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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 412 by mmeineke, Wed Mar 26 21:50:33 2003 UTC vs.
Revision 1212 by chrisfen, Tue Jun 1 17:15:43 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 "OOPSEMinimizer.hpp"
14	+	//#include "ConstraintElement.hpp"
15	+	//#include "ConstraintPair.hpp"
16
17		#ifdef IS_MPI
18		#include "mpiBASS.h"
19		#include "mpiSimulation.hpp"
20		#endif
21
22	+	// some defines for ensemble and Forcefield  cases
23	+
24	+	#define NVE_ENS        0
25	+	#define NVT_ENS        1
26	+	#define NPTi_ENS       2
27	+	#define NPTf_ENS       3
28	+	#define NPTxyz_ENS     4
29	+
30	+
31	+	#define FF_DUFF  0
32	+	#define FF_LJ    1
33	+	#define FF_EAM   2
34	+	#define FF_H2O   3
35	+
36	+	using namespace std;
37	+
38	+	/**
39	+	* Check whether dividend is divisble by divisor or not
40	+	*/
41	+	bool isDivisible(double dividend, double divisor){
42	+	double tolerance = 0.000001;
43	+	double quotient;
44	+	double diff;
45	+	int intQuotient;
46	+
47	+	quotient = dividend / divisor;
48	+
49	+	if (quotient < 0)
50	+	quotient = -quotient;
51	+
52	+	intQuotient = int (quotient + tolerance);
53	+
54	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
55	+
56	+	if (diff <= tolerance)
57	+	return true;
58	+	else
59	+	return false;
60	+	}
61	+
62		SimSetup::SimSetup(){
63	+
64	+	initSuspend = false;
65	+	isInfoArray = 0;
66	+	nInfo = 1;
67	+
68		stamps = new MakeStamps();
69		globals = new Globals();
70	<
70	>
71	>
72		#ifdef IS_MPI
73	<	strcpy( checkPointMsg, "SimSetup creation successful" );
73	>	strcpy(checkPointMsg, "SimSetup creation successful");
74		MPIcheckPoint();
75		#endif // IS_MPI
76		}
#	Line 27 | Line 80 | SimSetup::~SimSetup(){
80		delete globals;
81		}
82
83	<	void SimSetup::parseFile( char* fileName ){
83	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
84	>	info = the_info;
85	>	nInfo = theNinfo;
86	>	isInfoArray = 1;
87	>	initSuspend = true;
88	>	}
89
90	+
91	+	void SimSetup::parseFile(char* fileName){
92		#ifdef IS_MPI
93	<	if( worldRank == 0 ){
93	>	if (worldRank == 0){
94		#endif // is_mpi
95	<
95	>
96		inFileName = fileName;
97	<	set_interface_stamps( stamps, globals );
98	<
97	>	set_interface_stamps(stamps, globals);
98	>
99		#ifdef IS_MPI
100		mpiEventInit();
101		#endif
102
103	<	yacc_BASS( fileName );
103	>	yacc_BASS(fileName);
104
105		#ifdef IS_MPI
106		throwMPIEvent(NULL);
107		}
108	<	else receiveParse();
108	>	else{
109	>	receiveParse();
110	>	}
111		#endif
112
113		}
114
115		#ifdef IS_MPI
116		void SimSetup::receiveParse(void){
117	<
118	<	set_interface_stamps( stamps, globals );
119	<	mpiEventInit();
120	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
117	>	set_interface_stamps(stamps, globals);
118	>	mpiEventInit();
119	>	MPIcheckPoint();
120	>	mpiEventLoop();
121		}
122
123		#endif // is_mpi
124
125	<	void SimSetup::createSim( void ){
125	>	void SimSetup::createSim(void){
126
127	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
127	>	// gather all of the information from the Bass file
128
129	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
129	>	gatherInfo();
130
131	<	// 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();
131	>	// creation of complex system objects
132
133	<	// 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 );
133	>	sysObjectsCreation();
134
135	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
135	>	// check on the post processing info
136
137	+	finalInfoCheck();
138
139	<	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	<	}
139	>	// initialize the system coordinates
140
141	<	#ifdef IS_MPI
142	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
141	>	if ( !initSuspend ){
142	>	initSystemCoords();
143
144	<
144	>	if( !(globals->getUseInitTime()) )
145	>	info[0].currentTime = 0.0;
146	>	}
147
148	<	// 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];
148	>	// make the output filenames
149
150	<	if( !the_globals->haveNMol() ){
151	<	// we don't have the total number of molecules, so we assume it is
152	<	// given in each component
150	>	makeOutNames();
151	>
152	>	#ifdef IS_MPI
153	>	mpiSim->mpiRefresh();
154	>	#endif
155
156	<	tot_nmol = 0;
120	<	for( i=0; i<n_components; i++ ){
156	>	// initialize the Fortran
157
158	<	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	<	}
158	>	initFortran();
159
160	<	tot_nmol += the_components[i]->getNMol();
161	<	components_nmol[i] = the_components[i]->getNMol();
162	<	}
163	<	}
164	<	else{
165	<	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	<	}
160	>	if (globals->haveMinimizer())
161	>	// make minimizer
162	>	makeMinimizer();
163	>	else
164	>	// make the integrator
165	>	makeIntegrator();
166
167	<	#ifdef IS_MPI
161	<	strcpy( checkPointMsg, "Have the number of components" );
162	<	MPIcheckPoint();
163	<	#endif // is_mpi
167	>	}
168
165	–	// make an array of molecule stamps that match the components used.
166	–	// also extract the used stamps out into a separate linked list
169
170	<	simnfo->nComponents = n_components;
171	<	simnfo->componentsNmol = components_nmol;
172	<	simnfo->compStamps = comp_stamps;
173	<	simnfo->headStamp = new LinkedMolStamp();
174	<
175	<	char* id;
176	<	LinkedMolStamp* headStamp = simnfo->headStamp;
177	<	LinkedMolStamp* currentStamp = NULL;
178	<	for( i=0; i<n_components; i++ ){
170	>	void SimSetup::makeMolecules(void){
171	>	int i, j, k;
172	>	int exI, exJ, exK, exL, slI, slJ;
173	>	int tempI, tempJ, tempK, tempL;
174	>	int molI;
175	>	int stampID, atomOffset, rbOffset;
176	>	molInit molInfo;
177	>	DirectionalAtom* dAtom;
178	>	RigidBody* myRB;
179	>	StuntDouble* mySD;
180	>	LinkedAssign* extras;
181	>	LinkedAssign* current_extra;
182	>	AtomStamp* currentAtom;
183	>	BondStamp* currentBond;
184	>	BendStamp* currentBend;
185	>	TorsionStamp* currentTorsion;
186	>	RigidBodyStamp* currentRigidBody;
187	>	CutoffGroupStamp* currentCutoffGroup;
188	>	CutoffGroup* myCutoffGroup;
189	>	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
190	>	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
191
192	<	id = the_components[i]->getType();
193	<	comp_stamps[i] = NULL;
194	<
181	<	// check to make sure the component isn't already in the list
192	>	bond_pair* theBonds;
193	>	bend_set* theBends;
194	>	torsion_set* theTorsions;
195
196	<	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	<	}
196	>	set<int> skipList;
197
198	<	#ifdef IS_MPI
199	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
200	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
198	>	double phi, theta, psi;
199	>	char* molName;
200	>	char rbName[100];
201
202	+	//ConstraintPair* consPair; //constraint pair
203	+	//ConstraintElement* consElement1;  //first element of constraint pair
204	+	//ConstraintElement* consElement2;  //second element of constraint pair
205	+	//int whichRigidBody;
206	+	//int consAtomIndex;  //index of constraint atom in rigid body's atom array
207	+	//vector<pair<int, int> > jointAtoms;
208	+	//init the forceField paramters
209
210	+	the_ff->readParams();
211
212	<	// caclulate the number of atoms, bonds, bends and torsions
212	>	// init the atoms
213
214	<	tot_atoms = 0;
214	<	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	<	}
214	>	int nMembers, nNew, rb1, rb2;
215
216	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
216	>	for (k = 0; k < nInfo; k++){
217	>	the_ff->setSimInfo(&(info[k]));
218
219	<	simnfo->n_atoms = tot_atoms;
220	<	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;
219	>	atomOffset = 0;
220	>	groupOffset = 0;
221
222	<
223	<	#ifdef IS_MPI
222	>	for (i = 0; i < info[k].n_mol; i++){
223	>	stampID = info[k].molecules[i].getStampID();
224	>	molName = comp_stamps[stampID]->getID();
225
226	<	// divide the molecules among processors here.
227	<
228	<	mpiSim = new mpiSimulation( simnfo );
229	<
230	<
226	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
227	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
228	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
229	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
230	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
231
232	<	globalIndex = mpiSim->divideLabor();
232	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
233	>
234	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
235
236	+	if (molInfo.nBonds > 0)
237	+	molInfo.myBonds = new Bond*[molInfo.nBonds];
238	+	else
239	+	molInfo.myBonds = NULL;
240
241	+	if (molInfo.nBends > 0)
242	+	molInfo.myBends = new Bend*[molInfo.nBends];
243	+	else
244	+	molInfo.myBends = NULL;
245
246	<	// set up the local variables
247	<
248	<	int localMol, allMol;
249	<	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++ ){
246	>	if (molInfo.nTorsions > 0)
247	>	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
248	>	else
249	>	molInfo.myTorsions = NULL;
250
251	<	for( j=0; j<components_nmol[i]; j++ ){
251	>	theBonds = new bond_pair[molInfo.nBonds];
252	>	theBends = new bend_set[molInfo.nBends];
253	>	theTorsions = new torsion_set[molInfo.nTorsions];
254
255	<	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	<
255	>	// make the Atoms
256
257	<	simnfo->n_atoms = mpiSim->getMyNlocal();
258	<
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	<	}
257	>	for (j = 0; j < molInfo.nAtoms; j++){
258	>	currentAtom = comp_stamps[stampID]->getAtom(j);
259
260	<	simnfo->n_bonds = local_bonds;
261	<	simnfo->n_bends = local_bends;
262	<	simnfo->n_torsions = local_torsions;
263	<	simnfo->n_SRI = local_SRI;
264	<	simnfo->n_mol = localMol;
260	>	if (currentAtom->haveOrientation()){
261	>	dAtom = new DirectionalAtom((j + atomOffset),
262	>	info[k].getConfiguration());
263	>	info[k].n_oriented++;
264	>	molInfo.myAtoms[j] = dAtom;
265
266	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
267	<	MPIcheckPoint();
268	<
298	<
299	<	#endif // is_mpi
300	<
266	>	// Directional Atoms have standard unit vectors which are oriented
267	>	// in space using the three Euler angles.  We assume the standard
268	>	// unit vector was originally along the z axis below.
269
270	<	// create the atom and short range interaction arrays
270	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
271	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
272	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
273
274	<	Atom::createArrays(simnfo->n_atoms);
275	<	the_atoms = new Atom*[simnfo->n_atoms];
276	<	the_molecules = new Molecule[simnfo->n_mol];
274	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
275	>
276	>	}
277	>	else{
278
279	+	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
280
281	<	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	<	}
281	>	}
282
283	<	// set the arrays into the SimInfo object
283	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
284	>	#ifdef IS_MPI
285
286	<	simnfo->atoms = the_atoms;
329	<	simnfo->sr_interactions = the_sris;
330	<	simnfo->nGlobalExcludes = 0;
331	<	simnfo->excludes = the_excludes;
286	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
287
288	+	#endif // is_mpi
289	+	}
290
291	<	// get some of the tricky things that may still be in the globals
291	>	// make the bonds
292	>	for (j = 0; j < molInfo.nBonds; j++){
293	>	currentBond = comp_stamps[stampID]->getBond(j);
294	>	theBonds[j].a = currentBond->getA() + atomOffset;
295	>	theBonds[j].b = currentBond->getB() + atomOffset;
296
297	<
298	<	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() ){
297	>	tempI = theBonds[j].a;
298	>	tempJ = theBonds[j].b;
299
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	–
300		#ifdef IS_MPI
301	<	strcpy( checkPointMsg, "Box size set up" );
302	<	MPIcheckPoint();
303	<	#endif // is_mpi
301	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
302	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
303	>	#else
304	>	exI = tempI + 1;
305	>	exJ = tempJ + 1;
306	>	#endif
307
308	+	info[k].excludes->addPair(exI, exJ);
309	+	}
310
311	<	// initialize the arrays
311	>	//make the bends
312	>	for (j = 0; j < molInfo.nBends; j++){
313	>	currentBend = comp_stamps[stampID]->getBend(j);
314	>	theBends[j].a = currentBend->getA() + atomOffset;
315	>	theBends[j].b = currentBend->getB() + atomOffset;
316	>	theBends[j].c = currentBend->getC() + atomOffset;
317
318	<	the_ff->setSimInfo( simnfo );
318	>	if (currentBend->haveExtras()){
319	>	extras = currentBend->getExtras();
320	>	current_extra = extras;
321
322	<	makeAtoms();
323	<	simnfo->identArray = new int[simnfo->n_atoms];
324	<	for(i=0; i<simnfo->n_atoms; i++){
325	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
326	<	}
327	<
328	<	if( tot_bonds ){
393	<	makeBonds();
394	<	}
322	>	while (current_extra != NULL){
323	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
324	>	switch (current_extra->getType()){
325	>	case 0:
326	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
327	>	theBends[j].isGhost = 1;
328	>	break;
329
330	<	if( tot_bends ){
331	<	makeBends();
332	<	}
330	>	case 1:
331	>	theBends[j].ghost = (int) current_extra->getDouble() +
332	>	atomOffset;
333	>	theBends[j].isGhost = 1;
334	>	break;
335
336	<	if( tot_torsions ){
337	<	makeTorsions();
338	<	}
336	>	default:
337	>	sprintf(painCave.errMsg,
338	>	"SimSetup Error: ghostVectorSource was neither a "
339	>	"double nor an int.\n"
340	>	"-->Bend[%d] in %s\n",
341	>	j, comp_stamps[stampID]->getID());
342	>	painCave.isFatal = 1;
343	>	simError();
344	>	}
345	>	}
346	>	else{
347	>	sprintf(painCave.errMsg,
348	>	"SimSetup Error: unhandled bend assignment:\n"
349	>	"    -->%s in Bend[%d] in %s\n",
350	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
351	>	painCave.isFatal = 1;
352	>	simError();
353	>	}
354
355	+	current_extra = current_extra->getNext();
356	+	}
357	+	}
358
359	<	if (the_globals->getUseRF() ) {
360	<	simnfo->useReactionField = 1;
361	<
362	<	if( !the_globals->haveECR() ){
363	<	sprintf( painCave.errMsg,
364	<	"SimSetup Warning: using default value of 1/2 the smallest "
365	<	"box length for the electrostaticCutoffRadius.\n"
366	<	"I hope you have a very fast processor!\n");
367	<	painCave.isFatal = 0;
368	<	simError();
369	<	double smallest;
370	<	smallest = simnfo->box_x;
371	<	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	<	}
359	>	if (theBends[j].isGhost) {
360	>
361	>	tempI = theBends[j].a;
362	>	tempJ = theBends[j].b;
363	>
364	>	#ifdef IS_MPI
365	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
366	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
367	>	#else
368	>	exI = tempI + 1;
369	>	exJ = tempJ + 1;
370	>	#endif
371	>	info[k].excludes->addPair(exI, exJ);
372
373	<	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	<	}
373	>	} else {
374
375	+	tempI = theBends[j].a;
376	+	tempJ = theBends[j].b;
377	+	tempK = theBends[j].c;
378	+
379		#ifdef IS_MPI
380	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
381	<	MPIcheckPoint();
382	<	#endif // is_mpi
380	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
381	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
382	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
383	>	#else
384	>	exI = tempI + 1;
385	>	exJ = tempJ + 1;
386	>	exK = tempK + 1;
387	>	#endif
388	>
389	>	info[k].excludes->addPair(exI, exK);
390	>	info[k].excludes->addPair(exI, exJ);
391	>	info[k].excludes->addPair(exJ, exK);
392	>	}
393	>	}
394
395	<	if( the_globals->haveInitialConfig() ){
396	<
397	<	InitializeFromFile* fileInit;
398	<	#ifdef IS_MPI // is_mpi
399	<	if( worldRank == 0 ){
400	<	#endif //is_mpi
401	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
395	>	for (j = 0; j < molInfo.nTorsions; j++){
396	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
397	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
398	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
399	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
400	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
401	>
402	>	tempI = theTorsions[j].a;
403	>	tempJ = theTorsions[j].b;
404	>	tempK = theTorsions[j].c;
405	>	tempL = theTorsions[j].d;
406	>
407		#ifdef IS_MPI
408	<	}else fileInit = new InitializeFromFile( NULL );
408	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
409	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
410	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
411	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
412	>	#else
413	>	exI = tempI + 1;
414	>	exJ = tempJ + 1;
415	>	exK = tempK + 1;
416	>	exL = tempL + 1;
417		#endif
494	–	fileInit->read_xyz( simnfo ); // default velocities on
418
419	<	delete fileInit;
420	<	}
421	<	else{
419	>	info[k].excludes->addPair(exI, exJ);
420	>	info[k].excludes->addPair(exI, exK);
421	>	info[k].excludes->addPair(exI, exL);
422	>	info[k].excludes->addPair(exJ, exK);
423	>	info[k].excludes->addPair(exJ, exL);
424	>	info[k].excludes->addPair(exK, exL);
425	>	}
426
427	<	#ifdef IS_MPI
427	>
428	>	molInfo.myRigidBodies.clear();
429	>
430	>	for (j = 0; j < molInfo.nRigidBodies; j++){
431
432	<	// no init from bass
433	<
504	<	sprintf( painCave.errMsg,
505	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
506	<	painCave.isFatal;
507	<	simError();
508	<
509	<	#else
432	>	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
433	>	nMembers = currentRigidBody->getNMembers();
434
435	<	initFromBass();
435	>	// Create the Rigid Body:
436
437	+	myRB = new RigidBody();
438
439	<	#endif
440	<	}
439	>	sprintf(rbName,"%s_RB_%d", molName, j);
440	>	myRB->setType(rbName);
441	>
442	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
443
444	<	#ifdef IS_MPI
445	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
519	<	MPIcheckPoint();
520	<	#endif // is_mpi
444	>	// molI is atom numbering inside this molecule
445	>	molI = currentRigidBody->getMember(rb1);
446
447	+	// tempI is atom numbering on local processor
448	+	tempI = molI + atomOffset;
449
450	<
451	<
452	<
450	>	// currentAtom is the AtomStamp (which we need for
451	>	// rigid body reference positions)
452	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
453
454	<
454	>	// When we add to the rigid body, add the atom itself and
455	>	// the stamp info:
456	>
457	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
458	>
459	>	// Add this atom to the Skip List for the integrators
460		#ifdef IS_MPI
461	<	if( worldRank == 0 ){
462	<	#endif // is_mpi
463	<
464	<	if( the_globals->haveFinalConfig() ){
465	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
466	<	}
467	<	else{
468	<	strcpy( simnfo->finalName, inFileName );
469	<	char* endTest;
470	<	int nameLength = strlen( simnfo->finalName );
471	<	endTest = &(simnfo->finalName[nameLength - 5]);
472	<	if( !strcmp( endTest, ".bass" ) ){
473	<	strcpy( endTest, ".eor" );
461	>	slI = info[k].atoms[tempI]->getGlobalIndex();
462	>	#else
463	>	slI = tempI;
464	>	#endif
465	>	skipList.insert(slI);
466	>
467	>	}
468	>
469	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
470	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
471	>
472	>	tempI = currentRigidBody->getMember(rb1);
473	>	tempJ = currentRigidBody->getMember(rb2);
474	>
475	>	// Some explanation is required here.
476	>	// Fortran indexing starts at 1, while c indexing starts at 0
477	>	// Also, in parallel computations, the GlobalIndex is
478	>	// used for the exclude list:
479	>
480	>	#ifdef IS_MPI
481	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
482	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
483	>	#else
484	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
485	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
486	>	#endif
487	>
488	>	info[k].excludes->addPair(exI, exJ);
489	>
490	>	}
491	>	}
492	>
493	>	molInfo.myRigidBodies.push_back(myRB);
494	>	info[k].rigidBodies.push_back(myRB);
495		}
496	<	else if( !strcmp( endTest, ".BASS" ) ){
497	<	strcpy( endTest, ".eor" );
498	<	}
499	<	else{
500	<	endTest = &(simnfo->finalName[nameLength - 4]);
501	<	if( !strcmp( endTest, ".bss" ) ){
502	<	strcpy( endTest, ".eor" );
503	<	}
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	<	}
496	>
497	>
498	>	//create cutoff group for molecule
499	>
500	>	cutoffAtomSet.clear();
501	>	molInfo.myCutoffGroups.clear();
502	>
503	>	for (j = 0; j < nCutoffGroups; j++){
504
505	<	if( the_globals->haveStatusTime() ){
506	<	simnfo->statusTime = the_globals->getStatusTime();
626	<	}
505	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
506	>	nMembers = currentCutoffGroup->getNMembers();
507
508	<	if( the_globals->haveThermalTime() ){
509	<	simnfo->thermalTime = the_globals->getThermalTime();
510	<	}
508	>	myCutoffGroup = new CutoffGroup();
509	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
510	>
511	>	for (int cg = 0; cg < nMembers; cg++) {
512
513	<	// check for the temperature set flag
513	>	// molI is atom numbering inside this molecule
514	>	molI = currentCutoffGroup->getMember(cg);
515
516	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
516	>	// tempI is atom numbering on local processor
517	>	tempI = molI + atomOffset;
518
519	+	#ifdef IS_MPI
520	+	globalID = info[k].atoms[tempI]->getGlobalIndex()
521	+	#else
522	+	globalID = info[k].atoms[tempI]->getIndex();
523	+	#endif
524
525	<	//   // make the longe range forces and the integrator
525	>	globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
526
527	<	//   new AllLong( simnfo );
527	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
528
529	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
530	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
531	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
532	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
529	>	cutoffAtomSet.insert(tempI);
530	>	}
531	>
532	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
533	>	groupOffset++;
534
535	+	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
536
537	+	//creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
538
539	<	// initialize the Fortran
649	<
650	<	simnfo->refreshSim();
651	<
652	<	if( !strcmp( simnfo->mixingRule, "standard") ){
653	<	the_ff->initForceField( LB_MIXING_RULE );
654	<	}
655	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
656	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
657	<	}
658	<	else{
659	<	sprintf( painCave.errMsg,
660	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
661	<	simnfo->mixingRule );
662	<	painCave.isFatal = 1;
663	<	simError();
664	<	}
539	>	for(j = 0; j < molInfo.nAtoms; j++){
540
541	<
541	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
542	>	myCutoffGroup = new CutoffGroup();
543	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
544	>	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
545		#ifdef IS_MPI
546	<	strcpy( checkPointMsg,
547	<	"Successfully intialized the mixingRule for Fortran." );
548	<	MPIcheckPoint();
549	<	#endif // is_mpi
550	<	}
546	>	globalID = info[k].atoms[atomOffset + j]->getGlobalIndex()
547	>	#else
548	>	globalID = info[k].atoms[atomOffset + j]->getIndex();
549	>	#endif
550	>	globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
551	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
552	>	groupOffset++;
553	>	}
554	>
555	>	}
556
557	+	// After this is all set up, scan through the atoms to
558	+	// see if they can be added to the integrableObjects:
559
560	<	void SimSetup::makeMolecules( void ){
560	>	molInfo.myIntegrableObjects.clear();
561	>
562
563	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
678	<	molInit info;
679	<	DirectionalAtom* dAtom;
680	<	LinkedAssign* extras;
681	<	LinkedAssign* current_extra;
682	<	AtomStamp* currentAtom;
683	<	BondStamp* currentBond;
684	<	BendStamp* currentBend;
685	<	TorsionStamp* currentTorsion;
686	<
687	<	//init the forceField paramters
563	>	for (j = 0; j < molInfo.nAtoms; j++){
564
565	<	the_ff->readParams();
565	>	#ifdef IS_MPI
566	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
567	>	#else
568	>	slJ = j+atomOffset;
569	>	#endif
570
571	<
692	<	// init the molecules
571	>	// if they aren't on the skip list, then they can be integrated
572
573	<	atomOffset = 0;
574	<	excludeOffset = 0;
575	<	for(i=0; i<simnfo->n_mol; i++){
576	<
577	<	stampID = the_molecules[i].getStampID();
573	>	if (skipList.find(slJ) == skipList.end()) {
574	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
575	>	info[k].integrableObjects.push_back(mySD);
576	>	molInfo.myIntegrableObjects.push_back(mySD);
577	>	}
578	>	}
579
580	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
701	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
702	<	info.nBends    = comp_stamps[stampID]->getNBends();
703	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
704	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
580	>	// all rigid bodies are integrated:
581
582	<	info.myAtoms = &the_atoms[atomOffset];
583	<	info.myExcludes = &the_excludes[excludeOffset];
584	<	info.myBonds = new Bond*[info.nBonds];
585	<	info.myBends = new Bend*[info.nBends];
586	<	info.myTorsions = new Torsions*[info.nTorsions];
582	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
583	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
584	>	info[k].integrableObjects.push_back(mySD);
585	>	molInfo.myIntegrableObjects.push_back(mySD);
586	>	}
587
588	<	theBonds = new bond_pair[info.nBonds];
589	<	theBends = new bend_set[info.nBends];
590	<	theTorsions = new torsion_set[info.nTorsions];
591	<
592	<	// make the Atoms
717	<
718	<	for(j=0; j<info.nAtoms; j++){
588	>
589	>	/*
590	>
591	>	//creat ConstraintPair.
592	>	molInfo.myConstraintPair.clear();
593
594	<	currentAtom = theComponents[stampID]->getAtom( j );
595	<	if( currentAtom->haveOrientation() ){
596	<
597	<	dAtom = new DirectionalAtom(j + atomOffset);
598	<	simnfo->n_oriented++;
599	<	info.myAtoms[j] = dAtom;
600	<
601	<	ux = currentAtom->getOrntX();
602	<	uy = currentAtom->getOrntY();
603	<	uz = currentAtom->getOrntZ();
604	<
605	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
606	<
607	<	u = sqrt( uSqr );
608	<	ux = ux / u;
609	<	uy = uy / u;
610	<	uz = uz / u;
611	<
612	<	dAtom->setSUx( ux );
613	<	dAtom->setSUy( uy );
614	<	dAtom->setSUz( uz );
615	<	}
616	<	else{
617	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
618	<	}
619	<	info.myAtoms[j]->setType( currentAtom->getType() );
620	<
621	<	#ifdef IS_MPI
622	<
623	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
624	<
625	<	#endif // is_mpi
626	<	}
627	<
628	<	// make the bonds
629	<	for(j=0; j<info.nBonds; j++){
630	<
631	<	currentBond = comp_stamps[stampID]->getBond( j );
632	<	theBonds[j].a = currentBond->getA() + atomOffset;
633	<	theBonds[j].b = currentBond->getB() + atomOffset;
634	<
635	<	exI = theBonds[i].a;
636	<	exJ = theBonds[i].b;
637	<
638	<	// exclude_I must always be the smaller of the pair
639	<	if( exI > exJ ){
640	<	tempEx = exI;
641	<	exI = exJ;
642	<	exJ = tempEx;
643	<	}
644	<	#ifdef IS_MPI
645	<	tempEx = exI;
646	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
647	<	tempEx = exJ;
648	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
649	<
650	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
651	<	#else  // isn't MPI
652	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
653	<	#endif  //is_mpi
654	<	}
655	<	excludeOffset += info.nBonds;
656	<
657	<	//make the bends
658	<	for(j=0; j<info.nBends; j++){
659	<
660	<	currentBend = comp_stamps[stampID]->getBend( j );
661	<	theBends[j].a = currentBend->getA() + atomOffset;
662	<	theBends[j].b = currentBend->getB() + atomOffset;
663	<	theBends[j].c = currentBend->getC() + atomOffset;
664	<
665	<	if( currentBend->haveExtras() ){
666	<
667	<	extras = current_bend->getExtras();
668	<	current_extra = extras;
669	<
670	<	while( current_extra != NULL ){
671	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
672	<
673	<	switch( current_extra->getType() ){
674	<
675	<	case 0:
676	<	theBends[j].ghost =
677	<	current_extra->getInt() + atomOffset;
678	<	theBends[j].isGhost = 1;
679	<	break;
680	<
681	<	case 1:
682	<	theBends[j].ghost =
683	<	(int)current_extra->getDouble() + atomOffset;
684	<	theBends[j].isGhost = 1;
685	<	break;
686	<
687	<	default:
688	<	sprintf( painCave.errMsg,
689	<	"SimSetup Error: ghostVectorSource was neiter a "
690	<	"double nor an int.\n"
691	<	"-->Bend[%d] in %s\n",
692	<	j, comp_stamps[stampID]->getID() );
693	<	painCave.isFatal = 1;
694	<	simError();
695	<	}
696	<	}
697	<
698	<	else{
699	<
700	<	sprintf( painCave.errMsg,
701	<	"SimSetup Error: unhandled bend assignment:\n"
702	<	"    -->%s in Bend[%d] in %s\n",
703	<	current_extra->getlhs(),
704	<	j, comp_stamps[stampID]->getID() );
705	<	painCave.isFatal = 1;
706	<	simError();
707	<	}
708	<
709	<	current_extra = current_extra->getNext();
710	<	}
711	<	}
712	<
713	<	if( !theBends[j].isGhost ){
714	<
715	<	exI = theBends[j].a;
716	<	exJ = theBends[j].c;
717	<	}
718	<	else{
719	<
720	<	exI = theBends[j].a;
721	<	exJ = theBends[j].b;
722	<	}
723	<
724	<	// exclude_I must always be the smaller of the pair
725	<	if( exI > exJ ){
726	<	tempEx = exI;
727	<	exI = exJ;
728	<	exJ = tempEx;
729	<	}
730	<	#ifdef IS_MPI
731	<	tempEx = exI;
732	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
733	<	tempEx = exJ;
734	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
735	<
736	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
737	<	#else  // isn't MPI
738	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
739	<	#endif  //is_mpi
740	<	}
741	<	excludeOffset += info.nBends;
742	<
743	<	for(j=0; j<info.nTorsions; j++){
744	<
745	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
746	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
747	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
748	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
749	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
750	<
751	<	exI = theTorsions[j].a;
752	<	exJ = theTorsions[j].d;
753	<
754	<	// exclude_I must always be the smaller of the pair
755	<	if( exI > exJ ){
756	<	tempEx = exI;
757	<	exI = exJ;
758	<	exJ = tempEx;
759	<	}
760	<	#ifdef IS_MPI
761	<	tempEx = exI;
762	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
763	<	tempEx = exJ;
764	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
765	<
766	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
767	<	#else  // isn't MPI
768	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
769	<	#endif  //is_mpi
770	<	}
771	<	excludeOffset += info.nTorsions;
772	<
773	<
774	<
775	<
776	<
777	<
778	<
779	<
780	<	void SimSetup::makeAtoms( void ){
781	<
782	<	int i, j, k, index;
783	<	double ux, uy, uz, uSqr, u;
784	<	AtomStamp* current_atom;
785	<
786	<	DirectionalAtom* dAtom;
787	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
788	<
789	<	lMolIndex = 0;
790	<	molIndex = 0;
791	<	index = 0;
792	<	for( i=0; i<n_components; i++ ){
793	<
794	<	for( j=0; j<components_nmol[i]; j++ ){
795	<
796	<	#ifdef IS_MPI
797	<	if( mpiSim->getMyMolStart() <= molIndex &&
798	<	molIndex <= mpiSim->getMyMolEnd() ){
799	<	#endif // is_mpi
800	<
801	<	molStart = index;
802	<	nMemb = comp_stamps[i]->getNAtoms();
803	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
804	<
805	<	current_atom = comp_stamps[i]->getAtom( k );
806	<	if( current_atom->haveOrientation() ){
807	<
808	<	dAtom = new DirectionalAtom(index);
809	<	simnfo->n_oriented++;
810	<	the_atoms[index] = dAtom;
811	<
812	<	ux = current_atom->getOrntX();
813	<	uy = current_atom->getOrntY();
814	<	uz = current_atom->getOrntZ();
815	<
816	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
817	<
818	<	u = sqrt( uSqr );
819	<	ux = ux / u;
820	<	uy = uy / u;
821	<	uz = uz / u;
822	<
823	<	dAtom->setSUx( ux );
824	<	dAtom->setSUy( uy );
825	<	dAtom->setSUz( uz );
826	<	}
827	<	else{
828	<	the_atoms[index] = new GeneralAtom(index);
829	<	}
830	<	the_atoms[index]->setType( current_atom->getType() );
831	<	the_atoms[index]->setIndex( index );
832	<
833	<	// increment the index and repeat;
834	<	index++;
835	<	}
836	<
837	<	molEnd = index -1;
838	<	the_molecules[lMolIndex].setNMembers( nMemb );
839	<	the_molecules[lMolIndex].setStartAtom( molStart );
840	<	the_molecules[lMolIndex].setEndAtom( molEnd );
841	<	the_molecules[lMolIndex].setStampID( i );
842	<	lMolIndex++;
843	<
844	<	#ifdef IS_MPI
845	<	}
846	<	#endif //is_mpi
847	<
848	<	molIndex++;
849	<	}
850	<	}
851	<
852	<	#ifdef IS_MPI
853	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
854	<
855	<	delete[] globalIndex;
856	<
857	<	mpiSim->mpiRefresh();
858	<	#endif //IS_MPI
859	<
860	<	the_ff->initializeAtoms();
861	<	}
862	<
863	<	void SimSetup::makeBonds( void ){
864	<
865	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
866	<	bond_pair* the_bonds;
867	<	BondStamp* current_bond;
868	<
869	<	the_bonds = new bond_pair[tot_bonds];
870	<	index = 0;
871	<	offset = 0;
872	<	molIndex = 0;
873	<
874	<	for( i=0; i<n_components; i++ ){
875	<
876	<	for( j=0; j<components_nmol[i]; j++ ){
877	<
878	<	#ifdef IS_MPI
879	<	if( mpiSim->getMyMolStart() <= molIndex &&
880	<	molIndex <= mpiSim->getMyMolEnd() ){
881	<	#endif // is_mpi
882	<
883	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
884	<
885	<	current_bond = comp_stamps[i]->getBond( k );
886	<	the_bonds[index].a = current_bond->getA() + offset;
887	<	the_bonds[index].b = current_bond->getB() + offset;
888	<
889	<	exI = the_bonds[index].a;
890	<	exJ = the_bonds[index].b;
891	<
892	<	// exclude_I must always be the smaller of the pair
893	<	if( exI > exJ ){
894	<	tempEx = exI;
895	<	exI = exJ;
896	<	exJ = tempEx;
897	<	}
898	<
899	<
900	<	#ifdef IS_MPI
901	<
902	<	the_excludes[index*2] =
903	<	the_atoms[exI]->getGlobalIndex() + 1;
904	<	the_excludes[index*2 + 1] =
905	<	the_atoms[exJ]->getGlobalIndex() + 1;
906	<
907	<	#else  // isn't MPI
908	<
909	<	the_excludes[index*2] =     exI + 1;
910	<	the_excludes[index*2 + 1] = exJ + 1;
911	<	// fortran index from 1 (hence the +1 in the indexing)
912	<	#endif  //is_mpi
913	<
914	<	// increment the index and repeat;
915	<	index++;
916	<	}
917	<	offset += comp_stamps[i]->getNAtoms();
918	<
919	<	#ifdef IS_MPI
920	<	}
921	<	#endif //is_mpi
922	<
923	<	molIndex++;
924	<	}
925	<	}
926	<
927	<	the_ff->initializeBonds( the_bonds );
928	<	}
929	<
930	<	void SimSetup::makeBends( void ){
931	<
932	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
933	<	bend_set* the_bends;
934	<	BendStamp* current_bend;
935	<	LinkedAssign* extras;
936	<	LinkedAssign* current_extra;
937	<
938	<
939	<	the_bends = new bend_set[tot_bends];
940	<	index = 0;
941	<	offset = 0;
942	<	molIndex = 0;
943	<	for( i=0; i<n_components; i++ ){
944	<
945	<	for( j=0; j<components_nmol[i]; j++ ){
946	<
947	<	#ifdef IS_MPI
948	<	if( mpiSim->getMyMolStart() <= molIndex &&
949	<	molIndex <= mpiSim->getMyMolEnd() ){
950	<	#endif // is_mpi
951	<
952	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
953	<
954	<	current_bend = comp_stamps[i]->getBend( k );
955	<	the_bends[index].a = current_bend->getA() + offset;
956	<	the_bends[index].b = current_bend->getB() + offset;
957	<	the_bends[index].c = current_bend->getC() + offset;
958	<
959	<	if( current_bend->haveExtras() ){
960	<
961	<	extras = current_bend->getExtras();
962	<	current_extra = extras;
963	<
964	<	while( current_extra != NULL ){
965	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
966	<
967	<	switch( current_extra->getType() ){
968	<
969	<	case 0:
970	<	the_bends[index].ghost =
971	<	current_extra->getInt() + offset;
972	<	the_bends[index].isGhost = 1;
973	<	break;
974	<
975	<	case 1:
976	<	the_bends[index].ghost =
977	<	(int)current_extra->getDouble() + offset;
978	<	the_bends[index].isGhost = 1;
979	<	break;
980	<
981	<	default:
982	<	sprintf( painCave.errMsg,
983	<	"SimSetup Error: ghostVectorSource was neiter a "
984	<	"double nor an int.\n"
985	<	"-->Bend[%d] in %s\n",
986	<	k, comp_stamps[i]->getID() );
987	<	painCave.isFatal = 1;
988	<	simError();
989	<	}
990	<	}
991	<
992	<	else{
993	<
994	<	sprintf( painCave.errMsg,
995	<	"SimSetup Error: unhandled bend assignment:\n"
996	<	"    -->%s in Bend[%d] in %s\n",
997	<	current_extra->getlhs(),
998	<	k, comp_stamps[i]->getID() );
999	<	painCave.isFatal = 1;
1000	<	simError();
1001	<	}
1002	<
1003	<	current_extra = current_extra->getNext();
1004	<	}
1005	<	}
1006	<
1007	<	if( !the_bends[index].isGhost ){
1008	<
1009	<	exI = the_bends[index].a;
1010	<	exJ = the_bends[index].c;
1011	<	}
1012	<	else{
1013	<
1014	<	exI = the_bends[index].a;
1015	<	exJ = the_bends[index].b;
1016	<	}
1017	<
1018	<	// exclude_I must always be the smaller of the pair
1019	<	if( exI > exJ ){
1020	<	tempEx = exI;
1021	<	exI = exJ;
1022	<	exJ = tempEx;
1023	<	}
1024	<
1025	<
1026	<	#ifdef IS_MPI
1027	<
1028	<	the_excludes[(index + tot_bonds)*2] =
1029	<	the_atoms[exI]->getGlobalIndex() + 1;
1030	<	the_excludes[(index + tot_bonds)*2 + 1] =
1031	<	the_atoms[exJ]->getGlobalIndex() + 1;
1032	<
1033	<	#else  // isn't MPI
1034	<
1035	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
1036	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1037	<	// fortran index from 1 (hence the +1 in the indexing)
1038	<	#endif  //is_mpi
1039	<
1040	<
1041	<	// increment the index and repeat;
1042	<	index++;
1043	<	}
1044	<	offset += comp_stamps[i]->getNAtoms();
1045	<
1046	<	#ifdef IS_MPI
1047	<	}
1048	<	#endif //is_mpi
1049	<
1050	<	molIndex++;
1051	<	}
1052	<	}
1053	<
1054	<	#ifdef IS_MPI
1055	<	sprintf( checkPointMsg,
1056	<	"Successfully created the bends list.\n" );
1057	<	MPIcheckPoint();
1058	<	#endif // is_mpi
1059	<
1060	<
1061	<	the_ff->initializeBends( the_bends );
1062	<	}
1063	<
1064	<	void SimSetup::makeTorsions( void ){
1065	<
1066	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
1067	<	torsion_set* the_torsions;
1068	<	TorsionStamp* current_torsion;
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++ ){
1075	<
1076	<	for( j=0; j<components_nmol[i]; j++ ){
1077	<
1078	<	#ifdef IS_MPI
1079	<	if( mpiSim->getMyMolStart() <= molIndex &&
1080	<	molIndex <= mpiSim->getMyMolEnd() ){
1081	<	#endif // is_mpi
1082	<
1083	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
1084	<
1085	<	current_torsion = comp_stamps[i]->getTorsion( k );
1086	<	the_torsions[index].a = current_torsion->getA() + offset;
1087	<	the_torsions[index].b = current_torsion->getB() + offset;
1088	<	the_torsions[index].c = current_torsion->getC() + offset;
1089	<	the_torsions[index].d = current_torsion->getD() + offset;
1090	<
1091	<	exI = the_torsions[index].a;
1092	<	exJ = the_torsions[index].d;
1093	<
1094	<
1095	<	// exclude_I must always be the smaller of the pair
1096	<	if( exI > exJ ){
1097	<	tempEx = exI;
1098	<	exI = exJ;
1099	<	exJ = tempEx;
1100	<	}
1101	<
1102	<
1103	<	#ifdef IS_MPI
1104	<
1105	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
1106	<	the_atoms[exI]->getGlobalIndex() + 1;
1107	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1108	<	the_atoms[exJ]->getGlobalIndex() + 1;
1109	<
1110	<	#else  // isn't MPI
1111	<
1112	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1113	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1114	<	// fortran indexes from 1 (hence the +1 in the indexing)
1115	<	#endif  //is_mpi
1116	<
1117	<
1118	<	// increment the index and repeat;
1119	<	index++;
1120	<	}
1121	<	offset += comp_stamps[i]->getNAtoms();
1122	<
1123	<	#ifdef IS_MPI
1124	<	}
1125	<	#endif //is_mpi
1126	<
1127	<	molIndex++;
1128	<	}
1129	<	}
1130	<
1131	<	the_ff->initializeTorsions( the_torsions );
1132	<	}
1133	<
1134	<	void SimSetup::initFromBass( void ){
1135	<
1136	<	int i, j, k;
1137	<	int n_cells;
1138	<	double cellx, celly, cellz;
1139	<	double temp1, temp2, temp3;
1140	<	int n_per_extra;
1141	<	int n_extra;
1142	<	int have_extra, done;
1143	<
1144	<	temp1 = (double)tot_nmol / 4.0;
1145	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1146	<	temp3 = ceil( temp2 );
1147	<
1148	<	have_extra =0;
1149	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1150	<	have_extra =1;
1151	<
1152	<	n_cells = (int)temp3 - 1;
1153	<	cellx = simnfo->box_x / temp3;
1154	<	celly = simnfo->box_y / temp3;
1155	<	cellz = simnfo->box_z / temp3;
1156	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1157	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1158	<	n_per_extra = (int)ceil( temp1 );
1159	<
1160	<	if( n_per_extra > 4){
1161	<	sprintf( painCave.errMsg,
1162	<	"SimSetup error. There has been an error in constructing"
1163	<	" the non-complete lattice.\n" );
1164	<	painCave.isFatal = 1;
1165	<	simError();
1166	<	}
1167	<	}
1168	<	else{
1169	<	n_cells = (int)temp3;
1170	<	cellx = simnfo->box_x / temp3;
1171	<	celly = simnfo->box_y / temp3;
1172	<	cellz = simnfo->box_z / temp3;
1173	<	}
1174	<
1175	<	current_mol = 0;
1176	<	current_comp_mol = 0;
1177	<	current_comp = 0;
1178	<	current_atom_ndx = 0;
1179	<
1180	<	for( i=0; i < n_cells ; i++ ){
1181	<	for( j=0; j < n_cells; j++ ){
1182	<	for( k=0; k < n_cells; k++ ){
1183	<
1184	<	makeElement( i * cellx,
1185	<	j * celly,
1186	<	k * cellz );
1187	<
1188	<	makeElement( i * cellx + 0.5 * cellx,
1189	<	j * celly + 0.5 * celly,
1190	<	k * cellz );
1191	<
1192	<	makeElement( i * cellx,
1193	<	j * celly + 0.5 * celly,
1194	<	k * cellz + 0.5 * cellz );
1195	<
1196	<	makeElement( i * cellx + 0.5 * cellx,
1197	<	j * celly,
1198	<	k * cellz + 0.5 * cellz );
1199	<	}
1200	<	}
1201	<	}
1202	<
1203	<	if( have_extra ){
1204	<	done = 0;
1205	<
1206	<	int start_ndx;
1207	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1208	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1209	<
1210	<	if( i < n_cells ){
1211	<
1212	<	if( j < n_cells ){
1213	<	start_ndx = n_cells;
1214	<	}
1215	<	else start_ndx = 0;
1216	<	}
1217	<	else start_ndx = 0;
1218	<
1219	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1220	<
1221	<	makeElement( i * cellx,
1222	<	j * celly,
1223	<	k * cellz );
1224	<	done = ( current_mol >= tot_nmol );
1225	<
1226	<	if( !done && n_per_extra > 1 ){
1227	<	makeElement( i * cellx + 0.5 * cellx,
1228	<	j * celly + 0.5 * celly,
1229	<	k * cellz );
1230	<	done = ( current_mol >= tot_nmol );
1231	<	}
1232	<
1233	<	if( !done && n_per_extra > 2){
1234	<	makeElement( i * cellx,
1235	<	j * celly + 0.5 * celly,
1236	<	k * cellz + 0.5 * cellz );
1237	<	done = ( current_mol >= tot_nmol );
1238	<	}
1239	<
1240	<	if( !done && n_per_extra > 3){
1241	<	makeElement( i * cellx + 0.5 * cellx,
1242	<	j * celly,
1243	<	k * cellz + 0.5 * cellz );
1244	<	done = ( current_mol >= tot_nmol );
1245	<	}
1246	<	}
1247	<	}
1248	<	}
1249	<	}
1250	<
1251	<
1252	<	for( i=0; i<simnfo->n_atoms; i++ ){
1253	<	simnfo->atoms[i]->set_vx( 0.0 );
1254	<	simnfo->atoms[i]->set_vy( 0.0 );
1255	<	simnfo->atoms[i]->set_vz( 0.0 );
1256	<	}
1257	<	}
1258	<
1259	<	void SimSetup::makeElement( double x, double y, double z ){
1260	<
1261	<	int k;
1262	<	AtomStamp* current_atom;
1263	<	DirectionalAtom* dAtom;
1264	<	double rotMat[3][3];
1265	<
1266	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1267	<
1268	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1269	<	if( !current_atom->havePosition() ){
1270	<	sprintf( painCave.errMsg,
1271	<	"SimSetup:initFromBass error.\n"
1272	<	"\tComponent %s, atom %s does not have a position specified.\n"
1273	<	"\tThe initialization routine is unable to give a start"
1274	<	" position.\n",
1275	<	comp_stamps[current_comp]->getID(),
1276	<	current_atom->getType() );
1277	<	painCave.isFatal = 1;
1278	<	simError();
1279	<	}
1280	<
1281	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1282	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1283	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1284	<
1285	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1286	<
1287	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1288	<
1289	<	rotMat[0][0] = 1.0;
1290	<	rotMat[0][1] = 0.0;
1291	<	rotMat[0][2] = 0.0;
1292	<
1293	<	rotMat[1][0] = 0.0;
1294	<	rotMat[1][1] = 1.0;
1295	<	rotMat[1][2] = 0.0;
1296	<
1297	<	rotMat[2][0] = 0.0;
1298	<	rotMat[2][1] = 0.0;
1299	<	rotMat[2][2] = 1.0;
1300	<
1301	<	dAtom->setA( rotMat );
1302	<	}
1303	<
1304	<	current_atom_ndx++;
1305	<	}
1306	<
1307	<	current_mol++;
1308	<	current_comp_mol++;
1309	<
1310	<	if( current_comp_mol >= components_nmol[current_comp] ){
1311	<
1312	<	current_comp_mol = 0;
1313	<	current_comp++;
1314	<	}
594	>	for (j = 0; j < molInfo.nBonds; j++){
595	>
596	>	//if both atoms are in the same rigid body, just skip it
597	>	currentBond = comp_stamps[stampID]->getBond(j);
598	>	if(!comp_stamps[stampID]->isBondInSameRigidBody(currentBond)){
599	>
600	>	tempI = currentBond->getA() + atomOffset;
601	>	if( comp_stamps[stampID]->isAtomInRigidBody(currentBond->getA(), whichRigidBody, consAtomIndex))
602	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
603	>	else
604	>	consElement1 = new ConstraintAtom(info[k].atoms[tempI]);
605	>
606	>	tempJ =  currentBond->getB() + atomOffset;
607	>	if(comp_stamps[stampID]->isAtomInRigidBody(currentBond->getB(), whichRigidBody, consAtomIndex))
608	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[whichRigidBody], consAtomIndex);
609	>	else
610	>	consElement2 = new ConstraintAtom(info[k].atoms[tempJ]);
611	>
612	>	consPair = new DistanceConstraintPair(consElement1, consElement2);
613	>	molInfo.myConstraintPairs.push_back(consPair);
614	>	}
615	>	}
616	>
617	>	//loop over rigid bodies, if two rigid bodies share same joint, creat a HingeConstraintPair
618	>	for (int rb1 = 0; rb1 < molInfo.nRigidBodies -1 ; rb1++){
619	>	for (int rb2 = rb1 + 1; rb2 < molInfo.nRigidBodies ; rb2++){
620	>
621	>	jointAtoms = comp_stamps[stampID]->getJointAtoms(rb1, rb2);
622	>
623	>	for(size_t m = 0; m < jointAtoms.size(); m++){
624	>	consElement1 = new ConstraintRigidBody(molInfo.myRigidBodies[rb1], jointAtoms[m].first);
625	>	consElement2 = new ConstraintRigidBody(molInfo.myRigidBodies[rb2], jointAtoms[m].second);
626	>
627	>	consPair = new JointConstraintPair(consElement1, consElement2);
628	>	molInfo.myConstraintPairs.push_back(consPair);
629	>	}
630	>
631	>	}
632	>	}
633	>
634	>	*/
635	>	// send the arrays off to the forceField for init.
636	>
637	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
638	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
639	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
640	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
641	>	theTorsions);
642	>
643	>	info[k].molecules[i].initialize(molInfo);
644	>
645	>
646	>	atomOffset += molInfo.nAtoms;
647	>	delete[] theBonds;
648	>	delete[] theBends;
649	>	delete[] theTorsions;
650	>	}
651	>	}
652	>
653	>	#ifdef IS_MPI
654	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
655	>	MPIcheckPoint();
656	>	#endif // is_mpi
657	>
658	>	}
659	>
660	>	void SimSetup::initFromBass(void){
661	>	int i, j, k;
662	>	int n_cells;
663	>	double cellx, celly, cellz;
664	>	double temp1, temp2, temp3;
665	>	int n_per_extra;
666	>	int n_extra;
667	>	int have_extra, done;
668	>
669	>	double vel[3];
670	>	vel[0] = 0.0;
671	>	vel[1] = 0.0;
672	>	vel[2] = 0.0;
673	>
674	>	temp1 = (double) tot_nmol / 4.0;
675	>	temp2 = pow(temp1, (1.0 / 3.0));
676	>	temp3 = ceil(temp2);
677	>
678	>	have_extra = 0;
679	>	if (temp2 < temp3){
680	>	// we have a non-complete lattice
681	>	have_extra = 1;
682	>
683	>	n_cells = (int) temp3 - 1;
684	>	cellx = info[0].boxL[0] / temp3;
685	>	celly = info[0].boxL[1] / temp3;
686	>	cellz = info[0].boxL[2] / temp3;
687	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
688	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
689	>	n_per_extra = (int) ceil(temp1);
690	>
691	>	if (n_per_extra > 4){
692	>	sprintf(painCave.errMsg,
693	>	"SimSetup error. There has been an error in constructing"
694	>	" the non-complete lattice.\n");
695	>	painCave.isFatal = 1;
696	>	simError();
697	>	}
698	>	}
699	>	else{
700	>	n_cells = (int) temp3;
701	>	cellx = info[0].boxL[0] / temp3;
702	>	celly = info[0].boxL[1] / temp3;
703	>	cellz = info[0].boxL[2] / temp3;
704	>	}
705	>
706	>	current_mol = 0;
707	>	current_comp_mol = 0;
708	>	current_comp = 0;
709	>	current_atom_ndx = 0;
710	>
711	>	for (i = 0; i < n_cells ; i++){
712	>	for (j = 0; j < n_cells; j++){
713	>	for (k = 0; k < n_cells; k++){
714	>	makeElement(i * cellx, j * celly, k * cellz);
715	>
716	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
717	>
718	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
719	>
720	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
721	>	}
722	>	}
723	>	}
724	>
725	>	if (have_extra){
726	>	done = 0;
727	>
728	>	int start_ndx;
729	>	for (i = 0; i < (n_cells + 1) && !done; i++){
730	>	for (j = 0; j < (n_cells + 1) && !done; j++){
731	>	if (i < n_cells){
732	>	if (j < n_cells){
733	>	start_ndx = n_cells;
734	>	}
735	>	else
736	>	start_ndx = 0;
737	>	}
738	>	else
739	>	start_ndx = 0;
740	>
741	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
742	>	makeElement(i * cellx, j * celly, k * cellz);
743	>	done = (current_mol >= tot_nmol);
744	>
745	>	if (!done && n_per_extra > 1){
746	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
747	>	k * cellz);
748	>	done = (current_mol >= tot_nmol);
749	>	}
750	>
751	>	if (!done && n_per_extra > 2){
752	>	makeElement(i * cellx, j * celly + 0.5 * celly,
753	>	k * cellz + 0.5 * cellz);
754	>	done = (current_mol >= tot_nmol);
755	>	}
756	>
757	>	if (!done && n_per_extra > 3){
758	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
759	>	k * cellz + 0.5 * cellz);
760	>	done = (current_mol >= tot_nmol);
761	>	}
762	>	}
763	>	}
764	>	}
765	>	}
766	>
767	>	for (i = 0; i < info[0].n_atoms; i++){
768	>	info[0].atoms[i]->setVel(vel);
769	>	}
770	>	}
771	>
772	>	void SimSetup::makeElement(double x, double y, double z){
773	>	int k;
774	>	AtomStamp* current_atom;
775	>	DirectionalAtom* dAtom;
776	>	double rotMat[3][3];
777	>	double pos[3];
778	>
779	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
780	>	current_atom = comp_stamps[current_comp]->getAtom(k);
781	>	if (!current_atom->havePosition()){
782	>	sprintf(painCave.errMsg,
783	>	"SimSetup:initFromBass error.\n"
784	>	"\tComponent %s, atom %s does not have a position specified.\n"
785	>	"\tThe initialization routine is unable to give a start"
786	>	" position.\n",
787	>	comp_stamps[current_comp]->getID(), current_atom->getType());
788	>	painCave.isFatal = 1;
789	>	simError();
790	>	}
791	>
792	>	pos[0] = x + current_atom->getPosX();
793	>	pos[1] = y + current_atom->getPosY();
794	>	pos[2] = z + current_atom->getPosZ();
795	>
796	>	info[0].atoms[current_atom_ndx]->setPos(pos);
797	>
798	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
799	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
800	>
801	>	rotMat[0][0] = 1.0;
802	>	rotMat[0][1] = 0.0;
803	>	rotMat[0][2] = 0.0;
804	>
805	>	rotMat[1][0] = 0.0;
806	>	rotMat[1][1] = 1.0;
807	>	rotMat[1][2] = 0.0;
808	>
809	>	rotMat[2][0] = 0.0;
810	>	rotMat[2][1] = 0.0;
811	>	rotMat[2][2] = 1.0;
812	>
813	>	dAtom->setA(rotMat);
814	>	}
815	>
816	>	current_atom_ndx++;
817	>	}
818	>
819	>	current_mol++;
820	>	current_comp_mol++;
821	>
822	>	if (current_comp_mol >= components_nmol[current_comp]){
823	>	current_comp_mol = 0;
824	>	current_comp++;
825	>	}
826	>	}
827	>
828	>
829	>	void SimSetup::gatherInfo(void){
830	>	int i;
831	>
832	>	ensembleCase = -1;
833	>	ffCase = -1;
834	>
835	>	// set the easy ones first
836	>
837	>	for (i = 0; i < nInfo; i++){
838	>	info[i].target_temp = globals->getTargetTemp();
839	>	info[i].dt = globals->getDt();
840	>	info[i].run_time = globals->getRunTime();
841	>	}
842	>	n_components = globals->getNComponents();
843	>
844	>
845	>	// get the forceField
846	>
847	>	strcpy(force_field, globals->getForceField());
848	>
849	>	if (!strcasecmp(force_field, "DUFF")){
850	>	ffCase = FF_DUFF;
851	>	}
852	>	else if (!strcasecmp(force_field, "LJ")){
853	>	ffCase = FF_LJ;
854	>	}
855	>	else if (!strcasecmp(force_field, "EAM")){
856	>	ffCase = FF_EAM;
857	>	}
858	>	else if (!strcasecmp(force_field, "WATER")){
859	>	ffCase = FF_H2O;
860	>	}
861	>	else{
862	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
863	>	force_field);
864	>	painCave.isFatal = 1;
865	>	simError();
866	>	}
867	>
868	>	// get the ensemble
869	>
870	>	strcpy(ensemble, globals->getEnsemble());
871	>
872	>	if (!strcasecmp(ensemble, "NVE")){
873	>	ensembleCase = NVE_ENS;
874	>	}
875	>	else if (!strcasecmp(ensemble, "NVT")){
876	>	ensembleCase = NVT_ENS;
877	>	}
878	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
879	>	ensembleCase = NPTi_ENS;
880	>	}
881	>	else if (!strcasecmp(ensemble, "NPTf")){
882	>	ensembleCase = NPTf_ENS;
883	>	}
884	>	else if (!strcasecmp(ensemble, "NPTxyz")){
885	>	ensembleCase = NPTxyz_ENS;
886	>	}
887	>	else{
888	>	sprintf(painCave.errMsg,
889	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
890	>	"\treverting to NVE for this simulation.\n",
891	>	ensemble);
892	>	painCave.isFatal = 0;
893	>	simError();
894	>	strcpy(ensemble, "NVE");
895	>	ensembleCase = NVE_ENS;
896	>	}
897	>
898	>	for (i = 0; i < nInfo; i++){
899	>	strcpy(info[i].ensemble, ensemble);
900	>
901	>	// get the mixing rule
902	>
903	>	strcpy(info[i].mixingRule, globals->getMixingRule());
904	>	info[i].usePBC = globals->getPBC();
905	>	}
906	>
907	>	// get the components and calculate the tot_nMol and indvidual n_mol
908	>
909	>	the_components = globals->getComponents();
910	>	components_nmol = new int[n_components];
911	>
912	>
913	>	if (!globals->haveNMol()){
914	>	// we don't have the total number of molecules, so we assume it is
915	>	// given in each component
916	>
917	>	tot_nmol = 0;
918	>	for (i = 0; i < n_components; i++){
919	>	if (!the_components[i]->haveNMol()){
920	>	// we have a problem
921	>	sprintf(painCave.errMsg,
922	>	"SimSetup Error. No global NMol or component NMol given.\n"
923	>	"\tCannot calculate the number of atoms.\n");
924	>	painCave.isFatal = 1;
925	>	simError();
926	>	}
927	>
928	>	tot_nmol += the_components[i]->getNMol();
929	>	components_nmol[i] = the_components[i]->getNMol();
930	>	}
931	>	}
932	>	else{
933	>	sprintf(painCave.errMsg,
934	>	"SimSetup error.\n"
935	>	"\tSorry, the ability to specify total"
936	>	" nMols and then give molfractions in the components\n"
937	>	"\tis not currently supported."
938	>	" Please give nMol in the components.\n");
939	>	painCave.isFatal = 1;
940	>	simError();
941	>	}
942	>
943	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
944	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
945	>	sprintf(painCave.errMsg,
946	>	"Sample time is not divisible by dt.\n"
947	>	"\tThis will result in samples that are not uniformly\n"
948	>	"\tdistributed in time.  If this is a problem, change\n"
949	>	"\tyour sampleTime variable.\n");
950	>	painCave.isFatal = 0;
951	>	simError();
952	>	}
953	>
954	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
955	>	sprintf(painCave.errMsg,
956	>	"Status time is not divisible by dt.\n"
957	>	"\tThis will result in status reports that are not uniformly\n"
958	>	"\tdistributed in time.  If this is a problem, change \n"
959	>	"\tyour statusTime variable.\n");
960	>	painCave.isFatal = 0;
961	>	simError();
962	>	}
963	>
964	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
965	>	sprintf(painCave.errMsg,
966	>	"Thermal time is not divisible by dt.\n"
967	>	"\tThis will result in thermalizations that are not uniformly\n"
968	>	"\tdistributed in time.  If this is a problem, change \n"
969	>	"\tyour thermalTime variable.\n");
970	>	painCave.isFatal = 0;
971	>	simError();
972	>	}
973	>
974	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
975	>	sprintf(painCave.errMsg,
976	>	"Reset time is not divisible by dt.\n"
977	>	"\tThis will result in integrator resets that are not uniformly\n"
978	>	"\tdistributed in time.  If this is a problem, change\n"
979	>	"\tyour resetTime variable.\n");
980	>	painCave.isFatal = 0;
981	>	simError();
982	>	}
983	>
984	>	// set the status, sample, and thermal kick times
985	>
986	>	for (i = 0; i < nInfo; i++){
987	>	if (globals->haveSampleTime()){
988	>	info[i].sampleTime = globals->getSampleTime();
989	>	info[i].statusTime = info[i].sampleTime;
990	>	}
991	>	else{
992	>	info[i].sampleTime = globals->getRunTime();
993	>	info[i].statusTime = info[i].sampleTime;
994	>	}
995	>
996	>	if (globals->haveStatusTime()){
997	>	info[i].statusTime = globals->getStatusTime();
998	>	}
999	>
1000	>	if (globals->haveThermalTime()){
1001	>	info[i].thermalTime = globals->getThermalTime();
1002	>	} else {
1003	>	info[i].thermalTime = globals->getRunTime();
1004	>	}
1005	>
1006	>	info[i].resetIntegrator = 0;
1007	>	if( globals->haveResetTime() ){
1008	>	info[i].resetTime = globals->getResetTime();
1009	>	info[i].resetIntegrator = 1;
1010	>	}
1011	>
1012	>	// check for the temperature set flag
1013	>
1014	>	if (globals->haveTempSet())
1015	>	info[i].setTemp = globals->getTempSet();
1016	>
1017	>	// check for the extended State init
1018	>
1019	>	info[i].useInitXSstate = globals->getUseInitXSstate();
1020	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
1021	>
1022	>	// check for thermodynamic integration
1023	>	if (globals->getUseSolidThermInt() && !globals->getUseLiquidThermInt()) {
1024	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1025	>	info[i].useSolidThermInt = globals->getUseSolidThermInt();
1026	>	info[i].thermIntLambda = globals->getThermIntLambda();
1027	>	info[i].thermIntK = globals->getThermIntK();
1028	>
1029	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
1030	>	info[i].restraint = myRestraint;
1031	>	}
1032	>	else {
1033	>	sprintf(painCave.errMsg,
1034	>	"SimSetup Error:\n"
1035	>	"\tKeyword useSolidThermInt was set to 'true' but\n"
1036	>	"\tthermodynamicIntegrationLambda (and/or\n"
1037	>	"\tthermodynamicIntegrationK) was not specified.\n"
1038	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1039	>	painCave.isFatal = 1;
1040	>	simError();
1041	>	}
1042	>	}
1043	>	else if(globals->getUseLiquidThermInt()) {
1044	>	if (globals->getUseSolidThermInt()) {
1045	>	sprintf( painCave.errMsg,
1046	>	"SimSetup Warning: It appears that you have both solid and\n"
1047	>	"\tliquid thermodynamic integration activated in your .bass\n"
1048	>	"\tfile. To avoid confusion, specify only one technique in\n"
1049	>	"\tyour .bass file. Liquid-state thermodynamic integration\n"
1050	>	"\twill be assumed for the current simulation. If this is not\n"
1051	>	"\twhat you desire, set useSolidThermInt to 'true' and\n"
1052	>	"\tuseLiquidThermInt to 'false' in your .bass file.\n");
1053	>	painCave.isFatal = 0;
1054	>	simError();
1055	>	}
1056	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1057	>	info[i].useLiquidThermInt = globals->getUseLiquidThermInt();
1058	>	info[i].thermIntLambda = globals->getThermIntLambda();
1059	>	info[i].thermIntK = globals->getThermIntK();
1060	>	}
1061	>	else {
1062	>	sprintf(painCave.errMsg,
1063	>	"SimSetup Error:\n"
1064	>	"\tKeyword useLiquidThermInt was set to 'true' but\n"
1065	>	"\tthermodynamicIntegrationLambda (and/or\n"
1066	>	"\tthermodynamicIntegrationK) was not specified.\n"
1067	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
1068	>	painCave.isFatal = 1;
1069	>	simError();
1070	>	}
1071	>	}
1072	>	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
1073	>	sprintf(painCave.errMsg,
1074	>	"SimSetup Warning: If you want to use Thermodynamic\n"
1075	>	"\tIntegration, set useSolidThermInt or useLiquidThermInt to\n"
1076	>	"\t'true' in your .bass file.  These keywords are set to\n"
1077	>	"\t'false' by default, so your lambda and/or k values are\n"
1078	>	"\tbeing ignored.\n");
1079	>	painCave.isFatal = 0;
1080	>	simError();
1081	>	}
1082	>	}
1083	>
1084	>	//setup seed for random number generator
1085	>	int seedValue;
1086	>
1087	>	if (globals->haveSeed()){
1088	>	seedValue = globals->getSeed();
1089	>
1090	>	if(seedValue / 1E9 == 0){
1091	>	sprintf(painCave.errMsg,
1092	>	"Seed for sprng library should contain at least 9 digits\n"
1093	>	"OOPSE will generate a seed for user\n");
1094	>	painCave.isFatal = 0;
1095	>	simError();
1096	>
1097	>	//using seed generated by system instead of invalid seed set by user
1098	>	#ifndef IS_MPI
1099	>	seedValue = make_sprng_seed();
1100	>	#else
1101	>	if (worldRank == 0){
1102	>	seedValue = make_sprng_seed();
1103	>	}
1104	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1105	>	#endif
1106	>	}
1107	>	}//end of if branch of globals->haveSeed()
1108	>	else{
1109	>
1110	>	#ifndef IS_MPI
1111	>	seedValue = make_sprng_seed();
1112	>	#else
1113	>	if (worldRank == 0){
1114	>	seedValue = make_sprng_seed();
1115	>	}
1116	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1117	>	#endif
1118	>	}//end of globals->haveSeed()
1119	>
1120	>	for (int i = 0; i < nInfo; i++){
1121	>	info[i].setSeed(seedValue);
1122	>	}
1123	>
1124	>	#ifdef IS_MPI
1125	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1126	>	MPIcheckPoint();
1127	>	#endif // is_mpi
1128	>	}
1129	>
1130	>
1131	>	void SimSetup::finalInfoCheck(void){
1132	>	int index;
1133	>	int usesDipoles;
1134	>	int usesCharges;
1135	>	int i;
1136	>
1137	>	for (i = 0; i < nInfo; i++){
1138	>	// check electrostatic parameters
1139	>
1140	>	index = 0;
1141	>	usesDipoles = 0;
1142	>	while ((index < info[i].n_atoms) && !usesDipoles){
1143	>	usesDipoles = (info[i].atoms[index])->hasDipole();
1144	>	index++;
1145	>	}
1146	>	index = 0;
1147	>	usesCharges = 0;
1148	>	while ((index < info[i].n_atoms) && !usesCharges){
1149	>	usesCharges= (info[i].atoms[index])->hasCharge();
1150	>	index++;
1151	>	}
1152	>	#ifdef IS_MPI
1153	>	int myUse = usesDipoles;
1154	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1155	>	#endif //is_mpi
1156	>
1157	>	double theRcut, theRsw;
1158	>
1159	>	if (globals->haveRcut()) {
1160	>	theRcut = globals->getRcut();
1161	>
1162	>	if (globals->haveRsw())
1163	>	theRsw = globals->getRsw();
1164	>	else
1165	>	theRsw = theRcut;
1166	>
1167	>	info[i].setDefaultRcut(theRcut, theRsw);
1168	>
1169	>	} else {
1170	>
1171	>	the_ff->calcRcut();
1172	>	theRcut = info[i].getRcut();
1173	>
1174	>	if (globals->haveRsw())
1175	>	theRsw = globals->getRsw();
1176	>	else
1177	>	theRsw = theRcut;
1178	>
1179	>	info[i].setDefaultRcut(theRcut, theRsw);
1180	>	}
1181	>
1182	>	if (globals->getUseRF()){
1183	>	info[i].useReactionField = 1;
1184	>
1185	>	if (!globals->haveRcut()){
1186	>	sprintf(painCave.errMsg,
1187	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1188	>	"\tOOPSE will use a default value of 15.0 angstroms"
1189	>	"\tfor the cutoffRadius.\n");
1190	>	painCave.isFatal = 0;
1191	>	simError();
1192	>	theRcut = 15.0;
1193	>	}
1194	>	else{
1195	>	theRcut = globals->getRcut();
1196	>	}
1197	>
1198	>	if (!globals->haveRsw()){
1199	>	sprintf(painCave.errMsg,
1200	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1201	>	"\tOOPSE will use a default value of\n"
1202	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1203	>	painCave.isFatal = 0;
1204	>	simError();
1205	>	theRsw = 0.95 * theRcut;
1206	>	}
1207	>	else{
1208	>	theRsw = globals->getRsw();
1209	>	}
1210	>
1211	>	info[i].setDefaultRcut(theRcut, theRsw);
1212	>
1213	>	if (!globals->haveDielectric()){
1214	>	sprintf(painCave.errMsg,
1215	>	"SimSetup Error: No Dielectric constant was set.\n"
1216	>	"\tYou are trying to use Reaction Field without"
1217	>	"\tsetting a dielectric constant!\n");
1218	>	painCave.isFatal = 1;
1219	>	simError();
1220	>	}
1221	>	info[i].dielectric = globals->getDielectric();
1222	>	}
1223	>	else{
1224	>	if (usesDipoles || usesCharges){
1225	>
1226	>	if (!globals->haveRcut()){
1227	>	sprintf(painCave.errMsg,
1228	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1229	>	"\tOOPSE will use a default value of 15.0 angstroms"
1230	>	"\tfor the cutoffRadius.\n");
1231	>	painCave.isFatal = 0;
1232	>	simError();
1233	>	theRcut = 15.0;
1234	>	}
1235	>	else{
1236	>	theRcut = globals->getRcut();
1237	>	}
1238	>
1239	>	if (!globals->haveRsw()){
1240	>	sprintf(painCave.errMsg,
1241	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1242	>	"\tOOPSE will use a default value of\n"
1243	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1244	>	painCave.isFatal = 0;
1245	>	simError();
1246	>	theRsw = 0.95 * theRcut;
1247	>	}
1248	>	else{
1249	>	theRsw = globals->getRsw();
1250	>	}
1251	>
1252	>	info[i].setDefaultRcut(theRcut, theRsw);
1253	>
1254	>	}
1255	>	}
1256	>	}
1257	>	#ifdef IS_MPI
1258	>	strcpy(checkPointMsg, "post processing checks out");
1259	>	MPIcheckPoint();
1260	>	#endif // is_mpi
1261	>
1262	>	// clean up the forcefield
1263	>	the_ff->cleanMe();
1264	>	}
1265	>
1266	>	void SimSetup::initSystemCoords(void){
1267	>	int i;
1268	>
1269	>	char* inName;
1270	>
1271	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1272	>
1273	>	for (i = 0; i < info[0].n_atoms; i++)
1274	>	info[0].atoms[i]->setCoords();
1275	>
1276	>	if (globals->haveInitialConfig()){
1277	>	InitializeFromFile* fileInit;
1278	>	#ifdef IS_MPI // is_mpi
1279	>	if (worldRank == 0){
1280	>	#endif //is_mpi
1281	>	inName = globals->getInitialConfig();
1282	>	fileInit = new InitializeFromFile(inName);
1283	>	#ifdef IS_MPI
1284	>	}
1285	>	else
1286	>	fileInit = new InitializeFromFile(NULL);
1287	>	#endif
1288	>	fileInit->readInit(info); // default velocities on
1289	>
1290	>	delete fileInit;
1291	>	}
1292	>	else{
1293	>
1294	>	// no init from bass
1295	>
1296	>	sprintf(painCave.errMsg,
1297	>	"Cannot intialize a simulation without an initial configuration file.\n");
1298	>	painCave.isFatal = 1;;
1299	>	simError();
1300	>
1301	>	}
1302	>
1303	>	#ifdef IS_MPI
1304	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1305	>	MPIcheckPoint();
1306	>	#endif // is_mpi
1307	>	}
1308	>
1309	>
1310	>	void SimSetup::makeOutNames(void){
1311	>	int k;
1312	>
1313	>
1314	>	for (k = 0; k < nInfo; k++){
1315	>	#ifdef IS_MPI
1316	>	if (worldRank == 0){
1317	>	#endif // is_mpi
1318	>
1319	>	if (globals->haveFinalConfig()){
1320	>	strcpy(info[k].finalName, globals->getFinalConfig());
1321	>	}
1322	>	else{
1323	>	strcpy(info[k].finalName, inFileName);
1324	>	char* endTest;
1325	>	int nameLength = strlen(info[k].finalName);
1326	>	endTest = &(info[k].finalName[nameLength - 5]);
1327	>	if (!strcmp(endTest, ".bass")){
1328	>	strcpy(endTest, ".eor");
1329	>	}
1330	>	else if (!strcmp(endTest, ".BASS")){
1331	>	strcpy(endTest, ".eor");
1332	>	}
1333	>	else{
1334	>	endTest = &(info[k].finalName[nameLength - 4]);
1335	>	if (!strcmp(endTest, ".bss")){
1336	>	strcpy(endTest, ".eor");
1337	>	}
1338	>	else if (!strcmp(endTest, ".mdl")){
1339	>	strcpy(endTest, ".eor");
1340	>	}
1341	>	else{
1342	>	strcat(info[k].finalName, ".eor");
1343	>	}
1344	>	}
1345	>	}
1346	>
1347	>	// make the sample and status out names
1348	>
1349	>	strcpy(info[k].sampleName, inFileName);
1350	>	char* endTest;
1351	>	int nameLength = strlen(info[k].sampleName);
1352	>	endTest = &(info[k].sampleName[nameLength - 5]);
1353	>	if (!strcmp(endTest, ".bass")){
1354	>	strcpy(endTest, ".dump");
1355	>	}
1356	>	else if (!strcmp(endTest, ".BASS")){
1357	>	strcpy(endTest, ".dump");
1358	>	}
1359	>	else{
1360	>	endTest = &(info[k].sampleName[nameLength - 4]);
1361	>	if (!strcmp(endTest, ".bss")){
1362	>	strcpy(endTest, ".dump");
1363	>	}
1364	>	else if (!strcmp(endTest, ".mdl")){
1365	>	strcpy(endTest, ".dump");
1366	>	}
1367	>	else{
1368	>	strcat(info[k].sampleName, ".dump");
1369	>	}
1370	>	}
1371	>
1372	>	strcpy(info[k].statusName, inFileName);
1373	>	nameLength = strlen(info[k].statusName);
1374	>	endTest = &(info[k].statusName[nameLength - 5]);
1375	>	if (!strcmp(endTest, ".bass")){
1376	>	strcpy(endTest, ".stat");
1377	>	}
1378	>	else if (!strcmp(endTest, ".BASS")){
1379	>	strcpy(endTest, ".stat");
1380	>	}
1381	>	else{
1382	>	endTest = &(info[k].statusName[nameLength - 4]);
1383	>	if (!strcmp(endTest, ".bss")){
1384	>	strcpy(endTest, ".stat");
1385	>	}
1386	>	else if (!strcmp(endTest, ".mdl")){
1387	>	strcpy(endTest, ".stat");
1388	>	}
1389	>	else{
1390	>	strcat(info[k].statusName, ".stat");
1391	>	}
1392	>	}
1393	>
1394	>	strcpy(info[k].rawPotName, inFileName);
1395	>	nameLength = strlen(info[k].rawPotName);
1396	>	endTest = &(info[k].rawPotName[nameLength - 5]);
1397	>	if (!strcmp(endTest, ".bass")){
1398	>	strcpy(endTest, ".raw");
1399	>	}
1400	>	else if (!strcmp(endTest, ".BASS")){
1401	>	strcpy(endTest, ".raw");
1402	>	}
1403	>	else{
1404	>	endTest = &(info[k].rawPotName[nameLength - 4]);
1405	>	if (!strcmp(endTest, ".bss")){
1406	>	strcpy(endTest, ".raw");
1407	>	}
1408	>	else if (!strcmp(endTest, ".mdl")){
1409	>	strcpy(endTest, ".raw");
1410	>	}
1411	>	else{
1412	>	strcat(info[k].rawPotName, ".raw");
1413	>	}
1414	>	}
1415	>
1416	>	#ifdef IS_MPI
1417	>
1418	>	}
1419	>	#endif // is_mpi
1420	>	}
1421	>	}
1422	>
1423	>
1424	>	void SimSetup::sysObjectsCreation(void){
1425	>	int i, k;
1426	>
1427	>	// create the forceField
1428	>
1429	>	createFF();
1430	>
1431	>	// extract componentList
1432	>
1433	>	compList();
1434	>
1435	>	// calc the number of atoms, bond, bends, and torsions
1436	>
1437	>	calcSysValues();
1438	>
1439	>	#ifdef IS_MPI
1440	>	// divide the molecules among the processors
1441	>
1442	>	mpiMolDivide();
1443	>	#endif //is_mpi
1444	>
1445	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1446	>
1447	>	makeSysArrays();
1448	>
1449	>	// make and initialize the molecules (all but atomic coordinates)
1450	>
1451	>	makeMolecules();
1452	>
1453	>	for (k = 0; k < nInfo; k++){
1454	>	info[k].identArray = new int[info[k].n_atoms];
1455	>	for (i = 0; i < info[k].n_atoms; i++){
1456	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1457	>	}
1458	>	}
1459	>	}
1460	>
1461	>
1462	>	void SimSetup::createFF(void){
1463	>	switch (ffCase){
1464	>	case FF_DUFF:
1465	>	the_ff = new DUFF();
1466	>	break;
1467	>
1468	>	case FF_LJ:
1469	>	the_ff = new LJFF();
1470	>	break;
1471	>
1472	>	case FF_EAM:
1473	>	the_ff = new EAM_FF();
1474	>	break;
1475	>
1476	>	case FF_H2O:
1477	>	the_ff = new WATER();
1478	>	break;
1479	>
1480	>	default:
1481	>	sprintf(painCave.errMsg,
1482	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1483	>	painCave.isFatal = 1;
1484	>	simError();
1485	>	}
1486	>
1487	>	#ifdef IS_MPI
1488	>	strcpy(checkPointMsg, "ForceField creation successful");
1489	>	MPIcheckPoint();
1490	>	#endif // is_mpi
1491	>	}
1492	>
1493	>
1494	>	void SimSetup::compList(void){
1495	>	int i;
1496	>	char* id;
1497	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1498	>	LinkedMolStamp* currentStamp = NULL;
1499	>	comp_stamps = new MoleculeStamp * [n_components];
1500	>	bool haveCutoffGroups;
1501	>
1502	>	haveCutoffGroups = false;
1503	>
1504	>	// make an array of molecule stamps that match the components used.
1505	>	// also extract the used stamps out into a separate linked list
1506	>
1507	>	for (i = 0; i < nInfo; i++){
1508	>	info[i].nComponents = n_components;
1509	>	info[i].componentsNmol = components_nmol;
1510	>	info[i].compStamps = comp_stamps;
1511	>	info[i].headStamp = headStamp;
1512	>	}
1513	>
1514	>
1515	>	for (i = 0; i < n_components; i++){
1516	>	id = the_components[i]->getType();
1517	>	comp_stamps[i] = NULL;
1518	>
1519	>	// check to make sure the component isn't already in the list
1520	>
1521	>	comp_stamps[i] = headStamp->match(id);
1522	>	if (comp_stamps[i] == NULL){
1523	>	// extract the component from the list;
1524	>
1525	>	currentStamp = stamps->extractMolStamp(id);
1526	>	if (currentStamp == NULL){
1527	>	sprintf(painCave.errMsg,
1528	>	"SimSetup error: Component \"%s\" was not found in the "
1529	>	"list of declared molecules\n",
1530	>	id);
1531	>	painCave.isFatal = 1;
1532	>	simError();
1533	>	}
1534	>
1535	>	headStamp->add(currentStamp);
1536	>	comp_stamps[i] = headStamp->match(id);
1537	>	}
1538	>
1539	>	if(comp_stamps[i]->getNCutoffGroups() > 0)
1540	>	haveCutoffGroups = true;
1541	>	}
1542	>
1543	>	for (i = 0; i < nInfo; i++)
1544	>	info[i].haveCutoffGroups = haveCutoffGroups;
1545	>
1546	>	#ifdef IS_MPI
1547	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1548	>	MPIcheckPoint();
1549	>	#endif // is_mpi
1550	>	}
1551	>
1552	>	void SimSetup::calcSysValues(void){
1553	>	int i, j;
1554	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1555	>
1556	>	int* molMembershipArray;
1557	>	CutoffGroupStamp* cg;
1558	>
1559	>	tot_atoms = 0;
1560	>	tot_bonds = 0;
1561	>	tot_bends = 0;
1562	>	tot_torsions = 0;
1563	>	tot_rigid = 0;
1564	>	tot_groups = 0;
1565	>	for (i = 0; i < n_components; i++){
1566	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1567	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1568	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1569	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1570	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1571	>
1572	>	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1573	>	atomsingroups = 0;
1574	>	for (j=0; j < ncutgroups; j++) {
1575	>	cg = comp_stamps[i]->getCutoffGroup(j);
1576	>	atomsingroups += cg->getNMembers();
1577	>	}
1578	>	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1579	>	tot_groups += components_nmol[i] * ngroupsinstamp;
1580	>	}
1581	>
1582	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1583	>	molMembershipArray = new int[tot_atoms];
1584	>
1585	>	for (i = 0; i < nInfo; i++){
1586	>	info[i].n_atoms = tot_atoms;
1587	>	info[i].n_bonds = tot_bonds;
1588	>	info[i].n_bends = tot_bends;
1589	>	info[i].n_torsions = tot_torsions;
1590	>	info[i].n_SRI = tot_SRI;
1591	>	info[i].n_mol = tot_nmol;
1592	>	info[i].ngroup = tot_groups;
1593	>	info[i].molMembershipArray = molMembershipArray;
1594	>	}
1595	>	}
1596	>
1597	>	#ifdef IS_MPI
1598	>
1599	>	void SimSetup::mpiMolDivide(void){
1600	>	int i, j, k;
1601	>	int localMol, allMol;
1602	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1603	>	int local_rigid, local_groups;
1604	>	vector<int> globalMolIndex;
1605	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1606	>	CutoffGroupStamp* cg;
1607	>
1608	>	mpiSim = new mpiSimulation(info);
1609	>
1610	>	mpiSim->divideLabor();
1611	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1612	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1613	>
1614	>	// set up the local variables
1615	>
1616	>	mol2proc = mpiSim->getMolToProcMap();
1617	>	molCompType = mpiSim->getMolComponentType();
1618	>
1619	>	allMol = 0;
1620	>	localMol = 0;
1621	>	local_atoms = 0;
1622	>	local_bonds = 0;
1623	>	local_bends = 0;
1624	>	local_torsions = 0;
1625	>	local_rigid = 0;
1626	>	local_groups = 0;
1627	>	globalAtomCounter = 0;
1628	>
1629	>	for (i = 0; i < n_components; i++){
1630	>	for (j = 0; j < components_nmol[i]; j++){
1631	>	if (mol2proc[allMol] == worldRank){
1632	>	local_atoms += comp_stamps[i]->getNAtoms();
1633	>	local_bonds += comp_stamps[i]->getNBonds();
1634	>	local_bends += comp_stamps[i]->getNBends();
1635	>	local_torsions += comp_stamps[i]->getNTorsions();
1636	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1637	>
1638	>	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1639	>	atomsingroups = 0;
1640	>	for (k=0; k < ncutgroups; k++) {
1641	>	cg = comp_stamps[i]->getCutoffGroup(k);
1642	>	atomsingroups += cg->getNMembers();
1643	>	}
1644	>	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1645	>	ncutgroups;
1646	>	local_groups += ngroupsinstamp;
1647	>
1648	>	localMol++;
1649	>	}
1650	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1651	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1652	>	globalAtomCounter++;
1653	>	}
1654	>
1655	>	allMol++;
1656	>	}
1657	>	}
1658	>	local_SRI = local_bonds + local_bends + local_torsions;
1659	>
1660	>	info[0].n_atoms = mpiSim->getNAtomsLocal();
1661	>
1662	>	if (local_atoms != info[0].n_atoms){
1663	>	sprintf(painCave.errMsg,
1664	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1665	>	"\tlocalAtom (%d) are not equal.\n",
1666	>	info[0].n_atoms, local_atoms);
1667	>	painCave.isFatal = 1;
1668	>	simError();
1669	>	}
1670	>
1671	>	info[0].ngroup = mpiSim->getNGroupsLocal();
1672	>	if (local_groups != info[0].ngroup){
1673	>	sprintf(painCave.errMsg,
1674	>	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1675	>	"\tlocalGroups (%d) are not equal.\n",
1676	>	info[0].ngroup, local_groups);
1677	>	painCave.isFatal = 1;
1678	>	simError();
1679	>	}
1680	>
1681	>	info[0].n_bonds = local_bonds;
1682	>	info[0].n_bends = local_bends;
1683	>	info[0].n_torsions = local_torsions;
1684	>	info[0].n_SRI = local_SRI;
1685	>	info[0].n_mol = localMol;
1686	>
1687	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1688	>	MPIcheckPoint();
1689	>	}
1690	>
1691	>	#endif // is_mpi
1692	>
1693	>
1694	>	void SimSetup::makeSysArrays(void){
1695	>
1696	>	#ifndef IS_MPI
1697	>	int k, j;
1698	>	#endif // is_mpi
1699	>	int i, l;
1700	>
1701	>	Atom** the_atoms;
1702	>	Molecule* the_molecules;
1703	>
1704	>	for (l = 0; l < nInfo; l++){
1705	>	// create the atom and short range interaction arrays
1706	>
1707	>	the_atoms = new Atom * [info[l].n_atoms];
1708	>	the_molecules = new Molecule[info[l].n_mol];
1709	>	int molIndex;
1710	>
1711	>	// initialize the molecule's stampID's
1712	>
1713	>	#ifdef IS_MPI
1714	>
1715	>
1716	>	molIndex = 0;
1717	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1718	>	if (mol2proc[i] == worldRank){
1719	>	the_molecules[molIndex].setStampID(molCompType[i]);
1720	>	the_molecules[molIndex].setMyIndex(molIndex);
1721	>	the_molecules[molIndex].setGlobalIndex(i);
1722	>	molIndex++;
1723	>	}
1724	>	}
1725	>
1726	>	#else // is_mpi
1727	>
1728	>	molIndex = 0;
1729	>	globalAtomCounter = 0;
1730	>	for (i = 0; i < n_components; i++){
1731	>	for (j = 0; j < components_nmol[i]; j++){
1732	>	the_molecules[molIndex].setStampID(i);
1733	>	the_molecules[molIndex].setMyIndex(molIndex);
1734	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1735	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1736	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1737	>	globalAtomCounter++;
1738	>	}
1739	>	molIndex++;
1740	>	}
1741	>	}
1742	>
1743	>
1744	>	#endif // is_mpi
1745	>
1746	>	info[l].globalExcludes = new int;
1747	>	info[l].globalExcludes[0] = 0;
1748	>
1749	>	// set the arrays into the SimInfo object
1750	>
1751	>	info[l].atoms = the_atoms;
1752	>	info[l].molecules = the_molecules;
1753	>	info[l].nGlobalExcludes = 0;
1754	>
1755	>	the_ff->setSimInfo(info);
1756	>	}
1757	>	}
1758	>
1759	>	void SimSetup::makeIntegrator(void){
1760	>	int k;
1761	>
1762	>	NVE<RealIntegrator>* myNVE = NULL;
1763	>	NVT<RealIntegrator>* myNVT = NULL;
1764	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1765	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1766	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1767	>
1768	>	for (k = 0; k < nInfo; k++){
1769	>	switch (ensembleCase){
1770	>	case NVE_ENS:
1771	>	if (globals->haveZconstraints()){
1772	>	setupZConstraint(info[k]);
1773	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1774	>	}
1775	>	else{
1776	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1777	>	}
1778	>
1779	>	info->the_integrator = myNVE;
1780	>	break;
1781	>
1782	>	case NVT_ENS:
1783	>	if (globals->haveZconstraints()){
1784	>	setupZConstraint(info[k]);
1785	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1786	>	}
1787	>	else
1788	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1789	>
1790	>	myNVT->setTargetTemp(globals->getTargetTemp());
1791	>
1792	>	if (globals->haveTauThermostat())
1793	>	myNVT->setTauThermostat(globals->getTauThermostat());
1794	>	else{
1795	>	sprintf(painCave.errMsg,
1796	>	"SimSetup error: If you use the NVT\n"
1797	>	"\tensemble, you must set tauThermostat.\n");
1798	>	painCave.isFatal = 1;
1799	>	simError();
1800	>	}
1801	>
1802	>	info->the_integrator = myNVT;
1803	>	break;
1804	>
1805	>	case NPTi_ENS:
1806	>	if (globals->haveZconstraints()){
1807	>	setupZConstraint(info[k]);
1808	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1809	>	}
1810	>	else
1811	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1812	>
1813	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1814	>
1815	>	if (globals->haveTargetPressure())
1816	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1817	>	else{
1818	>	sprintf(painCave.errMsg,
1819	>	"SimSetup error: If you use a constant pressure\n"
1820	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1821	>	painCave.isFatal = 1;
1822	>	simError();
1823	>	}
1824	>
1825	>	if (globals->haveTauThermostat())
1826	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1827	>	else{
1828	>	sprintf(painCave.errMsg,
1829	>	"SimSetup error: If you use an NPT\n"
1830	>	"\tensemble, you must set tauThermostat.\n");
1831	>	painCave.isFatal = 1;
1832	>	simError();
1833	>	}
1834	>
1835	>	if (globals->haveTauBarostat())
1836	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1837	>	else{
1838	>	sprintf(painCave.errMsg,
1839	>	"SimSetup error: If you use an NPT\n"
1840	>	"\tensemble, you must set tauBarostat.\n");
1841	>	painCave.isFatal = 1;
1842	>	simError();
1843	>	}
1844	>
1845	>	info->the_integrator = myNPTi;
1846	>	break;
1847	>
1848	>	case NPTf_ENS:
1849	>	if (globals->haveZconstraints()){
1850	>	setupZConstraint(info[k]);
1851	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1852	>	}
1853	>	else
1854	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1855	>
1856	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1857	>
1858	>	if (globals->haveTargetPressure())
1859	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1860	>	else{
1861	>	sprintf(painCave.errMsg,
1862	>	"SimSetup error: If you use a constant pressure\n"
1863	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1864	>	painCave.isFatal = 1;
1865	>	simError();
1866	>	}
1867	>
1868	>	if (globals->haveTauThermostat())
1869	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1870	>
1871	>	else{
1872	>	sprintf(painCave.errMsg,
1873	>	"SimSetup error: If you use an NPT\n"
1874	>	"\tensemble, you must set tauThermostat.\n");
1875	>	painCave.isFatal = 1;
1876	>	simError();
1877	>	}
1878	>
1879	>	if (globals->haveTauBarostat())
1880	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1881	>
1882	>	else{
1883	>	sprintf(painCave.errMsg,
1884	>	"SimSetup error: If you use an NPT\n"
1885	>	"\tensemble, you must set tauBarostat.\n");
1886	>	painCave.isFatal = 1;
1887	>	simError();
1888	>	}
1889	>
1890	>	info->the_integrator = myNPTf;
1891	>	break;
1892	>
1893	>	case NPTxyz_ENS:
1894	>	if (globals->haveZconstraints()){
1895	>	setupZConstraint(info[k]);
1896	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1897	>	}
1898	>	else
1899	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1900	>
1901	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1902	>
1903	>	if (globals->haveTargetPressure())
1904	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1905	>	else{
1906	>	sprintf(painCave.errMsg,
1907	>	"SimSetup error: If you use a constant pressure\n"
1908	>	"\tensemble, you must set targetPressure in the BASS file.\n");
1909	>	painCave.isFatal = 1;
1910	>	simError();
1911	>	}
1912	>
1913	>	if (globals->haveTauThermostat())
1914	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1915	>	else{
1916	>	sprintf(painCave.errMsg,
1917	>	"SimSetup error: If you use an NPT\n"
1918	>	"\tensemble, you must set tauThermostat.\n");
1919	>	painCave.isFatal = 1;
1920	>	simError();
1921	>	}
1922	>
1923	>	if (globals->haveTauBarostat())
1924	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1925	>	else{
1926	>	sprintf(painCave.errMsg,
1927	>	"SimSetup error: If you use an NPT\n"
1928	>	"\tensemble, you must set tauBarostat.\n");
1929	>	painCave.isFatal = 1;
1930	>	simError();
1931	>	}
1932	>
1933	>	info->the_integrator = myNPTxyz;
1934	>	break;
1935	>
1936	>	default:
1937	>	sprintf(painCave.errMsg,
1938	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1939	>	painCave.isFatal = 1;
1940	>	simError();
1941	>	}
1942	>	}
1943	>	}
1944	>
1945	>	void SimSetup::initFortran(void){
1946	>	info[0].refreshSim();
1947	>
1948	>	if (!strcmp(info[0].mixingRule, "standard")){
1949	>	the_ff->initForceField(LB_MIXING_RULE);
1950	>	}
1951	>	else if (!strcmp(info[0].mixingRule, "explicit")){
1952	>	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1953	>	}
1954	>	else{
1955	>	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1956	>	info[0].mixingRule);
1957	>	painCave.isFatal = 1;
1958	>	simError();
1959	>	}
1960	>
1961	>
1962	>	#ifdef IS_MPI
1963	>	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1964	>	MPIcheckPoint();
1965	>	#endif // is_mpi
1966	>	}
1967	>
1968	>	void SimSetup::setupZConstraint(SimInfo& theInfo){
1969	>	int nZConstraints;
1970	>	ZconStamp** zconStamp;
1971	>
1972	>	if (globals->haveZconstraintTime()){
1973	>	//add sample time of z-constraint  into SimInfo's property list
1974	>	DoubleData* zconsTimeProp = new DoubleData();
1975	>	zconsTimeProp->setID(ZCONSTIME_ID);
1976	>	zconsTimeProp->setData(globals->getZconsTime());
1977	>	theInfo.addProperty(zconsTimeProp);
1978	>	}
1979	>	else{
1980	>	sprintf(painCave.errMsg,
1981	>	"ZConstraint error: If you use a ZConstraint,\n"
1982	>	"\tyou must set zconsTime.\n");
1983	>	painCave.isFatal = 1;
1984	>	simError();
1985	>	}
1986	>
1987	>	//push zconsTol into siminfo, if user does not specify
1988	>	//value for zconsTol, a default value will be used
1989	>	DoubleData* zconsTol = new DoubleData();
1990	>	zconsTol->setID(ZCONSTOL_ID);
1991	>	if (globals->haveZconsTol()){
1992	>	zconsTol->setData(globals->getZconsTol());
1993	>	}
1994	>	else{
1995	>	double defaultZConsTol = 0.01;
1996	>	sprintf(painCave.errMsg,
1997	>	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1998	>	"\tOOPSE will use a default value of %f.\n"
1999	>	"\tTo set the tolerance, use the zconsTol variable.\n",
2000	>	defaultZConsTol);
2001	>	painCave.isFatal = 0;
2002	>	simError();
2003	>
2004	>	zconsTol->setData(defaultZConsTol);
2005	>	}
2006	>	theInfo.addProperty(zconsTol);
2007	>
2008	>	//set Force Subtraction Policy
2009	>	StringData* zconsForcePolicy = new StringData();
2010	>	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
2011	>
2012	>	if (globals->haveZconsForcePolicy()){
2013	>	zconsForcePolicy->setData(globals->getZconsForcePolicy());
2014	>	}
2015	>	else{
2016	>	sprintf(painCave.errMsg,
2017	>	"ZConstraint Warning: No force subtraction policy was set.\n"
2018	>	"\tOOPSE will use PolicyByMass.\n"
2019	>	"\tTo set the policy, use the zconsForcePolicy variable.\n");
2020	>	painCave.isFatal = 0;
2021	>	simError();
2022	>	zconsForcePolicy->setData("BYMASS");
2023	>	}
2024	>
2025	>	theInfo.addProperty(zconsForcePolicy);
2026	>
2027	>	//set zcons gap
2028	>	DoubleData* zconsGap = new DoubleData();
2029	>	zconsGap->setID(ZCONSGAP_ID);
2030	>
2031	>	if (globals->haveZConsGap()){
2032	>	zconsGap->setData(globals->getZconsGap());
2033	>	theInfo.addProperty(zconsGap);
2034	>	}
2035	>
2036	>	//set zcons fixtime
2037	>	DoubleData* zconsFixtime = new DoubleData();
2038	>	zconsFixtime->setID(ZCONSFIXTIME_ID);
2039	>
2040	>	if (globals->haveZConsFixTime()){
2041	>	zconsFixtime->setData(globals->getZconsFixtime());
2042	>	theInfo.addProperty(zconsFixtime);
2043	>	}
2044	>
2045	>	//set zconsUsingSMD
2046	>	IntData* zconsUsingSMD = new IntData();
2047	>	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2048	>
2049	>	if (globals->haveZConsUsingSMD()){
2050	>	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2051	>	theInfo.addProperty(zconsUsingSMD);
2052	>	}
2053	>
2054	>	//Determine the name of ouput file and add it into SimInfo's property list
2055	>	//Be careful, do not use inFileName, since it is a pointer which
2056	>	//point to a string at master node, and slave nodes do not contain that string
2057	>
2058	>	string zconsOutput(theInfo.finalName);
2059	>
2060	>	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
2061	>
2062	>	StringData* zconsFilename = new StringData();
2063	>	zconsFilename->setID(ZCONSFILENAME_ID);
2064	>	zconsFilename->setData(zconsOutput);
2065	>
2066	>	theInfo.addProperty(zconsFilename);
2067	>
2068	>	//setup index, pos and other parameters of z-constraint molecules
2069	>	nZConstraints = globals->getNzConstraints();
2070	>	theInfo.nZconstraints = nZConstraints;
2071	>
2072	>	zconStamp = globals->getZconStamp();
2073	>	ZConsParaItem tempParaItem;
2074	>
2075	>	ZConsParaData* zconsParaData = new ZConsParaData();
2076	>	zconsParaData->setID(ZCONSPARADATA_ID);
2077	>
2078	>	for (int i = 0; i < nZConstraints; i++){
2079	>	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
2080	>	tempParaItem.zPos = zconStamp[i]->getZpos();
2081	>	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2082	>	tempParaItem.kRatio = zconStamp[i]->getKratio();
2083	>	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2084	>	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2085	>	zconsParaData->addItem(tempParaItem);
2086	>	}
2087	>
2088	>	//check the uniqueness of index
2089	>	if(!zconsParaData->isIndexUnique()){
2090	>	sprintf(painCave.errMsg,
2091	>	"ZConstraint Error: molIndex is not unique!\n");
2092	>	painCave.isFatal = 1;
2093	>	simError();
2094	>	}
2095	>
2096	>	//sort the parameters by index of molecules
2097	>	zconsParaData->sortByIndex();
2098	>
2099	>	//push data into siminfo, therefore, we can retrieve later
2100	>	theInfo.addProperty(zconsParaData);
2101	>	}
2102	>
2103	>	void SimSetup::makeMinimizer(){
2104	>
2105	>	OOPSEMinimizer* myOOPSEMinimizer;
2106	>	MinimizerParameterSet* param;
2107	>	char minimizerName[100];
2108	>
2109	>	for (int i = 0; i < nInfo; i++){
2110	>
2111	>	//prepare parameter set for minimizer
2112	>	param = new MinimizerParameterSet();
2113	>	param->setDefaultParameter();
2114	>
2115	>	if (globals->haveMinimizer()){
2116	>	param->setFTol(globals->getMinFTol());
2117	>	}
2118	>
2119	>	if (globals->haveMinGTol()){
2120	>	param->setGTol(globals->getMinGTol());
2121	>	}
2122	>
2123	>	if (globals->haveMinMaxIter()){
2124	>	param->setMaxIteration(globals->getMinMaxIter());
2125	>	}
2126	>
2127	>	if (globals->haveMinWriteFrq()){
2128	>	param->setMaxIteration(globals->getMinMaxIter());
2129	>	}
2130	>
2131	>	if (globals->haveMinWriteFrq()){
2132	>	param->setWriteFrq(globals->getMinWriteFrq());
2133	>	}
2134	>
2135	>	if (globals->haveMinStepSize()){
2136	>	param->setStepSize(globals->getMinStepSize());
2137	>	}
2138	>
2139	>	if (globals->haveMinLSMaxIter()){
2140	>	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2141	>	}
2142	>
2143	>	if (globals->haveMinLSTol()){
2144	>	param->setLineSearchTol(globals->getMinLSTol());
2145	>	}
2146	>
2147	>	strcpy(minimizerName, globals->getMinimizer());
2148	>
2149	>	if (!strcasecmp(minimizerName, "CG")){
2150	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2151	>	}
2152	>	else if (!strcasecmp(minimizerName, "SD")){
2153	>	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2154	>	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2155	>	}
2156	>	else{
2157	>	sprintf(painCave.errMsg,
2158	>	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2159	>	painCave.isFatal = 0;
2160	>	simError();
2161	>
2162	>	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2163	>	}
2164	>	info[i].the_integrator = myOOPSEMinimizer;
2165	>
2166	>	//store the minimizer into simInfo
2167	>	info[i].the_minimizer = myOOPSEMinimizer;
2168	>	info[i].has_minimizer = true;
2169	>	}
2170	>
2171		}

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