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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 693 by tim, Wed Aug 13 19:21:53 2003 UTC vs.
Revision 778 by mmeineke, Fri Sep 19 20:00:27 2003 UTC

#	Line 3 | Line 3
3		#include <iostream>
4		#include <cmath>
5		#include <string>
6	+	#include <sprng.h>
7
8		#include "SimSetup.hpp"
9		#include "ReadWrite.hpp"
#	Line 31 | Line 32 | SimSetup::SimSetup(){
32		using namespace std;
33
34		SimSetup::SimSetup(){
34	–
35		isInfoArray = 0;
36		nInfo = 1;
37	<
37	>
38		stamps = new MakeStamps();
39		globals = new Globals();
40	<
41	<
40	>
41	>
42		#ifdef IS_MPI
43	<	strcpy( checkPointMsg, "SimSetup creation successful" );
43	>	strcpy(checkPointMsg, "SimSetup creation successful");
44		MPIcheckPoint();
45		#endif // IS_MPI
46		}
#	Line 50 | Line 50 | void SimSetup::setSimInfo( SimInfo* the_info, int theN
50		delete globals;
51		}
52
53	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
54	<	info = the_info;
55	<	nInfo = theNinfo;
56	<	isInfoArray = 1;
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	<
60	>	void SimSetup::parseFile(char* fileName){
61		#ifdef IS_MPI
62	<	if( worldRank == 0 ){
62	>	if (worldRank == 0){
63		#endif // is_mpi
64	<
64	>
65		inFileName = fileName;
66	<	set_interface_stamps( stamps, globals );
67	<
66	>	set_interface_stamps(stamps, globals);
67	>
68		#ifdef IS_MPI
69		mpiEventInit();
70		#endif
71
72	<	yacc_BASS( fileName );
72	>	yacc_BASS(fileName);
73
74		#ifdef IS_MPI
75		throwMPIEvent(NULL);
76		}
77	<	else receiveParse();
77	>	else{
78	>	receiveParse();
79	>	}
80		#endif
81
82		}
83
84		#ifdef IS_MPI
85		void SimSetup::receiveParse(void){
86	<
87	<	set_interface_stamps( stamps, globals );
88	<	mpiEventInit();
89	<	MPIcheckPoint();
89	<	mpiEventLoop();
90	<
86	>	set_interface_stamps(stamps, globals);
87	>	mpiEventInit();
88	>	MPIcheckPoint();
89	>	mpiEventLoop();
90		}
91
92		#endif // is_mpi
93
94		void SimSetup::createSim(void){
96	–
95		int i, j, k, globalAtomIndex;
96	<
96	>
97		// gather all of the information from the Bass file
98
99		gatherInfo();
#	Line 110 | Line 108 | void SimSetup::createSim(void){
108
109		// initialize the system coordinates
110
111	<	if( !isInfoArray ) initSystemCoords();
111	>	if (!isInfoArray){
112	>	initSystemCoords();
113	>	}
114
115		// make the output filenames
116
117		makeOutNames();
118	<
118	>
119		// make the integrator
120	<
120	>
121		makeIntegrator();
122	<
122	>
123		#ifdef IS_MPI
124		mpiSim->mpiRefresh();
125		#endif
#	Line 127 | Line 127 | void SimSetup::createSim(void){
127		// initialize the Fortran
128
129		initFortran();
130	–
131	–
132	–
130		}
131
132
133	<	void SimSetup::makeMolecules( void ){
134	<
138	<	int k,l;
133	>	void SimSetup::makeMolecules(void){
134	>	int k, l;
135		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
136		molInit molInfo;
137		DirectionalAtom* dAtom;
#	Line 150 | Line 146 | void SimSetup::makeMolecules( void ){
146		bend_set* theBends;
147		torsion_set* theTorsions;
148
149	<
149	>
150		//init the forceField paramters
151
152		the_ff->readParams();
153
154	<
154	>
155		// init the atoms
156
157		double ux, uy, uz, u, uSqr;
162	–
163	–	for(k=0; k<nInfo; k++){
164	–
165	–	the_ff->setSimInfo( &(info[k]) );
158
159	+	for (k = 0; k < nInfo; k++){
160	+	the_ff->setSimInfo(&(info[k]));
161	+
162		atomOffset = 0;
163		excludeOffset = 0;
164	<	for(i=0; i<info[k].n_mol; i++){
170	<
164	>	for (i = 0; i < info[k].n_mol; i++){
165		stampID = info[k].molecules[i].getStampID();
166
167	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
168	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
169	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
167	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
168	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
169	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
170		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
171		molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
172	<
172	>
173		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
174		molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
175	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
176	<	molInfo.myBends = new Bend*[molInfo.nBends];
177	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
175	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
176	>	molInfo.myBends = new Bend * [molInfo.nBends];
177	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
178
179		theBonds = new bond_pair[molInfo.nBonds];
180		theBends = new bend_set[molInfo.nBends];
181		theTorsions = new torsion_set[molInfo.nTorsions];
182	<
182	>
183		// make the Atoms
184	<
185	<	for(j=0; j<molInfo.nAtoms; j++){
186	<
187	<	currentAtom = comp_stamps[stampID]->getAtom( j );
188	<	if( currentAtom->haveOrientation() ){
189	<
190	<	dAtom = new DirectionalAtom( (j + atomOffset),
191	<	info[k].getConfiguration() );
192	<	info[k].n_oriented++;
193	<	molInfo.myAtoms[j] = dAtom;
194	<
195	<	ux = currentAtom->getOrntX();
196	<	uy = currentAtom->getOrntY();
197	<	uz = currentAtom->getOrntZ();
198	<
199	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
200	<
201	<	u = sqrt( uSqr );
202	<	ux = ux / u;
203	<	uy = uy / u;
204	<	uz = uz / u;
205	<
206	<	dAtom->setSUx( ux );
207	<	dAtom->setSUy( uy );
208	<	dAtom->setSUz( uz );
209	<	}
210	<	else{
211	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
212	<	info[k].getConfiguration() );
213	<	}
220	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221	<
184	>
185	>	for (j = 0; j < molInfo.nAtoms; j++){
186	>	currentAtom = comp_stamps[stampID]->getAtom(j);
187	>	if (currentAtom->haveOrientation()){
188	>	dAtom = new DirectionalAtom((j + atomOffset),
189	>	info[k].getConfiguration());
190	>	info[k].n_oriented++;
191	>	molInfo.myAtoms[j] = dAtom;
192	>
193	>	ux = currentAtom->getOrntX();
194	>	uy = currentAtom->getOrntY();
195	>	uz = currentAtom->getOrntZ();
196	>
197	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
198	>
199	>	u = sqrt(uSqr);
200	>	ux = ux / u;
201	>	uy = uy / u;
202	>	uz = uz / u;
203	>
204	>	dAtom->setSUx(ux);
205	>	dAtom->setSUy(uy);
206	>	dAtom->setSUz(uz);
207	>	}
208	>	else{
209	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
210	>	info[k].getConfiguration());
211	>	}
212	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
213	>
214		#ifdef IS_MPI
215	<
216	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
217	<
215	>
216	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
217	>
218		#endif // is_mpi
219		}
220	<
221	<	// make the bonds
222	<	for(j=0; j<molInfo.nBonds; j++){
223	<
224	<	currentBond = comp_stamps[stampID]->getBond( j );
225	<	theBonds[j].a = currentBond->getA() + atomOffset;
226	<	theBonds[j].b = currentBond->getB() + atomOffset;
227	<
228	<	exI = theBonds[j].a;
229	<	exJ = theBonds[j].b;
230	<
231	<	// exclude_I must always be the smaller of the pair
232	<	if( exI > exJ ){
233	<	tempEx = exI;
234	<	exI = exJ;
235	<	exJ = tempEx;
244	<	}
220	>
221	>	// make the bonds
222	>	for (j = 0; j < molInfo.nBonds; j++){
223	>	currentBond = comp_stamps[stampID]->getBond(j);
224	>	theBonds[j].a = currentBond->getA() + atomOffset;
225	>	theBonds[j].b = currentBond->getB() + atomOffset;
226	>
227	>	exI = theBonds[j].a;
228	>	exJ = theBonds[j].b;
229	>
230	>	// exclude_I must always be the smaller of the pair
231	>	if (exI > exJ){
232	>	tempEx = exI;
233	>	exI = exJ;
234	>	exJ = tempEx;
235	>	}
236		#ifdef IS_MPI
237	<	tempEx = exI;
238	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
239	<	tempEx = exJ;
240	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
241	<
242	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
237	>	tempEx = exI;
238	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
239	>	tempEx = exJ;
240	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
241	>
242	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
243		#else  // isn't MPI
244	<
245	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
244	>
245	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
246		#endif  //is_mpi
247		}
248		excludeOffset += molInfo.nBonds;
249	<
249	>
250		//make the bends
251	<	for(j=0; j<molInfo.nBends; j++){
252	<
253	<	currentBend = comp_stamps[stampID]->getBend( j );
254	<	theBends[j].a = currentBend->getA() + atomOffset;
255	<	theBends[j].b = currentBend->getB() + atomOffset;
256	<	theBends[j].c = currentBend->getC() + atomOffset;
257	<
258	<	if( currentBend->haveExtras() ){
259	<
260	<	extras = currentBend->getExtras();
261	<	current_extra = extras;
262	<
263	<	while( current_extra != NULL ){
264	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
265	<
266	<	switch( current_extra->getType() ){
267	<
268	<	case 0:
269	<	theBends[j].ghost =
270	<	current_extra->getInt() + atomOffset;
271	<	theBends[j].isGhost = 1;
272	<	break;
273	<
274	<	case 1:
275	<	theBends[j].ghost =
276	<	(int)current_extra->getDouble() + atomOffset;
277	<	theBends[j].isGhost = 1;
278	<	break;
279	<
280	<	default:
281	<	sprintf( painCave.errMsg,
282	<	"SimSetup Error: ghostVectorSource was neither a "
283	<	"double nor an int.\n"
284	<	"-->Bend[%d] in %s\n",
285	<	j, comp_stamps[stampID]->getID() );
286	<	painCave.isFatal = 1;
287	<	simError();
288	<	}
289	<	}
290	<
291	<	else{
292	<
293	<	sprintf( painCave.errMsg,
294	<	"SimSetup Error: unhandled bend assignment:\n"
295	<	"    -->%s in Bend[%d] in %s\n",
296	<	current_extra->getlhs(),
297	<	j, comp_stamps[stampID]->getID() );
298	<	painCave.isFatal = 1;
299	<	simError();
300	<	}
301	<
302	<	current_extra = current_extra->getNext();
303	<	}
304	<	}
305	<
306	<	if( !theBends[j].isGhost ){
307	<
308	<	exI = theBends[j].a;
309	<	exJ = theBends[j].c;
310	<	}
311	<	else{
312	<
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	<	}
251	>	for (j = 0; j < molInfo.nBends; j++){
252	>	currentBend = comp_stamps[stampID]->getBend(j);
253	>	theBends[j].a = currentBend->getA() + atomOffset;
254	>	theBends[j].b = currentBend->getB() + atomOffset;
255	>	theBends[j].c = currentBend->getC() + atomOffset;
256	>
257	>	if (currentBend->haveExtras()){
258	>	extras = currentBend->getExtras();
259	>	current_extra = extras;
260	>
261	>	while (current_extra != NULL){
262	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
263	>	switch (current_extra->getType()){
264	>	case 0:
265	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
266	>	theBends[j].isGhost = 1;
267	>	break;
268	>
269	>	case 1:
270	>	theBends[j].ghost = (int) current_extra->getDouble() +
271	>	atomOffset;
272	>	theBends[j].isGhost = 1;
273	>	break;
274	>
275	>	default:
276	>	sprintf(painCave.errMsg,
277	>	"SimSetup Error: ghostVectorSource was neither a "
278	>	"double nor an int.\n"
279	>	"-->Bend[%d] in %s\n",
280	>	j, comp_stamps[stampID]->getID());
281	>	painCave.isFatal = 1;
282	>	simError();
283	>	}
284	>	}
285	>	else{
286	>	sprintf(painCave.errMsg,
287	>	"SimSetup Error: unhandled bend assignment:\n"
288	>	"    -->%s in Bend[%d] in %s\n",
289	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
290	>	painCave.isFatal = 1;
291	>	simError();
292	>	}
293	>
294	>	current_extra = current_extra->getNext();
295	>	}
296	>	}
297	>
298	>	if (!theBends[j].isGhost){
299	>	exI = theBends[j].a;
300	>	exJ = theBends[j].c;
301	>	}
302	>	else{
303	>	exI = theBends[j].a;
304	>	exJ = theBends[j].b;
305	>	}
306	>
307	>	// exclude_I must always be the smaller of the pair
308	>	if (exI > exJ){
309	>	tempEx = exI;
310	>	exI = exJ;
311	>	exJ = tempEx;
312	>	}
313		#ifdef IS_MPI
314	<	tempEx = exI;
315	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
316	<	tempEx = exJ;
317	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
318	<
319	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
314	>	tempEx = exI;
315	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
316	>	tempEx = exJ;
317	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
318	>
319	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
320		#else  // isn't MPI
321	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
321	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
322		#endif  //is_mpi
323		}
324		excludeOffset += molInfo.nBends;
325	<
326	<	for(j=0; j<molInfo.nTorsions; j++){
327	<
328	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
329	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
330	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
331	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
332	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
333	<
334	<	exI = theTorsions[j].a;
335	<	exJ = theTorsions[j].d;
336	<
337	<	// exclude_I must always be the smaller of the pair
338	<	if( exI > exJ ){
339	<	tempEx = exI;
340	<	exI = exJ;
341	<	exJ = tempEx;
361	<	}
325	>
326	>	for (j = 0; j < molInfo.nTorsions; j++){
327	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
328	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
329	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
330	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
331	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
332	>
333	>	exI = theTorsions[j].a;
334	>	exJ = theTorsions[j].d;
335	>
336	>	// exclude_I must always be the smaller of the pair
337	>	if (exI > exJ){
338	>	tempEx = exI;
339	>	exI = exJ;
340	>	exJ = tempEx;
341	>	}
342		#ifdef IS_MPI
343	<	tempEx = exI;
344	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345	<	tempEx = exJ;
346	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
347	<
348	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
343	>	tempEx = exI;
344	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345	>	tempEx = exJ;
346	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
347	>
348	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
349		#else  // isn't MPI
350	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
350	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
351		#endif  //is_mpi
352		}
353		excludeOffset += molInfo.nTorsions;
354	<
355	<
354	>
355	>
356		// 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 );
357
358	<
358	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
359	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
360	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
361	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
362	>	theTorsions);
363	>
364	>
365	>	info[k].molecules[i].initialize(molInfo);
366	>
367	>
368		atomOffset += molInfo.nAtoms;
369		delete[] theBonds;
370		delete[] theBends;
371		delete[] theTorsions;
372		}
373		}
374	<
374	>
375		#ifdef IS_MPI
376	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
376	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
377		MPIcheckPoint();
378		#endif // is_mpi
379	<
379	>
380		// clean up the forcefield
381
382		the_ff->calcRcut();
383		the_ff->cleanMe();
403	–
384		}
385
386	<	void SimSetup::initFromBass( void ){
407	<
386	>	void SimSetup::initFromBass(void){
387		int i, j, k;
388		int n_cells;
389		double cellx, celly, cellz;
#	Line 418 | Line 397 | void SimSetup::initFromBass( void ){
397		vel[1] = 0.0;
398		vel[2] = 0.0;
399
400	<	temp1 = (double)tot_nmol / 4.0;
401	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
402	<	temp3 = ceil( temp2 );
400	>	temp1 = (double) tot_nmol / 4.0;
401	>	temp2 = pow(temp1, (1.0 / 3.0));
402	>	temp3 = ceil(temp2);
403
404	<	have_extra =0;
405	<	if( temp2 < temp3 ){ // we have a non-complete lattice
406	<	have_extra =1;
404	>	have_extra = 0;
405	>	if (temp2 < temp3){
406	>	// we have a non-complete lattice
407	>	have_extra = 1;
408
409	<	n_cells = (int)temp3 - 1;
409	>	n_cells = (int) temp3 - 1;
410		cellx = info[0].boxL[0] / temp3;
411		celly = info[0].boxL[1] / temp3;
412		cellz = info[0].boxL[2] / temp3;
413	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
414	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
415	<	n_per_extra = (int)ceil( temp1 );
413	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
414	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
415	>	n_per_extra = (int) ceil(temp1);
416
417	<	if( n_per_extra > 4){
418	<	sprintf( painCave.errMsg,
419	<	"SimSetup error. There has been an error in constructing"
420	<	" the non-complete lattice.\n" );
417	>	if (n_per_extra > 4){
418	>	sprintf(painCave.errMsg,
419	>	"SimSetup error. There has been an error in constructing"
420	>	" the non-complete lattice.\n");
421		painCave.isFatal = 1;
422		simError();
423		}
424		}
425		else{
426	<	n_cells = (int)temp3;
426	>	n_cells = (int) temp3;
427		cellx = info[0].boxL[0] / temp3;
428		celly = info[0].boxL[1] / temp3;
429		cellz = info[0].boxL[2] / temp3;
#	Line 454 | Line 434 | void SimSetup::initFromBass( void ){
434		current_comp = 0;
435		current_atom_ndx = 0;
436
437	<	for( i=0; i < n_cells ; i++ ){
438	<	for( j=0; j < n_cells; j++ ){
439	<	for( k=0; k < n_cells; k++ ){
437	>	for (i = 0; i < n_cells ; i++){
438	>	for (j = 0; j < n_cells; j++){
439	>	for (k = 0; k < n_cells; k++){
440	>	makeElement(i * cellx, j * celly, k * cellz);
441
442	<	makeElement( i * cellx,
462	<	j * celly,
463	<	k * cellz );
442	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
443
444	<	makeElement( i * cellx + 0.5 * cellx,
466	<	j * celly + 0.5 * celly,
467	<	k * cellz );
444	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
445
446	<	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 );
446	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
447		}
448		}
449		}
450
451	<	if( have_extra ){
451	>	if (have_extra){
452		done = 0;
453
454		int start_ndx;
455	<	for( i=0; i < (n_cells+1) && !done; i++ ){
456	<	for( j=0; j < (n_cells+1) && !done; j++ ){
455	>	for (i = 0; i < (n_cells + 1) && !done; i++){
456	>	for (j = 0; j < (n_cells + 1) && !done; j++){
457	>	if (i < n_cells){
458	>	if (j < n_cells){
459	>	start_ndx = n_cells;
460	>	}
461	>	else
462	>	start_ndx = 0;
463	>	}
464	>	else
465	>	start_ndx = 0;
466
467	<	if( i < n_cells ){
467	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
468	>	makeElement(i * cellx, j * celly, k * cellz);
469	>	done = (current_mol >= tot_nmol);
470
471	<	if( j < n_cells ){
472	<	start_ndx = n_cells;
473	<	}
474	<	else start_ndx = 0;
475	<	}
494	<	else start_ndx = 0;
471	>	if (!done && n_per_extra > 1){
472	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
473	>	k * cellz);
474	>	done = (current_mol >= tot_nmol);
475	>	}
476
477	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
478	<
479	<	makeElement( i * cellx,
480	<	j * celly,
481	<	k * cellz );
501	<	done = ( current_mol >= tot_nmol );
502	<
503	<	if( !done && n_per_extra > 1 ){
504	<	makeElement( i * cellx + 0.5 * cellx,
505	<	j * celly + 0.5 * celly,
506	<	k * cellz );
507	<	done = ( current_mol >= tot_nmol );
508	<	}
509	<
510	<	if( !done && n_per_extra > 2){
511	<	makeElement( i * cellx,
512	<	j * celly + 0.5 * celly,
513	<	k * cellz + 0.5 * cellz );
514	<	done = ( current_mol >= tot_nmol );
515	<	}
477	>	if (!done && n_per_extra > 2){
478	>	makeElement(i * cellx, j * celly + 0.5 * celly,
479	>	k * cellz + 0.5 * cellz);
480	>	done = (current_mol >= tot_nmol);
481	>	}
482
483	<	if( !done && n_per_extra > 3){
484	<	makeElement( i * cellx + 0.5 * cellx,
485	<	j * celly,
486	<	k * cellz + 0.5 * cellz );
487	<	done = ( current_mol >= tot_nmol );
488	<	}
523	<	}
483	>	if (!done && n_per_extra > 3){
484	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
485	>	k * cellz + 0.5 * cellz);
486	>	done = (current_mol >= tot_nmol);
487	>	}
488	>	}
489		}
490		}
491		}
492
493	<	for( i=0; i<info[0].n_atoms; i++ ){
494	<	info[0].atoms[i]->setVel( vel );
493	>	for (i = 0; i < info[0].n_atoms; i++){
494	>	info[0].atoms[i]->setVel(vel);
495		}
496		}
497
498	<	void SimSetup::makeElement( double x, double y, double z ){
534	<
498	>	void SimSetup::makeElement(double x, double y, double z){
499		int k;
500		AtomStamp* current_atom;
501		DirectionalAtom* dAtom;
502		double rotMat[3][3];
503		double pos[3];
504
505	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
506	<
507	<	current_atom = comp_stamps[current_comp]->getAtom( k );
508	<	if( !current_atom->havePosition() ){
509	<	sprintf( painCave.errMsg,
510	<	"SimSetup:initFromBass error.\n"
511	<	"\tComponent %s, atom %s does not have a position specified.\n"
512	<	"\tThe initialization routine is unable to give a start"
513	<	" position.\n",
550	<	comp_stamps[current_comp]->getID(),
551	<	current_atom->getType() );
505	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
506	>	current_atom = comp_stamps[current_comp]->getAtom(k);
507	>	if (!current_atom->havePosition()){
508	>	sprintf(painCave.errMsg,
509	>	"SimSetup:initFromBass error.\n"
510	>	"\tComponent %s, atom %s does not have a position specified.\n"
511	>	"\tThe initialization routine is unable to give a start"
512	>	" position.\n",
513	>	comp_stamps[current_comp]->getID(), current_atom->getType());
514		painCave.isFatal = 1;
515		simError();
516		}
517	<
517	>
518		pos[0] = x + current_atom->getPosX();
519		pos[1] = y + current_atom->getPosY();
520		pos[2] = z + current_atom->getPosZ();
559	–
560	–	info[0].atoms[current_atom_ndx]->setPos( pos );
521
522	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
522	>	info[0].atoms[current_atom_ndx]->setPos(pos);
523
524	<	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
524	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
525	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
526
527		rotMat[0][0] = 1.0;
528		rotMat[0][1] = 0.0;
#	Line 575 | Line 536 | void SimSetup::makeElement( double x, double y, double
536		rotMat[2][1] = 0.0;
537		rotMat[2][2] = 1.0;
538
539	<	dAtom->setA( rotMat );
539	>	dAtom->setA(rotMat);
540		}
541
542		current_atom_ndx++;
#	Line 584 | Line 545 | void SimSetup::makeElement( double x, double y, double
545		current_mol++;
546		current_comp_mol++;
547
548	<	if( current_comp_mol >= components_nmol[current_comp] ){
588	<
548	>	if (current_comp_mol >= components_nmol[current_comp]){
549		current_comp_mol = 0;
550		current_comp++;
551		}
552		}
553
554
555	<	void SimSetup::gatherInfo( void ){
556	<	int i,j,k;
555	>	void SimSetup::gatherInfo(void){
556	>	int i, j, k;
557
558		ensembleCase = -1;
559		ffCase = -1;
560
561		// set the easy ones first
562
563	<	for( i=0; i<nInfo; i++){
563	>	for (i = 0; i < nInfo; i++){
564		info[i].target_temp = globals->getTargetTemp();
565		info[i].dt = globals->getDt();
566		info[i].run_time = globals->getRunTime();
#	Line 610 | Line 570 | void SimSetup::gatherInfo( void ){
570
571		// get the forceField
572
573	<	strcpy( force_field, globals->getForceField() );
573	>	strcpy(force_field, globals->getForceField());
574
575	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
576	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
577	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
575	>	if (!strcasecmp(force_field, "DUFF")){
576	>	ffCase = FF_DUFF;
577	>	}
578	>	else if (!strcasecmp(force_field, "LJ")){
579	>	ffCase = FF_LJ;
580	>	}
581	>	else if (!strcasecmp(force_field, "EAM")){
582	>	ffCase = FF_EAM;
583	>	}
584		else{
585	<	sprintf( painCave.errMsg,
586	<	"SimSetup Error. Unrecognized force field -> %s\n",
587	<	force_field );
588	<	painCave.isFatal = 1;
623	<	simError();
585	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
586	>	force_field);
587	>	painCave.isFatal = 1;
588	>	simError();
589		}
590
591	<	// get the ensemble
591	>	// get the ensemble
592
593	<	strcpy( ensemble, globals->getEnsemble() );
593	>	strcpy(ensemble, globals->getEnsemble());
594
595	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
596	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
597	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
595	>	if (!strcasecmp(ensemble, "NVE")){
596	>	ensembleCase = NVE_ENS;
597	>	}
598	>	else if (!strcasecmp(ensemble, "NVT")){
599	>	ensembleCase = NVT_ENS;
600	>	}
601	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
602		ensembleCase = NPTi_ENS;
603	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
604	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
605	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
603	>	}
604	>	else if (!strcasecmp(ensemble, "NPTf")){
605	>	ensembleCase = NPTf_ENS;
606	>	}
607	>	else if (!strcasecmp(ensemble, "NPTim")){
608	>	ensembleCase = NPTim_ENS;
609	>	}
610	>	else if (!strcasecmp(ensemble, "NPTfm")){
611	>	ensembleCase = NPTfm_ENS;
612	>	}
613		else{
614	<	sprintf( painCave.errMsg,
615	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
616	<	"reverting to NVE for this simulation.\n",
617	<	ensemble );
618	<	painCave.isFatal = 0;
619	<	simError();
620	<	strcpy( ensemble, "NVE" );
621	<	ensembleCase = NVE_ENS;
614	>	sprintf(painCave.errMsg,
615	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
616	>	"reverting to NVE for this simulation.\n",
617	>	ensemble);
618	>	painCave.isFatal = 0;
619	>	simError();
620	>	strcpy(ensemble, "NVE");
621	>	ensembleCase = NVE_ENS;
622		}
647	–
648	–	for(i=0; i<nInfo; i++){
649	–
650	–	strcpy( info[i].ensemble, ensemble );
623
624	+	for (i = 0; i < nInfo; i++){
625	+	strcpy(info[i].ensemble, ensemble);
626	+
627		// get the mixing rule
628
629	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
629	>	strcpy(info[i].mixingRule, globals->getMixingRule());
630		info[i].usePBC = globals->getPBC();
631		}
632	<
632	>
633		// get the components and calculate the tot_nMol and indvidual n_mol
634	<
634	>
635		the_components = globals->getComponents();
636		components_nmol = new int[n_components];
637
638
639	<	if( !globals->haveNMol() ){
639	>	if (!globals->haveNMol()){
640		// we don't have the total number of molecules, so we assume it is
641		// given in each component
642
643		tot_nmol = 0;
644	<	for( i=0; i<n_components; i++ ){
645	<
646	<	if( !the_components[i]->haveNMol() ){
647	<	// we have a problem
648	<	sprintf( painCave.errMsg,
649	<	"SimSetup Error. No global NMol or component NMol"
650	<	" given. Cannot calculate the number of atoms.\n" );
651	<	painCave.isFatal = 1;
677	<	simError();
644	>	for (i = 0; i < n_components; i++){
645	>	if (!the_components[i]->haveNMol()){
646	>	// we have a problem
647	>	sprintf(painCave.errMsg,
648	>	"SimSetup Error. No global NMol or component NMol"
649	>	" given. Cannot calculate the number of atoms.\n");
650	>	painCave.isFatal = 1;
651	>	simError();
652		}
653
654		tot_nmol += the_components[i]->getNMol();
#	Line 682 | Line 656 | void SimSetup::gatherInfo( void ){
656		}
657		}
658		else{
659	<	sprintf( painCave.errMsg,
660	<	"SimSetup error.\n"
661	<	"\tSorry, the ability to specify total"
662	<	" nMols and then give molfractions in the components\n"
663	<	"\tis not currently supported."
664	<	" Please give nMol in the components.\n" );
659	>	sprintf(painCave.errMsg,
660	>	"SimSetup error.\n"
661	>	"\tSorry, the ability to specify total"
662	>	" nMols and then give molfractions in the components\n"
663	>	"\tis not currently supported."
664	>	" Please give nMol in the components.\n");
665		painCave.isFatal = 1;
666		simError();
667		}
668
669		// set the status, sample, and thermal kick times
696	–
697	–	for(i=0; i<nInfo; i++){
670
671	<	if( globals->haveSampleTime() ){
671	>	for (i = 0; i < nInfo; i++){
672	>	if (globals->haveSampleTime()){
673		info[i].sampleTime = globals->getSampleTime();
674		info[i].statusTime = info[i].sampleTime;
675		info[i].thermalTime = info[i].sampleTime;
#	Line 706 | Line 679 | void SimSetup::gatherInfo( void ){
679		info[i].statusTime = info[i].sampleTime;
680		info[i].thermalTime = info[i].sampleTime;
681		}
682	<
683	<	if( globals->haveStatusTime() ){
682	>
683	>	if (globals->haveStatusTime()){
684		info[i].statusTime = globals->getStatusTime();
685		}
686	<
687	<	if( globals->haveThermalTime() ){
686	>
687	>	if (globals->haveThermalTime()){
688		info[i].thermalTime = globals->getThermalTime();
689		}
690
691	+	info[i].resetIntegrator = 0;
692	+	if( globals->haveResetTime() ){
693	+	info[i].resetTime = globals->getResetTime();
694	+	info[i].resetIntegrator = 1;
695	+	}
696	+
697		// check for the temperature set flag
698
699	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
700	<
699	>	if (globals->haveTempSet())
700	>	info[i].setTemp = globals->getTempSet();
701	>
702		// get some of the tricky things that may still be in the globals
703	<
703	>
704		double boxVector[3];
705	<	if( globals->haveBox() ){
705	>	if (globals->haveBox()){
706		boxVector[0] = globals->getBox();
707		boxVector[1] = globals->getBox();
708		boxVector[2] = globals->getBox();
709	<
710	<	info[i].setBox( boxVector );
709	>
710	>	info[i].setBox(boxVector);
711		}
712	<	else if( globals->haveDensity() ){
733	<
712	>	else if (globals->haveDensity()){
713		double vol;
714	<	vol = (double)tot_nmol / globals->getDensity();
715	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
714	>	vol = (double) tot_nmol / globals->getDensity();
715	>	boxVector[0] = pow(vol, (1.0 / 3.0));
716		boxVector[1] = boxVector[0];
717		boxVector[2] = boxVector[0];
718	<
719	<	info[i].setBox( boxVector );
720	<	}
718	>
719	>	info[i].setBox(boxVector);
720	>	}
721		else{
722	<	if( !globals->haveBoxX() ){
723	<	sprintf( painCave.errMsg,
724	<	"SimSetup error, no periodic BoxX size given.\n" );
725	<	painCave.isFatal = 1;
726	<	simError();
722	>	if (!globals->haveBoxX()){
723	>	sprintf(painCave.errMsg,
724	>	"SimSetup error, no periodic BoxX size given.\n");
725	>	painCave.isFatal = 1;
726	>	simError();
727		}
728		boxVector[0] = globals->getBoxX();
729	<
730	<	if( !globals->haveBoxY() ){
731	<	sprintf( painCave.errMsg,
732	<	"SimSetup error, no periodic BoxY size given.\n" );
733	<	painCave.isFatal = 1;
734	<	simError();
729	>
730	>	if (!globals->haveBoxY()){
731	>	sprintf(painCave.errMsg,
732	>	"SimSetup error, no periodic BoxY size given.\n");
733	>	painCave.isFatal = 1;
734	>	simError();
735		}
736		boxVector[1] = globals->getBoxY();
737	<
738	<	if( !globals->haveBoxZ() ){
739	<	sprintf( painCave.errMsg,
740	<	"SimSetup error, no periodic BoxZ size given.\n" );
741	<	painCave.isFatal = 1;
742	<	simError();
737	>
738	>	if (!globals->haveBoxZ()){
739	>	sprintf(painCave.errMsg,
740	>	"SimSetup error, no periodic BoxZ size given.\n");
741	>	painCave.isFatal = 1;
742	>	simError();
743		}
744		boxVector[2] = globals->getBoxZ();
766	–
767	–	info[i].setBox( boxVector );
768	–	}
745
746	+	info[i].setBox(boxVector);
747	+	}
748		}
749	+
750	+	//setup seed for random number generator
751	+	int seedValue;
752	+
753	+	if (globals->haveSeed()){
754	+	seedValue = globals->getSeed();
755	+
756	+	if(seedValue / 1E9 == 0){
757	+	sprintf(painCave.errMsg,
758	+	"Seed for sprng library should contain at least 9 digits\n"
759	+	"OOPSE will generate a seed for user\n");
760	+	painCave.isFatal = 0;
761	+	simError();
762	+
763	+	//using seed generated by system instead of invalid seed set by user
764	+	#ifndef IS_MPI
765	+	seedValue = make_sprng_seed();
766	+	#else
767	+	if (worldRank == 0){
768	+	seedValue = make_sprng_seed();
769	+	}
770	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
771	+	#endif
772	+	}
773	+	}//end of if branch of globals->haveSeed()
774	+	else{
775
776	+	#ifndef IS_MPI
777	+	seedValue = make_sprng_seed();
778	+	#else
779	+	if (worldRank == 0){
780	+	seedValue = make_sprng_seed();
781	+	}
782	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
783	+	#endif
784	+	}//end of globals->haveSeed()
785	+
786	+	for (int i = 0; i < nInfo; i++){
787	+	info[i].setSeed(seedValue);
788	+	}
789	+
790		#ifdef IS_MPI
791	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
791	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
792		MPIcheckPoint();
793		#endif // is_mpi
776	–
794		}
795
796
797	<	void SimSetup::finalInfoCheck( void ){
797	>	void SimSetup::finalInfoCheck(void){
798		int index;
799		int usesDipoles;
800		int i;
801
802	<	for(i=0; i<nInfo; i++){
802	>	for (i = 0; i < nInfo; i++){
803		// check electrostatic parameters
804	<
804	>
805		index = 0;
806		usesDipoles = 0;
807	<	while( (index < info[i].n_atoms) && !usesDipoles ){
807	>	while ((index < info[i].n_atoms) && !usesDipoles){
808		usesDipoles = (info[i].atoms[index])->hasDipole();
809		index++;
810		}
811	<
811	>
812		#ifdef IS_MPI
813		int myUse = usesDipoles;
814	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
814	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
815		#endif //is_mpi
816	<
816	>
817		double theEcr, theEst;
818	<
819	<	if (globals->getUseRF() ) {
818	>
819	>	if (globals->getUseRF()){
820		info[i].useReactionField = 1;
821	<
822	<	if( !globals->haveECR() ){
823	<	sprintf( painCave.errMsg,
824	<	"SimSetup Warning: using default value of 1/2 the smallest "
825	<	"box length for the electrostaticCutoffRadius.\n"
826	<	"I hope you have a very fast processor!\n");
827	<	painCave.isFatal = 0;
828	<	simError();
829	<	double smallest;
830	<	smallest = info[i].boxL[0];
831	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
832	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
833	<	theEcr = 0.5 * smallest;
834	<	} else {
835	<	theEcr = globals->getECR();
821	>
822	>	if (!globals->haveECR()){
823	>	sprintf(painCave.errMsg,
824	>	"SimSetup Warning: using default value of 1/2 the smallest "
825	>	"box length for the electrostaticCutoffRadius.\n"
826	>	"I hope you have a very fast processor!\n");
827	>	painCave.isFatal = 0;
828	>	simError();
829	>	double smallest;
830	>	smallest = info[i].boxL[0];
831	>	if (info[i].boxL[1] <= smallest)
832	>	smallest = info[i].boxL[1];
833	>	if (info[i].boxL[2] <= smallest)
834	>	smallest = info[i].boxL[2];
835	>	theEcr = 0.5 * smallest;
836		}
837	<
838	<	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();
837	>	else{
838	>	theEcr = globals->getECR();
839		}
840	<
841	<	info[i].setEcr( theEcr, theEst );
842	<
843	<	if(!globals->haveDielectric() ){
844	<	sprintf( painCave.errMsg,
845	<	"SimSetup Error: You are trying to use Reaction Field without"
846	<	"setting a dielectric constant!\n"
847	<	);
840	<	painCave.isFatal = 1;
841	<	simError();
840	>
841	>	if (!globals->haveEST()){
842	>	sprintf(painCave.errMsg,
843	>	"SimSetup Warning: using default value of 0.05 * the "
844	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
845	>	painCave.isFatal = 0;
846	>	simError();
847	>	theEst = 0.05 * theEcr;
848		}
849	<	info[i].dielectric = globals->getDielectric();
850	<	}
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 );
849	>	else{
850	>	theEst = globals->getEST();
851		}
852	<	}
852	>
853	>	info[i].setEcr(theEcr, theEst);
854	>
855	>	if (!globals->haveDielectric()){
856	>	sprintf(painCave.errMsg,
857	>	"SimSetup Error: You are trying to use Reaction Field without"
858	>	"setting a dielectric constant!\n");
859	>	painCave.isFatal = 1;
860	>	simError();
861	>	}
862	>	info[i].dielectric = globals->getDielectric();
863	>	}
864	>	else{
865	>	if (usesDipoles){
866	>	if (!globals->haveECR()){
867	>	sprintf(painCave.errMsg,
868	>	"SimSetup Warning: using default value of 1/2 the smallest "
869	>	"box length for the electrostaticCutoffRadius.\n"
870	>	"I hope you have a very fast processor!\n");
871	>	painCave.isFatal = 0;
872	>	simError();
873	>	double smallest;
874	>	smallest = info[i].boxL[0];
875	>	if (info[i].boxL[1] <= smallest)
876	>	smallest = info[i].boxL[1];
877	>	if (info[i].boxL[2] <= smallest)
878	>	smallest = info[i].boxL[2];
879	>	theEcr = 0.5 * smallest;
880	>	}
881	>	else{
882	>	theEcr = globals->getECR();
883	>	}
884	>
885	>	if (!globals->haveEST()){
886	>	sprintf(painCave.errMsg,
887	>	"SimSetup Warning: using default value of 0.05 * the "
888	>	"electrostaticCutoffRadius for the "
889	>	"electrostaticSkinThickness\n");
890	>	painCave.isFatal = 0;
891	>	simError();
892	>	theEst = 0.05 * theEcr;
893	>	}
894	>	else{
895	>	theEst = globals->getEST();
896	>	}
897	>
898	>	info[i].setEcr(theEcr, theEst);
899	>	}
900	>	}
901		}
902
903		#ifdef IS_MPI
904	<	strcpy( checkPointMsg, "post processing checks out" );
904	>	strcpy(checkPointMsg, "post processing checks out");
905		MPIcheckPoint();
906		#endif // is_mpi
886	–
907		}
908
909	<	void SimSetup::initSystemCoords( void ){
909	>	void SimSetup::initSystemCoords(void){
910		int i;
911	<
911	>
912		char* inName;
913
914	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
915
916	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
917	<
918	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
919	<
899	<	if( globals->haveInitialConfig() ){
900	<
916	>	for (i = 0; i < info[0].n_atoms; i++)
917	>	info[0].atoms[i]->setCoords();
918	>
919	>	if (globals->haveInitialConfig()){
920		InitializeFromFile* fileInit;
921		#ifdef IS_MPI // is_mpi
922	<	if( worldRank == 0 ){
922	>	if (worldRank == 0){
923		#endif //is_mpi
924		inName = globals->getInitialConfig();
925		double* tempDouble = new double[1000000];
926	<	fileInit = new InitializeFromFile( inName );
926	>	fileInit = new InitializeFromFile(inName);
927		#ifdef IS_MPI
928	<	}else fileInit = new InitializeFromFile( NULL );
928	>	}
929	>	else
930	>	fileInit = new InitializeFromFile(NULL);
931		#endif
932	<	fileInit->readInit( info ); // default velocities on
933	<
932	>	fileInit->readInit(info); // default velocities on
933	>
934		delete fileInit;
935		}
936		else{
916	–
937		#ifdef IS_MPI
938	<
938	>
939		// no init from bass
940	<
941	<	sprintf( painCave.errMsg,
942	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
940	>
941	>	sprintf(painCave.errMsg,
942	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
943		painCave.isFatal;
944		simError();
945	<
945	>
946		#else
947	<
947	>
948		initFromBass();
949	<
950	<
949	>
950	>
951		#endif
952		}
953	<
953	>
954		#ifdef IS_MPI
955	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
955	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
956		MPIcheckPoint();
957		#endif // is_mpi
938	–
958		}
959
960
961	<	void SimSetup::makeOutNames( void ){
943	<
961	>	void SimSetup::makeOutNames(void){
962		int k;
963
946	–
947	–	for(k=0; k<nInfo; k++){
964
965	+	for (k = 0; k < nInfo; k++){
966		#ifdef IS_MPI
967	<	if( worldRank == 0 ){
967	>	if (worldRank == 0){
968		#endif // is_mpi
969	<
970	<	if( globals->haveFinalConfig() ){
971	<	strcpy( info[k].finalName, globals->getFinalConfig() );
969	>
970	>	if (globals->haveFinalConfig()){
971	>	strcpy(info[k].finalName, globals->getFinalConfig());
972		}
973		else{
974	<	strcpy( info[k].finalName, inFileName );
975	<	char* endTest;
976	<	int nameLength = strlen( info[k].finalName );
977	<	endTest = &(info[k].finalName[nameLength - 5]);
978	<	if( !strcmp( endTest, ".bass" ) ){
979	<	strcpy( endTest, ".eor" );
980	<	}
981	<	else if( !strcmp( endTest, ".BASS" ) ){
982	<	strcpy( endTest, ".eor" );
983	<	}
984	<	else{
985	<	endTest = &(info[k].finalName[nameLength - 4]);
986	<	if( !strcmp( endTest, ".bss" ) ){
987	<	strcpy( endTest, ".eor" );
988	<	}
989	<	else if( !strcmp( endTest, ".mdl" ) ){
990	<	strcpy( endTest, ".eor" );
991	<	}
992	<	else{
993	<	strcat( info[k].finalName, ".eor" );
994	<	}
995	<	}
974	>	strcpy(info[k].finalName, inFileName);
975	>	char* endTest;
976	>	int nameLength = strlen(info[k].finalName);
977	>	endTest = &(info[k].finalName[nameLength - 5]);
978	>	if (!strcmp(endTest, ".bass")){
979	>	strcpy(endTest, ".eor");
980	>	}
981	>	else if (!strcmp(endTest, ".BASS")){
982	>	strcpy(endTest, ".eor");
983	>	}
984	>	else{
985	>	endTest = &(info[k].finalName[nameLength - 4]);
986	>	if (!strcmp(endTest, ".bss")){
987	>	strcpy(endTest, ".eor");
988	>	}
989	>	else if (!strcmp(endTest, ".mdl")){
990	>	strcpy(endTest, ".eor");
991	>	}
992	>	else{
993	>	strcat(info[k].finalName, ".eor");
994	>	}
995	>	}
996		}
997	<
997	>
998		// make the sample and status out names
999	<
1000	<	strcpy( info[k].sampleName, inFileName );
999	>
1000	>	strcpy(info[k].sampleName, inFileName);
1001		char* endTest;
1002	<	int nameLength = strlen( info[k].sampleName );
1002	>	int nameLength = strlen(info[k].sampleName);
1003		endTest = &(info[k].sampleName[nameLength - 5]);
1004	<	if( !strcmp( endTest, ".bass" ) ){
1005	<	strcpy( endTest, ".dump" );
1004	>	if (!strcmp(endTest, ".bass")){
1005	>	strcpy(endTest, ".dump");
1006		}
1007	<	else if( !strcmp( endTest, ".BASS" ) ){
1008	<	strcpy( endTest, ".dump" );
1007	>	else if (!strcmp(endTest, ".BASS")){
1008	>	strcpy(endTest, ".dump");
1009		}
1010		else{
1011	<	endTest = &(info[k].sampleName[nameLength - 4]);
1012	<	if( !strcmp( endTest, ".bss" ) ){
1013	<	strcpy( endTest, ".dump" );
1014	<	}
1015	<	else if( !strcmp( endTest, ".mdl" ) ){
1016	<	strcpy( endTest, ".dump" );
1017	<	}
1018	<	else{
1019	<	strcat( info[k].sampleName, ".dump" );
1020	<	}
1011	>	endTest = &(info[k].sampleName[nameLength - 4]);
1012	>	if (!strcmp(endTest, ".bss")){
1013	>	strcpy(endTest, ".dump");
1014	>	}
1015	>	else if (!strcmp(endTest, ".mdl")){
1016	>	strcpy(endTest, ".dump");
1017	>	}
1018	>	else{
1019	>	strcat(info[k].sampleName, ".dump");
1020	>	}
1021		}
1022	<
1023	<	strcpy( info[k].statusName, inFileName );
1024	<	nameLength = strlen( info[k].statusName );
1022	>
1023	>	strcpy(info[k].statusName, inFileName);
1024	>	nameLength = strlen(info[k].statusName);
1025		endTest = &(info[k].statusName[nameLength - 5]);
1026	<	if( !strcmp( endTest, ".bass" ) ){
1027	<	strcpy( endTest, ".stat" );
1026	>	if (!strcmp(endTest, ".bass")){
1027	>	strcpy(endTest, ".stat");
1028		}
1029	<	else if( !strcmp( endTest, ".BASS" ) ){
1030	<	strcpy( endTest, ".stat" );
1029	>	else if (!strcmp(endTest, ".BASS")){
1030	>	strcpy(endTest, ".stat");
1031		}
1032		else{
1033	<	endTest = &(info[k].statusName[nameLength - 4]);
1034	<	if( !strcmp( endTest, ".bss" ) ){
1035	<	strcpy( endTest, ".stat" );
1036	<	}
1037	<	else if( !strcmp( endTest, ".mdl" ) ){
1038	<	strcpy( endTest, ".stat" );
1039	<	}
1040	<	else{
1041	<	strcat( info[k].statusName, ".stat" );
1042	<	}
1033	>	endTest = &(info[k].statusName[nameLength - 4]);
1034	>	if (!strcmp(endTest, ".bss")){
1035	>	strcpy(endTest, ".stat");
1036	>	}
1037	>	else if (!strcmp(endTest, ".mdl")){
1038	>	strcpy(endTest, ".stat");
1039	>	}
1040	>	else{
1041	>	strcat(info[k].statusName, ".stat");
1042	>	}
1043		}
1044	<
1044	>
1045		#ifdef IS_MPI
1046	+
1047		}
1048		#endif // is_mpi
1049		}
1050		}
1051
1052
1053	<	void SimSetup::sysObjectsCreation( void ){
1054	<
1055	<	int i,k;
1038	<
1053	>	void SimSetup::sysObjectsCreation(void){
1054	>	int i, k;
1055	>
1056		// create the forceField
1057
1058		createFF();
#	Line 1050 | Line 1067 | void SimSetup::sysObjectsCreation( void ){
1067
1068		#ifdef IS_MPI
1069		// divide the molecules among the processors
1070	<
1070	>
1071		mpiMolDivide();
1072		#endif //is_mpi
1073	<
1073	>
1074		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1075	<
1075	>
1076		makeSysArrays();
1077
1078		// make and initialize the molecules (all but atomic coordinates)
1079	<
1079	>
1080		makeMolecules();
1081	<
1082	<	for(k=0; k<nInfo; k++){
1081	>
1082	>	for (k = 0; k < nInfo; k++){
1083		info[k].identArray = new int[info[k].n_atoms];
1084	<	for(i=0; i<info[k].n_atoms; i++){
1084	>	for (i = 0; i < info[k].n_atoms; i++){
1085		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1086		}
1087		}
1088		}
1089
1090
1091	<	void SimSetup::createFF( void ){
1091	>	void SimSetup::createFF(void){
1092	>	switch (ffCase){
1093	>	case FF_DUFF:
1094	>	the_ff = new DUFF();
1095	>	break;
1096
1097	<	switch( ffCase ){
1097	>	case FF_LJ:
1098	>	the_ff = new LJFF();
1099	>	break;
1100
1101	<	case FF_DUFF:
1102	<	the_ff = new DUFF();
1103	<	break;
1101	>	case FF_EAM:
1102	>	the_ff = new EAM_FF();
1103	>	break;
1104
1105	<	case FF_LJ:
1106	<	the_ff = new LJFF();
1107	<	break;
1108	<
1109	<	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();
1105	>	default:
1106	>	sprintf(painCave.errMsg,
1107	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1108	>	painCave.isFatal = 1;
1109	>	simError();
1110		}
1111
1112		#ifdef IS_MPI
1113	<	strcpy( checkPointMsg, "ForceField creation successful" );
1113	>	strcpy(checkPointMsg, "ForceField creation successful");
1114		MPIcheckPoint();
1115		#endif // is_mpi
1101	–
1116		}
1117
1118
1119	<	void SimSetup::compList( void ){
1106	<
1119	>	void SimSetup::compList(void){
1120		int i;
1121		char* id;
1122		LinkedMolStamp* headStamp = new LinkedMolStamp();
1123		LinkedMolStamp* currentStamp = NULL;
1124	<	comp_stamps = new MoleculeStamp*[n_components];
1125	<
1124	>	comp_stamps = new MoleculeStamp * [n_components];
1125	>
1126		// make an array of molecule stamps that match the components used.
1127		// also extract the used stamps out into a separate linked list
1128	<
1129	<	for(i=0; i<nInfo; i++){
1128	>
1129	>	for (i = 0; i < nInfo; i++){
1130		info[i].nComponents = n_components;
1131		info[i].componentsNmol = components_nmol;
1132		info[i].compStamps = comp_stamps;
1133		info[i].headStamp = headStamp;
1134		}
1122	–
1135
1124	–	for( i=0; i<n_components; i++ ){
1136
1137	+	for (i = 0; i < n_components; i++){
1138		id = the_components[i]->getType();
1139		comp_stamps[i] = NULL;
1140	<
1140	>
1141		// check to make sure the component isn't already in the list
1142
1143	<	comp_stamps[i] = headStamp->match( id );
1144	<	if( comp_stamps[i] == NULL ){
1133	<
1143	>	comp_stamps[i] = headStamp->match(id);
1144	>	if (comp_stamps[i] == NULL){
1145		// extract the component from the list;
1146	<
1147	<	currentStamp = stamps->extractMolStamp( id );
1148	<	if( currentStamp == NULL ){
1149	<	sprintf( painCave.errMsg,
1150	<	"SimSetup error: Component \"%s\" was not found in the "
1151	<	"list of declared molecules\n",
1152	<	id );
1153	<	painCave.isFatal = 1;
1154	<	simError();
1146	>
1147	>	currentStamp = stamps->extractMolStamp(id);
1148	>	if (currentStamp == NULL){
1149	>	sprintf(painCave.errMsg,
1150	>	"SimSetup error: Component \"%s\" was not found in the "
1151	>	"list of declared molecules\n",
1152	>	id);
1153	>	painCave.isFatal = 1;
1154	>	simError();
1155		}
1156	<
1157	<	headStamp->add( currentStamp );
1158	<	comp_stamps[i] = headStamp->match( id );
1156	>
1157	>	headStamp->add(currentStamp);
1158	>	comp_stamps[i] = headStamp->match(id);
1159		}
1160		}
1161
1162		#ifdef IS_MPI
1163	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1163	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1164		MPIcheckPoint();
1165		#endif // is_mpi
1155	–
1156	–
1166		}
1167
1168	<	void SimSetup::calcSysValues( void ){
1168	>	void SimSetup::calcSysValues(void){
1169		int i, j, k;
1170	<
1171	<	int *molMembershipArray;
1172	<
1170	>
1171	>	int* molMembershipArray;
1172	>
1173		tot_atoms = 0;
1174		tot_bonds = 0;
1175		tot_bends = 0;
1176		tot_torsions = 0;
1177	<	for( i=0; i<n_components; i++ ){
1178	<
1179	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1180	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1172	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1177	>	for (i = 0; i < n_components; i++){
1178	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1179	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1180	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1181		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1182		}
1183	<
1183	>
1184		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1185		molMembershipArray = new int[tot_atoms];
1186	<
1187	<	for(i=0; i<nInfo; i++){
1186	>
1187	>	for (i = 0; i < nInfo; i++){
1188		info[i].n_atoms = tot_atoms;
1189		info[i].n_bonds = tot_bonds;
1190		info[i].n_bends = tot_bends;
1191		info[i].n_torsions = tot_torsions;
1192		info[i].n_SRI = tot_SRI;
1193		info[i].n_mol = tot_nmol;
1194	<
1194	>
1195		info[i].molMembershipArray = molMembershipArray;
1196	<	}
1196	>	}
1197		}
1198
1199		#ifdef IS_MPI
1200
1201	<	void SimSetup::mpiMolDivide( void ){
1194	<
1201	>	void SimSetup::mpiMolDivide(void){
1202		int i, j, k;
1203		int localMol, allMol;
1204		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1205
1206	<	mpiSim = new mpiSimulation( info );
1207	<
1206	>	mpiSim = new mpiSimulation(info);
1207	>
1208		globalIndex = mpiSim->divideLabor();
1209
1210		// set up the local variables
1211	<
1211	>
1212		mol2proc = mpiSim->getMolToProcMap();
1213		molCompType = mpiSim->getMolComponentType();
1214	<
1214	>
1215		allMol = 0;
1216		localMol = 0;
1217		local_atoms = 0;
#	Line 1214 | Line 1221 | void SimSetup::mpiMolDivide( void ){
1221		globalAtomIndex = 0;
1222
1223
1224	<	for( i=0; i<n_components; i++ ){
1225	<
1226	<	for( j=0; j<components_nmol[i]; j++ ){
1227	<
1228	<	if( mol2proc[allMol] == worldRank ){
1229	<
1230	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1231	<	local_bonds +=    comp_stamps[i]->getNBonds();
1225	<	local_bends +=    comp_stamps[i]->getNBends();
1226	<	local_torsions += comp_stamps[i]->getNTorsions();
1227	<	localMol++;
1224	>	for (i = 0; i < n_components; i++){
1225	>	for (j = 0; j < components_nmol[i]; j++){
1226	>	if (mol2proc[allMol] == worldRank){
1227	>	local_atoms += comp_stamps[i]->getNAtoms();
1228	>	local_bonds += comp_stamps[i]->getNBonds();
1229	>	local_bends += comp_stamps[i]->getNBends();
1230	>	local_torsions += comp_stamps[i]->getNTorsions();
1231	>	localMol++;
1232		}
1233	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1233	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1234		info[0].molMembershipArray[globalAtomIndex] = allMol;
1235		globalAtomIndex++;
1236		}
1237
1238	<	allMol++;
1238	>	allMol++;
1239		}
1240		}
1241		local_SRI = local_bonds + local_bends + local_torsions;
1242	<
1242	>
1243		info[0].n_atoms = mpiSim->getMyNlocal();
1244	<
1245	<	if( local_atoms != info[0].n_atoms ){
1246	<	sprintf( painCave.errMsg,
1247	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1248	<	" localAtom (%d) are not equal.\n",
1249	<	info[0].n_atoms,
1246	<	local_atoms );
1244	>
1245	>	if (local_atoms != info[0].n_atoms){
1246	>	sprintf(painCave.errMsg,
1247	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1248	>	" localAtom (%d) are not equal.\n",
1249	>	info[0].n_atoms, local_atoms);
1250		painCave.isFatal = 1;
1251		simError();
1252		}
#	Line 1254 | Line 1257 | void SimSetup::mpiMolDivide( void ){
1257		info[0].n_SRI = local_SRI;
1258		info[0].n_mol = localMol;
1259
1260	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1260	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1261		MPIcheckPoint();
1262		}
1263	<
1263	>
1264		#endif // is_mpi
1265
1266
1267	<	void SimSetup::makeSysArrays( void ){
1267	>	void SimSetup::makeSysArrays(void){
1268		int i, j, k, l;
1269
1270		Atom** the_atoms;
1271		Molecule* the_molecules;
1272		Exclude** the_excludes;
1273
1274	<
1275	<	for(l=0; l<nInfo; l++){
1273	<
1274	>
1275	>	for (l = 0; l < nInfo; l++){
1276		// create the atom and short range interaction arrays
1277	<
1278	<	the_atoms = new Atom*[info[l].n_atoms];
1277	>
1278	>	the_atoms = new Atom * [info[l].n_atoms];
1279		the_molecules = new Molecule[info[l].n_mol];
1280		int molIndex;
1281
1282		// initialize the molecule's stampID's
1283	<
1283	>
1284		#ifdef IS_MPI
1285	<
1286	<
1285	>
1286	>
1287		molIndex = 0;
1288	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1289	<
1290	<	if(mol2proc[i] == worldRank ){
1291	<	the_molecules[molIndex].setStampID( molCompType[i] );
1292	<	the_molecules[molIndex].setMyIndex( molIndex );
1293	<	the_molecules[molIndex].setGlobalIndex( i );
1292	<	molIndex++;
1288	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1289	>	if (mol2proc[i] == worldRank){
1290	>	the_molecules[molIndex].setStampID(molCompType[i]);
1291	>	the_molecules[molIndex].setMyIndex(molIndex);
1292	>	the_molecules[molIndex].setGlobalIndex(i);
1293	>	molIndex++;
1294		}
1295		}
1296	<
1296	>
1297		#else // is_mpi
1298	<
1298	>
1299		molIndex = 0;
1300		globalAtomIndex = 0;
1301	<	for(i=0; i<n_components; i++){
1302	<	for(j=0; j<components_nmol[i]; j++ ){
1303	<	the_molecules[molIndex].setStampID( i );
1304	<	the_molecules[molIndex].setMyIndex( molIndex );
1305	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1306	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1307	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1308	<	globalAtomIndex++;
1309	<	}
1310	<	molIndex++;
1301	>	for (i = 0; i < n_components; i++){
1302	>	for (j = 0; j < components_nmol[i]; j++){
1303	>	the_molecules[molIndex].setStampID(i);
1304	>	the_molecules[molIndex].setMyIndex(molIndex);
1305	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1306	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1307	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1308	>	globalAtomIndex++;
1309	>	}
1310	>	molIndex++;
1311		}
1312		}
1313	<
1314	<
1313	>
1314	>
1315		#endif // is_mpi
1316
1317
1318	<	if( info[l].n_SRI ){
1318	<
1318	>	if (info[l].n_SRI){
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);
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		else{
1328	<
1329	<	Exclude::createArray( 1 );
1330	<	the_excludes = new Exclude*;
1328	>	Exclude::createArray(1);
1329	>	the_excludes = new Exclude * ;
1330		the_excludes[0] = new Exclude(0);
1331	<	the_excludes[0]->setPair( 0,0 );
1331	>	the_excludes[0]->setPair(0, 0);
1332		info[l].globalExcludes = new int;
1333		info[l].globalExcludes[0] = 0;
1334		info[l].n_exclude = 0;
#	Line 1342 | Line 1341 | void SimSetup::makeSysArrays( void ){
1341		info[l].nGlobalExcludes = 0;
1342		info[l].excludes = the_excludes;
1343
1344	<	the_ff->setSimInfo( info );
1346	<
1344	>	the_ff->setSimInfo(info);
1345		}
1346		}
1347
1348	<	void SimSetup::makeIntegrator( void ){
1351	<
1348	>	void SimSetup::makeIntegrator(void){
1349		int k;
1350
1351	<	NVT<RealIntegrator>*  myNVT = NULL;
1352	<	NPTi<RealIntegrator>* myNPTi = NULL;
1351	>	NVT<RealIntegrator>* myNVT = NULL;
1352	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1353		NPTf<RealIntegrator>* myNPTf = NULL;
1354		NPTim<RealIntegrator>* myNPTim = NULL;
1355		NPTfm<RealIntegrator>* myNPTfm = NULL;
1356	<
1357	<	for(k=0; k<nInfo; k++){
1358	<
1359	<	switch( ensembleCase ){
1360	<
1361	<	case NVE_ENS:
1362	<	if (globals->haveZconstraints()){
1363	<	setupZConstraint(info[k]);
1364	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1365	<	}
1356	>
1357	>	for (k = 0; k < nInfo; k++){
1358	>	switch (ensembleCase){
1359	>	case NVE_ENS:
1360	>	if (globals->haveZconstraints()){
1361	>	setupZConstraint(info[k]);
1362	>	new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1363	>	}
1364	>	else
1365	>	new NVE<RealIntegrator>(&(info[k]), the_ff);
1366	>	break;
1367
1368	<	else
1369	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1370	<	break;
1371	<
1372	<	case NVT_ENS:
1373	<	if (globals->haveZconstraints()){
1374	<	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 );
1368	>	case NVT_ENS:
1369	>	if (globals->haveZconstraints()){
1370	>	setupZConstraint(info[k]);
1371	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1372	>	}
1373	>	else
1374	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1375
1376	<	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 );
1376	>	myNVT->setTargetTemp(globals->getTargetTemp());
1377
1378	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1379	<
1380	<	if (globals->haveTargetPressure())
1381	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1382	<	else {
1383	<	sprintf( painCave.errMsg,
1384	<	"SimSetup error: If you use a constant pressure\n"
1385	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1386	<	painCave.isFatal = 1;
1387	<	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 );
1378	>	if (globals->haveTauThermostat())
1379	>	myNVT->setTauThermostat(globals->getTauThermostat());
1380	>	else{
1381	>	sprintf(painCave.errMsg,
1382	>	"SimSetup error: If you use the NVT\n"
1383	>	"    ensemble, you must set tauThermostat.\n");
1384	>	painCave.isFatal = 1;
1385	>	simError();
1386	>	}
1387	>	break;
1388
1389	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1390	<
1391	<	if (globals->haveTargetPressure())
1392	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1393	<	else {
1394	<	sprintf( painCave.errMsg,
1395	<	"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 );
1389	>	case NPTi_ENS:
1390	>	if (globals->haveZconstraints()){
1391	>	setupZConstraint(info[k]);
1392	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1393	>	}
1394	>	else
1395	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1396
1397	<	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 );
1397	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1398
1399	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1400	<
1401	<	if (globals->haveTargetPressure())
1402	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1403	<	else {
1404	<	sprintf( painCave.errMsg,
1405	<	"SimSetup error: If you use a constant pressure\n"
1406	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1407	<	painCave.isFatal = 1;
1408	<	simError();
1409	<	}
1410	<
1411	<	if( globals->haveTauThermostat() )
1412	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1413	<	else{
1414	<	sprintf( painCave.errMsg,
1415	<	"SimSetup error: If you use an NPT\n"
1416	<	"    ensemble, you must set tauThermostat.\n");
1417	<	painCave.isFatal = 1;
1418	<	simError();
1419	<	}
1420	<
1421	<	if( globals->haveTauBarostat() )
1422	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1423	<	else{
1424	<	sprintf( painCave.errMsg,
1425	<	"SimSetup error: If you use an NPT\n"
1426	<	"    ensemble, you must set tauBarostat.\n");
1427	<	painCave.isFatal = 1;
1428	<	simError();
1429	<	}
1430	<	break;
1431	<
1432	<	default:
1433	<	sprintf( painCave.errMsg,
1434	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1435	<	painCave.isFatal = 1;
1436	<	simError();
1399	>	if (globals->haveTargetPressure())
1400	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1401	>	else{
1402	>	sprintf(painCave.errMsg,
1403	>	"SimSetup error: If you use a constant pressure\n"
1404	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1405	>	painCave.isFatal = 1;
1406	>	simError();
1407	>	}
1408	>
1409	>	if (globals->haveTauThermostat())
1410	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1411	>	else{
1412	>	sprintf(painCave.errMsg,
1413	>	"SimSetup error: If you use an NPT\n"
1414	>	"    ensemble, you must set tauThermostat.\n");
1415	>	painCave.isFatal = 1;
1416	>	simError();
1417	>	}
1418	>
1419	>	if (globals->haveTauBarostat())
1420	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1421	>	else{
1422	>	sprintf(painCave.errMsg,
1423	>	"SimSetup error: If you use an NPT\n"
1424	>	"    ensemble, you must set tauBarostat.\n");
1425	>	painCave.isFatal = 1;
1426	>	simError();
1427	>	}
1428	>	break;
1429	>
1430	>	case NPTf_ENS:
1431	>	if (globals->haveZconstraints()){
1432	>	setupZConstraint(info[k]);
1433	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff);
1434	>	}
1435	>	else
1436	>	myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff);
1437	>
1438	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1439	>
1440	>	if (globals->haveTargetPressure())
1441	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1442	>	else{
1443	>	sprintf(painCave.errMsg,
1444	>	"SimSetup error: If you use a constant pressure\n"
1445	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1446	>	painCave.isFatal = 1;
1447	>	simError();
1448	>	}
1449	>
1450	>	if (globals->haveTauThermostat())
1451	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1452	>	else{
1453	>	sprintf(painCave.errMsg,
1454	>	"SimSetup error: If you use an NPT\n"
1455	>	"    ensemble, you must set tauThermostat.\n");
1456	>	painCave.isFatal = 1;
1457	>	simError();
1458	>	}
1459	>
1460	>	if (globals->haveTauBarostat())
1461	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1462	>	else{
1463	>	sprintf(painCave.errMsg,
1464	>	"SimSetup error: If you use an NPT\n"
1465	>	"    ensemble, you must set tauBarostat.\n");
1466	>	painCave.isFatal = 1;
1467	>	simError();
1468	>	}
1469	>	break;
1470	>
1471	>	case NPTim_ENS:
1472	>	if (globals->haveZconstraints()){
1473	>	setupZConstraint(info[k]);
1474	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >(&(info[k]), the_ff);
1475	>	}
1476	>	else
1477	>	myNPTim = new NPTim<RealIntegrator>(&(info[k]), the_ff);
1478	>
1479	>	myNPTim->setTargetTemp(globals->getTargetTemp());
1480	>
1481	>	if (globals->haveTargetPressure())
1482	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1483	>	else{
1484	>	sprintf(painCave.errMsg,
1485	>	"SimSetup error: If you use a constant pressure\n"
1486	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1487	>	painCave.isFatal = 1;
1488	>	simError();
1489	>	}
1490	>
1491	>	if (globals->haveTauThermostat())
1492	>	myNPTim->setTauThermostat(globals->getTauThermostat());
1493	>	else{
1494	>	sprintf(painCave.errMsg,
1495	>	"SimSetup error: If you use an NPT\n"
1496	>	"    ensemble, you must set tauThermostat.\n");
1497	>	painCave.isFatal = 1;
1498	>	simError();
1499	>	}
1500	>
1501	>	if (globals->haveTauBarostat())
1502	>	myNPTim->setTauBarostat(globals->getTauBarostat());
1503	>	else{
1504	>	sprintf(painCave.errMsg,
1505	>	"SimSetup error: If you use an NPT\n"
1506	>	"    ensemble, you must set tauBarostat.\n");
1507	>	painCave.isFatal = 1;
1508	>	simError();
1509	>	}
1510	>	break;
1511	>
1512	>	case NPTfm_ENS:
1513	>	if (globals->haveZconstraints()){
1514	>	setupZConstraint(info[k]);
1515	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff);
1516	>	}
1517	>	else
1518	>	myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff);
1519	>
1520	>	myNPTfm->setTargetTemp(globals->getTargetTemp());
1521	>
1522	>	if (globals->haveTargetPressure())
1523	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1524	>	else{
1525	>	sprintf(painCave.errMsg,
1526	>	"SimSetup error: If you use a constant pressure\n"
1527	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1528	>	painCave.isFatal = 1;
1529	>	simError();
1530	>	}
1531	>
1532	>	if (globals->haveTauThermostat())
1533	>	myNPTfm->setTauThermostat(globals->getTauThermostat());
1534	>	else{
1535	>	sprintf(painCave.errMsg,
1536	>	"SimSetup error: If you use an NPT\n"
1537	>	"    ensemble, you must set tauThermostat.\n");
1538	>	painCave.isFatal = 1;
1539	>	simError();
1540	>	}
1541	>
1542	>	if (globals->haveTauBarostat())
1543	>	myNPTfm->setTauBarostat(globals->getTauBarostat());
1544	>	else{
1545	>	sprintf(painCave.errMsg,
1546	>	"SimSetup error: If you use an NPT\n"
1547	>	"    ensemble, you must set tauBarostat.\n");
1548	>	painCave.isFatal = 1;
1549	>	simError();
1550	>	}
1551	>	break;
1552	>
1553	>	default:
1554	>	sprintf(painCave.errMsg,
1555	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1556	>	painCave.isFatal = 1;
1557	>	simError();
1558		}
1559		}
1560		}
1561
1562	<	void SimSetup::initFortran( void ){
1570	<
1562	>	void SimSetup::initFortran(void){
1563		info[0].refreshSim();
1564	<
1565	<	if( !strcmp( info[0].mixingRule, "standard") ){
1566	<	the_ff->initForceField( LB_MIXING_RULE );
1564	>
1565	>	if (!strcmp(info[0].mixingRule, "standard")){
1566	>	the_ff->initForceField(LB_MIXING_RULE);
1567		}
1568	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1569	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1568	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1569	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1570		}
1571		else{
1572	<	sprintf( painCave.errMsg,
1573	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1582	<	info[0].mixingRule );
1572	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1573	>	info[0].mixingRule);
1574		painCave.isFatal = 1;
1575		simError();
1576		}
1577
1578
1579		#ifdef IS_MPI
1580	<	strcpy( checkPointMsg,
1590	<	"Successfully intialized the mixingRule for Fortran." );
1580	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1581		MPIcheckPoint();
1582		#endif // is_mpi
1593	–
1583		}
1584
1585	<	void SimSetup::setupZConstraint(SimInfo& theInfo)
1586	<	{
1587	<	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	<	}
1585	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1586	>	int nZConstraints;
1587	>	ZconStamp** zconStamp;
1588
1589	<	//
1590	<	nZConstraints = globals->getNzConstraints();
1591	<	theInfo.nZconstraints = nZConstraints;
1592	<
1593	<	zconStamp = globals->getZconStamp();
1594	<	ZConsParaItem tempParaItem;
1589	>	if (globals->haveZconstraintTime()){
1590	>	//add sample time of z-constraint  into SimInfo's property list
1591	>	DoubleData* zconsTimeProp = new DoubleData();
1592	>	zconsTimeProp->setID(ZCONSTIME_ID);
1593	>	zconsTimeProp->setData(globals->getZconsTime());
1594	>	theInfo.addProperty(zconsTimeProp);
1595	>	}
1596	>	else{
1597	>	sprintf(painCave.errMsg,
1598	>	"ZConstraint error: If you use an ZConstraint\n"
1599	>	" , you must set sample time.\n");
1600	>	painCave.isFatal = 1;
1601	>	simError();
1602	>	}
1603
1604	<	ZConsParaData* zconsParaData = new ZConsParaData();
1605	<	zconsParaData->setID(ZCONSPARADATA_ID);
1606	<
1607	<	for(int i = 0; i < nZConstraints; i++){
1604	>	//push zconsTol into siminfo, if user does not specify
1605	>	//value for zconsTol, a default value will be used
1606	>	DoubleData* zconsTol = new DoubleData();
1607	>	zconsTol->setID(ZCONSTOL_ID);
1608	>	if (globals->haveZconsTol()){
1609	>	zconsTol->setData(globals->getZconsTol());
1610	>	}
1611	>	else{
1612	>	double defaultZConsTol = 0.01;
1613	>	sprintf(painCave.errMsg,
1614	>	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1615	>	" , default value %f is used.\n",
1616	>	defaultZConsTol);
1617	>	painCave.isFatal = 0;
1618	>	simError();
1619	>
1620	>	zconsTol->setData(defaultZConsTol);
1621	>	}
1622	>	theInfo.addProperty(zconsTol);
1623	>
1624	>	//set Force Subtraction Policy
1625	>	StringData* zconsForcePolicy = new StringData();
1626	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1627	>
1628	>	if (globals->haveZconsForcePolicy()){
1629	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1630	>	}
1631	>	else{
1632	>	sprintf(painCave.errMsg,
1633	>	"ZConstraint Warning: User does not set force Subtraction policy, "
1634	>	"PolicyByMass is used\n");
1635	>	painCave.isFatal = 0;
1636	>	simError();
1637	>	zconsForcePolicy->setData("BYMASS");
1638	>	}
1639	>
1640	>	theInfo.addProperty(zconsForcePolicy);
1641	>
1642	>	//Determine the name of ouput file and add it into SimInfo's property list
1643	>	//Be careful, do not use inFileName, since it is a pointer which
1644	>	//point to a string at master node, and slave nodes do not contain that string
1645	>
1646	>	string zconsOutput(theInfo.finalName);
1647	>
1648	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1649	>
1650	>	StringData* zconsFilename = new StringData();
1651	>	zconsFilename->setID(ZCONSFILENAME_ID);
1652	>	zconsFilename->setData(zconsOutput);
1653	>
1654	>	theInfo.addProperty(zconsFilename);
1655	>
1656	>	//setup index, pos and other parameters of z-constraint molecules
1657	>	nZConstraints = globals->getNzConstraints();
1658	>	theInfo.nZconstraints = nZConstraints;
1659	>
1660	>	zconStamp = globals->getZconStamp();
1661	>	ZConsParaItem tempParaItem;
1662	>
1663	>	ZConsParaData* zconsParaData = new ZConsParaData();
1664	>	zconsParaData->setID(ZCONSPARADATA_ID);
1665	>
1666	>	for (int i = 0; i < nZConstraints; i++){
1667		tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1668		tempParaItem.zPos = zconStamp[i]->getZpos();
1669		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1670		tempParaItem.kRatio = zconStamp[i]->getKratio();
1671
1672		zconsParaData->addItem(tempParaItem);
1673	<	}
1673	>	}
1674
1675	<	//sort the parameters by index of molecules
1676	<	zconsParaData->sortByIndex();
1677	<
1678	<	//push data into siminfo, therefore, we can retrieve later
1679	<	theInfo.addProperty(zconsParaData);
1675	>	//check the uniqueness of index
1676	>	if(!zconsParaData->isIndexUnique()){
1677	>	sprintf(painCave.errMsg,
1678	>	"ZConstraint Error: molIndex is not unique\n");
1679	>	painCave.isFatal = 1;
1680	>	simError();
1681	>	}
1682
1683	<	//push zconsTol into siminfo, if user does not specify
1684	<	//value for zconsTol, a default value will be used
1685	<	DoubleData* zconsTol = new DoubleData();
1686	<	zconsTol->setID(ZCONSTOL_ID);
1687	<	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);
1683	>	//sort the parameters by index of molecules
1684	>	zconsParaData->sortByIndex();
1685	>
1686	>	//push data into siminfo, therefore, we can retrieve later
1687	>	theInfo.addProperty(zconsParaData);
1688		}

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