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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 489 by mmeineke, Thu Apr 10 20:08:56 2003 UTC vs.
Revision 1031 by tim, Fri Feb 6 18:58:06 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"
16		#include "mpiSimulation.hpp"
17		#endif
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 NPTxyz_ENS     4
26	+
27	+
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 27 | Line 77 | void SimSetup::parseFile( char* fileName ){
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();
59	<	mpiEventLoop();
60	<
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;
68	<	Globals* the_globals;
69	<	ExtendedSystem* the_extendedsystem;
70	<	int i, j;
124	>	// gather all of the information from the Bass file
125
126	<	// get the stamps and globals;
73	<	the_stamps = stamps;
74	<	the_globals = globals;
126	>	gatherInfo();
127
128	<	// set the easy ones first
77	<	simnfo->target_temp = the_globals->getTargetTemp();
78	<	simnfo->dt = the_globals->getDt();
79	<	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.
82	<	n_components = the_globals->getNComponents();
83	<	strcpy( force_field, the_globals->getForceField() );
130	>	sysObjectsCreation();
131
132	<	// get the ensemble and set up an extended system if we need it:
86	<	strcpy( ensemble, the_globals->getEnsemble() );
87	<	if( !strcasecmp( ensemble, "NPT" ) ) {
88	<	the_extendedsystem = new ExtendedSystem( simnfo );
89	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
90	<	if (the_globals->haveTargetPressure())
91	<	the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
92	<	else {
93	<	sprintf( painCave.errMsg,
94	<	"SimSetup error: If you use the constant pressure\n"
95	<	"    ensemble, you must set targetPressure.\n"
96	<	"    This was found in the BASS file.\n");
97	<	painCave.isFatal = 1;
98	<	simError();
99	<	}
132	>	// check on the post processing info
133
134	<	if (the_globals->haveTauThermostat())
102	<	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
103	<	else if (the_globals->haveQmass())
104	<	the_extendedsystem->setQmass(the_globals->getQmass());
105	<	else {
106	<	sprintf( painCave.errMsg,
107	<	"SimSetup error: If you use one of the constant temperature\n"
108	<	"    ensembles, you must set either tauThermostat or qMass.\n"
109	<	"    Neither of these was found in the BASS file.\n");
110	<	painCave.isFatal = 1;
111	<	simError();
112	<	}
134	>	finalInfoCheck();
135
136	<	if (the_globals->haveTauBarostat())
115	<	the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
116	<	else {
117	<	sprintf( painCave.errMsg,
118	<	"SimSetup error: If you use the constant pressure\n"
119	<	"    ensemble, you must set tauBarostat.\n"
120	<	"    This was found in the BASS file.\n");
121	<	painCave.isFatal = 1;
122	<	simError();
123	<	}
136	>	// initialize the system coordinates
137
138	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
139	<	the_extendedsystem = new ExtendedSystem( simnfo );
127	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
138	>	if ( !initSuspend ){
139	>	initSystemCoords();
140
141	<	if (the_globals->haveTauThermostat())
142	<	the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
131	<	else if (the_globals->haveQmass())
132	<	the_extendedsystem->setQmass(the_globals->getQmass());
133	<	else {
134	<	sprintf( painCave.errMsg,
135	<	"SimSetup error: If you use one of the constant temperature\n"
136	<	"    ensembles, you must set either tauThermostat or qMass.\n"
137	<	"    Neither of these was found in the BASS file.\n");
138	<	painCave.isFatal = 1;
139	<	simError();
140	<	}
141	<
142	<	} else if ( !strcasecmp( ensemble, "NVE") ) {
143	<	} else {
144	<	sprintf( painCave.errMsg,
145	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
146	<	"reverting to NVE for this simulation.\n",
147	<	ensemble );
148	<	painCave.isFatal = 0;
149	<	simError();
150	<	strcpy( ensemble, "NVE" );
141	>	if( !(globals->getUseInitTime()) )
142	>	info[0].currentTime = 0.0;
143		}
152	–	strcpy( simnfo->ensemble, ensemble );
144
145	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
155	<	simnfo->usePBC = the_globals->getPBC();
156	<
157	<	int usesDipoles = 0;
158	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
159	<	the_ff = new TraPPE_ExFF();
160	<	usesDipoles = 1;
161	<	}
162	<	else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
163	<	else{
164	<	sprintf( painCave.errMsg,
165	<	"SimSetup Error. Unrecognized force field -> %s\n",
166	<	force_field );
167	<	painCave.isFatal = 1;
168	<	simError();
169	<	}
145	>	// make the output filenames
146
147	<	#ifdef IS_MPI
172	<	strcpy( checkPointMsg, "ForceField creation successful" );
173	<	MPIcheckPoint();
174	<	#endif // is_mpi
147	>	makeOutNames();
148
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	<	// get the components and calculate the tot_nMol and indvidual n_mol
179	<	the_components = the_globals->getComponents();
180	<	components_nmol = new int[n_components];
181	<	comp_stamps = new MoleculeStamp*[n_components];
160	>	// initialize the Fortran
161
162	<	if( !the_globals->haveNMol() ){
163	<	// we don't have the total number of molecules, so we assume it is
185	<	// given in each component
162	>	initFortran();
163	>	}
164
187	–	tot_nmol = 0;
188	–	for( i=0; i<n_components; i++ ){
165
166	<	if( !the_components[i]->haveNMol() ){
167	<	// we have a problem
168	<	sprintf( painCave.errMsg,
169	<	"SimSetup Error. No global NMol or component NMol"
170	<	" given. Cannot calculate the number of atoms.\n" );
171	<	painCave.isFatal = 1;
172	<	simError();
173	<	}
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	<	tot_nmol += the_components[i]->getNMol();
179	<	components_nmol[i] = the_components[i]->getNMol();
180	<	}
202	<	}
203	<	else{
204	<	sprintf( painCave.errMsg,
205	<	"SimSetup error.\n"
206	<	"\tSorry, the ability to specify total"
207	<	" nMols and then give molfractions in the components\n"
208	<	"\tis not currently supported."
209	<	" Please give nMol in the components.\n" );
210	<	painCave.isFatal = 1;
211	<	simError();
212	<
213	<
214	<	//     tot_nmol = the_globals->getNMol();
215	<
216	<	//   //we have the total number of molecules, now we check for molfractions
217	<	//     for( i=0; i<n_components; i++ ){
218	<
219	<	//       if( !the_components[i]->haveMolFraction() ){
220	<
221	<	//  if( !the_components[i]->haveNMol() ){
222	<	//    //we have a problem
223	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
224	<	//              << " nMol was given in component
225	<
226	<	}
178	>	bond_pair* theBonds;
179	>	bend_set* theBends;
180	>	torsion_set* theTorsions;
181
182	<	#ifdef IS_MPI
229	<	strcpy( checkPointMsg, "Have the number of components" );
230	<	MPIcheckPoint();
231	<	#endif // is_mpi
182	>	//init the forceField paramters
183
184	<	// make an array of molecule stamps that match the components used.
234	<	// also extract the used stamps out into a separate linked list
184	>	the_ff->readParams();
185
236	–	simnfo->nComponents = n_components;
237	–	simnfo->componentsNmol = components_nmol;
238	–	simnfo->compStamps = comp_stamps;
239	–	simnfo->headStamp = new LinkedMolStamp();
240	–
241	–	char* id;
242	–	LinkedMolStamp* headStamp = simnfo->headStamp;
243	–	LinkedMolStamp* currentStamp = NULL;
244	–	for( i=0; i<n_components; i++ ){
186
187	<	id = the_components[i]->getType();
247	<	comp_stamps[i] = NULL;
248	<
249	<	// check to make sure the component isn't already in the list
187	>	// init the atoms
188
189	<	comp_stamps[i] = headStamp->match( id );
190	<	if( comp_stamps[i] == NULL ){
191	<
192	<	// extract the component from the list;
255	<
256	<	currentStamp = the_stamps->extractMolStamp( id );
257	<	if( currentStamp == NULL ){
258	<	sprintf( painCave.errMsg,
259	<	"SimSetup error: Component \"%s\" was not found in the "
260	<	"list of declared molecules\n",
261	<	id );
262	<	painCave.isFatal = 1;
263	<	simError();
264	<	}
265	<
266	<	headStamp->add( currentStamp );
267	<	comp_stamps[i] = headStamp->match( id );
268	<	}
269	<	}
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	<	#ifdef IS_MPI
195	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
273	<	MPIcheckPoint();
274	<	#endif // is_mpi
275	<
194	>	for (k = 0; k < nInfo; k++){
195	>	the_ff->setSimInfo(&(info[k]));
196
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	<	// caclulate the number of atoms, bonds, bends and torsions
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_atoms = 0;
215	<	tot_bonds = 0;
216	<	tot_bends = 0;
284	<	tot_torsions = 0;
285	<	for( i=0; i<n_components; i++ ){
286	<
287	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
288	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
289	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
290	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
291	<	}
214	>	theBonds = new bond_pair[molInfo.nBonds];
215	>	theBends = new bend_set[molInfo.nBends];
216	>	theTorsions = new torsion_set[molInfo.nTorsions];
217
218	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
218	>	// make the Atoms
219
220	<	simnfo->n_atoms = tot_atoms;
221	<	simnfo->n_bonds = tot_bonds;
222	<	simnfo->n_bends = tot_bends;
223	<	simnfo->n_torsions = tot_torsions;
224	<	simnfo->n_SRI = tot_SRI;
225	<	simnfo->n_mol = tot_nmol;
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	<
229	<	#ifdef IS_MPI
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	<	// divide the molecules among processors here.
233	<
234	<	mpiSim = new mpiSimulation( simnfo );
235	<
236	<
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	<	globalIndex = mpiSim->divideLabor();
248	>	sux = 0.0;
249	>	suy = 0.0;
250	>	suz = 1.0;
251
252	<	// set up the local variables
253	<
254	<	int localMol, allMol;
316	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
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	<	int* mol2proc = mpiSim->getMolToProcMap();
319	<	int* molCompType = mpiSim->getMolComponentType();
320	<
321	<	allMol = 0;
322	<	localMol = 0;
323	<	local_atoms = 0;
324	<	local_bonds = 0;
325	<	local_bends = 0;
326	<	local_torsions = 0;
327	<	for( i=0; i<n_components; i++ ){
256	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
257
258	<	for( j=0; j<components_nmol[i]; j++ ){
259	<
260	<	if( mol2proc[allMol] == worldRank ){
261	<
333	<	local_atoms +=    comp_stamps[i]->getNAtoms();
334	<	local_bonds +=    comp_stamps[i]->getNBonds();
335	<	local_bends +=    comp_stamps[i]->getNBends();
336	<	local_torsions += comp_stamps[i]->getNTorsions();
337	<	localMol++;
338	<	}
339	<	allMol++;
340	<	}
341	<	}
342	<	local_SRI = local_bonds + local_bends + local_torsions;
343	<
258	>	u = sqrt(uSqr);
259	>	ux = ux / u;
260	>	uy = uy / u;
261	>	uz = uz / u;
262
263	<	simnfo->n_atoms = mpiSim->getMyNlocal();
264	<
265	<	if( local_atoms != simnfo->n_atoms ){
266	<	sprintf( painCave.errMsg,
267	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
268	<	" localAtom (%d) are not equal.\n",
269	<	simnfo->n_atoms,
270	<	local_atoms );
271	<	painCave.isFatal = 1;
354	<	simError();
355	<	}
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
273	<	simnfo->n_bonds = local_bonds;
358	<	simnfo->n_bends = local_bends;
359	<	simnfo->n_torsions = local_torsions;
360	<	simnfo->n_SRI = local_SRI;
361	<	simnfo->n_mol = localMol;
273	>	#ifdef IS_MPI
274
275	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
276	<	MPIcheckPoint();
365	<
366	<
275	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
276	>
277		#endif // is_mpi
278	<
278	>	}
279
280	<	// create the atom and short range interaction arrays
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	<	Atom::createArrays(simnfo->n_atoms);
287	<	the_atoms = new Atom*[simnfo->n_atoms];
374	<	the_molecules = new Molecule[simnfo->n_mol];
375	<	int molIndex;
286	>	exI = theBonds[j].a;
287	>	exJ = theBonds[j].b;
288
289	<	// initialize the molecule's stampID's
290	<
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	<
296	>	tempEx = exI;
297	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
298	>	tempEx = exJ;
299	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
300
301	<	molIndex = 0;
302	<	for(i=0; i<mpiSim->getTotNmol(); i++){
384	<
385	<	if(mol2proc[i] == worldRank ){
386	<	the_molecules[molIndex].setStampID( molCompType[i] );
387	<	the_molecules[molIndex].setMyIndex( molIndex );
388	<	the_molecules[molIndex].setGlobalIndex( i );
389	<	molIndex++;
390	<	}
391	<	}
301	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
302	>	#else  // isn't MPI
303
304	<	#else // is_mpi
305	<
306	<	molIndex = 0;
307	<	for(i=0; i<n_components; i++){
397	<	for(j=0; j<components_nmol[i]; j++ ){
398	<	the_molecules[molIndex].setStampID( i );
399	<	the_molecules[molIndex].setMyIndex( molIndex );
400	<	the_molecules[molIndex].setGlobalIndex( molIndex );
401	<	molIndex++;
402	<	}
403	<	}
404	<
304	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
305	>	#endif  //is_mpi
306	>	}
307	>	excludeOffset += molInfo.nBonds;
308
309	<	#endif // is_mpi
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	+	if (currentBend->haveExtras()){
317	+	extras = currentBend->getExtras();
318	+	current_extra = extras;
319
320	<	if( simnfo->n_SRI ){
321	<
322	<	Exclude::createArray(simnfo->n_SRI);
323	<	the_excludes = new Exclude*[simnfo->n_SRI];
324	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
325	<	simnfo->globalExcludes = new int;
326	<	simnfo->n_exclude = simnfo->n_SRI;
416	<	}
417	<	else{
418	<
419	<	Exclude::createArray( 1 );
420	<	the_excludes = new Exclude*;
421	<	the_excludes[0] = new Exclude(0);
422	<	the_excludes[0]->setPair( 0,0 );
423	<	simnfo->globalExcludes = new int;
424	<	simnfo->globalExcludes[0] = 0;
425	<	simnfo->n_exclude = 0;
426	<	}
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	<	// set the arrays into the SimInfo object
328	>	case 1:
329	>	theBends[j].ghost = (int) current_extra->getDouble() +
330	>	atomOffset;
331	>	theBends[j].isGhost = 1;
332	>	break;
333
334	<	simnfo->atoms = the_atoms;
335	<	simnfo->molecules = the_molecules;
336	<	simnfo->nGlobalExcludes = 0;
337	<	simnfo->excludes = the_excludes;
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	<	// get some of the tricky things that may still be in the globals
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	<
367	<	if( the_globals->haveBox() ){
368	<	simnfo->box_x = the_globals->getBox();
369	<	simnfo->box_y = the_globals->getBox();
370	<	simnfo->box_z = the_globals->getBox();
371	<	}
372	<	else if( the_globals->haveDensity() ){
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	>	tempEx = exI;
374	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
375	>	tempEx = exJ;
376	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
377
378	<	double vol;
379	<	vol = (double)tot_nmol / the_globals->getDensity();
380	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
381	<	simnfo->box_y = simnfo->box_x;
382	<	simnfo->box_z = simnfo->box_x;
383	<	}
452	<	else{
453	<	if( !the_globals->haveBoxX() ){
454	<	sprintf( painCave.errMsg,
455	<	"SimSetup error, no periodic BoxX size given.\n" );
456	<	painCave.isFatal = 1;
457	<	simError();
458	<	}
459	<	simnfo->box_x = the_globals->getBoxX();
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	<	if( !the_globals->haveBoxY() ){
386	<	sprintf( painCave.errMsg,
387	<	"SimSetup error, no periodic BoxY size given.\n" );
388	<	painCave.isFatal = 1;
389	<	simError();
390	<	}
467	<	simnfo->box_y = the_globals->getBoxY();
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	<	if( !the_globals->haveBoxZ() ){
393	<	sprintf( painCave.errMsg,
471	<	"SimSetup error, no periodic BoxZ size given.\n" );
472	<	painCave.isFatal = 1;
473	<	simError();
474	<	}
475	<	simnfo->box_z = the_globals->getBoxZ();
476	<	}
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	<	strcpy( checkPointMsg, "Box size set up" );
403	<	MPIcheckPoint();
404	<	#endif // 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	<
408	<	// initialize the arrays
409	<
410	<	the_ff->setSimInfo( simnfo );
487	<
488	<	makeMolecules();
489	<	simnfo->identArray = new int[simnfo->n_atoms];
490	<	simnfo->molMembershipArray = new int[simnfo->n_atoms];
491	<	for(i=0; i<simnfo->n_atoms; i++){
492	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
493	<	}
494	<	for(i=0; i< simnfo->n_mol; i++) {
495	<	the_molecules[i].atomicRollCall(simnfo->molMembershipArray);
496	<	}
497	<
498	<	if (the_globals->getUseRF() ) {
499	<	simnfo->useReactionField = 1;
500	<
501	<	if( !the_globals->haveECR() ){
502	<	sprintf( painCave.errMsg,
503	<	"SimSetup Warning: using default value of 1/2 the smallest "
504	<	"box length for the electrostaticCutoffRadius.\n"
505	<	"I hope you have a very fast processor!\n");
506	<	painCave.isFatal = 0;
507	<	simError();
508	<	double smallest;
509	<	smallest = simnfo->box_x;
510	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
511	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
512	<	simnfo->ecr = 0.5 * smallest;
513	<	} else {
514	<	simnfo->ecr        = the_globals->getECR();
515	<	}
516	<
517	<	if( !the_globals->haveEST() ){
518	<	sprintf( painCave.errMsg,
519	<	"SimSetup Warning: using default value of 0.05 * the "
520	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
521	<	);
522	<	painCave.isFatal = 0;
523	<	simError();
524	<	simnfo->est = 0.05 * simnfo->ecr;
525	<	} else {
526	<	simnfo->est        = the_globals->getEST();
527	<	}
528	<
529	<	if(!the_globals->haveDielectric() ){
530	<	sprintf( painCave.errMsg,
531	<	"SimSetup Error: You are trying to use Reaction Field without"
532	<	"setting a dielectric constant!\n"
533	<	);
534	<	painCave.isFatal = 1;
535	<	simError();
536	<	}
537	<	simnfo->dielectric = the_globals->getDielectric();
538	<	} else {
539	<	if (usesDipoles) {
540	<
541	<	if( !the_globals->haveECR() ){
542	<	sprintf( painCave.errMsg,
543	<	"SimSetup Warning: using default value of 1/2 the smallest "
544	<	"box length for the electrostaticCutoffRadius.\n"
545	<	"I hope you have a very fast processor!\n");
546	<	painCave.isFatal = 0;
547	<	simError();
548	<	double smallest;
549	<	smallest = simnfo->box_x;
550	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
551	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
552	<	simnfo->ecr = 0.5 * smallest;
553	<	} else {
554	<	simnfo->ecr        = the_globals->getECR();
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	<
557	<	if( !the_globals->haveEST() ){
558	<	sprintf( painCave.errMsg,
559	<	"SimSetup Warning: using default value of 5%% of the "
560	<	"electrostaticCutoffRadius for the "
561	<	"electrostaticSkinThickness\n"
562	<	);
563	<	painCave.isFatal = 0;
564	<	simError();
565	<	simnfo->est = 0.05 * simnfo->ecr;
566	<	} else {
567	<	simnfo->est        = the_globals->getEST();
568	<	}
569	<	}
570	<	}
412	>	excludeOffset += molInfo.nTorsions;
413
572	–	#ifdef IS_MPI
573	–	strcpy( checkPointMsg, "electrostatic parameters check out" );
574	–	MPIcheckPoint();
575	–	#endif // is_mpi
414
415	<	if( the_globals->haveInitialConfig() ){
578	<
579	<	InitializeFromFile* fileInit;
580	<	#ifdef IS_MPI // is_mpi
581	<	if( worldRank == 0 ){
582	<	#endif //is_mpi
583	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
584	<	#ifdef IS_MPI
585	<	}else fileInit = new InitializeFromFile( NULL );
586	<	#endif
587	<	fileInit->read_xyz( simnfo ); // default velocities on
415	>	// send the arrays off to the forceField for init.
416
417	<	delete fileInit;
418	<	}
419	<	else{
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
593	–	#ifdef IS_MPI
423
424	<	// no init from bass
596	<
597	<	sprintf( painCave.errMsg,
598	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
599	<	painCave.isFatal;
600	<	simError();
601	<
602	<	#else
424	>	info[k].molecules[i].initialize(molInfo);
425
604	–	initFromBass();
426
427	+	atomOffset += molInfo.nAtoms;
428	+	delete[] theBonds;
429	+	delete[] theBends;
430	+	delete[] theTorsions;
431	+	}
432	+	}
433
607	–	#endif
608	–	}
609	–
434		#ifdef IS_MPI
435	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
435	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
436		MPIcheckPoint();
437		#endif // is_mpi
438
439	+	// clean up the forcefield
440
441	<
442	<
443	<
441	>	the_ff->calcRcut();
442	>	the_ff->cleanMe();
443	>	}
444
445	<
446	<	#ifdef IS_MPI
447	<	if( worldRank == 0 ){
448	<	#endif // is_mpi
449	<
450	<	if( the_globals->haveFinalConfig() ){
451	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
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 vel[3];
455	>	vel[0] = 0.0;
456	>	vel[1] = 0.0;
457	>	vel[2] = 0.0;
458	>
459	>	temp1 = (double) tot_nmol / 4.0;
460	>	temp2 = pow(temp1, (1.0 / 3.0));
461	>	temp3 = ceil(temp2);
462	>
463	>	have_extra = 0;
464	>	if (temp2 < temp3){
465	>	// we have a non-complete lattice
466	>	have_extra = 1;
467	>
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 (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		}
628	–	else{
629	–	strcpy( simnfo->finalName, inFileName );
630	–	char* endTest;
631	–	int nameLength = strlen( simnfo->finalName );
632	–	endTest = &(simnfo->finalName[nameLength - 5]);
633	–	if( !strcmp( endTest, ".bass" ) ){
634	–	strcpy( endTest, ".eor" );
635	–	}
636	–	else if( !strcmp( endTest, ".BASS" ) ){
637	–	strcpy( endTest, ".eor" );
638	–	}
639	–	else{
640	–	endTest = &(simnfo->finalName[nameLength - 4]);
641	–	if( !strcmp( endTest, ".bss" ) ){
642	–	strcpy( endTest, ".eor" );
643	–	}
644	–	else if( !strcmp( endTest, ".mdl" ) ){
645	–	strcpy( endTest, ".eor" );
646	–	}
647	–	else{
648	–	strcat( simnfo->finalName, ".eor" );
649	–	}
650	–	}
651	–	}
652	–
653	–	// make the sample and status out names
654	–
655	–	strcpy( simnfo->sampleName, inFileName );
656	–	char* endTest;
657	–	int nameLength = strlen( simnfo->sampleName );
658	–	endTest = &(simnfo->sampleName[nameLength - 5]);
659	–	if( !strcmp( endTest, ".bass" ) ){
660	–	strcpy( endTest, ".dump" );
661	–	}
662	–	else if( !strcmp( endTest, ".BASS" ) ){
663	–	strcpy( endTest, ".dump" );
664	–	}
665	–	else{
666	–	endTest = &(simnfo->sampleName[nameLength - 4]);
667	–	if( !strcmp( endTest, ".bss" ) ){
668	–	strcpy( endTest, ".dump" );
669	–	}
670	–	else if( !strcmp( endTest, ".mdl" ) ){
671	–	strcpy( endTest, ".dump" );
672	–	}
673	–	else{
674	–	strcat( simnfo->sampleName, ".dump" );
675	–	}
676	–	}
677	–
678	–	strcpy( simnfo->statusName, inFileName );
679	–	nameLength = strlen( simnfo->statusName );
680	–	endTest = &(simnfo->statusName[nameLength - 5]);
681	–	if( !strcmp( endTest, ".bass" ) ){
682	–	strcpy( endTest, ".stat" );
683	–	}
684	–	else if( !strcmp( endTest, ".BASS" ) ){
685	–	strcpy( endTest, ".stat" );
686	–	}
687	–	else{
688	–	endTest = &(simnfo->statusName[nameLength - 4]);
689	–	if( !strcmp( endTest, ".bss" ) ){
690	–	strcpy( endTest, ".stat" );
691	–	}
692	–	else if( !strcmp( endTest, ".mdl" ) ){
693	–	strcpy( endTest, ".stat" );
694	–	}
695	–	else{
696	–	strcat( simnfo->statusName, ".stat" );
697	–	}
698	–	}
699	–
700	–	#ifdef IS_MPI
483		}
702	–	#endif // is_mpi
703	–
704	–	// set the status, sample, and themal kick times
705	–
706	–	if( the_globals->haveSampleTime() ){
707	–	simnfo->sampleTime = the_globals->getSampleTime();
708	–	simnfo->statusTime = simnfo->sampleTime;
709	–	simnfo->thermalTime = simnfo->sampleTime;
710	–	}
484		else{
485	<	simnfo->sampleTime = the_globals->getRunTime();
486	<	simnfo->statusTime = simnfo->sampleTime;
487	<	simnfo->thermalTime = simnfo->sampleTime;
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	<	if( the_globals->haveStatusTime() ){
492	<	simnfo->statusTime = the_globals->getStatusTime();
493	<	}
491	>	current_mol = 0;
492	>	current_comp_mol = 0;
493	>	current_comp = 0;
494	>	current_atom_ndx = 0;
495
496	<	if( the_globals->haveThermalTime() ){
497	<	simnfo->thermalTime = the_globals->getThermalTime();
498	<	}
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	<	// check for the temperature set flag
501	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
502
503	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
503	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
504
505	+	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
506	+	}
507	+	}
508	+	}
509
510	<	//   // make the longe range forces and the integrator
510	>	if (have_extra){
511	>	done = 0;
512
513	<	//   new AllLong( simnfo );
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( !strcmp( force_field, "TraPPE_Ex" ) ){
531	<	new Symplectic(simnfo, the_ff, the_extendedsystem);
532	<	}
533	<	else if( !strcmp( force_field, "LJ" ) ){
534	<	new Verlet( *simnfo, the_ff, the_extendedsystem );
740	<	}
741	<	else {
742	<	std::cerr << "I'm a bug.\n";
743	<	fprintf( stderr, "Ima bug. stderr %s\n", force_field);
744	<	}
745	<	#ifdef IS_MPI
746	<	mpiSim->mpiRefresh();
747	<	#endif
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	<	// initialize the Fortran
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
552	<	simnfo->refreshSim();
553	<
754	<	if( !strcmp( simnfo->mixingRule, "standard") ){
755	<	the_ff->initForceField( LB_MIXING_RULE );
552	>	for (i = 0; i < info[0].n_atoms; i++){
553	>	info[0].atoms[i]->setVel(vel);
554		}
757	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
758	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
759	–	}
760	–	else{
761	–	sprintf( painCave.errMsg,
762	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
763	–	simnfo->mixingRule );
764	–	painCave.isFatal = 1;
765	–	simError();
766	–	}
767	–
768	–
769	–	#ifdef IS_MPI
770	–	strcpy( checkPointMsg,
771	–	"Successfully intialized the mixingRule for Fortran." );
772	–	MPIcheckPoint();
773	–	#endif // is_mpi
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	<	void SimSetup::makeMolecules( void ){
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
577	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
578	<	molInit info;
579	<	DirectionalAtom* dAtom;
782	<	LinkedAssign* extras;
783	<	LinkedAssign* current_extra;
784	<	AtomStamp* currentAtom;
785	<	BondStamp* currentBond;
786	<	BendStamp* currentBend;
787	<	TorsionStamp* currentTorsion;
577	>	pos[0] = x + current_atom->getPosX();
578	>	pos[1] = y + current_atom->getPosY();
579	>	pos[2] = z + current_atom->getPosZ();
580
581	<	bond_pair* theBonds;
790	<	bend_set* theBends;
791	<	torsion_set* theTorsions;
581	>	info[0].atoms[current_atom_ndx]->setPos(pos);
582
583	<
584	<	//init the forceField paramters
583	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
584	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
585
586	<	the_ff->readParams();
586	>	rotMat[0][0] = 1.0;
587	>	rotMat[0][1] = 0.0;
588	>	rotMat[0][2] = 0.0;
589
590	<
591	<	// init the atoms
590	>	rotMat[1][0] = 0.0;
591	>	rotMat[1][1] = 1.0;
592	>	rotMat[1][2] = 0.0;
593
594	<	double ux, uy, uz, u, uSqr;
595	<
596	<	atomOffset = 0;
804	<	excludeOffset = 0;
805	<	for(i=0; i<simnfo->n_mol; i++){
806	<
807	<	stampID = the_molecules[i].getStampID();
594	>	rotMat[2][0] = 0.0;
595	>	rotMat[2][1] = 0.0;
596	>	rotMat[2][2] = 1.0;
597
598	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
599	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
811	<	info.nBends    = comp_stamps[stampID]->getNBends();
812	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
813	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
598	>	dAtom->setA(rotMat);
599	>	}
600
601	<	info.myAtoms = &the_atoms[atomOffset];
602	<	info.myExcludes = &the_excludes[excludeOffset];
817	<	info.myBonds = new Bond*[info.nBonds];
818	<	info.myBends = new Bend*[info.nBends];
819	<	info.myTorsions = new Torsion*[info.nTorsions];
601	>	current_atom_ndx++;
602	>	}
603
604	<	theBonds = new bond_pair[info.nBonds];
605	<	theBends = new bend_set[info.nBends];
823	<	theTorsions = new torsion_set[info.nTorsions];
824	<
825	<	// make the Atoms
826	<
827	<	for(j=0; j<info.nAtoms; j++){
828	<
829	<	currentAtom = comp_stamps[stampID]->getAtom( j );
830	<	if( currentAtom->haveOrientation() ){
831	<
832	<	dAtom = new DirectionalAtom(j + atomOffset);
833	<	simnfo->n_oriented++;
834	<	info.myAtoms[j] = dAtom;
835	<
836	<	ux = currentAtom->getOrntX();
837	<	uy = currentAtom->getOrntY();
838	<	uz = currentAtom->getOrntZ();
839	<
840	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
841	<
842	<	u = sqrt( uSqr );
843	<	ux = ux / u;
844	<	uy = uy / u;
845	<	uz = uz / u;
846	<
847	<	dAtom->setSUx( ux );
848	<	dAtom->setSUy( uy );
849	<	dAtom->setSUz( uz );
850	<	}
851	<	else{
852	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
853	<	}
854	<	info.myAtoms[j]->setType( currentAtom->getType() );
855	<
856	<	#ifdef IS_MPI
857	<
858	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
859	<
860	<	#endif // is_mpi
861	<	}
862	<
863	<	// make the bonds
864	<	for(j=0; j<info.nBonds; j++){
865	<
866	<	currentBond = comp_stamps[stampID]->getBond( j );
867	<	theBonds[j].a = currentBond->getA() + atomOffset;
868	<	theBonds[j].b = currentBond->getB() + atomOffset;
604	>	current_mol++;
605	>	current_comp_mol++;
606
607	<	exI = theBonds[j].a;
608	<	exJ = theBonds[j].b;
607	>	if (current_comp_mol >= components_nmol[current_comp]){
608	>	current_comp_mol = 0;
609	>	current_comp++;
610	>	}
611	>	}
612
873	–	// exclude_I must always be the smaller of the pair
874	–	if( exI > exJ ){
875	–	tempEx = exI;
876	–	exI = exJ;
877	–	exJ = tempEx;
878	–	}
879	–	#ifdef IS_MPI
880	–	tempEx = exI;
881	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
882	–	tempEx = exJ;
883	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
884	–
885	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
886	–	#else  // isn't MPI
613
614	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
615	<	#endif  //is_mpi
890	<	}
891	<	excludeOffset += info.nBonds;
614	>	void SimSetup::gatherInfo(void){
615	>	int i;
616
617	<	//make the bends
618	<	for(j=0; j<info.nBends; j++){
895	<
896	<	currentBend = comp_stamps[stampID]->getBend( j );
897	<	theBends[j].a = currentBend->getA() + atomOffset;
898	<	theBends[j].b = currentBend->getB() + atomOffset;
899	<	theBends[j].c = currentBend->getC() + atomOffset;
900	<
901	<	if( currentBend->haveExtras() ){
902	<
903	<	extras = currentBend->getExtras();
904	<	current_extra = extras;
905	<
906	<	while( current_extra != NULL ){
907	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
908	<
909	<	switch( current_extra->getType() ){
910	<
911	<	case 0:
912	<	theBends[j].ghost =
913	<	current_extra->getInt() + atomOffset;
914	<	theBends[j].isGhost = 1;
915	<	break;
916	<
917	<	case 1:
918	<	theBends[j].ghost =
919	<	(int)current_extra->getDouble() + atomOffset;
920	<	theBends[j].isGhost = 1;
921	<	break;
922	<
923	<	default:
924	<	sprintf( painCave.errMsg,
925	<	"SimSetup Error: ghostVectorSource was neither a "
926	<	"double nor an int.\n"
927	<	"-->Bend[%d] in %s\n",
928	<	j, comp_stamps[stampID]->getID() );
929	<	painCave.isFatal = 1;
930	<	simError();
931	<	}
932	<	}
933	<
934	<	else{
935	<
936	<	sprintf( painCave.errMsg,
937	<	"SimSetup Error: unhandled bend assignment:\n"
938	<	"    -->%s in Bend[%d] in %s\n",
939	<	current_extra->getlhs(),
940	<	j, comp_stamps[stampID]->getID() );
941	<	painCave.isFatal = 1;
942	<	simError();
943	<	}
944	<
945	<	current_extra = current_extra->getNext();
946	<	}
947	<	}
948	<
949	<	if( !theBends[j].isGhost ){
950	<
951	<	exI = theBends[j].a;
952	<	exJ = theBends[j].c;
953	<	}
954	<	else{
955	<
956	<	exI = theBends[j].a;
957	<	exJ = theBends[j].b;
958	<	}
959	<
960	<	// exclude_I must always be the smaller of the pair
961	<	if( exI > exJ ){
962	<	tempEx = exI;
963	<	exI = exJ;
964	<	exJ = tempEx;
965	<	}
966	<	#ifdef IS_MPI
967	<	tempEx = exI;
968	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
969	<	tempEx = exJ;
970	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
971	<
972	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
973	<	#else  // isn't MPI
974	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
975	<	#endif  //is_mpi
976	<	}
977	<	excludeOffset += info.nBends;
617	>	ensembleCase = -1;
618	>	ffCase = -1;
619
620	<	for(j=0; j<info.nTorsions; j++){
980	<
981	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
982	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
983	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
984	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
985	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
986	<
987	<	exI = theTorsions[j].a;
988	<	exJ = theTorsions[j].d;
620	>	// set the easy ones first
621
622	<	// exclude_I must always be the smaller of the pair
623	<	if( exI > exJ ){
624	<	tempEx = exI;
625	<	exI = exJ;
626	<	exJ = tempEx;
627	<	}
996	<	#ifdef IS_MPI
997	<	tempEx = exI;
998	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
999	<	tempEx = exJ;
1000	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1001	<
1002	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1003	<	#else  // isn't MPI
1004	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1005	<	#endif  //is_mpi
1006	<	}
1007	<	excludeOffset += info.nTorsions;
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
1009	–
1010	–	// send the arrays off to the forceField for init.
629
630	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1013	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1014	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1015	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
630	>	// get the forceField
631
632	+	strcpy(force_field, globals->getForceField());
633
634	<	the_molecules[i].initialize( info );
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	<	atomOffset += info.nAtoms;
656	<	delete[] theBonds;
657	<	delete[] theBends;
658	<	delete[] theTorsions;
655	>	strcpy(ensemble, globals->getEnsemble());
656	>
657	>	if (!strcasecmp(ensemble, "NVE")){
658	>	ensembleCase = NVE_ENS;
659		}
660	+	else if (!strcasecmp(ensemble, "NVT")){
661	+	ensembleCase = NVT_ENS;
662	+	}
663	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
664	+	ensembleCase = NPTi_ENS;
665	+	}
666	+	else if (!strcasecmp(ensemble, "NPTf")){
667	+	ensembleCase = NPTf_ENS;
668	+	}
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	<	#ifdef IS_MPI
684	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1029	<	MPIcheckPoint();
1030	<	#endif // is_mpi
683	>	for (i = 0; i < nInfo; i++){
684	>	strcpy(info[i].ensemble, ensemble);
685
686	<	// clean up the forcefield
1033	<	the_ff->calcRcut();
1034	<	the_ff->cleanMe();
686	>	// get the mixing rule
687
688	<	}
688	>	strcpy(info[i].mixingRule, globals->getMixingRule());
689	>	info[i].usePBC = globals->getPBC();
690	>	}
691
692	<	void SimSetup::initFromBass( void ){
692	>	// get the components and calculate the tot_nMol and indvidual n_mol
693
694	<	int i, j, k;
695	<	int n_cells;
1042	<	double cellx, celly, cellz;
1043	<	double temp1, temp2, temp3;
1044	<	int n_per_extra;
1045	<	int n_extra;
1046	<	int have_extra, done;
694	>	the_components = globals->getComponents();
695	>	components_nmol = new int[n_components];
696
1048	–	temp1 = (double)tot_nmol / 4.0;
1049	–	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1050	–	temp3 = ceil( temp2 );
697
698	<	have_extra =0;
699	<	if( temp2 < temp3 ){ // we have a non-complete lattice
700	<	have_extra =1;
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	<	n_cells = (int)temp3 - 1;
703	<	cellx = simnfo->box_x / temp3;
704	<	celly = simnfo->box_y / temp3;
705	<	cellz = simnfo->box_z / temp3;
706	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
707	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
708	<	n_per_extra = (int)ceil( temp1 );
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	<	if( n_per_extra > 4){
714	<	sprintf( painCave.errMsg,
1066	<	"SimSetup error. There has been an error in constructing"
1067	<	" the non-complete lattice.\n" );
1068	<	painCave.isFatal = 1;
1069	<	simError();
713	>	tot_nmol += the_components[i]->getNMol();
714	>	components_nmol[i] = the_components[i]->getNMol();
715		}
716		}
717		else{
718	<	n_cells = (int)temp3;
719	<	cellx = simnfo->box_x / temp3;
720	<	celly = simnfo->box_y / temp3;
721	<	cellz = simnfo->box_z / temp3;
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	<	current_mol = 0;
729	<	current_comp_mol = 0;
730	<	current_comp = 0;
731	<	current_atom_ndx = 0;
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	<	for( i=0; i < n_cells ; i++ ){
740	<	for( j=0; j < n_cells; j++ ){
741	<	for( k=0; k < n_cells; k++ ){
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	<	makeElement( i * cellx,
750	<	j * celly,
751	<	k * cellz );
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	<	makeElement( i * cellx + 0.5 * cellx,
760	<	j * celly + 0.5 * celly,
761	<	k * cellz );
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	<	makeElement( i * cellx,
1097	<	j * celly + 0.5 * celly,
1098	<	k * cellz + 0.5 * cellz );
769	>	// set the status, sample, and thermal kick times
770
771	<	makeElement( i * cellx + 0.5 * cellx,
772	<	j * celly,
773	<	k * cellz + 0.5 * cellz );
774	<	}
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	<	}
777	>	else{
778	>	info[i].sampleTime = globals->getRunTime();
779	>	info[i].statusTime = info[i].sampleTime;
780	>	info[i].thermalTime = info[i].sampleTime;
781	>	}
782
783	<	if( have_extra ){
784	<	done = 0;
783	>	if (globals->haveStatusTime()){
784	>	info[i].statusTime = globals->getStatusTime();
785	>	}
786
787	<	int start_ndx;
788	<	for( i=0; i < (n_cells+1) && !done; i++ ){
789	<	for( j=0; j < (n_cells+1) && !done; j++ ){
787	>	if (globals->haveThermalTime()){
788	>	info[i].thermalTime = globals->getThermalTime();
789	>	}
790
791	<	if( i < n_cells ){
791	>	info[i].resetIntegrator = 0;
792	>	if( globals->haveResetTime() ){
793	>	info[i].resetTime = globals->getResetTime();
794	>	info[i].resetIntegrator = 1;
795	>	}
796
797	<	if( j < n_cells ){
798	<	start_ndx = n_cells;
799	<	}
800	<	else start_ndx = 0;
1120	<	}
1121	<	else start_ndx = 0;
797	>	// check for the temperature set flag
798	>
799	>	if (globals->haveTempSet())
800	>	info[i].setTemp = globals->getTempSet();
801
802	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
802	>	// check for the extended State init
803
804	<	makeElement( i * cellx,
805	<	j * celly,
806	<	k * cellz );
807	<	done = ( current_mol >= tot_nmol );
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( !done && n_per_extra > 1 ){
813	<	makeElement( i * cellx + 0.5 * cellx,
1132	<	j * celly + 0.5 * celly,
1133	<	k * cellz );
1134	<	done = ( current_mol >= tot_nmol );
1135	<	}
812	>	if (globals->haveSeed()){
813	>	seedValue = globals->getSeed();
814
815	<	if( !done && n_per_extra > 2){
816	<	makeElement( i * cellx,
817	<	j * celly + 0.5 * celly,
818	<	k * cellz + 0.5 * cellz );
819	<	done = ( current_mol >= tot_nmol );
820	<	}
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	<	if( !done && n_per_extra > 3){
823	<	makeElement( i * cellx + 0.5 * cellx,
824	<	j * celly,
825	<	k * cellz + 0.5 * cellz );
826	<	done = ( current_mol >= tot_nmol );
827	<	}
1150	<	}
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	<	}
832	>	}//end of if branch of globals->haveSeed()
833	>	else{
834	>
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	<
846	<	for( i=0; i<simnfo->n_atoms; i++ ){
1157	<	simnfo->atoms[i]->set_vx( 0.0 );
1158	<	simnfo->atoms[i]->set_vy( 0.0 );
1159	<	simnfo->atoms[i]->set_vz( 0.0 );
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
1163	–	void SimSetup::makeElement( double x, double y, double z ){
855
856	<	int k;
857	<	AtomStamp* current_atom;
858	<	DirectionalAtom* dAtom;
859	<	double rotMat[3][3];
856	>	void SimSetup::finalInfoCheck(void){
857	>	int index;
858	>	int usesDipoles;
859	>	int i;
860
861	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
861	>	for (i = 0; i < nInfo; i++){
862	>	// check electrostatic parameters
863
864	<	current_atom = comp_stamps[current_comp]->getAtom( k );
865	<	if( !current_atom->havePosition() ){
866	<	sprintf( painCave.errMsg,
867	<	"SimSetup:initFromBass error.\n"
868	<	"\tComponent %s, atom %s does not have a position specified.\n"
1177	<	"\tThe initialization routine is unable to give a start"
1178	<	" position.\n",
1179	<	comp_stamps[current_comp]->getID(),
1180	<	current_atom->getType() );
1181	<	painCave.isFatal = 1;
1182	<	simError();
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	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
872	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
873	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
871	>	#ifdef IS_MPI
872	>	int myUse = usesDipoles;
873	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
874	>	#endif //is_mpi
875
876	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
876	>	double theEcr, theEst;
877
878	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
878	>	if (globals->getUseRF()){
879	>	info[i].useReactionField = 1;
880
881	<	rotMat[0][0] = 1.0;
882	<	rotMat[0][1] = 0.0;
883	<	rotMat[0][2] = 0.0;
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	<	rotMat[1][0] = 0.0;
895	<	rotMat[1][1] = 1.0;
896	<	rotMat[1][2] = 0.0;
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	<	rotMat[2][0] = 0.0;
1202	<	rotMat[2][1] = 0.0;
1203	<	rotMat[2][2] = 1.0;
908	>	info[i].setDefaultEcr(theEcr, theEst);
909
910	<	dAtom->setA( rotMat );
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, "post processing checks out");
955	+	MPIcheckPoint();
956	+	#endif // is_mpi
957	+	}
958	+
959	+	void SimSetup::initSystemCoords(void){
960	+	int i;
961
962	<	current_atom_ndx++;
962	>	char* inName;
963	>
964	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
965	>
966	>	for (i = 0; i < info[0].n_atoms; i++)
967	>	info[0].atoms[i]->setCoords();
968	>
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	>	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	<	current_mol++;
997	<	current_comp_mol++;
996	>	#ifdef IS_MPI
997	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
998	>	MPIcheckPoint();
999	>	#endif // is_mpi
1000	>	}
1001
1214	–	if( current_comp_mol >= components_nmol[current_comp] ){
1002
1003	<	current_comp_mol = 0;
1004	<	current_comp++;
1003	>	void SimSetup::makeOutNames(void){
1004	>	int k;
1005	>
1006	>
1007	>	for (k = 0; k < nInfo; k++){
1008	>	#ifdef IS_MPI
1009	>	if (worldRank == 0){
1010	>	#endif // is_mpi
1011	>
1012	>	if (globals->haveFinalConfig()){
1013	>	strcpy(info[k].finalName, globals->getFinalConfig());
1014	>	}
1015	>	else{
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	>	}
1039	>
1040	>	// make the sample and status out names
1041	>
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	>	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	>	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	>	else if (!strcmp(endTest, ".BASS")){
1072	>	strcpy(endTest, ".stat");
1073	>	}
1074	>	else{
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	>	}
1086	>
1087	>	#ifdef IS_MPI
1088	>
1089	>	}
1090	>	#endif // is_mpi
1091		}
1092		}
1093	+
1094	+
1095	+	void SimSetup::sysObjectsCreation(void){
1096	+	int i, k;
1097	+
1098	+	// create the forceField
1099	+
1100	+	createFF();
1101	+
1102	+	// extract componentList
1103	+
1104	+	compList();
1105	+
1106	+	// calc the number of atoms, bond, bends, and torsions
1107	+
1108	+	calcSysValues();
1109	+
1110	+	#ifdef IS_MPI
1111	+	// divide the molecules among the processors
1112	+
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	+
1132	+
1133	+	void SimSetup::createFF(void){
1134	+	switch (ffCase){
1135	+	case FF_DUFF:
1136	+	the_ff = new DUFF();
1137	+	break;
1138	+
1139	+	case FF_LJ:
1140	+	the_ff = new LJFF();
1141	+	break;
1142	+
1143	+	case FF_EAM:
1144	+	the_ff = new EAM_FF();
1145	+	break;
1146	+
1147	+	case FF_H2O:
1148	+	the_ff = new WATER();
1149	+	break;
1150	+
1151	+	default:
1152	+	sprintf(painCave.errMsg,
1153	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1154	+	painCave.isFatal = 1;
1155	+	simError();
1156	+	}
1157	+
1158	+	#ifdef IS_MPI
1159	+	strcpy(checkPointMsg, "ForceField creation successful");
1160	+	MPIcheckPoint();
1161	+	#endif // is_mpi
1162	+	}
1163	+
1164	+
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	+	// 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	+	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	+
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	+	#ifdef IS_MPI
1209	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1210	+	MPIcheckPoint();
1211	+	#endif // is_mpi
1212	+	}
1213	+
1214	+	void SimSetup::calcSysValues(void){
1215	+	int i;
1216	+
1217	+	int* molMembershipArray;
1218	+
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	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1231	+	molMembershipArray = new int[tot_atoms];
1232	+
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	+	info[i].molMembershipArray = molMembershipArray;
1242	+	}
1243	+	}
1244	+
1245	+	#ifdef IS_MPI
1246	+
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	+	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	+	#endif // is_mpi
1311	+
1312	+
1313	+	void SimSetup::makeSysArrays(void){
1314	+
1315	+	#ifndef IS_MPI
1316	+	int k, j;
1317	+	#endif // is_mpi
1318	+	int i, l;
1319	+
1320	+	Atom** the_atoms;
1321	+	Molecule* the_molecules;
1322	+	Exclude** the_excludes;
1323	+
1324	+
1325	+	for (l = 0; l < nInfo; l++){
1326	+	// create the atom and short range interaction arrays
1327	+
1328	+	the_atoms = new Atom * [info[l].n_atoms];
1329	+	the_molecules = new Molecule[info[l].n_mol];
1330	+	int molIndex;
1331	+
1332	+	// initialize the molecule's stampID's
1333	+
1334	+	#ifdef IS_MPI
1335	+
1336	+
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	+	#else // is_mpi
1348	+
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	+
1364	+
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	+	//creat the object functor;
1729	+	objFunc = (ObjFunctor1*) new ClassMemObjFunctor1<OOPSEMinimizerBase>
1730	+	(myOOPSEMinimizerBase, &OOPSEMinimizerBase::calcGradient);
1731	+
1732	+	//creat output functor;
1733	+	outputFunc =  new ClassMemOutputFunctor<OOPSEMinimizerBase>
1734	+	(myOOPSEMinimizerBase, &OOPSEMinimizerBase::output);
1735	+
1736	+	//creat nonlinear model
1737	+	dim = myOOPSEMinimizerBase->getDim();
1738	+	nlp = new ConcreteNLModel1(dim, objFunc);
1739	+
1740	+	//prepare parameter set for minimizer
1741	+	param = new MinimizerParameterSet();
1742	+	param->setDefaultParameter();
1743	+
1744	+	if (globals->haveMinimizer()){
1745	+	param->setFTol(globals->getMinFTol());
1746	+	}
1747	+
1748	+	if (globals->haveMinGTol()){
1749	+	param->setGTol(globals->getMinGTol());
1750	+	}
1751	+
1752	+	if (globals->haveMinMaxIter()){
1753	+	param->setMaxIteration(globals->getMinMaxIter());
1754	+	}
1755	+
1756	+	if (globals->haveMinWriteFrq()){
1757	+	param->setMaxIteration(globals->getMinMaxIter());
1758	+	}
1759	+
1760	+	if (globals->haveMinWriteFrq()){
1761	+	param->setWriteFrq(globals->getMinWriteFrq());
1762	+	}
1763	+
1764	+	if (globals->haveMinResetFrq()){
1765	+	param->setResetFrq(globals->getMinResetFrq());
1766	+	}
1767	+
1768	+	if (globals->haveMinLSMaxIter()){
1769	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1770	+	}
1771	+
1772	+	if (globals->haveMinLSTol()){
1773	+	param->setLineSearchTol(globals->getMinLSTol());
1774	+	}
1775	+
1776	+	//creat the minimizer
1777	+	minimizer = new PRCGMinimizer(nlp, param);
1778	+	minimizer->setLineSearchStrategy(nlp, GoldenSection);
1779	+	minimizer->setOutputFunctor(outputFunc);
1780	+
1781	+	//store the minimizer into simInfo
1782	+	info[i].the_minimizer = minimizer;
1783	+	info[i].has_minimizer = true;
1784	+	}
1785	+	*/
1786	+	}

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