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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 555 by mmeineke, Tue Jun 17 21:56:15 2003 UTC vs.
Revision 1187 by chrisfen, Sat May 22 18:16:18 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"
12	+	#include "RigidBody.hpp"
13	+	//#include "ConjugateMinimizer.hpp"
14	+	#include "OOPSEMinimizer.hpp"
15
16		#ifdef IS_MPI
17		#include "mpiBASS.h"
18		#include "mpiSimulation.hpp"
19		#endif
20
21	+	// some defines for ensemble and Forcefield  cases
22	+
23	+	#define NVE_ENS        0
24	+	#define NVT_ENS        1
25	+	#define NPTi_ENS       2
26	+	#define NPTf_ENS       3
27	+	#define NPTxyz_ENS     4
28	+
29	+
30	+	#define FF_DUFF  0
31	+	#define FF_LJ    1
32	+	#define FF_EAM   2
33	+	#define FF_H2O   3
34	+
35	+	using namespace std;
36	+
37	+	/**
38	+	* Check whether dividend is divisble by divisor or not
39	+	*/
40	+	bool isDivisible(double dividend, double divisor){
41	+	double tolerance = 0.000001;
42	+	double quotient;
43	+	double diff;
44	+	int intQuotient;
45	+
46	+	quotient = dividend / divisor;
47	+
48	+	if (quotient < 0)
49	+	quotient = -quotient;
50	+
51	+	intQuotient = int (quotient + tolerance);
52	+
53	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
54	+
55	+	if (diff <= tolerance)
56	+	return true;
57	+	else
58	+	return false;
59	+	}
60	+
61		SimSetup::SimSetup(){
62	+
63	+	initSuspend = false;
64	+	isInfoArray = 0;
65	+	nInfo = 1;
66	+
67		stamps = new MakeStamps();
68		globals = new Globals();
69	<
69	>
70	>
71		#ifdef IS_MPI
72	<	strcpy( checkPointMsg, "SimSetup creation successful" );
72	>	strcpy(checkPointMsg, "SimSetup creation successful");
73		MPIcheckPoint();
74		#endif // IS_MPI
75		}
#	Line 27 | Line 79 | SimSetup::~SimSetup(){
79		delete globals;
80		}
81
82	<	void SimSetup::parseFile( char* fileName ){
82	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
83	>	info = the_info;
84	>	nInfo = theNinfo;
85	>	isInfoArray = 1;
86	>	initSuspend = true;
87	>	}
88
89	+
90	+	void SimSetup::parseFile(char* fileName){
91		#ifdef IS_MPI
92	<	if( worldRank == 0 ){
92	>	if (worldRank == 0){
93		#endif // is_mpi
94	<
94	>
95		inFileName = fileName;
96	<	set_interface_stamps( stamps, globals );
97	<
96	>	set_interface_stamps(stamps, globals);
97	>
98		#ifdef IS_MPI
99		mpiEventInit();
100		#endif
101
102	<	yacc_BASS( fileName );
102	>	yacc_BASS(fileName);
103
104		#ifdef IS_MPI
105		throwMPIEvent(NULL);
106		}
107	<	else receiveParse();
107	>	else{
108	>	receiveParse();
109	>	}
110		#endif
111
112		}
113
114		#ifdef IS_MPI
115		void SimSetup::receiveParse(void){
116	<
117	<	set_interface_stamps( stamps, globals );
118	<	mpiEventInit();
119	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
116	>	set_interface_stamps(stamps, globals);
117	>	mpiEventInit();
118	>	MPIcheckPoint();
119	>	mpiEventLoop();
120		}
121
122		#endif // is_mpi
123
124	<	void SimSetup::createSim( void ){
124	>	void SimSetup::createSim(void){
125
126	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	ExtendedSystem* the_extendedsystem;
70	<	int i, j, k, globalAtomIndex;
126	>	// gather all of the information from the Bass file
127
128	<	// get the stamps and globals;
73	<	the_stamps = stamps;
74	<	the_globals = globals;
128	>	gatherInfo();
129
130	<	// set the easy ones first
77	<	simnfo->target_temp = the_globals->getTargetTemp();
78	<	simnfo->dt = the_globals->getDt();
79	<	simnfo->run_time = the_globals->getRunTime();
130	>	// creation of complex system objects
131
132	<	// get the ones we know are there, yet still may need some work.
82	<	n_components = the_globals->getNComponents();
83	<	strcpy( force_field, the_globals->getForceField() );
132	>	sysObjectsCreation();
133
134	<	// get the ensemble and set up an extended system if we need it:
86	<	strcpy( ensemble, the_globals->getEnsemble() );
87	<	if( !strcasecmp( ensemble, "NPT" ) ) {
88	<	the_extendedsystem = new ExtendedSystem( simnfo );
89	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
90	<	if (the_globals->haveTargetPressure())
91	<	the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
92	<	else {
93	<	sprintf( painCave.errMsg,
94	<	"SimSetup error: If you use the constant pressure\n"
95	<	"    ensemble, you must set targetPressure.\n"
96	<	"    This was found in the BASS file.\n");
97	<	painCave.isFatal = 1;
98	<	simError();
99	<	}
134	>	// check on the post processing info
135
136	<	if (the_globals->haveTauThermostat())
102	<	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
103	<	else if (the_globals->haveQmass())
104	<	the_extendedsystem->setQmass(the_globals->getQmass());
105	<	else {
106	<	sprintf( painCave.errMsg,
107	<	"SimSetup error: If you use one of the constant temperature\n"
108	<	"    ensembles, you must set either tauThermostat or qMass.\n"
109	<	"    Neither of these was found in the BASS file.\n");
110	<	painCave.isFatal = 1;
111	<	simError();
112	<	}
136	>	finalInfoCheck();
137
138	<	if (the_globals->haveTauBarostat())
115	<	the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
116	<	else {
117	<	sprintf( painCave.errMsg,
118	<	"SimSetup error: If you use the constant pressure\n"
119	<	"    ensemble, you must set tauBarostat.\n"
120	<	"    This was found in the BASS file.\n");
121	<	painCave.isFatal = 1;
122	<	simError();
123	<	}
138	>	// initialize the system coordinates
139
140	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
141	<	the_extendedsystem = new ExtendedSystem( simnfo );
127	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
140	>	if ( !initSuspend ){
141	>	initSystemCoords();
142
143	<	if (the_globals->haveTauThermostat())
144	<	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
131	<	else if (the_globals->haveQmass())
132	<	the_extendedsystem->setQmass(the_globals->getQmass());
133	<	else {
134	<	sprintf( painCave.errMsg,
135	<	"SimSetup error: If you use one of the constant temperature\n"
136	<	"    ensembles, you must set either tauThermostat or qMass.\n"
137	<	"    Neither of these was found in the BASS file.\n");
138	<	painCave.isFatal = 1;
139	<	simError();
140	<	}
141	<
142	<	} else if ( !strcasecmp( ensemble, "NVE") ) {
143	<	} else {
144	<	sprintf( painCave.errMsg,
145	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
146	<	"reverting to NVE for this simulation.\n",
147	<	ensemble );
148	<	painCave.isFatal = 0;
149	<	simError();
150	<	strcpy( ensemble, "NVE" );
143	>	if( !(globals->getUseInitTime()) )
144	>	info[0].currentTime = 0.0;
145		}
152	–	strcpy( simnfo->ensemble, ensemble );
146
147	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
155	<	simnfo->usePBC = the_globals->getPBC();
156	<
157	<	int usesDipoles = 0;
158	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
159	<	the_ff = new TraPPE_ExFF();
160	<	usesDipoles = 1;
161	<	}
162	<	else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
163	<	else{
164	<	sprintf( painCave.errMsg,
165	<	"SimSetup Error. Unrecognized force field -> %s\n",
166	<	force_field );
167	<	painCave.isFatal = 1;
168	<	simError();
169	<	}
147	>	// make the output filenames
148
149	+	makeOutNames();
150	+
151		#ifdef IS_MPI
152	<	strcpy( checkPointMsg, "ForceField creation successful" );
153	<	MPIcheckPoint();
174	<	#endif // is_mpi
152	>	mpiSim->mpiRefresh();
153	>	#endif
154
155	<
155	>	// initialize the Fortran
156
157	<	// get the components and calculate the tot_nMol and indvidual n_mol
179	<	the_components = the_globals->getComponents();
180	<	components_nmol = new int[n_components];
181	<	comp_stamps = new MoleculeStamp*[n_components];
157	>	initFortran();
158
159	<	if( !the_globals->haveNMol() ){
160	<	// we don't have the total number of molecules, so we assume it is
161	<	// given in each component
159	>	if (globals->haveMinimizer())
160	>	// make minimizer
161	>	makeMinimizer();
162	>	else
163	>	// make the integrator
164	>	makeIntegrator();
165
166	<	tot_nmol = 0;
188	<	for( i=0; i<n_components; i++ ){
166	>	}
167
190	–	if( !the_components[i]->haveNMol() ){
191	–	// we have a problem
192	–	sprintf( painCave.errMsg,
193	–	"SimSetup Error. No global NMol or component NMol"
194	–	" given. Cannot calculate the number of atoms.\n" );
195	–	painCave.isFatal = 1;
196	–	simError();
197	–	}
168
169	<	tot_nmol += the_components[i]->getNMol();
170	<	components_nmol[i] = the_components[i]->getNMol();
171	<	}
172	<	}
173	<	else{
174	<	sprintf( painCave.errMsg,
175	<	"SimSetup error.\n"
176	<	"\tSorry, the ability to specify total"
177	<	" nMols and then give molfractions in the components\n"
178	<	"\tis not currently supported."
179	<	" Please give nMol in the components.\n" );
180	<	painCave.isFatal = 1;
181	<	simError();
182	<
183	<
184	<	//     tot_nmol = the_globals->getNMol();
185	<
186	<	//   //we have the total number of molecules, now we check for molfractions
187	<	//     for( i=0; i<n_components; i++ ){
188	<
189	<	//       if( !the_components[i]->haveMolFraction() ){
220	<
221	<	//  if( !the_components[i]->haveNMol() ){
222	<	//    //we have a problem
223	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
224	<	//              << " nMol was given in component
225	<
226	<	}
169	>	void SimSetup::makeMolecules(void){
170	>	int i, j, k;
171	>	int exI, exJ, exK, exL, slI, slJ;
172	>	int tempI, tempJ, tempK, tempL;
173	>	int molI;
174	>	int stampID, atomOffset, rbOffset;
175	>	molInit molInfo;
176	>	DirectionalAtom* dAtom;
177	>	RigidBody* myRB;
178	>	StuntDouble* mySD;
179	>	LinkedAssign* extras;
180	>	LinkedAssign* current_extra;
181	>	AtomStamp* currentAtom;
182	>	BondStamp* currentBond;
183	>	BendStamp* currentBend;
184	>	TorsionStamp* currentTorsion;
185	>	RigidBodyStamp* currentRigidBody;
186	>	CutoffGroupStamp* currentCutoffGroup;
187	>	CutoffGroup* myCutoffGroup;
188	>	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
189	>	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
190
191	<	#ifdef IS_MPI
192	<	strcpy( checkPointMsg, "Have the number of components" );
193	<	MPIcheckPoint();
194	<	#endif // is_mpi
191	>	bond_pair* theBonds;
192	>	bend_set* theBends;
193	>	torsion_set* theTorsions;
194	>
195	>	set<int> skipList;
196	>
197	>	double phi, theta, psi;
198	>	char* molName;
199	>	char rbName[100];
200	>
201	>	//init the forceField paramters
202	>
203	>	the_ff->readParams();
204	>
205	>	// init the atoms
206
207	<	// make an array of molecule stamps that match the components used.
234	<	// also extract the used stamps out into a separate linked list
207	>	int nMembers, nNew, rb1, rb2;
208
209	<	simnfo->nComponents = n_components;
210	<	simnfo->componentsNmol = components_nmol;
238	<	simnfo->compStamps = comp_stamps;
239	<	simnfo->headStamp = new LinkedMolStamp();
240	<
241	<	char* id;
242	<	LinkedMolStamp* headStamp = simnfo->headStamp;
243	<	LinkedMolStamp* currentStamp = NULL;
244	<	for( i=0; i<n_components; i++ ){
209	>	for (k = 0; k < nInfo; k++){
210	>	the_ff->setSimInfo(&(info[k]));
211
212	<	id = the_components[i]->getType();
247	<	comp_stamps[i] = NULL;
248	<
249	<	// check to make sure the component isn't already in the list
212	>	atomOffset = 0;
213
214	<	comp_stamps[i] = headStamp->match( id );
215	<	if( comp_stamps[i] == NULL ){
216	<
254	<	// extract the component from the list;
255	<
256	<	currentStamp = the_stamps->extractMolStamp( id );
257	<	if( currentStamp == NULL ){
258	<	sprintf( painCave.errMsg,
259	<	"SimSetup error: Component \"%s\" was not found in the "
260	<	"list of declared molecules\n",
261	<	id );
262	<	painCave.isFatal = 1;
263	<	simError();
264	<	}
265	<
266	<	headStamp->add( currentStamp );
267	<	comp_stamps[i] = headStamp->match( id );
268	<	}
269	<	}
214	>	for (i = 0; i < info[k].n_mol; i++){
215	>	stampID = info[k].molecules[i].getStampID();
216	>	molName = comp_stamps[stampID]->getID();
217
218	<	#ifdef IS_MPI
219	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
220	<	MPIcheckPoint();
221	<	#endif // is_mpi
222	<
218	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
219	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
220	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
221	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
222	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
223
224	+	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
225	+
226	+	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
227
228	+	if (molInfo.nBonds > 0)
229	+	molInfo.myBonds = new Bond*[molInfo.nBonds];
230	+	else
231	+	molInfo.myBonds = NULL;
232
233	<	// caclulate the number of atoms, bonds, bends and torsions
233	>	if (molInfo.nBends > 0)
234	>	molInfo.myBends = new Bend*[molInfo.nBends];
235	>	else
236	>	molInfo.myBends = NULL;
237
238	<	tot_atoms = 0;
239	<	tot_bonds = 0;
240	<	tot_bends = 0;
241	<	tot_torsions = 0;
285	<	for( i=0; i<n_components; i++ ){
286	<
287	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
288	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
289	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
290	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
291	<	}
238	>	if (molInfo.nTorsions > 0)
239	>	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
240	>	else
241	>	molInfo.myTorsions = NULL;
242
243	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
244	<
245	<	simnfo->n_atoms = tot_atoms;
296	<	simnfo->n_bonds = tot_bonds;
297	<	simnfo->n_bends = tot_bends;
298	<	simnfo->n_torsions = tot_torsions;
299	<	simnfo->n_SRI = tot_SRI;
300	<	simnfo->n_mol = tot_nmol;
301	<
302	<	simnfo->molMembershipArray = new int[tot_atoms];
303	<
304	<	#ifdef IS_MPI
305	<
306	<	// divide the molecules among processors here.
307	<
308	<	mpiSim = new mpiSimulation( simnfo );
309	<
310	<	globalIndex = mpiSim->divideLabor();
311	<
312	<	// set up the local variables
313	<
314	<	int localMol, allMol;
315	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
316	<
317	<	int* mol2proc = mpiSim->getMolToProcMap();
318	<	int* molCompType = mpiSim->getMolComponentType();
319	<
320	<	allMol = 0;
321	<	localMol = 0;
322	<	local_atoms = 0;
323	<	local_bonds = 0;
324	<	local_bends = 0;
325	<	local_torsions = 0;
326	<	globalAtomIndex = 0;
327	<
328	<
329	<	for( i=0; i<n_components; i++ ){
330	<
331	<	for( j=0; j<components_nmol[i]; j++ ){
243	>	theBonds = new bond_pair[molInfo.nBonds];
244	>	theBends = new bend_set[molInfo.nBends];
245	>	theTorsions = new torsion_set[molInfo.nTorsions];
246
247	<	if( mol2proc[allMol] == worldRank ){
334	<
335	<	local_atoms +=    comp_stamps[i]->getNAtoms();
336	<	local_bonds +=    comp_stamps[i]->getNBonds();
337	<	local_bends +=    comp_stamps[i]->getNBends();
338	<	local_torsions += comp_stamps[i]->getNTorsions();
339	<	localMol++;
340	<	}
341	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
342	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
343	<	globalAtomIndex++;
344	<	}
247	>	// make the Atoms
248
249	<	allMol++;
250	<	}
348	<	}
349	<	local_SRI = local_bonds + local_bends + local_torsions;
350	<
351	<	simnfo->n_atoms = mpiSim->getMyNlocal();
352	<
353	<	if( local_atoms != simnfo->n_atoms ){
354	<	sprintf( painCave.errMsg,
355	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
356	<	" localAtom (%d) are not equal.\n",
357	<	simnfo->n_atoms,
358	<	local_atoms );
359	<	painCave.isFatal = 1;
360	<	simError();
361	<	}
249	>	for (j = 0; j < molInfo.nAtoms; j++){
250	>	currentAtom = comp_stamps[stampID]->getAtom(j);
251
252	<	simnfo->n_bonds = local_bonds;
253	<	simnfo->n_bends = local_bends;
254	<	simnfo->n_torsions = local_torsions;
255	<	simnfo->n_SRI = local_SRI;
256	<	simnfo->n_mol = localMol;
252	>	if (currentAtom->haveOrientation()){
253	>	dAtom = new DirectionalAtom((j + atomOffset),
254	>	info[k].getConfiguration());
255	>	info[k].n_oriented++;
256	>	molInfo.myAtoms[j] = dAtom;
257
258	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
259	<	MPIcheckPoint();
260	<
372	<
373	<	#endif // is_mpi
374	<
258	>	// Directional Atoms have standard unit vectors which are oriented
259	>	// in space using the three Euler angles.  We assume the standard
260	>	// unit vector was originally along the z axis below.
261
262	<	// create the atom and short range interaction arrays
262	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
263	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
264	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
265
266	<	Atom::createArrays(simnfo->n_atoms);
267	<	the_atoms = new Atom*[simnfo->n_atoms];
268	<	the_molecules = new Molecule[simnfo->n_mol];
269	<	int molIndex;
266	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
267	>
268	>	}
269	>	else{
270
271	<	// initialize the molecule's stampID's
271	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
272
273	+	}
274	+
275	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
276		#ifdef IS_MPI
386	–
277
278	<	molIndex = 0;
389	<	for(i=0; i<mpiSim->getTotNmol(); i++){
390	<
391	<	if(mol2proc[i] == worldRank ){
392	<	the_molecules[molIndex].setStampID( molCompType[i] );
393	<	the_molecules[molIndex].setMyIndex( molIndex );
394	<	the_molecules[molIndex].setGlobalIndex( i );
395	<	molIndex++;
396	<	}
397	<	}
278	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
279
399	–	#else // is_mpi
400	–
401	–	molIndex = 0;
402	–	globalAtomIndex = 0;
403	–	for(i=0; i<n_components; i++){
404	–	for(j=0; j<components_nmol[i]; j++ ){
405	–	the_molecules[molIndex].setStampID( i );
406	–	the_molecules[molIndex].setMyIndex( molIndex );
407	–	the_molecules[molIndex].setGlobalIndex( molIndex );
408	–	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
409	–	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
410	–	globalAtomIndex++;
411	–	}
412	–	molIndex++;
413	–	}
414	–	}
415	–
416	–
280		#endif // is_mpi
281	+	}
282
283	+	// make the bonds
284	+	for (j = 0; j < molInfo.nBonds; j++){
285	+	currentBond = comp_stamps[stampID]->getBond(j);
286	+	theBonds[j].a = currentBond->getA() + atomOffset;
287	+	theBonds[j].b = currentBond->getB() + atomOffset;
288
289	<	if( simnfo->n_SRI ){
290	<
422	<	Exclude::createArray(simnfo->n_SRI);
423	<	the_excludes = new Exclude*[simnfo->n_SRI];
424	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
425	<	simnfo->globalExcludes = new int;
426	<	simnfo->n_exclude = simnfo->n_SRI;
427	<	}
428	<	else{
429	<
430	<	Exclude::createArray( 1 );
431	<	the_excludes = new Exclude*;
432	<	the_excludes[0] = new Exclude(0);
433	<	the_excludes[0]->setPair( 0,0 );
434	<	simnfo->globalExcludes = new int;
435	<	simnfo->globalExcludes[0] = 0;
436	<	simnfo->n_exclude = 0;
437	<	}
289	>	tempI = theBonds[j].a;
290	>	tempJ = theBonds[j].b;
291
292	<	// set the arrays into the SimInfo object
293	<
294	<	simnfo->atoms = the_atoms;
295	<	simnfo->molecules = the_molecules;
296	<	simnfo->nGlobalExcludes = 0;
297	<	simnfo->excludes = the_excludes;
292	>	#ifdef IS_MPI
293	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
294	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
295	>	#else
296	>	exI = tempI + 1;
297	>	exJ = tempJ + 1;
298	>	#endif
299
300	+	info[k].excludes->addPair(exI, exJ);
301	+	}
302
303	<	// get some of the tricky things that may still be in the globals
303	>	//make the bends
304	>	for (j = 0; j < molInfo.nBends; j++){
305	>	currentBend = comp_stamps[stampID]->getBend(j);
306	>	theBends[j].a = currentBend->getA() + atomOffset;
307	>	theBends[j].b = currentBend->getB() + atomOffset;
308	>	theBends[j].c = currentBend->getC() + atomOffset;
309
310	<
311	<	if( the_globals->haveBox() ){
312	<	simnfo->box_x = the_globals->getBox();
452	<	simnfo->box_y = the_globals->getBox();
453	<	simnfo->box_z = the_globals->getBox();
454	<	}
455	<	else if( the_globals->haveDensity() ){
310	>	if (currentBend->haveExtras()){
311	>	extras = currentBend->getExtras();
312	>	current_extra = extras;
313
314	<	double vol;
315	<	vol = (double)tot_nmol / the_globals->getDensity();
316	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
317	<	simnfo->box_y = simnfo->box_x;
318	<	simnfo->box_z = simnfo->box_x;
319	<	}
320	<	else{
464	<	if( !the_globals->haveBoxX() ){
465	<	sprintf( painCave.errMsg,
466	<	"SimSetup error, no periodic BoxX size given.\n" );
467	<	painCave.isFatal = 1;
468	<	simError();
469	<	}
470	<	simnfo->box_x = the_globals->getBoxX();
314	>	while (current_extra != NULL){
315	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
316	>	switch (current_extra->getType()){
317	>	case 0:
318	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
319	>	theBends[j].isGhost = 1;
320	>	break;
321
322	<	if( !the_globals->haveBoxY() ){
323	<	sprintf( painCave.errMsg,
324	<	"SimSetup error, no periodic BoxY size given.\n" );
325	<	painCave.isFatal = 1;
326	<	simError();
477	<	}
478	<	simnfo->box_y = the_globals->getBoxY();
322	>	case 1:
323	>	theBends[j].ghost = (int) current_extra->getDouble() +
324	>	atomOffset;
325	>	theBends[j].isGhost = 1;
326	>	break;
327
328	<	if( !the_globals->haveBoxZ() ){
329	<	sprintf( painCave.errMsg,
330	<	"SimSetup error, no periodic BoxZ size given.\n" );
331	<	painCave.isFatal = 1;
332	<	simError();
333	<	}
334	<	simnfo->box_z = the_globals->getBoxZ();
335	<	}
328	>	default:
329	>	sprintf(painCave.errMsg,
330	>	"SimSetup Error: ghostVectorSource was neither a "
331	>	"double nor an int.\n"
332	>	"-->Bend[%d] in %s\n",
333	>	j, comp_stamps[stampID]->getID());
334	>	painCave.isFatal = 1;
335	>	simError();
336	>	}
337	>	}
338	>	else{
339	>	sprintf(painCave.errMsg,
340	>	"SimSetup Error: unhandled bend assignment:\n"
341	>	"    -->%s in Bend[%d] in %s\n",
342	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
343	>	painCave.isFatal = 1;
344	>	simError();
345	>	}
346
347	+	current_extra = current_extra->getNext();
348	+	}
349	+	}
350	+
351	+	if (theBends[j].isGhost) {
352	+
353	+	tempI = theBends[j].a;
354	+	tempJ = theBends[j].b;
355	+
356		#ifdef IS_MPI
357	<	strcpy( checkPointMsg, "Box size set up" );
358	<	MPIcheckPoint();
359	<	#endif // is_mpi
357	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
358	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
359	>	#else
360	>	exI = tempI + 1;
361	>	exJ = tempJ + 1;
362	>	#endif
363	>	info[k].excludes->addPair(exI, exJ);
364
365	+	} else {
366
367	<	// initialize the arrays
368	<
369	<	the_ff->setSimInfo( simnfo );
370	<
499	<	makeMolecules();
500	<	simnfo->identArray = new int[simnfo->n_atoms];
501	<	for(i=0; i<simnfo->n_atoms; i++){
502	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
503	<	}
504	<
505	<	if (the_globals->getUseRF() ) {
506	<	simnfo->useReactionField = 1;
507	<
508	<	if( !the_globals->haveECR() ){
509	<	sprintf( painCave.errMsg,
510	<	"SimSetup Warning: using default value of 1/2 the smallest "
511	<	"box length for the electrostaticCutoffRadius.\n"
512	<	"I hope you have a very fast processor!\n");
513	<	painCave.isFatal = 0;
514	<	simError();
515	<	double smallest;
516	<	smallest = simnfo->box_x;
517	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
518	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
519	<	simnfo->ecr = 0.5 * smallest;
520	<	} else {
521	<	simnfo->ecr        = the_globals->getECR();
522	<	}
523	<
524	<	if( !the_globals->haveEST() ){
525	<	sprintf( painCave.errMsg,
526	<	"SimSetup Warning: using default value of 0.05 * the "
527	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
528	<	);
529	<	painCave.isFatal = 0;
530	<	simError();
531	<	simnfo->est = 0.05 * simnfo->ecr;
532	<	} else {
533	<	simnfo->est        = the_globals->getEST();
534	<	}
535	<
536	<	if(!the_globals->haveDielectric() ){
537	<	sprintf( painCave.errMsg,
538	<	"SimSetup Error: You are trying to use Reaction Field without"
539	<	"setting a dielectric constant!\n"
540	<	);
541	<	painCave.isFatal = 1;
542	<	simError();
543	<	}
544	<	simnfo->dielectric = the_globals->getDielectric();
545	<	} else {
546	<	if (usesDipoles) {
547	<
548	<	if( !the_globals->haveECR() ){
549	<	sprintf( painCave.errMsg,
550	<	"SimSetup Warning: using default value of 1/2 the smallest "
551	<	"box length for the electrostaticCutoffRadius.\n"
552	<	"I hope you have a very fast processor!\n");
553	<	painCave.isFatal = 0;
554	<	simError();
555	<	double smallest;
556	<	smallest = simnfo->box_x;
557	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
558	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
559	<	simnfo->ecr = 0.5 * smallest;
560	<	} else {
561	<	simnfo->ecr        = the_globals->getECR();
562	<	}
563	<
564	<	if( !the_globals->haveEST() ){
565	<	sprintf( painCave.errMsg,
566	<	"SimSetup Warning: using default value of 5%% of the "
567	<	"electrostaticCutoffRadius for the "
568	<	"electrostaticSkinThickness\n"
569	<	);
570	<	painCave.isFatal = 0;
571	<	simError();
572	<	simnfo->est = 0.05 * simnfo->ecr;
573	<	} else {
574	<	simnfo->est        = the_globals->getEST();
575	<	}
576	<	}
577	<	}
578	<
367	>	tempI = theBends[j].a;
368	>	tempJ = theBends[j].b;
369	>	tempK = theBends[j].c;
370	>
371		#ifdef IS_MPI
372	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
373	<	MPIcheckPoint();
374	<	#endif // is_mpi
375	<
376	<	if( the_globals->haveInitialConfig() ){
377	<
378	<	InitializeFromFile* fileInit;
587	<	#ifdef IS_MPI // is_mpi
588	<	if( worldRank == 0 ){
589	<	#endif //is_mpi
590	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
591	<	#ifdef IS_MPI
592	<	}else fileInit = new InitializeFromFile( NULL );
372	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
373	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
374	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
375	>	#else
376	>	exI = tempI + 1;
377	>	exJ = tempJ + 1;
378	>	exK = tempK + 1;
379		#endif
380	<	fileInit->read_xyz( simnfo ); // default velocities on
380	>
381	>	info[k].excludes->addPair(exI, exK);
382	>	info[k].excludes->addPair(exI, exJ);
383	>	info[k].excludes->addPair(exJ, exK);
384	>	}
385	>	}
386
387	<	delete fileInit;
388	<	}
389	<	else{
387	>	for (j = 0; j < molInfo.nTorsions; j++){
388	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
389	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
390	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
391	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
392	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
393
394	<	#ifdef IS_MPI
394	>	tempI = theTorsions[j].a;
395	>	tempJ = theTorsions[j].b;
396	>	tempK = theTorsions[j].c;
397	>	tempL = theTorsions[j].d;
398
399	<	// no init from bass
400	<
401	<	sprintf( painCave.errMsg,
402	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
403	<	painCave.isFatal;
607	<	simError();
608	<
399	>	#ifdef IS_MPI
400	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
401	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
402	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
403	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
404		#else
405	<
406	<	initFromBass();
407	<
408	<
405	>	exI = tempI + 1;
406	>	exJ = tempJ + 1;
407	>	exK = tempK + 1;
408	>	exL = tempL + 1;
409		#endif
615	–	}
410
411	<	#ifdef IS_MPI
412	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
413	<	MPIcheckPoint();
414	<	#endif // is_mpi
411	>	info[k].excludes->addPair(exI, exJ);
412	>	info[k].excludes->addPair(exI, exK);
413	>	info[k].excludes->addPair(exI, exL);
414	>	info[k].excludes->addPair(exJ, exK);
415	>	info[k].excludes->addPair(exJ, exL);
416	>	info[k].excludes->addPair(exK, exL);
417	>	}
418
419	+
420	+	molInfo.myRigidBodies.clear();
421	+
422	+	for (j = 0; j < molInfo.nRigidBodies; j++){
423
424	<
425	<
625	<
424	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
425	>	nMembers = currentRigidBody->getNMembers();
426
427	<
427	>	// Create the Rigid Body:
428	>
429	>	myRB = new RigidBody();
430	>
431	>	sprintf(rbName,"%s_RB_%d", molName, j);
432	>	myRB->setType(rbName);
433	>
434	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
435	>
436	>	// molI is atom numbering inside this molecule
437	>	molI = currentRigidBody->getMember(rb1);
438	>
439	>	// tempI is atom numbering on local processor
440	>	tempI = molI + atomOffset;
441	>
442	>	// currentAtom is the AtomStamp (which we need for
443	>	// rigid body reference positions)
444	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
445	>
446	>	// When we add to the rigid body, add the atom itself and
447	>	// the stamp info:
448	>
449	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
450	>
451	>	// Add this atom to the Skip List for the integrators
452		#ifdef IS_MPI
453	<	if( worldRank == 0 ){
454	<	#endif // is_mpi
455	<
456	<	if( the_globals->haveFinalConfig() ){
457	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
458	<	}
459	<	else{
460	<	strcpy( simnfo->finalName, inFileName );
461	<	char* endTest;
462	<	int nameLength = strlen( simnfo->finalName );
463	<	endTest = &(simnfo->finalName[nameLength - 5]);
464	<	if( !strcmp( endTest, ".bass" ) ){
465	<	strcpy( endTest, ".eor" );
466	<	}
467	<	else if( !strcmp( endTest, ".BASS" ) ){
468	<	strcpy( endTest, ".eor" );
469	<	}
470	<	else{
471	<	endTest = &(simnfo->finalName[nameLength - 4]);
648	<	if( !strcmp( endTest, ".bss" ) ){
649	<	strcpy( endTest, ".eor" );
650	<	}
651	<	else if( !strcmp( endTest, ".mdl" ) ){
652	<	strcpy( endTest, ".eor" );
653	<	}
654	<	else{
655	<	strcat( simnfo->finalName, ".eor" );
656	<	}
657	<	}
658	<	}
659	<
660	<	// make the sample and status out names
661	<
662	<	strcpy( simnfo->sampleName, inFileName );
663	<	char* endTest;
664	<	int nameLength = strlen( simnfo->sampleName );
665	<	endTest = &(simnfo->sampleName[nameLength - 5]);
666	<	if( !strcmp( endTest, ".bass" ) ){
667	<	strcpy( endTest, ".dump" );
668	<	}
669	<	else if( !strcmp( endTest, ".BASS" ) ){
670	<	strcpy( endTest, ".dump" );
671	<	}
672	<	else{
673	<	endTest = &(simnfo->sampleName[nameLength - 4]);
674	<	if( !strcmp( endTest, ".bss" ) ){
675	<	strcpy( endTest, ".dump" );
676	<	}
677	<	else if( !strcmp( endTest, ".mdl" ) ){
678	<	strcpy( endTest, ".dump" );
679	<	}
680	<	else{
681	<	strcat( simnfo->sampleName, ".dump" );
682	<	}
683	<	}
684	<
685	<	strcpy( simnfo->statusName, inFileName );
686	<	nameLength = strlen( simnfo->statusName );
687	<	endTest = &(simnfo->statusName[nameLength - 5]);
688	<	if( !strcmp( endTest, ".bass" ) ){
689	<	strcpy( endTest, ".stat" );
690	<	}
691	<	else if( !strcmp( endTest, ".BASS" ) ){
692	<	strcpy( endTest, ".stat" );
693	<	}
694	<	else{
695	<	endTest = &(simnfo->statusName[nameLength - 4]);
696	<	if( !strcmp( endTest, ".bss" ) ){
697	<	strcpy( endTest, ".stat" );
698	<	}
699	<	else if( !strcmp( endTest, ".mdl" ) ){
700	<	strcpy( endTest, ".stat" );
701	<	}
702	<	else{
703	<	strcat( simnfo->statusName, ".stat" );
704	<	}
705	<	}
706	<
453	>	slI = info[k].atoms[tempI]->getGlobalIndex();
454	>	#else
455	>	slI = tempI;
456	>	#endif
457	>	skipList.insert(slI);
458	>
459	>	}
460	>
461	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
462	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
463	>
464	>	tempI = currentRigidBody->getMember(rb1);
465	>	tempJ = currentRigidBody->getMember(rb2);
466	>
467	>	// Some explanation is required here.
468	>	// Fortran indexing starts at 1, while c indexing starts at 0
469	>	// Also, in parallel computations, the GlobalIndex is
470	>	// used for the exclude list:
471	>
472		#ifdef IS_MPI
473	<	}
474	<	#endif // is_mpi
475	<
476	<	// set the status, sample, and themal kick times
477	<
478	<	if( the_globals->haveSampleTime() ){
479	<	simnfo->sampleTime = the_globals->getSampleTime();
480	<	simnfo->statusTime = simnfo->sampleTime;
481	<	simnfo->thermalTime = simnfo->sampleTime;
482	<	}
483	<	else{
719	<	simnfo->sampleTime = the_globals->getRunTime();
720	<	simnfo->statusTime = simnfo->sampleTime;
721	<	simnfo->thermalTime = simnfo->sampleTime;
722	<	}
473	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
474	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
475	>	#else
476	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
477	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
478	>	#endif
479	>
480	>	info[k].excludes->addPair(exI, exJ);
481	>
482	>	}
483	>	}
484
485	<	if( the_globals->haveStatusTime() ){
486	<	simnfo->statusTime = the_globals->getStatusTime();
487	<	}
485	>	molInfo.myRigidBodies.push_back(myRB);
486	>	info[k].rigidBodies.push_back(myRB);
487	>	}
488	>
489
490	<	if( the_globals->haveThermalTime() ){
729	<	simnfo->thermalTime = the_globals->getThermalTime();
730	<	}
490	>	//create cutoff group for molecule
491
492	<	// check for the temperature set flag
492	>	cutoffAtomSet.clear();
493	>	molInfo.myCutoffGroups.clear();
494	>
495	>	for (j = 0; j < nCutoffGroups; j++){
496
497	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
497	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
498	>	nMembers = currentCutoffGroup->getNMembers();
499
500	+	myCutoffGroup = new CutoffGroup();
501	+
502	+	for (int cg = 0; cg < nMembers; cg++) {
503
504	<	// make the integrator
504	>	// molI is atom numbering inside this molecule
505	>	molI = currentCutoffGroup->getMember(cg);
506
507	+	// tempI is atom numbering on local processor
508	+	tempI = molI + atomOffset;
509	+
510	+	myCutoffGroup->addAtom(info[k].atoms[tempI]);
511
512	<	if( !strcmp( ensemble, "TraPPE_Ex" ) ){
513	<	new Symplectic(simnfo, the_ff, the_extendedsystem);
742	<	}
743	<	else if( !strcmp( force_field, "LJ" ) ){
744	<	new Verlet( *simnfo, the_ff, the_extendedsystem );
745	<	}
512	>	cutoffAtomSet.insert(tempI);
513	>	}
514
515	<	#ifdef IS_MPI
516	<	mpiSim->mpiRefresh();
749	<	#endif
515	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
516	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
517
518	<	// initialize the Fortran
518	>	//creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
519
520	+	for(j = 0; j < molInfo.nAtoms; j++){
521
522	<	simnfo->refreshSim();
523	<
524	<	if( !strcmp( simnfo->mixingRule, "standard") ){
525	<	the_ff->initForceField( LB_MIXING_RULE );
526	<	}
527	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
528	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
761	<	}
762	<	else{
763	<	sprintf( painCave.errMsg,
764	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
765	<	simnfo->mixingRule );
766	<	painCave.isFatal = 1;
767	<	simError();
768	<	}
522	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
523	>	myCutoffGroup = new CutoffGroup();
524	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
525	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
526	>	}
527	>
528	>	}
529
530	+
531
771	–	#ifdef IS_MPI
772	–	strcpy( checkPointMsg,
773	–	"Successfully intialized the mixingRule for Fortran." );
774	–	MPIcheckPoint();
775	–	#endif // is_mpi
776	–	}
532
533	+	// After this is all set up, scan through the atoms to
534	+	// see if they can be added to the integrableObjects:
535
536	<	void SimSetup::makeMolecules( void ){
536	>	molInfo.myIntegrableObjects.clear();
537	>
538
539	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
782	<	molInit info;
783	<	DirectionalAtom* dAtom;
784	<	LinkedAssign* extras;
785	<	LinkedAssign* current_extra;
786	<	AtomStamp* currentAtom;
787	<	BondStamp* currentBond;
788	<	BendStamp* currentBend;
789	<	TorsionStamp* currentTorsion;
539	>	for (j = 0; j < molInfo.nAtoms; j++){
540
791	–	bond_pair* theBonds;
792	–	bend_set* theBends;
793	–	torsion_set* theTorsions;
794	–
795	–
796	–	//init the forceField paramters
797	–
798	–	the_ff->readParams();
799	–
800	–
801	–	// init the atoms
802	–
803	–	double ux, uy, uz, u, uSqr;
804	–
805	–	atomOffset = 0;
806	–	excludeOffset = 0;
807	–	for(i=0; i<simnfo->n_mol; i++){
808	–
809	–	stampID = the_molecules[i].getStampID();
810	–
811	–	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
812	–	info.nBonds    = comp_stamps[stampID]->getNBonds();
813	–	info.nBends    = comp_stamps[stampID]->getNBends();
814	–	info.nTorsions = comp_stamps[stampID]->getNTorsions();
815	–	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
816	–
817	–	info.myAtoms = &the_atoms[atomOffset];
818	–	info.myExcludes = &the_excludes[excludeOffset];
819	–	info.myBonds = new Bond*[info.nBonds];
820	–	info.myBends = new Bend*[info.nBends];
821	–	info.myTorsions = new Torsion*[info.nTorsions];
822	–
823	–	theBonds = new bond_pair[info.nBonds];
824	–	theBends = new bend_set[info.nBends];
825	–	theTorsions = new torsion_set[info.nTorsions];
826	–
827	–	// make the Atoms
828	–
829	–	for(j=0; j<info.nAtoms; j++){
830	–
831	–	currentAtom = comp_stamps[stampID]->getAtom( j );
832	–	if( currentAtom->haveOrientation() ){
833	–
834	–	dAtom = new DirectionalAtom(j + atomOffset);
835	–	simnfo->n_oriented++;
836	–	info.myAtoms[j] = dAtom;
837	–
838	–	ux = currentAtom->getOrntX();
839	–	uy = currentAtom->getOrntY();
840	–	uz = currentAtom->getOrntZ();
841	–
842	–	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
843	–
844	–	u = sqrt( uSqr );
845	–	ux = ux / u;
846	–	uy = uy / u;
847	–	uz = uz / u;
848	–
849	–	dAtom->setSUx( ux );
850	–	dAtom->setSUy( uy );
851	–	dAtom->setSUz( uz );
852	–	}
853	–	else{
854	–	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
855	–	}
856	–	info.myAtoms[j]->setType( currentAtom->getType() );
857	–
541		#ifdef IS_MPI
542	<
543	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
544	<
545	<	#endif // is_mpi
863	<	}
864	<
865	<	// make the bonds
866	<	for(j=0; j<info.nBonds; j++){
867	<
868	<	currentBond = comp_stamps[stampID]->getBond( j );
869	<	theBonds[j].a = currentBond->getA() + atomOffset;
870	<	theBonds[j].b = currentBond->getB() + atomOffset;
542	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
543	>	#else
544	>	slJ = j+atomOffset;
545	>	#endif
546
547	<	exI = theBonds[j].a;
873	<	exJ = theBonds[j].b;
547	>	// if they aren't on the skip list, then they can be integrated
548
549	<	// exclude_I must always be the smaller of the pair
550	<	if( exI > exJ ){
551	<	tempEx = exI;
552	<	exI = exJ;
553	<	exJ = tempEx;
549	>	if (skipList.find(slJ) == skipList.end()) {
550	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
551	>	info[k].integrableObjects.push_back(mySD);
552	>	molInfo.myIntegrableObjects.push_back(mySD);
553	>	}
554		}
881	–	#ifdef IS_MPI
882	–	tempEx = exI;
883	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
884	–	tempEx = exJ;
885	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
886	–
887	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
888	–	#else  // isn't MPI
555
556	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
891	<	#endif  //is_mpi
892	<	}
893	<	excludeOffset += info.nBonds;
556	>	// all rigid bodies are integrated:
557
558	<	//make the bends
559	<	for(j=0; j<info.nBends; j++){
560	<
561	<	currentBend = comp_stamps[stampID]->getBend( j );
899	<	theBends[j].a = currentBend->getA() + atomOffset;
900	<	theBends[j].b = currentBend->getB() + atomOffset;
901	<	theBends[j].c = currentBend->getC() + atomOffset;
902	<
903	<	if( currentBend->haveExtras() ){
904	<
905	<	extras = currentBend->getExtras();
906	<	current_extra = extras;
907	<
908	<	while( current_extra != NULL ){
909	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
910	<
911	<	switch( current_extra->getType() ){
912	<
913	<	case 0:
914	<	theBends[j].ghost =
915	<	current_extra->getInt() + atomOffset;
916	<	theBends[j].isGhost = 1;
917	<	break;
918	<
919	<	case 1:
920	<	theBends[j].ghost =
921	<	(int)current_extra->getDouble() + atomOffset;
922	<	theBends[j].isGhost = 1;
923	<	break;
924	<
925	<	default:
926	<	sprintf( painCave.errMsg,
927	<	"SimSetup Error: ghostVectorSource was neither a "
928	<	"double nor an int.\n"
929	<	"-->Bend[%d] in %s\n",
930	<	j, comp_stamps[stampID]->getID() );
931	<	painCave.isFatal = 1;
932	<	simError();
933	<	}
934	<	}
935	<
936	<	else{
937	<
938	<	sprintf( painCave.errMsg,
939	<	"SimSetup Error: unhandled bend assignment:\n"
940	<	"    -->%s in Bend[%d] in %s\n",
941	<	current_extra->getlhs(),
942	<	j, comp_stamps[stampID]->getID() );
943	<	painCave.isFatal = 1;
944	<	simError();
945	<	}
946	<
947	<	current_extra = current_extra->getNext();
948	<	}
558	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
559	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
560	>	info[k].integrableObjects.push_back(mySD);
561	>	molInfo.myIntegrableObjects.push_back(mySD);
562		}
563	<
951	<	if( !theBends[j].isGhost ){
952	<
953	<	exI = theBends[j].a;
954	<	exJ = theBends[j].c;
955	<	}
956	<	else{
957	<
958	<	exI = theBends[j].a;
959	<	exJ = theBends[j].b;
960	<	}
563	>
564
565	<	// exclude_I must always be the smaller of the pair
963	<	if( exI > exJ ){
964	<	tempEx = exI;
965	<	exI = exJ;
966	<	exJ = tempEx;
967	<	}
968	<	#ifdef IS_MPI
969	<	tempEx = exI;
970	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
971	<	tempEx = exJ;
972	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
565	>	// send the arrays off to the forceField for init.
566
567	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
568	<	#else  // isn't MPI
569	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
570	<	#endif  //is_mpi
571	<	}
979	<	excludeOffset += info.nBends;
980	<
981	<	for(j=0; j<info.nTorsions; j++){
982	<
983	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
984	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
985	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
986	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
987	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
988	<
989	<	exI = theTorsions[j].a;
990	<	exJ = theTorsions[j].d;
567	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
568	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
569	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
570	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
571	>	theTorsions);
572
573	<	// exclude_I must always be the smaller of the pair
993	<	if( exI > exJ ){
994	<	tempEx = exI;
995	<	exI = exJ;
996	<	exJ = tempEx;
997	<	}
998	<	#ifdef IS_MPI
999	<	tempEx = exI;
1000	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1001	<	tempEx = exJ;
1002	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1003	<
1004	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1005	<	#else  // isn't MPI
1006	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1007	<	#endif  //is_mpi
1008	<	}
1009	<	excludeOffset += info.nTorsions;
573	>	info[k].molecules[i].initialize(molInfo);
574
1011	–
1012	–	// send the arrays off to the forceField for init.
575
576	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
577	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
578	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
579	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
580	<
1019	<
1020	<	the_molecules[i].initialize( info );
1021	<
1022	<
1023	<	atomOffset += info.nAtoms;
1024	<	delete[] theBonds;
1025	<	delete[] theBends;
1026	<	delete[] theTorsions;
576	>	atomOffset += molInfo.nAtoms;
577	>	delete[] theBonds;
578	>	delete[] theBends;
579	>	delete[] theTorsions;
580	>	}
581		}
582
583		#ifdef IS_MPI
584	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
584	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
585		MPIcheckPoint();
586		#endif // is_mpi
587
1034	–	// clean up the forcefield
1035	–	the_ff->calcRcut();
1036	–	the_ff->cleanMe();
1037	–
588		}
589
590	<	void SimSetup::initFromBass( void ){
1041	<
590	>	void SimSetup::initFromBass(void){
591		int i, j, k;
592		int n_cells;
593		double cellx, celly, cellz;
#	Line 1047 | Line 596 | void SimSetup::initFromBass( void ){
596		int n_extra;
597		int have_extra, done;
598
599	<	temp1 = (double)tot_nmol / 4.0;
600	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
601	<	temp3 = ceil( temp2 );
599	>	double vel[3];
600	>	vel[0] = 0.0;
601	>	vel[1] = 0.0;
602	>	vel[2] = 0.0;
603
604	<	have_extra =0;
605	<	if( temp2 < temp3 ){ // we have a non-complete lattice
606	<	have_extra =1;
604	>	temp1 = (double) tot_nmol / 4.0;
605	>	temp2 = pow(temp1, (1.0 / 3.0));
606	>	temp3 = ceil(temp2);
607
608	<	n_cells = (int)temp3 - 1;
609	<	cellx = simnfo->box_x / temp3;
610	<	celly = simnfo->box_y / temp3;
611	<	cellz = simnfo->box_z / temp3;
1062	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1063	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1064	<	n_per_extra = (int)ceil( temp1 );
608	>	have_extra = 0;
609	>	if (temp2 < temp3){
610	>	// we have a non-complete lattice
611	>	have_extra = 1;
612
613	<	if( n_per_extra > 4){
614	<	sprintf( painCave.errMsg,
615	<	"SimSetup error. There has been an error in constructing"
616	<	" the non-complete lattice.\n" );
613	>	n_cells = (int) temp3 - 1;
614	>	cellx = info[0].boxL[0] / temp3;
615	>	celly = info[0].boxL[1] / temp3;
616	>	cellz = info[0].boxL[2] / temp3;
617	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
618	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
619	>	n_per_extra = (int) ceil(temp1);
620	>
621	>	if (n_per_extra > 4){
622	>	sprintf(painCave.errMsg,
623	>	"SimSetup error. There has been an error in constructing"
624	>	" the non-complete lattice.\n");
625		painCave.isFatal = 1;
626		simError();
627		}
628		}
629		else{
630	<	n_cells = (int)temp3;
631	<	cellx = simnfo->box_x / temp3;
632	<	celly = simnfo->box_y / temp3;
633	<	cellz = simnfo->box_z / temp3;
630	>	n_cells = (int) temp3;
631	>	cellx = info[0].boxL[0] / temp3;
632	>	celly = info[0].boxL[1] / temp3;
633	>	cellz = info[0].boxL[2] / temp3;
634		}
635
636		current_mol = 0;
#	Line 1083 | Line 638 | void SimSetup::initFromBass( void ){
638		current_comp = 0;
639		current_atom_ndx = 0;
640
641	<	for( i=0; i < n_cells ; i++ ){
642	<	for( j=0; j < n_cells; j++ ){
643	<	for( k=0; k < n_cells; k++ ){
641	>	for (i = 0; i < n_cells ; i++){
642	>	for (j = 0; j < n_cells; j++){
643	>	for (k = 0; k < n_cells; k++){
644	>	makeElement(i * cellx, j * celly, k * cellz);
645
646	<	makeElement( i * cellx,
1091	<	j * celly,
1092	<	k * cellz );
646	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
647
648	<	makeElement( i * cellx + 0.5 * cellx,
1095	<	j * celly + 0.5 * celly,
1096	<	k * cellz );
648	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
649
650	<	makeElement( i * cellx,
1099	<	j * celly + 0.5 * celly,
1100	<	k * cellz + 0.5 * cellz );
1101	<
1102	<	makeElement( i * cellx + 0.5 * cellx,
1103	<	j * celly,
1104	<	k * cellz + 0.5 * cellz );
650	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
651		}
652		}
653		}
654
655	<	if( have_extra ){
655	>	if (have_extra){
656		done = 0;
657
658		int start_ndx;
659	<	for( i=0; i < (n_cells+1) && !done; i++ ){
660	<	for( j=0; j < (n_cells+1) && !done; j++ ){
659	>	for (i = 0; i < (n_cells + 1) && !done; i++){
660	>	for (j = 0; j < (n_cells + 1) && !done; j++){
661	>	if (i < n_cells){
662	>	if (j < n_cells){
663	>	start_ndx = n_cells;
664	>	}
665	>	else
666	>	start_ndx = 0;
667	>	}
668	>	else
669	>	start_ndx = 0;
670
671	<	if( i < n_cells ){
671	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
672	>	makeElement(i * cellx, j * celly, k * cellz);
673	>	done = (current_mol >= tot_nmol);
674
675	<	if( j < n_cells ){
676	<	start_ndx = n_cells;
677	<	}
678	<	else start_ndx = 0;
679	<	}
1123	<	else start_ndx = 0;
675	>	if (!done && n_per_extra > 1){
676	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
677	>	k * cellz);
678	>	done = (current_mol >= tot_nmol);
679	>	}
680
681	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
681	>	if (!done && n_per_extra > 2){
682	>	makeElement(i * cellx, j * celly + 0.5 * celly,
683	>	k * cellz + 0.5 * cellz);
684	>	done = (current_mol >= tot_nmol);
685	>	}
686
687	<	makeElement( i * cellx,
688	<	j * celly,
689	<	k * cellz );
690	<	done = ( current_mol >= tot_nmol );
691	<
692	<	if( !done && n_per_extra > 1 ){
1133	<	makeElement( i * cellx + 0.5 * cellx,
1134	<	j * celly + 0.5 * celly,
1135	<	k * cellz );
1136	<	done = ( current_mol >= tot_nmol );
1137	<	}
1138	<
1139	<	if( !done && n_per_extra > 2){
1140	<	makeElement( i * cellx,
1141	<	j * celly + 0.5 * celly,
1142	<	k * cellz + 0.5 * cellz );
1143	<	done = ( current_mol >= tot_nmol );
1144	<	}
1145	<
1146	<	if( !done && n_per_extra > 3){
1147	<	makeElement( i * cellx + 0.5 * cellx,
1148	<	j * celly,
1149	<	k * cellz + 0.5 * cellz );
1150	<	done = ( current_mol >= tot_nmol );
1151	<	}
1152	<	}
687	>	if (!done && n_per_extra > 3){
688	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
689	>	k * cellz + 0.5 * cellz);
690	>	done = (current_mol >= tot_nmol);
691	>	}
692	>	}
693		}
694		}
695		}
696
697	<
698	<	for( i=0; i<simnfo->n_atoms; i++ ){
1159	<	simnfo->atoms[i]->set_vx( 0.0 );
1160	<	simnfo->atoms[i]->set_vy( 0.0 );
1161	<	simnfo->atoms[i]->set_vz( 0.0 );
697	>	for (i = 0; i < info[0].n_atoms; i++){
698	>	info[0].atoms[i]->setVel(vel);
699		}
700		}
701
702	<	void SimSetup::makeElement( double x, double y, double z ){
1166	<
702	>	void SimSetup::makeElement(double x, double y, double z){
703		int k;
704		AtomStamp* current_atom;
705		DirectionalAtom* dAtom;
706		double rotMat[3][3];
707	+	double pos[3];
708
709	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
710	<
711	<	current_atom = comp_stamps[current_comp]->getAtom( k );
712	<	if( !current_atom->havePosition() ){
713	<	sprintf( painCave.errMsg,
714	<	"SimSetup:initFromBass error.\n"
715	<	"\tComponent %s, atom %s does not have a position specified.\n"
716	<	"\tThe initialization routine is unable to give a start"
717	<	" position.\n",
1181	<	comp_stamps[current_comp]->getID(),
1182	<	current_atom->getType() );
709	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
710	>	current_atom = comp_stamps[current_comp]->getAtom(k);
711	>	if (!current_atom->havePosition()){
712	>	sprintf(painCave.errMsg,
713	>	"SimSetup:initFromBass error.\n"
714	>	"\tComponent %s, atom %s does not have a position specified.\n"
715	>	"\tThe initialization routine is unable to give a start"
716	>	" position.\n",
717	>	comp_stamps[current_comp]->getID(), current_atom->getType());
718		painCave.isFatal = 1;
719		simError();
720		}
721
722	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
723	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
724	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
722	>	pos[0] = x + current_atom->getPosX();
723	>	pos[1] = y + current_atom->getPosY();
724	>	pos[2] = z + current_atom->getPosZ();
725
726	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
726	>	info[0].atoms[current_atom_ndx]->setPos(pos);
727
728	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
728	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
729	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
730
731		rotMat[0][0] = 1.0;
732		rotMat[0][1] = 0.0;
#	Line 1204 | Line 740 | void SimSetup::makeElement( double x, double y, double
740		rotMat[2][1] = 0.0;
741		rotMat[2][2] = 1.0;
742
743	<	dAtom->setA( rotMat );
743	>	dAtom->setA(rotMat);
744		}
745
746		current_atom_ndx++;
#	Line 1213 | Line 749 | void SimSetup::makeElement( double x, double y, double
749		current_mol++;
750		current_comp_mol++;
751
752	<	if( current_comp_mol >= components_nmol[current_comp] ){
1217	<
752	>	if (current_comp_mol >= components_nmol[current_comp]){
753		current_comp_mol = 0;
754		current_comp++;
755	+	}
756	+	}
757	+
758	+
759	+	void SimSetup::gatherInfo(void){
760	+	int i;
761	+
762	+	ensembleCase = -1;
763	+	ffCase = -1;
764	+
765	+	// set the easy ones first
766	+
767	+	for (i = 0; i < nInfo; i++){
768	+	info[i].target_temp = globals->getTargetTemp();
769	+	info[i].dt = globals->getDt();
770	+	info[i].run_time = globals->getRunTime();
771	+	}
772	+	n_components = globals->getNComponents();
773	+
774	+
775	+	// get the forceField
776	+
777	+	strcpy(force_field, globals->getForceField());
778	+
779	+	if (!strcasecmp(force_field, "DUFF")){
780	+	ffCase = FF_DUFF;
781	+	}
782	+	else if (!strcasecmp(force_field, "LJ")){
783	+	ffCase = FF_LJ;
784	+	}
785	+	else if (!strcasecmp(force_field, "EAM")){
786	+	ffCase = FF_EAM;
787	+	}
788	+	else if (!strcasecmp(force_field, "WATER")){
789	+	ffCase = FF_H2O;
790	+	}
791	+	else{
792	+	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
793	+	force_field);
794	+	painCave.isFatal = 1;
795	+	simError();
796	+	}
797	+
798	+	// get the ensemble
799	+
800	+	strcpy(ensemble, globals->getEnsemble());
801	+
802	+	if (!strcasecmp(ensemble, "NVE")){
803	+	ensembleCase = NVE_ENS;
804	+	}
805	+	else if (!strcasecmp(ensemble, "NVT")){
806	+	ensembleCase = NVT_ENS;
807	+	}
808	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
809	+	ensembleCase = NPTi_ENS;
810	+	}
811	+	else if (!strcasecmp(ensemble, "NPTf")){
812	+	ensembleCase = NPTf_ENS;
813	+	}
814	+	else if (!strcasecmp(ensemble, "NPTxyz")){
815	+	ensembleCase = NPTxyz_ENS;
816	+	}
817	+	else{
818	+	sprintf(painCave.errMsg,
819	+	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
820	+	"\treverting to NVE for this simulation.\n",
821	+	ensemble);
822	+	painCave.isFatal = 0;
823	+	simError();
824	+	strcpy(ensemble, "NVE");
825	+	ensembleCase = NVE_ENS;
826	+	}
827	+
828	+	for (i = 0; i < nInfo; i++){
829	+	strcpy(info[i].ensemble, ensemble);
830	+
831	+	// get the mixing rule
832	+
833	+	strcpy(info[i].mixingRule, globals->getMixingRule());
834	+	info[i].usePBC = globals->getPBC();
835	+	}
836	+
837	+	// get the components and calculate the tot_nMol and indvidual n_mol
838	+
839	+	the_components = globals->getComponents();
840	+	components_nmol = new int[n_components];
841	+
842	+
843	+	if (!globals->haveNMol()){
844	+	// we don't have the total number of molecules, so we assume it is
845	+	// given in each component
846	+
847	+	tot_nmol = 0;
848	+	for (i = 0; i < n_components; i++){
849	+	if (!the_components[i]->haveNMol()){
850	+	// we have a problem
851	+	sprintf(painCave.errMsg,
852	+	"SimSetup Error. No global NMol or component NMol given.\n"
853	+	"\tCannot calculate the number of atoms.\n");
854	+	painCave.isFatal = 1;
855	+	simError();
856	+	}
857	+
858	+	tot_nmol += the_components[i]->getNMol();
859	+	components_nmol[i] = the_components[i]->getNMol();
860	+	}
861	+	}
862	+	else{
863	+	sprintf(painCave.errMsg,
864	+	"SimSetup error.\n"
865	+	"\tSorry, the ability to specify total"
866	+	" nMols and then give molfractions in the components\n"
867	+	"\tis not currently supported."
868	+	" Please give nMol in the components.\n");
869	+	painCave.isFatal = 1;
870	+	simError();
871	+	}
872	+
873	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
874	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
875	+	sprintf(painCave.errMsg,
876	+	"Sample time is not divisible by dt.\n"
877	+	"\tThis will result in samples that are not uniformly\n"
878	+	"\tdistributed in time.  If this is a problem, change\n"
879	+	"\tyour sampleTime variable.\n");
880	+	painCave.isFatal = 0;
881	+	simError();
882	+	}
883	+
884	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
885	+	sprintf(painCave.errMsg,
886	+	"Status time is not divisible by dt.\n"
887	+	"\tThis will result in status reports that are not uniformly\n"
888	+	"\tdistributed in time.  If this is a problem, change \n"
889	+	"\tyour statusTime variable.\n");
890	+	painCave.isFatal = 0;
891	+	simError();
892	+	}
893	+
894	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
895	+	sprintf(painCave.errMsg,
896	+	"Thermal time is not divisible by dt.\n"
897	+	"\tThis will result in thermalizations that are not uniformly\n"
898	+	"\tdistributed in time.  If this is a problem, change \n"
899	+	"\tyour thermalTime variable.\n");
900	+	painCave.isFatal = 0;
901	+	simError();
902	+	}
903	+
904	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
905	+	sprintf(painCave.errMsg,
906	+	"Reset time is not divisible by dt.\n"
907	+	"\tThis will result in integrator resets that are not uniformly\n"
908	+	"\tdistributed in time.  If this is a problem, change\n"
909	+	"\tyour resetTime variable.\n");
910	+	painCave.isFatal = 0;
911	+	simError();
912	+	}
913	+
914	+	// set the status, sample, and thermal kick times
915	+
916	+	for (i = 0; i < nInfo; i++){
917	+	if (globals->haveSampleTime()){
918	+	info[i].sampleTime = globals->getSampleTime();
919	+	info[i].statusTime = info[i].sampleTime;
920	+	}
921	+	else{
922	+	info[i].sampleTime = globals->getRunTime();
923	+	info[i].statusTime = info[i].sampleTime;
924	+	}
925	+
926	+	if (globals->haveStatusTime()){
927	+	info[i].statusTime = globals->getStatusTime();
928	+	}
929	+
930	+	if (globals->haveThermalTime()){
931	+	info[i].thermalTime = globals->getThermalTime();
932	+	} else {
933	+	info[i].thermalTime = globals->getRunTime();
934	+	}
935	+
936	+	info[i].resetIntegrator = 0;
937	+	if( globals->haveResetTime() ){
938	+	info[i].resetTime = globals->getResetTime();
939	+	info[i].resetIntegrator = 1;
940	+	}
941	+
942	+	// check for the temperature set flag
943	+
944	+	if (globals->haveTempSet())
945	+	info[i].setTemp = globals->getTempSet();
946	+
947	+	// check for the extended State init
948	+
949	+	info[i].useInitXSstate = globals->getUseInitXSstate();
950	+	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
951	+
952	+	// check for thermodynamic integration
953	+	if (globals->getUseThermInt()) {
954	+	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
955	+	info[i].useThermInt = globals->getUseThermInt();
956	+	info[i].thermIntLambda = globals->getThermIntLambda();
957	+	info[i].thermIntK = globals->getThermIntK();
958	+
959	+	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
960	+	info[i].restraint = myRestraint;
961	+	}
962	+	else {
963	+	sprintf(painCave.errMsg,
964	+	"SimSetup Error:\n"
965	+	"\tKeyword useThermInt was set to 'true' but\n"
966	+	"\tthermodynamicIntegrationLambda (and/or\n"
967	+	"\tthermodynamicIntegrationK) was not specified.\n"
968	+	"\tPlease provide a lambda value and k value in your .bass file.\n");
969	+	painCave.isFatal = 1;
970	+	simError();
971	+	}
972	+	}
973	+	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
974	+	sprintf(painCave.errMsg,
975	+	"SimSetup Warning: If you want to use Thermodynamic\n"
976	+	"\tIntegration, set useThermInt to 'true' in your .bass file.\n"
977	+	"\tThe useThermInt keyword is 'false' by default, so your\n"
978	+	"\tlambda and/or k values are being ignored.\n");
979	+	painCave.isFatal = 0;
980	+	simError();
981	+	}
982	+	}
983	+
984	+	//setup seed for random number generator
985	+	int seedValue;
986	+
987	+	if (globals->haveSeed()){
988	+	seedValue = globals->getSeed();
989	+
990	+	if(seedValue / 1E9 == 0){
991	+	sprintf(painCave.errMsg,
992	+	"Seed for sprng library should contain at least 9 digits\n"
993	+	"OOPSE will generate a seed for user\n");
994	+	painCave.isFatal = 0;
995	+	simError();
996	+
997	+	//using seed generated by system instead of invalid seed set by user
998	+	#ifndef IS_MPI
999	+	seedValue = make_sprng_seed();
1000	+	#else
1001	+	if (worldRank == 0){
1002	+	seedValue = make_sprng_seed();
1003	+	}
1004	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1005	+	#endif
1006	+	}
1007	+	}//end of if branch of globals->haveSeed()
1008	+	else{
1009	+
1010	+	#ifndef IS_MPI
1011	+	seedValue = make_sprng_seed();
1012	+	#else
1013	+	if (worldRank == 0){
1014	+	seedValue = make_sprng_seed();
1015	+	}
1016	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1017	+	#endif
1018	+	}//end of globals->haveSeed()
1019	+
1020	+	for (int i = 0; i < nInfo; i++){
1021	+	info[i].setSeed(seedValue);
1022	+	}
1023	+
1024	+	#ifdef IS_MPI
1025	+	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1026	+	MPIcheckPoint();
1027	+	#endif // is_mpi
1028	+	}
1029	+
1030	+
1031	+	void SimSetup::finalInfoCheck(void){
1032	+	int index;
1033	+	int usesDipoles;
1034	+	int usesCharges;
1035	+	int i;
1036	+
1037	+	for (i = 0; i < nInfo; i++){
1038	+	// check electrostatic parameters
1039	+
1040	+	index = 0;
1041	+	usesDipoles = 0;
1042	+	while ((index < info[i].n_atoms) && !usesDipoles){
1043	+	usesDipoles = (info[i].atoms[index])->hasDipole();
1044	+	index++;
1045	+	}
1046	+	index = 0;
1047	+	usesCharges = 0;
1048	+	while ((index < info[i].n_atoms) && !usesCharges){
1049	+	usesCharges= (info[i].atoms[index])->hasCharge();
1050	+	index++;
1051	+	}
1052	+	#ifdef IS_MPI
1053	+	int myUse = usesDipoles;
1054	+	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1055	+	#endif //is_mpi
1056	+
1057	+	double theRcut, theRsw;
1058	+
1059	+	if (globals->haveRcut()) {
1060	+	theRcut = globals->getRcut();
1061	+
1062	+	if (globals->haveRsw())
1063	+	theRsw = globals->getRsw();
1064	+	else
1065	+	theRsw = theRcut;
1066	+
1067	+	info[i].setDefaultRcut(theRcut, theRsw);
1068	+
1069	+	} else {
1070	+
1071	+	the_ff->calcRcut();
1072	+	theRcut = info[i].getRcut();
1073	+
1074	+	if (globals->haveRsw())
1075	+	theRsw = globals->getRsw();
1076	+	else
1077	+	theRsw = theRcut;
1078	+
1079	+	info[i].setDefaultRcut(theRcut, theRsw);
1080	+	}
1081	+
1082	+	if (globals->getUseRF()){
1083	+	info[i].useReactionField = 1;
1084	+
1085	+	if (!globals->haveRcut()){
1086	+	sprintf(painCave.errMsg,
1087	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1088	+	"\tOOPSE will use a default value of 15.0 angstroms"
1089	+	"\tfor the cutoffRadius.\n");
1090	+	painCave.isFatal = 0;
1091	+	simError();
1092	+	theRcut = 15.0;
1093	+	}
1094	+	else{
1095	+	theRcut = globals->getRcut();
1096	+	}
1097	+
1098	+	if (!globals->haveRsw()){
1099	+	sprintf(painCave.errMsg,
1100	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1101	+	"\tOOPSE will use a default value of\n"
1102	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1103	+	painCave.isFatal = 0;
1104	+	simError();
1105	+	theRsw = 0.95 * theRcut;
1106	+	}
1107	+	else{
1108	+	theRsw = globals->getRsw();
1109	+	}
1110	+
1111	+	info[i].setDefaultRcut(theRcut, theRsw);
1112	+
1113	+	if (!globals->haveDielectric()){
1114	+	sprintf(painCave.errMsg,
1115	+	"SimSetup Error: No Dielectric constant was set.\n"
1116	+	"\tYou are trying to use Reaction Field without"
1117	+	"\tsetting a dielectric constant!\n");
1118	+	painCave.isFatal = 1;
1119	+	simError();
1120	+	}
1121	+	info[i].dielectric = globals->getDielectric();
1122	+	}
1123	+	else{
1124	+	if (usesDipoles || usesCharges){
1125	+
1126	+	if (!globals->haveRcut()){
1127	+	sprintf(painCave.errMsg,
1128	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1129	+	"\tOOPSE will use a default value of 15.0 angstroms"
1130	+	"\tfor the cutoffRadius.\n");
1131	+	painCave.isFatal = 0;
1132	+	simError();
1133	+	theRcut = 15.0;
1134	+	}
1135	+	else{
1136	+	theRcut = globals->getRcut();
1137	+	}
1138	+
1139	+	if (!globals->haveRsw()){
1140	+	sprintf(painCave.errMsg,
1141	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1142	+	"\tOOPSE will use a default value of\n"
1143	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1144	+	painCave.isFatal = 0;
1145	+	simError();
1146	+	theRsw = 0.95 * theRcut;
1147	+	}
1148	+	else{
1149	+	theRsw = globals->getRsw();
1150	+	}
1151	+
1152	+	info[i].setDefaultRcut(theRcut, theRsw);
1153	+
1154	+	}
1155	+	}
1156	+	}
1157	+	#ifdef IS_MPI
1158	+	strcpy(checkPointMsg, "post processing checks out");
1159	+	MPIcheckPoint();
1160	+	#endif // is_mpi
1161	+
1162	+	// clean up the forcefield
1163	+	the_ff->cleanMe();
1164	+	}
1165	+
1166	+	void SimSetup::initSystemCoords(void){
1167	+	int i;
1168	+
1169	+	char* inName;
1170	+
1171	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1172	+
1173	+	for (i = 0; i < info[0].n_atoms; i++)
1174	+	info[0].atoms[i]->setCoords();
1175	+
1176	+	if (globals->haveInitialConfig()){
1177	+	InitializeFromFile* fileInit;
1178	+	#ifdef IS_MPI // is_mpi
1179	+	if (worldRank == 0){
1180	+	#endif //is_mpi
1181	+	inName = globals->getInitialConfig();
1182	+	fileInit = new InitializeFromFile(inName);
1183	+	#ifdef IS_MPI
1184	+	}
1185	+	else
1186	+	fileInit = new InitializeFromFile(NULL);
1187	+	#endif
1188	+	fileInit->readInit(info); // default velocities on
1189	+
1190	+	delete fileInit;
1191		}
1192	+	else{
1193	+
1194	+	// no init from bass
1195	+
1196	+	sprintf(painCave.errMsg,
1197	+	"Cannot intialize a simulation without an initial configuration file.\n");
1198	+	painCave.isFatal = 1;;
1199	+	simError();
1200	+
1201	+	}
1202	+
1203	+	#ifdef IS_MPI
1204	+	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1205	+	MPIcheckPoint();
1206	+	#endif // is_mpi
1207		}
1208	+
1209	+
1210	+	void SimSetup::makeOutNames(void){
1211	+	int k;
1212	+
1213	+
1214	+	for (k = 0; k < nInfo; k++){
1215	+	#ifdef IS_MPI
1216	+	if (worldRank == 0){
1217	+	#endif // is_mpi
1218	+
1219	+	if (globals->haveFinalConfig()){
1220	+	strcpy(info[k].finalName, globals->getFinalConfig());
1221	+	}
1222	+	else{
1223	+	strcpy(info[k].finalName, inFileName);
1224	+	char* endTest;
1225	+	int nameLength = strlen(info[k].finalName);
1226	+	endTest = &(info[k].finalName[nameLength - 5]);
1227	+	if (!strcmp(endTest, ".bass")){
1228	+	strcpy(endTest, ".eor");
1229	+	}
1230	+	else if (!strcmp(endTest, ".BASS")){
1231	+	strcpy(endTest, ".eor");
1232	+	}
1233	+	else{
1234	+	endTest = &(info[k].finalName[nameLength - 4]);
1235	+	if (!strcmp(endTest, ".bss")){
1236	+	strcpy(endTest, ".eor");
1237	+	}
1238	+	else if (!strcmp(endTest, ".mdl")){
1239	+	strcpy(endTest, ".eor");
1240	+	}
1241	+	else{
1242	+	strcat(info[k].finalName, ".eor");
1243	+	}
1244	+	}
1245	+	}
1246	+
1247	+	// make the sample and status out names
1248	+
1249	+	strcpy(info[k].sampleName, inFileName);
1250	+	char* endTest;
1251	+	int nameLength = strlen(info[k].sampleName);
1252	+	endTest = &(info[k].sampleName[nameLength - 5]);
1253	+	if (!strcmp(endTest, ".bass")){
1254	+	strcpy(endTest, ".dump");
1255	+	}
1256	+	else if (!strcmp(endTest, ".BASS")){
1257	+	strcpy(endTest, ".dump");
1258	+	}
1259	+	else{
1260	+	endTest = &(info[k].sampleName[nameLength - 4]);
1261	+	if (!strcmp(endTest, ".bss")){
1262	+	strcpy(endTest, ".dump");
1263	+	}
1264	+	else if (!strcmp(endTest, ".mdl")){
1265	+	strcpy(endTest, ".dump");
1266	+	}
1267	+	else{
1268	+	strcat(info[k].sampleName, ".dump");
1269	+	}
1270	+	}
1271	+
1272	+	strcpy(info[k].statusName, inFileName);
1273	+	nameLength = strlen(info[k].statusName);
1274	+	endTest = &(info[k].statusName[nameLength - 5]);
1275	+	if (!strcmp(endTest, ".bass")){
1276	+	strcpy(endTest, ".stat");
1277	+	}
1278	+	else if (!strcmp(endTest, ".BASS")){
1279	+	strcpy(endTest, ".stat");
1280	+	}
1281	+	else{
1282	+	endTest = &(info[k].statusName[nameLength - 4]);
1283	+	if (!strcmp(endTest, ".bss")){
1284	+	strcpy(endTest, ".stat");
1285	+	}
1286	+	else if (!strcmp(endTest, ".mdl")){
1287	+	strcpy(endTest, ".stat");
1288	+	}
1289	+	else{
1290	+	strcat(info[k].statusName, ".stat");
1291	+	}
1292	+	}
1293	+
1294	+	strcpy(info[k].rawPotName, inFileName);
1295	+	nameLength = strlen(info[k].rawPotName);
1296	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1297	+	if (!strcmp(endTest, ".bass")){
1298	+	strcpy(endTest, ".raw");
1299	+	}
1300	+	else if (!strcmp(endTest, ".BASS")){
1301	+	strcpy(endTest, ".raw");
1302	+	}
1303	+	else{
1304	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1305	+	if (!strcmp(endTest, ".bss")){
1306	+	strcpy(endTest, ".raw");
1307	+	}
1308	+	else if (!strcmp(endTest, ".mdl")){
1309	+	strcpy(endTest, ".raw");
1310	+	}
1311	+	else{
1312	+	strcat(info[k].rawPotName, ".raw");
1313	+	}
1314	+	}
1315	+
1316	+	#ifdef IS_MPI
1317	+
1318	+	}
1319	+	#endif // is_mpi
1320	+	}
1321	+	}
1322	+
1323	+
1324	+	void SimSetup::sysObjectsCreation(void){
1325	+	int i, k;
1326	+
1327	+	// create the forceField
1328	+
1329	+	createFF();
1330	+
1331	+	// extract componentList
1332	+
1333	+	compList();
1334	+
1335	+	// calc the number of atoms, bond, bends, and torsions
1336	+
1337	+	calcSysValues();
1338	+
1339	+	#ifdef IS_MPI
1340	+	// divide the molecules among the processors
1341	+
1342	+	mpiMolDivide();
1343	+	#endif //is_mpi
1344	+
1345	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1346	+
1347	+	makeSysArrays();
1348	+
1349	+	// make and initialize the molecules (all but atomic coordinates)
1350	+
1351	+	makeMolecules();
1352	+
1353	+	for (k = 0; k < nInfo; k++){
1354	+	info[k].identArray = new int[info[k].n_atoms];
1355	+	for (i = 0; i < info[k].n_atoms; i++){
1356	+	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1357	+	}
1358	+	}
1359	+	}
1360	+
1361	+
1362	+	void SimSetup::createFF(void){
1363	+	switch (ffCase){
1364	+	case FF_DUFF:
1365	+	the_ff = new DUFF();
1366	+	break;
1367	+
1368	+	case FF_LJ:
1369	+	the_ff = new LJFF();
1370	+	break;
1371	+
1372	+	case FF_EAM:
1373	+	the_ff = new EAM_FF();
1374	+	break;
1375	+
1376	+	case FF_H2O:
1377	+	the_ff = new WATER();
1378	+	break;
1379	+
1380	+	default:
1381	+	sprintf(painCave.errMsg,
1382	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1383	+	painCave.isFatal = 1;
1384	+	simError();
1385	+	}
1386	+
1387	+	#ifdef IS_MPI
1388	+	strcpy(checkPointMsg, "ForceField creation successful");
1389	+	MPIcheckPoint();
1390	+	#endif // is_mpi
1391	+	}
1392	+
1393	+
1394	+	void SimSetup::compList(void){
1395	+	int i;
1396	+	char* id;
1397	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1398	+	LinkedMolStamp* currentStamp = NULL;
1399	+	comp_stamps = new MoleculeStamp * [n_components];
1400	+	bool haveCutoffGroups;
1401	+
1402	+	haveCutoffGroups = false;
1403	+
1404	+	// make an array of molecule stamps that match the components used.
1405	+	// also extract the used stamps out into a separate linked list
1406	+
1407	+	for (i = 0; i < nInfo; i++){
1408	+	info[i].nComponents = n_components;
1409	+	info[i].componentsNmol = components_nmol;
1410	+	info[i].compStamps = comp_stamps;
1411	+	info[i].headStamp = headStamp;
1412	+	}
1413	+
1414	+
1415	+	for (i = 0; i < n_components; i++){
1416	+	id = the_components[i]->getType();
1417	+	comp_stamps[i] = NULL;
1418	+
1419	+	// check to make sure the component isn't already in the list
1420	+
1421	+	comp_stamps[i] = headStamp->match(id);
1422	+	if (comp_stamps[i] == NULL){
1423	+	// extract the component from the list;
1424	+
1425	+	currentStamp = stamps->extractMolStamp(id);
1426	+	if (currentStamp == NULL){
1427	+	sprintf(painCave.errMsg,
1428	+	"SimSetup error: Component \"%s\" was not found in the "
1429	+	"list of declared molecules\n",
1430	+	id);
1431	+	painCave.isFatal = 1;
1432	+	simError();
1433	+	}
1434	+
1435	+	headStamp->add(currentStamp);
1436	+	comp_stamps[i] = headStamp->match(id);
1437	+	}
1438	+
1439	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1440	+	haveCutoffGroups = true;
1441	+	}
1442	+
1443	+	for (i = 0; i < nInfo; i++)
1444	+	info[i].haveCutoffGroups = haveCutoffGroups;
1445	+
1446	+	#ifdef IS_MPI
1447	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1448	+	MPIcheckPoint();
1449	+	#endif // is_mpi
1450	+	}
1451	+
1452	+	void SimSetup::calcSysValues(void){
1453	+	int i;
1454	+
1455	+	int* molMembershipArray;
1456	+
1457	+	tot_atoms = 0;
1458	+	tot_bonds = 0;
1459	+	tot_bends = 0;
1460	+	tot_torsions = 0;
1461	+	tot_rigid = 0;
1462	+	for (i = 0; i < n_components; i++){
1463	+	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1464	+	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1465	+	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1466	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1467	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1468	+	}
1469	+
1470	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1471	+	molMembershipArray = new int[tot_atoms];
1472	+
1473	+	for (i = 0; i < nInfo; i++){
1474	+	info[i].n_atoms = tot_atoms;
1475	+	info[i].n_bonds = tot_bonds;
1476	+	info[i].n_bends = tot_bends;
1477	+	info[i].n_torsions = tot_torsions;
1478	+	info[i].n_SRI = tot_SRI;
1479	+	info[i].n_mol = tot_nmol;
1480	+
1481	+	info[i].molMembershipArray = molMembershipArray;
1482	+	}
1483	+	}
1484	+
1485	+	#ifdef IS_MPI
1486	+
1487	+	void SimSetup::mpiMolDivide(void){
1488	+	int i, j, k;
1489	+	int localMol, allMol;
1490	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1491	+	int local_rigid;
1492	+	vector<int> globalMolIndex;
1493	+
1494	+	mpiSim = new mpiSimulation(info);
1495	+
1496	+	mpiSim->divideLabor();
1497	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1498	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1499	+
1500	+	// set up the local variables
1501	+
1502	+	mol2proc = mpiSim->getMolToProcMap();
1503	+	molCompType = mpiSim->getMolComponentType();
1504	+
1505	+	allMol = 0;
1506	+	localMol = 0;
1507	+	local_atoms = 0;
1508	+	local_bonds = 0;
1509	+	local_bends = 0;
1510	+	local_torsions = 0;
1511	+	local_rigid = 0;
1512	+	globalAtomCounter = 0;
1513	+
1514	+	for (i = 0; i < n_components; i++){
1515	+	for (j = 0; j < components_nmol[i]; j++){
1516	+	if (mol2proc[allMol] == worldRank){
1517	+	local_atoms += comp_stamps[i]->getNAtoms();
1518	+	local_bonds += comp_stamps[i]->getNBonds();
1519	+	local_bends += comp_stamps[i]->getNBends();
1520	+	local_torsions += comp_stamps[i]->getNTorsions();
1521	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1522	+	localMol++;
1523	+	}
1524	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1525	+	info[0].molMembershipArray[globalAtomCounter] = allMol;
1526	+	globalAtomCounter++;
1527	+	}
1528	+
1529	+	allMol++;
1530	+	}
1531	+	}
1532	+	local_SRI = local_bonds + local_bends + local_torsions;
1533	+
1534	+	info[0].n_atoms = mpiSim->getMyNlocal();
1535	+
1536	+
1537	+	if (local_atoms != info[0].n_atoms){
1538	+	sprintf(painCave.errMsg,
1539	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1540	+	"\tlocalAtom (%d) are not equal.\n",
1541	+	info[0].n_atoms, local_atoms);
1542	+	painCave.isFatal = 1;
1543	+	simError();
1544	+	}
1545	+
1546	+	info[0].n_bonds = local_bonds;
1547	+	info[0].n_bends = local_bends;
1548	+	info[0].n_torsions = local_torsions;
1549	+	info[0].n_SRI = local_SRI;
1550	+	info[0].n_mol = localMol;
1551	+
1552	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1553	+	MPIcheckPoint();
1554	+	}
1555	+
1556	+	#endif // is_mpi
1557	+
1558	+
1559	+	void SimSetup::makeSysArrays(void){
1560	+
1561	+	#ifndef IS_MPI
1562	+	int k, j;
1563	+	#endif // is_mpi
1564	+	int i, l;
1565	+
1566	+	Atom** the_atoms;
1567	+	Molecule* the_molecules;
1568	+
1569	+	for (l = 0; l < nInfo; l++){
1570	+	// create the atom and short range interaction arrays
1571	+
1572	+	the_atoms = new Atom * [info[l].n_atoms];
1573	+	the_molecules = new Molecule[info[l].n_mol];
1574	+	int molIndex;
1575	+
1576	+	// initialize the molecule's stampID's
1577	+
1578	+	#ifdef IS_MPI
1579	+
1580	+
1581	+	molIndex = 0;
1582	+	for (i = 0; i < mpiSim->getTotNmol(); i++){
1583	+	if (mol2proc[i] == worldRank){
1584	+	the_molecules[molIndex].setStampID(molCompType[i]);
1585	+	the_molecules[molIndex].setMyIndex(molIndex);
1586	+	the_molecules[molIndex].setGlobalIndex(i);
1587	+	molIndex++;
1588	+	}
1589	+	}
1590	+
1591	+	#else // is_mpi
1592	+
1593	+	molIndex = 0;
1594	+	globalAtomCounter = 0;
1595	+	for (i = 0; i < n_components; i++){
1596	+	for (j = 0; j < components_nmol[i]; j++){
1597	+	the_molecules[molIndex].setStampID(i);
1598	+	the_molecules[molIndex].setMyIndex(molIndex);
1599	+	the_molecules[molIndex].setGlobalIndex(molIndex);
1600	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1601	+	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1602	+	globalAtomCounter++;
1603	+	}
1604	+	molIndex++;
1605	+	}
1606	+	}
1607	+
1608	+
1609	+	#endif // is_mpi
1610	+
1611	+	info[l].globalExcludes = new int;
1612	+	info[l].globalExcludes[0] = 0;
1613	+
1614	+	// set the arrays into the SimInfo object
1615	+
1616	+	info[l].atoms = the_atoms;
1617	+	info[l].molecules = the_molecules;
1618	+	info[l].nGlobalExcludes = 0;
1619	+
1620	+	the_ff->setSimInfo(info);
1621	+	}
1622	+	}
1623	+
1624	+	void SimSetup::makeIntegrator(void){
1625	+	int k;
1626	+
1627	+	NVE<RealIntegrator>* myNVE = NULL;
1628	+	NVT<RealIntegrator>* myNVT = NULL;
1629	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1630	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1631	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1632	+
1633	+	for (k = 0; k < nInfo; k++){
1634	+	switch (ensembleCase){
1635	+	case NVE_ENS:
1636	+	if (globals->haveZconstraints()){
1637	+	setupZConstraint(info[k]);
1638	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1639	+	}
1640	+	else{
1641	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1642	+	}
1643	+
1644	+	info->the_integrator = myNVE;
1645	+	break;
1646	+
1647	+	case NVT_ENS:
1648	+	if (globals->haveZconstraints()){
1649	+	setupZConstraint(info[k]);
1650	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1651	+	}
1652	+	else
1653	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1654	+
1655	+	myNVT->setTargetTemp(globals->getTargetTemp());
1656	+
1657	+	if (globals->haveTauThermostat())
1658	+	myNVT->setTauThermostat(globals->getTauThermostat());
1659	+	else{
1660	+	sprintf(painCave.errMsg,
1661	+	"SimSetup error: If you use the NVT\n"
1662	+	"\tensemble, you must set tauThermostat.\n");
1663	+	painCave.isFatal = 1;
1664	+	simError();
1665	+	}
1666	+
1667	+	info->the_integrator = myNVT;
1668	+	break;
1669	+
1670	+	case NPTi_ENS:
1671	+	if (globals->haveZconstraints()){
1672	+	setupZConstraint(info[k]);
1673	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1674	+	}
1675	+	else
1676	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1677	+
1678	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1679	+
1680	+	if (globals->haveTargetPressure())
1681	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1682	+	else{
1683	+	sprintf(painCave.errMsg,
1684	+	"SimSetup error: If you use a constant pressure\n"
1685	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1686	+	painCave.isFatal = 1;
1687	+	simError();
1688	+	}
1689	+
1690	+	if (globals->haveTauThermostat())
1691	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1692	+	else{
1693	+	sprintf(painCave.errMsg,
1694	+	"SimSetup error: If you use an NPT\n"
1695	+	"\tensemble, you must set tauThermostat.\n");
1696	+	painCave.isFatal = 1;
1697	+	simError();
1698	+	}
1699	+
1700	+	if (globals->haveTauBarostat())
1701	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1702	+	else{
1703	+	sprintf(painCave.errMsg,
1704	+	"SimSetup error: If you use an NPT\n"
1705	+	"\tensemble, you must set tauBarostat.\n");
1706	+	painCave.isFatal = 1;
1707	+	simError();
1708	+	}
1709	+
1710	+	info->the_integrator = myNPTi;
1711	+	break;
1712	+
1713	+	case NPTf_ENS:
1714	+	if (globals->haveZconstraints()){
1715	+	setupZConstraint(info[k]);
1716	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1717	+	}
1718	+	else
1719	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1720	+
1721	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1722	+
1723	+	if (globals->haveTargetPressure())
1724	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1725	+	else{
1726	+	sprintf(painCave.errMsg,
1727	+	"SimSetup error: If you use a constant pressure\n"
1728	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1729	+	painCave.isFatal = 1;
1730	+	simError();
1731	+	}
1732	+
1733	+	if (globals->haveTauThermostat())
1734	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1735	+
1736	+	else{
1737	+	sprintf(painCave.errMsg,
1738	+	"SimSetup error: If you use an NPT\n"
1739	+	"\tensemble, you must set tauThermostat.\n");
1740	+	painCave.isFatal = 1;
1741	+	simError();
1742	+	}
1743	+
1744	+	if (globals->haveTauBarostat())
1745	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1746	+
1747	+	else{
1748	+	sprintf(painCave.errMsg,
1749	+	"SimSetup error: If you use an NPT\n"
1750	+	"\tensemble, you must set tauBarostat.\n");
1751	+	painCave.isFatal = 1;
1752	+	simError();
1753	+	}
1754	+
1755	+	info->the_integrator = myNPTf;
1756	+	break;
1757	+
1758	+	case NPTxyz_ENS:
1759	+	if (globals->haveZconstraints()){
1760	+	setupZConstraint(info[k]);
1761	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1762	+	}
1763	+	else
1764	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1765	+
1766	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1767	+
1768	+	if (globals->haveTargetPressure())
1769	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1770	+	else{
1771	+	sprintf(painCave.errMsg,
1772	+	"SimSetup error: If you use a constant pressure\n"
1773	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1774	+	painCave.isFatal = 1;
1775	+	simError();
1776	+	}
1777	+
1778	+	if (globals->haveTauThermostat())
1779	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1780	+	else{
1781	+	sprintf(painCave.errMsg,
1782	+	"SimSetup error: If you use an NPT\n"
1783	+	"\tensemble, you must set tauThermostat.\n");
1784	+	painCave.isFatal = 1;
1785	+	simError();
1786	+	}
1787	+
1788	+	if (globals->haveTauBarostat())
1789	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1790	+	else{
1791	+	sprintf(painCave.errMsg,
1792	+	"SimSetup error: If you use an NPT\n"
1793	+	"\tensemble, you must set tauBarostat.\n");
1794	+	painCave.isFatal = 1;
1795	+	simError();
1796	+	}
1797	+
1798	+	info->the_integrator = myNPTxyz;
1799	+	break;
1800	+
1801	+	default:
1802	+	sprintf(painCave.errMsg,
1803	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1804	+	painCave.isFatal = 1;
1805	+	simError();
1806	+	}
1807	+	}
1808	+	}
1809	+
1810	+	void SimSetup::initFortran(void){
1811	+	info[0].refreshSim();
1812	+
1813	+	if (!strcmp(info[0].mixingRule, "standard")){
1814	+	the_ff->initForceField(LB_MIXING_RULE);
1815	+	}
1816	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1817	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1818	+	}
1819	+	else{
1820	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1821	+	info[0].mixingRule);
1822	+	painCave.isFatal = 1;
1823	+	simError();
1824	+	}
1825	+
1826	+
1827	+	#ifdef IS_MPI
1828	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1829	+	MPIcheckPoint();
1830	+	#endif // is_mpi
1831	+	}
1832	+
1833	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1834	+	int nZConstraints;
1835	+	ZconStamp** zconStamp;
1836	+
1837	+	if (globals->haveZconstraintTime()){
1838	+	//add sample time of z-constraint  into SimInfo's property list
1839	+	DoubleData* zconsTimeProp = new DoubleData();
1840	+	zconsTimeProp->setID(ZCONSTIME_ID);
1841	+	zconsTimeProp->setData(globals->getZconsTime());
1842	+	theInfo.addProperty(zconsTimeProp);
1843	+	}
1844	+	else{
1845	+	sprintf(painCave.errMsg,
1846	+	"ZConstraint error: If you use a ZConstraint,\n"
1847	+	"\tyou must set zconsTime.\n");
1848	+	painCave.isFatal = 1;
1849	+	simError();
1850	+	}
1851	+
1852	+	//push zconsTol into siminfo, if user does not specify
1853	+	//value for zconsTol, a default value will be used
1854	+	DoubleData* zconsTol = new DoubleData();
1855	+	zconsTol->setID(ZCONSTOL_ID);
1856	+	if (globals->haveZconsTol()){
1857	+	zconsTol->setData(globals->getZconsTol());
1858	+	}
1859	+	else{
1860	+	double defaultZConsTol = 0.01;
1861	+	sprintf(painCave.errMsg,
1862	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1863	+	"\tOOPSE will use a default value of %f.\n"
1864	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1865	+	defaultZConsTol);
1866	+	painCave.isFatal = 0;
1867	+	simError();
1868	+
1869	+	zconsTol->setData(defaultZConsTol);
1870	+	}
1871	+	theInfo.addProperty(zconsTol);
1872	+
1873	+	//set Force Subtraction Policy
1874	+	StringData* zconsForcePolicy = new StringData();
1875	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1876	+
1877	+	if (globals->haveZconsForcePolicy()){
1878	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1879	+	}
1880	+	else{
1881	+	sprintf(painCave.errMsg,
1882	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1883	+	"\tOOPSE will use PolicyByMass.\n"
1884	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1885	+	painCave.isFatal = 0;
1886	+	simError();
1887	+	zconsForcePolicy->setData("BYMASS");
1888	+	}
1889	+
1890	+	theInfo.addProperty(zconsForcePolicy);
1891	+
1892	+	//set zcons gap
1893	+	DoubleData* zconsGap = new DoubleData();
1894	+	zconsGap->setID(ZCONSGAP_ID);
1895	+
1896	+	if (globals->haveZConsGap()){
1897	+	zconsGap->setData(globals->getZconsGap());
1898	+	theInfo.addProperty(zconsGap);
1899	+	}
1900	+
1901	+	//set zcons fixtime
1902	+	DoubleData* zconsFixtime = new DoubleData();
1903	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1904	+
1905	+	if (globals->haveZConsFixTime()){
1906	+	zconsFixtime->setData(globals->getZconsFixtime());
1907	+	theInfo.addProperty(zconsFixtime);
1908	+	}
1909	+
1910	+	//set zconsUsingSMD
1911	+	IntData* zconsUsingSMD = new IntData();
1912	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1913	+
1914	+	if (globals->haveZConsUsingSMD()){
1915	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1916	+	theInfo.addProperty(zconsUsingSMD);
1917	+	}
1918	+
1919	+	//Determine the name of ouput file and add it into SimInfo's property list
1920	+	//Be careful, do not use inFileName, since it is a pointer which
1921	+	//point to a string at master node, and slave nodes do not contain that string
1922	+
1923	+	string zconsOutput(theInfo.finalName);
1924	+
1925	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1926	+
1927	+	StringData* zconsFilename = new StringData();
1928	+	zconsFilename->setID(ZCONSFILENAME_ID);
1929	+	zconsFilename->setData(zconsOutput);
1930	+
1931	+	theInfo.addProperty(zconsFilename);
1932	+
1933	+	//setup index, pos and other parameters of z-constraint molecules
1934	+	nZConstraints = globals->getNzConstraints();
1935	+	theInfo.nZconstraints = nZConstraints;
1936	+
1937	+	zconStamp = globals->getZconStamp();
1938	+	ZConsParaItem tempParaItem;
1939	+
1940	+	ZConsParaData* zconsParaData = new ZConsParaData();
1941	+	zconsParaData->setID(ZCONSPARADATA_ID);
1942	+
1943	+	for (int i = 0; i < nZConstraints; i++){
1944	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1945	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1946	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1947	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1948	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1949	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1950	+	zconsParaData->addItem(tempParaItem);
1951	+	}
1952	+
1953	+	//check the uniqueness of index
1954	+	if(!zconsParaData->isIndexUnique()){
1955	+	sprintf(painCave.errMsg,
1956	+	"ZConstraint Error: molIndex is not unique!\n");
1957	+	painCave.isFatal = 1;
1958	+	simError();
1959	+	}
1960	+
1961	+	//sort the parameters by index of molecules
1962	+	zconsParaData->sortByIndex();
1963	+
1964	+	//push data into siminfo, therefore, we can retrieve later
1965	+	theInfo.addProperty(zconsParaData);
1966	+	}
1967	+
1968	+	void SimSetup::makeMinimizer(){
1969	+
1970	+	OOPSEMinimizer* myOOPSEMinimizer;
1971	+	MinimizerParameterSet* param;
1972	+	char minimizerName[100];
1973	+
1974	+	for (int i = 0; i < nInfo; i++){
1975	+
1976	+	//prepare parameter set for minimizer
1977	+	param = new MinimizerParameterSet();
1978	+	param->setDefaultParameter();
1979	+
1980	+	if (globals->haveMinimizer()){
1981	+	param->setFTol(globals->getMinFTol());
1982	+	}
1983	+
1984	+	if (globals->haveMinGTol()){
1985	+	param->setGTol(globals->getMinGTol());
1986	+	}
1987	+
1988	+	if (globals->haveMinMaxIter()){
1989	+	param->setMaxIteration(globals->getMinMaxIter());
1990	+	}
1991	+
1992	+	if (globals->haveMinWriteFrq()){
1993	+	param->setMaxIteration(globals->getMinMaxIter());
1994	+	}
1995	+
1996	+	if (globals->haveMinWriteFrq()){
1997	+	param->setWriteFrq(globals->getMinWriteFrq());
1998	+	}
1999	+
2000	+	if (globals->haveMinStepSize()){
2001	+	param->setStepSize(globals->getMinStepSize());
2002	+	}
2003	+
2004	+	if (globals->haveMinLSMaxIter()){
2005	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2006	+	}
2007	+
2008	+	if (globals->haveMinLSTol()){
2009	+	param->setLineSearchTol(globals->getMinLSTol());
2010	+	}
2011	+
2012	+	strcpy(minimizerName, globals->getMinimizer());
2013	+
2014	+	if (!strcasecmp(minimizerName, "CG")){
2015	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2016	+	}
2017	+	else if (!strcasecmp(minimizerName, "SD")){
2018	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2019	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2020	+	}
2021	+	else{
2022	+	sprintf(painCave.errMsg,
2023	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2024	+	painCave.isFatal = 0;
2025	+	simError();
2026	+
2027	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2028	+	}
2029	+	info[i].the_integrator = myOOPSEMinimizer;
2030	+
2031	+	//store the minimizer into simInfo
2032	+	info[i].the_minimizer = myOOPSEMinimizer;
2033	+	info[i].has_minimizer = true;
2034	+	}
2035	+
2036	+	}

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