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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 407 by mmeineke, Wed Mar 26 20:22:02 2003 UTC vs.
Revision 708 by tim, Wed Aug 20 22:23:34 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6	+	#include <sys/time.h>
7
8		#include "SimSetup.hpp"
9	+	#include "ReadWrite.hpp"
10		#include "parse_me.h"
11		#include "Integrator.hpp"
12		#include "simError.h"
#	Line 12 | Line 16 | SimSetup::SimSetup(){
16		#include "mpiSimulation.hpp"
17		#endif
18
19	+	// some defines for ensemble and Forcefield  cases
20	+
21	+	#define NVE_ENS        0
22	+	#define NVT_ENS        1
23	+	#define NPTi_ENS       2
24	+	#define NPTf_ENS       3
25	+	#define NPTim_ENS      4
26	+	#define NPTfm_ENS      5
27	+
28	+	#define FF_DUFF 0
29	+	#define FF_LJ   1
30	+	#define FF_EAM  2
31	+
32	+	using namespace std;
33	+
34		SimSetup::SimSetup(){
35	+
36	+	isInfoArray = 0;
37	+	nInfo = 1;
38	+
39		stamps = new MakeStamps();
40		globals = new Globals();
41
42	+
43		#ifdef IS_MPI
44		strcpy( checkPointMsg, "SimSetup creation successful" );
45		MPIcheckPoint();
#	Line 27 | Line 51 | void SimSetup::parseFile( char* fileName ){
51		delete globals;
52		}
53
54	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
55	+	info = the_info;
56	+	nInfo = theNinfo;
57	+	isInfoArray = 1;
58	+	}
59	+
60	+
61		void SimSetup::parseFile( char* fileName ){
62
63		#ifdef IS_MPI
#	Line 62 | Line 93 | void SimSetup::createSim( void ){
93
94		#endif // is_mpi
95
96	<	void SimSetup::createSim( void ){
96	>	void SimSetup::createSim(void){
97
98	<	MakeStamps *the_stamps;
99	<	Globals* the_globals;
100	<	int i, j;
98	>	int i, j, k, globalAtomIndex;
99	>
100	>	// gather all of the information from the Bass file
101
102	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
102	>	gatherInfo();
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	>	// creation of complex system objects
105
106	<	// 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 );
106	>	sysObjectsCreation();
107
108	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
108	>	// check on the post processing info
109
110	+	finalInfoCheck();
111
112	<	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	<	}
112	>	// initialize the system coordinates
113
114	+	if( !isInfoArray ) initSystemCoords();
115	+
116	+	// make the output filenames
117	+
118	+	makeOutNames();
119	+
120	+	// make the integrator
121	+
122	+	makeIntegrator();
123	+
124		#ifdef IS_MPI
125	<	strcpy( checkPointMsg, "ForceField creation successful" );
126	<	MPIcheckPoint();
106	<	#endif // is_mpi
125	>	mpiSim->mpiRefresh();
126	>	#endif
127
128	+	// initialize the Fortran
129	+
130	+	initFortran();
131	+
132	+
133	+
134	+	}
135	+
136	+
137	+	void SimSetup::makeMolecules( void ){
138	+
139	+	int k,l;
140	+	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
141	+	molInit molInfo;
142	+	DirectionalAtom* dAtom;
143	+	LinkedAssign* extras;
144	+	LinkedAssign* current_extra;
145	+	AtomStamp* currentAtom;
146	+	BondStamp* currentBond;
147	+	BendStamp* currentBend;
148	+	TorsionStamp* currentTorsion;
149	+
150	+	bond_pair* theBonds;
151	+	bend_set* theBends;
152	+	torsion_set* theTorsions;
153	+
154
155	+	//init the forceField paramters
156
157	<	// 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];
157	>	the_ff->readParams();
158
159	<	if( !the_globals->haveNMol() ){
160	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
159	>
160	>	// init the atoms
161
162	<	tot_nmol = 0;
163	<	for( i=0; i<n_components; i++ ){
162	>	double ux, uy, uz, u, uSqr;
163	>
164	>	for(k=0; k<nInfo; k++){
165	>
166	>	the_ff->setSimInfo( &(info[k]) );
167
168	<	if( !the_components[i]->haveNMol() ){
169	<	// we have a problem
170	<	sprintf( painCave.errMsg,
171	<	"SimSetup Error. No global NMol or component NMol"
172	<	" given. Cannot calculate the number of atoms.\n" );
127	<	painCave.isFatal = 1;
128	<	simError();
129	<	}
168	>	atomOffset = 0;
169	>	excludeOffset = 0;
170	>	for(i=0; i<info[k].n_mol; i++){
171	>
172	>	stampID = info[k].molecules[i].getStampID();
173
174	<	tot_nmol += the_components[i]->getNMol();
175	<	components_nmol[i] = the_components[i]->getNMol();
176	<	}
177	<	}
178	<	else{
179	<	sprintf( painCave.errMsg,
180	<	"SimSetup error.\n"
181	<	"\tSorry, the ability to specify total"
182	<	" nMols and then give molfractions in the components\n"
183	<	"\tis not currently supported."
184	<	" Please give nMol in the components.\n" );
185	<	painCave.isFatal = 1;
186	<	simError();
174	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
175	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
176	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
177	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
178	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
179	>
180	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
181	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
182	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
183	>	molInfo.myBends = new Bend*[molInfo.nBends];
184	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
185	>
186	>	theBonds = new bond_pair[molInfo.nBonds];
187	>	theBends = new bend_set[molInfo.nBends];
188	>	theTorsions = new torsion_set[molInfo.nTorsions];
189
190	+	// make the Atoms
191
192	<	//     tot_nmol = the_globals->getNMol();
192	>	for(j=0; j<molInfo.nAtoms; j++){
193	>
194	>	currentAtom = comp_stamps[stampID]->getAtom( j );
195	>	if( currentAtom->haveOrientation() ){
196
197	<	//   //we have the total number of molecules, now we check for molfractions
198	<	//     for( i=0; i<n_components; i++ ){
197	>	dAtom = new DirectionalAtom( (j + atomOffset),
198	>	info[k].getConfiguration() );
199	>	info[k].n_oriented++;
200	>	molInfo.myAtoms[j] = dAtom;
201
202	<	//       if( !the_components[i]->haveMolFraction() ){
202	>	ux = currentAtom->getOrntX();
203	>	uy = currentAtom->getOrntY();
204	>	uz = currentAtom->getOrntZ();
205
206	<	//  if( !the_components[i]->haveNMol() ){
154	<	//    //we have a problem
155	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
156	<	//              << " nMol was given in component
206	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
207
208	+	u = sqrt( uSqr );
209	+	ux = ux / u;
210	+	uy = uy / u;
211	+	uz = uz / u;
212	+
213	+	dAtom->setSUx( ux );
214	+	dAtom->setSUy( uy );
215	+	dAtom->setSUz( uz );
216		}
217	<
217	>	else{
218	>	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
219	>	info[k].getConfiguration() );
220	>	}
221	>	molInfo.myAtoms[j]->setType( currentAtom->getType() );
222	>
223		#ifdef IS_MPI
224	<	strcpy( checkPointMsg, "Have the number of components" );
225	<	MPIcheckPoint();
224	>
225	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
226	>
227		#endif // is_mpi
228	<
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;
228	>	}
229
230	<	// check to make sure the component isn't already in the list
231	<
183	<	comp_stamps[i] = headStamp->match( id );
184	<	if( comp_stamps[i] == NULL ){
230	>	// make the bonds
231	>	for(j=0; j<molInfo.nBonds; j++){
232
233	<	// extract the component from the list;
233	>	currentBond = comp_stamps[stampID]->getBond( j );
234	>	theBonds[j].a = currentBond->getA() + atomOffset;
235	>	theBonds[j].b = currentBond->getB() + atomOffset;
236	>
237	>	exI = theBonds[j].a;
238	>	exJ = theBonds[j].b;
239	>
240	>	// exclude_I must always be the smaller of the pair
241	>	if( exI > exJ ){
242	>	tempEx = exI;
243	>	exI = exJ;
244	>	exJ = tempEx;
245	>	}
246	>	#ifdef IS_MPI
247	>	tempEx = exI;
248	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
249	>	tempEx = exJ;
250	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
251	>
252	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
253	>	#else  // isn't MPI
254	>
255	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
256	>	#endif  //is_mpi
257	>	}
258	>	excludeOffset += molInfo.nBonds;
259
260	<	currentStamp = the_stamps->extractMolStamp( id );
261	<	if( currentStamp == NULL ){
262	<	sprintf( painCave.errMsg,
263	<	"SimSetup error: Component \"%s\" was not found in the "
264	<	"list of declared molecules\n",
265	<	id );
266	<	painCave.isFatal = 1;
267	<	simError();
260	>	//make the bends
261	>	for(j=0; j<molInfo.nBends; j++){
262	>
263	>	currentBend = comp_stamps[stampID]->getBend( j );
264	>	theBends[j].a = currentBend->getA() + atomOffset;
265	>	theBends[j].b = currentBend->getB() + atomOffset;
266	>	theBends[j].c = currentBend->getC() + atomOffset;
267	>
268	>	if( currentBend->haveExtras() ){
269	>
270	>	extras = currentBend->getExtras();
271	>	current_extra = extras;
272	>
273	>	while( current_extra != NULL ){
274	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
275	>
276	>	switch( current_extra->getType() ){
277	>
278	>	case 0:
279	>	theBends[j].ghost =
280	>	current_extra->getInt() + atomOffset;
281	>	theBends[j].isGhost = 1;
282	>	break;
283	>
284	>	case 1:
285	>	theBends[j].ghost =
286	>	(int)current_extra->getDouble() + atomOffset;
287	>	theBends[j].isGhost = 1;
288	>	break;
289	>
290	>	default:
291	>	sprintf( painCave.errMsg,
292	>	"SimSetup Error: ghostVectorSource was neither a "
293	>	"double nor an int.\n"
294	>	"-->Bend[%d] in %s\n",
295	>	j, comp_stamps[stampID]->getID() );
296	>	painCave.isFatal = 1;
297	>	simError();
298	>	}
299		}
300
301	<	headStamp->add( currentStamp );
302	<	comp_stamps[i] = headStamp->match( id );
301	>	else{
302	>
303	>	sprintf( painCave.errMsg,
304	>	"SimSetup Error: unhandled bend assignment:\n"
305	>	"    -->%s in Bend[%d] in %s\n",
306	>	current_extra->getlhs(),
307	>	j, comp_stamps[stampID]->getID() );
308	>	painCave.isFatal = 1;
309	>	simError();
310	>	}
311	>
312	>	current_extra = current_extra->getNext();
313		}
314		}
202	–
203	–	#ifdef IS_MPI
204	–	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
205	–	MPIcheckPoint();
206	–	#endif // is_mpi
315
316	<
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++ ){
316	>	if( !theBends[j].isGhost ){
317
318	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
319	<	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();
318	>	exI = theBends[j].a;
319	>	exJ = theBends[j].c;
320		}
321	<
322	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
323	<
324	<	simnfo->n_atoms = tot_atoms;
325	<	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	<
321	>	else{
322	>
323	>	exI = theBends[j].a;
324	>	exJ = theBends[j].b;
325	>	}
326
327	+	// exclude_I must always be the smaller of the pair
328	+	if( exI > exJ ){
329	+	tempEx = exI;
330	+	exI = exJ;
331	+	exJ = tempEx;
332	+	}
333		#ifdef IS_MPI
334	<
335	<	// divide the molecules among processors here.
334	>	tempEx = exI;
335	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
336	>	tempEx = exJ;
337	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
338	>
339	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
340	>	#else  // isn't MPI
341	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
342	>	#endif  //is_mpi
343	>	}
344	>	excludeOffset += molInfo.nBends;
345	>
346	>	for(j=0; j<molInfo.nTorsions; j++){
347
348	<	mpiSim = new mpiSimulation( simnfo );
348	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
349	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
350	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
351	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
352	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
353
354	+	exI = theTorsions[j].a;
355	+	exJ = theTorsions[j].d;
356
357	<
358	<	globalIndex = mpiSim->divideLabor();
359	<
360	<
361	<
362	<	// set up the local variables
357	>	// exclude_I must always be the smaller of the pair
358	>	if( exI > exJ ){
359	>	tempEx = exI;
360	>	exI = exJ;
361	>	exJ = tempEx;
362	>	}
363	>	#ifdef IS_MPI
364	>	tempEx = exI;
365	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
366	>	tempEx = exJ;
367	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
368
369	<	int localMol, allMol;
370	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
371	<
372	<	allMol = 0;
373	<	localMol = 0;
374	<	local_atoms = 0;
375	<	local_bonds = 0;
376	<	local_bends = 0;
377	<	local_torsions = 0;
378	<	for( i=0; i<n_components; i++ ){
369	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
370	>	#else  // isn't MPI
371	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
372	>	#endif  //is_mpi
373	>	}
374	>	excludeOffset += molInfo.nTorsions;
375	>
376	>
377	>	// send the arrays off to the forceField for init.
378	>
379	>	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
380	>	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
381	>	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
382	>	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
383	>
384	>
385	>	info[k].molecules[i].initialize( molInfo );
386
260	–	for( j=0; j<components_nmol[i]; j++ ){
387
388	<	if( mpiSim->getMyMolStart() <= allMol &&
389	<	allMol <= mpiSim->getMyMolEnd() ){
390	<
391	<	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++;
388	>	atomOffset += molInfo.nAtoms;
389	>	delete[] theBonds;
390	>	delete[] theBends;
391	>	delete[] theTorsions;
392		}
393		}
274	–	local_SRI = local_bonds + local_bends + local_torsions;
394
395	<
396	<	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." );
395	>	#ifdef IS_MPI
396	>	sprintf( checkPointMsg, "all molecules initialized succesfully" );
397		MPIcheckPoint();
297	–
298	–
398		#endif // is_mpi
399
400	+	// clean up the forcefield
401
402	<	// create the atom and short range interaction arrays
402	>	the_ff->calcRcut();
403	>	the_ff->cleanMe();
404	>
405	>	}
406
407	<	Atom::createArrays(simnfo->n_atoms);
305	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
407	>	void SimSetup::initFromBass( void ){
408
409	+	int i, j, k;
410	+	int n_cells;
411	+	double cellx, celly, cellz;
412	+	double temp1, temp2, temp3;
413	+	int n_per_extra;
414	+	int n_extra;
415	+	int have_extra, done;
416
417	<	if( simnfo->n_SRI ){
418	<	the_sris = new SRI*[simnfo->n_SRI];
419	<	the_excludes = new int[2 * simnfo->n_SRI];
420	<	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;
417	>	double vel[3];
418	>	vel[0] = 0.0;
419	>	vel[1] = 0.0;
420	>	vel[2] = 0.0;
421
422	<	simnfo->n_exclude = 1;
423	<	}
422	>	temp1 = (double)tot_nmol / 4.0;
423	>	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
424	>	temp3 = ceil( temp2 );
425
426	<	// set the arrays into the SimInfo object
426	>	have_extra =0;
427	>	if( temp2 < temp3 ){ // we have a non-complete lattice
428	>	have_extra =1;
429
430	<	simnfo->atoms = the_atoms;
431	<	simnfo->sr_interactions = the_sris;
432	<	simnfo->nGlobalExcludes = 0;
433	<	simnfo->excludes = the_excludes;
430	>	n_cells = (int)temp3 - 1;
431	>	cellx = info[0].boxL[0] / temp3;
432	>	celly = info[0].boxL[1] / temp3;
433	>	cellz = info[0].boxL[2] / temp3;
434	>	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
435	>	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
436	>	n_per_extra = (int)ceil( temp1 );
437
438	<
334	<	// get some of the tricky things that may still be in the globals
335	<
336	<
337	<	if( the_globals->haveBox() ){
338	<	simnfo->box_x = the_globals->getBox();
339	<	simnfo->box_y = the_globals->getBox();
340	<	simnfo->box_z = the_globals->getBox();
341	<	}
342	<	else if( the_globals->haveDensity() ){
343	<
344	<	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() ){
438	>	if( n_per_extra > 4){
439		sprintf( painCave.errMsg,
440	<	"SimSetup error, no periodic BoxX size given.\n" );
440	>	"SimSetup error. There has been an error in constructing"
441	>	" the non-complete lattice.\n" );
442		painCave.isFatal = 1;
443		simError();
444		}
445	<	simnfo->box_x = the_globals->getBoxX();
446	<
447	<	if( !the_globals->haveBoxY() ){
448	<	sprintf( painCave.errMsg,
449	<	"SimSetup error, no periodic BoxY size given.\n" );
450	<	painCave.isFatal = 1;
451	<	simError();
445	>	}
446	>	else{
447	>	n_cells = (int)temp3;
448	>	cellx = info[0].boxL[0] / temp3;
449	>	celly = info[0].boxL[1] / temp3;
450	>	cellz = info[0].boxL[2] / temp3;
451	>	}
452	>
453	>	current_mol = 0;
454	>	current_comp_mol = 0;
455	>	current_comp = 0;
456	>	current_atom_ndx = 0;
457	>
458	>	for( i=0; i < n_cells ; i++ ){
459	>	for( j=0; j < n_cells; j++ ){
460	>	for( k=0; k < n_cells; k++ ){
461	>
462	>	makeElement( i * cellx,
463	>	j * celly,
464	>	k * cellz );
465	>
466	>	makeElement( i * cellx + 0.5 * cellx,
467	>	j * celly + 0.5 * celly,
468	>	k * cellz );
469	>
470	>	makeElement( i * cellx,
471	>	j * celly + 0.5 * celly,
472	>	k * cellz + 0.5 * cellz );
473	>
474	>	makeElement( i * cellx + 0.5 * cellx,
475	>	j * celly,
476	>	k * cellz + 0.5 * cellz );
477	>	}
478		}
479	<	simnfo->box_y = the_globals->getBoxY();
479	>	}
480
481	<	if( !the_globals->haveBoxZ() ){
482	<	sprintf( painCave.errMsg,
483	<	"SimSetup error, no periodic BoxZ size given.\n" );
484	<	painCave.isFatal = 1;
485	<	simError();
481	>	if( have_extra ){
482	>	done = 0;
483	>
484	>	int start_ndx;
485	>	for( i=0; i < (n_cells+1) && !done; i++ ){
486	>	for( j=0; j < (n_cells+1) && !done; j++ ){
487	>
488	>	if( i < n_cells ){
489	>
490	>	if( j < n_cells ){
491	>	start_ndx = n_cells;
492		}
493	<	simnfo->box_z = the_globals->getBoxZ();
493	>	else start_ndx = 0;
494		}
495	+	else start_ndx = 0;
496
497	<	#ifdef IS_MPI
377	<	strcpy( checkPointMsg, "Box size set up" );
378	<	MPIcheckPoint();
379	<	#endif // is_mpi
497	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
498
499	+	makeElement( i * cellx,
500	+	j * celly,
501	+	k * cellz );
502	+	done = ( current_mol >= tot_nmol );
503
504	<	// initialize the arrays
504	>	if( !done && n_per_extra > 1 ){
505	>	makeElement( i * cellx + 0.5 * cellx,
506	>	j * celly + 0.5 * celly,
507	>	k * cellz );
508	>	done = ( current_mol >= tot_nmol );
509	>	}
510
511	<	the_ff->setSimInfo( simnfo );
511	>	if( !done && n_per_extra > 2){
512	>	makeElement( i * cellx,
513	>	j * celly + 0.5 * celly,
514	>	k * cellz + 0.5 * cellz );
515	>	done = ( current_mol >= tot_nmol );
516	>	}
517
518	<	makeAtoms();
519	<	simnfo->identArray = new int[simnfo->n_atoms];
520	<	for(i=0; i<simnfo->n_atoms; i++){
521	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
518	>	if( !done && n_per_extra > 3){
519	>	makeElement( i * cellx + 0.5 * cellx,
520	>	j * celly,
521	>	k * cellz + 0.5 * cellz );
522	>	done = ( current_mol >= tot_nmol );
523	>	}
524		}
525	<
526	<	if( tot_bonds ){
393	<	makeBonds();
525	>	}
526	>	}
527		}
528
529	<	if( tot_bends ){
530	<	makeBends();
529	>	for( i=0; i<info[0].n_atoms; i++ ){
530	>	info[0].atoms[i]->setVel( vel );
531		}
532	+	}
533
534	<	if( tot_torsions ){
401	<	makeTorsions();
402	<	}
534	>	void SimSetup::makeElement( double x, double y, double z ){
535
536	+	int k;
537	+	AtomStamp* current_atom;
538	+	DirectionalAtom* dAtom;
539	+	double rotMat[3][3];
540	+	double pos[3];
541
542	<	if (the_globals->getUseRF() ) {
406	<	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	<	}
542	>	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
543
544	<	if( !the_globals->haveEST() ){
544	>	current_atom = comp_stamps[current_comp]->getAtom( k );
545	>	if( !current_atom->havePosition() ){
546		sprintf( painCave.errMsg,
547	<	"SimSetup Warning: using default value of 0.05 * the "
548	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
549	<	);
550	<	painCave.isFatal = 0;
551	<	simError();
552	<	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	<	);
547	>	"SimSetup:initFromBass error.\n"
548	>	"\tComponent %s, atom %s does not have a position specified.\n"
549	>	"\tThe initialization routine is unable to give a start"
550	>	" position.\n",
551	>	comp_stamps[current_comp]->getID(),
552	>	current_atom->getType() );
553		painCave.isFatal = 1;
554		simError();
555		}
556	<	simnfo->dielectric = the_globals->getDielectric();
557	<	} else {
558	<	if (simnfo->n_dipoles) {
559	<
560	<	if( !the_globals->haveECR() ){
561	<	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	<	}
556	>
557	>	pos[0] = x + current_atom->getPosX();
558	>	pos[1] = y + current_atom->getPosY();
559	>	pos[2] = z + current_atom->getPosZ();
560	>
561	>	info[0].atoms[current_atom_ndx]->setPos( pos );
562
563	<	#ifdef IS_MPI
480	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
481	<	MPIcheckPoint();
482	<	#endif // is_mpi
563	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
564
565	<	if( the_globals->haveInitialConfig() ){
485	<
486	<	InitializeFromFile* fileInit;
487	<	#ifdef IS_MPI // is_mpi
488	<	if( worldRank == 0 ){
489	<	#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
565	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
566
567	<	delete fileInit;
568	<	}
569	<	else{
567	>	rotMat[0][0] = 1.0;
568	>	rotMat[0][1] = 0.0;
569	>	rotMat[0][2] = 0.0;
570
571	<	#ifdef IS_MPI
571	>	rotMat[1][0] = 0.0;
572	>	rotMat[1][1] = 1.0;
573	>	rotMat[1][2] = 0.0;
574
575	<	// no init from bass
576	<
577	<	sprintf( painCave.errMsg,
505	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
506	<	painCave.isFatal;
507	<	simError();
508	<
509	<	#else
575	>	rotMat[2][0] = 0.0;
576	>	rotMat[2][1] = 0.0;
577	>	rotMat[2][2] = 1.0;
578
579	<	initFromBass();
579	>	dAtom->setA( rotMat );
580	>	}
581
582	+	current_atom_ndx++;
583	+	}
584
585	<	#endif
586	<	}
585	>	current_mol++;
586	>	current_comp_mol++;
587
588	<	#ifdef IS_MPI
518	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
519	<	MPIcheckPoint();
520	<	#endif // is_mpi
588	>	if( current_comp_mol >= components_nmol[current_comp] ){
589
590	+	current_comp_mol = 0;
591	+	current_comp++;
592	+	}
593	+	}
594
523	–
524	–
525	–
595
596	<
597	<	#ifdef IS_MPI
529	<	if( worldRank == 0 ){
530	<	#endif // is_mpi
531	<
532	<	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	<	}
596	>	void SimSetup::gatherInfo( void ){
597	>	int i,j,k;
598
599	<	if( the_globals->haveStatusTime() ){
600	<	simnfo->statusTime = the_globals->getStatusTime();
626	<	}
599	>	ensembleCase = -1;
600	>	ffCase = -1;
601
602	<	if( the_globals->haveThermalTime() ){
603	<	simnfo->thermalTime = the_globals->getThermalTime();
602	>	// set the easy ones first
603	>
604	>	for( i=0; i<nInfo; i++){
605	>	info[i].target_temp = globals->getTargetTemp();
606	>	info[i].dt = globals->getDt();
607	>	info[i].run_time = globals->getRunTime();
608		}
609	+	n_components = globals->getNComponents();
610
632	–	// check for the temperature set flag
611
612	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
612	>	// get the forceField
613
614	+	strcpy( force_field, globals->getForceField() );
615
616	<	//   // make the longe range forces and the integrator
617	<
618	<	//   new AllLong( simnfo );
640	<
641	<	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 );
654	<	}
655	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
656	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
657	<	}
616	>	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
617	>	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
618	>	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
619		else{
620		sprintf( painCave.errMsg,
621	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
622	<	simnfo->mixingRule );
621	>	"SimSetup Error. Unrecognized force field -> %s\n",
622	>	force_field );
623		painCave.isFatal = 1;
624		simError();
625		}
626
627	+	// get the ensemble
628
629	<	#ifdef IS_MPI
668	<	strcpy( checkPointMsg,
669	<	"Successfully intialized the mixingRule for Fortran." );
670	<	MPIcheckPoint();
671	<	#endif // is_mpi
672	<	}
629	>	strcpy( ensemble, globals->getEnsemble() );
630
631	+	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
632	+	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
633	+	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
634	+	ensembleCase = NPTi_ENS;
635	+	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
636	+	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
637	+	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
638	+	else{
639	+	sprintf( painCave.errMsg,
640	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
641	+	"reverting to NVE for this simulation.\n",
642	+	ensemble );
643	+	painCave.isFatal = 0;
644	+	simError();
645	+	strcpy( ensemble, "NVE" );
646	+	ensembleCase = NVE_ENS;
647	+	}
648	+
649	+	for(i=0; i<nInfo; i++){
650	+
651	+	strcpy( info[i].ensemble, ensemble );
652
653	<	void SimSetup::makeMolecules( void ){
653	>	// get the mixing rule
654
655	<	int i, j, exI, exJ, tempEx, stampID, atomOffset;
656	<	molInit info;
657	<	DirectionalAtom* dAtom;
680	<	AtomStamp* currentAtom;
681	<	BondStamp* currentBond;
682	<	BendStamp* currentBend;
683	<	TorsionStamp* currentTorsion;
655	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
656	>	info[i].usePBC = globals->getPBC();
657	>	}
658
659	<	//init the forceField paramters
659	>	// get the components and calculate the tot_nMol and indvidual n_mol
660	>
661	>	the_components = globals->getComponents();
662	>	components_nmol = new int[n_components];
663
687	–	the_ff->readParams();
664
665	<
666	<	// init the molecules
665	>	if( !globals->haveNMol() ){
666	>	// we don't have the total number of molecules, so we assume it is
667	>	// given in each component
668
669	<	atomOffset = 0;
670	<	for(i=0; i<simnfo->n_mol; i++){
694	<
695	<	stampID = the_molecules[i].getStampID();
669	>	tot_nmol = 0;
670	>	for( i=0; i<n_components; i++ ){
671
672	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
673	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
674	<	info.nBends    = comp_stamps[stampID]->getNBends();
675	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
676	<
677	<	info.myAtoms = &the_atoms[atomOffset];
678	<	info.myBonds = new Bond*[info.nBonds];
679	<	info.myBends = new Bend*[info.nBends];
705	<	info.myTorsions = new Torsions*[info.nTorsions];
672	>	if( !the_components[i]->haveNMol() ){
673	>	// we have a problem
674	>	sprintf( painCave.errMsg,
675	>	"SimSetup Error. No global NMol or component NMol"
676	>	" given. Cannot calculate the number of atoms.\n" );
677	>	painCave.isFatal = 1;
678	>	simError();
679	>	}
680
681	<	theBonds = new bond_pair[info.nBonds];
682	<	theBends = new bend_set[info.nBends];
683	<	theTorsions = new torsion_set[info.nTorsions];
684	<
685	<	// make the Atoms
686	<
687	<	for(j=0; j<info.nAtoms; j++){
688	<
689	<	currentAtom = theComponents[stampID]->getAtom( j );
690	<	if( currentAtom->haveOrientation() ){
691	<
692	<	dAtom = new DirectionalAtom(j + atomOffset);
693	<	simnfo->n_oriented++;
694	<	info.myAtoms[j] = dAtom;
695	<
696	<	ux = currentAtom->getOrntX();
697	<	uy = currentAtom->getOrntY();
698	<	uz = currentAtom->getOrntZ();
699	<
700	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
701	<
702	<	u = sqrt( uSqr );
703	<	ux = ux / u;
704	<	uy = uy / u;
705	<	uz = uz / u;
706	<
707	<	dAtom->setSUx( ux );
708	<	dAtom->setSUy( uy );
709	<	dAtom->setSUz( uz );
736	<	}
737	<	else{
738	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
739	<	}
740	<	info.myAtoms[j]->setType( currentAtom->getType() );
681	>	tot_nmol += the_components[i]->getNMol();
682	>	components_nmol[i] = the_components[i]->getNMol();
683	>	}
684	>	}
685	>	else{
686	>	sprintf( painCave.errMsg,
687	>	"SimSetup error.\n"
688	>	"\tSorry, the ability to specify total"
689	>	" nMols and then give molfractions in the components\n"
690	>	"\tis not currently supported."
691	>	" Please give nMol in the components.\n" );
692	>	painCave.isFatal = 1;
693	>	simError();
694	>	}
695	>
696	>	// set the status, sample, and thermal kick times
697	>
698	>	for(i=0; i<nInfo; i++){
699	>
700	>	if( globals->haveSampleTime() ){
701	>	info[i].sampleTime = globals->getSampleTime();
702	>	info[i].statusTime = info[i].sampleTime;
703	>	info[i].thermalTime = info[i].sampleTime;
704	>	}
705	>	else{
706	>	info[i].sampleTime = globals->getRunTime();
707	>	info[i].statusTime = info[i].sampleTime;
708	>	info[i].thermalTime = info[i].sampleTime;
709	>	}
710
711	<	#ifdef IS_MPI
712	<
713	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
745	<
746	<	#endif // is_mpi
747	<	}
711	>	if( globals->haveStatusTime() ){
712	>	info[i].statusTime = globals->getStatusTime();
713	>	}
714
715	<	// make the bonds
716	<	for(j=0; j<nBonds; j++){
717	<
752	<	currentBond = comp_stamps[stampID]->getBond( j );
753	<	theBonds[j].a = currentBond->getA() + atomOffset;
754	<	theBonds[j].b = currentBond->getB() + atomOffset;
715	>	if( globals->haveThermalTime() ){
716	>	info[i].thermalTime = globals->getThermalTime();
717	>	}
718
719	<	exI = theBonds[i].a;
757	<	exJ = theBonds[i].b;
719	>	// check for the temperature set flag
720
721	<	// exclude_I must always be the smaller of the pair
722	<	if( exI > exJ ){
723	<	tempEx = exI;
724	<	exI = exJ;
725	<	exJ = tempEx;
721	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
722	>
723	>	// get some of the tricky things that may still be in the globals
724	>
725	>	double boxVector[3];
726	>	if( globals->haveBox() ){
727	>	boxVector[0] = globals->getBox();
728	>	boxVector[1] = globals->getBox();
729	>	boxVector[2] = globals->getBox();
730	>
731	>	info[i].setBox( boxVector );
732	>	}
733	>	else if( globals->haveDensity() ){
734	>
735	>	double vol;
736	>	vol = (double)tot_nmol / globals->getDensity();
737	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
738	>	boxVector[1] = boxVector[0];
739	>	boxVector[2] = boxVector[0];
740	>
741	>	info[i].setBox( boxVector );
742	>	}
743	>	else{
744	>	if( !globals->haveBoxX() ){
745	>	sprintf( painCave.errMsg,
746	>	"SimSetup error, no periodic BoxX size given.\n" );
747	>	painCave.isFatal = 1;
748	>	simError();
749		}
750	<	#ifdef IS_MPI
750	>	boxVector[0] = globals->getBoxX();
751
752	<	the_excludes[index*2] =
753	<	the_atoms[exI]->getGlobalIndex() + 1;
754	<	the_excludes[index*2 + 1] =
755	<	the_atoms[exJ]->getGlobalIndex() + 1;
752	>	if( !globals->haveBoxY() ){
753	>	sprintf( painCave.errMsg,
754	>	"SimSetup error, no periodic BoxY size given.\n" );
755	>	painCave.isFatal = 1;
756	>	simError();
757	>	}
758	>	boxVector[1] = globals->getBoxY();
759
760	<	#else  // isn't MPI
760	>	if( !globals->haveBoxZ() ){
761	>	sprintf( painCave.errMsg,
762	>	"SimSetup error, no periodic BoxZ size given.\n" );
763	>	painCave.isFatal = 1;
764	>	simError();
765	>	}
766	>	boxVector[2] = globals->getBoxZ();
767
768	<	the_excludes[index*2] =     exI + 1;
769	<	the_excludes[index*2 + 1] = exJ + 1;
776	<	// fortran index from 1 (hence the +1 in the indexing)
777	<
778	<	#endif  //is_mpi
779	<
768	>	info[i].setBox( boxVector );
769	>	}
770		}
771
772	+	int seedValue;
773	+	struct timeval now_time_val;
774	+	struct timezone time_zone;
775
776	+	if(globals->haveSeed()){
777	+	seedValue = globals->getSeed();
778	+	}
779	+	else{
780	+	#ifndef IS_MPI
781	+	gettimeofday(&now_time_val, &time_zone);  // get the time now
782	+	seedValue = (int) now_time_val.tv_sec;      //  convert to epoch time
783	+	#else
784	+	if(worldRank == 0){
785	+	gettimeofday(&now_time_val, &time_zone);  // get the time now
786	+	seedValue = (int) now_time_val.tv_sec;      //  convert to epoch time
787	+	}
788	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
789	+	#endif
790	+	}
791
792	+	for(int i = 0; i < nInfo; i++){
793	+	info[i].setSeed(seedValue);
794	+	}
795
796	+	#ifdef IS_MPI
797	+	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
798	+	MPIcheckPoint();
799	+	#endif // is_mpi
800
801	+	}
802
803
804	+	void SimSetup::finalInfoCheck( void ){
805	+	int index;
806	+	int usesDipoles;
807	+	int i;
808
809	+	for(i=0; i<nInfo; i++){
810	+	// check electrostatic parameters
811	+
812	+	index = 0;
813	+	usesDipoles = 0;
814	+	while( (index < info[i].n_atoms) && !usesDipoles ){
815	+	usesDipoles = (info[i].atoms[index])->hasDipole();
816	+	index++;
817	+	}
818	+
819	+	#ifdef IS_MPI
820	+	int myUse = usesDipoles;
821	+	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
822	+	#endif //is_mpi
823	+
824	+	double theEcr, theEst;
825	+
826	+	if (globals->getUseRF() ) {
827	+	info[i].useReactionField = 1;
828	+
829	+	if( !globals->haveECR() ){
830	+	sprintf( painCave.errMsg,
831	+	"SimSetup Warning: using default value of 1/2 the smallest "
832	+	"box length for the electrostaticCutoffRadius.\n"
833	+	"I hope you have a very fast processor!\n");
834	+	painCave.isFatal = 0;
835	+	simError();
836	+	double smallest;
837	+	smallest = info[i].boxL[0];
838	+	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
839	+	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
840	+	theEcr = 0.5 * smallest;
841	+	} else {
842	+	theEcr = globals->getECR();
843	+	}
844	+
845	+	if( !globals->haveEST() ){
846	+	sprintf( painCave.errMsg,
847	+	"SimSetup Warning: using default value of 0.05 * the "
848	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
849	+	);
850	+	painCave.isFatal = 0;
851	+	simError();
852	+	theEst = 0.05 * theEcr;
853	+	} else {
854	+	theEst= globals->getEST();
855	+	}
856	+
857	+	info[i].setEcr( theEcr, theEst );
858	+
859	+	if(!globals->haveDielectric() ){
860	+	sprintf( painCave.errMsg,
861	+	"SimSetup Error: You are trying to use Reaction Field without"
862	+	"setting a dielectric constant!\n"
863	+	);
864	+	painCave.isFatal = 1;
865	+	simError();
866	+	}
867	+	info[i].dielectric = globals->getDielectric();
868	+	}
869	+	else {
870	+	if (usesDipoles) {
871	+
872	+	if( !globals->haveECR() ){
873	+	sprintf( painCave.errMsg,
874	+	"SimSetup Warning: using default value of 1/2 the smallest "
875	+	"box length for the electrostaticCutoffRadius.\n"
876	+	"I hope you have a very fast processor!\n");
877	+	painCave.isFatal = 0;
878	+	simError();
879	+	double smallest;
880	+	smallest = info[i].boxL[0];
881	+	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
882	+	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
883	+	theEcr = 0.5 * smallest;
884	+	} else {
885	+	theEcr = globals->getECR();
886	+	}
887	+
888	+	if( !globals->haveEST() ){
889	+	sprintf( painCave.errMsg,
890	+	"SimSetup Warning: using default value of 0.05 * the "
891	+	"electrostaticCutoffRadius for the "
892	+	"electrostaticSkinThickness\n"
893	+	);
894	+	painCave.isFatal = 0;
895	+	simError();
896	+	theEst = 0.05 * theEcr;
897	+	} else {
898	+	theEst= globals->getEST();
899	+	}
900	+
901	+	info[i].setEcr( theEcr, theEst );
902	+	}
903	+	}
904	+	}
905
906	+	#ifdef IS_MPI
907	+	strcpy( checkPointMsg, "post processing checks out" );
908	+	MPIcheckPoint();
909	+	#endif // is_mpi
910
911	+	}
912
913	+	void SimSetup::initSystemCoords( void ){
914	+	int i;
915	+
916	+	char* inName;
917
918	+	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
919
920	+	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
921	+
922	+	if( globals->haveInitialConfig() ){
923	+
924	+	InitializeFromFile* fileInit;
925	+	#ifdef IS_MPI // is_mpi
926	+	if( worldRank == 0 ){
927	+	#endif //is_mpi
928	+	inName = globals->getInitialConfig();
929	+	double* tempDouble = new double[1000000];
930	+	fileInit = new InitializeFromFile( inName );
931	+	#ifdef IS_MPI
932	+	}else fileInit = new InitializeFromFile( NULL );
933	+	#endif
934	+	fileInit->readInit( info ); // default velocities on
935	+
936	+	delete fileInit;
937	+	}
938	+	else{
939	+
940	+	#ifdef IS_MPI
941	+
942	+	// no init from bass
943	+
944	+	sprintf( painCave.errMsg,
945	+	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
946	+	painCave.isFatal;
947	+	simError();
948	+
949	+	#else
950	+
951	+	initFromBass();
952	+
953	+
954	+	#endif
955	+	}
956	+
957	+	#ifdef IS_MPI
958	+	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
959	+	MPIcheckPoint();
960	+	#endif // is_mpi
961	+
962	+	}
963
964
965	<	void SimSetup::makeAtoms( void ){
965	>	void SimSetup::makeOutNames( void ){
966	>
967	>	int k;
968
969	<	int i, j, k, index;
970	<	double ux, uy, uz, uSqr, u;
800	<	AtomStamp* current_atom;
969	>
970	>	for(k=0; k<nInfo; k++){
971
802	–	DirectionalAtom* dAtom;
803	–	int molIndex, molStart, molEnd, nMemb, lMolIndex;
804	–
805	–	lMolIndex = 0;
806	–	molIndex = 0;
807	–	index = 0;
808	–	for( i=0; i<n_components; i++ ){
809	–
810	–	for( j=0; j<components_nmol[i]; j++ ){
811	–
972		#ifdef IS_MPI
973	<	if( mpiSim->getMyMolStart() <= molIndex &&
974	<	molIndex <= mpiSim->getMyMolEnd() ){
815	<	#endif // is_mpi
816	<
817	<	molStart = index;
818	<	nMemb = comp_stamps[i]->getNAtoms();
819	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
820	<
821	<	current_atom = comp_stamps[i]->getAtom( k );
822	<	if( current_atom->haveOrientation() ){
823	<
824	<	dAtom = new DirectionalAtom(index);
825	<	simnfo->n_oriented++;
826	<	the_atoms[index] = dAtom;
827	<
828	<	ux = current_atom->getOrntX();
829	<	uy = current_atom->getOrntY();
830	<	uz = current_atom->getOrntZ();
831	<
832	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
833	<
834	<	u = sqrt( uSqr );
835	<	ux = ux / u;
836	<	uy = uy / u;
837	<	uz = uz / u;
838	<
839	<	dAtom->setSUx( ux );
840	<	dAtom->setSUy( uy );
841	<	dAtom->setSUz( uz );
842	<	}
843	<	else{
844	<	the_atoms[index] = new GeneralAtom(index);
845	<	}
846	<	the_atoms[index]->setType( current_atom->getType() );
847	<	the_atoms[index]->setIndex( index );
848	<
849	<	// increment the index and repeat;
850	<	index++;
851	<	}
852	<
853	<	molEnd = index -1;
854	<	the_molecules[lMolIndex].setNMembers( nMemb );
855	<	the_molecules[lMolIndex].setStartAtom( molStart );
856	<	the_molecules[lMolIndex].setEndAtom( molEnd );
857	<	the_molecules[lMolIndex].setStampID( i );
858	<	lMolIndex++;
859	<
860	<	#ifdef IS_MPI
861	<	}
862	<	#endif //is_mpi
973	>	if( worldRank == 0 ){
974	>	#endif // is_mpi
975
976	<	molIndex++;
976	>	if( globals->haveFinalConfig() ){
977	>	strcpy( info[k].finalName, globals->getFinalConfig() );
978	>	}
979	>	else{
980	>	strcpy( info[k].finalName, inFileName );
981	>	char* endTest;
982	>	int nameLength = strlen( info[k].finalName );
983	>	endTest = &(info[k].finalName[nameLength - 5]);
984	>	if( !strcmp( endTest, ".bass" ) ){
985	>	strcpy( endTest, ".eor" );
986	>	}
987	>	else if( !strcmp( endTest, ".BASS" ) ){
988	>	strcpy( endTest, ".eor" );
989	>	}
990	>	else{
991	>	endTest = &(info[k].finalName[nameLength - 4]);
992	>	if( !strcmp( endTest, ".bss" ) ){
993	>	strcpy( endTest, ".eor" );
994		}
995	+	else if( !strcmp( endTest, ".mdl" ) ){
996	+	strcpy( endTest, ".eor" );
997	+	}
998	+	else{
999	+	strcat( info[k].finalName, ".eor" );
1000	+	}
1001		}
1002	<
1002	>	}
1003	>
1004	>	// make the sample and status out names
1005	>
1006	>	strcpy( info[k].sampleName, inFileName );
1007	>	char* endTest;
1008	>	int nameLength = strlen( info[k].sampleName );
1009	>	endTest = &(info[k].sampleName[nameLength - 5]);
1010	>	if( !strcmp( endTest, ".bass" ) ){
1011	>	strcpy( endTest, ".dump" );
1012	>	}
1013	>	else if( !strcmp( endTest, ".BASS" ) ){
1014	>	strcpy( endTest, ".dump" );
1015	>	}
1016	>	else{
1017	>	endTest = &(info[k].sampleName[nameLength - 4]);
1018	>	if( !strcmp( endTest, ".bss" ) ){
1019	>	strcpy( endTest, ".dump" );
1020	>	}
1021	>	else if( !strcmp( endTest, ".mdl" ) ){
1022	>	strcpy( endTest, ".dump" );
1023	>	}
1024	>	else{
1025	>	strcat( info[k].sampleName, ".dump" );
1026	>	}
1027	>	}
1028	>
1029	>	strcpy( info[k].statusName, inFileName );
1030	>	nameLength = strlen( info[k].statusName );
1031	>	endTest = &(info[k].statusName[nameLength - 5]);
1032	>	if( !strcmp( endTest, ".bass" ) ){
1033	>	strcpy( endTest, ".stat" );
1034	>	}
1035	>	else if( !strcmp( endTest, ".BASS" ) ){
1036	>	strcpy( endTest, ".stat" );
1037	>	}
1038	>	else{
1039	>	endTest = &(info[k].statusName[nameLength - 4]);
1040	>	if( !strcmp( endTest, ".bss" ) ){
1041	>	strcpy( endTest, ".stat" );
1042	>	}
1043	>	else if( !strcmp( endTest, ".mdl" ) ){
1044	>	strcpy( endTest, ".stat" );
1045	>	}
1046	>	else{
1047	>	strcat( info[k].statusName, ".stat" );
1048	>	}
1049	>	}
1050	>
1051		#ifdef IS_MPI
1052	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
1053	<
1054	<	delete[] globalIndex;
872	<
873	<	mpiSim->mpiRefresh();
874	<	#endif //IS_MPI
875	<
876	<	the_ff->initializeAtoms();
1052	>	}
1053	>	#endif // is_mpi
1054	>	}
1055		}
1056
879	–	void SimSetup::makeBonds( void ){
1057
1058	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1059	<	bond_pair* the_bonds;
1060	<	BondStamp* current_bond;
1058	>	void SimSetup::sysObjectsCreation( void ){
1059	>
1060	>	int i,k;
1061	>
1062	>	// create the forceField
1063
1064	<	the_bonds = new bond_pair[tot_bonds];
886	<	index = 0;
887	<	offset = 0;
888	<	molIndex = 0;
1064	>	createFF();
1065
1066	<	for( i=0; i<n_components; i++ ){
1066	>	// extract componentList
1067
1068	<	for( j=0; j<components_nmol[i]; j++ ){
1068	>	compList();
1069
1070	<	#ifdef IS_MPI
895	<	if( mpiSim->getMyMolStart() <= molIndex &&
896	<	molIndex <= mpiSim->getMyMolEnd() ){
897	<	#endif // is_mpi
898	<
899	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
900	<
901	<	current_bond = comp_stamps[i]->getBond( k );
902	<	the_bonds[index].a = current_bond->getA() + offset;
903	<	the_bonds[index].b = current_bond->getB() + offset;
1070	>	// calc the number of atoms, bond, bends, and torsions
1071
1072	<	exI = the_bonds[index].a;
906	<	exJ = the_bonds[index].b;
1072	>	calcSysValues();
1073
908	–	// exclude_I must always be the smaller of the pair
909	–	if( exI > exJ ){
910	–	tempEx = exI;
911	–	exI = exJ;
912	–	exJ = tempEx;
913	–	}
914	–
915	–
1074		#ifdef IS_MPI
1075	<
1076	<	the_excludes[index*2] =
1077	<	the_atoms[exI]->getGlobalIndex() + 1;
920	<	the_excludes[index*2 + 1] =
921	<	the_atoms[exJ]->getGlobalIndex() + 1;
922	<
923	<	#else  // isn't MPI
924	<
925	<	the_excludes[index*2] =     exI + 1;
926	<	the_excludes[index*2 + 1] = exJ + 1;
927	<	// fortran index from 1 (hence the +1 in the indexing)
928	<	#endif  //is_mpi
929	<
930	<	// increment the index and repeat;
931	<	index++;
932	<	}
933	<	offset += comp_stamps[i]->getNAtoms();
934	<
935	<	#ifdef IS_MPI
936	<	}
1075	>	// divide the molecules among the processors
1076	>
1077	>	mpiMolDivide();
1078		#endif //is_mpi
1079	<
1080	<	molIndex++;
1081	<	}
1082	<	}
1079	>
1080	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1081	>
1082	>	makeSysArrays();
1083
1084	<	the_ff->initializeBonds( the_bonds );
1084	>	// make and initialize the molecules (all but atomic coordinates)
1085	>
1086	>	makeMolecules();
1087	>
1088	>	for(k=0; k<nInfo; k++){
1089	>	info[k].identArray = new int[info[k].n_atoms];
1090	>	for(i=0; i<info[k].n_atoms; i++){
1091	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1092	>	}
1093	>	}
1094		}
1095
946	–	void SimSetup::makeBends( void ){
1096
1097	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
949	<	bend_set* the_bends;
950	<	BendStamp* current_bend;
951	<	LinkedAssign* extras;
952	<	LinkedAssign* current_extra;
953	<
1097	>	void SimSetup::createFF( void ){
1098
1099	<	the_bends = new bend_set[tot_bends];
956	<	index = 0;
957	<	offset = 0;
958	<	molIndex = 0;
959	<	for( i=0; i<n_components; i++ ){
1099	>	switch( ffCase ){
1100
1101	<	for( j=0; j<components_nmol[i]; j++ ){
1101	>	case FF_DUFF:
1102	>	the_ff = new DUFF();
1103	>	break;
1104
1105	<	#ifdef IS_MPI
1106	<	if( mpiSim->getMyMolStart() <= molIndex &&
1107	<	molIndex <= mpiSim->getMyMolEnd() ){
966	<	#endif // is_mpi
1105	>	case FF_LJ:
1106	>	the_ff = new LJFF();
1107	>	break;
1108
1109	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
1110	<
1111	<	current_bend = comp_stamps[i]->getBend( k );
971	<	the_bends[index].a = current_bend->getA() + offset;
972	<	the_bends[index].b = current_bend->getB() + offset;
973	<	the_bends[index].c = current_bend->getC() + offset;
974	<
975	<	if( current_bend->haveExtras() ){
976	<
977	<	extras = current_bend->getExtras();
978	<	current_extra = extras;
979	<
980	<	while( current_extra != NULL ){
981	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
982	<
983	<	switch( current_extra->getType() ){
984	<
985	<	case 0:
986	<	the_bends[index].ghost =
987	<	current_extra->getInt() + offset;
988	<	the_bends[index].isGhost = 1;
989	<	break;
990	<
991	<	case 1:
992	<	the_bends[index].ghost =
993	<	(int)current_extra->getDouble() + offset;
994	<	the_bends[index].isGhost = 1;
995	<	break;
996	<
997	<	default:
998	<	sprintf( painCave.errMsg,
999	<	"SimSetup Error: ghostVectorSource was neiter a "
1000	<	"double nor an int.\n"
1001	<	"-->Bend[%d] in %s\n",
1002	<	k, comp_stamps[i]->getID() );
1003	<	painCave.isFatal = 1;
1004	<	simError();
1005	<	}
1006	<	}
1007	<
1008	<	else{
1009	<
1010	<	sprintf( painCave.errMsg,
1011	<	"SimSetup Error: unhandled bend assignment:\n"
1012	<	"    -->%s in Bend[%d] in %s\n",
1013	<	current_extra->getlhs(),
1014	<	k, comp_stamps[i]->getID() );
1015	<	painCave.isFatal = 1;
1016	<	simError();
1017	<	}
1018	<
1019	<	current_extra = current_extra->getNext();
1020	<	}
1021	<	}
1022	<
1023	<	if( !the_bends[index].isGhost ){
1024	<
1025	<	exI = the_bends[index].a;
1026	<	exJ = the_bends[index].c;
1027	<	}
1028	<	else{
1029	<
1030	<	exI = the_bends[index].a;
1031	<	exJ = the_bends[index].b;
1032	<	}
1033	<
1034	<	// exclude_I must always be the smaller of the pair
1035	<	if( exI > exJ ){
1036	<	tempEx = exI;
1037	<	exI = exJ;
1038	<	exJ = tempEx;
1039	<	}
1109	>	case FF_EAM:
1110	>	the_ff = new EAM_FF();
1111	>	break;
1112
1113	<
1114	<	#ifdef IS_MPI
1115	<
1116	<	the_excludes[(index + tot_bonds)*2] =
1117	<	the_atoms[exI]->getGlobalIndex() + 1;
1046	<	the_excludes[(index + tot_bonds)*2 + 1] =
1047	<	the_atoms[exJ]->getGlobalIndex() + 1;
1048	<
1049	<	#else  // isn't MPI
1050	<
1051	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
1052	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1053	<	// fortran index from 1 (hence the +1 in the indexing)
1054	<	#endif  //is_mpi
1055	<
1056	<
1057	<	// increment the index and repeat;
1058	<	index++;
1059	<	}
1060	<	offset += comp_stamps[i]->getNAtoms();
1061	<
1062	<	#ifdef IS_MPI
1063	<	}
1064	<	#endif //is_mpi
1065	<
1066	<	molIndex++;
1067	<	}
1113	>	default:
1114	>	sprintf( painCave.errMsg,
1115	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1116	>	painCave.isFatal = 1;
1117	>	simError();
1118		}
1119
1120		#ifdef IS_MPI
1121	<	sprintf( checkPointMsg,
1072	<	"Successfully created the bends list.\n" );
1121	>	strcpy( checkPointMsg, "ForceField creation successful" );
1122		MPIcheckPoint();
1123		#endif // is_mpi
1075	–
1124
1077	–	the_ff->initializeBends( the_bends );
1125		}
1126
1080	–	void SimSetup::makeTorsions( void ){
1127
1128	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1083	<	torsion_set* the_torsions;
1084	<	TorsionStamp* current_torsion;
1128	>	void SimSetup::compList( void ){
1129
1130	<	the_torsions = new torsion_set[tot_torsions];
1131	<	index = 0;
1132	<	offset = 0;
1133	<	molIndex = 0;
1134	<	for( i=0; i<n_components; i++ ){
1135	<
1136	<	for( j=0; j<components_nmol[i]; j++ ){
1137	<
1138	<	#ifdef IS_MPI
1139	<	if( mpiSim->getMyMolStart() <= molIndex &&
1140	<	molIndex <= mpiSim->getMyMolEnd() ){
1141	<	#endif // is_mpi
1142	<
1143	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1144	<
1145	<	current_torsion = comp_stamps[i]->getTorsion( k );
1102	<	the_torsions[index].a = current_torsion->getA() + offset;
1103	<	the_torsions[index].b = current_torsion->getB() + offset;
1104	<	the_torsions[index].c = current_torsion->getC() + offset;
1105	<	the_torsions[index].d = current_torsion->getD() + offset;
1106	<
1107	<	exI = the_torsions[index].a;
1108	<	exJ = the_torsions[index].d;
1109	<
1110	<
1111	<	// exclude_I must always be the smaller of the pair
1112	<	if( exI > exJ ){
1113	<	tempEx = exI;
1114	<	exI = exJ;
1115	<	exJ = tempEx;
1116	<	}
1130	>	int i;
1131	>	char* id;
1132	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1133	>	LinkedMolStamp* currentStamp = NULL;
1134	>	comp_stamps = new MoleculeStamp*[n_components];
1135	>
1136	>	// make an array of molecule stamps that match the components used.
1137	>	// also extract the used stamps out into a separate linked list
1138	>
1139	>	for(i=0; i<nInfo; i++){
1140	>	info[i].nComponents = n_components;
1141	>	info[i].componentsNmol = components_nmol;
1142	>	info[i].compStamps = comp_stamps;
1143	>	info[i].headStamp = headStamp;
1144	>	}
1145	>
1146
1147	+	for( i=0; i<n_components; i++ ){
1148
1149	<	#ifdef IS_MPI
1150	<
1151	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
1152	<	the_atoms[exI]->getGlobalIndex() + 1;
1123	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1124	<	the_atoms[exJ]->getGlobalIndex() + 1;
1125	<
1126	<	#else  // isn't MPI
1127	<
1128	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1129	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1130	<	// fortran indexes from 1 (hence the +1 in the indexing)
1131	<	#endif  //is_mpi
1132	<
1149	>	id = the_components[i]->getType();
1150	>	comp_stamps[i] = NULL;
1151	>
1152	>	// check to make sure the component isn't already in the list
1153
1154	<	// increment the index and repeat;
1155	<	index++;
1154	>	comp_stamps[i] = headStamp->match( id );
1155	>	if( comp_stamps[i] == NULL ){
1156	>
1157	>	// extract the component from the list;
1158	>
1159	>	currentStamp = stamps->extractMolStamp( id );
1160	>	if( currentStamp == NULL ){
1161	>	sprintf( painCave.errMsg,
1162	>	"SimSetup error: Component \"%s\" was not found in the "
1163	>	"list of declared molecules\n",
1164	>	id );
1165	>	painCave.isFatal = 1;
1166	>	simError();
1167		}
1168	<	offset += comp_stamps[i]->getNAtoms();
1168	>
1169	>	headStamp->add( currentStamp );
1170	>	comp_stamps[i] = headStamp->match( id );
1171	>	}
1172	>	}
1173
1174		#ifdef IS_MPI
1175	<	}
1176	<	#endif //is_mpi
1175	>	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1176	>	MPIcheckPoint();
1177	>	#endif // is_mpi
1178
1143	–	molIndex++;
1144	–	}
1145	–	}
1179
1147	–	the_ff->initializeTorsions( the_torsions );
1180		}
1181
1182	<	void SimSetup::initFromBass( void ){
1182	>	void SimSetup::calcSysValues( void ){
1183	>	int i, j, k;
1184	>
1185	>	int *molMembershipArray;
1186	>
1187	>	tot_atoms = 0;
1188	>	tot_bonds = 0;
1189	>	tot_bends = 0;
1190	>	tot_torsions = 0;
1191	>	for( i=0; i<n_components; i++ ){
1192	>
1193	>	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1194	>	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1195	>	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1196	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1197	>	}
1198	>
1199	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1200	>	molMembershipArray = new int[tot_atoms];
1201	>
1202	>	for(i=0; i<nInfo; i++){
1203	>	info[i].n_atoms = tot_atoms;
1204	>	info[i].n_bonds = tot_bonds;
1205	>	info[i].n_bends = tot_bends;
1206	>	info[i].n_torsions = tot_torsions;
1207	>	info[i].n_SRI = tot_SRI;
1208	>	info[i].n_mol = tot_nmol;
1209	>
1210	>	info[i].molMembershipArray = molMembershipArray;
1211	>	}
1212	>	}
1213
1214	+	#ifdef IS_MPI
1215	+
1216	+	void SimSetup::mpiMolDivide( void ){
1217	+
1218		int i, j, k;
1219	<	int n_cells;
1220	<	double cellx, celly, cellz;
1155	<	double temp1, temp2, temp3;
1156	<	int n_per_extra;
1157	<	int n_extra;
1158	<	int have_extra, done;
1219	>	int localMol, allMol;
1220	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1221
1222	<	temp1 = (double)tot_nmol / 4.0;
1223	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1224	<	temp3 = ceil( temp2 );
1222	>	mpiSim = new mpiSimulation( info );
1223	>
1224	>	globalIndex = mpiSim->divideLabor();
1225
1226	<	have_extra =0;
1227	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1228	<	have_extra =1;
1226	>	// set up the local variables
1227	>
1228	>	mol2proc = mpiSim->getMolToProcMap();
1229	>	molCompType = mpiSim->getMolComponentType();
1230	>
1231	>	allMol = 0;
1232	>	localMol = 0;
1233	>	local_atoms = 0;
1234	>	local_bonds = 0;
1235	>	local_bends = 0;
1236	>	local_torsions = 0;
1237	>	globalAtomIndex = 0;
1238
1168	–	n_cells = (int)temp3 - 1;
1169	–	cellx = simnfo->box_x / temp3;
1170	–	celly = simnfo->box_y / temp3;
1171	–	cellz = simnfo->box_z / temp3;
1172	–	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1173	–	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1174	–	n_per_extra = (int)ceil( temp1 );
1239
1240	<	if( n_per_extra > 4){
1241	<	sprintf( painCave.errMsg,
1242	<	"SimSetup error. There has been an error in constructing"
1243	<	" the non-complete lattice.\n" );
1244	<	painCave.isFatal = 1;
1245	<	simError();
1240	>	for( i=0; i<n_components; i++ ){
1241	>
1242	>	for( j=0; j<components_nmol[i]; j++ ){
1243	>
1244	>	if( mol2proc[allMol] == worldRank ){
1245	>
1246	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1247	>	local_bonds +=    comp_stamps[i]->getNBonds();
1248	>	local_bends +=    comp_stamps[i]->getNBends();
1249	>	local_torsions += comp_stamps[i]->getNTorsions();
1250	>	localMol++;
1251	>	}
1252	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1253	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1254	>	globalAtomIndex++;
1255	>	}
1256	>
1257	>	allMol++;
1258		}
1259		}
1260	<	else{
1261	<	n_cells = (int)temp3;
1262	<	cellx = simnfo->box_x / temp3;
1263	<	celly = simnfo->box_y / temp3;
1264	<	cellz = simnfo->box_z / temp3;
1260	>	local_SRI = local_bonds + local_bends + local_torsions;
1261	>
1262	>	info[0].n_atoms = mpiSim->getMyNlocal();
1263	>
1264	>	if( local_atoms != info[0].n_atoms ){
1265	>	sprintf( painCave.errMsg,
1266	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1267	>	" localAtom (%d) are not equal.\n",
1268	>	info[0].n_atoms,
1269	>	local_atoms );
1270	>	painCave.isFatal = 1;
1271	>	simError();
1272		}
1273
1274	<	current_mol = 0;
1275	<	current_comp_mol = 0;
1276	<	current_comp = 0;
1277	<	current_atom_ndx = 0;
1274	>	info[0].n_bonds = local_bonds;
1275	>	info[0].n_bends = local_bends;
1276	>	info[0].n_torsions = local_torsions;
1277	>	info[0].n_SRI = local_SRI;
1278	>	info[0].n_mol = localMol;
1279
1280	<	for( i=0; i < n_cells ; i++ ){
1281	<	for( j=0; j < n_cells; j++ ){
1282	<	for( k=0; k < n_cells; k++ ){
1280	>	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1281	>	MPIcheckPoint();
1282	>	}
1283	>
1284	>	#endif // is_mpi
1285
1200	–	makeElement( i * cellx,
1201	–	j * celly,
1202	–	k * cellz );
1286
1287	<	makeElement( i * cellx + 0.5 * cellx,
1288	<	j * celly + 0.5 * celly,
1206	<	k * cellz );
1287	>	void SimSetup::makeSysArrays( void ){
1288	>	int i, j, k, l;
1289
1290	<	makeElement( i * cellx,
1291	<	j * celly + 0.5 * celly,
1292	<	k * cellz + 0.5 * cellz );
1290	>	Atom** the_atoms;
1291	>	Molecule* the_molecules;
1292	>	Exclude** the_excludes;
1293
1294	<	makeElement( i * cellx + 0.5 * cellx,
1295	<	j * celly,
1296	<	k * cellz + 0.5 * cellz );
1294	>
1295	>	for(l=0; l<nInfo; l++){
1296	>
1297	>	// create the atom and short range interaction arrays
1298	>
1299	>	the_atoms = new Atom*[info[l].n_atoms];
1300	>	the_molecules = new Molecule[info[l].n_mol];
1301	>	int molIndex;
1302	>
1303	>	// initialize the molecule's stampID's
1304	>
1305	>	#ifdef IS_MPI
1306	>
1307	>
1308	>	molIndex = 0;
1309	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1310	>
1311	>	if(mol2proc[i] == worldRank ){
1312	>	the_molecules[molIndex].setStampID( molCompType[i] );
1313	>	the_molecules[molIndex].setMyIndex( molIndex );
1314	>	the_molecules[molIndex].setGlobalIndex( i );
1315	>	molIndex++;
1316		}
1317		}
1318	+
1319	+	#else // is_mpi
1320	+
1321	+	molIndex = 0;
1322	+	globalAtomIndex = 0;
1323	+	for(i=0; i<n_components; i++){
1324	+	for(j=0; j<components_nmol[i]; j++ ){
1325	+	the_molecules[molIndex].setStampID( i );
1326	+	the_molecules[molIndex].setMyIndex( molIndex );
1327	+	the_molecules[molIndex].setGlobalIndex( molIndex );
1328	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1329	+	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1330	+	globalAtomIndex++;
1331		}
1332	+	molIndex++;
1333	+	}
1334	+	}
1335	+
1336	+
1337	+	#endif // is_mpi
1338
1219	–	if( have_extra ){
1220	–	done = 0;
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++ ){
1343	<
1344	<	if( i < n_cells ){
1345	<
1228	<	if( j < n_cells ){
1229	<	start_ndx = n_cells;
1230	<	}
1231	<	else start_ndx = 0;
1232	<	}
1233	<	else start_ndx = 0;
1234	<
1235	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1236	<
1237	<	makeElement( i * cellx,
1238	<	j * celly,
1239	<	k * cellz );
1240	<	done = ( current_mol >= tot_nmol );
1241	<
1242	<	if( !done && n_per_extra > 1 ){
1243	<	makeElement( i * cellx + 0.5 * cellx,
1244	<	j * celly + 0.5 * celly,
1245	<	k * cellz );
1246	<	done = ( current_mol >= tot_nmol );
1247	<	}
1248	<
1249	<	if( !done && n_per_extra > 2){
1250	<	makeElement( i * cellx,
1251	<	j * celly + 0.5 * celly,
1252	<	k * cellz + 0.5 * cellz );
1253	<	done = ( current_mol >= tot_nmol );
1254	<	}
1255	<
1256	<	if( !done && n_per_extra > 3){
1257	<	makeElement( i * cellx + 0.5 * cellx,
1258	<	j * celly,
1259	<	k * cellz + 0.5 * cellz );
1260	<	done = ( current_mol >= tot_nmol );
1261	<	}
1262	<	}
1340	>	if( info[l].n_SRI ){
1341	>
1342	>	Exclude::createArray(info[l].n_SRI);
1343	>	the_excludes = new Exclude*[info[l].n_SRI];
1344	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1345	>	the_excludes[ex] = new Exclude(ex);
1346		}
1347	+	info[l].globalExcludes = new int;
1348	+	info[l].n_exclude = info[l].n_SRI;
1349		}
1350	<	}
1350	>	else{
1351	>
1352	>	Exclude::createArray( 1 );
1353	>	the_excludes = new Exclude*;
1354	>	the_excludes[0] = new Exclude(0);
1355	>	the_excludes[0]->setPair( 0,0 );
1356	>	info[l].globalExcludes = new int;
1357	>	info[l].globalExcludes[0] = 0;
1358	>	info[l].n_exclude = 0;
1359	>	}
1360
1361	+	// set the arrays into the SimInfo object
1362
1363	<	for( i=0; i<simnfo->n_atoms; i++ ){
1364	<	simnfo->atoms[i]->set_vx( 0.0 );
1365	<	simnfo->atoms[i]->set_vy( 0.0 );
1366	<	simnfo->atoms[i]->set_vz( 0.0 );
1363	>	info[l].atoms = the_atoms;
1364	>	info[l].molecules = the_molecules;
1365	>	info[l].nGlobalExcludes = 0;
1366	>	info[l].excludes = the_excludes;
1367	>
1368	>	the_ff->setSimInfo( info );
1369	>
1370		}
1371		}
1372
1373	<	void SimSetup::makeElement( double x, double y, double z ){
1373	>	void SimSetup::makeIntegrator( void ){
1374
1375		int k;
1278	–	AtomStamp* current_atom;
1279	–	DirectionalAtom* dAtom;
1280	–	double rotMat[3][3];
1376
1377	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1377	>	NVT<RealIntegrator>*  myNVT = NULL;
1378	>	NPTi<RealIntegrator>* myNPTi = NULL;
1379	>	NPTf<RealIntegrator>* myNPTf = NULL;
1380	>	NPTim<RealIntegrator>* myNPTim = NULL;
1381	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1382	>
1383	>	for(k=0; k<nInfo; k++){
1384	>
1385	>	switch( ensembleCase ){
1386	>
1387	>	case NVE_ENS:
1388	>	if (globals->haveZconstraints()){
1389	>	setupZConstraint(info[k]);
1390	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1391	>	}
1392
1393	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1394	<	if( !current_atom->havePosition() ){
1393	>	else
1394	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1395	>	break;
1396	>
1397	>	case NVT_ENS:
1398	>	if (globals->haveZconstraints()){
1399	>	setupZConstraint(info[k]);
1400	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1401	>	}
1402	>	else
1403	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1404	>
1405	>	myNVT->setTargetTemp(globals->getTargetTemp());
1406	>
1407	>	if (globals->haveTauThermostat())
1408	>	myNVT->setTauThermostat(globals->getTauThermostat());
1409	>
1410	>	else {
1411	>	sprintf( painCave.errMsg,
1412	>	"SimSetup error: If you use the NVT\n"
1413	>	"    ensemble, you must set tauThermostat.\n");
1414	>	painCave.isFatal = 1;
1415	>	simError();
1416	>	}
1417	>	break;
1418	>
1419	>	case NPTi_ENS:
1420	>	if (globals->haveZconstraints()){
1421	>	setupZConstraint(info[k]);
1422	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1423	>	}
1424	>	else
1425	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1426	>
1427	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1428	>
1429	>	if (globals->haveTargetPressure())
1430	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1431	>	else {
1432	>	sprintf( painCave.errMsg,
1433	>	"SimSetup error: If you use a constant pressure\n"
1434	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1435	>	painCave.isFatal = 1;
1436	>	simError();
1437	>	}
1438	>
1439	>	if( globals->haveTauThermostat() )
1440	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1441	>	else{
1442	>	sprintf( painCave.errMsg,
1443	>	"SimSetup error: If you use an NPT\n"
1444	>	"    ensemble, you must set tauThermostat.\n");
1445	>	painCave.isFatal = 1;
1446	>	simError();
1447	>	}
1448	>
1449	>	if( globals->haveTauBarostat() )
1450	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1451	>	else{
1452	>	sprintf( painCave.errMsg,
1453	>	"SimSetup error: If you use an NPT\n"
1454	>	"    ensemble, you must set tauBarostat.\n");
1455	>	painCave.isFatal = 1;
1456	>	simError();
1457	>	}
1458	>	break;
1459	>
1460	>	case NPTf_ENS:
1461	>	if (globals->haveZconstraints()){
1462	>	setupZConstraint(info[k]);
1463	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1464	>	}
1465	>	else
1466	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1467	>
1468	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1469	>
1470	>	if (globals->haveTargetPressure())
1471	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1472	>	else {
1473	>	sprintf( painCave.errMsg,
1474	>	"SimSetup error: If you use a constant pressure\n"
1475	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1476	>	painCave.isFatal = 1;
1477	>	simError();
1478	>	}
1479	>
1480	>	if( globals->haveTauThermostat() )
1481	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1482	>	else{
1483	>	sprintf( painCave.errMsg,
1484	>	"SimSetup error: If you use an NPT\n"
1485	>	"    ensemble, you must set tauThermostat.\n");
1486	>	painCave.isFatal = 1;
1487	>	simError();
1488	>	}
1489	>
1490	>	if( globals->haveTauBarostat() )
1491	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1492	>	else{
1493	>	sprintf( painCave.errMsg,
1494	>	"SimSetup error: If you use an NPT\n"
1495	>	"    ensemble, you must set tauBarostat.\n");
1496	>	painCave.isFatal = 1;
1497	>	simError();
1498	>	}
1499	>	break;
1500	>
1501	>	case NPTim_ENS:
1502	>	if (globals->haveZconstraints()){
1503	>	setupZConstraint(info[k]);
1504	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1505	>	}
1506	>	else
1507	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1508	>
1509	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1510	>
1511	>	if (globals->haveTargetPressure())
1512	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1513	>	else {
1514	>	sprintf( painCave.errMsg,
1515	>	"SimSetup error: If you use a constant pressure\n"
1516	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1517	>	painCave.isFatal = 1;
1518	>	simError();
1519	>	}
1520	>
1521	>	if( globals->haveTauThermostat() )
1522	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1523	>	else{
1524	>	sprintf( painCave.errMsg,
1525	>	"SimSetup error: If you use an NPT\n"
1526	>	"    ensemble, you must set tauThermostat.\n");
1527	>	painCave.isFatal = 1;
1528	>	simError();
1529	>	}
1530	>
1531	>	if( globals->haveTauBarostat() )
1532	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1533	>	else{
1534	>	sprintf( painCave.errMsg,
1535	>	"SimSetup error: If you use an NPT\n"
1536	>	"    ensemble, you must set tauBarostat.\n");
1537	>	painCave.isFatal = 1;
1538	>	simError();
1539	>	}
1540	>	break;
1541	>
1542	>	case NPTfm_ENS:
1543	>	if (globals->haveZconstraints()){
1544	>	setupZConstraint(info[k]);
1545	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1546	>	}
1547	>	else
1548	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1549	>
1550	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1551	>
1552	>	if (globals->haveTargetPressure())
1553	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1554	>	else {
1555	>	sprintf( painCave.errMsg,
1556	>	"SimSetup error: If you use a constant pressure\n"
1557	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1558	>	painCave.isFatal = 1;
1559	>	simError();
1560	>	}
1561	>
1562	>	if( globals->haveTauThermostat() )
1563	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1564	>	else{
1565	>	sprintf( painCave.errMsg,
1566	>	"SimSetup error: If you use an NPT\n"
1567	>	"    ensemble, you must set tauThermostat.\n");
1568	>	painCave.isFatal = 1;
1569	>	simError();
1570	>	}
1571	>
1572	>	if( globals->haveTauBarostat() )
1573	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1574	>	else{
1575	>	sprintf( painCave.errMsg,
1576	>	"SimSetup error: If you use an NPT\n"
1577	>	"    ensemble, you must set tauBarostat.\n");
1578	>	painCave.isFatal = 1;
1579	>	simError();
1580	>	}
1581	>	break;
1582	>
1583	>	default:
1584		sprintf( painCave.errMsg,
1585	<	"SimSetup:initFromBass error.\n"
1288	<	"\tComponent %s, atom %s does not have a position specified.\n"
1289	<	"\tThe initialization routine is unable to give a start"
1290	<	" position.\n",
1291	<	comp_stamps[current_comp]->getID(),
1292	<	current_atom->getType() );
1585	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1586		painCave.isFatal = 1;
1587		simError();
1588		}
1589	+	}
1590	+	}
1591
1592	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1298	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1299	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1592	>	void SimSetup::initFortran( void ){
1593
1594	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1594	>	info[0].refreshSim();
1595	>
1596	>	if( !strcmp( info[0].mixingRule, "standard") ){
1597	>	the_ff->initForceField( LB_MIXING_RULE );
1598	>	}
1599	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1600	>	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1601	>	}
1602	>	else{
1603	>	sprintf( painCave.errMsg,
1604	>	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1605	>	info[0].mixingRule );
1606	>	painCave.isFatal = 1;
1607	>	simError();
1608	>	}
1609
1303	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1610
1611	<	rotMat[0][0] = 1.0;
1612	<	rotMat[0][1] = 0.0;
1613	<	rotMat[0][2] = 0.0;
1611	>	#ifdef IS_MPI
1612	>	strcpy( checkPointMsg,
1613	>	"Successfully intialized the mixingRule for Fortran." );
1614	>	MPIcheckPoint();
1615	>	#endif // is_mpi
1616
1617	<	rotMat[1][0] = 0.0;
1310	<	rotMat[1][1] = 1.0;
1311	<	rotMat[1][2] = 0.0;
1617	>	}
1618
1619	<	rotMat[2][0] = 0.0;
1620	<	rotMat[2][1] = 0.0;
1621	<	rotMat[2][2] = 1.0;
1619	>	void SimSetup::setupZConstraint(SimInfo& theInfo)
1620	>	{
1621	>	int nZConstraints;
1622	>	ZconStamp** zconStamp;
1623
1624	<	dAtom->setA( rotMat );
1625	<	}
1624	>	if(globals->haveZconstraintTime()){
1625	>
1626	>	//add sample time of z-constraint  into SimInfo's property list
1627	>	DoubleData* zconsTimeProp = new DoubleData();
1628	>	zconsTimeProp->setID(ZCONSTIME_ID);
1629	>	zconsTimeProp->setData(globals->getZconsTime());
1630	>	theInfo.addProperty(zconsTimeProp);
1631	>	}
1632	>	else{
1633	>	sprintf( painCave.errMsg,
1634	>	"ZConstraint error: If you use an ZConstraint\n"
1635	>	" , you must set sample time.\n");
1636	>	painCave.isFatal = 1;
1637	>	simError();
1638	>	}
1639
1640	<	current_atom_ndx++;
1640	>	//push zconsTol into siminfo, if user does not specify
1641	>	//value for zconsTol, a default value will be used
1642	>	DoubleData* zconsTol = new DoubleData();
1643	>	zconsTol->setID(ZCONSTOL_ID);
1644	>	if(globals->haveZconsTol()){
1645	>	zconsTol->setData(globals->getZconsTol());
1646		}
1647	+	else{
1648	+	double defaultZConsTol = 0.01;
1649	+	sprintf( painCave.errMsg,
1650	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1651	+	" , default value %f is used.\n", defaultZConsTol);
1652	+	painCave.isFatal = 0;
1653	+	simError();
1654
1655	<	current_mol++;
1656	<	current_comp_mol++;
1655	>	zconsTol->setData(defaultZConsTol);
1656	>	}
1657	>	theInfo.addProperty(zconsTol);
1658
1659	<	if( current_comp_mol >= components_nmol[current_comp] ){
1659	>	//set Force Substraction Policy
1660	>	StringData* zconsForcePolicy =  new StringData();
1661	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1662	>
1663	>	if(globals->haveZconsForcePolicy()){
1664	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1665	>	}
1666	>	else{
1667	>	sprintf( painCave.errMsg,
1668	>	"ZConstraint Warning: User does not set force substraction policy, "
1669	>	"average force substraction policy is used\n");
1670	>	painCave.isFatal = 0;
1671	>	simError();
1672	>	zconsForcePolicy->setData("BYNUMBER");
1673	>	}
1674	>
1675	>	theInfo.addProperty(zconsForcePolicy);
1676	>
1677	>	//Determine the name of ouput file and add it into SimInfo's property list
1678	>	//Be careful, do not use inFileName, since it is a pointer which
1679	>	//point to a string at master node, and slave nodes do not contain that string
1680	>
1681	>	string zconsOutput(theInfo.finalName);
1682	>
1683	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1684	>
1685	>	StringData* zconsFilename = new StringData();
1686	>	zconsFilename->setID(ZCONSFILENAME_ID);
1687	>	zconsFilename->setData(zconsOutput);
1688	>
1689	>	theInfo.addProperty(zconsFilename);
1690	>
1691	>	//setup index, pos and other parameters of z-constraint molecules
1692	>	nZConstraints = globals->getNzConstraints();
1693	>	theInfo.nZconstraints = nZConstraints;
1694
1695	<	current_comp_mol = 0;
1696	<	current_comp++;
1695	>	zconStamp = globals->getZconStamp();
1696	>	ZConsParaItem tempParaItem;
1697	>
1698	>	ZConsParaData* zconsParaData = new ZConsParaData();
1699	>	zconsParaData->setID(ZCONSPARADATA_ID);
1700	>
1701	>	for(int i = 0; i < nZConstraints; i++){
1702	>	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1703	>	tempParaItem.zPos = zconStamp[i]->getZpos();
1704	>	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1705	>	tempParaItem.kRatio = zconStamp[i]->getKratio();
1706	>
1707	>	zconsParaData->addItem(tempParaItem);
1708		}
1709	+
1710	+	//sort the parameters by index of molecules
1711	+	zconsParaData->sortByIndex();
1712	+
1713	+	//push data into siminfo, therefore, we can retrieve later
1714	+	theInfo.addProperty(zconsParaData);
1715	+
1716		}

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