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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 708 by tim, Wed Aug 20 22:23:34 2003 UTC vs.
Revision 733 by tim, Wed Aug 27 19:23:29 2003 UTC

#	Line 3 | Line 3
3		#include <iostream>
4		#include <cmath>
5		#include <string>
6	<	#include <sys/time.h>
6	>	#include <sprng.h>
7
8		#include "SimSetup.hpp"
9		#include "ReadWrite.hpp"
#	Line 32 | Line 32 | SimSetup::SimSetup(){
32		using namespace std;
33
34		SimSetup::SimSetup(){
35	–
35		isInfoArray = 0;
36		nInfo = 1;
37	<
37	>
38		stamps = new MakeStamps();
39		globals = new Globals();
40	<
41	<
40	>
41	>
42		#ifdef IS_MPI
43	<	strcpy( checkPointMsg, "SimSetup creation successful" );
43	>	strcpy(checkPointMsg, "SimSetup creation successful");
44		MPIcheckPoint();
45		#endif // IS_MPI
46		}
#	Line 51 | Line 50 | SimSetup::~SimSetup(){
50		delete globals;
51		}
52
53	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
54	<	info = the_info;
55	<	nInfo = theNinfo;
56	<	isInfoArray = 1;
53	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
54	>	info = the_info;
55	>	nInfo = theNinfo;
56	>	isInfoArray = 1;
57		}
58
59
60	<	void SimSetup::parseFile( char* fileName ){
62	<
60	>	void SimSetup::parseFile(char* fileName){
61		#ifdef IS_MPI
62	<	if( worldRank == 0 ){
62	>	if (worldRank == 0){
63		#endif // is_mpi
64	<
64	>
65		inFileName = fileName;
66	<	set_interface_stamps( stamps, globals );
67	<
66	>	set_interface_stamps(stamps, globals);
67	>
68		#ifdef IS_MPI
69		mpiEventInit();
70		#endif
71
72	<	yacc_BASS( fileName );
72	>	yacc_BASS(fileName);
73
74		#ifdef IS_MPI
75		throwMPIEvent(NULL);
76		}
77	<	else receiveParse();
77	>	else{
78	>	receiveParse();
79	>	}
80		#endif
81
82		}
83
84		#ifdef IS_MPI
85		void SimSetup::receiveParse(void){
86	<
87	<	set_interface_stamps( stamps, globals );
88	<	mpiEventInit();
89	<	MPIcheckPoint();
90	<	mpiEventLoop();
91	<
86	>	set_interface_stamps(stamps, globals);
87	>	mpiEventInit();
88	>	MPIcheckPoint();
89	>	mpiEventLoop();
90		}
91
92		#endif // is_mpi
93
94		void SimSetup::createSim(void){
97	–
95		int i, j, k, globalAtomIndex;
96	<
96	>
97		// gather all of the information from the Bass file
98
99		gatherInfo();
#	Line 111 | Line 108 | void SimSetup::createSim(void){
108
109		// initialize the system coordinates
110
111	<	if( !isInfoArray ) initSystemCoords();
111	>	if (!isInfoArray){
112	>	initSystemCoords();
113	>	}
114
115		// make the output filenames
116
117		makeOutNames();
118	<
118	>
119		// make the integrator
120	<
120	>
121		makeIntegrator();
122	<
122	>
123		#ifdef IS_MPI
124		mpiSim->mpiRefresh();
125		#endif
#	Line 128 | Line 127 | void SimSetup::createSim(void){
127		// initialize the Fortran
128
129		initFortran();
131	–
132	–
133	–
130		}
131
132
133	<	void SimSetup::makeMolecules( void ){
134	<
139	<	int k,l;
133	>	void SimSetup::makeMolecules(void){
134	>	int k, l;
135		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
136		molInit molInfo;
137		DirectionalAtom* dAtom;
#	Line 151 | Line 146 | void SimSetup::makeMolecules( void ){
146		bend_set* theBends;
147		torsion_set* theTorsions;
148
149	<
149	>
150		//init the forceField paramters
151
152		the_ff->readParams();
153
154	<
154	>
155		// init the atoms
156
157		double ux, uy, uz, u, uSqr;
163	–
164	–	for(k=0; k<nInfo; k++){
165	–
166	–	the_ff->setSimInfo( &(info[k]) );
158
159	+	for (k = 0; k < nInfo; k++){
160	+	the_ff->setSimInfo(&(info[k]));
161	+
162		atomOffset = 0;
163		excludeOffset = 0;
164	<	for(i=0; i<info[k].n_mol; i++){
171	<
164	>	for (i = 0; i < info[k].n_mol; i++){
165		stampID = info[k].molecules[i].getStampID();
166
167	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
168	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
169	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
167	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
168	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
169	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
170		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
171		molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
172	<
172	>
173		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
174		molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
175	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
176	<	molInfo.myBends = new Bend*[molInfo.nBends];
177	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
175	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
176	>	molInfo.myBends = new Bend * [molInfo.nBends];
177	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
178
179		theBonds = new bond_pair[molInfo.nBonds];
180		theBends = new bend_set[molInfo.nBends];
181		theTorsions = new torsion_set[molInfo.nTorsions];
182	<
182	>
183		// make the Atoms
184	<
185	<	for(j=0; j<molInfo.nAtoms; j++){
186	<
187	<	currentAtom = comp_stamps[stampID]->getAtom( j );
188	<	if( currentAtom->haveOrientation() ){
189	<
190	<	dAtom = new DirectionalAtom( (j + atomOffset),
191	<	info[k].getConfiguration() );
192	<	info[k].n_oriented++;
193	<	molInfo.myAtoms[j] = dAtom;
194	<
195	<	ux = currentAtom->getOrntX();
196	<	uy = currentAtom->getOrntY();
197	<	uz = currentAtom->getOrntZ();
198	<
199	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
200	<
201	<	u = sqrt( uSqr );
202	<	ux = ux / u;
203	<	uy = uy / u;
204	<	uz = uz / u;
205	<
206	<	dAtom->setSUx( ux );
207	<	dAtom->setSUy( uy );
208	<	dAtom->setSUz( uz );
209	<	}
210	<	else{
211	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
212	<	info[k].getConfiguration() );
213	<	}
221	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
222	<
184	>
185	>	for (j = 0; j < molInfo.nAtoms; j++){
186	>	currentAtom = comp_stamps[stampID]->getAtom(j);
187	>	if (currentAtom->haveOrientation()){
188	>	dAtom = new DirectionalAtom((j + atomOffset),
189	>	info[k].getConfiguration());
190	>	info[k].n_oriented++;
191	>	molInfo.myAtoms[j] = dAtom;
192	>
193	>	ux = currentAtom->getOrntX();
194	>	uy = currentAtom->getOrntY();
195	>	uz = currentAtom->getOrntZ();
196	>
197	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
198	>
199	>	u = sqrt(uSqr);
200	>	ux = ux / u;
201	>	uy = uy / u;
202	>	uz = uz / u;
203	>
204	>	dAtom->setSUx(ux);
205	>	dAtom->setSUy(uy);
206	>	dAtom->setSUz(uz);
207	>	}
208	>	else{
209	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
210	>	info[k].getConfiguration());
211	>	}
212	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
213	>
214		#ifdef IS_MPI
215	<
216	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
217	<
215	>
216	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
217	>
218		#endif // is_mpi
219		}
220	<
221	<	// make the bonds
222	<	for(j=0; j<molInfo.nBonds; j++){
223	<
224	<	currentBond = comp_stamps[stampID]->getBond( j );
225	<	theBonds[j].a = currentBond->getA() + atomOffset;
226	<	theBonds[j].b = currentBond->getB() + atomOffset;
227	<
228	<	exI = theBonds[j].a;
229	<	exJ = theBonds[j].b;
230	<
231	<	// exclude_I must always be the smaller of the pair
232	<	if( exI > exJ ){
233	<	tempEx = exI;
234	<	exI = exJ;
235	<	exJ = tempEx;
245	<	}
220	>
221	>	// make the bonds
222	>	for (j = 0; j < molInfo.nBonds; j++){
223	>	currentBond = comp_stamps[stampID]->getBond(j);
224	>	theBonds[j].a = currentBond->getA() + atomOffset;
225	>	theBonds[j].b = currentBond->getB() + atomOffset;
226	>
227	>	exI = theBonds[j].a;
228	>	exJ = theBonds[j].b;
229	>
230	>	// exclude_I must always be the smaller of the pair
231	>	if (exI > exJ){
232	>	tempEx = exI;
233	>	exI = exJ;
234	>	exJ = tempEx;
235	>	}
236		#ifdef IS_MPI
237	<	tempEx = exI;
238	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
239	<	tempEx = exJ;
240	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
241	<
242	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
237	>	tempEx = exI;
238	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
239	>	tempEx = exJ;
240	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
241	>
242	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
243		#else  // isn't MPI
244	<
245	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
244	>
245	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
246		#endif  //is_mpi
247		}
248		excludeOffset += molInfo.nBonds;
249	<
249	>
250		//make the bends
251	<	for(j=0; j<molInfo.nBends; j++){
252	<
253	<	currentBend = comp_stamps[stampID]->getBend( j );
254	<	theBends[j].a = currentBend->getA() + atomOffset;
255	<	theBends[j].b = currentBend->getB() + atomOffset;
256	<	theBends[j].c = currentBend->getC() + atomOffset;
257	<
258	<	if( currentBend->haveExtras() ){
259	<
260	<	extras = currentBend->getExtras();
261	<	current_extra = extras;
262	<
263	<	while( current_extra != NULL ){
264	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
265	<
266	<	switch( current_extra->getType() ){
267	<
268	<	case 0:
269	<	theBends[j].ghost =
270	<	current_extra->getInt() + atomOffset;
271	<	theBends[j].isGhost = 1;
272	<	break;
273	<
274	<	case 1:
275	<	theBends[j].ghost =
276	<	(int)current_extra->getDouble() + atomOffset;
277	<	theBends[j].isGhost = 1;
278	<	break;
279	<
280	<	default:
281	<	sprintf( painCave.errMsg,
282	<	"SimSetup Error: ghostVectorSource was neither a "
283	<	"double nor an int.\n"
284	<	"-->Bend[%d] in %s\n",
285	<	j, comp_stamps[stampID]->getID() );
286	<	painCave.isFatal = 1;
287	<	simError();
288	<	}
289	<	}
290	<
291	<	else{
292	<
293	<	sprintf( painCave.errMsg,
294	<	"SimSetup Error: unhandled bend assignment:\n"
295	<	"    -->%s in Bend[%d] in %s\n",
296	<	current_extra->getlhs(),
297	<	j, comp_stamps[stampID]->getID() );
298	<	painCave.isFatal = 1;
299	<	simError();
300	<	}
301	<
302	<	current_extra = current_extra->getNext();
303	<	}
304	<	}
305	<
306	<	if( !theBends[j].isGhost ){
307	<
308	<	exI = theBends[j].a;
309	<	exJ = theBends[j].c;
310	<	}
311	<	else{
312	<
323	<	exI = theBends[j].a;
324	<	exJ = theBends[j].b;
325	<	}
326	<
327	<	// exclude_I must always be the smaller of the pair
328	<	if( exI > exJ ){
329	<	tempEx = exI;
330	<	exI = exJ;
331	<	exJ = tempEx;
332	<	}
251	>	for (j = 0; j < molInfo.nBends; j++){
252	>	currentBend = comp_stamps[stampID]->getBend(j);
253	>	theBends[j].a = currentBend->getA() + atomOffset;
254	>	theBends[j].b = currentBend->getB() + atomOffset;
255	>	theBends[j].c = currentBend->getC() + atomOffset;
256	>
257	>	if (currentBend->haveExtras()){
258	>	extras = currentBend->getExtras();
259	>	current_extra = extras;
260	>
261	>	while (current_extra != NULL){
262	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
263	>	switch (current_extra->getType()){
264	>	case 0:
265	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
266	>	theBends[j].isGhost = 1;
267	>	break;
268	>
269	>	case 1:
270	>	theBends[j].ghost = (int) current_extra->getDouble() +
271	>	atomOffset;
272	>	theBends[j].isGhost = 1;
273	>	break;
274	>
275	>	default:
276	>	sprintf(painCave.errMsg,
277	>	"SimSetup Error: ghostVectorSource was neither a "
278	>	"double nor an int.\n"
279	>	"-->Bend[%d] in %s\n",
280	>	j, comp_stamps[stampID]->getID());
281	>	painCave.isFatal = 1;
282	>	simError();
283	>	}
284	>	}
285	>	else{
286	>	sprintf(painCave.errMsg,
287	>	"SimSetup Error: unhandled bend assignment:\n"
288	>	"    -->%s in Bend[%d] in %s\n",
289	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
290	>	painCave.isFatal = 1;
291	>	simError();
292	>	}
293	>
294	>	current_extra = current_extra->getNext();
295	>	}
296	>	}
297	>
298	>	if (!theBends[j].isGhost){
299	>	exI = theBends[j].a;
300	>	exJ = theBends[j].c;
301	>	}
302	>	else{
303	>	exI = theBends[j].a;
304	>	exJ = theBends[j].b;
305	>	}
306	>
307	>	// exclude_I must always be the smaller of the pair
308	>	if (exI > exJ){
309	>	tempEx = exI;
310	>	exI = exJ;
311	>	exJ = tempEx;
312	>	}
313		#ifdef IS_MPI
314	<	tempEx = exI;
315	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
316	<	tempEx = exJ;
317	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
318	<
319	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
314	>	tempEx = exI;
315	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
316	>	tempEx = exJ;
317	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
318	>
319	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
320		#else  // isn't MPI
321	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
321	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
322		#endif  //is_mpi
323		}
324		excludeOffset += molInfo.nBends;
325	<
326	<	for(j=0; j<molInfo.nTorsions; j++){
327	<
328	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
329	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
330	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
331	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
332	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
333	<
334	<	exI = theTorsions[j].a;
335	<	exJ = theTorsions[j].d;
336	<
337	<	// exclude_I must always be the smaller of the pair
338	<	if( exI > exJ ){
339	<	tempEx = exI;
340	<	exI = exJ;
341	<	exJ = tempEx;
362	<	}
325	>
326	>	for (j = 0; j < molInfo.nTorsions; j++){
327	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
328	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
329	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
330	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
331	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
332	>
333	>	exI = theTorsions[j].a;
334	>	exJ = theTorsions[j].d;
335	>
336	>	// exclude_I must always be the smaller of the pair
337	>	if (exI > exJ){
338	>	tempEx = exI;
339	>	exI = exJ;
340	>	exJ = tempEx;
341	>	}
342		#ifdef IS_MPI
343	<	tempEx = exI;
344	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345	<	tempEx = exJ;
346	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
347	<
348	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
343	>	tempEx = exI;
344	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345	>	tempEx = exJ;
346	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
347	>
348	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
349		#else  // isn't MPI
350	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
350	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
351		#endif  //is_mpi
352		}
353		excludeOffset += molInfo.nTorsions;
354	<
355	<
354	>
355	>
356		// send the arrays off to the forceField for init.
378	–
379	–	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
380	–	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
381	–	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
382	–	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
383	–
384	–
385	–	info[k].molecules[i].initialize( molInfo );
357
358	<
358	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
359	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
360	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
361	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
362	>	theTorsions);
363	>
364	>
365	>	info[k].molecules[i].initialize(molInfo);
366	>
367	>
368		atomOffset += molInfo.nAtoms;
369		delete[] theBonds;
370		delete[] theBends;
371		delete[] theTorsions;
372		}
373		}
374	<
374	>
375		#ifdef IS_MPI
376	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
376	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
377		MPIcheckPoint();
378		#endif // is_mpi
379	<
379	>
380		// clean up the forcefield
381
382		the_ff->calcRcut();
383		the_ff->cleanMe();
404	–
384		}
385
386	<	void SimSetup::initFromBass( void ){
408	<
386	>	void SimSetup::initFromBass(void){
387		int i, j, k;
388		int n_cells;
389		double cellx, celly, cellz;
#	Line 419 | Line 397 | void SimSetup::initFromBass( void ){
397		vel[1] = 0.0;
398		vel[2] = 0.0;
399
400	<	temp1 = (double)tot_nmol / 4.0;
401	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
402	<	temp3 = ceil( temp2 );
400	>	temp1 = (double) tot_nmol / 4.0;
401	>	temp2 = pow(temp1, (1.0 / 3.0));
402	>	temp3 = ceil(temp2);
403
404	<	have_extra =0;
405	<	if( temp2 < temp3 ){ // we have a non-complete lattice
406	<	have_extra =1;
404	>	have_extra = 0;
405	>	if (temp2 < temp3){
406	>	// we have a non-complete lattice
407	>	have_extra = 1;
408
409	<	n_cells = (int)temp3 - 1;
409	>	n_cells = (int) temp3 - 1;
410		cellx = info[0].boxL[0] / temp3;
411		celly = info[0].boxL[1] / temp3;
412		cellz = info[0].boxL[2] / temp3;
413	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
414	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
415	<	n_per_extra = (int)ceil( temp1 );
413	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
414	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
415	>	n_per_extra = (int) ceil(temp1);
416
417	<	if( n_per_extra > 4){
418	<	sprintf( painCave.errMsg,
419	<	"SimSetup error. There has been an error in constructing"
420	<	" the non-complete lattice.\n" );
417	>	if (n_per_extra > 4){
418	>	sprintf(painCave.errMsg,
419	>	"SimSetup error. There has been an error in constructing"
420	>	" the non-complete lattice.\n");
421		painCave.isFatal = 1;
422		simError();
423		}
424		}
425		else{
426	<	n_cells = (int)temp3;
426	>	n_cells = (int) temp3;
427		cellx = info[0].boxL[0] / temp3;
428		celly = info[0].boxL[1] / temp3;
429		cellz = info[0].boxL[2] / temp3;
#	Line 455 | Line 434 | void SimSetup::initFromBass( void ){
434		current_comp = 0;
435		current_atom_ndx = 0;
436
437	<	for( i=0; i < n_cells ; i++ ){
438	<	for( j=0; j < n_cells; j++ ){
439	<	for( k=0; k < n_cells; k++ ){
437	>	for (i = 0; i < n_cells ; i++){
438	>	for (j = 0; j < n_cells; j++){
439	>	for (k = 0; k < n_cells; k++){
440	>	makeElement(i * cellx, j * celly, k * cellz);
441
442	<	makeElement( i * cellx,
463	<	j * celly,
464	<	k * cellz );
442	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
443
444	<	makeElement( i * cellx + 0.5 * cellx,
467	<	j * celly + 0.5 * celly,
468	<	k * cellz );
444	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
445
446	<	makeElement( i * cellx,
471	<	j * celly + 0.5 * celly,
472	<	k * cellz + 0.5 * cellz );
473	<
474	<	makeElement( i * cellx + 0.5 * cellx,
475	<	j * celly,
476	<	k * cellz + 0.5 * cellz );
446	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
447		}
448		}
449		}
450
451	<	if( have_extra ){
451	>	if (have_extra){
452		done = 0;
453
454		int start_ndx;
455	<	for( i=0; i < (n_cells+1) && !done; i++ ){
456	<	for( j=0; j < (n_cells+1) && !done; j++ ){
455	>	for (i = 0; i < (n_cells + 1) && !done; i++){
456	>	for (j = 0; j < (n_cells + 1) && !done; j++){
457	>	if (i < n_cells){
458	>	if (j < n_cells){
459	>	start_ndx = n_cells;
460	>	}
461	>	else
462	>	start_ndx = 0;
463	>	}
464	>	else
465	>	start_ndx = 0;
466
467	<	if( i < n_cells ){
467	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
468	>	makeElement(i * cellx, j * celly, k * cellz);
469	>	done = (current_mol >= tot_nmol);
470
471	<	if( j < n_cells ){
472	<	start_ndx = n_cells;
473	<	}
474	<	else start_ndx = 0;
475	<	}
495	<	else start_ndx = 0;
471	>	if (!done && n_per_extra > 1){
472	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
473	>	k * cellz);
474	>	done = (current_mol >= tot_nmol);
475	>	}
476
477	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
478	<
479	<	makeElement( i * cellx,
480	<	j * celly,
481	<	k * cellz );
502	<	done = ( current_mol >= tot_nmol );
503	<
504	<	if( !done && n_per_extra > 1 ){
505	<	makeElement( i * cellx + 0.5 * cellx,
506	<	j * celly + 0.5 * celly,
507	<	k * cellz );
508	<	done = ( current_mol >= tot_nmol );
509	<	}
510	<
511	<	if( !done && n_per_extra > 2){
512	<	makeElement( i * cellx,
513	<	j * celly + 0.5 * celly,
514	<	k * cellz + 0.5 * cellz );
515	<	done = ( current_mol >= tot_nmol );
516	<	}
477	>	if (!done && n_per_extra > 2){
478	>	makeElement(i * cellx, j * celly + 0.5 * celly,
479	>	k * cellz + 0.5 * cellz);
480	>	done = (current_mol >= tot_nmol);
481	>	}
482
483	<	if( !done && n_per_extra > 3){
484	<	makeElement( i * cellx + 0.5 * cellx,
485	<	j * celly,
486	<	k * cellz + 0.5 * cellz );
487	<	done = ( current_mol >= tot_nmol );
488	<	}
524	<	}
483	>	if (!done && n_per_extra > 3){
484	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
485	>	k * cellz + 0.5 * cellz);
486	>	done = (current_mol >= tot_nmol);
487	>	}
488	>	}
489		}
490		}
491		}
492
493	<	for( i=0; i<info[0].n_atoms; i++ ){
494	<	info[0].atoms[i]->setVel( vel );
493	>	for (i = 0; i < info[0].n_atoms; i++){
494	>	info[0].atoms[i]->setVel(vel);
495		}
496		}
497
498	<	void SimSetup::makeElement( double x, double y, double z ){
535	<
498	>	void SimSetup::makeElement(double x, double y, double z){
499		int k;
500		AtomStamp* current_atom;
501		DirectionalAtom* dAtom;
502		double rotMat[3][3];
503		double pos[3];
504
505	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
506	<
507	<	current_atom = comp_stamps[current_comp]->getAtom( k );
508	<	if( !current_atom->havePosition() ){
509	<	sprintf( painCave.errMsg,
510	<	"SimSetup:initFromBass error.\n"
511	<	"\tComponent %s, atom %s does not have a position specified.\n"
512	<	"\tThe initialization routine is unable to give a start"
513	<	" position.\n",
551	<	comp_stamps[current_comp]->getID(),
552	<	current_atom->getType() );
505	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
506	>	current_atom = comp_stamps[current_comp]->getAtom(k);
507	>	if (!current_atom->havePosition()){
508	>	sprintf(painCave.errMsg,
509	>	"SimSetup:initFromBass error.\n"
510	>	"\tComponent %s, atom %s does not have a position specified.\n"
511	>	"\tThe initialization routine is unable to give a start"
512	>	" position.\n",
513	>	comp_stamps[current_comp]->getID(), current_atom->getType());
514		painCave.isFatal = 1;
515		simError();
516		}
517	<
517	>
518		pos[0] = x + current_atom->getPosX();
519		pos[1] = y + current_atom->getPosY();
520		pos[2] = z + current_atom->getPosZ();
560	–
561	–	info[0].atoms[current_atom_ndx]->setPos( pos );
521
522	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
522	>	info[0].atoms[current_atom_ndx]->setPos(pos);
523
524	<	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
524	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
525	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
526
527		rotMat[0][0] = 1.0;
528		rotMat[0][1] = 0.0;
#	Line 576 | Line 536 | void SimSetup::makeElement( double x, double y, double
536		rotMat[2][1] = 0.0;
537		rotMat[2][2] = 1.0;
538
539	<	dAtom->setA( rotMat );
539	>	dAtom->setA(rotMat);
540		}
541
542		current_atom_ndx++;
#	Line 585 | Line 545 | void SimSetup::makeElement( double x, double y, double
545		current_mol++;
546		current_comp_mol++;
547
548	<	if( current_comp_mol >= components_nmol[current_comp] ){
589	<
548	>	if (current_comp_mol >= components_nmol[current_comp]){
549		current_comp_mol = 0;
550		current_comp++;
551		}
552		}
553
554
555	<	void SimSetup::gatherInfo( void ){
556	<	int i,j,k;
555	>	void SimSetup::gatherInfo(void){
556	>	int i, j, k;
557
558		ensembleCase = -1;
559		ffCase = -1;
560
561		// set the easy ones first
562
563	<	for( i=0; i<nInfo; i++){
563	>	for (i = 0; i < nInfo; i++){
564		info[i].target_temp = globals->getTargetTemp();
565		info[i].dt = globals->getDt();
566		info[i].run_time = globals->getRunTime();
#	Line 611 | Line 570 | void SimSetup::gatherInfo( void ){
570
571		// get the forceField
572
573	<	strcpy( force_field, globals->getForceField() );
573	>	strcpy(force_field, globals->getForceField());
574
575	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
576	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
577	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
575	>	if (!strcasecmp(force_field, "DUFF")){
576	>	ffCase = FF_DUFF;
577	>	}
578	>	else if (!strcasecmp(force_field, "LJ")){
579	>	ffCase = FF_LJ;
580	>	}
581	>	else if (!strcasecmp(force_field, "EAM")){
582	>	ffCase = FF_EAM;
583	>	}
584		else{
585	<	sprintf( painCave.errMsg,
586	<	"SimSetup Error. Unrecognized force field -> %s\n",
587	<	force_field );
588	<	painCave.isFatal = 1;
624	<	simError();
585	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
586	>	force_field);
587	>	painCave.isFatal = 1;
588	>	simError();
589		}
590
591	<	// get the ensemble
591	>	// get the ensemble
592
593	<	strcpy( ensemble, globals->getEnsemble() );
593	>	strcpy(ensemble, globals->getEnsemble());
594
595	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
596	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
597	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
595	>	if (!strcasecmp(ensemble, "NVE")){
596	>	ensembleCase = NVE_ENS;
597	>	}
598	>	else if (!strcasecmp(ensemble, "NVT")){
599	>	ensembleCase = NVT_ENS;
600	>	}
601	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
602		ensembleCase = NPTi_ENS;
603	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
604	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
605	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
603	>	}
604	>	else if (!strcasecmp(ensemble, "NPTf")){
605	>	ensembleCase = NPTf_ENS;
606	>	}
607	>	else if (!strcasecmp(ensemble, "NPTim")){
608	>	ensembleCase = NPTim_ENS;
609	>	}
610	>	else if (!strcasecmp(ensemble, "NPTfm")){
611	>	ensembleCase = NPTfm_ENS;
612	>	}
613		else{
614	<	sprintf( painCave.errMsg,
615	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
616	<	"reverting to NVE for this simulation.\n",
617	<	ensemble );
618	<	painCave.isFatal = 0;
619	<	simError();
620	<	strcpy( ensemble, "NVE" );
621	<	ensembleCase = NVE_ENS;
614	>	sprintf(painCave.errMsg,
615	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
616	>	"reverting to NVE for this simulation.\n",
617	>	ensemble);
618	>	painCave.isFatal = 0;
619	>	simError();
620	>	strcpy(ensemble, "NVE");
621	>	ensembleCase = NVE_ENS;
622		}
648	–
649	–	for(i=0; i<nInfo; i++){
650	–
651	–	strcpy( info[i].ensemble, ensemble );
623
624	+	for (i = 0; i < nInfo; i++){
625	+	strcpy(info[i].ensemble, ensemble);
626	+
627		// get the mixing rule
628
629	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
629	>	strcpy(info[i].mixingRule, globals->getMixingRule());
630		info[i].usePBC = globals->getPBC();
631		}
632	<
632	>
633		// get the components and calculate the tot_nMol and indvidual n_mol
634	<
634	>
635		the_components = globals->getComponents();
636		components_nmol = new int[n_components];
637
638
639	<	if( !globals->haveNMol() ){
639	>	if (!globals->haveNMol()){
640		// we don't have the total number of molecules, so we assume it is
641		// given in each component
642
643		tot_nmol = 0;
644	<	for( i=0; i<n_components; i++ ){
645	<
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;
678	<	simError();
644	>	for (i = 0; i < n_components; i++){
645	>	if (!the_components[i]->haveNMol()){
646	>	// we have a problem
647	>	sprintf(painCave.errMsg,
648	>	"SimSetup Error. No global NMol or component NMol"
649	>	" given. Cannot calculate the number of atoms.\n");
650	>	painCave.isFatal = 1;
651	>	simError();
652		}
653
654		tot_nmol += the_components[i]->getNMol();
#	Line 683 | Line 656 | void SimSetup::gatherInfo( void ){
656		}
657		}
658		else{
659	<	sprintf( painCave.errMsg,
660	<	"SimSetup error.\n"
661	<	"\tSorry, the ability to specify total"
662	<	" nMols and then give molfractions in the components\n"
663	<	"\tis not currently supported."
664	<	" Please give nMol in the components.\n" );
659	>	sprintf(painCave.errMsg,
660	>	"SimSetup error.\n"
661	>	"\tSorry, the ability to specify total"
662	>	" nMols and then give molfractions in the components\n"
663	>	"\tis not currently supported."
664	>	" Please give nMol in the components.\n");
665		painCave.isFatal = 1;
666		simError();
667		}
668
669		// set the status, sample, and thermal kick times
697	–
698	–	for(i=0; i<nInfo; i++){
670
671	<	if( globals->haveSampleTime() ){
671	>	for (i = 0; i < nInfo; i++){
672	>	if (globals->haveSampleTime()){
673		info[i].sampleTime = globals->getSampleTime();
674		info[i].statusTime = info[i].sampleTime;
675		info[i].thermalTime = info[i].sampleTime;
#	Line 707 | Line 679 | void SimSetup::gatherInfo( void ){
679		info[i].statusTime = info[i].sampleTime;
680		info[i].thermalTime = info[i].sampleTime;
681		}
682	<
683	<	if( globals->haveStatusTime() ){
682	>
683	>	if (globals->haveStatusTime()){
684		info[i].statusTime = globals->getStatusTime();
685		}
686	<
687	<	if( globals->haveThermalTime() ){
686	>
687	>	if (globals->haveThermalTime()){
688		info[i].thermalTime = globals->getThermalTime();
689		}
690
691		// check for the temperature set flag
692
693	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
694	<
693	>	if (globals->haveTempSet())
694	>	info[i].setTemp = globals->getTempSet();
695	>
696		// get some of the tricky things that may still be in the globals
697	<
697	>
698		double boxVector[3];
699	<	if( globals->haveBox() ){
699	>	if (globals->haveBox()){
700		boxVector[0] = globals->getBox();
701		boxVector[1] = globals->getBox();
702		boxVector[2] = globals->getBox();
703	<
704	<	info[i].setBox( boxVector );
703	>
704	>	info[i].setBox(boxVector);
705		}
706	<	else if( globals->haveDensity() ){
734	<
706	>	else if (globals->haveDensity()){
707		double vol;
708	<	vol = (double)tot_nmol / globals->getDensity();
709	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
708	>	vol = (double) tot_nmol / globals->getDensity();
709	>	boxVector[0] = pow(vol, (1.0 / 3.0));
710		boxVector[1] = boxVector[0];
711		boxVector[2] = boxVector[0];
712	<
713	<	info[i].setBox( boxVector );
714	<	}
712	>
713	>	info[i].setBox(boxVector);
714	>	}
715		else{
716	<	if( !globals->haveBoxX() ){
717	<	sprintf( painCave.errMsg,
718	<	"SimSetup error, no periodic BoxX size given.\n" );
719	<	painCave.isFatal = 1;
720	<	simError();
716	>	if (!globals->haveBoxX()){
717	>	sprintf(painCave.errMsg,
718	>	"SimSetup error, no periodic BoxX size given.\n");
719	>	painCave.isFatal = 1;
720	>	simError();
721		}
722		boxVector[0] = globals->getBoxX();
723	<
724	<	if( !globals->haveBoxY() ){
725	<	sprintf( painCave.errMsg,
726	<	"SimSetup error, no periodic BoxY size given.\n" );
727	<	painCave.isFatal = 1;
728	<	simError();
723	>
724	>	if (!globals->haveBoxY()){
725	>	sprintf(painCave.errMsg,
726	>	"SimSetup error, no periodic BoxY size given.\n");
727	>	painCave.isFatal = 1;
728	>	simError();
729		}
730		boxVector[1] = globals->getBoxY();
731	<
732	<	if( !globals->haveBoxZ() ){
733	<	sprintf( painCave.errMsg,
734	<	"SimSetup error, no periodic BoxZ size given.\n" );
735	<	painCave.isFatal = 1;
736	<	simError();
731	>
732	>	if (!globals->haveBoxZ()){
733	>	sprintf(painCave.errMsg,
734	>	"SimSetup error, no periodic BoxZ size given.\n");
735	>	painCave.isFatal = 1;
736	>	simError();
737		}
738		boxVector[2] = globals->getBoxZ();
739	<
740	<	info[i].setBox( boxVector );
739	>
740	>	info[i].setBox(boxVector);
741		}
742		}
743
744	+	//setup seed for random number generator
745		int seedValue;
773	–	struct timeval now_time_val;
774	–	struct timezone time_zone;
746
747	<	if(globals->haveSeed()){
747	>	if (globals->haveSeed()){
748		seedValue = globals->getSeed();
749	<	}
749	>
750	>	if(seedValue / 1E9 == 0){
751	>	sprintf(painCave.errMsg,
752	>	"Seed for sprng library should contain at least 9 digits\n"
753	>	"OOPSE will generate a seed for user\n");
754	>	painCave.isFatal = 0;
755	>	simError();
756	>
757	>	//using seed generated by system instead of invalid seed set by user
758	>	#ifndef IS_MPI
759	>	seedValue = make_sprng_seed();
760	>	#else
761	>	if (worldRank == 0){
762	>	seedValue = make_sprng_seed();
763	>	}
764	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
765	>	#endif
766	>	}
767	>	}//end of if branch of globals->haveSeed()
768		else{
769	+
770		#ifndef IS_MPI
771	<	gettimeofday(&now_time_val, &time_zone);  // get the time now
782	<	seedValue = (int) now_time_val.tv_sec;      //  convert to epoch time
771	>	seedValue = make_sprng_seed();
772		#else
773	<	if(worldRank == 0){
774	<	gettimeofday(&now_time_val, &time_zone);  // get the time now
786	<	seedValue = (int) now_time_val.tv_sec;      //  convert to epoch time
773	>	if (worldRank == 0){
774	>	seedValue = make_sprng_seed();
775		}
776	<	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
776	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
777		#endif
778	<	}
778	>	}//end of globals->haveSeed()
779
780	<	for(int i = 0; i < nInfo; i++){
780	>	for (int i = 0; i < nInfo; i++){
781		info[i].setSeed(seedValue);
782		}
783
784		#ifdef IS_MPI
785	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
785	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
786		MPIcheckPoint();
787		#endif // is_mpi
800	–
788		}
789
790
791	<	void SimSetup::finalInfoCheck( void ){
791	>	void SimSetup::finalInfoCheck(void){
792		int index;
793		int usesDipoles;
794		int i;
795
796	<	for(i=0; i<nInfo; i++){
796	>	for (i = 0; i < nInfo; i++){
797		// check electrostatic parameters
798	<
798	>
799		index = 0;
800		usesDipoles = 0;
801	<	while( (index < info[i].n_atoms) && !usesDipoles ){
801	>	while ((index < info[i].n_atoms) && !usesDipoles){
802		usesDipoles = (info[i].atoms[index])->hasDipole();
803		index++;
804		}
805	<
805	>
806		#ifdef IS_MPI
807		int myUse = usesDipoles;
808	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
808	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
809		#endif //is_mpi
810	<
810	>
811		double theEcr, theEst;
812	<
813	<	if (globals->getUseRF() ) {
812	>
813	>	if (globals->getUseRF()){
814		info[i].useReactionField = 1;
815	<
816	<	if( !globals->haveECR() ){
817	<	sprintf( painCave.errMsg,
818	<	"SimSetup Warning: using default value of 1/2 the smallest "
819	<	"box length for the electrostaticCutoffRadius.\n"
820	<	"I hope you have a very fast processor!\n");
821	<	painCave.isFatal = 0;
822	<	simError();
823	<	double smallest;
824	<	smallest = info[i].boxL[0];
825	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
826	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
827	<	theEcr = 0.5 * smallest;
828	<	} else {
829	<	theEcr = globals->getECR();
815	>
816	>	if (!globals->haveECR()){
817	>	sprintf(painCave.errMsg,
818	>	"SimSetup Warning: using default value of 1/2 the smallest "
819	>	"box length for the electrostaticCutoffRadius.\n"
820	>	"I hope you have a very fast processor!\n");
821	>	painCave.isFatal = 0;
822	>	simError();
823	>	double smallest;
824	>	smallest = info[i].boxL[0];
825	>	if (info[i].boxL[1] <= smallest)
826	>	smallest = info[i].boxL[1];
827	>	if (info[i].boxL[2] <= smallest)
828	>	smallest = info[i].boxL[2];
829	>	theEcr = 0.5 * smallest;
830		}
831	<
832	<	if( !globals->haveEST() ){
846	<	sprintf( painCave.errMsg,
847	<	"SimSetup Warning: using default value of 0.05 * the "
848	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
849	<	);
850	<	painCave.isFatal = 0;
851	<	simError();
852	<	theEst = 0.05 * theEcr;
853	<	} else {
854	<	theEst= globals->getEST();
831	>	else{
832	>	theEcr = globals->getECR();
833		}
834	<
835	<	info[i].setEcr( theEcr, theEst );
836	<
837	<	if(!globals->haveDielectric() ){
838	<	sprintf( painCave.errMsg,
839	<	"SimSetup Error: You are trying to use Reaction Field without"
840	<	"setting a dielectric constant!\n"
841	<	);
864	<	painCave.isFatal = 1;
865	<	simError();
834	>
835	>	if (!globals->haveEST()){
836	>	sprintf(painCave.errMsg,
837	>	"SimSetup Warning: using default value of 0.05 * the "
838	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
839	>	painCave.isFatal = 0;
840	>	simError();
841	>	theEst = 0.05 * theEcr;
842		}
843	<	info[i].dielectric = globals->getDielectric();
844	<	}
869	<	else {
870	<	if (usesDipoles) {
871	<
872	<	if( !globals->haveECR() ){
873	<	sprintf( painCave.errMsg,
874	<	"SimSetup Warning: using default value of 1/2 the smallest "
875	<	"box length for the electrostaticCutoffRadius.\n"
876	<	"I hope you have a very fast processor!\n");
877	<	painCave.isFatal = 0;
878	<	simError();
879	<	double smallest;
880	<	smallest = info[i].boxL[0];
881	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
882	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
883	<	theEcr = 0.5 * smallest;
884	<	} else {
885	<	theEcr = globals->getECR();
886	<	}
887	<
888	<	if( !globals->haveEST() ){
889	<	sprintf( painCave.errMsg,
890	<	"SimSetup Warning: using default value of 0.05 * the "
891	<	"electrostaticCutoffRadius for the "
892	<	"electrostaticSkinThickness\n"
893	<	);
894	<	painCave.isFatal = 0;
895	<	simError();
896	<	theEst = 0.05 * theEcr;
897	<	} else {
898	<	theEst= globals->getEST();
899	<	}
900	<
901	<	info[i].setEcr( theEcr, theEst );
843	>	else{
844	>	theEst = globals->getEST();
845		}
846	<	}
846	>
847	>	info[i].setEcr(theEcr, theEst);
848	>
849	>	if (!globals->haveDielectric()){
850	>	sprintf(painCave.errMsg,
851	>	"SimSetup Error: You are trying to use Reaction Field without"
852	>	"setting a dielectric constant!\n");
853	>	painCave.isFatal = 1;
854	>	simError();
855	>	}
856	>	info[i].dielectric = globals->getDielectric();
857	>	}
858	>	else{
859	>	if (usesDipoles){
860	>	if (!globals->haveECR()){
861	>	sprintf(painCave.errMsg,
862	>	"SimSetup Warning: using default value of 1/2 the smallest "
863	>	"box length for the electrostaticCutoffRadius.\n"
864	>	"I hope you have a very fast processor!\n");
865	>	painCave.isFatal = 0;
866	>	simError();
867	>	double smallest;
868	>	smallest = info[i].boxL[0];
869	>	if (info[i].boxL[1] <= smallest)
870	>	smallest = info[i].boxL[1];
871	>	if (info[i].boxL[2] <= smallest)
872	>	smallest = info[i].boxL[2];
873	>	theEcr = 0.5 * smallest;
874	>	}
875	>	else{
876	>	theEcr = globals->getECR();
877	>	}
878	>
879	>	if (!globals->haveEST()){
880	>	sprintf(painCave.errMsg,
881	>	"SimSetup Warning: using default value of 0.05 * the "
882	>	"electrostaticCutoffRadius for the "
883	>	"electrostaticSkinThickness\n");
884	>	painCave.isFatal = 0;
885	>	simError();
886	>	theEst = 0.05 * theEcr;
887	>	}
888	>	else{
889	>	theEst = globals->getEST();
890	>	}
891	>
892	>	info[i].setEcr(theEcr, theEst);
893	>	}
894	>	}
895		}
896
897		#ifdef IS_MPI
898	<	strcpy( checkPointMsg, "post processing checks out" );
898	>	strcpy(checkPointMsg, "post processing checks out");
899		MPIcheckPoint();
900		#endif // is_mpi
910	–
901		}
902
903	<	void SimSetup::initSystemCoords( void ){
903	>	void SimSetup::initSystemCoords(void){
904		int i;
905	<
905	>
906		char* inName;
907
908	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
908	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
909
910	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
911	<
912	<	if( globals->haveInitialConfig() ){
913	<
914	<	InitializeFromFile* fileInit;
915	<	#ifdef IS_MPI // is_mpi
916	<	if( worldRank == 0 ){
910	>	for (i = 0; i < info[0].n_atoms; i++)
911	>	info[0].atoms[i]->setCoords();
912	>
913	>	if (globals->haveInitialConfig()){
914	>	InitializeFromFile* fileInit;
915	>	#ifdef IS_MPI // is_mpi
916	>	if (worldRank == 0){
917		#endif //is_mpi
918		inName = globals->getInitialConfig();
919		double* tempDouble = new double[1000000];
920	<	fileInit = new InitializeFromFile( inName );
920	>	fileInit = new InitializeFromFile(inName);
921		#ifdef IS_MPI
922	<	}else fileInit = new InitializeFromFile( NULL );
922	>	}
923	>	else
924	>	fileInit = new InitializeFromFile(NULL);
925		#endif
926	<	fileInit->readInit( info ); // default velocities on
927	<
926	>	fileInit->readInit(info); // default velocities on
927	>
928		delete fileInit;
929		}
930		else{
939	–
931		#ifdef IS_MPI
932	<
932	>
933		// no init from bass
934	<
935	<	sprintf( painCave.errMsg,
936	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
934	>
935	>	sprintf(painCave.errMsg,
936	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
937		painCave.isFatal;
938		simError();
939	<
939	>
940		#else
941	<
941	>
942		initFromBass();
943	<
944	<
943	>
944	>
945		#endif
946		}
947	<
947	>
948		#ifdef IS_MPI
949	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
949	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
950		MPIcheckPoint();
951		#endif // is_mpi
961	–
952		}
953
954
955	<	void SimSetup::makeOutNames( void ){
966	<
955	>	void SimSetup::makeOutNames(void){
956		int k;
957
969	–
970	–	for(k=0; k<nInfo; k++){
958
959	+	for (k = 0; k < nInfo; k++){
960		#ifdef IS_MPI
961	<	if( worldRank == 0 ){
961	>	if (worldRank == 0){
962		#endif // is_mpi
963	<
964	<	if( globals->haveFinalConfig() ){
965	<	strcpy( info[k].finalName, globals->getFinalConfig() );
963	>
964	>	if (globals->haveFinalConfig()){
965	>	strcpy(info[k].finalName, globals->getFinalConfig());
966		}
967		else{
968	<	strcpy( info[k].finalName, inFileName );
969	<	char* endTest;
970	<	int nameLength = strlen( info[k].finalName );
971	<	endTest = &(info[k].finalName[nameLength - 5]);
972	<	if( !strcmp( endTest, ".bass" ) ){
973	<	strcpy( endTest, ".eor" );
974	<	}
975	<	else if( !strcmp( endTest, ".BASS" ) ){
976	<	strcpy( endTest, ".eor" );
977	<	}
978	<	else{
979	<	endTest = &(info[k].finalName[nameLength - 4]);
980	<	if( !strcmp( endTest, ".bss" ) ){
981	<	strcpy( endTest, ".eor" );
982	<	}
983	<	else if( !strcmp( endTest, ".mdl" ) ){
984	<	strcpy( endTest, ".eor" );
985	<	}
986	<	else{
987	<	strcat( info[k].finalName, ".eor" );
988	<	}
989	<	}
968	>	strcpy(info[k].finalName, inFileName);
969	>	char* endTest;
970	>	int nameLength = strlen(info[k].finalName);
971	>	endTest = &(info[k].finalName[nameLength - 5]);
972	>	if (!strcmp(endTest, ".bass")){
973	>	strcpy(endTest, ".eor");
974	>	}
975	>	else if (!strcmp(endTest, ".BASS")){
976	>	strcpy(endTest, ".eor");
977	>	}
978	>	else{
979	>	endTest = &(info[k].finalName[nameLength - 4]);
980	>	if (!strcmp(endTest, ".bss")){
981	>	strcpy(endTest, ".eor");
982	>	}
983	>	else if (!strcmp(endTest, ".mdl")){
984	>	strcpy(endTest, ".eor");
985	>	}
986	>	else{
987	>	strcat(info[k].finalName, ".eor");
988	>	}
989	>	}
990		}
991	<
991	>
992		// make the sample and status out names
993	<
994	<	strcpy( info[k].sampleName, inFileName );
993	>
994	>	strcpy(info[k].sampleName, inFileName);
995		char* endTest;
996	<	int nameLength = strlen( info[k].sampleName );
996	>	int nameLength = strlen(info[k].sampleName);
997		endTest = &(info[k].sampleName[nameLength - 5]);
998	<	if( !strcmp( endTest, ".bass" ) ){
999	<	strcpy( endTest, ".dump" );
998	>	if (!strcmp(endTest, ".bass")){
999	>	strcpy(endTest, ".dump");
1000		}
1001	<	else if( !strcmp( endTest, ".BASS" ) ){
1002	<	strcpy( endTest, ".dump" );
1001	>	else if (!strcmp(endTest, ".BASS")){
1002	>	strcpy(endTest, ".dump");
1003		}
1004		else{
1005	<	endTest = &(info[k].sampleName[nameLength - 4]);
1006	<	if( !strcmp( endTest, ".bss" ) ){
1007	<	strcpy( endTest, ".dump" );
1008	<	}
1009	<	else if( !strcmp( endTest, ".mdl" ) ){
1010	<	strcpy( endTest, ".dump" );
1011	<	}
1012	<	else{
1013	<	strcat( info[k].sampleName, ".dump" );
1014	<	}
1005	>	endTest = &(info[k].sampleName[nameLength - 4]);
1006	>	if (!strcmp(endTest, ".bss")){
1007	>	strcpy(endTest, ".dump");
1008	>	}
1009	>	else if (!strcmp(endTest, ".mdl")){
1010	>	strcpy(endTest, ".dump");
1011	>	}
1012	>	else{
1013	>	strcat(info[k].sampleName, ".dump");
1014	>	}
1015		}
1016	<
1017	<	strcpy( info[k].statusName, inFileName );
1018	<	nameLength = strlen( info[k].statusName );
1016	>
1017	>	strcpy(info[k].statusName, inFileName);
1018	>	nameLength = strlen(info[k].statusName);
1019		endTest = &(info[k].statusName[nameLength - 5]);
1020	<	if( !strcmp( endTest, ".bass" ) ){
1021	<	strcpy( endTest, ".stat" );
1020	>	if (!strcmp(endTest, ".bass")){
1021	>	strcpy(endTest, ".stat");
1022		}
1023	<	else if( !strcmp( endTest, ".BASS" ) ){
1024	<	strcpy( endTest, ".stat" );
1023	>	else if (!strcmp(endTest, ".BASS")){
1024	>	strcpy(endTest, ".stat");
1025		}
1026		else{
1027	<	endTest = &(info[k].statusName[nameLength - 4]);
1028	<	if( !strcmp( endTest, ".bss" ) ){
1029	<	strcpy( endTest, ".stat" );
1030	<	}
1031	<	else if( !strcmp( endTest, ".mdl" ) ){
1032	<	strcpy( endTest, ".stat" );
1033	<	}
1034	<	else{
1035	<	strcat( info[k].statusName, ".stat" );
1036	<	}
1027	>	endTest = &(info[k].statusName[nameLength - 4]);
1028	>	if (!strcmp(endTest, ".bss")){
1029	>	strcpy(endTest, ".stat");
1030	>	}
1031	>	else if (!strcmp(endTest, ".mdl")){
1032	>	strcpy(endTest, ".stat");
1033	>	}
1034	>	else{
1035	>	strcat(info[k].statusName, ".stat");
1036	>	}
1037		}
1038	<
1038	>
1039		#ifdef IS_MPI
1040	+
1041		}
1042		#endif // is_mpi
1043		}
1044		}
1045
1046
1047	<	void SimSetup::sysObjectsCreation( void ){
1048	<
1049	<	int i,k;
1061	<
1047	>	void SimSetup::sysObjectsCreation(void){
1048	>	int i, k;
1049	>
1050		// create the forceField
1051
1052		createFF();
#	Line 1073 | Line 1061 | void SimSetup::sysObjectsCreation( void ){
1061
1062		#ifdef IS_MPI
1063		// divide the molecules among the processors
1064	<
1064	>
1065		mpiMolDivide();
1066		#endif //is_mpi
1067	<
1067	>
1068		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1069	<
1069	>
1070		makeSysArrays();
1071
1072		// make and initialize the molecules (all but atomic coordinates)
1073	<
1073	>
1074		makeMolecules();
1075	<
1076	<	for(k=0; k<nInfo; k++){
1075	>
1076	>	for (k = 0; k < nInfo; k++){
1077		info[k].identArray = new int[info[k].n_atoms];
1078	<	for(i=0; i<info[k].n_atoms; i++){
1078	>	for (i = 0; i < info[k].n_atoms; i++){
1079		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1080		}
1081		}
1082		}
1083
1084
1085	<	void SimSetup::createFF( void ){
1085	>	void SimSetup::createFF(void){
1086	>	switch (ffCase){
1087	>	case FF_DUFF:
1088	>	the_ff = new DUFF();
1089	>	break;
1090
1091	<	switch( ffCase ){
1091	>	case FF_LJ:
1092	>	the_ff = new LJFF();
1093	>	break;
1094
1095	<	case FF_DUFF:
1096	<	the_ff = new DUFF();
1097	<	break;
1095	>	case FF_EAM:
1096	>	the_ff = new EAM_FF();
1097	>	break;
1098
1099	<	case FF_LJ:
1100	<	the_ff = new LJFF();
1101	<	break;
1102	<
1103	<	case FF_EAM:
1110	<	the_ff = new EAM_FF();
1111	<	break;
1112	<
1113	<	default:
1114	<	sprintf( painCave.errMsg,
1115	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1116	<	painCave.isFatal = 1;
1117	<	simError();
1099	>	default:
1100	>	sprintf(painCave.errMsg,
1101	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1102	>	painCave.isFatal = 1;
1103	>	simError();
1104		}
1105
1106		#ifdef IS_MPI
1107	<	strcpy( checkPointMsg, "ForceField creation successful" );
1107	>	strcpy(checkPointMsg, "ForceField creation successful");
1108		MPIcheckPoint();
1109		#endif // is_mpi
1124	–
1110		}
1111
1112
1113	<	void SimSetup::compList( void ){
1129	<
1113	>	void SimSetup::compList(void){
1114		int i;
1115		char* id;
1116		LinkedMolStamp* headStamp = new LinkedMolStamp();
1117		LinkedMolStamp* currentStamp = NULL;
1118	<	comp_stamps = new MoleculeStamp*[n_components];
1119	<
1118	>	comp_stamps = new MoleculeStamp * [n_components];
1119	>
1120		// make an array of molecule stamps that match the components used.
1121		// also extract the used stamps out into a separate linked list
1122	<
1123	<	for(i=0; i<nInfo; i++){
1122	>
1123	>	for (i = 0; i < nInfo; i++){
1124		info[i].nComponents = n_components;
1125		info[i].componentsNmol = components_nmol;
1126		info[i].compStamps = comp_stamps;
1127		info[i].headStamp = headStamp;
1128		}
1145	–
1129
1147	–	for( i=0; i<n_components; i++ ){
1130
1131	+	for (i = 0; i < n_components; i++){
1132		id = the_components[i]->getType();
1133		comp_stamps[i] = NULL;
1134	<
1134	>
1135		// check to make sure the component isn't already in the list
1136
1137	<	comp_stamps[i] = headStamp->match( id );
1138	<	if( comp_stamps[i] == NULL ){
1156	<
1137	>	comp_stamps[i] = headStamp->match(id);
1138	>	if (comp_stamps[i] == NULL){
1139		// extract the component from the list;
1140	<
1141	<	currentStamp = stamps->extractMolStamp( id );
1142	<	if( currentStamp == NULL ){
1143	<	sprintf( painCave.errMsg,
1144	<	"SimSetup error: Component \"%s\" was not found in the "
1145	<	"list of declared molecules\n",
1146	<	id );
1147	<	painCave.isFatal = 1;
1148	<	simError();
1140	>
1141	>	currentStamp = stamps->extractMolStamp(id);
1142	>	if (currentStamp == NULL){
1143	>	sprintf(painCave.errMsg,
1144	>	"SimSetup error: Component \"%s\" was not found in the "
1145	>	"list of declared molecules\n",
1146	>	id);
1147	>	painCave.isFatal = 1;
1148	>	simError();
1149		}
1150	<
1151	<	headStamp->add( currentStamp );
1152	<	comp_stamps[i] = headStamp->match( id );
1150	>
1151	>	headStamp->add(currentStamp);
1152	>	comp_stamps[i] = headStamp->match(id);
1153		}
1154		}
1155
1156		#ifdef IS_MPI
1157	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1157	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1158		MPIcheckPoint();
1159		#endif // is_mpi
1178	–
1179	–
1160		}
1161
1162	<	void SimSetup::calcSysValues( void ){
1162	>	void SimSetup::calcSysValues(void){
1163		int i, j, k;
1164	<
1165	<	int *molMembershipArray;
1166	<
1164	>
1165	>	int* molMembershipArray;
1166	>
1167		tot_atoms = 0;
1168		tot_bonds = 0;
1169		tot_bends = 0;
1170		tot_torsions = 0;
1171	<	for( i=0; i<n_components; i++ ){
1172	<
1173	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1174	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1195	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1171	>	for (i = 0; i < n_components; i++){
1172	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1173	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1174	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1175		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1176		}
1177	<
1177	>
1178		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1179		molMembershipArray = new int[tot_atoms];
1180	<
1181	<	for(i=0; i<nInfo; i++){
1180	>
1181	>	for (i = 0; i < nInfo; i++){
1182		info[i].n_atoms = tot_atoms;
1183		info[i].n_bonds = tot_bonds;
1184		info[i].n_bends = tot_bends;
1185		info[i].n_torsions = tot_torsions;
1186		info[i].n_SRI = tot_SRI;
1187		info[i].n_mol = tot_nmol;
1188	<
1188	>
1189		info[i].molMembershipArray = molMembershipArray;
1190	<	}
1190	>	}
1191		}
1192
1193		#ifdef IS_MPI
1194
1195	<	void SimSetup::mpiMolDivide( void ){
1217	<
1195	>	void SimSetup::mpiMolDivide(void){
1196		int i, j, k;
1197		int localMol, allMol;
1198		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1199
1200	<	mpiSim = new mpiSimulation( info );
1201	<
1200	>	mpiSim = new mpiSimulation(info);
1201	>
1202		globalIndex = mpiSim->divideLabor();
1203
1204		// set up the local variables
1205	<
1205	>
1206		mol2proc = mpiSim->getMolToProcMap();
1207		molCompType = mpiSim->getMolComponentType();
1208	<
1208	>
1209		allMol = 0;
1210		localMol = 0;
1211		local_atoms = 0;
#	Line 1237 | Line 1215 | void SimSetup::mpiMolDivide( void ){
1215		globalAtomIndex = 0;
1216
1217
1218	<	for( i=0; i<n_components; i++ ){
1219	<
1220	<	for( j=0; j<components_nmol[i]; j++ ){
1221	<
1222	<	if( mol2proc[allMol] == worldRank ){
1223	<
1224	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1225	<	local_bonds +=    comp_stamps[i]->getNBonds();
1248	<	local_bends +=    comp_stamps[i]->getNBends();
1249	<	local_torsions += comp_stamps[i]->getNTorsions();
1250	<	localMol++;
1218	>	for (i = 0; i < n_components; i++){
1219	>	for (j = 0; j < components_nmol[i]; j++){
1220	>	if (mol2proc[allMol] == worldRank){
1221	>	local_atoms += comp_stamps[i]->getNAtoms();
1222	>	local_bonds += comp_stamps[i]->getNBonds();
1223	>	local_bends += comp_stamps[i]->getNBends();
1224	>	local_torsions += comp_stamps[i]->getNTorsions();
1225	>	localMol++;
1226		}
1227	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1227	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1228		info[0].molMembershipArray[globalAtomIndex] = allMol;
1229		globalAtomIndex++;
1230		}
1231
1232	<	allMol++;
1232	>	allMol++;
1233		}
1234		}
1235		local_SRI = local_bonds + local_bends + local_torsions;
1236	<
1236	>
1237		info[0].n_atoms = mpiSim->getMyNlocal();
1238	<
1239	<	if( local_atoms != info[0].n_atoms ){
1240	<	sprintf( painCave.errMsg,
1241	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1242	<	" localAtom (%d) are not equal.\n",
1243	<	info[0].n_atoms,
1269	<	local_atoms );
1238	>
1239	>	if (local_atoms != info[0].n_atoms){
1240	>	sprintf(painCave.errMsg,
1241	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1242	>	" localAtom (%d) are not equal.\n",
1243	>	info[0].n_atoms, local_atoms);
1244		painCave.isFatal = 1;
1245		simError();
1246		}
#	Line 1277 | Line 1251 | void SimSetup::mpiMolDivide( void ){
1251		info[0].n_SRI = local_SRI;
1252		info[0].n_mol = localMol;
1253
1254	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1254	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1255		MPIcheckPoint();
1256		}
1257	<
1257	>
1258		#endif // is_mpi
1259
1260
1261	<	void SimSetup::makeSysArrays( void ){
1261	>	void SimSetup::makeSysArrays(void){
1262		int i, j, k, l;
1263
1264		Atom** the_atoms;
1265		Molecule* the_molecules;
1266		Exclude** the_excludes;
1267
1268	<
1269	<	for(l=0; l<nInfo; l++){
1296	<
1268	>
1269	>	for (l = 0; l < nInfo; l++){
1270		// create the atom and short range interaction arrays
1271	<
1272	<	the_atoms = new Atom*[info[l].n_atoms];
1271	>
1272	>	the_atoms = new Atom * [info[l].n_atoms];
1273		the_molecules = new Molecule[info[l].n_mol];
1274		int molIndex;
1275
1276		// initialize the molecule's stampID's
1277	<
1277	>
1278		#ifdef IS_MPI
1279	<
1280	<
1279	>
1280	>
1281		molIndex = 0;
1282	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1283	<
1284	<	if(mol2proc[i] == worldRank ){
1285	<	the_molecules[molIndex].setStampID( molCompType[i] );
1286	<	the_molecules[molIndex].setMyIndex( molIndex );
1287	<	the_molecules[molIndex].setGlobalIndex( i );
1315	<	molIndex++;
1282	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1283	>	if (mol2proc[i] == worldRank){
1284	>	the_molecules[molIndex].setStampID(molCompType[i]);
1285	>	the_molecules[molIndex].setMyIndex(molIndex);
1286	>	the_molecules[molIndex].setGlobalIndex(i);
1287	>	molIndex++;
1288		}
1289		}
1290	<
1290	>
1291		#else // is_mpi
1292	<
1292	>
1293		molIndex = 0;
1294		globalAtomIndex = 0;
1295	<	for(i=0; i<n_components; i++){
1296	<	for(j=0; j<components_nmol[i]; j++ ){
1297	<	the_molecules[molIndex].setStampID( i );
1298	<	the_molecules[molIndex].setMyIndex( molIndex );
1299	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1300	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1301	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1302	<	globalAtomIndex++;
1303	<	}
1304	<	molIndex++;
1295	>	for (i = 0; i < n_components; i++){
1296	>	for (j = 0; j < components_nmol[i]; j++){
1297	>	the_molecules[molIndex].setStampID(i);
1298	>	the_molecules[molIndex].setMyIndex(molIndex);
1299	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1300	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1301	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1302	>	globalAtomIndex++;
1303	>	}
1304	>	molIndex++;
1305		}
1306		}
1307	<
1308	<
1307	>
1308	>
1309		#endif // is_mpi
1310
1311
1312	<	if( info[l].n_SRI ){
1341	<
1312	>	if (info[l].n_SRI){
1313		Exclude::createArray(info[l].n_SRI);
1314	<	the_excludes = new Exclude*[info[l].n_SRI];
1315	<	for( int ex=0; ex<info[l].n_SRI; ex++){
1316	<	the_excludes[ex] = new Exclude(ex);
1314	>	the_excludes = new Exclude * [info[l].n_SRI];
1315	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1316	>	the_excludes[ex] = new Exclude(ex);
1317		}
1318		info[l].globalExcludes = new int;
1319		info[l].n_exclude = info[l].n_SRI;
1320		}
1321		else{
1322	<
1323	<	Exclude::createArray( 1 );
1353	<	the_excludes = new Exclude*;
1322	>	Exclude::createArray(1);
1323	>	the_excludes = new Exclude * ;
1324		the_excludes[0] = new Exclude(0);
1325	<	the_excludes[0]->setPair( 0,0 );
1325	>	the_excludes[0]->setPair(0, 0);
1326		info[l].globalExcludes = new int;
1327		info[l].globalExcludes[0] = 0;
1328		info[l].n_exclude = 0;
#	Line 1365 | Line 1335 | void SimSetup::makeSysArrays( void ){
1335		info[l].nGlobalExcludes = 0;
1336		info[l].excludes = the_excludes;
1337
1338	<	the_ff->setSimInfo( info );
1369	<
1338	>	the_ff->setSimInfo(info);
1339		}
1340		}
1341
1342	<	void SimSetup::makeIntegrator( void ){
1374	<
1342	>	void SimSetup::makeIntegrator(void){
1343		int k;
1344
1345	<	NVT<RealIntegrator>*  myNVT = NULL;
1345	>	NVT<RealIntegrator>* myNVT = NULL;
1346		NPTi<RealIntegrator>* myNPTi = NULL;
1347		NPTf<RealIntegrator>* myNPTf = NULL;
1348		NPTim<RealIntegrator>* myNPTim = NULL;
1349		NPTfm<RealIntegrator>* myNPTfm = NULL;
1350	<
1351	<	for(k=0; k<nInfo; k++){
1352	<
1353	<	switch( ensembleCase ){
1354	<
1355	<	case NVE_ENS:
1356	<	if (globals->haveZconstraints()){
1357	<	setupZConstraint(info[k]);
1358	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1359	<	}
1360	<
1393	<	else
1394	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1395	<	break;
1396	<
1397	<	case NVT_ENS:
1398	<	if (globals->haveZconstraints()){
1399	<	setupZConstraint(info[k]);
1400	<	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1401	<	}
1402	<	else
1403	<	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1350	>
1351	>	for (k = 0; k < nInfo; k++){
1352	>	switch (ensembleCase){
1353	>	case NVE_ENS:
1354	>	if (globals->haveZconstraints()){
1355	>	setupZConstraint(info[k]);
1356	>	new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1357	>	}
1358	>	else
1359	>	new NVE<RealIntegrator>(&(info[k]), the_ff);
1360	>	break;
1361
1362	+	case NVT_ENS:
1363	+	if (globals->haveZconstraints()){
1364	+	setupZConstraint(info[k]);
1365	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1366	+	}
1367	+	else
1368	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1369	+
1370		myNVT->setTargetTemp(globals->getTargetTemp());
1371	<
1372	<	if (globals->haveTauThermostat())
1371	>
1372	>	if (globals->haveTauThermostat())
1373		myNVT->setTauThermostat(globals->getTauThermostat());
1374	<
1375	<	else {
1376	<	sprintf( painCave.errMsg,
1377	<	"SimSetup error: If you use the NVT\n"
1413	<	"    ensemble, you must set tauThermostat.\n");
1374	>	else{
1375	>	sprintf(painCave.errMsg,
1376	>	"SimSetup error: If you use the NVT\n"
1377	>	"    ensemble, you must set tauThermostat.\n");
1378		painCave.isFatal = 1;
1379		simError();
1380		}
1381		break;
1418	–
1419	–	case NPTi_ENS:
1420	–	if (globals->haveZconstraints()){
1421	–	setupZConstraint(info[k]);
1422	–	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1423	–	}
1424	–	else
1425	–	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1382
1383	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1384	<
1385	<	if (globals->haveTargetPressure())
1386	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1387	<	else {
1388	<	sprintf( painCave.errMsg,
1389	<	"SimSetup error: If you use a constant pressure\n"
1434	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1435	<	painCave.isFatal = 1;
1436	<	simError();
1437	<	}
1438	<
1439	<	if( globals->haveTauThermostat() )
1440	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1441	<	else{
1442	<	sprintf( painCave.errMsg,
1443	<	"SimSetup error: If you use an NPT\n"
1444	<	"    ensemble, you must set tauThermostat.\n");
1445	<	painCave.isFatal = 1;
1446	<	simError();
1447	<	}
1448	<
1449	<	if( globals->haveTauBarostat() )
1450	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1451	<	else{
1452	<	sprintf( painCave.errMsg,
1453	<	"SimSetup error: If you use an NPT\n"
1454	<	"    ensemble, you must set tauBarostat.\n");
1455	<	painCave.isFatal = 1;
1456	<	simError();
1457	<	}
1458	<	break;
1459	<
1460	<	case NPTf_ENS:
1461	<	if (globals->haveZconstraints()){
1462	<	setupZConstraint(info[k]);
1463	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1464	<	}
1465	<	else
1466	<	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1383	>	case NPTi_ENS:
1384	>	if (globals->haveZconstraints()){
1385	>	setupZConstraint(info[k]);
1386	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >(&(info[k]), the_ff);
1387	>	}
1388	>	else
1389	>	myNPTi = new NPTi<RealIntegrator>(&(info[k]), the_ff);
1390
1391	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1469	<
1470	<	if (globals->haveTargetPressure())
1471	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1472	<	else {
1473	<	sprintf( painCave.errMsg,
1474	<	"SimSetup error: If you use a constant pressure\n"
1475	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1476	<	painCave.isFatal = 1;
1477	<	simError();
1478	<	}
1479	<
1480	<	if( globals->haveTauThermostat() )
1481	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1482	<	else{
1483	<	sprintf( painCave.errMsg,
1484	<	"SimSetup error: If you use an NPT\n"
1485	<	"    ensemble, you must set tauThermostat.\n");
1486	<	painCave.isFatal = 1;
1487	<	simError();
1488	<	}
1489	<
1490	<	if( globals->haveTauBarostat() )
1491	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1492	<	else{
1493	<	sprintf( painCave.errMsg,
1494	<	"SimSetup error: If you use an NPT\n"
1495	<	"    ensemble, you must set tauBarostat.\n");
1496	<	painCave.isFatal = 1;
1497	<	simError();
1498	<	}
1499	<	break;
1500	<
1501	<	case NPTim_ENS:
1502	<	if (globals->haveZconstraints()){
1503	<	setupZConstraint(info[k]);
1504	<	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1505	<	}
1506	<	else
1507	<	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1391	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1392
1393	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1394	<
1395	<	if (globals->haveTargetPressure())
1396	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1513	<	else {
1514	<	sprintf( painCave.errMsg,
1393	>	if (globals->haveTargetPressure())
1394	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1395	>	else{
1396	>	sprintf(painCave.errMsg,
1397		"SimSetup error: If you use a constant pressure\n"
1398		"    ensemble, you must set targetPressure in the BASS file.\n");
1399	<	painCave.isFatal = 1;
1400	<	simError();
1401	<	}
1402	<
1403	<	if( globals->haveTauThermostat() )
1404	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1405	<	else{
1406	<	sprintf( painCave.errMsg,
1399	>	painCave.isFatal = 1;
1400	>	simError();
1401	>	}
1402	>
1403	>	if (globals->haveTauThermostat())
1404	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1405	>	else{
1406	>	sprintf(painCave.errMsg,
1407		"SimSetup error: If you use an NPT\n"
1408		"    ensemble, you must set tauThermostat.\n");
1409	<	painCave.isFatal = 1;
1410	<	simError();
1411	<	}
1530	<
1531	<	if( globals->haveTauBarostat() )
1532	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1533	<	else{
1534	<	sprintf( painCave.errMsg,
1535	<	"SimSetup error: If you use an NPT\n"
1536	<	"    ensemble, you must set tauBarostat.\n");
1537	<	painCave.isFatal = 1;
1538	<	simError();
1539	<	}
1540	<	break;
1541	<
1542	<	case NPTfm_ENS:
1543	<	if (globals->haveZconstraints()){
1544	<	setupZConstraint(info[k]);
1545	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1546	<	}
1547	<	else
1548	<	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1409	>	painCave.isFatal = 1;
1410	>	simError();
1411	>	}
1412
1413	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1413	>	if (globals->haveTauBarostat())
1414	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1415	>	else{
1416	>	sprintf(painCave.errMsg,
1417	>	"SimSetup error: If you use an NPT\n"
1418	>	"    ensemble, you must set tauBarostat.\n");
1419	>	painCave.isFatal = 1;
1420	>	simError();
1421	>	}
1422	>	break;
1423
1424	<	if (globals->haveTargetPressure())
1425	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1426	<	else {
1427	<	sprintf( painCave.errMsg,
1424	>	case NPTf_ENS:
1425	>	if (globals->haveZconstraints()){
1426	>	setupZConstraint(info[k]);
1427	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff);
1428	>	}
1429	>	else
1430	>	myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff);
1431	>
1432	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1433	>
1434	>	if (globals->haveTargetPressure())
1435	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1436	>	else{
1437	>	sprintf(painCave.errMsg,
1438		"SimSetup error: If you use a constant pressure\n"
1439		"    ensemble, you must set targetPressure in the BASS file.\n");
1440	<	painCave.isFatal = 1;
1441	<	simError();
1442	<	}
1440	>	painCave.isFatal = 1;
1441	>	simError();
1442	>	}
1443
1444	<	if( globals->haveTauThermostat() )
1445	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1446	<	else{
1447	<	sprintf( painCave.errMsg,
1444	>	if (globals->haveTauThermostat())
1445	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1446	>	else{
1447	>	sprintf(painCave.errMsg,
1448		"SimSetup error: If you use an NPT\n"
1449		"    ensemble, you must set tauThermostat.\n");
1450	<	painCave.isFatal = 1;
1451	<	simError();
1452	<	}
1450	>	painCave.isFatal = 1;
1451	>	simError();
1452	>	}
1453
1454	<	if( globals->haveTauBarostat() )
1455	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1456	<	else{
1457	<	sprintf( painCave.errMsg,
1454	>	if (globals->haveTauBarostat())
1455	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1456	>	else{
1457	>	sprintf(painCave.errMsg,
1458		"SimSetup error: If you use an NPT\n"
1459		"    ensemble, you must set tauBarostat.\n");
1460	+	painCave.isFatal = 1;
1461	+	simError();
1462	+	}
1463	+	break;
1464	+
1465	+	case NPTim_ENS:
1466	+	if (globals->haveZconstraints()){
1467	+	setupZConstraint(info[k]);
1468	+	myNPTim = new ZConstraint<NPTim<RealIntegrator> >(&(info[k]), the_ff);
1469	+	}
1470	+	else
1471	+	myNPTim = new NPTim<RealIntegrator>(&(info[k]), the_ff);
1472	+
1473	+	myNPTim->setTargetTemp(globals->getTargetTemp());
1474	+
1475	+	if (globals->haveTargetPressure())
1476	+	myNPTim->setTargetPressure(globals->getTargetPressure());
1477	+	else{
1478	+	sprintf(painCave.errMsg,
1479	+	"SimSetup error: If you use a constant pressure\n"
1480	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1481	+	painCave.isFatal = 1;
1482	+	simError();
1483	+	}
1484	+
1485	+	if (globals->haveTauThermostat())
1486	+	myNPTim->setTauThermostat(globals->getTauThermostat());
1487	+	else{
1488	+	sprintf(painCave.errMsg,
1489	+	"SimSetup error: If you use an NPT\n"
1490	+	"    ensemble, you must set tauThermostat.\n");
1491	+	painCave.isFatal = 1;
1492	+	simError();
1493	+	}
1494	+
1495	+	if (globals->haveTauBarostat())
1496	+	myNPTim->setTauBarostat(globals->getTauBarostat());
1497	+	else{
1498	+	sprintf(painCave.errMsg,
1499	+	"SimSetup error: If you use an NPT\n"
1500	+	"    ensemble, you must set tauBarostat.\n");
1501	+	painCave.isFatal = 1;
1502	+	simError();
1503	+	}
1504	+	break;
1505	+
1506	+	case NPTfm_ENS:
1507	+	if (globals->haveZconstraints()){
1508	+	setupZConstraint(info[k]);
1509	+	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff);
1510	+	}
1511	+	else
1512	+	myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff);
1513	+
1514	+	myNPTfm->setTargetTemp(globals->getTargetTemp());
1515	+
1516	+	if (globals->haveTargetPressure())
1517	+	myNPTfm->setTargetPressure(globals->getTargetPressure());
1518	+	else{
1519	+	sprintf(painCave.errMsg,
1520	+	"SimSetup error: If you use a constant pressure\n"
1521	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1522	+	painCave.isFatal = 1;
1523	+	simError();
1524	+	}
1525	+
1526	+	if (globals->haveTauThermostat())
1527	+	myNPTfm->setTauThermostat(globals->getTauThermostat());
1528	+	else{
1529	+	sprintf(painCave.errMsg,
1530	+	"SimSetup error: If you use an NPT\n"
1531	+	"    ensemble, you must set tauThermostat.\n");
1532	+	painCave.isFatal = 1;
1533	+	simError();
1534	+	}
1535	+
1536	+	if (globals->haveTauBarostat())
1537	+	myNPTfm->setTauBarostat(globals->getTauBarostat());
1538	+	else{
1539	+	sprintf(painCave.errMsg,
1540	+	"SimSetup error: If you use an NPT\n"
1541	+	"    ensemble, you must set tauBarostat.\n");
1542	+	painCave.isFatal = 1;
1543	+	simError();
1544	+	}
1545	+	break;
1546	+
1547	+	default:
1548	+	sprintf(painCave.errMsg,
1549	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1550		painCave.isFatal = 1;
1551		simError();
1580	–	}
1581	–	break;
1582	–
1583	–	default:
1584	–	sprintf( painCave.errMsg,
1585	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1586	–	painCave.isFatal = 1;
1587	–	simError();
1552		}
1553		}
1554		}
1555
1556	<	void SimSetup::initFortran( void ){
1593	<
1556	>	void SimSetup::initFortran(void){
1557		info[0].refreshSim();
1558	<
1559	<	if( !strcmp( info[0].mixingRule, "standard") ){
1560	<	the_ff->initForceField( LB_MIXING_RULE );
1558	>
1559	>	if (!strcmp(info[0].mixingRule, "standard")){
1560	>	the_ff->initForceField(LB_MIXING_RULE);
1561		}
1562	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1563	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1562	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1563	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1564		}
1565		else{
1566	<	sprintf( painCave.errMsg,
1567	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1605	<	info[0].mixingRule );
1566	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1567	>	info[0].mixingRule);
1568		painCave.isFatal = 1;
1569		simError();
1570		}
1571
1572
1573		#ifdef IS_MPI
1574	<	strcpy( checkPointMsg,
1613	<	"Successfully intialized the mixingRule for Fortran." );
1574	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1575		MPIcheckPoint();
1576		#endif // is_mpi
1616	–
1577		}
1578
1579	<	void SimSetup::setupZConstraint(SimInfo& theInfo)
1620	<	{
1579	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1580		int nZConstraints;
1581		ZconStamp** zconStamp;
1582
1583	<	if(globals->haveZconstraintTime()){
1625	<
1583	>	if (globals->haveZconstraintTime()){
1584		//add sample time of z-constraint  into SimInfo's property list
1585		DoubleData* zconsTimeProp = new DoubleData();
1586		zconsTimeProp->setID(ZCONSTIME_ID);
#	Line 1630 | Line 1588 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1588		theInfo.addProperty(zconsTimeProp);
1589		}
1590		else{
1591	<	sprintf( painCave.errMsg,
1592	<	"ZConstraint error: If you use an ZConstraint\n"
1593	<	" , you must set sample time.\n");
1591	>	sprintf(painCave.errMsg,
1592	>	"ZConstraint error: If you use an ZConstraint\n"
1593	>	" , you must set sample time.\n");
1594		painCave.isFatal = 1;
1595	<	simError();
1595	>	simError();
1596		}
1597
1598		//push zconsTol into siminfo, if user does not specify
1599		//value for zconsTol, a default value will be used
1600		DoubleData* zconsTol = new DoubleData();
1601		zconsTol->setID(ZCONSTOL_ID);
1602	<	if(globals->haveZconsTol()){
1602	>	if (globals->haveZconsTol()){
1603		zconsTol->setData(globals->getZconsTol());
1604		}
1605		else{
1606	<	double defaultZConsTol = 0.01;
1607	<	sprintf( painCave.errMsg,
1608	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1609	<	" , default value %f is used.\n", defaultZConsTol);
1606	>	double defaultZConsTol = 0.01;
1607	>	sprintf(painCave.errMsg,
1608	>	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1609	>	" , default value %f is used.\n",
1610	>	defaultZConsTol);
1611		painCave.isFatal = 0;
1612		simError();
1613
#	Line 1657 | Line 1616 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1616		theInfo.addProperty(zconsTol);
1617
1618		//set Force Substraction Policy
1619	<	StringData* zconsForcePolicy =  new StringData();
1619	>	StringData* zconsForcePolicy = new StringData();
1620		zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1621	<
1622	<	if(globals->haveZconsForcePolicy()){
1621	>
1622	>	if (globals->haveZconsForcePolicy()){
1623		zconsForcePolicy->setData(globals->getZconsForcePolicy());
1624	<	}
1624	>	}
1625		else{
1626	<	sprintf( painCave.errMsg,
1627	<	"ZConstraint Warning: User does not set force substraction policy, "
1628	<	"average force substraction policy is used\n");
1629	<	painCave.isFatal = 0;
1630	<	simError();
1631	<	zconsForcePolicy->setData("BYNUMBER");
1626	>	sprintf(painCave.errMsg,
1627	>	"ZConstraint Warning: User does not set force substraction policy, "
1628	>	"average force substraction policy is used\n");
1629	>	painCave.isFatal = 0;
1630	>	simError();
1631	>	zconsForcePolicy->setData("BYNUMBER");
1632		}
1633	<
1634	<	theInfo.addProperty(zconsForcePolicy);
1635	<
1633	>
1634	>	theInfo.addProperty(zconsForcePolicy);
1635	>
1636		//Determine the name of ouput file and add it into SimInfo's property list
1637		//Be careful, do not use inFileName, since it is a pointer which
1638		//point to a string at master node, and slave nodes do not contain that string
1639	<
1639	>
1640		string zconsOutput(theInfo.finalName);
1641	<
1641	>
1642		zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1643	<
1643	>
1644		StringData* zconsFilename = new StringData();
1645		zconsFilename->setID(ZCONSFILENAME_ID);
1646		zconsFilename->setData(zconsOutput);
1647	<
1647	>
1648		theInfo.addProperty(zconsFilename);
1649	<
1649	>
1650		//setup index, pos and other parameters of z-constraint molecules
1651		nZConstraints = globals->getNzConstraints();
1652		theInfo.nZconstraints = nZConstraints;
#	Line 1697 | Line 1656 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1656
1657		ZConsParaData* zconsParaData = new ZConsParaData();
1658		zconsParaData->setID(ZCONSPARADATA_ID);
1659	<
1660	<	for(int i = 0; i < nZConstraints; i++){
1659	>
1660	>	for (int i = 0; i < nZConstraints; i++){
1661		tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1662		tempParaItem.zPos = zconStamp[i]->getZpos();
1663		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
#	Line 1709 | Line 1668 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1668
1669		//sort the parameters by index of molecules
1670		zconsParaData->sortByIndex();
1671	<
1671	>
1672		//push data into siminfo, therefore, we can retrieve later
1673		theInfo.addProperty(zconsParaData);
1715	–
1674		}

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