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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 823 by mmeineke, Mon Oct 27 22:07:48 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	<
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		SimSetup::SimSetup(){
34	+
35	+	initSuspend = false;
36	+	isInfoArray = 0;
37	+	nInfo = 1;
38	+
39		stamps = new MakeStamps();
40		globals = new Globals();
41	<
41	>
42	>
43		#ifdef IS_MPI
44	<	strcpy( checkPointMsg, "SimSetup creation successful" );
44	>	strcpy(checkPointMsg, "SimSetup creation successful");
45		MPIcheckPoint();
46		#endif // IS_MPI
47		}
#	Line 41 | Line 51 | void SimSetup::parseFile( char* fileName ){
51		delete globals;
52		}
53
54	<	void SimSetup::parseFile( char* fileName ){
54	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
55	>	info = the_info;
56	>	nInfo = theNinfo;
57	>	isInfoArray = 1;
58	>	initSuspend = true;
59	>	}
60
61	+
62	+	void SimSetup::parseFile(char* fileName){
63		#ifdef IS_MPI
64	<	if( worldRank == 0 ){
64	>	if (worldRank == 0){
65		#endif // is_mpi
66	<
66	>
67		inFileName = fileName;
68	<	set_interface_stamps( stamps, globals );
69	<
68	>	set_interface_stamps(stamps, globals);
69	>
70		#ifdef IS_MPI
71		mpiEventInit();
72		#endif
73
74	<	yacc_BASS( fileName );
74	>	yacc_BASS(fileName);
75
76		#ifdef IS_MPI
77		throwMPIEvent(NULL);
78		}
79	<	else receiveParse();
79	>	else{
80	>	receiveParse();
81	>	}
82		#endif
83
84		}
85
86		#ifdef IS_MPI
87		void SimSetup::receiveParse(void){
88	<
89	<	set_interface_stamps( stamps, globals );
90	<	mpiEventInit();
91	<	MPIcheckPoint();
73	<	mpiEventLoop();
74	<
88	>	set_interface_stamps(stamps, globals);
89	>	mpiEventInit();
90	>	MPIcheckPoint();
91	>	mpiEventLoop();
92		}
93
94		#endif // is_mpi
95
96	<	void SimSetup::createSim( void ){
96	>	void SimSetup::createSim(void){
97
81	–	int i, j, k, globalAtomIndex;
82	–
98		// gather all of the information from the Bass file
99	<
99	>
100		gatherInfo();
101
102		// creation of complex system objects
#	Line 89 | Line 104 | void SimSetup::createSim( void ){
104		sysObjectsCreation();
105
106		// check on the post processing info
107	<
107	>
108		finalInfoCheck();
109
110		// initialize the system coordinates
111
112	<	initSystemCoords();
113	<
112	>	if ( !initSuspend ){
113	>	initSystemCoords();
114
115	+	if( !(globals->getUseInitTime()) )
116	+	info[0].currentTime = 0.0;
117	+	}
118	+
119		// make the output filenames
120
121		makeOutNames();
122	<
122	>
123		// make the integrator
124	<
124	>
125		makeIntegrator();
126	<
126	>
127		#ifdef IS_MPI
128		mpiSim->mpiRefresh();
129		#endif
#	Line 112 | Line 131 | void SimSetup::createSim( void ){
131		// initialize the Fortran
132
133		initFortran();
115	–
116	–
117	–
134		}
135
136
137	<	void SimSetup::makeMolecules( void ){
138	<
137	>	void SimSetup::makeMolecules(void){
138	>	int k;
139		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140		molInit molInfo;
141		DirectionalAtom* dAtom;
#	Line 134 | Line 150 | void SimSetup::makeMolecules( void ){
150		bend_set* theBends;
151		torsion_set* theTorsions;
152
153	<
153	>
154		//init the forceField paramters
155
156		the_ff->readParams();
157
158	<
158	>
159		// init the atoms
160
161		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();
162
163	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
164	<	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;
163	>	for (k = 0; k < nInfo; k++){
164	>	the_ff->setSimInfo(&(info[k]));
165
166	<	molInfo.myAtoms = &the_atoms[atomOffset];
167	<	molInfo.myExcludes = &the_excludes[excludeOffset];
168	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
169	<	molInfo.myBends = new Bend*[molInfo.nBends];
163	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
166	>	atomOffset = 0;
167	>	excludeOffset = 0;
168	>	for (i = 0; i < info[k].n_mol; i++){
169	>	stampID = info[k].molecules[i].getStampID();
170
171	<	theBonds = new bond_pair[molInfo.nBonds];
172	<	theBends = new bend_set[molInfo.nBends];
173	<	theTorsions = new torsion_set[molInfo.nTorsions];
174	<
175	<	// make the Atoms
176	<
177	<	for(j=0; j<molInfo.nAtoms; j++){
178	<
179	<	currentAtom = comp_stamps[stampID]->getAtom( j );
180	<	if( currentAtom->haveOrientation() ){
181	<
182	<	dAtom = new DirectionalAtom(j + atomOffset);
183	<	info->n_oriented++;
184	<	molInfo.myAtoms[j] = dAtom;
185	<
186	<	ux = currentAtom->getOrntX();
187	<	uy = currentAtom->getOrntY();
188	<	uz = currentAtom->getOrntZ();
189	<
190	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
191	<
192	<	u = sqrt( uSqr );
193	<	ux = ux / u;
194	<	uy = uy / u;
195	<	uz = uz / u;
196	<
197	<	dAtom->setSUx( ux );
198	<	dAtom->setSUy( uy );
199	<	dAtom->setSUz( uz );
200	<	}
201	<	else{
202	<	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
203	<	}
204	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
205	<
171	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
172	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
173	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
174	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
175	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
176	>
177	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
178	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
179	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
180	>	molInfo.myBends = new Bend * [molInfo.nBends];
181	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
182	>
183	>	theBonds = new bond_pair[molInfo.nBonds];
184	>	theBends = new bend_set[molInfo.nBends];
185	>	theTorsions = new torsion_set[molInfo.nTorsions];
186	>
187	>	// make the Atoms
188	>
189	>	for (j = 0; j < molInfo.nAtoms; j++){
190	>	currentAtom = comp_stamps[stampID]->getAtom(j);
191	>	if (currentAtom->haveOrientation()){
192	>	dAtom = new DirectionalAtom((j + atomOffset),
193	>	info[k].getConfiguration());
194	>	info[k].n_oriented++;
195	>	molInfo.myAtoms[j] = dAtom;
196	>
197	>	ux = currentAtom->getOrntX();
198	>	uy = currentAtom->getOrntY();
199	>	uz = currentAtom->getOrntZ();
200	>
201	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
202	>
203	>	u = sqrt(uSqr);
204	>	ux = ux / u;
205	>	uy = uy / u;
206	>	uz = uz / u;
207	>
208	>	dAtom->setSUx(ux);
209	>	dAtom->setSUy(uy);
210	>	dAtom->setSUz(uz);
211	>	}
212	>	else{
213	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
214	>	info[k].getConfiguration());
215	>	}
216	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
217	>
218		#ifdef IS_MPI
219	<
220	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
221	<
219	>
220	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
221	>
222		#endif // is_mpi
223	<	}
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;
223	>	}
224
225	<	exI = theBonds[j].a;
226	<	exJ = theBonds[j].b;
225	>	// make the bonds
226	>	for (j = 0; j < molInfo.nBonds; j++){
227	>	currentBond = comp_stamps[stampID]->getBond(j);
228	>	theBonds[j].a = currentBond->getA() + atomOffset;
229	>	theBonds[j].b = currentBond->getB() + atomOffset;
230
231	<	// exclude_I must always be the smaller of the pair
232	<	if( exI > exJ ){
233	<	tempEx = exI;
234	<	exI = exJ;
235	<	exJ = tempEx;
236	<	}
231	>	exI = theBonds[j].a;
232	>	exJ = theBonds[j].b;
233	>
234	>	// exclude_I must always be the smaller of the pair
235	>	if (exI > exJ){
236	>	tempEx = exI;
237	>	exI = exJ;
238	>	exJ = tempEx;
239	>	}
240		#ifdef IS_MPI
241	<	tempEx = exI;
242	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
243	<	tempEx = exJ;
244	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
245	<
246	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
241	>	tempEx = exI;
242	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
243	>	tempEx = exJ;
244	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
245	>
246	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
247		#else  // isn't MPI
248
249	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
249	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
250		#endif  //is_mpi
251	<	}
252	<	excludeOffset += molInfo.nBonds;
251	>	}
252	>	excludeOffset += molInfo.nBonds;
253
254	<	//make the bends
255	<	for(j=0; j<molInfo.nBends; j++){
256	<
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	<
264	<	extras = currentBend->getExtras();
265	<	current_extra = extras;
266	<
267	<	while( current_extra != NULL ){
268	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
269	<
270	<	switch( current_extra->getType() ){
271	<
272	<	case 0:
273	<	theBends[j].ghost =
274	<	current_extra->getInt() + atomOffset;
275	<	theBends[j].isGhost = 1;
276	<	break;
277	<
278	<	case 1:
279	<	theBends[j].ghost =
280	<	(int)current_extra->getDouble() + atomOffset;
281	<	theBends[j].isGhost = 1;
282	<	break;
283	<
284	<	default:
285	<	sprintf( painCave.errMsg,
286	<	"SimSetup Error: ghostVectorSource was neither a "
287	<	"double nor an int.\n"
288	<	"-->Bend[%d] in %s\n",
289	<	j, comp_stamps[stampID]->getID() );
290	<	painCave.isFatal = 1;
291	<	simError();
292	<	}
293	<	}
294	<
295	<	else{
296	<
297	<	sprintf( painCave.errMsg,
298	<	"SimSetup Error: unhandled bend assignment:\n"
299	<	"    -->%s in Bend[%d] in %s\n",
300	<	current_extra->getlhs(),
301	<	j, comp_stamps[stampID]->getID() );
302	<	painCave.isFatal = 1;
303	<	simError();
304	<	}
305	<
306	<	current_extra = current_extra->getNext();
307	<	}
308	<	}
309	<
310	<	if( !theBends[j].isGhost ){
311	<
312	<	exI = theBends[j].a;
313	<	exJ = theBends[j].c;
314	<	}
315	<	else{
316	<
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	<	}
254	>	//make the bends
255	>	for (j = 0; j < molInfo.nBends; j++){
256	>	currentBend = comp_stamps[stampID]->getBend(j);
257	>	theBends[j].a = currentBend->getA() + atomOffset;
258	>	theBends[j].b = currentBend->getB() + atomOffset;
259	>	theBends[j].c = currentBend->getC() + atomOffset;
260	>
261	>	if (currentBend->haveExtras()){
262	>	extras = currentBend->getExtras();
263	>	current_extra = extras;
264	>
265	>	while (current_extra != NULL){
266	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
267	>	switch (current_extra->getType()){
268	>	case 0:
269	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
270	>	theBends[j].isGhost = 1;
271	>	break;
272	>
273	>	case 1:
274	>	theBends[j].ghost = (int) current_extra->getDouble() +
275	>	atomOffset;
276	>	theBends[j].isGhost = 1;
277	>	break;
278	>
279	>	default:
280	>	sprintf(painCave.errMsg,
281	>	"SimSetup Error: ghostVectorSource was neither a "
282	>	"double nor an int.\n"
283	>	"-->Bend[%d] in %s\n",
284	>	j, comp_stamps[stampID]->getID());
285	>	painCave.isFatal = 1;
286	>	simError();
287	>	}
288	>	}
289	>	else{
290	>	sprintf(painCave.errMsg,
291	>	"SimSetup Error: unhandled bend assignment:\n"
292	>	"    -->%s in Bend[%d] in %s\n",
293	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
294	>	painCave.isFatal = 1;
295	>	simError();
296	>	}
297	>
298	>	current_extra = current_extra->getNext();
299	>	}
300	>	}
301	>
302	>	if (!theBends[j].isGhost){
303	>	exI = theBends[j].a;
304	>	exJ = theBends[j].c;
305	>	}
306	>	else{
307	>	exI = theBends[j].a;
308	>	exJ = theBends[j].b;
309	>	}
310	>
311	>	// exclude_I must always be the smaller of the pair
312	>	if (exI > exJ){
313	>	tempEx = exI;
314	>	exI = exJ;
315	>	exJ = tempEx;
316	>	}
317		#ifdef IS_MPI
318	<	tempEx = exI;
319	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
320	<	tempEx = exJ;
321	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
322	<
323	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
318	>	tempEx = exI;
319	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
320	>	tempEx = exJ;
321	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
322	>
323	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
324		#else  // isn't MPI
325	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
325	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
326		#endif  //is_mpi
327	<	}
328	<	excludeOffset += molInfo.nBends;
327	>	}
328	>	excludeOffset += molInfo.nBends;
329
330	<	for(j=0; j<molInfo.nTorsions; j++){
331	<
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;
329	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
330	<
331	<	exI = theTorsions[j].a;
332	<	exJ = theTorsions[j].d;
330	>	for (j = 0; j < molInfo.nTorsions; j++){
331	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
332	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
333	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
334	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
335	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
336
337	<	// exclude_I must always be the smaller of the pair
338	<	if( exI > exJ ){
339	<	tempEx = exI;
340	<	exI = exJ;
341	<	exJ = tempEx;
342	<	}
337	>	exI = theTorsions[j].a;
338	>	exJ = theTorsions[j].d;
339	>
340	>	// exclude_I must always be the smaller of the pair
341	>	if (exI > exJ){
342	>	tempEx = exI;
343	>	exI = exJ;
344	>	exJ = tempEx;
345	>	}
346		#ifdef IS_MPI
347	<	tempEx = exI;
348	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
349	<	tempEx = exJ;
350	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
351	<
352	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
347	>	tempEx = exI;
348	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
349	>	tempEx = exJ;
350	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
351	>
352	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
353		#else  // isn't MPI
354	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
354	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
355		#endif  //is_mpi
356	<	}
357	<	excludeOffset += molInfo.nTorsions;
356	>	}
357	>	excludeOffset += molInfo.nTorsions;
358
353	–
354	–	// send the arrays off to the forceField for init.
359
360	<	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 );
360	>	// send the arrays off to the forceField for init.
361
362	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
363	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
364	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
365	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
366	+	theTorsions);
367
362	–	the_molecules[i].initialize( molInfo );
368
369	+	info[k].molecules[i].initialize(molInfo);
370
371	<	atomOffset += molInfo.nAtoms;
372	<	delete[] theBonds;
373	<	delete[] theBends;
374	<	delete[] theTorsions;
371	>
372	>	atomOffset += molInfo.nAtoms;
373	>	delete[] theBonds;
374	>	delete[] theBends;
375	>	delete[] theTorsions;
376	>	}
377		}
378
379		#ifdef IS_MPI
380	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
380	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
381		MPIcheckPoint();
382		#endif // is_mpi
383
384		// clean up the forcefield
385	+
386		the_ff->calcRcut();
387		the_ff->cleanMe();
379	–
388		}
389
390	<	void SimSetup::initFromBass( void ){
383	<
390	>	void SimSetup::initFromBass(void){
391		int i, j, k;
392		int n_cells;
393		double cellx, celly, cellz;
#	Line 389 | Line 396 | void SimSetup::initFromBass( void ){
396		int n_extra;
397		int have_extra, done;
398
399	<	temp1 = (double)tot_nmol / 4.0;
400	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
401	<	temp3 = ceil( temp2 );
399	>	double vel[3];
400	>	vel[0] = 0.0;
401	>	vel[1] = 0.0;
402	>	vel[2] = 0.0;
403
404	<	have_extra =0;
405	<	if( temp2 < temp3 ){ // we have a non-complete lattice
406	<	have_extra =1;
404	>	temp1 = (double) tot_nmol / 4.0;
405	>	temp2 = pow(temp1, (1.0 / 3.0));
406	>	temp3 = ceil(temp2);
407
408	<	n_cells = (int)temp3 - 1;
409	<	cellx = info->boxL[0] / temp3;
410	<	celly = info->boxL[1] / temp3;
411	<	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 );
408	>	have_extra = 0;
409	>	if (temp2 < temp3){
410	>	// we have a non-complete lattice
411	>	have_extra = 1;
412
413	<	if( n_per_extra > 4){
414	<	sprintf( painCave.errMsg,
415	<	"SimSetup error. There has been an error in constructing"
416	<	" the non-complete lattice.\n" );
413	>	n_cells = (int) temp3 - 1;
414	>	cellx = info[0].boxL[0] / temp3;
415	>	celly = info[0].boxL[1] / temp3;
416	>	cellz = info[0].boxL[2] / temp3;
417	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
418	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
419	>	n_per_extra = (int) ceil(temp1);
420	>
421	>	if (n_per_extra > 4){
422	>	sprintf(painCave.errMsg,
423	>	"SimSetup error. There has been an error in constructing"
424	>	" the non-complete lattice.\n");
425		painCave.isFatal = 1;
426		simError();
427		}
428		}
429		else{
430	<	n_cells = (int)temp3;
431	<	cellx = info->boxL[0] / temp3;
432	<	celly = info->boxL[1] / temp3;
433	<	cellz = info->boxL[2] / temp3;
430	>	n_cells = (int) temp3;
431	>	cellx = info[0].boxL[0] / temp3;
432	>	celly = info[0].boxL[1] / temp3;
433	>	cellz = info[0].boxL[2] / temp3;
434		}
435
436		current_mol = 0;
#	Line 425 | Line 438 | void SimSetup::initFromBass( void ){
438		current_comp = 0;
439		current_atom_ndx = 0;
440
441	<	for( i=0; i < n_cells ; i++ ){
442	<	for( j=0; j < n_cells; j++ ){
443	<	for( k=0; k < n_cells; k++ ){
441	>	for (i = 0; i < n_cells ; i++){
442	>	for (j = 0; j < n_cells; j++){
443	>	for (k = 0; k < n_cells; k++){
444	>	makeElement(i * cellx, j * celly, k * cellz);
445
446	<	makeElement( i * cellx,
433	<	j * celly,
434	<	k * cellz );
446	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
447
448	<	makeElement( i * cellx + 0.5 * cellx,
437	<	j * celly + 0.5 * celly,
438	<	k * cellz );
448	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
449
450	<	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 );
450	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
451		}
452		}
453		}
454
455	<	if( have_extra ){
455	>	if (have_extra){
456		done = 0;
457
458		int start_ndx;
459	<	for( i=0; i < (n_cells+1) && !done; i++ ){
460	<	for( j=0; j < (n_cells+1) && !done; j++ ){
459	>	for (i = 0; i < (n_cells + 1) && !done; i++){
460	>	for (j = 0; j < (n_cells + 1) && !done; j++){
461	>	if (i < n_cells){
462	>	if (j < n_cells){
463	>	start_ndx = n_cells;
464	>	}
465	>	else
466	>	start_ndx = 0;
467	>	}
468	>	else
469	>	start_ndx = 0;
470
471	<	if( i < n_cells ){
471	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
472	>	makeElement(i * cellx, j * celly, k * cellz);
473	>	done = (current_mol >= tot_nmol);
474
475	<	if( j < n_cells ){
476	<	start_ndx = n_cells;
477	<	}
478	<	else start_ndx = 0;
479	<	}
465	<	else start_ndx = 0;
475	>	if (!done && n_per_extra > 1){
476	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
477	>	k * cellz);
478	>	done = (current_mol >= tot_nmol);
479	>	}
480
481	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
481	>	if (!done && n_per_extra > 2){
482	>	makeElement(i * cellx, j * celly + 0.5 * celly,
483	>	k * cellz + 0.5 * cellz);
484	>	done = (current_mol >= tot_nmol);
485	>	}
486
487	<	makeElement( i * cellx,
488	<	j * celly,
489	<	k * cellz );
490	<	done = ( current_mol >= tot_nmol );
491	<
492	<	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	<	}
487	>	if (!done && n_per_extra > 3){
488	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
489	>	k * cellz + 0.5 * cellz);
490	>	done = (current_mol >= tot_nmol);
491	>	}
492	>	}
493		}
494		}
495		}
496
497	<
498	<	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 );
497	>	for (i = 0; i < info[0].n_atoms; i++){
498	>	info[0].atoms[i]->setVel(vel);
499		}
500		}
501
502	<	void SimSetup::makeElement( double x, double y, double z ){
508	<
502	>	void SimSetup::makeElement(double x, double y, double z){
503		int k;
504		AtomStamp* current_atom;
505		DirectionalAtom* dAtom;
506		double rotMat[3][3];
507	+	double pos[3];
508
509	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
510	<
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",
523	<	comp_stamps[current_comp]->getID(),
524	<	current_atom->getType() );
509	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
510	>	current_atom = comp_stamps[current_comp]->getAtom(k);
511	>	if (!current_atom->havePosition()){
512	>	sprintf(painCave.errMsg,
513	>	"SimSetup:initFromBass error.\n"
514	>	"\tComponent %s, atom %s does not have a position specified.\n"
515	>	"\tThe initialization routine is unable to give a start"
516	>	" position.\n",
517	>	comp_stamps[current_comp]->getID(), current_atom->getType());
518		painCave.isFatal = 1;
519		simError();
520		}
521
522	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
523	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
524	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
522	>	pos[0] = x + current_atom->getPosX();
523	>	pos[1] = y + current_atom->getPosY();
524	>	pos[2] = z + current_atom->getPosZ();
525
526	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
526	>	info[0].atoms[current_atom_ndx]->setPos(pos);
527
528	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
528	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
529	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
530
531		rotMat[0][0] = 1.0;
532		rotMat[0][1] = 0.0;
#	Line 546 | Line 540 | void SimSetup::makeElement( double x, double y, double
540		rotMat[2][1] = 0.0;
541		rotMat[2][2] = 1.0;
542
543	<	dAtom->setA( rotMat );
543	>	dAtom->setA(rotMat);
544		}
545
546		current_atom_ndx++;
#	Line 555 | Line 549 | void SimSetup::makeElement( double x, double y, double
549		current_mol++;
550		current_comp_mol++;
551
552	<	if( current_comp_mol >= components_nmol[current_comp] ){
559	<
552	>	if (current_comp_mol >= components_nmol[current_comp]){
553		current_comp_mol = 0;
554		current_comp++;
555		}
556		}
557
558
559	<	void SimSetup::gatherInfo( void ){
560	<	int i,j,k;
559	>	void SimSetup::gatherInfo(void){
560	>	int i;
561
562		ensembleCase = -1;
563		ffCase = -1;
564
572	–	// get the stamps and globals;
573	–	stamps = stamps;
574	–	globals = globals;
575	–
565		// set the easy ones first
566	<	info->target_temp = globals->getTargetTemp();
567	<	info->dt = globals->getDt();
568	<	info->run_time = globals->getRunTime();
566	>
567	>	for (i = 0; i < nInfo; i++){
568	>	info[i].target_temp = globals->getTargetTemp();
569	>	info[i].dt = globals->getDt();
570	>	info[i].run_time = globals->getRunTime();
571	>	}
572		n_components = globals->getNComponents();
573
574
575		// get the forceField
576
577	<	strcpy( force_field, globals->getForceField() );
577	>	strcpy(force_field, globals->getForceField());
578
579	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
580	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
579	>	if (!strcasecmp(force_field, "DUFF")){
580	>	ffCase = FF_DUFF;
581	>	}
582	>	else if (!strcasecmp(force_field, "LJ")){
583	>	ffCase = FF_LJ;
584	>	}
585	>	else if (!strcasecmp(force_field, "EAM")){
586	>	ffCase = FF_EAM;
587	>	}
588		else{
589	<	sprintf( painCave.errMsg,
590	<	"SimSetup Error. Unrecognized force field -> %s\n",
591	<	force_field );
592	<	painCave.isFatal = 1;
594	<	simError();
589	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
590	>	force_field);
591	>	painCave.isFatal = 1;
592	>	simError();
593		}
594
595	<	// get the ensemble
595	>	// get the ensemble
596
597	<	strcpy( ensemble, globals->getEnsemble() );
597	>	strcpy(ensemble, globals->getEnsemble());
598
599	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
600	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
601	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
599	>	if (!strcasecmp(ensemble, "NVE")){
600	>	ensembleCase = NVE_ENS;
601	>	}
602	>	else if (!strcasecmp(ensemble, "NVT")){
603	>	ensembleCase = NVT_ENS;
604	>	}
605	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
606		ensembleCase = NPTi_ENS;
607	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
608	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
609	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
607	>	}
608	>	else if (!strcasecmp(ensemble, "NPTf")){
609	>	ensembleCase = NPTf_ENS;
610	>	}
611	>	else if (!strcasecmp(ensemble, "NPTxyz")){
612	>	ensembleCase = NPTxyz_ENS;
613	>	}
614		else{
615	<	sprintf( painCave.errMsg,
616	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
617	<	"reverting to NVE for this simulation.\n",
618	<	ensemble );
619	<	painCave.isFatal = 0;
620	<	simError();
621	<	strcpy( ensemble, "NVE" );
622	<	ensembleCase = NVE_ENS;
615	>	sprintf(painCave.errMsg,
616	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
617	>	"reverting to NVE for this simulation.\n",
618	>	ensemble);
619	>	painCave.isFatal = 0;
620	>	simError();
621	>	strcpy(ensemble, "NVE");
622	>	ensembleCase = NVE_ENS;
623		}
618	–	strcpy( info->ensemble, ensemble );
624
625	<	// get the mixing rule
625	>	for (i = 0; i < nInfo; i++){
626	>	strcpy(info[i].ensemble, ensemble);
627
628	<	strcpy( info->mixingRule, globals->getMixingRule() );
629	<	info->usePBC = globals->getPBC();
630	<
631	<
628	>	// get the mixing rule
629	>
630	>	strcpy(info[i].mixingRule, globals->getMixingRule());
631	>	info[i].usePBC = globals->getPBC();
632	>	}
633	>
634		// get the components and calculate the tot_nMol and indvidual n_mol
635	<
635	>
636		the_components = globals->getComponents();
637		components_nmol = new int[n_components];
638
639
640	<	if( !globals->haveNMol() ){
640	>	if (!globals->haveNMol()){
641		// we don't have the total number of molecules, so we assume it is
642		// given in each component
643
644		tot_nmol = 0;
645	<	for( i=0; i<n_components; i++ ){
646	<
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;
645	<	simError();
645	>	for (i = 0; i < n_components; i++){
646	>	if (!the_components[i]->haveNMol()){
647	>	// we have a problem
648	>	sprintf(painCave.errMsg,
649	>	"SimSetup Error. No global NMol or component NMol"
650	>	" given. Cannot calculate the number of atoms.\n");
651	>	painCave.isFatal = 1;
652	>	simError();
653		}
654
655		tot_nmol += the_components[i]->getNMol();
#	Line 650 | Line 657 | void SimSetup::gatherInfo( void ){
657		}
658		}
659		else{
660	<	sprintf( painCave.errMsg,
661	<	"SimSetup error.\n"
662	<	"\tSorry, the ability to specify total"
663	<	" nMols and then give molfractions in the components\n"
664	<	"\tis not currently supported."
665	<	" Please give nMol in the components.\n" );
660	>	sprintf(painCave.errMsg,
661	>	"SimSetup error.\n"
662	>	"\tSorry, the ability to specify total"
663	>	" nMols and then give molfractions in the components\n"
664	>	"\tis not currently supported."
665	>	" Please give nMol in the components.\n");
666		painCave.isFatal = 1;
667		simError();
668		}
669
670		// set the status, sample, and thermal kick times
664	–
665	–	if( globals->haveSampleTime() ){
666	–	info->sampleTime = globals->getSampleTime();
667	–	info->statusTime = info->sampleTime;
668	–	info->thermalTime = info->sampleTime;
669	–	}
670	–	else{
671	–	info->sampleTime = globals->getRunTime();
672	–	info->statusTime = info->sampleTime;
673	–	info->thermalTime = info->sampleTime;
674	–	}
671
672	<	if( globals->haveStatusTime() ){
673	<	info->statusTime = globals->getStatusTime();
674	<	}
672	>	for (i = 0; i < nInfo; i++){
673	>	if (globals->haveSampleTime()){
674	>	info[i].sampleTime = globals->getSampleTime();
675	>	info[i].statusTime = info[i].sampleTime;
676	>	info[i].thermalTime = info[i].sampleTime;
677	>	}
678	>	else{
679	>	info[i].sampleTime = globals->getRunTime();
680	>	info[i].statusTime = info[i].sampleTime;
681	>	info[i].thermalTime = info[i].sampleTime;
682	>	}
683
684	<	if( globals->haveThermalTime() ){
685	<	info->thermalTime = globals->getThermalTime();
686	<	}
684	>	if (globals->haveStatusTime()){
685	>	info[i].statusTime = globals->getStatusTime();
686	>	}
687
688	<	// check for the temperature set flag
688	>	if (globals->haveThermalTime()){
689	>	info[i].thermalTime = globals->getThermalTime();
690	>	}
691
692	<	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
692	>	info[i].resetIntegrator = 0;
693	>	if( globals->haveResetTime() ){
694	>	info[i].resetTime = globals->getResetTime();
695	>	info[i].resetIntegrator = 1;
696	>	}
697
698	<	// get some of the tricky things that may still be in the globals
698	>	// check for the temperature set flag
699
700	<	double boxVector[3];
701	<	if( globals->haveBox() ){
692	<	boxVector[0] = globals->getBox();
693	<	boxVector[1] = globals->getBox();
694	<	boxVector[2] = globals->getBox();
695	<
696	<	info->setBox( boxVector );
697	<	}
698	<	else if( globals->haveDensity() ){
700	>	if (globals->haveTempSet())
701	>	info[i].setTemp = globals->getTempSet();
702
703	<	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];
703	>	// get some of the tricky things that may still be in the globals
704
705	<	info->setBox( boxVector );
706	<	}
707	<	else{
708	<	if( !globals->haveBoxX() ){
709	<	sprintf( painCave.errMsg,
711	<	"SimSetup error, no periodic BoxX size given.\n" );
712	<	painCave.isFatal = 1;
713	<	simError();
714	<	}
715	<	boxVector[0] = globals->getBoxX();
705	>	double boxVector[3];
706	>	if (globals->haveBox()){
707	>	boxVector[0] = globals->getBox();
708	>	boxVector[1] = globals->getBox();
709	>	boxVector[2] = globals->getBox();
710
711	<	if( !globals->haveBoxY() ){
718	<	sprintf( painCave.errMsg,
719	<	"SimSetup error, no periodic BoxY size given.\n" );
720	<	painCave.isFatal = 1;
721	<	simError();
711	>	info[i].setBox(boxVector);
712		}
713	<	boxVector[1] = globals->getBoxY();
713	>	else if (globals->haveDensity()){
714	>	double vol;
715	>	vol = (double) tot_nmol / globals->getDensity();
716	>	boxVector[0] = pow(vol, (1.0 / 3.0));
717	>	boxVector[1] = boxVector[0];
718	>	boxVector[2] = boxVector[0];
719
720	<	if( !globals->haveBoxZ() ){
726	<	sprintf( painCave.errMsg,
727	<	"SimSetup error, no periodic BoxZ size given.\n" );
728	<	painCave.isFatal = 1;
729	<	simError();
720	>	info[i].setBox(boxVector);
721		}
722	<	boxVector[2] = globals->getBoxZ();
722	>	else{
723	>	if (!globals->haveBoxX()){
724	>	sprintf(painCave.errMsg,
725	>	"SimSetup error, no periodic BoxX size given.\n");
726	>	painCave.isFatal = 1;
727	>	simError();
728	>	}
729	>	boxVector[0] = globals->getBoxX();
730
731	<	info->setBox( boxVector );
731	>	if (!globals->haveBoxY()){
732	>	sprintf(painCave.errMsg,
733	>	"SimSetup error, no periodic BoxY size given.\n");
734	>	painCave.isFatal = 1;
735	>	simError();
736	>	}
737	>	boxVector[1] = globals->getBoxY();
738	>
739	>	if (!globals->haveBoxZ()){
740	>	sprintf(painCave.errMsg,
741	>	"SimSetup error, no periodic BoxZ size given.\n");
742	>	painCave.isFatal = 1;
743	>	simError();
744	>	}
745	>	boxVector[2] = globals->getBoxZ();
746	>
747	>	info[i].setBox(boxVector);
748	>	}
749		}
750
751	+	//setup seed for random number generator
752	+	int seedValue;
753
754	+	if (globals->haveSeed()){
755	+	seedValue = globals->getSeed();
756	+
757	+	if(seedValue / 1E9 == 0){
758	+	sprintf(painCave.errMsg,
759	+	"Seed for sprng library should contain at least 9 digits\n"
760	+	"OOPSE will generate a seed for user\n");
761	+	painCave.isFatal = 0;
762	+	simError();
763	+
764	+	//using seed generated by system instead of invalid seed set by user
765	+	#ifndef IS_MPI
766	+	seedValue = make_sprng_seed();
767	+	#else
768	+	if (worldRank == 0){
769	+	seedValue = make_sprng_seed();
770	+	}
771	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
772	+	#endif
773	+	}
774	+	}//end of if branch of globals->haveSeed()
775	+	else{
776
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	+	}//end of globals->haveSeed()
786	+
787	+	for (int i = 0; i < nInfo; i++){
788	+	info[i].setSeed(seedValue);
789	+	}
790	+
791		#ifdef IS_MPI
792	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
792	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
793		MPIcheckPoint();
794		#endif // is_mpi
742	–
795		}
796
797
798	<	void SimSetup::finalInfoCheck( void ){
798	>	void SimSetup::finalInfoCheck(void){
799		int index;
800		int usesDipoles;
801	<
801	>	int i;
802
803	<	// check electrostatic parameters
804	<
805	<	index = 0;
806	<	usesDipoles = 0;
807	<	while( (index < info->n_atoms) && !usesDipoles ){
808	<	usesDipoles = ((info->atoms)[index])->hasDipole();
809	<	index++;
810	<	}
811	<
803	>	for (i = 0; i < nInfo; i++){
804	>	// check electrostatic parameters
805	>
806	>	index = 0;
807	>	usesDipoles = 0;
808	>	while ((index < info[i].n_atoms) && !usesDipoles){
809	>	usesDipoles = (info[i].atoms[index])->hasDipole();
810	>	index++;
811	>	}
812	>
813		#ifdef IS_MPI
814	<	int myUse = usesDipoles;
815	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
814	>	int myUse = usesDipoles;
815	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816		#endif //is_mpi
817
818	<	double theEcr, theEst;
818	>	double theEcr, theEst;
819
820	<	if (globals->getUseRF() ) {
821	<	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	<	}
820	>	if (globals->getUseRF()){
821	>	info[i].useReactionField = 1;
822
823	<	if( !globals->haveEST() ){
824	<	sprintf( painCave.errMsg,
825	<	"SimSetup Warning: using default value of 0.05 * the "
826	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
827	<	);
828	<	painCave.isFatal = 0;
829	<	simError();
830	<	theEst = 0.05 * theEcr;
831	<	} else {
832	<	theEst= globals->getEST();
833	<	}
834	<
835	<	info->setEcr( theEcr, theEst );
836	<
800	<	if(!globals->haveDielectric() ){
801	<	sprintf( painCave.errMsg,
802	<	"SimSetup Error: You are trying to use Reaction Field without"
803	<	"setting a dielectric constant!\n"
804	<	);
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();
823	>	if (!globals->haveECR()){
824	>	sprintf(painCave.errMsg,
825	>	"SimSetup Warning: using default value of 1/2 the smallest "
826	>	"box length for the electrostaticCutoffRadius.\n"
827	>	"I hope you have a very fast processor!\n");
828	>	painCave.isFatal = 0;
829	>	simError();
830	>	double smallest;
831	>	smallest = info[i].boxL[0];
832	>	if (info[i].boxL[1] <= smallest)
833	>	smallest = info[i].boxL[1];
834	>	if (info[i].boxL[2] <= smallest)
835	>	smallest = info[i].boxL[2];
836	>	theEcr = 0.5 * smallest;
837		}
838	<
839	<	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();
838	>	else{
839	>	theEcr = globals->getECR();
840		}
841
842	<	info->setEcr( theEcr, theEst );
842	>	if (!globals->haveEST()){
843	>	sprintf(painCave.errMsg,
844	>	"SimSetup Warning: using default value of 0.05 * the "
845	>	"electrostaticCutoffRadius for the 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].setEcr(theEcr, theEst);
855	>
856	>	if (!globals->haveDielectric()){
857	>	sprintf(painCave.errMsg,
858	>	"SimSetup Error: You are trying to use Reaction Field without"
859	>	"setting a dielectric constant!\n");
860	>	painCave.isFatal = 1;
861	>	simError();
862	>	}
863	>	info[i].dielectric = globals->getDielectric();
864		}
865	<	}
865	>	else{
866	>	if (usesDipoles){
867	>	if (!globals->haveECR()){
868	>	sprintf(painCave.errMsg,
869	>	"SimSetup Warning: using default value of 1/2 the smallest "
870	>	"box length for the electrostaticCutoffRadius.\n"
871	>	"I hope you have a very fast processor!\n");
872	>	painCave.isFatal = 0;
873	>	simError();
874	>	double smallest;
875	>	smallest = info[i].boxL[0];
876	>	if (info[i].boxL[1] <= smallest)
877	>	smallest = info[i].boxL[1];
878	>	if (info[i].boxL[2] <= smallest)
879	>	smallest = info[i].boxL[2];
880	>	theEcr = 0.5 * smallest;
881	>	}
882	>	else{
883	>	theEcr = globals->getECR();
884	>	}
885
886	+	if (!globals->haveEST()){
887	+	sprintf(painCave.errMsg,
888	+	"SimSetup Warning: using default value of 0.05 * the "
889	+	"electrostaticCutoffRadius for the "
890	+	"electrostaticSkinThickness\n");
891	+	painCave.isFatal = 0;
892	+	simError();
893	+	theEst = 0.05 * theEcr;
894	+	}
895	+	else{
896	+	theEst = globals->getEST();
897	+	}
898	+
899	+	info[i].setEcr(theEcr, theEst);
900	+	}
901	+	}
902	+	}
903	+
904		#ifdef IS_MPI
905	<	strcpy( checkPointMsg, "post processing checks out" );
905	>	strcpy(checkPointMsg, "post processing checks out");
906		MPIcheckPoint();
907		#endif // is_mpi
850	–
908		}
909
910	<	void SimSetup::initSystemCoords( void ){
910	>	void SimSetup::initSystemCoords(void){
911	>	int i;
912
913	<	if( globals->haveInitialConfig() ){
914	<
915	<	InitializeFromFile* fileInit;
913	>	char* inName;
914	>
915	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
916	>
917	>	for (i = 0; i < info[0].n_atoms; i++)
918	>	info[0].atoms[i]->setCoords();
919	>
920	>	if (globals->haveInitialConfig()){
921	>	InitializeFromFile* fileInit;
922		#ifdef IS_MPI // is_mpi
923	<	if( worldRank == 0 ){
923	>	if (worldRank == 0){
924		#endif //is_mpi
925	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
925	>	inName = globals->getInitialConfig();
926	>	fileInit = new InitializeFromFile(inName);
927		#ifdef IS_MPI
928	<	}else fileInit = new InitializeFromFile( NULL );
928	>	}
929	>	else
930	>	fileInit = new InitializeFromFile(NULL);
931		#endif
932	<	fileInit->read_xyz( info ); // default velocities on
932	>	fileInit->readInit(info); // default velocities on
933
934	<	delete fileInit;
935	<	}
936	<	else{
870	<
934	>	delete fileInit;
935	>	}
936	>	else{
937		#ifdef IS_MPI
938
939	<	// no init from bass
940	<
941	<	sprintf( painCave.errMsg,
942	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
943	<	painCave.isFatal;
944	<	simError();
945	<
939	>	// no init from bass
940	>
941	>	sprintf(painCave.errMsg,
942	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
943	>	painCave.isFatal = 1;;
944	>	simError();
945	>
946		#else
947
948	<	initFromBass();
948	>	initFromBass();
949
950
951		#endif
952	<	}
952	>	}
953
954		#ifdef IS_MPI
955	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
955	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
956		MPIcheckPoint();
957		#endif // is_mpi
892	–
958		}
959
960
961	<	void SimSetup::makeOutNames( void ){
961	>	void SimSetup::makeOutNames(void){
962	>	int k;
963
964	+
965	+	for (k = 0; k < nInfo; k++){
966		#ifdef IS_MPI
967	<	if( worldRank == 0 ){
967	>	if (worldRank == 0){
968		#endif // is_mpi
969	<
970	<	if( globals->haveFinalConfig() ){
971	<	strcpy( info->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" );
969	>
970	>	if (globals->haveFinalConfig()){
971	>	strcpy(info[k].finalName, globals->getFinalConfig());
972		}
913	–	else if( !strcmp( endTest, ".BASS" ) ){
914	–	strcpy( endTest, ".eor" );
915	–	}
973		else{
974	<	endTest = &(info->finalName[nameLength - 4]);
975	<	if( !strcmp( endTest, ".bss" ) ){
976	<	strcpy( endTest, ".eor" );
977	<	}
978	<	else if( !strcmp( endTest, ".mdl" ) ){
979	<	strcpy( endTest, ".eor" );
980	<	}
981	<	else{
982	<	strcat( info->finalName, ".eor" );
983	<	}
974	>	strcpy(info[k].finalName, inFileName);
975	>	char* endTest;
976	>	int nameLength = strlen(info[k].finalName);
977	>	endTest = &(info[k].finalName[nameLength - 5]);
978	>	if (!strcmp(endTest, ".bass")){
979	>	strcpy(endTest, ".eor");
980	>	}
981	>	else if (!strcmp(endTest, ".BASS")){
982	>	strcpy(endTest, ".eor");
983	>	}
984	>	else{
985	>	endTest = &(info[k].finalName[nameLength - 4]);
986	>	if (!strcmp(endTest, ".bss")){
987	>	strcpy(endTest, ".eor");
988	>	}
989	>	else if (!strcmp(endTest, ".mdl")){
990	>	strcpy(endTest, ".eor");
991	>	}
992	>	else{
993	>	strcat(info[k].finalName, ".eor");
994	>	}
995	>	}
996		}
997	<	}
998	<
999	<	// make the sample and status out names
1000	<
1001	<	strcpy( info->sampleName, inFileName );
1002	<	char* endTest;
1003	<	int nameLength = strlen( info->sampleName );
1004	<	endTest = &(info->sampleName[nameLength - 5]);
1005	<	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" );
997	>
998	>	// make the sample and status out names
999	>
1000	>	strcpy(info[k].sampleName, inFileName);
1001	>	char* endTest;
1002	>	int nameLength = strlen(info[k].sampleName);
1003	>	endTest = &(info[k].sampleName[nameLength - 5]);
1004	>	if (!strcmp(endTest, ".bass")){
1005	>	strcpy(endTest, ".dump");
1006		}
1007	<	else if( !strcmp( endTest, ".mdl" ) ){
1008	<	strcpy( endTest, ".dump" );
1007	>	else if (!strcmp(endTest, ".BASS")){
1008	>	strcpy(endTest, ".dump");
1009		}
1010		else{
1011	<	strcat( info->sampleName, ".dump" );
1011	>	endTest = &(info[k].sampleName[nameLength - 4]);
1012	>	if (!strcmp(endTest, ".bss")){
1013	>	strcpy(endTest, ".dump");
1014	>	}
1015	>	else if (!strcmp(endTest, ".mdl")){
1016	>	strcpy(endTest, ".dump");
1017	>	}
1018	>	else{
1019	>	strcat(info[k].sampleName, ".dump");
1020	>	}
1021		}
1022	<	}
1023	<
1024	<	strcpy( info->statusName, inFileName );
1025	<	nameLength = strlen( info->statusName );
1026	<	endTest = &(info->statusName[nameLength - 5]);
1027	<	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" );
1022	>
1023	>	strcpy(info[k].statusName, inFileName);
1024	>	nameLength = strlen(info[k].statusName);
1025	>	endTest = &(info[k].statusName[nameLength - 5]);
1026	>	if (!strcmp(endTest, ".bass")){
1027	>	strcpy(endTest, ".stat");
1028		}
1029	<	else if( !strcmp( endTest, ".mdl" ) ){
1030	<	strcpy( endTest, ".stat" );
1029	>	else if (!strcmp(endTest, ".BASS")){
1030	>	strcpy(endTest, ".stat");
1031		}
1032		else{
1033	<	strcat( info->statusName, ".stat" );
1033	>	endTest = &(info[k].statusName[nameLength - 4]);
1034	>	if (!strcmp(endTest, ".bss")){
1035	>	strcpy(endTest, ".stat");
1036	>	}
1037	>	else if (!strcmp(endTest, ".mdl")){
1038	>	strcpy(endTest, ".stat");
1039	>	}
1040	>	else{
1041	>	strcat(info[k].statusName, ".stat");
1042	>	}
1043		}
1044	<	}
976	<
1044	>
1045		#ifdef IS_MPI
978	–	}
979	–	#endif // is_mpi
1046
1047	+	}
1048	+	#endif // is_mpi
1049	+	}
1050		}
1051
1052
1053	<	void SimSetup::sysObjectsCreation( void ){
1053	>	void SimSetup::sysObjectsCreation(void){
1054	>	int i, k;
1055
986	–	int i;
987	–
1056		// create the forceField
1057
1058		createFF();
#	Line 999 | Line 1067 | void SimSetup::sysObjectsCreation( void ){
1067
1068		#ifdef IS_MPI
1069		// divide the molecules among the processors
1070	<
1070	>
1071		mpiMolDivide();
1072		#endif //is_mpi
1073	<
1073	>
1074		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1075	<
1075	>
1076		makeSysArrays();
1077
1078		// make and initialize the molecules (all but atomic coordinates)
1079	<
1079	>
1080		makeMolecules();
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	–
1081
1082	<
1082	>	for (k = 0; k < nInfo; k++){
1083	>	info[k].identArray = new int[info[k].n_atoms];
1084	>	for (i = 0; i < info[k].n_atoms; i++){
1085	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1086	>	}
1087	>	}
1088		}
1089
1090
1091	<	void SimSetup::createFF( void ){
1091	>	void SimSetup::createFF(void){
1092	>	switch (ffCase){
1093	>	case FF_DUFF:
1094	>	the_ff = new DUFF();
1095	>	break;
1096
1097	<	switch( ffCase ){
1097	>	case FF_LJ:
1098	>	the_ff = new LJFF();
1099	>	break;
1100
1101	<	case FF_DUFF:
1102	<	the_ff = new DUFF();
1103	<	break;
1101	>	case FF_EAM:
1102	>	the_ff = new EAM_FF();
1103	>	break;
1104
1105	<	case FF_LJ:
1106	<	the_ff = new LJFF();
1107	<	break;
1108	<
1109	<	default:
1036	<	sprintf( painCave.errMsg,
1037	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1038	<	painCave.isFatal = 1;
1039	<	simError();
1105	>	default:
1106	>	sprintf(painCave.errMsg,
1107	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1108	>	painCave.isFatal = 1;
1109	>	simError();
1110		}
1111
1112		#ifdef IS_MPI
1113	<	strcpy( checkPointMsg, "ForceField creation successful" );
1113	>	strcpy(checkPointMsg, "ForceField creation successful");
1114		MPIcheckPoint();
1115		#endif // is_mpi
1046	–
1116		}
1117
1118
1119	<	void SimSetup::compList( void ){
1051	<
1119	>	void SimSetup::compList(void){
1120		int i;
1121	+	char* id;
1122	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1123	+	LinkedMolStamp* currentStamp = NULL;
1124	+	comp_stamps = new MoleculeStamp * [n_components];
1125
1054	–	comp_stamps = new MoleculeStamp*[n_components];
1055	–
1126		// make an array of molecule stamps that match the components used.
1127		// also extract the used stamps out into a separate linked list
1128
1129	<	info->nComponents = n_components;
1130	<	info->componentsNmol = components_nmol;
1131	<	info->compStamps = comp_stamps;
1132	<	info->headStamp = new LinkedMolStamp();
1133	<
1134	<	char* id;
1065	<	LinkedMolStamp* headStamp = info->headStamp;
1066	<	LinkedMolStamp* currentStamp = NULL;
1067	<	for( i=0; i<n_components; i++ ){
1129	>	for (i = 0; i < nInfo; i++){
1130	>	info[i].nComponents = n_components;
1131	>	info[i].componentsNmol = components_nmol;
1132	>	info[i].compStamps = comp_stamps;
1133	>	info[i].headStamp = headStamp;
1134	>	}
1135
1136	+
1137	+	for (i = 0; i < n_components; i++){
1138		id = the_components[i]->getType();
1139		comp_stamps[i] = NULL;
1140	<
1140	>
1141		// check to make sure the component isn't already in the list
1142
1143	<	comp_stamps[i] = headStamp->match( id );
1144	<	if( comp_stamps[i] == NULL ){
1076	<
1143	>	comp_stamps[i] = headStamp->match(id);
1144	>	if (comp_stamps[i] == NULL){
1145		// extract the component from the list;
1146	<
1147	<	currentStamp = stamps->extractMolStamp( id );
1148	<	if( currentStamp == NULL ){
1149	<	sprintf( painCave.errMsg,
1150	<	"SimSetup error: Component \"%s\" was not found in the "
1151	<	"list of declared molecules\n",
1152	<	id );
1153	<	painCave.isFatal = 1;
1154	<	simError();
1146	>
1147	>	currentStamp = stamps->extractMolStamp(id);
1148	>	if (currentStamp == NULL){
1149	>	sprintf(painCave.errMsg,
1150	>	"SimSetup error: Component \"%s\" was not found in the "
1151	>	"list of declared molecules\n",
1152	>	id);
1153	>	painCave.isFatal = 1;
1154	>	simError();
1155		}
1156	<
1157	<	headStamp->add( currentStamp );
1158	<	comp_stamps[i] = headStamp->match( id );
1156	>
1157	>	headStamp->add(currentStamp);
1158	>	comp_stamps[i] = headStamp->match(id);
1159		}
1160		}
1161
1162		#ifdef IS_MPI
1163	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1163	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1164		MPIcheckPoint();
1165		#endif // is_mpi
1098	–
1099	–
1166		}
1167
1168	<	void SimSetup::calcSysValues( void ){
1169	<	int i, j, k;
1168	>	void SimSetup::calcSysValues(void){
1169	>	int i;
1170
1171	+	int* molMembershipArray;
1172
1173		tot_atoms = 0;
1174		tot_bonds = 0;
1175		tot_bends = 0;
1176		tot_torsions = 0;
1177	<	for( i=0; i<n_components; i++ ){
1178	<
1179	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1180	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1114	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1177	>	for (i = 0; i < n_components; i++){
1178	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1179	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1180	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1181		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1182		}
1183
1184		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1185	+	molMembershipArray = new int[tot_atoms];
1186
1187	<	info->n_atoms = tot_atoms;
1188	<	info->n_bonds = tot_bonds;
1189	<	info->n_bends = tot_bends;
1190	<	info->n_torsions = tot_torsions;
1191	<	info->n_SRI = tot_SRI;
1192	<	info->n_mol = tot_nmol;
1193	<
1194	<	info->molMembershipArray = new int[tot_atoms];
1187	>	for (i = 0; i < nInfo; i++){
1188	>	info[i].n_atoms = tot_atoms;
1189	>	info[i].n_bonds = tot_bonds;
1190	>	info[i].n_bends = tot_bends;
1191	>	info[i].n_torsions = tot_torsions;
1192	>	info[i].n_SRI = tot_SRI;
1193	>	info[i].n_mol = tot_nmol;
1194	>
1195	>	info[i].molMembershipArray = molMembershipArray;
1196	>	}
1197		}
1198
1130	–
1199		#ifdef IS_MPI
1200
1201	<	void SimSetup::mpiMolDivide( void ){
1134	<
1201	>	void SimSetup::mpiMolDivide(void){
1202		int i, j, k;
1203		int localMol, allMol;
1204		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1205
1206	<	mpiSim = new mpiSimulation( info );
1207	<
1206	>	mpiSim = new mpiSimulation(info);
1207	>
1208		globalIndex = mpiSim->divideLabor();
1209
1210		// set up the local variables
1211	<
1211	>
1212		mol2proc = mpiSim->getMolToProcMap();
1213		molCompType = mpiSim->getMolComponentType();
1214	<
1214	>
1215		allMol = 0;
1216		localMol = 0;
1217		local_atoms = 0;
#	Line 1154 | Line 1221 | void SimSetup::mpiMolDivide( void ){
1221		globalAtomIndex = 0;
1222
1223
1224	<	for( i=0; i<n_components; i++ ){
1225	<
1226	<	for( j=0; j<components_nmol[i]; j++ ){
1227	<
1228	<	if( mol2proc[allMol] == worldRank ){
1229	<
1230	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1231	<	local_bonds +=    comp_stamps[i]->getNBonds();
1165	<	local_bends +=    comp_stamps[i]->getNBends();
1166	<	local_torsions += comp_stamps[i]->getNTorsions();
1167	<	localMol++;
1224	>	for (i = 0; i < n_components; i++){
1225	>	for (j = 0; j < components_nmol[i]; j++){
1226	>	if (mol2proc[allMol] == worldRank){
1227	>	local_atoms += comp_stamps[i]->getNAtoms();
1228	>	local_bonds += comp_stamps[i]->getNBonds();
1229	>	local_bends += comp_stamps[i]->getNBends();
1230	>	local_torsions += comp_stamps[i]->getNTorsions();
1231	>	localMol++;
1232		}
1233	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1234	<	info->molMembershipArray[globalAtomIndex] = allMol;
1233	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1234	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1235		globalAtomIndex++;
1236		}
1237
1238	<	allMol++;
1238	>	allMol++;
1239		}
1240		}
1241		local_SRI = local_bonds + local_bends + local_torsions;
1242	<
1243	<	info->n_atoms = mpiSim->getMyNlocal();
1244	<
1245	<	if( local_atoms != info->n_atoms ){
1246	<	sprintf( painCave.errMsg,
1247	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1248	<	" localAtom (%d) are not equal.\n",
1249	<	info->n_atoms,
1186	<	local_atoms );
1242	>
1243	>	info[0].n_atoms = mpiSim->getMyNlocal();
1244	>
1245	>	if (local_atoms != info[0].n_atoms){
1246	>	sprintf(painCave.errMsg,
1247	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1248	>	" localAtom (%d) are not equal.\n",
1249	>	info[0].n_atoms, local_atoms);
1250		painCave.isFatal = 1;
1251		simError();
1252		}
1253
1254	<	info->n_bonds = local_bonds;
1255	<	info->n_bends = local_bends;
1256	<	info->n_torsions = local_torsions;
1257	<	info->n_SRI = local_SRI;
1258	<	info->n_mol = localMol;
1254	>	info[0].n_bonds = local_bonds;
1255	>	info[0].n_bends = local_bends;
1256	>	info[0].n_torsions = local_torsions;
1257	>	info[0].n_SRI = local_SRI;
1258	>	info[0].n_mol = localMol;
1259
1260	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1260	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1261		MPIcheckPoint();
1262		}
1263	<
1263	>
1264		#endif // is_mpi
1265
1266
1267	<	void SimSetup::makeSysArrays( void ){
1268	<	int i, j, k;
1267	>	void SimSetup::makeSysArrays(void){
1268	>
1269	>	#ifndef IS_MPI
1270	>	int k, j;
1271	>	#endif // is_mpi
1272	>	int i, l;
1273
1274	+	Atom** the_atoms;
1275	+	Molecule* the_molecules;
1276	+	Exclude** the_excludes;
1277
1208	–	// create the atom and short range interaction arrays
1278
1279	<	Atom::createArrays(info->n_atoms);
1280	<	the_atoms = new Atom*[info->n_atoms];
1212	<	the_molecules = new Molecule[info->n_mol];
1213	<	int molIndex;
1279	>	for (l = 0; l < nInfo; l++){
1280	>	// create the atom and short range interaction arrays
1281
1282	<	// initialize the molecule's stampID's
1282	>	the_atoms = new Atom * [info[l].n_atoms];
1283	>	the_molecules = new Molecule[info[l].n_mol];
1284	>	int molIndex;
1285
1286	+	// initialize the molecule's stampID's
1287	+
1288		#ifdef IS_MPI
1218	–
1289
1290	<	molIndex = 0;
1291	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1292	<
1293	<	if(mol2proc[i] == worldRank ){
1294	<	the_molecules[molIndex].setStampID( molCompType[i] );
1295	<	the_molecules[molIndex].setMyIndex( molIndex );
1296	<	the_molecules[molIndex].setGlobalIndex( i );
1297	<	molIndex++;
1290	>
1291	>	molIndex = 0;
1292	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1293	>	if (mol2proc[i] == worldRank){
1294	>	the_molecules[molIndex].setStampID(molCompType[i]);
1295	>	the_molecules[molIndex].setMyIndex(molIndex);
1296	>	the_molecules[molIndex].setGlobalIndex(i);
1297	>	molIndex++;
1298	>	}
1299		}
1229	–	}
1300
1301		#else // is_mpi
1302	<
1303	<	molIndex = 0;
1304	<	globalAtomIndex = 0;
1305	<	for(i=0; i<n_components; i++){
1306	<	for(j=0; j<components_nmol[i]; j++ ){
1307	<	the_molecules[molIndex].setStampID( i );
1308	<	the_molecules[molIndex].setMyIndex( molIndex );
1309	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1310	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1311	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1312	<	globalAtomIndex++;
1302	>
1303	>	molIndex = 0;
1304	>	globalAtomIndex = 0;
1305	>	for (i = 0; i < n_components; i++){
1306	>	for (j = 0; j < components_nmol[i]; j++){
1307	>	the_molecules[molIndex].setStampID(i);
1308	>	the_molecules[molIndex].setMyIndex(molIndex);
1309	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1310	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1311	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1312	>	globalAtomIndex++;
1313	>	}
1314	>	molIndex++;
1315		}
1244	–	molIndex++;
1316		}
1246	–	}
1247	–
1317
1318	+
1319		#endif // is_mpi
1320
1321
1322	<	if( info->n_SRI ){
1323	<
1324	<	Exclude::createArray(info->n_SRI);
1325	<	the_excludes = new Exclude*[info->n_SRI];
1326	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1327	<	info->globalExcludes = new int;
1328	<	info->n_exclude = info->n_SRI;
1329	<	}
1330	<	else{
1331	<
1332	<	Exclude::createArray( 1 );
1333	<	the_excludes = new Exclude*;
1334	<	the_excludes[0] = new Exclude(0);
1335	<	the_excludes[0]->setPair( 0,0 );
1336	<	info->globalExcludes = new int;
1337	<	info->globalExcludes[0] = 0;
1338	<	info->n_exclude = 0;
1339	<	}
1322	>	if (info[l].n_SRI){
1323	>	Exclude::createArray(info[l].n_SRI);
1324	>	the_excludes = new Exclude * [info[l].n_SRI];
1325	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1326	>	the_excludes[ex] = new Exclude(ex);
1327	>	}
1328	>	info[l].globalExcludes = new int;
1329	>	info[l].n_exclude = info[l].n_SRI;
1330	>	}
1331	>	else{
1332	>	Exclude::createArray(1);
1333	>	the_excludes = new Exclude * ;
1334	>	the_excludes[0] = new Exclude(0);
1335	>	the_excludes[0]->setPair(0, 0);
1336	>	info[l].globalExcludes = new int;
1337	>	info[l].globalExcludes[0] = 0;
1338	>	info[l].n_exclude = 0;
1339	>	}
1340
1341	<	// set the arrays into the SimInfo object
1341	>	// set the arrays into the SimInfo object
1342
1343	<	info->atoms = the_atoms;
1344	<	info->molecules = the_molecules;
1345	<	info->nGlobalExcludes = 0;
1346	<	info->excludes = the_excludes;
1343	>	info[l].atoms = the_atoms;
1344	>	info[l].molecules = the_molecules;
1345	>	info[l].nGlobalExcludes = 0;
1346	>	info[l].excludes = the_excludes;
1347
1348	<	the_ff->setSimInfo( info );
1349	<
1348	>	the_ff->setSimInfo(info);
1349	>	}
1350		}
1351
1352	<	void SimSetup::makeIntegrator( void ){
1352	>	void SimSetup::makeIntegrator(void){
1353	>	int k;
1354
1355	<	NVT*  myNVT = NULL;
1356	<	NPTi* myNPTi = NULL;
1357	<	NPTf* myNPTf = NULL;
1358	<	NPTim* myNPTim = NULL;
1359	<	NPTfm* myNPTfm = NULL;
1355	>	NVE<RealIntegrator>* myNVE = NULL;
1356	>	NVT<RealIntegrator>* myNVT = NULL;
1357	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1358	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1359	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1360	>
1361	>	for (k = 0; k < nInfo; k++){
1362	>	switch (ensembleCase){
1363	>	case NVE_ENS:
1364	>	if (globals->haveZconstraints()){
1365	>	setupZConstraint(info[k]);
1366	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1367	>	}
1368	>	else{
1369	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1370	>	}
1371	>
1372	>	info->the_integrator = myNVE;
1373	>	break;
1374
1375	<	switch( ensembleCase ){
1375	>	case NVT_ENS:
1376	>	if (globals->haveZconstraints()){
1377	>	setupZConstraint(info[k]);
1378	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1379	>	}
1380	>	else
1381	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1382
1383	<	case NVE_ENS:
1293	<	new NVE( info, the_ff );
1294	<	break;
1383	>	myNVT->setTargetTemp(globals->getTargetTemp());
1384
1385	<	case NVT_ENS:
1386	<	myNVT = new NVT( info, the_ff );
1387	<	myNVT->setTargetTemp(globals->getTargetTemp());
1385	>	if (globals->haveTauThermostat())
1386	>	myNVT->setTauThermostat(globals->getTauThermostat());
1387	>	else{
1388	>	sprintf(painCave.errMsg,
1389	>	"SimSetup error: If you use the NVT\n"
1390	>	"    ensemble, you must set tauThermostat.\n");
1391	>	painCave.isFatal = 1;
1392	>	simError();
1393	>	}
1394
1395	<	if (globals->haveTauThermostat())
1396	<	myNVT->setTauThermostat(globals->getTauThermostat());
1395	>	info->the_integrator = myNVT;
1396	>	break;
1397
1398	<	else {
1399	<	sprintf( painCave.errMsg,
1400	<	"SimSetup error: If you use the NVT\n"
1401	<	"    ensemble, you must set tauThermostat.\n");
1402	<	painCave.isFatal = 1;
1403	<	simError();
1404	<	}
1310	<	break;
1398	>	case NPTi_ENS:
1399	>	if (globals->haveZconstraints()){
1400	>	setupZConstraint(info[k]);
1401	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1402	>	}
1403	>	else
1404	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1405
1406	<	case NPTi_ENS:
1313	<	myNPTi = new NPTi( info, the_ff );
1314	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1406	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1407
1408	<	if (globals->haveTargetPressure())
1409	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1410	<	else {
1411	<	sprintf( painCave.errMsg,
1412	<	"SimSetup error: If you use a constant pressure\n"
1413	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1414	<	painCave.isFatal = 1;
1415	<	simError();
1416	<	}
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	<	}
1408	>	if (globals->haveTargetPressure())
1409	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1410	>	else{
1411	>	sprintf(painCave.errMsg,
1412	>	"SimSetup error: If you use a constant pressure\n"
1413	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1414	>	painCave.isFatal = 1;
1415	>	simError();
1416	>	}
1417
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	<	}
1345	<	break;
1418	>	if (globals->haveTauThermostat())
1419	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1420	>	else{
1421	>	sprintf(painCave.errMsg,
1422	>	"SimSetup error: If you use an NPT\n"
1423	>	"    ensemble, you must set tauThermostat.\n");
1424	>	painCave.isFatal = 1;
1425	>	simError();
1426	>	}
1427
1428	<	case NPTf_ENS:
1429	<	myNPTf = new NPTf( info, the_ff );
1430	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1428	>	if (globals->haveTauBarostat())
1429	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1430	>	else{
1431	>	sprintf(painCave.errMsg,
1432	>	"SimSetup error: If you use an NPT\n"
1433	>	"    ensemble, you must set tauBarostat.\n");
1434	>	painCave.isFatal = 1;
1435	>	simError();
1436	>	}
1437
1438	<	if (globals->haveTargetPressure())
1439	<	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	<	}
1438	>	info->the_integrator = myNPTi;
1439	>	break;
1440
1441	<	if( globals->haveTauThermostat() )
1442	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1443	<	else{
1444	<	sprintf( painCave.errMsg,
1445	<	"SimSetup error: If you use an NPT\n"
1446	<	"    ensemble, you must set tauThermostat.\n");
1447	<	painCave.isFatal = 1;
1368	<	simError();
1369	<	}
1441	>	case NPTf_ENS:
1442	>	if (globals->haveZconstraints()){
1443	>	setupZConstraint(info[k]);
1444	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1445	>	}
1446	>	else
1447	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1448
1449	<	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());
1449	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1450
1451	<	if (globals->haveTargetPressure())
1452	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1453	<	else {
1454	<	sprintf( painCave.errMsg,
1455	<	"SimSetup error: If you use a constant pressure\n"
1456	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1457	<	painCave.isFatal = 1;
1458	<	simError();
1459	<	}
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	<	}
1451	>	if (globals->haveTargetPressure())
1452	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1453	>	else{
1454	>	sprintf(painCave.errMsg,
1455	>	"SimSetup error: If you use a constant pressure\n"
1456	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1457	>	painCave.isFatal = 1;
1458	>	simError();
1459	>	}
1460
1461	<	if( globals->haveTauBarostat() )
1462	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1463	<	else{
1464	<	sprintf( painCave.errMsg,
1465	<	"SimSetup error: If you use an NPT\n"
1466	<	"    ensemble, you must set tauBarostat.\n");
1467	<	painCave.isFatal = 1;
1468	<	simError();
1469	<	}
1415	<	break;
1461	>	if (globals->haveTauThermostat())
1462	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1463	>	else{
1464	>	sprintf(painCave.errMsg,
1465	>	"SimSetup error: If you use an NPT\n"
1466	>	"    ensemble, you must set tauThermostat.\n");
1467	>	painCave.isFatal = 1;
1468	>	simError();
1469	>	}
1470
1471	<	case NPTfm_ENS:
1472	<	myNPTfm = new NPTfm( info, the_ff );
1473	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1471	>	if (globals->haveTauBarostat())
1472	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1473	>	else{
1474	>	sprintf(painCave.errMsg,
1475	>	"SimSetup error: If you use an NPT\n"
1476	>	"    ensemble, you must set tauBarostat.\n");
1477	>	painCave.isFatal = 1;
1478	>	simError();
1479	>	}
1480
1481	<	if (globals->haveTargetPressure())
1482	<	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	<	}
1481	>	info->the_integrator = myNPTf;
1482	>	break;
1483
1484	<	if( globals->haveTauBarostat() )
1485	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1486	<	else{
1487	<	sprintf( painCave.errMsg,
1488	<	"SimSetup error: If you use an NPT\n"
1489	<	"    ensemble, you must set tauBarostat.\n");
1490	<	painCave.isFatal = 1;
1448	<	simError();
1449	<	}
1450	<	break;
1484	>	case NPTxyz_ENS:
1485	>	if (globals->haveZconstraints()){
1486	>	setupZConstraint(info[k]);
1487	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1488	>	}
1489	>	else
1490	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1491
1492	<	default:
1453	<	sprintf( painCave.errMsg,
1454	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1455	<	painCave.isFatal = 1;
1456	<	simError();
1457	<	}
1492	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1493
1494	+	if (globals->haveTargetPressure())
1495	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1496	+	else{
1497	+	sprintf(painCave.errMsg,
1498	+	"SimSetup error: If you use a constant pressure\n"
1499	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1500	+	painCave.isFatal = 1;
1501	+	simError();
1502	+	}
1503	+
1504	+	if (globals->haveTauThermostat())
1505	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1506	+	else{
1507	+	sprintf(painCave.errMsg,
1508	+	"SimSetup error: If you use an NPT\n"
1509	+	"    ensemble, you must set tauThermostat.\n");
1510	+	painCave.isFatal = 1;
1511	+	simError();
1512	+	}
1513	+
1514	+	if (globals->haveTauBarostat())
1515	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1516	+	else{
1517	+	sprintf(painCave.errMsg,
1518	+	"SimSetup error: If you use an NPT\n"
1519	+	"    ensemble, you must set tauBarostat.\n");
1520	+	painCave.isFatal = 1;
1521	+	simError();
1522	+	}
1523	+
1524	+	info->the_integrator = myNPTxyz;
1525	+	break;
1526	+
1527	+	default:
1528	+	sprintf(painCave.errMsg,
1529	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1530	+	painCave.isFatal = 1;
1531	+	simError();
1532	+	}
1533	+	}
1534		}
1535
1536	<	void SimSetup::initFortran( void ){
1536	>	void SimSetup::initFortran(void){
1537	>	info[0].refreshSim();
1538
1539	<	info->refreshSim();
1540	<
1465	<	if( !strcmp( info->mixingRule, "standard") ){
1466	<	the_ff->initForceField( LB_MIXING_RULE );
1539	>	if (!strcmp(info[0].mixingRule, "standard")){
1540	>	the_ff->initForceField(LB_MIXING_RULE);
1541		}
1542	<	else if( !strcmp( info->mixingRule, "explicit") ){
1543	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1542	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1543	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1544		}
1545		else{
1546	<	sprintf( painCave.errMsg,
1547	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1474	<	info->mixingRule );
1546	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1547	>	info[0].mixingRule);
1548		painCave.isFatal = 1;
1549		simError();
1550		}
1551
1552
1553		#ifdef IS_MPI
1554	<	strcpy( checkPointMsg,
1482	<	"Successfully intialized the mixingRule for Fortran." );
1554	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1555		MPIcheckPoint();
1556		#endif // is_mpi
1557	+	}
1558
1559	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1560	+	int nZConstraints;
1561	+	ZconStamp** zconStamp;
1562	+
1563	+	if (globals->haveZconstraintTime()){
1564	+	//add sample time of z-constraint  into SimInfo's property list
1565	+	DoubleData* zconsTimeProp = new DoubleData();
1566	+	zconsTimeProp->setID(ZCONSTIME_ID);
1567	+	zconsTimeProp->setData(globals->getZconsTime());
1568	+	theInfo.addProperty(zconsTimeProp);
1569	+	}
1570	+	else{
1571	+	sprintf(painCave.errMsg,
1572	+	"ZConstraint error: If you use an ZConstraint\n"
1573	+	" , you must set sample time.\n");
1574	+	painCave.isFatal = 1;
1575	+	simError();
1576	+	}
1577	+
1578	+	//push zconsTol into siminfo, if user does not specify
1579	+	//value for zconsTol, a default value will be used
1580	+	DoubleData* zconsTol = new DoubleData();
1581	+	zconsTol->setID(ZCONSTOL_ID);
1582	+	if (globals->haveZconsTol()){
1583	+	zconsTol->setData(globals->getZconsTol());
1584	+	}
1585	+	else{
1586	+	double defaultZConsTol = 0.01;
1587	+	sprintf(painCave.errMsg,
1588	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1589	+	" , default value %f is used.\n",
1590	+	defaultZConsTol);
1591	+	painCave.isFatal = 0;
1592	+	simError();
1593	+
1594	+	zconsTol->setData(defaultZConsTol);
1595	+	}
1596	+	theInfo.addProperty(zconsTol);
1597	+
1598	+	//set Force Subtraction Policy
1599	+	StringData* zconsForcePolicy = new StringData();
1600	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1601	+
1602	+	if (globals->haveZconsForcePolicy()){
1603	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1604	+	}
1605	+	else{
1606	+	sprintf(painCave.errMsg,
1607	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1608	+	"PolicyByMass is used\n");
1609	+	painCave.isFatal = 0;
1610	+	simError();
1611	+	zconsForcePolicy->setData("BYMASS");
1612	+	}
1613	+
1614	+	theInfo.addProperty(zconsForcePolicy);
1615	+
1616	+	//Determine the name of ouput file and add it into SimInfo's property list
1617	+	//Be careful, do not use inFileName, since it is a pointer which
1618	+	//point to a string at master node, and slave nodes do not contain that string
1619	+
1620	+	string zconsOutput(theInfo.finalName);
1621	+
1622	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1623	+
1624	+	StringData* zconsFilename = new StringData();
1625	+	zconsFilename->setID(ZCONSFILENAME_ID);
1626	+	zconsFilename->setData(zconsOutput);
1627	+
1628	+	theInfo.addProperty(zconsFilename);
1629	+
1630	+	//setup index, pos and other parameters of z-constraint molecules
1631	+	nZConstraints = globals->getNzConstraints();
1632	+	theInfo.nZconstraints = nZConstraints;
1633	+
1634	+	zconStamp = globals->getZconStamp();
1635	+	ZConsParaItem tempParaItem;
1636	+
1637	+	ZConsParaData* zconsParaData = new ZConsParaData();
1638	+	zconsParaData->setID(ZCONSPARADATA_ID);
1639	+
1640	+	for (int i = 0; i < nZConstraints; i++){
1641	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1642	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1643	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1644	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1645	+
1646	+	zconsParaData->addItem(tempParaItem);
1647	+	}
1648	+
1649	+	//check the uniqueness of index
1650	+	if(!zconsParaData->isIndexUnique()){
1651	+	sprintf(painCave.errMsg,
1652	+	"ZConstraint Error: molIndex is not unique\n");
1653	+	painCave.isFatal = 1;
1654	+	simError();
1655	+	}
1656	+
1657	+	//sort the parameters by index of molecules
1658	+	zconsParaData->sortByIndex();
1659	+
1660	+	//push data into siminfo, therefore, we can retrieve later
1661	+	theInfo.addProperty(zconsParaData);
1662		}

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