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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 429 by mmeineke, Thu Mar 27 21:52:21 2003 UTC vs.
Revision 841 by mmeineke, Wed Oct 29 17:55:28 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
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 | SimSetup::~SimSetup(){
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	>	// initialize the system coordinates
107
108	+	if ( !initSuspend ){
109	+	initSystemCoords();
110
111	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
112	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
113	<	else{
94	<	sprintf( painCave.errMsg,
95	<	"SimSetup Error. Unrecognized force field -> %s\n",
96	<	force_field );
97	<	painCave.isFatal = 1;
98	<	simError();
99	<	}
111	>	if( !(globals->getUseInitTime()) )
112	>	info[0].currentTime = 0.0;
113	>	}
114
115	<	#ifdef IS_MPI
102	<	strcpy( checkPointMsg, "ForceField creation successful" );
103	<	MPIcheckPoint();
104	<	#endif // is_mpi
115	>	// check on the post processing info
116
117	<
117	>	finalInfoCheck();
118
119	<	// get the components and calculate the tot_nMol and indvidual n_mol
109	<	the_components = the_globals->getComponents();
110	<	components_nmol = new int[n_components];
111	<	comp_stamps = new MoleculeStamp*[n_components];
119	>	// make the output filenames
120
121	<	if( !the_globals->haveNMol() ){
114	<	// we don't have the total number of molecules, so we assume it is
115	<	// given in each component
121	>	makeOutNames();
122
123	<	tot_nmol = 0;
118	<	for( i=0; i<n_components; i++ ){
123	>	// make the integrator
124
125	<	if( !the_components[i]->haveNMol() ){
121	<	// we have a problem
122	<	sprintf( painCave.errMsg,
123	<	"SimSetup Error. No global NMol or component NMol"
124	<	" given. Cannot calculate the number of atoms.\n" );
125	<	painCave.isFatal = 1;
126	<	simError();
127	<	}
125	>	makeIntegrator();
126
129	–	tot_nmol += the_components[i]->getNMol();
130	–	components_nmol[i] = the_components[i]->getNMol();
131	–	}
132	–	}
133	–	else{
134	–	sprintf( painCave.errMsg,
135	–	"SimSetup error.\n"
136	–	"\tSorry, the ability to specify total"
137	–	" nMols and then give molfractions in the components\n"
138	–	"\tis not currently supported."
139	–	" Please give nMol in the components.\n" );
140	–	painCave.isFatal = 1;
141	–	simError();
142	–
143	–
144	–	//     tot_nmol = the_globals->getNMol();
145	–
146	–	//   //we have the total number of molecules, now we check for molfractions
147	–	//     for( i=0; i<n_components; i++ ){
148	–
149	–	//       if( !the_components[i]->haveMolFraction() ){
150	–
151	–	//  if( !the_components[i]->haveNMol() ){
152	–	//    //we have a problem
153	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
154	–	//              << " nMol was given in component
155	–
156	–	}
157	–
127		#ifdef IS_MPI
128	<	strcpy( checkPointMsg, "Have the number of components" );
129	<	MPIcheckPoint();
161	<	#endif // is_mpi
128	>	mpiSim->mpiRefresh();
129	>	#endif
130
131	<	// make an array of molecule stamps that match the components used.
164	<	// 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;
168	<	simnfo->compStamps = comp_stamps;
169	<	simnfo->headStamp = new LinkedMolStamp();
170	<
171	<	char* id;
172	<	LinkedMolStamp* headStamp = simnfo->headStamp;
173	<	LinkedMolStamp* currentStamp = NULL;
174	<	for( i=0; i<n_components; i++ ){
133	>	initFortran();
134	>	}
135
176	–	id = the_components[i]->getType();
177	–	comp_stamps[i] = NULL;
178	–
179	–	// 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 );
192	<	painCave.isFatal = 1;
193	<	simError();
194	<	}
195	<
196	<	headStamp->add( currentStamp );
197	<	comp_stamps[i] = headStamp->match( id );
198	<	}
199	<	}
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();
204	<	#endif // is_mpi
205	<
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
211	–	tot_atoms = 0;
212	–	tot_bonds = 0;
213	–	tot_bends = 0;
214	–	tot_torsions = 0;
215	–	for( i=0; i<n_components; i++ ){
216	–
217	–	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
218	–	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
219	–	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
220	–	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
221	–	}
158
159	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
159	>	// init the atoms
160
161	<	simnfo->n_atoms = tot_atoms;
226	<	simnfo->n_bonds = tot_bonds;
227	<	simnfo->n_bends = tot_bends;
228	<	simnfo->n_torsions = tot_torsions;
229	<	simnfo->n_SRI = tot_SRI;
230	<	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	<
239	<
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
246	<
247	<	int localMol, allMol;
248	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
187	>	// make the Atoms
188
189	<	int* mol2proc = mpiSim->getMolToProcMap();
190	<	int* molCompType = mpiSim->getMolComponentType();
191	<
192	<	allMol = 0;
193	<	localMol = 0;
194	<	local_atoms = 0;
195	<	local_bonds = 0;
257	<	local_bends = 0;
258	<	local_torsions = 0;
259	<	for( i=0; i<n_components; i++ ){
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	<	for( j=0; j<components_nmol[i]; j++ ){
198	<
199	<	if( mol2proc[j] == worldRank ){
264	<
265	<	local_atoms +=    comp_stamps[i]->getNAtoms();
266	<	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	<
197	>	ux = currentAtom->getOrntX();
198	>	uy = currentAtom->getOrntY();
199	>	uz = currentAtom->getOrntZ();
200
201	<	simnfo->n_atoms = mpiSim->getMyNlocal();
278	<
279	<	if( local_atoms != simnfo->n_atoms ){
280	<	sprintf( painCave.errMsg,
281	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282	<	" localAtom (%d) are not equal.\n",
283	<	simnfo->n_atoms,
284	<	local_atoms );
285	<	painCave.isFatal = 1;
286	<	simError();
287	<	}
201	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
202
203	<	simnfo->n_bonds = local_bonds;
204	<	simnfo->n_bends = local_bends;
205	<	simnfo->n_torsions = local_torsions;
206	<	simnfo->n_SRI = local_SRI;
293	<	simnfo->n_mol = localMol;
203	>	u = sqrt(uSqr);
204	>	ux = ux / u;
205	>	uy = uy / u;
206	>	uz = uz / u;
207
208	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
209	<	MPIcheckPoint();
210	<
211	<
212	<	#endif // is_mpi
213	<
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	<	// create the atom and short range interaction arrays
218	>	#ifdef IS_MPI
219
220	<	Atom::createArrays(simnfo->n_atoms);
305	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
307	<	int molIndex;
220	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
221
222	<	// initialize the molecule's stampID's
222	>	#endif // is_mpi
223	>	}
224
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	+	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	<
241	>	tempEx = exI;
242	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
243	>	tempEx = exJ;
244	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
245
246	<	molIndex = 0;
247	<	for(i=0; i<mpiSim->getTotNmol(); i++){
316	<
317	<	if(mol2proc[i] == worldRank ){
318	<	the_molecules[molIndex].setStampID( molCompType[i] );
319	<	molIndex++;
320	<	}
321	<	}
246	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
247	>	#else  // isn't MPI
248
249	<	#else // is_mpi
250	<
251	<	molIndex = 0;
252	<	for(i=0; i<n_components; i++){
327	<	for(j=0; j<components_nmol[i]; j++ ){
328	<	the_molecules[molIndex].setStampID( i );
329	<	molIndex++;
330	<	}
331	<	}
332	<
249	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
250	>	#endif  //is_mpi
251	>	}
252	>	excludeOffset += molInfo.nBonds;
253
254	<	#endif // is_mpi
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	<	if( simnfo->n_SRI ){
266	<	Exclude::createArray(simnfo->n_SRI);
267	<	the_excludes = new Exclude*[simnfo->n_SRI];
268	<	simnfo->globalExcludes = new int;
269	<	simnfo->n_exclude = tot_SRI;
270	<	}
271	<	else{
344	<
345	<	Exclude::createArray( 1 );
346	<	the_excludes = new Exclude*;
347	<	the_excludes[0] = new Exclude(0);
348	<	the_excludes[0]->setPair( 0,0 );
349	<	simnfo->globalExcludes = new int;
350	<	simnfo->globalExcludes[0] = 0;
351	<	simnfo->n_exclude = 0;
352	<	}
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	<	// set the arrays into the SimInfo object
273	>	case 1:
274	>	theBends[j].ghost = (int) current_extra->getDouble() +
275	>	atomOffset;
276	>	theBends[j].isGhost = 1;
277	>	break;
278
279	<	simnfo->atoms = the_atoms;
280	<	simnfo->molecules = the_molecules;
281	<	simnfo->nGlobalExcludes = 0;
282	<	simnfo->excludes = the_excludes;
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	+	current_extra = current_extra->getNext();
299	+	}
300	+	}
301
302	<	// get some of the tricky things that may still be in the globals
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	<
312	<	if( the_globals->haveBox() ){
313	<	simnfo->box_x = the_globals->getBox();
314	<	simnfo->box_y = the_globals->getBox();
315	<	simnfo->box_z = the_globals->getBox();
316	<	}
317	<	else if( the_globals->haveDensity() ){
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	>	tempEx = exI;
319	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
320	>	tempEx = exJ;
321	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
322
323	<	double vol;
324	<	vol = (double)tot_nmol / the_globals->getDensity();
325	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
326	<	simnfo->box_y = simnfo->box_x;
327	<	simnfo->box_z = simnfo->box_x;
328	<	}
378	<	else{
379	<	if( !the_globals->haveBoxX() ){
380	<	sprintf( painCave.errMsg,
381	<	"SimSetup error, no periodic BoxX size given.\n" );
382	<	painCave.isFatal = 1;
383	<	simError();
384	<	}
385	<	simnfo->box_x = the_globals->getBoxX();
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	<	if( !the_globals->haveBoxY() ){
331	<	sprintf( painCave.errMsg,
332	<	"SimSetup error, no periodic BoxY size given.\n" );
333	<	painCave.isFatal = 1;
334	<	simError();
335	<	}
393	<	simnfo->box_y = the_globals->getBoxY();
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	<	if( !the_globals->haveBoxZ() ){
338	<	sprintf( painCave.errMsg,
339	<	"SimSetup error, no periodic BoxZ size given.\n" );
340	<	painCave.isFatal = 1;
341	<	simError();
337	>	exI = theTorsions[j].a;
338	>	exJ = theTorsions[j].d;
339	>
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	>
359	>
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	>
368	>
369	>	info[k].molecules[i].initialize(molInfo);
370	>
371	>
372	>	atomOffset += molInfo.nAtoms;
373	>	delete[] theBonds;
374	>	delete[] theBends;
375	>	delete[] theTorsions;
376		}
401	–	simnfo->box_z = the_globals->getBoxZ();
377		}
378
379		#ifdef IS_MPI
380	<	strcpy( checkPointMsg, "Box size set up" );
380	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
381		MPIcheckPoint();
382		#endif // is_mpi
383
384	+	// clean up the forcefield
385
386	<	// initialize the arrays
386	>	the_ff->calcRcut();
387	>	the_ff->cleanMe();
388	>	}
389
390	<	the_ff->setSimInfo( simnfo );
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	<	makeMolecules();
400	<	simnfo->identArray = new int[simnfo->n_atoms];
401	<	for(i=0; i<simnfo->n_atoms; i++){
402	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
418	<	}
419	<
420	<	if (the_globals->getUseRF() ) {
421	<	simnfo->useReactionField = 1;
422	<
423	<	if( !the_globals->haveECR() ){
424	<	sprintf( painCave.errMsg,
425	<	"SimSetup Warning: using default value of 1/2 the smallest "
426	<	"box length for the electrostaticCutoffRadius.\n"
427	<	"I hope you have a very fast processor!\n");
428	<	painCave.isFatal = 0;
429	<	simError();
430	<	double smallest;
431	<	smallest = simnfo->box_x;
432	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
433	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
434	<	simnfo->ecr = 0.5 * smallest;
435	<	} else {
436	<	simnfo->ecr        = the_globals->getECR();
437	<	}
399	>	double vel[3];
400	>	vel[0] = 0.0;
401	>	vel[1] = 0.0;
402	>	vel[2] = 0.0;
403
404	<	if( !the_globals->haveEST() ){
405	<	sprintf( painCave.errMsg,
406	<	"SimSetup Warning: using default value of 0.05 * the "
407	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
408	<	);
409	<	painCave.isFatal = 0;
410	<	simError();
411	<	simnfo->est = 0.05 * simnfo->ecr;
412	<	} else {
413	<	simnfo->est        = the_globals->getEST();
414	<	}
415	<
416	<	if(!the_globals->haveDielectric() ){
417	<	sprintf( painCave.errMsg,
418	<	"SimSetup Error: You are trying to use Reaction Field without"
419	<	"setting a dielectric constant!\n"
420	<	);
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	>	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	>	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	<	simnfo->dielectric = the_globals->getDielectric();
429	<	} else {
430	<	if (simnfo->n_dipoles) {
431	<
432	<	if( !the_globals->haveECR() ){
433	<	sprintf( painCave.errMsg,
434	<	"SimSetup Warning: using default value of 1/2 the smallest"
435	<	"box length for the electrostaticCutoffRadius.\n"
436	<	"I hope you have a very fast processor!\n");
437	<	painCave.isFatal = 0;
438	<	simError();
439	<	double smallest;
440	<	smallest = simnfo->box_x;
441	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
442	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
443	<	simnfo->ecr = 0.5 * smallest;
444	<	} else {
445	<	simnfo->ecr        = the_globals->getECR();
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	>	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	>	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		}
478	–
479	–	if( !the_globals->haveEST() ){
480	–	sprintf( painCave.errMsg,
481	–	"SimSetup Warning: using default value of 5% of the"
482	–	"electrostaticCutoffRadius for the "
483	–	"electrostaticSkinThickness\n"
484	–	);
485	–	painCave.isFatal = 0;
486	–	simError();
487	–	simnfo->est = 0.05 * simnfo->ecr;
488	–	} else {
489	–	simnfo->est        = the_globals->getEST();
490	–	}
452		}
453	<	}
453	>	}
454
455	<	#ifdef IS_MPI
456	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
496	<	MPIcheckPoint();
497	<	#endif // is_mpi
455	>	if (have_extra){
456	>	done = 0;
457
458	<	if( the_globals->haveInitialConfig() ){
459	<
460	<	InitializeFromFile* fileInit;
461	<	#ifdef IS_MPI // is_mpi
462	<	if( worldRank == 0 ){
463	<	#endif //is_mpi
464	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
465	<	#ifdef IS_MPI
466	<	}else fileInit = new InitializeFromFile( NULL );
467	<	#endif
468	<	fileInit->read_xyz( simnfo ); // default velocities on
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	<	delete fileInit;
472	<	}
473	<	else{
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	<	#ifdef IS_MPI
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	<	// no init from bass
482	<
483	<	sprintf( painCave.errMsg,
484	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
485	<	painCave.isFatal;
522	<	simError();
523	<
524	<	#else
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	<	initFromBass();
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	>	}
495	>	}
496
497	+	for (i = 0; i < info[0].n_atoms; i++){
498	+	info[0].atoms[i]->setVel(vel);
499	+	}
500	+	}
501
502	<	#endif
503	<	}
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	<	#ifdef IS_MPI
510	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
511	<	MPIcheckPoint();
512	<	#endif // is_mpi
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	<
539	<
540	<
526	>	info[0].atoms[current_atom_ndx]->setPos(pos);
527
528	<
529	<	#ifdef IS_MPI
530	<	if( worldRank == 0 ){
531	<	#endif // is_mpi
532	<
533	<	if( the_globals->haveFinalConfig() ){
534	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
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		}
550	–	else{
551	–	strcpy( simnfo->finalName, inFileName );
552	–	char* endTest;
553	–	int nameLength = strlen( simnfo->finalName );
554	–	endTest = &(simnfo->finalName[nameLength - 5]);
555	–	if( !strcmp( endTest, ".bass" ) ){
556	–	strcpy( endTest, ".eor" );
557	–	}
558	–	else if( !strcmp( endTest, ".BASS" ) ){
559	–	strcpy( endTest, ".eor" );
560	–	}
561	–	else{
562	–	endTest = &(simnfo->finalName[nameLength - 4]);
563	–	if( !strcmp( endTest, ".bss" ) ){
564	–	strcpy( endTest, ".eor" );
565	–	}
566	–	else if( !strcmp( endTest, ".mdl" ) ){
567	–	strcpy( endTest, ".eor" );
568	–	}
569	–	else{
570	–	strcat( simnfo->finalName, ".eor" );
571	–	}
572	–	}
573	–	}
574	–
575	–	// make the sample and status out names
576	–
577	–	strcpy( simnfo->sampleName, inFileName );
578	–	char* endTest;
579	–	int nameLength = strlen( simnfo->sampleName );
580	–	endTest = &(simnfo->sampleName[nameLength - 5]);
581	–	if( !strcmp( endTest, ".bass" ) ){
582	–	strcpy( endTest, ".dump" );
583	–	}
584	–	else if( !strcmp( endTest, ".BASS" ) ){
585	–	strcpy( endTest, ".dump" );
586	–	}
587	–	else{
588	–	endTest = &(simnfo->sampleName[nameLength - 4]);
589	–	if( !strcmp( endTest, ".bss" ) ){
590	–	strcpy( endTest, ".dump" );
591	–	}
592	–	else if( !strcmp( endTest, ".mdl" ) ){
593	–	strcpy( endTest, ".dump" );
594	–	}
595	–	else{
596	–	strcat( simnfo->sampleName, ".dump" );
597	–	}
598	–	}
599	–
600	–	strcpy( simnfo->statusName, inFileName );
601	–	nameLength = strlen( simnfo->statusName );
602	–	endTest = &(simnfo->statusName[nameLength - 5]);
603	–	if( !strcmp( endTest, ".bass" ) ){
604	–	strcpy( endTest, ".stat" );
605	–	}
606	–	else if( !strcmp( endTest, ".BASS" ) ){
607	–	strcpy( endTest, ".stat" );
608	–	}
609	–	else{
610	–	endTest = &(simnfo->statusName[nameLength - 4]);
611	–	if( !strcmp( endTest, ".bss" ) ){
612	–	strcpy( endTest, ".stat" );
613	–	}
614	–	else if( !strcmp( endTest, ".mdl" ) ){
615	–	strcpy( endTest, ".stat" );
616	–	}
617	–	else{
618	–	strcat( simnfo->statusName, ".stat" );
619	–	}
620	–	}
621	–
622	–	#ifdef IS_MPI
623	–	}
624	–	#endif // is_mpi
625	–
626	–	// set the status, sample, and themal kick times
627	–
628	–	if( the_globals->haveSampleTime() ){
629	–	simnfo->sampleTime = the_globals->getSampleTime();
630	–	simnfo->statusTime = simnfo->sampleTime;
631	–	simnfo->thermalTime = simnfo->sampleTime;
632	–	}
633	–	else{
634	–	simnfo->sampleTime = the_globals->getRunTime();
635	–	simnfo->statusTime = simnfo->sampleTime;
636	–	simnfo->thermalTime = simnfo->sampleTime;
637	–	}
545
546	<	if( the_globals->haveStatusTime() ){
640	<	simnfo->statusTime = the_globals->getStatusTime();
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
647	–	// 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
656	–	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
657	–	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	<
663	<	simnfo->refreshSim();
664	<
665	<	if( !strcmp( simnfo->mixingRule, "standard") ){
666	<	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;
676	<	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
681	<	strcpy( checkPointMsg,
682	<	"Successfully intialized the mixingRule for Fortran." );
683	<	MPIcheckPoint();
684	<	#endif // is_mpi
685	<	}
686	<
687	<
688	<	void SimSetup::makeMolecules( void ){
689	<
690	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
691	<	molInit info;
692	<	DirectionalAtom* dAtom;
693	<	LinkedAssign* extras;
694	<	LinkedAssign* current_extra;
695	<	AtomStamp* currentAtom;
696	<	BondStamp* currentBond;
697	<	BendStamp* currentBend;
698	<	TorsionStamp* currentTorsion;
699	<
700	<	bond_pair* theBonds;
701	<	bend_set* theBends;
702	<	torsion_set* theTorsions;
703	<
704	<
705	<	//init the forceField paramters
706	<
707	<	the_ff->readParams();
708	<
709	<
710	<	// init the atoms
711	<
712	<	double ux, uy, uz, u, uSqr;
713	<
714	<	atomOffset = 0;
715	<	excludeOffset = 0;
716	<	for(i=0; i<simnfo->n_mol; i++){
717	<
718	<	stampID = the_molecules[i].getStampID();
719	<
720	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
721	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
722	<	info.nBends    = comp_stamps[stampID]->getNBends();
723	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
724	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
725	<
726	<	info.myAtoms = &the_atoms[atomOffset];
727	<	info.myExcludes = &the_excludes[excludeOffset];
728	<	info.myBonds = new Bond*[info.nBonds];
729	<	info.myBends = new Bend*[info.nBends];
730	<	info.myTorsions = new Torsion*[info.nTorsions];
731	<
732	<	theBonds = new bond_pair[info.nBonds];
733	<	theBends = new bend_set[info.nBends];
734	<	theTorsions = new torsion_set[info.nTorsions];
735	<
736	<	// make the Atoms
737	<
738	<	for(j=0; j<info.nAtoms; j++){
739	<
740	<	currentAtom = comp_stamps[stampID]->getAtom( j );
741	<	if( currentAtom->haveOrientation() ){
742	<
743	<	dAtom = new DirectionalAtom(j + atomOffset);
744	<	simnfo->n_oriented++;
745	<	info.myAtoms[j] = dAtom;
746	<
747	<	ux = currentAtom->getOrntX();
748	<	uy = currentAtom->getOrntY();
749	<	uz = currentAtom->getOrntZ();
750	<
751	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
752	<
753	<	u = sqrt( uSqr );
754	<	ux = ux / u;
755	<	uy = uy / u;
756	<	uz = uz / u;
757	<
758	<	dAtom->setSUx( ux );
759	<	dAtom->setSUy( uy );
760	<	dAtom->setSUz( uz );
761	<	}
762	<	else{
763	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
764	<	}
765	<	info.myAtoms[j]->setType( currentAtom->getType() );
766	<
767	<	#ifdef IS_MPI
768	<
769	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
770	<
771	<	#endif // is_mpi
772	<	}
773	<
774	<	// make the bonds
775	<	for(j=0; j<info.nBonds; j++){
776	<
777	<	currentBond = comp_stamps[stampID]->getBond( j );
778	<	theBonds[j].a = currentBond->getA() + atomOffset;
779	<	theBonds[j].b = currentBond->getB() + atomOffset;
597	>	strcpy(ensemble, globals->getEnsemble());
598
599	<	exI = theBonds[i].a;
600	<	exJ = theBonds[i].b;
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	<	// exclude_I must always be the smaller of the pair
626	<	if( exI > exJ ){
786	<	tempEx = exI;
787	<	exI = exJ;
788	<	exJ = tempEx;
789	<	}
790	<	#ifdef IS_MPI
791	<	tempEx = exI;
792	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
793	<	tempEx = exJ;
794	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
795	<
796	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
797	<	#else  // isn't MPI
798	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
799	<	#endif  //is_mpi
800	<	}
801	<	excludeOffset += info.nBonds;
625	>	for (i = 0; i < nInfo; i++){
626	>	strcpy(info[i].ensemble, ensemble);
627
628	<	//make the bends
804	<	for(j=0; j<info.nBends; j++){
805	<
806	<	currentBend = comp_stamps[stampID]->getBend( j );
807	<	theBends[j].a = currentBend->getA() + atomOffset;
808	<	theBends[j].b = currentBend->getB() + atomOffset;
809	<	theBends[j].c = currentBend->getC() + atomOffset;
810	<
811	<	if( currentBend->haveExtras() ){
812	<
813	<	extras = currentBend->getExtras();
814	<	current_extra = extras;
815	<
816	<	while( current_extra != NULL ){
817	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
818	<
819	<	switch( current_extra->getType() ){
820	<
821	<	case 0:
822	<	theBends[j].ghost =
823	<	current_extra->getInt() + atomOffset;
824	<	theBends[j].isGhost = 1;
825	<	break;
826	<
827	<	case 1:
828	<	theBends[j].ghost =
829	<	(int)current_extra->getDouble() + atomOffset;
830	<	theBends[j].isGhost = 1;
831	<	break;
832	<
833	<	default:
834	<	sprintf( painCave.errMsg,
835	<	"SimSetup Error: ghostVectorSource was neiter a "
836	<	"double nor an int.\n"
837	<	"-->Bend[%d] in %s\n",
838	<	j, comp_stamps[stampID]->getID() );
839	<	painCave.isFatal = 1;
840	<	simError();
841	<	}
842	<	}
843	<
844	<	else{
845	<
846	<	sprintf( painCave.errMsg,
847	<	"SimSetup Error: unhandled bend assignment:\n"
848	<	"    -->%s in Bend[%d] in %s\n",
849	<	current_extra->getlhs(),
850	<	j, comp_stamps[stampID]->getID() );
851	<	painCave.isFatal = 1;
852	<	simError();
853	<	}
854	<
855	<	current_extra = current_extra->getNext();
856	<	}
857	<	}
858	<
859	<	if( !theBends[j].isGhost ){
860	<
861	<	exI = theBends[j].a;
862	<	exJ = theBends[j].c;
863	<	}
864	<	else{
865	<
866	<	exI = theBends[j].a;
867	<	exJ = theBends[j].b;
868	<	}
869	<
870	<	// exclude_I must always be the smaller of the pair
871	<	if( exI > exJ ){
872	<	tempEx = exI;
873	<	exI = exJ;
874	<	exJ = tempEx;
875	<	}
876	<	#ifdef IS_MPI
877	<	tempEx = exI;
878	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
879	<	tempEx = exJ;
880	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
881	<
882	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
883	<	#else  // isn't MPI
884	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
885	<	#endif  //is_mpi
886	<	}
887	<	excludeOffset += info.nBends;
628	>	// get the mixing rule
629
630	<	for(j=0; j<info.nTorsions; j++){
631	<
891	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
892	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
893	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
894	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
895	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
896	<
897	<	exI = theTorsions[j].a;
898	<	exJ = theTorsions[j].d;
899	<
900	<	// exclude_I must always be the smaller of the pair
901	<	if( exI > exJ ){
902	<	tempEx = exI;
903	<	exI = exJ;
904	<	exJ = tempEx;
905	<	}
906	<	#ifdef IS_MPI
907	<	tempEx = exI;
908	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
909	<	tempEx = exJ;
910	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
911	<
912	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
913	<	#else  // isn't MPI
914	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
915	<	#endif  //is_mpi
916	<	}
917	<	excludeOffset += info.nTorsions;
918	<
919	<
920	<	// send the arrays off to the forceField for init.
921	<
922	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
923	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
924	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
925	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
926	<
927	<
928	<	the_molecules[i].initialize( info );
929	<	atomOffset += info.nAtoms;
930	<	delete[] theBonds;
931	<	delete[] theBends;
932	<	delete[] theTorsions;
630	>	strcpy(info[i].mixingRule, globals->getMixingRule());
631	>	info[i].usePBC = globals->getPBC();
632		}
633
634	<	// clean up the forcefield
936	<	the_ff->calcRcut();
937	<	the_ff->cleanMe();
938	<	}
634	>	// get the components and calculate the tot_nMol and indvidual n_mol
635
636	<	void SimSetup::initFromBass( void ){
636	>	the_components = globals->getComponents();
637	>	components_nmol = new int[n_components];
638
942	–	int i, j, k;
943	–	int n_cells;
944	–	double cellx, celly, cellz;
945	–	double temp1, temp2, temp3;
946	–	int n_per_extra;
947	–	int n_extra;
948	–	int have_extra, done;
639
640	<	temp1 = (double)tot_nmol / 4.0;
641	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
642	<	temp3 = ceil( temp2 );
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	<	have_extra =0;
645	<	if( temp2 < temp3 ){ // we have a non-complete lattice
646	<	have_extra =1;
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	>	}
654
655	<	n_cells = (int)temp3 - 1;
656	<	cellx = simnfo->box_x / temp3;
960	<	celly = simnfo->box_y / temp3;
961	<	cellz = simnfo->box_z / temp3;
962	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
963	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
964	<	n_per_extra = (int)ceil( temp1 );
965	<
966	<	if( n_per_extra > 4){
967	<	sprintf( painCave.errMsg,
968	<	"SimSetup error. There has been an error in constructing"
969	<	" the non-complete lattice.\n" );
970	<	painCave.isFatal = 1;
971	<	simError();
655	>	tot_nmol += the_components[i]->getNMol();
656	>	components_nmol[i] = the_components[i]->getNMol();
657		}
658		}
659		else{
660	<	n_cells = (int)temp3;
661	<	cellx = simnfo->box_x / temp3;
662	<	celly = simnfo->box_y / temp3;
663	<	cellz = simnfo->box_z / temp3;
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	<	current_mol = 0;
982	<	current_comp_mol = 0;
983	<	current_comp = 0;
984	<	current_atom_ndx = 0;
670	>	// set the status, sample, and thermal kick times
671
672	<	for( i=0; i < n_cells ; i++ ){
673	<	for( j=0; j < n_cells; j++ ){
674	<	for( k=0; k < n_cells; k++ ){
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	>	else{
679	>	info[i].sampleTime = globals->getRunTime();
680	>	info[i].statusTime = info[i].sampleTime;
681	>	info[i].thermalTime = info[i].sampleTime;
682	>	}
683
684	<	makeElement( i * cellx,
685	<	j * celly,
686	<	k * cellz );
684	>	if (globals->haveStatusTime()){
685	>	info[i].statusTime = globals->getStatusTime();
686	>	}
687
688	<	makeElement( i * cellx + 0.5 * cellx,
689	<	j * celly + 0.5 * celly,
690	<	k * cellz );
688	>	if (globals->haveThermalTime()){
689	>	info[i].thermalTime = globals->getThermalTime();
690	>	}
691
692	<	makeElement( i * cellx,
693	<	j * celly + 0.5 * celly,
694	<	k * cellz + 0.5 * cellz );
695	<
1002	<	makeElement( i * cellx + 0.5 * cellx,
1003	<	j * celly,
1004	<	k * cellz + 0.5 * cellz );
1005	<	}
692	>	info[i].resetIntegrator = 0;
693	>	if( globals->haveResetTime() ){
694	>	info[i].resetTime = globals->getResetTime();
695	>	info[i].resetIntegrator = 1;
696		}
697	+
698	+	// check for the temperature set flag
699	+
700	+	if (globals->haveTempSet())
701	+	info[i].setTemp = globals->getTempSet();
702	+
703		}
704	+
705	+	//setup seed for random number generator
706	+	int seedValue;
707
708	<	if( have_extra ){
709	<	done = 0;
708	>	if (globals->haveSeed()){
709	>	seedValue = globals->getSeed();
710
711	<	int start_ndx;
712	<	for( i=0; i < (n_cells+1) && !done; i++ ){
713	<	for( j=0; j < (n_cells+1) && !done; j++ ){
714	<
715	<	if( i < n_cells ){
711	>	if(seedValue / 1E9 == 0){
712	>	sprintf(painCave.errMsg,
713	>	"Seed for sprng library should contain at least 9 digits\n"
714	>	"OOPSE will generate a seed for user\n");
715	>	painCave.isFatal = 0;
716	>	simError();
717
718	<	if( j < n_cells ){
719	<	start_ndx = n_cells;
720	<	}
721	<	else start_ndx = 0;
722	<	}
723	<	else start_ndx = 0;
718	>	//using seed generated by system instead of invalid seed set by user
719	>	#ifndef IS_MPI
720	>	seedValue = make_sprng_seed();
721	>	#else
722	>	if (worldRank == 0){
723	>	seedValue = make_sprng_seed();
724	>	}
725	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
726	>	#endif
727	>	}
728	>	}//end of if branch of globals->haveSeed()
729	>	else{
730	>
731	>	#ifndef IS_MPI
732	>	seedValue = make_sprng_seed();
733	>	#else
734	>	if (worldRank == 0){
735	>	seedValue = make_sprng_seed();
736	>	}
737	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
738	>	#endif
739	>	}//end of globals->haveSeed()
740
741	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
741	>	for (int i = 0; i < nInfo; i++){
742	>	info[i].setSeed(seedValue);
743	>	}
744
745	<	makeElement( i * cellx,
746	<	j * celly,
747	<	k * cellz );
748	<	done = ( current_mol >= tot_nmol );
745	>	#ifdef IS_MPI
746	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
747	>	MPIcheckPoint();
748	>	#endif // is_mpi
749	>	}
750
1032	–	if( !done && n_per_extra > 1 ){
1033	–	makeElement( i * cellx + 0.5 * cellx,
1034	–	j * celly + 0.5 * celly,
1035	–	k * cellz );
1036	–	done = ( current_mol >= tot_nmol );
1037	–	}
751
752	<	if( !done && n_per_extra > 2){
753	<	makeElement( i * cellx,
754	<	j * celly + 0.5 * celly,
755	<	k * cellz + 0.5 * cellz );
1043	<	done = ( current_mol >= tot_nmol );
1044	<	}
752	>	void SimSetup::finalInfoCheck(void){
753	>	int index;
754	>	int usesDipoles;
755	>	int i;
756
757	<	if( !done && n_per_extra > 3){
758	<	makeElement( i * cellx + 0.5 * cellx,
759	<	j * celly,
760	<	k * cellz + 0.5 * cellz );
761	<	done = ( current_mol >= tot_nmol );
762	<	}
763	<	}
757	>	for (i = 0; i < nInfo; i++){
758	>	// check electrostatic parameters
759	>
760	>	index = 0;
761	>	usesDipoles = 0;
762	>	while ((index < info[i].n_atoms) && !usesDipoles){
763	>	usesDipoles = (info[i].atoms[index])->hasDipole();
764	>	index++;
765	>	}
766	>
767	>	#ifdef IS_MPI
768	>	int myUse = usesDipoles;
769	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770	>	#endif //is_mpi
771	>
772	>	double theEcr, theEst;
773	>
774	>	if (globals->getUseRF()){
775	>	info[i].useReactionField = 1;
776	>
777	>	if (!globals->haveECR()){
778	>	sprintf(painCave.errMsg,
779	>	"SimSetup Warning: using default value of 1/2 the smallest "
780	>	"box length for the electrostaticCutoffRadius.\n"
781	>	"I hope you have a very fast processor!\n");
782	>	painCave.isFatal = 0;
783	>	simError();
784	>	double smallest;
785	>	smallest = info[i].boxL[0];
786	>	if (info[i].boxL[1] <= smallest)
787	>	smallest = info[i].boxL[1];
788	>	if (info[i].boxL[2] <= smallest)
789	>	smallest = info[i].boxL[2];
790	>	theEcr = 0.5 * smallest;
791		}
792	+	else{
793	+	theEcr = globals->getECR();
794	+	}
795	+
796	+	if (!globals->haveEST()){
797	+	sprintf(painCave.errMsg,
798	+	"SimSetup Warning: using default value of 0.05 * the "
799	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
800	+	painCave.isFatal = 0;
801	+	simError();
802	+	theEst = 0.05 * theEcr;
803	+	}
804	+	else{
805	+	theEst = globals->getEST();
806	+	}
807	+
808	+	info[i].setDefaultEcr(theEcr, theEst);
809	+
810	+	if (!globals->haveDielectric()){
811	+	sprintf(painCave.errMsg,
812	+	"SimSetup Error: You are trying to use Reaction Field without"
813	+	"setting a dielectric constant!\n");
814	+	painCave.isFatal = 1;
815	+	simError();
816	+	}
817	+	info[i].dielectric = globals->getDielectric();
818		}
819	+	else{
820	+	if (usesDipoles){
821	+	if (!globals->haveECR()){
822	+	sprintf(painCave.errMsg,
823	+	"SimSetup Warning: using default value of 1/2 the smallest "
824	+	"box length for the electrostaticCutoffRadius.\n"
825	+	"I hope you have a very fast processor!\n");
826	+	painCave.isFatal = 0;
827	+	simError();
828	+	double smallest;
829	+	smallest = info[i].boxL[0];
830	+	if (info[i].boxL[1] <= smallest)
831	+	smallest = info[i].boxL[1];
832	+	if (info[i].boxL[2] <= smallest)
833	+	smallest = info[i].boxL[2];
834	+	theEcr = 0.5 * smallest;
835	+	}
836	+	else{
837	+	theEcr = globals->getECR();
838	+	}
839	+
840	+	if (!globals->haveEST()){
841	+	sprintf(painCave.errMsg,
842	+	"SimSetup Warning: using default value of 0.05 * the "
843	+	"electrostaticCutoffRadius for the "
844	+	"electrostaticSkinThickness\n");
845	+	painCave.isFatal = 0;
846	+	simError();
847	+	theEst = 0.05 * theEcr;
848	+	}
849	+	else{
850	+	theEst = globals->getEST();
851	+	}
852	+
853	+	info[i].setDefaultEcr(theEcr, theEst);
854	+	}
855	+	}
856		}
857
858	+	#ifdef IS_MPI
859	+	strcpy(checkPointMsg, "post processing checks out");
860	+	MPIcheckPoint();
861	+	#endif // is_mpi
862	+	}
863
864	<	for( i=0; i<simnfo->n_atoms; i++ ){
865	<	simnfo->atoms[i]->set_vx( 0.0 );
866	<	simnfo->atoms[i]->set_vy( 0.0 );
867	<	simnfo->atoms[i]->set_vz( 0.0 );
864	>	void SimSetup::initSystemCoords(void){
865	>	int i;
866	>
867	>	char* inName;
868	>
869	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
870	>
871	>	for (i = 0; i < info[0].n_atoms; i++)
872	>	info[0].atoms[i]->setCoords();
873	>
874	>	if (globals->haveInitialConfig()){
875	>	InitializeFromFile* fileInit;
876	>	#ifdef IS_MPI // is_mpi
877	>	if (worldRank == 0){
878	>	#endif //is_mpi
879	>	inName = globals->getInitialConfig();
880	>	fileInit = new InitializeFromFile(inName);
881	>	#ifdef IS_MPI
882	>	}
883	>	else
884	>	fileInit = new InitializeFromFile(NULL);
885	>	#endif
886	>	fileInit->readInit(info); // default velocities on
887	>
888	>	delete fileInit;
889		}
890	+	else{
891	+	#ifdef IS_MPI
892	+
893	+	// no init from bass
894	+
895	+	sprintf(painCave.errMsg,
896	+	"Cannot intialize a parallel simulation without an initial configuration file.\n");
897	+	painCave.isFatal = 1;;
898	+	simError();
899	+
900	+	#else
901	+
902	+	initFromBass();
903	+
904	+
905	+	#endif
906	+	}
907	+
908	+	#ifdef IS_MPI
909	+	strcpy(checkPointMsg, "Successfully read in the initial configuration");
910	+	MPIcheckPoint();
911	+	#endif // is_mpi
912		}
913
1065	–	void SimSetup::makeElement( double x, double y, double z ){
914
915	+	void SimSetup::makeOutNames(void){
916		int k;
1068	–	AtomStamp* current_atom;
1069	–	DirectionalAtom* dAtom;
1070	–	double rotMat[3][3];
917
1072	–	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
918
919	<	current_atom = comp_stamps[current_comp]->getAtom( k );
920	<	if( !current_atom->havePosition() ){
921	<	sprintf( painCave.errMsg,
922	<	"SimSetup:initFromBass error.\n"
923	<	"\tComponent %s, atom %s does not have a position specified.\n"
924	<	"\tThe initialization routine is unable to give a start"
925	<	" position.\n",
926	<	comp_stamps[current_comp]->getID(),
927	<	current_atom->getType() );
919	>	for (k = 0; k < nInfo; k++){
920	>	#ifdef IS_MPI
921	>	if (worldRank == 0){
922	>	#endif // is_mpi
923	>
924	>	if (globals->haveFinalConfig()){
925	>	strcpy(info[k].finalName, globals->getFinalConfig());
926	>	}
927	>	else{
928	>	strcpy(info[k].finalName, inFileName);
929	>	char* endTest;
930	>	int nameLength = strlen(info[k].finalName);
931	>	endTest = &(info[k].finalName[nameLength - 5]);
932	>	if (!strcmp(endTest, ".bass")){
933	>	strcpy(endTest, ".eor");
934	>	}
935	>	else if (!strcmp(endTest, ".BASS")){
936	>	strcpy(endTest, ".eor");
937	>	}
938	>	else{
939	>	endTest = &(info[k].finalName[nameLength - 4]);
940	>	if (!strcmp(endTest, ".bss")){
941	>	strcpy(endTest, ".eor");
942	>	}
943	>	else if (!strcmp(endTest, ".mdl")){
944	>	strcpy(endTest, ".eor");
945	>	}
946	>	else{
947	>	strcat(info[k].finalName, ".eor");
948	>	}
949	>	}
950	>	}
951	>
952	>	// make the sample and status out names
953	>
954	>	strcpy(info[k].sampleName, inFileName);
955	>	char* endTest;
956	>	int nameLength = strlen(info[k].sampleName);
957	>	endTest = &(info[k].sampleName[nameLength - 5]);
958	>	if (!strcmp(endTest, ".bass")){
959	>	strcpy(endTest, ".dump");
960	>	}
961	>	else if (!strcmp(endTest, ".BASS")){
962	>	strcpy(endTest, ".dump");
963	>	}
964	>	else{
965	>	endTest = &(info[k].sampleName[nameLength - 4]);
966	>	if (!strcmp(endTest, ".bss")){
967	>	strcpy(endTest, ".dump");
968	>	}
969	>	else if (!strcmp(endTest, ".mdl")){
970	>	strcpy(endTest, ".dump");
971	>	}
972	>	else{
973	>	strcat(info[k].sampleName, ".dump");
974	>	}
975	>	}
976	>
977	>	strcpy(info[k].statusName, inFileName);
978	>	nameLength = strlen(info[k].statusName);
979	>	endTest = &(info[k].statusName[nameLength - 5]);
980	>	if (!strcmp(endTest, ".bass")){
981	>	strcpy(endTest, ".stat");
982	>	}
983	>	else if (!strcmp(endTest, ".BASS")){
984	>	strcpy(endTest, ".stat");
985	>	}
986	>	else{
987	>	endTest = &(info[k].statusName[nameLength - 4]);
988	>	if (!strcmp(endTest, ".bss")){
989	>	strcpy(endTest, ".stat");
990	>	}
991	>	else if (!strcmp(endTest, ".mdl")){
992	>	strcpy(endTest, ".stat");
993	>	}
994	>	else{
995	>	strcat(info[k].statusName, ".stat");
996	>	}
997	>	}
998	>
999	>	#ifdef IS_MPI
1000	>
1001	>	}
1002	>	#endif // is_mpi
1003	>	}
1004	>	}
1005	>
1006	>
1007	>	void SimSetup::sysObjectsCreation(void){
1008	>	int i, k;
1009	>
1010	>	// create the forceField
1011	>
1012	>	createFF();
1013	>
1014	>	// extract componentList
1015	>
1016	>	compList();
1017	>
1018	>	// calc the number of atoms, bond, bends, and torsions
1019	>
1020	>	calcSysValues();
1021	>
1022	>	#ifdef IS_MPI
1023	>	// divide the molecules among the processors
1024	>
1025	>	mpiMolDivide();
1026	>	#endif //is_mpi
1027	>
1028	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1029	>
1030	>	makeSysArrays();
1031	>
1032	>	// make and initialize the molecules (all but atomic coordinates)
1033	>
1034	>	makeMolecules();
1035	>
1036	>	for (k = 0; k < nInfo; k++){
1037	>	info[k].identArray = new int[info[k].n_atoms];
1038	>	for (i = 0; i < info[k].n_atoms; i++){
1039	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1040	>	}
1041	>	}
1042	>	}
1043	>
1044	>
1045	>	void SimSetup::createFF(void){
1046	>	switch (ffCase){
1047	>	case FF_DUFF:
1048	>	the_ff = new DUFF();
1049	>	break;
1050	>
1051	>	case FF_LJ:
1052	>	the_ff = new LJFF();
1053	>	break;
1054	>
1055	>	case FF_EAM:
1056	>	the_ff = new EAM_FF();
1057	>	break;
1058	>
1059	>	default:
1060	>	sprintf(painCave.errMsg,
1061	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1062		painCave.isFatal = 1;
1063		simError();
1064	+	}
1065	+
1066	+	#ifdef IS_MPI
1067	+	strcpy(checkPointMsg, "ForceField creation successful");
1068	+	MPIcheckPoint();
1069	+	#endif // is_mpi
1070	+	}
1071	+
1072	+
1073	+	void SimSetup::compList(void){
1074	+	int i;
1075	+	char* id;
1076	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1077	+	LinkedMolStamp* currentStamp = NULL;
1078	+	comp_stamps = new MoleculeStamp * [n_components];
1079	+
1080	+	// make an array of molecule stamps that match the components used.
1081	+	// also extract the used stamps out into a separate linked list
1082	+
1083	+	for (i = 0; i < nInfo; i++){
1084	+	info[i].nComponents = n_components;
1085	+	info[i].componentsNmol = components_nmol;
1086	+	info[i].compStamps = comp_stamps;
1087	+	info[i].headStamp = headStamp;
1088	+	}
1089	+
1090	+
1091	+	for (i = 0; i < n_components; i++){
1092	+	id = the_components[i]->getType();
1093	+	comp_stamps[i] = NULL;
1094	+
1095	+	// check to make sure the component isn't already in the list
1096	+
1097	+	comp_stamps[i] = headStamp->match(id);
1098	+	if (comp_stamps[i] == NULL){
1099	+	// extract the component from the list;
1100	+
1101	+	currentStamp = stamps->extractMolStamp(id);
1102	+	if (currentStamp == NULL){
1103	+	sprintf(painCave.errMsg,
1104	+	"SimSetup error: Component \"%s\" was not found in the "
1105	+	"list of declared molecules\n",
1106	+	id);
1107	+	painCave.isFatal = 1;
1108	+	simError();
1109	+	}
1110	+
1111	+	headStamp->add(currentStamp);
1112	+	comp_stamps[i] = headStamp->match(id);
1113		}
1114	+	}
1115
1116	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1117	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1118	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1116	>	#ifdef IS_MPI
1117	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1118	>	MPIcheckPoint();
1119	>	#endif // is_mpi
1120	>	}
1121
1122	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1122	>	void SimSetup::calcSysValues(void){
1123	>	int i;
1124
1125	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1125	>	int* molMembershipArray;
1126
1127	<	rotMat[0][0] = 1.0;
1128	<	rotMat[0][1] = 0.0;
1129	<	rotMat[0][2] = 0.0;
1127	>	tot_atoms = 0;
1128	>	tot_bonds = 0;
1129	>	tot_bends = 0;
1130	>	tot_torsions = 0;
1131	>	for (i = 0; i < n_components; i++){
1132	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1133	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1134	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1135	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1136	>	}
1137
1138	<	rotMat[1][0] = 0.0;
1139	<	rotMat[1][1] = 1.0;
1101	<	rotMat[1][2] = 0.0;
1138	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1139	>	molMembershipArray = new int[tot_atoms];
1140
1141	<	rotMat[2][0] = 0.0;
1142	<	rotMat[2][1] = 0.0;
1143	<	rotMat[2][2] = 1.0;
1141	>	for (i = 0; i < nInfo; i++){
1142	>	info[i].n_atoms = tot_atoms;
1143	>	info[i].n_bonds = tot_bonds;
1144	>	info[i].n_bends = tot_bends;
1145	>	info[i].n_torsions = tot_torsions;
1146	>	info[i].n_SRI = tot_SRI;
1147	>	info[i].n_mol = tot_nmol;
1148
1149	<	dAtom->setA( rotMat );
1149	>	info[i].molMembershipArray = molMembershipArray;
1150	>	}
1151	>	}
1152	>
1153	>	#ifdef IS_MPI
1154	>
1155	>	void SimSetup::mpiMolDivide(void){
1156	>	int i, j, k;
1157	>	int localMol, allMol;
1158	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1159	>
1160	>	mpiSim = new mpiSimulation(info);
1161	>
1162	>	globalIndex = mpiSim->divideLabor();
1163	>
1164	>	// set up the local variables
1165	>
1166	>	mol2proc = mpiSim->getMolToProcMap();
1167	>	molCompType = mpiSim->getMolComponentType();
1168	>
1169	>	allMol = 0;
1170	>	localMol = 0;
1171	>	local_atoms = 0;
1172	>	local_bonds = 0;
1173	>	local_bends = 0;
1174	>	local_torsions = 0;
1175	>	globalAtomIndex = 0;
1176	>
1177	>
1178	>	for (i = 0; i < n_components; i++){
1179	>	for (j = 0; j < components_nmol[i]; j++){
1180	>	if (mol2proc[allMol] == worldRank){
1181	>	local_atoms += comp_stamps[i]->getNAtoms();
1182	>	local_bonds += comp_stamps[i]->getNBonds();
1183	>	local_bends += comp_stamps[i]->getNBends();
1184	>	local_torsions += comp_stamps[i]->getNTorsions();
1185	>	localMol++;
1186	>	}
1187	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1188	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1189	>	globalAtomIndex++;
1190	>	}
1191	>
1192	>	allMol++;
1193		}
1194	+	}
1195	+	local_SRI = local_bonds + local_bends + local_torsions;
1196
1197	<	current_atom_ndx++;
1197	>	info[0].n_atoms = mpiSim->getMyNlocal();
1198	>
1199	>	if (local_atoms != info[0].n_atoms){
1200	>	sprintf(painCave.errMsg,
1201	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1202	>	" localAtom (%d) are not equal.\n",
1203	>	info[0].n_atoms, local_atoms);
1204	>	painCave.isFatal = 1;
1205	>	simError();
1206		}
1207
1208	<	current_mol++;
1209	<	current_comp_mol++;
1208	>	info[0].n_bonds = local_bonds;
1209	>	info[0].n_bends = local_bends;
1210	>	info[0].n_torsions = local_torsions;
1211	>	info[0].n_SRI = local_SRI;
1212	>	info[0].n_mol = localMol;
1213
1214	<	if( current_comp_mol >= components_nmol[current_comp] ){
1214	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1215	>	MPIcheckPoint();
1216	>	}
1217
1218	<	current_comp_mol = 0;
1219	<	current_comp++;
1218	>	#endif // is_mpi
1219	>
1220	>
1221	>	void SimSetup::makeSysArrays(void){
1222	>
1223	>	#ifndef IS_MPI
1224	>	int k, j;
1225	>	#endif // is_mpi
1226	>	int i, l;
1227	>
1228	>	Atom** the_atoms;
1229	>	Molecule* the_molecules;
1230	>	Exclude** the_excludes;
1231	>
1232	>
1233	>	for (l = 0; l < nInfo; l++){
1234	>	// create the atom and short range interaction arrays
1235	>
1236	>	the_atoms = new Atom * [info[l].n_atoms];
1237	>	the_molecules = new Molecule[info[l].n_mol];
1238	>	int molIndex;
1239	>
1240	>	// initialize the molecule's stampID's
1241	>
1242	>	#ifdef IS_MPI
1243	>
1244	>
1245	>	molIndex = 0;
1246	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1247	>	if (mol2proc[i] == worldRank){
1248	>	the_molecules[molIndex].setStampID(molCompType[i]);
1249	>	the_molecules[molIndex].setMyIndex(molIndex);
1250	>	the_molecules[molIndex].setGlobalIndex(i);
1251	>	molIndex++;
1252	>	}
1253	>	}
1254	>
1255	>	#else // is_mpi
1256	>
1257	>	molIndex = 0;
1258	>	globalAtomIndex = 0;
1259	>	for (i = 0; i < n_components; i++){
1260	>	for (j = 0; j < components_nmol[i]; j++){
1261	>	the_molecules[molIndex].setStampID(i);
1262	>	the_molecules[molIndex].setMyIndex(molIndex);
1263	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1264	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1265	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1266	>	globalAtomIndex++;
1267	>	}
1268	>	molIndex++;
1269	>	}
1270	>	}
1271	>
1272	>
1273	>	#endif // is_mpi
1274	>
1275	>
1276	>	if (info[l].n_SRI){
1277	>	Exclude::createArray(info[l].n_SRI);
1278	>	the_excludes = new Exclude * [info[l].n_SRI];
1279	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1280	>	the_excludes[ex] = new Exclude(ex);
1281	>	}
1282	>	info[l].globalExcludes = new int;
1283	>	info[l].n_exclude = info[l].n_SRI;
1284	>	}
1285	>	else{
1286	>	Exclude::createArray(1);
1287	>	the_excludes = new Exclude * ;
1288	>	the_excludes[0] = new Exclude(0);
1289	>	the_excludes[0]->setPair(0, 0);
1290	>	info[l].globalExcludes = new int;
1291	>	info[l].globalExcludes[0] = 0;
1292	>	info[l].n_exclude = 0;
1293	>	}
1294	>
1295	>	// set the arrays into the SimInfo object
1296	>
1297	>	info[l].atoms = the_atoms;
1298	>	info[l].molecules = the_molecules;
1299	>	info[l].nGlobalExcludes = 0;
1300	>	info[l].excludes = the_excludes;
1301	>
1302	>	the_ff->setSimInfo(info);
1303	>	}
1304	>	}
1305	>
1306	>	void SimSetup::makeIntegrator(void){
1307	>	int k;
1308	>
1309	>	NVE<RealIntegrator>* myNVE = NULL;
1310	>	NVT<RealIntegrator>* myNVT = NULL;
1311	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1312	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1313	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1314	>
1315	>	for (k = 0; k < nInfo; k++){
1316	>	switch (ensembleCase){
1317	>	case NVE_ENS:
1318	>	if (globals->haveZconstraints()){
1319	>	setupZConstraint(info[k]);
1320	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1321	>	}
1322	>	else{
1323	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1324	>	}
1325	>
1326	>	info->the_integrator = myNVE;
1327	>	break;
1328	>
1329	>	case NVT_ENS:
1330	>	if (globals->haveZconstraints()){
1331	>	setupZConstraint(info[k]);
1332	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1333	>	}
1334	>	else
1335	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1336	>
1337	>	myNVT->setTargetTemp(globals->getTargetTemp());
1338	>
1339	>	if (globals->haveTauThermostat())
1340	>	myNVT->setTauThermostat(globals->getTauThermostat());
1341	>	else{
1342	>	sprintf(painCave.errMsg,
1343	>	"SimSetup error: If you use the NVT\n"
1344	>	"    ensemble, you must set tauThermostat.\n");
1345	>	painCave.isFatal = 1;
1346	>	simError();
1347	>	}
1348	>
1349	>	info->the_integrator = myNVT;
1350	>	break;
1351	>
1352	>	case NPTi_ENS:
1353	>	if (globals->haveZconstraints()){
1354	>	setupZConstraint(info[k]);
1355	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1356	>	}
1357	>	else
1358	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1359	>
1360	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1361	>
1362	>	if (globals->haveTargetPressure())
1363	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1364	>	else{
1365	>	sprintf(painCave.errMsg,
1366	>	"SimSetup error: If you use a constant pressure\n"
1367	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1368	>	painCave.isFatal = 1;
1369	>	simError();
1370	>	}
1371	>
1372	>	if (globals->haveTauThermostat())
1373	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1374	>	else{
1375	>	sprintf(painCave.errMsg,
1376	>	"SimSetup error: If you use an NPT\n"
1377	>	"    ensemble, you must set tauThermostat.\n");
1378	>	painCave.isFatal = 1;
1379	>	simError();
1380	>	}
1381	>
1382	>	if (globals->haveTauBarostat())
1383	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1384	>	else{
1385	>	sprintf(painCave.errMsg,
1386	>	"SimSetup error: If you use an NPT\n"
1387	>	"    ensemble, you must set tauBarostat.\n");
1388	>	painCave.isFatal = 1;
1389	>	simError();
1390	>	}
1391	>
1392	>	info->the_integrator = myNPTi;
1393	>	break;
1394	>
1395	>	case NPTf_ENS:
1396	>	if (globals->haveZconstraints()){
1397	>	setupZConstraint(info[k]);
1398	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1399	>	}
1400	>	else
1401	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1402	>
1403	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1404	>
1405	>	if (globals->haveTargetPressure())
1406	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1407	>	else{
1408	>	sprintf(painCave.errMsg,
1409	>	"SimSetup error: If you use a constant pressure\n"
1410	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1411	>	painCave.isFatal = 1;
1412	>	simError();
1413	>	}
1414	>
1415	>	if (globals->haveTauThermostat())
1416	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1417	>	else{
1418	>	sprintf(painCave.errMsg,
1419	>	"SimSetup error: If you use an NPT\n"
1420	>	"    ensemble, you must set tauThermostat.\n");
1421	>	painCave.isFatal = 1;
1422	>	simError();
1423	>	}
1424	>
1425	>	if (globals->haveTauBarostat())
1426	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1427	>	else{
1428	>	sprintf(painCave.errMsg,
1429	>	"SimSetup error: If you use an NPT\n"
1430	>	"    ensemble, you must set tauBarostat.\n");
1431	>	painCave.isFatal = 1;
1432	>	simError();
1433	>	}
1434	>
1435	>	info->the_integrator = myNPTf;
1436	>	break;
1437	>
1438	>	case NPTxyz_ENS:
1439	>	if (globals->haveZconstraints()){
1440	>	setupZConstraint(info[k]);
1441	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1442	>	}
1443	>	else
1444	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1445	>
1446	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1447	>
1448	>	if (globals->haveTargetPressure())
1449	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1450	>	else{
1451	>	sprintf(painCave.errMsg,
1452	>	"SimSetup error: If you use a constant pressure\n"
1453	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1454	>	painCave.isFatal = 1;
1455	>	simError();
1456	>	}
1457	>
1458	>	if (globals->haveTauThermostat())
1459	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1460	>	else{
1461	>	sprintf(painCave.errMsg,
1462	>	"SimSetup error: If you use an NPT\n"
1463	>	"    ensemble, you must set tauThermostat.\n");
1464	>	painCave.isFatal = 1;
1465	>	simError();
1466	>	}
1467	>
1468	>	if (globals->haveTauBarostat())
1469	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1470	>	else{
1471	>	sprintf(painCave.errMsg,
1472	>	"SimSetup error: If you use an NPT\n"
1473	>	"    ensemble, you must set tauBarostat.\n");
1474	>	painCave.isFatal = 1;
1475	>	simError();
1476	>	}
1477	>
1478	>	info->the_integrator = myNPTxyz;
1479	>	break;
1480	>
1481	>	default:
1482	>	sprintf(painCave.errMsg,
1483	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1484	>	painCave.isFatal = 1;
1485	>	simError();
1486	>	}
1487		}
1488		}
1489	+
1490	+	void SimSetup::initFortran(void){
1491	+	info[0].refreshSim();
1492	+
1493	+	if (!strcmp(info[0].mixingRule, "standard")){
1494	+	the_ff->initForceField(LB_MIXING_RULE);
1495	+	}
1496	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1497	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1498	+	}
1499	+	else{
1500	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1501	+	info[0].mixingRule);
1502	+	painCave.isFatal = 1;
1503	+	simError();
1504	+	}
1505	+
1506	+
1507	+	#ifdef IS_MPI
1508	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1509	+	MPIcheckPoint();
1510	+	#endif // is_mpi
1511	+	}
1512	+
1513	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1514	+	int nZConstraints;
1515	+	ZconStamp** zconStamp;
1516	+
1517	+	if (globals->haveZconstraintTime()){
1518	+	//add sample time of z-constraint  into SimInfo's property list
1519	+	DoubleData* zconsTimeProp = new DoubleData();
1520	+	zconsTimeProp->setID(ZCONSTIME_ID);
1521	+	zconsTimeProp->setData(globals->getZconsTime());
1522	+	theInfo.addProperty(zconsTimeProp);
1523	+	}
1524	+	else{
1525	+	sprintf(painCave.errMsg,
1526	+	"ZConstraint error: If you use an ZConstraint\n"
1527	+	" , you must set sample time.\n");
1528	+	painCave.isFatal = 1;
1529	+	simError();
1530	+	}
1531	+
1532	+	//push zconsTol into siminfo, if user does not specify
1533	+	//value for zconsTol, a default value will be used
1534	+	DoubleData* zconsTol = new DoubleData();
1535	+	zconsTol->setID(ZCONSTOL_ID);
1536	+	if (globals->haveZconsTol()){
1537	+	zconsTol->setData(globals->getZconsTol());
1538	+	}
1539	+	else{
1540	+	double defaultZConsTol = 0.01;
1541	+	sprintf(painCave.errMsg,
1542	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1543	+	" , default value %f is used.\n",
1544	+	defaultZConsTol);
1545	+	painCave.isFatal = 0;
1546	+	simError();
1547	+
1548	+	zconsTol->setData(defaultZConsTol);
1549	+	}
1550	+	theInfo.addProperty(zconsTol);
1551	+
1552	+	//set Force Subtraction Policy
1553	+	StringData* zconsForcePolicy = new StringData();
1554	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1555	+
1556	+	if (globals->haveZconsForcePolicy()){
1557	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1558	+	}
1559	+	else{
1560	+	sprintf(painCave.errMsg,
1561	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1562	+	"PolicyByMass is used\n");
1563	+	painCave.isFatal = 0;
1564	+	simError();
1565	+	zconsForcePolicy->setData("BYMASS");
1566	+	}
1567	+
1568	+	theInfo.addProperty(zconsForcePolicy);
1569	+
1570	+	//Determine the name of ouput file and add it into SimInfo's property list
1571	+	//Be careful, do not use inFileName, since it is a pointer which
1572	+	//point to a string at master node, and slave nodes do not contain that string
1573	+
1574	+	string zconsOutput(theInfo.finalName);
1575	+
1576	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1577	+
1578	+	StringData* zconsFilename = new StringData();
1579	+	zconsFilename->setID(ZCONSFILENAME_ID);
1580	+	zconsFilename->setData(zconsOutput);
1581	+
1582	+	theInfo.addProperty(zconsFilename);
1583	+
1584	+	//setup index, pos and other parameters of z-constraint molecules
1585	+	nZConstraints = globals->getNzConstraints();
1586	+	theInfo.nZconstraints = nZConstraints;
1587	+
1588	+	zconStamp = globals->getZconStamp();
1589	+	ZConsParaItem tempParaItem;
1590	+
1591	+	ZConsParaData* zconsParaData = new ZConsParaData();
1592	+	zconsParaData->setID(ZCONSPARADATA_ID);
1593	+
1594	+	for (int i = 0; i < nZConstraints; i++){
1595	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1596	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1597	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1598	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1599	+
1600	+	zconsParaData->addItem(tempParaItem);
1601	+	}
1602	+
1603	+	//check the uniqueness of index
1604	+	if(!zconsParaData->isIndexUnique()){
1605	+	sprintf(painCave.errMsg,
1606	+	"ZConstraint Error: molIndex is not unique\n");
1607	+	painCave.isFatal = 1;
1608	+	simError();
1609	+	}
1610	+
1611	+	//sort the parameters by index of molecules
1612	+	zconsParaData->sortByIndex();
1613	+
1614	+	//push data into siminfo, therefore, we can retrieve later
1615	+	theInfo.addProperty(zconsParaData);
1616	+	}

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