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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 412 by mmeineke, Wed Mar 26 21:50:33 2003 UTC vs.
Revision 859 by mmeineke, Mon Nov 10 21:50:36 2003 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 12 | Line 15 | SimSetup::SimSetup(){
15		#include "mpiSimulation.hpp"
16		#endif
17
18	+	// some defines for ensemble and Forcefield  cases
19	+
20	+	#define NVE_ENS        0
21	+	#define NVT_ENS        1
22	+	#define NPTi_ENS       2
23	+	#define NPTf_ENS       3
24	+	#define NPTxyz_ENS     4
25	+
26	+
27	+	#define FF_DUFF 0
28	+	#define FF_LJ   1
29	+	#define FF_EAM  2
30	+
31	+	using namespace std;
32	+
33		SimSetup::SimSetup(){
34	+
35	+	initSuspend = false;
36	+	isInfoArray = 0;
37	+	nInfo = 1;
38	+
39		stamps = new MakeStamps();
40		globals = new Globals();
41	<
41	>
42	>
43		#ifdef IS_MPI
44	<	strcpy( checkPointMsg, "SimSetup creation successful" );
44	>	strcpy(checkPointMsg, "SimSetup creation successful");
45		MPIcheckPoint();
46		#endif // IS_MPI
47		}
#	Line 27 | Line 51 | void SimSetup::parseFile( char* fileName ){
51		delete globals;
52		}
53
54	<	void SimSetup::parseFile( char* fileName ){
54	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
55	>	info = the_info;
56	>	nInfo = theNinfo;
57	>	isInfoArray = 1;
58	>	initSuspend = true;
59	>	}
60
61	+
62	+	void SimSetup::parseFile(char* fileName){
63		#ifdef IS_MPI
64	<	if( worldRank == 0 ){
64	>	if (worldRank == 0){
65		#endif // is_mpi
66	<
66	>
67		inFileName = fileName;
68	<	set_interface_stamps( stamps, globals );
69	<
68	>	set_interface_stamps(stamps, globals);
69	>
70		#ifdef IS_MPI
71		mpiEventInit();
72		#endif
73
74	<	yacc_BASS( fileName );
74	>	yacc_BASS(fileName);
75
76		#ifdef IS_MPI
77		throwMPIEvent(NULL);
78		}
79	<	else receiveParse();
79	>	else{
80	>	receiveParse();
81	>	}
82		#endif
83
84		}
85
86		#ifdef IS_MPI
87		void SimSetup::receiveParse(void){
88	<
89	<	set_interface_stamps( stamps, globals );
90	<	mpiEventInit();
91	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
88	>	set_interface_stamps(stamps, globals);
89	>	mpiEventInit();
90	>	MPIcheckPoint();
91	>	mpiEventLoop();
92		}
93
94		#endif // is_mpi
95
96	<	void SimSetup::createSim( void ){
96	>	void SimSetup::createSim(void){
97
98	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
98	>	// gather all of the information from the Bass file
99
100	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
100	>	gatherInfo();
101
102	<	// 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();
102	>	// creation of complex system objects
103
104	<	// 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 );
104	>	sysObjectsCreation();
105
106	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
106	>	// check on the post processing info
107
108	+	finalInfoCheck();
109
110	<	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	<	}
110	>	// initialize the system coordinates
111
112	<	#ifdef IS_MPI
113	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
112	>	if ( !initSuspend ){
113	>	initSystemCoords();
114
115	<
115	>	if( !(globals->getUseInitTime()) )
116	>	info[0].currentTime = 0.0;
117	>	}
118
119	<	// 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];
119	>	// make the output filenames
120
121	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
121	>	makeOutNames();
122
123	<	tot_nmol = 0;
120	<	for( i=0; i<n_components; i++ ){
123	>	// make the integrator
124
125	<	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	<	}
125	>	makeIntegrator();
126
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	–
127		#ifdef IS_MPI
128	<	strcpy( checkPointMsg, "Have the number of components" );
129	<	MPIcheckPoint();
163	<	#endif // is_mpi
128	>	mpiSim->mpiRefresh();
129	>	#endif
130
131	<	// make an array of molecule stamps that match the components used.
166	<	// also extract the used stamps out into a separate linked list
131	>	// initialize the Fortran
132
133	<	simnfo->nComponents = n_components;
134	<	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++ ){
133	>	initFortran();
134	>	}
135
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
136
137	<	comp_stamps[i] = headStamp->match( id );
138	<	if( comp_stamps[i] == NULL ){
139	<
140	<	// extract the component from the list;
141	<
142	<	currentStamp = the_stamps->extractMolStamp( id );
143	<	if( currentStamp == NULL ){
144	<	sprintf( painCave.errMsg,
145	<	"SimSetup error: Component \"%s\" was not found in the "
146	<	"list of declared molecules\n",
147	<	id );
194	<	painCave.isFatal = 1;
195	<	simError();
196	<	}
197	<
198	<	headStamp->add( currentStamp );
199	<	comp_stamps[i] = headStamp->match( id );
200	<	}
201	<	}
137	>	void SimSetup::makeMolecules(void){
138	>	int k;
139	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140	>	molInit molInfo;
141	>	DirectionalAtom* dAtom;
142	>	LinkedAssign* extras;
143	>	LinkedAssign* current_extra;
144	>	AtomStamp* currentAtom;
145	>	BondStamp* currentBond;
146	>	BendStamp* currentBend;
147	>	TorsionStamp* currentTorsion;
148
149	<	#ifdef IS_MPI
150	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
151	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
149	>	bond_pair* theBonds;
150	>	bend_set* theBends;
151	>	torsion_set* theTorsions;
152
153
154	+	//init the forceField paramters
155
156	<	// caclulate the number of atoms, bonds, bends and torsions
156	>	the_ff->readParams();
157
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	–	}
158
159	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
159	>	// init the atoms
160
161	<	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;
161	>	double ux, uy, uz, u, uSqr;
162
163	<
164	<	#ifdef IS_MPI
163	>	for (k = 0; k < nInfo; k++){
164	>	the_ff->setSimInfo(&(info[k]));
165
166	<	// divide the molecules among processors here.
167	<
168	<	mpiSim = new mpiSimulation( simnfo );
169	<
241	<
166	>	atomOffset = 0;
167	>	excludeOffset = 0;
168	>	for (i = 0; i < info[k].n_mol; i++){
169	>	stampID = info[k].molecules[i].getStampID();
170
171	<	globalIndex = mpiSim->divideLabor();
171	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
172	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
173	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
174	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
175	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
176
177	+	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
178	+	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
179	+	molInfo.myBonds = new Bond * [molInfo.nBonds];
180	+	molInfo.myBends = new Bend * [molInfo.nBends];
181	+	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
182
183	+	theBonds = new bond_pair[molInfo.nBonds];
184	+	theBends = new bend_set[molInfo.nBends];
185	+	theTorsions = new torsion_set[molInfo.nTorsions];
186
187	<	// 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++ ){
187	>	// make the Atoms
188
189	<	for( j=0; j<components_nmol[i]; j++ ){
190	<
191	<	if( mpiSim->getMyMolStart() <= allMol &&
192	<	allMol <= mpiSim->getMyMolEnd() ){
193	<
194	<	local_atoms +=    comp_stamps[i]->getNAtoms();
195	<	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	<
189	>	for (j = 0; j < molInfo.nAtoms; j++){
190	>	currentAtom = comp_stamps[stampID]->getAtom(j);
191	>	if (currentAtom->haveOrientation()){
192	>	dAtom = new DirectionalAtom((j + atomOffset),
193	>	info[k].getConfiguration());
194	>	info[k].n_oriented++;
195	>	molInfo.myAtoms[j] = dAtom;
196
197	<	simnfo->n_atoms = mpiSim->getMyNlocal();
198	<
199	<	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	<	}
197	>	ux = currentAtom->getOrntX();
198	>	uy = currentAtom->getOrntY();
199	>	uz = currentAtom->getOrntZ();
200
201	<	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;
201	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
202
203	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
204	<	MPIcheckPoint();
205	<
206	<
203	>	u = sqrt(uSqr);
204	>	ux = ux / u;
205	>	uy = uy / u;
206	>	uz = uz / u;
207	>
208	>	dAtom->setSUx(ux);
209	>	dAtom->setSUy(uy);
210	>	dAtom->setSUz(uz);
211	>	}
212	>	else{
213	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
214	>	info[k].getConfiguration());
215	>	}
216	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
217	>
218	>	#ifdef IS_MPI
219	>
220	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
221	>
222		#endif // is_mpi
223	<
223	>	}
224
225	<	// create the atom and short range interaction arrays
225	>	// make the bonds
226	>	for (j = 0; j < molInfo.nBonds; j++){
227	>	currentBond = comp_stamps[stampID]->getBond(j);
228	>	theBonds[j].a = currentBond->getA() + atomOffset;
229	>	theBonds[j].b = currentBond->getB() + atomOffset;
230
231	<	Atom::createArrays(simnfo->n_atoms);
232	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
231	>	exI = theBonds[j].a;
232	>	exJ = theBonds[j].b;
233
234	+	// exclude_I must always be the smaller of the pair
235	+	if (exI > exJ){
236	+	tempEx = exI;
237	+	exI = exJ;
238	+	exJ = tempEx;
239	+	}
240	+	#ifdef IS_MPI
241	+	tempEx = exI;
242	+	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
243	+	tempEx = exJ;
244	+	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
245
246	<	if( simnfo->n_SRI ){
247	<	Exclude::createArray(simnfo->n_SRI);
311	<	the_excludes = new Exclude*[simnfo->n_SRI];
312	<	simnfo->globalExcludes = new int;
313	<	simnfo->n_exclude = tot_SRI;
314	<	}
315	<	else{
316	<
317	<	Exclude::createArray( 1 );
318	<	the_excludes = new Exclude*;
319	<	the_excludes[0] = new Exclude(0);
320	<	the_excludes[0]->setPair( 0,0 );
321	<	simnfo->globalExcludes = new int;
322	<	simnfo->globalExcludes[0] = 0;
323	<	simnfo->n_exclude = 0;
324	<	}
246	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
247	>	#else  // isn't MPI
248
249	<	// set the arrays into the SimInfo object
249	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
250	>	#endif  //is_mpi
251	>	}
252	>	excludeOffset += molInfo.nBonds;
253
254	<	simnfo->atoms = the_atoms;
255	<	simnfo->sr_interactions = the_sris;
256	<	simnfo->nGlobalExcludes = 0;
257	<	simnfo->excludes = the_excludes;
254	>	//make the bends
255	>	for (j = 0; j < molInfo.nBends; j++){
256	>	currentBend = comp_stamps[stampID]->getBend(j);
257	>	theBends[j].a = currentBend->getA() + atomOffset;
258	>	theBends[j].b = currentBend->getB() + atomOffset;
259	>	theBends[j].c = currentBend->getC() + atomOffset;
260
261	+	if (currentBend->haveExtras()){
262	+	extras = currentBend->getExtras();
263	+	current_extra = extras;
264
265	<	// get some of the tricky things that may still be in the globals
265	>	while (current_extra != NULL){
266	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
267	>	switch (current_extra->getType()){
268	>	case 0:
269	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
270	>	theBends[j].isGhost = 1;
271	>	break;
272
273	<
274	<	if( the_globals->haveBox() ){
275	<	simnfo->box_x = the_globals->getBox();
276	<	simnfo->box_y = the_globals->getBox();
277	<	simnfo->box_z = the_globals->getBox();
341	<	}
342	<	else if( the_globals->haveDensity() ){
273	>	case 1:
274	>	theBends[j].ghost = (int) current_extra->getDouble() +
275	>	atomOffset;
276	>	theBends[j].isGhost = 1;
277	>	break;
278
279	<	double vol;
280	<	vol = (double)tot_nmol / the_globals->getDensity();
281	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
282	<	simnfo->box_y = simnfo->box_x;
283	<	simnfo->box_z = simnfo->box_x;
284	<	}
285	<	else{
286	<	if( !the_globals->haveBoxX() ){
287	<	sprintf( painCave.errMsg,
288	<	"SimSetup error, no periodic BoxX size given.\n" );
289	<	painCave.isFatal = 1;
290	<	simError();
291	<	}
292	<	simnfo->box_x = the_globals->getBoxX();
279	>	default:
280	>	sprintf(painCave.errMsg,
281	>	"SimSetup Error: ghostVectorSource was neither a "
282	>	"double nor an int.\n"
283	>	"-->Bend[%d] in %s\n",
284	>	j, comp_stamps[stampID]->getID());
285	>	painCave.isFatal = 1;
286	>	simError();
287	>	}
288	>	}
289	>	else{
290	>	sprintf(painCave.errMsg,
291	>	"SimSetup Error: unhandled bend assignment:\n"
292	>	"    -->%s in Bend[%d] in %s\n",
293	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
294	>	painCave.isFatal = 1;
295	>	simError();
296	>	}
297
298	<	if( !the_globals->haveBoxY() ){
299	<	sprintf( painCave.errMsg,
300	<	"SimSetup error, no periodic BoxY size given.\n" );
362	<	painCave.isFatal = 1;
363	<	simError();
364	<	}
365	<	simnfo->box_y = the_globals->getBoxY();
298	>	current_extra = current_extra->getNext();
299	>	}
300	>	}
301
302	<	if( !the_globals->haveBoxZ() ){
303	<	sprintf( painCave.errMsg,
304	<	"SimSetup error, no periodic BoxZ size given.\n" );
305	<	painCave.isFatal = 1;
306	<	simError();
307	<	}
308	<	simnfo->box_z = the_globals->getBoxZ();
309	<	}
302	>	if (!theBends[j].isGhost){
303	>	exI = theBends[j].a;
304	>	exJ = theBends[j].c;
305	>	}
306	>	else{
307	>	exI = theBends[j].a;
308	>	exJ = theBends[j].b;
309	>	}
310
311	+	// exclude_I must always be the smaller of the pair
312	+	if (exI > exJ){
313	+	tempEx = exI;
314	+	exI = exJ;
315	+	exJ = tempEx;
316	+	}
317		#ifdef IS_MPI
318	<	strcpy( checkPointMsg, "Box size set up" );
319	<	MPIcheckPoint();
320	<	#endif // is_mpi
318	>	tempEx = exI;
319	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
320	>	tempEx = exJ;
321	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
322
323	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
324	+	#else  // isn't MPI
325	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
326	+	#endif  //is_mpi
327	+	}
328	+	excludeOffset += molInfo.nBends;
329
330	<	// initialize the arrays
330	>	for (j = 0; j < molInfo.nTorsions; j++){
331	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
332	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
333	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
334	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
335	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
336
337	<	the_ff->setSimInfo( simnfo );
337	>	exI = theTorsions[j].a;
338	>	exJ = theTorsions[j].d;
339
340	<	makeAtoms();
341	<	simnfo->identArray = new int[simnfo->n_atoms];
342	<	for(i=0; i<simnfo->n_atoms; i++){
343	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
344	<	}
345	<
346	<	if( tot_bonds ){
347	<	makeBonds();
348	<	}
340	>	// exclude_I must always be the smaller of the pair
341	>	if (exI > exJ){
342	>	tempEx = exI;
343	>	exI = exJ;
344	>	exJ = tempEx;
345	>	}
346	>	#ifdef IS_MPI
347	>	tempEx = exI;
348	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
349	>	tempEx = exJ;
350	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
351	>
352	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
353	>	#else  // isn't MPI
354	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
355	>	#endif  //is_mpi
356	>	}
357	>	excludeOffset += molInfo.nTorsions;
358
396	–	if( tot_bends ){
397	–	makeBends();
398	–	}
359
360	<	if( tot_torsions ){
401	<	makeTorsions();
402	<	}
360	>	// send the arrays off to the forceField for init.
361
362	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
363	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
364	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
365	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
366	+	theTorsions);
367
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	–	}
368
369	<	if( !the_globals->haveEST() ){
370	<	sprintf( painCave.errMsg,
371	<	"SimSetup Warning: using default value of 0.05 * the "
372	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
373	<	);
374	<	painCave.isFatal = 0;
375	<	simError();
431	<	simnfo->est = 0.05 * simnfo->ecr;
432	<	} else {
433	<	simnfo->est        = the_globals->getEST();
369	>	info[k].molecules[i].initialize(molInfo);
370	>
371	>
372	>	atomOffset += molInfo.nAtoms;
373	>	delete[] theBonds;
374	>	delete[] theBends;
375	>	delete[] theTorsions;
376		}
377	<
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	<	}
377	>	}
378
379		#ifdef IS_MPI
380	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
380	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
381		MPIcheckPoint();
382		#endif // is_mpi
383
384	<	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
384	>	// clean up the forcefield
385
386	<	delete fileInit;
387	<	}
388	<	else{
386	>	the_ff->calcRcut();
387	>	the_ff->cleanMe();
388	>	}
389
390	<	#ifdef IS_MPI
390	>	void SimSetup::initFromBass(void){
391	>	int i, j, k;
392	>	int n_cells;
393	>	double cellx, celly, cellz;
394	>	double temp1, temp2, temp3;
395	>	int n_per_extra;
396	>	int n_extra;
397	>	int have_extra, done;
398
399	<	// no init from bass
400	<
401	<	sprintf( painCave.errMsg,
402	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
506	<	painCave.isFatal;
507	<	simError();
508	<
509	<	#else
399	>	double vel[3];
400	>	vel[0] = 0.0;
401	>	vel[1] = 0.0;
402	>	vel[2] = 0.0;
403
404	<	initFromBass();
404	>	temp1 = (double) tot_nmol / 4.0;
405	>	temp2 = pow(temp1, (1.0 / 3.0));
406	>	temp3 = ceil(temp2);
407
408	+	have_extra = 0;
409	+	if (temp2 < temp3){
410	+	// we have a non-complete lattice
411	+	have_extra = 1;
412
413	<	#endif
414	<	}
413	>	n_cells = (int) temp3 - 1;
414	>	cellx = info[0].boxL[0] / temp3;
415	>	celly = info[0].boxL[1] / temp3;
416	>	cellz = info[0].boxL[2] / temp3;
417	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
418	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
419	>	n_per_extra = (int) ceil(temp1);
420
421	<	#ifdef IS_MPI
422	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
423	<	MPIcheckPoint();
424	<	#endif // is_mpi
421	>	if (n_per_extra > 4){
422	>	sprintf(painCave.errMsg,
423	>	"SimSetup error. There has been an error in constructing"
424	>	" the non-complete lattice.\n");
425	>	painCave.isFatal = 1;
426	>	simError();
427	>	}
428	>	}
429	>	else{
430	>	n_cells = (int) temp3;
431	>	cellx = info[0].boxL[0] / temp3;
432	>	celly = info[0].boxL[1] / temp3;
433	>	cellz = info[0].boxL[2] / temp3;
434	>	}
435
436	+	current_mol = 0;
437	+	current_comp_mol = 0;
438	+	current_comp = 0;
439	+	current_atom_ndx = 0;
440
441	<
442	<
443	<
441	>	for (i = 0; i < n_cells ; i++){
442	>	for (j = 0; j < n_cells; j++){
443	>	for (k = 0; k < n_cells; k++){
444	>	makeElement(i * cellx, j * celly, k * cellz);
445
446	<
447	<	#ifdef IS_MPI
448	<	if( worldRank == 0 ){
449	<	#endif // is_mpi
450	<
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" );
446	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
447	>
448	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
449	>
450	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
451		}
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	–	}
452		}
453	<
454	<	// make the sample and status out names
455	<
456	<	strcpy( simnfo->sampleName, inFileName );
457	<	char* endTest;
458	<	int nameLength = strlen( simnfo->sampleName );
459	<	endTest = &(simnfo->sampleName[nameLength - 5]);
460	<	if( !strcmp( endTest, ".bass" ) ){
461	<	strcpy( endTest, ".dump" );
462	<	}
463	<	else if( !strcmp( endTest, ".BASS" ) ){
464	<	strcpy( endTest, ".dump" );
465	<	}
466	<	else{
467	<	endTest = &(simnfo->sampleName[nameLength - 4]);
468	<	if( !strcmp( endTest, ".bss" ) ){
469	<	strcpy( endTest, ".dump" );
470	<	}
471	<	else if( !strcmp( endTest, ".mdl" ) ){
472	<	strcpy( endTest, ".dump" );
473	<	}
474	<	else{
475	<	strcat( simnfo->sampleName, ".dump" );
476	<	}
477	<	}
478	<
479	<	strcpy( simnfo->statusName, inFileName );
480	<	nameLength = strlen( simnfo->statusName );
481	<	endTest = &(simnfo->statusName[nameLength - 5]);
482	<	if( !strcmp( endTest, ".bass" ) ){
483	<	strcpy( endTest, ".stat" );
484	<	}
485	<	else if( !strcmp( endTest, ".BASS" ) ){
486	<	strcpy( endTest, ".stat" );
487	<	}
488	<	else{
489	<	endTest = &(simnfo->statusName[nameLength - 4]);
490	<	if( !strcmp( endTest, ".bss" ) ){
491	<	strcpy( endTest, ".stat" );
492	<	}
599	<	else if( !strcmp( endTest, ".mdl" ) ){
600	<	strcpy( endTest, ".stat" );
601	<	}
602	<	else{
603	<	strcat( simnfo->statusName, ".stat" );
453	>	}
454	>
455	>	if (have_extra){
456	>	done = 0;
457	>
458	>	int start_ndx;
459	>	for (i = 0; i < (n_cells + 1) && !done; i++){
460	>	for (j = 0; j < (n_cells + 1) && !done; j++){
461	>	if (i < n_cells){
462	>	if (j < n_cells){
463	>	start_ndx = n_cells;
464	>	}
465	>	else
466	>	start_ndx = 0;
467	>	}
468	>	else
469	>	start_ndx = 0;
470	>
471	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
472	>	makeElement(i * cellx, j * celly, k * cellz);
473	>	done = (current_mol >= tot_nmol);
474	>
475	>	if (!done && n_per_extra > 1){
476	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
477	>	k * cellz);
478	>	done = (current_mol >= tot_nmol);
479	>	}
480	>
481	>	if (!done && n_per_extra > 2){
482	>	makeElement(i * cellx, j * celly + 0.5 * celly,
483	>	k * cellz + 0.5 * cellz);
484	>	done = (current_mol >= tot_nmol);
485	>	}
486	>
487	>	if (!done && n_per_extra > 3){
488	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
489	>	k * cellz + 0.5 * cellz);
490	>	done = (current_mol >= tot_nmol);
491	>	}
492	>	}
493		}
494		}
606	–
607	–	#ifdef IS_MPI
495		}
496	<	#endif // is_mpi
497	<
498	<	// 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;
496	>
497	>	for (i = 0; i < info[0].n_atoms; i++){
498	>	info[0].atoms[i]->setVel(vel);
499		}
500	<	else{
619	<	simnfo->sampleTime = the_globals->getRunTime();
620	<	simnfo->statusTime = simnfo->sampleTime;
621	<	simnfo->thermalTime = simnfo->sampleTime;
622	<	}
500	>	}
501
502	<	if( the_globals->haveStatusTime() ){
503	<	simnfo->statusTime = the_globals->getStatusTime();
502	>	void SimSetup::makeElement(double x, double y, double z){
503	>	int k;
504	>	AtomStamp* current_atom;
505	>	DirectionalAtom* dAtom;
506	>	double rotMat[3][3];
507	>	double pos[3];
508	>
509	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
510	>	current_atom = comp_stamps[current_comp]->getAtom(k);
511	>	if (!current_atom->havePosition()){
512	>	sprintf(painCave.errMsg,
513	>	"SimSetup:initFromBass error.\n"
514	>	"\tComponent %s, atom %s does not have a position specified.\n"
515	>	"\tThe initialization routine is unable to give a start"
516	>	" position.\n",
517	>	comp_stamps[current_comp]->getID(), current_atom->getType());
518	>	painCave.isFatal = 1;
519	>	simError();
520	>	}
521	>
522	>	pos[0] = x + current_atom->getPosX();
523	>	pos[1] = y + current_atom->getPosY();
524	>	pos[2] = z + current_atom->getPosZ();
525	>
526	>	info[0].atoms[current_atom_ndx]->setPos(pos);
527	>
528	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
529	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
530	>
531	>	rotMat[0][0] = 1.0;
532	>	rotMat[0][1] = 0.0;
533	>	rotMat[0][2] = 0.0;
534	>
535	>	rotMat[1][0] = 0.0;
536	>	rotMat[1][1] = 1.0;
537	>	rotMat[1][2] = 0.0;
538	>
539	>	rotMat[2][0] = 0.0;
540	>	rotMat[2][1] = 0.0;
541	>	rotMat[2][2] = 1.0;
542	>
543	>	dAtom->setA(rotMat);
544	>	}
545	>
546	>	current_atom_ndx++;
547		}
548
549	<	if( the_globals->haveThermalTime() ){
550	<	simnfo->thermalTime = the_globals->getThermalTime();
549	>	current_mol++;
550	>	current_comp_mol++;
551	>
552	>	if (current_comp_mol >= components_nmol[current_comp]){
553	>	current_comp_mol = 0;
554	>	current_comp++;
555		}
556	+	}
557
632	–	// check for the temperature set flag
558
559	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
559	>	void SimSetup::gatherInfo(void){
560	>	int i;
561
562	+	ensembleCase = -1;
563	+	ffCase = -1;
564
565	<	//   // make the longe range forces and the integrator
565	>	// set the easy ones first
566
567	<	//   new AllLong( simnfo );
567	>	for (i = 0; i < nInfo; i++){
568	>	info[i].target_temp = globals->getTargetTemp();
569	>	info[i].dt = globals->getDt();
570	>	info[i].run_time = globals->getRunTime();
571	>	}
572	>	n_components = globals->getNComponents();
573
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 );
574
575	+	// get the forceField
576
577	+	strcpy(force_field, globals->getForceField());
578
579	<	// initialize the Fortran
580	<
650	<	simnfo->refreshSim();
651	<
652	<	if( !strcmp( simnfo->mixingRule, "standard") ){
653	<	the_ff->initForceField( LB_MIXING_RULE );
579	>	if (!strcasecmp(force_field, "DUFF")){
580	>	ffCase = FF_DUFF;
581		}
582	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
583	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
582	>	else if (!strcasecmp(force_field, "LJ")){
583	>	ffCase = FF_LJ;
584		}
585	+	else if (!strcasecmp(force_field, "EAM")){
586	+	ffCase = FF_EAM;
587	+	}
588		else{
589	<	sprintf( painCave.errMsg,
590	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
591	<	simnfo->mixingRule );
592	<	painCave.isFatal = 1;
663	<	simError();
589	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
590	>	force_field);
591	>	painCave.isFatal = 1;
592	>	simError();
593		}
594
595	+	// get the ensemble
596
597	<	#ifdef IS_MPI
668	<	strcpy( checkPointMsg,
669	<	"Successfully intialized the mixingRule for Fortran." );
670	<	MPIcheckPoint();
671	<	#endif // is_mpi
672	<	}
597	>	strcpy(ensemble, globals->getEnsemble());
598
599	+	if (!strcasecmp(ensemble, "NVE")){
600	+	ensembleCase = NVE_ENS;
601	+	}
602	+	else if (!strcasecmp(ensemble, "NVT")){
603	+	ensembleCase = NVT_ENS;
604	+	}
605	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
606	+	ensembleCase = NPTi_ENS;
607	+	}
608	+	else if (!strcasecmp(ensemble, "NPTf")){
609	+	ensembleCase = NPTf_ENS;
610	+	}
611	+	else if (!strcasecmp(ensemble, "NPTxyz")){
612	+	ensembleCase = NPTxyz_ENS;
613	+	}
614	+	else{
615	+	sprintf(painCave.errMsg,
616	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
617	+	"reverting to NVE for this simulation.\n",
618	+	ensemble);
619	+	painCave.isFatal = 0;
620	+	simError();
621	+	strcpy(ensemble, "NVE");
622	+	ensembleCase = NVE_ENS;
623	+	}
624
625	<	void SimSetup::makeMolecules( void ){
625	>	for (i = 0; i < nInfo; i++){
626	>	strcpy(info[i].ensemble, ensemble);
627
628	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
678	<	molInit info;
679	<	DirectionalAtom* dAtom;
680	<	LinkedAssign* extras;
681	<	LinkedAssign* current_extra;
682	<	AtomStamp* currentAtom;
683	<	BondStamp* currentBond;
684	<	BendStamp* currentBend;
685	<	TorsionStamp* currentTorsion;
686	<
687	<	//init the forceField paramters
628	>	// get the mixing rule
629
630	<	the_ff->readParams();
630	>	strcpy(info[i].mixingRule, globals->getMixingRule());
631	>	info[i].usePBC = globals->getPBC();
632	>	}
633
634	<
692	<	// init the molecules
634	>	// get the components and calculate the tot_nMol and indvidual n_mol
635
636	<	atomOffset = 0;
637	<	excludeOffset = 0;
696	<	for(i=0; i<simnfo->n_mol; i++){
697	<
698	<	stampID = the_molecules[i].getStampID();
636	>	the_components = globals->getComponents();
637	>	components_nmol = new int[n_components];
638
700	–	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
701	–	info.nBonds    = comp_stamps[stampID]->getNBonds();
702	–	info.nBends    = comp_stamps[stampID]->getNBends();
703	–	info.nTorsions = comp_stamps[stampID]->getNTorsions();
704	–	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
639
640	<	info.myAtoms = &the_atoms[atomOffset];
641	<	info.myExcludes = &the_excludes[excludeOffset];
642	<	info.myBonds = new Bond*[info.nBonds];
709	<	info.myBends = new Bend*[info.nBends];
710	<	info.myTorsions = new Torsions*[info.nTorsions];
640	>	if (!globals->haveNMol()){
641	>	// we don't have the total number of molecules, so we assume it is
642	>	// given in each component
643
644	<	theBonds = new bond_pair[info.nBonds];
645	<	theBends = new bend_set[info.nBends];
646	<	theTorsions = new torsion_set[info.nTorsions];
647	<
648	<	// make the Atoms
649	<
650	<	for(j=0; j<info.nAtoms; j++){
651	<
652	<	currentAtom = theComponents[stampID]->getAtom( j );
721	<	if( currentAtom->haveOrientation() ){
722	<
723	<	dAtom = new DirectionalAtom(j + atomOffset);
724	<	simnfo->n_oriented++;
725	<	info.myAtoms[j] = dAtom;
726	<
727	<	ux = currentAtom->getOrntX();
728	<	uy = currentAtom->getOrntY();
729	<	uz = currentAtom->getOrntZ();
730	<
731	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
732	<
733	<	u = sqrt( uSqr );
734	<	ux = ux / u;
735	<	uy = uy / u;
736	<	uz = uz / u;
737	<
738	<	dAtom->setSUx( ux );
739	<	dAtom->setSUy( uy );
740	<	dAtom->setSUz( uz );
644	>	tot_nmol = 0;
645	>	for (i = 0; i < n_components; i++){
646	>	if (!the_components[i]->haveNMol()){
647	>	// we have a problem
648	>	sprintf(painCave.errMsg,
649	>	"SimSetup Error. No global NMol or component NMol"
650	>	" given. Cannot calculate the number of atoms.\n");
651	>	painCave.isFatal = 1;
652	>	simError();
653		}
742	–	else{
743	–	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
744	–	}
745	–	info.myAtoms[j]->setType( currentAtom->getType() );
746	–
747	–	#ifdef IS_MPI
748	–
749	–	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
750	–
751	–	#endif // is_mpi
752	–	}
753	–
754	–	// make the bonds
755	–	for(j=0; j<info.nBonds; j++){
756	–
757	–	currentBond = comp_stamps[stampID]->getBond( j );
758	–	theBonds[j].a = currentBond->getA() + atomOffset;
759	–	theBonds[j].b = currentBond->getB() + atomOffset;
654
655	<	exI = theBonds[i].a;
656	<	exJ = theBonds[i].b;
655	>	tot_nmol += the_components[i]->getNMol();
656	>	components_nmol[i] = the_components[i]->getNMol();
657	>	}
658	>	}
659	>	else{
660	>	sprintf(painCave.errMsg,
661	>	"SimSetup error.\n"
662	>	"\tSorry, the ability to specify total"
663	>	" nMols and then give molfractions in the components\n"
664	>	"\tis not currently supported."
665	>	" Please give nMol in the components.\n");
666	>	painCave.isFatal = 1;
667	>	simError();
668	>	}
669
670	<	// exclude_I must always be the smaller of the pair
671	<	if( exI > exJ ){
672	<	tempEx = exI;
673	<	exI = exJ;
674	<	exJ = tempEx;
675	<	}
676	<	#ifdef IS_MPI
771	<	tempEx = exI;
772	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
773	<	tempEx = exJ;
774	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
775	<
776	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
777	<	#else  // isn't MPI
778	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
779	<	#endif  //is_mpi
670	>	// set the status, sample, and thermal kick times
671	>
672	>	for (i = 0; i < nInfo; i++){
673	>	if (globals->haveSampleTime()){
674	>	info[i].sampleTime = globals->getSampleTime();
675	>	info[i].statusTime = info[i].sampleTime;
676	>	info[i].thermalTime = info[i].sampleTime;
677		}
678	<	excludeOffset += info.nBonds;
678	>	else{
679	>	info[i].sampleTime = globals->getRunTime();
680	>	info[i].statusTime = info[i].sampleTime;
681	>	info[i].thermalTime = info[i].sampleTime;
682	>	}
683
684	<	//make the bends
685	<	for(j=0; j<info.nBends; j++){
785	<
786	<	currentBend = comp_stamps[stampID]->getBend( j );
787	<	theBends[j].a = currentBend->getA() + atomOffset;
788	<	theBends[j].b = currentBend->getB() + atomOffset;
789	<	theBends[j].c = currentBend->getC() + atomOffset;
790	<
791	<	if( currentBend->haveExtras() ){
792	<
793	<	extras = current_bend->getExtras();
794	<	current_extra = extras;
795	<
796	<	while( current_extra != NULL ){
797	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
798	<
799	<	switch( current_extra->getType() ){
800	<
801	<	case 0:
802	<	theBends[j].ghost =
803	<	current_extra->getInt() + atomOffset;
804	<	theBends[j].isGhost = 1;
805	<	break;
806	<
807	<	case 1:
808	<	theBends[j].ghost =
809	<	(int)current_extra->getDouble() + atomOffset;
810	<	theBends[j].isGhost = 1;
811	<	break;
812	<
813	<	default:
814	<	sprintf( painCave.errMsg,
815	<	"SimSetup Error: ghostVectorSource was neiter a "
816	<	"double nor an int.\n"
817	<	"-->Bend[%d] in %s\n",
818	<	j, comp_stamps[stampID]->getID() );
819	<	painCave.isFatal = 1;
820	<	simError();
821	<	}
822	<	}
823	<
824	<	else{
825	<
826	<	sprintf( painCave.errMsg,
827	<	"SimSetup Error: unhandled bend assignment:\n"
828	<	"    -->%s in Bend[%d] in %s\n",
829	<	current_extra->getlhs(),
830	<	j, comp_stamps[stampID]->getID() );
831	<	painCave.isFatal = 1;
832	<	simError();
833	<	}
834	<
835	<	current_extra = current_extra->getNext();
836	<	}
837	<	}
838	<
839	<	if( !theBends[j].isGhost ){
840	<
841	<	exI = theBends[j].a;
842	<	exJ = theBends[j].c;
843	<	}
844	<	else{
845	<
846	<	exI = theBends[j].a;
847	<	exJ = theBends[j].b;
848	<	}
849	<
850	<	// exclude_I must always be the smaller of the pair
851	<	if( exI > exJ ){
852	<	tempEx = exI;
853	<	exI = exJ;
854	<	exJ = tempEx;
855	<	}
856	<	#ifdef IS_MPI
857	<	tempEx = exI;
858	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
859	<	tempEx = exJ;
860	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
861	<
862	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
863	<	#else  // isn't MPI
864	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
865	<	#endif  //is_mpi
684	>	if (globals->haveStatusTime()){
685	>	info[i].statusTime = globals->getStatusTime();
686		}
867	–	excludeOffset += info.nBends;
687
688	<	for(j=0; j<info.nTorsions; j++){
689	<
690	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
872	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
873	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
874	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
875	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
876	<
877	<	exI = theTorsions[j].a;
878	<	exJ = theTorsions[j].d;
688	>	if (globals->haveThermalTime()){
689	>	info[i].thermalTime = globals->getThermalTime();
690	>	}
691
692	<	// exclude_I must always be the smaller of the pair
693	<	if( exI > exJ ){
694	<	tempEx = exI;
695	<	exI = exJ;
884	<	exJ = tempEx;
885	<	}
886	<	#ifdef IS_MPI
887	<	tempEx = exI;
888	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
889	<	tempEx = exJ;
890	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
891	<
892	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
893	<	#else  // isn't MPI
894	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
895	<	#endif  //is_mpi
692	>	info[i].resetIntegrator = 0;
693	>	if( globals->haveResetTime() ){
694	>	info[i].resetTime = globals->getResetTime();
695	>	info[i].resetIntegrator = 1;
696		}
897	–	excludeOffset += info.nTorsions;
697
698	+	// check for the temperature set flag
699
700	+	if (globals->haveTempSet())
701	+	info[i].setTemp = globals->getTempSet();
702
703	+	// check for the extended State init
704
705	+	info[i].useInitXSstate = globals->getUseInitXSstate();
706	+	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
707	+
708	+	}
709	+
710	+	//setup seed for random number generator
711	+	int seedValue;
712
713	+	if (globals->haveSeed()){
714	+	seedValue = globals->getSeed();
715
716	+	if(seedValue / 1E9 == 0){
717	+	sprintf(painCave.errMsg,
718	+	"Seed for sprng library should contain at least 9 digits\n"
719	+	"OOPSE will generate a seed for user\n");
720	+	painCave.isFatal = 0;
721	+	simError();
722
723	<
724	<	void SimSetup::makeAtoms( void ){
725	<
726	<	int i, j, k, index;
727	<	double ux, uy, uz, uSqr, u;
728	<	AtomStamp* current_atom;
911	<
912	<	DirectionalAtom* dAtom;
913	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
914	<
915	<	lMolIndex = 0;
916	<	molIndex = 0;
917	<	index = 0;
918	<	for( i=0; i<n_components; i++ ){
919	<
920	<	for( j=0; j<components_nmol[i]; j++ ){
921	<
922	<	#ifdef IS_MPI
923	<	if( mpiSim->getMyMolStart() <= molIndex &&
924	<	molIndex <= mpiSim->getMyMolEnd() ){
925	<	#endif // is_mpi
926	<
927	<	molStart = index;
928	<	nMemb = comp_stamps[i]->getNAtoms();
929	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
930	<
931	<	current_atom = comp_stamps[i]->getAtom( k );
932	<	if( current_atom->haveOrientation() ){
933	<
934	<	dAtom = new DirectionalAtom(index);
935	<	simnfo->n_oriented++;
936	<	the_atoms[index] = dAtom;
937	<
938	<	ux = current_atom->getOrntX();
939	<	uy = current_atom->getOrntY();
940	<	uz = current_atom->getOrntZ();
941	<
942	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
943	<
944	<	u = sqrt( uSqr );
945	<	ux = ux / u;
946	<	uy = uy / u;
947	<	uz = uz / u;
948	<
949	<	dAtom->setSUx( ux );
950	<	dAtom->setSUy( uy );
951	<	dAtom->setSUz( uz );
952	<	}
953	<	else{
954	<	the_atoms[index] = new GeneralAtom(index);
955	<	}
956	<	the_atoms[index]->setType( current_atom->getType() );
957	<	the_atoms[index]->setIndex( index );
958	<
959	<	// increment the index and repeat;
960	<	index++;
961	<	}
962	<
963	<	molEnd = index -1;
964	<	the_molecules[lMolIndex].setNMembers( nMemb );
965	<	the_molecules[lMolIndex].setStartAtom( molStart );
966	<	the_molecules[lMolIndex].setEndAtom( molEnd );
967	<	the_molecules[lMolIndex].setStampID( i );
968	<	lMolIndex++;
969	<
970	<	#ifdef IS_MPI
723	>	//using seed generated by system instead of invalid seed set by user
724	>	#ifndef IS_MPI
725	>	seedValue = make_sprng_seed();
726	>	#else
727	>	if (worldRank == 0){
728	>	seedValue = make_sprng_seed();
729		}
730	<	#endif //is_mpi
731	<
974	<	molIndex++;
730	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
731	>	#endif
732		}
733	+	}//end of if branch of globals->haveSeed()
734	+	else{
735	+
736	+	#ifndef IS_MPI
737	+	seedValue = make_sprng_seed();
738	+	#else
739	+	if (worldRank == 0){
740	+	seedValue = make_sprng_seed();
741	+	}
742	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
743	+	#endif
744	+	}//end of globals->haveSeed()
745	+
746	+	for (int i = 0; i < nInfo; i++){
747	+	info[i].setSeed(seedValue);
748		}
749
750		#ifdef IS_MPI
751	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
752	<
753	<	delete[] globalIndex;
982	<
983	<	mpiSim->mpiRefresh();
984	<	#endif //IS_MPI
985	<
986	<	the_ff->initializeAtoms();
751	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
752	>	MPIcheckPoint();
753	>	#endif // is_mpi
754		}
755
989	–	void SimSetup::makeBonds( void ){
756
757	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
758	<	bond_pair* the_bonds;
759	<	BondStamp* current_bond;
757	>	void SimSetup::finalInfoCheck(void){
758	>	int index;
759	>	int usesDipoles;
760	>	int i;
761
762	<	the_bonds = new bond_pair[tot_bonds];
763	<	index = 0;
997	<	offset = 0;
998	<	molIndex = 0;
762	>	for (i = 0; i < nInfo; i++){
763	>	// check electrostatic parameters
764
765	<	for( i=0; i<n_components; i++ ){
765	>	index = 0;
766	>	usesDipoles = 0;
767	>	while ((index < info[i].n_atoms) && !usesDipoles){
768	>	usesDipoles = (info[i].atoms[index])->hasDipole();
769	>	index++;
770	>	}
771
1002	–	for( j=0; j<components_nmol[i]; j++ ){
1003	–
772		#ifdef IS_MPI
773	<	if( mpiSim->getMyMolStart() <= molIndex &&
774	<	molIndex <= mpiSim->getMyMolEnd() ){
775	<	#endif // is_mpi
1008	<
1009	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
1010	<
1011	<	current_bond = comp_stamps[i]->getBond( k );
1012	<	the_bonds[index].a = current_bond->getA() + offset;
1013	<	the_bonds[index].b = current_bond->getB() + offset;
773	>	int myUse = usesDipoles;
774	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
775	>	#endif //is_mpi
776
777	<	exI = the_bonds[index].a;
1016	<	exJ = the_bonds[index].b;
777	>	double theEcr, theEst;
778
779	<	// exclude_I must always be the smaller of the pair
780	<	if( exI > exJ ){
1020	<	tempEx = exI;
1021	<	exI = exJ;
1022	<	exJ = tempEx;
1023	<	}
779	>	if (globals->getUseRF()){
780	>	info[i].useReactionField = 1;
781
782	<
783	<	#ifdef IS_MPI
782	>	if (!globals->haveECR()){
783	>	sprintf(painCave.errMsg,
784	>	"SimSetup Warning: using default value of 15.0 angstroms"
785	>	"box length for the electrostaticCutoffRadius.\n");
786	>	painCave.isFatal = 0;
787	>	simError();
788	>	theEcr = 15.0;
789	>	}
790	>	else{
791	>	theEcr = globals->getECR();
792	>	}
793
794	<	the_excludes[index*2] =
795	<	the_atoms[exI]->getGlobalIndex() + 1;
796	<	the_excludes[index*2 + 1] =
797	<	the_atoms[exJ]->getGlobalIndex() + 1;
794	>	if (!globals->haveEST()){
795	>	sprintf(painCave.errMsg,
796	>	"SimSetup Warning: using default value of 0.05 * the "
797	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
798	>	painCave.isFatal = 0;
799	>	simError();
800	>	theEst = 0.05 * theEcr;
801	>	}
802	>	else{
803	>	theEst = globals->getEST();
804	>	}
805
806	<	#else  // isn't MPI
807	<
808	<	the_excludes[index*2] =     exI + 1;
809	<	the_excludes[index*2 + 1] = exJ + 1;
810	<	// fortran index from 1 (hence the +1 in the indexing)
811	<	#endif  //is_mpi
812	<
813	<	// increment the index and repeat;
814	<	index++;
815	<	}
816	<	offset += comp_stamps[i]->getNAtoms();
806	>	info[i].setDefaultEcr(theEcr, theEst);
807	>
808	>	if (!globals->haveDielectric()){
809	>	sprintf(painCave.errMsg,
810	>	"SimSetup Error: You are trying to use Reaction Field without"
811	>	"setting a dielectric constant!\n");
812	>	painCave.isFatal = 1;
813	>	simError();
814	>	}
815	>	info[i].dielectric = globals->getDielectric();
816	>	}
817	>	else{
818	>	if (usesDipoles){
819	>	if (!globals->haveECR()){
820	>	sprintf(painCave.errMsg,
821	>	"SimSetup Warning: using default value of 15.0 angstroms"
822	>	"box length for the electrostaticCutoffRadius.\n");
823	>	painCave.isFatal = 0;
824	>	simError();
825	>	theEcr = 15.0;
826	>	}
827	>	else{
828	>	theEcr = globals->getECR();
829	>	}
830
831	<	#ifdef IS_MPI
831	>	if (!globals->haveEST()){
832	>	sprintf(painCave.errMsg,
833	>	"SimSetup Warning: using default value of 0.05 * the "
834	>	"electrostaticCutoffRadius for the "
835	>	"electrostaticSkinThickness\n");
836	>	painCave.isFatal = 0;
837	>	simError();
838	>	theEst = 0.05 * theEcr;
839	>	}
840	>	else{
841	>	theEst = globals->getEST();
842	>	}
843	>
844	>	info[i].setDefaultEcr(theEcr, theEst);
845		}
846	+	}
847	+	}
848	+	#ifdef IS_MPI
849	+	strcpy(checkPointMsg, "post processing checks out");
850	+	MPIcheckPoint();
851	+	#endif // is_mpi
852	+	}
853	+
854	+	void SimSetup::initSystemCoords(void){
855	+	int i;
856	+
857	+	char* inName;
858	+
859	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
860	+
861	+	for (i = 0; i < info[0].n_atoms; i++)
862	+	info[0].atoms[i]->setCoords();
863	+
864	+	if (globals->haveInitialConfig()){
865	+	InitializeFromFile* fileInit;
866	+	#ifdef IS_MPI // is_mpi
867	+	if (worldRank == 0){
868		#endif //is_mpi
869	<
870	<	molIndex++;
871	<	}
869	>	inName = globals->getInitialConfig();
870	>	fileInit = new InitializeFromFile(inName);
871	>	#ifdef IS_MPI
872	>	}
873	>	else
874	>	fileInit = new InitializeFromFile(NULL);
875	>	#endif
876	>	fileInit->readInit(info); // default velocities on
877	>
878	>	delete fileInit;
879		}
880	+	else{
881	+
882	+	// no init from bass
883	+
884	+	sprintf(painCave.errMsg,
885	+	"Cannot intialize a simulation without an initial configuration file.\n");
886	+	painCave.isFatal = 1;;
887	+	simError();
888	+
889	+	}
890
891	<	the_ff->initializeBonds( the_bonds );
891	>	#ifdef IS_MPI
892	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
893	>	MPIcheckPoint();
894	>	#endif // is_mpi
895		}
896
1056	–	void SimSetup::makeBends( void ){
897
898	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
899	<	bend_set* the_bends;
1060	<	BendStamp* current_bend;
1061	<	LinkedAssign* extras;
1062	<	LinkedAssign* current_extra;
1063	<
898	>	void SimSetup::makeOutNames(void){
899	>	int k;
900
1065	–	the_bends = new bend_set[tot_bends];
1066	–	index = 0;
1067	–	offset = 0;
1068	–	molIndex = 0;
1069	–	for( i=0; i<n_components; i++ ){
901
902	<	for( j=0; j<components_nmol[i]; j++ ){
1072	<
902	>	for (k = 0; k < nInfo; k++){
903		#ifdef IS_MPI
904	<	if( mpiSim->getMyMolStart() <= molIndex &&
905	<	molIndex <= mpiSim->getMyMolEnd() ){
1076	<	#endif // is_mpi
904	>	if (worldRank == 0){
905	>	#endif // is_mpi
906
907	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
908	<
909	<	current_bend = comp_stamps[i]->getBend( k );
910	<	the_bends[index].a = current_bend->getA() + offset;
911	<	the_bends[index].b = current_bend->getB() + offset;
912	<	the_bends[index].c = current_bend->getC() + offset;
913	<
914	<	if( current_bend->haveExtras() ){
915	<
916	<	extras = current_bend->getExtras();
917	<	current_extra = extras;
918	<
919	<	while( current_extra != NULL ){
920	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
921	<
922	<	switch( current_extra->getType() ){
923	<
924	<	case 0:
925	<	the_bends[index].ghost =
926	<	current_extra->getInt() + offset;
927	<	the_bends[index].isGhost = 1;
928	<	break;
929	<
930	<	case 1:
931	<	the_bends[index].ghost =
932	<	(int)current_extra->getDouble() + offset;
933	<	the_bends[index].isGhost = 1;
1105	<	break;
1106	<
1107	<	default:
1108	<	sprintf( painCave.errMsg,
1109	<	"SimSetup Error: ghostVectorSource was neiter a "
1110	<	"double nor an int.\n"
1111	<	"-->Bend[%d] in %s\n",
1112	<	k, comp_stamps[i]->getID() );
1113	<	painCave.isFatal = 1;
1114	<	simError();
1115	<	}
1116	<	}
1117	<
1118	<	else{
1119	<
1120	<	sprintf( painCave.errMsg,
1121	<	"SimSetup Error: unhandled bend assignment:\n"
1122	<	"    -->%s in Bend[%d] in %s\n",
1123	<	current_extra->getlhs(),
1124	<	k, comp_stamps[i]->getID() );
1125	<	painCave.isFatal = 1;
1126	<	simError();
1127	<	}
1128	<
1129	<	current_extra = current_extra->getNext();
1130	<	}
1131	<	}
1132	<
1133	<	if( !the_bends[index].isGhost ){
1134	<
1135	<	exI = the_bends[index].a;
1136	<	exJ = the_bends[index].c;
1137	<	}
1138	<	else{
1139	<
1140	<	exI = the_bends[index].a;
1141	<	exJ = the_bends[index].b;
1142	<	}
1143	<
1144	<	// exclude_I must always be the smaller of the pair
1145	<	if( exI > exJ ){
1146	<	tempEx = exI;
1147	<	exI = exJ;
1148	<	exJ = tempEx;
1149	<	}
907	>	if (globals->haveFinalConfig()){
908	>	strcpy(info[k].finalName, globals->getFinalConfig());
909	>	}
910	>	else{
911	>	strcpy(info[k].finalName, inFileName);
912	>	char* endTest;
913	>	int nameLength = strlen(info[k].finalName);
914	>	endTest = &(info[k].finalName[nameLength - 5]);
915	>	if (!strcmp(endTest, ".bass")){
916	>	strcpy(endTest, ".eor");
917	>	}
918	>	else if (!strcmp(endTest, ".BASS")){
919	>	strcpy(endTest, ".eor");
920	>	}
921	>	else{
922	>	endTest = &(info[k].finalName[nameLength - 4]);
923	>	if (!strcmp(endTest, ".bss")){
924	>	strcpy(endTest, ".eor");
925	>	}
926	>	else if (!strcmp(endTest, ".mdl")){
927	>	strcpy(endTest, ".eor");
928	>	}
929	>	else{
930	>	strcat(info[k].finalName, ".eor");
931	>	}
932	>	}
933	>	}
934
935	+	// make the sample and status out names
936
937	+	strcpy(info[k].sampleName, inFileName);
938	+	char* endTest;
939	+	int nameLength = strlen(info[k].sampleName);
940	+	endTest = &(info[k].sampleName[nameLength - 5]);
941	+	if (!strcmp(endTest, ".bass")){
942	+	strcpy(endTest, ".dump");
943	+	}
944	+	else if (!strcmp(endTest, ".BASS")){
945	+	strcpy(endTest, ".dump");
946	+	}
947	+	else{
948	+	endTest = &(info[k].sampleName[nameLength - 4]);
949	+	if (!strcmp(endTest, ".bss")){
950	+	strcpy(endTest, ".dump");
951	+	}
952	+	else if (!strcmp(endTest, ".mdl")){
953	+	strcpy(endTest, ".dump");
954	+	}
955	+	else{
956	+	strcat(info[k].sampleName, ".dump");
957	+	}
958	+	}
959	+
960	+	strcpy(info[k].statusName, inFileName);
961	+	nameLength = strlen(info[k].statusName);
962	+	endTest = &(info[k].statusName[nameLength - 5]);
963	+	if (!strcmp(endTest, ".bass")){
964	+	strcpy(endTest, ".stat");
965	+	}
966	+	else if (!strcmp(endTest, ".BASS")){
967	+	strcpy(endTest, ".stat");
968	+	}
969	+	else{
970	+	endTest = &(info[k].statusName[nameLength - 4]);
971	+	if (!strcmp(endTest, ".bss")){
972	+	strcpy(endTest, ".stat");
973	+	}
974	+	else if (!strcmp(endTest, ".mdl")){
975	+	strcpy(endTest, ".stat");
976	+	}
977	+	else{
978	+	strcat(info[k].statusName, ".stat");
979	+	}
980	+	}
981	+
982		#ifdef IS_MPI
983
984	<	the_excludes[(index + tot_bonds)*2] =
985	<	the_atoms[exI]->getGlobalIndex() + 1;
986	<	the_excludes[(index + tot_bonds)*2 + 1] =
987	<	the_atoms[exJ]->getGlobalIndex() + 1;
988	<
989	<	#else  // isn't MPI
990	<
991	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
992	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
993	<	// fortran index from 1 (hence the +1 in the indexing)
994	<	#endif  //is_mpi
995	<
996	<
997	<	// increment the index and repeat;
998	<	index++;
999	<	}
1000	<	offset += comp_stamps[i]->getNAtoms();
1001	<
984	>	}
985	>	#endif // is_mpi
986	>	}
987	>	}
988	>
989	>
990	>	void SimSetup::sysObjectsCreation(void){
991	>	int i, k;
992	>
993	>	// create the forceField
994	>
995	>	createFF();
996	>
997	>	// extract componentList
998	>
999	>	compList();
1000	>
1001	>	// calc the number of atoms, bond, bends, and torsions
1002	>
1003	>	calcSysValues();
1004	>
1005		#ifdef IS_MPI
1006	<	}
1006	>	// divide the molecules among the processors
1007	>
1008	>	mpiMolDivide();
1009		#endif //is_mpi
1010
1011	<	molIndex++;
1011	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1012	>
1013	>	makeSysArrays();
1014	>
1015	>	// make and initialize the molecules (all but atomic coordinates)
1016	>
1017	>	makeMolecules();
1018	>
1019	>	for (k = 0; k < nInfo; k++){
1020	>	info[k].identArray = new int[info[k].n_atoms];
1021	>	for (i = 0; i < info[k].n_atoms; i++){
1022	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1023	>	}
1024	>	}
1025	>	}
1026	>
1027	>
1028	>	void SimSetup::createFF(void){
1029	>	switch (ffCase){
1030	>	case FF_DUFF:
1031	>	the_ff = new DUFF();
1032	>	break;
1033	>
1034	>	case FF_LJ:
1035	>	the_ff = new LJFF();
1036	>	break;
1037	>
1038	>	case FF_EAM:
1039	>	the_ff = new EAM_FF();
1040	>	break;
1041	>
1042	>	default:
1043	>	sprintf(painCave.errMsg,
1044	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1045	>	painCave.isFatal = 1;
1046	>	simError();
1047	>	}
1048	>
1049	>	#ifdef IS_MPI
1050	>	strcpy(checkPointMsg, "ForceField creation successful");
1051	>	MPIcheckPoint();
1052	>	#endif // is_mpi
1053	>	}
1054	>
1055	>
1056	>	void SimSetup::compList(void){
1057	>	int i;
1058	>	char* id;
1059	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1060	>	LinkedMolStamp* currentStamp = NULL;
1061	>	comp_stamps = new MoleculeStamp * [n_components];
1062	>
1063	>	// make an array of molecule stamps that match the components used.
1064	>	// also extract the used stamps out into a separate linked list
1065	>
1066	>	for (i = 0; i < nInfo; i++){
1067	>	info[i].nComponents = n_components;
1068	>	info[i].componentsNmol = components_nmol;
1069	>	info[i].compStamps = comp_stamps;
1070	>	info[i].headStamp = headStamp;
1071	>	}
1072	>
1073	>
1074	>	for (i = 0; i < n_components; i++){
1075	>	id = the_components[i]->getType();
1076	>	comp_stamps[i] = NULL;
1077	>
1078	>	// check to make sure the component isn't already in the list
1079	>
1080	>	comp_stamps[i] = headStamp->match(id);
1081	>	if (comp_stamps[i] == NULL){
1082	>	// extract the component from the list;
1083	>
1084	>	currentStamp = stamps->extractMolStamp(id);
1085	>	if (currentStamp == NULL){
1086	>	sprintf(painCave.errMsg,
1087	>	"SimSetup error: Component \"%s\" was not found in the "
1088	>	"list of declared molecules\n",
1089	>	id);
1090	>	painCave.isFatal = 1;
1091	>	simError();
1092	>	}
1093	>
1094	>	headStamp->add(currentStamp);
1095	>	comp_stamps[i] = headStamp->match(id);
1096		}
1097		}
1098
1099		#ifdef IS_MPI
1100	<	sprintf( checkPointMsg,
1182	<	"Successfully created the bends list.\n" );
1100	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1101		MPIcheckPoint();
1102		#endif // is_mpi
1185	–
1186	–
1187	–	the_ff->initializeBends( the_bends );
1103		}
1104
1105	<	void SimSetup::makeTorsions( void ){
1105	>	void SimSetup::calcSysValues(void){
1106	>	int i;
1107
1108	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1193	<	torsion_set* the_torsions;
1194	<	TorsionStamp* current_torsion;
1108	>	int* molMembershipArray;
1109
1110	<	the_torsions = new torsion_set[tot_torsions];
1111	<	index = 0;
1112	<	offset = 0;
1113	<	molIndex = 0;
1114	<	for( i=0; i<n_components; i++ ){
1110	>	tot_atoms = 0;
1111	>	tot_bonds = 0;
1112	>	tot_bends = 0;
1113	>	tot_torsions = 0;
1114	>	for (i = 0; i < n_components; i++){
1115	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1116	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1117	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1118	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1119	>	}
1120
1121	<	for( j=0; j<components_nmol[i]; j++ ){
1121	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1122	>	molMembershipArray = new int[tot_atoms];
1123
1124	+	for (i = 0; i < nInfo; i++){
1125	+	info[i].n_atoms = tot_atoms;
1126	+	info[i].n_bonds = tot_bonds;
1127	+	info[i].n_bends = tot_bends;
1128	+	info[i].n_torsions = tot_torsions;
1129	+	info[i].n_SRI = tot_SRI;
1130	+	info[i].n_mol = tot_nmol;
1131	+
1132	+	info[i].molMembershipArray = molMembershipArray;
1133	+	}
1134	+	}
1135	+
1136		#ifdef IS_MPI
1205	–	if( mpiSim->getMyMolStart() <= molIndex &&
1206	–	molIndex <= mpiSim->getMyMolEnd() ){
1207	–	#endif // is_mpi
1137
1138	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1138	>	void SimSetup::mpiMolDivide(void){
1139	>	int i, j, k;
1140	>	int localMol, allMol;
1141	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1142
1143	<	current_torsion = comp_stamps[i]->getTorsion( k );
1212	<	the_torsions[index].a = current_torsion->getA() + offset;
1213	<	the_torsions[index].b = current_torsion->getB() + offset;
1214	<	the_torsions[index].c = current_torsion->getC() + offset;
1215	<	the_torsions[index].d = current_torsion->getD() + offset;
1143	>	mpiSim = new mpiSimulation(info);
1144
1145	<	exI = the_torsions[index].a;
1218	<	exJ = the_torsions[index].d;
1145	>	globalIndex = mpiSim->divideLabor();
1146
1147	<
1221	<	// exclude_I must always be the smaller of the pair
1222	<	if( exI > exJ ){
1223	<	tempEx = exI;
1224	<	exI = exJ;
1225	<	exJ = tempEx;
1226	<	}
1147	>	// set up the local variables
1148
1149	+	mol2proc = mpiSim->getMolToProcMap();
1150	+	molCompType = mpiSim->getMolComponentType();
1151
1152	<	#ifdef IS_MPI
1153	<
1154	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
1155	<	the_atoms[exI]->getGlobalIndex() + 1;
1156	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1157	<	the_atoms[exJ]->getGlobalIndex() + 1;
1158	<
1236	<	#else  // isn't MPI
1237	<
1238	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1239	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1240	<	// fortran indexes from 1 (hence the +1 in the indexing)
1241	<	#endif  //is_mpi
1242	<
1152	>	allMol = 0;
1153	>	localMol = 0;
1154	>	local_atoms = 0;
1155	>	local_bonds = 0;
1156	>	local_bends = 0;
1157	>	local_torsions = 0;
1158	>	globalAtomIndex = 0;
1159
1244	–	// increment the index and repeat;
1245	–	index++;
1246	–	}
1247	–	offset += comp_stamps[i]->getNAtoms();
1160
1161	<	#ifdef IS_MPI
1161	>	for (i = 0; i < n_components; i++){
1162	>	for (j = 0; j < components_nmol[i]; j++){
1163	>	if (mol2proc[allMol] == worldRank){
1164	>	local_atoms += comp_stamps[i]->getNAtoms();
1165	>	local_bonds += comp_stamps[i]->getNBonds();
1166	>	local_bends += comp_stamps[i]->getNBends();
1167	>	local_torsions += comp_stamps[i]->getNTorsions();
1168	>	localMol++;
1169	>	}
1170	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1171	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1172	>	globalAtomIndex++;
1173		}
1251	–	#endif //is_mpi
1174
1175	<	molIndex++;
1175	>	allMol++;
1176		}
1177		}
1178	+	local_SRI = local_bonds + local_bends + local_torsions;
1179
1180	<	the_ff->initializeTorsions( the_torsions );
1258	<	}
1180	>	info[0].n_atoms = mpiSim->getMyNlocal();
1181
1182	<	void SimSetup::initFromBass( void ){
1182	>	if (local_atoms != info[0].n_atoms){
1183	>	sprintf(painCave.errMsg,
1184	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1185	>	" localAtom (%d) are not equal.\n",
1186	>	info[0].n_atoms, local_atoms);
1187	>	painCave.isFatal = 1;
1188	>	simError();
1189	>	}
1190
1191	<	int i, j, k;
1192	<	int n_cells;
1193	<	double cellx, celly, cellz;
1194	<	double temp1, temp2, temp3;
1195	<	int n_per_extra;
1267	<	int n_extra;
1268	<	int have_extra, done;
1191	>	info[0].n_bonds = local_bonds;
1192	>	info[0].n_bends = local_bends;
1193	>	info[0].n_torsions = local_torsions;
1194	>	info[0].n_SRI = local_SRI;
1195	>	info[0].n_mol = localMol;
1196
1197	<	temp1 = (double)tot_nmol / 4.0;
1198	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1199	<	temp3 = ceil( temp2 );
1197	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1198	>	MPIcheckPoint();
1199	>	}
1200
1201	<	have_extra =0;
1275	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1276	<	have_extra =1;
1201	>	#endif // is_mpi
1202
1278	–	n_cells = (int)temp3 - 1;
1279	–	cellx = simnfo->box_x / temp3;
1280	–	celly = simnfo->box_y / temp3;
1281	–	cellz = simnfo->box_z / temp3;
1282	–	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1283	–	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1284	–	n_per_extra = (int)ceil( temp1 );
1203
1204	<	if( n_per_extra > 4){
1205	<	sprintf( painCave.errMsg,
1206	<	"SimSetup error. There has been an error in constructing"
1207	<	" the non-complete lattice.\n" );
1208	<	painCave.isFatal = 1;
1209	<	simError();
1292	<	}
1293	<	}
1294	<	else{
1295	<	n_cells = (int)temp3;
1296	<	cellx = simnfo->box_x / temp3;
1297	<	celly = simnfo->box_y / temp3;
1298	<	cellz = simnfo->box_z / temp3;
1299	<	}
1204	>	void SimSetup::makeSysArrays(void){
1205	>
1206	>	#ifndef IS_MPI
1207	>	int k, j;
1208	>	#endif // is_mpi
1209	>	int i, l;
1210
1211	<	current_mol = 0;
1212	<	current_comp_mol = 0;
1213	<	current_comp = 0;
1304	<	current_atom_ndx = 0;
1211	>	Atom** the_atoms;
1212	>	Molecule* the_molecules;
1213	>	Exclude** the_excludes;
1214
1306	–	for( i=0; i < n_cells ; i++ ){
1307	–	for( j=0; j < n_cells; j++ ){
1308	–	for( k=0; k < n_cells; k++ ){
1215
1216	<	makeElement( i * cellx,
1217	<	j * celly,
1312	<	k * cellz );
1216	>	for (l = 0; l < nInfo; l++){
1217	>	// create the atom and short range interaction arrays
1218
1219	<	makeElement( i * cellx + 0.5 * cellx,
1220	<	j * celly + 0.5 * celly,
1221	<	k * cellz );
1219	>	the_atoms = new Atom * [info[l].n_atoms];
1220	>	the_molecules = new Molecule[info[l].n_mol];
1221	>	int molIndex;
1222
1223	<	makeElement( i * cellx,
1319	<	j * celly + 0.5 * celly,
1320	<	k * cellz + 0.5 * cellz );
1223	>	// initialize the molecule's stampID's
1224
1225	<	makeElement( i * cellx + 0.5 * cellx,
1226	<	j * celly,
1227	<	k * cellz + 0.5 * cellz );
1225	>	#ifdef IS_MPI
1226	>
1227	>
1228	>	molIndex = 0;
1229	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1230	>	if (mol2proc[i] == worldRank){
1231	>	the_molecules[molIndex].setStampID(molCompType[i]);
1232	>	the_molecules[molIndex].setMyIndex(molIndex);
1233	>	the_molecules[molIndex].setGlobalIndex(i);
1234	>	molIndex++;
1235		}
1236		}
1327	–	}
1237
1238	<	if( have_extra ){
1330	<	done = 0;
1238	>	#else // is_mpi
1239
1240	<	int start_ndx;
1241	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1242	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1240	>	molIndex = 0;
1241	>	globalAtomIndex = 0;
1242	>	for (i = 0; i < n_components; i++){
1243	>	for (j = 0; j < components_nmol[i]; j++){
1244	>	the_molecules[molIndex].setStampID(i);
1245	>	the_molecules[molIndex].setMyIndex(molIndex);
1246	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1247	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1248	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1249	>	globalAtomIndex++;
1250	>	}
1251	>	molIndex++;
1252	>	}
1253	>	}
1254
1336	–	if( i < n_cells ){
1255
1256	<	if( j < n_cells ){
1339	<	start_ndx = n_cells;
1340	<	}
1341	<	else start_ndx = 0;
1342	<	}
1343	<	else start_ndx = 0;
1256	>	#endif // is_mpi
1257
1345	–	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1258
1259	<	makeElement( i * cellx,
1260	<	j * celly,
1261	<	k * cellz );
1262	<	done = ( current_mol >= tot_nmol );
1263	<
1352	<	if( !done && n_per_extra > 1 ){
1353	<	makeElement( i * cellx + 0.5 * cellx,
1354	<	j * celly + 0.5 * celly,
1355	<	k * cellz );
1356	<	done = ( current_mol >= tot_nmol );
1357	<	}
1358	<
1359	<	if( !done && n_per_extra > 2){
1360	<	makeElement( i * cellx,
1361	<	j * celly + 0.5 * celly,
1362	<	k * cellz + 0.5 * cellz );
1363	<	done = ( current_mol >= tot_nmol );
1364	<	}
1365	<
1366	<	if( !done && n_per_extra > 3){
1367	<	makeElement( i * cellx + 0.5 * cellx,
1368	<	j * celly,
1369	<	k * cellz + 0.5 * cellz );
1370	<	done = ( current_mol >= tot_nmol );
1371	<	}
1372	<	}
1259	>	if (info[l].n_SRI){
1260	>	Exclude::createArray(info[l].n_SRI);
1261	>	the_excludes = new Exclude * [info[l].n_SRI];
1262	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1263	>	the_excludes[ex] = new Exclude(ex);
1264		}
1265	+	info[l].globalExcludes = new int;
1266	+	info[l].n_exclude = info[l].n_SRI;
1267		}
1268	<	}
1268	>	else{
1269	>	Exclude::createArray(1);
1270	>	the_excludes = new Exclude * ;
1271	>	the_excludes[0] = new Exclude(0);
1272	>	the_excludes[0]->setPair(0, 0);
1273	>	info[l].globalExcludes = new int;
1274	>	info[l].globalExcludes[0] = 0;
1275	>	info[l].n_exclude = 0;
1276	>	}
1277
1278	+	// set the arrays into the SimInfo object
1279
1280	<	for( i=0; i<simnfo->n_atoms; i++ ){
1281	<	simnfo->atoms[i]->set_vx( 0.0 );
1282	<	simnfo->atoms[i]->set_vy( 0.0 );
1283	<	simnfo->atoms[i]->set_vz( 0.0 );
1280	>	info[l].atoms = the_atoms;
1281	>	info[l].molecules = the_molecules;
1282	>	info[l].nGlobalExcludes = 0;
1283	>	info[l].excludes = the_excludes;
1284	>
1285	>	the_ff->setSimInfo(info);
1286		}
1287		}
1288
1289	<	void SimSetup::makeElement( double x, double y, double z ){
1386	<
1289	>	void SimSetup::makeIntegrator(void){
1290		int k;
1388	–	AtomStamp* current_atom;
1389	–	DirectionalAtom* dAtom;
1390	–	double rotMat[3][3];
1291
1292	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1292	>	NVE<RealIntegrator>* myNVE = NULL;
1293	>	NVT<RealIntegrator>* myNVT = NULL;
1294	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1295	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1296	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1297	>
1298	>	for (k = 0; k < nInfo; k++){
1299	>	switch (ensembleCase){
1300	>	case NVE_ENS:
1301	>	if (globals->haveZconstraints()){
1302	>	setupZConstraint(info[k]);
1303	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1304	>	}
1305	>	else{
1306	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1307	>	}
1308	>
1309	>	info->the_integrator = myNVE;
1310	>	break;
1311
1312	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1313	<	if( !current_atom->havePosition() ){
1314	<	sprintf( painCave.errMsg,
1315	<	"SimSetup:initFromBass error.\n"
1316	<	"\tComponent %s, atom %s does not have a position specified.\n"
1317	<	"\tThe initialization routine is unable to give a start"
1318	<	" position.\n",
1401	<	comp_stamps[current_comp]->getID(),
1402	<	current_atom->getType() );
1403	<	painCave.isFatal = 1;
1404	<	simError();
1405	<	}
1312	>	case NVT_ENS:
1313	>	if (globals->haveZconstraints()){
1314	>	setupZConstraint(info[k]);
1315	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1316	>	}
1317	>	else
1318	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1319
1320	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1408	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1409	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1320	>	myNVT->setTargetTemp(globals->getTargetTemp());
1321
1322	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1322	>	if (globals->haveTauThermostat())
1323	>	myNVT->setTauThermostat(globals->getTauThermostat());
1324	>	else{
1325	>	sprintf(painCave.errMsg,
1326	>	"SimSetup error: If you use the NVT\n"
1327	>	"    ensemble, you must set tauThermostat.\n");
1328	>	painCave.isFatal = 1;
1329	>	simError();
1330	>	}
1331
1332	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1332	>	info->the_integrator = myNVT;
1333	>	break;
1334
1335	<	rotMat[0][0] = 1.0;
1336	<	rotMat[0][1] = 0.0;
1337	<	rotMat[0][2] = 0.0;
1335	>	case NPTi_ENS:
1336	>	if (globals->haveZconstraints()){
1337	>	setupZConstraint(info[k]);
1338	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1339	>	}
1340	>	else
1341	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1342
1343	<	rotMat[1][0] = 0.0;
1420	<	rotMat[1][1] = 1.0;
1421	<	rotMat[1][2] = 0.0;
1343	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1344
1345	<	rotMat[2][0] = 0.0;
1346	<	rotMat[2][1] = 0.0;
1347	<	rotMat[2][2] = 1.0;
1345	>	if (globals->haveTargetPressure())
1346	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1347	>	else{
1348	>	sprintf(painCave.errMsg,
1349	>	"SimSetup error: If you use a constant pressure\n"
1350	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1351	>	painCave.isFatal = 1;
1352	>	simError();
1353	>	}
1354
1355	<	dAtom->setA( rotMat );
1355	>	if (globals->haveTauThermostat())
1356	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1357	>	else{
1358	>	sprintf(painCave.errMsg,
1359	>	"SimSetup error: If you use an NPT\n"
1360	>	"    ensemble, you must set tauThermostat.\n");
1361	>	painCave.isFatal = 1;
1362	>	simError();
1363	>	}
1364	>
1365	>	if (globals->haveTauBarostat())
1366	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1367	>	else{
1368	>	sprintf(painCave.errMsg,
1369	>	"SimSetup error: If you use an NPT\n"
1370	>	"    ensemble, you must set tauBarostat.\n");
1371	>	painCave.isFatal = 1;
1372	>	simError();
1373	>	}
1374	>
1375	>	info->the_integrator = myNPTi;
1376	>	break;
1377	>
1378	>	case NPTf_ENS:
1379	>	if (globals->haveZconstraints()){
1380	>	setupZConstraint(info[k]);
1381	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1382	>	}
1383	>	else
1384	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1385	>
1386	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1387	>
1388	>	if (globals->haveTargetPressure())
1389	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1390	>	else{
1391	>	sprintf(painCave.errMsg,
1392	>	"SimSetup error: If you use a constant pressure\n"
1393	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1394	>	painCave.isFatal = 1;
1395	>	simError();
1396	>	}
1397	>
1398	>	if (globals->haveTauThermostat())
1399	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1400	>
1401	>	else{
1402	>	sprintf(painCave.errMsg,
1403	>	"SimSetup error: If you use an NPT\n"
1404	>	"    ensemble, you must set tauThermostat.\n");
1405	>	painCave.isFatal = 1;
1406	>	simError();
1407	>	}
1408	>
1409	>	if (globals->haveTauBarostat())
1410	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1411	>
1412	>	else{
1413	>	sprintf(painCave.errMsg,
1414	>	"SimSetup error: If you use an NPT\n"
1415	>	"    ensemble, you must set tauBarostat.\n");
1416	>	painCave.isFatal = 1;
1417	>	simError();
1418	>	}
1419	>
1420	>	info->the_integrator = myNPTf;
1421	>	break;
1422	>
1423	>	case NPTxyz_ENS:
1424	>	if (globals->haveZconstraints()){
1425	>	setupZConstraint(info[k]);
1426	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1427	>	}
1428	>	else
1429	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1430	>
1431	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1432	>
1433	>	if (globals->haveTargetPressure())
1434	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1435	>	else{
1436	>	sprintf(painCave.errMsg,
1437	>	"SimSetup error: If you use a constant pressure\n"
1438	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1439	>	painCave.isFatal = 1;
1440	>	simError();
1441	>	}
1442	>
1443	>	if (globals->haveTauThermostat())
1444	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1445	>	else{
1446	>	sprintf(painCave.errMsg,
1447	>	"SimSetup error: If you use an NPT\n"
1448	>	"    ensemble, you must set tauThermostat.\n");
1449	>	painCave.isFatal = 1;
1450	>	simError();
1451	>	}
1452	>
1453	>	if (globals->haveTauBarostat())
1454	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1455	>	else{
1456	>	sprintf(painCave.errMsg,
1457	>	"SimSetup error: If you use an NPT\n"
1458	>	"    ensemble, you must set tauBarostat.\n");
1459	>	painCave.isFatal = 1;
1460	>	simError();
1461	>	}
1462	>
1463	>	info->the_integrator = myNPTxyz;
1464	>	break;
1465	>
1466	>	default:
1467	>	sprintf(painCave.errMsg,
1468	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1469	>	painCave.isFatal = 1;
1470	>	simError();
1471		}
1472	+	}
1473	+	}
1474
1475	<	current_atom_ndx++;
1475	>	void SimSetup::initFortran(void){
1476	>	info[0].refreshSim();
1477	>
1478	>	if (!strcmp(info[0].mixingRule, "standard")){
1479	>	the_ff->initForceField(LB_MIXING_RULE);
1480		}
1481	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1482	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1483	+	}
1484	+	else{
1485	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1486	+	info[0].mixingRule);
1487	+	painCave.isFatal = 1;
1488	+	simError();
1489	+	}
1490
1433	–	current_mol++;
1434	–	current_comp_mol++;
1491
1492	<	if( current_comp_mol >= components_nmol[current_comp] ){
1492	>	#ifdef IS_MPI
1493	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1494	>	MPIcheckPoint();
1495	>	#endif // is_mpi
1496	>	}
1497
1498	<	current_comp_mol = 0;
1499	<	current_comp++;
1498	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1499	>	int nZConstraints;
1500	>	ZconStamp** zconStamp;
1501	>
1502	>	if (globals->haveZconstraintTime()){
1503	>	//add sample time of z-constraint  into SimInfo's property list
1504	>	DoubleData* zconsTimeProp = new DoubleData();
1505	>	zconsTimeProp->setID(ZCONSTIME_ID);
1506	>	zconsTimeProp->setData(globals->getZconsTime());
1507	>	theInfo.addProperty(zconsTimeProp);
1508		}
1509	+	else{
1510	+	sprintf(painCave.errMsg,
1511	+	"ZConstraint error: If you use an ZConstraint\n"
1512	+	" , you must set sample time.\n");
1513	+	painCave.isFatal = 1;
1514	+	simError();
1515	+	}
1516	+
1517	+	//push zconsTol into siminfo, if user does not specify
1518	+	//value for zconsTol, a default value will be used
1519	+	DoubleData* zconsTol = new DoubleData();
1520	+	zconsTol->setID(ZCONSTOL_ID);
1521	+	if (globals->haveZconsTol()){
1522	+	zconsTol->setData(globals->getZconsTol());
1523	+	}
1524	+	else{
1525	+	double defaultZConsTol = 0.01;
1526	+	sprintf(painCave.errMsg,
1527	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1528	+	" , default value %f is used.\n",
1529	+	defaultZConsTol);
1530	+	painCave.isFatal = 0;
1531	+	simError();
1532	+
1533	+	zconsTol->setData(defaultZConsTol);
1534	+	}
1535	+	theInfo.addProperty(zconsTol);
1536	+
1537	+	//set Force Subtraction Policy
1538	+	StringData* zconsForcePolicy = new StringData();
1539	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1540	+
1541	+	if (globals->haveZconsForcePolicy()){
1542	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1543	+	}
1544	+	else{
1545	+	sprintf(painCave.errMsg,
1546	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1547	+	"PolicyByMass is used\n");
1548	+	painCave.isFatal = 0;
1549	+	simError();
1550	+	zconsForcePolicy->setData("BYMASS");
1551	+	}
1552	+
1553	+	theInfo.addProperty(zconsForcePolicy);
1554	+
1555	+	//Determine the name of ouput file and add it into SimInfo's property list
1556	+	//Be careful, do not use inFileName, since it is a pointer which
1557	+	//point to a string at master node, and slave nodes do not contain that string
1558	+
1559	+	string zconsOutput(theInfo.finalName);
1560	+
1561	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1562	+
1563	+	StringData* zconsFilename = new StringData();
1564	+	zconsFilename->setID(ZCONSFILENAME_ID);
1565	+	zconsFilename->setData(zconsOutput);
1566	+
1567	+	theInfo.addProperty(zconsFilename);
1568	+
1569	+	//setup index, pos and other parameters of z-constraint molecules
1570	+	nZConstraints = globals->getNzConstraints();
1571	+	theInfo.nZconstraints = nZConstraints;
1572	+
1573	+	zconStamp = globals->getZconStamp();
1574	+	ZConsParaItem tempParaItem;
1575	+
1576	+	ZConsParaData* zconsParaData = new ZConsParaData();
1577	+	zconsParaData->setID(ZCONSPARADATA_ID);
1578	+
1579	+	for (int i = 0; i < nZConstraints; i++){
1580	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1581	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1582	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1583	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1584	+
1585	+	zconsParaData->addItem(tempParaItem);
1586	+	}
1587	+
1588	+	//check the uniqueness of index
1589	+	if(!zconsParaData->isIndexUnique()){
1590	+	sprintf(painCave.errMsg,
1591	+	"ZConstraint Error: molIndex is not unique\n");
1592	+	painCave.isFatal = 1;
1593	+	simError();
1594	+	}
1595	+
1596	+	//sort the parameters by index of molecules
1597	+	zconsParaData->sortByIndex();
1598	+
1599	+	//push data into siminfo, therefore, we can retrieve later
1600	+	theInfo.addProperty(zconsParaData);
1601		}

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