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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 707 by mmeineke, Wed Aug 20 19:42:31 2003 UTC vs.
Revision 855 by mmeineke, Thu Nov 6 22:01:37 2003 UTC

#	Line 1 | Line 1
1		#include <algorithm>
2	<	#include <cstdlib>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
4	>	#include <math.h>
5		#include <string>
6	<
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8		#include "ReadWrite.hpp"
9		#include "parse_me.h"
#	Line 21 | Line 21
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
24	>	#define NPTxyz_ENS     4
25
26	+
27		#define FF_DUFF 0
28		#define FF_LJ   1
29		#define FF_EAM  2
#	Line 32 | Line 32 | SimSetup::SimSetup(){
32
33		SimSetup::SimSetup(){
34
35	+	initSuspend = false;
36		isInfoArray = 0;
37		nInfo = 1;
38	<
38	>
39		stamps = new MakeStamps();
40		globals = new Globals();
41	<
42	<
41	>
42	>
43		#ifdef IS_MPI
44	<	strcpy( checkPointMsg, "SimSetup creation successful" );
44	>	strcpy(checkPointMsg, "SimSetup creation successful");
45		MPIcheckPoint();
46		#endif // IS_MPI
47		}
#	Line 50 | Line 51 | void SimSetup::setSimInfo( SimInfo* the_info, int theN
51		delete globals;
52		}
53
54	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
55	<	info = the_info;
56	<	nInfo = theNinfo;
57	<	isInfoArray = 1;
54	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
55	>	info = the_info;
56	>	nInfo = theNinfo;
57	>	isInfoArray = 1;
58	>	initSuspend = true;
59		}
60
61
62	<	void SimSetup::parseFile( char* fileName ){
61	<
62	>	void SimSetup::parseFile(char* fileName){
63		#ifdef IS_MPI
64	<	if( worldRank == 0 ){
64	>	if (worldRank == 0){
65		#endif // is_mpi
66	<
66	>
67		inFileName = fileName;
68	<	set_interface_stamps( stamps, globals );
69	<
68	>	set_interface_stamps(stamps, globals);
69	>
70		#ifdef IS_MPI
71		mpiEventInit();
72		#endif
73
74	<	yacc_BASS( fileName );
74	>	yacc_BASS(fileName);
75
76		#ifdef IS_MPI
77		throwMPIEvent(NULL);
78		}
79	<	else receiveParse();
79	>	else{
80	>	receiveParse();
81	>	}
82		#endif
83
84		}
85
86		#ifdef IS_MPI
87		void SimSetup::receiveParse(void){
88	<
89	<	set_interface_stamps( stamps, globals );
90	<	mpiEventInit();
91	<	MPIcheckPoint();
89	<	mpiEventLoop();
90	<
88	>	set_interface_stamps(stamps, globals);
89	>	mpiEventInit();
90	>	MPIcheckPoint();
91	>	mpiEventLoop();
92		}
93
94		#endif // is_mpi
95
96		void SimSetup::createSim(void){
97
97	–	int i, j, k, globalAtomIndex;
98	–
98		// gather all of the information from the Bass file
99
100		gatherInfo();
#	Line 104 | Line 103 | void SimSetup::createSim(void){
103
104		sysObjectsCreation();
105
106	<	// check on the post processing info
106	>	// initialize the system coordinates
107
108	<	finalInfoCheck();
108	>	if ( !initSuspend ){
109	>	initSystemCoords();
110
111	<	// initialize the system coordinates
111	>	if( !(globals->getUseInitTime()) )
112	>	info[0].currentTime = 0.0;
113	>	}
114
115	<	if( !isInfoArray ) initSystemCoords();
115	>	// check on the post processing info
116
117	+	finalInfoCheck();
118	+
119		// make the output filenames
120
121		makeOutNames();
122	<
122	>
123		// make the integrator
124	<
124	>
125		makeIntegrator();
126	<
126	>
127		#ifdef IS_MPI
128		mpiSim->mpiRefresh();
129		#endif
#	Line 127 | Line 131 | void SimSetup::createSim(void){
131		// initialize the Fortran
132
133		initFortran();
130	–
131	–
132	–
134		}
135
136
137	<	void SimSetup::makeMolecules( void ){
138	<
138	<	int k,l;
137	>	void SimSetup::makeMolecules(void){
138	>	int k;
139		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140		molInit molInfo;
141		DirectionalAtom* dAtom;
#	Line 150 | Line 150 | void SimSetup::makeMolecules( void ){
150		bend_set* theBends;
151		torsion_set* theTorsions;
152
153	<
153	>
154		//init the forceField paramters
155
156		the_ff->readParams();
157
158	<
158	>
159		// init the atoms
160
161		double ux, uy, uz, u, uSqr;
162	–
163	–	for(k=0; k<nInfo; k++){
164	–
165	–	the_ff->setSimInfo( &(info[k]) );
162
163	+	for (k = 0; k < nInfo; k++){
164	+	the_ff->setSimInfo(&(info[k]));
165	+
166		atomOffset = 0;
167		excludeOffset = 0;
168	<	for(i=0; i<info[k].n_mol; i++){
170	<
168	>	for (i = 0; i < info[k].n_mol; i++){
169		stampID = info[k].molecules[i].getStampID();
170
171	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
172	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
173	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
171	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
172	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
173	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
174		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
175		molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
176	<
176	>
177		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
178		molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
179	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
180	<	molInfo.myBends = new Bend*[molInfo.nBends];
181	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
179	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
180	>	molInfo.myBends = new Bend * [molInfo.nBends];
181	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
182
183		theBonds = new bond_pair[molInfo.nBonds];
184		theBends = new bend_set[molInfo.nBends];
185		theTorsions = new torsion_set[molInfo.nTorsions];
186	<
187	<	// make the Atoms
188	<
189	<	for(j=0; j<molInfo.nAtoms; j++){
190	<
191	<	currentAtom = comp_stamps[stampID]->getAtom( j );
192	<	if( currentAtom->haveOrientation() ){
193	<
194	<	dAtom = new DirectionalAtom( (j + atomOffset),
195	<	info[k].getConfiguration() );
196	<	info[k].n_oriented++;
197	<	molInfo.myAtoms[j] = dAtom;
198	<
199	<	ux = currentAtom->getOrntX();
200	<	uy = currentAtom->getOrntY();
201	<	uz = currentAtom->getOrntZ();
202	<
203	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
204	<
205	<	u = sqrt( uSqr );
206	<	ux = ux / u;
207	<	uy = uy / u;
208	<	uz = uz / u;
209	<
210	<	dAtom->setSUx( ux );
211	<	dAtom->setSUy( uy );
212	<	dAtom->setSUz( uz );
213	<	}
214	<	else{
215	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
216	<	info[k].getConfiguration() );
217	<	}
220	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
221	<
186	>
187	>	// make the Atoms
188	>
189	>	for (j = 0; j < molInfo.nAtoms; j++){
190	>	currentAtom = comp_stamps[stampID]->getAtom(j);
191	>	if (currentAtom->haveOrientation()){
192	>	dAtom = new DirectionalAtom((j + atomOffset),
193	>	info[k].getConfiguration());
194	>	info[k].n_oriented++;
195	>	molInfo.myAtoms[j] = dAtom;
196	>
197	>	ux = currentAtom->getOrntX();
198	>	uy = currentAtom->getOrntY();
199	>	uz = currentAtom->getOrntZ();
200	>
201	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
202	>
203	>	u = sqrt(uSqr);
204	>	ux = ux / u;
205	>	uy = uy / u;
206	>	uz = uz / u;
207	>
208	>	dAtom->setSUx(ux);
209	>	dAtom->setSUy(uy);
210	>	dAtom->setSUz(uz);
211	>	}
212	>	else{
213	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
214	>	info[k].getConfiguration());
215	>	}
216	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
217	>
218		#ifdef IS_MPI
219	<
220	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
221	<
219	>
220	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
221	>
222		#endif // is_mpi
223		}
224	<
225	<	// make the bonds
226	<	for(j=0; j<molInfo.nBonds; j++){
227	<
228	<	currentBond = comp_stamps[stampID]->getBond( j );
229	<	theBonds[j].a = currentBond->getA() + atomOffset;
230	<	theBonds[j].b = currentBond->getB() + atomOffset;
231	<
232	<	exI = theBonds[j].a;
233	<	exJ = theBonds[j].b;
234	<
235	<	// exclude_I must always be the smaller of the pair
236	<	if( exI > exJ ){
237	<	tempEx = exI;
238	<	exI = exJ;
239	<	exJ = tempEx;
244	<	}
224	>
225	>	// make the bonds
226	>	for (j = 0; j < molInfo.nBonds; j++){
227	>	currentBond = comp_stamps[stampID]->getBond(j);
228	>	theBonds[j].a = currentBond->getA() + atomOffset;
229	>	theBonds[j].b = currentBond->getB() + atomOffset;
230	>
231	>	exI = theBonds[j].a;
232	>	exJ = theBonds[j].b;
233	>
234	>	// exclude_I must always be the smaller of the pair
235	>	if (exI > exJ){
236	>	tempEx = exI;
237	>	exI = exJ;
238	>	exJ = tempEx;
239	>	}
240		#ifdef IS_MPI
241	<	tempEx = exI;
242	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
243	<	tempEx = exJ;
244	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
245	<
246	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
241	>	tempEx = exI;
242	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
243	>	tempEx = exJ;
244	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
245	>
246	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
247		#else  // isn't MPI
248	<
249	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
248	>
249	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
250		#endif  //is_mpi
251		}
252		excludeOffset += molInfo.nBonds;
253	<
253	>
254		//make the bends
255	<	for(j=0; j<molInfo.nBends; j++){
256	<
257	<	currentBend = comp_stamps[stampID]->getBend( j );
258	<	theBends[j].a = currentBend->getA() + atomOffset;
259	<	theBends[j].b = currentBend->getB() + atomOffset;
260	<	theBends[j].c = currentBend->getC() + atomOffset;
261	<
262	<	if( currentBend->haveExtras() ){
263	<
264	<	extras = currentBend->getExtras();
265	<	current_extra = extras;
266	<
267	<	while( current_extra != NULL ){
268	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
269	<
270	<	switch( current_extra->getType() ){
271	<
272	<	case 0:
273	<	theBends[j].ghost =
274	<	current_extra->getInt() + atomOffset;
275	<	theBends[j].isGhost = 1;
276	<	break;
277	<
278	<	case 1:
279	<	theBends[j].ghost =
280	<	(int)current_extra->getDouble() + atomOffset;
281	<	theBends[j].isGhost = 1;
282	<	break;
283	<
284	<	default:
285	<	sprintf( painCave.errMsg,
286	<	"SimSetup Error: ghostVectorSource was neither a "
287	<	"double nor an int.\n"
288	<	"-->Bend[%d] in %s\n",
289	<	j, comp_stamps[stampID]->getID() );
290	<	painCave.isFatal = 1;
291	<	simError();
255	>	for (j = 0; j < molInfo.nBends; j++){
256	>	currentBend = comp_stamps[stampID]->getBend(j);
257	>	theBends[j].a = currentBend->getA() + atomOffset;
258	>	theBends[j].b = currentBend->getB() + atomOffset;
259	>	theBends[j].c = currentBend->getC() + atomOffset;
260	>
261	>	if (currentBend->haveExtras()){
262	>	extras = currentBend->getExtras();
263	>	current_extra = extras;
264	>
265	>	while (current_extra != NULL){
266	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
267	>	switch (current_extra->getType()){
268	>	case 0:
269	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
270	>	theBends[j].isGhost = 1;
271	>	break;
272	>
273	>	case 1:
274	>	theBends[j].ghost = (int) current_extra->getDouble() +
275	>	atomOffset;
276	>	theBends[j].isGhost = 1;
277	>	break;
278	>
279	>	default:
280	>	sprintf(painCave.errMsg,
281	>	"SimSetup Error: ghostVectorSource was neither a "
282	>	"double nor an int.\n"
283	>	"-->Bend[%d] in %s\n",
284	>	j, comp_stamps[stampID]->getID());
285	>	painCave.isFatal = 1;
286	>	simError();
287	>	}
288	>	}
289	>	else{
290	>	sprintf(painCave.errMsg,
291	>	"SimSetup Error: unhandled bend assignment:\n"
292	>	"    -->%s in Bend[%d] in %s\n",
293	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
294	>	painCave.isFatal = 1;
295	>	simError();
296	>	}
297	>
298	>	current_extra = current_extra->getNext();
299	>	}
300		}
301	<	}
302	<
303	<	else{
304	<
305	<	sprintf( painCave.errMsg,
306	<	"SimSetup Error: unhandled bend assignment:\n"
307	<	"    -->%s in Bend[%d] in %s\n",
308	<	current_extra->getlhs(),
309	<	j, comp_stamps[stampID]->getID() );
310	<	painCave.isFatal = 1;
311	<	simError();
312	<	}
313	<
314	<	current_extra = current_extra->getNext();
315	<	}
316	<	}
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	<	}
301	>
302	>	if (!theBends[j].isGhost){
303	>	exI = theBends[j].a;
304	>	exJ = theBends[j].c;
305	>	}
306	>	else{
307	>	exI = theBends[j].a;
308	>	exJ = theBends[j].b;
309	>	}
310	>
311	>	// exclude_I must always be the smaller of the pair
312	>	if (exI > exJ){
313	>	tempEx = exI;
314	>	exI = exJ;
315	>	exJ = tempEx;
316	>	}
317		#ifdef IS_MPI
318	<	tempEx = exI;
319	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
320	<	tempEx = exJ;
321	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
322	<
323	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
318	>	tempEx = exI;
319	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
320	>	tempEx = exJ;
321	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
322	>
323	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
324		#else  // isn't MPI
325	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
325	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
326		#endif  //is_mpi
327		}
328		excludeOffset += molInfo.nBends;
329	<
330	<	for(j=0; j<molInfo.nTorsions; j++){
331	<
332	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
333	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
334	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
335	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
336	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
337	<
338	<	exI = theTorsions[j].a;
339	<	exJ = theTorsions[j].d;
340	<
341	<	// exclude_I must always be the smaller of the pair
342	<	if( exI > exJ ){
343	<	tempEx = exI;
344	<	exI = exJ;
345	<	exJ = tempEx;
361	<	}
329	>
330	>	for (j = 0; j < molInfo.nTorsions; j++){
331	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
332	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
333	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
334	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
335	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
336	>
337	>	exI = theTorsions[j].a;
338	>	exJ = theTorsions[j].d;
339	>
340	>	// exclude_I must always be the smaller of the pair
341	>	if (exI > exJ){
342	>	tempEx = exI;
343	>	exI = exJ;
344	>	exJ = tempEx;
345	>	}
346		#ifdef IS_MPI
347	<	tempEx = exI;
348	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
349	<	tempEx = exJ;
350	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
351	<
352	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
347	>	tempEx = exI;
348	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
349	>	tempEx = exJ;
350	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
351	>
352	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
353		#else  // isn't MPI
354	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
354	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
355		#endif  //is_mpi
356		}
357		excludeOffset += molInfo.nTorsions;
358	<
359	<
358	>
359	>
360		// 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 );
361
362	<
362	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
363	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
364	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
365	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
366	>	theTorsions);
367	>
368	>
369	>	info[k].molecules[i].initialize(molInfo);
370	>
371	>
372		atomOffset += molInfo.nAtoms;
373		delete[] theBonds;
374		delete[] theBends;
375		delete[] theTorsions;
376		}
377		}
378	<
378	>
379		#ifdef IS_MPI
380	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
380	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
381		MPIcheckPoint();
382		#endif // is_mpi
383	<
383	>
384		// clean up the forcefield
385
386		the_ff->calcRcut();
387		the_ff->cleanMe();
403	–
388		}
389
390	<	void SimSetup::initFromBass( void ){
407	<
390	>	void SimSetup::initFromBass(void){
391		int i, j, k;
392		int n_cells;
393		double cellx, celly, cellz;
#	Line 418 | Line 401 | void SimSetup::initFromBass( void ){
401		vel[1] = 0.0;
402		vel[2] = 0.0;
403
404	<	temp1 = (double)tot_nmol / 4.0;
405	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
406	<	temp3 = ceil( temp2 );
404	>	temp1 = (double) tot_nmol / 4.0;
405	>	temp2 = pow(temp1, (1.0 / 3.0));
406	>	temp3 = ceil(temp2);
407
408	<	have_extra =0;
409	<	if( temp2 < temp3 ){ // we have a non-complete lattice
410	<	have_extra =1;
408	>	have_extra = 0;
409	>	if (temp2 < temp3){
410	>	// we have a non-complete lattice
411	>	have_extra = 1;
412
413	<	n_cells = (int)temp3 - 1;
413	>	n_cells = (int) temp3 - 1;
414		cellx = info[0].boxL[0] / temp3;
415		celly = info[0].boxL[1] / temp3;
416		cellz = info[0].boxL[2] / temp3;
417	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
418	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
419	<	n_per_extra = (int)ceil( temp1 );
417	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
418	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
419	>	n_per_extra = (int) ceil(temp1);
420
421	<	if( n_per_extra > 4){
422	<	sprintf( painCave.errMsg,
423	<	"SimSetup error. There has been an error in constructing"
424	<	" the non-complete lattice.\n" );
421	>	if (n_per_extra > 4){
422	>	sprintf(painCave.errMsg,
423	>	"SimSetup error. There has been an error in constructing"
424	>	" the non-complete lattice.\n");
425		painCave.isFatal = 1;
426		simError();
427		}
428		}
429		else{
430	<	n_cells = (int)temp3;
430	>	n_cells = (int) temp3;
431		cellx = info[0].boxL[0] / temp3;
432		celly = info[0].boxL[1] / temp3;
433		cellz = info[0].boxL[2] / temp3;
#	Line 454 | Line 438 | void SimSetup::initFromBass( void ){
438		current_comp = 0;
439		current_atom_ndx = 0;
440
441	<	for( i=0; i < n_cells ; i++ ){
442	<	for( j=0; j < n_cells; j++ ){
443	<	for( k=0; k < n_cells; k++ ){
441	>	for (i = 0; i < n_cells ; i++){
442	>	for (j = 0; j < n_cells; j++){
443	>	for (k = 0; k < n_cells; k++){
444	>	makeElement(i * cellx, j * celly, k * cellz);
445
446	<	makeElement( i * cellx,
462	<	j * celly,
463	<	k * cellz );
446	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
447
448	<	makeElement( i * cellx + 0.5 * cellx,
466	<	j * celly + 0.5 * celly,
467	<	k * cellz );
448	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
449
450	<	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 );
450	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
451		}
452		}
453		}
454
455	<	if( have_extra ){
455	>	if (have_extra){
456		done = 0;
457
458		int start_ndx;
459	<	for( i=0; i < (n_cells+1) && !done; i++ ){
460	<	for( j=0; j < (n_cells+1) && !done; j++ ){
459	>	for (i = 0; i < (n_cells + 1) && !done; i++){
460	>	for (j = 0; j < (n_cells + 1) && !done; j++){
461	>	if (i < n_cells){
462	>	if (j < n_cells){
463	>	start_ndx = n_cells;
464	>	}
465	>	else
466	>	start_ndx = 0;
467	>	}
468	>	else
469	>	start_ndx = 0;
470
471	<	if( i < n_cells ){
471	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
472	>	makeElement(i * cellx, j * celly, k * cellz);
473	>	done = (current_mol >= tot_nmol);
474
475	<	if( j < n_cells ){
476	<	start_ndx = n_cells;
477	<	}
478	<	else start_ndx = 0;
479	<	}
494	<	else start_ndx = 0;
495	<
496	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
475	>	if (!done && n_per_extra > 1){
476	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
477	>	k * cellz);
478	>	done = (current_mol >= tot_nmol);
479	>	}
480
481	<	makeElement( i * cellx,
482	<	j * celly,
483	<	k * cellz );
484	<	done = ( current_mol >= tot_nmol );
481	>	if (!done && n_per_extra > 2){
482	>	makeElement(i * cellx, j * celly + 0.5 * celly,
483	>	k * cellz + 0.5 * cellz);
484	>	done = (current_mol >= tot_nmol);
485	>	}
486
487	<	if( !done && n_per_extra > 1 ){
488	<	makeElement( i * cellx + 0.5 * cellx,
489	<	j * celly + 0.5 * celly,
490	<	k * cellz );
491	<	done = ( current_mol >= tot_nmol );
492	<	}
509	<
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	<	}
487	>	if (!done && n_per_extra > 3){
488	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
489	>	k * cellz + 0.5 * cellz);
490	>	done = (current_mol >= tot_nmol);
491	>	}
492	>	}
493		}
494		}
495		}
496
497	<	for( i=0; i<info[0].n_atoms; i++ ){
498	<	info[0].atoms[i]->setVel( vel );
497	>	for (i = 0; i < info[0].n_atoms; i++){
498	>	info[0].atoms[i]->setVel(vel);
499		}
500		}
501
502	<	void SimSetup::makeElement( double x, double y, double z ){
534	<
502	>	void SimSetup::makeElement(double x, double y, double z){
503		int k;
504		AtomStamp* current_atom;
505		DirectionalAtom* dAtom;
506		double rotMat[3][3];
507		double pos[3];
508
509	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
510	<
511	<	current_atom = comp_stamps[current_comp]->getAtom( k );
512	<	if( !current_atom->havePosition() ){
513	<	sprintf( painCave.errMsg,
514	<	"SimSetup:initFromBass error.\n"
515	<	"\tComponent %s, atom %s does not have a position specified.\n"
516	<	"\tThe initialization routine is unable to give a start"
517	<	" position.\n",
550	<	comp_stamps[current_comp]->getID(),
551	<	current_atom->getType() );
509	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
510	>	current_atom = comp_stamps[current_comp]->getAtom(k);
511	>	if (!current_atom->havePosition()){
512	>	sprintf(painCave.errMsg,
513	>	"SimSetup:initFromBass error.\n"
514	>	"\tComponent %s, atom %s does not have a position specified.\n"
515	>	"\tThe initialization routine is unable to give a start"
516	>	" position.\n",
517	>	comp_stamps[current_comp]->getID(), current_atom->getType());
518		painCave.isFatal = 1;
519		simError();
520		}
521	<
521	>
522		pos[0] = x + current_atom->getPosX();
523		pos[1] = y + current_atom->getPosY();
524		pos[2] = z + current_atom->getPosZ();
559	–
560	–	info[0].atoms[current_atom_ndx]->setPos( pos );
525
526	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
526	>	info[0].atoms[current_atom_ndx]->setPos(pos);
527
528	<	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
528	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
529	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
530
531		rotMat[0][0] = 1.0;
532		rotMat[0][1] = 0.0;
#	Line 575 | Line 540 | void SimSetup::makeElement( double x, double y, double
540		rotMat[2][1] = 0.0;
541		rotMat[2][2] = 1.0;
542
543	<	dAtom->setA( rotMat );
543	>	dAtom->setA(rotMat);
544		}
545
546		current_atom_ndx++;
#	Line 584 | Line 549 | void SimSetup::makeElement( double x, double y, double
549		current_mol++;
550		current_comp_mol++;
551
552	<	if( current_comp_mol >= components_nmol[current_comp] ){
588	<
552	>	if (current_comp_mol >= components_nmol[current_comp]){
553		current_comp_mol = 0;
554		current_comp++;
555		}
556		}
557
558
559	<	void SimSetup::gatherInfo( void ){
560	<	int i,j,k;
559	>	void SimSetup::gatherInfo(void){
560	>	int i;
561
562		ensembleCase = -1;
563		ffCase = -1;
564
565		// set the easy ones first
566
567	<	for( i=0; i<nInfo; i++){
567	>	for (i = 0; i < nInfo; i++){
568		info[i].target_temp = globals->getTargetTemp();
569		info[i].dt = globals->getDt();
570		info[i].run_time = globals->getRunTime();
#	Line 610 | Line 574 | void SimSetup::gatherInfo( void ){
574
575		// get the forceField
576
577	<	strcpy( force_field, globals->getForceField() );
577	>	strcpy(force_field, globals->getForceField());
578
579	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
580	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
581	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
579	>	if (!strcasecmp(force_field, "DUFF")){
580	>	ffCase = FF_DUFF;
581	>	}
582	>	else if (!strcasecmp(force_field, "LJ")){
583	>	ffCase = FF_LJ;
584	>	}
585	>	else if (!strcasecmp(force_field, "EAM")){
586	>	ffCase = FF_EAM;
587	>	}
588		else{
589	<	sprintf( painCave.errMsg,
590	<	"SimSetup Error. Unrecognized force field -> %s\n",
591	<	force_field );
592	<	painCave.isFatal = 1;
623	<	simError();
589	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
590	>	force_field);
591	>	painCave.isFatal = 1;
592	>	simError();
593		}
594
595	<	// get the ensemble
595	>	// get the ensemble
596
597	<	strcpy( ensemble, globals->getEnsemble() );
597	>	strcpy(ensemble, globals->getEnsemble());
598
599	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
600	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
601	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
599	>	if (!strcasecmp(ensemble, "NVE")){
600	>	ensembleCase = NVE_ENS;
601	>	}
602	>	else if (!strcasecmp(ensemble, "NVT")){
603	>	ensembleCase = NVT_ENS;
604	>	}
605	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
606		ensembleCase = NPTi_ENS;
607	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
608	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
609	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
607	>	}
608	>	else if (!strcasecmp(ensemble, "NPTf")){
609	>	ensembleCase = NPTf_ENS;
610	>	}
611	>	else if (!strcasecmp(ensemble, "NPTxyz")){
612	>	ensembleCase = NPTxyz_ENS;
613	>	}
614		else{
615	<	sprintf( painCave.errMsg,
616	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
617	<	"reverting to NVE for this simulation.\n",
618	<	ensemble );
619	<	painCave.isFatal = 0;
620	<	simError();
621	<	strcpy( ensemble, "NVE" );
622	<	ensembleCase = NVE_ENS;
615	>	sprintf(painCave.errMsg,
616	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
617	>	"reverting to NVE for this simulation.\n",
618	>	ensemble);
619	>	painCave.isFatal = 0;
620	>	simError();
621	>	strcpy(ensemble, "NVE");
622	>	ensembleCase = NVE_ENS;
623		}
647	–
648	–	for(i=0; i<nInfo; i++){
649	–
650	–	strcpy( info[i].ensemble, ensemble );
624
625	+	for (i = 0; i < nInfo; i++){
626	+	strcpy(info[i].ensemble, ensemble);
627	+
628		// get the mixing rule
629
630	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
630	>	strcpy(info[i].mixingRule, globals->getMixingRule());
631		info[i].usePBC = globals->getPBC();
632		}
633	<
633	>
634		// get the components and calculate the tot_nMol and indvidual n_mol
635	<
635	>
636		the_components = globals->getComponents();
637		components_nmol = new int[n_components];
638
639
640	<	if( !globals->haveNMol() ){
640	>	if (!globals->haveNMol()){
641		// we don't have the total number of molecules, so we assume it is
642		// given in each component
643
644		tot_nmol = 0;
645	<	for( i=0; i<n_components; i++ ){
646	<
647	<	if( !the_components[i]->haveNMol() ){
648	<	// we have a problem
649	<	sprintf( painCave.errMsg,
650	<	"SimSetup Error. No global NMol or component NMol"
651	<	" given. Cannot calculate the number of atoms.\n" );
652	<	painCave.isFatal = 1;
677	<	simError();
645	>	for (i = 0; i < n_components; i++){
646	>	if (!the_components[i]->haveNMol()){
647	>	// we have a problem
648	>	sprintf(painCave.errMsg,
649	>	"SimSetup Error. No global NMol or component NMol"
650	>	" given. Cannot calculate the number of atoms.\n");
651	>	painCave.isFatal = 1;
652	>	simError();
653		}
654
655		tot_nmol += the_components[i]->getNMol();
#	Line 682 | Line 657 | void SimSetup::gatherInfo( void ){
657		}
658		}
659		else{
660	<	sprintf( painCave.errMsg,
661	<	"SimSetup error.\n"
662	<	"\tSorry, the ability to specify total"
663	<	" nMols and then give molfractions in the components\n"
664	<	"\tis not currently supported."
665	<	" Please give nMol in the components.\n" );
660	>	sprintf(painCave.errMsg,
661	>	"SimSetup error.\n"
662	>	"\tSorry, the ability to specify total"
663	>	" nMols and then give molfractions in the components\n"
664	>	"\tis not currently supported."
665	>	" Please give nMol in the components.\n");
666		painCave.isFatal = 1;
667		simError();
668		}
669
670		// set the status, sample, and thermal kick times
696	–
697	–	for(i=0; i<nInfo; i++){
671
672	<	if( globals->haveSampleTime() ){
672	>	for (i = 0; i < nInfo; i++){
673	>	if (globals->haveSampleTime()){
674		info[i].sampleTime = globals->getSampleTime();
675		info[i].statusTime = info[i].sampleTime;
676		info[i].thermalTime = info[i].sampleTime;
#	Line 706 | Line 680 | void SimSetup::gatherInfo( void ){
680		info[i].statusTime = info[i].sampleTime;
681		info[i].thermalTime = info[i].sampleTime;
682		}
683	<
684	<	if( globals->haveStatusTime() ){
683	>
684	>	if (globals->haveStatusTime()){
685		info[i].statusTime = globals->getStatusTime();
686		}
687	<
688	<	if( globals->haveThermalTime() ){
687	>
688	>	if (globals->haveThermalTime()){
689		info[i].thermalTime = globals->getThermalTime();
690		}
691
692	+	info[i].resetIntegrator = 0;
693	+	if( globals->haveResetTime() ){
694	+	info[i].resetTime = globals->getResetTime();
695	+	info[i].resetIntegrator = 1;
696	+	}
697	+
698		// check for the temperature set flag
699	+
700	+	if (globals->haveTempSet())
701	+	info[i].setTemp = globals->getTempSet();
702
703	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
703	>	// check for the extended State init
704	>
705	>	info[i].useInitXSstate = globals->getUseInitXSstate();
706	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
707
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 );
708		}
709	<	else{
710	<	if( !globals->haveBoxX() ){
711	<	sprintf( painCave.errMsg,
712	<	"SimSetup error, no periodic BoxX size given.\n" );
713	<	painCave.isFatal = 1;
714	<	simError();
709	>
710	>	//setup seed for random number generator
711	>	int seedValue;
712	>
713	>	if (globals->haveSeed()){
714	>	seedValue = globals->getSeed();
715	>
716	>	if(seedValue / 1E9 == 0){
717	>	sprintf(painCave.errMsg,
718	>	"Seed for sprng library should contain at least 9 digits\n"
719	>	"OOPSE will generate a seed for user\n");
720	>	painCave.isFatal = 0;
721	>	simError();
722	>
723	>	//using seed generated by system instead of invalid seed set by user
724	>	#ifndef IS_MPI
725	>	seedValue = make_sprng_seed();
726	>	#else
727	>	if (worldRank == 0){
728	>	seedValue = make_sprng_seed();
729		}
730	<	boxVector[0] = globals->getBoxX();
731	<
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 );
730	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
731	>	#endif
732		}
733	+	}//end of if branch of globals->haveSeed()
734	+	else{
735	+
736	+	#ifndef IS_MPI
737	+	seedValue = make_sprng_seed();
738	+	#else
739	+	if (worldRank == 0){
740	+	seedValue = make_sprng_seed();
741	+	}
742	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
743	+	#endif
744	+	}//end of globals->haveSeed()
745
746	+	for (int i = 0; i < nInfo; i++){
747	+	info[i].setSeed(seedValue);
748		}
749	<
749	>
750		#ifdef IS_MPI
751	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
751	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
752		MPIcheckPoint();
753		#endif // is_mpi
776	–
754		}
755
756
757	<	void SimSetup::finalInfoCheck( void ){
757	>	void SimSetup::finalInfoCheck(void){
758		int index;
759		int usesDipoles;
760		int i;
761
762	<	for(i=0; i<nInfo; i++){
762	>	for (i = 0; i < nInfo; i++){
763		// check electrostatic parameters
764	<
764	>
765		index = 0;
766		usesDipoles = 0;
767	<	while( (index < info[i].n_atoms) && !usesDipoles ){
767	>	while ((index < info[i].n_atoms) && !usesDipoles){
768		usesDipoles = (info[i].atoms[index])->hasDipole();
769		index++;
770		}
771	<
771	>
772		#ifdef IS_MPI
773		int myUse = usesDipoles;
774	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
774	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
775		#endif //is_mpi
776	<
776	>
777		double theEcr, theEst;
778	<
779	<	if (globals->getUseRF() ) {
778	>
779	>	if (globals->getUseRF()){
780		info[i].useReactionField = 1;
781	<
782	<	if( !globals->haveECR() ){
783	<	sprintf( painCave.errMsg,
784	<	"SimSetup Warning: using default value of 1/2 the smallest "
785	<	"box length for the electrostaticCutoffRadius.\n"
786	<	"I hope you have a very fast processor!\n");
787	<	painCave.isFatal = 0;
788	<	simError();
789	<	double smallest;
790	<	smallest = info[i].boxL[0];
791	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
792	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
793	<	theEcr = 0.5 * smallest;
794	<	} else {
795	<	theEcr = globals->getECR();
781	>
782	>	if (!globals->haveECR()){
783	>	sprintf(painCave.errMsg,
784	>	"SimSetup Warning: using default value of 1/2 the smallest "
785	>	"box length for the electrostaticCutoffRadius.\n"
786	>	"I hope you have a very fast processor!\n");
787	>	painCave.isFatal = 0;
788	>	simError();
789	>	double smallest;
790	>	smallest = info[i].boxL[0];
791	>	if (info[i].boxL[1] <= smallest)
792	>	smallest = info[i].boxL[1];
793	>	if (info[i].boxL[2] <= smallest)
794	>	smallest = info[i].boxL[2];
795	>	theEcr = 0.5 * smallest;
796		}
797	<
798	<	if( !globals->haveEST() ){
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();
797	>	else{
798	>	theEcr = globals->getECR();
799		}
800	<
801	<	info[i].setEcr( theEcr, theEst );
802	<
803	<	if(!globals->haveDielectric() ){
804	<	sprintf( painCave.errMsg,
805	<	"SimSetup Error: You are trying to use Reaction Field without"
806	<	"setting a dielectric constant!\n"
807	<	);
840	<	painCave.isFatal = 1;
841	<	simError();
800	>
801	>	if (!globals->haveEST()){
802	>	sprintf(painCave.errMsg,
803	>	"SimSetup Warning: using default value of 0.05 * the "
804	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
805	>	painCave.isFatal = 0;
806	>	simError();
807	>	theEst = 0.05 * theEcr;
808		}
809	<	info[i].dielectric = globals->getDielectric();
810	<	}
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 );
809	>	else{
810	>	theEst = globals->getEST();
811		}
812	<	}
812	>
813	>	info[i].setDefaultEcr(theEcr, theEst);
814	>
815	>	if (!globals->haveDielectric()){
816	>	sprintf(painCave.errMsg,
817	>	"SimSetup Error: You are trying to use Reaction Field without"
818	>	"setting a dielectric constant!\n");
819	>	painCave.isFatal = 1;
820	>	simError();
821	>	}
822	>	info[i].dielectric = globals->getDielectric();
823	>	}
824	>	else{
825	>	if (usesDipoles){
826	>	if (!globals->haveECR()){
827	>	sprintf(painCave.errMsg,
828	>	"SimSetup Warning: using default value of 1/2 the smallest "
829	>	"box length for the electrostaticCutoffRadius.\n"
830	>	"I hope you have a very fast processor!\n");
831	>	painCave.isFatal = 0;
832	>	simError();
833	>	double smallest;
834	>	smallest = info[i].boxL[0];
835	>	if (info[i].boxL[1] <= smallest)
836	>	smallest = info[i].boxL[1];
837	>	if (info[i].boxL[2] <= smallest)
838	>	smallest = info[i].boxL[2];
839	>	theEcr = 0.5 * smallest;
840	>	}
841	>	else{
842	>	theEcr = globals->getECR();
843	>	}
844	>
845	>	if (!globals->haveEST()){
846	>	sprintf(painCave.errMsg,
847	>	"SimSetup Warning: using default value of 0.05 * the "
848	>	"electrostaticCutoffRadius for the "
849	>	"electrostaticSkinThickness\n");
850	>	painCave.isFatal = 0;
851	>	simError();
852	>	theEst = 0.05 * theEcr;
853	>	}
854	>	else{
855	>	theEst = globals->getEST();
856	>	}
857	>
858	>	info[i].setDefaultEcr(theEcr, theEst);
859	>	}
860	>	}
861	>
862	>	if( !initSuspend )
863	>	info[i].checkCutOffs();
864		}
865
866		#ifdef IS_MPI
867	<	strcpy( checkPointMsg, "post processing checks out" );
867	>	strcpy(checkPointMsg, "post processing checks out");
868		MPIcheckPoint();
869		#endif // is_mpi
886	–
870		}
871
872	<	void SimSetup::initSystemCoords( void ){
872	>	void SimSetup::initSystemCoords(void){
873		int i;
874	<
874	>
875		char* inName;
876
877	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
877	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
878
879	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
880	<
881	<	if( globals->haveInitialConfig() ){
882	<
879	>	for (i = 0; i < info[0].n_atoms; i++)
880	>	info[0].atoms[i]->setCoords();
881	>
882	>	if (globals->haveInitialConfig()){
883		InitializeFromFile* fileInit;
884		#ifdef IS_MPI // is_mpi
885	<	if( worldRank == 0 ){
885	>	if (worldRank == 0){
886		#endif //is_mpi
887		inName = globals->getInitialConfig();
888	<	double* tempDouble = new double[1000000];
906	<	fileInit = new InitializeFromFile( inName );
888	>	fileInit = new InitializeFromFile(inName);
889		#ifdef IS_MPI
890	<	}else fileInit = new InitializeFromFile( NULL );
890	>	}
891	>	else
892	>	fileInit = new InitializeFromFile(NULL);
893		#endif
894	<	fileInit->readInit( info ); // default velocities on
895	<
894	>	fileInit->readInit(info); // default velocities on
895	>
896		delete fileInit;
897		}
898		else{
915	–
899		#ifdef IS_MPI
900	<
900	>
901		// no init from bass
902	<
903	<	sprintf( painCave.errMsg,
904	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
905	<	painCave.isFatal;
902	>
903	>	sprintf(painCave.errMsg,
904	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
905	>	painCave.isFatal = 1;;
906		simError();
907	<
907	>
908		#else
909	<
909	>
910		initFromBass();
911	<
912	<
911	>
912	>
913		#endif
914		}
915	<
915	>
916		#ifdef IS_MPI
917	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
917	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
918		MPIcheckPoint();
919		#endif // is_mpi
937	–
920		}
921
922
923	<	void SimSetup::makeOutNames( void ){
942	<
923	>	void SimSetup::makeOutNames(void){
924		int k;
925
945	–
946	–	for(k=0; k<nInfo; k++){
926
927	+	for (k = 0; k < nInfo; k++){
928		#ifdef IS_MPI
929	<	if( worldRank == 0 ){
929	>	if (worldRank == 0){
930		#endif // is_mpi
931	<
932	<	if( globals->haveFinalConfig() ){
933	<	strcpy( info[k].finalName, globals->getFinalConfig() );
931	>
932	>	if (globals->haveFinalConfig()){
933	>	strcpy(info[k].finalName, globals->getFinalConfig());
934		}
935		else{
936	<	strcpy( info[k].finalName, inFileName );
937	<	char* endTest;
938	<	int nameLength = strlen( info[k].finalName );
939	<	endTest = &(info[k].finalName[nameLength - 5]);
940	<	if( !strcmp( endTest, ".bass" ) ){
941	<	strcpy( endTest, ".eor" );
942	<	}
943	<	else if( !strcmp( endTest, ".BASS" ) ){
944	<	strcpy( endTest, ".eor" );
945	<	}
946	<	else{
947	<	endTest = &(info[k].finalName[nameLength - 4]);
948	<	if( !strcmp( endTest, ".bss" ) ){
949	<	strcpy( endTest, ".eor" );
950	<	}
951	<	else if( !strcmp( endTest, ".mdl" ) ){
952	<	strcpy( endTest, ".eor" );
953	<	}
954	<	else{
955	<	strcat( info[k].finalName, ".eor" );
956	<	}
957	<	}
936	>	strcpy(info[k].finalName, inFileName);
937	>	char* endTest;
938	>	int nameLength = strlen(info[k].finalName);
939	>	endTest = &(info[k].finalName[nameLength - 5]);
940	>	if (!strcmp(endTest, ".bass")){
941	>	strcpy(endTest, ".eor");
942	>	}
943	>	else if (!strcmp(endTest, ".BASS")){
944	>	strcpy(endTest, ".eor");
945	>	}
946	>	else{
947	>	endTest = &(info[k].finalName[nameLength - 4]);
948	>	if (!strcmp(endTest, ".bss")){
949	>	strcpy(endTest, ".eor");
950	>	}
951	>	else if (!strcmp(endTest, ".mdl")){
952	>	strcpy(endTest, ".eor");
953	>	}
954	>	else{
955	>	strcat(info[k].finalName, ".eor");
956	>	}
957	>	}
958		}
959	<
959	>
960		// make the sample and status out names
961	<
962	<	strcpy( info[k].sampleName, inFileName );
961	>
962	>	strcpy(info[k].sampleName, inFileName);
963		char* endTest;
964	<	int nameLength = strlen( info[k].sampleName );
964	>	int nameLength = strlen(info[k].sampleName);
965		endTest = &(info[k].sampleName[nameLength - 5]);
966	<	if( !strcmp( endTest, ".bass" ) ){
967	<	strcpy( endTest, ".dump" );
966	>	if (!strcmp(endTest, ".bass")){
967	>	strcpy(endTest, ".dump");
968		}
969	<	else if( !strcmp( endTest, ".BASS" ) ){
970	<	strcpy( endTest, ".dump" );
969	>	else if (!strcmp(endTest, ".BASS")){
970	>	strcpy(endTest, ".dump");
971		}
972		else{
973	<	endTest = &(info[k].sampleName[nameLength - 4]);
974	<	if( !strcmp( endTest, ".bss" ) ){
975	<	strcpy( endTest, ".dump" );
976	<	}
977	<	else if( !strcmp( endTest, ".mdl" ) ){
978	<	strcpy( endTest, ".dump" );
979	<	}
980	<	else{
981	<	strcat( info[k].sampleName, ".dump" );
982	<	}
973	>	endTest = &(info[k].sampleName[nameLength - 4]);
974	>	if (!strcmp(endTest, ".bss")){
975	>	strcpy(endTest, ".dump");
976	>	}
977	>	else if (!strcmp(endTest, ".mdl")){
978	>	strcpy(endTest, ".dump");
979	>	}
980	>	else{
981	>	strcat(info[k].sampleName, ".dump");
982	>	}
983		}
984	<
985	<	strcpy( info[k].statusName, inFileName );
986	<	nameLength = strlen( info[k].statusName );
984	>
985	>	strcpy(info[k].statusName, inFileName);
986	>	nameLength = strlen(info[k].statusName);
987		endTest = &(info[k].statusName[nameLength - 5]);
988	<	if( !strcmp( endTest, ".bass" ) ){
989	<	strcpy( endTest, ".stat" );
988	>	if (!strcmp(endTest, ".bass")){
989	>	strcpy(endTest, ".stat");
990		}
991	<	else if( !strcmp( endTest, ".BASS" ) ){
992	<	strcpy( endTest, ".stat" );
991	>	else if (!strcmp(endTest, ".BASS")){
992	>	strcpy(endTest, ".stat");
993		}
994		else{
995	<	endTest = &(info[k].statusName[nameLength - 4]);
996	<	if( !strcmp( endTest, ".bss" ) ){
997	<	strcpy( endTest, ".stat" );
998	<	}
999	<	else if( !strcmp( endTest, ".mdl" ) ){
1000	<	strcpy( endTest, ".stat" );
1001	<	}
1002	<	else{
1003	<	strcat( info[k].statusName, ".stat" );
1004	<	}
995	>	endTest = &(info[k].statusName[nameLength - 4]);
996	>	if (!strcmp(endTest, ".bss")){
997	>	strcpy(endTest, ".stat");
998	>	}
999	>	else if (!strcmp(endTest, ".mdl")){
1000	>	strcpy(endTest, ".stat");
1001	>	}
1002	>	else{
1003	>	strcat(info[k].statusName, ".stat");
1004	>	}
1005		}
1006	<
1006	>
1007		#ifdef IS_MPI
1008	+
1009		}
1010		#endif // is_mpi
1011		}
1012		}
1013
1014
1015	<	void SimSetup::sysObjectsCreation( void ){
1016	<
1017	<	int i,k;
1037	<
1015	>	void SimSetup::sysObjectsCreation(void){
1016	>	int i, k;
1017	>
1018		// create the forceField
1019
1020		createFF();
#	Line 1049 | Line 1029 | void SimSetup::sysObjectsCreation( void ){
1029
1030		#ifdef IS_MPI
1031		// divide the molecules among the processors
1032	<
1032	>
1033		mpiMolDivide();
1034		#endif //is_mpi
1035	<
1035	>
1036		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1037	<
1037	>
1038		makeSysArrays();
1039
1040		// make and initialize the molecules (all but atomic coordinates)
1041	<
1041	>
1042		makeMolecules();
1043	<
1044	<	for(k=0; k<nInfo; k++){
1043	>
1044	>	for (k = 0; k < nInfo; k++){
1045		info[k].identArray = new int[info[k].n_atoms];
1046	<	for(i=0; i<info[k].n_atoms; i++){
1046	>	for (i = 0; i < info[k].n_atoms; i++){
1047		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1048		}
1049		}
1050		}
1051
1052
1053	<	void SimSetup::createFF( void ){
1053	>	void SimSetup::createFF(void){
1054	>	switch (ffCase){
1055	>	case FF_DUFF:
1056	>	the_ff = new DUFF();
1057	>	break;
1058
1059	<	switch( ffCase ){
1059	>	case FF_LJ:
1060	>	the_ff = new LJFF();
1061	>	break;
1062
1063	<	case FF_DUFF:
1064	<	the_ff = new DUFF();
1065	<	break;
1063	>	case FF_EAM:
1064	>	the_ff = new EAM_FF();
1065	>	break;
1066
1067	<	case FF_LJ:
1068	<	the_ff = new LJFF();
1069	<	break;
1070	<
1071	<	case FF_EAM:
1086	<	the_ff = new EAM_FF();
1087	<	break;
1088	<
1089	<	default:
1090	<	sprintf( painCave.errMsg,
1091	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1092	<	painCave.isFatal = 1;
1093	<	simError();
1067	>	default:
1068	>	sprintf(painCave.errMsg,
1069	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1070	>	painCave.isFatal = 1;
1071	>	simError();
1072		}
1073
1074		#ifdef IS_MPI
1075	<	strcpy( checkPointMsg, "ForceField creation successful" );
1075	>	strcpy(checkPointMsg, "ForceField creation successful");
1076		MPIcheckPoint();
1077		#endif // is_mpi
1100	–
1078		}
1079
1080
1081	<	void SimSetup::compList( void ){
1105	<
1081	>	void SimSetup::compList(void){
1082		int i;
1083		char* id;
1084		LinkedMolStamp* headStamp = new LinkedMolStamp();
1085		LinkedMolStamp* currentStamp = NULL;
1086	<	comp_stamps = new MoleculeStamp*[n_components];
1087	<
1086	>	comp_stamps = new MoleculeStamp * [n_components];
1087	>
1088		// make an array of molecule stamps that match the components used.
1089		// also extract the used stamps out into a separate linked list
1090	<
1091	<	for(i=0; i<nInfo; i++){
1090	>
1091	>	for (i = 0; i < nInfo; i++){
1092		info[i].nComponents = n_components;
1093		info[i].componentsNmol = components_nmol;
1094		info[i].compStamps = comp_stamps;
1095		info[i].headStamp = headStamp;
1096		}
1121	–
1097
1098	<	for( i=0; i<n_components; i++ ){
1099	<
1098	>
1099	>	for (i = 0; i < n_components; i++){
1100		id = the_components[i]->getType();
1101		comp_stamps[i] = NULL;
1102	<
1102	>
1103		// check to make sure the component isn't already in the list
1104
1105	<	comp_stamps[i] = headStamp->match( id );
1106	<	if( comp_stamps[i] == NULL ){
1132	<
1105	>	comp_stamps[i] = headStamp->match(id);
1106	>	if (comp_stamps[i] == NULL){
1107		// extract the component from the list;
1108	<
1109	<	currentStamp = stamps->extractMolStamp( id );
1110	<	if( currentStamp == NULL ){
1111	<	sprintf( painCave.errMsg,
1112	<	"SimSetup error: Component \"%s\" was not found in the "
1113	<	"list of declared molecules\n",
1114	<	id );
1115	<	painCave.isFatal = 1;
1116	<	simError();
1108	>
1109	>	currentStamp = stamps->extractMolStamp(id);
1110	>	if (currentStamp == NULL){
1111	>	sprintf(painCave.errMsg,
1112	>	"SimSetup error: Component \"%s\" was not found in the "
1113	>	"list of declared molecules\n",
1114	>	id);
1115	>	painCave.isFatal = 1;
1116	>	simError();
1117		}
1118	<
1119	<	headStamp->add( currentStamp );
1120	<	comp_stamps[i] = headStamp->match( id );
1118	>
1119	>	headStamp->add(currentStamp);
1120	>	comp_stamps[i] = headStamp->match(id);
1121		}
1122		}
1123
1124		#ifdef IS_MPI
1125	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1125	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1126		MPIcheckPoint();
1127		#endif // is_mpi
1128	+	}
1129
1130	+	void SimSetup::calcSysValues(void){
1131	+	int i;
1132
1133	<	}
1133	>	int* molMembershipArray;
1134
1158	–	void SimSetup::calcSysValues( void ){
1159	–	int i, j, k;
1160	–
1161	–	int *molMembershipArray;
1162	–
1135		tot_atoms = 0;
1136		tot_bonds = 0;
1137		tot_bends = 0;
1138		tot_torsions = 0;
1139	<	for( i=0; i<n_components; i++ ){
1140	<
1141	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1142	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1171	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1139	>	for (i = 0; i < n_components; i++){
1140	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1141	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1142	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1143		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1144		}
1145	<
1145	>
1146		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1147		molMembershipArray = new int[tot_atoms];
1148	<
1149	<	for(i=0; i<nInfo; i++){
1148	>
1149	>	for (i = 0; i < nInfo; i++){
1150		info[i].n_atoms = tot_atoms;
1151		info[i].n_bonds = tot_bonds;
1152		info[i].n_bends = tot_bends;
1153		info[i].n_torsions = tot_torsions;
1154		info[i].n_SRI = tot_SRI;
1155		info[i].n_mol = tot_nmol;
1156	<
1156	>
1157		info[i].molMembershipArray = molMembershipArray;
1158	<	}
1158	>	}
1159		}
1160
1161		#ifdef IS_MPI
1162
1163	<	void SimSetup::mpiMolDivide( void ){
1193	<
1163	>	void SimSetup::mpiMolDivide(void){
1164		int i, j, k;
1165		int localMol, allMol;
1166		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1167
1168	<	mpiSim = new mpiSimulation( info );
1169	<
1168	>	mpiSim = new mpiSimulation(info);
1169	>
1170		globalIndex = mpiSim->divideLabor();
1171
1172		// set up the local variables
1173	<
1173	>
1174		mol2proc = mpiSim->getMolToProcMap();
1175		molCompType = mpiSim->getMolComponentType();
1176	<
1176	>
1177		allMol = 0;
1178		localMol = 0;
1179		local_atoms = 0;
#	Line 1213 | Line 1183 | void SimSetup::mpiMolDivide( void ){
1183		globalAtomIndex = 0;
1184
1185
1186	<	for( i=0; i<n_components; i++ ){
1187	<
1188	<	for( j=0; j<components_nmol[i]; j++ ){
1189	<
1190	<	if( mol2proc[allMol] == worldRank ){
1191	<
1192	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1193	<	local_bonds +=    comp_stamps[i]->getNBonds();
1224	<	local_bends +=    comp_stamps[i]->getNBends();
1225	<	local_torsions += comp_stamps[i]->getNTorsions();
1226	<	localMol++;
1186	>	for (i = 0; i < n_components; i++){
1187	>	for (j = 0; j < components_nmol[i]; j++){
1188	>	if (mol2proc[allMol] == worldRank){
1189	>	local_atoms += comp_stamps[i]->getNAtoms();
1190	>	local_bonds += comp_stamps[i]->getNBonds();
1191	>	local_bends += comp_stamps[i]->getNBends();
1192	>	local_torsions += comp_stamps[i]->getNTorsions();
1193	>	localMol++;
1194		}
1195	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1195	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1196		info[0].molMembershipArray[globalAtomIndex] = allMol;
1197		globalAtomIndex++;
1198		}
1199
1200	<	allMol++;
1200	>	allMol++;
1201		}
1202		}
1203		local_SRI = local_bonds + local_bends + local_torsions;
1204	<
1204	>
1205		info[0].n_atoms = mpiSim->getMyNlocal();
1206	<
1207	<	if( local_atoms != info[0].n_atoms ){
1208	<	sprintf( painCave.errMsg,
1209	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1210	<	" localAtom (%d) are not equal.\n",
1211	<	info[0].n_atoms,
1245	<	local_atoms );
1206	>
1207	>	if (local_atoms != info[0].n_atoms){
1208	>	sprintf(painCave.errMsg,
1209	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1210	>	" localAtom (%d) are not equal.\n",
1211	>	info[0].n_atoms, local_atoms);
1212		painCave.isFatal = 1;
1213		simError();
1214		}
#	Line 1253 | Line 1219 | void SimSetup::mpiMolDivide( void ){
1219		info[0].n_SRI = local_SRI;
1220		info[0].n_mol = localMol;
1221
1222	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1222	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1223		MPIcheckPoint();
1224		}
1225	<
1225	>
1226		#endif // is_mpi
1227
1228
1229	<	void SimSetup::makeSysArrays( void ){
1230	<	int i, j, k, l;
1229	>	void SimSetup::makeSysArrays(void){
1230	>
1231	>	#ifndef IS_MPI
1232	>	int k, j;
1233	>	#endif // is_mpi
1234	>	int i, l;
1235
1236		Atom** the_atoms;
1237		Molecule* the_molecules;
1238		Exclude** the_excludes;
1239
1240	<
1241	<	for(l=0; l<nInfo; l++){
1272	<
1240	>
1241	>	for (l = 0; l < nInfo; l++){
1242		// create the atom and short range interaction arrays
1243	<
1244	<	the_atoms = new Atom*[info[l].n_atoms];
1243	>
1244	>	the_atoms = new Atom * [info[l].n_atoms];
1245		the_molecules = new Molecule[info[l].n_mol];
1246		int molIndex;
1247
1248		// initialize the molecule's stampID's
1249	<
1249	>
1250		#ifdef IS_MPI
1251	<
1252	<
1251	>
1252	>
1253		molIndex = 0;
1254	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1255	<
1256	<	if(mol2proc[i] == worldRank ){
1257	<	the_molecules[molIndex].setStampID( molCompType[i] );
1258	<	the_molecules[molIndex].setMyIndex( molIndex );
1259	<	the_molecules[molIndex].setGlobalIndex( i );
1291	<	molIndex++;
1254	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1255	>	if (mol2proc[i] == worldRank){
1256	>	the_molecules[molIndex].setStampID(molCompType[i]);
1257	>	the_molecules[molIndex].setMyIndex(molIndex);
1258	>	the_molecules[molIndex].setGlobalIndex(i);
1259	>	molIndex++;
1260		}
1261		}
1262	<
1262	>
1263		#else // is_mpi
1264	<
1264	>
1265		molIndex = 0;
1266		globalAtomIndex = 0;
1267	<	for(i=0; i<n_components; i++){
1268	<	for(j=0; j<components_nmol[i]; j++ ){
1269	<	the_molecules[molIndex].setStampID( i );
1270	<	the_molecules[molIndex].setMyIndex( molIndex );
1271	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1272	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1273	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1274	<	globalAtomIndex++;
1275	<	}
1276	<	molIndex++;
1267	>	for (i = 0; i < n_components; i++){
1268	>	for (j = 0; j < components_nmol[i]; j++){
1269	>	the_molecules[molIndex].setStampID(i);
1270	>	the_molecules[molIndex].setMyIndex(molIndex);
1271	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1272	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1273	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1274	>	globalAtomIndex++;
1275	>	}
1276	>	molIndex++;
1277		}
1278		}
1279	<
1280	<
1279	>
1280	>
1281		#endif // is_mpi
1282
1283
1284	<	if( info[l].n_SRI ){
1317	<
1284	>	if (info[l].n_SRI){
1285		Exclude::createArray(info[l].n_SRI);
1286	<	the_excludes = new Exclude*[info[l].n_SRI];
1287	<	for( int ex=0; ex<info[l].n_SRI; ex++){
1288	<	the_excludes[ex] = new Exclude(ex);
1286	>	the_excludes = new Exclude * [info[l].n_SRI];
1287	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1288	>	the_excludes[ex] = new Exclude(ex);
1289		}
1290		info[l].globalExcludes = new int;
1291		info[l].n_exclude = info[l].n_SRI;
1292		}
1293		else{
1294	<
1295	<	Exclude::createArray( 1 );
1329	<	the_excludes = new Exclude*;
1294	>	Exclude::createArray(1);
1295	>	the_excludes = new Exclude * ;
1296		the_excludes[0] = new Exclude(0);
1297	<	the_excludes[0]->setPair( 0,0 );
1297	>	the_excludes[0]->setPair(0, 0);
1298		info[l].globalExcludes = new int;
1299		info[l].globalExcludes[0] = 0;
1300		info[l].n_exclude = 0;
#	Line 1341 | Line 1307 | void SimSetup::makeSysArrays( void ){
1307		info[l].nGlobalExcludes = 0;
1308		info[l].excludes = the_excludes;
1309
1310	<	the_ff->setSimInfo( info );
1345	<
1310	>	the_ff->setSimInfo(info);
1311		}
1312		}
1313
1314	<	void SimSetup::makeIntegrator( void ){
1350	<
1314	>	void SimSetup::makeIntegrator(void){
1315		int k;
1316
1317	<	NVT<RealIntegrator>*  myNVT = NULL;
1318	<	NPTi<RealIntegrator>* myNPTi = NULL;
1319	<	NPTf<RealIntegrator>* myNPTf = NULL;
1320	<	NPTim<RealIntegrator>* myNPTim = NULL;
1321	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1322	<
1323	<	for(k=0; k<nInfo; k++){
1324	<
1325	<	switch( ensembleCase ){
1326	<
1327	<	case NVE_ENS:
1328	<	if (globals->haveZconstraints()){
1329	<	setupZConstraint(info[k]);
1330	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1331	<	}
1317	>	NVE<RealIntegrator>* myNVE = NULL;
1318	>	NVT<RealIntegrator>* myNVT = NULL;
1319	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1320	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1321	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1322	>
1323	>	for (k = 0; k < nInfo; k++){
1324	>	switch (ensembleCase){
1325	>	case NVE_ENS:
1326	>	if (globals->haveZconstraints()){
1327	>	setupZConstraint(info[k]);
1328	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1329	>	}
1330	>	else{
1331	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1332	>	}
1333	>
1334	>	info->the_integrator = myNVE;
1335	>	break;
1336
1337	<	else
1338	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1339	<	break;
1340	<
1341	<	case NVT_ENS:
1342	<	if (globals->haveZconstraints()){
1343	<	setupZConstraint(info[k]);
1376	<	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1377	<	}
1378	<	else
1379	<	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1337	>	case NVT_ENS:
1338	>	if (globals->haveZconstraints()){
1339	>	setupZConstraint(info[k]);
1340	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1341	>	}
1342	>	else
1343	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1344
1345		myNVT->setTargetTemp(globals->getTargetTemp());
1346	<
1347	<	if (globals->haveTauThermostat())
1346	>
1347	>	if (globals->haveTauThermostat())
1348		myNVT->setTauThermostat(globals->getTauThermostat());
1349	<
1350	<	else {
1351	<	sprintf( painCave.errMsg,
1352	<	"SimSetup error: If you use the NVT\n"
1389	<	"    ensemble, you must set tauThermostat.\n");
1349	>	else{
1350	>	sprintf(painCave.errMsg,
1351	>	"SimSetup error: If you use the NVT\n"
1352	>	"    ensemble, you must set tauThermostat.\n");
1353		painCave.isFatal = 1;
1354		simError();
1355		}
1356	+
1357	+	info->the_integrator = myNVT;
1358		break;
1394	–
1395	–	case NPTi_ENS:
1396	–	if (globals->haveZconstraints()){
1397	–	setupZConstraint(info[k]);
1398	–	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1399	–	}
1400	–	else
1401	–	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1359
1360	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1361	<
1362	<	if (globals->haveTargetPressure())
1363	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1364	<	else {
1365	<	sprintf( painCave.errMsg,
1366	<	"SimSetup error: If you use a constant pressure\n"
1410	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1411	<	painCave.isFatal = 1;
1412	<	simError();
1413	<	}
1414	<
1415	<	if( globals->haveTauThermostat() )
1416	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1417	<	else{
1418	<	sprintf( painCave.errMsg,
1419	<	"SimSetup error: If you use an NPT\n"
1420	<	"    ensemble, you must set tauThermostat.\n");
1421	<	painCave.isFatal = 1;
1422	<	simError();
1423	<	}
1424	<
1425	<	if( globals->haveTauBarostat() )
1426	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1427	<	else{
1428	<	sprintf( painCave.errMsg,
1429	<	"SimSetup error: If you use an NPT\n"
1430	<	"    ensemble, you must set tauBarostat.\n");
1431	<	painCave.isFatal = 1;
1432	<	simError();
1433	<	}
1434	<	break;
1435	<
1436	<	case NPTf_ENS:
1437	<	if (globals->haveZconstraints()){
1438	<	setupZConstraint(info[k]);
1439	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1440	<	}
1441	<	else
1442	<	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1360	>	case NPTi_ENS:
1361	>	if (globals->haveZconstraints()){
1362	>	setupZConstraint(info[k]);
1363	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1364	>	}
1365	>	else
1366	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1367
1368	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1445	<
1446	<	if (globals->haveTargetPressure())
1447	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1448	<	else {
1449	<	sprintf( painCave.errMsg,
1450	<	"SimSetup error: If you use a constant pressure\n"
1451	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1452	<	painCave.isFatal = 1;
1453	<	simError();
1454	<	}
1455	<
1456	<	if( globals->haveTauThermostat() )
1457	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1458	<	else{
1459	<	sprintf( painCave.errMsg,
1460	<	"SimSetup error: If you use an NPT\n"
1461	<	"    ensemble, you must set tauThermostat.\n");
1462	<	painCave.isFatal = 1;
1463	<	simError();
1464	<	}
1465	<
1466	<	if( globals->haveTauBarostat() )
1467	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1468	<	else{
1469	<	sprintf( painCave.errMsg,
1470	<	"SimSetup error: If you use an NPT\n"
1471	<	"    ensemble, you must set tauBarostat.\n");
1472	<	painCave.isFatal = 1;
1473	<	simError();
1474	<	}
1475	<	break;
1476	<
1477	<	case NPTim_ENS:
1478	<	if (globals->haveZconstraints()){
1479	<	setupZConstraint(info[k]);
1480	<	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1481	<	}
1482	<	else
1483	<	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1368	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1369
1370	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1371	<
1372	<	if (globals->haveTargetPressure())
1373	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1489	<	else {
1490	<	sprintf( painCave.errMsg,
1370	>	if (globals->haveTargetPressure())
1371	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1372	>	else{
1373	>	sprintf(painCave.errMsg,
1374		"SimSetup error: If you use a constant pressure\n"
1375		"    ensemble, you must set targetPressure in the BASS file.\n");
1376	<	painCave.isFatal = 1;
1377	<	simError();
1378	<	}
1379	<
1380	<	if( globals->haveTauThermostat() )
1381	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1382	<	else{
1383	<	sprintf( painCave.errMsg,
1376	>	painCave.isFatal = 1;
1377	>	simError();
1378	>	}
1379	>
1380	>	if (globals->haveTauThermostat())
1381	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1382	>	else{
1383	>	sprintf(painCave.errMsg,
1384		"SimSetup error: If you use an NPT\n"
1385		"    ensemble, you must set tauThermostat.\n");
1386	<	painCave.isFatal = 1;
1387	<	simError();
1388	<	}
1506	<
1507	<	if( globals->haveTauBarostat() )
1508	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1509	<	else{
1510	<	sprintf( painCave.errMsg,
1511	<	"SimSetup error: If you use an NPT\n"
1512	<	"    ensemble, you must set tauBarostat.\n");
1513	<	painCave.isFatal = 1;
1514	<	simError();
1515	<	}
1516	<	break;
1517	<
1518	<	case NPTfm_ENS:
1519	<	if (globals->haveZconstraints()){
1520	<	setupZConstraint(info[k]);
1521	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1522	<	}
1523	<	else
1524	<	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1386	>	painCave.isFatal = 1;
1387	>	simError();
1388	>	}
1389
1390	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1391	<
1392	<	if (globals->haveTargetPressure())
1393	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1530	<	else {
1531	<	sprintf( painCave.errMsg,
1532	<	"SimSetup error: If you use a constant pressure\n"
1533	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1534	<	painCave.isFatal = 1;
1535	<	simError();
1536	<	}
1537	<
1538	<	if( globals->haveTauThermostat() )
1539	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1540	<	else{
1541	<	sprintf( painCave.errMsg,
1390	>	if (globals->haveTauBarostat())
1391	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1392	>	else{
1393	>	sprintf(painCave.errMsg,
1394		"SimSetup error: If you use an NPT\n"
1395	<	"    ensemble, you must set tauThermostat.\n");
1396	<	painCave.isFatal = 1;
1397	<	simError();
1398	<	}
1395	>	"    ensemble, you must set tauBarostat.\n");
1396	>	painCave.isFatal = 1;
1397	>	simError();
1398	>	}
1399
1400	<	if( globals->haveTauBarostat() )
1401	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1402	<	else{
1403	<	sprintf( painCave.errMsg,
1400	>	info->the_integrator = myNPTi;
1401	>	break;
1402	>
1403	>	case NPTf_ENS:
1404	>	if (globals->haveZconstraints()){
1405	>	setupZConstraint(info[k]);
1406	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1407	>	}
1408	>	else
1409	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1410	>
1411	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1412	>
1413	>	if (globals->haveTargetPressure())
1414	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1415	>	else{
1416	>	sprintf(painCave.errMsg,
1417	>	"SimSetup error: If you use a constant pressure\n"
1418	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1419	>	painCave.isFatal = 1;
1420	>	simError();
1421	>	}
1422	>
1423	>	if (globals->haveTauThermostat())
1424	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1425	>
1426	>	else{
1427	>	sprintf(painCave.errMsg,
1428		"SimSetup error: If you use an NPT\n"
1429	+	"    ensemble, you must set tauThermostat.\n");
1430	+	painCave.isFatal = 1;
1431	+	simError();
1432	+	}
1433	+
1434	+	if (globals->haveTauBarostat())
1435	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1436	+
1437	+	else{
1438	+	sprintf(painCave.errMsg,
1439	+	"SimSetup error: If you use an NPT\n"
1440		"    ensemble, you must set tauBarostat.\n");
1441	+	painCave.isFatal = 1;
1442	+	simError();
1443	+	}
1444	+
1445	+	info->the_integrator = myNPTf;
1446	+	break;
1447	+
1448	+	case NPTxyz_ENS:
1449	+	if (globals->haveZconstraints()){
1450	+	setupZConstraint(info[k]);
1451	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1452	+	}
1453	+	else
1454	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1455	+
1456	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1457	+
1458	+	if (globals->haveTargetPressure())
1459	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1460	+	else{
1461	+	sprintf(painCave.errMsg,
1462	+	"SimSetup error: If you use a constant pressure\n"
1463	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1464	+	painCave.isFatal = 1;
1465	+	simError();
1466	+	}
1467	+
1468	+	if (globals->haveTauThermostat())
1469	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1470	+	else{
1471	+	sprintf(painCave.errMsg,
1472	+	"SimSetup error: If you use an NPT\n"
1473	+	"    ensemble, you must set tauThermostat.\n");
1474	+	painCave.isFatal = 1;
1475	+	simError();
1476	+	}
1477	+
1478	+	if (globals->haveTauBarostat())
1479	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1480	+	else{
1481	+	sprintf(painCave.errMsg,
1482	+	"SimSetup error: If you use an NPT\n"
1483	+	"    ensemble, you must set tauBarostat.\n");
1484	+	painCave.isFatal = 1;
1485	+	simError();
1486	+	}
1487	+
1488	+	info->the_integrator = myNPTxyz;
1489	+	break;
1490	+
1491	+	default:
1492	+	sprintf(painCave.errMsg,
1493	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1494		painCave.isFatal = 1;
1495		simError();
1556	–	}
1557	–	break;
1558	–
1559	–	default:
1560	–	sprintf( painCave.errMsg,
1561	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1562	–	painCave.isFatal = 1;
1563	–	simError();
1496		}
1497		}
1498		}
1499
1500	<	void SimSetup::initFortran( void ){
1569	<
1500	>	void SimSetup::initFortran(void){
1501		info[0].refreshSim();
1502	<
1503	<	if( !strcmp( info[0].mixingRule, "standard") ){
1504	<	the_ff->initForceField( LB_MIXING_RULE );
1502	>
1503	>	if (!strcmp(info[0].mixingRule, "standard")){
1504	>	the_ff->initForceField(LB_MIXING_RULE);
1505		}
1506	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1507	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1506	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1507	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1508		}
1509		else{
1510	<	sprintf( painCave.errMsg,
1511	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1581	<	info[0].mixingRule );
1510	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1511	>	info[0].mixingRule);
1512		painCave.isFatal = 1;
1513		simError();
1514		}
1515
1516
1517		#ifdef IS_MPI
1518	<	strcpy( checkPointMsg,
1589	<	"Successfully intialized the mixingRule for Fortran." );
1518	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1519		MPIcheckPoint();
1520		#endif // is_mpi
1592	–
1521		}
1522
1523	<	void SimSetup::setupZConstraint(SimInfo& theInfo)
1596	<	{
1523	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1524		int nZConstraints;
1525		ZconStamp** zconStamp;
1526
1527	<	if(globals->haveZconstraintTime()){
1601	<
1527	>	if (globals->haveZconstraintTime()){
1528		//add sample time of z-constraint  into SimInfo's property list
1529		DoubleData* zconsTimeProp = new DoubleData();
1530		zconsTimeProp->setID(ZCONSTIME_ID);
#	Line 1606 | Line 1532 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1532		theInfo.addProperty(zconsTimeProp);
1533		}
1534		else{
1535	<	sprintf( painCave.errMsg,
1536	<	"ZConstraint error: If you use an ZConstraint\n"
1537	<	" , you must set sample time.\n");
1535	>	sprintf(painCave.errMsg,
1536	>	"ZConstraint error: If you use an ZConstraint\n"
1537	>	" , you must set sample time.\n");
1538		painCave.isFatal = 1;
1539	<	simError();
1539	>	simError();
1540		}
1541
1542		//push zconsTol into siminfo, if user does not specify
1543		//value for zconsTol, a default value will be used
1544		DoubleData* zconsTol = new DoubleData();
1545		zconsTol->setID(ZCONSTOL_ID);
1546	<	if(globals->haveZconsTol()){
1546	>	if (globals->haveZconsTol()){
1547		zconsTol->setData(globals->getZconsTol());
1548		}
1549		else{
1550	<	double defaultZConsTol = 0.01;
1551	<	sprintf( painCave.errMsg,
1552	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1553	<	" , default value %f is used.\n", defaultZConsTol);
1550	>	double defaultZConsTol = 0.01;
1551	>	sprintf(painCave.errMsg,
1552	>	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1553	>	" , default value %f is used.\n",
1554	>	defaultZConsTol);
1555		painCave.isFatal = 0;
1556		simError();
1557
#	Line 1632 | Line 1559 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1559		}
1560		theInfo.addProperty(zconsTol);
1561
1562	<	//set Force Substraction Policy
1563	<	StringData* zconsForcePolicy =  new StringData();
1562	>	//set Force Subtraction Policy
1563	>	StringData* zconsForcePolicy = new StringData();
1564		zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1565	<
1566	<	if(globals->haveZconsForcePolicy()){
1565	>
1566	>	if (globals->haveZconsForcePolicy()){
1567		zconsForcePolicy->setData(globals->getZconsForcePolicy());
1568	<	}
1568	>	}
1569		else{
1570	<	sprintf( painCave.errMsg,
1571	<	"ZConstraint Warning: User does not set force substraction policy, "
1572	<	"average force substraction policy is used\n");
1573	<	painCave.isFatal = 0;
1574	<	simError();
1575	<	zconsForcePolicy->setData("BYNUMBER");
1570	>	sprintf(painCave.errMsg,
1571	>	"ZConstraint Warning: User does not set force Subtraction policy, "
1572	>	"PolicyByMass is used\n");
1573	>	painCave.isFatal = 0;
1574	>	simError();
1575	>	zconsForcePolicy->setData("BYMASS");
1576		}
1577	<
1578	<	theInfo.addProperty(zconsForcePolicy);
1579	<
1577	>
1578	>	theInfo.addProperty(zconsForcePolicy);
1579	>
1580		//Determine the name of ouput file and add it into SimInfo's property list
1581		//Be careful, do not use inFileName, since it is a pointer which
1582		//point to a string at master node, and slave nodes do not contain that string
1583	<
1583	>
1584		string zconsOutput(theInfo.finalName);
1585	<
1585	>
1586		zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1587	<
1587	>
1588		StringData* zconsFilename = new StringData();
1589		zconsFilename->setID(ZCONSFILENAME_ID);
1590		zconsFilename->setData(zconsOutput);
1591	<
1591	>
1592		theInfo.addProperty(zconsFilename);
1593	<
1593	>
1594		//setup index, pos and other parameters of z-constraint molecules
1595		nZConstraints = globals->getNzConstraints();
1596		theInfo.nZconstraints = nZConstraints;
#	Line 1673 | Line 1600 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1600
1601		ZConsParaData* zconsParaData = new ZConsParaData();
1602		zconsParaData->setID(ZCONSPARADATA_ID);
1603	<
1604	<	for(int i = 0; i < nZConstraints; i++){
1603	>
1604	>	for (int i = 0; i < nZConstraints; i++){
1605		tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1606		tempParaItem.zPos = zconStamp[i]->getZpos();
1607		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
#	Line 1683 | Line 1610 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1610		zconsParaData->addItem(tempParaItem);
1611		}
1612
1613	+	//check the uniqueness of index
1614	+	if(!zconsParaData->isIndexUnique()){
1615	+	sprintf(painCave.errMsg,
1616	+	"ZConstraint Error: molIndex is not unique\n");
1617	+	painCave.isFatal = 1;
1618	+	simError();
1619	+	}
1620	+
1621		//sort the parameters by index of molecules
1622		zconsParaData->sortByIndex();
1623
1624		//push data into siminfo, therefore, we can retrieve later
1625		theInfo.addProperty(zconsParaData);
1691	–
1626		}

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