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root/group/branches/new-templateless/OOPSE/libmdtools/SimSetup.cpp

Comparing:
trunk/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 689 by tim, Tue Aug 12 19:56:49 2003 UTC vs.
branches/new-templateless/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 850 by mmeineke, Mon Nov 3 22:07:17 2003 UTC

#	Line 1 | Line 1
1		#include <algorithm>
2	<	#include <cstdlib>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
4	>	#include <math.h>
5		#include <string>
6	+	#include <sprng.h>
7
8		#include "SimSetup.hpp"
9		#include "ReadWrite.hpp"
#	Line 21 | Line 22
22		#define NVT_ENS        1
23		#define NPTi_ENS       2
24		#define NPTf_ENS       3
25	<	#define NPTim_ENS      4
25	<	#define NPTfm_ENS      5
25	>	#define NPTxyz_ENS     4
26
27	+
28		#define FF_DUFF 0
29		#define FF_LJ   1
30		#define FF_EAM  2
#	Line 32 | Line 33 | SimSetup::SimSetup(){
33
34		SimSetup::SimSetup(){
35
36	+	initSuspend = false;
37		isInfoArray = 0;
38		nInfo = 1;
39	<
39	>
40		stamps = new MakeStamps();
41		globals = new Globals();
42	<
43	<
42	>
43	>
44		#ifdef IS_MPI
45	<	strcpy( checkPointMsg, "SimSetup creation successful" );
45	>	strcpy(checkPointMsg, "SimSetup creation successful");
46		MPIcheckPoint();
47		#endif // IS_MPI
48		}
#	Line 50 | Line 52 | SimSetup::~SimSetup(){
52		delete globals;
53		}
54
55	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
56	<	info = the_info;
57	<	nInfo = theNinfo;
58	<	isInfoArray = 1;
55	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
56	>	info = the_info;
57	>	nInfo = theNinfo;
58	>	isInfoArray = 1;
59	>	initSuspend = true;
60		}
61
62
63	<	void SimSetup::parseFile( char* fileName ){
61	<
63	>	void SimSetup::parseFile(char* fileName){
64		#ifdef IS_MPI
65	<	if( worldRank == 0 ){
65	>	if (worldRank == 0){
66		#endif // is_mpi
67	<
67	>
68		inFileName = fileName;
69	<	set_interface_stamps( stamps, globals );
70	<
69	>	set_interface_stamps(stamps, globals);
70	>
71		#ifdef IS_MPI
72		mpiEventInit();
73		#endif
74
75	<	yacc_BASS( fileName );
75	>	yacc_BASS(fileName);
76
77		#ifdef IS_MPI
78		throwMPIEvent(NULL);
79		}
80	<	else receiveParse();
80	>	else{
81	>	receiveParse();
82	>	}
83		#endif
84
85		}
86
87		#ifdef IS_MPI
88		void SimSetup::receiveParse(void){
89	<
90	<	set_interface_stamps( stamps, globals );
91	<	mpiEventInit();
92	<	MPIcheckPoint();
89	<	mpiEventLoop();
90	<
89	>	set_interface_stamps(stamps, globals);
90	>	mpiEventInit();
91	>	MPIcheckPoint();
92	>	mpiEventLoop();
93		}
94
95		#endif // is_mpi
96
97		void SimSetup::createSim(void){
98
97	–	int i, j, k, globalAtomIndex;
98	–
99		// gather all of the information from the Bass file
100
101	–	std::cerr << "gathering info\n";
102	–
101		gatherInfo();
102
103		// creation of complex system objects
104
107	–	std::cerr << "creating system objects\n";
108	–
105		sysObjectsCreation();
106
107	<	// check on the post processing info
112	<
113	<	std::cerr << "performing final info check.\n";
107	>	// initialize the system coordinates
108
109	<	finalInfoCheck();
109	>	if ( !initSuspend ){
110	>	initSystemCoords();
111
112	<	// initialize the system coordinates
112	>	if( !(globals->getUseInitTime()) )
113	>	info[0].currentTime = 0.0;
114	>	}
115
116	<	std::cerr << "about to init coords\n";
116	>	// check on the post processing info
117
118	<	if( !isInfoArray ) initSystemCoords();
118	>	finalInfoCheck();
119
120		// make the output filenames
121
122		makeOutNames();
123	<
123	>
124		// make the integrator
125	<
125	>
126		makeIntegrator();
127	<
127	>
128		#ifdef IS_MPI
129		mpiSim->mpiRefresh();
130		#endif
#	Line 135 | Line 132 | void SimSetup::createSim(void){
132		// initialize the Fortran
133
134		initFortran();
138	–
139	–
140	–
135		}
136
137
138	<	void SimSetup::makeMolecules( void ){
139	<
146	<	int k,l;
138	>	void SimSetup::makeMolecules(void){
139	>	int k;
140		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
141		molInit molInfo;
142		DirectionalAtom* dAtom;
#	Line 158 | Line 151 | void SimSetup::makeMolecules( void ){
151		bend_set* theBends;
152		torsion_set* theTorsions;
153
154	<
154	>
155		//init the forceField paramters
156
157		the_ff->readParams();
158
159	<
159	>
160		// init the atoms
161
162		double ux, uy, uz, u, uSqr;
170	–
171	–	for(k=0; k<nInfo; k++){
172	–
173	–	the_ff->setSimInfo( &(info[k]) );
163
164	+	for (k = 0; k < nInfo; k++){
165	+	the_ff->setSimInfo(&(info[k]));
166	+
167		atomOffset = 0;
168		excludeOffset = 0;
169	<	for(i=0; i<info[k].n_mol; i++){
178	<
169	>	for (i = 0; i < info[k].n_mol; i++){
170		stampID = info[k].molecules[i].getStampID();
171
172	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
173	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
174	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
172	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
173	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
174	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
175		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
176		molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
177	<
177	>
178		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
179		molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
180	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
181	<	molInfo.myBends = new Bend*[molInfo.nBends];
182	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
180	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
181	>	molInfo.myBends = new Bend * [molInfo.nBends];
182	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
183
184		theBonds = new bond_pair[molInfo.nBonds];
185		theBends = new bend_set[molInfo.nBends];
186		theTorsions = new torsion_set[molInfo.nTorsions];
187	<
187	>
188		// make the Atoms
189	<
190	<	for(j=0; j<molInfo.nAtoms; j++){
191	<
192	<	currentAtom = comp_stamps[stampID]->getAtom( j );
193	<	if( currentAtom->haveOrientation() ){
194	<
195	<	dAtom = new DirectionalAtom( (j + atomOffset),
196	<	info[k].getConfiguration() );
197	<	info[k].n_oriented++;
198	<	molInfo.myAtoms[j] = dAtom;
199	<
200	<	ux = currentAtom->getOrntX();
201	<	uy = currentAtom->getOrntY();
202	<	uz = currentAtom->getOrntZ();
203	<
204	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
205	<
206	<	u = sqrt( uSqr );
207	<	ux = ux / u;
208	<	uy = uy / u;
209	<	uz = uz / u;
210	<
211	<	dAtom->setSUx( ux );
212	<	dAtom->setSUy( uy );
213	<	dAtom->setSUz( uz );
214	<	}
215	<	else{
216	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
217	<	info[k].getConfiguration() );
218	<	}
228	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
229	<
189	>
190	>	for (j = 0; j < molInfo.nAtoms; j++){
191	>	currentAtom = comp_stamps[stampID]->getAtom(j);
192	>	if (currentAtom->haveOrientation()){
193	>	dAtom = new DirectionalAtom((j + atomOffset),
194	>	info[k].getConfiguration());
195	>	info[k].n_oriented++;
196	>	molInfo.myAtoms[j] = dAtom;
197	>
198	>	ux = currentAtom->getOrntX();
199	>	uy = currentAtom->getOrntY();
200	>	uz = currentAtom->getOrntZ();
201	>
202	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
203	>
204	>	u = sqrt(uSqr);
205	>	ux = ux / u;
206	>	uy = uy / u;
207	>	uz = uz / u;
208	>
209	>	dAtom->setSUx(ux);
210	>	dAtom->setSUy(uy);
211	>	dAtom->setSUz(uz);
212	>	}
213	>	else{
214	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
215	>	info[k].getConfiguration());
216	>	}
217	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
218	>
219		#ifdef IS_MPI
220	<
221	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
222	<
220	>
221	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
222	>
223		#endif // is_mpi
224		}
225	<
226	<	// make the bonds
227	<	for(j=0; j<molInfo.nBonds; j++){
228	<
229	<	currentBond = comp_stamps[stampID]->getBond( j );
230	<	theBonds[j].a = currentBond->getA() + atomOffset;
231	<	theBonds[j].b = currentBond->getB() + atomOffset;
232	<
233	<	exI = theBonds[j].a;
234	<	exJ = theBonds[j].b;
235	<
236	<	// exclude_I must always be the smaller of the pair
237	<	if( exI > exJ ){
238	<	tempEx = exI;
239	<	exI = exJ;
240	<	exJ = tempEx;
252	<	}
225	>
226	>	// make the bonds
227	>	for (j = 0; j < molInfo.nBonds; j++){
228	>	currentBond = comp_stamps[stampID]->getBond(j);
229	>	theBonds[j].a = currentBond->getA() + atomOffset;
230	>	theBonds[j].b = currentBond->getB() + atomOffset;
231	>
232	>	exI = theBonds[j].a;
233	>	exJ = theBonds[j].b;
234	>
235	>	// exclude_I must always be the smaller of the pair
236	>	if (exI > exJ){
237	>	tempEx = exI;
238	>	exI = exJ;
239	>	exJ = tempEx;
240	>	}
241		#ifdef IS_MPI
242	<	tempEx = exI;
243	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
244	<	tempEx = exJ;
245	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
246	<
247	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
242	>	tempEx = exI;
243	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
244	>	tempEx = exJ;
245	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
246	>
247	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
248		#else  // isn't MPI
249	<
250	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
249	>
250	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
251		#endif  //is_mpi
252		}
253		excludeOffset += molInfo.nBonds;
254	<
254	>
255		//make the bends
256	<	for(j=0; j<molInfo.nBends; j++){
257	<
258	<	currentBend = comp_stamps[stampID]->getBend( j );
259	<	theBends[j].a = currentBend->getA() + atomOffset;
260	<	theBends[j].b = currentBend->getB() + atomOffset;
261	<	theBends[j].c = currentBend->getC() + atomOffset;
262	<
263	<	if( currentBend->haveExtras() ){
264	<
265	<	extras = currentBend->getExtras();
266	<	current_extra = extras;
267	<
268	<	while( current_extra != NULL ){
269	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
270	<
271	<	switch( current_extra->getType() ){
272	<
273	<	case 0:
274	<	theBends[j].ghost =
275	<	current_extra->getInt() + atomOffset;
276	<	theBends[j].isGhost = 1;
277	<	break;
278	<
279	<	case 1:
280	<	theBends[j].ghost =
281	<	(int)current_extra->getDouble() + atomOffset;
282	<	theBends[j].isGhost = 1;
283	<	break;
284	<
285	<	default:
286	<	sprintf( painCave.errMsg,
287	<	"SimSetup Error: ghostVectorSource was neither a "
288	<	"double nor an int.\n"
289	<	"-->Bend[%d] in %s\n",
290	<	j, comp_stamps[stampID]->getID() );
291	<	painCave.isFatal = 1;
292	<	simError();
293	<	}
294	<	}
295	<
296	<	else{
297	<
298	<	sprintf( painCave.errMsg,
299	<	"SimSetup Error: unhandled bend assignment:\n"
300	<	"    -->%s in Bend[%d] in %s\n",
301	<	current_extra->getlhs(),
302	<	j, comp_stamps[stampID]->getID() );
303	<	painCave.isFatal = 1;
304	<	simError();
305	<	}
306	<
307	<	current_extra = current_extra->getNext();
308	<	}
309	<	}
310	<
311	<	if( !theBends[j].isGhost ){
312	<
313	<	exI = theBends[j].a;
314	<	exJ = theBends[j].c;
315	<	}
316	<	else{
317	<
330	<	exI = theBends[j].a;
331	<	exJ = theBends[j].b;
332	<	}
333	<
334	<	// exclude_I must always be the smaller of the pair
335	<	if( exI > exJ ){
336	<	tempEx = exI;
337	<	exI = exJ;
338	<	exJ = tempEx;
339	<	}
256	>	for (j = 0; j < molInfo.nBends; j++){
257	>	currentBend = comp_stamps[stampID]->getBend(j);
258	>	theBends[j].a = currentBend->getA() + atomOffset;
259	>	theBends[j].b = currentBend->getB() + atomOffset;
260	>	theBends[j].c = currentBend->getC() + atomOffset;
261	>
262	>	if (currentBend->haveExtras()){
263	>	extras = currentBend->getExtras();
264	>	current_extra = extras;
265	>
266	>	while (current_extra != NULL){
267	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
268	>	switch (current_extra->getType()){
269	>	case 0:
270	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
271	>	theBends[j].isGhost = 1;
272	>	break;
273	>
274	>	case 1:
275	>	theBends[j].ghost = (int) current_extra->getDouble() +
276	>	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	>	else{
291	>	sprintf(painCave.errMsg,
292	>	"SimSetup Error: unhandled bend assignment:\n"
293	>	"    -->%s in Bend[%d] in %s\n",
294	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
295	>	painCave.isFatal = 1;
296	>	simError();
297	>	}
298	>
299	>	current_extra = current_extra->getNext();
300	>	}
301	>	}
302	>
303	>	if (!theBends[j].isGhost){
304	>	exI = theBends[j].a;
305	>	exJ = theBends[j].c;
306	>	}
307	>	else{
308	>	exI = theBends[j].a;
309	>	exJ = theBends[j].b;
310	>	}
311	>
312	>	// exclude_I must always be the smaller of the pair
313	>	if (exI > exJ){
314	>	tempEx = exI;
315	>	exI = exJ;
316	>	exJ = tempEx;
317	>	}
318		#ifdef IS_MPI
319	<	tempEx = exI;
320	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
321	<	tempEx = exJ;
322	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
323	<
324	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
319	>	tempEx = exI;
320	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
321	>	tempEx = exJ;
322	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
323	>
324	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
325		#else  // isn't MPI
326	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
326	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
327		#endif  //is_mpi
328		}
329		excludeOffset += molInfo.nBends;
330	<
331	<	for(j=0; j<molInfo.nTorsions; j++){
332	<
333	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
334	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
335	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
336	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
337	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
338	<
339	<	exI = theTorsions[j].a;
340	<	exJ = theTorsions[j].d;
341	<
342	<	// exclude_I must always be the smaller of the pair
343	<	if( exI > exJ ){
344	<	tempEx = exI;
345	<	exI = exJ;
346	<	exJ = tempEx;
369	<	}
330	>
331	>	for (j = 0; j < molInfo.nTorsions; j++){
332	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
333	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
334	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
335	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
336	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
337	>
338	>	exI = theTorsions[j].a;
339	>	exJ = theTorsions[j].d;
340	>
341	>	// exclude_I must always be the smaller of the pair
342	>	if (exI > exJ){
343	>	tempEx = exI;
344	>	exI = exJ;
345	>	exJ = tempEx;
346	>	}
347		#ifdef IS_MPI
348	<	tempEx = exI;
349	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
350	<	tempEx = exJ;
351	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
352	<
353	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
348	>	tempEx = exI;
349	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
350	>	tempEx = exJ;
351	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
352	>
353	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
354		#else  // isn't MPI
355	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
355	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
356		#endif  //is_mpi
357		}
358		excludeOffset += molInfo.nTorsions;
359	<
360	<
359	>
360	>
361		// send the arrays off to the forceField for init.
385	–
386	–	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
387	–	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
388	–	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
389	–	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
390	–
391	–
392	–	info[k].molecules[i].initialize( molInfo );
362
363	<
363	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
364	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
365	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
366	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
367	>	theTorsions);
368	>
369	>
370	>	info[k].molecules[i].initialize(molInfo);
371	>
372	>
373		atomOffset += molInfo.nAtoms;
374		delete[] theBonds;
375		delete[] theBends;
376		delete[] theTorsions;
377		}
378		}
379	<
379	>
380		#ifdef IS_MPI
381	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
381	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
382		MPIcheckPoint();
383		#endif // is_mpi
384	<
384	>
385		// clean up the forcefield
386
387		the_ff->calcRcut();
388		the_ff->cleanMe();
411	–
389		}
390
391	<	void SimSetup::initFromBass( void ){
415	<
391	>	void SimSetup::initFromBass(void){
392		int i, j, k;
393		int n_cells;
394		double cellx, celly, cellz;
#	Line 426 | Line 402 | void SimSetup::initFromBass( void ){
402		vel[1] = 0.0;
403		vel[2] = 0.0;
404
405	<	temp1 = (double)tot_nmol / 4.0;
406	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
407	<	temp3 = ceil( temp2 );
405	>	temp1 = (double) tot_nmol / 4.0;
406	>	temp2 = pow(temp1, (1.0 / 3.0));
407	>	temp3 = ceil(temp2);
408
409	<	have_extra =0;
410	<	if( temp2 < temp3 ){ // we have a non-complete lattice
411	<	have_extra =1;
409	>	have_extra = 0;
410	>	if (temp2 < temp3){
411	>	// we have a non-complete lattice
412	>	have_extra = 1;
413
414	<	n_cells = (int)temp3 - 1;
414	>	n_cells = (int) temp3 - 1;
415		cellx = info[0].boxL[0] / temp3;
416		celly = info[0].boxL[1] / temp3;
417		cellz = info[0].boxL[2] / temp3;
418	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
419	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
420	<	n_per_extra = (int)ceil( temp1 );
418	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
419	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
420	>	n_per_extra = (int) ceil(temp1);
421
422	<	if( n_per_extra > 4){
423	<	sprintf( painCave.errMsg,
424	<	"SimSetup error. There has been an error in constructing"
425	<	" the non-complete lattice.\n" );
422	>	if (n_per_extra > 4){
423	>	sprintf(painCave.errMsg,
424	>	"SimSetup error. There has been an error in constructing"
425	>	" the non-complete lattice.\n");
426		painCave.isFatal = 1;
427		simError();
428		}
429		}
430		else{
431	<	n_cells = (int)temp3;
431	>	n_cells = (int) temp3;
432		cellx = info[0].boxL[0] / temp3;
433		celly = info[0].boxL[1] / temp3;
434		cellz = info[0].boxL[2] / temp3;
#	Line 462 | Line 439 | void SimSetup::initFromBass( void ){
439		current_comp = 0;
440		current_atom_ndx = 0;
441
442	<	for( i=0; i < n_cells ; i++ ){
443	<	for( j=0; j < n_cells; j++ ){
444	<	for( k=0; k < n_cells; k++ ){
442	>	for (i = 0; i < n_cells ; i++){
443	>	for (j = 0; j < n_cells; j++){
444	>	for (k = 0; k < n_cells; k++){
445	>	makeElement(i * cellx, j * celly, k * cellz);
446
447	<	makeElement( i * cellx,
470	<	j * celly,
471	<	k * cellz );
447	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
448
449	<	makeElement( i * cellx + 0.5 * cellx,
474	<	j * celly + 0.5 * celly,
475	<	k * cellz );
449	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
450
451	<	makeElement( i * cellx,
478	<	j * celly + 0.5 * celly,
479	<	k * cellz + 0.5 * cellz );
480	<
481	<	makeElement( i * cellx + 0.5 * cellx,
482	<	j * celly,
483	<	k * cellz + 0.5 * cellz );
451	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
452		}
453		}
454		}
455
456	<	if( have_extra ){
456	>	if (have_extra){
457		done = 0;
458
459		int start_ndx;
460	<	for( i=0; i < (n_cells+1) && !done; i++ ){
461	<	for( j=0; j < (n_cells+1) && !done; j++ ){
460	>	for (i = 0; i < (n_cells + 1) && !done; i++){
461	>	for (j = 0; j < (n_cells + 1) && !done; j++){
462	>	if (i < n_cells){
463	>	if (j < n_cells){
464	>	start_ndx = n_cells;
465	>	}
466	>	else
467	>	start_ndx = 0;
468	>	}
469	>	else
470	>	start_ndx = 0;
471
472	<	if( i < n_cells ){
472	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
473	>	makeElement(i * cellx, j * celly, k * cellz);
474	>	done = (current_mol >= tot_nmol);
475
476	<	if( j < n_cells ){
477	<	start_ndx = n_cells;
478	<	}
479	<	else start_ndx = 0;
480	<	}
502	<	else start_ndx = 0;
476	>	if (!done && n_per_extra > 1){
477	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
478	>	k * cellz);
479	>	done = (current_mol >= tot_nmol);
480	>	}
481
482	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
482	>	if (!done && n_per_extra > 2){
483	>	makeElement(i * cellx, j * celly + 0.5 * celly,
484	>	k * cellz + 0.5 * cellz);
485	>	done = (current_mol >= tot_nmol);
486	>	}
487
488	<	makeElement( i * cellx,
489	<	j * celly,
490	<	k * cellz );
491	<	done = ( current_mol >= tot_nmol );
492	<
493	<	if( !done && n_per_extra > 1 ){
512	<	makeElement( i * cellx + 0.5 * cellx,
513	<	j * celly + 0.5 * celly,
514	<	k * cellz );
515	<	done = ( current_mol >= tot_nmol );
516	<	}
517	<
518	<	if( !done && n_per_extra > 2){
519	<	makeElement( i * cellx,
520	<	j * celly + 0.5 * celly,
521	<	k * cellz + 0.5 * cellz );
522	<	done = ( current_mol >= tot_nmol );
523	<	}
524	<
525	<	if( !done && n_per_extra > 3){
526	<	makeElement( i * cellx + 0.5 * cellx,
527	<	j * celly,
528	<	k * cellz + 0.5 * cellz );
529	<	done = ( current_mol >= tot_nmol );
530	<	}
531	<	}
488	>	if (!done && n_per_extra > 3){
489	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
490	>	k * cellz + 0.5 * cellz);
491	>	done = (current_mol >= tot_nmol);
492	>	}
493	>	}
494		}
495		}
496		}
497
498	<	for( i=0; i<info[0].n_atoms; i++ ){
499	<	info[0].atoms[i]->setVel( vel );
498	>	for (i = 0; i < info[0].n_atoms; i++){
499	>	info[0].atoms[i]->setVel(vel);
500		}
501		}
502
503	<	void SimSetup::makeElement( double x, double y, double z ){
542	<
503	>	void SimSetup::makeElement(double x, double y, double z){
504		int k;
505		AtomStamp* current_atom;
506		DirectionalAtom* dAtom;
507		double rotMat[3][3];
508		double pos[3];
509
510	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
511	<
512	<	current_atom = comp_stamps[current_comp]->getAtom( k );
513	<	if( !current_atom->havePosition() ){
514	<	sprintf( painCave.errMsg,
515	<	"SimSetup:initFromBass error.\n"
516	<	"\tComponent %s, atom %s does not have a position specified.\n"
517	<	"\tThe initialization routine is unable to give a start"
518	<	" position.\n",
558	<	comp_stamps[current_comp]->getID(),
559	<	current_atom->getType() );
510	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
511	>	current_atom = comp_stamps[current_comp]->getAtom(k);
512	>	if (!current_atom->havePosition()){
513	>	sprintf(painCave.errMsg,
514	>	"SimSetup:initFromBass error.\n"
515	>	"\tComponent %s, atom %s does not have a position specified.\n"
516	>	"\tThe initialization routine is unable to give a start"
517	>	" position.\n",
518	>	comp_stamps[current_comp]->getID(), current_atom->getType());
519		painCave.isFatal = 1;
520		simError();
521		}
522	<
522	>
523		pos[0] = x + current_atom->getPosX();
524		pos[1] = y + current_atom->getPosY();
525		pos[2] = z + current_atom->getPosZ();
567	–
568	–	info[0].atoms[current_atom_ndx]->setPos( pos );
526
527	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
527	>	info[0].atoms[current_atom_ndx]->setPos(pos);
528
529	<	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
529	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
530	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
531
532		rotMat[0][0] = 1.0;
533		rotMat[0][1] = 0.0;
#	Line 583 | Line 541 | void SimSetup::makeElement( double x, double y, double
541		rotMat[2][1] = 0.0;
542		rotMat[2][2] = 1.0;
543
544	<	dAtom->setA( rotMat );
544	>	dAtom->setA(rotMat);
545		}
546
547		current_atom_ndx++;
#	Line 592 | Line 550 | void SimSetup::makeElement( double x, double y, double
550		current_mol++;
551		current_comp_mol++;
552
553	<	if( current_comp_mol >= components_nmol[current_comp] ){
596	<
553	>	if (current_comp_mol >= components_nmol[current_comp]){
554		current_comp_mol = 0;
555		current_comp++;
556		}
557		}
558
559
560	<	void SimSetup::gatherInfo( void ){
561	<	int i,j,k;
560	>	void SimSetup::gatherInfo(void){
561	>	int i;
562
563		ensembleCase = -1;
564		ffCase = -1;
565
566		// set the easy ones first
567
568	<	for( i=0; i<nInfo; i++){
568	>	for (i = 0; i < nInfo; i++){
569		info[i].target_temp = globals->getTargetTemp();
570		info[i].dt = globals->getDt();
571		info[i].run_time = globals->getRunTime();
#	Line 618 | Line 575 | void SimSetup::gatherInfo( void ){
575
576		// get the forceField
577
578	<	strcpy( force_field, globals->getForceField() );
578	>	strcpy(force_field, globals->getForceField());
579
580	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
581	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
582	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
580	>	if (!strcasecmp(force_field, "DUFF")){
581	>	ffCase = FF_DUFF;
582	>	}
583	>	else if (!strcasecmp(force_field, "LJ")){
584	>	ffCase = FF_LJ;
585	>	}
586	>	else if (!strcasecmp(force_field, "EAM")){
587	>	ffCase = FF_EAM;
588	>	}
589		else{
590	<	sprintf( painCave.errMsg,
591	<	"SimSetup Error. Unrecognized force field -> %s\n",
592	<	force_field );
593	<	painCave.isFatal = 1;
631	<	simError();
590	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
591	>	force_field);
592	>	painCave.isFatal = 1;
593	>	simError();
594		}
595
596	<	// get the ensemble
596	>	// get the ensemble
597
598	<	strcpy( ensemble, globals->getEnsemble() );
598	>	strcpy(ensemble, globals->getEnsemble());
599
600	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
601	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
602	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
600	>	if (!strcasecmp(ensemble, "NVE")){
601	>	ensembleCase = NVE_ENS;
602	>	}
603	>	else if (!strcasecmp(ensemble, "NVT")){
604	>	ensembleCase = NVT_ENS;
605	>	}
606	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
607		ensembleCase = NPTi_ENS;
608	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
609	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
610	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
608	>	}
609	>	else if (!strcasecmp(ensemble, "NPTf")){
610	>	ensembleCase = NPTf_ENS;
611	>	}
612	>	else if (!strcasecmp(ensemble, "NPTxyz")){
613	>	ensembleCase = NPTxyz_ENS;
614	>	}
615		else{
616	<	sprintf( painCave.errMsg,
617	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
618	<	"reverting to NVE for this simulation.\n",
619	<	ensemble );
620	<	painCave.isFatal = 0;
621	<	simError();
622	<	strcpy( ensemble, "NVE" );
623	<	ensembleCase = NVE_ENS;
616	>	sprintf(painCave.errMsg,
617	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
618	>	"reverting to NVE for this simulation.\n",
619	>	ensemble);
620	>	painCave.isFatal = 0;
621	>	simError();
622	>	strcpy(ensemble, "NVE");
623	>	ensembleCase = NVE_ENS;
624		}
655	–
656	–	for(i=0; i<nInfo; i++){
657	–
658	–	strcpy( info[i].ensemble, ensemble );
625
626	+	for (i = 0; i < nInfo; i++){
627	+	strcpy(info[i].ensemble, ensemble);
628	+
629		// get the mixing rule
630
631	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
631	>	strcpy(info[i].mixingRule, globals->getMixingRule());
632		info[i].usePBC = globals->getPBC();
633		}
634	<
634	>
635		// get the components and calculate the tot_nMol and indvidual n_mol
636	<
636	>
637		the_components = globals->getComponents();
638		components_nmol = new int[n_components];
639
640
641	<	if( !globals->haveNMol() ){
641	>	if (!globals->haveNMol()){
642		// we don't have the total number of molecules, so we assume it is
643		// given in each component
644
645		tot_nmol = 0;
646	<	for( i=0; i<n_components; i++ ){
647	<
648	<	if( !the_components[i]->haveNMol() ){
649	<	// we have a problem
650	<	sprintf( painCave.errMsg,
651	<	"SimSetup Error. No global NMol or component NMol"
652	<	" given. Cannot calculate the number of atoms.\n" );
653	<	painCave.isFatal = 1;
685	<	simError();
646	>	for (i = 0; i < n_components; i++){
647	>	if (!the_components[i]->haveNMol()){
648	>	// we have a problem
649	>	sprintf(painCave.errMsg,
650	>	"SimSetup Error. No global NMol or component NMol"
651	>	" given. Cannot calculate the number of atoms.\n");
652	>	painCave.isFatal = 1;
653	>	simError();
654		}
655
656		tot_nmol += the_components[i]->getNMol();
#	Line 690 | Line 658 | void SimSetup::gatherInfo( void ){
658		}
659		}
660		else{
661	<	sprintf( painCave.errMsg,
662	<	"SimSetup error.\n"
663	<	"\tSorry, the ability to specify total"
664	<	" nMols and then give molfractions in the components\n"
665	<	"\tis not currently supported."
666	<	" Please give nMol in the components.\n" );
661	>	sprintf(painCave.errMsg,
662	>	"SimSetup error.\n"
663	>	"\tSorry, the ability to specify total"
664	>	" nMols and then give molfractions in the components\n"
665	>	"\tis not currently supported."
666	>	" Please give nMol in the components.\n");
667		painCave.isFatal = 1;
668		simError();
669		}
670
671		// set the status, sample, and thermal kick times
704	–
705	–	for(i=0; i<nInfo; i++){
672
673	<	if( globals->haveSampleTime() ){
673	>	for (i = 0; i < nInfo; i++){
674	>	if (globals->haveSampleTime()){
675		info[i].sampleTime = globals->getSampleTime();
676		info[i].statusTime = info[i].sampleTime;
677		info[i].thermalTime = info[i].sampleTime;
#	Line 714 | Line 681 | void SimSetup::gatherInfo( void ){
681		info[i].statusTime = info[i].sampleTime;
682		info[i].thermalTime = info[i].sampleTime;
683		}
684	<
685	<	if( globals->haveStatusTime() ){
684	>
685	>	if (globals->haveStatusTime()){
686		info[i].statusTime = globals->getStatusTime();
687		}
688	<
689	<	if( globals->haveThermalTime() ){
688	>
689	>	if (globals->haveThermalTime()){
690		info[i].thermalTime = globals->getThermalTime();
691		}
692
693	<	// check for the temperature set flag
693	>	info[i].resetIntegrator = 0;
694	>	if( globals->haveResetTime() ){
695	>	info[i].resetTime = globals->getResetTime();
696	>	info[i].resetIntegrator = 1;
697	>	}
698
699	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
699	>	// check for the temperature set flag
700
701	<	// get some of the tricky things that may still be in the globals
701	>	if (globals->haveTempSet())
702	>	info[i].setTemp = globals->getTempSet();
703
732	–	double boxVector[3];
733	–	if( globals->haveBox() ){
734	–	boxVector[0] = globals->getBox();
735	–	boxVector[1] = globals->getBox();
736	–	boxVector[2] = globals->getBox();
737	–
738	–	info[i].setBox( boxVector );
739	–	}
740	–	else if( globals->haveDensity() ){
741	–
742	–	double vol;
743	–	vol = (double)tot_nmol / globals->getDensity();
744	–	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
745	–	boxVector[1] = boxVector[0];
746	–	boxVector[2] = boxVector[0];
747	–
748	–	info[i].setBox( boxVector );
704		}
705	<	else{
706	<	if( !globals->haveBoxX() ){
707	<	sprintf( painCave.errMsg,
708	<	"SimSetup error, no periodic BoxX size given.\n" );
709	<	painCave.isFatal = 1;
710	<	simError();
705	>
706	>	//setup seed for random number generator
707	>	int seedValue;
708	>
709	>	if (globals->haveSeed()){
710	>	seedValue = globals->getSeed();
711	>
712	>	if(seedValue / 1E9 == 0){
713	>	sprintf(painCave.errMsg,
714	>	"Seed for sprng library should contain at least 9 digits\n"
715	>	"OOPSE will generate a seed for user\n");
716	>	painCave.isFatal = 0;
717	>	simError();
718	>
719	>	//using seed generated by system instead of invalid seed set by user
720	>	#ifndef IS_MPI
721	>	seedValue = make_sprng_seed();
722	>	#else
723	>	if (worldRank == 0){
724	>	seedValue = make_sprng_seed();
725		}
726	<	boxVector[0] = globals->getBoxX();
727	<
759	<	if( !globals->haveBoxY() ){
760	<	sprintf( painCave.errMsg,
761	<	"SimSetup error, no periodic BoxY size given.\n" );
762	<	painCave.isFatal = 1;
763	<	simError();
764	<	}
765	<	boxVector[1] = globals->getBoxY();
766	<
767	<	if( !globals->haveBoxZ() ){
768	<	sprintf( painCave.errMsg,
769	<	"SimSetup error, no periodic BoxZ size given.\n" );
770	<	painCave.isFatal = 1;
771	<	simError();
772	<	}
773	<	boxVector[2] = globals->getBoxZ();
774	<
775	<	info[i].setBox( boxVector );
726	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
727	>	#endif
728		}
729	+	}//end of if branch of globals->haveSeed()
730	+	else{
731	+
732	+	#ifndef IS_MPI
733	+	seedValue = make_sprng_seed();
734	+	#else
735	+	if (worldRank == 0){
736	+	seedValue = make_sprng_seed();
737	+	}
738	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
739	+	#endif
740	+	}//end of globals->haveSeed()
741
742	+	for (int i = 0; i < nInfo; i++){
743	+	info[i].setSeed(seedValue);
744		}
745	<
745	>
746		#ifdef IS_MPI
747	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
747	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
748		MPIcheckPoint();
749		#endif // is_mpi
784	–
750		}
751
752
753	<	void SimSetup::finalInfoCheck( void ){
753	>	void SimSetup::finalInfoCheck(void){
754		int index;
755		int usesDipoles;
756		int i;
757
758	<	for(i=0; i<nInfo; i++){
758	>	for (i = 0; i < nInfo; i++){
759		// check electrostatic parameters
760	<
760	>
761		index = 0;
762		usesDipoles = 0;
763	<	while( (index < info[i].n_atoms) && !usesDipoles ){
763	>	while ((index < info[i].n_atoms) && !usesDipoles){
764		usesDipoles = (info[i].atoms[index])->hasDipole();
765		index++;
766		}
767	<
767	>
768		#ifdef IS_MPI
769		int myUse = usesDipoles;
770	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
770	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
771		#endif //is_mpi
772	<
772	>
773		double theEcr, theEst;
774	<
775	<	if (globals->getUseRF() ) {
774	>
775	>	if (globals->getUseRF()){
776		info[i].useReactionField = 1;
777	<
778	<	if( !globals->haveECR() ){
779	<	sprintf( painCave.errMsg,
780	<	"SimSetup Warning: using default value of 1/2 the smallest "
781	<	"box length for the electrostaticCutoffRadius.\n"
782	<	"I hope you have a very fast processor!\n");
783	<	painCave.isFatal = 0;
784	<	simError();
785	<	double smallest;
786	<	smallest = info[i].boxL[0];
787	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
788	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
789	<	theEcr = 0.5 * smallest;
790	<	} else {
791	<	theEcr = globals->getECR();
777	>
778	>	if (!globals->haveECR()){
779	>	sprintf(painCave.errMsg,
780	>	"SimSetup Warning: using default value of 1/2 the smallest "
781	>	"box length for the electrostaticCutoffRadius.\n"
782	>	"I hope you have a very fast processor!\n");
783	>	painCave.isFatal = 0;
784	>	simError();
785	>	double smallest;
786	>	smallest = info[i].boxL[0];
787	>	if (info[i].boxL[1] <= smallest)
788	>	smallest = info[i].boxL[1];
789	>	if (info[i].boxL[2] <= smallest)
790	>	smallest = info[i].boxL[2];
791	>	theEcr = 0.5 * smallest;
792		}
793	<
794	<	if( !globals->haveEST() ){
830	<	sprintf( painCave.errMsg,
831	<	"SimSetup Warning: using default value of 0.05 * the "
832	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
833	<	);
834	<	painCave.isFatal = 0;
835	<	simError();
836	<	theEst = 0.05 * theEcr;
837	<	} else {
838	<	theEst= globals->getEST();
793	>	else{
794	>	theEcr = globals->getECR();
795		}
796	<
797	<	info[i].setEcr( theEcr, theEst );
798	<
799	<	if(!globals->haveDielectric() ){
800	<	sprintf( painCave.errMsg,
801	<	"SimSetup Error: You are trying to use Reaction Field without"
802	<	"setting a dielectric constant!\n"
803	<	);
848	<	painCave.isFatal = 1;
849	<	simError();
796	>
797	>	if (!globals->haveEST()){
798	>	sprintf(painCave.errMsg,
799	>	"SimSetup Warning: using default value of 0.05 * the "
800	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
801	>	painCave.isFatal = 0;
802	>	simError();
803	>	theEst = 0.05 * theEcr;
804		}
805	<	info[i].dielectric = globals->getDielectric();
806	<	}
853	<	else {
854	<	if (usesDipoles) {
855	<
856	<	if( !globals->haveECR() ){
857	<	sprintf( painCave.errMsg,
858	<	"SimSetup Warning: using default value of 1/2 the smallest "
859	<	"box length for the electrostaticCutoffRadius.\n"
860	<	"I hope you have a very fast processor!\n");
861	<	painCave.isFatal = 0;
862	<	simError();
863	<	double smallest;
864	<	smallest = info[i].boxL[0];
865	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
866	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
867	<	theEcr = 0.5 * smallest;
868	<	} else {
869	<	theEcr = globals->getECR();
870	<	}
871	<
872	<	if( !globals->haveEST() ){
873	<	sprintf( painCave.errMsg,
874	<	"SimSetup Warning: using default value of 0.05 * the "
875	<	"electrostaticCutoffRadius for the "
876	<	"electrostaticSkinThickness\n"
877	<	);
878	<	painCave.isFatal = 0;
879	<	simError();
880	<	theEst = 0.05 * theEcr;
881	<	} else {
882	<	theEst= globals->getEST();
883	<	}
884	<
885	<	info[i].setEcr( theEcr, theEst );
805	>	else{
806	>	theEst = globals->getEST();
807		}
808	<	}
808	>
809	>	info[i].setDefaultEcr(theEcr, theEst);
810	>
811	>	if (!globals->haveDielectric()){
812	>	sprintf(painCave.errMsg,
813	>	"SimSetup Error: You are trying to use Reaction Field without"
814	>	"setting a dielectric constant!\n");
815	>	painCave.isFatal = 1;
816	>	simError();
817	>	}
818	>	info[i].dielectric = globals->getDielectric();
819	>	}
820	>	else{
821	>	if (usesDipoles){
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	>	else{
838	>	theEcr = globals->getECR();
839	>	}
840	>
841	>	if (!globals->haveEST()){
842	>	sprintf(painCave.errMsg,
843	>	"SimSetup Warning: using default value of 0.05 * the "
844	>	"electrostaticCutoffRadius for the "
845	>	"electrostaticSkinThickness\n");
846	>	painCave.isFatal = 0;
847	>	simError();
848	>	theEst = 0.05 * theEcr;
849	>	}
850	>	else{
851	>	theEst = globals->getEST();
852	>	}
853	>
854	>	info[i].setDefaultEcr(theEcr, theEst);
855	>	}
856	>	}
857	>	info[i].checkCutOffs();
858		}
859
860		#ifdef IS_MPI
861	<	strcpy( checkPointMsg, "post processing checks out" );
861	>	strcpy(checkPointMsg, "post processing checks out");
862		MPIcheckPoint();
863		#endif // is_mpi
894	–
864		}
865
866	<	void SimSetup::initSystemCoords( void ){
866	>	void SimSetup::initSystemCoords(void){
867		int i;
868	<
868	>
869		char* inName;
870
871	<	std::cerr << "Setting atom Coords\n";
871	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
872
873	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
874	<
875	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
876	<
908	<	if( globals->haveInitialConfig() ){
909	<
873	>	for (i = 0; i < info[0].n_atoms; i++)
874	>	info[0].atoms[i]->setCoords();
875	>
876	>	if (globals->haveInitialConfig()){
877		InitializeFromFile* fileInit;
878		#ifdef IS_MPI // is_mpi
879	<	if( worldRank == 0 ){
879	>	if (worldRank == 0){
880		#endif //is_mpi
881		inName = globals->getInitialConfig();
882	<	fileInit = new InitializeFromFile( inName );
882	>	fileInit = new InitializeFromFile(inName);
883		#ifdef IS_MPI
884	<	}else fileInit = new InitializeFromFile( NULL );
884	>	}
885	>	else
886	>	fileInit = new InitializeFromFile(NULL);
887		#endif
888	<	fileInit->readInit( info ); // default velocities on
889	<
888	>	fileInit->readInit(info); // default velocities on
889	>
890		delete fileInit;
891		}
892		else{
924	–
893		#ifdef IS_MPI
894	<
894	>
895		// no init from bass
896	<
897	<	sprintf( painCave.errMsg,
898	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
899	<	painCave.isFatal;
896	>
897	>	sprintf(painCave.errMsg,
898	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
899	>	painCave.isFatal = 1;;
900		simError();
901	<
901	>
902		#else
903	<
903	>
904		initFromBass();
905	<
906	<
905	>
906	>
907		#endif
908		}
909	<
909	>
910		#ifdef IS_MPI
911	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
911	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
912		MPIcheckPoint();
913		#endif // is_mpi
946	–
914		}
915
916
917	<	void SimSetup::makeOutNames( void ){
951	<
917	>	void SimSetup::makeOutNames(void){
918		int k;
919
954	–
955	–	for(k=0; k<nInfo; k++){
920
921	+	for (k = 0; k < nInfo; k++){
922		#ifdef IS_MPI
923	<	if( worldRank == 0 ){
923	>	if (worldRank == 0){
924		#endif // is_mpi
925	<
926	<	if( globals->haveFinalConfig() ){
927	<	strcpy( info[k].finalName, globals->getFinalConfig() );
925	>
926	>	if (globals->haveFinalConfig()){
927	>	strcpy(info[k].finalName, globals->getFinalConfig());
928		}
929		else{
930	<	strcpy( info[k].finalName, inFileName );
931	<	char* endTest;
932	<	int nameLength = strlen( info[k].finalName );
933	<	endTest = &(info[k].finalName[nameLength - 5]);
934	<	if( !strcmp( endTest, ".bass" ) ){
935	<	strcpy( endTest, ".eor" );
936	<	}
937	<	else if( !strcmp( endTest, ".BASS" ) ){
938	<	strcpy( endTest, ".eor" );
939	<	}
940	<	else{
941	<	endTest = &(info[k].finalName[nameLength - 4]);
942	<	if( !strcmp( endTest, ".bss" ) ){
943	<	strcpy( endTest, ".eor" );
944	<	}
945	<	else if( !strcmp( endTest, ".mdl" ) ){
946	<	strcpy( endTest, ".eor" );
947	<	}
948	<	else{
949	<	strcat( info[k].finalName, ".eor" );
950	<	}
951	<	}
930	>	strcpy(info[k].finalName, inFileName);
931	>	char* endTest;
932	>	int nameLength = strlen(info[k].finalName);
933	>	endTest = &(info[k].finalName[nameLength - 5]);
934	>	if (!strcmp(endTest, ".bass")){
935	>	strcpy(endTest, ".eor");
936	>	}
937	>	else if (!strcmp(endTest, ".BASS")){
938	>	strcpy(endTest, ".eor");
939	>	}
940	>	else{
941	>	endTest = &(info[k].finalName[nameLength - 4]);
942	>	if (!strcmp(endTest, ".bss")){
943	>	strcpy(endTest, ".eor");
944	>	}
945	>	else if (!strcmp(endTest, ".mdl")){
946	>	strcpy(endTest, ".eor");
947	>	}
948	>	else{
949	>	strcat(info[k].finalName, ".eor");
950	>	}
951	>	}
952		}
953	<
953	>
954		// make the sample and status out names
955	<
956	<	strcpy( info[k].sampleName, inFileName );
955	>
956	>	strcpy(info[k].sampleName, inFileName);
957		char* endTest;
958	<	int nameLength = strlen( info[k].sampleName );
958	>	int nameLength = strlen(info[k].sampleName);
959		endTest = &(info[k].sampleName[nameLength - 5]);
960	<	if( !strcmp( endTest, ".bass" ) ){
961	<	strcpy( endTest, ".dump" );
960	>	if (!strcmp(endTest, ".bass")){
961	>	strcpy(endTest, ".dump");
962		}
963	<	else if( !strcmp( endTest, ".BASS" ) ){
964	<	strcpy( endTest, ".dump" );
963	>	else if (!strcmp(endTest, ".BASS")){
964	>	strcpy(endTest, ".dump");
965		}
966		else{
967	<	endTest = &(info[k].sampleName[nameLength - 4]);
968	<	if( !strcmp( endTest, ".bss" ) ){
969	<	strcpy( endTest, ".dump" );
970	<	}
971	<	else if( !strcmp( endTest, ".mdl" ) ){
972	<	strcpy( endTest, ".dump" );
973	<	}
974	<	else{
975	<	strcat( info[k].sampleName, ".dump" );
976	<	}
967	>	endTest = &(info[k].sampleName[nameLength - 4]);
968	>	if (!strcmp(endTest, ".bss")){
969	>	strcpy(endTest, ".dump");
970	>	}
971	>	else if (!strcmp(endTest, ".mdl")){
972	>	strcpy(endTest, ".dump");
973	>	}
974	>	else{
975	>	strcat(info[k].sampleName, ".dump");
976	>	}
977		}
978	<
979	<	strcpy( info[k].statusName, inFileName );
980	<	nameLength = strlen( info[k].statusName );
978	>
979	>	strcpy(info[k].statusName, inFileName);
980	>	nameLength = strlen(info[k].statusName);
981		endTest = &(info[k].statusName[nameLength - 5]);
982	<	if( !strcmp( endTest, ".bass" ) ){
983	<	strcpy( endTest, ".stat" );
982	>	if (!strcmp(endTest, ".bass")){
983	>	strcpy(endTest, ".stat");
984		}
985	<	else if( !strcmp( endTest, ".BASS" ) ){
986	<	strcpy( endTest, ".stat" );
985	>	else if (!strcmp(endTest, ".BASS")){
986	>	strcpy(endTest, ".stat");
987		}
988		else{
989	<	endTest = &(info[k].statusName[nameLength - 4]);
990	<	if( !strcmp( endTest, ".bss" ) ){
991	<	strcpy( endTest, ".stat" );
992	<	}
993	<	else if( !strcmp( endTest, ".mdl" ) ){
994	<	strcpy( endTest, ".stat" );
995	<	}
996	<	else{
997	<	strcat( info[k].statusName, ".stat" );
998	<	}
989	>	endTest = &(info[k].statusName[nameLength - 4]);
990	>	if (!strcmp(endTest, ".bss")){
991	>	strcpy(endTest, ".stat");
992	>	}
993	>	else if (!strcmp(endTest, ".mdl")){
994	>	strcpy(endTest, ".stat");
995	>	}
996	>	else{
997	>	strcat(info[k].statusName, ".stat");
998	>	}
999		}
1000	<
1000	>
1001		#ifdef IS_MPI
1002	+
1003		}
1004		#endif // is_mpi
1005		}
1006		}
1007
1008
1009	<	void SimSetup::sysObjectsCreation( void ){
1010	<
1011	<	int i,k;
1046	<
1009	>	void SimSetup::sysObjectsCreation(void){
1010	>	int i, k;
1011	>
1012		// create the forceField
1013
1014		createFF();
#	Line 1058 | Line 1023 | void SimSetup::sysObjectsCreation( void ){
1023
1024		#ifdef IS_MPI
1025		// divide the molecules among the processors
1026	<
1026	>
1027		mpiMolDivide();
1028		#endif //is_mpi
1029	<
1029	>
1030		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1031	<
1031	>
1032		makeSysArrays();
1033
1034		// make and initialize the molecules (all but atomic coordinates)
1035	<
1035	>
1036		makeMolecules();
1037	<
1038	<	for(k=0; k<nInfo; k++){
1037	>
1038	>	for (k = 0; k < nInfo; k++){
1039		info[k].identArray = new int[info[k].n_atoms];
1040	<	for(i=0; i<info[k].n_atoms; i++){
1040	>	for (i = 0; i < info[k].n_atoms; i++){
1041		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1042		}
1043		}
1044		}
1045
1046
1047	<	void SimSetup::createFF( void ){
1047	>	void SimSetup::createFF(void){
1048	>	switch (ffCase){
1049	>	case FF_DUFF:
1050	>	the_ff = new DUFF();
1051	>	break;
1052
1053	<	switch( ffCase ){
1053	>	case FF_LJ:
1054	>	the_ff = new LJFF();
1055	>	break;
1056
1057	<	case FF_DUFF:
1058	<	the_ff = new DUFF();
1059	<	break;
1057	>	case FF_EAM:
1058	>	the_ff = new EAM_FF();
1059	>	break;
1060
1061	<	case FF_LJ:
1062	<	the_ff = new LJFF();
1063	<	break;
1064	<
1065	<	case FF_EAM:
1095	<	the_ff = new EAM_FF();
1096	<	break;
1097	<
1098	<	default:
1099	<	sprintf( painCave.errMsg,
1100	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1101	<	painCave.isFatal = 1;
1102	<	simError();
1061	>	default:
1062	>	sprintf(painCave.errMsg,
1063	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1064	>	painCave.isFatal = 1;
1065	>	simError();
1066		}
1067
1068		#ifdef IS_MPI
1069	<	strcpy( checkPointMsg, "ForceField creation successful" );
1069	>	strcpy(checkPointMsg, "ForceField creation successful");
1070		MPIcheckPoint();
1071		#endif // is_mpi
1109	–
1072		}
1073
1074
1075	<	void SimSetup::compList( void ){
1114	<
1075	>	void SimSetup::compList(void){
1076		int i;
1077		char* id;
1078		LinkedMolStamp* headStamp = new LinkedMolStamp();
1079		LinkedMolStamp* currentStamp = NULL;
1080	<	comp_stamps = new MoleculeStamp*[n_components];
1081	<
1080	>	comp_stamps = new MoleculeStamp * [n_components];
1081	>
1082		// make an array of molecule stamps that match the components used.
1083		// also extract the used stamps out into a separate linked list
1084	<
1085	<	for(i=0; i<nInfo; i++){
1084	>
1085	>	for (i = 0; i < nInfo; i++){
1086		info[i].nComponents = n_components;
1087		info[i].componentsNmol = components_nmol;
1088		info[i].compStamps = comp_stamps;
1089		info[i].headStamp = headStamp;
1090		}
1091	<
1091	>
1092
1093	<	for( i=0; i<n_components; i++ ){
1133	<
1093	>	for (i = 0; i < n_components; i++){
1094		id = the_components[i]->getType();
1095		comp_stamps[i] = NULL;
1096	<
1096	>
1097		// check to make sure the component isn't already in the list
1098
1099	<	comp_stamps[i] = headStamp->match( id );
1100	<	if( comp_stamps[i] == NULL ){
1141	<
1099	>	comp_stamps[i] = headStamp->match(id);
1100	>	if (comp_stamps[i] == NULL){
1101		// extract the component from the list;
1102	<
1103	<	currentStamp = stamps->extractMolStamp( id );
1104	<	if( currentStamp == NULL ){
1105	<	sprintf( painCave.errMsg,
1106	<	"SimSetup error: Component \"%s\" was not found in the "
1107	<	"list of declared molecules\n",
1108	<	id );
1109	<	painCave.isFatal = 1;
1110	<	simError();
1102	>
1103	>	currentStamp = stamps->extractMolStamp(id);
1104	>	if (currentStamp == NULL){
1105	>	sprintf(painCave.errMsg,
1106	>	"SimSetup error: Component \"%s\" was not found in the "
1107	>	"list of declared molecules\n",
1108	>	id);
1109	>	painCave.isFatal = 1;
1110	>	simError();
1111		}
1112	<
1113	<	headStamp->add( currentStamp );
1114	<	comp_stamps[i] = headStamp->match( id );
1112	>
1113	>	headStamp->add(currentStamp);
1114	>	comp_stamps[i] = headStamp->match(id);
1115		}
1116		}
1117
1118		#ifdef IS_MPI
1119	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1119	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1120		MPIcheckPoint();
1121		#endif // is_mpi
1122	+	}
1123
1124	+	void SimSetup::calcSysValues(void){
1125	+	int i;
1126
1127	<	}
1127	>	int* molMembershipArray;
1128
1167	–	void SimSetup::calcSysValues( void ){
1168	–	int i, j, k;
1169	–
1170	–	int *molMembershipArray;
1171	–
1129		tot_atoms = 0;
1130		tot_bonds = 0;
1131		tot_bends = 0;
1132		tot_torsions = 0;
1133	<	for( i=0; i<n_components; i++ ){
1134	<
1135	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1136	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1180	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1133	>	for (i = 0; i < n_components; i++){
1134	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1135	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1136	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1137		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1138		}
1139	<
1139	>
1140		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1141		molMembershipArray = new int[tot_atoms];
1142	<
1143	<	for(i=0; i<nInfo; i++){
1142	>
1143	>	for (i = 0; i < nInfo; i++){
1144		info[i].n_atoms = tot_atoms;
1145		info[i].n_bonds = tot_bonds;
1146		info[i].n_bends = tot_bends;
1147		info[i].n_torsions = tot_torsions;
1148		info[i].n_SRI = tot_SRI;
1149		info[i].n_mol = tot_nmol;
1150	<
1150	>
1151		info[i].molMembershipArray = molMembershipArray;
1152	<	}
1152	>	}
1153		}
1154
1155		#ifdef IS_MPI
1156
1157	<	void SimSetup::mpiMolDivide( void ){
1202	<
1157	>	void SimSetup::mpiMolDivide(void){
1158		int i, j, k;
1159		int localMol, allMol;
1160		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1161
1162	<	mpiSim = new mpiSimulation( info );
1163	<
1162	>	mpiSim = new mpiSimulation(info);
1163	>
1164		globalIndex = mpiSim->divideLabor();
1165
1166		// set up the local variables
1167	<
1167	>
1168		mol2proc = mpiSim->getMolToProcMap();
1169		molCompType = mpiSim->getMolComponentType();
1170	<
1170	>
1171		allMol = 0;
1172		localMol = 0;
1173		local_atoms = 0;
#	Line 1222 | Line 1177 | void SimSetup::mpiMolDivide( void ){
1177		globalAtomIndex = 0;
1178
1179
1180	<	for( i=0; i<n_components; i++ ){
1181	<
1182	<	for( j=0; j<components_nmol[i]; j++ ){
1183	<
1184	<	if( mol2proc[allMol] == worldRank ){
1185	<
1186	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1187	<	local_bonds +=    comp_stamps[i]->getNBonds();
1233	<	local_bends +=    comp_stamps[i]->getNBends();
1234	<	local_torsions += comp_stamps[i]->getNTorsions();
1235	<	localMol++;
1180	>	for (i = 0; i < n_components; i++){
1181	>	for (j = 0; j < components_nmol[i]; j++){
1182	>	if (mol2proc[allMol] == worldRank){
1183	>	local_atoms += comp_stamps[i]->getNAtoms();
1184	>	local_bonds += comp_stamps[i]->getNBonds();
1185	>	local_bends += comp_stamps[i]->getNBends();
1186	>	local_torsions += comp_stamps[i]->getNTorsions();
1187	>	localMol++;
1188		}
1189	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1189	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1190		info[0].molMembershipArray[globalAtomIndex] = allMol;
1191		globalAtomIndex++;
1192		}
1193
1194	<	allMol++;
1194	>	allMol++;
1195		}
1196		}
1197		local_SRI = local_bonds + local_bends + local_torsions;
1198	<
1198	>
1199		info[0].n_atoms = mpiSim->getMyNlocal();
1200	<
1201	<	if( local_atoms != info[0].n_atoms ){
1202	<	sprintf( painCave.errMsg,
1203	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1204	<	" localAtom (%d) are not equal.\n",
1205	<	info[0].n_atoms,
1254	<	local_atoms );
1200	>
1201	>	if (local_atoms != info[0].n_atoms){
1202	>	sprintf(painCave.errMsg,
1203	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1204	>	" localAtom (%d) are not equal.\n",
1205	>	info[0].n_atoms, local_atoms);
1206		painCave.isFatal = 1;
1207		simError();
1208		}
#	Line 1262 | Line 1213 | void SimSetup::mpiMolDivide( void ){
1213		info[0].n_SRI = local_SRI;
1214		info[0].n_mol = localMol;
1215
1216	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1216	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1217		MPIcheckPoint();
1218		}
1219	<
1219	>
1220		#endif // is_mpi
1221
1222
1223	<	void SimSetup::makeSysArrays( void ){
1224	<	int i, j, k, l;
1223	>	void SimSetup::makeSysArrays(void){
1224	>
1225	>	#ifndef IS_MPI
1226	>	int k, j;
1227	>	#endif // is_mpi
1228	>	int i, l;
1229
1230		Atom** the_atoms;
1231		Molecule* the_molecules;
1232		Exclude** the_excludes;
1233
1234	<
1235	<	for(l=0; l<nInfo; l++){
1281	<
1234	>
1235	>	for (l = 0; l < nInfo; l++){
1236		// create the atom and short range interaction arrays
1237	<
1238	<	the_atoms = new Atom*[info[l].n_atoms];
1237	>
1238	>	the_atoms = new Atom * [info[l].n_atoms];
1239		the_molecules = new Molecule[info[l].n_mol];
1240		int molIndex;
1241
1242		// initialize the molecule's stampID's
1243	<
1243	>
1244		#ifdef IS_MPI
1245	<
1246	<
1245	>
1246	>
1247		molIndex = 0;
1248	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1249	<
1250	<	if(mol2proc[i] == worldRank ){
1251	<	the_molecules[molIndex].setStampID( molCompType[i] );
1252	<	the_molecules[molIndex].setMyIndex( molIndex );
1253	<	the_molecules[molIndex].setGlobalIndex( i );
1300	<	molIndex++;
1248	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1249	>	if (mol2proc[i] == worldRank){
1250	>	the_molecules[molIndex].setStampID(molCompType[i]);
1251	>	the_molecules[molIndex].setMyIndex(molIndex);
1252	>	the_molecules[molIndex].setGlobalIndex(i);
1253	>	molIndex++;
1254		}
1255		}
1256	<
1256	>
1257		#else // is_mpi
1258	<
1258	>
1259		molIndex = 0;
1260		globalAtomIndex = 0;
1261	<	for(i=0; i<n_components; i++){
1262	<	for(j=0; j<components_nmol[i]; j++ ){
1263	<	the_molecules[molIndex].setStampID( i );
1264	<	the_molecules[molIndex].setMyIndex( molIndex );
1265	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1266	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1267	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1268	<	globalAtomIndex++;
1269	<	}
1270	<	molIndex++;
1261	>	for (i = 0; i < n_components; i++){
1262	>	for (j = 0; j < components_nmol[i]; j++){
1263	>	the_molecules[molIndex].setStampID(i);
1264	>	the_molecules[molIndex].setMyIndex(molIndex);
1265	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1266	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1267	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1268	>	globalAtomIndex++;
1269	>	}
1270	>	molIndex++;
1271		}
1272		}
1273	<
1274	<
1273	>
1274	>
1275		#endif // is_mpi
1276
1277
1278	<	if( info[l].n_SRI ){
1326	<
1278	>	if (info[l].n_SRI){
1279		Exclude::createArray(info[l].n_SRI);
1280	<	the_excludes = new Exclude*[info[l].n_SRI];
1281	<	for( int ex=0; ex<info[l].n_SRI; ex++){
1282	<	the_excludes[ex] = new Exclude(ex);
1280	>	the_excludes = new Exclude * [info[l].n_SRI];
1281	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1282	>	the_excludes[ex] = new Exclude(ex);
1283		}
1284		info[l].globalExcludes = new int;
1285		info[l].n_exclude = info[l].n_SRI;
1286		}
1287		else{
1288	<
1289	<	Exclude::createArray( 1 );
1338	<	the_excludes = new Exclude*;
1288	>	Exclude::createArray(1);
1289	>	the_excludes = new Exclude * ;
1290		the_excludes[0] = new Exclude(0);
1291	<	the_excludes[0]->setPair( 0,0 );
1291	>	the_excludes[0]->setPair(0, 0);
1292		info[l].globalExcludes = new int;
1293		info[l].globalExcludes[0] = 0;
1294		info[l].n_exclude = 0;
#	Line 1350 | Line 1301 | void SimSetup::makeSysArrays( void ){
1301		info[l].nGlobalExcludes = 0;
1302		info[l].excludes = the_excludes;
1303
1304	<	the_ff->setSimInfo( info );
1354	<
1304	>	the_ff->setSimInfo(info);
1305		}
1306		}
1307
1308	<	void SimSetup::makeIntegrator( void ){
1359	<
1308	>	void SimSetup::makeIntegrator(void){
1309		int k;
1310
1311	<	NVT<RealIntegrator>*  myNVT = NULL;
1312	<	NPTi<RealIntegrator>* myNPTi = NULL;
1313	<	NPTf<RealIntegrator>* myNPTf = NULL;
1314	<	NPTim<RealIntegrator>* myNPTim = NULL;
1315	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1316	<
1317	<	for(k=0; k<nInfo; k++){
1318	<
1370	<	switch( ensembleCase ){
1371	<
1311	>	NVE* myNVE = NULL;
1312	>	NVT* myNVT = NULL;
1313	>	NPTi* myNPTi = NULL;
1314	>	NPTf* myNPTf = NULL;
1315	>	NPTxyz* myNPTxyz = NULL;
1316	>
1317	>	for (k = 0; k < nInfo; k++){
1318	>	switch (ensembleCase){
1319		case NVE_ENS:
1320	<	if (globals->haveZconstraints()){
1321	<	setupZConstraint(info[k]);
1322	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1323	<	}
1324	<
1325	<	else
1326	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1320	>	if (globals->haveZconstraints()){
1321	>
1322	>	std::cerr << "ZConstraint is temporarily disabled\n";
1323	>
1324	>	//      setupZConstraint(info[k]);
1325	>	//      myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1326	>	}
1327	>
1328	>	//       else{
1329	>	myNVE = new NVE(&(info[k]), the_ff);
1330	>	//       }
1331	>
1332	>	info->the_integrator = myNVE;
1333		break;
1334
1335		case NVT_ENS:
1336	<	if (globals->haveZconstraints()){
1337	<	setupZConstraint(info[k]);
1338	<	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1339	<	}
1340	<	else
1341	<	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1342	<
1336	>	if (globals->haveZconstraints()){
1337	>
1338	>	std::cerr << "ZConstraint is temporarily disabled\n";
1339	>
1340	>	//      setupZConstraint(info[k]);
1341	>	//      myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1342	>	}
1343	>	// else
1344	>	myNVT = new NVT(&(info[k]), the_ff);
1345	>
1346		myNVT->setTargetTemp(globals->getTargetTemp());
1347
1348	<	if (globals->haveTauThermostat())
1348	>	if (globals->haveTauThermostat())
1349		myNVT->setTauThermostat(globals->getTauThermostat());
1350	<
1351	<	else {
1352	<	sprintf( painCave.errMsg,
1353	<	"SimSetup error: If you use the NVT\n"
1398	<	"    ensemble, you must set tauThermostat.\n");
1350	>	else{
1351	>	sprintf(painCave.errMsg,
1352	>	"SimSetup error: If you use the NVT\n"
1353	>	"    ensemble, you must set tauThermostat.\n");
1354		painCave.isFatal = 1;
1355		simError();
1356		}
1357	+
1358	+	info->the_integrator = myNVT;
1359		break;
1360
1361		case NPTi_ENS:
1362	<	if (globals->haveZconstraints()){
1363	<	setupZConstraint(info[k]);
1364	<	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1365	<	}
1366	<	else
1367	<	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1368	<
1369	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1362	>	if (globals->haveZconstraints()){
1363	>
1364	>	std::cerr << "ZConstraint is temporarily disabled\n";
1365	>
1366	>	//        setupZConstraint(info[k]);
1367	>	//           myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1368	>	}
1369	>	// else
1370	>	myNPTi = new NPTi(&(info[k]), the_ff);
1371
1372	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1373	+
1374		if (globals->haveTargetPressure())
1375		myNPTi->setTargetPressure(globals->getTargetPressure());
1376	<	else {
1377	<	sprintf( painCave.errMsg,
1378	<	"SimSetup error: If you use a constant pressure\n"
1379	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1376	>	else{
1377	>	sprintf(painCave.errMsg,
1378	>	"SimSetup error: If you use a constant pressure\n"
1379	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1380		painCave.isFatal = 1;
1381		simError();
1382		}
1383
1384	<	if( globals->haveTauThermostat() )
1385	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1384	>	if (globals->haveTauThermostat())
1385	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1386		else{
1387	<	sprintf( painCave.errMsg,
1388	<	"SimSetup error: If you use an NPT\n"
1389	<	"    ensemble, you must set tauThermostat.\n");
1387	>	sprintf(painCave.errMsg,
1388	>	"SimSetup error: If you use an NPT\n"
1389	>	"    ensemble, you must set tauThermostat.\n");
1390		painCave.isFatal = 1;
1391		simError();
1392		}
1393
1394	<	if( globals->haveTauBarostat() )
1395	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1394	>	if (globals->haveTauBarostat())
1395	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1396		else{
1397	<	sprintf( painCave.errMsg,
1398	<	"SimSetup error: If you use an NPT\n"
1399	<	"    ensemble, you must set tauBarostat.\n");
1397	>	sprintf(painCave.errMsg,
1398	>	"SimSetup error: If you use an NPT\n"
1399	>	"    ensemble, you must set tauBarostat.\n");
1400		painCave.isFatal = 1;
1401		simError();
1402		}
1403	+
1404	+	info->the_integrator = myNPTi;
1405		break;
1406
1407		case NPTf_ENS:
1408	<	if (globals->haveZconstraints()){
1447	<	setupZConstraint(info[k]);
1448	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1449	<	}
1450	<	else
1451	<	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1408	>	if (globals->haveZconstraints()){
1409
1410	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1410	>	std::cerr << "ZConstraint is temporarily disabled\n";
1411	>
1412	>	//      setupZConstraint(info[k]);
1413	>	//      myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1414	>	}
1415	>	//       else
1416	>	myNPTf = new NPTf(&(info[k]), the_ff);
1417
1418	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1419	+
1420		if (globals->haveTargetPressure())
1421		myNPTf->setTargetPressure(globals->getTargetPressure());
1422	<	else {
1423	<	sprintf( painCave.errMsg,
1424	<	"SimSetup error: If you use a constant pressure\n"
1425	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1422	>	else{
1423	>	sprintf(painCave.errMsg,
1424	>	"SimSetup error: If you use a constant pressure\n"
1425	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1426		painCave.isFatal = 1;
1427		simError();
1428		}
1429
1430	<	if( globals->haveTauThermostat() )
1431	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1467	<	else{
1468	<	sprintf( painCave.errMsg,
1469	<	"SimSetup error: If you use an NPT\n"
1470	<	"    ensemble, you must set tauThermostat.\n");
1471	<	painCave.isFatal = 1;
1472	<	simError();
1473	<	}
1430	>	if (globals->haveTauThermostat())
1431	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1432
1475	–	if( globals->haveTauBarostat() )
1476	–	myNPTf->setTauBarostat( globals->getTauBarostat() );
1433		else{
1434	<	sprintf( painCave.errMsg,
1435	<	"SimSetup error: If you use an NPT\n"
1436	<	"    ensemble, you must set tauBarostat.\n");
1434	>	sprintf(painCave.errMsg,
1435	>	"SimSetup error: If you use an NPT\n"
1436	>	"    ensemble, you must set tauThermostat.\n");
1437		painCave.isFatal = 1;
1438		simError();
1439		}
1484	–	break;
1440
1441	<	case NPTim_ENS:
1442	<	if (globals->haveZconstraints()){
1488	<	setupZConstraint(info[k]);
1489	<	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1490	<	}
1491	<	else
1492	<	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1493	<
1494	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1441	>	if (globals->haveTauBarostat())
1442	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1443
1496	–	if (globals->haveTargetPressure())
1497	–	myNPTim->setTargetPressure(globals->getTargetPressure());
1498	–	else {
1499	–	sprintf( painCave.errMsg,
1500	–	"SimSetup error: If you use a constant pressure\n"
1501	–	"    ensemble, you must set targetPressure in the BASS file.\n");
1502	–	painCave.isFatal = 1;
1503	–	simError();
1504	–	}
1505	–
1506	–	if( globals->haveTauThermostat() )
1507	–	myNPTim->setTauThermostat( globals->getTauThermostat() );
1444		else{
1445	<	sprintf( painCave.errMsg,
1446	<	"SimSetup error: If you use an NPT\n"
1447	<	"    ensemble, you must set tauThermostat.\n");
1445	>	sprintf(painCave.errMsg,
1446	>	"SimSetup error: If you use an NPT\n"
1447	>	"    ensemble, you must set tauBarostat.\n");
1448		painCave.isFatal = 1;
1449		simError();
1450		}
1451
1452	<	if( globals->haveTauBarostat() )
1517	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1518	<	else{
1519	<	sprintf( painCave.errMsg,
1520	<	"SimSetup error: If you use an NPT\n"
1521	<	"    ensemble, you must set tauBarostat.\n");
1522	<	painCave.isFatal = 1;
1523	<	simError();
1524	<	}
1452	>	info->the_integrator = myNPTf;
1453		break;
1454
1455	<	case NPTfm_ENS:
1456	<	if (globals->haveZconstraints()){
1457	<	setupZConstraint(info[k]);
1458	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1459	<	}
1460	<	else
1461	<	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1455	>	case NPTxyz_ENS:
1456	>	if (globals->haveZconstraints()){
1457	>
1458	>	std::cerr << "ZConstraint is temporarily disabled\n";
1459	>
1460	>	//      setupZConstraint(info[k]);
1461	>	//      myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1462	>	}
1463	>	//       else
1464	>	myNPTxyz = new NPTxyz(&(info[k]), the_ff);
1465
1466	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1466	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1467
1468		if (globals->haveTargetPressure())
1469	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1470	<	else {
1471	<	sprintf( painCave.errMsg,
1472	<	"SimSetup error: If you use a constant pressure\n"
1473	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1469	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1470	>	else{
1471	>	sprintf(painCave.errMsg,
1472	>	"SimSetup error: If you use a constant pressure\n"
1473	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1474		painCave.isFatal = 1;
1475		simError();
1476	<	}
1476	>	}
1477
1478	<	if( globals->haveTauThermostat() )
1479	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1478	>	if (globals->haveTauThermostat())
1479	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1480		else{
1481	<	sprintf( painCave.errMsg,
1482	<	"SimSetup error: If you use an NPT\n"
1483	<	"    ensemble, you must set tauThermostat.\n");
1481	>	sprintf(painCave.errMsg,
1482	>	"SimSetup error: If you use an NPT\n"
1483	>	"    ensemble, you must set tauThermostat.\n");
1484		painCave.isFatal = 1;
1485		simError();
1486		}
1487
1488	<	if( globals->haveTauBarostat() )
1489	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1488	>	if (globals->haveTauBarostat())
1489	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1490		else{
1491	<	sprintf( painCave.errMsg,
1492	<	"SimSetup error: If you use an NPT\n"
1493	<	"    ensemble, you must set tauBarostat.\n");
1491	>	sprintf(painCave.errMsg,
1492	>	"SimSetup error: If you use an NPT\n"
1493	>	"    ensemble, you must set tauBarostat.\n");
1494		painCave.isFatal = 1;
1495		simError();
1496		}
1497	+
1498	+	info->the_integrator = myNPTxyz;
1499		break;
1500
1501		default:
1502	<	sprintf( painCave.errMsg,
1503	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1502	>	sprintf(painCave.errMsg,
1503	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1504		painCave.isFatal = 1;
1505		simError();
1506		}
1507		}
1508		}
1509
1510	<	void SimSetup::initFortran( void ){
1578	<
1510	>	void SimSetup::initFortran(void){
1511		info[0].refreshSim();
1512	<
1513	<	if( !strcmp( info[0].mixingRule, "standard") ){
1514	<	the_ff->initForceField( LB_MIXING_RULE );
1512	>
1513	>	if (!strcmp(info[0].mixingRule, "standard")){
1514	>	the_ff->initForceField(LB_MIXING_RULE);
1515		}
1516	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1517	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1516	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1517	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1518		}
1519		else{
1520	<	sprintf( painCave.errMsg,
1521	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1590	<	info[0].mixingRule );
1520	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1521	>	info[0].mixingRule);
1522		painCave.isFatal = 1;
1523		simError();
1524		}
1525
1526
1527		#ifdef IS_MPI
1528	<	strcpy( checkPointMsg,
1598	<	"Successfully intialized the mixingRule for Fortran." );
1528	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1529		MPIcheckPoint();
1530		#endif // is_mpi
1601	–
1531		}
1532
1533	<	void SimSetup::setupZConstraint(SimInfo& theInfo)
1534	<	{
1535	<	int nZConstraints;
1607	<	ZconStamp** zconStamp;
1608	<
1609	<	if(globals->haveZconstraintTime()){
1610	<
1611	<	//add sample time of z-constraint  into SimInfo's property list
1612	<	DoubleData* zconsTimeProp = new DoubleData();
1613	<	zconsTimeProp->setID(ZCONSTIME_ID);
1614	<	zconsTimeProp->setData(globals->getZconsTime());
1615	<	theInfo.addProperty(zconsTimeProp);
1616	<	}
1617	<	else{
1618	<	sprintf( painCave.errMsg,
1619	<	"ZConstraint error: If you use an ZConstraint\n"
1620	<	" , you must set sample time.\n");
1621	<	painCave.isFatal = 1;
1622	<	simError();
1623	<	}
1533	>	// void SimSetup::setupZConstraint(SimInfo& theInfo){
1534	>	//   int nZConstraints;
1535	>	//   ZconStamp** zconStamp;
1536
1537	<	//
1538	<	nZConstraints = globals->getNzConstraints();
1539	<	zconStamp = globals->getZconStamp();
1540	<	ZConsParaItem tempParaItem;
1537	>	//   if (globals->haveZconstraintTime()){
1538	>	//     //add sample time of z-constraint  into SimInfo's property list
1539	>	//     DoubleData* zconsTimeProp = new DoubleData();
1540	>	//     zconsTimeProp->setID(ZCONSTIME_ID);
1541	>	//     zconsTimeProp->setData(globals->getZconsTime());
1542	>	//     theInfo.addProperty(zconsTimeProp);
1543	>	//   }
1544	>	//   else{
1545	>	//     sprintf(painCave.errMsg,
1546	>	//             "ZConstraint error: If you use an ZConstraint\n"
1547	>	//             " , you must set sample time.\n");
1548	>	//     painCave.isFatal = 1;
1549	>	//     simError();
1550	>	//   }
1551
1552	<	ZConsParaData* zconsParaData = new ZConsParaData();
1553	<	zconsParaData->setID(ZCONSPARADATA_ID);
1554	<
1555	<	for(int i = 0; i < nZConstraints; i++){
1556	<	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1557	<	tempParaItem.zPos = zconStamp[i]->getZpos();
1558	<	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1559	<	tempParaItem.kRatio = zconStamp[i]->getKratio();
1552	>	//   //push zconsTol into siminfo, if user does not specify
1553	>	//   //value for zconsTol, a default value will be used
1554	>	//   DoubleData* zconsTol = new DoubleData();
1555	>	//   zconsTol->setID(ZCONSTOL_ID);
1556	>	//   if (globals->haveZconsTol()){
1557	>	//     zconsTol->setData(globals->getZconsTol());
1558	>	//   }
1559	>	//   else{
1560	>	//     double defaultZConsTol = 0.01;
1561	>	//     sprintf(painCave.errMsg,
1562	>	//             "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1563	>	//             " , default value %f is used.\n",
1564	>	//             defaultZConsTol);
1565	>	//     painCave.isFatal = 0;
1566	>	//     simError();
1567
1568	<	zconsParaData->addItem(tempParaItem);
1569	<	}
1568	>	//     zconsTol->setData(defaultZConsTol);
1569	>	//   }
1570	>	//   theInfo.addProperty(zconsTol);
1571
1572	<	//sort the parameters by index of molecules
1573	<	zconsParaData->sortByIndex();
1574	<
1645	<	//push data into siminfo, therefore, we can retrieve later
1646	<	theInfo.addProperty(zconsParaData);
1572	>	//   //set Force Subtraction Policy
1573	>	//   StringData* zconsForcePolicy = new StringData();
1574	>	//   zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1575
1576	<	//push zconsTol into siminfo, if user does not specify
1577	<	//value for zconsTol, a default value will be used
1578	<	DoubleData* zconsTol = new DoubleData();
1579	<	zconsTol->setID(ZCONSTOL_ID);
1580	<	if(globals->haveZconsTol()){
1581	<	zconsTol->setData(globals->getZconsTol());
1582	<	}
1583	<	else{
1584	<	double defaultZConsTol = 1E-6;
1585	<	sprintf( painCave.errMsg,
1586	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1659	<	" , default value %f is used.\n", defaultZConsTol);
1660	<	painCave.isFatal = 0;
1661	<	simError();
1576	>	//   if (globals->haveZconsForcePolicy()){
1577	>	//     zconsForcePolicy->setData(globals->getZconsForcePolicy());
1578	>	//   }
1579	>	//   else{
1580	>	//     sprintf(painCave.errMsg,
1581	>	//             "ZConstraint Warning: User does not set force Subtraction policy, "
1582	>	//             "PolicyByMass is used\n");
1583	>	//     painCave.isFatal = 0;
1584	>	//     simError();
1585	>	//     zconsForcePolicy->setData("BYMASS");
1586	>	//   }
1587
1588	<	zconsTol->setData(defaultZConsTol);
1589	<	}
1590	<	theInfo.addProperty(zconsTol);
1591	<
1592	<	//Determine the name of ouput file and add it into SimInfo's property list
1593	<	//Be careful, do not use inFileName, since it is a pointer which
1594	<	//point to a string at master node, and slave nodes do not contain that string
1595	<
1596	<	string zconsOutput(theInfo.finalName);
1597	<
1598	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1599	<
1600	<	StringData* zconsFilename = new StringData();
1601	<	zconsFilename->setID(ZCONSFILENAME_ID);
1602	<	zconsFilename->setData(zconsOutput);
1603	<
1604	<	theInfo.addProperty(zconsFilename);
1605	<	}
1588	>	//   theInfo.addProperty(zconsForcePolicy);
1589	>
1590	>	//   //Determine the name of ouput file and add it into SimInfo's property list
1591	>	//   //Be careful, do not use inFileName, since it is a pointer which
1592	>	//   //point to a string at master node, and slave nodes do not contain that string
1593	>
1594	>	//   string zconsOutput(theInfo.finalName);
1595	>
1596	>	//   zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1597	>
1598	>	//   StringData* zconsFilename = new StringData();
1599	>	//   zconsFilename->setID(ZCONSFILENAME_ID);
1600	>	//   zconsFilename->setData(zconsOutput);
1601	>
1602	>	//   theInfo.addProperty(zconsFilename);
1603	>
1604	>	//   //setup index, pos and other parameters of z-constraint molecules
1605	>	//   nZConstraints = globals->getNzConstraints();
1606	>	//   theInfo.nZconstraints = nZConstraints;
1607	>
1608	>	//   zconStamp = globals->getZconStamp();
1609	>	//   ZConsParaItem tempParaItem;
1610	>
1611	>	//   ZConsParaData* zconsParaData = new ZConsParaData();
1612	>	//   zconsParaData->setID(ZCONSPARADATA_ID);
1613	>
1614	>	//   for (int i = 0; i < nZConstraints; i++){
1615	>	//     tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1616	>	//     tempParaItem.zPos = zconStamp[i]->getZpos();
1617	>	//     tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1618	>	//     tempParaItem.kRatio = zconStamp[i]->getKratio();
1619	>
1620	>	//     zconsParaData->addItem(tempParaItem);
1621	>	//   }
1622	>
1623	>	//   //check the uniqueness of index
1624	>	//   if(!zconsParaData->isIndexUnique()){
1625	>	//     sprintf(painCave.errMsg,
1626	>	//             "ZConstraint Error: molIndex is not unique\n");
1627	>	//     painCave.isFatal = 1;
1628	>	//     simError();
1629	>	//   }
1630	>
1631	>	//   //sort the parameters by index of molecules
1632	>	//   zconsParaData->sortByIndex();
1633	>
1634	>	//   //push data into siminfo, therefore, we can retrieve later
1635	>	//   theInfo.addProperty(zconsParaData);
1636	>	// }

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