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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 780 by mmeineke, Mon Sep 22 21:23:25 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 22 | Line 22
22		#define NVT_ENS        1
23		#define NPTi_ENS       2
24		#define NPTf_ENS       3
25	–	#define NPTim_ENS      4
26	–	#define NPTfm_ENS      5
25
26		#define FF_DUFF 0
27		#define FF_LJ   1
#	Line 32 | Line 30 | SimSetup::SimSetup(){
30		using namespace std;
31
32		SimSetup::SimSetup(){
35	–
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 51 | Line 48 | void SimSetup::setSimInfo( SimInfo* the_info, int theN
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 ){
62	<
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();
90	<	mpiEventLoop();
91	<
84	>	set_interface_stamps(stamps, globals);
85	>	mpiEventInit();
86	>	MPIcheckPoint();
87	>	mpiEventLoop();
88		}
89
90		#endif // is_mpi
91
92		void SimSetup::createSim(void){
97	–
93		int i, j, k, globalAtomIndex;
94	<
94	>
95		// gather all of the information from the Bass file
96
97		gatherInfo();
#	Line 111 | Line 106 | void SimSetup::createSim(void){
106
107		// initialize the system coordinates
108
109	<	if( !isInfoArray ) initSystemCoords();
109	>	if (!isInfoArray){
110	>	initSystemCoords();
111	>	}
112
113		// make the output filenames
114
115		makeOutNames();
116	<
116	>
117		// make the integrator
118	<
118	>
119		makeIntegrator();
120	<
120	>
121		#ifdef IS_MPI
122		mpiSim->mpiRefresh();
123		#endif
#	Line 128 | Line 125 | void SimSetup::createSim(void){
125		// initialize the Fortran
126
127		initFortran();
131	–
132	–
133	–
128		}
129
130
131	<	void SimSetup::makeMolecules( void ){
132	<
139	<	int k,l;
131	>	void SimSetup::makeMolecules(void){
132	>	int k, l;
133		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
134		molInit molInfo;
135		DirectionalAtom* dAtom;
#	Line 151 | Line 144 | void SimSetup::makeMolecules( void ){
144		bend_set* theBends;
145		torsion_set* theTorsions;
146
147	<
147	>
148		//init the forceField paramters
149
150		the_ff->readParams();
151
152	<
152	>
153		// init the atoms
154
155		double ux, uy, uz, u, uSqr;
163	–
164	–	for(k=0; k<nInfo; k++){
165	–
166	–	the_ff->setSimInfo( &(info[k]) );
156
157	+	for (k = 0; k < nInfo; k++){
158	+	the_ff->setSimInfo(&(info[k]));
159	+
160		atomOffset = 0;
161		excludeOffset = 0;
162	<	for(i=0; i<info[k].n_mol; i++){
171	<
162	>	for (i = 0; i < info[k].n_mol; i++){
163		stampID = info[k].molecules[i].getStampID();
164
165	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
166	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
167	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
165	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
166	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
167	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
168		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
169		molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
170	<
170	>
171		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
172		molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
173	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
174	<	molInfo.myBends = new Bend*[molInfo.nBends];
175	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
173	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
174	>	molInfo.myBends = new Bend * [molInfo.nBends];
175	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
176
177		theBonds = new bond_pair[molInfo.nBonds];
178		theBends = new bend_set[molInfo.nBends];
179		theTorsions = new torsion_set[molInfo.nTorsions];
180	<
180	>
181		// make the Atoms
182	<
183	<	for(j=0; j<molInfo.nAtoms; j++){
184	<
185	<	currentAtom = comp_stamps[stampID]->getAtom( j );
186	<	if( currentAtom->haveOrientation() ){
187	<
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	<	}
221	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
222	<
182	>
183	>	for (j = 0; j < molInfo.nAtoms; j++){
184	>	currentAtom = comp_stamps[stampID]->getAtom(j);
185	>	if (currentAtom->haveOrientation()){
186	>	dAtom = new DirectionalAtom((j + atomOffset),
187	>	info[k].getConfiguration());
188	>	info[k].n_oriented++;
189	>	molInfo.myAtoms[j] = dAtom;
190	>
191	>	ux = currentAtom->getOrntX();
192	>	uy = currentAtom->getOrntY();
193	>	uz = currentAtom->getOrntZ();
194	>
195	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
196	>
197	>	u = sqrt(uSqr);
198	>	ux = ux / u;
199	>	uy = uy / u;
200	>	uz = uz / u;
201	>
202	>	dAtom->setSUx(ux);
203	>	dAtom->setSUy(uy);
204	>	dAtom->setSUz(uz);
205	>	}
206	>	else{
207	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
208	>	info[k].getConfiguration());
209	>	}
210	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
211	>
212		#ifdef IS_MPI
213	<
214	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
215	<
213	>
214	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
215	>
216		#endif // is_mpi
217		}
218	<
219	<	// make the bonds
220	<	for(j=0; j<molInfo.nBonds; j++){
221	<
222	<	currentBond = comp_stamps[stampID]->getBond( j );
223	<	theBonds[j].a = currentBond->getA() + atomOffset;
224	<	theBonds[j].b = currentBond->getB() + atomOffset;
225	<
226	<	exI = theBonds[j].a;
227	<	exJ = theBonds[j].b;
228	<
229	<	// exclude_I must always be the smaller of the pair
230	<	if( exI > exJ ){
231	<	tempEx = exI;
232	<	exI = exJ;
233	<	exJ = tempEx;
245	<	}
218	>
219	>	// make the bonds
220	>	for (j = 0; j < molInfo.nBonds; j++){
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;
233	>	}
234		#ifdef IS_MPI
235	<	tempEx = exI;
236	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
237	<	tempEx = exJ;
238	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
239	<
240	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
235	>	tempEx = exI;
236	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
237	>	tempEx = exJ;
238	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
239	>
240	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
241		#else  // isn't MPI
242	<
243	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
242	>
243	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
244		#endif  //is_mpi
245		}
246		excludeOffset += molInfo.nBonds;
247	<
247	>
248		//make the bends
249	<	for(j=0; j<molInfo.nBends; j++){
250	<
251	<	currentBend = comp_stamps[stampID]->getBend( j );
252	<	theBends[j].a = currentBend->getA() + atomOffset;
253	<	theBends[j].b = currentBend->getB() + atomOffset;
254	<	theBends[j].c = currentBend->getC() + atomOffset;
255	<
256	<	if( currentBend->haveExtras() ){
257	<
258	<	extras = currentBend->getExtras();
259	<	current_extra = extras;
260	<
261	<	while( current_extra != NULL ){
262	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
263	<
264	<	switch( current_extra->getType() ){
265	<
266	<	case 0:
267	<	theBends[j].ghost =
268	<	current_extra->getInt() + atomOffset;
269	<	theBends[j].isGhost = 1;
270	<	break;
271	<
272	<	case 1:
273	<	theBends[j].ghost =
274	<	(int)current_extra->getDouble() + atomOffset;
275	<	theBends[j].isGhost = 1;
276	<	break;
277	<
278	<	default:
279	<	sprintf( painCave.errMsg,
280	<	"SimSetup Error: ghostVectorSource was neither a "
281	<	"double nor an int.\n"
282	<	"-->Bend[%d] in %s\n",
283	<	j, comp_stamps[stampID]->getID() );
284	<	painCave.isFatal = 1;
285	<	simError();
249	>	for (j = 0; j < molInfo.nBends; j++){
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	>	extras = currentBend->getExtras();
257	>	current_extra = extras;
258	>
259	>	while (current_extra != NULL){
260	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
261	>	switch (current_extra->getType()){
262	>	case 0:
263	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
264	>	theBends[j].isGhost = 1;
265	>	break;
266	>
267	>	case 1:
268	>	theBends[j].ghost = (int) current_extra->getDouble() +
269	>	atomOffset;
270	>	theBends[j].isGhost = 1;
271	>	break;
272	>
273	>	default:
274	>	sprintf(painCave.errMsg,
275	>	"SimSetup Error: ghostVectorSource was neither a "
276	>	"double nor an int.\n"
277	>	"-->Bend[%d] in %s\n",
278	>	j, comp_stamps[stampID]->getID());
279	>	painCave.isFatal = 1;
280	>	simError();
281	>	}
282	>	}
283	>	else{
284	>	sprintf(painCave.errMsg,
285	>	"SimSetup Error: unhandled bend assignment:\n"
286	>	"    -->%s in Bend[%d] in %s\n",
287	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
288	>	painCave.isFatal = 1;
289	>	simError();
290	>	}
291	>
292	>	current_extra = current_extra->getNext();
293	>	}
294		}
295	<	}
296	<
297	<	else{
298	<
299	<	sprintf( painCave.errMsg,
300	<	"SimSetup Error: unhandled bend assignment:\n"
301	<	"    -->%s in Bend[%d] in %s\n",
302	<	current_extra->getlhs(),
303	<	j, comp_stamps[stampID]->getID() );
304	<	painCave.isFatal = 1;
305	<	simError();
306	<	}
307	<
308	<	current_extra = current_extra->getNext();
309	<	}
310	<	}
315	<
316	<	if( !theBends[j].isGhost ){
317	<
318	<	exI = theBends[j].a;
319	<	exJ = theBends[j].c;
320	<	}
321	<	else{
322	<
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	<	}
295	>
296	>	if (!theBends[j].isGhost){
297	>	exI = theBends[j].a;
298	>	exJ = theBends[j].c;
299	>	}
300	>	else{
301	>	exI = theBends[j].a;
302	>	exJ = theBends[j].b;
303	>	}
304	>
305	>	// exclude_I must always be the smaller of the pair
306	>	if (exI > exJ){
307	>	tempEx = exI;
308	>	exI = exJ;
309	>	exJ = tempEx;
310	>	}
311		#ifdef IS_MPI
312	<	tempEx = exI;
313	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
314	<	tempEx = exJ;
315	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
316	<
317	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
312	>	tempEx = exI;
313	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
314	>	tempEx = exJ;
315	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
316	>
317	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
318		#else  // isn't MPI
319	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
319	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
320		#endif  //is_mpi
321		}
322		excludeOffset += molInfo.nBends;
323	<
324	<	for(j=0; j<molInfo.nTorsions; j++){
325	<
326	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
327	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
328	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
329	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
330	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
331	<
332	<	exI = theTorsions[j].a;
333	<	exJ = theTorsions[j].d;
334	<
335	<	// exclude_I must always be the smaller of the pair
336	<	if( exI > exJ ){
337	<	tempEx = exI;
338	<	exI = exJ;
339	<	exJ = tempEx;
362	<	}
323	>
324	>	for (j = 0; j < molInfo.nTorsions; j++){
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;
339	>	}
340		#ifdef IS_MPI
341	<	tempEx = exI;
342	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
343	<	tempEx = exJ;
344	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345	<
346	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
341	>	tempEx = exI;
342	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
343	>	tempEx = exJ;
344	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345	>
346	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
347		#else  // isn't MPI
348	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
348	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
349		#endif  //is_mpi
350		}
351		excludeOffset += molInfo.nTorsions;
352	<
353	<
352	>
353	>
354		// 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 );
355
356	<
356	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
357	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
358	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
359	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
360	>	theTorsions);
361	>
362	>
363	>	info[k].molecules[i].initialize(molInfo);
364	>
365	>
366		atomOffset += molInfo.nAtoms;
367		delete[] theBonds;
368		delete[] theBends;
369		delete[] theTorsions;
370		}
371		}
372	<
372	>
373		#ifdef IS_MPI
374	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
374	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
375		MPIcheckPoint();
376		#endif // is_mpi
377	<
377	>
378		// clean up the forcefield
379
380		the_ff->calcRcut();
381		the_ff->cleanMe();
404	–
382		}
383
384	<	void SimSetup::initFromBass( void ){
408	<
384	>	void SimSetup::initFromBass(void){
385		int i, j, k;
386		int n_cells;
387		double cellx, celly, cellz;
#	Line 419 | Line 395 | void SimSetup::initFromBass( void ){
395		vel[1] = 0.0;
396		vel[2] = 0.0;
397
398	<	temp1 = (double)tot_nmol / 4.0;
399	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
400	<	temp3 = ceil( temp2 );
398	>	temp1 = (double) tot_nmol / 4.0;
399	>	temp2 = pow(temp1, (1.0 / 3.0));
400	>	temp3 = ceil(temp2);
401
402	<	have_extra =0;
403	<	if( temp2 < temp3 ){ // we have a non-complete lattice
404	<	have_extra =1;
402	>	have_extra = 0;
403	>	if (temp2 < temp3){
404	>	// we have a non-complete lattice
405	>	have_extra = 1;
406
407	<	n_cells = (int)temp3 - 1;
407	>	n_cells = (int) temp3 - 1;
408		cellx = info[0].boxL[0] / temp3;
409		celly = info[0].boxL[1] / temp3;
410		cellz = info[0].boxL[2] / temp3;
411	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
412	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
413	<	n_per_extra = (int)ceil( temp1 );
411	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
412	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
413	>	n_per_extra = (int) ceil(temp1);
414
415	<	if( n_per_extra > 4){
416	<	sprintf( painCave.errMsg,
417	<	"SimSetup error. There has been an error in constructing"
418	<	" the non-complete lattice.\n" );
415	>	if (n_per_extra > 4){
416	>	sprintf(painCave.errMsg,
417	>	"SimSetup error. There has been an error in constructing"
418	>	" the non-complete lattice.\n");
419		painCave.isFatal = 1;
420		simError();
421		}
422		}
423		else{
424	<	n_cells = (int)temp3;
424	>	n_cells = (int) temp3;
425		cellx = info[0].boxL[0] / temp3;
426		celly = info[0].boxL[1] / temp3;
427		cellz = info[0].boxL[2] / temp3;
#	Line 455 | Line 432 | void SimSetup::initFromBass( void ){
432		current_comp = 0;
433		current_atom_ndx = 0;
434
435	<	for( i=0; i < n_cells ; i++ ){
436	<	for( j=0; j < n_cells; j++ ){
437	<	for( k=0; k < n_cells; k++ ){
435	>	for (i = 0; i < n_cells ; i++){
436	>	for (j = 0; j < n_cells; j++){
437	>	for (k = 0; k < n_cells; k++){
438	>	makeElement(i * cellx, j * celly, k * cellz);
439
440	<	makeElement( i * cellx,
463	<	j * celly,
464	<	k * cellz );
440	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
441
442	<	makeElement( i * cellx + 0.5 * cellx,
467	<	j * celly + 0.5 * celly,
468	<	k * cellz );
442	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
443
444	<	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 );
444	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
445		}
446		}
447		}
448
449	<	if( have_extra ){
449	>	if (have_extra){
450		done = 0;
451
452		int start_ndx;
453	<	for( i=0; i < (n_cells+1) && !done; i++ ){
454	<	for( j=0; j < (n_cells+1) && !done; j++ ){
453	>	for (i = 0; i < (n_cells + 1) && !done; i++){
454	>	for (j = 0; j < (n_cells + 1) && !done; j++){
455	>	if (i < n_cells){
456	>	if (j < n_cells){
457	>	start_ndx = n_cells;
458	>	}
459	>	else
460	>	start_ndx = 0;
461	>	}
462	>	else
463	>	start_ndx = 0;
464
465	<	if( i < n_cells ){
465	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
466	>	makeElement(i * cellx, j * celly, k * cellz);
467	>	done = (current_mol >= tot_nmol);
468
469	<	if( j < n_cells ){
470	<	start_ndx = n_cells;
471	<	}
472	<	else start_ndx = 0;
473	<	}
495	<	else start_ndx = 0;
469	>	if (!done && n_per_extra > 1){
470	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
471	>	k * cellz);
472	>	done = (current_mol >= tot_nmol);
473	>	}
474
475	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
476	<
477	<	makeElement( i * cellx,
478	<	j * celly,
479	<	k * cellz );
502	<	done = ( current_mol >= tot_nmol );
475	>	if (!done && n_per_extra > 2){
476	>	makeElement(i * cellx, j * celly + 0.5 * celly,
477	>	k * cellz + 0.5 * cellz);
478	>	done = (current_mol >= tot_nmol);
479	>	}
480
481	<	if( !done && n_per_extra > 1 ){
482	<	makeElement( i * cellx + 0.5 * cellx,
483	<	j * celly + 0.5 * celly,
484	<	k * cellz );
485	<	done = ( current_mol >= tot_nmol );
486	<	}
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	<	}
517	<
518	<	if( !done && n_per_extra > 3){
519	<	makeElement( i * cellx + 0.5 * cellx,
520	<	j * celly,
521	<	k * cellz + 0.5 * cellz );
522	<	done = ( current_mol >= tot_nmol );
523	<	}
524	<	}
481	>	if (!done && n_per_extra > 3){
482	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
483	>	k * cellz + 0.5 * cellz);
484	>	done = (current_mol >= tot_nmol);
485	>	}
486	>	}
487		}
488		}
489		}
490
491	<	for( i=0; i<info[0].n_atoms; i++ ){
492	<	info[0].atoms[i]->setVel( vel );
491	>	for (i = 0; i < info[0].n_atoms; i++){
492	>	info[0].atoms[i]->setVel(vel);
493		}
494		}
495
496	<	void SimSetup::makeElement( double x, double y, double z ){
535	<
496	>	void SimSetup::makeElement(double x, double y, double z){
497		int k;
498		AtomStamp* current_atom;
499		DirectionalAtom* dAtom;
500		double rotMat[3][3];
501		double pos[3];
502
503	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
504	<
505	<	current_atom = comp_stamps[current_comp]->getAtom( k );
506	<	if( !current_atom->havePosition() ){
507	<	sprintf( painCave.errMsg,
508	<	"SimSetup:initFromBass error.\n"
509	<	"\tComponent %s, atom %s does not have a position specified.\n"
510	<	"\tThe initialization routine is unable to give a start"
511	<	" position.\n",
551	<	comp_stamps[current_comp]->getID(),
552	<	current_atom->getType() );
503	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
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",
511	>	comp_stamps[current_comp]->getID(), current_atom->getType());
512		painCave.isFatal = 1;
513		simError();
514		}
515	<
515	>
516		pos[0] = x + current_atom->getPosX();
517		pos[1] = y + current_atom->getPosY();
518		pos[2] = z + current_atom->getPosZ();
560	–
561	–	info[0].atoms[current_atom_ndx]->setPos( pos );
519
520	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
520	>	info[0].atoms[current_atom_ndx]->setPos(pos);
521
522	<	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
522	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
523	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
524
525		rotMat[0][0] = 1.0;
526		rotMat[0][1] = 0.0;
#	Line 576 | Line 534 | void SimSetup::makeElement( double x, double y, double
534		rotMat[2][1] = 0.0;
535		rotMat[2][2] = 1.0;
536
537	<	dAtom->setA( rotMat );
537	>	dAtom->setA(rotMat);
538		}
539
540		current_atom_ndx++;
#	Line 585 | Line 543 | void SimSetup::makeElement( double x, double y, double
543		current_mol++;
544		current_comp_mol++;
545
546	<	if( current_comp_mol >= components_nmol[current_comp] ){
589	<
546	>	if (current_comp_mol >= components_nmol[current_comp]){
547		current_comp_mol = 0;
548		current_comp++;
549		}
550		}
551
552
553	<	void SimSetup::gatherInfo( void ){
554	<	int i,j,k;
553	>	void SimSetup::gatherInfo(void){
554	>	int i, j, k;
555
556		ensembleCase = -1;
557		ffCase = -1;
558
559		// set the easy ones first
560
561	<	for( i=0; i<nInfo; i++){
561	>	for (i = 0; i < nInfo; i++){
562		info[i].target_temp = globals->getTargetTemp();
563		info[i].dt = globals->getDt();
564		info[i].run_time = globals->getRunTime();
#	Line 611 | Line 568 | void SimSetup::gatherInfo( void ){
568
569		// get the forceField
570
571	<	strcpy( force_field, globals->getForceField() );
571	>	strcpy(force_field, globals->getForceField());
572
573	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
574	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
575	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
573	>	if (!strcasecmp(force_field, "DUFF")){
574	>	ffCase = FF_DUFF;
575	>	}
576	>	else if (!strcasecmp(force_field, "LJ")){
577	>	ffCase = FF_LJ;
578	>	}
579	>	else if (!strcasecmp(force_field, "EAM")){
580	>	ffCase = FF_EAM;
581	>	}
582		else{
583	<	sprintf( painCave.errMsg,
584	<	"SimSetup Error. Unrecognized force field -> %s\n",
585	<	force_field );
586	<	painCave.isFatal = 1;
624	<	simError();
583	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
584	>	force_field);
585	>	painCave.isFatal = 1;
586	>	simError();
587		}
588
589	<	// get the ensemble
589	>	// get the ensemble
590
591	<	strcpy( ensemble, globals->getEnsemble() );
591	>	strcpy(ensemble, globals->getEnsemble());
592
593	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
594	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
595	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
593	>	if (!strcasecmp(ensemble, "NVE")){
594	>	ensembleCase = NVE_ENS;
595	>	}
596	>	else if (!strcasecmp(ensemble, "NVT")){
597	>	ensembleCase = NVT_ENS;
598	>	}
599	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
600		ensembleCase = NPTi_ENS;
601	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
602	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
603	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
601	>	}
602	>	else if (!strcasecmp(ensemble, "NPTf")){
603	>	ensembleCase = NPTf_ENS;
604	>	}
605		else{
606	<	sprintf( painCave.errMsg,
607	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
608	<	"reverting to NVE for this simulation.\n",
609	<	ensemble );
610	<	painCave.isFatal = 0;
611	<	simError();
612	<	strcpy( ensemble, "NVE" );
613	<	ensembleCase = NVE_ENS;
606	>	sprintf(painCave.errMsg,
607	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
608	>	"reverting to NVE for this simulation.\n",
609	>	ensemble);
610	>	painCave.isFatal = 0;
611	>	simError();
612	>	strcpy(ensemble, "NVE");
613	>	ensembleCase = NVE_ENS;
614		}
648	–
649	–	for(i=0; i<nInfo; i++){
650	–
651	–	strcpy( info[i].ensemble, ensemble );
615
616	+	for (i = 0; i < nInfo; i++){
617	+	strcpy(info[i].ensemble, ensemble);
618	+
619		// get the mixing rule
620
621	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
621	>	strcpy(info[i].mixingRule, globals->getMixingRule());
622		info[i].usePBC = globals->getPBC();
623		}
624	<
624	>
625		// get the components and calculate the tot_nMol and indvidual n_mol
626	<
626	>
627		the_components = globals->getComponents();
628		components_nmol = new int[n_components];
629
630
631	<	if( !globals->haveNMol() ){
631	>	if (!globals->haveNMol()){
632		// we don't have the total number of molecules, so we assume it is
633		// given in each component
634
635		tot_nmol = 0;
636	<	for( i=0; i<n_components; i++ ){
637	<
638	<	if( !the_components[i]->haveNMol() ){
639	<	// we have a problem
640	<	sprintf( painCave.errMsg,
641	<	"SimSetup Error. No global NMol or component NMol"
642	<	" given. Cannot calculate the number of atoms.\n" );
643	<	painCave.isFatal = 1;
678	<	simError();
636	>	for (i = 0; i < n_components; i++){
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;
643	>	simError();
644		}
645
646		tot_nmol += the_components[i]->getNMol();
#	Line 683 | Line 648 | void SimSetup::gatherInfo( void ){
648		}
649		}
650		else{
651	<	sprintf( painCave.errMsg,
652	<	"SimSetup error.\n"
653	<	"\tSorry, the ability to specify total"
654	<	" nMols and then give molfractions in the components\n"
655	<	"\tis not currently supported."
656	<	" Please give nMol in the components.\n" );
651	>	sprintf(painCave.errMsg,
652	>	"SimSetup error.\n"
653	>	"\tSorry, the ability to specify total"
654	>	" nMols and then give molfractions in the components\n"
655	>	"\tis not currently supported."
656	>	" Please give nMol in the components.\n");
657		painCave.isFatal = 1;
658		simError();
659		}
660
661		// set the status, sample, and thermal kick times
697	–
698	–	for(i=0; i<nInfo; i++){
662
663	<	if( globals->haveSampleTime() ){
663	>	for (i = 0; i < nInfo; i++){
664	>	if (globals->haveSampleTime()){
665		info[i].sampleTime = globals->getSampleTime();
666		info[i].statusTime = info[i].sampleTime;
667		info[i].thermalTime = info[i].sampleTime;
#	Line 707 | Line 671 | void SimSetup::gatherInfo( void ){
671		info[i].statusTime = info[i].sampleTime;
672		info[i].thermalTime = info[i].sampleTime;
673		}
674	<
675	<	if( globals->haveStatusTime() ){
674	>
675	>	if (globals->haveStatusTime()){
676		info[i].statusTime = globals->getStatusTime();
677		}
678	<
679	<	if( globals->haveThermalTime() ){
678	>
679	>	if (globals->haveThermalTime()){
680		info[i].thermalTime = globals->getThermalTime();
681		}
682
683	+	info[i].resetIntegrator = 0;
684	+	if( globals->haveResetTime() ){
685	+	info[i].resetTime = globals->getResetTime();
686	+	info[i].resetIntegrator = 1;
687	+	}
688	+
689		// check for the temperature set flag
690
691	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
692	<
691	>	if (globals->haveTempSet())
692	>	info[i].setTemp = globals->getTempSet();
693	>
694		// get some of the tricky things that may still be in the globals
695	<
695	>
696		double boxVector[3];
697	<	if( globals->haveBox() ){
697	>	if (globals->haveBox()){
698		boxVector[0] = globals->getBox();
699		boxVector[1] = globals->getBox();
700		boxVector[2] = globals->getBox();
701	<
702	<	info[i].setBox( boxVector );
701	>
702	>	info[i].setBox(boxVector);
703		}
704	<	else if( globals->haveDensity() ){
734	<
704	>	else if (globals->haveDensity()){
705		double vol;
706	<	vol = (double)tot_nmol / globals->getDensity();
707	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
706	>	vol = (double) tot_nmol / globals->getDensity();
707	>	boxVector[0] = pow(vol, (1.0 / 3.0));
708		boxVector[1] = boxVector[0];
709		boxVector[2] = boxVector[0];
710	<
711	<	info[i].setBox( boxVector );
712	<	}
710	>
711	>	info[i].setBox(boxVector);
712	>	}
713		else{
714	<	if( !globals->haveBoxX() ){
715	<	sprintf( painCave.errMsg,
716	<	"SimSetup error, no periodic BoxX size given.\n" );
717	<	painCave.isFatal = 1;
718	<	simError();
714	>	if (!globals->haveBoxX()){
715	>	sprintf(painCave.errMsg,
716	>	"SimSetup error, no periodic BoxX size given.\n");
717	>	painCave.isFatal = 1;
718	>	simError();
719		}
720		boxVector[0] = globals->getBoxX();
721	<
722	<	if( !globals->haveBoxY() ){
723	<	sprintf( painCave.errMsg,
724	<	"SimSetup error, no periodic BoxY size given.\n" );
725	<	painCave.isFatal = 1;
726	<	simError();
721	>
722	>	if (!globals->haveBoxY()){
723	>	sprintf(painCave.errMsg,
724	>	"SimSetup error, no periodic BoxY size given.\n");
725	>	painCave.isFatal = 1;
726	>	simError();
727		}
728		boxVector[1] = globals->getBoxY();
729	<
730	<	if( !globals->haveBoxZ() ){
731	<	sprintf( painCave.errMsg,
732	<	"SimSetup error, no periodic BoxZ size given.\n" );
733	<	painCave.isFatal = 1;
734	<	simError();
729	>
730	>	if (!globals->haveBoxZ()){
731	>	sprintf(painCave.errMsg,
732	>	"SimSetup error, no periodic BoxZ size given.\n");
733	>	painCave.isFatal = 1;
734	>	simError();
735		}
736		boxVector[2] = globals->getBoxZ();
737	<
738	<	info[i].setBox( boxVector );
737	>
738	>	info[i].setBox(boxVector);
739		}
740		}
741
742	+	//setup seed for random number generator
743		int seedValue;
773	–	struct timeval now_time_val;
774	–	struct timezone time_zone;
744
745	<	if(globals->haveSeed()){
745	>	if (globals->haveSeed()){
746		seedValue = globals->getSeed();
747	<	}
747	>
748	>	if(seedValue / 1E9 == 0){
749	>	sprintf(painCave.errMsg,
750	>	"Seed for sprng library should contain at least 9 digits\n"
751	>	"OOPSE will generate a seed for user\n");
752	>	painCave.isFatal = 0;
753	>	simError();
754	>
755	>	//using seed generated by system instead of invalid seed set by user
756	>	#ifndef IS_MPI
757	>	seedValue = make_sprng_seed();
758	>	#else
759	>	if (worldRank == 0){
760	>	seedValue = make_sprng_seed();
761	>	}
762	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
763	>	#endif
764	>	}
765	>	}//end of if branch of globals->haveSeed()
766		else{
767	+
768		#ifndef IS_MPI
769	<	gettimeofday(&now_time_val, &time_zone);  // get the time now
782	<	seedValue = (int) now_time_val.tv_sec;      //  convert to epoch time
769	>	seedValue = make_sprng_seed();
770		#else
771	<	if(worldRank == 0){
772	<	gettimeofday(&now_time_val, &time_zone);  // get the time now
786	<	seedValue = (int) now_time_val.tv_sec;      //  convert to epoch time
771	>	if (worldRank == 0){
772	>	seedValue = make_sprng_seed();
773		}
774	<	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
774	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
775		#endif
776	<	}
776	>	}//end of globals->haveSeed()
777
778	<	for(int i = 0; i < nInfo; i++){
778	>	for (int i = 0; i < nInfo; i++){
779		info[i].setSeed(seedValue);
780		}
781
782		#ifdef IS_MPI
783	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
783	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
784		MPIcheckPoint();
785		#endif // is_mpi
800	–
786		}
787
788
789	<	void SimSetup::finalInfoCheck( void ){
789	>	void SimSetup::finalInfoCheck(void){
790		int index;
791		int usesDipoles;
792		int i;
793
794	<	for(i=0; i<nInfo; i++){
794	>	for (i = 0; i < nInfo; i++){
795		// check electrostatic parameters
796	<
796	>
797		index = 0;
798		usesDipoles = 0;
799	<	while( (index < info[i].n_atoms) && !usesDipoles ){
799	>	while ((index < info[i].n_atoms) && !usesDipoles){
800		usesDipoles = (info[i].atoms[index])->hasDipole();
801		index++;
802		}
803	<
803	>
804		#ifdef IS_MPI
805		int myUse = usesDipoles;
806	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
806	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
807		#endif //is_mpi
808	<
808	>
809		double theEcr, theEst;
810	<
811	<	if (globals->getUseRF() ) {
810	>
811	>	if (globals->getUseRF()){
812		info[i].useReactionField = 1;
813	<
814	<	if( !globals->haveECR() ){
815	<	sprintf( painCave.errMsg,
816	<	"SimSetup Warning: using default value of 1/2 the smallest "
817	<	"box length for the electrostaticCutoffRadius.\n"
818	<	"I hope you have a very fast processor!\n");
819	<	painCave.isFatal = 0;
820	<	simError();
821	<	double smallest;
822	<	smallest = info[i].boxL[0];
823	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
824	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
825	<	theEcr = 0.5 * smallest;
826	<	} else {
827	<	theEcr = globals->getECR();
813	>
814	>	if (!globals->haveECR()){
815	>	sprintf(painCave.errMsg,
816	>	"SimSetup Warning: using default value of 1/2 the smallest "
817	>	"box length for the electrostaticCutoffRadius.\n"
818	>	"I hope you have a very fast processor!\n");
819	>	painCave.isFatal = 0;
820	>	simError();
821	>	double smallest;
822	>	smallest = info[i].boxL[0];
823	>	if (info[i].boxL[1] <= smallest)
824	>	smallest = info[i].boxL[1];
825	>	if (info[i].boxL[2] <= smallest)
826	>	smallest = info[i].boxL[2];
827	>	theEcr = 0.5 * smallest;
828		}
829	<
830	<	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();
829	>	else{
830	>	theEcr = globals->getECR();
831		}
832	<
833	<	info[i].setEcr( theEcr, theEst );
834	<
835	<	if(!globals->haveDielectric() ){
836	<	sprintf( painCave.errMsg,
837	<	"SimSetup Error: You are trying to use Reaction Field without"
838	<	"setting a dielectric constant!\n"
839	<	);
864	<	painCave.isFatal = 1;
865	<	simError();
832	>
833	>	if (!globals->haveEST()){
834	>	sprintf(painCave.errMsg,
835	>	"SimSetup Warning: using default value of 0.05 * the "
836	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
837	>	painCave.isFatal = 0;
838	>	simError();
839	>	theEst = 0.05 * theEcr;
840		}
841	<	info[i].dielectric = globals->getDielectric();
842	<	}
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 );
841	>	else{
842	>	theEst = globals->getEST();
843		}
844	<	}
844	>
845	>	info[i].setEcr(theEcr, theEst);
846	>
847	>	if (!globals->haveDielectric()){
848	>	sprintf(painCave.errMsg,
849	>	"SimSetup Error: You are trying to use Reaction Field without"
850	>	"setting a dielectric constant!\n");
851	>	painCave.isFatal = 1;
852	>	simError();
853	>	}
854	>	info[i].dielectric = globals->getDielectric();
855	>	}
856	>	else{
857	>	if (usesDipoles){
858	>	if (!globals->haveECR()){
859	>	sprintf(painCave.errMsg,
860	>	"SimSetup Warning: using default value of 1/2 the smallest "
861	>	"box length for the electrostaticCutoffRadius.\n"
862	>	"I hope you have a very fast processor!\n");
863	>	painCave.isFatal = 0;
864	>	simError();
865	>	double smallest;
866	>	smallest = info[i].boxL[0];
867	>	if (info[i].boxL[1] <= smallest)
868	>	smallest = info[i].boxL[1];
869	>	if (info[i].boxL[2] <= smallest)
870	>	smallest = info[i].boxL[2];
871	>	theEcr = 0.5 * smallest;
872	>	}
873	>	else{
874	>	theEcr = globals->getECR();
875	>	}
876	>
877	>	if (!globals->haveEST()){
878	>	sprintf(painCave.errMsg,
879	>	"SimSetup Warning: using default value of 0.05 * the "
880	>	"electrostaticCutoffRadius for the "
881	>	"electrostaticSkinThickness\n");
882	>	painCave.isFatal = 0;
883	>	simError();
884	>	theEst = 0.05 * theEcr;
885	>	}
886	>	else{
887	>	theEst = globals->getEST();
888	>	}
889	>
890	>	info[i].setEcr(theEcr, theEst);
891	>	}
892	>	}
893		}
894
895		#ifdef IS_MPI
896	<	strcpy( checkPointMsg, "post processing checks out" );
896	>	strcpy(checkPointMsg, "post processing checks out");
897		MPIcheckPoint();
898		#endif // is_mpi
910	–
899		}
900
901	<	void SimSetup::initSystemCoords( void ){
901	>	void SimSetup::initSystemCoords(void){
902		int i;
903	<
903	>
904		char* inName;
905
906	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
906	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
907
908	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
909	<
910	<	if( globals->haveInitialConfig() ){
911	<
908	>	for (i = 0; i < info[0].n_atoms; i++)
909	>	info[0].atoms[i]->setCoords();
910	>
911	>	if (globals->haveInitialConfig()){
912		InitializeFromFile* fileInit;
913		#ifdef IS_MPI // is_mpi
914	<	if( worldRank == 0 ){
914	>	if (worldRank == 0){
915		#endif //is_mpi
916		inName = globals->getInitialConfig();
917		double* tempDouble = new double[1000000];
918	<	fileInit = new InitializeFromFile( inName );
918	>	fileInit = new InitializeFromFile(inName);
919		#ifdef IS_MPI
920	<	}else fileInit = new InitializeFromFile( NULL );
920	>	}
921	>	else
922	>	fileInit = new InitializeFromFile(NULL);
923		#endif
924	<	fileInit->readInit( info ); // default velocities on
925	<
924	>	fileInit->readInit(info); // default velocities on
925	>
926		delete fileInit;
927		}
928		else{
939	–
929		#ifdef IS_MPI
930	<
930	>
931		// no init from bass
932	<
933	<	sprintf( painCave.errMsg,
934	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
932	>
933	>	sprintf(painCave.errMsg,
934	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
935		painCave.isFatal;
936		simError();
937	<
937	>
938		#else
939	<
939	>
940		initFromBass();
941	<
942	<
941	>
942	>
943		#endif
944		}
945	<
945	>
946		#ifdef IS_MPI
947	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
947	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
948		MPIcheckPoint();
949		#endif // is_mpi
961	–
950		}
951
952
953	<	void SimSetup::makeOutNames( void ){
966	<
953	>	void SimSetup::makeOutNames(void){
954		int k;
955
969	–
970	–	for(k=0; k<nInfo; k++){
956
957	+	for (k = 0; k < nInfo; k++){
958		#ifdef IS_MPI
959	<	if( worldRank == 0 ){
959	>	if (worldRank == 0){
960		#endif // is_mpi
961	<
962	<	if( globals->haveFinalConfig() ){
963	<	strcpy( info[k].finalName, globals->getFinalConfig() );
961	>
962	>	if (globals->haveFinalConfig()){
963	>	strcpy(info[k].finalName, globals->getFinalConfig());
964		}
965		else{
966	<	strcpy( info[k].finalName, inFileName );
967	<	char* endTest;
968	<	int nameLength = strlen( info[k].finalName );
969	<	endTest = &(info[k].finalName[nameLength - 5]);
970	<	if( !strcmp( endTest, ".bass" ) ){
971	<	strcpy( endTest, ".eor" );
972	<	}
973	<	else if( !strcmp( endTest, ".BASS" ) ){
974	<	strcpy( endTest, ".eor" );
975	<	}
976	<	else{
977	<	endTest = &(info[k].finalName[nameLength - 4]);
978	<	if( !strcmp( endTest, ".bss" ) ){
979	<	strcpy( endTest, ".eor" );
980	<	}
981	<	else if( !strcmp( endTest, ".mdl" ) ){
982	<	strcpy( endTest, ".eor" );
983	<	}
984	<	else{
985	<	strcat( info[k].finalName, ".eor" );
986	<	}
987	<	}
966	>	strcpy(info[k].finalName, inFileName);
967	>	char* endTest;
968	>	int nameLength = strlen(info[k].finalName);
969	>	endTest = &(info[k].finalName[nameLength - 5]);
970	>	if (!strcmp(endTest, ".bass")){
971	>	strcpy(endTest, ".eor");
972	>	}
973	>	else if (!strcmp(endTest, ".BASS")){
974	>	strcpy(endTest, ".eor");
975	>	}
976	>	else{
977	>	endTest = &(info[k].finalName[nameLength - 4]);
978	>	if (!strcmp(endTest, ".bss")){
979	>	strcpy(endTest, ".eor");
980	>	}
981	>	else if (!strcmp(endTest, ".mdl")){
982	>	strcpy(endTest, ".eor");
983	>	}
984	>	else{
985	>	strcat(info[k].finalName, ".eor");
986	>	}
987	>	}
988		}
989	<
989	>
990		// make the sample and status out names
991	<
992	<	strcpy( info[k].sampleName, inFileName );
991	>
992	>	strcpy(info[k].sampleName, inFileName);
993		char* endTest;
994	<	int nameLength = strlen( info[k].sampleName );
994	>	int nameLength = strlen(info[k].sampleName);
995		endTest = &(info[k].sampleName[nameLength - 5]);
996	<	if( !strcmp( endTest, ".bass" ) ){
997	<	strcpy( endTest, ".dump" );
996	>	if (!strcmp(endTest, ".bass")){
997	>	strcpy(endTest, ".dump");
998		}
999	<	else if( !strcmp( endTest, ".BASS" ) ){
1000	<	strcpy( endTest, ".dump" );
999	>	else if (!strcmp(endTest, ".BASS")){
1000	>	strcpy(endTest, ".dump");
1001		}
1002		else{
1003	<	endTest = &(info[k].sampleName[nameLength - 4]);
1004	<	if( !strcmp( endTest, ".bss" ) ){
1005	<	strcpy( endTest, ".dump" );
1006	<	}
1007	<	else if( !strcmp( endTest, ".mdl" ) ){
1008	<	strcpy( endTest, ".dump" );
1009	<	}
1010	<	else{
1011	<	strcat( info[k].sampleName, ".dump" );
1012	<	}
1003	>	endTest = &(info[k].sampleName[nameLength - 4]);
1004	>	if (!strcmp(endTest, ".bss")){
1005	>	strcpy(endTest, ".dump");
1006	>	}
1007	>	else if (!strcmp(endTest, ".mdl")){
1008	>	strcpy(endTest, ".dump");
1009	>	}
1010	>	else{
1011	>	strcat(info[k].sampleName, ".dump");
1012	>	}
1013		}
1014	<
1015	<	strcpy( info[k].statusName, inFileName );
1016	<	nameLength = strlen( info[k].statusName );
1014	>
1015	>	strcpy(info[k].statusName, inFileName);
1016	>	nameLength = strlen(info[k].statusName);
1017		endTest = &(info[k].statusName[nameLength - 5]);
1018	<	if( !strcmp( endTest, ".bass" ) ){
1019	<	strcpy( endTest, ".stat" );
1018	>	if (!strcmp(endTest, ".bass")){
1019	>	strcpy(endTest, ".stat");
1020		}
1021	<	else if( !strcmp( endTest, ".BASS" ) ){
1022	<	strcpy( endTest, ".stat" );
1021	>	else if (!strcmp(endTest, ".BASS")){
1022	>	strcpy(endTest, ".stat");
1023		}
1024		else{
1025	<	endTest = &(info[k].statusName[nameLength - 4]);
1026	<	if( !strcmp( endTest, ".bss" ) ){
1027	<	strcpy( endTest, ".stat" );
1028	<	}
1029	<	else if( !strcmp( endTest, ".mdl" ) ){
1030	<	strcpy( endTest, ".stat" );
1031	<	}
1032	<	else{
1033	<	strcat( info[k].statusName, ".stat" );
1034	<	}
1025	>	endTest = &(info[k].statusName[nameLength - 4]);
1026	>	if (!strcmp(endTest, ".bss")){
1027	>	strcpy(endTest, ".stat");
1028	>	}
1029	>	else if (!strcmp(endTest, ".mdl")){
1030	>	strcpy(endTest, ".stat");
1031	>	}
1032	>	else{
1033	>	strcat(info[k].statusName, ".stat");
1034	>	}
1035		}
1036	<
1036	>
1037		#ifdef IS_MPI
1038	+
1039		}
1040		#endif // is_mpi
1041		}
1042		}
1043
1044
1045	<	void SimSetup::sysObjectsCreation( void ){
1046	<
1047	<	int i,k;
1061	<
1045	>	void SimSetup::sysObjectsCreation(void){
1046	>	int i, k;
1047	>
1048		// create the forceField
1049
1050		createFF();
#	Line 1073 | Line 1059 | void SimSetup::sysObjectsCreation( void ){
1059
1060		#ifdef IS_MPI
1061		// divide the molecules among the processors
1062	<
1062	>
1063		mpiMolDivide();
1064		#endif //is_mpi
1065	<
1065	>
1066		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1067	<
1067	>
1068		makeSysArrays();
1069
1070		// make and initialize the molecules (all but atomic coordinates)
1071	<
1071	>
1072		makeMolecules();
1073	<
1074	<	for(k=0; k<nInfo; k++){
1073	>
1074	>	for (k = 0; k < nInfo; k++){
1075		info[k].identArray = new int[info[k].n_atoms];
1076	<	for(i=0; i<info[k].n_atoms; i++){
1076	>	for (i = 0; i < info[k].n_atoms; i++){
1077		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1078		}
1079		}
1080		}
1081
1082
1083	<	void SimSetup::createFF( void ){
1083	>	void SimSetup::createFF(void){
1084	>	switch (ffCase){
1085	>	case FF_DUFF:
1086	>	the_ff = new DUFF();
1087	>	break;
1088
1089	<	switch( ffCase ){
1089	>	case FF_LJ:
1090	>	the_ff = new LJFF();
1091	>	break;
1092
1093	<	case FF_DUFF:
1094	<	the_ff = new DUFF();
1095	<	break;
1093	>	case FF_EAM:
1094	>	the_ff = new EAM_FF();
1095	>	break;
1096
1097	<	case FF_LJ:
1098	<	the_ff = new LJFF();
1099	<	break;
1100	<
1101	<	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();
1097	>	default:
1098	>	sprintf(painCave.errMsg,
1099	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1100	>	painCave.isFatal = 1;
1101	>	simError();
1102		}
1103
1104		#ifdef IS_MPI
1105	<	strcpy( checkPointMsg, "ForceField creation successful" );
1105	>	strcpy(checkPointMsg, "ForceField creation successful");
1106		MPIcheckPoint();
1107		#endif // is_mpi
1124	–
1108		}
1109
1110
1111	<	void SimSetup::compList( void ){
1129	<
1111	>	void SimSetup::compList(void){
1112		int i;
1113		char* id;
1114		LinkedMolStamp* headStamp = new LinkedMolStamp();
1115		LinkedMolStamp* currentStamp = NULL;
1116	<	comp_stamps = new MoleculeStamp*[n_components];
1117	<
1116	>	comp_stamps = new MoleculeStamp * [n_components];
1117	>
1118		// make an array of molecule stamps that match the components used.
1119		// also extract the used stamps out into a separate linked list
1120	<
1121	<	for(i=0; i<nInfo; i++){
1120	>
1121	>	for (i = 0; i < nInfo; i++){
1122		info[i].nComponents = n_components;
1123		info[i].componentsNmol = components_nmol;
1124		info[i].compStamps = comp_stamps;
1125		info[i].headStamp = headStamp;
1126		}
1145	–
1127
1147	–	for( i=0; i<n_components; i++ ){
1128
1129	+	for (i = 0; i < n_components; i++){
1130		id = the_components[i]->getType();
1131		comp_stamps[i] = NULL;
1132	<
1132	>
1133		// check to make sure the component isn't already in the list
1134
1135	<	comp_stamps[i] = headStamp->match( id );
1136	<	if( comp_stamps[i] == NULL ){
1156	<
1135	>	comp_stamps[i] = headStamp->match(id);
1136	>	if (comp_stamps[i] == NULL){
1137		// extract the component from the list;
1138	<
1139	<	currentStamp = stamps->extractMolStamp( id );
1140	<	if( currentStamp == NULL ){
1141	<	sprintf( painCave.errMsg,
1142	<	"SimSetup error: Component \"%s\" was not found in the "
1143	<	"list of declared molecules\n",
1144	<	id );
1145	<	painCave.isFatal = 1;
1146	<	simError();
1138	>
1139	>	currentStamp = stamps->extractMolStamp(id);
1140	>	if (currentStamp == NULL){
1141	>	sprintf(painCave.errMsg,
1142	>	"SimSetup error: Component \"%s\" was not found in the "
1143	>	"list of declared molecules\n",
1144	>	id);
1145	>	painCave.isFatal = 1;
1146	>	simError();
1147		}
1148	<
1149	<	headStamp->add( currentStamp );
1150	<	comp_stamps[i] = headStamp->match( id );
1148	>
1149	>	headStamp->add(currentStamp);
1150	>	comp_stamps[i] = headStamp->match(id);
1151		}
1152		}
1153
1154		#ifdef IS_MPI
1155	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1155	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1156		MPIcheckPoint();
1157		#endif // is_mpi
1178	–
1179	–
1158		}
1159
1160	<	void SimSetup::calcSysValues( void ){
1160	>	void SimSetup::calcSysValues(void){
1161		int i, j, k;
1162	<
1163	<	int *molMembershipArray;
1164	<
1162	>
1163	>	int* molMembershipArray;
1164	>
1165		tot_atoms = 0;
1166		tot_bonds = 0;
1167		tot_bends = 0;
1168		tot_torsions = 0;
1169	<	for( i=0; i<n_components; i++ ){
1170	<
1171	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1172	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1195	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1169	>	for (i = 0; i < n_components; i++){
1170	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1171	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1172	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1173		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1174		}
1175	<
1175	>
1176		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1177		molMembershipArray = new int[tot_atoms];
1178	<
1179	<	for(i=0; i<nInfo; i++){
1178	>
1179	>	for (i = 0; i < nInfo; i++){
1180		info[i].n_atoms = tot_atoms;
1181		info[i].n_bonds = tot_bonds;
1182		info[i].n_bends = tot_bends;
1183		info[i].n_torsions = tot_torsions;
1184		info[i].n_SRI = tot_SRI;
1185		info[i].n_mol = tot_nmol;
1186	<
1186	>
1187		info[i].molMembershipArray = molMembershipArray;
1188	<	}
1188	>	}
1189		}
1190
1191		#ifdef IS_MPI
1192
1193	<	void SimSetup::mpiMolDivide( void ){
1217	<
1193	>	void SimSetup::mpiMolDivide(void){
1194		int i, j, k;
1195		int localMol, allMol;
1196		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1197
1198	<	mpiSim = new mpiSimulation( info );
1199	<
1198	>	mpiSim = new mpiSimulation(info);
1199	>
1200		globalIndex = mpiSim->divideLabor();
1201
1202		// set up the local variables
1203	<
1203	>
1204		mol2proc = mpiSim->getMolToProcMap();
1205		molCompType = mpiSim->getMolComponentType();
1206	<
1206	>
1207		allMol = 0;
1208		localMol = 0;
1209		local_atoms = 0;
#	Line 1237 | Line 1213 | void SimSetup::mpiMolDivide( void ){
1213		globalAtomIndex = 0;
1214
1215
1216	<	for( i=0; i<n_components; i++ ){
1217	<
1218	<	for( j=0; j<components_nmol[i]; j++ ){
1219	<
1220	<	if( mol2proc[allMol] == worldRank ){
1221	<
1222	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1223	<	local_bonds +=    comp_stamps[i]->getNBonds();
1248	<	local_bends +=    comp_stamps[i]->getNBends();
1249	<	local_torsions += comp_stamps[i]->getNTorsions();
1250	<	localMol++;
1216	>	for (i = 0; i < n_components; i++){
1217	>	for (j = 0; j < components_nmol[i]; j++){
1218	>	if (mol2proc[allMol] == worldRank){
1219	>	local_atoms += comp_stamps[i]->getNAtoms();
1220	>	local_bonds += comp_stamps[i]->getNBonds();
1221	>	local_bends += comp_stamps[i]->getNBends();
1222	>	local_torsions += comp_stamps[i]->getNTorsions();
1223	>	localMol++;
1224		}
1225	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1225	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1226		info[0].molMembershipArray[globalAtomIndex] = allMol;
1227		globalAtomIndex++;
1228		}
1229
1230	<	allMol++;
1230	>	allMol++;
1231		}
1232		}
1233		local_SRI = local_bonds + local_bends + local_torsions;
1234	<
1234	>
1235		info[0].n_atoms = mpiSim->getMyNlocal();
1236	<
1237	<	if( local_atoms != info[0].n_atoms ){
1238	<	sprintf( painCave.errMsg,
1239	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1240	<	" localAtom (%d) are not equal.\n",
1241	<	info[0].n_atoms,
1269	<	local_atoms );
1236	>
1237	>	if (local_atoms != info[0].n_atoms){
1238	>	sprintf(painCave.errMsg,
1239	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1240	>	" localAtom (%d) are not equal.\n",
1241	>	info[0].n_atoms, local_atoms);
1242		painCave.isFatal = 1;
1243		simError();
1244		}
#	Line 1277 | Line 1249 | void SimSetup::mpiMolDivide( void ){
1249		info[0].n_SRI = local_SRI;
1250		info[0].n_mol = localMol;
1251
1252	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1252	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1253		MPIcheckPoint();
1254		}
1255	<
1255	>
1256		#endif // is_mpi
1257
1258
1259	<	void SimSetup::makeSysArrays( void ){
1259	>	void SimSetup::makeSysArrays(void){
1260		int i, j, k, l;
1261
1262		Atom** the_atoms;
1263		Molecule* the_molecules;
1264		Exclude** the_excludes;
1265
1266	<
1267	<	for(l=0; l<nInfo; l++){
1296	<
1266	>
1267	>	for (l = 0; l < nInfo; l++){
1268		// create the atom and short range interaction arrays
1269	<
1270	<	the_atoms = new Atom*[info[l].n_atoms];
1269	>
1270	>	the_atoms = new Atom * [info[l].n_atoms];
1271		the_molecules = new Molecule[info[l].n_mol];
1272		int molIndex;
1273
1274		// initialize the molecule's stampID's
1275	<
1275	>
1276		#ifdef IS_MPI
1277	<
1278	<
1277	>
1278	>
1279		molIndex = 0;
1280	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1281	<
1282	<	if(mol2proc[i] == worldRank ){
1283	<	the_molecules[molIndex].setStampID( molCompType[i] );
1284	<	the_molecules[molIndex].setMyIndex( molIndex );
1285	<	the_molecules[molIndex].setGlobalIndex( i );
1315	<	molIndex++;
1280	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1281	>	if (mol2proc[i] == worldRank){
1282	>	the_molecules[molIndex].setStampID(molCompType[i]);
1283	>	the_molecules[molIndex].setMyIndex(molIndex);
1284	>	the_molecules[molIndex].setGlobalIndex(i);
1285	>	molIndex++;
1286		}
1287		}
1288	<
1288	>
1289		#else // is_mpi
1290	<
1290	>
1291		molIndex = 0;
1292		globalAtomIndex = 0;
1293	<	for(i=0; i<n_components; i++){
1294	<	for(j=0; j<components_nmol[i]; j++ ){
1295	<	the_molecules[molIndex].setStampID( i );
1296	<	the_molecules[molIndex].setMyIndex( molIndex );
1297	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1298	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1299	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1300	<	globalAtomIndex++;
1301	<	}
1302	<	molIndex++;
1293	>	for (i = 0; i < n_components; i++){
1294	>	for (j = 0; j < components_nmol[i]; j++){
1295	>	the_molecules[molIndex].setStampID(i);
1296	>	the_molecules[molIndex].setMyIndex(molIndex);
1297	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1298	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1299	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1300	>	globalAtomIndex++;
1301	>	}
1302	>	molIndex++;
1303		}
1304		}
1305	<
1306	<
1305	>
1306	>
1307		#endif // is_mpi
1308
1309
1310	<	if( info[l].n_SRI ){
1341	<
1310	>	if (info[l].n_SRI){
1311		Exclude::createArray(info[l].n_SRI);
1312	<	the_excludes = new Exclude*[info[l].n_SRI];
1313	<	for( int ex=0; ex<info[l].n_SRI; ex++){
1314	<	the_excludes[ex] = new Exclude(ex);
1312	>	the_excludes = new Exclude * [info[l].n_SRI];
1313	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1314	>	the_excludes[ex] = new Exclude(ex);
1315		}
1316		info[l].globalExcludes = new int;
1317		info[l].n_exclude = info[l].n_SRI;
1318		}
1319		else{
1320	<
1321	<	Exclude::createArray( 1 );
1353	<	the_excludes = new Exclude*;
1320	>	Exclude::createArray(1);
1321	>	the_excludes = new Exclude * ;
1322		the_excludes[0] = new Exclude(0);
1323	<	the_excludes[0]->setPair( 0,0 );
1323	>	the_excludes[0]->setPair(0, 0);
1324		info[l].globalExcludes = new int;
1325		info[l].globalExcludes[0] = 0;
1326		info[l].n_exclude = 0;
#	Line 1365 | Line 1333 | void SimSetup::makeSysArrays( void ){
1333		info[l].nGlobalExcludes = 0;
1334		info[l].excludes = the_excludes;
1335
1336	<	the_ff->setSimInfo( info );
1369	<
1336	>	the_ff->setSimInfo(info);
1337		}
1338		}
1339
1340	<	void SimSetup::makeIntegrator( void ){
1374	<
1340	>	void SimSetup::makeIntegrator(void){
1341		int k;
1342
1343	<	NVT<RealIntegrator>*  myNVT = NULL;
1344	<	NPTi<RealIntegrator>* myNPTi = NULL;
1345	<	NPTf<RealIntegrator>* myNPTf = NULL;
1346	<	NPTim<RealIntegrator>* myNPTim = NULL;
1347	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1348	<
1349	<	for(k=0; k<nInfo; k++){
1350	<
1351	<	switch( ensembleCase ){
1352	<
1353	<	case NVE_ENS:
1354	<	if (globals->haveZconstraints()){
1355	<	setupZConstraint(info[k]);
1356	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1391	<	}
1343	>	NVT<RealIntegrator>* myNVT = NULL;
1344	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1345	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1346	>
1347	>	for (k = 0; k < nInfo; k++){
1348	>	switch (ensembleCase){
1349	>	case NVE_ENS:
1350	>	if (globals->haveZconstraints()){
1351	>	setupZConstraint(info[k]);
1352	>	new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1353	>	}
1354	>	else
1355	>	new NVE<RealIntegrator>(&(info[k]), the_ff);
1356	>	break;
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]);
1400	<	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1401	<	}
1402	<	else
1403	<	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1358	>	case NVT_ENS:
1359	>	if (globals->haveZconstraints()){
1360	>	setupZConstraint(info[k]);
1361	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1362	>	}
1363	>	else
1364	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1365
1366		myNVT->setTargetTemp(globals->getTargetTemp());
1367	<
1368	<	if (globals->haveTauThermostat())
1367	>
1368	>	if (globals->haveTauThermostat())
1369		myNVT->setTauThermostat(globals->getTauThermostat());
1370	<
1371	<	else {
1372	<	sprintf( painCave.errMsg,
1373	<	"SimSetup error: If you use the NVT\n"
1413	<	"    ensemble, you must set tauThermostat.\n");
1370	>	else{
1371	>	sprintf(painCave.errMsg,
1372	>	"SimSetup error: If you use the NVT\n"
1373	>	"    ensemble, you must set tauThermostat.\n");
1374		painCave.isFatal = 1;
1375		simError();
1376		}
1377		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 );
1378
1379	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1380	<
1381	<	if (globals->haveTargetPressure())
1382	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1383	<	else {
1384	<	sprintf( painCave.errMsg,
1385	<	"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 );
1379	>	case NPTi_ENS:
1380	>	if (globals->haveZconstraints()){
1381	>	setupZConstraint(info[k]);
1382	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1383	>	}
1384	>	else
1385	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1386
1387	<	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 );
1387	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1388
1389	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1390	<
1391	<	if (globals->haveTargetPressure())
1392	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1513	<	else {
1514	<	sprintf( painCave.errMsg,
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"
1394		"    ensemble, you must set targetPressure in the BASS file.\n");
1395	<	painCave.isFatal = 1;
1396	<	simError();
1397	<	}
1520	<
1521	<	if( globals->haveTauThermostat() )
1522	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1523	<	else{
1524	<	sprintf( painCave.errMsg,
1525	<	"SimSetup error: If you use an NPT\n"
1526	<	"    ensemble, you must set tauThermostat.\n");
1527	<	painCave.isFatal = 1;
1528	<	simError();
1529	<	}
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 );
1395	>	painCave.isFatal = 1;
1396	>	simError();
1397	>	}
1398
1399	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1399	>	if (globals->haveTauThermostat())
1400	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1401	>	else{
1402	>	sprintf(painCave.errMsg,
1403	>	"SimSetup error: If you use an NPT\n"
1404	>	"    ensemble, you must set tauThermostat.\n");
1405	>	painCave.isFatal = 1;
1406	>	simError();
1407	>	}
1408
1409	<	if (globals->haveTargetPressure())
1410	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1411	<	else {
1412	<	sprintf( painCave.errMsg,
1409	>	if (globals->haveTauBarostat())
1410	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1411	>	else{
1412	>	sprintf(painCave.errMsg,
1413	>	"SimSetup error: If you use an NPT\n"
1414	>	"    ensemble, you must set tauBarostat.\n");
1415	>	painCave.isFatal = 1;
1416	>	simError();
1417	>	}
1418	>	break;
1419	>
1420	>	case NPTf_ENS:
1421	>	if (globals->haveZconstraints()){
1422	>	setupZConstraint(info[k]);
1423	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1424	>	}
1425	>	else
1426	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1427	>
1428	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1429	>
1430	>	if (globals->haveTargetPressure())
1431	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1432	>	else{
1433	>	sprintf(painCave.errMsg,
1434		"SimSetup error: If you use a constant pressure\n"
1435		"    ensemble, you must set targetPressure in the BASS file.\n");
1436	<	painCave.isFatal = 1;
1437	<	simError();
1438	<	}
1436	>	painCave.isFatal = 1;
1437	>	simError();
1438	>	}
1439
1440	<	if( globals->haveTauThermostat() )
1441	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1442	<	else{
1443	<	sprintf( painCave.errMsg,
1440	>	if (globals->haveTauThermostat())
1441	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1442	>	else{
1443	>	sprintf(painCave.errMsg,
1444		"SimSetup error: If you use an NPT\n"
1445		"    ensemble, you must set tauThermostat.\n");
1446	<	painCave.isFatal = 1;
1447	<	simError();
1448	<	}
1446	>	painCave.isFatal = 1;
1447	>	simError();
1448	>	}
1449
1450	<	if( globals->haveTauBarostat() )
1451	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1452	<	else{
1453	<	sprintf( painCave.errMsg,
1450	>	if (globals->haveTauBarostat())
1451	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1452	>	else{
1453	>	sprintf(painCave.errMsg,
1454		"SimSetup error: If you use an NPT\n"
1455		"    ensemble, you must set tauBarostat.\n");
1456	+	painCave.isFatal = 1;
1457	+	simError();
1458	+	}
1459	+	break;
1460	+
1461	+	default:
1462	+	sprintf(painCave.errMsg,
1463	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1464		painCave.isFatal = 1;
1465		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();
1466		}
1467		}
1468		}
1469
1470	<	void SimSetup::initFortran( void ){
1593	<
1470	>	void SimSetup::initFortran(void){
1471		info[0].refreshSim();
1472	<
1473	<	if( !strcmp( info[0].mixingRule, "standard") ){
1474	<	the_ff->initForceField( LB_MIXING_RULE );
1472	>
1473	>	if (!strcmp(info[0].mixingRule, "standard")){
1474	>	the_ff->initForceField(LB_MIXING_RULE);
1475		}
1476	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1477	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1476	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1477	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1478		}
1479		else{
1480	<	sprintf( painCave.errMsg,
1481	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1605	<	info[0].mixingRule );
1480	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1481	>	info[0].mixingRule);
1482		painCave.isFatal = 1;
1483		simError();
1484		}
1485
1486
1487		#ifdef IS_MPI
1488	<	strcpy( checkPointMsg,
1613	<	"Successfully intialized the mixingRule for Fortran." );
1488	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1489		MPIcheckPoint();
1490		#endif // is_mpi
1616	–
1491		}
1492
1493	<	void SimSetup::setupZConstraint(SimInfo& theInfo)
1620	<	{
1493	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1494		int nZConstraints;
1495		ZconStamp** zconStamp;
1496
1497	<	if(globals->haveZconstraintTime()){
1625	<
1497	>	if (globals->haveZconstraintTime()){
1498		//add sample time of z-constraint  into SimInfo's property list
1499		DoubleData* zconsTimeProp = new DoubleData();
1500		zconsTimeProp->setID(ZCONSTIME_ID);
#	Line 1630 | Line 1502 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1502		theInfo.addProperty(zconsTimeProp);
1503		}
1504		else{
1505	<	sprintf( painCave.errMsg,
1506	<	"ZConstraint error: If you use an ZConstraint\n"
1507	<	" , you must set sample time.\n");
1505	>	sprintf(painCave.errMsg,
1506	>	"ZConstraint error: If you use an ZConstraint\n"
1507	>	" , you must set sample time.\n");
1508		painCave.isFatal = 1;
1509	<	simError();
1509	>	simError();
1510		}
1511
1512		//push zconsTol into siminfo, if user does not specify
1513		//value for zconsTol, a default value will be used
1514		DoubleData* zconsTol = new DoubleData();
1515		zconsTol->setID(ZCONSTOL_ID);
1516	<	if(globals->haveZconsTol()){
1516	>	if (globals->haveZconsTol()){
1517		zconsTol->setData(globals->getZconsTol());
1518		}
1519		else{
1520	<	double defaultZConsTol = 0.01;
1521	<	sprintf( painCave.errMsg,
1522	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1523	<	" , default value %f is used.\n", defaultZConsTol);
1520	>	double defaultZConsTol = 0.01;
1521	>	sprintf(painCave.errMsg,
1522	>	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1523	>	" , default value %f is used.\n",
1524	>	defaultZConsTol);
1525		painCave.isFatal = 0;
1526		simError();
1527
#	Line 1656 | Line 1529 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1529		}
1530		theInfo.addProperty(zconsTol);
1531
1532	<	//set Force Substraction Policy
1533	<	StringData* zconsForcePolicy =  new StringData();
1532	>	//set Force Subtraction Policy
1533	>	StringData* zconsForcePolicy = new StringData();
1534		zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1535	<
1536	<	if(globals->haveZconsForcePolicy()){
1535	>
1536	>	if (globals->haveZconsForcePolicy()){
1537		zconsForcePolicy->setData(globals->getZconsForcePolicy());
1538	<	}
1538	>	}
1539		else{
1540	<	sprintf( painCave.errMsg,
1541	<	"ZConstraint Warning: User does not set force substraction policy, "
1542	<	"average force substraction policy is used\n");
1543	<	painCave.isFatal = 0;
1544	<	simError();
1545	<	zconsForcePolicy->setData("BYNUMBER");
1540	>	sprintf(painCave.errMsg,
1541	>	"ZConstraint Warning: User does not set force Subtraction policy, "
1542	>	"PolicyByMass is used\n");
1543	>	painCave.isFatal = 0;
1544	>	simError();
1545	>	zconsForcePolicy->setData("BYMASS");
1546		}
1547	<
1548	<	theInfo.addProperty(zconsForcePolicy);
1549	<
1547	>
1548	>	theInfo.addProperty(zconsForcePolicy);
1549	>
1550		//Determine the name of ouput file and add it into SimInfo's property list
1551		//Be careful, do not use inFileName, since it is a pointer which
1552		//point to a string at master node, and slave nodes do not contain that string
1553	<
1553	>
1554		string zconsOutput(theInfo.finalName);
1555	<
1555	>
1556		zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1557	<
1557	>
1558		StringData* zconsFilename = new StringData();
1559		zconsFilename->setID(ZCONSFILENAME_ID);
1560		zconsFilename->setData(zconsOutput);
1561	<
1561	>
1562		theInfo.addProperty(zconsFilename);
1563	<
1563	>
1564		//setup index, pos and other parameters of z-constraint molecules
1565		nZConstraints = globals->getNzConstraints();
1566		theInfo.nZconstraints = nZConstraints;
#	Line 1697 | Line 1570 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1570
1571		ZConsParaData* zconsParaData = new ZConsParaData();
1572		zconsParaData->setID(ZCONSPARADATA_ID);
1573	<
1574	<	for(int i = 0; i < nZConstraints; i++){
1573	>
1574	>	for (int i = 0; i < nZConstraints; i++){
1575		tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1576		tempParaItem.zPos = zconStamp[i]->getZpos();
1577		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
#	Line 1707 | Line 1580 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1580		zconsParaData->addItem(tempParaItem);
1581		}
1582
1583	+	//check the uniqueness of index
1584	+	if(!zconsParaData->isIndexUnique()){
1585	+	sprintf(painCave.errMsg,
1586	+	"ZConstraint Error: molIndex is not unique\n");
1587	+	painCave.isFatal = 1;
1588	+	simError();
1589	+	}
1590	+
1591		//sort the parameters by index of molecules
1592		zconsParaData->sortByIndex();
1593
1594		//push data into siminfo, therefore, we can retrieve later
1595		theInfo.addProperty(zconsParaData);
1715	–
1596		}

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