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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 708 by tim, Wed Aug 20 22:23:34 2003 UTC vs.
Revision 841 by mmeineke, Wed Oct 29 17:55:28 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	<	#include <sys/time.h>
7	<
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8		#include "ReadWrite.hpp"
9		#include "parse_me.h"
#	Line 22 | Line 21
21		#define NVT_ENS        1
22		#define NPTi_ENS       2
23		#define NPTf_ENS       3
24	<	#define NPTim_ENS      4
26	<	#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 33 | 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 51 | 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 ){
62	<
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();
90	<	mpiEventLoop();
91	<
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
98	–	int i, j, k, globalAtomIndex;
99	–
98		// gather all of the information from the Bass file
99
100		gatherInfo();
#	Line 105 | 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 128 | Line 131 | void SimSetup::createSim(void){
131		// initialize the Fortran
132
133		initFortran();
131	–
132	–
133	–
134		}
135
136
137	<	void SimSetup::makeMolecules( void ){
138	<
139	<	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 151 | 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;
163	–
164	–	for(k=0; k<nInfo; k++){
165	–
166	–	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++){
171	<
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	<
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	<	}
221	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
222	<
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;
245	<	}
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	<	}
315	<
316	<	if( !theBends[j].isGhost ){
317	<
318	<	exI = theBends[j].a;
319	<	exJ = theBends[j].c;
320	<	}
321	<	else{
322	<
323	<	exI = theBends[j].a;
324	<	exJ = theBends[j].b;
325	<	}
326	<
327	<	// exclude_I must always be the smaller of the pair
328	<	if( exI > exJ ){
329	<	tempEx = exI;
330	<	exI = exJ;
331	<	exJ = tempEx;
332	<	}
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;
362	<	}
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.
378	–
379	–	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
380	–	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
381	–	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
382	–	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
383	–
384	–
385	–	info[k].molecules[i].initialize( molInfo );
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();
404	–
388		}
389
390	<	void SimSetup::initFromBass( void ){
408	<
390	>	void SimSetup::initFromBass(void){
391		int i, j, k;
392		int n_cells;
393		double cellx, celly, cellz;
#	Line 419 | 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 455 | 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,
463	<	j * celly,
464	<	k * cellz );
446	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
447
448	<	makeElement( i * cellx + 0.5 * cellx,
467	<	j * celly + 0.5 * celly,
468	<	k * cellz );
448	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
449
450	<	makeElement( i * cellx,
471	<	j * celly + 0.5 * celly,
472	<	k * cellz + 0.5 * cellz );
473	<
474	<	makeElement( i * cellx + 0.5 * cellx,
475	<	j * celly,
476	<	k * cellz + 0.5 * cellz );
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	<	}
495	<	else start_ndx = 0;
475	>	if (!done && n_per_extra > 1){
476	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
477	>	k * cellz);
478	>	done = (current_mol >= tot_nmol);
479	>	}
480
481	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
481	>	if (!done && n_per_extra > 2){
482	>	makeElement(i * cellx, j * celly + 0.5 * celly,
483	>	k * cellz + 0.5 * cellz);
484	>	done = (current_mol >= tot_nmol);
485	>	}
486
487	<	makeElement( i * cellx,
488	<	j * celly,
489	<	k * cellz );
490	<	done = ( current_mol >= tot_nmol );
491	<
492	<	if( !done && n_per_extra > 1 ){
505	<	makeElement( i * cellx + 0.5 * cellx,
506	<	j * celly + 0.5 * celly,
507	<	k * cellz );
508	<	done = ( current_mol >= tot_nmol );
509	<	}
510	<
511	<	if( !done && n_per_extra > 2){
512	<	makeElement( i * cellx,
513	<	j * celly + 0.5 * celly,
514	<	k * cellz + 0.5 * cellz );
515	<	done = ( current_mol >= tot_nmol );
516	<	}
517	<
518	<	if( !done && n_per_extra > 3){
519	<	makeElement( i * cellx + 0.5 * cellx,
520	<	j * celly,
521	<	k * cellz + 0.5 * cellz );
522	<	done = ( current_mol >= tot_nmol );
523	<	}
524	<	}
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 ){
535	<
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",
551	<	comp_stamps[current_comp]->getID(),
552	<	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();
560	–
561	–	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 576 | 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 585 | 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] ){
589	<
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 611 | 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;
624	<	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		}
648	–
649	–	for(i=0; i<nInfo; i++){
650	–
651	–	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;
678	<	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 683 | 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
697	–
698	–	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 707 | 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	<	// check for the temperature set flag
692	>	info[i].resetIntegrator = 0;
693	>	if( globals->haveResetTime() ){
694	>	info[i].resetTime = globals->getResetTime();
695	>	info[i].resetIntegrator = 1;
696	>	}
697
698	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
698	>	// check for the temperature set flag
699
700	<	// get some of the tricky things that may still be in the globals
700	>	if (globals->haveTempSet())
701	>	info[i].setTemp = globals->getTempSet();
702
725	–	double boxVector[3];
726	–	if( globals->haveBox() ){
727	–	boxVector[0] = globals->getBox();
728	–	boxVector[1] = globals->getBox();
729	–	boxVector[2] = globals->getBox();
730	–
731	–	info[i].setBox( boxVector );
732	–	}
733	–	else if( globals->haveDensity() ){
734	–
735	–	double vol;
736	–	vol = (double)tot_nmol / globals->getDensity();
737	–	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
738	–	boxVector[1] = boxVector[0];
739	–	boxVector[2] = boxVector[0];
740	–
741	–	info[i].setBox( boxVector );
703		}
704	<	else{
705	<	if( !globals->haveBoxX() ){
706	<	sprintf( painCave.errMsg,
707	<	"SimSetup error, no periodic BoxX size given.\n" );
708	<	painCave.isFatal = 1;
709	<	simError();
749	<	}
750	<	boxVector[0] = globals->getBoxX();
751	<
752	<	if( !globals->haveBoxY() ){
753	<	sprintf( painCave.errMsg,
754	<	"SimSetup error, no periodic BoxY size given.\n" );
755	<	painCave.isFatal = 1;
756	<	simError();
757	<	}
758	<	boxVector[1] = globals->getBoxY();
759	<
760	<	if( !globals->haveBoxZ() ){
761	<	sprintf( painCave.errMsg,
762	<	"SimSetup error, no periodic BoxZ size given.\n" );
763	<	painCave.isFatal = 1;
764	<	simError();
765	<	}
766	<	boxVector[2] = globals->getBoxZ();
767	<
768	<	info[i].setBox( boxVector );
769	<	}
770	<	}
704	>
705	>	//setup seed for random number generator
706	>	int seedValue;
707	>
708	>	if (globals->haveSeed()){
709	>	seedValue = globals->getSeed();
710
711	<	int seedValue;
712	<	struct timeval now_time_val;
713	<	struct timezone time_zone;
711	>	if(seedValue / 1E9 == 0){
712	>	sprintf(painCave.errMsg,
713	>	"Seed for sprng library should contain at least 9 digits\n"
714	>	"OOPSE will generate a seed for user\n");
715	>	painCave.isFatal = 0;
716	>	simError();
717
718	<	if(globals->haveSeed()){
719	<	seedValue = globals->getSeed();
720	<	}
718	>	//using seed generated by system instead of invalid seed set by user
719	>	#ifndef IS_MPI
720	>	seedValue = make_sprng_seed();
721	>	#else
722	>	if (worldRank == 0){
723	>	seedValue = make_sprng_seed();
724	>	}
725	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
726	>	#endif
727	>	}
728	>	}//end of if branch of globals->haveSeed()
729		else{
730	+
731		#ifndef IS_MPI
732	<	gettimeofday(&now_time_val, &time_zone);  // get the time now
782	<	seedValue = (int) now_time_val.tv_sec;      //  convert to epoch time
732	>	seedValue = make_sprng_seed();
733		#else
734	<	if(worldRank == 0){
735	<	gettimeofday(&now_time_val, &time_zone);  // get the time now
786	<	seedValue = (int) now_time_val.tv_sec;      //  convert to epoch time
734	>	if (worldRank == 0){
735	>	seedValue = make_sprng_seed();
736		}
737	<	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
737	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
738		#endif
739	<	}
739	>	}//end of globals->haveSeed()
740
741	<	for(int i = 0; i < nInfo; i++){
741	>	for (int i = 0; i < nInfo; i++){
742		info[i].setSeed(seedValue);
743		}
744
745		#ifdef IS_MPI
746	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
746	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
747		MPIcheckPoint();
748		#endif // is_mpi
800	–
749		}
750
751
752	<	void SimSetup::finalInfoCheck( void ){
752	>	void SimSetup::finalInfoCheck(void){
753		int index;
754		int usesDipoles;
755		int i;
756
757	<	for(i=0; i<nInfo; i++){
757	>	for (i = 0; i < nInfo; i++){
758		// check electrostatic parameters
759	<
759	>
760		index = 0;
761		usesDipoles = 0;
762	<	while( (index < info[i].n_atoms) && !usesDipoles ){
762	>	while ((index < info[i].n_atoms) && !usesDipoles){
763		usesDipoles = (info[i].atoms[index])->hasDipole();
764		index++;
765		}
766	<
766	>
767		#ifdef IS_MPI
768		int myUse = usesDipoles;
769	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
769	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770		#endif //is_mpi
771	<
771	>
772		double theEcr, theEst;
773	<
774	<	if (globals->getUseRF() ) {
773	>
774	>	if (globals->getUseRF()){
775		info[i].useReactionField = 1;
776	<
777	<	if( !globals->haveECR() ){
778	<	sprintf( painCave.errMsg,
779	<	"SimSetup Warning: using default value of 1/2 the smallest "
780	<	"box length for the electrostaticCutoffRadius.\n"
781	<	"I hope you have a very fast processor!\n");
782	<	painCave.isFatal = 0;
783	<	simError();
784	<	double smallest;
785	<	smallest = info[i].boxL[0];
786	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
787	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
788	<	theEcr = 0.5 * smallest;
789	<	} else {
790	<	theEcr = globals->getECR();
776	>
777	>	if (!globals->haveECR()){
778	>	sprintf(painCave.errMsg,
779	>	"SimSetup Warning: using default value of 1/2 the smallest "
780	>	"box length for the electrostaticCutoffRadius.\n"
781	>	"I hope you have a very fast processor!\n");
782	>	painCave.isFatal = 0;
783	>	simError();
784	>	double smallest;
785	>	smallest = info[i].boxL[0];
786	>	if (info[i].boxL[1] <= smallest)
787	>	smallest = info[i].boxL[1];
788	>	if (info[i].boxL[2] <= smallest)
789	>	smallest = info[i].boxL[2];
790	>	theEcr = 0.5 * smallest;
791		}
792	<
793	<	if( !globals->haveEST() ){
846	<	sprintf( painCave.errMsg,
847	<	"SimSetup Warning: using default value of 0.05 * the "
848	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
849	<	);
850	<	painCave.isFatal = 0;
851	<	simError();
852	<	theEst = 0.05 * theEcr;
853	<	} else {
854	<	theEst= globals->getEST();
792	>	else{
793	>	theEcr = globals->getECR();
794		}
795	<
796	<	info[i].setEcr( theEcr, theEst );
797	<
798	<	if(!globals->haveDielectric() ){
799	<	sprintf( painCave.errMsg,
800	<	"SimSetup Error: You are trying to use Reaction Field without"
801	<	"setting a dielectric constant!\n"
802	<	);
864	<	painCave.isFatal = 1;
865	<	simError();
795	>
796	>	if (!globals->haveEST()){
797	>	sprintf(painCave.errMsg,
798	>	"SimSetup Warning: using default value of 0.05 * the "
799	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
800	>	painCave.isFatal = 0;
801	>	simError();
802	>	theEst = 0.05 * theEcr;
803		}
804	<	info[i].dielectric = globals->getDielectric();
805	<	}
869	<	else {
870	<	if (usesDipoles) {
871	<
872	<	if( !globals->haveECR() ){
873	<	sprintf( painCave.errMsg,
874	<	"SimSetup Warning: using default value of 1/2 the smallest "
875	<	"box length for the electrostaticCutoffRadius.\n"
876	<	"I hope you have a very fast processor!\n");
877	<	painCave.isFatal = 0;
878	<	simError();
879	<	double smallest;
880	<	smallest = info[i].boxL[0];
881	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
882	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
883	<	theEcr = 0.5 * smallest;
884	<	} else {
885	<	theEcr = globals->getECR();
886	<	}
887	<
888	<	if( !globals->haveEST() ){
889	<	sprintf( painCave.errMsg,
890	<	"SimSetup Warning: using default value of 0.05 * the "
891	<	"electrostaticCutoffRadius for the "
892	<	"electrostaticSkinThickness\n"
893	<	);
894	<	painCave.isFatal = 0;
895	<	simError();
896	<	theEst = 0.05 * theEcr;
897	<	} else {
898	<	theEst= globals->getEST();
899	<	}
900	<
901	<	info[i].setEcr( theEcr, theEst );
804	>	else{
805	>	theEst = globals->getEST();
806		}
807	<	}
807	>
808	>	info[i].setDefaultEcr(theEcr, theEst);
809	>
810	>	if (!globals->haveDielectric()){
811	>	sprintf(painCave.errMsg,
812	>	"SimSetup Error: You are trying to use Reaction Field without"
813	>	"setting a dielectric constant!\n");
814	>	painCave.isFatal = 1;
815	>	simError();
816	>	}
817	>	info[i].dielectric = globals->getDielectric();
818	>	}
819	>	else{
820	>	if (usesDipoles){
821	>	if (!globals->haveECR()){
822	>	sprintf(painCave.errMsg,
823	>	"SimSetup Warning: using default value of 1/2 the smallest "
824	>	"box length for the electrostaticCutoffRadius.\n"
825	>	"I hope you have a very fast processor!\n");
826	>	painCave.isFatal = 0;
827	>	simError();
828	>	double smallest;
829	>	smallest = info[i].boxL[0];
830	>	if (info[i].boxL[1] <= smallest)
831	>	smallest = info[i].boxL[1];
832	>	if (info[i].boxL[2] <= smallest)
833	>	smallest = info[i].boxL[2];
834	>	theEcr = 0.5 * smallest;
835	>	}
836	>	else{
837	>	theEcr = globals->getECR();
838	>	}
839	>
840	>	if (!globals->haveEST()){
841	>	sprintf(painCave.errMsg,
842	>	"SimSetup Warning: using default value of 0.05 * the "
843	>	"electrostaticCutoffRadius for the "
844	>	"electrostaticSkinThickness\n");
845	>	painCave.isFatal = 0;
846	>	simError();
847	>	theEst = 0.05 * theEcr;
848	>	}
849	>	else{
850	>	theEst = globals->getEST();
851	>	}
852	>
853	>	info[i].setDefaultEcr(theEcr, theEst);
854	>	}
855	>	}
856		}
857
858		#ifdef IS_MPI
859	<	strcpy( checkPointMsg, "post processing checks out" );
859	>	strcpy(checkPointMsg, "post processing checks out");
860		MPIcheckPoint();
861		#endif // is_mpi
910	–
862		}
863
864	<	void SimSetup::initSystemCoords( void ){
864	>	void SimSetup::initSystemCoords(void){
865		int i;
866	<
866	>
867		char* inName;
868
869	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
869	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
870
871	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
872	<
873	<	if( globals->haveInitialConfig() ){
874	<
871	>	for (i = 0; i < info[0].n_atoms; i++)
872	>	info[0].atoms[i]->setCoords();
873	>
874	>	if (globals->haveInitialConfig()){
875		InitializeFromFile* fileInit;
876		#ifdef IS_MPI // is_mpi
877	<	if( worldRank == 0 ){
877	>	if (worldRank == 0){
878		#endif //is_mpi
879		inName = globals->getInitialConfig();
880	<	double* tempDouble = new double[1000000];
930	<	fileInit = new InitializeFromFile( inName );
880	>	fileInit = new InitializeFromFile(inName);
881		#ifdef IS_MPI
882	<	}else fileInit = new InitializeFromFile( NULL );
882	>	}
883	>	else
884	>	fileInit = new InitializeFromFile(NULL);
885		#endif
886	<	fileInit->readInit( info ); // default velocities on
887	<
886	>	fileInit->readInit(info); // default velocities on
887	>
888		delete fileInit;
889		}
890		else{
939	–
891		#ifdef IS_MPI
892	<
892	>
893		// no init from bass
894	<
895	<	sprintf( painCave.errMsg,
896	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
897	<	painCave.isFatal;
894	>
895	>	sprintf(painCave.errMsg,
896	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
897	>	painCave.isFatal = 1;;
898		simError();
899	<
899	>
900		#else
901	<
901	>
902		initFromBass();
903	<
904	<
903	>
904	>
905		#endif
906		}
907	<
907	>
908		#ifdef IS_MPI
909	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
909	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
910		MPIcheckPoint();
911		#endif // is_mpi
961	–
912		}
913
914
915	<	void SimSetup::makeOutNames( void ){
966	<
915	>	void SimSetup::makeOutNames(void){
916		int k;
917
969	–
970	–	for(k=0; k<nInfo; k++){
918
919	+	for (k = 0; k < nInfo; k++){
920		#ifdef IS_MPI
921	<	if( worldRank == 0 ){
921	>	if (worldRank == 0){
922		#endif // is_mpi
923	<
924	<	if( globals->haveFinalConfig() ){
925	<	strcpy( info[k].finalName, globals->getFinalConfig() );
923	>
924	>	if (globals->haveFinalConfig()){
925	>	strcpy(info[k].finalName, globals->getFinalConfig());
926		}
927		else{
928	<	strcpy( info[k].finalName, inFileName );
929	<	char* endTest;
930	<	int nameLength = strlen( info[k].finalName );
931	<	endTest = &(info[k].finalName[nameLength - 5]);
932	<	if( !strcmp( endTest, ".bass" ) ){
933	<	strcpy( endTest, ".eor" );
934	<	}
935	<	else if( !strcmp( endTest, ".BASS" ) ){
936	<	strcpy( endTest, ".eor" );
937	<	}
938	<	else{
939	<	endTest = &(info[k].finalName[nameLength - 4]);
940	<	if( !strcmp( endTest, ".bss" ) ){
941	<	strcpy( endTest, ".eor" );
942	<	}
943	<	else if( !strcmp( endTest, ".mdl" ) ){
944	<	strcpy( endTest, ".eor" );
945	<	}
946	<	else{
947	<	strcat( info[k].finalName, ".eor" );
948	<	}
949	<	}
928	>	strcpy(info[k].finalName, inFileName);
929	>	char* endTest;
930	>	int nameLength = strlen(info[k].finalName);
931	>	endTest = &(info[k].finalName[nameLength - 5]);
932	>	if (!strcmp(endTest, ".bass")){
933	>	strcpy(endTest, ".eor");
934	>	}
935	>	else if (!strcmp(endTest, ".BASS")){
936	>	strcpy(endTest, ".eor");
937	>	}
938	>	else{
939	>	endTest = &(info[k].finalName[nameLength - 4]);
940	>	if (!strcmp(endTest, ".bss")){
941	>	strcpy(endTest, ".eor");
942	>	}
943	>	else if (!strcmp(endTest, ".mdl")){
944	>	strcpy(endTest, ".eor");
945	>	}
946	>	else{
947	>	strcat(info[k].finalName, ".eor");
948	>	}
949	>	}
950		}
951	<
951	>
952		// make the sample and status out names
953	<
954	<	strcpy( info[k].sampleName, inFileName );
953	>
954	>	strcpy(info[k].sampleName, inFileName);
955		char* endTest;
956	<	int nameLength = strlen( info[k].sampleName );
956	>	int nameLength = strlen(info[k].sampleName);
957		endTest = &(info[k].sampleName[nameLength - 5]);
958	<	if( !strcmp( endTest, ".bass" ) ){
959	<	strcpy( endTest, ".dump" );
958	>	if (!strcmp(endTest, ".bass")){
959	>	strcpy(endTest, ".dump");
960		}
961	<	else if( !strcmp( endTest, ".BASS" ) ){
962	<	strcpy( endTest, ".dump" );
961	>	else if (!strcmp(endTest, ".BASS")){
962	>	strcpy(endTest, ".dump");
963		}
964		else{
965	<	endTest = &(info[k].sampleName[nameLength - 4]);
966	<	if( !strcmp( endTest, ".bss" ) ){
967	<	strcpy( endTest, ".dump" );
968	<	}
969	<	else if( !strcmp( endTest, ".mdl" ) ){
970	<	strcpy( endTest, ".dump" );
971	<	}
972	<	else{
973	<	strcat( info[k].sampleName, ".dump" );
974	<	}
965	>	endTest = &(info[k].sampleName[nameLength - 4]);
966	>	if (!strcmp(endTest, ".bss")){
967	>	strcpy(endTest, ".dump");
968	>	}
969	>	else if (!strcmp(endTest, ".mdl")){
970	>	strcpy(endTest, ".dump");
971	>	}
972	>	else{
973	>	strcat(info[k].sampleName, ".dump");
974	>	}
975		}
976	<
977	<	strcpy( info[k].statusName, inFileName );
978	<	nameLength = strlen( info[k].statusName );
976	>
977	>	strcpy(info[k].statusName, inFileName);
978	>	nameLength = strlen(info[k].statusName);
979		endTest = &(info[k].statusName[nameLength - 5]);
980	<	if( !strcmp( endTest, ".bass" ) ){
981	<	strcpy( endTest, ".stat" );
980	>	if (!strcmp(endTest, ".bass")){
981	>	strcpy(endTest, ".stat");
982		}
983	<	else if( !strcmp( endTest, ".BASS" ) ){
984	<	strcpy( endTest, ".stat" );
983	>	else if (!strcmp(endTest, ".BASS")){
984	>	strcpy(endTest, ".stat");
985		}
986		else{
987	<	endTest = &(info[k].statusName[nameLength - 4]);
988	<	if( !strcmp( endTest, ".bss" ) ){
989	<	strcpy( endTest, ".stat" );
990	<	}
991	<	else if( !strcmp( endTest, ".mdl" ) ){
992	<	strcpy( endTest, ".stat" );
993	<	}
994	<	else{
995	<	strcat( info[k].statusName, ".stat" );
996	<	}
987	>	endTest = &(info[k].statusName[nameLength - 4]);
988	>	if (!strcmp(endTest, ".bss")){
989	>	strcpy(endTest, ".stat");
990	>	}
991	>	else if (!strcmp(endTest, ".mdl")){
992	>	strcpy(endTest, ".stat");
993	>	}
994	>	else{
995	>	strcat(info[k].statusName, ".stat");
996	>	}
997		}
998	<
998	>
999		#ifdef IS_MPI
1000	+
1001		}
1002		#endif // is_mpi
1003		}
1004		}
1005
1006
1007	<	void SimSetup::sysObjectsCreation( void ){
1008	<
1009	<	int i,k;
1061	<
1007	>	void SimSetup::sysObjectsCreation(void){
1008	>	int i, k;
1009	>
1010		// create the forceField
1011
1012		createFF();
#	Line 1073 | Line 1021 | void SimSetup::sysObjectsCreation( void ){
1021
1022		#ifdef IS_MPI
1023		// divide the molecules among the processors
1024	<
1024	>
1025		mpiMolDivide();
1026		#endif //is_mpi
1027	<
1027	>
1028		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1029	<
1029	>
1030		makeSysArrays();
1031
1032		// make and initialize the molecules (all but atomic coordinates)
1033	<
1033	>
1034		makeMolecules();
1035	<
1036	<	for(k=0; k<nInfo; k++){
1035	>
1036	>	for (k = 0; k < nInfo; k++){
1037		info[k].identArray = new int[info[k].n_atoms];
1038	<	for(i=0; i<info[k].n_atoms; i++){
1038	>	for (i = 0; i < info[k].n_atoms; i++){
1039		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1040		}
1041		}
1042		}
1043
1044
1045	<	void SimSetup::createFF( void ){
1045	>	void SimSetup::createFF(void){
1046	>	switch (ffCase){
1047	>	case FF_DUFF:
1048	>	the_ff = new DUFF();
1049	>	break;
1050
1051	<	switch( ffCase ){
1051	>	case FF_LJ:
1052	>	the_ff = new LJFF();
1053	>	break;
1054
1055	<	case FF_DUFF:
1056	<	the_ff = new DUFF();
1057	<	break;
1055	>	case FF_EAM:
1056	>	the_ff = new EAM_FF();
1057	>	break;
1058
1059	<	case FF_LJ:
1060	<	the_ff = new LJFF();
1061	<	break;
1062	<
1063	<	case FF_EAM:
1110	<	the_ff = new EAM_FF();
1111	<	break;
1112	<
1113	<	default:
1114	<	sprintf( painCave.errMsg,
1115	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1116	<	painCave.isFatal = 1;
1117	<	simError();
1059	>	default:
1060	>	sprintf(painCave.errMsg,
1061	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1062	>	painCave.isFatal = 1;
1063	>	simError();
1064		}
1065
1066		#ifdef IS_MPI
1067	<	strcpy( checkPointMsg, "ForceField creation successful" );
1067	>	strcpy(checkPointMsg, "ForceField creation successful");
1068		MPIcheckPoint();
1069		#endif // is_mpi
1124	–
1070		}
1071
1072
1073	<	void SimSetup::compList( void ){
1129	<
1073	>	void SimSetup::compList(void){
1074		int i;
1075		char* id;
1076		LinkedMolStamp* headStamp = new LinkedMolStamp();
1077		LinkedMolStamp* currentStamp = NULL;
1078	<	comp_stamps = new MoleculeStamp*[n_components];
1079	<
1078	>	comp_stamps = new MoleculeStamp * [n_components];
1079	>
1080		// make an array of molecule stamps that match the components used.
1081		// also extract the used stamps out into a separate linked list
1082	<
1083	<	for(i=0; i<nInfo; i++){
1082	>
1083	>	for (i = 0; i < nInfo; i++){
1084		info[i].nComponents = n_components;
1085		info[i].componentsNmol = components_nmol;
1086		info[i].compStamps = comp_stamps;
1087		info[i].headStamp = headStamp;
1088		}
1145	–
1089
1147	–	for( i=0; i<n_components; i++ ){
1090
1091	+	for (i = 0; i < n_components; i++){
1092		id = the_components[i]->getType();
1093		comp_stamps[i] = NULL;
1094	<
1094	>
1095		// check to make sure the component isn't already in the list
1096
1097	<	comp_stamps[i] = headStamp->match( id );
1098	<	if( comp_stamps[i] == NULL ){
1156	<
1097	>	comp_stamps[i] = headStamp->match(id);
1098	>	if (comp_stamps[i] == NULL){
1099		// extract the component from the list;
1100	<
1101	<	currentStamp = stamps->extractMolStamp( id );
1102	<	if( currentStamp == NULL ){
1103	<	sprintf( painCave.errMsg,
1104	<	"SimSetup error: Component \"%s\" was not found in the "
1105	<	"list of declared molecules\n",
1106	<	id );
1107	<	painCave.isFatal = 1;
1108	<	simError();
1100	>
1101	>	currentStamp = stamps->extractMolStamp(id);
1102	>	if (currentStamp == NULL){
1103	>	sprintf(painCave.errMsg,
1104	>	"SimSetup error: Component \"%s\" was not found in the "
1105	>	"list of declared molecules\n",
1106	>	id);
1107	>	painCave.isFatal = 1;
1108	>	simError();
1109		}
1110	<
1111	<	headStamp->add( currentStamp );
1112	<	comp_stamps[i] = headStamp->match( id );
1110	>
1111	>	headStamp->add(currentStamp);
1112	>	comp_stamps[i] = headStamp->match(id);
1113		}
1114		}
1115
1116		#ifdef IS_MPI
1117	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1117	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1118		MPIcheckPoint();
1119		#endif // is_mpi
1120	+	}
1121
1122	+	void SimSetup::calcSysValues(void){
1123	+	int i;
1124
1125	<	}
1125	>	int* molMembershipArray;
1126
1182	–	void SimSetup::calcSysValues( void ){
1183	–	int i, j, k;
1184	–
1185	–	int *molMembershipArray;
1186	–
1127		tot_atoms = 0;
1128		tot_bonds = 0;
1129		tot_bends = 0;
1130		tot_torsions = 0;
1131	<	for( i=0; i<n_components; i++ ){
1132	<
1133	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1134	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1195	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1131	>	for (i = 0; i < n_components; i++){
1132	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1133	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1134	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1135		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1136		}
1137	<
1137	>
1138		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1139		molMembershipArray = new int[tot_atoms];
1140	<
1141	<	for(i=0; i<nInfo; i++){
1140	>
1141	>	for (i = 0; i < nInfo; i++){
1142		info[i].n_atoms = tot_atoms;
1143		info[i].n_bonds = tot_bonds;
1144		info[i].n_bends = tot_bends;
1145		info[i].n_torsions = tot_torsions;
1146		info[i].n_SRI = tot_SRI;
1147		info[i].n_mol = tot_nmol;
1148	<
1148	>
1149		info[i].molMembershipArray = molMembershipArray;
1150	<	}
1150	>	}
1151		}
1152
1153		#ifdef IS_MPI
1154
1155	<	void SimSetup::mpiMolDivide( void ){
1217	<
1155	>	void SimSetup::mpiMolDivide(void){
1156		int i, j, k;
1157		int localMol, allMol;
1158		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1159
1160	<	mpiSim = new mpiSimulation( info );
1161	<
1160	>	mpiSim = new mpiSimulation(info);
1161	>
1162		globalIndex = mpiSim->divideLabor();
1163
1164		// set up the local variables
1165	<
1165	>
1166		mol2proc = mpiSim->getMolToProcMap();
1167		molCompType = mpiSim->getMolComponentType();
1168	<
1168	>
1169		allMol = 0;
1170		localMol = 0;
1171		local_atoms = 0;
#	Line 1237 | Line 1175 | void SimSetup::mpiMolDivide( void ){
1175		globalAtomIndex = 0;
1176
1177
1178	<	for( i=0; i<n_components; i++ ){
1179	<
1180	<	for( j=0; j<components_nmol[i]; j++ ){
1181	<
1182	<	if( mol2proc[allMol] == worldRank ){
1183	<
1184	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1185	<	local_bonds +=    comp_stamps[i]->getNBonds();
1248	<	local_bends +=    comp_stamps[i]->getNBends();
1249	<	local_torsions += comp_stamps[i]->getNTorsions();
1250	<	localMol++;
1178	>	for (i = 0; i < n_components; i++){
1179	>	for (j = 0; j < components_nmol[i]; j++){
1180	>	if (mol2proc[allMol] == worldRank){
1181	>	local_atoms += comp_stamps[i]->getNAtoms();
1182	>	local_bonds += comp_stamps[i]->getNBonds();
1183	>	local_bends += comp_stamps[i]->getNBends();
1184	>	local_torsions += comp_stamps[i]->getNTorsions();
1185	>	localMol++;
1186		}
1187	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1187	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1188		info[0].molMembershipArray[globalAtomIndex] = allMol;
1189		globalAtomIndex++;
1190		}
1191
1192	<	allMol++;
1192	>	allMol++;
1193		}
1194		}
1195		local_SRI = local_bonds + local_bends + local_torsions;
1196	<
1196	>
1197		info[0].n_atoms = mpiSim->getMyNlocal();
1198	<
1199	<	if( local_atoms != info[0].n_atoms ){
1200	<	sprintf( painCave.errMsg,
1201	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1202	<	" localAtom (%d) are not equal.\n",
1203	<	info[0].n_atoms,
1269	<	local_atoms );
1198	>
1199	>	if (local_atoms != info[0].n_atoms){
1200	>	sprintf(painCave.errMsg,
1201	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1202	>	" localAtom (%d) are not equal.\n",
1203	>	info[0].n_atoms, local_atoms);
1204		painCave.isFatal = 1;
1205		simError();
1206		}
#	Line 1277 | Line 1211 | void SimSetup::mpiMolDivide( void ){
1211		info[0].n_SRI = local_SRI;
1212		info[0].n_mol = localMol;
1213
1214	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1214	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1215		MPIcheckPoint();
1216		}
1217	<
1217	>
1218		#endif // is_mpi
1219
1220
1221	<	void SimSetup::makeSysArrays( void ){
1222	<	int i, j, k, l;
1221	>	void SimSetup::makeSysArrays(void){
1222	>
1223	>	#ifndef IS_MPI
1224	>	int k, j;
1225	>	#endif // is_mpi
1226	>	int i, l;
1227
1228		Atom** the_atoms;
1229		Molecule* the_molecules;
1230		Exclude** the_excludes;
1231
1232	<
1233	<	for(l=0; l<nInfo; l++){
1296	<
1232	>
1233	>	for (l = 0; l < nInfo; l++){
1234		// create the atom and short range interaction arrays
1235	<
1236	<	the_atoms = new Atom*[info[l].n_atoms];
1235	>
1236	>	the_atoms = new Atom * [info[l].n_atoms];
1237		the_molecules = new Molecule[info[l].n_mol];
1238		int molIndex;
1239
1240		// initialize the molecule's stampID's
1241	<
1241	>
1242		#ifdef IS_MPI
1243	<
1244	<
1243	>
1244	>
1245		molIndex = 0;
1246	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1247	<
1248	<	if(mol2proc[i] == worldRank ){
1249	<	the_molecules[molIndex].setStampID( molCompType[i] );
1250	<	the_molecules[molIndex].setMyIndex( molIndex );
1251	<	the_molecules[molIndex].setGlobalIndex( i );
1315	<	molIndex++;
1246	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1247	>	if (mol2proc[i] == worldRank){
1248	>	the_molecules[molIndex].setStampID(molCompType[i]);
1249	>	the_molecules[molIndex].setMyIndex(molIndex);
1250	>	the_molecules[molIndex].setGlobalIndex(i);
1251	>	molIndex++;
1252		}
1253		}
1254	<
1254	>
1255		#else // is_mpi
1256	<
1256	>
1257		molIndex = 0;
1258		globalAtomIndex = 0;
1259	<	for(i=0; i<n_components; i++){
1260	<	for(j=0; j<components_nmol[i]; j++ ){
1261	<	the_molecules[molIndex].setStampID( i );
1262	<	the_molecules[molIndex].setMyIndex( molIndex );
1263	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1264	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1265	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1266	<	globalAtomIndex++;
1267	<	}
1268	<	molIndex++;
1259	>	for (i = 0; i < n_components; i++){
1260	>	for (j = 0; j < components_nmol[i]; j++){
1261	>	the_molecules[molIndex].setStampID(i);
1262	>	the_molecules[molIndex].setMyIndex(molIndex);
1263	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1264	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1265	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1266	>	globalAtomIndex++;
1267	>	}
1268	>	molIndex++;
1269		}
1270		}
1271	<
1272	<
1271	>
1272	>
1273		#endif // is_mpi
1274
1275
1276	<	if( info[l].n_SRI ){
1341	<
1276	>	if (info[l].n_SRI){
1277		Exclude::createArray(info[l].n_SRI);
1278	<	the_excludes = new Exclude*[info[l].n_SRI];
1279	<	for( int ex=0; ex<info[l].n_SRI; ex++){
1280	<	the_excludes[ex] = new Exclude(ex);
1278	>	the_excludes = new Exclude * [info[l].n_SRI];
1279	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1280	>	the_excludes[ex] = new Exclude(ex);
1281		}
1282		info[l].globalExcludes = new int;
1283		info[l].n_exclude = info[l].n_SRI;
1284		}
1285		else{
1286	<
1287	<	Exclude::createArray( 1 );
1353	<	the_excludes = new Exclude*;
1286	>	Exclude::createArray(1);
1287	>	the_excludes = new Exclude * ;
1288		the_excludes[0] = new Exclude(0);
1289	<	the_excludes[0]->setPair( 0,0 );
1289	>	the_excludes[0]->setPair(0, 0);
1290		info[l].globalExcludes = new int;
1291		info[l].globalExcludes[0] = 0;
1292		info[l].n_exclude = 0;
#	Line 1365 | Line 1299 | void SimSetup::makeSysArrays( void ){
1299		info[l].nGlobalExcludes = 0;
1300		info[l].excludes = the_excludes;
1301
1302	<	the_ff->setSimInfo( info );
1369	<
1302	>	the_ff->setSimInfo(info);
1303		}
1304		}
1305
1306	<	void SimSetup::makeIntegrator( void ){
1374	<
1306	>	void SimSetup::makeIntegrator(void){
1307		int k;
1308
1309	<	NVT<RealIntegrator>*  myNVT = NULL;
1310	<	NPTi<RealIntegrator>* myNPTi = NULL;
1311	<	NPTf<RealIntegrator>* myNPTf = NULL;
1312	<	NPTim<RealIntegrator>* myNPTim = NULL;
1313	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1314	<
1315	<	for(k=0; k<nInfo; k++){
1316	<
1317	<	switch( ensembleCase ){
1318	<
1319	<	case NVE_ENS:
1320	<	if (globals->haveZconstraints()){
1321	<	setupZConstraint(info[k]);
1322	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1323	<	}
1309	>	NVE<RealIntegrator>* myNVE = NULL;
1310	>	NVT<RealIntegrator>* myNVT = NULL;
1311	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1312	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1313	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1314	>
1315	>	for (k = 0; k < nInfo; k++){
1316	>	switch (ensembleCase){
1317	>	case NVE_ENS:
1318	>	if (globals->haveZconstraints()){
1319	>	setupZConstraint(info[k]);
1320	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1321	>	}
1322	>	else{
1323	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1324	>	}
1325	>
1326	>	info->the_integrator = myNVE;
1327	>	break;
1328
1329	<	else
1330	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1331	<	break;
1332	<
1333	<	case NVT_ENS:
1334	<	if (globals->haveZconstraints()){
1335	<	setupZConstraint(info[k]);
1400	<	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1401	<	}
1402	<	else
1403	<	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1329	>	case NVT_ENS:
1330	>	if (globals->haveZconstraints()){
1331	>	setupZConstraint(info[k]);
1332	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1333	>	}
1334	>	else
1335	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1336
1337		myNVT->setTargetTemp(globals->getTargetTemp());
1338	<
1339	<	if (globals->haveTauThermostat())
1338	>
1339	>	if (globals->haveTauThermostat())
1340		myNVT->setTauThermostat(globals->getTauThermostat());
1341	<
1342	<	else {
1343	<	sprintf( painCave.errMsg,
1344	<	"SimSetup error: If you use the NVT\n"
1413	<	"    ensemble, you must set tauThermostat.\n");
1341	>	else{
1342	>	sprintf(painCave.errMsg,
1343	>	"SimSetup error: If you use the NVT\n"
1344	>	"    ensemble, you must set tauThermostat.\n");
1345		painCave.isFatal = 1;
1346		simError();
1347		}
1348	+
1349	+	info->the_integrator = myNVT;
1350		break;
1418	–
1419	–	case NPTi_ENS:
1420	–	if (globals->haveZconstraints()){
1421	–	setupZConstraint(info[k]);
1422	–	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1423	–	}
1424	–	else
1425	–	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1351
1352	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1353	<
1354	<	if (globals->haveTargetPressure())
1355	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1356	<	else {
1357	<	sprintf( painCave.errMsg,
1358	<	"SimSetup error: If you use a constant pressure\n"
1434	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1435	<	painCave.isFatal = 1;
1436	<	simError();
1437	<	}
1438	<
1439	<	if( globals->haveTauThermostat() )
1440	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1441	<	else{
1442	<	sprintf( painCave.errMsg,
1443	<	"SimSetup error: If you use an NPT\n"
1444	<	"    ensemble, you must set tauThermostat.\n");
1445	<	painCave.isFatal = 1;
1446	<	simError();
1447	<	}
1448	<
1449	<	if( globals->haveTauBarostat() )
1450	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1451	<	else{
1452	<	sprintf( painCave.errMsg,
1453	<	"SimSetup error: If you use an NPT\n"
1454	<	"    ensemble, you must set tauBarostat.\n");
1455	<	painCave.isFatal = 1;
1456	<	simError();
1457	<	}
1458	<	break;
1459	<
1460	<	case NPTf_ENS:
1461	<	if (globals->haveZconstraints()){
1462	<	setupZConstraint(info[k]);
1463	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1464	<	}
1465	<	else
1466	<	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1352	>	case NPTi_ENS:
1353	>	if (globals->haveZconstraints()){
1354	>	setupZConstraint(info[k]);
1355	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1356	>	}
1357	>	else
1358	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1359
1360	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1469	<
1470	<	if (globals->haveTargetPressure())
1471	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1472	<	else {
1473	<	sprintf( painCave.errMsg,
1474	<	"SimSetup error: If you use a constant pressure\n"
1475	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1476	<	painCave.isFatal = 1;
1477	<	simError();
1478	<	}
1479	<
1480	<	if( globals->haveTauThermostat() )
1481	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1482	<	else{
1483	<	sprintf( painCave.errMsg,
1484	<	"SimSetup error: If you use an NPT\n"
1485	<	"    ensemble, you must set tauThermostat.\n");
1486	<	painCave.isFatal = 1;
1487	<	simError();
1488	<	}
1489	<
1490	<	if( globals->haveTauBarostat() )
1491	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1492	<	else{
1493	<	sprintf( painCave.errMsg,
1494	<	"SimSetup error: If you use an NPT\n"
1495	<	"    ensemble, you must set tauBarostat.\n");
1496	<	painCave.isFatal = 1;
1497	<	simError();
1498	<	}
1499	<	break;
1500	<
1501	<	case NPTim_ENS:
1502	<	if (globals->haveZconstraints()){
1503	<	setupZConstraint(info[k]);
1504	<	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1505	<	}
1506	<	else
1507	<	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1360	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1361
1362	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1363	<
1364	<	if (globals->haveTargetPressure())
1365	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1513	<	else {
1514	<	sprintf( painCave.errMsg,
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"
1367		"    ensemble, you must set targetPressure in the BASS file.\n");
1368	<	painCave.isFatal = 1;
1369	<	simError();
1370	<	}
1371	<
1372	<	if( globals->haveTauThermostat() )
1373	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1374	<	else{
1375	<	sprintf( painCave.errMsg,
1368	>	painCave.isFatal = 1;
1369	>	simError();
1370	>	}
1371	>
1372	>	if (globals->haveTauThermostat())
1373	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1374	>	else{
1375	>	sprintf(painCave.errMsg,
1376		"SimSetup error: If you use an NPT\n"
1377		"    ensemble, you must set tauThermostat.\n");
1378	<	painCave.isFatal = 1;
1379	<	simError();
1380	<	}
1530	<
1531	<	if( globals->haveTauBarostat() )
1532	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1533	<	else{
1534	<	sprintf( painCave.errMsg,
1535	<	"SimSetup error: If you use an NPT\n"
1536	<	"    ensemble, you must set tauBarostat.\n");
1537	<	painCave.isFatal = 1;
1538	<	simError();
1539	<	}
1540	<	break;
1541	<
1542	<	case NPTfm_ENS:
1543	<	if (globals->haveZconstraints()){
1544	<	setupZConstraint(info[k]);
1545	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1546	<	}
1547	<	else
1548	<	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1378	>	painCave.isFatal = 1;
1379	>	simError();
1380	>	}
1381
1382	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1383	<
1384	<	if (globals->haveTargetPressure())
1385	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1554	<	else {
1555	<	sprintf( painCave.errMsg,
1556	<	"SimSetup error: If you use a constant pressure\n"
1557	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1558	<	painCave.isFatal = 1;
1559	<	simError();
1560	<	}
1561	<
1562	<	if( globals->haveTauThermostat() )
1563	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1564	<	else{
1565	<	sprintf( painCave.errMsg,
1382	>	if (globals->haveTauBarostat())
1383	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1384	>	else{
1385	>	sprintf(painCave.errMsg,
1386		"SimSetup error: If you use an NPT\n"
1387	<	"    ensemble, you must set tauThermostat.\n");
1388	<	painCave.isFatal = 1;
1389	<	simError();
1390	<	}
1387	>	"    ensemble, you must set tauBarostat.\n");
1388	>	painCave.isFatal = 1;
1389	>	simError();
1390	>	}
1391
1392	<	if( globals->haveTauBarostat() )
1393	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1394	<	else{
1395	<	sprintf( painCave.errMsg,
1392	>	info->the_integrator = myNPTi;
1393	>	break;
1394	>
1395	>	case NPTf_ENS:
1396	>	if (globals->haveZconstraints()){
1397	>	setupZConstraint(info[k]);
1398	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1399	>	}
1400	>	else
1401	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1402	>
1403	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1404	>
1405	>	if (globals->haveTargetPressure())
1406	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1407	>	else{
1408	>	sprintf(painCave.errMsg,
1409	>	"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	>	myNPTf->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	+	myNPTf->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	+
1435	+	info->the_integrator = myNPTf;
1436	+	break;
1437	+
1438	+	case NPTxyz_ENS:
1439	+	if (globals->haveZconstraints()){
1440	+	setupZConstraint(info[k]);
1441	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1442	+	}
1443	+	else
1444	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1445	+
1446	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1447	+
1448	+	if (globals->haveTargetPressure())
1449	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1450	+	else{
1451	+	sprintf(painCave.errMsg,
1452	+	"SimSetup error: If you use a constant pressure\n"
1453	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1454	+	painCave.isFatal = 1;
1455	+	simError();
1456	+	}
1457	+
1458	+	if (globals->haveTauThermostat())
1459	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1460	+	else{
1461	+	sprintf(painCave.errMsg,
1462	+	"SimSetup error: If you use an NPT\n"
1463	+	"    ensemble, you must set tauThermostat.\n");
1464	+	painCave.isFatal = 1;
1465	+	simError();
1466	+	}
1467	+
1468	+	if (globals->haveTauBarostat())
1469	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1470	+	else{
1471	+	sprintf(painCave.errMsg,
1472	+	"SimSetup error: If you use an NPT\n"
1473	+	"    ensemble, you must set tauBarostat.\n");
1474	+	painCave.isFatal = 1;
1475	+	simError();
1476	+	}
1477	+
1478	+	info->the_integrator = myNPTxyz;
1479	+	break;
1480	+
1481	+	default:
1482	+	sprintf(painCave.errMsg,
1483	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1484		painCave.isFatal = 1;
1485		simError();
1580	–	}
1581	–	break;
1582	–
1583	–	default:
1584	–	sprintf( painCave.errMsg,
1585	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1586	–	painCave.isFatal = 1;
1587	–	simError();
1486		}
1487		}
1488		}
1489
1490	<	void SimSetup::initFortran( void ){
1593	<
1490	>	void SimSetup::initFortran(void){
1491		info[0].refreshSim();
1492	<
1493	<	if( !strcmp( info[0].mixingRule, "standard") ){
1494	<	the_ff->initForceField( LB_MIXING_RULE );
1492	>
1493	>	if (!strcmp(info[0].mixingRule, "standard")){
1494	>	the_ff->initForceField(LB_MIXING_RULE);
1495		}
1496	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1497	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1496	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1497	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1498		}
1499		else{
1500	<	sprintf( painCave.errMsg,
1501	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1605	<	info[0].mixingRule );
1500	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1501	>	info[0].mixingRule);
1502		painCave.isFatal = 1;
1503		simError();
1504		}
1505
1506
1507		#ifdef IS_MPI
1508	<	strcpy( checkPointMsg,
1613	<	"Successfully intialized the mixingRule for Fortran." );
1508	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1509		MPIcheckPoint();
1510		#endif // is_mpi
1616	–
1511		}
1512
1513	<	void SimSetup::setupZConstraint(SimInfo& theInfo)
1620	<	{
1513	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1514		int nZConstraints;
1515		ZconStamp** zconStamp;
1516
1517	<	if(globals->haveZconstraintTime()){
1625	<
1517	>	if (globals->haveZconstraintTime()){
1518		//add sample time of z-constraint  into SimInfo's property list
1519		DoubleData* zconsTimeProp = new DoubleData();
1520		zconsTimeProp->setID(ZCONSTIME_ID);
#	Line 1630 | Line 1522 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1522		theInfo.addProperty(zconsTimeProp);
1523		}
1524		else{
1525	<	sprintf( painCave.errMsg,
1526	<	"ZConstraint error: If you use an ZConstraint\n"
1527	<	" , you must set sample time.\n");
1525	>	sprintf(painCave.errMsg,
1526	>	"ZConstraint error: If you use an ZConstraint\n"
1527	>	" , you must set sample time.\n");
1528		painCave.isFatal = 1;
1529	<	simError();
1529	>	simError();
1530		}
1531
1532		//push zconsTol into siminfo, if user does not specify
1533		//value for zconsTol, a default value will be used
1534		DoubleData* zconsTol = new DoubleData();
1535		zconsTol->setID(ZCONSTOL_ID);
1536	<	if(globals->haveZconsTol()){
1536	>	if (globals->haveZconsTol()){
1537		zconsTol->setData(globals->getZconsTol());
1538		}
1539		else{
1540	<	double defaultZConsTol = 0.01;
1541	<	sprintf( painCave.errMsg,
1542	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1543	<	" , default value %f is used.\n", defaultZConsTol);
1540	>	double defaultZConsTol = 0.01;
1541	>	sprintf(painCave.errMsg,
1542	>	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1543	>	" , default value %f is used.\n",
1544	>	defaultZConsTol);
1545		painCave.isFatal = 0;
1546		simError();
1547
#	Line 1656 | Line 1549 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1549		}
1550		theInfo.addProperty(zconsTol);
1551
1552	<	//set Force Substraction Policy
1553	<	StringData* zconsForcePolicy =  new StringData();
1552	>	//set Force Subtraction Policy
1553	>	StringData* zconsForcePolicy = new StringData();
1554		zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1555	<
1556	<	if(globals->haveZconsForcePolicy()){
1555	>
1556	>	if (globals->haveZconsForcePolicy()){
1557		zconsForcePolicy->setData(globals->getZconsForcePolicy());
1558	<	}
1558	>	}
1559		else{
1560	<	sprintf( painCave.errMsg,
1561	<	"ZConstraint Warning: User does not set force substraction policy, "
1562	<	"average force substraction policy is used\n");
1563	<	painCave.isFatal = 0;
1564	<	simError();
1565	<	zconsForcePolicy->setData("BYNUMBER");
1560	>	sprintf(painCave.errMsg,
1561	>	"ZConstraint Warning: User does not set force Subtraction policy, "
1562	>	"PolicyByMass is used\n");
1563	>	painCave.isFatal = 0;
1564	>	simError();
1565	>	zconsForcePolicy->setData("BYMASS");
1566		}
1567	<
1568	<	theInfo.addProperty(zconsForcePolicy);
1569	<
1567	>
1568	>	theInfo.addProperty(zconsForcePolicy);
1569	>
1570		//Determine the name of ouput file and add it into SimInfo's property list
1571		//Be careful, do not use inFileName, since it is a pointer which
1572		//point to a string at master node, and slave nodes do not contain that string
1573	<
1573	>
1574		string zconsOutput(theInfo.finalName);
1575	<
1575	>
1576		zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1577	<
1577	>
1578		StringData* zconsFilename = new StringData();
1579		zconsFilename->setID(ZCONSFILENAME_ID);
1580		zconsFilename->setData(zconsOutput);
1581	<
1581	>
1582		theInfo.addProperty(zconsFilename);
1583	<
1583	>
1584		//setup index, pos and other parameters of z-constraint molecules
1585		nZConstraints = globals->getNzConstraints();
1586		theInfo.nZconstraints = nZConstraints;
#	Line 1697 | Line 1590 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1590
1591		ZConsParaData* zconsParaData = new ZConsParaData();
1592		zconsParaData->setID(ZCONSPARADATA_ID);
1593	<
1594	<	for(int i = 0; i < nZConstraints; i++){
1593	>
1594	>	for (int i = 0; i < nZConstraints; i++){
1595		tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1596		tempParaItem.zPos = zconStamp[i]->getZpos();
1597		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
#	Line 1707 | Line 1600 | void SimSetup::setupZConstraint(SimInfo& theInfo)
1600		zconsParaData->addItem(tempParaItem);
1601		}
1602
1603	+	//check the uniqueness of index
1604	+	if(!zconsParaData->isIndexUnique()){
1605	+	sprintf(painCave.errMsg,
1606	+	"ZConstraint Error: molIndex is not unique\n");
1607	+	painCave.isFatal = 1;
1608	+	simError();
1609	+	}
1610	+
1611		//sort the parameters by index of molecules
1612		zconsParaData->sortByIndex();
1613
1614		//push data into siminfo, therefore, we can retrieve later
1615		theInfo.addProperty(zconsParaData);
1715	–
1616		}

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