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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 1129 by tim, Thu Apr 22 03:29:30 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	<
216	<	//   //we have the total number of molecules, now we check for molfractions
217	<	//     for( i=0; i<n_components; i++ ){
218	<
219	<	//       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
187	<	#ifdef IS_MPI
188	<	strcpy( checkPointMsg, "Have the number of components" );
189	<	MPIcheckPoint();
190	<	#endif // is_mpi
187	>	bond_pair* theBonds;
188	>	bend_set* theBends;
189	>	torsion_set* theTorsions;
190	>
191	>	set<int> skipList;
192	>
193	>	double phi, theta, psi;
194	>	char* molName;
195	>	char rbName[100];
196	>
197	>	//init the forceField paramters
198	>
199	>	the_ff->readParams();
200	>
201	>	// init the atoms
202	>
203	>	int nMembers, nNew, rb1, rb2;
204
205	<	// make an array of molecule stamps that match the components used.
206	<	// also extract the used stamps out into a separate linked list
205	>	for (k = 0; k < nInfo; k++){
206	>	the_ff->setSimInfo(&(info[k]));
207
208	<	simnfo->nComponents = n_components;
237	<	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++ ){
208	>	atomOffset = 0;
209
210	<	id = the_components[i]->getType();
211	<	comp_stamps[i] = NULL;
212	<
249	<	// check to make sure the component isn't already in the list
210	>	for (i = 0; i < info[k].n_mol; i++){
211	>	stampID = info[k].molecules[i].getStampID();
212	>	molName = comp_stamps[stampID]->getID();
213
214	<	comp_stamps[i] = headStamp->match( id );
215	<	if( comp_stamps[i] == NULL ){
214	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
215	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
216	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
217	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
218	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
219
220	<	// extract the component from the list;
220	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
221	>
222	>	if (molInfo.nBonds > 0)
223	>	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
224	>	else
225	>	molInfo.myBonds = NULL;
226	>
227	>	if (molInfo.nBends > 0)
228	>	molInfo.myBends = new (Bend *) [molInfo.nBends];
229	>	else
230	>	molInfo.myBends = NULL;
231	>
232	>	if (molInfo.nTorsions > 0)
233	>	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
234	>	else
235	>	molInfo.myTorsions = NULL;
236	>
237	>	theBonds = new bond_pair[molInfo.nBonds];
238	>	theBends = new bend_set[molInfo.nBends];
239	>	theTorsions = new torsion_set[molInfo.nTorsions];
240
241	<	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	<	}
241	>	// make the Atoms
242
243	<	#ifdef IS_MPI
244	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
273	<	MPIcheckPoint();
274	<	#endif // is_mpi
275	<
243	>	for (j = 0; j < molInfo.nAtoms; j++){
244	>	currentAtom = comp_stamps[stampID]->getAtom(j);
245
246	+	if (currentAtom->haveOrientation()){
247	+	dAtom = new DirectionalAtom((j + atomOffset),
248	+	info[k].getConfiguration());
249	+	info[k].n_oriented++;
250	+	molInfo.myAtoms[j] = dAtom;
251
252	+	// Directional Atoms have standard unit vectors which are oriented
253	+	// in space using the three Euler angles.  We assume the standard
254	+	// unit vector was originally along the z axis below.
255
256	<	// caclulate the number of atoms, bonds, bends and torsions
256	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
257	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
258	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
259
260	<	tot_atoms = 0;
261	<	tot_bonds = 0;
262	<	tot_bends = 0;
263	<	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	<	}
260	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
261	>
262	>	}
263	>	else{
264
265	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
265	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
266
267	<	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];
267	>	}
268
269	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
270		#ifdef IS_MPI
271
272	<	// divide the molecules among processors here.
307	<
308	<	mpiSim = new mpiSimulation( simnfo );
309	<
310	<	globalIndex = mpiSim->divideLabor();
272	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
273
274	<	// set up the local variables
275	<
314	<	int localMol, allMol;
315	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
274	>	#endif // is_mpi
275	>	}
276
277	<	int* mol2proc = mpiSim->getMolToProcMap();
278	<	int* molCompType = mpiSim->getMolComponentType();
279	<
280	<	allMol = 0;
281	<	localMol = 0;
322	<	local_atoms = 0;
323	<	local_bonds = 0;
324	<	local_bends = 0;
325	<	local_torsions = 0;
326	<	globalAtomIndex = 0;
277	>	// make the bonds
278	>	for (j = 0; j < molInfo.nBonds; j++){
279	>	currentBond = comp_stamps[stampID]->getBond(j);
280	>	theBonds[j].a = currentBond->getA() + atomOffset;
281	>	theBonds[j].b = currentBond->getB() + atomOffset;
282
283	+	tempI = theBonds[j].a;
284	+	tempJ = theBonds[j].b;
285
286	<	for( i=0; i<n_components; i++ ){
286	>	#ifdef IS_MPI
287	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
288	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
289	>	#else
290	>	exI = tempI + 1;
291	>	exJ = tempJ + 1;
292	>	#endif
293
294	<	for( j=0; j<components_nmol[i]; j++ ){
332	<
333	<	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++;
294	>	info[k].excludes->addPair(exI, exJ);
295		}
296
297	<	allMol++;
298	<	}
299	<	}
300	<	local_SRI = local_bonds + local_bends + local_torsions;
301	<
302	<	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	<	}
297	>	//make the bends
298	>	for (j = 0; j < molInfo.nBends; j++){
299	>	currentBend = comp_stamps[stampID]->getBend(j);
300	>	theBends[j].a = currentBend->getA() + atomOffset;
301	>	theBends[j].b = currentBend->getB() + atomOffset;
302	>	theBends[j].c = currentBend->getC() + atomOffset;
303
304	<	simnfo->n_bonds = local_bonds;
305	<	simnfo->n_bends = local_bends;
306	<	simnfo->n_torsions = local_torsions;
366	<	simnfo->n_SRI = local_SRI;
367	<	simnfo->n_mol = localMol;
304	>	if (currentBend->haveExtras()){
305	>	extras = currentBend->getExtras();
306	>	current_extra = extras;
307
308	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
309	<	MPIcheckPoint();
310	<
311	<
312	<	#endif // is_mpi
313	<
308	>	while (current_extra != NULL){
309	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
310	>	switch (current_extra->getType()){
311	>	case 0:
312	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
313	>	theBends[j].isGhost = 1;
314	>	break;
315
316	<	// create the atom and short range interaction arrays
316	>	case 1:
317	>	theBends[j].ghost = (int) current_extra->getDouble() +
318	>	atomOffset;
319	>	theBends[j].isGhost = 1;
320	>	break;
321
322	<	Atom::createArrays(simnfo->n_atoms);
323	<	the_atoms = new Atom*[simnfo->n_atoms];
324	<	the_molecules = new Molecule[simnfo->n_mol];
325	<	int molIndex;
322	>	default:
323	>	sprintf(painCave.errMsg,
324	>	"SimSetup Error: ghostVectorSource was neither a "
325	>	"double nor an int.\n"
326	>	"-->Bend[%d] in %s\n",
327	>	j, comp_stamps[stampID]->getID());
328	>	painCave.isFatal = 1;
329	>	simError();
330	>	}
331	>	}
332	>	else{
333	>	sprintf(painCave.errMsg,
334	>	"SimSetup Error: unhandled bend assignment:\n"
335	>	"    -->%s in Bend[%d] in %s\n",
336	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
337	>	painCave.isFatal = 1;
338	>	simError();
339	>	}
340
341	<	// initialize the molecule's stampID's
341	>	current_extra = current_extra->getNext();
342	>	}
343	>	}
344
345	+	if (theBends[j].isGhost) {
346	+
347	+	tempI = theBends[j].a;
348	+	tempJ = theBends[j].b;
349	+
350		#ifdef IS_MPI
351	<
351	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
352	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
353	>	#else
354	>	exI = tempI + 1;
355	>	exJ = tempJ + 1;
356	>	#endif
357	>	info[k].excludes->addPair(exI, exJ);
358
359	<	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	<	}
359	>	} else {
360
361	<	#else // is_mpi
362	<
363	<	molIndex = 0;
364	<	globalAtomIndex = 0;
365	<	for(i=0; i<n_components; i++){
366	<	for(j=0; j<components_nmol[i]; j++ ){
367	<	the_molecules[molIndex].setStampID( i );
368	<	the_molecules[molIndex].setMyIndex( molIndex );
369	<	the_molecules[molIndex].setGlobalIndex( molIndex );
370	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
371	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
372	<	globalAtomIndex++;
361	>	tempI = theBends[j].a;
362	>	tempJ = theBends[j].b;
363	>	tempK = theBends[j].c;
364	>
365	>	#ifdef IS_MPI
366	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
367	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
368	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
369	>	#else
370	>	exI = tempI + 1;
371	>	exJ = tempJ + 1;
372	>	exK = tempK + 1;
373	>	#endif
374	>
375	>	info[k].excludes->addPair(exI, exK);
376	>	info[k].excludes->addPair(exI, exJ);
377	>	info[k].excludes->addPair(exJ, exK);
378	>	}
379		}
412	–	molIndex++;
413	–	}
414	–	}
415	–
380
381	<	#endif // is_mpi
381	>	for (j = 0; j < molInfo.nTorsions; j++){
382	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
383	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
384	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
385	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
386	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
387
388	+	tempI = theTorsions[j].a;
389	+	tempJ = theTorsions[j].b;
390	+	tempK = theTorsions[j].c;
391	+	tempL = theTorsions[j].d;
392
393	<	if( simnfo->n_SRI ){
394	<
395	<	Exclude::createArray(simnfo->n_SRI);
396	<	the_excludes = new Exclude*[simnfo->n_SRI];
397	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
398	<	simnfo->globalExcludes = new int;
399	<	simnfo->n_exclude = simnfo->n_SRI;
400	<	}
401	<	else{
402	<
403	<	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	<	}
393	>	#ifdef IS_MPI
394	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
395	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
396	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
397	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
398	>	#else
399	>	exI = tempI + 1;
400	>	exJ = tempJ + 1;
401	>	exK = tempK + 1;
402	>	exL = tempL + 1;
403	>	#endif
404
405	<	// set the arrays into the SimInfo object
405	>	info[k].excludes->addPair(exI, exJ);
406	>	info[k].excludes->addPair(exI, exK);
407	>	info[k].excludes->addPair(exI, exL);
408	>	info[k].excludes->addPair(exJ, exK);
409	>	info[k].excludes->addPair(exJ, exL);
410	>	info[k].excludes->addPair(exK, exL);
411	>	}
412
413	<	simnfo->atoms = the_atoms;
414	<	simnfo->molecules = the_molecules;
415	<	simnfo->nGlobalExcludes = 0;
416	<	simnfo->excludes = the_excludes;
413	>
414	>	molInfo.myRigidBodies.clear();
415	>
416	>	for (j = 0; j < molInfo.nRigidBodies; j++){
417
418	+	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
419	+	nMembers = currentRigidBody->getNMembers();
420
421	<	// get some of the tricky things that may still be in the globals
421	>	// Create the Rigid Body:
422
423	<
450	<	if( the_globals->haveBox() ){
451	<	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() ){
423	>	myRB = new RigidBody();
424
425	<	double vol;
426	<	vol = (double)tot_nmol / the_globals->getDensity();
427	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
428	<	simnfo->box_y = simnfo->box_x;
461	<	simnfo->box_z = simnfo->box_x;
462	<	}
463	<	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();
425	>	sprintf(rbName,"%s_RB_%d", molName, j);
426	>	myRB->setType(rbName);
427	>
428	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
429
430	<	if( !the_globals->haveBoxY() ){
431	<	sprintf( painCave.errMsg,
474	<	"SimSetup error, no periodic BoxY size given.\n" );
475	<	painCave.isFatal = 1;
476	<	simError();
477	<	}
478	<	simnfo->box_y = the_globals->getBoxY();
430	>	// molI is atom numbering inside this molecule
431	>	molI = currentRigidBody->getMember(rb1);
432
433	<	if( !the_globals->haveBoxZ() ){
434	<	sprintf( painCave.errMsg,
482	<	"SimSetup error, no periodic BoxZ size given.\n" );
483	<	painCave.isFatal = 1;
484	<	simError();
485	<	}
486	<	simnfo->box_z = the_globals->getBoxZ();
487	<	}
433	>	// tempI is atom numbering on local processor
434	>	tempI = molI + atomOffset;
435
436	<	#ifdef IS_MPI
437	<	strcpy( checkPointMsg, "Box size set up" );
438	<	MPIcheckPoint();
492	<	#endif // is_mpi
436	>	// currentAtom is the AtomStamp (which we need for
437	>	// rigid body reference positions)
438	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
439
440	+	// When we add to the rigid body, add the atom itself and
441	+	// the stamp info:
442
443	<	// initialize the arrays
443	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
444	>
445	>	// Add this atom to the Skip List for the integrators
446	>	#ifdef IS_MPI
447	>	slI = info[k].atoms[tempI]->getGlobalIndex();
448	>	#else
449	>	slI = tempI;
450	>	#endif
451	>	skipList.insert(slI);
452	>
453	>	}
454	>
455	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
456	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
457	>
458	>	tempI = currentRigidBody->getMember(rb1);
459	>	tempJ = currentRigidBody->getMember(rb2);
460	>
461	>	// Some explanation is required here.
462	>	// Fortran indexing starts at 1, while c indexing starts at 0
463	>	// Also, in parallel computations, the GlobalIndex is
464	>	// used for the exclude list:
465	>
466	>	#ifdef IS_MPI
467	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
468	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
469	>	#else
470	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
471	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
472	>	#endif
473	>
474	>	info[k].excludes->addPair(exI, exJ);
475	>
476	>	}
477	>	}
478
479	<	the_ff->setSimInfo( simnfo );
479	>	molInfo.myRigidBodies.push_back(myRB);
480	>	info[k].rigidBodies.push_back(myRB);
481	>	}
482	>
483
484	<	makeMolecules();
485	<	simnfo->identArray = new int[simnfo->n_atoms];
486	<	for(i=0; i<simnfo->n_atoms; i++){
487	<	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) {
484	>	// After this is all set up, scan through the atoms to
485	>	// see if they can be added to the integrableObjects:
486	>
487	>	molInfo.myIntegrableObjects.clear();
488
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	–	}
489
490	<	#ifdef IS_MPI
580	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
581	<	MPIcheckPoint();
582	<	#endif // is_mpi
490	>	for (j = 0; j < molInfo.nAtoms; j++){
491
584	–	if( the_globals->haveInitialConfig() ){
585	–
586	–	InitializeFromFile* fileInit;
587	–	#ifdef IS_MPI // is_mpi
588	–	if( worldRank == 0 ){
589	–	#endif //is_mpi
590	–	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
492		#ifdef IS_MPI
493	<	}else fileInit = new InitializeFromFile( NULL );
493	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
494	>	#else
495	>	slJ = j+atomOffset;
496		#endif
594	–	fileInit->read_xyz( simnfo ); // default velocities on
497
498	<	delete fileInit;
597	<	}
598	<	else{
498	>	// if they aren't on the skip list, then they can be integrated
499
500	<	#ifdef IS_MPI
500	>	if (skipList.find(slJ) == skipList.end()) {
501	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
502	>	info[k].integrableObjects.push_back(mySD);
503	>	molInfo.myIntegrableObjects.push_back(mySD);
504	>	}
505	>	}
506
507	<	// no init from bass
603	<
604	<	sprintf( painCave.errMsg,
605	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
606	<	painCave.isFatal;
607	<	simError();
608	<
609	<	#else
507	>	// all rigid bodies are integrated:
508
509	<	initFromBass();
509	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
510	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
511	>	info[k].integrableObjects.push_back(mySD);
512	>	molInfo.myIntegrableObjects.push_back(mySD);
513	>	}
514	>
515	>
516	>	// send the arrays off to the forceField for init.
517	>
518	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
519	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
520	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
521	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
522	>	theTorsions);
523
524	+	info[k].molecules[i].initialize(molInfo);
525
614	–	#endif
615	–	}
526
527	+	atomOffset += molInfo.nAtoms;
528	+	delete[] theBonds;
529	+	delete[] theBends;
530	+	delete[] theTorsions;
531	+	}
532	+	}
533	+
534		#ifdef IS_MPI
535	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
535	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
536		MPIcheckPoint();
537		#endif // is_mpi
538
539	+	// clean up the forcefield
540
541	<
624	<
625	<
541	>	if (!globals->haveLJrcut()){
542
543	<
544	<	#ifdef IS_MPI
545	<	if( worldRank == 0 ){
630	<	#endif // is_mpi
543	>	the_ff->calcRcut();
544	>
545	>	} else {
546
547	<	if( the_globals->haveFinalConfig() ){
633	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
634	<	}
635	<	else{
636	<	strcpy( simnfo->finalName, inFileName );
637	<	char* endTest;
638	<	int nameLength = strlen( simnfo->finalName );
639	<	endTest = &(simnfo->finalName[nameLength - 5]);
640	<	if( !strcmp( endTest, ".bass" ) ){
641	<	strcpy( endTest, ".eor" );
642	<	}
643	<	else if( !strcmp( endTest, ".BASS" ) ){
644	<	strcpy( endTest, ".eor" );
645	<	}
646	<	else{
647	<	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	<
707	<	#ifdef IS_MPI
547	>	the_ff->setRcut( globals->getLJrcut() );
548		}
709	–	#endif // is_mpi
710	–
711	–	// set the status, sample, and themal kick times
712	–
713	–	if( the_globals->haveSampleTime() ){
714	–	simnfo->sampleTime = the_globals->getSampleTime();
715	–	simnfo->statusTime = simnfo->sampleTime;
716	–	simnfo->thermalTime = simnfo->sampleTime;
717	–	}
718	–	else{
719	–	simnfo->sampleTime = the_globals->getRunTime();
720	–	simnfo->statusTime = simnfo->sampleTime;
721	–	simnfo->thermalTime = simnfo->sampleTime;
722	–	}
549
550	<	if( the_globals->haveStatusTime() ){
551	<	simnfo->statusTime = the_globals->getStatusTime();
726	<	}
550	>	the_ff->cleanMe();
551	>	}
552
553	<	if( the_globals->haveThermalTime() ){
554	<	simnfo->thermalTime = the_globals->getThermalTime();
555	<	}
553	>	void SimSetup::initFromBass(void){
554	>	int i, j, k;
555	>	int n_cells;
556	>	double cellx, celly, cellz;
557	>	double temp1, temp2, temp3;
558	>	int n_per_extra;
559	>	int n_extra;
560	>	int have_extra, done;
561
562	<	// check for the temperature set flag
562	>	double vel[3];
563	>	vel[0] = 0.0;
564	>	vel[1] = 0.0;
565	>	vel[2] = 0.0;
566
567	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
567	>	temp1 = (double) tot_nmol / 4.0;
568	>	temp2 = pow(temp1, (1.0 / 3.0));
569	>	temp3 = ceil(temp2);
570
571	<
572	<	// make the integrator
571	>	have_extra = 0;
572	>	if (temp2 < temp3){
573	>	// we have a non-complete lattice
574	>	have_extra = 1;
575
576	+	n_cells = (int) temp3 - 1;
577	+	cellx = info[0].boxL[0] / temp3;
578	+	celly = info[0].boxL[1] / temp3;
579	+	cellz = info[0].boxL[2] / temp3;
580	+	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
581	+	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
582	+	n_per_extra = (int) ceil(temp1);
583
584	<	if( !strcmp( ensemble, "TraPPE_Ex" ) ){
585	<	new Symplectic(simnfo, the_ff, the_extendedsystem);
586	<	}
587	<	else if( !strcmp( force_field, "LJ" ) ){
744	<	new Verlet( *simnfo, the_ff, the_extendedsystem );
745	<	}
746	<
747	<	#ifdef IS_MPI
748	<	mpiSim->mpiRefresh();
749	<	#endif
750	<
751	<	// initialize the Fortran
752	<
753	<
754	<	simnfo->refreshSim();
755	<
756	<	if( !strcmp( simnfo->mixingRule, "standard") ){
757	<	the_ff->initForceField( LB_MIXING_RULE );
758	<	}
759	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
760	<	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	<	}
769	<
770	<
771	<	#ifdef IS_MPI
772	<	strcpy( checkPointMsg,
773	<	"Successfully intialized the mixingRule for Fortran." );
774	<	MPIcheckPoint();
775	<	#endif // is_mpi
776	<	}
777	<
778	<
779	<	void SimSetup::makeMolecules( void ){
780	<
781	<	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;
790	<
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	<
858	<	#ifdef IS_MPI
859	<
860	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
861	<
862	<	#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;
871	<
872	<	exI = theBonds[j].a;
873	<	exJ = theBonds[j].b;
874	<
875	<	// exclude_I must always be the smaller of the pair
876	<	if( exI > exJ ){
877	<	tempEx = exI;
878	<	exI = exJ;
879	<	exJ = tempEx;
880	<	}
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
889	<
890	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
891	<	#endif  //is_mpi
892	<	}
893	<	excludeOffset += info.nBonds;
894	<
895	<	//make the bends
896	<	for(j=0; j<info.nBends; j++){
897	<
898	<	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	<	}
949	<	}
950	<
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	<	}
961	<
962	<	// 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;
973	<
974	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
975	<	#else  // isn't MPI
976	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
977	<	#endif  //is_mpi
978	<	}
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;
991	<
992	<	// 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;
1010	<
1011	<
1012	<	// send the arrays off to the forceField for init.
1013	<
1014	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1015	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1016	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1017	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1018	<
1019	<
1020	<	the_molecules[i].initialize( info );
1021	<
1022	<
1023	<	atomOffset += info.nAtoms;
1024	<	delete[] theBonds;
1025	<	delete[] theBends;
1026	<	delete[] theTorsions;
1027	<	}
1028	<
1029	<	#ifdef IS_MPI
1030	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1031	<	MPIcheckPoint();
1032	<	#endif // is_mpi
1033	<
1034	<	// clean up the forcefield
1035	<	the_ff->calcRcut();
1036	<	the_ff->cleanMe();
1037	<
1038	<	}
1039	<
1040	<	void SimSetup::initFromBass( void ){
1041	<
1042	<	int i, j, k;
1043	<	int n_cells;
1044	<	double cellx, celly, cellz;
1045	<	double temp1, temp2, temp3;
1046	<	int n_per_extra;
1047	<	int n_extra;
1048	<	int have_extra, done;
1049	<
1050	<	temp1 = (double)tot_nmol / 4.0;
1051	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1052	<	temp3 = ceil( temp2 );
1053	<
1054	<	have_extra =0;
1055	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1056	<	have_extra =1;
1057	<
1058	<	n_cells = (int)temp3 - 1;
1059	<	cellx = simnfo->box_x / temp3;
1060	<	celly = simnfo->box_y / temp3;
1061	<	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 );
1065	<
1066	<	if( n_per_extra > 4){
1067	<	sprintf( painCave.errMsg,
1068	<	"SimSetup error. There has been an error in constructing"
1069	<	" the non-complete lattice.\n" );
584	>	if (n_per_extra > 4){
585	>	sprintf(painCave.errMsg,
586	>	"SimSetup error. There has been an error in constructing"
587	>	" the non-complete lattice.\n");
588		painCave.isFatal = 1;
589		simError();
590		}
591		}
592		else{
593	<	n_cells = (int)temp3;
594	<	cellx = simnfo->box_x / temp3;
595	<	celly = simnfo->box_y / temp3;
596	<	cellz = simnfo->box_z / temp3;
593	>	n_cells = (int) temp3;
594	>	cellx = info[0].boxL[0] / temp3;
595	>	celly = info[0].boxL[1] / temp3;
596	>	cellz = info[0].boxL[2] / temp3;
597		}
598
599		current_mol = 0;
#	Line 1083 | Line 601 | void SimSetup::initFromBass( void ){
601		current_comp = 0;
602		current_atom_ndx = 0;
603
604	<	for( i=0; i < n_cells ; i++ ){
605	<	for( j=0; j < n_cells; j++ ){
606	<	for( k=0; k < n_cells; k++ ){
604	>	for (i = 0; i < n_cells ; i++){
605	>	for (j = 0; j < n_cells; j++){
606	>	for (k = 0; k < n_cells; k++){
607	>	makeElement(i * cellx, j * celly, k * cellz);
608
609	<	makeElement( i * cellx,
1091	<	j * celly,
1092	<	k * cellz );
609	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
610
611	<	makeElement( i * cellx + 0.5 * cellx,
1095	<	j * celly + 0.5 * celly,
1096	<	k * cellz );
611	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
612
613	<	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 );
613	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
614		}
615		}
616		}
617
618	<	if( have_extra ){
618	>	if (have_extra){
619		done = 0;
620
621		int start_ndx;
622	<	for( i=0; i < (n_cells+1) && !done; i++ ){
623	<	for( j=0; j < (n_cells+1) && !done; j++ ){
622	>	for (i = 0; i < (n_cells + 1) && !done; i++){
623	>	for (j = 0; j < (n_cells + 1) && !done; j++){
624	>	if (i < n_cells){
625	>	if (j < n_cells){
626	>	start_ndx = n_cells;
627	>	}
628	>	else
629	>	start_ndx = 0;
630	>	}
631	>	else
632	>	start_ndx = 0;
633
634	<	if( i < n_cells ){
634	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
635	>	makeElement(i * cellx, j * celly, k * cellz);
636	>	done = (current_mol >= tot_nmol);
637
638	<	if( j < n_cells ){
639	<	start_ndx = n_cells;
640	<	}
641	<	else start_ndx = 0;
642	<	}
1123	<	else start_ndx = 0;
638	>	if (!done && n_per_extra > 1){
639	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
640	>	k * cellz);
641	>	done = (current_mol >= tot_nmol);
642	>	}
643
644	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
644	>	if (!done && n_per_extra > 2){
645	>	makeElement(i * cellx, j * celly + 0.5 * celly,
646	>	k * cellz + 0.5 * cellz);
647	>	done = (current_mol >= tot_nmol);
648	>	}
649
650	<	makeElement( i * cellx,
651	<	j * celly,
652	<	k * cellz );
653	<	done = ( current_mol >= tot_nmol );
654	<
655	<	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	<	}
650	>	if (!done && n_per_extra > 3){
651	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
652	>	k * cellz + 0.5 * cellz);
653	>	done = (current_mol >= tot_nmol);
654	>	}
655	>	}
656		}
657		}
658		}
659
660	<
661	<	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 );
660	>	for (i = 0; i < info[0].n_atoms; i++){
661	>	info[0].atoms[i]->setVel(vel);
662		}
663		}
664
665	<	void SimSetup::makeElement( double x, double y, double z ){
1166	<
665	>	void SimSetup::makeElement(double x, double y, double z){
666		int k;
667		AtomStamp* current_atom;
668		DirectionalAtom* dAtom;
669		double rotMat[3][3];
670	+	double pos[3];
671
672	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
673	<
674	<	current_atom = comp_stamps[current_comp]->getAtom( k );
675	<	if( !current_atom->havePosition() ){
676	<	sprintf( painCave.errMsg,
677	<	"SimSetup:initFromBass error.\n"
678	<	"\tComponent %s, atom %s does not have a position specified.\n"
679	<	"\tThe initialization routine is unable to give a start"
680	<	" position.\n",
1181	<	comp_stamps[current_comp]->getID(),
1182	<	current_atom->getType() );
672	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
673	>	current_atom = comp_stamps[current_comp]->getAtom(k);
674	>	if (!current_atom->havePosition()){
675	>	sprintf(painCave.errMsg,
676	>	"SimSetup:initFromBass error.\n"
677	>	"\tComponent %s, atom %s does not have a position specified.\n"
678	>	"\tThe initialization routine is unable to give a start"
679	>	" position.\n",
680	>	comp_stamps[current_comp]->getID(), current_atom->getType());
681		painCave.isFatal = 1;
682		simError();
683		}
684
685	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
686	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
687	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
685	>	pos[0] = x + current_atom->getPosX();
686	>	pos[1] = y + current_atom->getPosY();
687	>	pos[2] = z + current_atom->getPosZ();
688
689	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
689	>	info[0].atoms[current_atom_ndx]->setPos(pos);
690
691	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
691	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
692	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
693
694		rotMat[0][0] = 1.0;
695		rotMat[0][1] = 0.0;
#	Line 1204 | Line 703 | void SimSetup::makeElement( double x, double y, double
703		rotMat[2][1] = 0.0;
704		rotMat[2][2] = 1.0;
705
706	<	dAtom->setA( rotMat );
706	>	dAtom->setA(rotMat);
707		}
708
709		current_atom_ndx++;
#	Line 1213 | Line 712 | void SimSetup::makeElement( double x, double y, double
712		current_mol++;
713		current_comp_mol++;
714
715	<	if( current_comp_mol >= components_nmol[current_comp] ){
1217	<
715	>	if (current_comp_mol >= components_nmol[current_comp]){
716		current_comp_mol = 0;
717		current_comp++;
718	+	}
719	+	}
720	+
721	+
722	+	void SimSetup::gatherInfo(void){
723	+	int i;
724	+
725	+	ensembleCase = -1;
726	+	ffCase = -1;
727	+
728	+	// set the easy ones first
729	+
730	+	for (i = 0; i < nInfo; i++){
731	+	info[i].target_temp = globals->getTargetTemp();
732	+	info[i].dt = globals->getDt();
733	+	info[i].run_time = globals->getRunTime();
734	+	}
735	+	n_components = globals->getNComponents();
736	+
737	+
738	+	// get the forceField
739	+
740	+	strcpy(force_field, globals->getForceField());
741	+
742	+	if (!strcasecmp(force_field, "DUFF")){
743	+	ffCase = FF_DUFF;
744	+	}
745	+	else if (!strcasecmp(force_field, "LJ")){
746	+	ffCase = FF_LJ;
747	+	}
748	+	else if (!strcasecmp(force_field, "EAM")){
749	+	ffCase = FF_EAM;
750	+	}
751	+	else if (!strcasecmp(force_field, "WATER")){
752	+	ffCase = FF_H2O;
753	+	}
754	+	else{
755	+	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
756	+	force_field);
757	+	painCave.isFatal = 1;
758	+	simError();
759	+	}
760	+
761	+	// get the ensemble
762	+
763	+	strcpy(ensemble, globals->getEnsemble());
764	+
765	+	if (!strcasecmp(ensemble, "NVE")){
766	+	ensembleCase = NVE_ENS;
767	+	}
768	+	else if (!strcasecmp(ensemble, "NVT")){
769	+	ensembleCase = NVT_ENS;
770	+	}
771	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
772	+	ensembleCase = NPTi_ENS;
773	+	}
774	+	else if (!strcasecmp(ensemble, "NPTf")){
775	+	ensembleCase = NPTf_ENS;
776	+	}
777	+	else if (!strcasecmp(ensemble, "NPTxyz")){
778	+	ensembleCase = NPTxyz_ENS;
779	+	}
780	+	else{
781	+	sprintf(painCave.errMsg,
782	+	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
783	+	"\treverting to NVE for this simulation.\n",
784	+	ensemble);
785	+	painCave.isFatal = 0;
786	+	simError();
787	+	strcpy(ensemble, "NVE");
788	+	ensembleCase = NVE_ENS;
789	+	}
790	+
791	+	for (i = 0; i < nInfo; i++){
792	+	strcpy(info[i].ensemble, ensemble);
793	+
794	+	// get the mixing rule
795	+
796	+	strcpy(info[i].mixingRule, globals->getMixingRule());
797	+	info[i].usePBC = globals->getPBC();
798	+	}
799	+
800	+	// get the components and calculate the tot_nMol and indvidual n_mol
801	+
802	+	the_components = globals->getComponents();
803	+	components_nmol = new int[n_components];
804	+
805	+
806	+	if (!globals->haveNMol()){
807	+	// we don't have the total number of molecules, so we assume it is
808	+	// given in each component
809	+
810	+	tot_nmol = 0;
811	+	for (i = 0; i < n_components; i++){
812	+	if (!the_components[i]->haveNMol()){
813	+	// we have a problem
814	+	sprintf(painCave.errMsg,
815	+	"SimSetup Error. No global NMol or component NMol given.\n"
816	+	"\tCannot calculate the number of atoms.\n");
817	+	painCave.isFatal = 1;
818	+	simError();
819	+	}
820	+
821	+	tot_nmol += the_components[i]->getNMol();
822	+	components_nmol[i] = the_components[i]->getNMol();
823	+	}
824	+	}
825	+	else{
826	+	sprintf(painCave.errMsg,
827	+	"SimSetup error.\n"
828	+	"\tSorry, the ability to specify total"
829	+	" nMols and then give molfractions in the components\n"
830	+	"\tis not currently supported."
831	+	" Please give nMol in the components.\n");
832	+	painCave.isFatal = 1;
833	+	simError();
834	+	}
835	+
836	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
837	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
838	+	sprintf(painCave.errMsg,
839	+	"Sample time is not divisible by dt.\n"
840	+	"\tThis will result in samples that are not uniformly\n"
841	+	"\tdistributed in time.  If this is a problem, change\n"
842	+	"\tyour sampleTime variable.\n");
843	+	painCave.isFatal = 0;
844	+	simError();
845	+	}
846	+
847	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
848	+	sprintf(painCave.errMsg,
849	+	"Status time is not divisible by dt.\n"
850	+	"\tThis will result in status reports that are not uniformly\n"
851	+	"\tdistributed in time.  If this is a problem, change \n"
852	+	"\tyour statusTime variable.\n");
853	+	painCave.isFatal = 0;
854	+	simError();
855	+	}
856	+
857	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
858	+	sprintf(painCave.errMsg,
859	+	"Thermal time is not divisible by dt.\n"
860	+	"\tThis will result in thermalizations that are not uniformly\n"
861	+	"\tdistributed in time.  If this is a problem, change \n"
862	+	"\tyour thermalTime variable.\n");
863	+	painCave.isFatal = 0;
864	+	simError();
865	+	}
866	+
867	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
868	+	sprintf(painCave.errMsg,
869	+	"Reset time is not divisible by dt.\n"
870	+	"\tThis will result in integrator resets that are not uniformly\n"
871	+	"\tdistributed in time.  If this is a problem, change\n"
872	+	"\tyour resetTime variable.\n");
873	+	painCave.isFatal = 0;
874	+	simError();
875	+	}
876	+
877	+	// set the status, sample, and thermal kick times
878	+
879	+	for (i = 0; i < nInfo; i++){
880	+	if (globals->haveSampleTime()){
881	+	info[i].sampleTime = globals->getSampleTime();
882	+	info[i].statusTime = info[i].sampleTime;
883	+	}
884	+	else{
885	+	info[i].sampleTime = globals->getRunTime();
886	+	info[i].statusTime = info[i].sampleTime;
887	+	}
888	+
889	+	if (globals->haveStatusTime()){
890	+	info[i].statusTime = globals->getStatusTime();
891	+	}
892	+
893	+	if (globals->haveThermalTime()){
894	+	info[i].thermalTime = globals->getThermalTime();
895	+	} else {
896	+	info[i].thermalTime = globals->getRunTime();
897	+	}
898	+
899	+	info[i].resetIntegrator = 0;
900	+	if( globals->haveResetTime() ){
901	+	info[i].resetTime = globals->getResetTime();
902	+	info[i].resetIntegrator = 1;
903	+	}
904	+
905	+	// check for the temperature set flag
906	+
907	+	if (globals->haveTempSet())
908	+	info[i].setTemp = globals->getTempSet();
909	+
910	+	// check for the extended State init
911	+
912	+	info[i].useInitXSstate = globals->getUseInitXSstate();
913	+	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
914	+
915	+	}
916	+
917	+	//setup seed for random number generator
918	+	int seedValue;
919	+
920	+	if (globals->haveSeed()){
921	+	seedValue = globals->getSeed();
922	+
923	+	if(seedValue / 1E9 == 0){
924	+	sprintf(painCave.errMsg,
925	+	"Seed for sprng library should contain at least 9 digits\n"
926	+	"OOPSE will generate a seed for user\n");
927	+	painCave.isFatal = 0;
928	+	simError();
929	+
930	+	//using seed generated by system instead of invalid seed set by user
931	+	#ifndef IS_MPI
932	+	seedValue = make_sprng_seed();
933	+	#else
934	+	if (worldRank == 0){
935	+	seedValue = make_sprng_seed();
936	+	}
937	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
938	+	#endif
939	+	}
940	+	}//end of if branch of globals->haveSeed()
941	+	else{
942	+
943	+	#ifndef IS_MPI
944	+	seedValue = make_sprng_seed();
945	+	#else
946	+	if (worldRank == 0){
947	+	seedValue = make_sprng_seed();
948	+	}
949	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
950	+	#endif
951	+	}//end of globals->haveSeed()
952	+
953	+	for (int i = 0; i < nInfo; i++){
954	+	info[i].setSeed(seedValue);
955	+	}
956	+
957	+	#ifdef IS_MPI
958	+	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
959	+	MPIcheckPoint();
960	+	#endif // is_mpi
961	+	}
962	+
963	+
964	+	void SimSetup::finalInfoCheck(void){
965	+	int index;
966	+	int usesDipoles;
967	+	int usesCharges;
968	+	int i;
969	+
970	+	for (i = 0; i < nInfo; i++){
971	+	// check electrostatic parameters
972	+
973	+	index = 0;
974	+	usesDipoles = 0;
975	+	while ((index < info[i].n_atoms) && !usesDipoles){
976	+	usesDipoles = (info[i].atoms[index])->hasDipole();
977	+	index++;
978	+	}
979	+	index = 0;
980	+	usesCharges = 0;
981	+	while ((index < info[i].n_atoms) && !usesCharges){
982	+	usesCharges= (info[i].atoms[index])->hasCharge();
983	+	index++;
984	+	}
985	+	#ifdef IS_MPI
986	+	int myUse = usesDipoles;
987	+	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
988	+	#endif //is_mpi
989	+
990	+	double theEcr, theEst;
991	+
992	+	if (globals->getUseRF()){
993	+	info[i].useReactionField = 1;
994	+
995	+	if (!globals->haveECR()){
996	+	sprintf(painCave.errMsg,
997	+	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
998	+	"\tOOPSE will use a default value of 15.0 angstroms"
999	+	"\tfor the electrostaticCutoffRadius.\n");
1000	+	painCave.isFatal = 0;
1001	+	simError();
1002	+	theEcr = 15.0;
1003	+	}
1004	+	else{
1005	+	theEcr = globals->getECR();
1006	+	}
1007	+
1008	+	if (!globals->haveEST()){
1009	+	sprintf(painCave.errMsg,
1010	+	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1011	+	"\tOOPSE will use a default value of\n"
1012	+	"\t0.05 * electrostaticCutoffRadius\n"
1013	+	"\tfor the electrostaticSkinThickness\n");
1014	+	painCave.isFatal = 0;
1015	+	simError();
1016	+	theEst = 0.05 * theEcr;
1017	+	}
1018	+	else{
1019	+	theEst = globals->getEST();
1020	+	}
1021	+
1022	+	info[i].setDefaultEcr(theEcr, theEst);
1023	+
1024	+	if (!globals->haveDielectric()){
1025	+	sprintf(painCave.errMsg,
1026	+	"SimSetup Error: No Dielectric constant was set.\n"
1027	+	"\tYou are trying to use Reaction Field without"
1028	+	"\tsetting a dielectric constant!\n");
1029	+	painCave.isFatal = 1;
1030	+	simError();
1031	+	}
1032	+	info[i].dielectric = globals->getDielectric();
1033	+	}
1034	+	else{
1035	+	if (usesDipoles || usesCharges){
1036	+	if (!globals->haveECR()){
1037	+	sprintf(painCave.errMsg,
1038	+	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1039	+	"\tOOPSE will use a default value of 15.0 angstroms"
1040	+	"\tfor the electrostaticCutoffRadius.\n");
1041	+	painCave.isFatal = 0;
1042	+	simError();
1043	+	theEcr = 15.0;
1044	+	}
1045	+	else{
1046	+	theEcr = globals->getECR();
1047	+	}
1048	+
1049	+	if (!globals->haveEST()){
1050	+	sprintf(painCave.errMsg,
1051	+	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1052	+	"\tOOPSE will use a default value of\n"
1053	+	"\t0.05 * electrostaticCutoffRadius\n"
1054	+	"\tfor the electrostaticSkinThickness\n");
1055	+	painCave.isFatal = 0;
1056	+	simError();
1057	+	theEst = 0.05 * theEcr;
1058	+	}
1059	+	else{
1060	+	theEst = globals->getEST();
1061	+	}
1062	+
1063	+	info[i].setDefaultEcr(theEcr, theEst);
1064	+	}
1065	+	}
1066	+	}
1067	+	#ifdef IS_MPI
1068	+	strcpy(checkPointMsg, "post processing checks out");
1069	+	MPIcheckPoint();
1070	+	#endif // is_mpi
1071	+	}
1072	+
1073	+	void SimSetup::initSystemCoords(void){
1074	+	int i;
1075	+
1076	+	char* inName;
1077	+
1078	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1079	+
1080	+	for (i = 0; i < info[0].n_atoms; i++)
1081	+	info[0].atoms[i]->setCoords();
1082	+
1083	+	if (globals->haveInitialConfig()){
1084	+	InitializeFromFile* fileInit;
1085	+	#ifdef IS_MPI // is_mpi
1086	+	if (worldRank == 0){
1087	+	#endif //is_mpi
1088	+	inName = globals->getInitialConfig();
1089	+	fileInit = new InitializeFromFile(inName);
1090	+	#ifdef IS_MPI
1091	+	}
1092	+	else
1093	+	fileInit = new InitializeFromFile(NULL);
1094	+	#endif
1095	+	fileInit->readInit(info); // default velocities on
1096	+
1097	+	delete fileInit;
1098	+	}
1099	+	else{
1100	+
1101	+	// no init from bass
1102	+
1103	+	sprintf(painCave.errMsg,
1104	+	"Cannot intialize a simulation without an initial configuration file.\n");
1105	+	painCave.isFatal = 1;;
1106	+	simError();
1107	+
1108	+	}
1109	+
1110	+	#ifdef IS_MPI
1111	+	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1112	+	MPIcheckPoint();
1113	+	#endif // is_mpi
1114	+	}
1115	+
1116	+
1117	+	void SimSetup::makeOutNames(void){
1118	+	int k;
1119	+
1120	+
1121	+	for (k = 0; k < nInfo; k++){
1122	+	#ifdef IS_MPI
1123	+	if (worldRank == 0){
1124	+	#endif // is_mpi
1125	+
1126	+	if (globals->haveFinalConfig()){
1127	+	strcpy(info[k].finalName, globals->getFinalConfig());
1128	+	}
1129	+	else{
1130	+	strcpy(info[k].finalName, inFileName);
1131	+	char* endTest;
1132	+	int nameLength = strlen(info[k].finalName);
1133	+	endTest = &(info[k].finalName[nameLength - 5]);
1134	+	if (!strcmp(endTest, ".bass")){
1135	+	strcpy(endTest, ".eor");
1136	+	}
1137	+	else if (!strcmp(endTest, ".BASS")){
1138	+	strcpy(endTest, ".eor");
1139	+	}
1140	+	else{
1141	+	endTest = &(info[k].finalName[nameLength - 4]);
1142	+	if (!strcmp(endTest, ".bss")){
1143	+	strcpy(endTest, ".eor");
1144	+	}
1145	+	else if (!strcmp(endTest, ".mdl")){
1146	+	strcpy(endTest, ".eor");
1147	+	}
1148	+	else{
1149	+	strcat(info[k].finalName, ".eor");
1150	+	}
1151	+	}
1152	+	}
1153	+
1154	+	// make the sample and status out names
1155	+
1156	+	strcpy(info[k].sampleName, inFileName);
1157	+	char* endTest;
1158	+	int nameLength = strlen(info[k].sampleName);
1159	+	endTest = &(info[k].sampleName[nameLength - 5]);
1160	+	if (!strcmp(endTest, ".bass")){
1161	+	strcpy(endTest, ".dump");
1162	+	}
1163	+	else if (!strcmp(endTest, ".BASS")){
1164	+	strcpy(endTest, ".dump");
1165	+	}
1166	+	else{
1167	+	endTest = &(info[k].sampleName[nameLength - 4]);
1168	+	if (!strcmp(endTest, ".bss")){
1169	+	strcpy(endTest, ".dump");
1170	+	}
1171	+	else if (!strcmp(endTest, ".mdl")){
1172	+	strcpy(endTest, ".dump");
1173	+	}
1174	+	else{
1175	+	strcat(info[k].sampleName, ".dump");
1176	+	}
1177	+	}
1178	+
1179	+	strcpy(info[k].statusName, inFileName);
1180	+	nameLength = strlen(info[k].statusName);
1181	+	endTest = &(info[k].statusName[nameLength - 5]);
1182	+	if (!strcmp(endTest, ".bass")){
1183	+	strcpy(endTest, ".stat");
1184	+	}
1185	+	else if (!strcmp(endTest, ".BASS")){
1186	+	strcpy(endTest, ".stat");
1187	+	}
1188	+	else{
1189	+	endTest = &(info[k].statusName[nameLength - 4]);
1190	+	if (!strcmp(endTest, ".bss")){
1191	+	strcpy(endTest, ".stat");
1192	+	}
1193	+	else if (!strcmp(endTest, ".mdl")){
1194	+	strcpy(endTest, ".stat");
1195	+	}
1196	+	else{
1197	+	strcat(info[k].statusName, ".stat");
1198	+	}
1199	+	}
1200	+
1201	+	#ifdef IS_MPI
1202	+
1203	+	}
1204	+	#endif // is_mpi
1205	+	}
1206	+	}
1207	+
1208	+
1209	+	void SimSetup::sysObjectsCreation(void){
1210	+	int i, k;
1211	+
1212	+	// create the forceField
1213	+
1214	+	createFF();
1215	+
1216	+	// extract componentList
1217	+
1218	+	compList();
1219	+
1220	+	// calc the number of atoms, bond, bends, and torsions
1221	+
1222	+	calcSysValues();
1223	+
1224	+	#ifdef IS_MPI
1225	+	// divide the molecules among the processors
1226	+
1227	+	mpiMolDivide();
1228	+	#endif //is_mpi
1229	+
1230	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1231	+
1232	+	makeSysArrays();
1233	+
1234	+	// make and initialize the molecules (all but atomic coordinates)
1235	+
1236	+	makeMolecules();
1237	+
1238	+	for (k = 0; k < nInfo; k++){
1239	+	info[k].identArray = new int[info[k].n_atoms];
1240	+	for (i = 0; i < info[k].n_atoms; i++){
1241	+	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1242	+	}
1243	+	}
1244	+	}
1245	+
1246	+
1247	+	void SimSetup::createFF(void){
1248	+	switch (ffCase){
1249	+	case FF_DUFF:
1250	+	the_ff = new DUFF();
1251	+	break;
1252	+
1253	+	case FF_LJ:
1254	+	the_ff = new LJFF();
1255	+	break;
1256	+
1257	+	case FF_EAM:
1258	+	the_ff = new EAM_FF();
1259	+	break;
1260	+
1261	+	case FF_H2O:
1262	+	the_ff = new WATER();
1263	+	break;
1264	+
1265	+	default:
1266	+	sprintf(painCave.errMsg,
1267	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1268	+	painCave.isFatal = 1;
1269	+	simError();
1270	+	}
1271	+
1272	+	#ifdef IS_MPI
1273	+	strcpy(checkPointMsg, "ForceField creation successful");
1274	+	MPIcheckPoint();
1275	+	#endif // is_mpi
1276	+	}
1277	+
1278	+
1279	+	void SimSetup::compList(void){
1280	+	int i;
1281	+	char* id;
1282	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1283	+	LinkedMolStamp* currentStamp = NULL;
1284	+	comp_stamps = new MoleculeStamp * [n_components];
1285	+
1286	+	// make an array of molecule stamps that match the components used.
1287	+	// also extract the used stamps out into a separate linked list
1288	+
1289	+	for (i = 0; i < nInfo; i++){
1290	+	info[i].nComponents = n_components;
1291	+	info[i].componentsNmol = components_nmol;
1292	+	info[i].compStamps = comp_stamps;
1293	+	info[i].headStamp = headStamp;
1294	+	}
1295	+
1296	+
1297	+	for (i = 0; i < n_components; i++){
1298	+	id = the_components[i]->getType();
1299	+	comp_stamps[i] = NULL;
1300	+
1301	+	// check to make sure the component isn't already in the list
1302	+
1303	+	comp_stamps[i] = headStamp->match(id);
1304	+	if (comp_stamps[i] == NULL){
1305	+	// extract the component from the list;
1306	+
1307	+	currentStamp = stamps->extractMolStamp(id);
1308	+	if (currentStamp == NULL){
1309	+	sprintf(painCave.errMsg,
1310	+	"SimSetup error: Component \"%s\" was not found in the "
1311	+	"list of declared molecules\n",
1312	+	id);
1313	+	painCave.isFatal = 1;
1314	+	simError();
1315	+	}
1316	+
1317	+	headStamp->add(currentStamp);
1318	+	comp_stamps[i] = headStamp->match(id);
1319	+	}
1320	+	}
1321	+
1322	+	#ifdef IS_MPI
1323	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1324	+	MPIcheckPoint();
1325	+	#endif // is_mpi
1326	+	}
1327	+
1328	+	void SimSetup::calcSysValues(void){
1329	+	int i;
1330	+
1331	+	int* molMembershipArray;
1332	+
1333	+	tot_atoms = 0;
1334	+	tot_bonds = 0;
1335	+	tot_bends = 0;
1336	+	tot_torsions = 0;
1337	+	tot_rigid = 0;
1338	+	for (i = 0; i < n_components; i++){
1339	+	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1340	+	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1341	+	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1342	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1343	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1344	+	}
1345	+
1346	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1347	+	molMembershipArray = new int[tot_atoms];
1348	+
1349	+	for (i = 0; i < nInfo; i++){
1350	+	info[i].n_atoms = tot_atoms;
1351	+	info[i].n_bonds = tot_bonds;
1352	+	info[i].n_bends = tot_bends;
1353	+	info[i].n_torsions = tot_torsions;
1354	+	info[i].n_SRI = tot_SRI;
1355	+	info[i].n_mol = tot_nmol;
1356	+
1357	+	info[i].molMembershipArray = molMembershipArray;
1358	+	}
1359	+	}
1360	+
1361	+	#ifdef IS_MPI
1362	+
1363	+	void SimSetup::mpiMolDivide(void){
1364	+	int i, j, k;
1365	+	int localMol, allMol;
1366	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1367	+	int local_rigid;
1368	+	vector<int> globalMolIndex;
1369	+
1370	+	mpiSim = new mpiSimulation(info);
1371	+
1372	+	mpiSim->divideLabor();
1373	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1374	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1375	+
1376	+	// set up the local variables
1377	+
1378	+	mol2proc = mpiSim->getMolToProcMap();
1379	+	molCompType = mpiSim->getMolComponentType();
1380	+
1381	+	allMol = 0;
1382	+	localMol = 0;
1383	+	local_atoms = 0;
1384	+	local_bonds = 0;
1385	+	local_bends = 0;
1386	+	local_torsions = 0;
1387	+	local_rigid = 0;
1388	+	globalAtomCounter = 0;
1389	+
1390	+	for (i = 0; i < n_components; i++){
1391	+	for (j = 0; j < components_nmol[i]; j++){
1392	+	if (mol2proc[allMol] == worldRank){
1393	+	local_atoms += comp_stamps[i]->getNAtoms();
1394	+	local_bonds += comp_stamps[i]->getNBonds();
1395	+	local_bends += comp_stamps[i]->getNBends();
1396	+	local_torsions += comp_stamps[i]->getNTorsions();
1397	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1398	+	localMol++;
1399	+	}
1400	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1401	+	info[0].molMembershipArray[globalAtomCounter] = allMol;
1402	+	globalAtomCounter++;
1403	+	}
1404	+
1405	+	allMol++;
1406	+	}
1407	+	}
1408	+	local_SRI = local_bonds + local_bends + local_torsions;
1409	+
1410	+	info[0].n_atoms = mpiSim->getMyNlocal();
1411	+
1412	+
1413	+	if (local_atoms != info[0].n_atoms){
1414	+	sprintf(painCave.errMsg,
1415	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1416	+	"\tlocalAtom (%d) are not equal.\n",
1417	+	info[0].n_atoms, local_atoms);
1418	+	painCave.isFatal = 1;
1419	+	simError();
1420	+	}
1421	+
1422	+	info[0].n_bonds = local_bonds;
1423	+	info[0].n_bends = local_bends;
1424	+	info[0].n_torsions = local_torsions;
1425	+	info[0].n_SRI = local_SRI;
1426	+	info[0].n_mol = localMol;
1427	+
1428	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1429	+	MPIcheckPoint();
1430	+	}
1431	+
1432	+	#endif // is_mpi
1433	+
1434	+
1435	+	void SimSetup::makeSysArrays(void){
1436	+
1437	+	#ifndef IS_MPI
1438	+	int k, j;
1439	+	#endif // is_mpi
1440	+	int i, l;
1441	+
1442	+	Atom** the_atoms;
1443	+	Molecule* the_molecules;
1444	+
1445	+	for (l = 0; l < nInfo; l++){
1446	+	// create the atom and short range interaction arrays
1447	+
1448	+	the_atoms = new Atom * [info[l].n_atoms];
1449	+	the_molecules = new Molecule[info[l].n_mol];
1450	+	int molIndex;
1451	+
1452	+	// initialize the molecule's stampID's
1453	+
1454	+	#ifdef IS_MPI
1455	+
1456	+
1457	+	molIndex = 0;
1458	+	for (i = 0; i < mpiSim->getTotNmol(); i++){
1459	+	if (mol2proc[i] == worldRank){
1460	+	the_molecules[molIndex].setStampID(molCompType[i]);
1461	+	the_molecules[molIndex].setMyIndex(molIndex);
1462	+	the_molecules[molIndex].setGlobalIndex(i);
1463	+	molIndex++;
1464	+	}
1465	+	}
1466	+
1467	+	#else // is_mpi
1468	+
1469	+	molIndex = 0;
1470	+	globalAtomCounter = 0;
1471	+	for (i = 0; i < n_components; i++){
1472	+	for (j = 0; j < components_nmol[i]; j++){
1473	+	the_molecules[molIndex].setStampID(i);
1474	+	the_molecules[molIndex].setMyIndex(molIndex);
1475	+	the_molecules[molIndex].setGlobalIndex(molIndex);
1476	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1477	+	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1478	+	globalAtomCounter++;
1479	+	}
1480	+	molIndex++;
1481	+	}
1482	+	}
1483	+
1484	+
1485	+	#endif // is_mpi
1486	+
1487	+	info[l].globalExcludes = new int;
1488	+	info[l].globalExcludes[0] = 0;
1489	+
1490	+	// set the arrays into the SimInfo object
1491	+
1492	+	info[l].atoms = the_atoms;
1493	+	info[l].molecules = the_molecules;
1494	+	info[l].nGlobalExcludes = 0;
1495	+
1496	+	the_ff->setSimInfo(info);
1497	+	}
1498	+	}
1499	+
1500	+	void SimSetup::makeIntegrator(void){
1501	+	int k;
1502	+
1503	+	NVE<RealIntegrator>* myNVE = NULL;
1504	+	NVT<RealIntegrator>* myNVT = NULL;
1505	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1506	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1507	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1508	+
1509	+	for (k = 0; k < nInfo; k++){
1510	+	switch (ensembleCase){
1511	+	case NVE_ENS:
1512	+	if (globals->haveZconstraints()){
1513	+	setupZConstraint(info[k]);
1514	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1515	+	}
1516	+	else{
1517	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1518	+	}
1519	+
1520	+	info->the_integrator = myNVE;
1521	+	break;
1522	+
1523	+	case NVT_ENS:
1524	+	if (globals->haveZconstraints()){
1525	+	setupZConstraint(info[k]);
1526	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1527	+	}
1528	+	else
1529	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1530	+
1531	+	myNVT->setTargetTemp(globals->getTargetTemp());
1532	+
1533	+	if (globals->haveTauThermostat())
1534	+	myNVT->setTauThermostat(globals->getTauThermostat());
1535	+	else{
1536	+	sprintf(painCave.errMsg,
1537	+	"SimSetup error: If you use the NVT\n"
1538	+	"\tensemble, you must set tauThermostat.\n");
1539	+	painCave.isFatal = 1;
1540	+	simError();
1541	+	}
1542	+
1543	+	info->the_integrator = myNVT;
1544	+	break;
1545	+
1546	+	case NPTi_ENS:
1547	+	if (globals->haveZconstraints()){
1548	+	setupZConstraint(info[k]);
1549	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1550	+	}
1551	+	else
1552	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1553	+
1554	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1555	+
1556	+	if (globals->haveTargetPressure())
1557	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1558	+	else{
1559	+	sprintf(painCave.errMsg,
1560	+	"SimSetup error: If you use a constant pressure\n"
1561	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1562	+	painCave.isFatal = 1;
1563	+	simError();
1564	+	}
1565	+
1566	+	if (globals->haveTauThermostat())
1567	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1568	+	else{
1569	+	sprintf(painCave.errMsg,
1570	+	"SimSetup error: If you use an NPT\n"
1571	+	"\tensemble, you must set tauThermostat.\n");
1572	+	painCave.isFatal = 1;
1573	+	simError();
1574	+	}
1575	+
1576	+	if (globals->haveTauBarostat())
1577	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1578	+	else{
1579	+	sprintf(painCave.errMsg,
1580	+	"SimSetup error: If you use an NPT\n"
1581	+	"\tensemble, you must set tauBarostat.\n");
1582	+	painCave.isFatal = 1;
1583	+	simError();
1584	+	}
1585	+
1586	+	info->the_integrator = myNPTi;
1587	+	break;
1588	+
1589	+	case NPTf_ENS:
1590	+	if (globals->haveZconstraints()){
1591	+	setupZConstraint(info[k]);
1592	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1593	+	}
1594	+	else
1595	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1596	+
1597	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1598	+
1599	+	if (globals->haveTargetPressure())
1600	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1601	+	else{
1602	+	sprintf(painCave.errMsg,
1603	+	"SimSetup error: If you use a constant pressure\n"
1604	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1605	+	painCave.isFatal = 1;
1606	+	simError();
1607	+	}
1608	+
1609	+	if (globals->haveTauThermostat())
1610	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1611	+
1612	+	else{
1613	+	sprintf(painCave.errMsg,
1614	+	"SimSetup error: If you use an NPT\n"
1615	+	"\tensemble, you must set tauThermostat.\n");
1616	+	painCave.isFatal = 1;
1617	+	simError();
1618	+	}
1619	+
1620	+	if (globals->haveTauBarostat())
1621	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1622	+
1623	+	else{
1624	+	sprintf(painCave.errMsg,
1625	+	"SimSetup error: If you use an NPT\n"
1626	+	"\tensemble, you must set tauBarostat.\n");
1627	+	painCave.isFatal = 1;
1628	+	simError();
1629	+	}
1630	+
1631	+	info->the_integrator = myNPTf;
1632	+	break;
1633	+
1634	+	case NPTxyz_ENS:
1635	+	if (globals->haveZconstraints()){
1636	+	setupZConstraint(info[k]);
1637	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1638	+	}
1639	+	else
1640	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1641	+
1642	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1643	+
1644	+	if (globals->haveTargetPressure())
1645	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1646	+	else{
1647	+	sprintf(painCave.errMsg,
1648	+	"SimSetup error: If you use a constant pressure\n"
1649	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1650	+	painCave.isFatal = 1;
1651	+	simError();
1652	+	}
1653	+
1654	+	if (globals->haveTauThermostat())
1655	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1656	+	else{
1657	+	sprintf(painCave.errMsg,
1658	+	"SimSetup error: If you use an NPT\n"
1659	+	"\tensemble, you must set tauThermostat.\n");
1660	+	painCave.isFatal = 1;
1661	+	simError();
1662	+	}
1663	+
1664	+	if (globals->haveTauBarostat())
1665	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1666	+	else{
1667	+	sprintf(painCave.errMsg,
1668	+	"SimSetup error: If you use an NPT\n"
1669	+	"\tensemble, you must set tauBarostat.\n");
1670	+	painCave.isFatal = 1;
1671	+	simError();
1672	+	}
1673	+
1674	+	info->the_integrator = myNPTxyz;
1675	+	break;
1676	+
1677	+	default:
1678	+	sprintf(painCave.errMsg,
1679	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1680	+	painCave.isFatal = 1;
1681	+	simError();
1682	+	}
1683		}
1684		}
1685	+
1686	+	void SimSetup::initFortran(void){
1687	+	info[0].refreshSim();
1688	+
1689	+	if (!strcmp(info[0].mixingRule, "standard")){
1690	+	the_ff->initForceField(LB_MIXING_RULE);
1691	+	}
1692	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1693	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1694	+	}
1695	+	else{
1696	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1697	+	info[0].mixingRule);
1698	+	painCave.isFatal = 1;
1699	+	simError();
1700	+	}
1701	+
1702	+
1703	+	#ifdef IS_MPI
1704	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1705	+	MPIcheckPoint();
1706	+	#endif // is_mpi
1707	+	}
1708	+
1709	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1710	+	int nZConstraints;
1711	+	ZconStamp** zconStamp;
1712	+
1713	+	if (globals->haveZconstraintTime()){
1714	+	//add sample time of z-constraint  into SimInfo's property list
1715	+	DoubleData* zconsTimeProp = new DoubleData();
1716	+	zconsTimeProp->setID(ZCONSTIME_ID);
1717	+	zconsTimeProp->setData(globals->getZconsTime());
1718	+	theInfo.addProperty(zconsTimeProp);
1719	+	}
1720	+	else{
1721	+	sprintf(painCave.errMsg,
1722	+	"ZConstraint error: If you use a ZConstraint,\n"
1723	+	"\tyou must set zconsTime.\n");
1724	+	painCave.isFatal = 1;
1725	+	simError();
1726	+	}
1727	+
1728	+	//push zconsTol into siminfo, if user does not specify
1729	+	//value for zconsTol, a default value will be used
1730	+	DoubleData* zconsTol = new DoubleData();
1731	+	zconsTol->setID(ZCONSTOL_ID);
1732	+	if (globals->haveZconsTol()){
1733	+	zconsTol->setData(globals->getZconsTol());
1734	+	}
1735	+	else{
1736	+	double defaultZConsTol = 0.01;
1737	+	sprintf(painCave.errMsg,
1738	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1739	+	"\tOOPSE will use a default value of %f.\n"
1740	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1741	+	defaultZConsTol);
1742	+	painCave.isFatal = 0;
1743	+	simError();
1744	+
1745	+	zconsTol->setData(defaultZConsTol);
1746	+	}
1747	+	theInfo.addProperty(zconsTol);
1748	+
1749	+	//set Force Subtraction Policy
1750	+	StringData* zconsForcePolicy = new StringData();
1751	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1752	+
1753	+	if (globals->haveZconsForcePolicy()){
1754	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1755	+	}
1756	+	else{
1757	+	sprintf(painCave.errMsg,
1758	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1759	+	"\tOOPSE will use PolicyByMass.\n"
1760	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1761	+	painCave.isFatal = 0;
1762	+	simError();
1763	+	zconsForcePolicy->setData("BYMASS");
1764	+	}
1765	+
1766	+	theInfo.addProperty(zconsForcePolicy);
1767	+
1768	+	//set zcons gap
1769	+	DoubleData* zconsGap = new DoubleData();
1770	+	zconsGap->setID(ZCONSGAP_ID);
1771	+
1772	+	if (globals->haveZConsGap()){
1773	+	zconsGap->setData(globals->getZconsGap());
1774	+	theInfo.addProperty(zconsGap);
1775	+	}
1776	+
1777	+	//set zcons fixtime
1778	+	DoubleData* zconsFixtime = new DoubleData();
1779	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1780	+
1781	+	if (globals->haveZConsFixTime()){
1782	+	zconsFixtime->setData(globals->getZconsFixtime());
1783	+	theInfo.addProperty(zconsFixtime);
1784	+	}
1785	+
1786	+	//set zconsUsingSMD
1787	+	IntData* zconsUsingSMD = new IntData();
1788	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1789	+
1790	+	if (globals->haveZConsUsingSMD()){
1791	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1792	+	theInfo.addProperty(zconsUsingSMD);
1793	+	}
1794	+
1795	+	//Determine the name of ouput file and add it into SimInfo's property list
1796	+	//Be careful, do not use inFileName, since it is a pointer which
1797	+	//point to a string at master node, and slave nodes do not contain that string
1798	+
1799	+	string zconsOutput(theInfo.finalName);
1800	+
1801	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1802	+
1803	+	StringData* zconsFilename = new StringData();
1804	+	zconsFilename->setID(ZCONSFILENAME_ID);
1805	+	zconsFilename->setData(zconsOutput);
1806	+
1807	+	theInfo.addProperty(zconsFilename);
1808	+
1809	+	//setup index, pos and other parameters of z-constraint molecules
1810	+	nZConstraints = globals->getNzConstraints();
1811	+	theInfo.nZconstraints = nZConstraints;
1812	+
1813	+	zconStamp = globals->getZconStamp();
1814	+	ZConsParaItem tempParaItem;
1815	+
1816	+	ZConsParaData* zconsParaData = new ZConsParaData();
1817	+	zconsParaData->setID(ZCONSPARADATA_ID);
1818	+
1819	+	for (int i = 0; i < nZConstraints; i++){
1820	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1821	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1822	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1823	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1824	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1825	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1826	+	zconsParaData->addItem(tempParaItem);
1827	+	}
1828	+
1829	+	//check the uniqueness of index
1830	+	if(!zconsParaData->isIndexUnique()){
1831	+	sprintf(painCave.errMsg,
1832	+	"ZConstraint Error: molIndex is not unique!\n");
1833	+	painCave.isFatal = 1;
1834	+	simError();
1835	+	}
1836	+
1837	+	//sort the parameters by index of molecules
1838	+	zconsParaData->sortByIndex();
1839	+
1840	+	//push data into siminfo, therefore, we can retrieve later
1841	+	theInfo.addProperty(zconsParaData);
1842	+	}
1843	+
1844	+	void SimSetup::makeMinimizer(){
1845	+
1846	+	OOPSEMinimizer* myOOPSEMinimizer;
1847	+	MinimizerParameterSet* param;
1848	+	char minimizerName[100];
1849	+
1850	+	for (int i = 0; i < nInfo; i++){
1851	+
1852	+	//prepare parameter set for minimizer
1853	+	param = new MinimizerParameterSet();
1854	+	param->setDefaultParameter();
1855	+
1856	+	if (globals->haveMinimizer()){
1857	+	param->setFTol(globals->getMinFTol());
1858	+	}
1859	+
1860	+	if (globals->haveMinGTol()){
1861	+	param->setGTol(globals->getMinGTol());
1862	+	}
1863	+
1864	+	if (globals->haveMinMaxIter()){
1865	+	param->setMaxIteration(globals->getMinMaxIter());
1866	+	}
1867	+
1868	+	if (globals->haveMinWriteFrq()){
1869	+	param->setMaxIteration(globals->getMinMaxIter());
1870	+	}
1871	+
1872	+	if (globals->haveMinWriteFrq()){
1873	+	param->setWriteFrq(globals->getMinWriteFrq());
1874	+	}
1875	+
1876	+	if (globals->haveMinStepSize()){
1877	+	param->setStepSize(globals->getMinStepSize());
1878	+	}
1879	+
1880	+	if (globals->haveMinLSMaxIter()){
1881	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1882	+	}
1883	+
1884	+	if (globals->haveMinLSTol()){
1885	+	param->setLineSearchTol(globals->getMinLSTol());
1886	+	}
1887	+
1888	+	strcpy(minimizerName, globals->getMinimizer());
1889	+
1890	+	if (!strcasecmp(minimizerName, "CG")){
1891	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1892	+	}
1893	+	else if (!strcasecmp(minimizerName, "SD")){
1894	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1895	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1896	+	}
1897	+	else{
1898	+	sprintf(painCave.errMsg,
1899	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1900	+	painCave.isFatal = 0;
1901	+	simError();
1902	+
1903	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1904	+	}
1905	+	info[i].the_integrator = myOOPSEMinimizer;
1906	+
1907	+	//store the minimizer into simInfo
1908	+	info[i].the_minimizer = myOOPSEMinimizer;
1909	+	info[i].has_minimizer = true;
1910	+	}
1911	+
1912	+	}

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