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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 616 by mmeineke, Tue Jul 15 18:52:16 2003 UTC vs.
Revision 708 by tim, Wed Aug 20 22:23:34 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6	+	#include <sys/time.h>
7
8		#include "SimSetup.hpp"
9	+	#include "ReadWrite.hpp"
10		#include "parse_me.h"
11		#include "Integrator.hpp"
12		#include "simError.h"
#	Line 14 | Line 18
18
19		// some defines for ensemble and Forcefield  cases
20
21	<	#define NVE_ENS   0
22	<	#define NVT_ENS   1
23	<	#define NPTi_ENS  2
24	<	#define NPTf_ENS  3
25	<	#define NPTim_ENS 4
26	<	#define NPTfm_ENS 5
21	>	#define NVE_ENS        0
22	>	#define NVT_ENS        1
23	>	#define NPTi_ENS       2
24	>	#define NPTf_ENS       3
25	>	#define NPTim_ENS      4
26	>	#define NPTfm_ENS      5
27
24	–
28		#define FF_DUFF 0
29		#define FF_LJ   1
30	+	#define FF_EAM  2
31
32	+	using namespace std;
33
34		SimSetup::SimSetup(){
35	+
36	+	isInfoArray = 0;
37	+	nInfo = 1;
38	+
39		stamps = new MakeStamps();
40		globals = new Globals();
41
42	+
43		#ifdef IS_MPI
44		strcpy( checkPointMsg, "SimSetup creation successful" );
45		MPIcheckPoint();
#	Line 41 | Line 51 | SimSetup::~SimSetup(){
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	+	}
59	+
60	+
61		void SimSetup::parseFile( char* fileName ){
62
63		#ifdef IS_MPI
#	Line 76 | Line 93 | void SimSetup::receiveParse(void){
93
94		#endif // is_mpi
95
96	<	void SimSetup::createSim( void ){
96	>	void SimSetup::createSim(void){
97
98		int i, j, k, globalAtomIndex;
99
100		// gather all of the information from the Bass file
101	<
101	>
102		gatherInfo();
103
104		// creation of complex system objects
#	Line 89 | Line 106 | void SimSetup::createSim( void ){
106		sysObjectsCreation();
107
108		// check on the post processing info
109	<
109	>
110		finalInfoCheck();
111
112		// initialize the system coordinates
113
114	<	initSystemCoords();
98	<
114	>	if( !isInfoArray ) initSystemCoords();
115
116		// make the output filenames
117
#	Line 120 | Line 136 | void SimSetup::makeMolecules( void ){
136
137		void SimSetup::makeMolecules( void ){
138
139	+	int k,l;
140		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
141		molInit molInfo;
142		DirectionalAtom* dAtom;
#	Line 144 | Line 161 | void SimSetup::makeMolecules( void ){
161
162		double ux, uy, uz, u, uSqr;
163
164	<	atomOffset = 0;
148	<	excludeOffset = 0;
149	<	for(i=0; i<info->n_mol; i++){
164	>	for(k=0; k<nInfo; k++){
165
166	<	stampID = the_molecules[i].getStampID();
166	>	the_ff->setSimInfo( &(info[k]) );
167
168	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
169	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
170	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
171	<	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
172	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
168	>	atomOffset = 0;
169	>	excludeOffset = 0;
170	>	for(i=0; i<info[k].n_mol; i++){
171	>
172	>	stampID = info[k].molecules[i].getStampID();
173
174	<	molInfo.myAtoms = &the_atoms[atomOffset];
175	<	molInfo.myExcludes = &the_excludes[excludeOffset];
176	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
177	<	molInfo.myBends = new Bend*[molInfo.nBends];
178	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
174	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
175	>	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;
179	>
180	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
181	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
182	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
183	>	molInfo.myBends = new Bend*[molInfo.nBends];
184	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
185
186	<	theBonds = new bond_pair[molInfo.nBonds];
187	<	theBends = new bend_set[molInfo.nBends];
188	<	theTorsions = new torsion_set[molInfo.nTorsions];
186	>	theBonds = new bond_pair[molInfo.nBonds];
187	>	theBends = new bend_set[molInfo.nBends];
188	>	theTorsions = new torsion_set[molInfo.nTorsions];
189
190	<	// make the Atoms
190	>	// make the Atoms
191
192	<	for(j=0; j<molInfo.nAtoms; j++){
193	<
194	<	currentAtom = comp_stamps[stampID]->getAtom( j );
195	<	if( currentAtom->haveOrientation() ){
175	<
176	<	dAtom = new DirectionalAtom(j + atomOffset);
177	<	info->n_oriented++;
178	<	molInfo.myAtoms[j] = dAtom;
179	<
180	<	ux = currentAtom->getOrntX();
181	<	uy = currentAtom->getOrntY();
182	<	uz = currentAtom->getOrntZ();
183	<
184	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
185	<
186	<	u = sqrt( uSqr );
187	<	ux = ux / u;
188	<	uy = uy / u;
189	<	uz = uz / u;
190	<
191	<	dAtom->setSUx( ux );
192	<	dAtom->setSUy( uy );
193	<	dAtom->setSUz( uz );
194	<	}
195	<	else{
196	<	molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset);
197	<	}
198	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
192	>	for(j=0; j<molInfo.nAtoms; j++){
193	>
194	>	currentAtom = comp_stamps[stampID]->getAtom( j );
195	>	if( currentAtom->haveOrientation() ){
196
197	+	dAtom = new DirectionalAtom( (j + atomOffset),
198	+	info[k].getConfiguration() );
199	+	info[k].n_oriented++;
200	+	molInfo.myAtoms[j] = dAtom;
201	+
202	+	ux = currentAtom->getOrntX();
203	+	uy = currentAtom->getOrntY();
204	+	uz = currentAtom->getOrntZ();
205	+
206	+	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
207	+
208	+	u = sqrt( uSqr );
209	+	ux = ux / u;
210	+	uy = uy / u;
211	+	uz = uz / u;
212	+
213	+	dAtom->setSUx( ux );
214	+	dAtom->setSUy( uy );
215	+	dAtom->setSUz( uz );
216	+	}
217	+	else{
218	+	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
219	+	info[k].getConfiguration() );
220	+	}
221	+	molInfo.myAtoms[j]->setType( currentAtom->getType() );
222	+
223		#ifdef IS_MPI
224
225	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
225	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
226
227		#endif // is_mpi
228	<	}
228	>	}
229
230		// make the bonds
231	<	for(j=0; j<molInfo.nBonds; j++){
231	>	for(j=0; j<molInfo.nBonds; j++){
232
233	<	currentBond = comp_stamps[stampID]->getBond( j );
234	<	theBonds[j].a = currentBond->getA() + atomOffset;
235	<	theBonds[j].b = currentBond->getB() + atomOffset;
236	<
237	<	exI = theBonds[j].a;
238	<	exJ = theBonds[j].b;
239	<
240	<	// exclude_I must always be the smaller of the pair
241	<	if( exI > exJ ){
242	<	tempEx = exI;
243	<	exI = exJ;
244	<	exJ = tempEx;
245	<	}
233	>	currentBond = comp_stamps[stampID]->getBond( j );
234	>	theBonds[j].a = currentBond->getA() + atomOffset;
235	>	theBonds[j].b = currentBond->getB() + atomOffset;
236	>
237	>	exI = theBonds[j].a;
238	>	exJ = theBonds[j].b;
239	>
240	>	// exclude_I must always be the smaller of the pair
241	>	if( exI > exJ ){
242	>	tempEx = exI;
243	>	exI = exJ;
244	>	exJ = tempEx;
245	>	}
246		#ifdef IS_MPI
247	<	tempEx = exI;
248	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
249	<	tempEx = exJ;
250	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
251	<
252	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
247	>	tempEx = exI;
248	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
249	>	tempEx = exJ;
250	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
251	>
252	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
253		#else  // isn't MPI
254	<
255	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
254	>
255	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
256		#endif  //is_mpi
234	–	}
235	–	excludeOffset += molInfo.nBonds;
236	–
237	–	//make the bends
238	–	for(j=0; j<molInfo.nBends; j++){
239	–
240	–	currentBend = comp_stamps[stampID]->getBend( j );
241	–	theBends[j].a = currentBend->getA() + atomOffset;
242	–	theBends[j].b = currentBend->getB() + atomOffset;
243	–	theBends[j].c = currentBend->getC() + atomOffset;
244	–
245	–	if( currentBend->haveExtras() ){
246	–
247	–	extras = currentBend->getExtras();
248	–	current_extra = extras;
249	–
250	–	while( current_extra != NULL ){
251	–	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
252	–
253	–	switch( current_extra->getType() ){
254	–
255	–	case 0:
256	–	theBends[j].ghost =
257	–	current_extra->getInt() + atomOffset;
258	–	theBends[j].isGhost = 1;
259	–	break;
260	–
261	–	case 1:
262	–	theBends[j].ghost =
263	–	(int)current_extra->getDouble() + atomOffset;
264	–	theBends[j].isGhost = 1;
265	–	break;
266	–
267	–	default:
268	–	sprintf( painCave.errMsg,
269	–	"SimSetup Error: ghostVectorSource was neither a "
270	–	"double nor an int.\n"
271	–	"-->Bend[%d] in %s\n",
272	–	j, comp_stamps[stampID]->getID() );
273	–	painCave.isFatal = 1;
274	–	simError();
275	–	}
276	–	}
277	–
278	–	else{
279	–
280	–	sprintf( painCave.errMsg,
281	–	"SimSetup Error: unhandled bend assignment:\n"
282	–	"    -->%s in Bend[%d] in %s\n",
283	–	current_extra->getlhs(),
284	–	j, comp_stamps[stampID]->getID() );
285	–	painCave.isFatal = 1;
286	–	simError();
287	–	}
288	–
289	–	current_extra = current_extra->getNext();
290	–	}
257		}
258	<
293	<	if( !theBends[j].isGhost ){
294	<
295	<	exI = theBends[j].a;
296	<	exJ = theBends[j].c;
297	<	}
298	<	else{
299	<
300	<	exI = theBends[j].a;
301	<	exJ = theBends[j].b;
302	<	}
258	>	excludeOffset += molInfo.nBonds;
259
260	<	// exclude_I must always be the smaller of the pair
261	<	if( exI > exJ ){
262	<	tempEx = exI;
263	<	exI = exJ;
264	<	exJ = tempEx;
265	<	}
266	<	#ifdef IS_MPI
267	<	tempEx = exI;
268	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
269	<	tempEx = exJ;
270	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
271	<
272	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
273	<	#else  // isn't MPI
274	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
275	<	#endif  //is_mpi
276	<	}
277	<	excludeOffset += molInfo.nBends;
278	<
279	<	for(j=0; j<molInfo.nTorsions; j++){
260	>	//make the bends
261	>	for(j=0; j<molInfo.nBends; j++){
262	>
263	>	currentBend = comp_stamps[stampID]->getBend( j );
264	>	theBends[j].a = currentBend->getA() + atomOffset;
265	>	theBends[j].b = currentBend->getB() + atomOffset;
266	>	theBends[j].c = currentBend->getC() + atomOffset;
267	>
268	>	if( currentBend->haveExtras() ){
269	>
270	>	extras = currentBend->getExtras();
271	>	current_extra = extras;
272	>
273	>	while( current_extra != NULL ){
274	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
275	>
276	>	switch( current_extra->getType() ){
277	>
278	>	case 0:
279	>	theBends[j].ghost =
280	>	current_extra->getInt() + atomOffset;
281	>	theBends[j].isGhost = 1;
282	>	break;
283	>
284	>	case 1:
285	>	theBends[j].ghost =
286	>	(int)current_extra->getDouble() + atomOffset;
287	>	theBends[j].isGhost = 1;
288	>	break;
289	>
290	>	default:
291	>	sprintf( painCave.errMsg,
292	>	"SimSetup Error: ghostVectorSource was neither a "
293	>	"double nor an int.\n"
294	>	"-->Bend[%d] in %s\n",
295	>	j, comp_stamps[stampID]->getID() );
296	>	painCave.isFatal = 1;
297	>	simError();
298	>	}
299	>	}
300
301	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
302	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
303	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
304	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
305	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
306	<
307	<	exI = theTorsions[j].a;
308	<	exJ = theTorsions[j].d;
309	<
334	<	// exclude_I must always be the smaller of the pair
335	<	if( exI > exJ ){
336	<	tempEx = exI;
337	<	exI = exJ;
338	<	exJ = tempEx;
301	>	else{
302	>
303	>	sprintf( painCave.errMsg,
304	>	"SimSetup Error: unhandled bend assignment:\n"
305	>	"    -->%s in Bend[%d] in %s\n",
306	>	current_extra->getlhs(),
307	>	j, comp_stamps[stampID]->getID() );
308	>	painCave.isFatal = 1;
309	>	simError();
310		}
311	+
312	+	current_extra = current_extra->getNext();
313	+	}
314	+	}
315	+
316	+	if( !theBends[j].isGhost ){
317	+
318	+	exI = theBends[j].a;
319	+	exJ = theBends[j].c;
320	+	}
321	+	else{
322	+
323	+	exI = theBends[j].a;
324	+	exJ = theBends[j].b;
325	+	}
326	+
327	+	// exclude_I must always be the smaller of the pair
328	+	if( exI > exJ ){
329	+	tempEx = exI;
330	+	exI = exJ;
331	+	exJ = tempEx;
332	+	}
333		#ifdef IS_MPI
334	<	tempEx = exI;
335	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
336	<	tempEx = exJ;
337	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
334	>	tempEx = exI;
335	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
336	>	tempEx = exJ;
337	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
338
339	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
339	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
340		#else  // isn't MPI
341	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
341	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
342		#endif  //is_mpi
343	<	}
344	<	excludeOffset += molInfo.nTorsions;
345	<
346	<
347	<	// send the arrays off to the forceField for init.
348	<
349	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
350	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
351	<	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
352	<	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
353	<
354	<
355	<	the_molecules[i].initialize( molInfo );
356	<
357	<
358	<	atomOffset += molInfo.nAtoms;
359	<	delete[] theBonds;
360	<	delete[] theBends;
361	<	delete[] theTorsions;
343	>	}
344	>	excludeOffset += molInfo.nBends;
345	>
346	>	for(j=0; j<molInfo.nTorsions; j++){
347	>
348	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
349	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
350	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
351	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
352	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
353	>
354	>	exI = theTorsions[j].a;
355	>	exJ = theTorsions[j].d;
356	>
357	>	// exclude_I must always be the smaller of the pair
358	>	if( exI > exJ ){
359	>	tempEx = exI;
360	>	exI = exJ;
361	>	exJ = tempEx;
362		}
363	+	#ifdef IS_MPI
364	+	tempEx = exI;
365	+	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
366	+	tempEx = exJ;
367	+	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
368	+
369	+	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
370	+	#else  // isn't MPI
371	+	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
372	+	#endif  //is_mpi
373	+	}
374	+	excludeOffset += molInfo.nTorsions;
375	+
376	+
377	+	// send the arrays off to the forceField for init.
378	+
379	+	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
380	+	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
381	+	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
382	+	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
383	+
384	+
385	+	info[k].molecules[i].initialize( molInfo );
386
387	+
388	+	atomOffset += molInfo.nAtoms;
389	+	delete[] theBonds;
390	+	delete[] theBends;
391	+	delete[] theTorsions;
392	+	}
393	+	}
394	+
395		#ifdef IS_MPI
396		sprintf( checkPointMsg, "all molecules initialized succesfully" );
397		MPIcheckPoint();
398		#endif // is_mpi
399	<
399	>
400		// clean up the forcefield
401	+
402		the_ff->calcRcut();
403		the_ff->cleanMe();
404	<
404	>
405		}
406
407		void SimSetup::initFromBass( void ){
#	Line 389 | Line 414 | void SimSetup::initFromBass( void ){
414		int n_extra;
415		int have_extra, done;
416
417	+	double vel[3];
418	+	vel[0] = 0.0;
419	+	vel[1] = 0.0;
420	+	vel[2] = 0.0;
421	+
422		temp1 = (double)tot_nmol / 4.0;
423		temp2 = pow( temp1, ( 1.0 / 3.0 ) );
424		temp3 = ceil( temp2 );
#	Line 398 | Line 428 | void SimSetup::initFromBass( void ){
428		have_extra =1;
429
430		n_cells = (int)temp3 - 1;
431	<	cellx = info->boxLx / temp3;
432	<	celly = info->boxLy / temp3;
433	<	cellz = info->boxLz / temp3;
431	>	cellx = info[0].boxL[0] / temp3;
432	>	celly = info[0].boxL[1] / temp3;
433	>	cellz = info[0].boxL[2] / temp3;
434		n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
435		temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
436		n_per_extra = (int)ceil( temp1 );
437
438		if( n_per_extra > 4){
439		sprintf( painCave.errMsg,
440	<	"SimSetup error. There has been an error in constructing"
441	<	" the non-complete lattice.\n" );
440	>	"SimSetup error. There has been an error in constructing"
441	>	" the non-complete lattice.\n" );
442		painCave.isFatal = 1;
443		simError();
444		}
445		}
446		else{
447		n_cells = (int)temp3;
448	<	cellx = info->boxLx / temp3;
449	<	celly = info->boxLy / temp3;
450	<	cellz = info->boxLz / temp3;
448	>	cellx = info[0].boxL[0] / temp3;
449	>	celly = info[0].boxL[1] / temp3;
450	>	cellz = info[0].boxL[2] / temp3;
451		}
452
453		current_mol = 0;
#	Line 429 | Line 459 | void SimSetup::initFromBass( void ){
459		for( j=0; j < n_cells; j++ ){
460		for( k=0; k < n_cells; k++ ){
461
462	<	makeElement( i * cellx,
463	<	j * celly,
464	<	k * cellz );
462	>	makeElement( i * cellx,
463	>	j * celly,
464	>	k * cellz );
465
466	<	makeElement( i * cellx + 0.5 * cellx,
467	<	j * celly + 0.5 * celly,
468	<	k * cellz );
466	>	makeElement( i * cellx + 0.5 * cellx,
467	>	j * celly + 0.5 * celly,
468	>	k * cellz );
469
470	<	makeElement( i * cellx,
471	<	j * celly + 0.5 * celly,
472	<	k * cellz + 0.5 * cellz );
470	>	makeElement( i * cellx,
471	>	j * celly + 0.5 * celly,
472	>	k * cellz + 0.5 * cellz );
473
474	<	makeElement( i * cellx + 0.5 * cellx,
475	<	j * celly,
476	<	k * cellz + 0.5 * cellz );
474	>	makeElement( i * cellx + 0.5 * cellx,
475	>	j * celly,
476	>	k * cellz + 0.5 * cellz );
477		}
478		}
479		}
#	Line 455 | Line 485 | void SimSetup::initFromBass( void ){
485		for( i=0; i < (n_cells+1) && !done; i++ ){
486		for( j=0; j < (n_cells+1) && !done; j++ ){
487
488	<	if( i < n_cells ){
488	>	if( i < n_cells ){
489
490	<	if( j < n_cells ){
491	<	start_ndx = n_cells;
492	<	}
493	<	else start_ndx = 0;
494	<	}
495	<	else start_ndx = 0;
490	>	if( j < n_cells ){
491	>	start_ndx = n_cells;
492	>	}
493	>	else start_ndx = 0;
494	>	}
495	>	else start_ndx = 0;
496
497	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
497	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
498
499	<	makeElement( i * cellx,
500	<	j * celly,
501	<	k * cellz );
502	<	done = ( current_mol >= tot_nmol );
499	>	makeElement( i * cellx,
500	>	j * celly,
501	>	k * cellz );
502	>	done = ( current_mol >= tot_nmol );
503
504	<	if( !done && n_per_extra > 1 ){
505	<	makeElement( i * cellx + 0.5 * cellx,
506	<	j * celly + 0.5 * celly,
507	<	k * cellz );
508	<	done = ( current_mol >= tot_nmol );
509	<	}
504	>	if( !done && n_per_extra > 1 ){
505	>	makeElement( i * cellx + 0.5 * cellx,
506	>	j * celly + 0.5 * celly,
507	>	k * cellz );
508	>	done = ( current_mol >= tot_nmol );
509	>	}
510
511	<	if( !done && n_per_extra > 2){
512	<	makeElement( i * cellx,
513	<	j * celly + 0.5 * celly,
514	<	k * cellz + 0.5 * cellz );
515	<	done = ( current_mol >= tot_nmol );
516	<	}
511	>	if( !done && n_per_extra > 2){
512	>	makeElement( i * cellx,
513	>	j * celly + 0.5 * celly,
514	>	k * cellz + 0.5 * cellz );
515	>	done = ( current_mol >= tot_nmol );
516	>	}
517
518	<	if( !done && n_per_extra > 3){
519	<	makeElement( i * cellx + 0.5 * cellx,
520	<	j * celly,
521	<	k * cellz + 0.5 * cellz );
522	<	done = ( current_mol >= tot_nmol );
523	<	}
524	<	}
518	>	if( !done && n_per_extra > 3){
519	>	makeElement( i * cellx + 0.5 * cellx,
520	>	j * celly,
521	>	k * cellz + 0.5 * cellz );
522	>	done = ( current_mol >= tot_nmol );
523	>	}
524	>	}
525		}
526		}
527		}
528
529	<
530	<	for( i=0; i<info->n_atoms; i++ ){
501	<	info->atoms[i]->set_vx( 0.0 );
502	<	info->atoms[i]->set_vy( 0.0 );
503	<	info->atoms[i]->set_vz( 0.0 );
529	>	for( i=0; i<info[0].n_atoms; i++ ){
530	>	info[0].atoms[i]->setVel( vel );
531		}
532		}
533
#	Line 510 | Line 537 | void SimSetup::makeElement( double x, double y, double
537		AtomStamp* current_atom;
538		DirectionalAtom* dAtom;
539		double rotMat[3][3];
540	+	double pos[3];
541
542		for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
543
544		current_atom = comp_stamps[current_comp]->getAtom( k );
545		if( !current_atom->havePosition() ){
546		sprintf( painCave.errMsg,
547	<	"SimSetup:initFromBass error.\n"
548	<	"\tComponent %s, atom %s does not have a position specified.\n"
549	<	"\tThe initialization routine is unable to give a start"
550	<	" position.\n",
551	<	comp_stamps[current_comp]->getID(),
552	<	current_atom->getType() );
547	>	"SimSetup:initFromBass error.\n"
548	>	"\tComponent %s, atom %s does not have a position specified.\n"
549	>	"\tThe initialization routine is unable to give a start"
550	>	" position.\n",
551	>	comp_stamps[current_comp]->getID(),
552	>	current_atom->getType() );
553		painCave.isFatal = 1;
554		simError();
555		}
556	+
557	+	pos[0] = x + current_atom->getPosX();
558	+	pos[1] = y + current_atom->getPosY();
559	+	pos[2] = z + current_atom->getPosZ();
560	+
561	+	info[0].atoms[current_atom_ndx]->setPos( pos );
562
563	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
530	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
531	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
563	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
564
565	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
565	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
566
535	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
536	–
567		rotMat[0][0] = 1.0;
568		rotMat[0][1] = 0.0;
569		rotMat[0][2] = 0.0;
#	Line 569 | Line 599 | void SimSetup::gatherInfo( void ){
599		ensembleCase = -1;
600		ffCase = -1;
601
572	–	// get the stamps and globals;
573	–	stamps = stamps;
574	–	globals = globals;
575	–
602		// set the easy ones first
603	<	info->target_temp = globals->getTargetTemp();
604	<	info->dt = globals->getDt();
605	<	info->run_time = globals->getRunTime();
603	>
604	>	for( i=0; i<nInfo; i++){
605	>	info[i].target_temp = globals->getTargetTemp();
606	>	info[i].dt = globals->getDt();
607	>	info[i].run_time = globals->getRunTime();
608	>	}
609		n_components = globals->getNComponents();
610
611
#	Line 586 | Line 615 | void SimSetup::gatherInfo( void ){
615
616		if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
617		else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
618	+	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
619		else{
620		sprintf( painCave.errMsg,
621	<	"SimSetup Error. Unrecognized force field -> %s\n",
622	<	force_field );
621	>	"SimSetup Error. Unrecognized force field -> %s\n",
622	>	force_field );
623		painCave.isFatal = 1;
624		simError();
625		}
#	Line 607 | Line 637 | void SimSetup::gatherInfo( void ){
637		else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
638		else{
639		sprintf( painCave.errMsg,
640	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
640	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
641		"reverting to NVE for this simulation.\n",
642	<	ensemble );
642	>	ensemble );
643		painCave.isFatal = 0;
644		simError();
645		strcpy( ensemble, "NVE" );
646		ensembleCase = NVE_ENS;
647		}
648	<	strcpy( info->ensemble, ensemble );
648	>
649	>	for(i=0; i<nInfo; i++){
650	>
651	>	strcpy( info[i].ensemble, ensemble );
652
653	<	// get the mixing rule
653	>	// get the mixing rule
654
655	<	strcpy( info->mixingRule, globals->getMixingRule() );
656	<	info->usePBC = globals->getPBC();
657	<
655	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
656	>	info[i].usePBC = globals->getPBC();
657	>	}
658
659		// get the components and calculate the tot_nMol and indvidual n_mol
660
#	Line 637 | Line 670 | void SimSetup::gatherInfo( void ){
670		for( i=0; i<n_components; i++ ){
671
672		if( !the_components[i]->haveNMol() ){
673	<	// we have a problem
674	<	sprintf( painCave.errMsg,
675	<	"SimSetup Error. No global NMol or component NMol"
676	<	" given. Cannot calculate the number of atoms.\n" );
677	<	painCave.isFatal = 1;
678	<	simError();
673	>	// we have a problem
674	>	sprintf( painCave.errMsg,
675	>	"SimSetup Error. No global NMol or component NMol"
676	>	" given. Cannot calculate the number of atoms.\n" );
677	>	painCave.isFatal = 1;
678	>	simError();
679		}
680
681		tot_nmol += the_components[i]->getNMol();
#	Line 651 | Line 684 | void SimSetup::gatherInfo( void ){
684		}
685		else{
686		sprintf( painCave.errMsg,
687	<	"SimSetup error.\n"
688	<	"\tSorry, the ability to specify total"
689	<	" nMols and then give molfractions in the components\n"
690	<	"\tis not currently supported."
691	<	" Please give nMol in the components.\n" );
687	>	"SimSetup error.\n"
688	>	"\tSorry, the ability to specify total"
689	>	" nMols and then give molfractions in the components\n"
690	>	"\tis not currently supported."
691	>	" Please give nMol in the components.\n" );
692		painCave.isFatal = 1;
693		simError();
694		}
695
696		// set the status, sample, and thermal kick times
697
698	<	if( globals->haveSampleTime() ){
666	<	info->sampleTime = globals->getSampleTime();
667	<	info->statusTime = info->sampleTime;
668	<	info->thermalTime = info->sampleTime;
669	<	}
670	<	else{
671	<	info->sampleTime = globals->getRunTime();
672	<	info->statusTime = info->sampleTime;
673	<	info->thermalTime = info->sampleTime;
674	<	}
698	>	for(i=0; i<nInfo; i++){
699
700	<	if( globals->haveStatusTime() ){
701	<	info->statusTime = globals->getStatusTime();
702	<	}
700	>	if( globals->haveSampleTime() ){
701	>	info[i].sampleTime = globals->getSampleTime();
702	>	info[i].statusTime = info[i].sampleTime;
703	>	info[i].thermalTime = info[i].sampleTime;
704	>	}
705	>	else{
706	>	info[i].sampleTime = globals->getRunTime();
707	>	info[i].statusTime = info[i].sampleTime;
708	>	info[i].thermalTime = info[i].sampleTime;
709	>	}
710	>
711	>	if( globals->haveStatusTime() ){
712	>	info[i].statusTime = globals->getStatusTime();
713	>	}
714	>
715	>	if( globals->haveThermalTime() ){
716	>	info[i].thermalTime = globals->getThermalTime();
717	>	}
718
719	<	if( globals->haveThermalTime() ){
681	<	info->thermalTime = globals->getThermalTime();
682	<	}
719	>	// check for the temperature set flag
720
721	<	// check for the temperature set flag
685	<
686	<	if( globals->haveTempSet() ) info->setTemp = globals->getTempSet();
687	<
688	<	// get some of the tricky things that may still be in the globals
689	<
690	<	double boxVector[3];
691	<	if( globals->haveBox() ){
692	<	boxVector[0] = globals->getBox();
693	<	boxVector[1] = globals->getBox();
694	<	boxVector[2] = globals->getBox();
721	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
722
723	<	info->setBox( boxVector );
723	>	// get some of the tricky things that may still be in the globals
724	>
725	>	double boxVector[3];
726	>	if( globals->haveBox() ){
727	>	boxVector[0] = globals->getBox();
728	>	boxVector[1] = globals->getBox();
729	>	boxVector[2] = globals->getBox();
730	>
731	>	info[i].setBox( boxVector );
732	>	}
733	>	else if( globals->haveDensity() ){
734	>
735	>	double vol;
736	>	vol = (double)tot_nmol / globals->getDensity();
737	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
738	>	boxVector[1] = boxVector[0];
739	>	boxVector[2] = boxVector[0];
740	>
741	>	info[i].setBox( boxVector );
742		}
743	<	else if( globals->haveDensity() ){
743	>	else{
744	>	if( !globals->haveBoxX() ){
745	>	sprintf( painCave.errMsg,
746	>	"SimSetup error, no periodic BoxX size given.\n" );
747	>	painCave.isFatal = 1;
748	>	simError();
749	>	}
750	>	boxVector[0] = globals->getBoxX();
751	>
752	>	if( !globals->haveBoxY() ){
753	>	sprintf( painCave.errMsg,
754	>	"SimSetup error, no periodic BoxY size given.\n" );
755	>	painCave.isFatal = 1;
756	>	simError();
757	>	}
758	>	boxVector[1] = globals->getBoxY();
759	>
760	>	if( !globals->haveBoxZ() ){
761	>	sprintf( painCave.errMsg,
762	>	"SimSetup error, no periodic BoxZ size given.\n" );
763	>	painCave.isFatal = 1;
764	>	simError();
765	>	}
766	>	boxVector[2] = globals->getBoxZ();
767	>
768	>	info[i].setBox( boxVector );
769	>	}
770	>	}
771
772	<	double vol;
773	<	vol = (double)tot_nmol / globals->getDensity();
774	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
703	<	boxVector[1] = boxVector[0];
704	<	boxVector[2] = boxVector[0];
772	>	int seedValue;
773	>	struct timeval now_time_val;
774	>	struct timezone time_zone;
775
776	<	info->setBox( boxVector );
776	>	if(globals->haveSeed()){
777	>	seedValue = globals->getSeed();
778		}
779		else{
780	<	if( !globals->haveBoxX() ){
781	<	sprintf( painCave.errMsg,
782	<	"SimSetup error, no periodic BoxX size given.\n" );
783	<	painCave.isFatal = 1;
784	<	simError();
780	>	#ifndef IS_MPI
781	>	gettimeofday(&now_time_val, &time_zone);  // get the time now
782	>	seedValue = (int) now_time_val.tv_sec;      //  convert to epoch time
783	>	#else
784	>	if(worldRank == 0){
785	>	gettimeofday(&now_time_val, &time_zone);  // get the time now
786	>	seedValue = (int) now_time_val.tv_sec;      //  convert to epoch time
787		}
788	<	boxVector[0] = globals->getBoxX();
788	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
789	>	#endif
790	>	}
791
792	<	if( !globals->haveBoxY() ){
793	<	sprintf( painCave.errMsg,
719	<	"SimSetup error, no periodic BoxY size given.\n" );
720	<	painCave.isFatal = 1;
721	<	simError();
722	<	}
723	<	boxVector[1] = globals->getBoxY();
724	<
725	<	if( !globals->haveBoxZ() ){
726	<	sprintf( painCave.errMsg,
727	<	"SimSetup error, no periodic BoxZ size given.\n" );
728	<	painCave.isFatal = 1;
729	<	simError();
730	<	}
731	<	boxVector[2] = globals->getBoxZ();
732	<
733	<	info->setBox( boxVector );
792	>	for(int i = 0; i < nInfo; i++){
793	>	info[i].setSeed(seedValue);
794		}
795
736	–
737	–
796		#ifdef IS_MPI
797		strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
798		MPIcheckPoint();
#	Line 746 | Line 804 | void SimSetup::finalInfoCheck( void ){
804		void SimSetup::finalInfoCheck( void ){
805		int index;
806		int usesDipoles;
807	<
807	>	int i;
808
809	<	// check electrostatic parameters
810	<
753	<	index = 0;
754	<	usesDipoles = 0;
755	<	while( (index < info->n_atoms) && !usesDipoles ){
756	<	usesDipoles = ((info->atoms)[index])->hasDipole();
757	<	index++;
758	<	}
759	<
760	<	#ifdef IS_MPI
761	<	int myUse = usesDipoles;
762	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
763	<	#endif //is_mpi
764	<
765	<
766	<	if (globals->getUseRF() ) {
767	<	info->useReactionField = 1;
809	>	for(i=0; i<nInfo; i++){
810	>	// check electrostatic parameters
811
812	<	if( !globals->haveECR() ){
813	<	sprintf( painCave.errMsg,
814	<	"SimSetup Warning: using default value of 1/2 the smallest "
815	<	"box length for the electrostaticCutoffRadius.\n"
816	<	"I hope you have a very fast processor!\n");
774	<	painCave.isFatal = 0;
775	<	simError();
776	<	double smallest;
777	<	smallest = info->boxLx;
778	<	if (info->boxLy <= smallest) smallest = info->boxLy;
779	<	if (info->boxLz <= smallest) smallest = info->boxLz;
780	<	info->ecr = 0.5 * smallest;
781	<	} else {
782	<	info->ecr        = globals->getECR();
812	>	index = 0;
813	>	usesDipoles = 0;
814	>	while( (index < info[i].n_atoms) && !usesDipoles ){
815	>	usesDipoles = (info[i].atoms[index])->hasDipole();
816	>	index++;
817		}
784	–
785	–	if( !globals->haveEST() ){
786	–	sprintf( painCave.errMsg,
787	–	"SimSetup Warning: using default value of 0.05 * the "
788	–	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
789	–	);
790	–	painCave.isFatal = 0;
791	–	simError();
792	–	info->est = 0.05 * info->ecr;
793	–	} else {
794	–	info->est        = globals->getEST();
795	–	}
818
819	<	if(!globals->haveDielectric() ){
820	<	sprintf( painCave.errMsg,
821	<	"SimSetup Error: You are trying to use Reaction Field without"
822	<	"setting a dielectric constant!\n"
823	<	);
824	<	painCave.isFatal = 1;
825	<	simError();
826	<	}
827	<	info->dielectric = globals->getDielectric();
806	<	}
807	<	else {
808	<	if (usesDipoles) {
819	>	#ifdef IS_MPI
820	>	int myUse = usesDipoles;
821	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
822	>	#endif //is_mpi
823	>
824	>	double theEcr, theEst;
825	>
826	>	if (globals->getUseRF() ) {
827	>	info[i].useReactionField = 1;
828
829		if( !globals->haveECR() ){
830	<	sprintf( painCave.errMsg,
831	<	"SimSetup Warning: using default value of 1/2 the smallest "
832	<	"box length for the electrostaticCutoffRadius.\n"
833	<	"I hope you have a very fast processor!\n");
834	<	painCave.isFatal = 0;
835	<	simError();
836	<	double smallest;
837	<	smallest = info->boxLx;
838	<	if (info->boxLy <= smallest) smallest = info->boxLy;
839	<	if (info->boxLz <= smallest) smallest = info->boxLz;
840	<	info->ecr = 0.5 * smallest;
830	>	sprintf( painCave.errMsg,
831	>	"SimSetup Warning: using default value of 1/2 the smallest "
832	>	"box length for the electrostaticCutoffRadius.\n"
833	>	"I hope you have a very fast processor!\n");
834	>	painCave.isFatal = 0;
835	>	simError();
836	>	double smallest;
837	>	smallest = info[i].boxL[0];
838	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
839	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
840	>	theEcr = 0.5 * smallest;
841		} else {
842	<	info->ecr        = globals->getECR();
842	>	theEcr = globals->getECR();
843		}
844
845		if( !globals->haveEST() ){
846	<	sprintf( painCave.errMsg,
847	<	"SimSetup Warning: using default value of 5%% of the "
848	<	"electrostaticCutoffRadius for the "
849	<	"electrostaticSkinThickness\n"
850	<	);
851	<	painCave.isFatal = 0;
852	<	simError();
834	<	info->est = 0.05 * info->ecr;
846	>	sprintf( painCave.errMsg,
847	>	"SimSetup Warning: using default value of 0.05 * the "
848	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
849	>	);
850	>	painCave.isFatal = 0;
851	>	simError();
852	>	theEst = 0.05 * theEcr;
853		} else {
854	<	info->est        = globals->getEST();
854	>	theEst= globals->getEST();
855		}
856	<	}
857	<	}
856	>
857	>	info[i].setEcr( theEcr, theEst );
858	>
859	>	if(!globals->haveDielectric() ){
860	>	sprintf( painCave.errMsg,
861	>	"SimSetup Error: You are trying to use Reaction Field without"
862	>	"setting a dielectric constant!\n"
863	>	);
864	>	painCave.isFatal = 1;
865	>	simError();
866	>	}
867	>	info[i].dielectric = globals->getDielectric();
868	>	}
869	>	else {
870	>	if (usesDipoles) {
871	>
872	>	if( !globals->haveECR() ){
873	>	sprintf( painCave.errMsg,
874	>	"SimSetup Warning: using default value of 1/2 the smallest "
875	>	"box length for the electrostaticCutoffRadius.\n"
876	>	"I hope you have a very fast processor!\n");
877	>	painCave.isFatal = 0;
878	>	simError();
879	>	double smallest;
880	>	smallest = info[i].boxL[0];
881	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
882	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
883	>	theEcr = 0.5 * smallest;
884	>	} else {
885	>	theEcr = globals->getECR();
886	>	}
887	>
888	>	if( !globals->haveEST() ){
889	>	sprintf( painCave.errMsg,
890	>	"SimSetup Warning: using default value of 0.05 * the "
891	>	"electrostaticCutoffRadius for the "
892	>	"electrostaticSkinThickness\n"
893	>	);
894	>	painCave.isFatal = 0;
895	>	simError();
896	>	theEst = 0.05 * theEcr;
897	>	} else {
898	>	theEst= globals->getEST();
899	>	}
900	>
901	>	info[i].setEcr( theEcr, theEst );
902	>	}
903	>	}
904	>	}
905
906		#ifdef IS_MPI
907		strcpy( checkPointMsg, "post processing checks out" );
#	Line 846 | Line 911 | void SimSetup::initSystemCoords( void ){
911		}
912
913		void SimSetup::initSystemCoords( void ){
914	+	int i;
915	+
916	+	char* inName;
917
918	<	if( globals->haveInitialConfig() ){
919	<
920	<	InitializeFromFile* fileInit;
918	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
919	>
920	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
921	>
922	>	if( globals->haveInitialConfig() ){
923	>
924	>	InitializeFromFile* fileInit;
925		#ifdef IS_MPI // is_mpi
926	<	if( worldRank == 0 ){
926	>	if( worldRank == 0 ){
927		#endif //is_mpi
928	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
928	>	inName = globals->getInitialConfig();
929	>	double* tempDouble = new double[1000000];
930	>	fileInit = new InitializeFromFile( inName );
931		#ifdef IS_MPI
932	<	}else fileInit = new InitializeFromFile( NULL );
932	>	}else fileInit = new InitializeFromFile( NULL );
933		#endif
934	<	fileInit->read_xyz( info ); // default velocities on
935	<
936	<	delete fileInit;
937	<	}
938	<	else{
939	<
934	>	fileInit->readInit( info ); // default velocities on
935	>
936	>	delete fileInit;
937	>	}
938	>	else{
939	>
940		#ifdef IS_MPI
941	<
942	<	// no init from bass
943	<
944	<	sprintf( painCave.errMsg,
945	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
946	<	painCave.isFatal;
947	<	simError();
948	<
941	>
942	>	// no init from bass
943	>
944	>	sprintf( painCave.errMsg,
945	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
946	>	painCave.isFatal;
947	>	simError();
948	>
949		#else
950	<
951	<	initFromBass();
952	<
953	<
950	>
951	>	initFromBass();
952	>
953	>
954		#endif
955	<	}
956	<
955	>	}
956	>
957		#ifdef IS_MPI
958		strcpy( checkPointMsg, "Successfully read in the initial configuration" );
959		MPIcheckPoint();
960		#endif // is_mpi
961	<
961	>
962		}
963
964
965		void SimSetup::makeOutNames( void ){
966	+
967	+	int k;
968
969	+
970	+	for(k=0; k<nInfo; k++){
971	+
972		#ifdef IS_MPI
973	<	if( worldRank == 0 ){
973	>	if( worldRank == 0 ){
974		#endif // is_mpi
975	<
976	<	if( globals->haveFinalConfig() ){
977	<	strcpy( info->finalName, globals->getFinalConfig() );
975	>
976	>	if( globals->haveFinalConfig() ){
977	>	strcpy( info[k].finalName, globals->getFinalConfig() );
978	>	}
979	>	else{
980	>	strcpy( info[k].finalName, inFileName );
981	>	char* endTest;
982	>	int nameLength = strlen( info[k].finalName );
983	>	endTest = &(info[k].finalName[nameLength - 5]);
984	>	if( !strcmp( endTest, ".bass" ) ){
985	>	strcpy( endTest, ".eor" );
986	>	}
987	>	else if( !strcmp( endTest, ".BASS" ) ){
988	>	strcpy( endTest, ".eor" );
989	>	}
990	>	else{
991	>	endTest = &(info[k].finalName[nameLength - 4]);
992	>	if( !strcmp( endTest, ".bss" ) ){
993	>	strcpy( endTest, ".eor" );
994		}
995	+	else if( !strcmp( endTest, ".mdl" ) ){
996	+	strcpy( endTest, ".eor" );
997	+	}
998		else{
999	<	strcpy( info->finalName, inFileName );
999	>	strcat( info[k].finalName, ".eor" );
1000	>	}
1001	>	}
1002	>	}
1003	>
1004	>	// make the sample and status out names
1005	>
1006	>	strcpy( info[k].sampleName, inFileName );
1007		char* endTest;
1008	<	int nameLength = strlen( info->finalName );
1009	<	endTest = &(info->finalName[nameLength - 5]);
1008	>	int nameLength = strlen( info[k].sampleName );
1009	>	endTest = &(info[k].sampleName[nameLength - 5]);
1010		if( !strcmp( endTest, ".bass" ) ){
1011	<	strcpy( endTest, ".eor" );
1011	>	strcpy( endTest, ".dump" );
1012		}
1013		else if( !strcmp( endTest, ".BASS" ) ){
1014	<	strcpy( endTest, ".eor" );
1014	>	strcpy( endTest, ".dump" );
1015		}
1016		else{
1017	<	endTest = &(info->finalName[nameLength - 4]);
1018	<	if( !strcmp( endTest, ".bss" ) ){
1019	<	strcpy( endTest, ".eor" );
1020	<	}
1021	<	else if( !strcmp( endTest, ".mdl" ) ){
1022	<	strcpy( endTest, ".eor" );
1023	<	}
1024	<	else{
1025	<	strcat( info->finalName, ".eor" );
1026	<	}
1017	>	endTest = &(info[k].sampleName[nameLength - 4]);
1018	>	if( !strcmp( endTest, ".bss" ) ){
1019	>	strcpy( endTest, ".dump" );
1020	>	}
1021	>	else if( !strcmp( endTest, ".mdl" ) ){
1022	>	strcpy( endTest, ".dump" );
1023	>	}
1024	>	else{
1025	>	strcat( info[k].sampleName, ".dump" );
1026	>	}
1027		}
1028	<	}
1029	<
1030	<	// make the sample and status out names
1031	<
1032	<	strcpy( info->sampleName, inFileName );
1033	<	char* endTest;
929	<	int nameLength = strlen( info->sampleName );
930	<	endTest = &(info->sampleName[nameLength - 5]);
931	<	if( !strcmp( endTest, ".bass" ) ){
932	<	strcpy( endTest, ".dump" );
933	<	}
934	<	else if( !strcmp( endTest, ".BASS" ) ){
935	<	strcpy( endTest, ".dump" );
936	<	}
937	<	else{
938	<	endTest = &(info->sampleName[nameLength - 4]);
939	<	if( !strcmp( endTest, ".bss" ) ){
940	<	strcpy( endTest, ".dump" );
941	<	}
942	<	else if( !strcmp( endTest, ".mdl" ) ){
943	<	strcpy( endTest, ".dump" );
944	<	}
945	<	else{
946	<	strcat( info->sampleName, ".dump" );
1028	>
1029	>	strcpy( info[k].statusName, inFileName );
1030	>	nameLength = strlen( info[k].statusName );
1031	>	endTest = &(info[k].statusName[nameLength - 5]);
1032	>	if( !strcmp( endTest, ".bass" ) ){
1033	>	strcpy( endTest, ".stat" );
1034		}
1035	<	}
1036	<
950	<	strcpy( info->statusName, inFileName );
951	<	nameLength = strlen( info->statusName );
952	<	endTest = &(info->statusName[nameLength - 5]);
953	<	if( !strcmp( endTest, ".bass" ) ){
954	<	strcpy( endTest, ".stat" );
955	<	}
956	<	else if( !strcmp( endTest, ".BASS" ) ){
957	<	strcpy( endTest, ".stat" );
958	<	}
959	<	else{
960	<	endTest = &(info->statusName[nameLength - 4]);
961	<	if( !strcmp( endTest, ".bss" ) ){
962	<	strcpy( endTest, ".stat" );
1035	>	else if( !strcmp( endTest, ".BASS" ) ){
1036	>	strcpy( endTest, ".stat" );
1037		}
964	–	else if( !strcmp( endTest, ".mdl" ) ){
965	–	strcpy( endTest, ".stat" );
966	–	}
1038		else{
1039	<	strcat( info->statusName, ".stat" );
1039	>	endTest = &(info[k].statusName[nameLength - 4]);
1040	>	if( !strcmp( endTest, ".bss" ) ){
1041	>	strcpy( endTest, ".stat" );
1042	>	}
1043	>	else if( !strcmp( endTest, ".mdl" ) ){
1044	>	strcpy( endTest, ".stat" );
1045	>	}
1046	>	else{
1047	>	strcat( info[k].statusName, ".stat" );
1048	>	}
1049		}
1050	<	}
971	<
1050	>
1051		#ifdef IS_MPI
1052	<	}
1052	>	}
1053		#endif // is_mpi
1054	<
1054	>	}
1055		}
1056
1057
1058		void SimSetup::sysObjectsCreation( void ){
1059	<
1060	<	int i;
1061	<
1059	>
1060	>	int i,k;
1061	>
1062		// create the forceField
1063
1064		createFF();
#	Line 999 | Line 1078 | void SimSetup::sysObjectsCreation( void ){
1078		#endif //is_mpi
1079
1080		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1081	<
1081	>
1082		makeSysArrays();
1083
1084		// make and initialize the molecules (all but atomic coordinates)
1085	<
1085	>
1086		makeMolecules();
1008	–	info->identArray = new int[info->n_atoms];
1009	–	for(i=0; i<info->n_atoms; i++){
1010	–	info->identArray[i] = the_atoms[i]->getIdent();
1011	–	}
1087
1088	<
1089	<
1088	>	for(k=0; k<nInfo; k++){
1089	>	info[k].identArray = new int[info[k].n_atoms];
1090	>	for(i=0; i<info[k].n_atoms; i++){
1091	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1092	>	}
1093	>	}
1094		}
1095
1096
#	Line 1027 | Line 1106 | void SimSetup::createFF( void ){
1106		the_ff = new LJFF();
1107		break;
1108
1109	+	case FF_EAM:
1110	+	the_ff = new EAM_FF();
1111	+	break;
1112	+
1113		default:
1114		sprintf( painCave.errMsg,
1115	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1115	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1116		painCave.isFatal = 1;
1117		simError();
1118		}
#	Line 1045 | Line 1128 | void SimSetup::compList( void ){
1128		void SimSetup::compList( void ){
1129
1130		int i;
1131	<
1131	>	char* id;
1132	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1133	>	LinkedMolStamp* currentStamp = NULL;
1134		comp_stamps = new MoleculeStamp*[n_components];
1135	<
1135	>
1136		// make an array of molecule stamps that match the components used.
1137		// also extract the used stamps out into a separate linked list
1053	–
1054	–	info->nComponents = n_components;
1055	–	info->componentsNmol = components_nmol;
1056	–	info->compStamps = comp_stamps;
1057	–	info->headStamp = new LinkedMolStamp();
1138
1139	<	char* id;
1140	<	LinkedMolStamp* headStamp = info->headStamp;
1141	<	LinkedMolStamp* currentStamp = NULL;
1139	>	for(i=0; i<nInfo; i++){
1140	>	info[i].nComponents = n_components;
1141	>	info[i].componentsNmol = components_nmol;
1142	>	info[i].compStamps = comp_stamps;
1143	>	info[i].headStamp = headStamp;
1144	>	}
1145	>
1146	>
1147		for( i=0; i<n_components; i++ ){
1148
1149		id = the_components[i]->getType();
#	Line 1073 | Line 1158 | void SimSetup::compList( void ){
1158
1159		currentStamp = stamps->extractMolStamp( id );
1160		if( currentStamp == NULL ){
1161	<	sprintf( painCave.errMsg,
1162	<	"SimSetup error: Component \"%s\" was not found in the "
1163	<	"list of declared molecules\n",
1164	<	id );
1165	<	painCave.isFatal = 1;
1166	<	simError();
1161	>	sprintf( painCave.errMsg,
1162	>	"SimSetup error: Component \"%s\" was not found in the "
1163	>	"list of declared molecules\n",
1164	>	id );
1165	>	painCave.isFatal = 1;
1166	>	simError();
1167		}
1168
1169		headStamp->add( currentStamp );
#	Line 1096 | Line 1181 | void SimSetup::calcSysValues( void ){
1181
1182		void SimSetup::calcSysValues( void ){
1183		int i, j, k;
1184	<
1185	<
1184	>
1185	>	int *molMembershipArray;
1186	>
1187		tot_atoms = 0;
1188		tot_bonds = 0;
1189		tot_bends = 0;
#	Line 1109 | Line 1195 | void SimSetup::calcSysValues( void ){
1195		tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1196		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1197		}
1198	<
1198	>
1199		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1200	<
1115	<	info->n_atoms = tot_atoms;
1116	<	info->n_bonds = tot_bonds;
1117	<	info->n_bends = tot_bends;
1118	<	info->n_torsions = tot_torsions;
1119	<	info->n_SRI = tot_SRI;
1120	<	info->n_mol = tot_nmol;
1200	>	molMembershipArray = new int[tot_atoms];
1201
1202	<	info->molMembershipArray = new int[tot_atoms];
1202	>	for(i=0; i<nInfo; i++){
1203	>	info[i].n_atoms = tot_atoms;
1204	>	info[i].n_bonds = tot_bonds;
1205	>	info[i].n_bends = tot_bends;
1206	>	info[i].n_torsions = tot_torsions;
1207	>	info[i].n_SRI = tot_SRI;
1208	>	info[i].n_mol = tot_nmol;
1209	>
1210	>	info[i].molMembershipArray = molMembershipArray;
1211	>	}
1212		}
1213
1125	–
1214		#ifdef IS_MPI
1215
1216		void SimSetup::mpiMolDivide( void ){
#	Line 1154 | Line 1242 | void SimSetup::mpiMolDivide( void ){
1242		for( j=0; j<components_nmol[i]; j++ ){
1243
1244		if( mol2proc[allMol] == worldRank ){
1245	<
1246	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1247	<	local_bonds +=    comp_stamps[i]->getNBonds();
1248	<	local_bends +=    comp_stamps[i]->getNBends();
1249	<	local_torsions += comp_stamps[i]->getNTorsions();
1250	<	localMol++;
1245	>
1246	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1247	>	local_bonds +=    comp_stamps[i]->getNBonds();
1248	>	local_bends +=    comp_stamps[i]->getNBends();
1249	>	local_torsions += comp_stamps[i]->getNTorsions();
1250	>	localMol++;
1251		}
1252		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1253	<	info->molMembershipArray[globalAtomIndex] = allMol;
1253	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1254		globalAtomIndex++;
1255		}
1256
#	Line 1171 | Line 1259 | void SimSetup::mpiMolDivide( void ){
1259		}
1260		local_SRI = local_bonds + local_bends + local_torsions;
1261
1262	<	info->n_atoms = mpiSim->getMyNlocal();
1262	>	info[0].n_atoms = mpiSim->getMyNlocal();
1263
1264	<	if( local_atoms != info->n_atoms ){
1264	>	if( local_atoms != info[0].n_atoms ){
1265		sprintf( painCave.errMsg,
1266	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1267	<	" localAtom (%d) are not equal.\n",
1268	<	info->n_atoms,
1269	<	local_atoms );
1266	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1267	>	" localAtom (%d) are not equal.\n",
1268	>	info[0].n_atoms,
1269	>	local_atoms );
1270		painCave.isFatal = 1;
1271		simError();
1272		}
1273
1274	<	info->n_bonds = local_bonds;
1275	<	info->n_bends = local_bends;
1276	<	info->n_torsions = local_torsions;
1277	<	info->n_SRI = local_SRI;
1278	<	info->n_mol = localMol;
1274	>	info[0].n_bonds = local_bonds;
1275	>	info[0].n_bends = local_bends;
1276	>	info[0].n_torsions = local_torsions;
1277	>	info[0].n_SRI = local_SRI;
1278	>	info[0].n_mol = localMol;
1279
1280		strcpy( checkPointMsg, "Passed nlocal consistency check." );
1281		MPIcheckPoint();
1282		}
1283	<
1283	>
1284		#endif // is_mpi
1285
1286
1287		void SimSetup::makeSysArrays( void ){
1288	<	int i, j, k;
1288	>	int i, j, k, l;
1289
1290	+	Atom** the_atoms;
1291	+	Molecule* the_molecules;
1292	+	Exclude** the_excludes;
1293
1203	–	// create the atom and short range interaction arrays
1204	–
1205	–	Atom::createArrays(info->n_atoms);
1206	–	the_atoms = new Atom*[info->n_atoms];
1207	–	the_molecules = new Molecule[info->n_mol];
1208	–	int molIndex;
1209	–
1210	–	// initialize the molecule's stampID's
1211	–
1212	–	#ifdef IS_MPI
1294
1295	+	for(l=0; l<nInfo; l++){
1296	+
1297	+	// create the atom and short range interaction arrays
1298	+
1299	+	the_atoms = new Atom*[info[l].n_atoms];
1300	+	the_molecules = new Molecule[info[l].n_mol];
1301	+	int molIndex;
1302
1303	<	molIndex = 0;
1216	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1303	>	// initialize the molecule's stampID's
1304
1305	<	if(mol2proc[i] == worldRank ){
1306	<	the_molecules[molIndex].setStampID( molCompType[i] );
1307	<	the_molecules[molIndex].setMyIndex( molIndex );
1308	<	the_molecules[molIndex].setGlobalIndex( i );
1309	<	molIndex++;
1305	>	#ifdef IS_MPI
1306	>
1307	>
1308	>	molIndex = 0;
1309	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1310	>
1311	>	if(mol2proc[i] == worldRank ){
1312	>	the_molecules[molIndex].setStampID( molCompType[i] );
1313	>	the_molecules[molIndex].setMyIndex( molIndex );
1314	>	the_molecules[molIndex].setGlobalIndex( i );
1315	>	molIndex++;
1316	>	}
1317		}
1318	<	}
1225	<
1318	>
1319		#else // is_mpi
1320	<
1321	<	molIndex = 0;
1322	<	globalAtomIndex = 0;
1323	<	for(i=0; i<n_components; i++){
1324	<	for(j=0; j<components_nmol[i]; j++ ){
1325	<	the_molecules[molIndex].setStampID( i );
1326	<	the_molecules[molIndex].setMyIndex( molIndex );
1327	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1328	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1329	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1330	<	globalAtomIndex++;
1320	>
1321	>	molIndex = 0;
1322	>	globalAtomIndex = 0;
1323	>	for(i=0; i<n_components; i++){
1324	>	for(j=0; j<components_nmol[i]; j++ ){
1325	>	the_molecules[molIndex].setStampID( i );
1326	>	the_molecules[molIndex].setMyIndex( molIndex );
1327	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1328	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1329	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1330	>	globalAtomIndex++;
1331	>	}
1332	>	molIndex++;
1333		}
1239	–	molIndex++;
1334		}
1241	–	}
1335
1336	<
1336	>
1337		#endif // is_mpi
1338
1339
1340	<	if( info->n_SRI ){
1340	>	if( info[l].n_SRI ){
1341
1342	<	Exclude::createArray(info->n_SRI);
1343	<	the_excludes = new Exclude*[info->n_SRI];
1344	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1345	<	info->globalExcludes = new int;
1346	<	info->n_exclude = info->n_SRI;
1347	<	}
1348	<	else{
1342	>	Exclude::createArray(info[l].n_SRI);
1343	>	the_excludes = new Exclude*[info[l].n_SRI];
1344	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1345	>	the_excludes[ex] = new Exclude(ex);
1346	>	}
1347	>	info[l].globalExcludes = new int;
1348	>	info[l].n_exclude = info[l].n_SRI;
1349	>	}
1350	>	else{
1351
1352	<	Exclude::createArray( 1 );
1353	<	the_excludes = new Exclude*;
1354	<	the_excludes[0] = new Exclude(0);
1355	<	the_excludes[0]->setPair( 0,0 );
1356	<	info->globalExcludes = new int;
1357	<	info->globalExcludes[0] = 0;
1358	<	info->n_exclude = 0;
1359	<	}
1352	>	Exclude::createArray( 1 );
1353	>	the_excludes = new Exclude*;
1354	>	the_excludes[0] = new Exclude(0);
1355	>	the_excludes[0]->setPair( 0,0 );
1356	>	info[l].globalExcludes = new int;
1357	>	info[l].globalExcludes[0] = 0;
1358	>	info[l].n_exclude = 0;
1359	>	}
1360
1361	<	// set the arrays into the SimInfo object
1361	>	// set the arrays into the SimInfo object
1362
1363	<	info->atoms = the_atoms;
1364	<	info->molecules = the_molecules;
1365	<	info->nGlobalExcludes = 0;
1366	<	info->excludes = the_excludes;
1363	>	info[l].atoms = the_atoms;
1364	>	info[l].molecules = the_molecules;
1365	>	info[l].nGlobalExcludes = 0;
1366	>	info[l].excludes = the_excludes;
1367
1368	<	the_ff->setSimInfo( info );
1369	<
1368	>	the_ff->setSimInfo( info );
1369	>
1370	>	}
1371		}
1372
1373		void SimSetup::makeIntegrator( void ){
1374
1375	<	NVT*  myNVT = NULL;
1280	<	NPTi* myNPTi = NULL;
1281	<	NPTf* myNPTf = NULL;
1282	<	NPTim* myNPTim = NULL;
1283	<	NPTfm* myNPTfm = NULL;
1375	>	int k;
1376
1377	<	switch( ensembleCase ){
1377	>	NVT<RealIntegrator>*  myNVT = NULL;
1378	>	NPTi<RealIntegrator>* myNPTi = NULL;
1379	>	NPTf<RealIntegrator>* myNPTf = NULL;
1380	>	NPTim<RealIntegrator>* myNPTim = NULL;
1381	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1382	>
1383	>	for(k=0; k<nInfo; k++){
1384	>
1385	>	switch( ensembleCase ){
1386	>
1387	>	case NVE_ENS:
1388	>	if (globals->haveZconstraints()){
1389	>	setupZConstraint(info[k]);
1390	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1391	>	}
1392
1393	<	case NVE_ENS:
1394	<	new NVE( info, the_ff );
1395	<	break;
1396	<
1397	<	case NVT_ENS:
1398	<	myNVT = new NVT( info, the_ff );
1399	<	myNVT->setTargetTemp(globals->getTargetTemp());
1400	<
1401	<	if (globals->haveTauThermostat())
1402	<	myNVT->setTauThermostat(globals->getTauThermostat());
1403	<
1298	<	else {
1299	<	sprintf( painCave.errMsg,
1300	<	"SimSetup error: If you use the NVT\n"
1301	<	"    ensemble, you must set tauThermostat.\n");
1302	<	painCave.isFatal = 1;
1303	<	simError();
1304	<	}
1305	<	break;
1393	>	else
1394	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1395	>	break;
1396	>
1397	>	case NVT_ENS:
1398	>	if (globals->haveZconstraints()){
1399	>	setupZConstraint(info[k]);
1400	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1401	>	}
1402	>	else
1403	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1404
1405	<	case NPTi_ENS:
1406	<	myNPTi = new NPTi( info, the_ff );
1407	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1405	>	myNVT->setTargetTemp(globals->getTargetTemp());
1406	>
1407	>	if (globals->haveTauThermostat())
1408	>	myNVT->setTauThermostat(globals->getTauThermostat());
1409	>
1410	>	else {
1411	>	sprintf( painCave.errMsg,
1412	>	"SimSetup error: If you use the NVT\n"
1413	>	"    ensemble, you must set tauThermostat.\n");
1414	>	painCave.isFatal = 1;
1415	>	simError();
1416	>	}
1417	>	break;
1418	>
1419	>	case NPTi_ENS:
1420	>	if (globals->haveZconstraints()){
1421	>	setupZConstraint(info[k]);
1422	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1423	>	}
1424	>	else
1425	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1426
1427	<	if (globals->haveTargetPressure())
1428	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1429	<	else {
1430	<	sprintf( painCave.errMsg,
1431	<	"SimSetup error: If you use a constant pressure\n"
1432	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1433	<	painCave.isFatal = 1;
1434	<	simError();
1435	<	}
1436	<
1437	<	if( globals->haveTauThermostat() )
1438	<	myNPTi->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	<	}
1427	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1428	>
1429	>	if (globals->haveTargetPressure())
1430	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1431	>	else {
1432	>	sprintf( painCave.errMsg,
1433	>	"SimSetup error: If you use a constant pressure\n"
1434	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1435	>	painCave.isFatal = 1;
1436	>	simError();
1437	>	}
1438	>
1439	>	if( globals->haveTauThermostat() )
1440	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1441	>	else{
1442	>	sprintf( painCave.errMsg,
1443	>	"SimSetup error: If you use an NPT\n"
1444	>	"    ensemble, you must set tauThermostat.\n");
1445	>	painCave.isFatal = 1;
1446	>	simError();
1447	>	}
1448	>
1449	>	if( globals->haveTauBarostat() )
1450	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1451	>	else{
1452	>	sprintf( painCave.errMsg,
1453	>	"SimSetup error: If you use an NPT\n"
1454	>	"    ensemble, you must set tauBarostat.\n");
1455	>	painCave.isFatal = 1;
1456	>	simError();
1457	>	}
1458	>	break;
1459	>
1460	>	case NPTf_ENS:
1461	>	if (globals->haveZconstraints()){
1462	>	setupZConstraint(info[k]);
1463	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1464	>	}
1465	>	else
1466	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1467
1468	<	if( globals->haveTauBarostat() )
1469	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1470	<	else{
1471	<	sprintf( painCave.errMsg,
1472	<	"SimSetup error: If you use an NPT\n"
1473	<	"    ensemble, you must set tauBarostat.\n");
1474	<	painCave.isFatal = 1;
1475	<	simError();
1476	<	}
1477	<	break;
1468	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1469	>
1470	>	if (globals->haveTargetPressure())
1471	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1472	>	else {
1473	>	sprintf( painCave.errMsg,
1474	>	"SimSetup error: If you use a constant pressure\n"
1475	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1476	>	painCave.isFatal = 1;
1477	>	simError();
1478	>	}
1479	>
1480	>	if( globals->haveTauThermostat() )
1481	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1482	>	else{
1483	>	sprintf( painCave.errMsg,
1484	>	"SimSetup error: If you use an NPT\n"
1485	>	"    ensemble, you must set tauThermostat.\n");
1486	>	painCave.isFatal = 1;
1487	>	simError();
1488	>	}
1489	>
1490	>	if( globals->haveTauBarostat() )
1491	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1492	>	else{
1493	>	sprintf( painCave.errMsg,
1494	>	"SimSetup error: If you use an NPT\n"
1495	>	"    ensemble, you must set tauBarostat.\n");
1496	>	painCave.isFatal = 1;
1497	>	simError();
1498	>	}
1499	>	break;
1500	>
1501	>	case NPTim_ENS:
1502	>	if (globals->haveZconstraints()){
1503	>	setupZConstraint(info[k]);
1504	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1505	>	}
1506	>	else
1507	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1508
1509	<	case NPTf_ENS:
1510	<	myNPTf = new NPTf( info, the_ff );
1511	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1509	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1510	>
1511	>	if (globals->haveTargetPressure())
1512	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1513	>	else {
1514	>	sprintf( painCave.errMsg,
1515	>	"SimSetup error: If you use a constant pressure\n"
1516	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1517	>	painCave.isFatal = 1;
1518	>	simError();
1519	>	}
1520	>
1521	>	if( globals->haveTauThermostat() )
1522	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1523	>	else{
1524	>	sprintf( painCave.errMsg,
1525	>	"SimSetup error: If you use an NPT\n"
1526	>	"    ensemble, you must set tauThermostat.\n");
1527	>	painCave.isFatal = 1;
1528	>	simError();
1529	>	}
1530	>
1531	>	if( globals->haveTauBarostat() )
1532	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1533	>	else{
1534	>	sprintf( painCave.errMsg,
1535	>	"SimSetup error: If you use an NPT\n"
1536	>	"    ensemble, you must set tauBarostat.\n");
1537	>	painCave.isFatal = 1;
1538	>	simError();
1539	>	}
1540	>	break;
1541	>
1542	>	case NPTfm_ENS:
1543	>	if (globals->haveZconstraints()){
1544	>	setupZConstraint(info[k]);
1545	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1546	>	}
1547	>	else
1548	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1549
1550	<	if (globals->haveTargetPressure())
1347	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1348	<	else {
1349	<	sprintf( painCave.errMsg,
1350	<	"SimSetup error: If you use a constant pressure\n"
1351	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1352	<	painCave.isFatal = 1;
1353	<	simError();
1354	<	}
1550	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1551
1552	<	if( globals->haveTauThermostat() )
1553	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1554	<	else{
1555	<	sprintf( painCave.errMsg,
1556	<	"SimSetup error: If you use an NPT\n"
1557	<	"    ensemble, you must set tauThermostat.\n");
1558	<	painCave.isFatal = 1;
1559	<	simError();
1560	<	}
1552	>	if (globals->haveTargetPressure())
1553	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1554	>	else {
1555	>	sprintf( painCave.errMsg,
1556	>	"SimSetup error: If you use a constant pressure\n"
1557	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1558	>	painCave.isFatal = 1;
1559	>	simError();
1560	>	}
1561
1562	<	if( globals->haveTauBarostat() )
1563	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1564	<	else{
1565	<	sprintf( painCave.errMsg,
1566	<	"SimSetup error: If you use an NPT\n"
1567	<	"    ensemble, you must set tauBarostat.\n");
1568	<	painCave.isFatal = 1;
1569	<	simError();
1570	<	}
1375	<	break;
1376	<
1377	<	case NPTim_ENS:
1378	<	myNPTim = new NPTim( info, the_ff );
1379	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1562	>	if( globals->haveTauThermostat() )
1563	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1564	>	else{
1565	>	sprintf( painCave.errMsg,
1566	>	"SimSetup error: If you use an NPT\n"
1567	>	"    ensemble, you must set tauThermostat.\n");
1568	>	painCave.isFatal = 1;
1569	>	simError();
1570	>	}
1571
1572	<	if (globals->haveTargetPressure())
1573	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1574	<	else {
1572	>	if( globals->haveTauBarostat() )
1573	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1574	>	else{
1575	>	sprintf( painCave.errMsg,
1576	>	"SimSetup error: If you use an NPT\n"
1577	>	"    ensemble, you must set tauBarostat.\n");
1578	>	painCave.isFatal = 1;
1579	>	simError();
1580	>	}
1581	>	break;
1582	>
1583	>	default:
1584		sprintf( painCave.errMsg,
1585	<	"SimSetup error: If you use a constant pressure\n"
1386	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1585	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1586		painCave.isFatal = 1;
1587		simError();
1588		}
1390	–
1391	–	if( globals->haveTauThermostat() )
1392	–	myNPTim->setTauThermostat( globals->getTauThermostat() );
1393	–	else{
1394	–	sprintf( painCave.errMsg,
1395	–	"SimSetup error: If you use an NPT\n"
1396	–	"    ensemble, you must set tauThermostat.\n");
1397	–	painCave.isFatal = 1;
1398	–	simError();
1399	–	}
1400	–
1401	–	if( globals->haveTauBarostat() )
1402	–	myNPTim->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;
1408	–	simError();
1409	–	}
1410	–	break;
1411	–
1412	–	case NPTfm_ENS:
1413	–	myNPTfm = new NPTfm( info, the_ff );
1414	–	myNPTfm->setTargetTemp( globals->getTargetTemp());
1415	–
1416	–	if (globals->haveTargetPressure())
1417	–	myNPTfm->setTargetPressure(globals->getTargetPressure());
1418	–	else {
1419	–	sprintf( painCave.errMsg,
1420	–	"SimSetup error: If you use a constant pressure\n"
1421	–	"    ensemble, you must set targetPressure in the BASS file.\n");
1422	–	painCave.isFatal = 1;
1423	–	simError();
1424	–	}
1425	–
1426	–	if( globals->haveTauThermostat() )
1427	–	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1428	–	else{
1429	–	sprintf( painCave.errMsg,
1430	–	"SimSetup error: If you use an NPT\n"
1431	–	"    ensemble, you must set tauThermostat.\n");
1432	–	painCave.isFatal = 1;
1433	–	simError();
1434	–	}
1435	–
1436	–	if( globals->haveTauBarostat() )
1437	–	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1438	–	else{
1439	–	sprintf( painCave.errMsg,
1440	–	"SimSetup error: If you use an NPT\n"
1441	–	"    ensemble, you must set tauBarostat.\n");
1442	–	painCave.isFatal = 1;
1443	–	simError();
1444	–	}
1445	–	break;
1446	–
1447	–	default:
1448	–	sprintf( painCave.errMsg,
1449	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1450	–	painCave.isFatal = 1;
1451	–	simError();
1589		}
1453	–
1590		}
1591
1592		void SimSetup::initFortran( void ){
1593
1594	<	info->refreshSim();
1594	>	info[0].refreshSim();
1595
1596	<	if( !strcmp( info->mixingRule, "standard") ){
1596	>	if( !strcmp( info[0].mixingRule, "standard") ){
1597		the_ff->initForceField( LB_MIXING_RULE );
1598		}
1599	<	else if( !strcmp( info->mixingRule, "explicit") ){
1599	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1600		the_ff->initForceField( EXPLICIT_MIXING_RULE );
1601		}
1602		else{
1603		sprintf( painCave.errMsg,
1604	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1605	<	info->mixingRule );
1604	>	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1605	>	info[0].mixingRule );
1606		painCave.isFatal = 1;
1607		simError();
1608		}
#	Line 1474 | Line 1610 | void SimSetup::initFortran( void ){
1610
1611		#ifdef IS_MPI
1612		strcpy( checkPointMsg,
1613	<	"Successfully intialized the mixingRule for Fortran." );
1613	>	"Successfully intialized the mixingRule for Fortran." );
1614		MPIcheckPoint();
1615		#endif // is_mpi
1616
1617		}
1618	+
1619	+	void SimSetup::setupZConstraint(SimInfo& theInfo)
1620	+	{
1621	+	int nZConstraints;
1622	+	ZconStamp** zconStamp;
1623	+
1624	+	if(globals->haveZconstraintTime()){
1625	+
1626	+	//add sample time of z-constraint  into SimInfo's property list
1627	+	DoubleData* zconsTimeProp = new DoubleData();
1628	+	zconsTimeProp->setID(ZCONSTIME_ID);
1629	+	zconsTimeProp->setData(globals->getZconsTime());
1630	+	theInfo.addProperty(zconsTimeProp);
1631	+	}
1632	+	else{
1633	+	sprintf( painCave.errMsg,
1634	+	"ZConstraint error: If you use an ZConstraint\n"
1635	+	" , you must set sample time.\n");
1636	+	painCave.isFatal = 1;
1637	+	simError();
1638	+	}
1639	+
1640	+	//push zconsTol into siminfo, if user does not specify
1641	+	//value for zconsTol, a default value will be used
1642	+	DoubleData* zconsTol = new DoubleData();
1643	+	zconsTol->setID(ZCONSTOL_ID);
1644	+	if(globals->haveZconsTol()){
1645	+	zconsTol->setData(globals->getZconsTol());
1646	+	}
1647	+	else{
1648	+	double defaultZConsTol = 0.01;
1649	+	sprintf( painCave.errMsg,
1650	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1651	+	" , default value %f is used.\n", defaultZConsTol);
1652	+	painCave.isFatal = 0;
1653	+	simError();
1654	+
1655	+	zconsTol->setData(defaultZConsTol);
1656	+	}
1657	+	theInfo.addProperty(zconsTol);
1658	+
1659	+	//set Force Substraction Policy
1660	+	StringData* zconsForcePolicy =  new StringData();
1661	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1662	+
1663	+	if(globals->haveZconsForcePolicy()){
1664	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1665	+	}
1666	+	else{
1667	+	sprintf( painCave.errMsg,
1668	+	"ZConstraint Warning: User does not set force substraction policy, "
1669	+	"average force substraction policy is used\n");
1670	+	painCave.isFatal = 0;
1671	+	simError();
1672	+	zconsForcePolicy->setData("BYNUMBER");
1673	+	}
1674	+
1675	+	theInfo.addProperty(zconsForcePolicy);
1676	+
1677	+	//Determine the name of ouput file and add it into SimInfo's property list
1678	+	//Be careful, do not use inFileName, since it is a pointer which
1679	+	//point to a string at master node, and slave nodes do not contain that string
1680	+
1681	+	string zconsOutput(theInfo.finalName);
1682	+
1683	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1684	+
1685	+	StringData* zconsFilename = new StringData();
1686	+	zconsFilename->setID(ZCONSFILENAME_ID);
1687	+	zconsFilename->setData(zconsOutput);
1688	+
1689	+	theInfo.addProperty(zconsFilename);
1690	+
1691	+	//setup index, pos and other parameters of z-constraint molecules
1692	+	nZConstraints = globals->getNzConstraints();
1693	+	theInfo.nZconstraints = nZConstraints;
1694	+
1695	+	zconStamp = globals->getZconStamp();
1696	+	ZConsParaItem tempParaItem;
1697	+
1698	+	ZConsParaData* zconsParaData = new ZConsParaData();
1699	+	zconsParaData->setID(ZCONSPARADATA_ID);
1700	+
1701	+	for(int i = 0; i < nZConstraints; i++){
1702	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1703	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1704	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1705	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1706	+
1707	+	zconsParaData->addItem(tempParaItem);
1708	+	}
1709	+
1710	+	//sort the parameters by index of molecules
1711	+	zconsParaData->sortByIndex();
1712	+
1713	+	//push data into siminfo, therefore, we can retrieve later
1714	+	theInfo.addProperty(zconsParaData);
1715	+
1716	+	}

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