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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 604 by gezelter, Tue Jul 15 03:08:00 2003 UTC vs.
Revision 983 by gezelter, Mon Jan 26 21:45:03 2004 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	Line 14 | Line 17
17
18		// some defines for ensemble and Forcefield  cases
19
20	<	#define NVE_ENS   0
21	<	#define NVT_ENS   1
22	<	#define NPTi_ENS  2
23	<	#define NPTf_ENS  3
24	<	#define NPTim_ENS 4
22	<	#define NPTfm_ENS 5
20	>	#define NVE_ENS        0
21	>	#define NVT_ENS        1
22	>	#define NPTi_ENS       2
23	>	#define NPTf_ENS       3
24	>	#define NPTxyz_ENS     4
25
26
27		#define FF_DUFF 0
28		#define FF_LJ   1
29	+	#define FF_EAM  2
30
31	+	using namespace std;
32
33	+	/**
34	+	* Check whether dividend is divisble by divisor or not
35	+	*/
36	+	bool isDivisible(double dividend, double divisor){
37	+	double tolerance = 0.000001;
38	+	double quotient;
39	+	double diff;
40	+	int intQuotient;
41	+
42	+	quotient = dividend / divisor;
43	+
44	+	if (quotient < 0)
45	+	quotient = -quotient;
46	+
47	+	intQuotient = int (quotient + tolerance);
48	+
49	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
50	+
51	+	if (diff <= tolerance)
52	+	return true;
53	+	else
54	+	return false;
55	+	}
56	+
57		SimSetup::SimSetup(){
58	+
59	+	initSuspend = false;
60	+	isInfoArray = 0;
61	+	nInfo = 1;
62	+
63		stamps = new MakeStamps();
64		globals = new Globals();
65	<
65	>
66	>
67		#ifdef IS_MPI
68	<	strcpy( checkPointMsg, "SimSetup creation successful" );
68	>	strcpy(checkPointMsg, "SimSetup creation successful");
69		MPIcheckPoint();
70		#endif // IS_MPI
71		}
#	Line 41 | Line 75 | void SimSetup::parseFile( char* fileName ){
75		delete globals;
76		}
77
78	<	void SimSetup::parseFile( char* fileName ){
78	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
79	>	info = the_info;
80	>	nInfo = theNinfo;
81	>	isInfoArray = 1;
82	>	initSuspend = true;
83	>	}
84
85	+
86	+	void SimSetup::parseFile(char* fileName){
87		#ifdef IS_MPI
88	<	if( worldRank == 0 ){
88	>	if (worldRank == 0){
89		#endif // is_mpi
90	<
90	>
91		inFileName = fileName;
92	<	set_interface_stamps( stamps, globals );
93	<
92	>	set_interface_stamps(stamps, globals);
93	>
94		#ifdef IS_MPI
95		mpiEventInit();
96		#endif
97
98	<	yacc_BASS( fileName );
98	>	yacc_BASS(fileName);
99
100		#ifdef IS_MPI
101		throwMPIEvent(NULL);
102		}
103	<	else receiveParse();
103	>	else{
104	>	receiveParse();
105	>	}
106		#endif
107
108		}
109
110		#ifdef IS_MPI
111		void SimSetup::receiveParse(void){
112	<
113	<	set_interface_stamps( stamps, globals );
114	<	mpiEventInit();
115	<	MPIcheckPoint();
73	<	mpiEventLoop();
74	<
112	>	set_interface_stamps(stamps, globals);
113	>	mpiEventInit();
114	>	MPIcheckPoint();
115	>	mpiEventLoop();
116		}
117
118		#endif // is_mpi
119
120	<	void SimSetup::createSim( void ){
120	>	void SimSetup::createSim(void){
121
122	<	MakeStamps *the_stamps;
82	<	Globals* the_globals;
83	<	int i, j, k, globalAtomIndex;
84	<
85	<	int ensembleCase;
86	<	int ffCase;
87	<
88	<	ensembleCase = -1;
89	<	ffCase = -1;
122	>	// gather all of the information from the Bass file
123
124	<	// get the stamps and globals;
92	<	the_stamps = stamps;
93	<	the_globals = globals;
124	>	gatherInfo();
125
126	<	// set the easy ones first
96	<	simnfo->target_temp = the_globals->getTargetTemp();
97	<	simnfo->dt = the_globals->getDt();
98	<	simnfo->run_time = the_globals->getRunTime();
126	>	// creation of complex system objects
127
128	<	// get the ones we know are there, yet still may need some work.
101	<	n_components = the_globals->getNComponents();
102	<	strcpy( force_field, the_globals->getForceField() );
128	>	sysObjectsCreation();
129
130	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
105	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
106	<	else{
107	<	sprintf( painCave.errMsg,
108	<	"SimSetup Error. Unrecognized force field -> %s\n",
109	<	force_field );
110	<	painCave.isFatal = 1;
111	<	simError();
112	<	}
130	>	// check on the post processing info
131
132	<	// get the ensemble:
115	<	strcpy( ensemble, the_globals->getEnsemble() );
132	>	finalInfoCheck();
133
134	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
118	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
119	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
120	<	ensembleCase = NPTi_ENS;
121	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
122	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
123	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
124	<	else{
125	<	sprintf( painCave.errMsg,
126	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
127	<	"reverting to NVE for this simulation.\n",
128	<	ensemble );
129	<	painCave.isFatal = 0;
130	<	simError();
131	<	strcpy( ensemble, "NVE" );
132	<	ensembleCase = NVE_ENS;
133	<	}
134	<	strcpy( simnfo->ensemble, ensemble );
134	>	// initialize the system coordinates
135
136	+	if ( !initSuspend ){
137	+	initSystemCoords();
138
139	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
140	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
141	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
140	<	//     if (the_globals->haveTargetPressure())
141	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
142	<	//     else {
143	<	//       sprintf( painCave.errMsg,
144	<	//                "SimSetup error: If you use the constant pressure\n"
145	<	//                "    ensemble, you must set targetPressure.\n"
146	<	//                "    This was found in the BASS file.\n");
147	<	//       painCave.isFatal = 1;
148	<	//       simError();
149	<	//     }
139	>	if( !(globals->getUseInitTime()) )
140	>	info[0].currentTime = 0.0;
141	>	}
142
143	<	//     if (the_globals->haveTauThermostat())
152	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
153	<	//     else if (the_globals->haveQmass())
154	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
155	<	//     else {
156	<	//       sprintf( painCave.errMsg,
157	<	//                "SimSetup error: If you use one of the constant temperature\n"
158	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
159	<	//                "    Neither of these was found in the BASS file.\n");
160	<	//       painCave.isFatal = 1;
161	<	//       simError();
162	<	//     }
143	>	// make the output filenames
144
145	<	//     if (the_globals->haveTauBarostat())
165	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
166	<	//     else {
167	<	//       sprintf( painCave.errMsg,
168	<	//                "SimSetup error: If you use the constant pressure\n"
169	<	//                "    ensemble, you must set tauBarostat.\n"
170	<	//                "    This was found in the BASS file.\n");
171	<	//       painCave.isFatal = 1;
172	<	//       simError();
173	<	//     }
145	>	makeOutNames();
146
147	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
176	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
177	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
147	>	// make the integrator
148
149	<	//     if (the_globals->haveTauThermostat())
180	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
181	<	//     else if (the_globals->haveQmass())
182	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
183	<	//     else {
184	<	//       sprintf( painCave.errMsg,
185	<	//                "SimSetup error: If you use one of the constant temperature\n"
186	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
187	<	//                "    Neither of these was found in the BASS file.\n");
188	<	//       painCave.isFatal = 1;
189	<	//       simError();
190	<	//     }
149	>	makeIntegrator();
150
151	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
152	<	simnfo->usePBC = the_globals->getPBC();
153	<
195	<	int usesDipoles = 0;
196	<	switch( ffCase ){
151	>	#ifdef IS_MPI
152	>	mpiSim->mpiRefresh();
153	>	#endif
154
155	<	case FF_DUFF:
199	<	the_ff = new DUFF();
200	<	usesDipoles = 1;
201	<	break;
155	>	// initialize the Fortran
156
157	<	case FF_LJ:
158	<	the_ff = new LJFF();
205	<	break;
157	>	initFortran();
158	>	}
159
207	–	default:
208	–	sprintf( painCave.errMsg,
209	–	"SimSetup Error. Unrecognized force field in case statement.\n");
210	–	painCave.isFatal = 1;
211	–	simError();
212	–	}
160
161	<	#ifdef IS_MPI
162	<	strcpy( checkPointMsg, "ForceField creation successful" );
163	<	MPIcheckPoint();
164	<	#endif // is_mpi
161	>	void SimSetup::makeMolecules(void){
162	>	int k;
163	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
164	>	molInit molInfo;
165	>	DirectionalAtom* dAtom;
166	>	LinkedAssign* extras;
167	>	LinkedAssign* current_extra;
168	>	AtomStamp* currentAtom;
169	>	BondStamp* currentBond;
170	>	BendStamp* currentBend;
171	>	TorsionStamp* currentTorsion;
172
173	<	// get the components and calculate the tot_nMol and indvidual n_mol
174	<	the_components = the_globals->getComponents();
175	<	components_nmol = new int[n_components];
222	<	comp_stamps = new MoleculeStamp*[n_components];
173	>	bond_pair* theBonds;
174	>	bend_set* theBends;
175	>	torsion_set* theTorsions;
176
177	<	if( !the_globals->haveNMol() ){
225	<	// we don't have the total number of molecules, so we assume it is
226	<	// given in each component
177	>	//init the forceField paramters
178
179	<	tot_nmol = 0;
229	<	for( i=0; i<n_components; i++ ){
179	>	the_ff->readParams();
180
231	–	if( !the_components[i]->haveNMol() ){
232	–	// we have a problem
233	–	sprintf( painCave.errMsg,
234	–	"SimSetup Error. No global NMol or component NMol"
235	–	" given. Cannot calculate the number of atoms.\n" );
236	–	painCave.isFatal = 1;
237	–	simError();
238	–	}
181
182	<	tot_nmol += the_components[i]->getNMol();
241	<	components_nmol[i] = the_components[i]->getNMol();
242	<	}
243	<	}
244	<	else{
245	<	sprintf( painCave.errMsg,
246	<	"SimSetup error.\n"
247	<	"\tSorry, the ability to specify total"
248	<	" nMols and then give molfractions in the components\n"
249	<	"\tis not currently supported."
250	<	" Please give nMol in the components.\n" );
251	<	painCave.isFatal = 1;
252	<	simError();
253	<
254	<
255	<	//     tot_nmol = the_globals->getNMol();
256	<
257	<	//   //we have the total number of molecules, now we check for molfractions
258	<	//     for( i=0; i<n_components; i++ ){
259	<
260	<	//       if( !the_components[i]->haveMolFraction() ){
261	<
262	<	//  if( !the_components[i]->haveNMol() ){
263	<	//    //we have a problem
264	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
265	<	//              << " nMol was given in component
266	<
267	<	}
182	>	// init the atoms
183
184	<	#ifdef IS_MPI
185	<	strcpy( checkPointMsg, "Have the number of components" );
186	<	MPIcheckPoint();
187	<	#endif // is_mpi
184	>	double phi, theta, psi;
185	>	double sux, suy, suz;
186	>	double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz;
187	>	double ux, uy, uz, u, uSqr;
188
189	<	// make an array of molecule stamps that match the components used.
190	<	// also extract the used stamps out into a separate linked list
189	>	for (k = 0; k < nInfo; k++){
190	>	the_ff->setSimInfo(&(info[k]));
191
192	<	simnfo->nComponents = n_components;
193	<	simnfo->componentsNmol = components_nmol;
194	<	simnfo->compStamps = comp_stamps;
195	<	simnfo->headStamp = new LinkedMolStamp();
281	<
282	<	char* id;
283	<	LinkedMolStamp* headStamp = simnfo->headStamp;
284	<	LinkedMolStamp* currentStamp = NULL;
285	<	for( i=0; i<n_components; i++ ){
192	>	atomOffset = 0;
193	>	excludeOffset = 0;
194	>	for (i = 0; i < info[k].n_mol; i++){
195	>	stampID = info[k].molecules[i].getStampID();
196
197	<	id = the_components[i]->getType();
198	<	comp_stamps[i] = NULL;
199	<
200	<	// check to make sure the component isn't already in the list
197	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
198	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
199	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
200	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
201	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
202
203	<	comp_stamps[i] = headStamp->match( id );
204	<	if( comp_stamps[i] == NULL ){
205	<
206	<	// extract the component from the list;
207	<
297	<	currentStamp = the_stamps->extractMolStamp( id );
298	<	if( currentStamp == NULL ){
299	<	sprintf( painCave.errMsg,
300	<	"SimSetup error: Component \"%s\" was not found in the "
301	<	"list of declared molecules\n",
302	<	id );
303	<	painCave.isFatal = 1;
304	<	simError();
305	<	}
306	<
307	<	headStamp->add( currentStamp );
308	<	comp_stamps[i] = headStamp->match( id );
309	<	}
310	<	}
203	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
204	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
205	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
206	>	molInfo.myBends = new Bend * [molInfo.nBends];
207	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
208
209	<	#ifdef IS_MPI
210	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
211	<	MPIcheckPoint();
315	<	#endif // is_mpi
316	<
209	>	theBonds = new bond_pair[molInfo.nBonds];
210	>	theBends = new bend_set[molInfo.nBends];
211	>	theTorsions = new torsion_set[molInfo.nTorsions];
212
213	+	// make the Atoms
214
215	+	for (j = 0; j < molInfo.nAtoms; j++){
216	+	currentAtom = comp_stamps[stampID]->getAtom(j);
217	+	if (currentAtom->haveOrientation()){
218	+	dAtom = new DirectionalAtom((j + atomOffset),
219	+	info[k].getConfiguration());
220	+	info[k].n_oriented++;
221	+	molInfo.myAtoms[j] = dAtom;
222
223	<	// caclulate the number of atoms, bonds, bends and torsions
223	>	// Directional Atoms have standard unit vectors which are oriented
224	>	// in space using the three Euler angles.  We assume the standard
225	>	// unit vector was originally along the z axis below.
226
227	<	tot_atoms = 0;
228	<	tot_bonds = 0;
229	<	tot_bends = 0;
230	<	tot_torsions = 0;
231	<	for( i=0; i<n_components; i++ ){
232	<
233	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
234	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
235	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
236	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
237	<	}
227	>	phi = currentAtom->getEulerPhi();
228	>	theta = currentAtom->getEulerTheta();
229	>	psi = currentAtom->getEulerPsi();
230	>
231	>	Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
232	>	Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
233	>	Axz = sin(theta) * sin(psi);
234	>
235	>	Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
236	>	Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
237	>	Ayz = sin(theta) * cos(psi);
238	>
239	>	Azx = sin(phi) * sin(theta);
240	>	Azy = -cos(phi) * sin(theta);
241	>	Azz = cos(theta);
242
243	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
243	>	sux = 0.0;
244	>	suy = 0.0;
245	>	suz = 1.0;
246
247	<	simnfo->n_atoms = tot_atoms;
248	<	simnfo->n_bonds = tot_bonds;
249	<	simnfo->n_bends = tot_bends;
339	<	simnfo->n_torsions = tot_torsions;
340	<	simnfo->n_SRI = tot_SRI;
341	<	simnfo->n_mol = tot_nmol;
342	<
343	<	simnfo->molMembershipArray = new int[tot_atoms];
247	>	ux = (Axx * sux) + (Ayx * suy) + (Azx * suz);
248	>	uy = (Axy * sux) + (Ayy * suy) + (Azy * suz);
249	>	uz = (Axz * sux) + (Ayz * suy) + (Azz * suz);
250
251	<	#ifdef IS_MPI
251	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
252
253	<	// divide the molecules among processors here.
254	<
255	<	mpiSim = new mpiSimulation( simnfo );
256	<
351	<	globalIndex = mpiSim->divideLabor();
253	>	u = sqrt(uSqr);
254	>	ux = ux / u;
255	>	uy = uy / u;
256	>	uz = uz / u;
257
258	<	// set up the local variables
259	<
260	<	int localMol, allMol;
261	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
258	>	dAtom->setSUx(ux);
259	>	dAtom->setSUy(uy);
260	>	dAtom->setSUz(uz);
261	>	}
262	>	else{
263	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
264	>	info[k].getConfiguration());
265	>	}
266	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
267
268	<	int* mol2proc = mpiSim->getMolToProcMap();
359	<	int* molCompType = mpiSim->getMolComponentType();
360	<
361	<	allMol = 0;
362	<	localMol = 0;
363	<	local_atoms = 0;
364	<	local_bonds = 0;
365	<	local_bends = 0;
366	<	local_torsions = 0;
367	<	globalAtomIndex = 0;
268	>	#ifdef IS_MPI
269
270	+	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
271
272	<	for( i=0; i<n_components; i++ ){
272	>	#endif // is_mpi
273	>	}
274
275	<	for( j=0; j<components_nmol[i]; j++ ){
276	<
277	<	if( mol2proc[allMol] == worldRank ){
278	<
279	<	local_atoms +=    comp_stamps[i]->getNAtoms();
377	<	local_bonds +=    comp_stamps[i]->getNBonds();
378	<	local_bends +=    comp_stamps[i]->getNBends();
379	<	local_torsions += comp_stamps[i]->getNTorsions();
380	<	localMol++;
381	<	}
382	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
383	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
384	<	globalAtomIndex++;
385	<	}
275	>	// make the bonds
276	>	for (j = 0; j < molInfo.nBonds; j++){
277	>	currentBond = comp_stamps[stampID]->getBond(j);
278	>	theBonds[j].a = currentBond->getA() + atomOffset;
279	>	theBonds[j].b = currentBond->getB() + atomOffset;
280
281	<	allMol++;
282	<	}
389	<	}
390	<	local_SRI = local_bonds + local_bends + local_torsions;
391	<
392	<	simnfo->n_atoms = mpiSim->getMyNlocal();
393	<
394	<	if( local_atoms != simnfo->n_atoms ){
395	<	sprintf( painCave.errMsg,
396	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
397	<	" localAtom (%d) are not equal.\n",
398	<	simnfo->n_atoms,
399	<	local_atoms );
400	<	painCave.isFatal = 1;
401	<	simError();
402	<	}
281	>	exI = theBonds[j].a;
282	>	exJ = theBonds[j].b;
283
284	<	simnfo->n_bonds = local_bonds;
285	<	simnfo->n_bends = local_bends;
286	<	simnfo->n_torsions = local_torsions;
287	<	simnfo->n_SRI = local_SRI;
288	<	simnfo->n_mol = localMol;
284	>	// exclude_I must always be the smaller of the pair
285	>	if (exI > exJ){
286	>	tempEx = exI;
287	>	exI = exJ;
288	>	exJ = tempEx;
289	>	}
290	>	#ifdef IS_MPI
291	>	tempEx = exI;
292	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
293	>	tempEx = exJ;
294	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
295
296	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
297	<	MPIcheckPoint();
412	<
413	<
414	<	#endif // is_mpi
415	<
296	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
297	>	#else  // isn't MPI
298
299	<	// create the atom and short range interaction arrays
299	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
300	>	#endif  //is_mpi
301	>	}
302	>	excludeOffset += molInfo.nBonds;
303
304	<	Atom::createArrays(simnfo->n_atoms);
305	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
307	<	int molIndex;
304	>	//make the bends
305	>	for (j = 0; j < molInfo.nBends; j++){
306	>	currentBend = comp_stamps[stampID]->getBend(j);
307	>	theBends[j].a = currentBend->getA() + atomOffset;
308	>	theBends[j].b = currentBend->getB() + atomOffset;
309	>	theBends[j].c = currentBend->getC() + atomOffset;
310
311	<	// initialize the molecule's stampID's
311	>	if (currentBend->haveExtras()){
312	>	extras = currentBend->getExtras();
313	>	current_extra = extras;
314	>
315	>	while (current_extra != NULL){
316	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
317	>	switch (current_extra->getType()){
318	>	case 0:
319	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
320	>	theBends[j].isGhost = 1;
321	>	break;
322	>
323	>	case 1:
324	>	theBends[j].ghost = (int) current_extra->getDouble() +
325	>	atomOffset;
326	>	theBends[j].isGhost = 1;
327	>	break;
328
329	+	default:
330	+	sprintf(painCave.errMsg,
331	+	"SimSetup Error: ghostVectorSource was neither a "
332	+	"double nor an int.\n"
333	+	"-->Bend[%d] in %s\n",
334	+	j, comp_stamps[stampID]->getID());
335	+	painCave.isFatal = 1;
336	+	simError();
337	+	}
338	+	}
339	+	else{
340	+	sprintf(painCave.errMsg,
341	+	"SimSetup Error: unhandled bend assignment:\n"
342	+	"    -->%s in Bend[%d] in %s\n",
343	+	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
344	+	painCave.isFatal = 1;
345	+	simError();
346	+	}
347	+
348	+	current_extra = current_extra->getNext();
349	+	}
350	+	}
351	+
352	+	if (!theBends[j].isGhost){
353	+	exI = theBends[j].a;
354	+	exJ = theBends[j].c;
355	+	}
356	+	else{
357	+	exI = theBends[j].a;
358	+	exJ = theBends[j].b;
359	+	}
360	+
361	+	// exclude_I must always be the smaller of the pair
362	+	if (exI > exJ){
363	+	tempEx = exI;
364	+	exI = exJ;
365	+	exJ = tempEx;
366	+	}
367		#ifdef IS_MPI
368	<
368	>	tempEx = exI;
369	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
370	>	tempEx = exJ;
371	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
372
373	<	molIndex = 0;
374	<	for(i=0; i<mpiSim->getTotNmol(); i++){
375	<
376	<	if(mol2proc[i] == worldRank ){
377	<	the_molecules[molIndex].setStampID( molCompType[i] );
378	<	the_molecules[molIndex].setMyIndex( molIndex );
435	<	the_molecules[molIndex].setGlobalIndex( i );
436	<	molIndex++;
437	<	}
438	<	}
373	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
374	>	#else  // isn't MPI
375	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
376	>	#endif  //is_mpi
377	>	}
378	>	excludeOffset += molInfo.nBends;
379
380	<	#else // is_mpi
381	<
382	<	molIndex = 0;
383	<	globalAtomIndex = 0;
384	<	for(i=0; i<n_components; i++){
385	<	for(j=0; j<components_nmol[i]; j++ ){
386	<	the_molecules[molIndex].setStampID( i );
387	<	the_molecules[molIndex].setMyIndex( molIndex );
388	<	the_molecules[molIndex].setGlobalIndex( molIndex );
389	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
390	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
391	<	globalAtomIndex++;
380	>	for (j = 0; j < molInfo.nTorsions; j++){
381	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
382	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
383	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
384	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
385	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
386	>
387	>	exI = theTorsions[j].a;
388	>	exJ = theTorsions[j].d;
389	>
390	>	// exclude_I must always be the smaller of the pair
391	>	if (exI > exJ){
392	>	tempEx = exI;
393	>	exI = exJ;
394	>	exJ = tempEx;
395	>	}
396	>	#ifdef IS_MPI
397	>	tempEx = exI;
398	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
399	>	tempEx = exJ;
400	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
401	>
402	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
403	>	#else  // isn't MPI
404	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
405	>	#endif  //is_mpi
406		}
407	<	molIndex++;
454	<	}
455	<	}
456	<
407	>	excludeOffset += molInfo.nTorsions;
408
458	–	#endif // is_mpi
409
410	+	// send the arrays off to the forceField for init.
411
412	<	if( simnfo->n_SRI ){
413	<
414	<	Exclude::createArray(simnfo->n_SRI);
415	<	the_excludes = new Exclude*[simnfo->n_SRI];
416	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
417	<	simnfo->globalExcludes = new int;
418	<	simnfo->n_exclude = simnfo->n_SRI;
412	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
413	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
414	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
415	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
416	>	theTorsions);
417	>
418	>
419	>	info[k].molecules[i].initialize(molInfo);
420	>
421	>
422	>	atomOffset += molInfo.nAtoms;
423	>	delete[] theBonds;
424	>	delete[] theBends;
425	>	delete[] theTorsions;
426	>	}
427		}
469	–	else{
470	–
471	–	Exclude::createArray( 1 );
472	–	the_excludes = new Exclude*;
473	–	the_excludes[0] = new Exclude(0);
474	–	the_excludes[0]->setPair( 0,0 );
475	–	simnfo->globalExcludes = new int;
476	–	simnfo->globalExcludes[0] = 0;
477	–	simnfo->n_exclude = 0;
478	–	}
428
429	<	// set the arrays into the SimInfo object
429	>	#ifdef IS_MPI
430	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
431	>	MPIcheckPoint();
432	>	#endif // is_mpi
433
434	<	simnfo->atoms = the_atoms;
483	<	simnfo->molecules = the_molecules;
484	<	simnfo->nGlobalExcludes = 0;
485	<	simnfo->excludes = the_excludes;
434	>	// clean up the forcefield
435
436	+	the_ff->calcRcut();
437	+	the_ff->cleanMe();
438	+	}
439
440	<	// get some of the tricky things that may still be in the globals
440	>	void SimSetup::initFromBass(void){
441	>	int i, j, k;
442	>	int n_cells;
443	>	double cellx, celly, cellz;
444	>	double temp1, temp2, temp3;
445	>	int n_per_extra;
446	>	int n_extra;
447	>	int have_extra, done;
448
449	<	double boxVector[3];
450	<	if( the_globals->haveBox() ){
451	<	boxVector[0] = the_globals->getBox();
452	<	boxVector[1] = the_globals->getBox();
494	<	boxVector[2] = the_globals->getBox();
495	<
496	<	simnfo->setBox( boxVector );
497	<	}
498	<	else if( the_globals->haveDensity() ){
449	>	double vel[3];
450	>	vel[0] = 0.0;
451	>	vel[1] = 0.0;
452	>	vel[2] = 0.0;
453
454	<	double vol;
455	<	vol = (double)tot_nmol / the_globals->getDensity();
456	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
503	<	boxVector[1] = boxVector[0];
504	<	boxVector[2] = boxVector[0];
454	>	temp1 = (double) tot_nmol / 4.0;
455	>	temp2 = pow(temp1, (1.0 / 3.0));
456	>	temp3 = ceil(temp2);
457
458	<	simnfo->setBox( boxVector );
459	<	}
460	<	else{
461	<	if( !the_globals->haveBoxX() ){
510	<	sprintf( painCave.errMsg,
511	<	"SimSetup error, no periodic BoxX size given.\n" );
512	<	painCave.isFatal = 1;
513	<	simError();
514	<	}
515	<	boxVector[0] = the_globals->getBoxX();
458	>	have_extra = 0;
459	>	if (temp2 < temp3){
460	>	// we have a non-complete lattice
461	>	have_extra = 1;
462
463	<	if( !the_globals->haveBoxY() ){
464	<	sprintf( painCave.errMsg,
465	<	"SimSetup error, no periodic BoxY size given.\n" );
466	<	painCave.isFatal = 1;
467	<	simError();
468	<	}
469	<	boxVector[1] = the_globals->getBoxY();
463	>	n_cells = (int) temp3 - 1;
464	>	cellx = info[0].boxL[0] / temp3;
465	>	celly = info[0].boxL[1] / temp3;
466	>	cellz = info[0].boxL[2] / temp3;
467	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
468	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
469	>	n_per_extra = (int) ceil(temp1);
470
471	<	if( !the_globals->haveBoxZ() ){
472	<	sprintf( painCave.errMsg,
473	<	"SimSetup error, no periodic BoxZ size given.\n" );
471	>	if (n_per_extra > 4){
472	>	sprintf(painCave.errMsg,
473	>	"SimSetup error. There has been an error in constructing"
474	>	" the non-complete lattice.\n");
475		painCave.isFatal = 1;
476		simError();
477		}
531	–	boxVector[2] = the_globals->getBoxZ();
532	–
533	–	simnfo->setBox( boxVector );
478		}
479	+	else{
480	+	n_cells = (int) temp3;
481	+	cellx = info[0].boxL[0] / temp3;
482	+	celly = info[0].boxL[1] / temp3;
483	+	cellz = info[0].boxL[2] / temp3;
484	+	}
485
486	<	#ifdef IS_MPI
487	<	strcpy( checkPointMsg, "Box size set up" );
488	<	MPIcheckPoint();
489	<	#endif // is_mpi
486	>	current_mol = 0;
487	>	current_comp_mol = 0;
488	>	current_comp = 0;
489	>	current_atom_ndx = 0;
490
491	+	for (i = 0; i < n_cells ; i++){
492	+	for (j = 0; j < n_cells; j++){
493	+	for (k = 0; k < n_cells; k++){
494	+	makeElement(i * cellx, j * celly, k * cellz);
495
496	<	// initialize the arrays
496	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
497
498	<	the_ff->setSimInfo( simnfo );
498	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
499
500	<	makeMolecules();
501	<	simnfo->identArray = new int[simnfo->n_atoms];
502	<	for(i=0; i<simnfo->n_atoms; i++){
549	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
500	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
501	>	}
502	>	}
503		}
504	<
505	<	if (the_globals->getUseRF() ) {
506	<	simnfo->useReactionField = 1;
554	<
555	<	if( !the_globals->haveECR() ){
556	<	sprintf( painCave.errMsg,
557	<	"SimSetup Warning: using default value of 1/2 the smallest "
558	<	"box length for the electrostaticCutoffRadius.\n"
559	<	"I hope you have a very fast processor!\n");
560	<	painCave.isFatal = 0;
561	<	simError();
562	<	double smallest;
563	<	smallest = simnfo->boxLx;
564	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
565	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
566	<	simnfo->ecr = 0.5 * smallest;
567	<	} else {
568	<	simnfo->ecr        = the_globals->getECR();
569	<	}
504	>
505	>	if (have_extra){
506	>	done = 0;
507
508	<	if( !the_globals->haveEST() ){
509	<	sprintf( painCave.errMsg,
510	<	"SimSetup Warning: using default value of 0.05 * the "
511	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
512	<	);
513	<	painCave.isFatal = 0;
514	<	simError();
515	<	simnfo->est = 0.05 * simnfo->ecr;
516	<	} else {
517	<	simnfo->est        = the_globals->getEST();
508	>	int start_ndx;
509	>	for (i = 0; i < (n_cells + 1) && !done; i++){
510	>	for (j = 0; j < (n_cells + 1) && !done; j++){
511	>	if (i < n_cells){
512	>	if (j < n_cells){
513	>	start_ndx = n_cells;
514	>	}
515	>	else
516	>	start_ndx = 0;
517	>	}
518	>	else
519	>	start_ndx = 0;
520	>
521	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
522	>	makeElement(i * cellx, j * celly, k * cellz);
523	>	done = (current_mol >= tot_nmol);
524	>
525	>	if (!done && n_per_extra > 1){
526	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
527	>	k * cellz);
528	>	done = (current_mol >= tot_nmol);
529	>	}
530	>
531	>	if (!done && n_per_extra > 2){
532	>	makeElement(i * cellx, j * celly + 0.5 * celly,
533	>	k * cellz + 0.5 * cellz);
534	>	done = (current_mol >= tot_nmol);
535	>	}
536	>
537	>	if (!done && n_per_extra > 3){
538	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
539	>	k * cellz + 0.5 * cellz);
540	>	done = (current_mol >= tot_nmol);
541	>	}
542	>	}
543	>	}
544		}
545	<
546	<	if(!the_globals->haveDielectric() ){
547	<	sprintf( painCave.errMsg,
548	<	"SimSetup Error: You are trying to use Reaction Field without"
549	<	"setting a dielectric constant!\n"
550	<	);
545	>	}
546	>
547	>	for (i = 0; i < info[0].n_atoms; i++){
548	>	info[0].atoms[i]->setVel(vel);
549	>	}
550	>	}
551	>
552	>	void SimSetup::makeElement(double x, double y, double z){
553	>	int k;
554	>	AtomStamp* current_atom;
555	>	DirectionalAtom* dAtom;
556	>	double rotMat[3][3];
557	>	double pos[3];
558	>
559	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
560	>	current_atom = comp_stamps[current_comp]->getAtom(k);
561	>	if (!current_atom->havePosition()){
562	>	sprintf(painCave.errMsg,
563	>	"SimSetup:initFromBass error.\n"
564	>	"\tComponent %s, atom %s does not have a position specified.\n"
565	>	"\tThe initialization routine is unable to give a start"
566	>	" position.\n",
567	>	comp_stamps[current_comp]->getID(), current_atom->getType());
568		painCave.isFatal = 1;
569		simError();
570		}
571	<	simnfo->dielectric = the_globals->getDielectric();
572	<	} else {
573	<	if (usesDipoles) {
574	<
575	<	if( !the_globals->haveECR() ){
576	<	sprintf( painCave.errMsg,
577	<	"SimSetup Warning: using default value of 1/2 the smallest "
578	<	"box length for the electrostaticCutoffRadius.\n"
579	<	"I hope you have a very fast processor!\n");
580	<	painCave.isFatal = 0;
581	<	simError();
582	<	double smallest;
583	<	smallest = simnfo->boxLx;
584	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
585	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
586	<	simnfo->ecr = 0.5 * smallest;
587	<	} else {
588	<	simnfo->ecr        = the_globals->getECR();
589	<	}
590	<
591	<	if( !the_globals->haveEST() ){
592	<	sprintf( painCave.errMsg,
593	<	"SimSetup Warning: using default value of 5%% of the "
614	<	"electrostaticCutoffRadius for the "
615	<	"electrostaticSkinThickness\n"
616	<	);
617	<	painCave.isFatal = 0;
618	<	simError();
619	<	simnfo->est = 0.05 * simnfo->ecr;
620	<	} else {
621	<	simnfo->est        = the_globals->getEST();
622	<	}
571	>
572	>	pos[0] = x + current_atom->getPosX();
573	>	pos[1] = y + current_atom->getPosY();
574	>	pos[2] = z + current_atom->getPosZ();
575	>
576	>	info[0].atoms[current_atom_ndx]->setPos(pos);
577	>
578	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
579	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
580	>
581	>	rotMat[0][0] = 1.0;
582	>	rotMat[0][1] = 0.0;
583	>	rotMat[0][2] = 0.0;
584	>
585	>	rotMat[1][0] = 0.0;
586	>	rotMat[1][1] = 1.0;
587	>	rotMat[1][2] = 0.0;
588	>
589	>	rotMat[2][0] = 0.0;
590	>	rotMat[2][1] = 0.0;
591	>	rotMat[2][2] = 1.0;
592	>
593	>	dAtom->setA(rotMat);
594		}
624	–	}
595
596	<	#ifdef IS_MPI
597	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
628	<	MPIcheckPoint();
629	<	#endif // is_mpi
596	>	current_atom_ndx++;
597	>	}
598
599	<	if( the_globals->haveInitialConfig() ){
600	<
633	<	InitializeFromFile* fileInit;
634	<	#ifdef IS_MPI // is_mpi
635	<	if( worldRank == 0 ){
636	<	#endif //is_mpi
637	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
638	<	#ifdef IS_MPI
639	<	}else fileInit = new InitializeFromFile( NULL );
640	<	#endif
641	<	fileInit->read_xyz( simnfo ); // default velocities on
599	>	current_mol++;
600	>	current_comp_mol++;
601
602	<	delete fileInit;
603	<	}
604	<	else{
602	>	if (current_comp_mol >= components_nmol[current_comp]){
603	>	current_comp_mol = 0;
604	>	current_comp++;
605	>	}
606	>	}
607
647	–	#ifdef IS_MPI
608
609	<	// no init from bass
610	<
651	<	sprintf( painCave.errMsg,
652	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
653	<	painCave.isFatal;
654	<	simError();
655	<
656	<	#else
609	>	void SimSetup::gatherInfo(void){
610	>	int i;
611
612	<	initFromBass();
612	>	ensembleCase = -1;
613	>	ffCase = -1;
614
615	+	// set the easy ones first
616
617	<	#endif
618	<	}
617	>	for (i = 0; i < nInfo; i++){
618	>	info[i].target_temp = globals->getTargetTemp();
619	>	info[i].dt = globals->getDt();
620	>	info[i].run_time = globals->getRunTime();
621	>	}
622	>	n_components = globals->getNComponents();
623
664	–	#ifdef IS_MPI
665	–	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
666	–	MPIcheckPoint();
667	–	#endif // is_mpi
624
625	+	// get the forceField
626
627	<
671	<
672	<
627	>	strcpy(force_field, globals->getForceField());
628
629	<
630	<	#ifdef IS_MPI
676	<	if( worldRank == 0 ){
677	<	#endif // is_mpi
678	<
679	<	if( the_globals->haveFinalConfig() ){
680	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
681	<	}
682	<	else{
683	<	strcpy( simnfo->finalName, inFileName );
684	<	char* endTest;
685	<	int nameLength = strlen( simnfo->finalName );
686	<	endTest = &(simnfo->finalName[nameLength - 5]);
687	<	if( !strcmp( endTest, ".bass" ) ){
688	<	strcpy( endTest, ".eor" );
689	<	}
690	<	else if( !strcmp( endTest, ".BASS" ) ){
691	<	strcpy( endTest, ".eor" );
692	<	}
693	<	else{
694	<	endTest = &(simnfo->finalName[nameLength - 4]);
695	<	if( !strcmp( endTest, ".bss" ) ){
696	<	strcpy( endTest, ".eor" );
697	<	}
698	<	else if( !strcmp( endTest, ".mdl" ) ){
699	<	strcpy( endTest, ".eor" );
700	<	}
701	<	else{
702	<	strcat( simnfo->finalName, ".eor" );
703	<	}
704	<	}
705	<	}
706	<
707	<	// make the sample and status out names
708	<
709	<	strcpy( simnfo->sampleName, inFileName );
710	<	char* endTest;
711	<	int nameLength = strlen( simnfo->sampleName );
712	<	endTest = &(simnfo->sampleName[nameLength - 5]);
713	<	if( !strcmp( endTest, ".bass" ) ){
714	<	strcpy( endTest, ".dump" );
715	<	}
716	<	else if( !strcmp( endTest, ".BASS" ) ){
717	<	strcpy( endTest, ".dump" );
718	<	}
719	<	else{
720	<	endTest = &(simnfo->sampleName[nameLength - 4]);
721	<	if( !strcmp( endTest, ".bss" ) ){
722	<	strcpy( endTest, ".dump" );
723	<	}
724	<	else if( !strcmp( endTest, ".mdl" ) ){
725	<	strcpy( endTest, ".dump" );
726	<	}
727	<	else{
728	<	strcat( simnfo->sampleName, ".dump" );
729	<	}
730	<	}
731	<
732	<	strcpy( simnfo->statusName, inFileName );
733	<	nameLength = strlen( simnfo->statusName );
734	<	endTest = &(simnfo->statusName[nameLength - 5]);
735	<	if( !strcmp( endTest, ".bass" ) ){
736	<	strcpy( endTest, ".stat" );
737	<	}
738	<	else if( !strcmp( endTest, ".BASS" ) ){
739	<	strcpy( endTest, ".stat" );
740	<	}
741	<	else{
742	<	endTest = &(simnfo->statusName[nameLength - 4]);
743	<	if( !strcmp( endTest, ".bss" ) ){
744	<	strcpy( endTest, ".stat" );
745	<	}
746	<	else if( !strcmp( endTest, ".mdl" ) ){
747	<	strcpy( endTest, ".stat" );
748	<	}
749	<	else{
750	<	strcat( simnfo->statusName, ".stat" );
751	<	}
752	<	}
753	<
754	<	#ifdef IS_MPI
629	>	if (!strcasecmp(force_field, "DUFF")){
630	>	ffCase = FF_DUFF;
631		}
632	<	#endif // is_mpi
633	<
758	<	// set the status, sample, and themal kick times
759	<
760	<	if( the_globals->haveSampleTime() ){
761	<	simnfo->sampleTime = the_globals->getSampleTime();
762	<	simnfo->statusTime = simnfo->sampleTime;
763	<	simnfo->thermalTime = simnfo->sampleTime;
632	>	else if (!strcasecmp(force_field, "LJ")){
633	>	ffCase = FF_LJ;
634		}
635	+	else if (!strcasecmp(force_field, "EAM")){
636	+	ffCase = FF_EAM;
637	+	}
638		else{
639	<	simnfo->sampleTime = the_globals->getRunTime();
640	<	simnfo->statusTime = simnfo->sampleTime;
641	<	simnfo->thermalTime = simnfo->sampleTime;
639	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
640	>	force_field);
641	>	painCave.isFatal = 1;
642	>	simError();
643		}
644
645	<	if( the_globals->haveStatusTime() ){
772	<	simnfo->statusTime = the_globals->getStatusTime();
773	<	}
645	>	// get the ensemble
646
647	<	if( the_globals->haveThermalTime() ){
648	<	simnfo->thermalTime = the_globals->getThermalTime();
647	>	strcpy(ensemble, globals->getEnsemble());
648	>
649	>	if (!strcasecmp(ensemble, "NVE")){
650	>	ensembleCase = NVE_ENS;
651		}
652	+	else if (!strcasecmp(ensemble, "NVT")){
653	+	ensembleCase = NVT_ENS;
654	+	}
655	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
656	+	ensembleCase = NPTi_ENS;
657	+	}
658	+	else if (!strcasecmp(ensemble, "NPTf")){
659	+	ensembleCase = NPTf_ENS;
660	+	}
661	+	else if (!strcasecmp(ensemble, "NPTxyz")){
662	+	ensembleCase = NPTxyz_ENS;
663	+	}
664	+	else{
665	+	sprintf(painCave.errMsg,
666	+	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
667	+	"\treverting to NVE for this simulation.\n",
668	+	ensemble);
669	+	painCave.isFatal = 0;
670	+	simError();
671	+	strcpy(ensemble, "NVE");
672	+	ensembleCase = NVE_ENS;
673	+	}
674
675	<	// check for the temperature set flag
675	>	for (i = 0; i < nInfo; i++){
676	>	strcpy(info[i].ensemble, ensemble);
677
678	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
678	>	// get the mixing rule
679
680	+	strcpy(info[i].mixingRule, globals->getMixingRule());
681	+	info[i].usePBC = globals->getPBC();
682	+	}
683
684	<	// make the integrator
785	<
786	<
787	<	NVT*  myNVT = NULL;
788	<	NPTi* myNPTi = NULL;
789	<	NPTf* myNPTf = NULL;
790	<	NPTim* myNPTim = NULL;
684	>	// get the components and calculate the tot_nMol and indvidual n_mol
685
686	<	switch( ensembleCase ){
686	>	the_components = globals->getComponents();
687	>	components_nmol = new int[n_components];
688
794	–	case NVE_ENS:
795	–	new NVE( simnfo, the_ff );
796	–	break;
689
690	<	case NVT_ENS:
691	<	myNVT = new NVT( simnfo, the_ff );
692	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
690	>	if (!globals->haveNMol()){
691	>	// we don't have the total number of molecules, so we assume it is
692	>	// given in each component
693
694	<	if (the_globals->haveTauThermostat())
695	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
694	>	tot_nmol = 0;
695	>	for (i = 0; i < n_components; i++){
696	>	if (!the_components[i]->haveNMol()){
697	>	// we have a problem
698	>	sprintf(painCave.errMsg,
699	>	"SimSetup Error. No global NMol or component NMol given.\n"
700	>	"\tCannot calculate the number of atoms.\n");
701	>	painCave.isFatal = 1;
702	>	simError();
703	>	}
704
705	<	else {
706	<	sprintf( painCave.errMsg,
807	<	"SimSetup error: If you use the NVT\n"
808	<	"    ensemble, you must set tauThermostat.\n");
809	<	painCave.isFatal = 1;
810	<	simError();
705	>	tot_nmol += the_components[i]->getNMol();
706	>	components_nmol[i] = the_components[i]->getNMol();
707		}
708	<	break;
708	>	}
709	>	else{
710	>	sprintf(painCave.errMsg,
711	>	"SimSetup error.\n"
712	>	"\tSorry, the ability to specify total"
713	>	" nMols and then give molfractions in the components\n"
714	>	"\tis not currently supported."
715	>	" Please give nMol in the components.\n");
716	>	painCave.isFatal = 1;
717	>	simError();
718	>	}
719
720	<	case NPTi_ENS:
721	<	myNPTi = new NPTi( simnfo, the_ff );
722	<	myNPTi->setTargetTemp( the_globals->getTargetTemp());
720	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
721	>	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
722	>	sprintf(painCave.errMsg,
723	>	"Sample time is not divisible by dt.\n"
724	>	"\tThis will result in samples that are not uniformly\n"
725	>	"\tdistributed in time.  If this is a problem, change\n"
726	>	"\tyour sampleTime variable.\n");
727	>	painCave.isFatal = 0;
728	>	simError();
729	>	}
730
731	<	if (the_globals->haveTargetPressure())
732	<	myNPTi->setTargetPressure(the_globals->getTargetPressure());
733	<	else {
734	<	sprintf( painCave.errMsg,
735	<	"SimSetup error: If you use a constant pressure\n"
736	<	"    ensemble, you must set targetPressure in the BASS file.\n");
737	<	painCave.isFatal = 1;
738	<	simError();
739	<	}
740	<
741	<	if( the_globals->haveTauThermostat() )
742	<	myNPTi->setTauThermostat( the_globals->getTauThermostat() );
743	<	else{
744	<	sprintf( painCave.errMsg,
745	<	"SimSetup error: If you use an NPT\n"
746	<	"    ensemble, you must set tauThermostat.\n");
747	<	painCave.isFatal = 1;
748	<	simError();
749	<	}
731	>	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
732	>	sprintf(painCave.errMsg,
733	>	"Status time is not divisible by dt.\n"
734	>	"\tThis will result in status reports that are not uniformly\n"
735	>	"\tdistributed in time.  If this is a problem, change \n"
736	>	"\tyour statusTime variable.\n");
737	>	painCave.isFatal = 0;
738	>	simError();
739	>	}
740	>
741	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
742	>	sprintf(painCave.errMsg,
743	>	"Thermal time is not divisible by dt.\n"
744	>	"\tThis will result in thermalizations that are not uniformly\n"
745	>	"\tdistributed in time.  If this is a problem, change \n"
746	>	"\tyour thermalTime variable.\n");
747	>	painCave.isFatal = 0;
748	>	simError();
749	>	}
750	>
751	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
752	>	sprintf(painCave.errMsg,
753	>	"Reset time is not divisible by dt.\n"
754	>	"\tThis will result in integrator resets that are not uniformly\n"
755	>	"\tdistributed in time.  If this is a problem, change\n"
756	>	"\tyour resetTime variable.\n");
757	>	painCave.isFatal = 0;
758	>	simError();
759	>	}
760
761	<	if( the_globals->haveTauBarostat() )
839	<	myNPTi->setTauBarostat( the_globals->getTauBarostat() );
840	<	else{
841	<	sprintf( painCave.errMsg,
842	<	"SimSetup error: If you use an NPT\n"
843	<	"    ensemble, you must set tauBarostat.\n");
844	<	painCave.isFatal = 1;
845	<	simError();
846	<	}
847	<	break;
761	>	// set the status, sample, and thermal kick times
762
763	<	case NPTf_ENS:
764	<	myNPTf = new NPTf( simnfo, the_ff );
765	<	myNPTf->setTargetTemp( the_globals->getTargetTemp());
766	<
767	<	if (the_globals->haveTargetPressure())
768	<	myNPTf->setTargetPressure(the_globals->getTargetPressure());
855	<	else {
856	<	sprintf( painCave.errMsg,
857	<	"SimSetup error: If you use a constant pressure\n"
858	<	"    ensemble, you must set targetPressure in the BASS file.\n");
859	<	painCave.isFatal = 1;
860	<	simError();
861	<	}
862	<
863	<	if( the_globals->haveTauThermostat() )
864	<	myNPTf->setTauThermostat( the_globals->getTauThermostat() );
763	>	for (i = 0; i < nInfo; i++){
764	>	if (globals->haveSampleTime()){
765	>	info[i].sampleTime = globals->getSampleTime();
766	>	info[i].statusTime = info[i].sampleTime;
767	>	info[i].thermalTime = info[i].sampleTime;
768	>	}
769		else{
770	<	sprintf( painCave.errMsg,
771	<	"SimSetup error: If you use an NPT\n"
772	<	"    ensemble, you must set tauThermostat.\n");
869	<	painCave.isFatal = 1;
870	<	simError();
770	>	info[i].sampleTime = globals->getRunTime();
771	>	info[i].statusTime = info[i].sampleTime;
772	>	info[i].thermalTime = info[i].sampleTime;
773		}
774
775	<	if( the_globals->haveTauBarostat() )
776	<	myNPTf->setTauBarostat( the_globals->getTauBarostat() );
875	<	else{
876	<	sprintf( painCave.errMsg,
877	<	"SimSetup error: If you use an NPT\n"
878	<	"    ensemble, you must set tauBarostat.\n");
879	<	painCave.isFatal = 1;
880	<	simError();
775	>	if (globals->haveStatusTime()){
776	>	info[i].statusTime = globals->getStatusTime();
777		}
882	–	break;
883	–
884	–	case NPTim_ENS:
885	–	myNPTim = new NPTim( simnfo, the_ff );
886	–	myNPTim->setTargetTemp( the_globals->getTargetTemp());
778
779	<	if (the_globals->haveTargetPressure())
780	<	myNPTim->setTargetPressure(the_globals->getTargetPressure());
890	<	else {
891	<	sprintf( painCave.errMsg,
892	<	"SimSetup error: If you use a constant pressure\n"
893	<	"    ensemble, you must set targetPressure in the BASS file.\n");
894	<	painCave.isFatal = 1;
895	<	simError();
779	>	if (globals->haveThermalTime()){
780	>	info[i].thermalTime = globals->getThermalTime();
781		}
897	–
898	–	if( the_globals->haveTauThermostat() )
899	–	myNPTim->setTauThermostat( the_globals->getTauThermostat() );
900	–	else{
901	–	sprintf( painCave.errMsg,
902	–	"SimSetup error: If you use an NPT\n"
903	–	"    ensemble, you must set tauThermostat.\n");
904	–	painCave.isFatal = 1;
905	–	simError();
906	–	}
782
783	<	if( the_globals->haveTauBarostat() )
784	<	myNPTim->setTauBarostat( the_globals->getTauBarostat() );
785	<	else{
786	<	sprintf( painCave.errMsg,
912	<	"SimSetup error: If you use an NPT\n"
913	<	"    ensemble, you must set tauBarostat.\n");
914	<	painCave.isFatal = 1;
915	<	simError();
783	>	info[i].resetIntegrator = 0;
784	>	if( globals->haveResetTime() ){
785	>	info[i].resetTime = globals->getResetTime();
786	>	info[i].resetIntegrator = 1;
787		}
917	–	break;
788
789	+	// check for the temperature set flag
790
791	+	if (globals->haveTempSet())
792	+	info[i].setTemp = globals->getTempSet();
793
794	<	default:
795	<	sprintf( painCave.errMsg,
796	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
797	<	painCave.isFatal = 1;
798	<	simError();
794	>	// check for the extended State init
795	>
796	>	info[i].useInitXSstate = globals->getUseInitXSstate();
797	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
798	>
799		}
800	+
801	+	//setup seed for random number generator
802	+	int seedValue;
803
804	+	if (globals->haveSeed()){
805	+	seedValue = globals->getSeed();
806
807	<	#ifdef IS_MPI
808	<	mpiSim->mpiRefresh();
807	>	if(seedValue / 1E9 == 0){
808	>	sprintf(painCave.errMsg,
809	>	"Seed for sprng library should contain at least 9 digits\n"
810	>	"OOPSE will generate a seed for user\n");
811	>	painCave.isFatal = 0;
812	>	simError();
813	>
814	>	//using seed generated by system instead of invalid seed set by user
815	>	#ifndef IS_MPI
816	>	seedValue = make_sprng_seed();
817	>	#else
818	>	if (worldRank == 0){
819	>	seedValue = make_sprng_seed();
820	>	}
821	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
822	>	#endif
823	>	}
824	>	}//end of if branch of globals->haveSeed()
825	>	else{
826	>
827	>	#ifndef IS_MPI
828	>	seedValue = make_sprng_seed();
829	>	#else
830	>	if (worldRank == 0){
831	>	seedValue = make_sprng_seed();
832	>	}
833	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
834		#endif
835	+	}//end of globals->haveSeed()
836
837	<	// initialize the Fortran
838	<
935	<
936	<	simnfo->refreshSim();
937	<
938	<	if( !strcmp( simnfo->mixingRule, "standard") ){
939	<	the_ff->initForceField( LB_MIXING_RULE );
837	>	for (int i = 0; i < nInfo; i++){
838	>	info[i].setSeed(seedValue);
839		}
941	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
942	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
943	–	}
944	–	else{
945	–	sprintf( painCave.errMsg,
946	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
947	–	simnfo->mixingRule );
948	–	painCave.isFatal = 1;
949	–	simError();
950	–	}
840
952	–
841		#ifdef IS_MPI
842	<	strcpy( checkPointMsg,
955	<	"Successfully intialized the mixingRule for Fortran." );
842	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
843		MPIcheckPoint();
844		#endif // is_mpi
845		}
846
847
848	<	void SimSetup::makeMolecules( void ){
848	>	void SimSetup::finalInfoCheck(void){
849	>	int index;
850	>	int usesDipoles;
851	>	int i;
852
853	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
854	<	molInit info;
965	<	DirectionalAtom* dAtom;
966	<	LinkedAssign* extras;
967	<	LinkedAssign* current_extra;
968	<	AtomStamp* currentAtom;
969	<	BondStamp* currentBond;
970	<	BendStamp* currentBend;
971	<	TorsionStamp* currentTorsion;
853	>	for (i = 0; i < nInfo; i++){
854	>	// check electrostatic parameters
855
856	<	bond_pair* theBonds;
857	<	bend_set* theBends;
858	<	torsion_set* theTorsions;
856	>	index = 0;
857	>	usesDipoles = 0;
858	>	while ((index < info[i].n_atoms) && !usesDipoles){
859	>	usesDipoles = (info[i].atoms[index])->hasDipole();
860	>	index++;
861	>	}
862
863	<
864	<	//init the forceField paramters
863	>	#ifdef IS_MPI
864	>	int myUse = usesDipoles;
865	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
866	>	#endif //is_mpi
867
868	<	the_ff->readParams();
868	>	double theEcr, theEst;
869
870	<
871	<	// init the atoms
870	>	if (globals->getUseRF()){
871	>	info[i].useReactionField = 1;
872
873	<	double ux, uy, uz, u, uSqr;
874	<
875	<	atomOffset = 0;
876	<	excludeOffset = 0;
877	<	for(i=0; i<simnfo->n_mol; i++){
878	<
879	<	stampID = the_molecules[i].getStampID();
880	<
993	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
994	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
995	<	info.nBends    = comp_stamps[stampID]->getNBends();
996	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
997	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
998	<
999	<	info.myAtoms = &the_atoms[atomOffset];
1000	<	info.myExcludes = &the_excludes[excludeOffset];
1001	<	info.myBonds = new Bond*[info.nBonds];
1002	<	info.myBends = new Bend*[info.nBends];
1003	<	info.myTorsions = new Torsion*[info.nTorsions];
1004	<
1005	<	theBonds = new bond_pair[info.nBonds];
1006	<	theBends = new bend_set[info.nBends];
1007	<	theTorsions = new torsion_set[info.nTorsions];
1008	<
1009	<	// make the Atoms
1010	<
1011	<	for(j=0; j<info.nAtoms; j++){
1012	<
1013	<	currentAtom = comp_stamps[stampID]->getAtom( j );
1014	<	if( currentAtom->haveOrientation() ){
1015	<
1016	<	dAtom = new DirectionalAtom(j + atomOffset);
1017	<	simnfo->n_oriented++;
1018	<	info.myAtoms[j] = dAtom;
1019	<
1020	<	ux = currentAtom->getOrntX();
1021	<	uy = currentAtom->getOrntY();
1022	<	uz = currentAtom->getOrntZ();
1023	<
1024	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
1025	<
1026	<	u = sqrt( uSqr );
1027	<	ux = ux / u;
1028	<	uy = uy / u;
1029	<	uz = uz / u;
1030	<
1031	<	dAtom->setSUx( ux );
1032	<	dAtom->setSUy( uy );
1033	<	dAtom->setSUz( uz );
873	>	if (!globals->haveECR()){
874	>	sprintf(painCave.errMsg,
875	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
876	>	"\tOOPSE will use a default value of 15.0 angstroms"
877	>	"\tfor the electrostaticCutoffRadius.\n");
878	>	painCave.isFatal = 0;
879	>	simError();
880	>	theEcr = 15.0;
881		}
882		else{
883	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
883	>	theEcr = globals->getECR();
884		}
1038	–	info.myAtoms[j]->setType( currentAtom->getType() );
1039	–
1040	–	#ifdef IS_MPI
1041	–
1042	–	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
1043	–
1044	–	#endif // is_mpi
1045	–	}
1046	–
1047	–	// make the bonds
1048	–	for(j=0; j<info.nBonds; j++){
1049	–
1050	–	currentBond = comp_stamps[stampID]->getBond( j );
1051	–	theBonds[j].a = currentBond->getA() + atomOffset;
1052	–	theBonds[j].b = currentBond->getB() + atomOffset;
885
886	<	exI = theBonds[j].a;
887	<	exJ = theBonds[j].b;
888	<
889	<	// exclude_I must always be the smaller of the pair
890	<	if( exI > exJ ){
891	<	tempEx = exI;
892	<	exI = exJ;
893	<	exJ = tempEx;
886	>	if (!globals->haveEST()){
887	>	sprintf(painCave.errMsg,
888	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
889	>	"\tOOPSE will use a default value of\n"
890	>	"\t0.05 * electrostaticCutoffRadius\n"
891	>	"\tfor the electrostaticSkinThickness\n");
892	>	painCave.isFatal = 0;
893	>	simError();
894	>	theEst = 0.05 * theEcr;
895		}
896	<	#ifdef IS_MPI
897	<	tempEx = exI;
898	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1066	<	tempEx = exJ;
1067	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1068	<
1069	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1070	<	#else  // isn't MPI
896	>	else{
897	>	theEst = globals->getEST();
898	>	}
899
900	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1073	<	#endif  //is_mpi
1074	<	}
1075	<	excludeOffset += info.nBonds;
900	>	info[i].setDefaultEcr(theEcr, theEst);
901
902	<	//make the bends
903	<	for(j=0; j<info.nBends; j++){
904	<
905	<	currentBend = comp_stamps[stampID]->getBend( j );
906	<	theBends[j].a = currentBend->getA() + atomOffset;
907	<	theBends[j].b = currentBend->getB() + atomOffset;
908	<	theBends[j].c = currentBend->getC() + atomOffset;
1084	<
1085	<	if( currentBend->haveExtras() ){
1086	<
1087	<	extras = currentBend->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	<	theBends[j].ghost =
1097	<	current_extra->getInt() + atomOffset;
1098	<	theBends[j].isGhost = 1;
1099	<	break;
1100	<
1101	<	case 1:
1102	<	theBends[j].ghost =
1103	<	(int)current_extra->getDouble() + atomOffset;
1104	<	theBends[j].isGhost = 1;
1105	<	break;
1106	<
1107	<	default:
1108	<	sprintf( painCave.errMsg,
1109	<	"SimSetup Error: ghostVectorSource was neither a "
1110	<	"double nor an int.\n"
1111	<	"-->Bend[%d] in %s\n",
1112	<	j, comp_stamps[stampID]->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	<	j, comp_stamps[stampID]->getID() );
1125	<	painCave.isFatal = 1;
1126	<	simError();
1127	<	}
1128	<
1129	<	current_extra = current_extra->getNext();
1130	<	}
902	>	if (!globals->haveDielectric()){
903	>	sprintf(painCave.errMsg,
904	>	"SimSetup Error: No Dielectric constant was set.\n"
905	>	"\tYou are trying to use Reaction Field without"
906	>	"\tsetting a dielectric constant!\n");
907	>	painCave.isFatal = 1;
908	>	simError();
909		}
910	<
911	<	if( !theBends[j].isGhost ){
912	<
913	<	exI = theBends[j].a;
914	<	exJ = theBends[j].c;
915	<	}
916	<	else{
910	>	info[i].dielectric = globals->getDielectric();
911	>	}
912	>	else{
913	>	if (usesDipoles){
914	>	if (!globals->haveECR()){
915	>	sprintf(painCave.errMsg,
916	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
917	>	"\tOOPSE will use a default value of 15.0 angstroms"
918	>	"\tfor the electrostaticCutoffRadius.\n");
919	>	painCave.isFatal = 0;
920	>	simError();
921	>	theEcr = 15.0;
922	>	}
923	>	else{
924	>	theEcr = globals->getECR();
925	>	}
926
927	<	exI = theBends[j].a;
928	<	exJ = theBends[j].b;
927	>	if (!globals->haveEST()){
928	>	sprintf(painCave.errMsg,
929	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
930	>	"\tOOPSE will use a default value of\n"
931	>	"\t0.05 * electrostaticCutoffRadius\n"
932	>	"\tfor the electrostaticSkinThickness\n");
933	>	painCave.isFatal = 0;
934	>	simError();
935	>	theEst = 0.05 * theEcr;
936	>	}
937	>	else{
938	>	theEst = globals->getEST();
939	>	}
940	>
941	>	info[i].setDefaultEcr(theEcr, theEst);
942		}
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	–	#ifdef IS_MPI
1151	–	tempEx = exI;
1152	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1153	–	tempEx = exJ;
1154	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1155	–
1156	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1157	–	#else  // isn't MPI
1158	–	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1159	–	#endif  //is_mpi
943		}
944	<	excludeOffset += info.nBends;
1162	<
1163	<	for(j=0; j<info.nTorsions; j++){
1164	<
1165	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1166	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1167	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1168	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1169	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1170	<
1171	<	exI = theTorsions[j].a;
1172	<	exJ = theTorsions[j].d;
1173	<
1174	<	// exclude_I must always be the smaller of the pair
1175	<	if( exI > exJ ){
1176	<	tempEx = exI;
1177	<	exI = exJ;
1178	<	exJ = tempEx;
1179	<	}
944	>	}
945		#ifdef IS_MPI
946	<	tempEx = exI;
947	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
948	<	tempEx = exJ;
949	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
950	<
951	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
952	<	#else  // isn't MPI
1188	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1189	<	#endif  //is_mpi
1190	<	}
1191	<	excludeOffset += info.nTorsions;
946	>	strcpy(checkPointMsg, "post processing checks out");
947	>	MPIcheckPoint();
948	>	#endif // is_mpi
949	>	}
950	>
951	>	void SimSetup::initSystemCoords(void){
952	>	int i;
953
954	<
1194	<	// send the arrays off to the forceField for init.
954	>	char* inName;
955
956	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1197	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1198	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1199	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
956	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
957
958	+	for (i = 0; i < info[0].n_atoms; i++)
959	+	info[0].atoms[i]->setCoords();
960
961	<	the_molecules[i].initialize( info );
961	>	if (globals->haveInitialConfig()){
962	>	InitializeFromFile* fileInit;
963	>	#ifdef IS_MPI // is_mpi
964	>	if (worldRank == 0){
965	>	#endif //is_mpi
966	>	inName = globals->getInitialConfig();
967	>	fileInit = new InitializeFromFile(inName);
968	>	#ifdef IS_MPI
969	>	}
970	>	else
971	>	fileInit = new InitializeFromFile(NULL);
972	>	#endif
973	>	fileInit->readInit(info); // default velocities on
974
975	<
1205	<	atomOffset += info.nAtoms;
1206	<	delete[] theBonds;
1207	<	delete[] theBends;
1208	<	delete[] theTorsions;
975	>	delete fileInit;
976		}
977	+	else{
978	+
979	+	// no init from bass
980	+
981	+	sprintf(painCave.errMsg,
982	+	"Cannot intialize a simulation without an initial configuration file.\n");
983	+	painCave.isFatal = 1;;
984	+	simError();
985	+
986	+	}
987
988		#ifdef IS_MPI
989	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
989	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
990		MPIcheckPoint();
991		#endif // is_mpi
992	+	}
993
1216	–	// clean up the forcefield
1217	–	the_ff->calcRcut();
1218	–	the_ff->cleanMe();
994
995	<	}
995	>	void SimSetup::makeOutNames(void){
996	>	int k;
997
1222	–	void SimSetup::initFromBass( void ){
998
999	<	int i, j, k;
1000	<	int n_cells;
1001	<	double cellx, celly, cellz;
1002	<	double temp1, temp2, temp3;
1228	<	int n_per_extra;
1229	<	int n_extra;
1230	<	int have_extra, done;
999	>	for (k = 0; k < nInfo; k++){
1000	>	#ifdef IS_MPI
1001	>	if (worldRank == 0){
1002	>	#endif // is_mpi
1003
1004	<	temp1 = (double)tot_nmol / 4.0;
1005	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1006	<	temp3 = ceil( temp2 );
1004	>	if (globals->haveFinalConfig()){
1005	>	strcpy(info[k].finalName, globals->getFinalConfig());
1006	>	}
1007	>	else{
1008	>	strcpy(info[k].finalName, inFileName);
1009	>	char* endTest;
1010	>	int nameLength = strlen(info[k].finalName);
1011	>	endTest = &(info[k].finalName[nameLength - 5]);
1012	>	if (!strcmp(endTest, ".bass")){
1013	>	strcpy(endTest, ".eor");
1014	>	}
1015	>	else if (!strcmp(endTest, ".BASS")){
1016	>	strcpy(endTest, ".eor");
1017	>	}
1018	>	else{
1019	>	endTest = &(info[k].finalName[nameLength - 4]);
1020	>	if (!strcmp(endTest, ".bss")){
1021	>	strcpy(endTest, ".eor");
1022	>	}
1023	>	else if (!strcmp(endTest, ".mdl")){
1024	>	strcpy(endTest, ".eor");
1025	>	}
1026	>	else{
1027	>	strcat(info[k].finalName, ".eor");
1028	>	}
1029	>	}
1030	>	}
1031
1032	<	have_extra =0;
1237	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1238	<	have_extra =1;
1032	>	// make the sample and status out names
1033
1034	<	n_cells = (int)temp3 - 1;
1035	<	cellx = simnfo->boxLx / temp3;
1036	<	celly = simnfo->boxLy / temp3;
1037	<	cellz = simnfo->boxLz / temp3;
1038	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1039	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1040	<	n_per_extra = (int)ceil( temp1 );
1034	>	strcpy(info[k].sampleName, inFileName);
1035	>	char* endTest;
1036	>	int nameLength = strlen(info[k].sampleName);
1037	>	endTest = &(info[k].sampleName[nameLength - 5]);
1038	>	if (!strcmp(endTest, ".bass")){
1039	>	strcpy(endTest, ".dump");
1040	>	}
1041	>	else if (!strcmp(endTest, ".BASS")){
1042	>	strcpy(endTest, ".dump");
1043	>	}
1044	>	else{
1045	>	endTest = &(info[k].sampleName[nameLength - 4]);
1046	>	if (!strcmp(endTest, ".bss")){
1047	>	strcpy(endTest, ".dump");
1048	>	}
1049	>	else if (!strcmp(endTest, ".mdl")){
1050	>	strcpy(endTest, ".dump");
1051	>	}
1052	>	else{
1053	>	strcat(info[k].sampleName, ".dump");
1054	>	}
1055	>	}
1056
1057	<	if( n_per_extra > 4){
1058	<	sprintf( painCave.errMsg,
1059	<	"SimSetup error. There has been an error in constructing"
1060	<	" the non-complete lattice.\n" );
1061	<	painCave.isFatal = 1;
1062	<	simError();
1057	>	strcpy(info[k].statusName, inFileName);
1058	>	nameLength = strlen(info[k].statusName);
1059	>	endTest = &(info[k].statusName[nameLength - 5]);
1060	>	if (!strcmp(endTest, ".bass")){
1061	>	strcpy(endTest, ".stat");
1062	>	}
1063	>	else if (!strcmp(endTest, ".BASS")){
1064	>	strcpy(endTest, ".stat");
1065	>	}
1066	>	else{
1067	>	endTest = &(info[k].statusName[nameLength - 4]);
1068	>	if (!strcmp(endTest, ".bss")){
1069	>	strcpy(endTest, ".stat");
1070	>	}
1071	>	else if (!strcmp(endTest, ".mdl")){
1072	>	strcpy(endTest, ".stat");
1073	>	}
1074	>	else{
1075	>	strcat(info[k].statusName, ".stat");
1076	>	}
1077	>	}
1078	>
1079	>	#ifdef IS_MPI
1080	>
1081		}
1082	+	#endif // is_mpi
1083		}
1084	<	else{
1257	<	n_cells = (int)temp3;
1258	<	cellx = simnfo->boxLx / temp3;
1259	<	celly = simnfo->boxLy / temp3;
1260	<	cellz = simnfo->boxLz / temp3;
1261	<	}
1084	>	}
1085
1263	–	current_mol = 0;
1264	–	current_comp_mol = 0;
1265	–	current_comp = 0;
1266	–	current_atom_ndx = 0;
1086
1087	<	for( i=0; i < n_cells ; i++ ){
1088	<	for( j=0; j < n_cells; j++ ){
1270	<	for( k=0; k < n_cells; k++ ){
1087	>	void SimSetup::sysObjectsCreation(void){
1088	>	int i, k;
1089
1090	<	makeElement( i * cellx,
1273	<	j * celly,
1274	<	k * cellz );
1090	>	// create the forceField
1091
1092	<	makeElement( i * cellx + 0.5 * cellx,
1277	<	j * celly + 0.5 * celly,
1278	<	k * cellz );
1092	>	createFF();
1093
1094	<	makeElement( i * cellx,
1281	<	j * celly + 0.5 * celly,
1282	<	k * cellz + 0.5 * cellz );
1094	>	// extract componentList
1095
1096	<	makeElement( i * cellx + 0.5 * cellx,
1097	<	j * celly,
1098	<	k * cellz + 0.5 * cellz );
1099	<	}
1096	>	compList();
1097	>
1098	>	// calc the number of atoms, bond, bends, and torsions
1099	>
1100	>	calcSysValues();
1101	>
1102	>	#ifdef IS_MPI
1103	>	// divide the molecules among the processors
1104	>
1105	>	mpiMolDivide();
1106	>	#endif //is_mpi
1107	>
1108	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1109	>
1110	>	makeSysArrays();
1111	>
1112	>	// make and initialize the molecules (all but atomic coordinates)
1113	>
1114	>	makeMolecules();
1115	>
1116	>	for (k = 0; k < nInfo; k++){
1117	>	info[k].identArray = new int[info[k].n_atoms];
1118	>	for (i = 0; i < info[k].n_atoms; i++){
1119	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1120		}
1121		}
1122	+	}
1123
1291	–	if( have_extra ){
1292	–	done = 0;
1124
1125	<	int start_ndx;
1126	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1127	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1125	>	void SimSetup::createFF(void){
1126	>	switch (ffCase){
1127	>	case FF_DUFF:
1128	>	the_ff = new DUFF();
1129	>	break;
1130
1131	<	if( i < n_cells ){
1131	>	case FF_LJ:
1132	>	the_ff = new LJFF();
1133	>	break;
1134
1135	<	if( j < n_cells ){
1136	<	start_ndx = n_cells;
1137	<	}
1303	<	else start_ndx = 0;
1304	<	}
1305	<	else start_ndx = 0;
1135	>	case FF_EAM:
1136	>	the_ff = new EAM_FF();
1137	>	break;
1138
1139	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1139	>	default:
1140	>	sprintf(painCave.errMsg,
1141	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1142	>	painCave.isFatal = 1;
1143	>	simError();
1144	>	}
1145
1146	<	makeElement( i * cellx,
1147	<	j * celly,
1148	<	k * cellz );
1149	<	done = ( current_mol >= tot_nmol );
1146	>	#ifdef IS_MPI
1147	>	strcpy(checkPointMsg, "ForceField creation successful");
1148	>	MPIcheckPoint();
1149	>	#endif // is_mpi
1150	>	}
1151
1314	–	if( !done && n_per_extra > 1 ){
1315	–	makeElement( i * cellx + 0.5 * cellx,
1316	–	j * celly + 0.5 * celly,
1317	–	k * cellz );
1318	–	done = ( current_mol >= tot_nmol );
1319	–	}
1152
1153	<	if( !done && n_per_extra > 2){
1154	<	makeElement( i * cellx,
1155	<	j * celly + 0.5 * celly,
1156	<	k * cellz + 0.5 * cellz );
1157	<	done = ( current_mol >= tot_nmol );
1158	<	}
1153	>	void SimSetup::compList(void){
1154	>	int i;
1155	>	char* id;
1156	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1157	>	LinkedMolStamp* currentStamp = NULL;
1158	>	comp_stamps = new MoleculeStamp * [n_components];
1159
1160	<	if( !done && n_per_extra > 3){
1161	<	makeElement( i * cellx + 0.5 * cellx,
1162	<	j * celly,
1163	<	k * cellz + 0.5 * cellz );
1164	<	done = ( current_mol >= tot_nmol );
1165	<	}
1166	<	}
1160	>	// make an array of molecule stamps that match the components used.
1161	>	// also extract the used stamps out into a separate linked list
1162	>
1163	>	for (i = 0; i < nInfo; i++){
1164	>	info[i].nComponents = n_components;
1165	>	info[i].componentsNmol = components_nmol;
1166	>	info[i].compStamps = comp_stamps;
1167	>	info[i].headStamp = headStamp;
1168	>	}
1169	>
1170	>
1171	>	for (i = 0; i < n_components; i++){
1172	>	id = the_components[i]->getType();
1173	>	comp_stamps[i] = NULL;
1174	>
1175	>	// check to make sure the component isn't already in the list
1176	>
1177	>	comp_stamps[i] = headStamp->match(id);
1178	>	if (comp_stamps[i] == NULL){
1179	>	// extract the component from the list;
1180	>
1181	>	currentStamp = stamps->extractMolStamp(id);
1182	>	if (currentStamp == NULL){
1183	>	sprintf(painCave.errMsg,
1184	>	"SimSetup error: Component \"%s\" was not found in the "
1185	>	"list of declared molecules\n",
1186	>	id);
1187	>	painCave.isFatal = 1;
1188	>	simError();
1189		}
1190	+
1191	+	headStamp->add(currentStamp);
1192	+	comp_stamps[i] = headStamp->match(id);
1193		}
1194		}
1195
1196	+	#ifdef IS_MPI
1197	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1198	+	MPIcheckPoint();
1199	+	#endif // is_mpi
1200	+	}
1201
1202	<	for( i=0; i<simnfo->n_atoms; i++ ){
1203	<	simnfo->atoms[i]->set_vx( 0.0 );
1204	<	simnfo->atoms[i]->set_vy( 0.0 );
1205	<	simnfo->atoms[i]->set_vz( 0.0 );
1202	>	void SimSetup::calcSysValues(void){
1203	>	int i;
1204	>
1205	>	int* molMembershipArray;
1206	>
1207	>	tot_atoms = 0;
1208	>	tot_bonds = 0;
1209	>	tot_bends = 0;
1210	>	tot_torsions = 0;
1211	>	for (i = 0; i < n_components; i++){
1212	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1213	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1214	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1215	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1216		}
1345	–	}
1217
1218	<	void SimSetup::makeElement( double x, double y, double z ){
1218	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1219	>	molMembershipArray = new int[tot_atoms];
1220
1221	<	int k;
1222	<	AtomStamp* current_atom;
1223	<	DirectionalAtom* dAtom;
1224	<	double rotMat[3][3];
1221	>	for (i = 0; i < nInfo; i++){
1222	>	info[i].n_atoms = tot_atoms;
1223	>	info[i].n_bonds = tot_bonds;
1224	>	info[i].n_bends = tot_bends;
1225	>	info[i].n_torsions = tot_torsions;
1226	>	info[i].n_SRI = tot_SRI;
1227	>	info[i].n_mol = tot_nmol;
1228
1229	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1229	>	info[i].molMembershipArray = molMembershipArray;
1230	>	}
1231	>	}
1232
1233	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1357	<	if( !current_atom->havePosition() ){
1358	<	sprintf( painCave.errMsg,
1359	<	"SimSetup:initFromBass error.\n"
1360	<	"\tComponent %s, atom %s does not have a position specified.\n"
1361	<	"\tThe initialization routine is unable to give a start"
1362	<	" position.\n",
1363	<	comp_stamps[current_comp]->getID(),
1364	<	current_atom->getType() );
1365	<	painCave.isFatal = 1;
1366	<	simError();
1367	<	}
1233	>	#ifdef IS_MPI
1234
1235	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1236	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1237	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1235	>	void SimSetup::mpiMolDivide(void){
1236	>	int i, j, k;
1237	>	int localMol, allMol;
1238	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1239
1240	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1240	>	mpiSim = new mpiSimulation(info);
1241
1242	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1242	>	globalIndex = mpiSim->divideLabor();
1243
1244	<	rotMat[0][0] = 1.0;
1378	<	rotMat[0][1] = 0.0;
1379	<	rotMat[0][2] = 0.0;
1244	>	// set up the local variables
1245
1246	<	rotMat[1][0] = 0.0;
1247	<	rotMat[1][1] = 1.0;
1383	<	rotMat[1][2] = 0.0;
1246	>	mol2proc = mpiSim->getMolToProcMap();
1247	>	molCompType = mpiSim->getMolComponentType();
1248
1249	<	rotMat[2][0] = 0.0;
1250	<	rotMat[2][1] = 0.0;
1251	<	rotMat[2][2] = 1.0;
1249	>	allMol = 0;
1250	>	localMol = 0;
1251	>	local_atoms = 0;
1252	>	local_bonds = 0;
1253	>	local_bends = 0;
1254	>	local_torsions = 0;
1255	>	globalAtomIndex = 0;
1256
1257	<	dAtom->setA( rotMat );
1257	>
1258	>	for (i = 0; i < n_components; i++){
1259	>	for (j = 0; j < components_nmol[i]; j++){
1260	>	if (mol2proc[allMol] == worldRank){
1261	>	local_atoms += comp_stamps[i]->getNAtoms();
1262	>	local_bonds += comp_stamps[i]->getNBonds();
1263	>	local_bends += comp_stamps[i]->getNBends();
1264	>	local_torsions += comp_stamps[i]->getNTorsions();
1265	>	localMol++;
1266	>	}
1267	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1268	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1269	>	globalAtomIndex++;
1270	>	}
1271	>
1272	>	allMol++;
1273		}
1274	+	}
1275	+	local_SRI = local_bonds + local_bends + local_torsions;
1276
1277	<	current_atom_ndx++;
1277	>	info[0].n_atoms = mpiSim->getMyNlocal();
1278	>
1279	>	if (local_atoms != info[0].n_atoms){
1280	>	sprintf(painCave.errMsg,
1281	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1282	>	"\tlocalAtom (%d) are not equal.\n",
1283	>	info[0].n_atoms, local_atoms);
1284	>	painCave.isFatal = 1;
1285	>	simError();
1286		}
1287
1288	<	current_mol++;
1289	<	current_comp_mol++;
1288	>	info[0].n_bonds = local_bonds;
1289	>	info[0].n_bends = local_bends;
1290	>	info[0].n_torsions = local_torsions;
1291	>	info[0].n_SRI = local_SRI;
1292	>	info[0].n_mol = localMol;
1293
1294	<	if( current_comp_mol >= components_nmol[current_comp] ){
1294	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1295	>	MPIcheckPoint();
1296	>	}
1297
1298	<	current_comp_mol = 0;
1299	<	current_comp++;
1298	>	#endif // is_mpi
1299	>
1300	>
1301	>	void SimSetup::makeSysArrays(void){
1302	>
1303	>	#ifndef IS_MPI
1304	>	int k, j;
1305	>	#endif // is_mpi
1306	>	int i, l;
1307	>
1308	>	Atom** the_atoms;
1309	>	Molecule* the_molecules;
1310	>	Exclude** the_excludes;
1311	>
1312	>
1313	>	for (l = 0; l < nInfo; l++){
1314	>	// create the atom and short range interaction arrays
1315	>
1316	>	the_atoms = new Atom * [info[l].n_atoms];
1317	>	the_molecules = new Molecule[info[l].n_mol];
1318	>	int molIndex;
1319	>
1320	>	// initialize the molecule's stampID's
1321	>
1322	>	#ifdef IS_MPI
1323	>
1324	>
1325	>	molIndex = 0;
1326	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1327	>	if (mol2proc[i] == worldRank){
1328	>	the_molecules[molIndex].setStampID(molCompType[i]);
1329	>	the_molecules[molIndex].setMyIndex(molIndex);
1330	>	the_molecules[molIndex].setGlobalIndex(i);
1331	>	molIndex++;
1332	>	}
1333	>	}
1334	>
1335	>	#else // is_mpi
1336	>
1337	>	molIndex = 0;
1338	>	globalAtomIndex = 0;
1339	>	for (i = 0; i < n_components; i++){
1340	>	for (j = 0; j < components_nmol[i]; j++){
1341	>	the_molecules[molIndex].setStampID(i);
1342	>	the_molecules[molIndex].setMyIndex(molIndex);
1343	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1344	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1345	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1346	>	globalAtomIndex++;
1347	>	}
1348	>	molIndex++;
1349	>	}
1350	>	}
1351	>
1352	>
1353	>	#endif // is_mpi
1354	>
1355	>
1356	>	if (info[l].n_SRI){
1357	>	Exclude::createArray(info[l].n_SRI);
1358	>	the_excludes = new Exclude * [info[l].n_SRI];
1359	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1360	>	the_excludes[ex] = new Exclude(ex);
1361	>	}
1362	>	info[l].globalExcludes = new int;
1363	>	info[l].n_exclude = info[l].n_SRI;
1364	>	}
1365	>	else{
1366	>	Exclude::createArray(1);
1367	>	the_excludes = new Exclude * ;
1368	>	the_excludes[0] = new Exclude(0);
1369	>	the_excludes[0]->setPair(0, 0);
1370	>	info[l].globalExcludes = new int;
1371	>	info[l].globalExcludes[0] = 0;
1372	>	info[l].n_exclude = 0;
1373	>	}
1374	>
1375	>	// set the arrays into the SimInfo object
1376	>
1377	>	info[l].atoms = the_atoms;
1378	>	info[l].molecules = the_molecules;
1379	>	info[l].nGlobalExcludes = 0;
1380	>	info[l].excludes = the_excludes;
1381	>
1382	>	the_ff->setSimInfo(info);
1383		}
1384		}
1385	+
1386	+	void SimSetup::makeIntegrator(void){
1387	+	int k;
1388	+
1389	+	NVE<RealIntegrator>* myNVE = NULL;
1390	+	NVT<RealIntegrator>* myNVT = NULL;
1391	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1392	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1393	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1394	+
1395	+	for (k = 0; k < nInfo; k++){
1396	+	switch (ensembleCase){
1397	+	case NVE_ENS:
1398	+	if (globals->haveZconstraints()){
1399	+	setupZConstraint(info[k]);
1400	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1401	+	}
1402	+	else{
1403	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1404	+	}
1405	+
1406	+	info->the_integrator = myNVE;
1407	+	break;
1408	+
1409	+	case NVT_ENS:
1410	+	if (globals->haveZconstraints()){
1411	+	setupZConstraint(info[k]);
1412	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1413	+	}
1414	+	else
1415	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1416	+
1417	+	myNVT->setTargetTemp(globals->getTargetTemp());
1418	+
1419	+	if (globals->haveTauThermostat())
1420	+	myNVT->setTauThermostat(globals->getTauThermostat());
1421	+	else{
1422	+	sprintf(painCave.errMsg,
1423	+	"SimSetup error: If you use the NVT\n"
1424	+	"\tensemble, you must set tauThermostat.\n");
1425	+	painCave.isFatal = 1;
1426	+	simError();
1427	+	}
1428	+
1429	+	info->the_integrator = myNVT;
1430	+	break;
1431	+
1432	+	case NPTi_ENS:
1433	+	if (globals->haveZconstraints()){
1434	+	setupZConstraint(info[k]);
1435	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1436	+	}
1437	+	else
1438	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1439	+
1440	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1441	+
1442	+	if (globals->haveTargetPressure())
1443	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1444	+	else{
1445	+	sprintf(painCave.errMsg,
1446	+	"SimSetup error: If you use a constant pressure\n"
1447	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1448	+	painCave.isFatal = 1;
1449	+	simError();
1450	+	}
1451	+
1452	+	if (globals->haveTauThermostat())
1453	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1454	+	else{
1455	+	sprintf(painCave.errMsg,
1456	+	"SimSetup error: If you use an NPT\n"
1457	+	"\tensemble, you must set tauThermostat.\n");
1458	+	painCave.isFatal = 1;
1459	+	simError();
1460	+	}
1461	+
1462	+	if (globals->haveTauBarostat())
1463	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1464	+	else{
1465	+	sprintf(painCave.errMsg,
1466	+	"SimSetup error: If you use an NPT\n"
1467	+	"\tensemble, you must set tauBarostat.\n");
1468	+	painCave.isFatal = 1;
1469	+	simError();
1470	+	}
1471	+
1472	+	info->the_integrator = myNPTi;
1473	+	break;
1474	+
1475	+	case NPTf_ENS:
1476	+	if (globals->haveZconstraints()){
1477	+	setupZConstraint(info[k]);
1478	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1479	+	}
1480	+	else
1481	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1482	+
1483	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1484	+
1485	+	if (globals->haveTargetPressure())
1486	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1487	+	else{
1488	+	sprintf(painCave.errMsg,
1489	+	"SimSetup error: If you use a constant pressure\n"
1490	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1491	+	painCave.isFatal = 1;
1492	+	simError();
1493	+	}
1494	+
1495	+	if (globals->haveTauThermostat())
1496	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1497	+
1498	+	else{
1499	+	sprintf(painCave.errMsg,
1500	+	"SimSetup error: If you use an NPT\n"
1501	+	"\tensemble, you must set tauThermostat.\n");
1502	+	painCave.isFatal = 1;
1503	+	simError();
1504	+	}
1505	+
1506	+	if (globals->haveTauBarostat())
1507	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1508	+
1509	+	else{
1510	+	sprintf(painCave.errMsg,
1511	+	"SimSetup error: If you use an NPT\n"
1512	+	"\tensemble, you must set tauBarostat.\n");
1513	+	painCave.isFatal = 1;
1514	+	simError();
1515	+	}
1516	+
1517	+	info->the_integrator = myNPTf;
1518	+	break;
1519	+
1520	+	case NPTxyz_ENS:
1521	+	if (globals->haveZconstraints()){
1522	+	setupZConstraint(info[k]);
1523	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1524	+	}
1525	+	else
1526	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1527	+
1528	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1529	+
1530	+	if (globals->haveTargetPressure())
1531	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1532	+	else{
1533	+	sprintf(painCave.errMsg,
1534	+	"SimSetup error: If you use a constant pressure\n"
1535	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1536	+	painCave.isFatal = 1;
1537	+	simError();
1538	+	}
1539	+
1540	+	if (globals->haveTauThermostat())
1541	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1542	+	else{
1543	+	sprintf(painCave.errMsg,
1544	+	"SimSetup error: If you use an NPT\n"
1545	+	"\tensemble, you must set tauThermostat.\n");
1546	+	painCave.isFatal = 1;
1547	+	simError();
1548	+	}
1549	+
1550	+	if (globals->haveTauBarostat())
1551	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1552	+	else{
1553	+	sprintf(painCave.errMsg,
1554	+	"SimSetup error: If you use an NPT\n"
1555	+	"\tensemble, you must set tauBarostat.\n");
1556	+	painCave.isFatal = 1;
1557	+	simError();
1558	+	}
1559	+
1560	+	info->the_integrator = myNPTxyz;
1561	+	break;
1562	+
1563	+	default:
1564	+	sprintf(painCave.errMsg,
1565	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1566	+	painCave.isFatal = 1;
1567	+	simError();
1568	+	}
1569	+	}
1570	+	}
1571	+
1572	+	void SimSetup::initFortran(void){
1573	+	info[0].refreshSim();
1574	+
1575	+	if (!strcmp(info[0].mixingRule, "standard")){
1576	+	the_ff->initForceField(LB_MIXING_RULE);
1577	+	}
1578	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1579	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1580	+	}
1581	+	else{
1582	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1583	+	info[0].mixingRule);
1584	+	painCave.isFatal = 1;
1585	+	simError();
1586	+	}
1587	+
1588	+
1589	+	#ifdef IS_MPI
1590	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1591	+	MPIcheckPoint();
1592	+	#endif // is_mpi
1593	+	}
1594	+
1595	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1596	+	int nZConstraints;
1597	+	ZconStamp** zconStamp;
1598	+
1599	+	if (globals->haveZconstraintTime()){
1600	+	//add sample time of z-constraint  into SimInfo's property list
1601	+	DoubleData* zconsTimeProp = new DoubleData();
1602	+	zconsTimeProp->setID(ZCONSTIME_ID);
1603	+	zconsTimeProp->setData(globals->getZconsTime());
1604	+	theInfo.addProperty(zconsTimeProp);
1605	+	}
1606	+	else{
1607	+	sprintf(painCave.errMsg,
1608	+	"ZConstraint error: If you use a ZConstraint,\n"
1609	+	"\tyou must set zconsTime.\n");
1610	+	painCave.isFatal = 1;
1611	+	simError();
1612	+	}
1613	+
1614	+	//push zconsTol into siminfo, if user does not specify
1615	+	//value for zconsTol, a default value will be used
1616	+	DoubleData* zconsTol = new DoubleData();
1617	+	zconsTol->setID(ZCONSTOL_ID);
1618	+	if (globals->haveZconsTol()){
1619	+	zconsTol->setData(globals->getZconsTol());
1620	+	}
1621	+	else{
1622	+	double defaultZConsTol = 0.01;
1623	+	sprintf(painCave.errMsg,
1624	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1625	+	"\tOOPSE will use a default value of %f.\n"
1626	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1627	+	defaultZConsTol);
1628	+	painCave.isFatal = 0;
1629	+	simError();
1630	+
1631	+	zconsTol->setData(defaultZConsTol);
1632	+	}
1633	+	theInfo.addProperty(zconsTol);
1634	+
1635	+	//set Force Subtraction Policy
1636	+	StringData* zconsForcePolicy = new StringData();
1637	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1638	+
1639	+	if (globals->haveZconsForcePolicy()){
1640	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1641	+	}
1642	+	else{
1643	+	sprintf(painCave.errMsg,
1644	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1645	+	"\tOOPSE will use PolicyByMass.\n"
1646	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1647	+	painCave.isFatal = 0;
1648	+	simError();
1649	+	zconsForcePolicy->setData("BYMASS");
1650	+	}
1651	+
1652	+	theInfo.addProperty(zconsForcePolicy);
1653	+
1654	+	//Determine the name of ouput file and add it into SimInfo's property list
1655	+	//Be careful, do not use inFileName, since it is a pointer which
1656	+	//point to a string at master node, and slave nodes do not contain that string
1657	+
1658	+	string zconsOutput(theInfo.finalName);
1659	+
1660	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1661	+
1662	+	StringData* zconsFilename = new StringData();
1663	+	zconsFilename->setID(ZCONSFILENAME_ID);
1664	+	zconsFilename->setData(zconsOutput);
1665	+
1666	+	theInfo.addProperty(zconsFilename);
1667	+
1668	+	//setup index, pos and other parameters of z-constraint molecules
1669	+	nZConstraints = globals->getNzConstraints();
1670	+	theInfo.nZconstraints = nZConstraints;
1671	+
1672	+	zconStamp = globals->getZconStamp();
1673	+	ZConsParaItem tempParaItem;
1674	+
1675	+	ZConsParaData* zconsParaData = new ZConsParaData();
1676	+	zconsParaData->setID(ZCONSPARADATA_ID);
1677	+
1678	+	for (int i = 0; i < nZConstraints; i++){
1679	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1680	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1681	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1682	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1683	+
1684	+	zconsParaData->addItem(tempParaItem);
1685	+	}
1686	+
1687	+	//check the uniqueness of index
1688	+	if(!zconsParaData->isIndexUnique()){
1689	+	sprintf(painCave.errMsg,
1690	+	"ZConstraint Error: molIndex is not unique!\n");
1691	+	painCave.isFatal = 1;
1692	+	simError();
1693	+	}
1694	+
1695	+	//sort the parameters by index of molecules
1696	+	zconsParaData->sortByIndex();
1697	+
1698	+	//push data into siminfo, therefore, we can retrieve later
1699	+	theInfo.addProperty(zconsParaData);
1700	+	}

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