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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 491 by mmeineke, Fri Apr 11 18:46:37 2003 UTC vs.
Revision 843 by mmeineke, Wed Oct 29 20:41:39 2003 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 12 | Line 15 | SimSetup::SimSetup(){
15		#include "mpiSimulation.hpp"
16		#endif
17
18	+	// some defines for ensemble and Forcefield  cases
19	+
20	+	#define NVE_ENS        0
21	+	#define NVT_ENS        1
22	+	#define NPTi_ENS       2
23	+	#define NPTf_ENS       3
24	+	#define NPTxyz_ENS     4
25	+
26	+
27	+	#define FF_DUFF 0
28	+	#define FF_LJ   1
29	+	#define FF_EAM  2
30	+
31	+	using namespace std;
32	+
33		SimSetup::SimSetup(){
34	+
35	+	initSuspend = false;
36	+	isInfoArray = 0;
37	+	nInfo = 1;
38	+
39		stamps = new MakeStamps();
40		globals = new Globals();
41	<
41	>
42	>
43		#ifdef IS_MPI
44	<	strcpy( checkPointMsg, "SimSetup creation successful" );
44	>	strcpy(checkPointMsg, "SimSetup creation successful");
45		MPIcheckPoint();
46		#endif // IS_MPI
47		}
#	Line 27 | Line 51 | void SimSetup::parseFile( char* fileName ){
51		delete globals;
52		}
53
54	<	void SimSetup::parseFile( char* fileName ){
54	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
55	>	info = the_info;
56	>	nInfo = theNinfo;
57	>	isInfoArray = 1;
58	>	initSuspend = true;
59	>	}
60
61	+
62	+	void SimSetup::parseFile(char* fileName){
63		#ifdef IS_MPI
64	<	if( worldRank == 0 ){
64	>	if (worldRank == 0){
65		#endif // is_mpi
66	<
66	>
67		inFileName = fileName;
68	<	set_interface_stamps( stamps, globals );
69	<
68	>	set_interface_stamps(stamps, globals);
69	>
70		#ifdef IS_MPI
71		mpiEventInit();
72		#endif
73
74	<	yacc_BASS( fileName );
74	>	yacc_BASS(fileName);
75
76		#ifdef IS_MPI
77		throwMPIEvent(NULL);
78		}
79	<	else receiveParse();
79	>	else{
80	>	receiveParse();
81	>	}
82		#endif
83
84		}
85
86		#ifdef IS_MPI
87		void SimSetup::receiveParse(void){
88	<
89	<	set_interface_stamps( stamps, globals );
90	<	mpiEventInit();
91	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
88	>	set_interface_stamps(stamps, globals);
89	>	mpiEventInit();
90	>	MPIcheckPoint();
91	>	mpiEventLoop();
92		}
93
94		#endif // is_mpi
95
96	<	void SimSetup::createSim( void ){
96	>	void SimSetup::createSim(void){
97
98	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	ExtendedSystem* the_extendedsystem;
70	<	int i, j, k, globalAtomIndex;
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	>	// initialize the system coordinates
107
108	<	if (the_globals->haveTauThermostat())
109	<	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	>	if ( !initSuspend ){
109	>	initSystemCoords();
110
111	<	if (the_globals->haveTauBarostat())
112	<	the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
113	<	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	<	}
111	>	if( !(globals->getUseInitTime()) )
112	>	info[0].currentTime = 0.0;
113	>	}
114
115	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
126	<	the_extendedsystem = new ExtendedSystem( simnfo );
127	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
115	>	// check on the post processing info
116
117	<	if (the_globals->haveTauThermostat())
130	<	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	<	}
117	>	finalInfoCheck();
118
119	<	} 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" );
151	<	}
152	<	strcpy( simnfo->ensemble, ensemble );
119	>	// make the output filenames
120
121	<	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	<	}
121	>	makeOutNames();
122
123	<	#ifdef IS_MPI
172	<	strcpy( checkPointMsg, "ForceField creation successful" );
173	<	MPIcheckPoint();
174	<	#endif // is_mpi
123	>	// make the integrator
124
125	<
125	>	makeIntegrator();
126
127	<	// get the components and calculate the tot_nMol and indvidual n_mol
128	<	the_components = the_globals->getComponents();
129	<	components_nmol = new int[n_components];
181	<	comp_stamps = new MoleculeStamp*[n_components];
127	>	#ifdef IS_MPI
128	>	mpiSim->mpiRefresh();
129	>	#endif
130
131	<	if( !the_globals->haveNMol() ){
184	<	// we don't have the total number of molecules, so we assume it is
185	<	// given in each component
131	>	// initialize the Fortran
132
133	<	tot_nmol = 0;
134	<	for( i=0; i<n_components; i++ ){
133	>	initFortran();
134	>	}
135
190	–	if( !the_components[i]->haveNMol() ){
191	–	// we have a problem
192	–	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	–	}
136
137	<	tot_nmol += the_components[i]->getNMol();
138	<	components_nmol[i] = the_components[i]->getNMol();
139	<	}
140	<	}
141	<	else{
142	<	sprintf( painCave.errMsg,
143	<	"SimSetup error.\n"
144	<	"\tSorry, the ability to specify total"
145	<	" nMols and then give molfractions in the components\n"
146	<	"\tis not currently supported."
147	<	" 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	<	}
137	>	void SimSetup::makeMolecules(void){
138	>	int k;
139	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140	>	molInit molInfo;
141	>	DirectionalAtom* dAtom;
142	>	LinkedAssign* extras;
143	>	LinkedAssign* current_extra;
144	>	AtomStamp* currentAtom;
145	>	BondStamp* currentBond;
146	>	BendStamp* currentBend;
147	>	TorsionStamp* currentTorsion;
148
149	<	#ifdef IS_MPI
150	<	strcpy( checkPointMsg, "Have the number of components" );
151	<	MPIcheckPoint();
231	<	#endif // is_mpi
149	>	bond_pair* theBonds;
150	>	bend_set* theBends;
151	>	torsion_set* theTorsions;
152
233	–	// make an array of molecule stamps that match the components used.
234	–	// also extract the used stamps out into a separate linked list
153
154	<	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++ ){
154	>	//init the forceField paramters
155
156	<	id = the_components[i]->getType();
247	<	comp_stamps[i] = NULL;
248	<
249	<	// check to make sure the component isn't already in the list
156	>	the_ff->readParams();
157
251	–	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	–	}
158
159	<	#ifdef IS_MPI
160	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
161	<	MPIcheckPoint();
274	<	#endif // is_mpi
275	<
159	>	// init the atoms
160	>
161	>	double ux, uy, uz, u, uSqr;
162
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	<	// caclulate the number of atoms, bonds, bends and torsions
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	<	tot_atoms = 0;
178	<	tot_bonds = 0;
179	<	tot_bends = 0;
180	<	tot_torsions = 0;
181	<	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	<	}
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_SRI = tot_bonds + tot_bends + tot_torsions;
183	>	theBonds = new bond_pair[molInfo.nBonds];
184	>	theBends = new bend_set[molInfo.nBends];
185	>	theTorsions = new torsion_set[molInfo.nTorsions];
186
187	<	simnfo->n_atoms = tot_atoms;
296	<	simnfo->n_bonds = tot_bonds;
297	<	simnfo->n_bends = tot_bends;
298	<	simnfo->n_torsions = tot_torsions;
299	<	simnfo->n_SRI = tot_SRI;
300	<	simnfo->n_mol = tot_nmol;
301	<
302	<	simnfo->molMembershipArray = new int[tot_atoms];
187	>	// make the Atoms
188
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	+	ux = currentAtom->getOrntX();
198	+	uy = currentAtom->getOrntY();
199	+	uz = currentAtom->getOrntZ();
200	+
201	+	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
202	+
203	+	u = sqrt(uSqr);
204	+	ux = ux / u;
205	+	uy = uy / u;
206	+	uz = uz / u;
207	+
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		#ifdef IS_MPI
219
220	<	// divide the molecules among processors here.
307	<
308	<	mpiSim = new mpiSimulation( simnfo );
309	<
310	<	globalIndex = mpiSim->divideLabor();
220	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
221
222	<	// set up the local variables
223	<
314	<	int localMol, allMol;
315	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
222	>	#endif // is_mpi
223	>	}
224
225	<	int* mol2proc = mpiSim->getMolToProcMap();
226	<	int* molCompType = mpiSim->getMolComponentType();
227	<
228	<	allMol = 0;
229	<	localMol = 0;
322	<	local_atoms = 0;
323	<	local_bonds = 0;
324	<	local_bends = 0;
325	<	local_torsions = 0;
326	<	globalAtomIndex = 0;
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	+	exI = theBonds[j].a;
232	+	exJ = theBonds[j].b;
233
234	<	for( i=0; i<n_components; i++ ){
234	>	// exclude_I must always be the smaller of the pair
235	>	if (exI > exJ){
236	>	tempEx = exI;
237	>	exI = exJ;
238	>	exJ = tempEx;
239	>	}
240	>	#ifdef IS_MPI
241	>	tempEx = exI;
242	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
243	>	tempEx = exJ;
244	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
245
246	<	for( j=0; j<components_nmol[i]; j++ ){
247	<
248	<	if( mol2proc[allMol] == worldRank ){
249	<
250	<	local_atoms +=    comp_stamps[i]->getNAtoms();
336	<	local_bonds +=    comp_stamps[i]->getNBonds();
337	<	local_bends +=    comp_stamps[i]->getNBends();
338	<	local_torsions += comp_stamps[i]->getNTorsions();
339	<	localMol++;
340	<	}
341	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
342	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
343	<	globalAtomIndex++;
246	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
247	>	#else  // isn't MPI
248	>
249	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
250	>	#endif  //is_mpi
251		}
252	+	excludeOffset += molInfo.nBonds;
253
254	<	allMol++;
255	<	}
256	<	}
257	<	local_SRI = local_bonds + local_bends + local_torsions;
258	<
259	<	simnfo->n_atoms = mpiSim->getMyNlocal();
352	<
353	<	if( local_atoms != simnfo->n_atoms ){
354	<	sprintf( painCave.errMsg,
355	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
356	<	" localAtom (%d) are not equal.\n",
357	<	simnfo->n_atoms,
358	<	local_atoms );
359	<	painCave.isFatal = 1;
360	<	simError();
361	<	}
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	<	simnfo->n_bonds = local_bonds;
262	<	simnfo->n_bends = local_bends;
263	<	simnfo->n_torsions = local_torsions;
366	<	simnfo->n_SRI = local_SRI;
367	<	simnfo->n_mol = localMol;
261	>	if (currentBend->haveExtras()){
262	>	extras = currentBend->getExtras();
263	>	current_extra = extras;
264
265	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
266	<	MPIcheckPoint();
267	<
268	<
269	<	#endif // is_mpi
270	<
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	<	// create the atom and short range interaction arrays
273	>	case 1:
274	>	theBends[j].ghost = (int) current_extra->getDouble() +
275	>	atomOffset;
276	>	theBends[j].isGhost = 1;
277	>	break;
278
279	<	Atom::createArrays(simnfo->n_atoms);
280	<	the_atoms = new Atom*[simnfo->n_atoms];
281	<	the_molecules = new Molecule[simnfo->n_mol];
282	<	int molIndex;
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	<	// initialize the molecule's stampID's
298	>	current_extra = current_extra->getNext();
299	>	}
300	>	}
301
302	+	if (!theBends[j].isGhost){
303	+	exI = theBends[j].a;
304	+	exJ = theBends[j].c;
305	+	}
306	+	else{
307	+	exI = theBends[j].a;
308	+	exJ = theBends[j].b;
309	+	}
310	+
311	+	// 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	<
318	>	tempEx = exI;
319	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
320	>	tempEx = exJ;
321	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
322
323	<	molIndex = 0;
324	<	for(i=0; i<mpiSim->getTotNmol(); i++){
325	<
326	<	if(mol2proc[i] == worldRank ){
392	<	the_molecules[molIndex].setStampID( molCompType[i] );
393	<	the_molecules[molIndex].setMyIndex( molIndex );
394	<	the_molecules[molIndex].setGlobalIndex( i );
395	<	molIndex++;
396	<	}
397	<	}
398	<
399	<	#else // is_mpi
400	<
401	<	molIndex = 0;
402	<	globalAtomIndex = 0;
403	<	for(i=0; i<n_components; i++){
404	<	for(j=0; j<components_nmol[i]; j++ ){
405	<	the_molecules[molIndex].setStampID( i );
406	<	the_molecules[molIndex].setMyIndex( molIndex );
407	<	the_molecules[molIndex].setGlobalIndex( molIndex );
408	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
409	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
410	<	globalAtomIndex++;
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	<	molIndex++;
413	<	}
414	<	}
415	<
328	>	excludeOffset += molInfo.nBends;
329
330	<	#endif // is_mpi
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	+	exI = theTorsions[j].a;
338	+	exJ = theTorsions[j].d;
339
340	<	if( simnfo->n_SRI ){
341	<
342	<	Exclude::createArray(simnfo->n_SRI);
343	<	the_excludes = new Exclude*[simnfo->n_SRI];
344	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
345	<	simnfo->globalExcludes = new int;
346	<	simnfo->n_exclude = simnfo->n_SRI;
347	<	}
348	<	else{
349	<
350	<	Exclude::createArray( 1 );
431	<	the_excludes = new Exclude*;
432	<	the_excludes[0] = new Exclude(0);
433	<	the_excludes[0]->setPair( 0,0 );
434	<	simnfo->globalExcludes = new int;
435	<	simnfo->globalExcludes[0] = 0;
436	<	simnfo->n_exclude = 0;
437	<	}
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	>	tempEx = exI;
348	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
349	>	tempEx = exJ;
350	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
351
352	<	// set the arrays into the SimInfo object
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
441	–	simnfo->atoms = the_atoms;
442	–	simnfo->molecules = the_molecules;
443	–	simnfo->nGlobalExcludes = 0;
444	–	simnfo->excludes = the_excludes;
359
360	+	// send the arrays off to the forceField for init.
361
362	<	// get some of the tricky things that may still be in the globals
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
449	–
450	–	if( the_globals->haveBox() ){
451	–	simnfo->box_x = the_globals->getBox();
452	–	simnfo->box_y = the_globals->getBox();
453	–	simnfo->box_z = the_globals->getBox();
454	–	}
455	–	else if( the_globals->haveDensity() ){
368
369	<	double vol;
458	<	vol = (double)tot_nmol / the_globals->getDensity();
459	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
460	<	simnfo->box_y = simnfo->box_x;
461	<	simnfo->box_z = simnfo->box_x;
462	<	}
463	<	else{
464	<	if( !the_globals->haveBoxX() ){
465	<	sprintf( painCave.errMsg,
466	<	"SimSetup error, no periodic BoxX size given.\n" );
467	<	painCave.isFatal = 1;
468	<	simError();
469	<	}
470	<	simnfo->box_x = the_globals->getBoxX();
369	>	info[k].molecules[i].initialize(molInfo);
370
472	–	if( !the_globals->haveBoxY() ){
473	–	sprintf( painCave.errMsg,
474	–	"SimSetup error, no periodic BoxY size given.\n" );
475	–	painCave.isFatal = 1;
476	–	simError();
477	–	}
478	–	simnfo->box_y = the_globals->getBoxY();
371
372	<	if( !the_globals->haveBoxZ() ){
373	<	sprintf( painCave.errMsg,
374	<	"SimSetup error, no periodic BoxZ size given.\n" );
375	<	painCave.isFatal = 1;
484	<	simError();
372	>	atomOffset += molInfo.nAtoms;
373	>	delete[] theBonds;
374	>	delete[] theBends;
375	>	delete[] theTorsions;
376		}
486	–	simnfo->box_z = the_globals->getBoxZ();
377		}
378
379		#ifdef IS_MPI
380	<	strcpy( checkPointMsg, "Box size set up" );
380	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
381		MPIcheckPoint();
382		#endif // is_mpi
383
384	+	// clean up the forcefield
385
386	<	// initialize the arrays
386	>	the_ff->calcRcut();
387	>	the_ff->cleanMe();
388	>	}
389
390	<	the_ff->setSimInfo( simnfo );
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	<	makeMolecules();
400	<	simnfo->identArray = new int[simnfo->n_atoms];
401	<	for(i=0; i<simnfo->n_atoms; i++){
402	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
503	<	}
504	<
505	<	if (the_globals->getUseRF() ) {
506	<	simnfo->useReactionField = 1;
507	<
508	<	if( !the_globals->haveECR() ){
509	<	sprintf( painCave.errMsg,
510	<	"SimSetup Warning: using default value of 1/2 the smallest "
511	<	"box length for the electrostaticCutoffRadius.\n"
512	<	"I hope you have a very fast processor!\n");
513	<	painCave.isFatal = 0;
514	<	simError();
515	<	double smallest;
516	<	smallest = simnfo->box_x;
517	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
518	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
519	<	simnfo->ecr = 0.5 * smallest;
520	<	} else {
521	<	simnfo->ecr        = the_globals->getECR();
522	<	}
399	>	double vel[3];
400	>	vel[0] = 0.0;
401	>	vel[1] = 0.0;
402	>	vel[2] = 0.0;
403
404	<	if( !the_globals->haveEST() ){
405	<	sprintf( painCave.errMsg,
406	<	"SimSetup Warning: using default value of 0.05 * the "
407	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
408	<	);
409	<	painCave.isFatal = 0;
410	<	simError();
411	<	simnfo->est = 0.05 * simnfo->ecr;
412	<	} else {
413	<	simnfo->est        = the_globals->getEST();
414	<	}
415	<
416	<	if(!the_globals->haveDielectric() ){
417	<	sprintf( painCave.errMsg,
418	<	"SimSetup Error: You are trying to use Reaction Field without"
419	<	"setting a dielectric constant!\n"
420	<	);
404	>	temp1 = (double) tot_nmol / 4.0;
405	>	temp2 = pow(temp1, (1.0 / 3.0));
406	>	temp3 = ceil(temp2);
407	>
408	>	have_extra = 0;
409	>	if (temp2 < temp3){
410	>	// we have a non-complete lattice
411	>	have_extra = 1;
412	>
413	>	n_cells = (int) temp3 - 1;
414	>	cellx = info[0].boxL[0] / temp3;
415	>	celly = info[0].boxL[1] / temp3;
416	>	cellz = info[0].boxL[2] / temp3;
417	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
418	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
419	>	n_per_extra = (int) ceil(temp1);
420	>
421	>	if (n_per_extra > 4){
422	>	sprintf(painCave.errMsg,
423	>	"SimSetup error. There has been an error in constructing"
424	>	" the non-complete lattice.\n");
425		painCave.isFatal = 1;
426		simError();
427		}
428	<	simnfo->dielectric = the_globals->getDielectric();
429	<	} else {
430	<	if (usesDipoles) {
431	<
432	<	if( !the_globals->haveECR() ){
433	<	sprintf( painCave.errMsg,
434	<	"SimSetup Warning: using default value of 1/2 the smallest "
551	<	"box length for the electrostaticCutoffRadius.\n"
552	<	"I hope you have a very fast processor!\n");
553	<	painCave.isFatal = 0;
554	<	simError();
555	<	double smallest;
556	<	smallest = simnfo->box_x;
557	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
558	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
559	<	simnfo->ecr = 0.5 * smallest;
560	<	} else {
561	<	simnfo->ecr        = the_globals->getECR();
562	<	}
563	<
564	<	if( !the_globals->haveEST() ){
565	<	sprintf( painCave.errMsg,
566	<	"SimSetup Warning: using default value of 5%% of the "
567	<	"electrostaticCutoffRadius for the "
568	<	"electrostaticSkinThickness\n"
569	<	);
570	<	painCave.isFatal = 0;
571	<	simError();
572	<	simnfo->est = 0.05 * simnfo->ecr;
573	<	} else {
574	<	simnfo->est        = the_globals->getEST();
575	<	}
576	<	}
577	<	}
428	>	}
429	>	else{
430	>	n_cells = (int) temp3;
431	>	cellx = info[0].boxL[0] / temp3;
432	>	celly = info[0].boxL[1] / temp3;
433	>	cellz = info[0].boxL[2] / temp3;
434	>	}
435
436	<	#ifdef IS_MPI
437	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
438	<	MPIcheckPoint();
439	<	#endif // is_mpi
436	>	current_mol = 0;
437	>	current_comp_mol = 0;
438	>	current_comp = 0;
439	>	current_atom_ndx = 0;
440
441	<	if( the_globals->haveInitialConfig() ){
442	<
443	<	InitializeFromFile* fileInit;
444	<	#ifdef IS_MPI // is_mpi
588	<	if( worldRank == 0 ){
589	<	#endif //is_mpi
590	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
591	<	#ifdef IS_MPI
592	<	}else fileInit = new InitializeFromFile( NULL );
593	<	#endif
594	<	fileInit->read_xyz( simnfo ); // default velocities on
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	<	delete fileInit;
597	<	}
598	<	else{
446	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
447
448	<	#ifdef IS_MPI
448	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
449
450	<	// no init from bass
451	<
452	<	sprintf( painCave.errMsg,
453	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
606	<	painCave.isFatal;
607	<	simError();
608	<
609	<	#else
450	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
451	>	}
452	>	}
453	>	}
454
455	<	initFromBass();
455	>	if (have_extra){
456	>	done = 0;
457
458	+	int start_ndx;
459	+	for (i = 0; i < (n_cells + 1) && !done; i++){
460	+	for (j = 0; j < (n_cells + 1) && !done; j++){
461	+	if (i < n_cells){
462	+	if (j < n_cells){
463	+	start_ndx = n_cells;
464	+	}
465	+	else
466	+	start_ndx = 0;
467	+	}
468	+	else
469	+	start_ndx = 0;
470
471	<	#endif
472	<	}
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	<	#ifdef IS_MPI
476	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
477	<	MPIcheckPoint();
478	<	#endif // is_mpi
475	>	if (!done && n_per_extra > 1){
476	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
477	>	k * cellz);
478	>	done = (current_mol >= tot_nmol);
479	>	}
480
481	+	if (!done && n_per_extra > 2){
482	+	makeElement(i * cellx, j * celly + 0.5 * celly,
483	+	k * cellz + 0.5 * cellz);
484	+	done = (current_mol >= tot_nmol);
485	+	}
486
487	<
488	<
489	<
490	<
491	<
492	<	#ifdef IS_MPI
629	<	if( worldRank == 0 ){
630	<	#endif // is_mpi
631	<
632	<	if( the_globals->haveFinalConfig() ){
633	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
634	<	}
635	<	else{
636	<	strcpy( simnfo->finalName, inFileName );
637	<	char* endTest;
638	<	int nameLength = strlen( simnfo->finalName );
639	<	endTest = &(simnfo->finalName[nameLength - 5]);
640	<	if( !strcmp( endTest, ".bass" ) ){
641	<	strcpy( endTest, ".eor" );
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		}
643	–	else if( !strcmp( endTest, ".BASS" ) ){
644	–	strcpy( endTest, ".eor" );
645	–	}
646	–	else{
647	–	endTest = &(simnfo->finalName[nameLength - 4]);
648	–	if( !strcmp( endTest, ".bss" ) ){
649	–	strcpy( endTest, ".eor" );
650	–	}
651	–	else if( !strcmp( endTest, ".mdl" ) ){
652	–	strcpy( endTest, ".eor" );
653	–	}
654	–	else{
655	–	strcat( simnfo->finalName, ".eor" );
656	–	}
657	–	}
494		}
659	–
660	–	// make the sample and status out names
661	–
662	–	strcpy( simnfo->sampleName, inFileName );
663	–	char* endTest;
664	–	int nameLength = strlen( simnfo->sampleName );
665	–	endTest = &(simnfo->sampleName[nameLength - 5]);
666	–	if( !strcmp( endTest, ".bass" ) ){
667	–	strcpy( endTest, ".dump" );
668	–	}
669	–	else if( !strcmp( endTest, ".BASS" ) ){
670	–	strcpy( endTest, ".dump" );
671	–	}
672	–	else{
673	–	endTest = &(simnfo->sampleName[nameLength - 4]);
674	–	if( !strcmp( endTest, ".bss" ) ){
675	–	strcpy( endTest, ".dump" );
676	–	}
677	–	else if( !strcmp( endTest, ".mdl" ) ){
678	–	strcpy( endTest, ".dump" );
679	–	}
680	–	else{
681	–	strcat( simnfo->sampleName, ".dump" );
682	–	}
683	–	}
684	–
685	–	strcpy( simnfo->statusName, inFileName );
686	–	nameLength = strlen( simnfo->statusName );
687	–	endTest = &(simnfo->statusName[nameLength - 5]);
688	–	if( !strcmp( endTest, ".bass" ) ){
689	–	strcpy( endTest, ".stat" );
690	–	}
691	–	else if( !strcmp( endTest, ".BASS" ) ){
692	–	strcpy( endTest, ".stat" );
693	–	}
694	–	else{
695	–	endTest = &(simnfo->statusName[nameLength - 4]);
696	–	if( !strcmp( endTest, ".bss" ) ){
697	–	strcpy( endTest, ".stat" );
698	–	}
699	–	else if( !strcmp( endTest, ".mdl" ) ){
700	–	strcpy( endTest, ".stat" );
701	–	}
702	–	else{
703	–	strcat( simnfo->statusName, ".stat" );
704	–	}
705	–	}
706	–
707	–	#ifdef IS_MPI
495		}
709	–	#endif // is_mpi
710	–
711	–	// set the status, sample, and themal kick times
712	–
713	–	if( the_globals->haveSampleTime() ){
714	–	simnfo->sampleTime = the_globals->getSampleTime();
715	–	simnfo->statusTime = simnfo->sampleTime;
716	–	simnfo->thermalTime = simnfo->sampleTime;
717	–	}
718	–	else{
719	–	simnfo->sampleTime = the_globals->getRunTime();
720	–	simnfo->statusTime = simnfo->sampleTime;
721	–	simnfo->thermalTime = simnfo->sampleTime;
722	–	}
496
497	<	if( the_globals->haveStatusTime() ){
498	<	simnfo->statusTime = the_globals->getStatusTime();
497	>	for (i = 0; i < info[0].n_atoms; i++){
498	>	info[0].atoms[i]->setVel(vel);
499		}
500	+	}
501
502	<	if( the_globals->haveThermalTime() ){
503	<	simnfo->thermalTime = the_globals->getThermalTime();
504	<	}
502	>	void SimSetup::makeElement(double x, double y, double z){
503	>	int k;
504	>	AtomStamp* current_atom;
505	>	DirectionalAtom* dAtom;
506	>	double rotMat[3][3];
507	>	double pos[3];
508
509	<	// check for the temperature set flag
509	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
510	>	current_atom = comp_stamps[current_comp]->getAtom(k);
511	>	if (!current_atom->havePosition()){
512	>	sprintf(painCave.errMsg,
513	>	"SimSetup:initFromBass error.\n"
514	>	"\tComponent %s, atom %s does not have a position specified.\n"
515	>	"\tThe initialization routine is unable to give a start"
516	>	" position.\n",
517	>	comp_stamps[current_comp]->getID(), current_atom->getType());
518	>	painCave.isFatal = 1;
519	>	simError();
520	>	}
521
522	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
522	>	pos[0] = x + current_atom->getPosX();
523	>	pos[1] = y + current_atom->getPosY();
524	>	pos[2] = z + current_atom->getPosZ();
525
526	+	info[0].atoms[current_atom_ndx]->setPos(pos);
527
528	<	//   // make the longe range forces and the integrator
528	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
529	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
530
531	<	//   new AllLong( simnfo );
531	>	rotMat[0][0] = 1.0;
532	>	rotMat[0][1] = 0.0;
533	>	rotMat[0][2] = 0.0;
534
535	+	rotMat[1][0] = 0.0;
536	+	rotMat[1][1] = 1.0;
537	+	rotMat[1][2] = 0.0;
538
539	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
540	<	new Symplectic(simnfo, the_ff, the_extendedsystem);
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		}
548	<	else if( !strcmp( force_field, "LJ" ) ){
549	<	new Verlet( *simnfo, the_ff, the_extendedsystem );
548	>
549	>	current_mol++;
550	>	current_comp_mol++;
551	>
552	>	if (current_comp_mol >= components_nmol[current_comp]){
553	>	current_comp_mol = 0;
554	>	current_comp++;
555		}
556	<	else {
749	<	std::cerr << "I'm a bug.\n";
750	<	fprintf( stderr, "Ima bug. stderr %s\n", force_field);
751	<	}
752	<	#ifdef IS_MPI
753	<	mpiSim->mpiRefresh();
754	<	#endif
556	>	}
557
756	–	// initialize the Fortran
558
559	+	void SimSetup::gatherInfo(void){
560	+	int i;
561
562	<	simnfo->refreshSim();
563	<
564	<	if( !strcmp( simnfo->mixingRule, "standard") ){
565	<	the_ff->initForceField( LB_MIXING_RULE );
566	<	}
567	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
568	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
562	>	ensembleCase = -1;
563	>	ffCase = -1;
564	>
565	>	// set the easy ones first
566	>
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	+
574	+
575	+	// get the forceField
576	+
577	+	strcpy(force_field, globals->getForceField());
578	+
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,
590	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
591	<	simnfo->mixingRule );
592	<	painCave.isFatal = 1;
772	<	simError();
589	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
590	>	force_field);
591	>	painCave.isFatal = 1;
592	>	simError();
593		}
594
595	+	// get the ensemble
596
597	<	#ifdef IS_MPI
777	<	strcpy( checkPointMsg,
778	<	"Successfully intialized the mixingRule for Fortran." );
779	<	MPIcheckPoint();
780	<	#endif // is_mpi
781	<	}
597	>	strcpy(ensemble, globals->getEnsemble());
598
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	<	void SimSetup::makeMolecules( void ){
625	>	for (i = 0; i < nInfo; i++){
626	>	strcpy(info[i].ensemble, ensemble);
627
628	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
787	<	molInit info;
788	<	DirectionalAtom* dAtom;
789	<	LinkedAssign* extras;
790	<	LinkedAssign* current_extra;
791	<	AtomStamp* currentAtom;
792	<	BondStamp* currentBond;
793	<	BendStamp* currentBend;
794	<	TorsionStamp* currentTorsion;
628	>	// get the mixing rule
629
630	<	bond_pair* theBonds;
631	<	bend_set* theBends;
632	<	torsion_set* theTorsions;
630	>	strcpy(info[i].mixingRule, globals->getMixingRule());
631	>	info[i].usePBC = globals->getPBC();
632	>	}
633
634	<
801	<	//init the forceField paramters
634	>	// get the components and calculate the tot_nMol and indvidual n_mol
635
636	<	the_ff->readParams();
636	>	the_components = globals->getComponents();
637	>	components_nmol = new int[n_components];
638
805	–
806	–	// init the atoms
639
640	<	double ux, uy, uz, u, uSqr;
641	<
642	<	atomOffset = 0;
811	<	excludeOffset = 0;
812	<	for(i=0; i<simnfo->n_mol; i++){
813	<
814	<	stampID = the_molecules[i].getStampID();
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	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
645	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
646	<	info.nBends    = comp_stamps[stampID]->getNBends();
647	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
648	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
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	<	info.myAtoms = &the_atoms[atomOffset];
656	<	info.myExcludes = &the_excludes[excludeOffset];
657	<	info.myBonds = new Bond*[info.nBonds];
658	<	info.myBends = new Bend*[info.nBends];
659	<	info.myTorsions = new Torsion*[info.nTorsions];
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	<	theBonds = new bond_pair[info.nBonds];
671	<	theBends = new bend_set[info.nBends];
672	<	theTorsions = new torsion_set[info.nTorsions];
670	>	// set the status, sample, and thermal kick times
671	>
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	>	if (globals->haveStatusTime()){
685	>	info[i].statusTime = globals->getStatusTime();
686	>	}
687	>
688	>	if (globals->haveThermalTime()){
689	>	info[i].thermalTime = globals->getThermalTime();
690	>	}
691	>
692	>	info[i].resetIntegrator = 0;
693	>	if( globals->haveResetTime() ){
694	>	info[i].resetTime = globals->getResetTime();
695	>	info[i].resetIntegrator = 1;
696	>	}
697	>
698	>	// check for the temperature set flag
699
700	<	// make the Atoms
700	>	if (globals->haveTempSet())
701	>	info[i].setTemp = globals->getTempSet();
702
703	<	for(j=0; j<info.nAtoms; j++){
704	<
705	<	currentAtom = comp_stamps[stampID]->getAtom( j );
706	<	if( currentAtom->haveOrientation() ){
707	<
708	<	dAtom = new DirectionalAtom(j + atomOffset);
709	<	simnfo->n_oriented++;
710	<	info.myAtoms[j] = dAtom;
711	<
712	<	ux = currentAtom->getOrntX();
713	<	uy = currentAtom->getOrntY();
714	<	uz = currentAtom->getOrntZ();
715	<
716	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
717	<
718	<	u = sqrt( uSqr );
719	<	ux = ux / u;
720	<	uy = uy / u;
721	<	uz = uz / u;
722	<
723	<	dAtom->setSUx( ux );
855	<	dAtom->setSUy( uy );
856	<	dAtom->setSUz( uz );
703	>	}
704	>
705	>	//setup seed for random number generator
706	>	int seedValue;
707	>
708	>	if (globals->haveSeed()){
709	>	seedValue = globals->getSeed();
710	>
711	>	if(seedValue / 1E9 == 0){
712	>	sprintf(painCave.errMsg,
713	>	"Seed for sprng library should contain at least 9 digits\n"
714	>	"OOPSE will generate a seed for user\n");
715	>	painCave.isFatal = 0;
716	>	simError();
717	>
718	>	//using seed generated by system instead of invalid seed set by user
719	>	#ifndef IS_MPI
720	>	seedValue = make_sprng_seed();
721	>	#else
722	>	if (worldRank == 0){
723	>	seedValue = make_sprng_seed();
724		}
725	<	else{
726	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
727	<	}
728	<	info.myAtoms[j]->setType( currentAtom->getType() );
725	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
726	>	#endif
727	>	}
728	>	}//end of if branch of globals->haveSeed()
729	>	else{
730
731	+	#ifndef IS_MPI
732	+	seedValue = make_sprng_seed();
733	+	#else
734	+	if (worldRank == 0){
735	+	seedValue = make_sprng_seed();
736	+	}
737	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
738	+	#endif
739	+	}//end of globals->haveSeed()
740	+
741	+	for (int i = 0; i < nInfo; i++){
742	+	info[i].setSeed(seedValue);
743	+	}
744	+
745		#ifdef IS_MPI
746	<
747	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
866	<
746	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
747	>	MPIcheckPoint();
748		#endif // is_mpi
749	<	}
869	<
870	<	// make the bonds
871	<	for(j=0; j<info.nBonds; j++){
872	<
873	<	currentBond = comp_stamps[stampID]->getBond( j );
874	<	theBonds[j].a = currentBond->getA() + atomOffset;
875	<	theBonds[j].b = currentBond->getB() + atomOffset;
749	>	}
750
877	–	exI = theBonds[j].a;
878	–	exJ = theBonds[j].b;
751
752	<	// exclude_I must always be the smaller of the pair
753	<	if( exI > exJ ){
754	<	tempEx = exI;
755	<	exI = exJ;
884	<	exJ = tempEx;
885	<	}
886	<	#ifdef IS_MPI
887	<	tempEx = exI;
888	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
889	<	tempEx = exJ;
890	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
891	<
892	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
893	<	#else  // isn't MPI
752	>	void SimSetup::finalInfoCheck(void){
753	>	int index;
754	>	int usesDipoles;
755	>	int i;
756
757	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
758	<	#endif  //is_mpi
757	>	for (i = 0; i < nInfo; i++){
758	>	// check electrostatic parameters
759	>
760	>	index = 0;
761	>	usesDipoles = 0;
762	>	while ((index < info[i].n_atoms) && !usesDipoles){
763	>	usesDipoles = (info[i].atoms[index])->hasDipole();
764	>	index++;
765		}
898	–	excludeOffset += info.nBonds;
766
767	<	//make the bends
768	<	for(j=0; j<info.nBends; j++){
769	<
770	<	currentBend = comp_stamps[stampID]->getBend( j );
771	<	theBends[j].a = currentBend->getA() + atomOffset;
772	<	theBends[j].b = currentBend->getB() + atomOffset;
773	<	theBends[j].c = currentBend->getC() + atomOffset;
774	<
775	<	if( currentBend->haveExtras() ){
776	<
777	<	extras = currentBend->getExtras();
778	<	current_extra = extras;
779	<
780	<	while( current_extra != NULL ){
781	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
782	<
783	<	switch( current_extra->getType() ){
784	<
785	<	case 0:
786	<	theBends[j].ghost =
787	<	current_extra->getInt() + atomOffset;
788	<	theBends[j].isGhost = 1;
789	<	break;
790	<
924	<	case 1:
925	<	theBends[j].ghost =
926	<	(int)current_extra->getDouble() + atomOffset;
927	<	theBends[j].isGhost = 1;
928	<	break;
929	<
930	<	default:
931	<	sprintf( painCave.errMsg,
932	<	"SimSetup Error: ghostVectorSource was neither a "
933	<	"double nor an int.\n"
934	<	"-->Bend[%d] in %s\n",
935	<	j, comp_stamps[stampID]->getID() );
936	<	painCave.isFatal = 1;
937	<	simError();
938	<	}
939	<	}
940	<
941	<	else{
942	<
943	<	sprintf( painCave.errMsg,
944	<	"SimSetup Error: unhandled bend assignment:\n"
945	<	"    -->%s in Bend[%d] in %s\n",
946	<	current_extra->getlhs(),
947	<	j, comp_stamps[stampID]->getID() );
948	<	painCave.isFatal = 1;
949	<	simError();
950	<	}
951	<
952	<	current_extra = current_extra->getNext();
953	<	}
767	>	#ifdef IS_MPI
768	>	int myUse = usesDipoles;
769	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770	>	#endif //is_mpi
771	>
772	>	double theEcr, theEst;
773	>
774	>	if (globals->getUseRF()){
775	>	info[i].useReactionField = 1;
776	>
777	>	if (!globals->haveECR()){
778	>	sprintf(painCave.errMsg,
779	>	"SimSetup Warning: using default value of 1/2 the smallest "
780	>	"box length for the electrostaticCutoffRadius.\n"
781	>	"I hope you have a very fast processor!\n");
782	>	painCave.isFatal = 0;
783	>	simError();
784	>	double smallest;
785	>	smallest = info[i].boxL[0];
786	>	if (info[i].boxL[1] <= smallest)
787	>	smallest = info[i].boxL[1];
788	>	if (info[i].boxL[2] <= smallest)
789	>	smallest = info[i].boxL[2];
790	>	theEcr = 0.5 * smallest;
791		}
792	<
793	<	if( !theBends[j].isGhost ){
957	<
958	<	exI = theBends[j].a;
959	<	exJ = theBends[j].c;
792	>	else{
793	>	theEcr = globals->getECR();
794		}
795	+
796	+	if (!globals->haveEST()){
797	+	sprintf(painCave.errMsg,
798	+	"SimSetup Warning: using default value of 0.05 * the "
799	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
800	+	painCave.isFatal = 0;
801	+	simError();
802	+	theEst = 0.05 * theEcr;
803	+	}
804		else{
805	<
963	<	exI = theBends[j].a;
964	<	exJ = theBends[j].b;
805	>	theEst = globals->getEST();
806		}
966	–
967	–	// exclude_I must always be the smaller of the pair
968	–	if( exI > exJ ){
969	–	tempEx = exI;
970	–	exI = exJ;
971	–	exJ = tempEx;
972	–	}
973	–	#ifdef IS_MPI
974	–	tempEx = exI;
975	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
976	–	tempEx = exJ;
977	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
978	–
979	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
980	–	#else  // isn't MPI
981	–	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
982	–	#endif  //is_mpi
983	–	}
984	–	excludeOffset += info.nBends;
807
808	<	for(j=0; j<info.nTorsions; j++){
987	<
988	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
989	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
990	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
991	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
992	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
993	<
994	<	exI = theTorsions[j].a;
995	<	exJ = theTorsions[j].d;
808	>	info[i].setDefaultEcr(theEcr, theEst);
809
810	<	// exclude_I must always be the smaller of the pair
811	<	if( exI > exJ ){
812	<	tempEx = exI;
813	<	exI = exJ;
814	<	exJ = tempEx;
810	>	if (!globals->haveDielectric()){
811	>	sprintf(painCave.errMsg,
812	>	"SimSetup Error: You are trying to use Reaction Field without"
813	>	"setting a dielectric constant!\n");
814	>	painCave.isFatal = 1;
815	>	simError();
816		}
817	<	#ifdef IS_MPI
1004	<	tempEx = exI;
1005	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1006	<	tempEx = exJ;
1007	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1008	<
1009	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1010	<	#else  // isn't MPI
1011	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1012	<	#endif  //is_mpi
817	>	info[i].dielectric = globals->getDielectric();
818		}
819	<	excludeOffset += info.nTorsions;
819	>	else{
820	>	if (usesDipoles){
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	<
841	<	// send the arrays off to the forceField for init.
840	>	if (!globals->haveEST()){
841	>	sprintf(painCave.errMsg,
842	>	"SimSetup Warning: using default value of 0.05 * the "
843	>	"electrostaticCutoffRadius for the "
844	>	"electrostaticSkinThickness\n");
845	>	painCave.isFatal = 0;
846	>	simError();
847	>	theEst = 0.05 * theEcr;
848	>	}
849	>	else{
850	>	theEst = globals->getEST();
851	>	}
852
853	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
854	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
855	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1022	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1023	<
1024	<
1025	<	the_molecules[i].initialize( info );
1026	<
1027	<
1028	<	atomOffset += info.nAtoms;
1029	<	delete[] theBonds;
1030	<	delete[] theBends;
1031	<	delete[] theTorsions;
853	>	info[i].setDefaultEcr(theEcr, theEst);
854	>	}
855	>	}
856		}
857
858		#ifdef IS_MPI
859	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
859	>	strcpy(checkPointMsg, "post processing checks out");
860		MPIcheckPoint();
861		#endif // is_mpi
1038	–
1039	–	// clean up the forcefield
1040	–	the_ff->calcRcut();
1041	–	the_ff->cleanMe();
1042	–
862		}
863
864	<	void SimSetup::initFromBass( void ){
864	>	void SimSetup::initSystemCoords(void){
865	>	int i;
866
867	<	int i, j, k;
1048	<	int n_cells;
1049	<	double cellx, celly, cellz;
1050	<	double temp1, temp2, temp3;
1051	<	int n_per_extra;
1052	<	int n_extra;
1053	<	int have_extra, done;
867	>	char* inName;
868
869	<	temp1 = (double)tot_nmol / 4.0;
1056	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1057	<	temp3 = ceil( temp2 );
869	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
870
871	<	have_extra =0;
872	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1061	<	have_extra =1;
871	>	for (i = 0; i < info[0].n_atoms; i++)
872	>	info[0].atoms[i]->setCoords();
873
874	<	n_cells = (int)temp3 - 1;
875	<	cellx = simnfo->box_x / temp3;
876	<	celly = simnfo->box_y / temp3;
877	<	cellz = simnfo->box_z / temp3;
878	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
879	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
880	<	n_per_extra = (int)ceil( temp1 );
881	<
1071	<	if( n_per_extra > 4){
1072	<	sprintf( painCave.errMsg,
1073	<	"SimSetup error. There has been an error in constructing"
1074	<	" the non-complete lattice.\n" );
1075	<	painCave.isFatal = 1;
1076	<	simError();
874	>	if (globals->haveInitialConfig()){
875	>	InitializeFromFile* fileInit;
876	>	#ifdef IS_MPI // is_mpi
877	>	if (worldRank == 0){
878	>	#endif //is_mpi
879	>	inName = globals->getInitialConfig();
880	>	fileInit = new InitializeFromFile(inName);
881	>	#ifdef IS_MPI
882		}
883	+	else
884	+	fileInit = new InitializeFromFile(NULL);
885	+	#endif
886	+	fileInit->readInit(info); // default velocities on
887	+
888	+	delete fileInit;
889		}
890		else{
891	<	n_cells = (int)temp3;
1081	<	cellx = simnfo->box_x / temp3;
1082	<	celly = simnfo->box_y / temp3;
1083	<	cellz = simnfo->box_z / temp3;
1084	<	}
891	>	#ifdef IS_MPI
892
893	<	current_mol = 0;
1087	<	current_comp_mol = 0;
1088	<	current_comp = 0;
1089	<	current_atom_ndx = 0;
893	>	// no init from bass
894
895	<	for( i=0; i < n_cells ; i++ ){
896	<	for( j=0; j < n_cells; j++ ){
897	<	for( k=0; k < n_cells; k++ ){
895	>	sprintf(painCave.errMsg,
896	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
897	>	painCave.isFatal = 1;;
898	>	simError();
899
900	<	makeElement( i * cellx,
1096	<	j * celly,
1097	<	k * cellz );
900	>	#else
901
902	<	makeElement( i * cellx + 0.5 * cellx,
1100	<	j * celly + 0.5 * celly,
1101	<	k * cellz );
902	>	initFromBass();
903
1103	–	makeElement( i * cellx,
1104	–	j * celly + 0.5 * celly,
1105	–	k * cellz + 0.5 * cellz );
904
905	<	makeElement( i * cellx + 0.5 * cellx,
1108	<	j * celly,
1109	<	k * cellz + 0.5 * cellz );
1110	<	}
1111	<	}
905	>	#endif
906		}
907
908	<	if( have_extra ){
909	<	done = 0;
910	<
911	<	int start_ndx;
1118	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1119	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1120	<
1121	<	if( i < n_cells ){
1122	<
1123	<	if( j < n_cells ){
1124	<	start_ndx = n_cells;
1125	<	}
1126	<	else start_ndx = 0;
1127	<	}
1128	<	else start_ndx = 0;
1129	<
1130	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1131	<
1132	<	makeElement( i * cellx,
1133	<	j * celly,
1134	<	k * cellz );
1135	<	done = ( current_mol >= tot_nmol );
1136	<
1137	<	if( !done && n_per_extra > 1 ){
1138	<	makeElement( i * cellx + 0.5 * cellx,
1139	<	j * celly + 0.5 * celly,
1140	<	k * cellz );
1141	<	done = ( current_mol >= tot_nmol );
1142	<	}
1143	<
1144	<	if( !done && n_per_extra > 2){
1145	<	makeElement( i * cellx,
1146	<	j * celly + 0.5 * celly,
1147	<	k * cellz + 0.5 * cellz );
1148	<	done = ( current_mol >= tot_nmol );
1149	<	}
1150	<
1151	<	if( !done && n_per_extra > 3){
1152	<	makeElement( i * cellx + 0.5 * cellx,
1153	<	j * celly,
1154	<	k * cellz + 0.5 * cellz );
1155	<	done = ( current_mol >= tot_nmol );
1156	<	}
1157	<	}
1158	<	}
1159	<	}
1160	<	}
1161	<
1162	<
1163	<	for( i=0; i<simnfo->n_atoms; i++ ){
1164	<	simnfo->atoms[i]->set_vx( 0.0 );
1165	<	simnfo->atoms[i]->set_vy( 0.0 );
1166	<	simnfo->atoms[i]->set_vz( 0.0 );
1167	<	}
908	>	#ifdef IS_MPI
909	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
910	>	MPIcheckPoint();
911	>	#endif // is_mpi
912		}
913
1170	–	void SimSetup::makeElement( double x, double y, double z ){
914
915	+	void SimSetup::makeOutNames(void){
916		int k;
1173	–	AtomStamp* current_atom;
1174	–	DirectionalAtom* dAtom;
1175	–	double rotMat[3][3];
917
1177	–	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
918
919	<	current_atom = comp_stamps[current_comp]->getAtom( k );
920	<	if( !current_atom->havePosition() ){
921	<	sprintf( painCave.errMsg,
922	<	"SimSetup:initFromBass error.\n"
1183	<	"\tComponent %s, atom %s does not have a position specified.\n"
1184	<	"\tThe initialization routine is unable to give a start"
1185	<	" position.\n",
1186	<	comp_stamps[current_comp]->getID(),
1187	<	current_atom->getType() );
1188	<	painCave.isFatal = 1;
1189	<	simError();
1190	<	}
919	>	for (k = 0; k < nInfo; k++){
920	>	#ifdef IS_MPI
921	>	if (worldRank == 0){
922	>	#endif // is_mpi
923
924	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
925	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
926	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
927	<
928	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
929	<
930	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
931	<
932	<	rotMat[0][0] = 1.0;
933	<	rotMat[0][1] = 0.0;
934	<	rotMat[0][2] = 0.0;
935	<
936	<	rotMat[1][0] = 0.0;
937	<	rotMat[1][1] = 1.0;
938	<	rotMat[1][2] = 0.0;
939	<
940	<	rotMat[2][0] = 0.0;
941	<	rotMat[2][1] = 0.0;
942	<	rotMat[2][2] = 1.0;
924	>	if (globals->haveFinalConfig()){
925	>	strcpy(info[k].finalName, globals->getFinalConfig());
926	>	}
927	>	else{
928	>	strcpy(info[k].finalName, inFileName);
929	>	char* endTest;
930	>	int nameLength = strlen(info[k].finalName);
931	>	endTest = &(info[k].finalName[nameLength - 5]);
932	>	if (!strcmp(endTest, ".bass")){
933	>	strcpy(endTest, ".eor");
934	>	}
935	>	else if (!strcmp(endTest, ".BASS")){
936	>	strcpy(endTest, ".eor");
937	>	}
938	>	else{
939	>	endTest = &(info[k].finalName[nameLength - 4]);
940	>	if (!strcmp(endTest, ".bss")){
941	>	strcpy(endTest, ".eor");
942	>	}
943	>	else if (!strcmp(endTest, ".mdl")){
944	>	strcpy(endTest, ".eor");
945	>	}
946	>	else{
947	>	strcat(info[k].finalName, ".eor");
948	>	}
949	>	}
950	>	}
951
952	<	dAtom->setA( rotMat );
952	>	// make the sample and status out names
953	>
954	>	strcpy(info[k].sampleName, inFileName);
955	>	char* endTest;
956	>	int nameLength = strlen(info[k].sampleName);
957	>	endTest = &(info[k].sampleName[nameLength - 5]);
958	>	if (!strcmp(endTest, ".bass")){
959	>	strcpy(endTest, ".dump");
960	>	}
961	>	else if (!strcmp(endTest, ".BASS")){
962	>	strcpy(endTest, ".dump");
963	>	}
964	>	else{
965	>	endTest = &(info[k].sampleName[nameLength - 4]);
966	>	if (!strcmp(endTest, ".bss")){
967	>	strcpy(endTest, ".dump");
968	>	}
969	>	else if (!strcmp(endTest, ".mdl")){
970	>	strcpy(endTest, ".dump");
971	>	}
972	>	else{
973	>	strcat(info[k].sampleName, ".dump");
974	>	}
975	>	}
976	>
977	>	strcpy(info[k].statusName, inFileName);
978	>	nameLength = strlen(info[k].statusName);
979	>	endTest = &(info[k].statusName[nameLength - 5]);
980	>	if (!strcmp(endTest, ".bass")){
981	>	strcpy(endTest, ".stat");
982	>	}
983	>	else if (!strcmp(endTest, ".BASS")){
984	>	strcpy(endTest, ".stat");
985	>	}
986	>	else{
987	>	endTest = &(info[k].statusName[nameLength - 4]);
988	>	if (!strcmp(endTest, ".bss")){
989	>	strcpy(endTest, ".stat");
990	>	}
991	>	else if (!strcmp(endTest, ".mdl")){
992	>	strcpy(endTest, ".stat");
993	>	}
994	>	else{
995	>	strcat(info[k].statusName, ".stat");
996	>	}
997	>	}
998	>
999	>	#ifdef IS_MPI
1000	>
1001		}
1002	+	#endif // is_mpi
1003	+	}
1004	+	}
1005
1006	<	current_atom_ndx++;
1006	>
1007	>	void SimSetup::sysObjectsCreation(void){
1008	>	int i, k;
1009	>
1010	>	// create the forceField
1011	>
1012	>	createFF();
1013	>
1014	>	// extract componentList
1015	>
1016	>	compList();
1017	>
1018	>	// calc the number of atoms, bond, bends, and torsions
1019	>
1020	>	calcSysValues();
1021	>
1022	>	#ifdef IS_MPI
1023	>	// divide the molecules among the processors
1024	>
1025	>	mpiMolDivide();
1026	>	#endif //is_mpi
1027	>
1028	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1029	>
1030	>	makeSysArrays();
1031	>
1032	>	// make and initialize the molecules (all but atomic coordinates)
1033	>
1034	>	makeMolecules();
1035	>
1036	>	for (k = 0; k < nInfo; k++){
1037	>	info[k].identArray = new int[info[k].n_atoms];
1038	>	for (i = 0; i < info[k].n_atoms; i++){
1039	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1040	>	}
1041		}
1042	+	}
1043
1218	–	current_mol++;
1219	–	current_comp_mol++;
1044
1045	<	if( current_comp_mol >= components_nmol[current_comp] ){
1045	>	void SimSetup::createFF(void){
1046	>	switch (ffCase){
1047	>	case FF_DUFF:
1048	>	the_ff = new DUFF();
1049	>	break;
1050
1051	<	current_comp_mol = 0;
1052	<	current_comp++;
1051	>	case FF_LJ:
1052	>	the_ff = new LJFF();
1053	>	break;
1054	>
1055	>	case FF_EAM:
1056	>	the_ff = new EAM_FF();
1057	>	break;
1058	>
1059	>	default:
1060	>	sprintf(painCave.errMsg,
1061	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1062	>	painCave.isFatal = 1;
1063	>	simError();
1064	>	}
1065	>
1066	>	#ifdef IS_MPI
1067	>	strcpy(checkPointMsg, "ForceField creation successful");
1068	>	MPIcheckPoint();
1069	>	#endif // is_mpi
1070	>	}
1071	>
1072	>
1073	>	void SimSetup::compList(void){
1074	>	int i;
1075	>	char* id;
1076	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1077	>	LinkedMolStamp* currentStamp = NULL;
1078	>	comp_stamps = new MoleculeStamp * [n_components];
1079	>
1080	>	// make an array of molecule stamps that match the components used.
1081	>	// also extract the used stamps out into a separate linked list
1082	>
1083	>	for (i = 0; i < nInfo; i++){
1084	>	info[i].nComponents = n_components;
1085	>	info[i].componentsNmol = components_nmol;
1086	>	info[i].compStamps = comp_stamps;
1087	>	info[i].headStamp = headStamp;
1088	>	}
1089	>
1090	>
1091	>	for (i = 0; i < n_components; i++){
1092	>	id = the_components[i]->getType();
1093	>	comp_stamps[i] = NULL;
1094	>
1095	>	// check to make sure the component isn't already in the list
1096	>
1097	>	comp_stamps[i] = headStamp->match(id);
1098	>	if (comp_stamps[i] == NULL){
1099	>	// extract the component from the list;
1100	>
1101	>	currentStamp = stamps->extractMolStamp(id);
1102	>	if (currentStamp == NULL){
1103	>	sprintf(painCave.errMsg,
1104	>	"SimSetup error: Component \"%s\" was not found in the "
1105	>	"list of declared molecules\n",
1106	>	id);
1107	>	painCave.isFatal = 1;
1108	>	simError();
1109	>	}
1110	>
1111	>	headStamp->add(currentStamp);
1112	>	comp_stamps[i] = headStamp->match(id);
1113	>	}
1114	>	}
1115	>
1116	>	#ifdef IS_MPI
1117	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1118	>	MPIcheckPoint();
1119	>	#endif // is_mpi
1120	>	}
1121	>
1122	>	void SimSetup::calcSysValues(void){
1123	>	int i;
1124	>
1125	>	int* molMembershipArray;
1126	>
1127	>	tot_atoms = 0;
1128	>	tot_bonds = 0;
1129	>	tot_bends = 0;
1130	>	tot_torsions = 0;
1131	>	for (i = 0; i < n_components; i++){
1132	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1133	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1134	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1135	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1136	>	}
1137	>
1138	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1139	>	molMembershipArray = new int[tot_atoms];
1140	>
1141	>	for (i = 0; i < nInfo; i++){
1142	>	info[i].n_atoms = tot_atoms;
1143	>	info[i].n_bonds = tot_bonds;
1144	>	info[i].n_bends = tot_bends;
1145	>	info[i].n_torsions = tot_torsions;
1146	>	info[i].n_SRI = tot_SRI;
1147	>	info[i].n_mol = tot_nmol;
1148	>
1149	>	info[i].molMembershipArray = molMembershipArray;
1150	>	}
1151	>	}
1152	>
1153	>	#ifdef IS_MPI
1154	>
1155	>	void SimSetup::mpiMolDivide(void){
1156	>	int i, j, k;
1157	>	int localMol, allMol;
1158	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1159	>
1160	>	mpiSim = new mpiSimulation(info);
1161	>
1162	>	globalIndex = mpiSim->divideLabor();
1163	>
1164	>	// set up the local variables
1165	>
1166	>	mol2proc = mpiSim->getMolToProcMap();
1167	>	molCompType = mpiSim->getMolComponentType();
1168	>
1169	>	allMol = 0;
1170	>	localMol = 0;
1171	>	local_atoms = 0;
1172	>	local_bonds = 0;
1173	>	local_bends = 0;
1174	>	local_torsions = 0;
1175	>	globalAtomIndex = 0;
1176	>
1177	>
1178	>	for (i = 0; i < n_components; i++){
1179	>	for (j = 0; j < components_nmol[i]; j++){
1180	>	if (mol2proc[allMol] == worldRank){
1181	>	local_atoms += comp_stamps[i]->getNAtoms();
1182	>	local_bonds += comp_stamps[i]->getNBonds();
1183	>	local_bends += comp_stamps[i]->getNBends();
1184	>	local_torsions += comp_stamps[i]->getNTorsions();
1185	>	localMol++;
1186	>	}
1187	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1188	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1189	>	globalAtomIndex++;
1190	>	}
1191	>
1192	>	allMol++;
1193	>	}
1194	>	}
1195	>	local_SRI = local_bonds + local_bends + local_torsions;
1196	>
1197	>	info[0].n_atoms = mpiSim->getMyNlocal();
1198	>
1199	>	if (local_atoms != info[0].n_atoms){
1200	>	sprintf(painCave.errMsg,
1201	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1202	>	" localAtom (%d) are not equal.\n",
1203	>	info[0].n_atoms, local_atoms);
1204	>	painCave.isFatal = 1;
1205	>	simError();
1206	>	}
1207	>
1208	>	info[0].n_bonds = local_bonds;
1209	>	info[0].n_bends = local_bends;
1210	>	info[0].n_torsions = local_torsions;
1211	>	info[0].n_SRI = local_SRI;
1212	>	info[0].n_mol = localMol;
1213	>
1214	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1215	>	MPIcheckPoint();
1216	>	}
1217	>
1218	>	#endif // is_mpi
1219	>
1220	>
1221	>	void SimSetup::makeSysArrays(void){
1222	>
1223	>	#ifndef IS_MPI
1224	>	int k, j;
1225	>	#endif // is_mpi
1226	>	int i, l;
1227	>
1228	>	Atom** the_atoms;
1229	>	Molecule* the_molecules;
1230	>	Exclude** the_excludes;
1231	>
1232	>
1233	>	for (l = 0; l < nInfo; l++){
1234	>	// create the atom and short range interaction arrays
1235	>
1236	>	the_atoms = new Atom * [info[l].n_atoms];
1237	>	the_molecules = new Molecule[info[l].n_mol];
1238	>	int molIndex;
1239	>
1240	>	// initialize the molecule's stampID's
1241	>
1242	>	#ifdef IS_MPI
1243	>
1244	>
1245	>	molIndex = 0;
1246	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1247	>	if (mol2proc[i] == worldRank){
1248	>	the_molecules[molIndex].setStampID(molCompType[i]);
1249	>	the_molecules[molIndex].setMyIndex(molIndex);
1250	>	the_molecules[molIndex].setGlobalIndex(i);
1251	>	molIndex++;
1252	>	}
1253	>	}
1254	>
1255	>	#else // is_mpi
1256	>
1257	>	molIndex = 0;
1258	>	globalAtomIndex = 0;
1259	>	for (i = 0; i < n_components; i++){
1260	>	for (j = 0; j < components_nmol[i]; j++){
1261	>	the_molecules[molIndex].setStampID(i);
1262	>	the_molecules[molIndex].setMyIndex(molIndex);
1263	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1264	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1265	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1266	>	globalAtomIndex++;
1267	>	}
1268	>	molIndex++;
1269	>	}
1270	>	}
1271	>
1272	>
1273	>	#endif // is_mpi
1274	>
1275	>
1276	>	if (info[l].n_SRI){
1277	>	Exclude::createArray(info[l].n_SRI);
1278	>	the_excludes = new Exclude * [info[l].n_SRI];
1279	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1280	>	the_excludes[ex] = new Exclude(ex);
1281	>	}
1282	>	info[l].globalExcludes = new int;
1283	>	info[l].n_exclude = info[l].n_SRI;
1284	>	}
1285	>	else{
1286	>	Exclude::createArray(1);
1287	>	the_excludes = new Exclude * ;
1288	>	the_excludes[0] = new Exclude(0);
1289	>	the_excludes[0]->setPair(0, 0);
1290	>	info[l].globalExcludes = new int;
1291	>	info[l].globalExcludes[0] = 0;
1292	>	info[l].n_exclude = 0;
1293	>	}
1294	>
1295	>	// set the arrays into the SimInfo object
1296	>
1297	>	info[l].atoms = the_atoms;
1298	>	info[l].molecules = the_molecules;
1299	>	info[l].nGlobalExcludes = 0;
1300	>	info[l].excludes = the_excludes;
1301	>
1302	>	the_ff->setSimInfo(info);
1303		}
1304		}
1305	+
1306	+	void SimSetup::makeIntegrator(void){
1307	+	int k;
1308	+
1309	+	NVE<RealIntegrator>* myNVE = NULL;
1310	+	NVT<RealIntegrator>* myNVT = NULL;
1311	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1312	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1313	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1314	+
1315	+	for (k = 0; k < nInfo; k++){
1316	+	switch (ensembleCase){
1317	+	case NVE_ENS:
1318	+	if (globals->haveZconstraints()){
1319	+	setupZConstraint(info[k]);
1320	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1321	+	}
1322	+	else{
1323	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1324	+	}
1325	+
1326	+	info->the_integrator = myNVE;
1327	+	break;
1328	+
1329	+	case NVT_ENS:
1330	+	if (globals->haveZconstraints()){
1331	+	setupZConstraint(info[k]);
1332	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1333	+	}
1334	+	else
1335	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1336	+
1337	+	myNVT->setTargetTemp(globals->getTargetTemp());
1338	+
1339	+	if (globals->haveTauThermostat())
1340	+	myNVT->setTauThermostat(globals->getTauThermostat());
1341	+	else{
1342	+	sprintf(painCave.errMsg,
1343	+	"SimSetup error: If you use the NVT\n"
1344	+	"    ensemble, you must set tauThermostat.\n");
1345	+	painCave.isFatal = 1;
1346	+	simError();
1347	+	}
1348	+
1349	+	info->the_integrator = myNVT;
1350	+	break;
1351	+
1352	+	case NPTi_ENS:
1353	+	if (globals->haveZconstraints()){
1354	+	setupZConstraint(info[k]);
1355	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1356	+	}
1357	+	else
1358	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1359	+
1360	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1361	+
1362	+	if (globals->haveTargetPressure())
1363	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1364	+	else{
1365	+	sprintf(painCave.errMsg,
1366	+	"SimSetup error: If you use a constant pressure\n"
1367	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1368	+	painCave.isFatal = 1;
1369	+	simError();
1370	+	}
1371	+
1372	+	if (globals->haveTauThermostat())
1373	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1374	+	else{
1375	+	sprintf(painCave.errMsg,
1376	+	"SimSetup error: If you use an NPT\n"
1377	+	"    ensemble, you must set tauThermostat.\n");
1378	+	painCave.isFatal = 1;
1379	+	simError();
1380	+	}
1381	+
1382	+	if (globals->haveTauBarostat())
1383	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1384	+	else{
1385	+	sprintf(painCave.errMsg,
1386	+	"SimSetup error: If you use an NPT\n"
1387	+	"    ensemble, you must set tauBarostat.\n");
1388	+	painCave.isFatal = 1;
1389	+	simError();
1390	+	}
1391	+
1392	+	info->the_integrator = myNPTi;
1393	+	break;
1394	+
1395	+	case NPTf_ENS:
1396	+	if (globals->haveZconstraints()){
1397	+	setupZConstraint(info[k]);
1398	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1399	+	}
1400	+	else
1401	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1402	+
1403	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1404	+
1405	+	if (globals->haveTargetPressure())
1406	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1407	+	else{
1408	+	sprintf(painCave.errMsg,
1409	+	"SimSetup error: If you use a constant pressure\n"
1410	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1411	+	painCave.isFatal = 1;
1412	+	simError();
1413	+	}
1414	+
1415	+	if (globals->haveTauThermostat())
1416	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1417	+
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	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1428	+
1429	+	else{
1430	+	sprintf(painCave.errMsg,
1431	+	"SimSetup error: If you use an NPT\n"
1432	+	"    ensemble, you must set tauBarostat.\n");
1433	+	painCave.isFatal = 1;
1434	+	simError();
1435	+	}
1436	+
1437	+	info->the_integrator = myNPTf;
1438	+	break;
1439	+
1440	+	case NPTxyz_ENS:
1441	+	if (globals->haveZconstraints()){
1442	+	setupZConstraint(info[k]);
1443	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1444	+	}
1445	+	else
1446	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1447	+
1448	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1449	+
1450	+	if (globals->haveTargetPressure())
1451	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1452	+	else{
1453	+	sprintf(painCave.errMsg,
1454	+	"SimSetup error: If you use a constant pressure\n"
1455	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1456	+	painCave.isFatal = 1;
1457	+	simError();
1458	+	}
1459	+
1460	+	if (globals->haveTauThermostat())
1461	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1462	+	else{
1463	+	sprintf(painCave.errMsg,
1464	+	"SimSetup error: If you use an NPT\n"
1465	+	"    ensemble, you must set tauThermostat.\n");
1466	+	painCave.isFatal = 1;
1467	+	simError();
1468	+	}
1469	+
1470	+	if (globals->haveTauBarostat())
1471	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1472	+	else{
1473	+	sprintf(painCave.errMsg,
1474	+	"SimSetup error: If you use an NPT\n"
1475	+	"    ensemble, you must set tauBarostat.\n");
1476	+	painCave.isFatal = 1;
1477	+	simError();
1478	+	}
1479	+
1480	+	info->the_integrator = myNPTxyz;
1481	+	break;
1482	+
1483	+	default:
1484	+	sprintf(painCave.errMsg,
1485	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1486	+	painCave.isFatal = 1;
1487	+	simError();
1488	+	}
1489	+	}
1490	+	}
1491	+
1492	+	void SimSetup::initFortran(void){
1493	+	info[0].refreshSim();
1494	+
1495	+	if (!strcmp(info[0].mixingRule, "standard")){
1496	+	the_ff->initForceField(LB_MIXING_RULE);
1497	+	}
1498	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1499	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1500	+	}
1501	+	else{
1502	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1503	+	info[0].mixingRule);
1504	+	painCave.isFatal = 1;
1505	+	simError();
1506	+	}
1507	+
1508	+
1509	+	#ifdef IS_MPI
1510	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1511	+	MPIcheckPoint();
1512	+	#endif // is_mpi
1513	+	}
1514	+
1515	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1516	+	int nZConstraints;
1517	+	ZconStamp** zconStamp;
1518	+
1519	+	if (globals->haveZconstraintTime()){
1520	+	//add sample time of z-constraint  into SimInfo's property list
1521	+	DoubleData* zconsTimeProp = new DoubleData();
1522	+	zconsTimeProp->setID(ZCONSTIME_ID);
1523	+	zconsTimeProp->setData(globals->getZconsTime());
1524	+	theInfo.addProperty(zconsTimeProp);
1525	+	}
1526	+	else{
1527	+	sprintf(painCave.errMsg,
1528	+	"ZConstraint error: If you use an ZConstraint\n"
1529	+	" , you must set sample time.\n");
1530	+	painCave.isFatal = 1;
1531	+	simError();
1532	+	}
1533	+
1534	+	//push zconsTol into siminfo, if user does not specify
1535	+	//value for zconsTol, a default value will be used
1536	+	DoubleData* zconsTol = new DoubleData();
1537	+	zconsTol->setID(ZCONSTOL_ID);
1538	+	if (globals->haveZconsTol()){
1539	+	zconsTol->setData(globals->getZconsTol());
1540	+	}
1541	+	else{
1542	+	double defaultZConsTol = 0.01;
1543	+	sprintf(painCave.errMsg,
1544	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1545	+	" , default value %f is used.\n",
1546	+	defaultZConsTol);
1547	+	painCave.isFatal = 0;
1548	+	simError();
1549	+
1550	+	zconsTol->setData(defaultZConsTol);
1551	+	}
1552	+	theInfo.addProperty(zconsTol);
1553	+
1554	+	//set Force Subtraction Policy
1555	+	StringData* zconsForcePolicy = new StringData();
1556	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1557	+
1558	+	if (globals->haveZconsForcePolicy()){
1559	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1560	+	}
1561	+	else{
1562	+	sprintf(painCave.errMsg,
1563	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1564	+	"PolicyByMass is used\n");
1565	+	painCave.isFatal = 0;
1566	+	simError();
1567	+	zconsForcePolicy->setData("BYMASS");
1568	+	}
1569	+
1570	+	theInfo.addProperty(zconsForcePolicy);
1571	+
1572	+	//Determine the name of ouput file and add it into SimInfo's property list
1573	+	//Be careful, do not use inFileName, since it is a pointer which
1574	+	//point to a string at master node, and slave nodes do not contain that string
1575	+
1576	+	string zconsOutput(theInfo.finalName);
1577	+
1578	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1579	+
1580	+	StringData* zconsFilename = new StringData();
1581	+	zconsFilename->setID(ZCONSFILENAME_ID);
1582	+	zconsFilename->setData(zconsOutput);
1583	+
1584	+	theInfo.addProperty(zconsFilename);
1585	+
1586	+	//setup index, pos and other parameters of z-constraint molecules
1587	+	nZConstraints = globals->getNzConstraints();
1588	+	theInfo.nZconstraints = nZConstraints;
1589	+
1590	+	zconStamp = globals->getZconStamp();
1591	+	ZConsParaItem tempParaItem;
1592	+
1593	+	ZConsParaData* zconsParaData = new ZConsParaData();
1594	+	zconsParaData->setID(ZCONSPARADATA_ID);
1595	+
1596	+	for (int i = 0; i < nZConstraints; i++){
1597	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1598	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1599	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1600	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1601	+
1602	+	zconsParaData->addItem(tempParaItem);
1603	+	}
1604	+
1605	+	//check the uniqueness of index
1606	+	if(!zconsParaData->isIndexUnique()){
1607	+	sprintf(painCave.errMsg,
1608	+	"ZConstraint Error: molIndex is not unique\n");
1609	+	painCave.isFatal = 1;
1610	+	simError();
1611	+	}
1612	+
1613	+	//sort the parameters by index of molecules
1614	+	zconsParaData->sortByIndex();
1615	+
1616	+	//push data into siminfo, therefore, we can retrieve later
1617	+	theInfo.addProperty(zconsParaData);
1618	+	}

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