals->haveBoxX() ){
744	>	sprintf( painCave.errMsg,
745	>	"SimSetup error, no periodic BoxX size given.\n" );
746	>	painCave.isFatal = 1;
747	>	simError();
748		}
749	<
750	<	if( !theBends[j].isGhost ){
751	<
752	<	exI = theBends[j].a;
753	<	exJ = theBends[j].c;
749	>	boxVector[0] = globals->getBoxX();
750	>
751	>	if( !globals->haveBoxY() ){
752	>	sprintf( painCave.errMsg,
753	>	"SimSetup error, no periodic BoxY size given.\n" );
754	>	painCave.isFatal = 1;
755	>	simError();
756		}
757	<	else{
871	<
872	<	exI = theBends[j].a;
873	<	exJ = theBends[j].b;
874	<	}
757	>	boxVector[1] = globals->getBoxY();
758
759	<	// exclude_I must always be the smaller of the pair
760	<	if( exI > exJ ){
761	<	tempEx = exI;
762	<	exI = exJ;
763	<	exJ = tempEx;
759	>	if( !globals->haveBoxZ() ){
760	>	sprintf( painCave.errMsg,
761	>	"SimSetup error, no periodic BoxZ size given.\n" );
762	>	painCave.isFatal = 1;
763	>	simError();
764		}
765	<	#ifdef IS_MPI
883	<	tempEx = exI;
884	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
885	<	tempEx = exJ;
886	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
765	>	boxVector[2] = globals->getBoxZ();
766
767	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
889	<	#else  // isn't MPI
890	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
891	<	#endif  //is_mpi
767	>	info[i].setBox( boxVector );
768		}
893	–	excludeOffset += info.nBends;
769
770	<	for(j=0; j<info.nTorsions; j++){
770	>	}
771	>
772	>	#ifdef IS_MPI
773	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
774	>	MPIcheckPoint();
775	>	#endif // is_mpi
776	>
777	>	}
778	>
779	>
780	>	void SimSetup::finalInfoCheck( void ){
781	>	int index;
782	>	int usesDipoles;
783	>	int i;
784	>
785	>	for(i=0; i<nInfo; i++){
786	>	// check electrostatic parameters
787	>
788	>	index = 0;
789	>	usesDipoles = 0;
790	>	while( (index < info[i].n_atoms) && !usesDipoles ){
791	>	usesDipoles = (info[i].atoms[index])->hasDipole();
792	>	index++;
793	>	}
794	>
795	>	#ifdef IS_MPI
796	>	int myUse = usesDipoles;
797	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
798	>	#endif //is_mpi
799	>
800	>	double theEcr, theEst;
801	>
802	>	if (globals->getUseRF() ) {
803	>	info[i].useReactionField = 1;
804
805	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
806	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
807	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
808	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
809	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
805	>	if( !globals->haveECR() ){
806	>	sprintf( painCave.errMsg,
807	>	"SimSetup Warning: using default value of 1/2 the smallest "
808	>	"box length for the electrostaticCutoffRadius.\n"
809	>	"I hope you have a very fast processor!\n");
810	>	painCave.isFatal = 0;
811	>	simError();
812	>	double smallest;
813	>	smallest = info[i].boxL[0];
814	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
815	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
816	>	theEcr = 0.5 * smallest;
817	>	} else {
818	>	theEcr = globals->getECR();
819	>	}
820
821	<	exI = theTorsions[j].a;
822	<	exJ = theTorsions[j].d;
823	<
824	<	// exclude_I must always be the smaller of the pair
825	<	if( exI > exJ ){
826	<	tempEx = exI;
827	<	exI = exJ;
828	<	exJ = tempEx;
821	>	if( !globals->haveEST() ){
822	>	sprintf( painCave.errMsg,
823	>	"SimSetup Warning: using default value of 0.05 * the "
824	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
825	>	);
826	>	painCave.isFatal = 0;
827	>	simError();
828	>	theEst = 0.05 * theEcr;
829	>	} else {
830	>	theEst= globals->getEST();
831		}
912	–	#ifdef IS_MPI
913	–	tempEx = exI;
914	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
915	–	tempEx = exJ;
916	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
832
833	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
834	<	#else  // isn't MPI
835	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
836	<	#endif  //is_mpi
837	<	}
838	<	excludeOffset += info.nTorsions;
839	<
840	<
841	<	// send the arrays off to the forceField for init.
842	<
843	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
844	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
845	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
846	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
833	>	info[i].setEcr( theEcr, theEst );
834	>
835	>	if(!globals->haveDielectric() ){
836	>	sprintf( painCave.errMsg,
837	>	"SimSetup Error: You are trying to use Reaction Field without"
838	>	"setting a dielectric constant!\n"
839	>	);
840	>	painCave.isFatal = 1;
841	>	simError();
842	>	}
843	>	info[i].dielectric = globals->getDielectric();
844	>	}
845	>	else {
846	>	if (usesDipoles) {
847	>
848	>	if( !globals->haveECR() ){
849	>	sprintf( painCave.errMsg,
850	>	"SimSetup Warning: using default value of 1/2 the smallest "
851	>	"box length for the electrostaticCutoffRadius.\n"
852	>	"I hope you have a very fast processor!\n");
853	>	painCave.isFatal = 0;
854	>	simError();
855	>	double smallest;
856	>	smallest = info[i].boxL[0];
857	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
858	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
859	>	theEcr = 0.5 * smallest;
860	>	} else {
861	>	theEcr = globals->getECR();
862	>	}
863	>
864	>	if( !globals->haveEST() ){
865	>	sprintf( painCave.errMsg,
866	>	"SimSetup Warning: using default value of 0.05 * the "
867	>	"electrostaticCutoffRadius for the "
868	>	"electrostaticSkinThickness\n"
869	>	);
870	>	painCave.isFatal = 0;
871	>	simError();
872	>	theEst = 0.05 * theEcr;
873	>	} else {
874	>	theEst= globals->getEST();
875	>	}
876	>
877	>	info[i].setEcr( theEcr, theEst );
878	>	}
879	>	}
880	>	}
881
882	+	#ifdef IS_MPI
883	+	strcpy( checkPointMsg, "post processing checks out" );
884	+	MPIcheckPoint();
885	+	#endif // is_mpi
886
887	<	the_molecules[i].initialize( info );
935	<	atomOffset += info.nAtoms;
936	<	delete[] theBonds;
937	<	delete[] theBends;
938	<	delete[] theTorsions;
939	<	}
887	>	}
888
889	+	void SimSetup::initSystemCoords( void ){
890	+	int i;
891	+
892	+	char* inName;
893	+
894	+	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
895	+
896	+	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
897	+
898	+	if( globals->haveInitialConfig() ){
899	+
900	+	InitializeFromFile* fileInit;
901	+	#ifdef IS_MPI // is_mpi
902	+	if( worldRank == 0 ){
903	+	#endif //is_mpi
904	+	inName = globals->getInitialConfig();
905	+	double* tempDouble = new double[1000000];
906	+	fileInit = new InitializeFromFile( inName );
907		#ifdef IS_MPI
908	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
908	>	}else fileInit = new InitializeFromFile( NULL );
909	>	#endif
910	>	fileInit->readInit( info ); // default velocities on
911	>
912	>	delete fileInit;
913	>	}
914	>	else{
915	>
916	>	#ifdef IS_MPI
917	>
918	>	// no init from bass
919	>
920	>	sprintf( painCave.errMsg,
921	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
922	>	painCave.isFatal;
923	>	simError();
924	>
925	>	#else
926	>
927	>	initFromBass();
928	>
929	>
930	>	#endif
931	>	}
932	>
933	>	#ifdef IS_MPI
934	>	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
935		MPIcheckPoint();
936		#endif // is_mpi
937	+
938	+	}
939
946	–	// clean up the forcefield
947	–	the_ff->calcRcut();
948	–	the_ff->cleanMe();
940
941	+	void SimSetup::makeOutNames( void ){
942	+
943	+	int k;
944	+
945	+
946	+	for(k=0; k<nInfo; k++){
947	+
948	+	#ifdef IS_MPI
949	+	if( worldRank == 0 ){
950	+	#endif // is_mpi
951	+
952	+	if( globals->haveFinalConfig() ){
953	+	strcpy( info[k].finalName, globals->getFinalConfig() );
954	+	}
955	+	else{
956	+	strcpy( info[k].finalName, inFileName );
957	+	char* endTest;
958	+	int nameLength = strlen( info[k].finalName );
959	+	endTest = &(info[k].finalName[nameLength - 5]);
960	+	if( !strcmp( endTest, ".bass" ) ){
961	+	strcpy( endTest, ".eor" );
962	+	}
963	+	else if( !strcmp( endTest, ".BASS" ) ){
964	+	strcpy( endTest, ".eor" );
965	+	}
966	+	else{
967	+	endTest = &(info[k].finalName[nameLength - 4]);
968	+	if( !strcmp( endTest, ".bss" ) ){
969	+	strcpy( endTest, ".eor" );
970	+	}
971	+	else if( !strcmp( endTest, ".mdl" ) ){
972	+	strcpy( endTest, ".eor" );
973	+	}
974	+	else{
975	+	strcat( info[k].finalName, ".eor" );
976	+	}
977	+	}
978	+	}
979	+
980	+	// make the sample and status out names
981	+
982	+	strcpy( info[k].sampleName, inFileName );
983	+	char* endTest;
984	+	int nameLength = strlen( info[k].sampleName );
985	+	endTest = &(info[k].sampleName[nameLength - 5]);
986	+	if( !strcmp( endTest, ".bass" ) ){
987	+	strcpy( endTest, ".dump" );
988	+	}
989	+	else if( !strcmp( endTest, ".BASS" ) ){
990	+	strcpy( endTest, ".dump" );
991	+	}
992	+	else{
993	+	endTest = &(info[k].sampleName[nameLength - 4]);
994	+	if( !strcmp( endTest, ".bss" ) ){
995	+	strcpy( endTest, ".dump" );
996	+	}
997	+	else if( !strcmp( endTest, ".mdl" ) ){
998	+	strcpy( endTest, ".dump" );
999	+	}
1000	+	else{
1001	+	strcat( info[k].sampleName, ".dump" );
1002	+	}
1003	+	}
1004	+
1005	+	strcpy( info[k].statusName, inFileName );
1006	+	nameLength = strlen( info[k].statusName );
1007	+	endTest = &(info[k].statusName[nameLength - 5]);
1008	+	if( !strcmp( endTest, ".bass" ) ){
1009	+	strcpy( endTest, ".stat" );
1010	+	}
1011	+	else if( !strcmp( endTest, ".BASS" ) ){
1012	+	strcpy( endTest, ".stat" );
1013	+	}
1014	+	else{
1015	+	endTest = &(info[k].statusName[nameLength - 4]);
1016	+	if( !strcmp( endTest, ".bss" ) ){
1017	+	strcpy( endTest, ".stat" );
1018	+	}
1019	+	else if( !strcmp( endTest, ".mdl" ) ){
1020	+	strcpy( endTest, ".stat" );
1021	+	}
1022	+	else{
1023	+	strcat( info[k].statusName, ".stat" );
1024	+	}
1025	+	}
1026	+
1027	+	#ifdef IS_MPI
1028	+	}
1029	+	#endif // is_mpi
1030	+	}
1031		}
1032
952	–	void SimSetup::initFromBass( void ){
1033
1034	<	int i, j, k;
1035	<	int n_cells;
1036	<	double cellx, celly, cellz;
1037	<	double temp1, temp2, temp3;
1038	<	int n_per_extra;
959	<	int n_extra;
960	<	int have_extra, done;
1034	>	void SimSetup::sysObjectsCreation( void ){
1035	>
1036	>	int i,k;
1037	>
1038	>	// create the forceField
1039
1040	<	temp1 = (double)tot_nmol / 4.0;
963	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
964	<	temp3 = ceil( temp2 );
1040	>	createFF();
1041
1042	<	have_extra =0;
967	<	if( temp2 < temp3 ){ // we have a non-complete lattice
968	<	have_extra =1;
1042	>	// extract componentList
1043
1044	<	n_cells = (int)temp3 - 1;
971	<	cellx = simnfo->box_x / temp3;
972	<	celly = simnfo->box_y / temp3;
973	<	cellz = simnfo->box_z / temp3;
974	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
975	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
976	<	n_per_extra = (int)ceil( temp1 );
1044	>	compList();
1045
1046	<	if( n_per_extra > 4){
1047	<	sprintf( painCave.errMsg,
1048	<	"SimSetup error. There has been an error in constructing"
1049	<	" the non-complete lattice.\n" );
1050	<	painCave.isFatal = 1;
1051	<	simError();
1046	>	// calc the number of atoms, bond, bends, and torsions
1047	>
1048	>	calcSysValues();
1049	>
1050	>	#ifdef IS_MPI
1051	>	// divide the molecules among the processors
1052	>
1053	>	mpiMolDivide();
1054	>	#endif //is_mpi
1055	>
1056	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1057	>
1058	>	makeSysArrays();
1059	>
1060	>	// make and initialize the molecules (all but atomic coordinates)
1061	>
1062	>	makeMolecules();
1063	>
1064	>	for(k=0; k<nInfo; k++){
1065	>	info[k].identArray = new int[info[k].n_atoms];
1066	>	for(i=0; i<info[k].n_atoms; i++){
1067	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1068		}
1069		}
1070	<	else{
1071	<	n_cells = (int)temp3;
1072	<	cellx = simnfo->box_x / temp3;
1073	<	celly = simnfo->box_y / temp3;
1074	<	cellz = simnfo->box_z / temp3;
1070	>	}
1071	>
1072	>
1073	>	void SimSetup::createFF( void ){
1074	>
1075	>	switch( ffCase ){
1076	>
1077	>	case FF_DUFF:
1078	>	the_ff = new DUFF();
1079	>	break;
1080	>
1081	>	case FF_LJ:
1082	>	the_ff = new LJFF();
1083	>	break;
1084	>
1085	>	case FF_EAM:
1086	>	the_ff = new EAM_FF();
1087	>	break;
1088	>
1089	>	default:
1090	>	sprintf( painCave.errMsg,
1091	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1092	>	painCave.isFatal = 1;
1093	>	simError();
1094	>	}
1095	>
1096	>	#ifdef IS_MPI
1097	>	strcpy( checkPointMsg, "ForceField creation successful" );
1098	>	MPIcheckPoint();
1099	>	#endif // is_mpi
1100	>
1101	>	}
1102	>
1103	>
1104	>	void SimSetup::compList( void ){
1105	>
1106	>	int i;
1107	>	char* id;
1108	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1109	>	LinkedMolStamp* currentStamp = NULL;
1110	>	comp_stamps = new MoleculeStamp*[n_components];
1111	>
1112	>	// make an array of molecule stamps that match the components used.
1113	>	// also extract the used stamps out into a separate linked list
1114	>
1115	>	for(i=0; i<nInfo; i++){
1116	>	info[i].nComponents = n_components;
1117	>	info[i].componentsNmol = components_nmol;
1118	>	info[i].compStamps = comp_stamps;
1119	>	info[i].headStamp = headStamp;
1120	>	}
1121	>
1122	>
1123	>	for( i=0; i<n_components; i++ ){
1124	>
1125	>	id = the_components[i]->getType();
1126	>	comp_stamps[i] = NULL;
1127	>
1128	>	// check to make sure the component isn't already in the list
1129	>
1130	>	comp_stamps[i] = headStamp->match( id );
1131	>	if( comp_stamps[i] == NULL ){
1132	>
1133	>	// extract the component from the list;
1134	>
1135	>	currentStamp = stamps->extractMolStamp( id );
1136	>	if( currentStamp == NULL ){
1137	>	sprintf( painCave.errMsg,
1138	>	"SimSetup error: Component \"%s\" was not found in the "
1139	>	"list of declared molecules\n",
1140	>	id );
1141	>	painCave.isFatal = 1;
1142	>	simError();
1143	>	}
1144	>
1145	>	headStamp->add( currentStamp );
1146	>	comp_stamps[i] = headStamp->match( id );
1147	>	}
1148	>	}
1149	>
1150	>	#ifdef IS_MPI
1151	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1152	>	MPIcheckPoint();
1153	>	#endif // is_mpi
1154	>
1155	>
1156	>	}
1157	>
1158	>	void SimSetup::calcSysValues( void ){
1159	>	int i, j, k;
1160	>
1161	>	int *molMembershipArray;
1162	>
1163	>	tot_atoms = 0;
1164	>	tot_bonds = 0;
1165	>	tot_bends = 0;
1166	>	tot_torsions = 0;
1167	>	for( i=0; i<n_components; i++ ){
1168	>
1169	>	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1170	>	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1171	>	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1172	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1173		}
1174	+
1175	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1176	+	molMembershipArray = new int[tot_atoms];
1177	+
1178	+	for(i=0; i<nInfo; i++){
1179	+	info[i].n_atoms = tot_atoms;
1180	+	info[i].n_bonds = tot_bonds;
1181	+	info[i].n_bends = tot_bends;
1182	+	info[i].n_torsions = tot_torsions;
1183	+	info[i].n_SRI = tot_SRI;
1184	+	info[i].n_mol = tot_nmol;
1185	+
1186	+	info[i].molMembershipArray = molMembershipArray;
1187	+	}
1188	+	}
1189
1190	<	current_mol = 0;
994	<	current_comp_mol = 0;
995	<	current_comp = 0;
996	<	current_atom_ndx = 0;
1190	>	#ifdef IS_MPI
1191
1192	<	for( i=0; i < n_cells ; i++ ){
1193	<	for( j=0; j < n_cells; j++ ){
1194	<	for( k=0; k < n_cells; k++ ){
1192	>	void SimSetup::mpiMolDivide( void ){
1193	>
1194	>	int i, j, k;
1195	>	int localMol, allMol;
1196	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1197
1198	<	makeElement( i * cellx,
1199	<	j * celly,
1200	<	k * cellz );
1198	>	mpiSim = new mpiSimulation( info );
1199	>
1200	>	globalIndex = mpiSim->divideLabor();
1201
1202	<	makeElement( i * cellx + 0.5 * cellx,
1203	<	j * celly + 0.5 * celly,
1204	<	k * cellz );
1202	>	// set up the local variables
1203	>
1204	>	mol2proc = mpiSim->getMolToProcMap();
1205	>	molCompType = mpiSim->getMolComponentType();
1206	>
1207	>	allMol = 0;
1208	>	localMol = 0;
1209	>	local_atoms = 0;
1210	>	local_bonds = 0;
1211	>	local_bends = 0;
1212	>	local_torsions = 0;
1213	>	globalAtomIndex = 0;
1214
1010	–	makeElement( i * cellx,
1011	–	j * celly + 0.5 * celly,
1012	–	k * cellz + 0.5 * cellz );
1215
1216	<	makeElement( i * cellx + 0.5 * cellx,
1217	<	j * celly,
1218	<	k * cellz + 0.5 * cellz );
1216	>	for( i=0; i<n_components; i++ ){
1217	>
1218	>	for( j=0; j<components_nmol[i]; j++ ){
1219	>
1220	>	if( mol2proc[allMol] == worldRank ){
1221	>
1222	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1223	>	local_bonds +=    comp_stamps[i]->getNBonds();
1224	>	local_bends +=    comp_stamps[i]->getNBends();
1225	>	local_torsions += comp_stamps[i]->getNTorsions();
1226	>	localMol++;
1227	>	}
1228	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1229	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1230	>	globalAtomIndex++;
1231		}
1232	+
1233	+	allMol++;
1234		}
1235		}
1236	+	local_SRI = local_bonds + local_bends + local_torsions;
1237	+
1238	+	info[0].n_atoms = mpiSim->getMyNlocal();
1239	+
1240	+	if( local_atoms != info[0].n_atoms ){
1241	+	sprintf( painCave.errMsg,
1242	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1243	+	" localAtom (%d) are not equal.\n",
1244	+	info[0].n_atoms,
1245	+	local_atoms );
1246	+	painCave.isFatal = 1;
1247	+	simError();
1248	+	}
1249
1250	<	if( have_extra ){
1251	<	done = 0;
1250	>	info[0].n_bonds = local_bonds;
1251	>	info[0].n_bends = local_bends;
1252	>	info[0].n_torsions = local_torsions;
1253	>	info[0].n_SRI = local_SRI;
1254	>	info[0].n_mol = localMol;
1255
1256	<	int start_ndx;
1257	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1258	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1256	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1257	>	MPIcheckPoint();
1258	>	}
1259	>
1260	>	#endif // is_mpi
1261
1028	–	if( i < n_cells ){
1262
1263	<	if( j < n_cells ){
1264	<	start_ndx = n_cells;
1032	<	}
1033	<	else start_ndx = 0;
1034	<	}
1035	<	else start_ndx = 0;
1263	>	void SimSetup::makeSysArrays( void ){
1264	>	int i, j, k, l;
1265
1266	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1266	>	Atom** the_atoms;
1267	>	Molecule* the_molecules;
1268	>	Exclude** the_excludes;
1269
1270	<	makeElement( i * cellx,
1271	<	j * celly,
1272	<	k * cellz );
1273	<	done = ( current_mol >= tot_nmol );
1270	>
1271	>	for(l=0; l<nInfo; l++){
1272	>
1273	>	// create the atom and short range interaction arrays
1274	>
1275	>	the_atoms = new Atom*[info[l].n_atoms];
1276	>	the_molecules = new Molecule[info[l].n_mol];
1277	>	int molIndex;
1278
1279	<	if( !done && n_per_extra > 1 ){
1280	<	makeElement( i * cellx + 0.5 * cellx,
1281	<	j * celly + 0.5 * celly,
1282	<	k * cellz );
1283	<	done = ( current_mol >= tot_nmol );
1284	<	}
1279	>	// initialize the molecule's stampID's
1280	>
1281	>	#ifdef IS_MPI
1282	>
1283	>
1284	>	molIndex = 0;
1285	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1286	>
1287	>	if(mol2proc[i] == worldRank ){
1288	>	the_molecules[molIndex].setStampID( molCompType[i] );
1289	>	the_molecules[molIndex].setMyIndex( molIndex );
1290	>	the_molecules[molIndex].setGlobalIndex( i );
1291	>	molIndex++;
1292	>	}
1293	>	}
1294	>
1295	>	#else // is_mpi
1296	>
1297	>	molIndex = 0;
1298	>	globalAtomIndex = 0;
1299	>	for(i=0; i<n_components; i++){
1300	>	for(j=0; j<components_nmol[i]; j++ ){
1301	>	the_molecules[molIndex].setStampID( i );
1302	>	the_molecules[molIndex].setMyIndex( molIndex );
1303	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1304	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1305	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1306	>	globalAtomIndex++;
1307	>	}
1308	>	molIndex++;
1309	>	}
1310	>	}
1311	>
1312	>
1313	>	#endif // is_mpi
1314
1051	–	if( !done && n_per_extra > 2){
1052	–	makeElement( i * cellx,
1053	–	j * celly + 0.5 * celly,
1054	–	k * cellz + 0.5 * cellz );
1055	–	done = ( current_mol >= tot_nmol );
1056	–	}
1315
1316	<	if( !done && n_per_extra > 3){
1317	<	makeElement( i * cellx + 0.5 * cellx,
1318	<	j * celly,
1319	<	k * cellz + 0.5 * cellz );
1320	<	done = ( current_mol >= tot_nmol );
1321	<	}
1064	<	}
1316	>	if( info[l].n_SRI ){
1317	>
1318	>	Exclude::createArray(info[l].n_SRI);
1319	>	the_excludes = new Exclude*[info[l].n_SRI];
1320	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1321	>	the_excludes[ex] = new Exclude(ex);
1322		}
1323	+	info[l].globalExcludes = new int;
1324	+	info[l].n_exclude = info[l].n_SRI;
1325		}
1326	<	}
1326	>	else{
1327	>
1328	>	Exclude::createArray( 1 );
1329	>	the_excludes = new Exclude*;
1330	>	the_excludes[0] = new Exclude(0);
1331	>	the_excludes[0]->setPair( 0,0 );
1332	>	info[l].globalExcludes = new int;
1333	>	info[l].globalExcludes[0] = 0;
1334	>	info[l].n_exclude = 0;
1335	>	}
1336
1337	+	// set the arrays into the SimInfo object
1338
1339	<	for( i=0; i<simnfo->n_atoms; i++ ){
1340	<	simnfo->atoms[i]->set_vx( 0.0 );
1341	<	simnfo->atoms[i]->set_vy( 0.0 );
1342	<	simnfo->atoms[i]->set_vz( 0.0 );
1339	>	info[l].atoms = the_atoms;
1340	>	info[l].molecules = the_molecules;
1341	>	info[l].nGlobalExcludes = 0;
1342	>	info[l].excludes = the_excludes;
1343	>
1344	>	the_ff->setSimInfo( info );
1345	>
1346		}
1347		}
1348
1349	<	void SimSetup::makeElement( double x, double y, double z ){
1349	>	void SimSetup::makeIntegrator( void ){
1350
1351		int k;
1080	–	AtomStamp* current_atom;
1081	–	DirectionalAtom* dAtom;
1082	–	double rotMat[3][3];
1352
1353	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1353	>	NVT<RealIntegrator>*  myNVT = NULL;
1354	>	NPTi<RealIntegrator>* myNPTi = NULL;
1355	>	NPTf<RealIntegrator>* myNPTf = NULL;
1356	>	NPTim<RealIntegrator>* myNPTim = NULL;
1357	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1358	>
1359	>	for(k=0; k<nInfo; k++){
1360	>
1361	>	switch( ensembleCase ){
1362	>
1363	>	case NVE_ENS:
1364	>	if (globals->haveZconstraints()){
1365	>	setupZConstraint(info[k]);
1366	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1367	>	}
1368
1369	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1370	<	if( !current_atom->havePosition() ){
1369	>	else
1370	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1371	>	break;
1372	>
1373	>	case NVT_ENS:
1374	>	if (globals->haveZconstraints()){
1375	>	setupZConstraint(info[k]);
1376	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1377	>	}
1378	>	else
1379	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1380	>
1381	>	myNVT->setTargetTemp(globals->getTargetTemp());
1382	>
1383	>	if (globals->haveTauThermostat())
1384	>	myNVT->setTauThermostat(globals->getTauThermostat());
1385	>
1386	>	else {
1387	>	sprintf( painCave.errMsg,
1388	>	"SimSetup error: If you use the NVT\n"
1389	>	"    ensemble, you must set tauThermostat.\n");
1390	>	painCave.isFatal = 1;
1391	>	simError();
1392	>	}
1393	>	break;
1394	>
1395	>	case NPTi_ENS:
1396	>	if (globals->haveZconstraints()){
1397	>	setupZConstraint(info[k]);
1398	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1399	>	}
1400	>	else
1401	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1402	>
1403	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1404	>
1405	>	if (globals->haveTargetPressure())
1406	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1407	>	else {
1408	>	sprintf( painCave.errMsg,
1409	>	"SimSetup error: If you use a constant pressure\n"
1410	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1411	>	painCave.isFatal = 1;
1412	>	simError();
1413	>	}
1414	>
1415	>	if( globals->haveTauThermostat() )
1416	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1417	>	else{
1418	>	sprintf( painCave.errMsg,
1419	>	"SimSetup error: If you use an NPT\n"
1420	>	"    ensemble, you must set tauThermostat.\n");
1421	>	painCave.isFatal = 1;
1422	>	simError();
1423	>	}
1424	>
1425	>	if( globals->haveTauBarostat() )
1426	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1427	>	else{
1428	>	sprintf( painCave.errMsg,
1429	>	"SimSetup error: If you use an NPT\n"
1430	>	"    ensemble, you must set tauBarostat.\n");
1431	>	painCave.isFatal = 1;
1432	>	simError();
1433	>	}
1434	>	break;
1435	>
1436	>	case NPTf_ENS:
1437	>	if (globals->haveZconstraints()){
1438	>	setupZConstraint(info[k]);
1439	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1440	>	}
1441	>	else
1442	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1443	>
1444	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1445	>
1446	>	if (globals->haveTargetPressure())
1447	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1448	>	else {
1449	>	sprintf( painCave.errMsg,
1450	>	"SimSetup error: If you use a constant pressure\n"
1451	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1452	>	painCave.isFatal = 1;
1453	>	simError();
1454	>	}
1455	>
1456	>	if( globals->haveTauThermostat() )
1457	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1458	>	else{
1459	>	sprintf( painCave.errMsg,
1460	>	"SimSetup error: If you use an NPT\n"
1461	>	"    ensemble, you must set tauThermostat.\n");
1462	>	painCave.isFatal = 1;
1463	>	simError();
1464	>	}
1465	>
1466	>	if( globals->haveTauBarostat() )
1467	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1468	>	else{
1469	>	sprintf( painCave.errMsg,
1470	>	"SimSetup error: If you use an NPT\n"
1471	>	"    ensemble, you must set tauBarostat.\n");
1472	>	painCave.isFatal = 1;
1473	>	simError();
1474	>	}
1475	>	break;
1476	>
1477	>	case NPTim_ENS:
1478	>	if (globals->haveZconstraints()){
1479	>	setupZConstraint(info[k]);
1480	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1481	>	}
1482	>	else
1483	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1484	>
1485	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1486	>
1487	>	if (globals->haveTargetPressure())
1488	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1489	>	else {
1490	>	sprintf( painCave.errMsg,
1491	>	"SimSetup error: If you use a constant pressure\n"
1492	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1493	>	painCave.isFatal = 1;
1494	>	simError();
1495	>	}
1496	>
1497	>	if( globals->haveTauThermostat() )
1498	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1499	>	else{
1500	>	sprintf( painCave.errMsg,
1501	>	"SimSetup error: If you use an NPT\n"
1502	>	"    ensemble, you must set tauThermostat.\n");
1503	>	painCave.isFatal = 1;
1504	>	simError();
1505	>	}
1506	>
1507	>	if( globals->haveTauBarostat() )
1508	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1509	>	else{
1510	>	sprintf( painCave.errMsg,
1511	>	"SimSetup error: If you use an NPT\n"
1512	>	"    ensemble, you must set tauBarostat.\n");
1513	>	painCave.isFatal = 1;
1514	>	simError();
1515	>	}
1516	>	break;
1517	>
1518	>	case NPTfm_ENS:
1519	>	if (globals->haveZconstraints()){
1520	>	setupZConstraint(info[k]);
1521	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1522	>	}
1523	>	else
1524	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1525	>
1526	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1527	>
1528	>	if (globals->haveTargetPressure())
1529	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1530	>	else {
1531	>	sprintf( painCave.errMsg,
1532	>	"SimSetup error: If you use a constant pressure\n"
1533	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1534	>	painCave.isFatal = 1;
1535	>	simError();
1536	>	}
1537	>
1538	>	if( globals->haveTauThermostat() )
1539	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1540	>	else{
1541	>	sprintf( painCave.errMsg,
1542	>	"SimSetup error: If you use an NPT\n"
1543	>	"    ensemble, you must set tauThermostat.\n");
1544	>	painCave.isFatal = 1;
1545	>	simError();
1546	>	}
1547	>
1548	>	if( globals->haveTauBarostat() )
1549	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1550	>	else{
1551	>	sprintf( painCave.errMsg,
1552	>	"SimSetup error: If you use an NPT\n"
1553	>	"    ensemble, you must set tauBarostat.\n");
1554	>	painCave.isFatal = 1;
1555	>	simError();
1556	>	}
1557	>	break;
1558	>
1559	>	default:
1560		sprintf( painCave.errMsg,
1561	<	"SimSetup:initFromBass error.\n"
1090	<	"\tComponent %s, atom %s does not have a position specified.\n"
1091	<	"\tThe initialization routine is unable to give a start"
1092	<	" position.\n",
1093	<	comp_stamps[current_comp]->getID(),
1094	<	current_atom->getType() );
1561	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1562		painCave.isFatal = 1;
1563		simError();
1564		}
1565	+	}
1566	+	}
1567
1568	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1100	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1101	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1568	>	void SimSetup::initFortran( void ){
1569
1570	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1570	>	info[0].refreshSim();
1571	>
1572	>	if( !strcmp( info[0].mixingRule, "standard") ){
1573	>	the_ff->initForceField( LB_MIXING_RULE );
1574	>	}
1575	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1576	>	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1577	>	}
1578	>	else{
1579	>	sprintf( painCave.errMsg,
1580	>	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1581	>	info[0].mixingRule );
1582	>	painCave.isFatal = 1;
1583	>	simError();
1584	>	}
1585
1105	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1586
1587	<	rotMat[0][0] = 1.0;
1588	<	rotMat[0][1] = 0.0;
1589	<	rotMat[0][2] = 0.0;
1587	>	#ifdef IS_MPI
1588	>	strcpy( checkPointMsg,
1589	>	"Successfully intialized the mixingRule for Fortran." );
1590	>	MPIcheckPoint();
1591	>	#endif // is_mpi
1592
1593	<	rotMat[1][0] = 0.0;
1112	<	rotMat[1][1] = 1.0;
1113	<	rotMat[1][2] = 0.0;
1593	>	}
1594
1595	<	rotMat[2][0] = 0.0;
1596	<	rotMat[2][1] = 0.0;
1597	<	rotMat[2][2] = 1.0;
1595	>	void SimSetup::setupZConstraint(SimInfo& theInfo)
1596	>	{
1597	>	int nZConstraints;
1598	>	ZconStamp** zconStamp;
1599
1600	<	dAtom->setA( rotMat );
1601	<	}
1600	>	if(globals->haveZconstraintTime()){
1601	>
1602	>	//add sample time of z-constraint  into SimInfo's property list
1603	>	DoubleData* zconsTimeProp = new DoubleData();
1604	>	zconsTimeProp->setID(ZCONSTIME_ID);
1605	>	zconsTimeProp->setData(globals->getZconsTime());
1606	>	theInfo.addProperty(zconsTimeProp);
1607	>	}
1608	>	else{
1609	>	sprintf( painCave.errMsg,
1610	>	"ZConstraint error: If you use an ZConstraint\n"
1611	>	" , you must set sample time.\n");
1612	>	painCave.isFatal = 1;
1613	>	simError();
1614	>	}
1615
1616	<	current_atom_ndx++;
1616	>	//push zconsTol into siminfo, if user does not specify
1617	>	//value for zconsTol, a default value will be used
1618	>	DoubleData* zconsTol = new DoubleData();
1619	>	zconsTol->setID(ZCONSTOL_ID);
1620	>	if(globals->haveZconsTol()){
1621	>	zconsTol->setData(globals->getZconsTol());
1622		}
1623	+	else{
1624	+	double defaultZConsTol = 0.01;
1625	+	sprintf( painCave.errMsg,
1626	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1627	+	" , default value %f is used.\n", defaultZConsTol);
1628	+	painCave.isFatal = 0;
1629	+	simError();
1630
1631	<	current_mol++;
1632	<	current_comp_mol++;
1631	>	zconsTol->setData(defaultZConsTol);
1632	>	}
1633	>	theInfo.addProperty(zconsTol);
1634
1635	<	if( current_comp_mol >= components_nmol[current_comp] ){
1635	>	//set Force Substraction Policy
1636	>	StringData* zconsForcePolicy =  new StringData();
1637	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1638	>
1639	>	if(globals->haveZconsForcePolicy()){
1640	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1641	>	}
1642	>	else{
1643	>	sprintf( painCave.errMsg,
1644	>	"ZConstraint Warning: User does not set force substraction policy, "
1645	>	"average force substraction policy is used\n");
1646	>	painCave.isFatal = 0;
1647	>	simError();
1648	>	zconsForcePolicy->setData("BYNUMBER");
1649	>	}
1650	>
1651	>	theInfo.addProperty(zconsForcePolicy);
1652	>
1653	>	//Determine the name of ouput file and add it into SimInfo's property list
1654	>	//Be careful, do not use inFileName, since it is a pointer which
1655	>	//point to a string at master node, and slave nodes do not contain that string
1656	>
1657	>	string zconsOutput(theInfo.finalName);
1658	>
1659	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1660	>
1661	>	StringData* zconsFilename = new StringData();
1662	>	zconsFilename->setID(ZCONSFILENAME_ID);
1663	>	zconsFilename->setData(zconsOutput);
1664	>
1665	>	theInfo.addProperty(zconsFilename);
1666	>
1667	>	//setup index, pos and other parameters of z-constraint molecules
1668	>	nZConstraints = globals->getNzConstraints();
1669	>	theInfo.nZconstraints = nZConstraints;
1670
1671	<	current_comp_mol = 0;
1672	<	current_comp++;
1671	>	zconStamp = globals->getZconStamp();
1672	>	ZConsParaItem tempParaItem;
1673	>
1674	>	ZConsParaData* zconsParaData = new ZConsParaData();
1675	>	zconsParaData->setID(ZCONSPARADATA_ID);
1676	>
1677	>	for(int i = 0; i < nZConstraints; i++){
1678	>	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1679	>	tempParaItem.zPos = zconStamp[i]->getZpos();
1680	>	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1681	>	tempParaItem.kRatio = zconStamp[i]->getKratio();
1682	>
1683	>	zconsParaData->addItem(tempParaItem);
1684		}
1685	+
1686	+	//sort the parameters by index of molecules
1687	+	zconsParaData->sortByIndex();
1688	+
1689	+	//push data into siminfo, therefore, we can retrieve later
1690	+	theInfo.addProperty(zconsParaData);
1691	+
1692		}

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