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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 438 by chuckv, Mon Mar 31 21:50:59 2003 UTC vs.
Revision 778 by mmeineke, Fri Sep 19 20:00:27 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 12 | Line 16
16		#include "mpiSimulation.hpp"
17		#endif
18
19	+	// some defines for ensemble and Forcefield  cases
20	+
21	+	#define NVE_ENS        0
22	+	#define NVT_ENS        1
23	+	#define NPTi_ENS       2
24	+	#define NPTf_ENS       3
25	+	#define NPTim_ENS      4
26	+	#define NPTfm_ENS      5
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 27 | Line 50 | SimSetup::~SimSetup(){
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();
59	<	mpiEventLoop();
60	<
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	>	int i, j, k, globalAtomIndex;
96
97	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
97	>	// gather all of the information from the Bass file
98
99	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
99	>	gatherInfo();
100
101	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	simnfo->run_time = the_globals->getRunTime();
101	>	// creation of complex system objects
102
103	<	// get the ones we know are there, yet still may need some work.
81	<	n_components = the_globals->getNComponents();
82	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
103	>	sysObjectsCreation();
104
105	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
105	>	// check on the post processing info
106
107	+	finalInfoCheck();
108
109	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
92	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
93	<	else{
94	<	sprintf( painCave.errMsg,
95	<	"SimSetup Error. Unrecognized force field -> %s\n",
96	<	force_field );
97	<	painCave.isFatal = 1;
98	<	simError();
99	<	}
109	>	// initialize the system coordinates
110
111	<	#ifdef IS_MPI
112	<	strcpy( checkPointMsg, "ForceField creation successful" );
113	<	MPIcheckPoint();
104	<	#endif // is_mpi
111	>	if (!isInfoArray){
112	>	initSystemCoords();
113	>	}
114
115	<
115	>	// make the output filenames
116
117	<	// get the components and calculate the tot_nMol and indvidual n_mol
109	<	the_components = the_globals->getComponents();
110	<	components_nmol = new int[n_components];
111	<	comp_stamps = new MoleculeStamp*[n_components];
117	>	makeOutNames();
118
119	<	if( !the_globals->haveNMol() ){
114	<	// we don't have the total number of molecules, so we assume it is
115	<	// given in each component
119	>	// make the integrator
120
121	<	tot_nmol = 0;
118	<	for( i=0; i<n_components; i++ ){
121	>	makeIntegrator();
122
120	–	if( !the_components[i]->haveNMol() ){
121	–	// we have a problem
122	–	sprintf( painCave.errMsg,
123	–	"SimSetup Error. No global NMol or component NMol"
124	–	" given. Cannot calculate the number of atoms.\n" );
125	–	painCave.isFatal = 1;
126	–	simError();
127	–	}
128	–
129	–	tot_nmol += the_components[i]->getNMol();
130	–	components_nmol[i] = the_components[i]->getNMol();
131	–	}
132	–	}
133	–	else{
134	–	sprintf( painCave.errMsg,
135	–	"SimSetup error.\n"
136	–	"\tSorry, the ability to specify total"
137	–	" nMols and then give molfractions in the components\n"
138	–	"\tis not currently supported."
139	–	" Please give nMol in the components.\n" );
140	–	painCave.isFatal = 1;
141	–	simError();
142	–
143	–
144	–	//     tot_nmol = the_globals->getNMol();
145	–
146	–	//   //we have the total number of molecules, now we check for molfractions
147	–	//     for( i=0; i<n_components; i++ ){
148	–
149	–	//       if( !the_components[i]->haveMolFraction() ){
150	–
151	–	//  if( !the_components[i]->haveNMol() ){
152	–	//    //we have a problem
153	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
154	–	//              << " nMol was given in component
155	–
156	–	}
157	–
123		#ifdef IS_MPI
124	<	strcpy( checkPointMsg, "Have the number of components" );
125	<	MPIcheckPoint();
161	<	#endif // is_mpi
124	>	mpiSim->mpiRefresh();
125	>	#endif
126
127	<	// make an array of molecule stamps that match the components used.
164	<	// also extract the used stamps out into a separate linked list
127	>	// initialize the Fortran
128
129	<	simnfo->nComponents = n_components;
130	<	simnfo->componentsNmol = components_nmol;
168	<	simnfo->compStamps = comp_stamps;
169	<	simnfo->headStamp = new LinkedMolStamp();
170	<
171	<	char* id;
172	<	LinkedMolStamp* headStamp = simnfo->headStamp;
173	<	LinkedMolStamp* currentStamp = NULL;
174	<	for( i=0; i<n_components; i++ ){
129	>	initFortran();
130	>	}
131
176	–	id = the_components[i]->getType();
177	–	comp_stamps[i] = NULL;
178	–
179	–	// check to make sure the component isn't already in the list
132
133	<	comp_stamps[i] = headStamp->match( id );
134	<	if( comp_stamps[i] == NULL ){
135	<
136	<	// extract the component from the list;
137	<
138	<	currentStamp = the_stamps->extractMolStamp( id );
139	<	if( currentStamp == NULL ){
140	<	sprintf( painCave.errMsg,
141	<	"SimSetup error: Component \"%s\" was not found in the "
142	<	"list of declared molecules\n",
143	<	id );
192	<	painCave.isFatal = 1;
193	<	simError();
194	<	}
195	<
196	<	headStamp->add( currentStamp );
197	<	comp_stamps[i] = headStamp->match( id );
198	<	}
199	<	}
133	>	void SimSetup::makeMolecules(void){
134	>	int k, l;
135	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
136	>	molInit molInfo;
137	>	DirectionalAtom* dAtom;
138	>	LinkedAssign* extras;
139	>	LinkedAssign* current_extra;
140	>	AtomStamp* currentAtom;
141	>	BondStamp* currentBond;
142	>	BendStamp* currentBend;
143	>	TorsionStamp* currentTorsion;
144
145	<	#ifdef IS_MPI
146	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
147	<	MPIcheckPoint();
204	<	#endif // is_mpi
205	<
145	>	bond_pair* theBonds;
146	>	bend_set* theBends;
147	>	torsion_set* theTorsions;
148
149
150	+	//init the forceField paramters
151
152	<	// caclulate the number of atoms, bonds, bends and torsions
152	>	the_ff->readParams();
153
211	–	tot_atoms = 0;
212	–	tot_bonds = 0;
213	–	tot_bends = 0;
214	–	tot_torsions = 0;
215	–	for( i=0; i<n_components; i++ ){
216	–
217	–	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
218	–	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
219	–	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
220	–	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
221	–	}
154
155	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
155	>	// init the atoms
156
157	<	simnfo->n_atoms = tot_atoms;
226	<	simnfo->n_bonds = tot_bonds;
227	<	simnfo->n_bends = tot_bends;
228	<	simnfo->n_torsions = tot_torsions;
229	<	simnfo->n_SRI = tot_SRI;
230	<	simnfo->n_mol = tot_nmol;
157	>	double ux, uy, uz, u, uSqr;
158
159	<
160	<	#ifdef IS_MPI
159	>	for (k = 0; k < nInfo; k++){
160	>	the_ff->setSimInfo(&(info[k]));
161
162	<	// divide the molecules among processors here.
163	<
164	<	mpiSim = new mpiSimulation( simnfo );
165	<
239	<
162	>	atomOffset = 0;
163	>	excludeOffset = 0;
164	>	for (i = 0; i < info[k].n_mol; i++){
165	>	stampID = info[k].molecules[i].getStampID();
166
167	<	globalIndex = mpiSim->divideLabor();
167	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
168	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
169	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
170	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
171	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
172
173	<	// set up the local variables
174	<
175	<	int localMol, allMol;
176	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
173	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
174	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
175	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
176	>	molInfo.myBends = new Bend * [molInfo.nBends];
177	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
178
179	<	int* mol2proc = mpiSim->getMolToProcMap();
180	<	int* molCompType = mpiSim->getMolComponentType();
181	<
251	<	allMol = 0;
252	<	localMol = 0;
253	<	local_atoms = 0;
254	<	local_bonds = 0;
255	<	local_bends = 0;
256	<	local_torsions = 0;
257	<	for( i=0; i<n_components; i++ ){
179	>	theBonds = new bond_pair[molInfo.nBonds];
180	>	theBends = new bend_set[molInfo.nBends];
181	>	theTorsions = new torsion_set[molInfo.nTorsions];
182
183	<	for( j=0; j<components_nmol[i]; j++ ){
260	<
261	<	if( mol2proc[j] == worldRank ){
262	<
263	<	local_atoms +=    comp_stamps[i]->getNAtoms();
264	<	local_bonds +=    comp_stamps[i]->getNBonds();
265	<	local_bends +=    comp_stamps[i]->getNBends();
266	<	local_torsions += comp_stamps[i]->getNTorsions();
267	<	localMol++;
268	<	}
269	<	allMol++;
270	<	}
271	<	}
272	<	local_SRI = local_bonds + local_bends + local_torsions;
273	<
183	>	// make the Atoms
184
185	<	simnfo->n_atoms = mpiSim->getMyNlocal();
186	<
187	<	if( local_atoms != simnfo->n_atoms ){
188	<	sprintf( painCave.errMsg,
189	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
190	<	" localAtom (%d) are not equal.\n",
191	<	simnfo->n_atoms,
282	<	local_atoms );
283	<	painCave.isFatal = 1;
284	<	simError();
285	<	}
185	>	for (j = 0; j < molInfo.nAtoms; j++){
186	>	currentAtom = comp_stamps[stampID]->getAtom(j);
187	>	if (currentAtom->haveOrientation()){
188	>	dAtom = new DirectionalAtom((j + atomOffset),
189	>	info[k].getConfiguration());
190	>	info[k].n_oriented++;
191	>	molInfo.myAtoms[j] = dAtom;
192
193	<	simnfo->n_bonds = local_bonds;
194	<	simnfo->n_bends = local_bends;
195	<	simnfo->n_torsions = local_torsions;
290	<	simnfo->n_SRI = local_SRI;
291	<	simnfo->n_mol = localMol;
193	>	ux = currentAtom->getOrntX();
194	>	uy = currentAtom->getOrntY();
195	>	uz = currentAtom->getOrntZ();
196
197	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
294	<	MPIcheckPoint();
295	<
296	<
297	<	#endif // is_mpi
298	<
197	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
198
199	<	// create the atom and short range interaction arrays
199	>	u = sqrt(uSqr);
200	>	ux = ux / u;
201	>	uy = uy / u;
202	>	uz = uz / u;
203
204	<	Atom::createArrays(simnfo->n_atoms);
205	<	the_atoms = new Atom*[simnfo->n_atoms];
206	<	the_molecules = new Molecule[simnfo->n_mol];
207	<	int molIndex;
204	>	dAtom->setSUx(ux);
205	>	dAtom->setSUy(uy);
206	>	dAtom->setSUz(uz);
207	>	}
208	>	else{
209	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
210	>	info[k].getConfiguration());
211	>	}
212	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
213
307	–	// initialize the molecule's stampID's
308	–
214		#ifdef IS_MPI
310	–
215
216	<	molIndex = 0;
313	<	for(i=0; i<mpiSim->getTotNmol(); i++){
314	<
315	<	if(mol2proc[i] == worldRank ){
316	<	the_molecules[molIndex].setStampID( molCompType[i] );
317	<	the_molecules[molIndex].setMyIndex( molIndex );
318	<	molIndex++;
319	<	}
320	<	}
216	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
217
322	–	#else // is_mpi
323	–
324	–	molIndex = 0;
325	–	for(i=0; i<n_components; i++){
326	–	for(j=0; j<components_nmol[i]; j++ ){
327	–	the_molecules[molIndex].setStampID( i );
328	–	the_molecules[molIndex].setMyIndex( molIndex );
329	–	molIndex++;
330	–	}
331	–	}
332	–
333	–
218		#endif // is_mpi
219	+	}
220
221	+	// make the bonds
222	+	for (j = 0; j < molInfo.nBonds; j++){
223	+	currentBond = comp_stamps[stampID]->getBond(j);
224	+	theBonds[j].a = currentBond->getA() + atomOffset;
225	+	theBonds[j].b = currentBond->getB() + atomOffset;
226
227	<	if( simnfo->n_SRI ){
228	<
339	<	std::cerr << "n_SRI = " << simnfo->n_SRI << "\n";
340	<
341	<	Exclude::createArray(simnfo->n_SRI);
342	<	the_excludes = new Exclude*[simnfo->n_SRI];
343	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
344	<	simnfo->globalExcludes = new int;
345	<	simnfo->n_exclude = simnfo->n_SRI;
346	<	}
347	<	else{
348	<
349	<	Exclude::createArray( 1 );
350	<	the_excludes = new Exclude*;
351	<	the_excludes[0] = new Exclude(0);
352	<	the_excludes[0]->setPair( 0,0 );
353	<	simnfo->globalExcludes = new int;
354	<	simnfo->globalExcludes[0] = 0;
355	<	simnfo->n_exclude = 0;
356	<	}
227	>	exI = theBonds[j].a;
228	>	exJ = theBonds[j].b;
229
230	<	// set the arrays into the SimInfo object
230	>	// exclude_I must always be the smaller of the pair
231	>	if (exI > exJ){
232	>	tempEx = exI;
233	>	exI = exJ;
234	>	exJ = tempEx;
235	>	}
236	>	#ifdef IS_MPI
237	>	tempEx = exI;
238	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
239	>	tempEx = exJ;
240	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
241
242	<	simnfo->atoms = the_atoms;
243	<	simnfo->molecules = the_molecules;
362	<	simnfo->nGlobalExcludes = 0;
363	<	simnfo->excludes = the_excludes;
242	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
243	>	#else  // isn't MPI
244
245	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
246	+	#endif  //is_mpi
247	+	}
248	+	excludeOffset += molInfo.nBonds;
249
250	<	// get some of the tricky things that may still be in the globals
250	>	//make the bends
251	>	for (j = 0; j < molInfo.nBends; j++){
252	>	currentBend = comp_stamps[stampID]->getBend(j);
253	>	theBends[j].a = currentBend->getA() + atomOffset;
254	>	theBends[j].b = currentBend->getB() + atomOffset;
255	>	theBends[j].c = currentBend->getC() + atomOffset;
256
257	<
258	<	if( the_globals->haveBox() ){
259	<	simnfo->box_x = the_globals->getBox();
371	<	simnfo->box_y = the_globals->getBox();
372	<	simnfo->box_z = the_globals->getBox();
373	<	}
374	<	else if( the_globals->haveDensity() ){
257	>	if (currentBend->haveExtras()){
258	>	extras = currentBend->getExtras();
259	>	current_extra = extras;
260
261	<	double vol;
262	<	vol = (double)tot_nmol / the_globals->getDensity();
263	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
264	<	simnfo->box_y = simnfo->box_x;
265	<	simnfo->box_z = simnfo->box_x;
266	<	}
267	<	else{
383	<	if( !the_globals->haveBoxX() ){
384	<	sprintf( painCave.errMsg,
385	<	"SimSetup error, no periodic BoxX size given.\n" );
386	<	painCave.isFatal = 1;
387	<	simError();
388	<	}
389	<	simnfo->box_x = the_globals->getBoxX();
261	>	while (current_extra != NULL){
262	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
263	>	switch (current_extra->getType()){
264	>	case 0:
265	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
266	>	theBends[j].isGhost = 1;
267	>	break;
268
269	<	if( !the_globals->haveBoxY() ){
270	<	sprintf( painCave.errMsg,
271	<	"SimSetup error, no periodic BoxY size given.\n" );
272	<	painCave.isFatal = 1;
273	<	simError();
396	<	}
397	<	simnfo->box_y = the_globals->getBoxY();
269	>	case 1:
270	>	theBends[j].ghost = (int) current_extra->getDouble() +
271	>	atomOffset;
272	>	theBends[j].isGhost = 1;
273	>	break;
274
275	<	if( !the_globals->haveBoxZ() ){
276	<	sprintf( painCave.errMsg,
277	<	"SimSetup error, no periodic BoxZ size given.\n" );
278	<	painCave.isFatal = 1;
279	<	simError();
280	<	}
281	<	simnfo->box_z = the_globals->getBoxZ();
282	<	}
275	>	default:
276	>	sprintf(painCave.errMsg,
277	>	"SimSetup Error: ghostVectorSource was neither a "
278	>	"double nor an int.\n"
279	>	"-->Bend[%d] in %s\n",
280	>	j, comp_stamps[stampID]->getID());
281	>	painCave.isFatal = 1;
282	>	simError();
283	>	}
284	>	}
285	>	else{
286	>	sprintf(painCave.errMsg,
287	>	"SimSetup Error: unhandled bend assignment:\n"
288	>	"    -->%s in Bend[%d] in %s\n",
289	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
290	>	painCave.isFatal = 1;
291	>	simError();
292	>	}
293
294	+	current_extra = current_extra->getNext();
295	+	}
296	+	}
297	+
298	+	if (!theBends[j].isGhost){
299	+	exI = theBends[j].a;
300	+	exJ = theBends[j].c;
301	+	}
302	+	else{
303	+	exI = theBends[j].a;
304	+	exJ = theBends[j].b;
305	+	}
306	+
307	+	// exclude_I must always be the smaller of the pair
308	+	if (exI > exJ){
309	+	tempEx = exI;
310	+	exI = exJ;
311	+	exJ = tempEx;
312	+	}
313		#ifdef IS_MPI
314	<	strcpy( checkPointMsg, "Box size set up" );
315	<	MPIcheckPoint();
316	<	#endif // is_mpi
314	>	tempEx = exI;
315	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
316	>	tempEx = exJ;
317	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
318
319	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
320	+	#else  // isn't MPI
321	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
322	+	#endif  //is_mpi
323	+	}
324	+	excludeOffset += molInfo.nBends;
325
326	<	// initialize the arrays
326	>	for (j = 0; j < molInfo.nTorsions; j++){
327	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
328	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
329	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
330	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
331	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
332
333	<	the_ff->setSimInfo( simnfo );
333	>	exI = theTorsions[j].a;
334	>	exJ = theTorsions[j].d;
335
336	<	makeMolecules();
337	<	simnfo->identArray = new int[simnfo->n_atoms];
338	<	for(i=0; i<simnfo->n_atoms; i++){
339	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
340	<	}
341	<
342	<	if (the_globals->getUseRF() ) {
343	<	simnfo->useReactionField = 1;
344	<
345	<	if( !the_globals->haveECR() ){
346	<	sprintf( painCave.errMsg,
429	<	"SimSetup Warning: using default value of 1/2 the smallest "
430	<	"box length for the electrostaticCutoffRadius.\n"
431	<	"I hope you have a very fast processor!\n");
432	<	painCave.isFatal = 0;
433	<	simError();
434	<	double smallest;
435	<	smallest = simnfo->box_x;
436	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
437	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
438	<	simnfo->ecr = 0.5 * smallest;
439	<	} else {
440	<	simnfo->ecr        = the_globals->getECR();
441	<	}
336	>	// exclude_I must always be the smaller of the pair
337	>	if (exI > exJ){
338	>	tempEx = exI;
339	>	exI = exJ;
340	>	exJ = tempEx;
341	>	}
342	>	#ifdef IS_MPI
343	>	tempEx = exI;
344	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345	>	tempEx = exJ;
346	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
347
348	<	if( !the_globals->haveEST() ){
349	<	sprintf( painCave.errMsg,
350	<	"SimSetup Warning: using default value of 0.05 * the "
351	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
447	<	);
448	<	painCave.isFatal = 0;
449	<	simError();
450	<	simnfo->est = 0.05 * simnfo->ecr;
451	<	} else {
452	<	simnfo->est        = the_globals->getEST();
453	<	}
454	<
455	<	if(!the_globals->haveDielectric() ){
456	<	sprintf( painCave.errMsg,
457	<	"SimSetup Error: You are trying to use Reaction Field without"
458	<	"setting a dielectric constant!\n"
459	<	);
460	<	painCave.isFatal = 1;
461	<	simError();
462	<	}
463	<	simnfo->dielectric = the_globals->getDielectric();
464	<	} else {
465	<	if (simnfo->n_dipoles) {
466	<
467	<	if( !the_globals->haveECR() ){
468	<	sprintf( painCave.errMsg,
469	<	"SimSetup Warning: using default value of 1/2 the smallest"
470	<	"box length for the electrostaticCutoffRadius.\n"
471	<	"I hope you have a very fast processor!\n");
472	<	painCave.isFatal = 0;
473	<	simError();
474	<	double smallest;
475	<	smallest = simnfo->box_x;
476	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
477	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
478	<	simnfo->ecr = 0.5 * smallest;
479	<	} else {
480	<	simnfo->ecr        = the_globals->getECR();
348	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
349	>	#else  // isn't MPI
350	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
351	>	#endif  //is_mpi
352		}
353	<
483	<	if( !the_globals->haveEST() ){
484	<	sprintf( painCave.errMsg,
485	<	"SimSetup Warning: using default value of 5% of the"
486	<	"electrostaticCutoffRadius for the "
487	<	"electrostaticSkinThickness\n"
488	<	);
489	<	painCave.isFatal = 0;
490	<	simError();
491	<	simnfo->est = 0.05 * simnfo->ecr;
492	<	} else {
493	<	simnfo->est        = the_globals->getEST();
494	<	}
495	<	}
496	<	}
353	>	excludeOffset += molInfo.nTorsions;
354
498	–	#ifdef IS_MPI
499	–	strcpy( checkPointMsg, "electrostatic parameters check out" );
500	–	MPIcheckPoint();
501	–	#endif // is_mpi
355
356	<	if( the_globals->haveInitialConfig() ){
504	<
505	<	InitializeFromFile* fileInit;
506	<	#ifdef IS_MPI // is_mpi
507	<	if( worldRank == 0 ){
508	<	#endif //is_mpi
509	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
510	<	#ifdef IS_MPI
511	<	}else fileInit = new InitializeFromFile( NULL );
512	<	#endif
513	<	fileInit->read_xyz( simnfo ); // default velocities on
356	>	// send the arrays off to the forceField for init.
357
358	<	delete fileInit;
359	<	}
360	<	else{
358	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
359	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
360	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
361	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
362	>	theTorsions);
363
519	–	#ifdef IS_MPI
364
365	<	// no init from bass
522	<
523	<	sprintf( painCave.errMsg,
524	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
525	<	painCave.isFatal;
526	<	simError();
527	<
528	<	#else
365	>	info[k].molecules[i].initialize(molInfo);
366
530	–	initFromBass();
367
368	+	atomOffset += molInfo.nAtoms;
369	+	delete[] theBonds;
370	+	delete[] theBends;
371	+	delete[] theTorsions;
372	+	}
373	+	}
374
533	–	#endif
534	–	}
535	–
375		#ifdef IS_MPI
376	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
376	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
377		MPIcheckPoint();
378		#endif // is_mpi
379
380	+	// clean up the forcefield
381
382	<
383	<
384	<
382	>	the_ff->calcRcut();
383	>	the_ff->cleanMe();
384	>	}
385
386	<
387	<	#ifdef IS_MPI
388	<	if( worldRank == 0 ){
389	<	#endif // is_mpi
390	<
391	<	if( the_globals->haveFinalConfig() ){
392	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
393	<	}
554	<	else{
555	<	strcpy( simnfo->finalName, inFileName );
556	<	char* endTest;
557	<	int nameLength = strlen( simnfo->finalName );
558	<	endTest = &(simnfo->finalName[nameLength - 5]);
559	<	if( !strcmp( endTest, ".bass" ) ){
560	<	strcpy( endTest, ".eor" );
561	<	}
562	<	else if( !strcmp( endTest, ".BASS" ) ){
563	<	strcpy( endTest, ".eor" );
564	<	}
565	<	else{
566	<	endTest = &(simnfo->finalName[nameLength - 4]);
567	<	if( !strcmp( endTest, ".bss" ) ){
568	<	strcpy( endTest, ".eor" );
569	<	}
570	<	else if( !strcmp( endTest, ".mdl" ) ){
571	<	strcpy( endTest, ".eor" );
572	<	}
573	<	else{
574	<	strcat( simnfo->finalName, ".eor" );
575	<	}
576	<	}
577	<	}
578	<
579	<	// make the sample and status out names
580	<
581	<	strcpy( simnfo->sampleName, inFileName );
582	<	char* endTest;
583	<	int nameLength = strlen( simnfo->sampleName );
584	<	endTest = &(simnfo->sampleName[nameLength - 5]);
585	<	if( !strcmp( endTest, ".bass" ) ){
586	<	strcpy( endTest, ".dump" );
587	<	}
588	<	else if( !strcmp( endTest, ".BASS" ) ){
589	<	strcpy( endTest, ".dump" );
590	<	}
591	<	else{
592	<	endTest = &(simnfo->sampleName[nameLength - 4]);
593	<	if( !strcmp( endTest, ".bss" ) ){
594	<	strcpy( endTest, ".dump" );
595	<	}
596	<	else if( !strcmp( endTest, ".mdl" ) ){
597	<	strcpy( endTest, ".dump" );
598	<	}
599	<	else{
600	<	strcat( simnfo->sampleName, ".dump" );
601	<	}
602	<	}
603	<
604	<	strcpy( simnfo->statusName, inFileName );
605	<	nameLength = strlen( simnfo->statusName );
606	<	endTest = &(simnfo->statusName[nameLength - 5]);
607	<	if( !strcmp( endTest, ".bass" ) ){
608	<	strcpy( endTest, ".stat" );
609	<	}
610	<	else if( !strcmp( endTest, ".BASS" ) ){
611	<	strcpy( endTest, ".stat" );
612	<	}
613	<	else{
614	<	endTest = &(simnfo->statusName[nameLength - 4]);
615	<	if( !strcmp( endTest, ".bss" ) ){
616	<	strcpy( endTest, ".stat" );
617	<	}
618	<	else if( !strcmp( endTest, ".mdl" ) ){
619	<	strcpy( endTest, ".stat" );
620	<	}
621	<	else{
622	<	strcat( simnfo->statusName, ".stat" );
623	<	}
624	<	}
625	<
626	<	#ifdef IS_MPI
627	<	}
628	<	#endif // is_mpi
629	<
630	<	// set the status, sample, and themal kick times
631	<
632	<	if( the_globals->haveSampleTime() ){
633	<	simnfo->sampleTime = the_globals->getSampleTime();
634	<	simnfo->statusTime = simnfo->sampleTime;
635	<	simnfo->thermalTime = simnfo->sampleTime;
636	<	}
637	<	else{
638	<	simnfo->sampleTime = the_globals->getRunTime();
639	<	simnfo->statusTime = simnfo->sampleTime;
640	<	simnfo->thermalTime = simnfo->sampleTime;
641	<	}
386	>	void SimSetup::initFromBass(void){
387	>	int i, j, k;
388	>	int n_cells;
389	>	double cellx, celly, cellz;
390	>	double temp1, temp2, temp3;
391	>	int n_per_extra;
392	>	int n_extra;
393	>	int have_extra, done;
394
395	<	if( the_globals->haveStatusTime() ){
396	<	simnfo->statusTime = the_globals->getStatusTime();
397	<	}
395	>	double vel[3];
396	>	vel[0] = 0.0;
397	>	vel[1] = 0.0;
398	>	vel[2] = 0.0;
399
400	<	if( the_globals->haveThermalTime() ){
401	<	simnfo->thermalTime = the_globals->getThermalTime();
402	<	}
400	>	temp1 = (double) tot_nmol / 4.0;
401	>	temp2 = pow(temp1, (1.0 / 3.0));
402	>	temp3 = ceil(temp2);
403
404	<	// check for the temperature set flag
404	>	have_extra = 0;
405	>	if (temp2 < temp3){
406	>	// we have a non-complete lattice
407	>	have_extra = 1;
408
409	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
409	>	n_cells = (int) temp3 - 1;
410	>	cellx = info[0].boxL[0] / temp3;
411	>	celly = info[0].boxL[1] / temp3;
412	>	cellz = info[0].boxL[2] / temp3;
413	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
414	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
415	>	n_per_extra = (int) ceil(temp1);
416
417	+	if (n_per_extra > 4){
418	+	sprintf(painCave.errMsg,
419	+	"SimSetup error. There has been an error in constructing"
420	+	" the non-complete lattice.\n");
421	+	painCave.isFatal = 1;
422	+	simError();
423	+	}
424	+	}
425	+	else{
426	+	n_cells = (int) temp3;
427	+	cellx = info[0].boxL[0] / temp3;
428	+	celly = info[0].boxL[1] / temp3;
429	+	cellz = info[0].boxL[2] / temp3;
430	+	}
431
432	<	//   // make the longe range forces and the integrator
432	>	current_mol = 0;
433	>	current_comp_mol = 0;
434	>	current_comp = 0;
435	>	current_atom_ndx = 0;
436
437	<	//   new AllLong( simnfo );
437	>	for (i = 0; i < n_cells ; i++){
438	>	for (j = 0; j < n_cells; j++){
439	>	for (k = 0; k < n_cells; k++){
440	>	makeElement(i * cellx, j * celly, k * cellz);
441
442	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
661	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
442	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
443
444	<	#ifdef IS_MPI
664	<	mpiSim->mpiRefresh();
665	<	#endif
444	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
445
446	<	// initialize the Fortran
446	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
447	>	}
448	>	}
449	>	}
450
451	+	if (have_extra){
452	+	done = 0;
453
454	<	simnfo->refreshSim();
455	<
456	<	if( !strcmp( simnfo->mixingRule, "standard") ){
457	<	the_ff->initForceField( LB_MIXING_RULE );
454	>	int start_ndx;
455	>	for (i = 0; i < (n_cells + 1) && !done; i++){
456	>	for (j = 0; j < (n_cells + 1) && !done; j++){
457	>	if (i < n_cells){
458	>	if (j < n_cells){
459	>	start_ndx = n_cells;
460	>	}
461	>	else
462	>	start_ndx = 0;
463	>	}
464	>	else
465	>	start_ndx = 0;
466	>
467	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
468	>	makeElement(i * cellx, j * celly, k * cellz);
469	>	done = (current_mol >= tot_nmol);
470	>
471	>	if (!done && n_per_extra > 1){
472	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
473	>	k * cellz);
474	>	done = (current_mol >= tot_nmol);
475	>	}
476	>
477	>	if (!done && n_per_extra > 2){
478	>	makeElement(i * cellx, j * celly + 0.5 * celly,
479	>	k * cellz + 0.5 * cellz);
480	>	done = (current_mol >= tot_nmol);
481	>	}
482	>
483	>	if (!done && n_per_extra > 3){
484	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
485	>	k * cellz + 0.5 * cellz);
486	>	done = (current_mol >= tot_nmol);
487	>	}
488	>	}
489	>	}
490	>	}
491		}
492	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
493	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
492	>
493	>	for (i = 0; i < info[0].n_atoms; i++){
494	>	info[0].atoms[i]->setVel(vel);
495		}
496	<	else{
497	<	sprintf( painCave.errMsg,
498	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
499	<	simnfo->mixingRule );
500	<	painCave.isFatal = 1;
501	<	simError();
496	>	}
497	>
498	>	void SimSetup::makeElement(double x, double y, double z){
499	>	int k;
500	>	AtomStamp* current_atom;
501	>	DirectionalAtom* dAtom;
502	>	double rotMat[3][3];
503	>	double pos[3];
504	>
505	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
506	>	current_atom = comp_stamps[current_comp]->getAtom(k);
507	>	if (!current_atom->havePosition()){
508	>	sprintf(painCave.errMsg,
509	>	"SimSetup:initFromBass error.\n"
510	>	"\tComponent %s, atom %s does not have a position specified.\n"
511	>	"\tThe initialization routine is unable to give a start"
512	>	" position.\n",
513	>	comp_stamps[current_comp]->getID(), current_atom->getType());
514	>	painCave.isFatal = 1;
515	>	simError();
516	>	}
517	>
518	>	pos[0] = x + current_atom->getPosX();
519	>	pos[1] = y + current_atom->getPosY();
520	>	pos[2] = z + current_atom->getPosZ();
521	>
522	>	info[0].atoms[current_atom_ndx]->setPos(pos);
523	>
524	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
525	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
526	>
527	>	rotMat[0][0] = 1.0;
528	>	rotMat[0][1] = 0.0;
529	>	rotMat[0][2] = 0.0;
530	>
531	>	rotMat[1][0] = 0.0;
532	>	rotMat[1][1] = 1.0;
533	>	rotMat[1][2] = 0.0;
534	>
535	>	rotMat[2][0] = 0.0;
536	>	rotMat[2][1] = 0.0;
537	>	rotMat[2][2] = 1.0;
538	>
539	>	dAtom->setA(rotMat);
540	>	}
541	>
542	>	current_atom_ndx++;
543		}
544
545	+	current_mol++;
546	+	current_comp_mol++;
547
548	<	#ifdef IS_MPI
549	<	strcpy( checkPointMsg,
550	<	"Successfully intialized the mixingRule for Fortran." );
551	<	MPIcheckPoint();
691	<	#endif // is_mpi
548	>	if (current_comp_mol >= components_nmol[current_comp]){
549	>	current_comp_mol = 0;
550	>	current_comp++;
551	>	}
552		}
553
554
555	<	void SimSetup::makeMolecules( void ){
555	>	void SimSetup::gatherInfo(void){
556	>	int i, j, k;
557
558	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
559	<	molInit info;
699	<	DirectionalAtom* dAtom;
700	<	LinkedAssign* extras;
701	<	LinkedAssign* current_extra;
702	<	AtomStamp* currentAtom;
703	<	BondStamp* currentBond;
704	<	BendStamp* currentBend;
705	<	TorsionStamp* currentTorsion;
558	>	ensembleCase = -1;
559	>	ffCase = -1;
560
561	<	bond_pair* theBonds;
708	<	bend_set* theBends;
709	<	torsion_set* theTorsions;
561	>	// set the easy ones first
562
563	<
564	<	//init the forceField paramters
563	>	for (i = 0; i < nInfo; i++){
564	>	info[i].target_temp = globals->getTargetTemp();
565	>	info[i].dt = globals->getDt();
566	>	info[i].run_time = globals->getRunTime();
567	>	}
568	>	n_components = globals->getNComponents();
569
714	–	the_ff->readParams();
570
571	<
717	<	// init the atoms
571	>	// get the forceField
572
573	<	double ux, uy, uz, u, uSqr;
720	<
721	<	atomOffset = 0;
722	<	excludeOffset = 0;
723	<	for(i=0; i<simnfo->n_mol; i++){
724	<
725	<	stampID = the_molecules[i].getStampID();
573	>	strcpy(force_field, globals->getForceField());
574
575	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
576	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
577	<	info.nBends    = comp_stamps[stampID]->getNBends();
578	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
579	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
575	>	if (!strcasecmp(force_field, "DUFF")){
576	>	ffCase = FF_DUFF;
577	>	}
578	>	else if (!strcasecmp(force_field, "LJ")){
579	>	ffCase = FF_LJ;
580	>	}
581	>	else if (!strcasecmp(force_field, "EAM")){
582	>	ffCase = FF_EAM;
583	>	}
584	>	else{
585	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
586	>	force_field);
587	>	painCave.isFatal = 1;
588	>	simError();
589	>	}
590
591	<	info.myAtoms = &the_atoms[atomOffset];
734	<	info.myExcludes = &the_excludes[excludeOffset];
735	<	info.myBonds = new Bond*[info.nBonds];
736	<	info.myBends = new Bend*[info.nBends];
737	<	info.myTorsions = new Torsion*[info.nTorsions];
591	>	// get the ensemble
592
593	<	theBonds = new bond_pair[info.nBonds];
740	<	theBends = new bend_set[info.nBends];
741	<	theTorsions = new torsion_set[info.nTorsions];
742	<
743	<	// make the Atoms
744	<
745	<	for(j=0; j<info.nAtoms; j++){
746	<
747	<	currentAtom = comp_stamps[stampID]->getAtom( j );
748	<	if( currentAtom->haveOrientation() ){
749	<
750	<	dAtom = new DirectionalAtom(j + atomOffset);
751	<	simnfo->n_oriented++;
752	<	info.myAtoms[j] = dAtom;
753	<
754	<	ux = currentAtom->getOrntX();
755	<	uy = currentAtom->getOrntY();
756	<	uz = currentAtom->getOrntZ();
757	<
758	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
759	<
760	<	u = sqrt( uSqr );
761	<	ux = ux / u;
762	<	uy = uy / u;
763	<	uz = uz / u;
764	<
765	<	dAtom->setSUx( ux );
766	<	dAtom->setSUy( uy );
767	<	dAtom->setSUz( uz );
768	<	}
769	<	else{
770	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
771	<	}
772	<	info.myAtoms[j]->setType( currentAtom->getType() );
773	<
774	<	#ifdef IS_MPI
775	<
776	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
777	<
778	<	#endif // is_mpi
779	<	}
780	<
781	<	// make the bonds
782	<	for(j=0; j<info.nBonds; j++){
783	<
784	<	currentBond = comp_stamps[stampID]->getBond( j );
785	<	theBonds[j].a = currentBond->getA() + atomOffset;
786	<	theBonds[j].b = currentBond->getB() + atomOffset;
593	>	strcpy(ensemble, globals->getEnsemble());
594
595	<	exI = theBonds[j].a;
596	<	exJ = theBonds[j].b;
595	>	if (!strcasecmp(ensemble, "NVE")){
596	>	ensembleCase = NVE_ENS;
597	>	}
598	>	else if (!strcasecmp(ensemble, "NVT")){
599	>	ensembleCase = NVT_ENS;
600	>	}
601	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
602	>	ensembleCase = NPTi_ENS;
603	>	}
604	>	else if (!strcasecmp(ensemble, "NPTf")){
605	>	ensembleCase = NPTf_ENS;
606	>	}
607	>	else if (!strcasecmp(ensemble, "NPTim")){
608	>	ensembleCase = NPTim_ENS;
609	>	}
610	>	else if (!strcasecmp(ensemble, "NPTfm")){
611	>	ensembleCase = NPTfm_ENS;
612	>	}
613	>	else{
614	>	sprintf(painCave.errMsg,
615	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
616	>	"reverting to NVE for this simulation.\n",
617	>	ensemble);
618	>	painCave.isFatal = 0;
619	>	simError();
620	>	strcpy(ensemble, "NVE");
621	>	ensembleCase = NVE_ENS;
622	>	}
623
624	<	// exclude_I must always be the smaller of the pair
625	<	if( exI > exJ ){
793	<	tempEx = exI;
794	<	exI = exJ;
795	<	exJ = tempEx;
796	<	}
797	<	#ifdef IS_MPI
798	<	tempEx = exI;
799	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
800	<	tempEx = exJ;
801	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
802	<
803	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
804	<	#else  // isn't MPI
624	>	for (i = 0; i < nInfo; i++){
625	>	strcpy(info[i].ensemble, ensemble);
626
627	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
807	<	#endif  //is_mpi
808	<	}
809	<	excludeOffset += info.nBonds;
627	>	// get the mixing rule
628
629	<	//make the bends
630	<	for(j=0; j<info.nBends; j++){
631	<
814	<	currentBend = comp_stamps[stampID]->getBend( j );
815	<	theBends[j].a = currentBend->getA() + atomOffset;
816	<	theBends[j].b = currentBend->getB() + atomOffset;
817	<	theBends[j].c = currentBend->getC() + atomOffset;
818	<
819	<	if( currentBend->haveExtras() ){
820	<
821	<	extras = currentBend->getExtras();
822	<	current_extra = extras;
823	<
824	<	while( current_extra != NULL ){
825	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
826	<
827	<	switch( current_extra->getType() ){
828	<
829	<	case 0:
830	<	theBends[j].ghost =
831	<	current_extra->getInt() + atomOffset;
832	<	theBends[j].isGhost = 1;
833	<	break;
834	<
835	<	case 1:
836	<	theBends[j].ghost =
837	<	(int)current_extra->getDouble() + atomOffset;
838	<	theBends[j].isGhost = 1;
839	<	break;
840	<
841	<	default:
842	<	sprintf( painCave.errMsg,
843	<	"SimSetup Error: ghostVectorSource was neither a "
844	<	"double nor an int.\n"
845	<	"-->Bend[%d] in %s\n",
846	<	j, comp_stamps[stampID]->getID() );
847	<	painCave.isFatal = 1;
848	<	simError();
849	<	}
850	<	}
851	<
852	<	else{
853	<
854	<	sprintf( painCave.errMsg,
855	<	"SimSetup Error: unhandled bend assignment:\n"
856	<	"    -->%s in Bend[%d] in %s\n",
857	<	current_extra->getlhs(),
858	<	j, comp_stamps[stampID]->getID() );
859	<	painCave.isFatal = 1;
860	<	simError();
861	<	}
862	<
863	<	current_extra = current_extra->getNext();
864	<	}
865	<	}
866	<
867	<	if( !theBends[j].isGhost ){
868	<
869	<	exI = theBends[j].a;
870	<	exJ = theBends[j].c;
871	<	}
872	<	else{
873	<
874	<	exI = theBends[j].a;
875	<	exJ = theBends[j].b;
876	<	}
877	<
878	<	// exclude_I must always be the smaller of the pair
879	<	if( exI > exJ ){
880	<	tempEx = exI;
881	<	exI = exJ;
882	<	exJ = tempEx;
883	<	}
884	<	#ifdef IS_MPI
885	<	tempEx = exI;
886	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
887	<	tempEx = exJ;
888	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
889	<
890	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
891	<	#else  // isn't MPI
892	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
893	<	#endif  //is_mpi
894	<	}
895	<	excludeOffset += info.nBends;
629	>	strcpy(info[i].mixingRule, globals->getMixingRule());
630	>	info[i].usePBC = globals->getPBC();
631	>	}
632
633	<	for(j=0; j<info.nTorsions; j++){
898	<
899	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
900	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
901	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
902	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
903	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
904	<
905	<	exI = theTorsions[j].a;
906	<	exJ = theTorsions[j].d;
633	>	// get the components and calculate the tot_nMol and indvidual n_mol
634
635	<	// exclude_I must always be the smaller of the pair
636	<	if( exI > exJ ){
910	<	tempEx = exI;
911	<	exI = exJ;
912	<	exJ = tempEx;
913	<	}
914	<	#ifdef IS_MPI
915	<	tempEx = exI;
916	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
917	<	tempEx = exJ;
918	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
919	<
920	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
921	<	#else  // isn't MPI
922	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
923	<	#endif  //is_mpi
924	<	}
925	<	excludeOffset += info.nTorsions;
635	>	the_components = globals->getComponents();
636	>	components_nmol = new int[n_components];
637
927	–
928	–	// send the arrays off to the forceField for init.
638
639	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
640	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
641	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
933	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
639	>	if (!globals->haveNMol()){
640	>	// we don't have the total number of molecules, so we assume it is
641	>	// given in each component
642
643	+	tot_nmol = 0;
644	+	for (i = 0; i < n_components; i++){
645	+	if (!the_components[i]->haveNMol()){
646	+	// we have a problem
647	+	sprintf(painCave.errMsg,
648	+	"SimSetup Error. No global NMol or component NMol"
649	+	" given. Cannot calculate the number of atoms.\n");
650	+	painCave.isFatal = 1;
651	+	simError();
652	+	}
653
654	<	the_molecules[i].initialize( info );
654	>	tot_nmol += the_components[i]->getNMol();
655	>	components_nmol[i] = the_components[i]->getNMol();
656	>	}
657	>	}
658	>	else{
659	>	sprintf(painCave.errMsg,
660	>	"SimSetup error.\n"
661	>	"\tSorry, the ability to specify total"
662	>	" nMols and then give molfractions in the components\n"
663	>	"\tis not currently supported."
664	>	" Please give nMol in the components.\n");
665	>	painCave.isFatal = 1;
666	>	simError();
667	>	}
668
669	+	// set the status, sample, and thermal kick times
670
671	<	atomOffset += info.nAtoms;
672	<	delete[] theBonds;
673	<	delete[] theBends;
674	<	delete[] theTorsions;
675	<	}
671	>	for (i = 0; i < nInfo; i++){
672	>	if (globals->haveSampleTime()){
673	>	info[i].sampleTime = globals->getSampleTime();
674	>	info[i].statusTime = info[i].sampleTime;
675	>	info[i].thermalTime = info[i].sampleTime;
676	>	}
677	>	else{
678	>	info[i].sampleTime = globals->getRunTime();
679	>	info[i].statusTime = info[i].sampleTime;
680	>	info[i].thermalTime = info[i].sampleTime;
681	>	}
682
683	<	#ifdef IS_MPI
684	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
685	<	MPIcheckPoint();
948	<	#endif // is_mpi
683	>	if (globals->haveStatusTime()){
684	>	info[i].statusTime = globals->getStatusTime();
685	>	}
686
687	<	// clean up the forcefield
688	<	the_ff->calcRcut();
689	<	the_ff->cleanMe();
687	>	if (globals->haveThermalTime()){
688	>	info[i].thermalTime = globals->getThermalTime();
689	>	}
690
691	<	}
691	>	info[i].resetIntegrator = 0;
692	>	if( globals->haveResetTime() ){
693	>	info[i].resetTime = globals->getResetTime();
694	>	info[i].resetIntegrator = 1;
695	>	}
696
697	<	void SimSetup::initFromBass( void ){
697	>	// check for the temperature set flag
698
699	<	int i, j, k;
700	<	int n_cells;
960	<	double cellx, celly, cellz;
961	<	double temp1, temp2, temp3;
962	<	int n_per_extra;
963	<	int n_extra;
964	<	int have_extra, done;
699	>	if (globals->haveTempSet())
700	>	info[i].setTemp = globals->getTempSet();
701
702	<	temp1 = (double)tot_nmol / 4.0;
967	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
968	<	temp3 = ceil( temp2 );
702	>	// get some of the tricky things that may still be in the globals
703
704	<	have_extra =0;
705	<	if( temp2 < temp3 ){ // we have a non-complete lattice
706	<	have_extra =1;
704	>	double boxVector[3];
705	>	if (globals->haveBox()){
706	>	boxVector[0] = globals->getBox();
707	>	boxVector[1] = globals->getBox();
708	>	boxVector[2] = globals->getBox();
709
710	<	n_cells = (int)temp3 - 1;
711	<	cellx = simnfo->box_x / temp3;
712	<	celly = simnfo->box_y / temp3;
713	<	cellz = simnfo->box_z / temp3;
714	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
715	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
716	<	n_per_extra = (int)ceil( temp1 );
710	>	info[i].setBox(boxVector);
711	>	}
712	>	else if (globals->haveDensity()){
713	>	double vol;
714	>	vol = (double) tot_nmol / globals->getDensity();
715	>	boxVector[0] = pow(vol, (1.0 / 3.0));
716	>	boxVector[1] = boxVector[0];
717	>	boxVector[2] = boxVector[0];
718
719	<	if( n_per_extra > 4){
983	<	sprintf( painCave.errMsg,
984	<	"SimSetup error. There has been an error in constructing"
985	<	" the non-complete lattice.\n" );
986	<	painCave.isFatal = 1;
987	<	simError();
719	>	info[i].setBox(boxVector);
720		}
721	<	}
722	<	else{
723	<	n_cells = (int)temp3;
724	<	cellx = simnfo->box_x / temp3;
725	<	celly = simnfo->box_y / temp3;
726	<	cellz = simnfo->box_z / temp3;
727	<	}
721	>	else{
722	>	if (!globals->haveBoxX()){
723	>	sprintf(painCave.errMsg,
724	>	"SimSetup error, no periodic BoxX size given.\n");
725	>	painCave.isFatal = 1;
726	>	simError();
727	>	}
728	>	boxVector[0] = globals->getBoxX();
729
730	<	current_mol = 0;
731	<	current_comp_mol = 0;
732	<	current_comp = 0;
733	<	current_atom_ndx = 0;
734	<
735	<	for( i=0; i < n_cells ; i++ ){
736	<	for( j=0; j < n_cells; j++ ){
1004	<	for( k=0; k < n_cells; k++ ){
1005	<
1006	<	makeElement( i * cellx,
1007	<	j * celly,
1008	<	k * cellz );
1009	<
1010	<	makeElement( i * cellx + 0.5 * cellx,
1011	<	j * celly + 0.5 * celly,
1012	<	k * cellz );
1013	<
1014	<	makeElement( i * cellx,
1015	<	j * celly + 0.5 * celly,
1016	<	k * cellz + 0.5 * cellz );
730	>	if (!globals->haveBoxY()){
731	>	sprintf(painCave.errMsg,
732	>	"SimSetup error, no periodic BoxY size given.\n");
733	>	painCave.isFatal = 1;
734	>	simError();
735	>	}
736	>	boxVector[1] = globals->getBoxY();
737
738	<	makeElement( i * cellx + 0.5 * cellx,
739	<	j * celly,
740	<	k * cellz + 0.5 * cellz );
738	>	if (!globals->haveBoxZ()){
739	>	sprintf(painCave.errMsg,
740	>	"SimSetup error, no periodic BoxZ size given.\n");
741	>	painCave.isFatal = 1;
742	>	simError();
743		}
744	+	boxVector[2] = globals->getBoxZ();
745	+
746	+	info[i].setBox(boxVector);
747		}
748		}
749
750	<	if( have_extra ){
751	<	done = 0;
750	>	//setup seed for random number generator
751	>	int seedValue;
752
753	<	int start_ndx;
754	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1030	<	for( j=0; j < (n_cells+1) && !done; j++ ){
753	>	if (globals->haveSeed()){
754	>	seedValue = globals->getSeed();
755
756	<	if( i < n_cells ){
756	>	if(seedValue / 1E9 == 0){
757	>	sprintf(painCave.errMsg,
758	>	"Seed for sprng library should contain at least 9 digits\n"
759	>	"OOPSE will generate a seed for user\n");
760	>	painCave.isFatal = 0;
761	>	simError();
762
763	<	if( j < n_cells ){
764	<	start_ndx = n_cells;
765	<	}
766	<	else start_ndx = 0;
767	<	}
768	<	else start_ndx = 0;
763	>	//using seed generated by system instead of invalid seed set by user
764	>	#ifndef IS_MPI
765	>	seedValue = make_sprng_seed();
766	>	#else
767	>	if (worldRank == 0){
768	>	seedValue = make_sprng_seed();
769	>	}
770	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
771	>	#endif
772	>	}
773	>	}//end of if branch of globals->haveSeed()
774	>	else{
775	>
776	>	#ifndef IS_MPI
777	>	seedValue = make_sprng_seed();
778	>	#else
779	>	if (worldRank == 0){
780	>	seedValue = make_sprng_seed();
781	>	}
782	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
783	>	#endif
784	>	}//end of globals->haveSeed()
785
786	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
786	>	for (int i = 0; i < nInfo; i++){
787	>	info[i].setSeed(seedValue);
788	>	}
789
790	<	makeElement( i * cellx,
791	<	j * celly,
792	<	k * cellz );
793	<	done = ( current_mol >= tot_nmol );
790	>	#ifdef IS_MPI
791	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
792	>	MPIcheckPoint();
793	>	#endif // is_mpi
794	>	}
795
1048	–	if( !done && n_per_extra > 1 ){
1049	–	makeElement( i * cellx + 0.5 * cellx,
1050	–	j * celly + 0.5 * celly,
1051	–	k * cellz );
1052	–	done = ( current_mol >= tot_nmol );
1053	–	}
796
797	<	if( !done && n_per_extra > 2){
798	<	makeElement( i * cellx,
799	<	j * celly + 0.5 * celly,
800	<	k * cellz + 0.5 * cellz );
1059	<	done = ( current_mol >= tot_nmol );
1060	<	}
797	>	void SimSetup::finalInfoCheck(void){
798	>	int index;
799	>	int usesDipoles;
800	>	int i;
801
802	<	if( !done && n_per_extra > 3){
803	<	makeElement( i * cellx + 0.5 * cellx,
804	<	j * celly,
805	<	k * cellz + 0.5 * cellz );
806	<	done = ( current_mol >= tot_nmol );
807	<	}
808	<	}
802	>	for (i = 0; i < nInfo; i++){
803	>	// check electrostatic parameters
804	>
805	>	index = 0;
806	>	usesDipoles = 0;
807	>	while ((index < info[i].n_atoms) && !usesDipoles){
808	>	usesDipoles = (info[i].atoms[index])->hasDipole();
809	>	index++;
810	>	}
811	>
812	>	#ifdef IS_MPI
813	>	int myUse = usesDipoles;
814	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
815	>	#endif //is_mpi
816	>
817	>	double theEcr, theEst;
818	>
819	>	if (globals->getUseRF()){
820	>	info[i].useReactionField = 1;
821	>
822	>	if (!globals->haveECR()){
823	>	sprintf(painCave.errMsg,
824	>	"SimSetup Warning: using default value of 1/2 the smallest "
825	>	"box length for the electrostaticCutoffRadius.\n"
826	>	"I hope you have a very fast processor!\n");
827	>	painCave.isFatal = 0;
828	>	simError();
829	>	double smallest;
830	>	smallest = info[i].boxL[0];
831	>	if (info[i].boxL[1] <= smallest)
832	>	smallest = info[i].boxL[1];
833	>	if (info[i].boxL[2] <= smallest)
834	>	smallest = info[i].boxL[2];
835	>	theEcr = 0.5 * smallest;
836		}
837	+	else{
838	+	theEcr = globals->getECR();
839	+	}
840	+
841	+	if (!globals->haveEST()){
842	+	sprintf(painCave.errMsg,
843	+	"SimSetup Warning: using default value of 0.05 * the "
844	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
845	+	painCave.isFatal = 0;
846	+	simError();
847	+	theEst = 0.05 * theEcr;
848	+	}
849	+	else{
850	+	theEst = globals->getEST();
851	+	}
852	+
853	+	info[i].setEcr(theEcr, theEst);
854	+
855	+	if (!globals->haveDielectric()){
856	+	sprintf(painCave.errMsg,
857	+	"SimSetup Error: You are trying to use Reaction Field without"
858	+	"setting a dielectric constant!\n");
859	+	painCave.isFatal = 1;
860	+	simError();
861	+	}
862	+	info[i].dielectric = globals->getDielectric();
863		}
864	<	}
864	>	else{
865	>	if (usesDipoles){
866	>	if (!globals->haveECR()){
867	>	sprintf(painCave.errMsg,
868	>	"SimSetup Warning: using default value of 1/2 the smallest "
869	>	"box length for the electrostaticCutoffRadius.\n"
870	>	"I hope you have a very fast processor!\n");
871	>	painCave.isFatal = 0;
872	>	simError();
873	>	double smallest;
874	>	smallest = info[i].boxL[0];
875	>	if (info[i].boxL[1] <= smallest)
876	>	smallest = info[i].boxL[1];
877	>	if (info[i].boxL[2] <= smallest)
878	>	smallest = info[i].boxL[2];
879	>	theEcr = 0.5 * smallest;
880	>	}
881	>	else{
882	>	theEcr = globals->getECR();
883	>	}
884
885	+	if (!globals->haveEST()){
886	+	sprintf(painCave.errMsg,
887	+	"SimSetup Warning: using default value of 0.05 * the "
888	+	"electrostaticCutoffRadius for the "
889	+	"electrostaticSkinThickness\n");
890	+	painCave.isFatal = 0;
891	+	simError();
892	+	theEst = 0.05 * theEcr;
893	+	}
894	+	else{
895	+	theEst = globals->getEST();
896	+	}
897
898	<	for( i=0; i<simnfo->n_atoms; i++ ){
899	<	simnfo->atoms[i]->set_vx( 0.0 );
900	<	simnfo->atoms[i]->set_vy( 0.0 );
1077	<	simnfo->atoms[i]->set_vz( 0.0 );
898	>	info[i].setEcr(theEcr, theEst);
899	>	}
900	>	}
901		}
902	+
903	+	#ifdef IS_MPI
904	+	strcpy(checkPointMsg, "post processing checks out");
905	+	MPIcheckPoint();
906	+	#endif // is_mpi
907		}
908
909	<	void SimSetup::makeElement( double x, double y, double z ){
909	>	void SimSetup::initSystemCoords(void){
910	>	int i;
911
912	<	int k;
1084	<	AtomStamp* current_atom;
1085	<	DirectionalAtom* dAtom;
1086	<	double rotMat[3][3];
912	>	char* inName;
913
914	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
914	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
915
916	<	current_atom = comp_stamps[current_comp]->getAtom( k );
917	<	if( !current_atom->havePosition() ){
918	<	sprintf( painCave.errMsg,
919	<	"SimSetup:initFromBass error.\n"
920	<	"\tComponent %s, atom %s does not have a position specified.\n"
921	<	"\tThe initialization routine is unable to give a start"
922	<	" position.\n",
923	<	comp_stamps[current_comp]->getID(),
924	<	current_atom->getType() );
925	<	painCave.isFatal = 1;
926	<	simError();
916	>	for (i = 0; i < info[0].n_atoms; i++)
917	>	info[0].atoms[i]->setCoords();
918	>
919	>	if (globals->haveInitialConfig()){
920	>	InitializeFromFile* fileInit;
921	>	#ifdef IS_MPI // is_mpi
922	>	if (worldRank == 0){
923	>	#endif //is_mpi
924	>	inName = globals->getInitialConfig();
925	>	double* tempDouble = new double[1000000];
926	>	fileInit = new InitializeFromFile(inName);
927	>	#ifdef IS_MPI
928		}
929	+	else
930	+	fileInit = new InitializeFromFile(NULL);
931	+	#endif
932	+	fileInit->readInit(info); // default velocities on
933
934	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
935	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
936	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
934	>	delete fileInit;
935	>	}
936	>	else{
937	>	#ifdef IS_MPI
938
939	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
939	>	// no init from bass
940
941	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
941	>	sprintf(painCave.errMsg,
942	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
943	>	painCave.isFatal;
944	>	simError();
945
946	<	rotMat[0][0] = 1.0;
1112	<	rotMat[0][1] = 0.0;
1113	<	rotMat[0][2] = 0.0;
946	>	#else
947
948	<	rotMat[1][0] = 0.0;
1116	<	rotMat[1][1] = 1.0;
1117	<	rotMat[1][2] = 0.0;
948	>	initFromBass();
949
1119	–	rotMat[2][0] = 0.0;
1120	–	rotMat[2][1] = 0.0;
1121	–	rotMat[2][2] = 1.0;
950
951	<	dAtom->setA( rotMat );
1124	<	}
1125	<
1126	<	current_atom_ndx++;
951	>	#endif
952		}
953
954	<	current_mol++;
955	<	current_comp_mol++;
954	>	#ifdef IS_MPI
955	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
956	>	MPIcheckPoint();
957	>	#endif // is_mpi
958	>	}
959
1132	–	if( current_comp_mol >= components_nmol[current_comp] ){
960
961	<	current_comp_mol = 0;
962	<	current_comp++;
961	>	void SimSetup::makeOutNames(void){
962	>	int k;
963	>
964	>
965	>	for (k = 0; k < nInfo; k++){
966	>	#ifdef IS_MPI
967	>	if (worldRank == 0){
968	>	#endif // is_mpi
969	>
970	>	if (globals->haveFinalConfig()){
971	>	strcpy(info[k].finalName, globals->getFinalConfig());
972	>	}
973	>	else{
974	>	strcpy(info[k].finalName, inFileName);
975	>	char* endTest;
976	>	int nameLength = strlen(info[k].finalName);
977	>	endTest = &(info[k].finalName[nameLength - 5]);
978	>	if (!strcmp(endTest, ".bass")){
979	>	strcpy(endTest, ".eor");
980	>	}
981	>	else if (!strcmp(endTest, ".BASS")){
982	>	strcpy(endTest, ".eor");
983	>	}
984	>	else{
985	>	endTest = &(info[k].finalName[nameLength - 4]);
986	>	if (!strcmp(endTest, ".bss")){
987	>	strcpy(endTest, ".eor");
988	>	}
989	>	else if (!strcmp(endTest, ".mdl")){
990	>	strcpy(endTest, ".eor");
991	>	}
992	>	else{
993	>	strcat(info[k].finalName, ".eor");
994	>	}
995	>	}
996	>	}
997	>
998	>	// make the sample and status out names
999	>
1000	>	strcpy(info[k].sampleName, inFileName);
1001	>	char* endTest;
1002	>	int nameLength = strlen(info[k].sampleName);
1003	>	endTest = &(info[k].sampleName[nameLength - 5]);
1004	>	if (!strcmp(endTest, ".bass")){
1005	>	strcpy(endTest, ".dump");
1006	>	}
1007	>	else if (!strcmp(endTest, ".BASS")){
1008	>	strcpy(endTest, ".dump");
1009	>	}
1010	>	else{
1011	>	endTest = &(info[k].sampleName[nameLength - 4]);
1012	>	if (!strcmp(endTest, ".bss")){
1013	>	strcpy(endTest, ".dump");
1014	>	}
1015	>	else if (!strcmp(endTest, ".mdl")){
1016	>	strcpy(endTest, ".dump");
1017	>	}
1018	>	else{
1019	>	strcat(info[k].sampleName, ".dump");
1020	>	}
1021	>	}
1022	>
1023	>	strcpy(info[k].statusName, inFileName);
1024	>	nameLength = strlen(info[k].statusName);
1025	>	endTest = &(info[k].statusName[nameLength - 5]);
1026	>	if (!strcmp(endTest, ".bass")){
1027	>	strcpy(endTest, ".stat");
1028	>	}
1029	>	else if (!strcmp(endTest, ".BASS")){
1030	>	strcpy(endTest, ".stat");
1031	>	}
1032	>	else{
1033	>	endTest = &(info[k].statusName[nameLength - 4]);
1034	>	if (!strcmp(endTest, ".bss")){
1035	>	strcpy(endTest, ".stat");
1036	>	}
1037	>	else if (!strcmp(endTest, ".mdl")){
1038	>	strcpy(endTest, ".stat");
1039	>	}
1040	>	else{
1041	>	strcat(info[k].statusName, ".stat");
1042	>	}
1043	>	}
1044	>
1045	>	#ifdef IS_MPI
1046	>
1047	>	}
1048	>	#endif // is_mpi
1049		}
1050		}
1051	+
1052	+
1053	+	void SimSetup::sysObjectsCreation(void){
1054	+	int i, k;
1055	+
1056	+	// create the forceField
1057	+
1058	+	createFF();
1059	+
1060	+	// extract componentList
1061	+
1062	+	compList();
1063	+
1064	+	// calc the number of atoms, bond, bends, and torsions
1065	+
1066	+	calcSysValues();
1067	+
1068	+	#ifdef IS_MPI
1069	+	// divide the molecules among the processors
1070	+
1071	+	mpiMolDivide();
1072	+	#endif //is_mpi
1073	+
1074	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1075	+
1076	+	makeSysArrays();
1077	+
1078	+	// make and initialize the molecules (all but atomic coordinates)
1079	+
1080	+	makeMolecules();
1081	+
1082	+	for (k = 0; k < nInfo; k++){
1083	+	info[k].identArray = new int[info[k].n_atoms];
1084	+	for (i = 0; i < info[k].n_atoms; i++){
1085	+	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1086	+	}
1087	+	}
1088	+	}
1089	+
1090	+
1091	+	void SimSetup::createFF(void){
1092	+	switch (ffCase){
1093	+	case FF_DUFF:
1094	+	the_ff = new DUFF();
1095	+	break;
1096	+
1097	+	case FF_LJ:
1098	+	the_ff = new LJFF();
1099	+	break;
1100	+
1101	+	case FF_EAM:
1102	+	the_ff = new EAM_FF();
1103	+	break;
1104	+
1105	+	default:
1106	+	sprintf(painCave.errMsg,
1107	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1108	+	painCave.isFatal = 1;
1109	+	simError();
1110	+	}
1111	+
1112	+	#ifdef IS_MPI
1113	+	strcpy(checkPointMsg, "ForceField creation successful");
1114	+	MPIcheckPoint();
1115	+	#endif // is_mpi
1116	+	}
1117	+
1118	+
1119	+	void SimSetup::compList(void){
1120	+	int i;
1121	+	char* id;
1122	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1123	+	LinkedMolStamp* currentStamp = NULL;
1124	+	comp_stamps = new MoleculeStamp * [n_components];
1125	+
1126	+	// make an array of molecule stamps that match the components used.
1127	+	// also extract the used stamps out into a separate linked list
1128	+
1129	+	for (i = 0; i < nInfo; i++){
1130	+	info[i].nComponents = n_components;
1131	+	info[i].componentsNmol = components_nmol;
1132	+	info[i].compStamps = comp_stamps;
1133	+	info[i].headStamp = headStamp;
1134	+	}
1135	+
1136	+
1137	+	for (i = 0; i < n_components; i++){
1138	+	id = the_components[i]->getType();
1139	+	comp_stamps[i] = NULL;
1140	+
1141	+	// check to make sure the component isn't already in the list
1142	+
1143	+	comp_stamps[i] = headStamp->match(id);
1144	+	if (comp_stamps[i] == NULL){
1145	+	// extract the component from the list;
1146	+
1147	+	currentStamp = stamps->extractMolStamp(id);
1148	+	if (currentStamp == NULL){
1149	+	sprintf(painCave.errMsg,
1150	+	"SimSetup error: Component \"%s\" was not found in the "
1151	+	"list of declared molecules\n",
1152	+	id);
1153	+	painCave.isFatal = 1;
1154	+	simError();
1155	+	}
1156	+
1157	+	headStamp->add(currentStamp);
1158	+	comp_stamps[i] = headStamp->match(id);
1159	+	}
1160	+	}
1161	+
1162	+	#ifdef IS_MPI
1163	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1164	+	MPIcheckPoint();
1165	+	#endif // is_mpi
1166	+	}
1167	+
1168	+	void SimSetup::calcSysValues(void){
1169	+	int i, j, k;
1170	+
1171	+	int* molMembershipArray;
1172	+
1173	+	tot_atoms = 0;
1174	+	tot_bonds = 0;
1175	+	tot_bends = 0;
1176	+	tot_torsions = 0;
1177	+	for (i = 0; i < n_components; i++){
1178	+	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1179	+	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1180	+	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1181	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1182	+	}
1183	+
1184	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1185	+	molMembershipArray = new int[tot_atoms];
1186	+
1187	+	for (i = 0; i < nInfo; i++){
1188	+	info[i].n_atoms = tot_atoms;
1189	+	info[i].n_bonds = tot_bonds;
1190	+	info[i].n_bends = tot_bends;
1191	+	info[i].n_torsions = tot_torsions;
1192	+	info[i].n_SRI = tot_SRI;
1193	+	info[i].n_mol = tot_nmol;
1194	+
1195	+	info[i].molMembershipArray = molMembershipArray;
1196	+	}
1197	+	}
1198	+
1199	+	#ifdef IS_MPI
1200	+
1201	+	void SimSetup::mpiMolDivide(void){
1202	+	int i, j, k;
1203	+	int localMol, allMol;
1204	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1205	+
1206	+	mpiSim = new mpiSimulation(info);
1207	+
1208	+	globalIndex = mpiSim->divideLabor();
1209	+
1210	+	// set up the local variables
1211	+
1212	+	mol2proc = mpiSim->getMolToProcMap();
1213	+	molCompType = mpiSim->getMolComponentType();
1214	+
1215	+	allMol = 0;
1216	+	localMol = 0;
1217	+	local_atoms = 0;
1218	+	local_bonds = 0;
1219	+	local_bends = 0;
1220	+	local_torsions = 0;
1221	+	globalAtomIndex = 0;
1222	+
1223	+
1224	+	for (i = 0; i < n_components; i++){
1225	+	for (j = 0; j < components_nmol[i]; j++){
1226	+	if (mol2proc[allMol] == worldRank){
1227	+	local_atoms += comp_stamps[i]->getNAtoms();
1228	+	local_bonds += comp_stamps[i]->getNBonds();
1229	+	local_bends += comp_stamps[i]->getNBends();
1230	+	local_torsions += comp_stamps[i]->getNTorsions();
1231	+	localMol++;
1232	+	}
1233	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1234	+	info[0].molMembershipArray[globalAtomIndex] = allMol;
1235	+	globalAtomIndex++;
1236	+	}
1237	+
1238	+	allMol++;
1239	+	}
1240	+	}
1241	+	local_SRI = local_bonds + local_bends + local_torsions;
1242	+
1243	+	info[0].n_atoms = mpiSim->getMyNlocal();
1244	+
1245	+	if (local_atoms != info[0].n_atoms){
1246	+	sprintf(painCave.errMsg,
1247	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1248	+	" localAtom (%d) are not equal.\n",
1249	+	info[0].n_atoms, local_atoms);
1250	+	painCave.isFatal = 1;
1251	+	simError();
1252	+	}
1253	+
1254	+	info[0].n_bonds = local_bonds;
1255	+	info[0].n_bends = local_bends;
1256	+	info[0].n_torsions = local_torsions;
1257	+	info[0].n_SRI = local_SRI;
1258	+	info[0].n_mol = localMol;
1259	+
1260	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1261	+	MPIcheckPoint();
1262	+	}
1263	+
1264	+	#endif // is_mpi
1265	+
1266	+
1267	+	void SimSetup::makeSysArrays(void){
1268	+	int i, j, k, l;
1269	+
1270	+	Atom** the_atoms;
1271	+	Molecule* the_molecules;
1272	+	Exclude** the_excludes;
1273	+
1274	+
1275	+	for (l = 0; l < nInfo; l++){
1276	+	// create the atom and short range interaction arrays
1277	+
1278	+	the_atoms = new Atom * [info[l].n_atoms];
1279	+	the_molecules = new Molecule[info[l].n_mol];
1280	+	int molIndex;
1281	+
1282	+	// initialize the molecule's stampID's
1283	+
1284	+	#ifdef IS_MPI
1285	+
1286	+
1287	+	molIndex = 0;
1288	+	for (i = 0; i < mpiSim->getTotNmol(); i++){
1289	+	if (mol2proc[i] == worldRank){
1290	+	the_molecules[molIndex].setStampID(molCompType[i]);
1291	+	the_molecules[molIndex].setMyIndex(molIndex);
1292	+	the_molecules[molIndex].setGlobalIndex(i);
1293	+	molIndex++;
1294	+	}
1295	+	}
1296	+
1297	+	#else // is_mpi
1298	+
1299	+	molIndex = 0;
1300	+	globalAtomIndex = 0;
1301	+	for (i = 0; i < n_components; i++){
1302	+	for (j = 0; j < components_nmol[i]; j++){
1303	+	the_molecules[molIndex].setStampID(i);
1304	+	the_molecules[molIndex].setMyIndex(molIndex);
1305	+	the_molecules[molIndex].setGlobalIndex(molIndex);
1306	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1307	+	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1308	+	globalAtomIndex++;
1309	+	}
1310	+	molIndex++;
1311	+	}
1312	+	}
1313	+
1314	+
1315	+	#endif // is_mpi
1316	+
1317	+
1318	+	if (info[l].n_SRI){
1319	+	Exclude::createArray(info[l].n_SRI);
1320	+	the_excludes = new Exclude * [info[l].n_SRI];
1321	+	for (int ex = 0; ex < info[l].n_SRI; ex++){
1322	+	the_excludes[ex] = new Exclude(ex);
1323	+	}
1324	+	info[l].globalExcludes = new int;
1325	+	info[l].n_exclude = info[l].n_SRI;
1326	+	}
1327	+	else{
1328	+	Exclude::createArray(1);
1329	+	the_excludes = new Exclude * ;
1330	+	the_excludes[0] = new Exclude(0);
1331	+	the_excludes[0]->setPair(0, 0);
1332	+	info[l].globalExcludes = new int;
1333	+	info[l].globalExcludes[0] = 0;
1334	+	info[l].n_exclude = 0;
1335	+	}
1336	+
1337	+	// set the arrays into the SimInfo object
1338	+
1339	+	info[l].atoms = the_atoms;
1340	+	info[l].molecules = the_molecules;
1341	+	info[l].nGlobalExcludes = 0;
1342	+	info[l].excludes = the_excludes;
1343	+
1344	+	the_ff->setSimInfo(info);
1345	+	}
1346	+	}
1347	+
1348	+	void SimSetup::makeIntegrator(void){
1349	+	int k;
1350	+
1351	+	NVT<RealIntegrator>* myNVT = NULL;
1352	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1353	+	NPTf<RealIntegrator>* myNPTf = NULL;
1354	+	NPTim<RealIntegrator>* myNPTim = NULL;
1355	+	NPTfm<RealIntegrator>* myNPTfm = NULL;
1356	+
1357	+	for (k = 0; k < nInfo; k++){
1358	+	switch (ensembleCase){
1359	+	case NVE_ENS:
1360	+	if (globals->haveZconstraints()){
1361	+	setupZConstraint(info[k]);
1362	+	new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1363	+	}
1364	+	else
1365	+	new NVE<RealIntegrator>(&(info[k]), the_ff);
1366	+	break;
1367	+
1368	+	case NVT_ENS:
1369	+	if (globals->haveZconstraints()){
1370	+	setupZConstraint(info[k]);
1371	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1372	+	}
1373	+	else
1374	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1375	+
1376	+	myNVT->setTargetTemp(globals->getTargetTemp());
1377	+
1378	+	if (globals->haveTauThermostat())
1379	+	myNVT->setTauThermostat(globals->getTauThermostat());
1380	+	else{
1381	+	sprintf(painCave.errMsg,
1382	+	"SimSetup error: If you use the NVT\n"
1383	+	"    ensemble, you must set tauThermostat.\n");
1384	+	painCave.isFatal = 1;
1385	+	simError();
1386	+	}
1387	+	break;
1388	+
1389	+	case NPTi_ENS:
1390	+	if (globals->haveZconstraints()){
1391	+	setupZConstraint(info[k]);
1392	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1393	+	}
1394	+	else
1395	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1396	+
1397	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1398	+
1399	+	if (globals->haveTargetPressure())
1400	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1401	+	else{
1402	+	sprintf(painCave.errMsg,
1403	+	"SimSetup error: If you use a constant pressure\n"
1404	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1405	+	painCave.isFatal = 1;
1406	+	simError();
1407	+	}
1408	+
1409	+	if (globals->haveTauThermostat())
1410	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1411	+	else{
1412	+	sprintf(painCave.errMsg,
1413	+	"SimSetup error: If you use an NPT\n"
1414	+	"    ensemble, you must set tauThermostat.\n");
1415	+	painCave.isFatal = 1;
1416	+	simError();
1417	+	}
1418	+
1419	+	if (globals->haveTauBarostat())
1420	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1421	+	else{
1422	+	sprintf(painCave.errMsg,
1423	+	"SimSetup error: If you use an NPT\n"
1424	+	"    ensemble, you must set tauBarostat.\n");
1425	+	painCave.isFatal = 1;
1426	+	simError();
1427	+	}
1428	+	break;
1429	+
1430	+	case NPTf_ENS:
1431	+	if (globals->haveZconstraints()){
1432	+	setupZConstraint(info[k]);
1433	+	myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff);
1434	+	}
1435	+	else
1436	+	myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff);
1437	+
1438	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1439	+
1440	+	if (globals->haveTargetPressure())
1441	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1442	+	else{
1443	+	sprintf(painCave.errMsg,
1444	+	"SimSetup error: If you use a constant pressure\n"
1445	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1446	+	painCave.isFatal = 1;
1447	+	simError();
1448	+	}
1449	+
1450	+	if (globals->haveTauThermostat())
1451	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1452	+	else{
1453	+	sprintf(painCave.errMsg,
1454	+	"SimSetup error: If you use an NPT\n"
1455	+	"    ensemble, you must set tauThermostat.\n");
1456	+	painCave.isFatal = 1;
1457	+	simError();
1458	+	}
1459	+
1460	+	if (globals->haveTauBarostat())
1461	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1462	+	else{
1463	+	sprintf(painCave.errMsg,
1464	+	"SimSetup error: If you use an NPT\n"
1465	+	"    ensemble, you must set tauBarostat.\n");
1466	+	painCave.isFatal = 1;
1467	+	simError();
1468	+	}
1469	+	break;
1470	+
1471	+	case NPTim_ENS:
1472	+	if (globals->haveZconstraints()){
1473	+	setupZConstraint(info[k]);
1474	+	myNPTim = new ZConstraint<NPTim<RealIntegrator> >(&(info[k]), the_ff);
1475	+	}
1476	+	else
1477	+	myNPTim = new NPTim<RealIntegrator>(&(info[k]), the_ff);
1478	+
1479	+	myNPTim->setTargetTemp(globals->getTargetTemp());
1480	+
1481	+	if (globals->haveTargetPressure())
1482	+	myNPTim->setTargetPressure(globals->getTargetPressure());
1483	+	else{
1484	+	sprintf(painCave.errMsg,
1485	+	"SimSetup error: If you use a constant pressure\n"
1486	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1487	+	painCave.isFatal = 1;
1488	+	simError();
1489	+	}
1490	+
1491	+	if (globals->haveTauThermostat())
1492	+	myNPTim->setTauThermostat(globals->getTauThermostat());
1493	+	else{
1494	+	sprintf(painCave.errMsg,
1495	+	"SimSetup error: If you use an NPT\n"
1496	+	"    ensemble, you must set tauThermostat.\n");
1497	+	painCave.isFatal = 1;
1498	+	simError();
1499	+	}
1500	+
1501	+	if (globals->haveTauBarostat())
1502	+	myNPTim->setTauBarostat(globals->getTauBarostat());
1503	+	else{
1504	+	sprintf(painCave.errMsg,
1505	+	"SimSetup error: If you use an NPT\n"
1506	+	"    ensemble, you must set tauBarostat.\n");
1507	+	painCave.isFatal = 1;
1508	+	simError();
1509	+	}
1510	+	break;
1511	+
1512	+	case NPTfm_ENS:
1513	+	if (globals->haveZconstraints()){
1514	+	setupZConstraint(info[k]);
1515	+	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff);
1516	+	}
1517	+	else
1518	+	myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff);
1519	+
1520	+	myNPTfm->setTargetTemp(globals->getTargetTemp());
1521	+
1522	+	if (globals->haveTargetPressure())
1523	+	myNPTfm->setTargetPressure(globals->getTargetPressure());
1524	+	else{
1525	+	sprintf(painCave.errMsg,
1526	+	"SimSetup error: If you use a constant pressure\n"
1527	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1528	+	painCave.isFatal = 1;
1529	+	simError();
1530	+	}
1531	+
1532	+	if (globals->haveTauThermostat())
1533	+	myNPTfm->setTauThermostat(globals->getTauThermostat());
1534	+	else{
1535	+	sprintf(painCave.errMsg,
1536	+	"SimSetup error: If you use an NPT\n"
1537	+	"    ensemble, you must set tauThermostat.\n");
1538	+	painCave.isFatal = 1;
1539	+	simError();
1540	+	}
1541	+
1542	+	if (globals->haveTauBarostat())
1543	+	myNPTfm->setTauBarostat(globals->getTauBarostat());
1544	+	else{
1545	+	sprintf(painCave.errMsg,
1546	+	"SimSetup error: If you use an NPT\n"
1547	+	"    ensemble, you must set tauBarostat.\n");
1548	+	painCave.isFatal = 1;
1549	+	simError();
1550	+	}
1551	+	break;
1552	+
1553	+	default:
1554	+	sprintf(painCave.errMsg,
1555	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1556	+	painCave.isFatal = 1;
1557	+	simError();
1558	+	}
1559	+	}
1560	+	}
1561	+
1562	+	void SimSetup::initFortran(void){
1563	+	info[0].refreshSim();
1564	+
1565	+	if (!strcmp(info[0].mixingRule, "standard")){
1566	+	the_ff->initForceField(LB_MIXING_RULE);
1567	+	}
1568	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1569	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1570	+	}
1571	+	else{
1572	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1573	+	info[0].mixingRule);
1574	+	painCave.isFatal = 1;
1575	+	simError();
1576	+	}
1577	+
1578	+
1579	+	#ifdef IS_MPI
1580	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1581	+	MPIcheckPoint();
1582	+	#endif // is_mpi
1583	+	}
1584	+
1585	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1586	+	int nZConstraints;
1587	+	ZconStamp** zconStamp;
1588	+
1589	+	if (globals->haveZconstraintTime()){
1590	+	//add sample time of z-constraint  into SimInfo's property list
1591	+	DoubleData* zconsTimeProp = new DoubleData();
1592	+	zconsTimeProp->setID(ZCONSTIME_ID);
1593	+	zconsTimeProp->setData(globals->getZconsTime());
1594	+	theInfo.addProperty(zconsTimeProp);
1595	+	}
1596	+	else{
1597	+	sprintf(painCave.errMsg,
1598	+	"ZConstraint error: If you use an ZConstraint\n"
1599	+	" , you must set sample time.\n");
1600	+	painCave.isFatal = 1;
1601	+	simError();
1602	+	}
1603	+
1604	+	//push zconsTol into siminfo, if user does not specify
1605	+	//value for zconsTol, a default value will be used
1606	+	DoubleData* zconsTol = new DoubleData();
1607	+	zconsTol->setID(ZCONSTOL_ID);
1608	+	if (globals->haveZconsTol()){
1609	+	zconsTol->setData(globals->getZconsTol());
1610	+	}
1611	+	else{
1612	+	double defaultZConsTol = 0.01;
1613	+	sprintf(painCave.errMsg,
1614	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1615	+	" , default value %f is used.\n",
1616	+	defaultZConsTol);
1617	+	painCave.isFatal = 0;
1618	+	simError();
1619	+
1620	+	zconsTol->setData(defaultZConsTol);
1621	+	}
1622	+	theInfo.addProperty(zconsTol);
1623	+
1624	+	//set Force Subtraction Policy
1625	+	StringData* zconsForcePolicy = new StringData();
1626	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1627	+
1628	+	if (globals->haveZconsForcePolicy()){
1629	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1630	+	}
1631	+	else{
1632	+	sprintf(painCave.errMsg,
1633	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1634	+	"PolicyByMass is used\n");
1635	+	painCave.isFatal = 0;
1636	+	simError();
1637	+	zconsForcePolicy->setData("BYMASS");
1638	+	}
1639	+
1640	+	theInfo.addProperty(zconsForcePolicy);
1641	+
1642	+	//Determine the name of ouput file and add it into SimInfo's property list
1643	+	//Be careful, do not use inFileName, since it is a pointer which
1644	+	//point to a string at master node, and slave nodes do not contain that string
1645	+
1646	+	string zconsOutput(theInfo.finalName);
1647	+
1648	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1649	+
1650	+	StringData* zconsFilename = new StringData();
1651	+	zconsFilename->setID(ZCONSFILENAME_ID);
1652	+	zconsFilename->setData(zconsOutput);
1653	+
1654	+	theInfo.addProperty(zconsFilename);
1655	+
1656	+	//setup index, pos and other parameters of z-constraint molecules
1657	+	nZConstraints = globals->getNzConstraints();
1658	+	theInfo.nZconstraints = nZConstraints;
1659	+
1660	+	zconStamp = globals->getZconStamp();
1661	+	ZConsParaItem tempParaItem;
1662	+
1663	+	ZConsParaData* zconsParaData = new ZConsParaData();
1664	+	zconsParaData->setID(ZCONSPARADATA_ID);
1665	+
1666	+	for (int i = 0; i < nZConstraints; i++){
1667	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1668	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1669	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1670	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1671	+
1672	+	zconsParaData->addItem(tempParaItem);
1673	+	}
1674	+
1675	+	//check the uniqueness of index
1676	+	if(!zconsParaData->isIndexUnique()){
1677	+	sprintf(painCave.errMsg,
1678	+	"ZConstraint Error: molIndex is not unique\n");
1679	+	painCave.isFatal = 1;
1680	+	simError();
1681	+	}
1682	+
1683	+	//sort the parameters by index of molecules
1684	+	zconsParaData->sortByIndex();
1685	+
1686	+	//push data into siminfo, therefore, we can retrieve later
1687	+	theInfo.addProperty(zconsParaData);
1688	+	}

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