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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 604 by gezelter, Tue Jul 15 03:08:00 2003 UTC vs.
Revision 1093 by tim, Wed Mar 17 14:22:59 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"
#	Line 14 | Line 19
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 NPTim_ENS 4
22	<	#define NPTfm_ENS 5
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
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 41 | Line 78 | void SimSetup::parseFile( char* fileName ){
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();
73	<	mpiEventLoop();
74	<
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;
82	<	Globals* the_globals;
83	<	int i, j, k, globalAtomIndex;
84	<
85	<	int ensembleCase;
86	<	int ffCase;
87	<
88	<	ensembleCase = -1;
89	<	ffCase = -1;
125	>	// gather all of the information from the Bass file
126
127	<	// get the stamps and globals;
92	<	the_stamps = stamps;
93	<	the_globals = globals;
127	>	gatherInfo();
128
129	<	// set the easy ones first
96	<	simnfo->target_temp = the_globals->getTargetTemp();
97	<	simnfo->dt = the_globals->getDt();
98	<	simnfo->run_time = the_globals->getRunTime();
129	>	// creation of complex system objects
130
131	<	// get the ones we know are there, yet still may need some work.
101	<	n_components = the_globals->getNComponents();
102	<	strcpy( force_field, the_globals->getForceField() );
131	>	sysObjectsCreation();
132
133	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
105	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
106	<	else{
107	<	sprintf( painCave.errMsg,
108	<	"SimSetup Error. Unrecognized force field -> %s\n",
109	<	force_field );
110	<	painCave.isFatal = 1;
111	<	simError();
112	<	}
133	>	// check on the post processing info
134
135	<	// get the ensemble:
115	<	strcpy( ensemble, the_globals->getEnsemble() );
135	>	finalInfoCheck();
136
137	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
138	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
139	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
140	<	ensembleCase = NPTi_ENS;
141	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
142	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
143	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
124	<	else{
125	<	sprintf( painCave.errMsg,
126	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
127	<	"reverting to NVE for this simulation.\n",
128	<	ensemble );
129	<	painCave.isFatal = 0;
130	<	simError();
131	<	strcpy( ensemble, "NVE" );
132	<	ensembleCase = NVE_ENS;
137	>	// initialize the system coordinates
138	>
139	>	if ( !initSuspend ){
140	>	initSystemCoords();
141	>
142	>	if( !(globals->getUseInitTime()) )
143	>	info[0].currentTime = 0.0;
144		}
134	–	strcpy( simnfo->ensemble, ensemble );
145
146	+	// make the output filenames
147
148	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
138	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
139	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
140	<	//     if (the_globals->haveTargetPressure())
141	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
142	<	//     else {
143	<	//       sprintf( painCave.errMsg,
144	<	//                "SimSetup error: If you use the constant pressure\n"
145	<	//                "    ensemble, you must set targetPressure.\n"
146	<	//                "    This was found in the BASS file.\n");
147	<	//       painCave.isFatal = 1;
148	<	//       simError();
149	<	//     }
148	>	makeOutNames();
149
150	<	//     if (the_globals->haveTauThermostat())
151	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
152	<	//     else if (the_globals->haveQmass())
153	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
154	<	//     else {
155	<	//       sprintf( painCave.errMsg,
156	<	//                "SimSetup error: If you use one of the constant temperature\n"
157	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
158	<	//                "    Neither of these was found in the BASS file.\n");
159	<	//       painCave.isFatal = 1;
161	<	//       simError();
162	<	//     }
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	<	//     if (the_globals->haveTauBarostat())
165	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
166	<	//     else {
167	<	//       sprintf( painCave.errMsg,
168	<	//                "SimSetup error: If you use the constant pressure\n"
169	<	//                "    ensemble, you must set tauBarostat.\n"
170	<	//                "    This was found in the BASS file.\n");
171	<	//       painCave.isFatal = 1;
172	<	//       simError();
173	<	//     }
161	>	// initialize the Fortran
162
163	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
164	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
177	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
163	>	initFortran();
164	>	}
165
179	–	//     if (the_globals->haveTauThermostat())
180	–	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
181	–	//     else if (the_globals->haveQmass())
182	–	//       the_extendedsystem->setQmass(the_globals->getQmass());
183	–	//     else {
184	–	//       sprintf( painCave.errMsg,
185	–	//                "SimSetup error: If you use one of the constant temperature\n"
186	–	//                "    ensembles, you must set either tauThermostat or qMass.\n"
187	–	//                "    Neither of these was found in the BASS file.\n");
188	–	//       painCave.isFatal = 1;
189	–	//       simError();
190	–	//     }
166
167	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
168	<	simnfo->usePBC = the_globals->getPBC();
169	<
170	<	int usesDipoles = 0;
171	<	switch( ffCase ){
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	<	case FF_DUFF:
180	<	the_ff = new DUFF();
181	<	usesDipoles = 1;
201	<	break;
179	>	bond_pair* theBonds;
180	>	bend_set* theBends;
181	>	torsion_set* theTorsions;
182
183	<	case FF_LJ:
204	<	the_ff = new LJFF();
205	<	break;
183	>	//init the forceField paramters
184
185	<	default:
208	<	sprintf( painCave.errMsg,
209	<	"SimSetup Error. Unrecognized force field in case statement.\n");
210	<	painCave.isFatal = 1;
211	<	simError();
212	<	}
185	>	the_ff->readParams();
186
214	–	#ifdef IS_MPI
215	–	strcpy( checkPointMsg, "ForceField creation successful" );
216	–	MPIcheckPoint();
217	–	#endif // is_mpi
187
188	<	// get the components and calculate the tot_nMol and indvidual n_mol
220	<	the_components = the_globals->getComponents();
221	<	components_nmol = new int[n_components];
222	<	comp_stamps = new MoleculeStamp*[n_components];
188	>	// init the atoms
189
190	<	if( !the_globals->haveNMol() ){
191	<	// we don't have the total number of molecules, so we assume it is
192	<	// given in each component
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	<	tot_nmol = 0;
196	<	for( i=0; i<n_components; i++ ){
195	>	for (k = 0; k < nInfo; k++){
196	>	the_ff->setSimInfo(&(info[k]));
197
198	<	if( !the_components[i]->haveNMol() ){
199	<	// we have a problem
200	<	sprintf( painCave.errMsg,
201	<	"SimSetup Error. No global NMol or component NMol"
202	<	" given. Cannot calculate the number of atoms.\n" );
203	<	painCave.isFatal = 1;
204	<	simError();
205	<	}
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	<	tot_nmol += the_components[i]->getNMol();
210	<	components_nmol[i] = the_components[i]->getNMol();
211	<	}
212	<	}
213	<	else{
245	<	sprintf( painCave.errMsg,
246	<	"SimSetup error.\n"
247	<	"\tSorry, the ability to specify total"
248	<	" nMols and then give molfractions in the components\n"
249	<	"\tis not currently supported."
250	<	" Please give nMol in the components.\n" );
251	<	painCave.isFatal = 1;
252	<	simError();
253	<
254	<
255	<	//     tot_nmol = the_globals->getNMol();
256	<
257	<	//   //we have the total number of molecules, now we check for molfractions
258	<	//     for( i=0; i<n_components; i++ ){
259	<
260	<	//       if( !the_components[i]->haveMolFraction() ){
261	<
262	<	//  if( !the_components[i]->haveNMol() ){
263	<	//    //we have a problem
264	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
265	<	//              << " nMol was given in component
266	<
267	<	}
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	<	#ifdef IS_MPI
216	<	strcpy( checkPointMsg, "Have the number of components" );
217	<	MPIcheckPoint();
272	<	#endif // is_mpi
215	>	theBonds = new bond_pair[molInfo.nBonds];
216	>	theBends = new bend_set[molInfo.nBends];
217	>	theTorsions = new torsion_set[molInfo.nTorsions];
218
219	<	// make an array of molecule stamps that match the components used.
275	<	// also extract the used stamps out into a separate linked list
219	>	// make the Atoms
220
221	<	simnfo->nComponents = n_components;
222	<	simnfo->componentsNmol = components_nmol;
223	<	simnfo->compStamps = comp_stamps;
224	<	simnfo->headStamp = new LinkedMolStamp();
225	<
226	<	char* id;
227	<	LinkedMolStamp* headStamp = simnfo->headStamp;
284	<	LinkedMolStamp* currentStamp = NULL;
285	<	for( i=0; i<n_components; i++ ){
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	<	id = the_components[i]->getType();
230	<	comp_stamps[i] = NULL;
231	<
290	<	// check to make sure the component isn't already in the list
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	<	comp_stamps[i] = headStamp->match( id );
234	<	if( comp_stamps[i] == NULL ){
235	<
236	<	// extract the component from the list;
237	<
238	<	currentStamp = the_stamps->extractMolStamp( id );
239	<	if( currentStamp == NULL ){
240	<	sprintf( painCave.errMsg,
241	<	"SimSetup error: Component \"%s\" was not found in the "
242	<	"list of declared molecules\n",
243	<	id );
244	<	painCave.isFatal = 1;
245	<	simError();
246	<	}
247	<
307	<	headStamp->add( currentStamp );
308	<	comp_stamps[i] = headStamp->match( id );
309	<	}
310	<	}
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	<	#ifdef IS_MPI
250	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
251	<	MPIcheckPoint();
315	<	#endif // is_mpi
316	<
249	>	sux = 0.0;
250	>	suy = 0.0;
251	>	suz = 1.0;
252
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	<	// caclulate the number of atoms, bonds, bends and torsions
259	>	u = sqrt(uSqr);
260	>	ux = ux / u;
261	>	uy = uy / u;
262	>	uz = uz / u;
263
264	<	tot_atoms = 0;
265	<	tot_bonds = 0;
266	<	tot_bends = 0;
267	<	tot_torsions = 0;
268	<	for( i=0; i<n_components; i++ ){
269	<
270	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
271	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
272	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
331	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
332	<	}
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
334	–	tot_SRI = tot_bonds + tot_bends + tot_torsions;
335	–
336	–	simnfo->n_atoms = tot_atoms;
337	–	simnfo->n_bonds = tot_bonds;
338	–	simnfo->n_bends = tot_bends;
339	–	simnfo->n_torsions = tot_torsions;
340	–	simnfo->n_SRI = tot_SRI;
341	–	simnfo->n_mol = tot_nmol;
342	–
343	–	simnfo->molMembershipArray = new int[tot_atoms];
344	–
274		#ifdef IS_MPI
275
276	<	// divide the molecules among processors here.
348	<
349	<	mpiSim = new mpiSimulation( simnfo );
350	<
351	<	globalIndex = mpiSim->divideLabor();
276	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
277
278	<	// set up the local variables
279	<
355	<	int localMol, allMol;
356	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
278	>	#endif // is_mpi
279	>	}
280
281	<	int* mol2proc = mpiSim->getMolToProcMap();
282	<	int* molCompType = mpiSim->getMolComponentType();
283	<
284	<	allMol = 0;
285	<	localMol = 0;
363	<	local_atoms = 0;
364	<	local_bonds = 0;
365	<	local_bends = 0;
366	<	local_torsions = 0;
367	<	globalAtomIndex = 0;
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	+	exI = theBonds[j].a;
288	+	exJ = theBonds[j].b;
289
290	<	for( i=0; i<n_components; i++ ){
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	>	tempEx = exI;
298	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
299	>	tempEx = exJ;
300	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
301
302	<	for( j=0; j<components_nmol[i]; j++ ){
303	<
304	<	if( mol2proc[allMol] == worldRank ){
305	<
306	<	local_atoms +=    comp_stamps[i]->getNAtoms();
377	<	local_bonds +=    comp_stamps[i]->getNBonds();
378	<	local_bends +=    comp_stamps[i]->getNBends();
379	<	local_torsions += comp_stamps[i]->getNTorsions();
380	<	localMol++;
381	<	}
382	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
383	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
384	<	globalAtomIndex++;
302	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
303	>	#else  // isn't MPI
304	>
305	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
306	>	#endif  //is_mpi
307		}
308	+	excludeOffset += molInfo.nBonds;
309
310	<	allMol++;
311	<	}
312	<	}
313	<	local_SRI = local_bonds + local_bends + local_torsions;
314	<
315	<	simnfo->n_atoms = mpiSim->getMyNlocal();
393	<
394	<	if( local_atoms != simnfo->n_atoms ){
395	<	sprintf( painCave.errMsg,
396	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
397	<	" localAtom (%d) are not equal.\n",
398	<	simnfo->n_atoms,
399	<	local_atoms );
400	<	painCave.isFatal = 1;
401	<	simError();
402	<	}
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	<	simnfo->n_bonds = local_bonds;
318	<	simnfo->n_bends = local_bends;
319	<	simnfo->n_torsions = local_torsions;
407	<	simnfo->n_SRI = local_SRI;
408	<	simnfo->n_mol = localMol;
409	<
410	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
411	<	MPIcheckPoint();
412	<
413	<
414	<	#endif // is_mpi
415	<
416	<
417	<	// create the atom and short range interaction arrays
418	<
419	<	Atom::createArrays(simnfo->n_atoms);
420	<	the_atoms = new Atom*[simnfo->n_atoms];
421	<	the_molecules = new Molecule[simnfo->n_mol];
422	<	int molIndex;
423	<
424	<	// initialize the molecule's stampID's
317	>	if (currentBend->haveExtras()){
318	>	extras = currentBend->getExtras();
319	>	current_extra = extras;
320
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	+	case 1:
330	+	theBends[j].ghost = (int) current_extra->getDouble() +
331	+	atomOffset;
332	+	theBends[j].isGhost = 1;
333	+	break;
334	+
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	+	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	+	// 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	<
374	>	tempEx = exI;
375	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
376	>	tempEx = exJ;
377	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
378
379	<	molIndex = 0;
380	<	for(i=0; i<mpiSim->getTotNmol(); i++){
381	<
382	<	if(mol2proc[i] == worldRank ){
383	<	the_molecules[molIndex].setStampID( molCompType[i] );
384	<	the_molecules[molIndex].setMyIndex( molIndex );
435	<	the_molecules[molIndex].setGlobalIndex( i );
436	<	molIndex++;
437	<	}
438	<	}
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	<	#else // is_mpi
387	<
388	<	molIndex = 0;
389	<	globalAtomIndex = 0;
390	<	for(i=0; i<n_components; i++){
391	<	for(j=0; j<components_nmol[i]; j++ ){
392	<	the_molecules[molIndex].setStampID( i );
393	<	the_molecules[molIndex].setMyIndex( molIndex );
394	<	the_molecules[molIndex].setGlobalIndex( molIndex );
395	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
396	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
397	<	globalAtomIndex++;
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	>	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	>	tempEx = exI;
404	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
405	>	tempEx = exJ;
406	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
407	>
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	<	molIndex++;
454	<	}
455	<	}
456	<
413	>	excludeOffset += molInfo.nTorsions;
414
458	–	#endif // is_mpi
415
416	+	// send the arrays off to the forceField for init.
417
418	<	if( simnfo->n_SRI ){
419	<
420	<	Exclude::createArray(simnfo->n_SRI);
421	<	the_excludes = new Exclude*[simnfo->n_SRI];
422	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
423	<	simnfo->globalExcludes = new int;
424	<	simnfo->n_exclude = simnfo->n_SRI;
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	>
424	>
425	>	info[k].molecules[i].initialize(molInfo);
426	>
427	>
428	>	atomOffset += molInfo.nAtoms;
429	>	delete[] theBonds;
430	>	delete[] theBends;
431	>	delete[] theTorsions;
432	>	}
433		}
469	–	else{
470	–
471	–	Exclude::createArray( 1 );
472	–	the_excludes = new Exclude*;
473	–	the_excludes[0] = new Exclude(0);
474	–	the_excludes[0]->setPair( 0,0 );
475	–	simnfo->globalExcludes = new int;
476	–	simnfo->globalExcludes[0] = 0;
477	–	simnfo->n_exclude = 0;
478	–	}
434
435	<	// set the arrays into the SimInfo object
435	>	#ifdef IS_MPI
436	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
437	>	MPIcheckPoint();
438	>	#endif // is_mpi
439
440	<	simnfo->atoms = the_atoms;
483	<	simnfo->molecules = the_molecules;
484	<	simnfo->nGlobalExcludes = 0;
485	<	simnfo->excludes = the_excludes;
440	>	// clean up the forcefield
441
442	+	the_ff->calcRcut();
443	+	the_ff->cleanMe();
444	+	}
445
446	<	// get some of the tricky things that may still be in the globals
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 boxVector[3];
456	<	if( the_globals->haveBox() ){
457	<	boxVector[0] = the_globals->getBox();
458	<	boxVector[1] = the_globals->getBox();
494	<	boxVector[2] = the_globals->getBox();
495	<
496	<	simnfo->setBox( boxVector );
497	<	}
498	<	else if( the_globals->haveDensity() ){
455	>	double vel[3];
456	>	vel[0] = 0.0;
457	>	vel[1] = 0.0;
458	>	vel[2] = 0.0;
459
460	<	double vol;
461	<	vol = (double)tot_nmol / the_globals->getDensity();
462	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
503	<	boxVector[1] = boxVector[0];
504	<	boxVector[2] = boxVector[0];
460	>	temp1 = (double) tot_nmol / 4.0;
461	>	temp2 = pow(temp1, (1.0 / 3.0));
462	>	temp3 = ceil(temp2);
463
464	<	simnfo->setBox( boxVector );
465	<	}
466	<	else{
467	<	if( !the_globals->haveBoxX() ){
510	<	sprintf( painCave.errMsg,
511	<	"SimSetup error, no periodic BoxX size given.\n" );
512	<	painCave.isFatal = 1;
513	<	simError();
514	<	}
515	<	boxVector[0] = the_globals->getBoxX();
464	>	have_extra = 0;
465	>	if (temp2 < temp3){
466	>	// we have a non-complete lattice
467	>	have_extra = 1;
468
469	<	if( !the_globals->haveBoxY() ){
470	<	sprintf( painCave.errMsg,
471	<	"SimSetup error, no periodic BoxY size given.\n" );
472	<	painCave.isFatal = 1;
473	<	simError();
474	<	}
475	<	boxVector[1] = the_globals->getBoxY();
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( !the_globals->haveBoxZ() ){
478	<	sprintf( painCave.errMsg,
479	<	"SimSetup error, no periodic BoxZ size given.\n" );
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		}
531	–	boxVector[2] = the_globals->getBoxZ();
532	–
533	–	simnfo->setBox( boxVector );
484		}
485	+	else{
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	<	#ifdef IS_MPI
493	<	strcpy( checkPointMsg, "Box size set up" );
494	<	MPIcheckPoint();
495	<	#endif // is_mpi
492	>	current_mol = 0;
493	>	current_comp_mol = 0;
494	>	current_comp = 0;
495	>	current_atom_ndx = 0;
496
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	<	// initialize the arrays
502	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
503
504	<	the_ff->setSimInfo( simnfo );
505	<
506	<	makeMolecules();
507	<	simnfo->identArray = new int[simnfo->n_atoms];
548	<	for(i=0; i<simnfo->n_atoms; i++){
549	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
550	<	}
551	<
552	<	if (the_globals->getUseRF() ) {
553	<	simnfo->useReactionField = 1;
554	<
555	<	if( !the_globals->haveECR() ){
556	<	sprintf( painCave.errMsg,
557	<	"SimSetup Warning: using default value of 1/2 the smallest "
558	<	"box length for the electrostaticCutoffRadius.\n"
559	<	"I hope you have a very fast processor!\n");
560	<	painCave.isFatal = 0;
561	<	simError();
562	<	double smallest;
563	<	smallest = simnfo->boxLx;
564	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
565	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
566	<	simnfo->ecr = 0.5 * smallest;
567	<	} else {
568	<	simnfo->ecr        = the_globals->getECR();
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	<	if( !the_globals->haveEST() ){
512	<	sprintf( painCave.errMsg,
513	<	"SimSetup Warning: using default value of 0.05 * the "
514	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
515	<	);
516	<	painCave.isFatal = 0;
517	<	simError();
518	<	simnfo->est = 0.05 * simnfo->ecr;
519	<	} else {
520	<	simnfo->est        = the_globals->getEST();
511	>	if (have_extra){
512	>	done = 0;
513	>
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 (!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	>	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	>	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	<	if(!the_globals->haveDielectric() ){
553	<	sprintf( painCave.errMsg,
554	<	"SimSetup Error: You are trying to use Reaction Field without"
555	<	"setting a dielectric constant!\n"
556	<	);
551	>	}
552	>
553	>	for (i = 0; i < info[0].n_atoms; i++){
554	>	info[0].atoms[i]->setVel(vel);
555	>	}
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	>	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	<	simnfo->dielectric = the_globals->getDielectric();
578	<	} else {
579	<	if (usesDipoles) {
580	<
581	<	if( !the_globals->haveECR() ){
582	<	sprintf( painCave.errMsg,
583	<	"SimSetup Warning: using default value of 1/2 the smallest "
584	<	"box length for the electrostaticCutoffRadius.\n"
585	<	"I hope you have a very fast processor!\n");
586	<	painCave.isFatal = 0;
587	<	simError();
588	<	double smallest;
589	<	smallest = simnfo->boxLx;
590	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
591	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
592	<	simnfo->ecr = 0.5 * smallest;
593	<	} else {
594	<	simnfo->ecr        = the_globals->getECR();
595	<	}
596	<
597	<	if( !the_globals->haveEST() ){
598	<	sprintf( painCave.errMsg,
599	<	"SimSetup Warning: using default value of 5%% of the "
614	<	"electrostaticCutoffRadius for the "
615	<	"electrostaticSkinThickness\n"
616	<	);
617	<	painCave.isFatal = 0;
618	<	simError();
619	<	simnfo->est = 0.05 * simnfo->ecr;
620	<	} else {
621	<	simnfo->est        = the_globals->getEST();
622	<	}
577	>
578	>	pos[0] = x + current_atom->getPosX();
579	>	pos[1] = y + current_atom->getPosY();
580	>	pos[2] = z + current_atom->getPosZ();
581	>
582	>	info[0].atoms[current_atom_ndx]->setPos(pos);
583	>
584	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
585	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
586	>
587	>	rotMat[0][0] = 1.0;
588	>	rotMat[0][1] = 0.0;
589	>	rotMat[0][2] = 0.0;
590	>
591	>	rotMat[1][0] = 0.0;
592	>	rotMat[1][1] = 1.0;
593	>	rotMat[1][2] = 0.0;
594	>
595	>	rotMat[2][0] = 0.0;
596	>	rotMat[2][1] = 0.0;
597	>	rotMat[2][2] = 1.0;
598	>
599	>	dAtom->setA(rotMat);
600		}
624	–	}
601
602	<	#ifdef IS_MPI
603	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
628	<	MPIcheckPoint();
629	<	#endif // is_mpi
602	>	current_atom_ndx++;
603	>	}
604
605	<	if( the_globals->haveInitialConfig() ){
606	<
633	<	InitializeFromFile* fileInit;
634	<	#ifdef IS_MPI // is_mpi
635	<	if( worldRank == 0 ){
636	<	#endif //is_mpi
637	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
638	<	#ifdef IS_MPI
639	<	}else fileInit = new InitializeFromFile( NULL );
640	<	#endif
641	<	fileInit->read_xyz( simnfo ); // default velocities on
605	>	current_mol++;
606	>	current_comp_mol++;
607
608	<	delete fileInit;
609	<	}
610	<	else{
608	>	if (current_comp_mol >= components_nmol[current_comp]){
609	>	current_comp_mol = 0;
610	>	current_comp++;
611	>	}
612	>	}
613
647	–	#ifdef IS_MPI
614
615	<	// no init from bass
616	<
651	<	sprintf( painCave.errMsg,
652	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
653	<	painCave.isFatal;
654	<	simError();
655	<
656	<	#else
615	>	void SimSetup::gatherInfo(void){
616	>	int i;
617
618	<	initFromBass();
618	>	ensembleCase = -1;
619	>	ffCase = -1;
620
621	+	// set the easy ones first
622
623	<	#endif
624	<	}
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
664	–	#ifdef IS_MPI
665	–	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
666	–	MPIcheckPoint();
667	–	#endif // is_mpi
630
631	+	// get the forceField
632
633	<
671	<
672	<
633	>	strcpy(force_field, globals->getForceField());
634
635	<
636	<	#ifdef IS_MPI
676	<	if( worldRank == 0 ){
677	<	#endif // is_mpi
678	<
679	<	if( the_globals->haveFinalConfig() ){
680	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
681	<	}
682	<	else{
683	<	strcpy( simnfo->finalName, inFileName );
684	<	char* endTest;
685	<	int nameLength = strlen( simnfo->finalName );
686	<	endTest = &(simnfo->finalName[nameLength - 5]);
687	<	if( !strcmp( endTest, ".bass" ) ){
688	<	strcpy( endTest, ".eor" );
689	<	}
690	<	else if( !strcmp( endTest, ".BASS" ) ){
691	<	strcpy( endTest, ".eor" );
692	<	}
693	<	else{
694	<	endTest = &(simnfo->finalName[nameLength - 4]);
695	<	if( !strcmp( endTest, ".bss" ) ){
696	<	strcpy( endTest, ".eor" );
697	<	}
698	<	else if( !strcmp( endTest, ".mdl" ) ){
699	<	strcpy( endTest, ".eor" );
700	<	}
701	<	else{
702	<	strcat( simnfo->finalName, ".eor" );
703	<	}
704	<	}
705	<	}
706	<
707	<	// make the sample and status out names
708	<
709	<	strcpy( simnfo->sampleName, inFileName );
710	<	char* endTest;
711	<	int nameLength = strlen( simnfo->sampleName );
712	<	endTest = &(simnfo->sampleName[nameLength - 5]);
713	<	if( !strcmp( endTest, ".bass" ) ){
714	<	strcpy( endTest, ".dump" );
715	<	}
716	<	else if( !strcmp( endTest, ".BASS" ) ){
717	<	strcpy( endTest, ".dump" );
718	<	}
719	<	else{
720	<	endTest = &(simnfo->sampleName[nameLength - 4]);
721	<	if( !strcmp( endTest, ".bss" ) ){
722	<	strcpy( endTest, ".dump" );
723	<	}
724	<	else if( !strcmp( endTest, ".mdl" ) ){
725	<	strcpy( endTest, ".dump" );
726	<	}
727	<	else{
728	<	strcat( simnfo->sampleName, ".dump" );
729	<	}
730	<	}
731	<
732	<	strcpy( simnfo->statusName, inFileName );
733	<	nameLength = strlen( simnfo->statusName );
734	<	endTest = &(simnfo->statusName[nameLength - 5]);
735	<	if( !strcmp( endTest, ".bass" ) ){
736	<	strcpy( endTest, ".stat" );
737	<	}
738	<	else if( !strcmp( endTest, ".BASS" ) ){
739	<	strcpy( endTest, ".stat" );
740	<	}
741	<	else{
742	<	endTest = &(simnfo->statusName[nameLength - 4]);
743	<	if( !strcmp( endTest, ".bss" ) ){
744	<	strcpy( endTest, ".stat" );
745	<	}
746	<	else if( !strcmp( endTest, ".mdl" ) ){
747	<	strcpy( endTest, ".stat" );
748	<	}
749	<	else{
750	<	strcat( simnfo->statusName, ".stat" );
751	<	}
752	<	}
753	<
754	<	#ifdef IS_MPI
635	>	if (!strcasecmp(force_field, "DUFF")){
636	>	ffCase = FF_DUFF;
637		}
638	<	#endif // is_mpi
639	<
758	<	// set the status, sample, and themal kick times
759	<
760	<	if( the_globals->haveSampleTime() ){
761	<	simnfo->sampleTime = the_globals->getSampleTime();
762	<	simnfo->statusTime = simnfo->sampleTime;
763	<	simnfo->thermalTime = simnfo->sampleTime;
638	>	else if (!strcasecmp(force_field, "LJ")){
639	>	ffCase = FF_LJ;
640		}
641	<	else{
642	<	simnfo->sampleTime = the_globals->getRunTime();
767	<	simnfo->statusTime = simnfo->sampleTime;
768	<	simnfo->thermalTime = simnfo->sampleTime;
641	>	else if (!strcasecmp(force_field, "EAM")){
642	>	ffCase = FF_EAM;
643		}
644	<
645	<	if( the_globals->haveStatusTime() ){
772	<	simnfo->statusTime = the_globals->getStatusTime();
644	>	else if (!strcasecmp(force_field, "WATER")){
645	>	ffCase = FF_H2O;
646		}
647	<
648	<	if( the_globals->haveThermalTime() ){
649	<	simnfo->thermalTime = the_globals->getThermalTime();
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	<	// check for the temperature set flag
654	>	// get the ensemble
655
656	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
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	<	// make the integrator
685	<
786	<
787	<	NVT*  myNVT = NULL;
788	<	NPTi* myNPTi = NULL;
789	<	NPTf* myNPTf = NULL;
790	<	NPTim* myNPTim = NULL;
684	>	for (i = 0; i < nInfo; i++){
685	>	strcpy(info[i].ensemble, ensemble);
686
687	<	switch( ensembleCase ){
687	>	// get the mixing rule
688
689	<	case NVE_ENS:
690	<	new NVE( simnfo, the_ff );
691	<	break;
689	>	strcpy(info[i].mixingRule, globals->getMixingRule());
690	>	info[i].usePBC = globals->getPBC();
691	>	}
692
693	<	case NVT_ENS:
799	<	myNVT = new NVT( simnfo, the_ff );
800	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
693	>	// get the components and calculate the tot_nMol and indvidual n_mol
694
695	<	if (the_globals->haveTauThermostat())
696	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
695	>	the_components = globals->getComponents();
696	>	components_nmol = new int[n_components];
697
805	–	else {
806	–	sprintf( painCave.errMsg,
807	–	"SimSetup error: If you use the NVT\n"
808	–	"    ensemble, you must set tauThermostat.\n");
809	–	painCave.isFatal = 1;
810	–	simError();
811	–	}
812	–	break;
698
699	<	case NPTi_ENS:
700	<	myNPTi = new NPTi( simnfo, the_ff );
701	<	myNPTi->setTargetTemp( the_globals->getTargetTemp());
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	<	if (the_globals->haveTargetPressure())
704	<	myNPTi->setTargetPressure(the_globals->getTargetPressure());
705	<	else {
706	<	sprintf( painCave.errMsg,
707	<	"SimSetup error: If you use a constant pressure\n"
708	<	"    ensemble, you must set targetPressure in the BASS file.\n");
709	<	painCave.isFatal = 1;
710	<	simError();
711	<	}
712	<
828	<	if( the_globals->haveTauThermostat() )
829	<	myNPTi->setTauThermostat( the_globals->getTauThermostat() );
830	<	else{
831	<	sprintf( painCave.errMsg,
832	<	"SimSetup error: If you use an NPT\n"
833	<	"    ensemble, you must set tauThermostat.\n");
834	<	painCave.isFatal = 1;
835	<	simError();
836	<	}
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( the_globals->haveTauBarostat() )
715	<	myNPTi->setTauBarostat( the_globals->getTauBarostat() );
840	<	else{
841	<	sprintf( painCave.errMsg,
842	<	"SimSetup error: If you use an NPT\n"
843	<	"    ensemble, you must set tauBarostat.\n");
844	<	painCave.isFatal = 1;
845	<	simError();
714	>	tot_nmol += the_components[i]->getNMol();
715	>	components_nmol[i] = the_components[i]->getNMol();
716		}
717	<	break;
717	>	}
718	>	else{
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	<	case NPTf_ENS:
730	<	myNPTf = new NPTf( simnfo, the_ff );
731	<	myNPTf->setTargetTemp( the_globals->getTargetTemp());
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	<	if (the_globals->haveTargetPressure())
741	<	myNPTf->setTargetPressure(the_globals->getTargetPressure());
742	<	else {
743	<	sprintf( painCave.errMsg,
744	<	"SimSetup error: If you use a constant pressure\n"
745	<	"    ensemble, you must set targetPressure in the BASS file.\n");
746	<	painCave.isFatal = 1;
747	<	simError();
748	<	}
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	<	if( the_globals->haveTauThermostat() )
751	<	myNPTf->setTauThermostat( the_globals->getTauThermostat() );
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	>	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	>	// set the status, sample, and thermal kick times
771	>
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		else{
779	<	sprintf( painCave.errMsg,
780	<	"SimSetup error: If you use an NPT\n"
781	<	"    ensemble, you must set tauThermostat.\n");
869	<	painCave.isFatal = 1;
870	<	simError();
779	>	info[i].sampleTime = globals->getRunTime();
780	>	info[i].statusTime = info[i].sampleTime;
781	>	info[i].thermalTime = info[i].sampleTime;
782		}
783
784	<	if( the_globals->haveTauBarostat() )
785	<	myNPTf->setTauBarostat( the_globals->getTauBarostat() );
875	<	else{
876	<	sprintf( painCave.errMsg,
877	<	"SimSetup error: If you use an NPT\n"
878	<	"    ensemble, you must set tauBarostat.\n");
879	<	painCave.isFatal = 1;
880	<	simError();
784	>	if (globals->haveStatusTime()){
785	>	info[i].statusTime = globals->getStatusTime();
786		}
882	–	break;
883	–
884	–	case NPTim_ENS:
885	–	myNPTim = new NPTim( simnfo, the_ff );
886	–	myNPTim->setTargetTemp( the_globals->getTargetTemp());
787
788	<	if (the_globals->haveTargetPressure())
789	<	myNPTim->setTargetPressure(the_globals->getTargetPressure());
890	<	else {
891	<	sprintf( painCave.errMsg,
892	<	"SimSetup error: If you use a constant pressure\n"
893	<	"    ensemble, you must set targetPressure in the BASS file.\n");
894	<	painCave.isFatal = 1;
895	<	simError();
788	>	if (globals->haveThermalTime()){
789	>	info[i].thermalTime = globals->getThermalTime();
790		}
791	<
792	<	if( the_globals->haveTauThermostat() )
793	<	myNPTim->setTauThermostat( the_globals->getTauThermostat() );
794	<	else{
795	<	sprintf( painCave.errMsg,
902	<	"SimSetup error: If you use an NPT\n"
903	<	"    ensemble, you must set tauThermostat.\n");
904	<	painCave.isFatal = 1;
905	<	simError();
791	>
792	>	info[i].resetIntegrator = 0;
793	>	if( globals->haveResetTime() ){
794	>	info[i].resetTime = globals->getResetTime();
795	>	info[i].resetIntegrator = 1;
796		}
797
798	<	if( the_globals->haveTauBarostat() )
799	<	myNPTim->setTauBarostat( the_globals->getTauBarostat() );
800	<	else{
801	<	sprintf( painCave.errMsg,
802	<	"SimSetup error: If you use an NPT\n"
803	<	"    ensemble, you must set tauBarostat.\n");
804	<	painCave.isFatal = 1;
798	>	// check for the temperature set flag
799	>
800	>	if (globals->haveTempSet())
801	>	info[i].setTemp = globals->getTempSet();
802	>
803	>	// check for the extended State init
804	>
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 (globals->haveSeed()){
814	>	seedValue = globals->getSeed();
815	>
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();
916	–	}
917	–	break;
822
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	+	}//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	<	default:
847	<	sprintf( painCave.errMsg,
923	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
924	<	painCave.isFatal = 1;
925	<	simError();
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
856
857	+	void SimSetup::finalInfoCheck(void){
858	+	int index;
859	+	int usesDipoles;
860	+	int i;
861	+
862	+	for (i = 0; i < nInfo; i++){
863	+	// check electrostatic parameters
864	+
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		#ifdef IS_MPI
873	<	mpiSim->mpiRefresh();
874	<	#endif
873	>	int myUse = usesDipoles;
874	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
875	>	#endif //is_mpi
876
877	<	// initialize the Fortran
877	>	double theEcr, theEst;
878
879	+	if (globals->getUseRF()){
880	+	info[i].useReactionField = 1;
881
882	<	simnfo->refreshSim();
883	<
884	<	if( !strcmp( simnfo->mixingRule, "standard") ){
885	<	the_ff->initForceField( LB_MIXING_RULE );
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	>	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	>	info[i].setDefaultEcr(theEcr, theEst);
910	>
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		}
941	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
942	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
943	–	}
944	–	else{
945	–	sprintf( painCave.errMsg,
946	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
947	–	simnfo->mixingRule );
948	–	painCave.isFatal = 1;
949	–	simError();
950	–	}
951	–
952	–
954		#ifdef IS_MPI
955	<	strcpy( checkPointMsg,
955	<	"Successfully intialized the mixingRule for Fortran." );
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	+	char* inName;
964
965	<	void SimSetup::makeMolecules( void ){
965	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
966
967	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
968	<	molInit info;
965	<	DirectionalAtom* dAtom;
966	<	LinkedAssign* extras;
967	<	LinkedAssign* current_extra;
968	<	AtomStamp* currentAtom;
969	<	BondStamp* currentBond;
970	<	BendStamp* currentBend;
971	<	TorsionStamp* currentTorsion;
967	>	for (i = 0; i < info[0].n_atoms; i++)
968	>	info[0].atoms[i]->setCoords();
969
970	<	bond_pair* theBonds;
971	<	bend_set* theBends;
972	<	torsion_set* theTorsions;
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	<
985	<	//init the forceField paramters
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	<	the_ff->readParams();
997	>	#ifdef IS_MPI
998	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
999	>	MPIcheckPoint();
1000	>	#endif // is_mpi
1001	>	}
1002
982	–
983	–	// init the atoms
1003
1004	<	double ux, uy, uz, u, uSqr;
1005	<
987	<	atomOffset = 0;
988	<	excludeOffset = 0;
989	<	for(i=0; i<simnfo->n_mol; i++){
990	<
991	<	stampID = the_molecules[i].getStampID();
1004	>	void SimSetup::makeOutNames(void){
1005	>	int k;
1006
993	–	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
994	–	info.nBonds    = comp_stamps[stampID]->getNBonds();
995	–	info.nBends    = comp_stamps[stampID]->getNBends();
996	–	info.nTorsions = comp_stamps[stampID]->getNTorsions();
997	–	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
1007
1008	<	info.myAtoms = &the_atoms[atomOffset];
1009	<	info.myExcludes = &the_excludes[excludeOffset];
1010	<	info.myBonds = new Bond*[info.nBonds];
1011	<	info.myBends = new Bend*[info.nBends];
1003	<	info.myTorsions = new Torsion*[info.nTorsions];
1008	>	for (k = 0; k < nInfo; k++){
1009	>	#ifdef IS_MPI
1010	>	if (worldRank == 0){
1011	>	#endif // is_mpi
1012
1013	<	theBonds = new bond_pair[info.nBonds];
1014	<	theBends = new bend_set[info.nBends];
1007	<	theTorsions = new torsion_set[info.nTorsions];
1008	<
1009	<	// make the Atoms
1010	<
1011	<	for(j=0; j<info.nAtoms; j++){
1012	<
1013	<	currentAtom = comp_stamps[stampID]->getAtom( j );
1014	<	if( currentAtom->haveOrientation() ){
1015	<
1016	<	dAtom = new DirectionalAtom(j + atomOffset);
1017	<	simnfo->n_oriented++;
1018	<	info.myAtoms[j] = dAtom;
1019	<
1020	<	ux = currentAtom->getOrntX();
1021	<	uy = currentAtom->getOrntY();
1022	<	uz = currentAtom->getOrntZ();
1023	<
1024	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
1025	<
1026	<	u = sqrt( uSqr );
1027	<	ux = ux / u;
1028	<	uy = uy / u;
1029	<	uz = uz / u;
1030	<
1031	<	dAtom->setSUx( ux );
1032	<	dAtom->setSUy( uy );
1033	<	dAtom->setSUz( uz );
1013	>	if (globals->haveFinalConfig()){
1014	>	strcpy(info[k].finalName, globals->getFinalConfig());
1015		}
1016		else{
1017	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
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		}
1038	–	info.myAtoms[j]->setType( currentAtom->getType() );
1039	–
1040	–	#ifdef IS_MPI
1041	–
1042	–	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
1043	–
1044	–	#endif // is_mpi
1045	–	}
1046	–
1047	–	// make the bonds
1048	–	for(j=0; j<info.nBonds; j++){
1049	–
1050	–	currentBond = comp_stamps[stampID]->getBond( j );
1051	–	theBonds[j].a = currentBond->getA() + atomOffset;
1052	–	theBonds[j].b = currentBond->getB() + atomOffset;
1040
1041	<	exI = theBonds[j].a;
1055	<	exJ = theBonds[j].b;
1041	>	// make the sample and status out names
1042
1043	<	// exclude_I must always be the smaller of the pair
1044	<	if( exI > exJ ){
1045	<	tempEx = exI;
1046	<	exI = exJ;
1047	<	exJ = tempEx;
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	<	#ifdef IS_MPI
1051	<	tempEx = exI;
1052	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1053	<	tempEx = exJ;
1054	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1055	<
1056	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1057	<	#else  // isn't MPI
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	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1067	<	#endif  //is_mpi
1068	<	}
1069	<	excludeOffset += info.nBonds;
1070	<
1077	<	//make the bends
1078	<	for(j=0; j<info.nBends; j++){
1079	<
1080	<	currentBend = comp_stamps[stampID]->getBend( j );
1081	<	theBends[j].a = currentBend->getA() + atomOffset;
1082	<	theBends[j].b = currentBend->getB() + atomOffset;
1083	<	theBends[j].c = currentBend->getC() + atomOffset;
1084	<
1085	<	if( currentBend->haveExtras() ){
1086	<
1087	<	extras = currentBend->getExtras();
1088	<	current_extra = extras;
1089	<
1090	<	while( current_extra != NULL ){
1091	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1092	<
1093	<	switch( current_extra->getType() ){
1094	<
1095	<	case 0:
1096	<	theBends[j].ghost =
1097	<	current_extra->getInt() + atomOffset;
1098	<	theBends[j].isGhost = 1;
1099	<	break;
1100	<
1101	<	case 1:
1102	<	theBends[j].ghost =
1103	<	(int)current_extra->getDouble() + atomOffset;
1104	<	theBends[j].isGhost = 1;
1105	<	break;
1106	<
1107	<	default:
1108	<	sprintf( painCave.errMsg,
1109	<	"SimSetup Error: ghostVectorSource was neither a "
1110	<	"double nor an int.\n"
1111	<	"-->Bend[%d] in %s\n",
1112	<	j, comp_stamps[stampID]->getID() );
1113	<	painCave.isFatal = 1;
1114	<	simError();
1115	<	}
1116	<	}
1117	<
1118	<	else{
1119	<
1120	<	sprintf( painCave.errMsg,
1121	<	"SimSetup Error: unhandled bend assignment:\n"
1122	<	"    -->%s in Bend[%d] in %s\n",
1123	<	current_extra->getlhs(),
1124	<	j, comp_stamps[stampID]->getID() );
1125	<	painCave.isFatal = 1;
1126	<	simError();
1127	<	}
1128	<
1129	<	current_extra = current_extra->getNext();
1130	<	}
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	<
1073	<	if( !theBends[j].isGhost ){
1134	<
1135	<	exI = theBends[j].a;
1136	<	exJ = theBends[j].c;
1072	>	else if (!strcmp(endTest, ".BASS")){
1073	>	strcpy(endTest, ".stat");
1074		}
1075		else{
1076	<
1077	<	exI = theBends[j].a;
1078	<	exJ = theBends[j].b;
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	<
1144	<	// exclude_I must always be the smaller of the pair
1145	<	if( exI > exJ ){
1146	<	tempEx = exI;
1147	<	exI = exJ;
1148	<	exJ = tempEx;
1149	<	}
1087	>
1088		#ifdef IS_MPI
1089	<	tempEx = exI;
1152	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1153	<	tempEx = exJ;
1154	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1155	<
1156	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1157	<	#else  // isn't MPI
1158	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1159	<	#endif  //is_mpi
1089	>
1090		}
1091	<	excludeOffset += info.nBends;
1091	>	#endif // is_mpi
1092	>	}
1093	>	}
1094
1163	–	for(j=0; j<info.nTorsions; j++){
1164	–
1165	–	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1166	–	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1167	–	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1168	–	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1169	–	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1170	–
1171	–	exI = theTorsions[j].a;
1172	–	exJ = theTorsions[j].d;
1095
1096	<	// exclude_I must always be the smaller of the pair
1097	<	if( exI > exJ ){
1176	<	tempEx = exI;
1177	<	exI = exJ;
1178	<	exJ = tempEx;
1179	<	}
1180	<	#ifdef IS_MPI
1181	<	tempEx = exI;
1182	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1183	<	tempEx = exJ;
1184	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1185	<
1186	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1187	<	#else  // isn't MPI
1188	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1189	<	#endif  //is_mpi
1190	<	}
1191	<	excludeOffset += info.nTorsions;
1096	>	void SimSetup::sysObjectsCreation(void){
1097	>	int i, k;
1098
1099	<
1194	<	// send the arrays off to the forceField for init.
1099	>	// create the forceField
1100
1101	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1197	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1198	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1199	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1101	>	createFF();
1102
1103	+	// extract componentList
1104
1105	<	the_molecules[i].initialize( info );
1105	>	compList();
1106
1107	+	// calc the number of atoms, bond, bends, and torsions
1108
1109	<	atomOffset += info.nAtoms;
1206	<	delete[] theBonds;
1207	<	delete[] theBends;
1208	<	delete[] theTorsions;
1209	<	}
1109	>	calcSysValues();
1110
1111		#ifdef IS_MPI
1112	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1213	<	MPIcheckPoint();
1214	<	#endif // is_mpi
1112	>	// divide the molecules among the processors
1113
1114	<	// clean up the forcefield
1115	<	the_ff->calcRcut();
1218	<	the_ff->cleanMe();
1114	>	mpiMolDivide();
1115	>	#endif //is_mpi
1116
1117	<	}
1117	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1118
1119	<	void SimSetup::initFromBass( void ){
1119	>	makeSysArrays();
1120
1121	<	int i, j, k;
1225	<	int n_cells;
1226	<	double cellx, celly, cellz;
1227	<	double temp1, temp2, temp3;
1228	<	int n_per_extra;
1229	<	int n_extra;
1230	<	int have_extra, done;
1121	>	// make and initialize the molecules (all but atomic coordinates)
1122
1123	<	temp1 = (double)tot_nmol / 4.0;
1233	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1234	<	temp3 = ceil( temp2 );
1123	>	makeMolecules();
1124
1125	<	have_extra =0;
1126	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1127	<	have_extra =1;
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
1240	–	n_cells = (int)temp3 - 1;
1241	–	cellx = simnfo->boxLx / temp3;
1242	–	celly = simnfo->boxLy / temp3;
1243	–	cellz = simnfo->boxLz / temp3;
1244	–	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1245	–	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1246	–	n_per_extra = (int)ceil( temp1 );
1133
1134	<	if( n_per_extra > 4){
1135	<	sprintf( painCave.errMsg,
1136	<	"SimSetup error. There has been an error in constructing"
1137	<	" the non-complete lattice.\n" );
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();
1254	–	}
1157		}
1256	–	else{
1257	–	n_cells = (int)temp3;
1258	–	cellx = simnfo->boxLx / temp3;
1259	–	celly = simnfo->boxLy / temp3;
1260	–	cellz = simnfo->boxLz / temp3;
1261	–	}
1158
1159	<	current_mol = 0;
1160	<	current_comp_mol = 0;
1161	<	current_comp = 0;
1162	<	current_atom_ndx = 0;
1159	>	#ifdef IS_MPI
1160	>	strcpy(checkPointMsg, "ForceField creation successful");
1161	>	MPIcheckPoint();
1162	>	#endif // is_mpi
1163	>	}
1164
1268	–	for( i=0; i < n_cells ; i++ ){
1269	–	for( j=0; j < n_cells; j++ ){
1270	–	for( k=0; k < n_cells; k++ ){
1165
1166	<	makeElement( i * cellx,
1167	<	j * celly,
1168	<	k * cellz );
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	<	makeElement( i * cellx + 0.5 * cellx,
1174	<	j * celly + 0.5 * celly,
1278	<	k * cellz );
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	<	makeElement( i * cellx,
1177	<	j * celly + 0.5 * celly,
1178	<	k * cellz + 0.5 * cellz );
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	<	makeElement( i * cellx + 0.5 * cellx,
1184	<	j * celly,
1185	<	k * cellz + 0.5 * cellz );
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	<	if( have_extra ){
1210	<	done = 0;
1209	>	#ifdef IS_MPI
1210	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1211	>	MPIcheckPoint();
1212	>	#endif // is_mpi
1213	>	}
1214
1215	<	int start_ndx;
1216	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1296	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1215	>	void SimSetup::calcSysValues(void){
1216	>	int i;
1217
1218	<	if( i < n_cells ){
1218	>	int* molMembershipArray;
1219
1220	<	if( j < n_cells ){
1221	<	start_ndx = n_cells;
1222	<	}
1223	<	else start_ndx = 0;
1224	<	}
1225	<	else start_ndx = 0;
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	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1231	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1232	>	molMembershipArray = new int[tot_atoms];
1233
1234	<	makeElement( i * cellx,
1235	<	j * celly,
1236	<	k * cellz );
1237	<	done = ( current_mol >= tot_nmol );
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	<	if( !done && n_per_extra > 1 ){
1243	<	makeElement( i * cellx + 0.5 * cellx,
1244	<	j * celly + 0.5 * celly,
1317	<	k * cellz );
1318	<	done = ( current_mol >= tot_nmol );
1319	<	}
1242	>	info[i].molMembershipArray = molMembershipArray;
1243	>	}
1244	>	}
1245
1246	<	if( !done && n_per_extra > 2){
1322	<	makeElement( i * cellx,
1323	<	j * celly + 0.5 * celly,
1324	<	k * cellz + 0.5 * cellz );
1325	<	done = ( current_mol >= tot_nmol );
1326	<	}
1246	>	#ifdef IS_MPI
1247
1248	<	if( !done && n_per_extra > 3){
1249	<	makeElement( i * cellx + 0.5 * cellx,
1250	<	j * celly,
1251	<	k * cellz + 0.5 * cellz );
1252	<	done = ( current_mol >= tot_nmol );
1253	<	}
1254	<	}
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	<	for( i=0; i<simnfo->n_atoms; i++ ){
1293	<	simnfo->atoms[i]->set_vx( 0.0 );
1294	<	simnfo->atoms[i]->set_vy( 0.0 );
1295	<	simnfo->atoms[i]->set_vz( 0.0 );
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	<	void SimSetup::makeElement( double x, double y, double z ){
1311	>	#endif // is_mpi
1312
1349	–	int k;
1350	–	AtomStamp* current_atom;
1351	–	DirectionalAtom* dAtom;
1352	–	double rotMat[3][3];
1313
1314	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1314	>	void SimSetup::makeSysArrays(void){
1315	>
1316	>	#ifndef IS_MPI
1317	>	int k, j;
1318	>	#endif // is_mpi
1319	>	int i, l;
1320
1321	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1322	<	if( !current_atom->havePosition() ){
1323	<	sprintf( painCave.errMsg,
1359	<	"SimSetup:initFromBass error.\n"
1360	<	"\tComponent %s, atom %s does not have a position specified.\n"
1361	<	"\tThe initialization routine is unable to give a start"
1362	<	" position.\n",
1363	<	comp_stamps[current_comp]->getID(),
1364	<	current_atom->getType() );
1365	<	painCave.isFatal = 1;
1366	<	simError();
1367	<	}
1321	>	Atom** the_atoms;
1322	>	Molecule* the_molecules;
1323	>	Exclude** the_excludes;
1324
1369	–	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1370	–	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1371	–	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1325
1326	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1326	>	for (l = 0; l < nInfo; l++){
1327	>	// create the atom and short range interaction arrays
1328
1329	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1329	>	the_atoms = new Atom * [info[l].n_atoms];
1330	>	the_molecules = new Molecule[info[l].n_mol];
1331	>	int molIndex;
1332
1333	<	rotMat[0][0] = 1.0;
1378	<	rotMat[0][1] = 0.0;
1379	<	rotMat[0][2] = 0.0;
1333	>	// initialize the molecule's stampID's
1334
1335	<	rotMat[1][0] = 0.0;
1382	<	rotMat[1][1] = 1.0;
1383	<	rotMat[1][2] = 0.0;
1335	>	#ifdef IS_MPI
1336
1385	–	rotMat[2][0] = 0.0;
1386	–	rotMat[2][1] = 0.0;
1387	–	rotMat[2][2] = 1.0;
1337
1338	<	dAtom->setA( rotMat );
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	<	current_atom_ndx++;
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	<	current_mol++;
1400	<	current_comp_mol++;
1399	>	void SimSetup::makeIntegrator(void){
1400	>	int k;
1401
1402	<	if( current_comp_mol >= components_nmol[current_comp] ){
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	<	current_comp_mol = 0;
1423	<	current_comp++;
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	+	//set zcons gap
1668	+	DoubleData* zconsGap = new DoubleData();
1669	+	zconsGap->setID(ZCONSGAP_ID);
1670	+
1671	+	if (globals->haveZConsGap()){
1672	+	zconsGap->setData(globals->getZconsGap());
1673	+	theInfo.addProperty(zconsGap);
1674	+	}
1675	+
1676	+	//set zcons fixtime
1677	+	DoubleData* zconsFixtime = new DoubleData();
1678	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1679	+
1680	+	if (globals->haveZConsFixTime()){
1681	+	zconsFixtime->setData(globals->getZconsFixtime());
1682	+	theInfo.addProperty(zconsFixtime);
1683	+	}
1684	+
1685	+	//set zconsUsingSMD
1686	+	IntData* zconsUsingSMD = new IntData();
1687	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1688	+
1689	+	if (globals->haveZConsUsingSMD()){
1690	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1691	+	theInfo.addProperty(zconsUsingSMD);
1692	+	}
1693	+
1694	+	//Determine the name of ouput file and add it into SimInfo's property list
1695	+	//Be careful, do not use inFileName, since it is a pointer which
1696	+	//point to a string at master node, and slave nodes do not contain that string
1697	+
1698	+	string zconsOutput(theInfo.finalName);
1699	+
1700	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1701	+
1702	+	StringData* zconsFilename = new StringData();
1703	+	zconsFilename->setID(ZCONSFILENAME_ID);
1704	+	zconsFilename->setData(zconsOutput);
1705	+
1706	+	theInfo.addProperty(zconsFilename);
1707	+
1708	+	//setup index, pos and other parameters of z-constraint molecules
1709	+	nZConstraints = globals->getNzConstraints();
1710	+	theInfo.nZconstraints = nZConstraints;
1711	+
1712	+	zconStamp = globals->getZconStamp();
1713	+	ZConsParaItem tempParaItem;
1714	+
1715	+	ZConsParaData* zconsParaData = new ZConsParaData();
1716	+	zconsParaData->setID(ZCONSPARADATA_ID);
1717	+
1718	+	for (int i = 0; i < nZConstraints; i++){
1719	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1720	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1721	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1722	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1723	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1724	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1725	+	zconsParaData->addItem(tempParaItem);
1726	+	}
1727	+
1728	+	//check the uniqueness of index
1729	+	if(!zconsParaData->isIndexUnique()){
1730	+	sprintf(painCave.errMsg,
1731	+	"ZConstraint Error: molIndex is not unique!\n");
1732	+	painCave.isFatal = 1;
1733	+	simError();
1734	+	}
1735	+
1736	+	//sort the parameters by index of molecules
1737	+	zconsParaData->sortByIndex();
1738	+
1739	+	//push data into siminfo, therefore, we can retrieve later
1740	+	theInfo.addProperty(zconsParaData);
1741	+	}
1742	+
1743	+	void SimSetup::makeMinimizer(){
1744	+
1745	+	OOPSEMinimizer* myOOPSEMinimizer;
1746	+	MinimizerParameterSet* param;
1747	+	char minimizerName[100];
1748	+
1749	+	for (int i = 0; i < nInfo; i++){
1750	+
1751	+	//prepare parameter set for minimizer
1752	+	param = new MinimizerParameterSet();
1753	+	param->setDefaultParameter();
1754	+
1755	+	if (globals->haveMinimizer()){
1756	+	param->setFTol(globals->getMinFTol());
1757	+	}
1758	+
1759	+	if (globals->haveMinGTol()){
1760	+	param->setGTol(globals->getMinGTol());
1761	+	}
1762	+
1763	+	if (globals->haveMinMaxIter()){
1764	+	param->setMaxIteration(globals->getMinMaxIter());
1765	+	}
1766	+
1767	+	if (globals->haveMinWriteFrq()){
1768	+	param->setMaxIteration(globals->getMinMaxIter());
1769	+	}
1770	+
1771	+	if (globals->haveMinWriteFrq()){
1772	+	param->setWriteFrq(globals->getMinWriteFrq());
1773	+	}
1774	+
1775	+	if (globals->haveMinStepSize()){
1776	+	param->setStepSize(globals->getMinStepSize());
1777	+	}
1778	+
1779	+	if (globals->haveMinLSMaxIter()){
1780	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1781	+	}
1782	+
1783	+	if (globals->haveMinLSTol()){
1784	+	param->setLineSearchTol(globals->getMinLSTol());
1785	+	}
1786	+
1787	+	strcpy(minimizerName, globals->getMinimizer());
1788	+
1789	+	if (!strcasecmp(minimizerName, "CG")){
1790	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1791	+	}
1792	+	else if (!strcasecmp(minimizerName, "SD")){
1793	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1794	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1795	+	}
1796	+	else{
1797	+	sprintf(painCave.errMsg,
1798	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1799	+	painCave.isFatal = 0;
1800	+	simError();
1801	+
1802	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1803	+	}
1804	+	info[i].the_integrator = myOOPSEMinimizer;
1805	+
1806	+	//store the minimizer into simInfo
1807	+	info[i].the_minimizer = myOOPSEMinimizer;
1808	+	info[i].has_minimizer = true;
1809	+	}
1810	+
1811	+	}

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