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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 412 by mmeineke, Wed Mar 26 21:50:33 2003 UTC vs.
Revision 782 by mmeineke, Tue Sep 23 20:34:31 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	+
26	+	#define FF_DUFF 0
27	+	#define FF_LJ   1
28	+	#define FF_EAM  2
29	+
30	+	using namespace std;
31	+
32		SimSetup::SimSetup(){
33	+	isInfoArray = 0;
34	+	nInfo = 1;
35	+
36		stamps = new MakeStamps();
37		globals = new Globals();
38	<
38	>
39	>
40		#ifdef IS_MPI
41	<	strcpy( checkPointMsg, "SimSetup creation successful" );
41	>	strcpy(checkPointMsg, "SimSetup creation successful");
42		MPIcheckPoint();
43		#endif // IS_MPI
44		}
#	Line 27 | Line 48 | void SimSetup::parseFile( char* fileName ){
48		delete globals;
49		}
50
51	<	void SimSetup::parseFile( char* fileName ){
51	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
52	>	info = the_info;
53	>	nInfo = theNinfo;
54	>	isInfoArray = 1;
55	>	}
56
57	+
58	+	void SimSetup::parseFile(char* fileName){
59		#ifdef IS_MPI
60	<	if( worldRank == 0 ){
60	>	if (worldRank == 0){
61		#endif // is_mpi
62	<
62	>
63		inFileName = fileName;
64	<	set_interface_stamps( stamps, globals );
65	<
64	>	set_interface_stamps(stamps, globals);
65	>
66		#ifdef IS_MPI
67		mpiEventInit();
68		#endif
69
70	<	yacc_BASS( fileName );
70	>	yacc_BASS(fileName);
71
72		#ifdef IS_MPI
73		throwMPIEvent(NULL);
74		}
75	<	else receiveParse();
75	>	else{
76	>	receiveParse();
77	>	}
78		#endif
79
80		}
81
82		#ifdef IS_MPI
83		void SimSetup::receiveParse(void){
84	<
85	<	set_interface_stamps( stamps, globals );
86	<	mpiEventInit();
87	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
84	>	set_interface_stamps(stamps, globals);
85	>	mpiEventInit();
86	>	MPIcheckPoint();
87	>	mpiEventLoop();
88		}
89
90		#endif // is_mpi
91
92	<	void SimSetup::createSim( void ){
92	>	void SimSetup::createSim(void){
93	>	int i, j, k, globalAtomIndex;
94
95	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
95	>	// gather all of the information from the Bass file
96
97	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
97	>	gatherInfo();
98
99	<	// 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();
99	>	// creation of complex system objects
100
101	<	// 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 );
101	>	sysObjectsCreation();
102
103	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
103	>	// check on the post processing info
104
105	+	finalInfoCheck();
106
107	<	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	<	}
107	>	// initialize the system coordinates
108
109	<	#ifdef IS_MPI
110	<	strcpy( checkPointMsg, "ForceField creation successful" );
111	<	MPIcheckPoint();
106	<	#endif // is_mpi
109	>	if (!isInfoArray){
110	>	initSystemCoords();
111	>	}
112
113	<
113	>	// make the output filenames
114
115	<	// 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];
115	>	makeOutNames();
116
117	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
117	>	// make the integrator
118
119	<	tot_nmol = 0;
120	<	for( i=0; i<n_components; i++ ){
119	>	makeIntegrator();
120
121	<	if( !the_components[i]->haveNMol() ){
122	<	// we have a problem
123	<	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	<	}
121	>	#ifdef IS_MPI
122	>	mpiSim->mpiRefresh();
123	>	#endif
124
125	<	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	<	}
125	>	// initialize the Fortran
126
127	<	#ifdef IS_MPI
128	<	strcpy( checkPointMsg, "Have the number of components" );
162	<	MPIcheckPoint();
163	<	#endif // is_mpi
127	>	initFortran();
128	>	}
129
165	–	// make an array of molecule stamps that match the components used.
166	–	// also extract the used stamps out into a separate linked list
130
131	<	simnfo->nComponents = n_components;
132	<	simnfo->componentsNmol = components_nmol;
133	<	simnfo->compStamps = comp_stamps;
134	<	simnfo->headStamp = new LinkedMolStamp();
135	<
136	<	char* id;
137	<	LinkedMolStamp* headStamp = simnfo->headStamp;
138	<	LinkedMolStamp* currentStamp = NULL;
139	<	for( i=0; i<n_components; i++ ){
131	>	void SimSetup::makeMolecules(void){
132	>	int k, l;
133	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
134	>	molInit molInfo;
135	>	DirectionalAtom* dAtom;
136	>	LinkedAssign* extras;
137	>	LinkedAssign* current_extra;
138	>	AtomStamp* currentAtom;
139	>	BondStamp* currentBond;
140	>	BendStamp* currentBend;
141	>	TorsionStamp* currentTorsion;
142
143	<	id = the_components[i]->getType();
144	<	comp_stamps[i] = NULL;
145	<
181	<	// check to make sure the component isn't already in the list
143	>	bond_pair* theBonds;
144	>	bend_set* theBends;
145	>	torsion_set* theTorsions;
146
183	–	comp_stamps[i] = headStamp->match( id );
184	–	if( comp_stamps[i] == NULL ){
185	–
186	–	// extract the component from the list;
187	–
188	–	currentStamp = the_stamps->extractMolStamp( id );
189	–	if( currentStamp == NULL ){
190	–	sprintf( painCave.errMsg,
191	–	"SimSetup error: Component \"%s\" was not found in the "
192	–	"list of declared molecules\n",
193	–	id );
194	–	painCave.isFatal = 1;
195	–	simError();
196	–	}
197	–
198	–	headStamp->add( currentStamp );
199	–	comp_stamps[i] = headStamp->match( id );
200	–	}
201	–	}
147
148	<	#ifdef IS_MPI
204	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
205	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
148	>	//init the forceField paramters
149
150	+	the_ff->readParams();
151
152
153	<	// caclulate the number of atoms, bonds, bends and torsions
153	>	// init the atoms
154
155	<	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	<	}
155	>	double ux, uy, uz, u, uSqr;
156
157	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
157	>	for (k = 0; k < nInfo; k++){
158	>	the_ff->setSimInfo(&(info[k]));
159
160	<	simnfo->n_atoms = tot_atoms;
161	<	simnfo->n_bonds = tot_bonds;
162	<	simnfo->n_bends = tot_bends;
163	<	simnfo->n_torsions = tot_torsions;
231	<	simnfo->n_SRI = tot_SRI;
232	<	simnfo->n_mol = tot_nmol;
160	>	atomOffset = 0;
161	>	excludeOffset = 0;
162	>	for (i = 0; i < info[k].n_mol; i++){
163	>	stampID = info[k].molecules[i].getStampID();
164
165	<
166	<	#ifdef IS_MPI
165	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
166	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
167	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
168	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
169	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
170
171	<	// divide the molecules among processors here.
172	<
173	<	mpiSim = new mpiSimulation( simnfo );
174	<
175	<
171	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
172	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
173	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
174	>	molInfo.myBends = new Bend * [molInfo.nBends];
175	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
176
177	<	globalIndex = mpiSim->divideLabor();
177	>	theBonds = new bond_pair[molInfo.nBonds];
178	>	theBends = new bend_set[molInfo.nBends];
179	>	theTorsions = new torsion_set[molInfo.nTorsions];
180
181	+	// make the Atoms
182
183	+	for (j = 0; j < molInfo.nAtoms; j++){
184	+	currentAtom = comp_stamps[stampID]->getAtom(j);
185	+	if (currentAtom->haveOrientation()){
186	+	dAtom = new DirectionalAtom((j + atomOffset),
187	+	info[k].getConfiguration());
188	+	info[k].n_oriented++;
189	+	molInfo.myAtoms[j] = dAtom;
190
191	<	// set up the local variables
192	<
193	<	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++ ){
191	>	ux = currentAtom->getOrntX();
192	>	uy = currentAtom->getOrntY();
193	>	uz = currentAtom->getOrntZ();
194
195	<	for( j=0; j<components_nmol[i]; j++ ){
261	<
262	<	if( mpiSim->getMyMolStart() <= allMol &&
263	<	allMol <= mpiSim->getMyMolEnd() ){
264	<
265	<	local_atoms +=    comp_stamps[i]->getNAtoms();
266	<	local_bonds +=    comp_stamps[i]->getNBonds();
267	<	local_bends +=    comp_stamps[i]->getNBends();
268	<	local_torsions += comp_stamps[i]->getNTorsions();
269	<	localMol++;
270	<	}
271	<	allMol++;
272	<	}
273	<	}
274	<	local_SRI = local_bonds + local_bends + local_torsions;
275	<
195	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
196
197	<	simnfo->n_atoms = mpiSim->getMyNlocal();
198	<
199	<	if( local_atoms != simnfo->n_atoms ){
200	<	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	>	u = sqrt(uSqr);
198	>	ux = ux / u;
199	>	uy = uy / u;
200	>	uz = uz / u;
201
202	<	simnfo->n_bonds = local_bonds;
203	<	simnfo->n_bends = local_bends;
204	<	simnfo->n_torsions = local_torsions;
205	<	simnfo->n_SRI = local_SRI;
206	<	simnfo->n_mol = localMol;
202	>	dAtom->setSUx(ux);
203	>	dAtom->setSUy(uy);
204	>	dAtom->setSUz(uz);
205	>	}
206	>	else{
207	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
208	>	info[k].getConfiguration());
209	>	}
210	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
211
212	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
213	<	MPIcheckPoint();
214	<
215	<
212	>	#ifdef IS_MPI
213	>
214	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
215	>
216		#endif // is_mpi
217	<
217	>	}
218
219	<	// create the atom and short range interaction arrays
219	>	// make the bonds
220	>	for (j = 0; j < molInfo.nBonds; j++){
221	>	currentBond = comp_stamps[stampID]->getBond(j);
222	>	theBonds[j].a = currentBond->getA() + atomOffset;
223	>	theBonds[j].b = currentBond->getB() + atomOffset;
224
225	<	Atom::createArrays(simnfo->n_atoms);
226	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
225	>	exI = theBonds[j].a;
226	>	exJ = theBonds[j].b;
227
228	+	// exclude_I must always be the smaller of the pair
229	+	if (exI > exJ){
230	+	tempEx = exI;
231	+	exI = exJ;
232	+	exJ = tempEx;
233	+	}
234	+	#ifdef IS_MPI
235	+	tempEx = exI;
236	+	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
237	+	tempEx = exJ;
238	+	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
239
240	<	if( simnfo->n_SRI ){
241	<	Exclude::createArray(simnfo->n_SRI);
311	<	the_excludes = new Exclude*[simnfo->n_SRI];
312	<	simnfo->globalExcludes = new int;
313	<	simnfo->n_exclude = tot_SRI;
314	<	}
315	<	else{
316	<
317	<	Exclude::createArray( 1 );
318	<	the_excludes = new Exclude*;
319	<	the_excludes[0] = new Exclude(0);
320	<	the_excludes[0]->setPair( 0,0 );
321	<	simnfo->globalExcludes = new int;
322	<	simnfo->globalExcludes[0] = 0;
323	<	simnfo->n_exclude = 0;
324	<	}
240	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
241	>	#else  // isn't MPI
242
243	<	// set the arrays into the SimInfo object
243	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
244	>	#endif  //is_mpi
245	>	}
246	>	excludeOffset += molInfo.nBonds;
247
248	<	simnfo->atoms = the_atoms;
249	<	simnfo->sr_interactions = the_sris;
250	<	simnfo->nGlobalExcludes = 0;
251	<	simnfo->excludes = the_excludes;
248	>	//make the bends
249	>	for (j = 0; j < molInfo.nBends; j++){
250	>	currentBend = comp_stamps[stampID]->getBend(j);
251	>	theBends[j].a = currentBend->getA() + atomOffset;
252	>	theBends[j].b = currentBend->getB() + atomOffset;
253	>	theBends[j].c = currentBend->getC() + atomOffset;
254
255	+	if (currentBend->haveExtras()){
256	+	extras = currentBend->getExtras();
257	+	current_extra = extras;
258
259	<	// get some of the tricky things that may still be in the globals
259	>	while (current_extra != NULL){
260	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
261	>	switch (current_extra->getType()){
262	>	case 0:
263	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
264	>	theBends[j].isGhost = 1;
265	>	break;
266
267	<
268	<	if( the_globals->haveBox() ){
269	<	simnfo->box_x = the_globals->getBox();
270	<	simnfo->box_y = the_globals->getBox();
271	<	simnfo->box_z = the_globals->getBox();
341	<	}
342	<	else if( the_globals->haveDensity() ){
267	>	case 1:
268	>	theBends[j].ghost = (int) current_extra->getDouble() +
269	>	atomOffset;
270	>	theBends[j].isGhost = 1;
271	>	break;
272
273	<	double vol;
274	<	vol = (double)tot_nmol / the_globals->getDensity();
275	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
276	<	simnfo->box_y = simnfo->box_x;
277	<	simnfo->box_z = simnfo->box_x;
278	<	}
279	<	else{
280	<	if( !the_globals->haveBoxX() ){
281	<	sprintf( painCave.errMsg,
282	<	"SimSetup error, no periodic BoxX size given.\n" );
283	<	painCave.isFatal = 1;
284	<	simError();
285	<	}
286	<	simnfo->box_x = the_globals->getBoxX();
273	>	default:
274	>	sprintf(painCave.errMsg,
275	>	"SimSetup Error: ghostVectorSource was neither a "
276	>	"double nor an int.\n"
277	>	"-->Bend[%d] in %s\n",
278	>	j, comp_stamps[stampID]->getID());
279	>	painCave.isFatal = 1;
280	>	simError();
281	>	}
282	>	}
283	>	else{
284	>	sprintf(painCave.errMsg,
285	>	"SimSetup Error: unhandled bend assignment:\n"
286	>	"    -->%s in Bend[%d] in %s\n",
287	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
288	>	painCave.isFatal = 1;
289	>	simError();
290	>	}
291
292	<	if( !the_globals->haveBoxY() ){
293	<	sprintf( painCave.errMsg,
294	<	"SimSetup error, no periodic BoxY size given.\n" );
362	<	painCave.isFatal = 1;
363	<	simError();
364	<	}
365	<	simnfo->box_y = the_globals->getBoxY();
292	>	current_extra = current_extra->getNext();
293	>	}
294	>	}
295
296	<	if( !the_globals->haveBoxZ() ){
297	<	sprintf( painCave.errMsg,
298	<	"SimSetup error, no periodic BoxZ size given.\n" );
299	<	painCave.isFatal = 1;
300	<	simError();
301	<	}
302	<	simnfo->box_z = the_globals->getBoxZ();
303	<	}
296	>	if (!theBends[j].isGhost){
297	>	exI = theBends[j].a;
298	>	exJ = theBends[j].c;
299	>	}
300	>	else{
301	>	exI = theBends[j].a;
302	>	exJ = theBends[j].b;
303	>	}
304
305	+	// exclude_I must always be the smaller of the pair
306	+	if (exI > exJ){
307	+	tempEx = exI;
308	+	exI = exJ;
309	+	exJ = tempEx;
310	+	}
311		#ifdef IS_MPI
312	<	strcpy( checkPointMsg, "Box size set up" );
313	<	MPIcheckPoint();
314	<	#endif // is_mpi
312	>	tempEx = exI;
313	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
314	>	tempEx = exJ;
315	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
316
317	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
318	+	#else  // isn't MPI
319	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
320	+	#endif  //is_mpi
321	+	}
322	+	excludeOffset += molInfo.nBends;
323
324	<	// initialize the arrays
324	>	for (j = 0; j < molInfo.nTorsions; j++){
325	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
326	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
327	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
328	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
329	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
330
331	<	the_ff->setSimInfo( simnfo );
331	>	exI = theTorsions[j].a;
332	>	exJ = theTorsions[j].d;
333
334	<	makeAtoms();
335	<	simnfo->identArray = new int[simnfo->n_atoms];
336	<	for(i=0; i<simnfo->n_atoms; i++){
337	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
338	<	}
339	<
340	<	if( tot_bonds ){
341	<	makeBonds();
342	<	}
334	>	// exclude_I must always be the smaller of the pair
335	>	if (exI > exJ){
336	>	tempEx = exI;
337	>	exI = exJ;
338	>	exJ = tempEx;
339	>	}
340	>	#ifdef IS_MPI
341	>	tempEx = exI;
342	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
343	>	tempEx = exJ;
344	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345	>
346	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
347	>	#else  // isn't MPI
348	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
349	>	#endif  //is_mpi
350	>	}
351	>	excludeOffset += molInfo.nTorsions;
352	>
353	>
354	>	// send the arrays off to the forceField for init.
355	>
356	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
357	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
358	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
359	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
360	>	theTorsions);
361	>
362	>
363	>	info[k].molecules[i].initialize(molInfo);
364
396	–	if( tot_bends ){
397	–	makeBends();
398	–	}
365
366	<	if( tot_torsions ){
367	<	makeTorsions();
366	>	atomOffset += molInfo.nAtoms;
367	>	delete[] theBonds;
368	>	delete[] theBends;
369	>	delete[] theTorsions;
370	>	}
371		}
372
373	+	#ifdef IS_MPI
374	+	sprintf(checkPointMsg, "all molecules initialized succesfully");
375	+	MPIcheckPoint();
376	+	#endif // is_mpi
377
378	<	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	<	}
378	>	// clean up the forcefield
379
380	<	if( !the_globals->haveEST() ){
381	<	sprintf( painCave.errMsg,
382	<	"SimSetup Warning: using default value of 0.05 * the "
383	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
384	<	);
385	<	painCave.isFatal = 0;
386	<	simError();
387	<	simnfo->est = 0.05 * simnfo->ecr;
388	<	} else {
389	<	simnfo->est        = the_globals->getEST();
390	<	}
391	<
392	<	if(!the_globals->haveDielectric() ){
393	<	sprintf( painCave.errMsg,
394	<	"SimSetup Error: You are trying to use Reaction Field without"
395	<	"setting a dielectric constant!\n"
396	<	);
380	>	the_ff->calcRcut();
381	>	the_ff->cleanMe();
382	>	}
383	>
384	>	void SimSetup::initFromBass(void){
385	>	int i, j, k;
386	>	int n_cells;
387	>	double cellx, celly, cellz;
388	>	double temp1, temp2, temp3;
389	>	int n_per_extra;
390	>	int n_extra;
391	>	int have_extra, done;
392	>
393	>	double vel[3];
394	>	vel[0] = 0.0;
395	>	vel[1] = 0.0;
396	>	vel[2] = 0.0;
397	>
398	>	temp1 = (double) tot_nmol / 4.0;
399	>	temp2 = pow(temp1, (1.0 / 3.0));
400	>	temp3 = ceil(temp2);
401	>
402	>	have_extra = 0;
403	>	if (temp2 < temp3){
404	>	// we have a non-complete lattice
405	>	have_extra = 1;
406	>
407	>	n_cells = (int) temp3 - 1;
408	>	cellx = info[0].boxL[0] / temp3;
409	>	celly = info[0].boxL[1] / temp3;
410	>	cellz = info[0].boxL[2] / temp3;
411	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
412	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
413	>	n_per_extra = (int) ceil(temp1);
414	>
415	>	if (n_per_extra > 4){
416	>	sprintf(painCave.errMsg,
417	>	"SimSetup error. There has been an error in constructing"
418	>	" the non-complete lattice.\n");
419		painCave.isFatal = 1;
420		simError();
421		}
422	<	simnfo->dielectric = the_globals->getDielectric();
423	<	} else {
424	<	if (simnfo->n_dipoles) {
425	<
426	<	if( !the_globals->haveECR() ){
427	<	sprintf( painCave.errMsg,
428	<	"SimSetup Warning: using default value of 1/2 the smallest"
429	<	"box length for the electrostaticCutoffRadius.\n"
430	<	"I hope you have a very fast processor!\n");
431	<	painCave.isFatal = 0;
432	<	simError();
433	<	double smallest;
434	<	smallest = simnfo->box_x;
435	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
436	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
437	<	simnfo->ecr = 0.5 * smallest;
438	<	} else {
439	<	simnfo->ecr        = the_globals->getECR();
422	>	}
423	>	else{
424	>	n_cells = (int) temp3;
425	>	cellx = info[0].boxL[0] / temp3;
426	>	celly = info[0].boxL[1] / temp3;
427	>	cellz = info[0].boxL[2] / temp3;
428	>	}
429	>
430	>	current_mol = 0;
431	>	current_comp_mol = 0;
432	>	current_comp = 0;
433	>	current_atom_ndx = 0;
434	>
435	>	for (i = 0; i < n_cells ; i++){
436	>	for (j = 0; j < n_cells; j++){
437	>	for (k = 0; k < n_cells; k++){
438	>	makeElement(i * cellx, j * celly, k * cellz);
439	>
440	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
441	>
442	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
443	>
444	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
445		}
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	–	}
446		}
447	<	}
447	>	}
448
449	<	#ifdef IS_MPI
450	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
481	<	MPIcheckPoint();
482	<	#endif // is_mpi
449	>	if (have_extra){
450	>	done = 0;
451
452	<	if( the_globals->haveInitialConfig() ){
453	<
454	<	InitializeFromFile* fileInit;
455	<	#ifdef IS_MPI // is_mpi
456	<	if( worldRank == 0 ){
457	<	#endif //is_mpi
458	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
459	<	#ifdef IS_MPI
460	<	}else fileInit = new InitializeFromFile( NULL );
461	<	#endif
462	<	fileInit->read_xyz( simnfo ); // default velocities on
452	>	int start_ndx;
453	>	for (i = 0; i < (n_cells + 1) && !done; i++){
454	>	for (j = 0; j < (n_cells + 1) && !done; j++){
455	>	if (i < n_cells){
456	>	if (j < n_cells){
457	>	start_ndx = n_cells;
458	>	}
459	>	else
460	>	start_ndx = 0;
461	>	}
462	>	else
463	>	start_ndx = 0;
464
465	<	delete fileInit;
466	<	}
467	<	else{
465	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
466	>	makeElement(i * cellx, j * celly, k * cellz);
467	>	done = (current_mol >= tot_nmol);
468
469	<	#ifdef IS_MPI
469	>	if (!done && n_per_extra > 1){
470	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
471	>	k * cellz);
472	>	done = (current_mol >= tot_nmol);
473	>	}
474
475	<	// no init from bass
476	<
477	<	sprintf( painCave.errMsg,
478	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
479	<	painCave.isFatal;
507	<	simError();
508	<
509	<	#else
475	>	if (!done && n_per_extra > 2){
476	>	makeElement(i * cellx, j * celly + 0.5 * celly,
477	>	k * cellz + 0.5 * cellz);
478	>	done = (current_mol >= tot_nmol);
479	>	}
480
481	<	initFromBass();
481	>	if (!done && n_per_extra > 3){
482	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
483	>	k * cellz + 0.5 * cellz);
484	>	done = (current_mol >= tot_nmol);
485	>	}
486	>	}
487	>	}
488	>	}
489	>	}
490
491	+	for (i = 0; i < info[0].n_atoms; i++){
492	+	info[0].atoms[i]->setVel(vel);
493	+	}
494	+	}
495
496	<	#endif
497	<	}
496	>	void SimSetup::makeElement(double x, double y, double z){
497	>	int k;
498	>	AtomStamp* current_atom;
499	>	DirectionalAtom* dAtom;
500	>	double rotMat[3][3];
501	>	double pos[3];
502
503	<	#ifdef IS_MPI
504	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
505	<	MPIcheckPoint();
506	<	#endif // is_mpi
503	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
504	>	current_atom = comp_stamps[current_comp]->getAtom(k);
505	>	if (!current_atom->havePosition()){
506	>	sprintf(painCave.errMsg,
507	>	"SimSetup:initFromBass error.\n"
508	>	"\tComponent %s, atom %s does not have a position specified.\n"
509	>	"\tThe initialization routine is unable to give a start"
510	>	" position.\n",
511	>	comp_stamps[current_comp]->getID(), current_atom->getType());
512	>	painCave.isFatal = 1;
513	>	simError();
514	>	}
515
516	+	pos[0] = x + current_atom->getPosX();
517	+	pos[1] = y + current_atom->getPosY();
518	+	pos[2] = z + current_atom->getPosZ();
519
520	<
524	<
525	<
520	>	info[0].atoms[current_atom_ndx]->setPos(pos);
521
522	<
523	<	#ifdef IS_MPI
524	<	if( worldRank == 0 ){
525	<	#endif // is_mpi
526	<
527	<	if( the_globals->haveFinalConfig() ){
528	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
522	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
523	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
524	>
525	>	rotMat[0][0] = 1.0;
526	>	rotMat[0][1] = 0.0;
527	>	rotMat[0][2] = 0.0;
528	>
529	>	rotMat[1][0] = 0.0;
530	>	rotMat[1][1] = 1.0;
531	>	rotMat[1][2] = 0.0;
532	>
533	>	rotMat[2][0] = 0.0;
534	>	rotMat[2][1] = 0.0;
535	>	rotMat[2][2] = 1.0;
536	>
537	>	dAtom->setA(rotMat);
538		}
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	–	}
539
540	<	if( the_globals->haveStatusTime() ){
625	<	simnfo->statusTime = the_globals->getStatusTime();
540	>	current_atom_ndx++;
541		}
542
543	<	if( the_globals->haveThermalTime() ){
544	<	simnfo->thermalTime = the_globals->getThermalTime();
543	>	current_mol++;
544	>	current_comp_mol++;
545	>
546	>	if (current_comp_mol >= components_nmol[current_comp]){
547	>	current_comp_mol = 0;
548	>	current_comp++;
549		}
550	+	}
551
632	–	// check for the temperature set flag
552
553	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
553	>	void SimSetup::gatherInfo(void){
554	>	int i, j, k;
555
556	+	ensembleCase = -1;
557	+	ffCase = -1;
558
559	<	//   // make the longe range forces and the integrator
559	>	// set the easy ones first
560
561	<	//   new AllLong( simnfo );
561	>	for (i = 0; i < nInfo; i++){
562	>	info[i].target_temp = globals->getTargetTemp();
563	>	info[i].dt = globals->getDt();
564	>	info[i].run_time = globals->getRunTime();
565	>	}
566	>	n_components = globals->getNComponents();
567
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 );
568
569	+	// get the forceField
570
571	+	strcpy(force_field, globals->getForceField());
572
573	<	// initialize the Fortran
574	<
650	<	simnfo->refreshSim();
651	<
652	<	if( !strcmp( simnfo->mixingRule, "standard") ){
653	<	the_ff->initForceField( LB_MIXING_RULE );
573	>	if (!strcasecmp(force_field, "DUFF")){
574	>	ffCase = FF_DUFF;
575		}
576	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
577	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
576	>	else if (!strcasecmp(force_field, "LJ")){
577	>	ffCase = FF_LJ;
578		}
579	+	else if (!strcasecmp(force_field, "EAM")){
580	+	ffCase = FF_EAM;
581	+	}
582		else{
583	<	sprintf( painCave.errMsg,
584	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
585	<	simnfo->mixingRule );
586	<	painCave.isFatal = 1;
663	<	simError();
583	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
584	>	force_field);
585	>	painCave.isFatal = 1;
586	>	simError();
587		}
588
589	+	// get the ensemble
590
591	<	#ifdef IS_MPI
668	<	strcpy( checkPointMsg,
669	<	"Successfully intialized the mixingRule for Fortran." );
670	<	MPIcheckPoint();
671	<	#endif // is_mpi
672	<	}
591	>	strcpy(ensemble, globals->getEnsemble());
592
593	+	if (!strcasecmp(ensemble, "NVE")){
594	+	ensembleCase = NVE_ENS;
595	+	}
596	+	else if (!strcasecmp(ensemble, "NVT")){
597	+	ensembleCase = NVT_ENS;
598	+	}
599	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
600	+	ensembleCase = NPTi_ENS;
601	+	}
602	+	else if (!strcasecmp(ensemble, "NPTf")){
603	+	ensembleCase = NPTf_ENS;
604	+	}
605	+	else{
606	+	sprintf(painCave.errMsg,
607	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
608	+	"reverting to NVE for this simulation.\n",
609	+	ensemble);
610	+	painCave.isFatal = 0;
611	+	simError();
612	+	strcpy(ensemble, "NVE");
613	+	ensembleCase = NVE_ENS;
614	+	}
615
616	<	void SimSetup::makeMolecules( void ){
616	>	for (i = 0; i < nInfo; i++){
617	>	strcpy(info[i].ensemble, ensemble);
618
619	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
678	<	molInit info;
679	<	DirectionalAtom* dAtom;
680	<	LinkedAssign* extras;
681	<	LinkedAssign* current_extra;
682	<	AtomStamp* currentAtom;
683	<	BondStamp* currentBond;
684	<	BendStamp* currentBend;
685	<	TorsionStamp* currentTorsion;
686	<
687	<	//init the forceField paramters
619	>	// get the mixing rule
620
621	<	the_ff->readParams();
621	>	strcpy(info[i].mixingRule, globals->getMixingRule());
622	>	info[i].usePBC = globals->getPBC();
623	>	}
624
625	<
692	<	// init the molecules
625	>	// get the components and calculate the tot_nMol and indvidual n_mol
626
627	<	atomOffset = 0;
628	<	excludeOffset = 0;
696	<	for(i=0; i<simnfo->n_mol; i++){
697	<
698	<	stampID = the_molecules[i].getStampID();
627	>	the_components = globals->getComponents();
628	>	components_nmol = new int[n_components];
629
700	–	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
701	–	info.nBonds    = comp_stamps[stampID]->getNBonds();
702	–	info.nBends    = comp_stamps[stampID]->getNBends();
703	–	info.nTorsions = comp_stamps[stampID]->getNTorsions();
704	–	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
630
631	<	info.myAtoms = &the_atoms[atomOffset];
632	<	info.myExcludes = &the_excludes[excludeOffset];
633	<	info.myBonds = new Bond*[info.nBonds];
634	<	info.myBends = new Bend*[info.nBends];
635	<	info.myTorsions = new Torsions*[info.nTorsions];
636	<
637	<	theBonds = new bond_pair[info.nBonds];
638	<	theBends = new bend_set[info.nBends];
639	<	theTorsions = new torsion_set[info.nTorsions];
640	<
641	<	// make the Atoms
642	<
643	<	for(j=0; j<info.nAtoms; j++){
719	<
720	<	currentAtom = theComponents[stampID]->getAtom( j );
721	<	if( currentAtom->haveOrientation() ){
722	<
723	<	dAtom = new DirectionalAtom(j + atomOffset);
724	<	simnfo->n_oriented++;
725	<	info.myAtoms[j] = dAtom;
726	<
727	<	ux = currentAtom->getOrntX();
728	<	uy = currentAtom->getOrntY();
729	<	uz = currentAtom->getOrntZ();
730	<
731	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
732	<
733	<	u = sqrt( uSqr );
734	<	ux = ux / u;
735	<	uy = uy / u;
736	<	uz = uz / u;
737	<
738	<	dAtom->setSUx( ux );
739	<	dAtom->setSUy( uy );
740	<	dAtom->setSUz( uz );
631	>	if (!globals->haveNMol()){
632	>	// we don't have the total number of molecules, so we assume it is
633	>	// given in each component
634	>
635	>	tot_nmol = 0;
636	>	for (i = 0; i < n_components; i++){
637	>	if (!the_components[i]->haveNMol()){
638	>	// we have a problem
639	>	sprintf(painCave.errMsg,
640	>	"SimSetup Error. No global NMol or component NMol"
641	>	" given. Cannot calculate the number of atoms.\n");
642	>	painCave.isFatal = 1;
643	>	simError();
644		}
742	–	else{
743	–	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
744	–	}
745	–	info.myAtoms[j]->setType( currentAtom->getType() );
746	–
747	–	#ifdef IS_MPI
748	–
749	–	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
750	–
751	–	#endif // is_mpi
752	–	}
753	–
754	–	// make the bonds
755	–	for(j=0; j<info.nBonds; j++){
756	–
757	–	currentBond = comp_stamps[stampID]->getBond( j );
758	–	theBonds[j].a = currentBond->getA() + atomOffset;
759	–	theBonds[j].b = currentBond->getB() + atomOffset;
645
646	<	exI = theBonds[i].a;
647	<	exJ = theBonds[i].b;
646	>	tot_nmol += the_components[i]->getNMol();
647	>	components_nmol[i] = the_components[i]->getNMol();
648	>	}
649	>	}
650	>	else{
651	>	sprintf(painCave.errMsg,
652	>	"SimSetup error.\n"
653	>	"\tSorry, the ability to specify total"
654	>	" nMols and then give molfractions in the components\n"
655	>	"\tis not currently supported."
656	>	" Please give nMol in the components.\n");
657	>	painCave.isFatal = 1;
658	>	simError();
659	>	}
660
661	<	// exclude_I must always be the smaller of the pair
662	<	if( exI > exJ ){
663	<	tempEx = exI;
664	<	exI = exJ;
665	<	exJ = tempEx;
666	<	}
667	<	#ifdef IS_MPI
771	<	tempEx = exI;
772	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
773	<	tempEx = exJ;
774	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
775	<
776	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
777	<	#else  // isn't MPI
778	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
779	<	#endif  //is_mpi
661	>	// set the status, sample, and thermal kick times
662	>
663	>	for (i = 0; i < nInfo; i++){
664	>	if (globals->haveSampleTime()){
665	>	info[i].sampleTime = globals->getSampleTime();
666	>	info[i].statusTime = info[i].sampleTime;
667	>	info[i].thermalTime = info[i].sampleTime;
668		}
669	<	excludeOffset += info.nBonds;
669	>	else{
670	>	info[i].sampleTime = globals->getRunTime();
671	>	info[i].statusTime = info[i].sampleTime;
672	>	info[i].thermalTime = info[i].sampleTime;
673	>	}
674
675	<	//make the bends
676	<	for(j=0; j<info.nBends; j++){
785	<
786	<	currentBend = comp_stamps[stampID]->getBend( j );
787	<	theBends[j].a = currentBend->getA() + atomOffset;
788	<	theBends[j].b = currentBend->getB() + atomOffset;
789	<	theBends[j].c = currentBend->getC() + atomOffset;
790	<
791	<	if( currentBend->haveExtras() ){
792	<
793	<	extras = current_bend->getExtras();
794	<	current_extra = extras;
795	<
796	<	while( current_extra != NULL ){
797	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
798	<
799	<	switch( current_extra->getType() ){
800	<
801	<	case 0:
802	<	theBends[j].ghost =
803	<	current_extra->getInt() + atomOffset;
804	<	theBends[j].isGhost = 1;
805	<	break;
806	<
807	<	case 1:
808	<	theBends[j].ghost =
809	<	(int)current_extra->getDouble() + atomOffset;
810	<	theBends[j].isGhost = 1;
811	<	break;
812	<
813	<	default:
814	<	sprintf( painCave.errMsg,
815	<	"SimSetup Error: ghostVectorSource was neiter a "
816	<	"double nor an int.\n"
817	<	"-->Bend[%d] in %s\n",
818	<	j, comp_stamps[stampID]->getID() );
819	<	painCave.isFatal = 1;
820	<	simError();
821	<	}
822	<	}
823	<
824	<	else{
825	<
826	<	sprintf( painCave.errMsg,
827	<	"SimSetup Error: unhandled bend assignment:\n"
828	<	"    -->%s in Bend[%d] in %s\n",
829	<	current_extra->getlhs(),
830	<	j, comp_stamps[stampID]->getID() );
831	<	painCave.isFatal = 1;
832	<	simError();
833	<	}
834	<
835	<	current_extra = current_extra->getNext();
836	<	}
837	<	}
838	<
839	<	if( !theBends[j].isGhost ){
840	<
841	<	exI = theBends[j].a;
842	<	exJ = theBends[j].c;
843	<	}
844	<	else{
845	<
846	<	exI = theBends[j].a;
847	<	exJ = theBends[j].b;
848	<	}
849	<
850	<	// exclude_I must always be the smaller of the pair
851	<	if( exI > exJ ){
852	<	tempEx = exI;
853	<	exI = exJ;
854	<	exJ = tempEx;
855	<	}
856	<	#ifdef IS_MPI
857	<	tempEx = exI;
858	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
859	<	tempEx = exJ;
860	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
861	<
862	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
863	<	#else  // isn't MPI
864	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
865	<	#endif  //is_mpi
675	>	if (globals->haveStatusTime()){
676	>	info[i].statusTime = globals->getStatusTime();
677		}
867	–	excludeOffset += info.nBends;
678
679	<	for(j=0; j<info.nTorsions; j++){
680	<
681	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
872	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
873	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
874	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
875	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
876	<
877	<	exI = theTorsions[j].a;
878	<	exJ = theTorsions[j].d;
679	>	if (globals->haveThermalTime()){
680	>	info[i].thermalTime = globals->getThermalTime();
681	>	}
682
683	<	// exclude_I must always be the smaller of the pair
684	<	if( exI > exJ ){
685	<	tempEx = exI;
686	<	exI = exJ;
884	<	exJ = tempEx;
885	<	}
886	<	#ifdef IS_MPI
887	<	tempEx = exI;
888	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
889	<	tempEx = exJ;
890	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
891	<
892	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
893	<	#else  // isn't MPI
894	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
895	<	#endif  //is_mpi
683	>	info[i].resetIntegrator = 0;
684	>	if( globals->haveResetTime() ){
685	>	info[i].resetTime = globals->getResetTime();
686	>	info[i].resetIntegrator = 1;
687		}
897	–	excludeOffset += info.nTorsions;
688
689	<
689	>	// check for the temperature set flag
690
691	+	if (globals->haveTempSet())
692	+	info[i].setTemp = globals->getTempSet();
693
694	+	// get some of the tricky things that may still be in the globals
695
696	+	double boxVector[3];
697	+	if (globals->haveBox()){
698	+	boxVector[0] = globals->getBox();
699	+	boxVector[1] = globals->getBox();
700	+	boxVector[2] = globals->getBox();
701
702	+	info[i].setBox(boxVector);
703	+	}
704	+	else if (globals->haveDensity()){
705	+	double vol;
706	+	vol = (double) tot_nmol / globals->getDensity();
707	+	boxVector[0] = pow(vol, (1.0 / 3.0));
708	+	boxVector[1] = boxVector[0];
709	+	boxVector[2] = boxVector[0];
710
711	+	info[i].setBox(boxVector);
712	+	}
713	+	else{
714	+	if (!globals->haveBoxX()){
715	+	sprintf(painCave.errMsg,
716	+	"SimSetup error, no periodic BoxX size given.\n");
717	+	painCave.isFatal = 1;
718	+	simError();
719	+	}
720	+	boxVector[0] = globals->getBoxX();
721
722	<	void SimSetup::makeAtoms( void ){
722	>	if (!globals->haveBoxY()){
723	>	sprintf(painCave.errMsg,
724	>	"SimSetup error, no periodic BoxY size given.\n");
725	>	painCave.isFatal = 1;
726	>	simError();
727	>	}
728	>	boxVector[1] = globals->getBoxY();
729
730	<	int i, j, k, index;
731	<	double ux, uy, uz, uSqr, u;
732	<	AtomStamp* current_atom;
730	>	if (!globals->haveBoxZ()){
731	>	sprintf(painCave.errMsg,
732	>	"SimSetup error, no periodic BoxZ size given.\n");
733	>	painCave.isFatal = 1;
734	>	simError();
735	>	}
736	>	boxVector[2] = globals->getBoxZ();
737
738	<	DirectionalAtom* dAtom;
739	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
738	>	info[i].setBox(boxVector);
739	>	}
740	>	}
741
742	<	lMolIndex = 0;
743	<	molIndex = 0;
917	<	index = 0;
918	<	for( i=0; i<n_components; i++ ){
742	>	//setup seed for random number generator
743	>	int seedValue;
744
745	<	for( j=0; j<components_nmol[i]; j++ ){
745	>	if (globals->haveSeed()){
746	>	seedValue = globals->getSeed();
747
748	<	#ifdef IS_MPI
749	<	if( mpiSim->getMyMolStart() <= molIndex &&
750	<	molIndex <= mpiSim->getMyMolEnd() ){
751	<	#endif // is_mpi
748	>	if(seedValue / 1E9 == 0){
749	>	sprintf(painCave.errMsg,
750	>	"Seed for sprng library should contain at least 9 digits\n"
751	>	"OOPSE will generate a seed for user\n");
752	>	painCave.isFatal = 0;
753	>	simError();
754
755	<	molStart = index;
756	<	nMemb = comp_stamps[i]->getNAtoms();
757	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
758	<
759	<	current_atom = comp_stamps[i]->getAtom( k );
760	<	if( current_atom->haveOrientation() ){
933	<
934	<	dAtom = new DirectionalAtom(index);
935	<	simnfo->n_oriented++;
936	<	the_atoms[index] = dAtom;
937	<
938	<	ux = current_atom->getOrntX();
939	<	uy = current_atom->getOrntY();
940	<	uz = current_atom->getOrntZ();
941	<
942	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
943	<
944	<	u = sqrt( uSqr );
945	<	ux = ux / u;
946	<	uy = uy / u;
947	<	uz = uz / u;
948	<
949	<	dAtom->setSUx( ux );
950	<	dAtom->setSUy( uy );
951	<	dAtom->setSUz( uz );
952	<	}
953	<	else{
954	<	the_atoms[index] = new GeneralAtom(index);
955	<	}
956	<	the_atoms[index]->setType( current_atom->getType() );
957	<	the_atoms[index]->setIndex( index );
958	<
959	<	// increment the index and repeat;
960	<	index++;
961	<	}
962	<
963	<	molEnd = index -1;
964	<	the_molecules[lMolIndex].setNMembers( nMemb );
965	<	the_molecules[lMolIndex].setStartAtom( molStart );
966	<	the_molecules[lMolIndex].setEndAtom( molEnd );
967	<	the_molecules[lMolIndex].setStampID( i );
968	<	lMolIndex++;
969	<
970	<	#ifdef IS_MPI
755	>	//using seed generated by system instead of invalid seed set by user
756	>	#ifndef IS_MPI
757	>	seedValue = make_sprng_seed();
758	>	#else
759	>	if (worldRank == 0){
760	>	seedValue = make_sprng_seed();
761		}
762	<	#endif //is_mpi
763	<
974	<	molIndex++;
762	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
763	>	#endif
764		}
765	+	}//end of if branch of globals->haveSeed()
766	+	else{
767	+
768	+	#ifndef IS_MPI
769	+	seedValue = make_sprng_seed();
770	+	#else
771	+	if (worldRank == 0){
772	+	seedValue = make_sprng_seed();
773	+	}
774	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
775	+	#endif
776	+	}//end of globals->haveSeed()
777	+
778	+	for (int i = 0; i < nInfo; i++){
779	+	info[i].setSeed(seedValue);
780		}
781
782		#ifdef IS_MPI
783	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
784	<
785	<	delete[] globalIndex;
982	<
983	<	mpiSim->mpiRefresh();
984	<	#endif //IS_MPI
985	<
986	<	the_ff->initializeAtoms();
783	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
784	>	MPIcheckPoint();
785	>	#endif // is_mpi
786		}
787
989	–	void SimSetup::makeBonds( void ){
788
789	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
790	<	bond_pair* the_bonds;
791	<	BondStamp* current_bond;
789	>	void SimSetup::finalInfoCheck(void){
790	>	int index;
791	>	int usesDipoles;
792	>	int i;
793
794	<	the_bonds = new bond_pair[tot_bonds];
795	<	index = 0;
997	<	offset = 0;
998	<	molIndex = 0;
999	<
1000	<	for( i=0; i<n_components; i++ ){
1001	<
1002	<	for( j=0; j<components_nmol[i]; j++ ){
1003	<
1004	<	#ifdef IS_MPI
1005	<	if( mpiSim->getMyMolStart() <= molIndex &&
1006	<	molIndex <= mpiSim->getMyMolEnd() ){
1007	<	#endif // is_mpi
1008	<
1009	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
1010	<
1011	<	current_bond = comp_stamps[i]->getBond( k );
1012	<	the_bonds[index].a = current_bond->getA() + offset;
1013	<	the_bonds[index].b = current_bond->getB() + offset;
1014	<
1015	<	exI = the_bonds[index].a;
1016	<	exJ = the_bonds[index].b;
794	>	for (i = 0; i < nInfo; i++){
795	>	// check electrostatic parameters
796
797	<	// exclude_I must always be the smaller of the pair
798	<	if( exI > exJ ){
799	<	tempEx = exI;
800	<	exI = exJ;
801	<	exJ = tempEx;
802	<	}
797	>	index = 0;
798	>	usesDipoles = 0;
799	>	while ((index < info[i].n_atoms) && !usesDipoles){
800	>	usesDipoles = (info[i].atoms[index])->hasDipole();
801	>	index++;
802	>	}
803
1025	–
804		#ifdef IS_MPI
805	<
806	<	the_excludes[index*2] =
1029	<	the_atoms[exI]->getGlobalIndex() + 1;
1030	<	the_excludes[index*2 + 1] =
1031	<	the_atoms[exJ]->getGlobalIndex() + 1;
1032	<
1033	<	#else  // isn't MPI
1034	<
1035	<	the_excludes[index*2] =     exI + 1;
1036	<	the_excludes[index*2 + 1] = exJ + 1;
1037	<	// fortran index from 1 (hence the +1 in the indexing)
1038	<	#endif  //is_mpi
1039	<
1040	<	// increment the index and repeat;
1041	<	index++;
1042	<	}
1043	<	offset += comp_stamps[i]->getNAtoms();
1044	<
1045	<	#ifdef IS_MPI
1046	<	}
805	>	int myUse = usesDipoles;
806	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
807		#endif //is_mpi
1048	–
1049	–	molIndex++;
1050	–	}
1051	–	}
808
809	<	the_ff->initializeBonds( the_bonds );
1054	<	}
809	>	double theEcr, theEst;
810
811	<	void SimSetup::makeBends( void ){
811	>	if (globals->getUseRF()){
812	>	info[i].useReactionField = 1;
813
814	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
815	<	bend_set* the_bends;
816	<	BendStamp* current_bend;
817	<	LinkedAssign* extras;
818	<	LinkedAssign* current_extra;
819	<
814	>	if (!globals->haveECR()){
815	>	sprintf(painCave.errMsg,
816	>	"SimSetup Warning: using default value of 1/2 the smallest "
817	>	"box length for the electrostaticCutoffRadius.\n"
818	>	"I hope you have a very fast processor!\n");
819	>	painCave.isFatal = 0;
820	>	simError();
821	>	double smallest;
822	>	smallest = info[i].boxL[0];
823	>	if (info[i].boxL[1] <= smallest)
824	>	smallest = info[i].boxL[1];
825	>	if (info[i].boxL[2] <= smallest)
826	>	smallest = info[i].boxL[2];
827	>	theEcr = 0.5 * smallest;
828	>	}
829	>	else{
830	>	theEcr = globals->getECR();
831	>	}
832
833	<	the_bends = new bend_set[tot_bends];
834	<	index = 0;
835	<	offset = 0;
836	<	molIndex = 0;
837	<	for( i=0; i<n_components; i++ ){
833	>	if (!globals->haveEST()){
834	>	sprintf(painCave.errMsg,
835	>	"SimSetup Warning: using default value of 0.05 * the "
836	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
837	>	painCave.isFatal = 0;
838	>	simError();
839	>	theEst = 0.05 * theEcr;
840	>	}
841	>	else{
842	>	theEst = globals->getEST();
843	>	}
844
845	<	for( j=0; j<components_nmol[i]; j++ ){
845	>	info[i].setEcr(theEcr, theEst);
846
847	<	#ifdef IS_MPI
848	<	if( mpiSim->getMyMolStart() <= molIndex &&
849	<	molIndex <= mpiSim->getMyMolEnd() ){
850	<	#endif // is_mpi
847	>	if (!globals->haveDielectric()){
848	>	sprintf(painCave.errMsg,
849	>	"SimSetup Error: You are trying to use Reaction Field without"
850	>	"setting a dielectric constant!\n");
851	>	painCave.isFatal = 1;
852	>	simError();
853	>	}
854	>	info[i].dielectric = globals->getDielectric();
855	>	}
856	>	else{
857	>	if (usesDipoles){
858	>	if (!globals->haveECR()){
859	>	sprintf(painCave.errMsg,
860	>	"SimSetup Warning: using default value of 1/2 the smallest "
861	>	"box length for the electrostaticCutoffRadius.\n"
862	>	"I hope you have a very fast processor!\n");
863	>	painCave.isFatal = 0;
864	>	simError();
865	>	double smallest;
866	>	smallest = info[i].boxL[0];
867	>	if (info[i].boxL[1] <= smallest)
868	>	smallest = info[i].boxL[1];
869	>	if (info[i].boxL[2] <= smallest)
870	>	smallest = info[i].boxL[2];
871	>	theEcr = 0.5 * smallest;
872	>	}
873	>	else{
874	>	theEcr = globals->getECR();
875	>	}
876
877	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
878	<
879	<	current_bend = comp_stamps[i]->getBend( k );
880	<	the_bends[index].a = current_bend->getA() + offset;
881	<	the_bends[index].b = current_bend->getB() + offset;
882	<	the_bends[index].c = current_bend->getC() + offset;
883	<
884	<	if( current_bend->haveExtras() ){
885	<
886	<	extras = current_bend->getExtras();
887	<	current_extra = extras;
888	<
1090	<	while( current_extra != NULL ){
1091	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1092	<
1093	<	switch( current_extra->getType() ){
1094	<
1095	<	case 0:
1096	<	the_bends[index].ghost =
1097	<	current_extra->getInt() + offset;
1098	<	the_bends[index].isGhost = 1;
1099	<	break;
1100	<
1101	<	case 1:
1102	<	the_bends[index].ghost =
1103	<	(int)current_extra->getDouble() + offset;
1104	<	the_bends[index].isGhost = 1;
1105	<	break;
1106	<
1107	<	default:
1108	<	sprintf( painCave.errMsg,
1109	<	"SimSetup Error: ghostVectorSource was neiter a "
1110	<	"double nor an int.\n"
1111	<	"-->Bend[%d] in %s\n",
1112	<	k, comp_stamps[i]->getID() );
1113	<	painCave.isFatal = 1;
1114	<	simError();
1115	<	}
1116	<	}
1117	<
1118	<	else{
1119	<
1120	<	sprintf( painCave.errMsg,
1121	<	"SimSetup Error: unhandled bend assignment:\n"
1122	<	"    -->%s in Bend[%d] in %s\n",
1123	<	current_extra->getlhs(),
1124	<	k, comp_stamps[i]->getID() );
1125	<	painCave.isFatal = 1;
1126	<	simError();
1127	<	}
1128	<
1129	<	current_extra = current_extra->getNext();
1130	<	}
1131	<	}
1132	<
1133	<	if( !the_bends[index].isGhost ){
1134	<
1135	<	exI = the_bends[index].a;
1136	<	exJ = the_bends[index].c;
1137	<	}
1138	<	else{
1139	<
1140	<	exI = the_bends[index].a;
1141	<	exJ = the_bends[index].b;
1142	<	}
1143	<
1144	<	// exclude_I must always be the smaller of the pair
1145	<	if( exI > exJ ){
1146	<	tempEx = exI;
1147	<	exI = exJ;
1148	<	exJ = tempEx;
1149	<	}
877	>	if (!globals->haveEST()){
878	>	sprintf(painCave.errMsg,
879	>	"SimSetup Warning: using default value of 0.05 * the "
880	>	"electrostaticCutoffRadius for the "
881	>	"electrostaticSkinThickness\n");
882	>	painCave.isFatal = 0;
883	>	simError();
884	>	theEst = 0.05 * theEcr;
885	>	}
886	>	else{
887	>	theEst = globals->getEST();
888	>	}
889
890	<
1152	<	#ifdef IS_MPI
1153	<
1154	<	the_excludes[(index + tot_bonds)*2] =
1155	<	the_atoms[exI]->getGlobalIndex() + 1;
1156	<	the_excludes[(index + tot_bonds)*2 + 1] =
1157	<	the_atoms[exJ]->getGlobalIndex() + 1;
1158	<
1159	<	#else  // isn't MPI
1160	<
1161	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
1162	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1163	<	// fortran index from 1 (hence the +1 in the indexing)
1164	<	#endif  //is_mpi
1165	<
1166	<
1167	<	// increment the index and repeat;
1168	<	index++;
1169	<	}
1170	<	offset += comp_stamps[i]->getNAtoms();
1171	<
1172	<	#ifdef IS_MPI
890	>	info[i].setEcr(theEcr, theEst);
891		}
1174	–	#endif //is_mpi
1175	–
1176	–	molIndex++;
892		}
893		}
894
895		#ifdef IS_MPI
896	<	sprintf( checkPointMsg,
1182	<	"Successfully created the bends list.\n" );
896	>	strcpy(checkPointMsg, "post processing checks out");
897		MPIcheckPoint();
898		#endif // is_mpi
1185	–
1186	–
1187	–	the_ff->initializeBends( the_bends );
899		}
900
901	<	void SimSetup::makeTorsions( void ){
901	>	void SimSetup::initSystemCoords(void){
902	>	int i;
903
904	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1193	<	torsion_set* the_torsions;
1194	<	TorsionStamp* current_torsion;
904	>	char* inName;
905
906	<	the_torsions = new torsion_set[tot_torsions];
1197	<	index = 0;
1198	<	offset = 0;
1199	<	molIndex = 0;
1200	<	for( i=0; i<n_components; i++ ){
906	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
907
908	<	for( j=0; j<components_nmol[i]; j++ ){
908	>	for (i = 0; i < info[0].n_atoms; i++)
909	>	info[0].atoms[i]->setCoords();
910
911	+	if (globals->haveInitialConfig()){
912	+	InitializeFromFile* fileInit;
913	+	#ifdef IS_MPI // is_mpi
914	+	if (worldRank == 0){
915	+	#endif //is_mpi
916	+	inName = globals->getInitialConfig();
917	+	double* tempDouble = new double[1000000];
918	+	fileInit = new InitializeFromFile(inName);
919		#ifdef IS_MPI
920	<	if( mpiSim->getMyMolStart() <= molIndex &&
921	<	molIndex <= mpiSim->getMyMolEnd() ){
922	<	#endif // is_mpi
920	>	}
921	>	else
922	>	fileInit = new InitializeFromFile(NULL);
923	>	#endif
924	>	fileInit->readInit(info); // default velocities on
925
926	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
926	>	delete fileInit;
927	>	}
928	>	else{
929	>	#ifdef IS_MPI
930
931	<	current_torsion = comp_stamps[i]->getTorsion( k );
1212	<	the_torsions[index].a = current_torsion->getA() + offset;
1213	<	the_torsions[index].b = current_torsion->getB() + offset;
1214	<	the_torsions[index].c = current_torsion->getC() + offset;
1215	<	the_torsions[index].d = current_torsion->getD() + offset;
931	>	// no init from bass
932
933	<	exI = the_torsions[index].a;
934	<	exJ = the_torsions[index].d;
933	>	sprintf(painCave.errMsg,
934	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
935	>	painCave.isFatal;
936	>	simError();
937
938	<
1221	<	// exclude_I must always be the smaller of the pair
1222	<	if( exI > exJ ){
1223	<	tempEx = exI;
1224	<	exI = exJ;
1225	<	exJ = tempEx;
1226	<	}
938	>	#else
939
940	+	initFromBass();
941
1229	–	#ifdef IS_MPI
1230	–
1231	–	the_excludes[(index + tot_bonds + tot_bends)*2] =
1232	–	the_atoms[exI]->getGlobalIndex() + 1;
1233	–	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1234	–	the_atoms[exJ]->getGlobalIndex() + 1;
1235	–
1236	–	#else  // isn't MPI
1237	–
1238	–	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1239	–	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1240	–	// fortran indexes from 1 (hence the +1 in the indexing)
1241	–	#endif  //is_mpi
1242	–
942
943	<	// increment the index and repeat;
1245	<	index++;
1246	<	}
1247	<	offset += comp_stamps[i]->getNAtoms();
1248	<
1249	<	#ifdef IS_MPI
1250	<	}
1251	<	#endif //is_mpi
1252	<
1253	<	molIndex++;
1254	<	}
943	>	#endif
944		}
945
946	<	the_ff->initializeTorsions( the_torsions );
946	>	#ifdef IS_MPI
947	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
948	>	MPIcheckPoint();
949	>	#endif // is_mpi
950		}
951
1260	–	void SimSetup::initFromBass( void ){
952
953	<	int i, j, k;
954	<	int n_cells;
1264	<	double cellx, celly, cellz;
1265	<	double temp1, temp2, temp3;
1266	<	int n_per_extra;
1267	<	int n_extra;
1268	<	int have_extra, done;
953	>	void SimSetup::makeOutNames(void){
954	>	int k;
955
1270	–	temp1 = (double)tot_nmol / 4.0;
1271	–	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1272	–	temp3 = ceil( temp2 );
956
957	<	have_extra =0;
958	<	if( temp2 < temp3 ){ // we have a non-complete lattice
959	<	have_extra =1;
957	>	for (k = 0; k < nInfo; k++){
958	>	#ifdef IS_MPI
959	>	if (worldRank == 0){
960	>	#endif // is_mpi
961
962	<	n_cells = (int)temp3 - 1;
963	<	cellx = simnfo->box_x / temp3;
964	<	celly = simnfo->box_y / temp3;
965	<	cellz = simnfo->box_z / temp3;
966	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
967	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
968	<	n_per_extra = (int)ceil( temp1 );
962	>	if (globals->haveFinalConfig()){
963	>	strcpy(info[k].finalName, globals->getFinalConfig());
964	>	}
965	>	else{
966	>	strcpy(info[k].finalName, inFileName);
967	>	char* endTest;
968	>	int nameLength = strlen(info[k].finalName);
969	>	endTest = &(info[k].finalName[nameLength - 5]);
970	>	if (!strcmp(endTest, ".bass")){
971	>	strcpy(endTest, ".eor");
972	>	}
973	>	else if (!strcmp(endTest, ".BASS")){
974	>	strcpy(endTest, ".eor");
975	>	}
976	>	else{
977	>	endTest = &(info[k].finalName[nameLength - 4]);
978	>	if (!strcmp(endTest, ".bss")){
979	>	strcpy(endTest, ".eor");
980	>	}
981	>	else if (!strcmp(endTest, ".mdl")){
982	>	strcpy(endTest, ".eor");
983	>	}
984	>	else{
985	>	strcat(info[k].finalName, ".eor");
986	>	}
987	>	}
988	>	}
989
990	<	if( n_per_extra > 4){
991	<	sprintf( painCave.errMsg,
992	<	"SimSetup error. There has been an error in constructing"
993	<	" the non-complete lattice.\n" );
994	<	painCave.isFatal = 1;
995	<	simError();
990	>	// make the sample and status out names
991	>
992	>	strcpy(info[k].sampleName, inFileName);
993	>	char* endTest;
994	>	int nameLength = strlen(info[k].sampleName);
995	>	endTest = &(info[k].sampleName[nameLength - 5]);
996	>	if (!strcmp(endTest, ".bass")){
997	>	strcpy(endTest, ".dump");
998	>	}
999	>	else if (!strcmp(endTest, ".BASS")){
1000	>	strcpy(endTest, ".dump");
1001	>	}
1002	>	else{
1003	>	endTest = &(info[k].sampleName[nameLength - 4]);
1004	>	if (!strcmp(endTest, ".bss")){
1005	>	strcpy(endTest, ".dump");
1006	>	}
1007	>	else if (!strcmp(endTest, ".mdl")){
1008	>	strcpy(endTest, ".dump");
1009	>	}
1010	>	else{
1011	>	strcat(info[k].sampleName, ".dump");
1012	>	}
1013	>	}
1014	>
1015	>	strcpy(info[k].statusName, inFileName);
1016	>	nameLength = strlen(info[k].statusName);
1017	>	endTest = &(info[k].statusName[nameLength - 5]);
1018	>	if (!strcmp(endTest, ".bass")){
1019	>	strcpy(endTest, ".stat");
1020	>	}
1021	>	else if (!strcmp(endTest, ".BASS")){
1022	>	strcpy(endTest, ".stat");
1023	>	}
1024	>	else{
1025	>	endTest = &(info[k].statusName[nameLength - 4]);
1026	>	if (!strcmp(endTest, ".bss")){
1027	>	strcpy(endTest, ".stat");
1028	>	}
1029	>	else if (!strcmp(endTest, ".mdl")){
1030	>	strcpy(endTest, ".stat");
1031	>	}
1032	>	else{
1033	>	strcat(info[k].statusName, ".stat");
1034	>	}
1035	>	}
1036	>
1037	>	#ifdef IS_MPI
1038	>
1039		}
1040	+	#endif // is_mpi
1041		}
1042	<	else{
1295	<	n_cells = (int)temp3;
1296	<	cellx = simnfo->box_x / temp3;
1297	<	celly = simnfo->box_y / temp3;
1298	<	cellz = simnfo->box_z / temp3;
1299	<	}
1042	>	}
1043
1301	–	current_mol = 0;
1302	–	current_comp_mol = 0;
1303	–	current_comp = 0;
1304	–	current_atom_ndx = 0;
1044
1045	<	for( i=0; i < n_cells ; i++ ){
1046	<	for( j=0; j < n_cells; j++ ){
1308	<	for( k=0; k < n_cells; k++ ){
1045	>	void SimSetup::sysObjectsCreation(void){
1046	>	int i, k;
1047
1048	<	makeElement( i * cellx,
1311	<	j * celly,
1312	<	k * cellz );
1048	>	// create the forceField
1049
1050	<	makeElement( i * cellx + 0.5 * cellx,
1315	<	j * celly + 0.5 * celly,
1316	<	k * cellz );
1050	>	createFF();
1051
1052	<	makeElement( i * cellx,
1319	<	j * celly + 0.5 * celly,
1320	<	k * cellz + 0.5 * cellz );
1052	>	// extract componentList
1053
1054	<	makeElement( i * cellx + 0.5 * cellx,
1055	<	j * celly,
1056	<	k * cellz + 0.5 * cellz );
1057	<	}
1054	>	compList();
1055	>
1056	>	// calc the number of atoms, bond, bends, and torsions
1057	>
1058	>	calcSysValues();
1059	>
1060	>	#ifdef IS_MPI
1061	>	// divide the molecules among the processors
1062	>
1063	>	mpiMolDivide();
1064	>	#endif //is_mpi
1065	>
1066	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1067	>
1068	>	makeSysArrays();
1069	>
1070	>	// make and initialize the molecules (all but atomic coordinates)
1071	>
1072	>	makeMolecules();
1073	>
1074	>	for (k = 0; k < nInfo; k++){
1075	>	info[k].identArray = new int[info[k].n_atoms];
1076	>	for (i = 0; i < info[k].n_atoms; i++){
1077	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1078		}
1079		}
1080	+	}
1081
1329	–	if( have_extra ){
1330	–	done = 0;
1082
1083	<	int start_ndx;
1084	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1085	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1083	>	void SimSetup::createFF(void){
1084	>	switch (ffCase){
1085	>	case FF_DUFF:
1086	>	the_ff = new DUFF();
1087	>	break;
1088
1089	<	if( i < n_cells ){
1089	>	case FF_LJ:
1090	>	the_ff = new LJFF();
1091	>	break;
1092
1093	<	if( j < n_cells ){
1094	<	start_ndx = n_cells;
1095	<	}
1341	<	else start_ndx = 0;
1342	<	}
1343	<	else start_ndx = 0;
1093	>	case FF_EAM:
1094	>	the_ff = new EAM_FF();
1095	>	break;
1096
1097	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1097	>	default:
1098	>	sprintf(painCave.errMsg,
1099	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1100	>	painCave.isFatal = 1;
1101	>	simError();
1102	>	}
1103
1104	<	makeElement( i * cellx,
1105	<	j * celly,
1106	<	k * cellz );
1107	<	done = ( current_mol >= tot_nmol );
1104	>	#ifdef IS_MPI
1105	>	strcpy(checkPointMsg, "ForceField creation successful");
1106	>	MPIcheckPoint();
1107	>	#endif // is_mpi
1108	>	}
1109
1352	–	if( !done && n_per_extra > 1 ){
1353	–	makeElement( i * cellx + 0.5 * cellx,
1354	–	j * celly + 0.5 * celly,
1355	–	k * cellz );
1356	–	done = ( current_mol >= tot_nmol );
1357	–	}
1110
1111	<	if( !done && n_per_extra > 2){
1112	<	makeElement( i * cellx,
1113	<	j * celly + 0.5 * celly,
1114	<	k * cellz + 0.5 * cellz );
1115	<	done = ( current_mol >= tot_nmol );
1116	<	}
1111	>	void SimSetup::compList(void){
1112	>	int i;
1113	>	char* id;
1114	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1115	>	LinkedMolStamp* currentStamp = NULL;
1116	>	comp_stamps = new MoleculeStamp * [n_components];
1117
1118	<	if( !done && n_per_extra > 3){
1119	<	makeElement( i * cellx + 0.5 * cellx,
1120	<	j * celly,
1121	<	k * cellz + 0.5 * cellz );
1122	<	done = ( current_mol >= tot_nmol );
1123	<	}
1124	<	}
1118	>	// make an array of molecule stamps that match the components used.
1119	>	// also extract the used stamps out into a separate linked list
1120	>
1121	>	for (i = 0; i < nInfo; i++){
1122	>	info[i].nComponents = n_components;
1123	>	info[i].componentsNmol = components_nmol;
1124	>	info[i].compStamps = comp_stamps;
1125	>	info[i].headStamp = headStamp;
1126	>	}
1127	>
1128	>
1129	>	for (i = 0; i < n_components; i++){
1130	>	id = the_components[i]->getType();
1131	>	comp_stamps[i] = NULL;
1132	>
1133	>	// check to make sure the component isn't already in the list
1134	>
1135	>	comp_stamps[i] = headStamp->match(id);
1136	>	if (comp_stamps[i] == NULL){
1137	>	// extract the component from the list;
1138	>
1139	>	currentStamp = stamps->extractMolStamp(id);
1140	>	if (currentStamp == NULL){
1141	>	sprintf(painCave.errMsg,
1142	>	"SimSetup error: Component \"%s\" was not found in the "
1143	>	"list of declared molecules\n",
1144	>	id);
1145	>	painCave.isFatal = 1;
1146	>	simError();
1147		}
1148	+
1149	+	headStamp->add(currentStamp);
1150	+	comp_stamps[i] = headStamp->match(id);
1151		}
1152		}
1153
1154	+	#ifdef IS_MPI
1155	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1156	+	MPIcheckPoint();
1157	+	#endif // is_mpi
1158	+	}
1159
1160	<	for( i=0; i<simnfo->n_atoms; i++ ){
1161	<	simnfo->atoms[i]->set_vx( 0.0 );
1162	<	simnfo->atoms[i]->set_vy( 0.0 );
1163	<	simnfo->atoms[i]->set_vz( 0.0 );
1160	>	void SimSetup::calcSysValues(void){
1161	>	int i, j, k;
1162	>
1163	>	int* molMembershipArray;
1164	>
1165	>	tot_atoms = 0;
1166	>	tot_bonds = 0;
1167	>	tot_bends = 0;
1168	>	tot_torsions = 0;
1169	>	for (i = 0; i < n_components; i++){
1170	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1171	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1172	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1173	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1174		}
1383	–	}
1175
1176	<	void SimSetup::makeElement( double x, double y, double z ){
1176	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1177	>	molMembershipArray = new int[tot_atoms];
1178
1179	<	int k;
1180	<	AtomStamp* current_atom;
1181	<	DirectionalAtom* dAtom;
1182	<	double rotMat[3][3];
1179	>	for (i = 0; i < nInfo; i++){
1180	>	info[i].n_atoms = tot_atoms;
1181	>	info[i].n_bonds = tot_bonds;
1182	>	info[i].n_bends = tot_bends;
1183	>	info[i].n_torsions = tot_torsions;
1184	>	info[i].n_SRI = tot_SRI;
1185	>	info[i].n_mol = tot_nmol;
1186
1187	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1187	>	info[i].molMembershipArray = molMembershipArray;
1188	>	}
1189	>	}
1190
1191	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1395	<	if( !current_atom->havePosition() ){
1396	<	sprintf( painCave.errMsg,
1397	<	"SimSetup:initFromBass error.\n"
1398	<	"\tComponent %s, atom %s does not have a position specified.\n"
1399	<	"\tThe initialization routine is unable to give a start"
1400	<	" position.\n",
1401	<	comp_stamps[current_comp]->getID(),
1402	<	current_atom->getType() );
1403	<	painCave.isFatal = 1;
1404	<	simError();
1405	<	}
1191	>	#ifdef IS_MPI
1192
1193	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1194	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1195	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1193	>	void SimSetup::mpiMolDivide(void){
1194	>	int i, j, k;
1195	>	int localMol, allMol;
1196	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1197
1198	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1198	>	mpiSim = new mpiSimulation(info);
1199
1200	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1200	>	globalIndex = mpiSim->divideLabor();
1201
1202	<	rotMat[0][0] = 1.0;
1416	<	rotMat[0][1] = 0.0;
1417	<	rotMat[0][2] = 0.0;
1202	>	// set up the local variables
1203
1204	<	rotMat[1][0] = 0.0;
1205	<	rotMat[1][1] = 1.0;
1421	<	rotMat[1][2] = 0.0;
1204	>	mol2proc = mpiSim->getMolToProcMap();
1205	>	molCompType = mpiSim->getMolComponentType();
1206
1207	<	rotMat[2][0] = 0.0;
1208	<	rotMat[2][1] = 0.0;
1209	<	rotMat[2][2] = 1.0;
1207	>	allMol = 0;
1208	>	localMol = 0;
1209	>	local_atoms = 0;
1210	>	local_bonds = 0;
1211	>	local_bends = 0;
1212	>	local_torsions = 0;
1213	>	globalAtomIndex = 0;
1214
1427	–	dAtom->setA( rotMat );
1428	–	}
1215
1216	<	current_atom_ndx++;
1216	>	for (i = 0; i < n_components; i++){
1217	>	for (j = 0; j < components_nmol[i]; j++){
1218	>	if (mol2proc[allMol] == worldRank){
1219	>	local_atoms += comp_stamps[i]->getNAtoms();
1220	>	local_bonds += comp_stamps[i]->getNBonds();
1221	>	local_bends += comp_stamps[i]->getNBends();
1222	>	local_torsions += comp_stamps[i]->getNTorsions();
1223	>	localMol++;
1224	>	}
1225	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1226	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1227	>	globalAtomIndex++;
1228	>	}
1229	>
1230	>	allMol++;
1231	>	}
1232		}
1233	+	local_SRI = local_bonds + local_bends + local_torsions;
1234
1235	<	current_mol++;
1434	<	current_comp_mol++;
1235	>	info[0].n_atoms = mpiSim->getMyNlocal();
1236
1237	<	if( current_comp_mol >= components_nmol[current_comp] ){
1237	>	if (local_atoms != info[0].n_atoms){
1238	>	sprintf(painCave.errMsg,
1239	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1240	>	" localAtom (%d) are not equal.\n",
1241	>	info[0].n_atoms, local_atoms);
1242	>	painCave.isFatal = 1;
1243	>	simError();
1244	>	}
1245
1246	<	current_comp_mol = 0;
1247	<	current_comp++;
1246	>	info[0].n_bonds = local_bonds;
1247	>	info[0].n_bends = local_bends;
1248	>	info[0].n_torsions = local_torsions;
1249	>	info[0].n_SRI = local_SRI;
1250	>	info[0].n_mol = localMol;
1251	>
1252	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1253	>	MPIcheckPoint();
1254	>	}
1255	>
1256	>	#endif // is_mpi
1257	>
1258	>
1259	>	void SimSetup::makeSysArrays(void){
1260	>	int i, j, k, l;
1261	>
1262	>	Atom** the_atoms;
1263	>	Molecule* the_molecules;
1264	>	Exclude** the_excludes;
1265	>
1266	>
1267	>	for (l = 0; l < nInfo; l++){
1268	>	// create the atom and short range interaction arrays
1269	>
1270	>	the_atoms = new Atom * [info[l].n_atoms];
1271	>	the_molecules = new Molecule[info[l].n_mol];
1272	>	int molIndex;
1273	>
1274	>	// initialize the molecule's stampID's
1275	>
1276	>	#ifdef IS_MPI
1277	>
1278	>
1279	>	molIndex = 0;
1280	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1281	>	if (mol2proc[i] == worldRank){
1282	>	the_molecules[molIndex].setStampID(molCompType[i]);
1283	>	the_molecules[molIndex].setMyIndex(molIndex);
1284	>	the_molecules[molIndex].setGlobalIndex(i);
1285	>	molIndex++;
1286	>	}
1287	>	}
1288	>
1289	>	#else // is_mpi
1290	>
1291	>	molIndex = 0;
1292	>	globalAtomIndex = 0;
1293	>	for (i = 0; i < n_components; i++){
1294	>	for (j = 0; j < components_nmol[i]; j++){
1295	>	the_molecules[molIndex].setStampID(i);
1296	>	the_molecules[molIndex].setMyIndex(molIndex);
1297	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1298	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1299	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1300	>	globalAtomIndex++;
1301	>	}
1302	>	molIndex++;
1303	>	}
1304	>	}
1305	>
1306	>
1307	>	#endif // is_mpi
1308	>
1309	>
1310	>	if (info[l].n_SRI){
1311	>	Exclude::createArray(info[l].n_SRI);
1312	>	the_excludes = new Exclude * [info[l].n_SRI];
1313	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1314	>	the_excludes[ex] = new Exclude(ex);
1315	>	}
1316	>	info[l].globalExcludes = new int;
1317	>	info[l].n_exclude = info[l].n_SRI;
1318	>	}
1319	>	else{
1320	>	Exclude::createArray(1);
1321	>	the_excludes = new Exclude * ;
1322	>	the_excludes[0] = new Exclude(0);
1323	>	the_excludes[0]->setPair(0, 0);
1324	>	info[l].globalExcludes = new int;
1325	>	info[l].globalExcludes[0] = 0;
1326	>	info[l].n_exclude = 0;
1327	>	}
1328	>
1329	>	// set the arrays into the SimInfo object
1330	>
1331	>	info[l].atoms = the_atoms;
1332	>	info[l].molecules = the_molecules;
1333	>	info[l].nGlobalExcludes = 0;
1334	>	info[l].excludes = the_excludes;
1335	>
1336	>	the_ff->setSimInfo(info);
1337		}
1338		}
1339	+
1340	+	void SimSetup::makeIntegrator(void){
1341	+	int k;
1342	+
1343	+	NVE<RealIntegrator>* myNVE = NULL;
1344	+	NVT<RealIntegrator>* myNVT = NULL;
1345	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1346	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1347	+
1348	+	for (k = 0; k < nInfo; k++){
1349	+	switch (ensembleCase){
1350	+	case NVE_ENS:
1351	+	if (globals->haveZconstraints()){
1352	+	setupZConstraint(info[k]);
1353	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1354	+	}
1355	+	else{
1356	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1357	+	}
1358	+
1359	+	info->the_integrator = myNVE;
1360	+	break;
1361	+
1362	+	case NVT_ENS:
1363	+	if (globals->haveZconstraints()){
1364	+	setupZConstraint(info[k]);
1365	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1366	+	}
1367	+	else
1368	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1369	+
1370	+	myNVT->setTargetTemp(globals->getTargetTemp());
1371	+
1372	+	if (globals->haveTauThermostat())
1373	+	myNVT->setTauThermostat(globals->getTauThermostat());
1374	+	else{
1375	+	sprintf(painCave.errMsg,
1376	+	"SimSetup error: If you use the NVT\n"
1377	+	"    ensemble, you must set tauThermostat.\n");
1378	+	painCave.isFatal = 1;
1379	+	simError();
1380	+	}
1381	+
1382	+	info->the_integrator = myNVT;
1383	+	break;
1384	+
1385	+	case NPTi_ENS:
1386	+	if (globals->haveZconstraints()){
1387	+	setupZConstraint(info[k]);
1388	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1389	+	}
1390	+	else
1391	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1392	+
1393	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1394	+
1395	+	if (globals->haveTargetPressure())
1396	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1397	+	else{
1398	+	sprintf(painCave.errMsg,
1399	+	"SimSetup error: If you use a constant pressure\n"
1400	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1401	+	painCave.isFatal = 1;
1402	+	simError();
1403	+	}
1404	+
1405	+	if (globals->haveTauThermostat())
1406	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1407	+	else{
1408	+	sprintf(painCave.errMsg,
1409	+	"SimSetup error: If you use an NPT\n"
1410	+	"    ensemble, you must set tauThermostat.\n");
1411	+	painCave.isFatal = 1;
1412	+	simError();
1413	+	}
1414	+
1415	+	if (globals->haveTauBarostat())
1416	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1417	+	else{
1418	+	sprintf(painCave.errMsg,
1419	+	"SimSetup error: If you use an NPT\n"
1420	+	"    ensemble, you must set tauBarostat.\n");
1421	+	painCave.isFatal = 1;
1422	+	simError();
1423	+	}
1424	+
1425	+	info->the_integrator = myNPTi;
1426	+	break;
1427	+
1428	+	case NPTf_ENS:
1429	+	if (globals->haveZconstraints()){
1430	+	setupZConstraint(info[k]);
1431	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1432	+	}
1433	+	else
1434	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1435	+
1436	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1437	+
1438	+	if (globals->haveTargetPressure())
1439	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1440	+	else{
1441	+	sprintf(painCave.errMsg,
1442	+	"SimSetup error: If you use a constant pressure\n"
1443	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1444	+	painCave.isFatal = 1;
1445	+	simError();
1446	+	}
1447	+
1448	+	if (globals->haveTauThermostat())
1449	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1450	+	else{
1451	+	sprintf(painCave.errMsg,
1452	+	"SimSetup error: If you use an NPT\n"
1453	+	"    ensemble, you must set tauThermostat.\n");
1454	+	painCave.isFatal = 1;
1455	+	simError();
1456	+	}
1457	+
1458	+	if (globals->haveTauBarostat())
1459	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1460	+	else{
1461	+	sprintf(painCave.errMsg,
1462	+	"SimSetup error: If you use an NPT\n"
1463	+	"    ensemble, you must set tauBarostat.\n");
1464	+	painCave.isFatal = 1;
1465	+	simError();
1466	+	}
1467	+
1468	+	info->the_integrator = myNPTf;
1469	+	break;
1470	+
1471	+	default:
1472	+	sprintf(painCave.errMsg,
1473	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1474	+	painCave.isFatal = 1;
1475	+	simError();
1476	+	}
1477	+	}
1478	+	}
1479	+
1480	+	void SimSetup::initFortran(void){
1481	+	info[0].refreshSim();
1482	+
1483	+	if (!strcmp(info[0].mixingRule, "standard")){
1484	+	the_ff->initForceField(LB_MIXING_RULE);
1485	+	}
1486	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1487	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1488	+	}
1489	+	else{
1490	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1491	+	info[0].mixingRule);
1492	+	painCave.isFatal = 1;
1493	+	simError();
1494	+	}
1495	+
1496	+
1497	+	#ifdef IS_MPI
1498	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1499	+	MPIcheckPoint();
1500	+	#endif // is_mpi
1501	+	}
1502	+
1503	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1504	+	int nZConstraints;
1505	+	ZconStamp** zconStamp;
1506	+
1507	+	if (globals->haveZconstraintTime()){
1508	+	//add sample time of z-constraint  into SimInfo's property list
1509	+	DoubleData* zconsTimeProp = new DoubleData();
1510	+	zconsTimeProp->setID(ZCONSTIME_ID);
1511	+	zconsTimeProp->setData(globals->getZconsTime());
1512	+	theInfo.addProperty(zconsTimeProp);
1513	+	}
1514	+	else{
1515	+	sprintf(painCave.errMsg,
1516	+	"ZConstraint error: If you use an ZConstraint\n"
1517	+	" , you must set sample time.\n");
1518	+	painCave.isFatal = 1;
1519	+	simError();
1520	+	}
1521	+
1522	+	//push zconsTol into siminfo, if user does not specify
1523	+	//value for zconsTol, a default value will be used
1524	+	DoubleData* zconsTol = new DoubleData();
1525	+	zconsTol->setID(ZCONSTOL_ID);
1526	+	if (globals->haveZconsTol()){
1527	+	zconsTol->setData(globals->getZconsTol());
1528	+	}
1529	+	else{
1530	+	double defaultZConsTol = 0.01;
1531	+	sprintf(painCave.errMsg,
1532	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1533	+	" , default value %f is used.\n",
1534	+	defaultZConsTol);
1535	+	painCave.isFatal = 0;
1536	+	simError();
1537	+
1538	+	zconsTol->setData(defaultZConsTol);
1539	+	}
1540	+	theInfo.addProperty(zconsTol);
1541	+
1542	+	//set Force Subtraction Policy
1543	+	StringData* zconsForcePolicy = new StringData();
1544	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1545	+
1546	+	if (globals->haveZconsForcePolicy()){
1547	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1548	+	}
1549	+	else{
1550	+	sprintf(painCave.errMsg,
1551	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1552	+	"PolicyByMass is used\n");
1553	+	painCave.isFatal = 0;
1554	+	simError();
1555	+	zconsForcePolicy->setData("BYMASS");
1556	+	}
1557	+
1558	+	theInfo.addProperty(zconsForcePolicy);
1559	+
1560	+	//Determine the name of ouput file and add it into SimInfo's property list
1561	+	//Be careful, do not use inFileName, since it is a pointer which
1562	+	//point to a string at master node, and slave nodes do not contain that string
1563	+
1564	+	string zconsOutput(theInfo.finalName);
1565	+
1566	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1567	+
1568	+	StringData* zconsFilename = new StringData();
1569	+	zconsFilename->setID(ZCONSFILENAME_ID);
1570	+	zconsFilename->setData(zconsOutput);
1571	+
1572	+	theInfo.addProperty(zconsFilename);
1573	+
1574	+	//setup index, pos and other parameters of z-constraint molecules
1575	+	nZConstraints = globals->getNzConstraints();
1576	+	theInfo.nZconstraints = nZConstraints;
1577	+
1578	+	zconStamp = globals->getZconStamp();
1579	+	ZConsParaItem tempParaItem;
1580	+
1581	+	ZConsParaData* zconsParaData = new ZConsParaData();
1582	+	zconsParaData->setID(ZCONSPARADATA_ID);
1583	+
1584	+	for (int i = 0; i < nZConstraints; i++){
1585	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1586	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1587	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1588	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1589	+
1590	+	zconsParaData->addItem(tempParaItem);
1591	+	}
1592	+
1593	+	//check the uniqueness of index
1594	+	if(!zconsParaData->isIndexUnique()){
1595	+	sprintf(painCave.errMsg,
1596	+	"ZConstraint Error: molIndex is not unique\n");
1597	+	painCave.isFatal = 1;
1598	+	simError();
1599	+	}
1600	+
1601	+	//sort the parameters by index of molecules
1602	+	zconsParaData->sortByIndex();
1603	+
1604	+	//push data into siminfo, therefore, we can retrieve later
1605	+	theInfo.addProperty(zconsParaData);
1606	+	}

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