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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 814 by mmeineke, Thu Oct 23 19:57:25 2003 UTC

#	Line 3 | Line 3
3		#include <iostream>
4		#include <cmath>
5		#include <string>
6	<
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8		#include "ReadWrite.hpp"
9		#include "parse_me.h"
#	Line 21 | Line 21
21		#define NVT_ENS        1
22		#define NPTi_ENS       2
23		#define NPTf_ENS       3
24	<	#define NPTim_ENS      4
25	<	#define NPTfm_ENS      5
24	>	#define NPTxyz_ENS     4
25
26	+
27		#define FF_DUFF 0
28		#define FF_LJ   1
29		#define FF_EAM  2
#	Line 31 | Line 31 | SimSetup::SimSetup(){
31		using namespace std;
32
33		SimSetup::SimSetup(){
34	–
34		isInfoArray = 0;
35		nInfo = 1;
36	<
36	>
37		stamps = new MakeStamps();
38		globals = new Globals();
39	<
40	<
39	>
40	>
41		#ifdef IS_MPI
42	<	strcpy( checkPointMsg, "SimSetup creation successful" );
42	>	strcpy(checkPointMsg, "SimSetup creation successful");
43		MPIcheckPoint();
44		#endif // IS_MPI
45		}
#	Line 50 | Line 49 | void SimSetup::setSimInfo( SimInfo* the_info, int theN
49		delete globals;
50		}
51
52	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
53	<	info = the_info;
54	<	nInfo = theNinfo;
55	<	isInfoArray = 1;
52	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
53	>	info = the_info;
54	>	nInfo = theNinfo;
55	>	isInfoArray = 1;
56		}
57
58
59	<	void SimSetup::parseFile( char* fileName ){
61	<
59	>	void SimSetup::parseFile(char* fileName){
60		#ifdef IS_MPI
61	<	if( worldRank == 0 ){
61	>	if (worldRank == 0){
62		#endif // is_mpi
63	<
63	>
64		inFileName = fileName;
65	<	set_interface_stamps( stamps, globals );
66	<
65	>	set_interface_stamps(stamps, globals);
66	>
67		#ifdef IS_MPI
68		mpiEventInit();
69		#endif
70
71	<	yacc_BASS( fileName );
71	>	yacc_BASS(fileName);
72
73		#ifdef IS_MPI
74		throwMPIEvent(NULL);
75		}
76	<	else receiveParse();
76	>	else{
77	>	receiveParse();
78	>	}
79		#endif
80
81		}
82
83		#ifdef IS_MPI
84		void SimSetup::receiveParse(void){
85	<
86	<	set_interface_stamps( stamps, globals );
87	<	mpiEventInit();
88	<	MPIcheckPoint();
89	<	mpiEventLoop();
90	<
85	>	set_interface_stamps(stamps, globals);
86	>	mpiEventInit();
87	>	MPIcheckPoint();
88	>	mpiEventLoop();
89		}
90
91		#endif // is_mpi
92
93		void SimSetup::createSim(void){
94
97	–	int i, j, k, globalAtomIndex;
98	–
95		// gather all of the information from the Bass file
96
97		gatherInfo();
#	Line 110 | Line 106 | void SimSetup::createSim(void){
106
107		// initialize the system coordinates
108
109	<	if( !isInfoArray ) initSystemCoords();
109	>	if (!isInfoArray){
110	>	initSystemCoords();
111
112	+	if( !(globals->getUseInitTime()) )
113	+	info[0].currentTime = 0.0;
114	+	}
115	+
116		// make the output filenames
117
118		makeOutNames();
119	<
119	>
120		// make the integrator
121	<
121	>
122		makeIntegrator();
123	<
123	>
124		#ifdef IS_MPI
125		mpiSim->mpiRefresh();
126		#endif
#	Line 127 | Line 128 | void SimSetup::createSim(void){
128		// initialize the Fortran
129
130		initFortran();
130	–
131	–
132	–
131		}
132
133
134	<	void SimSetup::makeMolecules( void ){
135	<
138	<	int k,l;
134	>	void SimSetup::makeMolecules(void){
135	>	int k;
136		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
137		molInit molInfo;
138		DirectionalAtom* dAtom;
#	Line 150 | Line 147 | void SimSetup::makeMolecules( void ){
147		bend_set* theBends;
148		torsion_set* theTorsions;
149
150	<
150	>
151		//init the forceField paramters
152
153		the_ff->readParams();
154
155	<
155	>
156		// init the atoms
157
158		double ux, uy, uz, u, uSqr;
162	–
163	–	for(k=0; k<nInfo; k++){
164	–
165	–	the_ff->setSimInfo( &(info[k]) );
159
160	+	for (k = 0; k < nInfo; k++){
161	+	the_ff->setSimInfo(&(info[k]));
162	+
163		atomOffset = 0;
164		excludeOffset = 0;
165	<	for(i=0; i<info[k].n_mol; i++){
170	<
165	>	for (i = 0; i < info[k].n_mol; i++){
166		stampID = info[k].molecules[i].getStampID();
167
168	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
169	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
170	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
168	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
169	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
170	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
171		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
172		molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
173	<
173	>
174		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
175		molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
176	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
177	<	molInfo.myBends = new Bend*[molInfo.nBends];
178	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
176	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
177	>	molInfo.myBends = new Bend * [molInfo.nBends];
178	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
179
180		theBonds = new bond_pair[molInfo.nBonds];
181		theBends = new bend_set[molInfo.nBends];
182		theTorsions = new torsion_set[molInfo.nTorsions];
183	<
183	>
184		// make the Atoms
185	<
186	<	for(j=0; j<molInfo.nAtoms; j++){
187	<
188	<	currentAtom = comp_stamps[stampID]->getAtom( j );
189	<	if( currentAtom->haveOrientation() ){
190	<
191	<	dAtom = new DirectionalAtom( (j + atomOffset),
192	<	info[k].getConfiguration() );
193	<	info[k].n_oriented++;
194	<	molInfo.myAtoms[j] = dAtom;
195	<
196	<	ux = currentAtom->getOrntX();
197	<	uy = currentAtom->getOrntY();
198	<	uz = currentAtom->getOrntZ();
199	<
200	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
201	<
202	<	u = sqrt( uSqr );
203	<	ux = ux / u;
204	<	uy = uy / u;
205	<	uz = uz / u;
206	<
207	<	dAtom->setSUx( ux );
208	<	dAtom->setSUy( uy );
209	<	dAtom->setSUz( uz );
210	<	}
211	<	else{
212	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
213	<	info[k].getConfiguration() );
214	<	}
220	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221	<
185	>
186	>	for (j = 0; j < molInfo.nAtoms; j++){
187	>	currentAtom = comp_stamps[stampID]->getAtom(j);
188	>	if (currentAtom->haveOrientation()){
189	>	dAtom = new DirectionalAtom((j + atomOffset),
190	>	info[k].getConfiguration());
191	>	info[k].n_oriented++;
192	>	molInfo.myAtoms[j] = dAtom;
193	>
194	>	ux = currentAtom->getOrntX();
195	>	uy = currentAtom->getOrntY();
196	>	uz = currentAtom->getOrntZ();
197	>
198	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
199	>
200	>	u = sqrt(uSqr);
201	>	ux = ux / u;
202	>	uy = uy / u;
203	>	uz = uz / u;
204	>
205	>	dAtom->setSUx(ux);
206	>	dAtom->setSUy(uy);
207	>	dAtom->setSUz(uz);
208	>	}
209	>	else{
210	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
211	>	info[k].getConfiguration());
212	>	}
213	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
214	>
215		#ifdef IS_MPI
216	<
217	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
218	<
216	>
217	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
218	>
219		#endif // is_mpi
220		}
221	<
222	<	// make the bonds
223	<	for(j=0; j<molInfo.nBonds; j++){
224	<
225	<	currentBond = comp_stamps[stampID]->getBond( j );
226	<	theBonds[j].a = currentBond->getA() + atomOffset;
227	<	theBonds[j].b = currentBond->getB() + atomOffset;
228	<
229	<	exI = theBonds[j].a;
230	<	exJ = theBonds[j].b;
231	<
232	<	// exclude_I must always be the smaller of the pair
233	<	if( exI > exJ ){
234	<	tempEx = exI;
235	<	exI = exJ;
236	<	exJ = tempEx;
244	<	}
221	>
222	>	// make the bonds
223	>	for (j = 0; j < molInfo.nBonds; j++){
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;
236	>	}
237		#ifdef IS_MPI
238	<	tempEx = exI;
239	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
240	<	tempEx = exJ;
241	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
242	<
243	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
238	>	tempEx = exI;
239	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
240	>	tempEx = exJ;
241	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
242	>
243	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
244		#else  // isn't MPI
245	<
246	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
245	>
246	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
247		#endif  //is_mpi
248		}
249		excludeOffset += molInfo.nBonds;
250	<
250	>
251		//make the bends
252	<	for(j=0; j<molInfo.nBends; j++){
253	<
254	<	currentBend = comp_stamps[stampID]->getBend( j );
255	<	theBends[j].a = currentBend->getA() + atomOffset;
256	<	theBends[j].b = currentBend->getB() + atomOffset;
257	<	theBends[j].c = currentBend->getC() + atomOffset;
258	<
259	<	if( currentBend->haveExtras() ){
260	<
261	<	extras = currentBend->getExtras();
262	<	current_extra = extras;
263	<
264	<	while( current_extra != NULL ){
265	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
266	<
267	<	switch( current_extra->getType() ){
268	<
269	<	case 0:
270	<	theBends[j].ghost =
271	<	current_extra->getInt() + atomOffset;
272	<	theBends[j].isGhost = 1;
273	<	break;
274	<
275	<	case 1:
276	<	theBends[j].ghost =
277	<	(int)current_extra->getDouble() + atomOffset;
278	<	theBends[j].isGhost = 1;
279	<	break;
280	<
281	<	default:
282	<	sprintf( painCave.errMsg,
283	<	"SimSetup Error: ghostVectorSource was neither a "
284	<	"double nor an int.\n"
285	<	"-->Bend[%d] in %s\n",
286	<	j, comp_stamps[stampID]->getID() );
287	<	painCave.isFatal = 1;
288	<	simError();
289	<	}
290	<	}
291	<
292	<	else{
293	<
294	<	sprintf( painCave.errMsg,
295	<	"SimSetup Error: unhandled bend assignment:\n"
296	<	"    -->%s in Bend[%d] in %s\n",
297	<	current_extra->getlhs(),
298	<	j, comp_stamps[stampID]->getID() );
299	<	painCave.isFatal = 1;
300	<	simError();
301	<	}
302	<
303	<	current_extra = current_extra->getNext();
304	<	}
305	<	}
306	<
307	<	if( !theBends[j].isGhost ){
308	<
309	<	exI = theBends[j].a;
310	<	exJ = theBends[j].c;
311	<	}
312	<	else{
313	<
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	<	}
252	>	for (j = 0; j < molInfo.nBends; j++){
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	>	extras = currentBend->getExtras();
260	>	current_extra = extras;
261	>
262	>	while (current_extra != NULL){
263	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
264	>	switch (current_extra->getType()){
265	>	case 0:
266	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
267	>	theBends[j].isGhost = 1;
268	>	break;
269	>
270	>	case 1:
271	>	theBends[j].ghost = (int) current_extra->getDouble() +
272	>	atomOffset;
273	>	theBends[j].isGhost = 1;
274	>	break;
275	>
276	>	default:
277	>	sprintf(painCave.errMsg,
278	>	"SimSetup Error: ghostVectorSource was neither a "
279	>	"double nor an int.\n"
280	>	"-->Bend[%d] in %s\n",
281	>	j, comp_stamps[stampID]->getID());
282	>	painCave.isFatal = 1;
283	>	simError();
284	>	}
285	>	}
286	>	else{
287	>	sprintf(painCave.errMsg,
288	>	"SimSetup Error: unhandled bend assignment:\n"
289	>	"    -->%s in Bend[%d] in %s\n",
290	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
291	>	painCave.isFatal = 1;
292	>	simError();
293	>	}
294	>
295	>	current_extra = current_extra->getNext();
296	>	}
297	>	}
298	>
299	>	if (!theBends[j].isGhost){
300	>	exI = theBends[j].a;
301	>	exJ = theBends[j].c;
302	>	}
303	>	else{
304	>	exI = theBends[j].a;
305	>	exJ = theBends[j].b;
306	>	}
307	>
308	>	// exclude_I must always be the smaller of the pair
309	>	if (exI > exJ){
310	>	tempEx = exI;
311	>	exI = exJ;
312	>	exJ = tempEx;
313	>	}
314		#ifdef IS_MPI
315	<	tempEx = exI;
316	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
317	<	tempEx = exJ;
318	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
319	<
320	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
315	>	tempEx = exI;
316	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
317	>	tempEx = exJ;
318	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
319	>
320	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
321		#else  // isn't MPI
322	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
322	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
323		#endif  //is_mpi
324		}
325		excludeOffset += molInfo.nBends;
326	<
327	<	for(j=0; j<molInfo.nTorsions; j++){
328	<
329	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
330	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
331	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
332	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
333	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
334	<
335	<	exI = theTorsions[j].a;
336	<	exJ = theTorsions[j].d;
337	<
338	<	// exclude_I must always be the smaller of the pair
339	<	if( exI > exJ ){
340	<	tempEx = exI;
341	<	exI = exJ;
342	<	exJ = tempEx;
361	<	}
326	>
327	>	for (j = 0; j < molInfo.nTorsions; j++){
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;
342	>	}
343		#ifdef IS_MPI
344	<	tempEx = exI;
345	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
346	<	tempEx = exJ;
347	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
348	<
349	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
344	>	tempEx = exI;
345	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
346	>	tempEx = exJ;
347	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
348	>
349	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
350		#else  // isn't MPI
351	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
351	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
352		#endif  //is_mpi
353		}
354		excludeOffset += molInfo.nTorsions;
355	<
356	<
355	>
356	>
357		// 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 );
358
359	<
359	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
360	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
361	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
362	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
363	>	theTorsions);
364	>
365	>
366	>	info[k].molecules[i].initialize(molInfo);
367	>
368	>
369		atomOffset += molInfo.nAtoms;
370		delete[] theBonds;
371		delete[] theBends;
372		delete[] theTorsions;
373		}
374		}
375	<
375	>
376		#ifdef IS_MPI
377	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
377	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
378		MPIcheckPoint();
379		#endif // is_mpi
380	<
380	>
381		// clean up the forcefield
382
383		the_ff->calcRcut();
384		the_ff->cleanMe();
403	–
385		}
386
387	<	void SimSetup::initFromBass( void ){
407	<
387	>	void SimSetup::initFromBass(void){
388		int i, j, k;
389		int n_cells;
390		double cellx, celly, cellz;
#	Line 418 | Line 398 | void SimSetup::initFromBass( void ){
398		vel[1] = 0.0;
399		vel[2] = 0.0;
400
401	<	temp1 = (double)tot_nmol / 4.0;
402	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
403	<	temp3 = ceil( temp2 );
401	>	temp1 = (double) tot_nmol / 4.0;
402	>	temp2 = pow(temp1, (1.0 / 3.0));
403	>	temp3 = ceil(temp2);
404
405	<	have_extra =0;
406	<	if( temp2 < temp3 ){ // we have a non-complete lattice
407	<	have_extra =1;
405	>	have_extra = 0;
406	>	if (temp2 < temp3){
407	>	// we have a non-complete lattice
408	>	have_extra = 1;
409
410	<	n_cells = (int)temp3 - 1;
410	>	n_cells = (int) temp3 - 1;
411		cellx = info[0].boxL[0] / temp3;
412		celly = info[0].boxL[1] / temp3;
413		cellz = info[0].boxL[2] / temp3;
414	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
415	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
416	<	n_per_extra = (int)ceil( temp1 );
414	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
415	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
416	>	n_per_extra = (int) ceil(temp1);
417
418	<	if( n_per_extra > 4){
419	<	sprintf( painCave.errMsg,
420	<	"SimSetup error. There has been an error in constructing"
421	<	" the non-complete lattice.\n" );
418	>	if (n_per_extra > 4){
419	>	sprintf(painCave.errMsg,
420	>	"SimSetup error. There has been an error in constructing"
421	>	" the non-complete lattice.\n");
422		painCave.isFatal = 1;
423		simError();
424		}
425		}
426		else{
427	<	n_cells = (int)temp3;
427	>	n_cells = (int) temp3;
428		cellx = info[0].boxL[0] / temp3;
429		celly = info[0].boxL[1] / temp3;
430		cellz = info[0].boxL[2] / temp3;
#	Line 454 | Line 435 | void SimSetup::initFromBass( void ){
435		current_comp = 0;
436		current_atom_ndx = 0;
437
438	<	for( i=0; i < n_cells ; i++ ){
439	<	for( j=0; j < n_cells; j++ ){
440	<	for( k=0; k < n_cells; k++ ){
438	>	for (i = 0; i < n_cells ; i++){
439	>	for (j = 0; j < n_cells; j++){
440	>	for (k = 0; k < n_cells; k++){
441	>	makeElement(i * cellx, j * celly, k * cellz);
442
443	<	makeElement( i * cellx,
462	<	j * celly,
463	<	k * cellz );
443	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
444
445	<	makeElement( i * cellx + 0.5 * cellx,
466	<	j * celly + 0.5 * celly,
467	<	k * cellz );
445	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
446
447	<	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 );
447	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
448		}
449		}
450		}
451
452	<	if( have_extra ){
452	>	if (have_extra){
453		done = 0;
454
455		int start_ndx;
456	<	for( i=0; i < (n_cells+1) && !done; i++ ){
457	<	for( j=0; j < (n_cells+1) && !done; j++ ){
456	>	for (i = 0; i < (n_cells + 1) && !done; i++){
457	>	for (j = 0; j < (n_cells + 1) && !done; j++){
458	>	if (i < n_cells){
459	>	if (j < n_cells){
460	>	start_ndx = n_cells;
461	>	}
462	>	else
463	>	start_ndx = 0;
464	>	}
465	>	else
466	>	start_ndx = 0;
467
468	<	if( i < n_cells ){
468	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
469	>	makeElement(i * cellx, j * celly, k * cellz);
470	>	done = (current_mol >= tot_nmol);
471
472	<	if( j < n_cells ){
473	<	start_ndx = n_cells;
474	<	}
475	<	else start_ndx = 0;
476	<	}
494	<	else start_ndx = 0;
472	>	if (!done && n_per_extra > 1){
473	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
474	>	k * cellz);
475	>	done = (current_mol >= tot_nmol);
476	>	}
477
478	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
479	<
480	<	makeElement( i * cellx,
481	<	j * celly,
482	<	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	<	}
478	>	if (!done && n_per_extra > 2){
479	>	makeElement(i * cellx, j * celly + 0.5 * celly,
480	>	k * cellz + 0.5 * cellz);
481	>	done = (current_mol >= tot_nmol);
482	>	}
483
484	<	if( !done && n_per_extra > 2){
485	<	makeElement( i * cellx,
486	<	j * celly + 0.5 * celly,
487	<	k * cellz + 0.5 * cellz );
488	<	done = ( current_mol >= tot_nmol );
489	<	}
516	<
517	<	if( !done && n_per_extra > 3){
518	<	makeElement( i * cellx + 0.5 * cellx,
519	<	j * celly,
520	<	k * cellz + 0.5 * cellz );
521	<	done = ( current_mol >= tot_nmol );
522	<	}
523	<	}
484	>	if (!done && n_per_extra > 3){
485	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
486	>	k * cellz + 0.5 * cellz);
487	>	done = (current_mol >= tot_nmol);
488	>	}
489	>	}
490		}
491		}
492		}
493
494	<	for( i=0; i<info[0].n_atoms; i++ ){
495	<	info[0].atoms[i]->setVel( vel );
494	>	for (i = 0; i < info[0].n_atoms; i++){
495	>	info[0].atoms[i]->setVel(vel);
496		}
497		}
498
499	<	void SimSetup::makeElement( double x, double y, double z ){
534	<
499	>	void SimSetup::makeElement(double x, double y, double z){
500		int k;
501		AtomStamp* current_atom;
502		DirectionalAtom* dAtom;
503		double rotMat[3][3];
504		double pos[3];
505
506	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
507	<
508	<	current_atom = comp_stamps[current_comp]->getAtom( k );
509	<	if( !current_atom->havePosition() ){
510	<	sprintf( painCave.errMsg,
511	<	"SimSetup:initFromBass error.\n"
512	<	"\tComponent %s, atom %s does not have a position specified.\n"
513	<	"\tThe initialization routine is unable to give a start"
514	<	" position.\n",
550	<	comp_stamps[current_comp]->getID(),
551	<	current_atom->getType() );
506	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
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",
514	>	comp_stamps[current_comp]->getID(), current_atom->getType());
515		painCave.isFatal = 1;
516		simError();
517		}
518	<
518	>
519		pos[0] = x + current_atom->getPosX();
520		pos[1] = y + current_atom->getPosY();
521		pos[2] = z + current_atom->getPosZ();
559	–
560	–	info[0].atoms[current_atom_ndx]->setPos( pos );
522
523	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
523	>	info[0].atoms[current_atom_ndx]->setPos(pos);
524
525	<	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
525	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
526	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
527
528		rotMat[0][0] = 1.0;
529		rotMat[0][1] = 0.0;
#	Line 575 | Line 537 | void SimSetup::makeElement( double x, double y, double
537		rotMat[2][1] = 0.0;
538		rotMat[2][2] = 1.0;
539
540	<	dAtom->setA( rotMat );
540	>	dAtom->setA(rotMat);
541		}
542
543		current_atom_ndx++;
#	Line 584 | Line 546 | void SimSetup::makeElement( double x, double y, double
546		current_mol++;
547		current_comp_mol++;
548
549	<	if( current_comp_mol >= components_nmol[current_comp] ){
588	<
549	>	if (current_comp_mol >= components_nmol[current_comp]){
550		current_comp_mol = 0;
551		current_comp++;
552		}
553		}
554
555
556	<	void SimSetup::gatherInfo( void ){
557	<	int i,j,k;
556	>	void SimSetup::gatherInfo(void){
557	>	int i;
558
559		ensembleCase = -1;
560		ffCase = -1;
561
562		// set the easy ones first
563
564	<	for( i=0; i<nInfo; i++){
564	>	for (i = 0; i < nInfo; i++){
565		info[i].target_temp = globals->getTargetTemp();
566		info[i].dt = globals->getDt();
567		info[i].run_time = globals->getRunTime();
#	Line 610 | Line 571 | void SimSetup::gatherInfo( void ){
571
572		// get the forceField
573
574	<	strcpy( force_field, globals->getForceField() );
574	>	strcpy(force_field, globals->getForceField());
575
576	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
577	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
578	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
576	>	if (!strcasecmp(force_field, "DUFF")){
577	>	ffCase = FF_DUFF;
578	>	}
579	>	else if (!strcasecmp(force_field, "LJ")){
580	>	ffCase = FF_LJ;
581	>	}
582	>	else if (!strcasecmp(force_field, "EAM")){
583	>	ffCase = FF_EAM;
584	>	}
585		else{
586	<	sprintf( painCave.errMsg,
587	<	"SimSetup Error. Unrecognized force field -> %s\n",
588	<	force_field );
589	<	painCave.isFatal = 1;
623	<	simError();
586	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
587	>	force_field);
588	>	painCave.isFatal = 1;
589	>	simError();
590		}
591
592	<	// get the ensemble
592	>	// get the ensemble
593
594	<	strcpy( ensemble, globals->getEnsemble() );
594	>	strcpy(ensemble, globals->getEnsemble());
595
596	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
597	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
598	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
596	>	if (!strcasecmp(ensemble, "NVE")){
597	>	ensembleCase = NVE_ENS;
598	>	}
599	>	else if (!strcasecmp(ensemble, "NVT")){
600	>	ensembleCase = NVT_ENS;
601	>	}
602	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
603		ensembleCase = NPTi_ENS;
604	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
605	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
606	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
604	>	}
605	>	else if (!strcasecmp(ensemble, "NPTf")){
606	>	ensembleCase = NPTf_ENS;
607	>	}
608	>	else if (!strcasecmp(ensemble, "NPTxyz")){
609	>	ensembleCase = NPTxyz_ENS;
610	>	}
611		else{
612	<	sprintf( painCave.errMsg,
613	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
614	<	"reverting to NVE for this simulation.\n",
615	<	ensemble );
616	<	painCave.isFatal = 0;
617	<	simError();
618	<	strcpy( ensemble, "NVE" );
619	<	ensembleCase = NVE_ENS;
612	>	sprintf(painCave.errMsg,
613	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
614	>	"reverting to NVE for this simulation.\n",
615	>	ensemble);
616	>	painCave.isFatal = 0;
617	>	simError();
618	>	strcpy(ensemble, "NVE");
619	>	ensembleCase = NVE_ENS;
620		}
647	–
648	–	for(i=0; i<nInfo; i++){
649	–
650	–	strcpy( info[i].ensemble, ensemble );
621
622	+	for (i = 0; i < nInfo; i++){
623	+	strcpy(info[i].ensemble, ensemble);
624	+
625		// get the mixing rule
626
627	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
627	>	strcpy(info[i].mixingRule, globals->getMixingRule());
628		info[i].usePBC = globals->getPBC();
629		}
630	<
630	>
631		// get the components and calculate the tot_nMol and indvidual n_mol
632	<
632	>
633		the_components = globals->getComponents();
634		components_nmol = new int[n_components];
635
636
637	<	if( !globals->haveNMol() ){
637	>	if (!globals->haveNMol()){
638		// we don't have the total number of molecules, so we assume it is
639		// given in each component
640
641		tot_nmol = 0;
642	<	for( i=0; i<n_components; i++ ){
643	<
644	<	if( !the_components[i]->haveNMol() ){
645	<	// we have a problem
646	<	sprintf( painCave.errMsg,
647	<	"SimSetup Error. No global NMol or component NMol"
648	<	" given. Cannot calculate the number of atoms.\n" );
649	<	painCave.isFatal = 1;
677	<	simError();
642	>	for (i = 0; i < n_components; i++){
643	>	if (!the_components[i]->haveNMol()){
644	>	// we have a problem
645	>	sprintf(painCave.errMsg,
646	>	"SimSetup Error. No global NMol or component NMol"
647	>	" given. Cannot calculate the number of atoms.\n");
648	>	painCave.isFatal = 1;
649	>	simError();
650		}
651
652		tot_nmol += the_components[i]->getNMol();
#	Line 682 | Line 654 | void SimSetup::gatherInfo( void ){
654		}
655		}
656		else{
657	<	sprintf( painCave.errMsg,
658	<	"SimSetup error.\n"
659	<	"\tSorry, the ability to specify total"
660	<	" nMols and then give molfractions in the components\n"
661	<	"\tis not currently supported."
662	<	" Please give nMol in the components.\n" );
657	>	sprintf(painCave.errMsg,
658	>	"SimSetup error.\n"
659	>	"\tSorry, the ability to specify total"
660	>	" nMols and then give molfractions in the components\n"
661	>	"\tis not currently supported."
662	>	" Please give nMol in the components.\n");
663		painCave.isFatal = 1;
664		simError();
665		}
666
667		// set the status, sample, and thermal kick times
696	–
697	–	for(i=0; i<nInfo; i++){
668
669	<	if( globals->haveSampleTime() ){
669	>	for (i = 0; i < nInfo; i++){
670	>	if (globals->haveSampleTime()){
671		info[i].sampleTime = globals->getSampleTime();
672		info[i].statusTime = info[i].sampleTime;
673		info[i].thermalTime = info[i].sampleTime;
#	Line 706 | Line 677 | void SimSetup::gatherInfo( void ){
677		info[i].statusTime = info[i].sampleTime;
678		info[i].thermalTime = info[i].sampleTime;
679		}
680	<
681	<	if( globals->haveStatusTime() ){
680	>
681	>	if (globals->haveStatusTime()){
682		info[i].statusTime = globals->getStatusTime();
683		}
684	<
685	<	if( globals->haveThermalTime() ){
684	>
685	>	if (globals->haveThermalTime()){
686		info[i].thermalTime = globals->getThermalTime();
687		}
688
689	+	info[i].resetIntegrator = 0;
690	+	if( globals->haveResetTime() ){
691	+	info[i].resetTime = globals->getResetTime();
692	+	info[i].resetIntegrator = 1;
693	+	}
694	+
695		// check for the temperature set flag
696
697	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
698	<
697	>	if (globals->haveTempSet())
698	>	info[i].setTemp = globals->getTempSet();
699	>
700		// get some of the tricky things that may still be in the globals
701	<
701	>
702		double boxVector[3];
703	<	if( globals->haveBox() ){
703	>	if (globals->haveBox()){
704		boxVector[0] = globals->getBox();
705		boxVector[1] = globals->getBox();
706		boxVector[2] = globals->getBox();
707	<
708	<	info[i].setBox( boxVector );
707	>
708	>	info[i].setBox(boxVector);
709		}
710	<	else if( globals->haveDensity() ){
733	<
710	>	else if (globals->haveDensity()){
711		double vol;
712	<	vol = (double)tot_nmol / globals->getDensity();
713	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
712	>	vol = (double) tot_nmol / globals->getDensity();
713	>	boxVector[0] = pow(vol, (1.0 / 3.0));
714		boxVector[1] = boxVector[0];
715		boxVector[2] = boxVector[0];
716	<
717	<	info[i].setBox( boxVector );
718	<	}
716	>
717	>	info[i].setBox(boxVector);
718	>	}
719		else{
720	<	if( !globals->haveBoxX() ){
721	<	sprintf( painCave.errMsg,
722	<	"SimSetup error, no periodic BoxX size given.\n" );
723	<	painCave.isFatal = 1;
724	<	simError();
720	>	if (!globals->haveBoxX()){
721	>	sprintf(painCave.errMsg,
722	>	"SimSetup error, no periodic BoxX size given.\n");
723	>	painCave.isFatal = 1;
724	>	simError();
725		}
726		boxVector[0] = globals->getBoxX();
727	<
728	<	if( !globals->haveBoxY() ){
729	<	sprintf( painCave.errMsg,
730	<	"SimSetup error, no periodic BoxY size given.\n" );
731	<	painCave.isFatal = 1;
732	<	simError();
756	<	}
757	<	boxVector[1] = globals->getBoxY();
758	<
759	<	if( !globals->haveBoxZ() ){
760	<	sprintf( painCave.errMsg,
761	<	"SimSetup error, no periodic BoxZ size given.\n" );
762	<	painCave.isFatal = 1;
763	<	simError();
727	>
728	>	if (!globals->haveBoxY()){
729	>	sprintf(painCave.errMsg,
730	>	"SimSetup error, no periodic BoxY size given.\n");
731	>	painCave.isFatal = 1;
732	>	simError();
733		}
734	+	boxVector[1] = globals->getBoxY();
735	+
736	+	if (!globals->haveBoxZ()){
737	+	sprintf(painCave.errMsg,
738	+	"SimSetup error, no periodic BoxZ size given.\n");
739	+	painCave.isFatal = 1;
740	+	simError();
741	+	}
742		boxVector[2] = globals->getBoxZ();
766	–
767	–	info[i].setBox( boxVector );
768	–	}
743
744	+	info[i].setBox(boxVector);
745	+	}
746		}
747	+
748	+	//setup seed for random number generator
749	+	int seedValue;
750	+
751	+	if (globals->haveSeed()){
752	+	seedValue = globals->getSeed();
753	+
754	+	if(seedValue / 1E9 == 0){
755	+	sprintf(painCave.errMsg,
756	+	"Seed for sprng library should contain at least 9 digits\n"
757	+	"OOPSE will generate a seed for user\n");
758	+	painCave.isFatal = 0;
759	+	simError();
760	+
761	+	//using seed generated by system instead of invalid seed set by user
762	+	#ifndef IS_MPI
763	+	seedValue = make_sprng_seed();
764	+	#else
765	+	if (worldRank == 0){
766	+	seedValue = make_sprng_seed();
767	+	}
768	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
769	+	#endif
770	+	}
771	+	}//end of if branch of globals->haveSeed()
772	+	else{
773
774	+	#ifndef IS_MPI
775	+	seedValue = make_sprng_seed();
776	+	#else
777	+	if (worldRank == 0){
778	+	seedValue = make_sprng_seed();
779	+	}
780	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
781	+	#endif
782	+	}//end of globals->haveSeed()
783	+
784	+	for (int i = 0; i < nInfo; i++){
785	+	info[i].setSeed(seedValue);
786	+	}
787	+
788		#ifdef IS_MPI
789	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
789	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
790		MPIcheckPoint();
791		#endif // is_mpi
776	–
792		}
793
794
795	<	void SimSetup::finalInfoCheck( void ){
795	>	void SimSetup::finalInfoCheck(void){
796		int index;
797		int usesDipoles;
798		int i;
799
800	<	for(i=0; i<nInfo; i++){
800	>	for (i = 0; i < nInfo; i++){
801		// check electrostatic parameters
802	<
802	>
803		index = 0;
804		usesDipoles = 0;
805	<	while( (index < info[i].n_atoms) && !usesDipoles ){
805	>	while ((index < info[i].n_atoms) && !usesDipoles){
806		usesDipoles = (info[i].atoms[index])->hasDipole();
807		index++;
808		}
809	<
809	>
810		#ifdef IS_MPI
811		int myUse = usesDipoles;
812	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
812	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813		#endif //is_mpi
814	<
814	>
815		double theEcr, theEst;
816	<
817	<	if (globals->getUseRF() ) {
816	>
817	>	if (globals->getUseRF()){
818		info[i].useReactionField = 1;
819	<
820	<	if( !globals->haveECR() ){
821	<	sprintf( painCave.errMsg,
822	<	"SimSetup Warning: using default value of 1/2 the smallest "
823	<	"box length for the electrostaticCutoffRadius.\n"
824	<	"I hope you have a very fast processor!\n");
825	<	painCave.isFatal = 0;
826	<	simError();
827	<	double smallest;
828	<	smallest = info[i].boxL[0];
829	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
830	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
831	<	theEcr = 0.5 * smallest;
832	<	} else {
833	<	theEcr = globals->getECR();
819	>
820	>	if (!globals->haveECR()){
821	>	sprintf(painCave.errMsg,
822	>	"SimSetup Warning: using default value of 1/2 the smallest "
823	>	"box length for the electrostaticCutoffRadius.\n"
824	>	"I hope you have a very fast processor!\n");
825	>	painCave.isFatal = 0;
826	>	simError();
827	>	double smallest;
828	>	smallest = info[i].boxL[0];
829	>	if (info[i].boxL[1] <= smallest)
830	>	smallest = info[i].boxL[1];
831	>	if (info[i].boxL[2] <= smallest)
832	>	smallest = info[i].boxL[2];
833	>	theEcr = 0.5 * smallest;
834		}
835	<
836	<	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();
835	>	else{
836	>	theEcr = globals->getECR();
837		}
838	<
839	<	info[i].setEcr( theEcr, theEst );
840	<
841	<	if(!globals->haveDielectric() ){
842	<	sprintf( painCave.errMsg,
843	<	"SimSetup Error: You are trying to use Reaction Field without"
844	<	"setting a dielectric constant!\n"
845	<	);
840	<	painCave.isFatal = 1;
841	<	simError();
838	>
839	>	if (!globals->haveEST()){
840	>	sprintf(painCave.errMsg,
841	>	"SimSetup Warning: using default value of 0.05 * the "
842	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
843	>	painCave.isFatal = 0;
844	>	simError();
845	>	theEst = 0.05 * theEcr;
846		}
847	<	info[i].dielectric = globals->getDielectric();
848	<	}
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 );
847	>	else{
848	>	theEst = globals->getEST();
849		}
850	<	}
850	>
851	>	info[i].setEcr(theEcr, theEst);
852	>
853	>	if (!globals->haveDielectric()){
854	>	sprintf(painCave.errMsg,
855	>	"SimSetup Error: You are trying to use Reaction Field without"
856	>	"setting a dielectric constant!\n");
857	>	painCave.isFatal = 1;
858	>	simError();
859	>	}
860	>	info[i].dielectric = globals->getDielectric();
861	>	}
862	>	else{
863	>	if (usesDipoles){
864	>	if (!globals->haveECR()){
865	>	sprintf(painCave.errMsg,
866	>	"SimSetup Warning: using default value of 1/2 the smallest "
867	>	"box length for the electrostaticCutoffRadius.\n"
868	>	"I hope you have a very fast processor!\n");
869	>	painCave.isFatal = 0;
870	>	simError();
871	>	double smallest;
872	>	smallest = info[i].boxL[0];
873	>	if (info[i].boxL[1] <= smallest)
874	>	smallest = info[i].boxL[1];
875	>	if (info[i].boxL[2] <= smallest)
876	>	smallest = info[i].boxL[2];
877	>	theEcr = 0.5 * smallest;
878	>	}
879	>	else{
880	>	theEcr = globals->getECR();
881	>	}
882	>
883	>	if (!globals->haveEST()){
884	>	sprintf(painCave.errMsg,
885	>	"SimSetup Warning: using default value of 0.05 * the "
886	>	"electrostaticCutoffRadius for the "
887	>	"electrostaticSkinThickness\n");
888	>	painCave.isFatal = 0;
889	>	simError();
890	>	theEst = 0.05 * theEcr;
891	>	}
892	>	else{
893	>	theEst = globals->getEST();
894	>	}
895	>
896	>	info[i].setEcr(theEcr, theEst);
897	>	}
898	>	}
899		}
900
901		#ifdef IS_MPI
902	<	strcpy( checkPointMsg, "post processing checks out" );
902	>	strcpy(checkPointMsg, "post processing checks out");
903		MPIcheckPoint();
904		#endif // is_mpi
886	–
905		}
906
907	<	void SimSetup::initSystemCoords( void ){
907	>	void SimSetup::initSystemCoords(void){
908		int i;
909	<
909	>
910		char* inName;
911
912	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
913
914	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
915	<
916	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
917	<
899	<	if( globals->haveInitialConfig() ){
900	<
914	>	for (i = 0; i < info[0].n_atoms; i++)
915	>	info[0].atoms[i]->setCoords();
916	>
917	>	if (globals->haveInitialConfig()){
918		InitializeFromFile* fileInit;
919		#ifdef IS_MPI // is_mpi
920	<	if( worldRank == 0 ){
920	>	if (worldRank == 0){
921		#endif //is_mpi
922		inName = globals->getInitialConfig();
923	<	double* tempDouble = new double[1000000];
907	<	fileInit = new InitializeFromFile( inName );
923	>	fileInit = new InitializeFromFile(inName);
924		#ifdef IS_MPI
925	<	}else fileInit = new InitializeFromFile( NULL );
925	>	}
926	>	else
927	>	fileInit = new InitializeFromFile(NULL);
928		#endif
929	<	fileInit->readInit( info ); // default velocities on
930	<
929	>	fileInit->readInit(info); // default velocities on
930	>
931		delete fileInit;
932		}
933		else{
916	–
934		#ifdef IS_MPI
935	<
935	>
936		// no init from bass
937	<
938	<	sprintf( painCave.errMsg,
939	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
940	<	painCave.isFatal;
937	>
938	>	sprintf(painCave.errMsg,
939	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
940	>	painCave.isFatal = 1;;
941		simError();
942	<
942	>
943		#else
944	<
944	>
945		initFromBass();
946	<
947	<
946	>
947	>
948		#endif
949		}
950	<
950	>
951		#ifdef IS_MPI
952	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
952	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
953		MPIcheckPoint();
954		#endif // is_mpi
938	–
955		}
956
957
958	<	void SimSetup::makeOutNames( void ){
943	<
958	>	void SimSetup::makeOutNames(void){
959		int k;
960
946	–
947	–	for(k=0; k<nInfo; k++){
961
962	+	for (k = 0; k < nInfo; k++){
963		#ifdef IS_MPI
964	<	if( worldRank == 0 ){
964	>	if (worldRank == 0){
965		#endif // is_mpi
966	<
967	<	if( globals->haveFinalConfig() ){
968	<	strcpy( info[k].finalName, globals->getFinalConfig() );
966	>
967	>	if (globals->haveFinalConfig()){
968	>	strcpy(info[k].finalName, globals->getFinalConfig());
969		}
970		else{
971	<	strcpy( info[k].finalName, inFileName );
972	<	char* endTest;
973	<	int nameLength = strlen( info[k].finalName );
974	<	endTest = &(info[k].finalName[nameLength - 5]);
975	<	if( !strcmp( endTest, ".bass" ) ){
976	<	strcpy( endTest, ".eor" );
977	<	}
978	<	else if( !strcmp( endTest, ".BASS" ) ){
979	<	strcpy( endTest, ".eor" );
980	<	}
981	<	else{
982	<	endTest = &(info[k].finalName[nameLength - 4]);
983	<	if( !strcmp( endTest, ".bss" ) ){
984	<	strcpy( endTest, ".eor" );
985	<	}
986	<	else if( !strcmp( endTest, ".mdl" ) ){
987	<	strcpy( endTest, ".eor" );
988	<	}
989	<	else{
990	<	strcat( info[k].finalName, ".eor" );
991	<	}
992	<	}
971	>	strcpy(info[k].finalName, inFileName);
972	>	char* endTest;
973	>	int nameLength = strlen(info[k].finalName);
974	>	endTest = &(info[k].finalName[nameLength - 5]);
975	>	if (!strcmp(endTest, ".bass")){
976	>	strcpy(endTest, ".eor");
977	>	}
978	>	else if (!strcmp(endTest, ".BASS")){
979	>	strcpy(endTest, ".eor");
980	>	}
981	>	else{
982	>	endTest = &(info[k].finalName[nameLength - 4]);
983	>	if (!strcmp(endTest, ".bss")){
984	>	strcpy(endTest, ".eor");
985	>	}
986	>	else if (!strcmp(endTest, ".mdl")){
987	>	strcpy(endTest, ".eor");
988	>	}
989	>	else{
990	>	strcat(info[k].finalName, ".eor");
991	>	}
992	>	}
993		}
994	<
994	>
995		// make the sample and status out names
996	<
997	<	strcpy( info[k].sampleName, inFileName );
996	>
997	>	strcpy(info[k].sampleName, inFileName);
998		char* endTest;
999	<	int nameLength = strlen( info[k].sampleName );
999	>	int nameLength = strlen(info[k].sampleName);
1000		endTest = &(info[k].sampleName[nameLength - 5]);
1001	<	if( !strcmp( endTest, ".bass" ) ){
1002	<	strcpy( endTest, ".dump" );
1001	>	if (!strcmp(endTest, ".bass")){
1002	>	strcpy(endTest, ".dump");
1003		}
1004	<	else if( !strcmp( endTest, ".BASS" ) ){
1005	<	strcpy( endTest, ".dump" );
1004	>	else if (!strcmp(endTest, ".BASS")){
1005	>	strcpy(endTest, ".dump");
1006		}
1007		else{
1008	<	endTest = &(info[k].sampleName[nameLength - 4]);
1009	<	if( !strcmp( endTest, ".bss" ) ){
1010	<	strcpy( endTest, ".dump" );
1011	<	}
1012	<	else if( !strcmp( endTest, ".mdl" ) ){
1013	<	strcpy( endTest, ".dump" );
1014	<	}
1015	<	else{
1016	<	strcat( info[k].sampleName, ".dump" );
1017	<	}
1008	>	endTest = &(info[k].sampleName[nameLength - 4]);
1009	>	if (!strcmp(endTest, ".bss")){
1010	>	strcpy(endTest, ".dump");
1011	>	}
1012	>	else if (!strcmp(endTest, ".mdl")){
1013	>	strcpy(endTest, ".dump");
1014	>	}
1015	>	else{
1016	>	strcat(info[k].sampleName, ".dump");
1017	>	}
1018		}
1019	<
1020	<	strcpy( info[k].statusName, inFileName );
1021	<	nameLength = strlen( info[k].statusName );
1019	>
1020	>	strcpy(info[k].statusName, inFileName);
1021	>	nameLength = strlen(info[k].statusName);
1022		endTest = &(info[k].statusName[nameLength - 5]);
1023	<	if( !strcmp( endTest, ".bass" ) ){
1024	<	strcpy( endTest, ".stat" );
1023	>	if (!strcmp(endTest, ".bass")){
1024	>	strcpy(endTest, ".stat");
1025		}
1026	<	else if( !strcmp( endTest, ".BASS" ) ){
1027	<	strcpy( endTest, ".stat" );
1026	>	else if (!strcmp(endTest, ".BASS")){
1027	>	strcpy(endTest, ".stat");
1028		}
1029		else{
1030	<	endTest = &(info[k].statusName[nameLength - 4]);
1031	<	if( !strcmp( endTest, ".bss" ) ){
1032	<	strcpy( endTest, ".stat" );
1033	<	}
1034	<	else if( !strcmp( endTest, ".mdl" ) ){
1035	<	strcpy( endTest, ".stat" );
1036	<	}
1037	<	else{
1038	<	strcat( info[k].statusName, ".stat" );
1039	<	}
1030	>	endTest = &(info[k].statusName[nameLength - 4]);
1031	>	if (!strcmp(endTest, ".bss")){
1032	>	strcpy(endTest, ".stat");
1033	>	}
1034	>	else if (!strcmp(endTest, ".mdl")){
1035	>	strcpy(endTest, ".stat");
1036	>	}
1037	>	else{
1038	>	strcat(info[k].statusName, ".stat");
1039	>	}
1040		}
1041	<
1041	>
1042		#ifdef IS_MPI
1043	+
1044		}
1045		#endif // is_mpi
1046		}
1047		}
1048
1049
1050	<	void SimSetup::sysObjectsCreation( void ){
1051	<
1052	<	int i,k;
1038	<
1050	>	void SimSetup::sysObjectsCreation(void){
1051	>	int i, k;
1052	>
1053		// create the forceField
1054
1055		createFF();
#	Line 1050 | Line 1064 | void SimSetup::sysObjectsCreation( void ){
1064
1065		#ifdef IS_MPI
1066		// divide the molecules among the processors
1067	<
1067	>
1068		mpiMolDivide();
1069		#endif //is_mpi
1070	<
1070	>
1071		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1072	<
1072	>
1073		makeSysArrays();
1074
1075		// make and initialize the molecules (all but atomic coordinates)
1076	<
1076	>
1077		makeMolecules();
1078	<
1079	<	for(k=0; k<nInfo; k++){
1078	>
1079	>	for (k = 0; k < nInfo; k++){
1080		info[k].identArray = new int[info[k].n_atoms];
1081	<	for(i=0; i<info[k].n_atoms; i++){
1081	>	for (i = 0; i < info[k].n_atoms; i++){
1082		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1083		}
1084		}
1085		}
1086
1087
1088	<	void SimSetup::createFF( void ){
1088	>	void SimSetup::createFF(void){
1089	>	switch (ffCase){
1090	>	case FF_DUFF:
1091	>	the_ff = new DUFF();
1092	>	break;
1093
1094	<	switch( ffCase ){
1094	>	case FF_LJ:
1095	>	the_ff = new LJFF();
1096	>	break;
1097
1098	<	case FF_DUFF:
1099	<	the_ff = new DUFF();
1100	<	break;
1098	>	case FF_EAM:
1099	>	the_ff = new EAM_FF();
1100	>	break;
1101
1102	<	case FF_LJ:
1103	<	the_ff = new LJFF();
1104	<	break;
1105	<
1106	<	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();
1102	>	default:
1103	>	sprintf(painCave.errMsg,
1104	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1105	>	painCave.isFatal = 1;
1106	>	simError();
1107		}
1108
1109		#ifdef IS_MPI
1110	<	strcpy( checkPointMsg, "ForceField creation successful" );
1110	>	strcpy(checkPointMsg, "ForceField creation successful");
1111		MPIcheckPoint();
1112		#endif // is_mpi
1101	–
1113		}
1114
1115
1116	<	void SimSetup::compList( void ){
1106	<
1116	>	void SimSetup::compList(void){
1117		int i;
1118		char* id;
1119		LinkedMolStamp* headStamp = new LinkedMolStamp();
1120		LinkedMolStamp* currentStamp = NULL;
1121	<	comp_stamps = new MoleculeStamp*[n_components];
1122	<
1121	>	comp_stamps = new MoleculeStamp * [n_components];
1122	>
1123		// make an array of molecule stamps that match the components used.
1124		// also extract the used stamps out into a separate linked list
1125	<
1126	<	for(i=0; i<nInfo; i++){
1125	>
1126	>	for (i = 0; i < nInfo; i++){
1127		info[i].nComponents = n_components;
1128		info[i].componentsNmol = components_nmol;
1129		info[i].compStamps = comp_stamps;
1130		info[i].headStamp = headStamp;
1131		}
1122	–
1132
1124	–	for( i=0; i<n_components; i++ ){
1133
1134	+	for (i = 0; i < n_components; i++){
1135		id = the_components[i]->getType();
1136		comp_stamps[i] = NULL;
1137	<
1137	>
1138		// check to make sure the component isn't already in the list
1139
1140	<	comp_stamps[i] = headStamp->match( id );
1141	<	if( comp_stamps[i] == NULL ){
1133	<
1140	>	comp_stamps[i] = headStamp->match(id);
1141	>	if (comp_stamps[i] == NULL){
1142		// extract the component from the list;
1143	<
1144	<	currentStamp = stamps->extractMolStamp( id );
1145	<	if( currentStamp == NULL ){
1146	<	sprintf( painCave.errMsg,
1147	<	"SimSetup error: Component \"%s\" was not found in the "
1148	<	"list of declared molecules\n",
1149	<	id );
1150	<	painCave.isFatal = 1;
1151	<	simError();
1143	>
1144	>	currentStamp = stamps->extractMolStamp(id);
1145	>	if (currentStamp == NULL){
1146	>	sprintf(painCave.errMsg,
1147	>	"SimSetup error: Component \"%s\" was not found in the "
1148	>	"list of declared molecules\n",
1149	>	id);
1150	>	painCave.isFatal = 1;
1151	>	simError();
1152		}
1153	<
1154	<	headStamp->add( currentStamp );
1155	<	comp_stamps[i] = headStamp->match( id );
1153	>
1154	>	headStamp->add(currentStamp);
1155	>	comp_stamps[i] = headStamp->match(id);
1156		}
1157		}
1158
1159		#ifdef IS_MPI
1160	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1160	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1161		MPIcheckPoint();
1162		#endif // is_mpi
1163	+	}
1164
1165	+	void SimSetup::calcSysValues(void){
1166	+	int i;
1167
1168	<	}
1168	>	int* molMembershipArray;
1169
1159	–	void SimSetup::calcSysValues( void ){
1160	–	int i, j, k;
1161	–
1162	–	int *molMembershipArray;
1163	–
1170		tot_atoms = 0;
1171		tot_bonds = 0;
1172		tot_bends = 0;
1173		tot_torsions = 0;
1174	<	for( i=0; i<n_components; i++ ){
1175	<
1176	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1177	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1172	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1174	>	for (i = 0; i < n_components; i++){
1175	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1176	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1177	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1178		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1179		}
1180	<
1180	>
1181		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1182		molMembershipArray = new int[tot_atoms];
1183	<
1184	<	for(i=0; i<nInfo; i++){
1183	>
1184	>	for (i = 0; i < nInfo; i++){
1185		info[i].n_atoms = tot_atoms;
1186		info[i].n_bonds = tot_bonds;
1187		info[i].n_bends = tot_bends;
1188		info[i].n_torsions = tot_torsions;
1189		info[i].n_SRI = tot_SRI;
1190		info[i].n_mol = tot_nmol;
1191	<
1191	>
1192		info[i].molMembershipArray = molMembershipArray;
1193	<	}
1193	>	}
1194		}
1195
1196		#ifdef IS_MPI
1197
1198	<	void SimSetup::mpiMolDivide( void ){
1194	<
1198	>	void SimSetup::mpiMolDivide(void){
1199		int i, j, k;
1200		int localMol, allMol;
1201		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1202
1203	<	mpiSim = new mpiSimulation( info );
1204	<
1203	>	mpiSim = new mpiSimulation(info);
1204	>
1205		globalIndex = mpiSim->divideLabor();
1206
1207		// set up the local variables
1208	<
1208	>
1209		mol2proc = mpiSim->getMolToProcMap();
1210		molCompType = mpiSim->getMolComponentType();
1211	<
1211	>
1212		allMol = 0;
1213		localMol = 0;
1214		local_atoms = 0;
#	Line 1214 | Line 1218 | void SimSetup::mpiMolDivide( void ){
1218		globalAtomIndex = 0;
1219
1220
1221	<	for( i=0; i<n_components; i++ ){
1222	<
1223	<	for( j=0; j<components_nmol[i]; j++ ){
1224	<
1225	<	if( mol2proc[allMol] == worldRank ){
1226	<
1227	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1228	<	local_bonds +=    comp_stamps[i]->getNBonds();
1225	<	local_bends +=    comp_stamps[i]->getNBends();
1226	<	local_torsions += comp_stamps[i]->getNTorsions();
1227	<	localMol++;
1221	>	for (i = 0; i < n_components; i++){
1222	>	for (j = 0; j < components_nmol[i]; j++){
1223	>	if (mol2proc[allMol] == worldRank){
1224	>	local_atoms += comp_stamps[i]->getNAtoms();
1225	>	local_bonds += comp_stamps[i]->getNBonds();
1226	>	local_bends += comp_stamps[i]->getNBends();
1227	>	local_torsions += comp_stamps[i]->getNTorsions();
1228	>	localMol++;
1229		}
1230	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1230	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1231		info[0].molMembershipArray[globalAtomIndex] = allMol;
1232		globalAtomIndex++;
1233		}
1234
1235	<	allMol++;
1235	>	allMol++;
1236		}
1237		}
1238		local_SRI = local_bonds + local_bends + local_torsions;
1239	<
1239	>
1240		info[0].n_atoms = mpiSim->getMyNlocal();
1241	<
1242	<	if( local_atoms != info[0].n_atoms ){
1243	<	sprintf( painCave.errMsg,
1244	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1245	<	" localAtom (%d) are not equal.\n",
1246	<	info[0].n_atoms,
1246	<	local_atoms );
1241	>
1242	>	if (local_atoms != info[0].n_atoms){
1243	>	sprintf(painCave.errMsg,
1244	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1245	>	" localAtom (%d) are not equal.\n",
1246	>	info[0].n_atoms, local_atoms);
1247		painCave.isFatal = 1;
1248		simError();
1249		}
#	Line 1254 | Line 1254 | void SimSetup::mpiMolDivide( void ){
1254		info[0].n_SRI = local_SRI;
1255		info[0].n_mol = localMol;
1256
1257	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1257	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1258		MPIcheckPoint();
1259		}
1260	<
1260	>
1261		#endif // is_mpi
1262
1263
1264	<	void SimSetup::makeSysArrays( void ){
1265	<	int i, j, k, l;
1264	>	void SimSetup::makeSysArrays(void){
1265	>
1266	>	#ifndef IS_MPI
1267	>	int k, j;
1268	>	#endif // is_mpi
1269	>	int i, l;
1270
1271		Atom** the_atoms;
1272		Molecule* the_molecules;
1273		Exclude** the_excludes;
1274
1275	<
1276	<	for(l=0; l<nInfo; l++){
1273	<
1275	>
1276	>	for (l = 0; l < nInfo; l++){
1277		// create the atom and short range interaction arrays
1278	<
1279	<	the_atoms = new Atom*[info[l].n_atoms];
1278	>
1279	>	the_atoms = new Atom * [info[l].n_atoms];
1280		the_molecules = new Molecule[info[l].n_mol];
1281		int molIndex;
1282
1283		// initialize the molecule's stampID's
1284	<
1284	>
1285		#ifdef IS_MPI
1286	<
1287	<
1286	>
1287	>
1288		molIndex = 0;
1289	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1290	<
1291	<	if(mol2proc[i] == worldRank ){
1292	<	the_molecules[molIndex].setStampID( molCompType[i] );
1293	<	the_molecules[molIndex].setMyIndex( molIndex );
1294	<	the_molecules[molIndex].setGlobalIndex( i );
1292	<	molIndex++;
1289	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1290	>	if (mol2proc[i] == worldRank){
1291	>	the_molecules[molIndex].setStampID(molCompType[i]);
1292	>	the_molecules[molIndex].setMyIndex(molIndex);
1293	>	the_molecules[molIndex].setGlobalIndex(i);
1294	>	molIndex++;
1295		}
1296		}
1297	<
1297	>
1298		#else // is_mpi
1299	<
1299	>
1300		molIndex = 0;
1301		globalAtomIndex = 0;
1302	<	for(i=0; i<n_components; i++){
1303	<	for(j=0; j<components_nmol[i]; j++ ){
1304	<	the_molecules[molIndex].setStampID( i );
1305	<	the_molecules[molIndex].setMyIndex( molIndex );
1306	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1307	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1308	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1309	<	globalAtomIndex++;
1310	<	}
1311	<	molIndex++;
1302	>	for (i = 0; i < n_components; i++){
1303	>	for (j = 0; j < components_nmol[i]; j++){
1304	>	the_molecules[molIndex].setStampID(i);
1305	>	the_molecules[molIndex].setMyIndex(molIndex);
1306	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1307	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1308	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1309	>	globalAtomIndex++;
1310	>	}
1311	>	molIndex++;
1312		}
1313		}
1314	<
1315	<
1314	>
1315	>
1316		#endif // is_mpi
1317
1318
1319	<	if( info[l].n_SRI ){
1318	<
1319	>	if (info[l].n_SRI){
1320		Exclude::createArray(info[l].n_SRI);
1321	<	the_excludes = new Exclude*[info[l].n_SRI];
1322	<	for( int ex=0; ex<info[l].n_SRI; ex++){
1323	<	the_excludes[ex] = new Exclude(ex);
1321	>	the_excludes = new Exclude * [info[l].n_SRI];
1322	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1323	>	the_excludes[ex] = new Exclude(ex);
1324		}
1325		info[l].globalExcludes = new int;
1326		info[l].n_exclude = info[l].n_SRI;
1327		}
1328		else{
1329	<
1330	<	Exclude::createArray( 1 );
1330	<	the_excludes = new Exclude*;
1329	>	Exclude::createArray(1);
1330	>	the_excludes = new Exclude * ;
1331		the_excludes[0] = new Exclude(0);
1332	<	the_excludes[0]->setPair( 0,0 );
1332	>	the_excludes[0]->setPair(0, 0);
1333		info[l].globalExcludes = new int;
1334		info[l].globalExcludes[0] = 0;
1335		info[l].n_exclude = 0;
#	Line 1342 | Line 1342 | void SimSetup::makeSysArrays( void ){
1342		info[l].nGlobalExcludes = 0;
1343		info[l].excludes = the_excludes;
1344
1345	<	the_ff->setSimInfo( info );
1346	<
1345	>	the_ff->setSimInfo(info);
1346		}
1347		}
1348
1349	<	void SimSetup::makeIntegrator( void ){
1351	<
1349	>	void SimSetup::makeIntegrator(void){
1350		int k;
1351
1352	<	NVT<RealIntegrator>*  myNVT = NULL;
1353	<	NPTi<RealIntegrator>* myNPTi = NULL;
1354	<	NPTf<RealIntegrator>* myNPTf = NULL;
1355	<	NPTim<RealIntegrator>* myNPTim = NULL;
1356	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1357	<
1358	<	for(k=0; k<nInfo; k++){
1359	<
1360	<	switch( ensembleCase ){
1361	<
1362	<	case NVE_ENS:
1363	<	if (globals->haveZconstraints()){
1364	<	setupZConstraint(info[k]);
1365	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1352	>	NVE<RealIntegrator>* myNVE = NULL;
1353	>	NVT<RealIntegrator>* myNVT = NULL;
1354	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1355	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1356	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1357	>
1358	>	for (k = 0; k < nInfo; k++){
1359	>	switch (ensembleCase){
1360	>	case NVE_ENS:
1361	>	if (globals->haveZconstraints()){
1362	>	setupZConstraint(info[k]);
1363	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1364	>	}
1365	>	else{
1366	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1367		}
1368	+
1369	+	info->the_integrator = myNVE;
1370	+	break;
1371
1372	<	else
1373	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1374	<	break;
1375	<
1376	<	case NVT_ENS:
1377	<	if (globals->haveZconstraints()){
1378	<	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 );
1372	>	case NVT_ENS:
1373	>	if (globals->haveZconstraints()){
1374	>	setupZConstraint(info[k]);
1375	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1376	>	}
1377	>	else
1378	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1379
1380	<	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 );
1380	>	myNVT->setTargetTemp(globals->getTargetTemp());
1381
1382	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1383	<
1384	<	if (globals->haveTargetPressure())
1385	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1386	<	else {
1387	<	sprintf( painCave.errMsg,
1388	<	"SimSetup error: If you use a constant pressure\n"
1389	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1390	<	painCave.isFatal = 1;
1413	<	simError();
1414	<	}
1415	<
1416	<	if( globals->haveTauThermostat() )
1417	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1418	<	else{
1419	<	sprintf( painCave.errMsg,
1420	<	"SimSetup error: If you use an NPT\n"
1421	<	"    ensemble, you must set tauThermostat.\n");
1422	<	painCave.isFatal = 1;
1423	<	simError();
1424	<	}
1425	<
1426	<	if( globals->haveTauBarostat() )
1427	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1428	<	else{
1429	<	sprintf( painCave.errMsg,
1430	<	"SimSetup error: If you use an NPT\n"
1431	<	"    ensemble, you must set tauBarostat.\n");
1432	<	painCave.isFatal = 1;
1433	<	simError();
1434	<	}
1435	<	break;
1436	<
1437	<	case NPTf_ENS:
1438	<	if (globals->haveZconstraints()){
1439	<	setupZConstraint(info[k]);
1440	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1441	<	}
1442	<	else
1443	<	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1382	>	if (globals->haveTauThermostat())
1383	>	myNVT->setTauThermostat(globals->getTauThermostat());
1384	>	else{
1385	>	sprintf(painCave.errMsg,
1386	>	"SimSetup error: If you use the NVT\n"
1387	>	"    ensemble, you must set tauThermostat.\n");
1388	>	painCave.isFatal = 1;
1389	>	simError();
1390	>	}
1391
1392	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1393	<
1447	<	if (globals->haveTargetPressure())
1448	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1449	<	else {
1450	<	sprintf( painCave.errMsg,
1451	<	"SimSetup error: If you use a constant pressure\n"
1452	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1453	<	painCave.isFatal = 1;
1454	<	simError();
1455	<	}
1456	<
1457	<	if( globals->haveTauThermostat() )
1458	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1459	<	else{
1460	<	sprintf( painCave.errMsg,
1461	<	"SimSetup error: If you use an NPT\n"
1462	<	"    ensemble, you must set tauThermostat.\n");
1463	<	painCave.isFatal = 1;
1464	<	simError();
1465	<	}
1466	<
1467	<	if( globals->haveTauBarostat() )
1468	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1469	<	else{
1470	<	sprintf( painCave.errMsg,
1471	<	"SimSetup error: If you use an NPT\n"
1472	<	"    ensemble, you must set tauBarostat.\n");
1473	<	painCave.isFatal = 1;
1474	<	simError();
1475	<	}
1476	<	break;
1477	<
1478	<	case NPTim_ENS:
1479	<	if (globals->haveZconstraints()){
1480	<	setupZConstraint(info[k]);
1481	<	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1482	<	}
1483	<	else
1484	<	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1392	>	info->the_integrator = myNVT;
1393	>	break;
1394
1395	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1396	<
1397	<	if (globals->haveTargetPressure())
1398	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1399	<	else {
1400	<	sprintf( painCave.errMsg,
1401	<	"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 );
1395	>	case NPTi_ENS:
1396	>	if (globals->haveZconstraints()){
1397	>	setupZConstraint(info[k]);
1398	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1399	>	}
1400	>	else
1401	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1402
1403	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1404	<
1405	<	if (globals->haveTargetPressure())
1406	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1407	<	else {
1408	<	sprintf( painCave.errMsg,
1409	<	"SimSetup error: If you use a constant pressure\n"
1410	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1411	<	painCave.isFatal = 1;
1412	<	simError();
1413	<	}
1414	<
1415	<	if( globals->haveTauThermostat() )
1416	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1417	<	else{
1418	<	sprintf( painCave.errMsg,
1419	<	"SimSetup error: If you use an NPT\n"
1420	<	"    ensemble, you must set tauThermostat.\n");
1421	<	painCave.isFatal = 1;
1422	<	simError();
1423	<	}
1424	<
1425	<	if( globals->haveTauBarostat() )
1426	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1427	<	else{
1428	<	sprintf( painCave.errMsg,
1429	<	"SimSetup error: If you use an NPT\n"
1430	<	"    ensemble, you must set tauBarostat.\n");
1431	<	painCave.isFatal = 1;
1432	<	simError();
1433	<	}
1434	<	break;
1435	<
1436	<	default:
1437	<	sprintf( painCave.errMsg,
1438	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1439	<	painCave.isFatal = 1;
1440	<	simError();
1403	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1404	>
1405	>	if (globals->haveTargetPressure())
1406	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1407	>	else{
1408	>	sprintf(painCave.errMsg,
1409	>	"SimSetup error: If you use a constant pressure\n"
1410	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1411	>	painCave.isFatal = 1;
1412	>	simError();
1413	>	}
1414	>
1415	>	if (globals->haveTauThermostat())
1416	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1417	>	else{
1418	>	sprintf(painCave.errMsg,
1419	>	"SimSetup error: If you use an NPT\n"
1420	>	"    ensemble, you must set tauThermostat.\n");
1421	>	painCave.isFatal = 1;
1422	>	simError();
1423	>	}
1424	>
1425	>	if (globals->haveTauBarostat())
1426	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1427	>	else{
1428	>	sprintf(painCave.errMsg,
1429	>	"SimSetup error: If you use an NPT\n"
1430	>	"    ensemble, you must set tauBarostat.\n");
1431	>	painCave.isFatal = 1;
1432	>	simError();
1433	>	}
1434	>
1435	>	info->the_integrator = myNPTi;
1436	>	break;
1437	>
1438	>	case NPTf_ENS:
1439	>	if (globals->haveZconstraints()){
1440	>	setupZConstraint(info[k]);
1441	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1442	>	}
1443	>	else
1444	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1445	>
1446	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1447	>
1448	>	if (globals->haveTargetPressure())
1449	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1450	>	else{
1451	>	sprintf(painCave.errMsg,
1452	>	"SimSetup error: If you use a constant pressure\n"
1453	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1454	>	painCave.isFatal = 1;
1455	>	simError();
1456	>	}
1457	>
1458	>	if (globals->haveTauThermostat())
1459	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1460	>	else{
1461	>	sprintf(painCave.errMsg,
1462	>	"SimSetup error: If you use an NPT\n"
1463	>	"    ensemble, you must set tauThermostat.\n");
1464	>	painCave.isFatal = 1;
1465	>	simError();
1466	>	}
1467	>
1468	>	if (globals->haveTauBarostat())
1469	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1470	>	else{
1471	>	sprintf(painCave.errMsg,
1472	>	"SimSetup error: If you use an NPT\n"
1473	>	"    ensemble, you must set tauBarostat.\n");
1474	>	painCave.isFatal = 1;
1475	>	simError();
1476	>	}
1477	>
1478	>	info->the_integrator = myNPTf;
1479	>	break;
1480	>
1481	>	case NPTxyz_ENS:
1482	>	if (globals->haveZconstraints()){
1483	>	setupZConstraint(info[k]);
1484	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1485	>	}
1486	>	else
1487	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1488	>
1489	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1490	>
1491	>	if (globals->haveTargetPressure())
1492	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1493	>	else{
1494	>	sprintf(painCave.errMsg,
1495	>	"SimSetup error: If you use a constant pressure\n"
1496	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1497	>	painCave.isFatal = 1;
1498	>	simError();
1499	>	}
1500	>
1501	>	if (globals->haveTauThermostat())
1502	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1503	>	else{
1504	>	sprintf(painCave.errMsg,
1505	>	"SimSetup error: If you use an NPT\n"
1506	>	"    ensemble, you must set tauThermostat.\n");
1507	>	painCave.isFatal = 1;
1508	>	simError();
1509	>	}
1510	>
1511	>	if (globals->haveTauBarostat())
1512	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1513	>	else{
1514	>	sprintf(painCave.errMsg,
1515	>	"SimSetup error: If you use an NPT\n"
1516	>	"    ensemble, you must set tauBarostat.\n");
1517	>	painCave.isFatal = 1;
1518	>	simError();
1519	>	}
1520	>
1521	>	info->the_integrator = myNPTxyz;
1522	>	break;
1523	>
1524	>	default:
1525	>	sprintf(painCave.errMsg,
1526	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1527	>	painCave.isFatal = 1;
1528	>	simError();
1529		}
1530		}
1531		}
1532
1533	<	void SimSetup::initFortran( void ){
1570	<
1533	>	void SimSetup::initFortran(void){
1534		info[0].refreshSim();
1535	<
1536	<	if( !strcmp( info[0].mixingRule, "standard") ){
1537	<	the_ff->initForceField( LB_MIXING_RULE );
1535	>
1536	>	if (!strcmp(info[0].mixingRule, "standard")){
1537	>	the_ff->initForceField(LB_MIXING_RULE);
1538		}
1539	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1540	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1539	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1540	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1541		}
1542		else{
1543	<	sprintf( painCave.errMsg,
1544	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1582	<	info[0].mixingRule );
1543	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1544	>	info[0].mixingRule);
1545		painCave.isFatal = 1;
1546		simError();
1547		}
1548
1549
1550		#ifdef IS_MPI
1551	<	strcpy( checkPointMsg,
1590	<	"Successfully intialized the mixingRule for Fortran." );
1551	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1552		MPIcheckPoint();
1553		#endif // is_mpi
1593	–
1554		}
1555
1556	<	void SimSetup::setupZConstraint(SimInfo& theInfo)
1557	<	{
1558	<	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	<	}
1556	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1557	>	int nZConstraints;
1558	>	ZconStamp** zconStamp;
1559
1560	<	//
1561	<	nZConstraints = globals->getNzConstraints();
1562	<	theInfo.nZconstraints = nZConstraints;
1563	<
1564	<	zconStamp = globals->getZconStamp();
1565	<	ZConsParaItem tempParaItem;
1560	>	if (globals->haveZconstraintTime()){
1561	>	//add sample time of z-constraint  into SimInfo's property list
1562	>	DoubleData* zconsTimeProp = new DoubleData();
1563	>	zconsTimeProp->setID(ZCONSTIME_ID);
1564	>	zconsTimeProp->setData(globals->getZconsTime());
1565	>	theInfo.addProperty(zconsTimeProp);
1566	>	}
1567	>	else{
1568	>	sprintf(painCave.errMsg,
1569	>	"ZConstraint error: If you use an ZConstraint\n"
1570	>	" , you must set sample time.\n");
1571	>	painCave.isFatal = 1;
1572	>	simError();
1573	>	}
1574
1575	<	ZConsParaData* zconsParaData = new ZConsParaData();
1576	<	zconsParaData->setID(ZCONSPARADATA_ID);
1577	<
1578	<	for(int i = 0; i < nZConstraints; i++){
1575	>	//push zconsTol into siminfo, if user does not specify
1576	>	//value for zconsTol, a default value will be used
1577	>	DoubleData* zconsTol = new DoubleData();
1578	>	zconsTol->setID(ZCONSTOL_ID);
1579	>	if (globals->haveZconsTol()){
1580	>	zconsTol->setData(globals->getZconsTol());
1581	>	}
1582	>	else{
1583	>	double defaultZConsTol = 0.01;
1584	>	sprintf(painCave.errMsg,
1585	>	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1586	>	" , default value %f is used.\n",
1587	>	defaultZConsTol);
1588	>	painCave.isFatal = 0;
1589	>	simError();
1590	>
1591	>	zconsTol->setData(defaultZConsTol);
1592	>	}
1593	>	theInfo.addProperty(zconsTol);
1594	>
1595	>	//set Force Subtraction Policy
1596	>	StringData* zconsForcePolicy = new StringData();
1597	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1598	>
1599	>	if (globals->haveZconsForcePolicy()){
1600	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1601	>	}
1602	>	else{
1603	>	sprintf(painCave.errMsg,
1604	>	"ZConstraint Warning: User does not set force Subtraction policy, "
1605	>	"PolicyByMass is used\n");
1606	>	painCave.isFatal = 0;
1607	>	simError();
1608	>	zconsForcePolicy->setData("BYMASS");
1609	>	}
1610	>
1611	>	theInfo.addProperty(zconsForcePolicy);
1612	>
1613	>	//Determine the name of ouput file and add it into SimInfo's property list
1614	>	//Be careful, do not use inFileName, since it is a pointer which
1615	>	//point to a string at master node, and slave nodes do not contain that string
1616	>
1617	>	string zconsOutput(theInfo.finalName);
1618	>
1619	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1620	>
1621	>	StringData* zconsFilename = new StringData();
1622	>	zconsFilename->setID(ZCONSFILENAME_ID);
1623	>	zconsFilename->setData(zconsOutput);
1624	>
1625	>	theInfo.addProperty(zconsFilename);
1626	>
1627	>	//setup index, pos and other parameters of z-constraint molecules
1628	>	nZConstraints = globals->getNzConstraints();
1629	>	theInfo.nZconstraints = nZConstraints;
1630	>
1631	>	zconStamp = globals->getZconStamp();
1632	>	ZConsParaItem tempParaItem;
1633	>
1634	>	ZConsParaData* zconsParaData = new ZConsParaData();
1635	>	zconsParaData->setID(ZCONSPARADATA_ID);
1636	>
1637	>	for (int i = 0; i < nZConstraints; i++){
1638		tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1639		tempParaItem.zPos = zconStamp[i]->getZpos();
1640		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1641		tempParaItem.kRatio = zconStamp[i]->getKratio();
1642
1643		zconsParaData->addItem(tempParaItem);
1644	<	}
1644	>	}
1645
1646	<	//sort the parameters by index of molecules
1647	<	zconsParaData->sortByIndex();
1648	<
1649	<	//push data into siminfo, therefore, we can retrieve later
1650	<	theInfo.addProperty(zconsParaData);
1646	>	//check the uniqueness of index
1647	>	if(!zconsParaData->isIndexUnique()){
1648	>	sprintf(painCave.errMsg,
1649	>	"ZConstraint Error: molIndex is not unique\n");
1650	>	painCave.isFatal = 1;
1651	>	simError();
1652	>	}
1653
1654	<	//push zconsTol into siminfo, if user does not specify
1655	<	//value for zconsTol, a default value will be used
1656	<	DoubleData* zconsTol = new DoubleData();
1657	<	zconsTol->setID(ZCONSTOL_ID);
1658	<	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);
1654	>	//sort the parameters by index of molecules
1655	>	zconsParaData->sortByIndex();
1656	>
1657	>	//push data into siminfo, therefore, we can retrieve later
1658	>	theInfo.addProperty(zconsParaData);
1659		}

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