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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 682 by tim, Tue Aug 12 17:51:33 2003 UTC vs.
Revision 965 by gezelter, Mon Jan 19 21:17:39 2004 UTC

#	Line 1 | Line 1
1		#include <algorithm>
2	<	#include <cstdlib>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
4	>	#include <math.h>
5		#include <string>
6	<
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 20 | Line 21
21		#define NVT_ENS        1
22		#define NPTi_ENS       2
23		#define NPTf_ENS       3
24	<	#define NPTim_ENS      4
24	<	#define NPTfm_ENS      5
24	>	#define NPTxyz_ENS     4
25
26	+
27		#define FF_DUFF 0
28		#define FF_LJ   1
29		#define FF_EAM  2
30
31		using namespace std;
32
33	+	/**
34	+	* Check whether dividend is divisble by divisor or not
35	+	*/
36	+	bool isDivisible(double dividend, double divisor){
37	+	double tolerance = 0.000001;
38	+	double quotient;
39	+	double diff;
40	+	int intQuotient;
41	+
42	+	quotient = dividend / divisor;
43	+
44	+	if (quotient < 0)
45	+	quotient = -quotient;
46	+
47	+	intQuotient = int (quotient + tolerance);
48	+
49	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
50	+
51	+	if (diff <= tolerance)
52	+	return true;
53	+	else
54	+	return false;
55	+	}
56	+
57		SimSetup::SimSetup(){
58
59	+	initSuspend = false;
60		isInfoArray = 0;
61		nInfo = 1;
62	<
62	>
63		stamps = new MakeStamps();
64		globals = new Globals();
65	<
66	<
65	>
66	>
67		#ifdef IS_MPI
68	<	strcpy( checkPointMsg, "SimSetup creation successful" );
68	>	strcpy(checkPointMsg, "SimSetup creation successful");
69		MPIcheckPoint();
70		#endif // IS_MPI
71		}
#	Line 49 | Line 75 | void SimSetup::setSimInfo( SimInfo* the_info, int theN
75		delete globals;
76		}
77
78	<	void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) {
79	<	info = the_info;
80	<	nInfo = theNinfo;
81	<	isInfoArray = 1;
78	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
79	>	info = the_info;
80	>	nInfo = theNinfo;
81	>	isInfoArray = 1;
82	>	initSuspend = true;
83		}
84
85
86	<	void SimSetup::parseFile( char* fileName ){
60	<
86	>	void SimSetup::parseFile(char* fileName){
87		#ifdef IS_MPI
88	<	if( worldRank == 0 ){
88	>	if (worldRank == 0){
89		#endif // is_mpi
90	<
90	>
91		inFileName = fileName;
92	<	set_interface_stamps( stamps, globals );
93	<
92	>	set_interface_stamps(stamps, globals);
93	>
94		#ifdef IS_MPI
95		mpiEventInit();
96		#endif
97
98	<	yacc_BASS( fileName );
98	>	yacc_BASS(fileName);
99
100		#ifdef IS_MPI
101		throwMPIEvent(NULL);
102		}
103	<	else receiveParse();
103	>	else{
104	>	receiveParse();
105	>	}
106		#endif
107
108		}
109
110		#ifdef IS_MPI
111		void SimSetup::receiveParse(void){
112	<
113	<	set_interface_stamps( stamps, globals );
114	<	mpiEventInit();
115	<	MPIcheckPoint();
88	<	mpiEventLoop();
89	<
112	>	set_interface_stamps(stamps, globals);
113	>	mpiEventInit();
114	>	MPIcheckPoint();
115	>	mpiEventLoop();
116		}
117
118		#endif // is_mpi
119
120		void SimSetup::createSim(void){
121
96	–	int i, j, k, globalAtomIndex;
97	–
122		// gather all of the information from the Bass file
123	<
123	>
124		gatherInfo();
125
126		// creation of complex system objects
#	Line 104 | Line 128 | void SimSetup::createSim(void){
128		sysObjectsCreation();
129
130		// check on the post processing info
131	<
131	>
132		finalInfoCheck();
133
134		// initialize the system coordinates
135
136	<	if( !isInfoArray ) initSystemCoords();
136	>	if ( !initSuspend ){
137	>	initSystemCoords();
138
139	+	if( !(globals->getUseInitTime()) )
140	+	info[0].currentTime = 0.0;
141	+	}
142	+
143		// make the output filenames
144
145		makeOutNames();
146	<
146	>
147		// make the integrator
148	<
148	>
149		makeIntegrator();
150	<
150	>
151		#ifdef IS_MPI
152		mpiSim->mpiRefresh();
153		#endif
#	Line 126 | Line 155 | void SimSetup::createSim(void){
155		// initialize the Fortran
156
157		initFortran();
129	–
130	–
131	–
158		}
159
160
161	<	void SimSetup::makeMolecules( void ){
162	<
137	<	int k,l;
161	>	void SimSetup::makeMolecules(void){
162	>	int k;
163		int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
164		molInit molInfo;
165		DirectionalAtom* dAtom;
#	Line 149 | Line 174 | void SimSetup::makeMolecules( void ){
174		bend_set* theBends;
175		torsion_set* theTorsions;
176
177	<
177	>
178		//init the forceField paramters
179
180		the_ff->readParams();
181
182	<
182	>
183		// init the atoms
184
185		double ux, uy, uz, u, uSqr;
161	–
162	–	for(k=0; k<nInfo; k++){
163	–
164	–	the_ff->setSimInfo( &(info[k]) );
186
187	+	for (k = 0; k < nInfo; k++){
188	+	the_ff->setSimInfo(&(info[k]));
189	+
190		atomOffset = 0;
191		excludeOffset = 0;
192	<	for(i=0; i<info[k].n_mol; i++){
169	<
192	>	for (i = 0; i < info[k].n_mol; i++){
193		stampID = info[k].molecules[i].getStampID();
194
195	<	molInfo.nAtoms    = comp_stamps[stampID]->getNAtoms();
196	<	molInfo.nBonds    = comp_stamps[stampID]->getNBonds();
197	<	molInfo.nBends    = comp_stamps[stampID]->getNBends();
195	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
196	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
197	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
198		molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
199		molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
200	<
200	>
201		molInfo.myAtoms = &(info[k].atoms[atomOffset]);
202		molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
203	<	molInfo.myBonds = new Bond*[molInfo.nBonds];
204	<	molInfo.myBends = new Bend*[molInfo.nBends];
205	<	molInfo.myTorsions = new Torsion*[molInfo.nTorsions];
203	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
204	>	molInfo.myBends = new Bend * [molInfo.nBends];
205	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
206
207		theBonds = new bond_pair[molInfo.nBonds];
208		theBends = new bend_set[molInfo.nBends];
209		theTorsions = new torsion_set[molInfo.nTorsions];
210	<
210	>
211		// make the Atoms
212	<
213	<	for(j=0; j<molInfo.nAtoms; j++){
214	<
215	<	currentAtom = comp_stamps[stampID]->getAtom( j );
216	<	if( currentAtom->haveOrientation() ){
217	<
218	<	dAtom = new DirectionalAtom( (j + atomOffset),
219	<	info[k].getConfiguration() );
220	<	info[k].n_oriented++;
221	<	molInfo.myAtoms[j] = dAtom;
222	<
223	<	ux = currentAtom->getOrntX();
224	<	uy = currentAtom->getOrntY();
225	<	uz = currentAtom->getOrntZ();
226	<
227	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
228	<
229	<	u = sqrt( uSqr );
230	<	ux = ux / u;
231	<	uy = uy / u;
232	<	uz = uz / u;
233	<
234	<	dAtom->setSUx( ux );
235	<	dAtom->setSUy( uy );
236	<	dAtom->setSUz( uz );
237	<	}
238	<	else{
239	<	molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset),
240	<	info[k].getConfiguration() );
241	<	}
219	<	molInfo.myAtoms[j]->setType( currentAtom->getType() );
220	<
212	>
213	>	for (j = 0; j < molInfo.nAtoms; j++){
214	>	currentAtom = comp_stamps[stampID]->getAtom(j);
215	>	if (currentAtom->haveOrientation()){
216	>	dAtom = new DirectionalAtom((j + atomOffset),
217	>	info[k].getConfiguration());
218	>	info[k].n_oriented++;
219	>	molInfo.myAtoms[j] = dAtom;
220	>
221	>	ux = currentAtom->getOrntX();
222	>	uy = currentAtom->getOrntY();
223	>	uz = currentAtom->getOrntZ();
224	>
225	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
226	>
227	>	u = sqrt(uSqr);
228	>	ux = ux / u;
229	>	uy = uy / u;
230	>	uz = uz / u;
231	>
232	>	dAtom->setSUx(ux);
233	>	dAtom->setSUy(uy);
234	>	dAtom->setSUz(uz);
235	>	}
236	>	else{
237	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
238	>	info[k].getConfiguration());
239	>	}
240	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
241	>
242		#ifdef IS_MPI
243	<
244	<	molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
245	<
243	>
244	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
245	>
246		#endif // is_mpi
247		}
248	<
249	<	// make the bonds
250	<	for(j=0; j<molInfo.nBonds; j++){
251	<
252	<	currentBond = comp_stamps[stampID]->getBond( j );
253	<	theBonds[j].a = currentBond->getA() + atomOffset;
254	<	theBonds[j].b = currentBond->getB() + atomOffset;
255	<
256	<	exI = theBonds[j].a;
257	<	exJ = theBonds[j].b;
258	<
259	<	// exclude_I must always be the smaller of the pair
260	<	if( exI > exJ ){
261	<	tempEx = exI;
262	<	exI = exJ;
263	<	exJ = tempEx;
243	<	}
248	>
249	>	// make the bonds
250	>	for (j = 0; j < molInfo.nBonds; j++){
251	>	currentBond = comp_stamps[stampID]->getBond(j);
252	>	theBonds[j].a = currentBond->getA() + atomOffset;
253	>	theBonds[j].b = currentBond->getB() + atomOffset;
254	>
255	>	exI = theBonds[j].a;
256	>	exJ = theBonds[j].b;
257	>
258	>	// exclude_I must always be the smaller of the pair
259	>	if (exI > exJ){
260	>	tempEx = exI;
261	>	exI = exJ;
262	>	exJ = tempEx;
263	>	}
264		#ifdef IS_MPI
265	<	tempEx = exI;
266	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
267	<	tempEx = exJ;
268	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
269	<
270	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
265	>	tempEx = exI;
266	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
267	>	tempEx = exJ;
268	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
269	>
270	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
271		#else  // isn't MPI
272	<
273	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
272	>
273	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
274		#endif  //is_mpi
275		}
276		excludeOffset += molInfo.nBonds;
277	<
277	>
278		//make the bends
279	<	for(j=0; j<molInfo.nBends; j++){
280	<
281	<	currentBend = comp_stamps[stampID]->getBend( j );
282	<	theBends[j].a = currentBend->getA() + atomOffset;
283	<	theBends[j].b = currentBend->getB() + atomOffset;
284	<	theBends[j].c = currentBend->getC() + atomOffset;
285	<
286	<	if( currentBend->haveExtras() ){
287	<
288	<	extras = currentBend->getExtras();
289	<	current_extra = extras;
290	<
291	<	while( current_extra != NULL ){
292	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
293	<
294	<	switch( current_extra->getType() ){
295	<
296	<	case 0:
297	<	theBends[j].ghost =
298	<	current_extra->getInt() + atomOffset;
299	<	theBends[j].isGhost = 1;
300	<	break;
301	<
302	<	case 1:
303	<	theBends[j].ghost =
304	<	(int)current_extra->getDouble() + atomOffset;
305	<	theBends[j].isGhost = 1;
306	<	break;
307	<
308	<	default:
309	<	sprintf( painCave.errMsg,
310	<	"SimSetup Error: ghostVectorSource was neither a "
311	<	"double nor an int.\n"
312	<	"-->Bend[%d] in %s\n",
313	<	j, comp_stamps[stampID]->getID() );
314	<	painCave.isFatal = 1;
315	<	simError();
316	<	}
317	<	}
318	<
319	<	else{
320	<
321	<	sprintf( painCave.errMsg,
322	<	"SimSetup Error: unhandled bend assignment:\n"
323	<	"    -->%s in Bend[%d] in %s\n",
324	<	current_extra->getlhs(),
325	<	j, comp_stamps[stampID]->getID() );
326	<	painCave.isFatal = 1;
327	<	simError();
328	<	}
329	<
330	<	current_extra = current_extra->getNext();
331	<	}
332	<	}
333	<
334	<	if( !theBends[j].isGhost ){
335	<
336	<	exI = theBends[j].a;
337	<	exJ = theBends[j].c;
338	<	}
339	<	else{
340	<
321	<	exI = theBends[j].a;
322	<	exJ = theBends[j].b;
323	<	}
324	<
325	<	// exclude_I must always be the smaller of the pair
326	<	if( exI > exJ ){
327	<	tempEx = exI;
328	<	exI = exJ;
329	<	exJ = tempEx;
330	<	}
279	>	for (j = 0; j < molInfo.nBends; j++){
280	>	currentBend = comp_stamps[stampID]->getBend(j);
281	>	theBends[j].a = currentBend->getA() + atomOffset;
282	>	theBends[j].b = currentBend->getB() + atomOffset;
283	>	theBends[j].c = currentBend->getC() + atomOffset;
284	>
285	>	if (currentBend->haveExtras()){
286	>	extras = currentBend->getExtras();
287	>	current_extra = extras;
288	>
289	>	while (current_extra != NULL){
290	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
291	>	switch (current_extra->getType()){
292	>	case 0:
293	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
294	>	theBends[j].isGhost = 1;
295	>	break;
296	>
297	>	case 1:
298	>	theBends[j].ghost = (int) current_extra->getDouble() +
299	>	atomOffset;
300	>	theBends[j].isGhost = 1;
301	>	break;
302	>
303	>	default:
304	>	sprintf(painCave.errMsg,
305	>	"SimSetup Error: ghostVectorSource was neither a "
306	>	"double nor an int.\n"
307	>	"-->Bend[%d] in %s\n",
308	>	j, comp_stamps[stampID]->getID());
309	>	painCave.isFatal = 1;
310	>	simError();
311	>	}
312	>	}
313	>	else{
314	>	sprintf(painCave.errMsg,
315	>	"SimSetup Error: unhandled bend assignment:\n"
316	>	"    -->%s in Bend[%d] in %s\n",
317	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
318	>	painCave.isFatal = 1;
319	>	simError();
320	>	}
321	>
322	>	current_extra = current_extra->getNext();
323	>	}
324	>	}
325	>
326	>	if (!theBends[j].isGhost){
327	>	exI = theBends[j].a;
328	>	exJ = theBends[j].c;
329	>	}
330	>	else{
331	>	exI = theBends[j].a;
332	>	exJ = theBends[j].b;
333	>	}
334	>
335	>	// exclude_I must always be the smaller of the pair
336	>	if (exI > exJ){
337	>	tempEx = exI;
338	>	exI = exJ;
339	>	exJ = tempEx;
340	>	}
341		#ifdef IS_MPI
342	<	tempEx = exI;
343	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
344	<	tempEx = exJ;
345	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
346	<
347	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
342	>	tempEx = exI;
343	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
344	>	tempEx = exJ;
345	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
346	>
347	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
348		#else  // isn't MPI
349	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
349	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
350		#endif  //is_mpi
351		}
352		excludeOffset += molInfo.nBends;
353	<
354	<	for(j=0; j<molInfo.nTorsions; j++){
355	<
356	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
357	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
358	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
359	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
360	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
361	<
362	<	exI = theTorsions[j].a;
363	<	exJ = theTorsions[j].d;
364	<
365	<	// exclude_I must always be the smaller of the pair
366	<	if( exI > exJ ){
367	<	tempEx = exI;
368	<	exI = exJ;
369	<	exJ = tempEx;
360	<	}
353	>
354	>	for (j = 0; j < molInfo.nTorsions; j++){
355	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
356	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
357	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
358	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
359	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
360	>
361	>	exI = theTorsions[j].a;
362	>	exJ = theTorsions[j].d;
363	>
364	>	// exclude_I must always be the smaller of the pair
365	>	if (exI > exJ){
366	>	tempEx = exI;
367	>	exI = exJ;
368	>	exJ = tempEx;
369	>	}
370		#ifdef IS_MPI
371	<	tempEx = exI;
372	<	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
373	<	tempEx = exJ;
374	<	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
375	<
376	<	info[k].excludes[j+excludeOffset]->setPair( exI, exJ );
371	>	tempEx = exI;
372	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
373	>	tempEx = exJ;
374	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
375	>
376	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
377		#else  // isn't MPI
378	<	info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
378	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
379		#endif  //is_mpi
380		}
381		excludeOffset += molInfo.nTorsions;
382	<
383	<
382	>
383	>
384		// send the arrays off to the forceField for init.
376	–
377	–	the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms );
378	–	the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds );
379	–	the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends );
380	–	the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions );
381	–
382	–
383	–	info[k].molecules[i].initialize( molInfo );
385
386	<
386	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
387	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
388	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
389	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
390	>	theTorsions);
391	>
392	>
393	>	info[k].molecules[i].initialize(molInfo);
394	>
395	>
396		atomOffset += molInfo.nAtoms;
397		delete[] theBonds;
398		delete[] theBends;
399		delete[] theTorsions;
400		}
401		}
402	<
402	>
403		#ifdef IS_MPI
404	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
404	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
405		MPIcheckPoint();
406		#endif // is_mpi
407	<
407	>
408		// clean up the forcefield
409
410		the_ff->calcRcut();
411		the_ff->cleanMe();
402	–
412		}
413
414	<	void SimSetup::initFromBass( void ){
406	<
414	>	void SimSetup::initFromBass(void){
415		int i, j, k;
416		int n_cells;
417		double cellx, celly, cellz;
#	Line 417 | Line 425 | void SimSetup::initFromBass( void ){
425		vel[1] = 0.0;
426		vel[2] = 0.0;
427
428	<	temp1 = (double)tot_nmol / 4.0;
429	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
430	<	temp3 = ceil( temp2 );
428	>	temp1 = (double) tot_nmol / 4.0;
429	>	temp2 = pow(temp1, (1.0 / 3.0));
430	>	temp3 = ceil(temp2);
431
432	<	have_extra =0;
433	<	if( temp2 < temp3 ){ // we have a non-complete lattice
434	<	have_extra =1;
432	>	have_extra = 0;
433	>	if (temp2 < temp3){
434	>	// we have a non-complete lattice
435	>	have_extra = 1;
436
437	<	n_cells = (int)temp3 - 1;
437	>	n_cells = (int) temp3 - 1;
438		cellx = info[0].boxL[0] / temp3;
439		celly = info[0].boxL[1] / temp3;
440		cellz = info[0].boxL[2] / temp3;
441	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
442	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
443	<	n_per_extra = (int)ceil( temp1 );
441	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
442	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
443	>	n_per_extra = (int) ceil(temp1);
444
445	<	if( n_per_extra > 4){
446	<	sprintf( painCave.errMsg,
447	<	"SimSetup error. There has been an error in constructing"
448	<	" the non-complete lattice.\n" );
445	>	if (n_per_extra > 4){
446	>	sprintf(painCave.errMsg,
447	>	"SimSetup error. There has been an error in constructing"
448	>	" the non-complete lattice.\n");
449		painCave.isFatal = 1;
450		simError();
451		}
452		}
453		else{
454	<	n_cells = (int)temp3;
454	>	n_cells = (int) temp3;
455		cellx = info[0].boxL[0] / temp3;
456		celly = info[0].boxL[1] / temp3;
457		cellz = info[0].boxL[2] / temp3;
#	Line 453 | Line 462 | void SimSetup::initFromBass( void ){
462		current_comp = 0;
463		current_atom_ndx = 0;
464
465	<	for( i=0; i < n_cells ; i++ ){
466	<	for( j=0; j < n_cells; j++ ){
467	<	for( k=0; k < n_cells; k++ ){
465	>	for (i = 0; i < n_cells ; i++){
466	>	for (j = 0; j < n_cells; j++){
467	>	for (k = 0; k < n_cells; k++){
468	>	makeElement(i * cellx, j * celly, k * cellz);
469
470	<	makeElement( i * cellx,
461	<	j * celly,
462	<	k * cellz );
470	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
471
472	<	makeElement( i * cellx + 0.5 * cellx,
465	<	j * celly + 0.5 * celly,
466	<	k * cellz );
472	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
473
474	<	makeElement( i * cellx,
469	<	j * celly + 0.5 * celly,
470	<	k * cellz + 0.5 * cellz );
471	<
472	<	makeElement( i * cellx + 0.5 * cellx,
473	<	j * celly,
474	<	k * cellz + 0.5 * cellz );
474	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
475		}
476		}
477		}
478
479	<	if( have_extra ){
479	>	if (have_extra){
480		done = 0;
481
482		int start_ndx;
483	<	for( i=0; i < (n_cells+1) && !done; i++ ){
484	<	for( j=0; j < (n_cells+1) && !done; j++ ){
483	>	for (i = 0; i < (n_cells + 1) && !done; i++){
484	>	for (j = 0; j < (n_cells + 1) && !done; j++){
485	>	if (i < n_cells){
486	>	if (j < n_cells){
487	>	start_ndx = n_cells;
488	>	}
489	>	else
490	>	start_ndx = 0;
491	>	}
492	>	else
493	>	start_ndx = 0;
494
495	<	if( i < n_cells ){
495	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
496	>	makeElement(i * cellx, j * celly, k * cellz);
497	>	done = (current_mol >= tot_nmol);
498
499	<	if( j < n_cells ){
500	<	start_ndx = n_cells;
501	<	}
502	<	else start_ndx = 0;
503	<	}
493	<	else start_ndx = 0;
499	>	if (!done && n_per_extra > 1){
500	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
501	>	k * cellz);
502	>	done = (current_mol >= tot_nmol);
503	>	}
504
505	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
505	>	if (!done && n_per_extra > 2){
506	>	makeElement(i * cellx, j * celly + 0.5 * celly,
507	>	k * cellz + 0.5 * cellz);
508	>	done = (current_mol >= tot_nmol);
509	>	}
510
511	<	makeElement( i * cellx,
512	<	j * celly,
513	<	k * cellz );
514	<	done = ( current_mol >= tot_nmol );
515	<
516	<	if( !done && n_per_extra > 1 ){
503	<	makeElement( i * cellx + 0.5 * cellx,
504	<	j * celly + 0.5 * celly,
505	<	k * cellz );
506	<	done = ( current_mol >= tot_nmol );
507	<	}
508	<
509	<	if( !done && n_per_extra > 2){
510	<	makeElement( i * cellx,
511	<	j * celly + 0.5 * celly,
512	<	k * cellz + 0.5 * cellz );
513	<	done = ( current_mol >= tot_nmol );
514	<	}
515	<
516	<	if( !done && n_per_extra > 3){
517	<	makeElement( i * cellx + 0.5 * cellx,
518	<	j * celly,
519	<	k * cellz + 0.5 * cellz );
520	<	done = ( current_mol >= tot_nmol );
521	<	}
522	<	}
511	>	if (!done && n_per_extra > 3){
512	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
513	>	k * cellz + 0.5 * cellz);
514	>	done = (current_mol >= tot_nmol);
515	>	}
516	>	}
517		}
518		}
519		}
520
521	<	for( i=0; i<info[0].n_atoms; i++ ){
522	<	info[0].atoms[i]->setVel( vel );
521	>	for (i = 0; i < info[0].n_atoms; i++){
522	>	info[0].atoms[i]->setVel(vel);
523		}
524		}
525
526	<	void SimSetup::makeElement( double x, double y, double z ){
533	<
526	>	void SimSetup::makeElement(double x, double y, double z){
527		int k;
528		AtomStamp* current_atom;
529		DirectionalAtom* dAtom;
530		double rotMat[3][3];
531		double pos[3];
532
533	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
534	<
535	<	current_atom = comp_stamps[current_comp]->getAtom( k );
536	<	if( !current_atom->havePosition() ){
537	<	sprintf( painCave.errMsg,
538	<	"SimSetup:initFromBass error.\n"
539	<	"\tComponent %s, atom %s does not have a position specified.\n"
540	<	"\tThe initialization routine is unable to give a start"
541	<	" position.\n",
549	<	comp_stamps[current_comp]->getID(),
550	<	current_atom->getType() );
533	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
534	>	current_atom = comp_stamps[current_comp]->getAtom(k);
535	>	if (!current_atom->havePosition()){
536	>	sprintf(painCave.errMsg,
537	>	"SimSetup:initFromBass error.\n"
538	>	"\tComponent %s, atom %s does not have a position specified.\n"
539	>	"\tThe initialization routine is unable to give a start"
540	>	" position.\n",
541	>	comp_stamps[current_comp]->getID(), current_atom->getType());
542		painCave.isFatal = 1;
543		simError();
544		}
545	<
545	>
546		pos[0] = x + current_atom->getPosX();
547		pos[1] = y + current_atom->getPosY();
548		pos[2] = z + current_atom->getPosZ();
558	–
559	–	info[0].atoms[current_atom_ndx]->setPos( pos );
549
550	<	if( info[0].atoms[current_atom_ndx]->isDirectional() ){
550	>	info[0].atoms[current_atom_ndx]->setPos(pos);
551
552	<	dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx];
552	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
553	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
554
555		rotMat[0][0] = 1.0;
556		rotMat[0][1] = 0.0;
#	Line 574 | Line 564 | void SimSetup::makeElement( double x, double y, double
564		rotMat[2][1] = 0.0;
565		rotMat[2][2] = 1.0;
566
567	<	dAtom->setA( rotMat );
567	>	dAtom->setA(rotMat);
568		}
569
570		current_atom_ndx++;
#	Line 583 | Line 573 | void SimSetup::makeElement( double x, double y, double
573		current_mol++;
574		current_comp_mol++;
575
576	<	if( current_comp_mol >= components_nmol[current_comp] ){
587	<
576	>	if (current_comp_mol >= components_nmol[current_comp]){
577		current_comp_mol = 0;
578		current_comp++;
579		}
580		}
581
582
583	<	void SimSetup::gatherInfo( void ){
584	<	int i,j,k;
583	>	void SimSetup::gatherInfo(void){
584	>	int i;
585
586		ensembleCase = -1;
587		ffCase = -1;
588
589		// set the easy ones first
590
591	<	for( i=0; i<nInfo; i++){
591	>	for (i = 0; i < nInfo; i++){
592		info[i].target_temp = globals->getTargetTemp();
593		info[i].dt = globals->getDt();
594		info[i].run_time = globals->getRunTime();
#	Line 609 | Line 598 | void SimSetup::gatherInfo( void ){
598
599		// get the forceField
600
601	<	strcpy( force_field, globals->getForceField() );
601	>	strcpy(force_field, globals->getForceField());
602
603	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
604	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
605	<	else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM;
603	>	if (!strcasecmp(force_field, "DUFF")){
604	>	ffCase = FF_DUFF;
605	>	}
606	>	else if (!strcasecmp(force_field, "LJ")){
607	>	ffCase = FF_LJ;
608	>	}
609	>	else if (!strcasecmp(force_field, "EAM")){
610	>	ffCase = FF_EAM;
611	>	}
612		else{
613	<	sprintf( painCave.errMsg,
614	<	"SimSetup Error. Unrecognized force field -> %s\n",
615	<	force_field );
616	<	painCave.isFatal = 1;
622	<	simError();
613	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
614	>	force_field);
615	>	painCave.isFatal = 1;
616	>	simError();
617		}
618
619	<	// get the ensemble
619	>	// get the ensemble
620
621	<	strcpy( ensemble, globals->getEnsemble() );
621	>	strcpy(ensemble, globals->getEnsemble());
622
623	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
624	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
625	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
623	>	if (!strcasecmp(ensemble, "NVE")){
624	>	ensembleCase = NVE_ENS;
625	>	}
626	>	else if (!strcasecmp(ensemble, "NVT")){
627	>	ensembleCase = NVT_ENS;
628	>	}
629	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
630		ensembleCase = NPTi_ENS;
631	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
632	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
633	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
631	>	}
632	>	else if (!strcasecmp(ensemble, "NPTf")){
633	>	ensembleCase = NPTf_ENS;
634	>	}
635	>	else if (!strcasecmp(ensemble, "NPTxyz")){
636	>	ensembleCase = NPTxyz_ENS;
637	>	}
638		else{
639	<	sprintf( painCave.errMsg,
640	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
641	<	"reverting to NVE for this simulation.\n",
642	<	ensemble );
643	<	painCave.isFatal = 0;
644	<	simError();
645	<	strcpy( ensemble, "NVE" );
646	<	ensembleCase = NVE_ENS;
639	>	sprintf(painCave.errMsg,
640	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
641	>	"\treverting to NVE for this simulation.\n",
642	>	ensemble);
643	>	painCave.isFatal = 0;
644	>	simError();
645	>	strcpy(ensemble, "NVE");
646	>	ensembleCase = NVE_ENS;
647		}
646	–
647	–	for(i=0; i<nInfo; i++){
648	–
649	–	strcpy( info[i].ensemble, ensemble );
648
649	+	for (i = 0; i < nInfo; i++){
650	+	strcpy(info[i].ensemble, ensemble);
651	+
652		// get the mixing rule
653
654	<	strcpy( info[i].mixingRule, globals->getMixingRule() );
654	>	strcpy(info[i].mixingRule, globals->getMixingRule());
655		info[i].usePBC = globals->getPBC();
656		}
657	<
657	>
658		// get the components and calculate the tot_nMol and indvidual n_mol
659	<
659	>
660		the_components = globals->getComponents();
661		components_nmol = new int[n_components];
662
663
664	<	if( !globals->haveNMol() ){
664	>	if (!globals->haveNMol()){
665		// we don't have the total number of molecules, so we assume it is
666		// given in each component
667
668		tot_nmol = 0;
669	<	for( i=0; i<n_components; i++ ){
670	<
671	<	if( !the_components[i]->haveNMol() ){
672	<	// we have a problem
673	<	sprintf( painCave.errMsg,
674	<	"SimSetup Error. No global NMol or component NMol"
675	<	" given. Cannot calculate the number of atoms.\n" );
676	<	painCave.isFatal = 1;
676	<	simError();
669	>	for (i = 0; i < n_components; i++){
670	>	if (!the_components[i]->haveNMol()){
671	>	// we have a problem
672	>	sprintf(painCave.errMsg,
673	>	"SimSetup Error. No global NMol or component NMol given.\n"
674	>	"\tCannot calculate the number of atoms.\n");
675	>	painCave.isFatal = 1;
676	>	simError();
677		}
678
679		tot_nmol += the_components[i]->getNMol();
#	Line 681 | Line 681 | void SimSetup::gatherInfo( void ){
681		}
682		}
683		else{
684	<	sprintf( painCave.errMsg,
685	<	"SimSetup error.\n"
686	<	"\tSorry, the ability to specify total"
687	<	" nMols and then give molfractions in the components\n"
688	<	"\tis not currently supported."
689	<	" Please give nMol in the components.\n" );
684	>	sprintf(painCave.errMsg,
685	>	"SimSetup error.\n"
686	>	"\tSorry, the ability to specify total"
687	>	" nMols and then give molfractions in the components\n"
688	>	"\tis not currently supported."
689	>	" Please give nMol in the components.\n");
690		painCave.isFatal = 1;
691		simError();
692		}
693
694	<	// set the status, sample, and thermal kick times
695	<
696	<	for(i=0; i<nInfo; i++){
694	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
695	>	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
696	>	sprintf(painCave.errMsg,
697	>	"Sample time is not divisible by dt.\n"
698	>	"\tThis will result in samples that are not uniformly\n"
699	>	"\tdistributed in time.  If this is a problem, change\n"
700	>	"\tyour sampleTime variable.\n");
701	>	painCave.isFatal = 0;
702	>	simError();
703	>	}
704
705	<	if( globals->haveSampleTime() ){
705	>	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
706	>	sprintf(painCave.errMsg,
707	>	"Status time is not divisible by dt.\n"
708	>	"\tThis will result in status reports that are not uniformly\n"
709	>	"\tdistributed in time.  If this is a problem, change \n"
710	>	"\tyour statusTime variable.\n");
711	>	painCave.isFatal = 0;
712	>	simError();
713	>	}
714	>
715	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
716	>	sprintf(painCave.errMsg,
717	>	"Thermal time is not divisible by dt.\n"
718	>	"\tThis will result in thermalizations that are not uniformly\n"
719	>	"\tdistributed in time.  If this is a problem, change \n"
720	>	"\tyour thermalTime variable.\n");
721	>	painCave.isFatal = 0;
722	>	simError();
723	>	}
724	>
725	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
726	>	sprintf(painCave.errMsg,
727	>	"Reset time is not divisible by dt.\n"
728	>	"\tThis will result in integrator resets that are not uniformly\n"
729	>	"\tdistributed in time.  If this is a problem, change\n"
730	>	"\tyour resetTime variable.\n");
731	>	painCave.isFatal = 0;
732	>	simError();
733	>	}
734	>
735	>	// set the status, sample, and thermal kick times
736	>
737	>	for (i = 0; i < nInfo; i++){
738	>	if (globals->haveSampleTime()){
739		info[i].sampleTime = globals->getSampleTime();
740		info[i].statusTime = info[i].sampleTime;
741		info[i].thermalTime = info[i].sampleTime;
#	Line 705 | Line 745 | void SimSetup::gatherInfo( void ){
745		info[i].statusTime = info[i].sampleTime;
746		info[i].thermalTime = info[i].sampleTime;
747		}
748	<
749	<	if( globals->haveStatusTime() ){
748	>
749	>	if (globals->haveStatusTime()){
750		info[i].statusTime = globals->getStatusTime();
751		}
752	<
753	<	if( globals->haveThermalTime() ){
752	>
753	>	if (globals->haveThermalTime()){
754		info[i].thermalTime = globals->getThermalTime();
755		}
756
757	+	info[i].resetIntegrator = 0;
758	+	if( globals->haveResetTime() ){
759	+	info[i].resetTime = globals->getResetTime();
760	+	info[i].resetIntegrator = 1;
761	+	}
762	+
763		// check for the temperature set flag
764	+
765	+	if (globals->haveTempSet())
766	+	info[i].setTemp = globals->getTempSet();
767
768	<	if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet();
768	>	// check for the extended State init
769	>
770	>	info[i].useInitXSstate = globals->getUseInitXSstate();
771	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
772
721	–	// get some of the tricky things that may still be in the globals
722	–
723	–	double boxVector[3];
724	–	if( globals->haveBox() ){
725	–	boxVector[0] = globals->getBox();
726	–	boxVector[1] = globals->getBox();
727	–	boxVector[2] = globals->getBox();
728	–
729	–	info[i].setBox( boxVector );
730	–	}
731	–	else if( globals->haveDensity() ){
732	–
733	–	double vol;
734	–	vol = (double)tot_nmol / globals->getDensity();
735	–	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
736	–	boxVector[1] = boxVector[0];
737	–	boxVector[2] = boxVector[0];
738	–
739	–	info[i].setBox( boxVector );
773		}
774	<	else{
775	<	if( !globals->haveBoxX() ){
776	<	sprintf( painCave.errMsg,
777	<	"SimSetup error, no periodic BoxX size given.\n" );
778	<	painCave.isFatal = 1;
779	<	simError();
774	>
775	>	//setup seed for random number generator
776	>	int seedValue;
777	>
778	>	if (globals->haveSeed()){
779	>	seedValue = globals->getSeed();
780	>
781	>	if(seedValue / 1E9 == 0){
782	>	sprintf(painCave.errMsg,
783	>	"Seed for sprng library should contain at least 9 digits\n"
784	>	"OOPSE will generate a seed for user\n");
785	>	painCave.isFatal = 0;
786	>	simError();
787	>
788	>	//using seed generated by system instead of invalid seed set by user
789	>	#ifndef IS_MPI
790	>	seedValue = make_sprng_seed();
791	>	#else
792	>	if (worldRank == 0){
793	>	seedValue = make_sprng_seed();
794		}
795	<	boxVector[0] = globals->getBoxX();
796	<
750	<	if( !globals->haveBoxY() ){
751	<	sprintf( painCave.errMsg,
752	<	"SimSetup error, no periodic BoxY size given.\n" );
753	<	painCave.isFatal = 1;
754	<	simError();
755	<	}
756	<	boxVector[1] = globals->getBoxY();
757	<
758	<	if( !globals->haveBoxZ() ){
759	<	sprintf( painCave.errMsg,
760	<	"SimSetup error, no periodic BoxZ size given.\n" );
761	<	painCave.isFatal = 1;
762	<	simError();
763	<	}
764	<	boxVector[2] = globals->getBoxZ();
765	<
766	<	info[i].setBox( boxVector );
795	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
796	>	#endif
797		}
798	+	}//end of if branch of globals->haveSeed()
799	+	else{
800	+
801	+	#ifndef IS_MPI
802	+	seedValue = make_sprng_seed();
803	+	#else
804	+	if (worldRank == 0){
805	+	seedValue = make_sprng_seed();
806	+	}
807	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
808	+	#endif
809	+	}//end of globals->haveSeed()
810
811	+	for (int i = 0; i < nInfo; i++){
812	+	info[i].setSeed(seedValue);
813		}
814	<
814	>
815		#ifdef IS_MPI
816	<	strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" );
816	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
817		MPIcheckPoint();
818		#endif // is_mpi
775	–
819		}
820
821
822	<	void SimSetup::finalInfoCheck( void ){
822	>	void SimSetup::finalInfoCheck(void){
823		int index;
824		int usesDipoles;
825		int i;
826
827	<	for(i=0; i<nInfo; i++){
827	>	for (i = 0; i < nInfo; i++){
828		// check electrostatic parameters
829	<
829	>
830		index = 0;
831		usesDipoles = 0;
832	<	while( (index < info[i].n_atoms) && !usesDipoles ){
832	>	while ((index < info[i].n_atoms) && !usesDipoles){
833		usesDipoles = (info[i].atoms[index])->hasDipole();
834		index++;
835		}
836	<
836	>
837		#ifdef IS_MPI
838		int myUse = usesDipoles;
839	<	MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD );
839	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
840		#endif //is_mpi
841	<
841	>
842		double theEcr, theEst;
843	<
844	<	if (globals->getUseRF() ) {
843	>
844	>	if (globals->getUseRF()){
845		info[i].useReactionField = 1;
846	<
847	<	if( !globals->haveECR() ){
848	<	sprintf( painCave.errMsg,
849	<	"SimSetup Warning: using default value of 1/2 the smallest "
850	<	"box length for the electrostaticCutoffRadius.\n"
851	<	"I hope you have a very fast processor!\n");
852	<	painCave.isFatal = 0;
853	<	simError();
854	<	double smallest;
812	<	smallest = info[i].boxL[0];
813	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
814	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
815	<	theEcr = 0.5 * smallest;
816	<	} else {
817	<	theEcr = globals->getECR();
846	>
847	>	if (!globals->haveECR()){
848	>	sprintf(painCave.errMsg,
849	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
850	>	"\tOOPSE will use a default value of 15.0 angstroms"
851	>	"\tfor the electrostaticCutoffRadius.\n");
852	>	painCave.isFatal = 0;
853	>	simError();
854	>	theEcr = 15.0;
855		}
856	<
857	<	if( !globals->haveEST() ){
821	<	sprintf( painCave.errMsg,
822	<	"SimSetup Warning: using default value of 0.05 * the "
823	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
824	<	);
825	<	painCave.isFatal = 0;
826	<	simError();
827	<	theEst = 0.05 * theEcr;
828	<	} else {
829	<	theEst= globals->getEST();
856	>	else{
857	>	theEcr = globals->getECR();
858		}
859	<
860	<	info[i].setEcr( theEcr, theEst );
861	<
862	<	if(!globals->haveDielectric() ){
863	<	sprintf( painCave.errMsg,
864	<	"SimSetup Error: You are trying to use Reaction Field without"
865	<	"setting a dielectric constant!\n"
866	<	);
867	<	painCave.isFatal = 1;
868	<	simError();
859	>
860	>	if (!globals->haveEST()){
861	>	sprintf(painCave.errMsg,
862	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
863	>	"\tOOPSE will use a default value of\n"
864	>	"\t0.05 * electrostaticCutoffRadius\n"
865	>	"\tfor the electrostaticSkinThickness\n");
866	>	painCave.isFatal = 0;
867	>	simError();
868	>	theEst = 0.05 * theEcr;
869		}
870	<	info[i].dielectric = globals->getDielectric();
871	<	}
872	<	else {
873	<	if (usesDipoles) {
874	<
875	<	if( !globals->haveECR() ){
876	<	sprintf( painCave.errMsg,
877	<	"SimSetup Warning: using default value of 1/2 the smallest "
878	<	"box length for the electrostaticCutoffRadius.\n"
879	<	"I hope you have a very fast processor!\n");
870	>	else{
871	>	theEst = globals->getEST();
872	>	}
873	>
874	>	info[i].setDefaultEcr(theEcr, theEst);
875	>
876	>	if (!globals->haveDielectric()){
877	>	sprintf(painCave.errMsg,
878	>	"SimSetup Error: No Dielectric constant was set.\n"
879	>	"\tYou are trying to use Reaction Field without"
880	>	"\tsetting a dielectric constant!\n");
881	>	painCave.isFatal = 1;
882	>	simError();
883	>	}
884	>	info[i].dielectric = globals->getDielectric();
885	>	}
886	>	else{
887	>	if (usesDipoles){
888	>	if (!globals->haveECR()){
889	>	sprintf(painCave.errMsg,
890	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
891	>	"\tOOPSE will use a default value of 15.0 angstroms"
892	>	"\tfor the electrostaticCutoffRadius.\n");
893		painCave.isFatal = 0;
894		simError();
895	<	double smallest;
896	<	smallest = info[i].boxL[0];
897	<	if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1];
898	<	if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2];
899	<	theEcr = 0.5 * smallest;
859	<	} else {
860	<	theEcr = globals->getECR();
861	<	}
895	>	theEcr = 15.0;
896	>	}
897	>	else{
898	>	theEcr = globals->getECR();
899	>	}
900
901	<	if( !globals->haveEST() ){
902	<	sprintf( painCave.errMsg,
903	<	"SimSetup Warning: using default value of 0.05 * the "
904	<	"electrostaticCutoffRadius for the "
905	<	"electrostaticSkinThickness\n"
906	<	);
907	<	painCave.isFatal = 0;
908	<	simError();
909	<	theEst = 0.05 * theEcr;
910	<	} else {
911	<	theEst= globals->getEST();
912	<	}
901	>	if (!globals->haveEST()){
902	>	sprintf(painCave.errMsg,
903	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
904	>	"\tOOPSE will use a default value of\n"
905	>	"\t0.05 * electrostaticCutoffRadius\n"
906	>	"\tfor the electrostaticSkinThickness\n");
907	>	painCave.isFatal = 0;
908	>	simError();
909	>	theEst = 0.05 * theEcr;
910	>	}
911	>	else{
912	>	theEst = globals->getEST();
913	>	}
914
915	<	info[i].setEcr( theEcr, theEst );
915	>	info[i].setDefaultEcr(theEcr, theEst);
916		}
917	<	}
917	>	}
918		}
880	–
919		#ifdef IS_MPI
920	<	strcpy( checkPointMsg, "post processing checks out" );
920	>	strcpy(checkPointMsg, "post processing checks out");
921		MPIcheckPoint();
922		#endif // is_mpi
885	–
923		}
887	–
888	–	void SimSetup::initSystemCoords( void ){
889	–	int i;
924
925	<	std::cerr << "Setting atom Coords\n";
925	>	void SimSetup::initSystemCoords(void){
926	>	int i;
927
928	<	(info[0].getConfiguration())->createArrays( info[0].n_atoms );
929	<
930	<	for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords();
931	<
932	<	if( globals->haveInitialConfig() ){
933	<
928	>	char* inName;
929	>
930	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
931	>
932	>	for (i = 0; i < info[0].n_atoms; i++)
933	>	info[0].atoms[i]->setCoords();
934	>
935	>	if (globals->haveInitialConfig()){
936		InitializeFromFile* fileInit;
937		#ifdef IS_MPI // is_mpi
938	<	if( worldRank == 0 ){
938	>	if (worldRank == 0){
939		#endif //is_mpi
940	<	fileInit = new InitializeFromFile( globals->getInitialConfig() );
940	>	inName = globals->getInitialConfig();
941	>	fileInit = new InitializeFromFile(inName);
942		#ifdef IS_MPI
943	<	}else fileInit = new InitializeFromFile( NULL );
943	>	}
944	>	else
945	>	fileInit = new InitializeFromFile(NULL);
946		#endif
947	<	fileInit->readInit( info ); // default velocities on
948	<
947	>	fileInit->readInit(info); // default velocities on
948	>
949		delete fileInit;
950		}
951		else{
952
913	–	#ifdef IS_MPI
914	–
953		// no init from bass
954
955	<	sprintf( painCave.errMsg,
956	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
957	<	painCave.isFatal;
955	>	sprintf(painCave.errMsg,
956	>	"Cannot intialize a simulation without an initial configuration file.\n");
957	>	painCave.isFatal = 1;;
958		simError();
959
922	–	#else
923	–
924	–	initFromBass();
925	–
926	–
927	–	#endif
960		}
961	<
961	>
962		#ifdef IS_MPI
963	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
963	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
964		MPIcheckPoint();
965		#endif // is_mpi
934	–
966		}
967
968
969	<	void SimSetup::makeOutNames( void ){
939	<
969	>	void SimSetup::makeOutNames(void){
970		int k;
971
942	–
943	–	for(k=0; k<nInfo; k++){
972
973	+	for (k = 0; k < nInfo; k++){
974		#ifdef IS_MPI
975	<	if( worldRank == 0 ){
975	>	if (worldRank == 0){
976		#endif // is_mpi
977	<
978	<	if( globals->haveFinalConfig() ){
979	<	strcpy( info[k].finalName, globals->getFinalConfig() );
977	>
978	>	if (globals->haveFinalConfig()){
979	>	strcpy(info[k].finalName, globals->getFinalConfig());
980		}
981		else{
982	<	strcpy( info[k].finalName, inFileName );
983	<	char* endTest;
984	<	int nameLength = strlen( info[k].finalName );
985	<	endTest = &(info[k].finalName[nameLength - 5]);
986	<	if( !strcmp( endTest, ".bass" ) ){
987	<	strcpy( endTest, ".eor" );
988	<	}
989	<	else if( !strcmp( endTest, ".BASS" ) ){
990	<	strcpy( endTest, ".eor" );
991	<	}
992	<	else{
993	<	endTest = &(info[k].finalName[nameLength - 4]);
994	<	if( !strcmp( endTest, ".bss" ) ){
995	<	strcpy( endTest, ".eor" );
996	<	}
997	<	else if( !strcmp( endTest, ".mdl" ) ){
998	<	strcpy( endTest, ".eor" );
999	<	}
1000	<	else{
1001	<	strcat( info[k].finalName, ".eor" );
1002	<	}
1003	<	}
982	>	strcpy(info[k].finalName, inFileName);
983	>	char* endTest;
984	>	int nameLength = strlen(info[k].finalName);
985	>	endTest = &(info[k].finalName[nameLength - 5]);
986	>	if (!strcmp(endTest, ".bass")){
987	>	strcpy(endTest, ".eor");
988	>	}
989	>	else if (!strcmp(endTest, ".BASS")){
990	>	strcpy(endTest, ".eor");
991	>	}
992	>	else{
993	>	endTest = &(info[k].finalName[nameLength - 4]);
994	>	if (!strcmp(endTest, ".bss")){
995	>	strcpy(endTest, ".eor");
996	>	}
997	>	else if (!strcmp(endTest, ".mdl")){
998	>	strcpy(endTest, ".eor");
999	>	}
1000	>	else{
1001	>	strcat(info[k].finalName, ".eor");
1002	>	}
1003	>	}
1004		}
1005	<
1005	>
1006		// make the sample and status out names
1007	<
1008	<	strcpy( info[k].sampleName, inFileName );
1007	>
1008	>	strcpy(info[k].sampleName, inFileName);
1009		char* endTest;
1010	<	int nameLength = strlen( info[k].sampleName );
1010	>	int nameLength = strlen(info[k].sampleName);
1011		endTest = &(info[k].sampleName[nameLength - 5]);
1012	<	if( !strcmp( endTest, ".bass" ) ){
1013	<	strcpy( endTest, ".dump" );
1012	>	if (!strcmp(endTest, ".bass")){
1013	>	strcpy(endTest, ".dump");
1014		}
1015	<	else if( !strcmp( endTest, ".BASS" ) ){
1016	<	strcpy( endTest, ".dump" );
1015	>	else if (!strcmp(endTest, ".BASS")){
1016	>	strcpy(endTest, ".dump");
1017		}
1018		else{
1019	<	endTest = &(info[k].sampleName[nameLength - 4]);
1020	<	if( !strcmp( endTest, ".bss" ) ){
1021	<	strcpy( endTest, ".dump" );
1022	<	}
1023	<	else if( !strcmp( endTest, ".mdl" ) ){
1024	<	strcpy( endTest, ".dump" );
1025	<	}
1026	<	else{
1027	<	strcat( info[k].sampleName, ".dump" );
1028	<	}
1019	>	endTest = &(info[k].sampleName[nameLength - 4]);
1020	>	if (!strcmp(endTest, ".bss")){
1021	>	strcpy(endTest, ".dump");
1022	>	}
1023	>	else if (!strcmp(endTest, ".mdl")){
1024	>	strcpy(endTest, ".dump");
1025	>	}
1026	>	else{
1027	>	strcat(info[k].sampleName, ".dump");
1028	>	}
1029		}
1030	<
1031	<	strcpy( info[k].statusName, inFileName );
1032	<	nameLength = strlen( info[k].statusName );
1030	>
1031	>	strcpy(info[k].statusName, inFileName);
1032	>	nameLength = strlen(info[k].statusName);
1033		endTest = &(info[k].statusName[nameLength - 5]);
1034	<	if( !strcmp( endTest, ".bass" ) ){
1035	<	strcpy( endTest, ".stat" );
1034	>	if (!strcmp(endTest, ".bass")){
1035	>	strcpy(endTest, ".stat");
1036		}
1037	<	else if( !strcmp( endTest, ".BASS" ) ){
1038	<	strcpy( endTest, ".stat" );
1037	>	else if (!strcmp(endTest, ".BASS")){
1038	>	strcpy(endTest, ".stat");
1039		}
1040		else{
1041	<	endTest = &(info[k].statusName[nameLength - 4]);
1042	<	if( !strcmp( endTest, ".bss" ) ){
1043	<	strcpy( endTest, ".stat" );
1044	<	}
1045	<	else if( !strcmp( endTest, ".mdl" ) ){
1046	<	strcpy( endTest, ".stat" );
1047	<	}
1048	<	else{
1049	<	strcat( info[k].statusName, ".stat" );
1050	<	}
1041	>	endTest = &(info[k].statusName[nameLength - 4]);
1042	>	if (!strcmp(endTest, ".bss")){
1043	>	strcpy(endTest, ".stat");
1044	>	}
1045	>	else if (!strcmp(endTest, ".mdl")){
1046	>	strcpy(endTest, ".stat");
1047	>	}
1048	>	else{
1049	>	strcat(info[k].statusName, ".stat");
1050	>	}
1051		}
1052	<
1052	>
1053		#ifdef IS_MPI
1054	+
1055		}
1056		#endif // is_mpi
1057		}
1058		}
1059
1060
1061	<	void SimSetup::sysObjectsCreation( void ){
1062	<
1063	<	int i,k;
1034	<
1061	>	void SimSetup::sysObjectsCreation(void){
1062	>	int i, k;
1063	>
1064		// create the forceField
1065	<
1065	>
1066		createFF();
1067
1068		// extract componentList
#	Line 1046 | Line 1075 | void SimSetup::sysObjectsCreation( void ){
1075
1076		#ifdef IS_MPI
1077		// divide the molecules among the processors
1078	<
1078	>
1079		mpiMolDivide();
1080		#endif //is_mpi
1081	<
1081	>
1082		// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1083	<
1083	>
1084		makeSysArrays();
1085
1086		// make and initialize the molecules (all but atomic coordinates)
1087	<
1087	>
1088		makeMolecules();
1089	<
1090	<	for(k=0; k<nInfo; k++){
1089	>
1090	>	for (k = 0; k < nInfo; k++){
1091		info[k].identArray = new int[info[k].n_atoms];
1092	<	for(i=0; i<info[k].n_atoms; i++){
1092	>	for (i = 0; i < info[k].n_atoms; i++){
1093		info[k].identArray[i] = info[k].atoms[i]->getIdent();
1094		}
1095		}
1096		}
1097
1098
1099	<	void SimSetup::createFF( void ){
1099	>	void SimSetup::createFF(void){
1100	>	switch (ffCase){
1101	>	case FF_DUFF:
1102	>	the_ff = new DUFF();
1103	>	break;
1104
1105	<	switch( ffCase ){
1105	>	case FF_LJ:
1106	>	the_ff = new LJFF();
1107	>	break;
1108
1109	<	case FF_DUFF:
1110	<	the_ff = new DUFF();
1111	<	break;
1109	>	case FF_EAM:
1110	>	the_ff = new EAM_FF();
1111	>	break;
1112
1113	<	case FF_LJ:
1114	<	the_ff = new LJFF();
1115	<	break;
1116	<
1117	<	case FF_EAM:
1083	<	the_ff = new EAM_FF();
1084	<	break;
1085	<
1086	<	default:
1087	<	sprintf( painCave.errMsg,
1088	<	"SimSetup Error. Unrecognized force field in case statement.\n");
1089	<	painCave.isFatal = 1;
1090	<	simError();
1113	>	default:
1114	>	sprintf(painCave.errMsg,
1115	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1116	>	painCave.isFatal = 1;
1117	>	simError();
1118		}
1119
1120		#ifdef IS_MPI
1121	<	strcpy( checkPointMsg, "ForceField creation successful" );
1121	>	strcpy(checkPointMsg, "ForceField creation successful");
1122		MPIcheckPoint();
1123		#endif // is_mpi
1097	–
1124		}
1125
1126
1127	<	void SimSetup::compList( void ){
1102	<
1127	>	void SimSetup::compList(void){
1128		int i;
1129		char* id;
1130		LinkedMolStamp* headStamp = new LinkedMolStamp();
1131		LinkedMolStamp* currentStamp = NULL;
1132	<	comp_stamps = new MoleculeStamp*[n_components];
1133	<
1132	>	comp_stamps = new MoleculeStamp * [n_components];
1133	>
1134		// make an array of molecule stamps that match the components used.
1135		// also extract the used stamps out into a separate linked list
1136	<
1137	<	for(i=0; i<nInfo; i++){
1136	>
1137	>	for (i = 0; i < nInfo; i++){
1138		info[i].nComponents = n_components;
1139		info[i].componentsNmol = components_nmol;
1140		info[i].compStamps = comp_stamps;
1141		info[i].headStamp = headStamp;
1142		}
1118	–
1143
1120	–	for( i=0; i<n_components; i++ ){
1144
1145	+	for (i = 0; i < n_components; i++){
1146		id = the_components[i]->getType();
1147		comp_stamps[i] = NULL;
1148	<
1148	>
1149		// check to make sure the component isn't already in the list
1150
1151	<	comp_stamps[i] = headStamp->match( id );
1152	<	if( comp_stamps[i] == NULL ){
1129	<
1151	>	comp_stamps[i] = headStamp->match(id);
1152	>	if (comp_stamps[i] == NULL){
1153		// extract the component from the list;
1154	<
1155	<	currentStamp = stamps->extractMolStamp( id );
1156	<	if( currentStamp == NULL ){
1157	<	sprintf( painCave.errMsg,
1158	<	"SimSetup error: Component \"%s\" was not found in the "
1159	<	"list of declared molecules\n",
1160	<	id );
1161	<	painCave.isFatal = 1;
1162	<	simError();
1154	>
1155	>	currentStamp = stamps->extractMolStamp(id);
1156	>	if (currentStamp == NULL){
1157	>	sprintf(painCave.errMsg,
1158	>	"SimSetup error: Component \"%s\" was not found in the "
1159	>	"list of declared molecules\n",
1160	>	id);
1161	>	painCave.isFatal = 1;
1162	>	simError();
1163		}
1164	<
1165	<	headStamp->add( currentStamp );
1166	<	comp_stamps[i] = headStamp->match( id );
1164	>
1165	>	headStamp->add(currentStamp);
1166	>	comp_stamps[i] = headStamp->match(id);
1167		}
1168		}
1169
1170		#ifdef IS_MPI
1171	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
1171	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1172		MPIcheckPoint();
1173		#endif // is_mpi
1174	+	}
1175
1176	+	void SimSetup::calcSysValues(void){
1177	+	int i;
1178
1179	<	}
1179	>	int* molMembershipArray;
1180
1155	–	void SimSetup::calcSysValues( void ){
1156	–	int i, j, k;
1157	–
1158	–	int *molMembershipArray;
1159	–
1181		tot_atoms = 0;
1182		tot_bonds = 0;
1183		tot_bends = 0;
1184		tot_torsions = 0;
1185	<	for( i=0; i<n_components; i++ ){
1186	<
1187	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
1188	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
1168	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
1185	>	for (i = 0; i < n_components; i++){
1186	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1187	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1188	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1189		tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1190		}
1191	<
1191	>
1192		tot_SRI = tot_bonds + tot_bends + tot_torsions;
1193		molMembershipArray = new int[tot_atoms];
1194	<
1195	<	for(i=0; i<nInfo; i++){
1194	>
1195	>	for (i = 0; i < nInfo; i++){
1196		info[i].n_atoms = tot_atoms;
1197		info[i].n_bonds = tot_bonds;
1198		info[i].n_bends = tot_bends;
1199		info[i].n_torsions = tot_torsions;
1200		info[i].n_SRI = tot_SRI;
1201		info[i].n_mol = tot_nmol;
1202	<
1202	>
1203		info[i].molMembershipArray = molMembershipArray;
1204	<	}
1204	>	}
1205		}
1206
1207		#ifdef IS_MPI
1208
1209	<	void SimSetup::mpiMolDivide( void ){
1190	<
1209	>	void SimSetup::mpiMolDivide(void){
1210		int i, j, k;
1211		int localMol, allMol;
1212		int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1213
1214	<	mpiSim = new mpiSimulation( info );
1215	<
1214	>	mpiSim = new mpiSimulation(info);
1215	>
1216		globalIndex = mpiSim->divideLabor();
1217
1218		// set up the local variables
1219	<
1219	>
1220		mol2proc = mpiSim->getMolToProcMap();
1221		molCompType = mpiSim->getMolComponentType();
1222	<
1222	>
1223		allMol = 0;
1224		localMol = 0;
1225		local_atoms = 0;
#	Line 1210 | Line 1229 | void SimSetup::mpiMolDivide( void ){
1229		globalAtomIndex = 0;
1230
1231
1232	<	for( i=0; i<n_components; i++ ){
1233	<
1234	<	for( j=0; j<components_nmol[i]; j++ ){
1235	<
1236	<	if( mol2proc[allMol] == worldRank ){
1237	<
1238	<	local_atoms +=    comp_stamps[i]->getNAtoms();
1239	<	local_bonds +=    comp_stamps[i]->getNBonds();
1221	<	local_bends +=    comp_stamps[i]->getNBends();
1222	<	local_torsions += comp_stamps[i]->getNTorsions();
1223	<	localMol++;
1232	>	for (i = 0; i < n_components; i++){
1233	>	for (j = 0; j < components_nmol[i]; j++){
1234	>	if (mol2proc[allMol] == worldRank){
1235	>	local_atoms += comp_stamps[i]->getNAtoms();
1236	>	local_bonds += comp_stamps[i]->getNBonds();
1237	>	local_bends += comp_stamps[i]->getNBends();
1238	>	local_torsions += comp_stamps[i]->getNTorsions();
1239	>	localMol++;
1240		}
1241	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1241	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1242		info[0].molMembershipArray[globalAtomIndex] = allMol;
1243		globalAtomIndex++;
1244		}
1245
1246	<	allMol++;
1246	>	allMol++;
1247		}
1248		}
1249		local_SRI = local_bonds + local_bends + local_torsions;
1250	<
1250	>
1251		info[0].n_atoms = mpiSim->getMyNlocal();
1252	<
1253	<	if( local_atoms != info[0].n_atoms ){
1254	<	sprintf( painCave.errMsg,
1255	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1256	<	" localAtom (%d) are not equal.\n",
1257	<	info[0].n_atoms,
1242	<	local_atoms );
1252	>
1253	>	if (local_atoms != info[0].n_atoms){
1254	>	sprintf(painCave.errMsg,
1255	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1256	>	"\tlocalAtom (%d) are not equal.\n",
1257	>	info[0].n_atoms, local_atoms);
1258		painCave.isFatal = 1;
1259		simError();
1260		}
#	Line 1250 | Line 1265 | void SimSetup::mpiMolDivide( void ){
1265		info[0].n_SRI = local_SRI;
1266		info[0].n_mol = localMol;
1267
1268	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
1268	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1269		MPIcheckPoint();
1270		}
1271	<
1271	>
1272		#endif // is_mpi
1273
1274
1275	<	void SimSetup::makeSysArrays( void ){
1276	<	int i, j, k, l;
1275	>	void SimSetup::makeSysArrays(void){
1276	>
1277	>	#ifndef IS_MPI
1278	>	int k, j;
1279	>	#endif // is_mpi
1280	>	int i, l;
1281
1282		Atom** the_atoms;
1283		Molecule* the_molecules;
1284		Exclude** the_excludes;
1285
1286	<
1287	<	for(l=0; l<nInfo; l++){
1269	<
1286	>
1287	>	for (l = 0; l < nInfo; l++){
1288		// create the atom and short range interaction arrays
1289	<
1290	<	the_atoms = new Atom*[info[l].n_atoms];
1289	>
1290	>	the_atoms = new Atom * [info[l].n_atoms];
1291		the_molecules = new Molecule[info[l].n_mol];
1292		int molIndex;
1293
1294		// initialize the molecule's stampID's
1295	<
1295	>
1296		#ifdef IS_MPI
1297	<
1298	<
1297	>
1298	>
1299		molIndex = 0;
1300	<	for(i=0; i<mpiSim->getTotNmol(); i++){
1301	<
1302	<	if(mol2proc[i] == worldRank ){
1303	<	the_molecules[molIndex].setStampID( molCompType[i] );
1304	<	the_molecules[molIndex].setMyIndex( molIndex );
1305	<	the_molecules[molIndex].setGlobalIndex( i );
1288	<	molIndex++;
1300	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1301	>	if (mol2proc[i] == worldRank){
1302	>	the_molecules[molIndex].setStampID(molCompType[i]);
1303	>	the_molecules[molIndex].setMyIndex(molIndex);
1304	>	the_molecules[molIndex].setGlobalIndex(i);
1305	>	molIndex++;
1306		}
1307		}
1308	<
1308	>
1309		#else // is_mpi
1310	<
1310	>
1311		molIndex = 0;
1312		globalAtomIndex = 0;
1313	<	for(i=0; i<n_components; i++){
1314	<	for(j=0; j<components_nmol[i]; j++ ){
1315	<	the_molecules[molIndex].setStampID( i );
1316	<	the_molecules[molIndex].setMyIndex( molIndex );
1317	<	the_molecules[molIndex].setGlobalIndex( molIndex );
1318	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
1319	<	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1320	<	globalAtomIndex++;
1321	<	}
1322	<	molIndex++;
1313	>	for (i = 0; i < n_components; i++){
1314	>	for (j = 0; j < components_nmol[i]; j++){
1315	>	the_molecules[molIndex].setStampID(i);
1316	>	the_molecules[molIndex].setMyIndex(molIndex);
1317	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1318	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1319	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1320	>	globalAtomIndex++;
1321	>	}
1322	>	molIndex++;
1323		}
1324		}
1325	<
1326	<
1325	>
1326	>
1327		#endif // is_mpi
1328
1329
1330	<	if( info[l].n_SRI ){
1314	<
1330	>	if (info[l].n_SRI){
1331		Exclude::createArray(info[l].n_SRI);
1332	<	the_excludes = new Exclude*[info[l].n_SRI];
1333	<	for( int ex=0; ex<info[l].n_SRI; ex++){
1334	<	the_excludes[ex] = new Exclude(ex);
1332	>	the_excludes = new Exclude * [info[l].n_SRI];
1333	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1334	>	the_excludes[ex] = new Exclude(ex);
1335		}
1336		info[l].globalExcludes = new int;
1337		info[l].n_exclude = info[l].n_SRI;
1338		}
1339		else{
1340	<
1341	<	Exclude::createArray( 1 );
1326	<	the_excludes = new Exclude*;
1340	>	Exclude::createArray(1);
1341	>	the_excludes = new Exclude * ;
1342		the_excludes[0] = new Exclude(0);
1343	<	the_excludes[0]->setPair( 0,0 );
1343	>	the_excludes[0]->setPair(0, 0);
1344		info[l].globalExcludes = new int;
1345		info[l].globalExcludes[0] = 0;
1346		info[l].n_exclude = 0;
#	Line 1338 | Line 1353 | void SimSetup::makeSysArrays( void ){
1353		info[l].nGlobalExcludes = 0;
1354		info[l].excludes = the_excludes;
1355
1356	<	the_ff->setSimInfo( info );
1342	<
1356	>	the_ff->setSimInfo(info);
1357		}
1358		}
1359
1360	<	void SimSetup::makeIntegrator( void ){
1347	<
1360	>	void SimSetup::makeIntegrator(void){
1361		int k;
1362
1363	<	NVT<RealIntegrator>*  myNVT = NULL;
1364	<	NPTi<RealIntegrator>* myNPTi = NULL;
1365	<	NPTf<RealIntegrator>* myNPTf = NULL;
1366	<	NPTim<RealIntegrator>* myNPTim = NULL;
1367	<	NPTfm<RealIntegrator>* myNPTfm = NULL;
1368	<
1369	<	for(k=0; k<nInfo; k++){
1370	<
1371	<	switch( ensembleCase ){
1372	<
1373	<	case NVE_ENS:
1374	<	if (globals->haveZconstraints()){
1375	<	setupZConstraint(info[k]);
1376	<	new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff );
1363	>	NVE<RealIntegrator>* myNVE = NULL;
1364	>	NVT<RealIntegrator>* myNVT = NULL;
1365	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1366	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1367	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1368	>
1369	>	for (k = 0; k < nInfo; k++){
1370	>	switch (ensembleCase){
1371	>	case NVE_ENS:
1372	>	if (globals->haveZconstraints()){
1373	>	setupZConstraint(info[k]);
1374	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1375	>	}
1376	>	else{
1377	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1378		}
1379	+
1380	+	info->the_integrator = myNVE;
1381	+	break;
1382
1383	<	else
1384	<	new NVE<RealIntegrator>( &(info[k]), the_ff );
1385	<	break;
1386	<
1387	<	case NVT_ENS:
1388	<	if (globals->haveZconstraints()){
1389	<	setupZConstraint(info[k]);
1373	<	myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff );
1374	<	}
1375	<	else
1376	<	myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff );
1383	>	case NVT_ENS:
1384	>	if (globals->haveZconstraints()){
1385	>	setupZConstraint(info[k]);
1386	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1387	>	}
1388	>	else
1389	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1390
1391	<	myNVT->setTargetTemp(globals->getTargetTemp());
1379	<
1380	<	if (globals->haveTauThermostat())
1381	<	myNVT->setTauThermostat(globals->getTauThermostat());
1382	<
1383	<	else {
1384	<	sprintf( painCave.errMsg,
1385	<	"SimSetup error: If you use the NVT\n"
1386	<	"    ensemble, you must set tauThermostat.\n");
1387	<	painCave.isFatal = 1;
1388	<	simError();
1389	<	}
1390	<	break;
1391	<
1392	<	case NPTi_ENS:
1393	<	if (globals->haveZconstraints()){
1394	<	setupZConstraint(info[k]);
1395	<	myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff );
1396	<	}
1397	<	else
1398	<	myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff );
1391	>	myNVT->setTargetTemp(globals->getTargetTemp());
1392
1393	<	myNPTi->setTargetTemp( globals->getTargetTemp() );
1394	<
1395	<	if (globals->haveTargetPressure())
1396	<	myNPTi->setTargetPressure(globals->getTargetPressure());
1397	<	else {
1398	<	sprintf( painCave.errMsg,
1399	<	"SimSetup error: If you use a constant pressure\n"
1400	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1401	<	painCave.isFatal = 1;
1409	<	simError();
1410	<	}
1411	<
1412	<	if( globals->haveTauThermostat() )
1413	<	myNPTi->setTauThermostat( globals->getTauThermostat() );
1414	<	else{
1415	<	sprintf( painCave.errMsg,
1416	<	"SimSetup error: If you use an NPT\n"
1417	<	"    ensemble, you must set tauThermostat.\n");
1418	<	painCave.isFatal = 1;
1419	<	simError();
1420	<	}
1421	<
1422	<	if( globals->haveTauBarostat() )
1423	<	myNPTi->setTauBarostat( globals->getTauBarostat() );
1424	<	else{
1425	<	sprintf( painCave.errMsg,
1426	<	"SimSetup error: If you use an NPT\n"
1427	<	"    ensemble, you must set tauBarostat.\n");
1428	<	painCave.isFatal = 1;
1429	<	simError();
1430	<	}
1431	<	break;
1432	<
1433	<	case NPTf_ENS:
1434	<	if (globals->haveZconstraints()){
1435	<	setupZConstraint(info[k]);
1436	<	myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff );
1437	<	}
1438	<	else
1439	<	myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff );
1393	>	if (globals->haveTauThermostat())
1394	>	myNVT->setTauThermostat(globals->getTauThermostat());
1395	>	else{
1396	>	sprintf(painCave.errMsg,
1397	>	"SimSetup error: If you use the NVT\n"
1398	>	"\tensemble, you must set tauThermostat.\n");
1399	>	painCave.isFatal = 1;
1400	>	simError();
1401	>	}
1402
1403	<	myNPTf->setTargetTemp( globals->getTargetTemp());
1404	<
1443	<	if (globals->haveTargetPressure())
1444	<	myNPTf->setTargetPressure(globals->getTargetPressure());
1445	<	else {
1446	<	sprintf( painCave.errMsg,
1447	<	"SimSetup error: If you use a constant pressure\n"
1448	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1449	<	painCave.isFatal = 1;
1450	<	simError();
1451	<	}
1452	<
1453	<	if( globals->haveTauThermostat() )
1454	<	myNPTf->setTauThermostat( globals->getTauThermostat() );
1455	<	else{
1456	<	sprintf( painCave.errMsg,
1457	<	"SimSetup error: If you use an NPT\n"
1458	<	"    ensemble, you must set tauThermostat.\n");
1459	<	painCave.isFatal = 1;
1460	<	simError();
1461	<	}
1462	<
1463	<	if( globals->haveTauBarostat() )
1464	<	myNPTf->setTauBarostat( globals->getTauBarostat() );
1465	<	else{
1466	<	sprintf( painCave.errMsg,
1467	<	"SimSetup error: If you use an NPT\n"
1468	<	"    ensemble, you must set tauBarostat.\n");
1469	<	painCave.isFatal = 1;
1470	<	simError();
1471	<	}
1472	<	break;
1473	<
1474	<	case NPTim_ENS:
1475	<	if (globals->haveZconstraints()){
1476	<	setupZConstraint(info[k]);
1477	<	myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff );
1478	<	}
1479	<	else
1480	<	myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff );
1403	>	info->the_integrator = myNVT;
1404	>	break;
1405
1406	<	myNPTim->setTargetTemp( globals->getTargetTemp());
1407	<
1408	<	if (globals->haveTargetPressure())
1409	<	myNPTim->setTargetPressure(globals->getTargetPressure());
1410	<	else {
1411	<	sprintf( painCave.errMsg,
1412	<	"SimSetup error: If you use a constant pressure\n"
1489	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1490	<	painCave.isFatal = 1;
1491	<	simError();
1492	<	}
1493	<
1494	<	if( globals->haveTauThermostat() )
1495	<	myNPTim->setTauThermostat( globals->getTauThermostat() );
1496	<	else{
1497	<	sprintf( painCave.errMsg,
1498	<	"SimSetup error: If you use an NPT\n"
1499	<	"    ensemble, you must set tauThermostat.\n");
1500	<	painCave.isFatal = 1;
1501	<	simError();
1502	<	}
1503	<
1504	<	if( globals->haveTauBarostat() )
1505	<	myNPTim->setTauBarostat( globals->getTauBarostat() );
1506	<	else{
1507	<	sprintf( painCave.errMsg,
1508	<	"SimSetup error: If you use an NPT\n"
1509	<	"    ensemble, you must set tauBarostat.\n");
1510	<	painCave.isFatal = 1;
1511	<	simError();
1512	<	}
1513	<	break;
1514	<
1515	<	case NPTfm_ENS:
1516	<	if (globals->haveZconstraints()){
1517	<	setupZConstraint(info[k]);
1518	<	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff );
1519	<	}
1520	<	else
1521	<	myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff );
1406	>	case NPTi_ENS:
1407	>	if (globals->haveZconstraints()){
1408	>	setupZConstraint(info[k]);
1409	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1410	>	}
1411	>	else
1412	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1413
1414	<	myNPTfm->setTargetTemp( globals->getTargetTemp());
1415	<
1416	<	if (globals->haveTargetPressure())
1417	<	myNPTfm->setTargetPressure(globals->getTargetPressure());
1418	<	else {
1419	<	sprintf( painCave.errMsg,
1420	<	"SimSetup error: If you use a constant pressure\n"
1421	<	"    ensemble, you must set targetPressure in the BASS file.\n");
1422	<	painCave.isFatal = 1;
1423	<	simError();
1424	<	}
1425	<
1426	<	if( globals->haveTauThermostat() )
1427	<	myNPTfm->setTauThermostat( globals->getTauThermostat() );
1428	<	else{
1429	<	sprintf( painCave.errMsg,
1430	<	"SimSetup error: If you use an NPT\n"
1431	<	"    ensemble, you must set tauThermostat.\n");
1432	<	painCave.isFatal = 1;
1433	<	simError();
1434	<	}
1435	<
1436	<	if( globals->haveTauBarostat() )
1437	<	myNPTfm->setTauBarostat( globals->getTauBarostat() );
1438	<	else{
1439	<	sprintf( painCave.errMsg,
1440	<	"SimSetup error: If you use an NPT\n"
1441	<	"    ensemble, you must set tauBarostat.\n");
1442	<	painCave.isFatal = 1;
1443	<	simError();
1444	<	}
1445	<	break;
1446	<
1447	<	default:
1448	<	sprintf( painCave.errMsg,
1449	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1450	<	painCave.isFatal = 1;
1451	<	simError();
1414	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1415	>
1416	>	if (globals->haveTargetPressure())
1417	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1418	>	else{
1419	>	sprintf(painCave.errMsg,
1420	>	"SimSetup error: If you use a constant pressure\n"
1421	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1422	>	painCave.isFatal = 1;
1423	>	simError();
1424	>	}
1425	>
1426	>	if (globals->haveTauThermostat())
1427	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1428	>	else{
1429	>	sprintf(painCave.errMsg,
1430	>	"SimSetup error: If you use an NPT\n"
1431	>	"\tensemble, you must set tauThermostat.\n");
1432	>	painCave.isFatal = 1;
1433	>	simError();
1434	>	}
1435	>
1436	>	if (globals->haveTauBarostat())
1437	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1438	>	else{
1439	>	sprintf(painCave.errMsg,
1440	>	"SimSetup error: If you use an NPT\n"
1441	>	"\tensemble, you must set tauBarostat.\n");
1442	>	painCave.isFatal = 1;
1443	>	simError();
1444	>	}
1445	>
1446	>	info->the_integrator = myNPTi;
1447	>	break;
1448	>
1449	>	case NPTf_ENS:
1450	>	if (globals->haveZconstraints()){
1451	>	setupZConstraint(info[k]);
1452	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1453	>	}
1454	>	else
1455	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1456	>
1457	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1458	>
1459	>	if (globals->haveTargetPressure())
1460	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1461	>	else{
1462	>	sprintf(painCave.errMsg,
1463	>	"SimSetup error: If you use a constant pressure\n"
1464	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1465	>	painCave.isFatal = 1;
1466	>	simError();
1467	>	}
1468	>
1469	>	if (globals->haveTauThermostat())
1470	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1471	>
1472	>	else{
1473	>	sprintf(painCave.errMsg,
1474	>	"SimSetup error: If you use an NPT\n"
1475	>	"\tensemble, you must set tauThermostat.\n");
1476	>	painCave.isFatal = 1;
1477	>	simError();
1478	>	}
1479	>
1480	>	if (globals->haveTauBarostat())
1481	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1482	>
1483	>	else{
1484	>	sprintf(painCave.errMsg,
1485	>	"SimSetup error: If you use an NPT\n"
1486	>	"\tensemble, you must set tauBarostat.\n");
1487	>	painCave.isFatal = 1;
1488	>	simError();
1489	>	}
1490	>
1491	>	info->the_integrator = myNPTf;
1492	>	break;
1493	>
1494	>	case NPTxyz_ENS:
1495	>	if (globals->haveZconstraints()){
1496	>	setupZConstraint(info[k]);
1497	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1498	>	}
1499	>	else
1500	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1501	>
1502	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1503	>
1504	>	if (globals->haveTargetPressure())
1505	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1506	>	else{
1507	>	sprintf(painCave.errMsg,
1508	>	"SimSetup error: If you use a constant pressure\n"
1509	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1510	>	painCave.isFatal = 1;
1511	>	simError();
1512	>	}
1513	>
1514	>	if (globals->haveTauThermostat())
1515	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1516	>	else{
1517	>	sprintf(painCave.errMsg,
1518	>	"SimSetup error: If you use an NPT\n"
1519	>	"\tensemble, you must set tauThermostat.\n");
1520	>	painCave.isFatal = 1;
1521	>	simError();
1522	>	}
1523	>
1524	>	if (globals->haveTauBarostat())
1525	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1526	>	else{
1527	>	sprintf(painCave.errMsg,
1528	>	"SimSetup error: If you use an NPT\n"
1529	>	"\tensemble, you must set tauBarostat.\n");
1530	>	painCave.isFatal = 1;
1531	>	simError();
1532	>	}
1533	>
1534	>	info->the_integrator = myNPTxyz;
1535	>	break;
1536	>
1537	>	default:
1538	>	sprintf(painCave.errMsg,
1539	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1540	>	painCave.isFatal = 1;
1541	>	simError();
1542		}
1543		}
1544		}
1545
1546	<	void SimSetup::initFortran( void ){
1566	<
1546	>	void SimSetup::initFortran(void){
1547		info[0].refreshSim();
1548	<
1549	<	if( !strcmp( info[0].mixingRule, "standard") ){
1550	<	the_ff->initForceField( LB_MIXING_RULE );
1548	>
1549	>	if (!strcmp(info[0].mixingRule, "standard")){
1550	>	the_ff->initForceField(LB_MIXING_RULE);
1551		}
1552	<	else if( !strcmp( info[0].mixingRule, "explicit") ){
1553	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
1552	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1553	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1554		}
1555		else{
1556	<	sprintf( painCave.errMsg,
1557	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
1578	<	info[0].mixingRule );
1556	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1557	>	info[0].mixingRule);
1558		painCave.isFatal = 1;
1559		simError();
1560		}
1561
1562
1563		#ifdef IS_MPI
1564	<	strcpy( checkPointMsg,
1586	<	"Successfully intialized the mixingRule for Fortran." );
1564	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1565		MPIcheckPoint();
1566		#endif // is_mpi
1589	–
1567		}
1568
1569	<	void SimSetup::setupZConstraint(SimInfo& theInfo)
1570	<	{
1571	<	int nZConstraints;
1595	<	ZconStamp** zconStamp;
1596	<
1597	<	if(globals->haveZconstraintTime()){
1598	<
1599	<	//add sample time of z-constraint  into SimInfo's property list
1600	<	DoubleData* zconsTimeProp = new DoubleData();
1601	<	zconsTimeProp->setID(ZCONSTIME_ID);
1602	<	zconsTimeProp->setData(globals->getZconsTime());
1603	<	theInfo.addProperty(zconsTimeProp);
1604	<	}
1605	<	else{
1606	<	sprintf( painCave.errMsg,
1607	<	"ZConstraint error: If you use an ZConstraint\n"
1608	<	" , you must set sample time.\n");
1609	<	painCave.isFatal = 1;
1610	<	simError();
1611	<	}
1569	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1570	>	int nZConstraints;
1571	>	ZconStamp** zconStamp;
1572
1573	<	//
1574	<	nZConstraints = globals->getNzConstraints();
1575	<	zconStamp = globals->getZconStamp();
1576	<	ZConsParaItem tempParaItem;
1573	>	if (globals->haveZconstraintTime()){
1574	>	//add sample time of z-constraint  into SimInfo's property list
1575	>	DoubleData* zconsTimeProp = new DoubleData();
1576	>	zconsTimeProp->setID(ZCONSTIME_ID);
1577	>	zconsTimeProp->setData(globals->getZconsTime());
1578	>	theInfo.addProperty(zconsTimeProp);
1579	>	}
1580	>	else{
1581	>	sprintf(painCave.errMsg,
1582	>	"ZConstraint error: If you use a ZConstraint,\n"
1583	>	"\tyou must set zconsTime.\n");
1584	>	painCave.isFatal = 1;
1585	>	simError();
1586	>	}
1587
1588	<	ZConsParaData* zconsParaData = new ZConsParaData();
1589	<	zconsParaData->setID(ZCONSPARADATA_ID);
1590	<
1591	<	for(int i = 0; i < nZConstraints; i++){
1588	>	//push zconsTol into siminfo, if user does not specify
1589	>	//value for zconsTol, a default value will be used
1590	>	DoubleData* zconsTol = new DoubleData();
1591	>	zconsTol->setID(ZCONSTOL_ID);
1592	>	if (globals->haveZconsTol()){
1593	>	zconsTol->setData(globals->getZconsTol());
1594	>	}
1595	>	else{
1596	>	double defaultZConsTol = 0.01;
1597	>	sprintf(painCave.errMsg,
1598	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1599	>	"\tOOPSE will use a default value of %f.\n"
1600	>	"\tTo set the tolerance, use the zconsTol variable.\n",
1601	>	defaultZConsTol);
1602	>	painCave.isFatal = 0;
1603	>	simError();
1604	>
1605	>	zconsTol->setData(defaultZConsTol);
1606	>	}
1607	>	theInfo.addProperty(zconsTol);
1608	>
1609	>	//set Force Subtraction Policy
1610	>	StringData* zconsForcePolicy = new StringData();
1611	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1612	>
1613	>	if (globals->haveZconsForcePolicy()){
1614	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1615	>	}
1616	>	else{
1617	>	sprintf(painCave.errMsg,
1618	>	"ZConstraint Warning: No force subtraction policy was set.\n"
1619	>	"\tOOPSE will use PolicyByMass.\n"
1620	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1621	>	painCave.isFatal = 0;
1622	>	simError();
1623	>	zconsForcePolicy->setData("BYMASS");
1624	>	}
1625	>
1626	>	theInfo.addProperty(zconsForcePolicy);
1627	>
1628	>	//Determine the name of ouput file and add it into SimInfo's property list
1629	>	//Be careful, do not use inFileName, since it is a pointer which
1630	>	//point to a string at master node, and slave nodes do not contain that string
1631	>
1632	>	string zconsOutput(theInfo.finalName);
1633	>
1634	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1635	>
1636	>	StringData* zconsFilename = new StringData();
1637	>	zconsFilename->setID(ZCONSFILENAME_ID);
1638	>	zconsFilename->setData(zconsOutput);
1639	>
1640	>	theInfo.addProperty(zconsFilename);
1641	>
1642	>	//setup index, pos and other parameters of z-constraint molecules
1643	>	nZConstraints = globals->getNzConstraints();
1644	>	theInfo.nZconstraints = nZConstraints;
1645	>
1646	>	zconStamp = globals->getZconStamp();
1647	>	ZConsParaItem tempParaItem;
1648	>
1649	>	ZConsParaData* zconsParaData = new ZConsParaData();
1650	>	zconsParaData->setID(ZCONSPARADATA_ID);
1651	>
1652	>	for (int i = 0; i < nZConstraints; i++){
1653		tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1654		tempParaItem.zPos = zconStamp[i]->getZpos();
1655		tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1656		tempParaItem.kRatio = zconStamp[i]->getKratio();
1657
1658		zconsParaData->addItem(tempParaItem);
1659	<	}
1659	>	}
1660
1661	<	//sort the parameters by index of molecules
1662	<	zconsParaData->sortByIndex();
1663	<
1664	<	//push data into siminfo, therefore, we can retrieve later
1665	<	theInfo.addProperty(zconsParaData);
1661	>	//check the uniqueness of index
1662	>	if(!zconsParaData->isIndexUnique()){
1663	>	sprintf(painCave.errMsg,
1664	>	"ZConstraint Error: molIndex is not unique!\n");
1665	>	painCave.isFatal = 1;
1666	>	simError();
1667	>	}
1668
1669	<	//push zconsTol into siminfo, if user does not specify
1670	<	//value for zconsTol, a default value will be used
1671	<	DoubleData* zconsTol = new DoubleData();
1672	<	zconsTol->setID(ZCONSTOL_ID);
1673	<	if(globals->haveZconsTol()){
1641	<	zconsTol->setData(globals->getZconsTol());
1642	<	}
1643	<	else{
1644	<	double defaultZConsTol = 1E-6;
1645	<	sprintf( painCave.errMsg,
1646	<	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1647	<	" , default value %f is used.\n", defaultZConsTol);
1648	<	painCave.isFatal = 0;
1649	<	simError();
1650	<
1651	<	zconsTol->setData(defaultZConsTol);
1652	<	}
1653	<	theInfo.addProperty(zconsTol);
1654	<
1655	<	//Determine the name of ouput file and add it into SimInfo's property list
1656	<	//Be careful, do not use inFileName, since it is a pointer which
1657	<	//point to a string at master node, and slave nodes do not contain that string
1658	<
1659	<	string zconsOutput(theInfo.finalName);
1660	<
1661	<	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1662	<
1663	<	StringData* zconsFilename = new StringData();
1664	<	zconsFilename->setID(ZCONSFILENAME_ID);
1665	<	zconsFilename->setData(zconsOutput);
1666	<
1667	<	theInfo.addProperty(zconsFilename);
1669	>	//sort the parameters by index of molecules
1670	>	zconsParaData->sortByIndex();
1671	>
1672	>	//push data into siminfo, therefore, we can retrieve later
1673	>	theInfo.addProperty(zconsParaData);
1674		}

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