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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 586 by mmeineke, Wed Jul 9 22:14:06 2003 UTC vs.
Revision 1214 by gezelter, Tue Jun 1 18:42:58 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 "OOPSEMinimizer.hpp"
14	+	//#include "ConstraintElement.hpp"
15	+	//#include "ConstraintPair.hpp"
16
17		#ifdef IS_MPI
18		#include "mpiBASS.h"
#	Line 14 | Line 21
21
22		// some defines for ensemble and Forcefield  cases
23
24	<	#define NVE_ENS  0
25	<	#define NVT_ENS  1
26	<	#define NPTi_ENS 2
27	<	#define NPTf_ENS 3
24	>	#define NVE_ENS        0
25	>	#define NVT_ENS        1
26	>	#define NPTi_ENS       2
27	>	#define NPTf_ENS       3
28	>	#define NPTxyz_ENS     4
29
30
31	<	#define FF_DUFF 0
32	<	#define FF_LJ   1
31	>	#define FF_DUFF  0
32	>	#define FF_LJ    1
33	>	#define FF_EAM   2
34	>	#define FF_H2O   3
35
36	+	using namespace std;
37
38	+	/**
39	+	* Check whether dividend is divisble by divisor or not
40	+	*/
41	+	bool isDivisible(double dividend, double divisor){
42	+	double tolerance = 0.000001;
43	+	double quotient;
44	+	double diff;
45	+	int intQuotient;
46	+
47	+	quotient = dividend / divisor;
48	+
49	+	if (quotient < 0)
50	+	quotient = -quotient;
51	+
52	+	intQuotient = int (quotient + tolerance);
53	+
54	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
55	+
56	+	if (diff <= tolerance)
57	+	return true;
58	+	else
59	+	return false;
60	+	}
61	+
62		SimSetup::SimSetup(){
63	+
64	+	initSuspend = false;
65	+	isInfoArray = 0;
66	+	nInfo = 1;
67	+
68		stamps = new MakeStamps();
69		globals = new Globals();
70	<
70	>
71	>
72		#ifdef IS_MPI
73	<	strcpy( checkPointMsg, "SimSetup creation successful" );
73	>	strcpy(checkPointMsg, "SimSetup creation successful");
74		MPIcheckPoint();
75		#endif // IS_MPI
76		}
#	Line 39 | Line 80 | SimSetup::~SimSetup(){
80		delete globals;
81		}
82
83	<	void SimSetup::parseFile( char* fileName ){
83	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
84	>	info = the_info;
85	>	nInfo = theNinfo;
86	>	isInfoArray = 1;
87	>	initSuspend = true;
88	>	}
89
90	+
91	+	void SimSetup::parseFile(char* fileName){
92		#ifdef IS_MPI
93	<	if( worldRank == 0 ){
93	>	if (worldRank == 0){
94		#endif // is_mpi
95	<
95	>
96		inFileName = fileName;
97	<	set_interface_stamps( stamps, globals );
98	<
97	>	set_interface_stamps(stamps, globals);
98	>
99		#ifdef IS_MPI
100		mpiEventInit();
101		#endif
102
103	<	yacc_BASS( fileName );
103	>	yacc_BASS(fileName);
104
105		#ifdef IS_MPI
106		throwMPIEvent(NULL);
107		}
108	<	else receiveParse();
108	>	else{
109	>	receiveParse();
110	>	}
111		#endif
112
113		}
114
115		#ifdef IS_MPI
116		void SimSetup::receiveParse(void){
117	<
118	<	set_interface_stamps( stamps, globals );
119	<	mpiEventInit();
120	<	MPIcheckPoint();
71	<	mpiEventLoop();
72	<
117	>	set_interface_stamps(stamps, globals);
118	>	mpiEventInit();
119	>	MPIcheckPoint();
120	>	mpiEventLoop();
121		}
122
123		#endif // is_mpi
124
125	<	void SimSetup::createSim( void ){
125	>	void SimSetup::createSim(void){
126
127	<	MakeStamps *the_stamps;
80	<	Globals* the_globals;
81	<	int i, j, k, globalAtomIndex;
82	<
83	<	int ensembleCase;
84	<	int ffCase;
85	<
86	<	ensembleCase = -1;
87	<	ffCase = -1;
127	>	// gather all of the information from the Bass file
128
129	<	// get the stamps and globals;
90	<	the_stamps = stamps;
91	<	the_globals = globals;
129	>	gatherInfo();
130
131	<	// set the easy ones first
94	<	simnfo->target_temp = the_globals->getTargetTemp();
95	<	simnfo->dt = the_globals->getDt();
96	<	simnfo->run_time = the_globals->getRunTime();
131	>	// creation of complex system objects
132
133	<	// get the ones we know are there, yet still may need some work.
99	<	n_components = the_globals->getNComponents();
100	<	strcpy( force_field, the_globals->getForceField() );
133	>	sysObjectsCreation();
134
135	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
103	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
104	<	else{
105	<	sprintf( painCave.errMsg,
106	<	"SimSetup Error. Unrecognized force field -> %s\n",
107	<	force_field );
108	<	painCave.isFatal = 1;
109	<	simError();
110	<	}
135	>	// check on the post processing info
136
137	<	// get the ensemble:
113	<	strcpy( ensemble, the_globals->getEnsemble() );
137	>	finalInfoCheck();
138
139	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
140	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
141	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
142	<	ensembleCase = NPTi_ENS;
143	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
144	<	else{
145	<	sprintf( painCave.errMsg,
122	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
123	<	"reverting to NVE for this simulation.\n",
124	<	ensemble );
125	<	painCave.isFatal = 0;
126	<	simError();
127	<	strcpy( ensemble, "NVE" );
128	<	ensembleCase = NVE_ENS;
139	>	// initialize the system coordinates
140	>
141	>	if ( !initSuspend ){
142	>	initSystemCoords();
143	>
144	>	if( !(globals->getUseInitTime()) )
145	>	info[0].currentTime = 0.0;
146		}
130	–	strcpy( simnfo->ensemble, ensemble );
147
148	+	// make the output filenames
149
150	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
151	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
152	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
153	<	//     if (the_globals->haveTargetPressure())
154	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
138	<	//     else {
139	<	//       sprintf( painCave.errMsg,
140	<	//                "SimSetup error: If you use the constant pressure\n"
141	<	//                "    ensemble, you must set targetPressure.\n"
142	<	//                "    This was found in the BASS file.\n");
143	<	//       painCave.isFatal = 1;
144	<	//       simError();
145	<	//     }
150	>	makeOutNames();
151	>
152	>	#ifdef IS_MPI
153	>	mpiSim->mpiRefresh();
154	>	#endif
155
156	<	//     if (the_globals->haveTauThermostat())
148	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
149	<	//     else if (the_globals->haveQmass())
150	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
151	<	//     else {
152	<	//       sprintf( painCave.errMsg,
153	<	//                "SimSetup error: If you use one of the constant temperature\n"
154	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
155	<	//                "    Neither of these was found in the BASS file.\n");
156	<	//       painCave.isFatal = 1;
157	<	//       simError();
158	<	//     }
156	>	// initialize the Fortran
157
158	<	//     if (the_globals->haveTauBarostat())
161	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
162	<	//     else {
163	<	//       sprintf( painCave.errMsg,
164	<	//                "SimSetup error: If you use the constant pressure\n"
165	<	//                "    ensemble, you must set tauBarostat.\n"
166	<	//                "    This was found in the BASS file.\n");
167	<	//       painCave.isFatal = 1;
168	<	//       simError();
169	<	//     }
158	>	initFortran();
159
160	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
161	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
162	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
160	>	if (globals->haveMinimizer())
161	>	// make minimizer
162	>	makeMinimizer();
163	>	else
164	>	// make the integrator
165	>	makeIntegrator();
166
167	<	//     if (the_globals->haveTauThermostat())
176	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
177	<	//     else if (the_globals->haveQmass())
178	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
179	<	//     else {
180	<	//       sprintf( painCave.errMsg,
181	<	//                "SimSetup error: If you use one of the constant temperature\n"
182	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
183	<	//                "    Neither of these was found in the BASS file.\n");
184	<	//       painCave.isFatal = 1;
185	<	//       simError();
186	<	//     }
167	>	}
168
188	–	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
189	–	simnfo->usePBC = the_globals->getPBC();
190	–
191	–	int usesDipoles = 0;
192	–	switch( ffCase ){
169
170	<	case FF_DUFF:
171	<	the_ff = new DUFF();
172	<	usesDipoles = 1;
173	<	break;
170	>	void SimSetup::makeMolecules(void){
171	>	int i, j, k;
172	>	int exI, exJ, exK, exL, slI, slJ;
173	>	int tempI, tempJ, tempK, tempL;
174	>	int molI, globalID;
175	>	int stampID, atomOffset, rbOffset, groupOffset;
176	>	molInit molInfo;
177	>	DirectionalAtom* dAtom;
178	>	RigidBody* myRB;
179	>	StuntDouble* mySD;
180	>	LinkedAssign* extras;
181	>	LinkedAssign* current_extra;
182	>	AtomStamp* currentAtom;
183	>	BondStamp* currentBond;
184	>	BendStamp* currentBend;
185	>	TorsionStamp* currentTorsion;
186	>	RigidBodyStamp* currentRigidBody;
187	>	CutoffGroupStamp* currentCutoffGroup;
188	>	CutoffGroup* myCutoffGroup;
189	>	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
190	>	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
191
192	<	case FF_LJ:
193	<	the_ff = new LJFF();
194	<	break;
192	>	bond_pair* theBonds;
193	>	bend_set* theBends;
194	>	torsion_set* theTorsions;
195
196	<	default:
204	<	sprintf( painCave.errMsg,
205	<	"SimSetup Error. Unrecognized force field in case statement.\n");
206	<	painCave.isFatal = 1;
207	<	simError();
208	<	}
196	>	set<int> skipList;
197
198	<	#ifdef IS_MPI
199	<	strcpy( checkPointMsg, "ForceField creation successful" );
200	<	MPIcheckPoint();
213	<	#endif // is_mpi
198	>	double phi, theta, psi;
199	>	char* molName;
200	>	char rbName[100];
201
202	<	// get the components and calculate the tot_nMol and indvidual n_mol
203	<	the_components = the_globals->getComponents();
204	<	components_nmol = new int[n_components];
205	<	comp_stamps = new MoleculeStamp*[n_components];
202	>	//ConstraintPair* consPair; //constraint pair
203	>	//ConstraintElement* consElement1;  //first element of constraint pair
204	>	//ConstraintElement* consElement2;  //second element of constraint pair
205	>	//int whichRigidBody;
206	>	//int consAtomIndex;  //index of constraint atom in rigid body's atom array
207	>	//vector<pair<int, int> > jointAtoms;
208	>	//init the forceField paramters
209
210	<	if( !the_globals->haveNMol() ){
221	<	// we don't have the total number of molecules, so we assume it is
222	<	// given in each component
210	>	the_ff->readParams();
211
212	<	tot_nmol = 0;
225	<	for( i=0; i<n_components; i++ ){
212	>	// init the atoms
213
214	<	if( !the_components[i]->haveNMol() ){
228	<	// we have a problem
229	<	sprintf( painCave.errMsg,
230	<	"SimSetup Error. No global NMol or component NMol"
231	<	" given. Cannot calculate the number of atoms.\n" );
232	<	painCave.isFatal = 1;
233	<	simError();
234	<	}
214	>	int nMembers, nNew, rb1, rb2;
215
216	<	tot_nmol += the_components[i]->getNMol();
217	<	components_nmol[i] = the_components[i]->getNMol();
238	<	}
239	<	}
240	<	else{
241	<	sprintf( painCave.errMsg,
242	<	"SimSetup error.\n"
243	<	"\tSorry, the ability to specify total"
244	<	" nMols and then give molfractions in the components\n"
245	<	"\tis not currently supported."
246	<	" Please give nMol in the components.\n" );
247	<	painCave.isFatal = 1;
248	<	simError();
249	<
250	<
251	<	//     tot_nmol = the_globals->getNMol();
252	<
253	<	//   //we have the total number of molecules, now we check for molfractions
254	<	//     for( i=0; i<n_components; i++ ){
255	<
256	<	//       if( !the_components[i]->haveMolFraction() ){
257	<
258	<	//  if( !the_components[i]->haveNMol() ){
259	<	//    //we have a problem
260	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
261	<	//              << " nMol was given in component
262	<
263	<	}
216	>	for (k = 0; k < nInfo; k++){
217	>	the_ff->setSimInfo(&(info[k]));
218
219		#ifdef IS_MPI
220	<	strcpy( checkPointMsg, "Have the number of components" );
221	<	MPIcheckPoint();
222	<	#endif // is_mpi
220	>	info[k].globalGroupMembership = new int[mpiSim->getNAtomsGlobal()];
221	>	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
222	>	info[k].globalGroupMembership[i] = 0;
223	>	#else
224	>	info[k].globalGroupMembership = new int[info[k].n_atoms];
225	>	for (i = 0; i < info[k].n_atoms; i++)
226	>	info[k].globalGroupMembership[i] = 0;
227	>	#endif
228
229	<	// make an array of molecule stamps that match the components used.
230	<	// also extract the used stamps out into a separate linked list
229	>	atomOffset = 0;
230	>	groupOffset = 0;
231
232	<	simnfo->nComponents = n_components;
233	<	simnfo->componentsNmol = components_nmol;
234	<	simnfo->compStamps = comp_stamps;
276	<	simnfo->headStamp = new LinkedMolStamp();
277	<
278	<	char* id;
279	<	LinkedMolStamp* headStamp = simnfo->headStamp;
280	<	LinkedMolStamp* currentStamp = NULL;
281	<	for( i=0; i<n_components; i++ ){
232	>	for (i = 0; i < info[k].n_mol; i++){
233	>	stampID = info[k].molecules[i].getStampID();
234	>	molName = comp_stamps[stampID]->getID();
235
236	<	id = the_components[i]->getType();
237	<	comp_stamps[i] = NULL;
238	<
239	<	// check to make sure the component isn't already in the list
236	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
237	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
238	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
239	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
240	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
241
242	<	comp_stamps[i] = headStamp->match( id );
289	<	if( comp_stamps[i] == NULL ){
242	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
243
244	<	// extract the component from the list;
292	<
293	<	currentStamp = the_stamps->extractMolStamp( id );
294	<	if( currentStamp == NULL ){
295	<	sprintf( painCave.errMsg,
296	<	"SimSetup error: Component \"%s\" was not found in the "
297	<	"list of declared molecules\n",
298	<	id );
299	<	painCave.isFatal = 1;
300	<	simError();
301	<	}
302	<
303	<	headStamp->add( currentStamp );
304	<	comp_stamps[i] = headStamp->match( id );
305	<	}
306	<	}
244	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
245
246	<	#ifdef IS_MPI
247	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
248	<	MPIcheckPoint();
249	<	#endif // is_mpi
312	<
246	>	if (molInfo.nBonds > 0)
247	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
248	>	else
249	>	molInfo.myBonds = NULL;
250
251	+	if (molInfo.nBends > 0)
252	+	molInfo.myBends = new Bend*[molInfo.nBends];
253	+	else
254	+	molInfo.myBends = NULL;
255
256	+	if (molInfo.nTorsions > 0)
257	+	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
258	+	else
259	+	molInfo.myTorsions = NULL;
260
261	<	// caclulate the number of atoms, bonds, bends and torsions
261	>	theBonds = new bond_pair[molInfo.nBonds];
262	>	theBends = new bend_set[molInfo.nBends];
263	>	theTorsions = new torsion_set[molInfo.nTorsions];
264	>
265	>	// make the Atoms
266
267	<	tot_atoms = 0;
268	<	tot_bonds = 0;
320	<	tot_bends = 0;
321	<	tot_torsions = 0;
322	<	for( i=0; i<n_components; i++ ){
323	<
324	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
325	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
326	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
327	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
328	<	}
267	>	for (j = 0; j < molInfo.nAtoms; j++){
268	>	currentAtom = comp_stamps[stampID]->getAtom(j);
269
270	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
270	>	if (currentAtom->haveOrientation()){
271	>	dAtom = new DirectionalAtom((j + atomOffset),
272	>	info[k].getConfiguration());
273	>	info[k].n_oriented++;
274	>	molInfo.myAtoms[j] = dAtom;
275
276	<	simnfo->n_atoms = tot_atoms;
277	<	simnfo->n_bonds = tot_bonds;
278	<	simnfo->n_bends = tot_bends;
335	<	simnfo->n_torsions = tot_torsions;
336	<	simnfo->n_SRI = tot_SRI;
337	<	simnfo->n_mol = tot_nmol;
338	<
339	<	simnfo->molMembershipArray = new int[tot_atoms];
276	>	// Directional Atoms have standard unit vectors which are oriented
277	>	// in space using the three Euler angles.  We assume the standard
278	>	// unit vector was originally along the z axis below.
279
280	<	#ifdef IS_MPI
280	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
281	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
282	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
283
284	<	// divide the molecules among processors here.
285	<
286	<	mpiSim = new mpiSimulation( simnfo );
287	<
347	<	globalIndex = mpiSim->divideLabor();
284	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
285	>
286	>	}
287	>	else{
288
289	<	// set up the local variables
350	<
351	<	int localMol, allMol;
352	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
289	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
290
291	<	int* mol2proc = mpiSim->getMolToProcMap();
355	<	int* molCompType = mpiSim->getMolComponentType();
356	<
357	<	allMol = 0;
358	<	localMol = 0;
359	<	local_atoms = 0;
360	<	local_bonds = 0;
361	<	local_bends = 0;
362	<	local_torsions = 0;
363	<	globalAtomIndex = 0;
291	>	}
292
293	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
294	+	#ifdef IS_MPI
295	+	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
296	+	#endif // is_mpi
297	+	}
298
299	<	for( i=0; i<n_components; i++ ){
299	>	// make the bonds
300	>	for (j = 0; j < molInfo.nBonds; j++){
301	>	currentBond = comp_stamps[stampID]->getBond(j);
302	>	theBonds[j].a = currentBond->getA() + atomOffset;
303	>	theBonds[j].b = currentBond->getB() + atomOffset;
304
305	<	for( j=0; j<components_nmol[i]; j++ ){
306	<
370	<	if( mol2proc[allMol] == worldRank ){
371	<
372	<	local_atoms +=    comp_stamps[i]->getNAtoms();
373	<	local_bonds +=    comp_stamps[i]->getNBonds();
374	<	local_bends +=    comp_stamps[i]->getNBends();
375	<	local_torsions += comp_stamps[i]->getNTorsions();
376	<	localMol++;
377	<	}
378	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
379	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
380	<	globalAtomIndex++;
381	<	}
305	>	tempI = theBonds[j].a;
306	>	tempJ = theBonds[j].b;
307
308	<	allMol++;
309	<	}
310	<	}
311	<	local_SRI = local_bonds + local_bends + local_torsions;
312	<
313	<	simnfo->n_atoms = mpiSim->getMyNlocal();
314	<
390	<	if( local_atoms != simnfo->n_atoms ){
391	<	sprintf( painCave.errMsg,
392	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
393	<	" localAtom (%d) are not equal.\n",
394	<	simnfo->n_atoms,
395	<	local_atoms );
396	<	painCave.isFatal = 1;
397	<	simError();
398	<	}
308	>	#ifdef IS_MPI
309	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
310	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
311	>	#else
312	>	exI = tempI + 1;
313	>	exJ = tempJ + 1;
314	>	#endif
315
316	<	simnfo->n_bonds = local_bonds;
317	<	simnfo->n_bends = local_bends;
402	<	simnfo->n_torsions = local_torsions;
403	<	simnfo->n_SRI = local_SRI;
404	<	simnfo->n_mol = localMol;
316	>	info[k].excludes->addPair(exI, exJ);
317	>	}
318
319	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
320	<	MPIcheckPoint();
321	<
322	<
323	<	#endif // is_mpi
324	<
319	>	//make the bends
320	>	for (j = 0; j < molInfo.nBends; j++){
321	>	currentBend = comp_stamps[stampID]->getBend(j);
322	>	theBends[j].a = currentBend->getA() + atomOffset;
323	>	theBends[j].b = currentBend->getB() + atomOffset;
324	>	theBends[j].c = currentBend->getC() + atomOffset;
325
326	<	// create the atom and short range interaction arrays
326	>	if (currentBend->haveExtras()){
327	>	extras = currentBend->getExtras();
328	>	current_extra = extras;
329
330	<	Atom::createArrays(simnfo->n_atoms);
331	<	the_atoms = new Atom*[simnfo->n_atoms];
332	<	the_molecules = new Molecule[simnfo->n_mol];
333	<	int molIndex;
330	>	while (current_extra != NULL){
331	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
332	>	switch (current_extra->getType()){
333	>	case 0:
334	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
335	>	theBends[j].isGhost = 1;
336	>	break;
337
338	<	// initialize the molecule's stampID's
338	>	case 1:
339	>	theBends[j].ghost = (int) current_extra->getDouble() +
340	>	atomOffset;
341	>	theBends[j].isGhost = 1;
342	>	break;
343
344	+	default:
345	+	sprintf(painCave.errMsg,
346	+	"SimSetup Error: ghostVectorSource was neither a "
347	+	"double nor an int.\n"
348	+	"-->Bend[%d] in %s\n",
349	+	j, comp_stamps[stampID]->getID());
350	+	painCave.isFatal = 1;
351	+	simError();
352	+	}
353	+	}
354	+	else{
355	+	sprintf(painCave.errMsg,
356	+	"SimSetup Error: unhandled bend assignment:\n"
357	+	"    -->%s in Bend[%d] in %s\n",
358	+	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
359	+	painCave.isFatal = 1;
360	+	simError();
361	+	}
362	+
363	+	current_extra = current_extra->getNext();
364	+	}
365	+	}
366	+
367	+	if (theBends[j].isGhost) {
368	+
369	+	tempI = theBends[j].a;
370	+	tempJ = theBends[j].b;
371	+
372		#ifdef IS_MPI
373	<
373	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
374	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
375	>	#else
376	>	exI = tempI + 1;
377	>	exJ = tempJ + 1;
378	>	#endif
379	>	info[k].excludes->addPair(exI, exJ);
380
381	<	molIndex = 0;
426	<	for(i=0; i<mpiSim->getTotNmol(); i++){
427	<
428	<	if(mol2proc[i] == worldRank ){
429	<	the_molecules[molIndex].setStampID( molCompType[i] );
430	<	the_molecules[molIndex].setMyIndex( molIndex );
431	<	the_molecules[molIndex].setGlobalIndex( i );
432	<	molIndex++;
433	<	}
434	<	}
381	>	} else {
382
383	<	#else // is_mpi
384	<
385	<	molIndex = 0;
386	<	globalAtomIndex = 0;
387	<	for(i=0; i<n_components; i++){
388	<	for(j=0; j<components_nmol[i]; j++ ){
389	<	the_molecules[molIndex].setStampID( i );
390	<	the_molecules[molIndex].setMyIndex( molIndex );
391	<	the_molecules[molIndex].setGlobalIndex( molIndex );
392	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
393	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
394	<	globalAtomIndex++;
383	>	tempI = theBends[j].a;
384	>	tempJ = theBends[j].b;
385	>	tempK = theBends[j].c;
386	>
387	>	#ifdef IS_MPI
388	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
389	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
390	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
391	>	#else
392	>	exI = tempI + 1;
393	>	exJ = tempJ + 1;
394	>	exK = tempK + 1;
395	>	#endif
396	>
397	>	info[k].excludes->addPair(exI, exK);
398	>	info[k].excludes->addPair(exI, exJ);
399	>	info[k].excludes->addPair(exJ, exK);
400	>	}
401		}
449	–	molIndex++;
450	–	}
451	–	}
452	–
402
403	<	#endif // is_mpi
403	>	for (j = 0; j < molInfo.nTorsions; j++){
404	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
405	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
406	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
407	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
408	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
409
410	+	tempI = theTorsions[j].a;
411	+	tempJ = theTorsions[j].b;
412	+	tempK = theTorsions[j].c;
413	+	tempL = theTorsions[j].d;
414
415	<	if( simnfo->n_SRI ){
416	<
417	<	Exclude::createArray(simnfo->n_SRI);
418	<	the_excludes = new Exclude*[simnfo->n_SRI];
419	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
420	<	simnfo->globalExcludes = new int;
421	<	simnfo->n_exclude = simnfo->n_SRI;
422	<	}
423	<	else{
424	<
425	<	Exclude::createArray( 1 );
468	<	the_excludes = new Exclude*;
469	<	the_excludes[0] = new Exclude(0);
470	<	the_excludes[0]->setPair( 0,0 );
471	<	simnfo->globalExcludes = new int;
472	<	simnfo->globalExcludes[0] = 0;
473	<	simnfo->n_exclude = 0;
474	<	}
415	>	#ifdef IS_MPI
416	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
417	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
418	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
419	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
420	>	#else
421	>	exI = tempI + 1;
422	>	exJ = tempJ + 1;
423	>	exK = tempK + 1;
424	>	exL = tempL + 1;
425	>	#endif
426
427	<	// set the arrays into the SimInfo object
427	>	info[k].excludes->addPair(exI, exJ);
428	>	info[k].excludes->addPair(exI, exK);
429	>	info[k].excludes->addPair(exI, exL);
430	>	info[k].excludes->addPair(exJ, exK);
431	>	info[k].excludes->addPair(exJ, exL);
432	>	info[k].excludes->addPair(exK, exL);
433	>	}
434
435	<	simnfo->atoms = the_atoms;
436	<	simnfo->molecules = the_molecules;
437	<	simnfo->nGlobalExcludes = 0;
438	<	simnfo->excludes = the_excludes;
435	>
436	>	molInfo.myRigidBodies.clear();
437	>
438	>	for (j = 0; j < molInfo.nRigidBodies; j++){
439
440	+	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
441	+	nMembers = currentRigidBody->getNMembers();
442
443	<	// get some of the tricky things that may still be in the globals
443	>	// Create the Rigid Body:
444
445	<	double boxVector[3];
487	<	if( the_globals->haveBox() ){
488	<	boxVector[0] = the_globals->getBox();
489	<	boxVector[1] = the_globals->getBox();
490	<	boxVector[2] = the_globals->getBox();
491	<
492	<	simnfo->setBox( boxVector );
493	<	}
494	<	else if( the_globals->haveDensity() ){
445	>	myRB = new RigidBody();
446
447	<	double vol;
448	<	vol = (double)tot_nmol / the_globals->getDensity();
449	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
450	<	boxVector[1] = boxVector[0];
500	<	boxVector[2] = boxVector[0];
447	>	sprintf(rbName,"%s_RB_%d", molName, j);
448	>	myRB->setType(rbName);
449	>
450	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
451
452	<	simnfo->setBox( boxVector );
453	<	}
504	<	else{
505	<	if( !the_globals->haveBoxX() ){
506	<	sprintf( painCave.errMsg,
507	<	"SimSetup error, no periodic BoxX size given.\n" );
508	<	painCave.isFatal = 1;
509	<	simError();
510	<	}
511	<	boxVector[0] = the_globals->getBoxX();
452	>	// molI is atom numbering inside this molecule
453	>	molI = currentRigidBody->getMember(rb1);
454
455	<	if( !the_globals->haveBoxY() ){
456	<	sprintf( painCave.errMsg,
515	<	"SimSetup error, no periodic BoxY size given.\n" );
516	<	painCave.isFatal = 1;
517	<	simError();
518	<	}
519	<	boxVector[1] = the_globals->getBoxY();
455	>	// tempI is atom numbering on local processor
456	>	tempI = molI + atomOffset;
457
458	<	if( !the_globals->haveBoxZ() ){
459	<	sprintf( painCave.errMsg,
460	<	"SimSetup error, no periodic BoxZ size given.\n" );
524	<	painCave.isFatal = 1;
525	<	simError();
526	<	}
527	<	boxVector[2] = the_globals->getBoxZ();
458	>	// currentAtom is the AtomStamp (which we need for
459	>	// rigid body reference positions)
460	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
461
462	<	simnfo->setBox( boxVector );
463	<	}
462	>	// When we add to the rigid body, add the atom itself and
463	>	// the stamp info:
464
465	+	myRB->addAtom(info[k].atoms[tempI], currentAtom);
466	+
467	+	// Add this atom to the Skip List for the integrators
468		#ifdef IS_MPI
469	<	strcpy( checkPointMsg, "Box size set up" );
470	<	MPIcheckPoint();
471	<	#endif // is_mpi
469	>	slI = info[k].atoms[tempI]->getGlobalIndex();
470	>	#else
471	>	slI = tempI;
472	>	#endif
473	>	skipList.insert(slI);
474	>
475	>	}
476	>
477	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
478	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
479	>
480	>	tempI = currentRigidBody->getMember(rb1);
481	>	tempJ = currentRigidBody->getMember(rb2);
482	>
483	>	// Some explanation is required here.
484	>	// Fortran indexing starts at 1, while c indexing starts at 0
485	>	// Also, in parallel computations, the GlobalIndex is
486	>	// used for the exclude list:
487	>
488	>	#ifdef IS_MPI
489	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
490	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
491	>	#else
492	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
493	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
494	>	#endif
495	>
496	>	info[k].excludes->addPair(exI, exJ);
497	>
498	>	}
499	>	}
500
501	+	molInfo.myRigidBodies.push_back(myRB);
502	+	info[k].rigidBodies.push_back(myRB);
503	+	}
504	+
505
506	<	// initialize the arrays
506	>	//create cutoff group for molecule
507
508	<	the_ff->setSimInfo( simnfo );
508	>	cutoffAtomSet.clear();
509	>	molInfo.myCutoffGroups.clear();
510	>
511	>	for (j = 0; j < nCutoffGroups; j++){
512
513	<	makeMolecules();
514	<	simnfo->identArray = new int[simnfo->n_atoms];
544	<	for(i=0; i<simnfo->n_atoms; i++){
545	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
546	<	}
547	<
548	<	if (the_globals->getUseRF() ) {
549	<	simnfo->useReactionField = 1;
550	<
551	<	if( !the_globals->haveECR() ){
552	<	sprintf( painCave.errMsg,
553	<	"SimSetup Warning: using default value of 1/2 the smallest "
554	<	"box length for the electrostaticCutoffRadius.\n"
555	<	"I hope you have a very fast processor!\n");
556	<	painCave.isFatal = 0;
557	<	simError();
558	<	double smallest;
559	<	smallest = simnfo->boxLx;
560	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
561	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
562	<	simnfo->ecr = 0.5 * smallest;
563	<	} else {
564	<	simnfo->ecr        = the_globals->getECR();
565	<	}
513	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
514	>	nMembers = currentCutoffGroup->getNMembers();
515
516	<	if( !the_globals->haveEST() ){
517	<	sprintf( painCave.errMsg,
569	<	"SimSetup Warning: using default value of 0.05 * the "
570	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
571	<	);
572	<	painCave.isFatal = 0;
573	<	simError();
574	<	simnfo->est = 0.05 * simnfo->ecr;
575	<	} else {
576	<	simnfo->est        = the_globals->getEST();
577	<	}
578	<
579	<	if(!the_globals->haveDielectric() ){
580	<	sprintf( painCave.errMsg,
581	<	"SimSetup Error: You are trying to use Reaction Field without"
582	<	"setting a dielectric constant!\n"
583	<	);
584	<	painCave.isFatal = 1;
585	<	simError();
586	<	}
587	<	simnfo->dielectric = the_globals->getDielectric();
588	<	} else {
589	<	if (usesDipoles) {
590	<
591	<	if( !the_globals->haveECR() ){
592	<	sprintf( painCave.errMsg,
593	<	"SimSetup Warning: using default value of 1/2 the smallest "
594	<	"box length for the electrostaticCutoffRadius.\n"
595	<	"I hope you have a very fast processor!\n");
596	<	painCave.isFatal = 0;
597	<	simError();
598	<	double smallest;
599	<	smallest = simnfo->boxLx;
600	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
601	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
602	<	simnfo->ecr = 0.5 * smallest;
603	<	} else {
604	<	simnfo->ecr        = the_globals->getECR();
605	<	}
606	<
607	<	if( !the_globals->haveEST() ){
608	<	sprintf( painCave.errMsg,
609	<	"SimSetup Warning: using default value of 5%% of the "
610	<	"electrostaticCutoffRadius for the "
611	<	"electrostaticSkinThickness\n"
612	<	);
613	<	painCave.isFatal = 0;
614	<	simError();
615	<	simnfo->est = 0.05 * simnfo->ecr;
616	<	} else {
617	<	simnfo->est        = the_globals->getEST();
618	<	}
619	<	}
620	<	}
621	<
516	>	myCutoffGroup = new CutoffGroup();
517	>
518		#ifdef IS_MPI
519	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
520	<	MPIcheckPoint();
521	<	#endif // is_mpi
519	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
520	>	#else
521	>	myCutoffGroup->setGlobalIndex(j + groupOffset);
522	>	#endif
523	>
524	>	for (int cg = 0; cg < nMembers; cg++) {
525
526	<	if( the_globals->haveInitialConfig() ){
527	<
528	<	InitializeFromFile* fileInit;
529	<	#ifdef IS_MPI // is_mpi
530	<	if( worldRank == 0 ){
531	<	#endif //is_mpi
633	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
526	>	// molI is atom numbering inside this molecule
527	>	molI = currentCutoffGroup->getMember(cg);
528	>
529	>	// tempI is atom numbering on local processor
530	>	tempI = molI + atomOffset;
531	>
532		#ifdef IS_MPI
533	<	}else fileInit = new InitializeFromFile( NULL );
533	>	globalID = info[k].atoms[tempI]->getGlobalIndex();
534	>	info[k].globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
535	>	#else
536	>	globalID = info[k].atoms[tempI]->getIndex();
537	>	info[k].globalGroupMembership[globalID] = j + groupOffset;
538		#endif
539	<	fileInit->read_xyz( simnfo ); // default velocities on
539	>
540
541	<	delete fileInit;
542	<	}
543	<	else{
541	>
542	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
543	>
544	>	cutoffAtomSet.insert(tempI);
545	>	}
546	>
547	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
548	>	groupOffset++;
549
550	<	#ifdef IS_MPI
550	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
551	>
552	>	//creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
553	>
554	>	for(j = 0; j < molInfo.nAtoms; j++){
555	>
556	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
557	>	myCutoffGroup = new CutoffGroup();
558	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
559
560	<	// no init from bass
561	<
562	<	sprintf( painCave.errMsg,
563	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
649	<	painCave.isFatal;
650	<	simError();
651	<
560	>	#ifdef IS_MPI
561	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
562	>	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
563	>	info[k].globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
564		#else
565	+	myCutoffGroup->setGlobalIndex(j + groupOffset);
566	+	globalID = info[k].atoms[atomOffset + j]->getIndex();
567	+	info[k].globalGroupMembership[globalID] = j+groupOffset;
568	+	#endif
569	+	molInfo.myCutoffGroups.push_back(myCutoffGroup);
570	+	groupOffset++;
571	+	}
572	+
573	+	}
574
575	<	initFromBass();
575	>	// After this is all set up, scan through the atoms to
576	>	// see if they can be added to the integrableObjects:
577
578	+	molInfo.myIntegrableObjects.clear();
579	+
580
581	<	#endif
658	<	}
581	>	for (j = 0; j < molInfo.nAtoms; j++){
582
583		#ifdef IS_MPI
584	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
585	<	MPIcheckPoint();
586	<	#endif // is_mpi
584	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
585	>	#else
586	>	slJ = j+atomOffset;
587	>	#endif
588
589	+	// if they aren't on the skip list, then they can be integrated
590
591	<
592	<
593	<
591	>	if (skipList.find(slJ) == skipList.end()) {
592	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
593	>	info[k].integrableObjects.push_back(mySD);
594	>	molInfo.myIntegrableObjects.push_back(mySD);
595	>	}
596	>	}
597
598	<
599	<	#ifdef IS_MPI
600	<	if( worldRank == 0 ){
601	<	#endif // is_mpi
602	<
603	<	if( the_globals->haveFinalConfig() ){
676	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
677	<	}
678	<	else{
679	<	strcpy( simnfo->finalName, inFileName );
680	<	char* endTest;
681	<	int nameLength = strlen( simnfo->finalName );
682	<	endTest = &(simnfo->finalName[nameLength - 5]);
683	<	if( !strcmp( endTest, ".bass" ) ){
684	<	strcpy( endTest, ".eor" );
598	>	// all rigid bodies are integrated:
599	>
600	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
601	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
602	>	info[k].integrableObjects.push_back(mySD);
603	>	molInfo.myIntegrableObjects.push_back(mySD);
604		}
605	<	else if( !strcmp( endTest, ".BASS" ) ){
606	<	strcpy( endTest, ".eor" );
607	<	}
608	<	else{
609	<	endTest = &(simnfo->finalName[nameLength - 4]);
610	<	if( !strcmp( endTest, ".bss" ) ){
611	<	strcpy( endTest, ".eor" );
612	<	}
613	<	else if( !strcmp( endTest, ".mdl" ) ){
614	<	strcpy( endTest, ".eor" );
615	<	}
616	<	else{
617	<	strcat( simnfo->finalName, ".eor" );
618	<	}
605	>
606	>
607	>	/*
608	>
609	>	//creat ConstraintPair.
610	>	molInfo.myConstraintPair.clear();
611	>
612	>	for (j = 0; j < molInfo.nBonds; j++){
613	>
614	>	//if both atoms are in the same rigid body, just skip it
615	>	currentBond = comp_stamps[stampID]->getBond(j);
616	>	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
617	>
618	>	tempI = currentBond->getA() + atomOffset;
619	>	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
620	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
621	>	else
622	>	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
623	>
624	>	tempJ =  currentBond->getB() + atomOffset;
625	>	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
626	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
627	>	else
628	>	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
629	>
630	>	consPair = new DistanceConstraintPair(consElement1, consElement2);
631	>	molInfo.myConstraintPairs.push_back(consPair);
632	>	}
633	>	}
634	>
635	>	//loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair
636	>	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
637	>	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
638	>
639	>	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
640	>
641	>	for(size_t m = 0; m < jointAtoms.size(); m++){
642	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
643	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
644	>
645	>	consPair = new JointConstraintPair(consElement1, consElement2);
646	>	molInfo.myConstraintPairs.push_back(consPair);
647	>	}
648	>
649	>	}
650		}
651	+
652	+	*/
653	+	// send the arrays off to the forceField for init.
654	+
655	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
656	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
657	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
658	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
659	+	theTorsions);
660	+
661	+	info[k].molecules[i].initialize(molInfo);
662	+
663	+
664	+	atomOffset += molInfo.nAtoms;
665	+	delete[] theBonds;
666	+	delete[] theBends;
667	+	delete[] theTorsions;
668		}
702	–
703	–	// make the sample and status out names
704	–
705	–	strcpy( simnfo->sampleName, inFileName );
706	–	char* endTest;
707	–	int nameLength = strlen( simnfo->sampleName );
708	–	endTest = &(simnfo->sampleName[nameLength - 5]);
709	–	if( !strcmp( endTest, ".bass" ) ){
710	–	strcpy( endTest, ".dump" );
711	–	}
712	–	else if( !strcmp( endTest, ".BASS" ) ){
713	–	strcpy( endTest, ".dump" );
714	–	}
715	–	else{
716	–	endTest = &(simnfo->sampleName[nameLength - 4]);
717	–	if( !strcmp( endTest, ".bss" ) ){
718	–	strcpy( endTest, ".dump" );
719	–	}
720	–	else if( !strcmp( endTest, ".mdl" ) ){
721	–	strcpy( endTest, ".dump" );
722	–	}
723	–	else{
724	–	strcat( simnfo->sampleName, ".dump" );
725	–	}
726	–	}
727	–
728	–	strcpy( simnfo->statusName, inFileName );
729	–	nameLength = strlen( simnfo->statusName );
730	–	endTest = &(simnfo->statusName[nameLength - 5]);
731	–	if( !strcmp( endTest, ".bass" ) ){
732	–	strcpy( endTest, ".stat" );
733	–	}
734	–	else if( !strcmp( endTest, ".BASS" ) ){
735	–	strcpy( endTest, ".stat" );
736	–	}
737	–	else{
738	–	endTest = &(simnfo->statusName[nameLength - 4]);
739	–	if( !strcmp( endTest, ".bss" ) ){
740	–	strcpy( endTest, ".stat" );
741	–	}
742	–	else if( !strcmp( endTest, ".mdl" ) ){
743	–	strcpy( endTest, ".stat" );
744	–	}
745	–	else{
746	–	strcat( simnfo->statusName, ".stat" );
747	–	}
748	–	}
749	–
750	–	#ifdef IS_MPI
751	–	}
752	–	#endif // is_mpi
753	–
754	–	// set the status, sample, and themal kick times
755	–
756	–	if( the_globals->haveSampleTime() ){
757	–	simnfo->sampleTime = the_globals->getSampleTime();
758	–	simnfo->statusTime = simnfo->sampleTime;
759	–	simnfo->thermalTime = simnfo->sampleTime;
760	–	}
761	–	else{
762	–	simnfo->sampleTime = the_globals->getRunTime();
763	–	simnfo->statusTime = simnfo->sampleTime;
764	–	simnfo->thermalTime = simnfo->sampleTime;
765	–	}
669
767	–	if( the_globals->haveStatusTime() ){
768	–	simnfo->statusTime = the_globals->getStatusTime();
769	–	}
670
771	–	if( the_globals->haveThermalTime() ){
772	–	simnfo->thermalTime = the_globals->getThermalTime();
773	–	}
671
672	<	// check for the temperature set flag
672	>	#ifdef IS_MPI
673	>	// Since the globalGroupMembership has been zero filled and we've only
674	>	// poked values into the atoms we know, we can do an Allreduce
675	>	// to get the full globalGroupMembership array (We think).
676	>	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
677	>	// docs said we could.
678
679	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
679	>	int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];
680
681	+	MPI_Allreduce(info[k].globalGroupMembership,
682	+	ggMjunk,
683	+	mpiSim->getNAtomsGlobal(),
684	+	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
685
686	<	// make the integrator
687	<
782	<
783	<	NVT*  myNVT = NULL;
784	<	NPTi* myNPTi = NULL;
785	<	NPTf* myNPTf = NULL;
786	<	switch( ensembleCase ){
686	>	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
687	>	info[k].globalGroupMembership[i] = ggMjunk[i];
688
689	<	case NVE_ENS:
690	<	new NVE( simnfo, the_ff );
691	<	break;
689	>	delete[] ggMjunk;
690	>
691	>	#endif
692
792	–	case NVT_ENS:
793	–	myNVT = new NVT( simnfo, the_ff );
794	–	myNVT->setTargetTemp(the_globals->getTargetTemp());
693
796	–	if (the_globals->haveTauThermostat())
797	–	myNVT->setTauThermostat(the_globals->getTauThermostat());
694
695	<	else {
800	<	sprintf( painCave.errMsg,
801	<	"SimSetup error: If you use the NVT\n"
802	<	"    ensemble, you must set tauThermostat.\n");
803	<	painCave.isFatal = 1;
804	<	simError();
805	<	}
806	<	break;
695	>	}
696
697	<	case NPTi_ENS:
698	<	myNPTi = new NPTi( simnfo, the_ff );
699	<	myNPTi->setTargetTemp( the_globals->getTargetTemp());
697	>	#ifdef IS_MPI
698	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
699	>	MPIcheckPoint();
700	>	#endif // is_mpi
701
702	<	if (the_globals->haveTargetPressure())
813	<	myNPTi->setTargetPressure(the_globals->getTargetPressure());
814	<	else {
815	<	sprintf( painCave.errMsg,
816	<	"SimSetup error: If you use a constant pressure\n"
817	<	"    ensemble, you must set targetPressure in the BASS file.\n");
818	<	painCave.isFatal = 1;
819	<	simError();
820	<	}
821	<
822	<	if( the_globals->haveTauThermostat() )
823	<	myNPTi->setTauThermostat( the_globals->getTauThermostat() );
824	<	else{
825	<	sprintf( painCave.errMsg,
826	<	"SimSetup error: If you use an NPT\n"
827	<	"    ensemble, you must set tauThermostat.\n");
828	<	painCave.isFatal = 1;
829	<	simError();
830	<	}
702	>	}
703
704	<	if( the_globals->haveTauBarostat() )
705	<	myNPTi->setTauBarostat( the_globals->getTauBarostat() );
706	<	else{
707	<	sprintf( painCave.errMsg,
708	<	"SimSetup error: If you use an NPT\n"
709	<	"    ensemble, you must set tauBarostat.\n");
710	<	painCave.isFatal = 1;
711	<	simError();
840	<	}
841	<	break;
704	>	void SimSetup::initFromBass(void){
705	>	int i, j, k;
706	>	int n_cells;
707	>	double cellx, celly, cellz;
708	>	double temp1, temp2, temp3;
709	>	int n_per_extra;
710	>	int n_extra;
711	>	int have_extra, done;
712
713	<	case NPTf_ENS:
714	<	myNPTf = new NPTf( simnfo, the_ff );
715	<	myNPTf->setTargetTemp( the_globals->getTargetTemp());
713	>	double vel[3];
714	>	vel[0] = 0.0;
715	>	vel[1] = 0.0;
716	>	vel[2] = 0.0;
717
718	<	if (the_globals->haveTargetPressure())
719	<	myNPTf->setTargetPressure(the_globals->getTargetPressure());
720	<	else {
850	<	sprintf( painCave.errMsg,
851	<	"SimSetup error: If you use a constant pressure\n"
852	<	"    ensemble, you must set targetPressure in the BASS file.\n");
853	<	painCave.isFatal = 1;
854	<	simError();
855	<	}
718	>	temp1 = (double) tot_nmol / 4.0;
719	>	temp2 = pow(temp1, (1.0 / 3.0));
720	>	temp3 = ceil(temp2);
721
722	<	if( the_globals->haveTauThermostat() )
723	<	myNPTf->setTauThermostat( the_globals->getTauThermostat() );
724	<	else{
725	<	sprintf( painCave.errMsg,
861	<	"SimSetup error: If you use an NPT\n"
862	<	"    ensemble, you must set tauThermostat.\n");
863	<	painCave.isFatal = 1;
864	<	simError();
865	<	}
722	>	have_extra = 0;
723	>	if (temp2 < temp3){
724	>	// we have a non-complete lattice
725	>	have_extra = 1;
726
727	<	if( the_globals->haveTauBarostat() )
728	<	myNPTf->setTauBarostat( the_globals->getTauBarostat() );
729	<	else{
730	<	sprintf( painCave.errMsg,
731	<	"SimSetup error: If you use an NPT\n"
732	<	"    ensemble, you must set tauBarostat.\n");
727	>	n_cells = (int) temp3 - 1;
728	>	cellx = info[0].boxL[0] / temp3;
729	>	celly = info[0].boxL[1] / temp3;
730	>	cellz = info[0].boxL[2] / temp3;
731	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
732	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
733	>	n_per_extra = (int) ceil(temp1);
734	>
735	>	if (n_per_extra > 4){
736	>	sprintf(painCave.errMsg,
737	>	"SimSetup error. There has been an error in constructing"
738	>	" the non-complete lattice.\n");
739		painCave.isFatal = 1;
740		simError();
741		}
876	–	break;
877	–
878	–
879	–
880	–	default:
881	–	sprintf( painCave.errMsg,
882	–	"SimSetup Error. Unrecognized ensemble in case statement.\n");
883	–	painCave.isFatal = 1;
884	–	simError();
742		}
743	+	else{
744	+	n_cells = (int) temp3;
745	+	cellx = info[0].boxL[0] / temp3;
746	+	celly = info[0].boxL[1] / temp3;
747	+	cellz = info[0].boxL[2] / temp3;
748	+	}
749
750	+	current_mol = 0;
751	+	current_comp_mol = 0;
752	+	current_comp = 0;
753	+	current_atom_ndx = 0;
754
755	<	#ifdef IS_MPI
756	<	mpiSim->mpiRefresh();
757	<	#endif
755	>	for (i = 0; i < n_cells ; i++){
756	>	for (j = 0; j < n_cells; j++){
757	>	for (k = 0; k < n_cells; k++){
758	>	makeElement(i * cellx, j * celly, k * cellz);
759
760	<	// initialize the Fortran
760	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
761
762	+	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
763
764	<	simnfo->refreshSim();
765	<
766	<	if( !strcmp( simnfo->mixingRule, "standard") ){
898	<	the_ff->initForceField( LB_MIXING_RULE );
764	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
765	>	}
766	>	}
767		}
768	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
769	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
768	>
769	>	if (have_extra){
770	>	done = 0;
771	>
772	>	int start_ndx;
773	>	for (i = 0; i < (n_cells + 1) && !done; i++){
774	>	for (j = 0; j < (n_cells + 1) && !done; j++){
775	>	if (i < n_cells){
776	>	if (j < n_cells){
777	>	start_ndx = n_cells;
778	>	}
779	>	else
780	>	start_ndx = 0;
781	>	}
782	>	else
783	>	start_ndx = 0;
784	>
785	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
786	>	makeElement(i * cellx, j * celly, k * cellz);
787	>	done = (current_mol >= tot_nmol);
788	>
789	>	if (!done && n_per_extra > 1){
790	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
791	>	k * cellz);
792	>	done = (current_mol >= tot_nmol);
793	>	}
794	>
795	>	if (!done && n_per_extra > 2){
796	>	makeElement(i * cellx, j * celly + 0.5 * celly,
797	>	k * cellz + 0.5 * cellz);
798	>	done = (current_mol >= tot_nmol);
799	>	}
800	>
801	>	if (!done && n_per_extra > 3){
802	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
803	>	k * cellz + 0.5 * cellz);
804	>	done = (current_mol >= tot_nmol);
805	>	}
806	>	}
807	>	}
808	>	}
809		}
810	<	else{
811	<	sprintf( painCave.errMsg,
812	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
906	<	simnfo->mixingRule );
907	<	painCave.isFatal = 1;
908	<	simError();
810	>
811	>	for (i = 0; i < info[0].n_atoms; i++){
812	>	info[0].atoms[i]->setVel(vel);
813		}
814	+	}
815
816	+	void SimSetup::makeElement(double x, double y, double z){
817	+	int k;
818	+	AtomStamp* current_atom;
819	+	DirectionalAtom* dAtom;
820	+	double rotMat[3][3];
821	+	double pos[3];
822
823	<	#ifdef IS_MPI
824	<	strcpy( checkPointMsg,
825	<	"Successfully intialized the mixingRule for Fortran." );
826	<	MPIcheckPoint();
827	<	#endif // is_mpi
823	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
824	>	current_atom = comp_stamps[current_comp]->getAtom(k);
825	>	if (!current_atom->havePosition()){
826	>	sprintf(painCave.errMsg,
827	>	"SimSetup:initFromBass error.\n"
828	>	"\tComponent %s, atom %s does not have a position specified.\n"
829	>	"\tThe initialization routine is unable to give a start"
830	>	" position.\n",
831	>	comp_stamps[current_comp]->getID(), current_atom->getType());
832	>	painCave.isFatal = 1;
833	>	simError();
834	>	}
835	>
836	>	pos[0] = x + current_atom->getPosX();
837	>	pos[1] = y + current_atom->getPosY();
838	>	pos[2] = z + current_atom->getPosZ();
839	>
840	>	info[0].atoms[current_atom_ndx]->setPos(pos);
841	>
842	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
843	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
844	>
845	>	rotMat[0][0] = 1.0;
846	>	rotMat[0][1] = 0.0;
847	>	rotMat[0][2] = 0.0;
848	>
849	>	rotMat[1][0] = 0.0;
850	>	rotMat[1][1] = 1.0;
851	>	rotMat[1][2] = 0.0;
852	>
853	>	rotMat[2][0] = 0.0;
854	>	rotMat[2][1] = 0.0;
855	>	rotMat[2][2] = 1.0;
856	>
857	>	dAtom->setA(rotMat);
858	>	}
859	>
860	>	current_atom_ndx++;
861	>	}
862	>
863	>	current_mol++;
864	>	current_comp_mol++;
865	>
866	>	if (current_comp_mol >= components_nmol[current_comp]){
867	>	current_comp_mol = 0;
868	>	current_comp++;
869	>	}
870		}
871
872
873	<	void SimSetup::makeMolecules( void ){
873	>	void SimSetup::gatherInfo(void){
874	>	int i;
875
876	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
877	<	molInit info;
924	<	DirectionalAtom* dAtom;
925	<	LinkedAssign* extras;
926	<	LinkedAssign* current_extra;
927	<	AtomStamp* currentAtom;
928	<	BondStamp* currentBond;
929	<	BendStamp* currentBend;
930	<	TorsionStamp* currentTorsion;
876	>	ensembleCase = -1;
877	>	ffCase = -1;
878
879	<	bond_pair* theBonds;
933	<	bend_set* theBends;
934	<	torsion_set* theTorsions;
879	>	// set the easy ones first
880
881	<
882	<	//init the forceField paramters
881	>	for (i = 0; i < nInfo; i++){
882	>	info[i].target_temp = globals->getTargetTemp();
883	>	info[i].dt = globals->getDt();
884	>	info[i].run_time = globals->getRunTime();
885	>	}
886	>	n_components = globals->getNComponents();
887
939	–	the_ff->readParams();
888
889	<
942	<	// init the atoms
889	>	// get the forceField
890
891	<	double ux, uy, uz, u, uSqr;
945	<
946	<	atomOffset = 0;
947	<	excludeOffset = 0;
948	<	for(i=0; i<simnfo->n_mol; i++){
949	<
950	<	stampID = the_molecules[i].getStampID();
891	>	strcpy(force_field, globals->getForceField());
892
893	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
894	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
895	<	info.nBends    = comp_stamps[stampID]->getNBends();
896	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
897	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
893	>	if (!strcasecmp(force_field, "DUFF")){
894	>	ffCase = FF_DUFF;
895	>	}
896	>	else if (!strcasecmp(force_field, "LJ")){
897	>	ffCase = FF_LJ;
898	>	}
899	>	else if (!strcasecmp(force_field, "EAM")){
900	>	ffCase = FF_EAM;
901	>	}
902	>	else if (!strcasecmp(force_field, "WATER")){
903	>	ffCase = FF_H2O;
904	>	}
905	>	else{
906	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
907	>	force_field);
908	>	painCave.isFatal = 1;
909	>	simError();
910	>	}
911
912	<	info.myAtoms = &the_atoms[atomOffset];
959	<	info.myExcludes = &the_excludes[excludeOffset];
960	<	info.myBonds = new Bond*[info.nBonds];
961	<	info.myBends = new Bend*[info.nBends];
962	<	info.myTorsions = new Torsion*[info.nTorsions];
912	>	// get the ensemble
913
914	<	theBonds = new bond_pair[info.nBonds];
915	<	theBends = new bend_set[info.nBends];
916	<	theTorsions = new torsion_set[info.nTorsions];
917	<
918	<	// make the Atoms
919	<
920	<	for(j=0; j<info.nAtoms; j++){
921	<
922	<	currentAtom = comp_stamps[stampID]->getAtom( j );
923	<	if( currentAtom->haveOrientation() ){
924	<
925	<	dAtom = new DirectionalAtom(j + atomOffset);
926	<	simnfo->n_oriented++;
927	<	info.myAtoms[j] = dAtom;
928	<
929	<	ux = currentAtom->getOrntX();
930	<	uy = currentAtom->getOrntY();
931	<	uz = currentAtom->getOrntZ();
932	<
933	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
934	<
935	<	u = sqrt( uSqr );
936	<	ux = ux / u;
937	<	uy = uy / u;
938	<	uz = uz / u;
939	<
940	<	dAtom->setSUx( ux );
941	<	dAtom->setSUy( uy );
942	<	dAtom->setSUz( uz );
943	<	}
944	<	else{
945	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
946	<	}
947	<	info.myAtoms[j]->setType( currentAtom->getType() );
948	<
949	<	#ifdef IS_MPI
950	<
951	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
952	<
953	<	#endif // is_mpi
954	<	}
955	<
956	<	// make the bonds
957	<	for(j=0; j<info.nBonds; j++){
958	<
959	<	currentBond = comp_stamps[stampID]->getBond( j );
960	<	theBonds[j].a = currentBond->getA() + atomOffset;
961	<	theBonds[j].b = currentBond->getB() + atomOffset;
914	>	strcpy(ensemble, globals->getEnsemble());
915	>
916	>	if (!strcasecmp(ensemble, "NVE")){
917	>	ensembleCase = NVE_ENS;
918	>	}
919	>	else if (!strcasecmp(ensemble, "NVT")){
920	>	ensembleCase = NVT_ENS;
921	>	}
922	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
923	>	ensembleCase = NPTi_ENS;
924	>	}
925	>	else if (!strcasecmp(ensemble, "NPTf")){
926	>	ensembleCase = NPTf_ENS;
927	>	}
928	>	else if (!strcasecmp(ensemble, "NPTxyz")){
929	>	ensembleCase = NPTxyz_ENS;
930	>	}
931	>	else{
932	>	sprintf(painCave.errMsg,
933	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
934	>	"\treverting to NVE for this simulation.\n",
935	>	ensemble);
936	>	painCave.isFatal = 0;
937	>	simError();
938	>	strcpy(ensemble, "NVE");
939	>	ensembleCase = NVE_ENS;
940	>	}
941	>
942	>	for (i = 0; i < nInfo; i++){
943	>	strcpy(info[i].ensemble, ensemble);
944	>
945	>	// get the mixing rule
946	>
947	>	strcpy(info[i].mixingRule, globals->getMixingRule());
948	>	info[i].usePBC = globals->getPBC();
949	>	}
950	>
951	>	// get the components and calculate the tot_nMol and indvidual n_mol
952	>
953	>	the_components = globals->getComponents();
954	>	components_nmol = new int[n_components];
955	>
956	>
957	>	if (!globals->haveNMol()){
958	>	// we don't have the total number of molecules, so we assume it is
959	>	// given in each component
960	>
961	>	tot_nmol = 0;
962	>	for (i = 0; i < n_components; i++){
963	>	if (!the_components[i]->haveNMol()){
964	>	// we have a problem
965	>	sprintf(painCave.errMsg,
966	>	"SimSetup Error. No global NMol or component NMol given.\n"
967	>	"\tCannot calculate the number of atoms.\n");
968	>	painCave.isFatal = 1;
969	>	simError();
970	>	}
971
972	<	exI = theBonds[j].a;
973	<	exJ = theBonds[j].b;
972	>	tot_nmol += the_components[i]->getNMol();
973	>	components_nmol[i] = the_components[i]->getNMol();
974	>	}
975	>	}
976	>	else{
977	>	sprintf(painCave.errMsg,
978	>	"SimSetup error.\n"
979	>	"\tSorry, the ability to specify total"
980	>	" nMols and then give molfractions in the components\n"
981	>	"\tis not currently supported."
982	>	" Please give nMol in the components.\n");
983	>	painCave.isFatal = 1;
984	>	simError();
985	>	}
986
987	<	// exclude_I must always be the smaller of the pair
988	<	if( exI > exJ ){
989	<	tempEx = exI;
990	<	exI = exJ;
991	<	exJ = tempEx;
992	<	}
993	<	#ifdef IS_MPI
994	<	tempEx = exI;
995	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
996	<	tempEx = exJ;
1026	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1027	<
1028	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1029	<	#else  // isn't MPI
987	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
988	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
989	>	sprintf(painCave.errMsg,
990	>	"Sample time is not divisible by dt.\n"
991	>	"\tThis will result in samples that are not uniformly\n"
992	>	"\tdistributed in time.  If this is a problem, change\n"
993	>	"\tyour sampleTime variable.\n");
994	>	painCave.isFatal = 0;
995	>	simError();
996	>	}
997
998	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
999	<	#endif  //is_mpi
998	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
999	>	sprintf(painCave.errMsg,
1000	>	"Status time is not divisible by dt.\n"
1001	>	"\tThis will result in status reports that are not uniformly\n"
1002	>	"\tdistributed in time.  If this is a problem, change \n"
1003	>	"\tyour statusTime variable.\n");
1004	>	painCave.isFatal = 0;
1005	>	simError();
1006	>	}
1007	>
1008	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
1009	>	sprintf(painCave.errMsg,
1010	>	"Thermal time is not divisible by dt.\n"
1011	>	"\tThis will result in thermalizations that are not uniformly\n"
1012	>	"\tdistributed in time.  If this is a problem, change \n"
1013	>	"\tyour thermalTime variable.\n");
1014	>	painCave.isFatal = 0;
1015	>	simError();
1016	>	}
1017	>
1018	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
1019	>	sprintf(painCave.errMsg,
1020	>	"Reset time is not divisible by dt.\n"
1021	>	"\tThis will result in integrator resets that are not uniformly\n"
1022	>	"\tdistributed in time.  If this is a problem, change\n"
1023	>	"\tyour resetTime variable.\n");
1024	>	painCave.isFatal = 0;
1025	>	simError();
1026	>	}
1027	>
1028	>	// set the status, sample, and thermal kick times
1029	>
1030	>	for (i = 0; i < nInfo; i++){
1031	>	if (globals->haveSampleTime()){
1032	>	info[i].sampleTime = globals->getSampleTime();
1033	>	info[i].statusTime = info[i].sampleTime;
1034		}
1035	<	excludeOffset += info.nBonds;
1035	>	else{
1036	>	info[i].sampleTime = globals->getRunTime();
1037	>	info[i].statusTime = info[i].sampleTime;
1038	>	}
1039
1040	<	//make the bends
1041	<	for(j=0; j<info.nBends; j++){
1038	<
1039	<	currentBend = comp_stamps[stampID]->getBend( j );
1040	<	theBends[j].a = currentBend->getA() + atomOffset;
1041	<	theBends[j].b = currentBend->getB() + atomOffset;
1042	<	theBends[j].c = currentBend->getC() + atomOffset;
1043	<
1044	<	if( currentBend->haveExtras() ){
1045	<
1046	<	extras = currentBend->getExtras();
1047	<	current_extra = extras;
1048	<
1049	<	while( current_extra != NULL ){
1050	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1051	<
1052	<	switch( current_extra->getType() ){
1053	<
1054	<	case 0:
1055	<	theBends[j].ghost =
1056	<	current_extra->getInt() + atomOffset;
1057	<	theBends[j].isGhost = 1;
1058	<	break;
1059	<
1060	<	case 1:
1061	<	theBends[j].ghost =
1062	<	(int)current_extra->getDouble() + atomOffset;
1063	<	theBends[j].isGhost = 1;
1064	<	break;
1065	<
1066	<	default:
1067	<	sprintf( painCave.errMsg,
1068	<	"SimSetup Error: ghostVectorSource was neither a "
1069	<	"double nor an int.\n"
1070	<	"-->Bend[%d] in %s\n",
1071	<	j, comp_stamps[stampID]->getID() );
1072	<	painCave.isFatal = 1;
1073	<	simError();
1074	<	}
1075	<	}
1076	<
1077	<	else{
1078	<
1079	<	sprintf( painCave.errMsg,
1080	<	"SimSetup Error: unhandled bend assignment:\n"
1081	<	"    -->%s in Bend[%d] in %s\n",
1082	<	current_extra->getlhs(),
1083	<	j, comp_stamps[stampID]->getID() );
1084	<	painCave.isFatal = 1;
1085	<	simError();
1086	<	}
1087	<
1088	<	current_extra = current_extra->getNext();
1089	<	}
1090	<	}
1091	<
1092	<	if( !theBends[j].isGhost ){
1093	<
1094	<	exI = theBends[j].a;
1095	<	exJ = theBends[j].c;
1096	<	}
1097	<	else{
1098	<
1099	<	exI = theBends[j].a;
1100	<	exJ = theBends[j].b;
1101	<	}
1102	<
1103	<	// exclude_I must always be the smaller of the pair
1104	<	if( exI > exJ ){
1105	<	tempEx = exI;
1106	<	exI = exJ;
1107	<	exJ = tempEx;
1108	<	}
1109	<	#ifdef IS_MPI
1110	<	tempEx = exI;
1111	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1112	<	tempEx = exJ;
1113	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1114	<
1115	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1116	<	#else  // isn't MPI
1117	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1118	<	#endif  //is_mpi
1040	>	if (globals->haveStatusTime()){
1041	>	info[i].statusTime = globals->getStatusTime();
1042		}
1120	–	excludeOffset += info.nBends;
1043
1044	<	for(j=0; j<info.nTorsions; j++){
1045	<
1046	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1047	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1048	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1127	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1128	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1129	<
1130	<	exI = theTorsions[j].a;
1131	<	exJ = theTorsions[j].d;
1044	>	if (globals->haveThermalTime()){
1045	>	info[i].thermalTime = globals->getThermalTime();
1046	>	} else {
1047	>	info[i].thermalTime = globals->getRunTime();
1048	>	}
1049
1050	<	// exclude_I must always be the smaller of the pair
1051	<	if( exI > exJ ){
1052	<	tempEx = exI;
1053	<	exI = exJ;
1137	<	exJ = tempEx;
1138	<	}
1139	<	#ifdef IS_MPI
1140	<	tempEx = exI;
1141	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1142	<	tempEx = exJ;
1143	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1144	<
1145	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1146	<	#else  // isn't MPI
1147	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1148	<	#endif  //is_mpi
1050	>	info[i].resetIntegrator = 0;
1051	>	if( globals->haveResetTime() ){
1052	>	info[i].resetTime = globals->getResetTime();
1053	>	info[i].resetIntegrator = 1;
1054		}
1150	–	excludeOffset += info.nTorsions;
1055
1056	+	// check for the temperature set flag
1057
1058	<	// send the arrays off to the forceField for init.
1058	>	if (globals->haveTempSet())
1059	>	info[i].setTemp = globals->getTempSet();
1060
1061	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1156	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1157	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1158	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1061	>	// check for the extended State init
1062
1063	+	info[i].useInitXSstate = globals->getUseInitXSstate();
1064	+	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1065
1066	<	the_molecules[i].initialize( info );
1067	<
1068	<
1069	<	atomOffset += info.nAtoms;
1070	<	delete[] theBonds;
1071	<	delete[] theBends;
1072	<	delete[] theTorsions;
1066	>	// check for thermodynamic integration
1067	>	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1068	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1069	>	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1070	>	info[i].thermIntLambda = globals->getThermIntLambda();
1071	>	info[i].thermIntK = globals->getThermIntK();
1072	>
1073	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1074	>	info[i].restraint = myRestraint;
1075	>	}
1076	>	else {
1077	>	sprintf(painCave.errMsg,
1078	>	"SimSetup Error:\n"
1079	>	"\tKeyword useSolidThermInt was set to 'true' but\n"
1080	>	"\tthermodynamicIntegrationLambda (and/or\n"
1081	>	"\tthermodynamicIntegrationK) was not specified.\n"
1082	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1083	>	painCave.isFatal = 1;
1084	>	simError();
1085	>	}
1086	>	}
1087	>	else if(globals->getUseLiquidThermInt()) {
1088	>	if (globals->getUseSolidThermInt()) {
1089	>	sprintf( painCave.errMsg,
1090	>	"SimSetup Warning: It appears that you have both solid and\n"
1091	>	"\tliquid thermodynamic integration activated in your .bass\n"
1092	>	"\tfile. To avoid confusion, specify only one technique in\n"
1093	>	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1094	>	"\twill be assumed for the current simulation. If this is not\n"
1095	>	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1096	>	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1097	>	painCave.isFatal = 0;
1098	>	simError();
1099	>	}
1100	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1101	>	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1102	>	info[i].thermIntLambda = globals->getThermIntLambda();
1103	>	info[i].thermIntK = globals->getThermIntK();
1104	>	}
1105	>	else {
1106	>	sprintf(painCave.errMsg,
1107	>	"SimSetup Error:\n"
1108	>	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1109	>	"\tthermodynamicIntegrationLambda (and/or\n"
1110	>	"\tthermodynamicIntegrationK) was not specified.\n"
1111	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1112	>	painCave.isFatal = 1;
1113	>	simError();
1114	>	}
1115	>	}
1116	>	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1117	>	sprintf(painCave.errMsg,
1118	>	"SimSetup Warning: If you want to use Thermodynamic\n"
1119	>	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1120	>	"\t'true' in your .bass file.  These keywords are set to\n"
1121	>	"\t'false' by default, so your lambda and/or k values are\n"
1122	>	"\tbeing ignored.\n");
1123	>	painCave.isFatal = 0;
1124	>	simError();
1125	>	}
1126		}
1127	+
1128	+	//setup seed for random number generator
1129	+	int seedValue;
1130
1131	+	if (globals->haveSeed()){
1132	+	seedValue = globals->getSeed();
1133	+
1134	+	if(seedValue / 1E9 == 0){
1135	+	sprintf(painCave.errMsg,
1136	+	"Seed for sprng library should contain at least 9 digits\n"
1137	+	"OOPSE will generate a seed for user\n");
1138	+	painCave.isFatal = 0;
1139	+	simError();
1140	+
1141	+	//using seed generated by system instead of invalid seed set by user
1142	+	#ifndef IS_MPI
1143	+	seedValue = make_sprng_seed();
1144	+	#else
1145	+	if (worldRank == 0){
1146	+	seedValue = make_sprng_seed();
1147	+	}
1148	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1149	+	#endif
1150	+	}
1151	+	}//end of if branch of globals->haveSeed()
1152	+	else{
1153	+
1154	+	#ifndef IS_MPI
1155	+	seedValue = make_sprng_seed();
1156	+	#else
1157	+	if (worldRank == 0){
1158	+	seedValue = make_sprng_seed();
1159	+	}
1160	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1161	+	#endif
1162	+	}//end of globals->haveSeed()
1163	+
1164	+	for (int i = 0; i < nInfo; i++){
1165	+	info[i].setSeed(seedValue);
1166	+	}
1167	+
1168		#ifdef IS_MPI
1169	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1169	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1170		MPIcheckPoint();
1171		#endif // is_mpi
1172	+	}
1173
1174	+
1175	+	void SimSetup::finalInfoCheck(void){
1176	+	int index;
1177	+	int usesDipoles;
1178	+	int usesCharges;
1179	+	int i;
1180	+
1181	+	for (i = 0; i < nInfo; i++){
1182	+	// check electrostatic parameters
1183	+
1184	+	index = 0;
1185	+	usesDipoles = 0;
1186	+	while ((index < info[i].n_atoms) && !usesDipoles){
1187	+	usesDipoles = (info[i].atoms[index])->hasDipole();
1188	+	index++;
1189	+	}
1190	+	index = 0;
1191	+	usesCharges = 0;
1192	+	while ((index < info[i].n_atoms) && !usesCharges){
1193	+	usesCharges= (info[i].atoms[index])->hasCharge();
1194	+	index++;
1195	+	}
1196	+	#ifdef IS_MPI
1197	+	int myUse = usesDipoles;
1198	+	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1199	+	#endif //is_mpi
1200	+
1201	+	double theRcut, theRsw;
1202	+
1203	+	if (globals->haveRcut()) {
1204	+	theRcut = globals->getRcut();
1205	+
1206	+	if (globals->haveRsw())
1207	+	theRsw = globals->getRsw();
1208	+	else
1209	+	theRsw = theRcut;
1210	+
1211	+	info[i].setDefaultRcut(theRcut, theRsw);
1212	+
1213	+	} else {
1214	+
1215	+	the_ff->calcRcut();
1216	+	theRcut = info[i].getRcut();
1217	+
1218	+	if (globals->haveRsw())
1219	+	theRsw = globals->getRsw();
1220	+	else
1221	+	theRsw = theRcut;
1222	+
1223	+	info[i].setDefaultRcut(theRcut, theRsw);
1224	+	}
1225	+
1226	+	if (globals->getUseRF()){
1227	+	info[i].useReactionField = 1;
1228	+
1229	+	if (!globals->haveRcut()){
1230	+	sprintf(painCave.errMsg,
1231	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1232	+	"\tOOPSE will use a default value of 15.0 angstroms"
1233	+	"\tfor the cutoffRadius.\n");
1234	+	painCave.isFatal = 0;
1235	+	simError();
1236	+	theRcut = 15.0;
1237	+	}
1238	+	else{
1239	+	theRcut = globals->getRcut();
1240	+	}
1241	+
1242	+	if (!globals->haveRsw()){
1243	+	sprintf(painCave.errMsg,
1244	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1245	+	"\tOOPSE will use a default value of\n"
1246	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1247	+	painCave.isFatal = 0;
1248	+	simError();
1249	+	theRsw = 0.95 * theRcut;
1250	+	}
1251	+	else{
1252	+	theRsw = globals->getRsw();
1253	+	}
1254	+
1255	+	info[i].setDefaultRcut(theRcut, theRsw);
1256	+
1257	+	if (!globals->haveDielectric()){
1258	+	sprintf(painCave.errMsg,
1259	+	"SimSetup Error: No Dielectric constant was set.\n"
1260	+	"\tYou are trying to use Reaction Field without"
1261	+	"\tsetting a dielectric constant!\n");
1262	+	painCave.isFatal = 1;
1263	+	simError();
1264	+	}
1265	+	info[i].dielectric = globals->getDielectric();
1266	+	}
1267	+	else{
1268	+	if (usesDipoles || usesCharges){
1269	+
1270	+	if (!globals->haveRcut()){
1271	+	sprintf(painCave.errMsg,
1272	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1273	+	"\tOOPSE will use a default value of 15.0 angstroms"
1274	+	"\tfor the cutoffRadius.\n");
1275	+	painCave.isFatal = 0;
1276	+	simError();
1277	+	theRcut = 15.0;
1278	+	}
1279	+	else{
1280	+	theRcut = globals->getRcut();
1281	+	}
1282	+
1283	+	if (!globals->haveRsw()){
1284	+	sprintf(painCave.errMsg,
1285	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1286	+	"\tOOPSE will use a default value of\n"
1287	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1288	+	painCave.isFatal = 0;
1289	+	simError();
1290	+	theRsw = 0.95 * theRcut;
1291	+	}
1292	+	else{
1293	+	theRsw = globals->getRsw();
1294	+	}
1295	+
1296	+	info[i].setDefaultRcut(theRcut, theRsw);
1297	+
1298	+	}
1299	+	}
1300	+	}
1301	+	#ifdef IS_MPI
1302	+	strcpy(checkPointMsg, "post processing checks out");
1303	+	MPIcheckPoint();
1304	+	#endif // is_mpi
1305	+
1306		// clean up the forcefield
1176	–	the_ff->calcRcut();
1307		the_ff->cleanMe();
1178	–
1308		}
1309	+
1310	+	void SimSetup::initSystemCoords(void){
1311	+	int i;
1312
1313	<	void SimSetup::initFromBass( void ){
1313	>	char* inName;
1314
1315	<	int i, j, k;
1184	<	int n_cells;
1185	<	double cellx, celly, cellz;
1186	<	double temp1, temp2, temp3;
1187	<	int n_per_extra;
1188	<	int n_extra;
1189	<	int have_extra, done;
1315	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1316
1317	<	temp1 = (double)tot_nmol / 4.0;
1318	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1193	<	temp3 = ceil( temp2 );
1317	>	for (i = 0; i < info[0].n_atoms; i++)
1318	>	info[0].atoms[i]->setCoords();
1319
1320	<	have_extra =0;
1321	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1322	<	have_extra =1;
1323	<
1324	<	n_cells = (int)temp3 - 1;
1325	<	cellx = simnfo->boxLx / temp3;
1326	<	celly = simnfo->boxLy / temp3;
1327	<	cellz = simnfo->boxLz / temp3;
1203	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1204	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1205	<	n_per_extra = (int)ceil( temp1 );
1206	<
1207	<	if( n_per_extra > 4){
1208	<	sprintf( painCave.errMsg,
1209	<	"SimSetup error. There has been an error in constructing"
1210	<	" the non-complete lattice.\n" );
1211	<	painCave.isFatal = 1;
1212	<	simError();
1320	>	if (globals->haveInitialConfig()){
1321	>	InitializeFromFile* fileInit;
1322	>	#ifdef IS_MPI // is_mpi
1323	>	if (worldRank == 0){
1324	>	#endif //is_mpi
1325	>	inName = globals->getInitialConfig();
1326	>	fileInit = new InitializeFromFile(inName);
1327	>	#ifdef IS_MPI
1328		}
1329	+	else
1330	+	fileInit = new InitializeFromFile(NULL);
1331	+	#endif
1332	+	fileInit->readInit(info); // default velocities on
1333	+
1334	+	delete fileInit;
1335		}
1336		else{
1337	<	n_cells = (int)temp3;
1338	<	cellx = simnfo->boxLx / temp3;
1339	<	celly = simnfo->boxLy / temp3;
1340	<	cellz = simnfo->boxLz / temp3;
1337	>
1338	>	// no init from bass
1339	>
1340	>	sprintf(painCave.errMsg,
1341	>	"Cannot intialize a simulation without an initial configuration file.\n");
1342	>	painCave.isFatal = 1;;
1343	>	simError();
1344	>
1345		}
1346
1347	<	current_mol = 0;
1348	<	current_comp_mol = 0;
1349	<	current_comp = 0;
1350	<	current_atom_ndx = 0;
1347	>	#ifdef IS_MPI
1348	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1349	>	MPIcheckPoint();
1350	>	#endif // is_mpi
1351	>	}
1352
1227	–	for( i=0; i < n_cells ; i++ ){
1228	–	for( j=0; j < n_cells; j++ ){
1229	–	for( k=0; k < n_cells; k++ ){
1353
1354	<	makeElement( i * cellx,
1355	<	j * celly,
1233	<	k * cellz );
1354	>	void SimSetup::makeOutNames(void){
1355	>	int k;
1356
1235	–	makeElement( i * cellx + 0.5 * cellx,
1236	–	j * celly + 0.5 * celly,
1237	–	k * cellz );
1357
1358	<	makeElement( i * cellx,
1359	<	j * celly + 0.5 * celly,
1360	<	k * cellz + 0.5 * cellz );
1358	>	for (k = 0; k < nInfo; k++){
1359	>	#ifdef IS_MPI
1360	>	if (worldRank == 0){
1361	>	#endif // is_mpi
1362
1363	<	makeElement( i * cellx + 0.5 * cellx,
1364	<	j * celly,
1245	<	k * cellz + 0.5 * cellz );
1363	>	if (globals->haveFinalConfig()){
1364	>	strcpy(info[k].finalName, globals->getFinalConfig());
1365		}
1366	+	else{
1367	+	strcpy(info[k].finalName, inFileName);
1368	+	char* endTest;
1369	+	int nameLength = strlen(info[k].finalName);
1370	+	endTest = &(info[k].finalName[nameLength - 5]);
1371	+	if (!strcmp(endTest, ".bass")){
1372	+	strcpy(endTest, ".eor");
1373	+	}
1374	+	else if (!strcmp(endTest, ".BASS")){
1375	+	strcpy(endTest, ".eor");
1376	+	}
1377	+	else{
1378	+	endTest = &(info[k].finalName[nameLength - 4]);
1379	+	if (!strcmp(endTest, ".bss")){
1380	+	strcpy(endTest, ".eor");
1381	+	}
1382	+	else if (!strcmp(endTest, ".mdl")){
1383	+	strcpy(endTest, ".eor");
1384	+	}
1385	+	else{
1386	+	strcat(info[k].finalName, ".eor");
1387	+	}
1388	+	}
1389	+	}
1390	+
1391	+	// make the sample and status out names
1392	+
1393	+	strcpy(info[k].sampleName, inFileName);
1394	+	char* endTest;
1395	+	int nameLength = strlen(info[k].sampleName);
1396	+	endTest = &(info[k].sampleName[nameLength - 5]);
1397	+	if (!strcmp(endTest, ".bass")){
1398	+	strcpy(endTest, ".dump");
1399	+	}
1400	+	else if (!strcmp(endTest, ".BASS")){
1401	+	strcpy(endTest, ".dump");
1402	+	}
1403	+	else{
1404	+	endTest = &(info[k].sampleName[nameLength - 4]);
1405	+	if (!strcmp(endTest, ".bss")){
1406	+	strcpy(endTest, ".dump");
1407	+	}
1408	+	else if (!strcmp(endTest, ".mdl")){
1409	+	strcpy(endTest, ".dump");
1410	+	}
1411	+	else{
1412	+	strcat(info[k].sampleName, ".dump");
1413	+	}
1414	+	}
1415	+
1416	+	strcpy(info[k].statusName, inFileName);
1417	+	nameLength = strlen(info[k].statusName);
1418	+	endTest = &(info[k].statusName[nameLength - 5]);
1419	+	if (!strcmp(endTest, ".bass")){
1420	+	strcpy(endTest, ".stat");
1421	+	}
1422	+	else if (!strcmp(endTest, ".BASS")){
1423	+	strcpy(endTest, ".stat");
1424	+	}
1425	+	else{
1426	+	endTest = &(info[k].statusName[nameLength - 4]);
1427	+	if (!strcmp(endTest, ".bss")){
1428	+	strcpy(endTest, ".stat");
1429	+	}
1430	+	else if (!strcmp(endTest, ".mdl")){
1431	+	strcpy(endTest, ".stat");
1432	+	}
1433	+	else{
1434	+	strcat(info[k].statusName, ".stat");
1435	+	}
1436	+	}
1437	+
1438	+	strcpy(info[k].rawPotName, inFileName);
1439	+	nameLength = strlen(info[k].rawPotName);
1440	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1441	+	if (!strcmp(endTest, ".bass")){
1442	+	strcpy(endTest, ".raw");
1443	+	}
1444	+	else if (!strcmp(endTest, ".BASS")){
1445	+	strcpy(endTest, ".raw");
1446	+	}
1447	+	else{
1448	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1449	+	if (!strcmp(endTest, ".bss")){
1450	+	strcpy(endTest, ".raw");
1451	+	}
1452	+	else if (!strcmp(endTest, ".mdl")){
1453	+	strcpy(endTest, ".raw");
1454	+	}
1455	+	else{
1456	+	strcat(info[k].rawPotName, ".raw");
1457	+	}
1458	+	}
1459	+
1460	+	#ifdef IS_MPI
1461	+
1462		}
1463	+	#endif // is_mpi
1464		}
1465	+	}
1466
1250	–	if( have_extra ){
1251	–	done = 0;
1467
1468	<	int start_ndx;
1469	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1255	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1468	>	void SimSetup::sysObjectsCreation(void){
1469	>	int i, k;
1470
1471	<	if( i < n_cells ){
1471	>	// create the forceField
1472
1473	<	if( j < n_cells ){
1260	<	start_ndx = n_cells;
1261	<	}
1262	<	else start_ndx = 0;
1263	<	}
1264	<	else start_ndx = 0;
1473	>	createFF();
1474
1475	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1475	>	// extract componentList
1476
1477	<	makeElement( i * cellx,
1269	<	j * celly,
1270	<	k * cellz );
1271	<	done = ( current_mol >= tot_nmol );
1477	>	compList();
1478
1479	<	if( !done && n_per_extra > 1 ){
1274	<	makeElement( i * cellx + 0.5 * cellx,
1275	<	j * celly + 0.5 * celly,
1276	<	k * cellz );
1277	<	done = ( current_mol >= tot_nmol );
1278	<	}
1479	>	// calc the number of atoms, bond, bends, and torsions
1480
1481	<	if( !done && n_per_extra > 2){
1281	<	makeElement( i * cellx,
1282	<	j * celly + 0.5 * celly,
1283	<	k * cellz + 0.5 * cellz );
1284	<	done = ( current_mol >= tot_nmol );
1285	<	}
1481	>	calcSysValues();
1482
1483	<	if( !done && n_per_extra > 3){
1484	<	makeElement( i * cellx + 0.5 * cellx,
1289	<	j * celly,
1290	<	k * cellz + 0.5 * cellz );
1291	<	done = ( current_mol >= tot_nmol );
1292	<	}
1293	<	}
1294	<	}
1295	<	}
1296	<	}
1483	>	#ifdef IS_MPI
1484	>	// divide the molecules among the processors
1485
1486	+	mpiMolDivide();
1487	+	#endif //is_mpi
1488
1489	<	for( i=0; i<simnfo->n_atoms; i++ ){
1490	<	simnfo->atoms[i]->set_vx( 0.0 );
1491	<	simnfo->atoms[i]->set_vy( 0.0 );
1492	<	simnfo->atoms[i]->set_vz( 0.0 );
1489	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1490	>
1491	>	makeSysArrays();
1492	>
1493	>	// make and initialize the molecules (all but atomic coordinates)
1494	>
1495	>	makeMolecules();
1496	>
1497	>	for (k = 0; k < nInfo; k++){
1498	>	info[k].identArray = new int[info[k].n_atoms];
1499	>	for (i = 0; i < info[k].n_atoms; i++){
1500	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1501	>	}
1502		}
1503		}
1504
1306	–	void SimSetup::makeElement( double x, double y, double z ){
1505
1506	<	int k;
1507	<	AtomStamp* current_atom;
1508	<	DirectionalAtom* dAtom;
1509	<	double rotMat[3][3];
1506	>	void SimSetup::createFF(void){
1507	>	switch (ffCase){
1508	>	case FF_DUFF:
1509	>	the_ff = new DUFF();
1510	>	break;
1511
1512	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1512	>	case FF_LJ:
1513	>	the_ff = new LJFF();
1514	>	break;
1515
1516	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1517	<	if( !current_atom->havePosition() ){
1518	<	sprintf( painCave.errMsg,
1519	<	"SimSetup:initFromBass error.\n"
1520	<	"\tComponent %s, atom %s does not have a position specified.\n"
1521	<	"\tThe initialization routine is unable to give a start"
1522	<	" position.\n",
1523	<	comp_stamps[current_comp]->getID(),
1524	<	current_atom->getType() );
1516	>	case FF_EAM:
1517	>	the_ff = new EAM_FF();
1518	>	break;
1519	>
1520	>	case FF_H2O:
1521	>	the_ff = new WATER();
1522	>	break;
1523	>
1524	>	default:
1525	>	sprintf(painCave.errMsg,
1526	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1527		painCave.isFatal = 1;
1528		simError();
1529	+	}
1530	+
1531	+	#ifdef IS_MPI
1532	+	strcpy(checkPointMsg, "ForceField creation successful");
1533	+	MPIcheckPoint();
1534	+	#endif // is_mpi
1535	+	}
1536	+
1537	+
1538	+	void SimSetup::compList(void){
1539	+	int i;
1540	+	char* id;
1541	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1542	+	LinkedMolStamp* currentStamp = NULL;
1543	+	comp_stamps = new MoleculeStamp * [n_components];
1544	+	bool haveCutoffGroups;
1545	+
1546	+	haveCutoffGroups = false;
1547	+
1548	+	// make an array of molecule stamps that match the components used.
1549	+	// also extract the used stamps out into a separate linked list
1550	+
1551	+	for (i = 0; i < nInfo; i++){
1552	+	info[i].nComponents = n_components;
1553	+	info[i].componentsNmol = components_nmol;
1554	+	info[i].compStamps = comp_stamps;
1555	+	info[i].headStamp = headStamp;
1556	+	}
1557	+
1558	+
1559	+	for (i = 0; i < n_components; i++){
1560	+	id = the_components[i]->getType();
1561	+	comp_stamps[i] = NULL;
1562	+
1563	+	// check to make sure the component isn't already in the list
1564	+
1565	+	comp_stamps[i] = headStamp->match(id);
1566	+	if (comp_stamps[i] == NULL){
1567	+	// extract the component from the list;
1568	+
1569	+	currentStamp = stamps->extractMolStamp(id);
1570	+	if (currentStamp == NULL){
1571	+	sprintf(painCave.errMsg,
1572	+	"SimSetup error: Component \"%s\" was not found in the "
1573	+	"list of declared molecules\n",
1574	+	id);
1575	+	painCave.isFatal = 1;
1576	+	simError();
1577	+	}
1578	+
1579	+	headStamp->add(currentStamp);
1580	+	comp_stamps[i] = headStamp->match(id);
1581		}
1582
1583	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1584	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1585	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1583	>	if(comp_stamps[i]->getNCutoffGroups() > 0)
1584	>	haveCutoffGroups = true;
1585	>	}
1586	>
1587	>	for (i = 0; i < nInfo; i++)
1588	>	info[i].haveCutoffGroups = haveCutoffGroups;
1589
1590	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1590	>	#ifdef IS_MPI
1591	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1592	>	MPIcheckPoint();
1593	>	#endif // is_mpi
1594	>	}
1595
1596	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1596	>	void SimSetup::calcSysValues(void){
1597	>	int i, j;
1598	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1599
1600	<	rotMat[0][0] = 1.0;
1601	<	rotMat[0][1] = 0.0;
1338	<	rotMat[0][2] = 0.0;
1600	>	int* molMembershipArray;
1601	>	CutoffGroupStamp* cg;
1602
1603	<	rotMat[1][0] = 0.0;
1604	<	rotMat[1][1] = 1.0;
1605	<	rotMat[1][2] = 0.0;
1603	>	tot_atoms = 0;
1604	>	tot_bonds = 0;
1605	>	tot_bends = 0;
1606	>	tot_torsions = 0;
1607	>	tot_rigid = 0;
1608	>	tot_groups = 0;
1609	>	for (i = 0; i < n_components; i++){
1610	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1611	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1612	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1613	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1614	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1615
1616	<	rotMat[2][0] = 0.0;
1617	<	rotMat[2][1] = 0.0;
1618	<	rotMat[2][2] = 1.0;
1616	>	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1617	>	atomsingroups = 0;
1618	>	for (j=0; j < ncutgroups; j++) {
1619	>	cg = comp_stamps[i]->getCutoffGroup(j);
1620	>	atomsingroups += cg->getNMembers();
1621	>	}
1622	>	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1623	>	tot_groups += components_nmol[i] * ngroupsinstamp;
1624	>	}
1625	>
1626	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1627	>	molMembershipArray = new int[tot_atoms];
1628
1629	<	dAtom->setA( rotMat );
1629	>	for (i = 0; i < nInfo; i++){
1630	>	info[i].n_atoms = tot_atoms;
1631	>	info[i].n_bonds = tot_bonds;
1632	>	info[i].n_bends = tot_bends;
1633	>	info[i].n_torsions = tot_torsions;
1634	>	info[i].n_SRI = tot_SRI;
1635	>	info[i].n_mol = tot_nmol;
1636	>	info[i].ngroup = tot_groups;
1637	>	info[i].molMembershipArray = molMembershipArray;
1638	>	}
1639	>	}
1640	>
1641	>	#ifdef IS_MPI
1642	>
1643	>	void SimSetup::mpiMolDivide(void){
1644	>	int i, j, k;
1645	>	int localMol, allMol;
1646	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1647	>	int local_rigid, local_groups;
1648	>	vector<int> globalMolIndex;
1649	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1650	>	CutoffGroupStamp* cg;
1651	>
1652	>	mpiSim = new mpiSimulation(info);
1653	>
1654	>	mpiSim->divideLabor();
1655	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1656	>	globalGroupIndex = mpiSim->getGlobalGroupIndex();
1657	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1658	>
1659	>	// set up the local variables
1660	>
1661	>	mol2proc = mpiSim->getMolToProcMap();
1662	>	molCompType = mpiSim->getMolComponentType();
1663	>
1664	>	allMol = 0;
1665	>	localMol = 0;
1666	>	local_atoms = 0;
1667	>	local_bonds = 0;
1668	>	local_bends = 0;
1669	>	local_torsions = 0;
1670	>	local_rigid = 0;
1671	>	local_groups = 0;
1672	>	globalAtomCounter = 0;
1673	>
1674	>	for (i = 0; i < n_components; i++){
1675	>	for (j = 0; j < components_nmol[i]; j++){
1676	>	if (mol2proc[allMol] == worldRank){
1677	>	local_atoms += comp_stamps[i]->getNAtoms();
1678	>	local_bonds += comp_stamps[i]->getNBonds();
1679	>	local_bends += comp_stamps[i]->getNBends();
1680	>	local_torsions += comp_stamps[i]->getNTorsions();
1681	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1682	>
1683	>	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1684	>	atomsingroups = 0;
1685	>	for (k=0; k < ncutgroups; k++) {
1686	>	cg = comp_stamps[i]->getCutoffGroup(k);
1687	>	atomsingroups += cg->getNMembers();
1688	>	}
1689	>	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1690	>	ncutgroups;
1691	>	local_groups += ngroupsinstamp;
1692	>
1693	>	localMol++;
1694	>	}
1695	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1696	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1697	>	globalAtomCounter++;
1698	>	}
1699	>
1700	>	allMol++;
1701		}
1702	+	}
1703	+	local_SRI = local_bonds + local_bends + local_torsions;
1704
1705	<	current_atom_ndx++;
1705	>	info[0].n_atoms = mpiSim->getNAtomsLocal();
1706	>
1707	>	if (local_atoms != info[0].n_atoms){
1708	>	sprintf(painCave.errMsg,
1709	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1710	>	"\tlocalAtom (%d) are not equal.\n",
1711	>	info[0].n_atoms, local_atoms);
1712	>	painCave.isFatal = 1;
1713	>	simError();
1714		}
1715
1716	<	current_mol++;
1717	<	current_comp_mol++;
1716	>	info[0].ngroup = mpiSim->getNGroupsLocal();
1717	>	if (local_groups != info[0].ngroup){
1718	>	sprintf(painCave.errMsg,
1719	>	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1720	>	"\tlocalGroups (%d) are not equal.\n",
1721	>	info[0].ngroup, local_groups);
1722	>	painCave.isFatal = 1;
1723	>	simError();
1724	>	}
1725	>
1726	>	info[0].n_bonds = local_bonds;
1727	>	info[0].n_bends = local_bends;
1728	>	info[0].n_torsions = local_torsions;
1729	>	info[0].n_SRI = local_SRI;
1730	>	info[0].n_mol = localMol;
1731
1732	<	if( current_comp_mol >= components_nmol[current_comp] ){
1732	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1733	>	MPIcheckPoint();
1734	>	}
1735
1736	<	current_comp_mol = 0;
1737	<	current_comp++;
1736	>	#endif // is_mpi
1737	>
1738	>
1739	>	void SimSetup::makeSysArrays(void){
1740	>
1741	>	#ifndef IS_MPI
1742	>	int k, j;
1743	>	#endif // is_mpi
1744	>	int i, l;
1745	>
1746	>	Atom** the_atoms;
1747	>	Molecule* the_molecules;
1748	>
1749	>	for (l = 0; l < nInfo; l++){
1750	>	// create the atom and short range interaction arrays
1751	>
1752	>	the_atoms = new Atom * [info[l].n_atoms];
1753	>	the_molecules = new Molecule[info[l].n_mol];
1754	>	int molIndex;
1755	>
1756	>	// initialize the molecule's stampID's
1757	>
1758	>	#ifdef IS_MPI
1759	>
1760	>
1761	>	molIndex = 0;
1762	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1763	>	if (mol2proc[i] == worldRank){
1764	>	the_molecules[molIndex].setStampID(molCompType[i]);
1765	>	the_molecules[molIndex].setMyIndex(molIndex);
1766	>	the_molecules[molIndex].setGlobalIndex(i);
1767	>	molIndex++;
1768	>	}
1769	>	}
1770	>
1771	>	#else // is_mpi
1772	>
1773	>	molIndex = 0;
1774	>	globalAtomCounter = 0;
1775	>	for (i = 0; i < n_components; i++){
1776	>	for (j = 0; j < components_nmol[i]; j++){
1777	>	the_molecules[molIndex].setStampID(i);
1778	>	the_molecules[molIndex].setMyIndex(molIndex);
1779	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1780	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1781	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1782	>	globalAtomCounter++;
1783	>	}
1784	>	molIndex++;
1785	>	}
1786	>	}
1787	>
1788	>
1789	>	#endif // is_mpi
1790	>
1791	>	info[l].globalExcludes = new int;
1792	>	info[l].globalExcludes[0] = 0;
1793	>
1794	>	// set the arrays into the SimInfo object
1795	>
1796	>	info[l].atoms = the_atoms;
1797	>	info[l].molecules = the_molecules;
1798	>	info[l].nGlobalExcludes = 0;
1799	>
1800	>	the_ff->setSimInfo(info);
1801		}
1802		}
1803	+
1804	+	void SimSetup::makeIntegrator(void){
1805	+	int k;
1806	+
1807	+	NVE<RealIntegrator>* myNVE = NULL;
1808	+	NVT<RealIntegrator>* myNVT = NULL;
1809	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1810	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1811	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1812	+
1813	+	for (k = 0; k < nInfo; k++){
1814	+	switch (ensembleCase){
1815	+	case NVE_ENS:
1816	+	if (globals->haveZconstraints()){
1817	+	setupZConstraint(info[k]);
1818	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1819	+	}
1820	+	else{
1821	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1822	+	}
1823	+
1824	+	info->the_integrator = myNVE;
1825	+	break;
1826	+
1827	+	case NVT_ENS:
1828	+	if (globals->haveZconstraints()){
1829	+	setupZConstraint(info[k]);
1830	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1831	+	}
1832	+	else
1833	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1834	+
1835	+	myNVT->setTargetTemp(globals->getTargetTemp());
1836	+
1837	+	if (globals->haveTauThermostat())
1838	+	myNVT->setTauThermostat(globals->getTauThermostat());
1839	+	else{
1840	+	sprintf(painCave.errMsg,
1841	+	"SimSetup error: If you use the NVT\n"
1842	+	"\tensemble, you must set tauThermostat.\n");
1843	+	painCave.isFatal = 1;
1844	+	simError();
1845	+	}
1846	+
1847	+	info->the_integrator = myNVT;
1848	+	break;
1849	+
1850	+	case NPTi_ENS:
1851	+	if (globals->haveZconstraints()){
1852	+	setupZConstraint(info[k]);
1853	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1854	+	}
1855	+	else
1856	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1857	+
1858	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1859	+
1860	+	if (globals->haveTargetPressure())
1861	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1862	+	else{
1863	+	sprintf(painCave.errMsg,
1864	+	"SimSetup error: If you use a constant pressure\n"
1865	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1866	+	painCave.isFatal = 1;
1867	+	simError();
1868	+	}
1869	+
1870	+	if (globals->haveTauThermostat())
1871	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1872	+	else{
1873	+	sprintf(painCave.errMsg,
1874	+	"SimSetup error: If you use an NPT\n"
1875	+	"\tensemble, you must set tauThermostat.\n");
1876	+	painCave.isFatal = 1;
1877	+	simError();
1878	+	}
1879	+
1880	+	if (globals->haveTauBarostat())
1881	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1882	+	else{
1883	+	sprintf(painCave.errMsg,
1884	+	"SimSetup error: If you use an NPT\n"
1885	+	"\tensemble, you must set tauBarostat.\n");
1886	+	painCave.isFatal = 1;
1887	+	simError();
1888	+	}
1889	+
1890	+	info->the_integrator = myNPTi;
1891	+	break;
1892	+
1893	+	case NPTf_ENS:
1894	+	if (globals->haveZconstraints()){
1895	+	setupZConstraint(info[k]);
1896	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1897	+	}
1898	+	else
1899	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1900	+
1901	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1902	+
1903	+	if (globals->haveTargetPressure())
1904	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1905	+	else{
1906	+	sprintf(painCave.errMsg,
1907	+	"SimSetup error: If you use a constant pressure\n"
1908	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1909	+	painCave.isFatal = 1;
1910	+	simError();
1911	+	}
1912	+
1913	+	if (globals->haveTauThermostat())
1914	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1915	+
1916	+	else{
1917	+	sprintf(painCave.errMsg,
1918	+	"SimSetup error: If you use an NPT\n"
1919	+	"\tensemble, you must set tauThermostat.\n");
1920	+	painCave.isFatal = 1;
1921	+	simError();
1922	+	}
1923	+
1924	+	if (globals->haveTauBarostat())
1925	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1926	+
1927	+	else{
1928	+	sprintf(painCave.errMsg,
1929	+	"SimSetup error: If you use an NPT\n"
1930	+	"\tensemble, you must set tauBarostat.\n");
1931	+	painCave.isFatal = 1;
1932	+	simError();
1933	+	}
1934	+
1935	+	info->the_integrator = myNPTf;
1936	+	break;
1937	+
1938	+	case NPTxyz_ENS:
1939	+	if (globals->haveZconstraints()){
1940	+	setupZConstraint(info[k]);
1941	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1942	+	}
1943	+	else
1944	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1945	+
1946	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1947	+
1948	+	if (globals->haveTargetPressure())
1949	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1950	+	else{
1951	+	sprintf(painCave.errMsg,
1952	+	"SimSetup error: If you use a constant pressure\n"
1953	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1954	+	painCave.isFatal = 1;
1955	+	simError();
1956	+	}
1957	+
1958	+	if (globals->haveTauThermostat())
1959	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1960	+	else{
1961	+	sprintf(painCave.errMsg,
1962	+	"SimSetup error: If you use an NPT\n"
1963	+	"\tensemble, you must set tauThermostat.\n");
1964	+	painCave.isFatal = 1;
1965	+	simError();
1966	+	}
1967	+
1968	+	if (globals->haveTauBarostat())
1969	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1970	+	else{
1971	+	sprintf(painCave.errMsg,
1972	+	"SimSetup error: If you use an NPT\n"
1973	+	"\tensemble, you must set tauBarostat.\n");
1974	+	painCave.isFatal = 1;
1975	+	simError();
1976	+	}
1977	+
1978	+	info->the_integrator = myNPTxyz;
1979	+	break;
1980	+
1981	+	default:
1982	+	sprintf(painCave.errMsg,
1983	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1984	+	painCave.isFatal = 1;
1985	+	simError();
1986	+	}
1987	+	}
1988	+	}
1989	+
1990	+	void SimSetup::initFortran(void){
1991	+	info[0].refreshSim();
1992	+
1993	+	if (!strcmp(info[0].mixingRule, "standard")){
1994	+	the_ff->initForceField(LB_MIXING_RULE);
1995	+	}
1996	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1997	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1998	+	}
1999	+	else{
2000	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
2001	+	info[0].mixingRule);
2002	+	painCave.isFatal = 1;
2003	+	simError();
2004	+	}
2005	+
2006	+
2007	+	#ifdef IS_MPI
2008	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
2009	+	MPIcheckPoint();
2010	+	#endif // is_mpi
2011	+	}
2012	+
2013	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
2014	+	int nZConstraints;
2015	+	ZconStamp** zconStamp;
2016	+
2017	+	if (globals->haveZconstraintTime()){
2018	+	//add sample time of z-constraint  into SimInfo's property list
2019	+	DoubleData* zconsTimeProp = new DoubleData();
2020	+	zconsTimeProp->setID(ZCONSTIME_ID);
2021	+	zconsTimeProp->setData(globals->getZconsTime());
2022	+	theInfo.addProperty(zconsTimeProp);
2023	+	}
2024	+	else{
2025	+	sprintf(painCave.errMsg,
2026	+	"ZConstraint error: If you use a ZConstraint,\n"
2027	+	"\tyou must set zconsTime.\n");
2028	+	painCave.isFatal = 1;
2029	+	simError();
2030	+	}
2031	+
2032	+	//push zconsTol into siminfo, if user does not specify
2033	+	//value for zconsTol, a default value will be used
2034	+	DoubleData* zconsTol = new DoubleData();
2035	+	zconsTol->setID(ZCONSTOL_ID);
2036	+	if (globals->haveZconsTol()){
2037	+	zconsTol->setData(globals->getZconsTol());
2038	+	}
2039	+	else{
2040	+	double defaultZConsTol = 0.01;
2041	+	sprintf(painCave.errMsg,
2042	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
2043	+	"\tOOPSE will use a default value of %f.\n"
2044	+	"\tTo set the tolerance, use the zconsTol variable.\n",
2045	+	defaultZConsTol);
2046	+	painCave.isFatal = 0;
2047	+	simError();
2048	+
2049	+	zconsTol->setData(defaultZConsTol);
2050	+	}
2051	+	theInfo.addProperty(zconsTol);
2052	+
2053	+	//set Force Subtraction Policy
2054	+	StringData* zconsForcePolicy = new StringData();
2055	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
2056	+
2057	+	if (globals->haveZconsForcePolicy()){
2058	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
2059	+	}
2060	+	else{
2061	+	sprintf(painCave.errMsg,
2062	+	"ZConstraint Warning: No force subtraction policy was set.\n"
2063	+	"\tOOPSE will use PolicyByMass.\n"
2064	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
2065	+	painCave.isFatal = 0;
2066	+	simError();
2067	+	zconsForcePolicy->setData("BYMASS");
2068	+	}
2069	+
2070	+	theInfo.addProperty(zconsForcePolicy);
2071	+
2072	+	//set zcons gap
2073	+	DoubleData* zconsGap = new DoubleData();
2074	+	zconsGap->setID(ZCONSGAP_ID);
2075	+
2076	+	if (globals->haveZConsGap()){
2077	+	zconsGap->setData(globals->getZconsGap());
2078	+	theInfo.addProperty(zconsGap);
2079	+	}
2080	+
2081	+	//set zcons fixtime
2082	+	DoubleData* zconsFixtime = new DoubleData();
2083	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
2084	+
2085	+	if (globals->haveZConsFixTime()){
2086	+	zconsFixtime->setData(globals->getZconsFixtime());
2087	+	theInfo.addProperty(zconsFixtime);
2088	+	}
2089	+
2090	+	//set zconsUsingSMD
2091	+	IntData* zconsUsingSMD = new IntData();
2092	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2093	+
2094	+	if (globals->haveZConsUsingSMD()){
2095	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2096	+	theInfo.addProperty(zconsUsingSMD);
2097	+	}
2098	+
2099	+	//Determine the name of ouput file and add it into SimInfo's property list
2100	+	//Be careful, do not use inFileName, since it is a pointer which
2101	+	//point to a string at master node, and slave nodes do not contain that string
2102	+
2103	+	string zconsOutput(theInfo.finalName);
2104	+
2105	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
2106	+
2107	+	StringData* zconsFilename = new StringData();
2108	+	zconsFilename->setID(ZCONSFILENAME_ID);
2109	+	zconsFilename->setData(zconsOutput);
2110	+
2111	+	theInfo.addProperty(zconsFilename);
2112	+
2113	+	//setup index, pos and other parameters of z-constraint molecules
2114	+	nZConstraints = globals->getNzConstraints();
2115	+	theInfo.nZconstraints = nZConstraints;
2116	+
2117	+	zconStamp = globals->getZconStamp();
2118	+	ZConsParaItem tempParaItem;
2119	+
2120	+	ZConsParaData* zconsParaData = new ZConsParaData();
2121	+	zconsParaData->setID(ZCONSPARADATA_ID);
2122	+
2123	+	for (int i = 0; i < nZConstraints; i++){
2124	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
2125	+	tempParaItem.zPos = zconStamp[i]->getZpos();
2126	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2127	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
2128	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2129	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2130	+	zconsParaData->addItem(tempParaItem);
2131	+	}
2132	+
2133	+	//check the uniqueness of index
2134	+	if(!zconsParaData->isIndexUnique()){
2135	+	sprintf(painCave.errMsg,
2136	+	"ZConstraint Error: molIndex is not unique!\n");
2137	+	painCave.isFatal = 1;
2138	+	simError();
2139	+	}
2140	+
2141	+	//sort the parameters by index of molecules
2142	+	zconsParaData->sortByIndex();
2143	+
2144	+	//push data into siminfo, therefore, we can retrieve later
2145	+	theInfo.addProperty(zconsParaData);
2146	+	}
2147	+
2148	+	void SimSetup::makeMinimizer(){
2149	+
2150	+	OOPSEMinimizer* myOOPSEMinimizer;
2151	+	MinimizerParameterSet* param;
2152	+	char minimizerName[100];
2153	+
2154	+	for (int i = 0; i < nInfo; i++){
2155	+
2156	+	//prepare parameter set for minimizer
2157	+	param = new MinimizerParameterSet();
2158	+	param->setDefaultParameter();
2159	+
2160	+	if (globals->haveMinimizer()){
2161	+	param->setFTol(globals->getMinFTol());
2162	+	}
2163	+
2164	+	if (globals->haveMinGTol()){
2165	+	param->setGTol(globals->getMinGTol());
2166	+	}
2167	+
2168	+	if (globals->haveMinMaxIter()){
2169	+	param->setMaxIteration(globals->getMinMaxIter());
2170	+	}
2171	+
2172	+	if (globals->haveMinWriteFrq()){
2173	+	param->setMaxIteration(globals->getMinMaxIter());
2174	+	}
2175	+
2176	+	if (globals->haveMinWriteFrq()){
2177	+	param->setWriteFrq(globals->getMinWriteFrq());
2178	+	}
2179	+
2180	+	if (globals->haveMinStepSize()){
2181	+	param->setStepSize(globals->getMinStepSize());
2182	+	}
2183	+
2184	+	if (globals->haveMinLSMaxIter()){
2185	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2186	+	}
2187	+
2188	+	if (globals->haveMinLSTol()){
2189	+	param->setLineSearchTol(globals->getMinLSTol());
2190	+	}
2191	+
2192	+	strcpy(minimizerName, globals->getMinimizer());
2193	+
2194	+	if (!strcasecmp(minimizerName, "CG")){
2195	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2196	+	}
2197	+	else if (!strcasecmp(minimizerName, "SD")){
2198	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2199	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2200	+	}
2201	+	else{
2202	+	sprintf(painCave.errMsg,
2203	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2204	+	painCave.isFatal = 0;
2205	+	simError();
2206	+
2207	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2208	+	}
2209	+	info[i].the_integrator = myOOPSEMinimizer;
2210	+
2211	+	//store the minimizer into simInfo
2212	+	info[i].the_minimizer = myOOPSEMinimizer;
2213	+	info[i].has_minimizer = true;
2214	+	}
2215	+
2216	+	}

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