ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 558 by mmeineke, Thu Jun 19 19:21:23 2003 UTC vs.
Revision 1139 by gezelter, Wed Apr 28 22:06:29 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" ) ) {
150	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
151	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
152	<	//     if (the_globals->haveTargetPressure())
153	<	//       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	>	#ifdef IS_MPI
152	>	mpiSim->mpiRefresh();
153	>	#endif
154
155	<	//     if (the_globals->haveTauThermostat())
144	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
145	<	//     else if (the_globals->haveQmass())
146	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
147	<	//     else {
148	<	//       sprintf( painCave.errMsg,
149	<	//                "SimSetup error: If you use one of the constant temperature\n"
150	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
151	<	//                "    Neither of these was found in the BASS file.\n");
152	<	//       painCave.isFatal = 1;
153	<	//       simError();
154	<	//     }
155	>	// initialize the Fortran
156
157	<	//     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	<	//     }
157	>	initFortran();
158
159	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
160	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
161	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
159	>	if (globals->haveMinimizer())
160	>	// make minimizer
161	>	makeMinimizer();
162	>	else
163	>	// make the integrator
164	>	makeIntegrator();
165
166	<	//     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	<	//     }
166	>	}
167
184	–	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
185	–	simnfo->usePBC = the_globals->getPBC();
186	–
187	–	int usesDipoles = 0;
188	–	switch( ffCase ){
168
169	<	case FF_DUFF:
170	<	the_ff = new DUFF();
171	<	usesDipoles = 1;
172	<	break;
169	>	void SimSetup::makeMolecules(void){
170	>	int i, j, k;
171	>	int exI, exJ, exK, exL, slI, slJ;
172	>	int tempI, tempJ, tempK, tempL;
173	>	int molI;
174	>	int stampID, atomOffset, rbOffset;
175	>	molInit molInfo;
176	>	DirectionalAtom* dAtom;
177	>	RigidBody* myRB;
178	>	StuntDouble* mySD;
179	>	LinkedAssign* extras;
180	>	LinkedAssign* current_extra;
181	>	AtomStamp* currentAtom;
182	>	BondStamp* currentBond;
183	>	BendStamp* currentBend;
184	>	TorsionStamp* currentTorsion;
185	>	RigidBodyStamp* currentRigidBody;
186
187	<	case FF_LJ:
188	<	the_ff = LJFF();
189	<	break;
187	>	bond_pair* theBonds;
188	>	bend_set* theBends;
189	>	torsion_set* theTorsions;
190
191	<	default:
200	<	sprintf( painCave.errMsg,
201	<	"SimSetup Error. Unrecognized force field in case statement.\n");
202	<	painCave.isFatal = 1;
203	<	simError();
204	<	}
191	>	set<int> skipList;
192
193	<	#ifdef IS_MPI
194	<	strcpy( checkPointMsg, "ForceField creation successful" );
195	<	MPIcheckPoint();
209	<	#endif // is_mpi
193	>	double phi, theta, psi;
194	>	char* molName;
195	>	char rbName[100];
196
197	<	// 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];
197	>	//init the forceField paramters
198
199	<	if( !the_globals->haveNMol() ){
217	<	// we don't have the total number of molecules, so we assume it is
218	<	// given in each component
199	>	the_ff->readParams();
200
201	<	tot_nmol = 0;
221	<	for( i=0; i<n_components; i++ ){
201	>	// init the atoms
202
203	<	if( !the_components[i]->haveNMol() ){
204	<	// we have a problem
205	<	sprintf( painCave.errMsg,
206	<	"SimSetup Error. No global NMol or component NMol"
207	<	" given. Cannot calculate the number of atoms.\n" );
208	<	painCave.isFatal = 1;
209	<	simError();
210	<	}
203	>	int nMembers, nNew, rb1, rb2;
204	>
205	>	for (k = 0; k < nInfo; k++){
206	>	the_ff->setSimInfo(&(info[k]));
207	>
208	>	atomOffset = 0;
209	>
210	>	for (i = 0; i < info[k].n_mol; i++){
211	>	stampID = info[k].molecules[i].getStampID();
212	>	molName = comp_stamps[stampID]->getID();
213	>
214	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
215	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
216	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
217	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
218	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
219	>
220	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
221
222	<	tot_nmol += the_components[i]->getNMol();
223	<	components_nmol[i] = the_components[i]->getNMol();
224	<	}
225	<	}
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	<	}
222	>	if (molInfo.nBonds > 0)
223	>	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
224	>	else
225	>	molInfo.myBonds = NULL;
226
227	<	#ifdef IS_MPI
228	<	strcpy( checkPointMsg, "Have the number of components" );
229	<	MPIcheckPoint();
230	<	#endif // is_mpi
227	>	if (molInfo.nBends > 0)
228	>	molInfo.myBends = new (Bend *) [molInfo.nBends];
229	>	else
230	>	molInfo.myBends = NULL;
231
232	<	// make an array of molecule stamps that match the components used.
233	<	// also extract the used stamps out into a separate linked list
232	>	if (molInfo.nTorsions > 0)
233	>	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
234	>	else
235	>	molInfo.myTorsions = NULL;
236
237	<	simnfo->nComponents = n_components;
238	<	simnfo->componentsNmol = components_nmol;
239	<	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 ){
237	>	theBonds = new bond_pair[molInfo.nBonds];
238	>	theBends = new bend_set[molInfo.nBends];
239	>	theTorsions = new torsion_set[molInfo.nTorsions];
240
241	<	// 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	<	}
241	>	// make the Atoms
242
243	<	#ifdef IS_MPI
244	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
306	<	MPIcheckPoint();
307	<	#endif // is_mpi
308	<
243	>	for (j = 0; j < molInfo.nAtoms; j++){
244	>	currentAtom = comp_stamps[stampID]->getAtom(j);
245
246	+	if (currentAtom->haveOrientation()){
247	+	dAtom = new DirectionalAtom((j + atomOffset),
248	+	info[k].getConfiguration());
249	+	info[k].n_oriented++;
250	+	molInfo.myAtoms[j] = dAtom;
251
252	+	// Directional Atoms have standard unit vectors which are oriented
253	+	// in space using the three Euler angles.  We assume the standard
254	+	// unit vector was originally along the z axis below.
255
256	<	// caclulate the number of atoms, bonds, bends and torsions
256	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
257	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
258	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
259
260	<	tot_atoms = 0;
261	<	tot_bonds = 0;
262	<	tot_bends = 0;
263	<	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	<	}
260	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
261	>
262	>	}
263	>	else{
264
265	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
265	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
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	>	}
268
269	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
270		#ifdef IS_MPI
271
272	<	// divide the molecules among processors here.
340	<
341	<	mpiSim = new mpiSimulation( simnfo );
342	<
343	<	globalIndex = mpiSim->divideLabor();
272	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
273
274	<	// set up the local variables
275	<
347	<	int localMol, allMol;
348	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
274	>	#endif // is_mpi
275	>	}
276
277	<	int* mol2proc = mpiSim->getMolToProcMap();
278	<	int* molCompType = mpiSim->getMolComponentType();
279	<
280	<	allMol = 0;
281	<	localMol = 0;
355	<	local_atoms = 0;
356	<	local_bonds = 0;
357	<	local_bends = 0;
358	<	local_torsions = 0;
359	<	globalAtomIndex = 0;
277	>	// make the bonds
278	>	for (j = 0; j < molInfo.nBonds; j++){
279	>	currentBond = comp_stamps[stampID]->getBond(j);
280	>	theBonds[j].a = currentBond->getA() + atomOffset;
281	>	theBonds[j].b = currentBond->getB() + atomOffset;
282
283	+	tempI = theBonds[j].a;
284	+	tempJ = theBonds[j].b;
285
286	<	for( i=0; i<n_components; i++ ){
286	>	#ifdef IS_MPI
287	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
288	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
289	>	#else
290	>	exI = tempI + 1;
291	>	exJ = tempJ + 1;
292	>	#endif
293
294	<	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++;
294	>	info[k].excludes->addPair(exI, exJ);
295		}
296
297	<	allMol++;
298	<	}
299	<	}
300	<	local_SRI = local_bonds + local_bends + local_torsions;
301	<
302	<	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	<	}
297	>	//make the bends
298	>	for (j = 0; j < molInfo.nBends; j++){
299	>	currentBend = comp_stamps[stampID]->getBend(j);
300	>	theBends[j].a = currentBend->getA() + atomOffset;
301	>	theBends[j].b = currentBend->getB() + atomOffset;
302	>	theBends[j].c = currentBend->getC() + atomOffset;
303
304	<	simnfo->n_bonds = local_bonds;
305	<	simnfo->n_bends = local_bends;
306	<	simnfo->n_torsions = local_torsions;
399	<	simnfo->n_SRI = local_SRI;
400	<	simnfo->n_mol = localMol;
304	>	if (currentBend->haveExtras()){
305	>	extras = currentBend->getExtras();
306	>	current_extra = extras;
307
308	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
309	<	MPIcheckPoint();
310	<
311	<
312	<	#endif // is_mpi
313	<
308	>	while (current_extra != NULL){
309	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
310	>	switch (current_extra->getType()){
311	>	case 0:
312	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
313	>	theBends[j].isGhost = 1;
314	>	break;
315
316	<	// create the atom and short range interaction arrays
316	>	case 1:
317	>	theBends[j].ghost = (int) current_extra->getDouble() +
318	>	atomOffset;
319	>	theBends[j].isGhost = 1;
320	>	break;
321
322	<	Atom::createArrays(simnfo->n_atoms);
323	<	the_atoms = new Atom*[simnfo->n_atoms];
324	<	the_molecules = new Molecule[simnfo->n_mol];
325	<	int molIndex;
326	<
327	<	// initialize the molecule's stampID's
322	>	default:
323	>	sprintf(painCave.errMsg,
324	>	"SimSetup Error: ghostVectorSource was neither a "
325	>	"double nor an int.\n"
326	>	"-->Bend[%d] in %s\n",
327	>	j, comp_stamps[stampID]->getID());
328	>	painCave.isFatal = 1;
329	>	simError();
330	>	}
331	>	}
332	>	else{
333	>	sprintf(painCave.errMsg,
334	>	"SimSetup Error: unhandled bend assignment:\n"
335	>	"    -->%s in Bend[%d] in %s\n",
336	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
337	>	painCave.isFatal = 1;
338	>	simError();
339	>	}
340
341	+	current_extra = current_extra->getNext();
342	+	}
343	+	}
344	+
345	+	if (theBends[j].isGhost) {
346	+
347	+	tempI = theBends[j].a;
348	+	tempJ = theBends[j].b;
349	+
350		#ifdef IS_MPI
351	<
351	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
352	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
353	>	#else
354	>	exI = tempI + 1;
355	>	exJ = tempJ + 1;
356	>	#endif
357	>	info[k].excludes->addPair(exI, exJ);
358
359	<	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	<	}
359	>	} else {
360
361	<	#else // is_mpi
362	<
363	<	molIndex = 0;
364	<	globalAtomIndex = 0;
365	<	for(i=0; i<n_components; i++){
366	<	for(j=0; j<components_nmol[i]; j++ ){
367	<	the_molecules[molIndex].setStampID( i );
368	<	the_molecules[molIndex].setMyIndex( molIndex );
369	<	the_molecules[molIndex].setGlobalIndex( molIndex );
370	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
371	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
372	<	globalAtomIndex++;
361	>	tempI = theBends[j].a;
362	>	tempJ = theBends[j].b;
363	>	tempK = theBends[j].c;
364	>
365	>	#ifdef IS_MPI
366	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
367	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
368	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
369	>	#else
370	>	exI = tempI + 1;
371	>	exJ = tempJ + 1;
372	>	exK = tempK + 1;
373	>	#endif
374	>
375	>	info[k].excludes->addPair(exI, exK);
376	>	info[k].excludes->addPair(exI, exJ);
377	>	info[k].excludes->addPair(exJ, exK);
378	>	}
379		}
445	–	molIndex++;
446	–	}
447	–	}
448	–
380
381	<	#endif // is_mpi
381	>	for (j = 0; j < molInfo.nTorsions; j++){
382	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
383	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
384	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
385	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
386	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
387
388	+	tempI = theTorsions[j].a;
389	+	tempJ = theTorsions[j].b;
390	+	tempK = theTorsions[j].c;
391	+	tempL = theTorsions[j].d;
392
393	<	if( simnfo->n_SRI ){
394	<
395	<	Exclude::createArray(simnfo->n_SRI);
396	<	the_excludes = new Exclude*[simnfo->n_SRI];
397	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
398	<	simnfo->globalExcludes = new int;
399	<	simnfo->n_exclude = simnfo->n_SRI;
400	<	}
401	<	else{
402	<
403	<	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	<	}
393	>	#ifdef IS_MPI
394	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
395	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
396	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
397	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
398	>	#else
399	>	exI = tempI + 1;
400	>	exJ = tempJ + 1;
401	>	exK = tempK + 1;
402	>	exL = tempL + 1;
403	>	#endif
404
405	<	// set the arrays into the SimInfo object
405	>	info[k].excludes->addPair(exI, exJ);
406	>	info[k].excludes->addPair(exI, exK);
407	>	info[k].excludes->addPair(exI, exL);
408	>	info[k].excludes->addPair(exJ, exK);
409	>	info[k].excludes->addPair(exJ, exL);
410	>	info[k].excludes->addPair(exK, exL);
411	>	}
412
413	<	simnfo->atoms = the_atoms;
414	<	simnfo->molecules = the_molecules;
415	<	simnfo->nGlobalExcludes = 0;
416	<	simnfo->excludes = the_excludes;
413	>
414	>	molInfo.myRigidBodies.clear();
415	>
416	>	for (j = 0; j < molInfo.nRigidBodies; j++){
417
418	+	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
419	+	nMembers = currentRigidBody->getNMembers();
420
421	<	// get some of the tricky things that may still be in the globals
421	>	// Create the Rigid Body:
422
423	<
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() ){
423	>	myRB = new RigidBody();
424
425	<	double vol;
426	<	vol = (double)tot_nmol / the_globals->getDensity();
427	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
428	<	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();
425	>	sprintf(rbName,"%s_RB_%d", molName, j);
426	>	myRB->setType(rbName);
427	>
428	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
429
430	<	if( !the_globals->haveBoxY() ){
431	<	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();
430	>	// molI is atom numbering inside this molecule
431	>	molI = currentRigidBody->getMember(rb1);
432
433	<	if( !the_globals->haveBoxZ() ){
434	<	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	<	}
433	>	// tempI is atom numbering on local processor
434	>	tempI = molI + atomOffset;
435
436	<	#ifdef IS_MPI
437	<	strcpy( checkPointMsg, "Box size set up" );
438	<	MPIcheckPoint();
525	<	#endif // is_mpi
436	>	// currentAtom is the AtomStamp (which we need for
437	>	// rigid body reference positions)
438	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
439
440	+	// When we add to the rigid body, add the atom itself and
441	+	// the stamp info:
442
443	<	// initialize the arrays
444	<
445	<	the_ff->setSimInfo( simnfo );
446	<
447	<	makeMolecules();
448	<	simnfo->identArray = new int[simnfo->n_atoms];
449	<	for(i=0; i<simnfo->n_atoms; i++){
450	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
451	<	}
452	<
453	<	if (the_globals->getUseRF() ) {
454	<	simnfo->useReactionField = 1;
455	<
456	<	if( !the_globals->haveECR() ){
457	<	sprintf( painCave.errMsg,
458	<	"SimSetup Warning: using default value of 1/2 the smallest "
459	<	"box length for the electrostaticCutoffRadius.\n"
460	<	"I hope you have a very fast processor!\n");
461	<	painCave.isFatal = 0;
462	<	simError();
463	<	double smallest;
464	<	smallest = simnfo->box_x;
465	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
466	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
467	<	simnfo->ecr = 0.5 * smallest;
468	<	} else {
469	<	simnfo->ecr        = the_globals->getECR();
470	<	}
471	<
472	<	if( !the_globals->haveEST() ){
473	<	sprintf( painCave.errMsg,
474	<	"SimSetup Warning: using default value of 0.05 * the "
475	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
476	<	);
477	<	painCave.isFatal = 0;
478	<	simError();
479	<	simnfo->est = 0.05 * simnfo->ecr;
480	<	} else {
566	<	simnfo->est        = the_globals->getEST();
567	<	}
568	<
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) {
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->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();
443	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
444	>
445	>	// Add this atom to the Skip List for the integrators
446	>	#ifdef IS_MPI
447	>	slI = info[k].atoms[tempI]->getGlobalIndex();
448	>	#else
449	>	slI = tempI;
450	>	#endif
451	>	skipList.insert(slI);
452	>
453	>	}
454	>
455	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
456	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
457	>
458	>	tempI = currentRigidBody->getMember(rb1);
459	>	tempJ = currentRigidBody->getMember(rb2);
460	>
461	>	// Some explanation is required here.
462	>	// Fortran indexing starts at 1, while c indexing starts at 0
463	>	// Also, in parallel computations, the GlobalIndex is
464	>	// used for the exclude list:
465	>
466	>	#ifdef IS_MPI
467	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
468	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
469	>	#else
470	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
471	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
472	>	#endif
473	>
474	>	info[k].excludes->addPair(exI, exJ);
475	>
476	>	}
477	>	}
478	>
479	>	molInfo.myRigidBodies.push_back(myRB);
480	>	info[k].rigidBodies.push_back(myRB);
481		}
482
597	–	if( !the_globals->haveEST() ){
598	–	sprintf( painCave.errMsg,
599	–	"SimSetup Warning: using default value of 5%% of the "
600	–	"electrostaticCutoffRadius for the "
601	–	"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	–	}
483
484	<	#ifdef IS_MPI
485	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
614	<	MPIcheckPoint();
615	<	#endif // is_mpi
484	>	// After this is all set up, scan through the atoms to
485	>	// see if they can be added to the integrableObjects:
486
487	<	if( the_globals->haveInitialConfig() ){
488	<
489	<	InitializeFromFile* fileInit;
490	<	#ifdef IS_MPI // is_mpi
491	<	if( worldRank == 0 ){
622	<	#endif //is_mpi
623	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
487	>	molInfo.myIntegrableObjects.clear();
488	>
489	>
490	>	for (j = 0; j < molInfo.nAtoms; j++){
491	>
492		#ifdef IS_MPI
493	<	}else fileInit = new InitializeFromFile( NULL );
493	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
494	>	#else
495	>	slJ = j+atomOffset;
496		#endif
627	–	fileInit->read_xyz( simnfo ); // default velocities on
497
498	<	delete fileInit;
630	<	}
631	<	else{
498	>	// if they aren't on the skip list, then they can be integrated
499
500	<	#ifdef IS_MPI
500	>	if (skipList.find(slJ) == skipList.end()) {
501	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
502	>	info[k].integrableObjects.push_back(mySD);
503	>	molInfo.myIntegrableObjects.push_back(mySD);
504	>	}
505	>	}
506
507	<	// 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
507	>	// all rigid bodies are integrated:
508
509	<	initFromBass();
509	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
510	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
511	>	info[k].integrableObjects.push_back(mySD);
512	>	molInfo.myIntegrableObjects.push_back(mySD);
513	>	}
514	>
515	>
516	>	// send the arrays off to the forceField for init.
517	>
518	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
519	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
520	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
521	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
522	>	theTorsions);
523
524	+	info[k].molecules[i].initialize(molInfo);
525
647	–	#endif
648	–	}
526
527	+	atomOffset += molInfo.nAtoms;
528	+	delete[] theBonds;
529	+	delete[] theBends;
530	+	delete[] theTorsions;
531	+	}
532	+	}
533	+
534		#ifdef IS_MPI
535	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
535	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
536		MPIcheckPoint();
537		#endif // is_mpi
538
539	+	// clean up the forcefield
540
541	<
657	<
658	<
541	>	if (!globals->haveLJrcut()){
542
543	<
544	<	#ifdef IS_MPI
545	<	if( worldRank == 0 ){
663	<	#endif // is_mpi
543	>	the_ff->calcRcut();
544	>
545	>	} else {
546
547	<	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
547	>	the_ff->setRcut( globals->getLJrcut() );
548		}
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	–	}
549
550	<	if( the_globals->haveStatusTime() ){
551	<	simnfo->statusTime = the_globals->getStatusTime();
759	<	}
550	>	the_ff->cleanMe();
551	>	}
552
553	<	if( the_globals->haveThermalTime() ){
762	<	simnfo->thermalTime = the_globals->getThermalTime();
763	<	}
764	<
765	<	// check for the temperature set flag
766	<
767	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
768	<
769	<
770	<	// make the integrator
771	<
772	<	switch( ensembleCase ){
773	<
774	<	case NVE_ENS:
775	<	new NVE( simnfo, the_ff );
776	<	break;
777	<
778	<	default:
779	<	sprintf( painCave.errMsg,
780	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
781	<	painCave.isFatal = 1;
782	<	simError();
783	<	}
784	<
785	<
786	<	#ifdef IS_MPI
787	<	mpiSim->mpiRefresh();
788	<	#endif
789	<
790	<	// initialize the Fortran
791	<
792	<
793	<	simnfo->refreshSim();
794	<
795	<	if( !strcmp( simnfo->mixingRule, "standard") ){
796	<	the_ff->initForceField( LB_MIXING_RULE );
797	<	}
798	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
799	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
800	<	}
801	<	else{
802	<	sprintf( painCave.errMsg,
803	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
804	<	simnfo->mixingRule );
805	<	painCave.isFatal = 1;
806	<	simError();
807	<	}
808	<
809	<
810	<	#ifdef IS_MPI
811	<	strcpy( checkPointMsg,
812	<	"Successfully intialized the mixingRule for Fortran." );
813	<	MPIcheckPoint();
814	<	#endif // is_mpi
815	<	}
816	<
817	<
818	<	void SimSetup::makeMolecules( void ){
819	<
820	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
821	<	molInit info;
822	<	DirectionalAtom* dAtom;
823	<	LinkedAssign* extras;
824	<	LinkedAssign* current_extra;
825	<	AtomStamp* currentAtom;
826	<	BondStamp* currentBond;
827	<	BendStamp* currentBend;
828	<	TorsionStamp* currentTorsion;
829	<
830	<	bond_pair* theBonds;
831	<	bend_set* theBends;
832	<	torsion_set* theTorsions;
833	<
834	<
835	<	//init the forceField paramters
836	<
837	<	the_ff->readParams();
838	<
839	<
840	<	// init the atoms
841	<
842	<	double ux, uy, uz, u, uSqr;
843	<
844	<	atomOffset = 0;
845	<	excludeOffset = 0;
846	<	for(i=0; i<simnfo->n_mol; i++){
847	<
848	<	stampID = the_molecules[i].getStampID();
849	<
850	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
851	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
852	<	info.nBends    = comp_stamps[stampID]->getNBends();
853	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
854	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
855	<
856	<	info.myAtoms = &the_atoms[atomOffset];
857	<	info.myExcludes = &the_excludes[excludeOffset];
858	<	info.myBonds = new Bond*[info.nBonds];
859	<	info.myBends = new Bend*[info.nBends];
860	<	info.myTorsions = new Torsion*[info.nTorsions];
861	<
862	<	theBonds = new bond_pair[info.nBonds];
863	<	theBends = new bend_set[info.nBends];
864	<	theTorsions = new torsion_set[info.nTorsions];
865	<
866	<	// make the Atoms
867	<
868	<	for(j=0; j<info.nAtoms; j++){
869	<
870	<	currentAtom = comp_stamps[stampID]->getAtom( j );
871	<	if( currentAtom->haveOrientation() ){
872	<
873	<	dAtom = new DirectionalAtom(j + atomOffset);
874	<	simnfo->n_oriented++;
875	<	info.myAtoms[j] = dAtom;
876	<
877	<	ux = currentAtom->getOrntX();
878	<	uy = currentAtom->getOrntY();
879	<	uz = currentAtom->getOrntZ();
880	<
881	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
882	<
883	<	u = sqrt( uSqr );
884	<	ux = ux / u;
885	<	uy = uy / u;
886	<	uz = uz / u;
887	<
888	<	dAtom->setSUx( ux );
889	<	dAtom->setSUy( uy );
890	<	dAtom->setSUz( uz );
891	<	}
892	<	else{
893	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
894	<	}
895	<	info.myAtoms[j]->setType( currentAtom->getType() );
896	<
897	<	#ifdef IS_MPI
898	<
899	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
900	<
901	<	#endif // is_mpi
902	<	}
903	<
904	<	// make the bonds
905	<	for(j=0; j<info.nBonds; j++){
906	<
907	<	currentBond = comp_stamps[stampID]->getBond( j );
908	<	theBonds[j].a = currentBond->getA() + atomOffset;
909	<	theBonds[j].b = currentBond->getB() + atomOffset;
910	<
911	<	exI = theBonds[j].a;
912	<	exJ = theBonds[j].b;
913	<
914	<	// exclude_I must always be the smaller of the pair
915	<	if( exI > exJ ){
916	<	tempEx = exI;
917	<	exI = exJ;
918	<	exJ = tempEx;
919	<	}
920	<	#ifdef IS_MPI
921	<	tempEx = exI;
922	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
923	<	tempEx = exJ;
924	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
925	<
926	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
927	<	#else  // isn't MPI
928	<
929	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
930	<	#endif  //is_mpi
931	<	}
932	<	excludeOffset += info.nBonds;
933	<
934	<	//make the bends
935	<	for(j=0; j<info.nBends; j++){
936	<
937	<	currentBend = comp_stamps[stampID]->getBend( j );
938	<	theBends[j].a = currentBend->getA() + atomOffset;
939	<	theBends[j].b = currentBend->getB() + atomOffset;
940	<	theBends[j].c = currentBend->getC() + atomOffset;
941	<
942	<	if( currentBend->haveExtras() ){
943	<
944	<	extras = currentBend->getExtras();
945	<	current_extra = extras;
946	<
947	<	while( current_extra != NULL ){
948	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
949	<
950	<	switch( current_extra->getType() ){
951	<
952	<	case 0:
953	<	theBends[j].ghost =
954	<	current_extra->getInt() + atomOffset;
955	<	theBends[j].isGhost = 1;
956	<	break;
957	<
958	<	case 1:
959	<	theBends[j].ghost =
960	<	(int)current_extra->getDouble() + atomOffset;
961	<	theBends[j].isGhost = 1;
962	<	break;
963	<
964	<	default:
965	<	sprintf( painCave.errMsg,
966	<	"SimSetup Error: ghostVectorSource was neither a "
967	<	"double nor an int.\n"
968	<	"-->Bend[%d] in %s\n",
969	<	j, comp_stamps[stampID]->getID() );
970	<	painCave.isFatal = 1;
971	<	simError();
972	<	}
973	<	}
974	<
975	<	else{
976	<
977	<	sprintf( painCave.errMsg,
978	<	"SimSetup Error: unhandled bend assignment:\n"
979	<	"    -->%s in Bend[%d] in %s\n",
980	<	current_extra->getlhs(),
981	<	j, comp_stamps[stampID]->getID() );
982	<	painCave.isFatal = 1;
983	<	simError();
984	<	}
985	<
986	<	current_extra = current_extra->getNext();
987	<	}
988	<	}
989	<
990	<	if( !theBends[j].isGhost ){
991	<
992	<	exI = theBends[j].a;
993	<	exJ = theBends[j].c;
994	<	}
995	<	else{
996	<
997	<	exI = theBends[j].a;
998	<	exJ = theBends[j].b;
999	<	}
1000	<
1001	<	// exclude_I must always be the smaller of the pair
1002	<	if( exI > exJ ){
1003	<	tempEx = exI;
1004	<	exI = exJ;
1005	<	exJ = tempEx;
1006	<	}
1007	<	#ifdef IS_MPI
1008	<	tempEx = exI;
1009	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1010	<	tempEx = exJ;
1011	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1012	<
1013	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1014	<	#else  // isn't MPI
1015	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1016	<	#endif  //is_mpi
1017	<	}
1018	<	excludeOffset += info.nBends;
1019	<
1020	<	for(j=0; j<info.nTorsions; j++){
1021	<
1022	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1023	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1024	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1025	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1026	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1027	<
1028	<	exI = theTorsions[j].a;
1029	<	exJ = theTorsions[j].d;
1030	<
1031	<	// exclude_I must always be the smaller of the pair
1032	<	if( exI > exJ ){
1033	<	tempEx = exI;
1034	<	exI = exJ;
1035	<	exJ = tempEx;
1036	<	}
1037	<	#ifdef IS_MPI
1038	<	tempEx = exI;
1039	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1040	<	tempEx = exJ;
1041	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1042	<
1043	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1044	<	#else  // isn't MPI
1045	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1046	<	#endif  //is_mpi
1047	<	}
1048	<	excludeOffset += info.nTorsions;
1049	<
1050	<
1051	<	// send the arrays off to the forceField for init.
1052	<
1053	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1054	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1055	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1056	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1057	<
1058	<
1059	<	the_molecules[i].initialize( info );
1060	<
1061	<
1062	<	atomOffset += info.nAtoms;
1063	<	delete[] theBonds;
1064	<	delete[] theBends;
1065	<	delete[] theTorsions;
1066	<	}
1067	<
1068	<	#ifdef IS_MPI
1069	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1070	<	MPIcheckPoint();
1071	<	#endif // is_mpi
1072	<
1073	<	// clean up the forcefield
1074	<	the_ff->calcRcut();
1075	<	the_ff->cleanMe();
1076	<
1077	<	}
1078	<
1079	<	void SimSetup::initFromBass( void ){
1080	<
553	>	void SimSetup::initFromBass(void){
554		int i, j, k;
555		int n_cells;
556		double cellx, celly, cellz;
#	Line 1086 | Line 559 | void SimSetup::initFromBass( void ){
559		int n_extra;
560		int have_extra, done;
561
562	<	temp1 = (double)tot_nmol / 4.0;
563	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
564	<	temp3 = ceil( temp2 );
562	>	double vel[3];
563	>	vel[0] = 0.0;
564	>	vel[1] = 0.0;
565	>	vel[2] = 0.0;
566
567	<	have_extra =0;
568	<	if( temp2 < temp3 ){ // we have a non-complete lattice
569	<	have_extra =1;
567	>	temp1 = (double) tot_nmol / 4.0;
568	>	temp2 = pow(temp1, (1.0 / 3.0));
569	>	temp3 = ceil(temp2);
570
571	<	n_cells = (int)temp3 - 1;
572	<	cellx = simnfo->box_x / temp3;
573	<	celly = simnfo->box_y / temp3;
574	<	cellz = simnfo->box_z / temp3;
1101	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1102	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1103	<	n_per_extra = (int)ceil( temp1 );
571	>	have_extra = 0;
572	>	if (temp2 < temp3){
573	>	// we have a non-complete lattice
574	>	have_extra = 1;
575
576	<	if( n_per_extra > 4){
577	<	sprintf( painCave.errMsg,
578	<	"SimSetup error. There has been an error in constructing"
579	<	" the non-complete lattice.\n" );
576	>	n_cells = (int) temp3 - 1;
577	>	cellx = info[0].boxL[0] / temp3;
578	>	celly = info[0].boxL[1] / temp3;
579	>	cellz = info[0].boxL[2] / temp3;
580	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
581	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
582	>	n_per_extra = (int) ceil(temp1);
583	>
584	>	if (n_per_extra > 4){
585	>	sprintf(painCave.errMsg,
586	>	"SimSetup error. There has been an error in constructing"
587	>	" the non-complete lattice.\n");
588		painCave.isFatal = 1;
589		simError();
590		}
591		}
592		else{
593	<	n_cells = (int)temp3;
594	<	cellx = simnfo->box_x / temp3;
595	<	celly = simnfo->box_y / temp3;
596	<	cellz = simnfo->box_z / temp3;
593	>	n_cells = (int) temp3;
594	>	cellx = info[0].boxL[0] / temp3;
595	>	celly = info[0].boxL[1] / temp3;
596	>	cellz = info[0].boxL[2] / temp3;
597		}
598
599		current_mol = 0;
#	Line 1122 | Line 601 | void SimSetup::initFromBass( void ){
601		current_comp = 0;
602		current_atom_ndx = 0;
603
604	<	for( i=0; i < n_cells ; i++ ){
605	<	for( j=0; j < n_cells; j++ ){
606	<	for( k=0; k < n_cells; k++ ){
604	>	for (i = 0; i < n_cells ; i++){
605	>	for (j = 0; j < n_cells; j++){
606	>	for (k = 0; k < n_cells; k++){
607	>	makeElement(i * cellx, j * celly, k * cellz);
608
609	<	makeElement( i * cellx,
1130	<	j * celly,
1131	<	k * cellz );
609	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
610
611	<	makeElement( i * cellx + 0.5 * cellx,
1134	<	j * celly + 0.5 * celly,
1135	<	k * cellz );
611	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
612
613	<	makeElement( i * cellx,
1138	<	j * celly + 0.5 * celly,
1139	<	k * cellz + 0.5 * cellz );
1140	<
1141	<	makeElement( i * cellx + 0.5 * cellx,
1142	<	j * celly,
1143	<	k * cellz + 0.5 * cellz );
613	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
614		}
615		}
616		}
617
618	<	if( have_extra ){
618	>	if (have_extra){
619		done = 0;
620
621		int start_ndx;
622	<	for( i=0; i < (n_cells+1) && !done; i++ ){
623	<	for( j=0; j < (n_cells+1) && !done; j++ ){
622	>	for (i = 0; i < (n_cells + 1) && !done; i++){
623	>	for (j = 0; j < (n_cells + 1) && !done; j++){
624	>	if (i < n_cells){
625	>	if (j < n_cells){
626	>	start_ndx = n_cells;
627	>	}
628	>	else
629	>	start_ndx = 0;
630	>	}
631	>	else
632	>	start_ndx = 0;
633
634	<	if( i < n_cells ){
634	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
635	>	makeElement(i * cellx, j * celly, k * cellz);
636	>	done = (current_mol >= tot_nmol);
637
638	<	if( j < n_cells ){
639	<	start_ndx = n_cells;
640	<	}
641	<	else start_ndx = 0;
642	<	}
1162	<	else start_ndx = 0;
638	>	if (!done && n_per_extra > 1){
639	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
640	>	k * cellz);
641	>	done = (current_mol >= tot_nmol);
642	>	}
643
644	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
645	<
646	<	makeElement( i * cellx,
647	<	j * celly,
648	<	k * cellz );
1169	<	done = ( current_mol >= tot_nmol );
1170	<
1171	<	if( !done && n_per_extra > 1 ){
1172	<	makeElement( i * cellx + 0.5 * cellx,
1173	<	j * celly + 0.5 * celly,
1174	<	k * cellz );
1175	<	done = ( current_mol >= tot_nmol );
1176	<	}
644	>	if (!done && n_per_extra > 2){
645	>	makeElement(i * cellx, j * celly + 0.5 * celly,
646	>	k * cellz + 0.5 * cellz);
647	>	done = (current_mol >= tot_nmol);
648	>	}
649
650	<	if( !done && n_per_extra > 2){
651	<	makeElement( i * cellx,
652	<	j * celly + 0.5 * celly,
653	<	k * cellz + 0.5 * cellz );
654	<	done = ( current_mol >= tot_nmol );
655	<	}
1184	<
1185	<	if( !done && n_per_extra > 3){
1186	<	makeElement( i * cellx + 0.5 * cellx,
1187	<	j * celly,
1188	<	k * cellz + 0.5 * cellz );
1189	<	done = ( current_mol >= tot_nmol );
1190	<	}
1191	<	}
650	>	if (!done && n_per_extra > 3){
651	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
652	>	k * cellz + 0.5 * cellz);
653	>	done = (current_mol >= tot_nmol);
654	>	}
655	>	}
656		}
657		}
658		}
659
660	<
661	<	for( i=0; i<simnfo->n_atoms; i++ ){
1198	<	simnfo->atoms[i]->set_vx( 0.0 );
1199	<	simnfo->atoms[i]->set_vy( 0.0 );
1200	<	simnfo->atoms[i]->set_vz( 0.0 );
660	>	for (i = 0; i < info[0].n_atoms; i++){
661	>	info[0].atoms[i]->setVel(vel);
662		}
663		}
664
665	<	void SimSetup::makeElement( double x, double y, double z ){
1205	<
665	>	void SimSetup::makeElement(double x, double y, double z){
666		int k;
667		AtomStamp* current_atom;
668		DirectionalAtom* dAtom;
669		double rotMat[3][3];
670	+	double pos[3];
671
672	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
673	<
674	<	current_atom = comp_stamps[current_comp]->getAtom( k );
675	<	if( !current_atom->havePosition() ){
676	<	sprintf( painCave.errMsg,
677	<	"SimSetup:initFromBass error.\n"
678	<	"\tComponent %s, atom %s does not have a position specified.\n"
679	<	"\tThe initialization routine is unable to give a start"
680	<	" position.\n",
1220	<	comp_stamps[current_comp]->getID(),
1221	<	current_atom->getType() );
672	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
673	>	current_atom = comp_stamps[current_comp]->getAtom(k);
674	>	if (!current_atom->havePosition()){
675	>	sprintf(painCave.errMsg,
676	>	"SimSetup:initFromBass error.\n"
677	>	"\tComponent %s, atom %s does not have a position specified.\n"
678	>	"\tThe initialization routine is unable to give a start"
679	>	" position.\n",
680	>	comp_stamps[current_comp]->getID(), current_atom->getType());
681		painCave.isFatal = 1;
682		simError();
683		}
684
685	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
686	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
687	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
685	>	pos[0] = x + current_atom->getPosX();
686	>	pos[1] = y + current_atom->getPosY();
687	>	pos[2] = z + current_atom->getPosZ();
688
689	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
689	>	info[0].atoms[current_atom_ndx]->setPos(pos);
690
691	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
691	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
692	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
693
694		rotMat[0][0] = 1.0;
695		rotMat[0][1] = 0.0;
#	Line 1243 | Line 703 | void SimSetup::makeElement( double x, double y, double
703		rotMat[2][1] = 0.0;
704		rotMat[2][2] = 1.0;
705
706	<	dAtom->setA( rotMat );
706	>	dAtom->setA(rotMat);
707		}
708
709		current_atom_ndx++;
#	Line 1251 | Line 711 | void SimSetup::makeElement( double x, double y, double
711
712		current_mol++;
713		current_comp_mol++;
714	+
715	+	if (current_comp_mol >= components_nmol[current_comp]){
716	+	current_comp_mol = 0;
717	+	current_comp++;
718	+	}
719	+	}
720	+
721	+
722	+	void SimSetup::gatherInfo(void){
723	+	int i;
724	+
725	+	ensembleCase = -1;
726	+	ffCase = -1;
727	+
728	+	// set the easy ones first
729	+
730	+	for (i = 0; i < nInfo; i++){
731	+	info[i].target_temp = globals->getTargetTemp();
732	+	info[i].dt = globals->getDt();
733	+	info[i].run_time = globals->getRunTime();
734	+	}
735	+	n_components = globals->getNComponents();
736	+
737	+
738	+	// get the forceField
739	+
740	+	strcpy(force_field, globals->getForceField());
741	+
742	+	if (!strcasecmp(force_field, "DUFF")){
743	+	ffCase = FF_DUFF;
744	+	}
745	+	else if (!strcasecmp(force_field, "LJ")){
746	+	ffCase = FF_LJ;
747	+	}
748	+	else if (!strcasecmp(force_field, "EAM")){
749	+	ffCase = FF_EAM;
750	+	}
751	+	else if (!strcasecmp(force_field, "WATER")){
752	+	ffCase = FF_H2O;
753	+	}
754	+	else{
755	+	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
756	+	force_field);
757	+	painCave.isFatal = 1;
758	+	simError();
759	+	}
760	+
761	+	// get the ensemble
762	+
763	+	strcpy(ensemble, globals->getEnsemble());
764	+
765	+	if (!strcasecmp(ensemble, "NVE")){
766	+	ensembleCase = NVE_ENS;
767	+	}
768	+	else if (!strcasecmp(ensemble, "NVT")){
769	+	ensembleCase = NVT_ENS;
770	+	}
771	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
772	+	ensembleCase = NPTi_ENS;
773	+	}
774	+	else if (!strcasecmp(ensemble, "NPTf")){
775	+	ensembleCase = NPTf_ENS;
776	+	}
777	+	else if (!strcasecmp(ensemble, "NPTxyz")){
778	+	ensembleCase = NPTxyz_ENS;
779	+	}
780	+	else{
781	+	sprintf(painCave.errMsg,
782	+	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
783	+	"\treverting to NVE for this simulation.\n",
784	+	ensemble);
785	+	painCave.isFatal = 0;
786	+	simError();
787	+	strcpy(ensemble, "NVE");
788	+	ensembleCase = NVE_ENS;
789	+	}
790	+
791	+	for (i = 0; i < nInfo; i++){
792	+	strcpy(info[i].ensemble, ensemble);
793	+
794	+	// get the mixing rule
795	+
796	+	strcpy(info[i].mixingRule, globals->getMixingRule());
797	+	info[i].usePBC = globals->getPBC();
798	+	}
799	+
800	+	// get the components and calculate the tot_nMol and indvidual n_mol
801	+
802	+	the_components = globals->getComponents();
803	+	components_nmol = new int[n_components];
804	+
805	+
806	+	if (!globals->haveNMol()){
807	+	// we don't have the total number of molecules, so we assume it is
808	+	// given in each component
809	+
810	+	tot_nmol = 0;
811	+	for (i = 0; i < n_components; i++){
812	+	if (!the_components[i]->haveNMol()){
813	+	// we have a problem
814	+	sprintf(painCave.errMsg,
815	+	"SimSetup Error. No global NMol or component NMol given.\n"
816	+	"\tCannot calculate the number of atoms.\n");
817	+	painCave.isFatal = 1;
818	+	simError();
819	+	}
820	+
821	+	tot_nmol += the_components[i]->getNMol();
822	+	components_nmol[i] = the_components[i]->getNMol();
823	+	}
824	+	}
825	+	else{
826	+	sprintf(painCave.errMsg,
827	+	"SimSetup error.\n"
828	+	"\tSorry, the ability to specify total"
829	+	" nMols and then give molfractions in the components\n"
830	+	"\tis not currently supported."
831	+	" Please give nMol in the components.\n");
832	+	painCave.isFatal = 1;
833	+	simError();
834	+	}
835	+
836	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
837	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
838	+	sprintf(painCave.errMsg,
839	+	"Sample time is not divisible by dt.\n"
840	+	"\tThis will result in samples that are not uniformly\n"
841	+	"\tdistributed in time.  If this is a problem, change\n"
842	+	"\tyour sampleTime variable.\n");
843	+	painCave.isFatal = 0;
844	+	simError();
845	+	}
846	+
847	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
848	+	sprintf(painCave.errMsg,
849	+	"Status time is not divisible by dt.\n"
850	+	"\tThis will result in status reports that are not uniformly\n"
851	+	"\tdistributed in time.  If this is a problem, change \n"
852	+	"\tyour statusTime variable.\n");
853	+	painCave.isFatal = 0;
854	+	simError();
855	+	}
856	+
857	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
858	+	sprintf(painCave.errMsg,
859	+	"Thermal time is not divisible by dt.\n"
860	+	"\tThis will result in thermalizations that are not uniformly\n"
861	+	"\tdistributed in time.  If this is a problem, change \n"
862	+	"\tyour thermalTime variable.\n");
863	+	painCave.isFatal = 0;
864	+	simError();
865	+	}
866	+
867	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
868	+	sprintf(painCave.errMsg,
869	+	"Reset time is not divisible by dt.\n"
870	+	"\tThis will result in integrator resets that are not uniformly\n"
871	+	"\tdistributed in time.  If this is a problem, change\n"
872	+	"\tyour resetTime variable.\n");
873	+	painCave.isFatal = 0;
874	+	simError();
875	+	}
876	+
877	+	// set the status, sample, and thermal kick times
878	+
879	+	for (i = 0; i < nInfo; i++){
880	+	if (globals->haveSampleTime()){
881	+	info[i].sampleTime = globals->getSampleTime();
882	+	info[i].statusTime = info[i].sampleTime;
883	+	}
884	+	else{
885	+	info[i].sampleTime = globals->getRunTime();
886	+	info[i].statusTime = info[i].sampleTime;
887	+	}
888	+
889	+	if (globals->haveStatusTime()){
890	+	info[i].statusTime = globals->getStatusTime();
891	+	}
892	+
893	+	if (globals->haveThermalTime()){
894	+	info[i].thermalTime = globals->getThermalTime();
895	+	} else {
896	+	info[i].thermalTime = globals->getRunTime();
897	+	}
898	+
899	+	info[i].resetIntegrator = 0;
900	+	if( globals->haveResetTime() ){
901	+	info[i].resetTime = globals->getResetTime();
902	+	info[i].resetIntegrator = 1;
903	+	}
904	+
905	+	// check for the temperature set flag
906	+
907	+	if (globals->haveTempSet())
908	+	info[i].setTemp = globals->getTempSet();
909	+
910	+	// check for the extended State init
911	+
912	+	info[i].useInitXSstate = globals->getUseInitXSstate();
913	+	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
914	+	info[i].useMolecularCutoffs = globals->getUseMolecularCutoffs();
915	+
916	+
917	+	}
918	+
919	+	//setup seed for random number generator
920	+	int seedValue;
921	+
922	+	if (globals->haveSeed()){
923	+	seedValue = globals->getSeed();
924	+
925	+	if(seedValue / 1E9 == 0){
926	+	sprintf(painCave.errMsg,
927	+	"Seed for sprng library should contain at least 9 digits\n"
928	+	"OOPSE will generate a seed for user\n");
929	+	painCave.isFatal = 0;
930	+	simError();
931	+
932	+	//using seed generated by system instead of invalid seed set by user
933	+	#ifndef IS_MPI
934	+	seedValue = make_sprng_seed();
935	+	#else
936	+	if (worldRank == 0){
937	+	seedValue = make_sprng_seed();
938	+	}
939	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
940	+	#endif
941	+	}
942	+	}//end of if branch of globals->haveSeed()
943	+	else{
944	+
945	+	#ifndef IS_MPI
946	+	seedValue = make_sprng_seed();
947	+	#else
948	+	if (worldRank == 0){
949	+	seedValue = make_sprng_seed();
950	+	}
951	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
952	+	#endif
953	+	}//end of globals->haveSeed()
954	+
955	+	for (int i = 0; i < nInfo; i++){
956	+	info[i].setSeed(seedValue);
957	+	}
958	+
959	+	#ifdef IS_MPI
960	+	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
961	+	MPIcheckPoint();
962	+	#endif // is_mpi
963	+	}
964	+
965	+
966	+	void SimSetup::finalInfoCheck(void){
967	+	int index;
968	+	int usesDipoles;
969	+	int usesCharges;
970	+	int i;
971	+
972	+	for (i = 0; i < nInfo; i++){
973	+	// check electrostatic parameters
974	+
975	+	index = 0;
976	+	usesDipoles = 0;
977	+	while ((index < info[i].n_atoms) && !usesDipoles){
978	+	usesDipoles = (info[i].atoms[index])->hasDipole();
979	+	index++;
980	+	}
981	+	index = 0;
982	+	usesCharges = 0;
983	+	while ((index < info[i].n_atoms) && !usesCharges){
984	+	usesCharges= (info[i].atoms[index])->hasCharge();
985	+	index++;
986	+	}
987	+	#ifdef IS_MPI
988	+	int myUse = usesDipoles;
989	+	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
990	+	#endif //is_mpi
991	+
992	+	double theEcr, theEst;
993	+
994	+	if (globals->getUseRF()){
995	+	info[i].useReactionField = 1;
996	+
997	+	if (!globals->haveECR()){
998	+	sprintf(painCave.errMsg,
999	+	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1000	+	"\tOOPSE will use a default value of 15.0 angstroms"
1001	+	"\tfor the electrostaticCutoffRadius.\n");
1002	+	painCave.isFatal = 0;
1003	+	simError();
1004	+	theEcr = 15.0;
1005	+	}
1006	+	else{
1007	+	theEcr = globals->getECR();
1008	+	}
1009	+
1010	+	if (!globals->haveEST()){
1011	+	sprintf(painCave.errMsg,
1012	+	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1013	+	"\tOOPSE will use a default value of\n"
1014	+	"\t0.05 * electrostaticCutoffRadius\n"
1015	+	"\tfor the electrostaticSkinThickness\n");
1016	+	painCave.isFatal = 0;
1017	+	simError();
1018	+	theEst = 0.05 * theEcr;
1019	+	}
1020	+	else{
1021	+	theEst = globals->getEST();
1022	+	}
1023	+
1024	+	info[i].setDefaultEcr(theEcr, theEst);
1025	+
1026	+	if (!globals->haveDielectric()){
1027	+	sprintf(painCave.errMsg,
1028	+	"SimSetup Error: No Dielectric constant was set.\n"
1029	+	"\tYou are trying to use Reaction Field without"
1030	+	"\tsetting a dielectric constant!\n");
1031	+	painCave.isFatal = 1;
1032	+	simError();
1033	+	}
1034	+	info[i].dielectric = globals->getDielectric();
1035	+	}
1036	+	else{
1037	+	if (usesDipoles || usesCharges){
1038	+	if (!globals->haveECR()){
1039	+	sprintf(painCave.errMsg,
1040	+	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1041	+	"\tOOPSE will use a default value of 15.0 angstroms"
1042	+	"\tfor the electrostaticCutoffRadius.\n");
1043	+	painCave.isFatal = 0;
1044	+	simError();
1045	+	theEcr = 15.0;
1046	+	}
1047	+	else{
1048	+	theEcr = globals->getECR();
1049	+	}
1050	+
1051	+	if (!globals->haveEST()){
1052	+	sprintf(painCave.errMsg,
1053	+	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1054	+	"\tOOPSE will use a default value of\n"
1055	+	"\t0.05 * electrostaticCutoffRadius\n"
1056	+	"\tfor the electrostaticSkinThickness\n");
1057	+	painCave.isFatal = 0;
1058	+	simError();
1059	+	theEst = 0.05 * theEcr;
1060	+	}
1061	+	else{
1062	+	theEst = globals->getEST();
1063	+	}
1064	+
1065	+	info[i].setDefaultEcr(theEcr, theEst);
1066	+	}
1067	+	}
1068	+	}
1069	+	#ifdef IS_MPI
1070	+	strcpy(checkPointMsg, "post processing checks out");
1071	+	MPIcheckPoint();
1072	+	#endif // is_mpi
1073	+	}
1074	+
1075	+	void SimSetup::initSystemCoords(void){
1076	+	int i;
1077	+
1078	+	char* inName;
1079
1080	<	if( current_comp_mol >= components_nmol[current_comp] ){
1080	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1081
1082	<	current_comp_mol = 0;
1083	<	current_comp++;
1082	>	for (i = 0; i < info[0].n_atoms; i++)
1083	>	info[0].atoms[i]->setCoords();
1084	>
1085	>	if (globals->haveInitialConfig()){
1086	>	InitializeFromFile* fileInit;
1087	>	#ifdef IS_MPI // is_mpi
1088	>	if (worldRank == 0){
1089	>	#endif //is_mpi
1090	>	inName = globals->getInitialConfig();
1091	>	fileInit = new InitializeFromFile(inName);
1092	>	#ifdef IS_MPI
1093	>	}
1094	>	else
1095	>	fileInit = new InitializeFromFile(NULL);
1096	>	#endif
1097	>	fileInit->readInit(info); // default velocities on
1098	>
1099	>	delete fileInit;
1100		}
1101	+	else{
1102	+
1103	+	// no init from bass
1104	+
1105	+	sprintf(painCave.errMsg,
1106	+	"Cannot intialize a simulation without an initial configuration file.\n");
1107	+	painCave.isFatal = 1;;
1108	+	simError();
1109	+
1110	+	}
1111	+
1112	+	#ifdef IS_MPI
1113	+	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1114	+	MPIcheckPoint();
1115	+	#endif // is_mpi
1116		}
1117	+
1118	+
1119	+	void SimSetup::makeOutNames(void){
1120	+	int k;
1121	+
1122	+
1123	+	for (k = 0; k < nInfo; k++){
1124	+	#ifdef IS_MPI
1125	+	if (worldRank == 0){
1126	+	#endif // is_mpi
1127	+
1128	+	if (globals->haveFinalConfig()){
1129	+	strcpy(info[k].finalName, globals->getFinalConfig());
1130	+	}
1131	+	else{
1132	+	strcpy(info[k].finalName, inFileName);
1133	+	char* endTest;
1134	+	int nameLength = strlen(info[k].finalName);
1135	+	endTest = &(info[k].finalName[nameLength - 5]);
1136	+	if (!strcmp(endTest, ".bass")){
1137	+	strcpy(endTest, ".eor");
1138	+	}
1139	+	else if (!strcmp(endTest, ".BASS")){
1140	+	strcpy(endTest, ".eor");
1141	+	}
1142	+	else{
1143	+	endTest = &(info[k].finalName[nameLength - 4]);
1144	+	if (!strcmp(endTest, ".bss")){
1145	+	strcpy(endTest, ".eor");
1146	+	}
1147	+	else if (!strcmp(endTest, ".mdl")){
1148	+	strcpy(endTest, ".eor");
1149	+	}
1150	+	else{
1151	+	strcat(info[k].finalName, ".eor");
1152	+	}
1153	+	}
1154	+	}
1155	+
1156	+	// make the sample and status out names
1157	+
1158	+	strcpy(info[k].sampleName, inFileName);
1159	+	char* endTest;
1160	+	int nameLength = strlen(info[k].sampleName);
1161	+	endTest = &(info[k].sampleName[nameLength - 5]);
1162	+	if (!strcmp(endTest, ".bass")){
1163	+	strcpy(endTest, ".dump");
1164	+	}
1165	+	else if (!strcmp(endTest, ".BASS")){
1166	+	strcpy(endTest, ".dump");
1167	+	}
1168	+	else{
1169	+	endTest = &(info[k].sampleName[nameLength - 4]);
1170	+	if (!strcmp(endTest, ".bss")){
1171	+	strcpy(endTest, ".dump");
1172	+	}
1173	+	else if (!strcmp(endTest, ".mdl")){
1174	+	strcpy(endTest, ".dump");
1175	+	}
1176	+	else{
1177	+	strcat(info[k].sampleName, ".dump");
1178	+	}
1179	+	}
1180	+
1181	+	strcpy(info[k].statusName, inFileName);
1182	+	nameLength = strlen(info[k].statusName);
1183	+	endTest = &(info[k].statusName[nameLength - 5]);
1184	+	if (!strcmp(endTest, ".bass")){
1185	+	strcpy(endTest, ".stat");
1186	+	}
1187	+	else if (!strcmp(endTest, ".BASS")){
1188	+	strcpy(endTest, ".stat");
1189	+	}
1190	+	else{
1191	+	endTest = &(info[k].statusName[nameLength - 4]);
1192	+	if (!strcmp(endTest, ".bss")){
1193	+	strcpy(endTest, ".stat");
1194	+	}
1195	+	else if (!strcmp(endTest, ".mdl")){
1196	+	strcpy(endTest, ".stat");
1197	+	}
1198	+	else{
1199	+	strcat(info[k].statusName, ".stat");
1200	+	}
1201	+	}
1202	+
1203	+	#ifdef IS_MPI
1204	+
1205	+	}
1206	+	#endif // is_mpi
1207	+	}
1208	+	}
1209	+
1210	+
1211	+	void SimSetup::sysObjectsCreation(void){
1212	+	int i, k;
1213	+
1214	+	// create the forceField
1215	+
1216	+	createFF();
1217	+
1218	+	// extract componentList
1219	+
1220	+	compList();
1221	+
1222	+	// calc the number of atoms, bond, bends, and torsions
1223	+
1224	+	calcSysValues();
1225	+
1226	+	#ifdef IS_MPI
1227	+	// divide the molecules among the processors
1228	+
1229	+	mpiMolDivide();
1230	+	#endif //is_mpi
1231	+
1232	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1233	+
1234	+	makeSysArrays();
1235	+
1236	+	// make and initialize the molecules (all but atomic coordinates)
1237	+
1238	+	makeMolecules();
1239	+
1240	+	for (k = 0; k < nInfo; k++){
1241	+	info[k].identArray = new int[info[k].n_atoms];
1242	+	for (i = 0; i < info[k].n_atoms; i++){
1243	+	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1244	+	}
1245	+	}
1246	+	}
1247	+
1248	+
1249	+	void SimSetup::createFF(void){
1250	+	switch (ffCase){
1251	+	case FF_DUFF:
1252	+	the_ff = new DUFF();
1253	+	break;
1254	+
1255	+	case FF_LJ:
1256	+	the_ff = new LJFF();
1257	+	break;
1258	+
1259	+	case FF_EAM:
1260	+	the_ff = new EAM_FF();
1261	+	break;
1262	+
1263	+	case FF_H2O:
1264	+	the_ff = new WATER();
1265	+	break;
1266	+
1267	+	default:
1268	+	sprintf(painCave.errMsg,
1269	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1270	+	painCave.isFatal = 1;
1271	+	simError();
1272	+	}
1273	+
1274	+	#ifdef IS_MPI
1275	+	strcpy(checkPointMsg, "ForceField creation successful");
1276	+	MPIcheckPoint();
1277	+	#endif // is_mpi
1278	+	}
1279	+
1280	+
1281	+	void SimSetup::compList(void){
1282	+	int i;
1283	+	char* id;
1284	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1285	+	LinkedMolStamp* currentStamp = NULL;
1286	+	comp_stamps = new MoleculeStamp * [n_components];
1287	+
1288	+	// make an array of molecule stamps that match the components used.
1289	+	// also extract the used stamps out into a separate linked list
1290	+
1291	+	for (i = 0; i < nInfo; i++){
1292	+	info[i].nComponents = n_components;
1293	+	info[i].componentsNmol = components_nmol;
1294	+	info[i].compStamps = comp_stamps;
1295	+	info[i].headStamp = headStamp;
1296	+	}
1297	+
1298	+
1299	+	for (i = 0; i < n_components; i++){
1300	+	id = the_components[i]->getType();
1301	+	comp_stamps[i] = NULL;
1302	+
1303	+	// check to make sure the component isn't already in the list
1304	+
1305	+	comp_stamps[i] = headStamp->match(id);
1306	+	if (comp_stamps[i] == NULL){
1307	+	// extract the component from the list;
1308	+
1309	+	currentStamp = stamps->extractMolStamp(id);
1310	+	if (currentStamp == NULL){
1311	+	sprintf(painCave.errMsg,
1312	+	"SimSetup error: Component \"%s\" was not found in the "
1313	+	"list of declared molecules\n",
1314	+	id);
1315	+	painCave.isFatal = 1;
1316	+	simError();
1317	+	}
1318	+
1319	+	headStamp->add(currentStamp);
1320	+	comp_stamps[i] = headStamp->match(id);
1321	+	}
1322	+	}
1323	+
1324	+	#ifdef IS_MPI
1325	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1326	+	MPIcheckPoint();
1327	+	#endif // is_mpi
1328	+	}
1329	+
1330	+	void SimSetup::calcSysValues(void){
1331	+	int i;
1332	+
1333	+	int* molMembershipArray;
1334	+
1335	+	tot_atoms = 0;
1336	+	tot_bonds = 0;
1337	+	tot_bends = 0;
1338	+	tot_torsions = 0;
1339	+	tot_rigid = 0;
1340	+	for (i = 0; i < n_components; i++){
1341	+	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1342	+	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1343	+	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1344	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1345	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1346	+	}
1347	+
1348	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1349	+	molMembershipArray = new int[tot_atoms];
1350	+
1351	+	for (i = 0; i < nInfo; i++){
1352	+	info[i].n_atoms = tot_atoms;
1353	+	info[i].n_bonds = tot_bonds;
1354	+	info[i].n_bends = tot_bends;
1355	+	info[i].n_torsions = tot_torsions;
1356	+	info[i].n_SRI = tot_SRI;
1357	+	info[i].n_mol = tot_nmol;
1358	+
1359	+	info[i].molMembershipArray = molMembershipArray;
1360	+	}
1361	+	}
1362	+
1363	+	#ifdef IS_MPI
1364	+
1365	+	void SimSetup::mpiMolDivide(void){
1366	+	int i, j, k;
1367	+	int localMol, allMol;
1368	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1369	+	int local_rigid;
1370	+	vector<int> globalMolIndex;
1371	+
1372	+	mpiSim = new mpiSimulation(info);
1373	+
1374	+	mpiSim->divideLabor();
1375	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1376	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1377	+
1378	+	// set up the local variables
1379	+
1380	+	mol2proc = mpiSim->getMolToProcMap();
1381	+	molCompType = mpiSim->getMolComponentType();
1382	+
1383	+	allMol = 0;
1384	+	localMol = 0;
1385	+	local_atoms = 0;
1386	+	local_bonds = 0;
1387	+	local_bends = 0;
1388	+	local_torsions = 0;
1389	+	local_rigid = 0;
1390	+	globalAtomCounter = 0;
1391	+
1392	+	for (i = 0; i < n_components; i++){
1393	+	for (j = 0; j < components_nmol[i]; j++){
1394	+	if (mol2proc[allMol] == worldRank){
1395	+	local_atoms += comp_stamps[i]->getNAtoms();
1396	+	local_bonds += comp_stamps[i]->getNBonds();
1397	+	local_bends += comp_stamps[i]->getNBends();
1398	+	local_torsions += comp_stamps[i]->getNTorsions();
1399	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1400	+	localMol++;
1401	+	}
1402	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1403	+	info[0].molMembershipArray[globalAtomCounter] = allMol;
1404	+	globalAtomCounter++;
1405	+	}
1406	+
1407	+	allMol++;
1408	+	}
1409	+	}
1410	+	local_SRI = local_bonds + local_bends + local_torsions;
1411	+
1412	+	info[0].n_atoms = mpiSim->getMyNlocal();
1413	+
1414	+
1415	+	if (local_atoms != info[0].n_atoms){
1416	+	sprintf(painCave.errMsg,
1417	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1418	+	"\tlocalAtom (%d) are not equal.\n",
1419	+	info[0].n_atoms, local_atoms);
1420	+	painCave.isFatal = 1;
1421	+	simError();
1422	+	}
1423	+
1424	+	info[0].n_bonds = local_bonds;
1425	+	info[0].n_bends = local_bends;
1426	+	info[0].n_torsions = local_torsions;
1427	+	info[0].n_SRI = local_SRI;
1428	+	info[0].n_mol = localMol;
1429	+
1430	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1431	+	MPIcheckPoint();
1432	+	}
1433	+
1434	+	#endif // is_mpi
1435	+
1436	+
1437	+	void SimSetup::makeSysArrays(void){
1438	+
1439	+	#ifndef IS_MPI
1440	+	int k, j;
1441	+	#endif // is_mpi
1442	+	int i, l;
1443	+
1444	+	Atom** the_atoms;
1445	+	Molecule* the_molecules;
1446	+
1447	+	for (l = 0; l < nInfo; l++){
1448	+	// create the atom and short range interaction arrays
1449	+
1450	+	the_atoms = new Atom * [info[l].n_atoms];
1451	+	the_molecules = new Molecule[info[l].n_mol];
1452	+	int molIndex;
1453	+
1454	+	// initialize the molecule's stampID's
1455	+
1456	+	#ifdef IS_MPI
1457	+
1458	+
1459	+	molIndex = 0;
1460	+	for (i = 0; i < mpiSim->getTotNmol(); i++){
1461	+	if (mol2proc[i] == worldRank){
1462	+	the_molecules[molIndex].setStampID(molCompType[i]);
1463	+	the_molecules[molIndex].setMyIndex(molIndex);
1464	+	the_molecules[molIndex].setGlobalIndex(i);
1465	+	molIndex++;
1466	+	}
1467	+	}
1468	+
1469	+	#else // is_mpi
1470	+
1471	+	molIndex = 0;
1472	+	globalAtomCounter = 0;
1473	+	for (i = 0; i < n_components; i++){
1474	+	for (j = 0; j < components_nmol[i]; j++){
1475	+	the_molecules[molIndex].setStampID(i);
1476	+	the_molecules[molIndex].setMyIndex(molIndex);
1477	+	the_molecules[molIndex].setGlobalIndex(molIndex);
1478	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1479	+	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1480	+	globalAtomCounter++;
1481	+	}
1482	+	molIndex++;
1483	+	}
1484	+	}
1485	+
1486	+
1487	+	#endif // is_mpi
1488	+
1489	+	info[l].globalExcludes = new int;
1490	+	info[l].globalExcludes[0] = 0;
1491	+
1492	+	// set the arrays into the SimInfo object
1493	+
1494	+	info[l].atoms = the_atoms;
1495	+	info[l].molecules = the_molecules;
1496	+	info[l].nGlobalExcludes = 0;
1497	+
1498	+	the_ff->setSimInfo(info);
1499	+	}
1500	+	}
1501	+
1502	+	void SimSetup::makeIntegrator(void){
1503	+	int k;
1504	+
1505	+	NVE<RealIntegrator>* myNVE = NULL;
1506	+	NVT<RealIntegrator>* myNVT = NULL;
1507	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1508	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1509	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1510	+
1511	+	for (k = 0; k < nInfo; k++){
1512	+	switch (ensembleCase){
1513	+	case NVE_ENS:
1514	+	if (globals->haveZconstraints()){
1515	+	setupZConstraint(info[k]);
1516	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1517	+	}
1518	+	else{
1519	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1520	+	}
1521	+
1522	+	info->the_integrator = myNVE;
1523	+	break;
1524	+
1525	+	case NVT_ENS:
1526	+	if (globals->haveZconstraints()){
1527	+	setupZConstraint(info[k]);
1528	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1529	+	}
1530	+	else
1531	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1532	+
1533	+	myNVT->setTargetTemp(globals->getTargetTemp());
1534	+
1535	+	if (globals->haveTauThermostat())
1536	+	myNVT->setTauThermostat(globals->getTauThermostat());
1537	+	else{
1538	+	sprintf(painCave.errMsg,
1539	+	"SimSetup error: If you use the NVT\n"
1540	+	"\tensemble, you must set tauThermostat.\n");
1541	+	painCave.isFatal = 1;
1542	+	simError();
1543	+	}
1544	+
1545	+	info->the_integrator = myNVT;
1546	+	break;
1547	+
1548	+	case NPTi_ENS:
1549	+	if (globals->haveZconstraints()){
1550	+	setupZConstraint(info[k]);
1551	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1552	+	}
1553	+	else
1554	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1555	+
1556	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1557	+
1558	+	if (globals->haveTargetPressure())
1559	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1560	+	else{
1561	+	sprintf(painCave.errMsg,
1562	+	"SimSetup error: If you use a constant pressure\n"
1563	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1564	+	painCave.isFatal = 1;
1565	+	simError();
1566	+	}
1567	+
1568	+	if (globals->haveTauThermostat())
1569	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1570	+	else{
1571	+	sprintf(painCave.errMsg,
1572	+	"SimSetup error: If you use an NPT\n"
1573	+	"\tensemble, you must set tauThermostat.\n");
1574	+	painCave.isFatal = 1;
1575	+	simError();
1576	+	}
1577	+
1578	+	if (globals->haveTauBarostat())
1579	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1580	+	else{
1581	+	sprintf(painCave.errMsg,
1582	+	"SimSetup error: If you use an NPT\n"
1583	+	"\tensemble, you must set tauBarostat.\n");
1584	+	painCave.isFatal = 1;
1585	+	simError();
1586	+	}
1587	+
1588	+	info->the_integrator = myNPTi;
1589	+	break;
1590	+
1591	+	case NPTf_ENS:
1592	+	if (globals->haveZconstraints()){
1593	+	setupZConstraint(info[k]);
1594	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1595	+	}
1596	+	else
1597	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1598	+
1599	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1600	+
1601	+	if (globals->haveTargetPressure())
1602	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1603	+	else{
1604	+	sprintf(painCave.errMsg,
1605	+	"SimSetup error: If you use a constant pressure\n"
1606	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1607	+	painCave.isFatal = 1;
1608	+	simError();
1609	+	}
1610	+
1611	+	if (globals->haveTauThermostat())
1612	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1613	+
1614	+	else{
1615	+	sprintf(painCave.errMsg,
1616	+	"SimSetup error: If you use an NPT\n"
1617	+	"\tensemble, you must set tauThermostat.\n");
1618	+	painCave.isFatal = 1;
1619	+	simError();
1620	+	}
1621	+
1622	+	if (globals->haveTauBarostat())
1623	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1624	+
1625	+	else{
1626	+	sprintf(painCave.errMsg,
1627	+	"SimSetup error: If you use an NPT\n"
1628	+	"\tensemble, you must set tauBarostat.\n");
1629	+	painCave.isFatal = 1;
1630	+	simError();
1631	+	}
1632	+
1633	+	info->the_integrator = myNPTf;
1634	+	break;
1635	+
1636	+	case NPTxyz_ENS:
1637	+	if (globals->haveZconstraints()){
1638	+	setupZConstraint(info[k]);
1639	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1640	+	}
1641	+	else
1642	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1643	+
1644	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1645	+
1646	+	if (globals->haveTargetPressure())
1647	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1648	+	else{
1649	+	sprintf(painCave.errMsg,
1650	+	"SimSetup error: If you use a constant pressure\n"
1651	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1652	+	painCave.isFatal = 1;
1653	+	simError();
1654	+	}
1655	+
1656	+	if (globals->haveTauThermostat())
1657	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1658	+	else{
1659	+	sprintf(painCave.errMsg,
1660	+	"SimSetup error: If you use an NPT\n"
1661	+	"\tensemble, you must set tauThermostat.\n");
1662	+	painCave.isFatal = 1;
1663	+	simError();
1664	+	}
1665	+
1666	+	if (globals->haveTauBarostat())
1667	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1668	+	else{
1669	+	sprintf(painCave.errMsg,
1670	+	"SimSetup error: If you use an NPT\n"
1671	+	"\tensemble, you must set tauBarostat.\n");
1672	+	painCave.isFatal = 1;
1673	+	simError();
1674	+	}
1675	+
1676	+	info->the_integrator = myNPTxyz;
1677	+	break;
1678	+
1679	+	default:
1680	+	sprintf(painCave.errMsg,
1681	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1682	+	painCave.isFatal = 1;
1683	+	simError();
1684	+	}
1685	+	}
1686	+	}
1687	+
1688	+	void SimSetup::initFortran(void){
1689	+	info[0].refreshSim();
1690	+
1691	+	if (!strcmp(info[0].mixingRule, "standard")){
1692	+	the_ff->initForceField(LB_MIXING_RULE);
1693	+	}
1694	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1695	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1696	+	}
1697	+	else{
1698	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1699	+	info[0].mixingRule);
1700	+	painCave.isFatal = 1;
1701	+	simError();
1702	+	}
1703	+
1704	+
1705	+	#ifdef IS_MPI
1706	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1707	+	MPIcheckPoint();
1708	+	#endif // is_mpi
1709	+	}
1710	+
1711	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1712	+	int nZConstraints;
1713	+	ZconStamp** zconStamp;
1714	+
1715	+	if (globals->haveZconstraintTime()){
1716	+	//add sample time of z-constraint  into SimInfo's property list
1717	+	DoubleData* zconsTimeProp = new DoubleData();
1718	+	zconsTimeProp->setID(ZCONSTIME_ID);
1719	+	zconsTimeProp->setData(globals->getZconsTime());
1720	+	theInfo.addProperty(zconsTimeProp);
1721	+	}
1722	+	else{
1723	+	sprintf(painCave.errMsg,
1724	+	"ZConstraint error: If you use a ZConstraint,\n"
1725	+	"\tyou must set zconsTime.\n");
1726	+	painCave.isFatal = 1;
1727	+	simError();
1728	+	}
1729	+
1730	+	//push zconsTol into siminfo, if user does not specify
1731	+	//value for zconsTol, a default value will be used
1732	+	DoubleData* zconsTol = new DoubleData();
1733	+	zconsTol->setID(ZCONSTOL_ID);
1734	+	if (globals->haveZconsTol()){
1735	+	zconsTol->setData(globals->getZconsTol());
1736	+	}
1737	+	else{
1738	+	double defaultZConsTol = 0.01;
1739	+	sprintf(painCave.errMsg,
1740	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1741	+	"\tOOPSE will use a default value of %f.\n"
1742	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1743	+	defaultZConsTol);
1744	+	painCave.isFatal = 0;
1745	+	simError();
1746	+
1747	+	zconsTol->setData(defaultZConsTol);
1748	+	}
1749	+	theInfo.addProperty(zconsTol);
1750	+
1751	+	//set Force Subtraction Policy
1752	+	StringData* zconsForcePolicy = new StringData();
1753	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1754	+
1755	+	if (globals->haveZconsForcePolicy()){
1756	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1757	+	}
1758	+	else{
1759	+	sprintf(painCave.errMsg,
1760	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1761	+	"\tOOPSE will use PolicyByMass.\n"
1762	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1763	+	painCave.isFatal = 0;
1764	+	simError();
1765	+	zconsForcePolicy->setData("BYMASS");
1766	+	}
1767	+
1768	+	theInfo.addProperty(zconsForcePolicy);
1769	+
1770	+	//set zcons gap
1771	+	DoubleData* zconsGap = new DoubleData();
1772	+	zconsGap->setID(ZCONSGAP_ID);
1773	+
1774	+	if (globals->haveZConsGap()){
1775	+	zconsGap->setData(globals->getZconsGap());
1776	+	theInfo.addProperty(zconsGap);
1777	+	}
1778	+
1779	+	//set zcons fixtime
1780	+	DoubleData* zconsFixtime = new DoubleData();
1781	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1782	+
1783	+	if (globals->haveZConsFixTime()){
1784	+	zconsFixtime->setData(globals->getZconsFixtime());
1785	+	theInfo.addProperty(zconsFixtime);
1786	+	}
1787	+
1788	+	//set zconsUsingSMD
1789	+	IntData* zconsUsingSMD = new IntData();
1790	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1791	+
1792	+	if (globals->haveZConsUsingSMD()){
1793	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1794	+	theInfo.addProperty(zconsUsingSMD);
1795	+	}
1796	+
1797	+	//Determine the name of ouput file and add it into SimInfo's property list
1798	+	//Be careful, do not use inFileName, since it is a pointer which
1799	+	//point to a string at master node, and slave nodes do not contain that string
1800	+
1801	+	string zconsOutput(theInfo.finalName);
1802	+
1803	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1804	+
1805	+	StringData* zconsFilename = new StringData();
1806	+	zconsFilename->setID(ZCONSFILENAME_ID);
1807	+	zconsFilename->setData(zconsOutput);
1808	+
1809	+	theInfo.addProperty(zconsFilename);
1810	+
1811	+	//setup index, pos and other parameters of z-constraint molecules
1812	+	nZConstraints = globals->getNzConstraints();
1813	+	theInfo.nZconstraints = nZConstraints;
1814	+
1815	+	zconStamp = globals->getZconStamp();
1816	+	ZConsParaItem tempParaItem;
1817	+
1818	+	ZConsParaData* zconsParaData = new ZConsParaData();
1819	+	zconsParaData->setID(ZCONSPARADATA_ID);
1820	+
1821	+	for (int i = 0; i < nZConstraints; i++){
1822	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1823	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1824	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1825	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1826	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1827	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1828	+	zconsParaData->addItem(tempParaItem);
1829	+	}
1830	+
1831	+	//check the uniqueness of index
1832	+	if(!zconsParaData->isIndexUnique()){
1833	+	sprintf(painCave.errMsg,
1834	+	"ZConstraint Error: molIndex is not unique!\n");
1835	+	painCave.isFatal = 1;
1836	+	simError();
1837	+	}
1838	+
1839	+	//sort the parameters by index of molecules
1840	+	zconsParaData->sortByIndex();
1841	+
1842	+	//push data into siminfo, therefore, we can retrieve later
1843	+	theInfo.addProperty(zconsParaData);
1844	+	}
1845	+
1846	+	void SimSetup::makeMinimizer(){
1847	+
1848	+	OOPSEMinimizer* myOOPSEMinimizer;
1849	+	MinimizerParameterSet* param;
1850	+	char minimizerName[100];
1851	+
1852	+	for (int i = 0; i < nInfo; i++){
1853	+
1854	+	//prepare parameter set for minimizer
1855	+	param = new MinimizerParameterSet();
1856	+	param->setDefaultParameter();
1857	+
1858	+	if (globals->haveMinimizer()){
1859	+	param->setFTol(globals->getMinFTol());
1860	+	}
1861	+
1862	+	if (globals->haveMinGTol()){
1863	+	param->setGTol(globals->getMinGTol());
1864	+	}
1865	+
1866	+	if (globals->haveMinMaxIter()){
1867	+	param->setMaxIteration(globals->getMinMaxIter());
1868	+	}
1869	+
1870	+	if (globals->haveMinWriteFrq()){
1871	+	param->setMaxIteration(globals->getMinMaxIter());
1872	+	}
1873	+
1874	+	if (globals->haveMinWriteFrq()){
1875	+	param->setWriteFrq(globals->getMinWriteFrq());
1876	+	}
1877	+
1878	+	if (globals->haveMinStepSize()){
1879	+	param->setStepSize(globals->getMinStepSize());
1880	+	}
1881	+
1882	+	if (globals->haveMinLSMaxIter()){
1883	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1884	+	}
1885	+
1886	+	if (globals->haveMinLSTol()){
1887	+	param->setLineSearchTol(globals->getMinLSTol());
1888	+	}
1889	+
1890	+	strcpy(minimizerName, globals->getMinimizer());
1891	+
1892	+	if (!strcasecmp(minimizerName, "CG")){
1893	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1894	+	}
1895	+	else if (!strcasecmp(minimizerName, "SD")){
1896	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1897	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1898	+	}
1899	+	else{
1900	+	sprintf(painCave.errMsg,
1901	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1902	+	painCave.isFatal = 0;
1903	+	simError();
1904	+
1905	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1906	+	}
1907	+	info[i].the_integrator = myOOPSEMinimizer;
1908	+
1909	+	//store the minimizer into simInfo
1910	+	info[i].the_minimizer = myOOPSEMinimizer;
1911	+	info[i].has_minimizer = true;
1912	+	}
1913	+
1914	+	}

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines