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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 407 by mmeineke, Wed Mar 26 20:22:02 2003 UTC vs.
Revision 1108 by tim, Wed Apr 14 15:37:41 2004 UTC

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

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