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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 778 by mmeineke, Fri Sep 19 20:00:27 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 NPTim_ENS      4
26	+	#define NPTfm_ENS      5
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	>	int i, j, k, globalAtomIndex;
96
97	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
97	>	// gather all of the information from the Bass file
98
99	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
99	>	gatherInfo();
100
101	<	// 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();
101	>	// creation of complex system objects
102
103	<	// 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 );
103	>	sysObjectsCreation();
104
105	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
105	>	// check on the post processing info
106
107	+	finalInfoCheck();
108
109	<	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	<	}
109	>	// initialize the system coordinates
110
111	<	#ifdef IS_MPI
112	<	strcpy( checkPointMsg, "ForceField creation successful" );
113	<	MPIcheckPoint();
106	<	#endif // is_mpi
111	>	if (!isInfoArray){
112	>	initSystemCoords();
113	>	}
114
115	<
115	>	// make the output filenames
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	>	makeOutNames();
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	>	// make the integrator
120
121	<	tot_nmol = 0;
120	<	for( i=0; i<n_components; i++ ){
121	>	makeIntegrator();
122
123	<	if( !the_components[i]->haveNMol() ){
124	<	// we have a problem
125	<	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	>	#ifdef IS_MPI
124	>	mpiSim->mpiRefresh();
125	>	#endif
126
127	<	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	<	}
127	>	// initialize the Fortran
128
129	<	#ifdef IS_MPI
130	<	strcpy( checkPointMsg, "Have the number of components" );
162	<	MPIcheckPoint();
163	<	#endif // is_mpi
129	>	initFortran();
130	>	}
131
165	–	// make an array of molecule stamps that match the components used.
166	–	// also extract the used stamps out into a separate linked list
132
133	<	simnfo->nComponents = n_components;
134	<	simnfo->componentsNmol = components_nmol;
135	<	simnfo->compStamps = comp_stamps;
136	<	simnfo->headStamp = new LinkedMolStamp();
137	<
138	<	char* id;
139	<	LinkedMolStamp* headStamp = simnfo->headStamp;
140	<	LinkedMolStamp* currentStamp = NULL;
141	<	for( i=0; i<n_components; i++ ){
133	>	void SimSetup::makeMolecules(void){
134	>	int k, l;
135	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
136	>	molInit molInfo;
137	>	DirectionalAtom* dAtom;
138	>	LinkedAssign* extras;
139	>	LinkedAssign* current_extra;
140	>	AtomStamp* currentAtom;
141	>	BondStamp* currentBond;
142	>	BendStamp* currentBend;
143	>	TorsionStamp* currentTorsion;
144
145	<	id = the_components[i]->getType();
146	<	comp_stamps[i] = NULL;
147	<
181	<	// check to make sure the component isn't already in the list
145	>	bond_pair* theBonds;
146	>	bend_set* theBends;
147	>	torsion_set* theTorsions;
148
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	–	}
149
150	<	#ifdef IS_MPI
204	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
205	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
150	>	//init the forceField paramters
151
152	+	the_ff->readParams();
153
154
155	<	// caclulate the number of atoms, bonds, bends and torsions
155	>	// init the atoms
156
157	<	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	<	}
157	>	double ux, uy, uz, u, uSqr;
158
159	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
159	>	for (k = 0; k < nInfo; k++){
160	>	the_ff->setSimInfo(&(info[k]));
161
162	<	simnfo->n_atoms = tot_atoms;
163	<	simnfo->n_bonds = tot_bonds;
164	<	simnfo->n_bends = tot_bends;
165	<	simnfo->n_torsions = tot_torsions;
231	<	simnfo->n_SRI = tot_SRI;
232	<	simnfo->n_mol = tot_nmol;
162	>	atomOffset = 0;
163	>	excludeOffset = 0;
164	>	for (i = 0; i < info[k].n_mol; i++){
165	>	stampID = info[k].molecules[i].getStampID();
166
167	<
168	<	#ifdef IS_MPI
167	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
168	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
169	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
170	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
171	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
172
173	<	// divide the molecules among processors here.
174	<
175	<	mpiSim = new mpiSimulation( simnfo );
176	<
177	<
173	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
174	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
175	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
176	>	molInfo.myBends = new Bend * [molInfo.nBends];
177	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
178
179	<	globalIndex = mpiSim->divideLabor();
179	>	theBonds = new bond_pair[molInfo.nBonds];
180	>	theBends = new bend_set[molInfo.nBends];
181	>	theTorsions = new torsion_set[molInfo.nTorsions];
182
183	+	// make the Atoms
184
185	+	for (j = 0; j < molInfo.nAtoms; j++){
186	+	currentAtom = comp_stamps[stampID]->getAtom(j);
187	+	if (currentAtom->haveOrientation()){
188	+	dAtom = new DirectionalAtom((j + atomOffset),
189	+	info[k].getConfiguration());
190	+	info[k].n_oriented++;
191	+	molInfo.myAtoms[j] = dAtom;
192
193	<	// set up the local variables
194	<
195	<	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++ ){
193	>	ux = currentAtom->getOrntX();
194	>	uy = currentAtom->getOrntY();
195	>	uz = currentAtom->getOrntZ();
196
197	<	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	<
197	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
198
199	<	simnfo->n_atoms = mpiSim->getMyNlocal();
200	<
201	<	if( local_atoms != simnfo->n_atoms ){
202	<	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	<	}
199	>	u = sqrt(uSqr);
200	>	ux = ux / u;
201	>	uy = uy / u;
202	>	uz = uz / u;
203
204	<	simnfo->n_bonds = local_bonds;
205	<	simnfo->n_bends = local_bends;
206	<	simnfo->n_torsions = local_torsions;
207	<	simnfo->n_SRI = local_SRI;
208	<	simnfo->n_mol = localMol;
204	>	dAtom->setSUx(ux);
205	>	dAtom->setSUy(uy);
206	>	dAtom->setSUz(uz);
207	>	}
208	>	else{
209	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
210	>	info[k].getConfiguration());
211	>	}
212	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
213
214	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
215	<	MPIcheckPoint();
216	<
217	<
214	>	#ifdef IS_MPI
215	>
216	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
217	>
218		#endif // is_mpi
219	<
219	>	}
220
221	<	// create the atom and short range interaction arrays
221	>	// make the bonds
222	>	for (j = 0; j < molInfo.nBonds; j++){
223	>	currentBond = comp_stamps[stampID]->getBond(j);
224	>	theBonds[j].a = currentBond->getA() + atomOffset;
225	>	theBonds[j].b = currentBond->getB() + atomOffset;
226
227	<	Atom::createArrays(simnfo->n_atoms);
228	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
227	>	exI = theBonds[j].a;
228	>	exJ = theBonds[j].b;
229
230	+	// exclude_I must always be the smaller of the pair
231	+	if (exI > exJ){
232	+	tempEx = exI;
233	+	exI = exJ;
234	+	exJ = tempEx;
235	+	}
236	+	#ifdef IS_MPI
237	+	tempEx = exI;
238	+	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
239	+	tempEx = exJ;
240	+	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
241
242	<	if( simnfo->n_SRI ){
243	<	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	<	}
242	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
243	>	#else  // isn't MPI
244
245	<	// set the arrays into the SimInfo object
245	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
246	>	#endif  //is_mpi
247	>	}
248	>	excludeOffset += molInfo.nBonds;
249
250	<	simnfo->atoms = the_atoms;
251	<	simnfo->sr_interactions = the_sris;
252	<	simnfo->nGlobalExcludes = 0;
253	<	simnfo->excludes = the_excludes;
250	>	//make the bends
251	>	for (j = 0; j < molInfo.nBends; j++){
252	>	currentBend = comp_stamps[stampID]->getBend(j);
253	>	theBends[j].a = currentBend->getA() + atomOffset;
254	>	theBends[j].b = currentBend->getB() + atomOffset;
255	>	theBends[j].c = currentBend->getC() + atomOffset;
256
257	+	if (currentBend->haveExtras()){
258	+	extras = currentBend->getExtras();
259	+	current_extra = extras;
260
261	<	// get some of the tricky things that may still be in the globals
261	>	while (current_extra != NULL){
262	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
263	>	switch (current_extra->getType()){
264	>	case 0:
265	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
266	>	theBends[j].isGhost = 1;
267	>	break;
268
269	<
270	<	if( the_globals->haveBox() ){
271	<	simnfo->box_x = the_globals->getBox();
272	<	simnfo->box_y = the_globals->getBox();
273	<	simnfo->box_z = the_globals->getBox();
341	<	}
342	<	else if( the_globals->haveDensity() ){
269	>	case 1:
270	>	theBends[j].ghost = (int) current_extra->getDouble() +
271	>	atomOffset;
272	>	theBends[j].isGhost = 1;
273	>	break;
274
275	<	double vol;
276	<	vol = (double)tot_nmol / the_globals->getDensity();
277	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
278	<	simnfo->box_y = simnfo->box_x;
279	<	simnfo->box_z = simnfo->box_x;
280	<	}
281	<	else{
282	<	if( !the_globals->haveBoxX() ){
283	<	sprintf( painCave.errMsg,
284	<	"SimSetup error, no periodic BoxX size given.\n" );
285	<	painCave.isFatal = 1;
286	<	simError();
287	<	}
288	<	simnfo->box_x = the_globals->getBoxX();
275	>	default:
276	>	sprintf(painCave.errMsg,
277	>	"SimSetup Error: ghostVectorSource was neither a "
278	>	"double nor an int.\n"
279	>	"-->Bend[%d] in %s\n",
280	>	j, comp_stamps[stampID]->getID());
281	>	painCave.isFatal = 1;
282	>	simError();
283	>	}
284	>	}
285	>	else{
286	>	sprintf(painCave.errMsg,
287	>	"SimSetup Error: unhandled bend assignment:\n"
288	>	"    -->%s in Bend[%d] in %s\n",
289	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
290	>	painCave.isFatal = 1;
291	>	simError();
292	>	}
293
294	<	if( !the_globals->haveBoxY() ){
295	<	sprintf( painCave.errMsg,
296	<	"SimSetup error, no periodic BoxY size given.\n" );
362	<	painCave.isFatal = 1;
363	<	simError();
364	<	}
365	<	simnfo->box_y = the_globals->getBoxY();
294	>	current_extra = current_extra->getNext();
295	>	}
296	>	}
297
298	<	if( !the_globals->haveBoxZ() ){
299	<	sprintf( painCave.errMsg,
300	<	"SimSetup error, no periodic BoxZ size given.\n" );
301	<	painCave.isFatal = 1;
302	<	simError();
303	<	}
304	<	simnfo->box_z = the_globals->getBoxZ();
305	<	}
298	>	if (!theBends[j].isGhost){
299	>	exI = theBends[j].a;
300	>	exJ = theBends[j].c;
301	>	}
302	>	else{
303	>	exI = theBends[j].a;
304	>	exJ = theBends[j].b;
305	>	}
306
307	+	// exclude_I must always be the smaller of the pair
308	+	if (exI > exJ){
309	+	tempEx = exI;
310	+	exI = exJ;
311	+	exJ = tempEx;
312	+	}
313		#ifdef IS_MPI
314	<	strcpy( checkPointMsg, "Box size set up" );
315	<	MPIcheckPoint();
316	<	#endif // is_mpi
314	>	tempEx = exI;
315	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
316	>	tempEx = exJ;
317	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
318
319	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
320	+	#else  // isn't MPI
321	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
322	+	#endif  //is_mpi
323	+	}
324	+	excludeOffset += molInfo.nBends;
325
326	<	// initialize the arrays
326	>	for (j = 0; j < molInfo.nTorsions; j++){
327	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
328	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
329	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
330	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
331	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
332
333	<	the_ff->setSimInfo( simnfo );
333	>	exI = theTorsions[j].a;
334	>	exJ = theTorsions[j].d;
335
336	<	makeAtoms();
337	<	simnfo->identArray = new int[simnfo->n_atoms];
338	<	for(i=0; i<simnfo->n_atoms; i++){
339	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
340	<	}
341	<
342	<	if( tot_bonds ){
343	<	makeBonds();
344	<	}
336	>	// exclude_I must always be the smaller of the pair
337	>	if (exI > exJ){
338	>	tempEx = exI;
339	>	exI = exJ;
340	>	exJ = tempEx;
341	>	}
342	>	#ifdef IS_MPI
343	>	tempEx = exI;
344	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345	>	tempEx = exJ;
346	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
347	>
348	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
349	>	#else  // isn't MPI
350	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
351	>	#endif  //is_mpi
352	>	}
353	>	excludeOffset += molInfo.nTorsions;
354	>
355	>
356	>	// send the arrays off to the forceField for init.
357	>
358	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
359	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
360	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
361	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
362	>	theTorsions);
363	>
364
365	<	if( tot_bends ){
397	<	makeBends();
398	<	}
365	>	info[k].molecules[i].initialize(molInfo);
366
367	<	if( tot_torsions ){
368	<	makeTorsions();
367	>
368	>	atomOffset += molInfo.nAtoms;
369	>	delete[] theBonds;
370	>	delete[] theBends;
371	>	delete[] theTorsions;
372	>	}
373		}
374
375	+	#ifdef IS_MPI
376	+	sprintf(checkPointMsg, "all molecules initialized succesfully");
377	+	MPIcheckPoint();
378	+	#endif // is_mpi
379
380	<	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	<	}
380	>	// clean up the forcefield
381
382	<	if( !the_globals->haveEST() ){
383	<	sprintf( painCave.errMsg,
384	<	"SimSetup Warning: using default value of 0.05 * the "
385	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
386	<	);
387	<	painCave.isFatal = 0;
388	<	simError();
389	<	simnfo->est = 0.05 * simnfo->ecr;
390	<	} else {
391	<	simnfo->est        = the_globals->getEST();
392	<	}
393	<
394	<	if(!the_globals->haveDielectric() ){
395	<	sprintf( painCave.errMsg,
396	<	"SimSetup Error: You are trying to use Reaction Field without"
397	<	"setting a dielectric constant!\n"
398	<	);
382	>	the_ff->calcRcut();
383	>	the_ff->cleanMe();
384	>	}
385	>
386	>	void SimSetup::initFromBass(void){
387	>	int i, j, k;
388	>	int n_cells;
389	>	double cellx, celly, cellz;
390	>	double temp1, temp2, temp3;
391	>	int n_per_extra;
392	>	int n_extra;
393	>	int have_extra, done;
394	>
395	>	double vel[3];
396	>	vel[0] = 0.0;
397	>	vel[1] = 0.0;
398	>	vel[2] = 0.0;
399	>
400	>	temp1 = (double) tot_nmol / 4.0;
401	>	temp2 = pow(temp1, (1.0 / 3.0));
402	>	temp3 = ceil(temp2);
403	>
404	>	have_extra = 0;
405	>	if (temp2 < temp3){
406	>	// we have a non-complete lattice
407	>	have_extra = 1;
408	>
409	>	n_cells = (int) temp3 - 1;
410	>	cellx = info[0].boxL[0] / temp3;
411	>	celly = info[0].boxL[1] / temp3;
412	>	cellz = info[0].boxL[2] / temp3;
413	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
414	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
415	>	n_per_extra = (int) ceil(temp1);
416	>
417	>	if (n_per_extra > 4){
418	>	sprintf(painCave.errMsg,
419	>	"SimSetup error. There has been an error in constructing"
420	>	" the non-complete lattice.\n");
421		painCave.isFatal = 1;
422		simError();
423		}
424	<	simnfo->dielectric = the_globals->getDielectric();
425	<	} else {
426	<	if (simnfo->n_dipoles) {
427	<
428	<	if( !the_globals->haveECR() ){
429	<	sprintf( painCave.errMsg,
430	<	"SimSetup Warning: using default value of 1/2 the smallest"
431	<	"box length for the electrostaticCutoffRadius.\n"
432	<	"I hope you have a very fast processor!\n");
433	<	painCave.isFatal = 0;
434	<	simError();
435	<	double smallest;
436	<	smallest = simnfo->box_x;
437	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
438	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
439	<	simnfo->ecr = 0.5 * smallest;
440	<	} else {
441	<	simnfo->ecr        = the_globals->getECR();
424	>	}
425	>	else{
426	>	n_cells = (int) temp3;
427	>	cellx = info[0].boxL[0] / temp3;
428	>	celly = info[0].boxL[1] / temp3;
429	>	cellz = info[0].boxL[2] / temp3;
430	>	}
431	>
432	>	current_mol = 0;
433	>	current_comp_mol = 0;
434	>	current_comp = 0;
435	>	current_atom_ndx = 0;
436	>
437	>	for (i = 0; i < n_cells ; i++){
438	>	for (j = 0; j < n_cells; j++){
439	>	for (k = 0; k < n_cells; k++){
440	>	makeElement(i * cellx, j * celly, k * cellz);
441	>
442	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
443	>
444	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
445	>
446	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
447		}
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	–	}
448		}
449	<	}
449	>	}
450
451	<	#ifdef IS_MPI
452	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
481	<	MPIcheckPoint();
482	<	#endif // is_mpi
451	>	if (have_extra){
452	>	done = 0;
453
454	<	if( the_globals->haveInitialConfig() ){
455	<
456	<	InitializeFromFile* fileInit;
457	<	#ifdef IS_MPI // is_mpi
458	<	if( worldRank == 0 ){
459	<	#endif //is_mpi
460	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
461	<	#ifdef IS_MPI
462	<	}else fileInit = new InitializeFromFile( NULL );
463	<	#endif
464	<	fileInit->read_xyz( simnfo ); // default velocities on
454	>	int start_ndx;
455	>	for (i = 0; i < (n_cells + 1) && !done; i++){
456	>	for (j = 0; j < (n_cells + 1) && !done; j++){
457	>	if (i < n_cells){
458	>	if (j < n_cells){
459	>	start_ndx = n_cells;
460	>	}
461	>	else
462	>	start_ndx = 0;
463	>	}
464	>	else
465	>	start_ndx = 0;
466
467	<	delete fileInit;
468	<	}
469	<	else{
467	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
468	>	makeElement(i * cellx, j * celly, k * cellz);
469	>	done = (current_mol >= tot_nmol);
470
471	<	#ifdef IS_MPI
471	>	if (!done && n_per_extra > 1){
472	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
473	>	k * cellz);
474	>	done = (current_mol >= tot_nmol);
475	>	}
476
477	<	// no init from bass
478	<
479	<	sprintf( painCave.errMsg,
480	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
481	<	painCave.isFatal;
507	<	simError();
508	<
509	<	#else
477	>	if (!done && n_per_extra > 2){
478	>	makeElement(i * cellx, j * celly + 0.5 * celly,
479	>	k * cellz + 0.5 * cellz);
480	>	done = (current_mol >= tot_nmol);
481	>	}
482
483	<	initFromBass();
483	>	if (!done && n_per_extra > 3){
484	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
485	>	k * cellz + 0.5 * cellz);
486	>	done = (current_mol >= tot_nmol);
487	>	}
488	>	}
489	>	}
490	>	}
491	>	}
492
493	+	for (i = 0; i < info[0].n_atoms; i++){
494	+	info[0].atoms[i]->setVel(vel);
495	+	}
496	+	}
497
498	<	#endif
499	<	}
498	>	void SimSetup::makeElement(double x, double y, double z){
499	>	int k;
500	>	AtomStamp* current_atom;
501	>	DirectionalAtom* dAtom;
502	>	double rotMat[3][3];
503	>	double pos[3];
504
505	<	#ifdef IS_MPI
506	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
507	<	MPIcheckPoint();
508	<	#endif // is_mpi
505	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
506	>	current_atom = comp_stamps[current_comp]->getAtom(k);
507	>	if (!current_atom->havePosition()){
508	>	sprintf(painCave.errMsg,
509	>	"SimSetup:initFromBass error.\n"
510	>	"\tComponent %s, atom %s does not have a position specified.\n"
511	>	"\tThe initialization routine is unable to give a start"
512	>	" position.\n",
513	>	comp_stamps[current_comp]->getID(), current_atom->getType());
514	>	painCave.isFatal = 1;
515	>	simError();
516	>	}
517
518	+	pos[0] = x + current_atom->getPosX();
519	+	pos[1] = y + current_atom->getPosY();
520	+	pos[2] = z + current_atom->getPosZ();
521
522	<
524	<
525	<
522	>	info[0].atoms[current_atom_ndx]->setPos(pos);
523
524	<
525	<	#ifdef IS_MPI
526	<	if( worldRank == 0 ){
527	<	#endif // is_mpi
528	<
529	<	if( the_globals->haveFinalConfig() ){
530	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
524	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
525	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
526	>
527	>	rotMat[0][0] = 1.0;
528	>	rotMat[0][1] = 0.0;
529	>	rotMat[0][2] = 0.0;
530	>
531	>	rotMat[1][0] = 0.0;
532	>	rotMat[1][1] = 1.0;
533	>	rotMat[1][2] = 0.0;
534	>
535	>	rotMat[2][0] = 0.0;
536	>	rotMat[2][1] = 0.0;
537	>	rotMat[2][2] = 1.0;
538	>
539	>	dAtom->setA(rotMat);
540		}
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	–	}
541
542	<	if( the_globals->haveStatusTime() ){
625	<	simnfo->statusTime = the_globals->getStatusTime();
542	>	current_atom_ndx++;
543		}
544
545	<	if( the_globals->haveThermalTime() ){
546	<	simnfo->thermalTime = the_globals->getThermalTime();
545	>	current_mol++;
546	>	current_comp_mol++;
547	>
548	>	if (current_comp_mol >= components_nmol[current_comp]){
549	>	current_comp_mol = 0;
550	>	current_comp++;
551		}
552	+	}
553
632	–	// check for the temperature set flag
554
555	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
555	>	void SimSetup::gatherInfo(void){
556	>	int i, j, k;
557
558	+	ensembleCase = -1;
559	+	ffCase = -1;
560
561	<	//   // make the longe range forces and the integrator
561	>	// set the easy ones first
562
563	<	//   new AllLong( simnfo );
563	>	for (i = 0; i < nInfo; i++){
564	>	info[i].target_temp = globals->getTargetTemp();
565	>	info[i].dt = globals->getDt();
566	>	info[i].run_time = globals->getRunTime();
567	>	}
568	>	n_components = globals->getNComponents();
569
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 );
570
571	+	// get the forceField
572
573	+	strcpy(force_field, globals->getForceField());
574
575	<	// initialize the Fortran
576	<
650	<	simnfo->refreshSim();
651	<
652	<	if( !strcmp( simnfo->mixingRule, "standard") ){
653	<	the_ff->initForceField( LB_MIXING_RULE );
575	>	if (!strcasecmp(force_field, "DUFF")){
576	>	ffCase = FF_DUFF;
577		}
578	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
579	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
578	>	else if (!strcasecmp(force_field, "LJ")){
579	>	ffCase = FF_LJ;
580		}
581	+	else if (!strcasecmp(force_field, "EAM")){
582	+	ffCase = FF_EAM;
583	+	}
584		else{
585	<	sprintf( painCave.errMsg,
586	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
587	<	simnfo->mixingRule );
588	<	painCave.isFatal = 1;
663	<	simError();
585	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
586	>	force_field);
587	>	painCave.isFatal = 1;
588	>	simError();
589		}
590
591	+	// get the ensemble
592
593	<	#ifdef IS_MPI
668	<	strcpy( checkPointMsg,
669	<	"Successfully intialized the mixingRule for Fortran." );
670	<	MPIcheckPoint();
671	<	#endif // is_mpi
672	<	}
593	>	strcpy(ensemble, globals->getEnsemble());
594
595	+	if (!strcasecmp(ensemble, "NVE")){
596	+	ensembleCase = NVE_ENS;
597	+	}
598	+	else if (!strcasecmp(ensemble, "NVT")){
599	+	ensembleCase = NVT_ENS;
600	+	}
601	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
602	+	ensembleCase = NPTi_ENS;
603	+	}
604	+	else if (!strcasecmp(ensemble, "NPTf")){
605	+	ensembleCase = NPTf_ENS;
606	+	}
607	+	else if (!strcasecmp(ensemble, "NPTim")){
608	+	ensembleCase = NPTim_ENS;
609	+	}
610	+	else if (!strcasecmp(ensemble, "NPTfm")){
611	+	ensembleCase = NPTfm_ENS;
612	+	}
613	+	else{
614	+	sprintf(painCave.errMsg,
615	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
616	+	"reverting to NVE for this simulation.\n",
617	+	ensemble);
618	+	painCave.isFatal = 0;
619	+	simError();
620	+	strcpy(ensemble, "NVE");
621	+	ensembleCase = NVE_ENS;
622	+	}
623
624	<	void SimSetup::makeMolecules( void ){
624	>	for (i = 0; i < nInfo; i++){
625	>	strcpy(info[i].ensemble, ensemble);
626
627	<	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
627	>	// get the mixing rule
628
629	<	the_ff->readParams();
629	>	strcpy(info[i].mixingRule, globals->getMixingRule());
630	>	info[i].usePBC = globals->getPBC();
631	>	}
632
633	<
692	<	// init the molecules
633	>	// get the components and calculate the tot_nMol and indvidual n_mol
634
635	<	atomOffset = 0;
636	<	excludeOffset = 0;
696	<	for(i=0; i<simnfo->n_mol; i++){
697	<
698	<	stampID = the_molecules[i].getStampID();
635	>	the_components = globals->getComponents();
636	>	components_nmol = new int[n_components];
637
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;
638
639	<	info.myAtoms = &the_atoms[atomOffset];
640	<	info.myExcludes = &the_excludes[excludeOffset];
641	<	info.myBonds = new Bond*[info.nBonds];
709	<	info.myBends = new Bend*[info.nBends];
710	<	info.myTorsions = new Torsions*[info.nTorsions];
639	>	if (!globals->haveNMol()){
640	>	// we don't have the total number of molecules, so we assume it is
641	>	// given in each component
642
643	<	theBonds = new bond_pair[info.nBonds];
644	<	theBends = new bend_set[info.nBends];
645	<	theTorsions = new torsion_set[info.nTorsions];
646	<
647	<	// make the Atoms
648	<
649	<	for(j=0; j<info.nAtoms; j++){
650	<
651	<	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 );
643	>	tot_nmol = 0;
644	>	for (i = 0; i < n_components; i++){
645	>	if (!the_components[i]->haveNMol()){
646	>	// we have a problem
647	>	sprintf(painCave.errMsg,
648	>	"SimSetup Error. No global NMol or component NMol"
649	>	" given. Cannot calculate the number of atoms.\n");
650	>	painCave.isFatal = 1;
651	>	simError();
652		}
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;
653
654	<	exI = theBonds[i].a;
655	<	exJ = theBonds[i].b;
654	>	tot_nmol += the_components[i]->getNMol();
655	>	components_nmol[i] = the_components[i]->getNMol();
656	>	}
657	>	}
658	>	else{
659	>	sprintf(painCave.errMsg,
660	>	"SimSetup error.\n"
661	>	"\tSorry, the ability to specify total"
662	>	" nMols and then give molfractions in the components\n"
663	>	"\tis not currently supported."
664	>	" Please give nMol in the components.\n");
665	>	painCave.isFatal = 1;
666	>	simError();
667	>	}
668
669	<	// exclude_I must always be the smaller of the pair
670	<	if( exI > exJ ){
671	<	tempEx = exI;
672	<	exI = exJ;
673	<	exJ = tempEx;
674	<	}
675	<	#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
669	>	// set the status, sample, and thermal kick times
670	>
671	>	for (i = 0; i < nInfo; i++){
672	>	if (globals->haveSampleTime()){
673	>	info[i].sampleTime = globals->getSampleTime();
674	>	info[i].statusTime = info[i].sampleTime;
675	>	info[i].thermalTime = info[i].sampleTime;
676		}
677	<	excludeOffset += info.nBonds;
677	>	else{
678	>	info[i].sampleTime = globals->getRunTime();
679	>	info[i].statusTime = info[i].sampleTime;
680	>	info[i].thermalTime = info[i].sampleTime;
681	>	}
682
683	<	//make the bends
684	<	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
683	>	if (globals->haveStatusTime()){
684	>	info[i].statusTime = globals->getStatusTime();
685		}
867	–	excludeOffset += info.nBends;
686
687	<	for(j=0; j<info.nTorsions; j++){
688	<
689	<	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;
687	>	if (globals->haveThermalTime()){
688	>	info[i].thermalTime = globals->getThermalTime();
689	>	}
690
691	<	// exclude_I must always be the smaller of the pair
692	<	if( exI > exJ ){
693	<	tempEx = exI;
694	<	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
691	>	info[i].resetIntegrator = 0;
692	>	if( globals->haveResetTime() ){
693	>	info[i].resetTime = globals->getResetTime();
694	>	info[i].resetIntegrator = 1;
695		}
897	–	excludeOffset += info.nTorsions;
696
697	<
697	>	// check for the temperature set flag
698
699	+	if (globals->haveTempSet())
700	+	info[i].setTemp = globals->getTempSet();
701
702	+	// get some of the tricky things that may still be in the globals
703
704	+	double boxVector[3];
705	+	if (globals->haveBox()){
706	+	boxVector[0] = globals->getBox();
707	+	boxVector[1] = globals->getBox();
708	+	boxVector[2] = globals->getBox();
709
710	+	info[i].setBox(boxVector);
711	+	}
712	+	else if (globals->haveDensity()){
713	+	double vol;
714	+	vol = (double) tot_nmol / globals->getDensity();
715	+	boxVector[0] = pow(vol, (1.0 / 3.0));
716	+	boxVector[1] = boxVector[0];
717	+	boxVector[2] = boxVector[0];
718
719	+	info[i].setBox(boxVector);
720	+	}
721	+	else{
722	+	if (!globals->haveBoxX()){
723	+	sprintf(painCave.errMsg,
724	+	"SimSetup error, no periodic BoxX size given.\n");
725	+	painCave.isFatal = 1;
726	+	simError();
727	+	}
728	+	boxVector[0] = globals->getBoxX();
729
730	<	void SimSetup::makeAtoms( void ){
730	>	if (!globals->haveBoxY()){
731	>	sprintf(painCave.errMsg,
732	>	"SimSetup error, no periodic BoxY size given.\n");
733	>	painCave.isFatal = 1;
734	>	simError();
735	>	}
736	>	boxVector[1] = globals->getBoxY();
737
738	<	int i, j, k, index;
739	<	double ux, uy, uz, uSqr, u;
740	<	AtomStamp* current_atom;
738	>	if (!globals->haveBoxZ()){
739	>	sprintf(painCave.errMsg,
740	>	"SimSetup error, no periodic BoxZ size given.\n");
741	>	painCave.isFatal = 1;
742	>	simError();
743	>	}
744	>	boxVector[2] = globals->getBoxZ();
745
746	<	DirectionalAtom* dAtom;
747	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
746	>	info[i].setBox(boxVector);
747	>	}
748	>	}
749
750	<	lMolIndex = 0;
751	<	molIndex = 0;
917	<	index = 0;
918	<	for( i=0; i<n_components; i++ ){
750	>	//setup seed for random number generator
751	>	int seedValue;
752
753	<	for( j=0; j<components_nmol[i]; j++ ){
753	>	if (globals->haveSeed()){
754	>	seedValue = globals->getSeed();
755
756	<	#ifdef IS_MPI
757	<	if( mpiSim->getMyMolStart() <= molIndex &&
758	<	molIndex <= mpiSim->getMyMolEnd() ){
759	<	#endif // is_mpi
756	>	if(seedValue / 1E9 == 0){
757	>	sprintf(painCave.errMsg,
758	>	"Seed for sprng library should contain at least 9 digits\n"
759	>	"OOPSE will generate a seed for user\n");
760	>	painCave.isFatal = 0;
761	>	simError();
762
763	<	molStart = index;
764	<	nMemb = comp_stamps[i]->getNAtoms();
765	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
766	<
767	<	current_atom = comp_stamps[i]->getAtom( k );
768	<	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
763	>	//using seed generated by system instead of invalid seed set by user
764	>	#ifndef IS_MPI
765	>	seedValue = make_sprng_seed();
766	>	#else
767	>	if (worldRank == 0){
768	>	seedValue = make_sprng_seed();
769		}
770	<	#endif //is_mpi
771	<
974	<	molIndex++;
770	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
771	>	#endif
772		}
773	+	}//end of if branch of globals->haveSeed()
774	+	else{
775	+
776	+	#ifndef IS_MPI
777	+	seedValue = make_sprng_seed();
778	+	#else
779	+	if (worldRank == 0){
780	+	seedValue = make_sprng_seed();
781	+	}
782	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
783	+	#endif
784	+	}//end of globals->haveSeed()
785	+
786	+	for (int i = 0; i < nInfo; i++){
787	+	info[i].setSeed(seedValue);
788		}
789
790		#ifdef IS_MPI
791	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
792	<
793	<	delete[] globalIndex;
982	<
983	<	mpiSim->mpiRefresh();
984	<	#endif //IS_MPI
985	<
986	<	the_ff->initializeAtoms();
791	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
792	>	MPIcheckPoint();
793	>	#endif // is_mpi
794		}
795
989	–	void SimSetup::makeBonds( void ){
796
797	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
798	<	bond_pair* the_bonds;
799	<	BondStamp* current_bond;
797	>	void SimSetup::finalInfoCheck(void){
798	>	int index;
799	>	int usesDipoles;
800	>	int i;
801
802	<	the_bonds = new bond_pair[tot_bonds];
803	<	index = 0;
997	<	offset = 0;
998	<	molIndex = 0;
802	>	for (i = 0; i < nInfo; i++){
803	>	// check electrostatic parameters
804
805	<	for( i=0; i<n_components; i++ ){
805	>	index = 0;
806	>	usesDipoles = 0;
807	>	while ((index < info[i].n_atoms) && !usesDipoles){
808	>	usesDipoles = (info[i].atoms[index])->hasDipole();
809	>	index++;
810	>	}
811
1002	–	for( j=0; j<components_nmol[i]; j++ ){
1003	–
812		#ifdef IS_MPI
813	<	if( mpiSim->getMyMolStart() <= molIndex &&
814	<	molIndex <= mpiSim->getMyMolEnd() ){
815	<	#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;
813	>	int myUse = usesDipoles;
814	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
815	>	#endif //is_mpi
816
817	<	exI = the_bonds[index].a;
1016	<	exJ = the_bonds[index].b;
817	>	double theEcr, theEst;
818
819	<	// exclude_I must always be the smaller of the pair
820	<	if( exI > exJ ){
1020	<	tempEx = exI;
1021	<	exI = exJ;
1022	<	exJ = tempEx;
1023	<	}
819	>	if (globals->getUseRF()){
820	>	info[i].useReactionField = 1;
821
822	<
823	<	#ifdef IS_MPI
822	>	if (!globals->haveECR()){
823	>	sprintf(painCave.errMsg,
824	>	"SimSetup Warning: using default value of 1/2 the smallest "
825	>	"box length for the electrostaticCutoffRadius.\n"
826	>	"I hope you have a very fast processor!\n");
827	>	painCave.isFatal = 0;
828	>	simError();
829	>	double smallest;
830	>	smallest = info[i].boxL[0];
831	>	if (info[i].boxL[1] <= smallest)
832	>	smallest = info[i].boxL[1];
833	>	if (info[i].boxL[2] <= smallest)
834	>	smallest = info[i].boxL[2];
835	>	theEcr = 0.5 * smallest;
836	>	}
837	>	else{
838	>	theEcr = globals->getECR();
839	>	}
840
841	<	the_excludes[index*2] =
842	<	the_atoms[exI]->getGlobalIndex() + 1;
843	<	the_excludes[index*2 + 1] =
844	<	the_atoms[exJ]->getGlobalIndex() + 1;
845	<
846	<	#else  // isn't MPI
847	<
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
841	>	if (!globals->haveEST()){
842	>	sprintf(painCave.errMsg,
843	>	"SimSetup Warning: using default value of 0.05 * the "
844	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
845	>	painCave.isFatal = 0;
846	>	simError();
847	>	theEst = 0.05 * theEcr;
848		}
849	<	#endif //is_mpi
850	<
851	<	molIndex++;
1050	<	}
1051	<	}
849	>	else{
850	>	theEst = globals->getEST();
851	>	}
852
853	<	the_ff->initializeBonds( the_bonds );
1054	<	}
853	>	info[i].setEcr(theEcr, theEst);
854
855	<	void SimSetup::makeBends( void ){
855	>	if (!globals->haveDielectric()){
856	>	sprintf(painCave.errMsg,
857	>	"SimSetup Error: You are trying to use Reaction Field without"
858	>	"setting a dielectric constant!\n");
859	>	painCave.isFatal = 1;
860	>	simError();
861	>	}
862	>	info[i].dielectric = globals->getDielectric();
863	>	}
864	>	else{
865	>	if (usesDipoles){
866	>	if (!globals->haveECR()){
867	>	sprintf(painCave.errMsg,
868	>	"SimSetup Warning: using default value of 1/2 the smallest "
869	>	"box length for the electrostaticCutoffRadius.\n"
870	>	"I hope you have a very fast processor!\n");
871	>	painCave.isFatal = 0;
872	>	simError();
873	>	double smallest;
874	>	smallest = info[i].boxL[0];
875	>	if (info[i].boxL[1] <= smallest)
876	>	smallest = info[i].boxL[1];
877	>	if (info[i].boxL[2] <= smallest)
878	>	smallest = info[i].boxL[2];
879	>	theEcr = 0.5 * smallest;
880	>	}
881	>	else{
882	>	theEcr = globals->getECR();
883	>	}
884
885	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
886	<	bend_set* the_bends;
887	<	BendStamp* current_bend;
888	<	LinkedAssign* extras;
889	<	LinkedAssign* current_extra;
890	<
885	>	if (!globals->haveEST()){
886	>	sprintf(painCave.errMsg,
887	>	"SimSetup Warning: using default value of 0.05 * the "
888	>	"electrostaticCutoffRadius for the "
889	>	"electrostaticSkinThickness\n");
890	>	painCave.isFatal = 0;
891	>	simError();
892	>	theEst = 0.05 * theEcr;
893	>	}
894	>	else{
895	>	theEst = globals->getEST();
896	>	}
897
898	<	the_bends = new bend_set[tot_bends];
1066	<	index = 0;
1067	<	offset = 0;
1068	<	molIndex = 0;
1069	<	for( i=0; i<n_components; i++ ){
1070	<
1071	<	for( j=0; j<components_nmol[i]; j++ ){
1072	<
1073	<	#ifdef IS_MPI
1074	<	if( mpiSim->getMyMolStart() <= molIndex &&
1075	<	molIndex <= mpiSim->getMyMolEnd() ){
1076	<	#endif // is_mpi
1077	<
1078	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
1079	<
1080	<	current_bend = comp_stamps[i]->getBend( k );
1081	<	the_bends[index].a = current_bend->getA() + offset;
1082	<	the_bends[index].b = current_bend->getB() + offset;
1083	<	the_bends[index].c = current_bend->getC() + offset;
1084	<
1085	<	if( current_bend->haveExtras() ){
1086	<
1087	<	extras = current_bend->getExtras();
1088	<	current_extra = extras;
1089	<
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	<	}
1150	<
1151	<
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
898	>	info[i].setEcr(theEcr, theEst);
899		}
1174	–	#endif //is_mpi
1175	–
1176	–	molIndex++;
900		}
901		}
902
903		#ifdef IS_MPI
904	<	sprintf( checkPointMsg,
1182	<	"Successfully created the bends list.\n" );
904	>	strcpy(checkPointMsg, "post processing checks out");
905		MPIcheckPoint();
906		#endif // is_mpi
1185	–
1186	–
1187	–	the_ff->initializeBends( the_bends );
907		}
908
909	<	void SimSetup::makeTorsions( void ){
909	>	void SimSetup::initSystemCoords(void){
910	>	int i;
911
912	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1193	<	torsion_set* the_torsions;
1194	<	TorsionStamp* current_torsion;
912	>	char* inName;
913
914	<	the_torsions = new torsion_set[tot_torsions];
1197	<	index = 0;
1198	<	offset = 0;
1199	<	molIndex = 0;
1200	<	for( i=0; i<n_components; i++ ){
914	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
915
916	<	for( j=0; j<components_nmol[i]; j++ ){
916	>	for (i = 0; i < info[0].n_atoms; i++)
917	>	info[0].atoms[i]->setCoords();
918
919	+	if (globals->haveInitialConfig()){
920	+	InitializeFromFile* fileInit;
921	+	#ifdef IS_MPI // is_mpi
922	+	if (worldRank == 0){
923	+	#endif //is_mpi
924	+	inName = globals->getInitialConfig();
925	+	double* tempDouble = new double[1000000];
926	+	fileInit = new InitializeFromFile(inName);
927		#ifdef IS_MPI
928	<	if( mpiSim->getMyMolStart() <= molIndex &&
929	<	molIndex <= mpiSim->getMyMolEnd() ){
930	<	#endif // is_mpi
928	>	}
929	>	else
930	>	fileInit = new InitializeFromFile(NULL);
931	>	#endif
932	>	fileInit->readInit(info); // default velocities on
933
934	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
934	>	delete fileInit;
935	>	}
936	>	else{
937	>	#ifdef IS_MPI
938
939	<	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;
939	>	// no init from bass
940
941	<	exI = the_torsions[index].a;
942	<	exJ = the_torsions[index].d;
941	>	sprintf(painCave.errMsg,
942	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
943	>	painCave.isFatal;
944	>	simError();
945
946	<
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	<	}
946	>	#else
947
948	+	initFromBass();
949
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	–
950
951	<	// increment the index and repeat;
952	<	index++;
1246	<	}
1247	<	offset += comp_stamps[i]->getNAtoms();
951	>	#endif
952	>	}
953
954		#ifdef IS_MPI
955	<	}
956	<	#endif //is_mpi
955	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
956	>	MPIcheckPoint();
957	>	#endif // is_mpi
958	>	}
959
1253	–	molIndex++;
1254	–	}
1255	–	}
960
961	<	the_ff->initializeTorsions( the_torsions );
962	<	}
961	>	void SimSetup::makeOutNames(void){
962	>	int k;
963
1260	–	void SimSetup::initFromBass( void ){
964
965	<	int i, j, k;
966	<	int n_cells;
967	<	double cellx, celly, cellz;
968	<	double temp1, temp2, temp3;
1266	<	int n_per_extra;
1267	<	int n_extra;
1268	<	int have_extra, done;
965	>	for (k = 0; k < nInfo; k++){
966	>	#ifdef IS_MPI
967	>	if (worldRank == 0){
968	>	#endif // is_mpi
969
970	<	temp1 = (double)tot_nmol / 4.0;
971	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
972	<	temp3 = ceil( temp2 );
970	>	if (globals->haveFinalConfig()){
971	>	strcpy(info[k].finalName, globals->getFinalConfig());
972	>	}
973	>	else{
974	>	strcpy(info[k].finalName, inFileName);
975	>	char* endTest;
976	>	int nameLength = strlen(info[k].finalName);
977	>	endTest = &(info[k].finalName[nameLength - 5]);
978	>	if (!strcmp(endTest, ".bass")){
979	>	strcpy(endTest, ".eor");
980	>	}
981	>	else if (!strcmp(endTest, ".BASS")){
982	>	strcpy(endTest, ".eor");
983	>	}
984	>	else{
985	>	endTest = &(info[k].finalName[nameLength - 4]);
986	>	if (!strcmp(endTest, ".bss")){
987	>	strcpy(endTest, ".eor");
988	>	}
989	>	else if (!strcmp(endTest, ".mdl")){
990	>	strcpy(endTest, ".eor");
991	>	}
992	>	else{
993	>	strcat(info[k].finalName, ".eor");
994	>	}
995	>	}
996	>	}
997
998	<	have_extra =0;
1275	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1276	<	have_extra =1;
998	>	// make the sample and status out names
999
1000	<	n_cells = (int)temp3 - 1;
1001	<	cellx = simnfo->box_x / temp3;
1002	<	celly = simnfo->box_y / temp3;
1003	<	cellz = simnfo->box_z / temp3;
1004	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1005	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1006	<	n_per_extra = (int)ceil( temp1 );
1000	>	strcpy(info[k].sampleName, inFileName);
1001	>	char* endTest;
1002	>	int nameLength = strlen(info[k].sampleName);
1003	>	endTest = &(info[k].sampleName[nameLength - 5]);
1004	>	if (!strcmp(endTest, ".bass")){
1005	>	strcpy(endTest, ".dump");
1006	>	}
1007	>	else if (!strcmp(endTest, ".BASS")){
1008	>	strcpy(endTest, ".dump");
1009	>	}
1010	>	else{
1011	>	endTest = &(info[k].sampleName[nameLength - 4]);
1012	>	if (!strcmp(endTest, ".bss")){
1013	>	strcpy(endTest, ".dump");
1014	>	}
1015	>	else if (!strcmp(endTest, ".mdl")){
1016	>	strcpy(endTest, ".dump");
1017	>	}
1018	>	else{
1019	>	strcat(info[k].sampleName, ".dump");
1020	>	}
1021	>	}
1022
1023	<	if( n_per_extra > 4){
1024	<	sprintf( painCave.errMsg,
1025	<	"SimSetup error. There has been an error in constructing"
1026	<	" the non-complete lattice.\n" );
1027	<	painCave.isFatal = 1;
1028	<	simError();
1023	>	strcpy(info[k].statusName, inFileName);
1024	>	nameLength = strlen(info[k].statusName);
1025	>	endTest = &(info[k].statusName[nameLength - 5]);
1026	>	if (!strcmp(endTest, ".bass")){
1027	>	strcpy(endTest, ".stat");
1028	>	}
1029	>	else if (!strcmp(endTest, ".BASS")){
1030	>	strcpy(endTest, ".stat");
1031	>	}
1032	>	else{
1033	>	endTest = &(info[k].statusName[nameLength - 4]);
1034	>	if (!strcmp(endTest, ".bss")){
1035	>	strcpy(endTest, ".stat");
1036	>	}
1037	>	else if (!strcmp(endTest, ".mdl")){
1038	>	strcpy(endTest, ".stat");
1039	>	}
1040	>	else{
1041	>	strcat(info[k].statusName, ".stat");
1042	>	}
1043	>	}
1044	>
1045	>	#ifdef IS_MPI
1046	>
1047		}
1048	+	#endif // is_mpi
1049		}
1050	<	else{
1051	<	n_cells = (int)temp3;
1052	<	cellx = simnfo->box_x / temp3;
1053	<	celly = simnfo->box_y / temp3;
1054	<	cellz = simnfo->box_z / temp3;
1050	>	}
1051	>
1052	>
1053	>	void SimSetup::sysObjectsCreation(void){
1054	>	int i, k;
1055	>
1056	>	// create the forceField
1057	>
1058	>	createFF();
1059	>
1060	>	// extract componentList
1061	>
1062	>	compList();
1063	>
1064	>	// calc the number of atoms, bond, bends, and torsions
1065	>
1066	>	calcSysValues();
1067	>
1068	>	#ifdef IS_MPI
1069	>	// divide the molecules among the processors
1070	>
1071	>	mpiMolDivide();
1072	>	#endif //is_mpi
1073	>
1074	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1075	>
1076	>	makeSysArrays();
1077	>
1078	>	// make and initialize the molecules (all but atomic coordinates)
1079	>
1080	>	makeMolecules();
1081	>
1082	>	for (k = 0; k < nInfo; k++){
1083	>	info[k].identArray = new int[info[k].n_atoms];
1084	>	for (i = 0; i < info[k].n_atoms; i++){
1085	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1086	>	}
1087		}
1088	+	}
1089
1301	–	current_mol = 0;
1302	–	current_comp_mol = 0;
1303	–	current_comp = 0;
1304	–	current_atom_ndx = 0;
1090
1091	<	for( i=0; i < n_cells ; i++ ){
1092	<	for( j=0; j < n_cells; j++ ){
1093	<	for( k=0; k < n_cells; k++ ){
1091	>	void SimSetup::createFF(void){
1092	>	switch (ffCase){
1093	>	case FF_DUFF:
1094	>	the_ff = new DUFF();
1095	>	break;
1096
1097	<	makeElement( i * cellx,
1098	<	j * celly,
1099	<	k * cellz );
1097	>	case FF_LJ:
1098	>	the_ff = new LJFF();
1099	>	break;
1100
1101	<	makeElement( i * cellx + 0.5 * cellx,
1102	<	j * celly + 0.5 * celly,
1103	<	k * cellz );
1101	>	case FF_EAM:
1102	>	the_ff = new EAM_FF();
1103	>	break;
1104
1105	<	makeElement( i * cellx,
1106	<	j * celly + 0.5 * celly,
1107	<	k * cellz + 0.5 * cellz );
1105	>	default:
1106	>	sprintf(painCave.errMsg,
1107	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1108	>	painCave.isFatal = 1;
1109	>	simError();
1110	>	}
1111
1112	<	makeElement( i * cellx + 0.5 * cellx,
1113	<	j * celly,
1114	<	k * cellz + 0.5 * cellz );
1112	>	#ifdef IS_MPI
1113	>	strcpy(checkPointMsg, "ForceField creation successful");
1114	>	MPIcheckPoint();
1115	>	#endif // is_mpi
1116	>	}
1117	>
1118	>
1119	>	void SimSetup::compList(void){
1120	>	int i;
1121	>	char* id;
1122	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1123	>	LinkedMolStamp* currentStamp = NULL;
1124	>	comp_stamps = new MoleculeStamp * [n_components];
1125	>
1126	>	// make an array of molecule stamps that match the components used.
1127	>	// also extract the used stamps out into a separate linked list
1128	>
1129	>	for (i = 0; i < nInfo; i++){
1130	>	info[i].nComponents = n_components;
1131	>	info[i].componentsNmol = components_nmol;
1132	>	info[i].compStamps = comp_stamps;
1133	>	info[i].headStamp = headStamp;
1134	>	}
1135	>
1136	>
1137	>	for (i = 0; i < n_components; i++){
1138	>	id = the_components[i]->getType();
1139	>	comp_stamps[i] = NULL;
1140	>
1141	>	// check to make sure the component isn't already in the list
1142	>
1143	>	comp_stamps[i] = headStamp->match(id);
1144	>	if (comp_stamps[i] == NULL){
1145	>	// extract the component from the list;
1146	>
1147	>	currentStamp = stamps->extractMolStamp(id);
1148	>	if (currentStamp == NULL){
1149	>	sprintf(painCave.errMsg,
1150	>	"SimSetup error: Component \"%s\" was not found in the "
1151	>	"list of declared molecules\n",
1152	>	id);
1153	>	painCave.isFatal = 1;
1154	>	simError();
1155		}
1156	+
1157	+	headStamp->add(currentStamp);
1158	+	comp_stamps[i] = headStamp->match(id);
1159		}
1160		}
1161
1162	<	if( have_extra ){
1163	<	done = 0;
1162	>	#ifdef IS_MPI
1163	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1164	>	MPIcheckPoint();
1165	>	#endif // is_mpi
1166	>	}
1167
1168	<	int start_ndx;
1169	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1334	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1168	>	void SimSetup::calcSysValues(void){
1169	>	int i, j, k;
1170
1171	<	if( i < n_cells ){
1171	>	int* molMembershipArray;
1172
1173	<	if( j < n_cells ){
1174	<	start_ndx = n_cells;
1175	<	}
1176	<	else start_ndx = 0;
1177	<	}
1178	<	else start_ndx = 0;
1173	>	tot_atoms = 0;
1174	>	tot_bonds = 0;
1175	>	tot_bends = 0;
1176	>	tot_torsions = 0;
1177	>	for (i = 0; i < n_components; i++){
1178	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1179	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1180	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1181	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1182	>	}
1183
1184	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1184	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1185	>	molMembershipArray = new int[tot_atoms];
1186
1187	<	makeElement( i * cellx,
1188	<	j * celly,
1189	<	k * cellz );
1190	<	done = ( current_mol >= tot_nmol );
1187	>	for (i = 0; i < nInfo; i++){
1188	>	info[i].n_atoms = tot_atoms;
1189	>	info[i].n_bonds = tot_bonds;
1190	>	info[i].n_bends = tot_bends;
1191	>	info[i].n_torsions = tot_torsions;
1192	>	info[i].n_SRI = tot_SRI;
1193	>	info[i].n_mol = tot_nmol;
1194
1195	<	if( !done && n_per_extra > 1 ){
1196	<	makeElement( i * cellx + 0.5 * cellx,
1197	<	j * celly + 0.5 * celly,
1355	<	k * cellz );
1356	<	done = ( current_mol >= tot_nmol );
1357	<	}
1195	>	info[i].molMembershipArray = molMembershipArray;
1196	>	}
1197	>	}
1198
1199	<	if( !done && n_per_extra > 2){
1360	<	makeElement( i * cellx,
1361	<	j * celly + 0.5 * celly,
1362	<	k * cellz + 0.5 * cellz );
1363	<	done = ( current_mol >= tot_nmol );
1364	<	}
1199	>	#ifdef IS_MPI
1200
1201	<	if( !done && n_per_extra > 3){
1202	<	makeElement( i * cellx + 0.5 * cellx,
1203	<	j * celly,
1204	<	k * cellz + 0.5 * cellz );
1205	<	done = ( current_mol >= tot_nmol );
1206	<	}
1207	<	}
1201	>	void SimSetup::mpiMolDivide(void){
1202	>	int i, j, k;
1203	>	int localMol, allMol;
1204	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1205	>
1206	>	mpiSim = new mpiSimulation(info);
1207	>
1208	>	globalIndex = mpiSim->divideLabor();
1209	>
1210	>	// set up the local variables
1211	>
1212	>	mol2proc = mpiSim->getMolToProcMap();
1213	>	molCompType = mpiSim->getMolComponentType();
1214	>
1215	>	allMol = 0;
1216	>	localMol = 0;
1217	>	local_atoms = 0;
1218	>	local_bonds = 0;
1219	>	local_bends = 0;
1220	>	local_torsions = 0;
1221	>	globalAtomIndex = 0;
1222	>
1223	>
1224	>	for (i = 0; i < n_components; i++){
1225	>	for (j = 0; j < components_nmol[i]; j++){
1226	>	if (mol2proc[allMol] == worldRank){
1227	>	local_atoms += comp_stamps[i]->getNAtoms();
1228	>	local_bonds += comp_stamps[i]->getNBonds();
1229	>	local_bends += comp_stamps[i]->getNBends();
1230	>	local_torsions += comp_stamps[i]->getNTorsions();
1231	>	localMol++;
1232	>	}
1233	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1234	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1235	>	globalAtomIndex++;
1236		}
1237	+
1238	+	allMol++;
1239		}
1240		}
1241	+	local_SRI = local_bonds + local_bends + local_torsions;
1242
1243	+	info[0].n_atoms = mpiSim->getMyNlocal();
1244
1245	<	for( i=0; i<simnfo->n_atoms; i++ ){
1246	<	simnfo->atoms[i]->set_vx( 0.0 );
1247	<	simnfo->atoms[i]->set_vy( 0.0 );
1248	<	simnfo->atoms[i]->set_vz( 0.0 );
1245	>	if (local_atoms != info[0].n_atoms){
1246	>	sprintf(painCave.errMsg,
1247	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1248	>	" localAtom (%d) are not equal.\n",
1249	>	info[0].n_atoms, local_atoms);
1250	>	painCave.isFatal = 1;
1251	>	simError();
1252		}
1253	+
1254	+	info[0].n_bonds = local_bonds;
1255	+	info[0].n_bends = local_bends;
1256	+	info[0].n_torsions = local_torsions;
1257	+	info[0].n_SRI = local_SRI;
1258	+	info[0].n_mol = localMol;
1259	+
1260	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1261	+	MPIcheckPoint();
1262		}
1263
1264	<	void SimSetup::makeElement( double x, double y, double z ){
1264	>	#endif // is_mpi
1265
1387	–	int k;
1388	–	AtomStamp* current_atom;
1389	–	DirectionalAtom* dAtom;
1390	–	double rotMat[3][3];
1266
1267	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1267	>	void SimSetup::makeSysArrays(void){
1268	>	int i, j, k, l;
1269
1270	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1271	<	if( !current_atom->havePosition() ){
1272	<	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	<	}
1270	>	Atom** the_atoms;
1271	>	Molecule* the_molecules;
1272	>	Exclude** the_excludes;
1273
1407	–	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1408	–	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1409	–	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1274
1275	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1275	>	for (l = 0; l < nInfo; l++){
1276	>	// create the atom and short range interaction arrays
1277
1278	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1278	>	the_atoms = new Atom * [info[l].n_atoms];
1279	>	the_molecules = new Molecule[info[l].n_mol];
1280	>	int molIndex;
1281
1282	<	rotMat[0][0] = 1.0;
1416	<	rotMat[0][1] = 0.0;
1417	<	rotMat[0][2] = 0.0;
1282	>	// initialize the molecule's stampID's
1283
1284	<	rotMat[1][0] = 0.0;
1420	<	rotMat[1][1] = 1.0;
1421	<	rotMat[1][2] = 0.0;
1284	>	#ifdef IS_MPI
1285
1423	–	rotMat[2][0] = 0.0;
1424	–	rotMat[2][1] = 0.0;
1425	–	rotMat[2][2] = 1.0;
1286
1287	<	dAtom->setA( rotMat );
1287	>	molIndex = 0;
1288	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1289	>	if (mol2proc[i] == worldRank){
1290	>	the_molecules[molIndex].setStampID(molCompType[i]);
1291	>	the_molecules[molIndex].setMyIndex(molIndex);
1292	>	the_molecules[molIndex].setGlobalIndex(i);
1293	>	molIndex++;
1294	>	}
1295		}
1296
1297	<	current_atom_ndx++;
1431	<	}
1297	>	#else // is_mpi
1298
1299	<	current_mol++;
1300	<	current_comp_mol++;
1299	>	molIndex = 0;
1300	>	globalAtomIndex = 0;
1301	>	for (i = 0; i < n_components; i++){
1302	>	for (j = 0; j < components_nmol[i]; j++){
1303	>	the_molecules[molIndex].setStampID(i);
1304	>	the_molecules[molIndex].setMyIndex(molIndex);
1305	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1306	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1307	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1308	>	globalAtomIndex++;
1309	>	}
1310	>	molIndex++;
1311	>	}
1312	>	}
1313
1436	–	if( current_comp_mol >= components_nmol[current_comp] ){
1314
1315	<	current_comp_mol = 0;
1316	<	current_comp++;
1315	>	#endif // is_mpi
1316	>
1317	>
1318	>	if (info[l].n_SRI){
1319	>	Exclude::createArray(info[l].n_SRI);
1320	>	the_excludes = new Exclude * [info[l].n_SRI];
1321	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1322	>	the_excludes[ex] = new Exclude(ex);
1323	>	}
1324	>	info[l].globalExcludes = new int;
1325	>	info[l].n_exclude = info[l].n_SRI;
1326	>	}
1327	>	else{
1328	>	Exclude::createArray(1);
1329	>	the_excludes = new Exclude * ;
1330	>	the_excludes[0] = new Exclude(0);
1331	>	the_excludes[0]->setPair(0, 0);
1332	>	info[l].globalExcludes = new int;
1333	>	info[l].globalExcludes[0] = 0;
1334	>	info[l].n_exclude = 0;
1335	>	}
1336	>
1337	>	// set the arrays into the SimInfo object
1338	>
1339	>	info[l].atoms = the_atoms;
1340	>	info[l].molecules = the_molecules;
1341	>	info[l].nGlobalExcludes = 0;
1342	>	info[l].excludes = the_excludes;
1343	>
1344	>	the_ff->setSimInfo(info);
1345		}
1346		}
1347	+
1348	+	void SimSetup::makeIntegrator(void){
1349	+	int k;
1350	+
1351	+	NVT<RealIntegrator>* myNVT = NULL;
1352	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1353	+	NPTf<RealIntegrator>* myNPTf = NULL;
1354	+	NPTim<RealIntegrator>* myNPTim = NULL;
1355	+	NPTfm<RealIntegrator>* myNPTfm = NULL;
1356	+
1357	+	for (k = 0; k < nInfo; k++){
1358	+	switch (ensembleCase){
1359	+	case NVE_ENS:
1360	+	if (globals->haveZconstraints()){
1361	+	setupZConstraint(info[k]);
1362	+	new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1363	+	}
1364	+	else
1365	+	new NVE<RealIntegrator>(&(info[k]), the_ff);
1366	+	break;
1367	+
1368	+	case NVT_ENS:
1369	+	if (globals->haveZconstraints()){
1370	+	setupZConstraint(info[k]);
1371	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1372	+	}
1373	+	else
1374	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1375	+
1376	+	myNVT->setTargetTemp(globals->getTargetTemp());
1377	+
1378	+	if (globals->haveTauThermostat())
1379	+	myNVT->setTauThermostat(globals->getTauThermostat());
1380	+	else{
1381	+	sprintf(painCave.errMsg,
1382	+	"SimSetup error: If you use the NVT\n"
1383	+	"    ensemble, you must set tauThermostat.\n");
1384	+	painCave.isFatal = 1;
1385	+	simError();
1386	+	}
1387	+	break;
1388	+
1389	+	case NPTi_ENS:
1390	+	if (globals->haveZconstraints()){
1391	+	setupZConstraint(info[k]);
1392	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1393	+	}
1394	+	else
1395	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1396	+
1397	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1398	+
1399	+	if (globals->haveTargetPressure())
1400	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1401	+	else{
1402	+	sprintf(painCave.errMsg,
1403	+	"SimSetup error: If you use a constant pressure\n"
1404	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1405	+	painCave.isFatal = 1;
1406	+	simError();
1407	+	}
1408	+
1409	+	if (globals->haveTauThermostat())
1410	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1411	+	else{
1412	+	sprintf(painCave.errMsg,
1413	+	"SimSetup error: If you use an NPT\n"
1414	+	"    ensemble, you must set tauThermostat.\n");
1415	+	painCave.isFatal = 1;
1416	+	simError();
1417	+	}
1418	+
1419	+	if (globals->haveTauBarostat())
1420	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1421	+	else{
1422	+	sprintf(painCave.errMsg,
1423	+	"SimSetup error: If you use an NPT\n"
1424	+	"    ensemble, you must set tauBarostat.\n");
1425	+	painCave.isFatal = 1;
1426	+	simError();
1427	+	}
1428	+	break;
1429	+
1430	+	case NPTf_ENS:
1431	+	if (globals->haveZconstraints()){
1432	+	setupZConstraint(info[k]);
1433	+	myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff);
1434	+	}
1435	+	else
1436	+	myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff);
1437	+
1438	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1439	+
1440	+	if (globals->haveTargetPressure())
1441	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1442	+	else{
1443	+	sprintf(painCave.errMsg,
1444	+	"SimSetup error: If you use a constant pressure\n"
1445	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1446	+	painCave.isFatal = 1;
1447	+	simError();
1448	+	}
1449	+
1450	+	if (globals->haveTauThermostat())
1451	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1452	+	else{
1453	+	sprintf(painCave.errMsg,
1454	+	"SimSetup error: If you use an NPT\n"
1455	+	"    ensemble, you must set tauThermostat.\n");
1456	+	painCave.isFatal = 1;
1457	+	simError();
1458	+	}
1459	+
1460	+	if (globals->haveTauBarostat())
1461	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1462	+	else{
1463	+	sprintf(painCave.errMsg,
1464	+	"SimSetup error: If you use an NPT\n"
1465	+	"    ensemble, you must set tauBarostat.\n");
1466	+	painCave.isFatal = 1;
1467	+	simError();
1468	+	}
1469	+	break;
1470	+
1471	+	case NPTim_ENS:
1472	+	if (globals->haveZconstraints()){
1473	+	setupZConstraint(info[k]);
1474	+	myNPTim = new ZConstraint<NPTim<RealIntegrator> >(&(info[k]), the_ff);
1475	+	}
1476	+	else
1477	+	myNPTim = new NPTim<RealIntegrator>(&(info[k]), the_ff);
1478	+
1479	+	myNPTim->setTargetTemp(globals->getTargetTemp());
1480	+
1481	+	if (globals->haveTargetPressure())
1482	+	myNPTim->setTargetPressure(globals->getTargetPressure());
1483	+	else{
1484	+	sprintf(painCave.errMsg,
1485	+	"SimSetup error: If you use a constant pressure\n"
1486	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1487	+	painCave.isFatal = 1;
1488	+	simError();
1489	+	}
1490	+
1491	+	if (globals->haveTauThermostat())
1492	+	myNPTim->setTauThermostat(globals->getTauThermostat());
1493	+	else{
1494	+	sprintf(painCave.errMsg,
1495	+	"SimSetup error: If you use an NPT\n"
1496	+	"    ensemble, you must set tauThermostat.\n");
1497	+	painCave.isFatal = 1;
1498	+	simError();
1499	+	}
1500	+
1501	+	if (globals->haveTauBarostat())
1502	+	myNPTim->setTauBarostat(globals->getTauBarostat());
1503	+	else{
1504	+	sprintf(painCave.errMsg,
1505	+	"SimSetup error: If you use an NPT\n"
1506	+	"    ensemble, you must set tauBarostat.\n");
1507	+	painCave.isFatal = 1;
1508	+	simError();
1509	+	}
1510	+	break;
1511	+
1512	+	case NPTfm_ENS:
1513	+	if (globals->haveZconstraints()){
1514	+	setupZConstraint(info[k]);
1515	+	myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff);
1516	+	}
1517	+	else
1518	+	myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff);
1519	+
1520	+	myNPTfm->setTargetTemp(globals->getTargetTemp());
1521	+
1522	+	if (globals->haveTargetPressure())
1523	+	myNPTfm->setTargetPressure(globals->getTargetPressure());
1524	+	else{
1525	+	sprintf(painCave.errMsg,
1526	+	"SimSetup error: If you use a constant pressure\n"
1527	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1528	+	painCave.isFatal = 1;
1529	+	simError();
1530	+	}
1531	+
1532	+	if (globals->haveTauThermostat())
1533	+	myNPTfm->setTauThermostat(globals->getTauThermostat());
1534	+	else{
1535	+	sprintf(painCave.errMsg,
1536	+	"SimSetup error: If you use an NPT\n"
1537	+	"    ensemble, you must set tauThermostat.\n");
1538	+	painCave.isFatal = 1;
1539	+	simError();
1540	+	}
1541	+
1542	+	if (globals->haveTauBarostat())
1543	+	myNPTfm->setTauBarostat(globals->getTauBarostat());
1544	+	else{
1545	+	sprintf(painCave.errMsg,
1546	+	"SimSetup error: If you use an NPT\n"
1547	+	"    ensemble, you must set tauBarostat.\n");
1548	+	painCave.isFatal = 1;
1549	+	simError();
1550	+	}
1551	+	break;
1552	+
1553	+	default:
1554	+	sprintf(painCave.errMsg,
1555	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1556	+	painCave.isFatal = 1;
1557	+	simError();
1558	+	}
1559	+	}
1560	+	}
1561	+
1562	+	void SimSetup::initFortran(void){
1563	+	info[0].refreshSim();
1564	+
1565	+	if (!strcmp(info[0].mixingRule, "standard")){
1566	+	the_ff->initForceField(LB_MIXING_RULE);
1567	+	}
1568	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1569	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1570	+	}
1571	+	else{
1572	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1573	+	info[0].mixingRule);
1574	+	painCave.isFatal = 1;
1575	+	simError();
1576	+	}
1577	+
1578	+
1579	+	#ifdef IS_MPI
1580	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1581	+	MPIcheckPoint();
1582	+	#endif // is_mpi
1583	+	}
1584	+
1585	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1586	+	int nZConstraints;
1587	+	ZconStamp** zconStamp;
1588	+
1589	+	if (globals->haveZconstraintTime()){
1590	+	//add sample time of z-constraint  into SimInfo's property list
1591	+	DoubleData* zconsTimeProp = new DoubleData();
1592	+	zconsTimeProp->setID(ZCONSTIME_ID);
1593	+	zconsTimeProp->setData(globals->getZconsTime());
1594	+	theInfo.addProperty(zconsTimeProp);
1595	+	}
1596	+	else{
1597	+	sprintf(painCave.errMsg,
1598	+	"ZConstraint error: If you use an ZConstraint\n"
1599	+	" , you must set sample time.\n");
1600	+	painCave.isFatal = 1;
1601	+	simError();
1602	+	}
1603	+
1604	+	//push zconsTol into siminfo, if user does not specify
1605	+	//value for zconsTol, a default value will be used
1606	+	DoubleData* zconsTol = new DoubleData();
1607	+	zconsTol->setID(ZCONSTOL_ID);
1608	+	if (globals->haveZconsTol()){
1609	+	zconsTol->setData(globals->getZconsTol());
1610	+	}
1611	+	else{
1612	+	double defaultZConsTol = 0.01;
1613	+	sprintf(painCave.errMsg,
1614	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1615	+	" , default value %f is used.\n",
1616	+	defaultZConsTol);
1617	+	painCave.isFatal = 0;
1618	+	simError();
1619	+
1620	+	zconsTol->setData(defaultZConsTol);
1621	+	}
1622	+	theInfo.addProperty(zconsTol);
1623	+
1624	+	//set Force Subtraction Policy
1625	+	StringData* zconsForcePolicy = new StringData();
1626	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1627	+
1628	+	if (globals->haveZconsForcePolicy()){
1629	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1630	+	}
1631	+	else{
1632	+	sprintf(painCave.errMsg,
1633	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1634	+	"PolicyByMass is used\n");
1635	+	painCave.isFatal = 0;
1636	+	simError();
1637	+	zconsForcePolicy->setData("BYMASS");
1638	+	}
1639	+
1640	+	theInfo.addProperty(zconsForcePolicy);
1641	+
1642	+	//Determine the name of ouput file and add it into SimInfo's property list
1643	+	//Be careful, do not use inFileName, since it is a pointer which
1644	+	//point to a string at master node, and slave nodes do not contain that string
1645	+
1646	+	string zconsOutput(theInfo.finalName);
1647	+
1648	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1649	+
1650	+	StringData* zconsFilename = new StringData();
1651	+	zconsFilename->setID(ZCONSFILENAME_ID);
1652	+	zconsFilename->setData(zconsOutput);
1653	+
1654	+	theInfo.addProperty(zconsFilename);
1655	+
1656	+	//setup index, pos and other parameters of z-constraint molecules
1657	+	nZConstraints = globals->getNzConstraints();
1658	+	theInfo.nZconstraints = nZConstraints;
1659	+
1660	+	zconStamp = globals->getZconStamp();
1661	+	ZConsParaItem tempParaItem;
1662	+
1663	+	ZConsParaData* zconsParaData = new ZConsParaData();
1664	+	zconsParaData->setID(ZCONSPARADATA_ID);
1665	+
1666	+	for (int i = 0; i < nZConstraints; i++){
1667	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1668	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1669	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1670	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1671	+
1672	+	zconsParaData->addItem(tempParaItem);
1673	+	}
1674	+
1675	+	//check the uniqueness of index
1676	+	if(!zconsParaData->isIndexUnique()){
1677	+	sprintf(painCave.errMsg,
1678	+	"ZConstraint Error: molIndex is not unique\n");
1679	+	painCave.isFatal = 1;
1680	+	simError();
1681	+	}
1682	+
1683	+	//sort the parameters by index of molecules
1684	+	zconsParaData->sortByIndex();
1685	+
1686	+	//push data into siminfo, therefore, we can retrieve later
1687	+	theInfo.addProperty(zconsParaData);
1688	+	}

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