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root/group/branches/new-templateless/OOPSE/libmdtools/SimSetup.cpp

Comparing:
trunk/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 407 by mmeineke, Wed Mar 26 20:22:02 2003 UTC vs.
branches/new-templateless/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 850 by mmeineke, Mon Nov 3 22:07:17 2003 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7
8		#include "SimSetup.hpp"
9	+	#include "ReadWrite.hpp"
10		#include "parse_me.h"
11		#include "Integrator.hpp"
12		#include "simError.h"
#	Line 12 | Line 16
16		#include "mpiSimulation.hpp"
17		#endif
18
19	+	// some defines for ensemble and Forcefield  cases
20	+
21	+	#define NVE_ENS        0
22	+	#define NVT_ENS        1
23	+	#define NPTi_ENS       2
24	+	#define NPTf_ENS       3
25	+	#define NPTxyz_ENS     4
26	+
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	+
36	+	initSuspend = false;
37	+	isInfoArray = 0;
38	+	nInfo = 1;
39	+
40		stamps = new MakeStamps();
41		globals = new Globals();
42	<
42	>
43	>
44		#ifdef IS_MPI
45	<	strcpy( checkPointMsg, "SimSetup creation successful" );
45	>	strcpy(checkPointMsg, "SimSetup creation successful");
46		MPIcheckPoint();
47		#endif // IS_MPI
48		}
#	Line 27 | Line 52 | SimSetup::~SimSetup(){
52		delete globals;
53		}
54
55	<	void SimSetup::parseFile( char* fileName ){
55	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
56	>	info = the_info;
57	>	nInfo = theNinfo;
58	>	isInfoArray = 1;
59	>	initSuspend = true;
60	>	}
61
62	+
63	+	void SimSetup::parseFile(char* fileName){
64		#ifdef IS_MPI
65	<	if( worldRank == 0 ){
65	>	if (worldRank == 0){
66		#endif // is_mpi
67	<
67	>
68		inFileName = fileName;
69	<	set_interface_stamps( stamps, globals );
70	<
69	>	set_interface_stamps(stamps, globals);
70	>
71		#ifdef IS_MPI
72		mpiEventInit();
73		#endif
74
75	<	yacc_BASS( fileName );
75	>	yacc_BASS(fileName);
76
77		#ifdef IS_MPI
78		throwMPIEvent(NULL);
79		}
80	<	else receiveParse();
80	>	else{
81	>	receiveParse();
82	>	}
83		#endif
84
85		}
86
87		#ifdef IS_MPI
88		void SimSetup::receiveParse(void){
89	<
90	<	set_interface_stamps( stamps, globals );
91	<	mpiEventInit();
92	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
89	>	set_interface_stamps(stamps, globals);
90	>	mpiEventInit();
91	>	MPIcheckPoint();
92	>	mpiEventLoop();
93		}
94
95		#endif // is_mpi
96
97	<	void SimSetup::createSim( void ){
97	>	void SimSetup::createSim(void){
98
99	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
99	>	// gather all of the information from the Bass file
100
101	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
101	>	gatherInfo();
102
103	<	// 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();
103	>	// creation of complex system objects
104
105	<	// 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 );
105	>	sysObjectsCreation();
106
107	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
107	>	// initialize the system coordinates
108
109	+	if ( !initSuspend ){
110	+	initSystemCoords();
111
112	<	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
113	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
114	<	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	<	}
112	>	if( !(globals->getUseInitTime()) )
113	>	info[0].currentTime = 0.0;
114	>	}
115
116	<	#ifdef IS_MPI
104	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
116	>	// check on the post processing info
117
118	<
118	>	finalInfoCheck();
119
120	<	// 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];
120	>	// make the output filenames
121
122	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
122	>	makeOutNames();
123
124	<	tot_nmol = 0;
120	<	for( i=0; i<n_components; i++ ){
124	>	// make the integrator
125
126	<	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	<	}
126	>	makeIntegrator();
127
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	–
128		#ifdef IS_MPI
129	<	strcpy( checkPointMsg, "Have the number of components" );
130	<	MPIcheckPoint();
163	<	#endif // is_mpi
129	>	mpiSim->mpiRefresh();
130	>	#endif
131
132	<	// make an array of molecule stamps that match the components used.
166	<	// also extract the used stamps out into a separate linked list
132	>	// initialize the Fortran
133
134	<	simnfo->nComponents = n_components;
135	<	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++ ){
134	>	initFortran();
135	>	}
136
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
137
138	<	comp_stamps[i] = headStamp->match( id );
139	<	if( comp_stamps[i] == NULL ){
140	<
141	<	// extract the component from the list;
142	<
143	<	currentStamp = the_stamps->extractMolStamp( id );
144	<	if( currentStamp == NULL ){
145	<	sprintf( painCave.errMsg,
146	<	"SimSetup error: Component \"%s\" was not found in the "
147	<	"list of declared molecules\n",
148	<	id );
194	<	painCave.isFatal = 1;
195	<	simError();
196	<	}
197	<
198	<	headStamp->add( currentStamp );
199	<	comp_stamps[i] = headStamp->match( id );
200	<	}
201	<	}
138	>	void SimSetup::makeMolecules(void){
139	>	int k;
140	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
141	>	molInit molInfo;
142	>	DirectionalAtom* dAtom;
143	>	LinkedAssign* extras;
144	>	LinkedAssign* current_extra;
145	>	AtomStamp* currentAtom;
146	>	BondStamp* currentBond;
147	>	BendStamp* currentBend;
148	>	TorsionStamp* currentTorsion;
149
150	<	#ifdef IS_MPI
151	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
152	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
150	>	bond_pair* theBonds;
151	>	bend_set* theBends;
152	>	torsion_set* theTorsions;
153
154
155	+	//init the forceField paramters
156
157	<	// caclulate the number of atoms, bonds, bends and torsions
157	>	the_ff->readParams();
158
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	–	}
159
160	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
160	>	// init the atoms
161
162	<	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;
162	>	double ux, uy, uz, u, uSqr;
163
164	<
165	<	#ifdef IS_MPI
164	>	for (k = 0; k < nInfo; k++){
165	>	the_ff->setSimInfo(&(info[k]));
166
167	<	// divide the molecules among processors here.
168	<
169	<	mpiSim = new mpiSimulation( simnfo );
170	<
241	<
167	>	atomOffset = 0;
168	>	excludeOffset = 0;
169	>	for (i = 0; i < info[k].n_mol; i++){
170	>	stampID = info[k].molecules[i].getStampID();
171
172	<	globalIndex = mpiSim->divideLabor();
172	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
173	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
174	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
175	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
176	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
177
178	+	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
179	+	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
180	+	molInfo.myBonds = new Bond * [molInfo.nBonds];
181	+	molInfo.myBends = new Bend * [molInfo.nBends];
182	+	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
183
184	+	theBonds = new bond_pair[molInfo.nBonds];
185	+	theBends = new bend_set[molInfo.nBends];
186	+	theTorsions = new torsion_set[molInfo.nTorsions];
187
188	<	// 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++ ){
188	>	// make the Atoms
189
190	<	for( j=0; j<components_nmol[i]; j++ ){
191	<
192	<	if( mpiSim->getMyMolStart() <= allMol &&
193	<	allMol <= mpiSim->getMyMolEnd() ){
194	<
195	<	local_atoms +=    comp_stamps[i]->getNAtoms();
196	<	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	<
190	>	for (j = 0; j < molInfo.nAtoms; j++){
191	>	currentAtom = comp_stamps[stampID]->getAtom(j);
192	>	if (currentAtom->haveOrientation()){
193	>	dAtom = new DirectionalAtom((j + atomOffset),
194	>	info[k].getConfiguration());
195	>	info[k].n_oriented++;
196	>	molInfo.myAtoms[j] = dAtom;
197
198	<	simnfo->n_atoms = mpiSim->getMyNlocal();
199	<
200	<	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	<	}
198	>	ux = currentAtom->getOrntX();
199	>	uy = currentAtom->getOrntY();
200	>	uz = currentAtom->getOrntZ();
201
202	<	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;
202	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
203
204	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
205	<	MPIcheckPoint();
206	<
207	<
299	<	#endif // is_mpi
300	<
204	>	u = sqrt(uSqr);
205	>	ux = ux / u;
206	>	uy = uy / u;
207	>	uz = uz / u;
208
209	<	// create the atom and short range interaction arrays
209	>	dAtom->setSUx(ux);
210	>	dAtom->setSUy(uy);
211	>	dAtom->setSUz(uz);
212	>	}
213	>	else{
214	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
215	>	info[k].getConfiguration());
216	>	}
217	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
218
219	<	Atom::createArrays(simnfo->n_atoms);
305	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
219	>	#ifdef IS_MPI
220
221	+	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
222
223	<	if( simnfo->n_SRI ){
224	<	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;
223	>	#endif // is_mpi
224	>	}
225
226	<	simnfo->n_exclude = 1;
227	<	}
226	>	// make the bonds
227	>	for (j = 0; j < molInfo.nBonds; j++){
228	>	currentBond = comp_stamps[stampID]->getBond(j);
229	>	theBonds[j].a = currentBond->getA() + atomOffset;
230	>	theBonds[j].b = currentBond->getB() + atomOffset;
231
232	<	// set the arrays into the SimInfo object
232	>	exI = theBonds[j].a;
233	>	exJ = theBonds[j].b;
234
235	<	simnfo->atoms = the_atoms;
236	<	simnfo->sr_interactions = the_sris;
237	<	simnfo->nGlobalExcludes = 0;
238	<	simnfo->excludes = the_excludes;
235	>	// exclude_I must always be the smaller of the pair
236	>	if (exI > exJ){
237	>	tempEx = exI;
238	>	exI = exJ;
239	>	exJ = tempEx;
240	>	}
241	>	#ifdef IS_MPI
242	>	tempEx = exI;
243	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
244	>	tempEx = exJ;
245	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
246
247	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
248	+	#else  // isn't MPI
249
250	<	// get some of the tricky things that may still be in the globals
250	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
251	>	#endif  //is_mpi
252	>	}
253	>	excludeOffset += molInfo.nBonds;
254
255	<
256	<	if( the_globals->haveBox() ){
257	<	simnfo->box_x = the_globals->getBox();
258	<	simnfo->box_y = the_globals->getBox();
259	<	simnfo->box_z = the_globals->getBox();
260	<	}
342	<	else if( the_globals->haveDensity() ){
255	>	//make the bends
256	>	for (j = 0; j < molInfo.nBends; j++){
257	>	currentBend = comp_stamps[stampID]->getBend(j);
258	>	theBends[j].a = currentBend->getA() + atomOffset;
259	>	theBends[j].b = currentBend->getB() + atomOffset;
260	>	theBends[j].c = currentBend->getC() + atomOffset;
261
262	<	double vol;
263	<	vol = (double)tot_nmol / the_globals->getDensity();
264	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
347	<	simnfo->box_y = simnfo->box_x;
348	<	simnfo->box_z = simnfo->box_x;
349	<	}
350	<	else{
351	<	if( !the_globals->haveBoxX() ){
352	<	sprintf( painCave.errMsg,
353	<	"SimSetup error, no periodic BoxX size given.\n" );
354	<	painCave.isFatal = 1;
355	<	simError();
356	<	}
357	<	simnfo->box_x = the_globals->getBoxX();
262	>	if (currentBend->haveExtras()){
263	>	extras = currentBend->getExtras();
264	>	current_extra = extras;
265
266	<	if( !the_globals->haveBoxY() ){
267	<	sprintf( painCave.errMsg,
268	<	"SimSetup error, no periodic BoxY size given.\n" );
269	<	painCave.isFatal = 1;
270	<	simError();
271	<	}
272	<	simnfo->box_y = the_globals->getBoxY();
266	>	while (current_extra != NULL){
267	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
268	>	switch (current_extra->getType()){
269	>	case 0:
270	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
271	>	theBends[j].isGhost = 1;
272	>	break;
273
274	<	if( !the_globals->haveBoxZ() ){
275	<	sprintf( painCave.errMsg,
276	<	"SimSetup error, no periodic BoxZ size given.\n" );
277	<	painCave.isFatal = 1;
278	<	simError();
372	<	}
373	<	simnfo->box_z = the_globals->getBoxZ();
374	<	}
274	>	case 1:
275	>	theBends[j].ghost = (int) current_extra->getDouble() +
276	>	atomOffset;
277	>	theBends[j].isGhost = 1;
278	>	break;
279
280	+	default:
281	+	sprintf(painCave.errMsg,
282	+	"SimSetup Error: ghostVectorSource was neither a "
283	+	"double nor an int.\n"
284	+	"-->Bend[%d] in %s\n",
285	+	j, comp_stamps[stampID]->getID());
286	+	painCave.isFatal = 1;
287	+	simError();
288	+	}
289	+	}
290	+	else{
291	+	sprintf(painCave.errMsg,
292	+	"SimSetup Error: unhandled bend assignment:\n"
293	+	"    -->%s in Bend[%d] in %s\n",
294	+	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
295	+	painCave.isFatal = 1;
296	+	simError();
297	+	}
298	+
299	+	current_extra = current_extra->getNext();
300	+	}
301	+	}
302	+
303	+	if (!theBends[j].isGhost){
304	+	exI = theBends[j].a;
305	+	exJ = theBends[j].c;
306	+	}
307	+	else{
308	+	exI = theBends[j].a;
309	+	exJ = theBends[j].b;
310	+	}
311	+
312	+	// exclude_I must always be the smaller of the pair
313	+	if (exI > exJ){
314	+	tempEx = exI;
315	+	exI = exJ;
316	+	exJ = tempEx;
317	+	}
318		#ifdef IS_MPI
319	<	strcpy( checkPointMsg, "Box size set up" );
320	<	MPIcheckPoint();
321	<	#endif // is_mpi
319	>	tempEx = exI;
320	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
321	>	tempEx = exJ;
322	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
323
324	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
325	+	#else  // isn't MPI
326	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
327	+	#endif  //is_mpi
328	+	}
329	+	excludeOffset += molInfo.nBends;
330
331	<	// initialize the arrays
331	>	for (j = 0; j < molInfo.nTorsions; j++){
332	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
333	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
334	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
335	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
336	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
337
338	<	the_ff->setSimInfo( simnfo );
338	>	exI = theTorsions[j].a;
339	>	exJ = theTorsions[j].d;
340
341	<	makeAtoms();
342	<	simnfo->identArray = new int[simnfo->n_atoms];
343	<	for(i=0; i<simnfo->n_atoms; i++){
344	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
345	<	}
346	<
347	<	if( tot_bonds ){
348	<	makeBonds();
349	<	}
341	>	// exclude_I must always be the smaller of the pair
342	>	if (exI > exJ){
343	>	tempEx = exI;
344	>	exI = exJ;
345	>	exJ = tempEx;
346	>	}
347	>	#ifdef IS_MPI
348	>	tempEx = exI;
349	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
350	>	tempEx = exJ;
351	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
352	>
353	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
354	>	#else  // isn't MPI
355	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
356	>	#endif  //is_mpi
357	>	}
358	>	excludeOffset += molInfo.nTorsions;
359	>
360	>
361	>	// send the arrays off to the forceField for init.
362
363	<	if( tot_bends ){
364	<	makeBends();
365	<	}
363	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
364	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
365	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
366	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
367	>	theTorsions);
368
400	–	if( tot_torsions ){
401	–	makeTorsions();
402	–	}
369
370	+	info[k].molecules[i].initialize(molInfo);
371
405	–	if (the_globals->getUseRF() ) {
406	–	simnfo->useReactionField = 1;
407	–
408	–	if( !the_globals->haveECR() ){
409	–	sprintf( painCave.errMsg,
410	–	"SimSetup Warning: using default value of 1/2 the smallest "
411	–	"box length for the electrostaticCutoffRadius.\n"
412	–	"I hope you have a very fast processor!\n");
413	–	painCave.isFatal = 0;
414	–	simError();
415	–	double smallest;
416	–	smallest = simnfo->box_x;
417	–	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
418	–	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
419	–	simnfo->ecr = 0.5 * smallest;
420	–	} else {
421	–	simnfo->ecr        = the_globals->getECR();
422	–	}
372
373	<	if( !the_globals->haveEST() ){
374	<	sprintf( painCave.errMsg,
375	<	"SimSetup Warning: using default value of 0.05 * the "
376	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
428	<	);
429	<	painCave.isFatal = 0;
430	<	simError();
431	<	simnfo->est = 0.05 * simnfo->ecr;
432	<	} else {
433	<	simnfo->est        = the_globals->getEST();
373	>	atomOffset += molInfo.nAtoms;
374	>	delete[] theBonds;
375	>	delete[] theBends;
376	>	delete[] theTorsions;
377		}
378	<
436	<	if(!the_globals->haveDielectric() ){
437	<	sprintf( painCave.errMsg,
438	<	"SimSetup Error: You are trying to use Reaction Field without"
439	<	"setting a dielectric constant!\n"
440	<	);
441	<	painCave.isFatal = 1;
442	<	simError();
443	<	}
444	<	simnfo->dielectric = the_globals->getDielectric();
445	<	} else {
446	<	if (simnfo->n_dipoles) {
447	<
448	<	if( !the_globals->haveECR() ){
449	<	sprintf( painCave.errMsg,
450	<	"SimSetup Warning: using default value of 1/2 the smallest"
451	<	"box length for the electrostaticCutoffRadius.\n"
452	<	"I hope you have a very fast processor!\n");
453	<	painCave.isFatal = 0;
454	<	simError();
455	<	double smallest;
456	<	smallest = simnfo->box_x;
457	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
458	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
459	<	simnfo->ecr = 0.5 * smallest;
460	<	} else {
461	<	simnfo->ecr        = the_globals->getECR();
462	<	}
463	<
464	<	if( !the_globals->haveEST() ){
465	<	sprintf( painCave.errMsg,
466	<	"SimSetup Warning: using default value of 5% of the"
467	<	"electrostaticCutoffRadius for the "
468	<	"electrostaticSkinThickness\n"
469	<	);
470	<	painCave.isFatal = 0;
471	<	simError();
472	<	simnfo->est = 0.05 * simnfo->ecr;
473	<	} else {
474	<	simnfo->est        = the_globals->getEST();
475	<	}
476	<	}
477	<	}
378	>	}
379
380		#ifdef IS_MPI
381	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
381	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
382		MPIcheckPoint();
383		#endif // is_mpi
384
385	<	if( the_globals->haveInitialConfig() ){
485	<
486	<	InitializeFromFile* fileInit;
487	<	#ifdef IS_MPI // is_mpi
488	<	if( worldRank == 0 ){
489	<	#endif //is_mpi
490	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
491	<	#ifdef IS_MPI
492	<	}else fileInit = new InitializeFromFile( NULL );
493	<	#endif
494	<	fileInit->read_xyz( simnfo ); // default velocities on
385	>	// clean up the forcefield
386
387	<	delete fileInit;
388	<	}
389	<	else{
387	>	the_ff->calcRcut();
388	>	the_ff->cleanMe();
389	>	}
390
391	<	#ifdef IS_MPI
391	>	void SimSetup::initFromBass(void){
392	>	int i, j, k;
393	>	int n_cells;
394	>	double cellx, celly, cellz;
395	>	double temp1, temp2, temp3;
396	>	int n_per_extra;
397	>	int n_extra;
398	>	int have_extra, done;
399
400	<	// no init from bass
401	<
402	<	sprintf( painCave.errMsg,
403	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
506	<	painCave.isFatal;
507	<	simError();
508	<
509	<	#else
400	>	double vel[3];
401	>	vel[0] = 0.0;
402	>	vel[1] = 0.0;
403	>	vel[2] = 0.0;
404
405	<	initFromBass();
405	>	temp1 = (double) tot_nmol / 4.0;
406	>	temp2 = pow(temp1, (1.0 / 3.0));
407	>	temp3 = ceil(temp2);
408
409	+	have_extra = 0;
410	+	if (temp2 < temp3){
411	+	// we have a non-complete lattice
412	+	have_extra = 1;
413
414	<	#endif
415	<	}
414	>	n_cells = (int) temp3 - 1;
415	>	cellx = info[0].boxL[0] / temp3;
416	>	celly = info[0].boxL[1] / temp3;
417	>	cellz = info[0].boxL[2] / temp3;
418	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
419	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
420	>	n_per_extra = (int) ceil(temp1);
421
422	<	#ifdef IS_MPI
423	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
424	<	MPIcheckPoint();
425	<	#endif // is_mpi
422	>	if (n_per_extra > 4){
423	>	sprintf(painCave.errMsg,
424	>	"SimSetup error. There has been an error in constructing"
425	>	" the non-complete lattice.\n");
426	>	painCave.isFatal = 1;
427	>	simError();
428	>	}
429	>	}
430	>	else{
431	>	n_cells = (int) temp3;
432	>	cellx = info[0].boxL[0] / temp3;
433	>	celly = info[0].boxL[1] / temp3;
434	>	cellz = info[0].boxL[2] / temp3;
435	>	}
436
437	+	current_mol = 0;
438	+	current_comp_mol = 0;
439	+	current_comp = 0;
440	+	current_atom_ndx = 0;
441
442	<
443	<
444	<
442	>	for (i = 0; i < n_cells ; i++){
443	>	for (j = 0; j < n_cells; j++){
444	>	for (k = 0; k < n_cells; k++){
445	>	makeElement(i * cellx, j * celly, k * cellz);
446
447	<
448	<	#ifdef IS_MPI
449	<	if( worldRank == 0 ){
450	<	#endif // is_mpi
451	<
532	<	if( the_globals->haveFinalConfig() ){
533	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
534	<	}
535	<	else{
536	<	strcpy( simnfo->finalName, inFileName );
537	<	char* endTest;
538	<	int nameLength = strlen( simnfo->finalName );
539	<	endTest = &(simnfo->finalName[nameLength - 5]);
540	<	if( !strcmp( endTest, ".bass" ) ){
541	<	strcpy( endTest, ".eor" );
447	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
448	>
449	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
450	>
451	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
452		}
543	–	else if( !strcmp( endTest, ".BASS" ) ){
544	–	strcpy( endTest, ".eor" );
545	–	}
546	–	else{
547	–	endTest = &(simnfo->finalName[nameLength - 4]);
548	–	if( !strcmp( endTest, ".bss" ) ){
549	–	strcpy( endTest, ".eor" );
550	–	}
551	–	else if( !strcmp( endTest, ".mdl" ) ){
552	–	strcpy( endTest, ".eor" );
553	–	}
554	–	else{
555	–	strcat( simnfo->finalName, ".eor" );
556	–	}
557	–	}
453		}
454	<
455	<	// make the sample and status out names
456	<
457	<	strcpy( simnfo->sampleName, inFileName );
458	<	char* endTest;
459	<	int nameLength = strlen( simnfo->sampleName );
460	<	endTest = &(simnfo->sampleName[nameLength - 5]);
461	<	if( !strcmp( endTest, ".bass" ) ){
462	<	strcpy( endTest, ".dump" );
463	<	}
464	<	else if( !strcmp( endTest, ".BASS" ) ){
465	<	strcpy( endTest, ".dump" );
466	<	}
467	<	else{
468	<	endTest = &(simnfo->sampleName[nameLength - 4]);
469	<	if( !strcmp( endTest, ".bss" ) ){
470	<	strcpy( endTest, ".dump" );
471	<	}
472	<	else if( !strcmp( endTest, ".mdl" ) ){
473	<	strcpy( endTest, ".dump" );
474	<	}
475	<	else{
476	<	strcat( simnfo->sampleName, ".dump" );
477	<	}
478	<	}
479	<
480	<	strcpy( simnfo->statusName, inFileName );
481	<	nameLength = strlen( simnfo->statusName );
482	<	endTest = &(simnfo->statusName[nameLength - 5]);
483	<	if( !strcmp( endTest, ".bass" ) ){
484	<	strcpy( endTest, ".stat" );
485	<	}
486	<	else if( !strcmp( endTest, ".BASS" ) ){
487	<	strcpy( endTest, ".stat" );
488	<	}
489	<	else{
490	<	endTest = &(simnfo->statusName[nameLength - 4]);
491	<	if( !strcmp( endTest, ".bss" ) ){
492	<	strcpy( endTest, ".stat" );
493	<	}
599	<	else if( !strcmp( endTest, ".mdl" ) ){
600	<	strcpy( endTest, ".stat" );
601	<	}
602	<	else{
603	<	strcat( simnfo->statusName, ".stat" );
454	>	}
455	>
456	>	if (have_extra){
457	>	done = 0;
458	>
459	>	int start_ndx;
460	>	for (i = 0; i < (n_cells + 1) && !done; i++){
461	>	for (j = 0; j < (n_cells + 1) && !done; j++){
462	>	if (i < n_cells){
463	>	if (j < n_cells){
464	>	start_ndx = n_cells;
465	>	}
466	>	else
467	>	start_ndx = 0;
468	>	}
469	>	else
470	>	start_ndx = 0;
471	>
472	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
473	>	makeElement(i * cellx, j * celly, k * cellz);
474	>	done = (current_mol >= tot_nmol);
475	>
476	>	if (!done && n_per_extra > 1){
477	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
478	>	k * cellz);
479	>	done = (current_mol >= tot_nmol);
480	>	}
481	>
482	>	if (!done && n_per_extra > 2){
483	>	makeElement(i * cellx, j * celly + 0.5 * celly,
484	>	k * cellz + 0.5 * cellz);
485	>	done = (current_mol >= tot_nmol);
486	>	}
487	>
488	>	if (!done && n_per_extra > 3){
489	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
490	>	k * cellz + 0.5 * cellz);
491	>	done = (current_mol >= tot_nmol);
492	>	}
493	>	}
494		}
495		}
606	–
607	–	#ifdef IS_MPI
496		}
497	<	#endif // is_mpi
498	<
499	<	// set the status, sample, and themal kick times
612	<
613	<	if( the_globals->haveSampleTime() ){
614	<	simnfo->sampleTime = the_globals->getSampleTime();
615	<	simnfo->statusTime = simnfo->sampleTime;
616	<	simnfo->thermalTime = simnfo->sampleTime;
497	>
498	>	for (i = 0; i < info[0].n_atoms; i++){
499	>	info[0].atoms[i]->setVel(vel);
500		}
501	<	else{
619	<	simnfo->sampleTime = the_globals->getRunTime();
620	<	simnfo->statusTime = simnfo->sampleTime;
621	<	simnfo->thermalTime = simnfo->sampleTime;
622	<	}
501	>	}
502
503	<	if( the_globals->haveStatusTime() ){
504	<	simnfo->statusTime = the_globals->getStatusTime();
503	>	void SimSetup::makeElement(double x, double y, double z){
504	>	int k;
505	>	AtomStamp* current_atom;
506	>	DirectionalAtom* dAtom;
507	>	double rotMat[3][3];
508	>	double pos[3];
509	>
510	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
511	>	current_atom = comp_stamps[current_comp]->getAtom(k);
512	>	if (!current_atom->havePosition()){
513	>	sprintf(painCave.errMsg,
514	>	"SimSetup:initFromBass error.\n"
515	>	"\tComponent %s, atom %s does not have a position specified.\n"
516	>	"\tThe initialization routine is unable to give a start"
517	>	" position.\n",
518	>	comp_stamps[current_comp]->getID(), current_atom->getType());
519	>	painCave.isFatal = 1;
520	>	simError();
521	>	}
522	>
523	>	pos[0] = x + current_atom->getPosX();
524	>	pos[1] = y + current_atom->getPosY();
525	>	pos[2] = z + current_atom->getPosZ();
526	>
527	>	info[0].atoms[current_atom_ndx]->setPos(pos);
528	>
529	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
530	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
531	>
532	>	rotMat[0][0] = 1.0;
533	>	rotMat[0][1] = 0.0;
534	>	rotMat[0][2] = 0.0;
535	>
536	>	rotMat[1][0] = 0.0;
537	>	rotMat[1][1] = 1.0;
538	>	rotMat[1][2] = 0.0;
539	>
540	>	rotMat[2][0] = 0.0;
541	>	rotMat[2][1] = 0.0;
542	>	rotMat[2][2] = 1.0;
543	>
544	>	dAtom->setA(rotMat);
545	>	}
546	>
547	>	current_atom_ndx++;
548		}
549
550	<	if( the_globals->haveThermalTime() ){
551	<	simnfo->thermalTime = the_globals->getThermalTime();
550	>	current_mol++;
551	>	current_comp_mol++;
552	>
553	>	if (current_comp_mol >= components_nmol[current_comp]){
554	>	current_comp_mol = 0;
555	>	current_comp++;
556		}
557	+	}
558
632	–	// check for the temperature set flag
559
560	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
560	>	void SimSetup::gatherInfo(void){
561	>	int i;
562
563	+	ensembleCase = -1;
564	+	ffCase = -1;
565
566	<	//   // make the longe range forces and the integrator
566	>	// set the easy ones first
567
568	<	//   new AllLong( simnfo );
568	>	for (i = 0; i < nInfo; i++){
569	>	info[i].target_temp = globals->getTargetTemp();
570	>	info[i].dt = globals->getDt();
571	>	info[i].run_time = globals->getRunTime();
572	>	}
573	>	n_components = globals->getNComponents();
574
641	–	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
642	–	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
643	–	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
644	–	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
575
576	+	// get the forceField
577
578	+	strcpy(force_field, globals->getForceField());
579
580	<	// initialize the Fortran
581	<
650	<	simnfo->refreshSim();
651	<
652	<	if( !strcmp( simnfo->mixingRule, "standard") ){
653	<	the_ff->initForceField( LB_MIXING_RULE );
580	>	if (!strcasecmp(force_field, "DUFF")){
581	>	ffCase = FF_DUFF;
582		}
583	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
584	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
583	>	else if (!strcasecmp(force_field, "LJ")){
584	>	ffCase = FF_LJ;
585		}
586	+	else if (!strcasecmp(force_field, "EAM")){
587	+	ffCase = FF_EAM;
588	+	}
589		else{
590	<	sprintf( painCave.errMsg,
591	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
592	<	simnfo->mixingRule );
593	<	painCave.isFatal = 1;
663	<	simError();
590	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
591	>	force_field);
592	>	painCave.isFatal = 1;
593	>	simError();
594		}
595
596	+	// get the ensemble
597
598	<	#ifdef IS_MPI
668	<	strcpy( checkPointMsg,
669	<	"Successfully intialized the mixingRule for Fortran." );
670	<	MPIcheckPoint();
671	<	#endif // is_mpi
672	<	}
598	>	strcpy(ensemble, globals->getEnsemble());
599
600	+	if (!strcasecmp(ensemble, "NVE")){
601	+	ensembleCase = NVE_ENS;
602	+	}
603	+	else if (!strcasecmp(ensemble, "NVT")){
604	+	ensembleCase = NVT_ENS;
605	+	}
606	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
607	+	ensembleCase = NPTi_ENS;
608	+	}
609	+	else if (!strcasecmp(ensemble, "NPTf")){
610	+	ensembleCase = NPTf_ENS;
611	+	}
612	+	else if (!strcasecmp(ensemble, "NPTxyz")){
613	+	ensembleCase = NPTxyz_ENS;
614	+	}
615	+	else{
616	+	sprintf(painCave.errMsg,
617	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
618	+	"reverting to NVE for this simulation.\n",
619	+	ensemble);
620	+	painCave.isFatal = 0;
621	+	simError();
622	+	strcpy(ensemble, "NVE");
623	+	ensembleCase = NVE_ENS;
624	+	}
625
626	<	void SimSetup::makeMolecules( void ){
626	>	for (i = 0; i < nInfo; i++){
627	>	strcpy(info[i].ensemble, ensemble);
628
629	<	int i, j, exI, exJ, tempEx, stampID, atomOffset;
678	<	molInit info;
679	<	DirectionalAtom* dAtom;
680	<	AtomStamp* currentAtom;
681	<	BondStamp* currentBond;
682	<	BendStamp* currentBend;
683	<	TorsionStamp* currentTorsion;
684	<
685	<	//init the forceField paramters
629	>	// get the mixing rule
630
631	<	the_ff->readParams();
631	>	strcpy(info[i].mixingRule, globals->getMixingRule());
632	>	info[i].usePBC = globals->getPBC();
633	>	}
634
635	<
690	<	// init the molecules
635	>	// get the components and calculate the tot_nMol and indvidual n_mol
636
637	<	atomOffset = 0;
638	<	for(i=0; i<simnfo->n_mol; i++){
694	<
695	<	stampID = the_molecules[i].getStampID();
637	>	the_components = globals->getComponents();
638	>	components_nmol = new int[n_components];
639
697	–	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
698	–	info.nBonds    = comp_stamps[stampID]->getNBonds();
699	–	info.nBends    = comp_stamps[stampID]->getNBends();
700	–	info.nTorsions = comp_stamps[stampID]->getNTorsions();
701	–
702	–	info.myAtoms = &the_atoms[atomOffset];
703	–	info.myBonds = new Bond*[info.nBonds];
704	–	info.myBends = new Bend*[info.nBends];
705	–	info.myTorsions = new Torsions*[info.nTorsions];
640
641	<	theBonds = new bond_pair[info.nBonds];
642	<	theBends = new bend_set[info.nBends];
643	<	theTorsions = new torsion_set[info.nTorsions];
710	<
711	<	// make the Atoms
712	<
713	<	for(j=0; j<info.nAtoms; j++){
714	<
715	<	currentAtom = theComponents[stampID]->getAtom( j );
716	<	if( currentAtom->haveOrientation() ){
717	<
718	<	dAtom = new DirectionalAtom(j + atomOffset);
719	<	simnfo->n_oriented++;
720	<	info.myAtoms[j] = dAtom;
721	<
722	<	ux = currentAtom->getOrntX();
723	<	uy = currentAtom->getOrntY();
724	<	uz = currentAtom->getOrntZ();
725	<
726	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
727	<
728	<	u = sqrt( uSqr );
729	<	ux = ux / u;
730	<	uy = uy / u;
731	<	uz = uz / u;
732	<
733	<	dAtom->setSUx( ux );
734	<	dAtom->setSUy( uy );
735	<	dAtom->setSUz( uz );
736	<	}
737	<	else{
738	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
739	<	}
740	<	info.myAtoms[j]->setType( currentAtom->getType() );
741	<
742	<	#ifdef IS_MPI
743	<
744	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
745	<
746	<	#endif // is_mpi
747	<	}
748	<
749	<	// make the bonds
750	<	for(j=0; j<nBonds; j++){
751	<
752	<	currentBond = comp_stamps[stampID]->getBond( j );
753	<	theBonds[j].a = currentBond->getA() + atomOffset;
754	<	theBonds[j].b = currentBond->getB() + atomOffset;
641	>	if (!globals->haveNMol()){
642	>	// we don't have the total number of molecules, so we assume it is
643	>	// given in each component
644
645	<	exI = theBonds[i].a;
646	<	exJ = theBonds[i].b;
647	<
648	<	// exclude_I must always be the smaller of the pair
649	<	if( exI > exJ ){
650	<	tempEx = exI;
651	<	exI = exJ;
652	<	exJ = tempEx;
645	>	tot_nmol = 0;
646	>	for (i = 0; i < n_components; i++){
647	>	if (!the_components[i]->haveNMol()){
648	>	// we have a problem
649	>	sprintf(painCave.errMsg,
650	>	"SimSetup Error. No global NMol or component NMol"
651	>	" given. Cannot calculate the number of atoms.\n");
652	>	painCave.isFatal = 1;
653	>	simError();
654		}
765	–	#ifdef IS_MPI
766	–
767	–	the_excludes[index*2] =
768	–	the_atoms[exI]->getGlobalIndex() + 1;
769	–	the_excludes[index*2 + 1] =
770	–	the_atoms[exJ]->getGlobalIndex() + 1;
771	–
772	–	#else  // isn't MPI
773	–
774	–	the_excludes[index*2] =     exI + 1;
775	–	the_excludes[index*2 + 1] = exJ + 1;
776	–	// fortran index from 1 (hence the +1 in the indexing)
655
656	<	#endif  //is_mpi
657	<
656	>	tot_nmol += the_components[i]->getNMol();
657	>	components_nmol[i] = the_components[i]->getNMol();
658	>	}
659		}
660	+	else{
661	+	sprintf(painCave.errMsg,
662	+	"SimSetup error.\n"
663	+	"\tSorry, the ability to specify total"
664	+	" nMols and then give molfractions in the components\n"
665	+	"\tis not currently supported."
666	+	" Please give nMol in the components.\n");
667	+	painCave.isFatal = 1;
668	+	simError();
669	+	}
670
671	+	// set the status, sample, and thermal kick times
672
673	+	for (i = 0; i < nInfo; i++){
674	+	if (globals->haveSampleTime()){
675	+	info[i].sampleTime = globals->getSampleTime();
676	+	info[i].statusTime = info[i].sampleTime;
677	+	info[i].thermalTime = info[i].sampleTime;
678	+	}
679	+	else{
680	+	info[i].sampleTime = globals->getRunTime();
681	+	info[i].statusTime = info[i].sampleTime;
682	+	info[i].thermalTime = info[i].sampleTime;
683	+	}
684
685	+	if (globals->haveStatusTime()){
686	+	info[i].statusTime = globals->getStatusTime();
687	+	}
688
689	+	if (globals->haveThermalTime()){
690	+	info[i].thermalTime = globals->getThermalTime();
691	+	}
692
693	+	info[i].resetIntegrator = 0;
694	+	if( globals->haveResetTime() ){
695	+	info[i].resetTime = globals->getResetTime();
696	+	info[i].resetIntegrator = 1;
697	+	}
698
699	+	// check for the temperature set flag
700	+
701	+	if (globals->haveTempSet())
702	+	info[i].setTemp = globals->getTempSet();
703	+
704	+	}
705	+
706	+	//setup seed for random number generator
707	+	int seedValue;
708
709	+	if (globals->haveSeed()){
710	+	seedValue = globals->getSeed();
711
712	+	if(seedValue / 1E9 == 0){
713	+	sprintf(painCave.errMsg,
714	+	"Seed for sprng library should contain at least 9 digits\n"
715	+	"OOPSE will generate a seed for user\n");
716	+	painCave.isFatal = 0;
717	+	simError();
718
719	+	//using seed generated by system instead of invalid seed set by user
720	+	#ifndef IS_MPI
721	+	seedValue = make_sprng_seed();
722	+	#else
723	+	if (worldRank == 0){
724	+	seedValue = make_sprng_seed();
725	+	}
726	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
727	+	#endif
728	+	}
729	+	}//end of if branch of globals->haveSeed()
730	+	else{
731	+
732	+	#ifndef IS_MPI
733	+	seedValue = make_sprng_seed();
734	+	#else
735	+	if (worldRank == 0){
736	+	seedValue = make_sprng_seed();
737	+	}
738	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
739	+	#endif
740	+	}//end of globals->haveSeed()
741
742	+	for (int i = 0; i < nInfo; i++){
743	+	info[i].setSeed(seedValue);
744	+	}
745
746	+	#ifdef IS_MPI
747	+	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
748	+	MPIcheckPoint();
749	+	#endif // is_mpi
750	+	}
751
752
753	+	void SimSetup::finalInfoCheck(void){
754	+	int index;
755	+	int usesDipoles;
756	+	int i;
757
758	+	for (i = 0; i < nInfo; i++){
759	+	// check electrostatic parameters
760
761	<	void SimSetup::makeAtoms( void ){
761	>	index = 0;
762	>	usesDipoles = 0;
763	>	while ((index < info[i].n_atoms) && !usesDipoles){
764	>	usesDipoles = (info[i].atoms[index])->hasDipole();
765	>	index++;
766	>	}
767
768	<	int i, j, k, index;
769	<	double ux, uy, uz, uSqr, u;
770	<	AtomStamp* current_atom;
768	>	#ifdef IS_MPI
769	>	int myUse = usesDipoles;
770	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
771	>	#endif //is_mpi
772
773	<	DirectionalAtom* dAtom;
803	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
773	>	double theEcr, theEst;
774
775	<	lMolIndex = 0;
776	<	molIndex = 0;
807	<	index = 0;
808	<	for( i=0; i<n_components; i++ ){
775	>	if (globals->getUseRF()){
776	>	info[i].useReactionField = 1;
777
778	<	for( j=0; j<components_nmol[i]; j++ ){
778	>	if (!globals->haveECR()){
779	>	sprintf(painCave.errMsg,
780	>	"SimSetup Warning: using default value of 1/2 the smallest "
781	>	"box length for the electrostaticCutoffRadius.\n"
782	>	"I hope you have a very fast processor!\n");
783	>	painCave.isFatal = 0;
784	>	simError();
785	>	double smallest;
786	>	smallest = info[i].boxL[0];
787	>	if (info[i].boxL[1] <= smallest)
788	>	smallest = info[i].boxL[1];
789	>	if (info[i].boxL[2] <= smallest)
790	>	smallest = info[i].boxL[2];
791	>	theEcr = 0.5 * smallest;
792	>	}
793	>	else{
794	>	theEcr = globals->getECR();
795	>	}
796
797	<	#ifdef IS_MPI
798	<	if( mpiSim->getMyMolStart() <= molIndex &&
799	<	molIndex <= mpiSim->getMyMolEnd() ){
800	<	#endif // is_mpi
797	>	if (!globals->haveEST()){
798	>	sprintf(painCave.errMsg,
799	>	"SimSetup Warning: using default value of 0.05 * the "
800	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
801	>	painCave.isFatal = 0;
802	>	simError();
803	>	theEst = 0.05 * theEcr;
804	>	}
805	>	else{
806	>	theEst = globals->getEST();
807	>	}
808
809	<	molStart = index;
818	<	nMemb = comp_stamps[i]->getNAtoms();
819	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
820	<
821	<	current_atom = comp_stamps[i]->getAtom( k );
822	<	if( current_atom->haveOrientation() ){
823	<
824	<	dAtom = new DirectionalAtom(index);
825	<	simnfo->n_oriented++;
826	<	the_atoms[index] = dAtom;
827	<
828	<	ux = current_atom->getOrntX();
829	<	uy = current_atom->getOrntY();
830	<	uz = current_atom->getOrntZ();
831	<
832	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
833	<
834	<	u = sqrt( uSqr );
835	<	ux = ux / u;
836	<	uy = uy / u;
837	<	uz = uz / u;
838	<
839	<	dAtom->setSUx( ux );
840	<	dAtom->setSUy( uy );
841	<	dAtom->setSUz( uz );
842	<	}
843	<	else{
844	<	the_atoms[index] = new GeneralAtom(index);
845	<	}
846	<	the_atoms[index]->setType( current_atom->getType() );
847	<	the_atoms[index]->setIndex( index );
848	<
849	<	// increment the index and repeat;
850	<	index++;
851	<	}
852	<
853	<	molEnd = index -1;
854	<	the_molecules[lMolIndex].setNMembers( nMemb );
855	<	the_molecules[lMolIndex].setStartAtom( molStart );
856	<	the_molecules[lMolIndex].setEndAtom( molEnd );
857	<	the_molecules[lMolIndex].setStampID( i );
858	<	lMolIndex++;
809	>	info[i].setDefaultEcr(theEcr, theEst);
810
811	<	#ifdef IS_MPI
811	>	if (!globals->haveDielectric()){
812	>	sprintf(painCave.errMsg,
813	>	"SimSetup Error: You are trying to use Reaction Field without"
814	>	"setting a dielectric constant!\n");
815	>	painCave.isFatal = 1;
816	>	simError();
817		}
818	<	#endif //is_mpi
863	<
864	<	molIndex++;
818	>	info[i].dielectric = globals->getDielectric();
819		}
820	+	else{
821	+	if (usesDipoles){
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 "
845	+	"electrostaticSkinThickness\n");
846	+	painCave.isFatal = 0;
847	+	simError();
848	+	theEst = 0.05 * theEcr;
849	+	}
850	+	else{
851	+	theEst = globals->getEST();
852	+	}
853	+
854	+	info[i].setDefaultEcr(theEcr, theEst);
855	+	}
856	+	}
857	+	info[i].checkCutOffs();
858		}
859
860		#ifdef IS_MPI
861	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
862	<
863	<	delete[] globalIndex;
872	<
873	<	mpiSim->mpiRefresh();
874	<	#endif //IS_MPI
875	<
876	<	the_ff->initializeAtoms();
861	>	strcpy(checkPointMsg, "post processing checks out");
862	>	MPIcheckPoint();
863	>	#endif // is_mpi
864		}
865
866	<	void SimSetup::makeBonds( void ){
866	>	void SimSetup::initSystemCoords(void){
867	>	int i;
868
869	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
882	<	bond_pair* the_bonds;
883	<	BondStamp* current_bond;
869	>	char* inName;
870
871	<	the_bonds = new bond_pair[tot_bonds];
886	<	index = 0;
887	<	offset = 0;
888	<	molIndex = 0;
871	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
872
873	<	for( i=0; i<n_components; i++ ){
873	>	for (i = 0; i < info[0].n_atoms; i++)
874	>	info[0].atoms[i]->setCoords();
875
876	<	for( j=0; j<components_nmol[i]; j++ ){
877	<
876	>	if (globals->haveInitialConfig()){
877	>	InitializeFromFile* fileInit;
878	>	#ifdef IS_MPI // is_mpi
879	>	if (worldRank == 0){
880	>	#endif //is_mpi
881	>	inName = globals->getInitialConfig();
882	>	fileInit = new InitializeFromFile(inName);
883		#ifdef IS_MPI
884	<	if( mpiSim->getMyMolStart() <= molIndex &&
885	<	molIndex <= mpiSim->getMyMolEnd() ){
886	<	#endif // is_mpi
887	<
888	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
900	<
901	<	current_bond = comp_stamps[i]->getBond( k );
902	<	the_bonds[index].a = current_bond->getA() + offset;
903	<	the_bonds[index].b = current_bond->getB() + offset;
884	>	}
885	>	else
886	>	fileInit = new InitializeFromFile(NULL);
887	>	#endif
888	>	fileInit->readInit(info); // default velocities on
889
890	<	exI = the_bonds[index].a;
891	<	exJ = the_bonds[index].b;
890	>	delete fileInit;
891	>	}
892	>	else{
893	>	#ifdef IS_MPI
894
895	<	// exclude_I must always be the smaller of the pair
909	<	if( exI > exJ ){
910	<	tempEx = exI;
911	<	exI = exJ;
912	<	exJ = tempEx;
913	<	}
895	>	// no init from bass
896
897	<
898	<	#ifdef IS_MPI
897	>	sprintf(painCave.errMsg,
898	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
899	>	painCave.isFatal = 1;;
900	>	simError();
901
902	<	the_excludes[index*2] =
919	<	the_atoms[exI]->getGlobalIndex() + 1;
920	<	the_excludes[index*2 + 1] =
921	<	the_atoms[exJ]->getGlobalIndex() + 1;
902	>	#else
903
904	<	#else  // isn't MPI
905	<
906	<	the_excludes[index*2] =     exI + 1;
907	<	the_excludes[index*2 + 1] = exJ + 1;
927	<	// fortran index from 1 (hence the +1 in the indexing)
928	<	#endif  //is_mpi
929	<
930	<	// increment the index and repeat;
931	<	index++;
932	<	}
933	<	offset += comp_stamps[i]->getNAtoms();
934	<
935	<	#ifdef IS_MPI
936	<	}
937	<	#endif //is_mpi
938	<
939	<	molIndex++;
940	<	}
904	>	initFromBass();
905	>
906	>
907	>	#endif
908		}
909
910	<	the_ff->initializeBonds( the_bonds );
910	>	#ifdef IS_MPI
911	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
912	>	MPIcheckPoint();
913	>	#endif // is_mpi
914		}
915
946	–	void SimSetup::makeBends( void ){
916
917	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
918	<	bend_set* the_bends;
950	<	BendStamp* current_bend;
951	<	LinkedAssign* extras;
952	<	LinkedAssign* current_extra;
953	<
917	>	void SimSetup::makeOutNames(void){
918	>	int k;
919
955	–	the_bends = new bend_set[tot_bends];
956	–	index = 0;
957	–	offset = 0;
958	–	molIndex = 0;
959	–	for( i=0; i<n_components; i++ ){
920
921	<	for( j=0; j<components_nmol[i]; j++ ){
962	<
921	>	for (k = 0; k < nInfo; k++){
922		#ifdef IS_MPI
923	<	if( mpiSim->getMyMolStart() <= molIndex &&
924	<	molIndex <= mpiSim->getMyMolEnd() ){
966	<	#endif // is_mpi
923	>	if (worldRank == 0){
924	>	#endif // is_mpi
925
926	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
927	<
928	<	current_bend = comp_stamps[i]->getBend( k );
929	<	the_bends[index].a = current_bend->getA() + offset;
930	<	the_bends[index].b = current_bend->getB() + offset;
931	<	the_bends[index].c = current_bend->getC() + offset;
932	<
933	<	if( current_bend->haveExtras() ){
934	<
935	<	extras = current_bend->getExtras();
936	<	current_extra = extras;
937	<
938	<	while( current_extra != NULL ){
939	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
940	<
941	<	switch( current_extra->getType() ){
942	<
943	<	case 0:
944	<	the_bends[index].ghost =
945	<	current_extra->getInt() + offset;
946	<	the_bends[index].isGhost = 1;
947	<	break;
948	<
949	<	case 1:
950	<	the_bends[index].ghost =
951	<	(int)current_extra->getDouble() + offset;
952	<	the_bends[index].isGhost = 1;
995	<	break;
996	<
997	<	default:
998	<	sprintf( painCave.errMsg,
999	<	"SimSetup Error: ghostVectorSource was neiter a "
1000	<	"double nor an int.\n"
1001	<	"-->Bend[%d] in %s\n",
1002	<	k, comp_stamps[i]->getID() );
1003	<	painCave.isFatal = 1;
1004	<	simError();
1005	<	}
1006	<	}
1007	<
1008	<	else{
1009	<
1010	<	sprintf( painCave.errMsg,
1011	<	"SimSetup Error: unhandled bend assignment:\n"
1012	<	"    -->%s in Bend[%d] in %s\n",
1013	<	current_extra->getlhs(),
1014	<	k, comp_stamps[i]->getID() );
1015	<	painCave.isFatal = 1;
1016	<	simError();
1017	<	}
1018	<
1019	<	current_extra = current_extra->getNext();
1020	<	}
1021	<	}
1022	<
1023	<	if( !the_bends[index].isGhost ){
1024	<
1025	<	exI = the_bends[index].a;
1026	<	exJ = the_bends[index].c;
1027	<	}
1028	<	else{
1029	<
1030	<	exI = the_bends[index].a;
1031	<	exJ = the_bends[index].b;
1032	<	}
1033	<
1034	<	// exclude_I must always be the smaller of the pair
1035	<	if( exI > exJ ){
1036	<	tempEx = exI;
1037	<	exI = exJ;
1038	<	exJ = tempEx;
1039	<	}
926	>	if (globals->haveFinalConfig()){
927	>	strcpy(info[k].finalName, globals->getFinalConfig());
928	>	}
929	>	else{
930	>	strcpy(info[k].finalName, inFileName);
931	>	char* endTest;
932	>	int nameLength = strlen(info[k].finalName);
933	>	endTest = &(info[k].finalName[nameLength - 5]);
934	>	if (!strcmp(endTest, ".bass")){
935	>	strcpy(endTest, ".eor");
936	>	}
937	>	else if (!strcmp(endTest, ".BASS")){
938	>	strcpy(endTest, ".eor");
939	>	}
940	>	else{
941	>	endTest = &(info[k].finalName[nameLength - 4]);
942	>	if (!strcmp(endTest, ".bss")){
943	>	strcpy(endTest, ".eor");
944	>	}
945	>	else if (!strcmp(endTest, ".mdl")){
946	>	strcpy(endTest, ".eor");
947	>	}
948	>	else{
949	>	strcat(info[k].finalName, ".eor");
950	>	}
951	>	}
952	>	}
953
954	+	// make the sample and status out names
955
956	<	#ifdef IS_MPI
956	>	strcpy(info[k].sampleName, inFileName);
957	>	char* endTest;
958	>	int nameLength = strlen(info[k].sampleName);
959	>	endTest = &(info[k].sampleName[nameLength - 5]);
960	>	if (!strcmp(endTest, ".bass")){
961	>	strcpy(endTest, ".dump");
962	>	}
963	>	else if (!strcmp(endTest, ".BASS")){
964	>	strcpy(endTest, ".dump");
965	>	}
966	>	else{
967	>	endTest = &(info[k].sampleName[nameLength - 4]);
968	>	if (!strcmp(endTest, ".bss")){
969	>	strcpy(endTest, ".dump");
970	>	}
971	>	else if (!strcmp(endTest, ".mdl")){
972	>	strcpy(endTest, ".dump");
973	>	}
974	>	else{
975	>	strcat(info[k].sampleName, ".dump");
976	>	}
977	>	}
978
979	<	the_excludes[(index + tot_bonds)*2] =
980	<	the_atoms[exI]->getGlobalIndex() + 1;
981	<	the_excludes[(index + tot_bonds)*2 + 1] =
982	<	the_atoms[exJ]->getGlobalIndex() + 1;
983	<
1049	<	#else  // isn't MPI
1050	<
1051	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
1052	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1053	<	// fortran index from 1 (hence the +1 in the indexing)
1054	<	#endif  //is_mpi
1055	<
1056	<
1057	<	// increment the index and repeat;
1058	<	index++;
1059	<	}
1060	<	offset += comp_stamps[i]->getNAtoms();
1061	<
1062	<	#ifdef IS_MPI
979	>	strcpy(info[k].statusName, inFileName);
980	>	nameLength = strlen(info[k].statusName);
981	>	endTest = &(info[k].statusName[nameLength - 5]);
982	>	if (!strcmp(endTest, ".bass")){
983	>	strcpy(endTest, ".stat");
984		}
985	<	#endif //is_mpi
985	>	else if (!strcmp(endTest, ".BASS")){
986	>	strcpy(endTest, ".stat");
987	>	}
988	>	else{
989	>	endTest = &(info[k].statusName[nameLength - 4]);
990	>	if (!strcmp(endTest, ".bss")){
991	>	strcpy(endTest, ".stat");
992	>	}
993	>	else if (!strcmp(endTest, ".mdl")){
994	>	strcpy(endTest, ".stat");
995	>	}
996	>	else{
997	>	strcat(info[k].statusName, ".stat");
998	>	}
999	>	}
1000
1001	<	molIndex++;
1001	>	#ifdef IS_MPI
1002	>
1003		}
1004	+	#endif // is_mpi
1005		}
1006	+	}
1007
1070	–	#ifdef IS_MPI
1071	–	sprintf( checkPointMsg,
1072	–	"Successfully created the bends list.\n" );
1073	–	MPIcheckPoint();
1074	–	#endif // is_mpi
1075	–
1008
1009	<	the_ff->initializeBends( the_bends );
1010	<	}
1009	>	void SimSetup::sysObjectsCreation(void){
1010	>	int i, k;
1011
1012	<	void SimSetup::makeTorsions( void ){
1012	>	// create the forceField
1013
1014	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1083	<	torsion_set* the_torsions;
1084	<	TorsionStamp* current_torsion;
1014	>	createFF();
1015
1016	<	the_torsions = new torsion_set[tot_torsions];
1087	<	index = 0;
1088	<	offset = 0;
1089	<	molIndex = 0;
1090	<	for( i=0; i<n_components; i++ ){
1016	>	// extract componentList
1017
1018	<	for( j=0; j<components_nmol[i]; j++ ){
1018	>	compList();
1019
1020	+	// calc the number of atoms, bond, bends, and torsions
1021	+
1022	+	calcSysValues();
1023	+
1024		#ifdef IS_MPI
1025	<	if( mpiSim->getMyMolStart() <= molIndex &&
1096	<	molIndex <= mpiSim->getMyMolEnd() ){
1097	<	#endif // is_mpi
1025	>	// divide the molecules among the processors
1026
1027	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1027	>	mpiMolDivide();
1028	>	#endif //is_mpi
1029
1030	<	current_torsion = comp_stamps[i]->getTorsion( k );
1102	<	the_torsions[index].a = current_torsion->getA() + offset;
1103	<	the_torsions[index].b = current_torsion->getB() + offset;
1104	<	the_torsions[index].c = current_torsion->getC() + offset;
1105	<	the_torsions[index].d = current_torsion->getD() + offset;
1030	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1031
1032	<	exI = the_torsions[index].a;
1108	<	exJ = the_torsions[index].d;
1032	>	makeSysArrays();
1033
1034	<
1111	<	// exclude_I must always be the smaller of the pair
1112	<	if( exI > exJ ){
1113	<	tempEx = exI;
1114	<	exI = exJ;
1115	<	exJ = tempEx;
1116	<	}
1034	>	// make and initialize the molecules (all but atomic coordinates)
1035
1036	+	makeMolecules();
1037
1038	<	#ifdef IS_MPI
1039	<
1040	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
1041	<	the_atoms[exI]->getGlobalIndex() + 1;
1042	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1043	<	the_atoms[exJ]->getGlobalIndex() + 1;
1044	<
1126	<	#else  // isn't MPI
1127	<
1128	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1129	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1130	<	// fortran indexes from 1 (hence the +1 in the indexing)
1131	<	#endif  //is_mpi
1132	<
1038	>	for (k = 0; k < nInfo; k++){
1039	>	info[k].identArray = new int[info[k].n_atoms];
1040	>	for (i = 0; i < info[k].n_atoms; i++){
1041	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1042	>	}
1043	>	}
1044	>	}
1045
1134	–	// increment the index and repeat;
1135	–	index++;
1136	–	}
1137	–	offset += comp_stamps[i]->getNAtoms();
1046
1047	+	void SimSetup::createFF(void){
1048	+	switch (ffCase){
1049	+	case FF_DUFF:
1050	+	the_ff = new DUFF();
1051	+	break;
1052	+
1053	+	case FF_LJ:
1054	+	the_ff = new LJFF();
1055	+	break;
1056	+
1057	+	case FF_EAM:
1058	+	the_ff = new EAM_FF();
1059	+	break;
1060	+
1061	+	default:
1062	+	sprintf(painCave.errMsg,
1063	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1064	+	painCave.isFatal = 1;
1065	+	simError();
1066	+	}
1067	+
1068		#ifdef IS_MPI
1069	<	}
1070	<	#endif //is_mpi
1069	>	strcpy(checkPointMsg, "ForceField creation successful");
1070	>	MPIcheckPoint();
1071	>	#endif // is_mpi
1072	>	}
1073
1143	–	molIndex++;
1144	–	}
1145	–	}
1074
1075	<	the_ff->initializeTorsions( the_torsions );
1076	<	}
1075	>	void SimSetup::compList(void){
1076	>	int i;
1077	>	char* id;
1078	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1079	>	LinkedMolStamp* currentStamp = NULL;
1080	>	comp_stamps = new MoleculeStamp * [n_components];
1081
1082	<	void SimSetup::initFromBass( void ){
1082	>	// make an array of molecule stamps that match the components used.
1083	>	// also extract the used stamps out into a separate linked list
1084
1085	<	int i, j, k;
1086	<	int n_cells;
1087	<	double cellx, celly, cellz;
1088	<	double temp1, temp2, temp3;
1089	<	int n_per_extra;
1090	<	int n_extra;
1158	<	int have_extra, done;
1085	>	for (i = 0; i < nInfo; i++){
1086	>	info[i].nComponents = n_components;
1087	>	info[i].componentsNmol = components_nmol;
1088	>	info[i].compStamps = comp_stamps;
1089	>	info[i].headStamp = headStamp;
1090	>	}
1091
1160	–	temp1 = (double)tot_nmol / 4.0;
1161	–	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1162	–	temp3 = ceil( temp2 );
1092
1093	<	have_extra =0;
1094	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1095	<	have_extra =1;
1093	>	for (i = 0; i < n_components; i++){
1094	>	id = the_components[i]->getType();
1095	>	comp_stamps[i] = NULL;
1096
1097	<	n_cells = (int)temp3 - 1;
1169	<	cellx = simnfo->box_x / temp3;
1170	<	celly = simnfo->box_y / temp3;
1171	<	cellz = simnfo->box_z / temp3;
1172	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1173	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1174	<	n_per_extra = (int)ceil( temp1 );
1097	>	// check to make sure the component isn't already in the list
1098
1099	<	if( n_per_extra > 4){
1100	<	sprintf( painCave.errMsg,
1101	<	"SimSetup error. There has been an error in constructing"
1102	<	" the non-complete lattice.\n" );
1103	<	painCave.isFatal = 1;
1104	<	simError();
1099	>	comp_stamps[i] = headStamp->match(id);
1100	>	if (comp_stamps[i] == NULL){
1101	>	// extract the component from the list;
1102	>
1103	>	currentStamp = stamps->extractMolStamp(id);
1104	>	if (currentStamp == NULL){
1105	>	sprintf(painCave.errMsg,
1106	>	"SimSetup error: Component \"%s\" was not found in the "
1107	>	"list of declared molecules\n",
1108	>	id);
1109	>	painCave.isFatal = 1;
1110	>	simError();
1111	>	}
1112	>
1113	>	headStamp->add(currentStamp);
1114	>	comp_stamps[i] = headStamp->match(id);
1115		}
1116		}
1184	–	else{
1185	–	n_cells = (int)temp3;
1186	–	cellx = simnfo->box_x / temp3;
1187	–	celly = simnfo->box_y / temp3;
1188	–	cellz = simnfo->box_z / temp3;
1189	–	}
1117
1118	<	current_mol = 0;
1119	<	current_comp_mol = 0;
1120	<	current_comp = 0;
1121	<	current_atom_ndx = 0;
1118	>	#ifdef IS_MPI
1119	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1120	>	MPIcheckPoint();
1121	>	#endif // is_mpi
1122	>	}
1123
1124	<	for( i=0; i < n_cells ; i++ ){
1125	<	for( j=0; j < n_cells; j++ ){
1198	<	for( k=0; k < n_cells; k++ ){
1124	>	void SimSetup::calcSysValues(void){
1125	>	int i;
1126
1127	<	makeElement( i * cellx,
1201	<	j * celly,
1202	<	k * cellz );
1127	>	int* molMembershipArray;
1128
1129	<	makeElement( i * cellx + 0.5 * cellx,
1130	<	j * celly + 0.5 * celly,
1131	<	k * cellz );
1129	>	tot_atoms = 0;
1130	>	tot_bonds = 0;
1131	>	tot_bends = 0;
1132	>	tot_torsions = 0;
1133	>	for (i = 0; i < n_components; i++){
1134	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1135	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1136	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1137	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1138	>	}
1139
1140	<	makeElement( i * cellx,
1141	<	j * celly + 0.5 * celly,
1210	<	k * cellz + 0.5 * cellz );
1140	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1141	>	molMembershipArray = new int[tot_atoms];
1142
1143	<	makeElement( i * cellx + 0.5 * cellx,
1144	<	j * celly,
1145	<	k * cellz + 0.5 * cellz );
1146	<	}
1147	<	}
1143	>	for (i = 0; i < nInfo; i++){
1144	>	info[i].n_atoms = tot_atoms;
1145	>	info[i].n_bonds = tot_bonds;
1146	>	info[i].n_bends = tot_bends;
1147	>	info[i].n_torsions = tot_torsions;
1148	>	info[i].n_SRI = tot_SRI;
1149	>	info[i].n_mol = tot_nmol;
1150	>
1151	>	info[i].molMembershipArray = molMembershipArray;
1152		}
1153	+	}
1154
1155	<	if( have_extra ){
1220	<	done = 0;
1155	>	#ifdef IS_MPI
1156
1157	<	int start_ndx;
1158	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1159	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1157	>	void SimSetup::mpiMolDivide(void){
1158	>	int i, j, k;
1159	>	int localMol, allMol;
1160	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1161
1162	<	if( i < n_cells ){
1162	>	mpiSim = new mpiSimulation(info);
1163
1164	<	if( j < n_cells ){
1229	<	start_ndx = n_cells;
1230	<	}
1231	<	else start_ndx = 0;
1232	<	}
1233	<	else start_ndx = 0;
1164	>	globalIndex = mpiSim->divideLabor();
1165
1166	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1166	>	// set up the local variables
1167
1168	<	makeElement( i * cellx,
1169	<	j * celly,
1239	<	k * cellz );
1240	<	done = ( current_mol >= tot_nmol );
1168	>	mol2proc = mpiSim->getMolToProcMap();
1169	>	molCompType = mpiSim->getMolComponentType();
1170
1171	<	if( !done && n_per_extra > 1 ){
1172	<	makeElement( i * cellx + 0.5 * cellx,
1173	<	j * celly + 0.5 * celly,
1174	<	k * cellz );
1175	<	done = ( current_mol >= tot_nmol );
1176	<	}
1171	>	allMol = 0;
1172	>	localMol = 0;
1173	>	local_atoms = 0;
1174	>	local_bonds = 0;
1175	>	local_bends = 0;
1176	>	local_torsions = 0;
1177	>	globalAtomIndex = 0;
1178
1249	–	if( !done && n_per_extra > 2){
1250	–	makeElement( i * cellx,
1251	–	j * celly + 0.5 * celly,
1252	–	k * cellz + 0.5 * cellz );
1253	–	done = ( current_mol >= tot_nmol );
1254	–	}
1179
1180	<	if( !done && n_per_extra > 3){
1181	<	makeElement( i * cellx + 0.5 * cellx,
1182	<	j * celly,
1183	<	k * cellz + 0.5 * cellz );
1184	<	done = ( current_mol >= tot_nmol );
1185	<	}
1186	<	}
1180	>	for (i = 0; i < n_components; i++){
1181	>	for (j = 0; j < components_nmol[i]; j++){
1182	>	if (mol2proc[allMol] == worldRank){
1183	>	local_atoms += comp_stamps[i]->getNAtoms();
1184	>	local_bonds += comp_stamps[i]->getNBonds();
1185	>	local_bends += comp_stamps[i]->getNBends();
1186	>	local_torsions += comp_stamps[i]->getNTorsions();
1187	>	localMol++;
1188	>	}
1189	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1190	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1191	>	globalAtomIndex++;
1192		}
1193	+
1194	+	allMol++;
1195		}
1196		}
1197	+	local_SRI = local_bonds + local_bends + local_torsions;
1198
1199	+	info[0].n_atoms = mpiSim->getMyNlocal();
1200
1201	<	for( i=0; i<simnfo->n_atoms; i++ ){
1202	<	simnfo->atoms[i]->set_vx( 0.0 );
1203	<	simnfo->atoms[i]->set_vy( 0.0 );
1204	<	simnfo->atoms[i]->set_vz( 0.0 );
1201	>	if (local_atoms != info[0].n_atoms){
1202	>	sprintf(painCave.errMsg,
1203	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1204	>	" localAtom (%d) are not equal.\n",
1205	>	info[0].n_atoms, local_atoms);
1206	>	painCave.isFatal = 1;
1207	>	simError();
1208		}
1209	+
1210	+	info[0].n_bonds = local_bonds;
1211	+	info[0].n_bends = local_bends;
1212	+	info[0].n_torsions = local_torsions;
1213	+	info[0].n_SRI = local_SRI;
1214	+	info[0].n_mol = localMol;
1215	+
1216	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1217	+	MPIcheckPoint();
1218		}
1219
1220	<	void SimSetup::makeElement( double x, double y, double z ){
1220	>	#endif // is_mpi
1221
1277	–	int k;
1278	–	AtomStamp* current_atom;
1279	–	DirectionalAtom* dAtom;
1280	–	double rotMat[3][3];
1222
1223	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1223	>	void SimSetup::makeSysArrays(void){
1224	>
1225	>	#ifndef IS_MPI
1226	>	int k, j;
1227	>	#endif // is_mpi
1228	>	int i, l;
1229
1230	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1231	<	if( !current_atom->havePosition() ){
1232	<	sprintf( painCave.errMsg,
1287	<	"SimSetup:initFromBass error.\n"
1288	<	"\tComponent %s, atom %s does not have a position specified.\n"
1289	<	"\tThe initialization routine is unable to give a start"
1290	<	" position.\n",
1291	<	comp_stamps[current_comp]->getID(),
1292	<	current_atom->getType() );
1293	<	painCave.isFatal = 1;
1294	<	simError();
1295	<	}
1230	>	Atom** the_atoms;
1231	>	Molecule* the_molecules;
1232	>	Exclude** the_excludes;
1233
1297	–	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1298	–	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1299	–	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1234
1235	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1235	>	for (l = 0; l < nInfo; l++){
1236	>	// create the atom and short range interaction arrays
1237
1238	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1238	>	the_atoms = new Atom * [info[l].n_atoms];
1239	>	the_molecules = new Molecule[info[l].n_mol];
1240	>	int molIndex;
1241
1242	<	rotMat[0][0] = 1.0;
1306	<	rotMat[0][1] = 0.0;
1307	<	rotMat[0][2] = 0.0;
1242	>	// initialize the molecule's stampID's
1243
1244	<	rotMat[1][0] = 0.0;
1310	<	rotMat[1][1] = 1.0;
1311	<	rotMat[1][2] = 0.0;
1244	>	#ifdef IS_MPI
1245
1313	–	rotMat[2][0] = 0.0;
1314	–	rotMat[2][1] = 0.0;
1315	–	rotMat[2][2] = 1.0;
1246
1247	<	dAtom->setA( rotMat );
1247	>	molIndex = 0;
1248	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1249	>	if (mol2proc[i] == worldRank){
1250	>	the_molecules[molIndex].setStampID(molCompType[i]);
1251	>	the_molecules[molIndex].setMyIndex(molIndex);
1252	>	the_molecules[molIndex].setGlobalIndex(i);
1253	>	molIndex++;
1254	>	}
1255		}
1256
1257	<	current_atom_ndx++;
1321	<	}
1257	>	#else // is_mpi
1258
1259	<	current_mol++;
1260	<	current_comp_mol++;
1259	>	molIndex = 0;
1260	>	globalAtomIndex = 0;
1261	>	for (i = 0; i < n_components; i++){
1262	>	for (j = 0; j < components_nmol[i]; j++){
1263	>	the_molecules[molIndex].setStampID(i);
1264	>	the_molecules[molIndex].setMyIndex(molIndex);
1265	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1266	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1267	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1268	>	globalAtomIndex++;
1269	>	}
1270	>	molIndex++;
1271	>	}
1272	>	}
1273
1326	–	if( current_comp_mol >= components_nmol[current_comp] ){
1274
1275	<	current_comp_mol = 0;
1276	<	current_comp++;
1275	>	#endif // is_mpi
1276	>
1277	>
1278	>	if (info[l].n_SRI){
1279	>	Exclude::createArray(info[l].n_SRI);
1280	>	the_excludes = new Exclude * [info[l].n_SRI];
1281	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1282	>	the_excludes[ex] = new Exclude(ex);
1283	>	}
1284	>	info[l].globalExcludes = new int;
1285	>	info[l].n_exclude = info[l].n_SRI;
1286	>	}
1287	>	else{
1288	>	Exclude::createArray(1);
1289	>	the_excludes = new Exclude * ;
1290	>	the_excludes[0] = new Exclude(0);
1291	>	the_excludes[0]->setPair(0, 0);
1292	>	info[l].globalExcludes = new int;
1293	>	info[l].globalExcludes[0] = 0;
1294	>	info[l].n_exclude = 0;
1295	>	}
1296	>
1297	>	// set the arrays into the SimInfo object
1298	>
1299	>	info[l].atoms = the_atoms;
1300	>	info[l].molecules = the_molecules;
1301	>	info[l].nGlobalExcludes = 0;
1302	>	info[l].excludes = the_excludes;
1303	>
1304	>	the_ff->setSimInfo(info);
1305		}
1306		}
1307	+
1308	+	void SimSetup::makeIntegrator(void){
1309	+	int k;
1310	+
1311	+	NVE* myNVE = NULL;
1312	+	NVT* myNVT = NULL;
1313	+	NPTi* myNPTi = NULL;
1314	+	NPTf* myNPTf = NULL;
1315	+	NPTxyz* myNPTxyz = NULL;
1316	+
1317	+	for (k = 0; k < nInfo; k++){
1318	+	switch (ensembleCase){
1319	+	case NVE_ENS:
1320	+	if (globals->haveZconstraints()){
1321	+
1322	+	std::cerr << "ZConstraint is temporarily disabled\n";
1323	+
1324	+	//      setupZConstraint(info[k]);
1325	+	//      myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1326	+	}
1327	+
1328	+	//       else{
1329	+	myNVE = new NVE(&(info[k]), the_ff);
1330	+	//       }
1331	+
1332	+	info->the_integrator = myNVE;
1333	+	break;
1334	+
1335	+	case NVT_ENS:
1336	+	if (globals->haveZconstraints()){
1337	+
1338	+	std::cerr << "ZConstraint is temporarily disabled\n";
1339	+
1340	+	//      setupZConstraint(info[k]);
1341	+	//      myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1342	+	}
1343	+	// else
1344	+	myNVT = new NVT(&(info[k]), the_ff);
1345	+
1346	+	myNVT->setTargetTemp(globals->getTargetTemp());
1347	+
1348	+	if (globals->haveTauThermostat())
1349	+	myNVT->setTauThermostat(globals->getTauThermostat());
1350	+	else{
1351	+	sprintf(painCave.errMsg,
1352	+	"SimSetup error: If you use the NVT\n"
1353	+	"    ensemble, you must set tauThermostat.\n");
1354	+	painCave.isFatal = 1;
1355	+	simError();
1356	+	}
1357	+
1358	+	info->the_integrator = myNVT;
1359	+	break;
1360	+
1361	+	case NPTi_ENS:
1362	+	if (globals->haveZconstraints()){
1363	+
1364	+	std::cerr << "ZConstraint is temporarily disabled\n";
1365	+
1366	+	//        setupZConstraint(info[k]);
1367	+	//           myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1368	+	}
1369	+	// else
1370	+	myNPTi = new NPTi(&(info[k]), the_ff);
1371	+
1372	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1373	+
1374	+	if (globals->haveTargetPressure())
1375	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1376	+	else{
1377	+	sprintf(painCave.errMsg,
1378	+	"SimSetup error: If you use a constant pressure\n"
1379	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1380	+	painCave.isFatal = 1;
1381	+	simError();
1382	+	}
1383	+
1384	+	if (globals->haveTauThermostat())
1385	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1386	+	else{
1387	+	sprintf(painCave.errMsg,
1388	+	"SimSetup error: If you use an NPT\n"
1389	+	"    ensemble, you must set tauThermostat.\n");
1390	+	painCave.isFatal = 1;
1391	+	simError();
1392	+	}
1393	+
1394	+	if (globals->haveTauBarostat())
1395	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1396	+	else{
1397	+	sprintf(painCave.errMsg,
1398	+	"SimSetup error: If you use an NPT\n"
1399	+	"    ensemble, you must set tauBarostat.\n");
1400	+	painCave.isFatal = 1;
1401	+	simError();
1402	+	}
1403	+
1404	+	info->the_integrator = myNPTi;
1405	+	break;
1406	+
1407	+	case NPTf_ENS:
1408	+	if (globals->haveZconstraints()){
1409	+
1410	+	std::cerr << "ZConstraint is temporarily disabled\n";
1411	+
1412	+	//      setupZConstraint(info[k]);
1413	+	//      myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1414	+	}
1415	+	//       else
1416	+	myNPTf = new NPTf(&(info[k]), the_ff);
1417	+
1418	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1419	+
1420	+	if (globals->haveTargetPressure())
1421	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1422	+	else{
1423	+	sprintf(painCave.errMsg,
1424	+	"SimSetup error: If you use a constant pressure\n"
1425	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1426	+	painCave.isFatal = 1;
1427	+	simError();
1428	+	}
1429	+
1430	+	if (globals->haveTauThermostat())
1431	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1432	+
1433	+	else{
1434	+	sprintf(painCave.errMsg,
1435	+	"SimSetup error: If you use an NPT\n"
1436	+	"    ensemble, you must set tauThermostat.\n");
1437	+	painCave.isFatal = 1;
1438	+	simError();
1439	+	}
1440	+
1441	+	if (globals->haveTauBarostat())
1442	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1443	+
1444	+	else{
1445	+	sprintf(painCave.errMsg,
1446	+	"SimSetup error: If you use an NPT\n"
1447	+	"    ensemble, you must set tauBarostat.\n");
1448	+	painCave.isFatal = 1;
1449	+	simError();
1450	+	}
1451	+
1452	+	info->the_integrator = myNPTf;
1453	+	break;
1454	+
1455	+	case NPTxyz_ENS:
1456	+	if (globals->haveZconstraints()){
1457	+
1458	+	std::cerr << "ZConstraint is temporarily disabled\n";
1459	+
1460	+	//      setupZConstraint(info[k]);
1461	+	//      myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1462	+	}
1463	+	//       else
1464	+	myNPTxyz = new NPTxyz(&(info[k]), the_ff);
1465	+
1466	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1467	+
1468	+	if (globals->haveTargetPressure())
1469	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1470	+	else{
1471	+	sprintf(painCave.errMsg,
1472	+	"SimSetup error: If you use a constant pressure\n"
1473	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1474	+	painCave.isFatal = 1;
1475	+	simError();
1476	+	}
1477	+
1478	+	if (globals->haveTauThermostat())
1479	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1480	+	else{
1481	+	sprintf(painCave.errMsg,
1482	+	"SimSetup error: If you use an NPT\n"
1483	+	"    ensemble, you must set tauThermostat.\n");
1484	+	painCave.isFatal = 1;
1485	+	simError();
1486	+	}
1487	+
1488	+	if (globals->haveTauBarostat())
1489	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1490	+	else{
1491	+	sprintf(painCave.errMsg,
1492	+	"SimSetup error: If you use an NPT\n"
1493	+	"    ensemble, you must set tauBarostat.\n");
1494	+	painCave.isFatal = 1;
1495	+	simError();
1496	+	}
1497	+
1498	+	info->the_integrator = myNPTxyz;
1499	+	break;
1500	+
1501	+	default:
1502	+	sprintf(painCave.errMsg,
1503	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1504	+	painCave.isFatal = 1;
1505	+	simError();
1506	+	}
1507	+	}
1508	+	}
1509	+
1510	+	void SimSetup::initFortran(void){
1511	+	info[0].refreshSim();
1512	+
1513	+	if (!strcmp(info[0].mixingRule, "standard")){
1514	+	the_ff->initForceField(LB_MIXING_RULE);
1515	+	}
1516	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1517	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1518	+	}
1519	+	else{
1520	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1521	+	info[0].mixingRule);
1522	+	painCave.isFatal = 1;
1523	+	simError();
1524	+	}
1525	+
1526	+
1527	+	#ifdef IS_MPI
1528	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1529	+	MPIcheckPoint();
1530	+	#endif // is_mpi
1531	+	}
1532	+
1533	+	// void SimSetup::setupZConstraint(SimInfo& theInfo){
1534	+	//   int nZConstraints;
1535	+	//   ZconStamp** zconStamp;
1536	+
1537	+	//   if (globals->haveZconstraintTime()){
1538	+	//     //add sample time of z-constraint  into SimInfo's property list
1539	+	//     DoubleData* zconsTimeProp = new DoubleData();
1540	+	//     zconsTimeProp->setID(ZCONSTIME_ID);
1541	+	//     zconsTimeProp->setData(globals->getZconsTime());
1542	+	//     theInfo.addProperty(zconsTimeProp);
1543	+	//   }
1544	+	//   else{
1545	+	//     sprintf(painCave.errMsg,
1546	+	//             "ZConstraint error: If you use an ZConstraint\n"
1547	+	//             " , you must set sample time.\n");
1548	+	//     painCave.isFatal = 1;
1549	+	//     simError();
1550	+	//   }
1551	+
1552	+	//   //push zconsTol into siminfo, if user does not specify
1553	+	//   //value for zconsTol, a default value will be used
1554	+	//   DoubleData* zconsTol = new DoubleData();
1555	+	//   zconsTol->setID(ZCONSTOL_ID);
1556	+	//   if (globals->haveZconsTol()){
1557	+	//     zconsTol->setData(globals->getZconsTol());
1558	+	//   }
1559	+	//   else{
1560	+	//     double defaultZConsTol = 0.01;
1561	+	//     sprintf(painCave.errMsg,
1562	+	//             "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1563	+	//             " , default value %f is used.\n",
1564	+	//             defaultZConsTol);
1565	+	//     painCave.isFatal = 0;
1566	+	//     simError();
1567	+
1568	+	//     zconsTol->setData(defaultZConsTol);
1569	+	//   }
1570	+	//   theInfo.addProperty(zconsTol);
1571	+
1572	+	//   //set Force Subtraction Policy
1573	+	//   StringData* zconsForcePolicy = new StringData();
1574	+	//   zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1575	+
1576	+	//   if (globals->haveZconsForcePolicy()){
1577	+	//     zconsForcePolicy->setData(globals->getZconsForcePolicy());
1578	+	//   }
1579	+	//   else{
1580	+	//     sprintf(painCave.errMsg,
1581	+	//             "ZConstraint Warning: User does not set force Subtraction policy, "
1582	+	//             "PolicyByMass is used\n");
1583	+	//     painCave.isFatal = 0;
1584	+	//     simError();
1585	+	//     zconsForcePolicy->setData("BYMASS");
1586	+	//   }
1587	+
1588	+	//   theInfo.addProperty(zconsForcePolicy);
1589	+
1590	+	//   //Determine the name of ouput file and add it into SimInfo's property list
1591	+	//   //Be careful, do not use inFileName, since it is a pointer which
1592	+	//   //point to a string at master node, and slave nodes do not contain that string
1593	+
1594	+	//   string zconsOutput(theInfo.finalName);
1595	+
1596	+	//   zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1597	+
1598	+	//   StringData* zconsFilename = new StringData();
1599	+	//   zconsFilename->setID(ZCONSFILENAME_ID);
1600	+	//   zconsFilename->setData(zconsOutput);
1601	+
1602	+	//   theInfo.addProperty(zconsFilename);
1603	+
1604	+	//   //setup index, pos and other parameters of z-constraint molecules
1605	+	//   nZConstraints = globals->getNzConstraints();
1606	+	//   theInfo.nZconstraints = nZConstraints;
1607	+
1608	+	//   zconStamp = globals->getZconStamp();
1609	+	//   ZConsParaItem tempParaItem;
1610	+
1611	+	//   ZConsParaData* zconsParaData = new ZConsParaData();
1612	+	//   zconsParaData->setID(ZCONSPARADATA_ID);
1613	+
1614	+	//   for (int i = 0; i < nZConstraints; i++){
1615	+	//     tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1616	+	//     tempParaItem.zPos = zconStamp[i]->getZpos();
1617	+	//     tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1618	+	//     tempParaItem.kRatio = zconStamp[i]->getKratio();
1619	+
1620	+	//     zconsParaData->addItem(tempParaItem);
1621	+	//   }
1622	+
1623	+	//   //check the uniqueness of index
1624	+	//   if(!zconsParaData->isIndexUnique()){
1625	+	//     sprintf(painCave.errMsg,
1626	+	//             "ZConstraint Error: molIndex is not unique\n");
1627	+	//     painCave.isFatal = 1;
1628	+	//     simError();
1629	+	//   }
1630	+
1631	+	//   //sort the parameters by index of molecules
1632	+	//   zconsParaData->sortByIndex();
1633	+
1634	+	//   //push data into siminfo, therefore, we can retrieve later
1635	+	//   theInfo.addProperty(zconsParaData);
1636	+	// }

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