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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 1097 by gezelter, Mon Apr 12 20:32:20 2004 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	#include "RigidBody.hpp"
13	+	//#include "ConjugateMinimizer.hpp"
14	+	#include "OOPSEMinimizer.hpp"
15
16		#ifdef IS_MPI
17		#include "mpiBASS.h"
#	Line 14 | Line 20
20
21		// some defines for ensemble and Forcefield  cases
22
23	<	#define NVE_ENS   0
24	<	#define NVT_ENS   1
25	<	#define NPTi_ENS  2
26	<	#define NPTf_ENS  3
27	<	#define NPTim_ENS 4
22	<	#define NPTfm_ENS 5
23	>	#define NVE_ENS        0
24	>	#define NVT_ENS        1
25	>	#define NPTi_ENS       2
26	>	#define NPTf_ENS       3
27	>	#define NPTxyz_ENS     4
28
29
30	<	#define FF_DUFF 0
31	<	#define FF_LJ   1
30	>	#define FF_DUFF  0
31	>	#define FF_LJ    1
32	>	#define FF_EAM   2
33	>	#define FF_H2O   3
34
35	+	using namespace std;
36
37	+	/**
38	+	* Check whether dividend is divisble by divisor or not
39	+	*/
40	+	bool isDivisible(double dividend, double divisor){
41	+	double tolerance = 0.000001;
42	+	double quotient;
43	+	double diff;
44	+	int intQuotient;
45	+
46	+	quotient = dividend / divisor;
47	+
48	+	if (quotient < 0)
49	+	quotient = -quotient;
50	+
51	+	intQuotient = int (quotient + tolerance);
52	+
53	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
54	+
55	+	if (diff <= tolerance)
56	+	return true;
57	+	else
58	+	return false;
59	+	}
60	+
61		SimSetup::SimSetup(){
62	+
63	+	initSuspend = false;
64	+	isInfoArray = 0;
65	+	nInfo = 1;
66	+
67		stamps = new MakeStamps();
68		globals = new Globals();
69	<
69	>
70	>
71		#ifdef IS_MPI
72	<	strcpy( checkPointMsg, "SimSetup creation successful" );
72	>	strcpy(checkPointMsg, "SimSetup creation successful");
73		MPIcheckPoint();
74		#endif // IS_MPI
75		}
#	Line 41 | Line 79 | void SimSetup::parseFile( char* fileName ){
79		delete globals;
80		}
81
82	<	void SimSetup::parseFile( char* fileName ){
82	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
83	>	info = the_info;
84	>	nInfo = theNinfo;
85	>	isInfoArray = 1;
86	>	initSuspend = true;
87	>	}
88
89	+
90	+	void SimSetup::parseFile(char* fileName){
91		#ifdef IS_MPI
92	<	if( worldRank == 0 ){
92	>	if (worldRank == 0){
93		#endif // is_mpi
94	<
94	>
95		inFileName = fileName;
96	<	set_interface_stamps( stamps, globals );
97	<
96	>	set_interface_stamps(stamps, globals);
97	>
98		#ifdef IS_MPI
99		mpiEventInit();
100		#endif
101
102	<	yacc_BASS( fileName );
102	>	yacc_BASS(fileName);
103
104		#ifdef IS_MPI
105		throwMPIEvent(NULL);
106		}
107	<	else receiveParse();
107	>	else{
108	>	receiveParse();
109	>	}
110		#endif
111
112		}
113
114		#ifdef IS_MPI
115		void SimSetup::receiveParse(void){
116	<
117	<	set_interface_stamps( stamps, globals );
118	<	mpiEventInit();
119	<	MPIcheckPoint();
73	<	mpiEventLoop();
74	<
116	>	set_interface_stamps(stamps, globals);
117	>	mpiEventInit();
118	>	MPIcheckPoint();
119	>	mpiEventLoop();
120		}
121
122		#endif // is_mpi
123
124	<	void SimSetup::createSim( void ){
124	>	void SimSetup::createSim(void){
125
126	<	MakeStamps *the_stamps;
82	<	Globals* the_globals;
83	<	int i, j, k, globalAtomIndex;
84	<
85	<	int ensembleCase;
86	<	int ffCase;
87	<
88	<	ensembleCase = -1;
89	<	ffCase = -1;
126	>	// gather all of the information from the Bass file
127
128	<	// get the stamps and globals;
92	<	the_stamps = stamps;
93	<	the_globals = globals;
128	>	gatherInfo();
129
130	<	// 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();
130	>	// creation of complex system objects
131
132	<	// 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() );
132	>	sysObjectsCreation();
133
134	<	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	<	}
134	>	// check on the post processing info
135
136	<	// get the ensemble:
115	<	strcpy( ensemble, the_globals->getEnsemble() );
136	>	finalInfoCheck();
137
138	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
139	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
140	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
141	<	ensembleCase = NPTi_ENS;
142	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
143	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
144	<	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;
138	>	// initialize the system coordinates
139	>
140	>	if ( !initSuspend ){
141	>	initSystemCoords();
142	>
143	>	if( !(globals->getUseInitTime()) )
144	>	info[0].currentTime = 0.0;
145		}
134	–	strcpy( simnfo->ensemble, ensemble );
146
147	+	// make the output filenames
148
149	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
138	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
139	<	//     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	<	//     }
149	>	makeOutNames();
150
151	<	//     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	<	//     }
151	>	if (globals->haveMinimizer())
152	>	// make minimizer
153	>	makeMinimizer();
154	>	else
155	>	// make the integrator
156	>	makeIntegrator();
157	>
158	>	#ifdef IS_MPI
159	>	mpiSim->mpiRefresh();
160	>	#endif
161
162	<	//     if (the_globals->haveTauBarostat())
165	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
166	<	//     else {
167	<	//       sprintf( painCave.errMsg,
168	<	//                "SimSetup error: If you use the constant pressure\n"
169	<	//                "    ensemble, you must set tauBarostat.\n"
170	<	//                "    This was found in the BASS file.\n");
171	<	//       painCave.isFatal = 1;
172	<	//       simError();
173	<	//     }
162	>	// initialize the Fortran
163
164	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
165	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
177	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
164	>	initFortran();
165	>	}
166
179	–	//     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	–	//     }
167
168	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
169	<	simnfo->usePBC = the_globals->getPBC();
170	<
171	<	int usesDipoles = 0;
172	<	switch( ffCase ){
168	>	void SimSetup::makeMolecules(void){
169	>	int i, j, k;
170	>	int exI, exJ, exK, exL, slI;
171	>	int tempI, tempJ, tempK, tempL;
172	>	int molI;
173	>	int stampID, atomOffset, rbOffset;
174	>	molInit molInfo;
175	>	DirectionalAtom* dAtom;
176	>	RigidBody* myRB;
177	>	StuntDouble* mySD;
178	>	LinkedAssign* extras;
179	>	LinkedAssign* current_extra;
180	>	AtomStamp* currentAtom;
181	>	BondStamp* currentBond;
182	>	BendStamp* currentBend;
183	>	TorsionStamp* currentTorsion;
184	>	RigidBodyStamp* currentRigidBody;
185
186	<	case FF_DUFF:
187	<	the_ff = new DUFF();
188	<	usesDipoles = 1;
201	<	break;
186	>	bond_pair* theBonds;
187	>	bend_set* theBends;
188	>	torsion_set* theTorsions;
189
190	<	case FF_LJ:
204	<	the_ff = new LJFF();
205	<	break;
190	>	set<int> skipList;
191
192	<	default:
208	<	sprintf( painCave.errMsg,
209	<	"SimSetup Error. Unrecognized force field in case statement.\n");
210	<	painCave.isFatal = 1;
211	<	simError();
212	<	}
192	>	double phi, theta, psi;
193
194	<	#ifdef IS_MPI
215	<	strcpy( checkPointMsg, "ForceField creation successful" );
216	<	MPIcheckPoint();
217	<	#endif // is_mpi
194	>	//init the forceField paramters
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	>	the_ff->readParams();
197
198	<	if( !the_globals->haveNMol() ){
225	<	// we don't have the total number of molecules, so we assume it is
226	<	// given in each component
198	>	// init the atoms
199
200	<	tot_nmol = 0;
229	<	for( i=0; i<n_components; i++ ){
200	>	int nMembers, nNew, rb1, rb2;
201
202	<	if( !the_components[i]->haveNMol() ){
203	<	// we have a problem
204	<	sprintf( painCave.errMsg,
205	<	"SimSetup Error. No global NMol or component NMol"
206	<	" given. Cannot calculate the number of atoms.\n" );
207	<	painCave.isFatal = 1;
208	<	simError();
209	<	}
202	>	for (k = 0; k < nInfo; k++){
203	>	the_ff->setSimInfo(&(info[k]));
204	>
205	>	atomOffset = 0;
206	>
207	>	for (i = 0; i < info[k].n_mol; i++){
208	>	stampID = info[k].molecules[i].getStampID();
209	>
210	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
211	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
212	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
213	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
214	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
215	>
216	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
217
218	<	tot_nmol += the_components[i]->getNMol();
219	<	components_nmol[i] = the_components[i]->getNMol();
220	<	}
221	<	}
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	<	}
218	>	if (molInfo.nBonds > 0)
219	>	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
220	>	else
221	>	molInfo.myBonds = NULL;
222
223	<	#ifdef IS_MPI
224	<	strcpy( checkPointMsg, "Have the number of components" );
225	<	MPIcheckPoint();
226	<	#endif // is_mpi
223	>	if (molInfo.nBends > 0)
224	>	molInfo.myBends = new (Bend *) [molInfo.nBends];
225	>	else
226	>	molInfo.myBends = NULL;
227
228	<	// make an array of molecule stamps that match the components used.
229	<	// also extract the used stamps out into a separate linked list
228	>	if (molInfo.nTorsions > 0)
229	>	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
230	>	else
231	>	molInfo.myTorsions = NULL;
232
233	<	simnfo->nComponents = n_components;
234	<	simnfo->componentsNmol = components_nmol;
235	<	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++ ){
286	<
287	<	id = the_components[i]->getType();
288	<	comp_stamps[i] = NULL;
289	<
290	<	// check to make sure the component isn't already in the list
291	<
292	<	comp_stamps[i] = headStamp->match( id );
293	<	if( comp_stamps[i] == NULL ){
233	>	theBonds = new bond_pair[molInfo.nBonds];
234	>	theBends = new bend_set[molInfo.nBends];
235	>	theTorsions = new torsion_set[molInfo.nTorsions];
236
237	<	// 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	<	}
237	>	// make the Atoms
238
239	<	#ifdef IS_MPI
240	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
314	<	MPIcheckPoint();
315	<	#endif // is_mpi
316	<
239	>	for (j = 0; j < molInfo.nAtoms; j++){
240	>	currentAtom = comp_stamps[stampID]->getAtom(j);
241
242	+	if (currentAtom->haveOrientation()){
243	+	dAtom = new DirectionalAtom((j + atomOffset),
244	+	info[k].getConfiguration());
245	+	info[k].n_oriented++;
246	+	molInfo.myAtoms[j] = dAtom;
247
248	+	// Directional Atoms have standard unit vectors which are oriented
249	+	// in space using the three Euler angles.  We assume the standard
250	+	// unit vector was originally along the z axis below.
251
252	<	// caclulate the number of atoms, bonds, bends and torsions
252	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
253	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
254	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
255
256	<	tot_atoms = 0;
257	<	tot_bonds = 0;
258	<	tot_bends = 0;
259	<	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	<	}
256	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
257	>
258	>	}
259	>	else{
260
261	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
261	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
262	>	}
263
264	<	simnfo->n_atoms = tot_atoms;
337	<	simnfo->n_bonds = tot_bonds;
338	<	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];
264	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
265
266		#ifdef IS_MPI
267
268	<	// divide the molecules among processors here.
348	<
349	<	mpiSim = new mpiSimulation( simnfo );
350	<
351	<	globalIndex = mpiSim->divideLabor();
268	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
269
270	<	// set up the local variables
271	<
355	<	int localMol, allMol;
356	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
270	>	#endif // is_mpi
271	>	}
272
273	<	int* mol2proc = mpiSim->getMolToProcMap();
274	<	int* molCompType = mpiSim->getMolComponentType();
275	<
276	<	allMol = 0;
277	<	localMol = 0;
363	<	local_atoms = 0;
364	<	local_bonds = 0;
365	<	local_bends = 0;
366	<	local_torsions = 0;
367	<	globalAtomIndex = 0;
273	>	// make the bonds
274	>	for (j = 0; j < molInfo.nBonds; j++){
275	>	currentBond = comp_stamps[stampID]->getBond(j);
276	>	theBonds[j].a = currentBond->getA() + atomOffset;
277	>	theBonds[j].b = currentBond->getB() + atomOffset;
278
279	+	tempI = theBonds[j].a;
280	+	tempJ = theBonds[j].b;
281
282	<	for( i=0; i<n_components; i++ ){
282	>	#ifdef IS_MPI
283	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
284	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
285	>	#else
286	>	exI = tempI + 1;
287	>	exJ = tempJ + 1;
288	>	#endif
289
290	<	for( j=0; j<components_nmol[i]; j++ ){
373	<
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++;
290	>	info[k].excludes->addPair(exI, exJ);
291		}
292
293	<	allMol++;
294	<	}
295	<	}
296	<	local_SRI = local_bonds + local_bends + local_torsions;
297	<
298	<	simnfo->n_atoms = mpiSim->getMyNlocal();
393	<
394	<	if( local_atoms != simnfo->n_atoms ){
395	<	sprintf( painCave.errMsg,
396	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
397	<	" localAtom (%d) are not equal.\n",
398	<	simnfo->n_atoms,
399	<	local_atoms );
400	<	painCave.isFatal = 1;
401	<	simError();
402	<	}
293	>	//make the bends
294	>	for (j = 0; j < molInfo.nBends; j++){
295	>	currentBend = comp_stamps[stampID]->getBend(j);
296	>	theBends[j].a = currentBend->getA() + atomOffset;
297	>	theBends[j].b = currentBend->getB() + atomOffset;
298	>	theBends[j].c = currentBend->getC() + atomOffset;
299
300	<	simnfo->n_bonds = local_bonds;
301	<	simnfo->n_bends = local_bends;
302	<	simnfo->n_torsions = local_torsions;
407	<	simnfo->n_SRI = local_SRI;
408	<	simnfo->n_mol = localMol;
300	>	if (currentBend->haveExtras()){
301	>	extras = currentBend->getExtras();
302	>	current_extra = extras;
303
304	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
305	<	MPIcheckPoint();
306	<
307	<
308	<	#endif // is_mpi
309	<
304	>	while (current_extra != NULL){
305	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
306	>	switch (current_extra->getType()){
307	>	case 0:
308	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
309	>	theBends[j].isGhost = 1;
310	>	break;
311
312	<	// create the atom and short range interaction arrays
312	>	case 1:
313	>	theBends[j].ghost = (int) current_extra->getDouble() +
314	>	atomOffset;
315	>	theBends[j].isGhost = 1;
316	>	break;
317
318	<	Atom::createArrays(simnfo->n_atoms);
319	<	the_atoms = new Atom*[simnfo->n_atoms];
320	<	the_molecules = new Molecule[simnfo->n_mol];
321	<	int molIndex;
322	<
323	<	// initialize the molecule's stampID's
318	>	default:
319	>	sprintf(painCave.errMsg,
320	>	"SimSetup Error: ghostVectorSource was neither a "
321	>	"double nor an int.\n"
322	>	"-->Bend[%d] in %s\n",
323	>	j, comp_stamps[stampID]->getID());
324	>	painCave.isFatal = 1;
325	>	simError();
326	>	}
327	>	}
328	>	else{
329	>	sprintf(painCave.errMsg,
330	>	"SimSetup Error: unhandled bend assignment:\n"
331	>	"    -->%s in Bend[%d] in %s\n",
332	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
333	>	painCave.isFatal = 1;
334	>	simError();
335	>	}
336
337	+	current_extra = current_extra->getNext();
338	+	}
339	+	}
340	+
341	+	if (theBends[j].isGhost) {
342	+
343	+	tempI = theBends[j].a;
344	+	tempJ = theBends[j].b;
345	+
346		#ifdef IS_MPI
347	<
347	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
348	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
349	>	#else
350	>	exI = tempI + 1;
351	>	exJ = tempJ + 1;
352	>	#endif
353	>	info[k].excludes->addPair(exI, exJ);
354
355	<	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	<	}
355	>	} else {
356
357	<	#else // is_mpi
358	<
359	<	molIndex = 0;
360	<	globalAtomIndex = 0;
361	<	for(i=0; i<n_components; i++){
362	<	for(j=0; j<components_nmol[i]; j++ ){
363	<	the_molecules[molIndex].setStampID( i );
364	<	the_molecules[molIndex].setMyIndex( molIndex );
365	<	the_molecules[molIndex].setGlobalIndex( molIndex );
366	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
367	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
368	<	globalAtomIndex++;
357	>	tempI = theBends[j].a;
358	>	tempJ = theBends[j].b;
359	>	tempK = theBends[j].c;
360	>
361	>	#ifdef IS_MPI
362	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
363	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
364	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
365	>	#else
366	>	exI = tempI + 1;
367	>	exJ = tempJ + 1;
368	>	exK = tempK + 1;
369	>	#endif
370	>
371	>	info[k].excludes->addPair(exI, exK);
372	>	info[k].excludes->addPair(exI, exJ);
373	>	info[k].excludes->addPair(exJ, exK);
374	>	}
375		}
453	–	molIndex++;
454	–	}
455	–	}
456	–
376
377	<	#endif // is_mpi
377	>	for (j = 0; j < molInfo.nTorsions; j++){
378	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
379	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
380	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
381	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
382	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
383
384	+	tempI = theTorsions[j].a;
385	+	tempJ = theTorsions[j].b;
386	+	tempK = theTorsions[j].c;
387	+	tempL = theTorsions[j].d;
388
389	<	if( simnfo->n_SRI ){
390	<
391	<	Exclude::createArray(simnfo->n_SRI);
392	<	the_excludes = new Exclude*[simnfo->n_SRI];
393	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
394	<	simnfo->globalExcludes = new int;
395	<	simnfo->n_exclude = simnfo->n_SRI;
396	<	}
397	<	else{
398	<
399	<	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	<	}
389	>	#ifdef IS_MPI
390	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
391	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
392	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
393	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
394	>	#else
395	>	exI = tempI + 1;
396	>	exJ = tempJ + 1;
397	>	exK = tempK + 1;
398	>	exL = tempL + 1;
399	>	#endif
400
401	<	// set the arrays into the SimInfo object
401	>	info[k].excludes->addPair(exI, exJ);
402	>	info[k].excludes->addPair(exI, exK);
403	>	info[k].excludes->addPair(exI, exL);
404	>	info[k].excludes->addPair(exJ, exK);
405	>	info[k].excludes->addPair(exJ, exL);
406	>	info[k].excludes->addPair(exK, exL);
407	>	}
408
409	<	simnfo->atoms = the_atoms;
483	<	simnfo->molecules = the_molecules;
484	<	simnfo->nGlobalExcludes = 0;
485	<	simnfo->excludes = the_excludes;
409	>	for (j = 0; j < molInfo.nRigidBodies; j++){
410
411	+	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
412	+	nMembers = currentRigidBody->getNMembers();
413
414	<	// get some of the tricky things that may still be in the globals
414	>	// Create the Rigid Body:
415
416	<	double boxVector[3];
417	<	if( the_globals->haveBox() ){
418	<	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() ){
416	>	myRB = new RigidBody();
417	>
418	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
419
420	<	double vol;
421	<	vol = (double)tot_nmol / the_globals->getDensity();
502	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
503	<	boxVector[1] = boxVector[0];
504	<	boxVector[2] = boxVector[0];
420	>	// molI is atom numbering inside this molecule
421	>	molI = currentRigidBody->getMember(rb1);
422
423	<	simnfo->setBox( boxVector );
424	<	}
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();
423	>	// tempI is atom numbering on local processor
424	>	tempI = molI + atomOffset;
425
426	<	if( !the_globals->haveBoxY() ){
427	<	sprintf( painCave.errMsg,
428	<	"SimSetup error, no periodic BoxY size given.\n" );
520	<	painCave.isFatal = 1;
521	<	simError();
522	<	}
523	<	boxVector[1] = the_globals->getBoxY();
426	>	// currentAtom is the AtomStamp (which we need for
427	>	// rigid body reference positions)
428	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
429
430	<	if( !the_globals->haveBoxZ() ){
431	<	sprintf( painCave.errMsg,
527	<	"SimSetup error, no periodic BoxZ size given.\n" );
528	<	painCave.isFatal = 1;
529	<	simError();
530	<	}
531	<	boxVector[2] = the_globals->getBoxZ();
430	>	// When we add to the rigid body, add the atom itself and
431	>	// the stamp info:
432
433	<	simnfo->setBox( boxVector );
434	<	}
435	<
433	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
434	>
435	>	// Add this atom to the Skip List for the integrators
436		#ifdef IS_MPI
437	<	strcpy( checkPointMsg, "Box size set up" );
438	<	MPIcheckPoint();
439	<	#endif // is_mpi
437	>	slI = info[k].atoms[tempI]->getGlobalIndex();
438	>	#else
439	>	slI = tempI;
440	>	#endif
441	>	skipList.insert(slI);
442	>
443	>	}
444	>
445	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
446	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
447	>
448	>	tempI = currentRigidBody->getMember(rb1);
449	>	tempJ = currentRigidBody->getMember(rb2);
450	>
451	>	// Some explanation is required here.
452	>	// Fortran indexing starts at 1, while c indexing starts at 0
453	>	// Also, in parallel computations, the GlobalIndex is
454	>	// used for the exclude list:
455	>
456	>	#ifdef IS_MPI
457	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
458	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
459	>	#else
460	>	exI = tempI + 1;
461	>	exJ = tempJ + 1;
462	>	#endif
463	>
464	>	info[k].excludes->addPair(exI, exJ);
465	>
466	>	}
467	>	}
468	>	}
469	>
470	>	// send the arrays off to the forceField for init.
471	>
472	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
473	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
474	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
475	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
476	>	theTorsions);
477
478	+	info[k].molecules[i].initialize(molInfo);
479
542	–	// initialize the arrays
480
481	<	the_ff->setSimInfo( simnfo );
481	>	atomOffset += molInfo.nAtoms;
482	>	delete[] theBonds;
483	>	delete[] theBends;
484	>	delete[] theTorsions;
485	>	}
486
487	<	makeMolecules();
547	<	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	<	}
487	>	// build up the integrableObjects vector:
488
489	<	if( !the_globals->haveEST() ){
572	<	sprintf( painCave.errMsg,
573	<	"SimSetup Warning: using default value of 0.05 * the "
574	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
575	<	);
576	<	painCave.isFatal = 0;
577	<	simError();
578	<	simnfo->est = 0.05 * simnfo->ecr;
579	<	} else {
580	<	simnfo->est        = the_globals->getEST();
581	<	}
582	<
583	<	if(!the_globals->haveDielectric() ){
584	<	sprintf( painCave.errMsg,
585	<	"SimSetup Error: You are trying to use Reaction Field without"
586	<	"setting a dielectric constant!\n"
587	<	);
588	<	painCave.isFatal = 1;
589	<	simError();
590	<	}
591	<	simnfo->dielectric = the_globals->getDielectric();
592	<	} else {
593	<	if (usesDipoles) {
489	>	for (i = 0; i < info[k].n_atoms; i++) {
490
491	<	if( !the_globals->haveECR() ){
492	<	sprintf( painCave.errMsg,
493	<	"SimSetup Warning: using default value of 1/2 the smallest "
494	<	"box length for the electrostaticCutoffRadius.\n"
495	<	"I hope you have a very fast processor!\n");
496	<	painCave.isFatal = 0;
497	<	simError();
498	<	double smallest;
499	<	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();
491	>	#ifdef IS_MPI
492	>	slI = info[k].atoms[i]->getGlobalIndex();
493	>	#else
494	>	slI = i;
495	>	#endif
496	>
497	>	if (skipList.find(slI) == skipList.end()) {
498	>	mySD = (StuntDouble *) info[k].atoms[i];
499	>	info[k].integrableObjects.push_back(mySD);
500		}
610	–
611	–	if( !the_globals->haveEST() ){
612	–	sprintf( painCave.errMsg,
613	–	"SimSetup Warning: using default value of 5%% of the "
614	–	"electrostaticCutoffRadius for the "
615	–	"electrostaticSkinThickness\n"
616	–	);
617	–	painCave.isFatal = 0;
618	–	simError();
619	–	simnfo->est = 0.05 * simnfo->ecr;
620	–	} else {
621	–	simnfo->est        = the_globals->getEST();
622	–	}
501		}
502	<	}
502	>	for (i = 0; i < info[k].rigidBodies.size(); i++) {
503	>	mySD = (StuntDouble *) info[k].rigidBodies[i];
504	>	info[k].integrableObjects.push_back(mySD);
505	>	}
506	>
507	>	}
508
509		#ifdef IS_MPI
510	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
510	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
511		MPIcheckPoint();
512		#endif // is_mpi
513
514	<	if( the_globals->haveInitialConfig() ){
632	<
633	<	InitializeFromFile* fileInit;
634	<	#ifdef IS_MPI // is_mpi
635	<	if( worldRank == 0 ){
636	<	#endif //is_mpi
637	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
638	<	#ifdef IS_MPI
639	<	}else fileInit = new InitializeFromFile( NULL );
640	<	#endif
641	<	fileInit->read_xyz( simnfo ); // default velocities on
514	>	// clean up the forcefield
515
516	<	delete fileInit;
644	<	}
645	<	else{
516	>	if (!globals->haveLJrcut()){
517
518	<	#ifdef IS_MPI
518	>	the_ff->calcRcut();
519
520	<	// no init from bass
521	<
522	<	sprintf( painCave.errMsg,
523	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
653	<	painCave.isFatal;
654	<	simError();
655	<
656	<	#else
520	>	} else {
521	>
522	>	the_ff->setRcut( globals->getLJrcut() );
523	>	}
524
525	<	initFromBass();
525	>	the_ff->cleanMe();
526	>	}
527
528	+	void SimSetup::initFromBass(void){
529	+	int i, j, k;
530	+	int n_cells;
531	+	double cellx, celly, cellz;
532	+	double temp1, temp2, temp3;
533	+	int n_per_extra;
534	+	int n_extra;
535	+	int have_extra, done;
536
537	<	#endif
538	<	}
537	>	double vel[3];
538	>	vel[0] = 0.0;
539	>	vel[1] = 0.0;
540	>	vel[2] = 0.0;
541
542	<	#ifdef IS_MPI
543	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
544	<	MPIcheckPoint();
667	<	#endif // is_mpi
542	>	temp1 = (double) tot_nmol / 4.0;
543	>	temp2 = pow(temp1, (1.0 / 3.0));
544	>	temp3 = ceil(temp2);
545
546	+	have_extra = 0;
547	+	if (temp2 < temp3){
548	+	// we have a non-complete lattice
549	+	have_extra = 1;
550
551	<
552	<
553	<
551	>	n_cells = (int) temp3 - 1;
552	>	cellx = info[0].boxL[0] / temp3;
553	>	celly = info[0].boxL[1] / temp3;
554	>	cellz = info[0].boxL[2] / temp3;
555	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
556	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
557	>	n_per_extra = (int) ceil(temp1);
558
559	<
560	<	#ifdef IS_MPI
561	<	if( worldRank == 0 ){
562	<	#endif // is_mpi
563	<
564	<	if( the_globals->haveFinalConfig() ){
680	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
559	>	if (n_per_extra > 4){
560	>	sprintf(painCave.errMsg,
561	>	"SimSetup error. There has been an error in constructing"
562	>	" the non-complete lattice.\n");
563	>	painCave.isFatal = 1;
564	>	simError();
565		}
566	<	else{
567	<	strcpy( simnfo->finalName, inFileName );
568	<	char* endTest;
569	<	int nameLength = strlen( simnfo->finalName );
570	<	endTest = &(simnfo->finalName[nameLength - 5]);
571	<	if( !strcmp( endTest, ".bass" ) ){
572	<	strcpy( endTest, ".eor" );
566	>	}
567	>	else{
568	>	n_cells = (int) temp3;
569	>	cellx = info[0].boxL[0] / temp3;
570	>	celly = info[0].boxL[1] / temp3;
571	>	cellz = info[0].boxL[2] / temp3;
572	>	}
573	>
574	>	current_mol = 0;
575	>	current_comp_mol = 0;
576	>	current_comp = 0;
577	>	current_atom_ndx = 0;
578	>
579	>	for (i = 0; i < n_cells ; i++){
580	>	for (j = 0; j < n_cells; j++){
581	>	for (k = 0; k < n_cells; k++){
582	>	makeElement(i * cellx, j * celly, k * cellz);
583	>
584	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
585	>
586	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
587	>
588	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
589		}
690	–	else if( !strcmp( endTest, ".BASS" ) ){
691	–	strcpy( endTest, ".eor" );
692	–	}
693	–	else{
694	–	endTest = &(simnfo->finalName[nameLength - 4]);
695	–	if( !strcmp( endTest, ".bss" ) ){
696	–	strcpy( endTest, ".eor" );
697	–	}
698	–	else if( !strcmp( endTest, ".mdl" ) ){
699	–	strcpy( endTest, ".eor" );
700	–	}
701	–	else{
702	–	strcat( simnfo->finalName, ".eor" );
703	–	}
704	–	}
590		}
706	–
707	–	// make the sample and status out names
708	–
709	–	strcpy( simnfo->sampleName, inFileName );
710	–	char* endTest;
711	–	int nameLength = strlen( simnfo->sampleName );
712	–	endTest = &(simnfo->sampleName[nameLength - 5]);
713	–	if( !strcmp( endTest, ".bass" ) ){
714	–	strcpy( endTest, ".dump" );
715	–	}
716	–	else if( !strcmp( endTest, ".BASS" ) ){
717	–	strcpy( endTest, ".dump" );
718	–	}
719	–	else{
720	–	endTest = &(simnfo->sampleName[nameLength - 4]);
721	–	if( !strcmp( endTest, ".bss" ) ){
722	–	strcpy( endTest, ".dump" );
723	–	}
724	–	else if( !strcmp( endTest, ".mdl" ) ){
725	–	strcpy( endTest, ".dump" );
726	–	}
727	–	else{
728	–	strcat( simnfo->sampleName, ".dump" );
729	–	}
730	–	}
731	–
732	–	strcpy( simnfo->statusName, inFileName );
733	–	nameLength = strlen( simnfo->statusName );
734	–	endTest = &(simnfo->statusName[nameLength - 5]);
735	–	if( !strcmp( endTest, ".bass" ) ){
736	–	strcpy( endTest, ".stat" );
737	–	}
738	–	else if( !strcmp( endTest, ".BASS" ) ){
739	–	strcpy( endTest, ".stat" );
740	–	}
741	–	else{
742	–	endTest = &(simnfo->statusName[nameLength - 4]);
743	–	if( !strcmp( endTest, ".bss" ) ){
744	–	strcpy( endTest, ".stat" );
745	–	}
746	–	else if( !strcmp( endTest, ".mdl" ) ){
747	–	strcpy( endTest, ".stat" );
748	–	}
749	–	else{
750	–	strcat( simnfo->statusName, ".stat" );
751	–	}
752	–	}
753	–
754	–	#ifdef IS_MPI
591		}
756	–	#endif // is_mpi
757	–
758	–	// set the status, sample, and themal kick times
759	–
760	–	if( the_globals->haveSampleTime() ){
761	–	simnfo->sampleTime = the_globals->getSampleTime();
762	–	simnfo->statusTime = simnfo->sampleTime;
763	–	simnfo->thermalTime = simnfo->sampleTime;
764	–	}
765	–	else{
766	–	simnfo->sampleTime = the_globals->getRunTime();
767	–	simnfo->statusTime = simnfo->sampleTime;
768	–	simnfo->thermalTime = simnfo->sampleTime;
769	–	}
592
593	<	if( the_globals->haveStatusTime() ){
594	<	simnfo->statusTime = the_globals->getStatusTime();
773	<	}
593	>	if (have_extra){
594	>	done = 0;
595
596	<	if( the_globals->haveThermalTime() ){
597	<	simnfo->thermalTime = the_globals->getThermalTime();
598	<	}
596	>	int start_ndx;
597	>	for (i = 0; i < (n_cells + 1) && !done; i++){
598	>	for (j = 0; j < (n_cells + 1) && !done; j++){
599	>	if (i < n_cells){
600	>	if (j < n_cells){
601	>	start_ndx = n_cells;
602	>	}
603	>	else
604	>	start_ndx = 0;
605	>	}
606	>	else
607	>	start_ndx = 0;
608
609	<	// check for the temperature set flag
609	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
610	>	makeElement(i * cellx, j * celly, k * cellz);
611	>	done = (current_mol >= tot_nmol);
612
613	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
613	>	if (!done && n_per_extra > 1){
614	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
615	>	k * cellz);
616	>	done = (current_mol >= tot_nmol);
617	>	}
618
619	+	if (!done && n_per_extra > 2){
620	+	makeElement(i * cellx, j * celly + 0.5 * celly,
621	+	k * cellz + 0.5 * cellz);
622	+	done = (current_mol >= tot_nmol);
623	+	}
624
625	<	// make the integrator
626	<
627	<
628	<	NVT*  myNVT = NULL;
629	<	NPTi* myNPTi = NULL;
630	<	NPTf* myNPTf = NULL;
631	<	NPTim* myNPTim = NULL;
791	<	NPTfm* myNPTfm = NULL;
792	<
793	<	switch( ensembleCase ){
794	<
795	<	case NVE_ENS:
796	<	new NVE( simnfo, the_ff );
797	<	break;
798	<
799	<	case NVT_ENS:
800	<	myNVT = new NVT( simnfo, the_ff );
801	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
802	<
803	<	if (the_globals->haveTauThermostat())
804	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
805	<
806	<	else {
807	<	sprintf( painCave.errMsg,
808	<	"SimSetup error: If you use the NVT\n"
809	<	"    ensemble, you must set tauThermostat.\n");
810	<	painCave.isFatal = 1;
811	<	simError();
625	>	if (!done && n_per_extra > 3){
626	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
627	>	k * cellz + 0.5 * cellz);
628	>	done = (current_mol >= tot_nmol);
629	>	}
630	>	}
631	>	}
632		}
633	<	break;
633	>	}
634
635	<	case NPTi_ENS:
636	<	myNPTi = new NPTi( simnfo, the_ff );
637	<	myNPTi->setTargetTemp( the_globals->getTargetTemp());
635	>	for (i = 0; i < info[0].n_atoms; i++){
636	>	info[0].atoms[i]->setVel(vel);
637	>	}
638	>	}
639
640	<	if (the_globals->haveTargetPressure())
641	<	myNPTi->setTargetPressure(the_globals->getTargetPressure());
642	<	else {
643	<	sprintf( painCave.errMsg,
644	<	"SimSetup error: If you use a constant pressure\n"
645	<	"    ensemble, you must set targetPressure in the BASS file.\n");
825	<	painCave.isFatal = 1;
826	<	simError();
827	<	}
828	<
829	<	if( the_globals->haveTauThermostat() )
830	<	myNPTi->setTauThermostat( the_globals->getTauThermostat() );
831	<	else{
832	<	sprintf( painCave.errMsg,
833	<	"SimSetup error: If you use an NPT\n"
834	<	"    ensemble, you must set tauThermostat.\n");
835	<	painCave.isFatal = 1;
836	<	simError();
837	<	}
640	>	void SimSetup::makeElement(double x, double y, double z){
641	>	int k;
642	>	AtomStamp* current_atom;
643	>	DirectionalAtom* dAtom;
644	>	double rotMat[3][3];
645	>	double pos[3];
646
647	<	if( the_globals->haveTauBarostat() )
648	<	myNPTi->setTauBarostat( the_globals->getTauBarostat() );
649	<	else{
650	<	sprintf( painCave.errMsg,
651	<	"SimSetup error: If you use an NPT\n"
652	<	"    ensemble, you must set tauBarostat.\n");
647	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
648	>	current_atom = comp_stamps[current_comp]->getAtom(k);
649	>	if (!current_atom->havePosition()){
650	>	sprintf(painCave.errMsg,
651	>	"SimSetup:initFromBass error.\n"
652	>	"\tComponent %s, atom %s does not have a position specified.\n"
653	>	"\tThe initialization routine is unable to give a start"
654	>	" position.\n",
655	>	comp_stamps[current_comp]->getID(), current_atom->getType());
656		painCave.isFatal = 1;
657		simError();
658		}
848	–	break;
659
660	<	case NPTf_ENS:
661	<	myNPTf = new NPTf( simnfo, the_ff );
662	<	myNPTf->setTargetTemp( the_globals->getTargetTemp());
660	>	pos[0] = x + current_atom->getPosX();
661	>	pos[1] = y + current_atom->getPosY();
662	>	pos[2] = z + current_atom->getPosZ();
663
664	<	if (the_globals->haveTargetPressure())
855	<	myNPTf->setTargetPressure(the_globals->getTargetPressure());
856	<	else {
857	<	sprintf( painCave.errMsg,
858	<	"SimSetup error: If you use a constant pressure\n"
859	<	"    ensemble, you must set targetPressure in the BASS file.\n");
860	<	painCave.isFatal = 1;
861	<	simError();
862	<	}
664	>	info[0].atoms[current_atom_ndx]->setPos(pos);
665
666	<	if( the_globals->haveTauThermostat() )
667	<	myNPTf->setTauThermostat( the_globals->getTauThermostat() );
866	<	else{
867	<	sprintf( painCave.errMsg,
868	<	"SimSetup error: If you use an NPT\n"
869	<	"    ensemble, you must set tauThermostat.\n");
870	<	painCave.isFatal = 1;
871	<	simError();
872	<	}
666	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
667	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
668
669	<	if( the_globals->haveTauBarostat() )
670	<	myNPTf->setTauBarostat( the_globals->getTauBarostat() );
671	<	else{
877	<	sprintf( painCave.errMsg,
878	<	"SimSetup error: If you use an NPT\n"
879	<	"    ensemble, you must set tauBarostat.\n");
880	<	painCave.isFatal = 1;
881	<	simError();
882	<	}
883	<	break;
884	<
885	<	case NPTim_ENS:
886	<	myNPTim = new NPTim( simnfo, the_ff );
887	<	myNPTim->setTargetTemp( the_globals->getTargetTemp());
669	>	rotMat[0][0] = 1.0;
670	>	rotMat[0][1] = 0.0;
671	>	rotMat[0][2] = 0.0;
672
673	<	if (the_globals->haveTargetPressure())
674	<	myNPTim->setTargetPressure(the_globals->getTargetPressure());
675	<	else {
892	<	sprintf( painCave.errMsg,
893	<	"SimSetup error: If you use a constant pressure\n"
894	<	"    ensemble, you must set targetPressure in the BASS file.\n");
895	<	painCave.isFatal = 1;
896	<	simError();
897	<	}
898	<
899	<	if( the_globals->haveTauThermostat() )
900	<	myNPTim->setTauThermostat( the_globals->getTauThermostat() );
901	<	else{
902	<	sprintf( painCave.errMsg,
903	<	"SimSetup error: If you use an NPT\n"
904	<	"    ensemble, you must set tauThermostat.\n");
905	<	painCave.isFatal = 1;
906	<	simError();
907	<	}
673	>	rotMat[1][0] = 0.0;
674	>	rotMat[1][1] = 1.0;
675	>	rotMat[1][2] = 0.0;
676
677	<	if( the_globals->haveTauBarostat() )
678	<	myNPTim->setTauBarostat( the_globals->getTauBarostat() );
679	<	else{
912	<	sprintf( painCave.errMsg,
913	<	"SimSetup error: If you use an NPT\n"
914	<	"    ensemble, you must set tauBarostat.\n");
915	<	painCave.isFatal = 1;
916	<	simError();
917	<	}
918	<	break;
677	>	rotMat[2][0] = 0.0;
678	>	rotMat[2][1] = 0.0;
679	>	rotMat[2][2] = 1.0;
680
681	<	case NPTfm_ENS:
921	<	myNPTfm = new NPTfm( simnfo, the_ff );
922	<	myNPTfm->setTargetTemp( the_globals->getTargetTemp());
923	<
924	<	if (the_globals->haveTargetPressure())
925	<	myNPTfm->setTargetPressure(the_globals->getTargetPressure());
926	<	else {
927	<	sprintf( painCave.errMsg,
928	<	"SimSetup error: If you use a constant pressure\n"
929	<	"    ensemble, you must set targetPressure in the BASS file.\n");
930	<	painCave.isFatal = 1;
931	<	simError();
932	<	}
933	<
934	<	if( the_globals->haveTauThermostat() )
935	<	myNPTfm->setTauThermostat( the_globals->getTauThermostat() );
936	<	else{
937	<	sprintf( painCave.errMsg,
938	<	"SimSetup error: If you use an NPT\n"
939	<	"    ensemble, you must set tauThermostat.\n");
940	<	painCave.isFatal = 1;
941	<	simError();
681	>	dAtom->setA(rotMat);
682		}
683
684	<	if( the_globals->haveTauBarostat() )
685	<	myNPTfm->setTauBarostat( the_globals->getTauBarostat() );
946	<	else{
947	<	sprintf( painCave.errMsg,
948	<	"SimSetup error: If you use an NPT\n"
949	<	"    ensemble, you must set tauBarostat.\n");
950	<	painCave.isFatal = 1;
951	<	simError();
952	<	}
953	<	break;
684	>	current_atom_ndx++;
685	>	}
686
687	<	default:
688	<	sprintf( painCave.errMsg,
689	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
690	<	painCave.isFatal = 1;
691	<	simError();
687	>	current_mol++;
688	>	current_comp_mol++;
689	>
690	>	if (current_comp_mol >= components_nmol[current_comp]){
691	>	current_comp_mol = 0;
692	>	current_comp++;
693		}
694	+	}
695
696
697	<	#ifdef IS_MPI
698	<	mpiSim->mpiRefresh();
965	<	#endif
697	>	void SimSetup::gatherInfo(void){
698	>	int i;
699
700	<	// initialize the Fortran
700	>	ensembleCase = -1;
701	>	ffCase = -1;
702
703	+	// set the easy ones first
704
705	<	simnfo->refreshSim();
706	<
707	<	if( !strcmp( simnfo->mixingRule, "standard") ){
708	<	the_ff->initForceField( LB_MIXING_RULE );
705	>	for (i = 0; i < nInfo; i++){
706	>	info[i].target_temp = globals->getTargetTemp();
707	>	info[i].dt = globals->getDt();
708	>	info[i].run_time = globals->getRunTime();
709		}
710	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
711	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
710	>	n_components = globals->getNComponents();
711	>
712	>
713	>	// get the forceField
714	>
715	>	strcpy(force_field, globals->getForceField());
716	>
717	>	if (!strcasecmp(force_field, "DUFF")){
718	>	ffCase = FF_DUFF;
719		}
720	+	else if (!strcasecmp(force_field, "LJ")){
721	+	ffCase = FF_LJ;
722	+	}
723	+	else if (!strcasecmp(force_field, "EAM")){
724	+	ffCase = FF_EAM;
725	+	}
726	+	else if (!strcasecmp(force_field, "WATER")){
727	+	ffCase = FF_H2O;
728	+	}
729		else{
730	<	sprintf( painCave.errMsg,
731	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
732	<	simnfo->mixingRule );
733	<	painCave.isFatal = 1;
983	<	simError();
730	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
731	>	force_field);
732	>	painCave.isFatal = 1;
733	>	simError();
734		}
735
736	+	// get the ensemble
737
738	<	#ifdef IS_MPI
988	<	strcpy( checkPointMsg,
989	<	"Successfully intialized the mixingRule for Fortran." );
990	<	MPIcheckPoint();
991	<	#endif // is_mpi
992	<	}
738	>	strcpy(ensemble, globals->getEnsemble());
739
740	+	if (!strcasecmp(ensemble, "NVE")){
741	+	ensembleCase = NVE_ENS;
742	+	}
743	+	else if (!strcasecmp(ensemble, "NVT")){
744	+	ensembleCase = NVT_ENS;
745	+	}
746	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
747	+	ensembleCase = NPTi_ENS;
748	+	}
749	+	else if (!strcasecmp(ensemble, "NPTf")){
750	+	ensembleCase = NPTf_ENS;
751	+	}
752	+	else if (!strcasecmp(ensemble, "NPTxyz")){
753	+	ensembleCase = NPTxyz_ENS;
754	+	}
755	+	else{
756	+	sprintf(painCave.errMsg,
757	+	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
758	+	"\treverting to NVE for this simulation.\n",
759	+	ensemble);
760	+	painCave.isFatal = 0;
761	+	simError();
762	+	strcpy(ensemble, "NVE");
763	+	ensembleCase = NVE_ENS;
764	+	}
765
766	<	void SimSetup::makeMolecules( void ){
766	>	for (i = 0; i < nInfo; i++){
767	>	strcpy(info[i].ensemble, ensemble);
768
769	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
998	<	molInit info;
999	<	DirectionalAtom* dAtom;
1000	<	LinkedAssign* extras;
1001	<	LinkedAssign* current_extra;
1002	<	AtomStamp* currentAtom;
1003	<	BondStamp* currentBond;
1004	<	BendStamp* currentBend;
1005	<	TorsionStamp* currentTorsion;
769	>	// get the mixing rule
770
771	<	bond_pair* theBonds;
772	<	bend_set* theBends;
773	<	torsion_set* theTorsions;
771	>	strcpy(info[i].mixingRule, globals->getMixingRule());
772	>	info[i].usePBC = globals->getPBC();
773	>	}
774
775	<
1012	<	//init the forceField paramters
775	>	// get the components and calculate the tot_nMol and indvidual n_mol
776
777	<	the_ff->readParams();
777	>	the_components = globals->getComponents();
778	>	components_nmol = new int[n_components];
779
1016	–
1017	–	// init the atoms
780
781	<	double ux, uy, uz, u, uSqr;
782	<
783	<	atomOffset = 0;
1022	<	excludeOffset = 0;
1023	<	for(i=0; i<simnfo->n_mol; i++){
1024	<
1025	<	stampID = the_molecules[i].getStampID();
781	>	if (!globals->haveNMol()){
782	>	// we don't have the total number of molecules, so we assume it is
783	>	// given in each component
784
785	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
786	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
787	<	info.nBends    = comp_stamps[stampID]->getNBends();
788	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
789	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
785	>	tot_nmol = 0;
786	>	for (i = 0; i < n_components; i++){
787	>	if (!the_components[i]->haveNMol()){
788	>	// we have a problem
789	>	sprintf(painCave.errMsg,
790	>	"SimSetup Error. No global NMol or component NMol given.\n"
791	>	"\tCannot calculate the number of atoms.\n");
792	>	painCave.isFatal = 1;
793	>	simError();
794	>	}
795
796	<	info.myAtoms = &the_atoms[atomOffset];
797	<	info.myExcludes = &the_excludes[excludeOffset];
798	<	info.myBonds = new Bond*[info.nBonds];
799	<	info.myBends = new Bend*[info.nBends];
800	<	info.myTorsions = new Torsion*[info.nTorsions];
796	>	tot_nmol += the_components[i]->getNMol();
797	>	components_nmol[i] = the_components[i]->getNMol();
798	>	}
799	>	}
800	>	else{
801	>	sprintf(painCave.errMsg,
802	>	"SimSetup error.\n"
803	>	"\tSorry, the ability to specify total"
804	>	" nMols and then give molfractions in the components\n"
805	>	"\tis not currently supported."
806	>	" Please give nMol in the components.\n");
807	>	painCave.isFatal = 1;
808	>	simError();
809	>	}
810
811	<	theBonds = new bond_pair[info.nBonds];
812	<	theBends = new bend_set[info.nBends];
813	<	theTorsions = new torsion_set[info.nTorsions];
814	<
815	<	// make the Atoms
816	<
817	<	for(j=0; j<info.nAtoms; j++){
818	<
819	<	currentAtom = comp_stamps[stampID]->getAtom( j );
820	<	if( currentAtom->haveOrientation() ){
821	<
822	<	dAtom = new DirectionalAtom(j + atomOffset);
823	<	simnfo->n_oriented++;
824	<	info.myAtoms[j] = dAtom;
825	<
826	<	ux = currentAtom->getOrntX();
827	<	uy = currentAtom->getOrntY();
828	<	uz = currentAtom->getOrntZ();
829	<
830	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
831	<
832	<	u = sqrt( uSqr );
833	<	ux = ux / u;
834	<	uy = uy / u;
835	<	uz = uz / u;
836	<
837	<	dAtom->setSUx( ux );
838	<	dAtom->setSUy( uy );
839	<	dAtom->setSUz( uz );
840	<	}
841	<	else{
842	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
843	<	}
844	<	info.myAtoms[j]->setType( currentAtom->getType() );
811	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
812	>	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
813	>	sprintf(painCave.errMsg,
814	>	"Sample time is not divisible by dt.\n"
815	>	"\tThis will result in samples that are not uniformly\n"
816	>	"\tdistributed in time.  If this is a problem, change\n"
817	>	"\tyour sampleTime variable.\n");
818	>	painCave.isFatal = 0;
819	>	simError();
820	>	}
821	>
822	>	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
823	>	sprintf(painCave.errMsg,
824	>	"Status time is not divisible by dt.\n"
825	>	"\tThis will result in status reports that are not uniformly\n"
826	>	"\tdistributed in time.  If this is a problem, change \n"
827	>	"\tyour statusTime variable.\n");
828	>	painCave.isFatal = 0;
829	>	simError();
830	>	}
831	>
832	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
833	>	sprintf(painCave.errMsg,
834	>	"Thermal time is not divisible by dt.\n"
835	>	"\tThis will result in thermalizations that are not uniformly\n"
836	>	"\tdistributed in time.  If this is a problem, change \n"
837	>	"\tyour thermalTime variable.\n");
838	>	painCave.isFatal = 0;
839	>	simError();
840	>	}
841	>
842	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
843	>	sprintf(painCave.errMsg,
844	>	"Reset time is not divisible by dt.\n"
845	>	"\tThis will result in integrator resets that are not uniformly\n"
846	>	"\tdistributed in time.  If this is a problem, change\n"
847	>	"\tyour resetTime variable.\n");
848	>	painCave.isFatal = 0;
849	>	simError();
850	>	}
851	>
852	>	// set the status, sample, and thermal kick times
853	>
854	>	for (i = 0; i < nInfo; i++){
855	>	if (globals->haveSampleTime()){
856	>	info[i].sampleTime = globals->getSampleTime();
857	>	info[i].statusTime = info[i].sampleTime;
858	>	info[i].thermalTime = info[i].sampleTime;
859	>	}
860	>	else{
861	>	info[i].sampleTime = globals->getRunTime();
862	>	info[i].statusTime = info[i].sampleTime;
863	>	info[i].thermalTime = info[i].sampleTime;
864	>	}
865	>
866	>	if (globals->haveStatusTime()){
867	>	info[i].statusTime = globals->getStatusTime();
868	>	}
869	>
870	>	if (globals->haveThermalTime()){
871	>	info[i].thermalTime = globals->getThermalTime();
872	>	}
873	>
874	>	info[i].resetIntegrator = 0;
875	>	if( globals->haveResetTime() ){
876	>	info[i].resetTime = globals->getResetTime();
877	>	info[i].resetIntegrator = 1;
878	>	}
879	>
880	>	// check for the temperature set flag
881
882	<	#ifdef IS_MPI
883	<
884	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
885	<
886	<	#endif // is_mpi
887	<	}
882	>	if (globals->haveTempSet())
883	>	info[i].setTemp = globals->getTempSet();
884	>
885	>	// check for the extended State init
886	>
887	>	info[i].useInitXSstate = globals->getUseInitXSstate();
888	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
889
890	<	// make the bonds
891	<	for(j=0; j<info.nBonds; j++){
892	<
893	<	currentBond = comp_stamps[stampID]->getBond( j );
1085	<	theBonds[j].a = currentBond->getA() + atomOffset;
1086	<	theBonds[j].b = currentBond->getB() + atomOffset;
890	>	}
891	>
892	>	//setup seed for random number generator
893	>	int seedValue;
894
895	<	exI = theBonds[j].a;
896	<	exJ = theBonds[j].b;
895	>	if (globals->haveSeed()){
896	>	seedValue = globals->getSeed();
897
898	<	// exclude_I must always be the smaller of the pair
899	<	if( exI > exJ ){
900	<	tempEx = exI;
901	<	exI = exJ;
902	<	exJ = tempEx;
898	>	if(seedValue / 1E9 == 0){
899	>	sprintf(painCave.errMsg,
900	>	"Seed for sprng library should contain at least 9 digits\n"
901	>	"OOPSE will generate a seed for user\n");
902	>	painCave.isFatal = 0;
903	>	simError();
904	>
905	>	//using seed generated by system instead of invalid seed set by user
906	>	#ifndef IS_MPI
907	>	seedValue = make_sprng_seed();
908	>	#else
909	>	if (worldRank == 0){
910	>	seedValue = make_sprng_seed();
911		}
912	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
913	+	#endif
914	+	}
915	+	}//end of if branch of globals->haveSeed()
916	+	else{
917	+
918	+	#ifndef IS_MPI
919	+	seedValue = make_sprng_seed();
920	+	#else
921	+	if (worldRank == 0){
922	+	seedValue = make_sprng_seed();
923	+	}
924	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
925	+	#endif
926	+	}//end of globals->haveSeed()
927	+
928	+	for (int i = 0; i < nInfo; i++){
929	+	info[i].setSeed(seedValue);
930	+	}
931	+
932		#ifdef IS_MPI
933	<	tempEx = exI;
934	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
935	<	tempEx = exJ;
936	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1102	<
1103	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1104	<	#else  // isn't MPI
933	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
934	>	MPIcheckPoint();
935	>	#endif // is_mpi
936	>	}
937
938	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
939	<	#endif  //is_mpi
938	>
939	>	void SimSetup::finalInfoCheck(void){
940	>	int index;
941	>	int usesDipoles;
942	>	int i;
943	>
944	>	for (i = 0; i < nInfo; i++){
945	>	// check electrostatic parameters
946	>
947	>	index = 0;
948	>	usesDipoles = 0;
949	>	while ((index < info[i].n_atoms) && !usesDipoles){
950	>	usesDipoles = (info[i].atoms[index])->hasDipole();
951	>	index++;
952		}
1109	–	excludeOffset += info.nBonds;
953
954	<	//make the bends
955	<	for(j=0; j<info.nBends; j++){
956	<
957	<	currentBend = comp_stamps[stampID]->getBend( j );
958	<	theBends[j].a = currentBend->getA() + atomOffset;
959	<	theBends[j].b = currentBend->getB() + atomOffset;
960	<	theBends[j].c = currentBend->getC() + atomOffset;
961	<
962	<	if( currentBend->haveExtras() ){
963	<
964	<	extras = currentBend->getExtras();
965	<	current_extra = extras;
966	<
967	<	while( current_extra != NULL ){
968	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
969	<
970	<	switch( current_extra->getType() ){
971	<
1129	<	case 0:
1130	<	theBends[j].ghost =
1131	<	current_extra->getInt() + atomOffset;
1132	<	theBends[j].isGhost = 1;
1133	<	break;
1134	<
1135	<	case 1:
1136	<	theBends[j].ghost =
1137	<	(int)current_extra->getDouble() + atomOffset;
1138	<	theBends[j].isGhost = 1;
1139	<	break;
1140	<
1141	<	default:
1142	<	sprintf( painCave.errMsg,
1143	<	"SimSetup Error: ghostVectorSource was neither a "
1144	<	"double nor an int.\n"
1145	<	"-->Bend[%d] in %s\n",
1146	<	j, comp_stamps[stampID]->getID() );
1147	<	painCave.isFatal = 1;
1148	<	simError();
1149	<	}
1150	<	}
1151	<
1152	<	else{
1153	<
1154	<	sprintf( painCave.errMsg,
1155	<	"SimSetup Error: unhandled bend assignment:\n"
1156	<	"    -->%s in Bend[%d] in %s\n",
1157	<	current_extra->getlhs(),
1158	<	j, comp_stamps[stampID]->getID() );
1159	<	painCave.isFatal = 1;
1160	<	simError();
1161	<	}
1162	<
1163	<	current_extra = current_extra->getNext();
1164	<	}
954	>	#ifdef IS_MPI
955	>	int myUse = usesDipoles;
956	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
957	>	#endif //is_mpi
958	>
959	>	double theEcr, theEst;
960	>
961	>	if (globals->getUseRF()){
962	>	info[i].useReactionField = 1;
963	>
964	>	if (!globals->haveECR()){
965	>	sprintf(painCave.errMsg,
966	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
967	>	"\tOOPSE will use a default value of 15.0 angstroms"
968	>	"\tfor the electrostaticCutoffRadius.\n");
969	>	painCave.isFatal = 0;
970	>	simError();
971	>	theEcr = 15.0;
972		}
1166	–
1167	–	if( !theBends[j].isGhost ){
1168	–
1169	–	exI = theBends[j].a;
1170	–	exJ = theBends[j].c;
1171	–	}
973		else{
974	<
1174	<	exI = theBends[j].a;
1175	<	exJ = theBends[j].b;
974	>	theEcr = globals->getECR();
975		}
976	<
977	<	// exclude_I must always be the smaller of the pair
978	<	if( exI > exJ ){
979	<	tempEx = exI;
980	<	exI = exJ;
981	<	exJ = tempEx;
976	>
977	>	if (!globals->haveEST()){
978	>	sprintf(painCave.errMsg,
979	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
980	>	"\tOOPSE will use a default value of\n"
981	>	"\t0.05 * electrostaticCutoffRadius\n"
982	>	"\tfor the electrostaticSkinThickness\n");
983	>	painCave.isFatal = 0;
984	>	simError();
985	>	theEst = 0.05 * theEcr;
986		}
987	<	#ifdef IS_MPI
988	<	tempEx = exI;
989	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1187	<	tempEx = exJ;
1188	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1189	<
1190	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1191	<	#else  // isn't MPI
1192	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1193	<	#endif  //is_mpi
1194	<	}
1195	<	excludeOffset += info.nBends;
987	>	else{
988	>	theEst = globals->getEST();
989	>	}
990
991	<	for(j=0; j<info.nTorsions; j++){
1198	<
1199	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1200	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1201	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1202	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1203	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1204	<
1205	<	exI = theTorsions[j].a;
1206	<	exJ = theTorsions[j].d;
991	>	info[i].setDefaultEcr(theEcr, theEst);
992
993	<	// exclude_I must always be the smaller of the pair
994	<	if( exI > exJ ){
995	<	tempEx = exI;
996	<	exI = exJ;
997	<	exJ = tempEx;
993	>	if (!globals->haveDielectric()){
994	>	sprintf(painCave.errMsg,
995	>	"SimSetup Error: No Dielectric constant was set.\n"
996	>	"\tYou are trying to use Reaction Field without"
997	>	"\tsetting a dielectric constant!\n");
998	>	painCave.isFatal = 1;
999	>	simError();
1000		}
1001	<	#ifdef IS_MPI
1215	<	tempEx = exI;
1216	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1217	<	tempEx = exJ;
1218	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1219	<
1220	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1221	<	#else  // isn't MPI
1222	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1223	<	#endif  //is_mpi
1001	>	info[i].dielectric = globals->getDielectric();
1002		}
1003	<	excludeOffset += info.nTorsions;
1003	>	else{
1004	>	if (usesDipoles){
1005	>	if (!globals->haveECR()){
1006	>	sprintf(painCave.errMsg,
1007	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1008	>	"\tOOPSE will use a default value of 15.0 angstroms"
1009	>	"\tfor the electrostaticCutoffRadius.\n");
1010	>	painCave.isFatal = 0;
1011	>	simError();
1012	>	theEcr = 15.0;
1013	>	}
1014	>	else{
1015	>	theEcr = globals->getECR();
1016	>	}
1017	>
1018	>	if (!globals->haveEST()){
1019	>	sprintf(painCave.errMsg,
1020	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1021	>	"\tOOPSE will use a default value of\n"
1022	>	"\t0.05 * electrostaticCutoffRadius\n"
1023	>	"\tfor the electrostaticSkinThickness\n");
1024	>	painCave.isFatal = 0;
1025	>	simError();
1026	>	theEst = 0.05 * theEcr;
1027	>	}
1028	>	else{
1029	>	theEst = globals->getEST();
1030	>	}
1031	>
1032	>	info[i].setDefaultEcr(theEcr, theEst);
1033	>	}
1034	>	}
1035	>	}
1036	>	#ifdef IS_MPI
1037	>	strcpy(checkPointMsg, "post processing checks out");
1038	>	MPIcheckPoint();
1039	>	#endif // is_mpi
1040	>	}
1041	>
1042	>	void SimSetup::initSystemCoords(void){
1043	>	int i;
1044
1045	<
1228	<	// send the arrays off to the forceField for init.
1045	>	char* inName;
1046
1047	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1231	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1232	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1233	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1047	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1048
1049	+	for (i = 0; i < info[0].n_atoms; i++)
1050	+	info[0].atoms[i]->setCoords();
1051
1052	<	the_molecules[i].initialize( info );
1052	>	if (globals->haveInitialConfig()){
1053	>	InitializeFromFile* fileInit;
1054	>	#ifdef IS_MPI // is_mpi
1055	>	if (worldRank == 0){
1056	>	#endif //is_mpi
1057	>	inName = globals->getInitialConfig();
1058	>	fileInit = new InitializeFromFile(inName);
1059	>	#ifdef IS_MPI
1060	>	}
1061	>	else
1062	>	fileInit = new InitializeFromFile(NULL);
1063	>	#endif
1064	>	fileInit->readInit(info); // default velocities on
1065
1066	<
1239	<	atomOffset += info.nAtoms;
1240	<	delete[] theBonds;
1241	<	delete[] theBends;
1242	<	delete[] theTorsions;
1066	>	delete fileInit;
1067		}
1068	+	else{
1069	+
1070	+	// no init from bass
1071	+
1072	+	sprintf(painCave.errMsg,
1073	+	"Cannot intialize a simulation without an initial configuration file.\n");
1074	+	painCave.isFatal = 1;;
1075	+	simError();
1076	+
1077	+	}
1078
1079		#ifdef IS_MPI
1080	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1080	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1081		MPIcheckPoint();
1082		#endif // is_mpi
1249	–
1250	–	// clean up the forcefield
1251	–	the_ff->calcRcut();
1252	–	the_ff->cleanMe();
1253	–
1083		}
1084
1256	–	void SimSetup::initFromBass( void ){
1085
1086	<	int i, j, k;
1087	<	int n_cells;
1260	<	double cellx, celly, cellz;
1261	<	double temp1, temp2, temp3;
1262	<	int n_per_extra;
1263	<	int n_extra;
1264	<	int have_extra, done;
1086	>	void SimSetup::makeOutNames(void){
1087	>	int k;
1088
1266	–	temp1 = (double)tot_nmol / 4.0;
1267	–	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1268	–	temp3 = ceil( temp2 );
1089
1090	<	have_extra =0;
1091	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1092	<	have_extra =1;
1090	>	for (k = 0; k < nInfo; k++){
1091	>	#ifdef IS_MPI
1092	>	if (worldRank == 0){
1093	>	#endif // is_mpi
1094
1095	<	n_cells = (int)temp3 - 1;
1096	<	cellx = simnfo->boxLx / temp3;
1097	<	celly = simnfo->boxLy / temp3;
1098	<	cellz = simnfo->boxLz / temp3;
1099	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1100	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1101	<	n_per_extra = (int)ceil( temp1 );
1095	>	if (globals->haveFinalConfig()){
1096	>	strcpy(info[k].finalName, globals->getFinalConfig());
1097	>	}
1098	>	else{
1099	>	strcpy(info[k].finalName, inFileName);
1100	>	char* endTest;
1101	>	int nameLength = strlen(info[k].finalName);
1102	>	endTest = &(info[k].finalName[nameLength - 5]);
1103	>	if (!strcmp(endTest, ".bass")){
1104	>	strcpy(endTest, ".eor");
1105	>	}
1106	>	else if (!strcmp(endTest, ".BASS")){
1107	>	strcpy(endTest, ".eor");
1108	>	}
1109	>	else{
1110	>	endTest = &(info[k].finalName[nameLength - 4]);
1111	>	if (!strcmp(endTest, ".bss")){
1112	>	strcpy(endTest, ".eor");
1113	>	}
1114	>	else if (!strcmp(endTest, ".mdl")){
1115	>	strcpy(endTest, ".eor");
1116	>	}
1117	>	else{
1118	>	strcat(info[k].finalName, ".eor");
1119	>	}
1120	>	}
1121	>	}
1122
1123	<	if( n_per_extra > 4){
1124	<	sprintf( painCave.errMsg,
1125	<	"SimSetup error. There has been an error in constructing"
1126	<	" the non-complete lattice.\n" );
1127	<	painCave.isFatal = 1;
1128	<	simError();
1123	>	// make the sample and status out names
1124	>
1125	>	strcpy(info[k].sampleName, inFileName);
1126	>	char* endTest;
1127	>	int nameLength = strlen(info[k].sampleName);
1128	>	endTest = &(info[k].sampleName[nameLength - 5]);
1129	>	if (!strcmp(endTest, ".bass")){
1130	>	strcpy(endTest, ".dump");
1131	>	}
1132	>	else if (!strcmp(endTest, ".BASS")){
1133	>	strcpy(endTest, ".dump");
1134	>	}
1135	>	else{
1136	>	endTest = &(info[k].sampleName[nameLength - 4]);
1137	>	if (!strcmp(endTest, ".bss")){
1138	>	strcpy(endTest, ".dump");
1139	>	}
1140	>	else if (!strcmp(endTest, ".mdl")){
1141	>	strcpy(endTest, ".dump");
1142	>	}
1143	>	else{
1144	>	strcat(info[k].sampleName, ".dump");
1145	>	}
1146	>	}
1147	>
1148	>	strcpy(info[k].statusName, inFileName);
1149	>	nameLength = strlen(info[k].statusName);
1150	>	endTest = &(info[k].statusName[nameLength - 5]);
1151	>	if (!strcmp(endTest, ".bass")){
1152	>	strcpy(endTest, ".stat");
1153	>	}
1154	>	else if (!strcmp(endTest, ".BASS")){
1155	>	strcpy(endTest, ".stat");
1156	>	}
1157	>	else{
1158	>	endTest = &(info[k].statusName[nameLength - 4]);
1159	>	if (!strcmp(endTest, ".bss")){
1160	>	strcpy(endTest, ".stat");
1161	>	}
1162	>	else if (!strcmp(endTest, ".mdl")){
1163	>	strcpy(endTest, ".stat");
1164	>	}
1165	>	else{
1166	>	strcat(info[k].statusName, ".stat");
1167	>	}
1168	>	}
1169	>
1170	>	#ifdef IS_MPI
1171	>
1172		}
1173	+	#endif // is_mpi
1174		}
1175	<	else{
1176	<	n_cells = (int)temp3;
1177	<	cellx = simnfo->boxLx / temp3;
1178	<	celly = simnfo->boxLy / temp3;
1179	<	cellz = simnfo->boxLz / temp3;
1175	>	}
1176	>
1177	>
1178	>	void SimSetup::sysObjectsCreation(void){
1179	>	int i, k;
1180	>
1181	>	// create the forceField
1182	>
1183	>	createFF();
1184	>
1185	>	// extract componentList
1186	>
1187	>	compList();
1188	>
1189	>	// calc the number of atoms, bond, bends, and torsions
1190	>
1191	>	calcSysValues();
1192	>
1193	>	#ifdef IS_MPI
1194	>	// divide the molecules among the processors
1195	>
1196	>	mpiMolDivide();
1197	>	#endif //is_mpi
1198	>
1199	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1200	>
1201	>	makeSysArrays();
1202	>
1203	>	// make and initialize the molecules (all but atomic coordinates)
1204	>
1205	>	makeMolecules();
1206	>
1207	>	for (k = 0; k < nInfo; k++){
1208	>	info[k].identArray = new int[info[k].n_atoms];
1209	>	for (i = 0; i < info[k].n_atoms; i++){
1210	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1211	>	}
1212		}
1213	+	}
1214
1297	–	current_mol = 0;
1298	–	current_comp_mol = 0;
1299	–	current_comp = 0;
1300	–	current_atom_ndx = 0;
1215
1216	<	for( i=0; i < n_cells ; i++ ){
1217	<	for( j=0; j < n_cells; j++ ){
1218	<	for( k=0; k < n_cells; k++ ){
1216	>	void SimSetup::createFF(void){
1217	>	switch (ffCase){
1218	>	case FF_DUFF:
1219	>	the_ff = new DUFF();
1220	>	break;
1221
1222	<	makeElement( i * cellx,
1223	<	j * celly,
1224	<	k * cellz );
1222	>	case FF_LJ:
1223	>	the_ff = new LJFF();
1224	>	break;
1225
1226	<	makeElement( i * cellx + 0.5 * cellx,
1227	<	j * celly + 0.5 * celly,
1228	<	k * cellz );
1226	>	case FF_EAM:
1227	>	the_ff = new EAM_FF();
1228	>	break;
1229
1230	<	makeElement( i * cellx,
1231	<	j * celly + 0.5 * celly,
1232	<	k * cellz + 0.5 * cellz );
1230	>	case FF_H2O:
1231	>	the_ff = new WATER();
1232	>	break;
1233
1234	<	makeElement( i * cellx + 0.5 * cellx,
1235	<	j * celly,
1236	<	k * cellz + 0.5 * cellz );
1234	>	default:
1235	>	sprintf(painCave.errMsg,
1236	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1237	>	painCave.isFatal = 1;
1238	>	simError();
1239	>	}
1240	>
1241	>	#ifdef IS_MPI
1242	>	strcpy(checkPointMsg, "ForceField creation successful");
1243	>	MPIcheckPoint();
1244	>	#endif // is_mpi
1245	>	}
1246	>
1247	>
1248	>	void SimSetup::compList(void){
1249	>	int i;
1250	>	char* id;
1251	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1252	>	LinkedMolStamp* currentStamp = NULL;
1253	>	comp_stamps = new MoleculeStamp * [n_components];
1254	>
1255	>	// make an array of molecule stamps that match the components used.
1256	>	// also extract the used stamps out into a separate linked list
1257	>
1258	>	for (i = 0; i < nInfo; i++){
1259	>	info[i].nComponents = n_components;
1260	>	info[i].componentsNmol = components_nmol;
1261	>	info[i].compStamps = comp_stamps;
1262	>	info[i].headStamp = headStamp;
1263	>	}
1264	>
1265	>
1266	>	for (i = 0; i < n_components; i++){
1267	>	id = the_components[i]->getType();
1268	>	comp_stamps[i] = NULL;
1269	>
1270	>	// check to make sure the component isn't already in the list
1271	>
1272	>	comp_stamps[i] = headStamp->match(id);
1273	>	if (comp_stamps[i] == NULL){
1274	>	// extract the component from the list;
1275	>
1276	>	currentStamp = stamps->extractMolStamp(id);
1277	>	if (currentStamp == NULL){
1278	>	sprintf(painCave.errMsg,
1279	>	"SimSetup error: Component \"%s\" was not found in the "
1280	>	"list of declared molecules\n",
1281	>	id);
1282	>	painCave.isFatal = 1;
1283	>	simError();
1284		}
1285	+
1286	+	headStamp->add(currentStamp);
1287	+	comp_stamps[i] = headStamp->match(id);
1288		}
1289		}
1290
1291	<	if( have_extra ){
1292	<	done = 0;
1291	>	#ifdef IS_MPI
1292	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1293	>	MPIcheckPoint();
1294	>	#endif // is_mpi
1295	>	}
1296
1297	<	int start_ndx;
1298	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1330	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1297	>	void SimSetup::calcSysValues(void){
1298	>	int i;
1299
1300	<	if( i < n_cells ){
1300	>	int* molMembershipArray;
1301
1302	<	if( j < n_cells ){
1303	<	start_ndx = n_cells;
1304	<	}
1305	<	else start_ndx = 0;
1306	<	}
1307	<	else start_ndx = 0;
1302	>	tot_atoms = 0;
1303	>	tot_bonds = 0;
1304	>	tot_bends = 0;
1305	>	tot_torsions = 0;
1306	>	tot_rigid = 0;
1307	>	for (i = 0; i < n_components; i++){
1308	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1309	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1310	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1311	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1312	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1313	>	}
1314	>
1315	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1316	>	molMembershipArray = new int[tot_atoms];
1317
1318	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1318	>	for (i = 0; i < nInfo; i++){
1319	>	info[i].n_atoms = tot_atoms;
1320	>	info[i].n_bonds = tot_bonds;
1321	>	info[i].n_bends = tot_bends;
1322	>	info[i].n_torsions = tot_torsions;
1323	>	info[i].n_SRI = tot_SRI;
1324	>	info[i].n_mol = tot_nmol;
1325
1326	<	makeElement( i * cellx,
1327	<	j * celly,
1328	<	k * cellz );
1346	<	done = ( current_mol >= tot_nmol );
1326	>	info[i].molMembershipArray = molMembershipArray;
1327	>	}
1328	>	}
1329
1330	<	if( !done && n_per_extra > 1 ){
1349	<	makeElement( i * cellx + 0.5 * cellx,
1350	<	j * celly + 0.5 * celly,
1351	<	k * cellz );
1352	<	done = ( current_mol >= tot_nmol );
1353	<	}
1330	>	#ifdef IS_MPI
1331
1332	<	if( !done && n_per_extra > 2){
1333	<	makeElement( i * cellx,
1334	<	j * celly + 0.5 * celly,
1335	<	k * cellz + 0.5 * cellz );
1336	<	done = ( current_mol >= tot_nmol );
1360	<	}
1332	>	void SimSetup::mpiMolDivide(void){
1333	>	int i, j, k;
1334	>	int localMol, allMol;
1335	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1336	>	int local_rigid;
1337
1338	<	if( !done && n_per_extra > 3){
1339	<	makeElement( i * cellx + 0.5 * cellx,
1340	<	j * celly,
1341	<	k * cellz + 0.5 * cellz );
1342	<	done = ( current_mol >= tot_nmol );
1343	<	}
1344	<	}
1338	>	mpiSim = new mpiSimulation(info);
1339	>
1340	>	globalIndex = mpiSim->divideLabor();
1341	>
1342	>	// set up the local variables
1343	>
1344	>	mol2proc = mpiSim->getMolToProcMap();
1345	>	molCompType = mpiSim->getMolComponentType();
1346	>
1347	>	allMol = 0;
1348	>	localMol = 0;
1349	>	local_atoms = 0;
1350	>	local_bonds = 0;
1351	>	local_bends = 0;
1352	>	local_torsions = 0;
1353	>	local_rigid = 0;
1354	>	globalAtomIndex = 0;
1355	>
1356	>	for (i = 0; i < n_components; i++){
1357	>	for (j = 0; j < components_nmol[i]; j++){
1358	>	if (mol2proc[allMol] == worldRank){
1359	>	local_atoms += comp_stamps[i]->getNAtoms();
1360	>	local_bonds += comp_stamps[i]->getNBonds();
1361	>	local_bends += comp_stamps[i]->getNBends();
1362	>	local_torsions += comp_stamps[i]->getNTorsions();
1363	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1364	>	localMol++;
1365	>	}
1366	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1367	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1368	>	globalAtomIndex++;
1369		}
1370	+
1371	+	allMol++;
1372		}
1373		}
1374	+	local_SRI = local_bonds + local_bends + local_torsions;
1375
1376	+	info[0].n_atoms = mpiSim->getMyNlocal();
1377	+
1378
1379	<	for( i=0; i<simnfo->n_atoms; i++ ){
1380	<	simnfo->atoms[i]->set_vx( 0.0 );
1381	<	simnfo->atoms[i]->set_vy( 0.0 );
1382	<	simnfo->atoms[i]->set_vz( 0.0 );
1379	>	if (local_atoms != info[0].n_atoms){
1380	>	sprintf(painCave.errMsg,
1381	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1382	>	"\tlocalAtom (%d) are not equal.\n",
1383	>	info[0].n_atoms, local_atoms);
1384	>	painCave.isFatal = 1;
1385	>	simError();
1386		}
1387	+
1388	+	info[0].n_bonds = local_bonds;
1389	+	info[0].n_bends = local_bends;
1390	+	info[0].n_torsions = local_torsions;
1391	+	info[0].n_SRI = local_SRI;
1392	+	info[0].n_mol = localMol;
1393	+
1394	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1395	+	MPIcheckPoint();
1396		}
1397
1398	<	void SimSetup::makeElement( double x, double y, double z ){
1398	>	#endif // is_mpi
1399
1383	–	int k;
1384	–	AtomStamp* current_atom;
1385	–	DirectionalAtom* dAtom;
1386	–	double rotMat[3][3];
1400
1401	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1401	>	void SimSetup::makeSysArrays(void){
1402	>
1403	>	#ifndef IS_MPI
1404	>	int k, j;
1405	>	#endif // is_mpi
1406	>	int i, l;
1407
1408	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1409	<	if( !current_atom->havePosition() ){
1392	<	sprintf( painCave.errMsg,
1393	<	"SimSetup:initFromBass error.\n"
1394	<	"\tComponent %s, atom %s does not have a position specified.\n"
1395	<	"\tThe initialization routine is unable to give a start"
1396	<	" position.\n",
1397	<	comp_stamps[current_comp]->getID(),
1398	<	current_atom->getType() );
1399	<	painCave.isFatal = 1;
1400	<	simError();
1401	<	}
1408	>	Atom** the_atoms;
1409	>	Molecule* the_molecules;
1410
1411	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1412	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1405	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1411	>	for (l = 0; l < nInfo; l++){
1412	>	// create the atom and short range interaction arrays
1413
1414	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1414	>	the_atoms = new Atom * [info[l].n_atoms];
1415	>	the_molecules = new Molecule[info[l].n_mol];
1416	>	int molIndex;
1417
1418	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1418	>	// initialize the molecule's stampID's
1419
1420	<	rotMat[0][0] = 1.0;
1412	<	rotMat[0][1] = 0.0;
1413	<	rotMat[0][2] = 0.0;
1420	>	#ifdef IS_MPI
1421
1415	–	rotMat[1][0] = 0.0;
1416	–	rotMat[1][1] = 1.0;
1417	–	rotMat[1][2] = 0.0;
1422
1423	<	rotMat[2][0] = 0.0;
1424	<	rotMat[2][1] = 0.0;
1425	<	rotMat[2][2] = 1.0;
1423	>	molIndex = 0;
1424	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1425	>	if (mol2proc[i] == worldRank){
1426	>	the_molecules[molIndex].setStampID(molCompType[i]);
1427	>	the_molecules[molIndex].setMyIndex(molIndex);
1428	>	the_molecules[molIndex].setGlobalIndex(i);
1429	>	molIndex++;
1430	>	}
1431	>	}
1432
1433	<	dAtom->setA( rotMat );
1433	>	#else // is_mpi
1434	>
1435	>	molIndex = 0;
1436	>	globalAtomIndex = 0;
1437	>	for (i = 0; i < n_components; i++){
1438	>	for (j = 0; j < components_nmol[i]; j++){
1439	>	the_molecules[molIndex].setStampID(i);
1440	>	the_molecules[molIndex].setMyIndex(molIndex);
1441	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1442	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1443	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1444	>	globalAtomIndex++;
1445	>	}
1446	>	molIndex++;
1447	>	}
1448		}
1449
1426	–	current_atom_ndx++;
1427	–	}
1450
1451	<	current_mol++;
1430	<	current_comp_mol++;
1451	>	#endif // is_mpi
1452
1453	<	if( current_comp_mol >= components_nmol[current_comp] ){
1453	>	info[l].globalExcludes = new int;
1454	>	info[l].globalExcludes[0] = 0;
1455	>
1456	>	// set the arrays into the SimInfo object
1457
1458	<	current_comp_mol = 0;
1459	<	current_comp++;
1458	>	info[l].atoms = the_atoms;
1459	>	info[l].molecules = the_molecules;
1460	>	info[l].nGlobalExcludes = 0;
1461	>
1462	>	the_ff->setSimInfo(info);
1463		}
1464		}
1465	+
1466	+	void SimSetup::makeIntegrator(void){
1467	+	int k;
1468	+
1469	+	NVE<RealIntegrator>* myNVE = NULL;
1470	+	NVT<RealIntegrator>* myNVT = NULL;
1471	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1472	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1473	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1474	+
1475	+	for (k = 0; k < nInfo; k++){
1476	+	switch (ensembleCase){
1477	+	case NVE_ENS:
1478	+	if (globals->haveZconstraints()){
1479	+	setupZConstraint(info[k]);
1480	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1481	+	}
1482	+	else{
1483	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1484	+	}
1485	+
1486	+	info->the_integrator = myNVE;
1487	+	break;
1488	+
1489	+	case NVT_ENS:
1490	+	if (globals->haveZconstraints()){
1491	+	setupZConstraint(info[k]);
1492	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1493	+	}
1494	+	else
1495	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1496	+
1497	+	myNVT->setTargetTemp(globals->getTargetTemp());
1498	+
1499	+	if (globals->haveTauThermostat())
1500	+	myNVT->setTauThermostat(globals->getTauThermostat());
1501	+	else{
1502	+	sprintf(painCave.errMsg,
1503	+	"SimSetup error: If you use the NVT\n"
1504	+	"\tensemble, you must set tauThermostat.\n");
1505	+	painCave.isFatal = 1;
1506	+	simError();
1507	+	}
1508	+
1509	+	info->the_integrator = myNVT;
1510	+	break;
1511	+
1512	+	case NPTi_ENS:
1513	+	if (globals->haveZconstraints()){
1514	+	setupZConstraint(info[k]);
1515	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1516	+	}
1517	+	else
1518	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1519	+
1520	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1521	+
1522	+	if (globals->haveTargetPressure())
1523	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1524	+	else{
1525	+	sprintf(painCave.errMsg,
1526	+	"SimSetup error: If you use a constant pressure\n"
1527	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1528	+	painCave.isFatal = 1;
1529	+	simError();
1530	+	}
1531	+
1532	+	if (globals->haveTauThermostat())
1533	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1534	+	else{
1535	+	sprintf(painCave.errMsg,
1536	+	"SimSetup error: If you use an NPT\n"
1537	+	"\tensemble, you must set tauThermostat.\n");
1538	+	painCave.isFatal = 1;
1539	+	simError();
1540	+	}
1541	+
1542	+	if (globals->haveTauBarostat())
1543	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1544	+	else{
1545	+	sprintf(painCave.errMsg,
1546	+	"SimSetup error: If you use an NPT\n"
1547	+	"\tensemble, you must set tauBarostat.\n");
1548	+	painCave.isFatal = 1;
1549	+	simError();
1550	+	}
1551	+
1552	+	info->the_integrator = myNPTi;
1553	+	break;
1554	+
1555	+	case NPTf_ENS:
1556	+	if (globals->haveZconstraints()){
1557	+	setupZConstraint(info[k]);
1558	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1559	+	}
1560	+	else
1561	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1562	+
1563	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1564	+
1565	+	if (globals->haveTargetPressure())
1566	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1567	+	else{
1568	+	sprintf(painCave.errMsg,
1569	+	"SimSetup error: If you use a constant pressure\n"
1570	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1571	+	painCave.isFatal = 1;
1572	+	simError();
1573	+	}
1574	+
1575	+	if (globals->haveTauThermostat())
1576	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1577	+
1578	+	else{
1579	+	sprintf(painCave.errMsg,
1580	+	"SimSetup error: If you use an NPT\n"
1581	+	"\tensemble, you must set tauThermostat.\n");
1582	+	painCave.isFatal = 1;
1583	+	simError();
1584	+	}
1585	+
1586	+	if (globals->haveTauBarostat())
1587	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1588	+
1589	+	else{
1590	+	sprintf(painCave.errMsg,
1591	+	"SimSetup error: If you use an NPT\n"
1592	+	"\tensemble, you must set tauBarostat.\n");
1593	+	painCave.isFatal = 1;
1594	+	simError();
1595	+	}
1596	+
1597	+	info->the_integrator = myNPTf;
1598	+	break;
1599	+
1600	+	case NPTxyz_ENS:
1601	+	if (globals->haveZconstraints()){
1602	+	setupZConstraint(info[k]);
1603	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1604	+	}
1605	+	else
1606	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1607	+
1608	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1609	+
1610	+	if (globals->haveTargetPressure())
1611	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1612	+	else{
1613	+	sprintf(painCave.errMsg,
1614	+	"SimSetup error: If you use a constant pressure\n"
1615	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1616	+	painCave.isFatal = 1;
1617	+	simError();
1618	+	}
1619	+
1620	+	if (globals->haveTauThermostat())
1621	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1622	+	else{
1623	+	sprintf(painCave.errMsg,
1624	+	"SimSetup error: If you use an NPT\n"
1625	+	"\tensemble, you must set tauThermostat.\n");
1626	+	painCave.isFatal = 1;
1627	+	simError();
1628	+	}
1629	+
1630	+	if (globals->haveTauBarostat())
1631	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1632	+	else{
1633	+	sprintf(painCave.errMsg,
1634	+	"SimSetup error: If you use an NPT\n"
1635	+	"\tensemble, you must set tauBarostat.\n");
1636	+	painCave.isFatal = 1;
1637	+	simError();
1638	+	}
1639	+
1640	+	info->the_integrator = myNPTxyz;
1641	+	break;
1642	+
1643	+	default:
1644	+	sprintf(painCave.errMsg,
1645	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1646	+	painCave.isFatal = 1;
1647	+	simError();
1648	+	}
1649	+	}
1650	+	}
1651	+
1652	+	void SimSetup::initFortran(void){
1653	+	info[0].refreshSim();
1654	+
1655	+	if (!strcmp(info[0].mixingRule, "standard")){
1656	+	the_ff->initForceField(LB_MIXING_RULE);
1657	+	}
1658	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1659	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1660	+	}
1661	+	else{
1662	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1663	+	info[0].mixingRule);
1664	+	painCave.isFatal = 1;
1665	+	simError();
1666	+	}
1667	+
1668	+
1669	+	#ifdef IS_MPI
1670	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1671	+	MPIcheckPoint();
1672	+	#endif // is_mpi
1673	+	}
1674	+
1675	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1676	+	int nZConstraints;
1677	+	ZconStamp** zconStamp;
1678	+
1679	+	if (globals->haveZconstraintTime()){
1680	+	//add sample time of z-constraint  into SimInfo's property list
1681	+	DoubleData* zconsTimeProp = new DoubleData();
1682	+	zconsTimeProp->setID(ZCONSTIME_ID);
1683	+	zconsTimeProp->setData(globals->getZconsTime());
1684	+	theInfo.addProperty(zconsTimeProp);
1685	+	}
1686	+	else{
1687	+	sprintf(painCave.errMsg,
1688	+	"ZConstraint error: If you use a ZConstraint,\n"
1689	+	"\tyou must set zconsTime.\n");
1690	+	painCave.isFatal = 1;
1691	+	simError();
1692	+	}
1693	+
1694	+	//push zconsTol into siminfo, if user does not specify
1695	+	//value for zconsTol, a default value will be used
1696	+	DoubleData* zconsTol = new DoubleData();
1697	+	zconsTol->setID(ZCONSTOL_ID);
1698	+	if (globals->haveZconsTol()){
1699	+	zconsTol->setData(globals->getZconsTol());
1700	+	}
1701	+	else{
1702	+	double defaultZConsTol = 0.01;
1703	+	sprintf(painCave.errMsg,
1704	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1705	+	"\tOOPSE will use a default value of %f.\n"
1706	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1707	+	defaultZConsTol);
1708	+	painCave.isFatal = 0;
1709	+	simError();
1710	+
1711	+	zconsTol->setData(defaultZConsTol);
1712	+	}
1713	+	theInfo.addProperty(zconsTol);
1714	+
1715	+	//set Force Subtraction Policy
1716	+	StringData* zconsForcePolicy = new StringData();
1717	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1718	+
1719	+	if (globals->haveZconsForcePolicy()){
1720	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1721	+	}
1722	+	else{
1723	+	sprintf(painCave.errMsg,
1724	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1725	+	"\tOOPSE will use PolicyByMass.\n"
1726	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1727	+	painCave.isFatal = 0;
1728	+	simError();
1729	+	zconsForcePolicy->setData("BYMASS");
1730	+	}
1731	+
1732	+	theInfo.addProperty(zconsForcePolicy);
1733	+
1734	+	//set zcons gap
1735	+	DoubleData* zconsGap = new DoubleData();
1736	+	zconsGap->setID(ZCONSGAP_ID);
1737	+
1738	+	if (globals->haveZConsGap()){
1739	+	zconsGap->setData(globals->getZconsGap());
1740	+	theInfo.addProperty(zconsGap);
1741	+	}
1742	+
1743	+	//set zcons fixtime
1744	+	DoubleData* zconsFixtime = new DoubleData();
1745	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1746	+
1747	+	if (globals->haveZConsFixTime()){
1748	+	zconsFixtime->setData(globals->getZconsFixtime());
1749	+	theInfo.addProperty(zconsFixtime);
1750	+	}
1751	+
1752	+	//set zconsUsingSMD
1753	+	IntData* zconsUsingSMD = new IntData();
1754	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1755	+
1756	+	if (globals->haveZConsUsingSMD()){
1757	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1758	+	theInfo.addProperty(zconsUsingSMD);
1759	+	}
1760	+
1761	+	//Determine the name of ouput file and add it into SimInfo's property list
1762	+	//Be careful, do not use inFileName, since it is a pointer which
1763	+	//point to a string at master node, and slave nodes do not contain that string
1764	+
1765	+	string zconsOutput(theInfo.finalName);
1766	+
1767	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1768	+
1769	+	StringData* zconsFilename = new StringData();
1770	+	zconsFilename->setID(ZCONSFILENAME_ID);
1771	+	zconsFilename->setData(zconsOutput);
1772	+
1773	+	theInfo.addProperty(zconsFilename);
1774	+
1775	+	//setup index, pos and other parameters of z-constraint molecules
1776	+	nZConstraints = globals->getNzConstraints();
1777	+	theInfo.nZconstraints = nZConstraints;
1778	+
1779	+	zconStamp = globals->getZconStamp();
1780	+	ZConsParaItem tempParaItem;
1781	+
1782	+	ZConsParaData* zconsParaData = new ZConsParaData();
1783	+	zconsParaData->setID(ZCONSPARADATA_ID);
1784	+
1785	+	for (int i = 0; i < nZConstraints; i++){
1786	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1787	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1788	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1789	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1790	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1791	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1792	+	zconsParaData->addItem(tempParaItem);
1793	+	}
1794	+
1795	+	//check the uniqueness of index
1796	+	if(!zconsParaData->isIndexUnique()){
1797	+	sprintf(painCave.errMsg,
1798	+	"ZConstraint Error: molIndex is not unique!\n");
1799	+	painCave.isFatal = 1;
1800	+	simError();
1801	+	}
1802	+
1803	+	//sort the parameters by index of molecules
1804	+	zconsParaData->sortByIndex();
1805	+
1806	+	//push data into siminfo, therefore, we can retrieve later
1807	+	theInfo.addProperty(zconsParaData);
1808	+	}
1809	+
1810	+	void SimSetup::makeMinimizer(){
1811	+
1812	+	OOPSEMinimizer* myOOPSEMinimizer;
1813	+	MinimizerParameterSet* param;
1814	+	char minimizerName[100];
1815	+
1816	+	for (int i = 0; i < nInfo; i++){
1817	+
1818	+	//prepare parameter set for minimizer
1819	+	param = new MinimizerParameterSet();
1820	+	param->setDefaultParameter();
1821	+
1822	+	if (globals->haveMinimizer()){
1823	+	param->setFTol(globals->getMinFTol());
1824	+	}
1825	+
1826	+	if (globals->haveMinGTol()){
1827	+	param->setGTol(globals->getMinGTol());
1828	+	}
1829	+
1830	+	if (globals->haveMinMaxIter()){
1831	+	param->setMaxIteration(globals->getMinMaxIter());
1832	+	}
1833	+
1834	+	if (globals->haveMinWriteFrq()){
1835	+	param->setMaxIteration(globals->getMinMaxIter());
1836	+	}
1837	+
1838	+	if (globals->haveMinWriteFrq()){
1839	+	param->setWriteFrq(globals->getMinWriteFrq());
1840	+	}
1841	+
1842	+	if (globals->haveMinStepSize()){
1843	+	param->setStepSize(globals->getMinStepSize());
1844	+	}
1845	+
1846	+	if (globals->haveMinLSMaxIter()){
1847	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1848	+	}
1849	+
1850	+	if (globals->haveMinLSTol()){
1851	+	param->setLineSearchTol(globals->getMinLSTol());
1852	+	}
1853	+
1854	+	strcpy(minimizerName, globals->getMinimizer());
1855	+
1856	+	if (!strcasecmp(minimizerName, "CG")){
1857	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1858	+	}
1859	+	else if (!strcasecmp(minimizerName, "SD")){
1860	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1861	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1862	+	}
1863	+	else{
1864	+	sprintf(painCave.errMsg,
1865	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1866	+	painCave.isFatal = 0;
1867	+	simError();
1868	+
1869	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1870	+	}
1871	+	info[i].the_integrator = myOOPSEMinimizer;
1872	+
1873	+	//store the minimizer into simInfo
1874	+	info[i].the_minimizer = myOOPSEMinimizer;
1875	+	info[i].has_minimizer = true;
1876	+	}
1877	+
1878	+	}

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