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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 414 by mmeineke, Wed Mar 26 22:02:36 2003 UTC vs.
Revision 1104 by gezelter, Tue Apr 13 16:26:03 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" ) ) 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	<	}
138	>	// initialize the system coordinates
139
140	<	#ifdef IS_MPI
141	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#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
111	<	the_components = the_globals->getComponents();
112	<	components_nmol = new int[n_components];
113	<	comp_stamps = new MoleculeStamp*[n_components];
147	>	// make the output filenames
148
149	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
149	>	makeOutNames();
150
151	<	tot_nmol = 0;
152	<	for( i=0; i<n_components; i++ ){
151	>	if (globals->haveMinimizer())
152	>	// make minimizer
153	>	makeMinimizer();
154	>	else
155	>	// make the integrator
156	>	makeIntegrator();
157	>
158	>	#ifdef IS_MPI
159	>	mpiSim->mpiRefresh();
160	>	#endif
161
162	<	if( !the_components[i]->haveNMol() ){
123	<	// we have a problem
124	<	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	<	}
162	>	// initialize the Fortran
163
164	<	tot_nmol += the_components[i]->getNMol();
165	<	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	<	}
164	>	initFortran();
165	>	}
166
160	–	#ifdef IS_MPI
161	–	strcpy( checkPointMsg, "Have the number of components" );
162	–	MPIcheckPoint();
163	–	#endif // is_mpi
167
168	<	// make an array of molecule stamps that match the components used.
169	<	// also extract the used stamps out into a separate linked list
168	>	void SimSetup::makeMolecules(void){
169	>	int i, j, k;
170	>	int exI, exJ, exK, exL, slI, slJ;
171	>	int tempI, tempJ, tempK, tempL;
172	>	int molI;
173	>	int stampID, atomOffset, rbOffset;
174	>	molInit molInfo;
175	>	DirectionalAtom* dAtom;
176	>	RigidBody* myRB;
177	>	StuntDouble* mySD;
178	>	LinkedAssign* extras;
179	>	LinkedAssign* current_extra;
180	>	AtomStamp* currentAtom;
181	>	BondStamp* currentBond;
182	>	BendStamp* currentBend;
183	>	TorsionStamp* currentTorsion;
184	>	RigidBodyStamp* currentRigidBody;
185
186	<	simnfo->nComponents = n_components;
187	<	simnfo->componentsNmol = components_nmol;
188	<	simnfo->compStamps = comp_stamps;
171	<	simnfo->headStamp = new LinkedMolStamp();
172	<
173	<	char* id;
174	<	LinkedMolStamp* headStamp = simnfo->headStamp;
175	<	LinkedMolStamp* currentStamp = NULL;
176	<	for( i=0; i<n_components; i++ ){
186	>	bond_pair* theBonds;
187	>	bend_set* theBends;
188	>	torsion_set* theTorsions;
189
190	<	id = the_components[i]->getType();
179	<	comp_stamps[i] = NULL;
180	<
181	<	// check to make sure the component isn't already in the list
190	>	set<int> skipList;
191
192	<	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	<	}
192	>	double phi, theta, psi;
193
194	<	#ifdef IS_MPI
204	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
205	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
194	>	//init the forceField paramters
195
196	+	the_ff->readParams();
197
198	+	// init the atoms
199
200	<	// caclulate the number of atoms, bonds, bends and torsions
200	>	int nMembers, nNew, rb1, rb2;
201
202	<	tot_atoms = 0;
203	<	tot_bonds = 0;
215	<	tot_bends = 0;
216	<	tot_torsions = 0;
217	<	for( i=0; i<n_components; i++ ){
218	<
219	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
220	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
221	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
222	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
223	<	}
202	>	for (k = 0; k < nInfo; k++){
203	>	the_ff->setSimInfo(&(info[k]));
204
205	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
205	>	atomOffset = 0;
206
207	<	simnfo->n_atoms = tot_atoms;
208	<	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;
207	>	for (i = 0; i < info[k].n_mol; i++){
208	>	stampID = info[k].molecules[i].getStampID();
209
210	<
211	<	#ifdef IS_MPI
210	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
211	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
212	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
213	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
214	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
215	>
216	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
217
218	<	// divide the molecules among processors here.
219	<
220	<	mpiSim = new mpiSimulation( simnfo );
221	<
241	<
218	>	if (molInfo.nBonds > 0)
219	>	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
220	>	else
221	>	molInfo.myBonds = NULL;
222
223	<	globalIndex = mpiSim->divideLabor();
223	>	if (molInfo.nBends > 0)
224	>	molInfo.myBends = new (Bend *) [molInfo.nBends];
225	>	else
226	>	molInfo.myBends = NULL;
227
228	+	if (molInfo.nTorsions > 0)
229	+	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
230	+	else
231	+	molInfo.myTorsions = NULL;
232
233	<
234	<	// set up the local variables
235	<
249	<	int localMol, allMol;
250	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
251	<
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++ ){
259	<
260	<	for( j=0; j<components_nmol[i]; j++ ){
233	>	theBonds = new bond_pair[molInfo.nBonds];
234	>	theBends = new bend_set[molInfo.nBends];
235	>	theTorsions = new torsion_set[molInfo.nTorsions];
236
237	<	if( mpiSim->getMyMolStart() <= allMol &&
263	<	allMol <= mpiSim->getMyMolEnd() ){
264	<
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	<
237	>	// make the Atoms
238
239	<	simnfo->n_atoms = mpiSim->getMyNlocal();
240	<
279	<	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	<	}
239	>	for (j = 0; j < molInfo.nAtoms; j++){
240	>	currentAtom = comp_stamps[stampID]->getAtom(j);
241
242	<	simnfo->n_bonds = local_bonds;
243	<	simnfo->n_bends = local_bends;
244	<	simnfo->n_torsions = local_torsions;
245	<	simnfo->n_SRI = local_SRI;
246	<	simnfo->n_mol = localMol;
242	>	if (currentAtom->haveOrientation()){
243	>	dAtom = new DirectionalAtom((j + atomOffset),
244	>	info[k].getConfiguration());
245	>	info[k].n_oriented++;
246	>	molInfo.myAtoms[j] = dAtom;
247
248	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
249	<	MPIcheckPoint();
250	<
298	<
299	<	#endif // is_mpi
300	<
248	>	// Directional Atoms have standard unit vectors which are oriented
249	>	// in space using the three Euler angles.  We assume the standard
250	>	// unit vector was originally along the z axis below.
251
252	<	// create the atom and short range interaction arrays
252	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
253	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
254	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
255
256	<	Atom::createArrays(simnfo->n_atoms);
257	<	the_atoms = new Atom*[simnfo->n_atoms];
258	<	the_molecules = new Molecule[simnfo->n_mol];
256	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
257	>
258	>	}
259	>	else{
260
261	+	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
262	+	}
263
264	<	if( simnfo->n_SRI ){
310	<	Exclude::createArray(simnfo->n_SRI);
311	<	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	<	}
264	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
265
266	<	// set the arrays into the SimInfo object
266	>	#ifdef IS_MPI
267
268	<	simnfo->atoms = the_atoms;
329	<	simnfo->sr_interactions = the_sris;
330	<	simnfo->nGlobalExcludes = 0;
331	<	simnfo->excludes = the_excludes;
268	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
269
270	+	#endif // is_mpi
271	+	}
272
273	<	// get some of the tricky things that may still be in the globals
273	>	// make the bonds
274	>	for (j = 0; j < molInfo.nBonds; j++){
275	>	currentBond = comp_stamps[stampID]->getBond(j);
276	>	theBonds[j].a = currentBond->getA() + atomOffset;
277	>	theBonds[j].b = currentBond->getB() + atomOffset;
278
279	<
280	<	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() ){
279	>	tempI = theBonds[j].a;
280	>	tempJ = theBonds[j].b;
281
344	–	double vol;
345	–	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();
358	–
359	–	if( !the_globals->haveBoxY() ){
360	–	sprintf( painCave.errMsg,
361	–	"SimSetup error, no periodic BoxY size given.\n" );
362	–	painCave.isFatal = 1;
363	–	simError();
364	–	}
365	–	simnfo->box_y = the_globals->getBoxY();
366	–
367	–	if( !the_globals->haveBoxZ() ){
368	–	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	–	}
375	–
282		#ifdef IS_MPI
283	<	strcpy( checkPointMsg, "Box size set up" );
284	<	MPIcheckPoint();
285	<	#endif // is_mpi
283	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
284	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
285	>	#else
286	>	exI = tempI + 1;
287	>	exJ = tempJ + 1;
288	>	#endif
289
290	+	info[k].excludes->addPair(exI, exJ);
291	+	}
292
293	<	// initialize the arrays
293	>	//make the bends
294	>	for (j = 0; j < molInfo.nBends; j++){
295	>	currentBend = comp_stamps[stampID]->getBend(j);
296	>	theBends[j].a = currentBend->getA() + atomOffset;
297	>	theBends[j].b = currentBend->getB() + atomOffset;
298	>	theBends[j].c = currentBend->getC() + atomOffset;
299
300	<	the_ff->setSimInfo( simnfo );
300	>	if (currentBend->haveExtras()){
301	>	extras = currentBend->getExtras();
302	>	current_extra = extras;
303
304	<	makeAtoms();
305	<	simnfo->identArray = new int[simnfo->n_atoms];
306	<	for(i=0; i<simnfo->n_atoms; i++){
307	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
308	<	}
309	<
310	<	if( tot_bonds ){
393	<	makeBonds();
394	<	}
304	>	while (current_extra != NULL){
305	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
306	>	switch (current_extra->getType()){
307	>	case 0:
308	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
309	>	theBends[j].isGhost = 1;
310	>	break;
311
312	<	if( tot_bends ){
313	<	makeBends();
314	<	}
312	>	case 1:
313	>	theBends[j].ghost = (int) current_extra->getDouble() +
314	>	atomOffset;
315	>	theBends[j].isGhost = 1;
316	>	break;
317
318	<	if( tot_torsions ){
319	<	makeTorsions();
320	<	}
318	>	default:
319	>	sprintf(painCave.errMsg,
320	>	"SimSetup Error: ghostVectorSource was neither a "
321	>	"double nor an int.\n"
322	>	"-->Bend[%d] in %s\n",
323	>	j, comp_stamps[stampID]->getID());
324	>	painCave.isFatal = 1;
325	>	simError();
326	>	}
327	>	}
328	>	else{
329	>	sprintf(painCave.errMsg,
330	>	"SimSetup Error: unhandled bend assignment:\n"
331	>	"    -->%s in Bend[%d] in %s\n",
332	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
333	>	painCave.isFatal = 1;
334	>	simError();
335	>	}
336
337	+	current_extra = current_extra->getNext();
338	+	}
339	+	}
340
341	<	if (the_globals->getUseRF() ) {
342	<	simnfo->useReactionField = 1;
343	<
344	<	if( !the_globals->haveECR() ){
345	<	sprintf( painCave.errMsg,
346	<	"SimSetup Warning: using default value of 1/2 the smallest "
347	<	"box length for the electrostaticCutoffRadius.\n"
348	<	"I hope you have a very fast processor!\n");
349	<	painCave.isFatal = 0;
350	<	simError();
351	<	double smallest;
352	<	smallest = simnfo->box_x;
353	<	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	<	}
341	>	if (theBends[j].isGhost) {
342	>
343	>	tempI = theBends[j].a;
344	>	tempJ = theBends[j].b;
345	>
346	>	#ifdef IS_MPI
347	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
348	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
349	>	#else
350	>	exI = tempI + 1;
351	>	exJ = tempJ + 1;
352	>	#endif
353	>	info[k].excludes->addPair(exI, exJ);
354
355	<	if( !the_globals->haveEST() ){
425	<	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	<	}
355	>	} else {
356
357	+	tempI = theBends[j].a;
358	+	tempJ = theBends[j].b;
359	+	tempK = theBends[j].c;
360	+
361		#ifdef IS_MPI
362	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
363	<	MPIcheckPoint();
364	<	#endif // is_mpi
362	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
363	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
364	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
365	>	#else
366	>	exI = tempI + 1;
367	>	exJ = tempJ + 1;
368	>	exK = tempK + 1;
369	>	#endif
370	>
371	>	info[k].excludes->addPair(exI, exK);
372	>	info[k].excludes->addPair(exI, exJ);
373	>	info[k].excludes->addPair(exJ, exK);
374	>	}
375	>	}
376
377	<	if( the_globals->haveInitialConfig() ){
378	<
379	<	InitializeFromFile* fileInit;
380	<	#ifdef IS_MPI // is_mpi
381	<	if( worldRank == 0 ){
382	<	#endif //is_mpi
383	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
377	>	for (j = 0; j < molInfo.nTorsions; j++){
378	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
379	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
380	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
381	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
382	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
383	>
384	>	tempI = theTorsions[j].a;
385	>	tempJ = theTorsions[j].b;
386	>	tempK = theTorsions[j].c;
387	>	tempL = theTorsions[j].d;
388	>
389		#ifdef IS_MPI
390	<	}else fileInit = new InitializeFromFile( NULL );
390	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
391	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
392	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
393	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
394	>	#else
395	>	exI = tempI + 1;
396	>	exJ = tempJ + 1;
397	>	exK = tempK + 1;
398	>	exL = tempL + 1;
399		#endif
494	–	fileInit->read_xyz( simnfo ); // default velocities on
400
401	<	delete fileInit;
402	<	}
403	<	else{
401	>	info[k].excludes->addPair(exI, exJ);
402	>	info[k].excludes->addPair(exI, exK);
403	>	info[k].excludes->addPair(exI, exL);
404	>	info[k].excludes->addPair(exJ, exK);
405	>	info[k].excludes->addPair(exJ, exL);
406	>	info[k].excludes->addPair(exK, exL);
407	>	}
408
409	<	#ifdef IS_MPI
409	>	for (j = 0; j < molInfo.nRigidBodies; j++){
410
411	<	// no init from bass
412	<
504	<	sprintf( painCave.errMsg,
505	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
506	<	painCave.isFatal;
507	<	simError();
508	<
509	<	#else
411	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
412	>	nMembers = currentRigidBody->getNMembers();
413
414	<	initFromBass();
414	>	// Create the Rigid Body:
415
416	+	myRB = new RigidBody();
417	+
418	+	for (rb1 = 0; rb1 < nMembers; rb1++) {
419
420	+	// molI is atom numbering inside this molecule
421	+	molI = currentRigidBody->getMember(rb1);
422	+
423	+	// tempI is atom numbering on local processor
424	+	tempI = molI + atomOffset;
425	+
426	+	// currentAtom is the AtomStamp (which we need for
427	+	// rigid body reference positions)
428	+	currentAtom = comp_stamps[stampID]->getAtom(molI);
429	+
430	+	// When we add to the rigid body, add the atom itself and
431	+	// the stamp info:
432	+
433	+	myRB->addAtom(info[k].atoms[tempI], currentAtom);
434	+
435	+	// Add this atom to the Skip List for the integrators
436	+	#ifdef IS_MPI
437	+	slI = info[k].atoms[tempI]->getGlobalIndex();
438	+	#else
439	+	slI = tempI;
440		#endif
441	<	}
441	>	skipList.insert(slI);
442	>
443	>	}
444	>
445	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
446	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
447	>
448	>	tempI = currentRigidBody->getMember(rb1);
449	>	tempJ = currentRigidBody->getMember(rb2);
450	>
451	>	// Some explanation is required here.
452	>	// Fortran indexing starts at 1, while c indexing starts at 0
453	>	// Also, in parallel computations, the GlobalIndex is
454	>	// used for the exclude list:
455	>
456	>	#ifdef IS_MPI
457	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
458	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
459	>	#else
460	>	exI = tempI + 1;
461	>	exJ = tempJ + 1;
462	>	#endif
463	>
464	>	info[k].excludes->addPair(exI, exJ);
465	>
466	>	}
467	>	}
468
469	+	molInfo.myRigidBodies.push_back(myRB);
470	+	info[k].rigidBodies.push_back(myRB);
471	+	}
472	+
473	+
474	+	// After this is all set up, scan through the atoms to
475	+	// see if they can be added to the integrableObjects:
476	+
477	+	for (j = 0; j < molInfo.nAtoms; j++){
478	+
479		#ifdef IS_MPI
480	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
481	<	MPIcheckPoint();
482	<	#endif // is_mpi
480	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
481	>	#else
482	>	slJ = j+atomOffset;
483	>	#endif
484
485	+	// if they aren't on the skip list, then they can be integrated
486
487	<
488	<
489	<
487	>	if (skipList.find(slJ) == skipList.end()) {
488	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
489	>	info[k].integrableObjects.push_back(mySD);
490	>	molInfo.myIntegrableObjects.push_back(mySD);
491	>	}
492	>	}
493
494	<
494	>	// all rigid bodies are integrated:
495	>
496	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
497	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
498	>	info[k].integrableObjects.push_back(mySD);
499	>	molInfo.myIntegrableObjects.push_back(mySD);
500	>	}
501	>
502	>
503	>	// send the arrays off to the forceField for init.
504	>
505	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
506	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
507	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
508	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
509	>	theTorsions);
510	>
511	>	info[k].molecules[i].initialize(molInfo);
512	>
513	>
514	>	atomOffset += molInfo.nAtoms;
515	>	delete[] theBonds;
516	>	delete[] theBends;
517	>	delete[] theTorsions;
518	>	}
519	>	}
520	>
521		#ifdef IS_MPI
522	<	if( worldRank == 0 ){
522	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
523	>	MPIcheckPoint();
524		#endif // is_mpi
531	–
532	–	if( the_globals->haveFinalConfig() ){
533	–	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
534	–	}
535	–	else{
536	–	strcpy( simnfo->finalName, inFileName );
537	–	char* endTest;
538	–	int nameLength = strlen( simnfo->finalName );
539	–	endTest = &(simnfo->finalName[nameLength - 5]);
540	–	if( !strcmp( endTest, ".bass" ) ){
541	–	strcpy( endTest, ".eor" );
542	–	}
543	–	else if( !strcmp( endTest, ".BASS" ) ){
544	–	strcpy( endTest, ".eor" );
545	–	}
546	–	else{
547	–	endTest = &(simnfo->finalName[nameLength - 4]);
548	–	if( !strcmp( endTest, ".bss" ) ){
549	–	strcpy( endTest, ".eor" );
550	–	}
551	–	else if( !strcmp( endTest, ".mdl" ) ){
552	–	strcpy( endTest, ".eor" );
553	–	}
554	–	else{
555	–	strcat( simnfo->finalName, ".eor" );
556	–	}
557	–	}
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" );
576	–	}
577	–	else if( !strcmp( endTest, ".mdl" ) ){
578	–	strcpy( endTest, ".dump" );
579	–	}
580	–	else{
581	–	strcat( simnfo->sampleName, ".dump" );
582	–	}
583	–	}
584	–
585	–	strcpy( simnfo->statusName, inFileName );
586	–	nameLength = strlen( simnfo->statusName );
587	–	endTest = &(simnfo->statusName[nameLength - 5]);
588	–	if( !strcmp( endTest, ".bass" ) ){
589	–	strcpy( endTest, ".stat" );
590	–	}
591	–	else if( !strcmp( endTest, ".BASS" ) ){
592	–	strcpy( endTest, ".stat" );
593	–	}
594	–	else{
595	–	endTest = &(simnfo->statusName[nameLength - 4]);
596	–	if( !strcmp( endTest, ".bss" ) ){
597	–	strcpy( endTest, ".stat" );
598	–	}
599	–	else if( !strcmp( endTest, ".mdl" ) ){
600	–	strcpy( endTest, ".stat" );
601	–	}
602	–	else{
603	–	strcat( simnfo->statusName, ".stat" );
604	–	}
605	–	}
606	–
607	–	#ifdef IS_MPI
608	–	}
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	–	}
525
526	<	if( the_globals->haveStatusTime() ){
625	<	simnfo->statusTime = the_globals->getStatusTime();
626	<	}
526	>	// clean up the forcefield
527
528	<	if( the_globals->haveThermalTime() ){
629	<	simnfo->thermalTime = the_globals->getThermalTime();
630	<	}
528	>	if (!globals->haveLJrcut()){
529
530	<	// check for the temperature set flag
530	>	the_ff->calcRcut();
531
532	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
532	>	} else {
533	>
534	>	the_ff->setRcut( globals->getLJrcut() );
535	>	}
536
537	+	the_ff->cleanMe();
538	+	}
539
540	<	//   // make the longe range forces and the integrator
540	>	void SimSetup::initFromBass(void){
541	>	int i, j, k;
542	>	int n_cells;
543	>	double cellx, celly, cellz;
544	>	double temp1, temp2, temp3;
545	>	int n_per_extra;
546	>	int n_extra;
547	>	int have_extra, done;
548
549	<	//   new AllLong( simnfo );
549	>	double vel[3];
550	>	vel[0] = 0.0;
551	>	vel[1] = 0.0;
552	>	vel[2] = 0.0;
553
554	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
555	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
556	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
644	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
554	>	temp1 = (double) tot_nmol / 4.0;
555	>	temp2 = pow(temp1, (1.0 / 3.0));
556	>	temp3 = ceil(temp2);
557
558	+	have_extra = 0;
559	+	if (temp2 < temp3){
560	+	// we have a non-complete lattice
561	+	have_extra = 1;
562
563	+	n_cells = (int) temp3 - 1;
564	+	cellx = info[0].boxL[0] / temp3;
565	+	celly = info[0].boxL[1] / temp3;
566	+	cellz = info[0].boxL[2] / temp3;
567	+	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
568	+	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
569	+	n_per_extra = (int) ceil(temp1);
570
571	<	// initialize the Fortran
572	<
573	<	simnfo->refreshSim();
574	<
575	<	if( !strcmp( simnfo->mixingRule, "standard") ){
576	<	the_ff->initForceField( LB_MIXING_RULE );
571	>	if (n_per_extra > 4){
572	>	sprintf(painCave.errMsg,
573	>	"SimSetup error. There has been an error in constructing"
574	>	" the non-complete lattice.\n");
575	>	painCave.isFatal = 1;
576	>	simError();
577	>	}
578		}
655	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
656	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
657	–	}
579		else{
580	<	sprintf( painCave.errMsg,
581	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
582	<	simnfo->mixingRule );
583	<	painCave.isFatal = 1;
663	<	simError();
580	>	n_cells = (int) temp3;
581	>	cellx = info[0].boxL[0] / temp3;
582	>	celly = info[0].boxL[1] / temp3;
583	>	cellz = info[0].boxL[2] / temp3;
584		}
585
586	+	current_mol = 0;
587	+	current_comp_mol = 0;
588	+	current_comp = 0;
589	+	current_atom_ndx = 0;
590
591	<	#ifdef IS_MPI
592	<	strcpy( checkPointMsg,
593	<	"Successfully intialized the mixingRule for Fortran." );
594	<	MPIcheckPoint();
671	<	#endif // is_mpi
672	<	}
591	>	for (i = 0; i < n_cells ; i++){
592	>	for (j = 0; j < n_cells; j++){
593	>	for (k = 0; k < n_cells; k++){
594	>	makeElement(i * cellx, j * celly, k * cellz);
595
596	+	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
597
598	<	void SimSetup::makeMolecules( void ){
598	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
599
600	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
601	<	molInit info;
602	<	DirectionalAtom* dAtom;
603	<	LinkedAssign* extras;
681	<	LinkedAssign* current_extra;
682	<	AtomStamp* currentAtom;
683	<	BondStamp* currentBond;
684	<	BendStamp* currentBend;
685	<	TorsionStamp* currentTorsion;
686	<
687	<	//init the forceField paramters
600	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
601	>	}
602	>	}
603	>	}
604
605	<	the_ff->readParams();
605	>	if (have_extra){
606	>	done = 0;
607
608	<
609	<	// init the molecules
608	>	int start_ndx;
609	>	for (i = 0; i < (n_cells + 1) && !done; i++){
610	>	for (j = 0; j < (n_cells + 1) && !done; j++){
611	>	if (i < n_cells){
612	>	if (j < n_cells){
613	>	start_ndx = n_cells;
614	>	}
615	>	else
616	>	start_ndx = 0;
617	>	}
618	>	else
619	>	start_ndx = 0;
620
621	<	atomOffset = 0;
622	<	excludeOffset = 0;
623	<	for(i=0; i<simnfo->n_mol; i++){
697	<
698	<	stampID = the_molecules[i].getStampID();
621	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
622	>	makeElement(i * cellx, j * celly, k * cellz);
623	>	done = (current_mol >= tot_nmol);
624
625	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
626	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
627	<	info.nBends    = comp_stamps[stampID]->getNBends();
628	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
629	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
625	>	if (!done && n_per_extra > 1){
626	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
627	>	k * cellz);
628	>	done = (current_mol >= tot_nmol);
629	>	}
630
631	<	info.myAtoms = &the_atoms[atomOffset];
632	<	info.myExcludes = &the_excludes[excludeOffset];
633	<	info.myBonds = new Bond*[info.nBonds];
634	<	info.myBends = new Bend*[info.nBends];
635	<	info.myTorsions = new Torsions*[info.nTorsions];
631	>	if (!done && n_per_extra > 2){
632	>	makeElement(i * cellx, j * celly + 0.5 * celly,
633	>	k * cellz + 0.5 * cellz);
634	>	done = (current_mol >= tot_nmol);
635	>	}
636
637	<	theBonds = new bond_pair[info.nBonds];
638	<	theBends = new bend_set[info.nBends];
639	<	theTorsions = new torsion_set[info.nTorsions];
640	<
641	<	// make the Atoms
642	<
718	<	for(j=0; j<info.nAtoms; j++){
719	<
720	<	currentAtom = theComponents[stampID]->getAtom( j );
721	<	if( currentAtom->haveOrientation() ){
722	<
723	<	dAtom = new DirectionalAtom(j + atomOffset);
724	<	simnfo->n_oriented++;
725	<	info.myAtoms[j] = dAtom;
726	<
727	<	ux = currentAtom->getOrntX();
728	<	uy = currentAtom->getOrntY();
729	<	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 );
637	>	if (!done && n_per_extra > 3){
638	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
639	>	k * cellz + 0.5 * cellz);
640	>	done = (current_mol >= tot_nmol);
641	>	}
642	>	}
643		}
644	<	else{
645	<	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;
644	>	}
645	>	}
646
647	<	exI = theBonds[i].a;
648	<	exJ = theBonds[i].b;
647	>	for (i = 0; i < info[0].n_atoms; i++){
648	>	info[0].atoms[i]->setVel(vel);
649	>	}
650	>	}
651
652	<	// exclude_I must always be the smaller of the pair
653	<	if( exI > exJ ){
654	<	tempEx = exI;
655	<	exI = exJ;
656	<	exJ = tempEx;
657	<	}
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;
652	>	void SimSetup::makeElement(double x, double y, double z){
653	>	int k;
654	>	AtomStamp* current_atom;
655	>	DirectionalAtom* dAtom;
656	>	double rotMat[3][3];
657	>	double pos[3];
658
659	<	//make the bends
660	<	for(j=0; j<info.nBends; j++){
661	<
662	<	currentBend = comp_stamps[stampID]->getBend( j );
663	<	theBends[j].a = currentBend->getA() + atomOffset;
664	<	theBends[j].b = currentBend->getB() + atomOffset;
665	<	theBends[j].c = currentBend->getC() + atomOffset;
666	<
667	<	if( currentBend->haveExtras() ){
668	<
669	<	extras = current_bend->getExtras();
794	<	current_extra = extras;
795	<
796	<	while( current_extra != NULL ){
797	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
798	<
799	<	switch( current_extra->getType() ){
800	<
801	<	case 0:
802	<	theBends[j].ghost =
803	<	current_extra->getInt() + atomOffset;
804	<	theBends[j].isGhost = 1;
805	<	break;
806	<
807	<	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
659	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
660	>	current_atom = comp_stamps[current_comp]->getAtom(k);
661	>	if (!current_atom->havePosition()){
662	>	sprintf(painCave.errMsg,
663	>	"SimSetup:initFromBass error.\n"
664	>	"\tComponent %s, atom %s does not have a position specified.\n"
665	>	"\tThe initialization routine is unable to give a start"
666	>	" position.\n",
667	>	comp_stamps[current_comp]->getID(), current_atom->getType());
668	>	painCave.isFatal = 1;
669	>	simError();
670		}
867	–	excludeOffset += info.nBends;
671
672	<	for(j=0; j<info.nTorsions; j++){
673	<
674	<	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;
672	>	pos[0] = x + current_atom->getPosX();
673	>	pos[1] = y + current_atom->getPosY();
674	>	pos[2] = z + current_atom->getPosZ();
675
676	<	// 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;
676	>	info[0].atoms[current_atom_ndx]->setPos(pos);
677
678	<
679	<	// send the arrays off to the forceField for init.
678	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
679	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
680
681	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
682	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
683	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
905	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
681	>	rotMat[0][0] = 1.0;
682	>	rotMat[0][1] = 0.0;
683	>	rotMat[0][2] = 0.0;
684
685	+	rotMat[1][0] = 0.0;
686	+	rotMat[1][1] = 1.0;
687	+	rotMat[1][2] = 0.0;
688
689	<	the_molecules[i].initialize( info );
690	<	atomOffset += info.nAtoms;
691	<	}
689	>	rotMat[2][0] = 0.0;
690	>	rotMat[2][1] = 0.0;
691	>	rotMat[2][2] = 1.0;
692
693	<	// clean up the forcefield
693	>	dAtom->setA(rotMat);
694	>	}
695
696	<	the_ff->cleanMe();
697	<	}
696	>	current_atom_ndx++;
697	>	}
698
699	+	current_mol++;
700	+	current_comp_mol++;
701
702	+	if (current_comp_mol >= components_nmol[current_comp]){
703	+	current_comp_mol = 0;
704	+	current_comp++;
705	+	}
706	+	}
707
919	–	void SimSetup::makeAtoms( void ){
708
709	<	int i, j, k, index;
710	<	double ux, uy, uz, uSqr, u;
923	<	AtomStamp* current_atom;
709	>	void SimSetup::gatherInfo(void){
710	>	int i;
711
712	<	DirectionalAtom* dAtom;
713	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
712	>	ensembleCase = -1;
713	>	ffCase = -1;
714
715	<	lMolIndex = 0;
929	<	molIndex = 0;
930	<	index = 0;
931	<	for( i=0; i<n_components; i++ ){
715	>	// set the easy ones first
716
717	<	for( j=0; j<components_nmol[i]; j++ ){
717	>	for (i = 0; i < nInfo; i++){
718	>	info[i].target_temp = globals->getTargetTemp();
719	>	info[i].dt = globals->getDt();
720	>	info[i].run_time = globals->getRunTime();
721	>	}
722	>	n_components = globals->getNComponents();
723
935	–	#ifdef IS_MPI
936	–	if( mpiSim->getMyMolStart() <= molIndex &&
937	–	molIndex <= mpiSim->getMyMolEnd() ){
938	–	#endif // is_mpi
724
725	<	molStart = index;
941	<	nMemb = comp_stamps[i]->getNAtoms();
942	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
943	<
944	<	current_atom = comp_stamps[i]->getAtom( k );
945	<	if( current_atom->haveOrientation() ){
946	<
947	<	dAtom = new DirectionalAtom(index);
948	<	simnfo->n_oriented++;
949	<	the_atoms[index] = dAtom;
950	<
951	<	ux = current_atom->getOrntX();
952	<	uy = current_atom->getOrntY();
953	<	uz = current_atom->getOrntZ();
954	<
955	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
956	<
957	<	u = sqrt( uSqr );
958	<	ux = ux / u;
959	<	uy = uy / u;
960	<	uz = uz / u;
961	<
962	<	dAtom->setSUx( ux );
963	<	dAtom->setSUy( uy );
964	<	dAtom->setSUz( uz );
965	<	}
966	<	else{
967	<	the_atoms[index] = new GeneralAtom(index);
968	<	}
969	<	the_atoms[index]->setType( current_atom->getType() );
970	<	the_atoms[index]->setIndex( index );
971	<
972	<	// increment the index and repeat;
973	<	index++;
974	<	}
975	<
976	<	molEnd = index -1;
977	<	the_molecules[lMolIndex].setNMembers( nMemb );
978	<	the_molecules[lMolIndex].setStartAtom( molStart );
979	<	the_molecules[lMolIndex].setEndAtom( molEnd );
980	<	the_molecules[lMolIndex].setStampID( i );
981	<	lMolIndex++;
725	>	// get the forceField
726
727	<	#ifdef IS_MPI
728	<	}
729	<	#endif //is_mpi
730	<
987	<	molIndex++;
988	<	}
727	>	strcpy(force_field, globals->getForceField());
728	>
729	>	if (!strcasecmp(force_field, "DUFF")){
730	>	ffCase = FF_DUFF;
731		}
732	+	else if (!strcasecmp(force_field, "LJ")){
733	+	ffCase = FF_LJ;
734	+	}
735	+	else if (!strcasecmp(force_field, "EAM")){
736	+	ffCase = FF_EAM;
737	+	}
738	+	else if (!strcasecmp(force_field, "WATER")){
739	+	ffCase = FF_H2O;
740	+	}
741	+	else{
742	+	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
743	+	force_field);
744	+	painCave.isFatal = 1;
745	+	simError();
746	+	}
747
748	<	#ifdef IS_MPI
992	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
993	<
994	<	delete[] globalIndex;
748	>	// get the ensemble
749
750	<	mpiSim->mpiRefresh();
997	<	#endif //IS_MPI
998	<
999	<	the_ff->initializeAtoms();
1000	<	}
750	>	strcpy(ensemble, globals->getEnsemble());
751
752	<	void SimSetup::makeBonds( void ){
752	>	if (!strcasecmp(ensemble, "NVE")){
753	>	ensembleCase = NVE_ENS;
754	>	}
755	>	else if (!strcasecmp(ensemble, "NVT")){
756	>	ensembleCase = NVT_ENS;
757	>	}
758	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
759	>	ensembleCase = NPTi_ENS;
760	>	}
761	>	else if (!strcasecmp(ensemble, "NPTf")){
762	>	ensembleCase = NPTf_ENS;
763	>	}
764	>	else if (!strcasecmp(ensemble, "NPTxyz")){
765	>	ensembleCase = NPTxyz_ENS;
766	>	}
767	>	else{
768	>	sprintf(painCave.errMsg,
769	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
770	>	"\treverting to NVE for this simulation.\n",
771	>	ensemble);
772	>	painCave.isFatal = 0;
773	>	simError();
774	>	strcpy(ensemble, "NVE");
775	>	ensembleCase = NVE_ENS;
776	>	}
777
778	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
779	<	bond_pair* the_bonds;
1006	<	BondStamp* current_bond;
778	>	for (i = 0; i < nInfo; i++){
779	>	strcpy(info[i].ensemble, ensemble);
780
781	<	the_bonds = new bond_pair[tot_bonds];
1009	<	index = 0;
1010	<	offset = 0;
1011	<	molIndex = 0;
781	>	// get the mixing rule
782
783	<	for( i=0; i<n_components; i++ ){
783	>	strcpy(info[i].mixingRule, globals->getMixingRule());
784	>	info[i].usePBC = globals->getPBC();
785	>	}
786
787	<	for( j=0; j<components_nmol[i]; j++ ){
787	>	// get the components and calculate the tot_nMol and indvidual n_mol
788
789	<	#ifdef IS_MPI
790	<	if( mpiSim->getMyMolStart() <= molIndex &&
1019	<	molIndex <= mpiSim->getMyMolEnd() ){
1020	<	#endif // is_mpi
1021	<
1022	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
1023	<
1024	<	current_bond = comp_stamps[i]->getBond( k );
1025	<	the_bonds[index].a = current_bond->getA() + offset;
1026	<	the_bonds[index].b = current_bond->getB() + offset;
789	>	the_components = globals->getComponents();
790	>	components_nmol = new int[n_components];
791
1028	–	exI = the_bonds[index].a;
1029	–	exJ = the_bonds[index].b;
792
793	<	// exclude_I must always be the smaller of the pair
794	<	if( exI > exJ ){
795	<	tempEx = exI;
1034	<	exI = exJ;
1035	<	exJ = tempEx;
1036	<	}
793	>	if (!globals->haveNMol()){
794	>	// we don't have the total number of molecules, so we assume it is
795	>	// given in each component
796
797	<
798	<	#ifdef IS_MPI
797	>	tot_nmol = 0;
798	>	for (i = 0; i < n_components; i++){
799	>	if (!the_components[i]->haveNMol()){
800	>	// we have a problem
801	>	sprintf(painCave.errMsg,
802	>	"SimSetup Error. No global NMol or component NMol given.\n"
803	>	"\tCannot calculate the number of atoms.\n");
804	>	painCave.isFatal = 1;
805	>	simError();
806	>	}
807
808	<	the_excludes[index*2] =
809	<	the_atoms[exI]->getGlobalIndex() + 1;
810	<	the_excludes[index*2 + 1] =
811	<	the_atoms[exJ]->getGlobalIndex() + 1;
808	>	tot_nmol += the_components[i]->getNMol();
809	>	components_nmol[i] = the_components[i]->getNMol();
810	>	}
811	>	}
812	>	else{
813	>	sprintf(painCave.errMsg,
814	>	"SimSetup error.\n"
815	>	"\tSorry, the ability to specify total"
816	>	" nMols and then give molfractions in the components\n"
817	>	"\tis not currently supported."
818	>	" Please give nMol in the components.\n");
819	>	painCave.isFatal = 1;
820	>	simError();
821	>	}
822
823	<	#else  // isn't MPI
824	<
825	<	the_excludes[index*2] =     exI + 1;
826	<	the_excludes[index*2 + 1] = exJ + 1;
827	<	// fortran index from 1 (hence the +1 in the indexing)
828	<	#endif  //is_mpi
829	<
830	<	// increment the index and repeat;
831	<	index++;
1055	<	}
1056	<	offset += comp_stamps[i]->getNAtoms();
1057	<
1058	<	#ifdef IS_MPI
1059	<	}
1060	<	#endif //is_mpi
1061	<
1062	<	molIndex++;
1063	<	}
823	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
824	>	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
825	>	sprintf(painCave.errMsg,
826	>	"Sample time is not divisible by dt.\n"
827	>	"\tThis will result in samples that are not uniformly\n"
828	>	"\tdistributed in time.  If this is a problem, change\n"
829	>	"\tyour sampleTime variable.\n");
830	>	painCave.isFatal = 0;
831	>	simError();
832		}
833
834	<	the_ff->initializeBonds( the_bonds );
835	<	}
834	>	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
835	>	sprintf(painCave.errMsg,
836	>	"Status time is not divisible by dt.\n"
837	>	"\tThis will result in status reports that are not uniformly\n"
838	>	"\tdistributed in time.  If this is a problem, change \n"
839	>	"\tyour statusTime variable.\n");
840	>	painCave.isFatal = 0;
841	>	simError();
842	>	}
843
844	<	void SimSetup::makeBends( void ){
844	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
845	>	sprintf(painCave.errMsg,
846	>	"Thermal time is not divisible by dt.\n"
847	>	"\tThis will result in thermalizations that are not uniformly\n"
848	>	"\tdistributed in time.  If this is a problem, change \n"
849	>	"\tyour thermalTime variable.\n");
850	>	painCave.isFatal = 0;
851	>	simError();
852	>	}
853
854	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
855	<	bend_set* the_bends;
856	<	BendStamp* current_bend;
857	<	LinkedAssign* extras;
858	<	LinkedAssign* current_extra;
854	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
855	>	sprintf(painCave.errMsg,
856	>	"Reset time is not divisible by dt.\n"
857	>	"\tThis will result in integrator resets that are not uniformly\n"
858	>	"\tdistributed in time.  If this is a problem, change\n"
859	>	"\tyour resetTime variable.\n");
860	>	painCave.isFatal = 0;
861	>	simError();
862	>	}
863	>
864	>	// set the status, sample, and thermal kick times
865	>
866	>	for (i = 0; i < nInfo; i++){
867	>	if (globals->haveSampleTime()){
868	>	info[i].sampleTime = globals->getSampleTime();
869	>	info[i].statusTime = info[i].sampleTime;
870	>	info[i].thermalTime = info[i].sampleTime;
871	>	}
872	>	else{
873	>	info[i].sampleTime = globals->getRunTime();
874	>	info[i].statusTime = info[i].sampleTime;
875	>	info[i].thermalTime = info[i].sampleTime;
876	>	}
877	>
878	>	if (globals->haveStatusTime()){
879	>	info[i].statusTime = globals->getStatusTime();
880	>	}
881	>
882	>	if (globals->haveThermalTime()){
883	>	info[i].thermalTime = globals->getThermalTime();
884	>	}
885	>
886	>	info[i].resetIntegrator = 0;
887	>	if( globals->haveResetTime() ){
888	>	info[i].resetTime = globals->getResetTime();
889	>	info[i].resetIntegrator = 1;
890	>	}
891	>
892	>	// check for the temperature set flag
893	>
894	>	if (globals->haveTempSet())
895	>	info[i].setTemp = globals->getTempSet();
896	>
897	>	// check for the extended State init
898	>
899	>	info[i].useInitXSstate = globals->getUseInitXSstate();
900	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
901	>
902	>	}
903
904	+	//setup seed for random number generator
905	+	int seedValue;
906
907	<	the_bends = new bend_set[tot_bends];
908	<	index = 0;
1080	<	offset = 0;
1081	<	molIndex = 0;
1082	<	for( i=0; i<n_components; i++ ){
907	>	if (globals->haveSeed()){
908	>	seedValue = globals->getSeed();
909
910	<	for( j=0; j<components_nmol[i]; j++ ){
910	>	if(seedValue / 1E9 == 0){
911	>	sprintf(painCave.errMsg,
912	>	"Seed for sprng library should contain at least 9 digits\n"
913	>	"OOPSE will generate a seed for user\n");
914	>	painCave.isFatal = 0;
915	>	simError();
916
917	+	//using seed generated by system instead of invalid seed set by user
918	+	#ifndef IS_MPI
919	+	seedValue = make_sprng_seed();
920	+	#else
921	+	if (worldRank == 0){
922	+	seedValue = make_sprng_seed();
923	+	}
924	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
925	+	#endif
926	+	}
927	+	}//end of if branch of globals->haveSeed()
928	+	else{
929	+
930	+	#ifndef IS_MPI
931	+	seedValue = make_sprng_seed();
932	+	#else
933	+	if (worldRank == 0){
934	+	seedValue = make_sprng_seed();
935	+	}
936	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
937	+	#endif
938	+	}//end of globals->haveSeed()
939	+
940	+	for (int i = 0; i < nInfo; i++){
941	+	info[i].setSeed(seedValue);
942	+	}
943	+
944		#ifdef IS_MPI
945	<	if( mpiSim->getMyMolStart() <= molIndex &&
946	<	molIndex <= mpiSim->getMyMolEnd() ){
947	<	#endif // is_mpi
945	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
946	>	MPIcheckPoint();
947	>	#endif // is_mpi
948	>	}
949
1091	–	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
1092	–
1093	–	current_bend = comp_stamps[i]->getBend( k );
1094	–	the_bends[index].a = current_bend->getA() + offset;
1095	–	the_bends[index].b = current_bend->getB() + offset;
1096	–	the_bends[index].c = current_bend->getC() + offset;
1097	–
1098	–	if( current_bend->haveExtras() ){
1099	–
1100	–	extras = current_bend->getExtras();
1101	–	current_extra = extras;
1102	–
1103	–	while( current_extra != NULL ){
1104	–	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1105	–
1106	–	switch( current_extra->getType() ){
1107	–
1108	–	case 0:
1109	–	the_bends[index].ghost =
1110	–	current_extra->getInt() + offset;
1111	–	the_bends[index].isGhost = 1;
1112	–	break;
1113	–
1114	–	case 1:
1115	–	the_bends[index].ghost =
1116	–	(int)current_extra->getDouble() + offset;
1117	–	the_bends[index].isGhost = 1;
1118	–	break;
1119	–
1120	–	default:
1121	–	sprintf( painCave.errMsg,
1122	–	"SimSetup Error: ghostVectorSource was neiter a "
1123	–	"double nor an int.\n"
1124	–	"-->Bend[%d] in %s\n",
1125	–	k, comp_stamps[i]->getID() );
1126	–	painCave.isFatal = 1;
1127	–	simError();
1128	–	}
1129	–	}
1130	–
1131	–	else{
1132	–
1133	–	sprintf( painCave.errMsg,
1134	–	"SimSetup Error: unhandled bend assignment:\n"
1135	–	"    -->%s in Bend[%d] in %s\n",
1136	–	current_extra->getlhs(),
1137	–	k, comp_stamps[i]->getID() );
1138	–	painCave.isFatal = 1;
1139	–	simError();
1140	–	}
1141	–
1142	–	current_extra = current_extra->getNext();
1143	–	}
1144	–	}
1145	–
1146	–	if( !the_bends[index].isGhost ){
1147	–
1148	–	exI = the_bends[index].a;
1149	–	exJ = the_bends[index].c;
1150	–	}
1151	–	else{
1152	–
1153	–	exI = the_bends[index].a;
1154	–	exJ = the_bends[index].b;
1155	–	}
1156	–
1157	–	// exclude_I must always be the smaller of the pair
1158	–	if( exI > exJ ){
1159	–	tempEx = exI;
1160	–	exI = exJ;
1161	–	exJ = tempEx;
1162	–	}
950
951	+	void SimSetup::finalInfoCheck(void){
952	+	int index;
953	+	int usesDipoles;
954	+	int i;
955
956	+	for (i = 0; i < nInfo; i++){
957	+	// check electrostatic parameters
958	+
959	+	index = 0;
960	+	usesDipoles = 0;
961	+	while ((index < info[i].n_atoms) && !usesDipoles){
962	+	usesDipoles = (info[i].atoms[index])->hasDipole();
963	+	index++;
964	+	}
965	+
966		#ifdef IS_MPI
967	+	int myUse = usesDipoles;
968	+	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
969	+	#endif //is_mpi
970
971	<	the_excludes[(index + tot_bonds)*2] =
972	<	the_atoms[exI]->getGlobalIndex() + 1;
973	<	the_excludes[(index + tot_bonds)*2 + 1] =
974	<	the_atoms[exJ]->getGlobalIndex() + 1;
975	<
976	<	#else  // isn't MPI
977	<
978	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
979	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
980	<	// fortran index from 1 (hence the +1 in the indexing)
981	<	#endif  //is_mpi
982	<
983	<
1180	<	// increment the index and repeat;
1181	<	index++;
1182	<	}
1183	<	offset += comp_stamps[i]->getNAtoms();
1184	<
1185	<	#ifdef IS_MPI
971	>	double theEcr, theEst;
972	>
973	>	if (globals->getUseRF()){
974	>	info[i].useReactionField = 1;
975	>
976	>	if (!globals->haveECR()){
977	>	sprintf(painCave.errMsg,
978	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
979	>	"\tOOPSE will use a default value of 15.0 angstroms"
980	>	"\tfor the electrostaticCutoffRadius.\n");
981	>	painCave.isFatal = 0;
982	>	simError();
983	>	theEcr = 15.0;
984		}
985	<	#endif //is_mpi
985	>	else{
986	>	theEcr = globals->getECR();
987	>	}
988
989	<	molIndex++;
989	>	if (!globals->haveEST()){
990	>	sprintf(painCave.errMsg,
991	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
992	>	"\tOOPSE will use a default value of\n"
993	>	"\t0.05 * electrostaticCutoffRadius\n"
994	>	"\tfor the electrostaticSkinThickness\n");
995	>	painCave.isFatal = 0;
996	>	simError();
997	>	theEst = 0.05 * theEcr;
998	>	}
999	>	else{
1000	>	theEst = globals->getEST();
1001	>	}
1002	>
1003	>	info[i].setDefaultEcr(theEcr, theEst);
1004	>
1005	>	if (!globals->haveDielectric()){
1006	>	sprintf(painCave.errMsg,
1007	>	"SimSetup Error: No Dielectric constant was set.\n"
1008	>	"\tYou are trying to use Reaction Field without"
1009	>	"\tsetting a dielectric constant!\n");
1010	>	painCave.isFatal = 1;
1011	>	simError();
1012	>	}
1013	>	info[i].dielectric = globals->getDielectric();
1014		}
1015	+	else{
1016	+	if (usesDipoles){
1017	+	if (!globals->haveECR()){
1018	+	sprintf(painCave.errMsg,
1019	+	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
1020	+	"\tOOPSE will use a default value of 15.0 angstroms"
1021	+	"\tfor the electrostaticCutoffRadius.\n");
1022	+	painCave.isFatal = 0;
1023	+	simError();
1024	+	theEcr = 15.0;
1025	+	}
1026	+	else{
1027	+	theEcr = globals->getECR();
1028	+	}
1029	+
1030	+	if (!globals->haveEST()){
1031	+	sprintf(painCave.errMsg,
1032	+	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
1033	+	"\tOOPSE will use a default value of\n"
1034	+	"\t0.05 * electrostaticCutoffRadius\n"
1035	+	"\tfor the electrostaticSkinThickness\n");
1036	+	painCave.isFatal = 0;
1037	+	simError();
1038	+	theEst = 0.05 * theEcr;
1039	+	}
1040	+	else{
1041	+	theEst = globals->getEST();
1042	+	}
1043	+
1044	+	info[i].setDefaultEcr(theEcr, theEst);
1045	+	}
1046	+	}
1047		}
1192	–
1048		#ifdef IS_MPI
1049	<	sprintf( checkPointMsg,
1195	<	"Successfully created the bends list.\n" );
1049	>	strcpy(checkPointMsg, "post processing checks out");
1050		MPIcheckPoint();
1051		#endif // is_mpi
1052	+	}
1053
1054	+	void SimSetup::initSystemCoords(void){
1055	+	int i;
1056
1057	<	the_ff->initializeBends( the_bends );
1201	<	}
1057	>	char* inName;
1058
1059	<	void SimSetup::makeTorsions( void ){
1059	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1060
1061	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1062	<	torsion_set* the_torsions;
1207	<	TorsionStamp* current_torsion;
1061	>	for (i = 0; i < info[0].n_atoms; i++)
1062	>	info[0].atoms[i]->setCoords();
1063
1064	<	the_torsions = new torsion_set[tot_torsions];
1065	<	index = 0;
1066	<	offset = 0;
1067	<	molIndex = 0;
1068	<	for( i=0; i<n_components; i++ ){
1069	<
1070	<	for( j=0; j<components_nmol[i]; j++ ){
1216	<
1064	>	if (globals->haveInitialConfig()){
1065	>	InitializeFromFile* fileInit;
1066	>	#ifdef IS_MPI // is_mpi
1067	>	if (worldRank == 0){
1068	>	#endif //is_mpi
1069	>	inName = globals->getInitialConfig();
1070	>	fileInit = new InitializeFromFile(inName);
1071		#ifdef IS_MPI
1218	–	if( mpiSim->getMyMolStart() <= molIndex &&
1219	–	molIndex <= mpiSim->getMyMolEnd() ){
1220	–	#endif // is_mpi
1221	–
1222	–	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1223	–
1224	–	current_torsion = comp_stamps[i]->getTorsion( k );
1225	–	the_torsions[index].a = current_torsion->getA() + offset;
1226	–	the_torsions[index].b = current_torsion->getB() + offset;
1227	–	the_torsions[index].c = current_torsion->getC() + offset;
1228	–	the_torsions[index].d = current_torsion->getD() + offset;
1229	–
1230	–	exI = the_torsions[index].a;
1231	–	exJ = the_torsions[index].d;
1232	–
1233	–
1234	–	// exclude_I must always be the smaller of the pair
1235	–	if( exI > exJ ){
1236	–	tempEx = exI;
1237	–	exI = exJ;
1238	–	exJ = tempEx;
1239	–	}
1240	–
1241	–
1242	–	#ifdef IS_MPI
1243	–
1244	–	the_excludes[(index + tot_bonds + tot_bends)*2] =
1245	–	the_atoms[exI]->getGlobalIndex() + 1;
1246	–	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1247	–	the_atoms[exJ]->getGlobalIndex() + 1;
1248	–
1249	–	#else  // isn't MPI
1250	–
1251	–	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1252	–	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1253	–	// fortran indexes from 1 (hence the +1 in the indexing)
1254	–	#endif  //is_mpi
1255	–
1256	–
1257	–	// increment the index and repeat;
1258	–	index++;
1259	–	}
1260	–	offset += comp_stamps[i]->getNAtoms();
1261	–
1262	–	#ifdef IS_MPI
1263	–	}
1264	–	#endif //is_mpi
1265	–
1266	–	molIndex++;
1072		}
1073	+	else
1074	+	fileInit = new InitializeFromFile(NULL);
1075	+	#endif
1076	+	fileInit->readInit(info); // default velocities on
1077	+
1078	+	delete fileInit;
1079		}
1080	+	else{
1081	+
1082	+	// no init from bass
1083	+
1084	+	sprintf(painCave.errMsg,
1085	+	"Cannot intialize a simulation without an initial configuration file.\n");
1086	+	painCave.isFatal = 1;;
1087	+	simError();
1088	+
1089	+	}
1090
1091	<	the_ff->initializeTorsions( the_torsions );
1091	>	#ifdef IS_MPI
1092	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1093	>	MPIcheckPoint();
1094	>	#endif // is_mpi
1095		}
1096
1273	–	void SimSetup::initFromBass( void ){
1097
1098	<	int i, j, k;
1099	<	int n_cells;
1277	<	double cellx, celly, cellz;
1278	<	double temp1, temp2, temp3;
1279	<	int n_per_extra;
1280	<	int n_extra;
1281	<	int have_extra, done;
1098	>	void SimSetup::makeOutNames(void){
1099	>	int k;
1100
1283	–	temp1 = (double)tot_nmol / 4.0;
1284	–	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1285	–	temp3 = ceil( temp2 );
1101
1102	<	have_extra =0;
1103	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1104	<	have_extra =1;
1105	<
1291	<	n_cells = (int)temp3 - 1;
1292	<	cellx = simnfo->box_x / temp3;
1293	<	celly = simnfo->box_y / temp3;
1294	<	cellz = simnfo->box_z / temp3;
1295	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1296	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1297	<	n_per_extra = (int)ceil( temp1 );
1102	>	for (k = 0; k < nInfo; k++){
1103	>	#ifdef IS_MPI
1104	>	if (worldRank == 0){
1105	>	#endif // is_mpi
1106
1107	<	if( n_per_extra > 4){
1108	<	sprintf( painCave.errMsg,
1109	<	"SimSetup error. There has been an error in constructing"
1110	<	" the non-complete lattice.\n" );
1111	<	painCave.isFatal = 1;
1112	<	simError();
1113	<	}
1114	<	}
1115	<	else{
1116	<	n_cells = (int)temp3;
1117	<	cellx = simnfo->box_x / temp3;
1118	<	celly = simnfo->box_y / temp3;
1119	<	cellz = simnfo->box_z / temp3;
1120	<	}
1107	>	if (globals->haveFinalConfig()){
1108	>	strcpy(info[k].finalName, globals->getFinalConfig());
1109	>	}
1110	>	else{
1111	>	strcpy(info[k].finalName, inFileName);
1112	>	char* endTest;
1113	>	int nameLength = strlen(info[k].finalName);
1114	>	endTest = &(info[k].finalName[nameLength - 5]);
1115	>	if (!strcmp(endTest, ".bass")){
1116	>	strcpy(endTest, ".eor");
1117	>	}
1118	>	else if (!strcmp(endTest, ".BASS")){
1119	>	strcpy(endTest, ".eor");
1120	>	}
1121	>	else{
1122	>	endTest = &(info[k].finalName[nameLength - 4]);
1123	>	if (!strcmp(endTest, ".bss")){
1124	>	strcpy(endTest, ".eor");
1125	>	}
1126	>	else if (!strcmp(endTest, ".mdl")){
1127	>	strcpy(endTest, ".eor");
1128	>	}
1129	>	else{
1130	>	strcat(info[k].finalName, ".eor");
1131	>	}
1132	>	}
1133	>	}
1134
1135	<	current_mol = 0;
1315	<	current_comp_mol = 0;
1316	<	current_comp = 0;
1317	<	current_atom_ndx = 0;
1135	>	// make the sample and status out names
1136
1137	<	for( i=0; i < n_cells ; i++ ){
1138	<	for( j=0; j < n_cells; j++ ){
1139	<	for( k=0; k < n_cells; k++ ){
1137	>	strcpy(info[k].sampleName, inFileName);
1138	>	char* endTest;
1139	>	int nameLength = strlen(info[k].sampleName);
1140	>	endTest = &(info[k].sampleName[nameLength - 5]);
1141	>	if (!strcmp(endTest, ".bass")){
1142	>	strcpy(endTest, ".dump");
1143	>	}
1144	>	else if (!strcmp(endTest, ".BASS")){
1145	>	strcpy(endTest, ".dump");
1146	>	}
1147	>	else{
1148	>	endTest = &(info[k].sampleName[nameLength - 4]);
1149	>	if (!strcmp(endTest, ".bss")){
1150	>	strcpy(endTest, ".dump");
1151	>	}
1152	>	else if (!strcmp(endTest, ".mdl")){
1153	>	strcpy(endTest, ".dump");
1154	>	}
1155	>	else{
1156	>	strcat(info[k].sampleName, ".dump");
1157	>	}
1158	>	}
1159
1160	<	makeElement( i * cellx,
1161	<	j * celly,
1162	<	k * cellz );
1160	>	strcpy(info[k].statusName, inFileName);
1161	>	nameLength = strlen(info[k].statusName);
1162	>	endTest = &(info[k].statusName[nameLength - 5]);
1163	>	if (!strcmp(endTest, ".bass")){
1164	>	strcpy(endTest, ".stat");
1165	>	}
1166	>	else if (!strcmp(endTest, ".BASS")){
1167	>	strcpy(endTest, ".stat");
1168	>	}
1169	>	else{
1170	>	endTest = &(info[k].statusName[nameLength - 4]);
1171	>	if (!strcmp(endTest, ".bss")){
1172	>	strcpy(endTest, ".stat");
1173	>	}
1174	>	else if (!strcmp(endTest, ".mdl")){
1175	>	strcpy(endTest, ".stat");
1176	>	}
1177	>	else{
1178	>	strcat(info[k].statusName, ".stat");
1179	>	}
1180	>	}
1181
1182	<	makeElement( i * cellx + 0.5 * cellx,
1328	<	j * celly + 0.5 * celly,
1329	<	k * cellz );
1182	>	#ifdef IS_MPI
1183
1331	–	makeElement( i * cellx,
1332	–	j * celly + 0.5 * celly,
1333	–	k * cellz + 0.5 * cellz );
1334	–
1335	–	makeElement( i * cellx + 0.5 * cellx,
1336	–	j * celly,
1337	–	k * cellz + 0.5 * cellz );
1338	–	}
1184		}
1185	+	#endif // is_mpi
1186		}
1187	+	}
1188
1342	–	if( have_extra ){
1343	–	done = 0;
1189
1190	<	int start_ndx;
1191	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1347	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1190	>	void SimSetup::sysObjectsCreation(void){
1191	>	int i, k;
1192
1193	<	if( i < n_cells ){
1193	>	// create the forceField
1194
1195	<	if( j < n_cells ){
1352	<	start_ndx = n_cells;
1353	<	}
1354	<	else start_ndx = 0;
1355	<	}
1356	<	else start_ndx = 0;
1195	>	createFF();
1196
1197	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1197	>	// extract componentList
1198
1199	<	makeElement( i * cellx,
1361	<	j * celly,
1362	<	k * cellz );
1363	<	done = ( current_mol >= tot_nmol );
1199	>	compList();
1200
1201	<	if( !done && n_per_extra > 1 ){
1366	<	makeElement( i * cellx + 0.5 * cellx,
1367	<	j * celly + 0.5 * celly,
1368	<	k * cellz );
1369	<	done = ( current_mol >= tot_nmol );
1370	<	}
1201	>	// calc the number of atoms, bond, bends, and torsions
1202
1203	<	if( !done && n_per_extra > 2){
1373	<	makeElement( i * cellx,
1374	<	j * celly + 0.5 * celly,
1375	<	k * cellz + 0.5 * cellz );
1376	<	done = ( current_mol >= tot_nmol );
1377	<	}
1203	>	calcSysValues();
1204
1205	<	if( !done && n_per_extra > 3){
1206	<	makeElement( i * cellx + 0.5 * cellx,
1381	<	j * celly,
1382	<	k * cellz + 0.5 * cellz );
1383	<	done = ( current_mol >= tot_nmol );
1384	<	}
1385	<	}
1386	<	}
1387	<	}
1388	<	}
1205	>	#ifdef IS_MPI
1206	>	// divide the molecules among the processors
1207
1208	+	mpiMolDivide();
1209	+	#endif //is_mpi
1210
1211	<	for( i=0; i<simnfo->n_atoms; i++ ){
1392	<	simnfo->atoms[i]->set_vx( 0.0 );
1393	<	simnfo->atoms[i]->set_vy( 0.0 );
1394	<	simnfo->atoms[i]->set_vz( 0.0 );
1395	<	}
1396	<	}
1211	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1212
1213	<	void SimSetup::makeElement( double x, double y, double z ){
1213	>	makeSysArrays();
1214
1215	<	int k;
1401	<	AtomStamp* current_atom;
1402	<	DirectionalAtom* dAtom;
1403	<	double rotMat[3][3];
1215	>	// make and initialize the molecules (all but atomic coordinates)
1216
1217	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1217	>	makeMolecules();
1218
1219	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1220	<	if( !current_atom->havePosition() ){
1221	<	sprintf( painCave.errMsg,
1222	<	"SimSetup:initFromBass error.\n"
1411	<	"\tComponent %s, atom %s does not have a position specified.\n"
1412	<	"\tThe initialization routine is unable to give a start"
1413	<	" position.\n",
1414	<	comp_stamps[current_comp]->getID(),
1415	<	current_atom->getType() );
1416	<	painCave.isFatal = 1;
1417	<	simError();
1219	>	for (k = 0; k < nInfo; k++){
1220	>	info[k].identArray = new int[info[k].n_atoms];
1221	>	for (i = 0; i < info[k].n_atoms; i++){
1222	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1223		}
1224	+	}
1225	+	}
1226
1420	–	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1421	–	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1422	–	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1227
1228	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1228	>	void SimSetup::createFF(void){
1229	>	switch (ffCase){
1230	>	case FF_DUFF:
1231	>	the_ff = new DUFF();
1232	>	break;
1233
1234	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1234	>	case FF_LJ:
1235	>	the_ff = new LJFF();
1236	>	break;
1237
1238	<	rotMat[0][0] = 1.0;
1239	<	rotMat[0][1] = 0.0;
1240	<	rotMat[0][2] = 0.0;
1238	>	case FF_EAM:
1239	>	the_ff = new EAM_FF();
1240	>	break;
1241
1242	<	rotMat[1][0] = 0.0;
1243	<	rotMat[1][1] = 1.0;
1244	<	rotMat[1][2] = 0.0;
1435	<
1436	<	rotMat[2][0] = 0.0;
1437	<	rotMat[2][1] = 0.0;
1438	<	rotMat[2][2] = 1.0;
1242	>	case FF_H2O:
1243	>	the_ff = new WATER();
1244	>	break;
1245
1246	<	dAtom->setA( rotMat );
1246	>	default:
1247	>	sprintf(painCave.errMsg,
1248	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1249	>	painCave.isFatal = 1;
1250	>	simError();
1251	>	}
1252	>
1253	>	#ifdef IS_MPI
1254	>	strcpy(checkPointMsg, "ForceField creation successful");
1255	>	MPIcheckPoint();
1256	>	#endif // is_mpi
1257	>	}
1258	>
1259	>
1260	>	void SimSetup::compList(void){
1261	>	int i;
1262	>	char* id;
1263	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1264	>	LinkedMolStamp* currentStamp = NULL;
1265	>	comp_stamps = new MoleculeStamp * [n_components];
1266	>
1267	>	// make an array of molecule stamps that match the components used.
1268	>	// also extract the used stamps out into a separate linked list
1269	>
1270	>	for (i = 0; i < nInfo; i++){
1271	>	info[i].nComponents = n_components;
1272	>	info[i].componentsNmol = components_nmol;
1273	>	info[i].compStamps = comp_stamps;
1274	>	info[i].headStamp = headStamp;
1275	>	}
1276	>
1277	>
1278	>	for (i = 0; i < n_components; i++){
1279	>	id = the_components[i]->getType();
1280	>	comp_stamps[i] = NULL;
1281	>
1282	>	// check to make sure the component isn't already in the list
1283	>
1284	>	comp_stamps[i] = headStamp->match(id);
1285	>	if (comp_stamps[i] == NULL){
1286	>	// extract the component from the list;
1287	>
1288	>	currentStamp = stamps->extractMolStamp(id);
1289	>	if (currentStamp == NULL){
1290	>	sprintf(painCave.errMsg,
1291	>	"SimSetup error: Component \"%s\" was not found in the "
1292	>	"list of declared molecules\n",
1293	>	id);
1294	>	painCave.isFatal = 1;
1295	>	simError();
1296	>	}
1297	>
1298	>	headStamp->add(currentStamp);
1299	>	comp_stamps[i] = headStamp->match(id);
1300		}
1301	+	}
1302
1303	<	current_atom_ndx++;
1303	>	#ifdef IS_MPI
1304	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1305	>	MPIcheckPoint();
1306	>	#endif // is_mpi
1307	>	}
1308	>
1309	>	void SimSetup::calcSysValues(void){
1310	>	int i;
1311	>
1312	>	int* molMembershipArray;
1313	>
1314	>	tot_atoms = 0;
1315	>	tot_bonds = 0;
1316	>	tot_bends = 0;
1317	>	tot_torsions = 0;
1318	>	tot_rigid = 0;
1319	>	for (i = 0; i < n_components; i++){
1320	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1321	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1322	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1323	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1324	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1325		}
1326	+
1327	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1328	+	molMembershipArray = new int[tot_atoms];
1329
1330	<	current_mol++;
1331	<	current_comp_mol++;
1330	>	for (i = 0; i < nInfo; i++){
1331	>	info[i].n_atoms = tot_atoms;
1332	>	info[i].n_bonds = tot_bonds;
1333	>	info[i].n_bends = tot_bends;
1334	>	info[i].n_torsions = tot_torsions;
1335	>	info[i].n_SRI = tot_SRI;
1336	>	info[i].n_mol = tot_nmol;
1337
1338	<	if( current_comp_mol >= components_nmol[current_comp] ){
1338	>	info[i].molMembershipArray = molMembershipArray;
1339	>	}
1340	>	}
1341	>
1342	>	#ifdef IS_MPI
1343	>
1344	>	void SimSetup::mpiMolDivide(void){
1345	>	int i, j, k;
1346	>	int localMol, allMol;
1347	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1348	>	int local_rigid;
1349	>
1350	>	mpiSim = new mpiSimulation(info);
1351	>
1352	>	globalIndex = mpiSim->divideLabor();
1353	>
1354	>	// set up the local variables
1355	>
1356	>	mol2proc = mpiSim->getMolToProcMap();
1357	>	molCompType = mpiSim->getMolComponentType();
1358	>
1359	>	allMol = 0;
1360	>	localMol = 0;
1361	>	local_atoms = 0;
1362	>	local_bonds = 0;
1363	>	local_bends = 0;
1364	>	local_torsions = 0;
1365	>	local_rigid = 0;
1366	>	globalAtomIndex = 0;
1367	>
1368	>	for (i = 0; i < n_components; i++){
1369	>	for (j = 0; j < components_nmol[i]; j++){
1370	>	if (mol2proc[allMol] == worldRank){
1371	>	local_atoms += comp_stamps[i]->getNAtoms();
1372	>	local_bonds += comp_stamps[i]->getNBonds();
1373	>	local_bends += comp_stamps[i]->getNBends();
1374	>	local_torsions += comp_stamps[i]->getNTorsions();
1375	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1376	>	localMol++;
1377	>	}
1378	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1379	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1380	>	globalAtomIndex++;
1381	>	}
1382	>
1383	>	allMol++;
1384	>	}
1385	>	}
1386	>	local_SRI = local_bonds + local_bends + local_torsions;
1387	>
1388	>	info[0].n_atoms = mpiSim->getMyNlocal();
1389	>
1390	>
1391	>	if (local_atoms != info[0].n_atoms){
1392	>	sprintf(painCave.errMsg,
1393	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1394	>	"\tlocalAtom (%d) are not equal.\n",
1395	>	info[0].n_atoms, local_atoms);
1396	>	painCave.isFatal = 1;
1397	>	simError();
1398	>	}
1399	>
1400	>	info[0].n_bonds = local_bonds;
1401	>	info[0].n_bends = local_bends;
1402	>	info[0].n_torsions = local_torsions;
1403	>	info[0].n_SRI = local_SRI;
1404	>	info[0].n_mol = localMol;
1405	>
1406	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1407	>	MPIcheckPoint();
1408	>	}
1409	>
1410	>	#endif // is_mpi
1411	>
1412	>
1413	>	void SimSetup::makeSysArrays(void){
1414	>
1415	>	#ifndef IS_MPI
1416	>	int k, j;
1417	>	#endif // is_mpi
1418	>	int i, l;
1419	>
1420	>	Atom** the_atoms;
1421	>	Molecule* the_molecules;
1422	>
1423	>	for (l = 0; l < nInfo; l++){
1424	>	// create the atom and short range interaction arrays
1425	>
1426	>	the_atoms = new Atom * [info[l].n_atoms];
1427	>	the_molecules = new Molecule[info[l].n_mol];
1428	>	int molIndex;
1429	>
1430	>	// initialize the molecule's stampID's
1431	>
1432	>	#ifdef IS_MPI
1433	>
1434	>
1435	>	molIndex = 0;
1436	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1437	>	if (mol2proc[i] == worldRank){
1438	>	the_molecules[molIndex].setStampID(molCompType[i]);
1439	>	the_molecules[molIndex].setMyIndex(molIndex);
1440	>	the_molecules[molIndex].setGlobalIndex(i);
1441	>	molIndex++;
1442	>	}
1443	>	}
1444	>
1445	>	#else // is_mpi
1446	>
1447	>	molIndex = 0;
1448	>	globalAtomIndex = 0;
1449	>	for (i = 0; i < n_components; i++){
1450	>	for (j = 0; j < components_nmol[i]; j++){
1451	>	the_molecules[molIndex].setStampID(i);
1452	>	the_molecules[molIndex].setMyIndex(molIndex);
1453	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1454	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1455	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1456	>	globalAtomIndex++;
1457	>	}
1458	>	molIndex++;
1459	>	}
1460	>	}
1461	>
1462	>
1463	>	#endif // is_mpi
1464	>
1465	>	info[l].globalExcludes = new int;
1466	>	info[l].globalExcludes[0] = 0;
1467	>
1468	>	// set the arrays into the SimInfo object
1469
1470	<	current_comp_mol = 0;
1471	<	current_comp++;
1470	>	info[l].atoms = the_atoms;
1471	>	info[l].molecules = the_molecules;
1472	>	info[l].nGlobalExcludes = 0;
1473	>
1474	>	the_ff->setSimInfo(info);
1475		}
1476		}
1477	+
1478	+	void SimSetup::makeIntegrator(void){
1479	+	int k;
1480	+
1481	+	NVE<RealIntegrator>* myNVE = NULL;
1482	+	NVT<RealIntegrator>* myNVT = NULL;
1483	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1484	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1485	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1486	+
1487	+	for (k = 0; k < nInfo; k++){
1488	+	switch (ensembleCase){
1489	+	case NVE_ENS:
1490	+	if (globals->haveZconstraints()){
1491	+	setupZConstraint(info[k]);
1492	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1493	+	}
1494	+	else{
1495	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1496	+	}
1497	+
1498	+	info->the_integrator = myNVE;
1499	+	break;
1500	+
1501	+	case NVT_ENS:
1502	+	if (globals->haveZconstraints()){
1503	+	setupZConstraint(info[k]);
1504	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1505	+	}
1506	+	else
1507	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1508	+
1509	+	myNVT->setTargetTemp(globals->getTargetTemp());
1510	+
1511	+	if (globals->haveTauThermostat())
1512	+	myNVT->setTauThermostat(globals->getTauThermostat());
1513	+	else{
1514	+	sprintf(painCave.errMsg,
1515	+	"SimSetup error: If you use the NVT\n"
1516	+	"\tensemble, you must set tauThermostat.\n");
1517	+	painCave.isFatal = 1;
1518	+	simError();
1519	+	}
1520	+
1521	+	info->the_integrator = myNVT;
1522	+	break;
1523	+
1524	+	case NPTi_ENS:
1525	+	if (globals->haveZconstraints()){
1526	+	setupZConstraint(info[k]);
1527	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1528	+	}
1529	+	else
1530	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1531	+
1532	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1533	+
1534	+	if (globals->haveTargetPressure())
1535	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1536	+	else{
1537	+	sprintf(painCave.errMsg,
1538	+	"SimSetup error: If you use a constant pressure\n"
1539	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1540	+	painCave.isFatal = 1;
1541	+	simError();
1542	+	}
1543	+
1544	+	if (globals->haveTauThermostat())
1545	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1546	+	else{
1547	+	sprintf(painCave.errMsg,
1548	+	"SimSetup error: If you use an NPT\n"
1549	+	"\tensemble, you must set tauThermostat.\n");
1550	+	painCave.isFatal = 1;
1551	+	simError();
1552	+	}
1553	+
1554	+	if (globals->haveTauBarostat())
1555	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1556	+	else{
1557	+	sprintf(painCave.errMsg,
1558	+	"SimSetup error: If you use an NPT\n"
1559	+	"\tensemble, you must set tauBarostat.\n");
1560	+	painCave.isFatal = 1;
1561	+	simError();
1562	+	}
1563	+
1564	+	info->the_integrator = myNPTi;
1565	+	break;
1566	+
1567	+	case NPTf_ENS:
1568	+	if (globals->haveZconstraints()){
1569	+	setupZConstraint(info[k]);
1570	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1571	+	}
1572	+	else
1573	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1574	+
1575	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1576	+
1577	+	if (globals->haveTargetPressure())
1578	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1579	+	else{
1580	+	sprintf(painCave.errMsg,
1581	+	"SimSetup error: If you use a constant pressure\n"
1582	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1583	+	painCave.isFatal = 1;
1584	+	simError();
1585	+	}
1586	+
1587	+	if (globals->haveTauThermostat())
1588	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1589	+
1590	+	else{
1591	+	sprintf(painCave.errMsg,
1592	+	"SimSetup error: If you use an NPT\n"
1593	+	"\tensemble, you must set tauThermostat.\n");
1594	+	painCave.isFatal = 1;
1595	+	simError();
1596	+	}
1597	+
1598	+	if (globals->haveTauBarostat())
1599	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1600	+
1601	+	else{
1602	+	sprintf(painCave.errMsg,
1603	+	"SimSetup error: If you use an NPT\n"
1604	+	"\tensemble, you must set tauBarostat.\n");
1605	+	painCave.isFatal = 1;
1606	+	simError();
1607	+	}
1608	+
1609	+	info->the_integrator = myNPTf;
1610	+	break;
1611	+
1612	+	case NPTxyz_ENS:
1613	+	if (globals->haveZconstraints()){
1614	+	setupZConstraint(info[k]);
1615	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1616	+	}
1617	+	else
1618	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1619	+
1620	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1621	+
1622	+	if (globals->haveTargetPressure())
1623	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1624	+	else{
1625	+	sprintf(painCave.errMsg,
1626	+	"SimSetup error: If you use a constant pressure\n"
1627	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1628	+	painCave.isFatal = 1;
1629	+	simError();
1630	+	}
1631	+
1632	+	if (globals->haveTauThermostat())
1633	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1634	+	else{
1635	+	sprintf(painCave.errMsg,
1636	+	"SimSetup error: If you use an NPT\n"
1637	+	"\tensemble, you must set tauThermostat.\n");
1638	+	painCave.isFatal = 1;
1639	+	simError();
1640	+	}
1641	+
1642	+	if (globals->haveTauBarostat())
1643	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1644	+	else{
1645	+	sprintf(painCave.errMsg,
1646	+	"SimSetup error: If you use an NPT\n"
1647	+	"\tensemble, you must set tauBarostat.\n");
1648	+	painCave.isFatal = 1;
1649	+	simError();
1650	+	}
1651	+
1652	+	info->the_integrator = myNPTxyz;
1653	+	break;
1654	+
1655	+	default:
1656	+	sprintf(painCave.errMsg,
1657	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1658	+	painCave.isFatal = 1;
1659	+	simError();
1660	+	}
1661	+	}
1662	+	}
1663	+
1664	+	void SimSetup::initFortran(void){
1665	+	info[0].refreshSim();
1666	+
1667	+	if (!strcmp(info[0].mixingRule, "standard")){
1668	+	the_ff->initForceField(LB_MIXING_RULE);
1669	+	}
1670	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1671	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1672	+	}
1673	+	else{
1674	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1675	+	info[0].mixingRule);
1676	+	painCave.isFatal = 1;
1677	+	simError();
1678	+	}
1679	+
1680	+
1681	+	#ifdef IS_MPI
1682	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1683	+	MPIcheckPoint();
1684	+	#endif // is_mpi
1685	+	}
1686	+
1687	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1688	+	int nZConstraints;
1689	+	ZconStamp** zconStamp;
1690	+
1691	+	if (globals->haveZconstraintTime()){
1692	+	//add sample time of z-constraint  into SimInfo's property list
1693	+	DoubleData* zconsTimeProp = new DoubleData();
1694	+	zconsTimeProp->setID(ZCONSTIME_ID);
1695	+	zconsTimeProp->setData(globals->getZconsTime());
1696	+	theInfo.addProperty(zconsTimeProp);
1697	+	}
1698	+	else{
1699	+	sprintf(painCave.errMsg,
1700	+	"ZConstraint error: If you use a ZConstraint,\n"
1701	+	"\tyou must set zconsTime.\n");
1702	+	painCave.isFatal = 1;
1703	+	simError();
1704	+	}
1705	+
1706	+	//push zconsTol into siminfo, if user does not specify
1707	+	//value for zconsTol, a default value will be used
1708	+	DoubleData* zconsTol = new DoubleData();
1709	+	zconsTol->setID(ZCONSTOL_ID);
1710	+	if (globals->haveZconsTol()){
1711	+	zconsTol->setData(globals->getZconsTol());
1712	+	}
1713	+	else{
1714	+	double defaultZConsTol = 0.01;
1715	+	sprintf(painCave.errMsg,
1716	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1717	+	"\tOOPSE will use a default value of %f.\n"
1718	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1719	+	defaultZConsTol);
1720	+	painCave.isFatal = 0;
1721	+	simError();
1722	+
1723	+	zconsTol->setData(defaultZConsTol);
1724	+	}
1725	+	theInfo.addProperty(zconsTol);
1726	+
1727	+	//set Force Subtraction Policy
1728	+	StringData* zconsForcePolicy = new StringData();
1729	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1730	+
1731	+	if (globals->haveZconsForcePolicy()){
1732	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1733	+	}
1734	+	else{
1735	+	sprintf(painCave.errMsg,
1736	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1737	+	"\tOOPSE will use PolicyByMass.\n"
1738	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1739	+	painCave.isFatal = 0;
1740	+	simError();
1741	+	zconsForcePolicy->setData("BYMASS");
1742	+	}
1743	+
1744	+	theInfo.addProperty(zconsForcePolicy);
1745	+
1746	+	//set zcons gap
1747	+	DoubleData* zconsGap = new DoubleData();
1748	+	zconsGap->setID(ZCONSGAP_ID);
1749	+
1750	+	if (globals->haveZConsGap()){
1751	+	zconsGap->setData(globals->getZconsGap());
1752	+	theInfo.addProperty(zconsGap);
1753	+	}
1754	+
1755	+	//set zcons fixtime
1756	+	DoubleData* zconsFixtime = new DoubleData();
1757	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1758	+
1759	+	if (globals->haveZConsFixTime()){
1760	+	zconsFixtime->setData(globals->getZconsFixtime());
1761	+	theInfo.addProperty(zconsFixtime);
1762	+	}
1763	+
1764	+	//set zconsUsingSMD
1765	+	IntData* zconsUsingSMD = new IntData();
1766	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1767	+
1768	+	if (globals->haveZConsUsingSMD()){
1769	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1770	+	theInfo.addProperty(zconsUsingSMD);
1771	+	}
1772	+
1773	+	//Determine the name of ouput file and add it into SimInfo's property list
1774	+	//Be careful, do not use inFileName, since it is a pointer which
1775	+	//point to a string at master node, and slave nodes do not contain that string
1776	+
1777	+	string zconsOutput(theInfo.finalName);
1778	+
1779	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1780	+
1781	+	StringData* zconsFilename = new StringData();
1782	+	zconsFilename->setID(ZCONSFILENAME_ID);
1783	+	zconsFilename->setData(zconsOutput);
1784	+
1785	+	theInfo.addProperty(zconsFilename);
1786	+
1787	+	//setup index, pos and other parameters of z-constraint molecules
1788	+	nZConstraints = globals->getNzConstraints();
1789	+	theInfo.nZconstraints = nZConstraints;
1790	+
1791	+	zconStamp = globals->getZconStamp();
1792	+	ZConsParaItem tempParaItem;
1793	+
1794	+	ZConsParaData* zconsParaData = new ZConsParaData();
1795	+	zconsParaData->setID(ZCONSPARADATA_ID);
1796	+
1797	+	for (int i = 0; i < nZConstraints; i++){
1798	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1799	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1800	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1801	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1802	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1803	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1804	+	zconsParaData->addItem(tempParaItem);
1805	+	}
1806	+
1807	+	//check the uniqueness of index
1808	+	if(!zconsParaData->isIndexUnique()){
1809	+	sprintf(painCave.errMsg,
1810	+	"ZConstraint Error: molIndex is not unique!\n");
1811	+	painCave.isFatal = 1;
1812	+	simError();
1813	+	}
1814	+
1815	+	//sort the parameters by index of molecules
1816	+	zconsParaData->sortByIndex();
1817	+
1818	+	//push data into siminfo, therefore, we can retrieve later
1819	+	theInfo.addProperty(zconsParaData);
1820	+	}
1821	+
1822	+	void SimSetup::makeMinimizer(){
1823	+
1824	+	OOPSEMinimizer* myOOPSEMinimizer;
1825	+	MinimizerParameterSet* param;
1826	+	char minimizerName[100];
1827	+
1828	+	for (int i = 0; i < nInfo; i++){
1829	+
1830	+	//prepare parameter set for minimizer
1831	+	param = new MinimizerParameterSet();
1832	+	param->setDefaultParameter();
1833	+
1834	+	if (globals->haveMinimizer()){
1835	+	param->setFTol(globals->getMinFTol());
1836	+	}
1837	+
1838	+	if (globals->haveMinGTol()){
1839	+	param->setGTol(globals->getMinGTol());
1840	+	}
1841	+
1842	+	if (globals->haveMinMaxIter()){
1843	+	param->setMaxIteration(globals->getMinMaxIter());
1844	+	}
1845	+
1846	+	if (globals->haveMinWriteFrq()){
1847	+	param->setMaxIteration(globals->getMinMaxIter());
1848	+	}
1849	+
1850	+	if (globals->haveMinWriteFrq()){
1851	+	param->setWriteFrq(globals->getMinWriteFrq());
1852	+	}
1853	+
1854	+	if (globals->haveMinStepSize()){
1855	+	param->setStepSize(globals->getMinStepSize());
1856	+	}
1857	+
1858	+	if (globals->haveMinLSMaxIter()){
1859	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1860	+	}
1861	+
1862	+	if (globals->haveMinLSTol()){
1863	+	param->setLineSearchTol(globals->getMinLSTol());
1864	+	}
1865	+
1866	+	strcpy(minimizerName, globals->getMinimizer());
1867	+
1868	+	if (!strcasecmp(minimizerName, "CG")){
1869	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1870	+	}
1871	+	else if (!strcasecmp(minimizerName, "SD")){
1872	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1873	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1874	+	}
1875	+	else{
1876	+	sprintf(painCave.errMsg,
1877	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1878	+	painCave.isFatal = 0;
1879	+	simError();
1880	+
1881	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1882	+	}
1883	+	info[i].the_integrator = myOOPSEMinimizer;
1884	+
1885	+	//store the minimizer into simInfo
1886	+	info[i].the_minimizer = myOOPSEMinimizer;
1887	+	info[i].has_minimizer = true;
1888	+	}
1889	+
1890	+	}

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