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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 561 by mmeineke, Fri Jun 20 20:29:36 2003 UTC vs.
Revision 812 by mmeineke, Wed Oct 22 21:17:32 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6	+	#include <sprng.h>
7
8		#include "SimSetup.hpp"
9	+	#include "ReadWrite.hpp"
10		#include "parse_me.h"
11		#include "Integrator.hpp"
12		#include "simError.h"
#	Line 14 | Line 18
18
19		// some defines for ensemble and Forcefield  cases
20
21	<	#define NVE_ENS 0
22	<	#define NVT_ENS 1
23	<	#define NPT_ENS 2
21	>	#define NVE_ENS        0
22	>	#define NVT_ENS        1
23	>	#define NPTi_ENS       2
24	>	#define NPTf_ENS       3
25	>	#define NPTxyz_ENS     4
26
27	+
28		#define FF_DUFF 0
29		#define FF_LJ   1
30	+	#define FF_EAM  2
31
32	+	using namespace std;
33
34		SimSetup::SimSetup(){
35	+	isInfoArray = 0;
36	+	nInfo = 1;
37	+
38		stamps = new MakeStamps();
39		globals = new Globals();
40	<
40	>
41	>
42		#ifdef IS_MPI
43	<	strcpy( checkPointMsg, "SimSetup creation successful" );
43	>	strcpy(checkPointMsg, "SimSetup creation successful");
44		MPIcheckPoint();
45		#endif // IS_MPI
46		}
#	Line 37 | Line 50 | void SimSetup::parseFile( char* fileName ){
50		delete globals;
51		}
52
53	<	void SimSetup::parseFile( char* fileName ){
53	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
54	>	info = the_info;
55	>	nInfo = theNinfo;
56	>	isInfoArray = 1;
57	>	}
58
59	+
60	+	void SimSetup::parseFile(char* fileName){
61		#ifdef IS_MPI
62	<	if( worldRank == 0 ){
62	>	if (worldRank == 0){
63		#endif // is_mpi
64	<
64	>
65		inFileName = fileName;
66	<	set_interface_stamps( stamps, globals );
67	<
66	>	set_interface_stamps(stamps, globals);
67	>
68		#ifdef IS_MPI
69		mpiEventInit();
70		#endif
71
72	<	yacc_BASS( fileName );
72	>	yacc_BASS(fileName);
73
74		#ifdef IS_MPI
75		throwMPIEvent(NULL);
76		}
77	<	else receiveParse();
77	>	else{
78	>	receiveParse();
79	>	}
80		#endif
81
82		}
83
84		#ifdef IS_MPI
85		void SimSetup::receiveParse(void){
86	<
87	<	set_interface_stamps( stamps, globals );
88	<	mpiEventInit();
89	<	MPIcheckPoint();
69	<	mpiEventLoop();
70	<
86	>	set_interface_stamps(stamps, globals);
87	>	mpiEventInit();
88	>	MPIcheckPoint();
89	>	mpiEventLoop();
90		}
91
92		#endif // is_mpi
93
94	<	void SimSetup::createSim( void ){
94	>	void SimSetup::createSim(void){
95
96	<	MakeStamps *the_stamps;
78	<	Globals* the_globals;
79	<	int i, j, k, globalAtomIndex;
80	<
81	<	int ensembleCase;
82	<	int ffCase;
83	<
84	<	ensembleCase = -1;
85	<	ffCase = -1;
96	>	// gather all of the information from the Bass file
97
98	<	// get the stamps and globals;
88	<	the_stamps = stamps;
89	<	the_globals = globals;
98	>	gatherInfo();
99
100	<	// set the easy ones first
92	<	simnfo->target_temp = the_globals->getTargetTemp();
93	<	simnfo->dt = the_globals->getDt();
94	<	simnfo->run_time = the_globals->getRunTime();
100	>	// creation of complex system objects
101
102	<	// get the ones we know are there, yet still may need some work.
97	<	n_components = the_globals->getNComponents();
98	<	strcpy( force_field, the_globals->getForceField() );
102	>	sysObjectsCreation();
103
104	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
101	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
102	<	else{
103	<	sprintf( painCave.errMsg,
104	<	"SimSetup Error. Unrecognized force field -> %s\n",
105	<	force_field );
106	<	painCave.isFatal = 1;
107	<	simError();
108	<	}
104	>	// check on the post processing info
105
106	<	// get the ensemble:
111	<	strcpy( ensemble, the_globals->getEnsemble() );
106	>	finalInfoCheck();
107
108	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
109	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
110	<	else if( !strcasecmp( ensemble, "NPT" )) ensembleCase = NPT_ENS;
111	<	else{
112	<	sprintf( painCave.errMsg,
113	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
114	<	"reverting to NVE for this simulation.\n",
120	<	ensemble );
121	<	painCave.isFatal = 0;
122	<	simError();
123	<	strcpy( ensemble, "NVE" );
124	<	ensembleCase = NVE_ENS;
108	>	// initialize the system coordinates
109	>
110	>	if (!isInfoArray){
111	>	initSystemCoords();
112	>
113	>	if( !(globals->getUseInitTime()) )
114	>	info[0].currentTime = 0.0;
115		}
126	–	strcpy( simnfo->ensemble, ensemble );
116
117	+	// make the output filenames
118
119	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
130	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
131	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
132	<	//     if (the_globals->haveTargetPressure())
133	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
134	<	//     else {
135	<	//       sprintf( painCave.errMsg,
136	<	//                "SimSetup error: If you use the constant pressure\n"
137	<	//                "    ensemble, you must set targetPressure.\n"
138	<	//                "    This was found in the BASS file.\n");
139	<	//       painCave.isFatal = 1;
140	<	//       simError();
141	<	//     }
119	>	makeOutNames();
120
121	<	//     if (the_globals->haveTauThermostat())
144	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
145	<	//     else if (the_globals->haveQmass())
146	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
147	<	//     else {
148	<	//       sprintf( painCave.errMsg,
149	<	//                "SimSetup error: If you use one of the constant temperature\n"
150	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
151	<	//                "    Neither of these was found in the BASS file.\n");
152	<	//       painCave.isFatal = 1;
153	<	//       simError();
154	<	//     }
121	>	// make the integrator
122
123	<	//     if (the_globals->haveTauBarostat())
157	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
158	<	//     else {
159	<	//       sprintf( painCave.errMsg,
160	<	//                "SimSetup error: If you use the constant pressure\n"
161	<	//                "    ensemble, you must set tauBarostat.\n"
162	<	//                "    This was found in the BASS file.\n");
163	<	//       painCave.isFatal = 1;
164	<	//       simError();
165	<	//     }
123	>	makeIntegrator();
124
125	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
126	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
127	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
125	>	#ifdef IS_MPI
126	>	mpiSim->mpiRefresh();
127	>	#endif
128
129	<	//     if (the_globals->haveTauThermostat())
172	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
173	<	//     else if (the_globals->haveQmass())
174	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
175	<	//     else {
176	<	//       sprintf( painCave.errMsg,
177	<	//                "SimSetup error: If you use one of the constant temperature\n"
178	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
179	<	//                "    Neither of these was found in the BASS file.\n");
180	<	//       painCave.isFatal = 1;
181	<	//       simError();
182	<	//     }
129	>	// initialize the Fortran
130
131	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
132	<	simnfo->usePBC = the_globals->getPBC();
186	<
187	<	int usesDipoles = 0;
188	<	switch( ffCase ){
131	>	initFortran();
132	>	}
133
190	–	case FF_DUFF:
191	–	the_ff = new DUFF();
192	–	usesDipoles = 1;
193	–	break;
134
135	<	case FF_LJ:
136	<	the_ff = new LJFF();
137	<	break;
135	>	void SimSetup::makeMolecules(void){
136	>	int k;
137	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
138	>	molInit molInfo;
139	>	DirectionalAtom* dAtom;
140	>	LinkedAssign* extras;
141	>	LinkedAssign* current_extra;
142	>	AtomStamp* currentAtom;
143	>	BondStamp* currentBond;
144	>	BendStamp* currentBend;
145	>	TorsionStamp* currentTorsion;
146
147	<	default:
148	<	sprintf( painCave.errMsg,
149	<	"SimSetup Error. Unrecognized force field in case statement.\n");
202	<	painCave.isFatal = 1;
203	<	simError();
204	<	}
147	>	bond_pair* theBonds;
148	>	bend_set* theBends;
149	>	torsion_set* theTorsions;
150
206	–	#ifdef IS_MPI
207	–	strcpy( checkPointMsg, "ForceField creation successful" );
208	–	MPIcheckPoint();
209	–	#endif // is_mpi
151
152	<	// get the components and calculate the tot_nMol and indvidual n_mol
212	<	the_components = the_globals->getComponents();
213	<	components_nmol = new int[n_components];
214	<	comp_stamps = new MoleculeStamp*[n_components];
152	>	//init the forceField paramters
153
154	<	if( !the_globals->haveNMol() ){
217	<	// we don't have the total number of molecules, so we assume it is
218	<	// given in each component
154	>	the_ff->readParams();
155
220	–	tot_nmol = 0;
221	–	for( i=0; i<n_components; i++ ){
156
157	<	if( !the_components[i]->haveNMol() ){
224	<	// we have a problem
225	<	sprintf( painCave.errMsg,
226	<	"SimSetup Error. No global NMol or component NMol"
227	<	" given. Cannot calculate the number of atoms.\n" );
228	<	painCave.isFatal = 1;
229	<	simError();
230	<	}
157	>	// init the atoms
158
159	<	tot_nmol += the_components[i]->getNMol();
233	<	components_nmol[i] = the_components[i]->getNMol();
234	<	}
235	<	}
236	<	else{
237	<	sprintf( painCave.errMsg,
238	<	"SimSetup error.\n"
239	<	"\tSorry, the ability to specify total"
240	<	" nMols and then give molfractions in the components\n"
241	<	"\tis not currently supported."
242	<	" Please give nMol in the components.\n" );
243	<	painCave.isFatal = 1;
244	<	simError();
245	<
246	<
247	<	//     tot_nmol = the_globals->getNMol();
248	<
249	<	//   //we have the total number of molecules, now we check for molfractions
250	<	//     for( i=0; i<n_components; i++ ){
251	<
252	<	//       if( !the_components[i]->haveMolFraction() ){
253	<
254	<	//  if( !the_components[i]->haveNMol() ){
255	<	//    //we have a problem
256	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
257	<	//              << " nMol was given in component
258	<
259	<	}
159	>	double ux, uy, uz, u, uSqr;
160
161	<	#ifdef IS_MPI
162	<	strcpy( checkPointMsg, "Have the number of components" );
263	<	MPIcheckPoint();
264	<	#endif // is_mpi
161	>	for (k = 0; k < nInfo; k++){
162	>	the_ff->setSimInfo(&(info[k]));
163
164	<	// make an array of molecule stamps that match the components used.
165	<	// also extract the used stamps out into a separate linked list
164	>	atomOffset = 0;
165	>	excludeOffset = 0;
166	>	for (i = 0; i < info[k].n_mol; i++){
167	>	stampID = info[k].molecules[i].getStampID();
168
169	<	simnfo->nComponents = n_components;
170	<	simnfo->componentsNmol = components_nmol;
171	<	simnfo->compStamps = comp_stamps;
172	<	simnfo->headStamp = new LinkedMolStamp();
173	<
274	<	char* id;
275	<	LinkedMolStamp* headStamp = simnfo->headStamp;
276	<	LinkedMolStamp* currentStamp = NULL;
277	<	for( i=0; i<n_components; i++ ){
169	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
170	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
171	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
172	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
173	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
174
175	<	id = the_components[i]->getType();
176	<	comp_stamps[i] = NULL;
177	<
178	<	// check to make sure the component isn't already in the list
175	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
176	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
177	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
178	>	molInfo.myBends = new Bend * [molInfo.nBends];
179	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
180
181	<	comp_stamps[i] = headStamp->match( id );
182	<	if( comp_stamps[i] == NULL ){
183	<
287	<	// extract the component from the list;
288	<
289	<	currentStamp = the_stamps->extractMolStamp( id );
290	<	if( currentStamp == NULL ){
291	<	sprintf( painCave.errMsg,
292	<	"SimSetup error: Component \"%s\" was not found in the "
293	<	"list of declared molecules\n",
294	<	id );
295	<	painCave.isFatal = 1;
296	<	simError();
297	<	}
298	<
299	<	headStamp->add( currentStamp );
300	<	comp_stamps[i] = headStamp->match( id );
301	<	}
302	<	}
181	>	theBonds = new bond_pair[molInfo.nBonds];
182	>	theBends = new bend_set[molInfo.nBends];
183	>	theTorsions = new torsion_set[molInfo.nTorsions];
184
185	<	#ifdef IS_MPI
305	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
306	<	MPIcheckPoint();
307	<	#endif // is_mpi
308	<
185	>	// make the Atoms
186
187	+	for (j = 0; j < molInfo.nAtoms; j++){
188	+	currentAtom = comp_stamps[stampID]->getAtom(j);
189	+	if (currentAtom->haveOrientation()){
190	+	dAtom = new DirectionalAtom((j + atomOffset),
191	+	info[k].getConfiguration());
192	+	info[k].n_oriented++;
193	+	molInfo.myAtoms[j] = dAtom;
194
195	+	ux = currentAtom->getOrntX();
196	+	uy = currentAtom->getOrntY();
197	+	uz = currentAtom->getOrntZ();
198
199	<	// caclulate the number of atoms, bonds, bends and torsions
199	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
200
201	<	tot_atoms = 0;
202	<	tot_bonds = 0;
203	<	tot_bends = 0;
204	<	tot_torsions = 0;
318	<	for( i=0; i<n_components; i++ ){
319	<
320	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
321	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
322	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
323	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
324	<	}
201	>	u = sqrt(uSqr);
202	>	ux = ux / u;
203	>	uy = uy / u;
204	>	uz = uz / u;
205
206	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
206	>	dAtom->setSUx(ux);
207	>	dAtom->setSUy(uy);
208	>	dAtom->setSUz(uz);
209	>	}
210	>	else{
211	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
212	>	info[k].getConfiguration());
213	>	}
214	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
215
328	–	simnfo->n_atoms = tot_atoms;
329	–	simnfo->n_bonds = tot_bonds;
330	–	simnfo->n_bends = tot_bends;
331	–	simnfo->n_torsions = tot_torsions;
332	–	simnfo->n_SRI = tot_SRI;
333	–	simnfo->n_mol = tot_nmol;
334	–
335	–	simnfo->molMembershipArray = new int[tot_atoms];
336	–
216		#ifdef IS_MPI
217
218	<	// divide the molecules among processors here.
340	<
341	<	mpiSim = new mpiSimulation( simnfo );
342	<
343	<	globalIndex = mpiSim->divideLabor();
218	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
219
220	<	// set up the local variables
221	<
347	<	int localMol, allMol;
348	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
220	>	#endif // is_mpi
221	>	}
222
223	<	int* mol2proc = mpiSim->getMolToProcMap();
224	<	int* molCompType = mpiSim->getMolComponentType();
225	<
226	<	allMol = 0;
227	<	localMol = 0;
355	<	local_atoms = 0;
356	<	local_bonds = 0;
357	<	local_bends = 0;
358	<	local_torsions = 0;
359	<	globalAtomIndex = 0;
223	>	// make the bonds
224	>	for (j = 0; j < molInfo.nBonds; j++){
225	>	currentBond = comp_stamps[stampID]->getBond(j);
226	>	theBonds[j].a = currentBond->getA() + atomOffset;
227	>	theBonds[j].b = currentBond->getB() + atomOffset;
228
229	+	exI = theBonds[j].a;
230	+	exJ = theBonds[j].b;
231
232	<	for( i=0; i<n_components; i++ ){
232	>	// exclude_I must always be the smaller of the pair
233	>	if (exI > exJ){
234	>	tempEx = exI;
235	>	exI = exJ;
236	>	exJ = tempEx;
237	>	}
238	>	#ifdef IS_MPI
239	>	tempEx = exI;
240	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
241	>	tempEx = exJ;
242	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
243
244	<	for( j=0; j<components_nmol[i]; j++ ){
245	<
246	<	if( mol2proc[allMol] == worldRank ){
247	<
248	<	local_atoms +=    comp_stamps[i]->getNAtoms();
369	<	local_bonds +=    comp_stamps[i]->getNBonds();
370	<	local_bends +=    comp_stamps[i]->getNBends();
371	<	local_torsions += comp_stamps[i]->getNTorsions();
372	<	localMol++;
373	<	}
374	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
375	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
376	<	globalAtomIndex++;
244	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
245	>	#else  // isn't MPI
246	>
247	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
248	>	#endif  //is_mpi
249		}
250	+	excludeOffset += molInfo.nBonds;
251
252	<	allMol++;
253	<	}
254	<	}
255	<	local_SRI = local_bonds + local_bends + local_torsions;
256	<
257	<	simnfo->n_atoms = mpiSim->getMyNlocal();
385	<
386	<	if( local_atoms != simnfo->n_atoms ){
387	<	sprintf( painCave.errMsg,
388	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
389	<	" localAtom (%d) are not equal.\n",
390	<	simnfo->n_atoms,
391	<	local_atoms );
392	<	painCave.isFatal = 1;
393	<	simError();
394	<	}
252	>	//make the bends
253	>	for (j = 0; j < molInfo.nBends; j++){
254	>	currentBend = comp_stamps[stampID]->getBend(j);
255	>	theBends[j].a = currentBend->getA() + atomOffset;
256	>	theBends[j].b = currentBend->getB() + atomOffset;
257	>	theBends[j].c = currentBend->getC() + atomOffset;
258
259	<	simnfo->n_bonds = local_bonds;
260	<	simnfo->n_bends = local_bends;
261	<	simnfo->n_torsions = local_torsions;
399	<	simnfo->n_SRI = local_SRI;
400	<	simnfo->n_mol = localMol;
259	>	if (currentBend->haveExtras()){
260	>	extras = currentBend->getExtras();
261	>	current_extra = extras;
262
263	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
264	<	MPIcheckPoint();
265	<
266	<
267	<	#endif // is_mpi
268	<
263	>	while (current_extra != NULL){
264	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
265	>	switch (current_extra->getType()){
266	>	case 0:
267	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
268	>	theBends[j].isGhost = 1;
269	>	break;
270
271	<	// create the atom and short range interaction arrays
271	>	case 1:
272	>	theBends[j].ghost = (int) current_extra->getDouble() +
273	>	atomOffset;
274	>	theBends[j].isGhost = 1;
275	>	break;
276
277	<	Atom::createArrays(simnfo->n_atoms);
278	<	the_atoms = new Atom*[simnfo->n_atoms];
279	<	the_molecules = new Molecule[simnfo->n_mol];
280	<	int molIndex;
277	>	default:
278	>	sprintf(painCave.errMsg,
279	>	"SimSetup Error: ghostVectorSource was neither a "
280	>	"double nor an int.\n"
281	>	"-->Bend[%d] in %s\n",
282	>	j, comp_stamps[stampID]->getID());
283	>	painCave.isFatal = 1;
284	>	simError();
285	>	}
286	>	}
287	>	else{
288	>	sprintf(painCave.errMsg,
289	>	"SimSetup Error: unhandled bend assignment:\n"
290	>	"    -->%s in Bend[%d] in %s\n",
291	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
292	>	painCave.isFatal = 1;
293	>	simError();
294	>	}
295
296	<	// initialize the molecule's stampID's
296	>	current_extra = current_extra->getNext();
297	>	}
298	>	}
299
300	+	if (!theBends[j].isGhost){
301	+	exI = theBends[j].a;
302	+	exJ = theBends[j].c;
303	+	}
304	+	else{
305	+	exI = theBends[j].a;
306	+	exJ = theBends[j].b;
307	+	}
308	+
309	+	// exclude_I must always be the smaller of the pair
310	+	if (exI > exJ){
311	+	tempEx = exI;
312	+	exI = exJ;
313	+	exJ = tempEx;
314	+	}
315		#ifdef IS_MPI
316	<
316	>	tempEx = exI;
317	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
318	>	tempEx = exJ;
319	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
320
321	<	molIndex = 0;
322	<	for(i=0; i<mpiSim->getTotNmol(); i++){
323	<
324	<	if(mol2proc[i] == worldRank ){
325	<	the_molecules[molIndex].setStampID( molCompType[i] );
326	<	the_molecules[molIndex].setMyIndex( molIndex );
427	<	the_molecules[molIndex].setGlobalIndex( i );
428	<	molIndex++;
429	<	}
430	<	}
321	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
322	>	#else  // isn't MPI
323	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
324	>	#endif  //is_mpi
325	>	}
326	>	excludeOffset += molInfo.nBends;
327
328	<	#else // is_mpi
329	<
330	<	molIndex = 0;
331	<	globalAtomIndex = 0;
332	<	for(i=0; i<n_components; i++){
333	<	for(j=0; j<components_nmol[i]; j++ ){
438	<	the_molecules[molIndex].setStampID( i );
439	<	the_molecules[molIndex].setMyIndex( molIndex );
440	<	the_molecules[molIndex].setGlobalIndex( molIndex );
441	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
442	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
443	<	globalAtomIndex++;
444	<	}
445	<	molIndex++;
446	<	}
447	<	}
448	<
328	>	for (j = 0; j < molInfo.nTorsions; j++){
329	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
330	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
331	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
332	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
333	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
334
335	<	#endif // is_mpi
335	>	exI = theTorsions[j].a;
336	>	exJ = theTorsions[j].d;
337
338	+	// exclude_I must always be the smaller of the pair
339	+	if (exI > exJ){
340	+	tempEx = exI;
341	+	exI = exJ;
342	+	exJ = tempEx;
343	+	}
344	+	#ifdef IS_MPI
345	+	tempEx = exI;
346	+	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
347	+	tempEx = exJ;
348	+	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
349
350	<	if( simnfo->n_SRI ){
351	<
352	<	Exclude::createArray(simnfo->n_SRI);
353	<	the_excludes = new Exclude*[simnfo->n_SRI];
354	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
355	<	simnfo->globalExcludes = new int;
459	<	simnfo->n_exclude = simnfo->n_SRI;
460	<	}
461	<	else{
462	<
463	<	Exclude::createArray( 1 );
464	<	the_excludes = new Exclude*;
465	<	the_excludes[0] = new Exclude(0);
466	<	the_excludes[0]->setPair( 0,0 );
467	<	simnfo->globalExcludes = new int;
468	<	simnfo->globalExcludes[0] = 0;
469	<	simnfo->n_exclude = 0;
470	<	}
350	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
351	>	#else  // isn't MPI
352	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
353	>	#endif  //is_mpi
354	>	}
355	>	excludeOffset += molInfo.nTorsions;
356
472	–	// set the arrays into the SimInfo object
357
358	<	simnfo->atoms = the_atoms;
475	<	simnfo->molecules = the_molecules;
476	<	simnfo->nGlobalExcludes = 0;
477	<	simnfo->excludes = the_excludes;
358	>	// send the arrays off to the forceField for init.
359
360	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
361	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
362	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
363	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
364	+	theTorsions);
365
480	–	// get some of the tricky things that may still be in the globals
366
367	<
483	<	if( the_globals->haveBox() ){
484	<	simnfo->box_x = the_globals->getBox();
485	<	simnfo->box_y = the_globals->getBox();
486	<	simnfo->box_z = the_globals->getBox();
487	<	}
488	<	else if( the_globals->haveDensity() ){
367	>	info[k].molecules[i].initialize(molInfo);
368
490	–	double vol;
491	–	vol = (double)tot_nmol / the_globals->getDensity();
492	–	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
493	–	simnfo->box_y = simnfo->box_x;
494	–	simnfo->box_z = simnfo->box_x;
495	–	}
496	–	else{
497	–	if( !the_globals->haveBoxX() ){
498	–	sprintf( painCave.errMsg,
499	–	"SimSetup error, no periodic BoxX size given.\n" );
500	–	painCave.isFatal = 1;
501	–	simError();
502	–	}
503	–	simnfo->box_x = the_globals->getBoxX();
369
370	<	if( !the_globals->haveBoxY() ){
371	<	sprintf( painCave.errMsg,
372	<	"SimSetup error, no periodic BoxY size given.\n" );
373	<	painCave.isFatal = 1;
509	<	simError();
370	>	atomOffset += molInfo.nAtoms;
371	>	delete[] theBonds;
372	>	delete[] theBends;
373	>	delete[] theTorsions;
374		}
511	–	simnfo->box_y = the_globals->getBoxY();
512	–
513	–	if( !the_globals->haveBoxZ() ){
514	–	sprintf( painCave.errMsg,
515	–	"SimSetup error, no periodic BoxZ size given.\n" );
516	–	painCave.isFatal = 1;
517	–	simError();
518	–	}
519	–	simnfo->box_z = the_globals->getBoxZ();
375		}
376
377		#ifdef IS_MPI
378	<	strcpy( checkPointMsg, "Box size set up" );
378	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
379		MPIcheckPoint();
380		#endif // is_mpi
381
382	+	// clean up the forcefield
383
384	<	// initialize the arrays
384	>	the_ff->calcRcut();
385	>	the_ff->cleanMe();
386	>	}
387
388	<	the_ff->setSimInfo( simnfo );
388	>	void SimSetup::initFromBass(void){
389	>	int i, j, k;
390	>	int n_cells;
391	>	double cellx, celly, cellz;
392	>	double temp1, temp2, temp3;
393	>	int n_per_extra;
394	>	int n_extra;
395	>	int have_extra, done;
396
397	<	makeMolecules();
398	<	simnfo->identArray = new int[simnfo->n_atoms];
399	<	for(i=0; i<simnfo->n_atoms; i++){
400	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
536	<	}
537	<
538	<	if (the_globals->getUseRF() ) {
539	<	simnfo->useReactionField = 1;
540	<
541	<	if( !the_globals->haveECR() ){
542	<	sprintf( painCave.errMsg,
543	<	"SimSetup Warning: using default value of 1/2 the smallest "
544	<	"box length for the electrostaticCutoffRadius.\n"
545	<	"I hope you have a very fast processor!\n");
546	<	painCave.isFatal = 0;
547	<	simError();
548	<	double smallest;
549	<	smallest = simnfo->box_x;
550	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
551	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
552	<	simnfo->ecr = 0.5 * smallest;
553	<	} else {
554	<	simnfo->ecr        = the_globals->getECR();
555	<	}
397	>	double vel[3];
398	>	vel[0] = 0.0;
399	>	vel[1] = 0.0;
400	>	vel[2] = 0.0;
401
402	<	if( !the_globals->haveEST() ){
403	<	sprintf( painCave.errMsg,
404	<	"SimSetup Warning: using default value of 0.05 * the "
405	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
406	<	);
407	<	painCave.isFatal = 0;
408	<	simError();
409	<	simnfo->est = 0.05 * simnfo->ecr;
410	<	} else {
411	<	simnfo->est        = the_globals->getEST();
412	<	}
413	<
414	<	if(!the_globals->haveDielectric() ){
415	<	sprintf( painCave.errMsg,
416	<	"SimSetup Error: You are trying to use Reaction Field without"
417	<	"setting a dielectric constant!\n"
418	<	);
402	>	temp1 = (double) tot_nmol / 4.0;
403	>	temp2 = pow(temp1, (1.0 / 3.0));
404	>	temp3 = ceil(temp2);
405	>
406	>	have_extra = 0;
407	>	if (temp2 < temp3){
408	>	// we have a non-complete lattice
409	>	have_extra = 1;
410	>
411	>	n_cells = (int) temp3 - 1;
412	>	cellx = info[0].boxL[0] / temp3;
413	>	celly = info[0].boxL[1] / temp3;
414	>	cellz = info[0].boxL[2] / temp3;
415	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
416	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
417	>	n_per_extra = (int) ceil(temp1);
418	>
419	>	if (n_per_extra > 4){
420	>	sprintf(painCave.errMsg,
421	>	"SimSetup error. There has been an error in constructing"
422	>	" the non-complete lattice.\n");
423		painCave.isFatal = 1;
424		simError();
425		}
426	<	simnfo->dielectric = the_globals->getDielectric();
427	<	} else {
428	<	if (usesDipoles) {
429	<
430	<	if( !the_globals->haveECR() ){
431	<	sprintf( painCave.errMsg,
432	<	"SimSetup Warning: using default value of 1/2 the smallest "
584	<	"box length for the electrostaticCutoffRadius.\n"
585	<	"I hope you have a very fast processor!\n");
586	<	painCave.isFatal = 0;
587	<	simError();
588	<	double smallest;
589	<	smallest = simnfo->box_x;
590	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
591	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
592	<	simnfo->ecr = 0.5 * smallest;
593	<	} else {
594	<	simnfo->ecr        = the_globals->getECR();
595	<	}
596	<
597	<	if( !the_globals->haveEST() ){
598	<	sprintf( painCave.errMsg,
599	<	"SimSetup Warning: using default value of 5%% of the "
600	<	"electrostaticCutoffRadius for the "
601	<	"electrostaticSkinThickness\n"
602	<	);
603	<	painCave.isFatal = 0;
604	<	simError();
605	<	simnfo->est = 0.05 * simnfo->ecr;
606	<	} else {
607	<	simnfo->est        = the_globals->getEST();
608	<	}
609	<	}
610	<	}
426	>	}
427	>	else{
428	>	n_cells = (int) temp3;
429	>	cellx = info[0].boxL[0] / temp3;
430	>	celly = info[0].boxL[1] / temp3;
431	>	cellz = info[0].boxL[2] / temp3;
432	>	}
433
434	<	#ifdef IS_MPI
435	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
436	<	MPIcheckPoint();
437	<	#endif // is_mpi
434	>	current_mol = 0;
435	>	current_comp_mol = 0;
436	>	current_comp = 0;
437	>	current_atom_ndx = 0;
438
439	<	if( the_globals->haveInitialConfig() ){
440	<
441	<	InitializeFromFile* fileInit;
442	<	#ifdef IS_MPI // is_mpi
621	<	if( worldRank == 0 ){
622	<	#endif //is_mpi
623	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
624	<	#ifdef IS_MPI
625	<	}else fileInit = new InitializeFromFile( NULL );
626	<	#endif
627	<	fileInit->read_xyz( simnfo ); // default velocities on
439	>	for (i = 0; i < n_cells ; i++){
440	>	for (j = 0; j < n_cells; j++){
441	>	for (k = 0; k < n_cells; k++){
442	>	makeElement(i * cellx, j * celly, k * cellz);
443
444	<	delete fileInit;
630	<	}
631	<	else{
444	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
445
446	<	#ifdef IS_MPI
446	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
447
448	<	// no init from bass
449	<
450	<	sprintf( painCave.errMsg,
451	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
639	<	painCave.isFatal;
640	<	simError();
641	<
642	<	#else
448	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
449	>	}
450	>	}
451	>	}
452
453	<	initFromBass();
453	>	if (have_extra){
454	>	done = 0;
455
456	+	int start_ndx;
457	+	for (i = 0; i < (n_cells + 1) && !done; i++){
458	+	for (j = 0; j < (n_cells + 1) && !done; j++){
459	+	if (i < n_cells){
460	+	if (j < n_cells){
461	+	start_ndx = n_cells;
462	+	}
463	+	else
464	+	start_ndx = 0;
465	+	}
466	+	else
467	+	start_ndx = 0;
468
469	<	#endif
470	<	}
469	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
470	>	makeElement(i * cellx, j * celly, k * cellz);
471	>	done = (current_mol >= tot_nmol);
472
473	<	#ifdef IS_MPI
474	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
475	<	MPIcheckPoint();
476	<	#endif // is_mpi
473	>	if (!done && n_per_extra > 1){
474	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
475	>	k * cellz);
476	>	done = (current_mol >= tot_nmol);
477	>	}
478
479	+	if (!done && n_per_extra > 2){
480	+	makeElement(i * cellx, j * celly + 0.5 * celly,
481	+	k * cellz + 0.5 * cellz);
482	+	done = (current_mol >= tot_nmol);
483	+	}
484
485	<
486	<
487	<
488	<
489	<
490	<	#ifdef IS_MPI
662	<	if( worldRank == 0 ){
663	<	#endif // is_mpi
664	<
665	<	if( the_globals->haveFinalConfig() ){
666	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
667	<	}
668	<	else{
669	<	strcpy( simnfo->finalName, inFileName );
670	<	char* endTest;
671	<	int nameLength = strlen( simnfo->finalName );
672	<	endTest = &(simnfo->finalName[nameLength - 5]);
673	<	if( !strcmp( endTest, ".bass" ) ){
674	<	strcpy( endTest, ".eor" );
485	>	if (!done && n_per_extra > 3){
486	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
487	>	k * cellz + 0.5 * cellz);
488	>	done = (current_mol >= tot_nmol);
489	>	}
490	>	}
491		}
676	–	else if( !strcmp( endTest, ".BASS" ) ){
677	–	strcpy( endTest, ".eor" );
678	–	}
679	–	else{
680	–	endTest = &(simnfo->finalName[nameLength - 4]);
681	–	if( !strcmp( endTest, ".bss" ) ){
682	–	strcpy( endTest, ".eor" );
683	–	}
684	–	else if( !strcmp( endTest, ".mdl" ) ){
685	–	strcpy( endTest, ".eor" );
686	–	}
687	–	else{
688	–	strcat( simnfo->finalName, ".eor" );
689	–	}
690	–	}
492		}
692	–
693	–	// make the sample and status out names
694	–
695	–	strcpy( simnfo->sampleName, inFileName );
696	–	char* endTest;
697	–	int nameLength = strlen( simnfo->sampleName );
698	–	endTest = &(simnfo->sampleName[nameLength - 5]);
699	–	if( !strcmp( endTest, ".bass" ) ){
700	–	strcpy( endTest, ".dump" );
701	–	}
702	–	else if( !strcmp( endTest, ".BASS" ) ){
703	–	strcpy( endTest, ".dump" );
704	–	}
705	–	else{
706	–	endTest = &(simnfo->sampleName[nameLength - 4]);
707	–	if( !strcmp( endTest, ".bss" ) ){
708	–	strcpy( endTest, ".dump" );
709	–	}
710	–	else if( !strcmp( endTest, ".mdl" ) ){
711	–	strcpy( endTest, ".dump" );
712	–	}
713	–	else{
714	–	strcat( simnfo->sampleName, ".dump" );
715	–	}
716	–	}
717	–
718	–	strcpy( simnfo->statusName, inFileName );
719	–	nameLength = strlen( simnfo->statusName );
720	–	endTest = &(simnfo->statusName[nameLength - 5]);
721	–	if( !strcmp( endTest, ".bass" ) ){
722	–	strcpy( endTest, ".stat" );
723	–	}
724	–	else if( !strcmp( endTest, ".BASS" ) ){
725	–	strcpy( endTest, ".stat" );
726	–	}
727	–	else{
728	–	endTest = &(simnfo->statusName[nameLength - 4]);
729	–	if( !strcmp( endTest, ".bss" ) ){
730	–	strcpy( endTest, ".stat" );
731	–	}
732	–	else if( !strcmp( endTest, ".mdl" ) ){
733	–	strcpy( endTest, ".stat" );
734	–	}
735	–	else{
736	–	strcat( simnfo->statusName, ".stat" );
737	–	}
738	–	}
739	–
740	–	#ifdef IS_MPI
493		}
742	–	#endif // is_mpi
743	–
744	–	// set the status, sample, and themal kick times
745	–
746	–	if( the_globals->haveSampleTime() ){
747	–	simnfo->sampleTime = the_globals->getSampleTime();
748	–	simnfo->statusTime = simnfo->sampleTime;
749	–	simnfo->thermalTime = simnfo->sampleTime;
750	–	}
751	–	else{
752	–	simnfo->sampleTime = the_globals->getRunTime();
753	–	simnfo->statusTime = simnfo->sampleTime;
754	–	simnfo->thermalTime = simnfo->sampleTime;
755	–	}
494
495	<	if( the_globals->haveStatusTime() ){
496	<	simnfo->statusTime = the_globals->getStatusTime();
495	>	for (i = 0; i < info[0].n_atoms; i++){
496	>	info[0].atoms[i]->setVel(vel);
497		}
498	+	}
499
500	<	if( the_globals->haveThermalTime() ){
501	<	simnfo->thermalTime = the_globals->getThermalTime();
502	<	}
500	>	void SimSetup::makeElement(double x, double y, double z){
501	>	int k;
502	>	AtomStamp* current_atom;
503	>	DirectionalAtom* dAtom;
504	>	double rotMat[3][3];
505	>	double pos[3];
506
507	<	// check for the temperature set flag
507	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
508	>	current_atom = comp_stamps[current_comp]->getAtom(k);
509	>	if (!current_atom->havePosition()){
510	>	sprintf(painCave.errMsg,
511	>	"SimSetup:initFromBass error.\n"
512	>	"\tComponent %s, atom %s does not have a position specified.\n"
513	>	"\tThe initialization routine is unable to give a start"
514	>	" position.\n",
515	>	comp_stamps[current_comp]->getID(), current_atom->getType());
516	>	painCave.isFatal = 1;
517	>	simError();
518	>	}
519
520	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
520	>	pos[0] = x + current_atom->getPosX();
521	>	pos[1] = y + current_atom->getPosY();
522	>	pos[2] = z + current_atom->getPosZ();
523
524	+	info[0].atoms[current_atom_ndx]->setPos(pos);
525
526	<	// make the integrator
527	<
772	<
773	<	NVT* myNVT = NULL;
774	<	switch( ensembleCase ){
526	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
527	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
528
529	<	case NVE_ENS:
530	<	new NVE( simnfo, the_ff );
531	<	break;
529	>	rotMat[0][0] = 1.0;
530	>	rotMat[0][1] = 0.0;
531	>	rotMat[0][2] = 0.0;
532
533	<	case NVT_ENS:
534	<	myNVT = new NVT( simnfo, the_ff );
535	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
533	>	rotMat[1][0] = 0.0;
534	>	rotMat[1][1] = 1.0;
535	>	rotMat[1][2] = 0.0;
536
537	<	if (the_globals->haveTauThermostat())
538	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
539	<	else if (the_globals->haveQmass())
540	<	myNVT->setQmass(the_globals->getQmass());
541	<	else {
789	<	sprintf( painCave.errMsg,
790	<	"SimSetup error: If you use the NVT\n"
791	<	"    ensemble, you must set either tauThermostat or qMass.\n"
792	<	"    Neither of these was found in the BASS file.\n");
793	<	painCave.isFatal = 1;
794	<	simError();
537	>	rotMat[2][0] = 0.0;
538	>	rotMat[2][1] = 0.0;
539	>	rotMat[2][2] = 1.0;
540	>
541	>	dAtom->setA(rotMat);
542		}
796	–	break;
543
544	<	default:
799	<	sprintf( painCave.errMsg,
800	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
801	<	painCave.isFatal = 1;
802	<	simError();
544	>	current_atom_ndx++;
545		}
546
547	<
548	<	#ifdef IS_MPI
807	<	mpiSim->mpiRefresh();
808	<	#endif
547	>	current_mol++;
548	>	current_comp_mol++;
549
550	<	// initialize the Fortran
550	>	if (current_comp_mol >= components_nmol[current_comp]){
551	>	current_comp_mol = 0;
552	>	current_comp++;
553	>	}
554	>	}
555
556
557	<	simnfo->refreshSim();
558	<
559	<	if( !strcmp( simnfo->mixingRule, "standard") ){
560	<	the_ff->initForceField( LB_MIXING_RULE );
557	>	void SimSetup::gatherInfo(void){
558	>	int i;
559	>
560	>	ensembleCase = -1;
561	>	ffCase = -1;
562	>
563	>	// set the easy ones first
564	>
565	>	for (i = 0; i < nInfo; i++){
566	>	info[i].target_temp = globals->getTargetTemp();
567	>	info[i].dt = globals->getDt();
568	>	info[i].run_time = globals->getRunTime();
569		}
570	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
571	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
570	>	n_components = globals->getNComponents();
571	>
572	>
573	>	// get the forceField
574	>
575	>	strcpy(force_field, globals->getForceField());
576	>
577	>	if (!strcasecmp(force_field, "DUFF")){
578	>	ffCase = FF_DUFF;
579		}
580	+	else if (!strcasecmp(force_field, "LJ")){
581	+	ffCase = FF_LJ;
582	+	}
583	+	else if (!strcasecmp(force_field, "EAM")){
584	+	ffCase = FF_EAM;
585	+	}
586		else{
587	<	sprintf( painCave.errMsg,
588	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
589	<	simnfo->mixingRule );
590	<	painCave.isFatal = 1;
826	<	simError();
587	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
588	>	force_field);
589	>	painCave.isFatal = 1;
590	>	simError();
591		}
592
593	+	// get the ensemble
594
595	<	#ifdef IS_MPI
831	<	strcpy( checkPointMsg,
832	<	"Successfully intialized the mixingRule for Fortran." );
833	<	MPIcheckPoint();
834	<	#endif // is_mpi
835	<	}
595	>	strcpy(ensemble, globals->getEnsemble());
596
597	+	if (!strcasecmp(ensemble, "NVE")){
598	+	ensembleCase = NVE_ENS;
599	+	}
600	+	else if (!strcasecmp(ensemble, "NVT")){
601	+	ensembleCase = NVT_ENS;
602	+	}
603	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
604	+	ensembleCase = NPTi_ENS;
605	+	}
606	+	else if (!strcasecmp(ensemble, "NPTf")){
607	+	ensembleCase = NPTf_ENS;
608	+	}
609	+	else if (!strcasecmp(ensemble, "NPTxyz")){
610	+	ensembleCase = NPTxyz_ENS;
611	+	}
612	+	else{
613	+	sprintf(painCave.errMsg,
614	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
615	+	"reverting to NVE for this simulation.\n",
616	+	ensemble);
617	+	painCave.isFatal = 0;
618	+	simError();
619	+	strcpy(ensemble, "NVE");
620	+	ensembleCase = NVE_ENS;
621	+	}
622
623	<	void SimSetup::makeMolecules( void ){
623	>	for (i = 0; i < nInfo; i++){
624	>	strcpy(info[i].ensemble, ensemble);
625
626	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
841	<	molInit info;
842	<	DirectionalAtom* dAtom;
843	<	LinkedAssign* extras;
844	<	LinkedAssign* current_extra;
845	<	AtomStamp* currentAtom;
846	<	BondStamp* currentBond;
847	<	BendStamp* currentBend;
848	<	TorsionStamp* currentTorsion;
626	>	// get the mixing rule
627
628	<	bond_pair* theBonds;
629	<	bend_set* theBends;
630	<	torsion_set* theTorsions;
628	>	strcpy(info[i].mixingRule, globals->getMixingRule());
629	>	info[i].usePBC = globals->getPBC();
630	>	}
631
632	<
855	<	//init the forceField paramters
632	>	// get the components and calculate the tot_nMol and indvidual n_mol
633
634	<	the_ff->readParams();
634	>	the_components = globals->getComponents();
635	>	components_nmol = new int[n_components];
636
859	–
860	–	// init the atoms
637
638	<	double ux, uy, uz, u, uSqr;
639	<
640	<	atomOffset = 0;
865	<	excludeOffset = 0;
866	<	for(i=0; i<simnfo->n_mol; i++){
867	<
868	<	stampID = the_molecules[i].getStampID();
638	>	if (!globals->haveNMol()){
639	>	// we don't have the total number of molecules, so we assume it is
640	>	// given in each component
641
642	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
643	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
644	<	info.nBends    = comp_stamps[stampID]->getNBends();
645	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
646	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
647	<
648	<	info.myAtoms = &the_atoms[atomOffset];
649	<	info.myExcludes = &the_excludes[excludeOffset];
650	<	info.myBonds = new Bond*[info.nBonds];
879	<	info.myBends = new Bend*[info.nBends];
880	<	info.myTorsions = new Torsion*[info.nTorsions];
881	<
882	<	theBonds = new bond_pair[info.nBonds];
883	<	theBends = new bend_set[info.nBends];
884	<	theTorsions = new torsion_set[info.nTorsions];
885	<
886	<	// make the Atoms
887	<
888	<	for(j=0; j<info.nAtoms; j++){
889	<
890	<	currentAtom = comp_stamps[stampID]->getAtom( j );
891	<	if( currentAtom->haveOrientation() ){
892	<
893	<	dAtom = new DirectionalAtom(j + atomOffset);
894	<	simnfo->n_oriented++;
895	<	info.myAtoms[j] = dAtom;
896	<
897	<	ux = currentAtom->getOrntX();
898	<	uy = currentAtom->getOrntY();
899	<	uz = currentAtom->getOrntZ();
900	<
901	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
902	<
903	<	u = sqrt( uSqr );
904	<	ux = ux / u;
905	<	uy = uy / u;
906	<	uz = uz / u;
907	<
908	<	dAtom->setSUx( ux );
909	<	dAtom->setSUy( uy );
910	<	dAtom->setSUz( uz );
642	>	tot_nmol = 0;
643	>	for (i = 0; i < n_components; i++){
644	>	if (!the_components[i]->haveNMol()){
645	>	// we have a problem
646	>	sprintf(painCave.errMsg,
647	>	"SimSetup Error. No global NMol or component NMol"
648	>	" given. Cannot calculate the number of atoms.\n");
649	>	painCave.isFatal = 1;
650	>	simError();
651		}
912	–	else{
913	–	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
914	–	}
915	–	info.myAtoms[j]->setType( currentAtom->getType() );
916	–
917	–	#ifdef IS_MPI
918	–
919	–	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
920	–
921	–	#endif // is_mpi
922	–	}
923	–
924	–	// make the bonds
925	–	for(j=0; j<info.nBonds; j++){
926	–
927	–	currentBond = comp_stamps[stampID]->getBond( j );
928	–	theBonds[j].a = currentBond->getA() + atomOffset;
929	–	theBonds[j].b = currentBond->getB() + atomOffset;
652
653	<	exI = theBonds[j].a;
654	<	exJ = theBonds[j].b;
653	>	tot_nmol += the_components[i]->getNMol();
654	>	components_nmol[i] = the_components[i]->getNMol();
655	>	}
656	>	}
657	>	else{
658	>	sprintf(painCave.errMsg,
659	>	"SimSetup error.\n"
660	>	"\tSorry, the ability to specify total"
661	>	" nMols and then give molfractions in the components\n"
662	>	"\tis not currently supported."
663	>	" Please give nMol in the components.\n");
664	>	painCave.isFatal = 1;
665	>	simError();
666	>	}
667
668	<	// exclude_I must always be the smaller of the pair
935	<	if( exI > exJ ){
936	<	tempEx = exI;
937	<	exI = exJ;
938	<	exJ = tempEx;
939	<	}
940	<	#ifdef IS_MPI
941	<	tempEx = exI;
942	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
943	<	tempEx = exJ;
944	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
945	<
946	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
947	<	#else  // isn't MPI
668	>	// set the status, sample, and thermal kick times
669
670	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
671	<	#endif  //is_mpi
670	>	for (i = 0; i < nInfo; i++){
671	>	if (globals->haveSampleTime()){
672	>	info[i].sampleTime = globals->getSampleTime();
673	>	info[i].statusTime = info[i].sampleTime;
674	>	info[i].thermalTime = info[i].sampleTime;
675		}
676	<	excludeOffset += info.nBonds;
676	>	else{
677	>	info[i].sampleTime = globals->getRunTime();
678	>	info[i].statusTime = info[i].sampleTime;
679	>	info[i].thermalTime = info[i].sampleTime;
680	>	}
681
682	<	//make the bends
683	<	for(j=0; j<info.nBends; j++){
956	<
957	<	currentBend = comp_stamps[stampID]->getBend( j );
958	<	theBends[j].a = currentBend->getA() + atomOffset;
959	<	theBends[j].b = currentBend->getB() + atomOffset;
960	<	theBends[j].c = currentBend->getC() + atomOffset;
961	<
962	<	if( currentBend->haveExtras() ){
963	<
964	<	extras = currentBend->getExtras();
965	<	current_extra = extras;
966	<
967	<	while( current_extra != NULL ){
968	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
969	<
970	<	switch( current_extra->getType() ){
971	<
972	<	case 0:
973	<	theBends[j].ghost =
974	<	current_extra->getInt() + atomOffset;
975	<	theBends[j].isGhost = 1;
976	<	break;
977	<
978	<	case 1:
979	<	theBends[j].ghost =
980	<	(int)current_extra->getDouble() + atomOffset;
981	<	theBends[j].isGhost = 1;
982	<	break;
983	<
984	<	default:
985	<	sprintf( painCave.errMsg,
986	<	"SimSetup Error: ghostVectorSource was neither a "
987	<	"double nor an int.\n"
988	<	"-->Bend[%d] in %s\n",
989	<	j, comp_stamps[stampID]->getID() );
990	<	painCave.isFatal = 1;
991	<	simError();
992	<	}
993	<	}
994	<
995	<	else{
996	<
997	<	sprintf( painCave.errMsg,
998	<	"SimSetup Error: unhandled bend assignment:\n"
999	<	"    -->%s in Bend[%d] in %s\n",
1000	<	current_extra->getlhs(),
1001	<	j, comp_stamps[stampID]->getID() );
1002	<	painCave.isFatal = 1;
1003	<	simError();
1004	<	}
1005	<
1006	<	current_extra = current_extra->getNext();
1007	<	}
1008	<	}
1009	<
1010	<	if( !theBends[j].isGhost ){
1011	<
1012	<	exI = theBends[j].a;
1013	<	exJ = theBends[j].c;
1014	<	}
1015	<	else{
1016	<
1017	<	exI = theBends[j].a;
1018	<	exJ = theBends[j].b;
1019	<	}
1020	<
1021	<	// exclude_I must always be the smaller of the pair
1022	<	if( exI > exJ ){
1023	<	tempEx = exI;
1024	<	exI = exJ;
1025	<	exJ = tempEx;
1026	<	}
1027	<	#ifdef IS_MPI
1028	<	tempEx = exI;
1029	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1030	<	tempEx = exJ;
1031	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1032	<
1033	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1034	<	#else  // isn't MPI
1035	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1036	<	#endif  //is_mpi
682	>	if (globals->haveStatusTime()){
683	>	info[i].statusTime = globals->getStatusTime();
684		}
1038	–	excludeOffset += info.nBends;
685
686	<	for(j=0; j<info.nTorsions; j++){
687	<
688	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1043	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1044	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1045	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1046	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1047	<
1048	<	exI = theTorsions[j].a;
1049	<	exJ = theTorsions[j].d;
686	>	if (globals->haveThermalTime()){
687	>	info[i].thermalTime = globals->getThermalTime();
688	>	}
689
690	<	// exclude_I must always be the smaller of the pair
691	<	if( exI > exJ ){
692	<	tempEx = exI;
693	<	exI = exJ;
1055	<	exJ = tempEx;
1056	<	}
1057	<	#ifdef IS_MPI
1058	<	tempEx = exI;
1059	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1060	<	tempEx = exJ;
1061	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1062	<
1063	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1064	<	#else  // isn't MPI
1065	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1066	<	#endif  //is_mpi
690	>	info[i].resetIntegrator = 0;
691	>	if( globals->haveResetTime() ){
692	>	info[i].resetTime = globals->getResetTime();
693	>	info[i].resetIntegrator = 1;
694		}
1068	–	excludeOffset += info.nTorsions;
695
696	<
1071	<	// send the arrays off to the forceField for init.
696	>	// check for the temperature set flag
697
698	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
699	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1075	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1076	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
698	>	if (globals->haveTempSet())
699	>	info[i].setTemp = globals->getTempSet();
700
701	+	// get some of the tricky things that may still be in the globals
702
703	<	the_molecules[i].initialize( info );
703	>	double boxVector[3];
704	>	if (globals->haveBox()){
705	>	boxVector[0] = globals->getBox();
706	>	boxVector[1] = globals->getBox();
707	>	boxVector[2] = globals->getBox();
708
709	+	info[i].setBox(boxVector);
710	+	}
711	+	else if (globals->haveDensity()){
712	+	double vol;
713	+	vol = (double) tot_nmol / globals->getDensity();
714	+	boxVector[0] = pow(vol, (1.0 / 3.0));
715	+	boxVector[1] = boxVector[0];
716	+	boxVector[2] = boxVector[0];
717
718	<	atomOffset += info.nAtoms;
719	<	delete[] theBonds;
720	<	delete[] theBends;
721	<	delete[] theTorsions;
722	<	}
718	>	info[i].setBox(boxVector);
719	>	}
720	>	else{
721	>	if (!globals->haveBoxX()){
722	>	sprintf(painCave.errMsg,
723	>	"SimSetup error, no periodic BoxX size given.\n");
724	>	painCave.isFatal = 1;
725	>	simError();
726	>	}
727	>	boxVector[0] = globals->getBoxX();
728
729	<	#ifdef IS_MPI
730	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
731	<	MPIcheckPoint();
732	<	#endif // is_mpi
729	>	if (!globals->haveBoxY()){
730	>	sprintf(painCave.errMsg,
731	>	"SimSetup error, no periodic BoxY size given.\n");
732	>	painCave.isFatal = 1;
733	>	simError();
734	>	}
735	>	boxVector[1] = globals->getBoxY();
736
737	<	// clean up the forcefield
738	<	the_ff->calcRcut();
739	<	the_ff->cleanMe();
737	>	if (!globals->haveBoxZ()){
738	>	sprintf(painCave.errMsg,
739	>	"SimSetup error, no periodic BoxZ size given.\n");
740	>	painCave.isFatal = 1;
741	>	simError();
742	>	}
743	>	boxVector[2] = globals->getBoxZ();
744
745	<	}
745	>	info[i].setBox(boxVector);
746	>	}
747	>	}
748
749	<	void SimSetup::initFromBass( void ){
749	>	//setup seed for random number generator
750	>	int seedValue;
751
752	<	int i, j, k;
753	<	int n_cells;
1103	<	double cellx, celly, cellz;
1104	<	double temp1, temp2, temp3;
1105	<	int n_per_extra;
1106	<	int n_extra;
1107	<	int have_extra, done;
752	>	if (globals->haveSeed()){
753	>	seedValue = globals->getSeed();
754
755	<	temp1 = (double)tot_nmol / 4.0;
756	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
757	<	temp3 = ceil( temp2 );
758	<
759	<	have_extra =0;
1114	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1115	<	have_extra =1;
1116	<
1117	<	n_cells = (int)temp3 - 1;
1118	<	cellx = simnfo->box_x / temp3;
1119	<	celly = simnfo->box_y / temp3;
1120	<	cellz = simnfo->box_z / temp3;
1121	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1122	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1123	<	n_per_extra = (int)ceil( temp1 );
1124	<
1125	<	if( n_per_extra > 4){
1126	<	sprintf( painCave.errMsg,
1127	<	"SimSetup error. There has been an error in constructing"
1128	<	" the non-complete lattice.\n" );
1129	<	painCave.isFatal = 1;
755	>	if(seedValue / 1E9 == 0){
756	>	sprintf(painCave.errMsg,
757	>	"Seed for sprng library should contain at least 9 digits\n"
758	>	"OOPSE will generate a seed for user\n");
759	>	painCave.isFatal = 0;
760		simError();
761	+
762	+	//using seed generated by system instead of invalid seed set by user
763	+	#ifndef IS_MPI
764	+	seedValue = make_sprng_seed();
765	+	#else
766	+	if (worldRank == 0){
767	+	seedValue = make_sprng_seed();
768	+	}
769	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
770	+	#endif
771		}
772	<	}
772	>	}//end of if branch of globals->haveSeed()
773		else{
774	<	n_cells = (int)temp3;
775	<	cellx = simnfo->box_x / temp3;
776	<	celly = simnfo->box_y / temp3;
777	<	cellz = simnfo->box_z / temp3;
774	>
775	>	#ifndef IS_MPI
776	>	seedValue = make_sprng_seed();
777	>	#else
778	>	if (worldRank == 0){
779	>	seedValue = make_sprng_seed();
780	>	}
781	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
782	>	#endif
783	>	}//end of globals->haveSeed()
784	>
785	>	for (int i = 0; i < nInfo; i++){
786	>	info[i].setSeed(seedValue);
787		}
788
789	<	current_mol = 0;
790	<	current_comp_mol = 0;
791	<	current_comp = 0;
792	<	current_atom_ndx = 0;
789	>	#ifdef IS_MPI
790	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
791	>	MPIcheckPoint();
792	>	#endif // is_mpi
793	>	}
794
1145	–	for( i=0; i < n_cells ; i++ ){
1146	–	for( j=0; j < n_cells; j++ ){
1147	–	for( k=0; k < n_cells; k++ ){
795
796	<	makeElement( i * cellx,
797	<	j * celly,
798	<	k * cellz );
796	>	void SimSetup::finalInfoCheck(void){
797	>	int index;
798	>	int usesDipoles;
799	>	int i;
800
801	<	makeElement( i * cellx + 0.5 * cellx,
802	<	j * celly + 0.5 * celly,
1155	<	k * cellz );
801	>	for (i = 0; i < nInfo; i++){
802	>	// check electrostatic parameters
803
804	<	makeElement( i * cellx,
805	<	j * celly + 0.5 * celly,
806	<	k * cellz + 0.5 * cellz );
807	<
808	<	makeElement( i * cellx + 0.5 * cellx,
1162	<	j * celly,
1163	<	k * cellz + 0.5 * cellz );
1164	<	}
804	>	index = 0;
805	>	usesDipoles = 0;
806	>	while ((index < info[i].n_atoms) && !usesDipoles){
807	>	usesDipoles = (info[i].atoms[index])->hasDipole();
808	>	index++;
809		}
1166	–	}
810
811	<	if( have_extra ){
812	<	done = 0;
811	>	#ifdef IS_MPI
812	>	int myUse = usesDipoles;
813	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814	>	#endif //is_mpi
815
816	<	int start_ndx;
1172	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1173	<	for( j=0; j < (n_cells+1) && !done; j++ ){
816	>	double theEcr, theEst;
817
818	<	if( i < n_cells ){
818	>	if (globals->getUseRF()){
819	>	info[i].useReactionField = 1;
820
821	<	if( j < n_cells ){
822	<	start_ndx = n_cells;
823	<	}
824	<	else start_ndx = 0;
825	<	}
826	<	else start_ndx = 0;
821	>	if (!globals->haveECR()){
822	>	sprintf(painCave.errMsg,
823	>	"SimSetup Warning: using default value of 1/2 the smallest "
824	>	"box length for the electrostaticCutoffRadius.\n"
825	>	"I hope you have a very fast processor!\n");
826	>	painCave.isFatal = 0;
827	>	simError();
828	>	double smallest;
829	>	smallest = info[i].boxL[0];
830	>	if (info[i].boxL[1] <= smallest)
831	>	smallest = info[i].boxL[1];
832	>	if (info[i].boxL[2] <= smallest)
833	>	smallest = info[i].boxL[2];
834	>	theEcr = 0.5 * smallest;
835	>	}
836	>	else{
837	>	theEcr = globals->getECR();
838	>	}
839
840	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
840	>	if (!globals->haveEST()){
841	>	sprintf(painCave.errMsg,
842	>	"SimSetup Warning: using default value of 0.05 * the "
843	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
844	>	painCave.isFatal = 0;
845	>	simError();
846	>	theEst = 0.05 * theEcr;
847	>	}
848	>	else{
849	>	theEst = globals->getEST();
850	>	}
851
852	<	makeElement( i * cellx,
1187	<	j * celly,
1188	<	k * cellz );
1189	<	done = ( current_mol >= tot_nmol );
852	>	info[i].setEcr(theEcr, theEst);
853
854	<	if( !done && n_per_extra > 1 ){
855	<	makeElement( i * cellx + 0.5 * cellx,
856	<	j * celly + 0.5 * celly,
857	<	k * cellz );
858	<	done = ( current_mol >= tot_nmol );
859	<	}
854	>	if (!globals->haveDielectric()){
855	>	sprintf(painCave.errMsg,
856	>	"SimSetup Error: You are trying to use Reaction Field without"
857	>	"setting a dielectric constant!\n");
858	>	painCave.isFatal = 1;
859	>	simError();
860	>	}
861	>	info[i].dielectric = globals->getDielectric();
862	>	}
863	>	else{
864	>	if (usesDipoles){
865	>	if (!globals->haveECR()){
866	>	sprintf(painCave.errMsg,
867	>	"SimSetup Warning: using default value of 1/2 the smallest "
868	>	"box length for the electrostaticCutoffRadius.\n"
869	>	"I hope you have a very fast processor!\n");
870	>	painCave.isFatal = 0;
871	>	simError();
872	>	double smallest;
873	>	smallest = info[i].boxL[0];
874	>	if (info[i].boxL[1] <= smallest)
875	>	smallest = info[i].boxL[1];
876	>	if (info[i].boxL[2] <= smallest)
877	>	smallest = info[i].boxL[2];
878	>	theEcr = 0.5 * smallest;
879	>	}
880	>	else{
881	>	theEcr = globals->getECR();
882	>	}
883
884	<	if( !done && n_per_extra > 2){
885	<	makeElement( i * cellx,
886	<	j * celly + 0.5 * celly,
887	<	k * cellz + 0.5 * cellz );
888	<	done = ( current_mol >= tot_nmol );
889	<	}
884	>	if (!globals->haveEST()){
885	>	sprintf(painCave.errMsg,
886	>	"SimSetup Warning: using default value of 0.05 * the "
887	>	"electrostaticCutoffRadius for the "
888	>	"electrostaticSkinThickness\n");
889	>	painCave.isFatal = 0;
890	>	simError();
891	>	theEst = 0.05 * theEcr;
892	>	}
893	>	else{
894	>	theEst = globals->getEST();
895	>	}
896
897	<	if( !done && n_per_extra > 3){
1206	<	makeElement( i * cellx + 0.5 * cellx,
1207	<	j * celly,
1208	<	k * cellz + 0.5 * cellz );
1209	<	done = ( current_mol >= tot_nmol );
1210	<	}
1211	<	}
897	>	info[i].setEcr(theEcr, theEst);
898		}
899		}
900		}
901
902	<
903	<	for( i=0; i<simnfo->n_atoms; i++ ){
904	<	simnfo->atoms[i]->set_vx( 0.0 );
905	<	simnfo->atoms[i]->set_vy( 0.0 );
1220	<	simnfo->atoms[i]->set_vz( 0.0 );
1221	<	}
902	>	#ifdef IS_MPI
903	>	strcpy(checkPointMsg, "post processing checks out");
904	>	MPIcheckPoint();
905	>	#endif // is_mpi
906		}
907
908	<	void SimSetup::makeElement( double x, double y, double z ){
908	>	void SimSetup::initSystemCoords(void){
909	>	int i;
910
911	<	int k;
1227	<	AtomStamp* current_atom;
1228	<	DirectionalAtom* dAtom;
1229	<	double rotMat[3][3];
911	>	char* inName;
912
913	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
913	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
914
915	<	current_atom = comp_stamps[current_comp]->getAtom( k );
916	<	if( !current_atom->havePosition() ){
917	<	sprintf( painCave.errMsg,
918	<	"SimSetup:initFromBass error.\n"
919	<	"\tComponent %s, atom %s does not have a position specified.\n"
920	<	"\tThe initialization routine is unable to give a start"
921	<	" position.\n",
922	<	comp_stamps[current_comp]->getID(),
923	<	current_atom->getType() );
924	<	painCave.isFatal = 1;
925	<	simError();
915	>	for (i = 0; i < info[0].n_atoms; i++)
916	>	info[0].atoms[i]->setCoords();
917	>
918	>	if (globals->haveInitialConfig()){
919	>	InitializeFromFile* fileInit;
920	>	#ifdef IS_MPI // is_mpi
921	>	if (worldRank == 0){
922	>	#endif //is_mpi
923	>	inName = globals->getInitialConfig();
924	>	fileInit = new InitializeFromFile(inName);
925	>	#ifdef IS_MPI
926		}
927	+	else
928	+	fileInit = new InitializeFromFile(NULL);
929	+	#endif
930	+	fileInit->readInit(info); // default velocities on
931
932	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
933	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
934	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
932	>	delete fileInit;
933	>	}
934	>	else{
935	>	#ifdef IS_MPI
936
937	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
937	>	// no init from bass
938
939	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
939	>	sprintf(painCave.errMsg,
940	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
941	>	painCave.isFatal = 1;;
942	>	simError();
943
944	<	rotMat[0][0] = 1.0;
1255	<	rotMat[0][1] = 0.0;
1256	<	rotMat[0][2] = 0.0;
944	>	#else
945
946	<	rotMat[1][0] = 0.0;
1259	<	rotMat[1][1] = 1.0;
1260	<	rotMat[1][2] = 0.0;
946	>	initFromBass();
947
1262	–	rotMat[2][0] = 0.0;
1263	–	rotMat[2][1] = 0.0;
1264	–	rotMat[2][2] = 1.0;
948
949	<	dAtom->setA( rotMat );
949	>	#endif
950	>	}
951	>
952	>	#ifdef IS_MPI
953	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
954	>	MPIcheckPoint();
955	>	#endif // is_mpi
956	>	}
957	>
958	>
959	>	void SimSetup::makeOutNames(void){
960	>	int k;
961	>
962	>
963	>	for (k = 0; k < nInfo; k++){
964	>	#ifdef IS_MPI
965	>	if (worldRank == 0){
966	>	#endif // is_mpi
967	>
968	>	if (globals->haveFinalConfig()){
969	>	strcpy(info[k].finalName, globals->getFinalConfig());
970	>	}
971	>	else{
972	>	strcpy(info[k].finalName, inFileName);
973	>	char* endTest;
974	>	int nameLength = strlen(info[k].finalName);
975	>	endTest = &(info[k].finalName[nameLength - 5]);
976	>	if (!strcmp(endTest, ".bass")){
977	>	strcpy(endTest, ".eor");
978	>	}
979	>	else if (!strcmp(endTest, ".BASS")){
980	>	strcpy(endTest, ".eor");
981	>	}
982	>	else{
983	>	endTest = &(info[k].finalName[nameLength - 4]);
984	>	if (!strcmp(endTest, ".bss")){
985	>	strcpy(endTest, ".eor");
986	>	}
987	>	else if (!strcmp(endTest, ".mdl")){
988	>	strcpy(endTest, ".eor");
989	>	}
990	>	else{
991	>	strcat(info[k].finalName, ".eor");
992	>	}
993	>	}
994	>	}
995	>
996	>	// make the sample and status out names
997	>
998	>	strcpy(info[k].sampleName, inFileName);
999	>	char* endTest;
1000	>	int nameLength = strlen(info[k].sampleName);
1001	>	endTest = &(info[k].sampleName[nameLength - 5]);
1002	>	if (!strcmp(endTest, ".bass")){
1003	>	strcpy(endTest, ".dump");
1004	>	}
1005	>	else if (!strcmp(endTest, ".BASS")){
1006	>	strcpy(endTest, ".dump");
1007	>	}
1008	>	else{
1009	>	endTest = &(info[k].sampleName[nameLength - 4]);
1010	>	if (!strcmp(endTest, ".bss")){
1011	>	strcpy(endTest, ".dump");
1012	>	}
1013	>	else if (!strcmp(endTest, ".mdl")){
1014	>	strcpy(endTest, ".dump");
1015	>	}
1016	>	else{
1017	>	strcat(info[k].sampleName, ".dump");
1018	>	}
1019	>	}
1020	>
1021	>	strcpy(info[k].statusName, inFileName);
1022	>	nameLength = strlen(info[k].statusName);
1023	>	endTest = &(info[k].statusName[nameLength - 5]);
1024	>	if (!strcmp(endTest, ".bass")){
1025	>	strcpy(endTest, ".stat");
1026	>	}
1027	>	else if (!strcmp(endTest, ".BASS")){
1028	>	strcpy(endTest, ".stat");
1029	>	}
1030	>	else{
1031	>	endTest = &(info[k].statusName[nameLength - 4]);
1032	>	if (!strcmp(endTest, ".bss")){
1033	>	strcpy(endTest, ".stat");
1034	>	}
1035	>	else if (!strcmp(endTest, ".mdl")){
1036	>	strcpy(endTest, ".stat");
1037	>	}
1038	>	else{
1039	>	strcat(info[k].statusName, ".stat");
1040	>	}
1041	>	}
1042	>
1043	>	#ifdef IS_MPI
1044	>
1045		}
1046	+	#endif // is_mpi
1047	+	}
1048	+	}
1049
1050	<	current_atom_ndx++;
1050	>
1051	>	void SimSetup::sysObjectsCreation(void){
1052	>	int i, k;
1053	>
1054	>	// create the forceField
1055	>
1056	>	createFF();
1057	>
1058	>	// extract componentList
1059	>
1060	>	compList();
1061	>
1062	>	// calc the number of atoms, bond, bends, and torsions
1063	>
1064	>	calcSysValues();
1065	>
1066	>	#ifdef IS_MPI
1067	>	// divide the molecules among the processors
1068	>
1069	>	mpiMolDivide();
1070	>	#endif //is_mpi
1071	>
1072	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1073	>
1074	>	makeSysArrays();
1075	>
1076	>	// make and initialize the molecules (all but atomic coordinates)
1077	>
1078	>	makeMolecules();
1079	>
1080	>	for (k = 0; k < nInfo; k++){
1081	>	info[k].identArray = new int[info[k].n_atoms];
1082	>	for (i = 0; i < info[k].n_atoms; i++){
1083	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1084	>	}
1085		}
1086	+	}
1087
1272	–	current_mol++;
1273	–	current_comp_mol++;
1088
1089	<	if( current_comp_mol >= components_nmol[current_comp] ){
1089	>	void SimSetup::createFF(void){
1090	>	switch (ffCase){
1091	>	case FF_DUFF:
1092	>	the_ff = new DUFF();
1093	>	break;
1094
1095	<	current_comp_mol = 0;
1096	<	current_comp++;
1095	>	case FF_LJ:
1096	>	the_ff = new LJFF();
1097	>	break;
1098	>
1099	>	case FF_EAM:
1100	>	the_ff = new EAM_FF();
1101	>	break;
1102	>
1103	>	default:
1104	>	sprintf(painCave.errMsg,
1105	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1106	>	painCave.isFatal = 1;
1107	>	simError();
1108		}
1109	+
1110	+	#ifdef IS_MPI
1111	+	strcpy(checkPointMsg, "ForceField creation successful");
1112	+	MPIcheckPoint();
1113	+	#endif // is_mpi
1114		}
1115	+
1116	+
1117	+	void SimSetup::compList(void){
1118	+	int i;
1119	+	char* id;
1120	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1121	+	LinkedMolStamp* currentStamp = NULL;
1122	+	comp_stamps = new MoleculeStamp * [n_components];
1123	+
1124	+	// make an array of molecule stamps that match the components used.
1125	+	// also extract the used stamps out into a separate linked list
1126	+
1127	+	for (i = 0; i < nInfo; i++){
1128	+	info[i].nComponents = n_components;
1129	+	info[i].componentsNmol = components_nmol;
1130	+	info[i].compStamps = comp_stamps;
1131	+	info[i].headStamp = headStamp;
1132	+	}
1133	+
1134	+
1135	+	for (i = 0; i < n_components; i++){
1136	+	id = the_components[i]->getType();
1137	+	comp_stamps[i] = NULL;
1138	+
1139	+	// check to make sure the component isn't already in the list
1140	+
1141	+	comp_stamps[i] = headStamp->match(id);
1142	+	if (comp_stamps[i] == NULL){
1143	+	// extract the component from the list;
1144	+
1145	+	currentStamp = stamps->extractMolStamp(id);
1146	+	if (currentStamp == NULL){
1147	+	sprintf(painCave.errMsg,
1148	+	"SimSetup error: Component \"%s\" was not found in the "
1149	+	"list of declared molecules\n",
1150	+	id);
1151	+	painCave.isFatal = 1;
1152	+	simError();
1153	+	}
1154	+
1155	+	headStamp->add(currentStamp);
1156	+	comp_stamps[i] = headStamp->match(id);
1157	+	}
1158	+	}
1159	+
1160	+	#ifdef IS_MPI
1161	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1162	+	MPIcheckPoint();
1163	+	#endif // is_mpi
1164	+	}
1165	+
1166	+	void SimSetup::calcSysValues(void){
1167	+	int i;
1168	+
1169	+	int* molMembershipArray;
1170	+
1171	+	tot_atoms = 0;
1172	+	tot_bonds = 0;
1173	+	tot_bends = 0;
1174	+	tot_torsions = 0;
1175	+	for (i = 0; i < n_components; i++){
1176	+	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1177	+	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1178	+	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1179	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1180	+	}
1181	+
1182	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1183	+	molMembershipArray = new int[tot_atoms];
1184	+
1185	+	for (i = 0; i < nInfo; i++){
1186	+	info[i].n_atoms = tot_atoms;
1187	+	info[i].n_bonds = tot_bonds;
1188	+	info[i].n_bends = tot_bends;
1189	+	info[i].n_torsions = tot_torsions;
1190	+	info[i].n_SRI = tot_SRI;
1191	+	info[i].n_mol = tot_nmol;
1192	+
1193	+	info[i].molMembershipArray = molMembershipArray;
1194	+	}
1195	+	}
1196	+
1197	+	#ifdef IS_MPI
1198	+
1199	+	void SimSetup::mpiMolDivide(void){
1200	+	int i, j, k;
1201	+	int localMol, allMol;
1202	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1203	+
1204	+	mpiSim = new mpiSimulation(info);
1205	+
1206	+	globalIndex = mpiSim->divideLabor();
1207	+
1208	+	// set up the local variables
1209	+
1210	+	mol2proc = mpiSim->getMolToProcMap();
1211	+	molCompType = mpiSim->getMolComponentType();
1212	+
1213	+	allMol = 0;
1214	+	localMol = 0;
1215	+	local_atoms = 0;
1216	+	local_bonds = 0;
1217	+	local_bends = 0;
1218	+	local_torsions = 0;
1219	+	globalAtomIndex = 0;
1220	+
1221	+
1222	+	for (i = 0; i < n_components; i++){
1223	+	for (j = 0; j < components_nmol[i]; j++){
1224	+	if (mol2proc[allMol] == worldRank){
1225	+	local_atoms += comp_stamps[i]->getNAtoms();
1226	+	local_bonds += comp_stamps[i]->getNBonds();
1227	+	local_bends += comp_stamps[i]->getNBends();
1228	+	local_torsions += comp_stamps[i]->getNTorsions();
1229	+	localMol++;
1230	+	}
1231	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1232	+	info[0].molMembershipArray[globalAtomIndex] = allMol;
1233	+	globalAtomIndex++;
1234	+	}
1235	+
1236	+	allMol++;
1237	+	}
1238	+	}
1239	+	local_SRI = local_bonds + local_bends + local_torsions;
1240	+
1241	+	info[0].n_atoms = mpiSim->getMyNlocal();
1242	+
1243	+	if (local_atoms != info[0].n_atoms){
1244	+	sprintf(painCave.errMsg,
1245	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1246	+	" localAtom (%d) are not equal.\n",
1247	+	info[0].n_atoms, local_atoms);
1248	+	painCave.isFatal = 1;
1249	+	simError();
1250	+	}
1251	+
1252	+	info[0].n_bonds = local_bonds;
1253	+	info[0].n_bends = local_bends;
1254	+	info[0].n_torsions = local_torsions;
1255	+	info[0].n_SRI = local_SRI;
1256	+	info[0].n_mol = localMol;
1257	+
1258	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1259	+	MPIcheckPoint();
1260	+	}
1261	+
1262	+	#endif // is_mpi
1263	+
1264	+
1265	+	void SimSetup::makeSysArrays(void){
1266	+
1267	+	#ifndef IS_MPI
1268	+	int k, j;
1269	+	#endif // is_mpi
1270	+	int i, l;
1271	+
1272	+	Atom** the_atoms;
1273	+	Molecule* the_molecules;
1274	+	Exclude** the_excludes;
1275	+
1276	+
1277	+	for (l = 0; l < nInfo; l++){
1278	+	// create the atom and short range interaction arrays
1279	+
1280	+	the_atoms = new Atom * [info[l].n_atoms];
1281	+	the_molecules = new Molecule[info[l].n_mol];
1282	+	int molIndex;
1283	+
1284	+	// initialize the molecule's stampID's
1285	+
1286	+	#ifdef IS_MPI
1287	+
1288	+
1289	+	molIndex = 0;
1290	+	for (i = 0; i < mpiSim->getTotNmol(); i++){
1291	+	if (mol2proc[i] == worldRank){
1292	+	the_molecules[molIndex].setStampID(molCompType[i]);
1293	+	the_molecules[molIndex].setMyIndex(molIndex);
1294	+	the_molecules[molIndex].setGlobalIndex(i);
1295	+	molIndex++;
1296	+	}
1297	+	}
1298	+
1299	+	#else // is_mpi
1300	+
1301	+	molIndex = 0;
1302	+	globalAtomIndex = 0;
1303	+	for (i = 0; i < n_components; i++){
1304	+	for (j = 0; j < components_nmol[i]; j++){
1305	+	the_molecules[molIndex].setStampID(i);
1306	+	the_molecules[molIndex].setMyIndex(molIndex);
1307	+	the_molecules[molIndex].setGlobalIndex(molIndex);
1308	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1309	+	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1310	+	globalAtomIndex++;
1311	+	}
1312	+	molIndex++;
1313	+	}
1314	+	}
1315	+
1316	+
1317	+	#endif // is_mpi
1318	+
1319	+
1320	+	if (info[l].n_SRI){
1321	+	Exclude::createArray(info[l].n_SRI);
1322	+	the_excludes = new Exclude * [info[l].n_SRI];
1323	+	for (int ex = 0; ex < info[l].n_SRI; ex++){
1324	+	the_excludes[ex] = new Exclude(ex);
1325	+	}
1326	+	info[l].globalExcludes = new int;
1327	+	info[l].n_exclude = info[l].n_SRI;
1328	+	}
1329	+	else{
1330	+	Exclude::createArray(1);
1331	+	the_excludes = new Exclude * ;
1332	+	the_excludes[0] = new Exclude(0);
1333	+	the_excludes[0]->setPair(0, 0);
1334	+	info[l].globalExcludes = new int;
1335	+	info[l].globalExcludes[0] = 0;
1336	+	info[l].n_exclude = 0;
1337	+	}
1338	+
1339	+	// set the arrays into the SimInfo object
1340	+
1341	+	info[l].atoms = the_atoms;
1342	+	info[l].molecules = the_molecules;
1343	+	info[l].nGlobalExcludes = 0;
1344	+	info[l].excludes = the_excludes;
1345	+
1346	+	the_ff->setSimInfo(info);
1347	+	}
1348	+	}
1349	+
1350	+	void SimSetup::makeIntegrator(void){
1351	+	int k;
1352	+
1353	+	NVE<RealIntegrator>* myNVE = NULL;
1354	+	NVT<RealIntegrator>* myNVT = NULL;
1355	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1356	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1357	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1358	+
1359	+	for (k = 0; k < nInfo; k++){
1360	+	switch (ensembleCase){
1361	+	case NVE_ENS:
1362	+	if (globals->haveZconstraints()){
1363	+	setupZConstraint(info[k]);
1364	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1365	+	}
1366	+	else{
1367	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1368	+	}
1369	+
1370	+	info->the_integrator = myNVE;
1371	+	break;
1372	+
1373	+	case NVT_ENS:
1374	+	if (globals->haveZconstraints()){
1375	+	setupZConstraint(info[k]);
1376	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1377	+	}
1378	+	else
1379	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1380	+
1381	+	myNVT->setTargetTemp(globals->getTargetTemp());
1382	+
1383	+	if (globals->haveTauThermostat())
1384	+	myNVT->setTauThermostat(globals->getTauThermostat());
1385	+	else{
1386	+	sprintf(painCave.errMsg,
1387	+	"SimSetup error: If you use the NVT\n"
1388	+	"    ensemble, you must set tauThermostat.\n");
1389	+	painCave.isFatal = 1;
1390	+	simError();
1391	+	}
1392	+
1393	+	info->the_integrator = myNVT;
1394	+	break;
1395	+
1396	+	case NPTi_ENS:
1397	+	if (globals->haveZconstraints()){
1398	+	setupZConstraint(info[k]);
1399	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1400	+	}
1401	+	else
1402	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1403	+
1404	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1405	+
1406	+	if (globals->haveTargetPressure())
1407	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1408	+	else{
1409	+	sprintf(painCave.errMsg,
1410	+	"SimSetup error: If you use a constant pressure\n"
1411	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1412	+	painCave.isFatal = 1;
1413	+	simError();
1414	+	}
1415	+
1416	+	if (globals->haveTauThermostat())
1417	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1418	+	else{
1419	+	sprintf(painCave.errMsg,
1420	+	"SimSetup error: If you use an NPT\n"
1421	+	"    ensemble, you must set tauThermostat.\n");
1422	+	painCave.isFatal = 1;
1423	+	simError();
1424	+	}
1425	+
1426	+	if (globals->haveTauBarostat())
1427	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1428	+	else{
1429	+	sprintf(painCave.errMsg,
1430	+	"SimSetup error: If you use an NPT\n"
1431	+	"    ensemble, you must set tauBarostat.\n");
1432	+	painCave.isFatal = 1;
1433	+	simError();
1434	+	}
1435	+
1436	+	info->the_integrator = myNPTi;
1437	+	break;
1438	+
1439	+	case NPTf_ENS:
1440	+	if (globals->haveZconstraints()){
1441	+	setupZConstraint(info[k]);
1442	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1443	+	}
1444	+	else
1445	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1446	+
1447	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1448	+
1449	+	if (globals->haveTargetPressure())
1450	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1451	+	else{
1452	+	sprintf(painCave.errMsg,
1453	+	"SimSetup error: If you use a constant pressure\n"
1454	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1455	+	painCave.isFatal = 1;
1456	+	simError();
1457	+	}
1458	+
1459	+	if (globals->haveTauThermostat())
1460	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1461	+	else{
1462	+	sprintf(painCave.errMsg,
1463	+	"SimSetup error: If you use an NPT\n"
1464	+	"    ensemble, you must set tauThermostat.\n");
1465	+	painCave.isFatal = 1;
1466	+	simError();
1467	+	}
1468	+
1469	+	if (globals->haveTauBarostat())
1470	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1471	+	else{
1472	+	sprintf(painCave.errMsg,
1473	+	"SimSetup error: If you use an NPT\n"
1474	+	"    ensemble, you must set tauBarostat.\n");
1475	+	painCave.isFatal = 1;
1476	+	simError();
1477	+	}
1478	+
1479	+	info->the_integrator = myNPTf;
1480	+	break;
1481	+
1482	+	case NPTxyz_ENS:
1483	+	if (globals->haveZconstraints()){
1484	+	setupZConstraint(info[k]);
1485	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1486	+	}
1487	+	else
1488	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1489	+
1490	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1491	+
1492	+	if (globals->haveTargetPressure())
1493	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1494	+	else{
1495	+	sprintf(painCave.errMsg,
1496	+	"SimSetup error: If you use a constant pressure\n"
1497	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1498	+	painCave.isFatal = 1;
1499	+	simError();
1500	+	}
1501	+
1502	+	if (globals->haveTauThermostat())
1503	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1504	+	else{
1505	+	sprintf(painCave.errMsg,
1506	+	"SimSetup error: If you use an NPT\n"
1507	+	"    ensemble, you must set tauThermostat.\n");
1508	+	painCave.isFatal = 1;
1509	+	simError();
1510	+	}
1511	+
1512	+	if (globals->haveTauBarostat())
1513	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1514	+	else{
1515	+	sprintf(painCave.errMsg,
1516	+	"SimSetup error: If you use an NPT\n"
1517	+	"    ensemble, you must set tauBarostat.\n");
1518	+	painCave.isFatal = 1;
1519	+	simError();
1520	+	}
1521	+
1522	+	info->the_integrator = myNPTxyz;
1523	+	break;
1524	+
1525	+	default:
1526	+	sprintf(painCave.errMsg,
1527	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1528	+	painCave.isFatal = 1;
1529	+	simError();
1530	+	}
1531	+	}
1532	+	}
1533	+
1534	+	void SimSetup::initFortran(void){
1535	+	info[0].refreshSim();
1536	+
1537	+	if (!strcmp(info[0].mixingRule, "standard")){
1538	+	the_ff->initForceField(LB_MIXING_RULE);
1539	+	}
1540	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1541	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1542	+	}
1543	+	else{
1544	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1545	+	info[0].mixingRule);
1546	+	painCave.isFatal = 1;
1547	+	simError();
1548	+	}
1549	+
1550	+
1551	+	#ifdef IS_MPI
1552	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1553	+	MPIcheckPoint();
1554	+	#endif // is_mpi
1555	+	}
1556	+
1557	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1558	+	int nZConstraints;
1559	+	ZconStamp** zconStamp;
1560	+
1561	+	if (globals->haveZconstraintTime()){
1562	+	//add sample time of z-constraint  into SimInfo's property list
1563	+	DoubleData* zconsTimeProp = new DoubleData();
1564	+	zconsTimeProp->setID(ZCONSTIME_ID);
1565	+	zconsTimeProp->setData(globals->getZconsTime());
1566	+	theInfo.addProperty(zconsTimeProp);
1567	+	}
1568	+	else{
1569	+	sprintf(painCave.errMsg,
1570	+	"ZConstraint error: If you use an ZConstraint\n"
1571	+	" , you must set sample time.\n");
1572	+	painCave.isFatal = 1;
1573	+	simError();
1574	+	}
1575	+
1576	+	//push zconsTol into siminfo, if user does not specify
1577	+	//value for zconsTol, a default value will be used
1578	+	DoubleData* zconsTol = new DoubleData();
1579	+	zconsTol->setID(ZCONSTOL_ID);
1580	+	if (globals->haveZconsTol()){
1581	+	zconsTol->setData(globals->getZconsTol());
1582	+	}
1583	+	else{
1584	+	double defaultZConsTol = 0.01;
1585	+	sprintf(painCave.errMsg,
1586	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1587	+	" , default value %f is used.\n",
1588	+	defaultZConsTol);
1589	+	painCave.isFatal = 0;
1590	+	simError();
1591	+
1592	+	zconsTol->setData(defaultZConsTol);
1593	+	}
1594	+	theInfo.addProperty(zconsTol);
1595	+
1596	+	//set Force Subtraction Policy
1597	+	StringData* zconsForcePolicy = new StringData();
1598	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1599	+
1600	+	if (globals->haveZconsForcePolicy()){
1601	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1602	+	}
1603	+	else{
1604	+	sprintf(painCave.errMsg,
1605	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1606	+	"PolicyByMass is used\n");
1607	+	painCave.isFatal = 0;
1608	+	simError();
1609	+	zconsForcePolicy->setData("BYMASS");
1610	+	}
1611	+
1612	+	theInfo.addProperty(zconsForcePolicy);
1613	+
1614	+	//Determine the name of ouput file and add it into SimInfo's property list
1615	+	//Be careful, do not use inFileName, since it is a pointer which
1616	+	//point to a string at master node, and slave nodes do not contain that string
1617	+
1618	+	string zconsOutput(theInfo.finalName);
1619	+
1620	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1621	+
1622	+	StringData* zconsFilename = new StringData();
1623	+	zconsFilename->setID(ZCONSFILENAME_ID);
1624	+	zconsFilename->setData(zconsOutput);
1625	+
1626	+	theInfo.addProperty(zconsFilename);
1627	+
1628	+	//setup index, pos and other parameters of z-constraint molecules
1629	+	nZConstraints = globals->getNzConstraints();
1630	+	theInfo.nZconstraints = nZConstraints;
1631	+
1632	+	zconStamp = globals->getZconStamp();
1633	+	ZConsParaItem tempParaItem;
1634	+
1635	+	ZConsParaData* zconsParaData = new ZConsParaData();
1636	+	zconsParaData->setID(ZCONSPARADATA_ID);
1637	+
1638	+	for (int i = 0; i < nZConstraints; i++){
1639	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1640	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1641	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1642	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1643	+
1644	+	zconsParaData->addItem(tempParaItem);
1645	+	}
1646	+
1647	+	//check the uniqueness of index
1648	+	if(!zconsParaData->isIndexUnique()){
1649	+	sprintf(painCave.errMsg,
1650	+	"ZConstraint Error: molIndex is not unique\n");
1651	+	painCave.isFatal = 1;
1652	+	simError();
1653	+	}
1654	+
1655	+	//sort the parameters by index of molecules
1656	+	zconsParaData->sortByIndex();
1657	+
1658	+	//push data into siminfo, therefore, we can retrieve later
1659	+	theInfo.addProperty(zconsParaData);
1660	+	}

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