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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 605 by gezelter, Tue Jul 15 03:27:24 2003 UTC vs.
Revision 1229 by gezelter, Thu Jun 3 20:02:25 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
28	<	#define NPTim_ENS 4
22	<	#define NPTfm_ENS 5
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 41 | 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();
73	<	mpiEventLoop();
74	<
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;
82	<	Globals* the_globals;
83	<	int i, j, k, globalAtomIndex;
84	<
85	<	int ensembleCase;
86	<	int ffCase;
87	<
88	<	ensembleCase = -1;
89	<	ffCase = -1;
127	>	// gather all of the information from the Bass file
128
129	<	// get the stamps and globals;
92	<	the_stamps = stamps;
93	<	the_globals = globals;
129	>	gatherInfo();
130
131	<	// set the easy ones first
96	<	simnfo->target_temp = the_globals->getTargetTemp();
97	<	simnfo->dt = the_globals->getDt();
98	<	simnfo->run_time = the_globals->getRunTime();
131	>	// creation of complex system objects
132
133	<	// get the ones we know are there, yet still may need some work.
101	<	n_components = the_globals->getNComponents();
102	<	strcpy( force_field, the_globals->getForceField() );
133	>	sysObjectsCreation();
134
135	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
105	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
106	<	else{
107	<	sprintf( painCave.errMsg,
108	<	"SimSetup Error. Unrecognized force field -> %s\n",
109	<	force_field );
110	<	painCave.isFatal = 1;
111	<	simError();
112	<	}
135	>	// check on the post processing info
136
137	<	// get the ensemble:
115	<	strcpy( ensemble, the_globals->getEnsemble() );
137	>	finalInfoCheck();
138
139	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
118	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
119	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
120	<	ensembleCase = NPTi_ENS;
121	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
122	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
123	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
124	<	else{
125	<	sprintf( painCave.errMsg,
126	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
127	<	"reverting to NVE for this simulation.\n",
128	<	ensemble );
129	<	painCave.isFatal = 0;
130	<	simError();
131	<	strcpy( ensemble, "NVE" );
132	<	ensembleCase = NVE_ENS;
133	<	}
134	<	strcpy( simnfo->ensemble, ensemble );
139	>	// initialize the system coordinates
140
141	+	if ( !initSuspend ){
142	+	initSystemCoords();
143
144	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
145	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
146	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
140	<	//     if (the_globals->haveTargetPressure())
141	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
142	<	//     else {
143	<	//       sprintf( painCave.errMsg,
144	<	//                "SimSetup error: If you use the constant pressure\n"
145	<	//                "    ensemble, you must set targetPressure.\n"
146	<	//                "    This was found in the BASS file.\n");
147	<	//       painCave.isFatal = 1;
148	<	//       simError();
149	<	//     }
144	>	if( !(globals->getUseInitTime()) )
145	>	info[0].currentTime = 0.0;
146	>	}
147
148	<	//     if (the_globals->haveTauThermostat())
152	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
153	<	//     else if (the_globals->haveQmass())
154	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
155	<	//     else {
156	<	//       sprintf( painCave.errMsg,
157	<	//                "SimSetup error: If you use one of the constant temperature\n"
158	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
159	<	//                "    Neither of these was found in the BASS file.\n");
160	<	//       painCave.isFatal = 1;
161	<	//       simError();
162	<	//     }
148	>	// make the output filenames
149
150	<	//     if (the_globals->haveTauBarostat())
151	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
152	<	//     else {
153	<	//       sprintf( painCave.errMsg,
154	<	//                "SimSetup error: If you use the constant pressure\n"
169	<	//                "    ensemble, you must set tauBarostat.\n"
170	<	//                "    This was found in the BASS file.\n");
171	<	//       painCave.isFatal = 1;
172	<	//       simError();
173	<	//     }
150	>	makeOutNames();
151	>
152	>	#ifdef IS_MPI
153	>	mpiSim->mpiRefresh();
154	>	#endif
155
156	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
176	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
177	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
156	>	// initialize the Fortran
157
158	<	//     if (the_globals->haveTauThermostat())
180	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
181	<	//     else if (the_globals->haveQmass())
182	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
183	<	//     else {
184	<	//       sprintf( painCave.errMsg,
185	<	//                "SimSetup error: If you use one of the constant temperature\n"
186	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
187	<	//                "    Neither of these was found in the BASS file.\n");
188	<	//       painCave.isFatal = 1;
189	<	//       simError();
190	<	//     }
158	>	initFortran();
159
160	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
161	<	simnfo->usePBC = the_globals->getPBC();
162	<
163	<	int usesDipoles = 0;
164	<	switch( ffCase ){
160	>	if (globals->haveMinimizer())
161	>	// make minimizer
162	>	makeMinimizer();
163	>	else
164	>	// make the integrator
165	>	makeIntegrator();
166
167	<	case FF_DUFF:
199	<	the_ff = new DUFF();
200	<	usesDipoles = 1;
201	<	break;
167	>	}
168
203	–	case FF_LJ:
204	–	the_ff = new LJFF();
205	–	break;
169
170	<	default:
171	<	sprintf( painCave.errMsg,
172	<	"SimSetup Error. Unrecognized force field in case statement.\n");
173	<	painCave.isFatal = 1;
174	<	simError();
175	<	}
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	<	#ifdef IS_MPI
193	<	strcpy( checkPointMsg, "ForceField creation successful" );
194	<	MPIcheckPoint();
217	<	#endif // is_mpi
192	>	bond_pair* theBonds;
193	>	bend_set* theBends;
194	>	torsion_set* theTorsions;
195
196	<	// get the components and calculate the tot_nMol and indvidual n_mol
220	<	the_components = the_globals->getComponents();
221	<	components_nmol = new int[n_components];
222	<	comp_stamps = new MoleculeStamp*[n_components];
196	>	set<int> skipList;
197
198	<	if( !the_globals->haveNMol() ){
199	<	// we don't have the total number of molecules, so we assume it is
200	<	// given in each component
198	>	double phi, theta, psi;
199	>	char* molName;
200	>	char rbName[100];
201
202	<	tot_nmol = 0;
203	<	for( i=0; i<n_components; i++ ){
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_components[i]->haveNMol() ){
232	<	// we have a problem
233	<	sprintf( painCave.errMsg,
234	<	"SimSetup Error. No global NMol or component NMol"
235	<	" given. Cannot calculate the number of atoms.\n" );
236	<	painCave.isFatal = 1;
237	<	simError();
238	<	}
210	>	the_ff->readParams();
211
212	<	tot_nmol += the_components[i]->getNMol();
241	<	components_nmol[i] = the_components[i]->getNMol();
242	<	}
243	<	}
244	<	else{
245	<	sprintf( painCave.errMsg,
246	<	"SimSetup error.\n"
247	<	"\tSorry, the ability to specify total"
248	<	" nMols and then give molfractions in the components\n"
249	<	"\tis not currently supported."
250	<	" Please give nMol in the components.\n" );
251	<	painCave.isFatal = 1;
252	<	simError();
253	<
254	<
255	<	//     tot_nmol = the_globals->getNMol();
256	<
257	<	//   //we have the total number of molecules, now we check for molfractions
258	<	//     for( i=0; i<n_components; i++ ){
259	<
260	<	//       if( !the_components[i]->haveMolFraction() ){
261	<
262	<	//  if( !the_components[i]->haveNMol() ){
263	<	//    //we have a problem
264	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
265	<	//              << " nMol was given in component
266	<
267	<	}
212	>	// init the atoms
213
214	+	int nMembers, nNew, rb1, rb2;
215	+
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;
280	<	simnfo->headStamp = new LinkedMolStamp();
281	<
282	<	char* id;
283	<	LinkedMolStamp* headStamp = simnfo->headStamp;
284	<	LinkedMolStamp* currentStamp = NULL;
285	<	for( i=0; i<n_components; i++ ){
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 );
293	<	if( comp_stamps[i] == NULL ){
242	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
243
244	<	// extract the component from the list;
296	<
297	<	currentStamp = the_stamps->extractMolStamp( id );
298	<	if( currentStamp == NULL ){
299	<	sprintf( painCave.errMsg,
300	<	"SimSetup error: Component \"%s\" was not found in the "
301	<	"list of declared molecules\n",
302	<	id );
303	<	painCave.isFatal = 1;
304	<	simError();
305	<	}
306	<
307	<	headStamp->add( currentStamp );
308	<	comp_stamps[i] = headStamp->match( id );
309	<	}
310	<	}
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
316	<
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;
324	<	tot_bends = 0;
325	<	tot_torsions = 0;
326	<	for( i=0; i<n_components; i++ ){
327	<
328	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
329	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
330	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
331	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
332	<	}
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;
339	<	simnfo->n_torsions = tot_torsions;
340	<	simnfo->n_SRI = tot_SRI;
341	<	simnfo->n_mol = tot_nmol;
342	<
343	<	simnfo->molMembershipArray = new int[tot_atoms];
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	<
351	<	globalIndex = mpiSim->divideLabor();
284	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
285	>
286	>	}
287	>	else{
288
289	<	// set up the local variables
354	<
355	<	int localMol, allMol;
356	<	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();
359	<	int* molCompType = mpiSim->getMolComponentType();
360	<
361	<	allMol = 0;
362	<	localMol = 0;
363	<	local_atoms = 0;
364	<	local_bonds = 0;
365	<	local_bends = 0;
366	<	local_torsions = 0;
367	<	globalAtomIndex = 0;
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	<
374	<	if( mol2proc[allMol] == worldRank ){
375	<
376	<	local_atoms +=    comp_stamps[i]->getNAtoms();
377	<	local_bonds +=    comp_stamps[i]->getNBonds();
378	<	local_bends +=    comp_stamps[i]->getNBends();
379	<	local_torsions += comp_stamps[i]->getNTorsions();
380	<	localMol++;
381	<	}
382	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
383	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
384	<	globalAtomIndex++;
385	<	}
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	<
394	<	if( local_atoms != simnfo->n_atoms ){
395	<	sprintf( painCave.errMsg,
396	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
397	<	" localAtom (%d) are not equal.\n",
398	<	simnfo->n_atoms,
399	<	local_atoms );
400	<	painCave.isFatal = 1;
401	<	simError();
402	<	}
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;
406	<	simnfo->n_torsions = local_torsions;
407	<	simnfo->n_SRI = local_SRI;
408	<	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;
334	<
335	<	// initialize the molecule's stampID's
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	+	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;
430	<	for(i=0; i<mpiSim->getTotNmol(); i++){
431	<
432	<	if(mol2proc[i] == worldRank ){
433	<	the_molecules[molIndex].setStampID( molCompType[i] );
434	<	the_molecules[molIndex].setMyIndex( molIndex );
435	<	the_molecules[molIndex].setGlobalIndex( i );
436	<	molIndex++;
437	<	}
438	<	}
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		}
453	–	molIndex++;
454	–	}
455	–	}
456	–
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 );
472	<	the_excludes = new Exclude*;
473	<	the_excludes[0] = new Exclude(0);
474	<	the_excludes[0]->setPair( 0,0 );
475	<	simnfo->globalExcludes = new int;
476	<	simnfo->globalExcludes[0] = 0;
477	<	simnfo->n_exclude = 0;
478	<	}
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];
491	<	if( the_globals->haveBox() ){
492	<	boxVector[0] = the_globals->getBox();
493	<	boxVector[1] = the_globals->getBox();
494	<	boxVector[2] = the_globals->getBox();
495	<
496	<	simnfo->setBox( boxVector );
497	<	}
498	<	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];
504	<	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	<	}
508	<	else{
509	<	if( !the_globals->haveBoxX() ){
510	<	sprintf( painCave.errMsg,
511	<	"SimSetup error, no periodic BoxX size given.\n" );
512	<	painCave.isFatal = 1;
513	<	simError();
514	<	}
515	<	boxVector[0] = the_globals->getBoxX();
452	>	// molI is atom numbering inside this molecule
453	>	molI = currentRigidBody->getMember(rb1);
454
455	<	if( !the_globals->haveBoxY() ){
456	<	sprintf( painCave.errMsg,
519	<	"SimSetup error, no periodic BoxY size given.\n" );
520	<	painCave.isFatal = 1;
521	<	simError();
522	<	}
523	<	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" );
528	<	painCave.isFatal = 1;
529	<	simError();
530	<	}
531	<	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];
548	<	for(i=0; i<simnfo->n_atoms; i++){
549	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
550	<	}
551	<
552	<	if (the_globals->getUseRF() ) {
553	<	simnfo->useReactionField = 1;
554	<
555	<	if( !the_globals->haveECR() ){
556	<	sprintf( painCave.errMsg,
557	<	"SimSetup Warning: using default value of 1/2 the smallest "
558	<	"box length for the electrostaticCutoffRadius.\n"
559	<	"I hope you have a very fast processor!\n");
560	<	painCave.isFatal = 0;
561	<	simError();
562	<	double smallest;
563	<	smallest = simnfo->boxLx;
564	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
565	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
566	<	simnfo->ecr = 0.5 * smallest;
567	<	} else {
568	<	simnfo->ecr        = the_globals->getECR();
569	<	}
513	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
514	>	nMembers = currentCutoffGroup->getNMembers();
515
516	<	if( !the_globals->haveEST() ){
517	<	sprintf( painCave.errMsg,
518	<	"SimSetup Warning: using default value of 0.05 * the "
519	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
520	<	);
521	<	painCave.isFatal = 0;
522	<	simError();
523	<	simnfo->est = 0.05 * simnfo->ecr;
524	<	} else {
525	<	simnfo->est        = the_globals->getEST();
526	<	}
527	<
528	<	if(!the_globals->haveDielectric() ){
529	<	sprintf( painCave.errMsg,
530	<	"SimSetup Error: You are trying to use Reaction Field without"
531	<	"setting a dielectric constant!\n"
532	<	);
533	<	painCave.isFatal = 1;
534	<	simError();
535	<	}
536	<	simnfo->dielectric = the_globals->getDielectric();
537	<	} else {
538	<	if (usesDipoles) {
516	>	myCutoffGroup = new CutoffGroup();
517	>
518	>	#ifdef IS_MPI
519	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
520	>	#else
521	>	myCutoffGroup->setGlobalIndex(groupOffset);
522	>	#endif
523	>
524	>	for (int cg = 0; cg < nMembers; cg++) {
525	>
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	>	globalID = info[k].atoms[tempI]->getGlobalIndex();
534	>	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
535	>	#else
536	>	globalID = info[k].atoms[tempI]->getIndex();
537	>	info[k].globalGroupMembership[globalID] = groupOffset;
538	>	#endif
539	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
540	>	cutoffAtomSet.insert(tempI);
541	>	}
542	>
543	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
544	>	groupOffset++;
545	>
546	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
547
595	–	if( !the_globals->haveECR() ){
596	–	sprintf( painCave.errMsg,
597	–	"SimSetup Warning: using default value of 1/2 the smallest "
598	–	"box length for the electrostaticCutoffRadius.\n"
599	–	"I hope you have a very fast processor!\n");
600	–	painCave.isFatal = 0;
601	–	simError();
602	–	double smallest;
603	–	smallest = simnfo->boxLx;
604	–	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
605	–	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
606	–	simnfo->ecr = 0.5 * smallest;
607	–	} else {
608	–	simnfo->ecr        = the_globals->getECR();
609	–	}
548
549	<	if( !the_globals->haveEST() ){
550	<	sprintf( painCave.errMsg,
551	<	"SimSetup Warning: using default value of 5%% of the "
552	<	"electrostaticCutoffRadius for the "
553	<	"electrostaticSkinThickness\n"
554	<	);
555	<	painCave.isFatal = 0;
556	<	simError();
557	<	simnfo->est = 0.05 * simnfo->ecr;
558	<	} else {
559	<	simnfo->est        = the_globals->getEST();
549	>	// create a cutoff group for every atom in current molecule which
550	>	// does not belong to cutoffgroup defined at mdl file
551	>
552	>	for(j = 0; j < molInfo.nAtoms; j++){
553	>
554	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
555	>	myCutoffGroup = new CutoffGroup();
556	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
557	>
558	>	#ifdef IS_MPI
559	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[groupOffset]);
560	>	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex();
561	>	info[k].globalGroupMembership[globalID] = globalGroupIndex[groupOffset];
562	>	#else
563	>	myCutoffGroup->setGlobalIndex(groupOffset);
564	>	globalID = info[k].atoms[atomOffset + j]->getIndex();
565	>	info[k].globalGroupMembership[globalID] = groupOffset;
566	>	#endif
567	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
568	>	groupOffset++;
569	>	}
570		}
623	–	}
624	–	}
571
572	<	#ifdef IS_MPI
573	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
628	<	MPIcheckPoint();
629	<	#endif // is_mpi
572	>	// After this is all set up, scan through the atoms to
573	>	// see if they can be added to the integrableObjects:
574
575	<	if( the_globals->haveInitialConfig() ){
576	<
577	<	InitializeFromFile* fileInit;
578	<	#ifdef IS_MPI // is_mpi
579	<	if( worldRank == 0 ){
636	<	#endif //is_mpi
637	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
575	>	molInfo.myIntegrableObjects.clear();
576	>
577	>
578	>	for (j = 0; j < molInfo.nAtoms; j++){
579	>
580		#ifdef IS_MPI
581	<	}else fileInit = new InitializeFromFile( NULL );
581	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
582	>	#else
583	>	slJ = j+atomOffset;
584		#endif
641	–	fileInit->read_xyz( simnfo ); // default velocities on
585
586	<	delete fileInit;
644	<	}
645	<	else{
586	>	// if they aren't on the skip list, then they can be integrated
587
588	<	#ifdef IS_MPI
588	>	if (skipList.find(slJ) == skipList.end()) {
589	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
590	>	info[k].integrableObjects.push_back(mySD);
591	>	molInfo.myIntegrableObjects.push_back(mySD);
592	>	}
593	>	}
594
595	<	// no init from bass
650	<
651	<	sprintf( painCave.errMsg,
652	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
653	<	painCave.isFatal;
654	<	simError();
655	<
656	<	#else
595	>	// all rigid bodies are integrated:
596
597	<	initFromBass();
597	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
598	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
599	>	info[k].integrableObjects.push_back(mySD);
600	>	molInfo.myIntegrableObjects.push_back(mySD);
601	>	}
602
603
604	<	#endif
662	<	}
604	>	/*
605
606	<	#ifdef IS_MPI
607	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
608	<	MPIcheckPoint();
609	<	#endif // is_mpi
606	>	//creat ConstraintPair.
607	>	molInfo.myConstraintPair.clear();
608	>
609	>	for (j = 0; j < molInfo.nBonds; j++){
610
611	+	//if both atoms are in the same rigid body, just skip it
612	+	currentBond = comp_stamps[stampID]->getBond(j);
613	+	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
614
615	<
616	<
617	<
615	>	tempI = currentBond->getA() + atomOffset;
616	>	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
617	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
618	>	else
619	>	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
620
621	<
622	<	#ifdef IS_MPI
623	<	if( worldRank == 0 ){
624	<	#endif // is_mpi
625	<
626	<	if( the_globals->haveFinalConfig() ){
627	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
628	<	}
629	<	else{
630	<	strcpy( simnfo->finalName, inFileName );
631	<	char* endTest;
632	<	int nameLength = strlen( simnfo->finalName );
633	<	endTest = &(simnfo->finalName[nameLength - 5]);
634	<	if( !strcmp( endTest, ".bass" ) ){
635	<	strcpy( endTest, ".eor" );
636	<	}
637	<	else if( !strcmp( endTest, ".BASS" ) ){
638	<	strcpy( endTest, ".eor" );
639	<	}
640	<	else{
641	<	endTest = &(simnfo->finalName[nameLength - 4]);
642	<	if( !strcmp( endTest, ".bss" ) ){
643	<	strcpy( endTest, ".eor" );
644	<	}
645	<	else if( !strcmp( endTest, ".mdl" ) ){
646	<	strcpy( endTest, ".eor" );
647	<	}
648	<	else{
649	<	strcat( simnfo->finalName, ".eor" );
650	<	}
651	<	}
652	<	}
653	<
654	<	// make the sample and status out names
655	<
656	<	strcpy( simnfo->sampleName, inFileName );
657	<	char* endTest;
658	<	int nameLength = strlen( simnfo->sampleName );
659	<	endTest = &(simnfo->sampleName[nameLength - 5]);
660	<	if( !strcmp( endTest, ".bass" ) ){
661	<	strcpy( endTest, ".dump" );
662	<	}
663	<	else if( !strcmp( endTest, ".BASS" ) ){
664	<	strcpy( endTest, ".dump" );
665	<	}
666	<	else{
667	<	endTest = &(simnfo->sampleName[nameLength - 4]);
668	<	if( !strcmp( endTest, ".bss" ) ){
669	<	strcpy( endTest, ".dump" );
670	<	}
671	<	else if( !strcmp( endTest, ".mdl" ) ){
672	<	strcpy( endTest, ".dump" );
673	<	}
674	<	else{
675	<	strcat( simnfo->sampleName, ".dump" );
676	<	}
677	<	}
678	<
679	<	strcpy( simnfo->statusName, inFileName );
680	<	nameLength = strlen( simnfo->statusName );
681	<	endTest = &(simnfo->statusName[nameLength - 5]);
682	<	if( !strcmp( endTest, ".bass" ) ){
683	<	strcpy( endTest, ".stat" );
684	<	}
685	<	else if( !strcmp( endTest, ".BASS" ) ){
686	<	strcpy( endTest, ".stat" );
687	<	}
688	<	else{
689	<	endTest = &(simnfo->statusName[nameLength - 4]);
690	<	if( !strcmp( endTest, ".bss" ) ){
691	<	strcpy( endTest, ".stat" );
692	<	}
693	<	else if( !strcmp( endTest, ".mdl" ) ){
694	<	strcpy( endTest, ".stat" );
695	<	}
696	<	else{
697	<	strcat( simnfo->statusName, ".stat" );
698	<	}
699	<	}
700	<
701	<	#ifdef IS_MPI
702	<	}
703	<	#endif // is_mpi
704	<
705	<	// set the status, sample, and themal kick times
706	<
707	<	if( the_globals->haveSampleTime() ){
708	<	simnfo->sampleTime = the_globals->getSampleTime();
709	<	simnfo->statusTime = simnfo->sampleTime;
710	<	simnfo->thermalTime = simnfo->sampleTime;
711	<	}
712	<	else{
713	<	simnfo->sampleTime = the_globals->getRunTime();
714	<	simnfo->statusTime = simnfo->sampleTime;
715	<	simnfo->thermalTime = simnfo->sampleTime;
716	<	}
717	<
718	<	if( the_globals->haveStatusTime() ){
719	<	simnfo->statusTime = the_globals->getStatusTime();
720	<	}
721	<
722	<	if( the_globals->haveThermalTime() ){
723	<	simnfo->thermalTime = the_globals->getThermalTime();
724	<	}
725	<
726	<	// check for the temperature set flag
727	<
728	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
729	<
730	<
731	<	// make the integrator
732	<
733	<
734	<	NVT*  myNVT = NULL;
735	<	NPTi* myNPTi = NULL;
736	<	NPTf* myNPTf = NULL;
737	<	NPTim* myNPTim = NULL;
738	<	NPTfm* myNPTfm = NULL;
739	<
740	<	switch( ensembleCase ){
741	<
742	<	case NVE_ENS:
743	<	new NVE( simnfo, the_ff );
744	<	break;
745	<
746	<	case NVT_ENS:
747	<	myNVT = new NVT( simnfo, the_ff );
748	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
749	<
750	<	if (the_globals->haveTauThermostat())
751	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
752	<
753	<	else {
754	<	sprintf( painCave.errMsg,
755	<	"SimSetup error: If you use the NVT\n"
756	<	"    ensemble, you must set tauThermostat.\n");
757	<	painCave.isFatal = 1;
758	<	simError();
759	<	}
760	<	break;
761	<
762	<	case NPTi_ENS:
763	<	myNPTi = new NPTi( simnfo, the_ff );
764	<	myNPTi->setTargetTemp( the_globals->getTargetTemp());
765	<
766	<	if (the_globals->haveTargetPressure())
767	<	myNPTi->setTargetPressure(the_globals->getTargetPressure());
768	<	else {
769	<	sprintf( painCave.errMsg,
770	<	"SimSetup error: If you use a constant pressure\n"
771	<	"    ensemble, you must set targetPressure in the BASS file.\n");
772	<	painCave.isFatal = 1;
773	<	simError();
774	<	}
775	<
776	<	if( the_globals->haveTauThermostat() )
777	<	myNPTi->setTauThermostat( the_globals->getTauThermostat() );
778	<	else{
779	<	sprintf( painCave.errMsg,
780	<	"SimSetup error: If you use an NPT\n"
781	<	"    ensemble, you must set tauThermostat.\n");
782	<	painCave.isFatal = 1;
783	<	simError();
784	<	}
785	<
786	<	if( the_globals->haveTauBarostat() )
787	<	myNPTi->setTauBarostat( the_globals->getTauBarostat() );
788	<	else{
789	<	sprintf( painCave.errMsg,
790	<	"SimSetup error: If you use an NPT\n"
791	<	"    ensemble, you must set tauBarostat.\n");
792	<	painCave.isFatal = 1;
793	<	simError();
794	<	}
795	<	break;
796	<
797	<	case NPTf_ENS:
798	<	myNPTf = new NPTf( simnfo, the_ff );
799	<	myNPTf->setTargetTemp( the_globals->getTargetTemp());
800	<
801	<	if (the_globals->haveTargetPressure())
802	<	myNPTf->setTargetPressure(the_globals->getTargetPressure());
803	<	else {
804	<	sprintf( painCave.errMsg,
805	<	"SimSetup error: If you use a constant pressure\n"
806	<	"    ensemble, you must set targetPressure in the BASS file.\n");
807	<	painCave.isFatal = 1;
808	<	simError();
809	<	}
810	<
811	<	if( the_globals->haveTauThermostat() )
812	<	myNPTf->setTauThermostat( the_globals->getTauThermostat() );
813	<	else{
814	<	sprintf( painCave.errMsg,
815	<	"SimSetup error: If you use an NPT\n"
816	<	"    ensemble, you must set tauThermostat.\n");
817	<	painCave.isFatal = 1;
818	<	simError();
819	<	}
820	<
821	<	if( the_globals->haveTauBarostat() )
822	<	myNPTf->setTauBarostat( the_globals->getTauBarostat() );
823	<	else{
824	<	sprintf( painCave.errMsg,
825	<	"SimSetup error: If you use an NPT\n"
826	<	"    ensemble, you must set tauBarostat.\n");
827	<	painCave.isFatal = 1;
828	<	simError();
829	<	}
830	<	break;
831	<
832	<	case NPTim_ENS:
833	<	myNPTim = new NPTim( simnfo, the_ff );
834	<	myNPTim->setTargetTemp( the_globals->getTargetTemp());
835	<
836	<	if (the_globals->haveTargetPressure())
837	<	myNPTim->setTargetPressure(the_globals->getTargetPressure());
838	<	else {
839	<	sprintf( painCave.errMsg,
840	<	"SimSetup error: If you use a constant pressure\n"
841	<	"    ensemble, you must set targetPressure in the BASS file.\n");
842	<	painCave.isFatal = 1;
843	<	simError();
844	<	}
845	<
846	<	if( the_globals->haveTauThermostat() )
847	<	myNPTim->setTauThermostat( the_globals->getTauThermostat() );
848	<	else{
849	<	sprintf( painCave.errMsg,
850	<	"SimSetup error: If you use an NPT\n"
851	<	"    ensemble, you must set tauThermostat.\n");
852	<	painCave.isFatal = 1;
853	<	simError();
854	<	}
855	<
856	<	if( the_globals->haveTauBarostat() )
857	<	myNPTim->setTauBarostat( the_globals->getTauBarostat() );
858	<	else{
859	<	sprintf( painCave.errMsg,
860	<	"SimSetup error: If you use an NPT\n"
861	<	"    ensemble, you must set tauBarostat.\n");
862	<	painCave.isFatal = 1;
863	<	simError();
864	<	}
865	<	break;
866	<
867	<	case NPTfm_ENS:
868	<	myNPTfm = new NPTfm( simnfo, the_ff );
869	<	myNPTfm->setTargetTemp( the_globals->getTargetTemp());
870	<
871	<	if (the_globals->haveTargetPressure())
872	<	myNPTfm->setTargetPressure(the_globals->getTargetPressure());
873	<	else {
874	<	sprintf( painCave.errMsg,
875	<	"SimSetup error: If you use a constant pressure\n"
876	<	"    ensemble, you must set targetPressure in the BASS file.\n");
877	<	painCave.isFatal = 1;
878	<	simError();
879	<	}
880	<
881	<	if( the_globals->haveTauThermostat() )
882	<	myNPTfm->setTauThermostat( the_globals->getTauThermostat() );
883	<	else{
884	<	sprintf( painCave.errMsg,
885	<	"SimSetup error: If you use an NPT\n"
886	<	"    ensemble, you must set tauThermostat.\n");
887	<	painCave.isFatal = 1;
888	<	simError();
889	<	}
890	<
891	<	if( the_globals->haveTauBarostat() )
892	<	myNPTfm->setTauBarostat( the_globals->getTauBarostat() );
893	<	else{
894	<	sprintf( painCave.errMsg,
895	<	"SimSetup error: If you use an NPT\n"
896	<	"    ensemble, you must set tauBarostat.\n");
897	<	painCave.isFatal = 1;
898	<	simError();
899	<	}
900	<	break;
901	<
902	<	default:
903	<	sprintf( painCave.errMsg,
904	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
905	<	painCave.isFatal = 1;
906	<	simError();
907	<	}
908	<
909	<
910	<	#ifdef IS_MPI
911	<	mpiSim->mpiRefresh();
912	<	#endif
913	<
914	<	// initialize the Fortran
915	<
916	<
917	<	simnfo->refreshSim();
918	<
919	<	if( !strcmp( simnfo->mixingRule, "standard") ){
920	<	the_ff->initForceField( LB_MIXING_RULE );
921	<	}
922	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
923	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
924	<	}
925	<	else{
926	<	sprintf( painCave.errMsg,
927	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
928	<	simnfo->mixingRule );
929	<	painCave.isFatal = 1;
930	<	simError();
931	<	}
932	<
933	<
934	<	#ifdef IS_MPI
935	<	strcpy( checkPointMsg,
936	<	"Successfully intialized the mixingRule for Fortran." );
937	<	MPIcheckPoint();
938	<	#endif // is_mpi
939	<	}
940	<
941	<
942	<	void SimSetup::makeMolecules( void ){
943	<
944	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
945	<	molInit info;
946	<	DirectionalAtom* dAtom;
947	<	LinkedAssign* extras;
948	<	LinkedAssign* current_extra;
949	<	AtomStamp* currentAtom;
950	<	BondStamp* currentBond;
951	<	BendStamp* currentBend;
952	<	TorsionStamp* currentTorsion;
953	<
954	<	bond_pair* theBonds;
955	<	bend_set* theBends;
956	<	torsion_set* theTorsions;
957	<
958	<
959	<	//init the forceField paramters
960	<
961	<	the_ff->readParams();
962	<
963	<
964	<	// init the atoms
965	<
966	<	double ux, uy, uz, u, uSqr;
967	<
968	<	atomOffset = 0;
969	<	excludeOffset = 0;
970	<	for(i=0; i<simnfo->n_mol; i++){
971	<
972	<	stampID = the_molecules[i].getStampID();
973	<
974	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
975	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
976	<	info.nBends    = comp_stamps[stampID]->getNBends();
977	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
978	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
979	<
980	<	info.myAtoms = &the_atoms[atomOffset];
981	<	info.myExcludes = &the_excludes[excludeOffset];
982	<	info.myBonds = new Bond*[info.nBonds];
983	<	info.myBends = new Bend*[info.nBends];
984	<	info.myTorsions = new Torsion*[info.nTorsions];
985	<
986	<	theBonds = new bond_pair[info.nBonds];
987	<	theBends = new bend_set[info.nBends];
988	<	theTorsions = new torsion_set[info.nTorsions];
989	<
990	<	// make the Atoms
991	<
992	<	for(j=0; j<info.nAtoms; j++){
993	<
994	<	currentAtom = comp_stamps[stampID]->getAtom( j );
995	<	if( currentAtom->haveOrientation() ){
996	<
997	<	dAtom = new DirectionalAtom(j + atomOffset);
998	<	simnfo->n_oriented++;
999	<	info.myAtoms[j] = dAtom;
1000	<
1001	<	ux = currentAtom->getOrntX();
1002	<	uy = currentAtom->getOrntY();
1003	<	uz = currentAtom->getOrntZ();
1004	<
1005	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
1006	<
1007	<	u = sqrt( uSqr );
1008	<	ux = ux / u;
1009	<	uy = uy / u;
1010	<	uz = uz / u;
1011	<
1012	<	dAtom->setSUx( ux );
1013	<	dAtom->setSUy( uy );
1014	<	dAtom->setSUz( uz );
1015	<	}
1016	<	else{
1017	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
1018	<	}
1019	<	info.myAtoms[j]->setType( currentAtom->getType() );
1020	<
1021	<	#ifdef IS_MPI
1022	<
1023	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
1024	<
1025	<	#endif // is_mpi
1026	<	}
1027	<
1028	<	// make the bonds
1029	<	for(j=0; j<info.nBonds; j++){
1030	<
1031	<	currentBond = comp_stamps[stampID]->getBond( j );
1032	<	theBonds[j].a = currentBond->getA() + atomOffset;
1033	<	theBonds[j].b = currentBond->getB() + atomOffset;
1034	<
1035	<	exI = theBonds[j].a;
1036	<	exJ = theBonds[j].b;
1037	<
1038	<	// exclude_I must always be the smaller of the pair
1039	<	if( exI > exJ ){
1040	<	tempEx = exI;
1041	<	exI = exJ;
1042	<	exJ = tempEx;
1043	<	}
1044	<	#ifdef IS_MPI
1045	<	tempEx = exI;
1046	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1047	<	tempEx = exJ;
1048	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1049	<
1050	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1051	<	#else  // isn't MPI
1052	<
1053	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1054	<	#endif  //is_mpi
1055	<	}
1056	<	excludeOffset += info.nBonds;
1057	<
1058	<	//make the bends
1059	<	for(j=0; j<info.nBends; j++){
1060	<
1061	<	currentBend = comp_stamps[stampID]->getBend( j );
1062	<	theBends[j].a = currentBend->getA() + atomOffset;
1063	<	theBends[j].b = currentBend->getB() + atomOffset;
1064	<	theBends[j].c = currentBend->getC() + atomOffset;
1065	<
1066	<	if( currentBend->haveExtras() ){
1067	<
1068	<	extras = currentBend->getExtras();
1069	<	current_extra = extras;
1070	<
1071	<	while( current_extra != NULL ){
1072	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1073	<
1074	<	switch( current_extra->getType() ){
1075	<
1076	<	case 0:
1077	<	theBends[j].ghost =
1078	<	current_extra->getInt() + atomOffset;
1079	<	theBends[j].isGhost = 1;
1080	<	break;
1081	<
1082	<	case 1:
1083	<	theBends[j].ghost =
1084	<	(int)current_extra->getDouble() + atomOffset;
1085	<	theBends[j].isGhost = 1;
1086	<	break;
1087	<
1088	<	default:
1089	<	sprintf( painCave.errMsg,
1090	<	"SimSetup Error: ghostVectorSource was neither a "
1091	<	"double nor an int.\n"
1092	<	"-->Bend[%d] in %s\n",
1093	<	j, comp_stamps[stampID]->getID() );
1094	<	painCave.isFatal = 1;
1095	<	simError();
1096	<	}
1097	<	}
1098	<
1099	<	else{
1100	<
1101	<	sprintf( painCave.errMsg,
1102	<	"SimSetup Error: unhandled bend assignment:\n"
1103	<	"    -->%s in Bend[%d] in %s\n",
1104	<	current_extra->getlhs(),
1105	<	j, comp_stamps[stampID]->getID() );
1106	<	painCave.isFatal = 1;
1107	<	simError();
1108	<	}
1109	<
1110	<	current_extra = current_extra->getNext();
1111	<	}
1112	<	}
1113	<
1114	<	if( !theBends[j].isGhost ){
1115	<
1116	<	exI = theBends[j].a;
1117	<	exJ = theBends[j].c;
1118	<	}
1119	<	else{
1120	<
1121	<	exI = theBends[j].a;
1122	<	exJ = theBends[j].b;
1123	<	}
1124	<
1125	<	// exclude_I must always be the smaller of the pair
1126	<	if( exI > exJ ){
1127	<	tempEx = exI;
1128	<	exI = exJ;
1129	<	exJ = tempEx;
1130	<	}
1131	<	#ifdef IS_MPI
1132	<	tempEx = exI;
1133	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1134	<	tempEx = exJ;
1135	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1136	<
1137	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1138	<	#else  // isn't MPI
1139	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1140	<	#endif  //is_mpi
1141	<	}
1142	<	excludeOffset += info.nBends;
1143	<
1144	<	for(j=0; j<info.nTorsions; j++){
1145	<
1146	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1147	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1148	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1149	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1150	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1151	<
1152	<	exI = theTorsions[j].a;
1153	<	exJ = theTorsions[j].d;
1154	<
1155	<	// exclude_I must always be the smaller of the pair
1156	<	if( exI > exJ ){
1157	<	tempEx = exI;
1158	<	exI = exJ;
1159	<	exJ = tempEx;
1160	<	}
1161	<	#ifdef IS_MPI
1162	<	tempEx = exI;
1163	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1164	<	tempEx = exJ;
1165	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1166	<
1167	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1168	<	#else  // isn't MPI
1169	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1170	<	#endif  //is_mpi
1171	<	}
1172	<	excludeOffset += info.nTorsions;
1173	<
1174	<
1175	<	// send the arrays off to the forceField for init.
1176	<
1177	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1178	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1179	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1180	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1181	<
1182	<
1183	<	the_molecules[i].initialize( info );
1184	<
1185	<
1186	<	atomOffset += info.nAtoms;
1187	<	delete[] theBonds;
1188	<	delete[] theBends;
1189	<	delete[] theTorsions;
1190	<	}
1191	<
1192	<	#ifdef IS_MPI
1193	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1194	<	MPIcheckPoint();
1195	<	#endif // is_mpi
1196	<
1197	<	// clean up the forcefield
1198	<	the_ff->calcRcut();
1199	<	the_ff->cleanMe();
1200	<
1201	<	}
1202	<
1203	<	void SimSetup::initFromBass( void ){
1204	<
1205	<	int i, j, k;
1206	<	int n_cells;
1207	<	double cellx, celly, cellz;
1208	<	double temp1, temp2, temp3;
1209	<	int n_per_extra;
1210	<	int n_extra;
1211	<	int have_extra, done;
1212	<
1213	<	temp1 = (double)tot_nmol / 4.0;
1214	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1215	<	temp3 = ceil( temp2 );
1216	<
1217	<	have_extra =0;
1218	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1219	<	have_extra =1;
1220	<
1221	<	n_cells = (int)temp3 - 1;
1222	<	cellx = simnfo->boxLx / temp3;
1223	<	celly = simnfo->boxLy / temp3;
1224	<	cellz = simnfo->boxLz / temp3;
1225	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1226	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1227	<	n_per_extra = (int)ceil( temp1 );
1228	<
1229	<	if( n_per_extra > 4){
1230	<	sprintf( painCave.errMsg,
1231	<	"SimSetup error. There has been an error in constructing"
1232	<	" the non-complete lattice.\n" );
1233	<	painCave.isFatal = 1;
1234	<	simError();
1235	<	}
1236	<	}
1237	<	else{
1238	<	n_cells = (int)temp3;
1239	<	cellx = simnfo->boxLx / temp3;
1240	<	celly = simnfo->boxLy / temp3;
1241	<	cellz = simnfo->boxLz / temp3;
1242	<	}
1243	<
1244	<	current_mol = 0;
1245	<	current_comp_mol = 0;
1246	<	current_comp = 0;
1247	<	current_atom_ndx = 0;
1248	<
1249	<	for( i=0; i < n_cells ; i++ ){
1250	<	for( j=0; j < n_cells; j++ ){
1251	<	for( k=0; k < n_cells; k++ ){
1252	<
1253	<	makeElement( i * cellx,
1254	<	j * celly,
1255	<	k * cellz );
1256	<
1257	<	makeElement( i * cellx + 0.5 * cellx,
1258	<	j * celly + 0.5 * celly,
1259	<	k * cellz );
1260	<
1261	<	makeElement( i * cellx,
1262	<	j * celly + 0.5 * celly,
1263	<	k * cellz + 0.5 * cellz );
1264	<
1265	<	makeElement( i * cellx + 0.5 * cellx,
1266	<	j * celly,
1267	<	k * cellz + 0.5 * cellz );
1268	<	}
1269	<	}
1270	<	}
1271	<
1272	<	if( have_extra ){
1273	<	done = 0;
1274	<
1275	<	int start_ndx;
1276	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1277	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1278	<
1279	<	if( i < n_cells ){
1280	<
1281	<	if( j < n_cells ){
1282	<	start_ndx = n_cells;
1283	<	}
1284	<	else start_ndx = 0;
1285	<	}
1286	<	else start_ndx = 0;
1287	<
1288	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1289	<
1290	<	makeElement( i * cellx,
1291	<	j * celly,
1292	<	k * cellz );
1293	<	done = ( current_mol >= tot_nmol );
1294	<
1295	<	if( !done && n_per_extra > 1 ){
1296	<	makeElement( i * cellx + 0.5 * cellx,
1297	<	j * celly + 0.5 * celly,
1298	<	k * cellz );
1299	<	done = ( current_mol >= tot_nmol );
1300	<	}
1301	<
1302	<	if( !done && n_per_extra > 2){
1303	<	makeElement( i * cellx,
1304	<	j * celly + 0.5 * celly,
1305	<	k * cellz + 0.5 * cellz );
1306	<	done = ( current_mol >= tot_nmol );
1307	<	}
1308	<
1309	<	if( !done && n_per_extra > 3){
1310	<	makeElement( i * cellx + 0.5 * cellx,
1311	<	j * celly,
1312	<	k * cellz + 0.5 * cellz );
1313	<	done = ( current_mol >= tot_nmol );
1314	<	}
1315	<	}
1316	<	}
1317	<	}
1318	<	}
1319	<
1320	<
1321	<	for( i=0; i<simnfo->n_atoms; i++ ){
1322	<	simnfo->atoms[i]->set_vx( 0.0 );
1323	<	simnfo->atoms[i]->set_vy( 0.0 );
1324	<	simnfo->atoms[i]->set_vz( 0.0 );
1325	<	}
1326	<	}
1327	<
1328	<	void SimSetup::makeElement( double x, double y, double z ){
1329	<
1330	<	int k;
1331	<	AtomStamp* current_atom;
1332	<	DirectionalAtom* dAtom;
1333	<	double rotMat[3][3];
1334	<
1335	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1336	<
1337	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1338	<	if( !current_atom->havePosition() ){
1339	<	sprintf( painCave.errMsg,
1340	<	"SimSetup:initFromBass error.\n"
1341	<	"\tComponent %s, atom %s does not have a position specified.\n"
1342	<	"\tThe initialization routine is unable to give a start"
1343	<	" position.\n",
1344	<	comp_stamps[current_comp]->getID(),
1345	<	current_atom->getType() );
1346	<	painCave.isFatal = 1;
1347	<	simError();
1348	<	}
1349	<
1350	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1351	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1352	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1353	<
1354	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1355	<
1356	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1357	<
1358	<	rotMat[0][0] = 1.0;
1359	<	rotMat[0][1] = 0.0;
1360	<	rotMat[0][2] = 0.0;
1361	<
1362	<	rotMat[1][0] = 0.0;
1363	<	rotMat[1][1] = 1.0;
1364	<	rotMat[1][2] = 0.0;
1365	<
1366	<	rotMat[2][0] = 0.0;
1367	<	rotMat[2][1] = 0.0;
1368	<	rotMat[2][2] = 1.0;
1369	<
1370	<	dAtom->setA( rotMat );
1371	<	}
1372	<
1373	<	current_atom_ndx++;
1374	<	}
1375	<
1376	<	current_mol++;
1377	<	current_comp_mol++;
1378	<
1379	<	if( current_comp_mol >= components_nmol[current_comp] ){
1380	<
1381	<	current_comp_mol = 0;
1382	<	current_comp++;
1383	<	}
621	>	tempJ =  currentBond->getB() + atomOffset;
622	>	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
623	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
624	>	else
625	>	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
626	>
627	>	consPair = new DistanceConstraintPair(consElement1, consElement2);
628	>	molInfo.myConstraintPairs.push_back(consPair);
629	>	}
630	>	}
631	>
632	>	//loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair
633	>	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
634	>	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
635	>
636	>	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
637	>
638	>	for(size_t m = 0; m < jointAtoms.size(); m++){
639	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
640	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
641	>
642	>	consPair = new JointConstraintPair(consElement1, consElement2);
643	>	molInfo.myConstraintPairs.push_back(consPair);
644	>	}
645	>
646	>	}
647	>	}
648	>
649	>	*/
650	>	// send the arrays off to the forceField for init.
651	>
652	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
653	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
654	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
655	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
656	>	theTorsions);
657	>
658	>	info[k].molecules[i].initialize(molInfo);
659	>
660	>
661	>	atomOffset += molInfo.nAtoms;
662	>	delete[] theBonds;
663	>	delete[] theBends;
664	>	delete[] theTorsions;
665	>	}
666	>
667	>
668	>
669	>	#ifdef IS_MPI
670	>	// Since the globalGroupMembership has been zero filled and we've only
671	>	// poked values into the atoms we know, we can do an Allreduce
672	>	// to get the full globalGroupMembership array (We think).
673	>	// This would be prettier if we could use MPI_IN_PLACE like the MPI-2
674	>	// docs said we could.
675	>
676	>	int* ggMjunk = new int[mpiSim->getNAtomsGlobal()];
677	>
678	>	MPI_Allreduce(info[k].globalGroupMembership,
679	>	ggMjunk,
680	>	mpiSim->getNAtomsGlobal(),
681	>	MPI_INT, MPI_SUM, MPI_COMM_WORLD);
682	>
683	>	for (i = 0; i < mpiSim->getNAtomsGlobal(); i++)
684	>	info[k].globalGroupMembership[i] = ggMjunk[i];
685	>
686	>	delete[] ggMjunk;
687	>
688	>	#endif
689	>
690	>
691	>
692	>	}
693	>
694	>	#ifdef IS_MPI
695	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
696	>	MPIcheckPoint();
697	>	#endif // is_mpi
698	>
699	>	}
700	>
701	>	void SimSetup::initFromBass(void){
702	>	int i, j, k;
703	>	int n_cells;
704	>	double cellx, celly, cellz;
705	>	double temp1, temp2, temp3;
706	>	int n_per_extra;
707	>	int n_extra;
708	>	int have_extra, done;
709	>
710	>	double vel[3];
711	>	vel[0] = 0.0;
712	>	vel[1] = 0.0;
713	>	vel[2] = 0.0;
714	>
715	>	temp1 = (double) tot_nmol / 4.0;
716	>	temp2 = pow(temp1, (1.0 / 3.0));
717	>	temp3 = ceil(temp2);
718	>
719	>	have_extra = 0;
720	>	if (temp2 < temp3){
721	>	// we have a non-complete lattice
722	>	have_extra = 1;
723	>
724	>	n_cells = (int) temp3 - 1;
725	>	cellx = info[0].boxL[0] / temp3;
726	>	celly = info[0].boxL[1] / temp3;
727	>	cellz = info[0].boxL[2] / temp3;
728	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
729	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
730	>	n_per_extra = (int) ceil(temp1);
731	>
732	>	if (n_per_extra > 4){
733	>	sprintf(painCave.errMsg,
734	>	"SimSetup error. There has been an error in constructing"
735	>	" the non-complete lattice.\n");
736	>	painCave.isFatal = 1;
737	>	simError();
738	>	}
739	>	}
740	>	else{
741	>	n_cells = (int) temp3;
742	>	cellx = info[0].boxL[0] / temp3;
743	>	celly = info[0].boxL[1] / temp3;
744	>	cellz = info[0].boxL[2] / temp3;
745	>	}
746	>
747	>	current_mol = 0;
748	>	current_comp_mol = 0;
749	>	current_comp = 0;
750	>	current_atom_ndx = 0;
751	>
752	>	for (i = 0; i < n_cells ; i++){
753	>	for (j = 0; j < n_cells; j++){
754	>	for (k = 0; k < n_cells; k++){
755	>	makeElement(i * cellx, j * celly, k * cellz);
756	>
757	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
758	>
759	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
760	>
761	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
762	>	}
763	>	}
764	>	}
765	>
766	>	if (have_extra){
767	>	done = 0;
768	>
769	>	int start_ndx;
770	>	for (i = 0; i < (n_cells + 1) && !done; i++){
771	>	for (j = 0; j < (n_cells + 1) && !done; j++){
772	>	if (i < n_cells){
773	>	if (j < n_cells){
774	>	start_ndx = n_cells;
775	>	}
776	>	else
777	>	start_ndx = 0;
778	>	}
779	>	else
780	>	start_ndx = 0;
781	>
782	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
783	>	makeElement(i * cellx, j * celly, k * cellz);
784	>	done = (current_mol >= tot_nmol);
785	>
786	>	if (!done && n_per_extra > 1){
787	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
788	>	k * cellz);
789	>	done = (current_mol >= tot_nmol);
790	>	}
791	>
792	>	if (!done && n_per_extra > 2){
793	>	makeElement(i * cellx, j * celly + 0.5 * celly,
794	>	k * cellz + 0.5 * cellz);
795	>	done = (current_mol >= tot_nmol);
796	>	}
797	>
798	>	if (!done && n_per_extra > 3){
799	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
800	>	k * cellz + 0.5 * cellz);
801	>	done = (current_mol >= tot_nmol);
802	>	}
803	>	}
804	>	}
805	>	}
806	>	}
807	>
808	>	for (i = 0; i < info[0].n_atoms; i++){
809	>	info[0].atoms[i]->setVel(vel);
810	>	}
811	>	}
812	>
813	>	void SimSetup::makeElement(double x, double y, double z){
814	>	int k;
815	>	AtomStamp* current_atom;
816	>	DirectionalAtom* dAtom;
817	>	double rotMat[3][3];
818	>	double pos[3];
819	>
820	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
821	>	current_atom = comp_stamps[current_comp]->getAtom(k);
822	>	if (!current_atom->havePosition()){
823	>	sprintf(painCave.errMsg,
824	>	"SimSetup:initFromBass error.\n"
825	>	"\tComponent %s, atom %s does not have a position specified.\n"
826	>	"\tThe initialization routine is unable to give a start"
827	>	" position.\n",
828	>	comp_stamps[current_comp]->getID(), current_atom->getType());
829	>	painCave.isFatal = 1;
830	>	simError();
831	>	}
832	>
833	>	pos[0] = x + current_atom->getPosX();
834	>	pos[1] = y + current_atom->getPosY();
835	>	pos[2] = z + current_atom->getPosZ();
836	>
837	>	info[0].atoms[current_atom_ndx]->setPos(pos);
838	>
839	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
840	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
841	>
842	>	rotMat[0][0] = 1.0;
843	>	rotMat[0][1] = 0.0;
844	>	rotMat[0][2] = 0.0;
845	>
846	>	rotMat[1][0] = 0.0;
847	>	rotMat[1][1] = 1.0;
848	>	rotMat[1][2] = 0.0;
849	>
850	>	rotMat[2][0] = 0.0;
851	>	rotMat[2][1] = 0.0;
852	>	rotMat[2][2] = 1.0;
853	>
854	>	dAtom->setA(rotMat);
855	>	}
856	>
857	>	current_atom_ndx++;
858	>	}
859	>
860	>	current_mol++;
861	>	current_comp_mol++;
862	>
863	>	if (current_comp_mol >= components_nmol[current_comp]){
864	>	current_comp_mol = 0;
865	>	current_comp++;
866	>	}
867	>	}
868	>
869	>
870	>	void SimSetup::gatherInfo(void){
871	>	int i;
872	>
873	>	ensembleCase = -1;
874	>	ffCase = -1;
875	>
876	>	// set the easy ones first
877	>
878	>	for (i = 0; i < nInfo; i++){
879	>	info[i].target_temp = globals->getTargetTemp();
880	>	info[i].dt = globals->getDt();
881	>	info[i].run_time = globals->getRunTime();
882	>	}
883	>	n_components = globals->getNComponents();
884	>
885	>
886	>	// get the forceField
887	>
888	>	strcpy(force_field, globals->getForceField());
889	>
890	>	if (!strcasecmp(force_field, "DUFF")){
891	>	ffCase = FF_DUFF;
892	>	}
893	>	else if (!strcasecmp(force_field, "LJ")){
894	>	ffCase = FF_LJ;
895	>	}
896	>	else if (!strcasecmp(force_field, "EAM")){
897	>	ffCase = FF_EAM;
898	>	}
899	>	else if (!strcasecmp(force_field, "WATER")){
900	>	ffCase = FF_H2O;
901	>	}
902	>	else{
903	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
904	>	force_field);
905	>	painCave.isFatal = 1;
906	>	simError();
907	>	}
908	>
909	>	// get the ensemble
910	>
911	>	strcpy(ensemble, globals->getEnsemble());
912	>
913	>	if (!strcasecmp(ensemble, "NVE")){
914	>	ensembleCase = NVE_ENS;
915	>	}
916	>	else if (!strcasecmp(ensemble, "NVT")){
917	>	ensembleCase = NVT_ENS;
918	>	}
919	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
920	>	ensembleCase = NPTi_ENS;
921	>	}
922	>	else if (!strcasecmp(ensemble, "NPTf")){
923	>	ensembleCase = NPTf_ENS;
924	>	}
925	>	else if (!strcasecmp(ensemble, "NPTxyz")){
926	>	ensembleCase = NPTxyz_ENS;
927	>	}
928	>	else{
929	>	sprintf(painCave.errMsg,
930	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
931	>	"\treverting to NVE for this simulation.\n",
932	>	ensemble);
933	>	painCave.isFatal = 0;
934	>	simError();
935	>	strcpy(ensemble, "NVE");
936	>	ensembleCase = NVE_ENS;
937	>	}
938	>
939	>	for (i = 0; i < nInfo; i++){
940	>	strcpy(info[i].ensemble, ensemble);
941	>
942	>	// get the mixing rule
943	>
944	>	strcpy(info[i].mixingRule, globals->getMixingRule());
945	>	info[i].usePBC = globals->getPBC();
946	>	}
947	>
948	>	// get the components and calculate the tot_nMol and indvidual n_mol
949	>
950	>	the_components = globals->getComponents();
951	>	components_nmol = new int[n_components];
952	>
953	>
954	>	if (!globals->haveNMol()){
955	>	// we don't have the total number of molecules, so we assume it is
956	>	// given in each component
957	>
958	>	tot_nmol = 0;
959	>	for (i = 0; i < n_components; i++){
960	>	if (!the_components[i]->haveNMol()){
961	>	// we have a problem
962	>	sprintf(painCave.errMsg,
963	>	"SimSetup Error. No global NMol or component NMol given.\n"
964	>	"\tCannot calculate the number of atoms.\n");
965	>	painCave.isFatal = 1;
966	>	simError();
967	>	}
968	>
969	>	tot_nmol += the_components[i]->getNMol();
970	>	components_nmol[i] = the_components[i]->getNMol();
971	>	}
972	>	}
973	>	else{
974	>	sprintf(painCave.errMsg,
975	>	"SimSetup error.\n"
976	>	"\tSorry, the ability to specify total"
977	>	" nMols and then give molfractions in the components\n"
978	>	"\tis not currently supported."
979	>	" Please give nMol in the components.\n");
980	>	painCave.isFatal = 1;
981	>	simError();
982	>	}
983	>
984	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
985	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
986	>	sprintf(painCave.errMsg,
987	>	"Sample time is not divisible by dt.\n"
988	>	"\tThis will result in samples that are not uniformly\n"
989	>	"\tdistributed in time.  If this is a problem, change\n"
990	>	"\tyour sampleTime variable.\n");
991	>	painCave.isFatal = 0;
992	>	simError();
993	>	}
994	>
995	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
996	>	sprintf(painCave.errMsg,
997	>	"Status time is not divisible by dt.\n"
998	>	"\tThis will result in status reports that are not uniformly\n"
999	>	"\tdistributed in time.  If this is a problem, change \n"
1000	>	"\tyour statusTime variable.\n");
1001	>	painCave.isFatal = 0;
1002	>	simError();
1003	>	}
1004	>
1005	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
1006	>	sprintf(painCave.errMsg,
1007	>	"Thermal time is not divisible by dt.\n"
1008	>	"\tThis will result in thermalizations that are not uniformly\n"
1009	>	"\tdistributed in time.  If this is a problem, change \n"
1010	>	"\tyour thermalTime variable.\n");
1011	>	painCave.isFatal = 0;
1012	>	simError();
1013	>	}
1014	>
1015	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
1016	>	sprintf(painCave.errMsg,
1017	>	"Reset time is not divisible by dt.\n"
1018	>	"\tThis will result in integrator resets that are not uniformly\n"
1019	>	"\tdistributed in time.  If this is a problem, change\n"
1020	>	"\tyour resetTime variable.\n");
1021	>	painCave.isFatal = 0;
1022	>	simError();
1023	>	}
1024	>
1025	>	// set the status, sample, and thermal kick times
1026	>
1027	>	for (i = 0; i < nInfo; i++){
1028	>	if (globals->haveSampleTime()){
1029	>	info[i].sampleTime = globals->getSampleTime();
1030	>	info[i].statusTime = info[i].sampleTime;
1031	>	}
1032	>	else{
1033	>	info[i].sampleTime = globals->getRunTime();
1034	>	info[i].statusTime = info[i].sampleTime;
1035	>	}
1036	>
1037	>	if (globals->haveStatusTime()){
1038	>	info[i].statusTime = globals->getStatusTime();
1039	>	}
1040	>
1041	>	if (globals->haveThermalTime()){
1042	>	info[i].thermalTime = globals->getThermalTime();
1043	>	} else {
1044	>	info[i].thermalTime = globals->getRunTime();
1045	>	}
1046	>
1047	>	info[i].resetIntegrator = 0;
1048	>	if( globals->haveResetTime() ){
1049	>	info[i].resetTime = globals->getResetTime();
1050	>	info[i].resetIntegrator = 1;
1051	>	}
1052	>
1053	>	// check for the temperature set flag
1054	>
1055	>	if (globals->haveTempSet())
1056	>	info[i].setTemp = globals->getTempSet();
1057	>
1058	>	// check for the extended State init
1059	>
1060	>	info[i].useInitXSstate = globals->getUseInitXSstate();
1061	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1062	>
1063	>	// check for thermodynamic integration
1064	>	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1065	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1066	>	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1067	>	info[i].thermIntLambda = globals->getThermIntLambda();
1068	>	info[i].thermIntK = globals->getThermIntK();
1069	>
1070	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1071	>	info[i].restraint = myRestraint;
1072	>	}
1073	>	else {
1074	>	sprintf(painCave.errMsg,
1075	>	"SimSetup Error:\n"
1076	>	"\tKeyword useSolidThermInt was set to 'true' but\n"
1077	>	"\tthermodynamicIntegrationLambda (and/or\n"
1078	>	"\tthermodynamicIntegrationK) was not specified.\n"
1079	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1080	>	painCave.isFatal = 1;
1081	>	simError();
1082	>	}
1083	>	}
1084	>	else if(globals->getUseLiquidThermInt()) {
1085	>	if (globals->getUseSolidThermInt()) {
1086	>	sprintf( painCave.errMsg,
1087	>	"SimSetup Warning: It appears that you have both solid and\n"
1088	>	"\tliquid thermodynamic integration activated in your .bass\n"
1089	>	"\tfile. To avoid confusion, specify only one technique in\n"
1090	>	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1091	>	"\twill be assumed for the current simulation. If this is not\n"
1092	>	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1093	>	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1094	>	painCave.isFatal = 0;
1095	>	simError();
1096	>	}
1097	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1098	>	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1099	>	info[i].thermIntLambda = globals->getThermIntLambda();
1100	>	info[i].thermIntK = globals->getThermIntK();
1101	>	}
1102	>	else {
1103	>	sprintf(painCave.errMsg,
1104	>	"SimSetup Error:\n"
1105	>	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1106	>	"\tthermodynamicIntegrationLambda (and/or\n"
1107	>	"\tthermodynamicIntegrationK) was not specified.\n"
1108	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1109	>	painCave.isFatal = 1;
1110	>	simError();
1111	>	}
1112	>	}
1113	>	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1114	>	sprintf(painCave.errMsg,
1115	>	"SimSetup Warning: If you want to use Thermodynamic\n"
1116	>	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1117	>	"\t'true' in your .bass file.  These keywords are set to\n"
1118	>	"\t'false' by default, so your lambda and/or k values are\n"
1119	>	"\tbeing ignored.\n");
1120	>	painCave.isFatal = 0;
1121	>	simError();
1122	>	}
1123	>	}
1124	>
1125	>	//setup seed for random number generator
1126	>	int seedValue;
1127	>
1128	>	if (globals->haveSeed()){
1129	>	seedValue = globals->getSeed();
1130	>
1131	>	if(seedValue / 1E9 == 0){
1132	>	sprintf(painCave.errMsg,
1133	>	"Seed for sprng library should contain at least 9 digits\n"
1134	>	"OOPSE will generate a seed for user\n");
1135	>	painCave.isFatal = 0;
1136	>	simError();
1137	>
1138	>	//using seed generated by system instead of invalid seed set by user
1139	>	#ifndef IS_MPI
1140	>	seedValue = make_sprng_seed();
1141	>	#else
1142	>	if (worldRank == 0){
1143	>	seedValue = make_sprng_seed();
1144	>	}
1145	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1146	>	#endif
1147	>	}
1148	>	}//end of if branch of globals->haveSeed()
1149	>	else{
1150	>
1151	>	#ifndef IS_MPI
1152	>	seedValue = make_sprng_seed();
1153	>	#else
1154	>	if (worldRank == 0){
1155	>	seedValue = make_sprng_seed();
1156	>	}
1157	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1158	>	#endif
1159	>	}//end of globals->haveSeed()
1160	>
1161	>	for (int i = 0; i < nInfo; i++){
1162	>	info[i].setSeed(seedValue);
1163	>	}
1164	>
1165	>	#ifdef IS_MPI
1166	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1167	>	MPIcheckPoint();
1168	>	#endif // is_mpi
1169	>	}
1170	>
1171	>
1172	>	void SimSetup::finalInfoCheck(void){
1173	>	int index;
1174	>	int usesDipoles;
1175	>	int usesCharges;
1176	>	int i;
1177	>
1178	>	for (i = 0; i < nInfo; i++){
1179	>	// check electrostatic parameters
1180	>
1181	>	index = 0;
1182	>	usesDipoles = 0;
1183	>	while ((index < info[i].n_atoms) && !usesDipoles){
1184	>	usesDipoles = (info[i].atoms[index])->hasDipole();
1185	>	index++;
1186	>	}
1187	>	index = 0;
1188	>	usesCharges = 0;
1189	>	while ((index < info[i].n_atoms) && !usesCharges){
1190	>	usesCharges= (info[i].atoms[index])->hasCharge();
1191	>	index++;
1192	>	}
1193	>	#ifdef IS_MPI
1194	>	int myUse = usesDipoles;
1195	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1196	>	#endif //is_mpi
1197	>
1198	>	double theRcut, theRsw;
1199	>
1200	>	if (globals->haveRcut()) {
1201	>	theRcut = globals->getRcut();
1202	>
1203	>	if (globals->haveRsw())
1204	>	theRsw = globals->getRsw();
1205	>	else
1206	>	theRsw = theRcut;
1207	>
1208	>	info[i].setDefaultRcut(theRcut, theRsw);
1209	>
1210	>	} else {
1211	>
1212	>	the_ff->calcRcut();
1213	>	theRcut = info[i].getRcut();
1214	>
1215	>	if (globals->haveRsw())
1216	>	theRsw = globals->getRsw();
1217	>	else
1218	>	theRsw = theRcut;
1219	>
1220	>	info[i].setDefaultRcut(theRcut, theRsw);
1221	>	}
1222	>
1223	>	if (globals->getUseRF()){
1224	>	info[i].useReactionField = 1;
1225	>
1226	>	if (!globals->haveRcut()){
1227	>	sprintf(painCave.errMsg,
1228	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1229	>	"\tOOPSE will use a default value of 15.0 angstroms"
1230	>	"\tfor the cutoffRadius.\n");
1231	>	painCave.isFatal = 0;
1232	>	simError();
1233	>	theRcut = 15.0;
1234	>	}
1235	>	else{
1236	>	theRcut = globals->getRcut();
1237	>	}
1238	>
1239	>	if (!globals->haveRsw()){
1240	>	sprintf(painCave.errMsg,
1241	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1242	>	"\tOOPSE will use a default value of\n"
1243	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1244	>	painCave.isFatal = 0;
1245	>	simError();
1246	>	theRsw = 0.95 * theRcut;
1247	>	}
1248	>	else{
1249	>	theRsw = globals->getRsw();
1250	>	}
1251	>
1252	>	info[i].setDefaultRcut(theRcut, theRsw);
1253	>
1254	>	if (!globals->haveDielectric()){
1255	>	sprintf(painCave.errMsg,
1256	>	"SimSetup Error: No Dielectric constant was set.\n"
1257	>	"\tYou are trying to use Reaction Field without"
1258	>	"\tsetting a dielectric constant!\n");
1259	>	painCave.isFatal = 1;
1260	>	simError();
1261	>	}
1262	>	info[i].dielectric = globals->getDielectric();
1263	>	}
1264	>	else{
1265	>	if (usesDipoles || usesCharges){
1266	>
1267	>	if (!globals->haveRcut()){
1268	>	sprintf(painCave.errMsg,
1269	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1270	>	"\tOOPSE will use a default value of 15.0 angstroms"
1271	>	"\tfor the cutoffRadius.\n");
1272	>	painCave.isFatal = 0;
1273	>	simError();
1274	>	theRcut = 15.0;
1275	>	}
1276	>	else{
1277	>	theRcut = globals->getRcut();
1278	>	}
1279	>
1280	>	if (!globals->haveRsw()){
1281	>	sprintf(painCave.errMsg,
1282	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1283	>	"\tOOPSE will use a default value of\n"
1284	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1285	>	painCave.isFatal = 0;
1286	>	simError();
1287	>	theRsw = 0.95 * theRcut;
1288	>	}
1289	>	else{
1290	>	theRsw = globals->getRsw();
1291	>	}
1292	>
1293	>	info[i].setDefaultRcut(theRcut, theRsw);
1294	>
1295	>	}
1296	>	}
1297	>	}
1298	>	#ifdef IS_MPI
1299	>	strcpy(checkPointMsg, "post processing checks out");
1300	>	MPIcheckPoint();
1301	>	#endif // is_mpi
1302	>
1303	>	// clean up the forcefield
1304	>	the_ff->cleanMe();
1305	>	}
1306	>
1307	>	void SimSetup::initSystemCoords(void){
1308	>	int i;
1309	>
1310	>	char* inName;
1311	>
1312	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1313	>
1314	>	for (i = 0; i < info[0].n_atoms; i++)
1315	>	info[0].atoms[i]->setCoords();
1316	>
1317	>	if (globals->haveInitialConfig()){
1318	>	InitializeFromFile* fileInit;
1319	>	#ifdef IS_MPI // is_mpi
1320	>	if (worldRank == 0){
1321	>	#endif //is_mpi
1322	>	inName = globals->getInitialConfig();
1323	>	fileInit = new InitializeFromFile(inName);
1324	>	#ifdef IS_MPI
1325	>	}
1326	>	else
1327	>	fileInit = new InitializeFromFile(NULL);
1328	>	#endif
1329	>	fileInit->readInit(info); // default velocities on
1330	>
1331	>	delete fileInit;
1332	>	}
1333	>	else{
1334	>
1335	>	// no init from bass
1336	>
1337	>	sprintf(painCave.errMsg,
1338	>	"Cannot intialize a simulation without an initial configuration file.\n");
1339	>	painCave.isFatal = 1;;
1340	>	simError();
1341	>
1342	>	}
1343	>
1344	>	#ifdef IS_MPI
1345	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1346	>	MPIcheckPoint();
1347	>	#endif // is_mpi
1348	>	}
1349	>
1350	>
1351	>	void SimSetup::makeOutNames(void){
1352	>	int k;
1353	>
1354	>
1355	>	for (k = 0; k < nInfo; k++){
1356	>	#ifdef IS_MPI
1357	>	if (worldRank == 0){
1358	>	#endif // is_mpi
1359	>
1360	>	if (globals->haveFinalConfig()){
1361	>	strcpy(info[k].finalName, globals->getFinalConfig());
1362	>	}
1363	>	else{
1364	>	strcpy(info[k].finalName, inFileName);
1365	>	char* endTest;
1366	>	int nameLength = strlen(info[k].finalName);
1367	>	endTest = &(info[k].finalName[nameLength - 5]);
1368	>	if (!strcmp(endTest, ".bass")){
1369	>	strcpy(endTest, ".eor");
1370	>	}
1371	>	else if (!strcmp(endTest, ".BASS")){
1372	>	strcpy(endTest, ".eor");
1373	>	}
1374	>	else{
1375	>	endTest = &(info[k].finalName[nameLength - 4]);
1376	>	if (!strcmp(endTest, ".bss")){
1377	>	strcpy(endTest, ".eor");
1378	>	}
1379	>	else if (!strcmp(endTest, ".mdl")){
1380	>	strcpy(endTest, ".eor");
1381	>	}
1382	>	else{
1383	>	strcat(info[k].finalName, ".eor");
1384	>	}
1385	>	}
1386	>	}
1387	>
1388	>	// make the sample and status out names
1389	>
1390	>	strcpy(info[k].sampleName, inFileName);
1391	>	char* endTest;
1392	>	int nameLength = strlen(info[k].sampleName);
1393	>	endTest = &(info[k].sampleName[nameLength - 5]);
1394	>	if (!strcmp(endTest, ".bass")){
1395	>	strcpy(endTest, ".dump");
1396	>	}
1397	>	else if (!strcmp(endTest, ".BASS")){
1398	>	strcpy(endTest, ".dump");
1399	>	}
1400	>	else{
1401	>	endTest = &(info[k].sampleName[nameLength - 4]);
1402	>	if (!strcmp(endTest, ".bss")){
1403	>	strcpy(endTest, ".dump");
1404	>	}
1405	>	else if (!strcmp(endTest, ".mdl")){
1406	>	strcpy(endTest, ".dump");
1407	>	}
1408	>	else{
1409	>	strcat(info[k].sampleName, ".dump");
1410	>	}
1411	>	}
1412	>
1413	>	strcpy(info[k].statusName, inFileName);
1414	>	nameLength = strlen(info[k].statusName);
1415	>	endTest = &(info[k].statusName[nameLength - 5]);
1416	>	if (!strcmp(endTest, ".bass")){
1417	>	strcpy(endTest, ".stat");
1418	>	}
1419	>	else if (!strcmp(endTest, ".BASS")){
1420	>	strcpy(endTest, ".stat");
1421	>	}
1422	>	else{
1423	>	endTest = &(info[k].statusName[nameLength - 4]);
1424	>	if (!strcmp(endTest, ".bss")){
1425	>	strcpy(endTest, ".stat");
1426	>	}
1427	>	else if (!strcmp(endTest, ".mdl")){
1428	>	strcpy(endTest, ".stat");
1429	>	}
1430	>	else{
1431	>	strcat(info[k].statusName, ".stat");
1432	>	}
1433	>	}
1434	>
1435	>	strcpy(info[k].rawPotName, inFileName);
1436	>	nameLength = strlen(info[k].rawPotName);
1437	>	endTest = &(info[k].rawPotName[nameLength - 5]);
1438	>	if (!strcmp(endTest, ".bass")){
1439	>	strcpy(endTest, ".raw");
1440	>	}
1441	>	else if (!strcmp(endTest, ".BASS")){
1442	>	strcpy(endTest, ".raw");
1443	>	}
1444	>	else{
1445	>	endTest = &(info[k].rawPotName[nameLength - 4]);
1446	>	if (!strcmp(endTest, ".bss")){
1447	>	strcpy(endTest, ".raw");
1448	>	}
1449	>	else if (!strcmp(endTest, ".mdl")){
1450	>	strcpy(endTest, ".raw");
1451	>	}
1452	>	else{
1453	>	strcat(info[k].rawPotName, ".raw");
1454	>	}
1455	>	}
1456	>
1457	>	#ifdef IS_MPI
1458	>
1459	>	}
1460	>	#endif // is_mpi
1461	>	}
1462	>	}
1463	>
1464	>
1465	>	void SimSetup::sysObjectsCreation(void){
1466	>	int i, k;
1467	>
1468	>	// create the forceField
1469	>
1470	>	createFF();
1471	>
1472	>	// extract componentList
1473	>
1474	>	compList();
1475	>
1476	>	// calc the number of atoms, bond, bends, and torsions
1477	>
1478	>	calcSysValues();
1479	>
1480	>	#ifdef IS_MPI
1481	>	// divide the molecules among the processors
1482	>
1483	>	mpiMolDivide();
1484	>	#endif //is_mpi
1485	>
1486	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1487	>
1488	>	makeSysArrays();
1489	>
1490	>	// make and initialize the molecules (all but atomic coordinates)
1491	>
1492	>	makeMolecules();
1493	>
1494	>	for (k = 0; k < nInfo; k++){
1495	>	info[k].identArray = new int[info[k].n_atoms];
1496	>	for (i = 0; i < info[k].n_atoms; i++){
1497	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1498	>	}
1499	>	}
1500	>	}
1501	>
1502	>
1503	>	void SimSetup::createFF(void){
1504	>	switch (ffCase){
1505	>	case FF_DUFF:
1506	>	the_ff = new DUFF();
1507	>	break;
1508	>
1509	>	case FF_LJ:
1510	>	the_ff = new LJFF();
1511	>	break;
1512	>
1513	>	case FF_EAM:
1514	>	the_ff = new EAM_FF();
1515	>	break;
1516	>
1517	>	case FF_H2O:
1518	>	the_ff = new WATER();
1519	>	break;
1520	>
1521	>	default:
1522	>	sprintf(painCave.errMsg,
1523	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1524	>	painCave.isFatal = 1;
1525	>	simError();
1526	>	}
1527	>
1528	>	#ifdef IS_MPI
1529	>	strcpy(checkPointMsg, "ForceField creation successful");
1530	>	MPIcheckPoint();
1531	>	#endif // is_mpi
1532	>	}
1533	>
1534	>
1535	>	void SimSetup::compList(void){
1536	>	int i;
1537	>	char* id;
1538	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1539	>	LinkedMolStamp* currentStamp = NULL;
1540	>	comp_stamps = new MoleculeStamp * [n_components];
1541	>	bool haveCutoffGroups;
1542	>
1543	>	haveCutoffGroups = false;
1544	>
1545	>	// make an array of molecule stamps that match the components used.
1546	>	// also extract the used stamps out into a separate linked list
1547	>
1548	>	for (i = 0; i < nInfo; i++){
1549	>	info[i].nComponents = n_components;
1550	>	info[i].componentsNmol = components_nmol;
1551	>	info[i].compStamps = comp_stamps;
1552	>	info[i].headStamp = headStamp;
1553	>	}
1554	>
1555	>
1556	>	for (i = 0; i < n_components; i++){
1557	>	id = the_components[i]->getType();
1558	>	comp_stamps[i] = NULL;
1559	>
1560	>	// check to make sure the component isn't already in the list
1561	>
1562	>	comp_stamps[i] = headStamp->match(id);
1563	>	if (comp_stamps[i] == NULL){
1564	>	// extract the component from the list;
1565	>
1566	>	currentStamp = stamps->extractMolStamp(id);
1567	>	if (currentStamp == NULL){
1568	>	sprintf(painCave.errMsg,
1569	>	"SimSetup error: Component \"%s\" was not found in the "
1570	>	"list of declared molecules\n",
1571	>	id);
1572	>	painCave.isFatal = 1;
1573	>	simError();
1574	>	}
1575	>
1576	>	headStamp->add(currentStamp);
1577	>	comp_stamps[i] = headStamp->match(id);
1578	>	}
1579	>
1580	>	if(comp_stamps[i]->getNCutoffGroups() > 0)
1581	>	haveCutoffGroups = true;
1582	>	}
1583	>
1584	>	for (i = 0; i < nInfo; i++)
1585	>	info[i].haveCutoffGroups = haveCutoffGroups;
1586	>
1587	>	#ifdef IS_MPI
1588	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1589	>	MPIcheckPoint();
1590	>	#endif // is_mpi
1591	>	}
1592	>
1593	>	void SimSetup::calcSysValues(void){
1594	>	int i, j;
1595	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1596	>
1597	>	int* molMembershipArray;
1598	>	CutoffGroupStamp* cg;
1599	>
1600	>	tot_atoms = 0;
1601	>	tot_bonds = 0;
1602	>	tot_bends = 0;
1603	>	tot_torsions = 0;
1604	>	tot_rigid = 0;
1605	>	tot_groups = 0;
1606	>	for (i = 0; i < n_components; i++){
1607	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1608	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1609	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1610	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1611	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1612	>
1613	>	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1614	>	atomsingroups = 0;
1615	>	for (j=0; j < ncutgroups; j++) {
1616	>	cg = comp_stamps[i]->getCutoffGroup(j);
1617	>	atomsingroups += cg->getNMembers();
1618	>	}
1619	>	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1620	>	tot_groups += components_nmol[i] * ngroupsinstamp;
1621	>	}
1622	>
1623	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1624	>	molMembershipArray = new int[tot_atoms];
1625	>
1626	>	for (i = 0; i < nInfo; i++){
1627	>	info[i].n_atoms = tot_atoms;
1628	>	info[i].n_bonds = tot_bonds;
1629	>	info[i].n_bends = tot_bends;
1630	>	info[i].n_torsions = tot_torsions;
1631	>	info[i].n_SRI = tot_SRI;
1632	>	info[i].n_mol = tot_nmol;
1633	>	info[i].ngroup = tot_groups;
1634	>	info[i].molMembershipArray = molMembershipArray;
1635	>	}
1636	>	}
1637	>
1638	>	#ifdef IS_MPI
1639	>
1640	>	void SimSetup::mpiMolDivide(void){
1641	>	int i, j, k;
1642	>	int localMol, allMol;
1643	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1644	>	int local_rigid, local_groups;
1645	>	vector<int> globalMolIndex;
1646	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1647	>	CutoffGroupStamp* cg;
1648	>
1649	>	mpiSim = new mpiSimulation(info);
1650	>
1651	>	mpiSim->divideLabor();
1652	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1653	>	globalGroupIndex = mpiSim->getGlobalGroupIndex();
1654	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1655	>
1656	>	// set up the local variables
1657	>
1658	>	mol2proc = mpiSim->getMolToProcMap();
1659	>	molCompType = mpiSim->getMolComponentType();
1660	>
1661	>	allMol = 0;
1662	>	localMol = 0;
1663	>	local_atoms = 0;
1664	>	local_bonds = 0;
1665	>	local_bends = 0;
1666	>	local_torsions = 0;
1667	>	local_rigid = 0;
1668	>	local_groups = 0;
1669	>	globalAtomCounter = 0;
1670	>
1671	>	for (i = 0; i < n_components; i++){
1672	>	for (j = 0; j < components_nmol[i]; j++){
1673	>	if (mol2proc[allMol] == worldRank){
1674	>	local_atoms += comp_stamps[i]->getNAtoms();
1675	>	local_bonds += comp_stamps[i]->getNBonds();
1676	>	local_bends += comp_stamps[i]->getNBends();
1677	>	local_torsions += comp_stamps[i]->getNTorsions();
1678	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1679	>
1680	>	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1681	>	atomsingroups = 0;
1682	>	for (k=0; k < ncutgroups; k++) {
1683	>	cg = comp_stamps[i]->getCutoffGroup(k);
1684	>	atomsingroups += cg->getNMembers();
1685	>	}
1686	>	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1687	>	ncutgroups;
1688	>	local_groups += ngroupsinstamp;
1689	>
1690	>	localMol++;
1691	>	}
1692	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1693	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1694	>	globalAtomCounter++;
1695	>	}
1696	>
1697	>	allMol++;
1698	>	}
1699	>	}
1700	>	local_SRI = local_bonds + local_bends + local_torsions;
1701	>
1702	>	info[0].n_atoms = mpiSim->getNAtomsLocal();
1703	>
1704	>	if (local_atoms != info[0].n_atoms){
1705	>	sprintf(painCave.errMsg,
1706	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1707	>	"\tlocalAtom (%d) are not equal.\n",
1708	>	info[0].n_atoms, local_atoms);
1709	>	painCave.isFatal = 1;
1710	>	simError();
1711	>	}
1712	>
1713	>	info[0].ngroup = mpiSim->getNGroupsLocal();
1714	>	if (local_groups != info[0].ngroup){
1715	>	sprintf(painCave.errMsg,
1716	>	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1717	>	"\tlocalGroups (%d) are not equal.\n",
1718	>	info[0].ngroup, local_groups);
1719	>	painCave.isFatal = 1;
1720	>	simError();
1721	>	}
1722	>
1723	>	info[0].n_bonds = local_bonds;
1724	>	info[0].n_bends = local_bends;
1725	>	info[0].n_torsions = local_torsions;
1726	>	info[0].n_SRI = local_SRI;
1727	>	info[0].n_mol = localMol;
1728	>
1729	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1730	>	MPIcheckPoint();
1731	>	}
1732	>
1733	>	#endif // is_mpi
1734	>
1735	>
1736	>	void SimSetup::makeSysArrays(void){
1737	>
1738	>	#ifndef IS_MPI
1739	>	int k, j;
1740	>	#endif // is_mpi
1741	>	int i, l;
1742	>
1743	>	Atom** the_atoms;
1744	>	Molecule* the_molecules;
1745	>
1746	>	for (l = 0; l < nInfo; l++){
1747	>	// create the atom and short range interaction arrays
1748	>
1749	>	the_atoms = new Atom * [info[l].n_atoms];
1750	>	the_molecules = new Molecule[info[l].n_mol];
1751	>	int molIndex;
1752	>
1753	>	// initialize the molecule's stampID's
1754	>
1755	>	#ifdef IS_MPI
1756	>
1757	>
1758	>	molIndex = 0;
1759	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1760	>	if (mol2proc[i] == worldRank){
1761	>	the_molecules[molIndex].setStampID(molCompType[i]);
1762	>	the_molecules[molIndex].setMyIndex(molIndex);
1763	>	the_molecules[molIndex].setGlobalIndex(i);
1764	>	molIndex++;
1765	>	}
1766	>	}
1767	>
1768	>	#else // is_mpi
1769	>
1770	>	molIndex = 0;
1771	>	globalAtomCounter = 0;
1772	>	for (i = 0; i < n_components; i++){
1773	>	for (j = 0; j < components_nmol[i]; j++){
1774	>	the_molecules[molIndex].setStampID(i);
1775	>	the_molecules[molIndex].setMyIndex(molIndex);
1776	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1777	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1778	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1779	>	globalAtomCounter++;
1780	>	}
1781	>	molIndex++;
1782	>	}
1783	>	}
1784	>
1785	>
1786	>	#endif // is_mpi
1787	>
1788	>	info[l].globalExcludes = new int;
1789	>	info[l].globalExcludes[0] = 0;
1790	>
1791	>	// set the arrays into the SimInfo object
1792	>
1793	>	info[l].atoms = the_atoms;
1794	>	info[l].molecules = the_molecules;
1795	>	info[l].nGlobalExcludes = 0;
1796	>
1797	>	the_ff->setSimInfo(info);
1798	>	}
1799	>	}
1800	>
1801	>	void SimSetup::makeIntegrator(void){
1802	>	int k;
1803	>
1804	>	NVE<RealIntegrator>* myNVE = NULL;
1805	>	NVT<RealIntegrator>* myNVT = NULL;
1806	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1807	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1808	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1809	>
1810	>	for (k = 0; k < nInfo; k++){
1811	>	switch (ensembleCase){
1812	>	case NVE_ENS:
1813	>	if (globals->haveZconstraints()){
1814	>	setupZConstraint(info[k]);
1815	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1816	>	}
1817	>	else{
1818	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1819	>	}
1820	>
1821	>	info->the_integrator = myNVE;
1822	>	break;
1823	>
1824	>	case NVT_ENS:
1825	>	if (globals->haveZconstraints()){
1826	>	setupZConstraint(info[k]);
1827	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1828	>	}
1829	>	else
1830	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1831	>
1832	>	myNVT->setTargetTemp(globals->getTargetTemp());
1833	>
1834	>	if (globals->haveTauThermostat())
1835	>	myNVT->setTauThermostat(globals->getTauThermostat());
1836	>	else{
1837	>	sprintf(painCave.errMsg,
1838	>	"SimSetup error: If you use the NVT\n"
1839	>	"\tensemble, you must set tauThermostat.\n");
1840	>	painCave.isFatal = 1;
1841	>	simError();
1842	>	}
1843	>
1844	>	info->the_integrator = myNVT;
1845	>	break;
1846	>
1847	>	case NPTi_ENS:
1848	>	if (globals->haveZconstraints()){
1849	>	setupZConstraint(info[k]);
1850	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1851	>	}
1852	>	else
1853	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1854	>
1855	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1856	>
1857	>	if (globals->haveTargetPressure())
1858	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1859	>	else{
1860	>	sprintf(painCave.errMsg,
1861	>	"SimSetup error: If you use a constant pressure\n"
1862	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1863	>	painCave.isFatal = 1;
1864	>	simError();
1865	>	}
1866	>
1867	>	if (globals->haveTauThermostat())
1868	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1869	>	else{
1870	>	sprintf(painCave.errMsg,
1871	>	"SimSetup error: If you use an NPT\n"
1872	>	"\tensemble, you must set tauThermostat.\n");
1873	>	painCave.isFatal = 1;
1874	>	simError();
1875	>	}
1876	>
1877	>	if (globals->haveTauBarostat())
1878	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1879	>	else{
1880	>	sprintf(painCave.errMsg,
1881	>	"SimSetup error: If you use an NPT\n"
1882	>	"\tensemble, you must set tauBarostat.\n");
1883	>	painCave.isFatal = 1;
1884	>	simError();
1885	>	}
1886	>
1887	>	info->the_integrator = myNPTi;
1888	>	break;
1889	>
1890	>	case NPTf_ENS:
1891	>	if (globals->haveZconstraints()){
1892	>	setupZConstraint(info[k]);
1893	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1894	>	}
1895	>	else
1896	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1897	>
1898	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1899	>
1900	>	if (globals->haveTargetPressure())
1901	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1902	>	else{
1903	>	sprintf(painCave.errMsg,
1904	>	"SimSetup error: If you use a constant pressure\n"
1905	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1906	>	painCave.isFatal = 1;
1907	>	simError();
1908	>	}
1909	>
1910	>	if (globals->haveTauThermostat())
1911	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1912	>
1913	>	else{
1914	>	sprintf(painCave.errMsg,
1915	>	"SimSetup error: If you use an NPT\n"
1916	>	"\tensemble, you must set tauThermostat.\n");
1917	>	painCave.isFatal = 1;
1918	>	simError();
1919	>	}
1920	>
1921	>	if (globals->haveTauBarostat())
1922	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1923	>
1924	>	else{
1925	>	sprintf(painCave.errMsg,
1926	>	"SimSetup error: If you use an NPT\n"
1927	>	"\tensemble, you must set tauBarostat.\n");
1928	>	painCave.isFatal = 1;
1929	>	simError();
1930	>	}
1931	>
1932	>	info->the_integrator = myNPTf;
1933	>	break;
1934	>
1935	>	case NPTxyz_ENS:
1936	>	if (globals->haveZconstraints()){
1937	>	setupZConstraint(info[k]);
1938	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1939	>	}
1940	>	else
1941	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1942	>
1943	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1944	>
1945	>	if (globals->haveTargetPressure())
1946	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1947	>	else{
1948	>	sprintf(painCave.errMsg,
1949	>	"SimSetup error: If you use a constant pressure\n"
1950	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1951	>	painCave.isFatal = 1;
1952	>	simError();
1953	>	}
1954	>
1955	>	if (globals->haveTauThermostat())
1956	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1957	>	else{
1958	>	sprintf(painCave.errMsg,
1959	>	"SimSetup error: If you use an NPT\n"
1960	>	"\tensemble, you must set tauThermostat.\n");
1961	>	painCave.isFatal = 1;
1962	>	simError();
1963	>	}
1964	>
1965	>	if (globals->haveTauBarostat())
1966	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1967	>	else{
1968	>	sprintf(painCave.errMsg,
1969	>	"SimSetup error: If you use an NPT\n"
1970	>	"\tensemble, you must set tauBarostat.\n");
1971	>	painCave.isFatal = 1;
1972	>	simError();
1973	>	}
1974	>
1975	>	info->the_integrator = myNPTxyz;
1976	>	break;
1977	>
1978	>	default:
1979	>	sprintf(painCave.errMsg,
1980	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1981	>	painCave.isFatal = 1;
1982	>	simError();
1983	>	}
1984	>	}
1985	>	}
1986	>
1987	>	void SimSetup::initFortran(void){
1988	>	info[0].refreshSim();
1989	>
1990	>	if (!strcmp(info[0].mixingRule, "standard")){
1991	>	the_ff->initForceField(LB_MIXING_RULE);
1992	>	}
1993	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1994	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1995	>	}
1996	>	else{
1997	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1998	>	info[0].mixingRule);
1999	>	painCave.isFatal = 1;
2000	>	simError();
2001	>	}
2002	>
2003	>
2004	>	#ifdef IS_MPI
2005	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
2006	>	MPIcheckPoint();
2007	>	#endif // is_mpi
2008	>	}
2009	>
2010	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
2011	>	int nZConstraints;
2012	>	ZconStamp** zconStamp;
2013	>
2014	>	if (globals->haveZconstraintTime()){
2015	>	//add sample time of z-constraint  into SimInfo's property list
2016	>	DoubleData* zconsTimeProp = new DoubleData();
2017	>	zconsTimeProp->setID(ZCONSTIME_ID);
2018	>	zconsTimeProp->setData(globals->getZconsTime());
2019	>	theInfo.addProperty(zconsTimeProp);
2020	>	}
2021	>	else{
2022	>	sprintf(painCave.errMsg,
2023	>	"ZConstraint error: If you use a ZConstraint,\n"
2024	>	"\tyou must set zconsTime.\n");
2025	>	painCave.isFatal = 1;
2026	>	simError();
2027	>	}
2028	>
2029	>	//push zconsTol into siminfo, if user does not specify
2030	>	//value for zconsTol, a default value will be used
2031	>	DoubleData* zconsTol = new DoubleData();
2032	>	zconsTol->setID(ZCONSTOL_ID);
2033	>	if (globals->haveZconsTol()){
2034	>	zconsTol->setData(globals->getZconsTol());
2035	>	}
2036	>	else{
2037	>	double defaultZConsTol = 0.01;
2038	>	sprintf(painCave.errMsg,
2039	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
2040	>	"\tOOPSE will use a default value of %f.\n"
2041	>	"\tTo set the tolerance, use the zconsTol variable.\n",
2042	>	defaultZConsTol);
2043	>	painCave.isFatal = 0;
2044	>	simError();
2045	>
2046	>	zconsTol->setData(defaultZConsTol);
2047	>	}
2048	>	theInfo.addProperty(zconsTol);
2049	>
2050	>	//set Force Subtraction Policy
2051	>	StringData* zconsForcePolicy = new StringData();
2052	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
2053	>
2054	>	if (globals->haveZconsForcePolicy()){
2055	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
2056	>	}
2057	>	else{
2058	>	sprintf(painCave.errMsg,
2059	>	"ZConstraint Warning: No force subtraction policy was set.\n"
2060	>	"\tOOPSE will use PolicyByMass.\n"
2061	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
2062	>	painCave.isFatal = 0;
2063	>	simError();
2064	>	zconsForcePolicy->setData("BYMASS");
2065	>	}
2066	>
2067	>	theInfo.addProperty(zconsForcePolicy);
2068	>
2069	>	//set zcons gap
2070	>	DoubleData* zconsGap = new DoubleData();
2071	>	zconsGap->setID(ZCONSGAP_ID);
2072	>
2073	>	if (globals->haveZConsGap()){
2074	>	zconsGap->setData(globals->getZconsGap());
2075	>	theInfo.addProperty(zconsGap);
2076	>	}
2077	>
2078	>	//set zcons fixtime
2079	>	DoubleData* zconsFixtime = new DoubleData();
2080	>	zconsFixtime->setID(ZCONSFIXTIME_ID);
2081	>
2082	>	if (globals->haveZConsFixTime()){
2083	>	zconsFixtime->setData(globals->getZconsFixtime());
2084	>	theInfo.addProperty(zconsFixtime);
2085	>	}
2086	>
2087	>	//set zconsUsingSMD
2088	>	IntData* zconsUsingSMD = new IntData();
2089	>	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2090	>
2091	>	if (globals->haveZConsUsingSMD()){
2092	>	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2093	>	theInfo.addProperty(zconsUsingSMD);
2094	>	}
2095	>
2096	>	//Determine the name of ouput file and add it into SimInfo's property list
2097	>	//Be careful, do not use inFileName, since it is a pointer which
2098	>	//point to a string at master node, and slave nodes do not contain that string
2099	>
2100	>	string zconsOutput(theInfo.finalName);
2101	>
2102	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
2103	>
2104	>	StringData* zconsFilename = new StringData();
2105	>	zconsFilename->setID(ZCONSFILENAME_ID);
2106	>	zconsFilename->setData(zconsOutput);
2107	>
2108	>	theInfo.addProperty(zconsFilename);
2109	>
2110	>	//setup index, pos and other parameters of z-constraint molecules
2111	>	nZConstraints = globals->getNzConstraints();
2112	>	theInfo.nZconstraints = nZConstraints;
2113	>
2114	>	zconStamp = globals->getZconStamp();
2115	>	ZConsParaItem tempParaItem;
2116	>
2117	>	ZConsParaData* zconsParaData = new ZConsParaData();
2118	>	zconsParaData->setID(ZCONSPARADATA_ID);
2119	>
2120	>	for (int i = 0; i < nZConstraints; i++){
2121	>	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
2122	>	tempParaItem.zPos = zconStamp[i]->getZpos();
2123	>	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2124	>	tempParaItem.kRatio = zconStamp[i]->getKratio();
2125	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2126	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2127	>	zconsParaData->addItem(tempParaItem);
2128	>	}
2129	>
2130	>	//check the uniqueness of index
2131	>	if(!zconsParaData->isIndexUnique()){
2132	>	sprintf(painCave.errMsg,
2133	>	"ZConstraint Error: molIndex is not unique!\n");
2134	>	painCave.isFatal = 1;
2135	>	simError();
2136	>	}
2137	>
2138	>	//sort the parameters by index of molecules
2139	>	zconsParaData->sortByIndex();
2140	>
2141	>	//push data into siminfo, therefore, we can retrieve later
2142	>	theInfo.addProperty(zconsParaData);
2143	>	}
2144	>
2145	>	void SimSetup::makeMinimizer(){
2146	>
2147	>	OOPSEMinimizer* myOOPSEMinimizer;
2148	>	MinimizerParameterSet* param;
2149	>	char minimizerName[100];
2150	>
2151	>	for (int i = 0; i < nInfo; i++){
2152	>
2153	>	//prepare parameter set for minimizer
2154	>	param = new MinimizerParameterSet();
2155	>	param->setDefaultParameter();
2156	>
2157	>	if (globals->haveMinimizer()){
2158	>	param->setFTol(globals->getMinFTol());
2159	>	}
2160	>
2161	>	if (globals->haveMinGTol()){
2162	>	param->setGTol(globals->getMinGTol());
2163	>	}
2164	>
2165	>	if (globals->haveMinMaxIter()){
2166	>	param->setMaxIteration(globals->getMinMaxIter());
2167	>	}
2168	>
2169	>	if (globals->haveMinWriteFrq()){
2170	>	param->setMaxIteration(globals->getMinMaxIter());
2171	>	}
2172	>
2173	>	if (globals->haveMinWriteFrq()){
2174	>	param->setWriteFrq(globals->getMinWriteFrq());
2175	>	}
2176	>
2177	>	if (globals->haveMinStepSize()){
2178	>	param->setStepSize(globals->getMinStepSize());
2179	>	}
2180	>
2181	>	if (globals->haveMinLSMaxIter()){
2182	>	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2183	>	}
2184	>
2185	>	if (globals->haveMinLSTol()){
2186	>	param->setLineSearchTol(globals->getMinLSTol());
2187	>	}
2188	>
2189	>	strcpy(minimizerName, globals->getMinimizer());
2190	>
2191	>	if (!strcasecmp(minimizerName, "CG")){
2192	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2193	>	}
2194	>	else if (!strcasecmp(minimizerName, "SD")){
2195	>	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2196	>	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2197	>	}
2198	>	else{
2199	>	sprintf(painCave.errMsg,
2200	>	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2201	>	painCave.isFatal = 0;
2202	>	simError();
2203	>
2204	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2205	>	}
2206	>	info[i].the_integrator = myOOPSEMinimizer;
2207	>
2208	>	//store the minimizer into simInfo
2209	>	info[i].the_minimizer = myOOPSEMinimizer;
2210	>	info[i].has_minimizer = true;
2211	>	}
2212	>
2213		}

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