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root/group/trunk/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.
Revision 812 by mmeineke, Wed Oct 22 21:17:32 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6	+	#include <sprng.h>
7
8		#include "SimSetup.hpp"
9	+	#include "ReadWrite.hpp"
10		#include "parse_me.h"
11		#include "Integrator.hpp"
12		#include "simError.h"
#	Line 12 | Line 16 | SimSetup::SimSetup(){
16		#include "mpiSimulation.hpp"
17		#endif
18
19	+	// some defines for ensemble and Forcefield  cases
20	+
21	+	#define NVE_ENS        0
22	+	#define NVT_ENS        1
23	+	#define NPTi_ENS       2
24	+	#define NPTf_ENS       3
25	+	#define NPTxyz_ENS     4
26	+
27	+
28	+	#define FF_DUFF 0
29	+	#define FF_LJ   1
30	+	#define FF_EAM  2
31	+
32	+	using namespace std;
33	+
34		SimSetup::SimSetup(){
35	+	isInfoArray = 0;
36	+	nInfo = 1;
37	+
38		stamps = new MakeStamps();
39		globals = new Globals();
40	<
40	>
41	>
42		#ifdef IS_MPI
43	<	strcpy( checkPointMsg, "SimSetup creation successful" );
43	>	strcpy(checkPointMsg, "SimSetup creation successful");
44		MPIcheckPoint();
45		#endif // IS_MPI
46		}
#	Line 27 | Line 50 | void SimSetup::parseFile( char* fileName ){
50		delete globals;
51		}
52
53	<	void SimSetup::parseFile( char* fileName ){
53	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
54	>	info = the_info;
55	>	nInfo = theNinfo;
56	>	isInfoArray = 1;
57	>	}
58
59	+
60	+	void SimSetup::parseFile(char* fileName){
61		#ifdef IS_MPI
62	<	if( worldRank == 0 ){
62	>	if (worldRank == 0){
63		#endif // is_mpi
64	<
64	>
65		inFileName = fileName;
66	<	set_interface_stamps( stamps, globals );
67	<
66	>	set_interface_stamps(stamps, globals);
67	>
68		#ifdef IS_MPI
69		mpiEventInit();
70		#endif
71
72	<	yacc_BASS( fileName );
72	>	yacc_BASS(fileName);
73
74		#ifdef IS_MPI
75		throwMPIEvent(NULL);
76		}
77	<	else receiveParse();
77	>	else{
78	>	receiveParse();
79	>	}
80		#endif
81
82		}
83
84		#ifdef IS_MPI
85		void SimSetup::receiveParse(void){
86	<
87	<	set_interface_stamps( stamps, globals );
88	<	mpiEventInit();
89	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
86	>	set_interface_stamps(stamps, globals);
87	>	mpiEventInit();
88	>	MPIcheckPoint();
89	>	mpiEventLoop();
90		}
91
92		#endif // is_mpi
93
94	<	void SimSetup::createSim( void ){
94	>	void SimSetup::createSim(void){
95
96	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
96	>	// gather all of the information from the Bass file
97
98	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
98	>	gatherInfo();
99
100	<	// 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();
100	>	// creation of complex system objects
101
102	<	// 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 );
102	>	sysObjectsCreation();
103
104	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
104	>	// check on the post processing info
105
106	+	finalInfoCheck();
107
108	<	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
92	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
93	<	else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
94	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
95	<	else{
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Error. Unrecognized force field -> %s\n",
98	<	force_field );
99	<	painCave.isFatal = 1;
100	<	simError();
101	<	}
108	>	// initialize the system coordinates
109
110	<	#ifdef IS_MPI
111	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
110	>	if (!isInfoArray){
111	>	initSystemCoords();
112
113	<
113	>	if( !(globals->getUseInitTime()) )
114	>	info[0].currentTime = 0.0;
115	>	}
116
117	<	// 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];
117	>	// make the output filenames
118
119	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
119	>	makeOutNames();
120
121	<	tot_nmol = 0;
120	<	for( i=0; i<n_components; i++ ){
121	>	// make the integrator
122
123	<	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	<	}
123	>	makeIntegrator();
124
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	–
125		#ifdef IS_MPI
126	<	strcpy( checkPointMsg, "Have the number of components" );
127	<	MPIcheckPoint();
163	<	#endif // is_mpi
126	>	mpiSim->mpiRefresh();
127	>	#endif
128
129	<	// make an array of molecule stamps that match the components used.
166	<	// also extract the used stamps out into a separate linked list
129	>	// initialize the Fortran
130
131	<	simnfo->nComponents = n_components;
132	<	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++ ){
131	>	initFortran();
132	>	}
133
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
134
135	<	comp_stamps[i] = headStamp->match( id );
136	<	if( comp_stamps[i] == NULL ){
137	<
138	<	// extract the component from the list;
139	<
140	<	currentStamp = the_stamps->extractMolStamp( id );
141	<	if( currentStamp == NULL ){
142	<	sprintf( painCave.errMsg,
143	<	"SimSetup error: Component \"%s\" was not found in the "
144	<	"list of declared molecules\n",
145	<	id );
194	<	painCave.isFatal = 1;
195	<	simError();
196	<	}
197	<
198	<	headStamp->add( currentStamp );
199	<	comp_stamps[i] = headStamp->match( id );
200	<	}
201	<	}
135	>	void SimSetup::makeMolecules(void){
136	>	int k;
137	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
138	>	molInit molInfo;
139	>	DirectionalAtom* dAtom;
140	>	LinkedAssign* extras;
141	>	LinkedAssign* current_extra;
142	>	AtomStamp* currentAtom;
143	>	BondStamp* currentBond;
144	>	BendStamp* currentBend;
145	>	TorsionStamp* currentTorsion;
146
147	<	#ifdef IS_MPI
148	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
149	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
147	>	bond_pair* theBonds;
148	>	bend_set* theBends;
149	>	torsion_set* theTorsions;
150
151
152	+	//init the forceField paramters
153
154	<	// caclulate the number of atoms, bonds, bends and torsions
154	>	the_ff->readParams();
155
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	–	}
156
157	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
157	>	// init the atoms
158
159	<	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;
159	>	double ux, uy, uz, u, uSqr;
160
161	<
162	<	#ifdef IS_MPI
161	>	for (k = 0; k < nInfo; k++){
162	>	the_ff->setSimInfo(&(info[k]));
163
164	<	// divide the molecules among processors here.
165	<
166	<	mpiSim = new mpiSimulation( simnfo );
167	<
241	<
164	>	atomOffset = 0;
165	>	excludeOffset = 0;
166	>	for (i = 0; i < info[k].n_mol; i++){
167	>	stampID = info[k].molecules[i].getStampID();
168
169	<	globalIndex = mpiSim->divideLabor();
169	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
170	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
171	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
172	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
173	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
174
175	+	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
176	+	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
177	+	molInfo.myBonds = new Bond * [molInfo.nBonds];
178	+	molInfo.myBends = new Bend * [molInfo.nBends];
179	+	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
180
181	+	theBonds = new bond_pair[molInfo.nBonds];
182	+	theBends = new bend_set[molInfo.nBends];
183	+	theTorsions = new torsion_set[molInfo.nTorsions];
184
185	<	// 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++ ){
185	>	// make the Atoms
186
187	<	for( j=0; j<components_nmol[i]; j++ ){
188	<
189	<	if( mpiSim->getMyMolStart() <= allMol &&
190	<	allMol <= mpiSim->getMyMolEnd() ){
191	<
192	<	local_atoms +=    comp_stamps[i]->getNAtoms();
193	<	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	<
187	>	for (j = 0; j < molInfo.nAtoms; j++){
188	>	currentAtom = comp_stamps[stampID]->getAtom(j);
189	>	if (currentAtom->haveOrientation()){
190	>	dAtom = new DirectionalAtom((j + atomOffset),
191	>	info[k].getConfiguration());
192	>	info[k].n_oriented++;
193	>	molInfo.myAtoms[j] = dAtom;
194
195	<	simnfo->n_atoms = mpiSim->getMyNlocal();
196	<
197	<	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	<	}
195	>	ux = currentAtom->getOrntX();
196	>	uy = currentAtom->getOrntY();
197	>	uz = currentAtom->getOrntZ();
198
199	<	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;
199	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
200
201	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
202	<	MPIcheckPoint();
203	<
204	<
201	>	u = sqrt(uSqr);
202	>	ux = ux / u;
203	>	uy = uy / u;
204	>	uz = uz / u;
205	>
206	>	dAtom->setSUx(ux);
207	>	dAtom->setSUy(uy);
208	>	dAtom->setSUz(uz);
209	>	}
210	>	else{
211	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
212	>	info[k].getConfiguration());
213	>	}
214	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
215	>
216	>	#ifdef IS_MPI
217	>
218	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
219	>
220		#endif // is_mpi
221	<
221	>	}
222
223	<	// create the atom and short range interaction arrays
223	>	// make the bonds
224	>	for (j = 0; j < molInfo.nBonds; j++){
225	>	currentBond = comp_stamps[stampID]->getBond(j);
226	>	theBonds[j].a = currentBond->getA() + atomOffset;
227	>	theBonds[j].b = currentBond->getB() + atomOffset;
228
229	<	Atom::createArrays(simnfo->n_atoms);
230	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
229	>	exI = theBonds[j].a;
230	>	exJ = theBonds[j].b;
231
232	+	// exclude_I must always be the smaller of the pair
233	+	if (exI > exJ){
234	+	tempEx = exI;
235	+	exI = exJ;
236	+	exJ = tempEx;
237	+	}
238	+	#ifdef IS_MPI
239	+	tempEx = exI;
240	+	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
241	+	tempEx = exJ;
242	+	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
243
244	<	if( simnfo->n_SRI ){
245	<	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;
244	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
245	>	#else  // isn't MPI
246
247	<	simnfo->n_exclude = 1;
248	<	}
247	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
248	>	#endif  //is_mpi
249	>	}
250	>	excludeOffset += molInfo.nBonds;
251
252	<	// set the arrays into the SimInfo object
252	>	//make the bends
253	>	for (j = 0; j < molInfo.nBends; j++){
254	>	currentBend = comp_stamps[stampID]->getBend(j);
255	>	theBends[j].a = currentBend->getA() + atomOffset;
256	>	theBends[j].b = currentBend->getB() + atomOffset;
257	>	theBends[j].c = currentBend->getC() + atomOffset;
258
259	<	simnfo->atoms = the_atoms;
260	<	simnfo->sr_interactions = the_sris;
261	<	simnfo->nGlobalExcludes = 0;
331	<	simnfo->excludes = the_excludes;
259	>	if (currentBend->haveExtras()){
260	>	extras = currentBend->getExtras();
261	>	current_extra = extras;
262
263	+	while (current_extra != NULL){
264	+	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
265	+	switch (current_extra->getType()){
266	+	case 0:
267	+	theBends[j].ghost = current_extra->getInt() + atomOffset;
268	+	theBends[j].isGhost = 1;
269	+	break;
270
271	<	// get some of the tricky things that may still be in the globals
271	>	case 1:
272	>	theBends[j].ghost = (int) current_extra->getDouble() +
273	>	atomOffset;
274	>	theBends[j].isGhost = 1;
275	>	break;
276
277	<
278	<	if( the_globals->haveBox() ){
279	<	simnfo->box_x = the_globals->getBox();
280	<	simnfo->box_y = the_globals->getBox();
281	<	simnfo->box_z = the_globals->getBox();
282	<	}
283	<	else if( the_globals->haveDensity() ){
277	>	default:
278	>	sprintf(painCave.errMsg,
279	>	"SimSetup Error: ghostVectorSource was neither a "
280	>	"double nor an int.\n"
281	>	"-->Bend[%d] in %s\n",
282	>	j, comp_stamps[stampID]->getID());
283	>	painCave.isFatal = 1;
284	>	simError();
285	>	}
286	>	}
287	>	else{
288	>	sprintf(painCave.errMsg,
289	>	"SimSetup Error: unhandled bend assignment:\n"
290	>	"    -->%s in Bend[%d] in %s\n",
291	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
292	>	painCave.isFatal = 1;
293	>	simError();
294	>	}
295
296	<	double vol;
297	<	vol = (double)tot_nmol / the_globals->getDensity();
298	<	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();
296	>	current_extra = current_extra->getNext();
297	>	}
298	>	}
299
300	<	if( !the_globals->haveBoxY() ){
301	<	sprintf( painCave.errMsg,
302	<	"SimSetup error, no periodic BoxY size given.\n" );
303	<	painCave.isFatal = 1;
304	<	simError();
305	<	}
306	<	simnfo->box_y = the_globals->getBoxY();
300	>	if (!theBends[j].isGhost){
301	>	exI = theBends[j].a;
302	>	exJ = theBends[j].c;
303	>	}
304	>	else{
305	>	exI = theBends[j].a;
306	>	exJ = theBends[j].b;
307	>	}
308
309	<	if( !the_globals->haveBoxZ() ){
310	<	sprintf( painCave.errMsg,
311	<	"SimSetup error, no periodic BoxZ size given.\n" );
312	<	painCave.isFatal = 1;
313	<	simError();
314	<	}
315	<	simnfo->box_z = the_globals->getBoxZ();
316	<	}
309	>	// exclude_I must always be the smaller of the pair
310	>	if (exI > exJ){
311	>	tempEx = exI;
312	>	exI = exJ;
313	>	exJ = tempEx;
314	>	}
315	>	#ifdef IS_MPI
316	>	tempEx = exI;
317	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
318	>	tempEx = exJ;
319	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
320
321	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
322	+	#else  // isn't MPI
323	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
324	+	#endif  //is_mpi
325	+	}
326	+	excludeOffset += molInfo.nBends;
327	+
328	+	for (j = 0; j < molInfo.nTorsions; j++){
329	+	currentTorsion = comp_stamps[stampID]->getTorsion(j);
330	+	theTorsions[j].a = currentTorsion->getA() + atomOffset;
331	+	theTorsions[j].b = currentTorsion->getB() + atomOffset;
332	+	theTorsions[j].c = currentTorsion->getC() + atomOffset;
333	+	theTorsions[j].d = currentTorsion->getD() + atomOffset;
334	+
335	+	exI = theTorsions[j].a;
336	+	exJ = theTorsions[j].d;
337	+
338	+	// exclude_I must always be the smaller of the pair
339	+	if (exI > exJ){
340	+	tempEx = exI;
341	+	exI = exJ;
342	+	exJ = tempEx;
343	+	}
344		#ifdef IS_MPI
345	<	strcpy( checkPointMsg, "Box size set up" );
346	<	MPIcheckPoint();
347	<	#endif // is_mpi
345	>	tempEx = exI;
346	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
347	>	tempEx = exJ;
348	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
349
350	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
351	+	#else  // isn't MPI
352	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
353	+	#endif  //is_mpi
354	+	}
355	+	excludeOffset += molInfo.nTorsions;
356
382	–	// initialize the arrays
357
358	<	the_ff->setSimInfo( simnfo );
358	>	// send the arrays off to the forceField for init.
359
360	<	makeAtoms();
361	<	simnfo->identArray = new int[simnfo->n_atoms];
362	<	for(i=0; i<simnfo->n_atoms; i++){
363	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
364	<	}
365	<
392	<	if( tot_bonds ){
393	<	makeBonds();
394	<	}
360	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
361	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
362	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
363	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
364	>	theTorsions);
365	>
366
367	<	if( tot_bends ){
397	<	makeBends();
398	<	}
367	>	info[k].molecules[i].initialize(molInfo);
368
369	<	if( tot_torsions ){
370	<	makeTorsions();
369	>
370	>	atomOffset += molInfo.nAtoms;
371	>	delete[] theBonds;
372	>	delete[] theBends;
373	>	delete[] theTorsions;
374	>	}
375		}
376
377	+	#ifdef IS_MPI
378	+	sprintf(checkPointMsg, "all molecules initialized succesfully");
379	+	MPIcheckPoint();
380	+	#endif // is_mpi
381
382	<	if (the_globals->getUseRF() ) {
406	<	simnfo->useReactionField = 1;
407	<
408	<	if( !the_globals->haveECR() ){
409	<	sprintf( painCave.errMsg,
410	<	"SimSetup Warning: using default value of 1/2 the smallest "
411	<	"box length for the electrostaticCutoffRadius.\n"
412	<	"I hope you have a very fast processor!\n");
413	<	painCave.isFatal = 0;
414	<	simError();
415	<	double smallest;
416	<	smallest = simnfo->box_x;
417	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
418	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
419	<	simnfo->ecr = 0.5 * smallest;
420	<	} else {
421	<	simnfo->ecr        = the_globals->getECR();
422	<	}
382	>	// clean up the forcefield
383
384	<	if( !the_globals->haveEST() ){
385	<	sprintf( painCave.errMsg,
386	<	"SimSetup Warning: using default value of 0.05 * the "
387	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
388	<	);
389	<	painCave.isFatal = 0;
390	<	simError();
391	<	simnfo->est = 0.05 * simnfo->ecr;
392	<	} else {
393	<	simnfo->est        = the_globals->getEST();
394	<	}
395	<
396	<	if(!the_globals->haveDielectric() ){
397	<	sprintf( painCave.errMsg,
398	<	"SimSetup Error: You are trying to use Reaction Field without"
399	<	"setting a dielectric constant!\n"
400	<	);
384	>	the_ff->calcRcut();
385	>	the_ff->cleanMe();
386	>	}
387	>
388	>	void SimSetup::initFromBass(void){
389	>	int i, j, k;
390	>	int n_cells;
391	>	double cellx, celly, cellz;
392	>	double temp1, temp2, temp3;
393	>	int n_per_extra;
394	>	int n_extra;
395	>	int have_extra, done;
396	>
397	>	double vel[3];
398	>	vel[0] = 0.0;
399	>	vel[1] = 0.0;
400	>	vel[2] = 0.0;
401	>
402	>	temp1 = (double) tot_nmol / 4.0;
403	>	temp2 = pow(temp1, (1.0 / 3.0));
404	>	temp3 = ceil(temp2);
405	>
406	>	have_extra = 0;
407	>	if (temp2 < temp3){
408	>	// we have a non-complete lattice
409	>	have_extra = 1;
410	>
411	>	n_cells = (int) temp3 - 1;
412	>	cellx = info[0].boxL[0] / temp3;
413	>	celly = info[0].boxL[1] / temp3;
414	>	cellz = info[0].boxL[2] / temp3;
415	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
416	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
417	>	n_per_extra = (int) ceil(temp1);
418	>
419	>	if (n_per_extra > 4){
420	>	sprintf(painCave.errMsg,
421	>	"SimSetup error. There has been an error in constructing"
422	>	" the non-complete lattice.\n");
423		painCave.isFatal = 1;
424		simError();
425		}
426	<	simnfo->dielectric = the_globals->getDielectric();
427	<	} else {
428	<	if (simnfo->n_dipoles) {
429	<
430	<	if( !the_globals->haveECR() ){
431	<	sprintf( painCave.errMsg,
432	<	"SimSetup Warning: using default value of 1/2 the smallest"
433	<	"box length for the electrostaticCutoffRadius.\n"
434	<	"I hope you have a very fast processor!\n");
435	<	painCave.isFatal = 0;
436	<	simError();
437	<	double smallest;
438	<	smallest = simnfo->box_x;
439	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
440	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
441	<	simnfo->ecr = 0.5 * smallest;
442	<	} else {
443	<	simnfo->ecr        = the_globals->getECR();
426	>	}
427	>	else{
428	>	n_cells = (int) temp3;
429	>	cellx = info[0].boxL[0] / temp3;
430	>	celly = info[0].boxL[1] / temp3;
431	>	cellz = info[0].boxL[2] / temp3;
432	>	}
433	>
434	>	current_mol = 0;
435	>	current_comp_mol = 0;
436	>	current_comp = 0;
437	>	current_atom_ndx = 0;
438	>
439	>	for (i = 0; i < n_cells ; i++){
440	>	for (j = 0; j < n_cells; j++){
441	>	for (k = 0; k < n_cells; k++){
442	>	makeElement(i * cellx, j * celly, k * cellz);
443	>
444	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
445	>
446	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
447	>
448	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
449		}
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	–	}
450		}
451	<	}
451	>	}
452
453	<	#ifdef IS_MPI
454	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
481	<	MPIcheckPoint();
482	<	#endif // is_mpi
453	>	if (have_extra){
454	>	done = 0;
455
456	<	if( the_globals->haveInitialConfig() ){
457	<
458	<	InitializeFromFile* fileInit;
459	<	#ifdef IS_MPI // is_mpi
460	<	if( worldRank == 0 ){
461	<	#endif //is_mpi
462	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
463	<	#ifdef IS_MPI
464	<	}else fileInit = new InitializeFromFile( NULL );
465	<	#endif
466	<	fileInit->read_xyz( simnfo ); // default velocities on
456	>	int start_ndx;
457	>	for (i = 0; i < (n_cells + 1) && !done; i++){
458	>	for (j = 0; j < (n_cells + 1) && !done; j++){
459	>	if (i < n_cells){
460	>	if (j < n_cells){
461	>	start_ndx = n_cells;
462	>	}
463	>	else
464	>	start_ndx = 0;
465	>	}
466	>	else
467	>	start_ndx = 0;
468
469	<	delete fileInit;
470	<	}
471	<	else{
469	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
470	>	makeElement(i * cellx, j * celly, k * cellz);
471	>	done = (current_mol >= tot_nmol);
472
473	<	#ifdef IS_MPI
473	>	if (!done && n_per_extra > 1){
474	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
475	>	k * cellz);
476	>	done = (current_mol >= tot_nmol);
477	>	}
478
479	<	// no init from bass
480	<
481	<	sprintf( painCave.errMsg,
482	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
483	<	painCave.isFatal;
507	<	simError();
508	<
509	<	#else
479	>	if (!done && n_per_extra > 2){
480	>	makeElement(i * cellx, j * celly + 0.5 * celly,
481	>	k * cellz + 0.5 * cellz);
482	>	done = (current_mol >= tot_nmol);
483	>	}
484
485	<	initFromBass();
485	>	if (!done && n_per_extra > 3){
486	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
487	>	k * cellz + 0.5 * cellz);
488	>	done = (current_mol >= tot_nmol);
489	>	}
490	>	}
491	>	}
492	>	}
493	>	}
494
495	+	for (i = 0; i < info[0].n_atoms; i++){
496	+	info[0].atoms[i]->setVel(vel);
497	+	}
498	+	}
499
500	<	#endif
501	<	}
500	>	void SimSetup::makeElement(double x, double y, double z){
501	>	int k;
502	>	AtomStamp* current_atom;
503	>	DirectionalAtom* dAtom;
504	>	double rotMat[3][3];
505	>	double pos[3];
506
507	<	#ifdef IS_MPI
508	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
509	<	MPIcheckPoint();
510	<	#endif // is_mpi
507	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
508	>	current_atom = comp_stamps[current_comp]->getAtom(k);
509	>	if (!current_atom->havePosition()){
510	>	sprintf(painCave.errMsg,
511	>	"SimSetup:initFromBass error.\n"
512	>	"\tComponent %s, atom %s does not have a position specified.\n"
513	>	"\tThe initialization routine is unable to give a start"
514	>	" position.\n",
515	>	comp_stamps[current_comp]->getID(), current_atom->getType());
516	>	painCave.isFatal = 1;
517	>	simError();
518	>	}
519
520	+	pos[0] = x + current_atom->getPosX();
521	+	pos[1] = y + current_atom->getPosY();
522	+	pos[2] = z + current_atom->getPosZ();
523
524	<
524	<
525	<
524	>	info[0].atoms[current_atom_ndx]->setPos(pos);
525
526	<
527	<	#ifdef IS_MPI
528	<	if( worldRank == 0 ){
529	<	#endif // is_mpi
530	<
531	<	if( the_globals->haveFinalConfig() ){
532	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
526	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
527	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
528	>
529	>	rotMat[0][0] = 1.0;
530	>	rotMat[0][1] = 0.0;
531	>	rotMat[0][2] = 0.0;
532	>
533	>	rotMat[1][0] = 0.0;
534	>	rotMat[1][1] = 1.0;
535	>	rotMat[1][2] = 0.0;
536	>
537	>	rotMat[2][0] = 0.0;
538	>	rotMat[2][1] = 0.0;
539	>	rotMat[2][2] = 1.0;
540	>
541	>	dAtom->setA(rotMat);
542		}
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
608	–	}
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	–	}
618	–	else{
619	–	simnfo->sampleTime = the_globals->getRunTime();
620	–	simnfo->statusTime = simnfo->sampleTime;
621	–	simnfo->thermalTime = simnfo->sampleTime;
622	–	}
543
544	<	if( the_globals->haveStatusTime() ){
625	<	simnfo->statusTime = the_globals->getStatusTime();
544	>	current_atom_ndx++;
545		}
546
547	<	if( the_globals->haveThermalTime() ){
548	<	simnfo->thermalTime = the_globals->getThermalTime();
547	>	current_mol++;
548	>	current_comp_mol++;
549	>
550	>	if (current_comp_mol >= components_nmol[current_comp]){
551	>	current_comp_mol = 0;
552	>	current_comp++;
553		}
554	+	}
555
632	–	// check for the temperature set flag
556
557	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
557	>	void SimSetup::gatherInfo(void){
558	>	int i;
559
560	+	ensembleCase = -1;
561	+	ffCase = -1;
562
563	<	//   // make the longe range forces and the integrator
563	>	// set the easy ones first
564
565	<	//   new AllLong( simnfo );
565	>	for (i = 0; i < nInfo; i++){
566	>	info[i].target_temp = globals->getTargetTemp();
567	>	info[i].dt = globals->getDt();
568	>	info[i].run_time = globals->getRunTime();
569	>	}
570	>	n_components = globals->getNComponents();
571
641	–	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
642	–	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
643	–	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
644	–	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
572
573	+	// get the forceField
574
575	+	strcpy(force_field, globals->getForceField());
576
577	<	// initialize the Fortran
578	<
650	<	simnfo->refreshSim();
651	<
652	<	if( !strcmp( simnfo->mixingRule, "standard") ){
653	<	the_ff->initForceField( LB_MIXING_RULE );
577	>	if (!strcasecmp(force_field, "DUFF")){
578	>	ffCase = FF_DUFF;
579		}
580	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
581	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
580	>	else if (!strcasecmp(force_field, "LJ")){
581	>	ffCase = FF_LJ;
582		}
583	+	else if (!strcasecmp(force_field, "EAM")){
584	+	ffCase = FF_EAM;
585	+	}
586		else{
587	<	sprintf( painCave.errMsg,
588	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
589	<	simnfo->mixingRule );
590	<	painCave.isFatal = 1;
663	<	simError();
587	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
588	>	force_field);
589	>	painCave.isFatal = 1;
590	>	simError();
591		}
592
593	+	// get the ensemble
594
595	<	#ifdef IS_MPI
668	<	strcpy( checkPointMsg,
669	<	"Successfully intialized the mixingRule for Fortran." );
670	<	MPIcheckPoint();
671	<	#endif // is_mpi
672	<	}
595	>	strcpy(ensemble, globals->getEnsemble());
596
597	+	if (!strcasecmp(ensemble, "NVE")){
598	+	ensembleCase = NVE_ENS;
599	+	}
600	+	else if (!strcasecmp(ensemble, "NVT")){
601	+	ensembleCase = NVT_ENS;
602	+	}
603	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
604	+	ensembleCase = NPTi_ENS;
605	+	}
606	+	else if (!strcasecmp(ensemble, "NPTf")){
607	+	ensembleCase = NPTf_ENS;
608	+	}
609	+	else if (!strcasecmp(ensemble, "NPTxyz")){
610	+	ensembleCase = NPTxyz_ENS;
611	+	}
612	+	else{
613	+	sprintf(painCave.errMsg,
614	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
615	+	"reverting to NVE for this simulation.\n",
616	+	ensemble);
617	+	painCave.isFatal = 0;
618	+	simError();
619	+	strcpy(ensemble, "NVE");
620	+	ensembleCase = NVE_ENS;
621	+	}
622
623	<	void SimSetup::makeMolecules( void ){
623	>	for (i = 0; i < nInfo; i++){
624	>	strcpy(info[i].ensemble, ensemble);
625
626	<	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
626	>	// get the mixing rule
627
628	<	the_ff->readParams();
628	>	strcpy(info[i].mixingRule, globals->getMixingRule());
629	>	info[i].usePBC = globals->getPBC();
630	>	}
631
632	<
690	<	// init the molecules
632	>	// get the components and calculate the tot_nMol and indvidual n_mol
633
634	<	atomOffset = 0;
635	<	for(i=0; i<simnfo->n_mol; i++){
694	<
695	<	stampID = the_molecules[i].getStampID();
634	>	the_components = globals->getComponents();
635	>	components_nmol = new int[n_components];
636
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];
637
638	<	theBonds = new bond_pair[info.nBonds];
639	<	theBends = new bend_set[info.nBends];
640	<	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;
638	>	if (!globals->haveNMol()){
639	>	// we don't have the total number of molecules, so we assume it is
640	>	// given in each component
641
642	<	exI = theBonds[i].a;
643	<	exJ = theBonds[i].b;
644	<
645	<	// exclude_I must always be the smaller of the pair
646	<	if( exI > exJ ){
647	<	tempEx = exI;
648	<	exI = exJ;
649	<	exJ = tempEx;
642	>	tot_nmol = 0;
643	>	for (i = 0; i < n_components; i++){
644	>	if (!the_components[i]->haveNMol()){
645	>	// we have a problem
646	>	sprintf(painCave.errMsg,
647	>	"SimSetup Error. No global NMol or component NMol"
648	>	" given. Cannot calculate the number of atoms.\n");
649	>	painCave.isFatal = 1;
650	>	simError();
651		}
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)
652
653	<	#endif  //is_mpi
654	<
653	>	tot_nmol += the_components[i]->getNMol();
654	>	components_nmol[i] = the_components[i]->getNMol();
655	>	}
656		}
657	+	else{
658	+	sprintf(painCave.errMsg,
659	+	"SimSetup error.\n"
660	+	"\tSorry, the ability to specify total"
661	+	" nMols and then give molfractions in the components\n"
662	+	"\tis not currently supported."
663	+	" Please give nMol in the components.\n");
664	+	painCave.isFatal = 1;
665	+	simError();
666	+	}
667
668	+	// set the status, sample, and thermal kick times
669
670	+	for (i = 0; i < nInfo; i++){
671	+	if (globals->haveSampleTime()){
672	+	info[i].sampleTime = globals->getSampleTime();
673	+	info[i].statusTime = info[i].sampleTime;
674	+	info[i].thermalTime = info[i].sampleTime;
675	+	}
676	+	else{
677	+	info[i].sampleTime = globals->getRunTime();
678	+	info[i].statusTime = info[i].sampleTime;
679	+	info[i].thermalTime = info[i].sampleTime;
680	+	}
681
682	+	if (globals->haveStatusTime()){
683	+	info[i].statusTime = globals->getStatusTime();
684	+	}
685
686	+	if (globals->haveThermalTime()){
687	+	info[i].thermalTime = globals->getThermalTime();
688	+	}
689
690	+	info[i].resetIntegrator = 0;
691	+	if( globals->haveResetTime() ){
692	+	info[i].resetTime = globals->getResetTime();
693	+	info[i].resetIntegrator = 1;
694	+	}
695
696	+	// check for the temperature set flag
697
698	+	if (globals->haveTempSet())
699	+	info[i].setTemp = globals->getTempSet();
700
701	+	// get some of the tricky things that may still be in the globals
702
703	+	double boxVector[3];
704	+	if (globals->haveBox()){
705	+	boxVector[0] = globals->getBox();
706	+	boxVector[1] = globals->getBox();
707	+	boxVector[2] = globals->getBox();
708
709	+	info[i].setBox(boxVector);
710	+	}
711	+	else if (globals->haveDensity()){
712	+	double vol;
713	+	vol = (double) tot_nmol / globals->getDensity();
714	+	boxVector[0] = pow(vol, (1.0 / 3.0));
715	+	boxVector[1] = boxVector[0];
716	+	boxVector[2] = boxVector[0];
717
718	+	info[i].setBox(boxVector);
719	+	}
720	+	else{
721	+	if (!globals->haveBoxX()){
722	+	sprintf(painCave.errMsg,
723	+	"SimSetup error, no periodic BoxX size given.\n");
724	+	painCave.isFatal = 1;
725	+	simError();
726	+	}
727	+	boxVector[0] = globals->getBoxX();
728
729	+	if (!globals->haveBoxY()){
730	+	sprintf(painCave.errMsg,
731	+	"SimSetup error, no periodic BoxY size given.\n");
732	+	painCave.isFatal = 1;
733	+	simError();
734	+	}
735	+	boxVector[1] = globals->getBoxY();
736
737	+	if (!globals->haveBoxZ()){
738	+	sprintf(painCave.errMsg,
739	+	"SimSetup error, no periodic BoxZ size given.\n");
740	+	painCave.isFatal = 1;
741	+	simError();
742	+	}
743	+	boxVector[2] = globals->getBoxZ();
744
745	+	info[i].setBox(boxVector);
746	+	}
747	+	}
748
749	<	void SimSetup::makeAtoms( void ){
749	>	//setup seed for random number generator
750	>	int seedValue;
751
752	<	int i, j, k, index;
753	<	double ux, uy, uz, uSqr, u;
800	<	AtomStamp* current_atom;
752	>	if (globals->haveSeed()){
753	>	seedValue = globals->getSeed();
754
755	<	DirectionalAtom* dAtom;
756	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
755	>	if(seedValue / 1E9 == 0){
756	>	sprintf(painCave.errMsg,
757	>	"Seed for sprng library should contain at least 9 digits\n"
758	>	"OOPSE will generate a seed for user\n");
759	>	painCave.isFatal = 0;
760	>	simError();
761
762	<	lMolIndex = 0;
763	<	molIndex = 0;
764	<	index = 0;
765	<	for( i=0; i<n_components; i++ ){
766	<
767	<	for( j=0; j<components_nmol[i]; j++ ){
811	<
812	<	#ifdef IS_MPI
813	<	if( mpiSim->getMyMolStart() <= molIndex &&
814	<	molIndex <= mpiSim->getMyMolEnd() ){
815	<	#endif // is_mpi
816	<
817	<	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++;
859	<
860	<	#ifdef IS_MPI
762	>	//using seed generated by system instead of invalid seed set by user
763	>	#ifndef IS_MPI
764	>	seedValue = make_sprng_seed();
765	>	#else
766	>	if (worldRank == 0){
767	>	seedValue = make_sprng_seed();
768		}
769	<	#endif //is_mpi
770	<
864	<	molIndex++;
769	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
770	>	#endif
771		}
772	+	}//end of if branch of globals->haveSeed()
773	+	else{
774	+
775	+	#ifndef IS_MPI
776	+	seedValue = make_sprng_seed();
777	+	#else
778	+	if (worldRank == 0){
779	+	seedValue = make_sprng_seed();
780	+	}
781	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
782	+	#endif
783	+	}//end of globals->haveSeed()
784	+
785	+	for (int i = 0; i < nInfo; i++){
786	+	info[i].setSeed(seedValue);
787		}
788
789		#ifdef IS_MPI
790	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
791	<
792	<	delete[] globalIndex;
872	<
873	<	mpiSim->mpiRefresh();
874	<	#endif //IS_MPI
875	<
876	<	the_ff->initializeAtoms();
790	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
791	>	MPIcheckPoint();
792	>	#endif // is_mpi
793		}
794
879	–	void SimSetup::makeBonds( void ){
795
796	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
797	<	bond_pair* the_bonds;
798	<	BondStamp* current_bond;
796	>	void SimSetup::finalInfoCheck(void){
797	>	int index;
798	>	int usesDipoles;
799	>	int i;
800
801	<	the_bonds = new bond_pair[tot_bonds];
802	<	index = 0;
887	<	offset = 0;
888	<	molIndex = 0;
801	>	for (i = 0; i < nInfo; i++){
802	>	// check electrostatic parameters
803
804	<	for( i=0; i<n_components; i++ ){
804	>	index = 0;
805	>	usesDipoles = 0;
806	>	while ((index < info[i].n_atoms) && !usesDipoles){
807	>	usesDipoles = (info[i].atoms[index])->hasDipole();
808	>	index++;
809	>	}
810
892	–	for( j=0; j<components_nmol[i]; j++ ){
893	–
811		#ifdef IS_MPI
812	<	if( mpiSim->getMyMolStart() <= molIndex &&
813	<	molIndex <= mpiSim->getMyMolEnd() ){
814	<	#endif // is_mpi
898	<
899	<	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;
812	>	int myUse = usesDipoles;
813	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
814	>	#endif //is_mpi
815
816	<	exI = the_bonds[index].a;
906	<	exJ = the_bonds[index].b;
816	>	double theEcr, theEst;
817
818	<	// exclude_I must always be the smaller of the pair
819	<	if( exI > exJ ){
910	<	tempEx = exI;
911	<	exI = exJ;
912	<	exJ = tempEx;
913	<	}
818	>	if (globals->getUseRF()){
819	>	info[i].useReactionField = 1;
820
821	<
822	<	#ifdef IS_MPI
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	<	the_excludes[index*2] =
841	<	the_atoms[exI]->getGlobalIndex() + 1;
842	<	the_excludes[index*2 + 1] =
843	<	the_atoms[exJ]->getGlobalIndex() + 1;
840	>	if (!globals->haveEST()){
841	>	sprintf(painCave.errMsg,
842	>	"SimSetup Warning: using default value of 0.05 * the "
843	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
844	>	painCave.isFatal = 0;
845	>	simError();
846	>	theEst = 0.05 * theEcr;
847	>	}
848	>	else{
849	>	theEst = globals->getEST();
850	>	}
851
852	<	#else  // isn't MPI
853	<
854	<	the_excludes[index*2] =     exI + 1;
855	<	the_excludes[index*2 + 1] = exJ + 1;
856	<	// fortran index from 1 (hence the +1 in the indexing)
857	<	#endif  //is_mpi
858	<
859	<	// increment the index and repeat;
931	<	index++;
932	<	}
933	<	offset += comp_stamps[i]->getNAtoms();
934	<
935	<	#ifdef IS_MPI
852	>	info[i].setEcr(theEcr, theEst);
853	>
854	>	if (!globals->haveDielectric()){
855	>	sprintf(painCave.errMsg,
856	>	"SimSetup Error: You are trying to use Reaction Field without"
857	>	"setting a dielectric constant!\n");
858	>	painCave.isFatal = 1;
859	>	simError();
860		}
861	<	#endif //is_mpi
862	<
863	<	molIndex++;
864	<	}
861	>	info[i].dielectric = globals->getDielectric();
862	>	}
863	>	else{
864	>	if (usesDipoles){
865	>	if (!globals->haveECR()){
866	>	sprintf(painCave.errMsg,
867	>	"SimSetup Warning: using default value of 1/2 the smallest "
868	>	"box length for the electrostaticCutoffRadius.\n"
869	>	"I hope you have a very fast processor!\n");
870	>	painCave.isFatal = 0;
871	>	simError();
872	>	double smallest;
873	>	smallest = info[i].boxL[0];
874	>	if (info[i].boxL[1] <= smallest)
875	>	smallest = info[i].boxL[1];
876	>	if (info[i].boxL[2] <= smallest)
877	>	smallest = info[i].boxL[2];
878	>	theEcr = 0.5 * smallest;
879	>	}
880	>	else{
881	>	theEcr = globals->getECR();
882	>	}
883	>
884	>	if (!globals->haveEST()){
885	>	sprintf(painCave.errMsg,
886	>	"SimSetup Warning: using default value of 0.05 * the "
887	>	"electrostaticCutoffRadius for the "
888	>	"electrostaticSkinThickness\n");
889	>	painCave.isFatal = 0;
890	>	simError();
891	>	theEst = 0.05 * theEcr;
892	>	}
893	>	else{
894	>	theEst = globals->getEST();
895	>	}
896	>
897	>	info[i].setEcr(theEcr, theEst);
898	>	}
899	>	}
900		}
901
902	<	the_ff->initializeBonds( the_bonds );
902	>	#ifdef IS_MPI
903	>	strcpy(checkPointMsg, "post processing checks out");
904	>	MPIcheckPoint();
905	>	#endif // is_mpi
906		}
907
908	<	void SimSetup::makeBends( void ){
908	>	void SimSetup::initSystemCoords(void){
909	>	int i;
910
911	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
949	<	bend_set* the_bends;
950	<	BendStamp* current_bend;
951	<	LinkedAssign* extras;
952	<	LinkedAssign* current_extra;
953	<
911	>	char* inName;
912
913	<	the_bends = new bend_set[tot_bends];
956	<	index = 0;
957	<	offset = 0;
958	<	molIndex = 0;
959	<	for( i=0; i<n_components; i++ ){
913	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
914
915	<	for( j=0; j<components_nmol[i]; j++ ){
915	>	for (i = 0; i < info[0].n_atoms; i++)
916	>	info[0].atoms[i]->setCoords();
917
918	+	if (globals->haveInitialConfig()){
919	+	InitializeFromFile* fileInit;
920	+	#ifdef IS_MPI // is_mpi
921	+	if (worldRank == 0){
922	+	#endif //is_mpi
923	+	inName = globals->getInitialConfig();
924	+	fileInit = new InitializeFromFile(inName);
925		#ifdef IS_MPI
926	<	if( mpiSim->getMyMolStart() <= molIndex &&
927	<	molIndex <= mpiSim->getMyMolEnd() ){
928	<	#endif // is_mpi
926	>	}
927	>	else
928	>	fileInit = new InitializeFromFile(NULL);
929	>	#endif
930	>	fileInit->readInit(info); // default velocities on
931
932	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
933	<
934	<	current_bend = comp_stamps[i]->getBend( k );
935	<	the_bends[index].a = current_bend->getA() + offset;
972	<	the_bends[index].b = current_bend->getB() + offset;
973	<	the_bends[index].c = current_bend->getC() + offset;
974	<
975	<	if( current_bend->haveExtras() ){
976	<
977	<	extras = current_bend->getExtras();
978	<	current_extra = extras;
979	<
980	<	while( current_extra != NULL ){
981	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
982	<
983	<	switch( current_extra->getType() ){
984	<
985	<	case 0:
986	<	the_bends[index].ghost =
987	<	current_extra->getInt() + offset;
988	<	the_bends[index].isGhost = 1;
989	<	break;
990	<
991	<	case 1:
992	<	the_bends[index].ghost =
993	<	(int)current_extra->getDouble() + offset;
994	<	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	<	}
932	>	delete fileInit;
933	>	}
934	>	else{
935	>	#ifdef IS_MPI
936
937	+	// no init from bass
938
939	<	#ifdef IS_MPI
939	>	sprintf(painCave.errMsg,
940	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
941	>	painCave.isFatal = 1;;
942	>	simError();
943
944	<	the_excludes[(index + tot_bonds)*2] =
1045	<	the_atoms[exI]->getGlobalIndex() + 1;
1046	<	the_excludes[(index + tot_bonds)*2 + 1] =
1047	<	the_atoms[exJ]->getGlobalIndex() + 1;
1048	<
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
1063	<	}
1064	<	#endif //is_mpi
944	>	#else
945
946	<	molIndex++;
947	<	}
946	>	initFromBass();
947	>
948	>
949	>	#endif
950		}
951
952		#ifdef IS_MPI
953	<	sprintf( checkPointMsg,
1072	<	"Successfully created the bends list.\n" );
953	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
954		MPIcheckPoint();
955		#endif // is_mpi
1075	–
1076	–
1077	–	the_ff->initializeBends( the_bends );
956		}
957
1080	–	void SimSetup::makeTorsions( void ){
958
959	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
960	<	torsion_set* the_torsions;
1084	<	TorsionStamp* current_torsion;
959	>	void SimSetup::makeOutNames(void){
960	>	int k;
961
1086	–	the_torsions = new torsion_set[tot_torsions];
1087	–	index = 0;
1088	–	offset = 0;
1089	–	molIndex = 0;
1090	–	for( i=0; i<n_components; i++ ){
962
963	<	for( j=0; j<components_nmol[i]; j++ ){
1093	<
963	>	for (k = 0; k < nInfo; k++){
964		#ifdef IS_MPI
965	<	if( mpiSim->getMyMolStart() <= molIndex &&
966	<	molIndex <= mpiSim->getMyMolEnd() ){
1097	<	#endif // is_mpi
965	>	if (worldRank == 0){
966	>	#endif // is_mpi
967
968	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
968	>	if (globals->haveFinalConfig()){
969	>	strcpy(info[k].finalName, globals->getFinalConfig());
970	>	}
971	>	else{
972	>	strcpy(info[k].finalName, inFileName);
973	>	char* endTest;
974	>	int nameLength = strlen(info[k].finalName);
975	>	endTest = &(info[k].finalName[nameLength - 5]);
976	>	if (!strcmp(endTest, ".bass")){
977	>	strcpy(endTest, ".eor");
978	>	}
979	>	else if (!strcmp(endTest, ".BASS")){
980	>	strcpy(endTest, ".eor");
981	>	}
982	>	else{
983	>	endTest = &(info[k].finalName[nameLength - 4]);
984	>	if (!strcmp(endTest, ".bss")){
985	>	strcpy(endTest, ".eor");
986	>	}
987	>	else if (!strcmp(endTest, ".mdl")){
988	>	strcpy(endTest, ".eor");
989	>	}
990	>	else{
991	>	strcat(info[k].finalName, ".eor");
992	>	}
993	>	}
994	>	}
995
996	<	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;
996	>	// make the sample and status out names
997
998	<	exI = the_torsions[index].a;
999	<	exJ = the_torsions[index].d;
998	>	strcpy(info[k].sampleName, inFileName);
999	>	char* endTest;
1000	>	int nameLength = strlen(info[k].sampleName);
1001	>	endTest = &(info[k].sampleName[nameLength - 5]);
1002	>	if (!strcmp(endTest, ".bass")){
1003	>	strcpy(endTest, ".dump");
1004	>	}
1005	>	else if (!strcmp(endTest, ".BASS")){
1006	>	strcpy(endTest, ".dump");
1007	>	}
1008	>	else{
1009	>	endTest = &(info[k].sampleName[nameLength - 4]);
1010	>	if (!strcmp(endTest, ".bss")){
1011	>	strcpy(endTest, ".dump");
1012	>	}
1013	>	else if (!strcmp(endTest, ".mdl")){
1014	>	strcpy(endTest, ".dump");
1015	>	}
1016	>	else{
1017	>	strcat(info[k].sampleName, ".dump");
1018	>	}
1019	>	}
1020
1021	<
1022	<	// exclude_I must always be the smaller of the pair
1023	<	if( exI > exJ ){
1024	<	tempEx = exI;
1025	<	exI = exJ;
1115	<	exJ = tempEx;
1116	<	}
1117	<
1118	<
1119	<	#ifdef IS_MPI
1120	<
1121	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
1122	<	the_atoms[exI]->getGlobalIndex() + 1;
1123	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1124	<	the_atoms[exJ]->getGlobalIndex() + 1;
1125	<
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	<
1133	<
1134	<	// increment the index and repeat;
1135	<	index++;
1021	>	strcpy(info[k].statusName, inFileName);
1022	>	nameLength = strlen(info[k].statusName);
1023	>	endTest = &(info[k].statusName[nameLength - 5]);
1024	>	if (!strcmp(endTest, ".bass")){
1025	>	strcpy(endTest, ".stat");
1026		}
1027	<	offset += comp_stamps[i]->getNAtoms();
1027	>	else if (!strcmp(endTest, ".BASS")){
1028	>	strcpy(endTest, ".stat");
1029	>	}
1030	>	else{
1031	>	endTest = &(info[k].statusName[nameLength - 4]);
1032	>	if (!strcmp(endTest, ".bss")){
1033	>	strcpy(endTest, ".stat");
1034	>	}
1035	>	else if (!strcmp(endTest, ".mdl")){
1036	>	strcpy(endTest, ".stat");
1037	>	}
1038	>	else{
1039	>	strcat(info[k].statusName, ".stat");
1040	>	}
1041	>	}
1042
1043		#ifdef IS_MPI
1140	–	}
1141	–	#endif //is_mpi
1044
1143	–	molIndex++;
1045		}
1046	+	#endif // is_mpi
1047		}
1146	–
1147	–	the_ff->initializeTorsions( the_torsions );
1048		}
1049
1150	–	void SimSetup::initFromBass( void ){
1050
1051	<	int i, j, k;
1052	<	int n_cells;
1154	<	double cellx, celly, cellz;
1155	<	double temp1, temp2, temp3;
1156	<	int n_per_extra;
1157	<	int n_extra;
1158	<	int have_extra, done;
1051	>	void SimSetup::sysObjectsCreation(void){
1052	>	int i, k;
1053
1054	<	temp1 = (double)tot_nmol / 4.0;
1161	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1162	<	temp3 = ceil( temp2 );
1054	>	// create the forceField
1055
1056	<	have_extra =0;
1165	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1166	<	have_extra =1;
1056	>	createFF();
1057
1058	<	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 );
1058	>	// extract componentList
1059
1060	<	if( n_per_extra > 4){
1061	<	sprintf( painCave.errMsg,
1062	<	"SimSetup error. There has been an error in constructing"
1063	<	" the non-complete lattice.\n" );
1060	>	compList();
1061	>
1062	>	// calc the number of atoms, bond, bends, and torsions
1063	>
1064	>	calcSysValues();
1065	>
1066	>	#ifdef IS_MPI
1067	>	// divide the molecules among the processors
1068	>
1069	>	mpiMolDivide();
1070	>	#endif //is_mpi
1071	>
1072	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1073	>
1074	>	makeSysArrays();
1075	>
1076	>	// make and initialize the molecules (all but atomic coordinates)
1077	>
1078	>	makeMolecules();
1079	>
1080	>	for (k = 0; k < nInfo; k++){
1081	>	info[k].identArray = new int[info[k].n_atoms];
1082	>	for (i = 0; i < info[k].n_atoms; i++){
1083	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1084	>	}
1085	>	}
1086	>	}
1087	>
1088	>
1089	>	void SimSetup::createFF(void){
1090	>	switch (ffCase){
1091	>	case FF_DUFF:
1092	>	the_ff = new DUFF();
1093	>	break;
1094	>
1095	>	case FF_LJ:
1096	>	the_ff = new LJFF();
1097	>	break;
1098	>
1099	>	case FF_EAM:
1100	>	the_ff = new EAM_FF();
1101	>	break;
1102	>
1103	>	default:
1104	>	sprintf(painCave.errMsg,
1105	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1106		painCave.isFatal = 1;
1107		simError();
1182	–	}
1108		}
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	–	}
1109
1110	<	current_mol = 0;
1111	<	current_comp_mol = 0;
1112	<	current_comp = 0;
1113	<	current_atom_ndx = 0;
1110	>	#ifdef IS_MPI
1111	>	strcpy(checkPointMsg, "ForceField creation successful");
1112	>	MPIcheckPoint();
1113	>	#endif // is_mpi
1114	>	}
1115
1196	–	for( i=0; i < n_cells ; i++ ){
1197	–	for( j=0; j < n_cells; j++ ){
1198	–	for( k=0; k < n_cells; k++ ){
1116
1117	<	makeElement( i * cellx,
1118	<	j * celly,
1119	<	k * cellz );
1117	>	void SimSetup::compList(void){
1118	>	int i;
1119	>	char* id;
1120	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1121	>	LinkedMolStamp* currentStamp = NULL;
1122	>	comp_stamps = new MoleculeStamp * [n_components];
1123
1124	<	makeElement( i * cellx + 0.5 * cellx,
1125	<	j * celly + 0.5 * celly,
1206	<	k * cellz );
1124	>	// make an array of molecule stamps that match the components used.
1125	>	// also extract the used stamps out into a separate linked list
1126
1127	<	makeElement( i * cellx,
1128	<	j * celly + 0.5 * celly,
1129	<	k * cellz + 0.5 * cellz );
1127	>	for (i = 0; i < nInfo; i++){
1128	>	info[i].nComponents = n_components;
1129	>	info[i].componentsNmol = components_nmol;
1130	>	info[i].compStamps = comp_stamps;
1131	>	info[i].headStamp = headStamp;
1132	>	}
1133
1134	<	makeElement( i * cellx + 0.5 * cellx,
1135	<	j * celly,
1136	<	k * cellz + 0.5 * cellz );
1134	>
1135	>	for (i = 0; i < n_components; i++){
1136	>	id = the_components[i]->getType();
1137	>	comp_stamps[i] = NULL;
1138	>
1139	>	// check to make sure the component isn't already in the list
1140	>
1141	>	comp_stamps[i] = headStamp->match(id);
1142	>	if (comp_stamps[i] == NULL){
1143	>	// extract the component from the list;
1144	>
1145	>	currentStamp = stamps->extractMolStamp(id);
1146	>	if (currentStamp == NULL){
1147	>	sprintf(painCave.errMsg,
1148	>	"SimSetup error: Component \"%s\" was not found in the "
1149	>	"list of declared molecules\n",
1150	>	id);
1151	>	painCave.isFatal = 1;
1152	>	simError();
1153		}
1154	+
1155	+	headStamp->add(currentStamp);
1156	+	comp_stamps[i] = headStamp->match(id);
1157		}
1158		}
1159
1160	<	if( have_extra ){
1161	<	done = 0;
1160	>	#ifdef IS_MPI
1161	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1162	>	MPIcheckPoint();
1163	>	#endif // is_mpi
1164	>	}
1165
1166	<	int start_ndx;
1167	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1224	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1166	>	void SimSetup::calcSysValues(void){
1167	>	int i;
1168
1169	<	if( i < n_cells ){
1169	>	int* molMembershipArray;
1170
1171	<	if( j < n_cells ){
1172	<	start_ndx = n_cells;
1173	<	}
1174	<	else start_ndx = 0;
1175	<	}
1176	<	else start_ndx = 0;
1171	>	tot_atoms = 0;
1172	>	tot_bonds = 0;
1173	>	tot_bends = 0;
1174	>	tot_torsions = 0;
1175	>	for (i = 0; i < n_components; i++){
1176	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1177	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1178	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1179	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1180	>	}
1181
1182	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1182	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1183	>	molMembershipArray = new int[tot_atoms];
1184
1185	<	makeElement( i * cellx,
1186	<	j * celly,
1187	<	k * cellz );
1188	<	done = ( current_mol >= tot_nmol );
1185	>	for (i = 0; i < nInfo; i++){
1186	>	info[i].n_atoms = tot_atoms;
1187	>	info[i].n_bonds = tot_bonds;
1188	>	info[i].n_bends = tot_bends;
1189	>	info[i].n_torsions = tot_torsions;
1190	>	info[i].n_SRI = tot_SRI;
1191	>	info[i].n_mol = tot_nmol;
1192
1193	<	if( !done && n_per_extra > 1 ){
1194	<	makeElement( i * cellx + 0.5 * cellx,
1195	<	j * celly + 0.5 * celly,
1245	<	k * cellz );
1246	<	done = ( current_mol >= tot_nmol );
1247	<	}
1193	>	info[i].molMembershipArray = molMembershipArray;
1194	>	}
1195	>	}
1196
1197	<	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	<	}
1197	>	#ifdef IS_MPI
1198
1199	<	if( !done && n_per_extra > 3){
1200	<	makeElement( i * cellx + 0.5 * cellx,
1201	<	j * celly,
1202	<	k * cellz + 0.5 * cellz );
1203	<	done = ( current_mol >= tot_nmol );
1204	<	}
1205	<	}
1199	>	void SimSetup::mpiMolDivide(void){
1200	>	int i, j, k;
1201	>	int localMol, allMol;
1202	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1203	>
1204	>	mpiSim = new mpiSimulation(info);
1205	>
1206	>	globalIndex = mpiSim->divideLabor();
1207	>
1208	>	// set up the local variables
1209	>
1210	>	mol2proc = mpiSim->getMolToProcMap();
1211	>	molCompType = mpiSim->getMolComponentType();
1212	>
1213	>	allMol = 0;
1214	>	localMol = 0;
1215	>	local_atoms = 0;
1216	>	local_bonds = 0;
1217	>	local_bends = 0;
1218	>	local_torsions = 0;
1219	>	globalAtomIndex = 0;
1220	>
1221	>
1222	>	for (i = 0; i < n_components; i++){
1223	>	for (j = 0; j < components_nmol[i]; j++){
1224	>	if (mol2proc[allMol] == worldRank){
1225	>	local_atoms += comp_stamps[i]->getNAtoms();
1226	>	local_bonds += comp_stamps[i]->getNBonds();
1227	>	local_bends += comp_stamps[i]->getNBends();
1228	>	local_torsions += comp_stamps[i]->getNTorsions();
1229	>	localMol++;
1230	>	}
1231	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1232	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1233	>	globalAtomIndex++;
1234		}
1235	+
1236	+	allMol++;
1237		}
1238		}
1239	+	local_SRI = local_bonds + local_bends + local_torsions;
1240
1241	+	info[0].n_atoms = mpiSim->getMyNlocal();
1242
1243	<	for( i=0; i<simnfo->n_atoms; i++ ){
1244	<	simnfo->atoms[i]->set_vx( 0.0 );
1245	<	simnfo->atoms[i]->set_vy( 0.0 );
1246	<	simnfo->atoms[i]->set_vz( 0.0 );
1243	>	if (local_atoms != info[0].n_atoms){
1244	>	sprintf(painCave.errMsg,
1245	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1246	>	" localAtom (%d) are not equal.\n",
1247	>	info[0].n_atoms, local_atoms);
1248	>	painCave.isFatal = 1;
1249	>	simError();
1250		}
1251	+
1252	+	info[0].n_bonds = local_bonds;
1253	+	info[0].n_bends = local_bends;
1254	+	info[0].n_torsions = local_torsions;
1255	+	info[0].n_SRI = local_SRI;
1256	+	info[0].n_mol = localMol;
1257	+
1258	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1259	+	MPIcheckPoint();
1260		}
1261
1262	<	void SimSetup::makeElement( double x, double y, double z ){
1262	>	#endif // is_mpi
1263
1277	–	int k;
1278	–	AtomStamp* current_atom;
1279	–	DirectionalAtom* dAtom;
1280	–	double rotMat[3][3];
1264
1265	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1265	>	void SimSetup::makeSysArrays(void){
1266	>
1267	>	#ifndef IS_MPI
1268	>	int k, j;
1269	>	#endif // is_mpi
1270	>	int i, l;
1271
1272	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1273	<	if( !current_atom->havePosition() ){
1274	<	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	<	}
1272	>	Atom** the_atoms;
1273	>	Molecule* the_molecules;
1274	>	Exclude** the_excludes;
1275
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() );
1276
1277	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1277	>	for (l = 0; l < nInfo; l++){
1278	>	// create the atom and short range interaction arrays
1279
1280	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1280	>	the_atoms = new Atom * [info[l].n_atoms];
1281	>	the_molecules = new Molecule[info[l].n_mol];
1282	>	int molIndex;
1283
1284	<	rotMat[0][0] = 1.0;
1306	<	rotMat[0][1] = 0.0;
1307	<	rotMat[0][2] = 0.0;
1284	>	// initialize the molecule's stampID's
1285
1286	<	rotMat[1][0] = 0.0;
1310	<	rotMat[1][1] = 1.0;
1311	<	rotMat[1][2] = 0.0;
1286	>	#ifdef IS_MPI
1287
1313	–	rotMat[2][0] = 0.0;
1314	–	rotMat[2][1] = 0.0;
1315	–	rotMat[2][2] = 1.0;
1288
1289	<	dAtom->setA( rotMat );
1289	>	molIndex = 0;
1290	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1291	>	if (mol2proc[i] == worldRank){
1292	>	the_molecules[molIndex].setStampID(molCompType[i]);
1293	>	the_molecules[molIndex].setMyIndex(molIndex);
1294	>	the_molecules[molIndex].setGlobalIndex(i);
1295	>	molIndex++;
1296	>	}
1297		}
1298
1299	<	current_atom_ndx++;
1321	<	}
1299	>	#else // is_mpi
1300
1301	<	current_mol++;
1302	<	current_comp_mol++;
1301	>	molIndex = 0;
1302	>	globalAtomIndex = 0;
1303	>	for (i = 0; i < n_components; i++){
1304	>	for (j = 0; j < components_nmol[i]; j++){
1305	>	the_molecules[molIndex].setStampID(i);
1306	>	the_molecules[molIndex].setMyIndex(molIndex);
1307	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1308	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1309	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1310	>	globalAtomIndex++;
1311	>	}
1312	>	molIndex++;
1313	>	}
1314	>	}
1315
1326	–	if( current_comp_mol >= components_nmol[current_comp] ){
1316
1317	<	current_comp_mol = 0;
1318	<	current_comp++;
1317	>	#endif // is_mpi
1318	>
1319	>
1320	>	if (info[l].n_SRI){
1321	>	Exclude::createArray(info[l].n_SRI);
1322	>	the_excludes = new Exclude * [info[l].n_SRI];
1323	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1324	>	the_excludes[ex] = new Exclude(ex);
1325	>	}
1326	>	info[l].globalExcludes = new int;
1327	>	info[l].n_exclude = info[l].n_SRI;
1328	>	}
1329	>	else{
1330	>	Exclude::createArray(1);
1331	>	the_excludes = new Exclude * ;
1332	>	the_excludes[0] = new Exclude(0);
1333	>	the_excludes[0]->setPair(0, 0);
1334	>	info[l].globalExcludes = new int;
1335	>	info[l].globalExcludes[0] = 0;
1336	>	info[l].n_exclude = 0;
1337	>	}
1338	>
1339	>	// set the arrays into the SimInfo object
1340	>
1341	>	info[l].atoms = the_atoms;
1342	>	info[l].molecules = the_molecules;
1343	>	info[l].nGlobalExcludes = 0;
1344	>	info[l].excludes = the_excludes;
1345	>
1346	>	the_ff->setSimInfo(info);
1347		}
1348		}
1349	+
1350	+	void SimSetup::makeIntegrator(void){
1351	+	int k;
1352	+
1353	+	NVE<RealIntegrator>* myNVE = NULL;
1354	+	NVT<RealIntegrator>* myNVT = NULL;
1355	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1356	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1357	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1358	+
1359	+	for (k = 0; k < nInfo; k++){
1360	+	switch (ensembleCase){
1361	+	case NVE_ENS:
1362	+	if (globals->haveZconstraints()){
1363	+	setupZConstraint(info[k]);
1364	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1365	+	}
1366	+	else{
1367	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1368	+	}
1369	+
1370	+	info->the_integrator = myNVE;
1371	+	break;
1372	+
1373	+	case NVT_ENS:
1374	+	if (globals->haveZconstraints()){
1375	+	setupZConstraint(info[k]);
1376	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1377	+	}
1378	+	else
1379	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1380	+
1381	+	myNVT->setTargetTemp(globals->getTargetTemp());
1382	+
1383	+	if (globals->haveTauThermostat())
1384	+	myNVT->setTauThermostat(globals->getTauThermostat());
1385	+	else{
1386	+	sprintf(painCave.errMsg,
1387	+	"SimSetup error: If you use the NVT\n"
1388	+	"    ensemble, you must set tauThermostat.\n");
1389	+	painCave.isFatal = 1;
1390	+	simError();
1391	+	}
1392	+
1393	+	info->the_integrator = myNVT;
1394	+	break;
1395	+
1396	+	case NPTi_ENS:
1397	+	if (globals->haveZconstraints()){
1398	+	setupZConstraint(info[k]);
1399	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1400	+	}
1401	+	else
1402	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1403	+
1404	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1405	+
1406	+	if (globals->haveTargetPressure())
1407	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1408	+	else{
1409	+	sprintf(painCave.errMsg,
1410	+	"SimSetup error: If you use a constant pressure\n"
1411	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1412	+	painCave.isFatal = 1;
1413	+	simError();
1414	+	}
1415	+
1416	+	if (globals->haveTauThermostat())
1417	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1418	+	else{
1419	+	sprintf(painCave.errMsg,
1420	+	"SimSetup error: If you use an NPT\n"
1421	+	"    ensemble, you must set tauThermostat.\n");
1422	+	painCave.isFatal = 1;
1423	+	simError();
1424	+	}
1425	+
1426	+	if (globals->haveTauBarostat())
1427	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1428	+	else{
1429	+	sprintf(painCave.errMsg,
1430	+	"SimSetup error: If you use an NPT\n"
1431	+	"    ensemble, you must set tauBarostat.\n");
1432	+	painCave.isFatal = 1;
1433	+	simError();
1434	+	}
1435	+
1436	+	info->the_integrator = myNPTi;
1437	+	break;
1438	+
1439	+	case NPTf_ENS:
1440	+	if (globals->haveZconstraints()){
1441	+	setupZConstraint(info[k]);
1442	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1443	+	}
1444	+	else
1445	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1446	+
1447	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1448	+
1449	+	if (globals->haveTargetPressure())
1450	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1451	+	else{
1452	+	sprintf(painCave.errMsg,
1453	+	"SimSetup error: If you use a constant pressure\n"
1454	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1455	+	painCave.isFatal = 1;
1456	+	simError();
1457	+	}
1458	+
1459	+	if (globals->haveTauThermostat())
1460	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1461	+	else{
1462	+	sprintf(painCave.errMsg,
1463	+	"SimSetup error: If you use an NPT\n"
1464	+	"    ensemble, you must set tauThermostat.\n");
1465	+	painCave.isFatal = 1;
1466	+	simError();
1467	+	}
1468	+
1469	+	if (globals->haveTauBarostat())
1470	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1471	+	else{
1472	+	sprintf(painCave.errMsg,
1473	+	"SimSetup error: If you use an NPT\n"
1474	+	"    ensemble, you must set tauBarostat.\n");
1475	+	painCave.isFatal = 1;
1476	+	simError();
1477	+	}
1478	+
1479	+	info->the_integrator = myNPTf;
1480	+	break;
1481	+
1482	+	case NPTxyz_ENS:
1483	+	if (globals->haveZconstraints()){
1484	+	setupZConstraint(info[k]);
1485	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1486	+	}
1487	+	else
1488	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1489	+
1490	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1491	+
1492	+	if (globals->haveTargetPressure())
1493	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1494	+	else{
1495	+	sprintf(painCave.errMsg,
1496	+	"SimSetup error: If you use a constant pressure\n"
1497	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1498	+	painCave.isFatal = 1;
1499	+	simError();
1500	+	}
1501	+
1502	+	if (globals->haveTauThermostat())
1503	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1504	+	else{
1505	+	sprintf(painCave.errMsg,
1506	+	"SimSetup error: If you use an NPT\n"
1507	+	"    ensemble, you must set tauThermostat.\n");
1508	+	painCave.isFatal = 1;
1509	+	simError();
1510	+	}
1511	+
1512	+	if (globals->haveTauBarostat())
1513	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1514	+	else{
1515	+	sprintf(painCave.errMsg,
1516	+	"SimSetup error: If you use an NPT\n"
1517	+	"    ensemble, you must set tauBarostat.\n");
1518	+	painCave.isFatal = 1;
1519	+	simError();
1520	+	}
1521	+
1522	+	info->the_integrator = myNPTxyz;
1523	+	break;
1524	+
1525	+	default:
1526	+	sprintf(painCave.errMsg,
1527	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1528	+	painCave.isFatal = 1;
1529	+	simError();
1530	+	}
1531	+	}
1532	+	}
1533	+
1534	+	void SimSetup::initFortran(void){
1535	+	info[0].refreshSim();
1536	+
1537	+	if (!strcmp(info[0].mixingRule, "standard")){
1538	+	the_ff->initForceField(LB_MIXING_RULE);
1539	+	}
1540	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1541	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1542	+	}
1543	+	else{
1544	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1545	+	info[0].mixingRule);
1546	+	painCave.isFatal = 1;
1547	+	simError();
1548	+	}
1549	+
1550	+
1551	+	#ifdef IS_MPI
1552	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1553	+	MPIcheckPoint();
1554	+	#endif // is_mpi
1555	+	}
1556	+
1557	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1558	+	int nZConstraints;
1559	+	ZconStamp** zconStamp;
1560	+
1561	+	if (globals->haveZconstraintTime()){
1562	+	//add sample time of z-constraint  into SimInfo's property list
1563	+	DoubleData* zconsTimeProp = new DoubleData();
1564	+	zconsTimeProp->setID(ZCONSTIME_ID);
1565	+	zconsTimeProp->setData(globals->getZconsTime());
1566	+	theInfo.addProperty(zconsTimeProp);
1567	+	}
1568	+	else{
1569	+	sprintf(painCave.errMsg,
1570	+	"ZConstraint error: If you use an ZConstraint\n"
1571	+	" , you must set sample time.\n");
1572	+	painCave.isFatal = 1;
1573	+	simError();
1574	+	}
1575	+
1576	+	//push zconsTol into siminfo, if user does not specify
1577	+	//value for zconsTol, a default value will be used
1578	+	DoubleData* zconsTol = new DoubleData();
1579	+	zconsTol->setID(ZCONSTOL_ID);
1580	+	if (globals->haveZconsTol()){
1581	+	zconsTol->setData(globals->getZconsTol());
1582	+	}
1583	+	else{
1584	+	double defaultZConsTol = 0.01;
1585	+	sprintf(painCave.errMsg,
1586	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1587	+	" , default value %f is used.\n",
1588	+	defaultZConsTol);
1589	+	painCave.isFatal = 0;
1590	+	simError();
1591	+
1592	+	zconsTol->setData(defaultZConsTol);
1593	+	}
1594	+	theInfo.addProperty(zconsTol);
1595	+
1596	+	//set Force Subtraction Policy
1597	+	StringData* zconsForcePolicy = new StringData();
1598	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1599	+
1600	+	if (globals->haveZconsForcePolicy()){
1601	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1602	+	}
1603	+	else{
1604	+	sprintf(painCave.errMsg,
1605	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1606	+	"PolicyByMass is used\n");
1607	+	painCave.isFatal = 0;
1608	+	simError();
1609	+	zconsForcePolicy->setData("BYMASS");
1610	+	}
1611	+
1612	+	theInfo.addProperty(zconsForcePolicy);
1613	+
1614	+	//Determine the name of ouput file and add it into SimInfo's property list
1615	+	//Be careful, do not use inFileName, since it is a pointer which
1616	+	//point to a string at master node, and slave nodes do not contain that string
1617	+
1618	+	string zconsOutput(theInfo.finalName);
1619	+
1620	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1621	+
1622	+	StringData* zconsFilename = new StringData();
1623	+	zconsFilename->setID(ZCONSFILENAME_ID);
1624	+	zconsFilename->setData(zconsOutput);
1625	+
1626	+	theInfo.addProperty(zconsFilename);
1627	+
1628	+	//setup index, pos and other parameters of z-constraint molecules
1629	+	nZConstraints = globals->getNzConstraints();
1630	+	theInfo.nZconstraints = nZConstraints;
1631	+
1632	+	zconStamp = globals->getZconStamp();
1633	+	ZConsParaItem tempParaItem;
1634	+
1635	+	ZConsParaData* zconsParaData = new ZConsParaData();
1636	+	zconsParaData->setID(ZCONSPARADATA_ID);
1637	+
1638	+	for (int i = 0; i < nZConstraints; i++){
1639	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1640	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1641	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1642	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1643	+
1644	+	zconsParaData->addItem(tempParaItem);
1645	+	}
1646	+
1647	+	//check the uniqueness of index
1648	+	if(!zconsParaData->isIndexUnique()){
1649	+	sprintf(painCave.errMsg,
1650	+	"ZConstraint Error: molIndex is not unique\n");
1651	+	painCave.isFatal = 1;
1652	+	simError();
1653	+	}
1654	+
1655	+	//sort the parameters by index of molecules
1656	+	zconsParaData->sortByIndex();
1657	+
1658	+	//push data into siminfo, therefore, we can retrieve later
1659	+	theInfo.addProperty(zconsParaData);
1660	+	}

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