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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 660 by tim, Thu Jul 31 19:59:34 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"
10		#include "parse_me.h"
11		#include "Integrator.hpp"
12		#include "simError.h"
#	Line 20 | Line 22
22		#define NVT_ENS        1
23		#define NPTi_ENS       2
24		#define NPTf_ENS       3
23	–	#define NPTim_ENS      4
24	–	#define NPTfm_ENS      5
25	–	#define NVEZCONS_ENS   6
26	–	#define NVTZCONS_ENS   7
27	–	#define NPTiZCONS_ENS  8
28	–	#define NPTfZCONS_ENS  9
29	–	#define NPTimZCONS_ENS 10
30	–	#define NPTfmZCONS_ENS 11
25
26		#define FF_DUFF 0
27		#define FF_LJ   1
#	Line 36 | Line 30 | SimSetup::SimSetup(){
30		using namespace std;
31
32		SimSetup::SimSetup(){
39	–
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 55 | 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;
55	<	}
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 ){
66	<
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();
94	<	mpiEventLoop();
95	<
84	>	set_interface_stamps(stamps, globals);
85	>	mpiEventInit();
86	>	MPIcheckPoint();
87	>	mpiEventLoop();
88		}
89
90		#endif // is_mpi
91
92	<	void SimSetup::createSim( void ){
92	>	void SimSetup::createSim(void){
93
102	–	int i, j, k, globalAtomIndex;
103	–
94		// gather all of the information from the Bass file
95	<
95	>
96		gatherInfo();
97
98		// creation of complex system objects
#	Line 110 | Line 100 | void SimSetup::createSim( void ){
100		sysObjectsCreation();
101
102		// check on the post processing info
103	<
103	>
104		finalInfoCheck();
105
106		// initialize the system coordinates
107
108	<	initSystemCoords();
109	<
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 133 | Line 124 | void SimSetup::createSim( void ){
124		// initialize the Fortran
125
126		initFortran();
136	–
137	–
138	–
127		}
128
129
130	<	void SimSetup::makeMolecules( void ){
131	<
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 155 | 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;
167	–
168	–	atomOffset = 0;
169	–	excludeOffset = 0;
170	–	for(i=0; i<info->n_mol; i++){
171	–
172	–	stampID = the_molecules[i].getStampID();
155
156	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
157	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
176	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
177	<	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
178	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
156	>	for (k = 0; k < nInfo; k++){
157	>	the_ff->setSimInfo(&(info[k]));
158
159	<	molInfo.myAtoms = &the_atoms[atomOffset];
160	<	molInfo.myExcludes = &the_excludes[excludeOffset];
161	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
162	<	molInfo.myBends = new Bend*[molInfo.nBends];
184	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
159	>	atomOffset = 0;
160	>	excludeOffset = 0;
161	>	for (i = 0; i < info[k].n_mol; i++){
162	>	stampID = info[k].molecules[i].getStampID();
163
164	<	theBonds = new bond_pair[molInfo.nBonds];
165	<	theBends = new bend_set[molInfo.nBends];
166	<	theTorsions = new torsion_set[molInfo.nTorsions];
167	<
168	<	// make the Atoms
169	<
170	<	for(j=0; j<molInfo.nAtoms; j++){
171	<
172	<	currentAtom = comp_stamps[stampID]->getAtom( j );
173	<	if( currentAtom->haveOrientation() ){
174	<
175	<	dAtom = new DirectionalAtom(j + atomOffset);
176	<	info->n_oriented++;
177	<	molInfo.myAtoms[j] = dAtom;
178	<
179	<	ux = currentAtom->getOrntX();
180	<	uy = currentAtom->getOrntY();
181	<	uz = currentAtom->getOrntZ();
182	<
183	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
184	<
185	<	u = sqrt( uSqr );
186	<	ux = ux / u;
187	<	uy = uy / u;
188	<	uz = uz / u;
189	<
190	<	dAtom->setSUx( ux );
191	<	dAtom->setSUy( uy );
192	<	dAtom->setSUz( uz );
193	<	}
194	<	else{
195	<	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
196	<	}
197	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
198	<
199	<	#ifdef IS_MPI
200	<
201	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
202	<
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	>
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];
175	>
176	>	theBonds = new bond_pair[molInfo.nBonds];
177	>	theBends = new bend_set[molInfo.nBends];
178	>	theTorsions = new torsion_set[molInfo.nTorsions];
179	>
180	>	// make the Atoms
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	>
215		#endif // is_mpi
216	<	}
227	<
228	<	// make the bonds
229	<	for(j=0; j<molInfo.nBonds; j++){
230	<
231	<	currentBond = comp_stamps[stampID]->getBond( j );
232	<	theBonds[j].a = currentBond->getA() + atomOffset;
233	<	theBonds[j].b = currentBond->getB() + atomOffset;
216	>	}
217
218	<	exI = theBonds[j].a;
219	<	exJ = theBonds[j].b;
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	<	// exclude_I must always be the smaller of the pair
225	<	if( exI > exJ ){
226	<	tempEx = exI;
227	<	exI = exJ;
228	<	exJ = tempEx;
229	<	}
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 = the_atoms[tempEx]->getGlobalIndex() + 1;
236	<	tempEx = exJ;
237	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
238	<
239	<	the_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	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
242	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
243		#endif  //is_mpi
244	<	}
245	<	excludeOffset += molInfo.nBonds;
244	>	}
245	>	excludeOffset += molInfo.nBonds;
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();
285	<	}
286	<	}
287	<
288	<	else{
289	<
290	<	sprintf( painCave.errMsg,
291	<	"SimSetup Error: unhandled bend assignment:\n"
292	<	"    -->%s in Bend[%d] in %s\n",
293	<	current_extra->getlhs(),
294	<	j, comp_stamps[stampID]->getID() );
295	<	painCave.isFatal = 1;
296	<	simError();
297	<	}
298	<
299	<	current_extra = current_extra->getNext();
300	<	}
301	<	}
302	<
303	<	if( !theBends[j].isGhost ){
304	<
305	<	exI = theBends[j].a;
306	<	exJ = theBends[j].c;
307	<	}
308	<	else{
309	<
321	<	exI = theBends[j].a;
322	<	exJ = theBends[j].b;
323	<	}
324	<
325	<	// exclude_I must always be the smaller of the pair
326	<	if( exI > exJ ){
327	<	tempEx = exI;
328	<	exI = exJ;
329	<	exJ = tempEx;
330	<	}
247	>	//make the bends
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	>	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 = the_atoms[tempEx]->getGlobalIndex() + 1;
313	<	tempEx = exJ;
314	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
315	<
316	<	the_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	<	the_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;
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;
350	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
351	<
352	<	exI = theTorsions[j].a;
353	<	exJ = theTorsions[j].d;
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	<	// exclude_I must always be the smaller of the pair
331	<	if( exI > exJ ){
332	<	tempEx = exI;
333	<	exI = exJ;
334	<	exJ = tempEx;
335	<	}
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 = the_atoms[tempEx]->getGlobalIndex() + 1;
342	<	tempEx = exJ;
343	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
344	<
345	<	the_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	<	the_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;
349	>	}
350	>	excludeOffset += molInfo.nTorsions;
351
374	–
375	–	// send the arrays off to the forceField for init.
352
353	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
378	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
379	<	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
380	<	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
353	>	// send the arrays off to the forceField for init.
354
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
383	–	the_molecules[i].initialize( molInfo );
361
362	+	info[k].molecules[i].initialize(molInfo);
363
364	<	atomOffset += molInfo.nAtoms;
365	<	delete[] theBonds;
366	<	delete[] theBends;
367	<	delete[] theTorsions;
364	>
365	>	atomOffset += molInfo.nAtoms;
366	>	delete[] theBonds;
367	>	delete[] theBends;
368	>	delete[] theTorsions;
369	>	}
370		}
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
377		// clean up the forcefield
378	+
379		the_ff->calcRcut();
380		the_ff->cleanMe();
400	–
381		}
382
383	<	void SimSetup::initFromBass( void ){
404	<
383	>	void SimSetup::initFromBass(void){
384		int i, j, k;
385		int n_cells;
386		double cellx, celly, cellz;
#	Line 410 | Line 389 | void SimSetup::initFromBass( void ){
389		int n_extra;
390		int have_extra, done;
391
392	<	temp1 = (double)tot_nmol / 4.0;
393	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
394	<	temp3 = ceil( temp2 );
392	>	double vel[3];
393	>	vel[0] = 0.0;
394	>	vel[1] = 0.0;
395	>	vel[2] = 0.0;
396
397	<	have_extra =0;
398	<	if( temp2 < temp3 ){ // we have a non-complete lattice
399	<	have_extra =1;
397	>	temp1 = (double) tot_nmol / 4.0;
398	>	temp2 = pow(temp1, (1.0 / 3.0));
399	>	temp3 = ceil(temp2);
400
401	<	n_cells = (int)temp3 - 1;
402	<	cellx = info->boxL[0] / temp3;
403	<	celly = info->boxL[1] / temp3;
404	<	cellz = info->boxL[2] / temp3;
425	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
426	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
427	<	n_per_extra = (int)ceil( temp1 );
401	>	have_extra = 0;
402	>	if (temp2 < temp3){
403	>	// we have a non-complete lattice
404	>	have_extra = 1;
405
406	<	if( n_per_extra > 4){
407	<	sprintf( painCave.errMsg,
408	<	"SimSetup error. There has been an error in constructing"
409	<	" the non-complete lattice.\n" );
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);
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");
418		painCave.isFatal = 1;
419		simError();
420		}
421		}
422		else{
423	<	n_cells = (int)temp3;
424	<	cellx = info->boxL[0] / temp3;
425	<	celly = info->boxL[1] / temp3;
426	<	cellz = info->boxL[2] / 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;
427		}
428
429		current_mol = 0;
#	Line 446 | 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,
454	<	j * celly,
455	<	k * cellz );
439	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
440
441	<	makeElement( i * cellx + 0.5 * cellx,
458	<	j * celly + 0.5 * celly,
459	<	k * cellz );
441	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
442
443	<	makeElement( i * cellx,
462	<	j * celly + 0.5 * celly,
463	<	k * cellz + 0.5 * cellz );
464	<
465	<	makeElement( i * cellx + 0.5 * cellx,
466	<	j * celly,
467	<	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	<	}
486	<	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++ ){
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	<	makeElement( i * cellx,
481	<	j * celly,
482	<	k * cellz );
483	<	done = ( current_mol >= tot_nmol );
484	<
485	<	if( !done && n_per_extra > 1 ){
496	<	makeElement( i * cellx + 0.5 * cellx,
497	<	j * celly + 0.5 * celly,
498	<	k * cellz );
499	<	done = ( current_mol >= tot_nmol );
500	<	}
501	<
502	<	if( !done && n_per_extra > 2){
503	<	makeElement( i * cellx,
504	<	j * celly + 0.5 * celly,
505	<	k * cellz + 0.5 * cellz );
506	<	done = ( current_mol >= tot_nmol );
507	<	}
508	<
509	<	if( !done && n_per_extra > 3){
510	<	makeElement( i * cellx + 0.5 * cellx,
511	<	j * celly,
512	<	k * cellz + 0.5 * cellz );
513	<	done = ( current_mol >= tot_nmol );
514	<	}
515	<	}
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	<
491	<	for( i=0; i<info->n_atoms; i++ ){
522	<	info->atoms[i]->set_vx( 0.0 );
523	<	info->atoms[i]->set_vy( 0.0 );
524	<	info->atoms[i]->set_vz( 0.0 );
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 ){
529	<
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",
544	<	comp_stamps[current_comp]->getID(),
545	<	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
515	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
516	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
517	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
515	>	pos[0] = x + current_atom->getPosX();
516	>	pos[1] = y + current_atom->getPosY();
517	>	pos[2] = z + current_atom->getPosZ();
518
519	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
519	>	info[0].atoms[current_atom_ndx]->setPos(pos);
520
521	<	dAtom = (DirectionalAtom *)the_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 567 | 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 576 | 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] ){
580	<
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
593	–	// get the stamps and globals;
594	–	stamps = stamps;
595	–	globals = globals;
596	–
558		// set the easy ones first
559	<	info->target_temp = globals->getTargetTemp();
560	<	info->dt = globals->getDt();
561	<	info->run_time = globals->getRunTime();
559	>
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();
564	>	}
565		n_components = globals->getNComponents();
566
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;
616	<	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;
603	<
631	<	else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS;
632	<	else if( !strcasecmp( ensemble, "NVTZCONS"))  ensembleCase = NVTZCONS_ENS;
633	<	else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPT"))
634	<	ensembleCase = NPTiZCONS_ENS;
635	<	else if( !strcasecmp( ensemble, "NPTfCONS"))  ensembleCase = NPTfZCONS_ENS;
636	<	else if( !strcasecmp( ensemble, "NPTimZCONS"))  ensembleCase = NPTimZCONS_ENS;
637	<	else if( !strcasecmp( ensemble, "NPTfmCONS"))  ensembleCase = NPTfmZCONS_ENS;
638	<
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		}
649	–	strcpy( info->ensemble, ensemble );
614
615	<	// get the mixing rule
615	>	for (i = 0; i < nInfo; i++){
616	>	strcpy(info[i].ensemble, ensemble);
617
618	<	strcpy( info->mixingRule, globals->getMixingRule() );
619	<	info->usePBC = globals->getPBC();
620	<
621	<
618	>	// get the mixing rule
619	>
620	>	strcpy(info[i].mixingRule, globals->getMixingRule());
621	>	info[i].usePBC = globals->getPBC();
622	>	}
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;
676	<	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 681 | 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
661	<
662	<	if( globals->haveSampleTime() ){
663	<	info->sampleTime = globals->getSampleTime();
664	<	info->statusTime = info->sampleTime;
665	<	info->thermalTime = info->sampleTime;
666	<	}
667	<	else{
668	<	info->sampleTime = globals->getRunTime();
669	<	info->statusTime = info->sampleTime;
670	<	info->thermalTime = info->sampleTime;
671	<	}
661	>
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;
667	>	}
668	>	else{
669	>	info[i].sampleTime = globals->getRunTime();
670	>	info[i].statusTime = info[i].sampleTime;
671	>	info[i].thermalTime = info[i].sampleTime;
672	>	}
673
674	<	if( globals->haveStatusTime() ){
675	<	info->statusTime = globals->getStatusTime();
676	<	}
674	>	if (globals->haveStatusTime()){
675	>	info[i].statusTime = globals->getStatusTime();
676	>	}
677
678	<	if( globals->haveThermalTime() ){
679	<	info->thermalTime = globals->getThermalTime();
680	<	}
678	>	if (globals->haveThermalTime()){
679	>	info[i].thermalTime = globals->getThermalTime();
680	>	}
681
682	<	// check for the temperature set flag
682	>	info[i].resetIntegrator = 0;
683	>	if( globals->haveResetTime() ){
684	>	info[i].resetTime = globals->getResetTime();
685	>	info[i].resetIntegrator = 1;
686	>	}
687
688	<	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
688	>	// check for the temperature set flag
689
690	<	// get some of the tricky things that may still be in the globals
690	>	if (globals->haveTempSet())
691	>	info[i].setTemp = globals->getTempSet();
692
693	<	double boxVector[3];
722	<	if( globals->haveBox() ){
723	<	boxVector[0] = globals->getBox();
724	<	boxVector[1] = globals->getBox();
725	<	boxVector[2] = globals->getBox();
726	<
727	<	info->setBox( boxVector );
728	<	}
729	<	else if( globals->haveDensity() ){
693	>	// get some of the tricky things that may still be in the globals
694
695	<	double vol;
696	<	vol = (double)tot_nmol / globals->getDensity();
697	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
698	<	boxVector[1] = boxVector[0];
699	<	boxVector[2] = boxVector[0];
695	>	double boxVector[3];
696	>	if (globals->haveBox()){
697	>	boxVector[0] = globals->getBox();
698	>	boxVector[1] = globals->getBox();
699	>	boxVector[2] = globals->getBox();
700
701	<	info->setBox( boxVector );
738	<	}
739	<	else{
740	<	if( !globals->haveBoxX() ){
741	<	sprintf( painCave.errMsg,
742	<	"SimSetup error, no periodic BoxX size given.\n" );
743	<	painCave.isFatal = 1;
744	<	simError();
701	>	info[i].setBox(boxVector);
702		}
703	<	boxVector[0] = globals->getBoxX();
703	>	else if (globals->haveDensity()){
704	>	double vol;
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	<	if( !globals->haveBoxY() ){
749	<	sprintf( painCave.errMsg,
750	<	"SimSetup error, no periodic BoxY size given.\n" );
751	<	painCave.isFatal = 1;
752	<	simError();
710	>	info[i].setBox(boxVector);
711		}
712	<	boxVector[1] = globals->getBoxY();
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();
718	>	}
719	>	boxVector[0] = globals->getBoxX();
720
721	<	if( !globals->haveBoxZ() ){
722	<	sprintf( painCave.errMsg,
723	<	"SimSetup error, no periodic BoxZ size given.\n" );
724	<	painCave.isFatal = 1;
725	<	simError();
726	<	}
727	<	boxVector[2] = globals->getBoxZ();
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	<	info->setBox( boxVector );
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();
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
773	–
785		}
786
787
788	<	void SimSetup::finalInfoCheck( void ){
788	>	void SimSetup::finalInfoCheck(void){
789		int index;
790		int usesDipoles;
791	<
791	>	int i;
792
793	<	// check electrostatic parameters
794	<
795	<	index = 0;
796	<	usesDipoles = 0;
797	<	while( (index < info->n_atoms) && !usesDipoles ){
798	<	usesDipoles = ((info->atoms)[index])->hasDipole();
799	<	index++;
800	<	}
801	<
793	>	for (i = 0; i < nInfo; i++){
794	>	// check electrostatic parameters
795	>
796	>	index = 0;
797	>	usesDipoles = 0;
798	>	while ((index < info[i].n_atoms) && !usesDipoles){
799	>	usesDipoles = (info[i].atoms[index])->hasDipole();
800	>	index++;
801	>	}
802	>
803		#ifdef IS_MPI
804	<	int myUse = usesDipoles;
805	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
804	>	int myUse = usesDipoles;
805	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
806		#endif //is_mpi
807
808	<	double theEcr, theEst;
808	>	double theEcr, theEst;
809
810	<	if (globals->getUseRF() ) {
811	<	info->useReactionField = 1;
800	<
801	<	if( !globals->haveECR() ){
802	<	sprintf( painCave.errMsg,
803	<	"SimSetup Warning: using default value of 1/2 the smallest "
804	<	"box length for the electrostaticCutoffRadius.\n"
805	<	"I hope you have a very fast processor!\n");
806	<	painCave.isFatal = 0;
807	<	simError();
808	<	double smallest;
809	<	smallest = info->boxL[0];
810	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
811	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
812	<	theEcr = 0.5 * smallest;
813	<	} else {
814	<	theEcr = globals->getECR();
815	<	}
810	>	if (globals->getUseRF()){
811	>	info[i].useReactionField = 1;
812
813	<	if( !globals->haveEST() ){
814	<	sprintf( painCave.errMsg,
815	<	"SimSetup Warning: using default value of 0.05 * the "
816	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
817	<	);
818	<	painCave.isFatal = 0;
819	<	simError();
820	<	theEst = 0.05 * theEcr;
821	<	} else {
822	<	theEst= globals->getEST();
823	<	}
824	<
825	<	info->setEcr( theEcr, theEst );
826	<
831	<	if(!globals->haveDielectric() ){
832	<	sprintf( painCave.errMsg,
833	<	"SimSetup Error: You are trying to use Reaction Field without"
834	<	"setting a dielectric constant!\n"
835	<	);
836	<	painCave.isFatal = 1;
837	<	simError();
838	<	}
839	<	info->dielectric = globals->getDielectric();
840	<	}
841	<	else {
842	<	if (usesDipoles) {
843	<
844	<	if( !globals->haveECR() ){
845	<	sprintf( painCave.errMsg,
846	<	"SimSetup Warning: using default value of 1/2 the smallest "
847	<	"box length for the electrostaticCutoffRadius.\n"
848	<	"I hope you have a very fast processor!\n");
849	<	painCave.isFatal = 0;
850	<	simError();
851	<	double smallest;
852	<	smallest = info->boxL[0];
853	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
854	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
855	<	theEcr = 0.5 * smallest;
856	<	} else {
857	<	theEcr = globals->getECR();
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() ){
861	<	sprintf( painCave.errMsg,
862	<	"SimSetup Warning: using default value of 0.05 * the "
863	<	"electrostaticCutoffRadius for the "
864	<	"electrostaticSkinThickness\n"
865	<	);
866	<	painCave.isFatal = 0;
867	<	simError();
868	<	theEst = 0.05 * theEcr;
869	<	} else {
870	<	theEst= globals->getEST();
828	>	else{
829	>	theEcr = globals->getECR();
830		}
831
832	<	info->setEcr( theEcr, theEst );
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	>	else{
841	>	theEst = globals->getEST();
842	>	}
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	<	}
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
881	–
898		}
899
900	<	void SimSetup::initSystemCoords( void ){
900	>	void SimSetup::initSystemCoords(void){
901	>	int i;
902
903	<	if( globals->haveInitialConfig() ){
904	<
905	<	InitializeFromFile* fileInit;
903	>	char* inName;
904	>
905	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
906	>
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	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
915	>	inName = globals->getInitialConfig();
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
922	>	fileInit->readInit(info); // default velocities on
923
924	<	delete fileInit;
925	<	}
926	<	else{
901	<
924	>	delete fileInit;
925	>	}
926	>	else{
927		#ifdef IS_MPI
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;
934	<	simError();
935	<
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 = 1;;
934	>	simError();
935	>
936		#else
937
938	<	initFromBass();
938	>	initFromBass();
939
940
941		#endif
942	<	}
942	>	}
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
923	–
948		}
949
950
951	<	void SimSetup::makeOutNames( void ){
951	>	void SimSetup::makeOutNames(void){
952	>	int k;
953
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->finalName, globals->getFinalConfig() );
935	<	}
936	<	else{
937	<	strcpy( info->finalName, inFileName );
938	<	char* endTest;
939	<	int nameLength = strlen( info->finalName );
940	<	endTest = &(info->finalName[nameLength - 5]);
941	<	if( !strcmp( endTest, ".bass" ) ){
942	<	strcpy( endTest, ".eor" );
959	>
960	>	if (globals->haveFinalConfig()){
961	>	strcpy(info[k].finalName, globals->getFinalConfig());
962		}
944	–	else if( !strcmp( endTest, ".BASS" ) ){
945	–	strcpy( endTest, ".eor" );
946	–	}
963		else{
964	<	endTest = &(info->finalName[nameLength - 4]);
965	<	if( !strcmp( endTest, ".bss" ) ){
966	<	strcpy( endTest, ".eor" );
967	<	}
968	<	else if( !strcmp( endTest, ".mdl" ) ){
969	<	strcpy( endTest, ".eor" );
970	<	}
971	<	else{
972	<	strcat( info->finalName, ".eor" );
973	<	}
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	<	}
988	<
989	<	// make the sample and status out names
990	<
991	<	strcpy( info->sampleName, inFileName );
992	<	char* endTest;
993	<	int nameLength = strlen( info->sampleName );
994	<	endTest = &(info->sampleName[nameLength - 5]);
995	<	if( !strcmp( endTest, ".bass" ) ){
968	<	strcpy( endTest, ".dump" );
969	<	}
970	<	else if( !strcmp( endTest, ".BASS" ) ){
971	<	strcpy( endTest, ".dump" );
972	<	}
973	<	else{
974	<	endTest = &(info->sampleName[nameLength - 4]);
975	<	if( !strcmp( endTest, ".bss" ) ){
976	<	strcpy( endTest, ".dump" );
987	>
988	>	// make the sample and status out names
989	>
990	>	strcpy(info[k].sampleName, inFileName);
991	>	char* endTest;
992	>	int nameLength = strlen(info[k].sampleName);
993	>	endTest = &(info[k].sampleName[nameLength - 5]);
994	>	if (!strcmp(endTest, ".bass")){
995	>	strcpy(endTest, ".dump");
996		}
997	<	else if( !strcmp( endTest, ".mdl" ) ){
998	<	strcpy( endTest, ".dump" );
997	>	else if (!strcmp(endTest, ".BASS")){
998	>	strcpy(endTest, ".dump");
999		}
1000		else{
1001	<	strcat( info->sampleName, ".dump" );
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	<
1014	<	strcpy( info->statusName, inFileName );
1015	<	nameLength = strlen( info->statusName );
1016	<	endTest = &(info->statusName[nameLength - 5]);
1017	<	if( !strcmp( endTest, ".bass" ) ){
990	<	strcpy( endTest, ".stat" );
991	<	}
992	<	else if( !strcmp( endTest, ".BASS" ) ){
993	<	strcpy( endTest, ".stat" );
994	<	}
995	<	else{
996	<	endTest = &(info->statusName[nameLength - 4]);
997	<	if( !strcmp( endTest, ".bss" ) ){
998	<	strcpy( endTest, ".stat" );
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");
1018		}
1019	<	else if( !strcmp( endTest, ".mdl" ) ){
1020	<	strcpy( endTest, ".stat" );
1019	>	else if (!strcmp(endTest, ".BASS")){
1020	>	strcpy(endTest, ".stat");
1021		}
1022		else{
1023	<	strcat( info->statusName, ".stat" );
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	<	}
1007	<
1034	>
1035		#ifdef IS_MPI
1009	–	}
1010	–	#endif // is_mpi
1036
1037	+	}
1038	+	#endif // is_mpi
1039	+	}
1040		}
1041
1042
1043	<	void SimSetup::sysObjectsCreation( void ){
1043	>	void SimSetup::sysObjectsCreation(void){
1044	>	int i, k;
1045
1017	–	int i;
1018	–
1046		// create the forceField
1047
1048		createFF();
#	Line 1030 | 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();
1044	–	info->identArray = new int[info->n_atoms];
1045	–	for(i=0; i<info->n_atoms; i++){
1046	–	info->identArray[i] = the_atoms[i]->getIdent();
1047	–	}
1048	–
1071
1072	<
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++){
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:
1067	<	the_ff = new EAM_FF();
1068	<	break;
1069	<
1070	<	default:
1071	<	sprintf( painCave.errMsg,
1072	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1073	<	painCave.isFatal = 1;
1074	<	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
1081	–
1106		}
1107
1108
1109	<	void SimSetup::compList( void ){
1086	<
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
1089	–	comp_stamps = new MoleculeStamp*[n_components];
1090	–
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	<	info->nComponents = n_components;
1120	<	info->componentsNmol = components_nmol;
1121	<	info->compStamps = comp_stamps;
1122	<	info->headStamp = new LinkedMolStamp();
1123	<
1124	<	char* id;
1100	<	LinkedMolStamp* headStamp = info->headStamp;
1101	<	LinkedMolStamp* currentStamp = NULL;
1102	<	for( i=0; i<n_components; i++ ){
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	>	}
1125
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 ){
1111	<
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
1133	–
1134	–
1156		}
1157
1158	<	void SimSetup::calcSysValues( void ){
1159	<	int i, j, k;
1158	>	void SimSetup::calcSysValues(void){
1159	>	int i;
1160
1161	+	int* molMembershipArray;
1162
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();
1149	<	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
1174		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1175	+	molMembershipArray = new int[tot_atoms];
1176
1177	<	info->n_atoms = tot_atoms;
1178	<	info->n_bonds = tot_bonds;
1179	<	info->n_bends = tot_bends;
1180	<	info->n_torsions = tot_torsions;
1181	<	info->n_SRI = tot_SRI;
1182	<	info->n_mol = tot_nmol;
1183	<
1184	<	info->molMembershipArray = new int[tot_atoms];
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	>
1185	>	info[i].molMembershipArray = molMembershipArray;
1186	>	}
1187		}
1188
1165	–
1189		#ifdef IS_MPI
1190
1191	<	void SimSetup::mpiMolDivide( void ){
1169	<
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 1189 | 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();
1200	<	local_bends +=    comp_stamps[i]->getNBends();
1201	<	local_torsions += comp_stamps[i]->getNTorsions();
1202	<	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++) {
1224	<	info->molMembershipArray[globalAtomIndex] = allMol;
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	<
1233	<	info->n_atoms = mpiSim->getMyNlocal();
1234	<
1235	<	if( local_atoms != info->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->n_atoms,
1221	<	local_atoms );
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, local_atoms);
1240		painCave.isFatal = 1;
1241		simError();
1242		}
1243
1244	<	info->n_bonds = local_bonds;
1245	<	info->n_bends = local_bends;
1246	<	info->n_torsions = local_torsions;
1247	<	info->n_SRI = local_SRI;
1248	<	info->n_mol = localMol;
1244	>	info[0].n_bonds = local_bonds;
1245	>	info[0].n_bends = local_bends;
1246	>	info[0].n_torsions = local_torsions;
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;
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
1243	–	// create the atom and short range interaction arrays
1268
1269	<	Atom::createArrays(info->n_atoms);
1270	<	the_atoms = new Atom*[info->n_atoms];
1247	<	the_molecules = new Molecule[info->n_mol];
1248	<	int molIndex;
1269	>	for (l = 0; l < nInfo; l++){
1270	>	// create the atom and short range interaction arrays
1271
1272	<	// initialize the molecule's stampID's
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	+
1278		#ifdef IS_MPI
1253	–
1279
1280	<	molIndex = 0;
1281	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1282	<
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++;
1280	>
1281	>	molIndex = 0;
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		}
1264	–	}
1290
1291		#else // is_mpi
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->molMembershipArray[globalAtomIndex] = molIndex;
1302	<	globalAtomIndex++;
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++;
1305		}
1279	–	molIndex++;
1306		}
1281	–	}
1282	–
1307
1308	+
1309		#endif // is_mpi
1310
1311
1312	<	if( info->n_SRI ){
1313	<
1314	<	Exclude::createArray(info->n_SRI);
1315	<	the_excludes = new Exclude*[info->n_SRI];
1316	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1317	<	info->globalExcludes = new int;
1318	<	info->n_exclude = info->n_SRI;
1319	<	}
1320	<	else{
1321	<
1322	<	Exclude::createArray( 1 );
1323	<	the_excludes = new Exclude*;
1324	<	the_excludes[0] = new Exclude(0);
1325	<	the_excludes[0]->setPair( 0,0 );
1326	<	info->globalExcludes = new int;
1327	<	info->globalExcludes[0] = 0;
1328	<	info->n_exclude = 0;
1329	<	}
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);
1317	>	}
1318	>	info[l].globalExcludes = new int;
1319	>	info[l].n_exclude = info[l].n_SRI;
1320	>	}
1321	>	else{
1322	>	Exclude::createArray(1);
1323	>	the_excludes = new Exclude * ;
1324	>	the_excludes[0] = new Exclude(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;
1329	>	}
1330
1331	<	// set the arrays into the SimInfo object
1331	>	// set the arrays into the SimInfo object
1332
1333	<	info->atoms = the_atoms;
1334	<	info->molecules = the_molecules;
1335	<	info->nGlobalExcludes = 0;
1336	<	info->excludes = the_excludes;
1333	>	info[l].atoms = the_atoms;
1334	>	info[l].molecules = the_molecules;
1335	>	info[l].nGlobalExcludes = 0;
1336	>	info[l].excludes = the_excludes;
1337
1338	<	the_ff->setSimInfo( info );
1339	<
1338	>	the_ff->setSimInfo(info);
1339	>	}
1340		}
1341
1342	<	void SimSetup::makeIntegrator( void ){
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;
1323	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1324	<	ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1325	<	ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL;
1326	<	ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL;
1327	<	ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL;
1328	<	ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL;
1329	<	ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL;
1330	<
1331	<	cerr << "setting integrator" <<endl;
1345	>	NVE<RealIntegrator>* myNVE = NULL;
1346	>	NVT<RealIntegrator>* myNVT = NULL;
1347	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1348	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1349
1350	<	switch( ensembleCase ){
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	<	case NVE_ENS:
1365	<	new NVE<RealIntegrator>( info, the_ff );
1366	<	break;
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	<	case NVT_ENS:
1340	<	myNVT = new NVT<RealIntegrator>( info, the_ff );
1341	<	myNVT->setTargetTemp(globals->getTargetTemp());
1372	>	myNVT->setTargetTemp(globals->getTargetTemp());
1373
1374	<	if (globals->haveTauThermostat())
1375	<	myNVT->setTauThermostat(globals->getTauThermostat());
1374	>	if (globals->haveTauThermostat())
1375	>	myNVT->setTauThermostat(globals->getTauThermostat());
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	<	else {
1385	<	sprintf( painCave.errMsg,
1348	<	"SimSetup error: If you use the NVT\n"
1349	<	"    ensemble, you must set tauThermostat.\n");
1350	<	painCave.isFatal = 1;
1351	<	simError();
1352	<	}
1353	<	break;
1384	>	info->the_integrator = myNVT;
1385	>	break;
1386
1387	<	case NPTi_ENS:
1388	<	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1389	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
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	<	if (globals->haveTargetPressure())
1360	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1361	<	else {
1362	<	sprintf( painCave.errMsg,
1363	<	"SimSetup error: If you use a constant pressure\n"
1364	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1365	<	painCave.isFatal = 1;
1366	<	simError();
1367	<	}
1368	<
1369	<	if( globals->haveTauThermostat() )
1370	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1371	<	else{
1372	<	sprintf( painCave.errMsg,
1373	<	"SimSetup error: If you use an NPT\n"
1374	<	"    ensemble, you must set tauThermostat.\n");
1375	<	painCave.isFatal = 1;
1376	<	simError();
1377	<	}
1395	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1396
1397	<	if( globals->haveTauBarostat() )
1398	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1399	<	else{
1400	<	sprintf( painCave.errMsg,
1401	<	"SimSetup error: If you use an NPT\n"
1402	<	"    ensemble, you must set tauBarostat.\n");
1403	<	painCave.isFatal = 1;
1404	<	simError();
1405	<	}
1388	<	break;
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	>	}
1406
1407	<	case NPTf_ENS:
1408	<	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1409	<	myNPTf->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	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1419	<	else {
1420	<	sprintf( painCave.errMsg,
1421	<	"SimSetup error: If you use a constant pressure\n"
1422	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1423	<	painCave.isFatal = 1;
1424	<	simError();
1425	<	}
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	<	if( globals->haveTauThermostat() )
1428	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1406	<	else{
1407	<	sprintf( painCave.errMsg,
1408	<	"SimSetup error: If you use an NPT\n"
1409	<	"    ensemble, you must set tauThermostat.\n");
1410	<	painCave.isFatal = 1;
1411	<	simError();
1412	<	}
1427	>	info->the_integrator = myNPTi;
1428	>	break;
1429
1430	<	if( globals->haveTauBarostat() )
1431	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1432	<	else{
1433	<	sprintf( painCave.errMsg,
1434	<	"SimSetup error: If you use an NPT\n"
1435	<	"    ensemble, you must set tauBarostat.\n");
1436	<	painCave.isFatal = 1;
1421	<	simError();
1422	<	}
1423	<	break;
1424	<
1425	<	case NPTim_ENS:
1426	<	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1427	<	myNPTim->setTargetTemp( globals->getTargetTemp());
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	<	if (globals->haveTargetPressure())
1430	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1431	<	else {
1432	<	sprintf( painCave.errMsg,
1433	<	"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	<	myNPTim->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	<	}
1438	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1439
1440	<	if( globals->haveTauBarostat() )
1441	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1442	<	else{
1443	<	sprintf( painCave.errMsg,
1444	<	"SimSetup error: If you use an NPT\n"
1445	<	"    ensemble, you must set tauBarostat.\n");
1446	<	painCave.isFatal = 1;
1447	<	simError();
1448	<	}
1458	<	break;
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	>	}
1449
1450	<	case NPTfm_ENS:
1451	<	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1452	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
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	>	}
1459
1460	<	if (globals->haveTargetPressure())
1461	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1462	<	else {
1463	<	sprintf( painCave.errMsg,
1464	<	"SimSetup error: If you use a constant pressure\n"
1465	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1466	<	painCave.isFatal = 1;
1467	<	simError();
1468	<	}
1473	<
1474	<	if( globals->haveTauThermostat() )
1475	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1476	<	else{
1477	<	sprintf( painCave.errMsg,
1478	<	"SimSetup error: If you use an NPT\n"
1479	<	"    ensemble, you must set tauThermostat.\n");
1480	<	painCave.isFatal = 1;
1481	<	simError();
1482	<	}
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	<	if( globals->haveTauBarostat() )
1471	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1486	<	else{
1487	<	sprintf( painCave.errMsg,
1488	<	"SimSetup error: If you use an NPT\n"
1489	<	"    ensemble, you must set tauBarostat.\n");
1490	<	painCave.isFatal = 1;
1491	<	simError();
1492	<	}
1493	<	break;
1494	<
1495	<	case NVEZCONS_ENS:
1470	>	info->the_integrator = myNPTf;
1471	>	break;
1472
1473	<
1474	<	//setup index of z-constraint molecules, z-constraint sampel time
1475	<	//and z-constraint force output name. These parameter should be known
1476	<	//before constructing the z-constraint integrator
1477	<	setupZConstraint();
1502	<
1503	<	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff );
1504	<
1505	<	break;
1506	<
1507	<
1508	<	case NVTZCONS_ENS:
1509	<
1510	<	setupZConstraint();
1511	<
1512	<	myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( info, the_ff );
1513	<	myNVTZCons->setTargetTemp(globals->getTargetTemp());
1514	<
1515	<	if (globals->haveTauThermostat())
1516	<	myNVTZCons->setTauThermostat(globals->getTauThermostat());
1517	<
1518	<	else {
1519	<	sprintf( painCave.errMsg,
1520	<	"SimSetup error: If you use the NVT\n"
1521	<	"    ensemble, you must set tauThermostat.\n");
1522	<	painCave.isFatal = 1;
1523	<	simError();
1524	<	}
1525	<	break;
1526	<
1527	<	case NPTiZCONS_ENS:
1528	<
1529	<	setupZConstraint();
1530	<
1531	<	myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( info, the_ff );
1532	<	myNPTiZCons->setTargetTemp( globals->getTargetTemp() );
1533	<
1534	<	if (globals->haveTargetPressure())
1535	<	myNPTiZCons->setTargetPressure(globals->getTargetPressure());
1536	<	else {
1537	<	sprintf( painCave.errMsg,
1538	<	"SimSetup error: If you use a constant pressure\n"
1539	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1540	<	painCave.isFatal = 1;
1541	<	simError();
1542	<	}
1543	<
1544	<	if( globals->haveTauThermostat() )
1545	<	myNPTiZCons->setTauThermostat( globals->getTauThermostat() );
1546	<	else{
1547	<	sprintf( painCave.errMsg,
1548	<	"SimSetup error: If you use an NPT\n"
1549	<	"    ensemble, you must set tauThermostat.\n");
1550	<	painCave.isFatal = 1;
1551	<	simError();
1473	>	default:
1474	>	sprintf(painCave.errMsg,
1475	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1476	>	painCave.isFatal = 1;
1477	>	simError();
1478		}
1553	–
1554	–	if( globals->haveTauBarostat() )
1555	–	myNPTiZCons->setTauBarostat( globals->getTauBarostat() );
1556	–	else{
1557	–	sprintf( painCave.errMsg,
1558	–	"SimSetup error: If you use an NPT\n"
1559	–	"    ensemble, you must set tauBarostat.\n");
1560	–	painCave.isFatal = 1;
1561	–	simError();
1562	–	}
1563	–
1564	–	break;
1565	–
1566	–	case NPTfZCONS_ENS:
1567	–
1568	–	setupZConstraint();
1569	–
1570	–	myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( info, the_ff );
1571	–	myNPTfZCons->setTargetTemp( globals->getTargetTemp());
1572	–
1573	–	if (globals->haveTargetPressure())
1574	–	myNPTfZCons->setTargetPressure(globals->getTargetPressure());
1575	–	else {
1576	–	sprintf( painCave.errMsg,
1577	–	"SimSetup error: If you use a constant pressure\n"
1578	–	"    ensemble, you must set targetPressure in the BASS file.\n");
1579	–	painCave.isFatal = 1;
1580	–	simError();
1581	–	}
1582	–
1583	–	if( globals->haveTauThermostat() )
1584	–	myNPTfZCons->setTauThermostat( globals->getTauThermostat() );
1585	–	else{
1586	–	sprintf( painCave.errMsg,
1587	–	"SimSetup error: If you use an NPT\n"
1588	–	"    ensemble, you must set tauThermostat.\n");
1589	–	painCave.isFatal = 1;
1590	–	simError();
1591	–	}
1592	–
1593	–	if( globals->haveTauBarostat() )
1594	–	myNPTfZCons->setTauBarostat( globals->getTauBarostat() );
1595	–	else{
1596	–	sprintf( painCave.errMsg,
1597	–	"SimSetup error: If you use an NPT\n"
1598	–	"    ensemble, you must set tauBarostat.\n");
1599	–	painCave.isFatal = 1;
1600	–	simError();
1601	–	}
1602	–
1603	–	break;
1604	–
1605	–	case NPTimZCONS_ENS:
1606	–
1607	–	setupZConstraint();
1608	–
1609	–	myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( info, the_ff );
1610	–	myNPTimZCons->setTargetTemp( globals->getTargetTemp());
1611	–
1612	–	if (globals->haveTargetPressure())
1613	–	myNPTimZCons->setTargetPressure(globals->getTargetPressure());
1614	–	else {
1615	–	sprintf( painCave.errMsg,
1616	–	"SimSetup error: If you use a constant pressure\n"
1617	–	"    ensemble, you must set targetPressure in the BASS file.\n");
1618	–	painCave.isFatal = 1;
1619	–	simError();
1620	–	}
1621	–
1622	–	if( globals->haveTauThermostat() )
1623	–	myNPTimZCons->setTauThermostat( globals->getTauThermostat() );
1624	–	else{
1625	–	sprintf( painCave.errMsg,
1626	–	"SimSetup error: If you use an NPT\n"
1627	–	"    ensemble, you must set tauThermostat.\n");
1628	–	painCave.isFatal = 1;
1629	–	simError();
1630	–	}
1631	–
1632	–	if( globals->haveTauBarostat() )
1633	–	myNPTimZCons->setTauBarostat( globals->getTauBarostat() );
1634	–	else{
1635	–	sprintf( painCave.errMsg,
1636	–	"SimSetup error: If you use an NPT\n"
1637	–	"    ensemble, you must set tauBarostat.\n");
1638	–	painCave.isFatal = 1;
1639	–	simError();
1640	–	}
1641	–
1642	–	break;
1643	–
1644	–	case NPTfmZCONS_ENS:
1645	–
1646	–	setupZConstraint();
1647	–
1648	–	myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( info, the_ff );
1649	–	myNPTfmZCons->setTargetTemp( globals->getTargetTemp());
1650	–
1651	–	if (globals->haveTargetPressure())
1652	–	myNPTfmZCons->setTargetPressure(globals->getTargetPressure());
1653	–	else {
1654	–	sprintf( painCave.errMsg,
1655	–	"SimSetup error: If you use a constant pressure\n"
1656	–	"    ensemble, you must set targetPressure in the BASS file.\n");
1657	–	painCave.isFatal = 1;
1658	–	simError();
1659	–	}
1660	–
1661	–	if( globals->haveTauThermostat() )
1662	–	myNPTfmZCons->setTauThermostat( globals->getTauThermostat() );
1663	–	else{
1664	–	sprintf( painCave.errMsg,
1665	–	"SimSetup error: If you use an NPT\n"
1666	–	"    ensemble, you must set tauThermostat.\n");
1667	–	painCave.isFatal = 1;
1668	–	simError();
1669	–	}
1670	–
1671	–	if( globals->haveTauBarostat() )
1672	–	myNPTfmZCons->setTauBarostat( globals->getTauBarostat() );
1673	–	else{
1674	–	sprintf( painCave.errMsg,
1675	–	"SimSetup error: If you use an NPT\n"
1676	–	"    ensemble, you must set tauBarostat.\n");
1677	–	painCave.isFatal = 1;
1678	–	simError();
1679	–	}
1680	–	break;
1681	–
1682	–
1683	–
1684	–	default:
1685	–	sprintf( painCave.errMsg,
1686	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1687	–	painCave.isFatal = 1;
1688	–	simError();
1479		}
1690	–
1480		}
1481
1482	<	void SimSetup::initFortran( void ){
1482	>	void SimSetup::initFortran(void){
1483	>	info[0].refreshSim();
1484
1485	<	info->refreshSim();
1486	<
1697	<	if( !strcmp( info->mixingRule, "standard") ){
1698	<	the_ff->initForceField( LB_MIXING_RULE );
1485	>	if (!strcmp(info[0].mixingRule, "standard")){
1486	>	the_ff->initForceField(LB_MIXING_RULE);
1487		}
1488	<	else if( !strcmp( info->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",
1706	<	info->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,
1714	<	"Successfully intialized the mixingRule for Fortran." );
1500	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1501		MPIcheckPoint();
1502		#endif // is_mpi
1717	–
1503		}
1504
1505	<	void SimSetup::setupZConstraint()
1506	<	{
1507	<	if(globals->haveZConsTime()){
1508	<
1509	<	//add sample time of z-constraint  into SimInfo's property list
1510	<	DoubleData* zconsTimeProp = new DoubleData();
1511	<	zconsTimeProp->setID("zconstime");
1512	<	zconsTimeProp->setData(globals->getZConsTime());
1513	<	info->addProperty(zconsTimeProp);
1505	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1506	>	int nZConstraints;
1507	>	ZconStamp** zconStamp;
1508	>
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);
1513	>	zconsTimeProp->setData(globals->getZconsTime());
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();
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()){
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",
1536	+	defaultZConsTol);
1537	+	painCave.isFatal = 0;
1538		simError();
1539	+
1540	+	zconsTol->setData(defaultZConsTol);
1541		}
1542	<
1543	<	if(globals->haveIndexOfAllZConsMols()){
1544	<
1545	<	//add index of z-constraint molecules into SimInfo's property list
1546	<	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1547	<
1548	<	//sort the index
1549	<	sort(tempIndex.begin(), tempIndex.end());
1745	<
1746	<	IndexData* zconsIndex = new IndexData();
1747	<	zconsIndex->setID("zconsindex");
1748	<	zconsIndex->setIndexData(tempIndex);
1749	<	info->addProperty(zconsIndex);
1542	>	theInfo.addProperty(zconsTol);
1543	>
1544	>	//set Force Subtraction Policy
1545	>	StringData* zconsForcePolicy = new StringData();
1546	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1547	>
1548	>	if (globals->haveZconsForcePolicy()){
1549	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1550		}
1551		else{
1552	<	sprintf( painCave.errMsg,
1553	<	"SimSetup error: If you use an ZConstraint\n"
1554	<	" , you must set index of z-constraint molecules.\n");
1555	<	painCave.isFatal = 1;
1556	<	simError();
1557	<
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	+
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	<
1566	<	string zconsOutput(info->finalName);
1567	<
1565	>
1566	>	string zconsOutput(theInfo.finalName);
1567	>
1568		zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1569	<
1569	>
1570		StringData* zconsFilename = new StringData();
1571	<	zconsFilename->setID("zconsfilename");
1571	>	zconsFilename->setID(ZCONSFILENAME_ID);
1572		zconsFilename->setData(zconsOutput);
1573
1574	<	info->addProperty(zconsFilename);
1574	>	theInfo.addProperty(zconsFilename);
1575
1576	+	//setup index, pos and other parameters of z-constraint molecules
1577	+	nZConstraints = globals->getNzConstraints();
1578	+	theInfo.nZconstraints = nZConstraints;
1579	+
1580	+	zconStamp = globals->getZconStamp();
1581	+	ZConsParaItem tempParaItem;
1582	+
1583	+	ZConsParaData* zconsParaData = new ZConsParaData();
1584	+	zconsParaData->setID(ZCONSPARADATA_ID);
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();
1590	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1591	+
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);
1608		}

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