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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 466 by gezelter, Mon Apr 7 14:30:36 2003 UTC vs.
Revision 859 by mmeineke, Mon Nov 10 21:50:36 2003 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
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	+
35	+	initSuspend = false;
36	+	isInfoArray = 0;
37	+	nInfo = 1;
38	+
39		stamps = new MakeStamps();
40		globals = new Globals();
41	<
41	>
42	>
43		#ifdef IS_MPI
44	<	strcpy( checkPointMsg, "SimSetup creation successful" );
44	>	strcpy(checkPointMsg, "SimSetup creation successful");
45		MPIcheckPoint();
46		#endif // IS_MPI
47		}
#	Line 27 | Line 51 | void SimSetup::parseFile( char* fileName ){
51		delete globals;
52		}
53
54	<	void SimSetup::parseFile( char* fileName ){
54	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
55	>	info = the_info;
56	>	nInfo = theNinfo;
57	>	isInfoArray = 1;
58	>	initSuspend = true;
59	>	}
60
61	+
62	+	void SimSetup::parseFile(char* fileName){
63		#ifdef IS_MPI
64	<	if( worldRank == 0 ){
64	>	if (worldRank == 0){
65		#endif // is_mpi
66	<
66	>
67		inFileName = fileName;
68	<	set_interface_stamps( stamps, globals );
69	<
68	>	set_interface_stamps(stamps, globals);
69	>
70		#ifdef IS_MPI
71		mpiEventInit();
72		#endif
73
74	<	yacc_BASS( fileName );
74	>	yacc_BASS(fileName);
75
76		#ifdef IS_MPI
77		throwMPIEvent(NULL);
78		}
79	<	else receiveParse();
79	>	else{
80	>	receiveParse();
81	>	}
82		#endif
83
84		}
85
86		#ifdef IS_MPI
87		void SimSetup::receiveParse(void){
88	<
89	<	set_interface_stamps( stamps, globals );
90	<	mpiEventInit();
91	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
88	>	set_interface_stamps(stamps, globals);
89	>	mpiEventInit();
90	>	MPIcheckPoint();
91	>	mpiEventLoop();
92		}
93
94		#endif // is_mpi
95
96	<	void SimSetup::createSim( void ){
96	>	void SimSetup::createSim(void){
97
98	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	ExtendedSystem* the_extendedsystem;
70	<	int i, j;
98	>	// gather all of the information from the Bass file
99
100	<	// get the stamps and globals;
73	<	the_stamps = stamps;
74	<	the_globals = globals;
100	>	gatherInfo();
101
102	<	// set the easy ones first
77	<	simnfo->target_temp = the_globals->getTargetTemp();
78	<	simnfo->dt = the_globals->getDt();
79	<	simnfo->run_time = the_globals->getRunTime();
102	>	// creation of complex system objects
103
104	<	// get the ones we know are there, yet still may need some work.
82	<	n_components = the_globals->getNComponents();
83	<	strcpy( force_field, the_globals->getForceField() );
104	>	sysObjectsCreation();
105
106	<	// get the ensemble and set up an extended system if we need it:
86	<	strcpy( ensemble, the_globals->getEnsemble() );
87	<	if( !strcasecmp( ensemble, "NPT" ) ) {
88	<	the_extendedsystem = new ExtendedSystem( simnfo );
89	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
90	<	the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
91	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
92	<	the_extendedsystem = new ExtendedSystem( simnfo );
93	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
94	<	} else if ( !strcasecmp( ensemble, "NVE") ) {
95	<	} else {
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
98	<	"reverting to NVE for this simulation.\n",
99	<	ensemble );
100	<	painCave.isFatal = 0;
101	<	simError();
102	<	strcpy( ensemble, "NVE" );
103	<	}
104	<	strcpy( simnfo->ensemble, ensemble );
106	>	// check on the post processing info
107
108	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
107	<	simnfo->usePBC = the_globals->getPBC();
108	<
109	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
110	<	else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
111	<	else{
112	<	sprintf( painCave.errMsg,
113	<	"SimSetup Error. Unrecognized force field -> %s\n",
114	<	force_field );
115	<	painCave.isFatal = 1;
116	<	simError();
117	<	}
108	>	finalInfoCheck();
109
110	<	#ifdef IS_MPI
120	<	strcpy( checkPointMsg, "ForceField creation successful" );
121	<	MPIcheckPoint();
122	<	#endif // is_mpi
110	>	// initialize the system coordinates
111
112	<
112	>	if ( !initSuspend ){
113	>	initSystemCoords();
114
115	<	// get the components and calculate the tot_nMol and indvidual n_mol
116	<	the_components = the_globals->getComponents();
117	<	components_nmol = new int[n_components];
129	<	comp_stamps = new MoleculeStamp*[n_components];
115	>	if( !(globals->getUseInitTime()) )
116	>	info[0].currentTime = 0.0;
117	>	}
118
119	<	if( !the_globals->haveNMol() ){
132	<	// we don't have the total number of molecules, so we assume it is
133	<	// given in each component
119	>	// make the output filenames
120
121	<	tot_nmol = 0;
136	<	for( i=0; i<n_components; i++ ){
121	>	makeOutNames();
122
123	<	if( !the_components[i]->haveNMol() ){
139	<	// we have a problem
140	<	sprintf( painCave.errMsg,
141	<	"SimSetup Error. No global NMol or component NMol"
142	<	" given. Cannot calculate the number of atoms.\n" );
143	<	painCave.isFatal = 1;
144	<	simError();
145	<	}
123	>	// make the integrator
124
125	<	tot_nmol += the_components[i]->getNMol();
148	<	components_nmol[i] = the_components[i]->getNMol();
149	<	}
150	<	}
151	<	else{
152	<	sprintf( painCave.errMsg,
153	<	"SimSetup error.\n"
154	<	"\tSorry, the ability to specify total"
155	<	" nMols and then give molfractions in the components\n"
156	<	"\tis not currently supported."
157	<	" Please give nMol in the components.\n" );
158	<	painCave.isFatal = 1;
159	<	simError();
160	<
161	<
162	<	//     tot_nmol = the_globals->getNMol();
163	<
164	<	//   //we have the total number of molecules, now we check for molfractions
165	<	//     for( i=0; i<n_components; i++ ){
166	<
167	<	//       if( !the_components[i]->haveMolFraction() ){
168	<
169	<	//  if( !the_components[i]->haveNMol() ){
170	<	//    //we have a problem
171	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
172	<	//              << " nMol was given in component
173	<
174	<	}
125	>	makeIntegrator();
126
127		#ifdef IS_MPI
128	<	strcpy( checkPointMsg, "Have the number of components" );
129	<	MPIcheckPoint();
179	<	#endif // is_mpi
128	>	mpiSim->mpiRefresh();
129	>	#endif
130
131	<	// make an array of molecule stamps that match the components used.
182	<	// also extract the used stamps out into a separate linked list
131	>	// initialize the Fortran
132
133	<	simnfo->nComponents = n_components;
134	<	simnfo->componentsNmol = components_nmol;
186	<	simnfo->compStamps = comp_stamps;
187	<	simnfo->headStamp = new LinkedMolStamp();
188	<
189	<	char* id;
190	<	LinkedMolStamp* headStamp = simnfo->headStamp;
191	<	LinkedMolStamp* currentStamp = NULL;
192	<	for( i=0; i<n_components; i++ ){
133	>	initFortran();
134	>	}
135
194	–	id = the_components[i]->getType();
195	–	comp_stamps[i] = NULL;
196	–
197	–	// check to make sure the component isn't already in the list
136
137	<	comp_stamps[i] = headStamp->match( id );
138	<	if( comp_stamps[i] == NULL ){
139	<
140	<	// extract the component from the list;
141	<
142	<	currentStamp = the_stamps->extractMolStamp( id );
143	<	if( currentStamp == NULL ){
144	<	sprintf( painCave.errMsg,
145	<	"SimSetup error: Component \"%s\" was not found in the "
146	<	"list of declared molecules\n",
147	<	id );
210	<	painCave.isFatal = 1;
211	<	simError();
212	<	}
213	<
214	<	headStamp->add( currentStamp );
215	<	comp_stamps[i] = headStamp->match( id );
216	<	}
217	<	}
137	>	void SimSetup::makeMolecules(void){
138	>	int k;
139	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140	>	molInit molInfo;
141	>	DirectionalAtom* dAtom;
142	>	LinkedAssign* extras;
143	>	LinkedAssign* current_extra;
144	>	AtomStamp* currentAtom;
145	>	BondStamp* currentBond;
146	>	BendStamp* currentBend;
147	>	TorsionStamp* currentTorsion;
148
149	<	#ifdef IS_MPI
150	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
151	<	MPIcheckPoint();
222	<	#endif // is_mpi
223	<
149	>	bond_pair* theBonds;
150	>	bend_set* theBends;
151	>	torsion_set* theTorsions;
152
153
154	+	//init the forceField paramters
155
156	<	// caclulate the number of atoms, bonds, bends and torsions
156	>	the_ff->readParams();
157
229	–	tot_atoms = 0;
230	–	tot_bonds = 0;
231	–	tot_bends = 0;
232	–	tot_torsions = 0;
233	–	for( i=0; i<n_components; i++ ){
234	–
235	–	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
236	–	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
237	–	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
238	–	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
239	–	}
158
159	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
159	>	// init the atoms
160
161	<	simnfo->n_atoms = tot_atoms;
244	<	simnfo->n_bonds = tot_bonds;
245	<	simnfo->n_bends = tot_bends;
246	<	simnfo->n_torsions = tot_torsions;
247	<	simnfo->n_SRI = tot_SRI;
248	<	simnfo->n_mol = tot_nmol;
161	>	double ux, uy, uz, u, uSqr;
162
163	<
164	<	#ifdef IS_MPI
163	>	for (k = 0; k < nInfo; k++){
164	>	the_ff->setSimInfo(&(info[k]));
165
166	<	// divide the molecules among processors here.
167	<
168	<	mpiSim = new mpiSimulation( simnfo );
169	<
257	<
166	>	atomOffset = 0;
167	>	excludeOffset = 0;
168	>	for (i = 0; i < info[k].n_mol; i++){
169	>	stampID = info[k].molecules[i].getStampID();
170
171	<	globalIndex = mpiSim->divideLabor();
171	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
172	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
173	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
174	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
175	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
176
177	<	// set up the local variables
178	<
179	<	int localMol, allMol;
180	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
177	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
178	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
179	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
180	>	molInfo.myBends = new Bend * [molInfo.nBends];
181	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
182
183	<	int* mol2proc = mpiSim->getMolToProcMap();
184	<	int* molCompType = mpiSim->getMolComponentType();
185	<
269	<	allMol = 0;
270	<	localMol = 0;
271	<	local_atoms = 0;
272	<	local_bonds = 0;
273	<	local_bends = 0;
274	<	local_torsions = 0;
275	<	for( i=0; i<n_components; i++ ){
183	>	theBonds = new bond_pair[molInfo.nBonds];
184	>	theBends = new bend_set[molInfo.nBends];
185	>	theTorsions = new torsion_set[molInfo.nTorsions];
186
187	<	for( j=0; j<components_nmol[i]; j++ ){
278	<
279	<	if( mol2proc[j] == worldRank ){
280	<
281	<	local_atoms +=    comp_stamps[i]->getNAtoms();
282	<	local_bonds +=    comp_stamps[i]->getNBonds();
283	<	local_bends +=    comp_stamps[i]->getNBends();
284	<	local_torsions += comp_stamps[i]->getNTorsions();
285	<	localMol++;
286	<	}
287	<	allMol++;
288	<	}
289	<	}
290	<	local_SRI = local_bonds + local_bends + local_torsions;
291	<
187	>	// make the Atoms
188
189	<	simnfo->n_atoms = mpiSim->getMyNlocal();
190	<
191	<	if( local_atoms != simnfo->n_atoms ){
192	<	sprintf( painCave.errMsg,
193	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
194	<	" localAtom (%d) are not equal.\n",
195	<	simnfo->n_atoms,
300	<	local_atoms );
301	<	painCave.isFatal = 1;
302	<	simError();
303	<	}
189	>	for (j = 0; j < molInfo.nAtoms; j++){
190	>	currentAtom = comp_stamps[stampID]->getAtom(j);
191	>	if (currentAtom->haveOrientation()){
192	>	dAtom = new DirectionalAtom((j + atomOffset),
193	>	info[k].getConfiguration());
194	>	info[k].n_oriented++;
195	>	molInfo.myAtoms[j] = dAtom;
196
197	<	simnfo->n_bonds = local_bonds;
198	<	simnfo->n_bends = local_bends;
199	<	simnfo->n_torsions = local_torsions;
308	<	simnfo->n_SRI = local_SRI;
309	<	simnfo->n_mol = localMol;
197	>	ux = currentAtom->getOrntX();
198	>	uy = currentAtom->getOrntY();
199	>	uz = currentAtom->getOrntZ();
200
201	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
312	<	MPIcheckPoint();
313	<
314	<
315	<	#endif // is_mpi
316	<
201	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
202
203	<	// create the atom and short range interaction arrays
203	>	u = sqrt(uSqr);
204	>	ux = ux / u;
205	>	uy = uy / u;
206	>	uz = uz / u;
207
208	<	Atom::createArrays(simnfo->n_atoms);
209	<	the_atoms = new Atom*[simnfo->n_atoms];
210	<	the_molecules = new Molecule[simnfo->n_mol];
211	<	int molIndex;
208	>	dAtom->setSUx(ux);
209	>	dAtom->setSUy(uy);
210	>	dAtom->setSUz(uz);
211	>	}
212	>	else{
213	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
214	>	info[k].getConfiguration());
215	>	}
216	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
217
325	–	// initialize the molecule's stampID's
326	–
218		#ifdef IS_MPI
328	–
219
220	<	molIndex = 0;
331	<	for(i=0; i<mpiSim->getTotNmol(); i++){
332	<
333	<	if(mol2proc[i] == worldRank ){
334	<	the_molecules[molIndex].setStampID( molCompType[i] );
335	<	the_molecules[molIndex].setMyIndex( molIndex );
336	<	molIndex++;
337	<	}
338	<	}
220	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
221
340	–	#else // is_mpi
341	–
342	–	molIndex = 0;
343	–	for(i=0; i<n_components; i++){
344	–	for(j=0; j<components_nmol[i]; j++ ){
345	–	the_molecules[molIndex].setStampID( i );
346	–	the_molecules[molIndex].setMyIndex( molIndex );
347	–	molIndex++;
348	–	}
349	–	}
350	–
351	–
222		#endif // is_mpi
223	+	}
224
225	+	// make the bonds
226	+	for (j = 0; j < molInfo.nBonds; j++){
227	+	currentBond = comp_stamps[stampID]->getBond(j);
228	+	theBonds[j].a = currentBond->getA() + atomOffset;
229	+	theBonds[j].b = currentBond->getB() + atomOffset;
230
231	<	if( simnfo->n_SRI ){
232	<
357	<	Exclude::createArray(simnfo->n_SRI);
358	<	the_excludes = new Exclude*[simnfo->n_SRI];
359	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
360	<	simnfo->globalExcludes = new int;
361	<	simnfo->n_exclude = simnfo->n_SRI;
362	<	}
363	<	else{
364	<
365	<	Exclude::createArray( 1 );
366	<	the_excludes = new Exclude*;
367	<	the_excludes[0] = new Exclude(0);
368	<	the_excludes[0]->setPair( 0,0 );
369	<	simnfo->globalExcludes = new int;
370	<	simnfo->globalExcludes[0] = 0;
371	<	simnfo->n_exclude = 0;
372	<	}
231	>	exI = theBonds[j].a;
232	>	exJ = theBonds[j].b;
233
234	<	// set the arrays into the SimInfo object
234	>	// exclude_I must always be the smaller of the pair
235	>	if (exI > exJ){
236	>	tempEx = exI;
237	>	exI = exJ;
238	>	exJ = tempEx;
239	>	}
240	>	#ifdef IS_MPI
241	>	tempEx = exI;
242	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
243	>	tempEx = exJ;
244	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
245
246	<	simnfo->atoms = the_atoms;
247	<	simnfo->molecules = the_molecules;
378	<	simnfo->nGlobalExcludes = 0;
379	<	simnfo->excludes = the_excludes;
246	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
247	>	#else  // isn't MPI
248
249	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
250	+	#endif  //is_mpi
251	+	}
252	+	excludeOffset += molInfo.nBonds;
253
254	<	// get some of the tricky things that may still be in the globals
254	>	//make the bends
255	>	for (j = 0; j < molInfo.nBends; j++){
256	>	currentBend = comp_stamps[stampID]->getBend(j);
257	>	theBends[j].a = currentBend->getA() + atomOffset;
258	>	theBends[j].b = currentBend->getB() + atomOffset;
259	>	theBends[j].c = currentBend->getC() + atomOffset;
260
261	<
262	<	if( the_globals->haveBox() ){
263	<	simnfo->box_x = the_globals->getBox();
387	<	simnfo->box_y = the_globals->getBox();
388	<	simnfo->box_z = the_globals->getBox();
389	<	}
390	<	else if( the_globals->haveDensity() ){
261	>	if (currentBend->haveExtras()){
262	>	extras = currentBend->getExtras();
263	>	current_extra = extras;
264
265	<	double vol;
266	<	vol = (double)tot_nmol / the_globals->getDensity();
267	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
268	<	simnfo->box_y = simnfo->box_x;
269	<	simnfo->box_z = simnfo->box_x;
270	<	}
271	<	else{
399	<	if( !the_globals->haveBoxX() ){
400	<	sprintf( painCave.errMsg,
401	<	"SimSetup error, no periodic BoxX size given.\n" );
402	<	painCave.isFatal = 1;
403	<	simError();
404	<	}
405	<	simnfo->box_x = the_globals->getBoxX();
265	>	while (current_extra != NULL){
266	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
267	>	switch (current_extra->getType()){
268	>	case 0:
269	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
270	>	theBends[j].isGhost = 1;
271	>	break;
272
273	<	if( !the_globals->haveBoxY() ){
274	<	sprintf( painCave.errMsg,
275	<	"SimSetup error, no periodic BoxY size given.\n" );
276	<	painCave.isFatal = 1;
277	<	simError();
412	<	}
413	<	simnfo->box_y = the_globals->getBoxY();
273	>	case 1:
274	>	theBends[j].ghost = (int) current_extra->getDouble() +
275	>	atomOffset;
276	>	theBends[j].isGhost = 1;
277	>	break;
278
279	<	if( !the_globals->haveBoxZ() ){
280	<	sprintf( painCave.errMsg,
281	<	"SimSetup error, no periodic BoxZ size given.\n" );
282	<	painCave.isFatal = 1;
283	<	simError();
284	<	}
285	<	simnfo->box_z = the_globals->getBoxZ();
286	<	}
279	>	default:
280	>	sprintf(painCave.errMsg,
281	>	"SimSetup Error: ghostVectorSource was neither a "
282	>	"double nor an int.\n"
283	>	"-->Bend[%d] in %s\n",
284	>	j, comp_stamps[stampID]->getID());
285	>	painCave.isFatal = 1;
286	>	simError();
287	>	}
288	>	}
289	>	else{
290	>	sprintf(painCave.errMsg,
291	>	"SimSetup Error: unhandled bend assignment:\n"
292	>	"    -->%s in Bend[%d] in %s\n",
293	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
294	>	painCave.isFatal = 1;
295	>	simError();
296	>	}
297
298	<	#ifdef IS_MPI
299	<	strcpy( checkPointMsg, "Box size set up" );
300	<	MPIcheckPoint();
427	<	#endif // is_mpi
298	>	current_extra = current_extra->getNext();
299	>	}
300	>	}
301
302	+	if (!theBends[j].isGhost){
303	+	exI = theBends[j].a;
304	+	exJ = theBends[j].c;
305	+	}
306	+	else{
307	+	exI = theBends[j].a;
308	+	exJ = theBends[j].b;
309	+	}
310
311	<	// initialize the arrays
311	>	// exclude_I must always be the smaller of the pair
312	>	if (exI > exJ){
313	>	tempEx = exI;
314	>	exI = exJ;
315	>	exJ = tempEx;
316	>	}
317	>	#ifdef IS_MPI
318	>	tempEx = exI;
319	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
320	>	tempEx = exJ;
321	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
322
323	<	the_ff->setSimInfo( simnfo );
323	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
324	>	#else  // isn't MPI
325	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
326	>	#endif  //is_mpi
327	>	}
328	>	excludeOffset += molInfo.nBends;
329
330	<	makeMolecules();
331	<	simnfo->identArray = new int[simnfo->n_atoms];
332	<	for(i=0; i<simnfo->n_atoms; i++){
333	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
334	<	}
335	<
440	<	if (the_globals->getUseRF() ) {
441	<	simnfo->useReactionField = 1;
442	<
443	<	if( !the_globals->haveECR() ){
444	<	sprintf( painCave.errMsg,
445	<	"SimSetup Warning: using default value of 1/2 the smallest "
446	<	"box length for the electrostaticCutoffRadius.\n"
447	<	"I hope you have a very fast processor!\n");
448	<	painCave.isFatal = 0;
449	<	simError();
450	<	double smallest;
451	<	smallest = simnfo->box_x;
452	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
453	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
454	<	simnfo->ecr = 0.5 * smallest;
455	<	} else {
456	<	simnfo->ecr        = the_globals->getECR();
457	<	}
330	>	for (j = 0; j < molInfo.nTorsions; j++){
331	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
332	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
333	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
334	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
335	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
336
337	<	if( !the_globals->haveEST() ){
338	<	sprintf( painCave.errMsg,
461	<	"SimSetup Warning: using default value of 0.05 * the "
462	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
463	<	);
464	<	painCave.isFatal = 0;
465	<	simError();
466	<	simnfo->est = 0.05 * simnfo->ecr;
467	<	} else {
468	<	simnfo->est        = the_globals->getEST();
469	<	}
470	<
471	<	if(!the_globals->haveDielectric() ){
472	<	sprintf( painCave.errMsg,
473	<	"SimSetup Error: You are trying to use Reaction Field without"
474	<	"setting a dielectric constant!\n"
475	<	);
476	<	painCave.isFatal = 1;
477	<	simError();
478	<	}
479	<	simnfo->dielectric = the_globals->getDielectric();
480	<	} else {
481	<	if (simnfo->n_dipoles) {
482	<
483	<	if( !the_globals->haveECR() ){
484	<	sprintf( painCave.errMsg,
485	<	"SimSetup Warning: using default value of 1/2 the smallest"
486	<	"box length for the electrostaticCutoffRadius.\n"
487	<	"I hope you have a very fast processor!\n");
488	<	painCave.isFatal = 0;
489	<	simError();
490	<	double smallest;
491	<	smallest = simnfo->box_x;
492	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
493	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
494	<	simnfo->ecr = 0.5 * smallest;
495	<	} else {
496	<	simnfo->ecr        = the_globals->getECR();
497	<	}
498	<
499	<	if( !the_globals->haveEST() ){
500	<	sprintf( painCave.errMsg,
501	<	"SimSetup Warning: using default value of 5% of the"
502	<	"electrostaticCutoffRadius for the "
503	<	"electrostaticSkinThickness\n"
504	<	);
505	<	painCave.isFatal = 0;
506	<	simError();
507	<	simnfo->est = 0.05 * simnfo->ecr;
508	<	} else {
509	<	simnfo->est        = the_globals->getEST();
510	<	}
511	<	}
512	<	}
337	>	exI = theTorsions[j].a;
338	>	exJ = theTorsions[j].d;
339
340	+	// exclude_I must always be the smaller of the pair
341	+	if (exI > exJ){
342	+	tempEx = exI;
343	+	exI = exJ;
344	+	exJ = tempEx;
345	+	}
346		#ifdef IS_MPI
347	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
348	<	MPIcheckPoint();
349	<	#endif // is_mpi
347	>	tempEx = exI;
348	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
349	>	tempEx = exJ;
350	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
351
352	<	if( the_globals->haveInitialConfig() ){
353	<
354	<	InitializeFromFile* fileInit;
355	<	#ifdef IS_MPI // is_mpi
356	<	if( worldRank == 0 ){
357	<	#endif //is_mpi
525	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
526	<	#ifdef IS_MPI
527	<	}else fileInit = new InitializeFromFile( NULL );
528	<	#endif
529	<	fileInit->read_xyz( simnfo ); // default velocities on
352	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
353	>	#else  // isn't MPI
354	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
355	>	#endif  //is_mpi
356	>	}
357	>	excludeOffset += molInfo.nTorsions;
358
531	–	delete fileInit;
532	–	}
533	–	else{
359
360	<	#ifdef IS_MPI
360	>	// send the arrays off to the forceField for init.
361
362	<	// no init from bass
363	<
364	<	sprintf( painCave.errMsg,
365	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
366	<	painCave.isFatal;
542	<	simError();
543	<
544	<	#else
362	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
363	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
364	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
365	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
366	>	theTorsions);
367
546	–	initFromBass();
368
369	+	info[k].molecules[i].initialize(molInfo);
370
549	–	#endif
550	–	}
371
372	+	atomOffset += molInfo.nAtoms;
373	+	delete[] theBonds;
374	+	delete[] theBends;
375	+	delete[] theTorsions;
376	+	}
377	+	}
378	+
379		#ifdef IS_MPI
380	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
380	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
381		MPIcheckPoint();
382		#endif // is_mpi
383
384	+	// clean up the forcefield
385
386	<
387	<
388	<
386	>	the_ff->calcRcut();
387	>	the_ff->cleanMe();
388	>	}
389
390	<
391	<	#ifdef IS_MPI
392	<	if( worldRank == 0 ){
393	<	#endif // is_mpi
394	<
395	<	if( the_globals->haveFinalConfig() ){
396	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
390	>	void SimSetup::initFromBass(void){
391	>	int i, j, k;
392	>	int n_cells;
393	>	double cellx, celly, cellz;
394	>	double temp1, temp2, temp3;
395	>	int n_per_extra;
396	>	int n_extra;
397	>	int have_extra, done;
398	>
399	>	double vel[3];
400	>	vel[0] = 0.0;
401	>	vel[1] = 0.0;
402	>	vel[2] = 0.0;
403	>
404	>	temp1 = (double) tot_nmol / 4.0;
405	>	temp2 = pow(temp1, (1.0 / 3.0));
406	>	temp3 = ceil(temp2);
407	>
408	>	have_extra = 0;
409	>	if (temp2 < temp3){
410	>	// we have a non-complete lattice
411	>	have_extra = 1;
412	>
413	>	n_cells = (int) temp3 - 1;
414	>	cellx = info[0].boxL[0] / temp3;
415	>	celly = info[0].boxL[1] / temp3;
416	>	cellz = info[0].boxL[2] / temp3;
417	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
418	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
419	>	n_per_extra = (int) ceil(temp1);
420	>
421	>	if (n_per_extra > 4){
422	>	sprintf(painCave.errMsg,
423	>	"SimSetup error. There has been an error in constructing"
424	>	" the non-complete lattice.\n");
425	>	painCave.isFatal = 1;
426	>	simError();
427		}
428	<	else{
429	<	strcpy( simnfo->finalName, inFileName );
430	<	char* endTest;
431	<	int nameLength = strlen( simnfo->finalName );
432	<	endTest = &(simnfo->finalName[nameLength - 5]);
433	<	if( !strcmp( endTest, ".bass" ) ){
434	<	strcpy( endTest, ".eor" );
435	<	}
436	<	else if( !strcmp( endTest, ".BASS" ) ){
437	<	strcpy( endTest, ".eor" );
438	<	}
439	<	else{
440	<	endTest = &(simnfo->finalName[nameLength - 4]);
441	<	if( !strcmp( endTest, ".bss" ) ){
442	<	strcpy( endTest, ".eor" );
443	<	}
444	<	else if( !strcmp( endTest, ".mdl" ) ){
445	<	strcpy( endTest, ".eor" );
446	<	}
447	<	else{
448	<	strcat( simnfo->finalName, ".eor" );
449	<	}
450	<	}
593	<	}
594	<
595	<	// make the sample and status out names
596	<
597	<	strcpy( simnfo->sampleName, inFileName );
598	<	char* endTest;
599	<	int nameLength = strlen( simnfo->sampleName );
600	<	endTest = &(simnfo->sampleName[nameLength - 5]);
601	<	if( !strcmp( endTest, ".bass" ) ){
602	<	strcpy( endTest, ".dump" );
603	<	}
604	<	else if( !strcmp( endTest, ".BASS" ) ){
605	<	strcpy( endTest, ".dump" );
606	<	}
607	<	else{
608	<	endTest = &(simnfo->sampleName[nameLength - 4]);
609	<	if( !strcmp( endTest, ".bss" ) ){
610	<	strcpy( endTest, ".dump" );
611	<	}
612	<	else if( !strcmp( endTest, ".mdl" ) ){
613	<	strcpy( endTest, ".dump" );
428	>	}
429	>	else{
430	>	n_cells = (int) temp3;
431	>	cellx = info[0].boxL[0] / temp3;
432	>	celly = info[0].boxL[1] / temp3;
433	>	cellz = info[0].boxL[2] / temp3;
434	>	}
435	>
436	>	current_mol = 0;
437	>	current_comp_mol = 0;
438	>	current_comp = 0;
439	>	current_atom_ndx = 0;
440	>
441	>	for (i = 0; i < n_cells ; i++){
442	>	for (j = 0; j < n_cells; j++){
443	>	for (k = 0; k < n_cells; k++){
444	>	makeElement(i * cellx, j * celly, k * cellz);
445	>
446	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
447	>
448	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
449	>
450	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
451		}
615	–	else{
616	–	strcat( simnfo->sampleName, ".dump" );
617	–	}
452		}
453	<
454	<	strcpy( simnfo->statusName, inFileName );
455	<	nameLength = strlen( simnfo->statusName );
456	<	endTest = &(simnfo->statusName[nameLength - 5]);
457	<	if( !strcmp( endTest, ".bass" ) ){
458	<	strcpy( endTest, ".stat" );
459	<	}
460	<	else if( !strcmp( endTest, ".BASS" ) ){
461	<	strcpy( endTest, ".stat" );
462	<	}
463	<	else{
464	<	endTest = &(simnfo->statusName[nameLength - 4]);
465	<	if( !strcmp( endTest, ".bss" ) ){
466	<	strcpy( endTest, ".stat" );
453	>	}
454	>
455	>	if (have_extra){
456	>	done = 0;
457	>
458	>	int start_ndx;
459	>	for (i = 0; i < (n_cells + 1) && !done; i++){
460	>	for (j = 0; j < (n_cells + 1) && !done; j++){
461	>	if (i < n_cells){
462	>	if (j < n_cells){
463	>	start_ndx = n_cells;
464	>	}
465	>	else
466	>	start_ndx = 0;
467	>	}
468	>	else
469	>	start_ndx = 0;
470	>
471	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
472	>	makeElement(i * cellx, j * celly, k * cellz);
473	>	done = (current_mol >= tot_nmol);
474	>
475	>	if (!done && n_per_extra > 1){
476	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
477	>	k * cellz);
478	>	done = (current_mol >= tot_nmol);
479	>	}
480	>
481	>	if (!done && n_per_extra > 2){
482	>	makeElement(i * cellx, j * celly + 0.5 * celly,
483	>	k * cellz + 0.5 * cellz);
484	>	done = (current_mol >= tot_nmol);
485	>	}
486	>
487	>	if (!done && n_per_extra > 3){
488	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
489	>	k * cellz + 0.5 * cellz);
490	>	done = (current_mol >= tot_nmol);
491	>	}
492	>	}
493		}
634	–	else if( !strcmp( endTest, ".mdl" ) ){
635	–	strcpy( endTest, ".stat" );
636	–	}
637	–	else{
638	–	strcat( simnfo->statusName, ".stat" );
639	–	}
494		}
641	–
642	–	#ifdef IS_MPI
495		}
644	–	#endif // is_mpi
645	–
646	–	// set the status, sample, and themal kick times
647	–
648	–	if( the_globals->haveSampleTime() ){
649	–	simnfo->sampleTime = the_globals->getSampleTime();
650	–	simnfo->statusTime = simnfo->sampleTime;
651	–	simnfo->thermalTime = simnfo->sampleTime;
652	–	}
653	–	else{
654	–	simnfo->sampleTime = the_globals->getRunTime();
655	–	simnfo->statusTime = simnfo->sampleTime;
656	–	simnfo->thermalTime = simnfo->sampleTime;
657	–	}
496
497	<	if( the_globals->haveStatusTime() ){
498	<	simnfo->statusTime = the_globals->getStatusTime();
497	>	for (i = 0; i < info[0].n_atoms; i++){
498	>	info[0].atoms[i]->setVel(vel);
499		}
500	+	}
501
502	<	if( the_globals->haveThermalTime() ){
503	<	simnfo->thermalTime = the_globals->getThermalTime();
504	<	}
502	>	void SimSetup::makeElement(double x, double y, double z){
503	>	int k;
504	>	AtomStamp* current_atom;
505	>	DirectionalAtom* dAtom;
506	>	double rotMat[3][3];
507	>	double pos[3];
508
509	<	// check for the temperature set flag
509	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
510	>	current_atom = comp_stamps[current_comp]->getAtom(k);
511	>	if (!current_atom->havePosition()){
512	>	sprintf(painCave.errMsg,
513	>	"SimSetup:initFromBass error.\n"
514	>	"\tComponent %s, atom %s does not have a position specified.\n"
515	>	"\tThe initialization routine is unable to give a start"
516	>	" position.\n",
517	>	comp_stamps[current_comp]->getID(), current_atom->getType());
518	>	painCave.isFatal = 1;
519	>	simError();
520	>	}
521
522	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
522	>	pos[0] = x + current_atom->getPosX();
523	>	pos[1] = y + current_atom->getPosY();
524	>	pos[2] = z + current_atom->getPosZ();
525
526	+	info[0].atoms[current_atom_ndx]->setPos(pos);
527
528	<	//   // make the longe range forces and the integrator
528	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
529	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
530
531	<	//   new AllLong( simnfo );
531	>	rotMat[0][0] = 1.0;
532	>	rotMat[0][1] = 0.0;
533	>	rotMat[0][2] = 0.0;
534
535	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic(simnfo,
536	<	the_ff,
537	<	the_extendedsystem);
679	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo,
680	<	the_ff,
681	<	the_extendedsystem );
535	>	rotMat[1][0] = 0.0;
536	>	rotMat[1][1] = 1.0;
537	>	rotMat[1][2] = 0.0;
538
539	<	#ifdef IS_MPI
540	<	mpiSim->mpiRefresh();
541	<	#endif
539	>	rotMat[2][0] = 0.0;
540	>	rotMat[2][1] = 0.0;
541	>	rotMat[2][2] = 1.0;
542
543	<	// initialize the Fortran
543	>	dAtom->setA(rotMat);
544	>	}
545
546	<
690	<	simnfo->refreshSim();
691	<
692	<	if( !strcmp( simnfo->mixingRule, "standard") ){
693	<	the_ff->initForceField( LB_MIXING_RULE );
546	>	current_atom_ndx++;
547		}
695	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
696	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
697	–	}
698	–	else{
699	–	sprintf( painCave.errMsg,
700	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
701	–	simnfo->mixingRule );
702	–	painCave.isFatal = 1;
703	–	simError();
704	–	}
548
549	+	current_mol++;
550	+	current_comp_mol++;
551
552	<	#ifdef IS_MPI
553	<	strcpy( checkPointMsg,
554	<	"Successfully intialized the mixingRule for Fortran." );
555	<	MPIcheckPoint();
711	<	#endif // is_mpi
552	>	if (current_comp_mol >= components_nmol[current_comp]){
553	>	current_comp_mol = 0;
554	>	current_comp++;
555	>	}
556		}
557
558
559	<	void SimSetup::makeMolecules( void ){
559	>	void SimSetup::gatherInfo(void){
560	>	int i;
561
562	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
563	<	molInit info;
719	<	DirectionalAtom* dAtom;
720	<	LinkedAssign* extras;
721	<	LinkedAssign* current_extra;
722	<	AtomStamp* currentAtom;
723	<	BondStamp* currentBond;
724	<	BendStamp* currentBend;
725	<	TorsionStamp* currentTorsion;
562	>	ensembleCase = -1;
563	>	ffCase = -1;
564
565	<	bond_pair* theBonds;
728	<	bend_set* theBends;
729	<	torsion_set* theTorsions;
565	>	// set the easy ones first
566
567	<
568	<	//init the forceField paramters
567	>	for (i = 0; i < nInfo; i++){
568	>	info[i].target_temp = globals->getTargetTemp();
569	>	info[i].dt = globals->getDt();
570	>	info[i].run_time = globals->getRunTime();
571	>	}
572	>	n_components = globals->getNComponents();
573
734	–	the_ff->readParams();
574
575	<
737	<	// init the atoms
575	>	// get the forceField
576
577	<	double ux, uy, uz, u, uSqr;
740	<
741	<	atomOffset = 0;
742	<	excludeOffset = 0;
743	<	for(i=0; i<simnfo->n_mol; i++){
744	<
745	<	stampID = the_molecules[i].getStampID();
577	>	strcpy(force_field, globals->getForceField());
578
579	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
580	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
581	<	info.nBends    = comp_stamps[stampID]->getNBends();
582	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
583	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
584	<
585	<	info.myAtoms = &the_atoms[atomOffset];
586	<	info.myExcludes = &the_excludes[excludeOffset];
587	<	info.myBonds = new Bond*[info.nBonds];
588	<	info.myBends = new Bend*[info.nBends];
589	<	info.myTorsions = new Torsion*[info.nTorsions];
579	>	if (!strcasecmp(force_field, "DUFF")){
580	>	ffCase = FF_DUFF;
581	>	}
582	>	else if (!strcasecmp(force_field, "LJ")){
583	>	ffCase = FF_LJ;
584	>	}
585	>	else if (!strcasecmp(force_field, "EAM")){
586	>	ffCase = FF_EAM;
587	>	}
588	>	else{
589	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
590	>	force_field);
591	>	painCave.isFatal = 1;
592	>	simError();
593	>	}
594
595	<	theBonds = new bond_pair[info.nBonds];
760	<	theBends = new bend_set[info.nBends];
761	<	theTorsions = new torsion_set[info.nTorsions];
762	<
763	<	// make the Atoms
764	<
765	<	for(j=0; j<info.nAtoms; j++){
766	<
767	<	currentAtom = comp_stamps[stampID]->getAtom( j );
768	<	if( currentAtom->haveOrientation() ){
769	<
770	<	dAtom = new DirectionalAtom(j + atomOffset);
771	<	simnfo->n_oriented++;
772	<	info.myAtoms[j] = dAtom;
773	<
774	<	ux = currentAtom->getOrntX();
775	<	uy = currentAtom->getOrntY();
776	<	uz = currentAtom->getOrntZ();
777	<
778	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
779	<
780	<	u = sqrt( uSqr );
781	<	ux = ux / u;
782	<	uy = uy / u;
783	<	uz = uz / u;
784	<
785	<	dAtom->setSUx( ux );
786	<	dAtom->setSUy( uy );
787	<	dAtom->setSUz( uz );
788	<	}
789	<	else{
790	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
791	<	}
792	<	info.myAtoms[j]->setType( currentAtom->getType() );
793	<
794	<	#ifdef IS_MPI
795	<
796	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
797	<
798	<	#endif // is_mpi
799	<	}
800	<
801	<	// make the bonds
802	<	for(j=0; j<info.nBonds; j++){
803	<
804	<	currentBond = comp_stamps[stampID]->getBond( j );
805	<	theBonds[j].a = currentBond->getA() + atomOffset;
806	<	theBonds[j].b = currentBond->getB() + atomOffset;
595	>	// get the ensemble
596
597	<	exI = theBonds[j].a;
809	<	exJ = theBonds[j].b;
597	>	strcpy(ensemble, globals->getEnsemble());
598
599	<	// exclude_I must always be the smaller of the pair
600	<	if( exI > exJ ){
601	<	tempEx = exI;
602	<	exI = exJ;
603	<	exJ = tempEx;
604	<	}
605	<	#ifdef IS_MPI
606	<	tempEx = exI;
607	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
608	<	tempEx = exJ;
609	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
610	<
611	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
612	<	#else  // isn't MPI
599	>	if (!strcasecmp(ensemble, "NVE")){
600	>	ensembleCase = NVE_ENS;
601	>	}
602	>	else if (!strcasecmp(ensemble, "NVT")){
603	>	ensembleCase = NVT_ENS;
604	>	}
605	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
606	>	ensembleCase = NPTi_ENS;
607	>	}
608	>	else if (!strcasecmp(ensemble, "NPTf")){
609	>	ensembleCase = NPTf_ENS;
610	>	}
611	>	else if (!strcasecmp(ensemble, "NPTxyz")){
612	>	ensembleCase = NPTxyz_ENS;
613	>	}
614	>	else{
615	>	sprintf(painCave.errMsg,
616	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
617	>	"reverting to NVE for this simulation.\n",
618	>	ensemble);
619	>	painCave.isFatal = 0;
620	>	simError();
621	>	strcpy(ensemble, "NVE");
622	>	ensembleCase = NVE_ENS;
623	>	}
624
625	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
626	<	#endif  //is_mpi
828	<	}
829	<	excludeOffset += info.nBonds;
625	>	for (i = 0; i < nInfo; i++){
626	>	strcpy(info[i].ensemble, ensemble);
627
628	<	//make the bends
832	<	for(j=0; j<info.nBends; j++){
833	<
834	<	currentBend = comp_stamps[stampID]->getBend( j );
835	<	theBends[j].a = currentBend->getA() + atomOffset;
836	<	theBends[j].b = currentBend->getB() + atomOffset;
837	<	theBends[j].c = currentBend->getC() + atomOffset;
838	<
839	<	if( currentBend->haveExtras() ){
840	<
841	<	extras = currentBend->getExtras();
842	<	current_extra = extras;
843	<
844	<	while( current_extra != NULL ){
845	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
846	<
847	<	switch( current_extra->getType() ){
848	<
849	<	case 0:
850	<	theBends[j].ghost =
851	<	current_extra->getInt() + atomOffset;
852	<	theBends[j].isGhost = 1;
853	<	break;
854	<
855	<	case 1:
856	<	theBends[j].ghost =
857	<	(int)current_extra->getDouble() + atomOffset;
858	<	theBends[j].isGhost = 1;
859	<	break;
860	<
861	<	default:
862	<	sprintf( painCave.errMsg,
863	<	"SimSetup Error: ghostVectorSource was neither a "
864	<	"double nor an int.\n"
865	<	"-->Bend[%d] in %s\n",
866	<	j, comp_stamps[stampID]->getID() );
867	<	painCave.isFatal = 1;
868	<	simError();
869	<	}
870	<	}
871	<
872	<	else{
873	<
874	<	sprintf( painCave.errMsg,
875	<	"SimSetup Error: unhandled bend assignment:\n"
876	<	"    -->%s in Bend[%d] in %s\n",
877	<	current_extra->getlhs(),
878	<	j, comp_stamps[stampID]->getID() );
879	<	painCave.isFatal = 1;
880	<	simError();
881	<	}
882	<
883	<	current_extra = current_extra->getNext();
884	<	}
885	<	}
886	<
887	<	if( !theBends[j].isGhost ){
888	<
889	<	exI = theBends[j].a;
890	<	exJ = theBends[j].c;
891	<	}
892	<	else{
893	<
894	<	exI = theBends[j].a;
895	<	exJ = theBends[j].b;
896	<	}
897	<
898	<	// exclude_I must always be the smaller of the pair
899	<	if( exI > exJ ){
900	<	tempEx = exI;
901	<	exI = exJ;
902	<	exJ = tempEx;
903	<	}
904	<	#ifdef IS_MPI
905	<	tempEx = exI;
906	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
907	<	tempEx = exJ;
908	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
909	<
910	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
911	<	#else  // isn't MPI
912	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
913	<	#endif  //is_mpi
914	<	}
915	<	excludeOffset += info.nBends;
628	>	// get the mixing rule
629
630	<	for(j=0; j<info.nTorsions; j++){
631	<
632	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
920	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
921	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
922	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
923	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
924	<
925	<	exI = theTorsions[j].a;
926	<	exJ = theTorsions[j].d;
630	>	strcpy(info[i].mixingRule, globals->getMixingRule());
631	>	info[i].usePBC = globals->getPBC();
632	>	}
633
634	<	// exclude_I must always be the smaller of the pair
929	<	if( exI > exJ ){
930	<	tempEx = exI;
931	<	exI = exJ;
932	<	exJ = tempEx;
933	<	}
934	<	#ifdef IS_MPI
935	<	tempEx = exI;
936	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
937	<	tempEx = exJ;
938	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
939	<
940	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
941	<	#else  // isn't MPI
942	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
943	<	#endif  //is_mpi
944	<	}
945	<	excludeOffset += info.nTorsions;
634	>	// get the components and calculate the tot_nMol and indvidual n_mol
635
636	<
637	<	// send the arrays off to the forceField for init.
636	>	the_components = globals->getComponents();
637	>	components_nmol = new int[n_components];
638
950	–	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
951	–	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
952	–	the_ff->initializeBends( info.nBends, info.myBends, theBends );
953	–	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
639
640	+	if (!globals->haveNMol()){
641	+	// we don't have the total number of molecules, so we assume it is
642	+	// given in each component
643
644	<	the_molecules[i].initialize( info );
644	>	tot_nmol = 0;
645	>	for (i = 0; i < n_components; i++){
646	>	if (!the_components[i]->haveNMol()){
647	>	// we have a problem
648	>	sprintf(painCave.errMsg,
649	>	"SimSetup Error. No global NMol or component NMol"
650	>	" given. Cannot calculate the number of atoms.\n");
651	>	painCave.isFatal = 1;
652	>	simError();
653	>	}
654
655	<
656	<	atomOffset += info.nAtoms;
657	<	delete[] theBonds;
961	<	delete[] theBends;
962	<	delete[] theTorsions;
655	>	tot_nmol += the_components[i]->getNMol();
656	>	components_nmol[i] = the_components[i]->getNMol();
657	>	}
658		}
659	+	else{
660	+	sprintf(painCave.errMsg,
661	+	"SimSetup error.\n"
662	+	"\tSorry, the ability to specify total"
663	+	" nMols and then give molfractions in the components\n"
664	+	"\tis not currently supported."
665	+	" Please give nMol in the components.\n");
666	+	painCave.isFatal = 1;
667	+	simError();
668	+	}
669
670	<	#ifdef IS_MPI
966	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
967	<	MPIcheckPoint();
968	<	#endif // is_mpi
670	>	// set the status, sample, and thermal kick times
671
672	<	// clean up the forcefield
673	<	the_ff->calcRcut();
674	<	the_ff->cleanMe();
672	>	for (i = 0; i < nInfo; i++){
673	>	if (globals->haveSampleTime()){
674	>	info[i].sampleTime = globals->getSampleTime();
675	>	info[i].statusTime = info[i].sampleTime;
676	>	info[i].thermalTime = info[i].sampleTime;
677	>	}
678	>	else{
679	>	info[i].sampleTime = globals->getRunTime();
680	>	info[i].statusTime = info[i].sampleTime;
681	>	info[i].thermalTime = info[i].sampleTime;
682	>	}
683
684	<	}
684	>	if (globals->haveStatusTime()){
685	>	info[i].statusTime = globals->getStatusTime();
686	>	}
687
688	<	void SimSetup::initFromBass( void ){
688	>	if (globals->haveThermalTime()){
689	>	info[i].thermalTime = globals->getThermalTime();
690	>	}
691
692	<	int i, j, k;
693	<	int n_cells;
694	<	double cellx, celly, cellz;
695	<	double temp1, temp2, temp3;
696	<	int n_per_extra;
983	<	int n_extra;
984	<	int have_extra, done;
692	>	info[i].resetIntegrator = 0;
693	>	if( globals->haveResetTime() ){
694	>	info[i].resetTime = globals->getResetTime();
695	>	info[i].resetIntegrator = 1;
696	>	}
697
698	<	temp1 = (double)tot_nmol / 4.0;
699	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
700	<	temp3 = ceil( temp2 );
698	>	// check for the temperature set flag
699	>
700	>	if (globals->haveTempSet())
701	>	info[i].setTemp = globals->getTempSet();
702
703	<	have_extra =0;
991	<	if( temp2 < temp3 ){ // we have a non-complete lattice
992	<	have_extra =1;
703	>	// check for the extended State init
704
705	<	n_cells = (int)temp3 - 1;
706	<	cellx = simnfo->box_x / temp3;
707	<	celly = simnfo->box_y / temp3;
997	<	cellz = simnfo->box_z / temp3;
998	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
999	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1000	<	n_per_extra = (int)ceil( temp1 );
1001	<
1002	<	if( n_per_extra > 4){
1003	<	sprintf( painCave.errMsg,
1004	<	"SimSetup error. There has been an error in constructing"
1005	<	" the non-complete lattice.\n" );
1006	<	painCave.isFatal = 1;
1007	<	simError();
1008	<	}
705	>	info[i].useInitXSstate = globals->getUseInitXSstate();
706	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
707	>
708		}
709	<	else{
710	<	n_cells = (int)temp3;
711	<	cellx = simnfo->box_x / temp3;
1013	<	celly = simnfo->box_y / temp3;
1014	<	cellz = simnfo->box_z / temp3;
1015	<	}
709	>
710	>	//setup seed for random number generator
711	>	int seedValue;
712
713	<	current_mol = 0;
714	<	current_comp_mol = 0;
1019	<	current_comp = 0;
1020	<	current_atom_ndx = 0;
713	>	if (globals->haveSeed()){
714	>	seedValue = globals->getSeed();
715
716	<	for( i=0; i < n_cells ; i++ ){
717	<	for( j=0; j < n_cells; j++ ){
718	<	for( k=0; k < n_cells; k++ ){
716	>	if(seedValue / 1E9 == 0){
717	>	sprintf(painCave.errMsg,
718	>	"Seed for sprng library should contain at least 9 digits\n"
719	>	"OOPSE will generate a seed for user\n");
720	>	painCave.isFatal = 0;
721	>	simError();
722
723	<	makeElement( i * cellx,
724	<	j * celly,
725	<	k * cellz );
726	<
727	<	makeElement( i * cellx + 0.5 * cellx,
728	<	j * celly + 0.5 * celly,
1032	<	k * cellz );
1033	<
1034	<	makeElement( i * cellx,
1035	<	j * celly + 0.5 * celly,
1036	<	k * cellz + 0.5 * cellz );
1037	<
1038	<	makeElement( i * cellx + 0.5 * cellx,
1039	<	j * celly,
1040	<	k * cellz + 0.5 * cellz );
723	>	//using seed generated by system instead of invalid seed set by user
724	>	#ifndef IS_MPI
725	>	seedValue = make_sprng_seed();
726	>	#else
727	>	if (worldRank == 0){
728	>	seedValue = make_sprng_seed();
729		}
730	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
731	+	#endif
732		}
733	+	}//end of if branch of globals->haveSeed()
734	+	else{
735	+
736	+	#ifndef IS_MPI
737	+	seedValue = make_sprng_seed();
738	+	#else
739	+	if (worldRank == 0){
740	+	seedValue = make_sprng_seed();
741	+	}
742	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
743	+	#endif
744	+	}//end of globals->haveSeed()
745	+
746	+	for (int i = 0; i < nInfo; i++){
747	+	info[i].setSeed(seedValue);
748		}
749
750	<	if( have_extra ){
751	<	done = 0;
750	>	#ifdef IS_MPI
751	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
752	>	MPIcheckPoint();
753	>	#endif // is_mpi
754	>	}
755
1048	–	int start_ndx;
1049	–	for( i=0; i < (n_cells+1) && !done; i++ ){
1050	–	for( j=0; j < (n_cells+1) && !done; j++ ){
756
757	<	if( i < n_cells ){
757	>	void SimSetup::finalInfoCheck(void){
758	>	int index;
759	>	int usesDipoles;
760	>	int i;
761
762	<	if( j < n_cells ){
763	<	start_ndx = n_cells;
1056	<	}
1057	<	else start_ndx = 0;
1058	<	}
1059	<	else start_ndx = 0;
762	>	for (i = 0; i < nInfo; i++){
763	>	// check electrostatic parameters
764
765	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
765	>	index = 0;
766	>	usesDipoles = 0;
767	>	while ((index < info[i].n_atoms) && !usesDipoles){
768	>	usesDipoles = (info[i].atoms[index])->hasDipole();
769	>	index++;
770	>	}
771
772	<	makeElement( i * cellx,
773	<	j * celly,
774	<	k * cellz );
775	<	done = ( current_mol >= tot_nmol );
772	>	#ifdef IS_MPI
773	>	int myUse = usesDipoles;
774	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
775	>	#endif //is_mpi
776
777	<	if( !done && n_per_extra > 1 ){
1069	<	makeElement( i * cellx + 0.5 * cellx,
1070	<	j * celly + 0.5 * celly,
1071	<	k * cellz );
1072	<	done = ( current_mol >= tot_nmol );
1073	<	}
777	>	double theEcr, theEst;
778
779	<	if( !done && n_per_extra > 2){
780	<	makeElement( i * cellx,
1077	<	j * celly + 0.5 * celly,
1078	<	k * cellz + 0.5 * cellz );
1079	<	done = ( current_mol >= tot_nmol );
1080	<	}
779	>	if (globals->getUseRF()){
780	>	info[i].useReactionField = 1;
781
782	<	if( !done && n_per_extra > 3){
783	<	makeElement( i * cellx + 0.5 * cellx,
784	<	j * celly,
785	<	k * cellz + 0.5 * cellz );
786	<	done = ( current_mol >= tot_nmol );
787	<	}
788	<	}
782	>	if (!globals->haveECR()){
783	>	sprintf(painCave.errMsg,
784	>	"SimSetup Warning: using default value of 15.0 angstroms"
785	>	"box length for the electrostaticCutoffRadius.\n");
786	>	painCave.isFatal = 0;
787	>	simError();
788	>	theEcr = 15.0;
789		}
790	<	}
791	<	}
790	>	else{
791	>	theEcr = globals->getECR();
792	>	}
793
794	+	if (!globals->haveEST()){
795	+	sprintf(painCave.errMsg,
796	+	"SimSetup Warning: using default value of 0.05 * the "
797	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
798	+	painCave.isFatal = 0;
799	+	simError();
800	+	theEst = 0.05 * theEcr;
801	+	}
802	+	else{
803	+	theEst = globals->getEST();
804	+	}
805
806	<	for( i=0; i<simnfo->n_atoms; i++ ){
807	<	simnfo->atoms[i]->set_vx( 0.0 );
808	<	simnfo->atoms[i]->set_vy( 0.0 );
809	<	simnfo->atoms[i]->set_vz( 0.0 );
806	>	info[i].setDefaultEcr(theEcr, theEst);
807	>
808	>	if (!globals->haveDielectric()){
809	>	sprintf(painCave.errMsg,
810	>	"SimSetup Error: You are trying to use Reaction Field without"
811	>	"setting a dielectric constant!\n");
812	>	painCave.isFatal = 1;
813	>	simError();
814	>	}
815	>	info[i].dielectric = globals->getDielectric();
816	>	}
817	>	else{
818	>	if (usesDipoles){
819	>	if (!globals->haveECR()){
820	>	sprintf(painCave.errMsg,
821	>	"SimSetup Warning: using default value of 15.0 angstroms"
822	>	"box length for the electrostaticCutoffRadius.\n");
823	>	painCave.isFatal = 0;
824	>	simError();
825	>	theEcr = 15.0;
826	>	}
827	>	else{
828	>	theEcr = globals->getECR();
829	>	}
830	>
831	>	if (!globals->haveEST()){
832	>	sprintf(painCave.errMsg,
833	>	"SimSetup Warning: using default value of 0.05 * the "
834	>	"electrostaticCutoffRadius for the "
835	>	"electrostaticSkinThickness\n");
836	>	painCave.isFatal = 0;
837	>	simError();
838	>	theEst = 0.05 * theEcr;
839	>	}
840	>	else{
841	>	theEst = globals->getEST();
842	>	}
843	>
844	>	info[i].setDefaultEcr(theEcr, theEst);
845	>	}
846	>	}
847		}
848	+	#ifdef IS_MPI
849	+	strcpy(checkPointMsg, "post processing checks out");
850	+	MPIcheckPoint();
851	+	#endif // is_mpi
852		}
853	+
854	+	void SimSetup::initSystemCoords(void){
855	+	int i;
856
857	<	void SimSetup::makeElement( double x, double y, double z ){
857	>	char* inName;
858
859	<	int k;
1104	<	AtomStamp* current_atom;
1105	<	DirectionalAtom* dAtom;
1106	<	double rotMat[3][3];
859	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
860
861	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
861	>	for (i = 0; i < info[0].n_atoms; i++)
862	>	info[0].atoms[i]->setCoords();
863
864	<	current_atom = comp_stamps[current_comp]->getAtom( k );
865	<	if( !current_atom->havePosition() ){
866	<	sprintf( painCave.errMsg,
867	<	"SimSetup:initFromBass error.\n"
868	<	"\tComponent %s, atom %s does not have a position specified.\n"
869	<	"\tThe initialization routine is unable to give a start"
870	<	" position.\n",
871	<	comp_stamps[current_comp]->getID(),
1118	<	current_atom->getType() );
1119	<	painCave.isFatal = 1;
1120	<	simError();
864	>	if (globals->haveInitialConfig()){
865	>	InitializeFromFile* fileInit;
866	>	#ifdef IS_MPI // is_mpi
867	>	if (worldRank == 0){
868	>	#endif //is_mpi
869	>	inName = globals->getInitialConfig();
870	>	fileInit = new InitializeFromFile(inName);
871	>	#ifdef IS_MPI
872		}
873	+	else
874	+	fileInit = new InitializeFromFile(NULL);
875	+	#endif
876	+	fileInit->readInit(info); // default velocities on
877
878	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
879	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
880	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
878	>	delete fileInit;
879	>	}
880	>	else{
881	>
882	>	// no init from bass
883	>
884	>	sprintf(painCave.errMsg,
885	>	"Cannot intialize a simulation without an initial configuration file.\n");
886	>	painCave.isFatal = 1;;
887	>	simError();
888	>
889	>	}
890
891	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
891	>	#ifdef IS_MPI
892	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
893	>	MPIcheckPoint();
894	>	#endif // is_mpi
895	>	}
896
1129	–	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
897
898	<	rotMat[0][0] = 1.0;
899	<	rotMat[0][1] = 0.0;
1133	<	rotMat[0][2] = 0.0;
898	>	void SimSetup::makeOutNames(void){
899	>	int k;
900
1135	–	rotMat[1][0] = 0.0;
1136	–	rotMat[1][1] = 1.0;
1137	–	rotMat[1][2] = 0.0;
901
902	<	rotMat[2][0] = 0.0;
903	<	rotMat[2][1] = 0.0;
904	<	rotMat[2][2] = 1.0;
902	>	for (k = 0; k < nInfo; k++){
903	>	#ifdef IS_MPI
904	>	if (worldRank == 0){
905	>	#endif // is_mpi
906
907	<	dAtom->setA( rotMat );
907	>	if (globals->haveFinalConfig()){
908	>	strcpy(info[k].finalName, globals->getFinalConfig());
909	>	}
910	>	else{
911	>	strcpy(info[k].finalName, inFileName);
912	>	char* endTest;
913	>	int nameLength = strlen(info[k].finalName);
914	>	endTest = &(info[k].finalName[nameLength - 5]);
915	>	if (!strcmp(endTest, ".bass")){
916	>	strcpy(endTest, ".eor");
917	>	}
918	>	else if (!strcmp(endTest, ".BASS")){
919	>	strcpy(endTest, ".eor");
920	>	}
921	>	else{
922	>	endTest = &(info[k].finalName[nameLength - 4]);
923	>	if (!strcmp(endTest, ".bss")){
924	>	strcpy(endTest, ".eor");
925	>	}
926	>	else if (!strcmp(endTest, ".mdl")){
927	>	strcpy(endTest, ".eor");
928	>	}
929	>	else{
930	>	strcat(info[k].finalName, ".eor");
931	>	}
932	>	}
933	>	}
934	>
935	>	// make the sample and status out names
936	>
937	>	strcpy(info[k].sampleName, inFileName);
938	>	char* endTest;
939	>	int nameLength = strlen(info[k].sampleName);
940	>	endTest = &(info[k].sampleName[nameLength - 5]);
941	>	if (!strcmp(endTest, ".bass")){
942	>	strcpy(endTest, ".dump");
943	>	}
944	>	else if (!strcmp(endTest, ".BASS")){
945	>	strcpy(endTest, ".dump");
946	>	}
947	>	else{
948	>	endTest = &(info[k].sampleName[nameLength - 4]);
949	>	if (!strcmp(endTest, ".bss")){
950	>	strcpy(endTest, ".dump");
951	>	}
952	>	else if (!strcmp(endTest, ".mdl")){
953	>	strcpy(endTest, ".dump");
954	>	}
955	>	else{
956	>	strcat(info[k].sampleName, ".dump");
957	>	}
958	>	}
959	>
960	>	strcpy(info[k].statusName, inFileName);
961	>	nameLength = strlen(info[k].statusName);
962	>	endTest = &(info[k].statusName[nameLength - 5]);
963	>	if (!strcmp(endTest, ".bass")){
964	>	strcpy(endTest, ".stat");
965	>	}
966	>	else if (!strcmp(endTest, ".BASS")){
967	>	strcpy(endTest, ".stat");
968	>	}
969	>	else{
970	>	endTest = &(info[k].statusName[nameLength - 4]);
971	>	if (!strcmp(endTest, ".bss")){
972	>	strcpy(endTest, ".stat");
973	>	}
974	>	else if (!strcmp(endTest, ".mdl")){
975	>	strcpy(endTest, ".stat");
976	>	}
977	>	else{
978	>	strcat(info[k].statusName, ".stat");
979	>	}
980	>	}
981	>
982	>	#ifdef IS_MPI
983	>
984		}
985	+	#endif // is_mpi
986	+	}
987	+	}
988
989	<	current_atom_ndx++;
989	>
990	>	void SimSetup::sysObjectsCreation(void){
991	>	int i, k;
992	>
993	>	// create the forceField
994	>
995	>	createFF();
996	>
997	>	// extract componentList
998	>
999	>	compList();
1000	>
1001	>	// calc the number of atoms, bond, bends, and torsions
1002	>
1003	>	calcSysValues();
1004	>
1005	>	#ifdef IS_MPI
1006	>	// divide the molecules among the processors
1007	>
1008	>	mpiMolDivide();
1009	>	#endif //is_mpi
1010	>
1011	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1012	>
1013	>	makeSysArrays();
1014	>
1015	>	// make and initialize the molecules (all but atomic coordinates)
1016	>
1017	>	makeMolecules();
1018	>
1019	>	for (k = 0; k < nInfo; k++){
1020	>	info[k].identArray = new int[info[k].n_atoms];
1021	>	for (i = 0; i < info[k].n_atoms; i++){
1022	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1023	>	}
1024		}
1025	+	}
1026
1149	–	current_mol++;
1150	–	current_comp_mol++;
1027
1028	<	if( current_comp_mol >= components_nmol[current_comp] ){
1028	>	void SimSetup::createFF(void){
1029	>	switch (ffCase){
1030	>	case FF_DUFF:
1031	>	the_ff = new DUFF();
1032	>	break;
1033
1034	<	current_comp_mol = 0;
1035	<	current_comp++;
1034	>	case FF_LJ:
1035	>	the_ff = new LJFF();
1036	>	break;
1037	>
1038	>	case FF_EAM:
1039	>	the_ff = new EAM_FF();
1040	>	break;
1041	>
1042	>	default:
1043	>	sprintf(painCave.errMsg,
1044	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1045	>	painCave.isFatal = 1;
1046	>	simError();
1047		}
1048	+
1049	+	#ifdef IS_MPI
1050	+	strcpy(checkPointMsg, "ForceField creation successful");
1051	+	MPIcheckPoint();
1052	+	#endif // is_mpi
1053		}
1054	+
1055	+
1056	+	void SimSetup::compList(void){
1057	+	int i;
1058	+	char* id;
1059	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1060	+	LinkedMolStamp* currentStamp = NULL;
1061	+	comp_stamps = new MoleculeStamp * [n_components];
1062	+
1063	+	// make an array of molecule stamps that match the components used.
1064	+	// also extract the used stamps out into a separate linked list
1065	+
1066	+	for (i = 0; i < nInfo; i++){
1067	+	info[i].nComponents = n_components;
1068	+	info[i].componentsNmol = components_nmol;
1069	+	info[i].compStamps = comp_stamps;
1070	+	info[i].headStamp = headStamp;
1071	+	}
1072	+
1073	+
1074	+	for (i = 0; i < n_components; i++){
1075	+	id = the_components[i]->getType();
1076	+	comp_stamps[i] = NULL;
1077	+
1078	+	// check to make sure the component isn't already in the list
1079	+
1080	+	comp_stamps[i] = headStamp->match(id);
1081	+	if (comp_stamps[i] == NULL){
1082	+	// extract the component from the list;
1083	+
1084	+	currentStamp = stamps->extractMolStamp(id);
1085	+	if (currentStamp == NULL){
1086	+	sprintf(painCave.errMsg,
1087	+	"SimSetup error: Component \"%s\" was not found in the "
1088	+	"list of declared molecules\n",
1089	+	id);
1090	+	painCave.isFatal = 1;
1091	+	simError();
1092	+	}
1093	+
1094	+	headStamp->add(currentStamp);
1095	+	comp_stamps[i] = headStamp->match(id);
1096	+	}
1097	+	}
1098	+
1099	+	#ifdef IS_MPI
1100	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1101	+	MPIcheckPoint();
1102	+	#endif // is_mpi
1103	+	}
1104	+
1105	+	void SimSetup::calcSysValues(void){
1106	+	int i;
1107	+
1108	+	int* molMembershipArray;
1109	+
1110	+	tot_atoms = 0;
1111	+	tot_bonds = 0;
1112	+	tot_bends = 0;
1113	+	tot_torsions = 0;
1114	+	for (i = 0; i < n_components; i++){
1115	+	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1116	+	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1117	+	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1118	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1119	+	}
1120	+
1121	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1122	+	molMembershipArray = new int[tot_atoms];
1123	+
1124	+	for (i = 0; i < nInfo; i++){
1125	+	info[i].n_atoms = tot_atoms;
1126	+	info[i].n_bonds = tot_bonds;
1127	+	info[i].n_bends = tot_bends;
1128	+	info[i].n_torsions = tot_torsions;
1129	+	info[i].n_SRI = tot_SRI;
1130	+	info[i].n_mol = tot_nmol;
1131	+
1132	+	info[i].molMembershipArray = molMembershipArray;
1133	+	}
1134	+	}
1135	+
1136	+	#ifdef IS_MPI
1137	+
1138	+	void SimSetup::mpiMolDivide(void){
1139	+	int i, j, k;
1140	+	int localMol, allMol;
1141	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1142	+
1143	+	mpiSim = new mpiSimulation(info);
1144	+
1145	+	globalIndex = mpiSim->divideLabor();
1146	+
1147	+	// set up the local variables
1148	+
1149	+	mol2proc = mpiSim->getMolToProcMap();
1150	+	molCompType = mpiSim->getMolComponentType();
1151	+
1152	+	allMol = 0;
1153	+	localMol = 0;
1154	+	local_atoms = 0;
1155	+	local_bonds = 0;
1156	+	local_bends = 0;
1157	+	local_torsions = 0;
1158	+	globalAtomIndex = 0;
1159	+
1160	+
1161	+	for (i = 0; i < n_components; i++){
1162	+	for (j = 0; j < components_nmol[i]; j++){
1163	+	if (mol2proc[allMol] == worldRank){
1164	+	local_atoms += comp_stamps[i]->getNAtoms();
1165	+	local_bonds += comp_stamps[i]->getNBonds();
1166	+	local_bends += comp_stamps[i]->getNBends();
1167	+	local_torsions += comp_stamps[i]->getNTorsions();
1168	+	localMol++;
1169	+	}
1170	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1171	+	info[0].molMembershipArray[globalAtomIndex] = allMol;
1172	+	globalAtomIndex++;
1173	+	}
1174	+
1175	+	allMol++;
1176	+	}
1177	+	}
1178	+	local_SRI = local_bonds + local_bends + local_torsions;
1179	+
1180	+	info[0].n_atoms = mpiSim->getMyNlocal();
1181	+
1182	+	if (local_atoms != info[0].n_atoms){
1183	+	sprintf(painCave.errMsg,
1184	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1185	+	" localAtom (%d) are not equal.\n",
1186	+	info[0].n_atoms, local_atoms);
1187	+	painCave.isFatal = 1;
1188	+	simError();
1189	+	}
1190	+
1191	+	info[0].n_bonds = local_bonds;
1192	+	info[0].n_bends = local_bends;
1193	+	info[0].n_torsions = local_torsions;
1194	+	info[0].n_SRI = local_SRI;
1195	+	info[0].n_mol = localMol;
1196	+
1197	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1198	+	MPIcheckPoint();
1199	+	}
1200	+
1201	+	#endif // is_mpi
1202	+
1203	+
1204	+	void SimSetup::makeSysArrays(void){
1205	+
1206	+	#ifndef IS_MPI
1207	+	int k, j;
1208	+	#endif // is_mpi
1209	+	int i, l;
1210	+
1211	+	Atom** the_atoms;
1212	+	Molecule* the_molecules;
1213	+	Exclude** the_excludes;
1214	+
1215	+
1216	+	for (l = 0; l < nInfo; l++){
1217	+	// create the atom and short range interaction arrays
1218	+
1219	+	the_atoms = new Atom * [info[l].n_atoms];
1220	+	the_molecules = new Molecule[info[l].n_mol];
1221	+	int molIndex;
1222	+
1223	+	// initialize the molecule's stampID's
1224	+
1225	+	#ifdef IS_MPI
1226	+
1227	+
1228	+	molIndex = 0;
1229	+	for (i = 0; i < mpiSim->getTotNmol(); i++){
1230	+	if (mol2proc[i] == worldRank){
1231	+	the_molecules[molIndex].setStampID(molCompType[i]);
1232	+	the_molecules[molIndex].setMyIndex(molIndex);
1233	+	the_molecules[molIndex].setGlobalIndex(i);
1234	+	molIndex++;
1235	+	}
1236	+	}
1237	+
1238	+	#else // is_mpi
1239	+
1240	+	molIndex = 0;
1241	+	globalAtomIndex = 0;
1242	+	for (i = 0; i < n_components; i++){
1243	+	for (j = 0; j < components_nmol[i]; j++){
1244	+	the_molecules[molIndex].setStampID(i);
1245	+	the_molecules[molIndex].setMyIndex(molIndex);
1246	+	the_molecules[molIndex].setGlobalIndex(molIndex);
1247	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1248	+	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1249	+	globalAtomIndex++;
1250	+	}
1251	+	molIndex++;
1252	+	}
1253	+	}
1254	+
1255	+
1256	+	#endif // is_mpi
1257	+
1258	+
1259	+	if (info[l].n_SRI){
1260	+	Exclude::createArray(info[l].n_SRI);
1261	+	the_excludes = new Exclude * [info[l].n_SRI];
1262	+	for (int ex = 0; ex < info[l].n_SRI; ex++){
1263	+	the_excludes[ex] = new Exclude(ex);
1264	+	}
1265	+	info[l].globalExcludes = new int;
1266	+	info[l].n_exclude = info[l].n_SRI;
1267	+	}
1268	+	else{
1269	+	Exclude::createArray(1);
1270	+	the_excludes = new Exclude * ;
1271	+	the_excludes[0] = new Exclude(0);
1272	+	the_excludes[0]->setPair(0, 0);
1273	+	info[l].globalExcludes = new int;
1274	+	info[l].globalExcludes[0] = 0;
1275	+	info[l].n_exclude = 0;
1276	+	}
1277	+
1278	+	// set the arrays into the SimInfo object
1279	+
1280	+	info[l].atoms = the_atoms;
1281	+	info[l].molecules = the_molecules;
1282	+	info[l].nGlobalExcludes = 0;
1283	+	info[l].excludes = the_excludes;
1284	+
1285	+	the_ff->setSimInfo(info);
1286	+	}
1287	+	}
1288	+
1289	+	void SimSetup::makeIntegrator(void){
1290	+	int k;
1291	+
1292	+	NVE<RealIntegrator>* myNVE = NULL;
1293	+	NVT<RealIntegrator>* myNVT = NULL;
1294	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1295	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1296	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1297	+
1298	+	for (k = 0; k < nInfo; k++){
1299	+	switch (ensembleCase){
1300	+	case NVE_ENS:
1301	+	if (globals->haveZconstraints()){
1302	+	setupZConstraint(info[k]);
1303	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1304	+	}
1305	+	else{
1306	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1307	+	}
1308	+
1309	+	info->the_integrator = myNVE;
1310	+	break;
1311	+
1312	+	case NVT_ENS:
1313	+	if (globals->haveZconstraints()){
1314	+	setupZConstraint(info[k]);
1315	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1316	+	}
1317	+	else
1318	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1319	+
1320	+	myNVT->setTargetTemp(globals->getTargetTemp());
1321	+
1322	+	if (globals->haveTauThermostat())
1323	+	myNVT->setTauThermostat(globals->getTauThermostat());
1324	+	else{
1325	+	sprintf(painCave.errMsg,
1326	+	"SimSetup error: If you use the NVT\n"
1327	+	"    ensemble, you must set tauThermostat.\n");
1328	+	painCave.isFatal = 1;
1329	+	simError();
1330	+	}
1331	+
1332	+	info->the_integrator = myNVT;
1333	+	break;
1334	+
1335	+	case NPTi_ENS:
1336	+	if (globals->haveZconstraints()){
1337	+	setupZConstraint(info[k]);
1338	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1339	+	}
1340	+	else
1341	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1342	+
1343	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1344	+
1345	+	if (globals->haveTargetPressure())
1346	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1347	+	else{
1348	+	sprintf(painCave.errMsg,
1349	+	"SimSetup error: If you use a constant pressure\n"
1350	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1351	+	painCave.isFatal = 1;
1352	+	simError();
1353	+	}
1354	+
1355	+	if (globals->haveTauThermostat())
1356	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1357	+	else{
1358	+	sprintf(painCave.errMsg,
1359	+	"SimSetup error: If you use an NPT\n"
1360	+	"    ensemble, you must set tauThermostat.\n");
1361	+	painCave.isFatal = 1;
1362	+	simError();
1363	+	}
1364	+
1365	+	if (globals->haveTauBarostat())
1366	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1367	+	else{
1368	+	sprintf(painCave.errMsg,
1369	+	"SimSetup error: If you use an NPT\n"
1370	+	"    ensemble, you must set tauBarostat.\n");
1371	+	painCave.isFatal = 1;
1372	+	simError();
1373	+	}
1374	+
1375	+	info->the_integrator = myNPTi;
1376	+	break;
1377	+
1378	+	case NPTf_ENS:
1379	+	if (globals->haveZconstraints()){
1380	+	setupZConstraint(info[k]);
1381	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1382	+	}
1383	+	else
1384	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1385	+
1386	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1387	+
1388	+	if (globals->haveTargetPressure())
1389	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1390	+	else{
1391	+	sprintf(painCave.errMsg,
1392	+	"SimSetup error: If you use a constant pressure\n"
1393	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1394	+	painCave.isFatal = 1;
1395	+	simError();
1396	+	}
1397	+
1398	+	if (globals->haveTauThermostat())
1399	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1400	+
1401	+	else{
1402	+	sprintf(painCave.errMsg,
1403	+	"SimSetup error: If you use an NPT\n"
1404	+	"    ensemble, you must set tauThermostat.\n");
1405	+	painCave.isFatal = 1;
1406	+	simError();
1407	+	}
1408	+
1409	+	if (globals->haveTauBarostat())
1410	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1411	+
1412	+	else{
1413	+	sprintf(painCave.errMsg,
1414	+	"SimSetup error: If you use an NPT\n"
1415	+	"    ensemble, you must set tauBarostat.\n");
1416	+	painCave.isFatal = 1;
1417	+	simError();
1418	+	}
1419	+
1420	+	info->the_integrator = myNPTf;
1421	+	break;
1422	+
1423	+	case NPTxyz_ENS:
1424	+	if (globals->haveZconstraints()){
1425	+	setupZConstraint(info[k]);
1426	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1427	+	}
1428	+	else
1429	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1430	+
1431	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1432	+
1433	+	if (globals->haveTargetPressure())
1434	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1435	+	else{
1436	+	sprintf(painCave.errMsg,
1437	+	"SimSetup error: If you use a constant pressure\n"
1438	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1439	+	painCave.isFatal = 1;
1440	+	simError();
1441	+	}
1442	+
1443	+	if (globals->haveTauThermostat())
1444	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1445	+	else{
1446	+	sprintf(painCave.errMsg,
1447	+	"SimSetup error: If you use an NPT\n"
1448	+	"    ensemble, you must set tauThermostat.\n");
1449	+	painCave.isFatal = 1;
1450	+	simError();
1451	+	}
1452	+
1453	+	if (globals->haveTauBarostat())
1454	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1455	+	else{
1456	+	sprintf(painCave.errMsg,
1457	+	"SimSetup error: If you use an NPT\n"
1458	+	"    ensemble, you must set tauBarostat.\n");
1459	+	painCave.isFatal = 1;
1460	+	simError();
1461	+	}
1462	+
1463	+	info->the_integrator = myNPTxyz;
1464	+	break;
1465	+
1466	+	default:
1467	+	sprintf(painCave.errMsg,
1468	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1469	+	painCave.isFatal = 1;
1470	+	simError();
1471	+	}
1472	+	}
1473	+	}
1474	+
1475	+	void SimSetup::initFortran(void){
1476	+	info[0].refreshSim();
1477	+
1478	+	if (!strcmp(info[0].mixingRule, "standard")){
1479	+	the_ff->initForceField(LB_MIXING_RULE);
1480	+	}
1481	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1482	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1483	+	}
1484	+	else{
1485	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1486	+	info[0].mixingRule);
1487	+	painCave.isFatal = 1;
1488	+	simError();
1489	+	}
1490	+
1491	+
1492	+	#ifdef IS_MPI
1493	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1494	+	MPIcheckPoint();
1495	+	#endif // is_mpi
1496	+	}
1497	+
1498	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1499	+	int nZConstraints;
1500	+	ZconStamp** zconStamp;
1501	+
1502	+	if (globals->haveZconstraintTime()){
1503	+	//add sample time of z-constraint  into SimInfo's property list
1504	+	DoubleData* zconsTimeProp = new DoubleData();
1505	+	zconsTimeProp->setID(ZCONSTIME_ID);
1506	+	zconsTimeProp->setData(globals->getZconsTime());
1507	+	theInfo.addProperty(zconsTimeProp);
1508	+	}
1509	+	else{
1510	+	sprintf(painCave.errMsg,
1511	+	"ZConstraint error: If you use an ZConstraint\n"
1512	+	" , you must set sample time.\n");
1513	+	painCave.isFatal = 1;
1514	+	simError();
1515	+	}
1516	+
1517	+	//push zconsTol into siminfo, if user does not specify
1518	+	//value for zconsTol, a default value will be used
1519	+	DoubleData* zconsTol = new DoubleData();
1520	+	zconsTol->setID(ZCONSTOL_ID);
1521	+	if (globals->haveZconsTol()){
1522	+	zconsTol->setData(globals->getZconsTol());
1523	+	}
1524	+	else{
1525	+	double defaultZConsTol = 0.01;
1526	+	sprintf(painCave.errMsg,
1527	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1528	+	" , default value %f is used.\n",
1529	+	defaultZConsTol);
1530	+	painCave.isFatal = 0;
1531	+	simError();
1532	+
1533	+	zconsTol->setData(defaultZConsTol);
1534	+	}
1535	+	theInfo.addProperty(zconsTol);
1536	+
1537	+	//set Force Subtraction Policy
1538	+	StringData* zconsForcePolicy = new StringData();
1539	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1540	+
1541	+	if (globals->haveZconsForcePolicy()){
1542	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1543	+	}
1544	+	else{
1545	+	sprintf(painCave.errMsg,
1546	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1547	+	"PolicyByMass is used\n");
1548	+	painCave.isFatal = 0;
1549	+	simError();
1550	+	zconsForcePolicy->setData("BYMASS");
1551	+	}
1552	+
1553	+	theInfo.addProperty(zconsForcePolicy);
1554	+
1555	+	//Determine the name of ouput file and add it into SimInfo's property list
1556	+	//Be careful, do not use inFileName, since it is a pointer which
1557	+	//point to a string at master node, and slave nodes do not contain that string
1558	+
1559	+	string zconsOutput(theInfo.finalName);
1560	+
1561	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1562	+
1563	+	StringData* zconsFilename = new StringData();
1564	+	zconsFilename->setID(ZCONSFILENAME_ID);
1565	+	zconsFilename->setData(zconsOutput);
1566	+
1567	+	theInfo.addProperty(zconsFilename);
1568	+
1569	+	//setup index, pos and other parameters of z-constraint molecules
1570	+	nZConstraints = globals->getNzConstraints();
1571	+	theInfo.nZconstraints = nZConstraints;
1572	+
1573	+	zconStamp = globals->getZconStamp();
1574	+	ZConsParaItem tempParaItem;
1575	+
1576	+	ZConsParaData* zconsParaData = new ZConsParaData();
1577	+	zconsParaData->setID(ZCONSPARADATA_ID);
1578	+
1579	+	for (int i = 0; i < nZConstraints; i++){
1580	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1581	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1582	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1583	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1584	+
1585	+	zconsParaData->addItem(tempParaItem);
1586	+	}
1587	+
1588	+	//check the uniqueness of index
1589	+	if(!zconsParaData->isIndexUnique()){
1590	+	sprintf(painCave.errMsg,
1591	+	"ZConstraint Error: molIndex is not unique\n");
1592	+	painCave.isFatal = 1;
1593	+	simError();
1594	+	}
1595	+
1596	+	//sort the parameters by index of molecules
1597	+	zconsParaData->sortByIndex();
1598	+
1599	+	//push data into siminfo, therefore, we can retrieve later
1600	+	theInfo.addProperty(zconsParaData);
1601	+	}

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