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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 626 by mmeineke, Wed Jul 16 21:30:56 2003 UTC vs.
Revision 962 by tim, Mon Jan 19 18:36:21 2004 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 14 | Line 17
17
18		// some defines for ensemble and Forcefield  cases
19
20	<	#define NVE_ENS   0
21	<	#define NVT_ENS   1
22	<	#define NPTi_ENS  2
23	<	#define NPTf_ENS  3
24	<	#define NPTim_ENS 4
22	<	#define NPTfm_ENS 5
20	>	#define NVE_ENS        0
21	>	#define NVT_ENS        1
22	>	#define NPTi_ENS       2
23	>	#define NPTf_ENS       3
24	>	#define NPTxyz_ENS     4
25
26
27		#define FF_DUFF 0
28		#define FF_LJ   1
29	+	#define FF_EAM  2
30
31	+	using namespace std;
32
33	+	/**
34	+	* Check whether dividend is divisble by divisor or not
35	+	*/
36	+	bool isDivisible(double dividend, double divisor){
37	+	double tolerance = 0.000001;
38	+	double quotient;
39	+	double diff;
40	+	int intQuotient;
41	+
42	+	quotient = dividend / divisor;
43	+
44	+	if (quotient < 0)
45	+	quotient = -quotient;
46	+
47	+	intQuotient = int (quotient + tolerance);
48	+
49	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
50	+
51	+	if (diff <= tolerance)
52	+	return true;
53	+	else
54	+	return false;
55	+	}
56	+
57		SimSetup::SimSetup(){
58	+
59	+	initSuspend = false;
60	+	isInfoArray = 0;
61	+	nInfo = 1;
62	+
63		stamps = new MakeStamps();
64		globals = new Globals();
65	<
65	>
66	>
67		#ifdef IS_MPI
68	<	strcpy( checkPointMsg, "SimSetup creation successful" );
68	>	strcpy(checkPointMsg, "SimSetup creation successful");
69		MPIcheckPoint();
70		#endif // IS_MPI
71		}
#	Line 41 | Line 75 | void SimSetup::parseFile( char* fileName ){
75		delete globals;
76		}
77
78	<	void SimSetup::parseFile( char* fileName ){
78	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
79	>	info = the_info;
80	>	nInfo = theNinfo;
81	>	isInfoArray = 1;
82	>	initSuspend = true;
83	>	}
84
85	+
86	+	void SimSetup::parseFile(char* fileName){
87		#ifdef IS_MPI
88	<	if( worldRank == 0 ){
88	>	if (worldRank == 0){
89		#endif // is_mpi
90	<
90	>
91		inFileName = fileName;
92	<	set_interface_stamps( stamps, globals );
93	<
92	>	set_interface_stamps(stamps, globals);
93	>
94		#ifdef IS_MPI
95		mpiEventInit();
96		#endif
97
98	<	yacc_BASS( fileName );
98	>	yacc_BASS(fileName);
99
100		#ifdef IS_MPI
101		throwMPIEvent(NULL);
102		}
103	<	else receiveParse();
103	>	else{
104	>	receiveParse();
105	>	}
106		#endif
107
108		}
109
110		#ifdef IS_MPI
111		void SimSetup::receiveParse(void){
112	<
113	<	set_interface_stamps( stamps, globals );
114	<	mpiEventInit();
115	<	MPIcheckPoint();
73	<	mpiEventLoop();
74	<
112	>	set_interface_stamps(stamps, globals);
113	>	mpiEventInit();
114	>	MPIcheckPoint();
115	>	mpiEventLoop();
116		}
117
118		#endif // is_mpi
119
120	<	void SimSetup::createSim( void ){
120	>	void SimSetup::createSim(void){
121
81	–	int i, j, k, globalAtomIndex;
82	–
122		// gather all of the information from the Bass file
123	<
123	>
124		gatherInfo();
125
126		// creation of complex system objects
#	Line 89 | Line 128 | void SimSetup::createSim( void ){
128		sysObjectsCreation();
129
130		// check on the post processing info
131	<
131	>
132		finalInfoCheck();
133
134		// initialize the system coordinates
135
136	<	initSystemCoords();
137	<
136	>	if ( !initSuspend ){
137	>	initSystemCoords();
138
139	+	if( !(globals->getUseInitTime()) )
140	+	info[0].currentTime = 0.0;
141	+	}
142	+
143		// make the output filenames
144
145		makeOutNames();
146	<
146	>
147		// make the integrator
148	<
148	>
149		makeIntegrator();
150	<
150	>
151		#ifdef IS_MPI
152		mpiSim->mpiRefresh();
153		#endif
#	Line 112 | Line 155 | void SimSetup::createSim( void ){
155		// initialize the Fortran
156
157		initFortran();
115	–
116	–
117	–
158		}
159
160
161	<	void SimSetup::makeMolecules( void ){
162	<
161	>	void SimSetup::makeMolecules(void){
162	>	int k;
163		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
164		molInit molInfo;
165		DirectionalAtom* dAtom;
#	Line 134 | Line 174 | void SimSetup::makeMolecules( void ){
174		bend_set* theBends;
175		torsion_set* theTorsions;
176
177	<
177	>
178		//init the forceField paramters
179
180		the_ff->readParams();
181
182	<
182	>
183		// init the atoms
184
185		double ux, uy, uz, u, uSqr;
146	–
147	–	atomOffset = 0;
148	–	excludeOffset = 0;
149	–	for(i=0; i<info->n_mol; i++){
150	–
151	–	stampID = the_molecules[i].getStampID();
186
187	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
188	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
155	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
156	<	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
157	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
187	>	for (k = 0; k < nInfo; k++){
188	>	the_ff->setSimInfo(&(info[k]));
189
190	<	molInfo.myAtoms = &the_atoms[atomOffset];
191	<	molInfo.myExcludes = &the_excludes[excludeOffset];
192	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
193	<	molInfo.myBends = new Bend*[molInfo.nBends];
163	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
190	>	atomOffset = 0;
191	>	excludeOffset = 0;
192	>	for (i = 0; i < info[k].n_mol; i++){
193	>	stampID = info[k].molecules[i].getStampID();
194
195	<	theBonds = new bond_pair[molInfo.nBonds];
196	<	theBends = new bend_set[molInfo.nBends];
197	<	theTorsions = new torsion_set[molInfo.nTorsions];
198	<
199	<	// make the Atoms
200	<
201	<	for(j=0; j<molInfo.nAtoms; j++){
202	<
203	<	currentAtom = comp_stamps[stampID]->getAtom( j );
204	<	if( currentAtom->haveOrientation() ){
205	<
206	<	dAtom = new DirectionalAtom(j + atomOffset);
207	<	info->n_oriented++;
208	<	molInfo.myAtoms[j] = dAtom;
209	<
210	<	ux = currentAtom->getOrntX();
211	<	uy = currentAtom->getOrntY();
212	<	uz = currentAtom->getOrntZ();
213	<
214	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
215	<
216	<	u = sqrt( uSqr );
217	<	ux = ux / u;
218	<	uy = uy / u;
219	<	uz = uz / u;
220	<
221	<	dAtom->setSUx( ux );
222	<	dAtom->setSUy( uy );
223	<	dAtom->setSUz( uz );
224	<	}
225	<	else{
226	<	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
227	<	}
228	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
229	<
195	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
196	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
197	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
198	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
199	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
200	>
201	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
202	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
203	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
204	>	molInfo.myBends = new Bend * [molInfo.nBends];
205	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
206	>
207	>	theBonds = new bond_pair[molInfo.nBonds];
208	>	theBends = new bend_set[molInfo.nBends];
209	>	theTorsions = new torsion_set[molInfo.nTorsions];
210	>
211	>	// make the Atoms
212	>
213	>	for (j = 0; j < molInfo.nAtoms; j++){
214	>	currentAtom = comp_stamps[stampID]->getAtom(j);
215	>	if (currentAtom->haveOrientation()){
216	>	dAtom = new DirectionalAtom((j + atomOffset),
217	>	info[k].getConfiguration());
218	>	info[k].n_oriented++;
219	>	molInfo.myAtoms[j] = dAtom;
220	>
221	>	ux = currentAtom->getOrntX();
222	>	uy = currentAtom->getOrntY();
223	>	uz = currentAtom->getOrntZ();
224	>
225	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
226	>
227	>	u = sqrt(uSqr);
228	>	ux = ux / u;
229	>	uy = uy / u;
230	>	uz = uz / u;
231	>
232	>	dAtom->setSUx(ux);
233	>	dAtom->setSUy(uy);
234	>	dAtom->setSUz(uz);
235	>	}
236	>	else{
237	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
238	>	info[k].getConfiguration());
239	>	}
240	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
241	>
242		#ifdef IS_MPI
243	<
244	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
245	<
243	>
244	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
245	>
246		#endif // is_mpi
247	<	}
206	<
207	<	// make the bonds
208	<	for(j=0; j<molInfo.nBonds; j++){
209	<
210	<	currentBond = comp_stamps[stampID]->getBond( j );
211	<	theBonds[j].a = currentBond->getA() + atomOffset;
212	<	theBonds[j].b = currentBond->getB() + atomOffset;
247	>	}
248
249	<	exI = theBonds[j].a;
250	<	exJ = theBonds[j].b;
249	>	// make the bonds
250	>	for (j = 0; j < molInfo.nBonds; j++){
251	>	currentBond = comp_stamps[stampID]->getBond(j);
252	>	theBonds[j].a = currentBond->getA() + atomOffset;
253	>	theBonds[j].b = currentBond->getB() + atomOffset;
254
255	<	// exclude_I must always be the smaller of the pair
256	<	if( exI > exJ ){
257	<	tempEx = exI;
258	<	exI = exJ;
259	<	exJ = tempEx;
260	<	}
255	>	exI = theBonds[j].a;
256	>	exJ = theBonds[j].b;
257	>
258	>	// exclude_I must always be the smaller of the pair
259	>	if (exI > exJ){
260	>	tempEx = exI;
261	>	exI = exJ;
262	>	exJ = tempEx;
263	>	}
264		#ifdef IS_MPI
265	<	tempEx = exI;
266	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
267	<	tempEx = exJ;
268	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
269	<
270	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
265	>	tempEx = exI;
266	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
267	>	tempEx = exJ;
268	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
269	>
270	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
271		#else  // isn't MPI
272
273	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
273	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
274		#endif  //is_mpi
275	<	}
276	<	excludeOffset += molInfo.nBonds;
275	>	}
276	>	excludeOffset += molInfo.nBonds;
277
278	<	//make the bends
279	<	for(j=0; j<molInfo.nBends; j++){
280	<
281	<	currentBend = comp_stamps[stampID]->getBend( j );
282	<	theBends[j].a = currentBend->getA() + atomOffset;
283	<	theBends[j].b = currentBend->getB() + atomOffset;
284	<	theBends[j].c = currentBend->getC() + atomOffset;
285	<
286	<	if( currentBend->haveExtras() ){
287	<
288	<	extras = currentBend->getExtras();
289	<	current_extra = extras;
290	<
291	<	while( current_extra != NULL ){
292	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
293	<
294	<	switch( current_extra->getType() ){
295	<
296	<	case 0:
297	<	theBends[j].ghost =
298	<	current_extra->getInt() + atomOffset;
299	<	theBends[j].isGhost = 1;
300	<	break;
301	<
302	<	case 1:
303	<	theBends[j].ghost =
304	<	(int)current_extra->getDouble() + atomOffset;
305	<	theBends[j].isGhost = 1;
306	<	break;
307	<
308	<	default:
309	<	sprintf( painCave.errMsg,
310	<	"SimSetup Error: ghostVectorSource was neither a "
311	<	"double nor an int.\n"
312	<	"-->Bend[%d] in %s\n",
313	<	j, comp_stamps[stampID]->getID() );
314	<	painCave.isFatal = 1;
315	<	simError();
316	<	}
317	<	}
318	<
319	<	else{
320	<
321	<	sprintf( painCave.errMsg,
322	<	"SimSetup Error: unhandled bend assignment:\n"
323	<	"    -->%s in Bend[%d] in %s\n",
324	<	current_extra->getlhs(),
325	<	j, comp_stamps[stampID]->getID() );
326	<	painCave.isFatal = 1;
327	<	simError();
328	<	}
329	<
330	<	current_extra = current_extra->getNext();
331	<	}
332	<	}
333	<
334	<	if( !theBends[j].isGhost ){
335	<
336	<	exI = theBends[j].a;
337	<	exJ = theBends[j].c;
338	<	}
339	<	else{
340	<
300	<	exI = theBends[j].a;
301	<	exJ = theBends[j].b;
302	<	}
303	<
304	<	// exclude_I must always be the smaller of the pair
305	<	if( exI > exJ ){
306	<	tempEx = exI;
307	<	exI = exJ;
308	<	exJ = tempEx;
309	<	}
278	>	//make the bends
279	>	for (j = 0; j < molInfo.nBends; j++){
280	>	currentBend = comp_stamps[stampID]->getBend(j);
281	>	theBends[j].a = currentBend->getA() + atomOffset;
282	>	theBends[j].b = currentBend->getB() + atomOffset;
283	>	theBends[j].c = currentBend->getC() + atomOffset;
284	>
285	>	if (currentBend->haveExtras()){
286	>	extras = currentBend->getExtras();
287	>	current_extra = extras;
288	>
289	>	while (current_extra != NULL){
290	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
291	>	switch (current_extra->getType()){
292	>	case 0:
293	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
294	>	theBends[j].isGhost = 1;
295	>	break;
296	>
297	>	case 1:
298	>	theBends[j].ghost = (int) current_extra->getDouble() +
299	>	atomOffset;
300	>	theBends[j].isGhost = 1;
301	>	break;
302	>
303	>	default:
304	>	sprintf(painCave.errMsg,
305	>	"SimSetup Error: ghostVectorSource was neither a "
306	>	"double nor an int.\n"
307	>	"-->Bend[%d] in %s\n",
308	>	j, comp_stamps[stampID]->getID());
309	>	painCave.isFatal = 1;
310	>	simError();
311	>	}
312	>	}
313	>	else{
314	>	sprintf(painCave.errMsg,
315	>	"SimSetup Error: unhandled bend assignment:\n"
316	>	"    -->%s in Bend[%d] in %s\n",
317	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
318	>	painCave.isFatal = 1;
319	>	simError();
320	>	}
321	>
322	>	current_extra = current_extra->getNext();
323	>	}
324	>	}
325	>
326	>	if (!theBends[j].isGhost){
327	>	exI = theBends[j].a;
328	>	exJ = theBends[j].c;
329	>	}
330	>	else{
331	>	exI = theBends[j].a;
332	>	exJ = theBends[j].b;
333	>	}
334	>
335	>	// exclude_I must always be the smaller of the pair
336	>	if (exI > exJ){
337	>	tempEx = exI;
338	>	exI = exJ;
339	>	exJ = tempEx;
340	>	}
341		#ifdef IS_MPI
342	<	tempEx = exI;
343	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
344	<	tempEx = exJ;
345	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
346	<
347	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
342	>	tempEx = exI;
343	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
344	>	tempEx = exJ;
345	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
346	>
347	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
348		#else  // isn't MPI
349	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
349	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
350		#endif  //is_mpi
351	<	}
352	<	excludeOffset += molInfo.nBends;
351	>	}
352	>	excludeOffset += molInfo.nBends;
353
354	<	for(j=0; j<molInfo.nTorsions; j++){
355	<
356	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
357	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
358	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
359	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
329	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
330	<
331	<	exI = theTorsions[j].a;
332	<	exJ = theTorsions[j].d;
354	>	for (j = 0; j < molInfo.nTorsions; j++){
355	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
356	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
357	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
358	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
359	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
360
361	<	// exclude_I must always be the smaller of the pair
362	<	if( exI > exJ ){
363	<	tempEx = exI;
364	<	exI = exJ;
365	<	exJ = tempEx;
366	<	}
361	>	exI = theTorsions[j].a;
362	>	exJ = theTorsions[j].d;
363	>
364	>	// exclude_I must always be the smaller of the pair
365	>	if (exI > exJ){
366	>	tempEx = exI;
367	>	exI = exJ;
368	>	exJ = tempEx;
369	>	}
370		#ifdef IS_MPI
371	<	tempEx = exI;
372	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
373	<	tempEx = exJ;
374	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
375	<
376	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
371	>	tempEx = exI;
372	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
373	>	tempEx = exJ;
374	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
375	>
376	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
377		#else  // isn't MPI
378	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
378	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
379		#endif  //is_mpi
380	<	}
381	<	excludeOffset += molInfo.nTorsions;
380	>	}
381	>	excludeOffset += molInfo.nTorsions;
382
353	–
354	–	// send the arrays off to the forceField for init.
383
384	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
357	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
358	<	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
359	<	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
384	>	// 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,
390	+	theTorsions);
391
362	–	the_molecules[i].initialize( molInfo );
392
393	+	info[k].molecules[i].initialize(molInfo);
394
395	<	atomOffset += molInfo.nAtoms;
396	<	delete[] theBonds;
397	<	delete[] theBends;
398	<	delete[] theTorsions;
395	>
396	>	atomOffset += molInfo.nAtoms;
397	>	delete[] theBonds;
398	>	delete[] theBends;
399	>	delete[] theTorsions;
400	>	}
401		}
402
403		#ifdef IS_MPI
404	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
404	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
405		MPIcheckPoint();
406		#endif // is_mpi
407
408		// clean up the forcefield
409	+
410		the_ff->calcRcut();
411		the_ff->cleanMe();
379	–
412		}
413
414	<	void SimSetup::initFromBass( void ){
383	<
414	>	void SimSetup::initFromBass(void){
415		int i, j, k;
416		int n_cells;
417		double cellx, celly, cellz;
#	Line 389 | Line 420 | void SimSetup::initFromBass( void ){
420		int n_extra;
421		int have_extra, done;
422
423	<	temp1 = (double)tot_nmol / 4.0;
424	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
425	<	temp3 = ceil( temp2 );
423	>	double vel[3];
424	>	vel[0] = 0.0;
425	>	vel[1] = 0.0;
426	>	vel[2] = 0.0;
427
428	<	have_extra =0;
429	<	if( temp2 < temp3 ){ // we have a non-complete lattice
430	<	have_extra =1;
428	>	temp1 = (double) tot_nmol / 4.0;
429	>	temp2 = pow(temp1, (1.0 / 3.0));
430	>	temp3 = ceil(temp2);
431
432	<	n_cells = (int)temp3 - 1;
433	<	cellx = info->boxL[0] / temp3;
434	<	celly = info->boxL[1] / temp3;
435	<	cellz = info->boxL[2] / temp3;
404	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
405	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
406	<	n_per_extra = (int)ceil( temp1 );
432	>	have_extra = 0;
433	>	if (temp2 < temp3){
434	>	// we have a non-complete lattice
435	>	have_extra = 1;
436
437	<	if( n_per_extra > 4){
438	<	sprintf( painCave.errMsg,
439	<	"SimSetup error. There has been an error in constructing"
440	<	" the non-complete lattice.\n" );
437	>	n_cells = (int) temp3 - 1;
438	>	cellx = info[0].boxL[0] / temp3;
439	>	celly = info[0].boxL[1] / temp3;
440	>	cellz = info[0].boxL[2] / temp3;
441	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
442	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
443	>	n_per_extra = (int) ceil(temp1);
444	>
445	>	if (n_per_extra > 4){
446	>	sprintf(painCave.errMsg,
447	>	"SimSetup error. There has been an error in constructing"
448	>	" the non-complete lattice.\n");
449		painCave.isFatal = 1;
450		simError();
451		}
452		}
453		else{
454	<	n_cells = (int)temp3;
455	<	cellx = info->boxL[0] / temp3;
456	<	celly = info->boxL[1] / temp3;
457	<	cellz = info->boxL[2] / temp3;
454	>	n_cells = (int) temp3;
455	>	cellx = info[0].boxL[0] / temp3;
456	>	celly = info[0].boxL[1] / temp3;
457	>	cellz = info[0].boxL[2] / temp3;
458		}
459
460		current_mol = 0;
#	Line 425 | Line 462 | void SimSetup::initFromBass( void ){
462		current_comp = 0;
463		current_atom_ndx = 0;
464
465	<	for( i=0; i < n_cells ; i++ ){
466	<	for( j=0; j < n_cells; j++ ){
467	<	for( k=0; k < n_cells; k++ ){
465	>	for (i = 0; i < n_cells ; i++){
466	>	for (j = 0; j < n_cells; j++){
467	>	for (k = 0; k < n_cells; k++){
468	>	makeElement(i * cellx, j * celly, k * cellz);
469
470	<	makeElement( i * cellx,
433	<	j * celly,
434	<	k * cellz );
470	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
471
472	<	makeElement( i * cellx + 0.5 * cellx,
437	<	j * celly + 0.5 * celly,
438	<	k * cellz );
472	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
473
474	<	makeElement( i * cellx,
441	<	j * celly + 0.5 * celly,
442	<	k * cellz + 0.5 * cellz );
443	<
444	<	makeElement( i * cellx + 0.5 * cellx,
445	<	j * celly,
446	<	k * cellz + 0.5 * cellz );
474	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
475		}
476		}
477		}
478
479	<	if( have_extra ){
479	>	if (have_extra){
480		done = 0;
481
482		int start_ndx;
483	<	for( i=0; i < (n_cells+1) && !done; i++ ){
484	<	for( j=0; j < (n_cells+1) && !done; j++ ){
483	>	for (i = 0; i < (n_cells + 1) && !done; i++){
484	>	for (j = 0; j < (n_cells + 1) && !done; j++){
485	>	if (i < n_cells){
486	>	if (j < n_cells){
487	>	start_ndx = n_cells;
488	>	}
489	>	else
490	>	start_ndx = 0;
491	>	}
492	>	else
493	>	start_ndx = 0;
494
495	<	if( i < n_cells ){
495	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
496	>	makeElement(i * cellx, j * celly, k * cellz);
497	>	done = (current_mol >= tot_nmol);
498
499	<	if( j < n_cells ){
500	<	start_ndx = n_cells;
501	<	}
502	<	else start_ndx = 0;
503	<	}
465	<	else start_ndx = 0;
499	>	if (!done && n_per_extra > 1){
500	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
501	>	k * cellz);
502	>	done = (current_mol >= tot_nmol);
503	>	}
504
505	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
505	>	if (!done && n_per_extra > 2){
506	>	makeElement(i * cellx, j * celly + 0.5 * celly,
507	>	k * cellz + 0.5 * cellz);
508	>	done = (current_mol >= tot_nmol);
509	>	}
510
511	<	makeElement( i * cellx,
512	<	j * celly,
513	<	k * cellz );
514	<	done = ( current_mol >= tot_nmol );
515	<
516	<	if( !done && n_per_extra > 1 ){
475	<	makeElement( i * cellx + 0.5 * cellx,
476	<	j * celly + 0.5 * celly,
477	<	k * cellz );
478	<	done = ( current_mol >= tot_nmol );
479	<	}
480	<
481	<	if( !done && n_per_extra > 2){
482	<	makeElement( i * cellx,
483	<	j * celly + 0.5 * celly,
484	<	k * cellz + 0.5 * cellz );
485	<	done = ( current_mol >= tot_nmol );
486	<	}
487	<
488	<	if( !done && n_per_extra > 3){
489	<	makeElement( i * cellx + 0.5 * cellx,
490	<	j * celly,
491	<	k * cellz + 0.5 * cellz );
492	<	done = ( current_mol >= tot_nmol );
493	<	}
494	<	}
511	>	if (!done && n_per_extra > 3){
512	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
513	>	k * cellz + 0.5 * cellz);
514	>	done = (current_mol >= tot_nmol);
515	>	}
516	>	}
517		}
518		}
519		}
520
521	<
522	<	for( i=0; i<info->n_atoms; i++ ){
501	<	info->atoms[i]->set_vx( 0.0 );
502	<	info->atoms[i]->set_vy( 0.0 );
503	<	info->atoms[i]->set_vz( 0.0 );
521	>	for (i = 0; i < info[0].n_atoms; i++){
522	>	info[0].atoms[i]->setVel(vel);
523		}
524		}
525
526	<	void SimSetup::makeElement( double x, double y, double z ){
508	<
526	>	void SimSetup::makeElement(double x, double y, double z){
527		int k;
528		AtomStamp* current_atom;
529		DirectionalAtom* dAtom;
530		double rotMat[3][3];
531	+	double pos[3];
532
533	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
534	<
535	<	current_atom = comp_stamps[current_comp]->getAtom( k );
536	<	if( !current_atom->havePosition() ){
537	<	sprintf( painCave.errMsg,
538	<	"SimSetup:initFromBass error.\n"
539	<	"\tComponent %s, atom %s does not have a position specified.\n"
540	<	"\tThe initialization routine is unable to give a start"
541	<	" position.\n",
523	<	comp_stamps[current_comp]->getID(),
524	<	current_atom->getType() );
533	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
534	>	current_atom = comp_stamps[current_comp]->getAtom(k);
535	>	if (!current_atom->havePosition()){
536	>	sprintf(painCave.errMsg,
537	>	"SimSetup:initFromBass error.\n"
538	>	"\tComponent %s, atom %s does not have a position specified.\n"
539	>	"\tThe initialization routine is unable to give a start"
540	>	" position.\n",
541	>	comp_stamps[current_comp]->getID(), current_atom->getType());
542		painCave.isFatal = 1;
543		simError();
544		}
545
546	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
547	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
548	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
546	>	pos[0] = x + current_atom->getPosX();
547	>	pos[1] = y + current_atom->getPosY();
548	>	pos[2] = z + current_atom->getPosZ();
549
550	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
550	>	info[0].atoms[current_atom_ndx]->setPos(pos);
551
552	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
552	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
553	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
554
555		rotMat[0][0] = 1.0;
556		rotMat[0][1] = 0.0;
#	Line 546 | Line 564 | void SimSetup::makeElement( double x, double y, double
564		rotMat[2][1] = 0.0;
565		rotMat[2][2] = 1.0;
566
567	<	dAtom->setA( rotMat );
567	>	dAtom->setA(rotMat);
568		}
569
570		current_atom_ndx++;
#	Line 555 | Line 573 | void SimSetup::makeElement( double x, double y, double
573		current_mol++;
574		current_comp_mol++;
575
576	<	if( current_comp_mol >= components_nmol[current_comp] ){
559	<
576	>	if (current_comp_mol >= components_nmol[current_comp]){
577		current_comp_mol = 0;
578		current_comp++;
579		}
580		}
581
582
583	<	void SimSetup::gatherInfo( void ){
584	<	int i,j,k;
583	>	void SimSetup::gatherInfo(void){
584	>	int i;
585
586		ensembleCase = -1;
587		ffCase = -1;
588
572	–	// get the stamps and globals;
573	–	stamps = stamps;
574	–	globals = globals;
575	–
589		// set the easy ones first
590	<	info->target_temp = globals->getTargetTemp();
591	<	info->dt = globals->getDt();
592	<	info->run_time = globals->getRunTime();
590	>
591	>	for (i = 0; i < nInfo; i++){
592	>	info[i].target_temp = globals->getTargetTemp();
593	>	info[i].dt = globals->getDt();
594	>	info[i].run_time = globals->getRunTime();
595	>	}
596		n_components = globals->getNComponents();
597
598
599		// get the forceField
600
601	<	strcpy( force_field, globals->getForceField() );
601	>	strcpy(force_field, globals->getForceField());
602
603	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
604	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
603	>	if (!strcasecmp(force_field, "DUFF")){
604	>	ffCase = FF_DUFF;
605	>	}
606	>	else if (!strcasecmp(force_field, "LJ")){
607	>	ffCase = FF_LJ;
608	>	}
609	>	else if (!strcasecmp(force_field, "EAM")){
610	>	ffCase = FF_EAM;
611	>	}
612		else{
613	<	sprintf( painCave.errMsg,
614	<	"SimSetup Error. Unrecognized force field -> %s\n",
615	<	force_field );
616	<	painCave.isFatal = 1;
594	<	simError();
613	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
614	>	force_field);
615	>	painCave.isFatal = 1;
616	>	simError();
617		}
618
619	<	// get the ensemble
619	>	// get the ensemble
620
621	<	strcpy( ensemble, globals->getEnsemble() );
621	>	strcpy(ensemble, globals->getEnsemble());
622
623	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
624	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
625	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
623	>	if (!strcasecmp(ensemble, "NVE")){
624	>	ensembleCase = NVE_ENS;
625	>	}
626	>	else if (!strcasecmp(ensemble, "NVT")){
627	>	ensembleCase = NVT_ENS;
628	>	}
629	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
630		ensembleCase = NPTi_ENS;
631	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
632	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
633	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
631	>	}
632	>	else if (!strcasecmp(ensemble, "NPTf")){
633	>	ensembleCase = NPTf_ENS;
634	>	}
635	>	else if (!strcasecmp(ensemble, "NPTxyz")){
636	>	ensembleCase = NPTxyz_ENS;
637	>	}
638		else{
639	<	sprintf( painCave.errMsg,
640	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
641	<	"reverting to NVE for this simulation.\n",
642	<	ensemble );
643	<	painCave.isFatal = 0;
644	<	simError();
645	<	strcpy( ensemble, "NVE" );
646	<	ensembleCase = NVE_ENS;
639	>	sprintf(painCave.errMsg,
640	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
641	>	"reverting to NVE for this simulation.\n",
642	>	ensemble);
643	>	painCave.isFatal = 0;
644	>	simError();
645	>	strcpy(ensemble, "NVE");
646	>	ensembleCase = NVE_ENS;
647		}
618	–	strcpy( info->ensemble, ensemble );
648
649	<	// get the mixing rule
649	>	for (i = 0; i < nInfo; i++){
650	>	strcpy(info[i].ensemble, ensemble);
651
652	<	strcpy( info->mixingRule, globals->getMixingRule() );
653	<	info->usePBC = globals->getPBC();
654	<
655	<
652	>	// get the mixing rule
653	>
654	>	strcpy(info[i].mixingRule, globals->getMixingRule());
655	>	info[i].usePBC = globals->getPBC();
656	>	}
657	>
658		// get the components and calculate the tot_nMol and indvidual n_mol
659	<
659	>
660		the_components = globals->getComponents();
661		components_nmol = new int[n_components];
662
663
664	<	if( !globals->haveNMol() ){
664	>	if (!globals->haveNMol()){
665		// we don't have the total number of molecules, so we assume it is
666		// given in each component
667
668		tot_nmol = 0;
669	<	for( i=0; i<n_components; i++ ){
670	<
671	<	if( !the_components[i]->haveNMol() ){
672	<	// we have a problem
673	<	sprintf( painCave.errMsg,
674	<	"SimSetup Error. No global NMol or component NMol"
675	<	" given. Cannot calculate the number of atoms.\n" );
676	<	painCave.isFatal = 1;
645	<	simError();
669	>	for (i = 0; i < n_components; i++){
670	>	if (!the_components[i]->haveNMol()){
671	>	// we have a problem
672	>	sprintf(painCave.errMsg,
673	>	"SimSetup Error. No global NMol or component NMol"
674	>	" given. Cannot calculate the number of atoms.\n");
675	>	painCave.isFatal = 1;
676	>	simError();
677		}
678
679		tot_nmol += the_components[i]->getNMol();
#	Line 650 | Line 681 | void SimSetup::gatherInfo( void ){
681		}
682		}
683		else{
684	<	sprintf( painCave.errMsg,
685	<	"SimSetup error.\n"
686	<	"\tSorry, the ability to specify total"
687	<	" nMols and then give molfractions in the components\n"
688	<	"\tis not currently supported."
689	<	" Please give nMol in the components.\n" );
684	>	sprintf(painCave.errMsg,
685	>	"SimSetup error.\n"
686	>	"\tSorry, the ability to specify total"
687	>	" nMols and then give molfractions in the components\n"
688	>	"\tis not currently supported."
689	>	" Please give nMol in the components.\n");
690		painCave.isFatal = 1;
691		simError();
692		}
693
694	<	// set the status, sample, and thermal kick times
695	<
696	<	if( globals->haveSampleTime() ){
697	<	info->sampleTime = globals->getSampleTime();
698	<	info->statusTime = info->sampleTime;
699	<	info->thermalTime = info->sampleTime;
694	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
695	>	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
696	>	sprintf(painCave.errMsg,
697	>	"Sample time is not divisible by dt \n");
698	>	painCave.isFatal = 0;
699	>	simError();
700		}
670	–	else{
671	–	info->sampleTime = globals->getRunTime();
672	–	info->statusTime = info->sampleTime;
673	–	info->thermalTime = info->sampleTime;
674	–	}
701
702	<	if( globals->haveStatusTime() ){
703	<	info->statusTime = globals->getStatusTime();
702	>	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
703	>	sprintf(painCave.errMsg,
704	>	"Status time is not divisible by dt\n");
705	>	painCave.isFatal = 0;
706	>	simError();
707		}
708
709	<	if( globals->haveThermalTime() ){
710	<	info->thermalTime = globals->getThermalTime();
711	<	}
709	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
710	>	sprintf(painCave.errMsg,
711	>	"Thermal time is not divisible by dt\n");
712	>	painCave.isFatal = 0;
713	>	simError();
714	>	}
715
716	<	// check for the temperature set flag
716	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
717	>	sprintf(painCave.errMsg,
718	>	"Reset time is not divisible by dt\n");
719	>	painCave.isFatal = 0;
720	>	simError();
721	>	}
722
723	<	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
723	>	// set the status, sample, and thermal kick times
724
725	<	// get some of the tricky things that may still be in the globals
725	>	for (i = 0; i < nInfo; i++){
726	>	if (globals->haveSampleTime()){
727	>	info[i].sampleTime = globals->getSampleTime();
728	>	info[i].statusTime = info[i].sampleTime;
729	>	info[i].thermalTime = info[i].sampleTime;
730	>	}
731	>	else{
732	>	info[i].sampleTime = globals->getRunTime();
733	>	info[i].statusTime = info[i].sampleTime;
734	>	info[i].thermalTime = info[i].sampleTime;
735	>	}
736
737	<	double boxVector[3];
738	<	if( globals->haveBox() ){
739	<	boxVector[0] = globals->getBox();
740	<	boxVector[1] = globals->getBox();
741	<	boxVector[2] = globals->getBox();
737	>	if (globals->haveStatusTime()){
738	>	info[i].statusTime = globals->getStatusTime();
739	>	}
740	>
741	>	if (globals->haveThermalTime()){
742	>	info[i].thermalTime = globals->getThermalTime();
743	>	}
744	>
745	>	info[i].resetIntegrator = 0;
746	>	if( globals->haveResetTime() ){
747	>	info[i].resetTime = globals->getResetTime();
748	>	info[i].resetIntegrator = 1;
749	>	}
750	>
751	>	// check for the temperature set flag
752
753	<	info->setBox( boxVector );
754	<	}
698	<	else if( globals->haveDensity() ){
753	>	if (globals->haveTempSet())
754	>	info[i].setTemp = globals->getTempSet();
755
756	<	double vol;
701	<	vol = (double)tot_nmol / globals->getDensity();
702	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
703	<	boxVector[1] = boxVector[0];
704	<	boxVector[2] = boxVector[0];
756	>	// check for the extended State init
757
758	<	info->setBox( boxVector );
758	>	info[i].useInitXSstate = globals->getUseInitXSstate();
759	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
760	>
761		}
762	<	else{
763	<	if( !globals->haveBoxX() ){
764	<	sprintf( painCave.errMsg,
711	<	"SimSetup error, no periodic BoxX size given.\n" );
712	<	painCave.isFatal = 1;
713	<	simError();
714	<	}
715	<	boxVector[0] = globals->getBoxX();
762	>
763	>	//setup seed for random number generator
764	>	int seedValue;
765
766	<	if( !globals->haveBoxY() ){
767	<	sprintf( painCave.errMsg,
719	<	"SimSetup error, no periodic BoxY size given.\n" );
720	<	painCave.isFatal = 1;
721	<	simError();
722	<	}
723	<	boxVector[1] = globals->getBoxY();
766	>	if (globals->haveSeed()){
767	>	seedValue = globals->getSeed();
768
769	<	if( !globals->haveBoxZ() ){
770	<	sprintf( painCave.errMsg,
771	<	"SimSetup error, no periodic BoxZ size given.\n" );
772	<	painCave.isFatal = 1;
769	>	if(seedValue / 1E9 == 0){
770	>	sprintf(painCave.errMsg,
771	>	"Seed for sprng library should contain at least 9 digits\n"
772	>	"OOPSE will generate a seed for user\n");
773	>	painCave.isFatal = 0;
774		simError();
775	+
776	+	//using seed generated by system instead of invalid seed set by user
777	+	#ifndef IS_MPI
778	+	seedValue = make_sprng_seed();
779	+	#else
780	+	if (worldRank == 0){
781	+	seedValue = make_sprng_seed();
782	+	}
783	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
784	+	#endif
785		}
786	<	boxVector[2] = globals->getBoxZ();
786	>	}//end of if branch of globals->haveSeed()
787	>	else{
788	>
789	>	#ifndef IS_MPI
790	>	seedValue = make_sprng_seed();
791	>	#else
792	>	if (worldRank == 0){
793	>	seedValue = make_sprng_seed();
794	>	}
795	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
796	>	#endif
797	>	}//end of globals->haveSeed()
798
799	<	info->setBox( boxVector );
799	>	for (int i = 0; i < nInfo; i++){
800	>	info[i].setSeed(seedValue);
801		}
802
736	–
737	–
803		#ifdef IS_MPI
804	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
804	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
805		MPIcheckPoint();
806		#endif // is_mpi
742	–
807		}
808
809
810	<	void SimSetup::finalInfoCheck( void ){
810	>	void SimSetup::finalInfoCheck(void){
811		int index;
812		int usesDipoles;
813	<
813	>	int i;
814
815	<	// check electrostatic parameters
816	<
817	<	index = 0;
818	<	usesDipoles = 0;
819	<	while( (index < info->n_atoms) && !usesDipoles ){
820	<	usesDipoles = ((info->atoms)[index])->hasDipole();
821	<	index++;
822	<	}
823	<
815	>	for (i = 0; i < nInfo; i++){
816	>	// check electrostatic parameters
817	>
818	>	index = 0;
819	>	usesDipoles = 0;
820	>	while ((index < info[i].n_atoms) && !usesDipoles){
821	>	usesDipoles = (info[i].atoms[index])->hasDipole();
822	>	index++;
823	>	}
824	>
825		#ifdef IS_MPI
826	<	int myUse = usesDipoles;
827	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
826	>	int myUse = usesDipoles;
827	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
828		#endif //is_mpi
829
830	<	double theEcr, theEst;
830	>	double theEcr, theEst;
831
832	<	if (globals->getUseRF() ) {
833	<	info->useReactionField = 1;
769	<
770	<	if( !globals->haveECR() ){
771	<	sprintf( painCave.errMsg,
772	<	"SimSetup Warning: using default value of 1/2 the smallest "
773	<	"box length for the electrostaticCutoffRadius.\n"
774	<	"I hope you have a very fast processor!\n");
775	<	painCave.isFatal = 0;
776	<	simError();
777	<	double smallest;
778	<	smallest = info->boxL[0];
779	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
780	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
781	<	theEcr = 0.5 * smallest;
782	<	} else {
783	<	theEcr = globals->getECR();
784	<	}
832	>	if (globals->getUseRF()){
833	>	info[i].useReactionField = 1;
834
835	<	if( !globals->haveEST() ){
836	<	sprintf( painCave.errMsg,
837	<	"SimSetup Warning: using default value of 0.05 * the "
838	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
839	<	);
840	<	painCave.isFatal = 0;
841	<	simError();
842	<	theEst = 0.05 * theEcr;
843	<	} else {
844	<	theEst= globals->getEST();
845	<	}
835	>	if (!globals->haveECR()){
836	>	sprintf(painCave.errMsg,
837	>	"SimSetup Warning: using default value of 15.0 angstroms"
838	>	"box length for the electrostaticCutoffRadius.\n");
839	>	painCave.isFatal = 0;
840	>	simError();
841	>	theEcr = 15.0;
842	>	}
843	>	else{
844	>	theEcr = globals->getECR();
845	>	}
846
847	<	info->setEcr( theEcr, theEst );
848	<
849	<	if(!globals->haveDielectric() ){
850	<	sprintf( painCave.errMsg,
851	<	"SimSetup Error: You are trying to use Reaction Field without"
852	<	"setting a dielectric constant!\n"
853	<	);
805	<	painCave.isFatal = 1;
806	<	simError();
807	<	}
808	<	info->dielectric = globals->getDielectric();
809	<	}
810	<	else {
811	<	if (usesDipoles) {
812	<
813	<	if( !globals->haveECR() ){
814	<	sprintf( painCave.errMsg,
815	<	"SimSetup Warning: using default value of 1/2 the smallest "
816	<	"box length for the electrostaticCutoffRadius.\n"
817	<	"I hope you have a very fast processor!\n");
818	<	painCave.isFatal = 0;
819	<	simError();
820	<	double smallest;
821	<	smallest = info->boxL[0];
822	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
823	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
824	<	theEcr = 0.5 * smallest;
825	<	} else {
826	<	theEcr = globals->getECR();
847	>	if (!globals->haveEST()){
848	>	sprintf(painCave.errMsg,
849	>	"SimSetup Warning: using default value of 0.05 * the "
850	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
851	>	painCave.isFatal = 0;
852	>	simError();
853	>	theEst = 0.05 * theEcr;
854		}
855	<
856	<	if( !globals->haveEST() ){
830	<	sprintf( painCave.errMsg,
831	<	"SimSetup Warning: using default value of 0.05 * the "
832	<	"electrostaticCutoffRadius for the "
833	<	"electrostaticSkinThickness\n"
834	<	);
835	<	painCave.isFatal = 0;
836	<	simError();
837	<	theEst = 0.05 * theEcr;
838	<	} else {
839	<	theEst= globals->getEST();
855	>	else{
856	>	theEst = globals->getEST();
857		}
858
859	<	info->setEcr( theEcr, theEst );
843	<	}
844	<	}
859	>	info[i].setDefaultEcr(theEcr, theEst);
860
861	+	if (!globals->haveDielectric()){
862	+	sprintf(painCave.errMsg,
863	+	"SimSetup Error: You are trying to use Reaction Field without"
864	+	"setting a dielectric constant!\n");
865	+	painCave.isFatal = 1;
866	+	simError();
867	+	}
868	+	info[i].dielectric = globals->getDielectric();
869	+	}
870	+	else{
871	+	if (usesDipoles){
872	+	if (!globals->haveECR()){
873	+	sprintf(painCave.errMsg,
874	+	"SimSetup Warning: using default value of 15.0 angstroms"
875	+	"box length for the electrostaticCutoffRadius.\n");
876	+	painCave.isFatal = 0;
877	+	simError();
878	+	theEcr = 15.0;
879	+	}
880	+	else{
881	+	theEcr = globals->getECR();
882	+	}
883	+
884	+	if (!globals->haveEST()){
885	+	sprintf(painCave.errMsg,
886	+	"SimSetup Warning: using default value of 0.05 * the "
887	+	"electrostaticCutoffRadius for the "
888	+	"electrostaticSkinThickness\n");
889	+	painCave.isFatal = 0;
890	+	simError();
891	+	theEst = 0.05 * theEcr;
892	+	}
893	+	else{
894	+	theEst = globals->getEST();
895	+	}
896	+
897	+	info[i].setDefaultEcr(theEcr, theEst);
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
850	–
905		}
906	+
907	+	void SimSetup::initSystemCoords(void){
908	+	int i;
909
910	<	void SimSetup::initSystemCoords( void ){
910	>	char* inName;
911
912	<	if( globals->haveInitialConfig() ){
913	<
914	<	InitializeFromFile* fileInit;
912	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
913	>
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	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
922	>	inName = globals->getInitialConfig();
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->read_xyz( info ); // default velocities on
929	>	fileInit->readInit(info); // default velocities on
930
931	<	delete fileInit;
932	<	}
933	<	else{
931	>	delete fileInit;
932	>	}
933	>	else{
934	>
935	>	// no init from bass
936	>
937	>	sprintf(painCave.errMsg,
938	>	"Cannot intialize a simulation without an initial configuration file.\n");
939	>	painCave.isFatal = 1;;
940	>	simError();
941	>
942	>	}
943
871	–	#ifdef IS_MPI
872	–
873	–	// no init from bass
874	–
875	–	sprintf( painCave.errMsg,
876	–	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
877	–	painCave.isFatal;
878	–	simError();
879	–
880	–	#else
881	–
882	–	initFromBass();
883	–
884	–
885	–	#endif
886	–	}
887	–
944		#ifdef IS_MPI
945	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
945	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
946		MPIcheckPoint();
947		#endif // is_mpi
892	–
948		}
949
950
951	<	void SimSetup::makeOutNames( void ){
951	>	void SimSetup::makeOutNames(void){
952	>	int k;
953
954	+
955	+	for (k = 0; k < nInfo; k++){
956		#ifdef IS_MPI
957	<	if( worldRank == 0 ){
957	>	if (worldRank == 0){
958		#endif // is_mpi
959	<
960	<	if( globals->haveFinalConfig() ){
961	<	strcpy( info->finalName, globals->getFinalConfig() );
904	<	}
905	<	else{
906	<	strcpy( info->finalName, inFileName );
907	<	char* endTest;
908	<	int nameLength = strlen( info->finalName );
909	<	endTest = &(info->finalName[nameLength - 5]);
910	<	if( !strcmp( endTest, ".bass" ) ){
911	<	strcpy( endTest, ".eor" );
959	>
960	>	if (globals->haveFinalConfig()){
961	>	strcpy(info[k].finalName, globals->getFinalConfig());
962		}
913	–	else if( !strcmp( endTest, ".BASS" ) ){
914	–	strcpy( endTest, ".eor" );
915	–	}
963		else{
964	<	endTest = &(info->finalName[nameLength - 4]);
965	<	if( !strcmp( endTest, ".bss" ) ){
966	<	strcpy( endTest, ".eor" );
967	<	}
968	<	else if( !strcmp( endTest, ".mdl" ) ){
969	<	strcpy( endTest, ".eor" );
970	<	}
971	<	else{
972	<	strcat( info->finalName, ".eor" );
973	<	}
964	>	strcpy(info[k].finalName, inFileName);
965	>	char* endTest;
966	>	int nameLength = strlen(info[k].finalName);
967	>	endTest = &(info[k].finalName[nameLength - 5]);
968	>	if (!strcmp(endTest, ".bass")){
969	>	strcpy(endTest, ".eor");
970	>	}
971	>	else if (!strcmp(endTest, ".BASS")){
972	>	strcpy(endTest, ".eor");
973	>	}
974	>	else{
975	>	endTest = &(info[k].finalName[nameLength - 4]);
976	>	if (!strcmp(endTest, ".bss")){
977	>	strcpy(endTest, ".eor");
978	>	}
979	>	else if (!strcmp(endTest, ".mdl")){
980	>	strcpy(endTest, ".eor");
981	>	}
982	>	else{
983	>	strcat(info[k].finalName, ".eor");
984	>	}
985	>	}
986		}
987	<	}
988	<
989	<	// make the sample and status out names
990	<
991	<	strcpy( info->sampleName, inFileName );
992	<	char* endTest;
993	<	int nameLength = strlen( info->sampleName );
994	<	endTest = &(info->sampleName[nameLength - 5]);
995	<	if( !strcmp( endTest, ".bass" ) ){
937	<	strcpy( endTest, ".dump" );
938	<	}
939	<	else if( !strcmp( endTest, ".BASS" ) ){
940	<	strcpy( endTest, ".dump" );
941	<	}
942	<	else{
943	<	endTest = &(info->sampleName[nameLength - 4]);
944	<	if( !strcmp( endTest, ".bss" ) ){
945	<	strcpy( endTest, ".dump" );
987	>
988	>	// make the sample and status out names
989	>
990	>	strcpy(info[k].sampleName, inFileName);
991	>	char* endTest;
992	>	int nameLength = strlen(info[k].sampleName);
993	>	endTest = &(info[k].sampleName[nameLength - 5]);
994	>	if (!strcmp(endTest, ".bass")){
995	>	strcpy(endTest, ".dump");
996		}
997	<	else if( !strcmp( endTest, ".mdl" ) ){
998	<	strcpy( endTest, ".dump" );
997	>	else if (!strcmp(endTest, ".BASS")){
998	>	strcpy(endTest, ".dump");
999		}
1000		else{
1001	<	strcat( info->sampleName, ".dump" );
1001	>	endTest = &(info[k].sampleName[nameLength - 4]);
1002	>	if (!strcmp(endTest, ".bss")){
1003	>	strcpy(endTest, ".dump");
1004	>	}
1005	>	else if (!strcmp(endTest, ".mdl")){
1006	>	strcpy(endTest, ".dump");
1007	>	}
1008	>	else{
1009	>	strcat(info[k].sampleName, ".dump");
1010	>	}
1011		}
1012	<	}
1013	<
1014	<	strcpy( info->statusName, inFileName );
1015	<	nameLength = strlen( info->statusName );
1016	<	endTest = &(info->statusName[nameLength - 5]);
1017	<	if( !strcmp( endTest, ".bass" ) ){
959	<	strcpy( endTest, ".stat" );
960	<	}
961	<	else if( !strcmp( endTest, ".BASS" ) ){
962	<	strcpy( endTest, ".stat" );
963	<	}
964	<	else{
965	<	endTest = &(info->statusName[nameLength - 4]);
966	<	if( !strcmp( endTest, ".bss" ) ){
967	<	strcpy( endTest, ".stat" );
1012	>
1013	>	strcpy(info[k].statusName, inFileName);
1014	>	nameLength = strlen(info[k].statusName);
1015	>	endTest = &(info[k].statusName[nameLength - 5]);
1016	>	if (!strcmp(endTest, ".bass")){
1017	>	strcpy(endTest, ".stat");
1018		}
1019	<	else if( !strcmp( endTest, ".mdl" ) ){
1020	<	strcpy( endTest, ".stat" );
1019	>	else if (!strcmp(endTest, ".BASS")){
1020	>	strcpy(endTest, ".stat");
1021		}
1022		else{
1023	<	strcat( info->statusName, ".stat" );
1023	>	endTest = &(info[k].statusName[nameLength - 4]);
1024	>	if (!strcmp(endTest, ".bss")){
1025	>	strcpy(endTest, ".stat");
1026	>	}
1027	>	else if (!strcmp(endTest, ".mdl")){
1028	>	strcpy(endTest, ".stat");
1029	>	}
1030	>	else{
1031	>	strcat(info[k].statusName, ".stat");
1032	>	}
1033		}
1034	<	}
976	<
1034	>
1035		#ifdef IS_MPI
978	–	}
979	–	#endif // is_mpi
1036
1037	+	}
1038	+	#endif // is_mpi
1039	+	}
1040		}
1041
1042
1043	<	void SimSetup::sysObjectsCreation( void ){
1043	>	void SimSetup::sysObjectsCreation(void){
1044	>	int i, k;
1045
986	–	int i;
987	–
1046		// create the forceField
1047
1048		createFF();
#	Line 999 | Line 1057 | void SimSetup::sysObjectsCreation( void ){
1057
1058		#ifdef IS_MPI
1059		// divide the molecules among the processors
1060	<
1060	>
1061		mpiMolDivide();
1062		#endif //is_mpi
1063	<
1063	>
1064		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1065	<
1065	>
1066		makeSysArrays();
1067
1068		// make and initialize the molecules (all but atomic coordinates)
1069	<
1069	>
1070		makeMolecules();
1013	–	info->identArray = new int[info->n_atoms];
1014	–	for(i=0; i<info->n_atoms; i++){
1015	–	info->identArray[i] = the_atoms[i]->getIdent();
1016	–	}
1017	–
1071
1072	<
1072	>	for (k = 0; k < nInfo; k++){
1073	>	info[k].identArray = new int[info[k].n_atoms];
1074	>	for (i = 0; i < info[k].n_atoms; i++){
1075	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1076	>	}
1077	>	}
1078		}
1079
1080
1081	<	void SimSetup::createFF( void ){
1081	>	void SimSetup::createFF(void){
1082	>	switch (ffCase){
1083	>	case FF_DUFF:
1084	>	the_ff = new DUFF();
1085	>	break;
1086
1087	<	switch( ffCase ){
1087	>	case FF_LJ:
1088	>	the_ff = new LJFF();
1089	>	break;
1090
1091	<	case FF_DUFF:
1092	<	the_ff = new DUFF();
1093	<	break;
1091	>	case FF_EAM:
1092	>	the_ff = new EAM_FF();
1093	>	break;
1094
1095	<	case FF_LJ:
1096	<	the_ff = new LJFF();
1097	<	break;
1098	<
1099	<	default:
1036	<	sprintf( painCave.errMsg,
1037	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1038	<	painCave.isFatal = 1;
1039	<	simError();
1095	>	default:
1096	>	sprintf(painCave.errMsg,
1097	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1098	>	painCave.isFatal = 1;
1099	>	simError();
1100		}
1101
1102		#ifdef IS_MPI
1103	<	strcpy( checkPointMsg, "ForceField creation successful" );
1103	>	strcpy(checkPointMsg, "ForceField creation successful");
1104		MPIcheckPoint();
1105		#endif // is_mpi
1046	–
1106		}
1107
1108
1109	<	void SimSetup::compList( void ){
1051	<
1109	>	void SimSetup::compList(void){
1110		int i;
1111	+	char* id;
1112	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1113	+	LinkedMolStamp* currentStamp = NULL;
1114	+	comp_stamps = new MoleculeStamp * [n_components];
1115
1054	–	comp_stamps = new MoleculeStamp*[n_components];
1055	–
1116		// make an array of molecule stamps that match the components used.
1117		// also extract the used stamps out into a separate linked list
1118
1119	<	info->nComponents = n_components;
1120	<	info->componentsNmol = components_nmol;
1121	<	info->compStamps = comp_stamps;
1122	<	info->headStamp = new LinkedMolStamp();
1123	<
1124	<	char* id;
1065	<	LinkedMolStamp* headStamp = info->headStamp;
1066	<	LinkedMolStamp* currentStamp = NULL;
1067	<	for( i=0; i<n_components; i++ ){
1119	>	for (i = 0; i < nInfo; i++){
1120	>	info[i].nComponents = n_components;
1121	>	info[i].componentsNmol = components_nmol;
1122	>	info[i].compStamps = comp_stamps;
1123	>	info[i].headStamp = headStamp;
1124	>	}
1125
1126	+
1127	+	for (i = 0; i < n_components; i++){
1128		id = the_components[i]->getType();
1129		comp_stamps[i] = NULL;
1130	<
1130	>
1131		// check to make sure the component isn't already in the list
1132
1133	<	comp_stamps[i] = headStamp->match( id );
1134	<	if( comp_stamps[i] == NULL ){
1076	<
1133	>	comp_stamps[i] = headStamp->match(id);
1134	>	if (comp_stamps[i] == NULL){
1135		// extract the component from the list;
1136	<
1137	<	currentStamp = stamps->extractMolStamp( id );
1138	<	if( currentStamp == NULL ){
1139	<	sprintf( painCave.errMsg,
1140	<	"SimSetup error: Component \"%s\" was not found in the "
1141	<	"list of declared molecules\n",
1142	<	id );
1143	<	painCave.isFatal = 1;
1144	<	simError();
1136	>
1137	>	currentStamp = stamps->extractMolStamp(id);
1138	>	if (currentStamp == NULL){
1139	>	sprintf(painCave.errMsg,
1140	>	"SimSetup error: Component \"%s\" was not found in the "
1141	>	"list of declared molecules\n",
1142	>	id);
1143	>	painCave.isFatal = 1;
1144	>	simError();
1145		}
1146	<
1147	<	headStamp->add( currentStamp );
1148	<	comp_stamps[i] = headStamp->match( id );
1146	>
1147	>	headStamp->add(currentStamp);
1148	>	comp_stamps[i] = headStamp->match(id);
1149		}
1150		}
1151
1152		#ifdef IS_MPI
1153	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1153	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1154		MPIcheckPoint();
1155		#endif // is_mpi
1098	–
1099	–
1156		}
1157
1158	<	void SimSetup::calcSysValues( void ){
1159	<	int i, j, k;
1158	>	void SimSetup::calcSysValues(void){
1159	>	int i;
1160
1161	+	int* molMembershipArray;
1162
1163		tot_atoms = 0;
1164		tot_bonds = 0;
1165		tot_bends = 0;
1166		tot_torsions = 0;
1167	<	for( i=0; i<n_components; i++ ){
1168	<
1169	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1170	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1114	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1167	>	for (i = 0; i < n_components; i++){
1168	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1169	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1170	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1171		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1172		}
1173
1174		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1175	+	molMembershipArray = new int[tot_atoms];
1176
1177	<	info->n_atoms = tot_atoms;
1178	<	info->n_bonds = tot_bonds;
1179	<	info->n_bends = tot_bends;
1180	<	info->n_torsions = tot_torsions;
1181	<	info->n_SRI = tot_SRI;
1182	<	info->n_mol = tot_nmol;
1183	<
1184	<	info->molMembershipArray = new int[tot_atoms];
1177	>	for (i = 0; i < nInfo; i++){
1178	>	info[i].n_atoms = tot_atoms;
1179	>	info[i].n_bonds = tot_bonds;
1180	>	info[i].n_bends = tot_bends;
1181	>	info[i].n_torsions = tot_torsions;
1182	>	info[i].n_SRI = tot_SRI;
1183	>	info[i].n_mol = tot_nmol;
1184	>
1185	>	info[i].molMembershipArray = molMembershipArray;
1186	>	}
1187		}
1188
1130	–
1189		#ifdef IS_MPI
1190
1191	<	void SimSetup::mpiMolDivide( void ){
1134	<
1191	>	void SimSetup::mpiMolDivide(void){
1192		int i, j, k;
1193		int localMol, allMol;
1194		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1195
1196	<	mpiSim = new mpiSimulation( info );
1197	<
1196	>	mpiSim = new mpiSimulation(info);
1197	>
1198		globalIndex = mpiSim->divideLabor();
1199
1200		// set up the local variables
1201	<
1201	>
1202		mol2proc = mpiSim->getMolToProcMap();
1203		molCompType = mpiSim->getMolComponentType();
1204	<
1204	>
1205		allMol = 0;
1206		localMol = 0;
1207		local_atoms = 0;
#	Line 1154 | Line 1211 | void SimSetup::mpiMolDivide( void ){
1211		globalAtomIndex = 0;
1212
1213
1214	<	for( i=0; i<n_components; i++ ){
1215	<
1216	<	for( j=0; j<components_nmol[i]; j++ ){
1217	<
1218	<	if( mol2proc[allMol] == worldRank ){
1219	<
1220	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1221	<	local_bonds +=    comp_stamps[i]->getNBonds();
1165	<	local_bends +=    comp_stamps[i]->getNBends();
1166	<	local_torsions += comp_stamps[i]->getNTorsions();
1167	<	localMol++;
1214	>	for (i = 0; i < n_components; i++){
1215	>	for (j = 0; j < components_nmol[i]; j++){
1216	>	if (mol2proc[allMol] == worldRank){
1217	>	local_atoms += comp_stamps[i]->getNAtoms();
1218	>	local_bonds += comp_stamps[i]->getNBonds();
1219	>	local_bends += comp_stamps[i]->getNBends();
1220	>	local_torsions += comp_stamps[i]->getNTorsions();
1221	>	localMol++;
1222		}
1223	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1224	<	info->molMembershipArray[globalAtomIndex] = allMol;
1223	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1224	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1225		globalAtomIndex++;
1226		}
1227
1228	<	allMol++;
1228	>	allMol++;
1229		}
1230		}
1231		local_SRI = local_bonds + local_bends + local_torsions;
1232	<
1233	<	info->n_atoms = mpiSim->getMyNlocal();
1234	<
1235	<	if( local_atoms != info->n_atoms ){
1236	<	sprintf( painCave.errMsg,
1237	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1238	<	" localAtom (%d) are not equal.\n",
1239	<	info->n_atoms,
1186	<	local_atoms );
1232	>
1233	>	info[0].n_atoms = mpiSim->getMyNlocal();
1234	>
1235	>	if (local_atoms != info[0].n_atoms){
1236	>	sprintf(painCave.errMsg,
1237	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1238	>	" localAtom (%d) are not equal.\n",
1239	>	info[0].n_atoms, local_atoms);
1240		painCave.isFatal = 1;
1241		simError();
1242		}
1243
1244	<	info->n_bonds = local_bonds;
1245	<	info->n_bends = local_bends;
1246	<	info->n_torsions = local_torsions;
1247	<	info->n_SRI = local_SRI;
1248	<	info->n_mol = localMol;
1244	>	info[0].n_bonds = local_bonds;
1245	>	info[0].n_bends = local_bends;
1246	>	info[0].n_torsions = local_torsions;
1247	>	info[0].n_SRI = local_SRI;
1248	>	info[0].n_mol = localMol;
1249
1250	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1250	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1251		MPIcheckPoint();
1252		}
1253	<
1253	>
1254		#endif // is_mpi
1255
1256
1257	<	void SimSetup::makeSysArrays( void ){
1258	<	int i, j, k;
1257	>	void SimSetup::makeSysArrays(void){
1258	>
1259	>	#ifndef IS_MPI
1260	>	int k, j;
1261	>	#endif // is_mpi
1262	>	int i, l;
1263
1264	+	Atom** the_atoms;
1265	+	Molecule* the_molecules;
1266	+	Exclude** the_excludes;
1267
1208	–	// create the atom and short range interaction arrays
1268
1269	<	Atom::createArrays(info->n_atoms);
1270	<	the_atoms = new Atom*[info->n_atoms];
1212	<	the_molecules = new Molecule[info->n_mol];
1213	<	int molIndex;
1269	>	for (l = 0; l < nInfo; l++){
1270	>	// create the atom and short range interaction arrays
1271
1272	<	// initialize the molecule's stampID's
1272	>	the_atoms = new Atom * [info[l].n_atoms];
1273	>	the_molecules = new Molecule[info[l].n_mol];
1274	>	int molIndex;
1275
1276	+	// initialize the molecule's stampID's
1277	+
1278		#ifdef IS_MPI
1218	–
1279
1280	<	molIndex = 0;
1281	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1282	<
1283	<	if(mol2proc[i] == worldRank ){
1284	<	the_molecules[molIndex].setStampID( molCompType[i] );
1285	<	the_molecules[molIndex].setMyIndex( molIndex );
1286	<	the_molecules[molIndex].setGlobalIndex( i );
1287	<	molIndex++;
1280	>
1281	>	molIndex = 0;
1282	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1283	>	if (mol2proc[i] == worldRank){
1284	>	the_molecules[molIndex].setStampID(molCompType[i]);
1285	>	the_molecules[molIndex].setMyIndex(molIndex);
1286	>	the_molecules[molIndex].setGlobalIndex(i);
1287	>	molIndex++;
1288	>	}
1289		}
1229	–	}
1290
1291		#else // is_mpi
1292	<
1293	<	molIndex = 0;
1294	<	globalAtomIndex = 0;
1295	<	for(i=0; i<n_components; i++){
1296	<	for(j=0; j<components_nmol[i]; j++ ){
1297	<	the_molecules[molIndex].setStampID( i );
1298	<	the_molecules[molIndex].setMyIndex( molIndex );
1299	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1300	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1301	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1302	<	globalAtomIndex++;
1292	>
1293	>	molIndex = 0;
1294	>	globalAtomIndex = 0;
1295	>	for (i = 0; i < n_components; i++){
1296	>	for (j = 0; j < components_nmol[i]; j++){
1297	>	the_molecules[molIndex].setStampID(i);
1298	>	the_molecules[molIndex].setMyIndex(molIndex);
1299	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1300	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1301	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1302	>	globalAtomIndex++;
1303	>	}
1304	>	molIndex++;
1305		}
1244	–	molIndex++;
1306		}
1246	–	}
1247	–
1307
1308	+
1309		#endif // is_mpi
1310
1311
1312	<	if( info->n_SRI ){
1313	<
1314	<	Exclude::createArray(info->n_SRI);
1315	<	the_excludes = new Exclude*[info->n_SRI];
1316	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1317	<	info->globalExcludes = new int;
1318	<	info->n_exclude = info->n_SRI;
1319	<	}
1320	<	else{
1321	<
1322	<	Exclude::createArray( 1 );
1323	<	the_excludes = new Exclude*;
1324	<	the_excludes[0] = new Exclude(0);
1325	<	the_excludes[0]->setPair( 0,0 );
1326	<	info->globalExcludes = new int;
1327	<	info->globalExcludes[0] = 0;
1328	<	info->n_exclude = 0;
1329	<	}
1312	>	if (info[l].n_SRI){
1313	>	Exclude::createArray(info[l].n_SRI);
1314	>	the_excludes = new Exclude * [info[l].n_SRI];
1315	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1316	>	the_excludes[ex] = new Exclude(ex);
1317	>	}
1318	>	info[l].globalExcludes = new int;
1319	>	info[l].n_exclude = info[l].n_SRI;
1320	>	}
1321	>	else{
1322	>	Exclude::createArray(1);
1323	>	the_excludes = new Exclude * ;
1324	>	the_excludes[0] = new Exclude(0);
1325	>	the_excludes[0]->setPair(0, 0);
1326	>	info[l].globalExcludes = new int;
1327	>	info[l].globalExcludes[0] = 0;
1328	>	info[l].n_exclude = 0;
1329	>	}
1330
1331	<	// set the arrays into the SimInfo object
1331	>	// set the arrays into the SimInfo object
1332
1333	<	info->atoms = the_atoms;
1334	<	info->molecules = the_molecules;
1335	<	info->nGlobalExcludes = 0;
1336	<	info->excludes = the_excludes;
1333	>	info[l].atoms = the_atoms;
1334	>	info[l].molecules = the_molecules;
1335	>	info[l].nGlobalExcludes = 0;
1336	>	info[l].excludes = the_excludes;
1337
1338	<	the_ff->setSimInfo( info );
1339	<
1338	>	the_ff->setSimInfo(info);
1339	>	}
1340		}
1341
1342	<	void SimSetup::makeIntegrator( void ){
1342	>	void SimSetup::makeIntegrator(void){
1343	>	int k;
1344
1345	<	NVT*  myNVT = NULL;
1346	<	NPTi* myNPTi = NULL;
1347	<	NPTf* myNPTf = NULL;
1348	<	NPTim* myNPTim = NULL;
1349	<	NPTfm* myNPTfm = NULL;
1345	>	NVE<RealIntegrator>* myNVE = NULL;
1346	>	NVT<RealIntegrator>* myNVT = NULL;
1347	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1348	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1349	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1350	>
1351	>	for (k = 0; k < nInfo; k++){
1352	>	switch (ensembleCase){
1353	>	case NVE_ENS:
1354	>	if (globals->haveZconstraints()){
1355	>	setupZConstraint(info[k]);
1356	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1357	>	}
1358	>	else{
1359	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1360	>	}
1361	>
1362	>	info->the_integrator = myNVE;
1363	>	break;
1364
1365	<	switch( ensembleCase ){
1365	>	case NVT_ENS:
1366	>	if (globals->haveZconstraints()){
1367	>	setupZConstraint(info[k]);
1368	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1369	>	}
1370	>	else
1371	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1372
1373	<	case NVE_ENS:
1293	<	new NVE( info, the_ff );
1294	<	break;
1373	>	myNVT->setTargetTemp(globals->getTargetTemp());
1374
1375	<	case NVT_ENS:
1376	<	myNVT = new NVT( info, the_ff );
1377	<	myNVT->setTargetTemp(globals->getTargetTemp());
1375	>	if (globals->haveTauThermostat())
1376	>	myNVT->setTauThermostat(globals->getTauThermostat());
1377	>	else{
1378	>	sprintf(painCave.errMsg,
1379	>	"SimSetup error: If you use the NVT\n"
1380	>	"    ensemble, you must set tauThermostat.\n");
1381	>	painCave.isFatal = 1;
1382	>	simError();
1383	>	}
1384
1385	<	if (globals->haveTauThermostat())
1386	<	myNVT->setTauThermostat(globals->getTauThermostat());
1385	>	info->the_integrator = myNVT;
1386	>	break;
1387
1388	<	else {
1389	<	sprintf( painCave.errMsg,
1390	<	"SimSetup error: If you use the NVT\n"
1391	<	"    ensemble, you must set tauThermostat.\n");
1392	<	painCave.isFatal = 1;
1393	<	simError();
1394	<	}
1310	<	break;
1388	>	case NPTi_ENS:
1389	>	if (globals->haveZconstraints()){
1390	>	setupZConstraint(info[k]);
1391	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1392	>	}
1393	>	else
1394	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1395
1396	<	case NPTi_ENS:
1313	<	myNPTi = new NPTi( info, the_ff );
1314	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1396	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1397
1398	<	if (globals->haveTargetPressure())
1399	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1400	<	else {
1401	<	sprintf( painCave.errMsg,
1402	<	"SimSetup error: If you use a constant pressure\n"
1403	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1404	<	painCave.isFatal = 1;
1405	<	simError();
1406	<	}
1325	<
1326	<	if( globals->haveTauThermostat() )
1327	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1328	<	else{
1329	<	sprintf( painCave.errMsg,
1330	<	"SimSetup error: If you use an NPT\n"
1331	<	"    ensemble, you must set tauThermostat.\n");
1332	<	painCave.isFatal = 1;
1333	<	simError();
1334	<	}
1398	>	if (globals->haveTargetPressure())
1399	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1400	>	else{
1401	>	sprintf(painCave.errMsg,
1402	>	"SimSetup error: If you use a constant pressure\n"
1403	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1404	>	painCave.isFatal = 1;
1405	>	simError();
1406	>	}
1407
1408	<	if( globals->haveTauBarostat() )
1409	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1410	<	else{
1411	<	sprintf( painCave.errMsg,
1412	<	"SimSetup error: If you use an NPT\n"
1413	<	"    ensemble, you must set tauBarostat.\n");
1414	<	painCave.isFatal = 1;
1415	<	simError();
1416	<	}
1345	<	break;
1408	>	if (globals->haveTauThermostat())
1409	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1410	>	else{
1411	>	sprintf(painCave.errMsg,
1412	>	"SimSetup error: If you use an NPT\n"
1413	>	"    ensemble, you must set tauThermostat.\n");
1414	>	painCave.isFatal = 1;
1415	>	simError();
1416	>	}
1417
1418	<	case NPTf_ENS:
1419	<	myNPTf = new NPTf( info, the_ff );
1420	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1418	>	if (globals->haveTauBarostat())
1419	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1420	>	else{
1421	>	sprintf(painCave.errMsg,
1422	>	"SimSetup error: If you use an NPT\n"
1423	>	"    ensemble, you must set tauBarostat.\n");
1424	>	painCave.isFatal = 1;
1425	>	simError();
1426	>	}
1427
1428	<	if (globals->haveTargetPressure())
1429	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1353	<	else {
1354	<	sprintf( painCave.errMsg,
1355	<	"SimSetup error: If you use a constant pressure\n"
1356	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1357	<	painCave.isFatal = 1;
1358	<	simError();
1359	<	}
1428	>	info->the_integrator = myNPTi;
1429	>	break;
1430
1431	<	if( globals->haveTauThermostat() )
1432	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1433	<	else{
1434	<	sprintf( painCave.errMsg,
1435	<	"SimSetup error: If you use an NPT\n"
1436	<	"    ensemble, you must set tauThermostat.\n");
1437	<	painCave.isFatal = 1;
1368	<	simError();
1369	<	}
1431	>	case NPTf_ENS:
1432	>	if (globals->haveZconstraints()){
1433	>	setupZConstraint(info[k]);
1434	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1435	>	}
1436	>	else
1437	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1438
1439	<	if( globals->haveTauBarostat() )
1372	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1373	<	else{
1374	<	sprintf( painCave.errMsg,
1375	<	"SimSetup error: If you use an NPT\n"
1376	<	"    ensemble, you must set tauBarostat.\n");
1377	<	painCave.isFatal = 1;
1378	<	simError();
1379	<	}
1380	<	break;
1381	<
1382	<	case NPTim_ENS:
1383	<	myNPTim = new NPTim( info, the_ff );
1384	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1439	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1440
1441	<	if (globals->haveTargetPressure())
1442	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1443	<	else {
1444	<	sprintf( painCave.errMsg,
1445	<	"SimSetup error: If you use a constant pressure\n"
1446	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1447	<	painCave.isFatal = 1;
1448	<	simError();
1449	<	}
1395	<
1396	<	if( globals->haveTauThermostat() )
1397	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1398	<	else{
1399	<	sprintf( painCave.errMsg,
1400	<	"SimSetup error: If you use an NPT\n"
1401	<	"    ensemble, you must set tauThermostat.\n");
1402	<	painCave.isFatal = 1;
1403	<	simError();
1404	<	}
1441	>	if (globals->haveTargetPressure())
1442	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1443	>	else{
1444	>	sprintf(painCave.errMsg,
1445	>	"SimSetup error: If you use a constant pressure\n"
1446	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1447	>	painCave.isFatal = 1;
1448	>	simError();
1449	>	}
1450
1451	<	if( globals->haveTauBarostat() )
1452	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1408	<	else{
1409	<	sprintf( painCave.errMsg,
1410	<	"SimSetup error: If you use an NPT\n"
1411	<	"    ensemble, you must set tauBarostat.\n");
1412	<	painCave.isFatal = 1;
1413	<	simError();
1414	<	}
1415	<	break;
1451	>	if (globals->haveTauThermostat())
1452	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1453
1454	<	case NPTfm_ENS:
1455	<	myNPTfm = new NPTfm( info, the_ff );
1456	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1454	>	else{
1455	>	sprintf(painCave.errMsg,
1456	>	"SimSetup error: If you use an NPT\n"
1457	>	"    ensemble, you must set tauThermostat.\n");
1458	>	painCave.isFatal = 1;
1459	>	simError();
1460	>	}
1461
1462	<	if (globals->haveTargetPressure())
1463	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1423	<	else {
1424	<	sprintf( painCave.errMsg,
1425	<	"SimSetup error: If you use a constant pressure\n"
1426	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1427	<	painCave.isFatal = 1;
1428	<	simError();
1429	<	}
1430	<
1431	<	if( globals->haveTauThermostat() )
1432	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1433	<	else{
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	<	}
1462	>	if (globals->haveTauBarostat())
1463	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1464
1465	<	if( globals->haveTauBarostat() )
1466	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1467	<	else{
1468	<	sprintf( painCave.errMsg,
1469	<	"SimSetup error: If you use an NPT\n"
1470	<	"    ensemble, you must set tauBarostat.\n");
1471	<	painCave.isFatal = 1;
1448	<	simError();
1449	<	}
1450	<	break;
1465	>	else{
1466	>	sprintf(painCave.errMsg,
1467	>	"SimSetup error: If you use an NPT\n"
1468	>	"    ensemble, you must set tauBarostat.\n");
1469	>	painCave.isFatal = 1;
1470	>	simError();
1471	>	}
1472
1473	<	default:
1474	<	sprintf( painCave.errMsg,
1454	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1455	<	painCave.isFatal = 1;
1456	<	simError();
1457	<	}
1473	>	info->the_integrator = myNPTf;
1474	>	break;
1475
1476	+	case NPTxyz_ENS:
1477	+	if (globals->haveZconstraints()){
1478	+	setupZConstraint(info[k]);
1479	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1480	+	}
1481	+	else
1482	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1483	+
1484	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1485	+
1486	+	if (globals->haveTargetPressure())
1487	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1488	+	else{
1489	+	sprintf(painCave.errMsg,
1490	+	"SimSetup error: If you use a constant pressure\n"
1491	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1492	+	painCave.isFatal = 1;
1493	+	simError();
1494	+	}
1495	+
1496	+	if (globals->haveTauThermostat())
1497	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1498	+	else{
1499	+	sprintf(painCave.errMsg,
1500	+	"SimSetup error: If you use an NPT\n"
1501	+	"    ensemble, you must set tauThermostat.\n");
1502	+	painCave.isFatal = 1;
1503	+	simError();
1504	+	}
1505	+
1506	+	if (globals->haveTauBarostat())
1507	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1508	+	else{
1509	+	sprintf(painCave.errMsg,
1510	+	"SimSetup error: If you use an NPT\n"
1511	+	"    ensemble, you must set tauBarostat.\n");
1512	+	painCave.isFatal = 1;
1513	+	simError();
1514	+	}
1515	+
1516	+	info->the_integrator = myNPTxyz;
1517	+	break;
1518	+
1519	+	default:
1520	+	sprintf(painCave.errMsg,
1521	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1522	+	painCave.isFatal = 1;
1523	+	simError();
1524	+	}
1525	+	}
1526		}
1527
1528	<	void SimSetup::initFortran( void ){
1528	>	void SimSetup::initFortran(void){
1529	>	info[0].refreshSim();
1530
1531	<	info->refreshSim();
1532	<
1465	<	if( !strcmp( info->mixingRule, "standard") ){
1466	<	the_ff->initForceField( LB_MIXING_RULE );
1531	>	if (!strcmp(info[0].mixingRule, "standard")){
1532	>	the_ff->initForceField(LB_MIXING_RULE);
1533		}
1534	<	else if( !strcmp( info->mixingRule, "explicit") ){
1535	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1534	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1535	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1536		}
1537		else{
1538	<	sprintf( painCave.errMsg,
1539	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1474	<	info->mixingRule );
1538	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1539	>	info[0].mixingRule);
1540		painCave.isFatal = 1;
1541		simError();
1542		}
1543
1544
1545		#ifdef IS_MPI
1546	<	strcpy( checkPointMsg,
1482	<	"Successfully intialized the mixingRule for Fortran." );
1546	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1547		MPIcheckPoint();
1548		#endif // is_mpi
1549	+	}
1550
1551	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1552	+	int nZConstraints;
1553	+	ZconStamp** zconStamp;
1554	+
1555	+	if (globals->haveZconstraintTime()){
1556	+	//add sample time of z-constraint  into SimInfo's property list
1557	+	DoubleData* zconsTimeProp = new DoubleData();
1558	+	zconsTimeProp->setID(ZCONSTIME_ID);
1559	+	zconsTimeProp->setData(globals->getZconsTime());
1560	+	theInfo.addProperty(zconsTimeProp);
1561	+	}
1562	+	else{
1563	+	sprintf(painCave.errMsg,
1564	+	"ZConstraint error: If you use an ZConstraint\n"
1565	+	" , you must set sample time.\n");
1566	+	painCave.isFatal = 1;
1567	+	simError();
1568	+	}
1569	+
1570	+	//push zconsTol into siminfo, if user does not specify
1571	+	//value for zconsTol, a default value will be used
1572	+	DoubleData* zconsTol = new DoubleData();
1573	+	zconsTol->setID(ZCONSTOL_ID);
1574	+	if (globals->haveZconsTol()){
1575	+	zconsTol->setData(globals->getZconsTol());
1576	+	}
1577	+	else{
1578	+	double defaultZConsTol = 0.01;
1579	+	sprintf(painCave.errMsg,
1580	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1581	+	" , default value %f is used.\n",
1582	+	defaultZConsTol);
1583	+	painCave.isFatal = 0;
1584	+	simError();
1585	+
1586	+	zconsTol->setData(defaultZConsTol);
1587	+	}
1588	+	theInfo.addProperty(zconsTol);
1589	+
1590	+	//set Force Subtraction Policy
1591	+	StringData* zconsForcePolicy = new StringData();
1592	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1593	+
1594	+	if (globals->haveZconsForcePolicy()){
1595	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1596	+	}
1597	+	else{
1598	+	sprintf(painCave.errMsg,
1599	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1600	+	"PolicyByMass is used\n");
1601	+	painCave.isFatal = 0;
1602	+	simError();
1603	+	zconsForcePolicy->setData("BYMASS");
1604	+	}
1605	+
1606	+	theInfo.addProperty(zconsForcePolicy);
1607	+
1608	+	//Determine the name of ouput file and add it into SimInfo's property list
1609	+	//Be careful, do not use inFileName, since it is a pointer which
1610	+	//point to a string at master node, and slave nodes do not contain that string
1611	+
1612	+	string zconsOutput(theInfo.finalName);
1613	+
1614	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1615	+
1616	+	StringData* zconsFilename = new StringData();
1617	+	zconsFilename->setID(ZCONSFILENAME_ID);
1618	+	zconsFilename->setData(zconsOutput);
1619	+
1620	+	theInfo.addProperty(zconsFilename);
1621	+
1622	+	//setup index, pos and other parameters of z-constraint molecules
1623	+	nZConstraints = globals->getNzConstraints();
1624	+	theInfo.nZconstraints = nZConstraints;
1625	+
1626	+	zconStamp = globals->getZconStamp();
1627	+	ZConsParaItem tempParaItem;
1628	+
1629	+	ZConsParaData* zconsParaData = new ZConsParaData();
1630	+	zconsParaData->setID(ZCONSPARADATA_ID);
1631	+
1632	+	for (int i = 0; i < nZConstraints; i++){
1633	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1634	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1635	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1636	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1637	+
1638	+	zconsParaData->addItem(tempParaItem);
1639	+	}
1640	+
1641	+	//check the uniqueness of index
1642	+	if(!zconsParaData->isIndexUnique()){
1643	+	sprintf(painCave.errMsg,
1644	+	"ZConstraint Error: molIndex is not unique\n");
1645	+	painCave.isFatal = 1;
1646	+	simError();
1647	+	}
1648	+
1649	+	//sort the parameters by index of molecules
1650	+	zconsParaData->sortByIndex();
1651	+
1652	+	//push data into siminfo, therefore, we can retrieve later
1653	+	theInfo.addProperty(zconsParaData);
1654		}

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