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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 412 by mmeineke, Wed Mar 26 21:50:33 2003 UTC vs.
Revision 693 by tim, Wed Aug 13 19:21:53 2003 UTC

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

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