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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 644 by mmeineke, Tue Jul 22 16:41:08 2003 UTC vs.
Revision 701 by tim, Wed Aug 20 14:34:04 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 14 | Line 17
17
18		// some defines for ensemble and Forcefield  cases
19
20	<	#define NVE_ENS   0
21	<	#define NVT_ENS   1
22	<	#define NPTi_ENS  2
23	<	#define NPTf_ENS  3
24	<	#define NPTim_ENS 4
25	<	#define NPTfm_ENS 5
20	>	#define NVE_ENS        0
21	>	#define NVT_ENS        1
22	>	#define NPTi_ENS       2
23	>	#define NPTf_ENS       3
24	>	#define NPTim_ENS      4
25	>	#define NPTfm_ENS      5
26
24	–
27		#define FF_DUFF 0
28		#define FF_LJ   1
29	+	#define FF_EAM  2
30
31	+	using namespace std;
32
33		SimSetup::SimSetup(){
34	+
35	+	isInfoArray = 0;
36	+	nInfo = 1;
37	+
38		stamps = new MakeStamps();
39		globals = new Globals();
40
41	+
42		#ifdef IS_MPI
43		strcpy( checkPointMsg, "SimSetup creation successful" );
44		MPIcheckPoint();
#	Line 41 | Line 50 | void SimSetup::parseFile( char* fileName ){
50		delete globals;
51		}
52
53	+	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
54	+	info = the_info;
55	+	nInfo = theNinfo;
56	+	isInfoArray = 1;
57	+	}
58	+
59	+
60		void SimSetup::parseFile( char* fileName ){
61
62		#ifdef IS_MPI
#	Line 76 | Line 92 | void SimSetup::createSim( void ){
92
93		#endif // is_mpi
94
95	<	void SimSetup::createSim( void ){
95	>	void SimSetup::createSim(void){
96
97		int i, j, k, globalAtomIndex;
98
99		// gather all of the information from the Bass file
100	<
100	>
101		gatherInfo();
102
103		// creation of complex system objects
#	Line 89 | Line 105 | void SimSetup::createSim( void ){
105		sysObjectsCreation();
106
107		// check on the post processing info
108	<
108	>
109		finalInfoCheck();
110
111		// initialize the system coordinates
112
113	<	initSystemCoords();
98	<
113	>	if( !isInfoArray ) initSystemCoords();
114
115		// make the output filenames
116
#	Line 120 | Line 135 | void SimSetup::makeMolecules( void ){
135
136		void SimSetup::makeMolecules( void ){
137
138	+	int k,l;
139		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140		molInit molInfo;
141		DirectionalAtom* dAtom;
#	Line 144 | Line 160 | void SimSetup::makeMolecules( void ){
160
161		double ux, uy, uz, u, uSqr;
162
163	<	atomOffset = 0;
148	<	excludeOffset = 0;
149	<	for(i=0; i<info->n_mol; i++){
163	>	for(k=0; k<nInfo; k++){
164
165	<	stampID = the_molecules[i].getStampID();
165	>	the_ff->setSimInfo( &(info[k]) );
166
167	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
168	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
169	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
170	<	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
171	<	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
167	>	atomOffset = 0;
168	>	excludeOffset = 0;
169	>	for(i=0; i<info[k].n_mol; i++){
170	>
171	>	stampID = info[k].molecules[i].getStampID();
172
173	<	molInfo.myAtoms = &the_atoms[atomOffset];
174	<	molInfo.myExcludes = &the_excludes[excludeOffset];
175	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
176	<	molInfo.myBends = new Bend*[molInfo.nBends];
177	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
173	>	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
174	>	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
175	>	molInfo.nBends    = comp_stamps[stampID]->getNBends();
176	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
177	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
178	>
179	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
180	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
181	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
182	>	molInfo.myBends = new Bend*[molInfo.nBends];
183	>	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
184
185	<	theBonds = new bond_pair[molInfo.nBonds];
186	<	theBends = new bend_set[molInfo.nBends];
187	<	theTorsions = new torsion_set[molInfo.nTorsions];
185	>	theBonds = new bond_pair[molInfo.nBonds];
186	>	theBends = new bend_set[molInfo.nBends];
187	>	theTorsions = new torsion_set[molInfo.nTorsions];
188
189	<	// make the Atoms
189	>	// make the Atoms
190
191	<	for(j=0; j<molInfo.nAtoms; j++){
192	<
193	<	currentAtom = comp_stamps[stampID]->getAtom( j );
194	<	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() );
191	>	for(j=0; j<molInfo.nAtoms; j++){
192	>
193	>	currentAtom = comp_stamps[stampID]->getAtom( j );
194	>	if( currentAtom->haveOrientation() ){
195
196	+	dAtom = new DirectionalAtom( (j + atomOffset),
197	+	info[k].getConfiguration() );
198	+	info[k].n_oriented++;
199	+	molInfo.myAtoms[j] = dAtom;
200	+
201	+	ux = currentAtom->getOrntX();
202	+	uy = currentAtom->getOrntY();
203	+	uz = currentAtom->getOrntZ();
204	+
205	+	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
206	+
207	+	u = sqrt( uSqr );
208	+	ux = ux / u;
209	+	uy = uy / u;
210	+	uz = uz / u;
211	+
212	+	dAtom->setSUx( ux );
213	+	dAtom->setSUy( uy );
214	+	dAtom->setSUz( uz );
215	+	}
216	+	else{
217	+	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
218	+	info[k].getConfiguration() );
219	+	}
220	+	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221	+
222		#ifdef IS_MPI
223
224	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
224	>	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
225
226		#endif // is_mpi
227	<	}
227	>	}
228
229		// make the bonds
230	<	for(j=0; j<molInfo.nBonds; j++){
230	>	for(j=0; j<molInfo.nBonds; j++){
231
232	<	currentBond = comp_stamps[stampID]->getBond( j );
233	<	theBonds[j].a = currentBond->getA() + atomOffset;
234	<	theBonds[j].b = currentBond->getB() + atomOffset;
235	<
236	<	exI = theBonds[j].a;
237	<	exJ = theBonds[j].b;
238	<
239	<	// exclude_I must always be the smaller of the pair
240	<	if( exI > exJ ){
241	<	tempEx = exI;
242	<	exI = exJ;
243	<	exJ = tempEx;
244	<	}
232	>	currentBond = comp_stamps[stampID]->getBond( j );
233	>	theBonds[j].a = currentBond->getA() + atomOffset;
234	>	theBonds[j].b = currentBond->getB() + atomOffset;
235	>
236	>	exI = theBonds[j].a;
237	>	exJ = theBonds[j].b;
238	>
239	>	// exclude_I must always be the smaller of the pair
240	>	if( exI > exJ ){
241	>	tempEx = exI;
242	>	exI = exJ;
243	>	exJ = tempEx;
244	>	}
245		#ifdef IS_MPI
246	<	tempEx = exI;
247	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
248	<	tempEx = exJ;
249	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
250	<
251	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
246	>	tempEx = exI;
247	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
248	>	tempEx = exJ;
249	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
250	>
251	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
252		#else  // isn't MPI
253	<
254	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
253	>
254	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
255		#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	–	}
256		}
257	<
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	<	}
257	>	excludeOffset += molInfo.nBonds;
258
259	<	// exclude_I must always be the smaller of the pair
260	<	if( exI > exJ ){
261	<	tempEx = exI;
262	<	exI = exJ;
263	<	exJ = tempEx;
264	<	}
265	<	#ifdef IS_MPI
266	<	tempEx = exI;
267	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
268	<	tempEx = exJ;
269	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
270	<
271	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
272	<	#else  // isn't MPI
273	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
274	<	#endif  //is_mpi
275	<	}
276	<	excludeOffset += molInfo.nBends;
277	<
278	<	for(j=0; j<molInfo.nTorsions; j++){
259	>	//make the bends
260	>	for(j=0; j<molInfo.nBends; j++){
261	>
262	>	currentBend = comp_stamps[stampID]->getBend( j );
263	>	theBends[j].a = currentBend->getA() + atomOffset;
264	>	theBends[j].b = currentBend->getB() + atomOffset;
265	>	theBends[j].c = currentBend->getC() + atomOffset;
266	>
267	>	if( currentBend->haveExtras() ){
268	>
269	>	extras = currentBend->getExtras();
270	>	current_extra = extras;
271	>
272	>	while( current_extra != NULL ){
273	>	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
274	>
275	>	switch( current_extra->getType() ){
276	>
277	>	case 0:
278	>	theBends[j].ghost =
279	>	current_extra->getInt() + atomOffset;
280	>	theBends[j].isGhost = 1;
281	>	break;
282	>
283	>	case 1:
284	>	theBends[j].ghost =
285	>	(int)current_extra->getDouble() + atomOffset;
286	>	theBends[j].isGhost = 1;
287	>	break;
288	>
289	>	default:
290	>	sprintf( painCave.errMsg,
291	>	"SimSetup Error: ghostVectorSource was neither a "
292	>	"double nor an int.\n"
293	>	"-->Bend[%d] in %s\n",
294	>	j, comp_stamps[stampID]->getID() );
295	>	painCave.isFatal = 1;
296	>	simError();
297	>	}
298	>	}
299
300	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
301	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
302	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
303	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
304	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
305	<
306	<	exI = theTorsions[j].a;
307	<	exJ = theTorsions[j].d;
308	<
334	<	// exclude_I must always be the smaller of the pair
335	<	if( exI > exJ ){
336	<	tempEx = exI;
337	<	exI = exJ;
338	<	exJ = tempEx;
300	>	else{
301	>
302	>	sprintf( painCave.errMsg,
303	>	"SimSetup Error: unhandled bend assignment:\n"
304	>	"    -->%s in Bend[%d] in %s\n",
305	>	current_extra->getlhs(),
306	>	j, comp_stamps[stampID]->getID() );
307	>	painCave.isFatal = 1;
308	>	simError();
309		}
310	+
311	+	current_extra = current_extra->getNext();
312	+	}
313	+	}
314	+
315	+	if( !theBends[j].isGhost ){
316	+
317	+	exI = theBends[j].a;
318	+	exJ = theBends[j].c;
319	+	}
320	+	else{
321	+
322	+	exI = theBends[j].a;
323	+	exJ = theBends[j].b;
324	+	}
325	+
326	+	// exclude_I must always be the smaller of the pair
327	+	if( exI > exJ ){
328	+	tempEx = exI;
329	+	exI = exJ;
330	+	exJ = tempEx;
331	+	}
332		#ifdef IS_MPI
333	<	tempEx = exI;
334	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
335	<	tempEx = exJ;
336	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
333	>	tempEx = exI;
334	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
335	>	tempEx = exJ;
336	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
337
338	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
338	>	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
339		#else  // isn't MPI
340	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
340	>	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
341		#endif  //is_mpi
342	<	}
343	<	excludeOffset += molInfo.nTorsions;
344	<
345	<
346	<	// send the arrays off to the forceField for init.
347	<
348	<	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
349	<	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
350	<	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
351	<	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
352	<
353	<
354	<	the_molecules[i].initialize( molInfo );
355	<
356	<
357	<	atomOffset += molInfo.nAtoms;
358	<	delete[] theBonds;
359	<	delete[] theBends;
360	<	delete[] theTorsions;
342	>	}
343	>	excludeOffset += molInfo.nBends;
344	>
345	>	for(j=0; j<molInfo.nTorsions; j++){
346	>
347	>	currentTorsion = comp_stamps[stampID]->getTorsion( j );
348	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
349	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
350	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
351	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
352	>
353	>	exI = theTorsions[j].a;
354	>	exJ = theTorsions[j].d;
355	>
356	>	// exclude_I must always be the smaller of the pair
357	>	if( exI > exJ ){
358	>	tempEx = exI;
359	>	exI = exJ;
360	>	exJ = tempEx;
361		}
362	+	#ifdef IS_MPI
363	+	tempEx = exI;
364	+	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
365	+	tempEx = exJ;
366	+	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
367	+
368	+	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
369	+	#else  // isn't MPI
370	+	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
371	+	#endif  //is_mpi
372	+	}
373	+	excludeOffset += molInfo.nTorsions;
374	+
375	+
376	+	// send the arrays off to the forceField for init.
377	+
378	+	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
379	+	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
380	+	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
381	+	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
382	+
383	+
384	+	info[k].molecules[i].initialize( molInfo );
385
386	+
387	+	atomOffset += molInfo.nAtoms;
388	+	delete[] theBonds;
389	+	delete[] theBends;
390	+	delete[] theTorsions;
391	+	}
392	+	}
393	+
394		#ifdef IS_MPI
395		sprintf( checkPointMsg, "all molecules initialized succesfully" );
396		MPIcheckPoint();
397		#endif // is_mpi
398	<
398	>
399		// clean up the forcefield
400	+
401		the_ff->calcRcut();
402		the_ff->cleanMe();
403	<
403	>
404		}
405
406		void SimSetup::initFromBass( void ){
#	Line 389 | Line 413 | void SimSetup::initFromBass( void ){
413		int n_extra;
414		int have_extra, done;
415
416	+	double vel[3];
417	+	vel[0] = 0.0;
418	+	vel[1] = 0.0;
419	+	vel[2] = 0.0;
420	+
421		temp1 = (double)tot_nmol / 4.0;
422		temp2 = pow( temp1, ( 1.0 / 3.0 ) );
423		temp3 = ceil( temp2 );
#	Line 398 | Line 427 | void SimSetup::initFromBass( void ){
427		have_extra =1;
428
429		n_cells = (int)temp3 - 1;
430	<	cellx = info->boxL[0] / temp3;
431	<	celly = info->boxL[1] / temp3;
432	<	cellz = info->boxL[2] / temp3;
430	>	cellx = info[0].boxL[0] / temp3;
431	>	celly = info[0].boxL[1] / temp3;
432	>	cellz = info[0].boxL[2] / temp3;
433		n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
434		temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
435		n_per_extra = (int)ceil( temp1 );
436
437		if( n_per_extra > 4){
438		sprintf( painCave.errMsg,
439	<	"SimSetup error. There has been an error in constructing"
440	<	" the non-complete lattice.\n" );
439	>	"SimSetup error. There has been an error in constructing"
440	>	" the non-complete lattice.\n" );
441		painCave.isFatal = 1;
442		simError();
443		}
444		}
445		else{
446		n_cells = (int)temp3;
447	<	cellx = info->boxL[0] / temp3;
448	<	celly = info->boxL[1] / temp3;
449	<	cellz = info->boxL[2] / temp3;
447	>	cellx = info[0].boxL[0] / temp3;
448	>	celly = info[0].boxL[1] / temp3;
449	>	cellz = info[0].boxL[2] / temp3;
450		}
451
452		current_mol = 0;
#	Line 429 | Line 458 | void SimSetup::initFromBass( void ){
458		for( j=0; j < n_cells; j++ ){
459		for( k=0; k < n_cells; k++ ){
460
461	<	makeElement( i * cellx,
462	<	j * celly,
463	<	k * cellz );
461	>	makeElement( i * cellx,
462	>	j * celly,
463	>	k * cellz );
464
465	<	makeElement( i * cellx + 0.5 * cellx,
466	<	j * celly + 0.5 * celly,
467	<	k * cellz );
465	>	makeElement( i * cellx + 0.5 * cellx,
466	>	j * celly + 0.5 * celly,
467	>	k * cellz );
468
469	<	makeElement( i * cellx,
470	<	j * celly + 0.5 * celly,
471	<	k * cellz + 0.5 * cellz );
469	>	makeElement( i * cellx,
470	>	j * celly + 0.5 * celly,
471	>	k * cellz + 0.5 * cellz );
472
473	<	makeElement( i * cellx + 0.5 * cellx,
474	<	j * celly,
475	<	k * cellz + 0.5 * cellz );
473	>	makeElement( i * cellx + 0.5 * cellx,
474	>	j * celly,
475	>	k * cellz + 0.5 * cellz );
476		}
477		}
478		}
#	Line 455 | Line 484 | void SimSetup::initFromBass( void ){
484		for( i=0; i < (n_cells+1) && !done; i++ ){
485		for( j=0; j < (n_cells+1) && !done; j++ ){
486
487	<	if( i < n_cells ){
487	>	if( i < n_cells ){
488
489	<	if( j < n_cells ){
490	<	start_ndx = n_cells;
491	<	}
492	<	else start_ndx = 0;
493	<	}
494	<	else start_ndx = 0;
489	>	if( j < n_cells ){
490	>	start_ndx = n_cells;
491	>	}
492	>	else start_ndx = 0;
493	>	}
494	>	else start_ndx = 0;
495
496	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
496	>	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
497
498	<	makeElement( i * cellx,
499	<	j * celly,
500	<	k * cellz );
501	<	done = ( current_mol >= tot_nmol );
473	<
474	<	if( !done && n_per_extra > 1 ){
475	<	makeElement( i * cellx + 0.5 * cellx,
476	<	j * celly + 0.5 * celly,
477	<	k * cellz );
478	<	done = ( current_mol >= tot_nmol );
479	<	}
498	>	makeElement( i * cellx,
499	>	j * celly,
500	>	k * cellz );
501	>	done = ( current_mol >= tot_nmol );
502
503	<	if( !done && n_per_extra > 2){
504	<	makeElement( i * cellx,
505	<	j * celly + 0.5 * celly,
506	<	k * cellz + 0.5 * cellz );
507	<	done = ( current_mol >= tot_nmol );
508	<	}
503	>	if( !done && n_per_extra > 1 ){
504	>	makeElement( i * cellx + 0.5 * cellx,
505	>	j * celly + 0.5 * celly,
506	>	k * cellz );
507	>	done = ( current_mol >= tot_nmol );
508	>	}
509
510	<	if( !done && n_per_extra > 3){
511	<	makeElement( i * cellx + 0.5 * cellx,
512	<	j * celly,
513	<	k * cellz + 0.5 * cellz );
514	<	done = ( current_mol >= tot_nmol );
515	<	}
516	<	}
510	>	if( !done && n_per_extra > 2){
511	>	makeElement( i * cellx,
512	>	j * celly + 0.5 * celly,
513	>	k * cellz + 0.5 * cellz );
514	>	done = ( current_mol >= tot_nmol );
515	>	}
516	>
517	>	if( !done && n_per_extra > 3){
518	>	makeElement( i * cellx + 0.5 * cellx,
519	>	j * celly,
520	>	k * cellz + 0.5 * cellz );
521	>	done = ( current_mol >= tot_nmol );
522	>	}
523	>	}
524		}
525		}
526		}
527
528	<
529	<	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 );
528	>	for( i=0; i<info[0].n_atoms; i++ ){
529	>	info[0].atoms[i]->setVel( vel );
530		}
531		}
532
#	Line 510 | Line 536 | void SimSetup::makeElement( double x, double y, double
536		AtomStamp* current_atom;
537		DirectionalAtom* dAtom;
538		double rotMat[3][3];
539	+	double pos[3];
540
541		for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
542
543		current_atom = comp_stamps[current_comp]->getAtom( k );
544		if( !current_atom->havePosition() ){
545		sprintf( painCave.errMsg,
546	<	"SimSetup:initFromBass error.\n"
547	<	"\tComponent %s, atom %s does not have a position specified.\n"
548	<	"\tThe initialization routine is unable to give a start"
549	<	" position.\n",
550	<	comp_stamps[current_comp]->getID(),
551	<	current_atom->getType() );
546	>	"SimSetup:initFromBass error.\n"
547	>	"\tComponent %s, atom %s does not have a position specified.\n"
548	>	"\tThe initialization routine is unable to give a start"
549	>	" position.\n",
550	>	comp_stamps[current_comp]->getID(),
551	>	current_atom->getType() );
552		painCave.isFatal = 1;
553		simError();
554		}
555	+
556	+	pos[0] = x + current_atom->getPosX();
557	+	pos[1] = y + current_atom->getPosY();
558	+	pos[2] = z + current_atom->getPosZ();
559	+
560	+	info[0].atoms[current_atom_ndx]->setPos( pos );
561
562	<	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() );
562	>	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
563
564	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
564	>	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
565
535	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
536	–
566		rotMat[0][0] = 1.0;
567		rotMat[0][1] = 0.0;
568		rotMat[0][2] = 0.0;
#	Line 569 | Line 598 | void SimSetup::gatherInfo( void ){
598		ensembleCase = -1;
599		ffCase = -1;
600
572	–	// get the stamps and globals;
573	–	stamps = stamps;
574	–	globals = globals;
575	–
601		// set the easy ones first
602	<	info->target_temp = globals->getTargetTemp();
603	<	info->dt = globals->getDt();
604	<	info->run_time = globals->getRunTime();
602	>
603	>	for( i=0; i<nInfo; i++){
604	>	info[i].target_temp = globals->getTargetTemp();
605	>	info[i].dt = globals->getDt();
606	>	info[i].run_time = globals->getRunTime();
607	>	}
608		n_components = globals->getNComponents();
609
610
#	Line 586 | Line 614 | void SimSetup::gatherInfo( void ){
614
615		if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
616		else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
617	+	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
618		else{
619		sprintf( painCave.errMsg,
620	<	"SimSetup Error. Unrecognized force field -> %s\n",
621	<	force_field );
620	>	"SimSetup Error. Unrecognized force field -> %s\n",
621	>	force_field );
622		painCave.isFatal = 1;
623		simError();
624		}
#	Line 607 | Line 636 | void SimSetup::gatherInfo( void ){
636		else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
637		else{
638		sprintf( painCave.errMsg,
639	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
639	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
640		"reverting to NVE for this simulation.\n",
641	<	ensemble );
641	>	ensemble );
642		painCave.isFatal = 0;
643		simError();
644		strcpy( ensemble, "NVE" );
645		ensembleCase = NVE_ENS;
646		}
647	<	strcpy( info->ensemble, ensemble );
647	>
648	>	for(i=0; i<nInfo; i++){
649	>
650	>	strcpy( info[i].ensemble, ensemble );
651
652	<	// get the mixing rule
652	>	// get the mixing rule
653
654	<	strcpy( info->mixingRule, globals->getMixingRule() );
655	<	info->usePBC = globals->getPBC();
656	<
654	>	strcpy( info[i].mixingRule, globals->getMixingRule() );
655	>	info[i].usePBC = globals->getPBC();
656	>	}
657
658		// get the components and calculate the tot_nMol and indvidual n_mol
659
#	Line 637 | Line 669 | void SimSetup::gatherInfo( void ){
669		for( i=0; i<n_components; i++ ){
670
671		if( !the_components[i]->haveNMol() ){
672	<	// we have a problem
673	<	sprintf( painCave.errMsg,
674	<	"SimSetup Error. No global NMol or component NMol"
675	<	" given. Cannot calculate the number of atoms.\n" );
676	<	painCave.isFatal = 1;
677	<	simError();
672	>	// we have a problem
673	>	sprintf( painCave.errMsg,
674	>	"SimSetup Error. No global NMol or component NMol"
675	>	" given. Cannot calculate the number of atoms.\n" );
676	>	painCave.isFatal = 1;
677	>	simError();
678		}
679
680		tot_nmol += the_components[i]->getNMol();
#	Line 651 | Line 683 | void SimSetup::gatherInfo( void ){
683		}
684		else{
685		sprintf( painCave.errMsg,
686	<	"SimSetup error.\n"
687	<	"\tSorry, the ability to specify total"
688	<	" nMols and then give molfractions in the components\n"
689	<	"\tis not currently supported."
690	<	" Please give nMol in the components.\n" );
686	>	"SimSetup error.\n"
687	>	"\tSorry, the ability to specify total"
688	>	" nMols and then give molfractions in the components\n"
689	>	"\tis not currently supported."
690	>	" Please give nMol in the components.\n" );
691		painCave.isFatal = 1;
692		simError();
693		}
694
695		// set the status, sample, and thermal kick times
696
697	<	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	<	}
697	>	for(i=0; i<nInfo; i++){
698
699	<	if( globals->haveStatusTime() ){
700	<	info->statusTime = globals->getStatusTime();
701	<	}
702	<
703	<	if( globals->haveThermalTime() ){
704	<	info->thermalTime = globals->getThermalTime();
705	<	}
706	<
707	<	// check for the temperature set flag
708	<
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();
699	>	if( globals->haveSampleTime() ){
700	>	info[i].sampleTime = globals->getSampleTime();
701	>	info[i].statusTime = info[i].sampleTime;
702	>	info[i].thermalTime = info[i].sampleTime;
703	>	}
704	>	else{
705	>	info[i].sampleTime = globals->getRunTime();
706	>	info[i].statusTime = info[i].sampleTime;
707	>	info[i].thermalTime = info[i].sampleTime;
708	>	}
709
710	<	info->setBox( boxVector );
711	<	}
698	<	else if( globals->haveDensity() ){
699	<
700	<	double vol;
701	<	vol = (double)tot_nmol / globals->getDensity();
702	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
703	<	boxVector[1] = boxVector[0];
704	<	boxVector[2] = boxVector[0];
705	<
706	<	info->setBox( boxVector );
707	<	}
708	<	else{
709	<	if( !globals->haveBoxX() ){
710	<	sprintf( painCave.errMsg,
711	<	"SimSetup error, no periodic BoxX size given.\n" );
712	<	painCave.isFatal = 1;
713	<	simError();
710	>	if( globals->haveStatusTime() ){
711	>	info[i].statusTime = globals->getStatusTime();
712		}
713	<	boxVector[0] = globals->getBoxX();
714	<
715	<	if( !globals->haveBoxY() ){
718	<	sprintf( painCave.errMsg,
719	<	"SimSetup error, no periodic BoxY size given.\n" );
720	<	painCave.isFatal = 1;
721	<	simError();
713	>
714	>	if( globals->haveThermalTime() ){
715	>	info[i].thermalTime = globals->getThermalTime();
716		}
723	–	boxVector[1] = globals->getBoxY();
717
718	<	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();
718	>	// check for the temperature set flag
719
720	<	info->setBox( boxVector );
720	>	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
721	>
722	>	// get some of the tricky things that may still be in the globals
723	>
724	>	double boxVector[3];
725	>	if( globals->haveBox() ){
726	>	boxVector[0] = globals->getBox();
727	>	boxVector[1] = globals->getBox();
728	>	boxVector[2] = globals->getBox();
729	>
730	>	info[i].setBox( boxVector );
731	>	}
732	>	else if( globals->haveDensity() ){
733	>
734	>	double vol;
735	>	vol = (double)tot_nmol / globals->getDensity();
736	>	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
737	>	boxVector[1] = boxVector[0];
738	>	boxVector[2] = boxVector[0];
739	>
740	>	info[i].setBox( boxVector );
741		}
742	<
742	>	else{
743	>	if( !globals->haveBoxX() ){
744	>	sprintf( painCave.errMsg,
745	>	"SimSetup error, no periodic BoxX size given.\n" );
746	>	painCave.isFatal = 1;
747	>	simError();
748	>	}
749	>	boxVector[0] = globals->getBoxX();
750	>
751	>	if( !globals->haveBoxY() ){
752	>	sprintf( painCave.errMsg,
753	>	"SimSetup error, no periodic BoxY size given.\n" );
754	>	painCave.isFatal = 1;
755	>	simError();
756	>	}
757	>	boxVector[1] = globals->getBoxY();
758	>
759	>	if( !globals->haveBoxZ() ){
760	>	sprintf( painCave.errMsg,
761	>	"SimSetup error, no periodic BoxZ size given.\n" );
762	>	painCave.isFatal = 1;
763	>	simError();
764	>	}
765	>	boxVector[2] = globals->getBoxZ();
766	>
767	>	info[i].setBox( boxVector );
768	>	}
769
770	+	}
771
772		#ifdef IS_MPI
773		strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
#	Line 746 | Line 780 | void SimSetup::finalInfoCheck( void ){
780		void SimSetup::finalInfoCheck( void ){
781		int index;
782		int usesDipoles;
783	<
783	>	int i;
784
785	<	// check electrostatic parameters
786	<
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	<	double theEcr, theEst;
766	<
767	<	if (globals->getUseRF() ) {
768	<	info->useReactionField = 1;
785	>	for(i=0; i<nInfo; i++){
786	>	// check electrostatic parameters
787
788	<	if( !globals->haveECR() ){
789	<	sprintf( painCave.errMsg,
790	<	"SimSetup Warning: using default value of 1/2 the smallest "
791	<	"box length for the electrostaticCutoffRadius.\n"
792	<	"I hope you have a very fast processor!\n");
775	<	painCave.isFatal = 0;
776	<	simError();
777	<	double smallest;
778	<	smallest = info->boxL[0];
779	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
780	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
781	<	theEcr = 0.5 * smallest;
782	<	} else {
783	<	theEcr = globals->getECR();
788	>	index = 0;
789	>	usesDipoles = 0;
790	>	while( (index < info[i].n_atoms) && !usesDipoles ){
791	>	usesDipoles = (info[i].atoms[index])->hasDipole();
792	>	index++;
793		}
785	–
786	–	if( !globals->haveEST() ){
787	–	sprintf( painCave.errMsg,
788	–	"SimSetup Warning: using default value of 0.05 * the "
789	–	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
790	–	);
791	–	painCave.isFatal = 0;
792	–	simError();
793	–	theEst = 0.05 * theEcr;
794	–	} else {
795	–	theEst= globals->getEST();
796	–	}
797	–
798	–	info->setEcr( theEcr, theEst );
794
795	<	if(!globals->haveDielectric() ){
796	<	sprintf( painCave.errMsg,
797	<	"SimSetup Error: You are trying to use Reaction Field without"
798	<	"setting a dielectric constant!\n"
799	<	);
800	<	painCave.isFatal = 1;
801	<	simError();
802	<	}
803	<	info->dielectric = globals->getDielectric();
809	<	}
810	<	else {
811	<	if (usesDipoles) {
795	>	#ifdef IS_MPI
796	>	int myUse = usesDipoles;
797	>	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
798	>	#endif //is_mpi
799	>
800	>	double theEcr, theEst;
801	>
802	>	if (globals->getUseRF() ) {
803	>	info[i].useReactionField = 1;
804
805		if( !globals->haveECR() ){
806	<	sprintf( painCave.errMsg,
807	<	"SimSetup Warning: using default value of 1/2 the smallest "
808	<	"box length for the electrostaticCutoffRadius.\n"
809	<	"I hope you have a very fast processor!\n");
810	<	painCave.isFatal = 0;
811	<	simError();
812	<	double smallest;
813	<	smallest = info->boxL[0];
814	<	if (info->boxL[1] <= smallest) smallest = info->boxL[1];
815	<	if (info->boxL[2] <= smallest) smallest = info->boxL[2];
816	<	theEcr = 0.5 * smallest;
806	>	sprintf( painCave.errMsg,
807	>	"SimSetup Warning: using default value of 1/2 the smallest "
808	>	"box length for the electrostaticCutoffRadius.\n"
809	>	"I hope you have a very fast processor!\n");
810	>	painCave.isFatal = 0;
811	>	simError();
812	>	double smallest;
813	>	smallest = info[i].boxL[0];
814	>	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
815	>	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
816	>	theEcr = 0.5 * smallest;
817		} else {
818	<	theEcr = globals->getECR();
818	>	theEcr = globals->getECR();
819		}
820
821		if( !globals->haveEST() ){
822	<	sprintf( painCave.errMsg,
823	<	"SimSetup Warning: using default value of 0.05 * the "
824	<	"electrostaticCutoffRadius for the "
825	<	"electrostaticSkinThickness\n"
826	<	);
827	<	painCave.isFatal = 0;
828	<	simError();
837	<	theEst = 0.05 * theEcr;
822	>	sprintf( painCave.errMsg,
823	>	"SimSetup Warning: using default value of 0.05 * the "
824	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
825	>	);
826	>	painCave.isFatal = 0;
827	>	simError();
828	>	theEst = 0.05 * theEcr;
829		} else {
830	<	theEst= globals->getEST();
830	>	theEst= globals->getEST();
831		}
832	+
833	+	info[i].setEcr( theEcr, theEst );
834	+
835	+	if(!globals->haveDielectric() ){
836	+	sprintf( painCave.errMsg,
837	+	"SimSetup Error: You are trying to use Reaction Field without"
838	+	"setting a dielectric constant!\n"
839	+	);
840	+	painCave.isFatal = 1;
841	+	simError();
842	+	}
843	+	info[i].dielectric = globals->getDielectric();
844	+	}
845	+	else {
846	+	if (usesDipoles) {
847	+
848	+	if( !globals->haveECR() ){
849	+	sprintf( painCave.errMsg,
850	+	"SimSetup Warning: using default value of 1/2 the smallest "
851	+	"box length for the electrostaticCutoffRadius.\n"
852	+	"I hope you have a very fast processor!\n");
853	+	painCave.isFatal = 0;
854	+	simError();
855	+	double smallest;
856	+	smallest = info[i].boxL[0];
857	+	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
858	+	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
859	+	theEcr = 0.5 * smallest;
860	+	} else {
861	+	theEcr = globals->getECR();
862	+	}
863	+
864	+	if( !globals->haveEST() ){
865	+	sprintf( painCave.errMsg,
866	+	"SimSetup Warning: using default value of 0.05 * the "
867	+	"electrostaticCutoffRadius for the "
868	+	"electrostaticSkinThickness\n"
869	+	);
870	+	painCave.isFatal = 0;
871	+	simError();
872	+	theEst = 0.05 * theEcr;
873	+	} else {
874	+	theEst= globals->getEST();
875	+	}
876	+
877	+	info[i].setEcr( theEcr, theEst );
878	+	}
879	+	}
880	+	}
881
842	–	info->setEcr( theEcr, theEst );
843	–	}
844	–	}
845	–
882		#ifdef IS_MPI
883		strcpy( checkPointMsg, "post processing checks out" );
884		MPIcheckPoint();
#	Line 851 | Line 887 | void SimSetup::initSystemCoords( void ){
887		}
888
889		void SimSetup::initSystemCoords( void ){
890	+	int i;
891	+
892	+	char* inName;
893
894	<	if( globals->haveInitialConfig() ){
895	<
896	<	InitializeFromFile* fileInit;
894	>
895	>	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
896	>
897	>	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
898	>
899	>	if( globals->haveInitialConfig() ){
900	>
901	>	InitializeFromFile* fileInit;
902		#ifdef IS_MPI // is_mpi
903	<	if( worldRank == 0 ){
903	>	if( worldRank == 0 ){
904		#endif //is_mpi
905	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
905	>	inName = globals->getInitialConfig();
906	>	double* tempDouble = new double[1000000];
907	>	fileInit = new InitializeFromFile( inName );
908		#ifdef IS_MPI
909	<	}else fileInit = new InitializeFromFile( NULL );
909	>	}else fileInit = new InitializeFromFile( NULL );
910		#endif
911	<	fileInit->readInit( info ); // default velocities on
912	<
913	<	delete fileInit;
914	<	}
915	<	else{
916	<
911	>	fileInit->readInit( info ); // default velocities on
912	>
913	>	delete fileInit;
914	>	}
915	>	else{
916	>
917		#ifdef IS_MPI
918	<
919	<	// no init from bass
920	<
921	<	sprintf( painCave.errMsg,
922	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
923	<	painCave.isFatal;
924	<	simError();
925	<
918	>
919	>	// no init from bass
920	>
921	>	sprintf( painCave.errMsg,
922	>	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
923	>	painCave.isFatal;
924	>	simError();
925	>
926		#else
927	<
928	<	initFromBass();
929	<
930	<
927	>
928	>	initFromBass();
929	>
930	>
931		#endif
932	<	}
933	<
932	>	}
933	>
934		#ifdef IS_MPI
935		strcpy( checkPointMsg, "Successfully read in the initial configuration" );
936		MPIcheckPoint();
937		#endif // is_mpi
938	<
938	>
939		}
940
941
942		void SimSetup::makeOutNames( void ){
943	+
944	+	int k;
945
946	+
947	+	for(k=0; k<nInfo; k++){
948	+
949		#ifdef IS_MPI
950	<	if( worldRank == 0 ){
950	>	if( worldRank == 0 ){
951		#endif // is_mpi
952	<
953	<	if( globals->haveFinalConfig() ){
954	<	strcpy( info->finalName, globals->getFinalConfig() );
952	>
953	>	if( globals->haveFinalConfig() ){
954	>	strcpy( info[k].finalName, globals->getFinalConfig() );
955	>	}
956	>	else{
957	>	strcpy( info[k].finalName, inFileName );
958	>	char* endTest;
959	>	int nameLength = strlen( info[k].finalName );
960	>	endTest = &(info[k].finalName[nameLength - 5]);
961	>	if( !strcmp( endTest, ".bass" ) ){
962	>	strcpy( endTest, ".eor" );
963	>	}
964	>	else if( !strcmp( endTest, ".BASS" ) ){
965	>	strcpy( endTest, ".eor" );
966	>	}
967	>	else{
968	>	endTest = &(info[k].finalName[nameLength - 4]);
969	>	if( !strcmp( endTest, ".bss" ) ){
970	>	strcpy( endTest, ".eor" );
971		}
972	+	else if( !strcmp( endTest, ".mdl" ) ){
973	+	strcpy( endTest, ".eor" );
974	+	}
975		else{
976	<	strcpy( info->finalName, inFileName );
976	>	strcat( info[k].finalName, ".eor" );
977	>	}
978	>	}
979	>	}
980	>
981	>	// make the sample and status out names
982	>
983	>	strcpy( info[k].sampleName, inFileName );
984		char* endTest;
985	<	int nameLength = strlen( info->finalName );
986	<	endTest = &(info->finalName[nameLength - 5]);
985	>	int nameLength = strlen( info[k].sampleName );
986	>	endTest = &(info[k].sampleName[nameLength - 5]);
987		if( !strcmp( endTest, ".bass" ) ){
988	<	strcpy( endTest, ".eor" );
988	>	strcpy( endTest, ".dump" );
989		}
990		else if( !strcmp( endTest, ".BASS" ) ){
991	<	strcpy( endTest, ".eor" );
991	>	strcpy( endTest, ".dump" );
992		}
993		else{
994	<	endTest = &(info->finalName[nameLength - 4]);
995	<	if( !strcmp( endTest, ".bss" ) ){
996	<	strcpy( endTest, ".eor" );
997	<	}
998	<	else if( !strcmp( endTest, ".mdl" ) ){
999	<	strcpy( endTest, ".eor" );
1000	<	}
1001	<	else{
1002	<	strcat( info->finalName, ".eor" );
1003	<	}
994	>	endTest = &(info[k].sampleName[nameLength - 4]);
995	>	if( !strcmp( endTest, ".bss" ) ){
996	>	strcpy( endTest, ".dump" );
997	>	}
998	>	else if( !strcmp( endTest, ".mdl" ) ){
999	>	strcpy( endTest, ".dump" );
1000	>	}
1001	>	else{
1002	>	strcat( info[k].sampleName, ".dump" );
1003	>	}
1004		}
1005	<	}
1006	<
1007	<	// make the sample and status out names
1008	<
1009	<	strcpy( info->sampleName, inFileName );
1010	<	char* endTest;
934	<	int nameLength = strlen( info->sampleName );
935	<	endTest = &(info->sampleName[nameLength - 5]);
936	<	if( !strcmp( endTest, ".bass" ) ){
937	<	strcpy( endTest, ".dump" );
938	<	}
939	<	else if( !strcmp( endTest, ".BASS" ) ){
940	<	strcpy( endTest, ".dump" );
941	<	}
942	<	else{
943	<	endTest = &(info->sampleName[nameLength - 4]);
944	<	if( !strcmp( endTest, ".bss" ) ){
945	<	strcpy( endTest, ".dump" );
1005	>
1006	>	strcpy( info[k].statusName, inFileName );
1007	>	nameLength = strlen( info[k].statusName );
1008	>	endTest = &(info[k].statusName[nameLength - 5]);
1009	>	if( !strcmp( endTest, ".bass" ) ){
1010	>	strcpy( endTest, ".stat" );
1011		}
1012	<	else if( !strcmp( endTest, ".mdl" ) ){
1013	<	strcpy( endTest, ".dump" );
949	<	}
950	<	else{
951	<	strcat( info->sampleName, ".dump" );
952	<	}
953	<	}
954	<
955	<	strcpy( info->statusName, inFileName );
956	<	nameLength = strlen( info->statusName );
957	<	endTest = &(info->statusName[nameLength - 5]);
958	<	if( !strcmp( endTest, ".bass" ) ){
959	<	strcpy( endTest, ".stat" );
960	<	}
961	<	else if( !strcmp( endTest, ".BASS" ) ){
962	<	strcpy( endTest, ".stat" );
963	<	}
964	<	else{
965	<	endTest = &(info->statusName[nameLength - 4]);
966	<	if( !strcmp( endTest, ".bss" ) ){
967	<	strcpy( endTest, ".stat" );
1012	>	else if( !strcmp( endTest, ".BASS" ) ){
1013	>	strcpy( endTest, ".stat" );
1014		}
969	–	else if( !strcmp( endTest, ".mdl" ) ){
970	–	strcpy( endTest, ".stat" );
971	–	}
1015		else{
1016	<	strcat( info->statusName, ".stat" );
1016	>	endTest = &(info[k].statusName[nameLength - 4]);
1017	>	if( !strcmp( endTest, ".bss" ) ){
1018	>	strcpy( endTest, ".stat" );
1019	>	}
1020	>	else if( !strcmp( endTest, ".mdl" ) ){
1021	>	strcpy( endTest, ".stat" );
1022	>	}
1023	>	else{
1024	>	strcat( info[k].statusName, ".stat" );
1025	>	}
1026		}
1027	<	}
976	<
1027	>
1028		#ifdef IS_MPI
1029	<	}
1029	>	}
1030		#endif // is_mpi
1031	<
1031	>	}
1032		}
1033
1034
1035		void SimSetup::sysObjectsCreation( void ){
1036	<
1037	<	int i;
1038	<
1036	>
1037	>	int i,k;
1038	>
1039		// create the forceField
1040
1041		createFF();
#	Line 1004 | Line 1055 | void SimSetup::sysObjectsCreation( void ){
1055		#endif //is_mpi
1056
1057		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1058	<
1058	>
1059		makeSysArrays();
1060
1061		// make and initialize the molecules (all but atomic coordinates)
1062	<
1062	>
1063		makeMolecules();
1013	–	info->identArray = new int[info->n_atoms];
1014	–	for(i=0; i<info->n_atoms; i++){
1015	–	info->identArray[i] = the_atoms[i]->getIdent();
1016	–	}
1064
1065	<
1066	<
1065	>	for(k=0; k<nInfo; k++){
1066	>	info[k].identArray = new int[info[k].n_atoms];
1067	>	for(i=0; i<info[k].n_atoms; i++){
1068	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1069	>	}
1070	>	}
1071		}
1072
1073
#	Line 1032 | Line 1083 | void SimSetup::createFF( void ){
1083		the_ff = new LJFF();
1084		break;
1085
1086	+	case FF_EAM:
1087	+	the_ff = new EAM_FF();
1088	+	break;
1089	+
1090		default:
1091		sprintf( painCave.errMsg,
1092	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1092	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1093		painCave.isFatal = 1;
1094		simError();
1095		}
#	Line 1050 | Line 1105 | void SimSetup::compList( void ){
1105		void SimSetup::compList( void ){
1106
1107		int i;
1108	<
1108	>	char* id;
1109	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1110	>	LinkedMolStamp* currentStamp = NULL;
1111		comp_stamps = new MoleculeStamp*[n_components];
1112	<
1112	>
1113		// make an array of molecule stamps that match the components used.
1114		// also extract the used stamps out into a separate linked list
1058	–
1059	–	info->nComponents = n_components;
1060	–	info->componentsNmol = components_nmol;
1061	–	info->compStamps = comp_stamps;
1062	–	info->headStamp = new LinkedMolStamp();
1115
1116	<	char* id;
1117	<	LinkedMolStamp* headStamp = info->headStamp;
1118	<	LinkedMolStamp* currentStamp = NULL;
1116	>	for(i=0; i<nInfo; i++){
1117	>	info[i].nComponents = n_components;
1118	>	info[i].componentsNmol = components_nmol;
1119	>	info[i].compStamps = comp_stamps;
1120	>	info[i].headStamp = headStamp;
1121	>	}
1122	>
1123	>
1124		for( i=0; i<n_components; i++ ){
1125
1126		id = the_components[i]->getType();
#	Line 1078 | Line 1135 | void SimSetup::compList( void ){
1135
1136		currentStamp = stamps->extractMolStamp( id );
1137		if( currentStamp == NULL ){
1138	<	sprintf( painCave.errMsg,
1139	<	"SimSetup error: Component \"%s\" was not found in the "
1140	<	"list of declared molecules\n",
1141	<	id );
1142	<	painCave.isFatal = 1;
1143	<	simError();
1138	>	sprintf( painCave.errMsg,
1139	>	"SimSetup error: Component \"%s\" was not found in the "
1140	>	"list of declared molecules\n",
1141	>	id );
1142	>	painCave.isFatal = 1;
1143	>	simError();
1144		}
1145
1146		headStamp->add( currentStamp );
#	Line 1101 | Line 1158 | void SimSetup::calcSysValues( void ){
1158
1159		void SimSetup::calcSysValues( void ){
1160		int i, j, k;
1161	<
1162	<
1161	>
1162	>	int *molMembershipArray;
1163	>
1164		tot_atoms = 0;
1165		tot_bonds = 0;
1166		tot_bends = 0;
#	Line 1114 | Line 1172 | void SimSetup::calcSysValues( void ){
1172		tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1173		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1174		}
1175	<
1175	>
1176		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1177	<
1120	<	info->n_atoms = tot_atoms;
1121	<	info->n_bonds = tot_bonds;
1122	<	info->n_bends = tot_bends;
1123	<	info->n_torsions = tot_torsions;
1124	<	info->n_SRI = tot_SRI;
1125	<	info->n_mol = tot_nmol;
1177	>	molMembershipArray = new int[tot_atoms];
1178
1179	<	info->molMembershipArray = new int[tot_atoms];
1179	>	for(i=0; i<nInfo; i++){
1180	>	info[i].n_atoms = tot_atoms;
1181	>	info[i].n_bonds = tot_bonds;
1182	>	info[i].n_bends = tot_bends;
1183	>	info[i].n_torsions = tot_torsions;
1184	>	info[i].n_SRI = tot_SRI;
1185	>	info[i].n_mol = tot_nmol;
1186	>
1187	>	info[i].molMembershipArray = molMembershipArray;
1188	>	}
1189		}
1190
1130	–
1191		#ifdef IS_MPI
1192
1193		void SimSetup::mpiMolDivide( void ){
#	Line 1159 | Line 1219 | void SimSetup::mpiMolDivide( void ){
1219		for( j=0; j<components_nmol[i]; j++ ){
1220
1221		if( mol2proc[allMol] == worldRank ){
1222	<
1223	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1224	<	local_bonds +=    comp_stamps[i]->getNBonds();
1225	<	local_bends +=    comp_stamps[i]->getNBends();
1226	<	local_torsions += comp_stamps[i]->getNTorsions();
1227	<	localMol++;
1222	>
1223	>	local_atoms +=    comp_stamps[i]->getNAtoms();
1224	>	local_bonds +=    comp_stamps[i]->getNBonds();
1225	>	local_bends +=    comp_stamps[i]->getNBends();
1226	>	local_torsions += comp_stamps[i]->getNTorsions();
1227	>	localMol++;
1228		}
1229		for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1230	<	info->molMembershipArray[globalAtomIndex] = allMol;
1230	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1231		globalAtomIndex++;
1232		}
1233
#	Line 1176 | Line 1236 | void SimSetup::mpiMolDivide( void ){
1236		}
1237		local_SRI = local_bonds + local_bends + local_torsions;
1238
1239	<	info->n_atoms = mpiSim->getMyNlocal();
1239	>	info[0].n_atoms = mpiSim->getMyNlocal();
1240
1241	<	if( local_atoms != info->n_atoms ){
1241	>	if( local_atoms != info[0].n_atoms ){
1242		sprintf( painCave.errMsg,
1243	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1244	<	" localAtom (%d) are not equal.\n",
1245	<	info->n_atoms,
1246	<	local_atoms );
1243	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1244	>	" localAtom (%d) are not equal.\n",
1245	>	info[0].n_atoms,
1246	>	local_atoms );
1247		painCave.isFatal = 1;
1248		simError();
1249		}
1250
1251	<	info->n_bonds = local_bonds;
1252	<	info->n_bends = local_bends;
1253	<	info->n_torsions = local_torsions;
1254	<	info->n_SRI = local_SRI;
1255	<	info->n_mol = localMol;
1251	>	info[0].n_bonds = local_bonds;
1252	>	info[0].n_bends = local_bends;
1253	>	info[0].n_torsions = local_torsions;
1254	>	info[0].n_SRI = local_SRI;
1255	>	info[0].n_mol = localMol;
1256
1257		strcpy( checkPointMsg, "Passed nlocal consistency check." );
1258		MPIcheckPoint();
1259		}
1260	<
1260	>
1261		#endif // is_mpi
1262
1263
1264		void SimSetup::makeSysArrays( void ){
1265	<	int i, j, k;
1265	>	int i, j, k, l;
1266
1267	+	Atom** the_atoms;
1268	+	Molecule* the_molecules;
1269	+	Exclude** the_excludes;
1270
1208	–	// create the atom and short range interaction arrays
1209	–
1210	–	Atom::createArrays(info->n_atoms);
1211	–	the_atoms = new Atom*[info->n_atoms];
1212	–	the_molecules = new Molecule[info->n_mol];
1213	–	int molIndex;
1214	–
1215	–	// initialize the molecule's stampID's
1216	–
1217	–	#ifdef IS_MPI
1271
1272	+	for(l=0; l<nInfo; l++){
1273	+
1274	+	// create the atom and short range interaction arrays
1275	+
1276	+	the_atoms = new Atom*[info[l].n_atoms];
1277	+	the_molecules = new Molecule[info[l].n_mol];
1278	+	int molIndex;
1279
1280	<	molIndex = 0;
1221	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1280	>	// initialize the molecule's stampID's
1281
1282	<	if(mol2proc[i] == worldRank ){
1283	<	the_molecules[molIndex].setStampID( molCompType[i] );
1284	<	the_molecules[molIndex].setMyIndex( molIndex );
1285	<	the_molecules[molIndex].setGlobalIndex( i );
1286	<	molIndex++;
1282	>	#ifdef IS_MPI
1283	>
1284	>
1285	>	molIndex = 0;
1286	>	for(i=0; i<mpiSim->getTotNmol(); i++){
1287	>
1288	>	if(mol2proc[i] == worldRank ){
1289	>	the_molecules[molIndex].setStampID( molCompType[i] );
1290	>	the_molecules[molIndex].setMyIndex( molIndex );
1291	>	the_molecules[molIndex].setGlobalIndex( i );
1292	>	molIndex++;
1293	>	}
1294		}
1295	<	}
1230	<
1295	>
1296		#else // is_mpi
1297	<
1298	<	molIndex = 0;
1299	<	globalAtomIndex = 0;
1300	<	for(i=0; i<n_components; i++){
1301	<	for(j=0; j<components_nmol[i]; j++ ){
1302	<	the_molecules[molIndex].setStampID( i );
1303	<	the_molecules[molIndex].setMyIndex( molIndex );
1304	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1305	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1306	<	info->molMembershipArray[globalAtomIndex] = molIndex;
1307	<	globalAtomIndex++;
1297	>
1298	>	molIndex = 0;
1299	>	globalAtomIndex = 0;
1300	>	for(i=0; i<n_components; i++){
1301	>	for(j=0; j<components_nmol[i]; j++ ){
1302	>	the_molecules[molIndex].setStampID( i );
1303	>	the_molecules[molIndex].setMyIndex( molIndex );
1304	>	the_molecules[molIndex].setGlobalIndex( molIndex );
1305	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1306	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1307	>	globalAtomIndex++;
1308	>	}
1309	>	molIndex++;
1310		}
1244	–	molIndex++;
1311		}
1246	–	}
1312
1313	<
1313	>
1314		#endif // is_mpi
1315
1316
1317	<	if( info->n_SRI ){
1317	>	if( info[l].n_SRI ){
1318
1319	<	Exclude::createArray(info->n_SRI);
1320	<	the_excludes = new Exclude*[info->n_SRI];
1321	<	for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
1322	<	info->globalExcludes = new int;
1323	<	info->n_exclude = info->n_SRI;
1324	<	}
1325	<	else{
1319	>	Exclude::createArray(info[l].n_SRI);
1320	>	the_excludes = new Exclude*[info[l].n_SRI];
1321	>	for( int ex=0; ex<info[l].n_SRI; ex++){
1322	>	the_excludes[ex] = new Exclude(ex);
1323	>	}
1324	>	info[l].globalExcludes = new int;
1325	>	info[l].n_exclude = info[l].n_SRI;
1326	>	}
1327	>	else{
1328
1329	<	Exclude::createArray( 1 );
1330	<	the_excludes = new Exclude*;
1331	<	the_excludes[0] = new Exclude(0);
1332	<	the_excludes[0]->setPair( 0,0 );
1333	<	info->globalExcludes = new int;
1334	<	info->globalExcludes[0] = 0;
1335	<	info->n_exclude = 0;
1336	<	}
1329	>	Exclude::createArray( 1 );
1330	>	the_excludes = new Exclude*;
1331	>	the_excludes[0] = new Exclude(0);
1332	>	the_excludes[0]->setPair( 0,0 );
1333	>	info[l].globalExcludes = new int;
1334	>	info[l].globalExcludes[0] = 0;
1335	>	info[l].n_exclude = 0;
1336	>	}
1337
1338	<	// set the arrays into the SimInfo object
1338	>	// set the arrays into the SimInfo object
1339
1340	<	info->atoms = the_atoms;
1341	<	info->molecules = the_molecules;
1342	<	info->nGlobalExcludes = 0;
1343	<	info->excludes = the_excludes;
1340	>	info[l].atoms = the_atoms;
1341	>	info[l].molecules = the_molecules;
1342	>	info[l].nGlobalExcludes = 0;
1343	>	info[l].excludes = the_excludes;
1344
1345	<	the_ff->setSimInfo( info );
1346	<
1345	>	the_ff->setSimInfo( info );
1346	>
1347	>	}
1348		}
1349
1350		void SimSetup::makeIntegrator( void ){
1351
1352	<	NVT*  myNVT = NULL;
1285	<	NPTi* myNPTi = NULL;
1286	<	NPTf* myNPTf = NULL;
1287	<	NPTim* myNPTim = NULL;
1288	<	NPTfm* myNPTfm = NULL;
1352	>	int k;
1353
1354	<	switch( ensembleCase ){
1354	>	NVT<RealIntegrator>*  myNVT = NULL;
1355	>	NPTi<RealIntegrator>* myNPTi = NULL;
1356	>	NPTf<RealIntegrator>* myNPTf = NULL;
1357	>	NPTim<RealIntegrator>* myNPTim = NULL;
1358	>	NPTfm<RealIntegrator>* myNPTfm = NULL;
1359	>
1360	>	for(k=0; k<nInfo; k++){
1361	>
1362	>	switch( ensembleCase ){
1363	>
1364	>	case NVE_ENS:
1365	>	if (globals->haveZconstraints()){
1366	>	setupZConstraint(info[k]);
1367	>	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1368	>	}
1369
1370	<	case NVE_ENS:
1371	<	new NVE( info, the_ff );
1372	<	break;
1373	<
1374	<	case NVT_ENS:
1375	<	myNVT = new NVT( info, the_ff );
1376	<	myNVT->setTargetTemp(globals->getTargetTemp());
1377	<
1378	<	if (globals->haveTauThermostat())
1379	<	myNVT->setTauThermostat(globals->getTauThermostat());
1380	<
1303	<	else {
1304	<	sprintf( painCave.errMsg,
1305	<	"SimSetup error: If you use the NVT\n"
1306	<	"    ensemble, you must set tauThermostat.\n");
1307	<	painCave.isFatal = 1;
1308	<	simError();
1309	<	}
1310	<	break;
1370	>	else
1371	>	new NVE<RealIntegrator>( &(info[k]), the_ff );
1372	>	break;
1373	>
1374	>	case NVT_ENS:
1375	>	if (globals->haveZconstraints()){
1376	>	setupZConstraint(info[k]);
1377	>	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1378	>	}
1379	>	else
1380	>	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1381
1382	<	case NPTi_ENS:
1383	<	myNPTi = new NPTi( info, the_ff );
1384	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1382	>	myNVT->setTargetTemp(globals->getTargetTemp());
1383	>
1384	>	if (globals->haveTauThermostat())
1385	>	myNVT->setTauThermostat(globals->getTauThermostat());
1386	>
1387	>	else {
1388	>	sprintf( painCave.errMsg,
1389	>	"SimSetup error: If you use the NVT\n"
1390	>	"    ensemble, you must set tauThermostat.\n");
1391	>	painCave.isFatal = 1;
1392	>	simError();
1393	>	}
1394	>	break;
1395	>
1396	>	case NPTi_ENS:
1397	>	if (globals->haveZconstraints()){
1398	>	setupZConstraint(info[k]);
1399	>	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1400	>	}
1401	>	else
1402	>	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1403
1404	<	if (globals->haveTargetPressure())
1405	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1406	<	else {
1407	<	sprintf( painCave.errMsg,
1408	<	"SimSetup error: If you use a constant pressure\n"
1409	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1410	<	painCave.isFatal = 1;
1411	<	simError();
1412	<	}
1413	<
1414	<	if( globals->haveTauThermostat() )
1415	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1416	<	else{
1417	<	sprintf( painCave.errMsg,
1418	<	"SimSetup error: If you use an NPT\n"
1419	<	"    ensemble, you must set tauThermostat.\n");
1420	<	painCave.isFatal = 1;
1421	<	simError();
1422	<	}
1404	>	myNPTi->setTargetTemp( globals->getTargetTemp() );
1405	>
1406	>	if (globals->haveTargetPressure())
1407	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1408	>	else {
1409	>	sprintf( painCave.errMsg,
1410	>	"SimSetup error: If you use a constant pressure\n"
1411	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1412	>	painCave.isFatal = 1;
1413	>	simError();
1414	>	}
1415	>
1416	>	if( globals->haveTauThermostat() )
1417	>	myNPTi->setTauThermostat( globals->getTauThermostat() );
1418	>	else{
1419	>	sprintf( painCave.errMsg,
1420	>	"SimSetup error: If you use an NPT\n"
1421	>	"    ensemble, you must set tauThermostat.\n");
1422	>	painCave.isFatal = 1;
1423	>	simError();
1424	>	}
1425	>
1426	>	if( globals->haveTauBarostat() )
1427	>	myNPTi->setTauBarostat( globals->getTauBarostat() );
1428	>	else{
1429	>	sprintf( painCave.errMsg,
1430	>	"SimSetup error: If you use an NPT\n"
1431	>	"    ensemble, you must set tauBarostat.\n");
1432	>	painCave.isFatal = 1;
1433	>	simError();
1434	>	}
1435	>	break;
1436	>
1437	>	case NPTf_ENS:
1438	>	if (globals->haveZconstraints()){
1439	>	setupZConstraint(info[k]);
1440	>	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1441	>	}
1442	>	else
1443	>	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1444
1445	<	if( globals->haveTauBarostat() )
1446	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1447	<	else{
1448	<	sprintf( painCave.errMsg,
1449	<	"SimSetup error: If you use an NPT\n"
1450	<	"    ensemble, you must set tauBarostat.\n");
1451	<	painCave.isFatal = 1;
1452	<	simError();
1453	<	}
1454	<	break;
1445	>	myNPTf->setTargetTemp( globals->getTargetTemp());
1446	>
1447	>	if (globals->haveTargetPressure())
1448	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1449	>	else {
1450	>	sprintf( painCave.errMsg,
1451	>	"SimSetup error: If you use a constant pressure\n"
1452	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1453	>	painCave.isFatal = 1;
1454	>	simError();
1455	>	}
1456	>
1457	>	if( globals->haveTauThermostat() )
1458	>	myNPTf->setTauThermostat( globals->getTauThermostat() );
1459	>	else{
1460	>	sprintf( painCave.errMsg,
1461	>	"SimSetup error: If you use an NPT\n"
1462	>	"    ensemble, you must set tauThermostat.\n");
1463	>	painCave.isFatal = 1;
1464	>	simError();
1465	>	}
1466	>
1467	>	if( globals->haveTauBarostat() )
1468	>	myNPTf->setTauBarostat( globals->getTauBarostat() );
1469	>	else{
1470	>	sprintf( painCave.errMsg,
1471	>	"SimSetup error: If you use an NPT\n"
1472	>	"    ensemble, you must set tauBarostat.\n");
1473	>	painCave.isFatal = 1;
1474	>	simError();
1475	>	}
1476	>	break;
1477	>
1478	>	case NPTim_ENS:
1479	>	if (globals->haveZconstraints()){
1480	>	setupZConstraint(info[k]);
1481	>	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1482	>	}
1483	>	else
1484	>	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1485
1486	<	case NPTf_ENS:
1487	<	myNPTf = new NPTf( info, the_ff );
1488	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1486	>	myNPTim->setTargetTemp( globals->getTargetTemp());
1487	>
1488	>	if (globals->haveTargetPressure())
1489	>	myNPTim->setTargetPressure(globals->getTargetPressure());
1490	>	else {
1491	>	sprintf( painCave.errMsg,
1492	>	"SimSetup error: If you use a constant pressure\n"
1493	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1494	>	painCave.isFatal = 1;
1495	>	simError();
1496	>	}
1497	>
1498	>	if( globals->haveTauThermostat() )
1499	>	myNPTim->setTauThermostat( globals->getTauThermostat() );
1500	>	else{
1501	>	sprintf( painCave.errMsg,
1502	>	"SimSetup error: If you use an NPT\n"
1503	>	"    ensemble, you must set tauThermostat.\n");
1504	>	painCave.isFatal = 1;
1505	>	simError();
1506	>	}
1507	>
1508	>	if( globals->haveTauBarostat() )
1509	>	myNPTim->setTauBarostat( globals->getTauBarostat() );
1510	>	else{
1511	>	sprintf( painCave.errMsg,
1512	>	"SimSetup error: If you use an NPT\n"
1513	>	"    ensemble, you must set tauBarostat.\n");
1514	>	painCave.isFatal = 1;
1515	>	simError();
1516	>	}
1517	>	break;
1518	>
1519	>	case NPTfm_ENS:
1520	>	if (globals->haveZconstraints()){
1521	>	setupZConstraint(info[k]);
1522	>	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1523	>	}
1524	>	else
1525	>	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1526
1527	<	if (globals->haveTargetPressure())
1352	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1353	<	else {
1354	<	sprintf( painCave.errMsg,
1355	<	"SimSetup error: If you use a constant pressure\n"
1356	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1357	<	painCave.isFatal = 1;
1358	<	simError();
1359	<	}
1527	>	myNPTfm->setTargetTemp( globals->getTargetTemp());
1528
1529	<	if( globals->haveTauThermostat() )
1530	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1531	<	else{
1532	<	sprintf( painCave.errMsg,
1533	<	"SimSetup error: If you use an NPT\n"
1534	<	"    ensemble, you must set tauThermostat.\n");
1535	<	painCave.isFatal = 1;
1536	<	simError();
1537	<	}
1529	>	if (globals->haveTargetPressure())
1530	>	myNPTfm->setTargetPressure(globals->getTargetPressure());
1531	>	else {
1532	>	sprintf( painCave.errMsg,
1533	>	"SimSetup error: If you use a constant pressure\n"
1534	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1535	>	painCave.isFatal = 1;
1536	>	simError();
1537	>	}
1538
1539	<	if( globals->haveTauBarostat() )
1540	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1541	<	else{
1542	<	sprintf( painCave.errMsg,
1543	<	"SimSetup error: If you use an NPT\n"
1544	<	"    ensemble, you must set tauBarostat.\n");
1545	<	painCave.isFatal = 1;
1546	<	simError();
1547	<	}
1380	<	break;
1381	<
1382	<	case NPTim_ENS:
1383	<	myNPTim = new NPTim( info, the_ff );
1384	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1539	>	if( globals->haveTauThermostat() )
1540	>	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1541	>	else{
1542	>	sprintf( painCave.errMsg,
1543	>	"SimSetup error: If you use an NPT\n"
1544	>	"    ensemble, you must set tauThermostat.\n");
1545	>	painCave.isFatal = 1;
1546	>	simError();
1547	>	}
1548
1549	<	if (globals->haveTargetPressure())
1550	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1551	<	else {
1549	>	if( globals->haveTauBarostat() )
1550	>	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1551	>	else{
1552	>	sprintf( painCave.errMsg,
1553	>	"SimSetup error: If you use an NPT\n"
1554	>	"    ensemble, you must set tauBarostat.\n");
1555	>	painCave.isFatal = 1;
1556	>	simError();
1557	>	}
1558	>	break;
1559	>
1560	>	default:
1561		sprintf( painCave.errMsg,
1562	<	"SimSetup error: If you use a constant pressure\n"
1391	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1562	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1563		painCave.isFatal = 1;
1564		simError();
1565		}
1395	–
1396	–	if( globals->haveTauThermostat() )
1397	–	myNPTim->setTauThermostat( globals->getTauThermostat() );
1398	–	else{
1399	–	sprintf( painCave.errMsg,
1400	–	"SimSetup error: If you use an NPT\n"
1401	–	"    ensemble, you must set tauThermostat.\n");
1402	–	painCave.isFatal = 1;
1403	–	simError();
1404	–	}
1405	–
1406	–	if( globals->haveTauBarostat() )
1407	–	myNPTim->setTauBarostat( globals->getTauBarostat() );
1408	–	else{
1409	–	sprintf( painCave.errMsg,
1410	–	"SimSetup error: If you use an NPT\n"
1411	–	"    ensemble, you must set tauBarostat.\n");
1412	–	painCave.isFatal = 1;
1413	–	simError();
1414	–	}
1415	–	break;
1416	–
1417	–	case NPTfm_ENS:
1418	–	myNPTfm = new NPTfm( info, the_ff );
1419	–	myNPTfm->setTargetTemp( globals->getTargetTemp());
1420	–
1421	–	if (globals->haveTargetPressure())
1422	–	myNPTfm->setTargetPressure(globals->getTargetPressure());
1423	–	else {
1424	–	sprintf( painCave.errMsg,
1425	–	"SimSetup error: If you use a constant pressure\n"
1426	–	"    ensemble, you must set targetPressure in the BASS file.\n");
1427	–	painCave.isFatal = 1;
1428	–	simError();
1429	–	}
1430	–
1431	–	if( globals->haveTauThermostat() )
1432	–	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1433	–	else{
1434	–	sprintf( painCave.errMsg,
1435	–	"SimSetup error: If you use an NPT\n"
1436	–	"    ensemble, you must set tauThermostat.\n");
1437	–	painCave.isFatal = 1;
1438	–	simError();
1439	–	}
1440	–
1441	–	if( globals->haveTauBarostat() )
1442	–	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1443	–	else{
1444	–	sprintf( painCave.errMsg,
1445	–	"SimSetup error: If you use an NPT\n"
1446	–	"    ensemble, you must set tauBarostat.\n");
1447	–	painCave.isFatal = 1;
1448	–	simError();
1449	–	}
1450	–	break;
1451	–
1452	–	default:
1453	–	sprintf( painCave.errMsg,
1454	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1455	–	painCave.isFatal = 1;
1456	–	simError();
1566		}
1458	–
1567		}
1568
1569		void SimSetup::initFortran( void ){
1570
1571	<	info->refreshSim();
1571	>	info[0].refreshSim();
1572
1573	<	if( !strcmp( info->mixingRule, "standard") ){
1573	>	if( !strcmp( info[0].mixingRule, "standard") ){
1574		the_ff->initForceField( LB_MIXING_RULE );
1575		}
1576	<	else if( !strcmp( info->mixingRule, "explicit") ){
1576	>	else if( !strcmp( info[0].mixingRule, "explicit") ){
1577		the_ff->initForceField( EXPLICIT_MIXING_RULE );
1578		}
1579		else{
1580		sprintf( painCave.errMsg,
1581	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1582	<	info->mixingRule );
1581	>	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1582	>	info[0].mixingRule );
1583		painCave.isFatal = 1;
1584		simError();
1585		}
#	Line 1479 | Line 1587 | void SimSetup::initFortran( void ){
1587
1588		#ifdef IS_MPI
1589		strcpy( checkPointMsg,
1590	<	"Successfully intialized the mixingRule for Fortran." );
1590	>	"Successfully intialized the mixingRule for Fortran." );
1591		MPIcheckPoint();
1592		#endif // is_mpi
1593
1594		}
1595	+
1596	+	void SimSetup::setupZConstraint(SimInfo& theInfo)
1597	+	{
1598	+	int nZConstraints;
1599	+	ZconStamp** zconStamp;
1600	+
1601	+	if(globals->haveZconstraintTime()){
1602	+
1603	+	//add sample time of z-constraint  into SimInfo's property list
1604	+	DoubleData* zconsTimeProp = new DoubleData();
1605	+	zconsTimeProp->setID(ZCONSTIME_ID);
1606	+	zconsTimeProp->setData(globals->getZconsTime());
1607	+	theInfo.addProperty(zconsTimeProp);
1608	+	}
1609	+	else{
1610	+	sprintf( painCave.errMsg,
1611	+	"ZConstraint error: If you use an ZConstraint\n"
1612	+	" , you must set sample time.\n");
1613	+	painCave.isFatal = 1;
1614	+	simError();
1615	+	}
1616	+
1617	+	//push zconsTol into siminfo, if user does not specify
1618	+	//value for zconsTol, a default value will be used
1619	+	DoubleData* zconsTol = new DoubleData();
1620	+	zconsTol->setID(ZCONSTOL_ID);
1621	+	if(globals->haveZconsTol()){
1622	+	zconsTol->setData(globals->getZconsTol());
1623	+	}
1624	+	else{
1625	+	double defaultZConsTol = 0.01;
1626	+	sprintf( painCave.errMsg,
1627	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1628	+	" , default value %f is used.\n", defaultZConsTol);
1629	+	painCave.isFatal = 0;
1630	+	simError();
1631	+
1632	+	zconsTol->setData(defaultZConsTol);
1633	+	}
1634	+	theInfo.addProperty(zconsTol);
1635	+
1636	+	//set Force Substraction Policy
1637	+	StringData* zconsForcePolicy =  new StringData();
1638	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1639	+
1640	+	if(globals->haveZconsForcePolicy()){
1641	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1642	+	}
1643	+	else{
1644	+	sprintf( painCave.errMsg,
1645	+	"ZConstraint Warning: User does not set force substraction policy, "
1646	+	"average force substraction policy is used\n");
1647	+	painCave.isFatal = 0;
1648	+	simError();
1649	+	zconsForcePolicy->setData("BYNUMBER");
1650	+	}
1651	+
1652	+	theInfo.addProperty(zconsForcePolicy);
1653	+
1654	+	//Determine the name of ouput file and add it into SimInfo's property list
1655	+	//Be careful, do not use inFileName, since it is a pointer which
1656	+	//point to a string at master node, and slave nodes do not contain that string
1657	+
1658	+	string zconsOutput(theInfo.finalName);
1659	+
1660	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1661	+
1662	+	StringData* zconsFilename = new StringData();
1663	+	zconsFilename->setID(ZCONSFILENAME_ID);
1664	+	zconsFilename->setData(zconsOutput);
1665	+
1666	+	theInfo.addProperty(zconsFilename);
1667	+
1668	+	//setup index, pos and other parameters of z-constraint molecules
1669	+	nZConstraints = globals->getNzConstraints();
1670	+	theInfo.nZconstraints = nZConstraints;
1671	+
1672	+	zconStamp = globals->getZconStamp();
1673	+	ZConsParaItem tempParaItem;
1674	+
1675	+	ZConsParaData* zconsParaData = new ZConsParaData();
1676	+	zconsParaData->setID(ZCONSPARADATA_ID);
1677	+
1678	+	for(int i = 0; i < nZConstraints; i++){
1679	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1680	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1681	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1682	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1683	+
1684	+	zconsParaData->addItem(tempParaItem);
1685	+	}
1686	+
1687	+	//sort the parameters by index of molecules
1688	+	zconsParaData->sortByIndex();
1689	+
1690	+	//push data into siminfo, therefore, we can retrieve later
1691	+	theInfo.addProperty(zconsParaData);
1692	+
1693	+	}

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