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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 558 by mmeineke, Thu Jun 19 19:21:23 2003 UTC vs.
Revision 1180 by chrisfen, Thu May 20 20:24:07 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 NPT_ENS 2
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
21	–	#define FF_DUFF 0
22	–	#define FF_LJ   1
29
30	+	#define FF_DUFF  0
31	+	#define FF_LJ    1
32	+	#define FF_EAM   2
33	+	#define FF_H2O   3
34
35	+	using namespace std;
36	+
37	+	/**
38	+	* Check whether dividend is divisble by divisor or not
39	+	*/
40	+	bool isDivisible(double dividend, double divisor){
41	+	double tolerance = 0.000001;
42	+	double quotient;
43	+	double diff;
44	+	int intQuotient;
45	+
46	+	quotient = dividend / divisor;
47	+
48	+	if (quotient < 0)
49	+	quotient = -quotient;
50	+
51	+	intQuotient = int (quotient + tolerance);
52	+
53	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
54	+
55	+	if (diff <= tolerance)
56	+	return true;
57	+	else
58	+	return false;
59	+	}
60	+
61		SimSetup::SimSetup(){
62	+
63	+	initSuspend = false;
64	+	isInfoArray = 0;
65	+	nInfo = 1;
66	+
67		stamps = new MakeStamps();
68		globals = new Globals();
69	<
69	>
70	>
71		#ifdef IS_MPI
72	<	strcpy( checkPointMsg, "SimSetup creation successful" );
72	>	strcpy(checkPointMsg, "SimSetup creation successful");
73		MPIcheckPoint();
74		#endif // IS_MPI
75		}
#	Line 37 | Line 79 | SimSetup::~SimSetup(){
79		delete globals;
80		}
81
82	<	void SimSetup::parseFile( char* fileName ){
82	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
83	>	info = the_info;
84	>	nInfo = theNinfo;
85	>	isInfoArray = 1;
86	>	initSuspend = true;
87	>	}
88
89	+
90	+	void SimSetup::parseFile(char* fileName){
91		#ifdef IS_MPI
92	<	if( worldRank == 0 ){
92	>	if (worldRank == 0){
93		#endif // is_mpi
94	<
94	>
95		inFileName = fileName;
96	<	set_interface_stamps( stamps, globals );
97	<
96	>	set_interface_stamps(stamps, globals);
97	>
98		#ifdef IS_MPI
99		mpiEventInit();
100		#endif
101
102	<	yacc_BASS( fileName );
102	>	yacc_BASS(fileName);
103
104		#ifdef IS_MPI
105		throwMPIEvent(NULL);
106		}
107	<	else receiveParse();
107	>	else{
108	>	receiveParse();
109	>	}
110		#endif
111
112		}
113
114		#ifdef IS_MPI
115		void SimSetup::receiveParse(void){
116	<
117	<	set_interface_stamps( stamps, globals );
118	<	mpiEventInit();
119	<	MPIcheckPoint();
69	<	mpiEventLoop();
70	<
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;
78	<	Globals* the_globals;
79	<	int i, j, k, globalAtomIndex;
80	<
81	<	int ensembleCase;
82	<	int ffCase;
83	<
84	<	ensembleCase = -1;
85	<	ffCase = -1;
126	>	// gather all of the information from the Bass file
127
128	<	// get the stamps and globals;
88	<	the_stamps = stamps;
89	<	the_globals = globals;
128	>	gatherInfo();
129
130	<	// set the easy ones first
92	<	simnfo->target_temp = the_globals->getTargetTemp();
93	<	simnfo->dt = the_globals->getDt();
94	<	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.
97	<	n_components = the_globals->getNComponents();
98	<	strcpy( force_field, the_globals->getForceField() );
132	>	sysObjectsCreation();
133
134	<	if( !strcasecmp( force_field, "DUFF" ))    ffCase = FF_DUFF;
101	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
102	<	else{
103	<	sprintf( painCave.errMsg,
104	<	"SimSetup Error. Unrecognized force field -> %s\n",
105	<	force_field );
106	<	painCave.isFatal = 1;
107	<	simError();
108	<	}
134	>	// check on the post processing info
135
136	<	// get the ensemble:
111	<	strcpy( ensemble, the_globals->getEnsemble() );
136	>	finalInfoCheck();
137
138	<	if( !strcasecmp( ensemble, "NVE" ))      ffCase = NVE_ENS;
139	<	else if( !strcasecmp( ensemble, "NVT" )) ffCase = NVT_ENS;
140	<	else if( !strcasecmp( ensemble, "NPT" )) ffCase = NPT_ENS;
141	<	else{
142	<	sprintf( painCave.errMsg,
143	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
144	<	"reverting to NVE for this simulation.\n",
120	<	ensemble );
121	<	painCave.isFatal = 0;
122	<	simError();
123	<	strcpy( ensemble, "NVE" );
124	<	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		}
126	–	strcpy( simnfo->ensemble, ensemble );
146
147	+	// make the output filenames
148
149	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
150	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
151	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
152	<	//     if (the_globals->haveTargetPressure())
153	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
134	<	//     else {
135	<	//       sprintf( painCave.errMsg,
136	<	//                "SimSetup error: If you use the constant pressure\n"
137	<	//                "    ensemble, you must set targetPressure.\n"
138	<	//                "    This was found in the BASS file.\n");
139	<	//       painCave.isFatal = 1;
140	<	//       simError();
141	<	//     }
149	>	makeOutNames();
150	>
151	>	#ifdef IS_MPI
152	>	mpiSim->mpiRefresh();
153	>	#endif
154
155	<	//     if (the_globals->haveTauThermostat())
144	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
145	<	//     else if (the_globals->haveQmass())
146	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
147	<	//     else {
148	<	//       sprintf( painCave.errMsg,
149	<	//                "SimSetup error: If you use one of the constant temperature\n"
150	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
151	<	//                "    Neither of these was found in the BASS file.\n");
152	<	//       painCave.isFatal = 1;
153	<	//       simError();
154	<	//     }
155	>	// initialize the Fortran
156
157	<	//     if (the_globals->haveTauBarostat())
157	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
158	<	//     else {
159	<	//       sprintf( painCave.errMsg,
160	<	//                "SimSetup error: If you use the constant pressure\n"
161	<	//                "    ensemble, you must set tauBarostat.\n"
162	<	//                "    This was found in the BASS file.\n");
163	<	//       painCave.isFatal = 1;
164	<	//       simError();
165	<	//     }
157	>	initFortran();
158
159	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
160	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
161	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
159	>	if (globals->haveMinimizer())
160	>	// make minimizer
161	>	makeMinimizer();
162	>	else
163	>	// make the integrator
164	>	makeIntegrator();
165
166	<	//     if (the_globals->haveTauThermostat())
172	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
173	<	//     else if (the_globals->haveQmass())
174	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
175	<	//     else {
176	<	//       sprintf( painCave.errMsg,
177	<	//                "SimSetup error: If you use one of the constant temperature\n"
178	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
179	<	//                "    Neither of these was found in the BASS file.\n");
180	<	//       painCave.isFatal = 1;
181	<	//       simError();
182	<	//     }
166	>	}
167
184	–	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
185	–	simnfo->usePBC = the_globals->getPBC();
186	–
187	–	int usesDipoles = 0;
188	–	switch( ffCase ){
168
169	<	case FF_DUFF:
170	<	the_ff = new DUFF();
171	<	usesDipoles = 1;
172	<	break;
169	>	void SimSetup::makeMolecules(void){
170	>	int i, j, k;
171	>	int exI, exJ, exK, exL, slI, slJ;
172	>	int tempI, tempJ, tempK, tempL;
173	>	int molI;
174	>	int stampID, atomOffset, rbOffset;
175	>	molInit molInfo;
176	>	DirectionalAtom* dAtom;
177	>	RigidBody* myRB;
178	>	StuntDouble* mySD;
179	>	LinkedAssign* extras;
180	>	LinkedAssign* current_extra;
181	>	AtomStamp* currentAtom;
182	>	BondStamp* currentBond;
183	>	BendStamp* currentBend;
184	>	TorsionStamp* currentTorsion;
185	>	RigidBodyStamp* currentRigidBody;
186	>	CutoffGroupStamp* currentCutoffGroup;
187	>	CutoffGroup* myCutoffGroup;
188	>	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
189	>	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
190
191	<	case FF_LJ:
192	<	the_ff = LJFF();
193	<	break;
191	>	bond_pair* theBonds;
192	>	bend_set* theBends;
193	>	torsion_set* theTorsions;
194
195	<	default:
200	<	sprintf( painCave.errMsg,
201	<	"SimSetup Error. Unrecognized force field in case statement.\n");
202	<	painCave.isFatal = 1;
203	<	simError();
204	<	}
195	>	set<int> skipList;
196
197	<	#ifdef IS_MPI
198	<	strcpy( checkPointMsg, "ForceField creation successful" );
199	<	MPIcheckPoint();
209	<	#endif // is_mpi
197	>	double phi, theta, psi;
198	>	char* molName;
199	>	char rbName[100];
200
201	<	// get the components and calculate the tot_nMol and indvidual n_mol
212	<	the_components = the_globals->getComponents();
213	<	components_nmol = new int[n_components];
214	<	comp_stamps = new MoleculeStamp*[n_components];
201	>	//init the forceField paramters
202
203	<	if( !the_globals->haveNMol() ){
217	<	// we don't have the total number of molecules, so we assume it is
218	<	// given in each component
203	>	the_ff->readParams();
204
205	<	tot_nmol = 0;
221	<	for( i=0; i<n_components; i++ ){
205	>	// init the atoms
206
207	<	if( !the_components[i]->haveNMol() ){
208	<	// we have a problem
209	<	sprintf( painCave.errMsg,
210	<	"SimSetup Error. No global NMol or component NMol"
211	<	" given. Cannot calculate the number of atoms.\n" );
212	<	painCave.isFatal = 1;
213	<	simError();
214	<	}
207	>	int nMembers, nNew, rb1, rb2;
208	>
209	>	for (k = 0; k < nInfo; k++){
210	>	the_ff->setSimInfo(&(info[k]));
211	>
212	>	atomOffset = 0;
213	>
214	>	for (i = 0; i < info[k].n_mol; i++){
215	>	stampID = info[k].molecules[i].getStampID();
216	>	molName = comp_stamps[stampID]->getID();
217
218	<	tot_nmol += the_components[i]->getNMol();
219	<	components_nmol[i] = the_components[i]->getNMol();
220	<	}
221	<	}
222	<	else{
237	<	sprintf( painCave.errMsg,
238	<	"SimSetup error.\n"
239	<	"\tSorry, the ability to specify total"
240	<	" nMols and then give molfractions in the components\n"
241	<	"\tis not currently supported."
242	<	" Please give nMol in the components.\n" );
243	<	painCave.isFatal = 1;
244	<	simError();
245	<
246	<
247	<	//     tot_nmol = the_globals->getNMol();
248	<
249	<	//   //we have the total number of molecules, now we check for molfractions
250	<	//     for( i=0; i<n_components; i++ ){
251	<
252	<	//       if( !the_components[i]->haveMolFraction() ){
253	<
254	<	//  if( !the_components[i]->haveNMol() ){
255	<	//    //we have a problem
256	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
257	<	//              << " nMol was given in component
258	<
259	<	}
218	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
219	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
220	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
221	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
222	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
223
224	<	#ifdef IS_MPI
225	<	strcpy( checkPointMsg, "Have the number of components" );
226	<	MPIcheckPoint();
264	<	#endif // is_mpi
224	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
225	>
226	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
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.nBonds > 0)
229	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
230	>	else
231	>	molInfo.myBonds = NULL;
232
233	<	simnfo->nComponents = n_components;
234	<	simnfo->componentsNmol = components_nmol;
235	<	simnfo->compStamps = comp_stamps;
236	<	simnfo->headStamp = new LinkedMolStamp();
273	<
274	<	char* id;
275	<	LinkedMolStamp* headStamp = simnfo->headStamp;
276	<	LinkedMolStamp* currentStamp = NULL;
277	<	for( i=0; i<n_components; i++ ){
233	>	if (molInfo.nBends > 0)
234	>	molInfo.myBends = new Bend*[molInfo.nBends];
235	>	else
236	>	molInfo.myBends = NULL;
237
238	<	id = the_components[i]->getType();
239	<	comp_stamps[i] = NULL;
240	<
241	<	// check to make sure the component isn't already in the list
238	>	if (molInfo.nTorsions > 0)
239	>	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
240	>	else
241	>	molInfo.myTorsions = NULL;
242
243	<	comp_stamps[i] = headStamp->match( id );
244	<	if( comp_stamps[i] == NULL ){
243	>	theBonds = new bond_pair[molInfo.nBonds];
244	>	theBends = new bend_set[molInfo.nBends];
245	>	theTorsions = new torsion_set[molInfo.nTorsions];
246
247	<	// extract the component from the list;
288	<
289	<	currentStamp = the_stamps->extractMolStamp( id );
290	<	if( currentStamp == NULL ){
291	<	sprintf( painCave.errMsg,
292	<	"SimSetup error: Component \"%s\" was not found in the "
293	<	"list of declared molecules\n",
294	<	id );
295	<	painCave.isFatal = 1;
296	<	simError();
297	<	}
298	<
299	<	headStamp->add( currentStamp );
300	<	comp_stamps[i] = headStamp->match( id );
301	<	}
302	<	}
247	>	// make the Atoms
248
249	<	#ifdef IS_MPI
250	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
306	<	MPIcheckPoint();
307	<	#endif // is_mpi
308	<
249	>	for (j = 0; j < molInfo.nAtoms; j++){
250	>	currentAtom = comp_stamps[stampID]->getAtom(j);
251
252	+	if (currentAtom->haveOrientation()){
253	+	dAtom = new DirectionalAtom((j + atomOffset),
254	+	info[k].getConfiguration());
255	+	info[k].n_oriented++;
256	+	molInfo.myAtoms[j] = dAtom;
257
258	+	// Directional Atoms have standard unit vectors which are oriented
259	+	// in space using the three Euler angles.  We assume the standard
260	+	// unit vector was originally along the z axis below.
261
262	<	// caclulate the number of atoms, bonds, bends and torsions
262	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
263	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
264	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
265
266	<	tot_atoms = 0;
267	<	tot_bonds = 0;
268	<	tot_bends = 0;
269	<	tot_torsions = 0;
318	<	for( i=0; i<n_components; i++ ){
319	<
320	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
321	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
322	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
323	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
324	<	}
266	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
267	>
268	>	}
269	>	else{
270
271	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
271	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
272
273	<	simnfo->n_atoms = tot_atoms;
329	<	simnfo->n_bonds = tot_bonds;
330	<	simnfo->n_bends = tot_bends;
331	<	simnfo->n_torsions = tot_torsions;
332	<	simnfo->n_SRI = tot_SRI;
333	<	simnfo->n_mol = tot_nmol;
334	<
335	<	simnfo->molMembershipArray = new int[tot_atoms];
273	>	}
274
275	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
276		#ifdef IS_MPI
277
278	<	// divide the molecules among processors here.
340	<
341	<	mpiSim = new mpiSimulation( simnfo );
342	<
343	<	globalIndex = mpiSim->divideLabor();
278	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
279
280	<	// set up the local variables
281	<
347	<	int localMol, allMol;
348	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
280	>	#endif // is_mpi
281	>	}
282
283	<	int* mol2proc = mpiSim->getMolToProcMap();
284	<	int* molCompType = mpiSim->getMolComponentType();
285	<
286	<	allMol = 0;
287	<	localMol = 0;
355	<	local_atoms = 0;
356	<	local_bonds = 0;
357	<	local_bends = 0;
358	<	local_torsions = 0;
359	<	globalAtomIndex = 0;
283	>	// make the bonds
284	>	for (j = 0; j < molInfo.nBonds; j++){
285	>	currentBond = comp_stamps[stampID]->getBond(j);
286	>	theBonds[j].a = currentBond->getA() + atomOffset;
287	>	theBonds[j].b = currentBond->getB() + atomOffset;
288
289	+	tempI = theBonds[j].a;
290	+	tempJ = theBonds[j].b;
291
292	<	for( i=0; i<n_components; i++ ){
292	>	#ifdef IS_MPI
293	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
294	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
295	>	#else
296	>	exI = tempI + 1;
297	>	exJ = tempJ + 1;
298	>	#endif
299
300	<	for( j=0; j<components_nmol[i]; j++ ){
365	<
366	<	if( mol2proc[allMol] == worldRank ){
367	<
368	<	local_atoms +=    comp_stamps[i]->getNAtoms();
369	<	local_bonds +=    comp_stamps[i]->getNBonds();
370	<	local_bends +=    comp_stamps[i]->getNBends();
371	<	local_torsions += comp_stamps[i]->getNTorsions();
372	<	localMol++;
373	<	}
374	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
375	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
376	<	globalAtomIndex++;
300	>	info[k].excludes->addPair(exI, exJ);
301		}
302
303	<	allMol++;
304	<	}
305	<	}
306	<	local_SRI = local_bonds + local_bends + local_torsions;
307	<
308	<	simnfo->n_atoms = mpiSim->getMyNlocal();
385	<
386	<	if( local_atoms != simnfo->n_atoms ){
387	<	sprintf( painCave.errMsg,
388	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
389	<	" localAtom (%d) are not equal.\n",
390	<	simnfo->n_atoms,
391	<	local_atoms );
392	<	painCave.isFatal = 1;
393	<	simError();
394	<	}
303	>	//make the bends
304	>	for (j = 0; j < molInfo.nBends; j++){
305	>	currentBend = comp_stamps[stampID]->getBend(j);
306	>	theBends[j].a = currentBend->getA() + atomOffset;
307	>	theBends[j].b = currentBend->getB() + atomOffset;
308	>	theBends[j].c = currentBend->getC() + atomOffset;
309
310	<	simnfo->n_bonds = local_bonds;
311	<	simnfo->n_bends = local_bends;
312	<	simnfo->n_torsions = local_torsions;
399	<	simnfo->n_SRI = local_SRI;
400	<	simnfo->n_mol = localMol;
310	>	if (currentBend->haveExtras()){
311	>	extras = currentBend->getExtras();
312	>	current_extra = extras;
313
314	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
315	<	MPIcheckPoint();
316	<
317	<
318	<	#endif // is_mpi
319	<
314	>	while (current_extra != NULL){
315	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
316	>	switch (current_extra->getType()){
317	>	case 0:
318	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
319	>	theBends[j].isGhost = 1;
320	>	break;
321
322	<	// create the atom and short range interaction arrays
322	>	case 1:
323	>	theBends[j].ghost = (int) current_extra->getDouble() +
324	>	atomOffset;
325	>	theBends[j].isGhost = 1;
326	>	break;
327
328	<	Atom::createArrays(simnfo->n_atoms);
329	<	the_atoms = new Atom*[simnfo->n_atoms];
330	<	the_molecules = new Molecule[simnfo->n_mol];
331	<	int molIndex;
332	<
333	<	// initialize the molecule's stampID's
328	>	default:
329	>	sprintf(painCave.errMsg,
330	>	"SimSetup Error: ghostVectorSource was neither a "
331	>	"double nor an int.\n"
332	>	"-->Bend[%d] in %s\n",
333	>	j, comp_stamps[stampID]->getID());
334	>	painCave.isFatal = 1;
335	>	simError();
336	>	}
337	>	}
338	>	else{
339	>	sprintf(painCave.errMsg,
340	>	"SimSetup Error: unhandled bend assignment:\n"
341	>	"    -->%s in Bend[%d] in %s\n",
342	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
343	>	painCave.isFatal = 1;
344	>	simError();
345	>	}
346
347	+	current_extra = current_extra->getNext();
348	+	}
349	+	}
350	+
351	+	if (theBends[j].isGhost) {
352	+
353	+	tempI = theBends[j].a;
354	+	tempJ = theBends[j].b;
355	+
356		#ifdef IS_MPI
357	<
357	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
358	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
359	>	#else
360	>	exI = tempI + 1;
361	>	exJ = tempJ + 1;
362	>	#endif
363	>	info[k].excludes->addPair(exI, exJ);
364
365	<	molIndex = 0;
422	<	for(i=0; i<mpiSim->getTotNmol(); i++){
423	<
424	<	if(mol2proc[i] == worldRank ){
425	<	the_molecules[molIndex].setStampID( molCompType[i] );
426	<	the_molecules[molIndex].setMyIndex( molIndex );
427	<	the_molecules[molIndex].setGlobalIndex( i );
428	<	molIndex++;
429	<	}
430	<	}
365	>	} else {
366
367	<	#else // is_mpi
368	<
369	<	molIndex = 0;
370	<	globalAtomIndex = 0;
371	<	for(i=0; i<n_components; i++){
372	<	for(j=0; j<components_nmol[i]; j++ ){
373	<	the_molecules[molIndex].setStampID( i );
374	<	the_molecules[molIndex].setMyIndex( molIndex );
375	<	the_molecules[molIndex].setGlobalIndex( molIndex );
376	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
377	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
378	<	globalAtomIndex++;
367	>	tempI = theBends[j].a;
368	>	tempJ = theBends[j].b;
369	>	tempK = theBends[j].c;
370	>
371	>	#ifdef IS_MPI
372	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
373	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
374	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
375	>	#else
376	>	exI = tempI + 1;
377	>	exJ = tempJ + 1;
378	>	exK = tempK + 1;
379	>	#endif
380	>
381	>	info[k].excludes->addPair(exI, exK);
382	>	info[k].excludes->addPair(exI, exJ);
383	>	info[k].excludes->addPair(exJ, exK);
384	>	}
385		}
445	–	molIndex++;
446	–	}
447	–	}
448	–
386
387	<	#endif // is_mpi
387	>	for (j = 0; j < molInfo.nTorsions; j++){
388	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
389	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
390	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
391	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
392	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
393
394	+	tempI = theTorsions[j].a;
395	+	tempJ = theTorsions[j].b;
396	+	tempK = theTorsions[j].c;
397	+	tempL = theTorsions[j].d;
398
399	<	if( simnfo->n_SRI ){
400	<
401	<	Exclude::createArray(simnfo->n_SRI);
402	<	the_excludes = new Exclude*[simnfo->n_SRI];
403	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
404	<	simnfo->globalExcludes = new int;
405	<	simnfo->n_exclude = simnfo->n_SRI;
406	<	}
407	<	else{
408	<
409	<	Exclude::createArray( 1 );
464	<	the_excludes = new Exclude*;
465	<	the_excludes[0] = new Exclude(0);
466	<	the_excludes[0]->setPair( 0,0 );
467	<	simnfo->globalExcludes = new int;
468	<	simnfo->globalExcludes[0] = 0;
469	<	simnfo->n_exclude = 0;
470	<	}
399	>	#ifdef IS_MPI
400	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
401	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
402	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
403	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
404	>	#else
405	>	exI = tempI + 1;
406	>	exJ = tempJ + 1;
407	>	exK = tempK + 1;
408	>	exL = tempL + 1;
409	>	#endif
410
411	<	// set the arrays into the SimInfo object
411	>	info[k].excludes->addPair(exI, exJ);
412	>	info[k].excludes->addPair(exI, exK);
413	>	info[k].excludes->addPair(exI, exL);
414	>	info[k].excludes->addPair(exJ, exK);
415	>	info[k].excludes->addPair(exJ, exL);
416	>	info[k].excludes->addPair(exK, exL);
417	>	}
418
419	<	simnfo->atoms = the_atoms;
420	<	simnfo->molecules = the_molecules;
421	<	simnfo->nGlobalExcludes = 0;
422	<	simnfo->excludes = the_excludes;
419	>
420	>	molInfo.myRigidBodies.clear();
421	>
422	>	for (j = 0; j < molInfo.nRigidBodies; j++){
423
424	+	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
425	+	nMembers = currentRigidBody->getNMembers();
426
427	<	// get some of the tricky things that may still be in the globals
427	>	// Create the Rigid Body:
428
429	<
483	<	if( the_globals->haveBox() ){
484	<	simnfo->box_x = the_globals->getBox();
485	<	simnfo->box_y = the_globals->getBox();
486	<	simnfo->box_z = the_globals->getBox();
487	<	}
488	<	else if( the_globals->haveDensity() ){
429	>	myRB = new RigidBody();
430
431	<	double vol;
432	<	vol = (double)tot_nmol / the_globals->getDensity();
433	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
434	<	simnfo->box_y = simnfo->box_x;
494	<	simnfo->box_z = simnfo->box_x;
495	<	}
496	<	else{
497	<	if( !the_globals->haveBoxX() ){
498	<	sprintf( painCave.errMsg,
499	<	"SimSetup error, no periodic BoxX size given.\n" );
500	<	painCave.isFatal = 1;
501	<	simError();
502	<	}
503	<	simnfo->box_x = the_globals->getBoxX();
431	>	sprintf(rbName,"%s_RB_%d", molName, j);
432	>	myRB->setType(rbName);
433	>
434	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
435
436	<	if( !the_globals->haveBoxY() ){
437	<	sprintf( painCave.errMsg,
507	<	"SimSetup error, no periodic BoxY size given.\n" );
508	<	painCave.isFatal = 1;
509	<	simError();
510	<	}
511	<	simnfo->box_y = the_globals->getBoxY();
436	>	// molI is atom numbering inside this molecule
437	>	molI = currentRigidBody->getMember(rb1);
438
439	<	if( !the_globals->haveBoxZ() ){
440	<	sprintf( painCave.errMsg,
515	<	"SimSetup error, no periodic BoxZ size given.\n" );
516	<	painCave.isFatal = 1;
517	<	simError();
518	<	}
519	<	simnfo->box_z = the_globals->getBoxZ();
520	<	}
439	>	// tempI is atom numbering on local processor
440	>	tempI = molI + atomOffset;
441
442	<	#ifdef IS_MPI
443	<	strcpy( checkPointMsg, "Box size set up" );
444	<	MPIcheckPoint();
525	<	#endif // is_mpi
442	>	// currentAtom is the AtomStamp (which we need for
443	>	// rigid body reference positions)
444	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
445
446	+	// When we add to the rigid body, add the atom itself and
447	+	// the stamp info:
448
449	<	// initialize the arrays
450	<
451	<	the_ff->setSimInfo( simnfo );
452	<
453	<	makeMolecules();
454	<	simnfo->identArray = new int[simnfo->n_atoms];
455	<	for(i=0; i<simnfo->n_atoms; i++){
456	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
457	<	}
458	<
459	<	if (the_globals->getUseRF() ) {
460	<	simnfo->useReactionField = 1;
461	<
462	<	if( !the_globals->haveECR() ){
463	<	sprintf( painCave.errMsg,
464	<	"SimSetup Warning: using default value of 1/2 the smallest "
465	<	"box length for the electrostaticCutoffRadius.\n"
466	<	"I hope you have a very fast processor!\n");
467	<	painCave.isFatal = 0;
468	<	simError();
469	<	double smallest;
470	<	smallest = simnfo->box_x;
471	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
472	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
473	<	simnfo->ecr = 0.5 * smallest;
474	<	} else {
475	<	simnfo->ecr        = the_globals->getECR();
476	<	}
477	<
478	<	if( !the_globals->haveEST() ){
479	<	sprintf( painCave.errMsg,
480	<	"SimSetup Warning: using default value of 0.05 * the "
481	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
482	<	);
483	<	painCave.isFatal = 0;
484	<	simError();
485	<	simnfo->est = 0.05 * simnfo->ecr;
486	<	} else {
566	<	simnfo->est        = the_globals->getEST();
567	<	}
568	<
569	<	if(!the_globals->haveDielectric() ){
570	<	sprintf( painCave.errMsg,
571	<	"SimSetup Error: You are trying to use Reaction Field without"
572	<	"setting a dielectric constant!\n"
573	<	);
574	<	painCave.isFatal = 1;
575	<	simError();
576	<	}
577	<	simnfo->dielectric = the_globals->getDielectric();
578	<	} else {
579	<	if (usesDipoles) {
580	<
581	<	if( !the_globals->haveECR() ){
582	<	sprintf( painCave.errMsg,
583	<	"SimSetup Warning: using default value of 1/2 the smallest "
584	<	"box length for the electrostaticCutoffRadius.\n"
585	<	"I hope you have a very fast processor!\n");
586	<	painCave.isFatal = 0;
587	<	simError();
588	<	double smallest;
589	<	smallest = simnfo->box_x;
590	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
591	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
592	<	simnfo->ecr = 0.5 * smallest;
593	<	} else {
594	<	simnfo->ecr        = the_globals->getECR();
449	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
450	>
451	>	// Add this atom to the Skip List for the integrators
452	>	#ifdef IS_MPI
453	>	slI = info[k].atoms[tempI]->getGlobalIndex();
454	>	#else
455	>	slI = tempI;
456	>	#endif
457	>	skipList.insert(slI);
458	>
459	>	}
460	>
461	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
462	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
463	>
464	>	tempI = currentRigidBody->getMember(rb1);
465	>	tempJ = currentRigidBody->getMember(rb2);
466	>
467	>	// Some explanation is required here.
468	>	// Fortran indexing starts at 1, while c indexing starts at 0
469	>	// Also, in parallel computations, the GlobalIndex is
470	>	// used for the exclude list:
471	>
472	>	#ifdef IS_MPI
473	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
474	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
475	>	#else
476	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
477	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
478	>	#endif
479	>
480	>	info[k].excludes->addPair(exI, exJ);
481	>
482	>	}
483	>	}
484	>
485	>	molInfo.myRigidBodies.push_back(myRB);
486	>	info[k].rigidBodies.push_back(myRB);
487		}
488
489	<	if( !the_globals->haveEST() ){
490	<	sprintf( painCave.errMsg,
491	<	"SimSetup Warning: using default value of 5%% of the "
492	<	"electrostaticCutoffRadius for the "
493	<	"electrostaticSkinThickness\n"
494	<	);
495	<	painCave.isFatal = 0;
496	<	simError();
497	<	simnfo->est = 0.05 * simnfo->ecr;
498	<	} else {
499	<	simnfo->est        = the_globals->getEST();
489	>
490	>	//create cutoff group for molecule
491	>
492	>	cutoffAtomSet.clear();
493	>	molInfo.myCutoffGroups.clear();
494	>
495	>	for (j = 0; j < nCutoffGroups; j++){
496	>
497	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
498	>	nMembers = currentCutoffGroup->getNMembers();
499	>
500	>	myCutoffGroup = new CutoffGroup();
501	>
502	>	for (int cg = 0; cg < nMembers; cg++) {
503	>
504	>	// molI is atom numbering inside this molecule
505	>	molI = currentCutoffGroup->getMember(cg);
506	>
507	>	// tempI is atom numbering on local processor
508	>	tempI = molI + atomOffset;
509	>
510	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
511	>
512	>	cutoffAtomSet.insert(tempI);
513	>	}
514	>
515	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
516	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
517	>
518	>	//creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
519	>
520	>	for(j = 0; j < molInfo.nAtoms; j++){
521	>
522	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
523	>	myCutoffGroup = new CutoffGroup();
524	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
525	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
526	>	}
527	>
528		}
609	–	}
610	–	}
529
530	<	#ifdef IS_MPI
613	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
614	<	MPIcheckPoint();
615	<	#endif // is_mpi
530	>
531
532	<	if( the_globals->haveInitialConfig() ){
533	<
534	<	InitializeFromFile* fileInit;
535	<	#ifdef IS_MPI // is_mpi
536	<	if( worldRank == 0 ){
537	<	#endif //is_mpi
538	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
532	>
533	>	// After this is all set up, scan through the atoms to
534	>	// see if they can be added to the integrableObjects:
535	>
536	>	molInfo.myIntegrableObjects.clear();
537	>
538	>
539	>	for (j = 0; j < molInfo.nAtoms; j++){
540	>
541		#ifdef IS_MPI
542	<	}else fileInit = new InitializeFromFile( NULL );
542	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
543	>	#else
544	>	slJ = j+atomOffset;
545		#endif
627	–	fileInit->read_xyz( simnfo ); // default velocities on
546
547	<	delete fileInit;
630	<	}
631	<	else{
547	>	// if they aren't on the skip list, then they can be integrated
548
549	<	#ifdef IS_MPI
549	>	if (skipList.find(slJ) == skipList.end()) {
550	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
551	>	info[k].integrableObjects.push_back(mySD);
552	>	molInfo.myIntegrableObjects.push_back(mySD);
553	>	}
554	>	}
555
556	<	// no init from bass
636	<
637	<	sprintf( painCave.errMsg,
638	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
639	<	painCave.isFatal;
640	<	simError();
641	<
642	<	#else
556	>	// all rigid bodies are integrated:
557
558	<	initFromBass();
558	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
559	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
560	>	info[k].integrableObjects.push_back(mySD);
561	>	molInfo.myIntegrableObjects.push_back(mySD);
562	>	}
563	>
564	>
565	>	// send the arrays off to the forceField for init.
566	>
567	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
568	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
569	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
570	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
571	>	theTorsions);
572
573	+	info[k].molecules[i].initialize(molInfo);
574
647	–	#endif
648	–	}
575
576	+	atomOffset += molInfo.nAtoms;
577	+	delete[] theBonds;
578	+	delete[] theBends;
579	+	delete[] theTorsions;
580	+	}
581	+	}
582	+
583		#ifdef IS_MPI
584	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
584	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
585		MPIcheckPoint();
586		#endif // is_mpi
587
588	+	}
589
590	<
591	<
592	<
590	>	void SimSetup::initFromBass(void){
591	>	int i, j, k;
592	>	int n_cells;
593	>	double cellx, celly, cellz;
594	>	double temp1, temp2, temp3;
595	>	int n_per_extra;
596	>	int n_extra;
597	>	int have_extra, done;
598
599	<
600	<	#ifdef IS_MPI
601	<	if( worldRank == 0 ){
602	<	#endif // is_mpi
603	<
604	<	if( the_globals->haveFinalConfig() ){
605	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
599	>	double vel[3];
600	>	vel[0] = 0.0;
601	>	vel[1] = 0.0;
602	>	vel[2] = 0.0;
603	>
604	>	temp1 = (double) tot_nmol / 4.0;
605	>	temp2 = pow(temp1, (1.0 / 3.0));
606	>	temp3 = ceil(temp2);
607	>
608	>	have_extra = 0;
609	>	if (temp2 < temp3){
610	>	// we have a non-complete lattice
611	>	have_extra = 1;
612	>
613	>	n_cells = (int) temp3 - 1;
614	>	cellx = info[0].boxL[0] / temp3;
615	>	celly = info[0].boxL[1] / temp3;
616	>	cellz = info[0].boxL[2] / temp3;
617	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
618	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
619	>	n_per_extra = (int) ceil(temp1);
620	>
621	>	if (n_per_extra > 4){
622	>	sprintf(painCave.errMsg,
623	>	"SimSetup error. There has been an error in constructing"
624	>	" the non-complete lattice.\n");
625	>	painCave.isFatal = 1;
626	>	simError();
627		}
668	–	else{
669	–	strcpy( simnfo->finalName, inFileName );
670	–	char* endTest;
671	–	int nameLength = strlen( simnfo->finalName );
672	–	endTest = &(simnfo->finalName[nameLength - 5]);
673	–	if( !strcmp( endTest, ".bass" ) ){
674	–	strcpy( endTest, ".eor" );
675	–	}
676	–	else if( !strcmp( endTest, ".BASS" ) ){
677	–	strcpy( endTest, ".eor" );
678	–	}
679	–	else{
680	–	endTest = &(simnfo->finalName[nameLength - 4]);
681	–	if( !strcmp( endTest, ".bss" ) ){
682	–	strcpy( endTest, ".eor" );
683	–	}
684	–	else if( !strcmp( endTest, ".mdl" ) ){
685	–	strcpy( endTest, ".eor" );
686	–	}
687	–	else{
688	–	strcat( simnfo->finalName, ".eor" );
689	–	}
690	–	}
691	–	}
692	–
693	–	// make the sample and status out names
694	–
695	–	strcpy( simnfo->sampleName, inFileName );
696	–	char* endTest;
697	–	int nameLength = strlen( simnfo->sampleName );
698	–	endTest = &(simnfo->sampleName[nameLength - 5]);
699	–	if( !strcmp( endTest, ".bass" ) ){
700	–	strcpy( endTest, ".dump" );
701	–	}
702	–	else if( !strcmp( endTest, ".BASS" ) ){
703	–	strcpy( endTest, ".dump" );
704	–	}
705	–	else{
706	–	endTest = &(simnfo->sampleName[nameLength - 4]);
707	–	if( !strcmp( endTest, ".bss" ) ){
708	–	strcpy( endTest, ".dump" );
709	–	}
710	–	else if( !strcmp( endTest, ".mdl" ) ){
711	–	strcpy( endTest, ".dump" );
712	–	}
713	–	else{
714	–	strcat( simnfo->sampleName, ".dump" );
715	–	}
716	–	}
717	–
718	–	strcpy( simnfo->statusName, inFileName );
719	–	nameLength = strlen( simnfo->statusName );
720	–	endTest = &(simnfo->statusName[nameLength - 5]);
721	–	if( !strcmp( endTest, ".bass" ) ){
722	–	strcpy( endTest, ".stat" );
723	–	}
724	–	else if( !strcmp( endTest, ".BASS" ) ){
725	–	strcpy( endTest, ".stat" );
726	–	}
727	–	else{
728	–	endTest = &(simnfo->statusName[nameLength - 4]);
729	–	if( !strcmp( endTest, ".bss" ) ){
730	–	strcpy( endTest, ".stat" );
731	–	}
732	–	else if( !strcmp( endTest, ".mdl" ) ){
733	–	strcpy( endTest, ".stat" );
734	–	}
735	–	else{
736	–	strcat( simnfo->statusName, ".stat" );
737	–	}
738	–	}
739	–
740	–	#ifdef IS_MPI
628		}
742	–	#endif // is_mpi
743	–
744	–	// set the status, sample, and themal kick times
745	–
746	–	if( the_globals->haveSampleTime() ){
747	–	simnfo->sampleTime = the_globals->getSampleTime();
748	–	simnfo->statusTime = simnfo->sampleTime;
749	–	simnfo->thermalTime = simnfo->sampleTime;
750	–	}
629		else{
630	<	simnfo->sampleTime = the_globals->getRunTime();
631	<	simnfo->statusTime = simnfo->sampleTime;
632	<	simnfo->thermalTime = simnfo->sampleTime;
630	>	n_cells = (int) temp3;
631	>	cellx = info[0].boxL[0] / temp3;
632	>	celly = info[0].boxL[1] / temp3;
633	>	cellz = info[0].boxL[2] / temp3;
634		}
635
636	<	if( the_globals->haveStatusTime() ){
637	<	simnfo->statusTime = the_globals->getStatusTime();
638	<	}
636	>	current_mol = 0;
637	>	current_comp_mol = 0;
638	>	current_comp = 0;
639	>	current_atom_ndx = 0;
640
641	<	if( the_globals->haveThermalTime() ){
642	<	simnfo->thermalTime = the_globals->getThermalTime();
641	>	for (i = 0; i < n_cells ; i++){
642	>	for (j = 0; j < n_cells; j++){
643	>	for (k = 0; k < n_cells; k++){
644	>	makeElement(i * cellx, j * celly, k * cellz);
645	>
646	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
647	>
648	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
649	>
650	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
651	>	}
652	>	}
653		}
654
655	<	// check for the temperature set flag
655	>	if (have_extra){
656	>	done = 0;
657
658	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
658	>	int start_ndx;
659	>	for (i = 0; i < (n_cells + 1) && !done; i++){
660	>	for (j = 0; j < (n_cells + 1) && !done; j++){
661	>	if (i < n_cells){
662	>	if (j < n_cells){
663	>	start_ndx = n_cells;
664	>	}
665	>	else
666	>	start_ndx = 0;
667	>	}
668	>	else
669	>	start_ndx = 0;
670
671	+	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
672	+	makeElement(i * cellx, j * celly, k * cellz);
673	+	done = (current_mol >= tot_nmol);
674
675	<	// make the integrator
675	>	if (!done && n_per_extra > 1){
676	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
677	>	k * cellz);
678	>	done = (current_mol >= tot_nmol);
679	>	}
680
681	<	switch( ensembleCase ){
681	>	if (!done && n_per_extra > 2){
682	>	makeElement(i * cellx, j * celly + 0.5 * celly,
683	>	k * cellz + 0.5 * cellz);
684	>	done = (current_mol >= tot_nmol);
685	>	}
686
687	<	case NVE_ENS:
688	<	new NVE( simnfo, the_ff );
689	<	break;
687	>	if (!done && n_per_extra > 3){
688	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
689	>	k * cellz + 0.5 * cellz);
690	>	done = (current_mol >= tot_nmol);
691	>	}
692	>	}
693	>	}
694	>	}
695	>	}
696
697	<	default:
698	<	sprintf( painCave.errMsg,
780	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
781	<	painCave.isFatal = 1;
782	<	simError();
697	>	for (i = 0; i < info[0].n_atoms; i++){
698	>	info[0].atoms[i]->setVel(vel);
699		}
700	+	}
701
702	+	void SimSetup::makeElement(double x, double y, double z){
703	+	int k;
704	+	AtomStamp* current_atom;
705	+	DirectionalAtom* dAtom;
706	+	double rotMat[3][3];
707	+	double pos[3];
708
709	<	#ifdef IS_MPI
710	<	mpiSim->mpiRefresh();
711	<	#endif
709	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
710	>	current_atom = comp_stamps[current_comp]->getAtom(k);
711	>	if (!current_atom->havePosition()){
712	>	sprintf(painCave.errMsg,
713	>	"SimSetup:initFromBass error.\n"
714	>	"\tComponent %s, atom %s does not have a position specified.\n"
715	>	"\tThe initialization routine is unable to give a start"
716	>	" position.\n",
717	>	comp_stamps[current_comp]->getID(), current_atom->getType());
718	>	painCave.isFatal = 1;
719	>	simError();
720	>	}
721
722	<	// initialize the Fortran
722	>	pos[0] = x + current_atom->getPosX();
723	>	pos[1] = y + current_atom->getPosY();
724	>	pos[2] = z + current_atom->getPosZ();
725
726	+	info[0].atoms[current_atom_ndx]->setPos(pos);
727
728	<	simnfo->refreshSim();
729	<
730	<	if( !strcmp( simnfo->mixingRule, "standard") ){
731	<	the_ff->initForceField( LB_MIXING_RULE );
728	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
729	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
730	>
731	>	rotMat[0][0] = 1.0;
732	>	rotMat[0][1] = 0.0;
733	>	rotMat[0][2] = 0.0;
734	>
735	>	rotMat[1][0] = 0.0;
736	>	rotMat[1][1] = 1.0;
737	>	rotMat[1][2] = 0.0;
738	>
739	>	rotMat[2][0] = 0.0;
740	>	rotMat[2][1] = 0.0;
741	>	rotMat[2][2] = 1.0;
742	>
743	>	dAtom->setA(rotMat);
744	>	}
745	>
746	>	current_atom_ndx++;
747		}
798	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
799	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
800	–	}
801	–	else{
802	–	sprintf( painCave.errMsg,
803	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
804	–	simnfo->mixingRule );
805	–	painCave.isFatal = 1;
806	–	simError();
807	–	}
748
749	+	current_mol++;
750	+	current_comp_mol++;
751
752	<	#ifdef IS_MPI
753	<	strcpy( checkPointMsg,
754	<	"Successfully intialized the mixingRule for Fortran." );
755	<	MPIcheckPoint();
814	<	#endif // is_mpi
752	>	if (current_comp_mol >= components_nmol[current_comp]){
753	>	current_comp_mol = 0;
754	>	current_comp++;
755	>	}
756		}
757
758
759	<	void SimSetup::makeMolecules( void ){
759	>	void SimSetup::gatherInfo(void){
760	>	int i;
761
762	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
763	<	molInit info;
822	<	DirectionalAtom* dAtom;
823	<	LinkedAssign* extras;
824	<	LinkedAssign* current_extra;
825	<	AtomStamp* currentAtom;
826	<	BondStamp* currentBond;
827	<	BendStamp* currentBend;
828	<	TorsionStamp* currentTorsion;
762	>	ensembleCase = -1;
763	>	ffCase = -1;
764
765	<	bond_pair* theBonds;
831	<	bend_set* theBends;
832	<	torsion_set* theTorsions;
765	>	// set the easy ones first
766
767	<
768	<	//init the forceField paramters
767	>	for (i = 0; i < nInfo; i++){
768	>	info[i].target_temp = globals->getTargetTemp();
769	>	info[i].dt = globals->getDt();
770	>	info[i].run_time = globals->getRunTime();
771	>	}
772	>	n_components = globals->getNComponents();
773
837	–	the_ff->readParams();
774
775	<
840	<	// init the atoms
775	>	// get the forceField
776
777	<	double ux, uy, uz, u, uSqr;
843	<
844	<	atomOffset = 0;
845	<	excludeOffset = 0;
846	<	for(i=0; i<simnfo->n_mol; i++){
847	<
848	<	stampID = the_molecules[i].getStampID();
777	>	strcpy(force_field, globals->getForceField());
778
779	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
780	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
781	<	info.nBends    = comp_stamps[stampID]->getNBends();
782	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
783	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
779	>	if (!strcasecmp(force_field, "DUFF")){
780	>	ffCase = FF_DUFF;
781	>	}
782	>	else if (!strcasecmp(force_field, "LJ")){
783	>	ffCase = FF_LJ;
784	>	}
785	>	else if (!strcasecmp(force_field, "EAM")){
786	>	ffCase = FF_EAM;
787	>	}
788	>	else if (!strcasecmp(force_field, "WATER")){
789	>	ffCase = FF_H2O;
790	>	}
791	>	else{
792	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
793	>	force_field);
794	>	painCave.isFatal = 1;
795	>	simError();
796	>	}
797
798	<	info.myAtoms = &the_atoms[atomOffset];
857	<	info.myExcludes = &the_excludes[excludeOffset];
858	<	info.myBonds = new Bond*[info.nBonds];
859	<	info.myBends = new Bend*[info.nBends];
860	<	info.myTorsions = new Torsion*[info.nTorsions];
798	>	// get the ensemble
799
800	<	theBonds = new bond_pair[info.nBonds];
801	<	theBends = new bend_set[info.nBends];
802	<	theTorsions = new torsion_set[info.nTorsions];
800	>	strcpy(ensemble, globals->getEnsemble());
801	>
802	>	if (!strcasecmp(ensemble, "NVE")){
803	>	ensembleCase = NVE_ENS;
804	>	}
805	>	else if (!strcasecmp(ensemble, "NVT")){
806	>	ensembleCase = NVT_ENS;
807	>	}
808	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
809	>	ensembleCase = NPTi_ENS;
810	>	}
811	>	else if (!strcasecmp(ensemble, "NPTf")){
812	>	ensembleCase = NPTf_ENS;
813	>	}
814	>	else if (!strcasecmp(ensemble, "NPTxyz")){
815	>	ensembleCase = NPTxyz_ENS;
816	>	}
817	>	else{
818	>	sprintf(painCave.errMsg,
819	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
820	>	"\treverting to NVE for this simulation.\n",
821	>	ensemble);
822	>	painCave.isFatal = 0;
823	>	simError();
824	>	strcpy(ensemble, "NVE");
825	>	ensembleCase = NVE_ENS;
826	>	}
827	>
828	>	for (i = 0; i < nInfo; i++){
829	>	strcpy(info[i].ensemble, ensemble);
830	>
831	>	// get the mixing rule
832	>
833	>	strcpy(info[i].mixingRule, globals->getMixingRule());
834	>	info[i].usePBC = globals->getPBC();
835	>	}
836	>
837	>	// get the components and calculate the tot_nMol and indvidual n_mol
838	>
839	>	the_components = globals->getComponents();
840	>	components_nmol = new int[n_components];
841	>
842	>
843	>	if (!globals->haveNMol()){
844	>	// we don't have the total number of molecules, so we assume it is
845	>	// given in each component
846	>
847	>	tot_nmol = 0;
848	>	for (i = 0; i < n_components; i++){
849	>	if (!the_components[i]->haveNMol()){
850	>	// we have a problem
851	>	sprintf(painCave.errMsg,
852	>	"SimSetup Error. No global NMol or component NMol given.\n"
853	>	"\tCannot calculate the number of atoms.\n");
854	>	painCave.isFatal = 1;
855	>	simError();
856	>	}
857	>
858	>	tot_nmol += the_components[i]->getNMol();
859	>	components_nmol[i] = the_components[i]->getNMol();
860	>	}
861	>	}
862	>	else{
863	>	sprintf(painCave.errMsg,
864	>	"SimSetup error.\n"
865	>	"\tSorry, the ability to specify total"
866	>	" nMols and then give molfractions in the components\n"
867	>	"\tis not currently supported."
868	>	" Please give nMol in the components.\n");
869	>	painCave.isFatal = 1;
870	>	simError();
871	>	}
872	>
873	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
874	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
875	>	sprintf(painCave.errMsg,
876	>	"Sample time is not divisible by dt.\n"
877	>	"\tThis will result in samples that are not uniformly\n"
878	>	"\tdistributed in time.  If this is a problem, change\n"
879	>	"\tyour sampleTime variable.\n");
880	>	painCave.isFatal = 0;
881	>	simError();
882	>	}
883	>
884	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
885	>	sprintf(painCave.errMsg,
886	>	"Status time is not divisible by dt.\n"
887	>	"\tThis will result in status reports that are not uniformly\n"
888	>	"\tdistributed in time.  If this is a problem, change \n"
889	>	"\tyour statusTime variable.\n");
890	>	painCave.isFatal = 0;
891	>	simError();
892	>	}
893	>
894	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
895	>	sprintf(painCave.errMsg,
896	>	"Thermal time is not divisible by dt.\n"
897	>	"\tThis will result in thermalizations that are not uniformly\n"
898	>	"\tdistributed in time.  If this is a problem, change \n"
899	>	"\tyour thermalTime variable.\n");
900	>	painCave.isFatal = 0;
901	>	simError();
902	>	}
903	>
904	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
905	>	sprintf(painCave.errMsg,
906	>	"Reset time is not divisible by dt.\n"
907	>	"\tThis will result in integrator resets that are not uniformly\n"
908	>	"\tdistributed in time.  If this is a problem, change\n"
909	>	"\tyour resetTime variable.\n");
910	>	painCave.isFatal = 0;
911	>	simError();
912	>	}
913	>
914	>	// set the status, sample, and thermal kick times
915	>
916	>	for (i = 0; i < nInfo; i++){
917	>	if (globals->haveSampleTime()){
918	>	info[i].sampleTime = globals->getSampleTime();
919	>	info[i].statusTime = info[i].sampleTime;
920	>	}
921	>	else{
922	>	info[i].sampleTime = globals->getRunTime();
923	>	info[i].statusTime = info[i].sampleTime;
924	>	}
925	>
926	>	if (globals->haveStatusTime()){
927	>	info[i].statusTime = globals->getStatusTime();
928	>	}
929	>
930	>	if (globals->haveThermalTime()){
931	>	info[i].thermalTime = globals->getThermalTime();
932	>	} else {
933	>	info[i].thermalTime = globals->getRunTime();
934	>	}
935	>
936	>	info[i].resetIntegrator = 0;
937	>	if( globals->haveResetTime() ){
938	>	info[i].resetTime = globals->getResetTime();
939	>	info[i].resetIntegrator = 1;
940	>	}
941	>
942	>	// check for the temperature set flag
943
944	<	// make the Atoms
945	<
946	<	for(j=0; j<info.nAtoms; j++){
944	>	if (globals->haveTempSet())
945	>	info[i].setTemp = globals->getTempSet();
946	>
947	>	// check for the extended State init
948	>
949	>	info[i].useInitXSstate = globals->getUseInitXSstate();
950	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
951	>
952	>	// check for thermodynamic integration
953	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
954	>	info[i].thermIntLambda = globals->getThermIntLambda();
955	>	info[i].thermIntK = globals->getThermIntK();
956	>	info[i].useThermInt = 1;
957
958	<	currentAtom = comp_stamps[stampID]->getAtom( j );
959	<	if( currentAtom->haveOrientation() ){
960	<
961	<	dAtom = new DirectionalAtom(j + atomOffset);
962	<	simnfo->n_oriented++;
963	<	info.myAtoms[j] = dAtom;
964	<
965	<	ux = currentAtom->getOrntX();
966	<	uy = currentAtom->getOrntY();
967	<	uz = currentAtom->getOrntZ();
968	<
969	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
970	<
971	<	u = sqrt( uSqr );
972	<	ux = ux / u;
973	<	uy = uy / u;
974	<	uz = uz / u;
975	<
976	<	dAtom->setSUx( ux );
977	<	dAtom->setSUy( uy );
978	<	dAtom->setSUz( uz );
979	<	}
980	<	else{
981	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
982	<	}
983	<	info.myAtoms[j]->setType( currentAtom->getType() );
958	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
959	>	info[i].restraint = myRestraint;
960	>	}
961	>	}
962	>
963	>	//setup seed for random number generator
964	>	int seedValue;
965	>
966	>	if (globals->haveSeed()){
967	>	seedValue = globals->getSeed();
968	>
969	>	if(seedValue / 1E9 == 0){
970	>	sprintf(painCave.errMsg,
971	>	"Seed for sprng library should contain at least 9 digits\n"
972	>	"OOPSE will generate a seed for user\n");
973	>	painCave.isFatal = 0;
974	>	simError();
975	>
976	>	//using seed generated by system instead of invalid seed set by user
977	>	#ifndef IS_MPI
978	>	seedValue = make_sprng_seed();
979	>	#else
980	>	if (worldRank == 0){
981	>	seedValue = make_sprng_seed();
982	>	}
983	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
984	>	#endif
985	>	}
986	>	}//end of if branch of globals->haveSeed()
987	>	else{
988
989	+	#ifndef IS_MPI
990	+	seedValue = make_sprng_seed();
991	+	#else
992	+	if (worldRank == 0){
993	+	seedValue = make_sprng_seed();
994	+	}
995	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
996	+	#endif
997	+	}//end of globals->haveSeed()
998	+
999	+	for (int i = 0; i < nInfo; i++){
1000	+	info[i].setSeed(seedValue);
1001	+	}
1002	+
1003		#ifdef IS_MPI
1004	<
1005	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
900	<
1004	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1005	>	MPIcheckPoint();
1006		#endif // is_mpi
1007	<	}
903	<
904	<	// make the bonds
905	<	for(j=0; j<info.nBonds; j++){
906	<
907	<	currentBond = comp_stamps[stampID]->getBond( j );
908	<	theBonds[j].a = currentBond->getA() + atomOffset;
909	<	theBonds[j].b = currentBond->getB() + atomOffset;
1007	>	}
1008
911	–	exI = theBonds[j].a;
912	–	exJ = theBonds[j].b;
1009
1010	<	// exclude_I must always be the smaller of the pair
1011	<	if( exI > exJ ){
1012	<	tempEx = exI;
1013	<	exI = exJ;
1014	<	exJ = tempEx;
1015	<	}
1010	>	void SimSetup::finalInfoCheck(void){
1011	>	int index;
1012	>	int usesDipoles;
1013	>	int usesCharges;
1014	>	int i;
1015	>
1016	>	for (i = 0; i < nInfo; i++){
1017	>	// check electrostatic parameters
1018	>
1019	>	index = 0;
1020	>	usesDipoles = 0;
1021	>	while ((index < info[i].n_atoms) && !usesDipoles){
1022	>	usesDipoles = (info[i].atoms[index])->hasDipole();
1023	>	index++;
1024	>	}
1025	>	index = 0;
1026	>	usesCharges = 0;
1027	>	while ((index < info[i].n_atoms) && !usesCharges){
1028	>	usesCharges= (info[i].atoms[index])->hasCharge();
1029	>	index++;
1030	>	}
1031		#ifdef IS_MPI
1032	<	tempEx = exI;
1033	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1034	<	tempEx = exJ;
1035	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1032	>	int myUse = usesDipoles;
1033	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1034	>	#endif //is_mpi
1035	>
1036	>	double theRcut, theRsw;
1037	>
1038	>	if (globals->haveRcut()) {
1039	>	theRcut = globals->getRcut();
1040	>
1041	>	if (globals->haveRsw())
1042	>	theRsw = globals->getRsw();
1043	>	else
1044	>	theRsw = theRcut;
1045
1046	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
927	<	#else  // isn't MPI
1046	>	info[i].setDefaultRcut(theRcut, theRsw);
1047
1048	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1049	<	#endif  //is_mpi
1048	>	} else {
1049	>
1050	>	the_ff->calcRcut();
1051	>	theRcut = info[i].getRcut();
1052	>
1053	>	if (globals->haveRsw())
1054	>	theRsw = globals->getRsw();
1055	>	else
1056	>	theRsw = theRcut;
1057	>
1058	>	info[i].setDefaultRcut(theRcut, theRsw);
1059		}
932	–	excludeOffset += info.nBonds;
1060
1061	<	//make the bends
1062	<	for(j=0; j<info.nBends; j++){
1061	>	if (globals->getUseRF()){
1062	>	info[i].useReactionField = 1;
1063
1064	<	currentBend = comp_stamps[stampID]->getBend( j );
1065	<	theBends[j].a = currentBend->getA() + atomOffset;
1066	<	theBends[j].b = currentBend->getB() + atomOffset;
1067	<	theBends[j].c = currentBend->getC() + atomOffset;
1068	<
1069	<	if( currentBend->haveExtras() ){
1070	<
1071	<	extras = currentBend->getExtras();
945	<	current_extra = extras;
946	<
947	<	while( current_extra != NULL ){
948	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
949	<
950	<	switch( current_extra->getType() ){
951	<
952	<	case 0:
953	<	theBends[j].ghost =
954	<	current_extra->getInt() + atomOffset;
955	<	theBends[j].isGhost = 1;
956	<	break;
957	<
958	<	case 1:
959	<	theBends[j].ghost =
960	<	(int)current_extra->getDouble() + atomOffset;
961	<	theBends[j].isGhost = 1;
962	<	break;
963	<
964	<	default:
965	<	sprintf( painCave.errMsg,
966	<	"SimSetup Error: ghostVectorSource was neither a "
967	<	"double nor an int.\n"
968	<	"-->Bend[%d] in %s\n",
969	<	j, comp_stamps[stampID]->getID() );
970	<	painCave.isFatal = 1;
971	<	simError();
972	<	}
973	<	}
974	<
975	<	else{
976	<
977	<	sprintf( painCave.errMsg,
978	<	"SimSetup Error: unhandled bend assignment:\n"
979	<	"    -->%s in Bend[%d] in %s\n",
980	<	current_extra->getlhs(),
981	<	j, comp_stamps[stampID]->getID() );
982	<	painCave.isFatal = 1;
983	<	simError();
984	<	}
985	<
986	<	current_extra = current_extra->getNext();
987	<	}
1064	>	if (!globals->haveRcut()){
1065	>	sprintf(painCave.errMsg,
1066	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1067	>	"\tOOPSE will use a default value of 15.0 angstroms"
1068	>	"\tfor the cutoffRadius.\n");
1069	>	painCave.isFatal = 0;
1070	>	simError();
1071	>	theRcut = 15.0;
1072		}
1073	<
1074	<	if( !theBends[j].isGhost ){
991	<
992	<	exI = theBends[j].a;
993	<	exJ = theBends[j].c;
1073	>	else{
1074	>	theRcut = globals->getRcut();
1075		}
1076	+
1077	+	if (!globals->haveRsw()){
1078	+	sprintf(painCave.errMsg,
1079	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1080	+	"\tOOPSE will use a default value of\n"
1081	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1082	+	painCave.isFatal = 0;
1083	+	simError();
1084	+	theRsw = 0.95 * theRcut;
1085	+	}
1086		else{
1087	<
997	<	exI = theBends[j].a;
998	<	exJ = theBends[j].b;
1087	>	theRsw = globals->getRsw();
1088		}
1089	<
1090	<	// exclude_I must always be the smaller of the pair
1091	<	if( exI > exJ ){
1092	<	tempEx = exI;
1093	<	exI = exJ;
1094	<	exJ = tempEx;
1089	>
1090	>	info[i].setDefaultRcut(theRcut, theRsw);
1091	>
1092	>	if (!globals->haveDielectric()){
1093	>	sprintf(painCave.errMsg,
1094	>	"SimSetup Error: No Dielectric constant was set.\n"
1095	>	"\tYou are trying to use Reaction Field without"
1096	>	"\tsetting a dielectric constant!\n");
1097	>	painCave.isFatal = 1;
1098	>	simError();
1099		}
1100	<	#ifdef IS_MPI
1008	<	tempEx = exI;
1009	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1010	<	tempEx = exJ;
1011	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1012	<
1013	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1014	<	#else  // isn't MPI
1015	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1016	<	#endif  //is_mpi
1100	>	info[i].dielectric = globals->getDielectric();
1101		}
1102	<	excludeOffset += info.nBends;
1102	>	else{
1103	>	if (usesDipoles || usesCharges){
1104
1105	<	for(j=0; j<info.nTorsions; j++){
1106	<
1107	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1108	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1109	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1110	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1111	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1112	<
1028	<	exI = theTorsions[j].a;
1029	<	exJ = theTorsions[j].d;
1030	<
1031	<	// exclude_I must always be the smaller of the pair
1032	<	if( exI > exJ ){
1033	<	tempEx = exI;
1034	<	exI = exJ;
1035	<	exJ = tempEx;
1105	>	if (!globals->haveRcut()){
1106	>	sprintf(painCave.errMsg,
1107	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1108	>	"\tOOPSE will use a default value of 15.0 angstroms"
1109	>	"\tfor the cutoffRadius.\n");
1110	>	painCave.isFatal = 0;
1111	>	simError();
1112	>	theRcut = 15.0;
1113		}
1114	<	#ifdef IS_MPI
1115	<	tempEx = exI;
1116	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1117	<	tempEx = exJ;
1118	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1119	<
1120	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1121	<	#else  // isn't MPI
1122	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1123	<	#endif  //is_mpi
1114	>	else{
1115	>	theRcut = globals->getRcut();
1116	>	}
1117	>
1118	>	if (!globals->haveRsw()){
1119	>	sprintf(painCave.errMsg,
1120	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1121	>	"\tOOPSE will use a default value of\n"
1122	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1123	>	painCave.isFatal = 0;
1124	>	simError();
1125	>	theRsw = 0.95 * theRcut;
1126	>	}
1127	>	else{
1128	>	theRsw = globals->getRsw();
1129	>	}
1130	>
1131	>	info[i].setDefaultRcut(theRcut, theRsw);
1132	>
1133	>	}
1134		}
1135	<	excludeOffset += info.nTorsions;
1135	>	}
1136	>	#ifdef IS_MPI
1137	>	strcpy(checkPointMsg, "post processing checks out");
1138	>	MPIcheckPoint();
1139	>	#endif // is_mpi
1140
1141	<
1142	<	// send the arrays off to the forceField for init.
1141	>	// clean up the forcefield
1142	>	the_ff->cleanMe();
1143	>	}
1144	>
1145	>	void SimSetup::initSystemCoords(void){
1146	>	int i;
1147
1148	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1054	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1055	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1056	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1148	>	char* inName;
1149
1150	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1151
1152	<	the_molecules[i].initialize( info );
1152	>	for (i = 0; i < info[0].n_atoms; i++)
1153	>	info[0].atoms[i]->setCoords();
1154
1155	+	if (globals->haveInitialConfig()){
1156	+	InitializeFromFile* fileInit;
1157	+	#ifdef IS_MPI // is_mpi
1158	+	if (worldRank == 0){
1159	+	#endif //is_mpi
1160	+	inName = globals->getInitialConfig();
1161	+	fileInit = new InitializeFromFile(inName);
1162	+	#ifdef IS_MPI
1163	+	}
1164	+	else
1165	+	fileInit = new InitializeFromFile(NULL);
1166	+	#endif
1167	+	fileInit->readInit(info); // default velocities on
1168
1169	<	atomOffset += info.nAtoms;
1063	<	delete[] theBonds;
1064	<	delete[] theBends;
1065	<	delete[] theTorsions;
1169	>	delete fileInit;
1170		}
1171	+	else{
1172	+
1173	+	// no init from bass
1174	+
1175	+	sprintf(painCave.errMsg,
1176	+	"Cannot intialize a simulation without an initial configuration file.\n");
1177	+	painCave.isFatal = 1;;
1178	+	simError();
1179	+
1180	+	}
1181
1182		#ifdef IS_MPI
1183	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1183	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1184		MPIcheckPoint();
1185		#endif // is_mpi
1186	+	}
1187
1073	–	// clean up the forcefield
1074	–	the_ff->calcRcut();
1075	–	the_ff->cleanMe();
1188
1189	<	}
1189	>	void SimSetup::makeOutNames(void){
1190	>	int k;
1191
1079	–	void SimSetup::initFromBass( void ){
1192
1193	<	int i, j, k;
1194	<	int n_cells;
1195	<	double cellx, celly, cellz;
1196	<	double temp1, temp2, temp3;
1085	<	int n_per_extra;
1086	<	int n_extra;
1087	<	int have_extra, done;
1193	>	for (k = 0; k < nInfo; k++){
1194	>	#ifdef IS_MPI
1195	>	if (worldRank == 0){
1196	>	#endif // is_mpi
1197
1198	<	temp1 = (double)tot_nmol / 4.0;
1199	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1200	<	temp3 = ceil( temp2 );
1198	>	if (globals->haveFinalConfig()){
1199	>	strcpy(info[k].finalName, globals->getFinalConfig());
1200	>	}
1201	>	else{
1202	>	strcpy(info[k].finalName, inFileName);
1203	>	char* endTest;
1204	>	int nameLength = strlen(info[k].finalName);
1205	>	endTest = &(info[k].finalName[nameLength - 5]);
1206	>	if (!strcmp(endTest, ".bass")){
1207	>	strcpy(endTest, ".eor");
1208	>	}
1209	>	else if (!strcmp(endTest, ".BASS")){
1210	>	strcpy(endTest, ".eor");
1211	>	}
1212	>	else{
1213	>	endTest = &(info[k].finalName[nameLength - 4]);
1214	>	if (!strcmp(endTest, ".bss")){
1215	>	strcpy(endTest, ".eor");
1216	>	}
1217	>	else if (!strcmp(endTest, ".mdl")){
1218	>	strcpy(endTest, ".eor");
1219	>	}
1220	>	else{
1221	>	strcat(info[k].finalName, ".eor");
1222	>	}
1223	>	}
1224	>	}
1225
1226	<	have_extra =0;
1094	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1095	<	have_extra =1;
1226	>	// make the sample and status out names
1227
1228	<	n_cells = (int)temp3 - 1;
1229	<	cellx = simnfo->box_x / temp3;
1230	<	celly = simnfo->box_y / temp3;
1231	<	cellz = simnfo->box_z / temp3;
1232	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1233	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1234	<	n_per_extra = (int)ceil( temp1 );
1228	>	strcpy(info[k].sampleName, inFileName);
1229	>	char* endTest;
1230	>	int nameLength = strlen(info[k].sampleName);
1231	>	endTest = &(info[k].sampleName[nameLength - 5]);
1232	>	if (!strcmp(endTest, ".bass")){
1233	>	strcpy(endTest, ".dump");
1234	>	}
1235	>	else if (!strcmp(endTest, ".BASS")){
1236	>	strcpy(endTest, ".dump");
1237	>	}
1238	>	else{
1239	>	endTest = &(info[k].sampleName[nameLength - 4]);
1240	>	if (!strcmp(endTest, ".bss")){
1241	>	strcpy(endTest, ".dump");
1242	>	}
1243	>	else if (!strcmp(endTest, ".mdl")){
1244	>	strcpy(endTest, ".dump");
1245	>	}
1246	>	else{
1247	>	strcat(info[k].sampleName, ".dump");
1248	>	}
1249	>	}
1250
1251	<	if( n_per_extra > 4){
1252	<	sprintf( painCave.errMsg,
1253	<	"SimSetup error. There has been an error in constructing"
1254	<	" the non-complete lattice.\n" );
1255	<	painCave.isFatal = 1;
1256	<	simError();
1251	>	strcpy(info[k].statusName, inFileName);
1252	>	nameLength = strlen(info[k].statusName);
1253	>	endTest = &(info[k].statusName[nameLength - 5]);
1254	>	if (!strcmp(endTest, ".bass")){
1255	>	strcpy(endTest, ".stat");
1256	>	}
1257	>	else if (!strcmp(endTest, ".BASS")){
1258	>	strcpy(endTest, ".stat");
1259	>	}
1260	>	else{
1261	>	endTest = &(info[k].statusName[nameLength - 4]);
1262	>	if (!strcmp(endTest, ".bss")){
1263	>	strcpy(endTest, ".stat");
1264	>	}
1265	>	else if (!strcmp(endTest, ".mdl")){
1266	>	strcpy(endTest, ".stat");
1267	>	}
1268	>	else{
1269	>	strcat(info[k].statusName, ".stat");
1270	>	}
1271	>	}
1272	>
1273	>	strcpy(info[k].rawPotName, inFileName);
1274	>	nameLength = strlen(info[k].rawPotName);
1275	>	endTest = &(info[k].rawPotName[nameLength - 5]);
1276	>	if (!strcmp(endTest, ".bass")){
1277	>	strcpy(endTest, ".raw");
1278	>	}
1279	>	else if (!strcmp(endTest, ".BASS")){
1280	>	strcpy(endTest, ".raw");
1281	>	}
1282	>	else{
1283	>	endTest = &(info[k].rawPotName[nameLength - 4]);
1284	>	if (!strcmp(endTest, ".bss")){
1285	>	strcpy(endTest, ".raw");
1286	>	}
1287	>	else if (!strcmp(endTest, ".mdl")){
1288	>	strcpy(endTest, ".raw");
1289	>	}
1290	>	else{
1291	>	strcat(info[k].rawPotName, ".raw");
1292	>	}
1293	>	}
1294	>
1295	>	#ifdef IS_MPI
1296	>
1297		}
1298	+	#endif // is_mpi
1299		}
1300	<	else{
1301	<	n_cells = (int)temp3;
1302	<	cellx = simnfo->box_x / temp3;
1303	<	celly = simnfo->box_y / temp3;
1304	<	cellz = simnfo->box_z / temp3;
1300	>	}
1301	>
1302	>
1303	>	void SimSetup::sysObjectsCreation(void){
1304	>	int i, k;
1305	>
1306	>	// create the forceField
1307	>
1308	>	createFF();
1309	>
1310	>	// extract componentList
1311	>
1312	>	compList();
1313	>
1314	>	// calc the number of atoms, bond, bends, and torsions
1315	>
1316	>	calcSysValues();
1317	>
1318	>	#ifdef IS_MPI
1319	>	// divide the molecules among the processors
1320	>
1321	>	mpiMolDivide();
1322	>	#endif //is_mpi
1323	>
1324	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1325	>
1326	>	makeSysArrays();
1327	>
1328	>	// make and initialize the molecules (all but atomic coordinates)
1329	>
1330	>	makeMolecules();
1331	>
1332	>	for (k = 0; k < nInfo; k++){
1333	>	info[k].identArray = new int[info[k].n_atoms];
1334	>	for (i = 0; i < info[k].n_atoms; i++){
1335	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1336	>	}
1337		}
1338	+	}
1339
1120	–	current_mol = 0;
1121	–	current_comp_mol = 0;
1122	–	current_comp = 0;
1123	–	current_atom_ndx = 0;
1340
1341	<	for( i=0; i < n_cells ; i++ ){
1342	<	for( j=0; j < n_cells; j++ ){
1343	<	for( k=0; k < n_cells; k++ ){
1341	>	void SimSetup::createFF(void){
1342	>	switch (ffCase){
1343	>	case FF_DUFF:
1344	>	the_ff = new DUFF();
1345	>	break;
1346
1347	<	makeElement( i * cellx,
1348	<	j * celly,
1349	<	k * cellz );
1347	>	case FF_LJ:
1348	>	the_ff = new LJFF();
1349	>	break;
1350
1351	<	makeElement( i * cellx + 0.5 * cellx,
1352	<	j * celly + 0.5 * celly,
1353	<	k * cellz );
1351	>	case FF_EAM:
1352	>	the_ff = new EAM_FF();
1353	>	break;
1354
1355	<	makeElement( i * cellx,
1356	<	j * celly + 0.5 * celly,
1357	<	k * cellz + 0.5 * cellz );
1355	>	case FF_H2O:
1356	>	the_ff = new WATER();
1357	>	break;
1358
1359	<	makeElement( i * cellx + 0.5 * cellx,
1360	<	j * celly,
1361	<	k * cellz + 0.5 * cellz );
1359	>	default:
1360	>	sprintf(painCave.errMsg,
1361	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1362	>	painCave.isFatal = 1;
1363	>	simError();
1364	>	}
1365	>
1366	>	#ifdef IS_MPI
1367	>	strcpy(checkPointMsg, "ForceField creation successful");
1368	>	MPIcheckPoint();
1369	>	#endif // is_mpi
1370	>	}
1371	>
1372	>
1373	>	void SimSetup::compList(void){
1374	>	int i;
1375	>	char* id;
1376	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1377	>	LinkedMolStamp* currentStamp = NULL;
1378	>	comp_stamps = new MoleculeStamp * [n_components];
1379	>	bool haveCutoffGroups;
1380	>
1381	>	haveCutoffGroups = false;
1382	>
1383	>	// make an array of molecule stamps that match the components used.
1384	>	// also extract the used stamps out into a separate linked list
1385	>
1386	>	for (i = 0; i < nInfo; i++){
1387	>	info[i].nComponents = n_components;
1388	>	info[i].componentsNmol = components_nmol;
1389	>	info[i].compStamps = comp_stamps;
1390	>	info[i].headStamp = headStamp;
1391	>	}
1392	>
1393	>
1394	>	for (i = 0; i < n_components; i++){
1395	>	id = the_components[i]->getType();
1396	>	comp_stamps[i] = NULL;
1397	>
1398	>	// check to make sure the component isn't already in the list
1399	>
1400	>	comp_stamps[i] = headStamp->match(id);
1401	>	if (comp_stamps[i] == NULL){
1402	>	// extract the component from the list;
1403	>
1404	>	currentStamp = stamps->extractMolStamp(id);
1405	>	if (currentStamp == NULL){
1406	>	sprintf(painCave.errMsg,
1407	>	"SimSetup error: Component \"%s\" was not found in the "
1408	>	"list of declared molecules\n",
1409	>	id);
1410	>	painCave.isFatal = 1;
1411	>	simError();
1412		}
1413	+
1414	+	headStamp->add(currentStamp);
1415	+	comp_stamps[i] = headStamp->match(id);
1416		}
1417	+
1418	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1419	+	haveCutoffGroups = true;
1420		}
1421	+
1422	+	for (i = 0; i < nInfo; i++)
1423	+	info[i].haveCutoffGroups = haveCutoffGroups;
1424
1425	<	if( have_extra ){
1426	<	done = 0;
1425	>	#ifdef IS_MPI
1426	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1427	>	MPIcheckPoint();
1428	>	#endif // is_mpi
1429	>	}
1430
1431	<	int start_ndx;
1432	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1153	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1431	>	void SimSetup::calcSysValues(void){
1432	>	int i;
1433
1434	<	if( i < n_cells ){
1434	>	int* molMembershipArray;
1435
1436	<	if( j < n_cells ){
1437	<	start_ndx = n_cells;
1438	<	}
1439	<	else start_ndx = 0;
1440	<	}
1441	<	else start_ndx = 0;
1436	>	tot_atoms = 0;
1437	>	tot_bonds = 0;
1438	>	tot_bends = 0;
1439	>	tot_torsions = 0;
1440	>	tot_rigid = 0;
1441	>	for (i = 0; i < n_components; i++){
1442	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1443	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1444	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1445	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1446	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1447	>	}
1448	>
1449	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1450	>	molMembershipArray = new int[tot_atoms];
1451
1452	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1452	>	for (i = 0; i < nInfo; i++){
1453	>	info[i].n_atoms = tot_atoms;
1454	>	info[i].n_bonds = tot_bonds;
1455	>	info[i].n_bends = tot_bends;
1456	>	info[i].n_torsions = tot_torsions;
1457	>	info[i].n_SRI = tot_SRI;
1458	>	info[i].n_mol = tot_nmol;
1459
1460	<	makeElement( i * cellx,
1461	<	j * celly,
1462	<	k * cellz );
1169	<	done = ( current_mol >= tot_nmol );
1460	>	info[i].molMembershipArray = molMembershipArray;
1461	>	}
1462	>	}
1463
1464	<	if( !done && n_per_extra > 1 ){
1172	<	makeElement( i * cellx + 0.5 * cellx,
1173	<	j * celly + 0.5 * celly,
1174	<	k * cellz );
1175	<	done = ( current_mol >= tot_nmol );
1176	<	}
1464	>	#ifdef IS_MPI
1465
1466	<	if( !done && n_per_extra > 2){
1467	<	makeElement( i * cellx,
1468	<	j * celly + 0.5 * celly,
1469	<	k * cellz + 0.5 * cellz );
1470	<	done = ( current_mol >= tot_nmol );
1471	<	}
1466	>	void SimSetup::mpiMolDivide(void){
1467	>	int i, j, k;
1468	>	int localMol, allMol;
1469	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1470	>	int local_rigid;
1471	>	vector<int> globalMolIndex;
1472
1473	<	if( !done && n_per_extra > 3){
1474	<	makeElement( i * cellx + 0.5 * cellx,
1475	<	j * celly,
1476	<	k * cellz + 0.5 * cellz );
1477	<	done = ( current_mol >= tot_nmol );
1478	<	}
1479	<	}
1473	>	mpiSim = new mpiSimulation(info);
1474	>
1475	>	mpiSim->divideLabor();
1476	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1477	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1478	>
1479	>	// set up the local variables
1480	>
1481	>	mol2proc = mpiSim->getMolToProcMap();
1482	>	molCompType = mpiSim->getMolComponentType();
1483	>
1484	>	allMol = 0;
1485	>	localMol = 0;
1486	>	local_atoms = 0;
1487	>	local_bonds = 0;
1488	>	local_bends = 0;
1489	>	local_torsions = 0;
1490	>	local_rigid = 0;
1491	>	globalAtomCounter = 0;
1492	>
1493	>	for (i = 0; i < n_components; i++){
1494	>	for (j = 0; j < components_nmol[i]; j++){
1495	>	if (mol2proc[allMol] == worldRank){
1496	>	local_atoms += comp_stamps[i]->getNAtoms();
1497	>	local_bonds += comp_stamps[i]->getNBonds();
1498	>	local_bends += comp_stamps[i]->getNBends();
1499	>	local_torsions += comp_stamps[i]->getNTorsions();
1500	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1501	>	localMol++;
1502	>	}
1503	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1504	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1505	>	globalAtomCounter++;
1506		}
1507	+
1508	+	allMol++;
1509		}
1510		}
1511	+	local_SRI = local_bonds + local_bends + local_torsions;
1512
1513	+	info[0].n_atoms = mpiSim->getMyNlocal();
1514	+
1515
1516	<	for( i=0; i<simnfo->n_atoms; i++ ){
1517	<	simnfo->atoms[i]->set_vx( 0.0 );
1518	<	simnfo->atoms[i]->set_vy( 0.0 );
1519	<	simnfo->atoms[i]->set_vz( 0.0 );
1516	>	if (local_atoms != info[0].n_atoms){
1517	>	sprintf(painCave.errMsg,
1518	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1519	>	"\tlocalAtom (%d) are not equal.\n",
1520	>	info[0].n_atoms, local_atoms);
1521	>	painCave.isFatal = 1;
1522	>	simError();
1523		}
1524	+
1525	+	info[0].n_bonds = local_bonds;
1526	+	info[0].n_bends = local_bends;
1527	+	info[0].n_torsions = local_torsions;
1528	+	info[0].n_SRI = local_SRI;
1529	+	info[0].n_mol = localMol;
1530	+
1531	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1532	+	MPIcheckPoint();
1533		}
1534
1535	<	void SimSetup::makeElement( double x, double y, double z ){
1535	>	#endif // is_mpi
1536
1206	–	int k;
1207	–	AtomStamp* current_atom;
1208	–	DirectionalAtom* dAtom;
1209	–	double rotMat[3][3];
1537
1538	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1538	>	void SimSetup::makeSysArrays(void){
1539	>
1540	>	#ifndef IS_MPI
1541	>	int k, j;
1542	>	#endif // is_mpi
1543	>	int i, l;
1544
1545	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1546	<	if( !current_atom->havePosition() ){
1215	<	sprintf( painCave.errMsg,
1216	<	"SimSetup:initFromBass error.\n"
1217	<	"\tComponent %s, atom %s does not have a position specified.\n"
1218	<	"\tThe initialization routine is unable to give a start"
1219	<	" position.\n",
1220	<	comp_stamps[current_comp]->getID(),
1221	<	current_atom->getType() );
1222	<	painCave.isFatal = 1;
1223	<	simError();
1224	<	}
1545	>	Atom** the_atoms;
1546	>	Molecule* the_molecules;
1547
1548	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1549	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1228	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1548	>	for (l = 0; l < nInfo; l++){
1549	>	// create the atom and short range interaction arrays
1550
1551	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1551	>	the_atoms = new Atom * [info[l].n_atoms];
1552	>	the_molecules = new Molecule[info[l].n_mol];
1553	>	int molIndex;
1554
1555	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1555	>	// initialize the molecule's stampID's
1556
1557	<	rotMat[0][0] = 1.0;
1235	<	rotMat[0][1] = 0.0;
1236	<	rotMat[0][2] = 0.0;
1557	>	#ifdef IS_MPI
1558
1238	–	rotMat[1][0] = 0.0;
1239	–	rotMat[1][1] = 1.0;
1240	–	rotMat[1][2] = 0.0;
1559
1560	<	rotMat[2][0] = 0.0;
1561	<	rotMat[2][1] = 0.0;
1562	<	rotMat[2][2] = 1.0;
1560	>	molIndex = 0;
1561	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1562	>	if (mol2proc[i] == worldRank){
1563	>	the_molecules[molIndex].setStampID(molCompType[i]);
1564	>	the_molecules[molIndex].setMyIndex(molIndex);
1565	>	the_molecules[molIndex].setGlobalIndex(i);
1566	>	molIndex++;
1567	>	}
1568	>	}
1569
1570	<	dAtom->setA( rotMat );
1570	>	#else // is_mpi
1571	>
1572	>	molIndex = 0;
1573	>	globalAtomCounter = 0;
1574	>	for (i = 0; i < n_components; i++){
1575	>	for (j = 0; j < components_nmol[i]; j++){
1576	>	the_molecules[molIndex].setStampID(i);
1577	>	the_molecules[molIndex].setMyIndex(molIndex);
1578	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1579	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1580	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1581	>	globalAtomCounter++;
1582	>	}
1583	>	molIndex++;
1584	>	}
1585		}
1586
1249	–	current_atom_ndx++;
1250	–	}
1587
1588	<	current_mol++;
1253	<	current_comp_mol++;
1588	>	#endif // is_mpi
1589
1590	<	if( current_comp_mol >= components_nmol[current_comp] ){
1590	>	info[l].globalExcludes = new int;
1591	>	info[l].globalExcludes[0] = 0;
1592	>
1593	>	// set the arrays into the SimInfo object
1594
1595	<	current_comp_mol = 0;
1596	<	current_comp++;
1595	>	info[l].atoms = the_atoms;
1596	>	info[l].molecules = the_molecules;
1597	>	info[l].nGlobalExcludes = 0;
1598	>
1599	>	the_ff->setSimInfo(info);
1600	>	}
1601	>	}
1602	>
1603	>	void SimSetup::makeIntegrator(void){
1604	>	int k;
1605	>
1606	>	NVE<RealIntegrator>* myNVE = NULL;
1607	>	NVT<RealIntegrator>* myNVT = NULL;
1608	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1609	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1610	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1611	>
1612	>	for (k = 0; k < nInfo; k++){
1613	>	switch (ensembleCase){
1614	>	case NVE_ENS:
1615	>	if (globals->haveZconstraints()){
1616	>	setupZConstraint(info[k]);
1617	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1618	>	}
1619	>	else{
1620	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1621	>	}
1622	>
1623	>	info->the_integrator = myNVE;
1624	>	break;
1625	>
1626	>	case NVT_ENS:
1627	>	if (globals->haveZconstraints()){
1628	>	setupZConstraint(info[k]);
1629	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1630	>	}
1631	>	else
1632	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1633	>
1634	>	myNVT->setTargetTemp(globals->getTargetTemp());
1635	>
1636	>	if (globals->haveTauThermostat())
1637	>	myNVT->setTauThermostat(globals->getTauThermostat());
1638	>	else{
1639	>	sprintf(painCave.errMsg,
1640	>	"SimSetup error: If you use the NVT\n"
1641	>	"\tensemble, you must set tauThermostat.\n");
1642	>	painCave.isFatal = 1;
1643	>	simError();
1644	>	}
1645	>
1646	>	info->the_integrator = myNVT;
1647	>	break;
1648	>
1649	>	case NPTi_ENS:
1650	>	if (globals->haveZconstraints()){
1651	>	setupZConstraint(info[k]);
1652	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1653	>	}
1654	>	else
1655	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1656	>
1657	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1658	>
1659	>	if (globals->haveTargetPressure())
1660	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1661	>	else{
1662	>	sprintf(painCave.errMsg,
1663	>	"SimSetup error: If you use a constant pressure\n"
1664	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1665	>	painCave.isFatal = 1;
1666	>	simError();
1667	>	}
1668	>
1669	>	if (globals->haveTauThermostat())
1670	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1671	>	else{
1672	>	sprintf(painCave.errMsg,
1673	>	"SimSetup error: If you use an NPT\n"
1674	>	"\tensemble, you must set tauThermostat.\n");
1675	>	painCave.isFatal = 1;
1676	>	simError();
1677	>	}
1678	>
1679	>	if (globals->haveTauBarostat())
1680	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1681	>	else{
1682	>	sprintf(painCave.errMsg,
1683	>	"SimSetup error: If you use an NPT\n"
1684	>	"\tensemble, you must set tauBarostat.\n");
1685	>	painCave.isFatal = 1;
1686	>	simError();
1687	>	}
1688	>
1689	>	info->the_integrator = myNPTi;
1690	>	break;
1691	>
1692	>	case NPTf_ENS:
1693	>	if (globals->haveZconstraints()){
1694	>	setupZConstraint(info[k]);
1695	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1696	>	}
1697	>	else
1698	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1699	>
1700	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1701	>
1702	>	if (globals->haveTargetPressure())
1703	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1704	>	else{
1705	>	sprintf(painCave.errMsg,
1706	>	"SimSetup error: If you use a constant pressure\n"
1707	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1708	>	painCave.isFatal = 1;
1709	>	simError();
1710	>	}
1711	>
1712	>	if (globals->haveTauThermostat())
1713	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1714	>
1715	>	else{
1716	>	sprintf(painCave.errMsg,
1717	>	"SimSetup error: If you use an NPT\n"
1718	>	"\tensemble, you must set tauThermostat.\n");
1719	>	painCave.isFatal = 1;
1720	>	simError();
1721	>	}
1722	>
1723	>	if (globals->haveTauBarostat())
1724	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1725	>
1726	>	else{
1727	>	sprintf(painCave.errMsg,
1728	>	"SimSetup error: If you use an NPT\n"
1729	>	"\tensemble, you must set tauBarostat.\n");
1730	>	painCave.isFatal = 1;
1731	>	simError();
1732	>	}
1733	>
1734	>	info->the_integrator = myNPTf;
1735	>	break;
1736	>
1737	>	case NPTxyz_ENS:
1738	>	if (globals->haveZconstraints()){
1739	>	setupZConstraint(info[k]);
1740	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1741	>	}
1742	>	else
1743	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1744	>
1745	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1746	>
1747	>	if (globals->haveTargetPressure())
1748	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1749	>	else{
1750	>	sprintf(painCave.errMsg,
1751	>	"SimSetup error: If you use a constant pressure\n"
1752	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1753	>	painCave.isFatal = 1;
1754	>	simError();
1755	>	}
1756	>
1757	>	if (globals->haveTauThermostat())
1758	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1759	>	else{
1760	>	sprintf(painCave.errMsg,
1761	>	"SimSetup error: If you use an NPT\n"
1762	>	"\tensemble, you must set tauThermostat.\n");
1763	>	painCave.isFatal = 1;
1764	>	simError();
1765	>	}
1766	>
1767	>	if (globals->haveTauBarostat())
1768	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1769	>	else{
1770	>	sprintf(painCave.errMsg,
1771	>	"SimSetup error: If you use an NPT\n"
1772	>	"\tensemble, you must set tauBarostat.\n");
1773	>	painCave.isFatal = 1;
1774	>	simError();
1775	>	}
1776	>
1777	>	info->the_integrator = myNPTxyz;
1778	>	break;
1779	>
1780	>	default:
1781	>	sprintf(painCave.errMsg,
1782	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1783	>	painCave.isFatal = 1;
1784	>	simError();
1785	>	}
1786		}
1787		}
1788	+
1789	+	void SimSetup::initFortran(void){
1790	+	info[0].refreshSim();
1791	+
1792	+	if (!strcmp(info[0].mixingRule, "standard")){
1793	+	the_ff->initForceField(LB_MIXING_RULE);
1794	+	}
1795	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1796	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1797	+	}
1798	+	else{
1799	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1800	+	info[0].mixingRule);
1801	+	painCave.isFatal = 1;
1802	+	simError();
1803	+	}
1804	+
1805	+
1806	+	#ifdef IS_MPI
1807	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1808	+	MPIcheckPoint();
1809	+	#endif // is_mpi
1810	+	}
1811	+
1812	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1813	+	int nZConstraints;
1814	+	ZconStamp** zconStamp;
1815	+
1816	+	if (globals->haveZconstraintTime()){
1817	+	//add sample time of z-constraint  into SimInfo's property list
1818	+	DoubleData* zconsTimeProp = new DoubleData();
1819	+	zconsTimeProp->setID(ZCONSTIME_ID);
1820	+	zconsTimeProp->setData(globals->getZconsTime());
1821	+	theInfo.addProperty(zconsTimeProp);
1822	+	}
1823	+	else{
1824	+	sprintf(painCave.errMsg,
1825	+	"ZConstraint error: If you use a ZConstraint,\n"
1826	+	"\tyou must set zconsTime.\n");
1827	+	painCave.isFatal = 1;
1828	+	simError();
1829	+	}
1830	+
1831	+	//push zconsTol into siminfo, if user does not specify
1832	+	//value for zconsTol, a default value will be used
1833	+	DoubleData* zconsTol = new DoubleData();
1834	+	zconsTol->setID(ZCONSTOL_ID);
1835	+	if (globals->haveZconsTol()){
1836	+	zconsTol->setData(globals->getZconsTol());
1837	+	}
1838	+	else{
1839	+	double defaultZConsTol = 0.01;
1840	+	sprintf(painCave.errMsg,
1841	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1842	+	"\tOOPSE will use a default value of %f.\n"
1843	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1844	+	defaultZConsTol);
1845	+	painCave.isFatal = 0;
1846	+	simError();
1847	+
1848	+	zconsTol->setData(defaultZConsTol);
1849	+	}
1850	+	theInfo.addProperty(zconsTol);
1851	+
1852	+	//set Force Subtraction Policy
1853	+	StringData* zconsForcePolicy = new StringData();
1854	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1855	+
1856	+	if (globals->haveZconsForcePolicy()){
1857	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1858	+	}
1859	+	else{
1860	+	sprintf(painCave.errMsg,
1861	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1862	+	"\tOOPSE will use PolicyByMass.\n"
1863	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1864	+	painCave.isFatal = 0;
1865	+	simError();
1866	+	zconsForcePolicy->setData("BYMASS");
1867	+	}
1868	+
1869	+	theInfo.addProperty(zconsForcePolicy);
1870	+
1871	+	//set zcons gap
1872	+	DoubleData* zconsGap = new DoubleData();
1873	+	zconsGap->setID(ZCONSGAP_ID);
1874	+
1875	+	if (globals->haveZConsGap()){
1876	+	zconsGap->setData(globals->getZconsGap());
1877	+	theInfo.addProperty(zconsGap);
1878	+	}
1879	+
1880	+	//set zcons fixtime
1881	+	DoubleData* zconsFixtime = new DoubleData();
1882	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1883	+
1884	+	if (globals->haveZConsFixTime()){
1885	+	zconsFixtime->setData(globals->getZconsFixtime());
1886	+	theInfo.addProperty(zconsFixtime);
1887	+	}
1888	+
1889	+	//set zconsUsingSMD
1890	+	IntData* zconsUsingSMD = new IntData();
1891	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1892	+
1893	+	if (globals->haveZConsUsingSMD()){
1894	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1895	+	theInfo.addProperty(zconsUsingSMD);
1896	+	}
1897	+
1898	+	//Determine the name of ouput file and add it into SimInfo's property list
1899	+	//Be careful, do not use inFileName, since it is a pointer which
1900	+	//point to a string at master node, and slave nodes do not contain that string
1901	+
1902	+	string zconsOutput(theInfo.finalName);
1903	+
1904	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1905	+
1906	+	StringData* zconsFilename = new StringData();
1907	+	zconsFilename->setID(ZCONSFILENAME_ID);
1908	+	zconsFilename->setData(zconsOutput);
1909	+
1910	+	theInfo.addProperty(zconsFilename);
1911	+
1912	+	//setup index, pos and other parameters of z-constraint molecules
1913	+	nZConstraints = globals->getNzConstraints();
1914	+	theInfo.nZconstraints = nZConstraints;
1915	+
1916	+	zconStamp = globals->getZconStamp();
1917	+	ZConsParaItem tempParaItem;
1918	+
1919	+	ZConsParaData* zconsParaData = new ZConsParaData();
1920	+	zconsParaData->setID(ZCONSPARADATA_ID);
1921	+
1922	+	for (int i = 0; i < nZConstraints; i++){
1923	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1924	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1925	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1926	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1927	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1928	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1929	+	zconsParaData->addItem(tempParaItem);
1930	+	}
1931	+
1932	+	//check the uniqueness of index
1933	+	if(!zconsParaData->isIndexUnique()){
1934	+	sprintf(painCave.errMsg,
1935	+	"ZConstraint Error: molIndex is not unique!\n");
1936	+	painCave.isFatal = 1;
1937	+	simError();
1938	+	}
1939	+
1940	+	//sort the parameters by index of molecules
1941	+	zconsParaData->sortByIndex();
1942	+
1943	+	//push data into siminfo, therefore, we can retrieve later
1944	+	theInfo.addProperty(zconsParaData);
1945	+	}
1946	+
1947	+	void SimSetup::makeMinimizer(){
1948	+
1949	+	OOPSEMinimizer* myOOPSEMinimizer;
1950	+	MinimizerParameterSet* param;
1951	+	char minimizerName[100];
1952	+
1953	+	for (int i = 0; i < nInfo; i++){
1954	+
1955	+	//prepare parameter set for minimizer
1956	+	param = new MinimizerParameterSet();
1957	+	param->setDefaultParameter();
1958	+
1959	+	if (globals->haveMinimizer()){
1960	+	param->setFTol(globals->getMinFTol());
1961	+	}
1962	+
1963	+	if (globals->haveMinGTol()){
1964	+	param->setGTol(globals->getMinGTol());
1965	+	}
1966	+
1967	+	if (globals->haveMinMaxIter()){
1968	+	param->setMaxIteration(globals->getMinMaxIter());
1969	+	}
1970	+
1971	+	if (globals->haveMinWriteFrq()){
1972	+	param->setMaxIteration(globals->getMinMaxIter());
1973	+	}
1974	+
1975	+	if (globals->haveMinWriteFrq()){
1976	+	param->setWriteFrq(globals->getMinWriteFrq());
1977	+	}
1978	+
1979	+	if (globals->haveMinStepSize()){
1980	+	param->setStepSize(globals->getMinStepSize());
1981	+	}
1982	+
1983	+	if (globals->haveMinLSMaxIter()){
1984	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1985	+	}
1986	+
1987	+	if (globals->haveMinLSTol()){
1988	+	param->setLineSearchTol(globals->getMinLSTol());
1989	+	}
1990	+
1991	+	strcpy(minimizerName, globals->getMinimizer());
1992	+
1993	+	if (!strcasecmp(minimizerName, "CG")){
1994	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1995	+	}
1996	+	else if (!strcasecmp(minimizerName, "SD")){
1997	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1998	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1999	+	}
2000	+	else{
2001	+	sprintf(painCave.errMsg,
2002	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2003	+	painCave.isFatal = 0;
2004	+	simError();
2005	+
2006	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2007	+	}
2008	+	info[i].the_integrator = myOOPSEMinimizer;
2009	+
2010	+	//store the minimizer into simInfo
2011	+	info[i].the_minimizer = myOOPSEMinimizer;
2012	+	info[i].has_minimizer = true;
2013	+	}
2014	+
2015	+	}

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