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

Comparing:
branches/mmeineke/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 377 by mmeineke, Fri Mar 21 17:42:12 2003 UTC vs.
trunk/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 787 by mmeineke, Thu Sep 25 19:27:15 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	+
26	+	#define FF_DUFF 0
27	+	#define FF_LJ   1
28	+	#define FF_EAM  2
29	+
30	+	using namespace std;
31	+
32		SimSetup::SimSetup(){
33	+	isInfoArray = 0;
34	+	nInfo = 1;
35	+
36		stamps = new MakeStamps();
37		globals = new Globals();
38	<
38	>
39	>
40		#ifdef IS_MPI
41	<	strcpy( checkPointMsg, "SimSetup creation successful" );
41	>	strcpy(checkPointMsg, "SimSetup creation successful");
42		MPIcheckPoint();
43		#endif // IS_MPI
44		}
#	Line 27 | Line 48 | void SimSetup::parseFile( char* fileName ){
48		delete globals;
49		}
50
51	<	void SimSetup::parseFile( char* fileName ){
51	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
52	>	info = the_info;
53	>	nInfo = theNinfo;
54	>	isInfoArray = 1;
55	>	}
56
57	+
58	+	void SimSetup::parseFile(char* fileName){
59		#ifdef IS_MPI
60	<	if( worldRank == 0 ){
60	>	if (worldRank == 0){
61		#endif // is_mpi
62	<
62	>
63		inFileName = fileName;
64	<	set_interface_stamps( stamps, globals );
65	<
64	>	set_interface_stamps(stamps, globals);
65	>
66		#ifdef IS_MPI
67		mpiEventInit();
68		#endif
69
70	<	yacc_BASS( fileName );
70	>	yacc_BASS(fileName);
71
72		#ifdef IS_MPI
73		throwMPIEvent(NULL);
74		}
75	<	else receiveParse();
75	>	else{
76	>	receiveParse();
77	>	}
78		#endif
79
80		}
81
82		#ifdef IS_MPI
83		void SimSetup::receiveParse(void){
84	<
85	<	set_interface_stamps( stamps, globals );
86	<	mpiEventInit();
87	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
84	>	set_interface_stamps(stamps, globals);
85	>	mpiEventInit();
86	>	MPIcheckPoint();
87	>	mpiEventLoop();
88		}
89
90		#endif // is_mpi
91
92	<	void SimSetup::createSim( void ){
92	>	void SimSetup::createSim(void){
93
94	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
94	>	// gather all of the information from the Bass file
95
96	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
96	>	gatherInfo();
97
98	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	simnfo->run_time = the_globals->getRunTime();
98	>	// creation of complex system objects
99
100	<	// get the ones we know are there, yet still may need some work.
81	<	n_components = the_globals->getNComponents();
82	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
100	>	sysObjectsCreation();
101
102	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
102	>	// check on the post processing info
103
104	+	finalInfoCheck();
105
106	<	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
92	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
93	<	else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
94	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
95	<	else{
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Error. Unrecognized force field -> %s\n",
98	<	force_field );
99	<	painCave.isFatal = 1;
100	<	simError();
101	<	}
106	>	// initialize the system coordinates
107
108	<	#ifdef IS_MPI
109	<	strcpy( checkPointMsg, "ForceField creation successful" );
110	<	MPIcheckPoint();
106	<	#endif // is_mpi
108	>	if (!isInfoArray){
109	>	initSystemCoords();
110	>	}
111
112	<
112	>	// make the output filenames
113
114	<	// get the components and calculate the tot_nMol and indvidual n_mol
111	<	the_components = the_globals->getComponents();
112	<	components_nmol = new int[n_components];
113	<	comp_stamps = new MoleculeStamp*[n_components];
114	>	makeOutNames();
115
116	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
116	>	// make the integrator
117
118	<	tot_nmol = 0;
120	<	for( i=0; i<n_components; i++ ){
118	>	makeIntegrator();
119
122	–	if( !the_components[i]->haveNMol() ){
123	–	// we have a problem
124	–	sprintf( painCave.errMsg,
125	–	"SimSetup Error. No global NMol or component NMol"
126	–	" given. Cannot calculate the number of atoms.\n" );
127	–	painCave.isFatal = 1;
128	–	simError();
129	–	}
130	–
131	–	tot_nmol += the_components[i]->getNMol();
132	–	components_nmol[i] = the_components[i]->getNMol();
133	–	}
134	–	}
135	–	else{
136	–	sprintf( painCave.errMsg,
137	–	"SimSetup error.\n"
138	–	"\tSorry, the ability to specify total"
139	–	" nMols and then give molfractions in the components\n"
140	–	"\tis not currently supported."
141	–	" Please give nMol in the components.\n" );
142	–	painCave.isFatal = 1;
143	–	simError();
144	–
145	–
146	–	//     tot_nmol = the_globals->getNMol();
147	–
148	–	//   //we have the total number of molecules, now we check for molfractions
149	–	//     for( i=0; i<n_components; i++ ){
150	–
151	–	//       if( !the_components[i]->haveMolFraction() ){
152	–
153	–	//  if( !the_components[i]->haveNMol() ){
154	–	//    //we have a problem
155	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
156	–	//              << " nMol was given in component
157	–
158	–	}
159	–
120		#ifdef IS_MPI
121	<	strcpy( checkPointMsg, "Have the number of components" );
122	<	MPIcheckPoint();
163	<	#endif // is_mpi
121	>	mpiSim->mpiRefresh();
122	>	#endif
123
124	<	// make an array of molecule stamps that match the components used.
166	<	// also extract the used stamps out into a separate linked list
124	>	// initialize the Fortran
125
126	<	simnfo->nComponents = n_components;
127	<	simnfo->componentsNmol = components_nmol;
170	<	simnfo->compStamps = comp_stamps;
171	<	simnfo->headStamp = new LinkedMolStamp();
172	<
173	<	char* id;
174	<	LinkedMolStamp* headStamp = simnfo->headStamp;
175	<	LinkedMolStamp* currentStamp = NULL;
176	<	for( i=0; i<n_components; i++ ){
126	>	initFortran();
127	>	}
128
178	–	id = the_components[i]->getType();
179	–	comp_stamps[i] = NULL;
180	–
181	–	// check to make sure the component isn't already in the list
129
130	<	comp_stamps[i] = headStamp->match( id );
131	<	if( comp_stamps[i] == NULL ){
132	<
133	<	// extract the component from the list;
134	<
135	<	currentStamp = the_stamps->extractMolStamp( id );
136	<	if( currentStamp == NULL ){
137	<	sprintf( painCave.errMsg,
138	<	"SimSetup error: Component \"%s\" was not found in the "
139	<	"list of declared molecules\n",
140	<	id );
194	<	painCave.isFatal = 1;
195	<	simError();
196	<	}
197	<
198	<	headStamp->add( currentStamp );
199	<	comp_stamps[i] = headStamp->match( id );
200	<	}
201	<	}
130	>	void SimSetup::makeMolecules(void){
131	>	int k;
132	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
133	>	molInit molInfo;
134	>	DirectionalAtom* dAtom;
135	>	LinkedAssign* extras;
136	>	LinkedAssign* current_extra;
137	>	AtomStamp* currentAtom;
138	>	BondStamp* currentBond;
139	>	BendStamp* currentBend;
140	>	TorsionStamp* currentTorsion;
141
142	<	#ifdef IS_MPI
143	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
144	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
142	>	bond_pair* theBonds;
143	>	bend_set* theBends;
144	>	torsion_set* theTorsions;
145
146
147	+	//init the forceField paramters
148
149	<	// caclulate the number of atoms, bonds, bends and torsions
149	>	the_ff->readParams();
150
213	–	tot_atoms = 0;
214	–	tot_bonds = 0;
215	–	tot_bends = 0;
216	–	tot_torsions = 0;
217	–	for( i=0; i<n_components; i++ ){
218	–
219	–	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
220	–	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
221	–	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
222	–	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
223	–	}
151
152	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
152	>	// init the atoms
153
154	<	simnfo->n_atoms = tot_atoms;
228	<	simnfo->n_bonds = tot_bonds;
229	<	simnfo->n_bends = tot_bends;
230	<	simnfo->n_torsions = tot_torsions;
231	<	simnfo->n_SRI = tot_SRI;
232	<	simnfo->n_mol = tot_nmol;
154	>	double ux, uy, uz, u, uSqr;
155
156	<
157	<	#ifdef IS_MPI
156	>	for (k = 0; k < nInfo; k++){
157	>	the_ff->setSimInfo(&(info[k]));
158
159	<	// divide the molecules among processors here.
160	<
161	<	mpiSim = new mpiSimulation( simnfo );
162	<
241	<
159	>	atomOffset = 0;
160	>	excludeOffset = 0;
161	>	for (i = 0; i < info[k].n_mol; i++){
162	>	stampID = info[k].molecules[i].getStampID();
163
164	<	globalIndex = mpiSim->divideLabor();
164	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
165	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
166	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
167	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
168	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
169
170	+	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
171	+	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
172	+	molInfo.myBonds = new Bond * [molInfo.nBonds];
173	+	molInfo.myBends = new Bend * [molInfo.nBends];
174	+	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
175
176	+	theBonds = new bond_pair[molInfo.nBonds];
177	+	theBends = new bend_set[molInfo.nBends];
178	+	theTorsions = new torsion_set[molInfo.nTorsions];
179
180	<	// set up the local variables
248	<
249	<	int localMol, allMol;
250	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
251	<
252	<	allMol = 0;
253	<	localMol = 0;
254	<	local_atoms = 0;
255	<	local_bonds = 0;
256	<	local_bends = 0;
257	<	local_torsions = 0;
258	<	for( i=0; i<n_components; i++ ){
180	>	// make the Atoms
181
182	<	for( j=0; j<components_nmol[i]; j++ ){
183	<
184	<	if( mpiSim->getMyMolStart() <= allMol &&
185	<	allMol <= mpiSim->getMyMolEnd() ){
186	<
187	<	local_atoms +=    comp_stamps[i]->getNAtoms();
188	<	local_bonds +=    comp_stamps[i]->getNBonds();
267	<	local_bends +=    comp_stamps[i]->getNBends();
268	<	local_torsions += comp_stamps[i]->getNTorsions();
269	<	localMol++;
270	<	}
271	<	allMol++;
272	<	}
273	<	}
274	<	local_SRI = local_bonds + local_bends + local_torsions;
275	<
182	>	for (j = 0; j < molInfo.nAtoms; j++){
183	>	currentAtom = comp_stamps[stampID]->getAtom(j);
184	>	if (currentAtom->haveOrientation()){
185	>	dAtom = new DirectionalAtom((j + atomOffset),
186	>	info[k].getConfiguration());
187	>	info[k].n_oriented++;
188	>	molInfo.myAtoms[j] = dAtom;
189
190	<	simnfo->n_atoms = mpiSim->getMyNlocal();
191	<
192	<	if( local_atoms != simnfo->n_atoms ){
280	<	sprintf( painCave.errMsg,
281	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282	<	" localAtom (%d) are note equal.\n",
283	<	simnfo->n_atoms,
284	<	local_atoms );
285	<	painCave.isFatal = 1;
286	<	simError();
287	<	}
190	>	ux = currentAtom->getOrntX();
191	>	uy = currentAtom->getOrntY();
192	>	uz = currentAtom->getOrntZ();
193
194	<	simnfo->n_bonds = local_bonds;
290	<	simnfo->n_bends = local_bends;
291	<	simnfo->n_torsions = local_torsions;
292	<	simnfo->n_SRI = local_SRI;
293	<	simnfo->n_mol = localMol;
194	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
195
196	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
197	<	MPIcheckPoint();
198	<
199	<
299	<	#endif // is_mpi
300	<
196	>	u = sqrt(uSqr);
197	>	ux = ux / u;
198	>	uy = uy / u;
199	>	uz = uz / u;
200
201	<	// create the atom and short range interaction arrays
201	>	dAtom->setSUx(ux);
202	>	dAtom->setSUy(uy);
203	>	dAtom->setSUz(uz);
204	>	}
205	>	else{
206	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
207	>	info[k].getConfiguration());
208	>	}
209	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
210
211	<	Atom::createArrays(simnfo->n_atoms);
305	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
211	>	#ifdef IS_MPI
212
213	+	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
214
215	<	if( simnfo->n_SRI ){
216	<	the_sris = new SRI*[simnfo->n_SRI];
311	<	the_excludes = new int[2 * simnfo->n_SRI];
312	<	simnfo->globalExcludes = new int;
313	<	simnfo->n_exclude = tot_SRI;
314	<	}
315	<	else{
316	<
317	<	the_excludes = new int[2];
318	<	the_excludes[0] = 0;
319	<	the_excludes[1] = 0;
320	<	simnfo->globalExcludes = new int;
321	<	simnfo->globalExcludes[0] = 0;
215	>	#endif // is_mpi
216	>	}
217
218	<	simnfo->n_exclude = 1;
219	<	}
218	>	// make the bonds
219	>	for (j = 0; j < molInfo.nBonds; j++){
220	>	currentBond = comp_stamps[stampID]->getBond(j);
221	>	theBonds[j].a = currentBond->getA() + atomOffset;
222	>	theBonds[j].b = currentBond->getB() + atomOffset;
223
224	<	// set the arrays into the SimInfo object
224	>	exI = theBonds[j].a;
225	>	exJ = theBonds[j].b;
226
227	<	simnfo->atoms = the_atoms;
228	<	simnfo->sr_interactions = the_sris;
229	<	simnfo->nGlobalExcludes = 0;
230	<	simnfo->excludes = the_excludes;
227	>	// exclude_I must always be the smaller of the pair
228	>	if (exI > exJ){
229	>	tempEx = exI;
230	>	exI = exJ;
231	>	exJ = tempEx;
232	>	}
233	>	#ifdef IS_MPI
234	>	tempEx = exI;
235	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
236	>	tempEx = exJ;
237	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
238
239	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
240	+	#else  // isn't MPI
241
242	<	// get some of the tricky things that may still be in the globals
242	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
243	>	#endif  //is_mpi
244	>	}
245	>	excludeOffset += molInfo.nBonds;
246
247	<	if( simnfo->n_dipoles ){
247	>	//make the bends
248	>	for (j = 0; j < molInfo.nBends; j++){
249	>	currentBend = comp_stamps[stampID]->getBend(j);
250	>	theBends[j].a = currentBend->getA() + atomOffset;
251	>	theBends[j].b = currentBend->getB() + atomOffset;
252	>	theBends[j].c = currentBend->getC() + atomOffset;
253
254	<	if( !the_globals->haveRRF() ){
255	<	sprintf( painCave.errMsg,
256	<	"SimSetup Error, system has dipoles, but no rRF was set.\n");
341	<	painCave.isFatal = 1;
342	<	simError();
343	<	}
344	<	if( !the_globals->haveDielectric() ){
345	<	sprintf( painCave.errMsg,
346	<	"SimSetup Error, system has dipoles, but no"
347	<	" dielectric was set.\n" );
348	<	painCave.isFatal = 1;
349	<	simError();
350	<	}
254	>	if (currentBend->haveExtras()){
255	>	extras = currentBend->getExtras();
256	>	current_extra = extras;
257
258	<	simnfo->rRF        = the_globals->getRRF();
259	<	simnfo->dielectric = the_globals->getDielectric();
260	<	}
258	>	while (current_extra != NULL){
259	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
260	>	switch (current_extra->getType()){
261	>	case 0:
262	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
263	>	theBends[j].isGhost = 1;
264	>	break;
265
266	<	#ifdef IS_MPI
267	<	strcpy( checkPointMsg, "rRf and dielectric check out" );
268	<	MPIcheckPoint();
269	<	#endif // is_mpi
270	<
361	<	if( the_globals->haveBox() ){
362	<	simnfo->box_x = the_globals->getBox();
363	<	simnfo->box_y = the_globals->getBox();
364	<	simnfo->box_z = the_globals->getBox();
365	<	}
366	<	else if( the_globals->haveDensity() ){
266	>	case 1:
267	>	theBends[j].ghost = (int) current_extra->getDouble() +
268	>	atomOffset;
269	>	theBends[j].isGhost = 1;
270	>	break;
271
272	<	double vol;
273	<	vol = (double)tot_nmol / the_globals->getDensity();
274	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
275	<	simnfo->box_y = simnfo->box_x;
276	<	simnfo->box_z = simnfo->box_x;
277	<	}
278	<	else{
279	<	if( !the_globals->haveBoxX() ){
280	<	sprintf( painCave.errMsg,
281	<	"SimSetup error, no periodic BoxX size given.\n" );
282	<	painCave.isFatal = 1;
283	<	simError();
284	<	}
285	<	simnfo->box_x = the_globals->getBoxX();
272	>	default:
273	>	sprintf(painCave.errMsg,
274	>	"SimSetup Error: ghostVectorSource was neither a "
275	>	"double nor an int.\n"
276	>	"-->Bend[%d] in %s\n",
277	>	j, comp_stamps[stampID]->getID());
278	>	painCave.isFatal = 1;
279	>	simError();
280	>	}
281	>	}
282	>	else{
283	>	sprintf(painCave.errMsg,
284	>	"SimSetup Error: unhandled bend assignment:\n"
285	>	"    -->%s in Bend[%d] in %s\n",
286	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
287	>	painCave.isFatal = 1;
288	>	simError();
289	>	}
290
291	<	if( !the_globals->haveBoxY() ){
292	<	sprintf( painCave.errMsg,
293	<	"SimSetup error, no periodic BoxY size given.\n" );
386	<	painCave.isFatal = 1;
387	<	simError();
388	<	}
389	<	simnfo->box_y = the_globals->getBoxY();
291	>	current_extra = current_extra->getNext();
292	>	}
293	>	}
294
295	<	if( !the_globals->haveBoxZ() ){
296	<	sprintf( painCave.errMsg,
297	<	"SimSetup error, no periodic BoxZ size given.\n" );
298	<	painCave.isFatal = 1;
299	<	simError();
300	<	}
301	<	simnfo->box_z = the_globals->getBoxZ();
302	<	}
295	>	if (!theBends[j].isGhost){
296	>	exI = theBends[j].a;
297	>	exJ = theBends[j].c;
298	>	}
299	>	else{
300	>	exI = theBends[j].a;
301	>	exJ = theBends[j].b;
302	>	}
303
304	+	// exclude_I must always be the smaller of the pair
305	+	if (exI > exJ){
306	+	tempEx = exI;
307	+	exI = exJ;
308	+	exJ = tempEx;
309	+	}
310		#ifdef IS_MPI
311	<	strcpy( checkPointMsg, "Box size set up" );
312	<	MPIcheckPoint();
313	<	#endif // is_mpi
311	>	tempEx = exI;
312	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
313	>	tempEx = exJ;
314	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
315
316	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
317	+	#else  // isn't MPI
318	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
319	+	#endif  //is_mpi
320	+	}
321	+	excludeOffset += molInfo.nBends;
322
323	<	// initialize the arrays
323	>	for (j = 0; j < molInfo.nTorsions; j++){
324	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
325	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
326	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
327	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
328	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
329
330	<	the_ff->setSimInfo( simnfo );
330	>	exI = theTorsions[j].a;
331	>	exJ = theTorsions[j].d;
332
333	<	makeAtoms();
334	<	simnfo->identArray = new int[simnfo->n_atoms];
335	<	for(i=0; i<simnfo->n_atoms; i++){
336	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
337	<	}
338	<
339	<	if( tot_bonds ){
340	<	makeBonds();
341	<	}
342	<
343	<	if( tot_bends ){
421	<	makeBends();
422	<	}
423	<
424	<	if( tot_torsions ){
425	<	makeTorsions();
426	<	}
333	>	// exclude_I must always be the smaller of the pair
334	>	if (exI > exJ){
335	>	tempEx = exI;
336	>	exI = exJ;
337	>	exJ = tempEx;
338	>	}
339	>	#ifdef IS_MPI
340	>	tempEx = exI;
341	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
342	>	tempEx = exJ;
343	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
344
345	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
346	+	#else  // isn't MPI
347	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
348	+	#endif  //is_mpi
349	+	}
350	+	excludeOffset += molInfo.nTorsions;
351
352
353	+	// send the arrays off to the forceField for init.
354
355	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
356	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
357	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
358	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
359	+	theTorsions);
360
361
362	<	if( the_globals->haveInitialConfig() ){
434	<
435	<	InitializeFromFile* fileInit;
436	<	#ifdef IS_MPI // is_mpi
437	<	if( worldRank == 0 ){
438	<	#endif //is_mpi
439	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
440	<	#ifdef IS_MPI
441	<	}else fileInit = new InitializeFromFile( NULL );
442	<	#endif
443	<	fileInit->read_xyz( simnfo ); // default velocities on
362	>	info[k].molecules[i].initialize(molInfo);
363
445	–	delete fileInit;
446	–	}
447	–	else{
364
365	<	#ifdef IS_MPI
365	>	atomOffset += molInfo.nAtoms;
366	>	delete[] theBonds;
367	>	delete[] theBends;
368	>	delete[] theTorsions;
369	>	}
370	>	}
371
372	<	// no init from bass
373	<
374	<	sprintf( painCave.errMsg,
375	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
455	<	painCave.isFatal;
456	<	simError();
457	<
458	<	#else
372	>	#ifdef IS_MPI
373	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
374	>	MPIcheckPoint();
375	>	#endif // is_mpi
376
377	<	initFromBass();
377	>	// clean up the forcefield
378
379	+	the_ff->calcRcut();
380	+	the_ff->cleanMe();
381	+	}
382
383	<	#endif
384	<	}
383	>	void SimSetup::initFromBass(void){
384	>	int i, j, k;
385	>	int n_cells;
386	>	double cellx, celly, cellz;
387	>	double temp1, temp2, temp3;
388	>	int n_per_extra;
389	>	int n_extra;
390	>	int have_extra, done;
391
392	<	#ifdef IS_MPI
393	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
394	<	MPIcheckPoint();
395	<	#endif // is_mpi
392	>	double vel[3];
393	>	vel[0] = 0.0;
394	>	vel[1] = 0.0;
395	>	vel[2] = 0.0;
396
397	+	temp1 = (double) tot_nmol / 4.0;
398	+	temp2 = pow(temp1, (1.0 / 3.0));
399	+	temp3 = ceil(temp2);
400
401	<
402	<
403	<
401	>	have_extra = 0;
402	>	if (temp2 < temp3){
403	>	// we have a non-complete lattice
404	>	have_extra = 1;
405
406	<
407	<	#ifdef IS_MPI
408	<	if( worldRank == 0 ){
409	<	#endif // is_mpi
410	<
411	<	if( the_globals->haveFinalConfig() ){
412	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
406	>	n_cells = (int) temp3 - 1;
407	>	cellx = info[0].boxL[0] / temp3;
408	>	celly = info[0].boxL[1] / temp3;
409	>	cellz = info[0].boxL[2] / temp3;
410	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
411	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
412	>	n_per_extra = (int) ceil(temp1);
413	>
414	>	if (n_per_extra > 4){
415	>	sprintf(painCave.errMsg,
416	>	"SimSetup error. There has been an error in constructing"
417	>	" the non-complete lattice.\n");
418	>	painCave.isFatal = 1;
419	>	simError();
420		}
484	–	else{
485	–	strcpy( simnfo->finalName, inFileName );
486	–	char* endTest;
487	–	int nameLength = strlen( simnfo->finalName );
488	–	endTest = &(simnfo->finalName[nameLength - 5]);
489	–	if( !strcmp( endTest, ".bass" ) ){
490	–	strcpy( endTest, ".eor" );
491	–	}
492	–	else if( !strcmp( endTest, ".BASS" ) ){
493	–	strcpy( endTest, ".eor" );
494	–	}
495	–	else{
496	–	endTest = &(simnfo->finalName[nameLength - 4]);
497	–	if( !strcmp( endTest, ".bss" ) ){
498	–	strcpy( endTest, ".eor" );
499	–	}
500	–	else if( !strcmp( endTest, ".mdl" ) ){
501	–	strcpy( endTest, ".eor" );
502	–	}
503	–	else{
504	–	strcat( simnfo->finalName, ".eor" );
505	–	}
506	–	}
507	–	}
508	–
509	–	// make the sample and status out names
510	–
511	–	strcpy( simnfo->sampleName, inFileName );
512	–	char* endTest;
513	–	int nameLength = strlen( simnfo->sampleName );
514	–	endTest = &(simnfo->sampleName[nameLength - 5]);
515	–	if( !strcmp( endTest, ".bass" ) ){
516	–	strcpy( endTest, ".dump" );
517	–	}
518	–	else if( !strcmp( endTest, ".BASS" ) ){
519	–	strcpy( endTest, ".dump" );
520	–	}
521	–	else{
522	–	endTest = &(simnfo->sampleName[nameLength - 4]);
523	–	if( !strcmp( endTest, ".bss" ) ){
524	–	strcpy( endTest, ".dump" );
525	–	}
526	–	else if( !strcmp( endTest, ".mdl" ) ){
527	–	strcpy( endTest, ".dump" );
528	–	}
529	–	else{
530	–	strcat( simnfo->sampleName, ".dump" );
531	–	}
532	–	}
533	–
534	–	strcpy( simnfo->statusName, inFileName );
535	–	nameLength = strlen( simnfo->statusName );
536	–	endTest = &(simnfo->statusName[nameLength - 5]);
537	–	if( !strcmp( endTest, ".bass" ) ){
538	–	strcpy( endTest, ".stat" );
539	–	}
540	–	else if( !strcmp( endTest, ".BASS" ) ){
541	–	strcpy( endTest, ".stat" );
542	–	}
543	–	else{
544	–	endTest = &(simnfo->statusName[nameLength - 4]);
545	–	if( !strcmp( endTest, ".bss" ) ){
546	–	strcpy( endTest, ".stat" );
547	–	}
548	–	else if( !strcmp( endTest, ".mdl" ) ){
549	–	strcpy( endTest, ".stat" );
550	–	}
551	–	else{
552	–	strcat( simnfo->statusName, ".stat" );
553	–	}
554	–	}
555	–
556	–	#ifdef IS_MPI
421		}
558	–	#endif // is_mpi
559	–
560	–	// set the status, sample, and themal kick times
561	–
562	–	if( the_globals->haveSampleTime() ){
563	–	simnfo->sampleTime = the_globals->getSampleTime();
564	–	simnfo->statusTime = simnfo->sampleTime;
565	–	simnfo->thermalTime = simnfo->sampleTime;
566	–	}
422		else{
423	<	simnfo->sampleTime = the_globals->getRunTime();
424	<	simnfo->statusTime = simnfo->sampleTime;
425	<	simnfo->thermalTime = simnfo->sampleTime;
423	>	n_cells = (int) temp3;
424	>	cellx = info[0].boxL[0] / temp3;
425	>	celly = info[0].boxL[1] / temp3;
426	>	cellz = info[0].boxL[2] / temp3;
427		}
428
429	<	if( the_globals->haveStatusTime() ){
430	<	simnfo->statusTime = the_globals->getStatusTime();
431	<	}
429	>	current_mol = 0;
430	>	current_comp_mol = 0;
431	>	current_comp = 0;
432	>	current_atom_ndx = 0;
433
434	<	if( the_globals->haveThermalTime() ){
435	<	simnfo->thermalTime = the_globals->getThermalTime();
436	<	}
434	>	for (i = 0; i < n_cells ; i++){
435	>	for (j = 0; j < n_cells; j++){
436	>	for (k = 0; k < n_cells; k++){
437	>	makeElement(i * cellx, j * celly, k * cellz);
438
439	<	// check for the temperature set flag
439	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
440
441	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
441	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
442
443	+	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
444	+	}
445	+	}
446	+	}
447
448	<	//   // make the longe range forces and the integrator
448	>	if (have_extra){
449	>	done = 0;
450
451	<	//   new AllLong( simnfo );
451	>	int start_ndx;
452	>	for (i = 0; i < (n_cells + 1) && !done; i++){
453	>	for (j = 0; j < (n_cells + 1) && !done; j++){
454	>	if (i < n_cells){
455	>	if (j < n_cells){
456	>	start_ndx = n_cells;
457	>	}
458	>	else
459	>	start_ndx = 0;
460	>	}
461	>	else
462	>	start_ndx = 0;
463
464	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
465	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
466	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
593	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
464	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
465	>	makeElement(i * cellx, j * celly, k * cellz);
466	>	done = (current_mol >= tot_nmol);
467
468	+	if (!done && n_per_extra > 1){
469	+	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
470	+	k * cellz);
471	+	done = (current_mol >= tot_nmol);
472	+	}
473
474	+	if (!done && n_per_extra > 2){
475	+	makeElement(i * cellx, j * celly + 0.5 * celly,
476	+	k * cellz + 0.5 * cellz);
477	+	done = (current_mol >= tot_nmol);
478	+	}
479
480	<	// initialize the Fortran
481	<
482	<	simnfo->refreshSim();
483	<
484	<	if( !strcmp( simnfo->mixingRule, "standard") ){
485	<	the_ff->initForceField( LB_MIXING_RULE );
480	>	if (!done && n_per_extra > 3){
481	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
482	>	k * cellz + 0.5 * cellz);
483	>	done = (current_mol >= tot_nmol);
484	>	}
485	>	}
486	>	}
487	>	}
488		}
489	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
490	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
489	>
490	>	for (i = 0; i < info[0].n_atoms; i++){
491	>	info[0].atoms[i]->setVel(vel);
492		}
493	+	}
494	+
495	+	void SimSetup::makeElement(double x, double y, double z){
496	+	int k;
497	+	AtomStamp* current_atom;
498	+	DirectionalAtom* dAtom;
499	+	double rotMat[3][3];
500	+	double pos[3];
501	+
502	+	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
503	+	current_atom = comp_stamps[current_comp]->getAtom(k);
504	+	if (!current_atom->havePosition()){
505	+	sprintf(painCave.errMsg,
506	+	"SimSetup:initFromBass error.\n"
507	+	"\tComponent %s, atom %s does not have a position specified.\n"
508	+	"\tThe initialization routine is unable to give a start"
509	+	" position.\n",
510	+	comp_stamps[current_comp]->getID(), current_atom->getType());
511	+	painCave.isFatal = 1;
512	+	simError();
513	+	}
514	+
515	+	pos[0] = x + current_atom->getPosX();
516	+	pos[1] = y + current_atom->getPosY();
517	+	pos[2] = z + current_atom->getPosZ();
518	+
519	+	info[0].atoms[current_atom_ndx]->setPos(pos);
520	+
521	+	if (info[0].atoms[current_atom_ndx]->isDirectional()){
522	+	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
523	+
524	+	rotMat[0][0] = 1.0;
525	+	rotMat[0][1] = 0.0;
526	+	rotMat[0][2] = 0.0;
527	+
528	+	rotMat[1][0] = 0.0;
529	+	rotMat[1][1] = 1.0;
530	+	rotMat[1][2] = 0.0;
531	+
532	+	rotMat[2][0] = 0.0;
533	+	rotMat[2][1] = 0.0;
534	+	rotMat[2][2] = 1.0;
535	+
536	+	dAtom->setA(rotMat);
537	+	}
538	+
539	+	current_atom_ndx++;
540	+	}
541	+
542	+	current_mol++;
543	+	current_comp_mol++;
544	+
545	+	if (current_comp_mol >= components_nmol[current_comp]){
546	+	current_comp_mol = 0;
547	+	current_comp++;
548	+	}
549	+	}
550	+
551	+
552	+	void SimSetup::gatherInfo(void){
553	+	int i;
554	+
555	+	ensembleCase = -1;
556	+	ffCase = -1;
557	+
558	+	// set the easy ones first
559	+
560	+	for (i = 0; i < nInfo; i++){
561	+	info[i].target_temp = globals->getTargetTemp();
562	+	info[i].dt = globals->getDt();
563	+	info[i].run_time = globals->getRunTime();
564	+	}
565	+	n_components = globals->getNComponents();
566	+
567	+
568	+	// get the forceField
569	+
570	+	strcpy(force_field, globals->getForceField());
571	+
572	+	if (!strcasecmp(force_field, "DUFF")){
573	+	ffCase = FF_DUFF;
574	+	}
575	+	else if (!strcasecmp(force_field, "LJ")){
576	+	ffCase = FF_LJ;
577	+	}
578	+	else if (!strcasecmp(force_field, "EAM")){
579	+	ffCase = FF_EAM;
580	+	}
581		else{
582	<	sprintf( painCave.errMsg,
583	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
584	<	simnfo->mixingRule );
582	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
583	>	force_field);
584	>	painCave.isFatal = 1;
585	>	simError();
586	>	}
587	>
588	>	// get the ensemble
589	>
590	>	strcpy(ensemble, globals->getEnsemble());
591	>
592	>	if (!strcasecmp(ensemble, "NVE")){
593	>	ensembleCase = NVE_ENS;
594	>	}
595	>	else if (!strcasecmp(ensemble, "NVT")){
596	>	ensembleCase = NVT_ENS;
597	>	}
598	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
599	>	ensembleCase = NPTi_ENS;
600	>	}
601	>	else if (!strcasecmp(ensemble, "NPTf")){
602	>	ensembleCase = NPTf_ENS;
603	>	}
604	>	else{
605	>	sprintf(painCave.errMsg,
606	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
607	>	"reverting to NVE for this simulation.\n",
608	>	ensemble);
609	>	painCave.isFatal = 0;
610	>	simError();
611	>	strcpy(ensemble, "NVE");
612	>	ensembleCase = NVE_ENS;
613	>	}
614	>
615	>	for (i = 0; i < nInfo; i++){
616	>	strcpy(info[i].ensemble, ensemble);
617	>
618	>	// get the mixing rule
619	>
620	>	strcpy(info[i].mixingRule, globals->getMixingRule());
621	>	info[i].usePBC = globals->getPBC();
622	>	}
623	>
624	>	// get the components and calculate the tot_nMol and indvidual n_mol
625	>
626	>	the_components = globals->getComponents();
627	>	components_nmol = new int[n_components];
628	>
629	>
630	>	if (!globals->haveNMol()){
631	>	// we don't have the total number of molecules, so we assume it is
632	>	// given in each component
633	>
634	>	tot_nmol = 0;
635	>	for (i = 0; i < n_components; i++){
636	>	if (!the_components[i]->haveNMol()){
637	>	// we have a problem
638	>	sprintf(painCave.errMsg,
639	>	"SimSetup Error. No global NMol or component NMol"
640	>	" given. Cannot calculate the number of atoms.\n");
641	>	painCave.isFatal = 1;
642	>	simError();
643	>	}
644	>
645	>	tot_nmol += the_components[i]->getNMol();
646	>	components_nmol[i] = the_components[i]->getNMol();
647	>	}
648	>	}
649	>	else{
650	>	sprintf(painCave.errMsg,
651	>	"SimSetup error.\n"
652	>	"\tSorry, the ability to specify total"
653	>	" nMols and then give molfractions in the components\n"
654	>	"\tis not currently supported."
655	>	" Please give nMol in the components.\n");
656		painCave.isFatal = 1;
657		simError();
658		}
659
660	+	// set the status, sample, and thermal kick times
661
662	<	#ifdef IS_MPI
663	<	strcpy( checkPointMsg,
664	<	"Successfully intialized the mixingRule for Fortran." );
665	<	MPIcheckPoint();
666	<	#endif // is_mpi
667	<	}
662	>	for (i = 0; i < nInfo; i++){
663	>	if (globals->haveSampleTime()){
664	>	info[i].sampleTime = globals->getSampleTime();
665	>	info[i].statusTime = info[i].sampleTime;
666	>	info[i].thermalTime = info[i].sampleTime;
667	>	}
668	>	else{
669	>	info[i].sampleTime = globals->getRunTime();
670	>	info[i].statusTime = info[i].sampleTime;
671	>	info[i].thermalTime = info[i].sampleTime;
672	>	}
673
674	<	void SimSetup::makeAtoms( void ){
674	>	if (globals->haveStatusTime()){
675	>	info[i].statusTime = globals->getStatusTime();
676	>	}
677
678	<	int i, j, k, index;
679	<	double ux, uy, uz, uSqr, u;
680	<	AtomStamp* current_atom;
678	>	if (globals->haveThermalTime()){
679	>	info[i].thermalTime = globals->getThermalTime();
680	>	}
681
682	<	DirectionalAtom* dAtom;
683	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
682	>	info[i].resetIntegrator = 0;
683	>	if( globals->haveResetTime() ){
684	>	info[i].resetTime = globals->getResetTime();
685	>	info[i].resetIntegrator = 1;
686	>	}
687
688	<	lMolIndex = 0;
633	<	molIndex = 0;
634	<	index = 0;
635	<	for( i=0; i<n_components; i++ ){
688	>	// check for the temperature set flag
689
690	<	for( j=0; j<components_nmol[i]; j++ ){
690	>	if (globals->haveTempSet())
691	>	info[i].setTemp = globals->getTempSet();
692
693	<	#ifdef IS_MPI
640	<	if( mpiSim->getMyMolStart() <= molIndex &&
641	<	molIndex <= mpiSim->getMyMolEnd() ){
642	<	#endif // is_mpi
693	>	// get some of the tricky things that may still be in the globals
694
695	<	molStart = index;
696	<	nMemb = comp_stamps[i]->getNAtoms();
697	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
698	<
699	<	current_atom = comp_stamps[i]->getAtom( k );
649	<	if( current_atom->haveOrientation() ){
650	<
651	<	dAtom = new DirectionalAtom(index);
652	<	simnfo->n_oriented++;
653	<	the_atoms[index] = dAtom;
654	<
655	<	ux = current_atom->getOrntX();
656	<	uy = current_atom->getOrntY();
657	<	uz = current_atom->getOrntZ();
658	<
659	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
660	<
661	<	u = sqrt( uSqr );
662	<	ux = ux / u;
663	<	uy = uy / u;
664	<	uz = uz / u;
665	<
666	<	dAtom->setSUx( ux );
667	<	dAtom->setSUy( uy );
668	<	dAtom->setSUz( uz );
669	<	}
670	<	else{
671	<	the_atoms[index] = new GeneralAtom(index);
672	<	}
673	<	the_atoms[index]->setType( current_atom->getType() );
674	<	the_atoms[index]->setIndex( index );
675	<
676	<	// increment the index and repeat;
677	<	index++;
678	<	}
679	<
680	<	molEnd = index -1;
681	<	the_molecules[lMolIndex].setNMembers( nMemb );
682	<	the_molecules[lMolIndex].setStartAtom( molStart );
683	<	the_molecules[lMolIndex].setEndAtom( molEnd );
684	<	the_molecules[lMolIndex].setStampID( i );
685	<	lMolIndex++;
695	>	double boxVector[3];
696	>	if (globals->haveBox()){
697	>	boxVector[0] = globals->getBox();
698	>	boxVector[1] = globals->getBox();
699	>	boxVector[2] = globals->getBox();
700
701	<	#ifdef IS_MPI
688	<	}
689	<	#endif //is_mpi
690	<
691	<	molIndex++;
701	>	info[i].setBox(boxVector);
702		}
703	<	}
703	>	else if (globals->haveDensity()){
704	>	double vol;
705	>	vol = (double) tot_nmol / globals->getDensity();
706	>	boxVector[0] = pow(vol, (1.0 / 3.0));
707	>	boxVector[1] = boxVector[0];
708	>	boxVector[2] = boxVector[0];
709
710	<	#ifdef IS_MPI
711	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
712	<
713	<	delete[] globalIndex;
710	>	info[i].setBox(boxVector);
711	>	}
712	>	else{
713	>	if (!globals->haveBoxX()){
714	>	sprintf(painCave.errMsg,
715	>	"SimSetup error, no periodic BoxX size given.\n");
716	>	painCave.isFatal = 1;
717	>	simError();
718	>	}
719	>	boxVector[0] = globals->getBoxX();
720
721	<	mpiSim->mpiRefresh();
722	<	#endif //IS_MPI
723	<
724	<	the_ff->initializeAtoms();
725	<	}
721	>	if (!globals->haveBoxY()){
722	>	sprintf(painCave.errMsg,
723	>	"SimSetup error, no periodic BoxY size given.\n");
724	>	painCave.isFatal = 1;
725	>	simError();
726	>	}
727	>	boxVector[1] = globals->getBoxY();
728
729	<	void SimSetup::makeBonds( void ){
730	<
731	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
732	<	bond_pair* the_bonds;
733	<	BondStamp* current_bond;
711	<
712	<	the_bonds = new bond_pair[tot_bonds];
713	<	index = 0;
714	<	offset = 0;
715	<	molIndex = 0;
716	<
717	<	for( i=0; i<n_components; i++ ){
718	<
719	<	for( j=0; j<components_nmol[i]; j++ ){
720	<
721	<	#ifdef IS_MPI
722	<	if( mpiSim->getMyMolStart() <= molIndex &&
723	<	molIndex <= mpiSim->getMyMolEnd() ){
724	<	#endif // is_mpi
725	<
726	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
727	<
728	<	current_bond = comp_stamps[i]->getBond( k );
729	<	the_bonds[index].a = current_bond->getA() + offset;
730	<	the_bonds[index].b = current_bond->getB() + offset;
731	<
732	<	exI = the_bonds[index].a;
733	<	exJ = the_bonds[index].b;
734	<
735	<	// exclude_I must always be the smaller of the pair
736	<	if( exI > exJ ){
737	<	tempEx = exI;
738	<	exI = exJ;
739	<	exJ = tempEx;
740	<	}
741	<
742	<
743	<	#ifdef IS_MPI
744	<
745	<	the_excludes[index*2] =
746	<	the_atoms[exI]->getGlobalIndex() + 1;
747	<	the_excludes[index*2 + 1] =
748	<	the_atoms[exJ]->getGlobalIndex() + 1;
749	<
750	<	#else  // isn't MPI
751	<
752	<	the_excludes[index*2] =     exI + 1;
753	<	the_excludes[index*2 + 1] = exJ + 1;
754	<	// fortran index from 1 (hence the +1 in the indexing)
755	<	#endif  //is_mpi
756	<
757	<	// increment the index and repeat;
758	<	index++;
759	<	}
760	<	offset += comp_stamps[i]->getNAtoms();
761	<
762	<	#ifdef IS_MPI
729	>	if (!globals->haveBoxZ()){
730	>	sprintf(painCave.errMsg,
731	>	"SimSetup error, no periodic BoxZ size given.\n");
732	>	painCave.isFatal = 1;
733	>	simError();
734		}
735	<	#endif //is_mpi
736	<
737	<	molIndex++;
738	<	}
735	>	boxVector[2] = globals->getBoxZ();
736	>
737	>	info[i].setBox(boxVector);
738	>	}
739		}
740
741	<	the_ff->initializeBonds( the_bonds );
742	<	}
741	>	//setup seed for random number generator
742	>	int seedValue;
743
744	<	void SimSetup::makeBends( void ){
744	>	if (globals->haveSeed()){
745	>	seedValue = globals->getSeed();
746
747	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
748	<	bend_set* the_bends;
749	<	BendStamp* current_bend;
750	<	LinkedAssign* extras;
751	<	LinkedAssign* current_extra;
752	<
747	>	if(seedValue / 1E9 == 0){
748	>	sprintf(painCave.errMsg,
749	>	"Seed for sprng library should contain at least 9 digits\n"
750	>	"OOPSE will generate a seed for user\n");
751	>	painCave.isFatal = 0;
752	>	simError();
753
754	<	the_bends = new bend_set[tot_bends];
755	<	index = 0;
756	<	offset = 0;
757	<	molIndex = 0;
758	<	for( i=0; i<n_components; i++ ){
759	<
788	<	for( j=0; j<components_nmol[i]; j++ ){
789	<
790	<	#ifdef IS_MPI
791	<	if( mpiSim->getMyMolStart() <= molIndex &&
792	<	molIndex <= mpiSim->getMyMolEnd() ){
793	<	#endif // is_mpi
794	<
795	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
796	<
797	<	current_bend = comp_stamps[i]->getBend( k );
798	<	the_bends[index].a = current_bend->getA() + offset;
799	<	the_bends[index].b = current_bend->getB() + offset;
800	<	the_bends[index].c = current_bend->getC() + offset;
801	<
802	<	if( current_bend->haveExtras() ){
803	<
804	<	extras = current_bend->getExtras();
805	<	current_extra = extras;
806	<
807	<	while( current_extra != NULL ){
808	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
809	<
810	<	switch( current_extra->getType() ){
811	<
812	<	case 0:
813	<	the_bends[index].ghost =
814	<	current_extra->getInt() + offset;
815	<	the_bends[index].isGhost = 1;
816	<	break;
817	<
818	<	case 1:
819	<	the_bends[index].ghost =
820	<	(int)current_extra->getDouble() + offset;
821	<	the_bends[index].isGhost = 1;
822	<	break;
823	<
824	<	default:
825	<	sprintf( painCave.errMsg,
826	<	"SimSetup Error: ghostVectorSource was neiter a "
827	<	"double nor an int.\n"
828	<	"-->Bend[%d] in %s\n",
829	<	k, comp_stamps[i]->getID() );
830	<	painCave.isFatal = 1;
831	<	simError();
832	<	}
833	<	}
834	<
835	<	else{
836	<
837	<	sprintf( painCave.errMsg,
838	<	"SimSetup Error: unhandled bend assignment:\n"
839	<	"    -->%s in Bend[%d] in %s\n",
840	<	current_extra->getlhs(),
841	<	k, comp_stamps[i]->getID() );
842	<	painCave.isFatal = 1;
843	<	simError();
844	<	}
845	<
846	<	current_extra = current_extra->getNext();
847	<	}
848	<	}
849	<
850	<	if( !the_bends[index].isGhost ){
851	<
852	<	exI = the_bends[index].a;
853	<	exJ = the_bends[index].c;
854	<	}
855	<	else{
856	<
857	<	exI = the_bends[index].a;
858	<	exJ = the_bends[index].b;
859	<	}
860	<
861	<	// exclude_I must always be the smaller of the pair
862	<	if( exI > exJ ){
863	<	tempEx = exI;
864	<	exI = exJ;
865	<	exJ = tempEx;
866	<	}
867	<
868	<
869	<	#ifdef IS_MPI
870	<
871	<	the_excludes[(index + tot_bonds)*2] =
872	<	the_atoms[exI]->getGlobalIndex() + 1;
873	<	the_excludes[(index + tot_bonds)*2 + 1] =
874	<	the_atoms[exJ]->getGlobalIndex() + 1;
875	<
876	<	#else  // isn't MPI
877	<
878	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
879	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
880	<	// fortran index from 1 (hence the +1 in the indexing)
881	<	#endif  //is_mpi
882	<
883	<
884	<	// increment the index and repeat;
885	<	index++;
886	<	}
887	<	offset += comp_stamps[i]->getNAtoms();
888	<
889	<	#ifdef IS_MPI
754	>	//using seed generated by system instead of invalid seed set by user
755	>	#ifndef IS_MPI
756	>	seedValue = make_sprng_seed();
757	>	#else
758	>	if (worldRank == 0){
759	>	seedValue = make_sprng_seed();
760		}
761	<	#endif //is_mpi
762	<
893	<	molIndex++;
761	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
762	>	#endif
763		}
764	+	}//end of if branch of globals->haveSeed()
765	+	else{
766	+
767	+	#ifndef IS_MPI
768	+	seedValue = make_sprng_seed();
769	+	#else
770	+	if (worldRank == 0){
771	+	seedValue = make_sprng_seed();
772	+	}
773	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
774	+	#endif
775	+	}//end of globals->haveSeed()
776	+
777	+	for (int i = 0; i < nInfo; i++){
778	+	info[i].setSeed(seedValue);
779		}
780
781		#ifdef IS_MPI
782	<	sprintf( checkPointMsg,
899	<	"Successfully created the bends list.\n" );
782	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
783		MPIcheckPoint();
784		#endif // is_mpi
902	–
903	–
904	–	the_ff->initializeBends( the_bends );
785		}
786
907	–	void SimSetup::makeTorsions( void ){
787
788	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
789	<	torsion_set* the_torsions;
790	<	TorsionStamp* current_torsion;
788	>	void SimSetup::finalInfoCheck(void){
789	>	int index;
790	>	int usesDipoles;
791	>	int i;
792
793	<	the_torsions = new torsion_set[tot_torsions];
794	<	index = 0;
915	<	offset = 0;
916	<	molIndex = 0;
917	<	for( i=0; i<n_components; i++ ){
793	>	for (i = 0; i < nInfo; i++){
794	>	// check electrostatic parameters
795
796	<	for( j=0; j<components_nmol[i]; j++ ){
796	>	index = 0;
797	>	usesDipoles = 0;
798	>	while ((index < info[i].n_atoms) && !usesDipoles){
799	>	usesDipoles = (info[i].atoms[index])->hasDipole();
800	>	index++;
801	>	}
802
803		#ifdef IS_MPI
804	<	if( mpiSim->getMyMolStart() <= molIndex &&
805	<	molIndex <= mpiSim->getMyMolEnd() ){
806	<	#endif // is_mpi
804	>	int myUse = usesDipoles;
805	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
806	>	#endif //is_mpi
807
808	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
808	>	double theEcr, theEst;
809
810	<	current_torsion = comp_stamps[i]->getTorsion( k );
811	<	the_torsions[index].a = current_torsion->getA() + offset;
930	<	the_torsions[index].b = current_torsion->getB() + offset;
931	<	the_torsions[index].c = current_torsion->getC() + offset;
932	<	the_torsions[index].d = current_torsion->getD() + offset;
810	>	if (globals->getUseRF()){
811	>	info[i].useReactionField = 1;
812
813	<	exI = the_torsions[index].a;
814	<	exJ = the_torsions[index].d;
815	<
816	<
817	<	// exclude_I must always be the smaller of the pair
818	<	if( exI > exJ ){
819	<	tempEx = exI;
820	<	exI = exJ;
821	<	exJ = tempEx;
822	<	}
813	>	if (!globals->haveECR()){
814	>	sprintf(painCave.errMsg,
815	>	"SimSetup Warning: using default value of 1/2 the smallest "
816	>	"box length for the electrostaticCutoffRadius.\n"
817	>	"I hope you have a very fast processor!\n");
818	>	painCave.isFatal = 0;
819	>	simError();
820	>	double smallest;
821	>	smallest = info[i].boxL[0];
822	>	if (info[i].boxL[1] <= smallest)
823	>	smallest = info[i].boxL[1];
824	>	if (info[i].boxL[2] <= smallest)
825	>	smallest = info[i].boxL[2];
826	>	theEcr = 0.5 * smallest;
827	>	}
828	>	else{
829	>	theEcr = globals->getECR();
830	>	}
831
832	+	if (!globals->haveEST()){
833	+	sprintf(painCave.errMsg,
834	+	"SimSetup Warning: using default value of 0.05 * the "
835	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
836	+	painCave.isFatal = 0;
837	+	simError();
838	+	theEst = 0.05 * theEcr;
839	+	}
840	+	else{
841	+	theEst = globals->getEST();
842	+	}
843
844	<	#ifdef IS_MPI
947	<
948	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
949	<	the_atoms[exI]->getGlobalIndex() + 1;
950	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
951	<	the_atoms[exJ]->getGlobalIndex() + 1;
952	<
953	<	#else  // isn't MPI
954	<
955	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
956	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
957	<	// fortran indexes from 1 (hence the +1 in the indexing)
958	<	#endif  //is_mpi
959	<
844	>	info[i].setEcr(theEcr, theEst);
845
846	<	// increment the index and repeat;
847	<	index++;
846	>	if (!globals->haveDielectric()){
847	>	sprintf(painCave.errMsg,
848	>	"SimSetup Error: You are trying to use Reaction Field without"
849	>	"setting a dielectric constant!\n");
850	>	painCave.isFatal = 1;
851	>	simError();
852		}
853	<	offset += comp_stamps[i]->getNAtoms();
853	>	info[i].dielectric = globals->getDielectric();
854	>	}
855	>	else{
856	>	if (usesDipoles){
857	>	if (!globals->haveECR()){
858	>	sprintf(painCave.errMsg,
859	>	"SimSetup Warning: using default value of 1/2 the smallest "
860	>	"box length for the electrostaticCutoffRadius.\n"
861	>	"I hope you have a very fast processor!\n");
862	>	painCave.isFatal = 0;
863	>	simError();
864	>	double smallest;
865	>	smallest = info[i].boxL[0];
866	>	if (info[i].boxL[1] <= smallest)
867	>	smallest = info[i].boxL[1];
868	>	if (info[i].boxL[2] <= smallest)
869	>	smallest = info[i].boxL[2];
870	>	theEcr = 0.5 * smallest;
871	>	}
872	>	else{
873	>	theEcr = globals->getECR();
874	>	}
875
876	<	#ifdef IS_MPI
877	<	}
878	<	#endif //is_mpi
876	>	if (!globals->haveEST()){
877	>	sprintf(painCave.errMsg,
878	>	"SimSetup Warning: using default value of 0.05 * the "
879	>	"electrostaticCutoffRadius for the "
880	>	"electrostaticSkinThickness\n");
881	>	painCave.isFatal = 0;
882	>	simError();
883	>	theEst = 0.05 * theEcr;
884	>	}
885	>	else{
886	>	theEst = globals->getEST();
887	>	}
888
889	<	molIndex++;
889	>	info[i].setEcr(theEcr, theEst);
890	>	}
891		}
892		}
893
894	<	the_ff->initializeTorsions( the_torsions );
894	>	#ifdef IS_MPI
895	>	strcpy(checkPointMsg, "post processing checks out");
896	>	MPIcheckPoint();
897	>	#endif // is_mpi
898		}
899
900	<	void SimSetup::initFromBass( void ){
900	>	void SimSetup::initSystemCoords(void){
901	>	int i;
902
903	<	int i, j, k;
980	<	int n_cells;
981	<	double cellx, celly, cellz;
982	<	double temp1, temp2, temp3;
983	<	int n_per_extra;
984	<	int n_extra;
985	<	int have_extra, done;
903	>	char* inName;
904
905	<	temp1 = (double)tot_nmol / 4.0;
988	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
989	<	temp3 = ceil( temp2 );
905	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
906
907	<	have_extra =0;
908	<	if( temp2 < temp3 ){ // we have a non-complete lattice
993	<	have_extra =1;
907	>	for (i = 0; i < info[0].n_atoms; i++)
908	>	info[0].atoms[i]->setCoords();
909
910	<	n_cells = (int)temp3 - 1;
911	<	cellx = simnfo->box_x / temp3;
912	<	celly = simnfo->box_y / temp3;
913	<	cellz = simnfo->box_z / temp3;
914	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
915	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
916	<	n_per_extra = (int)ceil( temp1 );
917	<
1003	<	if( n_per_extra > 4){
1004	<	sprintf( painCave.errMsg,
1005	<	"SimSetup error. There has been an error in constructing"
1006	<	" the non-complete lattice.\n" );
1007	<	painCave.isFatal = 1;
1008	<	simError();
910	>	if (globals->haveInitialConfig()){
911	>	InitializeFromFile* fileInit;
912	>	#ifdef IS_MPI // is_mpi
913	>	if (worldRank == 0){
914	>	#endif //is_mpi
915	>	inName = globals->getInitialConfig();
916	>	fileInit = new InitializeFromFile(inName);
917	>	#ifdef IS_MPI
918		}
919	+	else
920	+	fileInit = new InitializeFromFile(NULL);
921	+	#endif
922	+	fileInit->readInit(info); // default velocities on
923	+
924	+	delete fileInit;
925		}
926		else{
927	<	n_cells = (int)temp3;
928	<	cellx = simnfo->box_x / temp3;
929	<	celly = simnfo->box_y / temp3;
930	<	cellz = simnfo->box_z / temp3;
927	>	#ifdef IS_MPI
928	>
929	>	// no init from bass
930	>
931	>	sprintf(painCave.errMsg,
932	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
933	>	painCave.isFatal = 1;;
934	>	simError();
935	>
936	>	#else
937	>
938	>	initFromBass();
939	>
940	>
941	>	#endif
942		}
943
944	<	current_mol = 0;
945	<	current_comp_mol = 0;
946	<	current_comp = 0;
947	<	current_atom_ndx = 0;
944	>	#ifdef IS_MPI
945	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
946	>	MPIcheckPoint();
947	>	#endif // is_mpi
948	>	}
949
1023	–	for( i=0; i < n_cells ; i++ ){
1024	–	for( j=0; j < n_cells; j++ ){
1025	–	for( k=0; k < n_cells; k++ ){
950
951	<	makeElement( i * cellx,
952	<	j * celly,
1029	<	k * cellz );
951	>	void SimSetup::makeOutNames(void){
952	>	int k;
953
1031	–	makeElement( i * cellx + 0.5 * cellx,
1032	–	j * celly + 0.5 * celly,
1033	–	k * cellz );
954
955	<	makeElement( i * cellx,
956	<	j * celly + 0.5 * celly,
957	<	k * cellz + 0.5 * cellz );
955	>	for (k = 0; k < nInfo; k++){
956	>	#ifdef IS_MPI
957	>	if (worldRank == 0){
958	>	#endif // is_mpi
959
960	<	makeElement( i * cellx + 0.5 * cellx,
961	<	j * celly,
1041	<	k * cellz + 0.5 * cellz );
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
1046	–	if( have_extra ){
1047	–	done = 0;
1042
1043	<	int start_ndx;
1044	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1051	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1043	>	void SimSetup::sysObjectsCreation(void){
1044	>	int i, k;
1045
1046	<	if( i < n_cells ){
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
1055	–	if( j < n_cells ){
1056	–	start_ndx = n_cells;
1057	–	}
1058	–	else start_ndx = 0;
1059	–	}
1060	–	else start_ndx = 0;
1080
1081	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1081	>	void SimSetup::createFF(void){
1082	>	switch (ffCase){
1083	>	case FF_DUFF:
1084	>	the_ff = new DUFF();
1085	>	break;
1086
1087	<	makeElement( i * cellx,
1088	<	j * celly,
1089	<	k * cellz );
1067	<	done = ( current_mol >= tot_nmol );
1087	>	case FF_LJ:
1088	>	the_ff = new LJFF();
1089	>	break;
1090
1091	<	if( !done && n_per_extra > 1 ){
1092	<	makeElement( i * cellx + 0.5 * cellx,
1093	<	j * celly + 0.5 * celly,
1072	<	k * cellz );
1073	<	done = ( current_mol >= tot_nmol );
1074	<	}
1091	>	case FF_EAM:
1092	>	the_ff = new EAM_FF();
1093	>	break;
1094
1095	<	if( !done && n_per_extra > 2){
1096	<	makeElement( i * cellx,
1097	<	j * celly + 0.5 * celly,
1098	<	k * cellz + 0.5 * cellz );
1099	<	done = ( current_mol >= tot_nmol );
1100	<	}
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	<	if( !done && n_per_extra > 3){
1103	<	makeElement( i * cellx + 0.5 * cellx,
1104	<	j * celly,
1105	<	k * cellz + 0.5 * cellz );
1106	<	done = ( current_mol >= tot_nmol );
1107	<	}
1108	<	}
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	<	for( i=0; i<simnfo->n_atoms; i++ ){
1159	<	simnfo->atoms[i]->set_vx( 0.0 );
1160	<	simnfo->atoms[i]->set_vy( 0.0 );
1161	<	simnfo->atoms[i]->set_vz( 0.0 );
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	<	void SimSetup::makeElement( double x, double y, double z ){
1189	>	#ifdef IS_MPI
1190
1191	<	int k;
1192	<	AtomStamp* current_atom;
1193	<	DirectionalAtom* dAtom;
1194	<	double rotMat[3][3];
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	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1196	>	mpiSim = new mpiSimulation(info);
1197
1198	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1199	<	if( !current_atom->havePosition() ){
1200	<	sprintf( painCave.errMsg,
1201	<	"SimSetup:initFromBass error.\n"
1202	<	"\tComponent %s, atom %s does not have a position specified.\n"
1203	<	"\tThe initialization routine is unable to give a start"
1204	<	" position.\n",
1205	<	comp_stamps[current_comp]->getID(),
1206	<	current_atom->getType() );
1207	<	painCave.isFatal = 1;
1208	<	simError();
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	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1125	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1126	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1233	>	info[0].n_atoms = mpiSim->getMyNlocal();
1234
1235	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
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	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
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	<	rotMat[0][0] = 1.0;
1251	<	rotMat[0][1] = 0.0;
1252	<	rotMat[0][2] = 0.0;
1250	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1251	>	MPIcheckPoint();
1252	>	}
1253
1254	<	rotMat[1][0] = 0.0;
1137	<	rotMat[1][1] = 1.0;
1138	<	rotMat[1][2] = 0.0;
1254	>	#endif // is_mpi
1255
1140	–	rotMat[2][0] = 0.0;
1141	–	rotMat[2][1] = 0.0;
1142	–	rotMat[2][2] = 1.0;
1256
1257	<	dAtom->setA( rotMat );
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	<	current_atom_ndx++;
1148	<	}
1291	>	#else // is_mpi
1292
1293	<	current_mol++;
1294	<	current_comp_mol++;
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
1153	–	if( current_comp_mol >= components_nmol[current_comp] ){
1308
1309	<	current_comp_mol = 0;
1310	<	current_comp++;
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	+
1350	+	for (k = 0; k < nInfo; k++){
1351	+	switch (ensembleCase){
1352	+	case NVE_ENS:
1353	+	if (globals->haveZconstraints()){
1354	+	setupZConstraint(info[k]);
1355	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1356	+	}
1357	+	else{
1358	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1359	+	}
1360	+
1361	+	info->the_integrator = myNVE;
1362	+	break;
1363	+
1364	+	case NVT_ENS:
1365	+	if (globals->haveZconstraints()){
1366	+	setupZConstraint(info[k]);
1367	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1368	+	}
1369	+	else
1370	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1371	+
1372	+	myNVT->setTargetTemp(globals->getTargetTemp());
1373	+
1374	+	if (globals->haveTauThermostat())
1375	+	myNVT->setTauThermostat(globals->getTauThermostat());
1376	+	else{
1377	+	sprintf(painCave.errMsg,
1378	+	"SimSetup error: If you use the NVT\n"
1379	+	"    ensemble, you must set tauThermostat.\n");
1380	+	painCave.isFatal = 1;
1381	+	simError();
1382	+	}
1383	+
1384	+	info->the_integrator = myNVT;
1385	+	break;
1386	+
1387	+	case NPTi_ENS:
1388	+	if (globals->haveZconstraints()){
1389	+	setupZConstraint(info[k]);
1390	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1391	+	}
1392	+	else
1393	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1394	+
1395	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1396	+
1397	+	if (globals->haveTargetPressure())
1398	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1399	+	else{
1400	+	sprintf(painCave.errMsg,
1401	+	"SimSetup error: If you use a constant pressure\n"
1402	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1403	+	painCave.isFatal = 1;
1404	+	simError();
1405	+	}
1406	+
1407	+	if (globals->haveTauThermostat())
1408	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1409	+	else{
1410	+	sprintf(painCave.errMsg,
1411	+	"SimSetup error: If you use an NPT\n"
1412	+	"    ensemble, you must set tauThermostat.\n");
1413	+	painCave.isFatal = 1;
1414	+	simError();
1415	+	}
1416	+
1417	+	if (globals->haveTauBarostat())
1418	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1419	+	else{
1420	+	sprintf(painCave.errMsg,
1421	+	"SimSetup error: If you use an NPT\n"
1422	+	"    ensemble, you must set tauBarostat.\n");
1423	+	painCave.isFatal = 1;
1424	+	simError();
1425	+	}
1426	+
1427	+	info->the_integrator = myNPTi;
1428	+	break;
1429	+
1430	+	case NPTf_ENS:
1431	+	if (globals->haveZconstraints()){
1432	+	setupZConstraint(info[k]);
1433	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1434	+	}
1435	+	else
1436	+	myNPTf = new NPTf<NPT <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	+
1470	+	info->the_integrator = myNPTf;
1471	+	break;
1472	+
1473	+	default:
1474	+	sprintf(painCave.errMsg,
1475	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1476	+	painCave.isFatal = 1;
1477	+	simError();
1478	+	}
1479	+	}
1480	+	}
1481	+
1482	+	void SimSetup::initFortran(void){
1483	+	info[0].refreshSim();
1484	+
1485	+	if (!strcmp(info[0].mixingRule, "standard")){
1486	+	the_ff->initForceField(LB_MIXING_RULE);
1487	+	}
1488	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1489	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1490	+	}
1491	+	else{
1492	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1493	+	info[0].mixingRule);
1494	+	painCave.isFatal = 1;
1495	+	simError();
1496	+	}
1497	+
1498	+
1499	+	#ifdef IS_MPI
1500	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1501	+	MPIcheckPoint();
1502	+	#endif // is_mpi
1503	+	}
1504	+
1505	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1506	+	int nZConstraints;
1507	+	ZconStamp** zconStamp;
1508	+
1509	+	if (globals->haveZconstraintTime()){
1510	+	//add sample time of z-constraint  into SimInfo's property list
1511	+	DoubleData* zconsTimeProp = new DoubleData();
1512	+	zconsTimeProp->setID(ZCONSTIME_ID);
1513	+	zconsTimeProp->setData(globals->getZconsTime());
1514	+	theInfo.addProperty(zconsTimeProp);
1515	+	}
1516	+	else{
1517	+	sprintf(painCave.errMsg,
1518	+	"ZConstraint error: If you use an ZConstraint\n"
1519	+	" , you must set sample time.\n");
1520	+	painCave.isFatal = 1;
1521	+	simError();
1522	+	}
1523	+
1524	+	//push zconsTol into siminfo, if user does not specify
1525	+	//value for zconsTol, a default value will be used
1526	+	DoubleData* zconsTol = new DoubleData();
1527	+	zconsTol->setID(ZCONSTOL_ID);
1528	+	if (globals->haveZconsTol()){
1529	+	zconsTol->setData(globals->getZconsTol());
1530	+	}
1531	+	else{
1532	+	double defaultZConsTol = 0.01;
1533	+	sprintf(painCave.errMsg,
1534	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1535	+	" , default value %f is used.\n",
1536	+	defaultZConsTol);
1537	+	painCave.isFatal = 0;
1538	+	simError();
1539	+
1540	+	zconsTol->setData(defaultZConsTol);
1541	+	}
1542	+	theInfo.addProperty(zconsTol);
1543	+
1544	+	//set Force Subtraction Policy
1545	+	StringData* zconsForcePolicy = new StringData();
1546	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1547	+
1548	+	if (globals->haveZconsForcePolicy()){
1549	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1550	+	}
1551	+	else{
1552	+	sprintf(painCave.errMsg,
1553	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1554	+	"PolicyByMass is used\n");
1555	+	painCave.isFatal = 0;
1556	+	simError();
1557	+	zconsForcePolicy->setData("BYMASS");
1558	+	}
1559	+
1560	+	theInfo.addProperty(zconsForcePolicy);
1561	+
1562	+	//Determine the name of ouput file and add it into SimInfo's property list
1563	+	//Be careful, do not use inFileName, since it is a pointer which
1564	+	//point to a string at master node, and slave nodes do not contain that string
1565	+
1566	+	string zconsOutput(theInfo.finalName);
1567	+
1568	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1569	+
1570	+	StringData* zconsFilename = new StringData();
1571	+	zconsFilename->setID(ZCONSFILENAME_ID);
1572	+	zconsFilename->setData(zconsOutput);
1573	+
1574	+	theInfo.addProperty(zconsFilename);
1575	+
1576	+	//setup index, pos and other parameters of z-constraint molecules
1577	+	nZConstraints = globals->getNzConstraints();
1578	+	theInfo.nZconstraints = nZConstraints;
1579	+
1580	+	zconStamp = globals->getZconStamp();
1581	+	ZConsParaItem tempParaItem;
1582	+
1583	+	ZConsParaData* zconsParaData = new ZConsParaData();
1584	+	zconsParaData->setID(ZCONSPARADATA_ID);
1585	+
1586	+	for (int i = 0; i < nZConstraints; i++){
1587	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1588	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1589	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1590	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1591	+
1592	+	zconsParaData->addItem(tempParaItem);
1593	+	}
1594	+
1595	+	//check the uniqueness of index
1596	+	if(!zconsParaData->isIndexUnique()){
1597	+	sprintf(painCave.errMsg,
1598	+	"ZConstraint Error: molIndex is not unique\n");
1599	+	painCave.isFatal = 1;
1600	+	simError();
1601	+	}
1602	+
1603	+	//sort the parameters by index of molecules
1604	+	zconsParaData->sortByIndex();
1605	+
1606	+	//push data into siminfo, therefore, we can retrieve later
1607	+	theInfo.addProperty(zconsParaData);
1608	+	}

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