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

Comparing:
branches/mmeineke/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 682 by tim, Tue Aug 12 17:51:33 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6
7		#include "SimSetup.hpp"
8		#include "parse_me.h"
#	Line 12 | Line 14 | SimSetup::SimSetup(){
14		#include "mpiSimulation.hpp"
15		#endif
16
17	+	// some defines for ensemble and Forcefield  cases
18	+
19	+	#define NVE_ENS        0
20	+	#define NVT_ENS        1
21	+	#define NPTi_ENS       2
22	+	#define NPTf_ENS       3
23	+	#define NPTim_ENS      4
24	+	#define NPTfm_ENS      5
25	+
26	+	#define FF_DUFF 0
27	+	#define FF_LJ   1
28	+	#define FF_EAM  2
29	+
30	+	using namespace std;
31	+
32		SimSetup::SimSetup(){
33	+
34	+	isInfoArray = 0;
35	+	nInfo = 1;
36	+
37		stamps = new MakeStamps();
38		globals = new Globals();
39
40	+
41		#ifdef IS_MPI
42		strcpy( checkPointMsg, "SimSetup creation successful" );
43		MPIcheckPoint();
#	Line 27 | Line 49 | void SimSetup::parseFile( char* fileName ){
49		delete globals;
50		}
51
52	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
53	+	info = the_info;
54	+	nInfo = theNinfo;
55	+	isInfoArray = 1;
56	+	}
57	+
58	+
59		void SimSetup::parseFile( char* fileName ){
60
61		#ifdef IS_MPI
#	Line 62 | Line 91 | void SimSetup::createSim( void ){
91
92		#endif // is_mpi
93
94	<	void SimSetup::createSim( void ){
94	>	void SimSetup::createSim(void){
95
96	<	MakeStamps *the_stamps;
97	<	Globals* the_globals;
98	<	int i, j;
96	>	int i, j, k, globalAtomIndex;
97	>
98	>	// gather all of the information from the Bass file
99	>
100	>	gatherInfo();
101
102	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
102	>	// creation of complex system objects
103
104	<	// 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();
104	>	sysObjectsCreation();
105
106	<	// get the ones we know are there, yet still may need some work.
107	<	n_components = the_globals->getNComponents();
108	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
106	>	// check on the post processing info
107	>
108	>	finalInfoCheck();
109
110	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
110	>	// initialize the system coordinates
111
112	+	if( !isInfoArray ) initSystemCoords();
113
114	<	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	<	}
114	>	// make the output filenames
115
116	+	makeOutNames();
117	+
118	+	// make the integrator
119	+
120	+	makeIntegrator();
121	+
122		#ifdef IS_MPI
123	<	strcpy( checkPointMsg, "ForceField creation successful" );
124	<	MPIcheckPoint();
106	<	#endif // is_mpi
123	>	mpiSim->mpiRefresh();
124	>	#endif
125
126	<
126	>	// initialize the Fortran
127
128	<	// 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];
128	>	initFortran();
129
115	–	if( !the_globals->haveNMol() ){
116	–	// we don't have the total number of molecules, so we assume it is
117	–	// given in each component
130
119	–	tot_nmol = 0;
120	–	for( i=0; i<n_components; i++ ){
131
132	<	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
134	<	tot_nmol += the_components[i]->getNMol();
135	<	components_nmol[i] = the_components[i]->getNMol();
136	<	}
137	<	}
138	<	else{
139	<	sprintf( painCave.errMsg,
140	<	"SimSetup error.\n"
141	<	"\tSorry, the ability to specify total"
142	<	" nMols and then give molfractions in the components\n"
143	<	"\tis not currently supported."
144	<	" Please give nMol in the components.\n" );
145	<	painCave.isFatal = 1;
146	<	simError();
134	>
135	>	void SimSetup::makeMolecules( void ){
136	>
137	>	int k,l;
138	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
139	>	molInit molInfo;
140	>	DirectionalAtom* dAtom;
141	>	LinkedAssign* extras;
142	>	LinkedAssign* current_extra;
143	>	AtomStamp* currentAtom;
144	>	BondStamp* currentBond;
145	>	BendStamp* currentBend;
146	>	TorsionStamp* currentTorsion;
147	>
148	>	bond_pair* theBonds;
149	>	bend_set* theBends;
150	>	torsion_set* theTorsions;
151	>
152	>
153	>	//init the forceField paramters
154	>
155	>	the_ff->readParams();
156	>
157	>
158	>	// init the atoms
159	>
160	>	double ux, uy, uz, u, uSqr;
161	>
162	>	for(k=0; k<nInfo; k++){
163
164	+	the_ff->setSimInfo( &(info[k]) );
165	+
166	+	atomOffset = 0;
167	+	excludeOffset = 0;
168	+	for(i=0; i<info[k].n_mol; i++){
169
170	<	//     tot_nmol = the_globals->getNMol();
170	>	stampID = info[k].molecules[i].getStampID();
171	>
172	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
173	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
174	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
175	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
176	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
177	>
178	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
179	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
180	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
181	>	molInfo.myBends = new Bend*[molInfo.nBends];
182	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
183	>
184	>	theBonds = new bond_pair[molInfo.nBonds];
185	>	theBends = new bend_set[molInfo.nBends];
186	>	theTorsions = new torsion_set[molInfo.nTorsions];
187
188	<	//   //we have the total number of molecules, now we check for molfractions
149	<	//     for( i=0; i<n_components; i++ ){
188	>	// make the Atoms
189
190	<	//       if( !the_components[i]->haveMolFraction() ){
190	>	for(j=0; j<molInfo.nAtoms; j++){
191	>
192	>	currentAtom = comp_stamps[stampID]->getAtom( j );
193	>	if( currentAtom->haveOrientation() ){
194	>
195	>	dAtom = new DirectionalAtom( (j + atomOffset),
196	>	info[k].getConfiguration() );
197	>	info[k].n_oriented++;
198	>	molInfo.myAtoms[j] = dAtom;
199	>
200	>	ux = currentAtom->getOrntX();
201	>	uy = currentAtom->getOrntY();
202	>	uz = currentAtom->getOrntZ();
203	>
204	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
205	>
206	>	u = sqrt( uSqr );
207	>	ux = ux / u;
208	>	uy = uy / u;
209	>	uz = uz / u;
210	>
211	>	dAtom->setSUx( ux );
212	>	dAtom->setSUy( uy );
213	>	dAtom->setSUz( uz );
214	>	}
215	>	else{
216	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
217	>	info[k].getConfiguration() );
218	>	}
219	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
220
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	–	}
159	–
221		#ifdef IS_MPI
222	<	strcpy( checkPointMsg, "Have the number of components" );
223	<	MPIcheckPoint();
222	>
223	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
224	>
225		#endif // is_mpi
226	<
165	<	// make an array of molecule stamps that match the components used.
166	<	// also extract the used stamps out into a separate linked list
167	<
168	<	simnfo->nComponents = n_components;
169	<	simnfo->componentsNmol = components_nmol;
170	<	simnfo->compStamps = comp_stamps;
171	<	simnfo->headStamp = new LinkedMolStamp();
172	<
173	<	char* id;
174	<	LinkedMolStamp* headStamp = simnfo->headStamp;
175	<	LinkedMolStamp* currentStamp = NULL;
176	<	for( i=0; i<n_components; i++ ){
177	<
178	<	id = the_components[i]->getType();
179	<	comp_stamps[i] = NULL;
226	>	}
227
228	<	// check to make sure the component isn't already in the list
229	<
183	<	comp_stamps[i] = headStamp->match( id );
184	<	if( comp_stamps[i] == NULL ){
228	>	// make the bonds
229	>	for(j=0; j<molInfo.nBonds; j++){
230
231	<	// extract the component from the list;
231	>	currentBond = comp_stamps[stampID]->getBond( j );
232	>	theBonds[j].a = currentBond->getA() + atomOffset;
233	>	theBonds[j].b = currentBond->getB() + atomOffset;
234	>
235	>	exI = theBonds[j].a;
236	>	exJ = theBonds[j].b;
237	>
238	>	// exclude_I must always be the smaller of the pair
239	>	if( exI > exJ ){
240	>	tempEx = exI;
241	>	exI = exJ;
242	>	exJ = tempEx;
243	>	}
244	>	#ifdef IS_MPI
245	>	tempEx = exI;
246	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
247	>	tempEx = exJ;
248	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
249	>
250	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
251	>	#else  // isn't MPI
252	>
253	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
254	>	#endif  //is_mpi
255	>	}
256	>	excludeOffset += molInfo.nBonds;
257
258	<	currentStamp = the_stamps->extractMolStamp( id );
259	<	if( currentStamp == NULL ){
260	<	sprintf( painCave.errMsg,
261	<	"SimSetup error: Component \"%s\" was not found in the "
262	<	"list of declared molecules\n",
263	<	id );
264	<	painCave.isFatal = 1;
265	<	simError();
258	>	//make the bends
259	>	for(j=0; j<molInfo.nBends; j++){
260	>
261	>	currentBend = comp_stamps[stampID]->getBend( j );
262	>	theBends[j].a = currentBend->getA() + atomOffset;
263	>	theBends[j].b = currentBend->getB() + atomOffset;
264	>	theBends[j].c = currentBend->getC() + atomOffset;
265	>
266	>	if( currentBend->haveExtras() ){
267	>
268	>	extras = currentBend->getExtras();
269	>	current_extra = extras;
270	>
271	>	while( current_extra != NULL ){
272	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
273	>
274	>	switch( current_extra->getType() ){
275	>
276	>	case 0:
277	>	theBends[j].ghost =
278	>	current_extra->getInt() + atomOffset;
279	>	theBends[j].isGhost = 1;
280	>	break;
281	>
282	>	case 1:
283	>	theBends[j].ghost =
284	>	(int)current_extra->getDouble() + atomOffset;
285	>	theBends[j].isGhost = 1;
286	>	break;
287	>
288	>	default:
289	>	sprintf( painCave.errMsg,
290	>	"SimSetup Error: ghostVectorSource was neither a "
291	>	"double nor an int.\n"
292	>	"-->Bend[%d] in %s\n",
293	>	j, comp_stamps[stampID]->getID() );
294	>	painCave.isFatal = 1;
295	>	simError();
296	>	}
297	>	}
298	>
299	>	else{
300	>
301	>	sprintf( painCave.errMsg,
302	>	"SimSetup Error: unhandled bend assignment:\n"
303	>	"    -->%s in Bend[%d] in %s\n",
304	>	current_extra->getlhs(),
305	>	j, comp_stamps[stampID]->getID() );
306	>	painCave.isFatal = 1;
307	>	simError();
308	>	}
309	>
310	>	current_extra = current_extra->getNext();
311	>	}
312	>	}
313	>
314	>	if( !theBends[j].isGhost ){
315	>
316	>	exI = theBends[j].a;
317	>	exJ = theBends[j].c;
318	>	}
319	>	else{
320	>
321	>	exI = theBends[j].a;
322	>	exJ = theBends[j].b;
323	>	}
324	>
325	>	// exclude_I must always be the smaller of the pair
326	>	if( exI > exJ ){
327	>	tempEx = exI;
328	>	exI = exJ;
329	>	exJ = tempEx;
330	>	}
331	>	#ifdef IS_MPI
332	>	tempEx = exI;
333	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
334	>	tempEx = exJ;
335	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
336	>
337	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
338	>	#else  // isn't MPI
339	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
340	>	#endif  //is_mpi
341		}
342	+	excludeOffset += molInfo.nBends;
343
344	<	headStamp->add( currentStamp );
345	<	comp_stamps[i] = headStamp->match( id );
346	<	}
347	<	}
348	<
344	>	for(j=0; j<molInfo.nTorsions; j++){
345	>
346	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
347	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
348	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
349	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
350	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
351	>
352	>	exI = theTorsions[j].a;
353	>	exJ = theTorsions[j].d;
354	>
355	>	// exclude_I must always be the smaller of the pair
356	>	if( exI > exJ ){
357	>	tempEx = exI;
358	>	exI = exJ;
359	>	exJ = tempEx;
360	>	}
361		#ifdef IS_MPI
362	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
363	<	MPIcheckPoint();
364	<	#endif // is_mpi
365	<
362	>	tempEx = exI;
363	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
364	>	tempEx = exJ;
365	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
366	>
367	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
368	>	#else  // isn't MPI
369	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
370	>	#endif  //is_mpi
371	>	}
372	>	excludeOffset += molInfo.nTorsions;
373	>
374	>
375	>	// send the arrays off to the forceField for init.
376	>
377	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
378	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
379	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
380	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
381	>
382	>
383	>	info[k].molecules[i].initialize( molInfo );
384
209	–
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	–
234	–
235	–	#ifdef IS_MPI
236	–
237	–	// divide the molecules among processors here.
238	–
239	–	mpiSim = new mpiSimulation( simnfo );
240	–
241	–
242	–
243	–	globalIndex = mpiSim->divideLabor();
244	–
245	–
246	–
247	–	// set up the local variables
248	–
249	–	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++ ){
385
386	<	if( mpiSim->getMyMolStart() <= allMol &&
387	<	allMol <= mpiSim->getMyMolEnd() ){
388	<
389	<	local_atoms +=    comp_stamps[i]->getNAtoms();
266	<	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++;
386	>	atomOffset += molInfo.nAtoms;
387	>	delete[] theBonds;
388	>	delete[] theBends;
389	>	delete[] theTorsions;
390		}
391		}
274	–	local_SRI = local_bonds + local_bends + local_torsions;
392
393	<
394	<	simnfo->n_atoms = mpiSim->getMyNlocal();
278	<
279	<	if( local_atoms != simnfo->n_atoms ){
280	<	sprintf( painCave.errMsg,
281	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282	<	" localAtom (%d) are note equal.\n",
283	<	simnfo->n_atoms,
284	<	local_atoms );
285	<	painCave.isFatal = 1;
286	<	simError();
287	<	}
288	<
289	<	simnfo->n_bonds = local_bonds;
290	<	simnfo->n_bends = local_bends;
291	<	simnfo->n_torsions = local_torsions;
292	<	simnfo->n_SRI = local_SRI;
293	<	simnfo->n_mol = localMol;
294	<
295	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
393	>	#ifdef IS_MPI
394	>	sprintf( checkPointMsg, "all molecules initialized succesfully" );
395		MPIcheckPoint();
297	–
298	–
396		#endif // is_mpi
397
398	+	// clean up the forcefield
399
400	<	// create the atom and short range interaction arrays
400	>	the_ff->calcRcut();
401	>	the_ff->cleanMe();
402	>
403	>	}
404
405	<	Atom::createArrays(simnfo->n_atoms);
305	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
405	>	void SimSetup::initFromBass( void ){
406
407	+	int i, j, k;
408	+	int n_cells;
409	+	double cellx, celly, cellz;
410	+	double temp1, temp2, temp3;
411	+	int n_per_extra;
412	+	int n_extra;
413	+	int have_extra, done;
414
415	<	if( simnfo->n_SRI ){
416	<	the_sris = new SRI*[simnfo->n_SRI];
417	<	the_excludes = new int[2 * simnfo->n_SRI];
418	<	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;
415	>	double vel[3];
416	>	vel[0] = 0.0;
417	>	vel[1] = 0.0;
418	>	vel[2] = 0.0;
419
420	<	simnfo->n_exclude = 1;
421	<	}
420	>	temp1 = (double)tot_nmol / 4.0;
421	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
422	>	temp3 = ceil( temp2 );
423
424	<	// set the arrays into the SimInfo object
424	>	have_extra =0;
425	>	if( temp2 < temp3 ){ // we have a non-complete lattice
426	>	have_extra =1;
427
428	<	simnfo->atoms = the_atoms;
429	<	simnfo->sr_interactions = the_sris;
430	<	simnfo->nGlobalExcludes = 0;
431	<	simnfo->excludes = the_excludes;
428	>	n_cells = (int)temp3 - 1;
429	>	cellx = info[0].boxL[0] / temp3;
430	>	celly = info[0].boxL[1] / temp3;
431	>	cellz = info[0].boxL[2] / temp3;
432	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
433	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
434	>	n_per_extra = (int)ceil( temp1 );
435
436	<
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() ){
436	>	if( n_per_extra > 4){
437		sprintf( painCave.errMsg,
438	<	"SimSetup Error, system has dipoles, but no rRF was set.\n");
438	>	"SimSetup error. There has been an error in constructing"
439	>	" the non-complete lattice.\n" );
440		painCave.isFatal = 1;
441		simError();
442		}
443	<	if( !the_globals->haveDielectric() ){
444	<	sprintf( painCave.errMsg,
445	<	"SimSetup Error, system has dipoles, but no"
446	<	" dielectric was set.\n" );
447	<	painCave.isFatal = 1;
448	<	simError();
449	<	}
443	>	}
444	>	else{
445	>	n_cells = (int)temp3;
446	>	cellx = info[0].boxL[0] / temp3;
447	>	celly = info[0].boxL[1] / temp3;
448	>	cellz = info[0].boxL[2] / temp3;
449	>	}
450
451	<	simnfo->rRF        = the_globals->getRRF();
452	<	simnfo->dielectric = the_globals->getDielectric();
451	>	current_mol = 0;
452	>	current_comp_mol = 0;
453	>	current_comp = 0;
454	>	current_atom_ndx = 0;
455	>
456	>	for( i=0; i < n_cells ; i++ ){
457	>	for( j=0; j < n_cells; j++ ){
458	>	for( k=0; k < n_cells; k++ ){
459	>
460	>	makeElement( i * cellx,
461	>	j * celly,
462	>	k * cellz );
463	>
464	>	makeElement( i * cellx + 0.5 * cellx,
465	>	j * celly + 0.5 * celly,
466	>	k * cellz );
467	>
468	>	makeElement( i * cellx,
469	>	j * celly + 0.5 * celly,
470	>	k * cellz + 0.5 * cellz );
471	>
472	>	makeElement( i * cellx + 0.5 * cellx,
473	>	j * celly,
474	>	k * cellz + 0.5 * cellz );
475	>	}
476	>	}
477		}
478
479	<	#ifdef IS_MPI
480	<	strcpy( checkPointMsg, "rRf and dielectric check out" );
481	<	MPIcheckPoint();
482	<	#endif // is_mpi
483	<
484	<	if( the_globals->haveBox() ){
485	<	simnfo->box_x = the_globals->getBox();
486	<	simnfo->box_y = the_globals->getBox();
487	<	simnfo->box_z = the_globals->getBox();
479	>	if( have_extra ){
480	>	done = 0;
481	>
482	>	int start_ndx;
483	>	for( i=0; i < (n_cells+1) && !done; i++ ){
484	>	for( j=0; j < (n_cells+1) && !done; j++ ){
485	>
486	>	if( i < n_cells ){
487	>
488	>	if( j < n_cells ){
489	>	start_ndx = n_cells;
490	>	}
491	>	else start_ndx = 0;
492	>	}
493	>	else start_ndx = 0;
494	>
495	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
496	>
497	>	makeElement( i * cellx,
498	>	j * celly,
499	>	k * cellz );
500	>	done = ( current_mol >= tot_nmol );
501	>
502	>	if( !done && n_per_extra > 1 ){
503	>	makeElement( i * cellx + 0.5 * cellx,
504	>	j * celly + 0.5 * celly,
505	>	k * cellz );
506	>	done = ( current_mol >= tot_nmol );
507	>	}
508	>
509	>	if( !done && n_per_extra > 2){
510	>	makeElement( i * cellx,
511	>	j * celly + 0.5 * celly,
512	>	k * cellz + 0.5 * cellz );
513	>	done = ( current_mol >= tot_nmol );
514	>	}
515	>
516	>	if( !done && n_per_extra > 3){
517	>	makeElement( i * cellx + 0.5 * cellx,
518	>	j * celly,
519	>	k * cellz + 0.5 * cellz );
520	>	done = ( current_mol >= tot_nmol );
521	>	}
522	>	}
523	>	}
524	>	}
525		}
366	–	else if( the_globals->haveDensity() ){
526
527	<	double vol;
528	<	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;
527	>	for( i=0; i<info[0].n_atoms; i++ ){
528	>	info[0].atoms[i]->setVel( vel );
529		}
530	<	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();
530	>	}
531
532	<	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();
532	>	void SimSetup::makeElement( double x, double y, double z ){
533
534	<	if( !the_globals->haveBoxZ() ){
534	>	int k;
535	>	AtomStamp* current_atom;
536	>	DirectionalAtom* dAtom;
537	>	double rotMat[3][3];
538	>	double pos[3];
539	>
540	>	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
541	>
542	>	current_atom = comp_stamps[current_comp]->getAtom( k );
543	>	if( !current_atom->havePosition() ){
544		sprintf( painCave.errMsg,
545	<	"SimSetup error, no periodic BoxZ size given.\n" );
545	>	"SimSetup:initFromBass error.\n"
546	>	"\tComponent %s, atom %s does not have a position specified.\n"
547	>	"\tThe initialization routine is unable to give a start"
548	>	" position.\n",
549	>	comp_stamps[current_comp]->getID(),
550	>	current_atom->getType() );
551		painCave.isFatal = 1;
552		simError();
553		}
554	<	simnfo->box_z = the_globals->getBoxZ();
555	<	}
554	>
555	>	pos[0] = x + current_atom->getPosX();
556	>	pos[1] = y + current_atom->getPosY();
557	>	pos[2] = z + current_atom->getPosZ();
558	>
559	>	info[0].atoms[current_atom_ndx]->setPos( pos );
560
561	<	#ifdef IS_MPI
401	<	strcpy( checkPointMsg, "Box size set up" );
402	<	MPIcheckPoint();
403	<	#endif // is_mpi
561	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
562
563	+	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
564
565	<	// initialize the arrays
565	>	rotMat[0][0] = 1.0;
566	>	rotMat[0][1] = 0.0;
567	>	rotMat[0][2] = 0.0;
568
569	<	the_ff->setSimInfo( simnfo );
569	>	rotMat[1][0] = 0.0;
570	>	rotMat[1][1] = 1.0;
571	>	rotMat[1][2] = 0.0;
572
573	<	makeAtoms();
574	<	simnfo->identArray = new int[simnfo->n_atoms];
575	<	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	<	}
573	>	rotMat[2][0] = 0.0;
574	>	rotMat[2][1] = 0.0;
575	>	rotMat[2][2] = 1.0;
576
577	<	if( tot_bends ){
578	<	makeBends();
422	<	}
577	>	dAtom->setA( rotMat );
578	>	}
579
580	<	if( tot_torsions ){
425	<	makeTorsions();
580	>	current_atom_ndx++;
581		}
582
583	+	current_mol++;
584	+	current_comp_mol++;
585
586	+	if( current_comp_mol >= components_nmol[current_comp] ){
587
588	+	current_comp_mol = 0;
589	+	current_comp++;
590	+	}
591	+	}
592
593
594	+	void SimSetup::gatherInfo( void ){
595	+	int i,j,k;
596
597	<	if( the_globals->haveInitialConfig() ){
598	<
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
597	>	ensembleCase = -1;
598	>	ffCase = -1;
599
600	<	delete fileInit;
446	<	}
447	<	else{
600	>	// set the easy ones first
601
602	<	#ifdef IS_MPI
602	>	for( i=0; i<nInfo; i++){
603	>	info[i].target_temp = globals->getTargetTemp();
604	>	info[i].dt = globals->getDt();
605	>	info[i].run_time = globals->getRunTime();
606	>	}
607	>	n_components = globals->getNComponents();
608
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
609
610	<	initFromBass();
610	>	// get the forceField
611
612	+	strcpy( force_field, globals->getForceField() );
613
614	<	#endif
615	<	}
614	>	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
615	>	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
616	>	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
617	>	else{
618	>	sprintf( painCave.errMsg,
619	>	"SimSetup Error. Unrecognized force field -> %s\n",
620	>	force_field );
621	>	painCave.isFatal = 1;
622	>	simError();
623	>	}
624
625	<	#ifdef IS_MPI
467	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
468	<	MPIcheckPoint();
469	<	#endif // is_mpi
625	>	// get the ensemble
626
627	+	strcpy( ensemble, globals->getEnsemble() );
628
629	<
630	<
631	<
632	<
633	<
634	<	#ifdef IS_MPI
635	<	if( worldRank == 0 ){
636	<	#endif // is_mpi
637	<
638	<	if( the_globals->haveFinalConfig() ){
639	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
640	<	}
641	<	else{
642	<	strcpy( simnfo->finalName, inFileName );
643	<	char* endTest;
644	<	int nameLength = strlen( simnfo->finalName );
645	<	endTest = &(simnfo->finalName[nameLength - 5]);
646	<	if( !strcmp( endTest, ".bass" ) ){
647	<	strcpy( endTest, ".eor" );
629	>	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
630	>	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
631	>	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
632	>	ensembleCase = NPTi_ENS;
633	>	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
634	>	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
635	>	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
636	>	else{
637	>	sprintf( painCave.errMsg,
638	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
639	>	"reverting to NVE for this simulation.\n",
640	>	ensemble );
641	>	painCave.isFatal = 0;
642	>	simError();
643	>	strcpy( ensemble, "NVE" );
644	>	ensembleCase = NVE_ENS;
645	>	}
646	>
647	>	for(i=0; i<nInfo; i++){
648	>
649	>	strcpy( info[i].ensemble, ensemble );
650	>
651	>	// get the mixing rule
652	>
653	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
654	>	info[i].usePBC = globals->getPBC();
655	>	}
656	>
657	>	// get the components and calculate the tot_nMol and indvidual n_mol
658	>
659	>	the_components = globals->getComponents();
660	>	components_nmol = new int[n_components];
661	>
662	>
663	>	if( !globals->haveNMol() ){
664	>	// we don't have the total number of molecules, so we assume it is
665	>	// given in each component
666	>
667	>	tot_nmol = 0;
668	>	for( i=0; i<n_components; i++ ){
669	>
670	>	if( !the_components[i]->haveNMol() ){
671	>	// we have a problem
672	>	sprintf( painCave.errMsg,
673	>	"SimSetup Error. No global NMol or component NMol"
674	>	" given. Cannot calculate the number of atoms.\n" );
675	>	painCave.isFatal = 1;
676	>	simError();
677		}
678	<	else if( !strcmp( endTest, ".BASS" ) ){
679	<	strcpy( endTest, ".eor" );
680	<	}
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	<	}
678	>
679	>	tot_nmol += the_components[i]->getNMol();
680	>	components_nmol[i] = the_components[i]->getNMol();
681		}
682	<
683	<	// make the sample and status out names
684	<
685	<	strcpy( simnfo->sampleName, inFileName );
686	<	char* endTest;
687	<	int nameLength = strlen( simnfo->sampleName );
688	<	endTest = &(simnfo->sampleName[nameLength - 5]);
689	<	if( !strcmp( endTest, ".bass" ) ){
690	<	strcpy( endTest, ".dump" );
682	>	}
683	>	else{
684	>	sprintf( painCave.errMsg,
685	>	"SimSetup error.\n"
686	>	"\tSorry, the ability to specify total"
687	>	" nMols and then give molfractions in the components\n"
688	>	"\tis not currently supported."
689	>	" Please give nMol in the components.\n" );
690	>	painCave.isFatal = 1;
691	>	simError();
692	>	}
693	>
694	>	// set the status, sample, and thermal kick times
695	>
696	>	for(i=0; i<nInfo; i++){
697	>
698	>	if( globals->haveSampleTime() ){
699	>	info[i].sampleTime = globals->getSampleTime();
700	>	info[i].statusTime = info[i].sampleTime;
701	>	info[i].thermalTime = info[i].sampleTime;
702		}
518	–	else if( !strcmp( endTest, ".BASS" ) ){
519	–	strcpy( endTest, ".dump" );
520	–	}
703		else{
704	<	endTest = &(simnfo->sampleName[nameLength - 4]);
705	<	if( !strcmp( endTest, ".bss" ) ){
706	<	strcpy( endTest, ".dump" );
525	<	}
526	<	else if( !strcmp( endTest, ".mdl" ) ){
527	<	strcpy( endTest, ".dump" );
528	<	}
529	<	else{
530	<	strcat( simnfo->sampleName, ".dump" );
531	<	}
704	>	info[i].sampleTime = globals->getRunTime();
705	>	info[i].statusTime = info[i].sampleTime;
706	>	info[i].thermalTime = info[i].sampleTime;
707		}
708
709	<	strcpy( simnfo->statusName, inFileName );
710	<	nameLength = strlen( simnfo->statusName );
536	<	endTest = &(simnfo->statusName[nameLength - 5]);
537	<	if( !strcmp( endTest, ".bass" ) ){
538	<	strcpy( endTest, ".stat" );
709	>	if( globals->haveStatusTime() ){
710	>	info[i].statusTime = globals->getStatusTime();
711		}
712	<	else if( !strcmp( endTest, ".BASS" ) ){
713	<	strcpy( endTest, ".stat" );
712	>
713	>	if( globals->haveThermalTime() ){
714	>	info[i].thermalTime = globals->getThermalTime();
715		}
716	+
717	+	// check for the temperature set flag
718	+
719	+	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
720	+
721	+	// get some of the tricky things that may still be in the globals
722	+
723	+	double boxVector[3];
724	+	if( globals->haveBox() ){
725	+	boxVector[0] = globals->getBox();
726	+	boxVector[1] = globals->getBox();
727	+	boxVector[2] = globals->getBox();
728	+
729	+	info[i].setBox( boxVector );
730	+	}
731	+	else if( globals->haveDensity() ){
732	+
733	+	double vol;
734	+	vol = (double)tot_nmol / globals->getDensity();
735	+	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
736	+	boxVector[1] = boxVector[0];
737	+	boxVector[2] = boxVector[0];
738	+
739	+	info[i].setBox( boxVector );
740	+	}
741		else{
742	<	endTest = &(simnfo->statusName[nameLength - 4]);
743	<	if( !strcmp( endTest, ".bss" ) ){
744	<	strcpy( endTest, ".stat" );
742	>	if( !globals->haveBoxX() ){
743	>	sprintf( painCave.errMsg,
744	>	"SimSetup error, no periodic BoxX size given.\n" );
745	>	painCave.isFatal = 1;
746	>	simError();
747		}
748	<	else if( !strcmp( endTest, ".mdl" ) ){
749	<	strcpy( endTest, ".stat" );
748	>	boxVector[0] = globals->getBoxX();
749	>
750	>	if( !globals->haveBoxY() ){
751	>	sprintf( painCave.errMsg,
752	>	"SimSetup error, no periodic BoxY size given.\n" );
753	>	painCave.isFatal = 1;
754	>	simError();
755		}
756	<	else{
757	<	strcat( simnfo->statusName, ".stat" );
756	>	boxVector[1] = globals->getBoxY();
757	>
758	>	if( !globals->haveBoxZ() ){
759	>	sprintf( painCave.errMsg,
760	>	"SimSetup error, no periodic BoxZ size given.\n" );
761	>	painCave.isFatal = 1;
762	>	simError();
763		}
764	+	boxVector[2] = globals->getBoxZ();
765	+
766	+	info[i].setBox( boxVector );
767		}
768	+
769	+	}
770
771		#ifdef IS_MPI
772	<	}
772	>	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
773	>	MPIcheckPoint();
774		#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	–	}
775
776	<	if( the_globals->haveStatusTime() ){
574	<	simnfo->statusTime = the_globals->getStatusTime();
575	<	}
776	>	}
777
577	–	if( the_globals->haveThermalTime() ){
578	–	simnfo->thermalTime = the_globals->getThermalTime();
579	–	}
778
779	<	// check for the temperature set flag
779	>	void SimSetup::finalInfoCheck( void ){
780	>	int index;
781	>	int usesDipoles;
782	>	int i;
783
784	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
785	<
786	<
787	<	//   // make the longe range forces and the integrator
788	<
789	<	//   new AllLong( simnfo );
790	<
791	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
792	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
793	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
794	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
795	<
796	<
797	<
798	<	// initialize the Fortran
799	<
800	<	simnfo->refreshSim();
801	<
802	<	if( !strcmp( simnfo->mixingRule, "standard") ){
803	<	the_ff->initForceField( LB_MIXING_RULE );
804	<	}
805	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
806	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
807	<	}
808	<	else{
809	<	sprintf( painCave.errMsg,
810	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
811	<	simnfo->mixingRule );
812	<	painCave.isFatal = 1;
813	<	simError();
784	>	for(i=0; i<nInfo; i++){
785	>	// check electrostatic parameters
786	>
787	>	index = 0;
788	>	usesDipoles = 0;
789	>	while( (index < info[i].n_atoms) && !usesDipoles ){
790	>	usesDipoles = (info[i].atoms[index])->hasDipole();
791	>	index++;
792	>	}
793	>
794	>	#ifdef IS_MPI
795	>	int myUse = usesDipoles;
796	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
797	>	#endif //is_mpi
798	>
799	>	double theEcr, theEst;
800	>
801	>	if (globals->getUseRF() ) {
802	>	info[i].useReactionField = 1;
803	>
804	>	if( !globals->haveECR() ){
805	>	sprintf( painCave.errMsg,
806	>	"SimSetup Warning: using default value of 1/2 the smallest "
807	>	"box length for the electrostaticCutoffRadius.\n"
808	>	"I hope you have a very fast processor!\n");
809	>	painCave.isFatal = 0;
810	>	simError();
811	>	double smallest;
812	>	smallest = info[i].boxL[0];
813	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
814	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
815	>	theEcr = 0.5 * smallest;
816	>	} else {
817	>	theEcr = globals->getECR();
818	>	}
819	>
820	>	if( !globals->haveEST() ){
821	>	sprintf( painCave.errMsg,
822	>	"SimSetup Warning: using default value of 0.05 * the "
823	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
824	>	);
825	>	painCave.isFatal = 0;
826	>	simError();
827	>	theEst = 0.05 * theEcr;
828	>	} else {
829	>	theEst= globals->getEST();
830	>	}
831	>
832	>	info[i].setEcr( theEcr, theEst );
833	>
834	>	if(!globals->haveDielectric() ){
835	>	sprintf( painCave.errMsg,
836	>	"SimSetup Error: You are trying to use Reaction Field without"
837	>	"setting a dielectric constant!\n"
838	>	);
839	>	painCave.isFatal = 1;
840	>	simError();
841	>	}
842	>	info[i].dielectric = globals->getDielectric();
843	>	}
844	>	else {
845	>	if (usesDipoles) {
846	>
847	>	if( !globals->haveECR() ){
848	>	sprintf( painCave.errMsg,
849	>	"SimSetup Warning: using default value of 1/2 the smallest "
850	>	"box length for the electrostaticCutoffRadius.\n"
851	>	"I hope you have a very fast processor!\n");
852	>	painCave.isFatal = 0;
853	>	simError();
854	>	double smallest;
855	>	smallest = info[i].boxL[0];
856	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
857	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
858	>	theEcr = 0.5 * smallest;
859	>	} else {
860	>	theEcr = globals->getECR();
861	>	}
862	>
863	>	if( !globals->haveEST() ){
864	>	sprintf( painCave.errMsg,
865	>	"SimSetup Warning: using default value of 0.05 * the "
866	>	"electrostaticCutoffRadius for the "
867	>	"electrostaticSkinThickness\n"
868	>	);
869	>	painCave.isFatal = 0;
870	>	simError();
871	>	theEst = 0.05 * theEcr;
872	>	} else {
873	>	theEst= globals->getEST();
874	>	}
875	>
876	>	info[i].setEcr( theEcr, theEst );
877	>	}
878	>	}
879		}
880
615	–
881		#ifdef IS_MPI
882	<	strcpy( checkPointMsg,
618	<	"Successfully intialized the mixingRule for Fortran." );
882	>	strcpy( checkPointMsg, "post processing checks out" );
883		MPIcheckPoint();
884		#endif // is_mpi
885	+
886		}
887
888	<	void SimSetup::makeAtoms( void ){
888	>	void SimSetup::initSystemCoords( void ){
889	>	int i;
890	>
891	>	std::cerr << "Setting atom Coords\n";
892
893	<	int i, j, k, index;
894	<	double ux, uy, uz, uSqr, u;
895	<	AtomStamp* current_atom;
893	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
894	>
895	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
896	>
897	>	if( globals->haveInitialConfig() ){
898	>
899	>	InitializeFromFile* fileInit;
900	>	#ifdef IS_MPI // is_mpi
901	>	if( worldRank == 0 ){
902	>	#endif //is_mpi
903	>	fileInit = new InitializeFromFile( globals->getInitialConfig() );
904	>	#ifdef IS_MPI
905	>	}else fileInit = new InitializeFromFile( NULL );
906	>	#endif
907	>	fileInit->readInit( info ); // default velocities on
908	>
909	>	delete fileInit;
910	>	}
911	>	else{
912	>
913	>	#ifdef IS_MPI
914	>
915	>	// no init from bass
916	>
917	>	sprintf( painCave.errMsg,
918	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
919	>	painCave.isFatal;
920	>	simError();
921	>
922	>	#else
923	>
924	>	initFromBass();
925	>
926	>
927	>	#endif
928	>	}
929	>
930	>	#ifdef IS_MPI
931	>	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
932	>	MPIcheckPoint();
933	>	#endif // is_mpi
934	>
935	>	}
936
629	–	DirectionalAtom* dAtom;
630	–	int molIndex, molStart, molEnd, nMemb, lMolIndex;
937
938	<	lMolIndex = 0;
939	<	molIndex = 0;
940	<	index = 0;
635	<	for( i=0; i<n_components; i++ ){
938	>	void SimSetup::makeOutNames( void ){
939	>
940	>	int k;
941
942	<	for( j=0; j<components_nmol[i]; j++ ){
942	>
943	>	for(k=0; k<nInfo; k++){
944
945		#ifdef IS_MPI
946	<	if( mpiSim->getMyMolStart() <= molIndex &&
947	<	molIndex <= mpiSim->getMyMolEnd() ){
948	<	#endif // is_mpi
949	<
950	<	molStart = index;
951	<	nMemb = comp_stamps[i]->getNAtoms();
952	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
953	<
954	<	current_atom = comp_stamps[i]->getAtom( k );
955	<	if( current_atom->haveOrientation() ){
956	<
957	<	dAtom = new DirectionalAtom(index);
958	<	simnfo->n_oriented++;
959	<	the_atoms[index] = dAtom;
960	<
961	<	ux = current_atom->getOrntX();
962	<	uy = current_atom->getOrntY();
963	<	uz = current_atom->getOrntZ();
964	<
965	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
966	<
661	<	u = sqrt( uSqr );
662	<	ux = ux / u;
663	<	uy = uy / u;
664	<	uz = uz / u;
665	<
666	<	dAtom->setSUx( ux );
667	<	dAtom->setSUy( uy );
668	<	dAtom->setSUz( uz );
946	>	if( worldRank == 0 ){
947	>	#endif // is_mpi
948	>
949	>	if( globals->haveFinalConfig() ){
950	>	strcpy( info[k].finalName, globals->getFinalConfig() );
951	>	}
952	>	else{
953	>	strcpy( info[k].finalName, inFileName );
954	>	char* endTest;
955	>	int nameLength = strlen( info[k].finalName );
956	>	endTest = &(info[k].finalName[nameLength - 5]);
957	>	if( !strcmp( endTest, ".bass" ) ){
958	>	strcpy( endTest, ".eor" );
959	>	}
960	>	else if( !strcmp( endTest, ".BASS" ) ){
961	>	strcpy( endTest, ".eor" );
962	>	}
963	>	else{
964	>	endTest = &(info[k].finalName[nameLength - 4]);
965	>	if( !strcmp( endTest, ".bss" ) ){
966	>	strcpy( endTest, ".eor" );
967		}
968	+	else if( !strcmp( endTest, ".mdl" ) ){
969	+	strcpy( endTest, ".eor" );
970	+	}
971		else{
972	<	the_atoms[index] = new GeneralAtom(index);
972	>	strcat( info[k].finalName, ".eor" );
973		}
673	–	the_atoms[index]->setType( current_atom->getType() );
674	–	the_atoms[index]->setIndex( index );
675	–
676	–	// increment the index and repeat;
677	–	index++;
974		}
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
975		}
689	–	#endif //is_mpi
976
977	<	molIndex++;
977	>	// make the sample and status out names
978	>
979	>	strcpy( info[k].sampleName, inFileName );
980	>	char* endTest;
981	>	int nameLength = strlen( info[k].sampleName );
982	>	endTest = &(info[k].sampleName[nameLength - 5]);
983	>	if( !strcmp( endTest, ".bass" ) ){
984	>	strcpy( endTest, ".dump" );
985	>	}
986	>	else if( !strcmp( endTest, ".BASS" ) ){
987	>	strcpy( endTest, ".dump" );
988	>	}
989	>	else{
990	>	endTest = &(info[k].sampleName[nameLength - 4]);
991	>	if( !strcmp( endTest, ".bss" ) ){
992	>	strcpy( endTest, ".dump" );
993	>	}
994	>	else if( !strcmp( endTest, ".mdl" ) ){
995	>	strcpy( endTest, ".dump" );
996	>	}
997	>	else{
998	>	strcat( info[k].sampleName, ".dump" );
999	>	}
1000	>	}
1001	>
1002	>	strcpy( info[k].statusName, inFileName );
1003	>	nameLength = strlen( info[k].statusName );
1004	>	endTest = &(info[k].statusName[nameLength - 5]);
1005	>	if( !strcmp( endTest, ".bass" ) ){
1006	>	strcpy( endTest, ".stat" );
1007	>	}
1008	>	else if( !strcmp( endTest, ".BASS" ) ){
1009	>	strcpy( endTest, ".stat" );
1010	>	}
1011	>	else{
1012	>	endTest = &(info[k].statusName[nameLength - 4]);
1013	>	if( !strcmp( endTest, ".bss" ) ){
1014	>	strcpy( endTest, ".stat" );
1015	>	}
1016	>	else if( !strcmp( endTest, ".mdl" ) ){
1017	>	strcpy( endTest, ".stat" );
1018	>	}
1019	>	else{
1020	>	strcat( info[k].statusName, ".stat" );
1021	>	}
1022	>	}
1023	>
1024	>	#ifdef IS_MPI
1025		}
1026	+	#endif // is_mpi
1027		}
694	–
695	–	#ifdef IS_MPI
696	–	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
697	–
698	–	delete[] globalIndex;
699	–
700	–	mpiSim->mpiRefresh();
701	–	#endif //IS_MPI
702	–
703	–	the_ff->initializeAtoms();
1028		}
1029
706	–	void SimSetup::makeBonds( void ){
1030
1031	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1032	<	bond_pair* the_bonds;
1033	<	BondStamp* current_bond;
1031	>	void SimSetup::sysObjectsCreation( void ){
1032	>
1033	>	int i,k;
1034	>
1035	>	// create the forceField
1036	>
1037	>	createFF();
1038
1039	<	the_bonds = new bond_pair[tot_bonds];
713	<	index = 0;
714	<	offset = 0;
715	<	molIndex = 0;
1039	>	// extract componentList
1040
1041	<	for( i=0; i<n_components; i++ ){
1041	>	compList();
1042
1043	<	for( j=0; j<components_nmol[i]; j++ ){
1043	>	// calc the number of atoms, bond, bends, and torsions
1044
1045	<	#ifdef IS_MPI
722	<	if( mpiSim->getMyMolStart() <= molIndex &&
723	<	molIndex <= mpiSim->getMyMolEnd() ){
724	<	#endif // is_mpi
725	<
726	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
727	<
728	<	current_bond = comp_stamps[i]->getBond( k );
729	<	the_bonds[index].a = current_bond->getA() + offset;
730	<	the_bonds[index].b = current_bond->getB() + offset;
1045	>	calcSysValues();
1046
1047	<	exI = the_bonds[index].a;
1048	<	exJ = the_bonds[index].b;
1047	>	#ifdef IS_MPI
1048	>	// divide the molecules among the processors
1049	>
1050	>	mpiMolDivide();
1051	>	#endif //is_mpi
1052	>
1053	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1054	>
1055	>	makeSysArrays();
1056
1057	<	// exclude_I must always be the smaller of the pair
1058	<	if( exI > exJ ){
1059	<	tempEx = exI;
1060	<	exI = exJ;
1061	<	exJ = tempEx;
1062	<	}
1057	>	// make and initialize the molecules (all but atomic coordinates)
1058	>
1059	>	makeMolecules();
1060	>
1061	>	for(k=0; k<nInfo; k++){
1062	>	info[k].identArray = new int[info[k].n_atoms];
1063	>	for(i=0; i<info[k].n_atoms; i++){
1064	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1065	>	}
1066	>	}
1067	>	}
1068
742	–
743	–	#ifdef IS_MPI
1069
1070	<	the_excludes[index*2] =
746	<	the_atoms[exI]->getGlobalIndex() + 1;
747	<	the_excludes[index*2 + 1] =
748	<	the_atoms[exJ]->getGlobalIndex() + 1;
1070	>	void SimSetup::createFF( void ){
1071
1072	<	#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	<	}
1072	>	switch( ffCase ){
1073
1074	<	the_ff->initializeBonds( the_bonds );
1075	<	}
1074	>	case FF_DUFF:
1075	>	the_ff = new DUFF();
1076	>	break;
1077
1078	<	void SimSetup::makeBends( void ){
1078	>	case FF_LJ:
1079	>	the_ff = new LJFF();
1080	>	break;
1081
1082	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1083	<	bend_set* the_bends;
1084	<	BendStamp* current_bend;
778	<	LinkedAssign* extras;
779	<	LinkedAssign* current_extra;
780	<
1082	>	case FF_EAM:
1083	>	the_ff = new EAM_FF();
1084	>	break;
1085
1086	<	the_bends = new bend_set[tot_bends];
1087	<	index = 0;
1088	<	offset = 0;
1089	<	molIndex = 0;
1090	<	for( i=0; i<n_components; i++ ){
1086	>	default:
1087	>	sprintf( painCave.errMsg,
1088	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1089	>	painCave.isFatal = 1;
1090	>	simError();
1091	>	}
1092
788	–	for( j=0; j<components_nmol[i]; j++ ){
789	–
1093		#ifdef IS_MPI
1094	<	if( mpiSim->getMyMolStart() <= molIndex &&
1095	<	molIndex <= mpiSim->getMyMolEnd() ){
1096	<	#endif // is_mpi
1094	>	strcpy( checkPointMsg, "ForceField creation successful" );
1095	>	MPIcheckPoint();
1096	>	#endif // is_mpi
1097
1098	<	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	<	}
1098	>	}
1099
1100
1101	<	#ifdef IS_MPI
1101	>	void SimSetup::compList( void ){
1102
1103	<	the_excludes[(index + tot_bonds)*2] =
1104	<	the_atoms[exI]->getGlobalIndex() + 1;
1105	<	the_excludes[(index + tot_bonds)*2 + 1] =
1106	<	the_atoms[exJ]->getGlobalIndex() + 1;
1107	<
1108	<	#else  // isn't MPI
1109	<
1110	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
1111	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1112	<	// fortran index from 1 (hence the +1 in the indexing)
1113	<	#endif  //is_mpi
1114	<
1115	<
1116	<	// increment the index and repeat;
1117	<	index++;
1118	<	}
887	<	offset += comp_stamps[i]->getNAtoms();
888	<
889	<	#ifdef IS_MPI
890	<	}
891	<	#endif //is_mpi
1103	>	int i;
1104	>	char* id;
1105	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1106	>	LinkedMolStamp* currentStamp = NULL;
1107	>	comp_stamps = new MoleculeStamp*[n_components];
1108	>
1109	>	// make an array of molecule stamps that match the components used.
1110	>	// also extract the used stamps out into a separate linked list
1111	>
1112	>	for(i=0; i<nInfo; i++){
1113	>	info[i].nComponents = n_components;
1114	>	info[i].componentsNmol = components_nmol;
1115	>	info[i].compStamps = comp_stamps;
1116	>	info[i].headStamp = headStamp;
1117	>	}
1118	>
1119
1120	<	molIndex++;
1120	>	for( i=0; i<n_components; i++ ){
1121	>
1122	>	id = the_components[i]->getType();
1123	>	comp_stamps[i] = NULL;
1124	>
1125	>	// check to make sure the component isn't already in the list
1126	>
1127	>	comp_stamps[i] = headStamp->match( id );
1128	>	if( comp_stamps[i] == NULL ){
1129	>
1130	>	// extract the component from the list;
1131	>
1132	>	currentStamp = stamps->extractMolStamp( id );
1133	>	if( currentStamp == NULL ){
1134	>	sprintf( painCave.errMsg,
1135	>	"SimSetup error: Component \"%s\" was not found in the "
1136	>	"list of declared molecules\n",
1137	>	id );
1138	>	painCave.isFatal = 1;
1139	>	simError();
1140	>	}
1141	>
1142	>	headStamp->add( currentStamp );
1143	>	comp_stamps[i] = headStamp->match( id );
1144		}
1145		}
1146
1147		#ifdef IS_MPI
1148	<	sprintf( checkPointMsg,
899	<	"Successfully created the bends list.\n" );
1148	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1149		MPIcheckPoint();
1150		#endif // is_mpi
902	–
1151
1152	<	the_ff->initializeBends( the_bends );
1152	>
1153		}
1154
1155	<	void SimSetup::makeTorsions( void ){
1156	<
1157	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1158	<	torsion_set* the_torsions;
1159	<	TorsionStamp* current_torsion;
1160	<
1161	<	the_torsions = new torsion_set[tot_torsions];
1162	<	index = 0;
1163	<	offset = 0;
916	<	molIndex = 0;
1155	>	void SimSetup::calcSysValues( void ){
1156	>	int i, j, k;
1157	>
1158	>	int *molMembershipArray;
1159	>
1160	>	tot_atoms = 0;
1161	>	tot_bonds = 0;
1162	>	tot_bends = 0;
1163	>	tot_torsions = 0;
1164		for( i=0; i<n_components; i++ ){
1165	+
1166	+	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1167	+	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1168	+	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1169	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1170	+	}
1171	+
1172	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1173	+	molMembershipArray = new int[tot_atoms];
1174	+
1175	+	for(i=0; i<nInfo; i++){
1176	+	info[i].n_atoms = tot_atoms;
1177	+	info[i].n_bonds = tot_bonds;
1178	+	info[i].n_bends = tot_bends;
1179	+	info[i].n_torsions = tot_torsions;
1180	+	info[i].n_SRI = tot_SRI;
1181	+	info[i].n_mol = tot_nmol;
1182	+
1183	+	info[i].molMembershipArray = molMembershipArray;
1184	+	}
1185	+	}
1186
919	–	for( j=0; j<components_nmol[i]; j++ ){
920	–
1187		#ifdef IS_MPI
922	–	if( mpiSim->getMyMolStart() <= molIndex &&
923	–	molIndex <= mpiSim->getMyMolEnd() ){
924	–	#endif // is_mpi
1188
1189	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1189	>	void SimSetup::mpiMolDivide( void ){
1190	>
1191	>	int i, j, k;
1192	>	int localMol, allMol;
1193	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1194
1195	<	current_torsion = comp_stamps[i]->getTorsion( k );
1196	<	the_torsions[index].a = current_torsion->getA() + offset;
1197	<	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;
1195	>	mpiSim = new mpiSimulation( info );
1196	>
1197	>	globalIndex = mpiSim->divideLabor();
1198
1199	<	exI = the_torsions[index].a;
1200	<	exJ = the_torsions[index].d;
1199	>	// set up the local variables
1200	>
1201	>	mol2proc = mpiSim->getMolToProcMap();
1202	>	molCompType = mpiSim->getMolComponentType();
1203	>
1204	>	allMol = 0;
1205	>	localMol = 0;
1206	>	local_atoms = 0;
1207	>	local_bonds = 0;
1208	>	local_bends = 0;
1209	>	local_torsions = 0;
1210	>	globalAtomIndex = 0;
1211
937	–
938	–	// exclude_I must always be the smaller of the pair
939	–	if( exI > exJ ){
940	–	tempEx = exI;
941	–	exI = exJ;
942	–	exJ = tempEx;
943	–	}
1212
1213	+	for( i=0; i<n_components; i++ ){
1214
1215	<	#ifdef IS_MPI
1215	>	for( j=0; j<components_nmol[i]; j++ ){
1216	>
1217	>	if( mol2proc[allMol] == worldRank ){
1218
1219	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
1220	<	the_atoms[exI]->getGlobalIndex() + 1;
1221	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1222	<	the_atoms[exJ]->getGlobalIndex() + 1;
1223	<
1224	<	#else  // isn't MPI
1225	<
1226	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1227	<	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	<
960	<
961	<	// increment the index and repeat;
962	<	index++;
1219	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1220	>	local_bonds +=    comp_stamps[i]->getNBonds();
1221	>	local_bends +=    comp_stamps[i]->getNBends();
1222	>	local_torsions += comp_stamps[i]->getNTorsions();
1223	>	localMol++;
1224	>	}
1225	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1226	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1227	>	globalAtomIndex++;
1228		}
964	–	offset += comp_stamps[i]->getNAtoms();
1229
1230	<	#ifdef IS_MPI
967	<	}
968	<	#endif //is_mpi
969	<
970	<	molIndex++;
1230	>	allMol++;
1231		}
1232		}
1233	+	local_SRI = local_bonds + local_bends + local_torsions;
1234	+
1235	+	info[0].n_atoms = mpiSim->getMyNlocal();
1236	+
1237	+	if( local_atoms != info[0].n_atoms ){
1238	+	sprintf( painCave.errMsg,
1239	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1240	+	" localAtom (%d) are not equal.\n",
1241	+	info[0].n_atoms,
1242	+	local_atoms );
1243	+	painCave.isFatal = 1;
1244	+	simError();
1245	+	}
1246
1247	<	the_ff->initializeTorsions( the_torsions );
1247	>	info[0].n_bonds = local_bonds;
1248	>	info[0].n_bends = local_bends;
1249	>	info[0].n_torsions = local_torsions;
1250	>	info[0].n_SRI = local_SRI;
1251	>	info[0].n_mol = localMol;
1252	>
1253	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1254	>	MPIcheckPoint();
1255		}
1256	+
1257	+	#endif // is_mpi
1258
977	–	void SimSetup::initFromBass( void ){
1259
1260	<	int i, j, k;
1261	<	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;
1260	>	void SimSetup::makeSysArrays( void ){
1261	>	int i, j, k, l;
1262
1263	<	temp1 = (double)tot_nmol / 4.0;
1264	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1265	<	temp3 = ceil( temp2 );
1263	>	Atom** the_atoms;
1264	>	Molecule* the_molecules;
1265	>	Exclude** the_excludes;
1266
1267	<	have_extra =0;
1268	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1269	<	have_extra =1;
1267	>
1268	>	for(l=0; l<nInfo; l++){
1269	>
1270	>	// create the atom and short range interaction arrays
1271	>
1272	>	the_atoms = new Atom*[info[l].n_atoms];
1273	>	the_molecules = new Molecule[info[l].n_mol];
1274	>	int molIndex;
1275
1276	<	n_cells = (int)temp3 - 1;
1277	<	cellx = simnfo->box_x / temp3;
1278	<	celly = simnfo->box_y / temp3;
1279	<	cellz = simnfo->box_z / temp3;
1280	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1281	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1282	<	n_per_extra = (int)ceil( temp1 );
1283	<
1284	<	if( n_per_extra > 4){
1285	<	sprintf( painCave.errMsg,
1286	<	"SimSetup error. There has been an error in constructing"
1287	<	" the non-complete lattice.\n" );
1288	<	painCave.isFatal = 1;
1289	<	simError();
1276	>	// initialize the molecule's stampID's
1277	>
1278	>	#ifdef IS_MPI
1279	>
1280	>
1281	>	molIndex = 0;
1282	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1283	>
1284	>	if(mol2proc[i] == worldRank ){
1285	>	the_molecules[molIndex].setStampID( molCompType[i] );
1286	>	the_molecules[molIndex].setMyIndex( molIndex );
1287	>	the_molecules[molIndex].setGlobalIndex( i );
1288	>	molIndex++;
1289	>	}
1290		}
1291	<	}
1292	<	else{
1293	<	n_cells = (int)temp3;
1294	<	cellx = simnfo->box_x / temp3;
1295	<	celly = simnfo->box_y / temp3;
1296	<	cellz = simnfo->box_z / temp3;
1297	<	}
1291	>
1292	>	#else // is_mpi
1293	>
1294	>	molIndex = 0;
1295	>	globalAtomIndex = 0;
1296	>	for(i=0; i<n_components; i++){
1297	>	for(j=0; j<components_nmol[i]; j++ ){
1298	>	the_molecules[molIndex].setStampID( i );
1299	>	the_molecules[molIndex].setMyIndex( molIndex );
1300	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1301	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1302	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1303	>	globalAtomIndex++;
1304	>	}
1305	>	molIndex++;
1306	>	}
1307	>	}
1308	>
1309	>
1310	>	#endif // is_mpi
1311
1018	–	current_mol = 0;
1019	–	current_comp_mol = 0;
1020	–	current_comp = 0;
1021	–	current_atom_ndx = 0;
1312
1313	<	for( i=0; i < n_cells ; i++ ){
1314	<	for( j=0; j < n_cells; j++ ){
1315	<	for( k=0; k < n_cells; k++ ){
1313	>	if( info[l].n_SRI ){
1314	>
1315	>	Exclude::createArray(info[l].n_SRI);
1316	>	the_excludes = new Exclude*[info[l].n_SRI];
1317	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1318	>	the_excludes[ex] = new Exclude(ex);
1319	>	}
1320	>	info[l].globalExcludes = new int;
1321	>	info[l].n_exclude = info[l].n_SRI;
1322	>	}
1323	>	else{
1324	>
1325	>	Exclude::createArray( 1 );
1326	>	the_excludes = new Exclude*;
1327	>	the_excludes[0] = new Exclude(0);
1328	>	the_excludes[0]->setPair( 0,0 );
1329	>	info[l].globalExcludes = new int;
1330	>	info[l].globalExcludes[0] = 0;
1331	>	info[l].n_exclude = 0;
1332	>	}
1333
1334	<	makeElement( i * cellx,
1028	<	j * celly,
1029	<	k * cellz );
1334	>	// set the arrays into the SimInfo object
1335
1336	<	makeElement( i * cellx + 0.5 * cellx,
1337	<	j * celly + 0.5 * celly,
1338	<	k * cellz );
1336	>	info[l].atoms = the_atoms;
1337	>	info[l].molecules = the_molecules;
1338	>	info[l].nGlobalExcludes = 0;
1339	>	info[l].excludes = the_excludes;
1340
1341	<	makeElement( i * cellx,
1342	<	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	<	}
1341	>	the_ff->setSimInfo( info );
1342	>
1343		}
1344	+	}
1345
1346	<	if( have_extra ){
1047	<	done = 0;
1346	>	void SimSetup::makeIntegrator( void ){
1347
1348	<	int start_ndx;
1050	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1051	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1348	>	int k;
1349
1350	<	if( i < n_cells ){
1350	>	NVT<RealIntegrator>*  myNVT = NULL;
1351	>	NPTi<RealIntegrator>* myNPTi = NULL;
1352	>	NPTf<RealIntegrator>* myNPTf = NULL;
1353	>	NPTim<RealIntegrator>* myNPTim = NULL;
1354	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1355	>
1356	>	for(k=0; k<nInfo; k++){
1357	>
1358	>	switch( ensembleCase ){
1359	>
1360	>	case NVE_ENS:
1361	>	if (globals->haveZconstraints()){
1362	>	setupZConstraint(info[k]);
1363	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1364	>	}
1365
1366	<	if( j < n_cells ){
1367	<	start_ndx = n_cells;
1368	<	}
1369	<	else start_ndx = 0;
1366	>	else
1367	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1368	>	break;
1369	>
1370	>	case NVT_ENS:
1371	>	if (globals->haveZconstraints()){
1372	>	setupZConstraint(info[k]);
1373	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1374		}
1375	<	else start_ndx = 0;
1375	>	else
1376	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1377
1378	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1378	>	myNVT->setTargetTemp(globals->getTargetTemp());
1379	>
1380	>	if (globals->haveTauThermostat())
1381	>	myNVT->setTauThermostat(globals->getTauThermostat());
1382	>
1383	>	else {
1384	>	sprintf( painCave.errMsg,
1385	>	"SimSetup error: If you use the NVT\n"
1386	>	"    ensemble, you must set tauThermostat.\n");
1387	>	painCave.isFatal = 1;
1388	>	simError();
1389	>	}
1390	>	break;
1391	>
1392	>	case NPTi_ENS:
1393	>	if (globals->haveZconstraints()){
1394	>	setupZConstraint(info[k]);
1395	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1396	>	}
1397	>	else
1398	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1399
1400	<	makeElement( i * cellx,
1401	<	j * celly,
1402	<	k * cellz );
1403	<	done = ( current_mol >= tot_nmol );
1404	<
1405	<	if( !done && n_per_extra > 1 ){
1406	<	makeElement( i * cellx + 0.5 * cellx,
1407	<	j * celly + 0.5 * celly,
1408	<	k * cellz );
1409	<	done = ( current_mol >= tot_nmol );
1410	<	}
1411	<
1412	<	if( !done && n_per_extra > 2){
1413	<	makeElement( i * cellx,
1414	<	j * celly + 0.5 * celly,
1415	<	k * cellz + 0.5 * cellz );
1416	<	done = ( current_mol >= tot_nmol );
1417	<	}
1418	<
1419	<	if( !done && n_per_extra > 3){
1420	<	makeElement( i * cellx + 0.5 * cellx,
1421	<	j * celly,
1422	<	k * cellz + 0.5 * cellz );
1423	<	done = ( current_mol >= tot_nmol );
1424	<	}
1400	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1401	>
1402	>	if (globals->haveTargetPressure())
1403	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1404	>	else {
1405	>	sprintf( painCave.errMsg,
1406	>	"SimSetup error: If you use a constant pressure\n"
1407	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1408	>	painCave.isFatal = 1;
1409	>	simError();
1410	>	}
1411	>
1412	>	if( globals->haveTauThermostat() )
1413	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1414	>	else{
1415	>	sprintf( painCave.errMsg,
1416	>	"SimSetup error: If you use an NPT\n"
1417	>	"    ensemble, you must set tauThermostat.\n");
1418	>	painCave.isFatal = 1;
1419	>	simError();
1420	>	}
1421	>
1422	>	if( globals->haveTauBarostat() )
1423	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1424	>	else{
1425	>	sprintf( painCave.errMsg,
1426	>	"SimSetup error: If you use an NPT\n"
1427	>	"    ensemble, you must set tauBarostat.\n");
1428	>	painCave.isFatal = 1;
1429	>	simError();
1430	>	}
1431	>	break;
1432	>
1433	>	case NPTf_ENS:
1434	>	if (globals->haveZconstraints()){
1435	>	setupZConstraint(info[k]);
1436	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1437		}
1438	+	else
1439	+	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1440	+
1441	+	myNPTf->setTargetTemp( globals->getTargetTemp());
1442	+
1443	+	if (globals->haveTargetPressure())
1444	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1445	+	else {
1446	+	sprintf( painCave.errMsg,
1447	+	"SimSetup error: If you use a constant pressure\n"
1448	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1449	+	painCave.isFatal = 1;
1450	+	simError();
1451	+	}
1452	+
1453	+	if( globals->haveTauThermostat() )
1454	+	myNPTf->setTauThermostat( globals->getTauThermostat() );
1455	+	else{
1456	+	sprintf( painCave.errMsg,
1457	+	"SimSetup error: If you use an NPT\n"
1458	+	"    ensemble, you must set tauThermostat.\n");
1459	+	painCave.isFatal = 1;
1460	+	simError();
1461		}
1462	+
1463	+	if( globals->haveTauBarostat() )
1464	+	myNPTf->setTauBarostat( globals->getTauBarostat() );
1465	+	else{
1466	+	sprintf( painCave.errMsg,
1467	+	"SimSetup error: If you use an NPT\n"
1468	+	"    ensemble, you must set tauBarostat.\n");
1469	+	painCave.isFatal = 1;
1470	+	simError();
1471	+	}
1472	+	break;
1473	+
1474	+	case NPTim_ENS:
1475	+	if (globals->haveZconstraints()){
1476	+	setupZConstraint(info[k]);
1477	+	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1478	+	}
1479	+	else
1480	+	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1481	+
1482	+	myNPTim->setTargetTemp( globals->getTargetTemp());
1483	+
1484	+	if (globals->haveTargetPressure())
1485	+	myNPTim->setTargetPressure(globals->getTargetPressure());
1486	+	else {
1487	+	sprintf( painCave.errMsg,
1488	+	"SimSetup error: If you use a constant pressure\n"
1489	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1490	+	painCave.isFatal = 1;
1491	+	simError();
1492	+	}
1493	+
1494	+	if( globals->haveTauThermostat() )
1495	+	myNPTim->setTauThermostat( globals->getTauThermostat() );
1496	+	else{
1497	+	sprintf( painCave.errMsg,
1498	+	"SimSetup error: If you use an NPT\n"
1499	+	"    ensemble, you must set tauThermostat.\n");
1500	+	painCave.isFatal = 1;
1501	+	simError();
1502	+	}
1503	+
1504	+	if( globals->haveTauBarostat() )
1505	+	myNPTim->setTauBarostat( globals->getTauBarostat() );
1506	+	else{
1507	+	sprintf( painCave.errMsg,
1508	+	"SimSetup error: If you use an NPT\n"
1509	+	"    ensemble, you must set tauBarostat.\n");
1510	+	painCave.isFatal = 1;
1511	+	simError();
1512	+	}
1513	+	break;
1514	+
1515	+	case NPTfm_ENS:
1516	+	if (globals->haveZconstraints()){
1517	+	setupZConstraint(info[k]);
1518	+	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1519	+	}
1520	+	else
1521	+	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1522	+
1523	+	myNPTfm->setTargetTemp( globals->getTargetTemp());
1524	+
1525	+	if (globals->haveTargetPressure())
1526	+	myNPTfm->setTargetPressure(globals->getTargetPressure());
1527	+	else {
1528	+	sprintf( painCave.errMsg,
1529	+	"SimSetup error: If you use a constant pressure\n"
1530	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1531	+	painCave.isFatal = 1;
1532	+	simError();
1533	+	}
1534	+
1535	+	if( globals->haveTauThermostat() )
1536	+	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1537	+	else{
1538	+	sprintf( painCave.errMsg,
1539	+	"SimSetup error: If you use an NPT\n"
1540	+	"    ensemble, you must set tauThermostat.\n");
1541	+	painCave.isFatal = 1;
1542	+	simError();
1543	+	}
1544	+
1545	+	if( globals->haveTauBarostat() )
1546	+	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1547	+	else{
1548	+	sprintf( painCave.errMsg,
1549	+	"SimSetup error: If you use an NPT\n"
1550	+	"    ensemble, you must set tauBarostat.\n");
1551	+	painCave.isFatal = 1;
1552	+	simError();
1553	+	}
1554	+	break;
1555	+
1556	+	default:
1557	+	sprintf( painCave.errMsg,
1558	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1559	+	painCave.isFatal = 1;
1560	+	simError();
1561		}
1562		}
1563	+	}
1564
1565	+	void SimSetup::initFortran( void ){
1566
1567	<	for( i=0; i<simnfo->n_atoms; i++ ){
1568	<	simnfo->atoms[i]->set_vx( 0.0 );
1569	<	simnfo->atoms[i]->set_vy( 0.0 );
1570	<	simnfo->atoms[i]->set_vz( 0.0 );
1567	>	info[0].refreshSim();
1568	>
1569	>	if( !strcmp( info[0].mixingRule, "standard") ){
1570	>	the_ff->initForceField( LB_MIXING_RULE );
1571		}
1572	<	}
1572	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1573	>	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1574	>	}
1575	>	else{
1576	>	sprintf( painCave.errMsg,
1577	>	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1578	>	info[0].mixingRule );
1579	>	painCave.isFatal = 1;
1580	>	simError();
1581	>	}
1582
1102	–	void SimSetup::makeElement( double x, double y, double z ){
1583
1584	<	int k;
1585	<	AtomStamp* current_atom;
1586	<	DirectionalAtom* dAtom;
1587	<	double rotMat[3][3];
1584	>	#ifdef IS_MPI
1585	>	strcpy( checkPointMsg,
1586	>	"Successfully intialized the mixingRule for Fortran." );
1587	>	MPIcheckPoint();
1588	>	#endif // is_mpi
1589
1590	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1590	>	}
1591
1592	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1593	<	if( !current_atom->havePosition() ){
1592	>	void SimSetup::setupZConstraint(SimInfo& theInfo)
1593	>	{
1594	>	int nZConstraints;
1595	>	ZconStamp** zconStamp;
1596	>
1597	>	if(globals->haveZconstraintTime()){
1598	>
1599	>	//add sample time of z-constraint  into SimInfo's property list
1600	>	DoubleData* zconsTimeProp = new DoubleData();
1601	>	zconsTimeProp->setID(ZCONSTIME_ID);
1602	>	zconsTimeProp->setData(globals->getZconsTime());
1603	>	theInfo.addProperty(zconsTimeProp);
1604	>	}
1605	>	else{
1606		sprintf( painCave.errMsg,
1607	<	"SimSetup:initFromBass error.\n"
1608	<	"\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() );
1607	>	"ZConstraint error: If you use an ZConstraint\n"
1608	>	" , you must set sample time.\n");
1609		painCave.isFatal = 1;
1610	<	simError();
1610	>	simError();
1611		}
1612
1613	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1614	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1615	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1613	>	//
1614	>	nZConstraints = globals->getNzConstraints();
1615	>	zconStamp = globals->getZconStamp();
1616	>	ZConsParaItem tempParaItem;
1617
1618	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1618	>	ZConsParaData* zconsParaData = new ZConsParaData();
1619	>	zconsParaData->setID(ZCONSPARADATA_ID);
1620	>
1621	>	for(int i = 0; i < nZConstraints; i++){
1622	>	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1623	>	tempParaItem.zPos = zconStamp[i]->getZpos();
1624	>	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1625	>	tempParaItem.kRatio = zconStamp[i]->getKratio();
1626
1627	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1627	>	zconsParaData->addItem(tempParaItem);
1628	>	}
1629
1630	<	rotMat[0][0] = 1.0;
1631	<	rotMat[0][1] = 0.0;
1632	<	rotMat[0][2] = 0.0;
1630	>	//sort the parameters by index of molecules
1631	>	zconsParaData->sortByIndex();
1632	>
1633	>	//push data into siminfo, therefore, we can retrieve later
1634	>	theInfo.addProperty(zconsParaData);
1635
1636	<	rotMat[1][0] = 0.0;
1637	<	rotMat[1][1] = 1.0;
1638	<	rotMat[1][2] = 0.0;
1639	<
1640	<	rotMat[2][0] = 0.0;
1641	<	rotMat[2][1] = 0.0;
1142	<	rotMat[2][2] = 1.0;
1143	<
1144	<	dAtom->setA( rotMat );
1636	>	//push zconsTol into siminfo, if user does not specify
1637	>	//value for zconsTol, a default value will be used
1638	>	DoubleData* zconsTol = new DoubleData();
1639	>	zconsTol->setID(ZCONSTOL_ID);
1640	>	if(globals->haveZconsTol()){
1641	>	zconsTol->setData(globals->getZconsTol());
1642		}
1643	+	else{
1644	+	double defaultZConsTol = 1E-6;
1645	+	sprintf( painCave.errMsg,
1646	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1647	+	" , default value %f is used.\n", defaultZConsTol);
1648	+	painCave.isFatal = 0;
1649	+	simError();
1650
1651	<	current_atom_ndx++;
1652	<	}
1653	<
1654	<	current_mol++;
1655	<	current_comp_mol++;
1656	<
1657	<	if( current_comp_mol >= components_nmol[current_comp] ){
1658	<
1659	<	current_comp_mol = 0;
1660	<	current_comp++;
1661	<	}
1651	>	zconsTol->setData(defaultZConsTol);
1652	>	}
1653	>	theInfo.addProperty(zconsTol);
1654	>
1655	>	//Determine the name of ouput file and add it into SimInfo's property list
1656	>	//Be careful, do not use inFileName, since it is a pointer which
1657	>	//point to a string at master node, and slave nodes do not contain that string
1658	>
1659	>	string zconsOutput(theInfo.finalName);
1660	>
1661	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1662	>
1663	>	StringData* zconsFilename = new StringData();
1664	>	zconsFilename->setID(ZCONSFILENAME_ID);
1665	>	zconsFilename->setData(zconsOutput);
1666	>
1667	>	theInfo.addProperty(zconsFilename);
1668		}

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