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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 432 by chuckv, Thu Mar 27 23:33:40 2003 UTC vs.
Revision 1163 by gezelter, Wed May 12 14:30:12 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"
18		#include "mpiSimulation.hpp"
19		#endif
20
21	+	// some defines for ensemble and Forcefield  cases
22	+
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	+
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 27 | 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();
59	<	mpiEventLoop();
60	<
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;
68	<	Globals* the_globals;
69	<	int i, j;
126	>	// gather all of the information from the Bass file
127
128	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
128	>	gatherInfo();
129
130	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	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.
81	<	n_components = the_globals->getNComponents();
82	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
132	>	sysObjectsCreation();
133
134	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
134	>	// check on the post processing info
135
136	+	finalInfoCheck();
137
138	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
92	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
93	<	else{
94	<	sprintf( painCave.errMsg,
95	<	"SimSetup Error. Unrecognized force field -> %s\n",
96	<	force_field );
97	<	painCave.isFatal = 1;
98	<	simError();
99	<	}
138	>	// initialize the system coordinates
139
140	<	#ifdef IS_MPI
141	<	strcpy( checkPointMsg, "ForceField creation successful" );
103	<	MPIcheckPoint();
104	<	#endif // is_mpi
140	>	if ( !initSuspend ){
141	>	initSystemCoords();
142
143	<
143	>	if( !(globals->getUseInitTime()) )
144	>	info[0].currentTime = 0.0;
145	>	}
146
147	<	// get the components and calculate the tot_nMol and indvidual n_mol
109	<	the_components = the_globals->getComponents();
110	<	components_nmol = new int[n_components];
111	<	comp_stamps = new MoleculeStamp*[n_components];
147	>	// make the output filenames
148
149	<	if( !the_globals->haveNMol() ){
150	<	// we don't have the total number of molecules, so we assume it is
151	<	// given in each component
149	>	makeOutNames();
150	>
151	>	#ifdef IS_MPI
152	>	mpiSim->mpiRefresh();
153	>	#endif
154
155	<	tot_nmol = 0;
118	<	for( i=0; i<n_components; i++ ){
155	>	// initialize the Fortran
156
157	<	if( !the_components[i]->haveNMol() ){
121	<	// we have a problem
122	<	sprintf( painCave.errMsg,
123	<	"SimSetup Error. No global NMol or component NMol"
124	<	" given. Cannot calculate the number of atoms.\n" );
125	<	painCave.isFatal = 1;
126	<	simError();
127	<	}
157	>	initFortran();
158
159	<	tot_nmol += the_components[i]->getNMol();
160	<	components_nmol[i] = the_components[i]->getNMol();
161	<	}
162	<	}
163	<	else{
164	<	sprintf( painCave.errMsg,
135	<	"SimSetup error.\n"
136	<	"\tSorry, the ability to specify total"
137	<	" nMols and then give molfractions in the components\n"
138	<	"\tis not currently supported."
139	<	" Please give nMol in the components.\n" );
140	<	painCave.isFatal = 1;
141	<	simError();
142	<
143	<
144	<	//     tot_nmol = the_globals->getNMol();
145	<
146	<	//   //we have the total number of molecules, now we check for molfractions
147	<	//     for( i=0; i<n_components; i++ ){
148	<
149	<	//       if( !the_components[i]->haveMolFraction() ){
150	<
151	<	//  if( !the_components[i]->haveNMol() ){
152	<	//    //we have a problem
153	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
154	<	//              << " nMol was given in component
155	<
156	<	}
159	>	if (globals->haveMinimizer())
160	>	// make minimizer
161	>	makeMinimizer();
162	>	else
163	>	// make the integrator
164	>	makeIntegrator();
165
166	<	#ifdef IS_MPI
159	<	strcpy( checkPointMsg, "Have the number of components" );
160	<	MPIcheckPoint();
161	<	#endif // is_mpi
166	>	}
167
163	–	// make an array of molecule stamps that match the components used.
164	–	// also extract the used stamps out into a separate linked list
168
169	<	simnfo->nComponents = n_components;
170	<	simnfo->componentsNmol = components_nmol;
171	<	simnfo->compStamps = comp_stamps;
172	<	simnfo->headStamp = new LinkedMolStamp();
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	>	CutoffGroupStamp* currentCutoffGroup;
187	>	CutoffGroup* myCutoffGroup;
188
189	<	char* id;
190	<	LinkedMolStamp* headStamp = simnfo->headStamp;
191	<	LinkedMolStamp* currentStamp = NULL;
174	<	for( i=0; i<n_components; i++ ){
189	>	bond_pair* theBonds;
190	>	bend_set* theBends;
191	>	torsion_set* theTorsions;
192
193	<	id = the_components[i]->getType();
177	<	comp_stamps[i] = NULL;
178	<
179	<	// check to make sure the component isn't already in the list
193	>	set<int> skipList;
194
195	<	comp_stamps[i] = headStamp->match( id );
196	<	if( comp_stamps[i] == NULL ){
197	<
184	<	// extract the component from the list;
185	<
186	<	currentStamp = the_stamps->extractMolStamp( id );
187	<	if( currentStamp == NULL ){
188	<	sprintf( painCave.errMsg,
189	<	"SimSetup error: Component \"%s\" was not found in the "
190	<	"list of declared molecules\n",
191	<	id );
192	<	painCave.isFatal = 1;
193	<	simError();
194	<	}
195	<
196	<	headStamp->add( currentStamp );
197	<	comp_stamps[i] = headStamp->match( id );
198	<	}
199	<	}
195	>	double phi, theta, psi;
196	>	char* molName;
197	>	char rbName[100];
198
199	<	#ifdef IS_MPI
202	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
203	<	MPIcheckPoint();
204	<	#endif // is_mpi
205	<
199	>	//init the forceField paramters
200
201	+	the_ff->readParams();
202
203	+	// init the atoms
204
205	<	// caclulate the number of atoms, bonds, bends and torsions
205	>	int nMembers, nNew, rb1, rb2;
206
207	<	tot_atoms = 0;
208	<	tot_bonds = 0;
213	<	tot_bends = 0;
214	<	tot_torsions = 0;
215	<	for( i=0; i<n_components; i++ ){
216	<
217	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
218	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
219	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
220	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
221	<	}
207	>	for (k = 0; k < nInfo; k++){
208	>	the_ff->setSimInfo(&(info[k]));
209
210	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
210	>	atomOffset = 0;
211
212	<	simnfo->n_atoms = tot_atoms;
213	<	simnfo->n_bonds = tot_bonds;
214	<	simnfo->n_bends = tot_bends;
228	<	simnfo->n_torsions = tot_torsions;
229	<	simnfo->n_SRI = tot_SRI;
230	<	simnfo->n_mol = tot_nmol;
212	>	for (i = 0; i < info[k].n_mol; i++){
213	>	stampID = info[k].molecules[i].getStampID();
214	>	molName = comp_stamps[stampID]->getID();
215
216	<
217	<	#ifdef IS_MPI
216	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
217	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
218	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
219	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
220	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
221	>	molInfo.nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
222	>
223	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
224
225	<	// divide the molecules among processors here.
226	<
227	<	mpiSim = new mpiSimulation( simnfo );
228	<
239	<
225	>	if (molInfo.nBonds > 0)
226	>	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
227	>	else
228	>	molInfo.myBonds = NULL;
229
230	<	globalIndex = mpiSim->divideLabor();
230	>	if (molInfo.nBends > 0)
231	>	molInfo.myBends = new (Bend *) [molInfo.nBends];
232	>	else
233	>	molInfo.myBends = NULL;
234
235	<	// set up the local variables
236	<
237	<	int localMol, allMol;
238	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
235	>	if (molInfo.nTorsions > 0)
236	>	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
237	>	else
238	>	molInfo.myTorsions = NULL;
239
240	<	int* mol2proc = mpiSim->getMolToProcMap();
241	<	int* molCompType = mpiSim->getMolComponentType();
242	<
251	<	allMol = 0;
252	<	localMol = 0;
253	<	local_atoms = 0;
254	<	local_bonds = 0;
255	<	local_bends = 0;
256	<	local_torsions = 0;
257	<	for( i=0; i<n_components; i++ ){
258	<
259	<	for( j=0; j<components_nmol[i]; j++ ){
240	>	theBonds = new bond_pair[molInfo.nBonds];
241	>	theBends = new bend_set[molInfo.nBends];
242	>	theTorsions = new torsion_set[molInfo.nTorsions];
243
244	<	if( mol2proc[j] == worldRank ){
262	<
263	<	local_atoms +=    comp_stamps[i]->getNAtoms();
264	<	local_bonds +=    comp_stamps[i]->getNBonds();
265	<	local_bends +=    comp_stamps[i]->getNBends();
266	<	local_torsions += comp_stamps[i]->getNTorsions();
267	<	localMol++;
268	<	}
269	<	allMol++;
270	<	}
271	<	}
272	<	local_SRI = local_bonds + local_bends + local_torsions;
273	<
244	>	// make the Atoms
245
246	<	simnfo->n_atoms = mpiSim->getMyNlocal();
247	<
277	<	if( local_atoms != simnfo->n_atoms ){
278	<	sprintf( painCave.errMsg,
279	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
280	<	" localAtom (%d) are not equal.\n",
281	<	simnfo->n_atoms,
282	<	local_atoms );
283	<	painCave.isFatal = 1;
284	<	simError();
285	<	}
246	>	for (j = 0; j < molInfo.nAtoms; j++){
247	>	currentAtom = comp_stamps[stampID]->getAtom(j);
248
249	<	simnfo->n_bonds = local_bonds;
250	<	simnfo->n_bends = local_bends;
251	<	simnfo->n_torsions = local_torsions;
252	<	simnfo->n_SRI = local_SRI;
253	<	simnfo->n_mol = localMol;
249	>	if (currentAtom->haveOrientation()){
250	>	dAtom = new DirectionalAtom((j + atomOffset),
251	>	info[k].getConfiguration());
252	>	info[k].n_oriented++;
253	>	molInfo.myAtoms[j] = dAtom;
254
255	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
256	<	MPIcheckPoint();
257	<
296	<
297	<	#endif // is_mpi
298	<
255	>	// Directional Atoms have standard unit vectors which are oriented
256	>	// in space using the three Euler angles.  We assume the standard
257	>	// unit vector was originally along the z axis below.
258
259	<	// create the atom and short range interaction arrays
259	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
260	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
261	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
262
263	<	Atom::createArrays(simnfo->n_atoms);
264	<	the_atoms = new Atom*[simnfo->n_atoms];
265	<	the_molecules = new Molecule[simnfo->n_mol];
266	<	int molIndex;
263	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
264	>
265	>	}
266	>	else{
267
268	<	// initialize the molecule's stampID's
268	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
269
270	+	}
271	+
272	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
273		#ifdef IS_MPI
310	–
274
275	<	molIndex = 0;
313	<	for(i=0; i<mpiSim->getTotNmol(); i++){
314	<
315	<	if(mol2proc[i] == worldRank ){
316	<	the_molecules[molIndex].setStampID( molCompType[i] );
317	<	molIndex++;
318	<	}
319	<	}
275	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
276
321	–	#else // is_mpi
322	–
323	–	molIndex = 0;
324	–	for(i=0; i<n_components; i++){
325	–	for(j=0; j<components_nmol[i]; j++ ){
326	–	the_molecules[molIndex].setStampID( i );
327	–	molIndex++;
328	–	}
329	–	}
330	–
331	–
277		#endif // is_mpi
278	+	}
279
280	+	// make the bonds
281	+	for (j = 0; j < molInfo.nBonds; j++){
282	+	currentBond = comp_stamps[stampID]->getBond(j);
283	+	theBonds[j].a = currentBond->getA() + atomOffset;
284	+	theBonds[j].b = currentBond->getB() + atomOffset;
285
286	<	if( simnfo->n_SRI ){
287	<
337	<	std::cerr << "n_SRI = " << simnfo->n_SRI << "\n";
338	<
339	<	Exclude::createArray(simnfo->n_SRI);
340	<	the_excludes = new Exclude*[simnfo->n_SRI];
341	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
342	<	simnfo->globalExcludes = new int;
343	<	simnfo->n_exclude = tot_SRI;
344	<	}
345	<	else{
346	<
347	<	Exclude::createArray( 1 );
348	<	the_excludes = new Exclude*;
349	<	the_excludes[0] = new Exclude(0);
350	<	the_excludes[0]->setPair( 0,0 );
351	<	simnfo->globalExcludes = new int;
352	<	simnfo->globalExcludes[0] = 0;
353	<	simnfo->n_exclude = 0;
354	<	}
286	>	tempI = theBonds[j].a;
287	>	tempJ = theBonds[j].b;
288
289	<	// set the arrays into the SimInfo object
289	>	#ifdef IS_MPI
290	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
291	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
292	>	#else
293	>	exI = tempI + 1;
294	>	exJ = tempJ + 1;
295	>	#endif
296
297	<	simnfo->atoms = the_atoms;
298	<	simnfo->molecules = the_molecules;
360	<	simnfo->nGlobalExcludes = 0;
361	<	simnfo->excludes = the_excludes;
297	>	info[k].excludes->addPair(exI, exJ);
298	>	}
299
300	+	//make the bends
301	+	for (j = 0; j < molInfo.nBends; j++){
302	+	currentBend = comp_stamps[stampID]->getBend(j);
303	+	theBends[j].a = currentBend->getA() + atomOffset;
304	+	theBends[j].b = currentBend->getB() + atomOffset;
305	+	theBends[j].c = currentBend->getC() + atomOffset;
306
307	<	// get some of the tricky things that may still be in the globals
307	>	if (currentBend->haveExtras()){
308	>	extras = currentBend->getExtras();
309	>	current_extra = extras;
310
311	<
312	<	if( the_globals->haveBox() ){
313	<	simnfo->box_x = the_globals->getBox();
314	<	simnfo->box_y = the_globals->getBox();
315	<	simnfo->box_z = the_globals->getBox();
316	<	}
317	<	else if( the_globals->haveDensity() ){
311	>	while (current_extra != NULL){
312	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
313	>	switch (current_extra->getType()){
314	>	case 0:
315	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
316	>	theBends[j].isGhost = 1;
317	>	break;
318
319	<	double vol;
320	<	vol = (double)tot_nmol / the_globals->getDensity();
321	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
322	<	simnfo->box_y = simnfo->box_x;
323	<	simnfo->box_z = simnfo->box_x;
379	<	}
380	<	else{
381	<	if( !the_globals->haveBoxX() ){
382	<	sprintf( painCave.errMsg,
383	<	"SimSetup error, no periodic BoxX size given.\n" );
384	<	painCave.isFatal = 1;
385	<	simError();
386	<	}
387	<	simnfo->box_x = the_globals->getBoxX();
319	>	case 1:
320	>	theBends[j].ghost = (int) current_extra->getDouble() +
321	>	atomOffset;
322	>	theBends[j].isGhost = 1;
323	>	break;
324
325	<	if( !the_globals->haveBoxY() ){
326	<	sprintf( painCave.errMsg,
327	<	"SimSetup error, no periodic BoxY size given.\n" );
328	<	painCave.isFatal = 1;
329	<	simError();
330	<	}
331	<	simnfo->box_y = the_globals->getBoxY();
332	<
333	<	if( !the_globals->haveBoxZ() ){
334	<	sprintf( painCave.errMsg,
335	<	"SimSetup error, no periodic BoxZ size given.\n" );
336	<	painCave.isFatal = 1;
337	<	simError();
338	<	}
339	<	simnfo->box_z = the_globals->getBoxZ();
340	<	}
341	<
342	<	#ifdef IS_MPI
407	<	strcpy( checkPointMsg, "Box size set up" );
408	<	MPIcheckPoint();
409	<	#endif // is_mpi
325	>	default:
326	>	sprintf(painCave.errMsg,
327	>	"SimSetup Error: ghostVectorSource was neither a "
328	>	"double nor an int.\n"
329	>	"-->Bend[%d] in %s\n",
330	>	j, comp_stamps[stampID]->getID());
331	>	painCave.isFatal = 1;
332	>	simError();
333	>	}
334	>	}
335	>	else{
336	>	sprintf(painCave.errMsg,
337	>	"SimSetup Error: unhandled bend assignment:\n"
338	>	"    -->%s in Bend[%d] in %s\n",
339	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
340	>	painCave.isFatal = 1;
341	>	simError();
342	>	}
343
344	+	current_extra = current_extra->getNext();
345	+	}
346	+	}
347
348	<	// initialize the arrays
348	>	if (theBends[j].isGhost) {
349	>
350	>	tempI = theBends[j].a;
351	>	tempJ = theBends[j].b;
352	>
353	>	#ifdef IS_MPI
354	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
355	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
356	>	#else
357	>	exI = tempI + 1;
358	>	exJ = tempJ + 1;
359	>	#endif
360	>	info[k].excludes->addPair(exI, exJ);
361
362	<	the_ff->setSimInfo( simnfo );
362	>	} else {
363
364	<	makeMolecules();
365	<	simnfo->identArray = new int[simnfo->n_atoms];
366	<	for(i=0; i<simnfo->n_atoms; i++){
367	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
368	<	}
369	<
370	<	if (the_globals->getUseRF() ) {
371	<	simnfo->useReactionField = 1;
372	<
373	<	if( !the_globals->haveECR() ){
374	<	sprintf( painCave.errMsg,
375	<	"SimSetup Warning: using default value of 1/2 the smallest "
376	<	"box length for the electrostaticCutoffRadius.\n"
377	<	"I hope you have a very fast processor!\n");
378	<	painCave.isFatal = 0;
379	<	simError();
380	<	double smallest;
381	<	smallest = simnfo->box_x;
434	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
435	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
436	<	simnfo->ecr = 0.5 * smallest;
437	<	} else {
438	<	simnfo->ecr        = the_globals->getECR();
439	<	}
440	<
441	<	if( !the_globals->haveEST() ){
442	<	sprintf( painCave.errMsg,
443	<	"SimSetup Warning: using default value of 0.05 * the "
444	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
445	<	);
446	<	painCave.isFatal = 0;
447	<	simError();
448	<	simnfo->est = 0.05 * simnfo->ecr;
449	<	} else {
450	<	simnfo->est        = the_globals->getEST();
451	<	}
452	<
453	<	if(!the_globals->haveDielectric() ){
454	<	sprintf( painCave.errMsg,
455	<	"SimSetup Error: You are trying to use Reaction Field without"
456	<	"setting a dielectric constant!\n"
457	<	);
458	<	painCave.isFatal = 1;
459	<	simError();
460	<	}
461	<	simnfo->dielectric = the_globals->getDielectric();
462	<	} else {
463	<	if (simnfo->n_dipoles) {
464	<
465	<	if( !the_globals->haveECR() ){
466	<	sprintf( painCave.errMsg,
467	<	"SimSetup Warning: using default value of 1/2 the smallest"
468	<	"box length for the electrostaticCutoffRadius.\n"
469	<	"I hope you have a very fast processor!\n");
470	<	painCave.isFatal = 0;
471	<	simError();
472	<	double smallest;
473	<	smallest = simnfo->box_x;
474	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
475	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
476	<	simnfo->ecr = 0.5 * smallest;
477	<	} else {
478	<	simnfo->ecr        = the_globals->getECR();
364	>	tempI = theBends[j].a;
365	>	tempJ = theBends[j].b;
366	>	tempK = theBends[j].c;
367	>
368	>	#ifdef IS_MPI
369	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
370	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
371	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
372	>	#else
373	>	exI = tempI + 1;
374	>	exJ = tempJ + 1;
375	>	exK = tempK + 1;
376	>	#endif
377	>
378	>	info[k].excludes->addPair(exI, exK);
379	>	info[k].excludes->addPair(exI, exJ);
380	>	info[k].excludes->addPair(exJ, exK);
381	>	}
382		}
480	–
481	–	if( !the_globals->haveEST() ){
482	–	sprintf( painCave.errMsg,
483	–	"SimSetup Warning: using default value of 5% of the"
484	–	"electrostaticCutoffRadius for the "
485	–	"electrostaticSkinThickness\n"
486	–	);
487	–	painCave.isFatal = 0;
488	–	simError();
489	–	simnfo->est = 0.05 * simnfo->ecr;
490	–	} else {
491	–	simnfo->est        = the_globals->getEST();
492	–	}
493	–	}
494	–	}
383
384	<	#ifdef IS_MPI
385	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
386	<	MPIcheckPoint();
387	<	#endif // is_mpi
384	>	for (j = 0; j < molInfo.nTorsions; j++){
385	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
386	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
387	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
388	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
389	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
390
391	<	if( the_globals->haveInitialConfig() ){
392	<
393	<	InitializeFromFile* fileInit;
394	<	#ifdef IS_MPI // is_mpi
395	<	if( worldRank == 0 ){
506	<	#endif //is_mpi
507	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
391	>	tempI = theTorsions[j].a;
392	>	tempJ = theTorsions[j].b;
393	>	tempK = theTorsions[j].c;
394	>	tempL = theTorsions[j].d;
395	>
396		#ifdef IS_MPI
397	<	}else fileInit = new InitializeFromFile( NULL );
397	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
398	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
399	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
400	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
401	>	#else
402	>	exI = tempI + 1;
403	>	exJ = tempJ + 1;
404	>	exK = tempK + 1;
405	>	exL = tempL + 1;
406		#endif
511	–	fileInit->read_xyz( simnfo ); // default velocities on
407
408	<	delete fileInit;
409	<	}
410	<	else{
408	>	info[k].excludes->addPair(exI, exJ);
409	>	info[k].excludes->addPair(exI, exK);
410	>	info[k].excludes->addPair(exI, exL);
411	>	info[k].excludes->addPair(exJ, exK);
412	>	info[k].excludes->addPair(exJ, exL);
413	>	info[k].excludes->addPair(exK, exL);
414	>	}
415
416	<	#ifdef IS_MPI
416	>
417	>	molInfo.myRigidBodies.clear();
418	>
419	>	for (j = 0; j < molInfo.nRigidBodies; j++){
420
421	<	// no init from bass
422	<
521	<	sprintf( painCave.errMsg,
522	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
523	<	painCave.isFatal;
524	<	simError();
525	<
526	<	#else
421	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
422	>	nMembers = currentRigidBody->getNMembers();
423
424	<	initFromBass();
424	>	// Create the Rigid Body:
425
426	+	myRB = new RigidBody();
427
428	<	#endif
429	<	}
428	>	sprintf(rbName,"%s_RB_%d", molName, j);
429	>	myRB->setType(rbName);
430	>
431	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
432
433	<	#ifdef IS_MPI
434	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
536	<	MPIcheckPoint();
537	<	#endif // is_mpi
433	>	// molI is atom numbering inside this molecule
434	>	molI = currentRigidBody->getMember(rb1);
435
436	+	// tempI is atom numbering on local processor
437	+	tempI = molI + atomOffset;
438
439	<
440	<
441	<
439	>	// currentAtom is the AtomStamp (which we need for
440	>	// rigid body reference positions)
441	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
442
443	<
443	>	// When we add to the rigid body, add the atom itself and
444	>	// the stamp info:
445	>
446	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
447	>
448	>	// Add this atom to the Skip List for the integrators
449		#ifdef IS_MPI
450	<	if( worldRank == 0 ){
451	<	#endif // is_mpi
452	<
453	<	if( the_globals->haveFinalConfig() ){
454	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
455	<	}
456	<	else{
457	<	strcpy( simnfo->finalName, inFileName );
458	<	char* endTest;
459	<	int nameLength = strlen( simnfo->finalName );
460	<	endTest = &(simnfo->finalName[nameLength - 5]);
461	<	if( !strcmp( endTest, ".bass" ) ){
462	<	strcpy( endTest, ".eor" );
463	<	}
464	<	else if( !strcmp( endTest, ".BASS" ) ){
465	<	strcpy( endTest, ".eor" );
466	<	}
467	<	else{
468	<	endTest = &(simnfo->finalName[nameLength - 4]);
565	<	if( !strcmp( endTest, ".bss" ) ){
566	<	strcpy( endTest, ".eor" );
567	<	}
568	<	else if( !strcmp( endTest, ".mdl" ) ){
569	<	strcpy( endTest, ".eor" );
570	<	}
571	<	else{
572	<	strcat( simnfo->finalName, ".eor" );
573	<	}
574	<	}
575	<	}
576	<
577	<	// make the sample and status out names
578	<
579	<	strcpy( simnfo->sampleName, inFileName );
580	<	char* endTest;
581	<	int nameLength = strlen( simnfo->sampleName );
582	<	endTest = &(simnfo->sampleName[nameLength - 5]);
583	<	if( !strcmp( endTest, ".bass" ) ){
584	<	strcpy( endTest, ".dump" );
585	<	}
586	<	else if( !strcmp( endTest, ".BASS" ) ){
587	<	strcpy( endTest, ".dump" );
588	<	}
589	<	else{
590	<	endTest = &(simnfo->sampleName[nameLength - 4]);
591	<	if( !strcmp( endTest, ".bss" ) ){
592	<	strcpy( endTest, ".dump" );
593	<	}
594	<	else if( !strcmp( endTest, ".mdl" ) ){
595	<	strcpy( endTest, ".dump" );
596	<	}
597	<	else{
598	<	strcat( simnfo->sampleName, ".dump" );
599	<	}
600	<	}
601	<
602	<	strcpy( simnfo->statusName, inFileName );
603	<	nameLength = strlen( simnfo->statusName );
604	<	endTest = &(simnfo->statusName[nameLength - 5]);
605	<	if( !strcmp( endTest, ".bass" ) ){
606	<	strcpy( endTest, ".stat" );
607	<	}
608	<	else if( !strcmp( endTest, ".BASS" ) ){
609	<	strcpy( endTest, ".stat" );
610	<	}
611	<	else{
612	<	endTest = &(simnfo->statusName[nameLength - 4]);
613	<	if( !strcmp( endTest, ".bss" ) ){
614	<	strcpy( endTest, ".stat" );
615	<	}
616	<	else if( !strcmp( endTest, ".mdl" ) ){
617	<	strcpy( endTest, ".stat" );
618	<	}
619	<	else{
620	<	strcat( simnfo->statusName, ".stat" );
621	<	}
622	<	}
623	<
450	>	slI = info[k].atoms[tempI]->getGlobalIndex();
451	>	#else
452	>	slI = tempI;
453	>	#endif
454	>	skipList.insert(slI);
455	>
456	>	}
457	>
458	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
459	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
460	>
461	>	tempI = currentRigidBody->getMember(rb1);
462	>	tempJ = currentRigidBody->getMember(rb2);
463	>
464	>	// Some explanation is required here.
465	>	// Fortran indexing starts at 1, while c indexing starts at 0
466	>	// Also, in parallel computations, the GlobalIndex is
467	>	// used for the exclude list:
468	>
469		#ifdef IS_MPI
470	<	}
471	<	#endif // is_mpi
472	<
473	<	// set the status, sample, and themal kick times
474	<
475	<	if( the_globals->haveSampleTime() ){
476	<	simnfo->sampleTime = the_globals->getSampleTime();
477	<	simnfo->statusTime = simnfo->sampleTime;
478	<	simnfo->thermalTime = simnfo->sampleTime;
479	<	}
480	<	else{
636	<	simnfo->sampleTime = the_globals->getRunTime();
637	<	simnfo->statusTime = simnfo->sampleTime;
638	<	simnfo->thermalTime = simnfo->sampleTime;
639	<	}
470	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
471	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
472	>	#else
473	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
474	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
475	>	#endif
476	>
477	>	info[k].excludes->addPair(exI, exJ);
478	>
479	>	}
480	>	}
481
482	<	if( the_globals->haveStatusTime() ){
483	<	simnfo->statusTime = the_globals->getStatusTime();
484	<	}
482	>	molInfo.myRigidBodies.push_back(myRB);
483	>	info[k].rigidBodies.push_back(myRB);
484	>	}
485	>
486
487	<	if( the_globals->haveThermalTime() ){
488	<	simnfo->thermalTime = the_globals->getThermalTime();
489	<	}
487	>	//create cutoff group for molecule
488	>	molInfo.myCutoffGroups.clear();
489	>	for (j = 0; j < molInfo.nCutoffGroups; j++){
490
491	<	// check for the temperature set flag
491	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
492	>	nMembers = currentCutoffGroup->getNMembers();
493
494	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
494	>	myCutoffGroup = new CutoffGroup();
495	>
496	>	for (int cg = 0; cg < nMembers; cg++) {
497
498	+	// molI is atom numbering inside this molecule
499	+	molI = currentCutoffGroup->getMember(cg);
500
501	<	//   // make the longe range forces and the integrator
501	>	// tempI is atom numbering on local processor
502	>	tempI = molI + atomOffset;
503
504	<	//   new AllLong( simnfo );
504	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
505	>	}
506
507	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
508	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
507	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
508	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
509	>
510
511	+
512	+	// After this is all set up, scan through the atoms to
513	+	// see if they can be added to the integrableObjects:
514	+
515	+	molInfo.myIntegrableObjects.clear();
516	+
517	+
518	+	for (j = 0; j < molInfo.nAtoms; j++){
519	+
520		#ifdef IS_MPI
521	<	mpiSim->mpiRefresh();
521	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
522	>	#else
523	>	slJ = j+atomOffset;
524		#endif
525
526	<	// initialize the Fortran
526	>	// if they aren't on the skip list, then they can be integrated
527
528	+	if (skipList.find(slJ) == skipList.end()) {
529	+	mySD = (StuntDouble *) molInfo.myAtoms[j];
530	+	info[k].integrableObjects.push_back(mySD);
531	+	molInfo.myIntegrableObjects.push_back(mySD);
532	+	}
533	+	}
534
535	<	simnfo->refreshSim();
669	<
670	<	if( !strcmp( simnfo->mixingRule, "standard") ){
671	<	the_ff->initForceField( LB_MIXING_RULE );
672	<	}
673	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
674	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
675	<	}
676	<	else{
677	<	sprintf( painCave.errMsg,
678	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
679	<	simnfo->mixingRule );
680	<	painCave.isFatal = 1;
681	<	simError();
682	<	}
535	>	// all rigid bodies are integrated:
536
537	+	for (j = 0; j < molInfo.nRigidBodies; j++) {
538	+	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
539	+	info[k].integrableObjects.push_back(mySD);
540	+	molInfo.myIntegrableObjects.push_back(mySD);
541	+	}
542	+
543	+
544	+	// send the arrays off to the forceField for init.
545	+
546	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
547	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
548	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
549	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
550	+	theTorsions);
551
552	+	info[k].molecules[i].initialize(molInfo);
553	+
554	+
555	+	atomOffset += molInfo.nAtoms;
556	+	delete[] theBonds;
557	+	delete[] theBends;
558	+	delete[] theTorsions;
559	+	}
560	+	}
561	+
562		#ifdef IS_MPI
563	<	strcpy( checkPointMsg,
687	<	"Successfully intialized the mixingRule for Fortran." );
563	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
564		MPIcheckPoint();
565		#endif // is_mpi
566	+
567		}
568
569	+	void SimSetup::initFromBass(void){
570	+	int i, j, k;
571	+	int n_cells;
572	+	double cellx, celly, cellz;
573	+	double temp1, temp2, temp3;
574	+	int n_per_extra;
575	+	int n_extra;
576	+	int have_extra, done;
577
578	<	void SimSetup::makeMolecules( void ){
578	>	double vel[3];
579	>	vel[0] = 0.0;
580	>	vel[1] = 0.0;
581	>	vel[2] = 0.0;
582
583	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
584	<	molInit info;
585	<	DirectionalAtom* dAtom;
698	<	LinkedAssign* extras;
699	<	LinkedAssign* current_extra;
700	<	AtomStamp* currentAtom;
701	<	BondStamp* currentBond;
702	<	BendStamp* currentBend;
703	<	TorsionStamp* currentTorsion;
583	>	temp1 = (double) tot_nmol / 4.0;
584	>	temp2 = pow(temp1, (1.0 / 3.0));
585	>	temp3 = ceil(temp2);
586
587	<	bond_pair* theBonds;
588	<	bend_set* theBends;
589	<	torsion_set* theTorsions;
587	>	have_extra = 0;
588	>	if (temp2 < temp3){
589	>	// we have a non-complete lattice
590	>	have_extra = 1;
591
592	<
593	<	//init the forceField paramters
592	>	n_cells = (int) temp3 - 1;
593	>	cellx = info[0].boxL[0] / temp3;
594	>	celly = info[0].boxL[1] / temp3;
595	>	cellz = info[0].boxL[2] / temp3;
596	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
597	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
598	>	n_per_extra = (int) ceil(temp1);
599
600	<	the_ff->readParams();
601	<
602	<
603	<	// init the atoms
716	<
717	<	double ux, uy, uz, u, uSqr;
718	<
719	<	atomOffset = 0;
720	<	excludeOffset = 0;
721	<	for(i=0; i<simnfo->n_mol; i++){
722	<
723	<	stampID = the_molecules[i].getStampID();
724	<
725	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
726	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
727	<	info.nBends    = comp_stamps[stampID]->getNBends();
728	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
729	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
730	<
731	<	info.myAtoms = &the_atoms[atomOffset];
732	<	info.myExcludes = &the_excludes[excludeOffset];
733	<	info.myBonds = new Bond*[info.nBonds];
734	<	info.myBends = new Bend*[info.nBends];
735	<	info.myTorsions = new Torsion*[info.nTorsions];
736	<
737	<	theBonds = new bond_pair[info.nBonds];
738	<	theBends = new bend_set[info.nBends];
739	<	theTorsions = new torsion_set[info.nTorsions];
740	<
741	<	// make the Atoms
742	<
743	<	for(j=0; j<info.nAtoms; j++){
744	<
745	<	currentAtom = comp_stamps[stampID]->getAtom( j );
746	<	if( currentAtom->haveOrientation() ){
747	<
748	<	dAtom = new DirectionalAtom(j + atomOffset);
749	<	simnfo->n_oriented++;
750	<	info.myAtoms[j] = dAtom;
751	<
752	<	ux = currentAtom->getOrntX();
753	<	uy = currentAtom->getOrntY();
754	<	uz = currentAtom->getOrntZ();
755	<
756	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
757	<
758	<	u = sqrt( uSqr );
759	<	ux = ux / u;
760	<	uy = uy / u;
761	<	uz = uz / u;
762	<
763	<	dAtom->setSUx( ux );
764	<	dAtom->setSUy( uy );
765	<	dAtom->setSUz( uz );
766	<	}
767	<	else{
768	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
769	<	}
770	<	info.myAtoms[j]->setType( currentAtom->getType() );
771	<
772	<	#ifdef IS_MPI
773	<
774	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
775	<
776	<	#endif // is_mpi
777	<	}
778	<
779	<	// make the bonds
780	<	for(j=0; j<info.nBonds; j++){
781	<
782	<	currentBond = comp_stamps[stampID]->getBond( j );
783	<	theBonds[j].a = currentBond->getA() + atomOffset;
784	<	theBonds[j].b = currentBond->getB() + atomOffset;
785	<
786	<	exI = theBonds[i].a;
787	<	exJ = theBonds[i].b;
788	<
789	<	// exclude_I must always be the smaller of the pair
790	<	if( exI > exJ ){
791	<	tempEx = exI;
792	<	exI = exJ;
793	<	exJ = tempEx;
794	<	}
795	<	#ifdef IS_MPI
796	<	tempEx = exI;
797	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
798	<	tempEx = exJ;
799	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
800	<
801	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
802	<	#else  // isn't MPI
803	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
804	<	#endif  //is_mpi
805	<	}
806	<	excludeOffset += info.nBonds;
807	<
808	<	//make the bends
809	<	for(j=0; j<info.nBends; j++){
810	<
811	<	currentBend = comp_stamps[stampID]->getBend( j );
812	<	theBends[j].a = currentBend->getA() + atomOffset;
813	<	theBends[j].b = currentBend->getB() + atomOffset;
814	<	theBends[j].c = currentBend->getC() + atomOffset;
815	<
816	<	if( currentBend->haveExtras() ){
817	<
818	<	extras = currentBend->getExtras();
819	<	current_extra = extras;
820	<
821	<	while( current_extra != NULL ){
822	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
823	<
824	<	switch( current_extra->getType() ){
825	<
826	<	case 0:
827	<	theBends[j].ghost =
828	<	current_extra->getInt() + atomOffset;
829	<	theBends[j].isGhost = 1;
830	<	break;
831	<
832	<	case 1:
833	<	theBends[j].ghost =
834	<	(int)current_extra->getDouble() + atomOffset;
835	<	theBends[j].isGhost = 1;
836	<	break;
837	<
838	<	default:
839	<	sprintf( painCave.errMsg,
840	<	"SimSetup Error: ghostVectorSource was neiter a "
841	<	"double nor an int.\n"
842	<	"-->Bend[%d] in %s\n",
843	<	j, comp_stamps[stampID]->getID() );
844	<	painCave.isFatal = 1;
845	<	simError();
846	<	}
847	<	}
848	<
849	<	else{
850	<
851	<	sprintf( painCave.errMsg,
852	<	"SimSetup Error: unhandled bend assignment:\n"
853	<	"    -->%s in Bend[%d] in %s\n",
854	<	current_extra->getlhs(),
855	<	j, comp_stamps[stampID]->getID() );
856	<	painCave.isFatal = 1;
857	<	simError();
858	<	}
859	<
860	<	current_extra = current_extra->getNext();
861	<	}
862	<	}
863	<
864	<	if( !theBends[j].isGhost ){
865	<
866	<	exI = theBends[j].a;
867	<	exJ = theBends[j].c;
868	<	}
869	<	else{
870	<
871	<	exI = theBends[j].a;
872	<	exJ = theBends[j].b;
873	<	}
874	<
875	<	// exclude_I must always be the smaller of the pair
876	<	if( exI > exJ ){
877	<	tempEx = exI;
878	<	exI = exJ;
879	<	exJ = tempEx;
880	<	}
881	<	#ifdef IS_MPI
882	<	tempEx = exI;
883	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
884	<	tempEx = exJ;
885	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
886	<
887	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
888	<	#else  // isn't MPI
889	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
890	<	#endif  //is_mpi
891	<	}
892	<	excludeOffset += info.nBends;
893	<
894	<	for(j=0; j<info.nTorsions; j++){
895	<
896	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
897	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
898	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
899	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
900	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
901	<
902	<	exI = theTorsions[j].a;
903	<	exJ = theTorsions[j].d;
904	<
905	<	// exclude_I must always be the smaller of the pair
906	<	if( exI > exJ ){
907	<	tempEx = exI;
908	<	exI = exJ;
909	<	exJ = tempEx;
910	<	}
911	<	#ifdef IS_MPI
912	<	tempEx = exI;
913	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
914	<	tempEx = exJ;
915	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
916	<
917	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
918	<	#else  // isn't MPI
919	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
920	<	#endif  //is_mpi
921	<	}
922	<	excludeOffset += info.nTorsions;
923	<
924	<
925	<	// send the arrays off to the forceField for init.
926	<
927	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
928	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
929	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
930	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
931	<
932	<
933	<	the_molecules[i].initialize( info );
934	<	atomOffset += info.nAtoms;
935	<	delete[] theBonds;
936	<	delete[] theBends;
937	<	delete[] theTorsions;
938	<	}
939	<
940	<	// clean up the forcefield
941	<	the_ff->calcRcut();
942	<	the_ff->cleanMe();
943	<	}
944	<
945	<	void SimSetup::initFromBass( void ){
946	<
947	<	int i, j, k;
948	<	int n_cells;
949	<	double cellx, celly, cellz;
950	<	double temp1, temp2, temp3;
951	<	int n_per_extra;
952	<	int n_extra;
953	<	int have_extra, done;
954	<
955	<	temp1 = (double)tot_nmol / 4.0;
956	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
957	<	temp3 = ceil( temp2 );
958	<
959	<	have_extra =0;
960	<	if( temp2 < temp3 ){ // we have a non-complete lattice
961	<	have_extra =1;
962	<
963	<	n_cells = (int)temp3 - 1;
964	<	cellx = simnfo->box_x / temp3;
965	<	celly = simnfo->box_y / temp3;
966	<	cellz = simnfo->box_z / temp3;
967	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
968	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
969	<	n_per_extra = (int)ceil( temp1 );
970	<
971	<	if( n_per_extra > 4){
972	<	sprintf( painCave.errMsg,
973	<	"SimSetup error. There has been an error in constructing"
974	<	" the non-complete lattice.\n" );
600	>	if (n_per_extra > 4){
601	>	sprintf(painCave.errMsg,
602	>	"SimSetup error. There has been an error in constructing"
603	>	" the non-complete lattice.\n");
604		painCave.isFatal = 1;
605		simError();
606		}
607		}
608		else{
609	<	n_cells = (int)temp3;
610	<	cellx = simnfo->box_x / temp3;
611	<	celly = simnfo->box_y / temp3;
612	<	cellz = simnfo->box_z / temp3;
609	>	n_cells = (int) temp3;
610	>	cellx = info[0].boxL[0] / temp3;
611	>	celly = info[0].boxL[1] / temp3;
612	>	cellz = info[0].boxL[2] / temp3;
613		}
614
615		current_mol = 0;
#	Line 988 | Line 617 | void SimSetup::initFromBass( void ){
617		current_comp = 0;
618		current_atom_ndx = 0;
619
620	<	for( i=0; i < n_cells ; i++ ){
621	<	for( j=0; j < n_cells; j++ ){
622	<	for( k=0; k < n_cells; k++ ){
620	>	for (i = 0; i < n_cells ; i++){
621	>	for (j = 0; j < n_cells; j++){
622	>	for (k = 0; k < n_cells; k++){
623	>	makeElement(i * cellx, j * celly, k * cellz);
624
625	<	makeElement( i * cellx,
996	<	j * celly,
997	<	k * cellz );
625	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
626
627	<	makeElement( i * cellx + 0.5 * cellx,
1000	<	j * celly + 0.5 * celly,
1001	<	k * cellz );
627	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
628
629	<	makeElement( i * cellx,
1004	<	j * celly + 0.5 * celly,
1005	<	k * cellz + 0.5 * cellz );
1006	<
1007	<	makeElement( i * cellx + 0.5 * cellx,
1008	<	j * celly,
1009	<	k * cellz + 0.5 * cellz );
629	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
630		}
631		}
632		}
633
634	<	if( have_extra ){
634	>	if (have_extra){
635		done = 0;
636
637		int start_ndx;
638	<	for( i=0; i < (n_cells+1) && !done; i++ ){
639	<	for( j=0; j < (n_cells+1) && !done; j++ ){
638	>	for (i = 0; i < (n_cells + 1) && !done; i++){
639	>	for (j = 0; j < (n_cells + 1) && !done; j++){
640	>	if (i < n_cells){
641	>	if (j < n_cells){
642	>	start_ndx = n_cells;
643	>	}
644	>	else
645	>	start_ndx = 0;
646	>	}
647	>	else
648	>	start_ndx = 0;
649
650	<	if( i < n_cells ){
650	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
651	>	makeElement(i * cellx, j * celly, k * cellz);
652	>	done = (current_mol >= tot_nmol);
653
654	<	if( j < n_cells ){
655	<	start_ndx = n_cells;
656	<	}
657	<	else start_ndx = 0;
658	<	}
1028	<	else start_ndx = 0;
654	>	if (!done && n_per_extra > 1){
655	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
656	>	k * cellz);
657	>	done = (current_mol >= tot_nmol);
658	>	}
659
660	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
660	>	if (!done && n_per_extra > 2){
661	>	makeElement(i * cellx, j * celly + 0.5 * celly,
662	>	k * cellz + 0.5 * cellz);
663	>	done = (current_mol >= tot_nmol);
664	>	}
665
666	<	makeElement( i * cellx,
667	<	j * celly,
668	<	k * cellz );
669	<	done = ( current_mol >= tot_nmol );
670	<
671	<	if( !done && n_per_extra > 1 ){
1038	<	makeElement( i * cellx + 0.5 * cellx,
1039	<	j * celly + 0.5 * celly,
1040	<	k * cellz );
1041	<	done = ( current_mol >= tot_nmol );
1042	<	}
1043	<
1044	<	if( !done && n_per_extra > 2){
1045	<	makeElement( i * cellx,
1046	<	j * celly + 0.5 * celly,
1047	<	k * cellz + 0.5 * cellz );
1048	<	done = ( current_mol >= tot_nmol );
1049	<	}
1050	<
1051	<	if( !done && n_per_extra > 3){
1052	<	makeElement( i * cellx + 0.5 * cellx,
1053	<	j * celly,
1054	<	k * cellz + 0.5 * cellz );
1055	<	done = ( current_mol >= tot_nmol );
1056	<	}
1057	<	}
666	>	if (!done && n_per_extra > 3){
667	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
668	>	k * cellz + 0.5 * cellz);
669	>	done = (current_mol >= tot_nmol);
670	>	}
671	>	}
672		}
673		}
674		}
675
676	<
677	<	for( i=0; i<simnfo->n_atoms; i++ ){
1064	<	simnfo->atoms[i]->set_vx( 0.0 );
1065	<	simnfo->atoms[i]->set_vy( 0.0 );
1066	<	simnfo->atoms[i]->set_vz( 0.0 );
676	>	for (i = 0; i < info[0].n_atoms; i++){
677	>	info[0].atoms[i]->setVel(vel);
678		}
679		}
680
681	<	void SimSetup::makeElement( double x, double y, double z ){
1071	<
681	>	void SimSetup::makeElement(double x, double y, double z){
682		int k;
683		AtomStamp* current_atom;
684		DirectionalAtom* dAtom;
685		double rotMat[3][3];
686	+	double pos[3];
687
688	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
689	<
690	<	current_atom = comp_stamps[current_comp]->getAtom( k );
691	<	if( !current_atom->havePosition() ){
692	<	sprintf( painCave.errMsg,
693	<	"SimSetup:initFromBass error.\n"
694	<	"\tComponent %s, atom %s does not have a position specified.\n"
695	<	"\tThe initialization routine is unable to give a start"
696	<	" position.\n",
1086	<	comp_stamps[current_comp]->getID(),
1087	<	current_atom->getType() );
688	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
689	>	current_atom = comp_stamps[current_comp]->getAtom(k);
690	>	if (!current_atom->havePosition()){
691	>	sprintf(painCave.errMsg,
692	>	"SimSetup:initFromBass error.\n"
693	>	"\tComponent %s, atom %s does not have a position specified.\n"
694	>	"\tThe initialization routine is unable to give a start"
695	>	" position.\n",
696	>	comp_stamps[current_comp]->getID(), current_atom->getType());
697		painCave.isFatal = 1;
698		simError();
699		}
700
701	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
702	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
703	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
701	>	pos[0] = x + current_atom->getPosX();
702	>	pos[1] = y + current_atom->getPosY();
703	>	pos[2] = z + current_atom->getPosZ();
704
705	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
705	>	info[0].atoms[current_atom_ndx]->setPos(pos);
706
707	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
707	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
708	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
709
710		rotMat[0][0] = 1.0;
711		rotMat[0][1] = 0.0;
#	Line 1109 | Line 719 | void SimSetup::makeElement( double x, double y, double
719		rotMat[2][1] = 0.0;
720		rotMat[2][2] = 1.0;
721
722	<	dAtom->setA( rotMat );
722	>	dAtom->setA(rotMat);
723		}
724
725		current_atom_ndx++;
#	Line 1118 | Line 728 | void SimSetup::makeElement( double x, double y, double
728		current_mol++;
729		current_comp_mol++;
730
731	<	if( current_comp_mol >= components_nmol[current_comp] ){
1122	<
731	>	if (current_comp_mol >= components_nmol[current_comp]){
732		current_comp_mol = 0;
733		current_comp++;
734	+	}
735	+	}
736	+
737	+
738	+	void SimSetup::gatherInfo(void){
739	+	int i;
740	+
741	+	ensembleCase = -1;
742	+	ffCase = -1;
743	+
744	+	// set the easy ones first
745	+
746	+	for (i = 0; i < nInfo; i++){
747	+	info[i].target_temp = globals->getTargetTemp();
748	+	info[i].dt = globals->getDt();
749	+	info[i].run_time = globals->getRunTime();
750	+	}
751	+	n_components = globals->getNComponents();
752	+
753	+
754	+	// get the forceField
755	+
756	+	strcpy(force_field, globals->getForceField());
757	+
758	+	if (!strcasecmp(force_field, "DUFF")){
759	+	ffCase = FF_DUFF;
760	+	}
761	+	else if (!strcasecmp(force_field, "LJ")){
762	+	ffCase = FF_LJ;
763	+	}
764	+	else if (!strcasecmp(force_field, "EAM")){
765	+	ffCase = FF_EAM;
766	+	}
767	+	else if (!strcasecmp(force_field, "WATER")){
768	+	ffCase = FF_H2O;
769	+	}
770	+	else{
771	+	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
772	+	force_field);
773	+	painCave.isFatal = 1;
774	+	simError();
775	+	}
776	+
777	+	// get the ensemble
778	+
779	+	strcpy(ensemble, globals->getEnsemble());
780	+
781	+	if (!strcasecmp(ensemble, "NVE")){
782	+	ensembleCase = NVE_ENS;
783	+	}
784	+	else if (!strcasecmp(ensemble, "NVT")){
785	+	ensembleCase = NVT_ENS;
786	+	}
787	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
788	+	ensembleCase = NPTi_ENS;
789	+	}
790	+	else if (!strcasecmp(ensemble, "NPTf")){
791	+	ensembleCase = NPTf_ENS;
792	+	}
793	+	else if (!strcasecmp(ensemble, "NPTxyz")){
794	+	ensembleCase = NPTxyz_ENS;
795	+	}
796	+	else{
797	+	sprintf(painCave.errMsg,
798	+	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
799	+	"\treverting to NVE for this simulation.\n",
800	+	ensemble);
801	+	painCave.isFatal = 0;
802	+	simError();
803	+	strcpy(ensemble, "NVE");
804	+	ensembleCase = NVE_ENS;
805	+	}
806	+
807	+	for (i = 0; i < nInfo; i++){
808	+	strcpy(info[i].ensemble, ensemble);
809	+
810	+	// get the mixing rule
811	+
812	+	strcpy(info[i].mixingRule, globals->getMixingRule());
813	+	info[i].usePBC = globals->getPBC();
814	+	}
815	+
816	+	// get the components and calculate the tot_nMol and indvidual n_mol
817	+
818	+	the_components = globals->getComponents();
819	+	components_nmol = new int[n_components];
820	+
821	+
822	+	if (!globals->haveNMol()){
823	+	// we don't have the total number of molecules, so we assume it is
824	+	// given in each component
825	+
826	+	tot_nmol = 0;
827	+	for (i = 0; i < n_components; i++){
828	+	if (!the_components[i]->haveNMol()){
829	+	// we have a problem
830	+	sprintf(painCave.errMsg,
831	+	"SimSetup Error. No global NMol or component NMol given.\n"
832	+	"\tCannot calculate the number of atoms.\n");
833	+	painCave.isFatal = 1;
834	+	simError();
835	+	}
836	+
837	+	tot_nmol += the_components[i]->getNMol();
838	+	components_nmol[i] = the_components[i]->getNMol();
839	+	}
840	+	}
841	+	else{
842	+	sprintf(painCave.errMsg,
843	+	"SimSetup error.\n"
844	+	"\tSorry, the ability to specify total"
845	+	" nMols and then give molfractions in the components\n"
846	+	"\tis not currently supported."
847	+	" Please give nMol in the components.\n");
848	+	painCave.isFatal = 1;
849	+	simError();
850	+	}
851	+
852	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
853	+	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
854	+	sprintf(painCave.errMsg,
855	+	"Sample time is not divisible by dt.\n"
856	+	"\tThis will result in samples that are not uniformly\n"
857	+	"\tdistributed in time.  If this is a problem, change\n"
858	+	"\tyour sampleTime variable.\n");
859	+	painCave.isFatal = 0;
860	+	simError();
861	+	}
862	+
863	+	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
864	+	sprintf(painCave.errMsg,
865	+	"Status time is not divisible by dt.\n"
866	+	"\tThis will result in status reports that are not uniformly\n"
867	+	"\tdistributed in time.  If this is a problem, change \n"
868	+	"\tyour statusTime variable.\n");
869	+	painCave.isFatal = 0;
870	+	simError();
871	+	}
872	+
873	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
874	+	sprintf(painCave.errMsg,
875	+	"Thermal time is not divisible by dt.\n"
876	+	"\tThis will result in thermalizations that are not uniformly\n"
877	+	"\tdistributed in time.  If this is a problem, change \n"
878	+	"\tyour thermalTime variable.\n");
879	+	painCave.isFatal = 0;
880	+	simError();
881	+	}
882	+
883	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
884	+	sprintf(painCave.errMsg,
885	+	"Reset time is not divisible by dt.\n"
886	+	"\tThis will result in integrator resets that are not uniformly\n"
887	+	"\tdistributed in time.  If this is a problem, change\n"
888	+	"\tyour resetTime variable.\n");
889	+	painCave.isFatal = 0;
890	+	simError();
891	+	}
892	+
893	+	// set the status, sample, and thermal kick times
894	+
895	+	for (i = 0; i < nInfo; i++){
896	+	if (globals->haveSampleTime()){
897	+	info[i].sampleTime = globals->getSampleTime();
898	+	info[i].statusTime = info[i].sampleTime;
899	+	}
900	+	else{
901	+	info[i].sampleTime = globals->getRunTime();
902	+	info[i].statusTime = info[i].sampleTime;
903	+	}
904	+
905	+	if (globals->haveStatusTime()){
906	+	info[i].statusTime = globals->getStatusTime();
907	+	}
908	+
909	+	if (globals->haveThermalTime()){
910	+	info[i].thermalTime = globals->getThermalTime();
911	+	} else {
912	+	info[i].thermalTime = globals->getRunTime();
913	+	}
914	+
915	+	info[i].resetIntegrator = 0;
916	+	if( globals->haveResetTime() ){
917	+	info[i].resetTime = globals->getResetTime();
918	+	info[i].resetIntegrator = 1;
919	+	}
920	+
921	+	// check for the temperature set flag
922	+
923	+	if (globals->haveTempSet())
924	+	info[i].setTemp = globals->getTempSet();
925	+
926	+	// check for the extended State init
927	+
928	+	info[i].useInitXSstate = globals->getUseInitXSstate();
929	+	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
930	+
931	+	}
932	+
933	+	//setup seed for random number generator
934	+	int seedValue;
935	+
936	+	if (globals->haveSeed()){
937	+	seedValue = globals->getSeed();
938	+
939	+	if(seedValue / 1E9 == 0){
940	+	sprintf(painCave.errMsg,
941	+	"Seed for sprng library should contain at least 9 digits\n"
942	+	"OOPSE will generate a seed for user\n");
943	+	painCave.isFatal = 0;
944	+	simError();
945	+
946	+	//using seed generated by system instead of invalid seed set by user
947	+	#ifndef IS_MPI
948	+	seedValue = make_sprng_seed();
949	+	#else
950	+	if (worldRank == 0){
951	+	seedValue = make_sprng_seed();
952	+	}
953	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
954	+	#endif
955	+	}
956	+	}//end of if branch of globals->haveSeed()
957	+	else{
958	+
959	+	#ifndef IS_MPI
960	+	seedValue = make_sprng_seed();
961	+	#else
962	+	if (worldRank == 0){
963	+	seedValue = make_sprng_seed();
964	+	}
965	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
966	+	#endif
967	+	}//end of globals->haveSeed()
968	+
969	+	for (int i = 0; i < nInfo; i++){
970	+	info[i].setSeed(seedValue);
971	+	}
972	+
973	+	#ifdef IS_MPI
974	+	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
975	+	MPIcheckPoint();
976	+	#endif // is_mpi
977	+	}
978	+
979	+
980	+	void SimSetup::finalInfoCheck(void){
981	+	int index;
982	+	int usesDipoles;
983	+	int usesCharges;
984	+	int i;
985	+
986	+	for (i = 0; i < nInfo; i++){
987	+	// check electrostatic parameters
988	+
989	+	index = 0;
990	+	usesDipoles = 0;
991	+	while ((index < info[i].n_atoms) && !usesDipoles){
992	+	usesDipoles = (info[i].atoms[index])->hasDipole();
993	+	index++;
994	+	}
995	+	index = 0;
996	+	usesCharges = 0;
997	+	while ((index < info[i].n_atoms) && !usesCharges){
998	+	usesCharges= (info[i].atoms[index])->hasCharge();
999	+	index++;
1000	+	}
1001	+	#ifdef IS_MPI
1002	+	int myUse = usesDipoles;
1003	+	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1004	+	#endif //is_mpi
1005	+
1006	+	double theRcut, theRsw;
1007	+
1008	+	if (globals->haveRcut()) {
1009	+	theRcut = globals->getRcut();
1010	+
1011	+	if (globals->haveRsw())
1012	+	theRsw = globals->getRsw();
1013	+	else
1014	+	theRsw = theRcut;
1015	+
1016	+	info[i].setDefaultRcut(theRcut, theRsw);
1017	+
1018	+	} else {
1019	+
1020	+	the_ff->calcRcut();
1021	+	theRcut = info[i].getRcut();
1022	+
1023	+	if (globals->haveRsw())
1024	+	theRsw = globals->getRsw();
1025	+	else
1026	+	theRsw = theRcut;
1027	+
1028	+	info[i].setDefaultRcut(theRcut, theRsw);
1029	+	}
1030	+
1031	+	if (globals->getUseRF()){
1032	+	info[i].useReactionField = 1;
1033	+
1034	+	if (!globals->haveRcut()){
1035	+	sprintf(painCave.errMsg,
1036	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1037	+	"\tOOPSE will use a default value of 15.0 angstroms"
1038	+	"\tfor the cutoffRadius.\n");
1039	+	painCave.isFatal = 0;
1040	+	simError();
1041	+	theRcut = 15.0;
1042	+	}
1043	+	else{
1044	+	theRcut = globals->getRcut();
1045	+	}
1046	+
1047	+	if (!globals->haveRsw()){
1048	+	sprintf(painCave.errMsg,
1049	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1050	+	"\tOOPSE will use a default value of\n"
1051	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1052	+	painCave.isFatal = 0;
1053	+	simError();
1054	+	theRsw = 0.95 * theRcut;
1055	+	}
1056	+	else{
1057	+	theRsw = globals->getRsw();
1058	+	}
1059	+
1060	+	info[i].setDefaultRcut(theRcut, theRsw);
1061	+
1062	+	if (!globals->haveDielectric()){
1063	+	sprintf(painCave.errMsg,
1064	+	"SimSetup Error: No Dielectric constant was set.\n"
1065	+	"\tYou are trying to use Reaction Field without"
1066	+	"\tsetting a dielectric constant!\n");
1067	+	painCave.isFatal = 1;
1068	+	simError();
1069	+	}
1070	+	info[i].dielectric = globals->getDielectric();
1071	+	}
1072	+	else{
1073	+	if (usesDipoles || usesCharges){
1074	+
1075	+	if (!globals->haveRcut()){
1076	+	sprintf(painCave.errMsg,
1077	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1078	+	"\tOOPSE will use a default value of 15.0 angstroms"
1079	+	"\tfor the cutoffRadius.\n");
1080	+	painCave.isFatal = 0;
1081	+	simError();
1082	+	theRcut = 15.0;
1083	+	}
1084	+	else{
1085	+	theRcut = globals->getRcut();
1086	+	}
1087	+
1088	+	if (!globals->haveRsw()){
1089	+	sprintf(painCave.errMsg,
1090	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1091	+	"\tOOPSE will use a default value of\n"
1092	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1093	+	painCave.isFatal = 0;
1094	+	simError();
1095	+	theRsw = 0.95 * theRcut;
1096	+	}
1097	+	else{
1098	+	theRsw = globals->getRsw();
1099	+	}
1100	+
1101	+	info[i].setDefaultRcut(theRcut, theRsw);
1102	+
1103	+	}
1104	+	}
1105	+	}
1106	+	#ifdef IS_MPI
1107	+	strcpy(checkPointMsg, "post processing checks out");
1108	+	MPIcheckPoint();
1109	+	#endif // is_mpi
1110	+
1111	+	// clean up the forcefield
1112	+	the_ff->cleanMe();
1113	+	}
1114	+
1115	+	void SimSetup::initSystemCoords(void){
1116	+	int i;
1117	+
1118	+	char* inName;
1119	+
1120	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1121	+
1122	+	for (i = 0; i < info[0].n_atoms; i++)
1123	+	info[0].atoms[i]->setCoords();
1124	+
1125	+	if (globals->haveInitialConfig()){
1126	+	InitializeFromFile* fileInit;
1127	+	#ifdef IS_MPI // is_mpi
1128	+	if (worldRank == 0){
1129	+	#endif //is_mpi
1130	+	inName = globals->getInitialConfig();
1131	+	fileInit = new InitializeFromFile(inName);
1132	+	#ifdef IS_MPI
1133	+	}
1134	+	else
1135	+	fileInit = new InitializeFromFile(NULL);
1136	+	#endif
1137	+	fileInit->readInit(info); // default velocities on
1138	+
1139	+	delete fileInit;
1140	+	}
1141	+	else{
1142	+
1143	+	// no init from bass
1144	+
1145	+	sprintf(painCave.errMsg,
1146	+	"Cannot intialize a simulation without an initial configuration file.\n");
1147	+	painCave.isFatal = 1;;
1148	+	simError();
1149	+
1150	+	}
1151	+
1152	+	#ifdef IS_MPI
1153	+	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1154	+	MPIcheckPoint();
1155	+	#endif // is_mpi
1156	+	}
1157	+
1158	+
1159	+	void SimSetup::makeOutNames(void){
1160	+	int k;
1161	+
1162	+
1163	+	for (k = 0; k < nInfo; k++){
1164	+	#ifdef IS_MPI
1165	+	if (worldRank == 0){
1166	+	#endif // is_mpi
1167	+
1168	+	if (globals->haveFinalConfig()){
1169	+	strcpy(info[k].finalName, globals->getFinalConfig());
1170	+	}
1171	+	else{
1172	+	strcpy(info[k].finalName, inFileName);
1173	+	char* endTest;
1174	+	int nameLength = strlen(info[k].finalName);
1175	+	endTest = &(info[k].finalName[nameLength - 5]);
1176	+	if (!strcmp(endTest, ".bass")){
1177	+	strcpy(endTest, ".eor");
1178	+	}
1179	+	else if (!strcmp(endTest, ".BASS")){
1180	+	strcpy(endTest, ".eor");
1181	+	}
1182	+	else{
1183	+	endTest = &(info[k].finalName[nameLength - 4]);
1184	+	if (!strcmp(endTest, ".bss")){
1185	+	strcpy(endTest, ".eor");
1186	+	}
1187	+	else if (!strcmp(endTest, ".mdl")){
1188	+	strcpy(endTest, ".eor");
1189	+	}
1190	+	else{
1191	+	strcat(info[k].finalName, ".eor");
1192	+	}
1193	+	}
1194	+	}
1195	+
1196	+	// make the sample and status out names
1197	+
1198	+	strcpy(info[k].sampleName, inFileName);
1199	+	char* endTest;
1200	+	int nameLength = strlen(info[k].sampleName);
1201	+	endTest = &(info[k].sampleName[nameLength - 5]);
1202	+	if (!strcmp(endTest, ".bass")){
1203	+	strcpy(endTest, ".dump");
1204	+	}
1205	+	else if (!strcmp(endTest, ".BASS")){
1206	+	strcpy(endTest, ".dump");
1207	+	}
1208	+	else{
1209	+	endTest = &(info[k].sampleName[nameLength - 4]);
1210	+	if (!strcmp(endTest, ".bss")){
1211	+	strcpy(endTest, ".dump");
1212	+	}
1213	+	else if (!strcmp(endTest, ".mdl")){
1214	+	strcpy(endTest, ".dump");
1215	+	}
1216	+	else{
1217	+	strcat(info[k].sampleName, ".dump");
1218	+	}
1219	+	}
1220	+
1221	+	strcpy(info[k].statusName, inFileName);
1222	+	nameLength = strlen(info[k].statusName);
1223	+	endTest = &(info[k].statusName[nameLength - 5]);
1224	+	if (!strcmp(endTest, ".bass")){
1225	+	strcpy(endTest, ".stat");
1226	+	}
1227	+	else if (!strcmp(endTest, ".BASS")){
1228	+	strcpy(endTest, ".stat");
1229	+	}
1230	+	else{
1231	+	endTest = &(info[k].statusName[nameLength - 4]);
1232	+	if (!strcmp(endTest, ".bss")){
1233	+	strcpy(endTest, ".stat");
1234	+	}
1235	+	else if (!strcmp(endTest, ".mdl")){
1236	+	strcpy(endTest, ".stat");
1237	+	}
1238	+	else{
1239	+	strcat(info[k].statusName, ".stat");
1240	+	}
1241	+	}
1242	+
1243	+	#ifdef IS_MPI
1244	+
1245	+	}
1246	+	#endif // is_mpi
1247	+	}
1248	+	}
1249	+
1250	+
1251	+	void SimSetup::sysObjectsCreation(void){
1252	+	int i, k;
1253	+
1254	+	// create the forceField
1255	+
1256	+	createFF();
1257	+
1258	+	// extract componentList
1259	+
1260	+	compList();
1261	+
1262	+	// calc the number of atoms, bond, bends, and torsions
1263	+
1264	+	calcSysValues();
1265	+
1266	+	#ifdef IS_MPI
1267	+	// divide the molecules among the processors
1268	+
1269	+	mpiMolDivide();
1270	+	#endif //is_mpi
1271	+
1272	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1273	+
1274	+	makeSysArrays();
1275	+
1276	+	// make and initialize the molecules (all but atomic coordinates)
1277	+
1278	+	makeMolecules();
1279	+
1280	+	for (k = 0; k < nInfo; k++){
1281	+	info[k].identArray = new int[info[k].n_atoms];
1282	+	for (i = 0; i < info[k].n_atoms; i++){
1283	+	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1284	+	}
1285	+	}
1286	+	}
1287	+
1288	+
1289	+	void SimSetup::createFF(void){
1290	+	switch (ffCase){
1291	+	case FF_DUFF:
1292	+	the_ff = new DUFF();
1293	+	break;
1294	+
1295	+	case FF_LJ:
1296	+	the_ff = new LJFF();
1297	+	break;
1298	+
1299	+	case FF_EAM:
1300	+	the_ff = new EAM_FF();
1301	+	break;
1302	+
1303	+	case FF_H2O:
1304	+	the_ff = new WATER();
1305	+	break;
1306	+
1307	+	default:
1308	+	sprintf(painCave.errMsg,
1309	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1310	+	painCave.isFatal = 1;
1311	+	simError();
1312	+	}
1313	+
1314	+	#ifdef IS_MPI
1315	+	strcpy(checkPointMsg, "ForceField creation successful");
1316	+	MPIcheckPoint();
1317	+	#endif // is_mpi
1318	+	}
1319	+
1320	+
1321	+	void SimSetup::compList(void){
1322	+	int i;
1323	+	char* id;
1324	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1325	+	LinkedMolStamp* currentStamp = NULL;
1326	+	comp_stamps = new MoleculeStamp * [n_components];
1327	+	bool haveCutoffGroups;
1328	+
1329	+	haveCutoffGroups = false;
1330	+
1331	+	// make an array of molecule stamps that match the components used.
1332	+	// also extract the used stamps out into a separate linked list
1333	+
1334	+	for (i = 0; i < nInfo; i++){
1335	+	info[i].nComponents = n_components;
1336	+	info[i].componentsNmol = components_nmol;
1337	+	info[i].compStamps = comp_stamps;
1338	+	info[i].headStamp = headStamp;
1339	+	}
1340	+
1341	+
1342	+	for (i = 0; i < n_components; i++){
1343	+	id = the_components[i]->getType();
1344	+	comp_stamps[i] = NULL;
1345	+
1346	+	// check to make sure the component isn't already in the list
1347	+
1348	+	comp_stamps[i] = headStamp->match(id);
1349	+	if (comp_stamps[i] == NULL){
1350	+	// extract the component from the list;
1351	+
1352	+	currentStamp = stamps->extractMolStamp(id);
1353	+	if (currentStamp == NULL){
1354	+	sprintf(painCave.errMsg,
1355	+	"SimSetup error: Component \"%s\" was not found in the "
1356	+	"list of declared molecules\n",
1357	+	id);
1358	+	painCave.isFatal = 1;
1359	+	simError();
1360	+	}
1361	+
1362	+	headStamp->add(currentStamp);
1363	+	comp_stamps[i] = headStamp->match(id);
1364	+	}
1365	+
1366	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1367	+	haveCutoffGroups = true;
1368	+	}
1369	+
1370	+	for (i = 0; i < nInfo; i++)
1371	+	info[i].haveCutoffGroups = haveCutoffGroups;
1372	+
1373	+	#ifdef IS_MPI
1374	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1375	+	MPIcheckPoint();
1376	+	#endif // is_mpi
1377	+	}
1378	+
1379	+	void SimSetup::calcSysValues(void){
1380	+	int i;
1381	+
1382	+	int* molMembershipArray;
1383	+
1384	+	tot_atoms = 0;
1385	+	tot_bonds = 0;
1386	+	tot_bends = 0;
1387	+	tot_torsions = 0;
1388	+	tot_rigid = 0;
1389	+	for (i = 0; i < n_components; i++){
1390	+	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1391	+	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1392	+	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1393	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1394	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1395	+	}
1396	+
1397	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1398	+	molMembershipArray = new int[tot_atoms];
1399	+
1400	+	for (i = 0; i < nInfo; i++){
1401	+	info[i].n_atoms = tot_atoms;
1402	+	info[i].n_bonds = tot_bonds;
1403	+	info[i].n_bends = tot_bends;
1404	+	info[i].n_torsions = tot_torsions;
1405	+	info[i].n_SRI = tot_SRI;
1406	+	info[i].n_mol = tot_nmol;
1407	+
1408	+	info[i].molMembershipArray = molMembershipArray;
1409	+	}
1410	+	}
1411	+
1412	+	#ifdef IS_MPI
1413	+
1414	+	void SimSetup::mpiMolDivide(void){
1415	+	int i, j, k;
1416	+	int localMol, allMol;
1417	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1418	+	int local_rigid;
1419	+	vector<int> globalMolIndex;
1420	+
1421	+	mpiSim = new mpiSimulation(info);
1422	+
1423	+	mpiSim->divideLabor();
1424	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1425	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1426	+
1427	+	// set up the local variables
1428	+
1429	+	mol2proc = mpiSim->getMolToProcMap();
1430	+	molCompType = mpiSim->getMolComponentType();
1431	+
1432	+	allMol = 0;
1433	+	localMol = 0;
1434	+	local_atoms = 0;
1435	+	local_bonds = 0;
1436	+	local_bends = 0;
1437	+	local_torsions = 0;
1438	+	local_rigid = 0;
1439	+	globalAtomCounter = 0;
1440	+
1441	+	for (i = 0; i < n_components; i++){
1442	+	for (j = 0; j < components_nmol[i]; j++){
1443	+	if (mol2proc[allMol] == worldRank){
1444	+	local_atoms += comp_stamps[i]->getNAtoms();
1445	+	local_bonds += comp_stamps[i]->getNBonds();
1446	+	local_bends += comp_stamps[i]->getNBends();
1447	+	local_torsions += comp_stamps[i]->getNTorsions();
1448	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1449	+	localMol++;
1450	+	}
1451	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1452	+	info[0].molMembershipArray[globalAtomCounter] = allMol;
1453	+	globalAtomCounter++;
1454	+	}
1455	+
1456	+	allMol++;
1457	+	}
1458	+	}
1459	+	local_SRI = local_bonds + local_bends + local_torsions;
1460	+
1461	+	info[0].n_atoms = mpiSim->getMyNlocal();
1462	+
1463	+
1464	+	if (local_atoms != info[0].n_atoms){
1465	+	sprintf(painCave.errMsg,
1466	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1467	+	"\tlocalAtom (%d) are not equal.\n",
1468	+	info[0].n_atoms, local_atoms);
1469	+	painCave.isFatal = 1;
1470	+	simError();
1471	+	}
1472	+
1473	+	info[0].n_bonds = local_bonds;
1474	+	info[0].n_bends = local_bends;
1475	+	info[0].n_torsions = local_torsions;
1476	+	info[0].n_SRI = local_SRI;
1477	+	info[0].n_mol = localMol;
1478	+
1479	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1480	+	MPIcheckPoint();
1481	+	}
1482	+
1483	+	#endif // is_mpi
1484	+
1485	+
1486	+	void SimSetup::makeSysArrays(void){
1487	+
1488	+	#ifndef IS_MPI
1489	+	int k, j;
1490	+	#endif // is_mpi
1491	+	int i, l;
1492	+
1493	+	Atom** the_atoms;
1494	+	Molecule* the_molecules;
1495	+
1496	+	for (l = 0; l < nInfo; l++){
1497	+	// create the atom and short range interaction arrays
1498	+
1499	+	the_atoms = new Atom * [info[l].n_atoms];
1500	+	the_molecules = new Molecule[info[l].n_mol];
1501	+	int molIndex;
1502	+
1503	+	// initialize the molecule's stampID's
1504	+
1505	+	#ifdef IS_MPI
1506	+
1507	+
1508	+	molIndex = 0;
1509	+	for (i = 0; i < mpiSim->getTotNmol(); i++){
1510	+	if (mol2proc[i] == worldRank){
1511	+	the_molecules[molIndex].setStampID(molCompType[i]);
1512	+	the_molecules[molIndex].setMyIndex(molIndex);
1513	+	the_molecules[molIndex].setGlobalIndex(i);
1514	+	molIndex++;
1515	+	}
1516	+	}
1517	+
1518	+	#else // is_mpi
1519	+
1520	+	molIndex = 0;
1521	+	globalAtomCounter = 0;
1522	+	for (i = 0; i < n_components; i++){
1523	+	for (j = 0; j < components_nmol[i]; j++){
1524	+	the_molecules[molIndex].setStampID(i);
1525	+	the_molecules[molIndex].setMyIndex(molIndex);
1526	+	the_molecules[molIndex].setGlobalIndex(molIndex);
1527	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1528	+	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1529	+	globalAtomCounter++;
1530	+	}
1531	+	molIndex++;
1532	+	}
1533	+	}
1534	+
1535	+
1536	+	#endif // is_mpi
1537	+
1538	+	info[l].globalExcludes = new int;
1539	+	info[l].globalExcludes[0] = 0;
1540	+
1541	+	// set the arrays into the SimInfo object
1542	+
1543	+	info[l].atoms = the_atoms;
1544	+	info[l].molecules = the_molecules;
1545	+	info[l].nGlobalExcludes = 0;
1546	+
1547	+	the_ff->setSimInfo(info);
1548	+	}
1549	+	}
1550	+
1551	+	void SimSetup::makeIntegrator(void){
1552	+	int k;
1553	+
1554	+	NVE<RealIntegrator>* myNVE = NULL;
1555	+	NVT<RealIntegrator>* myNVT = NULL;
1556	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1557	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1558	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1559	+
1560	+	for (k = 0; k < nInfo; k++){
1561	+	switch (ensembleCase){
1562	+	case NVE_ENS:
1563	+	if (globals->haveZconstraints()){
1564	+	setupZConstraint(info[k]);
1565	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1566	+	}
1567	+	else{
1568	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1569	+	}
1570	+
1571	+	info->the_integrator = myNVE;
1572	+	break;
1573	+
1574	+	case NVT_ENS:
1575	+	if (globals->haveZconstraints()){
1576	+	setupZConstraint(info[k]);
1577	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1578	+	}
1579	+	else
1580	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1581	+
1582	+	myNVT->setTargetTemp(globals->getTargetTemp());
1583	+
1584	+	if (globals->haveTauThermostat())
1585	+	myNVT->setTauThermostat(globals->getTauThermostat());
1586	+	else{
1587	+	sprintf(painCave.errMsg,
1588	+	"SimSetup error: If you use the NVT\n"
1589	+	"\tensemble, you must set tauThermostat.\n");
1590	+	painCave.isFatal = 1;
1591	+	simError();
1592	+	}
1593	+
1594	+	info->the_integrator = myNVT;
1595	+	break;
1596	+
1597	+	case NPTi_ENS:
1598	+	if (globals->haveZconstraints()){
1599	+	setupZConstraint(info[k]);
1600	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1601	+	}
1602	+	else
1603	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1604	+
1605	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1606	+
1607	+	if (globals->haveTargetPressure())
1608	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1609	+	else{
1610	+	sprintf(painCave.errMsg,
1611	+	"SimSetup error: If you use a constant pressure\n"
1612	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1613	+	painCave.isFatal = 1;
1614	+	simError();
1615	+	}
1616	+
1617	+	if (globals->haveTauThermostat())
1618	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1619	+	else{
1620	+	sprintf(painCave.errMsg,
1621	+	"SimSetup error: If you use an NPT\n"
1622	+	"\tensemble, you must set tauThermostat.\n");
1623	+	painCave.isFatal = 1;
1624	+	simError();
1625	+	}
1626	+
1627	+	if (globals->haveTauBarostat())
1628	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1629	+	else{
1630	+	sprintf(painCave.errMsg,
1631	+	"SimSetup error: If you use an NPT\n"
1632	+	"\tensemble, you must set tauBarostat.\n");
1633	+	painCave.isFatal = 1;
1634	+	simError();
1635	+	}
1636	+
1637	+	info->the_integrator = myNPTi;
1638	+	break;
1639	+
1640	+	case NPTf_ENS:
1641	+	if (globals->haveZconstraints()){
1642	+	setupZConstraint(info[k]);
1643	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1644	+	}
1645	+	else
1646	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1647	+
1648	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1649	+
1650	+	if (globals->haveTargetPressure())
1651	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1652	+	else{
1653	+	sprintf(painCave.errMsg,
1654	+	"SimSetup error: If you use a constant pressure\n"
1655	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1656	+	painCave.isFatal = 1;
1657	+	simError();
1658	+	}
1659	+
1660	+	if (globals->haveTauThermostat())
1661	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1662	+
1663	+	else{
1664	+	sprintf(painCave.errMsg,
1665	+	"SimSetup error: If you use an NPT\n"
1666	+	"\tensemble, you must set tauThermostat.\n");
1667	+	painCave.isFatal = 1;
1668	+	simError();
1669	+	}
1670	+
1671	+	if (globals->haveTauBarostat())
1672	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1673	+
1674	+	else{
1675	+	sprintf(painCave.errMsg,
1676	+	"SimSetup error: If you use an NPT\n"
1677	+	"\tensemble, you must set tauBarostat.\n");
1678	+	painCave.isFatal = 1;
1679	+	simError();
1680	+	}
1681	+
1682	+	info->the_integrator = myNPTf;
1683	+	break;
1684	+
1685	+	case NPTxyz_ENS:
1686	+	if (globals->haveZconstraints()){
1687	+	setupZConstraint(info[k]);
1688	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1689	+	}
1690	+	else
1691	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1692	+
1693	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1694	+
1695	+	if (globals->haveTargetPressure())
1696	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1697	+	else{
1698	+	sprintf(painCave.errMsg,
1699	+	"SimSetup error: If you use a constant pressure\n"
1700	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1701	+	painCave.isFatal = 1;
1702	+	simError();
1703	+	}
1704	+
1705	+	if (globals->haveTauThermostat())
1706	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1707	+	else{
1708	+	sprintf(painCave.errMsg,
1709	+	"SimSetup error: If you use an NPT\n"
1710	+	"\tensemble, you must set tauThermostat.\n");
1711	+	painCave.isFatal = 1;
1712	+	simError();
1713	+	}
1714	+
1715	+	if (globals->haveTauBarostat())
1716	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1717	+	else{
1718	+	sprintf(painCave.errMsg,
1719	+	"SimSetup error: If you use an NPT\n"
1720	+	"\tensemble, you must set tauBarostat.\n");
1721	+	painCave.isFatal = 1;
1722	+	simError();
1723	+	}
1724	+
1725	+	info->the_integrator = myNPTxyz;
1726	+	break;
1727	+
1728	+	default:
1729	+	sprintf(painCave.errMsg,
1730	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1731	+	painCave.isFatal = 1;
1732	+	simError();
1733	+	}
1734		}
1735		}
1736	+
1737	+	void SimSetup::initFortran(void){
1738	+	info[0].refreshSim();
1739	+
1740	+	if (!strcmp(info[0].mixingRule, "standard")){
1741	+	the_ff->initForceField(LB_MIXING_RULE);
1742	+	}
1743	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1744	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1745	+	}
1746	+	else{
1747	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1748	+	info[0].mixingRule);
1749	+	painCave.isFatal = 1;
1750	+	simError();
1751	+	}
1752	+
1753	+
1754	+	#ifdef IS_MPI
1755	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1756	+	MPIcheckPoint();
1757	+	#endif // is_mpi
1758	+	}
1759	+
1760	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1761	+	int nZConstraints;
1762	+	ZconStamp** zconStamp;
1763	+
1764	+	if (globals->haveZconstraintTime()){
1765	+	//add sample time of z-constraint  into SimInfo's property list
1766	+	DoubleData* zconsTimeProp = new DoubleData();
1767	+	zconsTimeProp->setID(ZCONSTIME_ID);
1768	+	zconsTimeProp->setData(globals->getZconsTime());
1769	+	theInfo.addProperty(zconsTimeProp);
1770	+	}
1771	+	else{
1772	+	sprintf(painCave.errMsg,
1773	+	"ZConstraint error: If you use a ZConstraint,\n"
1774	+	"\tyou must set zconsTime.\n");
1775	+	painCave.isFatal = 1;
1776	+	simError();
1777	+	}
1778	+
1779	+	//push zconsTol into siminfo, if user does not specify
1780	+	//value for zconsTol, a default value will be used
1781	+	DoubleData* zconsTol = new DoubleData();
1782	+	zconsTol->setID(ZCONSTOL_ID);
1783	+	if (globals->haveZconsTol()){
1784	+	zconsTol->setData(globals->getZconsTol());
1785	+	}
1786	+	else{
1787	+	double defaultZConsTol = 0.01;
1788	+	sprintf(painCave.errMsg,
1789	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1790	+	"\tOOPSE will use a default value of %f.\n"
1791	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1792	+	defaultZConsTol);
1793	+	painCave.isFatal = 0;
1794	+	simError();
1795	+
1796	+	zconsTol->setData(defaultZConsTol);
1797	+	}
1798	+	theInfo.addProperty(zconsTol);
1799	+
1800	+	//set Force Subtraction Policy
1801	+	StringData* zconsForcePolicy = new StringData();
1802	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1803	+
1804	+	if (globals->haveZconsForcePolicy()){
1805	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1806	+	}
1807	+	else{
1808	+	sprintf(painCave.errMsg,
1809	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1810	+	"\tOOPSE will use PolicyByMass.\n"
1811	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1812	+	painCave.isFatal = 0;
1813	+	simError();
1814	+	zconsForcePolicy->setData("BYMASS");
1815	+	}
1816	+
1817	+	theInfo.addProperty(zconsForcePolicy);
1818	+
1819	+	//set zcons gap
1820	+	DoubleData* zconsGap = new DoubleData();
1821	+	zconsGap->setID(ZCONSGAP_ID);
1822	+
1823	+	if (globals->haveZConsGap()){
1824	+	zconsGap->setData(globals->getZconsGap());
1825	+	theInfo.addProperty(zconsGap);
1826	+	}
1827	+
1828	+	//set zcons fixtime
1829	+	DoubleData* zconsFixtime = new DoubleData();
1830	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1831	+
1832	+	if (globals->haveZConsFixTime()){
1833	+	zconsFixtime->setData(globals->getZconsFixtime());
1834	+	theInfo.addProperty(zconsFixtime);
1835	+	}
1836	+
1837	+	//set zconsUsingSMD
1838	+	IntData* zconsUsingSMD = new IntData();
1839	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1840	+
1841	+	if (globals->haveZConsUsingSMD()){
1842	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1843	+	theInfo.addProperty(zconsUsingSMD);
1844	+	}
1845	+
1846	+	//Determine the name of ouput file and add it into SimInfo's property list
1847	+	//Be careful, do not use inFileName, since it is a pointer which
1848	+	//point to a string at master node, and slave nodes do not contain that string
1849	+
1850	+	string zconsOutput(theInfo.finalName);
1851	+
1852	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1853	+
1854	+	StringData* zconsFilename = new StringData();
1855	+	zconsFilename->setID(ZCONSFILENAME_ID);
1856	+	zconsFilename->setData(zconsOutput);
1857	+
1858	+	theInfo.addProperty(zconsFilename);
1859	+
1860	+	//setup index, pos and other parameters of z-constraint molecules
1861	+	nZConstraints = globals->getNzConstraints();
1862	+	theInfo.nZconstraints = nZConstraints;
1863	+
1864	+	zconStamp = globals->getZconStamp();
1865	+	ZConsParaItem tempParaItem;
1866	+
1867	+	ZConsParaData* zconsParaData = new ZConsParaData();
1868	+	zconsParaData->setID(ZCONSPARADATA_ID);
1869	+
1870	+	for (int i = 0; i < nZConstraints; i++){
1871	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1872	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1873	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1874	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1875	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1876	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1877	+	zconsParaData->addItem(tempParaItem);
1878	+	}
1879	+
1880	+	//check the uniqueness of index
1881	+	if(!zconsParaData->isIndexUnique()){
1882	+	sprintf(painCave.errMsg,
1883	+	"ZConstraint Error: molIndex is not unique!\n");
1884	+	painCave.isFatal = 1;
1885	+	simError();
1886	+	}
1887	+
1888	+	//sort the parameters by index of molecules
1889	+	zconsParaData->sortByIndex();
1890	+
1891	+	//push data into siminfo, therefore, we can retrieve later
1892	+	theInfo.addProperty(zconsParaData);
1893	+	}
1894	+
1895	+	void SimSetup::makeMinimizer(){
1896	+
1897	+	OOPSEMinimizer* myOOPSEMinimizer;
1898	+	MinimizerParameterSet* param;
1899	+	char minimizerName[100];
1900	+
1901	+	for (int i = 0; i < nInfo; i++){
1902	+
1903	+	//prepare parameter set for minimizer
1904	+	param = new MinimizerParameterSet();
1905	+	param->setDefaultParameter();
1906	+
1907	+	if (globals->haveMinimizer()){
1908	+	param->setFTol(globals->getMinFTol());
1909	+	}
1910	+
1911	+	if (globals->haveMinGTol()){
1912	+	param->setGTol(globals->getMinGTol());
1913	+	}
1914	+
1915	+	if (globals->haveMinMaxIter()){
1916	+	param->setMaxIteration(globals->getMinMaxIter());
1917	+	}
1918	+
1919	+	if (globals->haveMinWriteFrq()){
1920	+	param->setMaxIteration(globals->getMinMaxIter());
1921	+	}
1922	+
1923	+	if (globals->haveMinWriteFrq()){
1924	+	param->setWriteFrq(globals->getMinWriteFrq());
1925	+	}
1926	+
1927	+	if (globals->haveMinStepSize()){
1928	+	param->setStepSize(globals->getMinStepSize());
1929	+	}
1930	+
1931	+	if (globals->haveMinLSMaxIter()){
1932	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1933	+	}
1934	+
1935	+	if (globals->haveMinLSTol()){
1936	+	param->setLineSearchTol(globals->getMinLSTol());
1937	+	}
1938	+
1939	+	strcpy(minimizerName, globals->getMinimizer());
1940	+
1941	+	if (!strcasecmp(minimizerName, "CG")){
1942	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1943	+	}
1944	+	else if (!strcasecmp(minimizerName, "SD")){
1945	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1946	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1947	+	}
1948	+	else{
1949	+	sprintf(painCave.errMsg,
1950	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1951	+	painCave.isFatal = 0;
1952	+	simError();
1953	+
1954	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1955	+	}
1956	+	info[i].the_integrator = myOOPSEMinimizer;
1957	+
1958	+	//store the minimizer into simInfo
1959	+	info[i].the_minimizer = myOOPSEMinimizer;
1960	+	info[i].has_minimizer = true;
1961	+	}
1962	+
1963	+	}

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