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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 701 by tim, Wed Aug 20 14:34:04 2003 UTC vs.
Revision 823 by mmeineke, Mon Oct 27 22:07:48 2003 UTC

#	Line 3 | Line 3
3		#include <iostream>
4		#include <cmath>
5		#include <string>
6	<
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8		#include "ReadWrite.hpp"
9		#include "parse_me.h"
#	Line 21 | Line 21
21		#define NVT_ENS        1
22		#define NPTi_ENS       2
23		#define NPTf_ENS       3
24	<	#define NPTim_ENS      4
25	<	#define NPTfm_ENS      5
24	>	#define NPTxyz_ENS     4
25
26	+
27		#define FF_DUFF 0
28		#define FF_LJ   1
29		#define FF_EAM  2
#	Line 32 | Line 32 | SimSetup::SimSetup(){
32
33		SimSetup::SimSetup(){
34
35	+	initSuspend = false;
36		isInfoArray = 0;
37		nInfo = 1;
38	<
38	>
39		stamps = new MakeStamps();
40		globals = new Globals();
41	<
42	<
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 50 | Line 51 | SimSetup::~SimSetup(){
51		delete globals;
52		}
53
54	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
55	<	info = the_info;
56	<	nInfo = theNinfo;
57	<	isInfoArray = 1;
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 ){
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();
89	<	mpiEventLoop();
90	<
88	>	set_interface_stamps(stamps, globals);
89	>	mpiEventInit();
90	>	MPIcheckPoint();
91	>	mpiEventLoop();
92		}
93
94		#endif // is_mpi
95
96		void SimSetup::createSim(void){
97
97	–	int i, j, k, globalAtomIndex;
98	–
98		// gather all of the information from the Bass file
99
100		gatherInfo();
#	Line 110 | Line 109 | void SimSetup::createSim(void){
109
110		// initialize the system coordinates
111
112	<	if( !isInfoArray ) initSystemCoords();
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 127 | Line 131 | void SimSetup::createSim(void){
131		// initialize the Fortran
132
133		initFortran();
130	–
131	–
132	–
134		}
135
136
137	<	void SimSetup::makeMolecules( void ){
138	<
138	<	int k,l;
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 150 | 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;
162	–
163	–	for(k=0; k<nInfo; k++){
164	–
165	–	the_ff->setSimInfo( &(info[k]) );
162
163	+	for (k = 0; k < nInfo; k++){
164	+	the_ff->setSimInfo(&(info[k]));
165	+
166		atomOffset = 0;
167		excludeOffset = 0;
168	<	for(i=0; i<info[k].n_mol; i++){
170	<
168	>	for (i = 0; i < info[k].n_mol; i++){
169		stampID = info[k].molecules[i].getStampID();
170
171	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
172	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
173	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
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	<
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];
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	<
186	>
187		// make the Atoms
188	<
189	<	for(j=0; j<molInfo.nAtoms; j++){
190	<
191	<	currentAtom = comp_stamps[stampID]->getAtom( j );
192	<	if( currentAtom->haveOrientation() ){
193	<
194	<	dAtom = new DirectionalAtom( (j + atomOffset),
195	<	info[k].getConfiguration() );
196	<	info[k].n_oriented++;
197	<	molInfo.myAtoms[j] = dAtom;
198	<
199	<	ux = currentAtom->getOrntX();
200	<	uy = currentAtom->getOrntY();
201	<	uz = currentAtom->getOrntZ();
202	<
203	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
204	<
205	<	u = sqrt( uSqr );
206	<	ux = ux / u;
207	<	uy = uy / u;
208	<	uz = uz / u;
209	<
210	<	dAtom->setSUx( ux );
211	<	dAtom->setSUy( uy );
212	<	dAtom->setSUz( uz );
213	<	}
214	<	else{
215	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
216	<	info[k].getConfiguration() );
217	<	}
220	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221	<
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		}
224	<
225	<	// make the bonds
226	<	for(j=0; j<molInfo.nBonds; j++){
227	<
228	<	currentBond = comp_stamps[stampID]->getBond( j );
229	<	theBonds[j].a = currentBond->getA() + atomOffset;
230	<	theBonds[j].b = currentBond->getB() + atomOffset;
231	<
232	<	exI = theBonds[j].a;
233	<	exJ = theBonds[j].b;
234	<
235	<	// exclude_I must always be the smaller of the pair
236	<	if( exI > exJ ){
237	<	tempEx = exI;
238	<	exI = exJ;
239	<	exJ = tempEx;
244	<	}
224	>
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	>	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 = 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 );
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	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
248	>
249	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
250		#endif  //is_mpi
251		}
252		excludeOffset += molInfo.nBonds;
253	<
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();
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	<
303	<	else{
304	<
305	<	sprintf( painCave.errMsg,
306	<	"SimSetup Error: unhandled bend assignment:\n"
307	<	"    -->%s in Bend[%d] in %s\n",
308	<	current_extra->getlhs(),
309	<	j, comp_stamps[stampID]->getID() );
310	<	painCave.isFatal = 1;
311	<	simError();
312	<	}
313	<
314	<	current_extra = current_extra->getNext();
315	<	}
316	<	}
314	<
315	<	if( !theBends[j].isGhost ){
316	<
317	<	exI = theBends[j].a;
318	<	exJ = theBends[j].c;
319	<	}
320	<	else{
321	<
322	<	exI = theBends[j].a;
323	<	exJ = theBends[j].b;
324	<	}
325	<
326	<	// exclude_I must always be the smaller of the pair
327	<	if( exI > exJ ){
328	<	tempEx = exI;
329	<	exI = exJ;
330	<	exJ = tempEx;
331	<	}
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 = 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 );
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	<	info[k].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;
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;
336	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
337	<
338	<	exI = theTorsions[j].a;
339	<	exJ = theTorsions[j].d;
340	<
341	<	// exclude_I must always be the smaller of the pair
342	<	if( exI > exJ ){
343	<	tempEx = exI;
344	<	exI = exJ;
345	<	exJ = tempEx;
361	<	}
329	>
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	>	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 = 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 );
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	<	info[k].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;
358	<
359	<
358	>
359	>
360		// send the arrays off to the forceField for init.
377	–
378	–	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
379	–	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
380	–	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
381	–	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
382	–
383	–
384	–	info[k].molecules[i].initialize( molInfo );
361
362	<
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	>
368	>
369	>	info[k].molecules[i].initialize(molInfo);
370	>
371	>
372		atomOffset += molInfo.nAtoms;
373		delete[] theBonds;
374		delete[] theBends;
375		delete[] theTorsions;
376		}
377		}
378	<
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	<
383	>
384		// clean up the forcefield
385
386		the_ff->calcRcut();
387		the_ff->cleanMe();
403	–
388		}
389
390	<	void SimSetup::initFromBass( void ){
407	<
390	>	void SimSetup::initFromBass(void){
391		int i, j, k;
392		int n_cells;
393		double cellx, celly, cellz;
#	Line 418 | Line 401 | void SimSetup::initFromBass( void ){
401		vel[1] = 0.0;
402		vel[2] = 0.0;
403
404	<	temp1 = (double)tot_nmol / 4.0;
405	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
406	<	temp3 = ceil( temp2 );
404	>	temp1 = (double) tot_nmol / 4.0;
405	>	temp2 = pow(temp1, (1.0 / 3.0));
406	>	temp3 = ceil(temp2);
407
408	<	have_extra =0;
409	<	if( temp2 < temp3 ){ // we have a non-complete lattice
410	<	have_extra =1;
408	>	have_extra = 0;
409	>	if (temp2 < temp3){
410	>	// we have a non-complete lattice
411	>	have_extra = 1;
412
413	<	n_cells = (int)temp3 - 1;
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 );
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" );
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;
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;
#	Line 454 | 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,
462	<	j * celly,
463	<	k * cellz );
446	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
447
448	<	makeElement( i * cellx + 0.5 * cellx,
466	<	j * celly + 0.5 * celly,
467	<	k * cellz );
448	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
449
450	<	makeElement( i * cellx,
470	<	j * celly + 0.5 * celly,
471	<	k * cellz + 0.5 * cellz );
472	<
473	<	makeElement( i * cellx + 0.5 * cellx,
474	<	j * celly,
475	<	k * cellz + 0.5 * cellz );
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	<	}
494	<	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++ ){
482	<
483	<	makeElement( i * cellx,
484	<	j * celly,
485	<	k * cellz );
501	<	done = ( current_mol >= tot_nmol );
502	<
503	<	if( !done && n_per_extra > 1 ){
504	<	makeElement( i * cellx + 0.5 * cellx,
505	<	j * celly + 0.5 * celly,
506	<	k * cellz );
507	<	done = ( current_mol >= tot_nmol );
508	<	}
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	<	if( !done && n_per_extra > 2){
488	<	makeElement( i * cellx,
489	<	j * celly + 0.5 * celly,
490	<	k * cellz + 0.5 * cellz );
491	<	done = ( current_mol >= tot_nmol );
492	<	}
516	<
517	<	if( !done && n_per_extra > 3){
518	<	makeElement( i * cellx + 0.5 * cellx,
519	<	j * celly,
520	<	k * cellz + 0.5 * cellz );
521	<	done = ( current_mol >= tot_nmol );
522	<	}
523	<	}
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	<	for( i=0; i<info[0].n_atoms; i++ ){
498	<	info[0].atoms[i]->setVel( vel );
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 ){
534	<
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",
550	<	comp_stamps[current_comp]->getID(),
551	<	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	<
521	>
522		pos[0] = x + current_atom->getPosX();
523		pos[1] = y + current_atom->getPosY();
524		pos[2] = z + current_atom->getPosZ();
559	–
560	–	info[0].atoms[current_atom_ndx]->setPos( pos );
525
526	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
526	>	info[0].atoms[current_atom_ndx]->setPos(pos);
527
528	<	dAtom = (DirectionalAtom *)info[0].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 575 | 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 584 | 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] ){
588	<
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
565		// set the easy ones first
566
567	<	for( i=0; i<nInfo; i++){
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();
#	Line 610 | Line 574 | void SimSetup::gatherInfo( void ){
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;
581	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
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;
623	<	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		}
647	–
648	–	for(i=0; i<nInfo; i++){
649	–
650	–	strcpy( info[i].ensemble, ensemble );
624
625	+	for (i = 0; i < nInfo; i++){
626	+	strcpy(info[i].ensemble, ensemble);
627	+
628		// get the mixing rule
629
630	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
630	>	strcpy(info[i].mixingRule, globals->getMixingRule());
631		info[i].usePBC = globals->getPBC();
632		}
633	<
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;
677	<	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 682 | 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
696	–
697	–	for(i=0; i<nInfo; i++){
671
672	<	if( globals->haveSampleTime() ){
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;
#	Line 706 | Line 680 | void SimSetup::gatherInfo( void ){
680		info[i].statusTime = info[i].sampleTime;
681		info[i].thermalTime = info[i].sampleTime;
682		}
683	<
684	<	if( globals->haveStatusTime() ){
683	>
684	>	if (globals->haveStatusTime()){
685		info[i].statusTime = globals->getStatusTime();
686		}
687	<
688	<	if( globals->haveThermalTime() ){
687	>
688	>	if (globals->haveThermalTime()){
689		info[i].thermalTime = globals->getThermalTime();
690		}
691
692	+	info[i].resetIntegrator = 0;
693	+	if( globals->haveResetTime() ){
694	+	info[i].resetTime = globals->getResetTime();
695	+	info[i].resetIntegrator = 1;
696	+	}
697	+
698		// check for the temperature set flag
699
700	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
701	<
700	>	if (globals->haveTempSet())
701	>	info[i].setTemp = globals->getTempSet();
702	>
703		// get some of the tricky things that may still be in the globals
704	<
704	>
705		double boxVector[3];
706	<	if( globals->haveBox() ){
706	>	if (globals->haveBox()){
707		boxVector[0] = globals->getBox();
708		boxVector[1] = globals->getBox();
709		boxVector[2] = globals->getBox();
710	<
711	<	info[i].setBox( boxVector );
710	>
711	>	info[i].setBox(boxVector);
712		}
713	<	else if( globals->haveDensity() ){
733	<
713	>	else if (globals->haveDensity()){
714		double vol;
715	<	vol = (double)tot_nmol / globals->getDensity();
716	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
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	<	info[i].setBox( boxVector );
721	<	}
719	>
720	>	info[i].setBox(boxVector);
721	>	}
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();
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	<	if( !globals->haveBoxY() ){
732	<	sprintf( painCave.errMsg,
733	<	"SimSetup error, no periodic BoxY size given.\n" );
734	<	painCave.isFatal = 1;
735	<	simError();
756	<	}
757	<	boxVector[1] = globals->getBoxY();
758	<
759	<	if( !globals->haveBoxZ() ){
760	<	sprintf( painCave.errMsg,
761	<	"SimSetup error, no periodic BoxZ size given.\n" );
762	<	painCave.isFatal = 1;
763	<	simError();
730	>
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();
766	–
767	–	info[i].setBox( boxVector );
768	–	}
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
776	–
795		}
796
797
798	<	void SimSetup::finalInfoCheck( void ){
798	>	void SimSetup::finalInfoCheck(void){
799		int index;
800		int usesDipoles;
801		int i;
802
803	<	for(i=0; i<nInfo; i++){
803	>	for (i = 0; i < nInfo; i++){
804		// check electrostatic parameters
805	<
805	>
806		index = 0;
807		usesDipoles = 0;
808	<	while( (index < info[i].n_atoms) && !usesDipoles ){
808	>	while ((index < info[i].n_atoms) && !usesDipoles){
809		usesDipoles = (info[i].atoms[index])->hasDipole();
810		index++;
811		}
812	<
812	>
813		#ifdef IS_MPI
814		int myUse = usesDipoles;
815	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
815	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816		#endif //is_mpi
817	<
817	>
818		double theEcr, theEst;
819	<
820	<	if (globals->getUseRF() ) {
819	>
820	>	if (globals->getUseRF()){
821		info[i].useReactionField = 1;
822	<
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) smallest = info[i].boxL[1];
833	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
834	<	theEcr = 0.5 * smallest;
835	<	} else {
836	<	theEcr = globals->getECR();
822	>
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() ){
822	<	sprintf( painCave.errMsg,
823	<	"SimSetup Warning: using default value of 0.05 * the "
824	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
825	<	);
826	<	painCave.isFatal = 0;
827	<	simError();
828	<	theEst = 0.05 * theEcr;
829	<	} else {
830	<	theEst= globals->getEST();
838	>	else{
839	>	theEcr = globals->getECR();
840		}
841	<
842	<	info[i].setEcr( theEcr, theEst );
843	<
844	<	if(!globals->haveDielectric() ){
845	<	sprintf( painCave.errMsg,
846	<	"SimSetup Error: You are trying to use Reaction Field without"
847	<	"setting a dielectric constant!\n"
848	<	);
840	<	painCave.isFatal = 1;
841	<	simError();
841	>
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	<	info[i].dielectric = globals->getDielectric();
851	<	}
845	<	else {
846	<	if (usesDipoles) {
847	<
848	<	if( !globals->haveECR() ){
849	<	sprintf( painCave.errMsg,
850	<	"SimSetup Warning: using default value of 1/2 the smallest "
851	<	"box length for the electrostaticCutoffRadius.\n"
852	<	"I hope you have a very fast processor!\n");
853	<	painCave.isFatal = 0;
854	<	simError();
855	<	double smallest;
856	<	smallest = info[i].boxL[0];
857	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
858	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
859	<	theEcr = 0.5 * smallest;
860	<	} else {
861	<	theEcr = globals->getECR();
862	<	}
863	<
864	<	if( !globals->haveEST() ){
865	<	sprintf( painCave.errMsg,
866	<	"SimSetup Warning: using default value of 0.05 * the "
867	<	"electrostaticCutoffRadius for the "
868	<	"electrostaticSkinThickness\n"
869	<	);
870	<	painCave.isFatal = 0;
871	<	simError();
872	<	theEst = 0.05 * theEcr;
873	<	} else {
874	<	theEst= globals->getEST();
875	<	}
876	<
877	<	info[i].setEcr( theEcr, theEst );
850	>	else{
851	>	theEst = globals->getEST();
852		}
853	<	}
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	>	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
886	–
908		}
909
910	<	void SimSetup::initSystemCoords( void ){
910	>	void SimSetup::initSystemCoords(void){
911		int i;
912	<
912	>
913		char* inName;
914
915	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
916
917	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
918	<
919	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
920	<
899	<	if( globals->haveInitialConfig() ){
900	<
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		inName = globals->getInitialConfig();
926	<	double* tempDouble = new double[1000000];
907	<	fileInit = new InitializeFromFile( inName );
926	>	fileInit = new InitializeFromFile(inName);
927		#ifdef IS_MPI
928	<	}else fileInit = new InitializeFromFile( NULL );
928	>	}
929	>	else
930	>	fileInit = new InitializeFromFile(NULL);
931		#endif
932	<	fileInit->readInit( info ); // default velocities on
933	<
932	>	fileInit->readInit(info); // default velocities on
933	>
934		delete fileInit;
935		}
936		else{
916	–
937		#ifdef IS_MPI
938	<
938	>
939		// no init from bass
940	<
941	<	sprintf( painCave.errMsg,
942	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
943	<	painCave.isFatal;
940	>
941	>	sprintf(painCave.errMsg,
942	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
943	>	painCave.isFatal = 1;;
944		simError();
945	<
945	>
946		#else
947	<
947	>
948		initFromBass();
949	<
950	<
949	>
950	>
951		#endif
952		}
953	<
953	>
954		#ifdef IS_MPI
955	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
955	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
956		MPIcheckPoint();
957		#endif // is_mpi
938	–
958		}
959
960
961	<	void SimSetup::makeOutNames( void ){
943	<
961	>	void SimSetup::makeOutNames(void){
962		int k;
963
946	–
947	–	for(k=0; k<nInfo; k++){
964
965	+	for (k = 0; k < nInfo; k++){
966		#ifdef IS_MPI
967	<	if( worldRank == 0 ){
967	>	if (worldRank == 0){
968		#endif // is_mpi
969	<
970	<	if( globals->haveFinalConfig() ){
971	<	strcpy( info[k].finalName, globals->getFinalConfig() );
969	>
970	>	if (globals->haveFinalConfig()){
971	>	strcpy(info[k].finalName, globals->getFinalConfig());
972		}
973		else{
974	<	strcpy( info[k].finalName, inFileName );
975	<	char* endTest;
976	<	int nameLength = strlen( info[k].finalName );
977	<	endTest = &(info[k].finalName[nameLength - 5]);
978	<	if( !strcmp( endTest, ".bass" ) ){
979	<	strcpy( endTest, ".eor" );
980	<	}
981	<	else if( !strcmp( endTest, ".BASS" ) ){
982	<	strcpy( endTest, ".eor" );
983	<	}
984	<	else{
985	<	endTest = &(info[k].finalName[nameLength - 4]);
986	<	if( !strcmp( endTest, ".bss" ) ){
987	<	strcpy( endTest, ".eor" );
988	<	}
989	<	else if( !strcmp( endTest, ".mdl" ) ){
990	<	strcpy( endTest, ".eor" );
991	<	}
992	<	else{
993	<	strcat( info[k].finalName, ".eor" );
994	<	}
995	<	}
974	>	strcpy(info[k].finalName, inFileName);
975	>	char* endTest;
976	>	int nameLength = strlen(info[k].finalName);
977	>	endTest = &(info[k].finalName[nameLength - 5]);
978	>	if (!strcmp(endTest, ".bass")){
979	>	strcpy(endTest, ".eor");
980	>	}
981	>	else if (!strcmp(endTest, ".BASS")){
982	>	strcpy(endTest, ".eor");
983	>	}
984	>	else{
985	>	endTest = &(info[k].finalName[nameLength - 4]);
986	>	if (!strcmp(endTest, ".bss")){
987	>	strcpy(endTest, ".eor");
988	>	}
989	>	else if (!strcmp(endTest, ".mdl")){
990	>	strcpy(endTest, ".eor");
991	>	}
992	>	else{
993	>	strcat(info[k].finalName, ".eor");
994	>	}
995	>	}
996		}
997	<
997	>
998		// make the sample and status out names
999	<
1000	<	strcpy( info[k].sampleName, inFileName );
999	>
1000	>	strcpy(info[k].sampleName, inFileName);
1001		char* endTest;
1002	<	int nameLength = strlen( info[k].sampleName );
1002	>	int nameLength = strlen(info[k].sampleName);
1003		endTest = &(info[k].sampleName[nameLength - 5]);
1004	<	if( !strcmp( endTest, ".bass" ) ){
1005	<	strcpy( endTest, ".dump" );
1004	>	if (!strcmp(endTest, ".bass")){
1005	>	strcpy(endTest, ".dump");
1006		}
1007	<	else if( !strcmp( endTest, ".BASS" ) ){
1008	<	strcpy( endTest, ".dump" );
1007	>	else if (!strcmp(endTest, ".BASS")){
1008	>	strcpy(endTest, ".dump");
1009		}
1010		else{
1011	<	endTest = &(info[k].sampleName[nameLength - 4]);
1012	<	if( !strcmp( endTest, ".bss" ) ){
1013	<	strcpy( endTest, ".dump" );
1014	<	}
1015	<	else if( !strcmp( endTest, ".mdl" ) ){
1016	<	strcpy( endTest, ".dump" );
1017	<	}
1018	<	else{
1019	<	strcat( info[k].sampleName, ".dump" );
1020	<	}
1011	>	endTest = &(info[k].sampleName[nameLength - 4]);
1012	>	if (!strcmp(endTest, ".bss")){
1013	>	strcpy(endTest, ".dump");
1014	>	}
1015	>	else if (!strcmp(endTest, ".mdl")){
1016	>	strcpy(endTest, ".dump");
1017	>	}
1018	>	else{
1019	>	strcat(info[k].sampleName, ".dump");
1020	>	}
1021		}
1022	<
1023	<	strcpy( info[k].statusName, inFileName );
1024	<	nameLength = strlen( info[k].statusName );
1022	>
1023	>	strcpy(info[k].statusName, inFileName);
1024	>	nameLength = strlen(info[k].statusName);
1025		endTest = &(info[k].statusName[nameLength - 5]);
1026	<	if( !strcmp( endTest, ".bass" ) ){
1027	<	strcpy( endTest, ".stat" );
1026	>	if (!strcmp(endTest, ".bass")){
1027	>	strcpy(endTest, ".stat");
1028		}
1029	<	else if( !strcmp( endTest, ".BASS" ) ){
1030	<	strcpy( endTest, ".stat" );
1029	>	else if (!strcmp(endTest, ".BASS")){
1030	>	strcpy(endTest, ".stat");
1031		}
1032		else{
1033	<	endTest = &(info[k].statusName[nameLength - 4]);
1034	<	if( !strcmp( endTest, ".bss" ) ){
1035	<	strcpy( endTest, ".stat" );
1036	<	}
1037	<	else if( !strcmp( endTest, ".mdl" ) ){
1038	<	strcpy( endTest, ".stat" );
1039	<	}
1040	<	else{
1041	<	strcat( info[k].statusName, ".stat" );
1042	<	}
1033	>	endTest = &(info[k].statusName[nameLength - 4]);
1034	>	if (!strcmp(endTest, ".bss")){
1035	>	strcpy(endTest, ".stat");
1036	>	}
1037	>	else if (!strcmp(endTest, ".mdl")){
1038	>	strcpy(endTest, ".stat");
1039	>	}
1040	>	else{
1041	>	strcat(info[k].statusName, ".stat");
1042	>	}
1043		}
1044	<
1044	>
1045		#ifdef IS_MPI
1046	+
1047		}
1048		#endif // is_mpi
1049		}
1050		}
1051
1052
1053	<	void SimSetup::sysObjectsCreation( void ){
1054	<
1055	<	int i,k;
1038	<
1053	>	void SimSetup::sysObjectsCreation(void){
1054	>	int i, k;
1055	>
1056		// create the forceField
1057
1058		createFF();
#	Line 1050 | Line 1067 | void SimSetup::sysObjectsCreation( void ){
1067
1068		#ifdef IS_MPI
1069		// divide the molecules among the processors
1070	<
1070	>
1071		mpiMolDivide();
1072		#endif //is_mpi
1073	<
1073	>
1074		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1075	<
1075	>
1076		makeSysArrays();
1077
1078		// make and initialize the molecules (all but atomic coordinates)
1079	<
1079	>
1080		makeMolecules();
1081	<
1082	<	for(k=0; k<nInfo; k++){
1081	>
1082	>	for (k = 0; k < nInfo; k++){
1083		info[k].identArray = new int[info[k].n_atoms];
1084	<	for(i=0; i<info[k].n_atoms; i++){
1084	>	for (i = 0; i < info[k].n_atoms; i++){
1085		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1086		}
1087		}
1088		}
1089
1090
1091	<	void SimSetup::createFF( void ){
1091	>	void SimSetup::createFF(void){
1092	>	switch (ffCase){
1093	>	case FF_DUFF:
1094	>	the_ff = new DUFF();
1095	>	break;
1096
1097	<	switch( ffCase ){
1097	>	case FF_LJ:
1098	>	the_ff = new LJFF();
1099	>	break;
1100
1101	<	case FF_DUFF:
1102	<	the_ff = new DUFF();
1103	<	break;
1101	>	case FF_EAM:
1102	>	the_ff = new EAM_FF();
1103	>	break;
1104
1105	<	case FF_LJ:
1106	<	the_ff = new LJFF();
1107	<	break;
1108	<
1109	<	case FF_EAM:
1087	<	the_ff = new EAM_FF();
1088	<	break;
1089	<
1090	<	default:
1091	<	sprintf( painCave.errMsg,
1092	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1093	<	painCave.isFatal = 1;
1094	<	simError();
1105	>	default:
1106	>	sprintf(painCave.errMsg,
1107	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1108	>	painCave.isFatal = 1;
1109	>	simError();
1110		}
1111
1112		#ifdef IS_MPI
1113	<	strcpy( checkPointMsg, "ForceField creation successful" );
1113	>	strcpy(checkPointMsg, "ForceField creation successful");
1114		MPIcheckPoint();
1115		#endif // is_mpi
1101	–
1116		}
1117
1118
1119	<	void SimSetup::compList( void ){
1106	<
1119	>	void SimSetup::compList(void){
1120		int i;
1121		char* id;
1122		LinkedMolStamp* headStamp = new LinkedMolStamp();
1123		LinkedMolStamp* currentStamp = NULL;
1124	<	comp_stamps = new MoleculeStamp*[n_components];
1125	<
1124	>	comp_stamps = new MoleculeStamp * [n_components];
1125	>
1126		// make an array of molecule stamps that match the components used.
1127		// also extract the used stamps out into a separate linked list
1128	<
1129	<	for(i=0; i<nInfo; i++){
1128	>
1129	>	for (i = 0; i < nInfo; i++){
1130		info[i].nComponents = n_components;
1131		info[i].componentsNmol = components_nmol;
1132		info[i].compStamps = comp_stamps;
1133		info[i].headStamp = headStamp;
1134		}
1122	–
1135
1124	–	for( i=0; i<n_components; i++ ){
1136
1137	+	for (i = 0; i < n_components; i++){
1138		id = the_components[i]->getType();
1139		comp_stamps[i] = NULL;
1140	<
1140	>
1141		// check to make sure the component isn't already in the list
1142
1143	<	comp_stamps[i] = headStamp->match( id );
1144	<	if( comp_stamps[i] == NULL ){
1133	<
1143	>	comp_stamps[i] = headStamp->match(id);
1144	>	if (comp_stamps[i] == NULL){
1145		// extract the component from the list;
1146	<
1147	<	currentStamp = stamps->extractMolStamp( id );
1148	<	if( currentStamp == NULL ){
1149	<	sprintf( painCave.errMsg,
1150	<	"SimSetup error: Component \"%s\" was not found in the "
1151	<	"list of declared molecules\n",
1152	<	id );
1153	<	painCave.isFatal = 1;
1154	<	simError();
1146	>
1147	>	currentStamp = stamps->extractMolStamp(id);
1148	>	if (currentStamp == NULL){
1149	>	sprintf(painCave.errMsg,
1150	>	"SimSetup error: Component \"%s\" was not found in the "
1151	>	"list of declared molecules\n",
1152	>	id);
1153	>	painCave.isFatal = 1;
1154	>	simError();
1155		}
1156	<
1157	<	headStamp->add( currentStamp );
1158	<	comp_stamps[i] = headStamp->match( id );
1156	>
1157	>	headStamp->add(currentStamp);
1158	>	comp_stamps[i] = headStamp->match(id);
1159		}
1160		}
1161
1162		#ifdef IS_MPI
1163	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1163	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1164		MPIcheckPoint();
1165		#endif // is_mpi
1166	+	}
1167
1168	+	void SimSetup::calcSysValues(void){
1169	+	int i;
1170
1171	<	}
1171	>	int* molMembershipArray;
1172
1159	–	void SimSetup::calcSysValues( void ){
1160	–	int i, j, k;
1161	–
1162	–	int *molMembershipArray;
1163	–
1173		tot_atoms = 0;
1174		tot_bonds = 0;
1175		tot_bends = 0;
1176		tot_torsions = 0;
1177	<	for( i=0; i<n_components; i++ ){
1178	<
1179	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1180	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1172	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1177	>	for (i = 0; i < n_components; i++){
1178	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1179	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1180	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1181		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1182		}
1183	<
1183	>
1184		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1185		molMembershipArray = new int[tot_atoms];
1186	<
1187	<	for(i=0; i<nInfo; i++){
1186	>
1187	>	for (i = 0; i < nInfo; i++){
1188		info[i].n_atoms = tot_atoms;
1189		info[i].n_bonds = tot_bonds;
1190		info[i].n_bends = tot_bends;
1191		info[i].n_torsions = tot_torsions;
1192		info[i].n_SRI = tot_SRI;
1193		info[i].n_mol = tot_nmol;
1194	<
1194	>
1195		info[i].molMembershipArray = molMembershipArray;
1196	<	}
1196	>	}
1197		}
1198
1199		#ifdef IS_MPI
1200
1201	<	void SimSetup::mpiMolDivide( void ){
1194	<
1201	>	void SimSetup::mpiMolDivide(void){
1202		int i, j, k;
1203		int localMol, allMol;
1204		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1205
1206	<	mpiSim = new mpiSimulation( info );
1207	<
1206	>	mpiSim = new mpiSimulation(info);
1207	>
1208		globalIndex = mpiSim->divideLabor();
1209
1210		// set up the local variables
1211	<
1211	>
1212		mol2proc = mpiSim->getMolToProcMap();
1213		molCompType = mpiSim->getMolComponentType();
1214	<
1214	>
1215		allMol = 0;
1216		localMol = 0;
1217		local_atoms = 0;
#	Line 1214 | Line 1221 | void SimSetup::mpiMolDivide( void ){
1221		globalAtomIndex = 0;
1222
1223
1224	<	for( i=0; i<n_components; i++ ){
1225	<
1226	<	for( j=0; j<components_nmol[i]; j++ ){
1227	<
1228	<	if( mol2proc[allMol] == worldRank ){
1229	<
1230	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1231	<	local_bonds +=    comp_stamps[i]->getNBonds();
1225	<	local_bends +=    comp_stamps[i]->getNBends();
1226	<	local_torsions += comp_stamps[i]->getNTorsions();
1227	<	localMol++;
1224	>	for (i = 0; i < n_components; i++){
1225	>	for (j = 0; j < components_nmol[i]; j++){
1226	>	if (mol2proc[allMol] == worldRank){
1227	>	local_atoms += comp_stamps[i]->getNAtoms();
1228	>	local_bonds += comp_stamps[i]->getNBonds();
1229	>	local_bends += comp_stamps[i]->getNBends();
1230	>	local_torsions += comp_stamps[i]->getNTorsions();
1231	>	localMol++;
1232		}
1233	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1233	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1234		info[0].molMembershipArray[globalAtomIndex] = allMol;
1235		globalAtomIndex++;
1236		}
1237
1238	<	allMol++;
1238	>	allMol++;
1239		}
1240		}
1241		local_SRI = local_bonds + local_bends + local_torsions;
1242	<
1242	>
1243		info[0].n_atoms = mpiSim->getMyNlocal();
1244	<
1245	<	if( local_atoms != info[0].n_atoms ){
1246	<	sprintf( painCave.errMsg,
1247	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1248	<	" localAtom (%d) are not equal.\n",
1249	<	info[0].n_atoms,
1246	<	local_atoms );
1244	>
1245	>	if (local_atoms != info[0].n_atoms){
1246	>	sprintf(painCave.errMsg,
1247	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1248	>	" localAtom (%d) are not equal.\n",
1249	>	info[0].n_atoms, local_atoms);
1250		painCave.isFatal = 1;
1251		simError();
1252		}
#	Line 1254 | Line 1257 | void SimSetup::mpiMolDivide( void ){
1257		info[0].n_SRI = local_SRI;
1258		info[0].n_mol = localMol;
1259
1260	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1260	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1261		MPIcheckPoint();
1262		}
1263	<
1263	>
1264		#endif // is_mpi
1265
1266
1267	<	void SimSetup::makeSysArrays( void ){
1268	<	int i, j, k, l;
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
1278	<
1279	<	for(l=0; l<nInfo; l++){
1273	<
1278	>
1279	>	for (l = 0; l < nInfo; l++){
1280		// create the atom and short range interaction arrays
1281	<
1282	<	the_atoms = new Atom*[info[l].n_atoms];
1281	>
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	<
1287	>
1288		#ifdef IS_MPI
1289	<
1290	<
1289	>
1290	>
1291		molIndex = 0;
1292	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1293	<
1294	<	if(mol2proc[i] == worldRank ){
1295	<	the_molecules[molIndex].setStampID( molCompType[i] );
1296	<	the_molecules[molIndex].setMyIndex( molIndex );
1297	<	the_molecules[molIndex].setGlobalIndex( i );
1292	<	molIndex++;
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		}
1300	<
1300	>
1301		#else // is_mpi
1302	<
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++;
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		}
1316		}
1317	<
1318	<
1317	>
1318	>
1319		#endif // is_mpi
1320
1321
1322	<	if( info[l].n_SRI ){
1318	<
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);
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	<
1333	<	Exclude::createArray( 1 );
1330	<	the_excludes = new Exclude*;
1332	>	Exclude::createArray(1);
1333	>	the_excludes = new Exclude * ;
1334		the_excludes[0] = new Exclude(0);
1335	<	the_excludes[0]->setPair( 0,0 );
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;
#	Line 1342 | Line 1345 | void SimSetup::makeSysArrays( void ){
1345		info[l].nGlobalExcludes = 0;
1346		info[l].excludes = the_excludes;
1347
1348	<	the_ff->setSimInfo( info );
1346	<
1348	>	the_ff->setSimInfo(info);
1349		}
1350		}
1351
1352	<	void SimSetup::makeIntegrator( void ){
1351	<
1352	>	void SimSetup::makeIntegrator(void){
1353		int k;
1354
1355	<	NVT<RealIntegrator>*  myNVT = NULL;
1356	<	NPTi<RealIntegrator>* myNPTi = NULL;
1357	<	NPTf<RealIntegrator>* myNPTf = NULL;
1358	<	NPTim<RealIntegrator>* myNPTim = NULL;
1359	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1360	<
1361	<	for(k=0; k<nInfo; k++){
1362	<
1363	<	switch( ensembleCase ){
1364	<
1365	<	case NVE_ENS:
1366	<	if (globals->haveZconstraints()){
1367	<	setupZConstraint(info[k]);
1368	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1369	<	}
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	<	else
1376	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1377	<	break;
1378	<
1379	<	case NVT_ENS:
1380	<	if (globals->haveZconstraints()){
1381	<	setupZConstraint(info[k]);
1377	<	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1378	<	}
1379	<	else
1380	<	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
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		myNVT->setTargetTemp(globals->getTargetTemp());
1384	<
1385	<	if (globals->haveTauThermostat())
1384	>
1385	>	if (globals->haveTauThermostat())
1386		myNVT->setTauThermostat(globals->getTauThermostat());
1387	<
1388	<	else {
1389	<	sprintf( painCave.errMsg,
1390	<	"SimSetup error: If you use the NVT\n"
1390	<	"    ensemble, you must set tauThermostat.\n");
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	+	info->the_integrator = myNVT;
1396		break;
1395	–
1396	–	case NPTi_ENS:
1397	–	if (globals->haveZconstraints()){
1398	–	setupZConstraint(info[k]);
1399	–	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1400	–	}
1401	–	else
1402	–	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1397
1398	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1399	<
1400	<	if (globals->haveTargetPressure())
1401	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1402	<	else {
1403	<	sprintf( painCave.errMsg,
1404	<	"SimSetup error: If you use a constant pressure\n"
1411	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1412	<	painCave.isFatal = 1;
1413	<	simError();
1414	<	}
1415	<
1416	<	if( globals->haveTauThermostat() )
1417	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1418	<	else{
1419	<	sprintf( painCave.errMsg,
1420	<	"SimSetup error: If you use an NPT\n"
1421	<	"    ensemble, you must set tauThermostat.\n");
1422	<	painCave.isFatal = 1;
1423	<	simError();
1424	<	}
1425	<
1426	<	if( globals->haveTauBarostat() )
1427	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1428	<	else{
1429	<	sprintf( painCave.errMsg,
1430	<	"SimSetup error: If you use an NPT\n"
1431	<	"    ensemble, you must set tauBarostat.\n");
1432	<	painCave.isFatal = 1;
1433	<	simError();
1434	<	}
1435	<	break;
1436	<
1437	<	case NPTf_ENS:
1438	<	if (globals->haveZconstraints()){
1439	<	setupZConstraint(info[k]);
1440	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1441	<	}
1442	<	else
1443	<	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
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	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1446	<
1447	<	if (globals->haveTargetPressure())
1448	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1449	<	else {
1450	<	sprintf( painCave.errMsg,
1451	<	"SimSetup error: If you use a constant pressure\n"
1452	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1453	<	painCave.isFatal = 1;
1454	<	simError();
1455	<	}
1456	<
1457	<	if( globals->haveTauThermostat() )
1458	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1459	<	else{
1460	<	sprintf( painCave.errMsg,
1461	<	"SimSetup error: If you use an NPT\n"
1462	<	"    ensemble, you must set tauThermostat.\n");
1463	<	painCave.isFatal = 1;
1464	<	simError();
1465	<	}
1466	<
1467	<	if( globals->haveTauBarostat() )
1468	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1469	<	else{
1470	<	sprintf( painCave.errMsg,
1471	<	"SimSetup error: If you use an NPT\n"
1472	<	"    ensemble, you must set tauBarostat.\n");
1473	<	painCave.isFatal = 1;
1474	<	simError();
1475	<	}
1476	<	break;
1477	<
1478	<	case NPTim_ENS:
1479	<	if (globals->haveZconstraints()){
1480	<	setupZConstraint(info[k]);
1481	<	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1482	<	}
1483	<	else
1484	<	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1406	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1407
1408	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1409	<
1410	<	if (globals->haveTargetPressure())
1411	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1490	<	else {
1491	<	sprintf( painCave.errMsg,
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->haveTauThermostat() )
1419	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1420	<	else{
1421	<	sprintf( painCave.errMsg,
1414	>	painCave.isFatal = 1;
1415	>	simError();
1416	>	}
1417	>
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	<	}
1507	<
1508	<	if( globals->haveTauBarostat() )
1509	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1510	<	else{
1511	<	sprintf( painCave.errMsg,
1512	<	"SimSetup error: If you use an NPT\n"
1513	<	"    ensemble, you must set tauBarostat.\n");
1514	<	painCave.isFatal = 1;
1515	<	simError();
1516	<	}
1517	<	break;
1518	<
1519	<	case NPTfm_ENS:
1520	<	if (globals->haveZconstraints()){
1521	<	setupZConstraint(info[k]);
1522	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1523	<	}
1524	<	else
1525	<	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1424	>	painCave.isFatal = 1;
1425	>	simError();
1426	>	}
1427
1428	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1429	<
1430	<	if (globals->haveTargetPressure())
1431	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1531	<	else {
1532	<	sprintf( painCave.errMsg,
1533	<	"SimSetup error: If you use a constant pressure\n"
1534	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1535	<	painCave.isFatal = 1;
1536	<	simError();
1537	<	}
1538	<
1539	<	if( globals->haveTauThermostat() )
1540	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1541	<	else{
1542	<	sprintf( painCave.errMsg,
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 tauThermostat.\n");
1434	<	painCave.isFatal = 1;
1435	<	simError();
1436	<	}
1433	>	"    ensemble, you must set tauBarostat.\n");
1434	>	painCave.isFatal = 1;
1435	>	simError();
1436	>	}
1437
1438	<	if( globals->haveTauBarostat() )
1439	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1440	<	else{
1441	<	sprintf( painCave.errMsg,
1438	>	info->the_integrator = myNPTi;
1439	>	break;
1440	>
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	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1450	>
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->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	+	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	+	info->the_integrator = myNPTf;
1482	+	break;
1483	+
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	+	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();
1557	–	}
1558	–	break;
1559	–
1560	–	default:
1561	–	sprintf( painCave.errMsg,
1562	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1563	–	painCave.isFatal = 1;
1564	–	simError();
1532		}
1533		}
1534		}
1535
1536	<	void SimSetup::initFortran( void ){
1570	<
1536	>	void SimSetup::initFortran(void){
1537		info[0].refreshSim();
1538	<
1539	<	if( !strcmp( info[0].mixingRule, "standard") ){
1540	<	the_ff->initForceField( LB_MIXING_RULE );
1538	>
1539	>	if (!strcmp(info[0].mixingRule, "standard")){
1540	>	the_ff->initForceField(LB_MIXING_RULE);
1541		}
1542	<	else if( !strcmp( info[0].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",
1582	<	info[0].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,
1590	<	"Successfully intialized the mixingRule for Fortran." );
1554	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1555		MPIcheckPoint();
1556		#endif // is_mpi
1593	–
1557		}
1558
1559	<	void SimSetup::setupZConstraint(SimInfo& theInfo)
1597	<	{
1559	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1560		int nZConstraints;
1561		ZconStamp** zconStamp;
1562
1563	<	if(globals->haveZconstraintTime()){
1602	<
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);
#	Line 1607 | Line 1568 | void SimSetup::setupZConstraint(SimInfo& theInfo)
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");
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();
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()){
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", defaultZConsTol);
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
#	Line 1633 | Line 1595 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1595		}
1596		theInfo.addProperty(zconsTol);
1597
1598	<	//set Force Substraction Policy
1599	<	StringData* zconsForcePolicy =  new StringData();
1598	>	//set Force Subtraction Policy
1599	>	StringData* zconsForcePolicy = new StringData();
1600		zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1601	<
1602	<	if(globals->haveZconsForcePolicy()){
1601	>
1602	>	if (globals->haveZconsForcePolicy()){
1603		zconsForcePolicy->setData(globals->getZconsForcePolicy());
1604	<	}
1604	>	}
1605		else{
1606	<	sprintf( painCave.errMsg,
1607	<	"ZConstraint Warning: User does not set force substraction policy, "
1608	<	"average force substraction policy is used\n");
1609	<	painCave.isFatal = 0;
1610	<	simError();
1611	<	zconsForcePolicy->setData("BYNUMBER");
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	<
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	<
1619	>
1620		string zconsOutput(theInfo.finalName);
1621	<
1621	>
1622		zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1623	<
1623	>
1624		StringData* zconsFilename = new StringData();
1625		zconsFilename->setID(ZCONSFILENAME_ID);
1626		zconsFilename->setData(zconsOutput);
1627	<
1627	>
1628		theInfo.addProperty(zconsFilename);
1629	<
1629	>
1630		//setup index, pos and other parameters of z-constraint molecules
1631		nZConstraints = globals->getNzConstraints();
1632		theInfo.nZconstraints = nZConstraints;
#	Line 1674 | Line 1636 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1636
1637		ZConsParaData* zconsParaData = new ZConsParaData();
1638		zconsParaData->setID(ZCONSPARADATA_ID);
1639	<
1640	<	for(int i = 0; i < nZConstraints; i++){
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();
#	Line 1684 | Line 1646 | void SimSetup::setupZConstraint(SimInfo& theInfo)
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);
1692	–
1662		}

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