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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 504 by mmeineke, Thu Apr 17 21:54:18 2003 UTC vs.
Revision 746 by mmeineke, Thu Sep 4 21:48:35 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 | SimSetup::SimSetup(){
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 | void SimSetup::parseFile( char* fileName ){
50		delete globals;
51		}
52
53	<	void SimSetup::parseFile( char* fileName ){
53	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
54	>	info = the_info;
55	>	nInfo = theNinfo;
56	>	isInfoArray = 1;
57	>	}
58
59	+
60	+	void SimSetup::parseFile(char* fileName){
61		#ifdef IS_MPI
62	<	if( worldRank == 0 ){
62	>	if (worldRank == 0){
63		#endif // is_mpi
64	<
64	>
65		inFileName = fileName;
66	<	set_interface_stamps( stamps, globals );
67	<
66	>	set_interface_stamps(stamps, globals);
67	>
68		#ifdef IS_MPI
69		mpiEventInit();
70		#endif
71
72	<	yacc_BASS( fileName );
72	>	yacc_BASS(fileName);
73
74		#ifdef IS_MPI
75		throwMPIEvent(NULL);
76		}
77	<	else receiveParse();
77	>	else{
78	>	receiveParse();
79	>	}
80		#endif
81
82		}
83
84		#ifdef IS_MPI
85		void SimSetup::receiveParse(void){
86	<
87	<	set_interface_stamps( stamps, globals );
88	<	mpiEventInit();
89	<	MPIcheckPoint();
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 ){
66	<
67	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	ExtendedSystem* the_extendedsystem;
94	>	void SimSetup::createSim(void){
95		int i, j, k, globalAtomIndex;
96
97	<	// get the stamps and globals;
73	<	the_stamps = stamps;
74	<	the_globals = globals;
97	>	// gather all of the information from the Bass file
98
99	<	// 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();
99	>	gatherInfo();
100
101	<	// 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() );
101	>	// creation of complex system objects
102
103	<	// 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	<	}
103	>	sysObjectsCreation();
104
105	<	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	<	}
105	>	// check on the post processing info
106
107	<	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	<	}
107	>	finalInfoCheck();
108
109	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
126	<	the_extendedsystem = new ExtendedSystem( simnfo );
127	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
109	>	// initialize the system coordinates
110
111	<	if (the_globals->haveTauThermostat())
112	<	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" );
111	>	if (!isInfoArray){
112	>	initSystemCoords();
113		}
152	–	strcpy( simnfo->ensemble, ensemble );
114
115	<	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	<	}
115	>	// make the output filenames
116
117	<	#ifdef IS_MPI
172	<	strcpy( checkPointMsg, "ForceField creation successful" );
173	<	MPIcheckPoint();
174	<	#endif // is_mpi
117	>	makeOutNames();
118
119	<
119	>	// make the integrator
120
121	<	// 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];
121	>	makeIntegrator();
122
123	<	if( !the_globals->haveNMol() ){
124	<	// we don't have the total number of molecules, so we assume it is
125	<	// given in each component
123	>	#ifdef IS_MPI
124	>	mpiSim->mpiRefresh();
125	>	#endif
126
127	<	tot_nmol = 0;
188	<	for( i=0; i<n_components; i++ ){
127	>	// initialize the Fortran
128
129	<	if( !the_components[i]->haveNMol() ){
130	<	// 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	<	}
129	>	initFortran();
130	>	}
131
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	–	}
132
133	<	#ifdef IS_MPI
134	<	strcpy( checkPointMsg, "Have the number of components" );
135	<	MPIcheckPoint();
136	<	#endif // is_mpi
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	<	// make an array of molecule stamps that match the components used.
146	<	// also extract the used stamps out into a separate linked list
145	>	bond_pair* theBonds;
146	>	bend_set* theBends;
147	>	torsion_set* theTorsions;
148
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++ ){
149
150	<	id = the_components[i]->getType();
247	<	comp_stamps[i] = NULL;
248	<
249	<	// check to make sure the component isn't already in the list
150	>	//init the forceField paramters
151
152	<	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	<	}
152	>	the_ff->readParams();
153
271	–	#ifdef IS_MPI
272	–	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
273	–	MPIcheckPoint();
274	–	#endif // is_mpi
275	–
154
155	+	// init the atoms
156
157	+	double ux, uy, uz, u, uSqr;
158
159	<	// caclulate the number of atoms, bonds, bends and torsions
159	>	for (k = 0; k < nInfo; k++){
160	>	the_ff->setSimInfo(&(info[k]));
161
162	<	tot_atoms = 0;
163	<	tot_bonds = 0;
164	<	tot_bends = 0;
165	<	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	<	}
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	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
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	<	simnfo->n_atoms = tot_atoms;
174	<	simnfo->n_bonds = tot_bonds;
175	<	simnfo->n_bends = tot_bends;
176	<	simnfo->n_torsions = tot_torsions;
177	<	simnfo->n_SRI = tot_SRI;
300	<	simnfo->n_mol = tot_nmol;
301	<
302	<	simnfo->molMembershipArray = new int[tot_atoms];
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	<	#ifdef IS_MPI
179	>	theBonds = new bond_pair[molInfo.nBonds];
180	>	theBends = new bend_set[molInfo.nBends];
181	>	theTorsions = new torsion_set[molInfo.nTorsions];
182
183	<	// divide the molecules among processors here.
307	<
308	<	mpiSim = new mpiSimulation( simnfo );
309	<
310	<	globalIndex = mpiSim->divideLabor();
183	>	// make the Atoms
184
185	<	// set up the local variables
186	<
187	<	int localMol, allMol;
188	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
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	<	int* mol2proc = mpiSim->getMolToProcMap();
194	<	int* molCompType = mpiSim->getMolComponentType();
195	<
320	<	allMol = 0;
321	<	localMol = 0;
322	<	local_atoms = 0;
323	<	local_bonds = 0;
324	<	local_bends = 0;
325	<	local_torsions = 0;
326	<	globalAtomIndex = 0;
193	>	ux = currentAtom->getOrntX();
194	>	uy = currentAtom->getOrntY();
195	>	uz = currentAtom->getOrntZ();
196
197	+	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
198
199	<	for( i=0; i<n_components; i++ ){
199	>	u = sqrt(uSqr);
200	>	ux = ux / u;
201	>	uy = uy / u;
202	>	uz = uz / u;
203
204	<	for( j=0; j<components_nmol[i]; j++ ){
205	<
206	<	if( mol2proc[allMol] == worldRank ){
207	<
208	<	local_atoms +=    comp_stamps[i]->getNAtoms();
209	<	local_bonds +=    comp_stamps[i]->getNBonds();
210	<	local_bends +=    comp_stamps[i]->getNBends();
211	<	local_torsions += comp_stamps[i]->getNTorsions();
212	<	localMol++;
340	<	}
341	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
342	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
343	<	globalAtomIndex++;
344	<	}
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
214	<	allMol++;
347	<	}
348	<	}
349	<	local_SRI = local_bonds + local_bends + local_torsions;
350	<
351	<	simnfo->n_atoms = mpiSim->getMyNlocal();
352	<
353	<	if( local_atoms != simnfo->n_atoms ){
354	<	sprintf( painCave.errMsg,
355	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
356	<	" localAtom (%d) are not equal.\n",
357	<	simnfo->n_atoms,
358	<	local_atoms );
359	<	painCave.isFatal = 1;
360	<	simError();
361	<	}
214	>	#ifdef IS_MPI
215
216	<	simnfo->n_bonds = local_bonds;
364	<	simnfo->n_bends = local_bends;
365	<	simnfo->n_torsions = local_torsions;
366	<	simnfo->n_SRI = local_SRI;
367	<	simnfo->n_mol = localMol;
216	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
217
369	–	strcpy( checkPointMsg, "Passed nlocal consistency check." );
370	–	MPIcheckPoint();
371	–
372	–
218		#endif // is_mpi
219	<
219	>	}
220
221	<	// create the atom and short range interaction arrays
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	<	Atom::createArrays(simnfo->n_atoms);
228	<	the_atoms = new Atom*[simnfo->n_atoms];
380	<	the_molecules = new Molecule[simnfo->n_mol];
381	<	int molIndex;
227	>	exI = theBonds[j].a;
228	>	exJ = theBonds[j].b;
229
230	<	// initialize the molecule's stampID's
231	<
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	<
237	>	tempEx = exI;
238	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
239	>	tempEx = exJ;
240	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
241
242	<	molIndex = 0;
243	<	for(i=0; i<mpiSim->getTotNmol(); i++){
390	<
391	<	if(mol2proc[i] == worldRank ){
392	<	the_molecules[molIndex].setStampID( molCompType[i] );
393	<	the_molecules[molIndex].setMyIndex( molIndex );
394	<	the_molecules[molIndex].setGlobalIndex( i );
395	<	molIndex++;
396	<	}
397	<	}
242	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
243	>	#else  // isn't MPI
244
245	<	#else // is_mpi
246	<
401	<	molIndex = 0;
402	<	globalAtomIndex = 0;
403	<	for(i=0; i<n_components; i++){
404	<	for(j=0; j<components_nmol[i]; j++ ){
405	<	the_molecules[molIndex].setStampID( i );
406	<	the_molecules[molIndex].setMyIndex( molIndex );
407	<	the_molecules[molIndex].setGlobalIndex( molIndex );
408	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
409	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
410	<	globalAtomIndex++;
245	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
246	>	#endif  //is_mpi
247		}
248	<	molIndex++;
413	<	}
414	<	}
415	<
248	>	excludeOffset += molInfo.nBonds;
249
250	<	#endif // is_mpi
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	+	if (currentBend->haveExtras()){
258	+	extras = currentBend->getExtras();
259	+	current_extra = extras;
260
261	<	if( simnfo->n_SRI ){
262	<
263	<	Exclude::createArray(simnfo->n_SRI);
264	<	the_excludes = new Exclude*[simnfo->n_SRI];
265	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
266	<	simnfo->globalExcludes = new int;
267	<	simnfo->n_exclude = simnfo->n_SRI;
427	<	}
428	<	else{
429	<
430	<	Exclude::createArray( 1 );
431	<	the_excludes = new Exclude*;
432	<	the_excludes[0] = new Exclude(0);
433	<	the_excludes[0]->setPair( 0,0 );
434	<	simnfo->globalExcludes = new int;
435	<	simnfo->globalExcludes[0] = 0;
436	<	simnfo->n_exclude = 0;
437	<	}
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	<	// set the arrays into the SimInfo object
269	>	case 1:
270	>	theBends[j].ghost = (int) current_extra->getDouble() +
271	>	atomOffset;
272	>	theBends[j].isGhost = 1;
273	>	break;
274
275	<	simnfo->atoms = the_atoms;
276	<	simnfo->molecules = the_molecules;
277	<	simnfo->nGlobalExcludes = 0;
278	<	simnfo->excludes = the_excludes;
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	<	// get some of the tricky things that may still be in the globals
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	<
308	<	if( the_globals->haveBox() ){
309	<	simnfo->box_x = the_globals->getBox();
310	<	simnfo->box_y = the_globals->getBox();
311	<	simnfo->box_z = the_globals->getBox();
312	<	}
313	<	else if( the_globals->haveDensity() ){
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	>	tempEx = exI;
315	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
316	>	tempEx = exJ;
317	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
318
319	<	double vol;
320	<	vol = (double)tot_nmol / the_globals->getDensity();
321	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
322	<	simnfo->box_y = simnfo->box_x;
323	<	simnfo->box_z = simnfo->box_x;
324	<	}
463	<	else{
464	<	if( !the_globals->haveBoxX() ){
465	<	sprintf( painCave.errMsg,
466	<	"SimSetup error, no periodic BoxX size given.\n" );
467	<	painCave.isFatal = 1;
468	<	simError();
469	<	}
470	<	simnfo->box_x = the_globals->getBoxX();
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	<	if( !the_globals->haveBoxY() ){
327	<	sprintf( painCave.errMsg,
328	<	"SimSetup error, no periodic BoxY size given.\n" );
329	<	painCave.isFatal = 1;
330	<	simError();
331	<	}
478	<	simnfo->box_y = the_globals->getBoxY();
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	<	if( !the_globals->haveBoxZ() ){
334	<	sprintf( painCave.errMsg,
482	<	"SimSetup error, no periodic BoxZ size given.\n" );
483	<	painCave.isFatal = 1;
484	<	simError();
485	<	}
486	<	simnfo->box_z = the_globals->getBoxZ();
487	<	}
333	>	exI = theTorsions[j].a;
334	>	exJ = theTorsions[j].d;
335
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	<	strcpy( checkPointMsg, "Box size set up" );
344	<	MPIcheckPoint();
345	<	#endif // 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	+	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	+	excludeOffset += molInfo.nTorsions;
354
495	–	// initialize the arrays
355
356	<	the_ff->setSimInfo( simnfo );
356	>	// send the arrays off to the forceField for init.
357
358	<	makeMolecules();
359	<	simnfo->identArray = new int[simnfo->n_atoms];
360	<	for(i=0; i<simnfo->n_atoms; i++){
361	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
362	<	}
504	<
505	<	if (the_globals->getUseRF() ) {
506	<	simnfo->useReactionField = 1;
507	<
508	<	if( !the_globals->haveECR() ){
509	<	sprintf( painCave.errMsg,
510	<	"SimSetup Warning: using default value of 1/2 the smallest "
511	<	"box length for the electrostaticCutoffRadius.\n"
512	<	"I hope you have a very fast processor!\n");
513	<	painCave.isFatal = 0;
514	<	simError();
515	<	double smallest;
516	<	smallest = simnfo->box_x;
517	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
518	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
519	<	simnfo->ecr = 0.5 * smallest;
520	<	} else {
521	<	simnfo->ecr        = the_globals->getECR();
522	<	}
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
364	<	if( !the_globals->haveEST() ){
365	<	sprintf( painCave.errMsg,
366	<	"SimSetup Warning: using default value of 0.05 * the "
367	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
368	<	);
369	<	painCave.isFatal = 0;
370	<	simError();
371	<	simnfo->est = 0.05 * simnfo->ecr;
532	<	} else {
533	<	simnfo->est        = the_globals->getEST();
364	>
365	>	info[k].molecules[i].initialize(molInfo);
366	>
367	>
368	>	atomOffset += molInfo.nAtoms;
369	>	delete[] theBonds;
370	>	delete[] theBends;
371	>	delete[] theTorsions;
372		}
373	<
536	<	if(!the_globals->haveDielectric() ){
537	<	sprintf( painCave.errMsg,
538	<	"SimSetup Error: You are trying to use Reaction Field without"
539	<	"setting a dielectric constant!\n"
540	<	);
541	<	painCave.isFatal = 1;
542	<	simError();
543	<	}
544	<	simnfo->dielectric = the_globals->getDielectric();
545	<	} else {
546	<	if (usesDipoles) {
547	<
548	<	if( !the_globals->haveECR() ){
549	<	sprintf( painCave.errMsg,
550	<	"SimSetup Warning: using default value of 1/2 the smallest "
551	<	"box length for the electrostaticCutoffRadius.\n"
552	<	"I hope you have a very fast processor!\n");
553	<	painCave.isFatal = 0;
554	<	simError();
555	<	double smallest;
556	<	smallest = simnfo->box_x;
557	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
558	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
559	<	simnfo->ecr = 0.5 * smallest;
560	<	} else {
561	<	simnfo->ecr        = the_globals->getECR();
562	<	}
563	<
564	<	if( !the_globals->haveEST() ){
565	<	sprintf( painCave.errMsg,
566	<	"SimSetup Warning: using default value of 5%% of the "
567	<	"electrostaticCutoffRadius for the "
568	<	"electrostaticSkinThickness\n"
569	<	);
570	<	painCave.isFatal = 0;
571	<	simError();
572	<	simnfo->est = 0.05 * simnfo->ecr;
573	<	} else {
574	<	simnfo->est        = the_globals->getEST();
575	<	}
576	<	}
577	<	}
373	>	}
374
375		#ifdef IS_MPI
376	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
376	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
377		MPIcheckPoint();
378		#endif // is_mpi
379
380	<	if( the_globals->haveInitialConfig() ){
585	<
586	<	InitializeFromFile* fileInit;
587	<	#ifdef IS_MPI // is_mpi
588	<	if( worldRank == 0 ){
589	<	#endif //is_mpi
590	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
591	<	#ifdef IS_MPI
592	<	}else fileInit = new InitializeFromFile( NULL );
593	<	#endif
594	<	fileInit->read_xyz( simnfo ); // default velocities on
380	>	// clean up the forcefield
381
382	<	delete fileInit;
383	<	}
384	<	else{
382	>	the_ff->calcRcut();
383	>	the_ff->cleanMe();
384	>	}
385
386	<	#ifdef IS_MPI
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	<	// no init from bass
396	<
397	<	sprintf( painCave.errMsg,
398	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
606	<	painCave.isFatal;
607	<	simError();
608	<
609	<	#else
395	>	double vel[3];
396	>	vel[0] = 0.0;
397	>	vel[1] = 0.0;
398	>	vel[2] = 0.0;
399
400	<	initFromBass();
400	>	temp1 = (double) tot_nmol / 4.0;
401	>	temp2 = pow(temp1, (1.0 / 3.0));
402	>	temp3 = ceil(temp2);
403
404	+	have_extra = 0;
405	+	if (temp2 < temp3){
406	+	// we have a non-complete lattice
407	+	have_extra = 1;
408
409	<	#endif
410	<	}
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	<	#ifdef IS_MPI
418	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
419	<	MPIcheckPoint();
420	<	#endif // is_mpi
421	<
422	<
623	<
624	<
625	<
626	<
627	<
628	<	#ifdef IS_MPI
629	<	if( worldRank == 0 ){
630	<	#endif // is_mpi
631	<
632	<	if( the_globals->haveFinalConfig() ){
633	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
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		}
635	–	else{
636	–	strcpy( simnfo->finalName, inFileName );
637	–	char* endTest;
638	–	int nameLength = strlen( simnfo->finalName );
639	–	endTest = &(simnfo->finalName[nameLength - 5]);
640	–	if( !strcmp( endTest, ".bass" ) ){
641	–	strcpy( endTest, ".eor" );
642	–	}
643	–	else if( !strcmp( endTest, ".BASS" ) ){
644	–	strcpy( endTest, ".eor" );
645	–	}
646	–	else{
647	–	endTest = &(simnfo->finalName[nameLength - 4]);
648	–	if( !strcmp( endTest, ".bss" ) ){
649	–	strcpy( endTest, ".eor" );
650	–	}
651	–	else if( !strcmp( endTest, ".mdl" ) ){
652	–	strcpy( endTest, ".eor" );
653	–	}
654	–	else{
655	–	strcat( simnfo->finalName, ".eor" );
656	–	}
657	–	}
658	–	}
659	–
660	–	// make the sample and status out names
661	–
662	–	strcpy( simnfo->sampleName, inFileName );
663	–	char* endTest;
664	–	int nameLength = strlen( simnfo->sampleName );
665	–	endTest = &(simnfo->sampleName[nameLength - 5]);
666	–	if( !strcmp( endTest, ".bass" ) ){
667	–	strcpy( endTest, ".dump" );
668	–	}
669	–	else if( !strcmp( endTest, ".BASS" ) ){
670	–	strcpy( endTest, ".dump" );
671	–	}
672	–	else{
673	–	endTest = &(simnfo->sampleName[nameLength - 4]);
674	–	if( !strcmp( endTest, ".bss" ) ){
675	–	strcpy( endTest, ".dump" );
676	–	}
677	–	else if( !strcmp( endTest, ".mdl" ) ){
678	–	strcpy( endTest, ".dump" );
679	–	}
680	–	else{
681	–	strcat( simnfo->sampleName, ".dump" );
682	–	}
683	–	}
684	–
685	–	strcpy( simnfo->statusName, inFileName );
686	–	nameLength = strlen( simnfo->statusName );
687	–	endTest = &(simnfo->statusName[nameLength - 5]);
688	–	if( !strcmp( endTest, ".bass" ) ){
689	–	strcpy( endTest, ".stat" );
690	–	}
691	–	else if( !strcmp( endTest, ".BASS" ) ){
692	–	strcpy( endTest, ".stat" );
693	–	}
694	–	else{
695	–	endTest = &(simnfo->statusName[nameLength - 4]);
696	–	if( !strcmp( endTest, ".bss" ) ){
697	–	strcpy( endTest, ".stat" );
698	–	}
699	–	else if( !strcmp( endTest, ".mdl" ) ){
700	–	strcpy( endTest, ".stat" );
701	–	}
702	–	else{
703	–	strcat( simnfo->statusName, ".stat" );
704	–	}
705	–	}
706	–
707	–	#ifdef IS_MPI
424		}
709	–	#endif // is_mpi
710	–
711	–	// set the status, sample, and themal kick times
712	–
713	–	if( the_globals->haveSampleTime() ){
714	–	simnfo->sampleTime = the_globals->getSampleTime();
715	–	simnfo->statusTime = simnfo->sampleTime;
716	–	simnfo->thermalTime = simnfo->sampleTime;
717	–	}
425		else{
426	<	simnfo->sampleTime = the_globals->getRunTime();
427	<	simnfo->statusTime = simnfo->sampleTime;
428	<	simnfo->thermalTime = simnfo->sampleTime;
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	<	if( the_globals->haveStatusTime() ){
433	<	simnfo->statusTime = the_globals->getStatusTime();
434	<	}
432	>	current_mol = 0;
433	>	current_comp_mol = 0;
434	>	current_comp = 0;
435	>	current_atom_ndx = 0;
436
437	<	if( the_globals->haveThermalTime() ){
438	<	simnfo->thermalTime = the_globals->getThermalTime();
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	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
443	>
444	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
445	>
446	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
447	>	}
448	>	}
449		}
450
451	<	// check for the temperature set flag
451	>	if (have_extra){
452	>	done = 0;
453
454	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
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	<	//   // make the longe range forces and the integrator
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	<	//   new AllLong( simnfo );
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
493	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
494	<	new Symplectic(simnfo, the_ff, the_extendedsystem);
493	>	for (i = 0; i < info[0].n_atoms; i++){
494	>	info[0].atoms[i]->setVel(vel);
495		}
496	<	else if( !strcmp( force_field, "LJ" ) ){
746	<	new Verlet( *simnfo, the_ff, the_extendedsystem );
747	<	}
496	>	}
497
498	<	#ifdef IS_MPI
499	<	mpiSim->mpiRefresh();
500	<	#endif
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	<	// initialize the Fortran
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	<	simnfo->refreshSim();
523	<
524	<	if( !strcmp( simnfo->mixingRule, "standard") ){
525	<	the_ff->initForceField( LB_MIXING_RULE );
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		}
761	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
762	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
763	–	}
764	–	else{
765	–	sprintf( painCave.errMsg,
766	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
767	–	simnfo->mixingRule );
768	–	painCave.isFatal = 1;
769	–	simError();
770	–	}
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();
777	<	#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;
785	<	DirectionalAtom* dAtom;
786	<	LinkedAssign* extras;
787	<	LinkedAssign* current_extra;
788	<	AtomStamp* currentAtom;
789	<	BondStamp* currentBond;
790	<	BendStamp* currentBend;
791	<	TorsionStamp* currentTorsion;
558	>	ensembleCase = -1;
559	>	ffCase = -1;
560
561	<	bond_pair* theBonds;
794	<	bend_set* theBends;
795	<	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
800	–	the_ff->readParams();
570
571	<
803	<	// init the atoms
571	>	// get the forceField
572
573	<	double ux, uy, uz, u, uSqr;
806	<
807	<	atomOffset = 0;
808	<	excludeOffset = 0;
809	<	for(i=0; i<simnfo->n_mol; i++){
810	<
811	<	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];
820	<	info.myExcludes = &the_excludes[excludeOffset];
821	<	info.myBonds = new Bond*[info.nBonds];
822	<	info.myBends = new Bend*[info.nBends];
823	<	info.myTorsions = new Torsion*[info.nTorsions];
591	>	// get the ensemble
592
593	<	theBonds = new bond_pair[info.nBonds];
826	<	theBends = new bend_set[info.nBends];
827	<	theTorsions = new torsion_set[info.nTorsions];
828	<
829	<	// make the Atoms
830	<
831	<	for(j=0; j<info.nAtoms; j++){
832	<
833	<	currentAtom = comp_stamps[stampID]->getAtom( j );
834	<	if( currentAtom->haveOrientation() ){
835	<
836	<	dAtom = new DirectionalAtom(j + atomOffset);
837	<	simnfo->n_oriented++;
838	<	info.myAtoms[j] = dAtom;
839	<
840	<	ux = currentAtom->getOrntX();
841	<	uy = currentAtom->getOrntY();
842	<	uz = currentAtom->getOrntZ();
843	<
844	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
845	<
846	<	u = sqrt( uSqr );
847	<	ux = ux / u;
848	<	uy = uy / u;
849	<	uz = uz / u;
850	<
851	<	dAtom->setSUx( ux );
852	<	dAtom->setSUy( uy );
853	<	dAtom->setSUz( uz );
854	<	}
855	<	else{
856	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
857	<	}
858	<	info.myAtoms[j]->setType( currentAtom->getType() );
859	<
860	<	#ifdef IS_MPI
861	<
862	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
863	<
864	<	#endif // is_mpi
865	<	}
866	<
867	<	// make the bonds
868	<	for(j=0; j<info.nBonds; j++){
869	<
870	<	currentBond = comp_stamps[stampID]->getBond( j );
871	<	theBonds[j].a = currentBond->getA() + atomOffset;
872	<	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 ){
879	<	tempEx = exI;
880	<	exI = exJ;
881	<	exJ = tempEx;
882	<	}
883	<	#ifdef IS_MPI
884	<	tempEx = exI;
885	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
886	<	tempEx = exJ;
887	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
888	<
889	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
890	<	#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) );
893	<	#endif  //is_mpi
894	<	}
895	<	excludeOffset += info.nBonds;
627	>	// get the mixing rule
628
629	<	//make the bends
630	<	for(j=0; j<info.nBends; j++){
631	<
900	<	currentBend = comp_stamps[stampID]->getBend( j );
901	<	theBends[j].a = currentBend->getA() + atomOffset;
902	<	theBends[j].b = currentBend->getB() + atomOffset;
903	<	theBends[j].c = currentBend->getC() + atomOffset;
904	<
905	<	if( currentBend->haveExtras() ){
906	<
907	<	extras = currentBend->getExtras();
908	<	current_extra = extras;
909	<
910	<	while( current_extra != NULL ){
911	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
912	<
913	<	switch( current_extra->getType() ){
914	<
915	<	case 0:
916	<	theBends[j].ghost =
917	<	current_extra->getInt() + atomOffset;
918	<	theBends[j].isGhost = 1;
919	<	break;
920	<
921	<	case 1:
922	<	theBends[j].ghost =
923	<	(int)current_extra->getDouble() + atomOffset;
924	<	theBends[j].isGhost = 1;
925	<	break;
926	<
927	<	default:
928	<	sprintf( painCave.errMsg,
929	<	"SimSetup Error: ghostVectorSource was neither a "
930	<	"double nor an int.\n"
931	<	"-->Bend[%d] in %s\n",
932	<	j, comp_stamps[stampID]->getID() );
933	<	painCave.isFatal = 1;
934	<	simError();
935	<	}
936	<	}
937	<
938	<	else{
939	<
940	<	sprintf( painCave.errMsg,
941	<	"SimSetup Error: unhandled bend assignment:\n"
942	<	"    -->%s in Bend[%d] in %s\n",
943	<	current_extra->getlhs(),
944	<	j, comp_stamps[stampID]->getID() );
945	<	painCave.isFatal = 1;
946	<	simError();
947	<	}
948	<
949	<	current_extra = current_extra->getNext();
950	<	}
951	<	}
952	<
953	<	if( !theBends[j].isGhost ){
954	<
955	<	exI = theBends[j].a;
956	<	exJ = theBends[j].c;
957	<	}
958	<	else{
959	<
960	<	exI = theBends[j].a;
961	<	exJ = theBends[j].b;
962	<	}
963	<
964	<	// exclude_I must always be the smaller of the pair
965	<	if( exI > exJ ){
966	<	tempEx = exI;
967	<	exI = exJ;
968	<	exJ = tempEx;
969	<	}
970	<	#ifdef IS_MPI
971	<	tempEx = exI;
972	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
973	<	tempEx = exJ;
974	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
975	<
976	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
977	<	#else  // isn't MPI
978	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
979	<	#endif  //is_mpi
980	<	}
981	<	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++){
984	<
985	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
986	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
987	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
988	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
989	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
990	<
991	<	exI = theTorsions[j].a;
992	<	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 ){
996	<	tempEx = exI;
997	<	exI = exJ;
998	<	exJ = tempEx;
999	<	}
1000	<	#ifdef IS_MPI
1001	<	tempEx = exI;
1002	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1003	<	tempEx = exJ;
1004	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1005	<
1006	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1007	<	#else  // isn't MPI
1008	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1009	<	#endif  //is_mpi
1010	<	}
1011	<	excludeOffset += info.nTorsions;
635	>	the_components = globals->getComponents();
636	>	components_nmol = new int[n_components];
637
1013	–
1014	–	// 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 );
1019	<	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 );
655	<
656	<
1025	<	atomOffset += info.nAtoms;
1026	<	delete[] theBonds;
1027	<	delete[] theBends;
1028	<	delete[] theTorsions;
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	<	#ifdef IS_MPI
1032	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1033	<	MPIcheckPoint();
1034	<	#endif // is_mpi
669	>	// set the status, sample, and thermal kick times
670
671	<	// clean up the forcefield
672	<	the_ff->calcRcut();
673	<	the_ff->cleanMe();
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	<	}
683	>	if (globals->haveStatusTime()){
684	>	info[i].statusTime = globals->getStatusTime();
685	>	}
686
687	<	void SimSetup::initFromBass( void ){
687	>	if (globals->haveThermalTime()){
688	>	info[i].thermalTime = globals->getThermalTime();
689	>	}
690
691	<	int i, j, k;
692	<	int n_cells;
693	<	double cellx, celly, cellz;
694	<	double temp1, temp2, temp3;
695	<	int n_per_extra;
1049	<	int n_extra;
1050	<	int have_extra, done;
691	>	info[i].resetIntegrator = 0;
692	>	if( globals->haveResetTime() ){
693	>	info[i].resetTime = globals->getResetTime();
694	>	info[i].resetIntegrator = 1;
695	>	}
696
697	<	temp1 = (double)tot_nmol / 4.0;
1053	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1054	<	temp3 = ceil( temp2 );
697	>	// check for the temperature set flag
698
699	<	have_extra =0;
700	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1058	<	have_extra =1;
699	>	if (globals->haveTempSet())
700	>	info[i].setTemp = globals->getTempSet();
701
702	<	n_cells = (int)temp3 - 1;
1061	<	cellx = simnfo->box_x / temp3;
1062	<	celly = simnfo->box_y / temp3;
1063	<	cellz = simnfo->box_z / temp3;
1064	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1065	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1066	<	n_per_extra = (int)ceil( temp1 );
702	>	// get some of the tricky things that may still be in the globals
703
704	<	if( n_per_extra > 4){
705	<	sprintf( painCave.errMsg,
706	<	"SimSetup error. There has been an error in constructing"
707	<	" the non-complete lattice.\n" );
708	<	painCave.isFatal = 1;
709	<	simError();
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	>	info[i].setBox(boxVector);
711		}
712	<	}
713	<	else{
714	<	n_cells = (int)temp3;
715	<	cellx = simnfo->box_x / temp3;
716	<	celly = simnfo->box_y / temp3;
717	<	cellz = simnfo->box_z / temp3;
1081	<	}
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	<	current_mol = 0;
720	<	current_comp_mol = 0;
721	<	current_comp = 0;
722	<	current_atom_ndx = 0;
719	>	info[i].setBox(boxVector);
720	>	}
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	<	for( i=0; i < n_cells ; i++ ){
731	<	for( j=0; j < n_cells; j++ ){
732	<	for( k=0; k < n_cells; k++ ){
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,
739	<	j * celly,
740	<	k * 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	<	makeElement( i * cellx + 0.5 * cellx,
747	<	j * celly + 0.5 * celly,
748	<	k * cellz );
746	>	info[i].setBox(boxVector);
747	>	}
748	>	}
749
750	<	makeElement( i * cellx,
751	<	j * celly + 0.5 * celly,
1102	<	k * cellz + 0.5 * cellz );
750	>	//setup seed for random number generator
751	>	int seedValue;
752
753	<	makeElement( i * cellx + 0.5 * cellx,
754	<	j * celly,
755	<	k * cellz + 0.5 * cellz );
753	>	if (globals->haveSeed()){
754	>	seedValue = globals->getSeed();
755	>
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	>	//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 (int i = 0; i < nInfo; i++){
787	+	info[i].setSeed(seedValue);
788		}
789
790	<	if( have_extra ){
791	<	done = 0;
790	>	#ifdef IS_MPI
791	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
792	>	MPIcheckPoint();
793	>	#endif // is_mpi
794	>	}
795
1114	–	int start_ndx;
1115	–	for( i=0; i < (n_cells+1) && !done; i++ ){
1116	–	for( j=0; j < (n_cells+1) && !done; j++ ){
796
797	<	if( i < n_cells ){
797	>	void SimSetup::finalInfoCheck(void){
798	>	int index;
799	>	int usesDipoles;
800	>	int i;
801
802	<	if( j < n_cells ){
803	<	start_ndx = n_cells;
1122	<	}
1123	<	else start_ndx = 0;
1124	<	}
1125	<	else start_ndx = 0;
802	>	for (i = 0; i < nInfo; i++){
803	>	// check electrostatic parameters
804
805	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
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	<	makeElement( i * cellx,
813	<	j * celly,
814	<	k * cellz );
815	<	done = ( current_mol >= tot_nmol );
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	<	if( !done && n_per_extra > 1 ){
1135	<	makeElement( i * cellx + 0.5 * cellx,
1136	<	j * celly + 0.5 * celly,
1137	<	k * cellz );
1138	<	done = ( current_mol >= tot_nmol );
1139	<	}
817	>	double theEcr, theEst;
818
819	<	if( !done && n_per_extra > 2){
820	<	makeElement( i * cellx,
1143	<	j * celly + 0.5 * celly,
1144	<	k * cellz + 0.5 * cellz );
1145	<	done = ( current_mol >= tot_nmol );
1146	<	}
819	>	if (globals->getUseRF()){
820	>	info[i].useReactionField = 1;
821
822	<	if( !done && n_per_extra > 3){
823	<	makeElement( i * cellx + 0.5 * cellx,
824	<	j * celly,
825	<	k * cellz + 0.5 * cellz );
826	<	done = ( current_mol >= tot_nmol );
827	<	}
828	<	}
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 );
1163	<	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;
1170	<	AtomStamp* current_atom;
1171	<	DirectionalAtom* dAtom;
1172	<	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;
1198	<	rotMat[0][1] = 0.0;
1199	<	rotMat[0][2] = 0.0;
946	>	#else
947
948	<	rotMat[1][0] = 0.0;
1202	<	rotMat[1][1] = 1.0;
1203	<	rotMat[1][2] = 0.0;
948	>	initFromBass();
949
1205	–	rotMat[2][0] = 0.0;
1206	–	rotMat[2][1] = 0.0;
1207	–	rotMat[2][2] = 1.0;
950
951	<	dAtom->setA( rotMat );
1210	<	}
1211	<
1212	<	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
1218	–	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<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<RealIntegrator> >(&(info[k]), the_ff);
1393	+	}
1394	+	else
1395	+	myNPTi = new NPTi<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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