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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 1041 by chrisfen, Mon Feb 9 14:48:57 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 "ConjugateMinimizer.hpp"
13
14		#ifdef IS_MPI
15		#include "mpiBASS.h"
#	Line 14 | Line 18
18
19		// some defines for ensemble and Forcefield  cases
20
21	<	#define NVE_ENS   0
22	<	#define NVT_ENS   1
23	<	#define NPTi_ENS  2
24	<	#define NPTf_ENS  3
25	<	#define NPTim_ENS 4
22	<	#define NPTfm_ENS 5
21	>	#define NVE_ENS        0
22	>	#define NVT_ENS        1
23	>	#define NPTi_ENS       2
24	>	#define NPTf_ENS       3
25	>	#define NPTxyz_ENS     4
26
27
28	<	#define FF_DUFF 0
29	<	#define FF_LJ   1
28	>	#define FF_DUFF  0
29	>	#define FF_LJ    1
30	>	#define FF_EAM   2
31	>	#define FF_H2O   3
32
33	+	using namespace std;
34
35	+	/**
36	+	* Check whether dividend is divisble by divisor or not
37	+	*/
38	+	bool isDivisible(double dividend, double divisor){
39	+	double tolerance = 0.000001;
40	+	double quotient;
41	+	double diff;
42	+	int intQuotient;
43	+
44	+	quotient = dividend / divisor;
45	+
46	+	if (quotient < 0)
47	+	quotient = -quotient;
48	+
49	+	intQuotient = int (quotient + tolerance);
50	+
51	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
52	+
53	+	if (diff <= tolerance)
54	+	return true;
55	+	else
56	+	return false;
57	+	}
58	+
59		SimSetup::SimSetup(){
60	+
61	+	initSuspend = false;
62	+	isInfoArray = 0;
63	+	nInfo = 1;
64	+
65		stamps = new MakeStamps();
66		globals = new Globals();
67	<
67	>
68	>
69		#ifdef IS_MPI
70	<	strcpy( checkPointMsg, "SimSetup creation successful" );
70	>	strcpy(checkPointMsg, "SimSetup creation successful");
71		MPIcheckPoint();
72		#endif // IS_MPI
73		}
#	Line 41 | Line 77 | SimSetup::~SimSetup(){
77		delete globals;
78		}
79
80	<	void SimSetup::parseFile( char* fileName ){
80	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
81	>	info = the_info;
82	>	nInfo = theNinfo;
83	>	isInfoArray = 1;
84	>	initSuspend = true;
85	>	}
86
87	+
88	+	void SimSetup::parseFile(char* fileName){
89		#ifdef IS_MPI
90	<	if( worldRank == 0 ){
90	>	if (worldRank == 0){
91		#endif // is_mpi
92	<
92	>
93		inFileName = fileName;
94	<	set_interface_stamps( stamps, globals );
95	<
94	>	set_interface_stamps(stamps, globals);
95	>
96		#ifdef IS_MPI
97		mpiEventInit();
98		#endif
99
100	<	yacc_BASS( fileName );
100	>	yacc_BASS(fileName);
101
102		#ifdef IS_MPI
103		throwMPIEvent(NULL);
104		}
105	<	else receiveParse();
105	>	else{
106	>	receiveParse();
107	>	}
108		#endif
109
110		}
111
112		#ifdef IS_MPI
113		void SimSetup::receiveParse(void){
114	<
115	<	set_interface_stamps( stamps, globals );
116	<	mpiEventInit();
117	<	MPIcheckPoint();
73	<	mpiEventLoop();
74	<
114	>	set_interface_stamps(stamps, globals);
115	>	mpiEventInit();
116	>	MPIcheckPoint();
117	>	mpiEventLoop();
118		}
119
120		#endif // is_mpi
121
122	<	void SimSetup::createSim( void ){
122	>	void SimSetup::createSim(void){
123
124	<	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;
124	>	// gather all of the information from the Bass file
125
126	<	// get the stamps and globals;
92	<	the_stamps = stamps;
93	<	the_globals = globals;
126	>	gatherInfo();
127
128	<	// 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();
128	>	// creation of complex system objects
129
130	<	// 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() );
130	>	sysObjectsCreation();
131
132	<	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	<	}
132	>	// check on the post processing info
133
134	<	// get the ensemble:
115	<	strcpy( ensemble, the_globals->getEnsemble() );
134	>	finalInfoCheck();
135
136	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
137	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
138	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
139	<	ensembleCase = NPTi_ENS;
140	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
141	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
142	<	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;
136	>	// initialize the system coordinates
137	>
138	>	if ( !initSuspend ){
139	>	initSystemCoords();
140	>
141	>	if( !(globals->getUseInitTime()) )
142	>	info[0].currentTime = 0.0;
143		}
134	–	strcpy( simnfo->ensemble, ensemble );
144
145	+	// make the output filenames
146
147	<	//   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	<	//     }
147	>	makeOutNames();
148
149	<	//     if (the_globals->haveTauThermostat())
150	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
151	<	//     else if (the_globals->haveQmass())
152	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
153	<	//     else {
154	<	//       sprintf( painCave.errMsg,
155	<	//                "SimSetup error: If you use one of the constant temperature\n"
156	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
157	<	//                "    Neither of these was found in the BASS file.\n");
158	<	//       painCave.isFatal = 1;
161	<	//       simError();
162	<	//     }
149	>	if (globals->haveMinimizer())
150	>	// make minimizer
151	>	makeMinimizer();
152	>	else
153	>	// make the integrator
154	>	makeIntegrator();
155	>
156	>	#ifdef IS_MPI
157	>	mpiSim->mpiRefresh();
158	>	#endif
159
160	<	//     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	<	//     }
160	>	// initialize the Fortran
161
162	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
163	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
177	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
162	>	initFortran();
163	>	}
164
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	–	//     }
165
166	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
167	<	simnfo->usePBC = the_globals->getPBC();
168	<
169	<	int usesDipoles = 0;
170	<	switch( ffCase ){
166	>	void SimSetup::makeMolecules(void){
167	>	int k;
168	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
169	>	molInit molInfo;
170	>	DirectionalAtom* dAtom;
171	>	LinkedAssign* extras;
172	>	LinkedAssign* current_extra;
173	>	AtomStamp* currentAtom;
174	>	BondStamp* currentBond;
175	>	BendStamp* currentBend;
176	>	TorsionStamp* currentTorsion;
177
178	<	case FF_DUFF:
179	<	the_ff = new DUFF();
180	<	usesDipoles = 1;
201	<	break;
178	>	bond_pair* theBonds;
179	>	bend_set* theBends;
180	>	torsion_set* theTorsions;
181
182	<	case FF_LJ:
204	<	the_ff = new LJFF();
205	<	break;
182	>	//init the forceField paramters
183
184	<	default:
208	<	sprintf( painCave.errMsg,
209	<	"SimSetup Error. Unrecognized force field in case statement.\n");
210	<	painCave.isFatal = 1;
211	<	simError();
212	<	}
184	>	the_ff->readParams();
185
214	–	#ifdef IS_MPI
215	–	strcpy( checkPointMsg, "ForceField creation successful" );
216	–	MPIcheckPoint();
217	–	#endif // is_mpi
186
187	<	// 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];
187	>	// init the atoms
188
189	<	if( !the_globals->haveNMol() ){
190	<	// we don't have the total number of molecules, so we assume it is
191	<	// given in each component
189	>	double phi, theta, psi;
190	>	double sux, suy, suz;
191	>	double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz;
192	>	double ux, uy, uz, u, uSqr;
193
194	<	tot_nmol = 0;
195	<	for( i=0; i<n_components; i++ ){
194	>	for (k = 0; k < nInfo; k++){
195	>	the_ff->setSimInfo(&(info[k]));
196
197	<	if( !the_components[i]->haveNMol() ){
198	<	// we have a problem
199	<	sprintf( painCave.errMsg,
200	<	"SimSetup Error. No global NMol or component NMol"
201	<	" given. Cannot calculate the number of atoms.\n" );
202	<	painCave.isFatal = 1;
203	<	simError();
204	<	}
197	>	atomOffset = 0;
198	>	excludeOffset = 0;
199	>	for (i = 0; i < info[k].n_mol; i++){
200	>	stampID = info[k].molecules[i].getStampID();
201	>
202	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
203	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
204	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
205	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
206	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
207	>
208	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
209	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
210	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
211	>	molInfo.myBends = new Bend * [molInfo.nBends];
212	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
213
214	<	tot_nmol += the_components[i]->getNMol();
215	<	components_nmol[i] = the_components[i]->getNMol();
216	<	}
243	<	}
244	<	else{
245	<	sprintf( painCave.errMsg,
246	<	"SimSetup error.\n"
247	<	"\tSorry, the ability to specify total"
248	<	" nMols and then give molfractions in the components\n"
249	<	"\tis not currently supported."
250	<	" Please give nMol in the components.\n" );
251	<	painCave.isFatal = 1;
252	<	simError();
253	<
254	<
255	<	//     tot_nmol = the_globals->getNMol();
256	<
257	<	//   //we have the total number of molecules, now we check for molfractions
258	<	//     for( i=0; i<n_components; i++ ){
259	<
260	<	//       if( !the_components[i]->haveMolFraction() ){
261	<
262	<	//  if( !the_components[i]->haveNMol() ){
263	<	//    //we have a problem
264	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
265	<	//              << " nMol was given in component
266	<
267	<	}
214	>	theBonds = new bond_pair[molInfo.nBonds];
215	>	theBends = new bend_set[molInfo.nBends];
216	>	theTorsions = new torsion_set[molInfo.nTorsions];
217
218	<	#ifdef IS_MPI
270	<	strcpy( checkPointMsg, "Have the number of components" );
271	<	MPIcheckPoint();
272	<	#endif // is_mpi
218	>	// make the Atoms
219
220	<	// make an array of molecule stamps that match the components used.
221	<	// also extract the used stamps out into a separate linked list
220	>	for (j = 0; j < molInfo.nAtoms; j++){
221	>	currentAtom = comp_stamps[stampID]->getAtom(j);
222	>	if (currentAtom->haveOrientation()){
223	>	dAtom = new DirectionalAtom((j + atomOffset),
224	>	info[k].getConfiguration());
225	>	info[k].n_oriented++;
226	>	molInfo.myAtoms[j] = dAtom;
227
228	<	simnfo->nComponents = n_components;
229	<	simnfo->componentsNmol = components_nmol;
230	<	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++ ){
228	>	// Directional Atoms have standard unit vectors which are oriented
229	>	// in space using the three Euler angles.  We assume the standard
230	>	// unit vector was originally along the z axis below.
231
232	<	id = the_components[i]->getType();
233	<	comp_stamps[i] = NULL;
234	<
235	<	// check to make sure the component isn't already in the list
232	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
233	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
234	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
235	>
236	>	Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
237	>	Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
238	>	Axz = sin(theta) * sin(psi);
239	>
240	>	Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
241	>	Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
242	>	Ayz = sin(theta) * cos(psi);
243	>
244	>	Azx = sin(phi) * sin(theta);
245	>	Azy = -cos(phi) * sin(theta);
246	>	Azz = cos(theta);
247
248	<	comp_stamps[i] = headStamp->match( id );
249	<	if( comp_stamps[i] == NULL ){
250	<
295	<	// 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	<	}
248	>	sux = 0.0;
249	>	suy = 0.0;
250	>	suz = 1.0;
251
252	<	#ifdef IS_MPI
253	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
254	<	MPIcheckPoint();
315	<	#endif // is_mpi
316	<
252	>	ux = (Axx * sux) + (Ayx * suy) + (Azx * suz);
253	>	uy = (Axy * sux) + (Ayy * suy) + (Azy * suz);
254	>	uz = (Axz * sux) + (Ayz * suy) + (Azz * suz);
255
256	+	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
257
258	+	u = sqrt(uSqr);
259	+	ux = ux / u;
260	+	uy = uy / u;
261	+	uz = uz / u;
262
263	<	// caclulate the number of atoms, bonds, bends and torsions
263	>	dAtom->setSUx(ux);
264	>	dAtom->setSUy(uy);
265	>	dAtom->setSUz(uz);
266	>	}
267	>	else{
268	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
269	>	info[k].getConfiguration());
270	>	}
271	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
272
322	–	tot_atoms = 0;
323	–	tot_bonds = 0;
324	–	tot_bends = 0;
325	–	tot_torsions = 0;
326	–	for( i=0; i<n_components; i++ ){
327	–
328	–	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
329	–	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
330	–	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
331	–	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
332	–	}
333	–
334	–	tot_SRI = tot_bonds + tot_bends + tot_torsions;
335	–
336	–	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];
344	–
273		#ifdef IS_MPI
274
275	<	// divide the molecules among processors here.
348	<
349	<	mpiSim = new mpiSimulation( simnfo );
350	<
351	<	globalIndex = mpiSim->divideLabor();
275	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
276
277	<	// set up the local variables
278	<
355	<	int localMol, allMol;
356	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
277	>	#endif // is_mpi
278	>	}
279
280	<	int* mol2proc = mpiSim->getMolToProcMap();
281	<	int* molCompType = mpiSim->getMolComponentType();
282	<
283	<	allMol = 0;
284	<	localMol = 0;
363	<	local_atoms = 0;
364	<	local_bonds = 0;
365	<	local_bends = 0;
366	<	local_torsions = 0;
367	<	globalAtomIndex = 0;
280	>	// make the bonds
281	>	for (j = 0; j < molInfo.nBonds; j++){
282	>	currentBond = comp_stamps[stampID]->getBond(j);
283	>	theBonds[j].a = currentBond->getA() + atomOffset;
284	>	theBonds[j].b = currentBond->getB() + atomOffset;
285
286	+	exI = theBonds[j].a;
287	+	exJ = theBonds[j].b;
288
289	<	for( i=0; i<n_components; i++ ){
289	>	// exclude_I must always be the smaller of the pair
290	>	if (exI > exJ){
291	>	tempEx = exI;
292	>	exI = exJ;
293	>	exJ = tempEx;
294	>	}
295	>	#ifdef IS_MPI
296	>	tempEx = exI;
297	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
298	>	tempEx = exJ;
299	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
300
301	<	for( j=0; j<components_nmol[i]; j++ ){
302	<
303	<	if( mol2proc[allMol] == worldRank ){
304	<
305	<	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++;
301	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
302	>	#else  // isn't MPI
303	>
304	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
305	>	#endif  //is_mpi
306		}
307	+	excludeOffset += molInfo.nBonds;
308
309	<	allMol++;
310	<	}
311	<	}
312	<	local_SRI = local_bonds + local_bends + local_torsions;
313	<
314	<	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	<	}
309	>	//make the bends
310	>	for (j = 0; j < molInfo.nBends; j++){
311	>	currentBend = comp_stamps[stampID]->getBend(j);
312	>	theBends[j].a = currentBend->getA() + atomOffset;
313	>	theBends[j].b = currentBend->getB() + atomOffset;
314	>	theBends[j].c = currentBend->getC() + atomOffset;
315
316	<	simnfo->n_bonds = local_bonds;
317	<	simnfo->n_bends = local_bends;
318	<	simnfo->n_torsions = local_torsions;
407	<	simnfo->n_SRI = local_SRI;
408	<	simnfo->n_mol = localMol;
316	>	if (currentBend->haveExtras()){
317	>	extras = currentBend->getExtras();
318	>	current_extra = extras;
319
320	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
321	<	MPIcheckPoint();
322	<
323	<
324	<	#endif // is_mpi
325	<
326	<
417	<	// create the atom and short range interaction arrays
418	<
419	<	Atom::createArrays(simnfo->n_atoms);
420	<	the_atoms = new Atom*[simnfo->n_atoms];
421	<	the_molecules = new Molecule[simnfo->n_mol];
422	<	int molIndex;
423	<
424	<	// initialize the molecule's stampID's
320	>	while (current_extra != NULL){
321	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
322	>	switch (current_extra->getType()){
323	>	case 0:
324	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
325	>	theBends[j].isGhost = 1;
326	>	break;
327
328	+	case 1:
329	+	theBends[j].ghost = (int) current_extra->getDouble() +
330	+	atomOffset;
331	+	theBends[j].isGhost = 1;
332	+	break;
333	+
334	+	default:
335	+	sprintf(painCave.errMsg,
336	+	"SimSetup Error: ghostVectorSource was neither a "
337	+	"double nor an int.\n"
338	+	"-->Bend[%d] in %s\n",
339	+	j, comp_stamps[stampID]->getID());
340	+	painCave.isFatal = 1;
341	+	simError();
342	+	}
343	+	}
344	+	else{
345	+	sprintf(painCave.errMsg,
346	+	"SimSetup Error: unhandled bend assignment:\n"
347	+	"    -->%s in Bend[%d] in %s\n",
348	+	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
349	+	painCave.isFatal = 1;
350	+	simError();
351	+	}
352	+
353	+	current_extra = current_extra->getNext();
354	+	}
355	+	}
356	+
357	+	if (!theBends[j].isGhost){
358	+	exI = theBends[j].a;
359	+	exJ = theBends[j].c;
360	+	}
361	+	else{
362	+	exI = theBends[j].a;
363	+	exJ = theBends[j].b;
364	+	}
365	+
366	+	// exclude_I must always be the smaller of the pair
367	+	if (exI > exJ){
368	+	tempEx = exI;
369	+	exI = exJ;
370	+	exJ = tempEx;
371	+	}
372		#ifdef IS_MPI
373	<
373	>	tempEx = exI;
374	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
375	>	tempEx = exJ;
376	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
377
378	<	molIndex = 0;
379	<	for(i=0; i<mpiSim->getTotNmol(); i++){
380	<
381	<	if(mol2proc[i] == worldRank ){
382	<	the_molecules[molIndex].setStampID( molCompType[i] );
383	<	the_molecules[molIndex].setMyIndex( molIndex );
435	<	the_molecules[molIndex].setGlobalIndex( i );
436	<	molIndex++;
437	<	}
438	<	}
378	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
379	>	#else  // isn't MPI
380	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
381	>	#endif  //is_mpi
382	>	}
383	>	excludeOffset += molInfo.nBends;
384
385	<	#else // is_mpi
386	<
387	<	molIndex = 0;
388	<	globalAtomIndex = 0;
389	<	for(i=0; i<n_components; i++){
390	<	for(j=0; j<components_nmol[i]; j++ ){
391	<	the_molecules[molIndex].setStampID( i );
392	<	the_molecules[molIndex].setMyIndex( molIndex );
393	<	the_molecules[molIndex].setGlobalIndex( molIndex );
394	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
395	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
396	<	globalAtomIndex++;
385	>	for (j = 0; j < molInfo.nTorsions; j++){
386	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
387	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
388	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
389	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
390	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
391	>
392	>	exI = theTorsions[j].a;
393	>	exJ = theTorsions[j].d;
394	>
395	>	// exclude_I must always be the smaller of the pair
396	>	if (exI > exJ){
397	>	tempEx = exI;
398	>	exI = exJ;
399	>	exJ = tempEx;
400	>	}
401	>	#ifdef IS_MPI
402	>	tempEx = exI;
403	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
404	>	tempEx = exJ;
405	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
406	>
407	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
408	>	#else  // isn't MPI
409	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
410	>	#endif  //is_mpi
411		}
412	<	molIndex++;
454	<	}
455	<	}
456	<
412	>	excludeOffset += molInfo.nTorsions;
413
458	–	#endif // is_mpi
414
415	+	// send the arrays off to the forceField for init.
416
417	<	if( simnfo->n_SRI ){
418	<
419	<	Exclude::createArray(simnfo->n_SRI);
420	<	the_excludes = new Exclude*[simnfo->n_SRI];
421	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
422	<	simnfo->globalExcludes = new int;
423	<	simnfo->n_exclude = simnfo->n_SRI;
417	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
418	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
419	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
420	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
421	>	theTorsions);
422	>
423	>
424	>	info[k].molecules[i].initialize(molInfo);
425	>
426	>
427	>	atomOffset += molInfo.nAtoms;
428	>	delete[] theBonds;
429	>	delete[] theBends;
430	>	delete[] theTorsions;
431	>	}
432		}
469	–	else{
470	–
471	–	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	–	}
433
434	<	// set the arrays into the SimInfo object
434	>	#ifdef IS_MPI
435	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
436	>	MPIcheckPoint();
437	>	#endif // is_mpi
438
439	<	simnfo->atoms = the_atoms;
483	<	simnfo->molecules = the_molecules;
484	<	simnfo->nGlobalExcludes = 0;
485	<	simnfo->excludes = the_excludes;
439	>	// clean up the forcefield
440
441	+	the_ff->calcRcut();
442	+	the_ff->cleanMe();
443	+	}
444
445	<	// get some of the tricky things that may still be in the globals
445	>	void SimSetup::initFromBass(void){
446	>	int i, j, k;
447	>	int n_cells;
448	>	double cellx, celly, cellz;
449	>	double temp1, temp2, temp3;
450	>	int n_per_extra;
451	>	int n_extra;
452	>	int have_extra, done;
453
454	<	double boxVector[3];
455	<	if( the_globals->haveBox() ){
456	<	boxVector[0] = the_globals->getBox();
457	<	boxVector[1] = the_globals->getBox();
494	<	boxVector[2] = the_globals->getBox();
495	<
496	<	simnfo->setBox( boxVector );
497	<	}
498	<	else if( the_globals->haveDensity() ){
454	>	double vel[3];
455	>	vel[0] = 0.0;
456	>	vel[1] = 0.0;
457	>	vel[2] = 0.0;
458
459	<	double vol;
460	<	vol = (double)tot_nmol / the_globals->getDensity();
461	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
503	<	boxVector[1] = boxVector[0];
504	<	boxVector[2] = boxVector[0];
459	>	temp1 = (double) tot_nmol / 4.0;
460	>	temp2 = pow(temp1, (1.0 / 3.0));
461	>	temp3 = ceil(temp2);
462
463	<	simnfo->setBox( boxVector );
464	<	}
465	<	else{
466	<	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();
463	>	have_extra = 0;
464	>	if (temp2 < temp3){
465	>	// we have a non-complete lattice
466	>	have_extra = 1;
467
468	<	if( !the_globals->haveBoxY() ){
469	<	sprintf( painCave.errMsg,
470	<	"SimSetup error, no periodic BoxY size given.\n" );
471	<	painCave.isFatal = 1;
472	<	simError();
473	<	}
474	<	boxVector[1] = the_globals->getBoxY();
468	>	n_cells = (int) temp3 - 1;
469	>	cellx = info[0].boxL[0] / temp3;
470	>	celly = info[0].boxL[1] / temp3;
471	>	cellz = info[0].boxL[2] / temp3;
472	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
473	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
474	>	n_per_extra = (int) ceil(temp1);
475
476	<	if( !the_globals->haveBoxZ() ){
477	<	sprintf( painCave.errMsg,
478	<	"SimSetup error, no periodic BoxZ size given.\n" );
476	>	if (n_per_extra > 4){
477	>	sprintf(painCave.errMsg,
478	>	"SimSetup error. There has been an error in constructing"
479	>	" the non-complete lattice.\n");
480		painCave.isFatal = 1;
481		simError();
482		}
531	–	boxVector[2] = the_globals->getBoxZ();
532	–
533	–	simnfo->setBox( boxVector );
483		}
484	+	else{
485	+	n_cells = (int) temp3;
486	+	cellx = info[0].boxL[0] / temp3;
487	+	celly = info[0].boxL[1] / temp3;
488	+	cellz = info[0].boxL[2] / temp3;
489	+	}
490
491	<	#ifdef IS_MPI
492	<	strcpy( checkPointMsg, "Box size set up" );
493	<	MPIcheckPoint();
494	<	#endif // is_mpi
491	>	current_mol = 0;
492	>	current_comp_mol = 0;
493	>	current_comp = 0;
494	>	current_atom_ndx = 0;
495
496	+	for (i = 0; i < n_cells ; i++){
497	+	for (j = 0; j < n_cells; j++){
498	+	for (k = 0; k < n_cells; k++){
499	+	makeElement(i * cellx, j * celly, k * cellz);
500
501	<	// initialize the arrays
501	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
502
503	<	the_ff->setSimInfo( simnfo );
503	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
504
505	<	makeMolecules();
506	<	simnfo->identArray = new int[simnfo->n_atoms];
507	<	for(i=0; i<simnfo->n_atoms; i++){
549	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
505	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
506	>	}
507	>	}
508		}
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	–	}
509
510	<	if( !the_globals->haveEST() ){
511	<	sprintf( painCave.errMsg,
512	<	"SimSetup Warning: using default value of 0.05 * the "
513	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
514	<	);
515	<	painCave.isFatal = 0;
516	<	simError();
517	<	simnfo->est = 0.05 * simnfo->ecr;
518	<	} else {
519	<	simnfo->est        = the_globals->getEST();
510	>	if (have_extra){
511	>	done = 0;
512	>
513	>	int start_ndx;
514	>	for (i = 0; i < (n_cells + 1) && !done; i++){
515	>	for (j = 0; j < (n_cells + 1) && !done; j++){
516	>	if (i < n_cells){
517	>	if (j < n_cells){
518	>	start_ndx = n_cells;
519	>	}
520	>	else
521	>	start_ndx = 0;
522	>	}
523	>	else
524	>	start_ndx = 0;
525	>
526	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
527	>	makeElement(i * cellx, j * celly, k * cellz);
528	>	done = (current_mol >= tot_nmol);
529	>
530	>	if (!done && n_per_extra > 1){
531	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
532	>	k * cellz);
533	>	done = (current_mol >= tot_nmol);
534	>	}
535	>
536	>	if (!done && n_per_extra > 2){
537	>	makeElement(i * cellx, j * celly + 0.5 * celly,
538	>	k * cellz + 0.5 * cellz);
539	>	done = (current_mol >= tot_nmol);
540	>	}
541	>
542	>	if (!done && n_per_extra > 3){
543	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
544	>	k * cellz + 0.5 * cellz);
545	>	done = (current_mol >= tot_nmol);
546	>	}
547	>	}
548	>	}
549		}
550	<
551	<	if(!the_globals->haveDielectric() ){
552	<	sprintf( painCave.errMsg,
553	<	"SimSetup Error: You are trying to use Reaction Field without"
554	<	"setting a dielectric constant!\n"
555	<	);
550	>	}
551	>
552	>	for (i = 0; i < info[0].n_atoms; i++){
553	>	info[0].atoms[i]->setVel(vel);
554	>	}
555	>	}
556	>
557	>	void SimSetup::makeElement(double x, double y, double z){
558	>	int k;
559	>	AtomStamp* current_atom;
560	>	DirectionalAtom* dAtom;
561	>	double rotMat[3][3];
562	>	double pos[3];
563	>
564	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
565	>	current_atom = comp_stamps[current_comp]->getAtom(k);
566	>	if (!current_atom->havePosition()){
567	>	sprintf(painCave.errMsg,
568	>	"SimSetup:initFromBass error.\n"
569	>	"\tComponent %s, atom %s does not have a position specified.\n"
570	>	"\tThe initialization routine is unable to give a start"
571	>	" position.\n",
572	>	comp_stamps[current_comp]->getID(), current_atom->getType());
573		painCave.isFatal = 1;
574		simError();
575		}
576	<	simnfo->dielectric = the_globals->getDielectric();
577	<	} else {
578	<	if (usesDipoles) {
579	<
580	<	if( !the_globals->haveECR() ){
581	<	sprintf( painCave.errMsg,
582	<	"SimSetup Warning: using default value of 1/2 the smallest "
583	<	"box length for the electrostaticCutoffRadius.\n"
584	<	"I hope you have a very fast processor!\n");
585	<	painCave.isFatal = 0;
586	<	simError();
587	<	double smallest;
588	<	smallest = simnfo->boxLx;
589	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
590	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
591	<	simnfo->ecr = 0.5 * smallest;
592	<	} else {
593	<	simnfo->ecr        = the_globals->getECR();
594	<	}
595	<
596	<	if( !the_globals->haveEST() ){
597	<	sprintf( painCave.errMsg,
598	<	"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	<	}
576	>
577	>	pos[0] = x + current_atom->getPosX();
578	>	pos[1] = y + current_atom->getPosY();
579	>	pos[2] = z + current_atom->getPosZ();
580	>
581	>	info[0].atoms[current_atom_ndx]->setPos(pos);
582	>
583	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
584	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
585	>
586	>	rotMat[0][0] = 1.0;
587	>	rotMat[0][1] = 0.0;
588	>	rotMat[0][2] = 0.0;
589	>
590	>	rotMat[1][0] = 0.0;
591	>	rotMat[1][1] = 1.0;
592	>	rotMat[1][2] = 0.0;
593	>
594	>	rotMat[2][0] = 0.0;
595	>	rotMat[2][1] = 0.0;
596	>	rotMat[2][2] = 1.0;
597	>
598	>	dAtom->setA(rotMat);
599		}
624	–	}
600
601	<	#ifdef IS_MPI
602	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
628	<	MPIcheckPoint();
629	<	#endif // is_mpi
601	>	current_atom_ndx++;
602	>	}
603
604	<	if( the_globals->haveInitialConfig() ){
605	<
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
604	>	current_mol++;
605	>	current_comp_mol++;
606
607	<	delete fileInit;
608	<	}
609	<	else{
607	>	if (current_comp_mol >= components_nmol[current_comp]){
608	>	current_comp_mol = 0;
609	>	current_comp++;
610	>	}
611	>	}
612
647	–	#ifdef IS_MPI
613
614	<	// no init from bass
615	<
651	<	sprintf( painCave.errMsg,
652	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
653	<	painCave.isFatal;
654	<	simError();
655	<
656	<	#else
614	>	void SimSetup::gatherInfo(void){
615	>	int i;
616
617	<	initFromBass();
617	>	ensembleCase = -1;
618	>	ffCase = -1;
619
620	+	// set the easy ones first
621
622	<	#endif
623	<	}
622	>	for (i = 0; i < nInfo; i++){
623	>	info[i].target_temp = globals->getTargetTemp();
624	>	info[i].dt = globals->getDt();
625	>	info[i].run_time = globals->getRunTime();
626	>	}
627	>	n_components = globals->getNComponents();
628
664	–	#ifdef IS_MPI
665	–	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
666	–	MPIcheckPoint();
667	–	#endif // is_mpi
629
630	+	// get the forceField
631
632	<
671	<
672	<
632	>	strcpy(force_field, globals->getForceField());
633
634	<
635	<	#ifdef IS_MPI
636	<	if( worldRank == 0 ){
637	<	#endif // is_mpi
638	<
639	<	if( the_globals->haveFinalConfig() ){
640	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
641	<	}
642	<	else{
643	<	strcpy( simnfo->finalName, inFileName );
644	<	char* endTest;
645	<	int nameLength = strlen( simnfo->finalName );
646	<	endTest = &(simnfo->finalName[nameLength - 5]);
647	<	if( !strcmp( endTest, ".bass" ) ){
648	<	strcpy( endTest, ".eor" );
649	<	}
650	<	else if( !strcmp( endTest, ".BASS" ) ){
651	<	strcpy( endTest, ".eor" );
652	<	}
653	<	else{
654	<	endTest = &(simnfo->finalName[nameLength - 4]);
655	<	if( !strcmp( endTest, ".bss" ) ){
656	<	strcpy( endTest, ".eor" );
657	<	}
658	<	else if( !strcmp( endTest, ".mdl" ) ){
699	<	strcpy( endTest, ".eor" );
700	<	}
701	<	else{
702	<	strcat( simnfo->finalName, ".eor" );
703	<	}
704	<	}
705	<	}
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
634	>	if (!strcasecmp(force_field, "DUFF")){
635	>	ffCase = FF_DUFF;
636	>	}
637	>	else if (!strcasecmp(force_field, "LJ")){
638	>	ffCase = FF_LJ;
639	>	}
640	>	else if (!strcasecmp(force_field, "EAM")){
641	>	ffCase = FF_EAM;
642	>	}
643	>	else if (!strcasecmp(force_field, "WATER")){
644	>	ffCase = FF_H2O;
645	>	}
646	>	else{
647	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
648	>	force_field);
649	>	painCave.isFatal = 1;
650	>	simError();
651	>	}
652	>
653	>	// get the ensemble
654	>
655	>	strcpy(ensemble, globals->getEnsemble());
656	>
657	>	if (!strcasecmp(ensemble, "NVE")){
658	>	ensembleCase = NVE_ENS;
659		}
660	<	#endif // is_mpi
661	<
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;
660	>	else if (!strcasecmp(ensemble, "NVT")){
661	>	ensembleCase = NVT_ENS;
662		}
663	<	else{
664	<	simnfo->sampleTime = the_globals->getRunTime();
767	<	simnfo->statusTime = simnfo->sampleTime;
768	<	simnfo->thermalTime = simnfo->sampleTime;
663	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
664	>	ensembleCase = NPTi_ENS;
665		}
666	<
667	<	if( the_globals->haveStatusTime() ){
772	<	simnfo->statusTime = the_globals->getStatusTime();
666	>	else if (!strcasecmp(ensemble, "NPTf")){
667	>	ensembleCase = NPTf_ENS;
668		}
669	<
670	<	if( the_globals->haveThermalTime() ){
776	<	simnfo->thermalTime = the_globals->getThermalTime();
669	>	else if (!strcasecmp(ensemble, "NPTxyz")){
670	>	ensembleCase = NPTxyz_ENS;
671		}
672	+	else{
673	+	sprintf(painCave.errMsg,
674	+	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
675	+	"\treverting to NVE for this simulation.\n",
676	+	ensemble);
677	+	painCave.isFatal = 0;
678	+	simError();
679	+	strcpy(ensemble, "NVE");
680	+	ensembleCase = NVE_ENS;
681	+	}
682
683	<	// check for the temperature set flag
683	>	for (i = 0; i < nInfo; i++){
684	>	strcpy(info[i].ensemble, ensemble);
685
686	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
686	>	// get the mixing rule
687
688	+	strcpy(info[i].mixingRule, globals->getMixingRule());
689	+	info[i].usePBC = globals->getPBC();
690	+	}
691
692	<	// make the integrator
785	<
786	<
787	<	NVT*  myNVT = NULL;
788	<	NPTi* myNPTi = NULL;
789	<	NPTf* myNPTf = NULL;
790	<	NPTim* myNPTim = NULL;
791	<	NPTfm* myNPTfm = NULL;
692	>	// get the components and calculate the tot_nMol and indvidual n_mol
693
694	<	switch( ensembleCase ){
694	>	the_components = globals->getComponents();
695	>	components_nmol = new int[n_components];
696
795	–	case NVE_ENS:
796	–	new NVE( simnfo, the_ff );
797	–	break;
697
698	<	case NVT_ENS:
699	<	myNVT = new NVT( simnfo, the_ff );
700	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
698	>	if (!globals->haveNMol()){
699	>	// we don't have the total number of molecules, so we assume it is
700	>	// given in each component
701
702	<	if (the_globals->haveTauThermostat())
703	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
702	>	tot_nmol = 0;
703	>	for (i = 0; i < n_components; i++){
704	>	if (!the_components[i]->haveNMol()){
705	>	// we have a problem
706	>	sprintf(painCave.errMsg,
707	>	"SimSetup Error. No global NMol or component NMol given.\n"
708	>	"\tCannot calculate the number of atoms.\n");
709	>	painCave.isFatal = 1;
710	>	simError();
711	>	}
712
713	<	else {
714	<	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();
713	>	tot_nmol += the_components[i]->getNMol();
714	>	components_nmol[i] = the_components[i]->getNMol();
715		}
716	<	break;
716	>	}
717	>	else{
718	>	sprintf(painCave.errMsg,
719	>	"SimSetup error.\n"
720	>	"\tSorry, the ability to specify total"
721	>	" nMols and then give molfractions in the components\n"
722	>	"\tis not currently supported."
723	>	" Please give nMol in the components.\n");
724	>	painCave.isFatal = 1;
725	>	simError();
726	>	}
727
728	<	case NPTi_ENS:
729	<	myNPTi = new NPTi( simnfo, the_ff );
730	<	myNPTi->setTargetTemp( the_globals->getTargetTemp());
728	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
729	>	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
730	>	sprintf(painCave.errMsg,
731	>	"Sample time is not divisible by dt.\n"
732	>	"\tThis will result in samples that are not uniformly\n"
733	>	"\tdistributed in time.  If this is a problem, change\n"
734	>	"\tyour sampleTime variable.\n");
735	>	painCave.isFatal = 0;
736	>	simError();
737	>	}
738
739	<	if (the_globals->haveTargetPressure())
740	<	myNPTi->setTargetPressure(the_globals->getTargetPressure());
741	<	else {
742	<	sprintf( painCave.errMsg,
743	<	"SimSetup error: If you use a constant pressure\n"
744	<	"    ensemble, you must set targetPressure in the BASS file.\n");
745	<	painCave.isFatal = 1;
746	<	simError();
747	<	}
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	<	}
739	>	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
740	>	sprintf(painCave.errMsg,
741	>	"Status time is not divisible by dt.\n"
742	>	"\tThis will result in status reports that are not uniformly\n"
743	>	"\tdistributed in time.  If this is a problem, change \n"
744	>	"\tyour statusTime variable.\n");
745	>	painCave.isFatal = 0;
746	>	simError();
747	>	}
748
749	<	if( the_globals->haveTauBarostat() )
750	<	myNPTi->setTauBarostat( the_globals->getTauBarostat() );
751	<	else{
752	<	sprintf( painCave.errMsg,
753	<	"SimSetup error: If you use an NPT\n"
754	<	"    ensemble, you must set tauBarostat.\n");
755	<	painCave.isFatal = 1;
756	<	simError();
757	<	}
848	<	break;
849	<
850	<	case NPTf_ENS:
851	<	myNPTf = new NPTf( simnfo, the_ff );
852	<	myNPTf->setTargetTemp( the_globals->getTargetTemp());
749	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
750	>	sprintf(painCave.errMsg,
751	>	"Thermal time is not divisible by dt.\n"
752	>	"\tThis will result in thermalizations that are not uniformly\n"
753	>	"\tdistributed in time.  If this is a problem, change \n"
754	>	"\tyour thermalTime variable.\n");
755	>	painCave.isFatal = 0;
756	>	simError();
757	>	}
758
759	<	if (the_globals->haveTargetPressure())
760	<	myNPTf->setTargetPressure(the_globals->getTargetPressure());
761	<	else {
762	<	sprintf( painCave.errMsg,
763	<	"SimSetup error: If you use a constant pressure\n"
764	<	"    ensemble, you must set targetPressure in the BASS file.\n");
765	<	painCave.isFatal = 1;
766	<	simError();
767	<	}
759	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
760	>	sprintf(painCave.errMsg,
761	>	"Reset time is not divisible by dt.\n"
762	>	"\tThis will result in integrator resets that are not uniformly\n"
763	>	"\tdistributed in time.  If this is a problem, change\n"
764	>	"\tyour resetTime variable.\n");
765	>	painCave.isFatal = 0;
766	>	simError();
767	>	}
768
769	<	if( the_globals->haveTauThermostat() )
770	<	myNPTf->setTauThermostat( the_globals->getTauThermostat() );
769	>	// set the status, sample, and thermal kick times
770	>
771	>	for (i = 0; i < nInfo; i++){
772	>	if (globals->haveSampleTime()){
773	>	info[i].sampleTime = globals->getSampleTime();
774	>	info[i].statusTime = info[i].sampleTime;
775	>	info[i].thermalTime = info[i].sampleTime;
776	>	}
777		else{
778	<	sprintf( painCave.errMsg,
779	<	"SimSetup error: If you use an NPT\n"
780	<	"    ensemble, you must set tauThermostat.\n");
870	<	painCave.isFatal = 1;
871	<	simError();
778	>	info[i].sampleTime = globals->getRunTime();
779	>	info[i].statusTime = info[i].sampleTime;
780	>	info[i].thermalTime = info[i].sampleTime;
781		}
782
783	<	if( the_globals->haveTauBarostat() )
784	<	myNPTf->setTauBarostat( the_globals->getTauBarostat() );
876	<	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();
783	>	if (globals->haveStatusTime()){
784	>	info[i].statusTime = globals->getStatusTime();
785		}
883	–	break;
884	–
885	–	case NPTim_ENS:
886	–	myNPTim = new NPTim( simnfo, the_ff );
887	–	myNPTim->setTargetTemp( the_globals->getTargetTemp());
786
787	<	if (the_globals->haveTargetPressure())
788	<	myNPTim->setTargetPressure(the_globals->getTargetPressure());
891	<	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();
787	>	if (globals->haveThermalTime()){
788	>	info[i].thermalTime = globals->getThermalTime();
789		}
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	–	}
790
791	<	if( the_globals->haveTauBarostat() )
792	<	myNPTim->setTauBarostat( the_globals->getTauBarostat() );
793	<	else{
794	<	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();
791	>	info[i].resetIntegrator = 0;
792	>	if( globals->haveResetTime() ){
793	>	info[i].resetTime = globals->getResetTime();
794	>	info[i].resetIntegrator = 1;
795		}
918	–	break;
796
797	<	case NPTfm_ENS:
798	<	myNPTfm = new NPTfm( simnfo, the_ff );
799	<	myNPTfm->setTargetTemp( the_globals->getTargetTemp());
797	>	// check for the temperature set flag
798	>
799	>	if (globals->haveTempSet())
800	>	info[i].setTemp = globals->getTempSet();
801
802	<	if (the_globals->haveTargetPressure())
803	<	myNPTfm->setTargetPressure(the_globals->getTargetPressure());
804	<	else {
805	<	sprintf( painCave.errMsg,
806	<	"SimSetup error: If you use a constant pressure\n"
807	<	"    ensemble, you must set targetPressure in the BASS file.\n");
808	<	painCave.isFatal = 1;
802	>	// check for the extended State init
803	>
804	>	info[i].useInitXSstate = globals->getUseInitXSstate();
805	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
806	>
807	>	}
808	>
809	>	//setup seed for random number generator
810	>	int seedValue;
811	>
812	>	if (globals->haveSeed()){
813	>	seedValue = globals->getSeed();
814	>
815	>	if(seedValue / 1E9 == 0){
816	>	sprintf(painCave.errMsg,
817	>	"Seed for sprng library should contain at least 9 digits\n"
818	>	"OOPSE will generate a seed for user\n");
819	>	painCave.isFatal = 0;
820		simError();
821	+
822	+	//using seed generated by system instead of invalid seed set by user
823	+	#ifndef IS_MPI
824	+	seedValue = make_sprng_seed();
825	+	#else
826	+	if (worldRank == 0){
827	+	seedValue = make_sprng_seed();
828	+	}
829	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
830	+	#endif
831		}
832	+	}//end of if branch of globals->haveSeed()
833	+	else{
834
835	<	if( the_globals->haveTauThermostat() )
836	<	myNPTfm->setTauThermostat( the_globals->getTauThermostat() );
837	<	else{
838	<	sprintf( painCave.errMsg,
839	<	"SimSetup error: If you use an NPT\n"
939	<	"    ensemble, you must set tauThermostat.\n");
940	<	painCave.isFatal = 1;
941	<	simError();
835	>	#ifndef IS_MPI
836	>	seedValue = make_sprng_seed();
837	>	#else
838	>	if (worldRank == 0){
839	>	seedValue = make_sprng_seed();
840		}
841	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
842	+	#endif
843	+	}//end of globals->haveSeed()
844
845	<	if( the_globals->haveTauBarostat() )
846	<	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;
954	<
955	<	default:
956	<	sprintf( painCave.errMsg,
957	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
958	<	painCave.isFatal = 1;
959	<	simError();
845	>	for (int i = 0; i < nInfo; i++){
846	>	info[i].setSeed(seedValue);
847		}
848	+
849	+	#ifdef IS_MPI
850	+	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
851	+	MPIcheckPoint();
852	+	#endif // is_mpi
853	+	}
854
855
856	+	void SimSetup::finalInfoCheck(void){
857	+	int index;
858	+	int usesDipoles;
859	+	int i;
860	+
861	+	for (i = 0; i < nInfo; i++){
862	+	// check electrostatic parameters
863	+
864	+	index = 0;
865	+	usesDipoles = 0;
866	+	while ((index < info[i].n_atoms) && !usesDipoles){
867	+	usesDipoles = (info[i].atoms[index])->hasDipole();
868	+	index++;
869	+	}
870	+
871		#ifdef IS_MPI
872	<	mpiSim->mpiRefresh();
873	<	#endif
872	>	int myUse = usesDipoles;
873	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
874	>	#endif //is_mpi
875
876	<	// initialize the Fortran
876	>	double theEcr, theEst;
877
878	+	if (globals->getUseRF()){
879	+	info[i].useReactionField = 1;
880
881	<	simnfo->refreshSim();
882	<
883	<	if( !strcmp( simnfo->mixingRule, "standard") ){
884	<	the_ff->initForceField( LB_MIXING_RULE );
885	<	}
886	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
887	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
888	<	}
889	<	else{
890	<	sprintf( painCave.errMsg,
891	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
892	<	simnfo->mixingRule );
982	<	painCave.isFatal = 1;
983	<	simError();
984	<	}
881	>	if (!globals->haveECR()){
882	>	sprintf(painCave.errMsg,
883	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
884	>	"\tOOPSE will use a default value of 15.0 angstroms"
885	>	"\tfor the electrostaticCutoffRadius.\n");
886	>	painCave.isFatal = 0;
887	>	simError();
888	>	theEcr = 15.0;
889	>	}
890	>	else{
891	>	theEcr = globals->getECR();
892	>	}
893
894	+	if (!globals->haveEST()){
895	+	sprintf(painCave.errMsg,
896	+	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
897	+	"\tOOPSE will use a default value of\n"
898	+	"\t0.05 * electrostaticCutoffRadius\n"
899	+	"\tfor the electrostaticSkinThickness\n");
900	+	painCave.isFatal = 0;
901	+	simError();
902	+	theEst = 0.05 * theEcr;
903	+	}
904	+	else{
905	+	theEst = globals->getEST();
906	+	}
907
908	+	info[i].setDefaultEcr(theEcr, theEst);
909	+
910	+	if (!globals->haveDielectric()){
911	+	sprintf(painCave.errMsg,
912	+	"SimSetup Error: No Dielectric constant was set.\n"
913	+	"\tYou are trying to use Reaction Field without"
914	+	"\tsetting a dielectric constant!\n");
915	+	painCave.isFatal = 1;
916	+	simError();
917	+	}
918	+	info[i].dielectric = globals->getDielectric();
919	+	}
920	+	else{
921	+	if (usesDipoles){
922	+	if (!globals->haveECR()){
923	+	sprintf(painCave.errMsg,
924	+	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
925	+	"\tOOPSE will use a default value of 15.0 angstroms"
926	+	"\tfor the electrostaticCutoffRadius.\n");
927	+	painCave.isFatal = 0;
928	+	simError();
929	+	theEcr = 15.0;
930	+	}
931	+	else{
932	+	theEcr = globals->getECR();
933	+	}
934	+
935	+	if (!globals->haveEST()){
936	+	sprintf(painCave.errMsg,
937	+	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
938	+	"\tOOPSE will use a default value of\n"
939	+	"\t0.05 * electrostaticCutoffRadius\n"
940	+	"\tfor the electrostaticSkinThickness\n");
941	+	painCave.isFatal = 0;
942	+	simError();
943	+	theEst = 0.05 * theEcr;
944	+	}
945	+	else{
946	+	theEst = globals->getEST();
947	+	}
948	+
949	+	info[i].setDefaultEcr(theEcr, theEst);
950	+	}
951	+	}
952	+	}
953		#ifdef IS_MPI
954	<	strcpy( checkPointMsg,
989	<	"Successfully intialized the mixingRule for Fortran." );
954	>	strcpy(checkPointMsg, "post processing checks out");
955		MPIcheckPoint();
956		#endif // is_mpi
957		}
958	+
959	+	void SimSetup::initSystemCoords(void){
960	+	int i;
961
962	+	char* inName;
963
964	<	void SimSetup::makeMolecules( void ){
964	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
965
966	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
967	<	molInit info;
999	<	DirectionalAtom* dAtom;
1000	<	LinkedAssign* extras;
1001	<	LinkedAssign* current_extra;
1002	<	AtomStamp* currentAtom;
1003	<	BondStamp* currentBond;
1004	<	BendStamp* currentBend;
1005	<	TorsionStamp* currentTorsion;
966	>	for (i = 0; i < info[0].n_atoms; i++)
967	>	info[0].atoms[i]->setCoords();
968
969	<	bond_pair* theBonds;
970	<	bend_set* theBends;
971	<	torsion_set* theTorsions;
969	>	if (globals->haveInitialConfig()){
970	>	InitializeFromFile* fileInit;
971	>	#ifdef IS_MPI // is_mpi
972	>	if (worldRank == 0){
973	>	#endif //is_mpi
974	>	inName = globals->getInitialConfig();
975	>	fileInit = new InitializeFromFile(inName);
976	>	#ifdef IS_MPI
977	>	}
978	>	else
979	>	fileInit = new InitializeFromFile(NULL);
980	>	#endif
981	>	fileInit->readInit(info); // default velocities on
982
983	<
984	<	//init the forceField paramters
983	>	delete fileInit;
984	>	}
985	>	else{
986	>
987	>	// no init from bass
988	>
989	>	sprintf(painCave.errMsg,
990	>	"Cannot intialize a simulation without an initial configuration file.\n");
991	>	painCave.isFatal = 1;;
992	>	simError();
993	>
994	>	}
995
996	<	the_ff->readParams();
996	>	#ifdef IS_MPI
997	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
998	>	MPIcheckPoint();
999	>	#endif // is_mpi
1000	>	}
1001
1016	–
1017	–	// init the atoms
1002
1003	<	double ux, uy, uz, u, uSqr;
1004	<
1021	<	atomOffset = 0;
1022	<	excludeOffset = 0;
1023	<	for(i=0; i<simnfo->n_mol; i++){
1024	<
1025	<	stampID = the_molecules[i].getStampID();
1003	>	void SimSetup::makeOutNames(void){
1004	>	int k;
1005
1027	–	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
1028	–	info.nBonds    = comp_stamps[stampID]->getNBonds();
1029	–	info.nBends    = comp_stamps[stampID]->getNBends();
1030	–	info.nTorsions = comp_stamps[stampID]->getNTorsions();
1031	–	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
1006
1007	<	info.myAtoms = &the_atoms[atomOffset];
1008	<	info.myExcludes = &the_excludes[excludeOffset];
1009	<	info.myBonds = new Bond*[info.nBonds];
1010	<	info.myBends = new Bend*[info.nBends];
1037	<	info.myTorsions = new Torsion*[info.nTorsions];
1007	>	for (k = 0; k < nInfo; k++){
1008	>	#ifdef IS_MPI
1009	>	if (worldRank == 0){
1010	>	#endif // is_mpi
1011
1012	<	theBonds = new bond_pair[info.nBonds];
1013	<	theBends = new bend_set[info.nBends];
1041	<	theTorsions = new torsion_set[info.nTorsions];
1042	<
1043	<	// make the Atoms
1044	<
1045	<	for(j=0; j<info.nAtoms; j++){
1046	<
1047	<	currentAtom = comp_stamps[stampID]->getAtom( j );
1048	<	if( currentAtom->haveOrientation() ){
1049	<
1050	<	dAtom = new DirectionalAtom(j + atomOffset);
1051	<	simnfo->n_oriented++;
1052	<	info.myAtoms[j] = dAtom;
1053	<
1054	<	ux = currentAtom->getOrntX();
1055	<	uy = currentAtom->getOrntY();
1056	<	uz = currentAtom->getOrntZ();
1057	<
1058	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
1059	<
1060	<	u = sqrt( uSqr );
1061	<	ux = ux / u;
1062	<	uy = uy / u;
1063	<	uz = uz / u;
1064	<
1065	<	dAtom->setSUx( ux );
1066	<	dAtom->setSUy( uy );
1067	<	dAtom->setSUz( uz );
1012	>	if (globals->haveFinalConfig()){
1013	>	strcpy(info[k].finalName, globals->getFinalConfig());
1014		}
1015		else{
1016	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
1016	>	strcpy(info[k].finalName, inFileName);
1017	>	char* endTest;
1018	>	int nameLength = strlen(info[k].finalName);
1019	>	endTest = &(info[k].finalName[nameLength - 5]);
1020	>	if (!strcmp(endTest, ".bass")){
1021	>	strcpy(endTest, ".eor");
1022	>	}
1023	>	else if (!strcmp(endTest, ".BASS")){
1024	>	strcpy(endTest, ".eor");
1025	>	}
1026	>	else{
1027	>	endTest = &(info[k].finalName[nameLength - 4]);
1028	>	if (!strcmp(endTest, ".bss")){
1029	>	strcpy(endTest, ".eor");
1030	>	}
1031	>	else if (!strcmp(endTest, ".mdl")){
1032	>	strcpy(endTest, ".eor");
1033	>	}
1034	>	else{
1035	>	strcat(info[k].finalName, ".eor");
1036	>	}
1037	>	}
1038		}
1072	–	info.myAtoms[j]->setType( currentAtom->getType() );
1073	–
1074	–	#ifdef IS_MPI
1075	–
1076	–	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
1077	–
1078	–	#endif // is_mpi
1079	–	}
1080	–
1081	–	// make the bonds
1082	–	for(j=0; j<info.nBonds; j++){
1083	–
1084	–	currentBond = comp_stamps[stampID]->getBond( j );
1085	–	theBonds[j].a = currentBond->getA() + atomOffset;
1086	–	theBonds[j].b = currentBond->getB() + atomOffset;
1039
1040	<	exI = theBonds[j].a;
1089	<	exJ = theBonds[j].b;
1040	>	// make the sample and status out names
1041
1042	<	// exclude_I must always be the smaller of the pair
1043	<	if( exI > exJ ){
1044	<	tempEx = exI;
1045	<	exI = exJ;
1046	<	exJ = tempEx;
1042	>	strcpy(info[k].sampleName, inFileName);
1043	>	char* endTest;
1044	>	int nameLength = strlen(info[k].sampleName);
1045	>	endTest = &(info[k].sampleName[nameLength - 5]);
1046	>	if (!strcmp(endTest, ".bass")){
1047	>	strcpy(endTest, ".dump");
1048		}
1049	<	#ifdef IS_MPI
1050	<	tempEx = exI;
1051	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1052	<	tempEx = exJ;
1053	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1054	<
1055	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1056	<	#else  // isn't MPI
1049	>	else if (!strcmp(endTest, ".BASS")){
1050	>	strcpy(endTest, ".dump");
1051	>	}
1052	>	else{
1053	>	endTest = &(info[k].sampleName[nameLength - 4]);
1054	>	if (!strcmp(endTest, ".bss")){
1055	>	strcpy(endTest, ".dump");
1056	>	}
1057	>	else if (!strcmp(endTest, ".mdl")){
1058	>	strcpy(endTest, ".dump");
1059	>	}
1060	>	else{
1061	>	strcat(info[k].sampleName, ".dump");
1062	>	}
1063	>	}
1064
1065	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1066	<	#endif  //is_mpi
1067	<	}
1068	<	excludeOffset += info.nBonds;
1069	<
1111	<	//make the bends
1112	<	for(j=0; j<info.nBends; j++){
1113	<
1114	<	currentBend = comp_stamps[stampID]->getBend( j );
1115	<	theBends[j].a = currentBend->getA() + atomOffset;
1116	<	theBends[j].b = currentBend->getB() + atomOffset;
1117	<	theBends[j].c = currentBend->getC() + atomOffset;
1118	<
1119	<	if( currentBend->haveExtras() ){
1120	<
1121	<	extras = currentBend->getExtras();
1122	<	current_extra = extras;
1123	<
1124	<	while( current_extra != NULL ){
1125	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1126	<
1127	<	switch( current_extra->getType() ){
1128	<
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	<	}
1065	>	strcpy(info[k].statusName, inFileName);
1066	>	nameLength = strlen(info[k].statusName);
1067	>	endTest = &(info[k].statusName[nameLength - 5]);
1068	>	if (!strcmp(endTest, ".bass")){
1069	>	strcpy(endTest, ".stat");
1070		}
1071	<
1072	<	if( !theBends[j].isGhost ){
1168	<
1169	<	exI = theBends[j].a;
1170	<	exJ = theBends[j].c;
1071	>	else if (!strcmp(endTest, ".BASS")){
1072	>	strcpy(endTest, ".stat");
1073		}
1074		else{
1075	<
1076	<	exI = theBends[j].a;
1077	<	exJ = theBends[j].b;
1075	>	endTest = &(info[k].statusName[nameLength - 4]);
1076	>	if (!strcmp(endTest, ".bss")){
1077	>	strcpy(endTest, ".stat");
1078	>	}
1079	>	else if (!strcmp(endTest, ".mdl")){
1080	>	strcpy(endTest, ".stat");
1081	>	}
1082	>	else{
1083	>	strcat(info[k].statusName, ".stat");
1084	>	}
1085		}
1177	–
1178	–	// exclude_I must always be the smaller of the pair
1179	–	if( exI > exJ ){
1180	–	tempEx = exI;
1181	–	exI = exJ;
1182	–	exJ = tempEx;
1183	–	}
1184	–	#ifdef IS_MPI
1185	–	tempEx = exI;
1186	–	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;
1086
1197	–	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;
1207	–
1208	–	// exclude_I must always be the smaller of the pair
1209	–	if( exI > exJ ){
1210	–	tempEx = exI;
1211	–	exI = exJ;
1212	–	exJ = tempEx;
1213	–	}
1087		#ifdef IS_MPI
1088	<	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
1088	>
1089		}
1090	<	excludeOffset += info.nTorsions;
1090	>	#endif // is_mpi
1091	>	}
1092	>	}
1093
1227	–
1228	–	// send the arrays off to the forceField for init.
1094
1095	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1096	<	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 );
1095	>	void SimSetup::sysObjectsCreation(void){
1096	>	int i, k;
1097
1098	+	// create the forceField
1099
1100	<	the_molecules[i].initialize( info );
1100	>	createFF();
1101
1102	+	// extract componentList
1103
1104	<	atomOffset += info.nAtoms;
1240	<	delete[] theBonds;
1241	<	delete[] theBends;
1242	<	delete[] theTorsions;
1243	<	}
1104	>	compList();
1105
1106	+	// calc the number of atoms, bond, bends, and torsions
1107	+
1108	+	calcSysValues();
1109	+
1110		#ifdef IS_MPI
1111	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1247	<	MPIcheckPoint();
1248	<	#endif // is_mpi
1111	>	// divide the molecules among the processors
1112
1113	<	// clean up the forcefield
1114	<	the_ff->calcRcut();
1252	<	the_ff->cleanMe();
1113	>	mpiMolDivide();
1114	>	#endif //is_mpi
1115
1116	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1117	+
1118	+	makeSysArrays();
1119	+
1120	+	// make and initialize the molecules (all but atomic coordinates)
1121	+
1122	+	makeMolecules();
1123	+
1124	+	for (k = 0; k < nInfo; k++){
1125	+	info[k].identArray = new int[info[k].n_atoms];
1126	+	for (i = 0; i < info[k].n_atoms; i++){
1127	+	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1128	+	}
1129	+	}
1130		}
1131
1256	–	void SimSetup::initFromBass( void ){
1132
1133	<	int i, j, k;
1134	<	int n_cells;
1135	<	double cellx, celly, cellz;
1136	<	double temp1, temp2, temp3;
1137	<	int n_per_extra;
1263	<	int n_extra;
1264	<	int have_extra, done;
1133	>	void SimSetup::createFF(void){
1134	>	switch (ffCase){
1135	>	case FF_DUFF:
1136	>	the_ff = new DUFF();
1137	>	break;
1138
1139	<	temp1 = (double)tot_nmol / 4.0;
1140	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1141	<	temp3 = ceil( temp2 );
1139	>	case FF_LJ:
1140	>	the_ff = new LJFF();
1141	>	break;
1142
1143	<	have_extra =0;
1144	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1145	<	have_extra =1;
1143	>	case FF_EAM:
1144	>	the_ff = new EAM_FF();
1145	>	break;
1146
1147	<	n_cells = (int)temp3 - 1;
1148	<	cellx = simnfo->boxLx / temp3;
1149	<	celly = simnfo->boxLy / temp3;
1277	<	cellz = simnfo->boxLz / temp3;
1278	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1279	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1280	<	n_per_extra = (int)ceil( temp1 );
1147	>	case FF_H2O:
1148	>	the_ff = new WATER();
1149	>	break;
1150
1151	<	if( n_per_extra > 4){
1152	<	sprintf( painCave.errMsg,
1153	<	"SimSetup error. There has been an error in constructing"
1285	<	" the non-complete lattice.\n" );
1151	>	default:
1152	>	sprintf(painCave.errMsg,
1153	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1154		painCave.isFatal = 1;
1155		simError();
1288	–	}
1156		}
1290	–	else{
1291	–	n_cells = (int)temp3;
1292	–	cellx = simnfo->boxLx / temp3;
1293	–	celly = simnfo->boxLy / temp3;
1294	–	cellz = simnfo->boxLz / temp3;
1295	–	}
1157
1158	<	current_mol = 0;
1159	<	current_comp_mol = 0;
1160	<	current_comp = 0;
1161	<	current_atom_ndx = 0;
1158	>	#ifdef IS_MPI
1159	>	strcpy(checkPointMsg, "ForceField creation successful");
1160	>	MPIcheckPoint();
1161	>	#endif // is_mpi
1162	>	}
1163
1302	–	for( i=0; i < n_cells ; i++ ){
1303	–	for( j=0; j < n_cells; j++ ){
1304	–	for( k=0; k < n_cells; k++ ){
1164
1165	<	makeElement( i * cellx,
1166	<	j * celly,
1167	<	k * cellz );
1165	>	void SimSetup::compList(void){
1166	>	int i;
1167	>	char* id;
1168	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1169	>	LinkedMolStamp* currentStamp = NULL;
1170	>	comp_stamps = new MoleculeStamp * [n_components];
1171
1172	<	makeElement( i * cellx + 0.5 * cellx,
1173	<	j * celly + 0.5 * celly,
1312	<	k * cellz );
1172	>	// make an array of molecule stamps that match the components used.
1173	>	// also extract the used stamps out into a separate linked list
1174
1175	<	makeElement( i * cellx,
1176	<	j * celly + 0.5 * celly,
1177	<	k * cellz + 0.5 * cellz );
1175	>	for (i = 0; i < nInfo; i++){
1176	>	info[i].nComponents = n_components;
1177	>	info[i].componentsNmol = components_nmol;
1178	>	info[i].compStamps = comp_stamps;
1179	>	info[i].headStamp = headStamp;
1180	>	}
1181
1182	<	makeElement( i * cellx + 0.5 * cellx,
1183	<	j * celly,
1184	<	k * cellz + 0.5 * cellz );
1182	>
1183	>	for (i = 0; i < n_components; i++){
1184	>	id = the_components[i]->getType();
1185	>	comp_stamps[i] = NULL;
1186	>
1187	>	// check to make sure the component isn't already in the list
1188	>
1189	>	comp_stamps[i] = headStamp->match(id);
1190	>	if (comp_stamps[i] == NULL){
1191	>	// extract the component from the list;
1192	>
1193	>	currentStamp = stamps->extractMolStamp(id);
1194	>	if (currentStamp == NULL){
1195	>	sprintf(painCave.errMsg,
1196	>	"SimSetup error: Component \"%s\" was not found in the "
1197	>	"list of declared molecules\n",
1198	>	id);
1199	>	painCave.isFatal = 1;
1200	>	simError();
1201		}
1202	+
1203	+	headStamp->add(currentStamp);
1204	+	comp_stamps[i] = headStamp->match(id);
1205		}
1206		}
1207
1208	<	if( have_extra ){
1209	<	done = 0;
1208	>	#ifdef IS_MPI
1209	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1210	>	MPIcheckPoint();
1211	>	#endif // is_mpi
1212	>	}
1213
1214	<	int start_ndx;
1215	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1330	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1214	>	void SimSetup::calcSysValues(void){
1215	>	int i;
1216
1217	<	if( i < n_cells ){
1217	>	int* molMembershipArray;
1218
1219	<	if( j < n_cells ){
1220	<	start_ndx = n_cells;
1221	<	}
1222	<	else start_ndx = 0;
1223	<	}
1224	<	else start_ndx = 0;
1219	>	tot_atoms = 0;
1220	>	tot_bonds = 0;
1221	>	tot_bends = 0;
1222	>	tot_torsions = 0;
1223	>	for (i = 0; i < n_components; i++){
1224	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1225	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1226	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1227	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1228	>	}
1229
1230	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1230	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1231	>	molMembershipArray = new int[tot_atoms];
1232
1233	<	makeElement( i * cellx,
1234	<	j * celly,
1235	<	k * cellz );
1236	<	done = ( current_mol >= tot_nmol );
1233	>	for (i = 0; i < nInfo; i++){
1234	>	info[i].n_atoms = tot_atoms;
1235	>	info[i].n_bonds = tot_bonds;
1236	>	info[i].n_bends = tot_bends;
1237	>	info[i].n_torsions = tot_torsions;
1238	>	info[i].n_SRI = tot_SRI;
1239	>	info[i].n_mol = tot_nmol;
1240
1241	<	if( !done && n_per_extra > 1 ){
1242	<	makeElement( i * cellx + 0.5 * cellx,
1243	<	j * celly + 0.5 * celly,
1351	<	k * cellz );
1352	<	done = ( current_mol >= tot_nmol );
1353	<	}
1241	>	info[i].molMembershipArray = molMembershipArray;
1242	>	}
1243	>	}
1244
1245	<	if( !done && n_per_extra > 2){
1356	<	makeElement( i * cellx,
1357	<	j * celly + 0.5 * celly,
1358	<	k * cellz + 0.5 * cellz );
1359	<	done = ( current_mol >= tot_nmol );
1360	<	}
1245	>	#ifdef IS_MPI
1246
1247	<	if( !done && n_per_extra > 3){
1248	<	makeElement( i * cellx + 0.5 * cellx,
1249	<	j * celly,
1250	<	k * cellz + 0.5 * cellz );
1251	<	done = ( current_mol >= tot_nmol );
1252	<	}
1253	<	}
1247	>	void SimSetup::mpiMolDivide(void){
1248	>	int i, j, k;
1249	>	int localMol, allMol;
1250	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1251	>
1252	>	mpiSim = new mpiSimulation(info);
1253	>
1254	>	globalIndex = mpiSim->divideLabor();
1255	>
1256	>	// set up the local variables
1257	>
1258	>	mol2proc = mpiSim->getMolToProcMap();
1259	>	molCompType = mpiSim->getMolComponentType();
1260	>
1261	>	allMol = 0;
1262	>	localMol = 0;
1263	>	local_atoms = 0;
1264	>	local_bonds = 0;
1265	>	local_bends = 0;
1266	>	local_torsions = 0;
1267	>	globalAtomIndex = 0;
1268	>
1269	>
1270	>	for (i = 0; i < n_components; i++){
1271	>	for (j = 0; j < components_nmol[i]; j++){
1272	>	if (mol2proc[allMol] == worldRank){
1273	>	local_atoms += comp_stamps[i]->getNAtoms();
1274	>	local_bonds += comp_stamps[i]->getNBonds();
1275	>	local_bends += comp_stamps[i]->getNBends();
1276	>	local_torsions += comp_stamps[i]->getNTorsions();
1277	>	localMol++;
1278	>	}
1279	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1280	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1281	>	globalAtomIndex++;
1282		}
1283	+
1284	+	allMol++;
1285		}
1286		}
1287	+	local_SRI = local_bonds + local_bends + local_torsions;
1288
1289	+	info[0].n_atoms = mpiSim->getMyNlocal();
1290
1291	<	for( i=0; i<simnfo->n_atoms; i++ ){
1292	<	simnfo->atoms[i]->set_vx( 0.0 );
1293	<	simnfo->atoms[i]->set_vy( 0.0 );
1294	<	simnfo->atoms[i]->set_vz( 0.0 );
1291	>	if (local_atoms != info[0].n_atoms){
1292	>	sprintf(painCave.errMsg,
1293	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1294	>	"\tlocalAtom (%d) are not equal.\n",
1295	>	info[0].n_atoms, local_atoms);
1296	>	painCave.isFatal = 1;
1297	>	simError();
1298		}
1299	+
1300	+	info[0].n_bonds = local_bonds;
1301	+	info[0].n_bends = local_bends;
1302	+	info[0].n_torsions = local_torsions;
1303	+	info[0].n_SRI = local_SRI;
1304	+	info[0].n_mol = localMol;
1305	+
1306	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1307	+	MPIcheckPoint();
1308		}
1309
1310	<	void SimSetup::makeElement( double x, double y, double z ){
1310	>	#endif // is_mpi
1311
1383	–	int k;
1384	–	AtomStamp* current_atom;
1385	–	DirectionalAtom* dAtom;
1386	–	double rotMat[3][3];
1312
1313	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1313	>	void SimSetup::makeSysArrays(void){
1314	>
1315	>	#ifndef IS_MPI
1316	>	int k, j;
1317	>	#endif // is_mpi
1318	>	int i, l;
1319
1320	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1321	<	if( !current_atom->havePosition() ){
1322	<	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	<	}
1320	>	Atom** the_atoms;
1321	>	Molecule* the_molecules;
1322	>	Exclude** the_excludes;
1323
1403	–	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1404	–	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1405	–	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1324
1325	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1325	>	for (l = 0; l < nInfo; l++){
1326	>	// create the atom and short range interaction arrays
1327
1328	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1328	>	the_atoms = new Atom * [info[l].n_atoms];
1329	>	the_molecules = new Molecule[info[l].n_mol];
1330	>	int molIndex;
1331
1332	<	rotMat[0][0] = 1.0;
1412	<	rotMat[0][1] = 0.0;
1413	<	rotMat[0][2] = 0.0;
1332	>	// initialize the molecule's stampID's
1333
1334	<	rotMat[1][0] = 0.0;
1416	<	rotMat[1][1] = 1.0;
1417	<	rotMat[1][2] = 0.0;
1334	>	#ifdef IS_MPI
1335
1419	–	rotMat[2][0] = 0.0;
1420	–	rotMat[2][1] = 0.0;
1421	–	rotMat[2][2] = 1.0;
1336
1337	<	dAtom->setA( rotMat );
1337	>	molIndex = 0;
1338	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1339	>	if (mol2proc[i] == worldRank){
1340	>	the_molecules[molIndex].setStampID(molCompType[i]);
1341	>	the_molecules[molIndex].setMyIndex(molIndex);
1342	>	the_molecules[molIndex].setGlobalIndex(i);
1343	>	molIndex++;
1344	>	}
1345		}
1346
1347	<	current_atom_ndx++;
1427	<	}
1347	>	#else // is_mpi
1348
1349	<	current_mol++;
1350	<	current_comp_mol++;
1349	>	molIndex = 0;
1350	>	globalAtomIndex = 0;
1351	>	for (i = 0; i < n_components; i++){
1352	>	for (j = 0; j < components_nmol[i]; j++){
1353	>	the_molecules[molIndex].setStampID(i);
1354	>	the_molecules[molIndex].setMyIndex(molIndex);
1355	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1356	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1357	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1358	>	globalAtomIndex++;
1359	>	}
1360	>	molIndex++;
1361	>	}
1362	>	}
1363
1432	–	if( current_comp_mol >= components_nmol[current_comp] ){
1364
1365	<	current_comp_mol = 0;
1366	<	current_comp++;
1365	>	#endif // is_mpi
1366	>
1367	>
1368	>	if (info[l].n_SRI){
1369	>	Exclude::createArray(info[l].n_SRI);
1370	>	the_excludes = new Exclude * [info[l].n_SRI];
1371	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1372	>	the_excludes[ex] = new Exclude(ex);
1373	>	}
1374	>	info[l].globalExcludes = new int;
1375	>	info[l].n_exclude = info[l].n_SRI;
1376	>	}
1377	>	else{
1378	>	Exclude::createArray(1);
1379	>	the_excludes = new Exclude * ;
1380	>	the_excludes[0] = new Exclude(0);
1381	>	the_excludes[0]->setPair(0, 0);
1382	>	info[l].globalExcludes = new int;
1383	>	info[l].globalExcludes[0] = 0;
1384	>	info[l].n_exclude = 0;
1385	>	}
1386	>
1387	>	// set the arrays into the SimInfo object
1388	>
1389	>	info[l].atoms = the_atoms;
1390	>	info[l].molecules = the_molecules;
1391	>	info[l].nGlobalExcludes = 0;
1392	>	info[l].excludes = the_excludes;
1393	>
1394	>	the_ff->setSimInfo(info);
1395		}
1396		}
1397	+
1398	+	void SimSetup::makeIntegrator(void){
1399	+	int k;
1400	+
1401	+	NVE<RealIntegrator>* myNVE = NULL;
1402	+	NVT<RealIntegrator>* myNVT = NULL;
1403	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1404	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1405	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1406	+
1407	+	for (k = 0; k < nInfo; k++){
1408	+	switch (ensembleCase){
1409	+	case NVE_ENS:
1410	+	if (globals->haveZconstraints()){
1411	+	setupZConstraint(info[k]);
1412	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1413	+	}
1414	+	else{
1415	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1416	+	}
1417	+
1418	+	info->the_integrator = myNVE;
1419	+	break;
1420	+
1421	+	case NVT_ENS:
1422	+	if (globals->haveZconstraints()){
1423	+	setupZConstraint(info[k]);
1424	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1425	+	}
1426	+	else
1427	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1428	+
1429	+	myNVT->setTargetTemp(globals->getTargetTemp());
1430	+
1431	+	if (globals->haveTauThermostat())
1432	+	myNVT->setTauThermostat(globals->getTauThermostat());
1433	+	else{
1434	+	sprintf(painCave.errMsg,
1435	+	"SimSetup error: If you use the NVT\n"
1436	+	"\tensemble, you must set tauThermostat.\n");
1437	+	painCave.isFatal = 1;
1438	+	simError();
1439	+	}
1440	+
1441	+	info->the_integrator = myNVT;
1442	+	break;
1443	+
1444	+	case NPTi_ENS:
1445	+	if (globals->haveZconstraints()){
1446	+	setupZConstraint(info[k]);
1447	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1448	+	}
1449	+	else
1450	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1451	+
1452	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1453	+
1454	+	if (globals->haveTargetPressure())
1455	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1456	+	else{
1457	+	sprintf(painCave.errMsg,
1458	+	"SimSetup error: If you use a constant pressure\n"
1459	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1460	+	painCave.isFatal = 1;
1461	+	simError();
1462	+	}
1463	+
1464	+	if (globals->haveTauThermostat())
1465	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1466	+	else{
1467	+	sprintf(painCave.errMsg,
1468	+	"SimSetup error: If you use an NPT\n"
1469	+	"\tensemble, you must set tauThermostat.\n");
1470	+	painCave.isFatal = 1;
1471	+	simError();
1472	+	}
1473	+
1474	+	if (globals->haveTauBarostat())
1475	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1476	+	else{
1477	+	sprintf(painCave.errMsg,
1478	+	"SimSetup error: If you use an NPT\n"
1479	+	"\tensemble, you must set tauBarostat.\n");
1480	+	painCave.isFatal = 1;
1481	+	simError();
1482	+	}
1483	+
1484	+	info->the_integrator = myNPTi;
1485	+	break;
1486	+
1487	+	case NPTf_ENS:
1488	+	if (globals->haveZconstraints()){
1489	+	setupZConstraint(info[k]);
1490	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1491	+	}
1492	+	else
1493	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1494	+
1495	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1496	+
1497	+	if (globals->haveTargetPressure())
1498	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1499	+	else{
1500	+	sprintf(painCave.errMsg,
1501	+	"SimSetup error: If you use a constant pressure\n"
1502	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1503	+	painCave.isFatal = 1;
1504	+	simError();
1505	+	}
1506	+
1507	+	if (globals->haveTauThermostat())
1508	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1509	+
1510	+	else{
1511	+	sprintf(painCave.errMsg,
1512	+	"SimSetup error: If you use an NPT\n"
1513	+	"\tensemble, you must set tauThermostat.\n");
1514	+	painCave.isFatal = 1;
1515	+	simError();
1516	+	}
1517	+
1518	+	if (globals->haveTauBarostat())
1519	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1520	+
1521	+	else{
1522	+	sprintf(painCave.errMsg,
1523	+	"SimSetup error: If you use an NPT\n"
1524	+	"\tensemble, you must set tauBarostat.\n");
1525	+	painCave.isFatal = 1;
1526	+	simError();
1527	+	}
1528	+
1529	+	info->the_integrator = myNPTf;
1530	+	break;
1531	+
1532	+	case NPTxyz_ENS:
1533	+	if (globals->haveZconstraints()){
1534	+	setupZConstraint(info[k]);
1535	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1536	+	}
1537	+	else
1538	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1539	+
1540	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1541	+
1542	+	if (globals->haveTargetPressure())
1543	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1544	+	else{
1545	+	sprintf(painCave.errMsg,
1546	+	"SimSetup error: If you use a constant pressure\n"
1547	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1548	+	painCave.isFatal = 1;
1549	+	simError();
1550	+	}
1551	+
1552	+	if (globals->haveTauThermostat())
1553	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1554	+	else{
1555	+	sprintf(painCave.errMsg,
1556	+	"SimSetup error: If you use an NPT\n"
1557	+	"\tensemble, you must set tauThermostat.\n");
1558	+	painCave.isFatal = 1;
1559	+	simError();
1560	+	}
1561	+
1562	+	if (globals->haveTauBarostat())
1563	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1564	+	else{
1565	+	sprintf(painCave.errMsg,
1566	+	"SimSetup error: If you use an NPT\n"
1567	+	"\tensemble, you must set tauBarostat.\n");
1568	+	painCave.isFatal = 1;
1569	+	simError();
1570	+	}
1571	+
1572	+	info->the_integrator = myNPTxyz;
1573	+	break;
1574	+
1575	+	default:
1576	+	sprintf(painCave.errMsg,
1577	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1578	+	painCave.isFatal = 1;
1579	+	simError();
1580	+	}
1581	+	}
1582	+	}
1583	+
1584	+	void SimSetup::initFortran(void){
1585	+	info[0].refreshSim();
1586	+
1587	+	if (!strcmp(info[0].mixingRule, "standard")){
1588	+	the_ff->initForceField(LB_MIXING_RULE);
1589	+	}
1590	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1591	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1592	+	}
1593	+	else{
1594	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1595	+	info[0].mixingRule);
1596	+	painCave.isFatal = 1;
1597	+	simError();
1598	+	}
1599	+
1600	+
1601	+	#ifdef IS_MPI
1602	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1603	+	MPIcheckPoint();
1604	+	#endif // is_mpi
1605	+	}
1606	+
1607	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1608	+	int nZConstraints;
1609	+	ZconStamp** zconStamp;
1610	+
1611	+	if (globals->haveZconstraintTime()){
1612	+	//add sample time of z-constraint  into SimInfo's property list
1613	+	DoubleData* zconsTimeProp = new DoubleData();
1614	+	zconsTimeProp->setID(ZCONSTIME_ID);
1615	+	zconsTimeProp->setData(globals->getZconsTime());
1616	+	theInfo.addProperty(zconsTimeProp);
1617	+	}
1618	+	else{
1619	+	sprintf(painCave.errMsg,
1620	+	"ZConstraint error: If you use a ZConstraint,\n"
1621	+	"\tyou must set zconsTime.\n");
1622	+	painCave.isFatal = 1;
1623	+	simError();
1624	+	}
1625	+
1626	+	//push zconsTol into siminfo, if user does not specify
1627	+	//value for zconsTol, a default value will be used
1628	+	DoubleData* zconsTol = new DoubleData();
1629	+	zconsTol->setID(ZCONSTOL_ID);
1630	+	if (globals->haveZconsTol()){
1631	+	zconsTol->setData(globals->getZconsTol());
1632	+	}
1633	+	else{
1634	+	double defaultZConsTol = 0.01;
1635	+	sprintf(painCave.errMsg,
1636	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1637	+	"\tOOPSE will use a default value of %f.\n"
1638	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1639	+	defaultZConsTol);
1640	+	painCave.isFatal = 0;
1641	+	simError();
1642	+
1643	+	zconsTol->setData(defaultZConsTol);
1644	+	}
1645	+	theInfo.addProperty(zconsTol);
1646	+
1647	+	//set Force Subtraction Policy
1648	+	StringData* zconsForcePolicy = new StringData();
1649	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1650	+
1651	+	if (globals->haveZconsForcePolicy()){
1652	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1653	+	}
1654	+	else{
1655	+	sprintf(painCave.errMsg,
1656	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1657	+	"\tOOPSE will use PolicyByMass.\n"
1658	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1659	+	painCave.isFatal = 0;
1660	+	simError();
1661	+	zconsForcePolicy->setData("BYMASS");
1662	+	}
1663	+
1664	+	theInfo.addProperty(zconsForcePolicy);
1665	+
1666	+	//Determine the name of ouput file and add it into SimInfo's property list
1667	+	//Be careful, do not use inFileName, since it is a pointer which
1668	+	//point to a string at master node, and slave nodes do not contain that string
1669	+
1670	+	string zconsOutput(theInfo.finalName);
1671	+
1672	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1673	+
1674	+	StringData* zconsFilename = new StringData();
1675	+	zconsFilename->setID(ZCONSFILENAME_ID);
1676	+	zconsFilename->setData(zconsOutput);
1677	+
1678	+	theInfo.addProperty(zconsFilename);
1679	+
1680	+	//setup index, pos and other parameters of z-constraint molecules
1681	+	nZConstraints = globals->getNzConstraints();
1682	+	theInfo.nZconstraints = nZConstraints;
1683	+
1684	+	zconStamp = globals->getZconStamp();
1685	+	ZConsParaItem tempParaItem;
1686	+
1687	+	ZConsParaData* zconsParaData = new ZConsParaData();
1688	+	zconsParaData->setID(ZCONSPARADATA_ID);
1689	+
1690	+	for (int i = 0; i < nZConstraints; i++){
1691	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1692	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1693	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1694	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1695	+
1696	+	zconsParaData->addItem(tempParaItem);
1697	+	}
1698	+
1699	+	//check the uniqueness of index
1700	+	if(!zconsParaData->isIndexUnique()){
1701	+	sprintf(painCave.errMsg,
1702	+	"ZConstraint Error: molIndex is not unique!\n");
1703	+	painCave.isFatal = 1;
1704	+	simError();
1705	+	}
1706	+
1707	+	//sort the parameters by index of molecules
1708	+	zconsParaData->sortByIndex();
1709	+
1710	+	//push data into siminfo, therefore, we can retrieve later
1711	+	theInfo.addProperty(zconsParaData);
1712	+	}
1713	+
1714	+	void SimSetup::makeMinimizer(){
1715	+
1716	+	OOPSEMinimizerBase* myOOPSEMinimizerBase;
1717	+	ObjFunctor1 * objFunc;
1718	+	OutputFunctor* outputFunc;
1719	+	ConcreteNLModel1* nlp;
1720	+	MinimizerParameterSet* param;
1721	+	ConjugateMinimizerBase* minimizer;
1722	+	int dim;
1723	+
1724	+	for (int i = 0; i < nInfo; i++){
1725	+	//creat
1726	+	myOOPSEMinimizerBase = new OOPSEMinimizerBase(&(info[i]), the_ff);
1727	+
1728	+	info[i].the_integrator = myOOPSEMinimizerBase;
1729	+	//creat the object functor;
1730	+	objFunc = (ObjFunctor1*) new ClassMemObjFunctor1<OOPSEMinimizerBase>
1731	+	(myOOPSEMinimizerBase, &OOPSEMinimizerBase::calcGradient);
1732	+
1733	+	//creat output functor;
1734	+	outputFunc =  new ClassMemOutputFunctor<OOPSEMinimizerBase>
1735	+	(myOOPSEMinimizerBase, &OOPSEMinimizerBase::output);
1736	+
1737	+	//creat nonlinear model
1738	+	dim = myOOPSEMinimizerBase->getDim();
1739	+	nlp = new ConcreteNLModel1(dim, objFunc);
1740	+
1741	+	nlp->setX(myOOPSEMinimizerBase->getCoor());
1742	+
1743	+	//prepare parameter set for minimizer
1744	+	param = new MinimizerParameterSet();
1745	+	param->setDefaultParameter();
1746	+
1747	+	if (globals->haveMinimizer()){
1748	+	param->setFTol(globals->getMinFTol());
1749	+	}
1750	+
1751	+	if (globals->haveMinGTol()){
1752	+	param->setGTol(globals->getMinGTol());
1753	+	}
1754	+
1755	+	if (globals->haveMinMaxIter()){
1756	+	param->setMaxIteration(globals->getMinMaxIter());
1757	+	}
1758	+
1759	+	if (globals->haveMinWriteFrq()){
1760	+	param->setMaxIteration(globals->getMinMaxIter());
1761	+	}
1762	+
1763	+	if (globals->haveMinWriteFrq()){
1764	+	param->setWriteFrq(globals->getMinWriteFrq());
1765	+	}
1766	+
1767	+	if (globals->haveMinResetFrq()){
1768	+	param->setResetFrq(globals->getMinResetFrq());
1769	+	}
1770	+
1771	+	if (globals->haveMinLSMaxIter()){
1772	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1773	+	}
1774	+
1775	+	if (globals->haveMinLSTol()){
1776	+	param->setLineSearchTol(globals->getMinLSTol());
1777	+	}
1778	+
1779	+	//creat the minimizer
1780	+	minimizer = new PRCGMinimizer(nlp, param);
1781	+	minimizer->setLineSearchStrategy(nlp, GoldenSection);
1782	+	minimizer->setOutputFunctor(outputFunc);
1783	+
1784	+	//store the minimizer into simInfo
1785	+	info[i].the_minimizer = minimizer;
1786	+	info[i].has_minimizer = true;
1787	+	}
1788	+
1789	+	}

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