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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 661 by tim, Fri Aug 1 16:18:13 2003 UTC vs.
Revision 859 by mmeineke, Mon Nov 10 21:50:36 2003 UTC

#	Line 1 | Line 1
1		#include <algorithm>
2	<	#include <cstdlib>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
4	>	#include <math.h>
5		#include <string>
6	<
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 20 | Line 21
21		#define NVT_ENS        1
22		#define NPTi_ENS       2
23		#define NPTf_ENS       3
24	<	#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
24	>	#define NPTxyz_ENS     4
25
26	+
27		#define FF_DUFF 0
28		#define FF_LJ   1
29		#define FF_EAM  2
#	Line 37 | Line 32 | SimSetup::SimSetup(){
32
33		SimSetup::SimSetup(){
34
35	+	initSuspend = false;
36		isInfoArray = 0;
37		nInfo = 1;
38	<
38	>
39		stamps = new MakeStamps();
40		globals = new Globals();
41	<
42	<
41	>
42	>
43		#ifdef IS_MPI
44	<	strcpy( checkPointMsg, "SimSetup creation successful" );
44	>	strcpy(checkPointMsg, "SimSetup creation successful");
45		MPIcheckPoint();
46		#endif // IS_MPI
47		}
#	Line 55 | Line 51 | void SimSetup::setSimInfo( SimInfo* the_info, int theN
51		delete globals;
52		}
53
54	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
55	<	info = the_info;
56	<	nInfo = theNinfo;
57	<	isInfoArray = 1;
58	<	}
54	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
55	>	info = the_info;
56	>	nInfo = theNinfo;
57	>	isInfoArray = 1;
58	>	initSuspend = true;
59	>	}
60
61
62	<	void SimSetup::parseFile( char* fileName ){
66	<
62	>	void SimSetup::parseFile(char* fileName){
63		#ifdef IS_MPI
64	<	if( worldRank == 0 ){
64	>	if (worldRank == 0){
65		#endif // is_mpi
66	<
66	>
67		inFileName = fileName;
68	<	set_interface_stamps( stamps, globals );
69	<
68	>	set_interface_stamps(stamps, globals);
69	>
70		#ifdef IS_MPI
71		mpiEventInit();
72		#endif
73
74	<	yacc_BASS( fileName );
74	>	yacc_BASS(fileName);
75
76		#ifdef IS_MPI
77		throwMPIEvent(NULL);
78		}
79	<	else receiveParse();
79	>	else{
80	>	receiveParse();
81	>	}
82		#endif
83
84		}
85
86		#ifdef IS_MPI
87		void SimSetup::receiveParse(void){
88	<
89	<	set_interface_stamps( stamps, globals );
90	<	mpiEventInit();
91	<	MPIcheckPoint();
94	<	mpiEventLoop();
95	<
88	>	set_interface_stamps(stamps, globals);
89	>	mpiEventInit();
90	>	MPIcheckPoint();
91	>	mpiEventLoop();
92		}
93
94		#endif // is_mpi
95
96	<	void SimSetup::createSim( void ){
96	>	void SimSetup::createSim(void){
97
102	–	int i, j, k, globalAtomIndex;
103	–
98		// gather all of the information from the Bass file
99	<
99	>
100		gatherInfo();
101
102		// creation of complex system objects
#	Line 110 | Line 104 | void SimSetup::createSim( void ){
104		sysObjectsCreation();
105
106		// check on the post processing info
107	<
107	>
108		finalInfoCheck();
109
110		// initialize the system coordinates
111
112	<	initSystemCoords();
113	<
112	>	if ( !initSuspend ){
113	>	initSystemCoords();
114
115	+	if( !(globals->getUseInitTime()) )
116	+	info[0].currentTime = 0.0;
117	+	}
118	+
119		// make the output filenames
120
121		makeOutNames();
122	<
122	>
123		// make the integrator
124	<
124	>
125		makeIntegrator();
126	<
126	>
127		#ifdef IS_MPI
128		mpiSim->mpiRefresh();
129		#endif
#	Line 133 | Line 131 | void SimSetup::createSim( void ){
131		// initialize the Fortran
132
133		initFortran();
136	–
137	–
138	–
134		}
135
136
137	<	void SimSetup::makeMolecules( void ){
138	<
137	>	void SimSetup::makeMolecules(void){
138	>	int k;
139		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140		molInit molInfo;
141		DirectionalAtom* dAtom;
#	Line 155 | Line 150 | void SimSetup::makeMolecules( void ){
150		bend_set* theBends;
151		torsion_set* theTorsions;
152
153	<
153	>
154		//init the forceField paramters
155
156		the_ff->readParams();
157
158	<
158	>
159		// init the atoms
160
161		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();
162
163	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
164	<	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;
163	>	for (k = 0; k < nInfo; k++){
164	>	the_ff->setSimInfo(&(info[k]));
165
166	<	molInfo.myAtoms = &the_atoms[atomOffset];
167	<	molInfo.myExcludes = &the_excludes[excludeOffset];
168	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
169	<	molInfo.myBends = new Bend*[molInfo.nBends];
184	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
166	>	atomOffset = 0;
167	>	excludeOffset = 0;
168	>	for (i = 0; i < info[k].n_mol; i++){
169	>	stampID = info[k].molecules[i].getStampID();
170
171	<	theBonds = new bond_pair[molInfo.nBonds];
172	<	theBends = new bend_set[molInfo.nBends];
173	<	theTorsions = new torsion_set[molInfo.nTorsions];
174	<
175	<	// make the Atoms
176	<
177	<	for(j=0; j<molInfo.nAtoms; j++){
178	<
179	<	currentAtom = comp_stamps[stampID]->getAtom( j );
180	<	if( currentAtom->haveOrientation() ){
181	<
182	<	dAtom = new DirectionalAtom(j + atomOffset);
183	<	info->n_oriented++;
184	<	molInfo.myAtoms[j] = dAtom;
185	<
186	<	ux = currentAtom->getOrntX();
187	<	uy = currentAtom->getOrntY();
188	<	uz = currentAtom->getOrntZ();
189	<
190	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
191	<
192	<	u = sqrt( uSqr );
193	<	ux = ux / u;
194	<	uy = uy / u;
195	<	uz = uz / u;
196	<
197	<	dAtom->setSUx( ux );
198	<	dAtom->setSUy( uy );
199	<	dAtom->setSUz( uz );
200	<	}
201	<	else{
202	<	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
203	<	}
204	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
205	<
171	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
172	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
173	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
174	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
175	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
176	>
177	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
178	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
179	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
180	>	molInfo.myBends = new Bend * [molInfo.nBends];
181	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
182	>
183	>	theBonds = new bond_pair[molInfo.nBonds];
184	>	theBends = new bend_set[molInfo.nBends];
185	>	theTorsions = new torsion_set[molInfo.nTorsions];
186	>
187	>	// make the Atoms
188	>
189	>	for (j = 0; j < molInfo.nAtoms; j++){
190	>	currentAtom = comp_stamps[stampID]->getAtom(j);
191	>	if (currentAtom->haveOrientation()){
192	>	dAtom = new DirectionalAtom((j + atomOffset),
193	>	info[k].getConfiguration());
194	>	info[k].n_oriented++;
195	>	molInfo.myAtoms[j] = dAtom;
196	>
197	>	ux = currentAtom->getOrntX();
198	>	uy = currentAtom->getOrntY();
199	>	uz = currentAtom->getOrntZ();
200	>
201	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
202	>
203	>	u = sqrt(uSqr);
204	>	ux = ux / u;
205	>	uy = uy / u;
206	>	uz = uz / u;
207	>
208	>	dAtom->setSUx(ux);
209	>	dAtom->setSUy(uy);
210	>	dAtom->setSUz(uz);
211	>	}
212	>	else{
213	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
214	>	info[k].getConfiguration());
215	>	}
216	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
217	>
218		#ifdef IS_MPI
219	<
220	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
221	<
219	>
220	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
221	>
222		#endif // is_mpi
223	<	}
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;
223	>	}
224
225	<	exI = theBonds[j].a;
226	<	exJ = theBonds[j].b;
225	>	// make the bonds
226	>	for (j = 0; j < molInfo.nBonds; j++){
227	>	currentBond = comp_stamps[stampID]->getBond(j);
228	>	theBonds[j].a = currentBond->getA() + atomOffset;
229	>	theBonds[j].b = currentBond->getB() + atomOffset;
230
231	<	// exclude_I must always be the smaller of the pair
232	<	if( exI > exJ ){
233	<	tempEx = exI;
234	<	exI = exJ;
235	<	exJ = tempEx;
236	<	}
231	>	exI = theBonds[j].a;
232	>	exJ = theBonds[j].b;
233	>
234	>	// exclude_I must always be the smaller of the pair
235	>	if (exI > exJ){
236	>	tempEx = exI;
237	>	exI = exJ;
238	>	exJ = tempEx;
239	>	}
240		#ifdef IS_MPI
241	<	tempEx = exI;
242	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
243	<	tempEx = exJ;
244	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
245	<
246	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
241	>	tempEx = exI;
242	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
243	>	tempEx = exJ;
244	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
245	>
246	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
247		#else  // isn't MPI
248
249	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
249	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
250		#endif  //is_mpi
251	<	}
252	<	excludeOffset += molInfo.nBonds;
251	>	}
252	>	excludeOffset += molInfo.nBonds;
253
254	<	//make the bends
255	<	for(j=0; j<molInfo.nBends; j++){
256	<
257	<	currentBend = comp_stamps[stampID]->getBend( j );
258	<	theBends[j].a = currentBend->getA() + atomOffset;
259	<	theBends[j].b = currentBend->getB() + atomOffset;
260	<	theBends[j].c = currentBend->getC() + atomOffset;
261	<
262	<	if( currentBend->haveExtras() ){
263	<
264	<	extras = currentBend->getExtras();
265	<	current_extra = extras;
266	<
267	<	while( current_extra != NULL ){
268	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
269	<
270	<	switch( current_extra->getType() ){
271	<
272	<	case 0:
273	<	theBends[j].ghost =
274	<	current_extra->getInt() + atomOffset;
275	<	theBends[j].isGhost = 1;
276	<	break;
277	<
278	<	case 1:
279	<	theBends[j].ghost =
280	<	(int)current_extra->getDouble() + atomOffset;
281	<	theBends[j].isGhost = 1;
282	<	break;
283	<
284	<	default:
285	<	sprintf( painCave.errMsg,
286	<	"SimSetup Error: ghostVectorSource was neither a "
287	<	"double nor an int.\n"
288	<	"-->Bend[%d] in %s\n",
289	<	j, comp_stamps[stampID]->getID() );
290	<	painCave.isFatal = 1;
291	<	simError();
292	<	}
293	<	}
294	<
295	<	else{
296	<
297	<	sprintf( painCave.errMsg,
298	<	"SimSetup Error: unhandled bend assignment:\n"
299	<	"    -->%s in Bend[%d] in %s\n",
300	<	current_extra->getlhs(),
301	<	j, comp_stamps[stampID]->getID() );
302	<	painCave.isFatal = 1;
303	<	simError();
304	<	}
305	<
306	<	current_extra = current_extra->getNext();
307	<	}
308	<	}
309	<
310	<	if( !theBends[j].isGhost ){
311	<
312	<	exI = theBends[j].a;
313	<	exJ = theBends[j].c;
314	<	}
315	<	else{
316	<
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	<	}
254	>	//make the bends
255	>	for (j = 0; j < molInfo.nBends; j++){
256	>	currentBend = comp_stamps[stampID]->getBend(j);
257	>	theBends[j].a = currentBend->getA() + atomOffset;
258	>	theBends[j].b = currentBend->getB() + atomOffset;
259	>	theBends[j].c = currentBend->getC() + atomOffset;
260	>
261	>	if (currentBend->haveExtras()){
262	>	extras = currentBend->getExtras();
263	>	current_extra = extras;
264	>
265	>	while (current_extra != NULL){
266	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
267	>	switch (current_extra->getType()){
268	>	case 0:
269	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
270	>	theBends[j].isGhost = 1;
271	>	break;
272	>
273	>	case 1:
274	>	theBends[j].ghost = (int) current_extra->getDouble() +
275	>	atomOffset;
276	>	theBends[j].isGhost = 1;
277	>	break;
278	>
279	>	default:
280	>	sprintf(painCave.errMsg,
281	>	"SimSetup Error: ghostVectorSource was neither a "
282	>	"double nor an int.\n"
283	>	"-->Bend[%d] in %s\n",
284	>	j, comp_stamps[stampID]->getID());
285	>	painCave.isFatal = 1;
286	>	simError();
287	>	}
288	>	}
289	>	else{
290	>	sprintf(painCave.errMsg,
291	>	"SimSetup Error: unhandled bend assignment:\n"
292	>	"    -->%s in Bend[%d] in %s\n",
293	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
294	>	painCave.isFatal = 1;
295	>	simError();
296	>	}
297	>
298	>	current_extra = current_extra->getNext();
299	>	}
300	>	}
301	>
302	>	if (!theBends[j].isGhost){
303	>	exI = theBends[j].a;
304	>	exJ = theBends[j].c;
305	>	}
306	>	else{
307	>	exI = theBends[j].a;
308	>	exJ = theBends[j].b;
309	>	}
310	>
311	>	// exclude_I must always be the smaller of the pair
312	>	if (exI > exJ){
313	>	tempEx = exI;
314	>	exI = exJ;
315	>	exJ = tempEx;
316	>	}
317		#ifdef IS_MPI
318	<	tempEx = exI;
319	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
320	<	tempEx = exJ;
321	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
322	<
323	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
318	>	tempEx = exI;
319	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
320	>	tempEx = exJ;
321	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
322	>
323	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
324		#else  // isn't MPI
325	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
325	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
326		#endif  //is_mpi
327	<	}
328	<	excludeOffset += molInfo.nBends;
327	>	}
328	>	excludeOffset += molInfo.nBends;
329
330	<	for(j=0; j<molInfo.nTorsions; j++){
331	<
332	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
333	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
334	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
335	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
350	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
351	<
352	<	exI = theTorsions[j].a;
353	<	exJ = theTorsions[j].d;
330	>	for (j = 0; j < molInfo.nTorsions; j++){
331	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
332	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
333	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
334	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
335	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
336
337	<	// exclude_I must always be the smaller of the pair
338	<	if( exI > exJ ){
339	<	tempEx = exI;
340	<	exI = exJ;
341	<	exJ = tempEx;
342	<	}
337	>	exI = theTorsions[j].a;
338	>	exJ = theTorsions[j].d;
339	>
340	>	// exclude_I must always be the smaller of the pair
341	>	if (exI > exJ){
342	>	tempEx = exI;
343	>	exI = exJ;
344	>	exJ = tempEx;
345	>	}
346		#ifdef IS_MPI
347	<	tempEx = exI;
348	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
349	<	tempEx = exJ;
350	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
351	<
352	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
347	>	tempEx = exI;
348	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
349	>	tempEx = exJ;
350	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
351	>
352	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
353		#else  // isn't MPI
354	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
354	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
355		#endif  //is_mpi
356	<	}
357	<	excludeOffset += molInfo.nTorsions;
356	>	}
357	>	excludeOffset += molInfo.nTorsions;
358
374	–
375	–	// send the arrays off to the forceField for init.
359
360	<	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 );
360	>	// send the arrays off to the forceField for init.
361
362	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
363	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
364	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
365	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
366	+	theTorsions);
367
383	–	the_molecules[i].initialize( molInfo );
368
369	+	info[k].molecules[i].initialize(molInfo);
370
371	<	atomOffset += molInfo.nAtoms;
372	<	delete[] theBonds;
373	<	delete[] theBends;
374	<	delete[] theTorsions;
371	>
372	>	atomOffset += molInfo.nAtoms;
373	>	delete[] theBonds;
374	>	delete[] theBends;
375	>	delete[] theTorsions;
376	>	}
377		}
378
379		#ifdef IS_MPI
380	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
380	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
381		MPIcheckPoint();
382		#endif // is_mpi
383
384		// clean up the forcefield
385	+
386		the_ff->calcRcut();
387		the_ff->cleanMe();
400	–
388		}
389
390	<	void SimSetup::initFromBass( void ){
404	<
390	>	void SimSetup::initFromBass(void){
391		int i, j, k;
392		int n_cells;
393		double cellx, celly, cellz;
#	Line 410 | Line 396 | void SimSetup::initFromBass( void ){
396		int n_extra;
397		int have_extra, done;
398
399	<	temp1 = (double)tot_nmol / 4.0;
400	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
401	<	temp3 = ceil( temp2 );
399	>	double vel[3];
400	>	vel[0] = 0.0;
401	>	vel[1] = 0.0;
402	>	vel[2] = 0.0;
403
404	<	have_extra =0;
405	<	if( temp2 < temp3 ){ // we have a non-complete lattice
406	<	have_extra =1;
404	>	temp1 = (double) tot_nmol / 4.0;
405	>	temp2 = pow(temp1, (1.0 / 3.0));
406	>	temp3 = ceil(temp2);
407
408	<	n_cells = (int)temp3 - 1;
409	<	cellx = info->boxL[0] / temp3;
410	<	celly = info->boxL[1] / temp3;
411	<	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 );
408	>	have_extra = 0;
409	>	if (temp2 < temp3){
410	>	// we have a non-complete lattice
411	>	have_extra = 1;
412
413	<	if( n_per_extra > 4){
414	<	sprintf( painCave.errMsg,
415	<	"SimSetup error. There has been an error in constructing"
416	<	" the non-complete lattice.\n" );
413	>	n_cells = (int) temp3 - 1;
414	>	cellx = info[0].boxL[0] / temp3;
415	>	celly = info[0].boxL[1] / temp3;
416	>	cellz = info[0].boxL[2] / temp3;
417	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
418	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
419	>	n_per_extra = (int) ceil(temp1);
420	>
421	>	if (n_per_extra > 4){
422	>	sprintf(painCave.errMsg,
423	>	"SimSetup error. There has been an error in constructing"
424	>	" the non-complete lattice.\n");
425		painCave.isFatal = 1;
426		simError();
427		}
428		}
429		else{
430	<	n_cells = (int)temp3;
431	<	cellx = info->boxL[0] / temp3;
432	<	celly = info->boxL[1] / temp3;
433	<	cellz = info->boxL[2] / temp3;
430	>	n_cells = (int) temp3;
431	>	cellx = info[0].boxL[0] / temp3;
432	>	celly = info[0].boxL[1] / temp3;
433	>	cellz = info[0].boxL[2] / temp3;
434		}
435
436		current_mol = 0;
#	Line 446 | Line 438 | void SimSetup::initFromBass( void ){
438		current_comp = 0;
439		current_atom_ndx = 0;
440
441	<	for( i=0; i < n_cells ; i++ ){
442	<	for( j=0; j < n_cells; j++ ){
443	<	for( k=0; k < n_cells; k++ ){
441	>	for (i = 0; i < n_cells ; i++){
442	>	for (j = 0; j < n_cells; j++){
443	>	for (k = 0; k < n_cells; k++){
444	>	makeElement(i * cellx, j * celly, k * cellz);
445
446	<	makeElement( i * cellx,
454	<	j * celly,
455	<	k * cellz );
446	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
447
448	<	makeElement( i * cellx + 0.5 * cellx,
458	<	j * celly + 0.5 * celly,
459	<	k * cellz );
448	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
449
450	<	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 );
450	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
451		}
452		}
453		}
454
455	<	if( have_extra ){
455	>	if (have_extra){
456		done = 0;
457
458		int start_ndx;
459	<	for( i=0; i < (n_cells+1) && !done; i++ ){
460	<	for( j=0; j < (n_cells+1) && !done; j++ ){
459	>	for (i = 0; i < (n_cells + 1) && !done; i++){
460	>	for (j = 0; j < (n_cells + 1) && !done; j++){
461	>	if (i < n_cells){
462	>	if (j < n_cells){
463	>	start_ndx = n_cells;
464	>	}
465	>	else
466	>	start_ndx = 0;
467	>	}
468	>	else
469	>	start_ndx = 0;
470
471	<	if( i < n_cells ){
471	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
472	>	makeElement(i * cellx, j * celly, k * cellz);
473	>	done = (current_mol >= tot_nmol);
474
475	<	if( j < n_cells ){
476	<	start_ndx = n_cells;
477	<	}
478	<	else start_ndx = 0;
479	<	}
486	<	else start_ndx = 0;
475	>	if (!done && n_per_extra > 1){
476	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
477	>	k * cellz);
478	>	done = (current_mol >= tot_nmol);
479	>	}
480
481	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
481	>	if (!done && n_per_extra > 2){
482	>	makeElement(i * cellx, j * celly + 0.5 * celly,
483	>	k * cellz + 0.5 * cellz);
484	>	done = (current_mol >= tot_nmol);
485	>	}
486
487	<	makeElement( i * cellx,
488	<	j * celly,
489	<	k * cellz );
490	<	done = ( current_mol >= tot_nmol );
491	<
492	<	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	<	}
487	>	if (!done && n_per_extra > 3){
488	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
489	>	k * cellz + 0.5 * cellz);
490	>	done = (current_mol >= tot_nmol);
491	>	}
492	>	}
493		}
494		}
495		}
496
497	<
498	<	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 );
497	>	for (i = 0; i < info[0].n_atoms; i++){
498	>	info[0].atoms[i]->setVel(vel);
499		}
500		}
501
502	<	void SimSetup::makeElement( double x, double y, double z ){
529	<
502	>	void SimSetup::makeElement(double x, double y, double z){
503		int k;
504		AtomStamp* current_atom;
505		DirectionalAtom* dAtom;
506		double rotMat[3][3];
507	+	double pos[3];
508
509	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
510	<
511	<	current_atom = comp_stamps[current_comp]->getAtom( k );
512	<	if( !current_atom->havePosition() ){
513	<	sprintf( painCave.errMsg,
514	<	"SimSetup:initFromBass error.\n"
515	<	"\tComponent %s, atom %s does not have a position specified.\n"
516	<	"\tThe initialization routine is unable to give a start"
517	<	" position.\n",
544	<	comp_stamps[current_comp]->getID(),
545	<	current_atom->getType() );
509	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
510	>	current_atom = comp_stamps[current_comp]->getAtom(k);
511	>	if (!current_atom->havePosition()){
512	>	sprintf(painCave.errMsg,
513	>	"SimSetup:initFromBass error.\n"
514	>	"\tComponent %s, atom %s does not have a position specified.\n"
515	>	"\tThe initialization routine is unable to give a start"
516	>	" position.\n",
517	>	comp_stamps[current_comp]->getID(), current_atom->getType());
518		painCave.isFatal = 1;
519		simError();
520		}
521
522	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
523	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
524	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
522	>	pos[0] = x + current_atom->getPosX();
523	>	pos[1] = y + current_atom->getPosY();
524	>	pos[2] = z + current_atom->getPosZ();
525
526	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
526	>	info[0].atoms[current_atom_ndx]->setPos(pos);
527
528	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
528	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
529	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
530
531		rotMat[0][0] = 1.0;
532		rotMat[0][1] = 0.0;
#	Line 567 | Line 540 | void SimSetup::makeElement( double x, double y, double
540		rotMat[2][1] = 0.0;
541		rotMat[2][2] = 1.0;
542
543	<	dAtom->setA( rotMat );
543	>	dAtom->setA(rotMat);
544		}
545
546		current_atom_ndx++;
#	Line 576 | Line 549 | void SimSetup::makeElement( double x, double y, double
549		current_mol++;
550		current_comp_mol++;
551
552	<	if( current_comp_mol >= components_nmol[current_comp] ){
580	<
552	>	if (current_comp_mol >= components_nmol[current_comp]){
553		current_comp_mol = 0;
554		current_comp++;
555		}
556		}
557
558
559	<	void SimSetup::gatherInfo( void ){
560	<	int i,j,k;
559	>	void SimSetup::gatherInfo(void){
560	>	int i;
561
562		ensembleCase = -1;
563		ffCase = -1;
564
593	–	// get the stamps and globals;
594	–	stamps = stamps;
595	–	globals = globals;
596	–
565		// set the easy ones first
566	<	info->target_temp = globals->getTargetTemp();
567	<	info->dt = globals->getDt();
568	<	info->run_time = globals->getRunTime();
566	>
567	>	for (i = 0; i < nInfo; i++){
568	>	info[i].target_temp = globals->getTargetTemp();
569	>	info[i].dt = globals->getDt();
570	>	info[i].run_time = globals->getRunTime();
571	>	}
572		n_components = globals->getNComponents();
573
574
575		// get the forceField
576
577	<	strcpy( force_field, globals->getForceField() );
577	>	strcpy(force_field, globals->getForceField());
578
579	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
580	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
581	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
579	>	if (!strcasecmp(force_field, "DUFF")){
580	>	ffCase = FF_DUFF;
581	>	}
582	>	else if (!strcasecmp(force_field, "LJ")){
583	>	ffCase = FF_LJ;
584	>	}
585	>	else if (!strcasecmp(force_field, "EAM")){
586	>	ffCase = FF_EAM;
587	>	}
588		else{
589	<	sprintf( painCave.errMsg,
590	<	"SimSetup Error. Unrecognized force field -> %s\n",
591	<	force_field );
592	<	painCave.isFatal = 1;
616	<	simError();
589	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
590	>	force_field);
591	>	painCave.isFatal = 1;
592	>	simError();
593		}
594
595	<	// get the ensemble
595	>	// get the ensemble
596
597	<	strcpy( ensemble, globals->getEnsemble() );
597	>	strcpy(ensemble, globals->getEnsemble());
598
599	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
600	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
601	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
599	>	if (!strcasecmp(ensemble, "NVE")){
600	>	ensembleCase = NVE_ENS;
601	>	}
602	>	else if (!strcasecmp(ensemble, "NVT")){
603	>	ensembleCase = NVT_ENS;
604	>	}
605	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
606		ensembleCase = NPTi_ENS;
607	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
608	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
609	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
610	<
611	<	else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS;
612	<	else if( !strcasecmp( ensemble, "NVTZCONS"))  ensembleCase = NVTZCONS_ENS;
613	<	else if( !strcasecmp( ensemble, "NPTiZCONS") || !strcasecmp( ensemble, "NPTZCONS"))
634	<	ensembleCase = NPTiZCONS_ENS;
635	<	else if( !strcasecmp( ensemble, "NPTfZCONS"))  ensembleCase = NPTfZCONS_ENS;
636	<	else if( !strcasecmp( ensemble, "NPTimZCONS"))  ensembleCase = NPTimZCONS_ENS;
637	<	else if( !strcasecmp( ensemble, "NPTfmZCONS"))  ensembleCase = NPTfmZCONS_ENS;
638	<
607	>	}
608	>	else if (!strcasecmp(ensemble, "NPTf")){
609	>	ensembleCase = NPTf_ENS;
610	>	}
611	>	else if (!strcasecmp(ensemble, "NPTxyz")){
612	>	ensembleCase = NPTxyz_ENS;
613	>	}
614		else{
615	<	sprintf( painCave.errMsg,
616	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
617	<	"reverting to NVE for this simulation.\n",
618	<	ensemble );
619	<	painCave.isFatal = 0;
620	<	simError();
621	<	strcpy( ensemble, "NVE" );
622	<	ensembleCase = NVE_ENS;
615	>	sprintf(painCave.errMsg,
616	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
617	>	"reverting to NVE for this simulation.\n",
618	>	ensemble);
619	>	painCave.isFatal = 0;
620	>	simError();
621	>	strcpy(ensemble, "NVE");
622	>	ensembleCase = NVE_ENS;
623		}
649	–	strcpy( info->ensemble, ensemble );
624
625	<	// get the mixing rule
625	>	for (i = 0; i < nInfo; i++){
626	>	strcpy(info[i].ensemble, ensemble);
627
628	<	strcpy( info->mixingRule, globals->getMixingRule() );
629	<	info->usePBC = globals->getPBC();
630	<
631	<
628	>	// get the mixing rule
629	>
630	>	strcpy(info[i].mixingRule, globals->getMixingRule());
631	>	info[i].usePBC = globals->getPBC();
632	>	}
633	>
634		// get the components and calculate the tot_nMol and indvidual n_mol
635	<
635	>
636		the_components = globals->getComponents();
637		components_nmol = new int[n_components];
638
639
640	<	if( !globals->haveNMol() ){
640	>	if (!globals->haveNMol()){
641		// we don't have the total number of molecules, so we assume it is
642		// given in each component
643
644		tot_nmol = 0;
645	<	for( i=0; i<n_components; i++ ){
646	<
647	<	if( !the_components[i]->haveNMol() ){
648	<	// we have a problem
649	<	sprintf( painCave.errMsg,
650	<	"SimSetup Error. No global NMol or component NMol"
651	<	" given. Cannot calculate the number of atoms.\n" );
652	<	painCave.isFatal = 1;
676	<	simError();
645	>	for (i = 0; i < n_components; i++){
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;
652	>	simError();
653		}
654
655		tot_nmol += the_components[i]->getNMol();
#	Line 681 | Line 657 | void SimSetup::gatherInfo( void ){
657		}
658		}
659		else{
660	<	sprintf( painCave.errMsg,
661	<	"SimSetup error.\n"
662	<	"\tSorry, the ability to specify total"
663	<	" nMols and then give molfractions in the components\n"
664	<	"\tis not currently supported."
665	<	" Please give nMol in the components.\n" );
660	>	sprintf(painCave.errMsg,
661	>	"SimSetup error.\n"
662	>	"\tSorry, the ability to specify total"
663	>	" nMols and then give molfractions in the components\n"
664	>	"\tis not currently supported."
665	>	" Please give nMol in the components.\n");
666		painCave.isFatal = 1;
667		simError();
668		}
669
670		// set the status, sample, and thermal kick times
695	–
696	–	if( globals->haveSampleTime() ){
697	–	info->sampleTime = globals->getSampleTime();
698	–	info->statusTime = info->sampleTime;
699	–	info->thermalTime = info->sampleTime;
700	–	}
701	–	else{
702	–	info->sampleTime = globals->getRunTime();
703	–	info->statusTime = info->sampleTime;
704	–	info->thermalTime = info->sampleTime;
705	–	}
671
672	<	if( globals->haveStatusTime() ){
673	<	info->statusTime = globals->getStatusTime();
674	<	}
672	>	for (i = 0; i < nInfo; i++){
673	>	if (globals->haveSampleTime()){
674	>	info[i].sampleTime = globals->getSampleTime();
675	>	info[i].statusTime = info[i].sampleTime;
676	>	info[i].thermalTime = info[i].sampleTime;
677	>	}
678	>	else{
679	>	info[i].sampleTime = globals->getRunTime();
680	>	info[i].statusTime = info[i].sampleTime;
681	>	info[i].thermalTime = info[i].sampleTime;
682	>	}
683
684	<	if( globals->haveThermalTime() ){
685	<	info->thermalTime = globals->getThermalTime();
686	<	}
684	>	if (globals->haveStatusTime()){
685	>	info[i].statusTime = globals->getStatusTime();
686	>	}
687
688	<	// check for the temperature set flag
688	>	if (globals->haveThermalTime()){
689	>	info[i].thermalTime = globals->getThermalTime();
690	>	}
691
692	<	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
692	>	info[i].resetIntegrator = 0;
693	>	if( globals->haveResetTime() ){
694	>	info[i].resetTime = globals->getResetTime();
695	>	info[i].resetIntegrator = 1;
696	>	}
697
698	<	// get some of the tricky things that may still be in the globals
698	>	// check for the temperature set flag
699	>
700	>	if (globals->haveTempSet())
701	>	info[i].setTemp = globals->getTempSet();
702
703	<	double boxVector[3];
704	<	if( globals->haveBox() ){
705	<	boxVector[0] = globals->getBox();
706	<	boxVector[1] = globals->getBox();
725	<	boxVector[2] = globals->getBox();
703	>	// check for the extended State init
704	>
705	>	info[i].useInitXSstate = globals->getUseInitXSstate();
706	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
707
727	–	info->setBox( boxVector );
708		}
709	<	else if( globals->haveDensity() ){
709	>
710	>	//setup seed for random number generator
711	>	int seedValue;
712
713	<	double vol;
714	<	vol = (double)tot_nmol / globals->getDensity();
733	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
734	<	boxVector[1] = boxVector[0];
735	<	boxVector[2] = boxVector[0];
713	>	if (globals->haveSeed()){
714	>	seedValue = globals->getSeed();
715
716	<	info->setBox( boxVector );
717	<	}
718	<	else{
719	<	if( !globals->haveBoxX() ){
720	<	sprintf( painCave.errMsg,
742	<	"SimSetup error, no periodic BoxX size given.\n" );
743	<	painCave.isFatal = 1;
716	>	if(seedValue / 1E9 == 0){
717	>	sprintf(painCave.errMsg,
718	>	"Seed for sprng library should contain at least 9 digits\n"
719	>	"OOPSE will generate a seed for user\n");
720	>	painCave.isFatal = 0;
721		simError();
745	–	}
746	–	boxVector[0] = globals->getBoxX();
722
723	<	if( !globals->haveBoxY() ){
724	<	sprintf( painCave.errMsg,
725	<	"SimSetup error, no periodic BoxY size given.\n" );
726	<	painCave.isFatal = 1;
727	<	simError();
723	>	//using seed generated by system instead of invalid seed set by user
724	>	#ifndef IS_MPI
725	>	seedValue = make_sprng_seed();
726	>	#else
727	>	if (worldRank == 0){
728	>	seedValue = make_sprng_seed();
729	>	}
730	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
731	>	#endif
732		}
733	<	boxVector[1] = globals->getBoxY();
734	<
735	<	if( !globals->haveBoxZ() ){
736	<	sprintf( painCave.errMsg,
737	<	"SimSetup error, no periodic BoxZ size given.\n" );
738	<	painCave.isFatal = 1;
739	<	simError();
733	>	}//end of if branch of globals->haveSeed()
734	>	else{
735	>
736	>	#ifndef IS_MPI
737	>	seedValue = make_sprng_seed();
738	>	#else
739	>	if (worldRank == 0){
740	>	seedValue = make_sprng_seed();
741		}
742	<	boxVector[2] = globals->getBoxZ();
742	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
743	>	#endif
744	>	}//end of globals->haveSeed()
745
746	<	info->setBox( boxVector );
746	>	for (int i = 0; i < nInfo; i++){
747	>	info[i].setSeed(seedValue);
748		}
749
767	–
768	–
750		#ifdef IS_MPI
751	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
751	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
752		MPIcheckPoint();
753		#endif // is_mpi
773	–
754		}
755
756
757	<	void SimSetup::finalInfoCheck( void ){
757	>	void SimSetup::finalInfoCheck(void){
758		int index;
759		int usesDipoles;
760	<
760	>	int i;
761
762	<	// check electrostatic parameters
763	<
764	<	index = 0;
765	<	usesDipoles = 0;
766	<	while( (index < info->n_atoms) && !usesDipoles ){
767	<	usesDipoles = ((info->atoms)[index])->hasDipole();
768	<	index++;
769	<	}
770	<
762	>	for (i = 0; i < nInfo; i++){
763	>	// check electrostatic parameters
764	>
765	>	index = 0;
766	>	usesDipoles = 0;
767	>	while ((index < info[i].n_atoms) && !usesDipoles){
768	>	usesDipoles = (info[i].atoms[index])->hasDipole();
769	>	index++;
770	>	}
771	>
772		#ifdef IS_MPI
773	<	int myUse = usesDipoles;
774	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
773	>	int myUse = usesDipoles;
774	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
775		#endif //is_mpi
776
777	<	double theEcr, theEst;
777	>	double theEcr, theEst;
778
779	<	if (globals->getUseRF() ) {
780	<	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	<	}
779	>	if (globals->getUseRF()){
780	>	info[i].useReactionField = 1;
781
782	<	if( !globals->haveEST() ){
783	<	sprintf( painCave.errMsg,
784	<	"SimSetup Warning: using default value of 0.05 * the "
785	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
786	<	);
787	<	painCave.isFatal = 0;
788	<	simError();
789	<	theEst = 0.05 * theEcr;
790	<	} else {
791	<	theEst= globals->getEST();
792	<	}
782	>	if (!globals->haveECR()){
783	>	sprintf(painCave.errMsg,
784	>	"SimSetup Warning: using default value of 15.0 angstroms"
785	>	"box length for the electrostaticCutoffRadius.\n");
786	>	painCave.isFatal = 0;
787	>	simError();
788	>	theEcr = 15.0;
789	>	}
790	>	else{
791	>	theEcr = globals->getECR();
792	>	}
793
794	<	info->setEcr( theEcr, theEst );
795	<
796	<	if(!globals->haveDielectric() ){
797	<	sprintf( painCave.errMsg,
798	<	"SimSetup Error: You are trying to use Reaction Field without"
799	<	"setting a dielectric constant!\n"
800	<	);
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();
794	>	if (!globals->haveEST()){
795	>	sprintf(painCave.errMsg,
796	>	"SimSetup Warning: using default value of 0.05 * the "
797	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
798	>	painCave.isFatal = 0;
799	>	simError();
800	>	theEst = 0.05 * theEcr;
801		}
802	<
803	<	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();
802	>	else{
803	>	theEst = globals->getEST();
804		}
805
806	<	info->setEcr( theEcr, theEst );
874	<	}
875	<	}
806	>	info[i].setDefaultEcr(theEcr, theEst);
807
808	+	if (!globals->haveDielectric()){
809	+	sprintf(painCave.errMsg,
810	+	"SimSetup Error: You are trying to use Reaction Field without"
811	+	"setting a dielectric constant!\n");
812	+	painCave.isFatal = 1;
813	+	simError();
814	+	}
815	+	info[i].dielectric = globals->getDielectric();
816	+	}
817	+	else{
818	+	if (usesDipoles){
819	+	if (!globals->haveECR()){
820	+	sprintf(painCave.errMsg,
821	+	"SimSetup Warning: using default value of 15.0 angstroms"
822	+	"box length for the electrostaticCutoffRadius.\n");
823	+	painCave.isFatal = 0;
824	+	simError();
825	+	theEcr = 15.0;
826	+	}
827	+	else{
828	+	theEcr = globals->getECR();
829	+	}
830	+
831	+	if (!globals->haveEST()){
832	+	sprintf(painCave.errMsg,
833	+	"SimSetup Warning: using default value of 0.05 * the "
834	+	"electrostaticCutoffRadius for the "
835	+	"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].setDefaultEcr(theEcr, theEst);
845	+	}
846	+	}
847	+	}
848		#ifdef IS_MPI
849	<	strcpy( checkPointMsg, "post processing checks out" );
849	>	strcpy(checkPointMsg, "post processing checks out");
850		MPIcheckPoint();
851		#endif // is_mpi
881	–
852		}
853	+
854	+	void SimSetup::initSystemCoords(void){
855	+	int i;
856
857	<	void SimSetup::initSystemCoords( void ){
857	>	char* inName;
858
859	<	if( globals->haveInitialConfig() ){
860	<
861	<	InitializeFromFile* fileInit;
859	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
860	>
861	>	for (i = 0; i < info[0].n_atoms; i++)
862	>	info[0].atoms[i]->setCoords();
863	>
864	>	if (globals->haveInitialConfig()){
865	>	InitializeFromFile* fileInit;
866		#ifdef IS_MPI // is_mpi
867	<	if( worldRank == 0 ){
867	>	if (worldRank == 0){
868		#endif //is_mpi
869	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
869	>	inName = globals->getInitialConfig();
870	>	fileInit = new InitializeFromFile(inName);
871		#ifdef IS_MPI
872	<	}else fileInit = new InitializeFromFile( NULL );
872	>	}
873	>	else
874	>	fileInit = new InitializeFromFile(NULL);
875		#endif
876	<	fileInit->readInit( info ); // default velocities on
876	>	fileInit->readInit(info); // default velocities on
877
878	<	delete fileInit;
879	<	}
880	<	else{
878	>	delete fileInit;
879	>	}
880	>	else{
881	>
882	>	// no init from bass
883	>
884	>	sprintf(painCave.errMsg,
885	>	"Cannot intialize a simulation without an initial configuration file.\n");
886	>	painCave.isFatal = 1;;
887	>	simError();
888	>
889	>	}
890
902	–	#ifdef IS_MPI
903	–
904	–	// no init from bass
905	–
906	–	sprintf( painCave.errMsg,
907	–	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
908	–	painCave.isFatal;
909	–	simError();
910	–
911	–	#else
912	–
913	–	initFromBass();
914	–
915	–
916	–	#endif
917	–	}
918	–
891		#ifdef IS_MPI
892	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
892	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
893		MPIcheckPoint();
894		#endif // is_mpi
923	–
895		}
896
897
898	<	void SimSetup::makeOutNames( void ){
898	>	void SimSetup::makeOutNames(void){
899	>	int k;
900
901	+
902	+	for (k = 0; k < nInfo; k++){
903		#ifdef IS_MPI
904	<	if( worldRank == 0 ){
904	>	if (worldRank == 0){
905		#endif // is_mpi
906	<
907	<	if( globals->haveFinalConfig() ){
908	<	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" );
906	>
907	>	if (globals->haveFinalConfig()){
908	>	strcpy(info[k].finalName, globals->getFinalConfig());
909		}
944	–	else if( !strcmp( endTest, ".BASS" ) ){
945	–	strcpy( endTest, ".eor" );
946	–	}
910		else{
911	<	endTest = &(info->finalName[nameLength - 4]);
912	<	if( !strcmp( endTest, ".bss" ) ){
913	<	strcpy( endTest, ".eor" );
914	<	}
915	<	else if( !strcmp( endTest, ".mdl" ) ){
916	<	strcpy( endTest, ".eor" );
917	<	}
918	<	else{
919	<	strcat( info->finalName, ".eor" );
920	<	}
921	<	}
922	<	}
923	<
924	<	// make the sample and status out names
925	<
926	<	strcpy( info->sampleName, inFileName );
927	<	char* endTest;
928	<	int nameLength = strlen( info->sampleName );
929	<	endTest = &(info->sampleName[nameLength - 5]);
930	<	if( !strcmp( endTest, ".bass" ) ){
931	<	strcpy( endTest, ".dump" );
932	<	}
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" );
911	>	strcpy(info[k].finalName, inFileName);
912	>	char* endTest;
913	>	int nameLength = strlen(info[k].finalName);
914	>	endTest = &(info[k].finalName[nameLength - 5]);
915	>	if (!strcmp(endTest, ".bass")){
916	>	strcpy(endTest, ".eor");
917	>	}
918	>	else if (!strcmp(endTest, ".BASS")){
919	>	strcpy(endTest, ".eor");
920	>	}
921	>	else{
922	>	endTest = &(info[k].finalName[nameLength - 4]);
923	>	if (!strcmp(endTest, ".bss")){
924	>	strcpy(endTest, ".eor");
925	>	}
926	>	else if (!strcmp(endTest, ".mdl")){
927	>	strcpy(endTest, ".eor");
928	>	}
929	>	else{
930	>	strcat(info[k].finalName, ".eor");
931	>	}
932	>	}
933		}
934	<	else if( !strcmp( endTest, ".mdl" ) ){
935	<	strcpy( endTest, ".dump" );
934	>
935	>	// make the sample and status out names
936	>
937	>	strcpy(info[k].sampleName, inFileName);
938	>	char* endTest;
939	>	int nameLength = strlen(info[k].sampleName);
940	>	endTest = &(info[k].sampleName[nameLength - 5]);
941	>	if (!strcmp(endTest, ".bass")){
942	>	strcpy(endTest, ".dump");
943		}
944	+	else if (!strcmp(endTest, ".BASS")){
945	+	strcpy(endTest, ".dump");
946	+	}
947		else{
948	<	strcat( info->sampleName, ".dump" );
948	>	endTest = &(info[k].sampleName[nameLength - 4]);
949	>	if (!strcmp(endTest, ".bss")){
950	>	strcpy(endTest, ".dump");
951	>	}
952	>	else if (!strcmp(endTest, ".mdl")){
953	>	strcpy(endTest, ".dump");
954	>	}
955	>	else{
956	>	strcat(info[k].sampleName, ".dump");
957	>	}
958		}
959	<	}
960	<
961	<	strcpy( info->statusName, inFileName );
962	<	nameLength = strlen( info->statusName );
963	<	endTest = &(info->statusName[nameLength - 5]);
964	<	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" );
959	>
960	>	strcpy(info[k].statusName, inFileName);
961	>	nameLength = strlen(info[k].statusName);
962	>	endTest = &(info[k].statusName[nameLength - 5]);
963	>	if (!strcmp(endTest, ".bass")){
964	>	strcpy(endTest, ".stat");
965		}
966	<	else if( !strcmp( endTest, ".mdl" ) ){
967	<	strcpy( endTest, ".stat" );
966	>	else if (!strcmp(endTest, ".BASS")){
967	>	strcpy(endTest, ".stat");
968		}
969		else{
970	<	strcat( info->statusName, ".stat" );
970	>	endTest = &(info[k].statusName[nameLength - 4]);
971	>	if (!strcmp(endTest, ".bss")){
972	>	strcpy(endTest, ".stat");
973	>	}
974	>	else if (!strcmp(endTest, ".mdl")){
975	>	strcpy(endTest, ".stat");
976	>	}
977	>	else{
978	>	strcat(info[k].statusName, ".stat");
979	>	}
980		}
981	<	}
1007	<
981	>
982		#ifdef IS_MPI
1009	–	}
1010	–	#endif // is_mpi
983
984	+	}
985	+	#endif // is_mpi
986	+	}
987		}
988
989
990	<	void SimSetup::sysObjectsCreation( void ){
990	>	void SimSetup::sysObjectsCreation(void){
991	>	int i, k;
992
1017	–	int i;
1018	–
993		// create the forceField
994
995		createFF();
#	Line 1030 | Line 1004 | void SimSetup::sysObjectsCreation( void ){
1004
1005		#ifdef IS_MPI
1006		// divide the molecules among the processors
1007	<
1007	>
1008		mpiMolDivide();
1009		#endif //is_mpi
1010	<
1010	>
1011		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1012	<
1012	>
1013		makeSysArrays();
1014
1015		// make and initialize the molecules (all but atomic coordinates)
1016	<
1016	>
1017		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	–
1018
1019	<
1019	>	for (k = 0; k < nInfo; k++){
1020	>	info[k].identArray = new int[info[k].n_atoms];
1021	>	for (i = 0; i < info[k].n_atoms; i++){
1022	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1023	>	}
1024	>	}
1025		}
1026
1027
1028	<	void SimSetup::createFF( void ){
1028	>	void SimSetup::createFF(void){
1029	>	switch (ffCase){
1030	>	case FF_DUFF:
1031	>	the_ff = new DUFF();
1032	>	break;
1033
1034	<	switch( ffCase ){
1034	>	case FF_LJ:
1035	>	the_ff = new LJFF();
1036	>	break;
1037
1038	<	case FF_DUFF:
1039	<	the_ff = new DUFF();
1040	<	break;
1038	>	case FF_EAM:
1039	>	the_ff = new EAM_FF();
1040	>	break;
1041
1042	<	case FF_LJ:
1043	<	the_ff = new LJFF();
1044	<	break;
1045	<
1046	<	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();
1042	>	default:
1043	>	sprintf(painCave.errMsg,
1044	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1045	>	painCave.isFatal = 1;
1046	>	simError();
1047		}
1048
1049		#ifdef IS_MPI
1050	<	strcpy( checkPointMsg, "ForceField creation successful" );
1050	>	strcpy(checkPointMsg, "ForceField creation successful");
1051		MPIcheckPoint();
1052		#endif // is_mpi
1081	–
1053		}
1054
1055
1056	<	void SimSetup::compList( void ){
1086	<
1056	>	void SimSetup::compList(void){
1057		int i;
1058	+	char* id;
1059	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1060	+	LinkedMolStamp* currentStamp = NULL;
1061	+	comp_stamps = new MoleculeStamp * [n_components];
1062
1089	–	comp_stamps = new MoleculeStamp*[n_components];
1090	–
1063		// make an array of molecule stamps that match the components used.
1064		// also extract the used stamps out into a separate linked list
1065
1066	<	info->nComponents = n_components;
1067	<	info->componentsNmol = components_nmol;
1068	<	info->compStamps = comp_stamps;
1069	<	info->headStamp = new LinkedMolStamp();
1070	<
1071	<	char* id;
1100	<	LinkedMolStamp* headStamp = info->headStamp;
1101	<	LinkedMolStamp* currentStamp = NULL;
1102	<	for( i=0; i<n_components; i++ ){
1066	>	for (i = 0; i < nInfo; i++){
1067	>	info[i].nComponents = n_components;
1068	>	info[i].componentsNmol = components_nmol;
1069	>	info[i].compStamps = comp_stamps;
1070	>	info[i].headStamp = headStamp;
1071	>	}
1072
1073	+
1074	+	for (i = 0; i < n_components; i++){
1075		id = the_components[i]->getType();
1076		comp_stamps[i] = NULL;
1077	<
1077	>
1078		// check to make sure the component isn't already in the list
1079
1080	<	comp_stamps[i] = headStamp->match( id );
1081	<	if( comp_stamps[i] == NULL ){
1111	<
1080	>	comp_stamps[i] = headStamp->match(id);
1081	>	if (comp_stamps[i] == NULL){
1082		// extract the component from the list;
1083	<
1084	<	currentStamp = stamps->extractMolStamp( id );
1085	<	if( currentStamp == NULL ){
1086	<	sprintf( painCave.errMsg,
1087	<	"SimSetup error: Component \"%s\" was not found in the "
1088	<	"list of declared molecules\n",
1089	<	id );
1090	<	painCave.isFatal = 1;
1091	<	simError();
1083	>
1084	>	currentStamp = stamps->extractMolStamp(id);
1085	>	if (currentStamp == NULL){
1086	>	sprintf(painCave.errMsg,
1087	>	"SimSetup error: Component \"%s\" was not found in the "
1088	>	"list of declared molecules\n",
1089	>	id);
1090	>	painCave.isFatal = 1;
1091	>	simError();
1092		}
1093	<
1094	<	headStamp->add( currentStamp );
1095	<	comp_stamps[i] = headStamp->match( id );
1093	>
1094	>	headStamp->add(currentStamp);
1095	>	comp_stamps[i] = headStamp->match(id);
1096		}
1097		}
1098
1099		#ifdef IS_MPI
1100	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1100	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1101		MPIcheckPoint();
1102		#endif // is_mpi
1133	–
1134	–
1103		}
1104
1105	<	void SimSetup::calcSysValues( void ){
1106	<	int i, j, k;
1105	>	void SimSetup::calcSysValues(void){
1106	>	int i;
1107
1108	+	int* molMembershipArray;
1109
1110		tot_atoms = 0;
1111		tot_bonds = 0;
1112		tot_bends = 0;
1113		tot_torsions = 0;
1114	<	for( i=0; i<n_components; i++ ){
1115	<
1116	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1117	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1149	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1114	>	for (i = 0; i < n_components; i++){
1115	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1116	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1117	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1118		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1119		}
1120
1121		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1122	+	molMembershipArray = new int[tot_atoms];
1123
1124	<	info->n_atoms = tot_atoms;
1125	<	info->n_bonds = tot_bonds;
1126	<	info->n_bends = tot_bends;
1127	<	info->n_torsions = tot_torsions;
1128	<	info->n_SRI = tot_SRI;
1129	<	info->n_mol = tot_nmol;
1130	<
1131	<	info->molMembershipArray = new int[tot_atoms];
1124	>	for (i = 0; i < nInfo; i++){
1125	>	info[i].n_atoms = tot_atoms;
1126	>	info[i].n_bonds = tot_bonds;
1127	>	info[i].n_bends = tot_bends;
1128	>	info[i].n_torsions = tot_torsions;
1129	>	info[i].n_SRI = tot_SRI;
1130	>	info[i].n_mol = tot_nmol;
1131	>
1132	>	info[i].molMembershipArray = molMembershipArray;
1133	>	}
1134		}
1135
1165	–
1136		#ifdef IS_MPI
1137
1138	<	void SimSetup::mpiMolDivide( void ){
1169	<
1138	>	void SimSetup::mpiMolDivide(void){
1139		int i, j, k;
1140		int localMol, allMol;
1141		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1142
1143	<	mpiSim = new mpiSimulation( info );
1144	<
1143	>	mpiSim = new mpiSimulation(info);
1144	>
1145		globalIndex = mpiSim->divideLabor();
1146
1147		// set up the local variables
1148	<
1148	>
1149		mol2proc = mpiSim->getMolToProcMap();
1150		molCompType = mpiSim->getMolComponentType();
1151	<
1151	>
1152		allMol = 0;
1153		localMol = 0;
1154		local_atoms = 0;
#	Line 1189 | Line 1158 | void SimSetup::mpiMolDivide( void ){
1158		globalAtomIndex = 0;
1159
1160
1161	<	for( i=0; i<n_components; i++ ){
1162	<
1163	<	for( j=0; j<components_nmol[i]; j++ ){
1164	<
1165	<	if( mol2proc[allMol] == worldRank ){
1166	<
1167	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1168	<	local_bonds +=    comp_stamps[i]->getNBonds();
1200	<	local_bends +=    comp_stamps[i]->getNBends();
1201	<	local_torsions += comp_stamps[i]->getNTorsions();
1202	<	localMol++;
1161	>	for (i = 0; i < n_components; i++){
1162	>	for (j = 0; j < components_nmol[i]; j++){
1163	>	if (mol2proc[allMol] == worldRank){
1164	>	local_atoms += comp_stamps[i]->getNAtoms();
1165	>	local_bonds += comp_stamps[i]->getNBonds();
1166	>	local_bends += comp_stamps[i]->getNBends();
1167	>	local_torsions += comp_stamps[i]->getNTorsions();
1168	>	localMol++;
1169		}
1170	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1171	<	info->molMembershipArray[globalAtomIndex] = allMol;
1170	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1171	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1172		globalAtomIndex++;
1173		}
1174
1175	<	allMol++;
1175	>	allMol++;
1176		}
1177		}
1178		local_SRI = local_bonds + local_bends + local_torsions;
1179	<
1180	<	info->n_atoms = mpiSim->getMyNlocal();
1181	<
1182	<	if( local_atoms != info->n_atoms ){
1183	<	sprintf( painCave.errMsg,
1184	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1185	<	" localAtom (%d) are not equal.\n",
1186	<	info->n_atoms,
1221	<	local_atoms );
1179	>
1180	>	info[0].n_atoms = mpiSim->getMyNlocal();
1181	>
1182	>	if (local_atoms != info[0].n_atoms){
1183	>	sprintf(painCave.errMsg,
1184	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1185	>	" localAtom (%d) are not equal.\n",
1186	>	info[0].n_atoms, local_atoms);
1187		painCave.isFatal = 1;
1188		simError();
1189		}
1190
1191	<	info->n_bonds = local_bonds;
1192	<	info->n_bends = local_bends;
1193	<	info->n_torsions = local_torsions;
1194	<	info->n_SRI = local_SRI;
1195	<	info->n_mol = localMol;
1191	>	info[0].n_bonds = local_bonds;
1192	>	info[0].n_bends = local_bends;
1193	>	info[0].n_torsions = local_torsions;
1194	>	info[0].n_SRI = local_SRI;
1195	>	info[0].n_mol = localMol;
1196
1197	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1197	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1198		MPIcheckPoint();
1199		}
1200	<
1200	>
1201		#endif // is_mpi
1202
1203
1204	<	void SimSetup::makeSysArrays( void ){
1205	<	int i, j, k;
1204	>	void SimSetup::makeSysArrays(void){
1205	>
1206	>	#ifndef IS_MPI
1207	>	int k, j;
1208	>	#endif // is_mpi
1209	>	int i, l;
1210
1211	+	Atom** the_atoms;
1212	+	Molecule* the_molecules;
1213	+	Exclude** the_excludes;
1214
1243	–	// create the atom and short range interaction arrays
1215
1216	<	Atom::createArrays(info->n_atoms);
1217	<	the_atoms = new Atom*[info->n_atoms];
1247	<	the_molecules = new Molecule[info->n_mol];
1248	<	int molIndex;
1216	>	for (l = 0; l < nInfo; l++){
1217	>	// create the atom and short range interaction arrays
1218
1219	<	// initialize the molecule's stampID's
1219	>	the_atoms = new Atom * [info[l].n_atoms];
1220	>	the_molecules = new Molecule[info[l].n_mol];
1221	>	int molIndex;
1222
1223	+	// initialize the molecule's stampID's
1224	+
1225		#ifdef IS_MPI
1253	–
1226
1227	<	molIndex = 0;
1228	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1229	<
1230	<	if(mol2proc[i] == worldRank ){
1231	<	the_molecules[molIndex].setStampID( molCompType[i] );
1232	<	the_molecules[molIndex].setMyIndex( molIndex );
1233	<	the_molecules[molIndex].setGlobalIndex( i );
1234	<	molIndex++;
1227	>
1228	>	molIndex = 0;
1229	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1230	>	if (mol2proc[i] == worldRank){
1231	>	the_molecules[molIndex].setStampID(molCompType[i]);
1232	>	the_molecules[molIndex].setMyIndex(molIndex);
1233	>	the_molecules[molIndex].setGlobalIndex(i);
1234	>	molIndex++;
1235	>	}
1236		}
1264	–	}
1237
1238		#else // is_mpi
1239	<
1240	<	molIndex = 0;
1241	<	globalAtomIndex = 0;
1242	<	for(i=0; i<n_components; i++){
1243	<	for(j=0; j<components_nmol[i]; j++ ){
1244	<	the_molecules[molIndex].setStampID( i );
1245	<	the_molecules[molIndex].setMyIndex( molIndex );
1246	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1247	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1248	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1249	<	globalAtomIndex++;
1239	>
1240	>	molIndex = 0;
1241	>	globalAtomIndex = 0;
1242	>	for (i = 0; i < n_components; i++){
1243	>	for (j = 0; j < components_nmol[i]; j++){
1244	>	the_molecules[molIndex].setStampID(i);
1245	>	the_molecules[molIndex].setMyIndex(molIndex);
1246	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1247	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1248	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1249	>	globalAtomIndex++;
1250	>	}
1251	>	molIndex++;
1252		}
1279	–	molIndex++;
1253		}
1281	–	}
1282	–
1254
1255	+
1256		#endif // is_mpi
1257
1258
1259	<	if( info->n_SRI ){
1260	<
1261	<	Exclude::createArray(info->n_SRI);
1262	<	the_excludes = new Exclude*[info->n_SRI];
1263	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1264	<	info->globalExcludes = new int;
1265	<	info->n_exclude = info->n_SRI;
1266	<	}
1267	<	else{
1268	<
1269	<	Exclude::createArray( 1 );
1270	<	the_excludes = new Exclude*;
1271	<	the_excludes[0] = new Exclude(0);
1272	<	the_excludes[0]->setPair( 0,0 );
1273	<	info->globalExcludes = new int;
1274	<	info->globalExcludes[0] = 0;
1275	<	info->n_exclude = 0;
1276	<	}
1259	>	if (info[l].n_SRI){
1260	>	Exclude::createArray(info[l].n_SRI);
1261	>	the_excludes = new Exclude * [info[l].n_SRI];
1262	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1263	>	the_excludes[ex] = new Exclude(ex);
1264	>	}
1265	>	info[l].globalExcludes = new int;
1266	>	info[l].n_exclude = info[l].n_SRI;
1267	>	}
1268	>	else{
1269	>	Exclude::createArray(1);
1270	>	the_excludes = new Exclude * ;
1271	>	the_excludes[0] = new Exclude(0);
1272	>	the_excludes[0]->setPair(0, 0);
1273	>	info[l].globalExcludes = new int;
1274	>	info[l].globalExcludes[0] = 0;
1275	>	info[l].n_exclude = 0;
1276	>	}
1277
1278	<	// set the arrays into the SimInfo object
1278	>	// set the arrays into the SimInfo object
1279
1280	<	info->atoms = the_atoms;
1281	<	info->molecules = the_molecules;
1282	<	info->nGlobalExcludes = 0;
1283	<	info->excludes = the_excludes;
1280	>	info[l].atoms = the_atoms;
1281	>	info[l].molecules = the_molecules;
1282	>	info[l].nGlobalExcludes = 0;
1283	>	info[l].excludes = the_excludes;
1284
1285	<	the_ff->setSimInfo( info );
1286	<
1285	>	the_ff->setSimInfo(info);
1286	>	}
1287		}
1288
1289	<	void SimSetup::makeIntegrator( void ){
1289	>	void SimSetup::makeIntegrator(void){
1290	>	int k;
1291
1292	<	NVT<RealIntegrator>*  myNVT = NULL;
1293	<	NPTi<RealIntegrator>* myNPTi = NULL;
1294	<	NPTf<RealIntegrator>* myNPTf = NULL;
1295	<	NPTim<RealIntegrator>* myNPTim = NULL;
1296	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1297	<	ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL;
1298	<	ZConstraint<NVT<RealIntegrator> >* myNVTZCons = NULL;
1299	<	ZConstraint<NPTi<RealIntegrator> >* myNPTiZCons = NULL;
1300	<	ZConstraint<NPTf<RealIntegrator> >* myNPTfZCons = NULL;
1301	<	ZConstraint<NPTim<RealIntegrator> >* myNPTimZCons = NULL;
1302	<	ZConstraint<NPTfm<RealIntegrator> >* myNPTfmZCons = NULL;
1303	<
1304	<	switch( ensembleCase ){
1292	>	NVE<RealIntegrator>* myNVE = NULL;
1293	>	NVT<RealIntegrator>* myNVT = NULL;
1294	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1295	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1296	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1297	>
1298	>	for (k = 0; k < nInfo; k++){
1299	>	switch (ensembleCase){
1300	>	case NVE_ENS:
1301	>	if (globals->haveZconstraints()){
1302	>	setupZConstraint(info[k]);
1303	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1304	>	}
1305	>	else{
1306	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1307	>	}
1308	>
1309	>	info->the_integrator = myNVE;
1310	>	break;
1311
1312	<	case NVE_ENS:
1313	<	new NVE<RealIntegrator>( info, the_ff );
1314	<	break;
1315	<
1316	<	case NVT_ENS:
1317	<	myNVT = new NVT<RealIntegrator>( info, the_ff );
1318	<	myNVT->setTargetTemp(globals->getTargetTemp());
1312	>	case NVT_ENS:
1313	>	if (globals->haveZconstraints()){
1314	>	setupZConstraint(info[k]);
1315	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1316	>	}
1317	>	else
1318	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1319
1320	<	if (globals->haveTauThermostat())
1342	<	myNVT->setTauThermostat(globals->getTauThermostat());
1320	>	myNVT->setTargetTemp(globals->getTargetTemp());
1321
1322	<	else {
1323	<	sprintf( painCave.errMsg,
1324	<	"SimSetup error: If you use the NVT\n"
1325	<	"    ensemble, you must set tauThermostat.\n");
1326	<	painCave.isFatal = 1;
1327	<	simError();
1328	<	}
1329	<	break;
1322	>	if (globals->haveTauThermostat())
1323	>	myNVT->setTauThermostat(globals->getTauThermostat());
1324	>	else{
1325	>	sprintf(painCave.errMsg,
1326	>	"SimSetup error: If you use the NVT\n"
1327	>	"    ensemble, you must set tauThermostat.\n");
1328	>	painCave.isFatal = 1;
1329	>	simError();
1330	>	}
1331
1332	<	case NPTi_ENS:
1333	<	myNPTi = new NPTi<RealIntegrator>( info, the_ff );
1355	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1332	>	info->the_integrator = myNVT;
1333	>	break;
1334
1335	<	if (globals->haveTargetPressure())
1336	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1337	<	else {
1338	<	sprintf( painCave.errMsg,
1339	<	"SimSetup error: If you use a constant pressure\n"
1340	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1341	<	painCave.isFatal = 1;
1364	<	simError();
1365	<	}
1366	<
1367	<	if( globals->haveTauThermostat() )
1368	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1369	<	else{
1370	<	sprintf( painCave.errMsg,
1371	<	"SimSetup error: If you use an NPT\n"
1372	<	"    ensemble, you must set tauThermostat.\n");
1373	<	painCave.isFatal = 1;
1374	<	simError();
1375	<	}
1335	>	case NPTi_ENS:
1336	>	if (globals->haveZconstraints()){
1337	>	setupZConstraint(info[k]);
1338	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1339	>	}
1340	>	else
1341	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1342
1343	<	if( globals->haveTauBarostat() )
1378	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1379	<	else{
1380	<	sprintf( painCave.errMsg,
1381	<	"SimSetup error: If you use an NPT\n"
1382	<	"    ensemble, you must set tauBarostat.\n");
1383	<	painCave.isFatal = 1;
1384	<	simError();
1385	<	}
1386	<	break;
1343	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1344
1345	<	case NPTf_ENS:
1346	<	myNPTf = new NPTf<RealIntegrator>( info, the_ff );
1347	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1345	>	if (globals->haveTargetPressure())
1346	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1347	>	else{
1348	>	sprintf(painCave.errMsg,
1349	>	"SimSetup error: If you use a constant pressure\n"
1350	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1351	>	painCave.isFatal = 1;
1352	>	simError();
1353	>	}
1354
1355	<	if (globals->haveTargetPressure())
1356	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1357	<	else {
1358	<	sprintf( painCave.errMsg,
1359	<	"SimSetup error: If you use a constant pressure\n"
1360	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1361	<	painCave.isFatal = 1;
1362	<	simError();
1363	<	}
1355	>	if (globals->haveTauThermostat())
1356	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1357	>	else{
1358	>	sprintf(painCave.errMsg,
1359	>	"SimSetup error: If you use an NPT\n"
1360	>	"    ensemble, you must set tauThermostat.\n");
1361	>	painCave.isFatal = 1;
1362	>	simError();
1363	>	}
1364
1365	<	if( globals->haveTauThermostat() )
1366	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1367	<	else{
1368	<	sprintf( painCave.errMsg,
1369	<	"SimSetup error: If you use an NPT\n"
1370	<	"    ensemble, you must set tauThermostat.\n");
1371	<	painCave.isFatal = 1;
1372	<	simError();
1373	<	}
1365	>	if (globals->haveTauBarostat())
1366	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1367	>	else{
1368	>	sprintf(painCave.errMsg,
1369	>	"SimSetup error: If you use an NPT\n"
1370	>	"    ensemble, you must set tauBarostat.\n");
1371	>	painCave.isFatal = 1;
1372	>	simError();
1373	>	}
1374
1375	<	if( globals->haveTauBarostat() )
1376	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1414	<	else{
1415	<	sprintf( painCave.errMsg,
1416	<	"SimSetup error: If you use an NPT\n"
1417	<	"    ensemble, you must set tauBarostat.\n");
1418	<	painCave.isFatal = 1;
1419	<	simError();
1420	<	}
1421	<	break;
1422	<
1423	<	case NPTim_ENS:
1424	<	myNPTim = new NPTim<RealIntegrator>( info, the_ff );
1425	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1375	>	info->the_integrator = myNPTi;
1376	>	break;
1377
1378	<	if (globals->haveTargetPressure())
1379	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1380	<	else {
1381	<	sprintf( painCave.errMsg,
1382	<	"SimSetup error: If you use a constant pressure\n"
1383	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1384	<	painCave.isFatal = 1;
1434	<	simError();
1435	<	}
1436	<
1437	<	if( globals->haveTauThermostat() )
1438	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1439	<	else{
1440	<	sprintf( painCave.errMsg,
1441	<	"SimSetup error: If you use an NPT\n"
1442	<	"    ensemble, you must set tauThermostat.\n");
1443	<	painCave.isFatal = 1;
1444	<	simError();
1445	<	}
1378	>	case NPTf_ENS:
1379	>	if (globals->haveZconstraints()){
1380	>	setupZConstraint(info[k]);
1381	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1382	>	}
1383	>	else
1384	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1385
1386	<	if( globals->haveTauBarostat() )
1448	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1449	<	else{
1450	<	sprintf( painCave.errMsg,
1451	<	"SimSetup error: If you use an NPT\n"
1452	<	"    ensemble, you must set tauBarostat.\n");
1453	<	painCave.isFatal = 1;
1454	<	simError();
1455	<	}
1456	<	break;
1386	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1387
1388	<	case NPTfm_ENS:
1389	<	myNPTfm = new NPTfm<RealIntegrator>( info, the_ff );
1390	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1388	>	if (globals->haveTargetPressure())
1389	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1390	>	else{
1391	>	sprintf(painCave.errMsg,
1392	>	"SimSetup error: If you use a constant pressure\n"
1393	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1394	>	painCave.isFatal = 1;
1395	>	simError();
1396	>	}
1397
1398	<	if (globals->haveTargetPressure())
1399	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1464	<	else {
1465	<	sprintf( painCave.errMsg,
1466	<	"SimSetup error: If you use a constant pressure\n"
1467	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1468	<	painCave.isFatal = 1;
1469	<	simError();
1470	<	}
1471	<
1472	<	if( globals->haveTauThermostat() )
1473	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1474	<	else{
1475	<	sprintf( painCave.errMsg,
1476	<	"SimSetup error: If you use an NPT\n"
1477	<	"    ensemble, you must set tauThermostat.\n");
1478	<	painCave.isFatal = 1;
1479	<	simError();
1480	<	}
1398	>	if (globals->haveTauThermostat())
1399	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1400
1401	<	if( globals->haveTauBarostat() )
1402	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1403	<	else{
1404	<	sprintf( painCave.errMsg,
1405	<	"SimSetup error: If you use an NPT\n"
1406	<	"    ensemble, you must set tauBarostat.\n");
1407	<	painCave.isFatal = 1;
1489	<	simError();
1490	<	}
1491	<	break;
1492	<
1493	<	case NVEZCONS_ENS:
1401	>	else{
1402	>	sprintf(painCave.errMsg,
1403	>	"SimSetup error: If you use an NPT\n"
1404	>	"    ensemble, you must set tauThermostat.\n");
1405	>	painCave.isFatal = 1;
1406	>	simError();
1407	>	}
1408
1409	+	if (globals->haveTauBarostat())
1410	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1411
1412	<	//setup index of z-constraint molecules, z-constraint sampel time
1413	<	//and z-constraint force output name. These parameter should be known
1414	<	//before constructing the z-constraint integrator
1415	<	setupZConstraint();
1416	<
1417	<	myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff );
1418	<
1503	<	break;
1504	<
1505	<
1506	<	case NVTZCONS_ENS:
1507	<
1508	<	setupZConstraint();
1509	<
1510	<	myNVTZCons = new ZConstraint<NVT<RealIntegrator> >( info, the_ff );
1511	<	myNVTZCons->setTargetTemp(globals->getTargetTemp());
1412	>	else{
1413	>	sprintf(painCave.errMsg,
1414	>	"SimSetup error: If you use an NPT\n"
1415	>	"    ensemble, you must set tauBarostat.\n");
1416	>	painCave.isFatal = 1;
1417	>	simError();
1418	>	}
1419
1420	<	if (globals->haveTauThermostat())
1421	<	myNVTZCons->setTauThermostat(globals->getTauThermostat());
1420	>	info->the_integrator = myNPTf;
1421	>	break;
1422
1423	<	else {
1424	<	sprintf( painCave.errMsg,
1425	<	"SimSetup error: If you use the NVT\n"
1426	<	"    ensemble, you must set tauThermostat.\n");
1427	<	painCave.isFatal = 1;
1428	<	simError();
1429	<	}
1523	<	break;
1524	<
1525	<	case NPTiZCONS_ENS:
1526	<
1527	<	setupZConstraint();
1528	<
1529	<	myNPTiZCons = new ZConstraint<NPTi<RealIntegrator> >( info, the_ff );
1530	<	myNPTiZCons->setTargetTemp( globals->getTargetTemp() );
1423	>	case NPTxyz_ENS:
1424	>	if (globals->haveZconstraints()){
1425	>	setupZConstraint(info[k]);
1426	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1427	>	}
1428	>	else
1429	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1430
1431	<	if (globals->haveTargetPressure())
1533	<	myNPTiZCons->setTargetPressure(globals->getTargetPressure());
1534	<	else {
1535	<	sprintf( painCave.errMsg,
1536	<	"SimSetup error: If you use a constant pressure\n"
1537	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1538	<	painCave.isFatal = 1;
1539	<	simError();
1540	<	}
1541	<
1542	<	if( globals->haveTauThermostat() )
1543	<	myNPTiZCons->setTauThermostat( globals->getTauThermostat() );
1544	<	else{
1545	<	sprintf( painCave.errMsg,
1546	<	"SimSetup error: If you use an NPT\n"
1547	<	"    ensemble, you must set tauThermostat.\n");
1548	<	painCave.isFatal = 1;
1549	<	simError();
1550	<	}
1431	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1432
1433	<	if( globals->haveTauBarostat() )
1434	<	myNPTiZCons->setTauBarostat( globals->getTauBarostat() );
1435	<	else{
1436	<	sprintf( painCave.errMsg,
1437	<	"SimSetup error: If you use an NPT\n"
1438	<	"    ensemble, you must set tauBarostat.\n");
1439	<	painCave.isFatal = 1;
1440	<	simError();
1441	<	}
1561	<
1562	<	break;
1563	<
1564	<	case NPTfZCONS_ENS:
1565	<
1566	<	setupZConstraint();
1567	<
1568	<	myNPTfZCons = new ZConstraint<NPTf<RealIntegrator> >( info, the_ff );
1569	<	myNPTfZCons->setTargetTemp( globals->getTargetTemp());
1433	>	if (globals->haveTargetPressure())
1434	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1435	>	else{
1436	>	sprintf(painCave.errMsg,
1437	>	"SimSetup error: If you use a constant pressure\n"
1438	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1439	>	painCave.isFatal = 1;
1440	>	simError();
1441	>	}
1442
1443	<	if (globals->haveTargetPressure())
1444	<	myNPTfZCons->setTargetPressure(globals->getTargetPressure());
1445	<	else {
1446	<	sprintf( painCave.errMsg,
1447	<	"SimSetup error: If you use a constant pressure\n"
1448	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1449	<	painCave.isFatal = 1;
1450	<	simError();
1451	<	}
1443	>	if (globals->haveTauThermostat())
1444	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1445	>	else{
1446	>	sprintf(painCave.errMsg,
1447	>	"SimSetup error: If you use an NPT\n"
1448	>	"    ensemble, you must set tauThermostat.\n");
1449	>	painCave.isFatal = 1;
1450	>	simError();
1451	>	}
1452
1453	<	if( globals->haveTauThermostat() )
1454	<	myNPTfZCons->setTauThermostat( globals->getTauThermostat() );
1455	<	else{
1456	<	sprintf( painCave.errMsg,
1457	<	"SimSetup error: If you use an NPT\n"
1458	<	"    ensemble, you must set tauThermostat.\n");
1459	<	painCave.isFatal = 1;
1460	<	simError();
1461	<	}
1453	>	if (globals->haveTauBarostat())
1454	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1455	>	else{
1456	>	sprintf(painCave.errMsg,
1457	>	"SimSetup error: If you use an NPT\n"
1458	>	"    ensemble, you must set tauBarostat.\n");
1459	>	painCave.isFatal = 1;
1460	>	simError();
1461	>	}
1462
1463	<	if( globals->haveTauBarostat() )
1464	<	myNPTfZCons->setTauBarostat( globals->getTauBarostat() );
1593	<	else{
1594	<	sprintf( painCave.errMsg,
1595	<	"SimSetup error: If you use an NPT\n"
1596	<	"    ensemble, you must set tauBarostat.\n");
1597	<	painCave.isFatal = 1;
1598	<	simError();
1599	<	}
1600	<
1601	<	break;
1602	<
1603	<	case NPTimZCONS_ENS:
1604	<
1605	<	setupZConstraint();
1606	<
1607	<	myNPTimZCons = new ZConstraint<NPTim<RealIntegrator> >( info, the_ff );
1608	<	myNPTimZCons->setTargetTemp( globals->getTargetTemp());
1463	>	info->the_integrator = myNPTxyz;
1464	>	break;
1465
1466	<	if (globals->haveTargetPressure())
1467	<	myNPTimZCons->setTargetPressure(globals->getTargetPressure());
1468	<	else {
1469	<	sprintf( painCave.errMsg,
1470	<	"SimSetup error: If you use a constant pressure\n"
1615	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1616	<	painCave.isFatal = 1;
1617	<	simError();
1466	>	default:
1467	>	sprintf(painCave.errMsg,
1468	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1469	>	painCave.isFatal = 1;
1470	>	simError();
1471		}
1619	–
1620	–	if( globals->haveTauThermostat() )
1621	–	myNPTimZCons->setTauThermostat( globals->getTauThermostat() );
1622	–	else{
1623	–	sprintf( painCave.errMsg,
1624	–	"SimSetup error: If you use an NPT\n"
1625	–	"    ensemble, you must set tauThermostat.\n");
1626	–	painCave.isFatal = 1;
1627	–	simError();
1628	–	}
1629	–
1630	–	if( globals->haveTauBarostat() )
1631	–	myNPTimZCons->setTauBarostat( globals->getTauBarostat() );
1632	–	else{
1633	–	sprintf( painCave.errMsg,
1634	–	"SimSetup error: If you use an NPT\n"
1635	–	"    ensemble, you must set tauBarostat.\n");
1636	–	painCave.isFatal = 1;
1637	–	simError();
1638	–	}
1639	–
1640	–	break;
1641	–
1642	–	case NPTfmZCONS_ENS:
1643	–
1644	–	setupZConstraint();
1645	–
1646	–	myNPTfmZCons = new ZConstraint<NPTfm<RealIntegrator> >( info, the_ff );
1647	–	myNPTfmZCons->setTargetTemp( globals->getTargetTemp());
1648	–
1649	–	if (globals->haveTargetPressure())
1650	–	myNPTfmZCons->setTargetPressure(globals->getTargetPressure());
1651	–	else {
1652	–	sprintf( painCave.errMsg,
1653	–	"SimSetup error: If you use a constant pressure\n"
1654	–	"    ensemble, you must set targetPressure in the BASS file.\n");
1655	–	painCave.isFatal = 1;
1656	–	simError();
1657	–	}
1658	–
1659	–	if( globals->haveTauThermostat() )
1660	–	myNPTfmZCons->setTauThermostat( globals->getTauThermostat() );
1661	–	else{
1662	–	sprintf( painCave.errMsg,
1663	–	"SimSetup error: If you use an NPT\n"
1664	–	"    ensemble, you must set tauThermostat.\n");
1665	–	painCave.isFatal = 1;
1666	–	simError();
1667	–	}
1668	–
1669	–	if( globals->haveTauBarostat() )
1670	–	myNPTfmZCons->setTauBarostat( globals->getTauBarostat() );
1671	–	else{
1672	–	sprintf( painCave.errMsg,
1673	–	"SimSetup error: If you use an NPT\n"
1674	–	"    ensemble, you must set tauBarostat.\n");
1675	–	painCave.isFatal = 1;
1676	–	simError();
1677	–	}
1678	–	break;
1679	–
1680	–
1681	–
1682	–	default:
1683	–	sprintf( painCave.errMsg,
1684	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1685	–	painCave.isFatal = 1;
1686	–	simError();
1472		}
1688	–
1473		}
1474
1475	<	void SimSetup::initFortran( void ){
1475	>	void SimSetup::initFortran(void){
1476	>	info[0].refreshSim();
1477
1478	<	info->refreshSim();
1479	<
1695	<	if( !strcmp( info->mixingRule, "standard") ){
1696	<	the_ff->initForceField( LB_MIXING_RULE );
1478	>	if (!strcmp(info[0].mixingRule, "standard")){
1479	>	the_ff->initForceField(LB_MIXING_RULE);
1480		}
1481	<	else if( !strcmp( info->mixingRule, "explicit") ){
1482	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1481	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1482	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1483		}
1484		else{
1485	<	sprintf( painCave.errMsg,
1486	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1704	<	info->mixingRule );
1485	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1486	>	info[0].mixingRule);
1487		painCave.isFatal = 1;
1488		simError();
1489		}
1490
1491
1492		#ifdef IS_MPI
1493	<	strcpy( checkPointMsg,
1712	<	"Successfully intialized the mixingRule for Fortran." );
1493	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1494		MPIcheckPoint();
1495		#endif // is_mpi
1715	–
1496		}
1497
1498	<	void SimSetup::setupZConstraint()
1499	<	{
1500	<	if(globals->haveZConsTime()){
1501	<
1502	<	//add sample time of z-constraint  into SimInfo's property list
1503	<	DoubleData* zconsTimeProp = new DoubleData();
1504	<	zconsTimeProp->setID("zconstime");
1505	<	zconsTimeProp->setData(globals->getZConsTime());
1506	<	info->addProperty(zconsTimeProp);
1498	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1499	>	int nZConstraints;
1500	>	ZconStamp** zconStamp;
1501	>
1502	>	if (globals->haveZconstraintTime()){
1503	>	//add sample time of z-constraint  into SimInfo's property list
1504	>	DoubleData* zconsTimeProp = new DoubleData();
1505	>	zconsTimeProp->setID(ZCONSTIME_ID);
1506	>	zconsTimeProp->setData(globals->getZconsTime());
1507	>	theInfo.addProperty(zconsTimeProp);
1508		}
1509		else{
1510	<	sprintf( painCave.errMsg,
1511	<	"ZConstraint error: If you use an ZConstraint\n"
1512	<	" , you must set sample time.\n");
1510	>	sprintf(painCave.errMsg,
1511	>	"ZConstraint error: If you use an ZConstraint\n"
1512	>	" , you must set sample time.\n");
1513		painCave.isFatal = 1;
1514	+	simError();
1515	+	}
1516	+
1517	+	//push zconsTol into siminfo, if user does not specify
1518	+	//value for zconsTol, a default value will be used
1519	+	DoubleData* zconsTol = new DoubleData();
1520	+	zconsTol->setID(ZCONSTOL_ID);
1521	+	if (globals->haveZconsTol()){
1522	+	zconsTol->setData(globals->getZconsTol());
1523	+	}
1524	+	else{
1525	+	double defaultZConsTol = 0.01;
1526	+	sprintf(painCave.errMsg,
1527	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1528	+	" , default value %f is used.\n",
1529	+	defaultZConsTol);
1530	+	painCave.isFatal = 0;
1531		simError();
1532	+
1533	+	zconsTol->setData(defaultZConsTol);
1534		}
1535	<
1536	<	if(globals->haveIndexOfAllZConsMols()){
1537	<
1538	<	//add index of z-constraint molecules into SimInfo's property list
1539	<	vector<int> tempIndex = globals->getIndexOfAllZConsMols();
1540	<
1541	<	//sort the index
1542	<	sort(tempIndex.begin(), tempIndex.end());
1743	<
1744	<	IndexData* zconsIndex = new IndexData();
1745	<	zconsIndex->setID("zconsindex");
1746	<	zconsIndex->setIndexData(tempIndex);
1747	<	info->addProperty(zconsIndex);
1535	>	theInfo.addProperty(zconsTol);
1536	>
1537	>	//set Force Subtraction Policy
1538	>	StringData* zconsForcePolicy = new StringData();
1539	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1540	>
1541	>	if (globals->haveZconsForcePolicy()){
1542	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1543		}
1544		else{
1545	<	sprintf( painCave.errMsg,
1546	<	"SimSetup error: If you use an ZConstraint\n"
1547	<	" , you must set index of z-constraint molecules.\n");
1548	<	painCave.isFatal = 1;
1549	<	simError();
1550	<
1545	>	sprintf(painCave.errMsg,
1546	>	"ZConstraint Warning: User does not set force Subtraction policy, "
1547	>	"PolicyByMass is used\n");
1548	>	painCave.isFatal = 0;
1549	>	simError();
1550	>	zconsForcePolicy->setData("BYMASS");
1551		}
1552
1553	+	theInfo.addProperty(zconsForcePolicy);
1554	+
1555		//Determine the name of ouput file and add it into SimInfo's property list
1556		//Be careful, do not use inFileName, since it is a pointer which
1557		//point to a string at master node, and slave nodes do not contain that string
1558	<
1559	<	string zconsOutput(info->finalName);
1560	<
1558	>
1559	>	string zconsOutput(theInfo.finalName);
1560	>
1561		zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1562	<
1562	>
1563		StringData* zconsFilename = new StringData();
1564	<	zconsFilename->setID("zconsfilename");
1564	>	zconsFilename->setID(ZCONSFILENAME_ID);
1565		zconsFilename->setData(zconsOutput);
1566
1567	<	info->addProperty(zconsFilename);
1567	>	theInfo.addProperty(zconsFilename);
1568
1569	+	//setup index, pos and other parameters of z-constraint molecules
1570	+	nZConstraints = globals->getNzConstraints();
1571	+	theInfo.nZconstraints = nZConstraints;
1572	+
1573	+	zconStamp = globals->getZconStamp();
1574	+	ZConsParaItem tempParaItem;
1575	+
1576	+	ZConsParaData* zconsParaData = new ZConsParaData();
1577	+	zconsParaData->setID(ZCONSPARADATA_ID);
1578	+
1579	+	for (int i = 0; i < nZConstraints; i++){
1580	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1581	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1582	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1583	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1584	+
1585	+	zconsParaData->addItem(tempParaItem);
1586	+	}
1587	+
1588	+	//check the uniqueness of index
1589	+	if(!zconsParaData->isIndexUnique()){
1590	+	sprintf(painCave.errMsg,
1591	+	"ZConstraint Error: molIndex is not unique\n");
1592	+	painCave.isFatal = 1;
1593	+	simError();
1594	+	}
1595	+
1596	+	//sort the parameters by index of molecules
1597	+	zconsParaData->sortByIndex();
1598	+
1599	+	//push data into siminfo, therefore, we can retrieve later
1600	+	theInfo.addProperty(zconsParaData);
1601		}

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