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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 489 by mmeineke, Thu Apr 10 20:08:56 2003 UTC vs.
Revision 962 by tim, Mon Jan 19 18:36:21 2004 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	+	/**
34	+	* Check whether dividend is divisble by divisor or not
35	+	*/
36	+	bool isDivisible(double dividend, double divisor){
37	+	double tolerance = 0.000001;
38	+	double quotient;
39	+	double diff;
40	+	int intQuotient;
41	+
42	+	quotient = dividend / divisor;
43	+
44	+	if (quotient < 0)
45	+	quotient = -quotient;
46	+
47	+	intQuotient = int (quotient + tolerance);
48	+
49	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
50	+
51	+	if (diff <= tolerance)
52	+	return true;
53	+	else
54	+	return false;
55	+	}
56	+
57		SimSetup::SimSetup(){
58	+
59	+	initSuspend = false;
60	+	isInfoArray = 0;
61	+	nInfo = 1;
62	+
63		stamps = new MakeStamps();
64		globals = new Globals();
65	<
65	>
66	>
67		#ifdef IS_MPI
68	<	strcpy( checkPointMsg, "SimSetup creation successful" );
68	>	strcpy(checkPointMsg, "SimSetup creation successful");
69		MPIcheckPoint();
70		#endif // IS_MPI
71		}
#	Line 27 | Line 75 | void SimSetup::parseFile( char* fileName ){
75		delete globals;
76		}
77
78	<	void SimSetup::parseFile( char* fileName ){
78	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
79	>	info = the_info;
80	>	nInfo = theNinfo;
81	>	isInfoArray = 1;
82	>	initSuspend = true;
83	>	}
84
85	+
86	+	void SimSetup::parseFile(char* fileName){
87		#ifdef IS_MPI
88	<	if( worldRank == 0 ){
88	>	if (worldRank == 0){
89		#endif // is_mpi
90	<
90	>
91		inFileName = fileName;
92	<	set_interface_stamps( stamps, globals );
93	<
92	>	set_interface_stamps(stamps, globals);
93	>
94		#ifdef IS_MPI
95		mpiEventInit();
96		#endif
97
98	<	yacc_BASS( fileName );
98	>	yacc_BASS(fileName);
99
100		#ifdef IS_MPI
101		throwMPIEvent(NULL);
102		}
103	<	else receiveParse();
103	>	else{
104	>	receiveParse();
105	>	}
106		#endif
107
108		}
109
110		#ifdef IS_MPI
111		void SimSetup::receiveParse(void){
112	<
113	<	set_interface_stamps( stamps, globals );
114	<	mpiEventInit();
115	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
112	>	set_interface_stamps(stamps, globals);
113	>	mpiEventInit();
114	>	MPIcheckPoint();
115	>	mpiEventLoop();
116		}
117
118		#endif // is_mpi
119
120	<	void SimSetup::createSim( void ){
120	>	void SimSetup::createSim(void){
121
122	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	ExtendedSystem* the_extendedsystem;
70	<	int i, j;
122	>	// gather all of the information from the Bass file
123
124	<	// get the stamps and globals;
73	<	the_stamps = stamps;
74	<	the_globals = globals;
124	>	gatherInfo();
125
126	<	// 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();
126	>	// creation of complex system objects
127
128	<	// 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() );
128	>	sysObjectsCreation();
129
130	<	// 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	<	}
130	>	// check on the post processing info
131
132	<	if (the_globals->haveTauThermostat())
102	<	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
103	<	else if (the_globals->haveQmass())
104	<	the_extendedsystem->setQmass(the_globals->getQmass());
105	<	else {
106	<	sprintf( painCave.errMsg,
107	<	"SimSetup error: If you use one of the constant temperature\n"
108	<	"    ensembles, you must set either tauThermostat or qMass.\n"
109	<	"    Neither of these was found in the BASS file.\n");
110	<	painCave.isFatal = 1;
111	<	simError();
112	<	}
132	>	finalInfoCheck();
133
134	<	if (the_globals->haveTauBarostat())
115	<	the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
116	<	else {
117	<	sprintf( painCave.errMsg,
118	<	"SimSetup error: If you use the constant pressure\n"
119	<	"    ensemble, you must set tauBarostat.\n"
120	<	"    This was found in the BASS file.\n");
121	<	painCave.isFatal = 1;
122	<	simError();
123	<	}
134	>	// initialize the system coordinates
135
136	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
137	<	the_extendedsystem = new ExtendedSystem( simnfo );
127	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
136	>	if ( !initSuspend ){
137	>	initSystemCoords();
138
139	<	if (the_globals->haveTauThermostat())
140	<	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
131	<	else if (the_globals->haveQmass())
132	<	the_extendedsystem->setQmass(the_globals->getQmass());
133	<	else {
134	<	sprintf( painCave.errMsg,
135	<	"SimSetup error: If you use one of the constant temperature\n"
136	<	"    ensembles, you must set either tauThermostat or qMass.\n"
137	<	"    Neither of these was found in the BASS file.\n");
138	<	painCave.isFatal = 1;
139	<	simError();
140	<	}
141	<
142	<	} else if ( !strcasecmp( ensemble, "NVE") ) {
143	<	} else {
144	<	sprintf( painCave.errMsg,
145	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
146	<	"reverting to NVE for this simulation.\n",
147	<	ensemble );
148	<	painCave.isFatal = 0;
149	<	simError();
150	<	strcpy( ensemble, "NVE" );
139	>	if( !(globals->getUseInitTime()) )
140	>	info[0].currentTime = 0.0;
141		}
152	–	strcpy( simnfo->ensemble, ensemble );
142
143	<	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	<	}
143	>	// make the output filenames
144
145	<	#ifdef IS_MPI
172	<	strcpy( checkPointMsg, "ForceField creation successful" );
173	<	MPIcheckPoint();
174	<	#endif // is_mpi
145	>	makeOutNames();
146
147	<
147	>	// make the integrator
148
149	<	// get the components and calculate the tot_nMol and indvidual n_mol
179	<	the_components = the_globals->getComponents();
180	<	components_nmol = new int[n_components];
181	<	comp_stamps = new MoleculeStamp*[n_components];
149	>	makeIntegrator();
150
151	<	if( !the_globals->haveNMol() ){
152	<	// we don't have the total number of molecules, so we assume it is
153	<	// given in each component
151	>	#ifdef IS_MPI
152	>	mpiSim->mpiRefresh();
153	>	#endif
154
155	<	tot_nmol = 0;
188	<	for( i=0; i<n_components; i++ ){
155	>	// initialize the Fortran
156
157	<	if( !the_components[i]->haveNMol() ){
158	<	// 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	<	}
157	>	initFortran();
158	>	}
159
199	–	tot_nmol += the_components[i]->getNMol();
200	–	components_nmol[i] = the_components[i]->getNMol();
201	–	}
202	–	}
203	–	else{
204	–	sprintf( painCave.errMsg,
205	–	"SimSetup error.\n"
206	–	"\tSorry, the ability to specify total"
207	–	" nMols and then give molfractions in the components\n"
208	–	"\tis not currently supported."
209	–	" Please give nMol in the components.\n" );
210	–	painCave.isFatal = 1;
211	–	simError();
212	–
213	–
214	–	//     tot_nmol = the_globals->getNMol();
215	–
216	–	//   //we have the total number of molecules, now we check for molfractions
217	–	//     for( i=0; i<n_components; i++ ){
218	–
219	–	//       if( !the_components[i]->haveMolFraction() ){
220	–
221	–	//  if( !the_components[i]->haveNMol() ){
222	–	//    //we have a problem
223	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
224	–	//              << " nMol was given in component
225	–
226	–	}
160
161	<	#ifdef IS_MPI
162	<	strcpy( checkPointMsg, "Have the number of components" );
163	<	MPIcheckPoint();
164	<	#endif // is_mpi
161	>	void SimSetup::makeMolecules(void){
162	>	int k;
163	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
164	>	molInit molInfo;
165	>	DirectionalAtom* dAtom;
166	>	LinkedAssign* extras;
167	>	LinkedAssign* current_extra;
168	>	AtomStamp* currentAtom;
169	>	BondStamp* currentBond;
170	>	BendStamp* currentBend;
171	>	TorsionStamp* currentTorsion;
172
173	<	// make an array of molecule stamps that match the components used.
174	<	// also extract the used stamps out into a separate linked list
173	>	bond_pair* theBonds;
174	>	bend_set* theBends;
175	>	torsion_set* theTorsions;
176
236	–	simnfo->nComponents = n_components;
237	–	simnfo->componentsNmol = components_nmol;
238	–	simnfo->compStamps = comp_stamps;
239	–	simnfo->headStamp = new LinkedMolStamp();
240	–
241	–	char* id;
242	–	LinkedMolStamp* headStamp = simnfo->headStamp;
243	–	LinkedMolStamp* currentStamp = NULL;
244	–	for( i=0; i<n_components; i++ ){
177
178	<	id = the_components[i]->getType();
247	<	comp_stamps[i] = NULL;
248	<
249	<	// check to make sure the component isn't already in the list
178	>	//init the forceField paramters
179
180	<	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	<	}
180	>	the_ff->readParams();
181
271	–	#ifdef IS_MPI
272	–	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
273	–	MPIcheckPoint();
274	–	#endif // is_mpi
275	–
182
183	+	// init the atoms
184
185	+	double ux, uy, uz, u, uSqr;
186
187	<	// caclulate the number of atoms, bonds, bends and torsions
187	>	for (k = 0; k < nInfo; k++){
188	>	the_ff->setSimInfo(&(info[k]));
189
190	<	tot_atoms = 0;
191	<	tot_bonds = 0;
192	<	tot_bends = 0;
193	<	tot_torsions = 0;
285	<	for( i=0; i<n_components; i++ ){
286	<
287	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
288	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
289	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
290	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
291	<	}
190	>	atomOffset = 0;
191	>	excludeOffset = 0;
192	>	for (i = 0; i < info[k].n_mol; i++){
193	>	stampID = info[k].molecules[i].getStampID();
194
195	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
195	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
196	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
197	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
198	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
199	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
200
201	<	simnfo->n_atoms = tot_atoms;
202	<	simnfo->n_bonds = tot_bonds;
203	<	simnfo->n_bends = tot_bends;
204	<	simnfo->n_torsions = tot_torsions;
205	<	simnfo->n_SRI = tot_SRI;
300	<	simnfo->n_mol = tot_nmol;
201	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
202	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
203	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
204	>	molInfo.myBends = new Bend * [molInfo.nBends];
205	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
206
207	<
208	<	#ifdef IS_MPI
207	>	theBonds = new bond_pair[molInfo.nBonds];
208	>	theBends = new bend_set[molInfo.nBends];
209	>	theTorsions = new torsion_set[molInfo.nTorsions];
210
211	<	// divide the molecules among processors here.
306	<
307	<	mpiSim = new mpiSimulation( simnfo );
308	<
309	<
211	>	// make the Atoms
212
213	<	globalIndex = mpiSim->divideLabor();
213	>	for (j = 0; j < molInfo.nAtoms; j++){
214	>	currentAtom = comp_stamps[stampID]->getAtom(j);
215	>	if (currentAtom->haveOrientation()){
216	>	dAtom = new DirectionalAtom((j + atomOffset),
217	>	info[k].getConfiguration());
218	>	info[k].n_oriented++;
219	>	molInfo.myAtoms[j] = dAtom;
220
221	<	// set up the local variables
222	<
223	<	int localMol, allMol;
316	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
221	>	ux = currentAtom->getOrntX();
222	>	uy = currentAtom->getOrntY();
223	>	uz = currentAtom->getOrntZ();
224
225	<	int* mol2proc = mpiSim->getMolToProcMap();
319	<	int* molCompType = mpiSim->getMolComponentType();
320	<
321	<	allMol = 0;
322	<	localMol = 0;
323	<	local_atoms = 0;
324	<	local_bonds = 0;
325	<	local_bends = 0;
326	<	local_torsions = 0;
327	<	for( i=0; i<n_components; i++ ){
225	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
226
227	<	for( j=0; j<components_nmol[i]; j++ ){
228	<
229	<	if( mol2proc[allMol] == worldRank ){
230	<
333	<	local_atoms +=    comp_stamps[i]->getNAtoms();
334	<	local_bonds +=    comp_stamps[i]->getNBonds();
335	<	local_bends +=    comp_stamps[i]->getNBends();
336	<	local_torsions += comp_stamps[i]->getNTorsions();
337	<	localMol++;
338	<	}
339	<	allMol++;
340	<	}
341	<	}
342	<	local_SRI = local_bonds + local_bends + local_torsions;
343	<
227	>	u = sqrt(uSqr);
228	>	ux = ux / u;
229	>	uy = uy / u;
230	>	uz = uz / u;
231
232	<	simnfo->n_atoms = mpiSim->getMyNlocal();
233	<
234	<	if( local_atoms != simnfo->n_atoms ){
235	<	sprintf( painCave.errMsg,
236	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
237	<	" localAtom (%d) are not equal.\n",
238	<	simnfo->n_atoms,
239	<	local_atoms );
240	<	painCave.isFatal = 1;
354	<	simError();
355	<	}
232	>	dAtom->setSUx(ux);
233	>	dAtom->setSUy(uy);
234	>	dAtom->setSUz(uz);
235	>	}
236	>	else{
237	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
238	>	info[k].getConfiguration());
239	>	}
240	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
241
242	<	simnfo->n_bonds = local_bonds;
358	<	simnfo->n_bends = local_bends;
359	<	simnfo->n_torsions = local_torsions;
360	<	simnfo->n_SRI = local_SRI;
361	<	simnfo->n_mol = localMol;
242	>	#ifdef IS_MPI
243
244	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
245	<	MPIcheckPoint();
365	<
366	<
244	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
245	>
246		#endif // is_mpi
247	<
247	>	}
248
249	<	// create the atom and short range interaction arrays
249	>	// make the bonds
250	>	for (j = 0; j < molInfo.nBonds; j++){
251	>	currentBond = comp_stamps[stampID]->getBond(j);
252	>	theBonds[j].a = currentBond->getA() + atomOffset;
253	>	theBonds[j].b = currentBond->getB() + atomOffset;
254
255	<	Atom::createArrays(simnfo->n_atoms);
256	<	the_atoms = new Atom*[simnfo->n_atoms];
374	<	the_molecules = new Molecule[simnfo->n_mol];
375	<	int molIndex;
255	>	exI = theBonds[j].a;
256	>	exJ = theBonds[j].b;
257
258	<	// initialize the molecule's stampID's
259	<
258	>	// exclude_I must always be the smaller of the pair
259	>	if (exI > exJ){
260	>	tempEx = exI;
261	>	exI = exJ;
262	>	exJ = tempEx;
263	>	}
264		#ifdef IS_MPI
265	<
265	>	tempEx = exI;
266	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
267	>	tempEx = exJ;
268	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
269
270	<	molIndex = 0;
271	<	for(i=0; i<mpiSim->getTotNmol(); i++){
384	<
385	<	if(mol2proc[i] == worldRank ){
386	<	the_molecules[molIndex].setStampID( molCompType[i] );
387	<	the_molecules[molIndex].setMyIndex( molIndex );
388	<	the_molecules[molIndex].setGlobalIndex( i );
389	<	molIndex++;
390	<	}
391	<	}
270	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
271	>	#else  // isn't MPI
272
273	<	#else // is_mpi
274	<
275	<	molIndex = 0;
276	<	for(i=0; i<n_components; i++){
397	<	for(j=0; j<components_nmol[i]; j++ ){
398	<	the_molecules[molIndex].setStampID( i );
399	<	the_molecules[molIndex].setMyIndex( molIndex );
400	<	the_molecules[molIndex].setGlobalIndex( molIndex );
401	<	molIndex++;
402	<	}
403	<	}
404	<
273	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
274	>	#endif  //is_mpi
275	>	}
276	>	excludeOffset += molInfo.nBonds;
277
278	<	#endif // is_mpi
278	>	//make the bends
279	>	for (j = 0; j < molInfo.nBends; j++){
280	>	currentBend = comp_stamps[stampID]->getBend(j);
281	>	theBends[j].a = currentBend->getA() + atomOffset;
282	>	theBends[j].b = currentBend->getB() + atomOffset;
283	>	theBends[j].c = currentBend->getC() + atomOffset;
284
285	+	if (currentBend->haveExtras()){
286	+	extras = currentBend->getExtras();
287	+	current_extra = extras;
288
289	<	if( simnfo->n_SRI ){
290	<
291	<	Exclude::createArray(simnfo->n_SRI);
292	<	the_excludes = new Exclude*[simnfo->n_SRI];
293	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
294	<	simnfo->globalExcludes = new int;
295	<	simnfo->n_exclude = simnfo->n_SRI;
416	<	}
417	<	else{
418	<
419	<	Exclude::createArray( 1 );
420	<	the_excludes = new Exclude*;
421	<	the_excludes[0] = new Exclude(0);
422	<	the_excludes[0]->setPair( 0,0 );
423	<	simnfo->globalExcludes = new int;
424	<	simnfo->globalExcludes[0] = 0;
425	<	simnfo->n_exclude = 0;
426	<	}
289	>	while (current_extra != NULL){
290	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
291	>	switch (current_extra->getType()){
292	>	case 0:
293	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
294	>	theBends[j].isGhost = 1;
295	>	break;
296
297	<	// set the arrays into the SimInfo object
297	>	case 1:
298	>	theBends[j].ghost = (int) current_extra->getDouble() +
299	>	atomOffset;
300	>	theBends[j].isGhost = 1;
301	>	break;
302
303	<	simnfo->atoms = the_atoms;
304	<	simnfo->molecules = the_molecules;
305	<	simnfo->nGlobalExcludes = 0;
306	<	simnfo->excludes = the_excludes;
303	>	default:
304	>	sprintf(painCave.errMsg,
305	>	"SimSetup Error: ghostVectorSource was neither a "
306	>	"double nor an int.\n"
307	>	"-->Bend[%d] in %s\n",
308	>	j, comp_stamps[stampID]->getID());
309	>	painCave.isFatal = 1;
310	>	simError();
311	>	}
312	>	}
313	>	else{
314	>	sprintf(painCave.errMsg,
315	>	"SimSetup Error: unhandled bend assignment:\n"
316	>	"    -->%s in Bend[%d] in %s\n",
317	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
318	>	painCave.isFatal = 1;
319	>	simError();
320	>	}
321
322	+	current_extra = current_extra->getNext();
323	+	}
324	+	}
325
326	<	// get some of the tricky things that may still be in the globals
326	>	if (!theBends[j].isGhost){
327	>	exI = theBends[j].a;
328	>	exJ = theBends[j].c;
329	>	}
330	>	else{
331	>	exI = theBends[j].a;
332	>	exJ = theBends[j].b;
333	>	}
334
335	<
336	<	if( the_globals->haveBox() ){
337	<	simnfo->box_x = the_globals->getBox();
338	<	simnfo->box_y = the_globals->getBox();
339	<	simnfo->box_z = the_globals->getBox();
340	<	}
341	<	else if( the_globals->haveDensity() ){
335	>	// exclude_I must always be the smaller of the pair
336	>	if (exI > exJ){
337	>	tempEx = exI;
338	>	exI = exJ;
339	>	exJ = tempEx;
340	>	}
341	>	#ifdef IS_MPI
342	>	tempEx = exI;
343	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
344	>	tempEx = exJ;
345	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
346
347	<	double vol;
348	<	vol = (double)tot_nmol / the_globals->getDensity();
349	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
350	<	simnfo->box_y = simnfo->box_x;
351	<	simnfo->box_z = simnfo->box_x;
352	<	}
452	<	else{
453	<	if( !the_globals->haveBoxX() ){
454	<	sprintf( painCave.errMsg,
455	<	"SimSetup error, no periodic BoxX size given.\n" );
456	<	painCave.isFatal = 1;
457	<	simError();
458	<	}
459	<	simnfo->box_x = the_globals->getBoxX();
347	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
348	>	#else  // isn't MPI
349	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
350	>	#endif  //is_mpi
351	>	}
352	>	excludeOffset += molInfo.nBends;
353
354	<	if( !the_globals->haveBoxY() ){
355	<	sprintf( painCave.errMsg,
356	<	"SimSetup error, no periodic BoxY size given.\n" );
357	<	painCave.isFatal = 1;
358	<	simError();
359	<	}
467	<	simnfo->box_y = the_globals->getBoxY();
354	>	for (j = 0; j < molInfo.nTorsions; j++){
355	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
356	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
357	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
358	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
359	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
360
361	<	if( !the_globals->haveBoxZ() ){
362	<	sprintf( painCave.errMsg,
471	<	"SimSetup error, no periodic BoxZ size given.\n" );
472	<	painCave.isFatal = 1;
473	<	simError();
474	<	}
475	<	simnfo->box_z = the_globals->getBoxZ();
476	<	}
361	>	exI = theTorsions[j].a;
362	>	exJ = theTorsions[j].d;
363
364	+	// exclude_I must always be the smaller of the pair
365	+	if (exI > exJ){
366	+	tempEx = exI;
367	+	exI = exJ;
368	+	exJ = tempEx;
369	+	}
370		#ifdef IS_MPI
371	<	strcpy( checkPointMsg, "Box size set up" );
372	<	MPIcheckPoint();
373	<	#endif // is_mpi
371	>	tempEx = exI;
372	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
373	>	tempEx = exJ;
374	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
375
376	<
377	<	// initialize the arrays
378	<
379	<	the_ff->setSimInfo( simnfo );
487	<
488	<	makeMolecules();
489	<	simnfo->identArray = new int[simnfo->n_atoms];
490	<	simnfo->molMembershipArray = new int[simnfo->n_atoms];
491	<	for(i=0; i<simnfo->n_atoms; i++){
492	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
493	<	}
494	<	for(i=0; i< simnfo->n_mol; i++) {
495	<	the_molecules[i].atomicRollCall(simnfo->molMembershipArray);
496	<	}
497	<
498	<	if (the_globals->getUseRF() ) {
499	<	simnfo->useReactionField = 1;
500	<
501	<	if( !the_globals->haveECR() ){
502	<	sprintf( painCave.errMsg,
503	<	"SimSetup Warning: using default value of 1/2 the smallest "
504	<	"box length for the electrostaticCutoffRadius.\n"
505	<	"I hope you have a very fast processor!\n");
506	<	painCave.isFatal = 0;
507	<	simError();
508	<	double smallest;
509	<	smallest = simnfo->box_x;
510	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
511	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
512	<	simnfo->ecr = 0.5 * smallest;
513	<	} else {
514	<	simnfo->ecr        = the_globals->getECR();
515	<	}
516	<
517	<	if( !the_globals->haveEST() ){
518	<	sprintf( painCave.errMsg,
519	<	"SimSetup Warning: using default value of 0.05 * the "
520	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
521	<	);
522	<	painCave.isFatal = 0;
523	<	simError();
524	<	simnfo->est = 0.05 * simnfo->ecr;
525	<	} else {
526	<	simnfo->est        = the_globals->getEST();
527	<	}
528	<
529	<	if(!the_globals->haveDielectric() ){
530	<	sprintf( painCave.errMsg,
531	<	"SimSetup Error: You are trying to use Reaction Field without"
532	<	"setting a dielectric constant!\n"
533	<	);
534	<	painCave.isFatal = 1;
535	<	simError();
536	<	}
537	<	simnfo->dielectric = the_globals->getDielectric();
538	<	} else {
539	<	if (usesDipoles) {
540	<
541	<	if( !the_globals->haveECR() ){
542	<	sprintf( painCave.errMsg,
543	<	"SimSetup Warning: using default value of 1/2 the smallest "
544	<	"box length for the electrostaticCutoffRadius.\n"
545	<	"I hope you have a very fast processor!\n");
546	<	painCave.isFatal = 0;
547	<	simError();
548	<	double smallest;
549	<	smallest = simnfo->box_x;
550	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
551	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
552	<	simnfo->ecr = 0.5 * smallest;
553	<	} else {
554	<	simnfo->ecr        = the_globals->getECR();
376	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
377	>	#else  // isn't MPI
378	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
379	>	#endif  //is_mpi
380		}
381	<
557	<	if( !the_globals->haveEST() ){
558	<	sprintf( painCave.errMsg,
559	<	"SimSetup Warning: using default value of 5%% of the "
560	<	"electrostaticCutoffRadius for the "
561	<	"electrostaticSkinThickness\n"
562	<	);
563	<	painCave.isFatal = 0;
564	<	simError();
565	<	simnfo->est = 0.05 * simnfo->ecr;
566	<	} else {
567	<	simnfo->est        = the_globals->getEST();
568	<	}
569	<	}
570	<	}
381	>	excludeOffset += molInfo.nTorsions;
382
572	–	#ifdef IS_MPI
573	–	strcpy( checkPointMsg, "electrostatic parameters check out" );
574	–	MPIcheckPoint();
575	–	#endif // is_mpi
383
384	<	if( the_globals->haveInitialConfig() ){
578	<
579	<	InitializeFromFile* fileInit;
580	<	#ifdef IS_MPI // is_mpi
581	<	if( worldRank == 0 ){
582	<	#endif //is_mpi
583	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
584	<	#ifdef IS_MPI
585	<	}else fileInit = new InitializeFromFile( NULL );
586	<	#endif
587	<	fileInit->read_xyz( simnfo ); // default velocities on
384	>	// send the arrays off to the forceField for init.
385
386	<	delete fileInit;
387	<	}
388	<	else{
386	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
387	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
388	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
389	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
390	>	theTorsions);
391
593	–	#ifdef IS_MPI
392
393	<	// no init from bass
596	<
597	<	sprintf( painCave.errMsg,
598	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
599	<	painCave.isFatal;
600	<	simError();
601	<
602	<	#else
393	>	info[k].molecules[i].initialize(molInfo);
394
604	–	initFromBass();
395
396	+	atomOffset += molInfo.nAtoms;
397	+	delete[] theBonds;
398	+	delete[] theBends;
399	+	delete[] theTorsions;
400	+	}
401	+	}
402
607	–	#endif
608	–	}
609	–
403		#ifdef IS_MPI
404	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
404	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
405		MPIcheckPoint();
406		#endif // is_mpi
407
408	+	// clean up the forcefield
409
410	<
411	<
412	<
410	>	the_ff->calcRcut();
411	>	the_ff->cleanMe();
412	>	}
413
414	<
415	<	#ifdef IS_MPI
416	<	if( worldRank == 0 ){
417	<	#endif // is_mpi
418	<
419	<	if( the_globals->haveFinalConfig() ){
420	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
414	>	void SimSetup::initFromBass(void){
415	>	int i, j, k;
416	>	int n_cells;
417	>	double cellx, celly, cellz;
418	>	double temp1, temp2, temp3;
419	>	int n_per_extra;
420	>	int n_extra;
421	>	int have_extra, done;
422	>
423	>	double vel[3];
424	>	vel[0] = 0.0;
425	>	vel[1] = 0.0;
426	>	vel[2] = 0.0;
427	>
428	>	temp1 = (double) tot_nmol / 4.0;
429	>	temp2 = pow(temp1, (1.0 / 3.0));
430	>	temp3 = ceil(temp2);
431	>
432	>	have_extra = 0;
433	>	if (temp2 < temp3){
434	>	// we have a non-complete lattice
435	>	have_extra = 1;
436	>
437	>	n_cells = (int) temp3 - 1;
438	>	cellx = info[0].boxL[0] / temp3;
439	>	celly = info[0].boxL[1] / temp3;
440	>	cellz = info[0].boxL[2] / temp3;
441	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
442	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
443	>	n_per_extra = (int) ceil(temp1);
444	>
445	>	if (n_per_extra > 4){
446	>	sprintf(painCave.errMsg,
447	>	"SimSetup error. There has been an error in constructing"
448	>	" the non-complete lattice.\n");
449	>	painCave.isFatal = 1;
450	>	simError();
451		}
628	–	else{
629	–	strcpy( simnfo->finalName, inFileName );
630	–	char* endTest;
631	–	int nameLength = strlen( simnfo->finalName );
632	–	endTest = &(simnfo->finalName[nameLength - 5]);
633	–	if( !strcmp( endTest, ".bass" ) ){
634	–	strcpy( endTest, ".eor" );
635	–	}
636	–	else if( !strcmp( endTest, ".BASS" ) ){
637	–	strcpy( endTest, ".eor" );
638	–	}
639	–	else{
640	–	endTest = &(simnfo->finalName[nameLength - 4]);
641	–	if( !strcmp( endTest, ".bss" ) ){
642	–	strcpy( endTest, ".eor" );
643	–	}
644	–	else if( !strcmp( endTest, ".mdl" ) ){
645	–	strcpy( endTest, ".eor" );
646	–	}
647	–	else{
648	–	strcat( simnfo->finalName, ".eor" );
649	–	}
650	–	}
651	–	}
652	–
653	–	// make the sample and status out names
654	–
655	–	strcpy( simnfo->sampleName, inFileName );
656	–	char* endTest;
657	–	int nameLength = strlen( simnfo->sampleName );
658	–	endTest = &(simnfo->sampleName[nameLength - 5]);
659	–	if( !strcmp( endTest, ".bass" ) ){
660	–	strcpy( endTest, ".dump" );
661	–	}
662	–	else if( !strcmp( endTest, ".BASS" ) ){
663	–	strcpy( endTest, ".dump" );
664	–	}
665	–	else{
666	–	endTest = &(simnfo->sampleName[nameLength - 4]);
667	–	if( !strcmp( endTest, ".bss" ) ){
668	–	strcpy( endTest, ".dump" );
669	–	}
670	–	else if( !strcmp( endTest, ".mdl" ) ){
671	–	strcpy( endTest, ".dump" );
672	–	}
673	–	else{
674	–	strcat( simnfo->sampleName, ".dump" );
675	–	}
676	–	}
677	–
678	–	strcpy( simnfo->statusName, inFileName );
679	–	nameLength = strlen( simnfo->statusName );
680	–	endTest = &(simnfo->statusName[nameLength - 5]);
681	–	if( !strcmp( endTest, ".bass" ) ){
682	–	strcpy( endTest, ".stat" );
683	–	}
684	–	else if( !strcmp( endTest, ".BASS" ) ){
685	–	strcpy( endTest, ".stat" );
686	–	}
687	–	else{
688	–	endTest = &(simnfo->statusName[nameLength - 4]);
689	–	if( !strcmp( endTest, ".bss" ) ){
690	–	strcpy( endTest, ".stat" );
691	–	}
692	–	else if( !strcmp( endTest, ".mdl" ) ){
693	–	strcpy( endTest, ".stat" );
694	–	}
695	–	else{
696	–	strcat( simnfo->statusName, ".stat" );
697	–	}
698	–	}
699	–
700	–	#ifdef IS_MPI
452		}
702	–	#endif // is_mpi
703	–
704	–	// set the status, sample, and themal kick times
705	–
706	–	if( the_globals->haveSampleTime() ){
707	–	simnfo->sampleTime = the_globals->getSampleTime();
708	–	simnfo->statusTime = simnfo->sampleTime;
709	–	simnfo->thermalTime = simnfo->sampleTime;
710	–	}
453		else{
454	<	simnfo->sampleTime = the_globals->getRunTime();
455	<	simnfo->statusTime = simnfo->sampleTime;
456	<	simnfo->thermalTime = simnfo->sampleTime;
454	>	n_cells = (int) temp3;
455	>	cellx = info[0].boxL[0] / temp3;
456	>	celly = info[0].boxL[1] / temp3;
457	>	cellz = info[0].boxL[2] / temp3;
458		}
459
460	<	if( the_globals->haveStatusTime() ){
461	<	simnfo->statusTime = the_globals->getStatusTime();
462	<	}
460	>	current_mol = 0;
461	>	current_comp_mol = 0;
462	>	current_comp = 0;
463	>	current_atom_ndx = 0;
464
465	<	if( the_globals->haveThermalTime() ){
466	<	simnfo->thermalTime = the_globals->getThermalTime();
467	<	}
465	>	for (i = 0; i < n_cells ; i++){
466	>	for (j = 0; j < n_cells; j++){
467	>	for (k = 0; k < n_cells; k++){
468	>	makeElement(i * cellx, j * celly, k * cellz);
469
470	<	// check for the temperature set flag
470	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
471
472	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
472	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
473
474	+	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
475	+	}
476	+	}
477	+	}
478
479	<	//   // make the longe range forces and the integrator
479	>	if (have_extra){
480	>	done = 0;
481
482	<	//   new AllLong( simnfo );
482	>	int start_ndx;
483	>	for (i = 0; i < (n_cells + 1) && !done; i++){
484	>	for (j = 0; j < (n_cells + 1) && !done; j++){
485	>	if (i < n_cells){
486	>	if (j < n_cells){
487	>	start_ndx = n_cells;
488	>	}
489	>	else
490	>	start_ndx = 0;
491	>	}
492	>	else
493	>	start_ndx = 0;
494
495	+	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
496	+	makeElement(i * cellx, j * celly, k * cellz);
497	+	done = (current_mol >= tot_nmol);
498
499	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
500	<	new Symplectic(simnfo, the_ff, the_extendedsystem);
501	<	}
502	<	else if( !strcmp( force_field, "LJ" ) ){
503	<	new Verlet( *simnfo, the_ff, the_extendedsystem );
740	<	}
741	<	else {
742	<	std::cerr << "I'm a bug.\n";
743	<	fprintf( stderr, "Ima bug. stderr %s\n", force_field);
744	<	}
745	<	#ifdef IS_MPI
746	<	mpiSim->mpiRefresh();
747	<	#endif
499	>	if (!done && n_per_extra > 1){
500	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
501	>	k * cellz);
502	>	done = (current_mol >= tot_nmol);
503	>	}
504
505	<	// initialize the Fortran
505	>	if (!done && n_per_extra > 2){
506	>	makeElement(i * cellx, j * celly + 0.5 * celly,
507	>	k * cellz + 0.5 * cellz);
508	>	done = (current_mol >= tot_nmol);
509	>	}
510
511	<
512	<	simnfo->refreshSim();
513	<
514	<	if( !strcmp( simnfo->mixingRule, "standard") ){
515	<	the_ff->initForceField( LB_MIXING_RULE );
511	>	if (!done && n_per_extra > 3){
512	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
513	>	k * cellz + 0.5 * cellz);
514	>	done = (current_mol >= tot_nmol);
515	>	}
516	>	}
517	>	}
518	>	}
519		}
757	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
758	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
759	–	}
760	–	else{
761	–	sprintf( painCave.errMsg,
762	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
763	–	simnfo->mixingRule );
764	–	painCave.isFatal = 1;
765	–	simError();
766	–	}
520
521	<
522	<	#ifdef IS_MPI
523	<	strcpy( checkPointMsg,
771	<	"Successfully intialized the mixingRule for Fortran." );
772	<	MPIcheckPoint();
773	<	#endif // is_mpi
521	>	for (i = 0; i < info[0].n_atoms; i++){
522	>	info[0].atoms[i]->setVel(vel);
523	>	}
524		}
525
526	<
527	<	void SimSetup::makeMolecules( void ){
528	<
779	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
780	<	molInit info;
526	>	void SimSetup::makeElement(double x, double y, double z){
527	>	int k;
528	>	AtomStamp* current_atom;
529		DirectionalAtom* dAtom;
530	<	LinkedAssign* extras;
531	<	LinkedAssign* current_extra;
784	<	AtomStamp* currentAtom;
785	<	BondStamp* currentBond;
786	<	BendStamp* currentBend;
787	<	TorsionStamp* currentTorsion;
530	>	double rotMat[3][3];
531	>	double pos[3];
532
533	<	bond_pair* theBonds;
534	<	bend_set* theBends;
535	<	torsion_set* theTorsions;
533	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
534	>	current_atom = comp_stamps[current_comp]->getAtom(k);
535	>	if (!current_atom->havePosition()){
536	>	sprintf(painCave.errMsg,
537	>	"SimSetup:initFromBass error.\n"
538	>	"\tComponent %s, atom %s does not have a position specified.\n"
539	>	"\tThe initialization routine is unable to give a start"
540	>	" position.\n",
541	>	comp_stamps[current_comp]->getID(), current_atom->getType());
542	>	painCave.isFatal = 1;
543	>	simError();
544	>	}
545
546	<
547	<	//init the forceField paramters
546	>	pos[0] = x + current_atom->getPosX();
547	>	pos[1] = y + current_atom->getPosY();
548	>	pos[2] = z + current_atom->getPosZ();
549
550	<	the_ff->readParams();
550	>	info[0].atoms[current_atom_ndx]->setPos(pos);
551
552	<
553	<	// init the atoms
552	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
553	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
554
555	<	double ux, uy, uz, u, uSqr;
556	<
557	<	atomOffset = 0;
804	<	excludeOffset = 0;
805	<	for(i=0; i<simnfo->n_mol; i++){
806	<
807	<	stampID = the_molecules[i].getStampID();
555	>	rotMat[0][0] = 1.0;
556	>	rotMat[0][1] = 0.0;
557	>	rotMat[0][2] = 0.0;
558
559	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
560	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
561	<	info.nBends    = comp_stamps[stampID]->getNBends();
812	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
813	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
559	>	rotMat[1][0] = 0.0;
560	>	rotMat[1][1] = 1.0;
561	>	rotMat[1][2] = 0.0;
562
563	<	info.myAtoms = &the_atoms[atomOffset];
564	<	info.myExcludes = &the_excludes[excludeOffset];
565	<	info.myBonds = new Bond*[info.nBonds];
818	<	info.myBends = new Bend*[info.nBends];
819	<	info.myTorsions = new Torsion*[info.nTorsions];
563	>	rotMat[2][0] = 0.0;
564	>	rotMat[2][1] = 0.0;
565	>	rotMat[2][2] = 1.0;
566
567	<	theBonds = new bond_pair[info.nBonds];
822	<	theBends = new bend_set[info.nBends];
823	<	theTorsions = new torsion_set[info.nTorsions];
824	<
825	<	// make the Atoms
826	<
827	<	for(j=0; j<info.nAtoms; j++){
828	<
829	<	currentAtom = comp_stamps[stampID]->getAtom( j );
830	<	if( currentAtom->haveOrientation() ){
831	<
832	<	dAtom = new DirectionalAtom(j + atomOffset);
833	<	simnfo->n_oriented++;
834	<	info.myAtoms[j] = dAtom;
835	<
836	<	ux = currentAtom->getOrntX();
837	<	uy = currentAtom->getOrntY();
838	<	uz = currentAtom->getOrntZ();
839	<
840	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
841	<
842	<	u = sqrt( uSqr );
843	<	ux = ux / u;
844	<	uy = uy / u;
845	<	uz = uz / u;
846	<
847	<	dAtom->setSUx( ux );
848	<	dAtom->setSUy( uy );
849	<	dAtom->setSUz( uz );
850	<	}
851	<	else{
852	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
853	<	}
854	<	info.myAtoms[j]->setType( currentAtom->getType() );
855	<
856	<	#ifdef IS_MPI
857	<
858	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
859	<
860	<	#endif // is_mpi
861	<	}
862	<
863	<	// make the bonds
864	<	for(j=0; j<info.nBonds; j++){
865	<
866	<	currentBond = comp_stamps[stampID]->getBond( j );
867	<	theBonds[j].a = currentBond->getA() + atomOffset;
868	<	theBonds[j].b = currentBond->getB() + atomOffset;
869	<
870	<	exI = theBonds[j].a;
871	<	exJ = theBonds[j].b;
872	<
873	<	// exclude_I must always be the smaller of the pair
874	<	if( exI > exJ ){
875	<	tempEx = exI;
876	<	exI = exJ;
877	<	exJ = tempEx;
878	<	}
879	<	#ifdef IS_MPI
880	<	tempEx = exI;
881	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
882	<	tempEx = exJ;
883	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
884	<
885	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
886	<	#else  // isn't MPI
887	<
888	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
889	<	#endif  //is_mpi
567	>	dAtom->setA(rotMat);
568		}
891	–	excludeOffset += info.nBonds;
569
570	<	//make the bends
571	<	for(j=0; j<info.nBends; j++){
895	<
896	<	currentBend = comp_stamps[stampID]->getBend( j );
897	<	theBends[j].a = currentBend->getA() + atomOffset;
898	<	theBends[j].b = currentBend->getB() + atomOffset;
899	<	theBends[j].c = currentBend->getC() + atomOffset;
900	<
901	<	if( currentBend->haveExtras() ){
902	<
903	<	extras = currentBend->getExtras();
904	<	current_extra = extras;
905	<
906	<	while( current_extra != NULL ){
907	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
908	<
909	<	switch( current_extra->getType() ){
910	<
911	<	case 0:
912	<	theBends[j].ghost =
913	<	current_extra->getInt() + atomOffset;
914	<	theBends[j].isGhost = 1;
915	<	break;
916	<
917	<	case 1:
918	<	theBends[j].ghost =
919	<	(int)current_extra->getDouble() + atomOffset;
920	<	theBends[j].isGhost = 1;
921	<	break;
922	<
923	<	default:
924	<	sprintf( painCave.errMsg,
925	<	"SimSetup Error: ghostVectorSource was neither a "
926	<	"double nor an int.\n"
927	<	"-->Bend[%d] in %s\n",
928	<	j, comp_stamps[stampID]->getID() );
929	<	painCave.isFatal = 1;
930	<	simError();
931	<	}
932	<	}
933	<
934	<	else{
935	<
936	<	sprintf( painCave.errMsg,
937	<	"SimSetup Error: unhandled bend assignment:\n"
938	<	"    -->%s in Bend[%d] in %s\n",
939	<	current_extra->getlhs(),
940	<	j, comp_stamps[stampID]->getID() );
941	<	painCave.isFatal = 1;
942	<	simError();
943	<	}
944	<
945	<	current_extra = current_extra->getNext();
946	<	}
947	<	}
948	<
949	<	if( !theBends[j].isGhost ){
950	<
951	<	exI = theBends[j].a;
952	<	exJ = theBends[j].c;
953	<	}
954	<	else{
955	<
956	<	exI = theBends[j].a;
957	<	exJ = theBends[j].b;
958	<	}
959	<
960	<	// exclude_I must always be the smaller of the pair
961	<	if( exI > exJ ){
962	<	tempEx = exI;
963	<	exI = exJ;
964	<	exJ = tempEx;
965	<	}
966	<	#ifdef IS_MPI
967	<	tempEx = exI;
968	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
969	<	tempEx = exJ;
970	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
971	<
972	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
973	<	#else  // isn't MPI
974	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
975	<	#endif  //is_mpi
976	<	}
977	<	excludeOffset += info.nBends;
570	>	current_atom_ndx++;
571	>	}
572
573	<	for(j=0; j<info.nTorsions; j++){
574	<
981	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
982	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
983	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
984	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
985	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
986	<
987	<	exI = theTorsions[j].a;
988	<	exJ = theTorsions[j].d;
573	>	current_mol++;
574	>	current_comp_mol++;
575
576	<	// exclude_I must always be the smaller of the pair
577	<	if( exI > exJ ){
578	<	tempEx = exI;
579	<	exI = exJ;
580	<	exJ = tempEx;
995	<	}
996	<	#ifdef IS_MPI
997	<	tempEx = exI;
998	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
999	<	tempEx = exJ;
1000	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1001	<
1002	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1003	<	#else  // isn't MPI
1004	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1005	<	#endif  //is_mpi
1006	<	}
1007	<	excludeOffset += info.nTorsions;
576	>	if (current_comp_mol >= components_nmol[current_comp]){
577	>	current_comp_mol = 0;
578	>	current_comp++;
579	>	}
580	>	}
581
1009	–
1010	–	// send the arrays off to the forceField for init.
582
583	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
584	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1014	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1015	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
583	>	void SimSetup::gatherInfo(void){
584	>	int i;
585
586	+	ensembleCase = -1;
587	+	ffCase = -1;
588
589	<	the_molecules[i].initialize( info );
589	>	// set the easy ones first
590
591	<
592	<	atomOffset += info.nAtoms;
593	<	delete[] theBonds;
594	<	delete[] theBends;
1024	<	delete[] theTorsions;
591	>	for (i = 0; i < nInfo; i++){
592	>	info[i].target_temp = globals->getTargetTemp();
593	>	info[i].dt = globals->getDt();
594	>	info[i].run_time = globals->getRunTime();
595		}
596	+	n_components = globals->getNComponents();
597
1027	–	#ifdef IS_MPI
1028	–	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1029	–	MPIcheckPoint();
1030	–	#endif // is_mpi
598
599	<	// clean up the forcefield
1033	<	the_ff->calcRcut();
1034	<	the_ff->cleanMe();
599	>	// get the forceField
600
601	<	}
601	>	strcpy(force_field, globals->getForceField());
602
603	<	void SimSetup::initFromBass( void ){
603	>	if (!strcasecmp(force_field, "DUFF")){
604	>	ffCase = FF_DUFF;
605	>	}
606	>	else if (!strcasecmp(force_field, "LJ")){
607	>	ffCase = FF_LJ;
608	>	}
609	>	else if (!strcasecmp(force_field, "EAM")){
610	>	ffCase = FF_EAM;
611	>	}
612	>	else{
613	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
614	>	force_field);
615	>	painCave.isFatal = 1;
616	>	simError();
617	>	}
618
619	<	int i, j, k;
1041	<	int n_cells;
1042	<	double cellx, celly, cellz;
1043	<	double temp1, temp2, temp3;
1044	<	int n_per_extra;
1045	<	int n_extra;
1046	<	int have_extra, done;
619	>	// get the ensemble
620
621	<	temp1 = (double)tot_nmol / 4.0;
1049	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1050	<	temp3 = ceil( temp2 );
621	>	strcpy(ensemble, globals->getEnsemble());
622
623	<	have_extra =0;
624	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1054	<	have_extra =1;
1055	<
1056	<	n_cells = (int)temp3 - 1;
1057	<	cellx = simnfo->box_x / temp3;
1058	<	celly = simnfo->box_y / temp3;
1059	<	cellz = simnfo->box_z / temp3;
1060	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1061	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1062	<	n_per_extra = (int)ceil( temp1 );
1063	<
1064	<	if( n_per_extra > 4){
1065	<	sprintf( painCave.errMsg,
1066	<	"SimSetup error. There has been an error in constructing"
1067	<	" the non-complete lattice.\n" );
1068	<	painCave.isFatal = 1;
1069	<	simError();
1070	<	}
623	>	if (!strcasecmp(ensemble, "NVE")){
624	>	ensembleCase = NVE_ENS;
625		}
626	<	else{
627	<	n_cells = (int)temp3;
1074	<	cellx = simnfo->box_x / temp3;
1075	<	celly = simnfo->box_y / temp3;
1076	<	cellz = simnfo->box_z / temp3;
626	>	else if (!strcasecmp(ensemble, "NVT")){
627	>	ensembleCase = NVT_ENS;
628		}
629	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
630	+	ensembleCase = NPTi_ENS;
631	+	}
632	+	else if (!strcasecmp(ensemble, "NPTf")){
633	+	ensembleCase = NPTf_ENS;
634	+	}
635	+	else if (!strcasecmp(ensemble, "NPTxyz")){
636	+	ensembleCase = NPTxyz_ENS;
637	+	}
638	+	else{
639	+	sprintf(painCave.errMsg,
640	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
641	+	"reverting to NVE for this simulation.\n",
642	+	ensemble);
643	+	painCave.isFatal = 0;
644	+	simError();
645	+	strcpy(ensemble, "NVE");
646	+	ensembleCase = NVE_ENS;
647	+	}
648
649	<	current_mol = 0;
650	<	current_comp_mol = 0;
1081	<	current_comp = 0;
1082	<	current_atom_ndx = 0;
649	>	for (i = 0; i < nInfo; i++){
650	>	strcpy(info[i].ensemble, ensemble);
651
652	<	for( i=0; i < n_cells ; i++ ){
1085	<	for( j=0; j < n_cells; j++ ){
1086	<	for( k=0; k < n_cells; k++ ){
652	>	// get the mixing rule
653
654	<	makeElement( i * cellx,
655	<	j * celly,
656	<	k * cellz );
654	>	strcpy(info[i].mixingRule, globals->getMixingRule());
655	>	info[i].usePBC = globals->getPBC();
656	>	}
657
658	<	makeElement( i * cellx + 0.5 * cellx,
1093	<	j * celly + 0.5 * celly,
1094	<	k * cellz );
658	>	// get the components and calculate the tot_nMol and indvidual n_mol
659
660	<	makeElement( i * cellx,
661	<	j * celly + 0.5 * celly,
1098	<	k * cellz + 0.5 * cellz );
660	>	the_components = globals->getComponents();
661	>	components_nmol = new int[n_components];
662
663	<	makeElement( i * cellx + 0.5 * cellx,
664	<	j * celly,
665	<	k * cellz + 0.5 * cellz );
663	>
664	>	if (!globals->haveNMol()){
665	>	// we don't have the total number of molecules, so we assume it is
666	>	// given in each component
667	>
668	>	tot_nmol = 0;
669	>	for (i = 0; i < n_components; i++){
670	>	if (!the_components[i]->haveNMol()){
671	>	// we have a problem
672	>	sprintf(painCave.errMsg,
673	>	"SimSetup Error. No global NMol or component NMol"
674	>	" given. Cannot calculate the number of atoms.\n");
675	>	painCave.isFatal = 1;
676	>	simError();
677		}
678	+
679	+	tot_nmol += the_components[i]->getNMol();
680	+	components_nmol[i] = the_components[i]->getNMol();
681		}
682		}
683	+	else{
684	+	sprintf(painCave.errMsg,
685	+	"SimSetup error.\n"
686	+	"\tSorry, the ability to specify total"
687	+	" nMols and then give molfractions in the components\n"
688	+	"\tis not currently supported."
689	+	" Please give nMol in the components.\n");
690	+	painCave.isFatal = 1;
691	+	simError();
692	+	}
693
694	<	if( have_extra ){
695	<	done = 0;
694	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
695	>	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
696	>	sprintf(painCave.errMsg,
697	>	"Sample time is not divisible by dt \n");
698	>	painCave.isFatal = 0;
699	>	simError();
700	>	}
701
702	<	int start_ndx;
703	<	for( i=0; i < (n_cells+1) && !done; i++ ){
704	<	for( j=0; j < (n_cells+1) && !done; j++ ){
702	>	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
703	>	sprintf(painCave.errMsg,
704	>	"Status time is not divisible by dt\n");
705	>	painCave.isFatal = 0;
706	>	simError();
707	>	}
708
709	<	if( i < n_cells ){
709	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
710	>	sprintf(painCave.errMsg,
711	>	"Thermal time is not divisible by dt\n");
712	>	painCave.isFatal = 0;
713	>	simError();
714	>	}
715
716	<	if( j < n_cells ){
717	<	start_ndx = n_cells;
718	<	}
719	<	else start_ndx = 0;
720	<	}
721	<	else start_ndx = 0;
716	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
717	>	sprintf(painCave.errMsg,
718	>	"Reset time is not divisible by dt\n");
719	>	painCave.isFatal = 0;
720	>	simError();
721	>	}
722
723	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
723	>	// set the status, sample, and thermal kick times
724
725	<	makeElement( i * cellx,
726	<	j * celly,
727	<	k * cellz );
728	<	done = ( current_mol >= tot_nmol );
725	>	for (i = 0; i < nInfo; i++){
726	>	if (globals->haveSampleTime()){
727	>	info[i].sampleTime = globals->getSampleTime();
728	>	info[i].statusTime = info[i].sampleTime;
729	>	info[i].thermalTime = info[i].sampleTime;
730	>	}
731	>	else{
732	>	info[i].sampleTime = globals->getRunTime();
733	>	info[i].statusTime = info[i].sampleTime;
734	>	info[i].thermalTime = info[i].sampleTime;
735	>	}
736
737	<	if( !done && n_per_extra > 1 ){
738	<	makeElement( i * cellx + 0.5 * cellx,
739	<	j * celly + 0.5 * celly,
1133	<	k * cellz );
1134	<	done = ( current_mol >= tot_nmol );
1135	<	}
737	>	if (globals->haveStatusTime()){
738	>	info[i].statusTime = globals->getStatusTime();
739	>	}
740
741	<	if( !done && n_per_extra > 2){
742	<	makeElement( i * cellx,
743	<	j * celly + 0.5 * celly,
1140	<	k * cellz + 0.5 * cellz );
1141	<	done = ( current_mol >= tot_nmol );
1142	<	}
741	>	if (globals->haveThermalTime()){
742	>	info[i].thermalTime = globals->getThermalTime();
743	>	}
744
745	<	if( !done && n_per_extra > 3){
746	<	makeElement( i * cellx + 0.5 * cellx,
747	<	j * celly,
748	<	k * cellz + 0.5 * cellz );
1148	<	done = ( current_mol >= tot_nmol );
1149	<	}
1150	<	}
1151	<	}
745	>	info[i].resetIntegrator = 0;
746	>	if( globals->haveResetTime() ){
747	>	info[i].resetTime = globals->getResetTime();
748	>	info[i].resetIntegrator = 1;
749		}
750	+
751	+	// check for the temperature set flag
752	+
753	+	if (globals->haveTempSet())
754	+	info[i].setTemp = globals->getTempSet();
755	+
756	+	// check for the extended State init
757	+
758	+	info[i].useInitXSstate = globals->getUseInitXSstate();
759	+	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
760	+
761		}
762	+
763	+	//setup seed for random number generator
764	+	int seedValue;
765
766	+	if (globals->haveSeed()){
767	+	seedValue = globals->getSeed();
768
769	<	for( i=0; i<simnfo->n_atoms; i++ ){
770	<	simnfo->atoms[i]->set_vx( 0.0 );
771	<	simnfo->atoms[i]->set_vy( 0.0 );
772	<	simnfo->atoms[i]->set_vz( 0.0 );
769	>	if(seedValue / 1E9 == 0){
770	>	sprintf(painCave.errMsg,
771	>	"Seed for sprng library should contain at least 9 digits\n"
772	>	"OOPSE will generate a seed for user\n");
773	>	painCave.isFatal = 0;
774	>	simError();
775	>
776	>	//using seed generated by system instead of invalid seed set by user
777	>	#ifndef IS_MPI
778	>	seedValue = make_sprng_seed();
779	>	#else
780	>	if (worldRank == 0){
781	>	seedValue = make_sprng_seed();
782	>	}
783	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
784	>	#endif
785	>	}
786	>	}//end of if branch of globals->haveSeed()
787	>	else{
788	>
789	>	#ifndef IS_MPI
790	>	seedValue = make_sprng_seed();
791	>	#else
792	>	if (worldRank == 0){
793	>	seedValue = make_sprng_seed();
794	>	}
795	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
796	>	#endif
797	>	}//end of globals->haveSeed()
798	>
799	>	for (int i = 0; i < nInfo; i++){
800	>	info[i].setSeed(seedValue);
801		}
802	+
803	+	#ifdef IS_MPI
804	+	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
805	+	MPIcheckPoint();
806	+	#endif // is_mpi
807		}
808
1163	–	void SimSetup::makeElement( double x, double y, double z ){
809
810	<	int k;
811	<	AtomStamp* current_atom;
812	<	DirectionalAtom* dAtom;
813	<	double rotMat[3][3];
810	>	void SimSetup::finalInfoCheck(void){
811	>	int index;
812	>	int usesDipoles;
813	>	int i;
814
815	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
815	>	for (i = 0; i < nInfo; i++){
816	>	// check electrostatic parameters
817
818	<	current_atom = comp_stamps[current_comp]->getAtom( k );
819	<	if( !current_atom->havePosition() ){
820	<	sprintf( painCave.errMsg,
821	<	"SimSetup:initFromBass error.\n"
822	<	"\tComponent %s, atom %s does not have a position specified.\n"
1177	<	"\tThe initialization routine is unable to give a start"
1178	<	" position.\n",
1179	<	comp_stamps[current_comp]->getID(),
1180	<	current_atom->getType() );
1181	<	painCave.isFatal = 1;
1182	<	simError();
818	>	index = 0;
819	>	usesDipoles = 0;
820	>	while ((index < info[i].n_atoms) && !usesDipoles){
821	>	usesDipoles = (info[i].atoms[index])->hasDipole();
822	>	index++;
823		}
824
825	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
826	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
827	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
825	>	#ifdef IS_MPI
826	>	int myUse = usesDipoles;
827	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
828	>	#endif //is_mpi
829
830	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
830	>	double theEcr, theEst;
831
832	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
832	>	if (globals->getUseRF()){
833	>	info[i].useReactionField = 1;
834
835	<	rotMat[0][0] = 1.0;
836	<	rotMat[0][1] = 0.0;
837	<	rotMat[0][2] = 0.0;
835	>	if (!globals->haveECR()){
836	>	sprintf(painCave.errMsg,
837	>	"SimSetup Warning: using default value of 15.0 angstroms"
838	>	"box length for the electrostaticCutoffRadius.\n");
839	>	painCave.isFatal = 0;
840	>	simError();
841	>	theEcr = 15.0;
842	>	}
843	>	else{
844	>	theEcr = globals->getECR();
845	>	}
846
847	<	rotMat[1][0] = 0.0;
848	<	rotMat[1][1] = 1.0;
849	<	rotMat[1][2] = 0.0;
847	>	if (!globals->haveEST()){
848	>	sprintf(painCave.errMsg,
849	>	"SimSetup Warning: using default value of 0.05 * the "
850	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
851	>	painCave.isFatal = 0;
852	>	simError();
853	>	theEst = 0.05 * theEcr;
854	>	}
855	>	else{
856	>	theEst = globals->getEST();
857	>	}
858
859	<	rotMat[2][0] = 0.0;
1202	<	rotMat[2][1] = 0.0;
1203	<	rotMat[2][2] = 1.0;
859	>	info[i].setDefaultEcr(theEcr, theEst);
860
861	<	dAtom->setA( rotMat );
861	>	if (!globals->haveDielectric()){
862	>	sprintf(painCave.errMsg,
863	>	"SimSetup Error: You are trying to use Reaction Field without"
864	>	"setting a dielectric constant!\n");
865	>	painCave.isFatal = 1;
866	>	simError();
867	>	}
868	>	info[i].dielectric = globals->getDielectric();
869		}
870	<
871	<	current_atom_ndx++;
870	>	else{
871	>	if (usesDipoles){
872	>	if (!globals->haveECR()){
873	>	sprintf(painCave.errMsg,
874	>	"SimSetup Warning: using default value of 15.0 angstroms"
875	>	"box length for the electrostaticCutoffRadius.\n");
876	>	painCave.isFatal = 0;
877	>	simError();
878	>	theEcr = 15.0;
879	>	}
880	>	else{
881	>	theEcr = globals->getECR();
882	>	}
883	>
884	>	if (!globals->haveEST()){
885	>	sprintf(painCave.errMsg,
886	>	"SimSetup Warning: using default value of 0.05 * the "
887	>	"electrostaticCutoffRadius for the "
888	>	"electrostaticSkinThickness\n");
889	>	painCave.isFatal = 0;
890	>	simError();
891	>	theEst = 0.05 * theEcr;
892	>	}
893	>	else{
894	>	theEst = globals->getEST();
895	>	}
896	>
897	>	info[i].setDefaultEcr(theEcr, theEst);
898	>	}
899	>	}
900		}
901	+	#ifdef IS_MPI
902	+	strcpy(checkPointMsg, "post processing checks out");
903	+	MPIcheckPoint();
904	+	#endif // is_mpi
905	+	}
906	+
907	+	void SimSetup::initSystemCoords(void){
908	+	int i;
909
910	<	current_mol++;
1212	<	current_comp_mol++;
910	>	char* inName;
911
912	<	if( current_comp_mol >= components_nmol[current_comp] ){
912	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
913
914	<	current_comp_mol = 0;
915	<	current_comp++;
914	>	for (i = 0; i < info[0].n_atoms; i++)
915	>	info[0].atoms[i]->setCoords();
916	>
917	>	if (globals->haveInitialConfig()){
918	>	InitializeFromFile* fileInit;
919	>	#ifdef IS_MPI // is_mpi
920	>	if (worldRank == 0){
921	>	#endif //is_mpi
922	>	inName = globals->getInitialConfig();
923	>	fileInit = new InitializeFromFile(inName);
924	>	#ifdef IS_MPI
925	>	}
926	>	else
927	>	fileInit = new InitializeFromFile(NULL);
928	>	#endif
929	>	fileInit->readInit(info); // default velocities on
930	>
931	>	delete fileInit;
932	>	}
933	>	else{
934	>
935	>	// no init from bass
936	>
937	>	sprintf(painCave.errMsg,
938	>	"Cannot intialize a simulation without an initial configuration file.\n");
939	>	painCave.isFatal = 1;;
940	>	simError();
941	>
942	>	}
943	>
944	>	#ifdef IS_MPI
945	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
946	>	MPIcheckPoint();
947	>	#endif // is_mpi
948	>	}
949	>
950	>
951	>	void SimSetup::makeOutNames(void){
952	>	int k;
953	>
954	>
955	>	for (k = 0; k < nInfo; k++){
956	>	#ifdef IS_MPI
957	>	if (worldRank == 0){
958	>	#endif // is_mpi
959	>
960	>	if (globals->haveFinalConfig()){
961	>	strcpy(info[k].finalName, globals->getFinalConfig());
962	>	}
963	>	else{
964	>	strcpy(info[k].finalName, inFileName);
965	>	char* endTest;
966	>	int nameLength = strlen(info[k].finalName);
967	>	endTest = &(info[k].finalName[nameLength - 5]);
968	>	if (!strcmp(endTest, ".bass")){
969	>	strcpy(endTest, ".eor");
970	>	}
971	>	else if (!strcmp(endTest, ".BASS")){
972	>	strcpy(endTest, ".eor");
973	>	}
974	>	else{
975	>	endTest = &(info[k].finalName[nameLength - 4]);
976	>	if (!strcmp(endTest, ".bss")){
977	>	strcpy(endTest, ".eor");
978	>	}
979	>	else if (!strcmp(endTest, ".mdl")){
980	>	strcpy(endTest, ".eor");
981	>	}
982	>	else{
983	>	strcat(info[k].finalName, ".eor");
984	>	}
985	>	}
986	>	}
987	>
988	>	// make the sample and status out names
989	>
990	>	strcpy(info[k].sampleName, inFileName);
991	>	char* endTest;
992	>	int nameLength = strlen(info[k].sampleName);
993	>	endTest = &(info[k].sampleName[nameLength - 5]);
994	>	if (!strcmp(endTest, ".bass")){
995	>	strcpy(endTest, ".dump");
996	>	}
997	>	else if (!strcmp(endTest, ".BASS")){
998	>	strcpy(endTest, ".dump");
999	>	}
1000	>	else{
1001	>	endTest = &(info[k].sampleName[nameLength - 4]);
1002	>	if (!strcmp(endTest, ".bss")){
1003	>	strcpy(endTest, ".dump");
1004	>	}
1005	>	else if (!strcmp(endTest, ".mdl")){
1006	>	strcpy(endTest, ".dump");
1007	>	}
1008	>	else{
1009	>	strcat(info[k].sampleName, ".dump");
1010	>	}
1011	>	}
1012	>
1013	>	strcpy(info[k].statusName, inFileName);
1014	>	nameLength = strlen(info[k].statusName);
1015	>	endTest = &(info[k].statusName[nameLength - 5]);
1016	>	if (!strcmp(endTest, ".bass")){
1017	>	strcpy(endTest, ".stat");
1018	>	}
1019	>	else if (!strcmp(endTest, ".BASS")){
1020	>	strcpy(endTest, ".stat");
1021	>	}
1022	>	else{
1023	>	endTest = &(info[k].statusName[nameLength - 4]);
1024	>	if (!strcmp(endTest, ".bss")){
1025	>	strcpy(endTest, ".stat");
1026	>	}
1027	>	else if (!strcmp(endTest, ".mdl")){
1028	>	strcpy(endTest, ".stat");
1029	>	}
1030	>	else{
1031	>	strcat(info[k].statusName, ".stat");
1032	>	}
1033	>	}
1034	>
1035	>	#ifdef IS_MPI
1036	>
1037	>	}
1038	>	#endif // is_mpi
1039	>	}
1040	>	}
1041	>
1042	>
1043	>	void SimSetup::sysObjectsCreation(void){
1044	>	int i, k;
1045	>
1046	>	// create the forceField
1047	>
1048	>	createFF();
1049	>
1050	>	// extract componentList
1051	>
1052	>	compList();
1053	>
1054	>	// calc the number of atoms, bond, bends, and torsions
1055	>
1056	>	calcSysValues();
1057	>
1058	>	#ifdef IS_MPI
1059	>	// divide the molecules among the processors
1060	>
1061	>	mpiMolDivide();
1062	>	#endif //is_mpi
1063	>
1064	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1065	>
1066	>	makeSysArrays();
1067	>
1068	>	// make and initialize the molecules (all but atomic coordinates)
1069	>
1070	>	makeMolecules();
1071	>
1072	>	for (k = 0; k < nInfo; k++){
1073	>	info[k].identArray = new int[info[k].n_atoms];
1074	>	for (i = 0; i < info[k].n_atoms; i++){
1075	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1076	>	}
1077	>	}
1078	>	}
1079	>
1080	>
1081	>	void SimSetup::createFF(void){
1082	>	switch (ffCase){
1083	>	case FF_DUFF:
1084	>	the_ff = new DUFF();
1085	>	break;
1086	>
1087	>	case FF_LJ:
1088	>	the_ff = new LJFF();
1089	>	break;
1090	>
1091	>	case FF_EAM:
1092	>	the_ff = new EAM_FF();
1093	>	break;
1094	>
1095	>	default:
1096	>	sprintf(painCave.errMsg,
1097	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1098	>	painCave.isFatal = 1;
1099	>	simError();
1100	>	}
1101	>
1102	>	#ifdef IS_MPI
1103	>	strcpy(checkPointMsg, "ForceField creation successful");
1104	>	MPIcheckPoint();
1105	>	#endif // is_mpi
1106	>	}
1107	>
1108	>
1109	>	void SimSetup::compList(void){
1110	>	int i;
1111	>	char* id;
1112	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1113	>	LinkedMolStamp* currentStamp = NULL;
1114	>	comp_stamps = new MoleculeStamp * [n_components];
1115	>
1116	>	// make an array of molecule stamps that match the components used.
1117	>	// also extract the used stamps out into a separate linked list
1118	>
1119	>	for (i = 0; i < nInfo; i++){
1120	>	info[i].nComponents = n_components;
1121	>	info[i].componentsNmol = components_nmol;
1122	>	info[i].compStamps = comp_stamps;
1123	>	info[i].headStamp = headStamp;
1124	>	}
1125	>
1126	>
1127	>	for (i = 0; i < n_components; i++){
1128	>	id = the_components[i]->getType();
1129	>	comp_stamps[i] = NULL;
1130	>
1131	>	// check to make sure the component isn't already in the list
1132	>
1133	>	comp_stamps[i] = headStamp->match(id);
1134	>	if (comp_stamps[i] == NULL){
1135	>	// extract the component from the list;
1136	>
1137	>	currentStamp = stamps->extractMolStamp(id);
1138	>	if (currentStamp == NULL){
1139	>	sprintf(painCave.errMsg,
1140	>	"SimSetup error: Component \"%s\" was not found in the "
1141	>	"list of declared molecules\n",
1142	>	id);
1143	>	painCave.isFatal = 1;
1144	>	simError();
1145	>	}
1146	>
1147	>	headStamp->add(currentStamp);
1148	>	comp_stamps[i] = headStamp->match(id);
1149	>	}
1150	>	}
1151	>
1152	>	#ifdef IS_MPI
1153	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1154	>	MPIcheckPoint();
1155	>	#endif // is_mpi
1156	>	}
1157	>
1158	>	void SimSetup::calcSysValues(void){
1159	>	int i;
1160	>
1161	>	int* molMembershipArray;
1162	>
1163	>	tot_atoms = 0;
1164	>	tot_bonds = 0;
1165	>	tot_bends = 0;
1166	>	tot_torsions = 0;
1167	>	for (i = 0; i < n_components; i++){
1168	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1169	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1170	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1171	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1172	>	}
1173	>
1174	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1175	>	molMembershipArray = new int[tot_atoms];
1176	>
1177	>	for (i = 0; i < nInfo; i++){
1178	>	info[i].n_atoms = tot_atoms;
1179	>	info[i].n_bonds = tot_bonds;
1180	>	info[i].n_bends = tot_bends;
1181	>	info[i].n_torsions = tot_torsions;
1182	>	info[i].n_SRI = tot_SRI;
1183	>	info[i].n_mol = tot_nmol;
1184	>
1185	>	info[i].molMembershipArray = molMembershipArray;
1186	>	}
1187	>	}
1188	>
1189	>	#ifdef IS_MPI
1190	>
1191	>	void SimSetup::mpiMolDivide(void){
1192	>	int i, j, k;
1193	>	int localMol, allMol;
1194	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1195	>
1196	>	mpiSim = new mpiSimulation(info);
1197	>
1198	>	globalIndex = mpiSim->divideLabor();
1199	>
1200	>	// set up the local variables
1201	>
1202	>	mol2proc = mpiSim->getMolToProcMap();
1203	>	molCompType = mpiSim->getMolComponentType();
1204	>
1205	>	allMol = 0;
1206	>	localMol = 0;
1207	>	local_atoms = 0;
1208	>	local_bonds = 0;
1209	>	local_bends = 0;
1210	>	local_torsions = 0;
1211	>	globalAtomIndex = 0;
1212	>
1213	>
1214	>	for (i = 0; i < n_components; i++){
1215	>	for (j = 0; j < components_nmol[i]; j++){
1216	>	if (mol2proc[allMol] == worldRank){
1217	>	local_atoms += comp_stamps[i]->getNAtoms();
1218	>	local_bonds += comp_stamps[i]->getNBonds();
1219	>	local_bends += comp_stamps[i]->getNBends();
1220	>	local_torsions += comp_stamps[i]->getNTorsions();
1221	>	localMol++;
1222	>	}
1223	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1224	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1225	>	globalAtomIndex++;
1226	>	}
1227	>
1228	>	allMol++;
1229	>	}
1230	>	}
1231	>	local_SRI = local_bonds + local_bends + local_torsions;
1232	>
1233	>	info[0].n_atoms = mpiSim->getMyNlocal();
1234	>
1235	>	if (local_atoms != info[0].n_atoms){
1236	>	sprintf(painCave.errMsg,
1237	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1238	>	" localAtom (%d) are not equal.\n",
1239	>	info[0].n_atoms, local_atoms);
1240	>	painCave.isFatal = 1;
1241	>	simError();
1242	>	}
1243	>
1244	>	info[0].n_bonds = local_bonds;
1245	>	info[0].n_bends = local_bends;
1246	>	info[0].n_torsions = local_torsions;
1247	>	info[0].n_SRI = local_SRI;
1248	>	info[0].n_mol = localMol;
1249	>
1250	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1251	>	MPIcheckPoint();
1252	>	}
1253	>
1254	>	#endif // is_mpi
1255	>
1256	>
1257	>	void SimSetup::makeSysArrays(void){
1258	>
1259	>	#ifndef IS_MPI
1260	>	int k, j;
1261	>	#endif // is_mpi
1262	>	int i, l;
1263	>
1264	>	Atom** the_atoms;
1265	>	Molecule* the_molecules;
1266	>	Exclude** the_excludes;
1267	>
1268	>
1269	>	for (l = 0; l < nInfo; l++){
1270	>	// create the atom and short range interaction arrays
1271	>
1272	>	the_atoms = new Atom * [info[l].n_atoms];
1273	>	the_molecules = new Molecule[info[l].n_mol];
1274	>	int molIndex;
1275	>
1276	>	// initialize the molecule's stampID's
1277	>
1278	>	#ifdef IS_MPI
1279	>
1280	>
1281	>	molIndex = 0;
1282	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1283	>	if (mol2proc[i] == worldRank){
1284	>	the_molecules[molIndex].setStampID(molCompType[i]);
1285	>	the_molecules[molIndex].setMyIndex(molIndex);
1286	>	the_molecules[molIndex].setGlobalIndex(i);
1287	>	molIndex++;
1288	>	}
1289	>	}
1290	>
1291	>	#else // is_mpi
1292	>
1293	>	molIndex = 0;
1294	>	globalAtomIndex = 0;
1295	>	for (i = 0; i < n_components; i++){
1296	>	for (j = 0; j < components_nmol[i]; j++){
1297	>	the_molecules[molIndex].setStampID(i);
1298	>	the_molecules[molIndex].setMyIndex(molIndex);
1299	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1300	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1301	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1302	>	globalAtomIndex++;
1303	>	}
1304	>	molIndex++;
1305	>	}
1306	>	}
1307	>
1308	>
1309	>	#endif // is_mpi
1310	>
1311	>
1312	>	if (info[l].n_SRI){
1313	>	Exclude::createArray(info[l].n_SRI);
1314	>	the_excludes = new Exclude * [info[l].n_SRI];
1315	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1316	>	the_excludes[ex] = new Exclude(ex);
1317	>	}
1318	>	info[l].globalExcludes = new int;
1319	>	info[l].n_exclude = info[l].n_SRI;
1320	>	}
1321	>	else{
1322	>	Exclude::createArray(1);
1323	>	the_excludes = new Exclude * ;
1324	>	the_excludes[0] = new Exclude(0);
1325	>	the_excludes[0]->setPair(0, 0);
1326	>	info[l].globalExcludes = new int;
1327	>	info[l].globalExcludes[0] = 0;
1328	>	info[l].n_exclude = 0;
1329	>	}
1330	>
1331	>	// set the arrays into the SimInfo object
1332	>
1333	>	info[l].atoms = the_atoms;
1334	>	info[l].molecules = the_molecules;
1335	>	info[l].nGlobalExcludes = 0;
1336	>	info[l].excludes = the_excludes;
1337	>
1338	>	the_ff->setSimInfo(info);
1339		}
1340		}
1341	+
1342	+	void SimSetup::makeIntegrator(void){
1343	+	int k;
1344	+
1345	+	NVE<RealIntegrator>* myNVE = NULL;
1346	+	NVT<RealIntegrator>* myNVT = NULL;
1347	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1348	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1349	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1350	+
1351	+	for (k = 0; k < nInfo; k++){
1352	+	switch (ensembleCase){
1353	+	case NVE_ENS:
1354	+	if (globals->haveZconstraints()){
1355	+	setupZConstraint(info[k]);
1356	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1357	+	}
1358	+	else{
1359	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1360	+	}
1361	+
1362	+	info->the_integrator = myNVE;
1363	+	break;
1364	+
1365	+	case NVT_ENS:
1366	+	if (globals->haveZconstraints()){
1367	+	setupZConstraint(info[k]);
1368	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1369	+	}
1370	+	else
1371	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1372	+
1373	+	myNVT->setTargetTemp(globals->getTargetTemp());
1374	+
1375	+	if (globals->haveTauThermostat())
1376	+	myNVT->setTauThermostat(globals->getTauThermostat());
1377	+	else{
1378	+	sprintf(painCave.errMsg,
1379	+	"SimSetup error: If you use the NVT\n"
1380	+	"    ensemble, you must set tauThermostat.\n");
1381	+	painCave.isFatal = 1;
1382	+	simError();
1383	+	}
1384	+
1385	+	info->the_integrator = myNVT;
1386	+	break;
1387	+
1388	+	case NPTi_ENS:
1389	+	if (globals->haveZconstraints()){
1390	+	setupZConstraint(info[k]);
1391	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1392	+	}
1393	+	else
1394	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1395	+
1396	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1397	+
1398	+	if (globals->haveTargetPressure())
1399	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1400	+	else{
1401	+	sprintf(painCave.errMsg,
1402	+	"SimSetup error: If you use a constant pressure\n"
1403	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1404	+	painCave.isFatal = 1;
1405	+	simError();
1406	+	}
1407	+
1408	+	if (globals->haveTauThermostat())
1409	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1410	+	else{
1411	+	sprintf(painCave.errMsg,
1412	+	"SimSetup error: If you use an NPT\n"
1413	+	"    ensemble, you must set tauThermostat.\n");
1414	+	painCave.isFatal = 1;
1415	+	simError();
1416	+	}
1417	+
1418	+	if (globals->haveTauBarostat())
1419	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1420	+	else{
1421	+	sprintf(painCave.errMsg,
1422	+	"SimSetup error: If you use an NPT\n"
1423	+	"    ensemble, you must set tauBarostat.\n");
1424	+	painCave.isFatal = 1;
1425	+	simError();
1426	+	}
1427	+
1428	+	info->the_integrator = myNPTi;
1429	+	break;
1430	+
1431	+	case NPTf_ENS:
1432	+	if (globals->haveZconstraints()){
1433	+	setupZConstraint(info[k]);
1434	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1435	+	}
1436	+	else
1437	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1438	+
1439	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1440	+
1441	+	if (globals->haveTargetPressure())
1442	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1443	+	else{
1444	+	sprintf(painCave.errMsg,
1445	+	"SimSetup error: If you use a constant pressure\n"
1446	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1447	+	painCave.isFatal = 1;
1448	+	simError();
1449	+	}
1450	+
1451	+	if (globals->haveTauThermostat())
1452	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1453	+
1454	+	else{
1455	+	sprintf(painCave.errMsg,
1456	+	"SimSetup error: If you use an NPT\n"
1457	+	"    ensemble, you must set tauThermostat.\n");
1458	+	painCave.isFatal = 1;
1459	+	simError();
1460	+	}
1461	+
1462	+	if (globals->haveTauBarostat())
1463	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1464	+
1465	+	else{
1466	+	sprintf(painCave.errMsg,
1467	+	"SimSetup error: If you use an NPT\n"
1468	+	"    ensemble, you must set tauBarostat.\n");
1469	+	painCave.isFatal = 1;
1470	+	simError();
1471	+	}
1472	+
1473	+	info->the_integrator = myNPTf;
1474	+	break;
1475	+
1476	+	case NPTxyz_ENS:
1477	+	if (globals->haveZconstraints()){
1478	+	setupZConstraint(info[k]);
1479	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1480	+	}
1481	+	else
1482	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1483	+
1484	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1485	+
1486	+	if (globals->haveTargetPressure())
1487	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1488	+	else{
1489	+	sprintf(painCave.errMsg,
1490	+	"SimSetup error: If you use a constant pressure\n"
1491	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1492	+	painCave.isFatal = 1;
1493	+	simError();
1494	+	}
1495	+
1496	+	if (globals->haveTauThermostat())
1497	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1498	+	else{
1499	+	sprintf(painCave.errMsg,
1500	+	"SimSetup error: If you use an NPT\n"
1501	+	"    ensemble, you must set tauThermostat.\n");
1502	+	painCave.isFatal = 1;
1503	+	simError();
1504	+	}
1505	+
1506	+	if (globals->haveTauBarostat())
1507	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1508	+	else{
1509	+	sprintf(painCave.errMsg,
1510	+	"SimSetup error: If you use an NPT\n"
1511	+	"    ensemble, you must set tauBarostat.\n");
1512	+	painCave.isFatal = 1;
1513	+	simError();
1514	+	}
1515	+
1516	+	info->the_integrator = myNPTxyz;
1517	+	break;
1518	+
1519	+	default:
1520	+	sprintf(painCave.errMsg,
1521	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1522	+	painCave.isFatal = 1;
1523	+	simError();
1524	+	}
1525	+	}
1526	+	}
1527	+
1528	+	void SimSetup::initFortran(void){
1529	+	info[0].refreshSim();
1530	+
1531	+	if (!strcmp(info[0].mixingRule, "standard")){
1532	+	the_ff->initForceField(LB_MIXING_RULE);
1533	+	}
1534	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1535	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1536	+	}
1537	+	else{
1538	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1539	+	info[0].mixingRule);
1540	+	painCave.isFatal = 1;
1541	+	simError();
1542	+	}
1543	+
1544	+
1545	+	#ifdef IS_MPI
1546	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1547	+	MPIcheckPoint();
1548	+	#endif // is_mpi
1549	+	}
1550	+
1551	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1552	+	int nZConstraints;
1553	+	ZconStamp** zconStamp;
1554	+
1555	+	if (globals->haveZconstraintTime()){
1556	+	//add sample time of z-constraint  into SimInfo's property list
1557	+	DoubleData* zconsTimeProp = new DoubleData();
1558	+	zconsTimeProp->setID(ZCONSTIME_ID);
1559	+	zconsTimeProp->setData(globals->getZconsTime());
1560	+	theInfo.addProperty(zconsTimeProp);
1561	+	}
1562	+	else{
1563	+	sprintf(painCave.errMsg,
1564	+	"ZConstraint error: If you use an ZConstraint\n"
1565	+	" , you must set sample time.\n");
1566	+	painCave.isFatal = 1;
1567	+	simError();
1568	+	}
1569	+
1570	+	//push zconsTol into siminfo, if user does not specify
1571	+	//value for zconsTol, a default value will be used
1572	+	DoubleData* zconsTol = new DoubleData();
1573	+	zconsTol->setID(ZCONSTOL_ID);
1574	+	if (globals->haveZconsTol()){
1575	+	zconsTol->setData(globals->getZconsTol());
1576	+	}
1577	+	else{
1578	+	double defaultZConsTol = 0.01;
1579	+	sprintf(painCave.errMsg,
1580	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1581	+	" , default value %f is used.\n",
1582	+	defaultZConsTol);
1583	+	painCave.isFatal = 0;
1584	+	simError();
1585	+
1586	+	zconsTol->setData(defaultZConsTol);
1587	+	}
1588	+	theInfo.addProperty(zconsTol);
1589	+
1590	+	//set Force Subtraction Policy
1591	+	StringData* zconsForcePolicy = new StringData();
1592	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1593	+
1594	+	if (globals->haveZconsForcePolicy()){
1595	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1596	+	}
1597	+	else{
1598	+	sprintf(painCave.errMsg,
1599	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1600	+	"PolicyByMass is used\n");
1601	+	painCave.isFatal = 0;
1602	+	simError();
1603	+	zconsForcePolicy->setData("BYMASS");
1604	+	}
1605	+
1606	+	theInfo.addProperty(zconsForcePolicy);
1607	+
1608	+	//Determine the name of ouput file and add it into SimInfo's property list
1609	+	//Be careful, do not use inFileName, since it is a pointer which
1610	+	//point to a string at master node, and slave nodes do not contain that string
1611	+
1612	+	string zconsOutput(theInfo.finalName);
1613	+
1614	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1615	+
1616	+	StringData* zconsFilename = new StringData();
1617	+	zconsFilename->setID(ZCONSFILENAME_ID);
1618	+	zconsFilename->setData(zconsOutput);
1619	+
1620	+	theInfo.addProperty(zconsFilename);
1621	+
1622	+	//setup index, pos and other parameters of z-constraint molecules
1623	+	nZConstraints = globals->getNzConstraints();
1624	+	theInfo.nZconstraints = nZConstraints;
1625	+
1626	+	zconStamp = globals->getZconStamp();
1627	+	ZConsParaItem tempParaItem;
1628	+
1629	+	ZConsParaData* zconsParaData = new ZConsParaData();
1630	+	zconsParaData->setID(ZCONSPARADATA_ID);
1631	+
1632	+	for (int i = 0; i < nZConstraints; i++){
1633	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1634	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1635	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1636	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1637	+
1638	+	zconsParaData->addItem(tempParaItem);
1639	+	}
1640	+
1641	+	//check the uniqueness of index
1642	+	if(!zconsParaData->isIndexUnique()){
1643	+	sprintf(painCave.errMsg,
1644	+	"ZConstraint Error: molIndex is not unique\n");
1645	+	painCave.isFatal = 1;
1646	+	simError();
1647	+	}
1648	+
1649	+	//sort the parameters by index of molecules
1650	+	zconsParaData->sortByIndex();
1651	+
1652	+	//push data into siminfo, therefore, we can retrieve later
1653	+	theInfo.addProperty(zconsParaData);
1654	+	}

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