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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 420 by mmeineke, Thu Mar 27 17:32:03 2003 UTC vs.
Revision 814 by mmeineke, Thu Oct 23 19:57:25 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	<
5	>	#include <string>
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 12 | Line 15 | SimSetup::SimSetup(){
15		#include "mpiSimulation.hpp"
16		#endif
17
18	+	// some defines for ensemble and Forcefield  cases
19	+
20	+	#define NVE_ENS        0
21	+	#define NVT_ENS        1
22	+	#define NPTi_ENS       2
23	+	#define NPTf_ENS       3
24	+	#define 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		SimSetup::SimSetup(){
34	+	isInfoArray = 0;
35	+	nInfo = 1;
36	+
37		stamps = new MakeStamps();
38		globals = new Globals();
39	<
39	>
40	>
41		#ifdef IS_MPI
42	<	strcpy( checkPointMsg, "SimSetup creation successful" );
42	>	strcpy(checkPointMsg, "SimSetup creation successful");
43		MPIcheckPoint();
44		#endif // IS_MPI
45		}
#	Line 27 | Line 49 | void SimSetup::parseFile( char* fileName ){
49		delete globals;
50		}
51
52	<	void SimSetup::parseFile( char* fileName ){
52	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
53	>	info = the_info;
54	>	nInfo = theNinfo;
55	>	isInfoArray = 1;
56	>	}
57
58	+
59	+	void SimSetup::parseFile(char* fileName){
60		#ifdef IS_MPI
61	<	if( worldRank == 0 ){
61	>	if (worldRank == 0){
62		#endif // is_mpi
63	<
63	>
64		inFileName = fileName;
65	<	set_interface_stamps( stamps, globals );
66	<
65	>	set_interface_stamps(stamps, globals);
66	>
67		#ifdef IS_MPI
68		mpiEventInit();
69		#endif
70
71	<	yacc_BASS( fileName );
71	>	yacc_BASS(fileName);
72
73		#ifdef IS_MPI
74		throwMPIEvent(NULL);
75		}
76	<	else receiveParse();
76	>	else{
77	>	receiveParse();
78	>	}
79		#endif
80
81		}
82
83		#ifdef IS_MPI
84		void SimSetup::receiveParse(void){
85	<
86	<	set_interface_stamps( stamps, globals );
87	<	mpiEventInit();
88	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
85	>	set_interface_stamps(stamps, globals);
86	>	mpiEventInit();
87	>	MPIcheckPoint();
88	>	mpiEventLoop();
89		}
90
91		#endif // is_mpi
92
93	<	void SimSetup::createSim( void ){
93	>	void SimSetup::createSim(void){
94
95	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
95	>	// gather all of the information from the Bass file
96
97	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
97	>	gatherInfo();
98
99	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	simnfo->run_time = the_globals->getRunTime();
99	>	// creation of complex system objects
100
101	<	// get the ones we know are there, yet still may need some work.
81	<	n_components = the_globals->getNComponents();
82	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
101	>	sysObjectsCreation();
102
103	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
103	>	// check on the post processing info
104
105	+	finalInfoCheck();
106
107	<	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
92	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
93	<	else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
94	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
95	<	else{
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Error. Unrecognized force field -> %s\n",
98	<	force_field );
99	<	painCave.isFatal = 1;
100	<	simError();
101	<	}
107	>	// initialize the system coordinates
108
109	<	#ifdef IS_MPI
110	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
109	>	if (!isInfoArray){
110	>	initSystemCoords();
111
112	<
112	>	if( !(globals->getUseInitTime()) )
113	>	info[0].currentTime = 0.0;
114	>	}
115
116	<	// get the components and calculate the tot_nMol and indvidual n_mol
111	<	the_components = the_globals->getComponents();
112	<	components_nmol = new int[n_components];
113	<	comp_stamps = new MoleculeStamp*[n_components];
116	>	// make the output filenames
117
118	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
118	>	makeOutNames();
119
120	<	tot_nmol = 0;
120	<	for( i=0; i<n_components; i++ ){
120	>	// make the integrator
121
122	<	if( !the_components[i]->haveNMol() ){
123	<	// we have a problem
124	<	sprintf( painCave.errMsg,
125	<	"SimSetup Error. No global NMol or component NMol"
126	<	" given. Cannot calculate the number of atoms.\n" );
127	<	painCave.isFatal = 1;
128	<	simError();
129	<	}
122	>	makeIntegrator();
123
131	–	tot_nmol += the_components[i]->getNMol();
132	–	components_nmol[i] = the_components[i]->getNMol();
133	–	}
134	–	}
135	–	else{
136	–	sprintf( painCave.errMsg,
137	–	"SimSetup error.\n"
138	–	"\tSorry, the ability to specify total"
139	–	" nMols and then give molfractions in the components\n"
140	–	"\tis not currently supported."
141	–	" Please give nMol in the components.\n" );
142	–	painCave.isFatal = 1;
143	–	simError();
144	–
145	–
146	–	//     tot_nmol = the_globals->getNMol();
147	–
148	–	//   //we have the total number of molecules, now we check for molfractions
149	–	//     for( i=0; i<n_components; i++ ){
150	–
151	–	//       if( !the_components[i]->haveMolFraction() ){
152	–
153	–	//  if( !the_components[i]->haveNMol() ){
154	–	//    //we have a problem
155	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
156	–	//              << " nMol was given in component
157	–
158	–	}
159	–
124		#ifdef IS_MPI
125	<	strcpy( checkPointMsg, "Have the number of components" );
126	<	MPIcheckPoint();
163	<	#endif // is_mpi
125	>	mpiSim->mpiRefresh();
126	>	#endif
127
128	<	// make an array of molecule stamps that match the components used.
166	<	// also extract the used stamps out into a separate linked list
128	>	// initialize the Fortran
129
130	<	simnfo->nComponents = n_components;
131	<	simnfo->componentsNmol = components_nmol;
170	<	simnfo->compStamps = comp_stamps;
171	<	simnfo->headStamp = new LinkedMolStamp();
172	<
173	<	char* id;
174	<	LinkedMolStamp* headStamp = simnfo->headStamp;
175	<	LinkedMolStamp* currentStamp = NULL;
176	<	for( i=0; i<n_components; i++ ){
130	>	initFortran();
131	>	}
132
178	–	id = the_components[i]->getType();
179	–	comp_stamps[i] = NULL;
180	–
181	–	// check to make sure the component isn't already in the list
133
134	<	comp_stamps[i] = headStamp->match( id );
135	<	if( comp_stamps[i] == NULL ){
136	<
137	<	// extract the component from the list;
138	<
139	<	currentStamp = the_stamps->extractMolStamp( id );
140	<	if( currentStamp == NULL ){
141	<	sprintf( painCave.errMsg,
142	<	"SimSetup error: Component \"%s\" was not found in the "
143	<	"list of declared molecules\n",
144	<	id );
194	<	painCave.isFatal = 1;
195	<	simError();
196	<	}
197	<
198	<	headStamp->add( currentStamp );
199	<	comp_stamps[i] = headStamp->match( id );
200	<	}
201	<	}
134	>	void SimSetup::makeMolecules(void){
135	>	int k;
136	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
137	>	molInit molInfo;
138	>	DirectionalAtom* dAtom;
139	>	LinkedAssign* extras;
140	>	LinkedAssign* current_extra;
141	>	AtomStamp* currentAtom;
142	>	BondStamp* currentBond;
143	>	BendStamp* currentBend;
144	>	TorsionStamp* currentTorsion;
145
146	<	#ifdef IS_MPI
147	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
148	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
146	>	bond_pair* theBonds;
147	>	bend_set* theBends;
148	>	torsion_set* theTorsions;
149
150
151	+	//init the forceField paramters
152
153	<	// caclulate the number of atoms, bonds, bends and torsions
153	>	the_ff->readParams();
154
213	–	tot_atoms = 0;
214	–	tot_bonds = 0;
215	–	tot_bends = 0;
216	–	tot_torsions = 0;
217	–	for( i=0; i<n_components; i++ ){
218	–
219	–	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
220	–	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
221	–	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
222	–	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
223	–	}
155
156	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
156	>	// init the atoms
157
158	<	simnfo->n_atoms = tot_atoms;
228	<	simnfo->n_bonds = tot_bonds;
229	<	simnfo->n_bends = tot_bends;
230	<	simnfo->n_torsions = tot_torsions;
231	<	simnfo->n_SRI = tot_SRI;
232	<	simnfo->n_mol = tot_nmol;
158	>	double ux, uy, uz, u, uSqr;
159
160	<
161	<	#ifdef IS_MPI
160	>	for (k = 0; k < nInfo; k++){
161	>	the_ff->setSimInfo(&(info[k]));
162
163	<	// divide the molecules among processors here.
164	<
165	<	mpiSim = new mpiSimulation( simnfo );
166	<
241	<
163	>	atomOffset = 0;
164	>	excludeOffset = 0;
165	>	for (i = 0; i < info[k].n_mol; i++){
166	>	stampID = info[k].molecules[i].getStampID();
167
168	<	globalIndex = mpiSim->divideLabor();
168	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
169	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
170	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
171	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
172	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
173
174	+	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
175	+	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
176	+	molInfo.myBonds = new Bond * [molInfo.nBonds];
177	+	molInfo.myBends = new Bend * [molInfo.nBends];
178	+	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
179
180	+	theBonds = new bond_pair[molInfo.nBonds];
181	+	theBends = new bend_set[molInfo.nBends];
182	+	theTorsions = new torsion_set[molInfo.nTorsions];
183
184	<	// set up the local variables
248	<
249	<	int localMol, allMol;
250	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
251	<
252	<	allMol = 0;
253	<	localMol = 0;
254	<	local_atoms = 0;
255	<	local_bonds = 0;
256	<	local_bends = 0;
257	<	local_torsions = 0;
258	<	for( i=0; i<n_components; i++ ){
184	>	// make the Atoms
185
186	<	for( j=0; j<components_nmol[i]; j++ ){
187	<
188	<	if( mpiSim->getMyMolStart() <= allMol &&
189	<	allMol <= mpiSim->getMyMolEnd() ){
190	<
191	<	local_atoms +=    comp_stamps[i]->getNAtoms();
192	<	local_bonds +=    comp_stamps[i]->getNBonds();
267	<	local_bends +=    comp_stamps[i]->getNBends();
268	<	local_torsions += comp_stamps[i]->getNTorsions();
269	<	localMol++;
270	<	}
271	<	allMol++;
272	<	}
273	<	}
274	<	local_SRI = local_bonds + local_bends + local_torsions;
275	<
186	>	for (j = 0; j < molInfo.nAtoms; j++){
187	>	currentAtom = comp_stamps[stampID]->getAtom(j);
188	>	if (currentAtom->haveOrientation()){
189	>	dAtom = new DirectionalAtom((j + atomOffset),
190	>	info[k].getConfiguration());
191	>	info[k].n_oriented++;
192	>	molInfo.myAtoms[j] = dAtom;
193
194	<	simnfo->n_atoms = mpiSim->getMyNlocal();
195	<
196	<	if( local_atoms != simnfo->n_atoms ){
280	<	sprintf( painCave.errMsg,
281	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282	<	" localAtom (%d) are note equal.\n",
283	<	simnfo->n_atoms,
284	<	local_atoms );
285	<	painCave.isFatal = 1;
286	<	simError();
287	<	}
194	>	ux = currentAtom->getOrntX();
195	>	uy = currentAtom->getOrntY();
196	>	uz = currentAtom->getOrntZ();
197
198	<	simnfo->n_bonds = local_bonds;
290	<	simnfo->n_bends = local_bends;
291	<	simnfo->n_torsions = local_torsions;
292	<	simnfo->n_SRI = local_SRI;
293	<	simnfo->n_mol = localMol;
198	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
199
200	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
201	<	MPIcheckPoint();
202	<
203	<
200	>	u = sqrt(uSqr);
201	>	ux = ux / u;
202	>	uy = uy / u;
203	>	uz = uz / u;
204	>
205	>	dAtom->setSUx(ux);
206	>	dAtom->setSUy(uy);
207	>	dAtom->setSUz(uz);
208	>	}
209	>	else{
210	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
211	>	info[k].getConfiguration());
212	>	}
213	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
214	>
215	>	#ifdef IS_MPI
216	>
217	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
218	>
219		#endif // is_mpi
220	<
220	>	}
221
222	<	// create the atom and short range interaction arrays
222	>	// make the bonds
223	>	for (j = 0; j < molInfo.nBonds; j++){
224	>	currentBond = comp_stamps[stampID]->getBond(j);
225	>	theBonds[j].a = currentBond->getA() + atomOffset;
226	>	theBonds[j].b = currentBond->getB() + atomOffset;
227
228	<	Atom::createArrays(simnfo->n_atoms);
229	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
228	>	exI = theBonds[j].a;
229	>	exJ = theBonds[j].b;
230
231	+	// exclude_I must always be the smaller of the pair
232	+	if (exI > exJ){
233	+	tempEx = exI;
234	+	exI = exJ;
235	+	exJ = tempEx;
236	+	}
237	+	#ifdef IS_MPI
238	+	tempEx = exI;
239	+	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
240	+	tempEx = exJ;
241	+	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
242
243	<	if( simnfo->n_SRI ){
244	<	Exclude::createArray(simnfo->n_SRI);
311	<	the_excludes = new Exclude*[simnfo->n_SRI];
312	<	simnfo->globalExcludes = new int;
313	<	simnfo->n_exclude = tot_SRI;
314	<	}
315	<	else{
316	<
317	<	Exclude::createArray( 1 );
318	<	the_excludes = new Exclude*;
319	<	the_excludes[0] = new Exclude(0);
320	<	the_excludes[0]->setPair( 0,0 );
321	<	simnfo->globalExcludes = new int;
322	<	simnfo->globalExcludes[0] = 0;
323	<	simnfo->n_exclude = 0;
324	<	}
243	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
244	>	#else  // isn't MPI
245
246	<	// set the arrays into the SimInfo object
246	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
247	>	#endif  //is_mpi
248	>	}
249	>	excludeOffset += molInfo.nBonds;
250
251	<	simnfo->atoms = the_atoms;
252	<	simnfo->sr_interactions = the_sris;
253	<	simnfo->nGlobalExcludes = 0;
254	<	simnfo->excludes = the_excludes;
251	>	//make the bends
252	>	for (j = 0; j < molInfo.nBends; j++){
253	>	currentBend = comp_stamps[stampID]->getBend(j);
254	>	theBends[j].a = currentBend->getA() + atomOffset;
255	>	theBends[j].b = currentBend->getB() + atomOffset;
256	>	theBends[j].c = currentBend->getC() + atomOffset;
257
258	+	if (currentBend->haveExtras()){
259	+	extras = currentBend->getExtras();
260	+	current_extra = extras;
261
262	<	// get some of the tricky things that may still be in the globals
262	>	while (current_extra != NULL){
263	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
264	>	switch (current_extra->getType()){
265	>	case 0:
266	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
267	>	theBends[j].isGhost = 1;
268	>	break;
269
270	<
271	<	if( the_globals->haveBox() ){
272	<	simnfo->box_x = the_globals->getBox();
273	<	simnfo->box_y = the_globals->getBox();
274	<	simnfo->box_z = the_globals->getBox();
341	<	}
342	<	else if( the_globals->haveDensity() ){
270	>	case 1:
271	>	theBends[j].ghost = (int) current_extra->getDouble() +
272	>	atomOffset;
273	>	theBends[j].isGhost = 1;
274	>	break;
275
276	<	double vol;
277	<	vol = (double)tot_nmol / the_globals->getDensity();
278	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
279	<	simnfo->box_y = simnfo->box_x;
280	<	simnfo->box_z = simnfo->box_x;
281	<	}
282	<	else{
283	<	if( !the_globals->haveBoxX() ){
284	<	sprintf( painCave.errMsg,
285	<	"SimSetup error, no periodic BoxX size given.\n" );
286	<	painCave.isFatal = 1;
287	<	simError();
288	<	}
289	<	simnfo->box_x = the_globals->getBoxX();
276	>	default:
277	>	sprintf(painCave.errMsg,
278	>	"SimSetup Error: ghostVectorSource was neither a "
279	>	"double nor an int.\n"
280	>	"-->Bend[%d] in %s\n",
281	>	j, comp_stamps[stampID]->getID());
282	>	painCave.isFatal = 1;
283	>	simError();
284	>	}
285	>	}
286	>	else{
287	>	sprintf(painCave.errMsg,
288	>	"SimSetup Error: unhandled bend assignment:\n"
289	>	"    -->%s in Bend[%d] in %s\n",
290	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
291	>	painCave.isFatal = 1;
292	>	simError();
293	>	}
294
295	<	if( !the_globals->haveBoxY() ){
296	<	sprintf( painCave.errMsg,
297	<	"SimSetup error, no periodic BoxY size given.\n" );
362	<	painCave.isFatal = 1;
363	<	simError();
364	<	}
365	<	simnfo->box_y = the_globals->getBoxY();
295	>	current_extra = current_extra->getNext();
296	>	}
297	>	}
298
299	<	if( !the_globals->haveBoxZ() ){
300	<	sprintf( painCave.errMsg,
301	<	"SimSetup error, no periodic BoxZ size given.\n" );
302	<	painCave.isFatal = 1;
303	<	simError();
304	<	}
305	<	simnfo->box_z = the_globals->getBoxZ();
306	<	}
299	>	if (!theBends[j].isGhost){
300	>	exI = theBends[j].a;
301	>	exJ = theBends[j].c;
302	>	}
303	>	else{
304	>	exI = theBends[j].a;
305	>	exJ = theBends[j].b;
306	>	}
307
308	+	// exclude_I must always be the smaller of the pair
309	+	if (exI > exJ){
310	+	tempEx = exI;
311	+	exI = exJ;
312	+	exJ = tempEx;
313	+	}
314		#ifdef IS_MPI
315	<	strcpy( checkPointMsg, "Box size set up" );
316	<	MPIcheckPoint();
317	<	#endif // is_mpi
315	>	tempEx = exI;
316	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
317	>	tempEx = exJ;
318	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
319
320	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
321	+	#else  // isn't MPI
322	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
323	+	#endif  //is_mpi
324	+	}
325	+	excludeOffset += molInfo.nBends;
326
327	<	// initialize the arrays
327	>	for (j = 0; j < molInfo.nTorsions; j++){
328	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
329	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
330	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
331	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
332	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
333
334	<	the_ff->setSimInfo( simnfo );
334	>	exI = theTorsions[j].a;
335	>	exJ = theTorsions[j].d;
336
337	<	makeAtoms();
338	<	simnfo->identArray = new int[simnfo->n_atoms];
339	<	for(i=0; i<simnfo->n_atoms; i++){
340	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
341	<	}
342	<
343	<	if( tot_bonds ){
344	<	makeBonds();
345	<	}
337	>	// exclude_I must always be the smaller of the pair
338	>	if (exI > exJ){
339	>	tempEx = exI;
340	>	exI = exJ;
341	>	exJ = tempEx;
342	>	}
343	>	#ifdef IS_MPI
344	>	tempEx = exI;
345	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
346	>	tempEx = exJ;
347	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
348	>
349	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
350	>	#else  // isn't MPI
351	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
352	>	#endif  //is_mpi
353	>	}
354	>	excludeOffset += molInfo.nTorsions;
355	>
356	>
357	>	// send the arrays off to the forceField for init.
358	>
359	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
360	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
361	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
362	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
363	>	theTorsions);
364
396	–	if( tot_bends ){
397	–	makeBends();
398	–	}
365
366	<	if( tot_torsions ){
401	<	makeTorsions();
402	<	}
366	>	info[k].molecules[i].initialize(molInfo);
367
368
369	<	if (the_globals->getUseRF() ) {
370	<	simnfo->useReactionField = 1;
371	<
372	<	if( !the_globals->haveECR() ){
409	<	sprintf( painCave.errMsg,
410	<	"SimSetup Warning: using default value of 1/2 the smallest "
411	<	"box length for the electrostaticCutoffRadius.\n"
412	<	"I hope you have a very fast processor!\n");
413	<	painCave.isFatal = 0;
414	<	simError();
415	<	double smallest;
416	<	smallest = simnfo->box_x;
417	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
418	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
419	<	simnfo->ecr = 0.5 * smallest;
420	<	} else {
421	<	simnfo->ecr        = the_globals->getECR();
369	>	atomOffset += molInfo.nAtoms;
370	>	delete[] theBonds;
371	>	delete[] theBends;
372	>	delete[] theTorsions;
373		}
374	+	}
375
424	–	if( !the_globals->haveEST() ){
425	–	sprintf( painCave.errMsg,
426	–	"SimSetup Warning: using default value of 0.05 * the "
427	–	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
428	–	);
429	–	painCave.isFatal = 0;
430	–	simError();
431	–	simnfo->est = 0.05 * simnfo->ecr;
432	–	} else {
433	–	simnfo->est        = the_globals->getEST();
434	–	}
435	–
436	–	if(!the_globals->haveDielectric() ){
437	–	sprintf( painCave.errMsg,
438	–	"SimSetup Error: You are trying to use Reaction Field without"
439	–	"setting a dielectric constant!\n"
440	–	);
441	–	painCave.isFatal = 1;
442	–	simError();
443	–	}
444	–	simnfo->dielectric = the_globals->getDielectric();
445	–	} else {
446	–	if (simnfo->n_dipoles) {
447	–
448	–	if( !the_globals->haveECR() ){
449	–	sprintf( painCave.errMsg,
450	–	"SimSetup Warning: using default value of 1/2 the smallest"
451	–	"box length for the electrostaticCutoffRadius.\n"
452	–	"I hope you have a very fast processor!\n");
453	–	painCave.isFatal = 0;
454	–	simError();
455	–	double smallest;
456	–	smallest = simnfo->box_x;
457	–	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
458	–	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
459	–	simnfo->ecr = 0.5 * smallest;
460	–	} else {
461	–	simnfo->ecr        = the_globals->getECR();
462	–	}
463	–
464	–	if( !the_globals->haveEST() ){
465	–	sprintf( painCave.errMsg,
466	–	"SimSetup Warning: using default value of 5% of the"
467	–	"electrostaticCutoffRadius for the "
468	–	"electrostaticSkinThickness\n"
469	–	);
470	–	painCave.isFatal = 0;
471	–	simError();
472	–	simnfo->est = 0.05 * simnfo->ecr;
473	–	} else {
474	–	simnfo->est        = the_globals->getEST();
475	–	}
476	–	}
477	–	}
478	–
376		#ifdef IS_MPI
377	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
377	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
378		MPIcheckPoint();
379		#endif // is_mpi
380
381	<	if( the_globals->haveInitialConfig() ){
485	<
486	<	InitializeFromFile* fileInit;
487	<	#ifdef IS_MPI // is_mpi
488	<	if( worldRank == 0 ){
489	<	#endif //is_mpi
490	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
491	<	#ifdef IS_MPI
492	<	}else fileInit = new InitializeFromFile( NULL );
493	<	#endif
494	<	fileInit->read_xyz( simnfo ); // default velocities on
381	>	// clean up the forcefield
382
383	<	delete fileInit;
384	<	}
385	<	else{
383	>	the_ff->calcRcut();
384	>	the_ff->cleanMe();
385	>	}
386
387	<	#ifdef IS_MPI
387	>	void SimSetup::initFromBass(void){
388	>	int i, j, k;
389	>	int n_cells;
390	>	double cellx, celly, cellz;
391	>	double temp1, temp2, temp3;
392	>	int n_per_extra;
393	>	int n_extra;
394	>	int have_extra, done;
395
396	<	// no init from bass
397	<
398	<	sprintf( painCave.errMsg,
399	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
506	<	painCave.isFatal;
507	<	simError();
508	<
509	<	#else
396	>	double vel[3];
397	>	vel[0] = 0.0;
398	>	vel[1] = 0.0;
399	>	vel[2] = 0.0;
400
401	<	initFromBass();
401	>	temp1 = (double) tot_nmol / 4.0;
402	>	temp2 = pow(temp1, (1.0 / 3.0));
403	>	temp3 = ceil(temp2);
404
405	+	have_extra = 0;
406	+	if (temp2 < temp3){
407	+	// we have a non-complete lattice
408	+	have_extra = 1;
409
410	<	#endif
411	<	}
410	>	n_cells = (int) temp3 - 1;
411	>	cellx = info[0].boxL[0] / temp3;
412	>	celly = info[0].boxL[1] / temp3;
413	>	cellz = info[0].boxL[2] / temp3;
414	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
415	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
416	>	n_per_extra = (int) ceil(temp1);
417
418	<	#ifdef IS_MPI
419	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
420	<	MPIcheckPoint();
421	<	#endif // is_mpi
422	<
423	<
523	<
524	<
525	<
526	<
527	<
528	<	#ifdef IS_MPI
529	<	if( worldRank == 0 ){
530	<	#endif // is_mpi
531	<
532	<	if( the_globals->haveFinalConfig() ){
533	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
418	>	if (n_per_extra > 4){
419	>	sprintf(painCave.errMsg,
420	>	"SimSetup error. There has been an error in constructing"
421	>	" the non-complete lattice.\n");
422	>	painCave.isFatal = 1;
423	>	simError();
424		}
535	–	else{
536	–	strcpy( simnfo->finalName, inFileName );
537	–	char* endTest;
538	–	int nameLength = strlen( simnfo->finalName );
539	–	endTest = &(simnfo->finalName[nameLength - 5]);
540	–	if( !strcmp( endTest, ".bass" ) ){
541	–	strcpy( endTest, ".eor" );
542	–	}
543	–	else if( !strcmp( endTest, ".BASS" ) ){
544	–	strcpy( endTest, ".eor" );
545	–	}
546	–	else{
547	–	endTest = &(simnfo->finalName[nameLength - 4]);
548	–	if( !strcmp( endTest, ".bss" ) ){
549	–	strcpy( endTest, ".eor" );
550	–	}
551	–	else if( !strcmp( endTest, ".mdl" ) ){
552	–	strcpy( endTest, ".eor" );
553	–	}
554	–	else{
555	–	strcat( simnfo->finalName, ".eor" );
556	–	}
557	–	}
558	–	}
559	–
560	–	// make the sample and status out names
561	–
562	–	strcpy( simnfo->sampleName, inFileName );
563	–	char* endTest;
564	–	int nameLength = strlen( simnfo->sampleName );
565	–	endTest = &(simnfo->sampleName[nameLength - 5]);
566	–	if( !strcmp( endTest, ".bass" ) ){
567	–	strcpy( endTest, ".dump" );
568	–	}
569	–	else if( !strcmp( endTest, ".BASS" ) ){
570	–	strcpy( endTest, ".dump" );
571	–	}
572	–	else{
573	–	endTest = &(simnfo->sampleName[nameLength - 4]);
574	–	if( !strcmp( endTest, ".bss" ) ){
575	–	strcpy( endTest, ".dump" );
576	–	}
577	–	else if( !strcmp( endTest, ".mdl" ) ){
578	–	strcpy( endTest, ".dump" );
579	–	}
580	–	else{
581	–	strcat( simnfo->sampleName, ".dump" );
582	–	}
583	–	}
584	–
585	–	strcpy( simnfo->statusName, inFileName );
586	–	nameLength = strlen( simnfo->statusName );
587	–	endTest = &(simnfo->statusName[nameLength - 5]);
588	–	if( !strcmp( endTest, ".bass" ) ){
589	–	strcpy( endTest, ".stat" );
590	–	}
591	–	else if( !strcmp( endTest, ".BASS" ) ){
592	–	strcpy( endTest, ".stat" );
593	–	}
594	–	else{
595	–	endTest = &(simnfo->statusName[nameLength - 4]);
596	–	if( !strcmp( endTest, ".bss" ) ){
597	–	strcpy( endTest, ".stat" );
598	–	}
599	–	else if( !strcmp( endTest, ".mdl" ) ){
600	–	strcpy( endTest, ".stat" );
601	–	}
602	–	else{
603	–	strcat( simnfo->statusName, ".stat" );
604	–	}
605	–	}
606	–
607	–	#ifdef IS_MPI
425		}
609	–	#endif // is_mpi
610	–
611	–	// set the status, sample, and themal kick times
612	–
613	–	if( the_globals->haveSampleTime() ){
614	–	simnfo->sampleTime = the_globals->getSampleTime();
615	–	simnfo->statusTime = simnfo->sampleTime;
616	–	simnfo->thermalTime = simnfo->sampleTime;
617	–	}
426		else{
427	<	simnfo->sampleTime = the_globals->getRunTime();
428	<	simnfo->statusTime = simnfo->sampleTime;
429	<	simnfo->thermalTime = simnfo->sampleTime;
427	>	n_cells = (int) temp3;
428	>	cellx = info[0].boxL[0] / temp3;
429	>	celly = info[0].boxL[1] / temp3;
430	>	cellz = info[0].boxL[2] / temp3;
431		}
432
433	<	if( the_globals->haveStatusTime() ){
434	<	simnfo->statusTime = the_globals->getStatusTime();
433	>	current_mol = 0;
434	>	current_comp_mol = 0;
435	>	current_comp = 0;
436	>	current_atom_ndx = 0;
437	>
438	>	for (i = 0; i < n_cells ; i++){
439	>	for (j = 0; j < n_cells; j++){
440	>	for (k = 0; k < n_cells; k++){
441	>	makeElement(i * cellx, j * celly, k * cellz);
442	>
443	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
444	>
445	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
446	>
447	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
448	>	}
449	>	}
450		}
451
452	<	if( the_globals->haveThermalTime() ){
453	<	simnfo->thermalTime = the_globals->getThermalTime();
452	>	if (have_extra){
453	>	done = 0;
454	>
455	>	int start_ndx;
456	>	for (i = 0; i < (n_cells + 1) && !done; i++){
457	>	for (j = 0; j < (n_cells + 1) && !done; j++){
458	>	if (i < n_cells){
459	>	if (j < n_cells){
460	>	start_ndx = n_cells;
461	>	}
462	>	else
463	>	start_ndx = 0;
464	>	}
465	>	else
466	>	start_ndx = 0;
467	>
468	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
469	>	makeElement(i * cellx, j * celly, k * cellz);
470	>	done = (current_mol >= tot_nmol);
471	>
472	>	if (!done && n_per_extra > 1){
473	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
474	>	k * cellz);
475	>	done = (current_mol >= tot_nmol);
476	>	}
477	>
478	>	if (!done && n_per_extra > 2){
479	>	makeElement(i * cellx, j * celly + 0.5 * celly,
480	>	k * cellz + 0.5 * cellz);
481	>	done = (current_mol >= tot_nmol);
482	>	}
483	>
484	>	if (!done && n_per_extra > 3){
485	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
486	>	k * cellz + 0.5 * cellz);
487	>	done = (current_mol >= tot_nmol);
488	>	}
489	>	}
490	>	}
491	>	}
492		}
493
494	<	// check for the temperature set flag
494	>	for (i = 0; i < info[0].n_atoms; i++){
495	>	info[0].atoms[i]->setVel(vel);
496	>	}
497	>	}
498
499	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
499	>	void SimSetup::makeElement(double x, double y, double z){
500	>	int k;
501	>	AtomStamp* current_atom;
502	>	DirectionalAtom* dAtom;
503	>	double rotMat[3][3];
504	>	double pos[3];
505
506	+	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
507	+	current_atom = comp_stamps[current_comp]->getAtom(k);
508	+	if (!current_atom->havePosition()){
509	+	sprintf(painCave.errMsg,
510	+	"SimSetup:initFromBass error.\n"
511	+	"\tComponent %s, atom %s does not have a position specified.\n"
512	+	"\tThe initialization routine is unable to give a start"
513	+	" position.\n",
514	+	comp_stamps[current_comp]->getID(), current_atom->getType());
515	+	painCave.isFatal = 1;
516	+	simError();
517	+	}
518
519	<	//   // make the longe range forces and the integrator
519	>	pos[0] = x + current_atom->getPosX();
520	>	pos[1] = y + current_atom->getPosY();
521	>	pos[2] = z + current_atom->getPosZ();
522
523	<	//   new AllLong( simnfo );
523	>	info[0].atoms[current_atom_ndx]->setPos(pos);
524
525	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
526	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
643	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
644	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
525	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
526	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
527
528	+	rotMat[0][0] = 1.0;
529	+	rotMat[0][1] = 0.0;
530	+	rotMat[0][2] = 0.0;
531
532	+	rotMat[1][0] = 0.0;
533	+	rotMat[1][1] = 1.0;
534	+	rotMat[1][2] = 0.0;
535
536	<	// initialize the Fortran
537	<
538	<	simnfo->refreshSim();
539	<
540	<	if( !strcmp( simnfo->mixingRule, "standard") ){
541	<	the_ff->initForceField( LB_MIXING_RULE );
536	>	rotMat[2][0] = 0.0;
537	>	rotMat[2][1] = 0.0;
538	>	rotMat[2][2] = 1.0;
539	>
540	>	dAtom->setA(rotMat);
541	>	}
542	>
543	>	current_atom_ndx++;
544		}
545	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
546	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
545	>
546	>	current_mol++;
547	>	current_comp_mol++;
548	>
549	>	if (current_comp_mol >= components_nmol[current_comp]){
550	>	current_comp_mol = 0;
551	>	current_comp++;
552		}
553	+	}
554	+
555	+
556	+	void SimSetup::gatherInfo(void){
557	+	int i;
558	+
559	+	ensembleCase = -1;
560	+	ffCase = -1;
561	+
562	+	// set the easy ones first
563	+
564	+	for (i = 0; i < nInfo; i++){
565	+	info[i].target_temp = globals->getTargetTemp();
566	+	info[i].dt = globals->getDt();
567	+	info[i].run_time = globals->getRunTime();
568	+	}
569	+	n_components = globals->getNComponents();
570	+
571	+
572	+	// get the forceField
573	+
574	+	strcpy(force_field, globals->getForceField());
575	+
576	+	if (!strcasecmp(force_field, "DUFF")){
577	+	ffCase = FF_DUFF;
578	+	}
579	+	else if (!strcasecmp(force_field, "LJ")){
580	+	ffCase = FF_LJ;
581	+	}
582	+	else if (!strcasecmp(force_field, "EAM")){
583	+	ffCase = FF_EAM;
584	+	}
585		else{
586	<	sprintf( painCave.errMsg,
587	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
588	<	simnfo->mixingRule );
589	<	painCave.isFatal = 1;
663	<	simError();
586	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
587	>	force_field);
588	>	painCave.isFatal = 1;
589	>	simError();
590		}
591
592	+	// get the ensemble
593
594	<	#ifdef IS_MPI
668	<	strcpy( checkPointMsg,
669	<	"Successfully intialized the mixingRule for Fortran." );
670	<	MPIcheckPoint();
671	<	#endif // is_mpi
672	<	}
594	>	strcpy(ensemble, globals->getEnsemble());
595
596	+	if (!strcasecmp(ensemble, "NVE")){
597	+	ensembleCase = NVE_ENS;
598	+	}
599	+	else if (!strcasecmp(ensemble, "NVT")){
600	+	ensembleCase = NVT_ENS;
601	+	}
602	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
603	+	ensembleCase = NPTi_ENS;
604	+	}
605	+	else if (!strcasecmp(ensemble, "NPTf")){
606	+	ensembleCase = NPTf_ENS;
607	+	}
608	+	else if (!strcasecmp(ensemble, "NPTxyz")){
609	+	ensembleCase = NPTxyz_ENS;
610	+	}
611	+	else{
612	+	sprintf(painCave.errMsg,
613	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
614	+	"reverting to NVE for this simulation.\n",
615	+	ensemble);
616	+	painCave.isFatal = 0;
617	+	simError();
618	+	strcpy(ensemble, "NVE");
619	+	ensembleCase = NVE_ENS;
620	+	}
621
622	<	void SimSetup::makeMolecules( void ){
622	>	for (i = 0; i < nInfo; i++){
623	>	strcpy(info[i].ensemble, ensemble);
624
625	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
678	<	molInit info;
679	<	DirectionalAtom* dAtom;
680	<	LinkedAssign* extras;
681	<	LinkedAssign* current_extra;
682	<	AtomStamp* currentAtom;
683	<	BondStamp* currentBond;
684	<	BendStamp* currentBend;
685	<	TorsionStamp* currentTorsion;
686	<
687	<	//init the forceField paramters
625	>	// get the mixing rule
626
627	<	the_ff->readParams();
627	>	strcpy(info[i].mixingRule, globals->getMixingRule());
628	>	info[i].usePBC = globals->getPBC();
629	>	}
630
631	<
692	<	// init the molecules
631	>	// get the components and calculate the tot_nMol and indvidual n_mol
632
633	<	atomOffset = 0;
634	<	excludeOffset = 0;
696	<	for(i=0; i<simnfo->n_mol; i++){
697	<
698	<	stampID = the_molecules[i].getStampID();
633	>	the_components = globals->getComponents();
634	>	components_nmol = new int[n_components];
635
700	–	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
701	–	info.nBonds    = comp_stamps[stampID]->getNBonds();
702	–	info.nBends    = comp_stamps[stampID]->getNBends();
703	–	info.nTorsions = comp_stamps[stampID]->getNTorsions();
704	–	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
636
637	<	info.myAtoms = &the_atoms[atomOffset];
638	<	info.myExcludes = &the_excludes[excludeOffset];
639	<	info.myBonds = new Bond*[info.nBonds];
709	<	info.myBends = new Bend*[info.nBends];
710	<	info.myTorsions = new Torsions*[info.nTorsions];
637	>	if (!globals->haveNMol()){
638	>	// we don't have the total number of molecules, so we assume it is
639	>	// given in each component
640
641	<	theBonds = new bond_pair[info.nBonds];
642	<	theBends = new bend_set[info.nBends];
643	<	theTorsions = new torsion_set[info.nTorsions];
644	<
645	<	// make the Atoms
646	<
647	<	for(j=0; j<info.nAtoms; j++){
648	<
649	<	currentAtom = theComponents[stampID]->getAtom( j );
721	<	if( currentAtom->haveOrientation() ){
722	<
723	<	dAtom = new DirectionalAtom(j + atomOffset);
724	<	simnfo->n_oriented++;
725	<	info.myAtoms[j] = dAtom;
726	<
727	<	ux = currentAtom->getOrntX();
728	<	uy = currentAtom->getOrntY();
729	<	uz = currentAtom->getOrntZ();
730	<
731	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
732	<
733	<	u = sqrt( uSqr );
734	<	ux = ux / u;
735	<	uy = uy / u;
736	<	uz = uz / u;
737	<
738	<	dAtom->setSUx( ux );
739	<	dAtom->setSUy( uy );
740	<	dAtom->setSUz( uz );
641	>	tot_nmol = 0;
642	>	for (i = 0; i < n_components; i++){
643	>	if (!the_components[i]->haveNMol()){
644	>	// we have a problem
645	>	sprintf(painCave.errMsg,
646	>	"SimSetup Error. No global NMol or component NMol"
647	>	" given. Cannot calculate the number of atoms.\n");
648	>	painCave.isFatal = 1;
649	>	simError();
650		}
742	–	else{
743	–	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
744	–	}
745	–	info.myAtoms[j]->setType( currentAtom->getType() );
746	–
747	–	#ifdef IS_MPI
748	–
749	–	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
750	–
751	–	#endif // is_mpi
752	–	}
753	–
754	–	// make the bonds
755	–	for(j=0; j<info.nBonds; j++){
756	–
757	–	currentBond = comp_stamps[stampID]->getBond( j );
758	–	theBonds[j].a = currentBond->getA() + atomOffset;
759	–	theBonds[j].b = currentBond->getB() + atomOffset;
651
652	<	exI = theBonds[i].a;
653	<	exJ = theBonds[i].b;
652	>	tot_nmol += the_components[i]->getNMol();
653	>	components_nmol[i] = the_components[i]->getNMol();
654	>	}
655	>	}
656	>	else{
657	>	sprintf(painCave.errMsg,
658	>	"SimSetup error.\n"
659	>	"\tSorry, the ability to specify total"
660	>	" nMols and then give molfractions in the components\n"
661	>	"\tis not currently supported."
662	>	" Please give nMol in the components.\n");
663	>	painCave.isFatal = 1;
664	>	simError();
665	>	}
666
667	<	// exclude_I must always be the smaller of the pair
668	<	if( exI > exJ ){
669	<	tempEx = exI;
670	<	exI = exJ;
671	<	exJ = tempEx;
672	<	}
673	<	#ifdef IS_MPI
771	<	tempEx = exI;
772	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
773	<	tempEx = exJ;
774	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
775	<
776	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
777	<	#else  // isn't MPI
778	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
779	<	#endif  //is_mpi
667	>	// set the status, sample, and thermal kick times
668	>
669	>	for (i = 0; i < nInfo; i++){
670	>	if (globals->haveSampleTime()){
671	>	info[i].sampleTime = globals->getSampleTime();
672	>	info[i].statusTime = info[i].sampleTime;
673	>	info[i].thermalTime = info[i].sampleTime;
674		}
675	<	excludeOffset += info.nBonds;
675	>	else{
676	>	info[i].sampleTime = globals->getRunTime();
677	>	info[i].statusTime = info[i].sampleTime;
678	>	info[i].thermalTime = info[i].sampleTime;
679	>	}
680
681	<	//make the bends
682	<	for(j=0; j<info.nBends; j++){
785	<
786	<	currentBend = comp_stamps[stampID]->getBend( j );
787	<	theBends[j].a = currentBend->getA() + atomOffset;
788	<	theBends[j].b = currentBend->getB() + atomOffset;
789	<	theBends[j].c = currentBend->getC() + atomOffset;
790	<
791	<	if( currentBend->haveExtras() ){
792	<
793	<	extras = current_bend->getExtras();
794	<	current_extra = extras;
795	<
796	<	while( current_extra != NULL ){
797	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
798	<
799	<	switch( current_extra->getType() ){
800	<
801	<	case 0:
802	<	theBends[j].ghost =
803	<	current_extra->getInt() + atomOffset;
804	<	theBends[j].isGhost = 1;
805	<	break;
806	<
807	<	case 1:
808	<	theBends[j].ghost =
809	<	(int)current_extra->getDouble() + atomOffset;
810	<	theBends[j].isGhost = 1;
811	<	break;
812	<
813	<	default:
814	<	sprintf( painCave.errMsg,
815	<	"SimSetup Error: ghostVectorSource was neiter a "
816	<	"double nor an int.\n"
817	<	"-->Bend[%d] in %s\n",
818	<	j, comp_stamps[stampID]->getID() );
819	<	painCave.isFatal = 1;
820	<	simError();
821	<	}
822	<	}
823	<
824	<	else{
825	<
826	<	sprintf( painCave.errMsg,
827	<	"SimSetup Error: unhandled bend assignment:\n"
828	<	"    -->%s in Bend[%d] in %s\n",
829	<	current_extra->getlhs(),
830	<	j, comp_stamps[stampID]->getID() );
831	<	painCave.isFatal = 1;
832	<	simError();
833	<	}
834	<
835	<	current_extra = current_extra->getNext();
836	<	}
837	<	}
838	<
839	<	if( !theBends[j].isGhost ){
840	<
841	<	exI = theBends[j].a;
842	<	exJ = theBends[j].c;
843	<	}
844	<	else{
845	<
846	<	exI = theBends[j].a;
847	<	exJ = theBends[j].b;
848	<	}
849	<
850	<	// exclude_I must always be the smaller of the pair
851	<	if( exI > exJ ){
852	<	tempEx = exI;
853	<	exI = exJ;
854	<	exJ = tempEx;
855	<	}
856	<	#ifdef IS_MPI
857	<	tempEx = exI;
858	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
859	<	tempEx = exJ;
860	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
861	<
862	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
863	<	#else  // isn't MPI
864	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
865	<	#endif  //is_mpi
681	>	if (globals->haveStatusTime()){
682	>	info[i].statusTime = globals->getStatusTime();
683		}
867	–	excludeOffset += info.nBends;
684
685	<	for(j=0; j<info.nTorsions; j++){
686	<
687	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
872	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
873	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
874	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
875	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
876	<
877	<	exI = theTorsions[j].a;
878	<	exJ = theTorsions[j].d;
685	>	if (globals->haveThermalTime()){
686	>	info[i].thermalTime = globals->getThermalTime();
687	>	}
688
689	<	// exclude_I must always be the smaller of the pair
690	<	if( exI > exJ ){
691	<	tempEx = exI;
692	<	exI = exJ;
884	<	exJ = tempEx;
885	<	}
886	<	#ifdef IS_MPI
887	<	tempEx = exI;
888	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
889	<	tempEx = exJ;
890	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
891	<
892	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
893	<	#else  // isn't MPI
894	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
895	<	#endif  //is_mpi
689	>	info[i].resetIntegrator = 0;
690	>	if( globals->haveResetTime() ){
691	>	info[i].resetTime = globals->getResetTime();
692	>	info[i].resetIntegrator = 1;
693		}
897	–	excludeOffset += info.nTorsions;
694
695	<
900	<	// send the arrays off to the forceField for init.
695	>	// check for the temperature set flag
696
697	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
698	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
904	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
905	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
697	>	if (globals->haveTempSet())
698	>	info[i].setTemp = globals->getTempSet();
699
700	+	// get some of the tricky things that may still be in the globals
701
702	<	the_molecules[i].initialize( info );
703	<	atomOffset += info.nAtoms;
704	<	}
702	>	double boxVector[3];
703	>	if (globals->haveBox()){
704	>	boxVector[0] = globals->getBox();
705	>	boxVector[1] = globals->getBox();
706	>	boxVector[2] = globals->getBox();
707
708	<	// clean up the forcefield
709	<	the_ff->calcRcut();
710	<	the_ff->cleanMe();
711	<	}
708	>	info[i].setBox(boxVector);
709	>	}
710	>	else if (globals->haveDensity()){
711	>	double vol;
712	>	vol = (double) tot_nmol / globals->getDensity();
713	>	boxVector[0] = pow(vol, (1.0 / 3.0));
714	>	boxVector[1] = boxVector[0];
715	>	boxVector[2] = boxVector[0];
716
717	<	void SimSetup::initFromBass( void ){
717	>	info[i].setBox(boxVector);
718	>	}
719	>	else{
720	>	if (!globals->haveBoxX()){
721	>	sprintf(painCave.errMsg,
722	>	"SimSetup error, no periodic BoxX size given.\n");
723	>	painCave.isFatal = 1;
724	>	simError();
725	>	}
726	>	boxVector[0] = globals->getBoxX();
727
728	<	int i, j, k;
729	<	int n_cells;
730	<	double cellx, celly, cellz;
731	<	double temp1, temp2, temp3;
732	<	int n_per_extra;
733	<	int n_extra;
734	<	int have_extra, done;
728	>	if (!globals->haveBoxY()){
729	>	sprintf(painCave.errMsg,
730	>	"SimSetup error, no periodic BoxY size given.\n");
731	>	painCave.isFatal = 1;
732	>	simError();
733	>	}
734	>	boxVector[1] = globals->getBoxY();
735
736	<	temp1 = (double)tot_nmol / 4.0;
737	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
738	<	temp3 = ceil( temp2 );
736	>	if (!globals->haveBoxZ()){
737	>	sprintf(painCave.errMsg,
738	>	"SimSetup error, no periodic BoxZ size given.\n");
739	>	painCave.isFatal = 1;
740	>	simError();
741	>	}
742	>	boxVector[2] = globals->getBoxZ();
743
744	<	have_extra =0;
932	<	if( temp2 < temp3 ){ // we have a non-complete lattice
933	<	have_extra =1;
934	<
935	<	n_cells = (int)temp3 - 1;
936	<	cellx = simnfo->box_x / temp3;
937	<	celly = simnfo->box_y / temp3;
938	<	cellz = simnfo->box_z / temp3;
939	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
940	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
941	<	n_per_extra = (int)ceil( temp1 );
942	<
943	<	if( n_per_extra > 4){
944	<	sprintf( painCave.errMsg,
945	<	"SimSetup error. There has been an error in constructing"
946	<	" the non-complete lattice.\n" );
947	<	painCave.isFatal = 1;
948	<	simError();
744	>	info[i].setBox(boxVector);
745		}
746		}
951	–	else{
952	–	n_cells = (int)temp3;
953	–	cellx = simnfo->box_x / temp3;
954	–	celly = simnfo->box_y / temp3;
955	–	cellz = simnfo->box_z / temp3;
956	–	}
747
748	<	current_mol = 0;
749	<	current_comp_mol = 0;
960	<	current_comp = 0;
961	<	current_atom_ndx = 0;
748	>	//setup seed for random number generator
749	>	int seedValue;
750
751	<	for( i=0; i < n_cells ; i++ ){
752	<	for( j=0; j < n_cells; j++ ){
965	<	for( k=0; k < n_cells; k++ ){
751	>	if (globals->haveSeed()){
752	>	seedValue = globals->getSeed();
753
754	<	makeElement( i * cellx,
755	<	j * celly,
756	<	k * cellz );
757	<
758	<	makeElement( i * cellx + 0.5 * cellx,
759	<	j * celly + 0.5 * celly,
973	<	k * cellz );
974	<
975	<	makeElement( i * cellx,
976	<	j * celly + 0.5 * celly,
977	<	k * cellz + 0.5 * cellz );
754	>	if(seedValue / 1E9 == 0){
755	>	sprintf(painCave.errMsg,
756	>	"Seed for sprng library should contain at least 9 digits\n"
757	>	"OOPSE will generate a seed for user\n");
758	>	painCave.isFatal = 0;
759	>	simError();
760
761	<	makeElement( i * cellx + 0.5 * cellx,
762	<	j * celly,
763	<	k * cellz + 0.5 * cellz );
761	>	//using seed generated by system instead of invalid seed set by user
762	>	#ifndef IS_MPI
763	>	seedValue = make_sprng_seed();
764	>	#else
765	>	if (worldRank == 0){
766	>	seedValue = make_sprng_seed();
767		}
768	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
769	+	#endif
770		}
771	+	}//end of if branch of globals->haveSeed()
772	+	else{
773	+
774	+	#ifndef IS_MPI
775	+	seedValue = make_sprng_seed();
776	+	#else
777	+	if (worldRank == 0){
778	+	seedValue = make_sprng_seed();
779	+	}
780	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
781	+	#endif
782	+	}//end of globals->haveSeed()
783	+
784	+	for (int i = 0; i < nInfo; i++){
785	+	info[i].setSeed(seedValue);
786		}
787
788	<	if( have_extra ){
789	<	done = 0;
788	>	#ifdef IS_MPI
789	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
790	>	MPIcheckPoint();
791	>	#endif // is_mpi
792	>	}
793
989	–	int start_ndx;
990	–	for( i=0; i < (n_cells+1) && !done; i++ ){
991	–	for( j=0; j < (n_cells+1) && !done; j++ ){
794
795	<	if( i < n_cells ){
795	>	void SimSetup::finalInfoCheck(void){
796	>	int index;
797	>	int usesDipoles;
798	>	int i;
799
800	<	if( j < n_cells ){
801	<	start_ndx = n_cells;
997	<	}
998	<	else start_ndx = 0;
999	<	}
1000	<	else start_ndx = 0;
800	>	for (i = 0; i < nInfo; i++){
801	>	// check electrostatic parameters
802
803	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
803	>	index = 0;
804	>	usesDipoles = 0;
805	>	while ((index < info[i].n_atoms) && !usesDipoles){
806	>	usesDipoles = (info[i].atoms[index])->hasDipole();
807	>	index++;
808	>	}
809
810	<	makeElement( i * cellx,
811	<	j * celly,
812	<	k * cellz );
813	<	done = ( current_mol >= tot_nmol );
810	>	#ifdef IS_MPI
811	>	int myUse = usesDipoles;
812	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
813	>	#endif //is_mpi
814
815	<	if( !done && n_per_extra > 1 ){
1010	<	makeElement( i * cellx + 0.5 * cellx,
1011	<	j * celly + 0.5 * celly,
1012	<	k * cellz );
1013	<	done = ( current_mol >= tot_nmol );
1014	<	}
815	>	double theEcr, theEst;
816
817	<	if( !done && n_per_extra > 2){
818	<	makeElement( i * cellx,
1018	<	j * celly + 0.5 * celly,
1019	<	k * cellz + 0.5 * cellz );
1020	<	done = ( current_mol >= tot_nmol );
1021	<	}
817	>	if (globals->getUseRF()){
818	>	info[i].useReactionField = 1;
819
820	<	if( !done && n_per_extra > 3){
821	<	makeElement( i * cellx + 0.5 * cellx,
822	<	j * celly,
823	<	k * cellz + 0.5 * cellz );
824	<	done = ( current_mol >= tot_nmol );
825	<	}
826	<	}
820	>	if (!globals->haveECR()){
821	>	sprintf(painCave.errMsg,
822	>	"SimSetup Warning: using default value of 1/2 the smallest "
823	>	"box length for the electrostaticCutoffRadius.\n"
824	>	"I hope you have a very fast processor!\n");
825	>	painCave.isFatal = 0;
826	>	simError();
827	>	double smallest;
828	>	smallest = info[i].boxL[0];
829	>	if (info[i].boxL[1] <= smallest)
830	>	smallest = info[i].boxL[1];
831	>	if (info[i].boxL[2] <= smallest)
832	>	smallest = info[i].boxL[2];
833	>	theEcr = 0.5 * smallest;
834		}
835	+	else{
836	+	theEcr = globals->getECR();
837	+	}
838	+
839	+	if (!globals->haveEST()){
840	+	sprintf(painCave.errMsg,
841	+	"SimSetup Warning: using default value of 0.05 * the "
842	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
843	+	painCave.isFatal = 0;
844	+	simError();
845	+	theEst = 0.05 * theEcr;
846	+	}
847	+	else{
848	+	theEst = globals->getEST();
849	+	}
850	+
851	+	info[i].setEcr(theEcr, theEst);
852	+
853	+	if (!globals->haveDielectric()){
854	+	sprintf(painCave.errMsg,
855	+	"SimSetup Error: You are trying to use Reaction Field without"
856	+	"setting a dielectric constant!\n");
857	+	painCave.isFatal = 1;
858	+	simError();
859	+	}
860	+	info[i].dielectric = globals->getDielectric();
861		}
862	<	}
862	>	else{
863	>	if (usesDipoles){
864	>	if (!globals->haveECR()){
865	>	sprintf(painCave.errMsg,
866	>	"SimSetup Warning: using default value of 1/2 the smallest "
867	>	"box length for the electrostaticCutoffRadius.\n"
868	>	"I hope you have a very fast processor!\n");
869	>	painCave.isFatal = 0;
870	>	simError();
871	>	double smallest;
872	>	smallest = info[i].boxL[0];
873	>	if (info[i].boxL[1] <= smallest)
874	>	smallest = info[i].boxL[1];
875	>	if (info[i].boxL[2] <= smallest)
876	>	smallest = info[i].boxL[2];
877	>	theEcr = 0.5 * smallest;
878	>	}
879	>	else{
880	>	theEcr = globals->getECR();
881	>	}
882
883	+	if (!globals->haveEST()){
884	+	sprintf(painCave.errMsg,
885	+	"SimSetup Warning: using default value of 0.05 * the "
886	+	"electrostaticCutoffRadius for the "
887	+	"electrostaticSkinThickness\n");
888	+	painCave.isFatal = 0;
889	+	simError();
890	+	theEst = 0.05 * theEcr;
891	+	}
892	+	else{
893	+	theEst = globals->getEST();
894	+	}
895
896	<	for( i=0; i<simnfo->n_atoms; i++ ){
897	<	simnfo->atoms[i]->set_vx( 0.0 );
898	<	simnfo->atoms[i]->set_vy( 0.0 );
1038	<	simnfo->atoms[i]->set_vz( 0.0 );
896	>	info[i].setEcr(theEcr, theEst);
897	>	}
898	>	}
899		}
900	+
901	+	#ifdef IS_MPI
902	+	strcpy(checkPointMsg, "post processing checks out");
903	+	MPIcheckPoint();
904	+	#endif // is_mpi
905		}
906
907	<	void SimSetup::makeElement( double x, double y, double z ){
907	>	void SimSetup::initSystemCoords(void){
908	>	int i;
909
910	<	int k;
1045	<	AtomStamp* current_atom;
1046	<	DirectionalAtom* dAtom;
1047	<	double rotMat[3][3];
910	>	char* inName;
911
912	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
912	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
913
914	<	current_atom = comp_stamps[current_comp]->getAtom( k );
915	<	if( !current_atom->havePosition() ){
916	<	sprintf( painCave.errMsg,
917	<	"SimSetup:initFromBass error.\n"
918	<	"\tComponent %s, atom %s does not have a position specified.\n"
919	<	"\tThe initialization routine is unable to give a start"
920	<	" position.\n",
921	<	comp_stamps[current_comp]->getID(),
922	<	current_atom->getType() );
923	<	painCave.isFatal = 1;
924	<	simError();
914	>	for (i = 0; i < info[0].n_atoms; i++)
915	>	info[0].atoms[i]->setCoords();
916	>
917	>	if (globals->haveInitialConfig()){
918	>	InitializeFromFile* fileInit;
919	>	#ifdef IS_MPI // is_mpi
920	>	if (worldRank == 0){
921	>	#endif //is_mpi
922	>	inName = globals->getInitialConfig();
923	>	fileInit = new InitializeFromFile(inName);
924	>	#ifdef IS_MPI
925		}
926	+	else
927	+	fileInit = new InitializeFromFile(NULL);
928	+	#endif
929	+	fileInit->readInit(info); // default velocities on
930
931	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
932	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
933	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
931	>	delete fileInit;
932	>	}
933	>	else{
934	>	#ifdef IS_MPI
935
936	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
936	>	// no init from bass
937
938	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
938	>	sprintf(painCave.errMsg,
939	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
940	>	painCave.isFatal = 1;;
941	>	simError();
942
943	<	rotMat[0][0] = 1.0;
1073	<	rotMat[0][1] = 0.0;
1074	<	rotMat[0][2] = 0.0;
943	>	#else
944
945	<	rotMat[1][0] = 0.0;
1077	<	rotMat[1][1] = 1.0;
1078	<	rotMat[1][2] = 0.0;
945	>	initFromBass();
946
1080	–	rotMat[2][0] = 0.0;
1081	–	rotMat[2][1] = 0.0;
1082	–	rotMat[2][2] = 1.0;
947
948	<	dAtom->setA( rotMat );
1085	<	}
1086	<
1087	<	current_atom_ndx++;
948	>	#endif
949		}
950
951	<	current_mol++;
952	<	current_comp_mol++;
951	>	#ifdef IS_MPI
952	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
953	>	MPIcheckPoint();
954	>	#endif // is_mpi
955	>	}
956
1093	–	if( current_comp_mol >= components_nmol[current_comp] ){
957
958	<	current_comp_mol = 0;
959	<	current_comp++;
958	>	void SimSetup::makeOutNames(void){
959	>	int k;
960	>
961	>
962	>	for (k = 0; k < nInfo; k++){
963	>	#ifdef IS_MPI
964	>	if (worldRank == 0){
965	>	#endif // is_mpi
966	>
967	>	if (globals->haveFinalConfig()){
968	>	strcpy(info[k].finalName, globals->getFinalConfig());
969	>	}
970	>	else{
971	>	strcpy(info[k].finalName, inFileName);
972	>	char* endTest;
973	>	int nameLength = strlen(info[k].finalName);
974	>	endTest = &(info[k].finalName[nameLength - 5]);
975	>	if (!strcmp(endTest, ".bass")){
976	>	strcpy(endTest, ".eor");
977	>	}
978	>	else if (!strcmp(endTest, ".BASS")){
979	>	strcpy(endTest, ".eor");
980	>	}
981	>	else{
982	>	endTest = &(info[k].finalName[nameLength - 4]);
983	>	if (!strcmp(endTest, ".bss")){
984	>	strcpy(endTest, ".eor");
985	>	}
986	>	else if (!strcmp(endTest, ".mdl")){
987	>	strcpy(endTest, ".eor");
988	>	}
989	>	else{
990	>	strcat(info[k].finalName, ".eor");
991	>	}
992	>	}
993	>	}
994	>
995	>	// make the sample and status out names
996	>
997	>	strcpy(info[k].sampleName, inFileName);
998	>	char* endTest;
999	>	int nameLength = strlen(info[k].sampleName);
1000	>	endTest = &(info[k].sampleName[nameLength - 5]);
1001	>	if (!strcmp(endTest, ".bass")){
1002	>	strcpy(endTest, ".dump");
1003	>	}
1004	>	else if (!strcmp(endTest, ".BASS")){
1005	>	strcpy(endTest, ".dump");
1006	>	}
1007	>	else{
1008	>	endTest = &(info[k].sampleName[nameLength - 4]);
1009	>	if (!strcmp(endTest, ".bss")){
1010	>	strcpy(endTest, ".dump");
1011	>	}
1012	>	else if (!strcmp(endTest, ".mdl")){
1013	>	strcpy(endTest, ".dump");
1014	>	}
1015	>	else{
1016	>	strcat(info[k].sampleName, ".dump");
1017	>	}
1018	>	}
1019	>
1020	>	strcpy(info[k].statusName, inFileName);
1021	>	nameLength = strlen(info[k].statusName);
1022	>	endTest = &(info[k].statusName[nameLength - 5]);
1023	>	if (!strcmp(endTest, ".bass")){
1024	>	strcpy(endTest, ".stat");
1025	>	}
1026	>	else if (!strcmp(endTest, ".BASS")){
1027	>	strcpy(endTest, ".stat");
1028	>	}
1029	>	else{
1030	>	endTest = &(info[k].statusName[nameLength - 4]);
1031	>	if (!strcmp(endTest, ".bss")){
1032	>	strcpy(endTest, ".stat");
1033	>	}
1034	>	else if (!strcmp(endTest, ".mdl")){
1035	>	strcpy(endTest, ".stat");
1036	>	}
1037	>	else{
1038	>	strcat(info[k].statusName, ".stat");
1039	>	}
1040	>	}
1041	>
1042	>	#ifdef IS_MPI
1043	>
1044	>	}
1045	>	#endif // is_mpi
1046		}
1047		}
1048	+
1049	+
1050	+	void SimSetup::sysObjectsCreation(void){
1051	+	int i, k;
1052	+
1053	+	// create the forceField
1054	+
1055	+	createFF();
1056	+
1057	+	// extract componentList
1058	+
1059	+	compList();
1060	+
1061	+	// calc the number of atoms, bond, bends, and torsions
1062	+
1063	+	calcSysValues();
1064	+
1065	+	#ifdef IS_MPI
1066	+	// divide the molecules among the processors
1067	+
1068	+	mpiMolDivide();
1069	+	#endif //is_mpi
1070	+
1071	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1072	+
1073	+	makeSysArrays();
1074	+
1075	+	// make and initialize the molecules (all but atomic coordinates)
1076	+
1077	+	makeMolecules();
1078	+
1079	+	for (k = 0; k < nInfo; k++){
1080	+	info[k].identArray = new int[info[k].n_atoms];
1081	+	for (i = 0; i < info[k].n_atoms; i++){
1082	+	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1083	+	}
1084	+	}
1085	+	}
1086	+
1087	+
1088	+	void SimSetup::createFF(void){
1089	+	switch (ffCase){
1090	+	case FF_DUFF:
1091	+	the_ff = new DUFF();
1092	+	break;
1093	+
1094	+	case FF_LJ:
1095	+	the_ff = new LJFF();
1096	+	break;
1097	+
1098	+	case FF_EAM:
1099	+	the_ff = new EAM_FF();
1100	+	break;
1101	+
1102	+	default:
1103	+	sprintf(painCave.errMsg,
1104	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1105	+	painCave.isFatal = 1;
1106	+	simError();
1107	+	}
1108	+
1109	+	#ifdef IS_MPI
1110	+	strcpy(checkPointMsg, "ForceField creation successful");
1111	+	MPIcheckPoint();
1112	+	#endif // is_mpi
1113	+	}
1114	+
1115	+
1116	+	void SimSetup::compList(void){
1117	+	int i;
1118	+	char* id;
1119	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1120	+	LinkedMolStamp* currentStamp = NULL;
1121	+	comp_stamps = new MoleculeStamp * [n_components];
1122	+
1123	+	// make an array of molecule stamps that match the components used.
1124	+	// also extract the used stamps out into a separate linked list
1125	+
1126	+	for (i = 0; i < nInfo; i++){
1127	+	info[i].nComponents = n_components;
1128	+	info[i].componentsNmol = components_nmol;
1129	+	info[i].compStamps = comp_stamps;
1130	+	info[i].headStamp = headStamp;
1131	+	}
1132	+
1133	+
1134	+	for (i = 0; i < n_components; i++){
1135	+	id = the_components[i]->getType();
1136	+	comp_stamps[i] = NULL;
1137	+
1138	+	// check to make sure the component isn't already in the list
1139	+
1140	+	comp_stamps[i] = headStamp->match(id);
1141	+	if (comp_stamps[i] == NULL){
1142	+	// extract the component from the list;
1143	+
1144	+	currentStamp = stamps->extractMolStamp(id);
1145	+	if (currentStamp == NULL){
1146	+	sprintf(painCave.errMsg,
1147	+	"SimSetup error: Component \"%s\" was not found in the "
1148	+	"list of declared molecules\n",
1149	+	id);
1150	+	painCave.isFatal = 1;
1151	+	simError();
1152	+	}
1153	+
1154	+	headStamp->add(currentStamp);
1155	+	comp_stamps[i] = headStamp->match(id);
1156	+	}
1157	+	}
1158	+
1159	+	#ifdef IS_MPI
1160	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1161	+	MPIcheckPoint();
1162	+	#endif // is_mpi
1163	+	}
1164	+
1165	+	void SimSetup::calcSysValues(void){
1166	+	int i;
1167	+
1168	+	int* molMembershipArray;
1169	+
1170	+	tot_atoms = 0;
1171	+	tot_bonds = 0;
1172	+	tot_bends = 0;
1173	+	tot_torsions = 0;
1174	+	for (i = 0; i < n_components; i++){
1175	+	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1176	+	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1177	+	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1178	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1179	+	}
1180	+
1181	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1182	+	molMembershipArray = new int[tot_atoms];
1183	+
1184	+	for (i = 0; i < nInfo; i++){
1185	+	info[i].n_atoms = tot_atoms;
1186	+	info[i].n_bonds = tot_bonds;
1187	+	info[i].n_bends = tot_bends;
1188	+	info[i].n_torsions = tot_torsions;
1189	+	info[i].n_SRI = tot_SRI;
1190	+	info[i].n_mol = tot_nmol;
1191	+
1192	+	info[i].molMembershipArray = molMembershipArray;
1193	+	}
1194	+	}
1195	+
1196	+	#ifdef IS_MPI
1197	+
1198	+	void SimSetup::mpiMolDivide(void){
1199	+	int i, j, k;
1200	+	int localMol, allMol;
1201	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1202	+
1203	+	mpiSim = new mpiSimulation(info);
1204	+
1205	+	globalIndex = mpiSim->divideLabor();
1206	+
1207	+	// set up the local variables
1208	+
1209	+	mol2proc = mpiSim->getMolToProcMap();
1210	+	molCompType = mpiSim->getMolComponentType();
1211	+
1212	+	allMol = 0;
1213	+	localMol = 0;
1214	+	local_atoms = 0;
1215	+	local_bonds = 0;
1216	+	local_bends = 0;
1217	+	local_torsions = 0;
1218	+	globalAtomIndex = 0;
1219	+
1220	+
1221	+	for (i = 0; i < n_components; i++){
1222	+	for (j = 0; j < components_nmol[i]; j++){
1223	+	if (mol2proc[allMol] == worldRank){
1224	+	local_atoms += comp_stamps[i]->getNAtoms();
1225	+	local_bonds += comp_stamps[i]->getNBonds();
1226	+	local_bends += comp_stamps[i]->getNBends();
1227	+	local_torsions += comp_stamps[i]->getNTorsions();
1228	+	localMol++;
1229	+	}
1230	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1231	+	info[0].molMembershipArray[globalAtomIndex] = allMol;
1232	+	globalAtomIndex++;
1233	+	}
1234	+
1235	+	allMol++;
1236	+	}
1237	+	}
1238	+	local_SRI = local_bonds + local_bends + local_torsions;
1239	+
1240	+	info[0].n_atoms = mpiSim->getMyNlocal();
1241	+
1242	+	if (local_atoms != info[0].n_atoms){
1243	+	sprintf(painCave.errMsg,
1244	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1245	+	" localAtom (%d) are not equal.\n",
1246	+	info[0].n_atoms, local_atoms);
1247	+	painCave.isFatal = 1;
1248	+	simError();
1249	+	}
1250	+
1251	+	info[0].n_bonds = local_bonds;
1252	+	info[0].n_bends = local_bends;
1253	+	info[0].n_torsions = local_torsions;
1254	+	info[0].n_SRI = local_SRI;
1255	+	info[0].n_mol = localMol;
1256	+
1257	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1258	+	MPIcheckPoint();
1259	+	}
1260	+
1261	+	#endif // is_mpi
1262	+
1263	+
1264	+	void SimSetup::makeSysArrays(void){
1265	+
1266	+	#ifndef IS_MPI
1267	+	int k, j;
1268	+	#endif // is_mpi
1269	+	int i, l;
1270	+
1271	+	Atom** the_atoms;
1272	+	Molecule* the_molecules;
1273	+	Exclude** the_excludes;
1274	+
1275	+
1276	+	for (l = 0; l < nInfo; l++){
1277	+	// create the atom and short range interaction arrays
1278	+
1279	+	the_atoms = new Atom * [info[l].n_atoms];
1280	+	the_molecules = new Molecule[info[l].n_mol];
1281	+	int molIndex;
1282	+
1283	+	// initialize the molecule's stampID's
1284	+
1285	+	#ifdef IS_MPI
1286	+
1287	+
1288	+	molIndex = 0;
1289	+	for (i = 0; i < mpiSim->getTotNmol(); i++){
1290	+	if (mol2proc[i] == worldRank){
1291	+	the_molecules[molIndex].setStampID(molCompType[i]);
1292	+	the_molecules[molIndex].setMyIndex(molIndex);
1293	+	the_molecules[molIndex].setGlobalIndex(i);
1294	+	molIndex++;
1295	+	}
1296	+	}
1297	+
1298	+	#else // is_mpi
1299	+
1300	+	molIndex = 0;
1301	+	globalAtomIndex = 0;
1302	+	for (i = 0; i < n_components; i++){
1303	+	for (j = 0; j < components_nmol[i]; j++){
1304	+	the_molecules[molIndex].setStampID(i);
1305	+	the_molecules[molIndex].setMyIndex(molIndex);
1306	+	the_molecules[molIndex].setGlobalIndex(molIndex);
1307	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1308	+	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1309	+	globalAtomIndex++;
1310	+	}
1311	+	molIndex++;
1312	+	}
1313	+	}
1314	+
1315	+
1316	+	#endif // is_mpi
1317	+
1318	+
1319	+	if (info[l].n_SRI){
1320	+	Exclude::createArray(info[l].n_SRI);
1321	+	the_excludes = new Exclude * [info[l].n_SRI];
1322	+	for (int ex = 0; ex < info[l].n_SRI; ex++){
1323	+	the_excludes[ex] = new Exclude(ex);
1324	+	}
1325	+	info[l].globalExcludes = new int;
1326	+	info[l].n_exclude = info[l].n_SRI;
1327	+	}
1328	+	else{
1329	+	Exclude::createArray(1);
1330	+	the_excludes = new Exclude * ;
1331	+	the_excludes[0] = new Exclude(0);
1332	+	the_excludes[0]->setPair(0, 0);
1333	+	info[l].globalExcludes = new int;
1334	+	info[l].globalExcludes[0] = 0;
1335	+	info[l].n_exclude = 0;
1336	+	}
1337	+
1338	+	// set the arrays into the SimInfo object
1339	+
1340	+	info[l].atoms = the_atoms;
1341	+	info[l].molecules = the_molecules;
1342	+	info[l].nGlobalExcludes = 0;
1343	+	info[l].excludes = the_excludes;
1344	+
1345	+	the_ff->setSimInfo(info);
1346	+	}
1347	+	}
1348	+
1349	+	void SimSetup::makeIntegrator(void){
1350	+	int k;
1351	+
1352	+	NVE<RealIntegrator>* myNVE = NULL;
1353	+	NVT<RealIntegrator>* myNVT = NULL;
1354	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1355	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1356	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1357	+
1358	+	for (k = 0; k < nInfo; k++){
1359	+	switch (ensembleCase){
1360	+	case NVE_ENS:
1361	+	if (globals->haveZconstraints()){
1362	+	setupZConstraint(info[k]);
1363	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1364	+	}
1365	+	else{
1366	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1367	+	}
1368	+
1369	+	info->the_integrator = myNVE;
1370	+	break;
1371	+
1372	+	case NVT_ENS:
1373	+	if (globals->haveZconstraints()){
1374	+	setupZConstraint(info[k]);
1375	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1376	+	}
1377	+	else
1378	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1379	+
1380	+	myNVT->setTargetTemp(globals->getTargetTemp());
1381	+
1382	+	if (globals->haveTauThermostat())
1383	+	myNVT->setTauThermostat(globals->getTauThermostat());
1384	+	else{
1385	+	sprintf(painCave.errMsg,
1386	+	"SimSetup error: If you use the NVT\n"
1387	+	"    ensemble, you must set tauThermostat.\n");
1388	+	painCave.isFatal = 1;
1389	+	simError();
1390	+	}
1391	+
1392	+	info->the_integrator = myNVT;
1393	+	break;
1394	+
1395	+	case NPTi_ENS:
1396	+	if (globals->haveZconstraints()){
1397	+	setupZConstraint(info[k]);
1398	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1399	+	}
1400	+	else
1401	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1402	+
1403	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1404	+
1405	+	if (globals->haveTargetPressure())
1406	+	myNPTi->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	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1417	+	else{
1418	+	sprintf(painCave.errMsg,
1419	+	"SimSetup error: If you use an NPT\n"
1420	+	"    ensemble, you must set tauThermostat.\n");
1421	+	painCave.isFatal = 1;
1422	+	simError();
1423	+	}
1424	+
1425	+	if (globals->haveTauBarostat())
1426	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1427	+	else{
1428	+	sprintf(painCave.errMsg,
1429	+	"SimSetup error: If you use an NPT\n"
1430	+	"    ensemble, you must set tauBarostat.\n");
1431	+	painCave.isFatal = 1;
1432	+	simError();
1433	+	}
1434	+
1435	+	info->the_integrator = myNPTi;
1436	+	break;
1437	+
1438	+	case NPTf_ENS:
1439	+	if (globals->haveZconstraints()){
1440	+	setupZConstraint(info[k]);
1441	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1442	+	}
1443	+	else
1444	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1445	+
1446	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1447	+
1448	+	if (globals->haveTargetPressure())
1449	+	myNPTf->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	+	myNPTf->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	+	myNPTf->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 = myNPTf;
1479	+	break;
1480	+
1481	+	case NPTxyz_ENS:
1482	+	if (globals->haveZconstraints()){
1483	+	setupZConstraint(info[k]);
1484	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1485	+	}
1486	+	else
1487	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1488	+
1489	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1490	+
1491	+	if (globals->haveTargetPressure())
1492	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1493	+	else{
1494	+	sprintf(painCave.errMsg,
1495	+	"SimSetup error: If you use a constant pressure\n"
1496	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1497	+	painCave.isFatal = 1;
1498	+	simError();
1499	+	}
1500	+
1501	+	if (globals->haveTauThermostat())
1502	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1503	+	else{
1504	+	sprintf(painCave.errMsg,
1505	+	"SimSetup error: If you use an NPT\n"
1506	+	"    ensemble, you must set tauThermostat.\n");
1507	+	painCave.isFatal = 1;
1508	+	simError();
1509	+	}
1510	+
1511	+	if (globals->haveTauBarostat())
1512	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1513	+	else{
1514	+	sprintf(painCave.errMsg,
1515	+	"SimSetup error: If you use an NPT\n"
1516	+	"    ensemble, you must set tauBarostat.\n");
1517	+	painCave.isFatal = 1;
1518	+	simError();
1519	+	}
1520	+
1521	+	info->the_integrator = myNPTxyz;
1522	+	break;
1523	+
1524	+	default:
1525	+	sprintf(painCave.errMsg,
1526	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1527	+	painCave.isFatal = 1;
1528	+	simError();
1529	+	}
1530	+	}
1531	+	}
1532	+
1533	+	void SimSetup::initFortran(void){
1534	+	info[0].refreshSim();
1535	+
1536	+	if (!strcmp(info[0].mixingRule, "standard")){
1537	+	the_ff->initForceField(LB_MIXING_RULE);
1538	+	}
1539	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1540	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1541	+	}
1542	+	else{
1543	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1544	+	info[0].mixingRule);
1545	+	painCave.isFatal = 1;
1546	+	simError();
1547	+	}
1548	+
1549	+
1550	+	#ifdef IS_MPI
1551	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1552	+	MPIcheckPoint();
1553	+	#endif // is_mpi
1554	+	}
1555	+
1556	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1557	+	int nZConstraints;
1558	+	ZconStamp** zconStamp;
1559	+
1560	+	if (globals->haveZconstraintTime()){
1561	+	//add sample time of z-constraint  into SimInfo's property list
1562	+	DoubleData* zconsTimeProp = new DoubleData();
1563	+	zconsTimeProp->setID(ZCONSTIME_ID);
1564	+	zconsTimeProp->setData(globals->getZconsTime());
1565	+	theInfo.addProperty(zconsTimeProp);
1566	+	}
1567	+	else{
1568	+	sprintf(painCave.errMsg,
1569	+	"ZConstraint error: If you use an ZConstraint\n"
1570	+	" , you must set sample time.\n");
1571	+	painCave.isFatal = 1;
1572	+	simError();
1573	+	}
1574	+
1575	+	//push zconsTol into siminfo, if user does not specify
1576	+	//value for zconsTol, a default value will be used
1577	+	DoubleData* zconsTol = new DoubleData();
1578	+	zconsTol->setID(ZCONSTOL_ID);
1579	+	if (globals->haveZconsTol()){
1580	+	zconsTol->setData(globals->getZconsTol());
1581	+	}
1582	+	else{
1583	+	double defaultZConsTol = 0.01;
1584	+	sprintf(painCave.errMsg,
1585	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1586	+	" , default value %f is used.\n",
1587	+	defaultZConsTol);
1588	+	painCave.isFatal = 0;
1589	+	simError();
1590	+
1591	+	zconsTol->setData(defaultZConsTol);
1592	+	}
1593	+	theInfo.addProperty(zconsTol);
1594	+
1595	+	//set Force Subtraction Policy
1596	+	StringData* zconsForcePolicy = new StringData();
1597	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1598	+
1599	+	if (globals->haveZconsForcePolicy()){
1600	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1601	+	}
1602	+	else{
1603	+	sprintf(painCave.errMsg,
1604	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1605	+	"PolicyByMass is used\n");
1606	+	painCave.isFatal = 0;
1607	+	simError();
1608	+	zconsForcePolicy->setData("BYMASS");
1609	+	}
1610	+
1611	+	theInfo.addProperty(zconsForcePolicy);
1612	+
1613	+	//Determine the name of ouput file and add it into SimInfo's property list
1614	+	//Be careful, do not use inFileName, since it is a pointer which
1615	+	//point to a string at master node, and slave nodes do not contain that string
1616	+
1617	+	string zconsOutput(theInfo.finalName);
1618	+
1619	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1620	+
1621	+	StringData* zconsFilename = new StringData();
1622	+	zconsFilename->setID(ZCONSFILENAME_ID);
1623	+	zconsFilename->setData(zconsOutput);
1624	+
1625	+	theInfo.addProperty(zconsFilename);
1626	+
1627	+	//setup index, pos and other parameters of z-constraint molecules
1628	+	nZConstraints = globals->getNzConstraints();
1629	+	theInfo.nZconstraints = nZConstraints;
1630	+
1631	+	zconStamp = globals->getZconStamp();
1632	+	ZConsParaItem tempParaItem;
1633	+
1634	+	ZConsParaData* zconsParaData = new ZConsParaData();
1635	+	zconsParaData->setID(ZCONSPARADATA_ID);
1636	+
1637	+	for (int i = 0; i < nZConstraints; i++){
1638	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1639	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1640	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1641	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1642	+
1643	+	zconsParaData->addItem(tempParaItem);
1644	+	}
1645	+
1646	+	//check the uniqueness of index
1647	+	if(!zconsParaData->isIndexUnique()){
1648	+	sprintf(painCave.errMsg,
1649	+	"ZConstraint Error: molIndex is not unique\n");
1650	+	painCave.isFatal = 1;
1651	+	simError();
1652	+	}
1653	+
1654	+	//sort the parameters by index of molecules
1655	+	zconsParaData->sortByIndex();
1656	+
1657	+	//push data into siminfo, therefore, we can retrieve later
1658	+	theInfo.addProperty(zconsParaData);
1659	+	}

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