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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 504 by mmeineke, Thu Apr 17 21:54:18 2003 UTC vs.
Revision 1066 by tim, Tue Feb 24 16:36:33 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	+	#include "OOPSEMinimizer.hpp"
14
15		#ifdef IS_MPI
16		#include "mpiBASS.h"
17		#include "mpiSimulation.hpp"
18		#endif
19
20	+	// some defines for ensemble and Forcefield  cases
21	+
22	+	#define NVE_ENS        0
23	+	#define NVT_ENS        1
24	+	#define NPTi_ENS       2
25	+	#define NPTf_ENS       3
26	+	#define NPTxyz_ENS     4
27	+
28	+
29	+	#define FF_DUFF  0
30	+	#define FF_LJ    1
31	+	#define FF_EAM   2
32	+	#define FF_H2O   3
33	+
34	+	using namespace std;
35	+
36	+	/**
37	+	* Check whether dividend is divisble by divisor or not
38	+	*/
39	+	bool isDivisible(double dividend, double divisor){
40	+	double tolerance = 0.000001;
41	+	double quotient;
42	+	double diff;
43	+	int intQuotient;
44	+
45	+	quotient = dividend / divisor;
46	+
47	+	if (quotient < 0)
48	+	quotient = -quotient;
49	+
50	+	intQuotient = int (quotient + tolerance);
51	+
52	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
53	+
54	+	if (diff <= tolerance)
55	+	return true;
56	+	else
57	+	return false;
58	+	}
59	+
60		SimSetup::SimSetup(){
61	+
62	+	initSuspend = false;
63	+	isInfoArray = 0;
64	+	nInfo = 1;
65	+
66		stamps = new MakeStamps();
67		globals = new Globals();
68	<
68	>
69	>
70		#ifdef IS_MPI
71	<	strcpy( checkPointMsg, "SimSetup creation successful" );
71	>	strcpy(checkPointMsg, "SimSetup creation successful");
72		MPIcheckPoint();
73		#endif // IS_MPI
74		}
#	Line 27 | Line 78 | SimSetup::~SimSetup(){
78		delete globals;
79		}
80
81	<	void SimSetup::parseFile( char* fileName ){
81	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
82	>	info = the_info;
83	>	nInfo = theNinfo;
84	>	isInfoArray = 1;
85	>	initSuspend = true;
86	>	}
87
88	+
89	+	void SimSetup::parseFile(char* fileName){
90		#ifdef IS_MPI
91	<	if( worldRank == 0 ){
91	>	if (worldRank == 0){
92		#endif // is_mpi
93	<
93	>
94		inFileName = fileName;
95	<	set_interface_stamps( stamps, globals );
96	<
95	>	set_interface_stamps(stamps, globals);
96	>
97		#ifdef IS_MPI
98		mpiEventInit();
99		#endif
100
101	<	yacc_BASS( fileName );
101	>	yacc_BASS(fileName);
102
103		#ifdef IS_MPI
104		throwMPIEvent(NULL);
105		}
106	<	else receiveParse();
106	>	else{
107	>	receiveParse();
108	>	}
109		#endif
110
111		}
112
113		#ifdef IS_MPI
114		void SimSetup::receiveParse(void){
115	<
116	<	set_interface_stamps( stamps, globals );
117	<	mpiEventInit();
118	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
115	>	set_interface_stamps(stamps, globals);
116	>	mpiEventInit();
117	>	MPIcheckPoint();
118	>	mpiEventLoop();
119		}
120
121		#endif // is_mpi
122
123	<	void SimSetup::createSim( void ){
123	>	void SimSetup::createSim(void){
124
125	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	ExtendedSystem* the_extendedsystem;
70	<	int i, j, k, globalAtomIndex;
125	>	// gather all of the information from the Bass file
126
127	<	// get the stamps and globals;
73	<	the_stamps = stamps;
74	<	the_globals = globals;
127	>	gatherInfo();
128
129	<	// 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();
129	>	// creation of complex system objects
130
131	<	// 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() );
131	>	sysObjectsCreation();
132
133	<	// 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	<	}
133	>	// check on the post processing info
134
135	<	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	<	}
135	>	finalInfoCheck();
136
137	<	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	<	}
137	>	// initialize the system coordinates
138
139	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
140	<	the_extendedsystem = new ExtendedSystem( simnfo );
127	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
139	>	if ( !initSuspend ){
140	>	initSystemCoords();
141
142	<	if (the_globals->haveTauThermostat())
143	<	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" );
142	>	if( !(globals->getUseInitTime()) )
143	>	info[0].currentTime = 0.0;
144		}
152	–	strcpy( simnfo->ensemble, ensemble );
145
146	<	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	<	}
146	>	// make the output filenames
147
148	<	#ifdef IS_MPI
172	<	strcpy( checkPointMsg, "ForceField creation successful" );
173	<	MPIcheckPoint();
174	<	#endif // is_mpi
148	>	makeOutNames();
149
150	+	if (globals->haveMinimizer())
151	+	// make minimizer
152	+	makeMinimizer();
153	+	else
154	+	// make the integrator
155	+	makeIntegrator();
156
157	+	#ifdef IS_MPI
158	+	mpiSim->mpiRefresh();
159	+	#endif
160
161	<	// 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];
161	>	// initialize the Fortran
162
163	<	if( !the_globals->haveNMol() ){
164	<	// we don't have the total number of molecules, so we assume it is
185	<	// given in each component
163	>	initFortran();
164	>	}
165
187	–	tot_nmol = 0;
188	–	for( i=0; i<n_components; i++ ){
166
167	<	if( !the_components[i]->haveNMol() ){
168	<	// we have a problem
169	<	sprintf( painCave.errMsg,
170	<	"SimSetup Error. No global NMol or component NMol"
171	<	" given. Cannot calculate the number of atoms.\n" );
172	<	painCave.isFatal = 1;
173	<	simError();
174	<	}
167	>	void SimSetup::makeMolecules(void){
168	>	int k;
169	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
170	>	molInit molInfo;
171	>	DirectionalAtom* dAtom;
172	>	LinkedAssign* extras;
173	>	LinkedAssign* current_extra;
174	>	AtomStamp* currentAtom;
175	>	BondStamp* currentBond;
176	>	BendStamp* currentBend;
177	>	TorsionStamp* currentTorsion;
178
179	<	tot_nmol += the_components[i]->getNMol();
180	<	components_nmol[i] = the_components[i]->getNMol();
181	<	}
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	<	}
179	>	bond_pair* theBonds;
180	>	bend_set* theBends;
181	>	torsion_set* theTorsions;
182
183	<	#ifdef IS_MPI
229	<	strcpy( checkPointMsg, "Have the number of components" );
230	<	MPIcheckPoint();
231	<	#endif // is_mpi
183	>	//init the forceField paramters
184
185	<	// make an array of molecule stamps that match the components used.
234	<	// also extract the used stamps out into a separate linked list
185	>	the_ff->readParams();
186
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++ ){
187
188	<	id = the_components[i]->getType();
247	<	comp_stamps[i] = NULL;
248	<
249	<	// check to make sure the component isn't already in the list
188	>	// init the atoms
189
190	<	comp_stamps[i] = headStamp->match( id );
191	<	if( comp_stamps[i] == NULL ){
192	<
193	<	// 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	<	}
190	>	double phi, theta, psi;
191	>	double sux, suy, suz;
192	>	double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz;
193	>	double ux, uy, uz, u, uSqr;
194
195	<	#ifdef IS_MPI
196	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
273	<	MPIcheckPoint();
274	<	#endif // is_mpi
275	<
195	>	for (k = 0; k < nInfo; k++){
196	>	the_ff->setSimInfo(&(info[k]));
197
198	+	atomOffset = 0;
199	+	excludeOffset = 0;
200	+	for (i = 0; i < info[k].n_mol; i++){
201	+	stampID = info[k].molecules[i].getStampID();
202
203	+	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
204	+	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
205	+	molInfo.nBends = comp_stamps[stampID]->getNBends();
206	+	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
207	+	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
208
209	<	// caclulate the number of atoms, bonds, bends and torsions
209	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
210	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
211	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
212	>	molInfo.myBends = new Bend * [molInfo.nBends];
213	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
214
215	<	tot_atoms = 0;
216	<	tot_bonds = 0;
217	<	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	<	}
215	>	theBonds = new bond_pair[molInfo.nBonds];
216	>	theBends = new bend_set[molInfo.nBends];
217	>	theTorsions = new torsion_set[molInfo.nTorsions];
218
219	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
219	>	// make the Atoms
220
221	<	simnfo->n_atoms = tot_atoms;
222	<	simnfo->n_bonds = tot_bonds;
223	<	simnfo->n_bends = tot_bends;
224	<	simnfo->n_torsions = tot_torsions;
225	<	simnfo->n_SRI = tot_SRI;
226	<	simnfo->n_mol = tot_nmol;
227	<
302	<	simnfo->molMembershipArray = new int[tot_atoms];
221	>	for (j = 0; j < molInfo.nAtoms; j++){
222	>	currentAtom = comp_stamps[stampID]->getAtom(j);
223	>	if (currentAtom->haveOrientation()){
224	>	dAtom = new DirectionalAtom((j + atomOffset),
225	>	info[k].getConfiguration());
226	>	info[k].n_oriented++;
227	>	molInfo.myAtoms[j] = dAtom;
228
229	<	#ifdef IS_MPI
229	>	// Directional Atoms have standard unit vectors which are oriented
230	>	// in space using the three Euler angles.  We assume the standard
231	>	// unit vector was originally along the z axis below.
232
233	<	// divide the molecules among processors here.
234	<
235	<	mpiSim = new mpiSimulation( simnfo );
236	<
237	<	globalIndex = mpiSim->divideLabor();
233	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
234	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
235	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
236	>
237	>	Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
238	>	Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
239	>	Axz = sin(theta) * sin(psi);
240	>
241	>	Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
242	>	Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
243	>	Ayz = sin(theta) * cos(psi);
244	>
245	>	Azx = sin(phi) * sin(theta);
246	>	Azy = -cos(phi) * sin(theta);
247	>	Azz = cos(theta);
248
249	<	// set up the local variables
250	<
251	<	int localMol, allMol;
315	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
249	>	sux = 0.0;
250	>	suy = 0.0;
251	>	suz = 1.0;
252
253	<	int* mol2proc = mpiSim->getMolToProcMap();
254	<	int* molCompType = mpiSim->getMolComponentType();
255	<
320	<	allMol = 0;
321	<	localMol = 0;
322	<	local_atoms = 0;
323	<	local_bonds = 0;
324	<	local_bends = 0;
325	<	local_torsions = 0;
326	<	globalAtomIndex = 0;
253	>	ux = (Axx * sux) + (Ayx * suy) + (Azx * suz);
254	>	uy = (Axy * sux) + (Ayy * suy) + (Azy * suz);
255	>	uz = (Axz * sux) + (Ayz * suy) + (Azz * suz);
256
257	+	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
258
259	<	for( i=0; i<n_components; i++ ){
259	>	u = sqrt(uSqr);
260	>	ux = ux / u;
261	>	uy = uy / u;
262	>	uz = uz / u;
263
264	<	for( j=0; j<components_nmol[i]; j++ ){
265	<
266	<	if( mol2proc[allMol] == worldRank ){
267	<
268	<	local_atoms +=    comp_stamps[i]->getNAtoms();
269	<	local_bonds +=    comp_stamps[i]->getNBonds();
270	<	local_bends +=    comp_stamps[i]->getNBends();
271	<	local_torsions += comp_stamps[i]->getNTorsions();
272	<	localMol++;
340	<	}
341	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
342	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
343	<	globalAtomIndex++;
344	<	}
264	>	dAtom->setSUx(ux);
265	>	dAtom->setSUy(uy);
266	>	dAtom->setSUz(uz);
267	>	}
268	>	else{
269	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
270	>	info[k].getConfiguration());
271	>	}
272	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
273
274	<	allMol++;
347	<	}
348	<	}
349	<	local_SRI = local_bonds + local_bends + local_torsions;
350	<
351	<	simnfo->n_atoms = mpiSim->getMyNlocal();
352	<
353	<	if( local_atoms != simnfo->n_atoms ){
354	<	sprintf( painCave.errMsg,
355	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
356	<	" localAtom (%d) are not equal.\n",
357	<	simnfo->n_atoms,
358	<	local_atoms );
359	<	painCave.isFatal = 1;
360	<	simError();
361	<	}
274	>	#ifdef IS_MPI
275
276	<	simnfo->n_bonds = local_bonds;
364	<	simnfo->n_bends = local_bends;
365	<	simnfo->n_torsions = local_torsions;
366	<	simnfo->n_SRI = local_SRI;
367	<	simnfo->n_mol = localMol;
276	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
277
369	–	strcpy( checkPointMsg, "Passed nlocal consistency check." );
370	–	MPIcheckPoint();
371	–
372	–
278		#endif // is_mpi
279	<
279	>	}
280
281	<	// create the atom and short range interaction arrays
281	>	// make the bonds
282	>	for (j = 0; j < molInfo.nBonds; j++){
283	>	currentBond = comp_stamps[stampID]->getBond(j);
284	>	theBonds[j].a = currentBond->getA() + atomOffset;
285	>	theBonds[j].b = currentBond->getB() + atomOffset;
286
287	<	Atom::createArrays(simnfo->n_atoms);
288	<	the_atoms = new Atom*[simnfo->n_atoms];
380	<	the_molecules = new Molecule[simnfo->n_mol];
381	<	int molIndex;
287	>	exI = theBonds[j].a;
288	>	exJ = theBonds[j].b;
289
290	<	// initialize the molecule's stampID's
291	<
290	>	// exclude_I must always be the smaller of the pair
291	>	if (exI > exJ){
292	>	tempEx = exI;
293	>	exI = exJ;
294	>	exJ = tempEx;
295	>	}
296		#ifdef IS_MPI
297	<
297	>	tempEx = exI;
298	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
299	>	tempEx = exJ;
300	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
301
302	<	molIndex = 0;
303	<	for(i=0; i<mpiSim->getTotNmol(); i++){
390	<
391	<	if(mol2proc[i] == worldRank ){
392	<	the_molecules[molIndex].setStampID( molCompType[i] );
393	<	the_molecules[molIndex].setMyIndex( molIndex );
394	<	the_molecules[molIndex].setGlobalIndex( i );
395	<	molIndex++;
396	<	}
397	<	}
302	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
303	>	#else  // isn't MPI
304
305	<	#else // is_mpi
306	<
401	<	molIndex = 0;
402	<	globalAtomIndex = 0;
403	<	for(i=0; i<n_components; i++){
404	<	for(j=0; j<components_nmol[i]; j++ ){
405	<	the_molecules[molIndex].setStampID( i );
406	<	the_molecules[molIndex].setMyIndex( molIndex );
407	<	the_molecules[molIndex].setGlobalIndex( molIndex );
408	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
409	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
410	<	globalAtomIndex++;
305	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
306	>	#endif  //is_mpi
307		}
308	<	molIndex++;
413	<	}
414	<	}
415	<
308	>	excludeOffset += molInfo.nBonds;
309
310	<	#endif // is_mpi
310	>	//make the bends
311	>	for (j = 0; j < molInfo.nBends; j++){
312	>	currentBend = comp_stamps[stampID]->getBend(j);
313	>	theBends[j].a = currentBend->getA() + atomOffset;
314	>	theBends[j].b = currentBend->getB() + atomOffset;
315	>	theBends[j].c = currentBend->getC() + atomOffset;
316
317	+	if (currentBend->haveExtras()){
318	+	extras = currentBend->getExtras();
319	+	current_extra = extras;
320
321	<	if( simnfo->n_SRI ){
322	<
323	<	Exclude::createArray(simnfo->n_SRI);
324	<	the_excludes = new Exclude*[simnfo->n_SRI];
325	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
326	<	simnfo->globalExcludes = new int;
327	<	simnfo->n_exclude = simnfo->n_SRI;
427	<	}
428	<	else{
429	<
430	<	Exclude::createArray( 1 );
431	<	the_excludes = new Exclude*;
432	<	the_excludes[0] = new Exclude(0);
433	<	the_excludes[0]->setPair( 0,0 );
434	<	simnfo->globalExcludes = new int;
435	<	simnfo->globalExcludes[0] = 0;
436	<	simnfo->n_exclude = 0;
437	<	}
321	>	while (current_extra != NULL){
322	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
323	>	switch (current_extra->getType()){
324	>	case 0:
325	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
326	>	theBends[j].isGhost = 1;
327	>	break;
328
329	<	// set the arrays into the SimInfo object
329	>	case 1:
330	>	theBends[j].ghost = (int) current_extra->getDouble() +
331	>	atomOffset;
332	>	theBends[j].isGhost = 1;
333	>	break;
334
335	<	simnfo->atoms = the_atoms;
336	<	simnfo->molecules = the_molecules;
337	<	simnfo->nGlobalExcludes = 0;
338	<	simnfo->excludes = the_excludes;
335	>	default:
336	>	sprintf(painCave.errMsg,
337	>	"SimSetup Error: ghostVectorSource was neither a "
338	>	"double nor an int.\n"
339	>	"-->Bend[%d] in %s\n",
340	>	j, comp_stamps[stampID]->getID());
341	>	painCave.isFatal = 1;
342	>	simError();
343	>	}
344	>	}
345	>	else{
346	>	sprintf(painCave.errMsg,
347	>	"SimSetup Error: unhandled bend assignment:\n"
348	>	"    -->%s in Bend[%d] in %s\n",
349	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
350	>	painCave.isFatal = 1;
351	>	simError();
352	>	}
353
354	+	current_extra = current_extra->getNext();
355	+	}
356	+	}
357
358	<	// get some of the tricky things that may still be in the globals
358	>	if (!theBends[j].isGhost){
359	>	exI = theBends[j].a;
360	>	exJ = theBends[j].c;
361	>	}
362	>	else{
363	>	exI = theBends[j].a;
364	>	exJ = theBends[j].b;
365	>	}
366
367	<
368	<	if( the_globals->haveBox() ){
369	<	simnfo->box_x = the_globals->getBox();
370	<	simnfo->box_y = the_globals->getBox();
371	<	simnfo->box_z = the_globals->getBox();
372	<	}
373	<	else if( the_globals->haveDensity() ){
367	>	// exclude_I must always be the smaller of the pair
368	>	if (exI > exJ){
369	>	tempEx = exI;
370	>	exI = exJ;
371	>	exJ = tempEx;
372	>	}
373	>	#ifdef IS_MPI
374	>	tempEx = exI;
375	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
376	>	tempEx = exJ;
377	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
378
379	<	double vol;
380	<	vol = (double)tot_nmol / the_globals->getDensity();
381	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
382	<	simnfo->box_y = simnfo->box_x;
383	<	simnfo->box_z = simnfo->box_x;
384	<	}
463	<	else{
464	<	if( !the_globals->haveBoxX() ){
465	<	sprintf( painCave.errMsg,
466	<	"SimSetup error, no periodic BoxX size given.\n" );
467	<	painCave.isFatal = 1;
468	<	simError();
469	<	}
470	<	simnfo->box_x = the_globals->getBoxX();
379	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
380	>	#else  // isn't MPI
381	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
382	>	#endif  //is_mpi
383	>	}
384	>	excludeOffset += molInfo.nBends;
385
386	<	if( !the_globals->haveBoxY() ){
387	<	sprintf( painCave.errMsg,
388	<	"SimSetup error, no periodic BoxY size given.\n" );
389	<	painCave.isFatal = 1;
390	<	simError();
391	<	}
478	<	simnfo->box_y = the_globals->getBoxY();
386	>	for (j = 0; j < molInfo.nTorsions; j++){
387	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
388	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
389	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
390	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
391	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
392
393	<	if( !the_globals->haveBoxZ() ){
394	<	sprintf( painCave.errMsg,
482	<	"SimSetup error, no periodic BoxZ size given.\n" );
483	<	painCave.isFatal = 1;
484	<	simError();
485	<	}
486	<	simnfo->box_z = the_globals->getBoxZ();
487	<	}
393	>	exI = theTorsions[j].a;
394	>	exJ = theTorsions[j].d;
395
396	+	// exclude_I must always be the smaller of the pair
397	+	if (exI > exJ){
398	+	tempEx = exI;
399	+	exI = exJ;
400	+	exJ = tempEx;
401	+	}
402		#ifdef IS_MPI
403	<	strcpy( checkPointMsg, "Box size set up" );
404	<	MPIcheckPoint();
405	<	#endif // is_mpi
403	>	tempEx = exI;
404	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
405	>	tempEx = exJ;
406	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
407
408	<
409	<	// initialize the arrays
410	<
411	<	the_ff->setSimInfo( simnfo );
498	<
499	<	makeMolecules();
500	<	simnfo->identArray = new int[simnfo->n_atoms];
501	<	for(i=0; i<simnfo->n_atoms; i++){
502	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
503	<	}
504	<
505	<	if (the_globals->getUseRF() ) {
506	<	simnfo->useReactionField = 1;
507	<
508	<	if( !the_globals->haveECR() ){
509	<	sprintf( painCave.errMsg,
510	<	"SimSetup Warning: using default value of 1/2 the smallest "
511	<	"box length for the electrostaticCutoffRadius.\n"
512	<	"I hope you have a very fast processor!\n");
513	<	painCave.isFatal = 0;
514	<	simError();
515	<	double smallest;
516	<	smallest = simnfo->box_x;
517	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
518	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
519	<	simnfo->ecr = 0.5 * smallest;
520	<	} else {
521	<	simnfo->ecr        = the_globals->getECR();
522	<	}
523	<
524	<	if( !the_globals->haveEST() ){
525	<	sprintf( painCave.errMsg,
526	<	"SimSetup Warning: using default value of 0.05 * the "
527	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
528	<	);
529	<	painCave.isFatal = 0;
530	<	simError();
531	<	simnfo->est = 0.05 * simnfo->ecr;
532	<	} else {
533	<	simnfo->est        = the_globals->getEST();
534	<	}
535	<
536	<	if(!the_globals->haveDielectric() ){
537	<	sprintf( painCave.errMsg,
538	<	"SimSetup Error: You are trying to use Reaction Field without"
539	<	"setting a dielectric constant!\n"
540	<	);
541	<	painCave.isFatal = 1;
542	<	simError();
543	<	}
544	<	simnfo->dielectric = the_globals->getDielectric();
545	<	} else {
546	<	if (usesDipoles) {
547	<
548	<	if( !the_globals->haveECR() ){
549	<	sprintf( painCave.errMsg,
550	<	"SimSetup Warning: using default value of 1/2 the smallest "
551	<	"box length for the electrostaticCutoffRadius.\n"
552	<	"I hope you have a very fast processor!\n");
553	<	painCave.isFatal = 0;
554	<	simError();
555	<	double smallest;
556	<	smallest = simnfo->box_x;
557	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
558	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
559	<	simnfo->ecr = 0.5 * smallest;
560	<	} else {
561	<	simnfo->ecr        = the_globals->getECR();
408	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
409	>	#else  // isn't MPI
410	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
411	>	#endif  //is_mpi
412		}
413	<
564	<	if( !the_globals->haveEST() ){
565	<	sprintf( painCave.errMsg,
566	<	"SimSetup Warning: using default value of 5%% of the "
567	<	"electrostaticCutoffRadius for the "
568	<	"electrostaticSkinThickness\n"
569	<	);
570	<	painCave.isFatal = 0;
571	<	simError();
572	<	simnfo->est = 0.05 * simnfo->ecr;
573	<	} else {
574	<	simnfo->est        = the_globals->getEST();
575	<	}
576	<	}
577	<	}
413	>	excludeOffset += molInfo.nTorsions;
414
579	–	#ifdef IS_MPI
580	–	strcpy( checkPointMsg, "electrostatic parameters check out" );
581	–	MPIcheckPoint();
582	–	#endif // is_mpi
415
416	<	if( the_globals->haveInitialConfig() ){
585	<
586	<	InitializeFromFile* fileInit;
587	<	#ifdef IS_MPI // is_mpi
588	<	if( worldRank == 0 ){
589	<	#endif //is_mpi
590	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
591	<	#ifdef IS_MPI
592	<	}else fileInit = new InitializeFromFile( NULL );
593	<	#endif
594	<	fileInit->read_xyz( simnfo ); // default velocities on
416	>	// send the arrays off to the forceField for init.
417
418	<	delete fileInit;
419	<	}
420	<	else{
421	<
422	<	#ifdef IS_MPI
418	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
419	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
420	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
421	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
422	>	theTorsions);
423
602	–	// no init from bass
603	–
604	–	sprintf( painCave.errMsg,
605	–	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
606	–	painCave.isFatal;
607	–	simError();
608	–
609	–	#else
424
425	<	initFromBass();
425	>	info[k].molecules[i].initialize(molInfo);
426
427
428	<	#endif
429	<	}
428	>	atomOffset += molInfo.nAtoms;
429	>	delete[] theBonds;
430	>	delete[] theBends;
431	>	delete[] theTorsions;
432	>	}
433	>	}
434
435		#ifdef IS_MPI
436	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
436	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
437		MPIcheckPoint();
438		#endif // is_mpi
439
440	+	// clean up the forcefield
441
442	<
443	<
444	<
442	>	the_ff->calcRcut();
443	>	the_ff->cleanMe();
444	>	}
445
446	<
447	<	#ifdef IS_MPI
448	<	if( worldRank == 0 ){
449	<	#endif // is_mpi
450	<
451	<	if( the_globals->haveFinalConfig() ){
452	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
446	>	void SimSetup::initFromBass(void){
447	>	int i, j, k;
448	>	int n_cells;
449	>	double cellx, celly, cellz;
450	>	double temp1, temp2, temp3;
451	>	int n_per_extra;
452	>	int n_extra;
453	>	int have_extra, done;
454	>
455	>	double vel[3];
456	>	vel[0] = 0.0;
457	>	vel[1] = 0.0;
458	>	vel[2] = 0.0;
459	>
460	>	temp1 = (double) tot_nmol / 4.0;
461	>	temp2 = pow(temp1, (1.0 / 3.0));
462	>	temp3 = ceil(temp2);
463	>
464	>	have_extra = 0;
465	>	if (temp2 < temp3){
466	>	// we have a non-complete lattice
467	>	have_extra = 1;
468	>
469	>	n_cells = (int) temp3 - 1;
470	>	cellx = info[0].boxL[0] / temp3;
471	>	celly = info[0].boxL[1] / temp3;
472	>	cellz = info[0].boxL[2] / temp3;
473	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
474	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
475	>	n_per_extra = (int) ceil(temp1);
476	>
477	>	if (n_per_extra > 4){
478	>	sprintf(painCave.errMsg,
479	>	"SimSetup error. There has been an error in constructing"
480	>	" the non-complete lattice.\n");
481	>	painCave.isFatal = 1;
482	>	simError();
483		}
635	–	else{
636	–	strcpy( simnfo->finalName, inFileName );
637	–	char* endTest;
638	–	int nameLength = strlen( simnfo->finalName );
639	–	endTest = &(simnfo->finalName[nameLength - 5]);
640	–	if( !strcmp( endTest, ".bass" ) ){
641	–	strcpy( endTest, ".eor" );
642	–	}
643	–	else if( !strcmp( endTest, ".BASS" ) ){
644	–	strcpy( endTest, ".eor" );
645	–	}
646	–	else{
647	–	endTest = &(simnfo->finalName[nameLength - 4]);
648	–	if( !strcmp( endTest, ".bss" ) ){
649	–	strcpy( endTest, ".eor" );
650	–	}
651	–	else if( !strcmp( endTest, ".mdl" ) ){
652	–	strcpy( endTest, ".eor" );
653	–	}
654	–	else{
655	–	strcat( simnfo->finalName, ".eor" );
656	–	}
657	–	}
658	–	}
659	–
660	–	// make the sample and status out names
661	–
662	–	strcpy( simnfo->sampleName, inFileName );
663	–	char* endTest;
664	–	int nameLength = strlen( simnfo->sampleName );
665	–	endTest = &(simnfo->sampleName[nameLength - 5]);
666	–	if( !strcmp( endTest, ".bass" ) ){
667	–	strcpy( endTest, ".dump" );
668	–	}
669	–	else if( !strcmp( endTest, ".BASS" ) ){
670	–	strcpy( endTest, ".dump" );
671	–	}
672	–	else{
673	–	endTest = &(simnfo->sampleName[nameLength - 4]);
674	–	if( !strcmp( endTest, ".bss" ) ){
675	–	strcpy( endTest, ".dump" );
676	–	}
677	–	else if( !strcmp( endTest, ".mdl" ) ){
678	–	strcpy( endTest, ".dump" );
679	–	}
680	–	else{
681	–	strcat( simnfo->sampleName, ".dump" );
682	–	}
683	–	}
684	–
685	–	strcpy( simnfo->statusName, inFileName );
686	–	nameLength = strlen( simnfo->statusName );
687	–	endTest = &(simnfo->statusName[nameLength - 5]);
688	–	if( !strcmp( endTest, ".bass" ) ){
689	–	strcpy( endTest, ".stat" );
690	–	}
691	–	else if( !strcmp( endTest, ".BASS" ) ){
692	–	strcpy( endTest, ".stat" );
693	–	}
694	–	else{
695	–	endTest = &(simnfo->statusName[nameLength - 4]);
696	–	if( !strcmp( endTest, ".bss" ) ){
697	–	strcpy( endTest, ".stat" );
698	–	}
699	–	else if( !strcmp( endTest, ".mdl" ) ){
700	–	strcpy( endTest, ".stat" );
701	–	}
702	–	else{
703	–	strcat( simnfo->statusName, ".stat" );
704	–	}
705	–	}
706	–
707	–	#ifdef IS_MPI
484		}
709	–	#endif // is_mpi
710	–
711	–	// set the status, sample, and themal kick times
712	–
713	–	if( the_globals->haveSampleTime() ){
714	–	simnfo->sampleTime = the_globals->getSampleTime();
715	–	simnfo->statusTime = simnfo->sampleTime;
716	–	simnfo->thermalTime = simnfo->sampleTime;
717	–	}
485		else{
486	<	simnfo->sampleTime = the_globals->getRunTime();
487	<	simnfo->statusTime = simnfo->sampleTime;
488	<	simnfo->thermalTime = simnfo->sampleTime;
486	>	n_cells = (int) temp3;
487	>	cellx = info[0].boxL[0] / temp3;
488	>	celly = info[0].boxL[1] / temp3;
489	>	cellz = info[0].boxL[2] / temp3;
490		}
491
492	<	if( the_globals->haveStatusTime() ){
493	<	simnfo->statusTime = the_globals->getStatusTime();
494	<	}
492	>	current_mol = 0;
493	>	current_comp_mol = 0;
494	>	current_comp = 0;
495	>	current_atom_ndx = 0;
496
497	<	if( the_globals->haveThermalTime() ){
498	<	simnfo->thermalTime = the_globals->getThermalTime();
499	<	}
497	>	for (i = 0; i < n_cells ; i++){
498	>	for (j = 0; j < n_cells; j++){
499	>	for (k = 0; k < n_cells; k++){
500	>	makeElement(i * cellx, j * celly, k * cellz);
501
502	<	// check for the temperature set flag
502	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
503
504	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
504	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
505
506	+	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
507	+	}
508	+	}
509	+	}
510
511	<	//   // make the longe range forces and the integrator
511	>	if (have_extra){
512	>	done = 0;
513
514	<	//   new AllLong( simnfo );
514	>	int start_ndx;
515	>	for (i = 0; i < (n_cells + 1) && !done; i++){
516	>	for (j = 0; j < (n_cells + 1) && !done; j++){
517	>	if (i < n_cells){
518	>	if (j < n_cells){
519	>	start_ndx = n_cells;
520	>	}
521	>	else
522	>	start_ndx = 0;
523	>	}
524	>	else
525	>	start_ndx = 0;
526
527	+	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
528	+	makeElement(i * cellx, j * celly, k * cellz);
529	+	done = (current_mol >= tot_nmol);
530
531	<	if( !strcmp( force_field, "TraPPE_Ex" ) ){
532	<	new Symplectic(simnfo, the_ff, the_extendedsystem);
533	<	}
534	<	else if( !strcmp( force_field, "LJ" ) ){
535	<	new Verlet( *simnfo, the_ff, the_extendedsystem );
747	<	}
531	>	if (!done && n_per_extra > 1){
532	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
533	>	k * cellz);
534	>	done = (current_mol >= tot_nmol);
535	>	}
536
537	<	#ifdef IS_MPI
538	<	mpiSim->mpiRefresh();
539	<	#endif
537	>	if (!done && n_per_extra > 2){
538	>	makeElement(i * cellx, j * celly + 0.5 * celly,
539	>	k * cellz + 0.5 * cellz);
540	>	done = (current_mol >= tot_nmol);
541	>	}
542
543	<	// initialize the Fortran
543	>	if (!done && n_per_extra > 3){
544	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
545	>	k * cellz + 0.5 * cellz);
546	>	done = (current_mol >= tot_nmol);
547	>	}
548	>	}
549	>	}
550	>	}
551	>	}
552
553	<
554	<	simnfo->refreshSim();
757	<
758	<	if( !strcmp( simnfo->mixingRule, "standard") ){
759	<	the_ff->initForceField( LB_MIXING_RULE );
553	>	for (i = 0; i < info[0].n_atoms; i++){
554	>	info[0].atoms[i]->setVel(vel);
555		}
761	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
762	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
763	–	}
764	–	else{
765	–	sprintf( painCave.errMsg,
766	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
767	–	simnfo->mixingRule );
768	–	painCave.isFatal = 1;
769	–	simError();
770	–	}
771	–
772	–
773	–	#ifdef IS_MPI
774	–	strcpy( checkPointMsg,
775	–	"Successfully intialized the mixingRule for Fortran." );
776	–	MPIcheckPoint();
777	–	#endif // is_mpi
556		}
557
558	+	void SimSetup::makeElement(double x, double y, double z){
559	+	int k;
560	+	AtomStamp* current_atom;
561	+	DirectionalAtom* dAtom;
562	+	double rotMat[3][3];
563	+	double pos[3];
564
565	<	void SimSetup::makeMolecules( void ){
565	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
566	>	current_atom = comp_stamps[current_comp]->getAtom(k);
567	>	if (!current_atom->havePosition()){
568	>	sprintf(painCave.errMsg,
569	>	"SimSetup:initFromBass error.\n"
570	>	"\tComponent %s, atom %s does not have a position specified.\n"
571	>	"\tThe initialization routine is unable to give a start"
572	>	" position.\n",
573	>	comp_stamps[current_comp]->getID(), current_atom->getType());
574	>	painCave.isFatal = 1;
575	>	simError();
576	>	}
577
578	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
579	<	molInit info;
580	<	DirectionalAtom* dAtom;
786	<	LinkedAssign* extras;
787	<	LinkedAssign* current_extra;
788	<	AtomStamp* currentAtom;
789	<	BondStamp* currentBond;
790	<	BendStamp* currentBend;
791	<	TorsionStamp* currentTorsion;
578	>	pos[0] = x + current_atom->getPosX();
579	>	pos[1] = y + current_atom->getPosY();
580	>	pos[2] = z + current_atom->getPosZ();
581
582	<	bond_pair* theBonds;
794	<	bend_set* theBends;
795	<	torsion_set* theTorsions;
582	>	info[0].atoms[current_atom_ndx]->setPos(pos);
583
584	<
585	<	//init the forceField paramters
584	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
585	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
586
587	<	the_ff->readParams();
587	>	rotMat[0][0] = 1.0;
588	>	rotMat[0][1] = 0.0;
589	>	rotMat[0][2] = 0.0;
590
591	<
592	<	// init the atoms
591	>	rotMat[1][0] = 0.0;
592	>	rotMat[1][1] = 1.0;
593	>	rotMat[1][2] = 0.0;
594
595	<	double ux, uy, uz, u, uSqr;
596	<
597	<	atomOffset = 0;
808	<	excludeOffset = 0;
809	<	for(i=0; i<simnfo->n_mol; i++){
810	<
811	<	stampID = the_molecules[i].getStampID();
595	>	rotMat[2][0] = 0.0;
596	>	rotMat[2][1] = 0.0;
597	>	rotMat[2][2] = 1.0;
598
599	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
600	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
815	<	info.nBends    = comp_stamps[stampID]->getNBends();
816	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
817	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
599	>	dAtom->setA(rotMat);
600	>	}
601
602	<	info.myAtoms = &the_atoms[atomOffset];
603	<	info.myExcludes = &the_excludes[excludeOffset];
821	<	info.myBonds = new Bond*[info.nBonds];
822	<	info.myBends = new Bend*[info.nBends];
823	<	info.myTorsions = new Torsion*[info.nTorsions];
602	>	current_atom_ndx++;
603	>	}
604
605	<	theBonds = new bond_pair[info.nBonds];
606	<	theBends = new bend_set[info.nBends];
827	<	theTorsions = new torsion_set[info.nTorsions];
828	<
829	<	// make the Atoms
830	<
831	<	for(j=0; j<info.nAtoms; j++){
832	<
833	<	currentAtom = comp_stamps[stampID]->getAtom( j );
834	<	if( currentAtom->haveOrientation() ){
835	<
836	<	dAtom = new DirectionalAtom(j + atomOffset);
837	<	simnfo->n_oriented++;
838	<	info.myAtoms[j] = dAtom;
839	<
840	<	ux = currentAtom->getOrntX();
841	<	uy = currentAtom->getOrntY();
842	<	uz = currentAtom->getOrntZ();
843	<
844	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
845	<
846	<	u = sqrt( uSqr );
847	<	ux = ux / u;
848	<	uy = uy / u;
849	<	uz = uz / u;
850	<
851	<	dAtom->setSUx( ux );
852	<	dAtom->setSUy( uy );
853	<	dAtom->setSUz( uz );
854	<	}
855	<	else{
856	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
857	<	}
858	<	info.myAtoms[j]->setType( currentAtom->getType() );
859	<
860	<	#ifdef IS_MPI
861	<
862	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
863	<
864	<	#endif // is_mpi
865	<	}
866	<
867	<	// make the bonds
868	<	for(j=0; j<info.nBonds; j++){
869	<
870	<	currentBond = comp_stamps[stampID]->getBond( j );
871	<	theBonds[j].a = currentBond->getA() + atomOffset;
872	<	theBonds[j].b = currentBond->getB() + atomOffset;
605	>	current_mol++;
606	>	current_comp_mol++;
607
608	<	exI = theBonds[j].a;
609	<	exJ = theBonds[j].b;
608	>	if (current_comp_mol >= components_nmol[current_comp]){
609	>	current_comp_mol = 0;
610	>	current_comp++;
611	>	}
612	>	}
613
877	–	// exclude_I must always be the smaller of the pair
878	–	if( exI > exJ ){
879	–	tempEx = exI;
880	–	exI = exJ;
881	–	exJ = tempEx;
882	–	}
883	–	#ifdef IS_MPI
884	–	tempEx = exI;
885	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
886	–	tempEx = exJ;
887	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
888	–
889	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
890	–	#else  // isn't MPI
614
615	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
616	<	#endif  //is_mpi
894	<	}
895	<	excludeOffset += info.nBonds;
615	>	void SimSetup::gatherInfo(void){
616	>	int i;
617
618	<	//make the bends
619	<	for(j=0; j<info.nBends; j++){
899	<
900	<	currentBend = comp_stamps[stampID]->getBend( j );
901	<	theBends[j].a = currentBend->getA() + atomOffset;
902	<	theBends[j].b = currentBend->getB() + atomOffset;
903	<	theBends[j].c = currentBend->getC() + atomOffset;
904	<
905	<	if( currentBend->haveExtras() ){
906	<
907	<	extras = currentBend->getExtras();
908	<	current_extra = extras;
909	<
910	<	while( current_extra != NULL ){
911	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
912	<
913	<	switch( current_extra->getType() ){
914	<
915	<	case 0:
916	<	theBends[j].ghost =
917	<	current_extra->getInt() + atomOffset;
918	<	theBends[j].isGhost = 1;
919	<	break;
920	<
921	<	case 1:
922	<	theBends[j].ghost =
923	<	(int)current_extra->getDouble() + atomOffset;
924	<	theBends[j].isGhost = 1;
925	<	break;
926	<
927	<	default:
928	<	sprintf( painCave.errMsg,
929	<	"SimSetup Error: ghostVectorSource was neither a "
930	<	"double nor an int.\n"
931	<	"-->Bend[%d] in %s\n",
932	<	j, comp_stamps[stampID]->getID() );
933	<	painCave.isFatal = 1;
934	<	simError();
935	<	}
936	<	}
937	<
938	<	else{
939	<
940	<	sprintf( painCave.errMsg,
941	<	"SimSetup Error: unhandled bend assignment:\n"
942	<	"    -->%s in Bend[%d] in %s\n",
943	<	current_extra->getlhs(),
944	<	j, comp_stamps[stampID]->getID() );
945	<	painCave.isFatal = 1;
946	<	simError();
947	<	}
948	<
949	<	current_extra = current_extra->getNext();
950	<	}
951	<	}
952	<
953	<	if( !theBends[j].isGhost ){
954	<
955	<	exI = theBends[j].a;
956	<	exJ = theBends[j].c;
957	<	}
958	<	else{
959	<
960	<	exI = theBends[j].a;
961	<	exJ = theBends[j].b;
962	<	}
963	<
964	<	// exclude_I must always be the smaller of the pair
965	<	if( exI > exJ ){
966	<	tempEx = exI;
967	<	exI = exJ;
968	<	exJ = tempEx;
969	<	}
970	<	#ifdef IS_MPI
971	<	tempEx = exI;
972	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
973	<	tempEx = exJ;
974	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
975	<
976	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
977	<	#else  // isn't MPI
978	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
979	<	#endif  //is_mpi
980	<	}
981	<	excludeOffset += info.nBends;
618	>	ensembleCase = -1;
619	>	ffCase = -1;
620
621	<	for(j=0; j<info.nTorsions; j++){
984	<
985	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
986	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
987	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
988	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
989	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
990	<
991	<	exI = theTorsions[j].a;
992	<	exJ = theTorsions[j].d;
621	>	// set the easy ones first
622
623	<	// exclude_I must always be the smaller of the pair
624	<	if( exI > exJ ){
625	<	tempEx = exI;
626	<	exI = exJ;
627	<	exJ = tempEx;
628	<	}
1000	<	#ifdef IS_MPI
1001	<	tempEx = exI;
1002	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1003	<	tempEx = exJ;
1004	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1005	<
1006	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1007	<	#else  // isn't MPI
1008	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1009	<	#endif  //is_mpi
1010	<	}
1011	<	excludeOffset += info.nTorsions;
623	>	for (i = 0; i < nInfo; i++){
624	>	info[i].target_temp = globals->getTargetTemp();
625	>	info[i].dt = globals->getDt();
626	>	info[i].run_time = globals->getRunTime();
627	>	}
628	>	n_components = globals->getNComponents();
629
1013	–
1014	–	// send the arrays off to the forceField for init.
630
631	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1017	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1018	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1019	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
631	>	// get the forceField
632
633	+	strcpy(force_field, globals->getForceField());
634
635	<	the_molecules[i].initialize( info );
635	>	if (!strcasecmp(force_field, "DUFF")){
636	>	ffCase = FF_DUFF;
637	>	}
638	>	else if (!strcasecmp(force_field, "LJ")){
639	>	ffCase = FF_LJ;
640	>	}
641	>	else if (!strcasecmp(force_field, "EAM")){
642	>	ffCase = FF_EAM;
643	>	}
644	>	else if (!strcasecmp(force_field, "WATER")){
645	>	ffCase = FF_H2O;
646	>	}
647	>	else{
648	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
649	>	force_field);
650	>	painCave.isFatal = 1;
651	>	simError();
652	>	}
653
654	+	// get the ensemble
655
656	<	atomOffset += info.nAtoms;
657	<	delete[] theBonds;
658	<	delete[] theBends;
659	<	delete[] theTorsions;
656	>	strcpy(ensemble, globals->getEnsemble());
657	>
658	>	if (!strcasecmp(ensemble, "NVE")){
659	>	ensembleCase = NVE_ENS;
660		}
661	+	else if (!strcasecmp(ensemble, "NVT")){
662	+	ensembleCase = NVT_ENS;
663	+	}
664	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
665	+	ensembleCase = NPTi_ENS;
666	+	}
667	+	else if (!strcasecmp(ensemble, "NPTf")){
668	+	ensembleCase = NPTf_ENS;
669	+	}
670	+	else if (!strcasecmp(ensemble, "NPTxyz")){
671	+	ensembleCase = NPTxyz_ENS;
672	+	}
673	+	else{
674	+	sprintf(painCave.errMsg,
675	+	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
676	+	"\treverting to NVE for this simulation.\n",
677	+	ensemble);
678	+	painCave.isFatal = 0;
679	+	simError();
680	+	strcpy(ensemble, "NVE");
681	+	ensembleCase = NVE_ENS;
682	+	}
683
684	<	#ifdef IS_MPI
685	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1033	<	MPIcheckPoint();
1034	<	#endif // is_mpi
684	>	for (i = 0; i < nInfo; i++){
685	>	strcpy(info[i].ensemble, ensemble);
686
687	<	// clean up the forcefield
1037	<	the_ff->calcRcut();
1038	<	the_ff->cleanMe();
687	>	// get the mixing rule
688
689	<	}
689	>	strcpy(info[i].mixingRule, globals->getMixingRule());
690	>	info[i].usePBC = globals->getPBC();
691	>	}
692
693	<	void SimSetup::initFromBass( void ){
693	>	// get the components and calculate the tot_nMol and indvidual n_mol
694
695	<	int i, j, k;
696	<	int n_cells;
1046	<	double cellx, celly, cellz;
1047	<	double temp1, temp2, temp3;
1048	<	int n_per_extra;
1049	<	int n_extra;
1050	<	int have_extra, done;
695	>	the_components = globals->getComponents();
696	>	components_nmol = new int[n_components];
697
1052	–	temp1 = (double)tot_nmol / 4.0;
1053	–	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1054	–	temp3 = ceil( temp2 );
698
699	<	have_extra =0;
700	<	if( temp2 < temp3 ){ // we have a non-complete lattice
701	<	have_extra =1;
699	>	if (!globals->haveNMol()){
700	>	// we don't have the total number of molecules, so we assume it is
701	>	// given in each component
702
703	<	n_cells = (int)temp3 - 1;
704	<	cellx = simnfo->box_x / temp3;
705	<	celly = simnfo->box_y / temp3;
706	<	cellz = simnfo->box_z / temp3;
707	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
708	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
709	<	n_per_extra = (int)ceil( temp1 );
703	>	tot_nmol = 0;
704	>	for (i = 0; i < n_components; i++){
705	>	if (!the_components[i]->haveNMol()){
706	>	// we have a problem
707	>	sprintf(painCave.errMsg,
708	>	"SimSetup Error. No global NMol or component NMol given.\n"
709	>	"\tCannot calculate the number of atoms.\n");
710	>	painCave.isFatal = 1;
711	>	simError();
712	>	}
713
714	<	if( n_per_extra > 4){
715	<	sprintf( painCave.errMsg,
1070	<	"SimSetup error. There has been an error in constructing"
1071	<	" the non-complete lattice.\n" );
1072	<	painCave.isFatal = 1;
1073	<	simError();
714	>	tot_nmol += the_components[i]->getNMol();
715	>	components_nmol[i] = the_components[i]->getNMol();
716		}
717		}
718		else{
719	<	n_cells = (int)temp3;
720	<	cellx = simnfo->box_x / temp3;
721	<	celly = simnfo->box_y / temp3;
722	<	cellz = simnfo->box_z / temp3;
719	>	sprintf(painCave.errMsg,
720	>	"SimSetup error.\n"
721	>	"\tSorry, the ability to specify total"
722	>	" nMols and then give molfractions in the components\n"
723	>	"\tis not currently supported."
724	>	" Please give nMol in the components.\n");
725	>	painCave.isFatal = 1;
726	>	simError();
727		}
728
729	<	current_mol = 0;
730	<	current_comp_mol = 0;
731	<	current_comp = 0;
732	<	current_atom_ndx = 0;
729	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
730	>	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
731	>	sprintf(painCave.errMsg,
732	>	"Sample time is not divisible by dt.\n"
733	>	"\tThis will result in samples that are not uniformly\n"
734	>	"\tdistributed in time.  If this is a problem, change\n"
735	>	"\tyour sampleTime variable.\n");
736	>	painCave.isFatal = 0;
737	>	simError();
738	>	}
739
740	<	for( i=0; i < n_cells ; i++ ){
741	<	for( j=0; j < n_cells; j++ ){
742	<	for( k=0; k < n_cells; k++ ){
740	>	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
741	>	sprintf(painCave.errMsg,
742	>	"Status time is not divisible by dt.\n"
743	>	"\tThis will result in status reports that are not uniformly\n"
744	>	"\tdistributed in time.  If this is a problem, change \n"
745	>	"\tyour statusTime variable.\n");
746	>	painCave.isFatal = 0;
747	>	simError();
748	>	}
749
750	<	makeElement( i * cellx,
751	<	j * celly,
752	<	k * cellz );
750	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
751	>	sprintf(painCave.errMsg,
752	>	"Thermal time is not divisible by dt.\n"
753	>	"\tThis will result in thermalizations that are not uniformly\n"
754	>	"\tdistributed in time.  If this is a problem, change \n"
755	>	"\tyour thermalTime variable.\n");
756	>	painCave.isFatal = 0;
757	>	simError();
758	>	}
759
760	<	makeElement( i * cellx + 0.5 * cellx,
761	<	j * celly + 0.5 * celly,
762	<	k * cellz );
760	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
761	>	sprintf(painCave.errMsg,
762	>	"Reset time is not divisible by dt.\n"
763	>	"\tThis will result in integrator resets that are not uniformly\n"
764	>	"\tdistributed in time.  If this is a problem, change\n"
765	>	"\tyour resetTime variable.\n");
766	>	painCave.isFatal = 0;
767	>	simError();
768	>	}
769
770	<	makeElement( i * cellx,
1101	<	j * celly + 0.5 * celly,
1102	<	k * cellz + 0.5 * cellz );
770	>	// set the status, sample, and thermal kick times
771
772	<	makeElement( i * cellx + 0.5 * cellx,
773	<	j * celly,
774	<	k * cellz + 0.5 * cellz );
775	<	}
772	>	for (i = 0; i < nInfo; i++){
773	>	if (globals->haveSampleTime()){
774	>	info[i].sampleTime = globals->getSampleTime();
775	>	info[i].statusTime = info[i].sampleTime;
776	>	info[i].thermalTime = info[i].sampleTime;
777		}
778	<	}
778	>	else{
779	>	info[i].sampleTime = globals->getRunTime();
780	>	info[i].statusTime = info[i].sampleTime;
781	>	info[i].thermalTime = info[i].sampleTime;
782	>	}
783
784	<	if( have_extra ){
785	<	done = 0;
784	>	if (globals->haveStatusTime()){
785	>	info[i].statusTime = globals->getStatusTime();
786	>	}
787
788	<	int start_ndx;
789	<	for( i=0; i < (n_cells+1) && !done; i++ ){
790	<	for( j=0; j < (n_cells+1) && !done; j++ ){
788	>	if (globals->haveThermalTime()){
789	>	info[i].thermalTime = globals->getThermalTime();
790	>	}
791
792	<	if( i < n_cells ){
792	>	info[i].resetIntegrator = 0;
793	>	if( globals->haveResetTime() ){
794	>	info[i].resetTime = globals->getResetTime();
795	>	info[i].resetIntegrator = 1;
796	>	}
797
798	<	if( j < n_cells ){
799	<	start_ndx = n_cells;
800	<	}
801	<	else start_ndx = 0;
1124	<	}
1125	<	else start_ndx = 0;
798	>	// check for the temperature set flag
799	>
800	>	if (globals->haveTempSet())
801	>	info[i].setTemp = globals->getTempSet();
802
803	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
803	>	// check for the extended State init
804
805	<	makeElement( i * cellx,
806	<	j * celly,
807	<	k * cellz );
808	<	done = ( current_mol >= tot_nmol );
805	>	info[i].useInitXSstate = globals->getUseInitXSstate();
806	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
807	>
808	>	}
809	>
810	>	//setup seed for random number generator
811	>	int seedValue;
812
813	<	if( !done && n_per_extra > 1 ){
814	<	makeElement( i * cellx + 0.5 * cellx,
1136	<	j * celly + 0.5 * celly,
1137	<	k * cellz );
1138	<	done = ( current_mol >= tot_nmol );
1139	<	}
813	>	if (globals->haveSeed()){
814	>	seedValue = globals->getSeed();
815
816	<	if( !done && n_per_extra > 2){
817	<	makeElement( i * cellx,
818	<	j * celly + 0.5 * celly,
819	<	k * cellz + 0.5 * cellz );
820	<	done = ( current_mol >= tot_nmol );
821	<	}
816	>	if(seedValue / 1E9 == 0){
817	>	sprintf(painCave.errMsg,
818	>	"Seed for sprng library should contain at least 9 digits\n"
819	>	"OOPSE will generate a seed for user\n");
820	>	painCave.isFatal = 0;
821	>	simError();
822
823	<	if( !done && n_per_extra > 3){
824	<	makeElement( i * cellx + 0.5 * cellx,
825	<	j * celly,
826	<	k * cellz + 0.5 * cellz );
827	<	done = ( current_mol >= tot_nmol );
828	<	}
1154	<	}
823	>	//using seed generated by system instead of invalid seed set by user
824	>	#ifndef IS_MPI
825	>	seedValue = make_sprng_seed();
826	>	#else
827	>	if (worldRank == 0){
828	>	seedValue = make_sprng_seed();
829		}
830	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
831	+	#endif
832		}
833	<	}
833	>	}//end of if branch of globals->haveSeed()
834	>	else{
835	>
836	>	#ifndef IS_MPI
837	>	seedValue = make_sprng_seed();
838	>	#else
839	>	if (worldRank == 0){
840	>	seedValue = make_sprng_seed();
841	>	}
842	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
843	>	#endif
844	>	}//end of globals->haveSeed()
845
846	<
847	<	for( i=0; i<simnfo->n_atoms; i++ ){
1161	<	simnfo->atoms[i]->set_vx( 0.0 );
1162	<	simnfo->atoms[i]->set_vy( 0.0 );
1163	<	simnfo->atoms[i]->set_vz( 0.0 );
846	>	for (int i = 0; i < nInfo; i++){
847	>	info[i].setSeed(seedValue);
848		}
849	+
850	+	#ifdef IS_MPI
851	+	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
852	+	MPIcheckPoint();
853	+	#endif // is_mpi
854		}
855
1167	–	void SimSetup::makeElement( double x, double y, double z ){
856
857	<	int k;
858	<	AtomStamp* current_atom;
859	<	DirectionalAtom* dAtom;
860	<	double rotMat[3][3];
857	>	void SimSetup::finalInfoCheck(void){
858	>	int index;
859	>	int usesDipoles;
860	>	int i;
861
862	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
862	>	for (i = 0; i < nInfo; i++){
863	>	// check electrostatic parameters
864
865	<	current_atom = comp_stamps[current_comp]->getAtom( k );
866	<	if( !current_atom->havePosition() ){
867	<	sprintf( painCave.errMsg,
868	<	"SimSetup:initFromBass error.\n"
869	<	"\tComponent %s, atom %s does not have a position specified.\n"
1181	<	"\tThe initialization routine is unable to give a start"
1182	<	" position.\n",
1183	<	comp_stamps[current_comp]->getID(),
1184	<	current_atom->getType() );
1185	<	painCave.isFatal = 1;
1186	<	simError();
865	>	index = 0;
866	>	usesDipoles = 0;
867	>	while ((index < info[i].n_atoms) && !usesDipoles){
868	>	usesDipoles = (info[i].atoms[index])->hasDipole();
869	>	index++;
870		}
871
872	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
873	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
874	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
872	>	#ifdef IS_MPI
873	>	int myUse = usesDipoles;
874	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
875	>	#endif //is_mpi
876
877	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
877	>	double theEcr, theEst;
878
879	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
879	>	if (globals->getUseRF()){
880	>	info[i].useReactionField = 1;
881
882	<	rotMat[0][0] = 1.0;
883	<	rotMat[0][1] = 0.0;
884	<	rotMat[0][2] = 0.0;
882	>	if (!globals->haveECR()){
883	>	sprintf(painCave.errMsg,
884	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
885	>	"\tOOPSE will use a default value of 15.0 angstroms"
886	>	"\tfor the electrostaticCutoffRadius.\n");
887	>	painCave.isFatal = 0;
888	>	simError();
889	>	theEcr = 15.0;
890	>	}
891	>	else{
892	>	theEcr = globals->getECR();
893	>	}
894
895	<	rotMat[1][0] = 0.0;
896	<	rotMat[1][1] = 1.0;
897	<	rotMat[1][2] = 0.0;
895	>	if (!globals->haveEST()){
896	>	sprintf(painCave.errMsg,
897	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
898	>	"\tOOPSE will use a default value of\n"
899	>	"\t0.05 * electrostaticCutoffRadius\n"
900	>	"\tfor the electrostaticSkinThickness\n");
901	>	painCave.isFatal = 0;
902	>	simError();
903	>	theEst = 0.05 * theEcr;
904	>	}
905	>	else{
906	>	theEst = globals->getEST();
907	>	}
908
909	<	rotMat[2][0] = 0.0;
1206	<	rotMat[2][1] = 0.0;
1207	<	rotMat[2][2] = 1.0;
909	>	info[i].setDefaultEcr(theEcr, theEst);
910
911	<	dAtom->setA( rotMat );
911	>	if (!globals->haveDielectric()){
912	>	sprintf(painCave.errMsg,
913	>	"SimSetup Error: No Dielectric constant was set.\n"
914	>	"\tYou are trying to use Reaction Field without"
915	>	"\tsetting a dielectric constant!\n");
916	>	painCave.isFatal = 1;
917	>	simError();
918	>	}
919	>	info[i].dielectric = globals->getDielectric();
920		}
921	+	else{
922	+	if (usesDipoles){
923	+	if (!globals->haveECR()){
924	+	sprintf(painCave.errMsg,
925	+	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
926	+	"\tOOPSE will use a default value of 15.0 angstroms"
927	+	"\tfor the electrostaticCutoffRadius.\n");
928	+	painCave.isFatal = 0;
929	+	simError();
930	+	theEcr = 15.0;
931	+	}
932	+	else{
933	+	theEcr = globals->getECR();
934	+	}
935	+
936	+	if (!globals->haveEST()){
937	+	sprintf(painCave.errMsg,
938	+	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
939	+	"\tOOPSE will use a default value of\n"
940	+	"\t0.05 * electrostaticCutoffRadius\n"
941	+	"\tfor the electrostaticSkinThickness\n");
942	+	painCave.isFatal = 0;
943	+	simError();
944	+	theEst = 0.05 * theEcr;
945	+	}
946	+	else{
947	+	theEst = globals->getEST();
948	+	}
949	+
950	+	info[i].setDefaultEcr(theEcr, theEst);
951	+	}
952	+	}
953	+	}
954	+	#ifdef IS_MPI
955	+	strcpy(checkPointMsg, "post processing checks out");
956	+	MPIcheckPoint();
957	+	#endif // is_mpi
958	+	}
959	+
960	+	void SimSetup::initSystemCoords(void){
961	+	int i;
962
963	<	current_atom_ndx++;
963	>	char* inName;
964	>
965	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
966	>
967	>	for (i = 0; i < info[0].n_atoms; i++)
968	>	info[0].atoms[i]->setCoords();
969	>
970	>	if (globals->haveInitialConfig()){
971	>	InitializeFromFile* fileInit;
972	>	#ifdef IS_MPI // is_mpi
973	>	if (worldRank == 0){
974	>	#endif //is_mpi
975	>	inName = globals->getInitialConfig();
976	>	fileInit = new InitializeFromFile(inName);
977	>	#ifdef IS_MPI
978	>	}
979	>	else
980	>	fileInit = new InitializeFromFile(NULL);
981	>	#endif
982	>	fileInit->readInit(info); // default velocities on
983	>
984	>	delete fileInit;
985		}
986	+	else{
987	+
988	+	// no init from bass
989	+
990	+	sprintf(painCave.errMsg,
991	+	"Cannot intialize a simulation without an initial configuration file.\n");
992	+	painCave.isFatal = 1;;
993	+	simError();
994	+
995	+	}
996
997	<	current_mol++;
998	<	current_comp_mol++;
997	>	#ifdef IS_MPI
998	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
999	>	MPIcheckPoint();
1000	>	#endif // is_mpi
1001	>	}
1002
1218	–	if( current_comp_mol >= components_nmol[current_comp] ){
1003
1004	<	current_comp_mol = 0;
1005	<	current_comp++;
1004	>	void SimSetup::makeOutNames(void){
1005	>	int k;
1006	>
1007	>
1008	>	for (k = 0; k < nInfo; k++){
1009	>	#ifdef IS_MPI
1010	>	if (worldRank == 0){
1011	>	#endif // is_mpi
1012	>
1013	>	if (globals->haveFinalConfig()){
1014	>	strcpy(info[k].finalName, globals->getFinalConfig());
1015	>	}
1016	>	else{
1017	>	strcpy(info[k].finalName, inFileName);
1018	>	char* endTest;
1019	>	int nameLength = strlen(info[k].finalName);
1020	>	endTest = &(info[k].finalName[nameLength - 5]);
1021	>	if (!strcmp(endTest, ".bass")){
1022	>	strcpy(endTest, ".eor");
1023	>	}
1024	>	else if (!strcmp(endTest, ".BASS")){
1025	>	strcpy(endTest, ".eor");
1026	>	}
1027	>	else{
1028	>	endTest = &(info[k].finalName[nameLength - 4]);
1029	>	if (!strcmp(endTest, ".bss")){
1030	>	strcpy(endTest, ".eor");
1031	>	}
1032	>	else if (!strcmp(endTest, ".mdl")){
1033	>	strcpy(endTest, ".eor");
1034	>	}
1035	>	else{
1036	>	strcat(info[k].finalName, ".eor");
1037	>	}
1038	>	}
1039	>	}
1040	>
1041	>	// make the sample and status out names
1042	>
1043	>	strcpy(info[k].sampleName, inFileName);
1044	>	char* endTest;
1045	>	int nameLength = strlen(info[k].sampleName);
1046	>	endTest = &(info[k].sampleName[nameLength - 5]);
1047	>	if (!strcmp(endTest, ".bass")){
1048	>	strcpy(endTest, ".dump");
1049	>	}
1050	>	else if (!strcmp(endTest, ".BASS")){
1051	>	strcpy(endTest, ".dump");
1052	>	}
1053	>	else{
1054	>	endTest = &(info[k].sampleName[nameLength - 4]);
1055	>	if (!strcmp(endTest, ".bss")){
1056	>	strcpy(endTest, ".dump");
1057	>	}
1058	>	else if (!strcmp(endTest, ".mdl")){
1059	>	strcpy(endTest, ".dump");
1060	>	}
1061	>	else{
1062	>	strcat(info[k].sampleName, ".dump");
1063	>	}
1064	>	}
1065	>
1066	>	strcpy(info[k].statusName, inFileName);
1067	>	nameLength = strlen(info[k].statusName);
1068	>	endTest = &(info[k].statusName[nameLength - 5]);
1069	>	if (!strcmp(endTest, ".bass")){
1070	>	strcpy(endTest, ".stat");
1071	>	}
1072	>	else if (!strcmp(endTest, ".BASS")){
1073	>	strcpy(endTest, ".stat");
1074	>	}
1075	>	else{
1076	>	endTest = &(info[k].statusName[nameLength - 4]);
1077	>	if (!strcmp(endTest, ".bss")){
1078	>	strcpy(endTest, ".stat");
1079	>	}
1080	>	else if (!strcmp(endTest, ".mdl")){
1081	>	strcpy(endTest, ".stat");
1082	>	}
1083	>	else{
1084	>	strcat(info[k].statusName, ".stat");
1085	>	}
1086	>	}
1087	>
1088	>	#ifdef IS_MPI
1089	>
1090	>	}
1091	>	#endif // is_mpi
1092	>	}
1093	>	}
1094	>
1095	>
1096	>	void SimSetup::sysObjectsCreation(void){
1097	>	int i, k;
1098	>
1099	>	// create the forceField
1100	>
1101	>	createFF();
1102	>
1103	>	// extract componentList
1104	>
1105	>	compList();
1106	>
1107	>	// calc the number of atoms, bond, bends, and torsions
1108	>
1109	>	calcSysValues();
1110	>
1111	>	#ifdef IS_MPI
1112	>	// divide the molecules among the processors
1113	>
1114	>	mpiMolDivide();
1115	>	#endif //is_mpi
1116	>
1117	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1118	>
1119	>	makeSysArrays();
1120	>
1121	>	// make and initialize the molecules (all but atomic coordinates)
1122	>
1123	>	makeMolecules();
1124	>
1125	>	for (k = 0; k < nInfo; k++){
1126	>	info[k].identArray = new int[info[k].n_atoms];
1127	>	for (i = 0; i < info[k].n_atoms; i++){
1128	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1129	>	}
1130	>	}
1131	>	}
1132	>
1133	>
1134	>	void SimSetup::createFF(void){
1135	>	switch (ffCase){
1136	>	case FF_DUFF:
1137	>	the_ff = new DUFF();
1138	>	break;
1139	>
1140	>	case FF_LJ:
1141	>	the_ff = new LJFF();
1142	>	break;
1143	>
1144	>	case FF_EAM:
1145	>	the_ff = new EAM_FF();
1146	>	break;
1147	>
1148	>	case FF_H2O:
1149	>	the_ff = new WATER();
1150	>	break;
1151	>
1152	>	default:
1153	>	sprintf(painCave.errMsg,
1154	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1155	>	painCave.isFatal = 1;
1156	>	simError();
1157	>	}
1158	>
1159	>	#ifdef IS_MPI
1160	>	strcpy(checkPointMsg, "ForceField creation successful");
1161	>	MPIcheckPoint();
1162	>	#endif // is_mpi
1163	>	}
1164	>
1165	>
1166	>	void SimSetup::compList(void){
1167	>	int i;
1168	>	char* id;
1169	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1170	>	LinkedMolStamp* currentStamp = NULL;
1171	>	comp_stamps = new MoleculeStamp * [n_components];
1172	>
1173	>	// make an array of molecule stamps that match the components used.
1174	>	// also extract the used stamps out into a separate linked list
1175	>
1176	>	for (i = 0; i < nInfo; i++){
1177	>	info[i].nComponents = n_components;
1178	>	info[i].componentsNmol = components_nmol;
1179	>	info[i].compStamps = comp_stamps;
1180	>	info[i].headStamp = headStamp;
1181	>	}
1182	>
1183	>
1184	>	for (i = 0; i < n_components; i++){
1185	>	id = the_components[i]->getType();
1186	>	comp_stamps[i] = NULL;
1187	>
1188	>	// check to make sure the component isn't already in the list
1189	>
1190	>	comp_stamps[i] = headStamp->match(id);
1191	>	if (comp_stamps[i] == NULL){
1192	>	// extract the component from the list;
1193	>
1194	>	currentStamp = stamps->extractMolStamp(id);
1195	>	if (currentStamp == NULL){
1196	>	sprintf(painCave.errMsg,
1197	>	"SimSetup error: Component \"%s\" was not found in the "
1198	>	"list of declared molecules\n",
1199	>	id);
1200	>	painCave.isFatal = 1;
1201	>	simError();
1202	>	}
1203	>
1204	>	headStamp->add(currentStamp);
1205	>	comp_stamps[i] = headStamp->match(id);
1206	>	}
1207	>	}
1208	>
1209	>	#ifdef IS_MPI
1210	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1211	>	MPIcheckPoint();
1212	>	#endif // is_mpi
1213	>	}
1214	>
1215	>	void SimSetup::calcSysValues(void){
1216	>	int i;
1217	>
1218	>	int* molMembershipArray;
1219	>
1220	>	tot_atoms = 0;
1221	>	tot_bonds = 0;
1222	>	tot_bends = 0;
1223	>	tot_torsions = 0;
1224	>	for (i = 0; i < n_components; i++){
1225	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1226	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1227	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1228	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1229	>	}
1230	>
1231	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1232	>	molMembershipArray = new int[tot_atoms];
1233	>
1234	>	for (i = 0; i < nInfo; i++){
1235	>	info[i].n_atoms = tot_atoms;
1236	>	info[i].n_bonds = tot_bonds;
1237	>	info[i].n_bends = tot_bends;
1238	>	info[i].n_torsions = tot_torsions;
1239	>	info[i].n_SRI = tot_SRI;
1240	>	info[i].n_mol = tot_nmol;
1241	>
1242	>	info[i].molMembershipArray = molMembershipArray;
1243	>	}
1244	>	}
1245	>
1246	>	#ifdef IS_MPI
1247	>
1248	>	void SimSetup::mpiMolDivide(void){
1249	>	int i, j, k;
1250	>	int localMol, allMol;
1251	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1252	>
1253	>	mpiSim = new mpiSimulation(info);
1254	>
1255	>	globalIndex = mpiSim->divideLabor();
1256	>
1257	>	// set up the local variables
1258	>
1259	>	mol2proc = mpiSim->getMolToProcMap();
1260	>	molCompType = mpiSim->getMolComponentType();
1261	>
1262	>	allMol = 0;
1263	>	localMol = 0;
1264	>	local_atoms = 0;
1265	>	local_bonds = 0;
1266	>	local_bends = 0;
1267	>	local_torsions = 0;
1268	>	globalAtomIndex = 0;
1269	>
1270	>
1271	>	for (i = 0; i < n_components; i++){
1272	>	for (j = 0; j < components_nmol[i]; j++){
1273	>	if (mol2proc[allMol] == worldRank){
1274	>	local_atoms += comp_stamps[i]->getNAtoms();
1275	>	local_bonds += comp_stamps[i]->getNBonds();
1276	>	local_bends += comp_stamps[i]->getNBends();
1277	>	local_torsions += comp_stamps[i]->getNTorsions();
1278	>	localMol++;
1279	>	}
1280	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1281	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1282	>	globalAtomIndex++;
1283	>	}
1284	>
1285	>	allMol++;
1286	>	}
1287	>	}
1288	>	local_SRI = local_bonds + local_bends + local_torsions;
1289	>
1290	>	info[0].n_atoms = mpiSim->getMyNlocal();
1291	>
1292	>	if (local_atoms != info[0].n_atoms){
1293	>	sprintf(painCave.errMsg,
1294	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1295	>	"\tlocalAtom (%d) are not equal.\n",
1296	>	info[0].n_atoms, local_atoms);
1297	>	painCave.isFatal = 1;
1298	>	simError();
1299	>	}
1300	>
1301	>	info[0].n_bonds = local_bonds;
1302	>	info[0].n_bends = local_bends;
1303	>	info[0].n_torsions = local_torsions;
1304	>	info[0].n_SRI = local_SRI;
1305	>	info[0].n_mol = localMol;
1306	>
1307	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1308	>	MPIcheckPoint();
1309	>	}
1310	>
1311	>	#endif // is_mpi
1312	>
1313	>
1314	>	void SimSetup::makeSysArrays(void){
1315	>
1316	>	#ifndef IS_MPI
1317	>	int k, j;
1318	>	#endif // is_mpi
1319	>	int i, l;
1320	>
1321	>	Atom** the_atoms;
1322	>	Molecule* the_molecules;
1323	>	Exclude** the_excludes;
1324	>
1325	>
1326	>	for (l = 0; l < nInfo; l++){
1327	>	// create the atom and short range interaction arrays
1328	>
1329	>	the_atoms = new Atom * [info[l].n_atoms];
1330	>	the_molecules = new Molecule[info[l].n_mol];
1331	>	int molIndex;
1332	>
1333	>	// initialize the molecule's stampID's
1334	>
1335	>	#ifdef IS_MPI
1336	>
1337	>
1338	>	molIndex = 0;
1339	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1340	>	if (mol2proc[i] == worldRank){
1341	>	the_molecules[molIndex].setStampID(molCompType[i]);
1342	>	the_molecules[molIndex].setMyIndex(molIndex);
1343	>	the_molecules[molIndex].setGlobalIndex(i);
1344	>	molIndex++;
1345	>	}
1346	>	}
1347	>
1348	>	#else // is_mpi
1349	>
1350	>	molIndex = 0;
1351	>	globalAtomIndex = 0;
1352	>	for (i = 0; i < n_components; i++){
1353	>	for (j = 0; j < components_nmol[i]; j++){
1354	>	the_molecules[molIndex].setStampID(i);
1355	>	the_molecules[molIndex].setMyIndex(molIndex);
1356	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1357	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1358	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1359	>	globalAtomIndex++;
1360	>	}
1361	>	molIndex++;
1362	>	}
1363	>	}
1364	>
1365	>
1366	>	#endif // is_mpi
1367	>
1368	>
1369	>	if (info[l].n_SRI){
1370	>	Exclude::createArray(info[l].n_SRI);
1371	>	the_excludes = new Exclude * [info[l].n_SRI];
1372	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1373	>	the_excludes[ex] = new Exclude(ex);
1374	>	}
1375	>	info[l].globalExcludes = new int;
1376	>	info[l].n_exclude = info[l].n_SRI;
1377	>	}
1378	>	else{
1379	>	Exclude::createArray(1);
1380	>	the_excludes = new Exclude * ;
1381	>	the_excludes[0] = new Exclude(0);
1382	>	the_excludes[0]->setPair(0, 0);
1383	>	info[l].globalExcludes = new int;
1384	>	info[l].globalExcludes[0] = 0;
1385	>	info[l].n_exclude = 0;
1386	>	}
1387	>
1388	>	// set the arrays into the SimInfo object
1389	>
1390	>	info[l].atoms = the_atoms;
1391	>	info[l].molecules = the_molecules;
1392	>	info[l].nGlobalExcludes = 0;
1393	>	info[l].excludes = the_excludes;
1394	>
1395	>	the_ff->setSimInfo(info);
1396	>	}
1397	>	}
1398	>
1399	>	void SimSetup::makeIntegrator(void){
1400	>	int k;
1401	>
1402	>	NVE<RealIntegrator>* myNVE = NULL;
1403	>	NVT<RealIntegrator>* myNVT = NULL;
1404	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1405	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1406	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1407	>
1408	>	for (k = 0; k < nInfo; k++){
1409	>	switch (ensembleCase){
1410	>	case NVE_ENS:
1411	>	if (globals->haveZconstraints()){
1412	>	setupZConstraint(info[k]);
1413	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1414	>	}
1415	>	else{
1416	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1417	>	}
1418	>
1419	>	info->the_integrator = myNVE;
1420	>	break;
1421	>
1422	>	case NVT_ENS:
1423	>	if (globals->haveZconstraints()){
1424	>	setupZConstraint(info[k]);
1425	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1426	>	}
1427	>	else
1428	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1429	>
1430	>	myNVT->setTargetTemp(globals->getTargetTemp());
1431	>
1432	>	if (globals->haveTauThermostat())
1433	>	myNVT->setTauThermostat(globals->getTauThermostat());
1434	>	else{
1435	>	sprintf(painCave.errMsg,
1436	>	"SimSetup error: If you use the NVT\n"
1437	>	"\tensemble, you must set tauThermostat.\n");
1438	>	painCave.isFatal = 1;
1439	>	simError();
1440	>	}
1441	>
1442	>	info->the_integrator = myNVT;
1443	>	break;
1444	>
1445	>	case NPTi_ENS:
1446	>	if (globals->haveZconstraints()){
1447	>	setupZConstraint(info[k]);
1448	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1449	>	}
1450	>	else
1451	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1452	>
1453	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1454	>
1455	>	if (globals->haveTargetPressure())
1456	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1457	>	else{
1458	>	sprintf(painCave.errMsg,
1459	>	"SimSetup error: If you use a constant pressure\n"
1460	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1461	>	painCave.isFatal = 1;
1462	>	simError();
1463	>	}
1464	>
1465	>	if (globals->haveTauThermostat())
1466	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1467	>	else{
1468	>	sprintf(painCave.errMsg,
1469	>	"SimSetup error: If you use an NPT\n"
1470	>	"\tensemble, you must set tauThermostat.\n");
1471	>	painCave.isFatal = 1;
1472	>	simError();
1473	>	}
1474	>
1475	>	if (globals->haveTauBarostat())
1476	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1477	>	else{
1478	>	sprintf(painCave.errMsg,
1479	>	"SimSetup error: If you use an NPT\n"
1480	>	"\tensemble, you must set tauBarostat.\n");
1481	>	painCave.isFatal = 1;
1482	>	simError();
1483	>	}
1484	>
1485	>	info->the_integrator = myNPTi;
1486	>	break;
1487	>
1488	>	case NPTf_ENS:
1489	>	if (globals->haveZconstraints()){
1490	>	setupZConstraint(info[k]);
1491	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1492	>	}
1493	>	else
1494	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1495	>
1496	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1497	>
1498	>	if (globals->haveTargetPressure())
1499	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1500	>	else{
1501	>	sprintf(painCave.errMsg,
1502	>	"SimSetup error: If you use a constant pressure\n"
1503	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1504	>	painCave.isFatal = 1;
1505	>	simError();
1506	>	}
1507	>
1508	>	if (globals->haveTauThermostat())
1509	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1510	>
1511	>	else{
1512	>	sprintf(painCave.errMsg,
1513	>	"SimSetup error: If you use an NPT\n"
1514	>	"\tensemble, you must set tauThermostat.\n");
1515	>	painCave.isFatal = 1;
1516	>	simError();
1517	>	}
1518	>
1519	>	if (globals->haveTauBarostat())
1520	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1521	>
1522	>	else{
1523	>	sprintf(painCave.errMsg,
1524	>	"SimSetup error: If you use an NPT\n"
1525	>	"\tensemble, you must set tauBarostat.\n");
1526	>	painCave.isFatal = 1;
1527	>	simError();
1528	>	}
1529	>
1530	>	info->the_integrator = myNPTf;
1531	>	break;
1532	>
1533	>	case NPTxyz_ENS:
1534	>	if (globals->haveZconstraints()){
1535	>	setupZConstraint(info[k]);
1536	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1537	>	}
1538	>	else
1539	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1540	>
1541	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1542	>
1543	>	if (globals->haveTargetPressure())
1544	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1545	>	else{
1546	>	sprintf(painCave.errMsg,
1547	>	"SimSetup error: If you use a constant pressure\n"
1548	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1549	>	painCave.isFatal = 1;
1550	>	simError();
1551	>	}
1552	>
1553	>	if (globals->haveTauThermostat())
1554	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1555	>	else{
1556	>	sprintf(painCave.errMsg,
1557	>	"SimSetup error: If you use an NPT\n"
1558	>	"\tensemble, you must set tauThermostat.\n");
1559	>	painCave.isFatal = 1;
1560	>	simError();
1561	>	}
1562	>
1563	>	if (globals->haveTauBarostat())
1564	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1565	>	else{
1566	>	sprintf(painCave.errMsg,
1567	>	"SimSetup error: If you use an NPT\n"
1568	>	"\tensemble, you must set tauBarostat.\n");
1569	>	painCave.isFatal = 1;
1570	>	simError();
1571	>	}
1572	>
1573	>	info->the_integrator = myNPTxyz;
1574	>	break;
1575	>
1576	>	default:
1577	>	sprintf(painCave.errMsg,
1578	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1579	>	painCave.isFatal = 1;
1580	>	simError();
1581	>	}
1582		}
1583		}
1584	+
1585	+	void SimSetup::initFortran(void){
1586	+	info[0].refreshSim();
1587	+
1588	+	if (!strcmp(info[0].mixingRule, "standard")){
1589	+	the_ff->initForceField(LB_MIXING_RULE);
1590	+	}
1591	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1592	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1593	+	}
1594	+	else{
1595	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1596	+	info[0].mixingRule);
1597	+	painCave.isFatal = 1;
1598	+	simError();
1599	+	}
1600	+
1601	+
1602	+	#ifdef IS_MPI
1603	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1604	+	MPIcheckPoint();
1605	+	#endif // is_mpi
1606	+	}
1607	+
1608	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1609	+	int nZConstraints;
1610	+	ZconStamp** zconStamp;
1611	+
1612	+	if (globals->haveZconstraintTime()){
1613	+	//add sample time of z-constraint  into SimInfo's property list
1614	+	DoubleData* zconsTimeProp = new DoubleData();
1615	+	zconsTimeProp->setID(ZCONSTIME_ID);
1616	+	zconsTimeProp->setData(globals->getZconsTime());
1617	+	theInfo.addProperty(zconsTimeProp);
1618	+	}
1619	+	else{
1620	+	sprintf(painCave.errMsg,
1621	+	"ZConstraint error: If you use a ZConstraint,\n"
1622	+	"\tyou must set zconsTime.\n");
1623	+	painCave.isFatal = 1;
1624	+	simError();
1625	+	}
1626	+
1627	+	//push zconsTol into siminfo, if user does not specify
1628	+	//value for zconsTol, a default value will be used
1629	+	DoubleData* zconsTol = new DoubleData();
1630	+	zconsTol->setID(ZCONSTOL_ID);
1631	+	if (globals->haveZconsTol()){
1632	+	zconsTol->setData(globals->getZconsTol());
1633	+	}
1634	+	else{
1635	+	double defaultZConsTol = 0.01;
1636	+	sprintf(painCave.errMsg,
1637	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1638	+	"\tOOPSE will use a default value of %f.\n"
1639	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1640	+	defaultZConsTol);
1641	+	painCave.isFatal = 0;
1642	+	simError();
1643	+
1644	+	zconsTol->setData(defaultZConsTol);
1645	+	}
1646	+	theInfo.addProperty(zconsTol);
1647	+
1648	+	//set Force Subtraction Policy
1649	+	StringData* zconsForcePolicy = new StringData();
1650	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1651	+
1652	+	if (globals->haveZconsForcePolicy()){
1653	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1654	+	}
1655	+	else{
1656	+	sprintf(painCave.errMsg,
1657	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1658	+	"\tOOPSE will use PolicyByMass.\n"
1659	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1660	+	painCave.isFatal = 0;
1661	+	simError();
1662	+	zconsForcePolicy->setData("BYMASS");
1663	+	}
1664	+
1665	+	theInfo.addProperty(zconsForcePolicy);
1666	+
1667	+	//Determine the name of ouput file and add it into SimInfo's property list
1668	+	//Be careful, do not use inFileName, since it is a pointer which
1669	+	//point to a string at master node, and slave nodes do not contain that string
1670	+
1671	+	string zconsOutput(theInfo.finalName);
1672	+
1673	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1674	+
1675	+	StringData* zconsFilename = new StringData();
1676	+	zconsFilename->setID(ZCONSFILENAME_ID);
1677	+	zconsFilename->setData(zconsOutput);
1678	+
1679	+	theInfo.addProperty(zconsFilename);
1680	+
1681	+	//setup index, pos and other parameters of z-constraint molecules
1682	+	nZConstraints = globals->getNzConstraints();
1683	+	theInfo.nZconstraints = nZConstraints;
1684	+
1685	+	zconStamp = globals->getZconStamp();
1686	+	ZConsParaItem tempParaItem;
1687	+
1688	+	ZConsParaData* zconsParaData = new ZConsParaData();
1689	+	zconsParaData->setID(ZCONSPARADATA_ID);
1690	+
1691	+	for (int i = 0; i < nZConstraints; i++){
1692	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1693	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1694	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1695	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1696	+
1697	+	zconsParaData->addItem(tempParaItem);
1698	+	}
1699	+
1700	+	//check the uniqueness of index
1701	+	if(!zconsParaData->isIndexUnique()){
1702	+	sprintf(painCave.errMsg,
1703	+	"ZConstraint Error: molIndex is not unique!\n");
1704	+	painCave.isFatal = 1;
1705	+	simError();
1706	+	}
1707	+
1708	+	//sort the parameters by index of molecules
1709	+	zconsParaData->sortByIndex();
1710	+
1711	+	//push data into siminfo, therefore, we can retrieve later
1712	+	theInfo.addProperty(zconsParaData);
1713	+	}
1714	+
1715	+	void SimSetup::makeMinimizer(){
1716	+
1717	+	OOPSEMinimizer* myOOPSEMinimizer;
1718	+	MinimizerParameterSet* param;
1719	+	char minimizerName[100];
1720	+
1721	+	for (int i = 0; i < nInfo; i++){
1722	+
1723	+	//prepare parameter set for minimizer
1724	+	param = new MinimizerParameterSet();
1725	+	param->setDefaultParameter();
1726	+
1727	+	if (globals->haveMinimizer()){
1728	+	param->setFTol(globals->getMinFTol());
1729	+	}
1730	+
1731	+	if (globals->haveMinGTol()){
1732	+	param->setGTol(globals->getMinGTol());
1733	+	}
1734	+
1735	+	if (globals->haveMinMaxIter()){
1736	+	param->setMaxIteration(globals->getMinMaxIter());
1737	+	}
1738	+
1739	+	if (globals->haveMinWriteFrq()){
1740	+	param->setMaxIteration(globals->getMinMaxIter());
1741	+	}
1742	+
1743	+	if (globals->haveMinWriteFrq()){
1744	+	param->setWriteFrq(globals->getMinWriteFrq());
1745	+	}
1746	+
1747	+	if (globals->haveMinStepSize()){
1748	+	param->setStepSize(globals->getMinStepSize());
1749	+	}
1750	+
1751	+	if (globals->haveMinLSMaxIter()){
1752	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1753	+	}
1754	+
1755	+	if (globals->haveMinLSTol()){
1756	+	param->setLineSearchTol(globals->getMinLSTol());
1757	+	}
1758	+
1759	+	strcpy(minimizerName, globals->getMinimizer());
1760	+
1761	+	if (!strcasecmp(minimizerName, "CG")){
1762	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1763	+	}
1764	+	else if (!strcasecmp(minimizerName, "SD")){
1765	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1766	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1767	+	}
1768	+	else{
1769	+	sprintf(painCave.errMsg,
1770	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1771	+	painCave.isFatal = 0;
1772	+	simError();
1773	+
1774	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1775	+	}
1776	+	info[i].the_integrator = myOOPSEMinimizer;
1777	+
1778	+	//store the minimizer into simInfo
1779	+	info[i].the_minimizer = myOOPSEMinimizer;
1780	+	info[i].has_minimizer = true;
1781	+	}
1782	+
1783	+	}

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