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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 487 by mmeineke, Thu Apr 10 16:27:21 2003 UTC vs.
Revision 829 by gezelter, Tue Oct 28 16:03:37 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
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 | SimSetup::~SimSetup(){
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	<	if (the_globals->haveTargetPressure())
91	<	the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
92	<	else {
93	<	sprintf( painCave.errMsg,
94	<	"SimSetup error: If you use the constant pressure\n"
95	<	"    ensemble, you must set targetPressure.\n"
96	<	"    This was found in the BASS file.\n");
97	<	painCave.isFatal = 1;
98	<	simError();
99	<	}
106	>	// check on the post processing info
107
108	<	if (the_globals->haveTauThermostat())
102	<	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
103	<	else if (the_globals->haveQmass())
104	<	the_extendedsystem->setQmass(the_globals->getQmass());
105	<	else {
106	<	sprintf( painCave.errMsg,
107	<	"SimSetup error: If you use one of the constant temperature\n"
108	<	"    ensembles, you must set either tauThermostat or qMass.\n"
109	<	"    Neither of these was found in the BASS file.\n");
110	<	painCave.isFatal = 1;
111	<	simError();
112	<	}
108	>	finalInfoCheck();
109
110	<	if (the_globals->haveTauBarostat())
115	<	the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
116	<	else {
117	<	sprintf( painCave.errMsg,
118	<	"SimSetup error: If you use the constant pressure\n"
119	<	"    ensemble, you must set tauBarostat.\n"
120	<	"    This was found in the BASS file.\n");
121	<	painCave.isFatal = 1;
122	<	simError();
123	<	}
110	>	// initialize the system coordinates
111
112	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
113	<	the_extendedsystem = new ExtendedSystem( simnfo );
127	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
112	>	if ( !initSuspend ){
113	>	initSystemCoords();
114
115	<	if (the_globals->haveTauThermostat())
116	<	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
131	<	else if (the_globals->haveQmass())
132	<	the_extendedsystem->setQmass(the_globals->getQmass());
133	<	else {
134	<	sprintf( painCave.errMsg,
135	<	"SimSetup error: If you use one of the constant temperature\n"
136	<	"    ensembles, you must set either tauThermostat or qMass.\n"
137	<	"    Neither of these was found in the BASS file.\n");
138	<	painCave.isFatal = 1;
139	<	simError();
140	<	}
141	<
142	<	} else if ( !strcasecmp( ensemble, "NVE") ) {
143	<	} else {
144	<	sprintf( painCave.errMsg,
145	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
146	<	"reverting to NVE for this simulation.\n",
147	<	ensemble );
148	<	painCave.isFatal = 0;
149	<	simError();
150	<	strcpy( ensemble, "NVE" );
115	>	if( !(globals->getUseInitTime()) )
116	>	info[0].currentTime = 0.0;
117		}
152	–	strcpy( simnfo->ensemble, ensemble );
118
119	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
155	<	simnfo->usePBC = the_globals->getPBC();
156	<
157	<	int usesDipoles = 0;
158	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
159	<	the_ff = new TraPPE_ExFF();
160	<	usesDipoles = 1;
161	<	}
162	<	else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
163	<	else{
164	<	sprintf( painCave.errMsg,
165	<	"SimSetup Error. Unrecognized force field -> %s\n",
166	<	force_field );
167	<	painCave.isFatal = 1;
168	<	simError();
169	<	}
119	>	// make the output filenames
120
121	+	makeOutNames();
122	+
123	+	// make the integrator
124	+
125	+	makeIntegrator();
126	+
127		#ifdef IS_MPI
128	<	strcpy( checkPointMsg, "ForceField creation successful" );
129	<	MPIcheckPoint();
174	<	#endif // is_mpi
128	>	mpiSim->mpiRefresh();
129	>	#endif
130
131	<
131	>	// initialize the Fortran
132
133	<	// get the components and calculate the tot_nMol and indvidual n_mol
134	<	the_components = the_globals->getComponents();
180	<	components_nmol = new int[n_components];
181	<	comp_stamps = new MoleculeStamp*[n_components];
133	>	initFortran();
134	>	}
135
183	–	if( !the_globals->haveNMol() ){
184	–	// we don't have the total number of molecules, so we assume it is
185	–	// given in each component
136
137	<	tot_nmol = 0;
138	<	for( i=0; i<n_components; i++ ){
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	<	if( !the_components[i]->haveNMol() ){
150	<	// we have a problem
151	<	sprintf( painCave.errMsg,
193	<	"SimSetup Error. No global NMol or component NMol"
194	<	" given. Cannot calculate the number of atoms.\n" );
195	<	painCave.isFatal = 1;
196	<	simError();
197	<	}
149	>	bond_pair* theBonds;
150	>	bend_set* theBends;
151	>	torsion_set* theTorsions;
152
199	–	tot_nmol += the_components[i]->getNMol();
200	–	components_nmol[i] = the_components[i]->getNMol();
201	–	}
202	–	}
203	–	else{
204	–	sprintf( painCave.errMsg,
205	–	"SimSetup error.\n"
206	–	"\tSorry, the ability to specify total"
207	–	" nMols and then give molfractions in the components\n"
208	–	"\tis not currently supported."
209	–	" Please give nMol in the components.\n" );
210	–	painCave.isFatal = 1;
211	–	simError();
212	–
213	–
214	–	//     tot_nmol = the_globals->getNMol();
215	–
216	–	//   //we have the total number of molecules, now we check for molfractions
217	–	//     for( i=0; i<n_components; i++ ){
218	–
219	–	//       if( !the_components[i]->haveMolFraction() ){
220	–
221	–	//  if( !the_components[i]->haveNMol() ){
222	–	//    //we have a problem
223	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
224	–	//              << " nMol was given in component
225	–
226	–	}
153
154	<	#ifdef IS_MPI
229	<	strcpy( checkPointMsg, "Have the number of components" );
230	<	MPIcheckPoint();
231	<	#endif // is_mpi
154	>	//init the forceField paramters
155
156	<	// make an array of molecule stamps that match the components used.
234	<	// also extract the used stamps out into a separate linked list
156	>	the_ff->readParams();
157
236	–	simnfo->nComponents = n_components;
237	–	simnfo->componentsNmol = components_nmol;
238	–	simnfo->compStamps = comp_stamps;
239	–	simnfo->headStamp = new LinkedMolStamp();
240	–
241	–	char* id;
242	–	LinkedMolStamp* headStamp = simnfo->headStamp;
243	–	LinkedMolStamp* currentStamp = NULL;
244	–	for( i=0; i<n_components; i++ ){
158
159	<	id = the_components[i]->getType();
247	<	comp_stamps[i] = NULL;
248	<
249	<	// check to make sure the component isn't already in the list
159	>	// init the atoms
160
161	<	comp_stamps[i] = headStamp->match( id );
252	<	if( comp_stamps[i] == NULL ){
253	<
254	<	// extract the component from the list;
255	<
256	<	currentStamp = the_stamps->extractMolStamp( id );
257	<	if( currentStamp == NULL ){
258	<	sprintf( painCave.errMsg,
259	<	"SimSetup error: Component \"%s\" was not found in the "
260	<	"list of declared molecules\n",
261	<	id );
262	<	painCave.isFatal = 1;
263	<	simError();
264	<	}
265	<
266	<	headStamp->add( currentStamp );
267	<	comp_stamps[i] = headStamp->match( id );
268	<	}
269	<	}
161	>	double ux, uy, uz, u, uSqr;
162
163	<	#ifdef IS_MPI
164	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
273	<	MPIcheckPoint();
274	<	#endif // is_mpi
275	<
163	>	for (k = 0; k < nInfo; k++){
164	>	the_ff->setSimInfo(&(info[k]));
165
166	+	atomOffset = 0;
167	+	excludeOffset = 0;
168	+	for (i = 0; i < info[k].n_mol; i++){
169	+	stampID = info[k].molecules[i].getStampID();
170
171	+	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
172	+	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
173	+	molInfo.nBends = comp_stamps[stampID]->getNBends();
174	+	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
175	+	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
176
177	<	// caclulate the number of atoms, bonds, bends and torsions
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	<	tot_atoms = 0;
184	<	tot_bonds = 0;
185	<	tot_bends = 0;
284	<	tot_torsions = 0;
285	<	for( i=0; i<n_components; i++ ){
286	<
287	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
288	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
289	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
290	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
291	<	}
183	>	theBonds = new bond_pair[molInfo.nBonds];
184	>	theBends = new bend_set[molInfo.nBends];
185	>	theTorsions = new torsion_set[molInfo.nTorsions];
186
187	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
187	>	// make the Atoms
188
189	<	simnfo->n_atoms = tot_atoms;
190	<	simnfo->n_bonds = tot_bonds;
191	<	simnfo->n_bends = tot_bends;
192	<	simnfo->n_torsions = tot_torsions;
193	<	simnfo->n_SRI = tot_SRI;
194	<	simnfo->n_mol = tot_nmol;
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	<
198	<	#ifdef IS_MPI
197	>	ux = currentAtom->getOrntX();
198	>	uy = currentAtom->getOrntY();
199	>	uz = currentAtom->getOrntZ();
200
201	<	// divide the molecules among processors here.
306	<
307	<	mpiSim = new mpiSimulation( simnfo );
308	<
309	<
201	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
202
203	<	globalIndex = mpiSim->divideLabor();
203	>	u = sqrt(uSqr);
204	>	ux = ux / u;
205	>	uy = uy / u;
206	>	uz = uz / u;
207
208	<	// set up the local variables
209	<
210	<	int localMol, allMol;
211	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
208	>	dAtom->setSUx(ux);
209	>	dAtom->setSUy(uy);
210	>	dAtom->setSUz(uz);
211	>	}
212	>	else{
213	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
214	>	info[k].getConfiguration());
215	>	}
216	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
217
218	<	int* mol2proc = mpiSim->getMolToProcMap();
319	<	int* molCompType = mpiSim->getMolComponentType();
320	<
321	<	allMol = 0;
322	<	localMol = 0;
323	<	local_atoms = 0;
324	<	local_bonds = 0;
325	<	local_bends = 0;
326	<	local_torsions = 0;
327	<	for( i=0; i<n_components; i++ ){
218	>	#ifdef IS_MPI
219
220	<	for( j=0; j<components_nmol[i]; j++ ){
330	<
331	<	if( mol2proc[allMol] == worldRank ){
332	<
333	<	local_atoms +=    comp_stamps[i]->getNAtoms();
334	<	local_bonds +=    comp_stamps[i]->getNBonds();
335	<	local_bends +=    comp_stamps[i]->getNBends();
336	<	local_torsions += comp_stamps[i]->getNTorsions();
337	<	localMol++;
338	<	}
339	<	allMol++;
340	<	}
341	<	}
342	<	local_SRI = local_bonds + local_bends + local_torsions;
343	<
220	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
221
345	–	simnfo->n_atoms = mpiSim->getMyNlocal();
346	–
347	–	if( local_atoms != simnfo->n_atoms ){
348	–	sprintf( painCave.errMsg,
349	–	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
350	–	" localAtom (%d) are not equal.\n",
351	–	simnfo->n_atoms,
352	–	local_atoms );
353	–	painCave.isFatal = 1;
354	–	simError();
355	–	}
356	–
357	–	simnfo->n_bonds = local_bonds;
358	–	simnfo->n_bends = local_bends;
359	–	simnfo->n_torsions = local_torsions;
360	–	simnfo->n_SRI = local_SRI;
361	–	simnfo->n_mol = localMol;
362	–
363	–	strcpy( checkPointMsg, "Passed nlocal consistency check." );
364	–	MPIcheckPoint();
365	–
366	–
222		#endif // is_mpi
223	<
223	>	}
224
225	<	// create the atom and short range interaction arrays
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	<	Atom::createArrays(simnfo->n_atoms);
232	<	the_atoms = new Atom*[simnfo->n_atoms];
374	<	the_molecules = new Molecule[simnfo->n_mol];
375	<	int molIndex;
231	>	exI = theBonds[j].a;
232	>	exJ = theBonds[j].b;
233
234	<	// initialize the molecule's stampID's
235	<
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	<
241	>	tempEx = exI;
242	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
243	>	tempEx = exJ;
244	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
245
246	<	molIndex = 0;
247	<	for(i=0; i<mpiSim->getTotNmol(); i++){
384	<
385	<	if(mol2proc[i] == worldRank ){
386	<	the_molecules[molIndex].setStampID( molCompType[i] );
387	<	the_molecules[molIndex].setMyIndex( molIndex );
388	<	molIndex++;
389	<	}
390	<	}
246	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
247	>	#else  // isn't MPI
248
249	<	#else // is_mpi
250	<
251	<	molIndex = 0;
252	<	for(i=0; i<n_components; i++){
396	<	for(j=0; j<components_nmol[i]; j++ ){
397	<	the_molecules[molIndex].setStampID( i );
398	<	the_molecules[molIndex].setMyIndex( molIndex );
399	<	molIndex++;
400	<	}
401	<	}
402	<
249	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
250	>	#endif  //is_mpi
251	>	}
252	>	excludeOffset += molInfo.nBonds;
253
254	<	#endif // is_mpi
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	+	if (currentBend->haveExtras()){
262	+	extras = currentBend->getExtras();
263	+	current_extra = extras;
264
265	<	if( simnfo->n_SRI ){
266	<
267	<	Exclude::createArray(simnfo->n_SRI);
268	<	the_excludes = new Exclude*[simnfo->n_SRI];
269	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
270	<	simnfo->globalExcludes = new int;
271	<	simnfo->n_exclude = simnfo->n_SRI;
414	<	}
415	<	else{
416	<
417	<	Exclude::createArray( 1 );
418	<	the_excludes = new Exclude*;
419	<	the_excludes[0] = new Exclude(0);
420	<	the_excludes[0]->setPair( 0,0 );
421	<	simnfo->globalExcludes = new int;
422	<	simnfo->globalExcludes[0] = 0;
423	<	simnfo->n_exclude = 0;
424	<	}
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	<	// set the arrays into the SimInfo object
273	>	case 1:
274	>	theBends[j].ghost = (int) current_extra->getDouble() +
275	>	atomOffset;
276	>	theBends[j].isGhost = 1;
277	>	break;
278
279	<	simnfo->atoms = the_atoms;
280	<	simnfo->molecules = the_molecules;
281	<	simnfo->nGlobalExcludes = 0;
282	<	simnfo->excludes = the_excludes;
279	>	default:
280	>	sprintf(painCave.errMsg,
281	>	"SimSetup Error: ghostVectorSource was neither a "
282	>	"double nor an int.\n"
283	>	"-->Bend[%d] in %s\n",
284	>	j, comp_stamps[stampID]->getID());
285	>	painCave.isFatal = 1;
286	>	simError();
287	>	}
288	>	}
289	>	else{
290	>	sprintf(painCave.errMsg,
291	>	"SimSetup Error: unhandled bend assignment:\n"
292	>	"    -->%s in Bend[%d] in %s\n",
293	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
294	>	painCave.isFatal = 1;
295	>	simError();
296	>	}
297
298	+	current_extra = current_extra->getNext();
299	+	}
300	+	}
301
302	<	// get some of the tricky things that may still be in the globals
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	<
312	<	if( the_globals->haveBox() ){
313	<	simnfo->box_x = the_globals->getBox();
314	<	simnfo->box_y = the_globals->getBox();
315	<	simnfo->box_z = the_globals->getBox();
316	<	}
317	<	else if( the_globals->haveDensity() ){
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	<	double vol;
324	<	vol = (double)tot_nmol / the_globals->getDensity();
325	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
326	<	simnfo->box_y = simnfo->box_x;
327	<	simnfo->box_z = simnfo->box_x;
328	<	}
450	<	else{
451	<	if( !the_globals->haveBoxX() ){
452	<	sprintf( painCave.errMsg,
453	<	"SimSetup error, no periodic BoxX size given.\n" );
454	<	painCave.isFatal = 1;
455	<	simError();
456	<	}
457	<	simnfo->box_x = the_globals->getBoxX();
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	<	if( !the_globals->haveBoxY() ){
331	<	sprintf( painCave.errMsg,
332	<	"SimSetup error, no periodic BoxY size given.\n" );
333	<	painCave.isFatal = 1;
334	<	simError();
335	<	}
465	<	simnfo->box_y = the_globals->getBoxY();
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->haveBoxZ() ){
338	<	sprintf( painCave.errMsg,
469	<	"SimSetup error, no periodic BoxZ size given.\n" );
470	<	painCave.isFatal = 1;
471	<	simError();
472	<	}
473	<	simnfo->box_z = the_globals->getBoxZ();
474	<	}
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, "Box size set up" );
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	+	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
482	–	// initialize the arrays
359
360	<	the_ff->setSimInfo( simnfo );
360	>	// send the arrays off to the forceField for init.
361
362	<	makeMolecules();
363	<	simnfo->identArray = new int[simnfo->n_atoms];
364	<	simnfo->molMembershipArray = new int[simnfo->n_atoms];
365	<	for(i=0; i<simnfo->n_atoms; i++){
366	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
491	<	}
492	<	for(i=0; i< simnfo->n_mol; i++) {
493	<	the_molecules[i].atomicRollCall(simnfo->molMembershipArray);
494	<	}
495	<
496	<	if (the_globals->getUseRF() ) {
497	<	simnfo->useReactionField = 1;
498	<
499	<	if( !the_globals->haveECR() ){
500	<	sprintf( painCave.errMsg,
501	<	"SimSetup Warning: using default value of 1/2 the smallest "
502	<	"box length for the electrostaticCutoffRadius.\n"
503	<	"I hope you have a very fast processor!\n");
504	<	painCave.isFatal = 0;
505	<	simError();
506	<	double smallest;
507	<	smallest = simnfo->box_x;
508	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
509	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
510	<	simnfo->ecr = 0.5 * smallest;
511	<	} else {
512	<	simnfo->ecr        = the_globals->getECR();
513	<	}
362	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
363	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
364	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
365	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
366	>	theTorsions);
367
368	<	if( !the_globals->haveEST() ){
369	<	sprintf( painCave.errMsg,
370	<	"SimSetup Warning: using default value of 0.05 * the "
371	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
372	<	);
373	<	painCave.isFatal = 0;
374	<	simError();
375	<	simnfo->est = 0.05 * simnfo->ecr;
523	<	} else {
524	<	simnfo->est        = the_globals->getEST();
368	>
369	>	info[k].molecules[i].initialize(molInfo);
370	>
371	>
372	>	atomOffset += molInfo.nAtoms;
373	>	delete[] theBonds;
374	>	delete[] theBends;
375	>	delete[] theTorsions;
376		}
377	<
527	<	if(!the_globals->haveDielectric() ){
528	<	sprintf( painCave.errMsg,
529	<	"SimSetup Error: You are trying to use Reaction Field without"
530	<	"setting a dielectric constant!\n"
531	<	);
532	<	painCave.isFatal = 1;
533	<	simError();
534	<	}
535	<	simnfo->dielectric = the_globals->getDielectric();
536	<	} else {
537	<	if (usesDipoles) {
538	<
539	<	if( !the_globals->haveECR() ){
540	<	sprintf( painCave.errMsg,
541	<	"SimSetup Warning: using default value of 1/2 the smallest "
542	<	"box length for the electrostaticCutoffRadius.\n"
543	<	"I hope you have a very fast processor!\n");
544	<	painCave.isFatal = 0;
545	<	simError();
546	<	double smallest;
547	<	smallest = simnfo->box_x;
548	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
549	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
550	<	simnfo->ecr = 0.5 * smallest;
551	<	} else {
552	<	simnfo->ecr        = the_globals->getECR();
553	<	}
554	<
555	<	if( !the_globals->haveEST() ){
556	<	sprintf( painCave.errMsg,
557	<	"SimSetup Warning: using default value of 5%% of the "
558	<	"electrostaticCutoffRadius for the "
559	<	"electrostaticSkinThickness\n"
560	<	);
561	<	painCave.isFatal = 0;
562	<	simError();
563	<	simnfo->est = 0.05 * simnfo->ecr;
564	<	} else {
565	<	simnfo->est        = the_globals->getEST();
566	<	}
567	<	}
568	<	}
377	>	}
378
379		#ifdef IS_MPI
380	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
380	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
381		MPIcheckPoint();
382		#endif // is_mpi
383
384	<	if( the_globals->haveInitialConfig() ){
576	<
577	<	InitializeFromFile* fileInit;
578	<	#ifdef IS_MPI // is_mpi
579	<	if( worldRank == 0 ){
580	<	#endif //is_mpi
581	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
582	<	#ifdef IS_MPI
583	<	}else fileInit = new InitializeFromFile( NULL );
584	<	#endif
585	<	fileInit->read_xyz( simnfo ); // default velocities on
384	>	// clean up the forcefield
385
386	<	delete fileInit;
387	<	}
388	<	else{
386	>	the_ff->calcRcut();
387	>	the_ff->cleanMe();
388	>	}
389
390	<	#ifdef IS_MPI
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	<	// no init from bass
400	<
401	<	sprintf( painCave.errMsg,
402	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
597	<	painCave.isFatal;
598	<	simError();
599	<
600	<	#else
399	>	double vel[3];
400	>	vel[0] = 0.0;
401	>	vel[1] = 0.0;
402	>	vel[2] = 0.0;
403
404	<	initFromBass();
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	<	#endif
414	<	}
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	<	#ifdef IS_MPI
422	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
423	<	MPIcheckPoint();
424	<	#endif // is_mpi
425	<
426	<
614	<
615	<
616	<
617	<
618	<
619	<	#ifdef IS_MPI
620	<	if( worldRank == 0 ){
621	<	#endif // is_mpi
622	<
623	<	if( the_globals->haveFinalConfig() ){
624	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
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		}
626	–	else{
627	–	strcpy( simnfo->finalName, inFileName );
628	–	char* endTest;
629	–	int nameLength = strlen( simnfo->finalName );
630	–	endTest = &(simnfo->finalName[nameLength - 5]);
631	–	if( !strcmp( endTest, ".bass" ) ){
632	–	strcpy( endTest, ".eor" );
633	–	}
634	–	else if( !strcmp( endTest, ".BASS" ) ){
635	–	strcpy( endTest, ".eor" );
636	–	}
637	–	else{
638	–	endTest = &(simnfo->finalName[nameLength - 4]);
639	–	if( !strcmp( endTest, ".bss" ) ){
640	–	strcpy( endTest, ".eor" );
641	–	}
642	–	else if( !strcmp( endTest, ".mdl" ) ){
643	–	strcpy( endTest, ".eor" );
644	–	}
645	–	else{
646	–	strcat( simnfo->finalName, ".eor" );
647	–	}
648	–	}
649	–	}
650	–
651	–	// make the sample and status out names
652	–
653	–	strcpy( simnfo->sampleName, inFileName );
654	–	char* endTest;
655	–	int nameLength = strlen( simnfo->sampleName );
656	–	endTest = &(simnfo->sampleName[nameLength - 5]);
657	–	if( !strcmp( endTest, ".bass" ) ){
658	–	strcpy( endTest, ".dump" );
659	–	}
660	–	else if( !strcmp( endTest, ".BASS" ) ){
661	–	strcpy( endTest, ".dump" );
662	–	}
663	–	else{
664	–	endTest = &(simnfo->sampleName[nameLength - 4]);
665	–	if( !strcmp( endTest, ".bss" ) ){
666	–	strcpy( endTest, ".dump" );
667	–	}
668	–	else if( !strcmp( endTest, ".mdl" ) ){
669	–	strcpy( endTest, ".dump" );
670	–	}
671	–	else{
672	–	strcat( simnfo->sampleName, ".dump" );
673	–	}
674	–	}
675	–
676	–	strcpy( simnfo->statusName, inFileName );
677	–	nameLength = strlen( simnfo->statusName );
678	–	endTest = &(simnfo->statusName[nameLength - 5]);
679	–	if( !strcmp( endTest, ".bass" ) ){
680	–	strcpy( endTest, ".stat" );
681	–	}
682	–	else if( !strcmp( endTest, ".BASS" ) ){
683	–	strcpy( endTest, ".stat" );
684	–	}
685	–	else{
686	–	endTest = &(simnfo->statusName[nameLength - 4]);
687	–	if( !strcmp( endTest, ".bss" ) ){
688	–	strcpy( endTest, ".stat" );
689	–	}
690	–	else if( !strcmp( endTest, ".mdl" ) ){
691	–	strcpy( endTest, ".stat" );
692	–	}
693	–	else{
694	–	strcat( simnfo->statusName, ".stat" );
695	–	}
696	–	}
697	–
698	–	#ifdef IS_MPI
428		}
700	–	#endif // is_mpi
701	–
702	–	// set the status, sample, and themal kick times
703	–
704	–	if( the_globals->haveSampleTime() ){
705	–	simnfo->sampleTime = the_globals->getSampleTime();
706	–	simnfo->statusTime = simnfo->sampleTime;
707	–	simnfo->thermalTime = simnfo->sampleTime;
708	–	}
429		else{
430	<	simnfo->sampleTime = the_globals->getRunTime();
431	<	simnfo->statusTime = simnfo->sampleTime;
432	<	simnfo->thermalTime = simnfo->sampleTime;
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	<	if( the_globals->haveStatusTime() ){
437	<	simnfo->statusTime = the_globals->getStatusTime();
438	<	}
436	>	current_mol = 0;
437	>	current_comp_mol = 0;
438	>	current_comp = 0;
439	>	current_atom_ndx = 0;
440
441	<	if( the_globals->haveThermalTime() ){
442	<	simnfo->thermalTime = the_globals->getThermalTime();
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	>	}
452	>	}
453		}
454
455	<	// check for the temperature set flag
455	>	if (have_extra){
456	>	done = 0;
457
458	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
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	<	//   // make the longe range forces and the integrator
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	<	//   new AllLong( simnfo );
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	+	}
494	+	}
495	+	}
496
497	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
498	<	new Symplectic(simnfo, the_ff, the_extendedsystem);
497	>	for (i = 0; i < info[0].n_atoms; i++){
498	>	info[0].atoms[i]->setVel(vel);
499		}
500	<	else if( !strcmp( force_field, "LJ" ) ){
737	<	new Verlet( *simnfo, the_ff, the_extendedsystem );
738	<	}
739	<	else {
740	<	std::cerr << "I'm a bug.\n";
741	<	fprintf( stderr, "Ima bug. stderr %s\n", force_field);
742	<	}
743	<	#ifdef IS_MPI
744	<	mpiSim->mpiRefresh();
745	<	#endif
500	>	}
501
502	<	// initialize the Fortran
502	>	void SimSetup::makeElement(double x, double y, double z){
503	>	int k;
504	>	AtomStamp* current_atom;
505	>	DirectionalAtom* dAtom;
506	>	double rotMat[3][3];
507	>	double pos[3];
508
509	+	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
510	+	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	<	simnfo->refreshSim();
523	<
524	<	if( !strcmp( simnfo->mixingRule, "standard") ){
525	<	the_ff->initForceField( LB_MIXING_RULE );
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	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
529	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
530	>
531	>	rotMat[0][0] = 1.0;
532	>	rotMat[0][1] = 0.0;
533	>	rotMat[0][2] = 0.0;
534	>
535	>	rotMat[1][0] = 0.0;
536	>	rotMat[1][1] = 1.0;
537	>	rotMat[1][2] = 0.0;
538	>
539	>	rotMat[2][0] = 0.0;
540	>	rotMat[2][1] = 0.0;
541	>	rotMat[2][2] = 1.0;
542	>
543	>	dAtom->setA(rotMat);
544	>	}
545	>
546	>	current_atom_ndx++;
547		}
755	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
756	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
757	–	}
758	–	else{
759	–	sprintf( painCave.errMsg,
760	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
761	–	simnfo->mixingRule );
762	–	painCave.isFatal = 1;
763	–	simError();
764	–	}
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();
771	<	#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;
779	<	DirectionalAtom* dAtom;
780	<	LinkedAssign* extras;
781	<	LinkedAssign* current_extra;
782	<	AtomStamp* currentAtom;
783	<	BondStamp* currentBond;
784	<	BendStamp* currentBend;
785	<	TorsionStamp* currentTorsion;
562	>	ensembleCase = -1;
563	>	ffCase = -1;
564
565	<	bond_pair* theBonds;
788	<	bend_set* theBends;
789	<	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
794	–	the_ff->readParams();
574
575	<
797	<	// init the atoms
575	>	// get the forceField
576
577	<	double ux, uy, uz, u, uSqr;
800	<
801	<	atomOffset = 0;
802	<	excludeOffset = 0;
803	<	for(i=0; i<simnfo->n_mol; i++){
804	<
805	<	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;
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	<	info.myAtoms = &the_atoms[atomOffset];
814	<	info.myExcludes = &the_excludes[excludeOffset];
815	<	info.myBonds = new Bond*[info.nBonds];
816	<	info.myBends = new Bend*[info.nBends];
817	<	info.myTorsions = new Torsion*[info.nTorsions];
595	>	// get the ensemble
596
597	<	theBonds = new bond_pair[info.nBonds];
820	<	theBends = new bend_set[info.nBends];
821	<	theTorsions = new torsion_set[info.nTorsions];
822	<
823	<	// make the Atoms
824	<
825	<	for(j=0; j<info.nAtoms; j++){
826	<
827	<	currentAtom = comp_stamps[stampID]->getAtom( j );
828	<	if( currentAtom->haveOrientation() ){
829	<
830	<	dAtom = new DirectionalAtom(j + atomOffset);
831	<	simnfo->n_oriented++;
832	<	info.myAtoms[j] = dAtom;
833	<
834	<	ux = currentAtom->getOrntX();
835	<	uy = currentAtom->getOrntY();
836	<	uz = currentAtom->getOrntZ();
837	<
838	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
839	<
840	<	u = sqrt( uSqr );
841	<	ux = ux / u;
842	<	uy = uy / u;
843	<	uz = uz / u;
844	<
845	<	dAtom->setSUx( ux );
846	<	dAtom->setSUy( uy );
847	<	dAtom->setSUz( uz );
848	<	}
849	<	else{
850	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
851	<	}
852	<	info.myAtoms[j]->setType( currentAtom->getType() );
853	<
854	<	#ifdef IS_MPI
855	<
856	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
857	<
858	<	#endif // is_mpi
859	<	}
860	<
861	<	// make the bonds
862	<	for(j=0; j<info.nBonds; j++){
863	<
864	<	currentBond = comp_stamps[stampID]->getBond( j );
865	<	theBonds[j].a = currentBond->getA() + atomOffset;
866	<	theBonds[j].b = currentBond->getB() + atomOffset;
597	>	strcpy(ensemble, globals->getEnsemble());
598
599	<	exI = theBonds[j].a;
600	<	exJ = theBonds[j].b;
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	<	// exclude_I must always be the smaller of the pair
626	<	if( exI > exJ ){
873	<	tempEx = exI;
874	<	exI = exJ;
875	<	exJ = tempEx;
876	<	}
877	<	#ifdef IS_MPI
878	<	tempEx = exI;
879	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
880	<	tempEx = exJ;
881	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
882	<
883	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
884	<	#else  // isn't MPI
625	>	for (i = 0; i < nInfo; i++){
626	>	strcpy(info[i].ensemble, ensemble);
627
628	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
887	<	#endif  //is_mpi
888	<	}
889	<	excludeOffset += info.nBonds;
628	>	// get the mixing rule
629
630	<	//make the bends
631	<	for(j=0; j<info.nBends; j++){
632	<
894	<	currentBend = comp_stamps[stampID]->getBend( j );
895	<	theBends[j].a = currentBend->getA() + atomOffset;
896	<	theBends[j].b = currentBend->getB() + atomOffset;
897	<	theBends[j].c = currentBend->getC() + atomOffset;
898	<
899	<	if( currentBend->haveExtras() ){
900	<
901	<	extras = currentBend->getExtras();
902	<	current_extra = extras;
903	<
904	<	while( current_extra != NULL ){
905	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
906	<
907	<	switch( current_extra->getType() ){
908	<
909	<	case 0:
910	<	theBends[j].ghost =
911	<	current_extra->getInt() + atomOffset;
912	<	theBends[j].isGhost = 1;
913	<	break;
914	<
915	<	case 1:
916	<	theBends[j].ghost =
917	<	(int)current_extra->getDouble() + atomOffset;
918	<	theBends[j].isGhost = 1;
919	<	break;
920	<
921	<	default:
922	<	sprintf( painCave.errMsg,
923	<	"SimSetup Error: ghostVectorSource was neither a "
924	<	"double nor an int.\n"
925	<	"-->Bend[%d] in %s\n",
926	<	j, comp_stamps[stampID]->getID() );
927	<	painCave.isFatal = 1;
928	<	simError();
929	<	}
930	<	}
931	<
932	<	else{
933	<
934	<	sprintf( painCave.errMsg,
935	<	"SimSetup Error: unhandled bend assignment:\n"
936	<	"    -->%s in Bend[%d] in %s\n",
937	<	current_extra->getlhs(),
938	<	j, comp_stamps[stampID]->getID() );
939	<	painCave.isFatal = 1;
940	<	simError();
941	<	}
942	<
943	<	current_extra = current_extra->getNext();
944	<	}
945	<	}
946	<
947	<	if( !theBends[j].isGhost ){
948	<
949	<	exI = theBends[j].a;
950	<	exJ = theBends[j].c;
951	<	}
952	<	else{
953	<
954	<	exI = theBends[j].a;
955	<	exJ = theBends[j].b;
956	<	}
957	<
958	<	// exclude_I must always be the smaller of the pair
959	<	if( exI > exJ ){
960	<	tempEx = exI;
961	<	exI = exJ;
962	<	exJ = tempEx;
963	<	}
964	<	#ifdef IS_MPI
965	<	tempEx = exI;
966	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
967	<	tempEx = exJ;
968	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
969	<
970	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
971	<	#else  // isn't MPI
972	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
973	<	#endif  //is_mpi
974	<	}
975	<	excludeOffset += info.nBends;
630	>	strcpy(info[i].mixingRule, globals->getMixingRule());
631	>	info[i].usePBC = globals->getPBC();
632	>	}
633
634	<	for(j=0; j<info.nTorsions; j++){
978	<
979	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
980	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
981	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
982	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
983	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
984	<
985	<	exI = theTorsions[j].a;
986	<	exJ = theTorsions[j].d;
634	>	// get the components and calculate the tot_nMol and indvidual n_mol
635
636	<	// exclude_I must always be the smaller of the pair
637	<	if( exI > exJ ){
990	<	tempEx = exI;
991	<	exI = exJ;
992	<	exJ = tempEx;
993	<	}
994	<	#ifdef IS_MPI
995	<	tempEx = exI;
996	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
997	<	tempEx = exJ;
998	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
999	<
1000	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1001	<	#else  // isn't MPI
1002	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1003	<	#endif  //is_mpi
1004	<	}
1005	<	excludeOffset += info.nTorsions;
636	>	the_components = globals->getComponents();
637	>	components_nmol = new int[n_components];
638
1007	–
1008	–	// send the arrays off to the forceField for init.
639
640	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
641	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
642	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1013	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
640	>	if (!globals->haveNMol()){
641	>	// we don't have the total number of molecules, so we assume it is
642	>	// given in each component
643
644	+	tot_nmol = 0;
645	+	for (i = 0; i < n_components; i++){
646	+	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	<	the_molecules[i].initialize( info );
656	<
657	<
1019	<	atomOffset += info.nAtoms;
1020	<	delete[] theBonds;
1021	<	delete[] theBends;
1022	<	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
1026	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1027	<	MPIcheckPoint();
1028	<	#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;
1043	<	int n_extra;
1044	<	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;
1047	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1048	<	temp3 = ceil( temp2 );
698	>	// check for the temperature set flag
699
700	<	have_extra =0;
701	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1052	<	have_extra =1;
700	>	if (globals->haveTempSet())
701	>	info[i].setTemp = globals->getTempSet();
702
703	<	n_cells = (int)temp3 - 1;
1055	<	cellx = simnfo->box_x / temp3;
1056	<	celly = simnfo->box_y / temp3;
1057	<	cellz = simnfo->box_z / temp3;
1058	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1059	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1060	<	n_per_extra = (int)ceil( temp1 );
703	>	// get some of the tricky things that may still be in the globals
704
705	<	if( n_per_extra > 4){
706	<	sprintf( painCave.errMsg,
707	<	"SimSetup error. There has been an error in constructing"
708	<	" the non-complete lattice.\n" );
709	<	painCave.isFatal = 1;
710	<	simError();
705	>	double boxVector[3];
706	>	if (globals->haveBox()){
707	>	boxVector[0] = globals->getBox();
708	>	boxVector[1] = globals->getBox();
709	>	boxVector[2] = globals->getBox();
710	>
711	>	info[i].setBox(boxVector);
712		}
713	<	}
714	<	else{
715	<	n_cells = (int)temp3;
716	<	cellx = simnfo->box_x / temp3;
717	<	celly = simnfo->box_y / temp3;
718	<	cellz = simnfo->box_z / temp3;
1075	<	}
713	>	else if (globals->haveDensity()){
714	>	double vol;
715	>	vol = (double) tot_nmol / globals->getDensity();
716	>	boxVector[0] = pow(vol, (1.0 / 3.0));
717	>	boxVector[1] = boxVector[0];
718	>	boxVector[2] = boxVector[0];
719
720	<	current_mol = 0;
721	<	current_comp_mol = 0;
722	<	current_comp = 0;
723	<	current_atom_ndx = 0;
720	>	info[i].setBox(boxVector);
721	>	}
722	>	else{
723	>	if (!globals->haveBoxX()){
724	>	sprintf(painCave.errMsg,
725	>	"SimSetup error, no periodic BoxX size given.\n");
726	>	painCave.isFatal = 1;
727	>	simError();
728	>	}
729	>	boxVector[0] = globals->getBoxX();
730
731	<	for( i=0; i < n_cells ; i++ ){
732	<	for( j=0; j < n_cells; j++ ){
733	<	for( k=0; k < n_cells; k++ ){
731	>	if (!globals->haveBoxY()){
732	>	sprintf(painCave.errMsg,
733	>	"SimSetup error, no periodic BoxY size given.\n");
734	>	painCave.isFatal = 1;
735	>	simError();
736	>	}
737	>	boxVector[1] = globals->getBoxY();
738
739	<	makeElement( i * cellx,
740	<	j * celly,
741	<	k * cellz );
739	>	if (!globals->haveBoxZ()){
740	>	sprintf(painCave.errMsg,
741	>	"SimSetup error, no periodic BoxZ size given.\n");
742	>	painCave.isFatal = 1;
743	>	simError();
744	>	}
745	>	boxVector[2] = globals->getBoxZ();
746
747	<	makeElement( i * cellx + 0.5 * cellx,
748	<	j * celly + 0.5 * celly,
749	<	k * cellz );
747	>	info[i].setBox(boxVector);
748	>	}
749	>	}
750
751	<	makeElement( i * cellx,
752	<	j * celly + 0.5 * celly,
1096	<	k * cellz + 0.5 * cellz );
751	>	//setup seed for random number generator
752	>	int seedValue;
753
754	<	makeElement( i * cellx + 0.5 * cellx,
755	<	j * celly,
756	<	k * cellz + 0.5 * cellz );
754	>	if (globals->haveSeed()){
755	>	seedValue = globals->getSeed();
756	>
757	>	if(seedValue / 1E9 == 0){
758	>	sprintf(painCave.errMsg,
759	>	"Seed for sprng library should contain at least 9 digits\n"
760	>	"OOPSE will generate a seed for user\n");
761	>	painCave.isFatal = 0;
762	>	simError();
763	>
764	>	//using seed generated by system instead of invalid seed set by user
765	>	#ifndef IS_MPI
766	>	seedValue = make_sprng_seed();
767	>	#else
768	>	if (worldRank == 0){
769	>	seedValue = make_sprng_seed();
770		}
771	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
772	+	#endif
773		}
774	+	}//end of if branch of globals->haveSeed()
775	+	else{
776	+
777	+	#ifndef IS_MPI
778	+	seedValue = make_sprng_seed();
779	+	#else
780	+	if (worldRank == 0){
781	+	seedValue = make_sprng_seed();
782	+	}
783	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
784	+	#endif
785	+	}//end of globals->haveSeed()
786	+
787	+	for (int i = 0; i < nInfo; i++){
788	+	info[i].setSeed(seedValue);
789		}
790
791	<	if( have_extra ){
792	<	done = 0;
791	>	#ifdef IS_MPI
792	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
793	>	MPIcheckPoint();
794	>	#endif // is_mpi
795	>	}
796
1108	–	int start_ndx;
1109	–	for( i=0; i < (n_cells+1) && !done; i++ ){
1110	–	for( j=0; j < (n_cells+1) && !done; j++ ){
797
798	<	if( i < n_cells ){
798	>	void SimSetup::finalInfoCheck(void){
799	>	int index;
800	>	int usesDipoles;
801	>	int i;
802
803	<	if( j < n_cells ){
804	<	start_ndx = n_cells;
1116	<	}
1117	<	else start_ndx = 0;
1118	<	}
1119	<	else start_ndx = 0;
803	>	for (i = 0; i < nInfo; i++){
804	>	// check electrostatic parameters
805
806	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
806	>	index = 0;
807	>	usesDipoles = 0;
808	>	while ((index < info[i].n_atoms) && !usesDipoles){
809	>	usesDipoles = (info[i].atoms[index])->hasDipole();
810	>	index++;
811	>	}
812
813	<	makeElement( i * cellx,
814	<	j * celly,
815	<	k * cellz );
816	<	done = ( current_mol >= tot_nmol );
813	>	#ifdef IS_MPI
814	>	int myUse = usesDipoles;
815	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
816	>	#endif //is_mpi
817
818	<	if( !done && n_per_extra > 1 ){
1129	<	makeElement( i * cellx + 0.5 * cellx,
1130	<	j * celly + 0.5 * celly,
1131	<	k * cellz );
1132	<	done = ( current_mol >= tot_nmol );
1133	<	}
818	>	double theEcr, theEst;
819
820	<	if( !done && n_per_extra > 2){
821	<	makeElement( i * cellx,
1137	<	j * celly + 0.5 * celly,
1138	<	k * cellz + 0.5 * cellz );
1139	<	done = ( current_mol >= tot_nmol );
1140	<	}
820	>	if (globals->getUseRF()){
821	>	info[i].useReactionField = 1;
822
823	<	if( !done && n_per_extra > 3){
824	<	makeElement( i * cellx + 0.5 * cellx,
825	<	j * celly,
826	<	k * cellz + 0.5 * cellz );
827	<	done = ( current_mol >= tot_nmol );
828	<	}
829	<	}
823	>	if (!globals->haveECR()){
824	>	sprintf(painCave.errMsg,
825	>	"SimSetup Warning: using default value of 1/2 the smallest "
826	>	"box length for the electrostaticCutoffRadius.\n"
827	>	"I hope you have a very fast processor!\n");
828	>	painCave.isFatal = 0;
829	>	simError();
830	>	double smallest;
831	>	smallest = info[i].boxL[0];
832	>	if (info[i].boxL[1] <= smallest)
833	>	smallest = info[i].boxL[1];
834	>	if (info[i].boxL[2] <= smallest)
835	>	smallest = info[i].boxL[2];
836	>	theEcr = 0.5 * smallest;
837		}
838	+	else{
839	+	theEcr = globals->getECR();
840	+	}
841	+
842	+	if (!globals->haveEST()){
843	+	sprintf(painCave.errMsg,
844	+	"SimSetup Warning: using default value of 0.05 * the "
845	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
846	+	painCave.isFatal = 0;
847	+	simError();
848	+	theEst = 0.05 * theEcr;
849	+	}
850	+	else{
851	+	theEst = globals->getEST();
852	+	}
853	+
854	+	info[i].setEcr(theEcr, theEst);
855	+
856	+	if (!globals->haveDielectric()){
857	+	sprintf(painCave.errMsg,
858	+	"SimSetup Error: You are trying to use Reaction Field without"
859	+	"setting a dielectric constant!\n");
860	+	painCave.isFatal = 1;
861	+	simError();
862	+	}
863	+	info[i].dielectric = globals->getDielectric();
864		}
865	<	}
865	>	else{
866	>	if (usesDipoles){
867	>	if (!globals->haveECR()){
868	>	sprintf(painCave.errMsg,
869	>	"SimSetup Warning: using default value of 1/2 the smallest "
870	>	"box length for the electrostaticCutoffRadius.\n"
871	>	"I hope you have a very fast processor!\n");
872	>	painCave.isFatal = 0;
873	>	simError();
874	>	double smallest;
875	>	smallest = info[i].boxL[0];
876	>	if (info[i].boxL[1] <= smallest)
877	>	smallest = info[i].boxL[1];
878	>	if (info[i].boxL[2] <= smallest)
879	>	smallest = info[i].boxL[2];
880	>	theEcr = 0.5 * smallest;
881	>	}
882	>	else{
883	>	theEcr = globals->getECR();
884	>	}
885
886	+	if (!globals->haveEST()){
887	+	sprintf(painCave.errMsg,
888	+	"SimSetup Warning: using default value of 0.05 * the "
889	+	"electrostaticCutoffRadius for the "
890	+	"electrostaticSkinThickness\n");
891	+	painCave.isFatal = 0;
892	+	simError();
893	+	theEst = 0.05 * theEcr;
894	+	}
895	+	else{
896	+	theEst = globals->getEST();
897	+	}
898
899	<	for( i=0; i<simnfo->n_atoms; i++ ){
900	<	simnfo->atoms[i]->set_vx( 0.0 );
901	<	simnfo->atoms[i]->set_vy( 0.0 );
1157	<	simnfo->atoms[i]->set_vz( 0.0 );
899	>	info[i].setEcr(theEcr, theEst);
900	>	}
901	>	}
902		}
903	+
904	+	#ifdef IS_MPI
905	+	strcpy(checkPointMsg, "post processing checks out");
906	+	MPIcheckPoint();
907	+	#endif // is_mpi
908		}
909
910	<	void SimSetup::makeElement( double x, double y, double z ){
910	>	void SimSetup::initSystemCoords(void){
911	>	int i;
912
913	<	int k;
1164	<	AtomStamp* current_atom;
1165	<	DirectionalAtom* dAtom;
1166	<	double rotMat[3][3];
913	>	char* inName;
914
915	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
915	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
916
917	<	current_atom = comp_stamps[current_comp]->getAtom( k );
918	<	if( !current_atom->havePosition() ){
919	<	sprintf( painCave.errMsg,
920	<	"SimSetup:initFromBass error.\n"
921	<	"\tComponent %s, atom %s does not have a position specified.\n"
922	<	"\tThe initialization routine is unable to give a start"
923	<	" position.\n",
924	<	comp_stamps[current_comp]->getID(),
925	<	current_atom->getType() );
926	<	painCave.isFatal = 1;
927	<	simError();
917	>	for (i = 0; i < info[0].n_atoms; i++)
918	>	info[0].atoms[i]->setCoords();
919	>
920	>	if (globals->haveInitialConfig()){
921	>	InitializeFromFile* fileInit;
922	>	#ifdef IS_MPI // is_mpi
923	>	if (worldRank == 0){
924	>	#endif //is_mpi
925	>	inName = globals->getInitialConfig();
926	>	fileInit = new InitializeFromFile(inName);
927	>	#ifdef IS_MPI
928		}
929	+	else
930	+	fileInit = new InitializeFromFile(NULL);
931	+	#endif
932	+	fileInit->readInit(info); // default velocities on
933
934	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
935	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
936	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
934	>	delete fileInit;
935	>	}
936	>	else{
937	>	#ifdef IS_MPI
938
939	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
939	>	// no init from bass
940
941	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
941	>	sprintf(painCave.errMsg,
942	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
943	>	painCave.isFatal = 1;;
944	>	simError();
945
946	<	rotMat[0][0] = 1.0;
1192	<	rotMat[0][1] = 0.0;
1193	<	rotMat[0][2] = 0.0;
946	>	#else
947
948	<	rotMat[1][0] = 0.0;
1196	<	rotMat[1][1] = 1.0;
1197	<	rotMat[1][2] = 0.0;
948	>	initFromBass();
949
1199	–	rotMat[2][0] = 0.0;
1200	–	rotMat[2][1] = 0.0;
1201	–	rotMat[2][2] = 1.0;
950
951	<	dAtom->setA( rotMat );
1204	<	}
1205	<
1206	<	current_atom_ndx++;
951	>	#endif
952		}
953
954	<	current_mol++;
955	<	current_comp_mol++;
954	>	#ifdef IS_MPI
955	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
956	>	MPIcheckPoint();
957	>	#endif // is_mpi
958	>	}
959
1212	–	if( current_comp_mol >= components_nmol[current_comp] ){
960
961	<	current_comp_mol = 0;
962	<	current_comp++;
961	>	void SimSetup::makeOutNames(void){
962	>	int k;
963	>
964	>
965	>	for (k = 0; k < nInfo; k++){
966	>	#ifdef IS_MPI
967	>	if (worldRank == 0){
968	>	#endif // is_mpi
969	>
970	>	if (globals->haveFinalConfig()){
971	>	strcpy(info[k].finalName, globals->getFinalConfig());
972	>	}
973	>	else{
974	>	strcpy(info[k].finalName, inFileName);
975	>	char* endTest;
976	>	int nameLength = strlen(info[k].finalName);
977	>	endTest = &(info[k].finalName[nameLength - 5]);
978	>	if (!strcmp(endTest, ".bass")){
979	>	strcpy(endTest, ".eor");
980	>	}
981	>	else if (!strcmp(endTest, ".BASS")){
982	>	strcpy(endTest, ".eor");
983	>	}
984	>	else{
985	>	endTest = &(info[k].finalName[nameLength - 4]);
986	>	if (!strcmp(endTest, ".bss")){
987	>	strcpy(endTest, ".eor");
988	>	}
989	>	else if (!strcmp(endTest, ".mdl")){
990	>	strcpy(endTest, ".eor");
991	>	}
992	>	else{
993	>	strcat(info[k].finalName, ".eor");
994	>	}
995	>	}
996	>	}
997	>
998	>	// make the sample and status out names
999	>
1000	>	strcpy(info[k].sampleName, inFileName);
1001	>	char* endTest;
1002	>	int nameLength = strlen(info[k].sampleName);
1003	>	endTest = &(info[k].sampleName[nameLength - 5]);
1004	>	if (!strcmp(endTest, ".bass")){
1005	>	strcpy(endTest, ".dump");
1006	>	}
1007	>	else if (!strcmp(endTest, ".BASS")){
1008	>	strcpy(endTest, ".dump");
1009	>	}
1010	>	else{
1011	>	endTest = &(info[k].sampleName[nameLength - 4]);
1012	>	if (!strcmp(endTest, ".bss")){
1013	>	strcpy(endTest, ".dump");
1014	>	}
1015	>	else if (!strcmp(endTest, ".mdl")){
1016	>	strcpy(endTest, ".dump");
1017	>	}
1018	>	else{
1019	>	strcat(info[k].sampleName, ".dump");
1020	>	}
1021	>	}
1022	>
1023	>	strcpy(info[k].statusName, inFileName);
1024	>	nameLength = strlen(info[k].statusName);
1025	>	endTest = &(info[k].statusName[nameLength - 5]);
1026	>	if (!strcmp(endTest, ".bass")){
1027	>	strcpy(endTest, ".stat");
1028	>	}
1029	>	else if (!strcmp(endTest, ".BASS")){
1030	>	strcpy(endTest, ".stat");
1031	>	}
1032	>	else{
1033	>	endTest = &(info[k].statusName[nameLength - 4]);
1034	>	if (!strcmp(endTest, ".bss")){
1035	>	strcpy(endTest, ".stat");
1036	>	}
1037	>	else if (!strcmp(endTest, ".mdl")){
1038	>	strcpy(endTest, ".stat");
1039	>	}
1040	>	else{
1041	>	strcat(info[k].statusName, ".stat");
1042	>	}
1043	>	}
1044	>
1045	>	#ifdef IS_MPI
1046	>
1047	>	}
1048	>	#endif // is_mpi
1049	>	}
1050	>	}
1051	>
1052	>
1053	>	void SimSetup::sysObjectsCreation(void){
1054	>	int i, k;
1055	>
1056	>	// create the forceField
1057	>
1058	>	createFF();
1059	>
1060	>	// extract componentList
1061	>
1062	>	compList();
1063	>
1064	>	// calc the number of atoms, bond, bends, and torsions
1065	>
1066	>	calcSysValues();
1067	>
1068	>	#ifdef IS_MPI
1069	>	// divide the molecules among the processors
1070	>
1071	>	mpiMolDivide();
1072	>	#endif //is_mpi
1073	>
1074	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1075	>
1076	>	makeSysArrays();
1077	>
1078	>	// make and initialize the molecules (all but atomic coordinates)
1079	>
1080	>	makeMolecules();
1081	>
1082	>	for (k = 0; k < nInfo; k++){
1083	>	info[k].identArray = new int[info[k].n_atoms];
1084	>	for (i = 0; i < info[k].n_atoms; i++){
1085	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1086	>	}
1087	>	}
1088	>	}
1089	>
1090	>
1091	>	void SimSetup::createFF(void){
1092	>	switch (ffCase){
1093	>	case FF_DUFF:
1094	>	the_ff = new DUFF();
1095	>	break;
1096	>
1097	>	case FF_LJ:
1098	>	the_ff = new LJFF();
1099	>	break;
1100	>
1101	>	case FF_EAM:
1102	>	the_ff = new EAM_FF();
1103	>	break;
1104	>
1105	>	default:
1106	>	sprintf(painCave.errMsg,
1107	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1108	>	painCave.isFatal = 1;
1109	>	simError();
1110	>	}
1111	>
1112	>	#ifdef IS_MPI
1113	>	strcpy(checkPointMsg, "ForceField creation successful");
1114	>	MPIcheckPoint();
1115	>	#endif // is_mpi
1116	>	}
1117	>
1118	>
1119	>	void SimSetup::compList(void){
1120	>	int i;
1121	>	char* id;
1122	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1123	>	LinkedMolStamp* currentStamp = NULL;
1124	>	comp_stamps = new MoleculeStamp * [n_components];
1125	>
1126	>	// make an array of molecule stamps that match the components used.
1127	>	// also extract the used stamps out into a separate linked list
1128	>
1129	>	for (i = 0; i < nInfo; i++){
1130	>	info[i].nComponents = n_components;
1131	>	info[i].componentsNmol = components_nmol;
1132	>	info[i].compStamps = comp_stamps;
1133	>	info[i].headStamp = headStamp;
1134	>	}
1135	>
1136	>
1137	>	for (i = 0; i < n_components; i++){
1138	>	id = the_components[i]->getType();
1139	>	comp_stamps[i] = NULL;
1140	>
1141	>	// check to make sure the component isn't already in the list
1142	>
1143	>	comp_stamps[i] = headStamp->match(id);
1144	>	if (comp_stamps[i] == NULL){
1145	>	// extract the component from the list;
1146	>
1147	>	currentStamp = stamps->extractMolStamp(id);
1148	>	if (currentStamp == NULL){
1149	>	sprintf(painCave.errMsg,
1150	>	"SimSetup error: Component \"%s\" was not found in the "
1151	>	"list of declared molecules\n",
1152	>	id);
1153	>	painCave.isFatal = 1;
1154	>	simError();
1155	>	}
1156	>
1157	>	headStamp->add(currentStamp);
1158	>	comp_stamps[i] = headStamp->match(id);
1159	>	}
1160	>	}
1161	>
1162	>	#ifdef IS_MPI
1163	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1164	>	MPIcheckPoint();
1165	>	#endif // is_mpi
1166	>	}
1167	>
1168	>	void SimSetup::calcSysValues(void){
1169	>	int i;
1170	>
1171	>	int* molMembershipArray;
1172	>
1173	>	tot_atoms = 0;
1174	>	tot_bonds = 0;
1175	>	tot_bends = 0;
1176	>	tot_torsions = 0;
1177	>	for (i = 0; i < n_components; i++){
1178	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1179	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1180	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1181	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1182	>	}
1183	>
1184	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1185	>	molMembershipArray = new int[tot_atoms];
1186	>
1187	>	for (i = 0; i < nInfo; i++){
1188	>	info[i].n_atoms = tot_atoms;
1189	>	info[i].n_bonds = tot_bonds;
1190	>	info[i].n_bends = tot_bends;
1191	>	info[i].n_torsions = tot_torsions;
1192	>	info[i].n_SRI = tot_SRI;
1193	>	info[i].n_mol = tot_nmol;
1194	>
1195	>	info[i].molMembershipArray = molMembershipArray;
1196	>	}
1197	>	}
1198	>
1199	>	#ifdef IS_MPI
1200	>
1201	>	void SimSetup::mpiMolDivide(void){
1202	>	int i, j, k;
1203	>	int localMol, allMol;
1204	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1205	>
1206	>	mpiSim = new mpiSimulation(info);
1207	>
1208	>	globalIndex = mpiSim->divideLabor();
1209	>
1210	>	// set up the local variables
1211	>
1212	>	mol2proc = mpiSim->getMolToProcMap();
1213	>	molCompType = mpiSim->getMolComponentType();
1214	>
1215	>	allMol = 0;
1216	>	localMol = 0;
1217	>	local_atoms = 0;
1218	>	local_bonds = 0;
1219	>	local_bends = 0;
1220	>	local_torsions = 0;
1221	>	globalAtomIndex = 0;
1222	>
1223	>
1224	>	for (i = 0; i < n_components; i++){
1225	>	for (j = 0; j < components_nmol[i]; j++){
1226	>	if (mol2proc[allMol] == worldRank){
1227	>	local_atoms += comp_stamps[i]->getNAtoms();
1228	>	local_bonds += comp_stamps[i]->getNBonds();
1229	>	local_bends += comp_stamps[i]->getNBends();
1230	>	local_torsions += comp_stamps[i]->getNTorsions();
1231	>	localMol++;
1232	>	}
1233	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1234	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1235	>	globalAtomIndex++;
1236	>	}
1237	>
1238	>	allMol++;
1239	>	}
1240	>	}
1241	>	local_SRI = local_bonds + local_bends + local_torsions;
1242	>
1243	>	info[0].n_atoms = mpiSim->getMyNlocal();
1244	>
1245	>	if (local_atoms != info[0].n_atoms){
1246	>	sprintf(painCave.errMsg,
1247	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1248	>	" localAtom (%d) are not equal.\n",
1249	>	info[0].n_atoms, local_atoms);
1250	>	painCave.isFatal = 1;
1251	>	simError();
1252	>	}
1253	>
1254	>	info[0].n_bonds = local_bonds;
1255	>	info[0].n_bends = local_bends;
1256	>	info[0].n_torsions = local_torsions;
1257	>	info[0].n_SRI = local_SRI;
1258	>	info[0].n_mol = localMol;
1259	>
1260	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1261	>	MPIcheckPoint();
1262	>	}
1263	>
1264	>	#endif // is_mpi
1265	>
1266	>
1267	>	void SimSetup::makeSysArrays(void){
1268	>
1269	>	#ifndef IS_MPI
1270	>	int k, j;
1271	>	#endif // is_mpi
1272	>	int i, l;
1273	>
1274	>	Atom** the_atoms;
1275	>	Molecule* the_molecules;
1276	>	Exclude** the_excludes;
1277	>
1278	>
1279	>	for (l = 0; l < nInfo; l++){
1280	>	// create the atom and short range interaction arrays
1281	>
1282	>	the_atoms = new Atom * [info[l].n_atoms];
1283	>	the_molecules = new Molecule[info[l].n_mol];
1284	>	int molIndex;
1285	>
1286	>	// initialize the molecule's stampID's
1287	>
1288	>	#ifdef IS_MPI
1289	>
1290	>
1291	>	molIndex = 0;
1292	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1293	>	if (mol2proc[i] == worldRank){
1294	>	the_molecules[molIndex].setStampID(molCompType[i]);
1295	>	the_molecules[molIndex].setMyIndex(molIndex);
1296	>	the_molecules[molIndex].setGlobalIndex(i);
1297	>	molIndex++;
1298	>	}
1299	>	}
1300	>
1301	>	#else // is_mpi
1302	>
1303	>	molIndex = 0;
1304	>	globalAtomIndex = 0;
1305	>	for (i = 0; i < n_components; i++){
1306	>	for (j = 0; j < components_nmol[i]; j++){
1307	>	the_molecules[molIndex].setStampID(i);
1308	>	the_molecules[molIndex].setMyIndex(molIndex);
1309	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1310	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1311	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1312	>	globalAtomIndex++;
1313	>	}
1314	>	molIndex++;
1315	>	}
1316	>	}
1317	>
1318	>
1319	>	#endif // is_mpi
1320	>
1321	>
1322	>	if (info[l].n_SRI){
1323	>	Exclude::createArray(info[l].n_SRI);
1324	>	the_excludes = new Exclude * [info[l].n_SRI];
1325	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1326	>	the_excludes[ex] = new Exclude(ex);
1327	>	}
1328	>	info[l].globalExcludes = new int;
1329	>	info[l].n_exclude = info[l].n_SRI;
1330	>	}
1331	>	else{
1332	>	Exclude::createArray(1);
1333	>	the_excludes = new Exclude * ;
1334	>	the_excludes[0] = new Exclude(0);
1335	>	the_excludes[0]->setPair(0, 0);
1336	>	info[l].globalExcludes = new int;
1337	>	info[l].globalExcludes[0] = 0;
1338	>	info[l].n_exclude = 0;
1339	>	}
1340	>
1341	>	// set the arrays into the SimInfo object
1342	>
1343	>	info[l].atoms = the_atoms;
1344	>	info[l].molecules = the_molecules;
1345	>	info[l].nGlobalExcludes = 0;
1346	>	info[l].excludes = the_excludes;
1347	>
1348	>	the_ff->setSimInfo(info);
1349		}
1350		}
1351	+
1352	+	void SimSetup::makeIntegrator(void){
1353	+	int k;
1354	+
1355	+	NVE<RealIntegrator>* myNVE = NULL;
1356	+	NVT<RealIntegrator>* myNVT = NULL;
1357	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1358	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1359	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1360	+
1361	+	for (k = 0; k < nInfo; k++){
1362	+	switch (ensembleCase){
1363	+	case NVE_ENS:
1364	+	if (globals->haveZconstraints()){
1365	+	setupZConstraint(info[k]);
1366	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1367	+	}
1368	+	else{
1369	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1370	+	}
1371	+
1372	+	info->the_integrator = myNVE;
1373	+	break;
1374	+
1375	+	case NVT_ENS:
1376	+	if (globals->haveZconstraints()){
1377	+	setupZConstraint(info[k]);
1378	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1379	+	}
1380	+	else
1381	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1382	+
1383	+	myNVT->setTargetTemp(globals->getTargetTemp());
1384	+
1385	+	if (globals->haveTauThermostat())
1386	+	myNVT->setTauThermostat(globals->getTauThermostat());
1387	+	else{
1388	+	sprintf(painCave.errMsg,
1389	+	"SimSetup error: If you use the NVT\n"
1390	+	"    ensemble, you must set tauThermostat.\n");
1391	+	painCave.isFatal = 1;
1392	+	simError();
1393	+	}
1394	+
1395	+	info->the_integrator = myNVT;
1396	+	break;
1397	+
1398	+	case NPTi_ENS:
1399	+	if (globals->haveZconstraints()){
1400	+	setupZConstraint(info[k]);
1401	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1402	+	}
1403	+	else
1404	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1405	+
1406	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1407	+
1408	+	if (globals->haveTargetPressure())
1409	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1410	+	else{
1411	+	sprintf(painCave.errMsg,
1412	+	"SimSetup error: If you use a constant pressure\n"
1413	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1414	+	painCave.isFatal = 1;
1415	+	simError();
1416	+	}
1417	+
1418	+	if (globals->haveTauThermostat())
1419	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1420	+	else{
1421	+	sprintf(painCave.errMsg,
1422	+	"SimSetup error: If you use an NPT\n"
1423	+	"    ensemble, you must set tauThermostat.\n");
1424	+	painCave.isFatal = 1;
1425	+	simError();
1426	+	}
1427	+
1428	+	if (globals->haveTauBarostat())
1429	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1430	+	else{
1431	+	sprintf(painCave.errMsg,
1432	+	"SimSetup error: If you use an NPT\n"
1433	+	"    ensemble, you must set tauBarostat.\n");
1434	+	painCave.isFatal = 1;
1435	+	simError();
1436	+	}
1437	+
1438	+	info->the_integrator = myNPTi;
1439	+	break;
1440	+
1441	+	case NPTf_ENS:
1442	+	if (globals->haveZconstraints()){
1443	+	setupZConstraint(info[k]);
1444	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1445	+	}
1446	+	else
1447	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1448	+
1449	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1450	+
1451	+	if (globals->haveTargetPressure())
1452	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1453	+	else{
1454	+	sprintf(painCave.errMsg,
1455	+	"SimSetup error: If you use a constant pressure\n"
1456	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1457	+	painCave.isFatal = 1;
1458	+	simError();
1459	+	}
1460	+
1461	+	if (globals->haveTauThermostat())
1462	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1463	+	else{
1464	+	sprintf(painCave.errMsg,
1465	+	"SimSetup error: If you use an NPT\n"
1466	+	"    ensemble, you must set tauThermostat.\n");
1467	+	painCave.isFatal = 1;
1468	+	simError();
1469	+	}
1470	+
1471	+	if (globals->haveTauBarostat())
1472	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1473	+	else{
1474	+	sprintf(painCave.errMsg,
1475	+	"SimSetup error: If you use an NPT\n"
1476	+	"    ensemble, you must set tauBarostat.\n");
1477	+	painCave.isFatal = 1;
1478	+	simError();
1479	+	}
1480	+
1481	+	info->the_integrator = myNPTf;
1482	+	break;
1483	+
1484	+	case NPTxyz_ENS:
1485	+	if (globals->haveZconstraints()){
1486	+	setupZConstraint(info[k]);
1487	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1488	+	}
1489	+	else
1490	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1491	+
1492	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1493	+
1494	+	if (globals->haveTargetPressure())
1495	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1496	+	else{
1497	+	sprintf(painCave.errMsg,
1498	+	"SimSetup error: If you use a constant pressure\n"
1499	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1500	+	painCave.isFatal = 1;
1501	+	simError();
1502	+	}
1503	+
1504	+	if (globals->haveTauThermostat())
1505	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1506	+	else{
1507	+	sprintf(painCave.errMsg,
1508	+	"SimSetup error: If you use an NPT\n"
1509	+	"    ensemble, you must set tauThermostat.\n");
1510	+	painCave.isFatal = 1;
1511	+	simError();
1512	+	}
1513	+
1514	+	if (globals->haveTauBarostat())
1515	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1516	+	else{
1517	+	sprintf(painCave.errMsg,
1518	+	"SimSetup error: If you use an NPT\n"
1519	+	"    ensemble, you must set tauBarostat.\n");
1520	+	painCave.isFatal = 1;
1521	+	simError();
1522	+	}
1523	+
1524	+	info->the_integrator = myNPTxyz;
1525	+	break;
1526	+
1527	+	default:
1528	+	sprintf(painCave.errMsg,
1529	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1530	+	painCave.isFatal = 1;
1531	+	simError();
1532	+	}
1533	+	}
1534	+	}
1535	+
1536	+	void SimSetup::initFortran(void){
1537	+	info[0].refreshSim();
1538	+
1539	+	if (!strcmp(info[0].mixingRule, "standard")){
1540	+	the_ff->initForceField(LB_MIXING_RULE);
1541	+	}
1542	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1543	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1544	+	}
1545	+	else{
1546	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1547	+	info[0].mixingRule);
1548	+	painCave.isFatal = 1;
1549	+	simError();
1550	+	}
1551	+
1552	+
1553	+	#ifdef IS_MPI
1554	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1555	+	MPIcheckPoint();
1556	+	#endif // is_mpi
1557	+	}
1558	+
1559	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1560	+	int nZConstraints;
1561	+	ZconStamp** zconStamp;
1562	+
1563	+	if (globals->haveZconstraintTime()){
1564	+	//add sample time of z-constraint  into SimInfo's property list
1565	+	DoubleData* zconsTimeProp = new DoubleData();
1566	+	zconsTimeProp->setID(ZCONSTIME_ID);
1567	+	zconsTimeProp->setData(globals->getZconsTime());
1568	+	theInfo.addProperty(zconsTimeProp);
1569	+	}
1570	+	else{
1571	+	sprintf(painCave.errMsg,
1572	+	"ZConstraint error: If you use an ZConstraint\n"
1573	+	" , you must set sample time.\n");
1574	+	painCave.isFatal = 1;
1575	+	simError();
1576	+	}
1577	+
1578	+	//push zconsTol into siminfo, if user does not specify
1579	+	//value for zconsTol, a default value will be used
1580	+	DoubleData* zconsTol = new DoubleData();
1581	+	zconsTol->setID(ZCONSTOL_ID);
1582	+	if (globals->haveZconsTol()){
1583	+	zconsTol->setData(globals->getZconsTol());
1584	+	}
1585	+	else{
1586	+	double defaultZConsTol = 0.01;
1587	+	sprintf(painCave.errMsg,
1588	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1589	+	" , default value %f is used.\n",
1590	+	defaultZConsTol);
1591	+	painCave.isFatal = 0;
1592	+	simError();
1593	+
1594	+	zconsTol->setData(defaultZConsTol);
1595	+	}
1596	+	theInfo.addProperty(zconsTol);
1597	+
1598	+	//set Force Subtraction Policy
1599	+	StringData* zconsForcePolicy = new StringData();
1600	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1601	+
1602	+	if (globals->haveZconsForcePolicy()){
1603	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1604	+	}
1605	+	else{
1606	+	sprintf(painCave.errMsg,
1607	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1608	+	"PolicyByMass is used\n");
1609	+	painCave.isFatal = 0;
1610	+	simError();
1611	+	zconsForcePolicy->setData("BYMASS");
1612	+	}
1613	+
1614	+	theInfo.addProperty(zconsForcePolicy);
1615	+
1616	+	//Determine the name of ouput file and add it into SimInfo's property list
1617	+	//Be careful, do not use inFileName, since it is a pointer which
1618	+	//point to a string at master node, and slave nodes do not contain that string
1619	+
1620	+	string zconsOutput(theInfo.finalName);
1621	+
1622	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1623	+
1624	+	StringData* zconsFilename = new StringData();
1625	+	zconsFilename->setID(ZCONSFILENAME_ID);
1626	+	zconsFilename->setData(zconsOutput);
1627	+
1628	+	theInfo.addProperty(zconsFilename);
1629	+
1630	+	//setup index, pos and other parameters of z-constraint molecules
1631	+	nZConstraints = globals->getNzConstraints();
1632	+	theInfo.nZconstraints = nZConstraints;
1633	+
1634	+	zconStamp = globals->getZconStamp();
1635	+	ZConsParaItem tempParaItem;
1636	+
1637	+	ZConsParaData* zconsParaData = new ZConsParaData();
1638	+	zconsParaData->setID(ZCONSPARADATA_ID);
1639	+
1640	+	for (int i = 0; i < nZConstraints; i++){
1641	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1642	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1643	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1644	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1645	+
1646	+	zconsParaData->addItem(tempParaItem);
1647	+	}
1648	+
1649	+	//check the uniqueness of index
1650	+	if(!zconsParaData->isIndexUnique()){
1651	+	sprintf(painCave.errMsg,
1652	+	"ZConstraint Error: molIndex is not unique\n");
1653	+	painCave.isFatal = 1;
1654	+	simError();
1655	+	}
1656	+
1657	+	//sort the parameters by index of molecules
1658	+	zconsParaData->sortByIndex();
1659	+
1660	+	//push data into siminfo, therefore, we can retrieve later
1661	+	theInfo.addProperty(zconsParaData);
1662	+	}

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