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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 738 by tim, Tue Sep 2 14:30:12 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 22 | Line 24
24		#define NPTf_ENS       3
25		#define NPTim_ENS      4
26		#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
27
28		#define FF_DUFF 0
29		#define FF_LJ   1
#	Line 36 | Line 32 | SimSetup::SimSetup(){
32		using namespace std;
33
34		SimSetup::SimSetup(){
39	–
35		isInfoArray = 0;
36		nInfo = 1;
37	<
37	>
38		stamps = new MakeStamps();
39		globals = new Globals();
40	<
41	<
40	>
41	>
42		#ifdef IS_MPI
43	<	strcpy( checkPointMsg, "SimSetup creation successful" );
43	>	strcpy(checkPointMsg, "SimSetup creation successful");
44		MPIcheckPoint();
45		#endif // IS_MPI
46		}
#	Line 55 | Line 50 | void SimSetup::setSimInfo( SimInfo* the_info, int theN
50		delete globals;
51		}
52
53	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
54	<	info = the_info;
55	<	nInfo = theNinfo;
56	<	isInfoArray = 1;
57	<	}
53	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
54	>	info = the_info;
55	>	nInfo = theNinfo;
56	>	isInfoArray = 1;
57	>	}
58
59
60	<	void SimSetup::parseFile( char* fileName ){
66	<
60	>	void SimSetup::parseFile(char* fileName){
61		#ifdef IS_MPI
62	<	if( worldRank == 0 ){
62	>	if (worldRank == 0){
63		#endif // is_mpi
64	<
64	>
65		inFileName = fileName;
66	<	set_interface_stamps( stamps, globals );
67	<
66	>	set_interface_stamps(stamps, globals);
67	>
68		#ifdef IS_MPI
69		mpiEventInit();
70		#endif
71
72	<	yacc_BASS( fileName );
72	>	yacc_BASS(fileName);
73
74		#ifdef IS_MPI
75		throwMPIEvent(NULL);
76		}
77	<	else receiveParse();
77	>	else{
78	>	receiveParse();
79	>	}
80		#endif
81
82		}
83
84		#ifdef IS_MPI
85		void SimSetup::receiveParse(void){
86	<
87	<	set_interface_stamps( stamps, globals );
88	<	mpiEventInit();
89	<	MPIcheckPoint();
94	<	mpiEventLoop();
95	<
86	>	set_interface_stamps(stamps, globals);
87	>	mpiEventInit();
88	>	MPIcheckPoint();
89	>	mpiEventLoop();
90		}
91
92		#endif // is_mpi
93
94	<	void SimSetup::createSim( void ){
101	<
94	>	void SimSetup::createSim(void){
95		int i, j, k, globalAtomIndex;
96	<
96	>
97		// gather all of the information from the Bass file
98	<
98	>
99		gatherInfo();
100
101		// creation of complex system objects
#	Line 110 | Line 103 | void SimSetup::createSim( void ){
103		sysObjectsCreation();
104
105		// check on the post processing info
106	<
106	>
107		finalInfoCheck();
108
109		// initialize the system coordinates
110
111	<	initSystemCoords();
112	<
111	>	if (!isInfoArray){
112	>	initSystemCoords();
113	>	}
114
115		// make the output filenames
116
117		makeOutNames();
118	<
118	>
119		// make the integrator
120	<
120	>
121		makeIntegrator();
122	<
122	>
123		#ifdef IS_MPI
124		mpiSim->mpiRefresh();
125		#endif
#	Line 133 | Line 127 | void SimSetup::createSim( void ){
127		// initialize the Fortran
128
129		initFortran();
136	–
137	–
138	–
130		}
131
132
133	<	void SimSetup::makeMolecules( void ){
134	<
133	>	void SimSetup::makeMolecules(void){
134	>	int k, l;
135		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
136		molInit molInfo;
137		DirectionalAtom* dAtom;
#	Line 155 | Line 146 | void SimSetup::makeMolecules( void ){
146		bend_set* theBends;
147		torsion_set* theTorsions;
148
149	<
149	>
150		//init the forceField paramters
151
152		the_ff->readParams();
153
154	<
154	>
155		// init the atoms
156
157		double ux, uy, uz, u, uSqr;
167	–
168	–	atomOffset = 0;
169	–	excludeOffset = 0;
170	–	for(i=0; i<info->n_mol; i++){
171	–
172	–	stampID = the_molecules[i].getStampID();
158
159	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
160	<	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;
159	>	for (k = 0; k < nInfo; k++){
160	>	the_ff->setSimInfo(&(info[k]));
161
162	<	molInfo.myAtoms = &the_atoms[atomOffset];
163	<	molInfo.myExcludes = &the_excludes[excludeOffset];
164	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
165	<	molInfo.myBends = new Bend*[molInfo.nBends];
184	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
162	>	atomOffset = 0;
163	>	excludeOffset = 0;
164	>	for (i = 0; i < info[k].n_mol; i++){
165	>	stampID = info[k].molecules[i].getStampID();
166
167	<	theBonds = new bond_pair[molInfo.nBonds];
168	<	theBends = new bend_set[molInfo.nBends];
169	<	theTorsions = new torsion_set[molInfo.nTorsions];
170	<
171	<	// make the Atoms
172	<
173	<	for(j=0; j<molInfo.nAtoms; j++){
174	<
175	<	currentAtom = comp_stamps[stampID]->getAtom( j );
176	<	if( currentAtom->haveOrientation() ){
177	<
178	<	dAtom = new DirectionalAtom(j + atomOffset);
179	<	info->n_oriented++;
180	<	molInfo.myAtoms[j] = dAtom;
181	<
182	<	ux = currentAtom->getOrntX();
183	<	uy = currentAtom->getOrntY();
184	<	uz = currentAtom->getOrntZ();
185	<
186	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
187	<
188	<	u = sqrt( uSqr );
189	<	ux = ux / u;
190	<	uy = uy / u;
191	<	uz = uz / u;
192	<
193	<	dAtom->setSUx( ux );
194	<	dAtom->setSUy( uy );
195	<	dAtom->setSUz( uz );
196	<	}
197	<	else{
198	<	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
199	<	}
200	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
201	<
202	<	#ifdef IS_MPI
203	<
204	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
205	<
167	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
168	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
169	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
170	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
171	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
172	>
173	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
174	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
175	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
176	>	molInfo.myBends = new Bend * [molInfo.nBends];
177	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
178	>
179	>	theBonds = new bond_pair[molInfo.nBonds];
180	>	theBends = new bend_set[molInfo.nBends];
181	>	theTorsions = new torsion_set[molInfo.nTorsions];
182	>
183	>	// make the Atoms
184	>
185	>	for (j = 0; j < molInfo.nAtoms; j++){
186	>	currentAtom = comp_stamps[stampID]->getAtom(j);
187	>	if (currentAtom->haveOrientation()){
188	>	dAtom = new DirectionalAtom((j + atomOffset),
189	>	info[k].getConfiguration());
190	>	info[k].n_oriented++;
191	>	molInfo.myAtoms[j] = dAtom;
192	>
193	>	ux = currentAtom->getOrntX();
194	>	uy = currentAtom->getOrntY();
195	>	uz = currentAtom->getOrntZ();
196	>
197	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
198	>
199	>	u = sqrt(uSqr);
200	>	ux = ux / u;
201	>	uy = uy / u;
202	>	uz = uz / u;
203	>
204	>	dAtom->setSUx(ux);
205	>	dAtom->setSUy(uy);
206	>	dAtom->setSUz(uz);
207	>	}
208	>	else{
209	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
210	>	info[k].getConfiguration());
211	>	}
212	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
213	>
214	>	#ifdef IS_MPI
215	>
216	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
217	>
218		#endif // is_mpi
219	<	}
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;
219	>	}
220
221	<	exI = theBonds[j].a;
222	<	exJ = theBonds[j].b;
221	>	// make the bonds
222	>	for (j = 0; j < molInfo.nBonds; j++){
223	>	currentBond = comp_stamps[stampID]->getBond(j);
224	>	theBonds[j].a = currentBond->getA() + atomOffset;
225	>	theBonds[j].b = currentBond->getB() + atomOffset;
226
227	<	// exclude_I must always be the smaller of the pair
228	<	if( exI > exJ ){
229	<	tempEx = exI;
230	<	exI = exJ;
231	<	exJ = tempEx;
232	<	}
227	>	exI = theBonds[j].a;
228	>	exJ = theBonds[j].b;
229	>
230	>	// exclude_I must always be the smaller of the pair
231	>	if (exI > exJ){
232	>	tempEx = exI;
233	>	exI = exJ;
234	>	exJ = tempEx;
235	>	}
236		#ifdef IS_MPI
237	<	tempEx = exI;
238	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
239	<	tempEx = exJ;
240	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
241	<
242	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
237	>	tempEx = exI;
238	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
239	>	tempEx = exJ;
240	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
241	>
242	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
243		#else  // isn't MPI
244
245	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
245	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
246		#endif  //is_mpi
247	<	}
248	<	excludeOffset += molInfo.nBonds;
247	>	}
248	>	excludeOffset += molInfo.nBonds;
249
250	<	//make the bends
251	<	for(j=0; j<molInfo.nBends; j++){
252	<
253	<	currentBend = comp_stamps[stampID]->getBend( j );
254	<	theBends[j].a = currentBend->getA() + atomOffset;
255	<	theBends[j].b = currentBend->getB() + atomOffset;
256	<	theBends[j].c = currentBend->getC() + atomOffset;
257	<
258	<	if( currentBend->haveExtras() ){
259	<
260	<	extras = currentBend->getExtras();
261	<	current_extra = extras;
262	<
263	<	while( current_extra != NULL ){
264	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
265	<
266	<	switch( current_extra->getType() ){
267	<
268	<	case 0:
269	<	theBends[j].ghost =
270	<	current_extra->getInt() + atomOffset;
271	<	theBends[j].isGhost = 1;
272	<	break;
273	<
274	<	case 1:
275	<	theBends[j].ghost =
276	<	(int)current_extra->getDouble() + atomOffset;
277	<	theBends[j].isGhost = 1;
278	<	break;
279	<
280	<	default:
281	<	sprintf( painCave.errMsg,
282	<	"SimSetup Error: ghostVectorSource was neither a "
283	<	"double nor an int.\n"
284	<	"-->Bend[%d] in %s\n",
285	<	j, comp_stamps[stampID]->getID() );
286	<	painCave.isFatal = 1;
287	<	simError();
288	<	}
289	<	}
290	<
291	<	else{
292	<
293	<	sprintf( painCave.errMsg,
294	<	"SimSetup Error: unhandled bend assignment:\n"
295	<	"    -->%s in Bend[%d] in %s\n",
296	<	current_extra->getlhs(),
297	<	j, comp_stamps[stampID]->getID() );
298	<	painCave.isFatal = 1;
299	<	simError();
300	<	}
301	<
302	<	current_extra = current_extra->getNext();
303	<	}
304	<	}
305	<
306	<	if( !theBends[j].isGhost ){
307	<
308	<	exI = theBends[j].a;
309	<	exJ = theBends[j].c;
310	<	}
311	<	else{
312	<
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	<	}
250	>	//make the bends
251	>	for (j = 0; j < molInfo.nBends; j++){
252	>	currentBend = comp_stamps[stampID]->getBend(j);
253	>	theBends[j].a = currentBend->getA() + atomOffset;
254	>	theBends[j].b = currentBend->getB() + atomOffset;
255	>	theBends[j].c = currentBend->getC() + atomOffset;
256	>
257	>	if (currentBend->haveExtras()){
258	>	extras = currentBend->getExtras();
259	>	current_extra = extras;
260	>
261	>	while (current_extra != NULL){
262	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
263	>	switch (current_extra->getType()){
264	>	case 0:
265	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
266	>	theBends[j].isGhost = 1;
267	>	break;
268	>
269	>	case 1:
270	>	theBends[j].ghost = (int) current_extra->getDouble() +
271	>	atomOffset;
272	>	theBends[j].isGhost = 1;
273	>	break;
274	>
275	>	default:
276	>	sprintf(painCave.errMsg,
277	>	"SimSetup Error: ghostVectorSource was neither a "
278	>	"double nor an int.\n"
279	>	"-->Bend[%d] in %s\n",
280	>	j, comp_stamps[stampID]->getID());
281	>	painCave.isFatal = 1;
282	>	simError();
283	>	}
284	>	}
285	>	else{
286	>	sprintf(painCave.errMsg,
287	>	"SimSetup Error: unhandled bend assignment:\n"
288	>	"    -->%s in Bend[%d] in %s\n",
289	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
290	>	painCave.isFatal = 1;
291	>	simError();
292	>	}
293	>
294	>	current_extra = current_extra->getNext();
295	>	}
296	>	}
297	>
298	>	if (!theBends[j].isGhost){
299	>	exI = theBends[j].a;
300	>	exJ = theBends[j].c;
301	>	}
302	>	else{
303	>	exI = theBends[j].a;
304	>	exJ = theBends[j].b;
305	>	}
306	>
307	>	// exclude_I must always be the smaller of the pair
308	>	if (exI > exJ){
309	>	tempEx = exI;
310	>	exI = exJ;
311	>	exJ = tempEx;
312	>	}
313		#ifdef IS_MPI
314	<	tempEx = exI;
315	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
316	<	tempEx = exJ;
317	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
318	<
319	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
314	>	tempEx = exI;
315	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
316	>	tempEx = exJ;
317	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
318	>
319	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
320		#else  // isn't MPI
321	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
321	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
322		#endif  //is_mpi
323	<	}
324	<	excludeOffset += molInfo.nBends;
323	>	}
324	>	excludeOffset += molInfo.nBends;
325
326	<	for(j=0; j<molInfo.nTorsions; j++){
327	<
328	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
329	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
330	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
331	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
350	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
351	<
352	<	exI = theTorsions[j].a;
353	<	exJ = theTorsions[j].d;
326	>	for (j = 0; j < molInfo.nTorsions; j++){
327	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
328	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
329	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
330	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
331	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
332
333	<	// exclude_I must always be the smaller of the pair
334	<	if( exI > exJ ){
335	<	tempEx = exI;
336	<	exI = exJ;
337	<	exJ = tempEx;
338	<	}
333	>	exI = theTorsions[j].a;
334	>	exJ = theTorsions[j].d;
335	>
336	>	// exclude_I must always be the smaller of the pair
337	>	if (exI > exJ){
338	>	tempEx = exI;
339	>	exI = exJ;
340	>	exJ = tempEx;
341	>	}
342		#ifdef IS_MPI
343	<	tempEx = exI;
344	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
345	<	tempEx = exJ;
346	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
347	<
348	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
343	>	tempEx = exI;
344	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345	>	tempEx = exJ;
346	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
347	>
348	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
349		#else  // isn't MPI
350	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
350	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
351		#endif  //is_mpi
352	<	}
353	<	excludeOffset += molInfo.nTorsions;
352	>	}
353	>	excludeOffset += molInfo.nTorsions;
354
374	–
375	–	// send the arrays off to the forceField for init.
355
356	<	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 );
356	>	// send the arrays off to the forceField for init.
357
358	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
359	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
360	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
361	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
362	+	theTorsions);
363
383	–	the_molecules[i].initialize( molInfo );
364
365	+	info[k].molecules[i].initialize(molInfo);
366
367	<	atomOffset += molInfo.nAtoms;
368	<	delete[] theBonds;
369	<	delete[] theBends;
370	<	delete[] theTorsions;
367	>
368	>	atomOffset += molInfo.nAtoms;
369	>	delete[] theBonds;
370	>	delete[] theBends;
371	>	delete[] theTorsions;
372	>	}
373		}
374
375		#ifdef IS_MPI
376	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
376	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
377		MPIcheckPoint();
378		#endif // is_mpi
379
380		// clean up the forcefield
381	+
382		the_ff->calcRcut();
383		the_ff->cleanMe();
400	–
384		}
385
386	<	void SimSetup::initFromBass( void ){
404	<
386	>	void SimSetup::initFromBass(void){
387		int i, j, k;
388		int n_cells;
389		double cellx, celly, cellz;
#	Line 410 | Line 392 | void SimSetup::initFromBass( void ){
392		int n_extra;
393		int have_extra, done;
394
395	<	temp1 = (double)tot_nmol / 4.0;
396	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
397	<	temp3 = ceil( temp2 );
395	>	double vel[3];
396	>	vel[0] = 0.0;
397	>	vel[1] = 0.0;
398	>	vel[2] = 0.0;
399
400	<	have_extra =0;
401	<	if( temp2 < temp3 ){ // we have a non-complete lattice
402	<	have_extra =1;
400	>	temp1 = (double) tot_nmol / 4.0;
401	>	temp2 = pow(temp1, (1.0 / 3.0));
402	>	temp3 = ceil(temp2);
403
404	<	n_cells = (int)temp3 - 1;
405	<	cellx = info->boxL[0] / temp3;
406	<	celly = info->boxL[1] / temp3;
407	<	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 );
404	>	have_extra = 0;
405	>	if (temp2 < temp3){
406	>	// we have a non-complete lattice
407	>	have_extra = 1;
408
409	<	if( n_per_extra > 4){
410	<	sprintf( painCave.errMsg,
411	<	"SimSetup error. There has been an error in constructing"
412	<	" the non-complete lattice.\n" );
409	>	n_cells = (int) temp3 - 1;
410	>	cellx = info[0].boxL[0] / temp3;
411	>	celly = info[0].boxL[1] / temp3;
412	>	cellz = info[0].boxL[2] / temp3;
413	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
414	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
415	>	n_per_extra = (int) ceil(temp1);
416	>
417	>	if (n_per_extra > 4){
418	>	sprintf(painCave.errMsg,
419	>	"SimSetup error. There has been an error in constructing"
420	>	" the non-complete lattice.\n");
421		painCave.isFatal = 1;
422		simError();
423		}
424		}
425		else{
426	<	n_cells = (int)temp3;
427	<	cellx = info->boxL[0] / temp3;
428	<	celly = info->boxL[1] / temp3;
429	<	cellz = info->boxL[2] / temp3;
426	>	n_cells = (int) temp3;
427	>	cellx = info[0].boxL[0] / temp3;
428	>	celly = info[0].boxL[1] / temp3;
429	>	cellz = info[0].boxL[2] / temp3;
430		}
431
432		current_mol = 0;
#	Line 446 | Line 434 | void SimSetup::initFromBass( void ){
434		current_comp = 0;
435		current_atom_ndx = 0;
436
437	<	for( i=0; i < n_cells ; i++ ){
438	<	for( j=0; j < n_cells; j++ ){
439	<	for( k=0; k < n_cells; k++ ){
437	>	for (i = 0; i < n_cells ; i++){
438	>	for (j = 0; j < n_cells; j++){
439	>	for (k = 0; k < n_cells; k++){
440	>	makeElement(i * cellx, j * celly, k * cellz);
441
442	<	makeElement( i * cellx,
454	<	j * celly,
455	<	k * cellz );
442	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
443
444	<	makeElement( i * cellx + 0.5 * cellx,
458	<	j * celly + 0.5 * celly,
459	<	k * cellz );
444	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
445
446	<	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 );
446	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
447		}
448		}
449		}
450
451	<	if( have_extra ){
451	>	if (have_extra){
452		done = 0;
453
454		int start_ndx;
455	<	for( i=0; i < (n_cells+1) && !done; i++ ){
456	<	for( j=0; j < (n_cells+1) && !done; j++ ){
455	>	for (i = 0; i < (n_cells + 1) && !done; i++){
456	>	for (j = 0; j < (n_cells + 1) && !done; j++){
457	>	if (i < n_cells){
458	>	if (j < n_cells){
459	>	start_ndx = n_cells;
460	>	}
461	>	else
462	>	start_ndx = 0;
463	>	}
464	>	else
465	>	start_ndx = 0;
466
467	<	if( i < n_cells ){
467	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
468	>	makeElement(i * cellx, j * celly, k * cellz);
469	>	done = (current_mol >= tot_nmol);
470
471	<	if( j < n_cells ){
472	<	start_ndx = n_cells;
473	<	}
474	<	else start_ndx = 0;
475	<	}
486	<	else start_ndx = 0;
471	>	if (!done && n_per_extra > 1){
472	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
473	>	k * cellz);
474	>	done = (current_mol >= tot_nmol);
475	>	}
476
477	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
477	>	if (!done && n_per_extra > 2){
478	>	makeElement(i * cellx, j * celly + 0.5 * celly,
479	>	k * cellz + 0.5 * cellz);
480	>	done = (current_mol >= tot_nmol);
481	>	}
482
483	<	makeElement( i * cellx,
484	<	j * celly,
485	<	k * cellz );
486	<	done = ( current_mol >= tot_nmol );
487	<
488	<	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	<	}
483	>	if (!done && n_per_extra > 3){
484	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
485	>	k * cellz + 0.5 * cellz);
486	>	done = (current_mol >= tot_nmol);
487	>	}
488	>	}
489		}
490		}
491		}
492
493	<
494	<	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 );
493	>	for (i = 0; i < info[0].n_atoms; i++){
494	>	info[0].atoms[i]->setVel(vel);
495		}
496		}
497
498	<	void SimSetup::makeElement( double x, double y, double z ){
529	<
498	>	void SimSetup::makeElement(double x, double y, double z){
499		int k;
500		AtomStamp* current_atom;
501		DirectionalAtom* dAtom;
502		double rotMat[3][3];
503	+	double pos[3];
504
505	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
506	<
507	<	current_atom = comp_stamps[current_comp]->getAtom( k );
508	<	if( !current_atom->havePosition() ){
509	<	sprintf( painCave.errMsg,
510	<	"SimSetup:initFromBass error.\n"
511	<	"\tComponent %s, atom %s does not have a position specified.\n"
512	<	"\tThe initialization routine is unable to give a start"
513	<	" position.\n",
544	<	comp_stamps[current_comp]->getID(),
545	<	current_atom->getType() );
505	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
506	>	current_atom = comp_stamps[current_comp]->getAtom(k);
507	>	if (!current_atom->havePosition()){
508	>	sprintf(painCave.errMsg,
509	>	"SimSetup:initFromBass error.\n"
510	>	"\tComponent %s, atom %s does not have a position specified.\n"
511	>	"\tThe initialization routine is unable to give a start"
512	>	" position.\n",
513	>	comp_stamps[current_comp]->getID(), current_atom->getType());
514		painCave.isFatal = 1;
515		simError();
516		}
517
518	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
519	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
520	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
518	>	pos[0] = x + current_atom->getPosX();
519	>	pos[1] = y + current_atom->getPosY();
520	>	pos[2] = z + current_atom->getPosZ();
521
522	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
522	>	info[0].atoms[current_atom_ndx]->setPos(pos);
523
524	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
524	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
525	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
526
527		rotMat[0][0] = 1.0;
528		rotMat[0][1] = 0.0;
#	Line 567 | Line 536 | void SimSetup::makeElement( double x, double y, double
536		rotMat[2][1] = 0.0;
537		rotMat[2][2] = 1.0;
538
539	<	dAtom->setA( rotMat );
539	>	dAtom->setA(rotMat);
540		}
541
542		current_atom_ndx++;
#	Line 576 | Line 545 | void SimSetup::makeElement( double x, double y, double
545		current_mol++;
546		current_comp_mol++;
547
548	<	if( current_comp_mol >= components_nmol[current_comp] ){
580	<
548	>	if (current_comp_mol >= components_nmol[current_comp]){
549		current_comp_mol = 0;
550		current_comp++;
551		}
552		}
553
554
555	<	void SimSetup::gatherInfo( void ){
556	<	int i,j,k;
555	>	void SimSetup::gatherInfo(void){
556	>	int i, j, k;
557
558		ensembleCase = -1;
559		ffCase = -1;
560
593	–	// get the stamps and globals;
594	–	stamps = stamps;
595	–	globals = globals;
596	–
561		// set the easy ones first
562	<	info->target_temp = globals->getTargetTemp();
563	<	info->dt = globals->getDt();
564	<	info->run_time = globals->getRunTime();
562	>
563	>	for (i = 0; i < nInfo; i++){
564	>	info[i].target_temp = globals->getTargetTemp();
565	>	info[i].dt = globals->getDt();
566	>	info[i].run_time = globals->getRunTime();
567	>	}
568		n_components = globals->getNComponents();
569
570
571		// get the forceField
572
573	<	strcpy( force_field, globals->getForceField() );
573	>	strcpy(force_field, globals->getForceField());
574
575	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
576	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
577	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
575	>	if (!strcasecmp(force_field, "DUFF")){
576	>	ffCase = FF_DUFF;
577	>	}
578	>	else if (!strcasecmp(force_field, "LJ")){
579	>	ffCase = FF_LJ;
580	>	}
581	>	else if (!strcasecmp(force_field, "EAM")){
582	>	ffCase = FF_EAM;
583	>	}
584		else{
585	<	sprintf( painCave.errMsg,
586	<	"SimSetup Error. Unrecognized force field -> %s\n",
587	<	force_field );
588	<	painCave.isFatal = 1;
616	<	simError();
585	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
586	>	force_field);
587	>	painCave.isFatal = 1;
588	>	simError();
589		}
590
591	<	// get the ensemble
591	>	// get the ensemble
592
593	<	strcpy( ensemble, globals->getEnsemble() );
593	>	strcpy(ensemble, globals->getEnsemble());
594
595	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
596	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
597	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
595	>	if (!strcasecmp(ensemble, "NVE")){
596	>	ensembleCase = NVE_ENS;
597	>	}
598	>	else if (!strcasecmp(ensemble, "NVT")){
599	>	ensembleCase = NVT_ENS;
600	>	}
601	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
602		ensembleCase = NPTi_ENS;
603	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
604	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
605	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
606	<
607	<	else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS;
608	<	else if( !strcasecmp( ensemble, "NVTZCONS"))  ensembleCase = NVTZCONS_ENS;
609	<	else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPT"))
610	<	ensembleCase = NPTiZCONS_ENS;
611	<	else if( !strcasecmp( ensemble, "NPTfCONS"))  ensembleCase = NPTfZCONS_ENS;
612	<	else if( !strcasecmp( ensemble, "NPTimZCONS"))  ensembleCase = NPTimZCONS_ENS;
637	<	else if( !strcasecmp( ensemble, "NPTfmCONS"))  ensembleCase = NPTfmZCONS_ENS;
638	<
603	>	}
604	>	else if (!strcasecmp(ensemble, "NPTf")){
605	>	ensembleCase = NPTf_ENS;
606	>	}
607	>	else if (!strcasecmp(ensemble, "NPTim")){
608	>	ensembleCase = NPTim_ENS;
609	>	}
610	>	else if (!strcasecmp(ensemble, "NPTfm")){
611	>	ensembleCase = NPTfm_ENS;
612	>	}
613		else{
614	<	sprintf( painCave.errMsg,
615	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
616	<	"reverting to NVE for this simulation.\n",
617	<	ensemble );
618	<	painCave.isFatal = 0;
619	<	simError();
620	<	strcpy( ensemble, "NVE" );
621	<	ensembleCase = NVE_ENS;
614	>	sprintf(painCave.errMsg,
615	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
616	>	"reverting to NVE for this simulation.\n",
617	>	ensemble);
618	>	painCave.isFatal = 0;
619	>	simError();
620	>	strcpy(ensemble, "NVE");
621	>	ensembleCase = NVE_ENS;
622		}
649	–	strcpy( info->ensemble, ensemble );
623
624	<	// get the mixing rule
624	>	for (i = 0; i < nInfo; i++){
625	>	strcpy(info[i].ensemble, ensemble);
626
627	<	strcpy( info->mixingRule, globals->getMixingRule() );
628	<	info->usePBC = globals->getPBC();
629	<
630	<
627	>	// get the mixing rule
628	>
629	>	strcpy(info[i].mixingRule, globals->getMixingRule());
630	>	info[i].usePBC = globals->getPBC();
631	>	}
632	>
633		// get the components and calculate the tot_nMol and indvidual n_mol
634	<
634	>
635		the_components = globals->getComponents();
636		components_nmol = new int[n_components];
637
638
639	<	if( !globals->haveNMol() ){
639	>	if (!globals->haveNMol()){
640		// we don't have the total number of molecules, so we assume it is
641		// given in each component
642
643		tot_nmol = 0;
644	<	for( i=0; i<n_components; i++ ){
645	<
646	<	if( !the_components[i]->haveNMol() ){
647	<	// we have a problem
648	<	sprintf( painCave.errMsg,
649	<	"SimSetup Error. No global NMol or component NMol"
650	<	" given. Cannot calculate the number of atoms.\n" );
651	<	painCave.isFatal = 1;
676	<	simError();
644	>	for (i = 0; i < n_components; i++){
645	>	if (!the_components[i]->haveNMol()){
646	>	// we have a problem
647	>	sprintf(painCave.errMsg,
648	>	"SimSetup Error. No global NMol or component NMol"
649	>	" given. Cannot calculate the number of atoms.\n");
650	>	painCave.isFatal = 1;
651	>	simError();
652		}
653
654		tot_nmol += the_components[i]->getNMol();
#	Line 681 | Line 656 | void SimSetup::gatherInfo( void ){
656		}
657		}
658		else{
659	<	sprintf( painCave.errMsg,
660	<	"SimSetup error.\n"
661	<	"\tSorry, the ability to specify total"
662	<	" nMols and then give molfractions in the components\n"
663	<	"\tis not currently supported."
664	<	" Please give nMol in the components.\n" );
659	>	sprintf(painCave.errMsg,
660	>	"SimSetup error.\n"
661	>	"\tSorry, the ability to specify total"
662	>	" nMols and then give molfractions in the components\n"
663	>	"\tis not currently supported."
664	>	" Please give nMol in the components.\n");
665		painCave.isFatal = 1;
666		simError();
667		}
668
669		// set the status, sample, and thermal kick times
670	<
671	<	if( globals->haveSampleTime() ){
672	<	info->sampleTime = globals->getSampleTime();
673	<	info->statusTime = info->sampleTime;
674	<	info->thermalTime = info->sampleTime;
675	<	}
676	<	else{
677	<	info->sampleTime = globals->getRunTime();
678	<	info->statusTime = info->sampleTime;
679	<	info->thermalTime = info->sampleTime;
680	<	}
670	>
671	>	for (i = 0; i < nInfo; i++){
672	>	if (globals->haveSampleTime()){
673	>	info[i].sampleTime = globals->getSampleTime();
674	>	info[i].statusTime = info[i].sampleTime;
675	>	info[i].thermalTime = info[i].sampleTime;
676	>	}
677	>	else{
678	>	info[i].sampleTime = globals->getRunTime();
679	>	info[i].statusTime = info[i].sampleTime;
680	>	info[i].thermalTime = info[i].sampleTime;
681	>	}
682
683	<	if( globals->haveStatusTime() ){
684	<	info->statusTime = globals->getStatusTime();
685	<	}
683	>	if (globals->haveStatusTime()){
684	>	info[i].statusTime = globals->getStatusTime();
685	>	}
686
687	<	if( globals->haveThermalTime() ){
688	<	info->thermalTime = globals->getThermalTime();
689	<	}
687	>	if (globals->haveThermalTime()){
688	>	info[i].thermalTime = globals->getThermalTime();
689	>	}
690
691	<	// check for the temperature set flag
691	>	// check for the temperature set flag
692
693	<	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
693	>	if (globals->haveTempSet())
694	>	info[i].setTemp = globals->getTempSet();
695
696	<	// get some of the tricky things that may still be in the globals
696	>	// get some of the tricky things that may still be in the globals
697
698	<	double boxVector[3];
699	<	if( globals->haveBox() ){
700	<	boxVector[0] = globals->getBox();
701	<	boxVector[1] = globals->getBox();
702	<	boxVector[2] = globals->getBox();
726	<
727	<	info->setBox( boxVector );
728	<	}
729	<	else if( globals->haveDensity() ){
698	>	double boxVector[3];
699	>	if (globals->haveBox()){
700	>	boxVector[0] = globals->getBox();
701	>	boxVector[1] = globals->getBox();
702	>	boxVector[2] = globals->getBox();
703
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];
704	>	info[i].setBox(boxVector);
705	>	}
706	>	else if (globals->haveDensity()){
707	>	double vol;
708	>	vol = (double) tot_nmol / globals->getDensity();
709	>	boxVector[0] = pow(vol, (1.0 / 3.0));
710	>	boxVector[1] = boxVector[0];
711	>	boxVector[2] = boxVector[0];
712
713	<	info->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();
713	>	info[i].setBox(boxVector);
714		}
715	<	boxVector[0] = globals->getBoxX();
715	>	else{
716	>	if (!globals->haveBoxX()){
717	>	sprintf(painCave.errMsg,
718	>	"SimSetup error, no periodic BoxX size given.\n");
719	>	painCave.isFatal = 1;
720	>	simError();
721	>	}
722	>	boxVector[0] = globals->getBoxX();
723
724	<	if( !globals->haveBoxY() ){
725	<	sprintf( painCave.errMsg,
726	<	"SimSetup error, no periodic BoxY size given.\n" );
727	<	painCave.isFatal = 1;
728	<	simError();
724	>	if (!globals->haveBoxY()){
725	>	sprintf(painCave.errMsg,
726	>	"SimSetup error, no periodic BoxY size given.\n");
727	>	painCave.isFatal = 1;
728	>	simError();
729	>	}
730	>	boxVector[1] = globals->getBoxY();
731	>
732	>	if (!globals->haveBoxZ()){
733	>	sprintf(painCave.errMsg,
734	>	"SimSetup error, no periodic BoxZ size given.\n");
735	>	painCave.isFatal = 1;
736	>	simError();
737	>	}
738	>	boxVector[2] = globals->getBoxZ();
739	>
740	>	info[i].setBox(boxVector);
741		}
742	<	boxVector[1] = globals->getBoxY();
742	>	}
743
744	<	if( !globals->haveBoxZ() ){
745	<	sprintf( painCave.errMsg,
746	<	"SimSetup error, no periodic BoxZ size given.\n" );
747	<	painCave.isFatal = 1;
744	>	//setup seed for random number generator
745	>	int seedValue;
746	>
747	>	if (globals->haveSeed()){
748	>	seedValue = globals->getSeed();
749	>
750	>	if(seedValue / 1E9 == 0){
751	>	sprintf(painCave.errMsg,
752	>	"Seed for sprng library should contain at least 9 digits\n"
753	>	"OOPSE will generate a seed for user\n");
754	>	painCave.isFatal = 0;
755		simError();
756	+
757	+	//using seed generated by system instead of invalid seed set by user
758	+	#ifndef IS_MPI
759	+	seedValue = make_sprng_seed();
760	+	#else
761	+	if (worldRank == 0){
762	+	seedValue = make_sprng_seed();
763	+	}
764	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
765	+	#endif
766		}
767	<	boxVector[2] = globals->getBoxZ();
767	>	}//end of if branch of globals->haveSeed()
768	>	else{
769	>
770	>	#ifndef IS_MPI
771	>	seedValue = make_sprng_seed();
772	>	#else
773	>	if (worldRank == 0){
774	>	seedValue = make_sprng_seed();
775	>	}
776	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
777	>	#endif
778	>	}//end of globals->haveSeed()
779
780	<	info->setBox( boxVector );
780	>	for (int i = 0; i < nInfo; i++){
781	>	info[i].setSeed(seedValue);
782		}
783
767	–
768	–
784		#ifdef IS_MPI
785	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
785	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
786		MPIcheckPoint();
787		#endif // is_mpi
773	–
788		}
789
790
791	<	void SimSetup::finalInfoCheck( void ){
791	>	void SimSetup::finalInfoCheck(void){
792		int index;
793		int usesDipoles;
794	<
794	>	int i;
795
796	<	// check electrostatic parameters
797	<
798	<	index = 0;
799	<	usesDipoles = 0;
800	<	while( (index < info->n_atoms) && !usesDipoles ){
801	<	usesDipoles = ((info->atoms)[index])->hasDipole();
802	<	index++;
803	<	}
804	<
796	>	for (i = 0; i < nInfo; i++){
797	>	// check electrostatic parameters
798	>
799	>	index = 0;
800	>	usesDipoles = 0;
801	>	while ((index < info[i].n_atoms) && !usesDipoles){
802	>	usesDipoles = (info[i].atoms[index])->hasDipole();
803	>	index++;
804	>	}
805	>
806		#ifdef IS_MPI
807	<	int myUse = usesDipoles;
808	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
807	>	int myUse = usesDipoles;
808	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
809		#endif //is_mpi
810
811	<	double theEcr, theEst;
811	>	double theEcr, theEst;
812
813	<	if (globals->getUseRF() ) {
814	<	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	<	}
813	>	if (globals->getUseRF()){
814	>	info[i].useReactionField = 1;
815
816	<	if( !globals->haveEST() ){
817	<	sprintf( painCave.errMsg,
818	<	"SimSetup Warning: using default value of 0.05 * the "
819	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
820	<	);
821	<	painCave.isFatal = 0;
822	<	simError();
823	<	theEst = 0.05 * theEcr;
824	<	} else {
825	<	theEst= globals->getEST();
826	<	}
827	<
828	<	info->setEcr( theEcr, theEst );
829	<
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();
816	>	if (!globals->haveECR()){
817	>	sprintf(painCave.errMsg,
818	>	"SimSetup Warning: using default value of 1/2 the smallest "
819	>	"box length for the electrostaticCutoffRadius.\n"
820	>	"I hope you have a very fast processor!\n");
821	>	painCave.isFatal = 0;
822	>	simError();
823	>	double smallest;
824	>	smallest = info[i].boxL[0];
825	>	if (info[i].boxL[1] <= smallest)
826	>	smallest = info[i].boxL[1];
827	>	if (info[i].boxL[2] <= smallest)
828	>	smallest = info[i].boxL[2];
829	>	theEcr = 0.5 * smallest;
830		}
831	<
832	<	if( !globals->haveEST() ){
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();
831	>	else{
832	>	theEcr = globals->getECR();
833		}
834
835	<	info->setEcr( theEcr, theEst );
835	>	if (!globals->haveEST()){
836	>	sprintf(painCave.errMsg,
837	>	"SimSetup Warning: using default value of 0.05 * the "
838	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
839	>	painCave.isFatal = 0;
840	>	simError();
841	>	theEst = 0.05 * theEcr;
842	>	}
843	>	else{
844	>	theEst = globals->getEST();
845	>	}
846	>
847	>	info[i].setEcr(theEcr, theEst);
848	>
849	>	if (!globals->haveDielectric()){
850	>	sprintf(painCave.errMsg,
851	>	"SimSetup Error: You are trying to use Reaction Field without"
852	>	"setting a dielectric constant!\n");
853	>	painCave.isFatal = 1;
854	>	simError();
855	>	}
856	>	info[i].dielectric = globals->getDielectric();
857		}
858	<	}
858	>	else{
859	>	if (usesDipoles){
860	>	if (!globals->haveECR()){
861	>	sprintf(painCave.errMsg,
862	>	"SimSetup Warning: using default value of 1/2 the smallest "
863	>	"box length for the electrostaticCutoffRadius.\n"
864	>	"I hope you have a very fast processor!\n");
865	>	painCave.isFatal = 0;
866	>	simError();
867	>	double smallest;
868	>	smallest = info[i].boxL[0];
869	>	if (info[i].boxL[1] <= smallest)
870	>	smallest = info[i].boxL[1];
871	>	if (info[i].boxL[2] <= smallest)
872	>	smallest = info[i].boxL[2];
873	>	theEcr = 0.5 * smallest;
874	>	}
875	>	else{
876	>	theEcr = globals->getECR();
877	>	}
878
879	+	if (!globals->haveEST()){
880	+	sprintf(painCave.errMsg,
881	+	"SimSetup Warning: using default value of 0.05 * the "
882	+	"electrostaticCutoffRadius for the "
883	+	"electrostaticSkinThickness\n");
884	+	painCave.isFatal = 0;
885	+	simError();
886	+	theEst = 0.05 * theEcr;
887	+	}
888	+	else{
889	+	theEst = globals->getEST();
890	+	}
891	+
892	+	info[i].setEcr(theEcr, theEst);
893	+	}
894	+	}
895	+	}
896	+
897		#ifdef IS_MPI
898	<	strcpy( checkPointMsg, "post processing checks out" );
898	>	strcpy(checkPointMsg, "post processing checks out");
899		MPIcheckPoint();
900		#endif // is_mpi
881	–
901		}
902
903	<	void SimSetup::initSystemCoords( void ){
903	>	void SimSetup::initSystemCoords(void){
904	>	int i;
905
906	<	if( globals->haveInitialConfig() ){
907	<
908	<	InitializeFromFile* fileInit;
906	>	char* inName;
907	>
908	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
909	>
910	>	for (i = 0; i < info[0].n_atoms; i++)
911	>	info[0].atoms[i]->setCoords();
912	>
913	>	if (globals->haveInitialConfig()){
914	>	InitializeFromFile* fileInit;
915		#ifdef IS_MPI // is_mpi
916	<	if( worldRank == 0 ){
916	>	if (worldRank == 0){
917		#endif //is_mpi
918	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
918	>	inName = globals->getInitialConfig();
919	>	double* tempDouble = new double[1000000];
920	>	fileInit = new InitializeFromFile(inName);
921		#ifdef IS_MPI
922	<	}else fileInit = new InitializeFromFile( NULL );
922	>	}
923	>	else
924	>	fileInit = new InitializeFromFile(NULL);
925		#endif
926	<	fileInit->readInit( info ); // default velocities on
926	>	fileInit->readInit(info); // default velocities on
927
928	<	delete fileInit;
929	<	}
930	<	else{
901	<
928	>	delete fileInit;
929	>	}
930	>	else{
931		#ifdef IS_MPI
932
933	<	// no init from bass
934	<
935	<	sprintf( painCave.errMsg,
936	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
937	<	painCave.isFatal;
938	<	simError();
939	<
933	>	// no init from bass
934	>
935	>	sprintf(painCave.errMsg,
936	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
937	>	painCave.isFatal;
938	>	simError();
939	>
940		#else
941
942	<	initFromBass();
942	>	initFromBass();
943
944
945		#endif
946	<	}
946	>	}
947
948		#ifdef IS_MPI
949	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
949	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
950		MPIcheckPoint();
951		#endif // is_mpi
923	–
952		}
953
954
955	<	void SimSetup::makeOutNames( void ){
955	>	void SimSetup::makeOutNames(void){
956	>	int k;
957
958	+
959	+	for (k = 0; k < nInfo; k++){
960		#ifdef IS_MPI
961	<	if( worldRank == 0 ){
961	>	if (worldRank == 0){
962		#endif // is_mpi
963	<
964	<	if( globals->haveFinalConfig() ){
965	<	strcpy( info->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" );
963	>
964	>	if (globals->haveFinalConfig()){
965	>	strcpy(info[k].finalName, globals->getFinalConfig());
966		}
967	<	else if( !strcmp( endTest, ".BASS" ) ){
968	<	strcpy( endTest, ".eor" );
967	>	else{
968	>	strcpy(info[k].finalName, inFileName);
969	>	char* endTest;
970	>	int nameLength = strlen(info[k].finalName);
971	>	endTest = &(info[k].finalName[nameLength - 5]);
972	>	if (!strcmp(endTest, ".bass")){
973	>	strcpy(endTest, ".eor");
974	>	}
975	>	else if (!strcmp(endTest, ".BASS")){
976	>	strcpy(endTest, ".eor");
977	>	}
978	>	else{
979	>	endTest = &(info[k].finalName[nameLength - 4]);
980	>	if (!strcmp(endTest, ".bss")){
981	>	strcpy(endTest, ".eor");
982	>	}
983	>	else if (!strcmp(endTest, ".mdl")){
984	>	strcpy(endTest, ".eor");
985	>	}
986	>	else{
987	>	strcat(info[k].finalName, ".eor");
988	>	}
989	>	}
990		}
991	<	else{
992	<	endTest = &(info->finalName[nameLength - 4]);
993	<	if( !strcmp( endTest, ".bss" ) ){
994	<	strcpy( endTest, ".eor" );
995	<	}
996	<	else if( !strcmp( endTest, ".mdl" ) ){
997	<	strcpy( endTest, ".eor" );
998	<	}
999	<	else{
956	<	strcat( info->finalName, ".eor" );
957	<	}
991	>
992	>	// make the sample and status out names
993	>
994	>	strcpy(info[k].sampleName, inFileName);
995	>	char* endTest;
996	>	int nameLength = strlen(info[k].sampleName);
997	>	endTest = &(info[k].sampleName[nameLength - 5]);
998	>	if (!strcmp(endTest, ".bass")){
999	>	strcpy(endTest, ".dump");
1000		}
1001	<	}
1002	<
961	<	// make the sample and status out names
962	<
963	<	strcpy( info->sampleName, inFileName );
964	<	char* endTest;
965	<	int nameLength = strlen( info->sampleName );
966	<	endTest = &(info->sampleName[nameLength - 5]);
967	<	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" );
1001	>	else if (!strcmp(endTest, ".BASS")){
1002	>	strcpy(endTest, ".dump");
1003		}
978	–	else if( !strcmp( endTest, ".mdl" ) ){
979	–	strcpy( endTest, ".dump" );
980	–	}
1004		else{
1005	<	strcat( info->sampleName, ".dump" );
1005	>	endTest = &(info[k].sampleName[nameLength - 4]);
1006	>	if (!strcmp(endTest, ".bss")){
1007	>	strcpy(endTest, ".dump");
1008	>	}
1009	>	else if (!strcmp(endTest, ".mdl")){
1010	>	strcpy(endTest, ".dump");
1011	>	}
1012	>	else{
1013	>	strcat(info[k].sampleName, ".dump");
1014	>	}
1015		}
1016	<	}
1017	<
1018	<	strcpy( info->statusName, inFileName );
1019	<	nameLength = strlen( info->statusName );
1020	<	endTest = &(info->statusName[nameLength - 5]);
1021	<	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" );
1016	>
1017	>	strcpy(info[k].statusName, inFileName);
1018	>	nameLength = strlen(info[k].statusName);
1019	>	endTest = &(info[k].statusName[nameLength - 5]);
1020	>	if (!strcmp(endTest, ".bass")){
1021	>	strcpy(endTest, ".stat");
1022		}
1023	<	else if( !strcmp( endTest, ".mdl" ) ){
1024	<	strcpy( endTest, ".stat" );
1023	>	else if (!strcmp(endTest, ".BASS")){
1024	>	strcpy(endTest, ".stat");
1025		}
1026		else{
1027	<	strcat( info->statusName, ".stat" );
1027	>	endTest = &(info[k].statusName[nameLength - 4]);
1028	>	if (!strcmp(endTest, ".bss")){
1029	>	strcpy(endTest, ".stat");
1030	>	}
1031	>	else if (!strcmp(endTest, ".mdl")){
1032	>	strcpy(endTest, ".stat");
1033	>	}
1034	>	else{
1035	>	strcat(info[k].statusName, ".stat");
1036	>	}
1037		}
1038	<	}
1007	<
1038	>
1039		#ifdef IS_MPI
1009	–	}
1010	–	#endif // is_mpi
1040
1041	+	}
1042	+	#endif // is_mpi
1043	+	}
1044		}
1045
1046
1047	<	void SimSetup::sysObjectsCreation( void ){
1047	>	void SimSetup::sysObjectsCreation(void){
1048	>	int i, k;
1049
1017	–	int i;
1018	–
1050		// create the forceField
1051
1052		createFF();
#	Line 1030 | Line 1061 | void SimSetup::sysObjectsCreation( void ){
1061
1062		#ifdef IS_MPI
1063		// divide the molecules among the processors
1064	<
1064	>
1065		mpiMolDivide();
1066		#endif //is_mpi
1067	<
1067	>
1068		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1069	<
1069	>
1070		makeSysArrays();
1071
1072		// make and initialize the molecules (all but atomic coordinates)
1073	<
1073	>
1074		makeMolecules();
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	–
1075
1076	<
1076	>	for (k = 0; k < nInfo; k++){
1077	>	info[k].identArray = new int[info[k].n_atoms];
1078	>	for (i = 0; i < info[k].n_atoms; i++){
1079	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1080	>	}
1081	>	}
1082		}
1083
1084
1085	<	void SimSetup::createFF( void ){
1085	>	void SimSetup::createFF(void){
1086	>	switch (ffCase){
1087	>	case FF_DUFF:
1088	>	the_ff = new DUFF();
1089	>	break;
1090
1091	<	switch( ffCase ){
1091	>	case FF_LJ:
1092	>	the_ff = new LJFF();
1093	>	break;
1094
1095	<	case FF_DUFF:
1096	<	the_ff = new DUFF();
1097	<	break;
1095	>	case FF_EAM:
1096	>	the_ff = new EAM_FF();
1097	>	break;
1098
1099	<	case FF_LJ:
1100	<	the_ff = new LJFF();
1101	<	break;
1102	<
1103	<	case FF_EAM:
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();
1099	>	default:
1100	>	sprintf(painCave.errMsg,
1101	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1102	>	painCave.isFatal = 1;
1103	>	simError();
1104		}
1105
1106		#ifdef IS_MPI
1107	<	strcpy( checkPointMsg, "ForceField creation successful" );
1107	>	strcpy(checkPointMsg, "ForceField creation successful");
1108		MPIcheckPoint();
1109		#endif // is_mpi
1081	–
1110		}
1111
1112
1113	<	void SimSetup::compList( void ){
1086	<
1113	>	void SimSetup::compList(void){
1114		int i;
1115	+	char* id;
1116	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1117	+	LinkedMolStamp* currentStamp = NULL;
1118	+	comp_stamps = new MoleculeStamp * [n_components];
1119
1089	–	comp_stamps = new MoleculeStamp*[n_components];
1090	–
1120		// make an array of molecule stamps that match the components used.
1121		// also extract the used stamps out into a separate linked list
1122
1123	<	info->nComponents = n_components;
1124	<	info->componentsNmol = components_nmol;
1125	<	info->compStamps = comp_stamps;
1126	<	info->headStamp = new LinkedMolStamp();
1127	<
1128	<	char* id;
1100	<	LinkedMolStamp* headStamp = info->headStamp;
1101	<	LinkedMolStamp* currentStamp = NULL;
1102	<	for( i=0; i<n_components; i++ ){
1123	>	for (i = 0; i < nInfo; i++){
1124	>	info[i].nComponents = n_components;
1125	>	info[i].componentsNmol = components_nmol;
1126	>	info[i].compStamps = comp_stamps;
1127	>	info[i].headStamp = headStamp;
1128	>	}
1129
1130	+
1131	+	for (i = 0; i < n_components; i++){
1132		id = the_components[i]->getType();
1133		comp_stamps[i] = NULL;
1134	<
1134	>
1135		// check to make sure the component isn't already in the list
1136
1137	<	comp_stamps[i] = headStamp->match( id );
1138	<	if( comp_stamps[i] == NULL ){
1111	<
1137	>	comp_stamps[i] = headStamp->match(id);
1138	>	if (comp_stamps[i] == NULL){
1139		// extract the component from the list;
1140	<
1141	<	currentStamp = stamps->extractMolStamp( id );
1142	<	if( currentStamp == NULL ){
1143	<	sprintf( painCave.errMsg,
1144	<	"SimSetup error: Component \"%s\" was not found in the "
1145	<	"list of declared molecules\n",
1146	<	id );
1147	<	painCave.isFatal = 1;
1148	<	simError();
1140	>
1141	>	currentStamp = stamps->extractMolStamp(id);
1142	>	if (currentStamp == NULL){
1143	>	sprintf(painCave.errMsg,
1144	>	"SimSetup error: Component \"%s\" was not found in the "
1145	>	"list of declared molecules\n",
1146	>	id);
1147	>	painCave.isFatal = 1;
1148	>	simError();
1149		}
1150	<
1151	<	headStamp->add( currentStamp );
1152	<	comp_stamps[i] = headStamp->match( id );
1150	>
1151	>	headStamp->add(currentStamp);
1152	>	comp_stamps[i] = headStamp->match(id);
1153		}
1154		}
1155
1156		#ifdef IS_MPI
1157	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1157	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1158		MPIcheckPoint();
1159		#endif // is_mpi
1133	–
1134	–
1160		}
1161
1162	<	void SimSetup::calcSysValues( void ){
1162	>	void SimSetup::calcSysValues(void){
1163		int i, j, k;
1164
1165	+	int* molMembershipArray;
1166
1167		tot_atoms = 0;
1168		tot_bonds = 0;
1169		tot_bends = 0;
1170		tot_torsions = 0;
1171	<	for( i=0; i<n_components; i++ ){
1172	<
1173	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1174	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1149	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1171	>	for (i = 0; i < n_components; i++){
1172	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1173	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1174	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1175		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1176		}
1177
1178		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1179	+	molMembershipArray = new int[tot_atoms];
1180
1181	<	info->n_atoms = tot_atoms;
1182	<	info->n_bonds = tot_bonds;
1183	<	info->n_bends = tot_bends;
1184	<	info->n_torsions = tot_torsions;
1185	<	info->n_SRI = tot_SRI;
1186	<	info->n_mol = tot_nmol;
1187	<
1188	<	info->molMembershipArray = new int[tot_atoms];
1181	>	for (i = 0; i < nInfo; i++){
1182	>	info[i].n_atoms = tot_atoms;
1183	>	info[i].n_bonds = tot_bonds;
1184	>	info[i].n_bends = tot_bends;
1185	>	info[i].n_torsions = tot_torsions;
1186	>	info[i].n_SRI = tot_SRI;
1187	>	info[i].n_mol = tot_nmol;
1188	>
1189	>	info[i].molMembershipArray = molMembershipArray;
1190	>	}
1191		}
1192
1165	–
1193		#ifdef IS_MPI
1194
1195	<	void SimSetup::mpiMolDivide( void ){
1169	<
1195	>	void SimSetup::mpiMolDivide(void){
1196		int i, j, k;
1197		int localMol, allMol;
1198		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1199
1200	<	mpiSim = new mpiSimulation( info );
1201	<
1200	>	mpiSim = new mpiSimulation(info);
1201	>
1202		globalIndex = mpiSim->divideLabor();
1203
1204		// set up the local variables
1205	<
1205	>
1206		mol2proc = mpiSim->getMolToProcMap();
1207		molCompType = mpiSim->getMolComponentType();
1208	<
1208	>
1209		allMol = 0;
1210		localMol = 0;
1211		local_atoms = 0;
#	Line 1189 | Line 1215 | void SimSetup::mpiMolDivide( void ){
1215		globalAtomIndex = 0;
1216
1217
1218	<	for( i=0; i<n_components; i++ ){
1219	<
1220	<	for( j=0; j<components_nmol[i]; j++ ){
1221	<
1222	<	if( mol2proc[allMol] == worldRank ){
1223	<
1224	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1225	<	local_bonds +=    comp_stamps[i]->getNBonds();
1200	<	local_bends +=    comp_stamps[i]->getNBends();
1201	<	local_torsions += comp_stamps[i]->getNTorsions();
1202	<	localMol++;
1218	>	for (i = 0; i < n_components; i++){
1219	>	for (j = 0; j < components_nmol[i]; j++){
1220	>	if (mol2proc[allMol] == worldRank){
1221	>	local_atoms += comp_stamps[i]->getNAtoms();
1222	>	local_bonds += comp_stamps[i]->getNBonds();
1223	>	local_bends += comp_stamps[i]->getNBends();
1224	>	local_torsions += comp_stamps[i]->getNTorsions();
1225	>	localMol++;
1226		}
1227	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1228	<	info->molMembershipArray[globalAtomIndex] = allMol;
1227	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1228	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1229		globalAtomIndex++;
1230		}
1231
1232	<	allMol++;
1232	>	allMol++;
1233		}
1234		}
1235		local_SRI = local_bonds + local_bends + local_torsions;
1236	<
1237	<	info->n_atoms = mpiSim->getMyNlocal();
1238	<
1239	<	if( local_atoms != info->n_atoms ){
1240	<	sprintf( painCave.errMsg,
1241	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1242	<	" localAtom (%d) are not equal.\n",
1243	<	info->n_atoms,
1221	<	local_atoms );
1236	>
1237	>	info[0].n_atoms = mpiSim->getMyNlocal();
1238	>
1239	>	if (local_atoms != info[0].n_atoms){
1240	>	sprintf(painCave.errMsg,
1241	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1242	>	" localAtom (%d) are not equal.\n",
1243	>	info[0].n_atoms, local_atoms);
1244		painCave.isFatal = 1;
1245		simError();
1246		}
1247
1248	<	info->n_bonds = local_bonds;
1249	<	info->n_bends = local_bends;
1250	<	info->n_torsions = local_torsions;
1251	<	info->n_SRI = local_SRI;
1252	<	info->n_mol = localMol;
1248	>	info[0].n_bonds = local_bonds;
1249	>	info[0].n_bends = local_bends;
1250	>	info[0].n_torsions = local_torsions;
1251	>	info[0].n_SRI = local_SRI;
1252	>	info[0].n_mol = localMol;
1253
1254	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1254	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1255		MPIcheckPoint();
1256		}
1257	<
1257	>
1258		#endif // is_mpi
1259
1260
1261	<	void SimSetup::makeSysArrays( void ){
1262	<	int i, j, k;
1261	>	void SimSetup::makeSysArrays(void){
1262	>	int i, j, k, l;
1263
1264	<
1265	<	// create the atom and short range interaction arrays
1264	>	Atom** the_atoms;
1265	>	Molecule* the_molecules;
1266	>	Exclude** the_excludes;
1267
1245	–	Atom::createArrays(info->n_atoms);
1246	–	the_atoms = new Atom*[info->n_atoms];
1247	–	the_molecules = new Molecule[info->n_mol];
1248	–	int molIndex;
1268
1269	<	// initialize the molecule's stampID's
1269	>	for (l = 0; l < nInfo; l++){
1270	>	// create the atom and short range interaction arrays
1271
1272	+	the_atoms = new Atom * [info[l].n_atoms];
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;
1345	>	NVT<RealIntegrator>* myNVT = NULL;
1346		NPTi<RealIntegrator>* myNPTi = NULL;
1347		NPTf<RealIntegrator>* myNPTf = NULL;
1348		NPTim<RealIntegrator>* myNPTim = NULL;
1349		NPTfm<RealIntegrator>* myNPTfm = NULL;
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;
1350
1351	<	switch( ensembleCase ){
1351	>	for (k = 0; k < nInfo; k++){
1352	>	switch (ensembleCase){
1353	>	case NVE_ENS:
1354	>	if (globals->haveZconstraints()){
1355	>	setupZConstraint(info[k]);
1356	>	new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1357	>	}
1358	>	else
1359	>	new NVE<RealIntegrator>(&(info[k]), the_ff);
1360	>	break;
1361
1362	<	case NVE_ENS:
1363	<	new NVE<RealIntegrator>( info, the_ff );
1364	<	break;
1362	>	case NVT_ENS:
1363	>	if (globals->haveZconstraints()){
1364	>	setupZConstraint(info[k]);
1365	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1366	>	}
1367	>	else
1368	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1369
1370	<	case NVT_ENS:
1340	<	myNVT = new NVT<RealIntegrator>( info, the_ff );
1341	<	myNVT->setTargetTemp(globals->getTargetTemp());
1370	>	myNVT->setTargetTemp(globals->getTargetTemp());
1371
1372	<	if (globals->haveTauThermostat())
1373	<	myNVT->setTauThermostat(globals->getTauThermostat());
1372	>	if (globals->haveTauThermostat())
1373	>	myNVT->setTauThermostat(globals->getTauThermostat());
1374	>	else{
1375	>	sprintf(painCave.errMsg,
1376	>	"SimSetup error: If you use the NVT\n"
1377	>	"    ensemble, you must set tauThermostat.\n");
1378	>	painCave.isFatal = 1;
1379	>	simError();
1380	>	}
1381	>	break;
1382
1383	<	else {
1384	<	sprintf( painCave.errMsg,
1385	<	"SimSetup error: If you use the NVT\n"
1386	<	"    ensemble, you must set tauThermostat.\n");
1387	<	painCave.isFatal = 1;
1388	<	simError();
1389	<	}
1353	<	break;
1383	>	case NPTi_ENS:
1384	>	if (globals->haveZconstraints()){
1385	>	setupZConstraint(info[k]);
1386	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >(&(info[k]), the_ff);
1387	>	}
1388	>	else
1389	>	myNPTi = new NPTi<RealIntegrator>(&(info[k]), the_ff);
1390
1391	<	case NPTi_ENS:
1356	<	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1357	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1391	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1392
1393	<	if (globals->haveTargetPressure())
1394	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1395	<	else {
1396	<	sprintf( painCave.errMsg,
1397	<	"SimSetup error: If you use a constant pressure\n"
1398	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1399	<	painCave.isFatal = 1;
1400	<	simError();
1401	<	}
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	<	}
1393	>	if (globals->haveTargetPressure())
1394	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1395	>	else{
1396	>	sprintf(painCave.errMsg,
1397	>	"SimSetup error: If you use a constant pressure\n"
1398	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1399	>	painCave.isFatal = 1;
1400	>	simError();
1401	>	}
1402
1403	<	if( globals->haveTauBarostat() )
1404	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1405	<	else{
1406	<	sprintf( painCave.errMsg,
1407	<	"SimSetup error: If you use an NPT\n"
1408	<	"    ensemble, you must set tauBarostat.\n");
1409	<	painCave.isFatal = 1;
1410	<	simError();
1411	<	}
1388	<	break;
1403	>	if (globals->haveTauThermostat())
1404	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1405	>	else{
1406	>	sprintf(painCave.errMsg,
1407	>	"SimSetup error: If you use an NPT\n"
1408	>	"    ensemble, you must set tauThermostat.\n");
1409	>	painCave.isFatal = 1;
1410	>	simError();
1411	>	}
1412
1413	<	case NPTf_ENS:
1414	<	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1415	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1413	>	if (globals->haveTauBarostat())
1414	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1415	>	else{
1416	>	sprintf(painCave.errMsg,
1417	>	"SimSetup error: If you use an NPT\n"
1418	>	"    ensemble, you must set tauBarostat.\n");
1419	>	painCave.isFatal = 1;
1420	>	simError();
1421	>	}
1422	>	break;
1423
1424	<	if (globals->haveTargetPressure())
1425	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1426	<	else {
1427	<	sprintf( painCave.errMsg,
1428	<	"SimSetup error: If you use a constant pressure\n"
1429	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1430	<	painCave.isFatal = 1;
1401	<	simError();
1402	<	}
1424	>	case NPTf_ENS:
1425	>	if (globals->haveZconstraints()){
1426	>	setupZConstraint(info[k]);
1427	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff);
1428	>	}
1429	>	else
1430	>	myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff);
1431
1432	<	if( globals->haveTauThermostat() )
1405	<	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	<	}
1432	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1433
1434	<	if( globals->haveTauBarostat() )
1435	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1436	<	else{
1437	<	sprintf( painCave.errMsg,
1438	<	"SimSetup error: If you use an NPT\n"
1439	<	"    ensemble, you must set tauBarostat.\n");
1440	<	painCave.isFatal = 1;
1441	<	simError();
1442	<	}
1423	<	break;
1424	<
1425	<	case NPTim_ENS:
1426	<	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1427	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1434	>	if (globals->haveTargetPressure())
1435	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1436	>	else{
1437	>	sprintf(painCave.errMsg,
1438	>	"SimSetup error: If you use a constant pressure\n"
1439	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1440	>	painCave.isFatal = 1;
1441	>	simError();
1442	>	}
1443
1444	<	if (globals->haveTargetPressure())
1445	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1446	<	else {
1447	<	sprintf( painCave.errMsg,
1448	<	"SimSetup error: If you use a constant pressure\n"
1449	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1450	<	painCave.isFatal = 1;
1451	<	simError();
1452	<	}
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	<	}
1444	>	if (globals->haveTauThermostat())
1445	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1446	>	else{
1447	>	sprintf(painCave.errMsg,
1448	>	"SimSetup error: If you use an NPT\n"
1449	>	"    ensemble, you must set tauThermostat.\n");
1450	>	painCave.isFatal = 1;
1451	>	simError();
1452	>	}
1453
1454	<	if( globals->haveTauBarostat() )
1455	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1456	<	else{
1457	<	sprintf( painCave.errMsg,
1458	<	"SimSetup error: If you use an NPT\n"
1459	<	"    ensemble, you must set tauBarostat.\n");
1460	<	painCave.isFatal = 1;
1461	<	simError();
1462	<	}
1463	<	break;
1454	>	if (globals->haveTauBarostat())
1455	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1456	>	else{
1457	>	sprintf(painCave.errMsg,
1458	>	"SimSetup error: If you use an NPT\n"
1459	>	"    ensemble, you must set tauBarostat.\n");
1460	>	painCave.isFatal = 1;
1461	>	simError();
1462	>	}
1463	>	break;
1464
1465	<	case NPTfm_ENS:
1466	<	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1467	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1465	>	case NPTim_ENS:
1466	>	if (globals->haveZconstraints()){
1467	>	setupZConstraint(info[k]);
1468	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >(&(info[k]), the_ff);
1469	>	}
1470	>	else
1471	>	myNPTim = new NPTim<RealIntegrator>(&(info[k]), the_ff);
1472
1473	<	if (globals->haveTargetPressure())
1465	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1466	<	else {
1467	<	sprintf( painCave.errMsg,
1468	<	"SimSetup error: If you use a constant pressure\n"
1469	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1470	<	painCave.isFatal = 1;
1471	<	simError();
1472	<	}
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	<	}
1473	>	myNPTim->setTargetTemp(globals->getTargetTemp());
1474
1475	<	if( globals->haveTauBarostat() )
1476	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1477	<	else{
1478	<	sprintf( painCave.errMsg,
1479	<	"SimSetup error: If you use an NPT\n"
1480	<	"    ensemble, you must set tauBarostat.\n");
1481	<	painCave.isFatal = 1;
1482	<	simError();
1483	<	}
1493	<	break;
1494	<
1495	<	case NVEZCONS_ENS:
1475	>	if (globals->haveTargetPressure())
1476	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1477	>	else{
1478	>	sprintf(painCave.errMsg,
1479	>	"SimSetup error: If you use a constant pressure\n"
1480	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1481	>	painCave.isFatal = 1;
1482	>	simError();
1483	>	}
1484
1485	+	if (globals->haveTauThermostat())
1486	+	myNPTim->setTauThermostat(globals->getTauThermostat());
1487	+	else{
1488	+	sprintf(painCave.errMsg,
1489	+	"SimSetup error: If you use an NPT\n"
1490	+	"    ensemble, you must set tauThermostat.\n");
1491	+	painCave.isFatal = 1;
1492	+	simError();
1493	+	}
1494
1495	<	//setup index of z-constraint molecules, z-constraint sampel time
1496	<	//and z-constraint force output name. These parameter should be known
1497	<	//before constructing the z-constraint integrator
1498	<	setupZConstraint();
1499	<
1500	<	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff );
1501	<
1502	<	break;
1503	<
1504	<
1508	<	case NVTZCONS_ENS:
1509	<
1510	<	setupZConstraint();
1511	<
1512	<	myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( info, the_ff );
1513	<	myNVTZCons->setTargetTemp(globals->getTargetTemp());
1495	>	if (globals->haveTauBarostat())
1496	>	myNPTim->setTauBarostat(globals->getTauBarostat());
1497	>	else{
1498	>	sprintf(painCave.errMsg,
1499	>	"SimSetup error: If you use an NPT\n"
1500	>	"    ensemble, you must set tauBarostat.\n");
1501	>	painCave.isFatal = 1;
1502	>	simError();
1503	>	}
1504	>	break;
1505
1506	<	if (globals->haveTauThermostat())
1507	<	myNVTZCons->setTauThermostat(globals->getTauThermostat());
1506	>	case NPTfm_ENS:
1507	>	if (globals->haveZconstraints()){
1508	>	setupZConstraint(info[k]);
1509	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff);
1510	>	}
1511	>	else
1512	>	myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff);
1513
1514	<	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() );
1514	>	myNPTfm->setTargetTemp(globals->getTargetTemp());
1515
1516	<	if (globals->haveTargetPressure())
1517	<	myNPTiZCons->setTargetPressure(globals->getTargetPressure());
1518	<	else {
1519	<	sprintf( painCave.errMsg,
1520	<	"SimSetup error: If you use a constant pressure\n"
1521	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1522	<	painCave.isFatal = 1;
1523	<	simError();
1524	<	}
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();
1552	<	}
1516	>	if (globals->haveTargetPressure())
1517	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1518	>	else{
1519	>	sprintf(painCave.errMsg,
1520	>	"SimSetup error: If you use a constant pressure\n"
1521	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1522	>	painCave.isFatal = 1;
1523	>	simError();
1524	>	}
1525
1526	<	if( globals->haveTauBarostat() )
1527	<	myNPTiZCons->setTauBarostat( globals->getTauBarostat() );
1528	<	else{
1529	<	sprintf( painCave.errMsg,
1530	<	"SimSetup error: If you use an NPT\n"
1531	<	"    ensemble, you must set tauBarostat.\n");
1532	<	painCave.isFatal = 1;
1533	<	simError();
1534	<	}
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());
1526	>	if (globals->haveTauThermostat())
1527	>	myNPTfm->setTauThermostat(globals->getTauThermostat());
1528	>	else{
1529	>	sprintf(painCave.errMsg,
1530	>	"SimSetup error: If you use an NPT\n"
1531	>	"    ensemble, you must set tauThermostat.\n");
1532	>	painCave.isFatal = 1;
1533	>	simError();
1534	>	}
1535
1536	<	if (globals->haveTargetPressure())
1537	<	myNPTfZCons->setTargetPressure(globals->getTargetPressure());
1538	<	else {
1539	<	sprintf( painCave.errMsg,
1540	<	"SimSetup error: If you use a constant pressure\n"
1541	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1542	<	painCave.isFatal = 1;
1543	<	simError();
1544	<	}
1536	>	if (globals->haveTauBarostat())
1537	>	myNPTfm->setTauBarostat(globals->getTauBarostat());
1538	>	else{
1539	>	sprintf(painCave.errMsg,
1540	>	"SimSetup error: If you use an NPT\n"
1541	>	"    ensemble, you must set tauBarostat.\n");
1542	>	painCave.isFatal = 1;
1543	>	simError();
1544	>	}
1545	>	break;
1546
1547	<	if( globals->haveTauThermostat() )
1548	<	myNPTfZCons->setTauThermostat( globals->getTauThermostat() );
1549	<	else{
1550	<	sprintf( painCave.errMsg,
1551	<	"SimSetup error: If you use an NPT\n"
1588	<	"    ensemble, you must set tauThermostat.\n");
1589	<	painCave.isFatal = 1;
1590	<	simError();
1547	>	default:
1548	>	sprintf(painCave.errMsg,
1549	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1550	>	painCave.isFatal = 1;
1551	>	simError();
1552		}
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();
1553		}
1690	–
1554		}
1555
1556	<	void SimSetup::initFortran( void ){
1556	>	void SimSetup::initFortran(void){
1557	>	info[0].refreshSim();
1558
1559	<	info->refreshSim();
1560	<
1697	<	if( !strcmp( info->mixingRule, "standard") ){
1698	<	the_ff->initForceField( LB_MIXING_RULE );
1559	>	if (!strcmp(info[0].mixingRule, "standard")){
1560	>	the_ff->initForceField(LB_MIXING_RULE);
1561		}
1562	<	else if( !strcmp( info->mixingRule, "explicit") ){
1563	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1562	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1563	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1564		}
1565		else{
1566	<	sprintf( painCave.errMsg,
1567	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1706	<	info->mixingRule );
1566	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1567	>	info[0].mixingRule);
1568		painCave.isFatal = 1;
1569		simError();
1570		}
1571
1572
1573		#ifdef IS_MPI
1574	<	strcpy( checkPointMsg,
1714	<	"Successfully intialized the mixingRule for Fortran." );
1574	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1575		MPIcheckPoint();
1576		#endif // is_mpi
1717	–
1577		}
1578
1579	<	void SimSetup::setupZConstraint()
1580	<	{
1581	<	if(globals->haveZConsTime()){
1582	<
1583	<	//add sample time of z-constraint  into SimInfo's property list
1584	<	DoubleData* zconsTimeProp = new DoubleData();
1585	<	zconsTimeProp->setID("zconstime");
1586	<	zconsTimeProp->setData(globals->getZConsTime());
1587	<	info->addProperty(zconsTimeProp);
1579	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1580	>	int nZConstraints;
1581	>	ZconStamp** zconStamp;
1582	>
1583	>	if (globals->haveZconstraintTime()){
1584	>	//add sample time of z-constraint  into SimInfo's property list
1585	>	DoubleData* zconsTimeProp = new DoubleData();
1586	>	zconsTimeProp->setID(ZCONSTIME_ID);
1587	>	zconsTimeProp->setData(globals->getZconsTime());
1588	>	theInfo.addProperty(zconsTimeProp);
1589		}
1590		else{
1591	<	sprintf( painCave.errMsg,
1592	<	"ZConstraint error: If you use an ZConstraint\n"
1593	<	" , you must set sample time.\n");
1591	>	sprintf(painCave.errMsg,
1592	>	"ZConstraint error: If you use an ZConstraint\n"
1593	>	" , you must set sample time.\n");
1594		painCave.isFatal = 1;
1595	+	simError();
1596	+	}
1597	+
1598	+	//push zconsTol into siminfo, if user does not specify
1599	+	//value for zconsTol, a default value will be used
1600	+	DoubleData* zconsTol = new DoubleData();
1601	+	zconsTol->setID(ZCONSTOL_ID);
1602	+	if (globals->haveZconsTol()){
1603	+	zconsTol->setData(globals->getZconsTol());
1604	+	}
1605	+	else{
1606	+	double defaultZConsTol = 0.01;
1607	+	sprintf(painCave.errMsg,
1608	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1609	+	" , default value %f is used.\n",
1610	+	defaultZConsTol);
1611	+	painCave.isFatal = 0;
1612		simError();
1613	+
1614	+	zconsTol->setData(defaultZConsTol);
1615		}
1616	<
1617	<	if(globals->haveIndexOfAllZConsMols()){
1618	<
1619	<	//add index of z-constraint molecules into SimInfo's property list
1620	<	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1621	<
1622	<	//sort the index
1623	<	sort(tempIndex.begin(), tempIndex.end());
1745	<
1746	<	IndexData* zconsIndex = new IndexData();
1747	<	zconsIndex->setID("zconsindex");
1748	<	zconsIndex->setIndexData(tempIndex);
1749	<	info->addProperty(zconsIndex);
1616	>	theInfo.addProperty(zconsTol);
1617	>
1618	>	//set Force Subtraction Policy
1619	>	StringData* zconsForcePolicy = new StringData();
1620	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1621	>
1622	>	if (globals->haveZconsForcePolicy()){
1623	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1624		}
1625		else{
1626	<	sprintf( painCave.errMsg,
1627	<	"SimSetup error: If you use an ZConstraint\n"
1628	<	" , you must set index of z-constraint molecules.\n");
1629	<	painCave.isFatal = 1;
1630	<	simError();
1631	<
1626	>	sprintf(painCave.errMsg,
1627	>	"ZConstraint Warning: User does not set force Subtraction policy, "
1628	>	"PolicyByMass is used\n");
1629	>	painCave.isFatal = 0;
1630	>	simError();
1631	>	zconsForcePolicy->setData("BYMASS");
1632		}
1633
1634	+	theInfo.addProperty(zconsForcePolicy);
1635	+
1636		//Determine the name of ouput file and add it into SimInfo's property list
1637		//Be careful, do not use inFileName, since it is a pointer which
1638		//point to a string at master node, and slave nodes do not contain that string
1639	<
1640	<	string zconsOutput(info->finalName);
1641	<
1639	>
1640	>	string zconsOutput(theInfo.finalName);
1641	>
1642		zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1643	<
1643	>
1644		StringData* zconsFilename = new StringData();
1645	<	zconsFilename->setID("zconsfilename");
1645	>	zconsFilename->setID(ZCONSFILENAME_ID);
1646		zconsFilename->setData(zconsOutput);
1647
1648	<	info->addProperty(zconsFilename);
1648	>	theInfo.addProperty(zconsFilename);
1649
1650	+	//setup index, pos and other parameters of z-constraint molecules
1651	+	nZConstraints = globals->getNzConstraints();
1652	+	theInfo.nZconstraints = nZConstraints;
1653	+
1654	+	zconStamp = globals->getZconStamp();
1655	+	ZConsParaItem tempParaItem;
1656	+
1657	+	ZConsParaData* zconsParaData = new ZConsParaData();
1658	+	zconsParaData->setID(ZCONSPARADATA_ID);
1659	+
1660	+	for (int i = 0; i < nZConstraints; i++){
1661	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1662	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1663	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1664	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1665	+
1666	+	zconsParaData->addItem(tempParaItem);
1667	+	}
1668	+
1669	+	//check the uniqueness of index
1670	+	if(!zconsParaData->isIndexUnique()){
1671	+	sprintf(painCave.errMsg,
1672	+	"ZConstraint Error: molIndex is not unique\n");
1673	+	painCave.isFatal = 1;
1674	+	simError();
1675	+	}
1676	+
1677	+	//sort the parameters by index of molecules
1678	+	zconsParaData->sortByIndex();
1679	+
1680	+	//push data into siminfo, therefore, we can retrieve later
1681	+	theInfo.addProperty(zconsParaData);
1682		}

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