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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 557 by mmeineke, Thu Jun 19 19:11:53 2003 UTC vs.
Revision 1108 by tim, Wed Apr 14 15:37:41 2004 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	#include "RigidBody.hpp"
13	+	//#include "ConjugateMinimizer.hpp"
14	+	#include "OOPSEMinimizer.hpp"
15
16		#ifdef IS_MPI
17		#include "mpiBASS.h"
#	Line 14 | Line 20
20
21		// some defines for ensemble and Forcefield  cases
22
23	<	#define NVE_ENS 0
24	<	#define NVT_ENS 1
25	<	#define NPT_ENS 2
23	>	#define NVE_ENS        0
24	>	#define NVT_ENS        1
25	>	#define NPTi_ENS       2
26	>	#define NPTf_ENS       3
27	>	#define NPTxyz_ENS     4
28
21	–	#define FF_DUFF 0
22	–	#define FF_LJ   1
29
30	+	#define FF_DUFF  0
31	+	#define FF_LJ    1
32	+	#define FF_EAM   2
33	+	#define FF_H2O   3
34
35	+	using namespace std;
36	+
37	+	/**
38	+	* Check whether dividend is divisble by divisor or not
39	+	*/
40	+	bool isDivisible(double dividend, double divisor){
41	+	double tolerance = 0.000001;
42	+	double quotient;
43	+	double diff;
44	+	int intQuotient;
45	+
46	+	quotient = dividend / divisor;
47	+
48	+	if (quotient < 0)
49	+	quotient = -quotient;
50	+
51	+	intQuotient = int (quotient + tolerance);
52	+
53	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
54	+
55	+	if (diff <= tolerance)
56	+	return true;
57	+	else
58	+	return false;
59	+	}
60	+
61		SimSetup::SimSetup(){
62	+
63	+	initSuspend = false;
64	+	isInfoArray = 0;
65	+	nInfo = 1;
66	+
67		stamps = new MakeStamps();
68		globals = new Globals();
69	<
69	>
70	>
71		#ifdef IS_MPI
72	<	strcpy( checkPointMsg, "SimSetup creation successful" );
72	>	strcpy(checkPointMsg, "SimSetup creation successful");
73		MPIcheckPoint();
74		#endif // IS_MPI
75		}
#	Line 37 | Line 79 | SimSetup::~SimSetup(){
79		delete globals;
80		}
81
82	<	void SimSetup::parseFile( char* fileName ){
82	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
83	>	info = the_info;
84	>	nInfo = theNinfo;
85	>	isInfoArray = 1;
86	>	initSuspend = true;
87	>	}
88
89	+
90	+	void SimSetup::parseFile(char* fileName){
91		#ifdef IS_MPI
92	<	if( worldRank == 0 ){
92	>	if (worldRank == 0){
93		#endif // is_mpi
94	<
94	>
95		inFileName = fileName;
96	<	set_interface_stamps( stamps, globals );
97	<
96	>	set_interface_stamps(stamps, globals);
97	>
98		#ifdef IS_MPI
99		mpiEventInit();
100		#endif
101
102	<	yacc_BASS( fileName );
102	>	yacc_BASS(fileName);
103
104		#ifdef IS_MPI
105		throwMPIEvent(NULL);
106		}
107	<	else receiveParse();
107	>	else{
108	>	receiveParse();
109	>	}
110		#endif
111
112		}
113
114		#ifdef IS_MPI
115		void SimSetup::receiveParse(void){
116	<
117	<	set_interface_stamps( stamps, globals );
118	<	mpiEventInit();
119	<	MPIcheckPoint();
69	<	mpiEventLoop();
70	<
116	>	set_interface_stamps(stamps, globals);
117	>	mpiEventInit();
118	>	MPIcheckPoint();
119	>	mpiEventLoop();
120		}
121
122		#endif // is_mpi
123
124	<	void SimSetup::createSim( void ){
124	>	void SimSetup::createSim(void){
125
126	<	MakeStamps *the_stamps;
78	<	Globals* the_globals;
79	<	int i, j, k, globalAtomIndex;
80	<
81	<	int ensembleCase;
82	<	int ffCase;
83	<
84	<	ensembleCase = -1;
85	<	ffCase = -1;
126	>	// gather all of the information from the Bass file
127
128	<	// get the stamps and globals;
88	<	the_stamps = stamps;
89	<	the_globals = globals;
128	>	gatherInfo();
129
130	<	// set the easy ones first
92	<	simnfo->target_temp = the_globals->getTargetTemp();
93	<	simnfo->dt = the_globals->getDt();
94	<	simnfo->run_time = the_globals->getRunTime();
130	>	// creation of complex system objects
131
132	<	// get the ones we know are there, yet still may need some work.
97	<	n_components = the_globals->getNComponents();
98	<	strcpy( force_field, the_globals->getForceField() );
132	>	sysObjectsCreation();
133
134	<	if( !strcasecmp( force_field, "DUFF" ))    ffCase = FF_DUFF;
101	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
102	<	else{
103	<	sprintf( painCave.errMsg,
104	<	"SimSetup Error. Unrecognized force field -> %s\n",
105	<	force_field );
106	<	painCave.isFatal = 1;
107	<	simError();
108	<	}
134	>	// check on the post processing info
135
136	<	// get the ensemble:
111	<	strcpy( ensemble, the_globals->getEnsemble() );
136	>	finalInfoCheck();
137
138	<	if( !strcasecmp( ensemble, "NVE" ))      ffCase = NVE_ENS;
139	<	else if( !strcasecmp( ensemble, "NVT" )) ffCase = NVT_ENS;
140	<	else if( !strcasecmp( ensemble, "NPT" )) ffCase = NPT_ENS;
141	<	else{
142	<	sprintf( painCave.errMsg,
143	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
144	<	"reverting to NVE for this simulation.\n",
120	<	ensemble );
121	<	painCave.isFatal = 0;
122	<	simError();
123	<	strcpy( ensemble, "NVE" );
124	<	ensembleCase = NVE_ENS;
138	>	// initialize the system coordinates
139	>
140	>	if ( !initSuspend ){
141	>	initSystemCoords();
142	>
143	>	if( !(globals->getUseInitTime()) )
144	>	info[0].currentTime = 0.0;
145		}
126	–	strcpy( simnfo->ensemble, ensemble );
146
147	+	// make the output filenames
148
149	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
130	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
131	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
132	<	//     if (the_globals->haveTargetPressure())
133	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
134	<	//     else {
135	<	//       sprintf( painCave.errMsg,
136	<	//                "SimSetup error: If you use the constant pressure\n"
137	<	//                "    ensemble, you must set targetPressure.\n"
138	<	//                "    This was found in the BASS file.\n");
139	<	//       painCave.isFatal = 1;
140	<	//       simError();
141	<	//     }
149	>	makeOutNames();
150
151	<	//     if (the_globals->haveTauThermostat())
152	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
153	<	//     else if (the_globals->haveQmass())
154	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
155	<	//     else {
156	<	//       sprintf( painCave.errMsg,
157	<	//                "SimSetup error: If you use one of the constant temperature\n"
158	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
159	<	//                "    Neither of these was found in the BASS file.\n");
160	<	//       painCave.isFatal = 1;
153	<	//       simError();
154	<	//     }
151	>	if (globals->haveMinimizer())
152	>	// make minimizer
153	>	makeMinimizer();
154	>	else
155	>	// make the integrator
156	>	makeIntegrator();
157	>
158	>	#ifdef IS_MPI
159	>	mpiSim->mpiRefresh();
160	>	#endif
161
162	<	//     if (the_globals->haveTauBarostat())
157	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
158	<	//     else {
159	<	//       sprintf( painCave.errMsg,
160	<	//                "SimSetup error: If you use the constant pressure\n"
161	<	//                "    ensemble, you must set tauBarostat.\n"
162	<	//                "    This was found in the BASS file.\n");
163	<	//       painCave.isFatal = 1;
164	<	//       simError();
165	<	//     }
162	>	// initialize the Fortran
163
164	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
165	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
169	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
164	>	initFortran();
165	>	}
166
171	–	//     if (the_globals->haveTauThermostat())
172	–	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
173	–	//     else if (the_globals->haveQmass())
174	–	//       the_extendedsystem->setQmass(the_globals->getQmass());
175	–	//     else {
176	–	//       sprintf( painCave.errMsg,
177	–	//                "SimSetup error: If you use one of the constant temperature\n"
178	–	//                "    ensembles, you must set either tauThermostat or qMass.\n"
179	–	//                "    Neither of these was found in the BASS file.\n");
180	–	//       painCave.isFatal = 1;
181	–	//       simError();
182	–	//     }
167
168	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
169	<	simnfo->usePBC = the_globals->getPBC();
170	<
171	<	int usesDipoles = 0;
172	<	switch( ffCase ){
168	>	void SimSetup::makeMolecules(void){
169	>	int i, j, k;
170	>	int exI, exJ, exK, exL, slI, slJ;
171	>	int tempI, tempJ, tempK, tempL;
172	>	int molI;
173	>	int stampID, atomOffset, rbOffset;
174	>	molInit molInfo;
175	>	DirectionalAtom* dAtom;
176	>	RigidBody* myRB;
177	>	StuntDouble* mySD;
178	>	LinkedAssign* extras;
179	>	LinkedAssign* current_extra;
180	>	AtomStamp* currentAtom;
181	>	BondStamp* currentBond;
182	>	BendStamp* currentBend;
183	>	TorsionStamp* currentTorsion;
184	>	RigidBodyStamp* currentRigidBody;
185
186	<	case FF_DUFF:
187	<	the_ff = new DUFF();
188	<	usesDipoles = 1;
193	<	break;
186	>	bond_pair* theBonds;
187	>	bend_set* theBends;
188	>	torsion_set* theTorsions;
189
190	<	case FF_LJ:
196	<	the_ff = LJFF();
197	<	break;
190	>	set<int> skipList;
191
192	<	default:
193	<	sprintf( painCave.errMsg,
194	<	"SimSetup Error. Unrecognized force field in case statement.\n");
202	<	painCave.isFatal = 1;
203	<	simError();
204	<	}
192	>	double phi, theta, psi;
193	>	char* molName;
194	>	char rbName[100];
195
196	<	#ifdef IS_MPI
207	<	strcpy( checkPointMsg, "ForceField creation successful" );
208	<	MPIcheckPoint();
209	<	#endif // is_mpi
196	>	//init the forceField paramters
197
198	<	// get the components and calculate the tot_nMol and indvidual n_mol
212	<	the_components = the_globals->getComponents();
213	<	components_nmol = new int[n_components];
214	<	comp_stamps = new MoleculeStamp*[n_components];
198	>	the_ff->readParams();
199
200	<	if( !the_globals->haveNMol() ){
217	<	// we don't have the total number of molecules, so we assume it is
218	<	// given in each component
200	>	// init the atoms
201
202	<	tot_nmol = 0;
221	<	for( i=0; i<n_components; i++ ){
202	>	int nMembers, nNew, rb1, rb2;
203
204	<	if( !the_components[i]->haveNMol() ){
205	<	// we have a problem
206	<	sprintf( painCave.errMsg,
207	<	"SimSetup Error. No global NMol or component NMol"
208	<	" given. Cannot calculate the number of atoms.\n" );
209	<	painCave.isFatal = 1;
210	<	simError();
211	<	}
204	>	for (k = 0; k < nInfo; k++){
205	>	the_ff->setSimInfo(&(info[k]));
206	>
207	>	atomOffset = 0;
208	>
209	>	for (i = 0; i < info[k].n_mol; i++){
210	>	stampID = info[k].molecules[i].getStampID();
211	>	molName = comp_stamps[stampID]->getID();
212	>
213	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
214	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
215	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
216	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
217	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
218	>
219	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
220
221	<	tot_nmol += the_components[i]->getNMol();
222	<	components_nmol[i] = the_components[i]->getNMol();
223	<	}
224	<	}
236	<	else{
237	<	sprintf( painCave.errMsg,
238	<	"SimSetup error.\n"
239	<	"\tSorry, the ability to specify total"
240	<	" nMols and then give molfractions in the components\n"
241	<	"\tis not currently supported."
242	<	" Please give nMol in the components.\n" );
243	<	painCave.isFatal = 1;
244	<	simError();
245	<
246	<
247	<	//     tot_nmol = the_globals->getNMol();
248	<
249	<	//   //we have the total number of molecules, now we check for molfractions
250	<	//     for( i=0; i<n_components; i++ ){
251	<
252	<	//       if( !the_components[i]->haveMolFraction() ){
253	<
254	<	//  if( !the_components[i]->haveNMol() ){
255	<	//    //we have a problem
256	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
257	<	//              << " nMol was given in component
258	<
259	<	}
221	>	if (molInfo.nBonds > 0)
222	>	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
223	>	else
224	>	molInfo.myBonds = NULL;
225
226	<	#ifdef IS_MPI
227	<	strcpy( checkPointMsg, "Have the number of components" );
228	<	MPIcheckPoint();
229	<	#endif // is_mpi
226	>	if (molInfo.nBends > 0)
227	>	molInfo.myBends = new (Bend *) [molInfo.nBends];
228	>	else
229	>	molInfo.myBends = NULL;
230
231	<	// make an array of molecule stamps that match the components used.
232	<	// also extract the used stamps out into a separate linked list
231	>	if (molInfo.nTorsions > 0)
232	>	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
233	>	else
234	>	molInfo.myTorsions = NULL;
235
236	<	simnfo->nComponents = n_components;
237	<	simnfo->componentsNmol = components_nmol;
238	<	simnfo->compStamps = comp_stamps;
272	<	simnfo->headStamp = new LinkedMolStamp();
273	<
274	<	char* id;
275	<	LinkedMolStamp* headStamp = simnfo->headStamp;
276	<	LinkedMolStamp* currentStamp = NULL;
277	<	for( i=0; i<n_components; i++ ){
278	<
279	<	id = the_components[i]->getType();
280	<	comp_stamps[i] = NULL;
281	<
282	<	// check to make sure the component isn't already in the list
283	<
284	<	comp_stamps[i] = headStamp->match( id );
285	<	if( comp_stamps[i] == NULL ){
236	>	theBonds = new bond_pair[molInfo.nBonds];
237	>	theBends = new bend_set[molInfo.nBends];
238	>	theTorsions = new torsion_set[molInfo.nTorsions];
239
240	<	// extract the component from the list;
288	<
289	<	currentStamp = the_stamps->extractMolStamp( id );
290	<	if( currentStamp == NULL ){
291	<	sprintf( painCave.errMsg,
292	<	"SimSetup error: Component \"%s\" was not found in the "
293	<	"list of declared molecules\n",
294	<	id );
295	<	painCave.isFatal = 1;
296	<	simError();
297	<	}
298	<
299	<	headStamp->add( currentStamp );
300	<	comp_stamps[i] = headStamp->match( id );
301	<	}
302	<	}
240	>	// make the Atoms
241
242	<	#ifdef IS_MPI
243	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
306	<	MPIcheckPoint();
307	<	#endif // is_mpi
308	<
242	>	for (j = 0; j < molInfo.nAtoms; j++){
243	>	currentAtom = comp_stamps[stampID]->getAtom(j);
244
245	+	if (currentAtom->haveOrientation()){
246	+	dAtom = new DirectionalAtom((j + atomOffset),
247	+	info[k].getConfiguration());
248	+	info[k].n_oriented++;
249	+	molInfo.myAtoms[j] = dAtom;
250
251	+	// Directional Atoms have standard unit vectors which are oriented
252	+	// in space using the three Euler angles.  We assume the standard
253	+	// unit vector was originally along the z axis below.
254
255	<	// caclulate the number of atoms, bonds, bends and torsions
255	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
256	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
257	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
258
259	<	tot_atoms = 0;
260	<	tot_bonds = 0;
261	<	tot_bends = 0;
262	<	tot_torsions = 0;
318	<	for( i=0; i<n_components; i++ ){
319	<
320	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
321	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
322	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
323	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
324	<	}
259	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
260	>
261	>	}
262	>	else{
263
264	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
264	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
265	>	}
266
267	<	simnfo->n_atoms = tot_atoms;
329	<	simnfo->n_bonds = tot_bonds;
330	<	simnfo->n_bends = tot_bends;
331	<	simnfo->n_torsions = tot_torsions;
332	<	simnfo->n_SRI = tot_SRI;
333	<	simnfo->n_mol = tot_nmol;
334	<
335	<	simnfo->molMembershipArray = new int[tot_atoms];
267	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
268
269		#ifdef IS_MPI
270
271	<	// divide the molecules among processors here.
340	<
341	<	mpiSim = new mpiSimulation( simnfo );
342	<
343	<	globalIndex = mpiSim->divideLabor();
271	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
272
273	<	// set up the local variables
274	<
347	<	int localMol, allMol;
348	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
273	>	#endif // is_mpi
274	>	}
275
276	<	int* mol2proc = mpiSim->getMolToProcMap();
277	<	int* molCompType = mpiSim->getMolComponentType();
278	<
279	<	allMol = 0;
280	<	localMol = 0;
355	<	local_atoms = 0;
356	<	local_bonds = 0;
357	<	local_bends = 0;
358	<	local_torsions = 0;
359	<	globalAtomIndex = 0;
276	>	// make the bonds
277	>	for (j = 0; j < molInfo.nBonds; j++){
278	>	currentBond = comp_stamps[stampID]->getBond(j);
279	>	theBonds[j].a = currentBond->getA() + atomOffset;
280	>	theBonds[j].b = currentBond->getB() + atomOffset;
281
282	+	tempI = theBonds[j].a;
283	+	tempJ = theBonds[j].b;
284
285	<	for( i=0; i<n_components; i++ ){
285	>	#ifdef IS_MPI
286	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
287	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
288	>	#else
289	>	exI = tempI + 1;
290	>	exJ = tempJ + 1;
291	>	#endif
292
293	<	for( j=0; j<components_nmol[i]; j++ ){
365	<
366	<	if( mol2proc[allMol] == worldRank ){
367	<
368	<	local_atoms +=    comp_stamps[i]->getNAtoms();
369	<	local_bonds +=    comp_stamps[i]->getNBonds();
370	<	local_bends +=    comp_stamps[i]->getNBends();
371	<	local_torsions += comp_stamps[i]->getNTorsions();
372	<	localMol++;
373	<	}
374	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
375	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
376	<	globalAtomIndex++;
293	>	info[k].excludes->addPair(exI, exJ);
294		}
295
296	<	allMol++;
297	<	}
298	<	}
299	<	local_SRI = local_bonds + local_bends + local_torsions;
300	<
301	<	simnfo->n_atoms = mpiSim->getMyNlocal();
385	<
386	<	if( local_atoms != simnfo->n_atoms ){
387	<	sprintf( painCave.errMsg,
388	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
389	<	" localAtom (%d) are not equal.\n",
390	<	simnfo->n_atoms,
391	<	local_atoms );
392	<	painCave.isFatal = 1;
393	<	simError();
394	<	}
296	>	//make the bends
297	>	for (j = 0; j < molInfo.nBends; j++){
298	>	currentBend = comp_stamps[stampID]->getBend(j);
299	>	theBends[j].a = currentBend->getA() + atomOffset;
300	>	theBends[j].b = currentBend->getB() + atomOffset;
301	>	theBends[j].c = currentBend->getC() + atomOffset;
302
303	<	simnfo->n_bonds = local_bonds;
304	<	simnfo->n_bends = local_bends;
305	<	simnfo->n_torsions = local_torsions;
399	<	simnfo->n_SRI = local_SRI;
400	<	simnfo->n_mol = localMol;
303	>	if (currentBend->haveExtras()){
304	>	extras = currentBend->getExtras();
305	>	current_extra = extras;
306
307	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
308	<	MPIcheckPoint();
309	<
310	<
311	<	#endif // is_mpi
312	<
307	>	while (current_extra != NULL){
308	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
309	>	switch (current_extra->getType()){
310	>	case 0:
311	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
312	>	theBends[j].isGhost = 1;
313	>	break;
314
315	<	// create the atom and short range interaction arrays
315	>	case 1:
316	>	theBends[j].ghost = (int) current_extra->getDouble() +
317	>	atomOffset;
318	>	theBends[j].isGhost = 1;
319	>	break;
320
321	<	Atom::createArrays(simnfo->n_atoms);
322	<	the_atoms = new Atom*[simnfo->n_atoms];
323	<	the_molecules = new Molecule[simnfo->n_mol];
324	<	int molIndex;
325	<
326	<	// initialize the molecule's stampID's
321	>	default:
322	>	sprintf(painCave.errMsg,
323	>	"SimSetup Error: ghostVectorSource was neither a "
324	>	"double nor an int.\n"
325	>	"-->Bend[%d] in %s\n",
326	>	j, comp_stamps[stampID]->getID());
327	>	painCave.isFatal = 1;
328	>	simError();
329	>	}
330	>	}
331	>	else{
332	>	sprintf(painCave.errMsg,
333	>	"SimSetup Error: unhandled bend assignment:\n"
334	>	"    -->%s in Bend[%d] in %s\n",
335	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
336	>	painCave.isFatal = 1;
337	>	simError();
338	>	}
339
340	+	current_extra = current_extra->getNext();
341	+	}
342	+	}
343	+
344	+	if (theBends[j].isGhost) {
345	+
346	+	tempI = theBends[j].a;
347	+	tempJ = theBends[j].b;
348	+
349		#ifdef IS_MPI
350	<
350	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
351	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
352	>	#else
353	>	exI = tempI + 1;
354	>	exJ = tempJ + 1;
355	>	#endif
356	>	info[k].excludes->addPair(exI, exJ);
357
358	<	molIndex = 0;
422	<	for(i=0; i<mpiSim->getTotNmol(); i++){
423	<
424	<	if(mol2proc[i] == worldRank ){
425	<	the_molecules[molIndex].setStampID( molCompType[i] );
426	<	the_molecules[molIndex].setMyIndex( molIndex );
427	<	the_molecules[molIndex].setGlobalIndex( i );
428	<	molIndex++;
429	<	}
430	<	}
358	>	} else {
359
360	<	#else // is_mpi
361	<
362	<	molIndex = 0;
363	<	globalAtomIndex = 0;
364	<	for(i=0; i<n_components; i++){
365	<	for(j=0; j<components_nmol[i]; j++ ){
366	<	the_molecules[molIndex].setStampID( i );
367	<	the_molecules[molIndex].setMyIndex( molIndex );
368	<	the_molecules[molIndex].setGlobalIndex( molIndex );
369	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
370	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
371	<	globalAtomIndex++;
360	>	tempI = theBends[j].a;
361	>	tempJ = theBends[j].b;
362	>	tempK = theBends[j].c;
363	>
364	>	#ifdef IS_MPI
365	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
366	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
367	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
368	>	#else
369	>	exI = tempI + 1;
370	>	exJ = tempJ + 1;
371	>	exK = tempK + 1;
372	>	#endif
373	>
374	>	info[k].excludes->addPair(exI, exK);
375	>	info[k].excludes->addPair(exI, exJ);
376	>	info[k].excludes->addPair(exJ, exK);
377	>	}
378		}
445	–	molIndex++;
446	–	}
447	–	}
448	–
379
380	<	#endif // is_mpi
380	>	for (j = 0; j < molInfo.nTorsions; j++){
381	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
382	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
383	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
384	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
385	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
386
387	+	tempI = theTorsions[j].a;
388	+	tempJ = theTorsions[j].b;
389	+	tempK = theTorsions[j].c;
390	+	tempL = theTorsions[j].d;
391
392	<	if( simnfo->n_SRI ){
393	<
394	<	Exclude::createArray(simnfo->n_SRI);
395	<	the_excludes = new Exclude*[simnfo->n_SRI];
396	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
397	<	simnfo->globalExcludes = new int;
398	<	simnfo->n_exclude = simnfo->n_SRI;
399	<	}
400	<	else{
401	<
402	<	Exclude::createArray( 1 );
464	<	the_excludes = new Exclude*;
465	<	the_excludes[0] = new Exclude(0);
466	<	the_excludes[0]->setPair( 0,0 );
467	<	simnfo->globalExcludes = new int;
468	<	simnfo->globalExcludes[0] = 0;
469	<	simnfo->n_exclude = 0;
470	<	}
392	>	#ifdef IS_MPI
393	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
394	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
395	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
396	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
397	>	#else
398	>	exI = tempI + 1;
399	>	exJ = tempJ + 1;
400	>	exK = tempK + 1;
401	>	exL = tempL + 1;
402	>	#endif
403
404	<	// set the arrays into the SimInfo object
404	>	info[k].excludes->addPair(exI, exJ);
405	>	info[k].excludes->addPair(exI, exK);
406	>	info[k].excludes->addPair(exI, exL);
407	>	info[k].excludes->addPair(exJ, exK);
408	>	info[k].excludes->addPair(exJ, exL);
409	>	info[k].excludes->addPair(exK, exL);
410	>	}
411
412	<	simnfo->atoms = the_atoms;
475	<	simnfo->molecules = the_molecules;
476	<	simnfo->nGlobalExcludes = 0;
477	<	simnfo->excludes = the_excludes;
412	>	for (j = 0; j < molInfo.nRigidBodies; j++){
413
414	+	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
415	+	nMembers = currentRigidBody->getNMembers();
416
417	<	// get some of the tricky things that may still be in the globals
417	>	// Create the Rigid Body:
418
419	<
483	<	if( the_globals->haveBox() ){
484	<	simnfo->box_x = the_globals->getBox();
485	<	simnfo->box_y = the_globals->getBox();
486	<	simnfo->box_z = the_globals->getBox();
487	<	}
488	<	else if( the_globals->haveDensity() ){
419	>	myRB = new RigidBody();
420
421	<	double vol;
422	<	vol = (double)tot_nmol / the_globals->getDensity();
423	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
424	<	simnfo->box_y = simnfo->box_x;
494	<	simnfo->box_z = simnfo->box_x;
495	<	}
496	<	else{
497	<	if( !the_globals->haveBoxX() ){
498	<	sprintf( painCave.errMsg,
499	<	"SimSetup error, no periodic BoxX size given.\n" );
500	<	painCave.isFatal = 1;
501	<	simError();
502	<	}
503	<	simnfo->box_x = the_globals->getBoxX();
421	>	sprintf(rbName,"%s_RB_%s", molName, j);
422	>	myRB->setType(rbName);
423	>
424	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
425
426	<	if( !the_globals->haveBoxY() ){
427	<	sprintf( painCave.errMsg,
507	<	"SimSetup error, no periodic BoxY size given.\n" );
508	<	painCave.isFatal = 1;
509	<	simError();
510	<	}
511	<	simnfo->box_y = the_globals->getBoxY();
426	>	// molI is atom numbering inside this molecule
427	>	molI = currentRigidBody->getMember(rb1);
428
429	<	if( !the_globals->haveBoxZ() ){
430	<	sprintf( painCave.errMsg,
515	<	"SimSetup error, no periodic BoxZ size given.\n" );
516	<	painCave.isFatal = 1;
517	<	simError();
518	<	}
519	<	simnfo->box_z = the_globals->getBoxZ();
520	<	}
429	>	// tempI is atom numbering on local processor
430	>	tempI = molI + atomOffset;
431
432	+	// currentAtom is the AtomStamp (which we need for
433	+	// rigid body reference positions)
434	+	currentAtom = comp_stamps[stampID]->getAtom(molI);
435	+
436	+	// When we add to the rigid body, add the atom itself and
437	+	// the stamp info:
438	+
439	+	myRB->addAtom(info[k].atoms[tempI], currentAtom);
440	+
441	+	// Add this atom to the Skip List for the integrators
442		#ifdef IS_MPI
443	<	strcpy( checkPointMsg, "Box size set up" );
444	<	MPIcheckPoint();
445	<	#endif // is_mpi
443	>	slI = info[k].atoms[tempI]->getGlobalIndex();
444	>	#else
445	>	slI = tempI;
446	>	#endif
447	>	skipList.insert(slI);
448	>
449	>	}
450	>
451	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
452	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
453	>
454	>	tempI = currentRigidBody->getMember(rb1);
455	>	tempJ = currentRigidBody->getMember(rb2);
456	>
457	>	// Some explanation is required here.
458	>	// Fortran indexing starts at 1, while c indexing starts at 0
459	>	// Also, in parallel computations, the GlobalIndex is
460	>	// used for the exclude list:
461	>
462	>	#ifdef IS_MPI
463	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
464	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
465	>	#else
466	>	exI = tempI + 1;
467	>	exJ = tempJ + 1;
468	>	#endif
469	>
470	>	info[k].excludes->addPair(exI, exJ);
471	>
472	>	}
473	>	}
474
475	+	molInfo.myRigidBodies.push_back(myRB);
476	+	info[k].rigidBodies.push_back(myRB);
477	+	}
478	+
479
480	<	// initialize the arrays
480	>	// After this is all set up, scan through the atoms to
481	>	// see if they can be added to the integrableObjects:
482
483	<	the_ff->setSimInfo( simnfo );
483	>	for (j = 0; j < molInfo.nAtoms; j++){
484
485	<	makeMolecules();
486	<	simnfo->identArray = new int[simnfo->n_atoms];
487	<	for(i=0; i<simnfo->n_atoms; i++){
488	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
489	<	}
537	<
538	<	if (the_globals->getUseRF() ) {
539	<	simnfo->useReactionField = 1;
540	<
541	<	if( !the_globals->haveECR() ){
542	<	sprintf( painCave.errMsg,
543	<	"SimSetup Warning: using default value of 1/2 the smallest "
544	<	"box length for the electrostaticCutoffRadius.\n"
545	<	"I hope you have a very fast processor!\n");
546	<	painCave.isFatal = 0;
547	<	simError();
548	<	double smallest;
549	<	smallest = simnfo->box_x;
550	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
551	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
552	<	simnfo->ecr = 0.5 * smallest;
553	<	} else {
554	<	simnfo->ecr        = the_globals->getECR();
555	<	}
485	>	#ifdef IS_MPI
486	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
487	>	#else
488	>	slJ = j+atomOffset;
489	>	#endif
490
491	<	if( !the_globals->haveEST() ){
492	<	sprintf( painCave.errMsg,
493	<	"SimSetup Warning: using default value of 0.05 * the "
494	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
495	<	);
496	<	painCave.isFatal = 0;
497	<	simError();
498	<	simnfo->est = 0.05 * simnfo->ecr;
499	<	} else {
500	<	simnfo->est        = the_globals->getEST();
501	<	}
491	>	// if they aren't on the skip list, then they can be integrated
492	>
493	>	if (skipList.find(slJ) == skipList.end()) {
494	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
495	>	info[k].integrableObjects.push_back(mySD);
496	>	molInfo.myIntegrableObjects.push_back(mySD);
497	>	}
498	>	}
499	>
500	>	// all rigid bodies are integrated:
501	>
502	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
503	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
504	>	info[k].integrableObjects.push_back(mySD);
505	>	molInfo.myIntegrableObjects.push_back(mySD);
506	>	}
507
569	–	if(!the_globals->haveDielectric() ){
570	–	sprintf( painCave.errMsg,
571	–	"SimSetup Error: You are trying to use Reaction Field without"
572	–	"setting a dielectric constant!\n"
573	–	);
574	–	painCave.isFatal = 1;
575	–	simError();
576	–	}
577	–	simnfo->dielectric = the_globals->getDielectric();
578	–	} else {
579	–	if (usesDipoles) {
508
509	<	if( !the_globals->haveECR() ){
582	<	sprintf( painCave.errMsg,
583	<	"SimSetup Warning: using default value of 1/2 the smallest "
584	<	"box length for the electrostaticCutoffRadius.\n"
585	<	"I hope you have a very fast processor!\n");
586	<	painCave.isFatal = 0;
587	<	simError();
588	<	double smallest;
589	<	smallest = simnfo->box_x;
590	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
591	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
592	<	simnfo->ecr = 0.5 * smallest;
593	<	} else {
594	<	simnfo->ecr        = the_globals->getECR();
595	<	}
509	>	// send the arrays off to the forceField for init.
510
511	<	if( !the_globals->haveEST() ){
512	<	sprintf( painCave.errMsg,
513	<	"SimSetup Warning: using default value of 5%% of the "
514	<	"electrostaticCutoffRadius for the "
515	<	"electrostaticSkinThickness\n"
602	<	);
603	<	painCave.isFatal = 0;
604	<	simError();
605	<	simnfo->est = 0.05 * simnfo->ecr;
606	<	} else {
607	<	simnfo->est        = the_globals->getEST();
608	<	}
609	<	}
610	<	}
511	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
512	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
513	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
514	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
515	>	theTorsions);
516
517	<	#ifdef IS_MPI
613	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
614	<	MPIcheckPoint();
615	<	#endif // is_mpi
517	>	info[k].molecules[i].initialize(molInfo);
518
617	–	if( the_globals->haveInitialConfig() ){
618	–
619	–	InitializeFromFile* fileInit;
620	–	#ifdef IS_MPI // is_mpi
621	–	if( worldRank == 0 ){
622	–	#endif //is_mpi
623	–	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
624	–	#ifdef IS_MPI
625	–	}else fileInit = new InitializeFromFile( NULL );
626	–	#endif
627	–	fileInit->read_xyz( simnfo ); // default velocities on
519
520	<	delete fileInit;
521	<	}
522	<	else{
520	>	atomOffset += molInfo.nAtoms;
521	>	delete[] theBonds;
522	>	delete[] theBends;
523	>	delete[] theTorsions;
524	>	}
525	>	}
526
633	–	#ifdef IS_MPI
634	–
635	–	// no init from bass
636	–
637	–	sprintf( painCave.errMsg,
638	–	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
639	–	painCave.isFatal;
640	–	simError();
641	–
642	–	#else
643	–
644	–	initFromBass();
645	–
646	–
647	–	#endif
648	–	}
649	–
527		#ifdef IS_MPI
528	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
528	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
529		MPIcheckPoint();
530		#endif // is_mpi
531
532	+	// clean up the forcefield
533
534	<
657	<
658	<
534	>	if (!globals->haveLJrcut()){
535
536	<
537	<	#ifdef IS_MPI
538	<	if( worldRank == 0 ){
663	<	#endif // is_mpi
536	>	the_ff->calcRcut();
537	>
538	>	} else {
539
540	<	if( the_globals->haveFinalConfig() ){
666	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
667	<	}
668	<	else{
669	<	strcpy( simnfo->finalName, inFileName );
670	<	char* endTest;
671	<	int nameLength = strlen( simnfo->finalName );
672	<	endTest = &(simnfo->finalName[nameLength - 5]);
673	<	if( !strcmp( endTest, ".bass" ) ){
674	<	strcpy( endTest, ".eor" );
675	<	}
676	<	else if( !strcmp( endTest, ".BASS" ) ){
677	<	strcpy( endTest, ".eor" );
678	<	}
679	<	else{
680	<	endTest = &(simnfo->finalName[nameLength - 4]);
681	<	if( !strcmp( endTest, ".bss" ) ){
682	<	strcpy( endTest, ".eor" );
683	<	}
684	<	else if( !strcmp( endTest, ".mdl" ) ){
685	<	strcpy( endTest, ".eor" );
686	<	}
687	<	else{
688	<	strcat( simnfo->finalName, ".eor" );
689	<	}
690	<	}
691	<	}
692	<
693	<	// make the sample and status out names
694	<
695	<	strcpy( simnfo->sampleName, inFileName );
696	<	char* endTest;
697	<	int nameLength = strlen( simnfo->sampleName );
698	<	endTest = &(simnfo->sampleName[nameLength - 5]);
699	<	if( !strcmp( endTest, ".bass" ) ){
700	<	strcpy( endTest, ".dump" );
701	<	}
702	<	else if( !strcmp( endTest, ".BASS" ) ){
703	<	strcpy( endTest, ".dump" );
704	<	}
705	<	else{
706	<	endTest = &(simnfo->sampleName[nameLength - 4]);
707	<	if( !strcmp( endTest, ".bss" ) ){
708	<	strcpy( endTest, ".dump" );
709	<	}
710	<	else if( !strcmp( endTest, ".mdl" ) ){
711	<	strcpy( endTest, ".dump" );
712	<	}
713	<	else{
714	<	strcat( simnfo->sampleName, ".dump" );
715	<	}
716	<	}
717	<
718	<	strcpy( simnfo->statusName, inFileName );
719	<	nameLength = strlen( simnfo->statusName );
720	<	endTest = &(simnfo->statusName[nameLength - 5]);
721	<	if( !strcmp( endTest, ".bass" ) ){
722	<	strcpy( endTest, ".stat" );
723	<	}
724	<	else if( !strcmp( endTest, ".BASS" ) ){
725	<	strcpy( endTest, ".stat" );
726	<	}
727	<	else{
728	<	endTest = &(simnfo->statusName[nameLength - 4]);
729	<	if( !strcmp( endTest, ".bss" ) ){
730	<	strcpy( endTest, ".stat" );
731	<	}
732	<	else if( !strcmp( endTest, ".mdl" ) ){
733	<	strcpy( endTest, ".stat" );
734	<	}
735	<	else{
736	<	strcat( simnfo->statusName, ".stat" );
737	<	}
738	<	}
739	<
740	<	#ifdef IS_MPI
540	>	the_ff->setRcut( globals->getLJrcut() );
541		}
742	–	#endif // is_mpi
743	–
744	–	// set the status, sample, and themal kick times
745	–
746	–	if( the_globals->haveSampleTime() ){
747	–	simnfo->sampleTime = the_globals->getSampleTime();
748	–	simnfo->statusTime = simnfo->sampleTime;
749	–	simnfo->thermalTime = simnfo->sampleTime;
750	–	}
751	–	else{
752	–	simnfo->sampleTime = the_globals->getRunTime();
753	–	simnfo->statusTime = simnfo->sampleTime;
754	–	simnfo->thermalTime = simnfo->sampleTime;
755	–	}
542
543	<	if( the_globals->haveStatusTime() ){
544	<	simnfo->statusTime = the_globals->getStatusTime();
759	<	}
543	>	the_ff->cleanMe();
544	>	}
545
546	<	if( the_globals->haveThermalTime() ){
547	<	simnfo->thermalTime = the_globals->getThermalTime();
548	<	}
546	>	void SimSetup::initFromBass(void){
547	>	int i, j, k;
548	>	int n_cells;
549	>	double cellx, celly, cellz;
550	>	double temp1, temp2, temp3;
551	>	int n_per_extra;
552	>	int n_extra;
553	>	int have_extra, done;
554
555	<	// check for the temperature set flag
555	>	double vel[3];
556	>	vel[0] = 0.0;
557	>	vel[1] = 0.0;
558	>	vel[2] = 0.0;
559
560	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
560	>	temp1 = (double) tot_nmol / 4.0;
561	>	temp2 = pow(temp1, (1.0 / 3.0));
562	>	temp3 = ceil(temp2);
563
564	+	have_extra = 0;
565	+	if (temp2 < temp3){
566	+	// we have a non-complete lattice
567	+	have_extra = 1;
568
569	<	// make the integrator
569	>	n_cells = (int) temp3 - 1;
570	>	cellx = info[0].boxL[0] / temp3;
571	>	celly = info[0].boxL[1] / temp3;
572	>	cellz = info[0].boxL[2] / temp3;
573	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
574	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
575	>	n_per_extra = (int) ceil(temp1);
576
577	<
578	<	if( !strcmp( ensemble, "TraPPE_Ex" ) ){
579	<	new Symplectic(simnfo, the_ff, the_extendedsystem);
580	<	}
776	<	else if( !strcmp( force_field, "LJ" ) ){
777	<	new Verlet( *simnfo, the_ff, the_extendedsystem );
778	<	}
779	<
780	<	#ifdef IS_MPI
781	<	mpiSim->mpiRefresh();
782	<	#endif
783	<
784	<	// initialize the Fortran
785	<
786	<
787	<	simnfo->refreshSim();
788	<
789	<	if( !strcmp( simnfo->mixingRule, "standard") ){
790	<	the_ff->initForceField( LB_MIXING_RULE );
791	<	}
792	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
793	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
794	<	}
795	<	else{
796	<	sprintf( painCave.errMsg,
797	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
798	<	simnfo->mixingRule );
799	<	painCave.isFatal = 1;
800	<	simError();
801	<	}
802	<
803	<
804	<	#ifdef IS_MPI
805	<	strcpy( checkPointMsg,
806	<	"Successfully intialized the mixingRule for Fortran." );
807	<	MPIcheckPoint();
808	<	#endif // is_mpi
809	<	}
810	<
811	<
812	<	void SimSetup::makeMolecules( void ){
813	<
814	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
815	<	molInit info;
816	<	DirectionalAtom* dAtom;
817	<	LinkedAssign* extras;
818	<	LinkedAssign* current_extra;
819	<	AtomStamp* currentAtom;
820	<	BondStamp* currentBond;
821	<	BendStamp* currentBend;
822	<	TorsionStamp* currentTorsion;
823	<
824	<	bond_pair* theBonds;
825	<	bend_set* theBends;
826	<	torsion_set* theTorsions;
827	<
828	<
829	<	//init the forceField paramters
830	<
831	<	the_ff->readParams();
832	<
833	<
834	<	// init the atoms
835	<
836	<	double ux, uy, uz, u, uSqr;
837	<
838	<	atomOffset = 0;
839	<	excludeOffset = 0;
840	<	for(i=0; i<simnfo->n_mol; i++){
841	<
842	<	stampID = the_molecules[i].getStampID();
843	<
844	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
845	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
846	<	info.nBends    = comp_stamps[stampID]->getNBends();
847	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
848	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
849	<
850	<	info.myAtoms = &the_atoms[atomOffset];
851	<	info.myExcludes = &the_excludes[excludeOffset];
852	<	info.myBonds = new Bond*[info.nBonds];
853	<	info.myBends = new Bend*[info.nBends];
854	<	info.myTorsions = new Torsion*[info.nTorsions];
855	<
856	<	theBonds = new bond_pair[info.nBonds];
857	<	theBends = new bend_set[info.nBends];
858	<	theTorsions = new torsion_set[info.nTorsions];
859	<
860	<	// make the Atoms
861	<
862	<	for(j=0; j<info.nAtoms; j++){
863	<
864	<	currentAtom = comp_stamps[stampID]->getAtom( j );
865	<	if( currentAtom->haveOrientation() ){
866	<
867	<	dAtom = new DirectionalAtom(j + atomOffset);
868	<	simnfo->n_oriented++;
869	<	info.myAtoms[j] = dAtom;
870	<
871	<	ux = currentAtom->getOrntX();
872	<	uy = currentAtom->getOrntY();
873	<	uz = currentAtom->getOrntZ();
874	<
875	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
876	<
877	<	u = sqrt( uSqr );
878	<	ux = ux / u;
879	<	uy = uy / u;
880	<	uz = uz / u;
881	<
882	<	dAtom->setSUx( ux );
883	<	dAtom->setSUy( uy );
884	<	dAtom->setSUz( uz );
885	<	}
886	<	else{
887	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
888	<	}
889	<	info.myAtoms[j]->setType( currentAtom->getType() );
890	<
891	<	#ifdef IS_MPI
892	<
893	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
894	<
895	<	#endif // is_mpi
896	<	}
897	<
898	<	// make the bonds
899	<	for(j=0; j<info.nBonds; j++){
900	<
901	<	currentBond = comp_stamps[stampID]->getBond( j );
902	<	theBonds[j].a = currentBond->getA() + atomOffset;
903	<	theBonds[j].b = currentBond->getB() + atomOffset;
904	<
905	<	exI = theBonds[j].a;
906	<	exJ = theBonds[j].b;
907	<
908	<	// exclude_I must always be the smaller of the pair
909	<	if( exI > exJ ){
910	<	tempEx = exI;
911	<	exI = exJ;
912	<	exJ = tempEx;
913	<	}
914	<	#ifdef IS_MPI
915	<	tempEx = exI;
916	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
917	<	tempEx = exJ;
918	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
919	<
920	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
921	<	#else  // isn't MPI
922	<
923	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
924	<	#endif  //is_mpi
925	<	}
926	<	excludeOffset += info.nBonds;
927	<
928	<	//make the bends
929	<	for(j=0; j<info.nBends; j++){
930	<
931	<	currentBend = comp_stamps[stampID]->getBend( j );
932	<	theBends[j].a = currentBend->getA() + atomOffset;
933	<	theBends[j].b = currentBend->getB() + atomOffset;
934	<	theBends[j].c = currentBend->getC() + atomOffset;
935	<
936	<	if( currentBend->haveExtras() ){
937	<
938	<	extras = currentBend->getExtras();
939	<	current_extra = extras;
940	<
941	<	while( current_extra != NULL ){
942	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
943	<
944	<	switch( current_extra->getType() ){
945	<
946	<	case 0:
947	<	theBends[j].ghost =
948	<	current_extra->getInt() + atomOffset;
949	<	theBends[j].isGhost = 1;
950	<	break;
951	<
952	<	case 1:
953	<	theBends[j].ghost =
954	<	(int)current_extra->getDouble() + atomOffset;
955	<	theBends[j].isGhost = 1;
956	<	break;
957	<
958	<	default:
959	<	sprintf( painCave.errMsg,
960	<	"SimSetup Error: ghostVectorSource was neither a "
961	<	"double nor an int.\n"
962	<	"-->Bend[%d] in %s\n",
963	<	j, comp_stamps[stampID]->getID() );
964	<	painCave.isFatal = 1;
965	<	simError();
966	<	}
967	<	}
968	<
969	<	else{
970	<
971	<	sprintf( painCave.errMsg,
972	<	"SimSetup Error: unhandled bend assignment:\n"
973	<	"    -->%s in Bend[%d] in %s\n",
974	<	current_extra->getlhs(),
975	<	j, comp_stamps[stampID]->getID() );
976	<	painCave.isFatal = 1;
977	<	simError();
978	<	}
979	<
980	<	current_extra = current_extra->getNext();
981	<	}
982	<	}
983	<
984	<	if( !theBends[j].isGhost ){
985	<
986	<	exI = theBends[j].a;
987	<	exJ = theBends[j].c;
988	<	}
989	<	else{
990	<
991	<	exI = theBends[j].a;
992	<	exJ = theBends[j].b;
993	<	}
994	<
995	<	// exclude_I must always be the smaller of the pair
996	<	if( exI > exJ ){
997	<	tempEx = exI;
998	<	exI = exJ;
999	<	exJ = tempEx;
1000	<	}
1001	<	#ifdef IS_MPI
1002	<	tempEx = exI;
1003	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1004	<	tempEx = exJ;
1005	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1006	<
1007	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1008	<	#else  // isn't MPI
1009	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1010	<	#endif  //is_mpi
1011	<	}
1012	<	excludeOffset += info.nBends;
1013	<
1014	<	for(j=0; j<info.nTorsions; j++){
1015	<
1016	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1017	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1018	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1019	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1020	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1021	<
1022	<	exI = theTorsions[j].a;
1023	<	exJ = theTorsions[j].d;
1024	<
1025	<	// exclude_I must always be the smaller of the pair
1026	<	if( exI > exJ ){
1027	<	tempEx = exI;
1028	<	exI = exJ;
1029	<	exJ = tempEx;
1030	<	}
1031	<	#ifdef IS_MPI
1032	<	tempEx = exI;
1033	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1034	<	tempEx = exJ;
1035	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1036	<
1037	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1038	<	#else  // isn't MPI
1039	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1040	<	#endif  //is_mpi
1041	<	}
1042	<	excludeOffset += info.nTorsions;
1043	<
1044	<
1045	<	// send the arrays off to the forceField for init.
1046	<
1047	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1048	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1049	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1050	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1051	<
1052	<
1053	<	the_molecules[i].initialize( info );
1054	<
1055	<
1056	<	atomOffset += info.nAtoms;
1057	<	delete[] theBonds;
1058	<	delete[] theBends;
1059	<	delete[] theTorsions;
1060	<	}
1061	<
1062	<	#ifdef IS_MPI
1063	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1064	<	MPIcheckPoint();
1065	<	#endif // is_mpi
1066	<
1067	<	// clean up the forcefield
1068	<	the_ff->calcRcut();
1069	<	the_ff->cleanMe();
1070	<
1071	<	}
1072	<
1073	<	void SimSetup::initFromBass( void ){
1074	<
1075	<	int i, j, k;
1076	<	int n_cells;
1077	<	double cellx, celly, cellz;
1078	<	double temp1, temp2, temp3;
1079	<	int n_per_extra;
1080	<	int n_extra;
1081	<	int have_extra, done;
1082	<
1083	<	temp1 = (double)tot_nmol / 4.0;
1084	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1085	<	temp3 = ceil( temp2 );
1086	<
1087	<	have_extra =0;
1088	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1089	<	have_extra =1;
1090	<
1091	<	n_cells = (int)temp3 - 1;
1092	<	cellx = simnfo->box_x / temp3;
1093	<	celly = simnfo->box_y / temp3;
1094	<	cellz = simnfo->box_z / temp3;
1095	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1096	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1097	<	n_per_extra = (int)ceil( temp1 );
1098	<
1099	<	if( n_per_extra > 4){
1100	<	sprintf( painCave.errMsg,
1101	<	"SimSetup error. There has been an error in constructing"
1102	<	" the non-complete lattice.\n" );
577	>	if (n_per_extra > 4){
578	>	sprintf(painCave.errMsg,
579	>	"SimSetup error. There has been an error in constructing"
580	>	" the non-complete lattice.\n");
581		painCave.isFatal = 1;
582		simError();
583		}
584		}
585		else{
586	<	n_cells = (int)temp3;
587	<	cellx = simnfo->box_x / temp3;
588	<	celly = simnfo->box_y / temp3;
589	<	cellz = simnfo->box_z / temp3;
586	>	n_cells = (int) temp3;
587	>	cellx = info[0].boxL[0] / temp3;
588	>	celly = info[0].boxL[1] / temp3;
589	>	cellz = info[0].boxL[2] / temp3;
590		}
591
592		current_mol = 0;
#	Line 1116 | Line 594 | void SimSetup::initFromBass( void ){
594		current_comp = 0;
595		current_atom_ndx = 0;
596
597	<	for( i=0; i < n_cells ; i++ ){
598	<	for( j=0; j < n_cells; j++ ){
599	<	for( k=0; k < n_cells; k++ ){
597	>	for (i = 0; i < n_cells ; i++){
598	>	for (j = 0; j < n_cells; j++){
599	>	for (k = 0; k < n_cells; k++){
600	>	makeElement(i * cellx, j * celly, k * cellz);
601
602	<	makeElement( i * cellx,
1124	<	j * celly,
1125	<	k * cellz );
602	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
603
604	<	makeElement( i * cellx + 0.5 * cellx,
1128	<	j * celly + 0.5 * celly,
1129	<	k * cellz );
604	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
605
606	<	makeElement( i * cellx,
1132	<	j * celly + 0.5 * celly,
1133	<	k * cellz + 0.5 * cellz );
1134	<
1135	<	makeElement( i * cellx + 0.5 * cellx,
1136	<	j * celly,
1137	<	k * cellz + 0.5 * cellz );
606	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
607		}
608		}
609		}
610
611	<	if( have_extra ){
611	>	if (have_extra){
612		done = 0;
613
614		int start_ndx;
615	<	for( i=0; i < (n_cells+1) && !done; i++ ){
616	<	for( j=0; j < (n_cells+1) && !done; j++ ){
615	>	for (i = 0; i < (n_cells + 1) && !done; i++){
616	>	for (j = 0; j < (n_cells + 1) && !done; j++){
617	>	if (i < n_cells){
618	>	if (j < n_cells){
619	>	start_ndx = n_cells;
620	>	}
621	>	else
622	>	start_ndx = 0;
623	>	}
624	>	else
625	>	start_ndx = 0;
626
627	<	if( i < n_cells ){
627	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
628	>	makeElement(i * cellx, j * celly, k * cellz);
629	>	done = (current_mol >= tot_nmol);
630
631	<	if( j < n_cells ){
632	<	start_ndx = n_cells;
633	<	}
634	<	else start_ndx = 0;
635	<	}
1156	<	else start_ndx = 0;
631	>	if (!done && n_per_extra > 1){
632	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
633	>	k * cellz);
634	>	done = (current_mol >= tot_nmol);
635	>	}
636
637	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
637	>	if (!done && n_per_extra > 2){
638	>	makeElement(i * cellx, j * celly + 0.5 * celly,
639	>	k * cellz + 0.5 * cellz);
640	>	done = (current_mol >= tot_nmol);
641	>	}
642
643	<	makeElement( i * cellx,
644	<	j * celly,
645	<	k * cellz );
646	<	done = ( current_mol >= tot_nmol );
647	<
648	<	if( !done && n_per_extra > 1 ){
1166	<	makeElement( i * cellx + 0.5 * cellx,
1167	<	j * celly + 0.5 * celly,
1168	<	k * cellz );
1169	<	done = ( current_mol >= tot_nmol );
1170	<	}
1171	<
1172	<	if( !done && n_per_extra > 2){
1173	<	makeElement( i * cellx,
1174	<	j * celly + 0.5 * celly,
1175	<	k * cellz + 0.5 * cellz );
1176	<	done = ( current_mol >= tot_nmol );
1177	<	}
1178	<
1179	<	if( !done && n_per_extra > 3){
1180	<	makeElement( i * cellx + 0.5 * cellx,
1181	<	j * celly,
1182	<	k * cellz + 0.5 * cellz );
1183	<	done = ( current_mol >= tot_nmol );
1184	<	}
1185	<	}
643	>	if (!done && n_per_extra > 3){
644	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
645	>	k * cellz + 0.5 * cellz);
646	>	done = (current_mol >= tot_nmol);
647	>	}
648	>	}
649		}
650		}
651		}
652
653	<
654	<	for( i=0; i<simnfo->n_atoms; i++ ){
1192	<	simnfo->atoms[i]->set_vx( 0.0 );
1193	<	simnfo->atoms[i]->set_vy( 0.0 );
1194	<	simnfo->atoms[i]->set_vz( 0.0 );
653	>	for (i = 0; i < info[0].n_atoms; i++){
654	>	info[0].atoms[i]->setVel(vel);
655		}
656		}
657
658	<	void SimSetup::makeElement( double x, double y, double z ){
1199	<
658	>	void SimSetup::makeElement(double x, double y, double z){
659		int k;
660		AtomStamp* current_atom;
661		DirectionalAtom* dAtom;
662		double rotMat[3][3];
663	+	double pos[3];
664
665	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
666	<
667	<	current_atom = comp_stamps[current_comp]->getAtom( k );
668	<	if( !current_atom->havePosition() ){
669	<	sprintf( painCave.errMsg,
670	<	"SimSetup:initFromBass error.\n"
671	<	"\tComponent %s, atom %s does not have a position specified.\n"
672	<	"\tThe initialization routine is unable to give a start"
673	<	" position.\n",
1214	<	comp_stamps[current_comp]->getID(),
1215	<	current_atom->getType() );
665	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
666	>	current_atom = comp_stamps[current_comp]->getAtom(k);
667	>	if (!current_atom->havePosition()){
668	>	sprintf(painCave.errMsg,
669	>	"SimSetup:initFromBass error.\n"
670	>	"\tComponent %s, atom %s does not have a position specified.\n"
671	>	"\tThe initialization routine is unable to give a start"
672	>	" position.\n",
673	>	comp_stamps[current_comp]->getID(), current_atom->getType());
674		painCave.isFatal = 1;
675		simError();
676		}
677
678	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
679	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
680	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
678	>	pos[0] = x + current_atom->getPosX();
679	>	pos[1] = y + current_atom->getPosY();
680	>	pos[2] = z + current_atom->getPosZ();
681
682	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
682	>	info[0].atoms[current_atom_ndx]->setPos(pos);
683
684	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
684	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
685	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
686
687		rotMat[0][0] = 1.0;
688		rotMat[0][1] = 0.0;
#	Line 1237 | Line 696 | void SimSetup::makeElement( double x, double y, double
696		rotMat[2][1] = 0.0;
697		rotMat[2][2] = 1.0;
698
699	<	dAtom->setA( rotMat );
699	>	dAtom->setA(rotMat);
700		}
701
702		current_atom_ndx++;
#	Line 1246 | Line 705 | void SimSetup::makeElement( double x, double y, double
705		current_mol++;
706		current_comp_mol++;
707
708	<	if( current_comp_mol >= components_nmol[current_comp] ){
1250	<
708	>	if (current_comp_mol >= components_nmol[current_comp]){
709		current_comp_mol = 0;
710		current_comp++;
711	+	}
712	+	}
713	+
714	+
715	+	void SimSetup::gatherInfo(void){
716	+	int i;
717	+
718	+	ensembleCase = -1;
719	+	ffCase = -1;
720	+
721	+	// set the easy ones first
722	+
723	+	for (i = 0; i < nInfo; i++){
724	+	info[i].target_temp = globals->getTargetTemp();
725	+	info[i].dt = globals->getDt();
726	+	info[i].run_time = globals->getRunTime();
727	+	}
728	+	n_components = globals->getNComponents();
729	+
730	+
731	+	// get the forceField
732	+
733	+	strcpy(force_field, globals->getForceField());
734	+
735	+	if (!strcasecmp(force_field, "DUFF")){
736	+	ffCase = FF_DUFF;
737	+	}
738	+	else if (!strcasecmp(force_field, "LJ")){
739	+	ffCase = FF_LJ;
740	+	}
741	+	else if (!strcasecmp(force_field, "EAM")){
742	+	ffCase = FF_EAM;
743	+	}
744	+	else if (!strcasecmp(force_field, "WATER")){
745	+	ffCase = FF_H2O;
746	+	}
747	+	else{
748	+	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
749	+	force_field);
750	+	painCave.isFatal = 1;
751	+	simError();
752	+	}
753	+
754	+	// get the ensemble
755	+
756	+	strcpy(ensemble, globals->getEnsemble());
757	+
758	+	if (!strcasecmp(ensemble, "NVE")){
759	+	ensembleCase = NVE_ENS;
760	+	}
761	+	else if (!strcasecmp(ensemble, "NVT")){
762	+	ensembleCase = NVT_ENS;
763	+	}
764	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
765	+	ensembleCase = NPTi_ENS;
766	+	}
767	+	else if (!strcasecmp(ensemble, "NPTf")){
768	+	ensembleCase = NPTf_ENS;
769	+	}
770	+	else if (!strcasecmp(ensemble, "NPTxyz")){
771	+	ensembleCase = NPTxyz_ENS;
772	+	}
773	+	else{
774	+	sprintf(painCave.errMsg,
775	+	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
776	+	"\treverting to NVE for this simulation.\n",
777	+	ensemble);
778	+	painCave.isFatal = 0;
779	+	simError();
780	+	strcpy(ensemble, "NVE");
781	+	ensembleCase = NVE_ENS;
782	+	}
783	+
784	+	for (i = 0; i < nInfo; i++){
785	+	strcpy(info[i].ensemble, ensemble);
786	+
787	+	// get the mixing rule
788	+
789	+	strcpy(info[i].mixingRule, globals->getMixingRule());
790	+	info[i].usePBC = globals->getPBC();
791	+	}
792	+
793	+	// get the components and calculate the tot_nMol and indvidual n_mol
794	+
795	+	the_components = globals->getComponents();
796	+	components_nmol = new int[n_components];
797	+
798	+
799	+	if (!globals->haveNMol()){
800	+	// we don't have the total number of molecules, so we assume it is
801	+	// given in each component
802	+
803	+	tot_nmol = 0;
804	+	for (i = 0; i < n_components; i++){
805	+	if (!the_components[i]->haveNMol()){
806	+	// we have a problem
807	+	sprintf(painCave.errMsg,
808	+	"SimSetup Error. No global NMol or component NMol given.\n"
809	+	"\tCannot calculate the number of atoms.\n");
810	+	painCave.isFatal = 1;
811	+	simError();
812	+	}
813	+
814	+	tot_nmol += the_components[i]->getNMol();
815	+	components_nmol[i] = the_components[i]->getNMol();
816	+	}
817	+	}
818	+	else{
819	+	sprintf(painCave.errMsg,
820	+	"SimSetup error.\n"
821	+	"\tSorry, the ability to specify total"
822	+	" nMols and then give molfractions in the components\n"
823	+	"\tis not currently supported."
824	+	" Please give nMol in the components.\n");
825	+	painCave.isFatal = 1;
826	+	simError();
827	+	}
828	+
829	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
830	+	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
831	+	sprintf(painCave.errMsg,
832	+	"Sample time is not divisible by dt.\n"
833	+	"\tThis will result in samples that are not uniformly\n"
834	+	"\tdistributed in time.  If this is a problem, change\n"
835	+	"\tyour sampleTime variable.\n");
836	+	painCave.isFatal = 0;
837	+	simError();
838	+	}
839	+
840	+	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
841	+	sprintf(painCave.errMsg,
842	+	"Status time is not divisible by dt.\n"
843	+	"\tThis will result in status reports that are not uniformly\n"
844	+	"\tdistributed in time.  If this is a problem, change \n"
845	+	"\tyour statusTime variable.\n");
846	+	painCave.isFatal = 0;
847	+	simError();
848	+	}
849	+
850	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
851	+	sprintf(painCave.errMsg,
852	+	"Thermal time is not divisible by dt.\n"
853	+	"\tThis will result in thermalizations that are not uniformly\n"
854	+	"\tdistributed in time.  If this is a problem, change \n"
855	+	"\tyour thermalTime variable.\n");
856	+	painCave.isFatal = 0;
857	+	simError();
858	+	}
859	+
860	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
861	+	sprintf(painCave.errMsg,
862	+	"Reset time is not divisible by dt.\n"
863	+	"\tThis will result in integrator resets that are not uniformly\n"
864	+	"\tdistributed in time.  If this is a problem, change\n"
865	+	"\tyour resetTime variable.\n");
866	+	painCave.isFatal = 0;
867	+	simError();
868	+	}
869	+
870	+	// set the status, sample, and thermal kick times
871	+
872	+	for (i = 0; i < nInfo; i++){
873	+	if (globals->haveSampleTime()){
874	+	info[i].sampleTime = globals->getSampleTime();
875	+	info[i].statusTime = info[i].sampleTime;
876	+	info[i].thermalTime = info[i].sampleTime;
877	+	}
878	+	else{
879	+	info[i].sampleTime = globals->getRunTime();
880	+	info[i].statusTime = info[i].sampleTime;
881	+	info[i].thermalTime = info[i].sampleTime;
882	+	}
883	+
884	+	if (globals->haveStatusTime()){
885	+	info[i].statusTime = globals->getStatusTime();
886	+	}
887	+
888	+	if (globals->haveThermalTime()){
889	+	info[i].thermalTime = globals->getThermalTime();
890	+	}
891	+
892	+	info[i].resetIntegrator = 0;
893	+	if( globals->haveResetTime() ){
894	+	info[i].resetTime = globals->getResetTime();
895	+	info[i].resetIntegrator = 1;
896	+	}
897	+
898	+	// check for the temperature set flag
899	+
900	+	if (globals->haveTempSet())
901	+	info[i].setTemp = globals->getTempSet();
902	+
903	+	// check for the extended State init
904	+
905	+	info[i].useInitXSstate = globals->getUseInitXSstate();
906	+	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
907	+
908	+	}
909	+
910	+	//setup seed for random number generator
911	+	int seedValue;
912	+
913	+	if (globals->haveSeed()){
914	+	seedValue = globals->getSeed();
915	+
916	+	if(seedValue / 1E9 == 0){
917	+	sprintf(painCave.errMsg,
918	+	"Seed for sprng library should contain at least 9 digits\n"
919	+	"OOPSE will generate a seed for user\n");
920	+	painCave.isFatal = 0;
921	+	simError();
922	+
923	+	//using seed generated by system instead of invalid seed set by user
924	+	#ifndef IS_MPI
925	+	seedValue = make_sprng_seed();
926	+	#else
927	+	if (worldRank == 0){
928	+	seedValue = make_sprng_seed();
929	+	}
930	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
931	+	#endif
932	+	}
933	+	}//end of if branch of globals->haveSeed()
934	+	else{
935	+
936	+	#ifndef IS_MPI
937	+	seedValue = make_sprng_seed();
938	+	#else
939	+	if (worldRank == 0){
940	+	seedValue = make_sprng_seed();
941	+	}
942	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
943	+	#endif
944	+	}//end of globals->haveSeed()
945	+
946	+	for (int i = 0; i < nInfo; i++){
947	+	info[i].setSeed(seedValue);
948	+	}
949	+
950	+	#ifdef IS_MPI
951	+	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
952	+	MPIcheckPoint();
953	+	#endif // is_mpi
954	+	}
955	+
956	+
957	+	void SimSetup::finalInfoCheck(void){
958	+	int index;
959	+	int usesDipoles;
960	+	int i;
961	+
962	+	for (i = 0; i < nInfo; i++){
963	+	// check electrostatic parameters
964	+
965	+	index = 0;
966	+	usesDipoles = 0;
967	+	while ((index < info[i].n_atoms) && !usesDipoles){
968	+	usesDipoles = (info[i].atoms[index])->hasDipole();
969	+	index++;
970	+	}
971	+
972	+	#ifdef IS_MPI
973	+	int myUse = usesDipoles;
974	+	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
975	+	#endif //is_mpi
976	+
977	+	double theEcr, theEst;
978	+
979	+	if (globals->getUseRF()){
980	+	info[i].useReactionField = 1;
981	+
982	+	if (!globals->haveECR()){
983	+	sprintf(painCave.errMsg,
984	+	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
985	+	"\tOOPSE will use a default value of 15.0 angstroms"
986	+	"\tfor the electrostaticCutoffRadius.\n");
987	+	painCave.isFatal = 0;
988	+	simError();
989	+	theEcr = 15.0;
990	+	}
991	+	else{
992	+	theEcr = globals->getECR();
993	+	}
994	+
995	+	if (!globals->haveEST()){
996	+	sprintf(painCave.errMsg,
997	+	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
998	+	"\tOOPSE will use a default value of\n"
999	+	"\t0.05 * electrostaticCutoffRadius\n"
1000	+	"\tfor the electrostaticSkinThickness\n");
1001	+	painCave.isFatal = 0;
1002	+	simError();
1003	+	theEst = 0.05 * theEcr;
1004	+	}
1005	+	else{
1006	+	theEst = globals->getEST();
1007	+	}
1008	+
1009	+	info[i].setDefaultEcr(theEcr, theEst);
1010	+
1011	+	if (!globals->haveDielectric()){
1012	+	sprintf(painCave.errMsg,
1013	+	"SimSetup Error: No Dielectric constant was set.\n"
1014	+	"\tYou are trying to use Reaction Field without"
1015	+	"\tsetting a dielectric constant!\n");
1016	+	painCave.isFatal = 1;
1017	+	simError();
1018	+	}
1019	+	info[i].dielectric = globals->getDielectric();
1020	+	}
1021	+	else{
1022	+	if (usesDipoles){
1023	+	if (!globals->haveECR()){
1024	+	sprintf(painCave.errMsg,
1025	+	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1026	+	"\tOOPSE will use a default value of 15.0 angstroms"
1027	+	"\tfor the electrostaticCutoffRadius.\n");
1028	+	painCave.isFatal = 0;
1029	+	simError();
1030	+	theEcr = 15.0;
1031	+	}
1032	+	else{
1033	+	theEcr = globals->getECR();
1034	+	}
1035	+
1036	+	if (!globals->haveEST()){
1037	+	sprintf(painCave.errMsg,
1038	+	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1039	+	"\tOOPSE will use a default value of\n"
1040	+	"\t0.05 * electrostaticCutoffRadius\n"
1041	+	"\tfor the electrostaticSkinThickness\n");
1042	+	painCave.isFatal = 0;
1043	+	simError();
1044	+	theEst = 0.05 * theEcr;
1045	+	}
1046	+	else{
1047	+	theEst = globals->getEST();
1048	+	}
1049	+
1050	+	info[i].setDefaultEcr(theEcr, theEst);
1051	+	}
1052	+	}
1053	+	}
1054	+	#ifdef IS_MPI
1055	+	strcpy(checkPointMsg, "post processing checks out");
1056	+	MPIcheckPoint();
1057	+	#endif // is_mpi
1058	+	}
1059	+
1060	+	void SimSetup::initSystemCoords(void){
1061	+	int i;
1062	+
1063	+	char* inName;
1064	+
1065	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1066	+
1067	+	for (i = 0; i < info[0].n_atoms; i++)
1068	+	info[0].atoms[i]->setCoords();
1069	+
1070	+	if (globals->haveInitialConfig()){
1071	+	InitializeFromFile* fileInit;
1072	+	#ifdef IS_MPI // is_mpi
1073	+	if (worldRank == 0){
1074	+	#endif //is_mpi
1075	+	inName = globals->getInitialConfig();
1076	+	fileInit = new InitializeFromFile(inName);
1077	+	#ifdef IS_MPI
1078	+	}
1079	+	else
1080	+	fileInit = new InitializeFromFile(NULL);
1081	+	#endif
1082	+	fileInit->readInit(info); // default velocities on
1083	+
1084	+	delete fileInit;
1085	+	}
1086	+	else{
1087	+
1088	+	// no init from bass
1089	+
1090	+	sprintf(painCave.errMsg,
1091	+	"Cannot intialize a simulation without an initial configuration file.\n");
1092	+	painCave.isFatal = 1;;
1093	+	simError();
1094	+
1095	+	}
1096	+
1097	+	#ifdef IS_MPI
1098	+	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1099	+	MPIcheckPoint();
1100	+	#endif // is_mpi
1101	+	}
1102	+
1103	+
1104	+	void SimSetup::makeOutNames(void){
1105	+	int k;
1106	+
1107	+
1108	+	for (k = 0; k < nInfo; k++){
1109	+	#ifdef IS_MPI
1110	+	if (worldRank == 0){
1111	+	#endif // is_mpi
1112	+
1113	+	if (globals->haveFinalConfig()){
1114	+	strcpy(info[k].finalName, globals->getFinalConfig());
1115	+	}
1116	+	else{
1117	+	strcpy(info[k].finalName, inFileName);
1118	+	char* endTest;
1119	+	int nameLength = strlen(info[k].finalName);
1120	+	endTest = &(info[k].finalName[nameLength - 5]);
1121	+	if (!strcmp(endTest, ".bass")){
1122	+	strcpy(endTest, ".eor");
1123	+	}
1124	+	else if (!strcmp(endTest, ".BASS")){
1125	+	strcpy(endTest, ".eor");
1126	+	}
1127	+	else{
1128	+	endTest = &(info[k].finalName[nameLength - 4]);
1129	+	if (!strcmp(endTest, ".bss")){
1130	+	strcpy(endTest, ".eor");
1131	+	}
1132	+	else if (!strcmp(endTest, ".mdl")){
1133	+	strcpy(endTest, ".eor");
1134	+	}
1135	+	else{
1136	+	strcat(info[k].finalName, ".eor");
1137	+	}
1138	+	}
1139	+	}
1140	+
1141	+	// make the sample and status out names
1142	+
1143	+	strcpy(info[k].sampleName, inFileName);
1144	+	char* endTest;
1145	+	int nameLength = strlen(info[k].sampleName);
1146	+	endTest = &(info[k].sampleName[nameLength - 5]);
1147	+	if (!strcmp(endTest, ".bass")){
1148	+	strcpy(endTest, ".dump");
1149	+	}
1150	+	else if (!strcmp(endTest, ".BASS")){
1151	+	strcpy(endTest, ".dump");
1152	+	}
1153	+	else{
1154	+	endTest = &(info[k].sampleName[nameLength - 4]);
1155	+	if (!strcmp(endTest, ".bss")){
1156	+	strcpy(endTest, ".dump");
1157	+	}
1158	+	else if (!strcmp(endTest, ".mdl")){
1159	+	strcpy(endTest, ".dump");
1160	+	}
1161	+	else{
1162	+	strcat(info[k].sampleName, ".dump");
1163	+	}
1164	+	}
1165	+
1166	+	strcpy(info[k].statusName, inFileName);
1167	+	nameLength = strlen(info[k].statusName);
1168	+	endTest = &(info[k].statusName[nameLength - 5]);
1169	+	if (!strcmp(endTest, ".bass")){
1170	+	strcpy(endTest, ".stat");
1171	+	}
1172	+	else if (!strcmp(endTest, ".BASS")){
1173	+	strcpy(endTest, ".stat");
1174	+	}
1175	+	else{
1176	+	endTest = &(info[k].statusName[nameLength - 4]);
1177	+	if (!strcmp(endTest, ".bss")){
1178	+	strcpy(endTest, ".stat");
1179	+	}
1180	+	else if (!strcmp(endTest, ".mdl")){
1181	+	strcpy(endTest, ".stat");
1182	+	}
1183	+	else{
1184	+	strcat(info[k].statusName, ".stat");
1185	+	}
1186	+	}
1187	+
1188	+	#ifdef IS_MPI
1189	+
1190	+	}
1191	+	#endif // is_mpi
1192	+	}
1193	+	}
1194	+
1195	+
1196	+	void SimSetup::sysObjectsCreation(void){
1197	+	int i, k;
1198	+
1199	+	// create the forceField
1200	+
1201	+	createFF();
1202	+
1203	+	// extract componentList
1204	+
1205	+	compList();
1206	+
1207	+	// calc the number of atoms, bond, bends, and torsions
1208	+
1209	+	calcSysValues();
1210	+
1211	+	#ifdef IS_MPI
1212	+	// divide the molecules among the processors
1213	+
1214	+	mpiMolDivide();
1215	+	#endif //is_mpi
1216	+
1217	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1218	+
1219	+	makeSysArrays();
1220	+
1221	+	// make and initialize the molecules (all but atomic coordinates)
1222	+
1223	+	makeMolecules();
1224	+
1225	+	for (k = 0; k < nInfo; k++){
1226	+	info[k].identArray = new int[info[k].n_atoms];
1227	+	for (i = 0; i < info[k].n_atoms; i++){
1228	+	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1229	+	}
1230	+	}
1231	+	}
1232	+
1233	+
1234	+	void SimSetup::createFF(void){
1235	+	switch (ffCase){
1236	+	case FF_DUFF:
1237	+	the_ff = new DUFF();
1238	+	break;
1239	+
1240	+	case FF_LJ:
1241	+	the_ff = new LJFF();
1242	+	break;
1243	+
1244	+	case FF_EAM:
1245	+	the_ff = new EAM_FF();
1246	+	break;
1247	+
1248	+	case FF_H2O:
1249	+	the_ff = new WATER();
1250	+	break;
1251	+
1252	+	default:
1253	+	sprintf(painCave.errMsg,
1254	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1255	+	painCave.isFatal = 1;
1256	+	simError();
1257	+	}
1258	+
1259	+	#ifdef IS_MPI
1260	+	strcpy(checkPointMsg, "ForceField creation successful");
1261	+	MPIcheckPoint();
1262	+	#endif // is_mpi
1263	+	}
1264	+
1265	+
1266	+	void SimSetup::compList(void){
1267	+	int i;
1268	+	char* id;
1269	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1270	+	LinkedMolStamp* currentStamp = NULL;
1271	+	comp_stamps = new MoleculeStamp * [n_components];
1272	+
1273	+	// make an array of molecule stamps that match the components used.
1274	+	// also extract the used stamps out into a separate linked list
1275	+
1276	+	for (i = 0; i < nInfo; i++){
1277	+	info[i].nComponents = n_components;
1278	+	info[i].componentsNmol = components_nmol;
1279	+	info[i].compStamps = comp_stamps;
1280	+	info[i].headStamp = headStamp;
1281	+	}
1282	+
1283	+
1284	+	for (i = 0; i < n_components; i++){
1285	+	id = the_components[i]->getType();
1286	+	comp_stamps[i] = NULL;
1287	+
1288	+	// check to make sure the component isn't already in the list
1289	+
1290	+	comp_stamps[i] = headStamp->match(id);
1291	+	if (comp_stamps[i] == NULL){
1292	+	// extract the component from the list;
1293	+
1294	+	currentStamp = stamps->extractMolStamp(id);
1295	+	if (currentStamp == NULL){
1296	+	sprintf(painCave.errMsg,
1297	+	"SimSetup error: Component \"%s\" was not found in the "
1298	+	"list of declared molecules\n",
1299	+	id);
1300	+	painCave.isFatal = 1;
1301	+	simError();
1302	+	}
1303	+
1304	+	headStamp->add(currentStamp);
1305	+	comp_stamps[i] = headStamp->match(id);
1306	+	}
1307	+	}
1308	+
1309	+	#ifdef IS_MPI
1310	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1311	+	MPIcheckPoint();
1312	+	#endif // is_mpi
1313	+	}
1314	+
1315	+	void SimSetup::calcSysValues(void){
1316	+	int i;
1317	+
1318	+	int* molMembershipArray;
1319	+
1320	+	tot_atoms = 0;
1321	+	tot_bonds = 0;
1322	+	tot_bends = 0;
1323	+	tot_torsions = 0;
1324	+	tot_rigid = 0;
1325	+	for (i = 0; i < n_components; i++){
1326	+	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1327	+	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1328	+	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1329	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1330	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1331	+	}
1332	+
1333	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1334	+	molMembershipArray = new int[tot_atoms];
1335	+
1336	+	for (i = 0; i < nInfo; i++){
1337	+	info[i].n_atoms = tot_atoms;
1338	+	info[i].n_bonds = tot_bonds;
1339	+	info[i].n_bends = tot_bends;
1340	+	info[i].n_torsions = tot_torsions;
1341	+	info[i].n_SRI = tot_SRI;
1342	+	info[i].n_mol = tot_nmol;
1343	+
1344	+	info[i].molMembershipArray = molMembershipArray;
1345	+	}
1346	+	}
1347	+
1348	+	#ifdef IS_MPI
1349	+
1350	+	void SimSetup::mpiMolDivide(void){
1351	+	int i, j, k;
1352	+	int localMol, allMol;
1353	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1354	+	int local_rigid;
1355	+	vector<int> globalAtomIndex;
1356	+	vector<int> globalMolIndex;
1357	+
1358	+	mpiSim = new mpiSimulation(info);
1359	+
1360	+	mpiSim->divideLabor();
1361	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1362	+	globalMolIndex = mpiSim->getGlobalMolIndex();
1363	+
1364	+	// set up the local variables
1365	+
1366	+	mol2proc = mpiSim->getMolToProcMap();
1367	+	molCompType = mpiSim->getMolComponentType();
1368	+
1369	+	allMol = 0;
1370	+	localMol = 0;
1371	+	local_atoms = 0;
1372	+	local_bonds = 0;
1373	+	local_bends = 0;
1374	+	local_torsions = 0;
1375	+	local_rigid = 0;
1376	+	globalAtomCounter = 0;
1377	+
1378	+	for (i = 0; i < n_components; i++){
1379	+	for (j = 0; j < components_nmol[i]; j++){
1380	+	if (mol2proc[allMol] == worldRank){
1381	+	local_atoms += comp_stamps[i]->getNAtoms();
1382	+	local_bonds += comp_stamps[i]->getNBonds();
1383	+	local_bends += comp_stamps[i]->getNBends();
1384	+	local_torsions += comp_stamps[i]->getNTorsions();
1385	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1386	+	localMol++;
1387	+	}
1388	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1389	+	info[0].molMembershipArray[globalAtomCounter] = allMol;
1390	+	globalAtomCounter++;
1391	+	}
1392	+
1393	+	allMol++;
1394	+	}
1395	+	}
1396	+	local_SRI = local_bonds + local_bends + local_torsions;
1397	+
1398	+	info[0].n_atoms = mpiSim->getMyNlocal();
1399	+
1400	+
1401	+	if (local_atoms != info[0].n_atoms){
1402	+	sprintf(painCave.errMsg,
1403	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1404	+	"\tlocalAtom (%d) are not equal.\n",
1405	+	info[0].n_atoms, local_atoms);
1406	+	painCave.isFatal = 1;
1407	+	simError();
1408	+	}
1409	+
1410	+	info[0].n_bonds = local_bonds;
1411	+	info[0].n_bends = local_bends;
1412	+	info[0].n_torsions = local_torsions;
1413	+	info[0].n_SRI = local_SRI;
1414	+	info[0].n_mol = localMol;
1415	+
1416	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1417	+	MPIcheckPoint();
1418	+	}
1419	+
1420	+	#endif // is_mpi
1421	+
1422	+
1423	+	void SimSetup::makeSysArrays(void){
1424	+
1425	+	#ifndef IS_MPI
1426	+	int k, j;
1427	+	#endif // is_mpi
1428	+	int i, l;
1429	+
1430	+	Atom** the_atoms;
1431	+	Molecule* the_molecules;
1432	+
1433	+	for (l = 0; l < nInfo; l++){
1434	+	// create the atom and short range interaction arrays
1435	+
1436	+	the_atoms = new Atom * [info[l].n_atoms];
1437	+	the_molecules = new Molecule[info[l].n_mol];
1438	+	int molIndex;
1439	+
1440	+	// initialize the molecule's stampID's
1441	+
1442	+	#ifdef IS_MPI
1443	+
1444	+
1445	+	molIndex = 0;
1446	+	for (i = 0; i < mpiSim->getTotNmol(); i++){
1447	+	if (mol2proc[i] == worldRank){
1448	+	the_molecules[molIndex].setStampID(molCompType[i]);
1449	+	the_molecules[molIndex].setMyIndex(molIndex);
1450	+	the_molecules[molIndex].setGlobalIndex(i);
1451	+	molIndex++;
1452	+	}
1453	+	}
1454	+
1455	+	#else // is_mpi
1456	+
1457	+	molIndex = 0;
1458	+	globalAtomCounter = 0;
1459	+	for (i = 0; i < n_components; i++){
1460	+	for (j = 0; j < components_nmol[i]; j++){
1461	+	the_molecules[molIndex].setStampID(i);
1462	+	the_molecules[molIndex].setMyIndex(molIndex);
1463	+	the_molecules[molIndex].setGlobalIndex(molIndex);
1464	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1465	+	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1466	+	globalAtomCounter++;
1467	+	}
1468	+	molIndex++;
1469	+	}
1470	+	}
1471	+
1472	+
1473	+	#endif // is_mpi
1474	+
1475	+	info[l].globalExcludes = new int;
1476	+	info[l].globalExcludes[0] = 0;
1477	+
1478	+	// set the arrays into the SimInfo object
1479	+
1480	+	info[l].atoms = the_atoms;
1481	+	info[l].molecules = the_molecules;
1482	+	info[l].nGlobalExcludes = 0;
1483	+
1484	+	the_ff->setSimInfo(info);
1485	+	}
1486	+	}
1487	+
1488	+	void SimSetup::makeIntegrator(void){
1489	+	int k;
1490	+
1491	+	NVE<RealIntegrator>* myNVE = NULL;
1492	+	NVT<RealIntegrator>* myNVT = NULL;
1493	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1494	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1495	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1496	+
1497	+	for (k = 0; k < nInfo; k++){
1498	+	switch (ensembleCase){
1499	+	case NVE_ENS:
1500	+	if (globals->haveZconstraints()){
1501	+	setupZConstraint(info[k]);
1502	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1503	+	}
1504	+	else{
1505	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1506	+	}
1507	+
1508	+	info->the_integrator = myNVE;
1509	+	break;
1510	+
1511	+	case NVT_ENS:
1512	+	if (globals->haveZconstraints()){
1513	+	setupZConstraint(info[k]);
1514	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1515	+	}
1516	+	else
1517	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1518	+
1519	+	myNVT->setTargetTemp(globals->getTargetTemp());
1520	+
1521	+	if (globals->haveTauThermostat())
1522	+	myNVT->setTauThermostat(globals->getTauThermostat());
1523	+	else{
1524	+	sprintf(painCave.errMsg,
1525	+	"SimSetup error: If you use the NVT\n"
1526	+	"\tensemble, you must set tauThermostat.\n");
1527	+	painCave.isFatal = 1;
1528	+	simError();
1529	+	}
1530	+
1531	+	info->the_integrator = myNVT;
1532	+	break;
1533	+
1534	+	case NPTi_ENS:
1535	+	if (globals->haveZconstraints()){
1536	+	setupZConstraint(info[k]);
1537	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1538	+	}
1539	+	else
1540	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1541	+
1542	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1543	+
1544	+	if (globals->haveTargetPressure())
1545	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1546	+	else{
1547	+	sprintf(painCave.errMsg,
1548	+	"SimSetup error: If you use a constant pressure\n"
1549	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1550	+	painCave.isFatal = 1;
1551	+	simError();
1552	+	}
1553	+
1554	+	if (globals->haveTauThermostat())
1555	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1556	+	else{
1557	+	sprintf(painCave.errMsg,
1558	+	"SimSetup error: If you use an NPT\n"
1559	+	"\tensemble, you must set tauThermostat.\n");
1560	+	painCave.isFatal = 1;
1561	+	simError();
1562	+	}
1563	+
1564	+	if (globals->haveTauBarostat())
1565	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1566	+	else{
1567	+	sprintf(painCave.errMsg,
1568	+	"SimSetup error: If you use an NPT\n"
1569	+	"\tensemble, you must set tauBarostat.\n");
1570	+	painCave.isFatal = 1;
1571	+	simError();
1572	+	}
1573	+
1574	+	info->the_integrator = myNPTi;
1575	+	break;
1576	+
1577	+	case NPTf_ENS:
1578	+	if (globals->haveZconstraints()){
1579	+	setupZConstraint(info[k]);
1580	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1581	+	}
1582	+	else
1583	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1584	+
1585	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1586	+
1587	+	if (globals->haveTargetPressure())
1588	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1589	+	else{
1590	+	sprintf(painCave.errMsg,
1591	+	"SimSetup error: If you use a constant pressure\n"
1592	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1593	+	painCave.isFatal = 1;
1594	+	simError();
1595	+	}
1596	+
1597	+	if (globals->haveTauThermostat())
1598	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1599	+
1600	+	else{
1601	+	sprintf(painCave.errMsg,
1602	+	"SimSetup error: If you use an NPT\n"
1603	+	"\tensemble, you must set tauThermostat.\n");
1604	+	painCave.isFatal = 1;
1605	+	simError();
1606	+	}
1607	+
1608	+	if (globals->haveTauBarostat())
1609	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1610	+
1611	+	else{
1612	+	sprintf(painCave.errMsg,
1613	+	"SimSetup error: If you use an NPT\n"
1614	+	"\tensemble, you must set tauBarostat.\n");
1615	+	painCave.isFatal = 1;
1616	+	simError();
1617	+	}
1618	+
1619	+	info->the_integrator = myNPTf;
1620	+	break;
1621	+
1622	+	case NPTxyz_ENS:
1623	+	if (globals->haveZconstraints()){
1624	+	setupZConstraint(info[k]);
1625	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1626	+	}
1627	+	else
1628	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1629	+
1630	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1631	+
1632	+	if (globals->haveTargetPressure())
1633	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1634	+	else{
1635	+	sprintf(painCave.errMsg,
1636	+	"SimSetup error: If you use a constant pressure\n"
1637	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1638	+	painCave.isFatal = 1;
1639	+	simError();
1640	+	}
1641	+
1642	+	if (globals->haveTauThermostat())
1643	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1644	+	else{
1645	+	sprintf(painCave.errMsg,
1646	+	"SimSetup error: If you use an NPT\n"
1647	+	"\tensemble, you must set tauThermostat.\n");
1648	+	painCave.isFatal = 1;
1649	+	simError();
1650	+	}
1651	+
1652	+	if (globals->haveTauBarostat())
1653	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1654	+	else{
1655	+	sprintf(painCave.errMsg,
1656	+	"SimSetup error: If you use an NPT\n"
1657	+	"\tensemble, you must set tauBarostat.\n");
1658	+	painCave.isFatal = 1;
1659	+	simError();
1660	+	}
1661	+
1662	+	info->the_integrator = myNPTxyz;
1663	+	break;
1664	+
1665	+	default:
1666	+	sprintf(painCave.errMsg,
1667	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1668	+	painCave.isFatal = 1;
1669	+	simError();
1670	+	}
1671		}
1672		}
1673	+
1674	+	void SimSetup::initFortran(void){
1675	+	info[0].refreshSim();
1676	+
1677	+	if (!strcmp(info[0].mixingRule, "standard")){
1678	+	the_ff->initForceField(LB_MIXING_RULE);
1679	+	}
1680	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1681	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1682	+	}
1683	+	else{
1684	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1685	+	info[0].mixingRule);
1686	+	painCave.isFatal = 1;
1687	+	simError();
1688	+	}
1689	+
1690	+
1691	+	#ifdef IS_MPI
1692	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1693	+	MPIcheckPoint();
1694	+	#endif // is_mpi
1695	+	}
1696	+
1697	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1698	+	int nZConstraints;
1699	+	ZconStamp** zconStamp;
1700	+
1701	+	if (globals->haveZconstraintTime()){
1702	+	//add sample time of z-constraint  into SimInfo's property list
1703	+	DoubleData* zconsTimeProp = new DoubleData();
1704	+	zconsTimeProp->setID(ZCONSTIME_ID);
1705	+	zconsTimeProp->setData(globals->getZconsTime());
1706	+	theInfo.addProperty(zconsTimeProp);
1707	+	}
1708	+	else{
1709	+	sprintf(painCave.errMsg,
1710	+	"ZConstraint error: If you use a ZConstraint,\n"
1711	+	"\tyou must set zconsTime.\n");
1712	+	painCave.isFatal = 1;
1713	+	simError();
1714	+	}
1715	+
1716	+	//push zconsTol into siminfo, if user does not specify
1717	+	//value for zconsTol, a default value will be used
1718	+	DoubleData* zconsTol = new DoubleData();
1719	+	zconsTol->setID(ZCONSTOL_ID);
1720	+	if (globals->haveZconsTol()){
1721	+	zconsTol->setData(globals->getZconsTol());
1722	+	}
1723	+	else{
1724	+	double defaultZConsTol = 0.01;
1725	+	sprintf(painCave.errMsg,
1726	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1727	+	"\tOOPSE will use a default value of %f.\n"
1728	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1729	+	defaultZConsTol);
1730	+	painCave.isFatal = 0;
1731	+	simError();
1732	+
1733	+	zconsTol->setData(defaultZConsTol);
1734	+	}
1735	+	theInfo.addProperty(zconsTol);
1736	+
1737	+	//set Force Subtraction Policy
1738	+	StringData* zconsForcePolicy = new StringData();
1739	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1740	+
1741	+	if (globals->haveZconsForcePolicy()){
1742	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1743	+	}
1744	+	else{
1745	+	sprintf(painCave.errMsg,
1746	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1747	+	"\tOOPSE will use PolicyByMass.\n"
1748	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1749	+	painCave.isFatal = 0;
1750	+	simError();
1751	+	zconsForcePolicy->setData("BYMASS");
1752	+	}
1753	+
1754	+	theInfo.addProperty(zconsForcePolicy);
1755	+
1756	+	//set zcons gap
1757	+	DoubleData* zconsGap = new DoubleData();
1758	+	zconsGap->setID(ZCONSGAP_ID);
1759	+
1760	+	if (globals->haveZConsGap()){
1761	+	zconsGap->setData(globals->getZconsGap());
1762	+	theInfo.addProperty(zconsGap);
1763	+	}
1764	+
1765	+	//set zcons fixtime
1766	+	DoubleData* zconsFixtime = new DoubleData();
1767	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1768	+
1769	+	if (globals->haveZConsFixTime()){
1770	+	zconsFixtime->setData(globals->getZconsFixtime());
1771	+	theInfo.addProperty(zconsFixtime);
1772	+	}
1773	+
1774	+	//set zconsUsingSMD
1775	+	IntData* zconsUsingSMD = new IntData();
1776	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1777	+
1778	+	if (globals->haveZConsUsingSMD()){
1779	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1780	+	theInfo.addProperty(zconsUsingSMD);
1781	+	}
1782	+
1783	+	//Determine the name of ouput file and add it into SimInfo's property list
1784	+	//Be careful, do not use inFileName, since it is a pointer which
1785	+	//point to a string at master node, and slave nodes do not contain that string
1786	+
1787	+	string zconsOutput(theInfo.finalName);
1788	+
1789	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1790	+
1791	+	StringData* zconsFilename = new StringData();
1792	+	zconsFilename->setID(ZCONSFILENAME_ID);
1793	+	zconsFilename->setData(zconsOutput);
1794	+
1795	+	theInfo.addProperty(zconsFilename);
1796	+
1797	+	//setup index, pos and other parameters of z-constraint molecules
1798	+	nZConstraints = globals->getNzConstraints();
1799	+	theInfo.nZconstraints = nZConstraints;
1800	+
1801	+	zconStamp = globals->getZconStamp();
1802	+	ZConsParaItem tempParaItem;
1803	+
1804	+	ZConsParaData* zconsParaData = new ZConsParaData();
1805	+	zconsParaData->setID(ZCONSPARADATA_ID);
1806	+
1807	+	for (int i = 0; i < nZConstraints; i++){
1808	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1809	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1810	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1811	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1812	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1813	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1814	+	zconsParaData->addItem(tempParaItem);
1815	+	}
1816	+
1817	+	//check the uniqueness of index
1818	+	if(!zconsParaData->isIndexUnique()){
1819	+	sprintf(painCave.errMsg,
1820	+	"ZConstraint Error: molIndex is not unique!\n");
1821	+	painCave.isFatal = 1;
1822	+	simError();
1823	+	}
1824	+
1825	+	//sort the parameters by index of molecules
1826	+	zconsParaData->sortByIndex();
1827	+
1828	+	//push data into siminfo, therefore, we can retrieve later
1829	+	theInfo.addProperty(zconsParaData);
1830	+	}
1831	+
1832	+	void SimSetup::makeMinimizer(){
1833	+
1834	+	OOPSEMinimizer* myOOPSEMinimizer;
1835	+	MinimizerParameterSet* param;
1836	+	char minimizerName[100];
1837	+
1838	+	for (int i = 0; i < nInfo; i++){
1839	+
1840	+	//prepare parameter set for minimizer
1841	+	param = new MinimizerParameterSet();
1842	+	param->setDefaultParameter();
1843	+
1844	+	if (globals->haveMinimizer()){
1845	+	param->setFTol(globals->getMinFTol());
1846	+	}
1847	+
1848	+	if (globals->haveMinGTol()){
1849	+	param->setGTol(globals->getMinGTol());
1850	+	}
1851	+
1852	+	if (globals->haveMinMaxIter()){
1853	+	param->setMaxIteration(globals->getMinMaxIter());
1854	+	}
1855	+
1856	+	if (globals->haveMinWriteFrq()){
1857	+	param->setMaxIteration(globals->getMinMaxIter());
1858	+	}
1859	+
1860	+	if (globals->haveMinWriteFrq()){
1861	+	param->setWriteFrq(globals->getMinWriteFrq());
1862	+	}
1863	+
1864	+	if (globals->haveMinStepSize()){
1865	+	param->setStepSize(globals->getMinStepSize());
1866	+	}
1867	+
1868	+	if (globals->haveMinLSMaxIter()){
1869	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1870	+	}
1871	+
1872	+	if (globals->haveMinLSTol()){
1873	+	param->setLineSearchTol(globals->getMinLSTol());
1874	+	}
1875	+
1876	+	strcpy(minimizerName, globals->getMinimizer());
1877	+
1878	+	if (!strcasecmp(minimizerName, "CG")){
1879	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1880	+	}
1881	+	else if (!strcasecmp(minimizerName, "SD")){
1882	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1883	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1884	+	}
1885	+	else{
1886	+	sprintf(painCave.errMsg,
1887	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1888	+	painCave.isFatal = 0;
1889	+	simError();
1890	+
1891	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1892	+	}
1893	+	info[i].the_integrator = myOOPSEMinimizer;
1894	+
1895	+	//store the minimizer into simInfo
1896	+	info[i].the_minimizer = myOOPSEMinimizer;
1897	+	info[i].has_minimizer = true;
1898	+	}
1899	+
1900	+	}

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