ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing:
trunk/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 407 by mmeineke, Wed Mar 26 20:22:02 2003 UTC vs.
branches/new-templateless/OOPSE/libmdtools/SimSetup.cpp (file contents), Revision 851 by mmeineke, Wed Nov 5 19:18:17 2003 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <stdlib.h>
2		#include <iostream>
3	<	#include <cmath>
3	>	#include <math.h>
4	>	#include <string.h>
5	>	#include <sprng.h>
6
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" ) ) the_ff = new TraPPEFF();
112	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
113	<	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	<	}
111	>	if( !(globals->getUseInitTime()) )
112	>	info[0].currentTime = 0.0;
113	>	}
114
115	<	#ifdef IS_MPI
104	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#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
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	<	the_sris = new SRI*[simnfo->n_SRI];
311	<	the_excludes = new int[2 * simnfo->n_SRI];
312	<	simnfo->globalExcludes = new int;
313	<	simnfo->n_exclude = tot_SRI;
314	<	}
315	<	else{
316	<
317	<	the_excludes = new int[2];
318	<	the_excludes[0] = 0;
319	<	the_excludes[1] = 0;
320	<	simnfo->globalExcludes = new int;
321	<	simnfo->globalExcludes[0] = 0;
246	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
247	>	#else  // isn't MPI
248
249	<	simnfo->n_exclude = 1;
250	<	}
249	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
250	>	#endif  //is_mpi
251	>	}
252	>	excludeOffset += molInfo.nBonds;
253
254	<	// set the arrays into the SimInfo object
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	<	simnfo->atoms = the_atoms;
262	<	simnfo->sr_interactions = the_sris;
263	<	simnfo->nGlobalExcludes = 0;
331	<	simnfo->excludes = the_excludes;
261	>	if (currentBend->haveExtras()){
262	>	extras = currentBend->getExtras();
263	>	current_extra = extras;
264
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	<	// get some of the tricky things that may still be in the globals
273	>	case 1:
274	>	theBends[j].ghost = (int) current_extra->getDouble() +
275	>	atomOffset;
276	>	theBends[j].isGhost = 1;
277	>	break;
278
279	<
280	<	if( the_globals->haveBox() ){
281	<	simnfo->box_x = the_globals->getBox();
282	<	simnfo->box_y = the_globals->getBox();
283	<	simnfo->box_z = the_globals->getBox();
284	<	}
285	<	else if( the_globals->haveDensity() ){
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	<	double vol;
299	<	vol = (double)tot_nmol / the_globals->getDensity();
300	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
347	<	simnfo->box_y = simnfo->box_x;
348	<	simnfo->box_z = simnfo->box_x;
349	<	}
350	<	else{
351	<	if( !the_globals->haveBoxX() ){
352	<	sprintf( painCave.errMsg,
353	<	"SimSetup error, no periodic BoxX size given.\n" );
354	<	painCave.isFatal = 1;
355	<	simError();
356	<	}
357	<	simnfo->box_x = the_globals->getBoxX();
298	>	current_extra = current_extra->getNext();
299	>	}
300	>	}
301
302	<	if( !the_globals->haveBoxY() ){
303	<	sprintf( painCave.errMsg,
304	<	"SimSetup error, no periodic BoxY size given.\n" );
305	<	painCave.isFatal = 1;
306	<	simError();
307	<	}
308	<	simnfo->box_y = the_globals->getBoxY();
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	<	if( !the_globals->haveBoxZ() ){
312	<	sprintf( painCave.errMsg,
313	<	"SimSetup error, no periodic BoxZ size given.\n" );
314	<	painCave.isFatal = 1;
315	<	simError();
316	<	}
317	<	simnfo->box_z = the_globals->getBoxZ();
318	<	}
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	+	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	+	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	+	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	<	strcpy( checkPointMsg, "Box size set up" );
348	<	MPIcheckPoint();
349	<	#endif // 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
382	–	// initialize the arrays
359
360	<	the_ff->setSimInfo( simnfo );
360	>	// send the arrays off to the forceField for init.
361
362	<	makeAtoms();
363	<	simnfo->identArray = new int[simnfo->n_atoms];
364	<	for(i=0; i<simnfo->n_atoms; i++){
365	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
366	<	}
391	<
392	<	if( tot_bonds ){
393	<	makeBonds();
394	<	}
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
396	–	if( tot_bends ){
397	–	makeBends();
398	–	}
368
369	<	if( tot_torsions ){
401	<	makeTorsions();
402	<	}
369	>	info[k].molecules[i].initialize(molInfo);
370
371
372	<	if (the_globals->getUseRF() ) {
373	<	simnfo->useReactionField = 1;
374	<
375	<	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();
372	>	atomOffset += molInfo.nAtoms;
373	>	delete[] theBonds;
374	>	delete[] theBends;
375	>	delete[] theTorsions;
376		}
377	+	}
378
424	–	if( !the_globals->haveEST() ){
425	–	sprintf( painCave.errMsg,
426	–	"SimSetup Warning: using default value of 0.05 * the "
427	–	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
428	–	);
429	–	painCave.isFatal = 0;
430	–	simError();
431	–	simnfo->est = 0.05 * simnfo->ecr;
432	–	} else {
433	–	simnfo->est        = the_globals->getEST();
434	–	}
435	–
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	–	}
478	–
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
425	<
426	<
523	<
524	<
525	<
526	<
527	<
528	<	#ifdef IS_MPI
529	<	if( worldRank == 0 ){
530	<	#endif // is_mpi
531	<
532	<	if( the_globals->haveFinalConfig() ){
533	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
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		}
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" );
542	–	}
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	–	}
558	–	}
559	–
560	–	// make the sample and status out names
561	–
562	–	strcpy( simnfo->sampleName, inFileName );
563	–	char* endTest;
564	–	int nameLength = strlen( simnfo->sampleName );
565	–	endTest = &(simnfo->sampleName[nameLength - 5]);
566	–	if( !strcmp( endTest, ".bass" ) ){
567	–	strcpy( endTest, ".dump" );
568	–	}
569	–	else if( !strcmp( endTest, ".BASS" ) ){
570	–	strcpy( endTest, ".dump" );
571	–	}
572	–	else{
573	–	endTest = &(simnfo->sampleName[nameLength - 4]);
574	–	if( !strcmp( endTest, ".bss" ) ){
575	–	strcpy( endTest, ".dump" );
576	–	}
577	–	else if( !strcmp( endTest, ".mdl" ) ){
578	–	strcpy( endTest, ".dump" );
579	–	}
580	–	else{
581	–	strcat( simnfo->sampleName, ".dump" );
582	–	}
583	–	}
584	–
585	–	strcpy( simnfo->statusName, inFileName );
586	–	nameLength = strlen( simnfo->statusName );
587	–	endTest = &(simnfo->statusName[nameLength - 5]);
588	–	if( !strcmp( endTest, ".bass" ) ){
589	–	strcpy( endTest, ".stat" );
590	–	}
591	–	else if( !strcmp( endTest, ".BASS" ) ){
592	–	strcpy( endTest, ".stat" );
593	–	}
594	–	else{
595	–	endTest = &(simnfo->statusName[nameLength - 4]);
596	–	if( !strcmp( endTest, ".bss" ) ){
597	–	strcpy( endTest, ".stat" );
598	–	}
599	–	else if( !strcmp( endTest, ".mdl" ) ){
600	–	strcpy( endTest, ".stat" );
601	–	}
602	–	else{
603	–	strcat( simnfo->statusName, ".stat" );
604	–	}
605	–	}
606	–
607	–	#ifdef IS_MPI
428		}
609	–	#endif // is_mpi
610	–
611	–	// 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;
617	–	}
429		else{
430	<	simnfo->sampleTime = the_globals->getRunTime();
431	<	simnfo->statusTime = simnfo->sampleTime;
432	<	simnfo->thermalTime = simnfo->sampleTime;
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	<	if( the_globals->haveStatusTime() ){
437	<	simnfo->statusTime = the_globals->getStatusTime();
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	>	}
452	>	}
453		}
454
455	<	if( the_globals->haveThermalTime() ){
456	<	simnfo->thermalTime = the_globals->getThermalTime();
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	>	}
495		}
496
497	<	// check for the temperature set flag
497	>	for (i = 0; i < info[0].n_atoms; i++){
498	>	info[0].atoms[i]->setVel(vel);
499	>	}
500	>	}
501
502	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
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	<	//   // make the longe range forces and the integrator
522	>	pos[0] = x + current_atom->getPosX();
523	>	pos[1] = y + current_atom->getPosY();
524	>	pos[2] = z + current_atom->getPosZ();
525
526	<	//   new AllLong( simnfo );
526	>	info[0].atoms[current_atom_ndx]->setPos(pos);
527
528	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
529	<	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 );
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	<	// initialize the Fortran
540	<
541	<	simnfo->refreshSim();
542	<
543	<	if( !strcmp( simnfo->mixingRule, "standard") ){
544	<	the_ff->initForceField( LB_MIXING_RULE );
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	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
549	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
548	>
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	+
558	+
559	+	void SimSetup::gatherInfo(void){
560	+	int i;
561	+
562	+	ensembleCase = -1;
563	+	ffCase = -1;
564	+
565	+	// set the easy ones first
566	+
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	+
574	+
575	+	// get the forceField
576	+
577	+	strcpy(force_field, globals->getForceField());
578	+
579	+	if (!strcasecmp(force_field, "DUFF")){
580	+	ffCase = FF_DUFF;
581	+	}
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;
678	<	molInit info;
679	<	DirectionalAtom* dAtom;
680	<	AtomStamp* currentAtom;
681	<	BondStamp* currentBond;
682	<	BendStamp* currentBend;
683	<	TorsionStamp* currentTorsion;
684	<
685	<	//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	<
690	<	// init the molecules
634	>	// get the components and calculate the tot_nMol and indvidual n_mol
635
636	<	atomOffset = 0;
637	<	for(i=0; i<simnfo->n_mol; i++){
694	<
695	<	stampID = the_molecules[i].getStampID();
636	>	the_components = globals->getComponents();
637	>	components_nmol = new int[n_components];
638
697	–	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
698	–	info.nBonds    = comp_stamps[stampID]->getNBonds();
699	–	info.nBends    = comp_stamps[stampID]->getNBends();
700	–	info.nTorsions = comp_stamps[stampID]->getNTorsions();
701	–
702	–	info.myAtoms = &the_atoms[atomOffset];
703	–	info.myBonds = new Bond*[info.nBonds];
704	–	info.myBends = new Bend*[info.nBends];
705	–	info.myTorsions = new Torsions*[info.nTorsions];
639
640	<	theBonds = new bond_pair[info.nBonds];
641	<	theBends = new bend_set[info.nBends];
642	<	theTorsions = new torsion_set[info.nTorsions];
710	<
711	<	// make the Atoms
712	<
713	<	for(j=0; j<info.nAtoms; j++){
714	<
715	<	currentAtom = theComponents[stampID]->getAtom( j );
716	<	if( currentAtom->haveOrientation() ){
717	<
718	<	dAtom = new DirectionalAtom(j + atomOffset);
719	<	simnfo->n_oriented++;
720	<	info.myAtoms[j] = dAtom;
721	<
722	<	ux = currentAtom->getOrntX();
723	<	uy = currentAtom->getOrntY();
724	<	uz = currentAtom->getOrntZ();
725	<
726	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
727	<
728	<	u = sqrt( uSqr );
729	<	ux = ux / u;
730	<	uy = uy / u;
731	<	uz = uz / u;
732	<
733	<	dAtom->setSUx( ux );
734	<	dAtom->setSUy( uy );
735	<	dAtom->setSUz( uz );
736	<	}
737	<	else{
738	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
739	<	}
740	<	info.myAtoms[j]->setType( currentAtom->getType() );
741	<
742	<	#ifdef IS_MPI
743	<
744	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
745	<
746	<	#endif // is_mpi
747	<	}
748	<
749	<	// make the bonds
750	<	for(j=0; j<nBonds; j++){
751	<
752	<	currentBond = comp_stamps[stampID]->getBond( j );
753	<	theBonds[j].a = currentBond->getA() + atomOffset;
754	<	theBonds[j].b = currentBond->getB() + atomOffset;
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	<	exI = theBonds[i].a;
645	<	exJ = theBonds[i].b;
646	<
647	<	// exclude_I must always be the smaller of the pair
648	<	if( exI > exJ ){
649	<	tempEx = exI;
650	<	exI = exJ;
651	<	exJ = tempEx;
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		}
765	–	#ifdef IS_MPI
766	–
767	–	the_excludes[index*2] =
768	–	the_atoms[exI]->getGlobalIndex() + 1;
769	–	the_excludes[index*2 + 1] =
770	–	the_atoms[exJ]->getGlobalIndex() + 1;
771	–
772	–	#else  // isn't MPI
773	–
774	–	the_excludes[index*2] =     exI + 1;
775	–	the_excludes[index*2 + 1] = exJ + 1;
776	–	// fortran index from 1 (hence the +1 in the indexing)
654
655	<	#endif  //is_mpi
656	<
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	+	// 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	+	else{
679	+	info[i].sampleTime = globals->getRunTime();
680	+	info[i].statusTime = info[i].sampleTime;
681	+	info[i].thermalTime = info[i].sampleTime;
682	+	}
683
684	+	if (globals->haveStatusTime()){
685	+	info[i].statusTime = globals->getStatusTime();
686	+	}
687
688	+	if (globals->haveThermalTime()){
689	+	info[i].thermalTime = globals->getThermalTime();
690	+	}
691
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 (globals->haveSeed()){
709	+	seedValue = globals->getSeed();
710
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	+	//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 (int i = 0; i < nInfo; i++){
742	+	info[i].setSeed(seedValue);
743	+	}
744
745	+	#ifdef IS_MPI
746	+	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
747	+	MPIcheckPoint();
748	+	#endif // is_mpi
749	+	}
750
751
752	+	void SimSetup::finalInfoCheck(void){
753	+	int index;
754	+	int usesDipoles;
755	+	int i;
756
757	+	for (i = 0; i < nInfo; i++){
758	+	// check electrostatic parameters
759
760	<	void SimSetup::makeAtoms( void ){
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	<	int i, j, k, index;
768	<	double ux, uy, uz, uSqr, u;
769	<	AtomStamp* current_atom;
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	<	DirectionalAtom* dAtom;
803	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
772	>	double theEcr, theEst;
773
774	<	lMolIndex = 0;
775	<	molIndex = 0;
807	<	index = 0;
808	<	for( i=0; i<n_components; i++ ){
774	>	if (globals->getUseRF()){
775	>	info[i].useReactionField = 1;
776
777	<	for( j=0; j<components_nmol[i]; j++ ){
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	<	#ifdef IS_MPI
797	<	if( mpiSim->getMyMolStart() <= molIndex &&
798	<	molIndex <= mpiSim->getMyMolEnd() ){
799	<	#endif // is_mpi
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	<	molStart = index;
818	<	nMemb = comp_stamps[i]->getNAtoms();
819	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
820	<
821	<	current_atom = comp_stamps[i]->getAtom( k );
822	<	if( current_atom->haveOrientation() ){
823	<
824	<	dAtom = new DirectionalAtom(index);
825	<	simnfo->n_oriented++;
826	<	the_atoms[index] = dAtom;
827	<
828	<	ux = current_atom->getOrntX();
829	<	uy = current_atom->getOrntY();
830	<	uz = current_atom->getOrntZ();
831	<
832	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
833	<
834	<	u = sqrt( uSqr );
835	<	ux = ux / u;
836	<	uy = uy / u;
837	<	uz = uz / u;
838	<
839	<	dAtom->setSUx( ux );
840	<	dAtom->setSUy( uy );
841	<	dAtom->setSUz( uz );
842	<	}
843	<	else{
844	<	the_atoms[index] = new GeneralAtom(index);
845	<	}
846	<	the_atoms[index]->setType( current_atom->getType() );
847	<	the_atoms[index]->setIndex( index );
848	<
849	<	// increment the index and repeat;
850	<	index++;
851	<	}
852	<
853	<	molEnd = index -1;
854	<	the_molecules[lMolIndex].setNMembers( nMemb );
855	<	the_molecules[lMolIndex].setStartAtom( molStart );
856	<	the_molecules[lMolIndex].setEndAtom( molEnd );
857	<	the_molecules[lMolIndex].setStampID( i );
858	<	lMolIndex++;
808	>	info[i].setDefaultEcr(theEcr, theEst);
809
810	<	#ifdef IS_MPI
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	<	#endif //is_mpi
863	<
864	<	molIndex++;
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	+	info[i].checkCutOffs();
857		}
858
859		#ifdef IS_MPI
860	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
861	<
862	<	delete[] globalIndex;
872	<
873	<	mpiSim->mpiRefresh();
874	<	#endif //IS_MPI
875	<
876	<	the_ff->initializeAtoms();
860	>	strcpy(checkPointMsg, "post processing checks out");
861	>	MPIcheckPoint();
862	>	#endif // is_mpi
863		}
864
865	<	void SimSetup::makeBonds( void ){
865	>	void SimSetup::initSystemCoords(void){
866	>	int i;
867
868	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
882	<	bond_pair* the_bonds;
883	<	BondStamp* current_bond;
868	>	char* inName;
869
870	<	the_bonds = new bond_pair[tot_bonds];
886	<	index = 0;
887	<	offset = 0;
888	<	molIndex = 0;
870	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
871
872	<	for( i=0; i<n_components; i++ ){
872	>	for (i = 0; i < info[0].n_atoms; i++)
873	>	info[0].atoms[i]->setCoords();
874
875	<	for( j=0; j<components_nmol[i]; j++ ){
876	<
875	>	if (globals->haveInitialConfig()){
876	>	InitializeFromFile* fileInit;
877	>	#ifdef IS_MPI // is_mpi
878	>	if (worldRank == 0){
879	>	#endif //is_mpi
880	>	inName = globals->getInitialConfig();
881	>	fileInit = new InitializeFromFile(inName);
882		#ifdef IS_MPI
883	<	if( mpiSim->getMyMolStart() <= molIndex &&
884	<	molIndex <= mpiSim->getMyMolEnd() ){
885	<	#endif // is_mpi
886	<
887	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
900	<
901	<	current_bond = comp_stamps[i]->getBond( k );
902	<	the_bonds[index].a = current_bond->getA() + offset;
903	<	the_bonds[index].b = current_bond->getB() + offset;
883	>	}
884	>	else
885	>	fileInit = new InitializeFromFile(NULL);
886	>	#endif
887	>	fileInit->readInit(info); // default velocities on
888
889	<	exI = the_bonds[index].a;
890	<	exJ = the_bonds[index].b;
889	>	delete fileInit;
890	>	}
891	>	else{
892	>	#ifdef IS_MPI
893
894	<	// exclude_I must always be the smaller of the pair
909	<	if( exI > exJ ){
910	<	tempEx = exI;
911	<	exI = exJ;
912	<	exJ = tempEx;
913	<	}
894	>	// no init from bass
895
896	<
897	<	#ifdef IS_MPI
896	>	sprintf(painCave.errMsg,
897	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
898	>	painCave.isFatal = 1;;
899	>	simError();
900
901	<	the_excludes[index*2] =
919	<	the_atoms[exI]->getGlobalIndex() + 1;
920	<	the_excludes[index*2 + 1] =
921	<	the_atoms[exJ]->getGlobalIndex() + 1;
901	>	#else
902
903	<	#else  // isn't MPI
904	<
905	<	the_excludes[index*2] =     exI + 1;
906	<	the_excludes[index*2 + 1] = exJ + 1;
927	<	// fortran index from 1 (hence the +1 in the indexing)
928	<	#endif  //is_mpi
929	<
930	<	// increment the index and repeat;
931	<	index++;
932	<	}
933	<	offset += comp_stamps[i]->getNAtoms();
934	<
935	<	#ifdef IS_MPI
936	<	}
937	<	#endif //is_mpi
938	<
939	<	molIndex++;
940	<	}
903	>	initFromBass();
904	>
905	>
906	>	#endif
907		}
908
909	<	the_ff->initializeBonds( the_bonds );
909	>	#ifdef IS_MPI
910	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
911	>	MPIcheckPoint();
912	>	#endif // is_mpi
913		}
914
946	–	void SimSetup::makeBends( void ){
915
916	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
917	<	bend_set* the_bends;
950	<	BendStamp* current_bend;
951	<	LinkedAssign* extras;
952	<	LinkedAssign* current_extra;
953	<
916	>	void SimSetup::makeOutNames(void){
917	>	int k;
918
955	–	the_bends = new bend_set[tot_bends];
956	–	index = 0;
957	–	offset = 0;
958	–	molIndex = 0;
959	–	for( i=0; i<n_components; i++ ){
919
920	<	for( j=0; j<components_nmol[i]; j++ ){
962	<
920	>	for (k = 0; k < nInfo; k++){
921		#ifdef IS_MPI
922	<	if( mpiSim->getMyMolStart() <= molIndex &&
923	<	molIndex <= mpiSim->getMyMolEnd() ){
966	<	#endif // is_mpi
922	>	if (worldRank == 0){
923	>	#endif // is_mpi
924
925	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
926	<
927	<	current_bend = comp_stamps[i]->getBend( k );
928	<	the_bends[index].a = current_bend->getA() + offset;
929	<	the_bends[index].b = current_bend->getB() + offset;
930	<	the_bends[index].c = current_bend->getC() + offset;
931	<
932	<	if( current_bend->haveExtras() ){
933	<
934	<	extras = current_bend->getExtras();
935	<	current_extra = extras;
936	<
937	<	while( current_extra != NULL ){
938	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
939	<
940	<	switch( current_extra->getType() ){
941	<
942	<	case 0:
943	<	the_bends[index].ghost =
944	<	current_extra->getInt() + offset;
945	<	the_bends[index].isGhost = 1;
946	<	break;
947	<
948	<	case 1:
949	<	the_bends[index].ghost =
950	<	(int)current_extra->getDouble() + offset;
951	<	the_bends[index].isGhost = 1;
995	<	break;
996	<
997	<	default:
998	<	sprintf( painCave.errMsg,
999	<	"SimSetup Error: ghostVectorSource was neiter a "
1000	<	"double nor an int.\n"
1001	<	"-->Bend[%d] in %s\n",
1002	<	k, comp_stamps[i]->getID() );
1003	<	painCave.isFatal = 1;
1004	<	simError();
1005	<	}
1006	<	}
1007	<
1008	<	else{
1009	<
1010	<	sprintf( painCave.errMsg,
1011	<	"SimSetup Error: unhandled bend assignment:\n"
1012	<	"    -->%s in Bend[%d] in %s\n",
1013	<	current_extra->getlhs(),
1014	<	k, comp_stamps[i]->getID() );
1015	<	painCave.isFatal = 1;
1016	<	simError();
1017	<	}
1018	<
1019	<	current_extra = current_extra->getNext();
1020	<	}
1021	<	}
1022	<
1023	<	if( !the_bends[index].isGhost ){
1024	<
1025	<	exI = the_bends[index].a;
1026	<	exJ = the_bends[index].c;
1027	<	}
1028	<	else{
1029	<
1030	<	exI = the_bends[index].a;
1031	<	exJ = the_bends[index].b;
1032	<	}
1033	<
1034	<	// exclude_I must always be the smaller of the pair
1035	<	if( exI > exJ ){
1036	<	tempEx = exI;
1037	<	exI = exJ;
1038	<	exJ = tempEx;
1039	<	}
925	>	if (globals->haveFinalConfig()){
926	>	strcpy(info[k].finalName, globals->getFinalConfig());
927	>	}
928	>	else{
929	>	strcpy(info[k].finalName, inFileName);
930	>	char* endTest;
931	>	int nameLength = strlen(info[k].finalName);
932	>	endTest = &(info[k].finalName[nameLength - 5]);
933	>	if (!strcmp(endTest, ".bass")){
934	>	strcpy(endTest, ".eor");
935	>	}
936	>	else if (!strcmp(endTest, ".BASS")){
937	>	strcpy(endTest, ".eor");
938	>	}
939	>	else{
940	>	endTest = &(info[k].finalName[nameLength - 4]);
941	>	if (!strcmp(endTest, ".bss")){
942	>	strcpy(endTest, ".eor");
943	>	}
944	>	else if (!strcmp(endTest, ".mdl")){
945	>	strcpy(endTest, ".eor");
946	>	}
947	>	else{
948	>	strcat(info[k].finalName, ".eor");
949	>	}
950	>	}
951	>	}
952
953	+	// make the sample and status out names
954
955	<	#ifdef IS_MPI
955	>	strcpy(info[k].sampleName, inFileName);
956	>	char* endTest;
957	>	int nameLength = strlen(info[k].sampleName);
958	>	endTest = &(info[k].sampleName[nameLength - 5]);
959	>	if (!strcmp(endTest, ".bass")){
960	>	strcpy(endTest, ".dump");
961	>	}
962	>	else if (!strcmp(endTest, ".BASS")){
963	>	strcpy(endTest, ".dump");
964	>	}
965	>	else{
966	>	endTest = &(info[k].sampleName[nameLength - 4]);
967	>	if (!strcmp(endTest, ".bss")){
968	>	strcpy(endTest, ".dump");
969	>	}
970	>	else if (!strcmp(endTest, ".mdl")){
971	>	strcpy(endTest, ".dump");
972	>	}
973	>	else{
974	>	strcat(info[k].sampleName, ".dump");
975	>	}
976	>	}
977
978	<	the_excludes[(index + tot_bonds)*2] =
979	<	the_atoms[exI]->getGlobalIndex() + 1;
980	<	the_excludes[(index + tot_bonds)*2 + 1] =
981	<	the_atoms[exJ]->getGlobalIndex() + 1;
982	<
1049	<	#else  // isn't MPI
1050	<
1051	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
1052	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1053	<	// fortran index from 1 (hence the +1 in the indexing)
1054	<	#endif  //is_mpi
1055	<
1056	<
1057	<	// increment the index and repeat;
1058	<	index++;
1059	<	}
1060	<	offset += comp_stamps[i]->getNAtoms();
1061	<
1062	<	#ifdef IS_MPI
978	>	strcpy(info[k].statusName, inFileName);
979	>	nameLength = strlen(info[k].statusName);
980	>	endTest = &(info[k].statusName[nameLength - 5]);
981	>	if (!strcmp(endTest, ".bass")){
982	>	strcpy(endTest, ".stat");
983		}
984	<	#endif //is_mpi
984	>	else if (!strcmp(endTest, ".BASS")){
985	>	strcpy(endTest, ".stat");
986	>	}
987	>	else{
988	>	endTest = &(info[k].statusName[nameLength - 4]);
989	>	if (!strcmp(endTest, ".bss")){
990	>	strcpy(endTest, ".stat");
991	>	}
992	>	else if (!strcmp(endTest, ".mdl")){
993	>	strcpy(endTest, ".stat");
994	>	}
995	>	else{
996	>	strcat(info[k].statusName, ".stat");
997	>	}
998	>	}
999
1000	<	molIndex++;
1000	>	#ifdef IS_MPI
1001	>
1002		}
1003	+	#endif // is_mpi
1004		}
1005	+	}
1006
1070	–	#ifdef IS_MPI
1071	–	sprintf( checkPointMsg,
1072	–	"Successfully created the bends list.\n" );
1073	–	MPIcheckPoint();
1074	–	#endif // is_mpi
1075	–
1007
1008	<	the_ff->initializeBends( the_bends );
1009	<	}
1008	>	void SimSetup::sysObjectsCreation(void){
1009	>	int i, k;
1010
1011	<	void SimSetup::makeTorsions( void ){
1011	>	// create the forceField
1012
1013	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1083	<	torsion_set* the_torsions;
1084	<	TorsionStamp* current_torsion;
1013	>	createFF();
1014
1015	<	the_torsions = new torsion_set[tot_torsions];
1087	<	index = 0;
1088	<	offset = 0;
1089	<	molIndex = 0;
1090	<	for( i=0; i<n_components; i++ ){
1015	>	// extract componentList
1016
1017	<	for( j=0; j<components_nmol[i]; j++ ){
1017	>	compList();
1018
1019	+	// calc the number of atoms, bond, bends, and torsions
1020	+
1021	+	calcSysValues();
1022	+
1023		#ifdef IS_MPI
1024	<	if( mpiSim->getMyMolStart() <= molIndex &&
1096	<	molIndex <= mpiSim->getMyMolEnd() ){
1097	<	#endif // is_mpi
1024	>	// divide the molecules among the processors
1025
1026	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1026	>	mpiMolDivide();
1027	>	#endif //is_mpi
1028
1029	<	current_torsion = comp_stamps[i]->getTorsion( k );
1102	<	the_torsions[index].a = current_torsion->getA() + offset;
1103	<	the_torsions[index].b = current_torsion->getB() + offset;
1104	<	the_torsions[index].c = current_torsion->getC() + offset;
1105	<	the_torsions[index].d = current_torsion->getD() + offset;
1029	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1030
1031	<	exI = the_torsions[index].a;
1108	<	exJ = the_torsions[index].d;
1031	>	makeSysArrays();
1032
1033	<
1111	<	// exclude_I must always be the smaller of the pair
1112	<	if( exI > exJ ){
1113	<	tempEx = exI;
1114	<	exI = exJ;
1115	<	exJ = tempEx;
1116	<	}
1033	>	// make and initialize the molecules (all but atomic coordinates)
1034
1035	+	makeMolecules();
1036
1037	<	#ifdef IS_MPI
1038	<
1039	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
1040	<	the_atoms[exI]->getGlobalIndex() + 1;
1041	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1042	<	the_atoms[exJ]->getGlobalIndex() + 1;
1043	<
1126	<	#else  // isn't MPI
1127	<
1128	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1129	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1130	<	// fortran indexes from 1 (hence the +1 in the indexing)
1131	<	#endif  //is_mpi
1132	<
1037	>	for (k = 0; k < nInfo; k++){
1038	>	info[k].identArray = new int[info[k].n_atoms];
1039	>	for (i = 0; i < info[k].n_atoms; i++){
1040	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1041	>	}
1042	>	}
1043	>	}
1044
1134	–	// increment the index and repeat;
1135	–	index++;
1136	–	}
1137	–	offset += comp_stamps[i]->getNAtoms();
1045
1046	+	void SimSetup::createFF(void){
1047	+	switch (ffCase){
1048	+	case FF_DUFF:
1049	+	the_ff = new DUFF();
1050	+	break;
1051	+
1052	+	case FF_LJ:
1053	+	the_ff = new LJFF();
1054	+	break;
1055	+
1056	+	case FF_EAM:
1057	+	the_ff = new EAM_FF();
1058	+	break;
1059	+
1060	+	default:
1061	+	sprintf(painCave.errMsg,
1062	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1063	+	painCave.isFatal = 1;
1064	+	simError();
1065	+	}
1066	+
1067		#ifdef IS_MPI
1068	<	}
1069	<	#endif //is_mpi
1068	>	strcpy(checkPointMsg, "ForceField creation successful");
1069	>	MPIcheckPoint();
1070	>	#endif // is_mpi
1071	>	}
1072
1143	–	molIndex++;
1144	–	}
1145	–	}
1073
1074	<	the_ff->initializeTorsions( the_torsions );
1075	<	}
1074	>	void SimSetup::compList(void){
1075	>	int i;
1076	>	char* id;
1077	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1078	>	LinkedMolStamp* currentStamp = NULL;
1079	>	comp_stamps = new MoleculeStamp * [n_components];
1080
1081	<	void SimSetup::initFromBass( void ){
1081	>	// make an array of molecule stamps that match the components used.
1082	>	// also extract the used stamps out into a separate linked list
1083
1084	<	int i, j, k;
1085	<	int n_cells;
1086	<	double cellx, celly, cellz;
1087	<	double temp1, temp2, temp3;
1088	<	int n_per_extra;
1089	<	int n_extra;
1158	<	int have_extra, done;
1084	>	for (i = 0; i < nInfo; i++){
1085	>	info[i].nComponents = n_components;
1086	>	info[i].componentsNmol = components_nmol;
1087	>	info[i].compStamps = comp_stamps;
1088	>	info[i].headStamp = headStamp;
1089	>	}
1090
1160	–	temp1 = (double)tot_nmol / 4.0;
1161	–	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1162	–	temp3 = ceil( temp2 );
1091
1092	<	have_extra =0;
1093	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1094	<	have_extra =1;
1092	>	for (i = 0; i < n_components; i++){
1093	>	id = the_components[i]->getType();
1094	>	comp_stamps[i] = NULL;
1095
1096	<	n_cells = (int)temp3 - 1;
1169	<	cellx = simnfo->box_x / temp3;
1170	<	celly = simnfo->box_y / temp3;
1171	<	cellz = simnfo->box_z / temp3;
1172	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1173	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1174	<	n_per_extra = (int)ceil( temp1 );
1096	>	// check to make sure the component isn't already in the list
1097
1098	<	if( n_per_extra > 4){
1099	<	sprintf( painCave.errMsg,
1100	<	"SimSetup error. There has been an error in constructing"
1101	<	" the non-complete lattice.\n" );
1102	<	painCave.isFatal = 1;
1103	<	simError();
1098	>	comp_stamps[i] = headStamp->match(id);
1099	>	if (comp_stamps[i] == NULL){
1100	>	// extract the component from the list;
1101	>
1102	>	currentStamp = stamps->extractMolStamp(id);
1103	>	if (currentStamp == NULL){
1104	>	sprintf(painCave.errMsg,
1105	>	"SimSetup error: Component \"%s\" was not found in the "
1106	>	"list of declared molecules\n",
1107	>	id);
1108	>	painCave.isFatal = 1;
1109	>	simError();
1110	>	}
1111	>
1112	>	headStamp->add(currentStamp);
1113	>	comp_stamps[i] = headStamp->match(id);
1114		}
1115		}
1184	–	else{
1185	–	n_cells = (int)temp3;
1186	–	cellx = simnfo->box_x / temp3;
1187	–	celly = simnfo->box_y / temp3;
1188	–	cellz = simnfo->box_z / temp3;
1189	–	}
1116
1117	<	current_mol = 0;
1118	<	current_comp_mol = 0;
1119	<	current_comp = 0;
1120	<	current_atom_ndx = 0;
1117	>	#ifdef IS_MPI
1118	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1119	>	MPIcheckPoint();
1120	>	#endif // is_mpi
1121	>	}
1122
1123	<	for( i=0; i < n_cells ; i++ ){
1124	<	for( j=0; j < n_cells; j++ ){
1198	<	for( k=0; k < n_cells; k++ ){
1123	>	void SimSetup::calcSysValues(void){
1124	>	int i;
1125
1126	<	makeElement( i * cellx,
1201	<	j * celly,
1202	<	k * cellz );
1126	>	int* molMembershipArray;
1127
1128	<	makeElement( i * cellx + 0.5 * cellx,
1129	<	j * celly + 0.5 * celly,
1130	<	k * cellz );
1128	>	tot_atoms = 0;
1129	>	tot_bonds = 0;
1130	>	tot_bends = 0;
1131	>	tot_torsions = 0;
1132	>	for (i = 0; i < n_components; i++){
1133	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1134	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1135	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1136	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1137	>	}
1138
1139	<	makeElement( i * cellx,
1140	<	j * celly + 0.5 * celly,
1210	<	k * cellz + 0.5 * cellz );
1139	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1140	>	molMembershipArray = new int[tot_atoms];
1141
1142	<	makeElement( i * cellx + 0.5 * cellx,
1143	<	j * celly,
1144	<	k * cellz + 0.5 * cellz );
1145	<	}
1146	<	}
1142	>	for (i = 0; i < nInfo; i++){
1143	>	info[i].n_atoms = tot_atoms;
1144	>	info[i].n_bonds = tot_bonds;
1145	>	info[i].n_bends = tot_bends;
1146	>	info[i].n_torsions = tot_torsions;
1147	>	info[i].n_SRI = tot_SRI;
1148	>	info[i].n_mol = tot_nmol;
1149	>
1150	>	info[i].molMembershipArray = molMembershipArray;
1151		}
1152	+	}
1153
1154	<	if( have_extra ){
1220	<	done = 0;
1154	>	#ifdef IS_MPI
1155
1156	<	int start_ndx;
1157	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1158	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1156	>	void SimSetup::mpiMolDivide(void){
1157	>	int i, j, k;
1158	>	int localMol, allMol;
1159	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1160
1161	<	if( i < n_cells ){
1161	>	mpiSim = new mpiSimulation(info);
1162
1163	<	if( j < n_cells ){
1229	<	start_ndx = n_cells;
1230	<	}
1231	<	else start_ndx = 0;
1232	<	}
1233	<	else start_ndx = 0;
1163	>	globalIndex = mpiSim->divideLabor();
1164
1165	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1165	>	// set up the local variables
1166
1167	<	makeElement( i * cellx,
1168	<	j * celly,
1239	<	k * cellz );
1240	<	done = ( current_mol >= tot_nmol );
1167	>	mol2proc = mpiSim->getMolToProcMap();
1168	>	molCompType = mpiSim->getMolComponentType();
1169
1170	<	if( !done && n_per_extra > 1 ){
1171	<	makeElement( i * cellx + 0.5 * cellx,
1172	<	j * celly + 0.5 * celly,
1173	<	k * cellz );
1174	<	done = ( current_mol >= tot_nmol );
1175	<	}
1170	>	allMol = 0;
1171	>	localMol = 0;
1172	>	local_atoms = 0;
1173	>	local_bonds = 0;
1174	>	local_bends = 0;
1175	>	local_torsions = 0;
1176	>	globalAtomIndex = 0;
1177
1249	–	if( !done && n_per_extra > 2){
1250	–	makeElement( i * cellx,
1251	–	j * celly + 0.5 * celly,
1252	–	k * cellz + 0.5 * cellz );
1253	–	done = ( current_mol >= tot_nmol );
1254	–	}
1178
1179	<	if( !done && n_per_extra > 3){
1180	<	makeElement( i * cellx + 0.5 * cellx,
1181	<	j * celly,
1182	<	k * cellz + 0.5 * cellz );
1183	<	done = ( current_mol >= tot_nmol );
1184	<	}
1185	<	}
1179	>	for (i = 0; i < n_components; i++){
1180	>	for (j = 0; j < components_nmol[i]; j++){
1181	>	if (mol2proc[allMol] == worldRank){
1182	>	local_atoms += comp_stamps[i]->getNAtoms();
1183	>	local_bonds += comp_stamps[i]->getNBonds();
1184	>	local_bends += comp_stamps[i]->getNBends();
1185	>	local_torsions += comp_stamps[i]->getNTorsions();
1186	>	localMol++;
1187	>	}
1188	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1189	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1190	>	globalAtomIndex++;
1191		}
1192	+
1193	+	allMol++;
1194		}
1195		}
1196	+	local_SRI = local_bonds + local_bends + local_torsions;
1197
1198	+	info[0].n_atoms = mpiSim->getMyNlocal();
1199
1200	<	for( i=0; i<simnfo->n_atoms; i++ ){
1201	<	simnfo->atoms[i]->set_vx( 0.0 );
1202	<	simnfo->atoms[i]->set_vy( 0.0 );
1203	<	simnfo->atoms[i]->set_vz( 0.0 );
1200	>	if (local_atoms != info[0].n_atoms){
1201	>	sprintf(painCave.errMsg,
1202	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1203	>	" localAtom (%d) are not equal.\n",
1204	>	info[0].n_atoms, local_atoms);
1205	>	painCave.isFatal = 1;
1206	>	simError();
1207		}
1208	+
1209	+	info[0].n_bonds = local_bonds;
1210	+	info[0].n_bends = local_bends;
1211	+	info[0].n_torsions = local_torsions;
1212	+	info[0].n_SRI = local_SRI;
1213	+	info[0].n_mol = localMol;
1214	+
1215	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1216	+	MPIcheckPoint();
1217		}
1218
1219	<	void SimSetup::makeElement( double x, double y, double z ){
1219	>	#endif // is_mpi
1220
1277	–	int k;
1278	–	AtomStamp* current_atom;
1279	–	DirectionalAtom* dAtom;
1280	–	double rotMat[3][3];
1221
1222	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1222	>	void SimSetup::makeSysArrays(void){
1223	>
1224	>	#ifndef IS_MPI
1225	>	int k, j;
1226	>	#endif // is_mpi
1227	>	int i, l;
1228
1229	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1230	<	if( !current_atom->havePosition() ){
1231	<	sprintf( painCave.errMsg,
1287	<	"SimSetup:initFromBass error.\n"
1288	<	"\tComponent %s, atom %s does not have a position specified.\n"
1289	<	"\tThe initialization routine is unable to give a start"
1290	<	" position.\n",
1291	<	comp_stamps[current_comp]->getID(),
1292	<	current_atom->getType() );
1293	<	painCave.isFatal = 1;
1294	<	simError();
1295	<	}
1229	>	Atom** the_atoms;
1230	>	Molecule* the_molecules;
1231	>	Exclude** the_excludes;
1232
1297	–	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1298	–	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1299	–	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1233
1234	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1234	>	for (l = 0; l < nInfo; l++){
1235	>	// create the atom and short range interaction arrays
1236
1237	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1237	>	the_atoms = new Atom * [info[l].n_atoms];
1238	>	the_molecules = new Molecule[info[l].n_mol];
1239	>	int molIndex;
1240
1241	<	rotMat[0][0] = 1.0;
1306	<	rotMat[0][1] = 0.0;
1307	<	rotMat[0][2] = 0.0;
1241	>	// initialize the molecule's stampID's
1242
1243	<	rotMat[1][0] = 0.0;
1310	<	rotMat[1][1] = 1.0;
1311	<	rotMat[1][2] = 0.0;
1243	>	#ifdef IS_MPI
1244
1313	–	rotMat[2][0] = 0.0;
1314	–	rotMat[2][1] = 0.0;
1315	–	rotMat[2][2] = 1.0;
1245
1246	<	dAtom->setA( rotMat );
1246	>	molIndex = 0;
1247	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1248	>	if (mol2proc[i] == worldRank){
1249	>	the_molecules[molIndex].setStampID(molCompType[i]);
1250	>	the_molecules[molIndex].setMyIndex(molIndex);
1251	>	the_molecules[molIndex].setGlobalIndex(i);
1252	>	molIndex++;
1253	>	}
1254		}
1255
1256	<	current_atom_ndx++;
1321	<	}
1256	>	#else // is_mpi
1257
1258	<	current_mol++;
1259	<	current_comp_mol++;
1258	>	molIndex = 0;
1259	>	globalAtomIndex = 0;
1260	>	for (i = 0; i < n_components; i++){
1261	>	for (j = 0; j < components_nmol[i]; j++){
1262	>	the_molecules[molIndex].setStampID(i);
1263	>	the_molecules[molIndex].setMyIndex(molIndex);
1264	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1265	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1266	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1267	>	globalAtomIndex++;
1268	>	}
1269	>	molIndex++;
1270	>	}
1271	>	}
1272
1326	–	if( current_comp_mol >= components_nmol[current_comp] ){
1273
1274	<	current_comp_mol = 0;
1275	<	current_comp++;
1274	>	#endif // is_mpi
1275	>
1276	>
1277	>	if (info[l].n_SRI){
1278	>	Exclude::createArray(info[l].n_SRI);
1279	>	the_excludes = new Exclude * [info[l].n_SRI];
1280	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1281	>	the_excludes[ex] = new Exclude(ex);
1282	>	}
1283	>	info[l].globalExcludes = new int;
1284	>	info[l].n_exclude = info[l].n_SRI;
1285	>	}
1286	>	else{
1287	>	Exclude::createArray(1);
1288	>	the_excludes = new Exclude * ;
1289	>	the_excludes[0] = new Exclude(0);
1290	>	the_excludes[0]->setPair(0, 0);
1291	>	info[l].globalExcludes = new int;
1292	>	info[l].globalExcludes[0] = 0;
1293	>	info[l].n_exclude = 0;
1294	>	}
1295	>
1296	>	// set the arrays into the SimInfo object
1297	>
1298	>	info[l].atoms = the_atoms;
1299	>	info[l].molecules = the_molecules;
1300	>	info[l].nGlobalExcludes = 0;
1301	>	info[l].excludes = the_excludes;
1302	>
1303	>	the_ff->setSimInfo(info);
1304		}
1305		}
1306	+
1307	+	void SimSetup::makeIntegrator(void){
1308	+	int k;
1309	+
1310	+	NVE* myNVE = NULL;
1311	+	NVT* myNVT = NULL;
1312	+	NPTi* myNPTi = NULL;
1313	+	NPTf* myNPTf = NULL;
1314	+	NPTxyz* myNPTxyz = NULL;
1315	+
1316	+	for (k = 0; k < nInfo; k++){
1317	+	switch (ensembleCase){
1318	+	case NVE_ENS:
1319	+	if (globals->haveZconstraints()){
1320	+
1321	+	std::cerr << "ZConstraint is temporarily disabled\n";
1322	+
1323	+	//      setupZConstraint(info[k]);
1324	+	//      myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1325	+	}
1326	+
1327	+	//       else{
1328	+	myNVE = new NVE(&(info[k]), the_ff);
1329	+	//       }
1330	+
1331	+	info->the_integrator = myNVE;
1332	+	break;
1333	+
1334	+	case NVT_ENS:
1335	+	if (globals->haveZconstraints()){
1336	+
1337	+	std::cerr << "ZConstraint is temporarily disabled\n";
1338	+
1339	+	//      setupZConstraint(info[k]);
1340	+	//      myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1341	+	}
1342	+	// else
1343	+	myNVT = new NVT(&(info[k]), the_ff);
1344	+
1345	+	myNVT->setTargetTemp(globals->getTargetTemp());
1346	+
1347	+	if (globals->haveTauThermostat())
1348	+	myNVT->setTauThermostat(globals->getTauThermostat());
1349	+	else{
1350	+	sprintf(painCave.errMsg,
1351	+	"SimSetup error: If you use the NVT\n"
1352	+	"    ensemble, you must set tauThermostat.\n");
1353	+	painCave.isFatal = 1;
1354	+	simError();
1355	+	}
1356	+
1357	+	info->the_integrator = myNVT;
1358	+	break;
1359	+
1360	+	case NPTi_ENS:
1361	+	if (globals->haveZconstraints()){
1362	+
1363	+	std::cerr << "ZConstraint is temporarily disabled\n";
1364	+
1365	+	//        setupZConstraint(info[k]);
1366	+	//           myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1367	+	}
1368	+	// else
1369	+	myNPTi = new NPTi(&(info[k]), the_ff);
1370	+
1371	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1372	+
1373	+	if (globals->haveTargetPressure())
1374	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1375	+	else{
1376	+	sprintf(painCave.errMsg,
1377	+	"SimSetup error: If you use a constant pressure\n"
1378	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1379	+	painCave.isFatal = 1;
1380	+	simError();
1381	+	}
1382	+
1383	+	if (globals->haveTauThermostat())
1384	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1385	+	else{
1386	+	sprintf(painCave.errMsg,
1387	+	"SimSetup error: If you use an NPT\n"
1388	+	"    ensemble, you must set tauThermostat.\n");
1389	+	painCave.isFatal = 1;
1390	+	simError();
1391	+	}
1392	+
1393	+	if (globals->haveTauBarostat())
1394	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1395	+	else{
1396	+	sprintf(painCave.errMsg,
1397	+	"SimSetup error: If you use an NPT\n"
1398	+	"    ensemble, you must set tauBarostat.\n");
1399	+	painCave.isFatal = 1;
1400	+	simError();
1401	+	}
1402	+
1403	+	info->the_integrator = myNPTi;
1404	+	break;
1405	+
1406	+	case NPTf_ENS:
1407	+	if (globals->haveZconstraints()){
1408	+
1409	+	std::cerr << "ZConstraint is temporarily disabled\n";
1410	+
1411	+	//      setupZConstraint(info[k]);
1412	+	//      myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1413	+	}
1414	+	//       else
1415	+	myNPTf = new NPTf(&(info[k]), the_ff);
1416	+
1417	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1418	+
1419	+	if (globals->haveTargetPressure())
1420	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1421	+	else{
1422	+	sprintf(painCave.errMsg,
1423	+	"SimSetup error: If you use a constant pressure\n"
1424	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1425	+	painCave.isFatal = 1;
1426	+	simError();
1427	+	}
1428	+
1429	+	if (globals->haveTauThermostat())
1430	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1431	+
1432	+	else{
1433	+	sprintf(painCave.errMsg,
1434	+	"SimSetup error: If you use an NPT\n"
1435	+	"    ensemble, you must set tauThermostat.\n");
1436	+	painCave.isFatal = 1;
1437	+	simError();
1438	+	}
1439	+
1440	+	if (globals->haveTauBarostat())
1441	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1442	+
1443	+	else{
1444	+	sprintf(painCave.errMsg,
1445	+	"SimSetup error: If you use an NPT\n"
1446	+	"    ensemble, you must set tauBarostat.\n");
1447	+	painCave.isFatal = 1;
1448	+	simError();
1449	+	}
1450	+
1451	+	info->the_integrator = myNPTf;
1452	+	break;
1453	+
1454	+	case NPTxyz_ENS:
1455	+	if (globals->haveZconstraints()){
1456	+
1457	+	std::cerr << "ZConstraint is temporarily disabled\n";
1458	+
1459	+	//      setupZConstraint(info[k]);
1460	+	//      myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1461	+	}
1462	+	//       else
1463	+	myNPTxyz = new NPTxyz(&(info[k]), the_ff);
1464	+
1465	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1466	+
1467	+	if (globals->haveTargetPressure())
1468	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1469	+	else{
1470	+	sprintf(painCave.errMsg,
1471	+	"SimSetup error: If you use a constant pressure\n"
1472	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1473	+	painCave.isFatal = 1;
1474	+	simError();
1475	+	}
1476	+
1477	+	if (globals->haveTauThermostat())
1478	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1479	+	else{
1480	+	sprintf(painCave.errMsg,
1481	+	"SimSetup error: If you use an NPT\n"
1482	+	"    ensemble, you must set tauThermostat.\n");
1483	+	painCave.isFatal = 1;
1484	+	simError();
1485	+	}
1486	+
1487	+	if (globals->haveTauBarostat())
1488	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1489	+	else{
1490	+	sprintf(painCave.errMsg,
1491	+	"SimSetup error: If you use an NPT\n"
1492	+	"    ensemble, you must set tauBarostat.\n");
1493	+	painCave.isFatal = 1;
1494	+	simError();
1495	+	}
1496	+
1497	+	info->the_integrator = myNPTxyz;
1498	+	break;
1499	+
1500	+	default:
1501	+	sprintf(painCave.errMsg,
1502	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1503	+	painCave.isFatal = 1;
1504	+	simError();
1505	+	}
1506	+	}
1507	+	}
1508	+
1509	+	void SimSetup::initFortran(void){
1510	+	info[0].refreshSim();
1511	+
1512	+	if (!strcmp(info[0].mixingRule, "standard")){
1513	+	the_ff->initForceField(LB_MIXING_RULE);
1514	+	}
1515	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1516	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1517	+	}
1518	+	else{
1519	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1520	+	info[0].mixingRule);
1521	+	painCave.isFatal = 1;
1522	+	simError();
1523	+	}
1524	+
1525	+
1526	+	#ifdef IS_MPI
1527	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1528	+	MPIcheckPoint();
1529	+	#endif // is_mpi
1530	+	}
1531	+
1532	+	// void SimSetup::setupZConstraint(SimInfo& theInfo){
1533	+	//   int nZConstraints;
1534	+	//   ZconStamp** zconStamp;
1535	+
1536	+	//   if (globals->haveZconstraintTime()){
1537	+	//     //add sample time of z-constraint  into SimInfo's property list
1538	+	//     DoubleData* zconsTimeProp = new DoubleData();
1539	+	//     zconsTimeProp->setID(ZCONSTIME_ID);
1540	+	//     zconsTimeProp->setData(globals->getZconsTime());
1541	+	//     theInfo.addProperty(zconsTimeProp);
1542	+	//   }
1543	+	//   else{
1544	+	//     sprintf(painCave.errMsg,
1545	+	//             "ZConstraint error: If you use an ZConstraint\n"
1546	+	//             " , you must set sample time.\n");
1547	+	//     painCave.isFatal = 1;
1548	+	//     simError();
1549	+	//   }
1550	+
1551	+	//   //push zconsTol into siminfo, if user does not specify
1552	+	//   //value for zconsTol, a default value will be used
1553	+	//   DoubleData* zconsTol = new DoubleData();
1554	+	//   zconsTol->setID(ZCONSTOL_ID);
1555	+	//   if (globals->haveZconsTol()){
1556	+	//     zconsTol->setData(globals->getZconsTol());
1557	+	//   }
1558	+	//   else{
1559	+	//     double defaultZConsTol = 0.01;
1560	+	//     sprintf(painCave.errMsg,
1561	+	//             "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1562	+	//             " , default value %f is used.\n",
1563	+	//             defaultZConsTol);
1564	+	//     painCave.isFatal = 0;
1565	+	//     simError();
1566	+
1567	+	//     zconsTol->setData(defaultZConsTol);
1568	+	//   }
1569	+	//   theInfo.addProperty(zconsTol);
1570	+
1571	+	//   //set Force Subtraction Policy
1572	+	//   StringData* zconsForcePolicy = new StringData();
1573	+	//   zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1574	+
1575	+	//   if (globals->haveZconsForcePolicy()){
1576	+	//     zconsForcePolicy->setData(globals->getZconsForcePolicy());
1577	+	//   }
1578	+	//   else{
1579	+	//     sprintf(painCave.errMsg,
1580	+	//             "ZConstraint Warning: User does not set force Subtraction policy, "
1581	+	//             "PolicyByMass is used\n");
1582	+	//     painCave.isFatal = 0;
1583	+	//     simError();
1584	+	//     zconsForcePolicy->setData("BYMASS");
1585	+	//   }
1586	+
1587	+	//   theInfo.addProperty(zconsForcePolicy);
1588	+
1589	+	//   //Determine the name of ouput file and add it into SimInfo's property list
1590	+	//   //Be careful, do not use inFileName, since it is a pointer which
1591	+	//   //point to a string at master node, and slave nodes do not contain that string
1592	+
1593	+	//   string zconsOutput(theInfo.finalName);
1594	+
1595	+	//   zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1596	+
1597	+	//   StringData* zconsFilename = new StringData();
1598	+	//   zconsFilename->setID(ZCONSFILENAME_ID);
1599	+	//   zconsFilename->setData(zconsOutput);
1600	+
1601	+	//   theInfo.addProperty(zconsFilename);
1602	+
1603	+	//   //setup index, pos and other parameters of z-constraint molecules
1604	+	//   nZConstraints = globals->getNzConstraints();
1605	+	//   theInfo.nZconstraints = nZConstraints;
1606	+
1607	+	//   zconStamp = globals->getZconStamp();
1608	+	//   ZConsParaItem tempParaItem;
1609	+
1610	+	//   ZConsParaData* zconsParaData = new ZConsParaData();
1611	+	//   zconsParaData->setID(ZCONSPARADATA_ID);
1612	+
1613	+	//   for (int i = 0; i < nZConstraints; i++){
1614	+	//     tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1615	+	//     tempParaItem.zPos = zconStamp[i]->getZpos();
1616	+	//     tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1617	+	//     tempParaItem.kRatio = zconStamp[i]->getKratio();
1618	+
1619	+	//     zconsParaData->addItem(tempParaItem);
1620	+	//   }
1621	+
1622	+	//   //check the uniqueness of index
1623	+	//   if(!zconsParaData->isIndexUnique()){
1624	+	//     sprintf(painCave.errMsg,
1625	+	//             "ZConstraint Error: molIndex is not unique\n");
1626	+	//     painCave.isFatal = 1;
1627	+	//     simError();
1628	+	//   }
1629	+
1630	+	//   //sort the parameters by index of molecules
1631	+	//   zconsParaData->sortByIndex();
1632	+
1633	+	//   //push data into siminfo, therefore, we can retrieve later
1634	+	//   theInfo.addProperty(zconsParaData);
1635	+	// }

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines