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root/group/branches/no-template-branch/OOPSE/libmdtools/SimSetup.cpp

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 378 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
Revision 690 by mmeineke, Tue Aug 12 21:44:06 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	<	int i, j;
97	>	int i, j, k, globalAtomIndex;
98	>
99	>	// gather all of the information from the Bass file
100
101	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
101	>	gatherInfo();
102
103	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	simnfo->run_time = the_globals->getRunTime();
103	>	// creation of complex system objects
104
105	<	// get the ones we know are there, yet still may need some work.
81	<	n_components = the_globals->getNComponents();
82	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
105	>	sysObjectsCreation();
106
107	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
107	>	// check on the post processing info
108
109	+	finalInfoCheck();
110
111	<	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
92	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
93	<	else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
94	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
95	<	else{
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Error. Unrecognized force field -> %s\n",
98	<	force_field );
99	<	painCave.isFatal = 1;
100	<	simError();
101	<	}
111	>	// initialize the system coordinates
112
113	<	#ifdef IS_MPI
104	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
113	>	if( !isInfoArray ) initSystemCoords();
114
115	+	// make the output filenames
116	+
117	+	makeOutNames();
118	+
119	+	// make the integrator
120
121	+	makeIntegrator();
122	+
123	+	#ifdef IS_MPI
124	+	mpiSim->mpiRefresh();
125	+	#endif
126
127	<	// get the components and calculate the tot_nMol and indvidual n_mol
111	<	the_components = the_globals->getComponents();
112	<	components_nmol = new int[n_components];
113	<	comp_stamps = new MoleculeStamp*[n_components];
127	>	// initialize the Fortran
128
129	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
129	>	initFortran();
130
119	–	tot_nmol = 0;
120	–	for( i=0; i<n_components; i++ ){
131
122	–	if( !the_components[i]->haveNMol() ){
123	–	// we have a problem
124	–	sprintf( painCave.errMsg,
125	–	"SimSetup Error. No global NMol or component NMol"
126	–	" given. Cannot calculate the number of atoms.\n" );
127	–	painCave.isFatal = 1;
128	–	simError();
129	–	}
132
133	<	tot_nmol += the_components[i]->getNMol();
132	<	components_nmol[i] = the_components[i]->getNMol();
133	<	}
134	<	}
135	<	else{
136	<	sprintf( painCave.errMsg,
137	<	"SimSetup error.\n"
138	<	"\tSorry, the ability to specify total"
139	<	" nMols and then give molfractions in the components\n"
140	<	"\tis not currently supported."
141	<	" Please give nMol in the components.\n" );
142	<	painCave.isFatal = 1;
143	<	simError();
144	<
145	<
146	<	//     tot_nmol = the_globals->getNMol();
147	<
148	<	//   //we have the total number of molecules, now we check for molfractions
149	<	//     for( i=0; i<n_components; i++ ){
150	<
151	<	//       if( !the_components[i]->haveMolFraction() ){
152	<
153	<	//  if( !the_components[i]->haveNMol() ){
154	<	//    //we have a problem
155	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
156	<	//              << " nMol was given in component
157	<
158	<	}
133	>	}
134
160	–	#ifdef IS_MPI
161	–	strcpy( checkPointMsg, "Have the number of components" );
162	–	MPIcheckPoint();
163	–	#endif // is_mpi
135
136	<	// make an array of molecule stamps that match the components used.
166	<	// also extract the used stamps out into a separate linked list
136	>	void SimSetup::makeMolecules( void ){
137
138	<	simnfo->nComponents = n_components;
139	<	simnfo->componentsNmol = components_nmol;
140	<	simnfo->compStamps = comp_stamps;
141	<	simnfo->headStamp = new LinkedMolStamp();
142	<
143	<	char* id;
144	<	LinkedMolStamp* headStamp = simnfo->headStamp;
145	<	LinkedMolStamp* currentStamp = NULL;
146	<	for( i=0; i<n_components; i++ ){
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	<	id = the_components[i]->getType();
150	<	comp_stamps[i] = NULL;
151	<
181	<	// check to make sure the component isn't already in the list
149	>	bond_pair* theBonds;
150	>	bend_set* theBends;
151	>	torsion_set* theTorsions;
152
183	–	comp_stamps[i] = headStamp->match( id );
184	–	if( comp_stamps[i] == NULL ){
185	–
186	–	// extract the component from the list;
187	–
188	–	currentStamp = the_stamps->extractMolStamp( id );
189	–	if( currentStamp == NULL ){
190	–	sprintf( painCave.errMsg,
191	–	"SimSetup error: Component \"%s\" was not found in the "
192	–	"list of declared molecules\n",
193	–	id );
194	–	painCave.isFatal = 1;
195	–	simError();
196	–	}
197	–
198	–	headStamp->add( currentStamp );
199	–	comp_stamps[i] = headStamp->match( id );
200	–	}
201	–	}
202	–
203	–	#ifdef IS_MPI
204	–	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
205	–	MPIcheckPoint();
206	–	#endif // is_mpi
153
154	+	//init the forceField paramters
155
156	+	the_ff->readParams();
157
210	–
211	–	// caclulate the number of atoms, bonds, bends and torsions
212	–
213	–	tot_atoms = 0;
214	–	tot_bonds = 0;
215	–	tot_bends = 0;
216	–	tot_torsions = 0;
217	–	for( i=0; i<n_components; i++ ){
218	–
219	–	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
220	–	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
221	–	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
222	–	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
223	–	}
224	–
225	–	tot_SRI = tot_bonds + tot_bends + tot_torsions;
226	–
227	–	simnfo->n_atoms = tot_atoms;
228	–	simnfo->n_bonds = tot_bonds;
229	–	simnfo->n_bends = tot_bends;
230	–	simnfo->n_torsions = tot_torsions;
231	–	simnfo->n_SRI = tot_SRI;
232	–	simnfo->n_mol = tot_nmol;
233	–
158
159	<	#ifdef IS_MPI
159	>	// init the atoms
160
161	<	// divide the molecules among processors here.
161	>	double ux, uy, uz, u, uSqr;
162
163	<	mpiSim = new mpiSimulation( simnfo );
164	<
165	<
163	>	for(k=0; k<nInfo; k++){
164	>
165	>	the_ff->setSimInfo( &(info[k]) );
166
167	<	globalIndex = mpiSim->divideLabor();
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	<
174	<
175	<	// set up the local variables
176	<
177	<	int localMol, allMol;
250	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
251	<
252	<	allMol = 0;
253	<	localMol = 0;
254	<	local_atoms = 0;
255	<	local_bonds = 0;
256	<	local_bends = 0;
257	<	local_torsions = 0;
258	<	for( i=0; i<n_components; i++ ){
259	<
260	<	for( j=0; j<components_nmol[i]; j++ ){
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( mpiSim->getMyMolStart() <= allMol &&
180	<	allMol <= mpiSim->getMyMolEnd() ){
181	<
182	<	local_atoms +=    comp_stamps[i]->getNAtoms();
183	<	local_bonds +=    comp_stamps[i]->getNBonds();
267	<	local_bends +=    comp_stamps[i]->getNBends();
268	<	local_torsions += comp_stamps[i]->getNTorsions();
269	<	localMol++;
270	<	}
271	<	allMol++;
272	<	}
273	<	}
274	<	local_SRI = local_bonds + local_bends + local_torsions;
275	<
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();
186	<
187	<	if( local_atoms != simnfo->n_atoms ){
188	<	sprintf( painCave.errMsg,
189	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
190	<	" localAtom (%d) are note equal.\n",
191	<	simnfo->n_atoms,
192	<	local_atoms );
193	<	painCave.isFatal = 1;
194	<	simError();
195	<	}
196	<
197	<	simnfo->n_bonds = local_bonds;
198	<	simnfo->n_bends = local_bends;
199	<	simnfo->n_torsions = local_torsions;
200	<	simnfo->n_SRI = local_SRI;
201	<	simnfo->n_mol = localMol;
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	>	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: 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	>	}
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	>	// 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	>	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	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
387	<	MPIcheckPoint();
386	>
387	>	atomOffset += molInfo.nAtoms;
388	>	delete[] theBonds;
389	>	delete[] theBends;
390	>	delete[] theTorsions;
391	>	}
392	>	}
393
394	<
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	<	// create the atom and short range interaction arrays
401	>	the_ff->calcRcut();
402	>	the_ff->cleanMe();
403	>
404	>	}
405
406	<	Atom::createArrays(simnfo->n_atoms);
305	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
406	>	void SimSetup::initFromBass( void ){
407
408	+	int i, j, k;
409	+	int n_cells;
410	+	double cellx, celly, cellz;
411	+	double temp1, temp2, temp3;
412	+	int n_per_extra;
413	+	int n_extra;
414	+	int have_extra, done;
415
416	<	if( simnfo->n_SRI ){
417	<	the_sris = new SRI*[simnfo->n_SRI];
418	<	the_excludes = new int[2 * simnfo->n_SRI];
419	<	simnfo->globalExcludes = new int;
313	<	simnfo->n_exclude = tot_SRI;
314	<	}
315	<	else{
316	<
317	<	the_excludes = new int[2];
318	<	the_excludes[0] = 0;
319	<	the_excludes[1] = 0;
320	<	simnfo->globalExcludes = new int;
321	<	simnfo->globalExcludes[0] = 0;
416	>	double vel[3];
417	>	vel[0] = 0.0;
418	>	vel[1] = 0.0;
419	>	vel[2] = 0.0;
420
421	<	simnfo->n_exclude = 1;
422	<	}
421	>	temp1 = (double)tot_nmol / 4.0;
422	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
423	>	temp3 = ceil( temp2 );
424
425	<	// set the arrays into the SimInfo object
425	>	have_extra =0;
426	>	if( temp2 < temp3 ){ // we have a non-complete lattice
427	>	have_extra =1;
428
429	<	simnfo->atoms = the_atoms;
430	<	simnfo->sr_interactions = the_sris;
431	<	simnfo->nGlobalExcludes = 0;
432	<	simnfo->excludes = the_excludes;
429	>	n_cells = (int)temp3 - 1;
430	>	cellx = info[0].boxL[0] / temp3;
431	>	celly = info[0].boxL[1] / temp3;
432	>	cellz = info[0].boxL[2] / temp3;
433	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
434	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
435	>	n_per_extra = (int)ceil( temp1 );
436
437	<
334	<	// get some of the tricky things that may still be in the globals
335	<
336	<	if( simnfo->n_dipoles ){
337	<
338	<	if( !the_globals->haveRRF() ){
437	>	if( n_per_extra > 4){
438		sprintf( painCave.errMsg,
439	<	"SimSetup Error, system has dipoles, but no rRF was set.\n");
439	>	"SimSetup error. There has been an error in constructing"
440	>	" the non-complete lattice.\n" );
441		painCave.isFatal = 1;
442		simError();
443		}
444	<	if( !the_globals->haveDielectric() ){
445	<	sprintf( painCave.errMsg,
446	<	"SimSetup Error, system has dipoles, but no"
447	<	" dielectric was set.\n" );
448	<	painCave.isFatal = 1;
449	<	simError();
450	<	}
444	>	}
445	>	else{
446	>	n_cells = (int)temp3;
447	>	cellx = info[0].boxL[0] / temp3;
448	>	celly = info[0].boxL[1] / temp3;
449	>	cellz = info[0].boxL[2] / temp3;
450	>	}
451
452	<	simnfo->rRF        = the_globals->getRRF();
453	<	simnfo->dielectric = the_globals->getDielectric();
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	>	makeElement( i * cellx,
462	>	j * celly,
463	>	k * cellz );
464	>
465	>	makeElement( i * cellx + 0.5 * cellx,
466	>	j * celly + 0.5 * celly,
467	>	k * cellz );
468	>
469	>	makeElement( i * cellx,
470	>	j * celly + 0.5 * celly,
471	>	k * cellz + 0.5 * cellz );
472	>
473	>	makeElement( i * cellx + 0.5 * cellx,
474	>	j * celly,
475	>	k * cellz + 0.5 * cellz );
476	>	}
477	>	}
478		}
479
480	<	#ifdef IS_MPI
481	<	strcpy( checkPointMsg, "rRf and dielectric check out" );
482	<	MPIcheckPoint();
483	<	#endif // is_mpi
484	<
485	<	if( the_globals->haveBox() ){
486	<	simnfo->box_x = the_globals->getBox();
487	<	simnfo->box_y = the_globals->getBox();
488	<	simnfo->box_z = the_globals->getBox();
480	>	if( have_extra ){
481	>	done = 0;
482	>
483	>	int start_ndx;
484	>	for( i=0; i < (n_cells+1) && !done; i++ ){
485	>	for( j=0; j < (n_cells+1) && !done; j++ ){
486	>
487	>	if( i < n_cells ){
488	>
489	>	if( j < n_cells ){
490	>	start_ndx = n_cells;
491	>	}
492	>	else start_ndx = 0;
493	>	}
494	>	else start_ndx = 0;
495	>
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	>	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	>	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( !done && n_per_extra > 3){
518	>	makeElement( i * cellx + 0.5 * cellx,
519	>	j * celly,
520	>	k * cellz + 0.5 * cellz );
521	>	done = ( current_mol >= tot_nmol );
522	>	}
523	>	}
524	>	}
525	>	}
526		}
366	–	else if( the_globals->haveDensity() ){
527
528	<	double vol;
529	<	vol = (double)tot_nmol / the_globals->getDensity();
370	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
371	<	simnfo->box_y = simnfo->box_x;
372	<	simnfo->box_z = simnfo->box_x;
528	>	for( i=0; i<info[0].n_atoms; i++ ){
529	>	info[0].atoms[i]->setVel( vel );
530		}
531	<	else{
375	<	if( !the_globals->haveBoxX() ){
376	<	sprintf( painCave.errMsg,
377	<	"SimSetup error, no periodic BoxX size given.\n" );
378	<	painCave.isFatal = 1;
379	<	simError();
380	<	}
381	<	simnfo->box_x = the_globals->getBoxX();
531	>	}
532
533	<	if( !the_globals->haveBoxY() ){
384	<	sprintf( painCave.errMsg,
385	<	"SimSetup error, no periodic BoxY size given.\n" );
386	<	painCave.isFatal = 1;
387	<	simError();
388	<	}
389	<	simnfo->box_y = the_globals->getBoxY();
533	>	void SimSetup::makeElement( double x, double y, double z ){
534
535	<	if( !the_globals->haveBoxZ() ){
535	>	int k;
536	>	AtomStamp* current_atom;
537	>	DirectionalAtom* dAtom;
538	>	double rotMat[3][3];
539	>	double pos[3];
540	>
541	>	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
542	>
543	>	current_atom = comp_stamps[current_comp]->getAtom( k );
544	>	if( !current_atom->havePosition() ){
545		sprintf( painCave.errMsg,
546	<	"SimSetup error, no periodic BoxZ size given.\n" );
546	>	"SimSetup:initFromBass error.\n"
547	>	"\tComponent %s, atom %s does not have a position specified.\n"
548	>	"\tThe initialization routine is unable to give a start"
549	>	" position.\n",
550	>	comp_stamps[current_comp]->getID(),
551	>	current_atom->getType() );
552		painCave.isFatal = 1;
553		simError();
554		}
555	<	simnfo->box_z = the_globals->getBoxZ();
556	<	}
555	>
556	>	pos[0] = x + current_atom->getPosX();
557	>	pos[1] = y + current_atom->getPosY();
558	>	pos[2] = z + current_atom->getPosZ();
559	>
560	>	info[0].atoms[current_atom_ndx]->setPos( pos );
561
562	<	#ifdef IS_MPI
401	<	strcpy( checkPointMsg, "Box size set up" );
402	<	MPIcheckPoint();
403	<	#endif // is_mpi
562	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
563
564	+	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
565
566	<	// initialize the arrays
566	>	rotMat[0][0] = 1.0;
567	>	rotMat[0][1] = 0.0;
568	>	rotMat[0][2] = 0.0;
569
570	<	the_ff->setSimInfo( simnfo );
570	>	rotMat[1][0] = 0.0;
571	>	rotMat[1][1] = 1.0;
572	>	rotMat[1][2] = 0.0;
573
574	<	makeAtoms();
575	<	simnfo->identArray = new int[simnfo->n_atoms];
576	<	for(i=0; i<simnfo->n_atoms; i++){
413	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
414	<	}
415	<
416	<	if( tot_bonds ){
417	<	makeBonds();
418	<	}
574	>	rotMat[2][0] = 0.0;
575	>	rotMat[2][1] = 0.0;
576	>	rotMat[2][2] = 1.0;
577
578	<	if( tot_bends ){
579	<	makeBends();
422	<	}
578	>	dAtom->setA( rotMat );
579	>	}
580
581	<	if( tot_torsions ){
425	<	makeTorsions();
581	>	current_atom_ndx++;
582		}
583
584	+	current_mol++;
585	+	current_comp_mol++;
586
587	+	if( current_comp_mol >= components_nmol[current_comp] ){
588
589	+	current_comp_mol = 0;
590	+	current_comp++;
591	+	}
592	+	}
593
594
595	+	void SimSetup::gatherInfo( void ){
596	+	int i,j,k;
597
598	<	if( the_globals->haveInitialConfig() ){
599	<
435	<	InitializeFromFile* fileInit;
436	<	#ifdef IS_MPI // is_mpi
437	<	if( worldRank == 0 ){
438	<	#endif //is_mpi
439	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
440	<	#ifdef IS_MPI
441	<	}else fileInit = new InitializeFromFile( NULL );
442	<	#endif
443	<	fileInit->read_xyz( simnfo ); // default velocities on
598	>	ensembleCase = -1;
599	>	ffCase = -1;
600
601	<	delete fileInit;
446	<	}
447	<	else{
601	>	// set the easy ones first
602
603	<	#ifdef IS_MPI
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
451	–	// no init from bass
452	–
453	–	sprintf( painCave.errMsg,
454	–	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
455	–	painCave.isFatal;
456	–	simError();
457	–
458	–	#else
610
611	<	initFromBass();
611	>	// get the forceField
612
613	+	strcpy( force_field, globals->getForceField() );
614
615	<	#endif
616	<	}
615	>	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
616	>	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
617	>	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
618	>	else{
619	>	sprintf( painCave.errMsg,
620	>	"SimSetup Error. Unrecognized force field -> %s\n",
621	>	force_field );
622	>	painCave.isFatal = 1;
623	>	simError();
624	>	}
625
626	<	#ifdef IS_MPI
467	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
468	<	MPIcheckPoint();
469	<	#endif // is_mpi
626	>	// get the ensemble
627
628	+	strcpy( ensemble, globals->getEnsemble() );
629
630	<
631	<
632	<
633	<
634	<
635	<	#ifdef IS_MPI
636	<	if( worldRank == 0 ){
637	<	#endif // is_mpi
638	<
639	<	if( the_globals->haveFinalConfig() ){
640	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
641	<	}
642	<	else{
643	<	strcpy( simnfo->finalName, inFileName );
644	<	char* endTest;
645	<	int nameLength = strlen( simnfo->finalName );
646	<	endTest = &(simnfo->finalName[nameLength - 5]);
647	<	if( !strcmp( endTest, ".bass" ) ){
648	<	strcpy( endTest, ".eor" );
630	>	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
631	>	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
632	>	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
633	>	ensembleCase = NPTi_ENS;
634	>	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
635	>	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
636	>	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
637	>	else{
638	>	sprintf( painCave.errMsg,
639	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
640	>	"reverting to NVE for this simulation.\n",
641	>	ensemble );
642	>	painCave.isFatal = 0;
643	>	simError();
644	>	strcpy( ensemble, "NVE" );
645	>	ensembleCase = NVE_ENS;
646	>	}
647	>
648	>	for(i=0; i<nInfo; i++){
649	>
650	>	strcpy( info[i].ensemble, ensemble );
651	>
652	>	// get the mixing rule
653	>
654	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
655	>	info[i].usePBC = globals->getPBC();
656	>	}
657	>
658	>	// get the components and calculate the tot_nMol and indvidual n_mol
659	>
660	>	the_components = globals->getComponents();
661	>	components_nmol = new int[n_components];
662	>
663	>
664	>	if( !globals->haveNMol() ){
665	>	// we don't have the total number of molecules, so we assume it is
666	>	// given in each component
667	>
668	>	tot_nmol = 0;
669	>	for( i=0; i<n_components; i++ ){
670	>
671	>	if( !the_components[i]->haveNMol() ){
672	>	// we have a problem
673	>	sprintf( painCave.errMsg,
674	>	"SimSetup Error. No global NMol or component NMol"
675	>	" given. Cannot calculate the number of atoms.\n" );
676	>	painCave.isFatal = 1;
677	>	simError();
678		}
679	<	else if( !strcmp( endTest, ".BASS" ) ){
680	<	strcpy( endTest, ".eor" );
681	<	}
495	<	else{
496	<	endTest = &(simnfo->finalName[nameLength - 4]);
497	<	if( !strcmp( endTest, ".bss" ) ){
498	<	strcpy( endTest, ".eor" );
499	<	}
500	<	else if( !strcmp( endTest, ".mdl" ) ){
501	<	strcpy( endTest, ".eor" );
502	<	}
503	<	else{
504	<	strcat( simnfo->finalName, ".eor" );
505	<	}
506	<	}
679	>
680	>	tot_nmol += the_components[i]->getNMol();
681	>	components_nmol[i] = the_components[i]->getNMol();
682		}
683	<
684	<	// make the sample and status out names
685	<
686	<	strcpy( simnfo->sampleName, inFileName );
687	<	char* endTest;
688	<	int nameLength = strlen( simnfo->sampleName );
689	<	endTest = &(simnfo->sampleName[nameLength - 5]);
690	<	if( !strcmp( endTest, ".bass" ) ){
691	<	strcpy( endTest, ".dump" );
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		}
518	–	else if( !strcmp( endTest, ".BASS" ) ){
519	–	strcpy( endTest, ".dump" );
520	–	}
704		else{
705	<	endTest = &(simnfo->sampleName[nameLength - 4]);
706	<	if( !strcmp( endTest, ".bss" ) ){
707	<	strcpy( endTest, ".dump" );
525	<	}
526	<	else if( !strcmp( endTest, ".mdl" ) ){
527	<	strcpy( endTest, ".dump" );
528	<	}
529	<	else{
530	<	strcat( simnfo->sampleName, ".dump" );
531	<	}
705	>	info[i].sampleTime = globals->getRunTime();
706	>	info[i].statusTime = info[i].sampleTime;
707	>	info[i].thermalTime = info[i].sampleTime;
708		}
709
710	<	strcpy( simnfo->statusName, inFileName );
711	<	nameLength = strlen( simnfo->statusName );
536	<	endTest = &(simnfo->statusName[nameLength - 5]);
537	<	if( !strcmp( endTest, ".bass" ) ){
538	<	strcpy( endTest, ".stat" );
710	>	if( globals->haveStatusTime() ){
711	>	info[i].statusTime = globals->getStatusTime();
712		}
713	<	else if( !strcmp( endTest, ".BASS" ) ){
714	<	strcpy( endTest, ".stat" );
713	>
714	>	if( globals->haveThermalTime() ){
715	>	info[i].thermalTime = globals->getThermalTime();
716		}
717	+
718	+	// check for the temperature set flag
719	+
720	+	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
721	+
722	+	// get some of the tricky things that may still be in the globals
723	+
724	+	double boxVector[3];
725	+	if( globals->haveBox() ){
726	+	boxVector[0] = globals->getBox();
727	+	boxVector[1] = globals->getBox();
728	+	boxVector[2] = globals->getBox();
729	+
730	+	info[i].setBox( boxVector );
731	+	}
732	+	else if( globals->haveDensity() ){
733	+
734	+	double vol;
735	+	vol = (double)tot_nmol / globals->getDensity();
736	+	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
737	+	boxVector[1] = boxVector[0];
738	+	boxVector[2] = boxVector[0];
739	+
740	+	info[i].setBox( boxVector );
741	+	}
742		else{
743	<	endTest = &(simnfo->statusName[nameLength - 4]);
744	<	if( !strcmp( endTest, ".bss" ) ){
745	<	strcpy( endTest, ".stat" );
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	<	else if( !strcmp( endTest, ".mdl" ) ){
750	<	strcpy( endTest, ".stat" );
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{
758	<	strcat( simnfo->statusName, ".stat" );
757	>	boxVector[1] = globals->getBoxY();
758	>
759	>	if( !globals->haveBoxZ() ){
760	>	sprintf( painCave.errMsg,
761	>	"SimSetup error, no periodic BoxZ size given.\n" );
762	>	painCave.isFatal = 1;
763	>	simError();
764		}
765	+	boxVector[2] = globals->getBoxZ();
766	+
767	+	info[i].setBox( boxVector );
768		}
769	+
770	+	}
771
772		#ifdef IS_MPI
773	<	}
773	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
774	>	MPIcheckPoint();
775		#endif // is_mpi
559	–
560	–	// set the status, sample, and themal kick times
561	–
562	–	if( the_globals->haveSampleTime() ){
563	–	simnfo->sampleTime = the_globals->getSampleTime();
564	–	simnfo->statusTime = simnfo->sampleTime;
565	–	simnfo->thermalTime = simnfo->sampleTime;
566	–	}
567	–	else{
568	–	simnfo->sampleTime = the_globals->getRunTime();
569	–	simnfo->statusTime = simnfo->sampleTime;
570	–	simnfo->thermalTime = simnfo->sampleTime;
571	–	}
776
777	<	if( the_globals->haveStatusTime() ){
574	<	simnfo->statusTime = the_globals->getStatusTime();
575	<	}
777	>	}
778
577	–	if( the_globals->haveThermalTime() ){
578	–	simnfo->thermalTime = the_globals->getThermalTime();
579	–	}
779
780	<	// check for the temperature set flag
780	>	void SimSetup::finalInfoCheck( void ){
781	>	int index;
782	>	int usesDipoles;
783	>	int i;
784
785	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
786	<
787	<
788	<	//   // make the longe range forces and the integrator
789	<
790	<	//   new AllLong( simnfo );
791	<
792	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
793	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
794	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
795	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
796	<
797	<
798	<
799	<	// initialize the Fortran
800	<
801	<	simnfo->refreshSim();
802	<
803	<	if( !strcmp( simnfo->mixingRule, "standard") ){
804	<	the_ff->initForceField( LB_MIXING_RULE );
805	<	}
806	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
807	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
808	<	}
809	<	else{
810	<	sprintf( painCave.errMsg,
811	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
812	<	simnfo->mixingRule );
813	<	painCave.isFatal = 1;
814	<	simError();
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	>	if( !globals->haveECR() ){
806	>	sprintf( painCave.errMsg,
807	>	"SimSetup Warning: using default value of 1/2 the smallest "
808	>	"box length for the electrostaticCutoffRadius.\n"
809	>	"I hope you have a very fast processor!\n");
810	>	painCave.isFatal = 0;
811	>	simError();
812	>	double smallest;
813	>	smallest = info[i].boxL[0];
814	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
815	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
816	>	theEcr = 0.5 * smallest;
817	>	} else {
818	>	theEcr = globals->getECR();
819	>	}
820	>
821	>	if( !globals->haveEST() ){
822	>	sprintf( painCave.errMsg,
823	>	"SimSetup Warning: using default value of 0.05 * the "
824	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
825	>	);
826	>	painCave.isFatal = 0;
827	>	simError();
828	>	theEst = 0.05 * theEcr;
829	>	} else {
830	>	theEst= globals->getEST();
831	>	}
832	>
833	>	info[i].setEcr( theEcr, theEst );
834	>
835	>	if(!globals->haveDielectric() ){
836	>	sprintf( painCave.errMsg,
837	>	"SimSetup Error: You are trying to use Reaction Field without"
838	>	"setting a dielectric constant!\n"
839	>	);
840	>	painCave.isFatal = 1;
841	>	simError();
842	>	}
843	>	info[i].dielectric = globals->getDielectric();
844	>	}
845	>	else {
846	>	if (usesDipoles) {
847	>
848	>	if( !globals->haveECR() ){
849	>	sprintf( painCave.errMsg,
850	>	"SimSetup Warning: using default value of 1/2 the smallest "
851	>	"box length for the electrostaticCutoffRadius.\n"
852	>	"I hope you have a very fast processor!\n");
853	>	painCave.isFatal = 0;
854	>	simError();
855	>	double smallest;
856	>	smallest = info[i].boxL[0];
857	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
858	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
859	>	theEcr = 0.5 * smallest;
860	>	} else {
861	>	theEcr = globals->getECR();
862	>	}
863	>
864	>	if( !globals->haveEST() ){
865	>	sprintf( painCave.errMsg,
866	>	"SimSetup Warning: using default value of 0.05 * the "
867	>	"electrostaticCutoffRadius for the "
868	>	"electrostaticSkinThickness\n"
869	>	);
870	>	painCave.isFatal = 0;
871	>	simError();
872	>	theEst = 0.05 * theEcr;
873	>	} else {
874	>	theEst= globals->getEST();
875	>	}
876	>
877	>	info[i].setEcr( theEcr, theEst );
878	>	}
879	>	}
880		}
881
615	–
882		#ifdef IS_MPI
883	<	strcpy( checkPointMsg,
618	<	"Successfully intialized the mixingRule for Fortran." );
883	>	strcpy( checkPointMsg, "post processing checks out" );
884		MPIcheckPoint();
885		#endif // is_mpi
886	+
887		}
888
889	<	void SimSetup::makeAtoms( void ){
889	>	void SimSetup::initSystemCoords( void ){
890	>	int i;
891	>
892	>	char* inName;
893
625	–	int i, j, k, index;
626	–	double ux, uy, uz, uSqr, u;
627	–	AtomStamp* current_atom;
894
895	<	DirectionalAtom* dAtom;
896	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
895	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
896	>
897	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
898	>
899	>	if( globals->haveInitialConfig() ){
900	>
901	>	InitializeFromFile* fileInit;
902	>	#ifdef IS_MPI // is_mpi
903	>	if( worldRank == 0 ){
904	>	#endif //is_mpi
905	>	inName = globals->getInitialConfig();
906	>	fileInit = new InitializeFromFile( inName );
907	>	#ifdef IS_MPI
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
632	–	lMolIndex = 0;
633	–	molIndex = 0;
634	–	index = 0;
635	–	for( i=0; i<n_components; i++ ){
940
941	<	for( j=0; j<components_nmol[i]; j++ ){
941	>	void SimSetup::makeOutNames( void ){
942	>
943	>	int k;
944
945	<	#ifdef IS_MPI
946	<	if( mpiSim->getMyMolStart() <= molIndex &&
641	<	molIndex <= mpiSim->getMyMolEnd() ){
642	<	#endif // is_mpi
945	>
946	>	for(k=0; k<nInfo; k++){
947
948	<	molStart = index;
949	<	nMemb = comp_stamps[i]->getNAtoms();
950	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
951	<
952	<	current_atom = comp_stamps[i]->getAtom( k );
953	<	if( current_atom->haveOrientation() ){
954	<
955	<	dAtom = new DirectionalAtom(index);
956	<	simnfo->n_oriented++;
957	<	the_atoms[index] = dAtom;
958	<
959	<	ux = current_atom->getOrntX();
960	<	uy = current_atom->getOrntY();
961	<	uz = current_atom->getOrntZ();
962	<
963	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
964	<
965	<	u = sqrt( uSqr );
966	<	ux = ux / u;
967	<	uy = uy / u;
968	<	uz = uz / u;
969	<
666	<	dAtom->setSUx( ux );
667	<	dAtom->setSUy( uy );
668	<	dAtom->setSUz( uz );
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	<	the_atoms[index] = new GeneralAtom(index);
975	>	strcat( info[k].finalName, ".eor" );
976		}
673	–	the_atoms[index]->setType( current_atom->getType() );
674	–	the_atoms[index]->setIndex( index );
675	–
676	–	// increment the index and repeat;
677	–	index++;
977		}
679	–
680	–	molEnd = index -1;
681	–	the_molecules[lMolIndex].setNMembers( nMemb );
682	–	the_molecules[lMolIndex].setStartAtom( molStart );
683	–	the_molecules[lMolIndex].setEndAtom( molEnd );
684	–	the_molecules[lMolIndex].setStampID( i );
685	–	lMolIndex++;
686	–
687	–	#ifdef IS_MPI
978		}
689	–	#endif //is_mpi
979
980	<	molIndex++;
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
695	–	#ifdef IS_MPI
696	–	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
697	–
698	–	delete[] globalIndex;
1033
1034	<	mpiSim->mpiRefresh();
1035	<	#endif //IS_MPI
1036	<
1037	<	the_ff->initializeAtoms();
1038	<	}
1034	>	void SimSetup::sysObjectsCreation( void ){
1035	>
1036	>	int i,k;
1037	>
1038	>	// create the forceField
1039
1040	<	void SimSetup::makeBonds( void ){
1040	>	createFF();
1041
1042	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
709	<	bond_pair* the_bonds;
710	<	BondStamp* current_bond;
1042	>	// extract componentList
1043
1044	<	the_bonds = new bond_pair[tot_bonds];
713	<	index = 0;
714	<	offset = 0;
715	<	molIndex = 0;
1044	>	compList();
1045
1046	<	for( i=0; i<n_components; i++ ){
1046	>	// calc the number of atoms, bond, bends, and torsions
1047
1048	<	for( j=0; j<components_nmol[i]; j++ ){
1048	>	calcSysValues();
1049
1050		#ifdef IS_MPI
1051	<	if( mpiSim->getMyMolStart() <= molIndex &&
1052	<	molIndex <= mpiSim->getMyMolEnd() ){
1053	<	#endif // is_mpi
1054	<
1055	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
1056	<
1057	<	current_bond = comp_stamps[i]->getBond( k );
1058	<	the_bonds[index].a = current_bond->getA() + offset;
730	<	the_bonds[index].b = current_bond->getB() + offset;
731	<
732	<	exI = the_bonds[index].a;
733	<	exJ = the_bonds[index].b;
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	<	// exclude_I must always be the smaller of the pair
1061	<	if( exI > exJ ){
1062	<	tempEx = exI;
1063	<	exI = exJ;
1064	<	exJ = tempEx;
1065	<	}
1060	>	// make and initialize the molecules (all but atomic coordinates)
1061	>
1062	>	makeMolecules();
1063	>
1064	>	for(k=0; k<nInfo; k++){
1065	>	info[k].identArray = new int[info[k].n_atoms];
1066	>	for(i=0; i<info[k].n_atoms; i++){
1067	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1068	>	}
1069	>	}
1070	>	}
1071
742	–
743	–	#ifdef IS_MPI
1072
1073	<	the_excludes[index*2] =
746	<	the_atoms[exI]->getGlobalIndex() + 1;
747	<	the_excludes[index*2 + 1] =
748	<	the_atoms[exJ]->getGlobalIndex() + 1;
1073	>	void SimSetup::createFF( void ){
1074
1075	<	#else  // isn't MPI
751	<
752	<	the_excludes[index*2] =     exI + 1;
753	<	the_excludes[index*2 + 1] = exJ + 1;
754	<	// fortran index from 1 (hence the +1 in the indexing)
755	<	#endif  //is_mpi
756	<
757	<	// increment the index and repeat;
758	<	index++;
759	<	}
760	<	offset += comp_stamps[i]->getNAtoms();
761	<
762	<	#ifdef IS_MPI
763	<	}
764	<	#endif //is_mpi
765	<
766	<	molIndex++;
767	<	}
768	<	}
1075	>	switch( ffCase ){
1076
1077	<	the_ff->initializeBonds( the_bonds );
1078	<	}
1077	>	case FF_DUFF:
1078	>	the_ff = new DUFF();
1079	>	break;
1080
1081	<	void SimSetup::makeBends( void ){
1081	>	case FF_LJ:
1082	>	the_ff = new LJFF();
1083	>	break;
1084
1085	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1086	<	bend_set* the_bends;
1087	<	BendStamp* current_bend;
778	<	LinkedAssign* extras;
779	<	LinkedAssign* current_extra;
780	<
1085	>	case FF_EAM:
1086	>	the_ff = new EAM_FF();
1087	>	break;
1088
1089	<	the_bends = new bend_set[tot_bends];
1090	<	index = 0;
1091	<	offset = 0;
1092	<	molIndex = 0;
1093	<	for( i=0; i<n_components; i++ ){
1089	>	default:
1090	>	sprintf( painCave.errMsg,
1091	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1092	>	painCave.isFatal = 1;
1093	>	simError();
1094	>	}
1095
788	–	for( j=0; j<components_nmol[i]; j++ ){
789	–
1096		#ifdef IS_MPI
1097	<	if( mpiSim->getMyMolStart() <= molIndex &&
1098	<	molIndex <= mpiSim->getMyMolEnd() ){
1099	<	#endif // is_mpi
1097	>	strcpy( checkPointMsg, "ForceField creation successful" );
1098	>	MPIcheckPoint();
1099	>	#endif // is_mpi
1100
1101	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
796	<
797	<	current_bend = comp_stamps[i]->getBend( k );
798	<	the_bends[index].a = current_bend->getA() + offset;
799	<	the_bends[index].b = current_bend->getB() + offset;
800	<	the_bends[index].c = current_bend->getC() + offset;
801	<
802	<	if( current_bend->haveExtras() ){
803	<
804	<	extras = current_bend->getExtras();
805	<	current_extra = extras;
806	<
807	<	while( current_extra != NULL ){
808	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
809	<
810	<	switch( current_extra->getType() ){
811	<
812	<	case 0:
813	<	the_bends[index].ghost =
814	<	current_extra->getInt() + offset;
815	<	the_bends[index].isGhost = 1;
816	<	break;
817	<
818	<	case 1:
819	<	the_bends[index].ghost =
820	<	(int)current_extra->getDouble() + offset;
821	<	the_bends[index].isGhost = 1;
822	<	break;
823	<
824	<	default:
825	<	sprintf( painCave.errMsg,
826	<	"SimSetup Error: ghostVectorSource was neiter a "
827	<	"double nor an int.\n"
828	<	"-->Bend[%d] in %s\n",
829	<	k, comp_stamps[i]->getID() );
830	<	painCave.isFatal = 1;
831	<	simError();
832	<	}
833	<	}
834	<
835	<	else{
836	<
837	<	sprintf( painCave.errMsg,
838	<	"SimSetup Error: unhandled bend assignment:\n"
839	<	"    -->%s in Bend[%d] in %s\n",
840	<	current_extra->getlhs(),
841	<	k, comp_stamps[i]->getID() );
842	<	painCave.isFatal = 1;
843	<	simError();
844	<	}
845	<
846	<	current_extra = current_extra->getNext();
847	<	}
848	<	}
849	<
850	<	if( !the_bends[index].isGhost ){
851	<
852	<	exI = the_bends[index].a;
853	<	exJ = the_bends[index].c;
854	<	}
855	<	else{
856	<
857	<	exI = the_bends[index].a;
858	<	exJ = the_bends[index].b;
859	<	}
860	<
861	<	// exclude_I must always be the smaller of the pair
862	<	if( exI > exJ ){
863	<	tempEx = exI;
864	<	exI = exJ;
865	<	exJ = tempEx;
866	<	}
1101	>	}
1102
1103
1104	<	#ifdef IS_MPI
1104	>	void SimSetup::compList( void ){
1105
1106	<	the_excludes[(index + tot_bonds)*2] =
1107	<	the_atoms[exI]->getGlobalIndex() + 1;
1108	<	the_excludes[(index + tot_bonds)*2 + 1] =
1109	<	the_atoms[exJ]->getGlobalIndex() + 1;
1110	<
1111	<	#else  // isn't MPI
1112	<
1113	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
1114	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1115	<	// fortran index from 1 (hence the +1 in the indexing)
1116	<	#endif  //is_mpi
1117	<
1118	<
1119	<	// increment the index and repeat;
1120	<	index++;
1121	<	}
887	<	offset += comp_stamps[i]->getNAtoms();
888	<
889	<	#ifdef IS_MPI
890	<	}
891	<	#endif //is_mpi
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	<	molIndex++;
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	<	sprintf( checkPointMsg,
899	<	"Successfully created the bends list.\n" );
1151	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1152		MPIcheckPoint();
1153		#endif // is_mpi
902	–
1154
1155	<	the_ff->initializeBends( the_bends );
1155	>
1156		}
1157
1158	<	void SimSetup::makeTorsions( void ){
1159	<
1160	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1161	<	torsion_set* the_torsions;
1162	<	TorsionStamp* current_torsion;
1163	<
1164	<	the_torsions = new torsion_set[tot_torsions];
1165	<	index = 0;
1166	<	offset = 0;
916	<	molIndex = 0;
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
919	–	for( j=0; j<components_nmol[i]; j++ ){
920	–
1190		#ifdef IS_MPI
922	–	if( mpiSim->getMyMolStart() <= molIndex &&
923	–	molIndex <= mpiSim->getMyMolEnd() ){
924	–	#endif // is_mpi
1191
1192	<	for( k=0; k<comp_stamps[i]->getNTorsions(); 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	<	current_torsion = comp_stamps[i]->getTorsion( k );
1199	<	the_torsions[index].a = current_torsion->getA() + offset;
1200	<	the_torsions[index].b = current_torsion->getB() + offset;
931	<	the_torsions[index].c = current_torsion->getC() + offset;
932	<	the_torsions[index].d = current_torsion->getD() + offset;
1198	>	mpiSim = new mpiSimulation( info );
1199	>
1200	>	globalIndex = mpiSim->divideLabor();
1201
1202	<	exI = the_torsions[index].a;
1203	<	exJ = the_torsions[index].d;
1204	<
1205	<
1206	<	// exclude_I must always be the smaller of the pair
1207	<	if( exI > exJ ){
1208	<	tempEx = exI;
1209	<	exI = exJ;
1210	<	exJ = tempEx;
1211	<	}
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
1215
1216	<	#ifdef IS_MPI
947	<
948	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
949	<	the_atoms[exI]->getGlobalIndex() + 1;
950	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
951	<	the_atoms[exJ]->getGlobalIndex() + 1;
952	<
953	<	#else  // isn't MPI
954	<
955	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
956	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
957	<	// fortran indexes from 1 (hence the +1 in the indexing)
958	<	#endif  //is_mpi
959	<
1216	>	for( i=0; i<n_components; i++ ){
1217
1218	<	// increment the index and repeat;
1219	<	index++;
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		}
964	–	offset += comp_stamps[i]->getNAtoms();
1232
1233	<	#ifdef IS_MPI
967	<	}
968	<	#endif //is_mpi
969	<
970	<	molIndex++;
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	<	the_ff->initializeTorsions( the_torsions );
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	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1257	>	MPIcheckPoint();
1258		}
1259	+
1260	+	#endif // is_mpi
1261
977	–	void SimSetup::initFromBass( void ){
1262
1263	<	int i, j, k;
1264	<	int n_cells;
981	<	double cellx, celly, cellz;
982	<	double temp1, temp2, temp3;
983	<	int n_per_extra;
984	<	int n_extra;
985	<	int have_extra, done;
1263	>	void SimSetup::makeSysArrays( void ){
1264	>	int i, j, k, l;
1265
1266	<	temp1 = (double)tot_nmol / 4.0;
1267	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1268	<	temp3 = ceil( temp2 );
1266	>	Atom** the_atoms;
1267	>	Molecule* the_molecules;
1268	>	Exclude** the_excludes;
1269
1270	<	have_extra =0;
1271	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1272	<	have_extra =1;
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	<	n_cells = (int)temp3 - 1;
1280	<	cellx = simnfo->box_x / temp3;
1281	<	celly = simnfo->box_y / temp3;
1282	<	cellz = simnfo->box_z / temp3;
1283	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1284	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1285	<	n_per_extra = (int)ceil( temp1 );
1286	<
1287	<	if( n_per_extra > 4){
1288	<	sprintf( painCave.errMsg,
1289	<	"SimSetup error. There has been an error in constructing"
1290	<	" the non-complete lattice.\n" );
1291	<	painCave.isFatal = 1;
1292	<	simError();
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{
1296	<	n_cells = (int)temp3;
1297	<	cellx = simnfo->box_x / temp3;
1298	<	celly = simnfo->box_y / temp3;
1299	<	cellz = simnfo->box_z / temp3;
1300	<	}
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
1018	–	current_mol = 0;
1019	–	current_comp_mol = 0;
1020	–	current_comp = 0;
1021	–	current_atom_ndx = 0;
1315
1316	<	for( i=0; i < n_cells ; i++ ){
1317	<	for( j=0; j < n_cells; j++ ){
1318	<	for( k=0; k < n_cells; k++ ){
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	>	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	<	makeElement( i * cellx,
1028	<	j * celly,
1029	<	k * cellz );
1337	>	// set the arrays into the SimInfo object
1338
1339	<	makeElement( i * cellx + 0.5 * cellx,
1340	<	j * celly + 0.5 * celly,
1341	<	k * cellz );
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	<	makeElement( i * cellx,
1345	<	j * celly + 0.5 * celly,
1037	<	k * cellz + 0.5 * cellz );
1038	<
1039	<	makeElement( i * cellx + 0.5 * cellx,
1040	<	j * celly,
1041	<	k * cellz + 0.5 * cellz );
1042	<	}
1043	<	}
1344	>	the_ff->setSimInfo( info );
1345	>
1346		}
1347	+	}
1348
1349	<	if( have_extra ){
1047	<	done = 0;
1349	>	void SimSetup::makeIntegrator( void ){
1350
1351	<	int start_ndx;
1050	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1051	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1351	>	int k;
1352
1353	<	if( i < n_cells ){
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	<	if( j < n_cells ){
1370	<	start_ndx = n_cells;
1371	<	}
1372	<	else start_ndx = 0;
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 start_ndx = 0;
1378	>	else
1379	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1380
1381	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
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	<	makeElement( i * cellx,
1404	<	j * celly,
1405	<	k * cellz );
1406	<	done = ( current_mol >= tot_nmol );
1407	<
1408	<	if( !done && n_per_extra > 1 ){
1409	<	makeElement( i * cellx + 0.5 * cellx,
1410	<	j * celly + 0.5 * celly,
1411	<	k * cellz );
1412	<	done = ( current_mol >= tot_nmol );
1413	<	}
1414	<
1415	<	if( !done && n_per_extra > 2){
1416	<	makeElement( i * cellx,
1417	<	j * celly + 0.5 * celly,
1418	<	k * cellz + 0.5 * cellz );
1419	<	done = ( current_mol >= tot_nmol );
1420	<	}
1421	<
1422	<	if( !done && n_per_extra > 3){
1423	<	makeElement( i * cellx + 0.5 * cellx,
1424	<	j * celly,
1425	<	k * cellz + 0.5 * cellz );
1426	<	done = ( current_mol >= tot_nmol );
1427	<	}
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 Error. Unrecognized ensemble in case statement.\n");
1562	+	painCave.isFatal = 1;
1563	+	simError();
1564		}
1565		}
1566	+	}
1567
1568	+	void SimSetup::initFortran( void ){
1569
1570	<	for( i=0; i<simnfo->n_atoms; i++ ){
1571	<	simnfo->atoms[i]->set_vx( 0.0 );
1572	<	simnfo->atoms[i]->set_vy( 0.0 );
1573	<	simnfo->atoms[i]->set_vz( 0.0 );
1570	>	info[0].refreshSim();
1571	>
1572	>	if( !strcmp( info[0].mixingRule, "standard") ){
1573	>	the_ff->initForceField( LB_MIXING_RULE );
1574		}
1575	<	}
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
1102	–	void SimSetup::makeElement( double x, double y, double z ){
1586
1587	<	int k;
1588	<	AtomStamp* current_atom;
1589	<	DirectionalAtom* dAtom;
1590	<	double rotMat[3][3];
1587	>	#ifdef IS_MPI
1588	>	strcpy( checkPointMsg,
1589	>	"Successfully intialized the mixingRule for Fortran." );
1590	>	MPIcheckPoint();
1591	>	#endif // is_mpi
1592
1593	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1593	>	}
1594
1595	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1596	<	if( !current_atom->havePosition() ){
1595	>	void SimSetup::setupZConstraint(SimInfo& theInfo)
1596	>	{
1597	>	int nZConstraints;
1598	>	ZconStamp** zconStamp;
1599	>
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	<	"SimSetup:initFromBass error.\n"
1611	<	"\tComponent %s, atom %s does not have a position specified.\n"
1116	<	"\tThe initialization routine is unable to give a start"
1117	<	" position.\n",
1118	<	comp_stamps[current_comp]->getID(),
1119	<	current_atom->getType() );
1610	>	"ZConstraint error: If you use an ZConstraint\n"
1611	>	" , you must set sample time.\n");
1612		painCave.isFatal = 1;
1613	<	simError();
1613	>	simError();
1614		}
1615
1616	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1617	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1618	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1616	>	//
1617	>	nZConstraints = globals->getNzConstraints();
1618	>	zconStamp = globals->getZconStamp();
1619	>	ZConsParaItem tempParaItem;
1620
1621	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1621	>	ZConsParaData* zconsParaData = new ZConsParaData();
1622	>	zconsParaData->setID(ZCONSPARADATA_ID);
1623	>
1624	>	for(int i = 0; i < nZConstraints; i++){
1625	>	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1626	>	tempParaItem.zPos = zconStamp[i]->getZpos();
1627	>	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1628	>	tempParaItem.kRatio = zconStamp[i]->getKratio();
1629
1630	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1630	>	zconsParaData->addItem(tempParaItem);
1631	>	}
1632
1633	<	rotMat[0][0] = 1.0;
1634	<	rotMat[0][1] = 0.0;
1635	<	rotMat[0][2] = 0.0;
1633	>	//sort the parameters by index of molecules
1634	>	zconsParaData->sortByIndex();
1635	>
1636	>	//push data into siminfo, therefore, we can retrieve later
1637	>	theInfo.addProperty(zconsParaData);
1638
1639	<	rotMat[1][0] = 0.0;
1640	<	rotMat[1][1] = 1.0;
1641	<	rotMat[1][2] = 0.0;
1642	<
1643	<	rotMat[2][0] = 0.0;
1644	<	rotMat[2][1] = 0.0;
1142	<	rotMat[2][2] = 1.0;
1143	<
1144	<	dAtom->setA( rotMat );
1639	>	//push zconsTol into siminfo, if user does not specify
1640	>	//value for zconsTol, a default value will be used
1641	>	DoubleData* zconsTol = new DoubleData();
1642	>	zconsTol->setID(ZCONSTOL_ID);
1643	>	if(globals->haveZconsTol()){
1644	>	zconsTol->setData(globals->getZconsTol());
1645		}
1646	+	else{
1647	+	double defaultZConsTol = 1E-6;
1648	+	sprintf( painCave.errMsg,
1649	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1650	+	" , default value %f is used.\n", defaultZConsTol);
1651	+	painCave.isFatal = 0;
1652	+	simError();
1653
1654	<	current_atom_ndx++;
1655	<	}
1656	<
1657	<	current_mol++;
1658	<	current_comp_mol++;
1659	<
1660	<	if( current_comp_mol >= components_nmol[current_comp] ){
1661	<
1662	<	current_comp_mol = 0;
1663	<	current_comp++;
1664	<	}
1654	>	zconsTol->setData(defaultZConsTol);
1655	>	}
1656	>	theInfo.addProperty(zconsTol);
1657	>
1658	>	//Determine the name of ouput file and add it into SimInfo's property list
1659	>	//Be careful, do not use inFileName, since it is a pointer which
1660	>	//point to a string at master node, and slave nodes do not contain that string
1661	>
1662	>	string zconsOutput(theInfo.finalName);
1663	>
1664	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1665	>
1666	>	StringData* zconsFilename = new StringData();
1667	>	zconsFilename->setID(ZCONSFILENAME_ID);
1668	>	zconsFilename->setData(zconsOutput);
1669	>
1670	>	theInfo.addProperty(zconsFilename);
1671		}

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