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root/group/branches/no-template-branch/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 787 by mmeineke, Thu Sep 25 19:27:15 2003 UTC

#	Line 3 | Line 3
3		#include <iostream>
4		#include <cmath>
5		#include <string>
6	+	#include <sprng.h>
7
8		#include "SimSetup.hpp"
9		#include "ReadWrite.hpp"
#	Line 21 | Line 22
22		#define NVT_ENS        1
23		#define NPTi_ENS       2
24		#define NPTf_ENS       3
24	–	#define NPTim_ENS      4
25	–	#define NPTfm_ENS      5
25
26		#define FF_DUFF 0
27		#define FF_LJ   1
#	Line 31 | Line 30 | SimSetup::SimSetup(){
30		using namespace std;
31
32		SimSetup::SimSetup(){
34	–
33		isInfoArray = 0;
34		nInfo = 1;
35	<
35	>
36		stamps = new MakeStamps();
37		globals = new Globals();
38	<
39	<
38	>
39	>
40		#ifdef IS_MPI
41	<	strcpy( checkPointMsg, "SimSetup creation successful" );
41	>	strcpy(checkPointMsg, "SimSetup creation successful");
42		MPIcheckPoint();
43		#endif // IS_MPI
44		}
#	Line 50 | Line 48 | SimSetup::~SimSetup(){
48		delete globals;
49		}
50
51	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
52	<	info = the_info;
53	<	nInfo = theNinfo;
54	<	isInfoArray = 1;
51	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
52	>	info = the_info;
53	>	nInfo = theNinfo;
54	>	isInfoArray = 1;
55		}
56
57
58	<	void SimSetup::parseFile( char* fileName ){
61	<
58	>	void SimSetup::parseFile(char* fileName){
59		#ifdef IS_MPI
60	<	if( worldRank == 0 ){
60	>	if (worldRank == 0){
61		#endif // is_mpi
62	<
62	>
63		inFileName = fileName;
64	<	set_interface_stamps( stamps, globals );
65	<
64	>	set_interface_stamps(stamps, globals);
65	>
66		#ifdef IS_MPI
67		mpiEventInit();
68		#endif
69
70	<	yacc_BASS( fileName );
70	>	yacc_BASS(fileName);
71
72		#ifdef IS_MPI
73		throwMPIEvent(NULL);
74		}
75	<	else receiveParse();
75	>	else{
76	>	receiveParse();
77	>	}
78		#endif
79
80		}
81
82		#ifdef IS_MPI
83		void SimSetup::receiveParse(void){
84	<
85	<	set_interface_stamps( stamps, globals );
86	<	mpiEventInit();
87	<	MPIcheckPoint();
89	<	mpiEventLoop();
90	<
84	>	set_interface_stamps(stamps, globals);
85	>	mpiEventInit();
86	>	MPIcheckPoint();
87	>	mpiEventLoop();
88		}
89
90		#endif // is_mpi
91
92		void SimSetup::createSim(void){
93
97	–	int i, j, k, globalAtomIndex;
98	–
94		// gather all of the information from the Bass file
95
96		gatherInfo();
#	Line 110 | Line 105 | void SimSetup::createSim(void){
105
106		// initialize the system coordinates
107
108	<	if( !isInfoArray ) initSystemCoords();
108	>	if (!isInfoArray){
109	>	initSystemCoords();
110	>	}
111
112		// make the output filenames
113
114		makeOutNames();
115	<
115	>
116		// make the integrator
117	<
117	>
118		makeIntegrator();
119	<
119	>
120		#ifdef IS_MPI
121		mpiSim->mpiRefresh();
122		#endif
#	Line 127 | Line 124 | void SimSetup::createSim(void){
124		// initialize the Fortran
125
126		initFortran();
130	–
131	–
132	–
127		}
128
129
130	<	void SimSetup::makeMolecules( void ){
131	<
138	<	int k,l;
130	>	void SimSetup::makeMolecules(void){
131	>	int k;
132		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
133		molInit molInfo;
134		DirectionalAtom* dAtom;
#	Line 150 | Line 143 | void SimSetup::makeMolecules( void ){
143		bend_set* theBends;
144		torsion_set* theTorsions;
145
146	<
146	>
147		//init the forceField paramters
148
149		the_ff->readParams();
150
151	<
151	>
152		// init the atoms
153
154		double ux, uy, uz, u, uSqr;
162	–
163	–	for(k=0; k<nInfo; k++){
164	–
165	–	the_ff->setSimInfo( &(info[k]) );
155
156	+	for (k = 0; k < nInfo; k++){
157	+	the_ff->setSimInfo(&(info[k]));
158	+
159		atomOffset = 0;
160		excludeOffset = 0;
161	<	for(i=0; i<info[k].n_mol; i++){
170	<
161	>	for (i = 0; i < info[k].n_mol; i++){
162		stampID = info[k].molecules[i].getStampID();
163
164	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
165	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
166	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
164	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
165	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
166	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
167		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
168		molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
169	<
169	>
170		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
171		molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
172	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
173	<	molInfo.myBends = new Bend*[molInfo.nBends];
174	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
172	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
173	>	molInfo.myBends = new Bend * [molInfo.nBends];
174	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
175
176		theBonds = new bond_pair[molInfo.nBonds];
177		theBends = new bend_set[molInfo.nBends];
178		theTorsions = new torsion_set[molInfo.nTorsions];
179	<
179	>
180		// make the Atoms
181	<
182	<	for(j=0; j<molInfo.nAtoms; j++){
183	<
184	<	currentAtom = comp_stamps[stampID]->getAtom( j );
185	<	if( currentAtom->haveOrientation() ){
186	<
187	<	dAtom = new DirectionalAtom( (j + atomOffset),
188	<	info[k].getConfiguration() );
189	<	info[k].n_oriented++;
190	<	molInfo.myAtoms[j] = dAtom;
191	<
192	<	ux = currentAtom->getOrntX();
193	<	uy = currentAtom->getOrntY();
194	<	uz = currentAtom->getOrntZ();
195	<
196	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
197	<
198	<	u = sqrt( uSqr );
199	<	ux = ux / u;
200	<	uy = uy / u;
201	<	uz = uz / u;
202	<
203	<	dAtom->setSUx( ux );
204	<	dAtom->setSUy( uy );
205	<	dAtom->setSUz( uz );
206	<	}
207	<	else{
208	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
209	<	info[k].getConfiguration() );
210	<	}
220	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221	<
181	>
182	>	for (j = 0; j < molInfo.nAtoms; j++){
183	>	currentAtom = comp_stamps[stampID]->getAtom(j);
184	>	if (currentAtom->haveOrientation()){
185	>	dAtom = new DirectionalAtom((j + atomOffset),
186	>	info[k].getConfiguration());
187	>	info[k].n_oriented++;
188	>	molInfo.myAtoms[j] = dAtom;
189	>
190	>	ux = currentAtom->getOrntX();
191	>	uy = currentAtom->getOrntY();
192	>	uz = currentAtom->getOrntZ();
193	>
194	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
195	>
196	>	u = sqrt(uSqr);
197	>	ux = ux / u;
198	>	uy = uy / u;
199	>	uz = uz / u;
200	>
201	>	dAtom->setSUx(ux);
202	>	dAtom->setSUy(uy);
203	>	dAtom->setSUz(uz);
204	>	}
205	>	else{
206	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
207	>	info[k].getConfiguration());
208	>	}
209	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
210	>
211		#ifdef IS_MPI
212	<
213	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
214	<
212	>
213	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
214	>
215		#endif // is_mpi
216		}
217	<
218	<	// make the bonds
219	<	for(j=0; j<molInfo.nBonds; j++){
220	<
221	<	currentBond = comp_stamps[stampID]->getBond( j );
222	<	theBonds[j].a = currentBond->getA() + atomOffset;
223	<	theBonds[j].b = currentBond->getB() + atomOffset;
224	<
225	<	exI = theBonds[j].a;
226	<	exJ = theBonds[j].b;
227	<
228	<	// exclude_I must always be the smaller of the pair
229	<	if( exI > exJ ){
230	<	tempEx = exI;
231	<	exI = exJ;
232	<	exJ = tempEx;
244	<	}
217	>
218	>	// make the bonds
219	>	for (j = 0; j < molInfo.nBonds; j++){
220	>	currentBond = comp_stamps[stampID]->getBond(j);
221	>	theBonds[j].a = currentBond->getA() + atomOffset;
222	>	theBonds[j].b = currentBond->getB() + atomOffset;
223	>
224	>	exI = theBonds[j].a;
225	>	exJ = theBonds[j].b;
226	>
227	>	// exclude_I must always be the smaller of the pair
228	>	if (exI > exJ){
229	>	tempEx = exI;
230	>	exI = exJ;
231	>	exJ = tempEx;
232	>	}
233		#ifdef IS_MPI
234	<	tempEx = exI;
235	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
236	<	tempEx = exJ;
237	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
238	<
239	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
234	>	tempEx = exI;
235	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
236	>	tempEx = exJ;
237	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
238	>
239	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
240		#else  // isn't MPI
241	<
242	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
241	>
242	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
243		#endif  //is_mpi
244		}
245		excludeOffset += molInfo.nBonds;
246	<
246	>
247		//make the bends
248	<	for(j=0; j<molInfo.nBends; j++){
249	<
250	<	currentBend = comp_stamps[stampID]->getBend( j );
251	<	theBends[j].a = currentBend->getA() + atomOffset;
252	<	theBends[j].b = currentBend->getB() + atomOffset;
253	<	theBends[j].c = currentBend->getC() + atomOffset;
254	<
255	<	if( currentBend->haveExtras() ){
256	<
257	<	extras = currentBend->getExtras();
258	<	current_extra = extras;
259	<
260	<	while( current_extra != NULL ){
261	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
262	<
263	<	switch( current_extra->getType() ){
264	<
265	<	case 0:
266	<	theBends[j].ghost =
267	<	current_extra->getInt() + atomOffset;
268	<	theBends[j].isGhost = 1;
269	<	break;
270	<
271	<	case 1:
272	<	theBends[j].ghost =
273	<	(int)current_extra->getDouble() + atomOffset;
274	<	theBends[j].isGhost = 1;
275	<	break;
276	<
277	<	default:
278	<	sprintf( painCave.errMsg,
279	<	"SimSetup Error: ghostVectorSource was neither a "
280	<	"double nor an int.\n"
281	<	"-->Bend[%d] in %s\n",
282	<	j, comp_stamps[stampID]->getID() );
283	<	painCave.isFatal = 1;
284	<	simError();
248	>	for (j = 0; j < molInfo.nBends; j++){
249	>	currentBend = comp_stamps[stampID]->getBend(j);
250	>	theBends[j].a = currentBend->getA() + atomOffset;
251	>	theBends[j].b = currentBend->getB() + atomOffset;
252	>	theBends[j].c = currentBend->getC() + atomOffset;
253	>
254	>	if (currentBend->haveExtras()){
255	>	extras = currentBend->getExtras();
256	>	current_extra = extras;
257	>
258	>	while (current_extra != NULL){
259	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
260	>	switch (current_extra->getType()){
261	>	case 0:
262	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
263	>	theBends[j].isGhost = 1;
264	>	break;
265	>
266	>	case 1:
267	>	theBends[j].ghost = (int) current_extra->getDouble() +
268	>	atomOffset;
269	>	theBends[j].isGhost = 1;
270	>	break;
271	>
272	>	default:
273	>	sprintf(painCave.errMsg,
274	>	"SimSetup Error: ghostVectorSource was neither a "
275	>	"double nor an int.\n"
276	>	"-->Bend[%d] in %s\n",
277	>	j, comp_stamps[stampID]->getID());
278	>	painCave.isFatal = 1;
279	>	simError();
280	>	}
281	>	}
282	>	else{
283	>	sprintf(painCave.errMsg,
284	>	"SimSetup Error: unhandled bend assignment:\n"
285	>	"    -->%s in Bend[%d] in %s\n",
286	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
287	>	painCave.isFatal = 1;
288	>	simError();
289	>	}
290	>
291	>	current_extra = current_extra->getNext();
292	>	}
293		}
294	<	}
295	<
296	<	else{
297	<
298	<	sprintf( painCave.errMsg,
299	<	"SimSetup Error: unhandled bend assignment:\n"
300	<	"    -->%s in Bend[%d] in %s\n",
301	<	current_extra->getlhs(),
302	<	j, comp_stamps[stampID]->getID() );
303	<	painCave.isFatal = 1;
304	<	simError();
305	<	}
306	<
307	<	current_extra = current_extra->getNext();
308	<	}
309	<	}
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	<	}
294	>
295	>	if (!theBends[j].isGhost){
296	>	exI = theBends[j].a;
297	>	exJ = theBends[j].c;
298	>	}
299	>	else{
300	>	exI = theBends[j].a;
301	>	exJ = theBends[j].b;
302	>	}
303	>
304	>	// exclude_I must always be the smaller of the pair
305	>	if (exI > exJ){
306	>	tempEx = exI;
307	>	exI = exJ;
308	>	exJ = tempEx;
309	>	}
310		#ifdef IS_MPI
311	<	tempEx = exI;
312	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
313	<	tempEx = exJ;
314	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
315	<
316	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
311	>	tempEx = exI;
312	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
313	>	tempEx = exJ;
314	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
315	>
316	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
317		#else  // isn't MPI
318	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
318	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
319		#endif  //is_mpi
320		}
321		excludeOffset += molInfo.nBends;
322	<
323	<	for(j=0; j<molInfo.nTorsions; j++){
324	<
325	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
326	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
327	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
328	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
329	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
330	<
331	<	exI = theTorsions[j].a;
332	<	exJ = theTorsions[j].d;
333	<
334	<	// exclude_I must always be the smaller of the pair
335	<	if( exI > exJ ){
336	<	tempEx = exI;
337	<	exI = exJ;
338	<	exJ = tempEx;
361	<	}
322	>
323	>	for (j = 0; j < molInfo.nTorsions; j++){
324	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
325	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
326	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
327	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
328	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
329	>
330	>	exI = theTorsions[j].a;
331	>	exJ = theTorsions[j].d;
332	>
333	>	// exclude_I must always be the smaller of the pair
334	>	if (exI > exJ){
335	>	tempEx = exI;
336	>	exI = exJ;
337	>	exJ = tempEx;
338	>	}
339		#ifdef IS_MPI
340	<	tempEx = exI;
341	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
342	<	tempEx = exJ;
343	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
344	<
345	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
340	>	tempEx = exI;
341	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
342	>	tempEx = exJ;
343	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
344	>
345	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
346		#else  // isn't MPI
347	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
347	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
348		#endif  //is_mpi
349		}
350		excludeOffset += molInfo.nTorsions;
351	<
352	<
351	>
352	>
353		// 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 );
354
355	<
355	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
356	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
357	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
358	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
359	>	theTorsions);
360	>
361	>
362	>	info[k].molecules[i].initialize(molInfo);
363	>
364	>
365		atomOffset += molInfo.nAtoms;
366		delete[] theBonds;
367		delete[] theBends;
368		delete[] theTorsions;
369		}
370		}
371	<
371	>
372		#ifdef IS_MPI
373	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
373	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
374		MPIcheckPoint();
375		#endif // is_mpi
376	<
376	>
377		// clean up the forcefield
378
379		the_ff->calcRcut();
380		the_ff->cleanMe();
403	–
381		}
382
383	<	void SimSetup::initFromBass( void ){
407	<
383	>	void SimSetup::initFromBass(void){
384		int i, j, k;
385		int n_cells;
386		double cellx, celly, cellz;
#	Line 418 | Line 394 | void SimSetup::initFromBass( void ){
394		vel[1] = 0.0;
395		vel[2] = 0.0;
396
397	<	temp1 = (double)tot_nmol / 4.0;
398	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
399	<	temp3 = ceil( temp2 );
397	>	temp1 = (double) tot_nmol / 4.0;
398	>	temp2 = pow(temp1, (1.0 / 3.0));
399	>	temp3 = ceil(temp2);
400
401	<	have_extra =0;
402	<	if( temp2 < temp3 ){ // we have a non-complete lattice
403	<	have_extra =1;
401	>	have_extra = 0;
402	>	if (temp2 < temp3){
403	>	// we have a non-complete lattice
404	>	have_extra = 1;
405
406	<	n_cells = (int)temp3 - 1;
406	>	n_cells = (int) temp3 - 1;
407		cellx = info[0].boxL[0] / temp3;
408		celly = info[0].boxL[1] / temp3;
409		cellz = info[0].boxL[2] / temp3;
410	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
411	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
412	<	n_per_extra = (int)ceil( temp1 );
410	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
411	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
412	>	n_per_extra = (int) ceil(temp1);
413
414	<	if( n_per_extra > 4){
415	<	sprintf( painCave.errMsg,
416	<	"SimSetup error. There has been an error in constructing"
417	<	" the non-complete lattice.\n" );
414	>	if (n_per_extra > 4){
415	>	sprintf(painCave.errMsg,
416	>	"SimSetup error. There has been an error in constructing"
417	>	" the non-complete lattice.\n");
418		painCave.isFatal = 1;
419		simError();
420		}
421		}
422		else{
423	<	n_cells = (int)temp3;
423	>	n_cells = (int) temp3;
424		cellx = info[0].boxL[0] / temp3;
425		celly = info[0].boxL[1] / temp3;
426		cellz = info[0].boxL[2] / temp3;
#	Line 454 | Line 431 | void SimSetup::initFromBass( void ){
431		current_comp = 0;
432		current_atom_ndx = 0;
433
434	<	for( i=0; i < n_cells ; i++ ){
435	<	for( j=0; j < n_cells; j++ ){
436	<	for( k=0; k < n_cells; k++ ){
434	>	for (i = 0; i < n_cells ; i++){
435	>	for (j = 0; j < n_cells; j++){
436	>	for (k = 0; k < n_cells; k++){
437	>	makeElement(i * cellx, j * celly, k * cellz);
438
439	<	makeElement( i * cellx,
462	<	j * celly,
463	<	k * cellz );
439	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
440
441	<	makeElement( i * cellx + 0.5 * cellx,
466	<	j * celly + 0.5 * celly,
467	<	k * cellz );
441	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
442
443	<	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 );
443	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
444		}
445		}
446		}
447
448	<	if( have_extra ){
448	>	if (have_extra){
449		done = 0;
450
451		int start_ndx;
452	<	for( i=0; i < (n_cells+1) && !done; i++ ){
453	<	for( j=0; j < (n_cells+1) && !done; j++ ){
452	>	for (i = 0; i < (n_cells + 1) && !done; i++){
453	>	for (j = 0; j < (n_cells + 1) && !done; j++){
454	>	if (i < n_cells){
455	>	if (j < n_cells){
456	>	start_ndx = n_cells;
457	>	}
458	>	else
459	>	start_ndx = 0;
460	>	}
461	>	else
462	>	start_ndx = 0;
463
464	<	if( i < n_cells ){
464	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
465	>	makeElement(i * cellx, j * celly, k * cellz);
466	>	done = (current_mol >= tot_nmol);
467
468	<	if( j < n_cells ){
469	<	start_ndx = n_cells;
470	<	}
471	<	else start_ndx = 0;
472	<	}
494	<	else start_ndx = 0;
468	>	if (!done && n_per_extra > 1){
469	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
470	>	k * cellz);
471	>	done = (current_mol >= tot_nmol);
472	>	}
473
474	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
475	<
476	<	makeElement( i * cellx,
477	<	j * celly,
478	<	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	<	}
474	>	if (!done && n_per_extra > 2){
475	>	makeElement(i * cellx, j * celly + 0.5 * celly,
476	>	k * cellz + 0.5 * cellz);
477	>	done = (current_mol >= tot_nmol);
478	>	}
479
480	<	if( !done && n_per_extra > 2){
481	<	makeElement( i * cellx,
482	<	j * celly + 0.5 * celly,
483	<	k * cellz + 0.5 * cellz );
484	<	done = ( current_mol >= tot_nmol );
485	<	}
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	<	}
480	>	if (!done && n_per_extra > 3){
481	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
482	>	k * cellz + 0.5 * cellz);
483	>	done = (current_mol >= tot_nmol);
484	>	}
485	>	}
486		}
487		}
488		}
489
490	<	for( i=0; i<info[0].n_atoms; i++ ){
491	<	info[0].atoms[i]->setVel( vel );
490	>	for (i = 0; i < info[0].n_atoms; i++){
491	>	info[0].atoms[i]->setVel(vel);
492		}
493		}
494
495	<	void SimSetup::makeElement( double x, double y, double z ){
534	<
495	>	void SimSetup::makeElement(double x, double y, double z){
496		int k;
497		AtomStamp* current_atom;
498		DirectionalAtom* dAtom;
499		double rotMat[3][3];
500		double pos[3];
501
502	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
503	<
504	<	current_atom = comp_stamps[current_comp]->getAtom( k );
505	<	if( !current_atom->havePosition() ){
506	<	sprintf( painCave.errMsg,
507	<	"SimSetup:initFromBass error.\n"
508	<	"\tComponent %s, atom %s does not have a position specified.\n"
509	<	"\tThe initialization routine is unable to give a start"
510	<	" position.\n",
550	<	comp_stamps[current_comp]->getID(),
551	<	current_atom->getType() );
502	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
503	>	current_atom = comp_stamps[current_comp]->getAtom(k);
504	>	if (!current_atom->havePosition()){
505	>	sprintf(painCave.errMsg,
506	>	"SimSetup:initFromBass error.\n"
507	>	"\tComponent %s, atom %s does not have a position specified.\n"
508	>	"\tThe initialization routine is unable to give a start"
509	>	" position.\n",
510	>	comp_stamps[current_comp]->getID(), current_atom->getType());
511		painCave.isFatal = 1;
512		simError();
513		}
514	<
514	>
515		pos[0] = x + current_atom->getPosX();
516		pos[1] = y + current_atom->getPosY();
517		pos[2] = z + current_atom->getPosZ();
559	–
560	–	info[0].atoms[current_atom_ndx]->setPos( pos );
518
519	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
519	>	info[0].atoms[current_atom_ndx]->setPos(pos);
520
521	<	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
521	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
522	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
523
524		rotMat[0][0] = 1.0;
525		rotMat[0][1] = 0.0;
#	Line 575 | Line 533 | void SimSetup::makeElement( double x, double y, double
533		rotMat[2][1] = 0.0;
534		rotMat[2][2] = 1.0;
535
536	<	dAtom->setA( rotMat );
536	>	dAtom->setA(rotMat);
537		}
538
539		current_atom_ndx++;
#	Line 584 | Line 542 | void SimSetup::makeElement( double x, double y, double
542		current_mol++;
543		current_comp_mol++;
544
545	<	if( current_comp_mol >= components_nmol[current_comp] ){
588	<
545	>	if (current_comp_mol >= components_nmol[current_comp]){
546		current_comp_mol = 0;
547		current_comp++;
548		}
549		}
550
551
552	<	void SimSetup::gatherInfo( void ){
553	<	int i,j,k;
552	>	void SimSetup::gatherInfo(void){
553	>	int i;
554
555		ensembleCase = -1;
556		ffCase = -1;
557
558		// set the easy ones first
559
560	<	for( i=0; i<nInfo; i++){
560	>	for (i = 0; i < nInfo; i++){
561		info[i].target_temp = globals->getTargetTemp();
562		info[i].dt = globals->getDt();
563		info[i].run_time = globals->getRunTime();
#	Line 610 | Line 567 | void SimSetup::gatherInfo( void ){
567
568		// get the forceField
569
570	<	strcpy( force_field, globals->getForceField() );
570	>	strcpy(force_field, globals->getForceField());
571
572	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
573	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
574	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
572	>	if (!strcasecmp(force_field, "DUFF")){
573	>	ffCase = FF_DUFF;
574	>	}
575	>	else if (!strcasecmp(force_field, "LJ")){
576	>	ffCase = FF_LJ;
577	>	}
578	>	else if (!strcasecmp(force_field, "EAM")){
579	>	ffCase = FF_EAM;
580	>	}
581		else{
582	<	sprintf( painCave.errMsg,
583	<	"SimSetup Error. Unrecognized force field -> %s\n",
584	<	force_field );
585	<	painCave.isFatal = 1;
623	<	simError();
582	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
583	>	force_field);
584	>	painCave.isFatal = 1;
585	>	simError();
586		}
587
588	<	// get the ensemble
588	>	// get the ensemble
589
590	<	strcpy( ensemble, globals->getEnsemble() );
590	>	strcpy(ensemble, globals->getEnsemble());
591
592	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
593	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
594	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
592	>	if (!strcasecmp(ensemble, "NVE")){
593	>	ensembleCase = NVE_ENS;
594	>	}
595	>	else if (!strcasecmp(ensemble, "NVT")){
596	>	ensembleCase = NVT_ENS;
597	>	}
598	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
599		ensembleCase = NPTi_ENS;
600	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
601	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
602	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
600	>	}
601	>	else if (!strcasecmp(ensemble, "NPTf")){
602	>	ensembleCase = NPTf_ENS;
603	>	}
604		else{
605	<	sprintf( painCave.errMsg,
606	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
607	<	"reverting to NVE for this simulation.\n",
608	<	ensemble );
609	<	painCave.isFatal = 0;
610	<	simError();
611	<	strcpy( ensemble, "NVE" );
612	<	ensembleCase = NVE_ENS;
605	>	sprintf(painCave.errMsg,
606	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
607	>	"reverting to NVE for this simulation.\n",
608	>	ensemble);
609	>	painCave.isFatal = 0;
610	>	simError();
611	>	strcpy(ensemble, "NVE");
612	>	ensembleCase = NVE_ENS;
613		}
647	–
648	–	for(i=0; i<nInfo; i++){
649	–
650	–	strcpy( info[i].ensemble, ensemble );
614
615	+	for (i = 0; i < nInfo; i++){
616	+	strcpy(info[i].ensemble, ensemble);
617	+
618		// get the mixing rule
619
620	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
620	>	strcpy(info[i].mixingRule, globals->getMixingRule());
621		info[i].usePBC = globals->getPBC();
622		}
623	<
623	>
624		// get the components and calculate the tot_nMol and indvidual n_mol
625	<
625	>
626		the_components = globals->getComponents();
627		components_nmol = new int[n_components];
628
629
630	<	if( !globals->haveNMol() ){
630	>	if (!globals->haveNMol()){
631		// we don't have the total number of molecules, so we assume it is
632		// given in each component
633
634		tot_nmol = 0;
635	<	for( i=0; i<n_components; i++ ){
636	<
637	<	if( !the_components[i]->haveNMol() ){
638	<	// we have a problem
639	<	sprintf( painCave.errMsg,
640	<	"SimSetup Error. No global NMol or component NMol"
641	<	" given. Cannot calculate the number of atoms.\n" );
642	<	painCave.isFatal = 1;
677	<	simError();
635	>	for (i = 0; i < n_components; i++){
636	>	if (!the_components[i]->haveNMol()){
637	>	// we have a problem
638	>	sprintf(painCave.errMsg,
639	>	"SimSetup Error. No global NMol or component NMol"
640	>	" given. Cannot calculate the number of atoms.\n");
641	>	painCave.isFatal = 1;
642	>	simError();
643		}
644
645		tot_nmol += the_components[i]->getNMol();
#	Line 682 | Line 647 | void SimSetup::gatherInfo( void ){
647		}
648		}
649		else{
650	<	sprintf( painCave.errMsg,
651	<	"SimSetup error.\n"
652	<	"\tSorry, the ability to specify total"
653	<	" nMols and then give molfractions in the components\n"
654	<	"\tis not currently supported."
655	<	" Please give nMol in the components.\n" );
650	>	sprintf(painCave.errMsg,
651	>	"SimSetup error.\n"
652	>	"\tSorry, the ability to specify total"
653	>	" nMols and then give molfractions in the components\n"
654	>	"\tis not currently supported."
655	>	" Please give nMol in the components.\n");
656		painCave.isFatal = 1;
657		simError();
658		}
659
660		// set the status, sample, and thermal kick times
696	–
697	–	for(i=0; i<nInfo; i++){
661
662	<	if( globals->haveSampleTime() ){
662	>	for (i = 0; i < nInfo; i++){
663	>	if (globals->haveSampleTime()){
664		info[i].sampleTime = globals->getSampleTime();
665		info[i].statusTime = info[i].sampleTime;
666		info[i].thermalTime = info[i].sampleTime;
#	Line 706 | Line 670 | void SimSetup::gatherInfo( void ){
670		info[i].statusTime = info[i].sampleTime;
671		info[i].thermalTime = info[i].sampleTime;
672		}
673	<
674	<	if( globals->haveStatusTime() ){
673	>
674	>	if (globals->haveStatusTime()){
675		info[i].statusTime = globals->getStatusTime();
676		}
677	<
678	<	if( globals->haveThermalTime() ){
677	>
678	>	if (globals->haveThermalTime()){
679		info[i].thermalTime = globals->getThermalTime();
680		}
681
682	+	info[i].resetIntegrator = 0;
683	+	if( globals->haveResetTime() ){
684	+	info[i].resetTime = globals->getResetTime();
685	+	info[i].resetIntegrator = 1;
686	+	}
687	+
688		// check for the temperature set flag
689
690	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
691	<
690	>	if (globals->haveTempSet())
691	>	info[i].setTemp = globals->getTempSet();
692	>
693		// get some of the tricky things that may still be in the globals
694	<
694	>
695		double boxVector[3];
696	<	if( globals->haveBox() ){
696	>	if (globals->haveBox()){
697		boxVector[0] = globals->getBox();
698		boxVector[1] = globals->getBox();
699		boxVector[2] = globals->getBox();
700	<
701	<	info[i].setBox( boxVector );
700	>
701	>	info[i].setBox(boxVector);
702		}
703	<	else if( globals->haveDensity() ){
733	<
703	>	else if (globals->haveDensity()){
704		double vol;
705	<	vol = (double)tot_nmol / globals->getDensity();
706	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
705	>	vol = (double) tot_nmol / globals->getDensity();
706	>	boxVector[0] = pow(vol, (1.0 / 3.0));
707		boxVector[1] = boxVector[0];
708		boxVector[2] = boxVector[0];
709	<
710	<	info[i].setBox( boxVector );
711	<	}
709	>
710	>	info[i].setBox(boxVector);
711	>	}
712		else{
713	<	if( !globals->haveBoxX() ){
714	<	sprintf( painCave.errMsg,
715	<	"SimSetup error, no periodic BoxX size given.\n" );
716	<	painCave.isFatal = 1;
717	<	simError();
713	>	if (!globals->haveBoxX()){
714	>	sprintf(painCave.errMsg,
715	>	"SimSetup error, no periodic BoxX size given.\n");
716	>	painCave.isFatal = 1;
717	>	simError();
718		}
719		boxVector[0] = globals->getBoxX();
720	<
721	<	if( !globals->haveBoxY() ){
722	<	sprintf( painCave.errMsg,
723	<	"SimSetup error, no periodic BoxY size given.\n" );
724	<	painCave.isFatal = 1;
725	<	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();
720	>
721	>	if (!globals->haveBoxY()){
722	>	sprintf(painCave.errMsg,
723	>	"SimSetup error, no periodic BoxY size given.\n");
724	>	painCave.isFatal = 1;
725	>	simError();
726		}
727	+	boxVector[1] = globals->getBoxY();
728	+
729	+	if (!globals->haveBoxZ()){
730	+	sprintf(painCave.errMsg,
731	+	"SimSetup error, no periodic BoxZ size given.\n");
732	+	painCave.isFatal = 1;
733	+	simError();
734	+	}
735		boxVector[2] = globals->getBoxZ();
766	–
767	–	info[i].setBox( boxVector );
768	–	}
736
737	+	info[i].setBox(boxVector);
738	+	}
739		}
740	+
741	+	//setup seed for random number generator
742	+	int seedValue;
743	+
744	+	if (globals->haveSeed()){
745	+	seedValue = globals->getSeed();
746	+
747	+	if(seedValue / 1E9 == 0){
748	+	sprintf(painCave.errMsg,
749	+	"Seed for sprng library should contain at least 9 digits\n"
750	+	"OOPSE will generate a seed for user\n");
751	+	painCave.isFatal = 0;
752	+	simError();
753	+
754	+	//using seed generated by system instead of invalid seed set by user
755	+	#ifndef IS_MPI
756	+	seedValue = make_sprng_seed();
757	+	#else
758	+	if (worldRank == 0){
759	+	seedValue = make_sprng_seed();
760	+	}
761	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
762	+	#endif
763	+	}
764	+	}//end of if branch of globals->haveSeed()
765	+	else{
766
767	+	#ifndef IS_MPI
768	+	seedValue = make_sprng_seed();
769	+	#else
770	+	if (worldRank == 0){
771	+	seedValue = make_sprng_seed();
772	+	}
773	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
774	+	#endif
775	+	}//end of globals->haveSeed()
776	+
777	+	for (int i = 0; i < nInfo; i++){
778	+	info[i].setSeed(seedValue);
779	+	}
780	+
781		#ifdef IS_MPI
782	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
782	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
783		MPIcheckPoint();
784		#endif // is_mpi
776	–
785		}
786
787
788	<	void SimSetup::finalInfoCheck( void ){
788	>	void SimSetup::finalInfoCheck(void){
789		int index;
790		int usesDipoles;
791		int i;
792
793	<	for(i=0; i<nInfo; i++){
793	>	for (i = 0; i < nInfo; i++){
794		// check electrostatic parameters
795	<
795	>
796		index = 0;
797		usesDipoles = 0;
798	<	while( (index < info[i].n_atoms) && !usesDipoles ){
798	>	while ((index < info[i].n_atoms) && !usesDipoles){
799		usesDipoles = (info[i].atoms[index])->hasDipole();
800		index++;
801		}
802	<
802	>
803		#ifdef IS_MPI
804		int myUse = usesDipoles;
805	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
805	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
806		#endif //is_mpi
807	<
807	>
808		double theEcr, theEst;
809	<
810	<	if (globals->getUseRF() ) {
809	>
810	>	if (globals->getUseRF()){
811		info[i].useReactionField = 1;
812	<
813	<	if( !globals->haveECR() ){
814	<	sprintf( painCave.errMsg,
815	<	"SimSetup Warning: using default value of 1/2 the smallest "
816	<	"box length for the electrostaticCutoffRadius.\n"
817	<	"I hope you have a very fast processor!\n");
818	<	painCave.isFatal = 0;
819	<	simError();
820	<	double smallest;
821	<	smallest = info[i].boxL[0];
822	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
823	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
824	<	theEcr = 0.5 * smallest;
825	<	} else {
826	<	theEcr = globals->getECR();
812	>
813	>	if (!globals->haveECR()){
814	>	sprintf(painCave.errMsg,
815	>	"SimSetup Warning: using default value of 1/2 the smallest "
816	>	"box length for the electrostaticCutoffRadius.\n"
817	>	"I hope you have a very fast processor!\n");
818	>	painCave.isFatal = 0;
819	>	simError();
820	>	double smallest;
821	>	smallest = info[i].boxL[0];
822	>	if (info[i].boxL[1] <= smallest)
823	>	smallest = info[i].boxL[1];
824	>	if (info[i].boxL[2] <= smallest)
825	>	smallest = info[i].boxL[2];
826	>	theEcr = 0.5 * smallest;
827		}
828	<
829	<	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();
828	>	else{
829	>	theEcr = globals->getECR();
830		}
831	<
832	<	info[i].setEcr( theEcr, theEst );
833	<
834	<	if(!globals->haveDielectric() ){
835	<	sprintf( painCave.errMsg,
836	<	"SimSetup Error: You are trying to use Reaction Field without"
837	<	"setting a dielectric constant!\n"
838	<	);
840	<	painCave.isFatal = 1;
841	<	simError();
831	>
832	>	if (!globals->haveEST()){
833	>	sprintf(painCave.errMsg,
834	>	"SimSetup Warning: using default value of 0.05 * the "
835	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
836	>	painCave.isFatal = 0;
837	>	simError();
838	>	theEst = 0.05 * theEcr;
839		}
840	<	info[i].dielectric = globals->getDielectric();
841	<	}
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 );
840	>	else{
841	>	theEst = globals->getEST();
842		}
843	<	}
843	>
844	>	info[i].setEcr(theEcr, theEst);
845	>
846	>	if (!globals->haveDielectric()){
847	>	sprintf(painCave.errMsg,
848	>	"SimSetup Error: You are trying to use Reaction Field without"
849	>	"setting a dielectric constant!\n");
850	>	painCave.isFatal = 1;
851	>	simError();
852	>	}
853	>	info[i].dielectric = globals->getDielectric();
854	>	}
855	>	else{
856	>	if (usesDipoles){
857	>	if (!globals->haveECR()){
858	>	sprintf(painCave.errMsg,
859	>	"SimSetup Warning: using default value of 1/2 the smallest "
860	>	"box length for the electrostaticCutoffRadius.\n"
861	>	"I hope you have a very fast processor!\n");
862	>	painCave.isFatal = 0;
863	>	simError();
864	>	double smallest;
865	>	smallest = info[i].boxL[0];
866	>	if (info[i].boxL[1] <= smallest)
867	>	smallest = info[i].boxL[1];
868	>	if (info[i].boxL[2] <= smallest)
869	>	smallest = info[i].boxL[2];
870	>	theEcr = 0.5 * smallest;
871	>	}
872	>	else{
873	>	theEcr = globals->getECR();
874	>	}
875	>
876	>	if (!globals->haveEST()){
877	>	sprintf(painCave.errMsg,
878	>	"SimSetup Warning: using default value of 0.05 * the "
879	>	"electrostaticCutoffRadius for the "
880	>	"electrostaticSkinThickness\n");
881	>	painCave.isFatal = 0;
882	>	simError();
883	>	theEst = 0.05 * theEcr;
884	>	}
885	>	else{
886	>	theEst = globals->getEST();
887	>	}
888	>
889	>	info[i].setEcr(theEcr, theEst);
890	>	}
891	>	}
892		}
893
894		#ifdef IS_MPI
895	<	strcpy( checkPointMsg, "post processing checks out" );
895	>	strcpy(checkPointMsg, "post processing checks out");
896		MPIcheckPoint();
897		#endif // is_mpi
886	–
898		}
899
900	<	void SimSetup::initSystemCoords( void ){
900	>	void SimSetup::initSystemCoords(void){
901		int i;
902	<
902	>
903		char* inName;
904
905	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
906
907	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
908	<
909	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
910	<
899	<	if( globals->haveInitialConfig() ){
900	<
907	>	for (i = 0; i < info[0].n_atoms; i++)
908	>	info[0].atoms[i]->setCoords();
909	>
910	>	if (globals->haveInitialConfig()){
911		InitializeFromFile* fileInit;
912		#ifdef IS_MPI // is_mpi
913	<	if( worldRank == 0 ){
913	>	if (worldRank == 0){
914		#endif //is_mpi
915		inName = globals->getInitialConfig();
916	<	double* tempDouble = new double[1000000];
907	<	fileInit = new InitializeFromFile( inName );
916	>	fileInit = new InitializeFromFile(inName);
917		#ifdef IS_MPI
918	<	}else fileInit = new InitializeFromFile( NULL );
918	>	}
919	>	else
920	>	fileInit = new InitializeFromFile(NULL);
921		#endif
922	<	fileInit->readInit( info ); // default velocities on
923	<
922	>	fileInit->readInit(info); // default velocities on
923	>
924		delete fileInit;
925		}
926		else{
916	–
927		#ifdef IS_MPI
928	<
928	>
929		// no init from bass
930	<
931	<	sprintf( painCave.errMsg,
932	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
933	<	painCave.isFatal;
930	>
931	>	sprintf(painCave.errMsg,
932	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
933	>	painCave.isFatal = 1;;
934		simError();
935	<
935	>
936		#else
937	<
937	>
938		initFromBass();
939	<
940	<
939	>
940	>
941		#endif
942		}
943	<
943	>
944		#ifdef IS_MPI
945	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
945	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
946		MPIcheckPoint();
947		#endif // is_mpi
938	–
948		}
949
950
951	<	void SimSetup::makeOutNames( void ){
943	<
951	>	void SimSetup::makeOutNames(void){
952		int k;
953
946	–
947	–	for(k=0; k<nInfo; k++){
954
955	+	for (k = 0; k < nInfo; k++){
956		#ifdef IS_MPI
957	<	if( worldRank == 0 ){
957	>	if (worldRank == 0){
958		#endif // is_mpi
959	<
960	<	if( globals->haveFinalConfig() ){
961	<	strcpy( info[k].finalName, globals->getFinalConfig() );
959	>
960	>	if (globals->haveFinalConfig()){
961	>	strcpy(info[k].finalName, globals->getFinalConfig());
962		}
963		else{
964	<	strcpy( info[k].finalName, inFileName );
965	<	char* endTest;
966	<	int nameLength = strlen( info[k].finalName );
967	<	endTest = &(info[k].finalName[nameLength - 5]);
968	<	if( !strcmp( endTest, ".bass" ) ){
969	<	strcpy( endTest, ".eor" );
970	<	}
971	<	else if( !strcmp( endTest, ".BASS" ) ){
972	<	strcpy( endTest, ".eor" );
973	<	}
974	<	else{
975	<	endTest = &(info[k].finalName[nameLength - 4]);
976	<	if( !strcmp( endTest, ".bss" ) ){
977	<	strcpy( endTest, ".eor" );
978	<	}
979	<	else if( !strcmp( endTest, ".mdl" ) ){
980	<	strcpy( endTest, ".eor" );
981	<	}
982	<	else{
983	<	strcat( info[k].finalName, ".eor" );
984	<	}
985	<	}
964	>	strcpy(info[k].finalName, inFileName);
965	>	char* endTest;
966	>	int nameLength = strlen(info[k].finalName);
967	>	endTest = &(info[k].finalName[nameLength - 5]);
968	>	if (!strcmp(endTest, ".bass")){
969	>	strcpy(endTest, ".eor");
970	>	}
971	>	else if (!strcmp(endTest, ".BASS")){
972	>	strcpy(endTest, ".eor");
973	>	}
974	>	else{
975	>	endTest = &(info[k].finalName[nameLength - 4]);
976	>	if (!strcmp(endTest, ".bss")){
977	>	strcpy(endTest, ".eor");
978	>	}
979	>	else if (!strcmp(endTest, ".mdl")){
980	>	strcpy(endTest, ".eor");
981	>	}
982	>	else{
983	>	strcat(info[k].finalName, ".eor");
984	>	}
985	>	}
986		}
987	<
987	>
988		// make the sample and status out names
989	<
990	<	strcpy( info[k].sampleName, inFileName );
989	>
990	>	strcpy(info[k].sampleName, inFileName);
991		char* endTest;
992	<	int nameLength = strlen( info[k].sampleName );
992	>	int nameLength = strlen(info[k].sampleName);
993		endTest = &(info[k].sampleName[nameLength - 5]);
994	<	if( !strcmp( endTest, ".bass" ) ){
995	<	strcpy( endTest, ".dump" );
994	>	if (!strcmp(endTest, ".bass")){
995	>	strcpy(endTest, ".dump");
996		}
997	<	else if( !strcmp( endTest, ".BASS" ) ){
998	<	strcpy( endTest, ".dump" );
997	>	else if (!strcmp(endTest, ".BASS")){
998	>	strcpy(endTest, ".dump");
999		}
1000		else{
1001	<	endTest = &(info[k].sampleName[nameLength - 4]);
1002	<	if( !strcmp( endTest, ".bss" ) ){
1003	<	strcpy( endTest, ".dump" );
1004	<	}
1005	<	else if( !strcmp( endTest, ".mdl" ) ){
1006	<	strcpy( endTest, ".dump" );
1007	<	}
1008	<	else{
1009	<	strcat( info[k].sampleName, ".dump" );
1010	<	}
1001	>	endTest = &(info[k].sampleName[nameLength - 4]);
1002	>	if (!strcmp(endTest, ".bss")){
1003	>	strcpy(endTest, ".dump");
1004	>	}
1005	>	else if (!strcmp(endTest, ".mdl")){
1006	>	strcpy(endTest, ".dump");
1007	>	}
1008	>	else{
1009	>	strcat(info[k].sampleName, ".dump");
1010	>	}
1011		}
1012	<
1013	<	strcpy( info[k].statusName, inFileName );
1014	<	nameLength = strlen( info[k].statusName );
1012	>
1013	>	strcpy(info[k].statusName, inFileName);
1014	>	nameLength = strlen(info[k].statusName);
1015		endTest = &(info[k].statusName[nameLength - 5]);
1016	<	if( !strcmp( endTest, ".bass" ) ){
1017	<	strcpy( endTest, ".stat" );
1016	>	if (!strcmp(endTest, ".bass")){
1017	>	strcpy(endTest, ".stat");
1018		}
1019	<	else if( !strcmp( endTest, ".BASS" ) ){
1020	<	strcpy( endTest, ".stat" );
1019	>	else if (!strcmp(endTest, ".BASS")){
1020	>	strcpy(endTest, ".stat");
1021		}
1022		else{
1023	<	endTest = &(info[k].statusName[nameLength - 4]);
1024	<	if( !strcmp( endTest, ".bss" ) ){
1025	<	strcpy( endTest, ".stat" );
1026	<	}
1027	<	else if( !strcmp( endTest, ".mdl" ) ){
1028	<	strcpy( endTest, ".stat" );
1029	<	}
1030	<	else{
1031	<	strcat( info[k].statusName, ".stat" );
1032	<	}
1023	>	endTest = &(info[k].statusName[nameLength - 4]);
1024	>	if (!strcmp(endTest, ".bss")){
1025	>	strcpy(endTest, ".stat");
1026	>	}
1027	>	else if (!strcmp(endTest, ".mdl")){
1028	>	strcpy(endTest, ".stat");
1029	>	}
1030	>	else{
1031	>	strcat(info[k].statusName, ".stat");
1032	>	}
1033		}
1034	<
1034	>
1035		#ifdef IS_MPI
1036	+
1037		}
1038		#endif // is_mpi
1039		}
1040		}
1041
1042
1043	<	void SimSetup::sysObjectsCreation( void ){
1044	<
1045	<	int i,k;
1038	<
1043	>	void SimSetup::sysObjectsCreation(void){
1044	>	int i, k;
1045	>
1046		// create the forceField
1047
1048		createFF();
#	Line 1050 | Line 1057 | void SimSetup::sysObjectsCreation( void ){
1057
1058		#ifdef IS_MPI
1059		// divide the molecules among the processors
1060	<
1060	>
1061		mpiMolDivide();
1062		#endif //is_mpi
1063	<
1063	>
1064		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1065	<
1065	>
1066		makeSysArrays();
1067
1068		// make and initialize the molecules (all but atomic coordinates)
1069	<
1069	>
1070		makeMolecules();
1071	<
1072	<	for(k=0; k<nInfo; k++){
1071	>
1072	>	for (k = 0; k < nInfo; k++){
1073		info[k].identArray = new int[info[k].n_atoms];
1074	<	for(i=0; i<info[k].n_atoms; i++){
1074	>	for (i = 0; i < info[k].n_atoms; i++){
1075		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1076		}
1077		}
1078		}
1079
1080
1081	<	void SimSetup::createFF( void ){
1081	>	void SimSetup::createFF(void){
1082	>	switch (ffCase){
1083	>	case FF_DUFF:
1084	>	the_ff = new DUFF();
1085	>	break;
1086
1087	<	switch( ffCase ){
1087	>	case FF_LJ:
1088	>	the_ff = new LJFF();
1089	>	break;
1090
1091	<	case FF_DUFF:
1092	<	the_ff = new DUFF();
1093	<	break;
1091	>	case FF_EAM:
1092	>	the_ff = new EAM_FF();
1093	>	break;
1094
1095	<	case FF_LJ:
1096	<	the_ff = new LJFF();
1097	<	break;
1098	<
1099	<	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();
1095	>	default:
1096	>	sprintf(painCave.errMsg,
1097	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1098	>	painCave.isFatal = 1;
1099	>	simError();
1100		}
1101
1102		#ifdef IS_MPI
1103	<	strcpy( checkPointMsg, "ForceField creation successful" );
1103	>	strcpy(checkPointMsg, "ForceField creation successful");
1104		MPIcheckPoint();
1105		#endif // is_mpi
1101	–
1106		}
1107
1108
1109	<	void SimSetup::compList( void ){
1106	<
1109	>	void SimSetup::compList(void){
1110		int i;
1111		char* id;
1112		LinkedMolStamp* headStamp = new LinkedMolStamp();
1113		LinkedMolStamp* currentStamp = NULL;
1114	<	comp_stamps = new MoleculeStamp*[n_components];
1115	<
1114	>	comp_stamps = new MoleculeStamp * [n_components];
1115	>
1116		// make an array of molecule stamps that match the components used.
1117		// also extract the used stamps out into a separate linked list
1118	<
1119	<	for(i=0; i<nInfo; i++){
1118	>
1119	>	for (i = 0; i < nInfo; i++){
1120		info[i].nComponents = n_components;
1121		info[i].componentsNmol = components_nmol;
1122		info[i].compStamps = comp_stamps;
1123		info[i].headStamp = headStamp;
1124		}
1122	–
1125
1124	–	for( i=0; i<n_components; i++ ){
1126
1127	+	for (i = 0; i < n_components; i++){
1128		id = the_components[i]->getType();
1129		comp_stamps[i] = NULL;
1130	<
1130	>
1131		// check to make sure the component isn't already in the list
1132
1133	<	comp_stamps[i] = headStamp->match( id );
1134	<	if( comp_stamps[i] == NULL ){
1133	<
1133	>	comp_stamps[i] = headStamp->match(id);
1134	>	if (comp_stamps[i] == NULL){
1135		// extract the component from the list;
1136	<
1137	<	currentStamp = stamps->extractMolStamp( id );
1138	<	if( currentStamp == NULL ){
1139	<	sprintf( painCave.errMsg,
1140	<	"SimSetup error: Component \"%s\" was not found in the "
1141	<	"list of declared molecules\n",
1142	<	id );
1143	<	painCave.isFatal = 1;
1144	<	simError();
1136	>
1137	>	currentStamp = stamps->extractMolStamp(id);
1138	>	if (currentStamp == NULL){
1139	>	sprintf(painCave.errMsg,
1140	>	"SimSetup error: Component \"%s\" was not found in the "
1141	>	"list of declared molecules\n",
1142	>	id);
1143	>	painCave.isFatal = 1;
1144	>	simError();
1145		}
1146	<
1147	<	headStamp->add( currentStamp );
1148	<	comp_stamps[i] = headStamp->match( id );
1146	>
1147	>	headStamp->add(currentStamp);
1148	>	comp_stamps[i] = headStamp->match(id);
1149		}
1150		}
1151
1152		#ifdef IS_MPI
1153	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1153	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1154		MPIcheckPoint();
1155		#endif // is_mpi
1156	+	}
1157
1158	+	void SimSetup::calcSysValues(void){
1159	+	int i;
1160
1161	<	}
1161	>	int* molMembershipArray;
1162
1159	–	void SimSetup::calcSysValues( void ){
1160	–	int i, j, k;
1161	–
1162	–	int *molMembershipArray;
1163	–
1163		tot_atoms = 0;
1164		tot_bonds = 0;
1165		tot_bends = 0;
1166		tot_torsions = 0;
1167	<	for( i=0; i<n_components; i++ ){
1168	<
1169	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1170	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1172	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1167	>	for (i = 0; i < n_components; i++){
1168	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1169	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1170	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1171		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1172		}
1173	<
1173	>
1174		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1175		molMembershipArray = new int[tot_atoms];
1176	<
1177	<	for(i=0; i<nInfo; i++){
1176	>
1177	>	for (i = 0; i < nInfo; i++){
1178		info[i].n_atoms = tot_atoms;
1179		info[i].n_bonds = tot_bonds;
1180		info[i].n_bends = tot_bends;
1181		info[i].n_torsions = tot_torsions;
1182		info[i].n_SRI = tot_SRI;
1183		info[i].n_mol = tot_nmol;
1184	<
1184	>
1185		info[i].molMembershipArray = molMembershipArray;
1186	<	}
1186	>	}
1187		}
1188
1189		#ifdef IS_MPI
1190
1191	<	void SimSetup::mpiMolDivide( void ){
1194	<
1191	>	void SimSetup::mpiMolDivide(void){
1192		int i, j, k;
1193		int localMol, allMol;
1194		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1195
1196	<	mpiSim = new mpiSimulation( info );
1197	<
1196	>	mpiSim = new mpiSimulation(info);
1197	>
1198		globalIndex = mpiSim->divideLabor();
1199
1200		// set up the local variables
1201	<
1201	>
1202		mol2proc = mpiSim->getMolToProcMap();
1203		molCompType = mpiSim->getMolComponentType();
1204	<
1204	>
1205		allMol = 0;
1206		localMol = 0;
1207		local_atoms = 0;
#	Line 1214 | Line 1211 | void SimSetup::mpiMolDivide( void ){
1211		globalAtomIndex = 0;
1212
1213
1214	<	for( i=0; i<n_components; i++ ){
1215	<
1216	<	for( j=0; j<components_nmol[i]; j++ ){
1217	<
1218	<	if( mol2proc[allMol] == worldRank ){
1219	<
1220	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1221	<	local_bonds +=    comp_stamps[i]->getNBonds();
1225	<	local_bends +=    comp_stamps[i]->getNBends();
1226	<	local_torsions += comp_stamps[i]->getNTorsions();
1227	<	localMol++;
1214	>	for (i = 0; i < n_components; i++){
1215	>	for (j = 0; j < components_nmol[i]; j++){
1216	>	if (mol2proc[allMol] == worldRank){
1217	>	local_atoms += comp_stamps[i]->getNAtoms();
1218	>	local_bonds += comp_stamps[i]->getNBonds();
1219	>	local_bends += comp_stamps[i]->getNBends();
1220	>	local_torsions += comp_stamps[i]->getNTorsions();
1221	>	localMol++;
1222		}
1223	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1223	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1224		info[0].molMembershipArray[globalAtomIndex] = allMol;
1225		globalAtomIndex++;
1226		}
1227
1228	<	allMol++;
1228	>	allMol++;
1229		}
1230		}
1231		local_SRI = local_bonds + local_bends + local_torsions;
1232	<
1232	>
1233		info[0].n_atoms = mpiSim->getMyNlocal();
1234	<
1235	<	if( local_atoms != info[0].n_atoms ){
1236	<	sprintf( painCave.errMsg,
1237	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1238	<	" localAtom (%d) are not equal.\n",
1239	<	info[0].n_atoms,
1246	<	local_atoms );
1234	>
1235	>	if (local_atoms != info[0].n_atoms){
1236	>	sprintf(painCave.errMsg,
1237	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1238	>	" localAtom (%d) are not equal.\n",
1239	>	info[0].n_atoms, local_atoms);
1240		painCave.isFatal = 1;
1241		simError();
1242		}
#	Line 1254 | Line 1247 | void SimSetup::mpiMolDivide( void ){
1247		info[0].n_SRI = local_SRI;
1248		info[0].n_mol = localMol;
1249
1250	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1250	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1251		MPIcheckPoint();
1252		}
1253	<
1253	>
1254		#endif // is_mpi
1255
1256
1257	<	void SimSetup::makeSysArrays( void ){
1258	<	int i, j, k, l;
1257	>	void SimSetup::makeSysArrays(void){
1258	>
1259	>	#ifndef IS_MPI
1260	>	int k, j;
1261	>	#endif // is_mpi
1262	>	int i, l;
1263
1264		Atom** the_atoms;
1265		Molecule* the_molecules;
1266		Exclude** the_excludes;
1267
1268	<
1269	<	for(l=0; l<nInfo; l++){
1273	<
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 );
1292	<	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 ){
1318	<
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 );
1330	<	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 1342 | Line 1335 | void SimSetup::makeSysArrays( void ){
1335		info[l].nGlobalExcludes = 0;
1336		info[l].excludes = the_excludes;
1337
1338	<	the_ff->setSimInfo( info );
1346	<
1338	>	the_ff->setSimInfo(info);
1339		}
1340		}
1341
1342	<	void SimSetup::makeIntegrator( void ){
1351	<
1342	>	void SimSetup::makeIntegrator(void){
1343		int k;
1344
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	<	}
1345	>	NVE<RealIntegrator>* myNVE = NULL;
1346	>	NVT<RealIntegrator>* myNVT = NULL;
1347	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1348	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1349	>
1350	>	for (k = 0; k < nInfo; k++){
1351	>	switch (ensembleCase){
1352	>	case NVE_ENS:
1353	>	if (globals->haveZconstraints()){
1354	>	setupZConstraint(info[k]);
1355	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1356	>	}
1357	>	else{
1358	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1359	>	}
1360	>
1361	>	info->the_integrator = myNVE;
1362	>	break;
1363
1364	<	else
1365	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1366	<	break;
1367	<
1368	<	case NVT_ENS:
1369	<	if (globals->haveZconstraints()){
1370	<	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 );
1364	>	case NVT_ENS:
1365	>	if (globals->haveZconstraints()){
1366	>	setupZConstraint(info[k]);
1367	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1368	>	}
1369	>	else
1370	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1371
1372		myNVT->setTargetTemp(globals->getTargetTemp());
1373	<
1374	<	if (globals->haveTauThermostat())
1373	>
1374	>	if (globals->haveTauThermostat())
1375		myNVT->setTauThermostat(globals->getTauThermostat());
1376	<
1377	<	else {
1378	<	sprintf( painCave.errMsg,
1379	<	"SimSetup error: If you use the NVT\n"
1390	<	"    ensemble, you must set tauThermostat.\n");
1376	>	else{
1377	>	sprintf(painCave.errMsg,
1378	>	"SimSetup error: If you use the NVT\n"
1379	>	"    ensemble, you must set tauThermostat.\n");
1380		painCave.isFatal = 1;
1381		simError();
1382		}
1383	+
1384	+	info->the_integrator = myNVT;
1385		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 );
1386
1387	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1388	<
1389	<	if (globals->haveTargetPressure())
1390	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1391	<	else {
1392	<	sprintf( painCave.errMsg,
1393	<	"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 );
1387	>	case NPTi_ENS:
1388	>	if (globals->haveZconstraints()){
1389	>	setupZConstraint(info[k]);
1390	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1391	>	}
1392	>	else
1393	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1394
1395	<	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 );
1395	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1396
1397	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1398	<
1399	<	if (globals->haveTargetPressure())
1400	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1490	<	else {
1491	<	sprintf( painCave.errMsg,
1397	>	if (globals->haveTargetPressure())
1398	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1399	>	else{
1400	>	sprintf(painCave.errMsg,
1401		"SimSetup error: If you use a constant pressure\n"
1402		"    ensemble, you must set targetPressure in the BASS file.\n");
1403	<	painCave.isFatal = 1;
1404	<	simError();
1405	<	}
1497	<
1498	<	if( globals->haveTauThermostat() )
1499	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1500	<	else{
1501	<	sprintf( painCave.errMsg,
1502	<	"SimSetup error: If you use an NPT\n"
1503	<	"    ensemble, you must set tauThermostat.\n");
1504	<	painCave.isFatal = 1;
1505	<	simError();
1506	<	}
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 );
1403	>	painCave.isFatal = 1;
1404	>	simError();
1405	>	}
1406
1407	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1407	>	if (globals->haveTauThermostat())
1408	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1409	>	else{
1410	>	sprintf(painCave.errMsg,
1411	>	"SimSetup error: If you use an NPT\n"
1412	>	"    ensemble, you must set tauThermostat.\n");
1413	>	painCave.isFatal = 1;
1414	>	simError();
1415	>	}
1416
1417	<	if (globals->haveTargetPressure())
1418	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1419	<	else {
1420	<	sprintf( painCave.errMsg,
1417	>	if (globals->haveTauBarostat())
1418	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1419	>	else{
1420	>	sprintf(painCave.errMsg,
1421	>	"SimSetup error: If you use an NPT\n"
1422	>	"    ensemble, you must set tauBarostat.\n");
1423	>	painCave.isFatal = 1;
1424	>	simError();
1425	>	}
1426	>
1427	>	info->the_integrator = myNPTi;
1428	>	break;
1429	>
1430	>	case NPTf_ENS:
1431	>	if (globals->haveZconstraints()){
1432	>	setupZConstraint(info[k]);
1433	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1434	>	}
1435	>	else
1436	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1437	>
1438	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1439	>
1440	>	if (globals->haveTargetPressure())
1441	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1442	>	else{
1443	>	sprintf(painCave.errMsg,
1444		"SimSetup error: If you use a constant pressure\n"
1445		"    ensemble, you must set targetPressure in the BASS file.\n");
1446	<	painCave.isFatal = 1;
1447	<	simError();
1448	<	}
1446	>	painCave.isFatal = 1;
1447	>	simError();
1448	>	}
1449
1450	<	if( globals->haveTauThermostat() )
1451	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1452	<	else{
1453	<	sprintf( painCave.errMsg,
1450	>	if (globals->haveTauThermostat())
1451	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1452	>	else{
1453	>	sprintf(painCave.errMsg,
1454		"SimSetup error: If you use an NPT\n"
1455		"    ensemble, you must set tauThermostat.\n");
1456	<	painCave.isFatal = 1;
1457	<	simError();
1458	<	}
1456	>	painCave.isFatal = 1;
1457	>	simError();
1458	>	}
1459
1460	<	if( globals->haveTauBarostat() )
1461	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1462	<	else{
1463	<	sprintf( painCave.errMsg,
1460	>	if (globals->haveTauBarostat())
1461	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1462	>	else{
1463	>	sprintf(painCave.errMsg,
1464		"SimSetup error: If you use an NPT\n"
1465		"    ensemble, you must set tauBarostat.\n");
1466	+	painCave.isFatal = 1;
1467	+	simError();
1468	+	}
1469	+
1470	+	info->the_integrator = myNPTf;
1471	+	break;
1472	+
1473	+	default:
1474	+	sprintf(painCave.errMsg,
1475	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1476		painCave.isFatal = 1;
1477		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();
1478		}
1479		}
1480		}
1481
1482	<	void SimSetup::initFortran( void ){
1570	<
1482	>	void SimSetup::initFortran(void){
1483		info[0].refreshSim();
1484	<
1485	<	if( !strcmp( info[0].mixingRule, "standard") ){
1486	<	the_ff->initForceField( LB_MIXING_RULE );
1484	>
1485	>	if (!strcmp(info[0].mixingRule, "standard")){
1486	>	the_ff->initForceField(LB_MIXING_RULE);
1487		}
1488	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1489	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1488	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1489	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1490		}
1491		else{
1492	<	sprintf( painCave.errMsg,
1493	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1582	<	info[0].mixingRule );
1492	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1493	>	info[0].mixingRule);
1494		painCave.isFatal = 1;
1495		simError();
1496		}
1497
1498
1499		#ifdef IS_MPI
1500	<	strcpy( checkPointMsg,
1590	<	"Successfully intialized the mixingRule for Fortran." );
1500	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1501		MPIcheckPoint();
1502		#endif // is_mpi
1593	–
1503		}
1504
1505	<	void SimSetup::setupZConstraint(SimInfo& theInfo)
1597	<	{
1505	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1506		int nZConstraints;
1507		ZconStamp** zconStamp;
1508
1509	<	if(globals->haveZconstraintTime()){
1602	<
1509	>	if (globals->haveZconstraintTime()){
1510		//add sample time of z-constraint  into SimInfo's property list
1511		DoubleData* zconsTimeProp = new DoubleData();
1512		zconsTimeProp->setID(ZCONSTIME_ID);
#	Line 1607 | Line 1514 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1514		theInfo.addProperty(zconsTimeProp);
1515		}
1516		else{
1517	<	sprintf( painCave.errMsg,
1518	<	"ZConstraint error: If you use an ZConstraint\n"
1519	<	" , you must set sample time.\n");
1517	>	sprintf(painCave.errMsg,
1518	>	"ZConstraint error: If you use an ZConstraint\n"
1519	>	" , you must set sample time.\n");
1520		painCave.isFatal = 1;
1521	<	simError();
1521	>	simError();
1522		}
1523
1524		//push zconsTol into siminfo, if user does not specify
1525		//value for zconsTol, a default value will be used
1526		DoubleData* zconsTol = new DoubleData();
1527		zconsTol->setID(ZCONSTOL_ID);
1528	<	if(globals->haveZconsTol()){
1528	>	if (globals->haveZconsTol()){
1529		zconsTol->setData(globals->getZconsTol());
1530		}
1531		else{
1532	<	double defaultZConsTol = 0.01;
1533	<	sprintf( painCave.errMsg,
1534	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1535	<	" , default value %f is used.\n", defaultZConsTol);
1532	>	double defaultZConsTol = 0.01;
1533	>	sprintf(painCave.errMsg,
1534	>	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1535	>	" , default value %f is used.\n",
1536	>	defaultZConsTol);
1537		painCave.isFatal = 0;
1538		simError();
1539
#	Line 1633 | Line 1541 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1541		}
1542		theInfo.addProperty(zconsTol);
1543
1544	<	//set Force Substraction Policy
1545	<	StringData* zconsForcePolicy =  new StringData();
1544	>	//set Force Subtraction Policy
1545	>	StringData* zconsForcePolicy = new StringData();
1546		zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1547	<
1548	<	if(globals->haveZconsForcePolicy()){
1547	>
1548	>	if (globals->haveZconsForcePolicy()){
1549		zconsForcePolicy->setData(globals->getZconsForcePolicy());
1550	<	}
1550	>	}
1551		else{
1552	<	sprintf( painCave.errMsg,
1553	<	"ZConstraint Warning: User does not set force substraction policy, "
1554	<	"average force substraction policy is used\n");
1555	<	painCave.isFatal = 0;
1556	<	simError();
1557	<	zconsForcePolicy->setData("BYNUMBER");
1552	>	sprintf(painCave.errMsg,
1553	>	"ZConstraint Warning: User does not set force Subtraction policy, "
1554	>	"PolicyByMass is used\n");
1555	>	painCave.isFatal = 0;
1556	>	simError();
1557	>	zconsForcePolicy->setData("BYMASS");
1558		}
1559	<
1560	<	theInfo.addProperty(zconsForcePolicy);
1561	<
1559	>
1560	>	theInfo.addProperty(zconsForcePolicy);
1561	>
1562		//Determine the name of ouput file and add it into SimInfo's property list
1563		//Be careful, do not use inFileName, since it is a pointer which
1564		//point to a string at master node, and slave nodes do not contain that string
1565	<
1565	>
1566		string zconsOutput(theInfo.finalName);
1567	<
1567	>
1568		zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1569	<
1569	>
1570		StringData* zconsFilename = new StringData();
1571		zconsFilename->setID(ZCONSFILENAME_ID);
1572		zconsFilename->setData(zconsOutput);
1573	<
1573	>
1574		theInfo.addProperty(zconsFilename);
1575	<
1575	>
1576		//setup index, pos and other parameters of z-constraint molecules
1577		nZConstraints = globals->getNzConstraints();
1578		theInfo.nZconstraints = nZConstraints;
#	Line 1674 | Line 1582 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1582
1583		ZConsParaData* zconsParaData = new ZConsParaData();
1584		zconsParaData->setID(ZCONSPARADATA_ID);
1585	<
1586	<	for(int i = 0; i < nZConstraints; i++){
1585	>
1586	>	for (int i = 0; i < nZConstraints; i++){
1587		tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1588		tempParaItem.zPos = zconStamp[i]->getZpos();
1589		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
#	Line 1684 | Line 1592 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1592		zconsParaData->addItem(tempParaItem);
1593		}
1594
1595	+	//check the uniqueness of index
1596	+	if(!zconsParaData->isIndexUnique()){
1597	+	sprintf(painCave.errMsg,
1598	+	"ZConstraint Error: molIndex is not unique\n");
1599	+	painCave.isFatal = 1;
1600	+	simError();
1601	+	}
1602	+
1603		//sort the parameters by index of molecules
1604		zconsParaData->sortByIndex();
1605
1606		//push data into siminfo, therefore, we can retrieve later
1607		theInfo.addProperty(zconsParaData);
1692	–
1608		}

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