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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 412 by mmeineke, Wed Mar 26 21:50:33 2003 UTC vs.
Revision 1091 by tim, Tue Mar 16 19:22:56 2004 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	//#include "ConjugateMinimizer.hpp"
13	+	#include "OOPSEMinimizer.hpp"
14
15		#ifdef IS_MPI
16		#include "mpiBASS.h"
17		#include "mpiSimulation.hpp"
18		#endif
19
20	+	// some defines for ensemble and Forcefield  cases
21	+
22	+	#define NVE_ENS        0
23	+	#define NVT_ENS        1
24	+	#define NPTi_ENS       2
25	+	#define NPTf_ENS       3
26	+	#define NPTxyz_ENS     4
27	+
28	+
29	+	#define FF_DUFF  0
30	+	#define FF_LJ    1
31	+	#define FF_EAM   2
32	+	#define FF_H2O   3
33	+
34	+	using namespace std;
35	+
36	+	/**
37	+	* Check whether dividend is divisble by divisor or not
38	+	*/
39	+	bool isDivisible(double dividend, double divisor){
40	+	double tolerance = 0.000001;
41	+	double quotient;
42	+	double diff;
43	+	int intQuotient;
44	+
45	+	quotient = dividend / divisor;
46	+
47	+	if (quotient < 0)
48	+	quotient = -quotient;
49	+
50	+	intQuotient = int (quotient + tolerance);
51	+
52	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
53	+
54	+	if (diff <= tolerance)
55	+	return true;
56	+	else
57	+	return false;
58	+	}
59	+
60		SimSetup::SimSetup(){
61	+
62	+	initSuspend = false;
63	+	isInfoArray = 0;
64	+	nInfo = 1;
65	+
66		stamps = new MakeStamps();
67		globals = new Globals();
68	<
68	>
69	>
70		#ifdef IS_MPI
71	<	strcpy( checkPointMsg, "SimSetup creation successful" );
71	>	strcpy(checkPointMsg, "SimSetup creation successful");
72		MPIcheckPoint();
73		#endif // IS_MPI
74		}
#	Line 27 | Line 78 | SimSetup::~SimSetup(){
78		delete globals;
79		}
80
81	<	void SimSetup::parseFile( char* fileName ){
81	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
82	>	info = the_info;
83	>	nInfo = theNinfo;
84	>	isInfoArray = 1;
85	>	initSuspend = true;
86	>	}
87
88	+
89	+	void SimSetup::parseFile(char* fileName){
90		#ifdef IS_MPI
91	<	if( worldRank == 0 ){
91	>	if (worldRank == 0){
92		#endif // is_mpi
93	<
93	>
94		inFileName = fileName;
95	<	set_interface_stamps( stamps, globals );
96	<
95	>	set_interface_stamps(stamps, globals);
96	>
97		#ifdef IS_MPI
98		mpiEventInit();
99		#endif
100
101	<	yacc_BASS( fileName );
101	>	yacc_BASS(fileName);
102
103		#ifdef IS_MPI
104		throwMPIEvent(NULL);
105		}
106	<	else receiveParse();
106	>	else{
107	>	receiveParse();
108	>	}
109		#endif
110
111		}
112
113		#ifdef IS_MPI
114		void SimSetup::receiveParse(void){
115	<
116	<	set_interface_stamps( stamps, globals );
117	<	mpiEventInit();
118	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
115	>	set_interface_stamps(stamps, globals);
116	>	mpiEventInit();
117	>	MPIcheckPoint();
118	>	mpiEventLoop();
119		}
120
121		#endif // is_mpi
122
123	<	void SimSetup::createSim( void ){
123	>	void SimSetup::createSim(void){
124
125	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
125	>	// gather all of the information from the Bass file
126
127	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
127	>	gatherInfo();
128
129	<	// 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();
129	>	// creation of complex system objects
130
131	<	// 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 );
131	>	sysObjectsCreation();
132
133	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
133	>	// check on the post processing info
134
135	+	finalInfoCheck();
136
137	<	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
92	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
93	<	else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
94	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
95	<	else{
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Error. Unrecognized force field -> %s\n",
98	<	force_field );
99	<	painCave.isFatal = 1;
100	<	simError();
101	<	}
137	>	// initialize the system coordinates
138
139	<	#ifdef IS_MPI
140	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
139	>	if ( !initSuspend ){
140	>	initSystemCoords();
141
142	<
142	>	if( !(globals->getUseInitTime()) )
143	>	info[0].currentTime = 0.0;
144	>	}
145
146	<	// get the components and calculate the tot_nMol and indvidual n_mol
111	<	the_components = the_globals->getComponents();
112	<	components_nmol = new int[n_components];
113	<	comp_stamps = new MoleculeStamp*[n_components];
146	>	// make the output filenames
147
148	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
148	>	makeOutNames();
149
150	<	tot_nmol = 0;
151	<	for( i=0; i<n_components; i++ ){
152	<
153	<	if( !the_components[i]->haveNMol() ){
154	<	// we have a problem
155	<	sprintf( painCave.errMsg,
125	<	"SimSetup Error. No global NMol or component NMol"
126	<	" given. Cannot calculate the number of atoms.\n" );
127	<	painCave.isFatal = 1;
128	<	simError();
129	<	}
130	<
131	<	tot_nmol += the_components[i]->getNMol();
132	<	components_nmol[i] = the_components[i]->getNMol();
133	<	}
134	<	}
135	<	else{
136	<	sprintf( painCave.errMsg,
137	<	"SimSetup error.\n"
138	<	"\tSorry, the ability to specify total"
139	<	" nMols and then give molfractions in the components\n"
140	<	"\tis not currently supported."
141	<	" Please give nMol in the components.\n" );
142	<	painCave.isFatal = 1;
143	<	simError();
144	<
145	<
146	<	//     tot_nmol = the_globals->getNMol();
147	<
148	<	//   //we have the total number of molecules, now we check for molfractions
149	<	//     for( i=0; i<n_components; i++ ){
150	<
151	<	//       if( !the_components[i]->haveMolFraction() ){
152	<
153	<	//  if( !the_components[i]->haveNMol() ){
154	<	//    //we have a problem
155	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
156	<	//              << " nMol was given in component
157	<
158	<	}
159	<
160	<	#ifdef IS_MPI
161	<	strcpy( checkPointMsg, "Have the number of components" );
162	<	MPIcheckPoint();
163	<	#endif // is_mpi
164	<
165	<	// make an array of molecule stamps that match the components used.
166	<	// also extract the used stamps out into a separate linked list
167	<
168	<	simnfo->nComponents = n_components;
169	<	simnfo->componentsNmol = components_nmol;
170	<	simnfo->compStamps = comp_stamps;
171	<	simnfo->headStamp = new LinkedMolStamp();
150	>	if (globals->haveMinimizer())
151	>	// make minimizer
152	>	makeMinimizer();
153	>	else
154	>	// make the integrator
155	>	makeIntegrator();
156
173	–	char* id;
174	–	LinkedMolStamp* headStamp = simnfo->headStamp;
175	–	LinkedMolStamp* currentStamp = NULL;
176	–	for( i=0; i<n_components; i++ ){
177	–
178	–	id = the_components[i]->getType();
179	–	comp_stamps[i] = NULL;
180	–
181	–	// check to make sure the component isn't already in the list
182	–
183	–	comp_stamps[i] = headStamp->match( id );
184	–	if( comp_stamps[i] == NULL ){
185	–
186	–	// extract the component from the list;
187	–
188	–	currentStamp = the_stamps->extractMolStamp( id );
189	–	if( currentStamp == NULL ){
190	–	sprintf( painCave.errMsg,
191	–	"SimSetup error: Component \"%s\" was not found in the "
192	–	"list of declared molecules\n",
193	–	id );
194	–	painCave.isFatal = 1;
195	–	simError();
196	–	}
197	–
198	–	headStamp->add( currentStamp );
199	–	comp_stamps[i] = headStamp->match( id );
200	–	}
201	–	}
202	–
157		#ifdef IS_MPI
158	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
159	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
158	>	mpiSim->mpiRefresh();
159	>	#endif
160
161	+	// initialize the Fortran
162
163	+	initFortran();
164	+	}
165
211	–	// caclulate the number of atoms, bonds, bends and torsions
166
167	<	tot_atoms = 0;
168	<	tot_bonds = 0;
169	<	tot_bends = 0;
170	<	tot_torsions = 0;
171	<	for( i=0; i<n_components; i++ ){
172	<
173	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
174	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
175	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
176	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
177	<	}
167	>	void SimSetup::makeMolecules(void){
168	>	int k;
169	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
170	>	molInit molInfo;
171	>	DirectionalAtom* dAtom;
172	>	LinkedAssign* extras;
173	>	LinkedAssign* current_extra;
174	>	AtomStamp* currentAtom;
175	>	BondStamp* currentBond;
176	>	BendStamp* currentBend;
177	>	TorsionStamp* currentTorsion;
178
179	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
179	>	bond_pair* theBonds;
180	>	bend_set* theBends;
181	>	torsion_set* theTorsions;
182
183	<	simnfo->n_atoms = tot_atoms;
228	<	simnfo->n_bonds = tot_bonds;
229	<	simnfo->n_bends = tot_bends;
230	<	simnfo->n_torsions = tot_torsions;
231	<	simnfo->n_SRI = tot_SRI;
232	<	simnfo->n_mol = tot_nmol;
183	>	//init the forceField paramters
184
185	<
235	<	#ifdef IS_MPI
185	>	the_ff->readParams();
186
237	–	// divide the molecules among processors here.
238	–
239	–	mpiSim = new mpiSimulation( simnfo );
240	–
241	–
187
188	<	globalIndex = mpiSim->divideLabor();
188	>	// init the atoms
189	>
190	>	double phi, theta, psi;
191	>	double sux, suy, suz;
192	>	double Axx, Axy, Axz, Ayx, Ayy, Ayz, Azx, Azy, Azz;
193	>	double ux, uy, uz, u, uSqr;
194
195	+	for (k = 0; k < nInfo; k++){
196	+	the_ff->setSimInfo(&(info[k]));
197
198	+	atomOffset = 0;
199	+	excludeOffset = 0;
200	+	for (i = 0; i < info[k].n_mol; i++){
201	+	stampID = info[k].molecules[i].getStampID();
202
203	<	// set up the local variables
204	<
205	<	int localMol, allMol;
206	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
207	<
252	<	allMol = 0;
253	<	localMol = 0;
254	<	local_atoms = 0;
255	<	local_bonds = 0;
256	<	local_bends = 0;
257	<	local_torsions = 0;
258	<	for( i=0; i<n_components; i++ ){
203	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
204	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
205	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
206	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
207	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
208
209	<	for( j=0; j<components_nmol[i]; j++ ){
210	<
211	<	if( mpiSim->getMyMolStart() <= allMol &&
212	<	allMol <= mpiSim->getMyMolEnd() ){
213	<
265	<	local_atoms +=    comp_stamps[i]->getNAtoms();
266	<	local_bonds +=    comp_stamps[i]->getNBonds();
267	<	local_bends +=    comp_stamps[i]->getNBends();
268	<	local_torsions += comp_stamps[i]->getNTorsions();
269	<	localMol++;
270	<	}
271	<	allMol++;
272	<	}
273	<	}
274	<	local_SRI = local_bonds + local_bends + local_torsions;
275	<
209	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
210	>	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
211	>	molInfo.myBonds = new Bond * [molInfo.nBonds];
212	>	molInfo.myBends = new Bend * [molInfo.nBends];
213	>	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
214
215	<	simnfo->n_atoms = mpiSim->getMyNlocal();
216	<
217	<	if( local_atoms != simnfo->n_atoms ){
280	<	sprintf( painCave.errMsg,
281	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282	<	" localAtom (%d) are note equal.\n",
283	<	simnfo->n_atoms,
284	<	local_atoms );
285	<	painCave.isFatal = 1;
286	<	simError();
287	<	}
215	>	theBonds = new bond_pair[molInfo.nBonds];
216	>	theBends = new bend_set[molInfo.nBends];
217	>	theTorsions = new torsion_set[molInfo.nTorsions];
218
219	<	simnfo->n_bonds = local_bonds;
290	<	simnfo->n_bends = local_bends;
291	<	simnfo->n_torsions = local_torsions;
292	<	simnfo->n_SRI = local_SRI;
293	<	simnfo->n_mol = localMol;
219	>	// make the Atoms
220
221	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
222	<	MPIcheckPoint();
223	<
224	<
225	<	#endif // is_mpi
226	<
221	>	for (j = 0; j < molInfo.nAtoms; j++){
222	>	currentAtom = comp_stamps[stampID]->getAtom(j);
223	>	if (currentAtom->haveOrientation()){
224	>	dAtom = new DirectionalAtom((j + atomOffset),
225	>	info[k].getConfiguration());
226	>	info[k].n_oriented++;
227	>	molInfo.myAtoms[j] = dAtom;
228
229	<	// create the atom and short range interaction arrays
229	>	// Directional Atoms have standard unit vectors which are oriented
230	>	// in space using the three Euler angles.  We assume the standard
231	>	// unit vector was originally along the z axis below.
232
233	<	Atom::createArrays(simnfo->n_atoms);
234	<	the_atoms = new Atom*[simnfo->n_atoms];
235	<	the_molecules = new Molecule[simnfo->n_mol];
233	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
234	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
235	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
236	>
237	>	Axx = (cos(phi) * cos(psi)) - (sin(phi) * cos(theta) * sin(psi));
238	>	Axy = (sin(phi) * cos(psi)) + (cos(phi) * cos(theta) * sin(psi));
239	>	Axz = sin(theta) * sin(psi);
240	>
241	>	Ayx = -(cos(phi) * sin(psi)) - (sin(phi) * cos(theta) * cos(psi));
242	>	Ayy = -(sin(phi) * sin(psi)) + (cos(phi) * cos(theta) * cos(psi));
243	>	Ayz = sin(theta) * cos(psi);
244	>
245	>	Azx = sin(phi) * sin(theta);
246	>	Azy = -cos(phi) * sin(theta);
247	>	Azz = cos(theta);
248
249	+	sux = 0.0;
250	+	suy = 0.0;
251	+	suz = 1.0;
252
253	<	if( simnfo->n_SRI ){
254	<	Exclude::createArray(simnfo->n_SRI);
255	<	the_excludes = new Exclude*[simnfo->n_SRI];
312	<	simnfo->globalExcludes = new int;
313	<	simnfo->n_exclude = tot_SRI;
314	<	}
315	<	else{
316	<
317	<	Exclude::createArray( 1 );
318	<	the_excludes = new Exclude*;
319	<	the_excludes[0] = new Exclude(0);
320	<	the_excludes[0]->setPair( 0,0 );
321	<	simnfo->globalExcludes = new int;
322	<	simnfo->globalExcludes[0] = 0;
323	<	simnfo->n_exclude = 0;
324	<	}
253	>	ux = (Axx * sux) + (Ayx * suy) + (Azx * suz);
254	>	uy = (Axy * sux) + (Ayy * suy) + (Azy * suz);
255	>	uz = (Axz * sux) + (Ayz * suy) + (Azz * suz);
256
257	<	// set the arrays into the SimInfo object
257	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
258
259	<	simnfo->atoms = the_atoms;
260	<	simnfo->sr_interactions = the_sris;
261	<	simnfo->nGlobalExcludes = 0;
262	<	simnfo->excludes = the_excludes;
259	>	u = sqrt(uSqr);
260	>	ux = ux / u;
261	>	uy = uy / u;
262	>	uz = uz / u;
263
264	+	dAtom->setSUx(ux);
265	+	dAtom->setSUy(uy);
266	+	dAtom->setSUz(uz);
267	+	}
268	+	else{
269	+	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
270	+	info[k].getConfiguration());
271	+	}
272	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
273
274	<	// get some of the tricky things that may still be in the globals
274	>	#ifdef IS_MPI
275
276	<
337	<	if( the_globals->haveBox() ){
338	<	simnfo->box_x = the_globals->getBox();
339	<	simnfo->box_y = the_globals->getBox();
340	<	simnfo->box_z = the_globals->getBox();
341	<	}
342	<	else if( the_globals->haveDensity() ){
276	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
277
278	<	double vol;
279	<	vol = (double)tot_nmol / the_globals->getDensity();
346	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
347	<	simnfo->box_y = simnfo->box_x;
348	<	simnfo->box_z = simnfo->box_x;
349	<	}
350	<	else{
351	<	if( !the_globals->haveBoxX() ){
352	<	sprintf( painCave.errMsg,
353	<	"SimSetup error, no periodic BoxX size given.\n" );
354	<	painCave.isFatal = 1;
355	<	simError();
356	<	}
357	<	simnfo->box_x = the_globals->getBoxX();
278	>	#endif // is_mpi
279	>	}
280
281	<	if( !the_globals->haveBoxY() ){
282	<	sprintf( painCave.errMsg,
283	<	"SimSetup error, no periodic BoxY size given.\n" );
284	<	painCave.isFatal = 1;
285	<	simError();
364	<	}
365	<	simnfo->box_y = the_globals->getBoxY();
281	>	// make the bonds
282	>	for (j = 0; j < molInfo.nBonds; j++){
283	>	currentBond = comp_stamps[stampID]->getBond(j);
284	>	theBonds[j].a = currentBond->getA() + atomOffset;
285	>	theBonds[j].b = currentBond->getB() + atomOffset;
286
287	<	if( !the_globals->haveBoxZ() ){
288	<	sprintf( painCave.errMsg,
369	<	"SimSetup error, no periodic BoxZ size given.\n" );
370	<	painCave.isFatal = 1;
371	<	simError();
372	<	}
373	<	simnfo->box_z = the_globals->getBoxZ();
374	<	}
287	>	exI = theBonds[j].a;
288	>	exJ = theBonds[j].b;
289
290	+	// exclude_I must always be the smaller of the pair
291	+	if (exI > exJ){
292	+	tempEx = exI;
293	+	exI = exJ;
294	+	exJ = tempEx;
295	+	}
296		#ifdef IS_MPI
297	<	strcpy( checkPointMsg, "Box size set up" );
298	<	MPIcheckPoint();
299	<	#endif // is_mpi
297	>	tempEx = exI;
298	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
299	>	tempEx = exJ;
300	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
301
302	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
303	+	#else  // isn't MPI
304
305	<	// initialize the arrays
305	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
306	>	#endif  //is_mpi
307	>	}
308	>	excludeOffset += molInfo.nBonds;
309
310	<	the_ff->setSimInfo( simnfo );
310	>	//make the bends
311	>	for (j = 0; j < molInfo.nBends; j++){
312	>	currentBend = comp_stamps[stampID]->getBend(j);
313	>	theBends[j].a = currentBend->getA() + atomOffset;
314	>	theBends[j].b = currentBend->getB() + atomOffset;
315	>	theBends[j].c = currentBend->getC() + atomOffset;
316
317	<	makeAtoms();
318	<	simnfo->identArray = new int[simnfo->n_atoms];
319	<	for(i=0; i<simnfo->n_atoms; i++){
320	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
321	<	}
322	<
323	<	if( tot_bonds ){
324	<	makeBonds();
325	<	}
317	>	if (currentBend->haveExtras()){
318	>	extras = currentBend->getExtras();
319	>	current_extra = extras;
320	>
321	>	while (current_extra != NULL){
322	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
323	>	switch (current_extra->getType()){
324	>	case 0:
325	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
326	>	theBends[j].isGhost = 1;
327	>	break;
328	>
329	>	case 1:
330	>	theBends[j].ghost = (int) current_extra->getDouble() +
331	>	atomOffset;
332	>	theBends[j].isGhost = 1;
333	>	break;
334	>
335	>	default:
336	>	sprintf(painCave.errMsg,
337	>	"SimSetup Error: ghostVectorSource was neither a "
338	>	"double nor an int.\n"
339	>	"-->Bend[%d] in %s\n",
340	>	j, comp_stamps[stampID]->getID());
341	>	painCave.isFatal = 1;
342	>	simError();
343	>	}
344	>	}
345	>	else{
346	>	sprintf(painCave.errMsg,
347	>	"SimSetup Error: unhandled bend assignment:\n"
348	>	"    -->%s in Bend[%d] in %s\n",
349	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
350	>	painCave.isFatal = 1;
351	>	simError();
352	>	}
353	>
354	>	current_extra = current_extra->getNext();
355	>	}
356	>	}
357
358	<	if( tot_bends ){
359	<	makeBends();
360	<	}
358	>	if (!theBends[j].isGhost){
359	>	exI = theBends[j].a;
360	>	exJ = theBends[j].c;
361	>	}
362	>	else{
363	>	exI = theBends[j].a;
364	>	exJ = theBends[j].b;
365	>	}
366
367	<	if( tot_torsions ){
368	<	makeTorsions();
369	<	}
367	>	// exclude_I must always be the smaller of the pair
368	>	if (exI > exJ){
369	>	tempEx = exI;
370	>	exI = exJ;
371	>	exJ = tempEx;
372	>	}
373	>	#ifdef IS_MPI
374	>	tempEx = exI;
375	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
376	>	tempEx = exJ;
377	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
378
379	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
380	+	#else  // isn't MPI
381	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
382	+	#endif  //is_mpi
383	+	}
384	+	excludeOffset += molInfo.nBends;
385
386	<	if (the_globals->getUseRF() ) {
387	<	simnfo->useReactionField = 1;
388	<
389	<	if( !the_globals->haveECR() ){
390	<	sprintf( painCave.errMsg,
391	<	"SimSetup Warning: using default value of 1/2 the smallest "
411	<	"box length for the electrostaticCutoffRadius.\n"
412	<	"I hope you have a very fast processor!\n");
413	<	painCave.isFatal = 0;
414	<	simError();
415	<	double smallest;
416	<	smallest = simnfo->box_x;
417	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
418	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
419	<	simnfo->ecr = 0.5 * smallest;
420	<	} else {
421	<	simnfo->ecr        = the_globals->getECR();
422	<	}
386	>	for (j = 0; j < molInfo.nTorsions; j++){
387	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
388	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
389	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
390	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
391	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
392
393	<	if( !the_globals->haveEST() ){
394	<	sprintf( painCave.errMsg,
426	<	"SimSetup Warning: using default value of 0.05 * the "
427	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
428	<	);
429	<	painCave.isFatal = 0;
430	<	simError();
431	<	simnfo->est = 0.05 * simnfo->ecr;
432	<	} else {
433	<	simnfo->est        = the_globals->getEST();
434	<	}
435	<
436	<	if(!the_globals->haveDielectric() ){
437	<	sprintf( painCave.errMsg,
438	<	"SimSetup Error: You are trying to use Reaction Field without"
439	<	"setting a dielectric constant!\n"
440	<	);
441	<	painCave.isFatal = 1;
442	<	simError();
443	<	}
444	<	simnfo->dielectric = the_globals->getDielectric();
445	<	} else {
446	<	if (simnfo->n_dipoles) {
447	<
448	<	if( !the_globals->haveECR() ){
449	<	sprintf( painCave.errMsg,
450	<	"SimSetup Warning: using default value of 1/2 the smallest"
451	<	"box length for the electrostaticCutoffRadius.\n"
452	<	"I hope you have a very fast processor!\n");
453	<	painCave.isFatal = 0;
454	<	simError();
455	<	double smallest;
456	<	smallest = simnfo->box_x;
457	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
458	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
459	<	simnfo->ecr = 0.5 * smallest;
460	<	} else {
461	<	simnfo->ecr        = the_globals->getECR();
462	<	}
463	<
464	<	if( !the_globals->haveEST() ){
465	<	sprintf( painCave.errMsg,
466	<	"SimSetup Warning: using default value of 5% of the"
467	<	"electrostaticCutoffRadius for the "
468	<	"electrostaticSkinThickness\n"
469	<	);
470	<	painCave.isFatal = 0;
471	<	simError();
472	<	simnfo->est = 0.05 * simnfo->ecr;
473	<	} else {
474	<	simnfo->est        = the_globals->getEST();
475	<	}
476	<	}
477	<	}
393	>	exI = theTorsions[j].a;
394	>	exJ = theTorsions[j].d;
395
396	+	// exclude_I must always be the smaller of the pair
397	+	if (exI > exJ){
398	+	tempEx = exI;
399	+	exI = exJ;
400	+	exJ = tempEx;
401	+	}
402		#ifdef IS_MPI
403	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
404	<	MPIcheckPoint();
405	<	#endif // is_mpi
403	>	tempEx = exI;
404	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
405	>	tempEx = exJ;
406	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
407
408	<	if( the_globals->haveInitialConfig() ){
409	<
410	<	InitializeFromFile* fileInit;
411	<	#ifdef IS_MPI // is_mpi
412	<	if( worldRank == 0 ){
413	<	#endif //is_mpi
490	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
491	<	#ifdef IS_MPI
492	<	}else fileInit = new InitializeFromFile( NULL );
493	<	#endif
494	<	fileInit->read_xyz( simnfo ); // default velocities on
408	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
409	>	#else  // isn't MPI
410	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
411	>	#endif  //is_mpi
412	>	}
413	>	excludeOffset += molInfo.nTorsions;
414
496	–	delete fileInit;
497	–	}
498	–	else{
415
416	<	#ifdef IS_MPI
416	>	// send the arrays off to the forceField for init.
417
418	<	// no init from bass
419	<
420	<	sprintf( painCave.errMsg,
421	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
422	<	painCave.isFatal;
507	<	simError();
508	<
509	<	#else
418	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
419	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
420	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
421	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
422	>	theTorsions);
423
511	–	initFromBass();
424
425	+	info[k].molecules[i].initialize(molInfo);
426
514	–	#endif
515	–	}
427
428	+	atomOffset += molInfo.nAtoms;
429	+	delete[] theBonds;
430	+	delete[] theBends;
431	+	delete[] theTorsions;
432	+	}
433	+	}
434	+
435		#ifdef IS_MPI
436	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
436	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
437		MPIcheckPoint();
438		#endif // is_mpi
439
440	+	// clean up the forcefield
441
442	<
443	<
444	<
442	>	the_ff->calcRcut();
443	>	the_ff->cleanMe();
444	>	}
445
446	<
447	<	#ifdef IS_MPI
448	<	if( worldRank == 0 ){
449	<	#endif // is_mpi
450	<
451	<	if( the_globals->haveFinalConfig() ){
452	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
446	>	void SimSetup::initFromBass(void){
447	>	int i, j, k;
448	>	int n_cells;
449	>	double cellx, celly, cellz;
450	>	double temp1, temp2, temp3;
451	>	int n_per_extra;
452	>	int n_extra;
453	>	int have_extra, done;
454	>
455	>	double vel[3];
456	>	vel[0] = 0.0;
457	>	vel[1] = 0.0;
458	>	vel[2] = 0.0;
459	>
460	>	temp1 = (double) tot_nmol / 4.0;
461	>	temp2 = pow(temp1, (1.0 / 3.0));
462	>	temp3 = ceil(temp2);
463	>
464	>	have_extra = 0;
465	>	if (temp2 < temp3){
466	>	// we have a non-complete lattice
467	>	have_extra = 1;
468	>
469	>	n_cells = (int) temp3 - 1;
470	>	cellx = info[0].boxL[0] / temp3;
471	>	celly = info[0].boxL[1] / temp3;
472	>	cellz = info[0].boxL[2] / temp3;
473	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
474	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
475	>	n_per_extra = (int) ceil(temp1);
476	>
477	>	if (n_per_extra > 4){
478	>	sprintf(painCave.errMsg,
479	>	"SimSetup error. There has been an error in constructing"
480	>	" the non-complete lattice.\n");
481	>	painCave.isFatal = 1;
482	>	simError();
483		}
484	<	else{
485	<	strcpy( simnfo->finalName, inFileName );
486	<	char* endTest;
487	<	int nameLength = strlen( simnfo->finalName );
488	<	endTest = &(simnfo->finalName[nameLength - 5]);
489	<	if( !strcmp( endTest, ".bass" ) ){
490	<	strcpy( endTest, ".eor" );
491	<	}
492	<	else if( !strcmp( endTest, ".BASS" ) ){
493	<	strcpy( endTest, ".eor" );
494	<	}
495	<	else{
496	<	endTest = &(simnfo->finalName[nameLength - 4]);
497	<	if( !strcmp( endTest, ".bss" ) ){
498	<	strcpy( endTest, ".eor" );
499	<	}
500	<	else if( !strcmp( endTest, ".mdl" ) ){
501	<	strcpy( endTest, ".eor" );
502	<	}
503	<	else{
504	<	strcat( simnfo->finalName, ".eor" );
505	<	}
506	<	}
558	<	}
559	<
560	<	// make the sample and status out names
561	<
562	<	strcpy( simnfo->sampleName, inFileName );
563	<	char* endTest;
564	<	int nameLength = strlen( simnfo->sampleName );
565	<	endTest = &(simnfo->sampleName[nameLength - 5]);
566	<	if( !strcmp( endTest, ".bass" ) ){
567	<	strcpy( endTest, ".dump" );
568	<	}
569	<	else if( !strcmp( endTest, ".BASS" ) ){
570	<	strcpy( endTest, ".dump" );
571	<	}
572	<	else{
573	<	endTest = &(simnfo->sampleName[nameLength - 4]);
574	<	if( !strcmp( endTest, ".bss" ) ){
575	<	strcpy( endTest, ".dump" );
484	>	}
485	>	else{
486	>	n_cells = (int) temp3;
487	>	cellx = info[0].boxL[0] / temp3;
488	>	celly = info[0].boxL[1] / temp3;
489	>	cellz = info[0].boxL[2] / temp3;
490	>	}
491	>
492	>	current_mol = 0;
493	>	current_comp_mol = 0;
494	>	current_comp = 0;
495	>	current_atom_ndx = 0;
496	>
497	>	for (i = 0; i < n_cells ; i++){
498	>	for (j = 0; j < n_cells; j++){
499	>	for (k = 0; k < n_cells; k++){
500	>	makeElement(i * cellx, j * celly, k * cellz);
501	>
502	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
503	>
504	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
505	>
506	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
507		}
577	–	else if( !strcmp( endTest, ".mdl" ) ){
578	–	strcpy( endTest, ".dump" );
579	–	}
580	–	else{
581	–	strcat( simnfo->sampleName, ".dump" );
582	–	}
508		}
509	<
510	<	strcpy( simnfo->statusName, inFileName );
511	<	nameLength = strlen( simnfo->statusName );
512	<	endTest = &(simnfo->statusName[nameLength - 5]);
513	<	if( !strcmp( endTest, ".bass" ) ){
514	<	strcpy( endTest, ".stat" );
515	<	}
516	<	else if( !strcmp( endTest, ".BASS" ) ){
517	<	strcpy( endTest, ".stat" );
518	<	}
519	<	else{
520	<	endTest = &(simnfo->statusName[nameLength - 4]);
521	<	if( !strcmp( endTest, ".bss" ) ){
522	<	strcpy( endTest, ".stat" );
509	>	}
510	>
511	>	if (have_extra){
512	>	done = 0;
513	>
514	>	int start_ndx;
515	>	for (i = 0; i < (n_cells + 1) && !done; i++){
516	>	for (j = 0; j < (n_cells + 1) && !done; j++){
517	>	if (i < n_cells){
518	>	if (j < n_cells){
519	>	start_ndx = n_cells;
520	>	}
521	>	else
522	>	start_ndx = 0;
523	>	}
524	>	else
525	>	start_ndx = 0;
526	>
527	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
528	>	makeElement(i * cellx, j * celly, k * cellz);
529	>	done = (current_mol >= tot_nmol);
530	>
531	>	if (!done && n_per_extra > 1){
532	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
533	>	k * cellz);
534	>	done = (current_mol >= tot_nmol);
535	>	}
536	>
537	>	if (!done && n_per_extra > 2){
538	>	makeElement(i * cellx, j * celly + 0.5 * celly,
539	>	k * cellz + 0.5 * cellz);
540	>	done = (current_mol >= tot_nmol);
541	>	}
542	>
543	>	if (!done && n_per_extra > 3){
544	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
545	>	k * cellz + 0.5 * cellz);
546	>	done = (current_mol >= tot_nmol);
547	>	}
548	>	}
549		}
599	–	else if( !strcmp( endTest, ".mdl" ) ){
600	–	strcpy( endTest, ".stat" );
601	–	}
602	–	else{
603	–	strcat( simnfo->statusName, ".stat" );
604	–	}
550		}
606	–
607	–	#ifdef IS_MPI
551		}
609	–	#endif // is_mpi
610	–
611	–	// set the status, sample, and themal kick times
612	–
613	–	if( the_globals->haveSampleTime() ){
614	–	simnfo->sampleTime = the_globals->getSampleTime();
615	–	simnfo->statusTime = simnfo->sampleTime;
616	–	simnfo->thermalTime = simnfo->sampleTime;
617	–	}
618	–	else{
619	–	simnfo->sampleTime = the_globals->getRunTime();
620	–	simnfo->statusTime = simnfo->sampleTime;
621	–	simnfo->thermalTime = simnfo->sampleTime;
622	–	}
552
553	<	if( the_globals->haveStatusTime() ){
554	<	simnfo->statusTime = the_globals->getStatusTime();
553	>	for (i = 0; i < info[0].n_atoms; i++){
554	>	info[0].atoms[i]->setVel(vel);
555		}
556	+	}
557
558	<	if( the_globals->haveThermalTime() ){
559	<	simnfo->thermalTime = the_globals->getThermalTime();
560	<	}
558	>	void SimSetup::makeElement(double x, double y, double z){
559	>	int k;
560	>	AtomStamp* current_atom;
561	>	DirectionalAtom* dAtom;
562	>	double rotMat[3][3];
563	>	double pos[3];
564
565	<	// check for the temperature set flag
565	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
566	>	current_atom = comp_stamps[current_comp]->getAtom(k);
567	>	if (!current_atom->havePosition()){
568	>	sprintf(painCave.errMsg,
569	>	"SimSetup:initFromBass error.\n"
570	>	"\tComponent %s, atom %s does not have a position specified.\n"
571	>	"\tThe initialization routine is unable to give a start"
572	>	" position.\n",
573	>	comp_stamps[current_comp]->getID(), current_atom->getType());
574	>	painCave.isFatal = 1;
575	>	simError();
576	>	}
577
578	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
578	>	pos[0] = x + current_atom->getPosX();
579	>	pos[1] = y + current_atom->getPosY();
580	>	pos[2] = z + current_atom->getPosZ();
581
582	+	info[0].atoms[current_atom_ndx]->setPos(pos);
583
584	<	//   // make the longe range forces and the integrator
584	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
585	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
586
587	<	//   new AllLong( simnfo );
587	>	rotMat[0][0] = 1.0;
588	>	rotMat[0][1] = 0.0;
589	>	rotMat[0][2] = 0.0;
590
591	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
592	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
593	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
644	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
591	>	rotMat[1][0] = 0.0;
592	>	rotMat[1][1] = 1.0;
593	>	rotMat[1][2] = 0.0;
594
595	+	rotMat[2][0] = 0.0;
596	+	rotMat[2][1] = 0.0;
597	+	rotMat[2][2] = 1.0;
598
599	+	dAtom->setA(rotMat);
600	+	}
601
602	<	// initialize the Fortran
649	<
650	<	simnfo->refreshSim();
651	<
652	<	if( !strcmp( simnfo->mixingRule, "standard") ){
653	<	the_ff->initForceField( LB_MIXING_RULE );
602	>	current_atom_ndx++;
603		}
655	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
656	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
657	–	}
658	–	else{
659	–	sprintf( painCave.errMsg,
660	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
661	–	simnfo->mixingRule );
662	–	painCave.isFatal = 1;
663	–	simError();
664	–	}
604
605	+	current_mol++;
606	+	current_comp_mol++;
607
608	<	#ifdef IS_MPI
609	<	strcpy( checkPointMsg,
610	<	"Successfully intialized the mixingRule for Fortran." );
611	<	MPIcheckPoint();
671	<	#endif // is_mpi
608	>	if (current_comp_mol >= components_nmol[current_comp]){
609	>	current_comp_mol = 0;
610	>	current_comp++;
611	>	}
612		}
613
614
615	<	void SimSetup::makeMolecules( void ){
615	>	void SimSetup::gatherInfo(void){
616	>	int i;
617
618	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
619	<	molInit info;
679	<	DirectionalAtom* dAtom;
680	<	LinkedAssign* extras;
681	<	LinkedAssign* current_extra;
682	<	AtomStamp* currentAtom;
683	<	BondStamp* currentBond;
684	<	BendStamp* currentBend;
685	<	TorsionStamp* currentTorsion;
686	<
687	<	//init the forceField paramters
618	>	ensembleCase = -1;
619	>	ffCase = -1;
620
621	<	the_ff->readParams();
621	>	// set the easy ones first
622
623	<
624	<	// init the molecules
623	>	for (i = 0; i < nInfo; i++){
624	>	info[i].target_temp = globals->getTargetTemp();
625	>	info[i].dt = globals->getDt();
626	>	info[i].run_time = globals->getRunTime();
627	>	}
628	>	n_components = globals->getNComponents();
629
694	–	atomOffset = 0;
695	–	excludeOffset = 0;
696	–	for(i=0; i<simnfo->n_mol; i++){
697	–
698	–	stampID = the_molecules[i].getStampID();
630
631	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
701	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
702	<	info.nBends    = comp_stamps[stampID]->getNBends();
703	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
704	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
631	>	// get the forceField
632
633	<	info.myAtoms = &the_atoms[atomOffset];
707	<	info.myExcludes = &the_excludes[excludeOffset];
708	<	info.myBonds = new Bond*[info.nBonds];
709	<	info.myBends = new Bend*[info.nBends];
710	<	info.myTorsions = new Torsions*[info.nTorsions];
633	>	strcpy(force_field, globals->getForceField());
634
635	<	theBonds = new bond_pair[info.nBonds];
636	<	theBends = new bend_set[info.nBends];
637	<	theTorsions = new torsion_set[info.nTorsions];
638	<
639	<	// make the Atoms
640	<
641	<	for(j=0; j<info.nAtoms; j++){
642	<
643	<	currentAtom = theComponents[stampID]->getAtom( j );
644	<	if( currentAtom->haveOrientation() ){
645	<
646	<	dAtom = new DirectionalAtom(j + atomOffset);
647	<	simnfo->n_oriented++;
648	<	info.myAtoms[j] = dAtom;
649	<
650	<	ux = currentAtom->getOrntX();
651	<	uy = currentAtom->getOrntY();
652	<	uz = currentAtom->getOrntZ();
730	<
731	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
732	<
733	<	u = sqrt( uSqr );
734	<	ux = ux / u;
735	<	uy = uy / u;
736	<	uz = uz / u;
737	<
738	<	dAtom->setSUx( ux );
739	<	dAtom->setSUy( uy );
740	<	dAtom->setSUz( uz );
741	<	}
742	<	else{
743	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
744	<	}
745	<	info.myAtoms[j]->setType( currentAtom->getType() );
746	<
747	<	#ifdef IS_MPI
748	<
749	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
750	<
751	<	#endif // is_mpi
752	<	}
753	<
754	<	// make the bonds
755	<	for(j=0; j<info.nBonds; j++){
756	<
757	<	currentBond = comp_stamps[stampID]->getBond( j );
758	<	theBonds[j].a = currentBond->getA() + atomOffset;
759	<	theBonds[j].b = currentBond->getB() + atomOffset;
635	>	if (!strcasecmp(force_field, "DUFF")){
636	>	ffCase = FF_DUFF;
637	>	}
638	>	else if (!strcasecmp(force_field, "LJ")){
639	>	ffCase = FF_LJ;
640	>	}
641	>	else if (!strcasecmp(force_field, "EAM")){
642	>	ffCase = FF_EAM;
643	>	}
644	>	else if (!strcasecmp(force_field, "WATER")){
645	>	ffCase = FF_H2O;
646	>	}
647	>	else{
648	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
649	>	force_field);
650	>	painCave.isFatal = 1;
651	>	simError();
652	>	}
653
654	<	exI = theBonds[i].a;
762	<	exJ = theBonds[i].b;
654	>	// get the ensemble
655
656	<	// exclude_I must always be the smaller of the pair
765	<	if( exI > exJ ){
766	<	tempEx = exI;
767	<	exI = exJ;
768	<	exJ = tempEx;
769	<	}
770	<	#ifdef IS_MPI
771	<	tempEx = exI;
772	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
773	<	tempEx = exJ;
774	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
775	<
776	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
777	<	#else  // isn't MPI
778	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
779	<	#endif  //is_mpi
780	<	}
781	<	excludeOffset += info.nBonds;
656	>	strcpy(ensemble, globals->getEnsemble());
657
658	<	//make the bends
659	<	for(j=0; j<info.nBends; j++){
660	<
661	<	currentBend = comp_stamps[stampID]->getBend( j );
662	<	theBends[j].a = currentBend->getA() + atomOffset;
663	<	theBends[j].b = currentBend->getB() + atomOffset;
664	<	theBends[j].c = currentBend->getC() + atomOffset;
665	<
666	<	if( currentBend->haveExtras() ){
667	<
668	<	extras = current_bend->getExtras();
669	<	current_extra = extras;
670	<
671	<	while( current_extra != NULL ){
672	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
673	<
674	<	switch( current_extra->getType() ){
675	<
676	<	case 0:
677	<	theBends[j].ghost =
678	<	current_extra->getInt() + atomOffset;
679	<	theBends[j].isGhost = 1;
680	<	break;
681	<
682	<	case 1:
808	<	theBends[j].ghost =
809	<	(int)current_extra->getDouble() + atomOffset;
810	<	theBends[j].isGhost = 1;
811	<	break;
812	<
813	<	default:
814	<	sprintf( painCave.errMsg,
815	<	"SimSetup Error: ghostVectorSource was neiter a "
816	<	"double nor an int.\n"
817	<	"-->Bend[%d] in %s\n",
818	<	j, comp_stamps[stampID]->getID() );
819	<	painCave.isFatal = 1;
820	<	simError();
821	<	}
822	<	}
823	<
824	<	else{
825	<
826	<	sprintf( painCave.errMsg,
827	<	"SimSetup Error: unhandled bend assignment:\n"
828	<	"    -->%s in Bend[%d] in %s\n",
829	<	current_extra->getlhs(),
830	<	j, comp_stamps[stampID]->getID() );
831	<	painCave.isFatal = 1;
832	<	simError();
833	<	}
834	<
835	<	current_extra = current_extra->getNext();
836	<	}
837	<	}
838	<
839	<	if( !theBends[j].isGhost ){
840	<
841	<	exI = theBends[j].a;
842	<	exJ = theBends[j].c;
843	<	}
844	<	else{
845	<
846	<	exI = theBends[j].a;
847	<	exJ = theBends[j].b;
848	<	}
849	<
850	<	// exclude_I must always be the smaller of the pair
851	<	if( exI > exJ ){
852	<	tempEx = exI;
853	<	exI = exJ;
854	<	exJ = tempEx;
855	<	}
856	<	#ifdef IS_MPI
857	<	tempEx = exI;
858	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
859	<	tempEx = exJ;
860	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
861	<
862	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
863	<	#else  // isn't MPI
864	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
865	<	#endif  //is_mpi
866	<	}
867	<	excludeOffset += info.nBends;
658	>	if (!strcasecmp(ensemble, "NVE")){
659	>	ensembleCase = NVE_ENS;
660	>	}
661	>	else if (!strcasecmp(ensemble, "NVT")){
662	>	ensembleCase = NVT_ENS;
663	>	}
664	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
665	>	ensembleCase = NPTi_ENS;
666	>	}
667	>	else if (!strcasecmp(ensemble, "NPTf")){
668	>	ensembleCase = NPTf_ENS;
669	>	}
670	>	else if (!strcasecmp(ensemble, "NPTxyz")){
671	>	ensembleCase = NPTxyz_ENS;
672	>	}
673	>	else{
674	>	sprintf(painCave.errMsg,
675	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
676	>	"\treverting to NVE for this simulation.\n",
677	>	ensemble);
678	>	painCave.isFatal = 0;
679	>	simError();
680	>	strcpy(ensemble, "NVE");
681	>	ensembleCase = NVE_ENS;
682	>	}
683
684	<	for(j=0; j<info.nTorsions; j++){
685	<
871	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
872	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
873	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
874	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
875	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
876	<
877	<	exI = theTorsions[j].a;
878	<	exJ = theTorsions[j].d;
684	>	for (i = 0; i < nInfo; i++){
685	>	strcpy(info[i].ensemble, ensemble);
686
687	<	// exclude_I must always be the smaller of the pair
881	<	if( exI > exJ ){
882	<	tempEx = exI;
883	<	exI = exJ;
884	<	exJ = tempEx;
885	<	}
886	<	#ifdef IS_MPI
887	<	tempEx = exI;
888	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
889	<	tempEx = exJ;
890	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
891	<
892	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
893	<	#else  // isn't MPI
894	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
895	<	#endif  //is_mpi
896	<	}
897	<	excludeOffset += info.nTorsions;
687	>	// get the mixing rule
688
689	<
689	>	strcpy(info[i].mixingRule, globals->getMixingRule());
690	>	info[i].usePBC = globals->getPBC();
691	>	}
692
693	+	// get the components and calculate the tot_nMol and indvidual n_mol
694
695	+	the_components = globals->getComponents();
696	+	components_nmol = new int[n_components];
697
698
699	+	if (!globals->haveNMol()){
700	+	// we don't have the total number of molecules, so we assume it is
701	+	// given in each component
702
703	+	tot_nmol = 0;
704	+	for (i = 0; i < n_components; i++){
705	+	if (!the_components[i]->haveNMol()){
706	+	// we have a problem
707	+	sprintf(painCave.errMsg,
708	+	"SimSetup Error. No global NMol or component NMol given.\n"
709	+	"\tCannot calculate the number of atoms.\n");
710	+	painCave.isFatal = 1;
711	+	simError();
712	+	}
713
714	<	void SimSetup::makeAtoms( void ){
714	>	tot_nmol += the_components[i]->getNMol();
715	>	components_nmol[i] = the_components[i]->getNMol();
716	>	}
717	>	}
718	>	else{
719	>	sprintf(painCave.errMsg,
720	>	"SimSetup error.\n"
721	>	"\tSorry, the ability to specify total"
722	>	" nMols and then give molfractions in the components\n"
723	>	"\tis not currently supported."
724	>	" Please give nMol in the components.\n");
725	>	painCave.isFatal = 1;
726	>	simError();
727	>	}
728
729	<	int i, j, k, index;
730	<	double ux, uy, uz, uSqr, u;
731	<	AtomStamp* current_atom;
729	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
730	>	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
731	>	sprintf(painCave.errMsg,
732	>	"Sample time is not divisible by dt.\n"
733	>	"\tThis will result in samples that are not uniformly\n"
734	>	"\tdistributed in time.  If this is a problem, change\n"
735	>	"\tyour sampleTime variable.\n");
736	>	painCave.isFatal = 0;
737	>	simError();
738	>	}
739
740	<	DirectionalAtom* dAtom;
741	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
740	>	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
741	>	sprintf(painCave.errMsg,
742	>	"Status time is not divisible by dt.\n"
743	>	"\tThis will result in status reports that are not uniformly\n"
744	>	"\tdistributed in time.  If this is a problem, change \n"
745	>	"\tyour statusTime variable.\n");
746	>	painCave.isFatal = 0;
747	>	simError();
748	>	}
749
750	<	lMolIndex = 0;
751	<	molIndex = 0;
752	<	index = 0;
753	<	for( i=0; i<n_components; i++ ){
750	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
751	>	sprintf(painCave.errMsg,
752	>	"Thermal time is not divisible by dt.\n"
753	>	"\tThis will result in thermalizations that are not uniformly\n"
754	>	"\tdistributed in time.  If this is a problem, change \n"
755	>	"\tyour thermalTime variable.\n");
756	>	painCave.isFatal = 0;
757	>	simError();
758	>	}
759
760	<	for( j=0; j<components_nmol[i]; j++ ){
760	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
761	>	sprintf(painCave.errMsg,
762	>	"Reset time is not divisible by dt.\n"
763	>	"\tThis will result in integrator resets that are not uniformly\n"
764	>	"\tdistributed in time.  If this is a problem, change\n"
765	>	"\tyour resetTime variable.\n");
766	>	painCave.isFatal = 0;
767	>	simError();
768	>	}
769
770	<	#ifdef IS_MPI
923	<	if( mpiSim->getMyMolStart() <= molIndex &&
924	<	molIndex <= mpiSim->getMyMolEnd() ){
925	<	#endif // is_mpi
770	>	// set the status, sample, and thermal kick times
771
772	<	molStart = index;
773	<	nMemb = comp_stamps[i]->getNAtoms();
774	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
775	<
776	<	current_atom = comp_stamps[i]->getAtom( k );
777	<	if( current_atom->haveOrientation() ){
778	<
779	<	dAtom = new DirectionalAtom(index);
780	<	simnfo->n_oriented++;
781	<	the_atoms[index] = dAtom;
782	<
938	<	ux = current_atom->getOrntX();
939	<	uy = current_atom->getOrntY();
940	<	uz = current_atom->getOrntZ();
941	<
942	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
943	<
944	<	u = sqrt( uSqr );
945	<	ux = ux / u;
946	<	uy = uy / u;
947	<	uz = uz / u;
948	<
949	<	dAtom->setSUx( ux );
950	<	dAtom->setSUy( uy );
951	<	dAtom->setSUz( uz );
952	<	}
953	<	else{
954	<	the_atoms[index] = new GeneralAtom(index);
955	<	}
956	<	the_atoms[index]->setType( current_atom->getType() );
957	<	the_atoms[index]->setIndex( index );
958	<
959	<	// increment the index and repeat;
960	<	index++;
961	<	}
962	<
963	<	molEnd = index -1;
964	<	the_molecules[lMolIndex].setNMembers( nMemb );
965	<	the_molecules[lMolIndex].setStartAtom( molStart );
966	<	the_molecules[lMolIndex].setEndAtom( molEnd );
967	<	the_molecules[lMolIndex].setStampID( i );
968	<	lMolIndex++;
772	>	for (i = 0; i < nInfo; i++){
773	>	if (globals->haveSampleTime()){
774	>	info[i].sampleTime = globals->getSampleTime();
775	>	info[i].statusTime = info[i].sampleTime;
776	>	info[i].thermalTime = info[i].sampleTime;
777	>	}
778	>	else{
779	>	info[i].sampleTime = globals->getRunTime();
780	>	info[i].statusTime = info[i].sampleTime;
781	>	info[i].thermalTime = info[i].sampleTime;
782	>	}
783
784	<	#ifdef IS_MPI
785	<	}
972	<	#endif //is_mpi
973	<
974	<	molIndex++;
784	>	if (globals->haveStatusTime()){
785	>	info[i].statusTime = globals->getStatusTime();
786		}
976	–	}
787
788	<	#ifdef IS_MPI
789	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
790	<
981	<	delete[] globalIndex;
788	>	if (globals->haveThermalTime()){
789	>	info[i].thermalTime = globals->getThermalTime();
790	>	}
791
792	<	mpiSim->mpiRefresh();
793	<	#endif //IS_MPI
794	<
795	<	the_ff->initializeAtoms();
796	<	}
792	>	info[i].resetIntegrator = 0;
793	>	if( globals->haveResetTime() ){
794	>	info[i].resetTime = globals->getResetTime();
795	>	info[i].resetIntegrator = 1;
796	>	}
797
798	<	void SimSetup::makeBonds( void ){
798	>	// check for the temperature set flag
799	>
800	>	if (globals->haveTempSet())
801	>	info[i].setTemp = globals->getTempSet();
802
803	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
992	<	bond_pair* the_bonds;
993	<	BondStamp* current_bond;
803	>	// check for the extended State init
804
805	<	the_bonds = new bond_pair[tot_bonds];
806	<	index = 0;
807	<	offset = 0;
808	<	molIndex = 0;
805	>	info[i].useInitXSstate = globals->getUseInitXSstate();
806	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
807	>
808	>	}
809	>
810	>	//setup seed for random number generator
811	>	int seedValue;
812
813	<	for( i=0; i<n_components; i++ ){
813	>	if (globals->haveSeed()){
814	>	seedValue = globals->getSeed();
815
816	<	for( j=0; j<components_nmol[i]; j++ ){
816	>	if(seedValue / 1E9 == 0){
817	>	sprintf(painCave.errMsg,
818	>	"Seed for sprng library should contain at least 9 digits\n"
819	>	"OOPSE will generate a seed for user\n");
820	>	painCave.isFatal = 0;
821	>	simError();
822
823	<	#ifdef IS_MPI
824	<	if( mpiSim->getMyMolStart() <= molIndex &&
825	<	molIndex <= mpiSim->getMyMolEnd() ){
826	<	#endif // is_mpi
827	<
828	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
829	<
830	<	current_bond = comp_stamps[i]->getBond( k );
831	<	the_bonds[index].a = current_bond->getA() + offset;
832	<	the_bonds[index].b = current_bond->getB() + offset;
833	<
834	<	exI = the_bonds[index].a;
835	<	exJ = the_bonds[index].b;
823	>	//using seed generated by system instead of invalid seed set by user
824	>	#ifndef IS_MPI
825	>	seedValue = make_sprng_seed();
826	>	#else
827	>	if (worldRank == 0){
828	>	seedValue = make_sprng_seed();
829	>	}
830	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
831	>	#endif
832	>	}
833	>	}//end of if branch of globals->haveSeed()
834	>	else{
835	>
836	>	#ifndef IS_MPI
837	>	seedValue = make_sprng_seed();
838	>	#else
839	>	if (worldRank == 0){
840	>	seedValue = make_sprng_seed();
841	>	}
842	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
843	>	#endif
844	>	}//end of globals->haveSeed()
845
846	<	// exclude_I must always be the smaller of the pair
847	<	if( exI > exJ ){
848	<	tempEx = exI;
849	<	exI = exJ;
1022	<	exJ = tempEx;
1023	<	}
1024	<
1025	<
846	>	for (int i = 0; i < nInfo; i++){
847	>	info[i].setSeed(seedValue);
848	>	}
849	>
850		#ifdef IS_MPI
851	+	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
852	+	MPIcheckPoint();
853	+	#endif // is_mpi
854	+	}
855
1028	–	the_excludes[index*2] =
1029	–	the_atoms[exI]->getGlobalIndex() + 1;
1030	–	the_excludes[index*2 + 1] =
1031	–	the_atoms[exJ]->getGlobalIndex() + 1;
856
857	<	#else  // isn't MPI
858	<
859	<	the_excludes[index*2] =     exI + 1;
860	<	the_excludes[index*2 + 1] = exJ + 1;
861	<	// fortran index from 1 (hence the +1 in the indexing)
862	<	#endif  //is_mpi
863	<
864	<	// increment the index and repeat;
865	<	index++;
866	<	}
867	<	offset += comp_stamps[i]->getNAtoms();
868	<
857	>	void SimSetup::finalInfoCheck(void){
858	>	int index;
859	>	int usesDipoles;
860	>	int i;
861	>
862	>	for (i = 0; i < nInfo; i++){
863	>	// check electrostatic parameters
864	>
865	>	index = 0;
866	>	usesDipoles = 0;
867	>	while ((index < info[i].n_atoms) && !usesDipoles){
868	>	usesDipoles = (info[i].atoms[index])->hasDipole();
869	>	index++;
870	>	}
871	>
872		#ifdef IS_MPI
873	<	}
873	>	int myUse = usesDipoles;
874	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
875		#endif //is_mpi
1048	–
1049	–	molIndex++;
1050	–	}
1051	–	}
876
877	<	the_ff->initializeBonds( the_bonds );
1054	<	}
877	>	double theEcr, theEst;
878
879	<	void SimSetup::makeBends( void ){
879	>	if (globals->getUseRF()){
880	>	info[i].useReactionField = 1;
881
882	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
883	<	bend_set* the_bends;
884	<	BendStamp* current_bend;
885	<	LinkedAssign* extras;
886	<	LinkedAssign* current_extra;
887	<
882	>	if (!globals->haveECR()){
883	>	sprintf(painCave.errMsg,
884	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
885	>	"\tOOPSE will use a default value of 15.0 angstroms"
886	>	"\tfor the electrostaticCutoffRadius.\n");
887	>	painCave.isFatal = 0;
888	>	simError();
889	>	theEcr = 15.0;
890	>	}
891	>	else{
892	>	theEcr = globals->getECR();
893	>	}
894
895	<	the_bends = new bend_set[tot_bends];
896	<	index = 0;
897	<	offset = 0;
898	<	molIndex = 0;
899	<	for( i=0; i<n_components; i++ ){
895	>	if (!globals->haveEST()){
896	>	sprintf(painCave.errMsg,
897	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
898	>	"\tOOPSE will use a default value of\n"
899	>	"\t0.05 * electrostaticCutoffRadius\n"
900	>	"\tfor the electrostaticSkinThickness\n");
901	>	painCave.isFatal = 0;
902	>	simError();
903	>	theEst = 0.05 * theEcr;
904	>	}
905	>	else{
906	>	theEst = globals->getEST();
907	>	}
908
909	<	for( j=0; j<components_nmol[i]; j++ ){
909	>	info[i].setDefaultEcr(theEcr, theEst);
910
911	+	if (!globals->haveDielectric()){
912	+	sprintf(painCave.errMsg,
913	+	"SimSetup Error: No Dielectric constant was set.\n"
914	+	"\tYou are trying to use Reaction Field without"
915	+	"\tsetting a dielectric constant!\n");
916	+	painCave.isFatal = 1;
917	+	simError();
918	+	}
919	+	info[i].dielectric = globals->getDielectric();
920	+	}
921	+	else{
922	+	if (usesDipoles){
923	+	if (!globals->haveECR()){
924	+	sprintf(painCave.errMsg,
925	+	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
926	+	"\tOOPSE will use a default value of 15.0 angstroms"
927	+	"\tfor the electrostaticCutoffRadius.\n");
928	+	painCave.isFatal = 0;
929	+	simError();
930	+	theEcr = 15.0;
931	+	}
932	+	else{
933	+	theEcr = globals->getECR();
934	+	}
935	+
936	+	if (!globals->haveEST()){
937	+	sprintf(painCave.errMsg,
938	+	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
939	+	"\tOOPSE will use a default value of\n"
940	+	"\t0.05 * electrostaticCutoffRadius\n"
941	+	"\tfor the electrostaticSkinThickness\n");
942	+	painCave.isFatal = 0;
943	+	simError();
944	+	theEst = 0.05 * theEcr;
945	+	}
946	+	else{
947	+	theEst = globals->getEST();
948	+	}
949	+
950	+	info[i].setDefaultEcr(theEcr, theEst);
951	+	}
952	+	}
953	+	}
954		#ifdef IS_MPI
955	<	if( mpiSim->getMyMolStart() <= molIndex &&
956	<	molIndex <= mpiSim->getMyMolEnd() ){
957	<	#endif // is_mpi
955	>	strcpy(checkPointMsg, "post processing checks out");
956	>	MPIcheckPoint();
957	>	#endif // is_mpi
958	>	}
959	>
960	>	void SimSetup::initSystemCoords(void){
961	>	int i;
962
963	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
1079	<
1080	<	current_bend = comp_stamps[i]->getBend( k );
1081	<	the_bends[index].a = current_bend->getA() + offset;
1082	<	the_bends[index].b = current_bend->getB() + offset;
1083	<	the_bends[index].c = current_bend->getC() + offset;
1084	<
1085	<	if( current_bend->haveExtras() ){
1086	<
1087	<	extras = current_bend->getExtras();
1088	<	current_extra = extras;
1089	<
1090	<	while( current_extra != NULL ){
1091	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1092	<
1093	<	switch( current_extra->getType() ){
1094	<
1095	<	case 0:
1096	<	the_bends[index].ghost =
1097	<	current_extra->getInt() + offset;
1098	<	the_bends[index].isGhost = 1;
1099	<	break;
1100	<
1101	<	case 1:
1102	<	the_bends[index].ghost =
1103	<	(int)current_extra->getDouble() + offset;
1104	<	the_bends[index].isGhost = 1;
1105	<	break;
1106	<
1107	<	default:
1108	<	sprintf( painCave.errMsg,
1109	<	"SimSetup Error: ghostVectorSource was neiter a "
1110	<	"double nor an int.\n"
1111	<	"-->Bend[%d] in %s\n",
1112	<	k, comp_stamps[i]->getID() );
1113	<	painCave.isFatal = 1;
1114	<	simError();
1115	<	}
1116	<	}
1117	<
1118	<	else{
1119	<
1120	<	sprintf( painCave.errMsg,
1121	<	"SimSetup Error: unhandled bend assignment:\n"
1122	<	"    -->%s in Bend[%d] in %s\n",
1123	<	current_extra->getlhs(),
1124	<	k, comp_stamps[i]->getID() );
1125	<	painCave.isFatal = 1;
1126	<	simError();
1127	<	}
1128	<
1129	<	current_extra = current_extra->getNext();
1130	<	}
1131	<	}
1132	<
1133	<	if( !the_bends[index].isGhost ){
1134	<
1135	<	exI = the_bends[index].a;
1136	<	exJ = the_bends[index].c;
1137	<	}
1138	<	else{
1139	<
1140	<	exI = the_bends[index].a;
1141	<	exJ = the_bends[index].b;
1142	<	}
1143	<
1144	<	// exclude_I must always be the smaller of the pair
1145	<	if( exI > exJ ){
1146	<	tempEx = exI;
1147	<	exI = exJ;
1148	<	exJ = tempEx;
1149	<	}
963	>	char* inName;
964
965	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
966
967	<	#ifdef IS_MPI
967	>	for (i = 0; i < info[0].n_atoms; i++)
968	>	info[0].atoms[i]->setCoords();
969
970	<	the_excludes[(index + tot_bonds)*2] =
971	<	the_atoms[exI]->getGlobalIndex() + 1;
972	<	the_excludes[(index + tot_bonds)*2 + 1] =
973	<	the_atoms[exJ]->getGlobalIndex() + 1;
1158	<
1159	<	#else  // isn't MPI
1160	<
1161	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
1162	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1163	<	// fortran index from 1 (hence the +1 in the indexing)
1164	<	#endif  //is_mpi
1165	<
1166	<
1167	<	// increment the index and repeat;
1168	<	index++;
1169	<	}
1170	<	offset += comp_stamps[i]->getNAtoms();
1171	<
1172	<	#ifdef IS_MPI
1173	<	}
970	>	if (globals->haveInitialConfig()){
971	>	InitializeFromFile* fileInit;
972	>	#ifdef IS_MPI // is_mpi
973	>	if (worldRank == 0){
974		#endif //is_mpi
975	<
976	<	molIndex++;
975	>	inName = globals->getInitialConfig();
976	>	fileInit = new InitializeFromFile(inName);
977	>	#ifdef IS_MPI
978		}
979	+	else
980	+	fileInit = new InitializeFromFile(NULL);
981	+	#endif
982	+	fileInit->readInit(info); // default velocities on
983	+
984	+	delete fileInit;
985		}
986	+	else{
987	+
988	+	// no init from bass
989	+
990	+	sprintf(painCave.errMsg,
991	+	"Cannot intialize a simulation without an initial configuration file.\n");
992	+	painCave.isFatal = 1;;
993	+	simError();
994	+
995	+	}
996
997		#ifdef IS_MPI
998	<	sprintf( checkPointMsg,
1182	<	"Successfully created the bends list.\n" );
998	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
999		MPIcheckPoint();
1000		#endif // is_mpi
1185	–
1186	–
1187	–	the_ff->initializeBends( the_bends );
1001		}
1002
1190	–	void SimSetup::makeTorsions( void ){
1003
1004	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1005	<	torsion_set* the_torsions;
1194	<	TorsionStamp* current_torsion;
1004	>	void SimSetup::makeOutNames(void){
1005	>	int k;
1006
1196	–	the_torsions = new torsion_set[tot_torsions];
1197	–	index = 0;
1198	–	offset = 0;
1199	–	molIndex = 0;
1200	–	for( i=0; i<n_components; i++ ){
1007
1008	<	for( j=0; j<components_nmol[i]; j++ ){
1008	>	for (k = 0; k < nInfo; k++){
1009	>	#ifdef IS_MPI
1010	>	if (worldRank == 0){
1011	>	#endif // is_mpi
1012
1013	+	if (globals->haveFinalConfig()){
1014	+	strcpy(info[k].finalName, globals->getFinalConfig());
1015	+	}
1016	+	else{
1017	+	strcpy(info[k].finalName, inFileName);
1018	+	char* endTest;
1019	+	int nameLength = strlen(info[k].finalName);
1020	+	endTest = &(info[k].finalName[nameLength - 5]);
1021	+	if (!strcmp(endTest, ".bass")){
1022	+	strcpy(endTest, ".eor");
1023	+	}
1024	+	else if (!strcmp(endTest, ".BASS")){
1025	+	strcpy(endTest, ".eor");
1026	+	}
1027	+	else{
1028	+	endTest = &(info[k].finalName[nameLength - 4]);
1029	+	if (!strcmp(endTest, ".bss")){
1030	+	strcpy(endTest, ".eor");
1031	+	}
1032	+	else if (!strcmp(endTest, ".mdl")){
1033	+	strcpy(endTest, ".eor");
1034	+	}
1035	+	else{
1036	+	strcat(info[k].finalName, ".eor");
1037	+	}
1038	+	}
1039	+	}
1040	+
1041	+	// make the sample and status out names
1042	+
1043	+	strcpy(info[k].sampleName, inFileName);
1044	+	char* endTest;
1045	+	int nameLength = strlen(info[k].sampleName);
1046	+	endTest = &(info[k].sampleName[nameLength - 5]);
1047	+	if (!strcmp(endTest, ".bass")){
1048	+	strcpy(endTest, ".dump");
1049	+	}
1050	+	else if (!strcmp(endTest, ".BASS")){
1051	+	strcpy(endTest, ".dump");
1052	+	}
1053	+	else{
1054	+	endTest = &(info[k].sampleName[nameLength - 4]);
1055	+	if (!strcmp(endTest, ".bss")){
1056	+	strcpy(endTest, ".dump");
1057	+	}
1058	+	else if (!strcmp(endTest, ".mdl")){
1059	+	strcpy(endTest, ".dump");
1060	+	}
1061	+	else{
1062	+	strcat(info[k].sampleName, ".dump");
1063	+	}
1064	+	}
1065	+
1066	+	strcpy(info[k].statusName, inFileName);
1067	+	nameLength = strlen(info[k].statusName);
1068	+	endTest = &(info[k].statusName[nameLength - 5]);
1069	+	if (!strcmp(endTest, ".bass")){
1070	+	strcpy(endTest, ".stat");
1071	+	}
1072	+	else if (!strcmp(endTest, ".BASS")){
1073	+	strcpy(endTest, ".stat");
1074	+	}
1075	+	else{
1076	+	endTest = &(info[k].statusName[nameLength - 4]);
1077	+	if (!strcmp(endTest, ".bss")){
1078	+	strcpy(endTest, ".stat");
1079	+	}
1080	+	else if (!strcmp(endTest, ".mdl")){
1081	+	strcpy(endTest, ".stat");
1082	+	}
1083	+	else{
1084	+	strcat(info[k].statusName, ".stat");
1085	+	}
1086	+	}
1087	+
1088		#ifdef IS_MPI
1205	–	if( mpiSim->getMyMolStart() <= molIndex &&
1206	–	molIndex <= mpiSim->getMyMolEnd() ){
1207	–	#endif // is_mpi
1089
1090	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1090	>	}
1091	>	#endif // is_mpi
1092	>	}
1093	>	}
1094
1211	–	current_torsion = comp_stamps[i]->getTorsion( k );
1212	–	the_torsions[index].a = current_torsion->getA() + offset;
1213	–	the_torsions[index].b = current_torsion->getB() + offset;
1214	–	the_torsions[index].c = current_torsion->getC() + offset;
1215	–	the_torsions[index].d = current_torsion->getD() + offset;
1095
1096	<	exI = the_torsions[index].a;
1097	<	exJ = the_torsions[index].d;
1096	>	void SimSetup::sysObjectsCreation(void){
1097	>	int i, k;
1098
1099	<
1100	<	// exclude_I must always be the smaller of the pair
1101	<	if( exI > exJ ){
1102	<	tempEx = exI;
1103	<	exI = exJ;
1104	<	exJ = tempEx;
1105	<	}
1099	>	// create the forceField
1100	>
1101	>	createFF();
1102	>
1103	>	// extract componentList
1104	>
1105	>	compList();
1106
1107	+	// calc the number of atoms, bond, bends, and torsions
1108
1109	+	calcSysValues();
1110	+
1111		#ifdef IS_MPI
1112	<
1231	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
1232	<	the_atoms[exI]->getGlobalIndex() + 1;
1233	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1234	<	the_atoms[exJ]->getGlobalIndex() + 1;
1235	<
1236	<	#else  // isn't MPI
1237	<
1238	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1239	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1240	<	// fortran indexes from 1 (hence the +1 in the indexing)
1241	<	#endif  //is_mpi
1242	<
1112	>	// divide the molecules among the processors
1113
1114	<	// increment the index and repeat;
1115	<	index++;
1246	<	}
1247	<	offset += comp_stamps[i]->getNAtoms();
1114	>	mpiMolDivide();
1115	>	#endif //is_mpi
1116
1117	<	#ifdef IS_MPI
1250	<	}
1251	<	#endif //is_mpi
1117	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1118
1119	<	molIndex++;
1119	>	makeSysArrays();
1120	>
1121	>	// make and initialize the molecules (all but atomic coordinates)
1122	>
1123	>	makeMolecules();
1124	>
1125	>	for (k = 0; k < nInfo; k++){
1126	>	info[k].identArray = new int[info[k].n_atoms];
1127	>	for (i = 0; i < info[k].n_atoms; i++){
1128	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1129		}
1130		}
1256	–
1257	–	the_ff->initializeTorsions( the_torsions );
1131		}
1132
1260	–	void SimSetup::initFromBass( void ){
1133
1134	<	int i, j, k;
1135	<	int n_cells;
1136	<	double cellx, celly, cellz;
1137	<	double temp1, temp2, temp3;
1138	<	int n_per_extra;
1267	<	int n_extra;
1268	<	int have_extra, done;
1134	>	void SimSetup::createFF(void){
1135	>	switch (ffCase){
1136	>	case FF_DUFF:
1137	>	the_ff = new DUFF();
1138	>	break;
1139
1140	<	temp1 = (double)tot_nmol / 4.0;
1141	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1142	<	temp3 = ceil( temp2 );
1140	>	case FF_LJ:
1141	>	the_ff = new LJFF();
1142	>	break;
1143
1144	<	have_extra =0;
1145	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1146	<	have_extra =1;
1144	>	case FF_EAM:
1145	>	the_ff = new EAM_FF();
1146	>	break;
1147
1148	<	n_cells = (int)temp3 - 1;
1149	<	cellx = simnfo->box_x / temp3;
1150	<	celly = simnfo->box_y / temp3;
1281	<	cellz = simnfo->box_z / temp3;
1282	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1283	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1284	<	n_per_extra = (int)ceil( temp1 );
1148	>	case FF_H2O:
1149	>	the_ff = new WATER();
1150	>	break;
1151
1152	<	if( n_per_extra > 4){
1153	<	sprintf( painCave.errMsg,
1154	<	"SimSetup error. There has been an error in constructing"
1289	<	" the non-complete lattice.\n" );
1152	>	default:
1153	>	sprintf(painCave.errMsg,
1154	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1155		painCave.isFatal = 1;
1156		simError();
1292	–	}
1157		}
1294	–	else{
1295	–	n_cells = (int)temp3;
1296	–	cellx = simnfo->box_x / temp3;
1297	–	celly = simnfo->box_y / temp3;
1298	–	cellz = simnfo->box_z / temp3;
1299	–	}
1158
1159	<	current_mol = 0;
1160	<	current_comp_mol = 0;
1161	<	current_comp = 0;
1162	<	current_atom_ndx = 0;
1159	>	#ifdef IS_MPI
1160	>	strcpy(checkPointMsg, "ForceField creation successful");
1161	>	MPIcheckPoint();
1162	>	#endif // is_mpi
1163	>	}
1164
1306	–	for( i=0; i < n_cells ; i++ ){
1307	–	for( j=0; j < n_cells; j++ ){
1308	–	for( k=0; k < n_cells; k++ ){
1165
1166	<	makeElement( i * cellx,
1167	<	j * celly,
1168	<	k * cellz );
1166	>	void SimSetup::compList(void){
1167	>	int i;
1168	>	char* id;
1169	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1170	>	LinkedMolStamp* currentStamp = NULL;
1171	>	comp_stamps = new MoleculeStamp * [n_components];
1172
1173	<	makeElement( i * cellx + 0.5 * cellx,
1174	<	j * celly + 0.5 * celly,
1316	<	k * cellz );
1173	>	// make an array of molecule stamps that match the components used.
1174	>	// also extract the used stamps out into a separate linked list
1175
1176	<	makeElement( i * cellx,
1177	<	j * celly + 0.5 * celly,
1178	<	k * cellz + 0.5 * cellz );
1176	>	for (i = 0; i < nInfo; i++){
1177	>	info[i].nComponents = n_components;
1178	>	info[i].componentsNmol = components_nmol;
1179	>	info[i].compStamps = comp_stamps;
1180	>	info[i].headStamp = headStamp;
1181	>	}
1182
1183	<	makeElement( i * cellx + 0.5 * cellx,
1184	<	j * celly,
1185	<	k * cellz + 0.5 * cellz );
1183	>
1184	>	for (i = 0; i < n_components; i++){
1185	>	id = the_components[i]->getType();
1186	>	comp_stamps[i] = NULL;
1187	>
1188	>	// check to make sure the component isn't already in the list
1189	>
1190	>	comp_stamps[i] = headStamp->match(id);
1191	>	if (comp_stamps[i] == NULL){
1192	>	// extract the component from the list;
1193	>
1194	>	currentStamp = stamps->extractMolStamp(id);
1195	>	if (currentStamp == NULL){
1196	>	sprintf(painCave.errMsg,
1197	>	"SimSetup error: Component \"%s\" was not found in the "
1198	>	"list of declared molecules\n",
1199	>	id);
1200	>	painCave.isFatal = 1;
1201	>	simError();
1202		}
1203	+
1204	+	headStamp->add(currentStamp);
1205	+	comp_stamps[i] = headStamp->match(id);
1206		}
1207		}
1208
1209	<	if( have_extra ){
1210	<	done = 0;
1209	>	#ifdef IS_MPI
1210	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1211	>	MPIcheckPoint();
1212	>	#endif // is_mpi
1213	>	}
1214
1215	<	int start_ndx;
1216	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1334	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1215	>	void SimSetup::calcSysValues(void){
1216	>	int i;
1217
1218	<	if( i < n_cells ){
1218	>	int* molMembershipArray;
1219
1220	<	if( j < n_cells ){
1221	<	start_ndx = n_cells;
1222	<	}
1223	<	else start_ndx = 0;
1224	<	}
1225	<	else start_ndx = 0;
1220	>	tot_atoms = 0;
1221	>	tot_bonds = 0;
1222	>	tot_bends = 0;
1223	>	tot_torsions = 0;
1224	>	for (i = 0; i < n_components; i++){
1225	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1226	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1227	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1228	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1229	>	}
1230
1231	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1231	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1232	>	molMembershipArray = new int[tot_atoms];
1233
1234	<	makeElement( i * cellx,
1235	<	j * celly,
1236	<	k * cellz );
1237	<	done = ( current_mol >= tot_nmol );
1234	>	for (i = 0; i < nInfo; i++){
1235	>	info[i].n_atoms = tot_atoms;
1236	>	info[i].n_bonds = tot_bonds;
1237	>	info[i].n_bends = tot_bends;
1238	>	info[i].n_torsions = tot_torsions;
1239	>	info[i].n_SRI = tot_SRI;
1240	>	info[i].n_mol = tot_nmol;
1241
1242	<	if( !done && n_per_extra > 1 ){
1243	<	makeElement( i * cellx + 0.5 * cellx,
1244	<	j * celly + 0.5 * celly,
1355	<	k * cellz );
1356	<	done = ( current_mol >= tot_nmol );
1357	<	}
1242	>	info[i].molMembershipArray = molMembershipArray;
1243	>	}
1244	>	}
1245
1246	<	if( !done && n_per_extra > 2){
1360	<	makeElement( i * cellx,
1361	<	j * celly + 0.5 * celly,
1362	<	k * cellz + 0.5 * cellz );
1363	<	done = ( current_mol >= tot_nmol );
1364	<	}
1246	>	#ifdef IS_MPI
1247
1248	<	if( !done && n_per_extra > 3){
1249	<	makeElement( i * cellx + 0.5 * cellx,
1250	<	j * celly,
1251	<	k * cellz + 0.5 * cellz );
1252	<	done = ( current_mol >= tot_nmol );
1253	<	}
1254	<	}
1248	>	void SimSetup::mpiMolDivide(void){
1249	>	int i, j, k;
1250	>	int localMol, allMol;
1251	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1252	>
1253	>	mpiSim = new mpiSimulation(info);
1254	>
1255	>	globalIndex = mpiSim->divideLabor();
1256	>
1257	>	// set up the local variables
1258	>
1259	>	mol2proc = mpiSim->getMolToProcMap();
1260	>	molCompType = mpiSim->getMolComponentType();
1261	>
1262	>	allMol = 0;
1263	>	localMol = 0;
1264	>	local_atoms = 0;
1265	>	local_bonds = 0;
1266	>	local_bends = 0;
1267	>	local_torsions = 0;
1268	>	globalAtomIndex = 0;
1269	>
1270	>
1271	>	for (i = 0; i < n_components; i++){
1272	>	for (j = 0; j < components_nmol[i]; j++){
1273	>	if (mol2proc[allMol] == worldRank){
1274	>	local_atoms += comp_stamps[i]->getNAtoms();
1275	>	local_bonds += comp_stamps[i]->getNBonds();
1276	>	local_bends += comp_stamps[i]->getNBends();
1277	>	local_torsions += comp_stamps[i]->getNTorsions();
1278	>	localMol++;
1279	>	}
1280	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1281	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1282	>	globalAtomIndex++;
1283		}
1284	+
1285	+	allMol++;
1286		}
1287		}
1288	+	local_SRI = local_bonds + local_bends + local_torsions;
1289
1290	+	info[0].n_atoms = mpiSim->getMyNlocal();
1291
1292	<	for( i=0; i<simnfo->n_atoms; i++ ){
1293	<	simnfo->atoms[i]->set_vx( 0.0 );
1294	<	simnfo->atoms[i]->set_vy( 0.0 );
1295	<	simnfo->atoms[i]->set_vz( 0.0 );
1292	>	if (local_atoms != info[0].n_atoms){
1293	>	sprintf(painCave.errMsg,
1294	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1295	>	"\tlocalAtom (%d) are not equal.\n",
1296	>	info[0].n_atoms, local_atoms);
1297	>	painCave.isFatal = 1;
1298	>	simError();
1299		}
1300	+
1301	+	info[0].n_bonds = local_bonds;
1302	+	info[0].n_bends = local_bends;
1303	+	info[0].n_torsions = local_torsions;
1304	+	info[0].n_SRI = local_SRI;
1305	+	info[0].n_mol = localMol;
1306	+
1307	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1308	+	MPIcheckPoint();
1309		}
1310
1311	<	void SimSetup::makeElement( double x, double y, double z ){
1311	>	#endif // is_mpi
1312
1387	–	int k;
1388	–	AtomStamp* current_atom;
1389	–	DirectionalAtom* dAtom;
1390	–	double rotMat[3][3];
1313
1314	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1314	>	void SimSetup::makeSysArrays(void){
1315	>
1316	>	#ifndef IS_MPI
1317	>	int k, j;
1318	>	#endif // is_mpi
1319	>	int i, l;
1320
1321	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1322	<	if( !current_atom->havePosition() ){
1323	<	sprintf( painCave.errMsg,
1397	<	"SimSetup:initFromBass error.\n"
1398	<	"\tComponent %s, atom %s does not have a position specified.\n"
1399	<	"\tThe initialization routine is unable to give a start"
1400	<	" position.\n",
1401	<	comp_stamps[current_comp]->getID(),
1402	<	current_atom->getType() );
1403	<	painCave.isFatal = 1;
1404	<	simError();
1405	<	}
1321	>	Atom** the_atoms;
1322	>	Molecule* the_molecules;
1323	>	Exclude** the_excludes;
1324
1407	–	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1408	–	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1409	–	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1325
1326	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1326	>	for (l = 0; l < nInfo; l++){
1327	>	// create the atom and short range interaction arrays
1328
1329	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1329	>	the_atoms = new Atom * [info[l].n_atoms];
1330	>	the_molecules = new Molecule[info[l].n_mol];
1331	>	int molIndex;
1332
1333	<	rotMat[0][0] = 1.0;
1416	<	rotMat[0][1] = 0.0;
1417	<	rotMat[0][2] = 0.0;
1333	>	// initialize the molecule's stampID's
1334
1335	<	rotMat[1][0] = 0.0;
1420	<	rotMat[1][1] = 1.0;
1421	<	rotMat[1][2] = 0.0;
1335	>	#ifdef IS_MPI
1336
1423	–	rotMat[2][0] = 0.0;
1424	–	rotMat[2][1] = 0.0;
1425	–	rotMat[2][2] = 1.0;
1337
1338	<	dAtom->setA( rotMat );
1338	>	molIndex = 0;
1339	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1340	>	if (mol2proc[i] == worldRank){
1341	>	the_molecules[molIndex].setStampID(molCompType[i]);
1342	>	the_molecules[molIndex].setMyIndex(molIndex);
1343	>	the_molecules[molIndex].setGlobalIndex(i);
1344	>	molIndex++;
1345	>	}
1346		}
1347
1348	<	current_atom_ndx++;
1431	<	}
1348	>	#else // is_mpi
1349
1350	<	current_mol++;
1351	<	current_comp_mol++;
1350	>	molIndex = 0;
1351	>	globalAtomIndex = 0;
1352	>	for (i = 0; i < n_components; i++){
1353	>	for (j = 0; j < components_nmol[i]; j++){
1354	>	the_molecules[molIndex].setStampID(i);
1355	>	the_molecules[molIndex].setMyIndex(molIndex);
1356	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1357	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1358	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1359	>	globalAtomIndex++;
1360	>	}
1361	>	molIndex++;
1362	>	}
1363	>	}
1364
1436	–	if( current_comp_mol >= components_nmol[current_comp] ){
1365
1366	<	current_comp_mol = 0;
1367	<	current_comp++;
1366	>	#endif // is_mpi
1367	>
1368	>
1369	>	if (info[l].n_SRI){
1370	>	Exclude::createArray(info[l].n_SRI);
1371	>	the_excludes = new Exclude * [info[l].n_SRI];
1372	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1373	>	the_excludes[ex] = new Exclude(ex);
1374	>	}
1375	>	info[l].globalExcludes = new int;
1376	>	info[l].n_exclude = info[l].n_SRI;
1377	>	}
1378	>	else{
1379	>	Exclude::createArray(1);
1380	>	the_excludes = new Exclude * ;
1381	>	the_excludes[0] = new Exclude(0);
1382	>	the_excludes[0]->setPair(0, 0);
1383	>	info[l].globalExcludes = new int;
1384	>	info[l].globalExcludes[0] = 0;
1385	>	info[l].n_exclude = 0;
1386	>	}
1387	>
1388	>	// set the arrays into the SimInfo object
1389	>
1390	>	info[l].atoms = the_atoms;
1391	>	info[l].molecules = the_molecules;
1392	>	info[l].nGlobalExcludes = 0;
1393	>	info[l].excludes = the_excludes;
1394	>
1395	>	the_ff->setSimInfo(info);
1396		}
1397		}
1398	+
1399	+	void SimSetup::makeIntegrator(void){
1400	+	int k;
1401	+
1402	+	NVE<RealIntegrator>* myNVE = NULL;
1403	+	NVT<RealIntegrator>* myNVT = NULL;
1404	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1405	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1406	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1407	+
1408	+	for (k = 0; k < nInfo; k++){
1409	+	switch (ensembleCase){
1410	+	case NVE_ENS:
1411	+	if (globals->haveZconstraints()){
1412	+	setupZConstraint(info[k]);
1413	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1414	+	}
1415	+	else{
1416	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1417	+	}
1418	+
1419	+	info->the_integrator = myNVE;
1420	+	break;
1421	+
1422	+	case NVT_ENS:
1423	+	if (globals->haveZconstraints()){
1424	+	setupZConstraint(info[k]);
1425	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1426	+	}
1427	+	else
1428	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1429	+
1430	+	myNVT->setTargetTemp(globals->getTargetTemp());
1431	+
1432	+	if (globals->haveTauThermostat())
1433	+	myNVT->setTauThermostat(globals->getTauThermostat());
1434	+	else{
1435	+	sprintf(painCave.errMsg,
1436	+	"SimSetup error: If you use the NVT\n"
1437	+	"\tensemble, you must set tauThermostat.\n");
1438	+	painCave.isFatal = 1;
1439	+	simError();
1440	+	}
1441	+
1442	+	info->the_integrator = myNVT;
1443	+	break;
1444	+
1445	+	case NPTi_ENS:
1446	+	if (globals->haveZconstraints()){
1447	+	setupZConstraint(info[k]);
1448	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1449	+	}
1450	+	else
1451	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1452	+
1453	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1454	+
1455	+	if (globals->haveTargetPressure())
1456	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1457	+	else{
1458	+	sprintf(painCave.errMsg,
1459	+	"SimSetup error: If you use a constant pressure\n"
1460	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1461	+	painCave.isFatal = 1;
1462	+	simError();
1463	+	}
1464	+
1465	+	if (globals->haveTauThermostat())
1466	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1467	+	else{
1468	+	sprintf(painCave.errMsg,
1469	+	"SimSetup error: If you use an NPT\n"
1470	+	"\tensemble, you must set tauThermostat.\n");
1471	+	painCave.isFatal = 1;
1472	+	simError();
1473	+	}
1474	+
1475	+	if (globals->haveTauBarostat())
1476	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1477	+	else{
1478	+	sprintf(painCave.errMsg,
1479	+	"SimSetup error: If you use an NPT\n"
1480	+	"\tensemble, you must set tauBarostat.\n");
1481	+	painCave.isFatal = 1;
1482	+	simError();
1483	+	}
1484	+
1485	+	info->the_integrator = myNPTi;
1486	+	break;
1487	+
1488	+	case NPTf_ENS:
1489	+	if (globals->haveZconstraints()){
1490	+	setupZConstraint(info[k]);
1491	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1492	+	}
1493	+	else
1494	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1495	+
1496	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1497	+
1498	+	if (globals->haveTargetPressure())
1499	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1500	+	else{
1501	+	sprintf(painCave.errMsg,
1502	+	"SimSetup error: If you use a constant pressure\n"
1503	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1504	+	painCave.isFatal = 1;
1505	+	simError();
1506	+	}
1507	+
1508	+	if (globals->haveTauThermostat())
1509	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1510	+
1511	+	else{
1512	+	sprintf(painCave.errMsg,
1513	+	"SimSetup error: If you use an NPT\n"
1514	+	"\tensemble, you must set tauThermostat.\n");
1515	+	painCave.isFatal = 1;
1516	+	simError();
1517	+	}
1518	+
1519	+	if (globals->haveTauBarostat())
1520	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1521	+
1522	+	else{
1523	+	sprintf(painCave.errMsg,
1524	+	"SimSetup error: If you use an NPT\n"
1525	+	"\tensemble, you must set tauBarostat.\n");
1526	+	painCave.isFatal = 1;
1527	+	simError();
1528	+	}
1529	+
1530	+	info->the_integrator = myNPTf;
1531	+	break;
1532	+
1533	+	case NPTxyz_ENS:
1534	+	if (globals->haveZconstraints()){
1535	+	setupZConstraint(info[k]);
1536	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1537	+	}
1538	+	else
1539	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1540	+
1541	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1542	+
1543	+	if (globals->haveTargetPressure())
1544	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1545	+	else{
1546	+	sprintf(painCave.errMsg,
1547	+	"SimSetup error: If you use a constant pressure\n"
1548	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1549	+	painCave.isFatal = 1;
1550	+	simError();
1551	+	}
1552	+
1553	+	if (globals->haveTauThermostat())
1554	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1555	+	else{
1556	+	sprintf(painCave.errMsg,
1557	+	"SimSetup error: If you use an NPT\n"
1558	+	"\tensemble, you must set tauThermostat.\n");
1559	+	painCave.isFatal = 1;
1560	+	simError();
1561	+	}
1562	+
1563	+	if (globals->haveTauBarostat())
1564	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1565	+	else{
1566	+	sprintf(painCave.errMsg,
1567	+	"SimSetup error: If you use an NPT\n"
1568	+	"\tensemble, you must set tauBarostat.\n");
1569	+	painCave.isFatal = 1;
1570	+	simError();
1571	+	}
1572	+
1573	+	info->the_integrator = myNPTxyz;
1574	+	break;
1575	+
1576	+	default:
1577	+	sprintf(painCave.errMsg,
1578	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1579	+	painCave.isFatal = 1;
1580	+	simError();
1581	+	}
1582	+	}
1583	+	}
1584	+
1585	+	void SimSetup::initFortran(void){
1586	+	info[0].refreshSim();
1587	+
1588	+	if (!strcmp(info[0].mixingRule, "standard")){
1589	+	the_ff->initForceField(LB_MIXING_RULE);
1590	+	}
1591	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1592	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1593	+	}
1594	+	else{
1595	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1596	+	info[0].mixingRule);
1597	+	painCave.isFatal = 1;
1598	+	simError();
1599	+	}
1600	+
1601	+
1602	+	#ifdef IS_MPI
1603	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1604	+	MPIcheckPoint();
1605	+	#endif // is_mpi
1606	+	}
1607	+
1608	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1609	+	int nZConstraints;
1610	+	ZconStamp** zconStamp;
1611	+
1612	+	if (globals->haveZconstraintTime()){
1613	+	//add sample time of z-constraint  into SimInfo's property list
1614	+	DoubleData* zconsTimeProp = new DoubleData();
1615	+	zconsTimeProp->setID(ZCONSTIME_ID);
1616	+	zconsTimeProp->setData(globals->getZconsTime());
1617	+	theInfo.addProperty(zconsTimeProp);
1618	+	}
1619	+	else{
1620	+	sprintf(painCave.errMsg,
1621	+	"ZConstraint error: If you use a ZConstraint,\n"
1622	+	"\tyou must set zconsTime.\n");
1623	+	painCave.isFatal = 1;
1624	+	simError();
1625	+	}
1626	+
1627	+	//push zconsTol into siminfo, if user does not specify
1628	+	//value for zconsTol, a default value will be used
1629	+	DoubleData* zconsTol = new DoubleData();
1630	+	zconsTol->setID(ZCONSTOL_ID);
1631	+	if (globals->haveZconsTol()){
1632	+	zconsTol->setData(globals->getZconsTol());
1633	+	}
1634	+	else{
1635	+	double defaultZConsTol = 0.01;
1636	+	sprintf(painCave.errMsg,
1637	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1638	+	"\tOOPSE will use a default value of %f.\n"
1639	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1640	+	defaultZConsTol);
1641	+	painCave.isFatal = 0;
1642	+	simError();
1643	+
1644	+	zconsTol->setData(defaultZConsTol);
1645	+	}
1646	+	theInfo.addProperty(zconsTol);
1647	+
1648	+	//set Force Subtraction Policy
1649	+	StringData* zconsForcePolicy = new StringData();
1650	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1651	+
1652	+	if (globals->haveZconsForcePolicy()){
1653	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1654	+	}
1655	+	else{
1656	+	sprintf(painCave.errMsg,
1657	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1658	+	"\tOOPSE will use PolicyByMass.\n"
1659	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1660	+	painCave.isFatal = 0;
1661	+	simError();
1662	+	zconsForcePolicy->setData("BYMASS");
1663	+	}
1664	+
1665	+	theInfo.addProperty(zconsForcePolicy);
1666	+
1667	+	//set zcons gap
1668	+	DoubleData* zconsGap = new DoubleData();
1669	+	zconsGap->setID(ZCONSGAP_ID);
1670	+
1671	+	if (globals->haveZConsGap()){
1672	+	zconsGap->setData(globals->getZconsGap());
1673	+	theInfo.addProperty(zconsGap);
1674	+	}
1675	+
1676	+	//set zcons fixtime
1677	+	DoubleData* zconsFixtime = new DoubleData();
1678	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1679	+
1680	+	if (globals->haveZConsFixTime()){
1681	+	zconsFixtime->setData(globals->getZconsFixtime());
1682	+	theInfo.addProperty(zconsFixtime);
1683	+	}
1684	+
1685	+
1686	+	//Determine the name of ouput file and add it into SimInfo's property list
1687	+	//Be careful, do not use inFileName, since it is a pointer which
1688	+	//point to a string at master node, and slave nodes do not contain that string
1689	+
1690	+	string zconsOutput(theInfo.finalName);
1691	+
1692	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1693	+
1694	+	StringData* zconsFilename = new StringData();
1695	+	zconsFilename->setID(ZCONSFILENAME_ID);
1696	+	zconsFilename->setData(zconsOutput);
1697	+
1698	+	theInfo.addProperty(zconsFilename);
1699	+
1700	+	//setup index, pos and other parameters of z-constraint molecules
1701	+	nZConstraints = globals->getNzConstraints();
1702	+	theInfo.nZconstraints = nZConstraints;
1703	+
1704	+	zconStamp = globals->getZconStamp();
1705	+	ZConsParaItem tempParaItem;
1706	+
1707	+	ZConsParaData* zconsParaData = new ZConsParaData();
1708	+	zconsParaData->setID(ZCONSPARADATA_ID);
1709	+
1710	+	for (int i = 0; i < nZConstraints; i++){
1711	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1712	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1713	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1714	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1715	+
1716	+	zconsParaData->addItem(tempParaItem);
1717	+	}
1718	+
1719	+	//check the uniqueness of index
1720	+	if(!zconsParaData->isIndexUnique()){
1721	+	sprintf(painCave.errMsg,
1722	+	"ZConstraint Error: molIndex is not unique!\n");
1723	+	painCave.isFatal = 1;
1724	+	simError();
1725	+	}
1726	+
1727	+	//sort the parameters by index of molecules
1728	+	zconsParaData->sortByIndex();
1729	+
1730	+	//push data into siminfo, therefore, we can retrieve later
1731	+	theInfo.addProperty(zconsParaData);
1732	+	}
1733	+
1734	+	void SimSetup::makeMinimizer(){
1735	+
1736	+	OOPSEMinimizer* myOOPSEMinimizer;
1737	+	MinimizerParameterSet* param;
1738	+	char minimizerName[100];
1739	+
1740	+	for (int i = 0; i < nInfo; i++){
1741	+
1742	+	//prepare parameter set for minimizer
1743	+	param = new MinimizerParameterSet();
1744	+	param->setDefaultParameter();
1745	+
1746	+	if (globals->haveMinimizer()){
1747	+	param->setFTol(globals->getMinFTol());
1748	+	}
1749	+
1750	+	if (globals->haveMinGTol()){
1751	+	param->setGTol(globals->getMinGTol());
1752	+	}
1753	+
1754	+	if (globals->haveMinMaxIter()){
1755	+	param->setMaxIteration(globals->getMinMaxIter());
1756	+	}
1757	+
1758	+	if (globals->haveMinWriteFrq()){
1759	+	param->setMaxIteration(globals->getMinMaxIter());
1760	+	}
1761	+
1762	+	if (globals->haveMinWriteFrq()){
1763	+	param->setWriteFrq(globals->getMinWriteFrq());
1764	+	}
1765	+
1766	+	if (globals->haveMinStepSize()){
1767	+	param->setStepSize(globals->getMinStepSize());
1768	+	}
1769	+
1770	+	if (globals->haveMinLSMaxIter()){
1771	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1772	+	}
1773	+
1774	+	if (globals->haveMinLSTol()){
1775	+	param->setLineSearchTol(globals->getMinLSTol());
1776	+	}
1777	+
1778	+	strcpy(minimizerName, globals->getMinimizer());
1779	+
1780	+	if (!strcasecmp(minimizerName, "CG")){
1781	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1782	+	}
1783	+	else if (!strcasecmp(minimizerName, "SD")){
1784	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1785	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1786	+	}
1787	+	else{
1788	+	sprintf(painCave.errMsg,
1789	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1790	+	painCave.isFatal = 0;
1791	+	simError();
1792	+
1793	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1794	+	}
1795	+	info[i].the_integrator = myOOPSEMinimizer;
1796	+
1797	+	//store the minimizer into simInfo
1798	+	info[i].the_minimizer = myOOPSEMinimizer;
1799	+	info[i].has_minimizer = true;
1800	+	}
1801	+
1802	+	}

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