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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 466 by gezelter, Mon Apr 7 14:30:36 2003 UTC vs.
Revision 1211 by tim, Tue Jun 1 15:57:30 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	<	ExtendedSystem* the_extendedsystem;
70	<	int i, j;
127	>	// gather all of the information from the Bass file
128
129	<	// get the stamps and globals;
73	<	the_stamps = stamps;
74	<	the_globals = globals;
129	>	gatherInfo();
130
131	<	// set the easy ones first
77	<	simnfo->target_temp = the_globals->getTargetTemp();
78	<	simnfo->dt = the_globals->getDt();
79	<	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.
82	<	n_components = the_globals->getNComponents();
83	<	strcpy( force_field, the_globals->getForceField() );
133	>	sysObjectsCreation();
134
135	<	// get the ensemble and set up an extended system if we need it:
86	<	strcpy( ensemble, the_globals->getEnsemble() );
87	<	if( !strcasecmp( ensemble, "NPT" ) ) {
88	<	the_extendedsystem = new ExtendedSystem( simnfo );
89	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
90	<	the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
91	<	} else if ( !strcasecmp( ensemble, "NVT") ) {
92	<	the_extendedsystem = new ExtendedSystem( simnfo );
93	<	the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
94	<	} else if ( !strcasecmp( ensemble, "NVE") ) {
95	<	} else {
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
98	<	"reverting to NVE for this simulation.\n",
99	<	ensemble );
100	<	painCave.isFatal = 0;
101	<	simError();
102	<	strcpy( ensemble, "NVE" );
103	<	}
104	<	strcpy( simnfo->ensemble, ensemble );
135	>	// check on the post processing info
136
137	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
107	<	simnfo->usePBC = the_globals->getPBC();
108	<
109	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
110	<	else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
111	<	else{
112	<	sprintf( painCave.errMsg,
113	<	"SimSetup Error. Unrecognized force field -> %s\n",
114	<	force_field );
115	<	painCave.isFatal = 1;
116	<	simError();
117	<	}
137	>	finalInfoCheck();
138
139	<	#ifdef IS_MPI
120	<	strcpy( checkPointMsg, "ForceField creation successful" );
121	<	MPIcheckPoint();
122	<	#endif // is_mpi
139	>	// initialize the system coordinates
140
141	<
141	>	if ( !initSuspend ){
142	>	initSystemCoords();
143
144	<	// get the components and calculate the tot_nMol and indvidual n_mol
145	<	the_components = the_globals->getComponents();
146	<	components_nmol = new int[n_components];
129	<	comp_stamps = new MoleculeStamp*[n_components];
144	>	if( !(globals->getUseInitTime()) )
145	>	info[0].currentTime = 0.0;
146	>	}
147
148	<	if( !the_globals->haveNMol() ){
132	<	// we don't have the total number of molecules, so we assume it is
133	<	// given in each component
148	>	// make the output filenames
149
150	<	tot_nmol = 0;
151	<	for( i=0; i<n_components; i++ ){
150	>	makeOutNames();
151	>
152	>	#ifdef IS_MPI
153	>	mpiSim->mpiRefresh();
154	>	#endif
155
156	<	if( !the_components[i]->haveNMol() ){
139	<	// we have a problem
140	<	sprintf( painCave.errMsg,
141	<	"SimSetup Error. No global NMol or component NMol"
142	<	" given. Cannot calculate the number of atoms.\n" );
143	<	painCave.isFatal = 1;
144	<	simError();
145	<	}
156	>	// initialize the Fortran
157
158	<	tot_nmol += the_components[i]->getNMol();
148	<	components_nmol[i] = the_components[i]->getNMol();
149	<	}
150	<	}
151	<	else{
152	<	sprintf( painCave.errMsg,
153	<	"SimSetup error.\n"
154	<	"\tSorry, the ability to specify total"
155	<	" nMols and then give molfractions in the components\n"
156	<	"\tis not currently supported."
157	<	" Please give nMol in the components.\n" );
158	<	painCave.isFatal = 1;
159	<	simError();
160	<
161	<
162	<	//     tot_nmol = the_globals->getNMol();
163	<
164	<	//   //we have the total number of molecules, now we check for molfractions
165	<	//     for( i=0; i<n_components; i++ ){
166	<
167	<	//       if( !the_components[i]->haveMolFraction() ){
168	<
169	<	//  if( !the_components[i]->haveNMol() ){
170	<	//    //we have a problem
171	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
172	<	//              << " nMol was given in component
173	<
174	<	}
158	>	initFortran();
159
160	<	#ifdef IS_MPI
161	<	strcpy( checkPointMsg, "Have the number of components" );
162	<	MPIcheckPoint();
163	<	#endif // is_mpi
160	>	if (globals->haveMinimizer())
161	>	// make minimizer
162	>	makeMinimizer();
163	>	else
164	>	// make the integrator
165	>	makeIntegrator();
166
167	<	// make an array of molecule stamps that match the components used.
182	<	// also extract the used stamps out into a separate linked list
167	>	}
168
184	–	simnfo->nComponents = n_components;
185	–	simnfo->componentsNmol = components_nmol;
186	–	simnfo->compStamps = comp_stamps;
187	–	simnfo->headStamp = new LinkedMolStamp();
188	–
189	–	char* id;
190	–	LinkedMolStamp* headStamp = simnfo->headStamp;
191	–	LinkedMolStamp* currentStamp = NULL;
192	–	for( i=0; i<n_components; i++ ){
169
170	<	id = the_components[i]->getType();
171	<	comp_stamps[i] = NULL;
172	<
173	<	// check to make sure the component isn't already in the list
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	<	comp_stamps[i] = headStamp->match( id );
193	<	if( comp_stamps[i] == NULL ){
194	<
202	<	// extract the component from the list;
203	<
204	<	currentStamp = the_stamps->extractMolStamp( id );
205	<	if( currentStamp == NULL ){
206	<	sprintf( painCave.errMsg,
207	<	"SimSetup error: Component \"%s\" was not found in the "
208	<	"list of declared molecules\n",
209	<	id );
210	<	painCave.isFatal = 1;
211	<	simError();
212	<	}
213	<
214	<	headStamp->add( currentStamp );
215	<	comp_stamps[i] = headStamp->match( id );
216	<	}
217	<	}
192	>	bond_pair* theBonds;
193	>	bend_set* theBends;
194	>	torsion_set* theTorsions;
195
196	<	#ifdef IS_MPI
220	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
221	<	MPIcheckPoint();
222	<	#endif // is_mpi
223	<
196	>	set<int> skipList;
197
198	+	double phi, theta, psi;
199	+	char* molName;
200	+	char rbName[100];
201
202	<
203	<	// caclulate the number of atoms, bonds, bends and torsions
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	<	tot_atoms = 0;
230	<	tot_bonds = 0;
231	<	tot_bends = 0;
232	<	tot_torsions = 0;
233	<	for( i=0; i<n_components; i++ ){
234	<
235	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
236	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
237	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
238	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
239	<	}
210	>	the_ff->readParams();
211
212	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
212	>	// init the atoms
213
214	<	simnfo->n_atoms = tot_atoms;
244	<	simnfo->n_bonds = tot_bonds;
245	<	simnfo->n_bends = tot_bends;
246	<	simnfo->n_torsions = tot_torsions;
247	<	simnfo->n_SRI = tot_SRI;
248	<	simnfo->n_mol = tot_nmol;
214	>	int nMembers, nNew, rb1, rb2;
215
216	<
217	<	#ifdef IS_MPI
216	>	for (k = 0; k < nInfo; k++){
217	>	the_ff->setSimInfo(&(info[k]));
218
219	<	// divide the molecules among processors here.
220	<
255	<	mpiSim = new mpiSimulation( simnfo );
256	<
257	<
219	>	atomOffset = 0;
220	>	groupOffset = 0;
221
222	<	globalIndex = mpiSim->divideLabor();
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	<	// set up the local variables
227	<
228	<	int localMol, allMol;
229	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
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	<	int* mol2proc = mpiSim->getMolToProcMap();
233	<	int* molCompType = mpiSim->getMolComponentType();
234	<
269	<	allMol = 0;
270	<	localMol = 0;
271	<	local_atoms = 0;
272	<	local_bonds = 0;
273	<	local_bends = 0;
274	<	local_torsions = 0;
275	<	for( i=0; i<n_components; i++ ){
232	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
233	>
234	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
235
236	<	for( j=0; j<components_nmol[i]; j++ ){
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	>	if (molInfo.nTorsions > 0)
247	>	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
248	>	else
249	>	molInfo.myTorsions = NULL;
250	>
251	>	theBonds = new bond_pair[molInfo.nBonds];
252	>	theBends = new bend_set[molInfo.nBends];
253	>	theTorsions = new torsion_set[molInfo.nTorsions];
254
255	<	if( mol2proc[j] == worldRank ){
280	<
281	<	local_atoms +=    comp_stamps[i]->getNAtoms();
282	<	local_bonds +=    comp_stamps[i]->getNBonds();
283	<	local_bends +=    comp_stamps[i]->getNBends();
284	<	local_torsions += comp_stamps[i]->getNTorsions();
285	<	localMol++;
286	<	}
287	<	allMol++;
288	<	}
289	<	}
290	<	local_SRI = local_bonds + local_bends + local_torsions;
291	<
255	>	// make the Atoms
256
257	<	simnfo->n_atoms = mpiSim->getMyNlocal();
258	<
295	<	if( local_atoms != simnfo->n_atoms ){
296	<	sprintf( painCave.errMsg,
297	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
298	<	" localAtom (%d) are not equal.\n",
299	<	simnfo->n_atoms,
300	<	local_atoms );
301	<	painCave.isFatal = 1;
302	<	simError();
303	<	}
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	<
314	<
315	<	#endif // is_mpi
316	<
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];
277	<	int molIndex;
274	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
275	>
276	>	}
277	>	else{
278
279	<	// initialize the molecule's stampID's
279	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
280
281	+	}
282	+
283	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
284		#ifdef IS_MPI
328	–
285
286	<	molIndex = 0;
331	<	for(i=0; i<mpiSim->getTotNmol(); i++){
332	<
333	<	if(mol2proc[i] == worldRank ){
334	<	the_molecules[molIndex].setStampID( molCompType[i] );
335	<	the_molecules[molIndex].setMyIndex( molIndex );
336	<	molIndex++;
337	<	}
338	<	}
286	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
287
340	–	#else // is_mpi
341	–
342	–	molIndex = 0;
343	–	for(i=0; i<n_components; i++){
344	–	for(j=0; j<components_nmol[i]; j++ ){
345	–	the_molecules[molIndex].setStampID( i );
346	–	the_molecules[molIndex].setMyIndex( molIndex );
347	–	molIndex++;
348	–	}
349	–	}
350	–
351	–
288		#endif // is_mpi
289	+	}
290
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	<	if( simnfo->n_SRI ){
298	<
357	<	Exclude::createArray(simnfo->n_SRI);
358	<	the_excludes = new Exclude*[simnfo->n_SRI];
359	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
360	<	simnfo->globalExcludes = new int;
361	<	simnfo->n_exclude = simnfo->n_SRI;
362	<	}
363	<	else{
364	<
365	<	Exclude::createArray( 1 );
366	<	the_excludes = new Exclude*;
367	<	the_excludes[0] = new Exclude(0);
368	<	the_excludes[0]->setPair( 0,0 );
369	<	simnfo->globalExcludes = new int;
370	<	simnfo->globalExcludes[0] = 0;
371	<	simnfo->n_exclude = 0;
372	<	}
297	>	tempI = theBonds[j].a;
298	>	tempJ = theBonds[j].b;
299
300	<	// set the arrays into the SimInfo object
300	>	#ifdef 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	<	simnfo->atoms = the_atoms;
309	<	simnfo->molecules = the_molecules;
378	<	simnfo->nGlobalExcludes = 0;
379	<	simnfo->excludes = the_excludes;
308	>	info[k].excludes->addPair(exI, exJ);
309	>	}
310
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	<	// get some of the tricky things that may still be in the globals
318	>	if (currentBend->haveExtras()){
319	>	extras = currentBend->getExtras();
320	>	current_extra = extras;
321
322	<
323	<	if( the_globals->haveBox() ){
324	<	simnfo->box_x = the_globals->getBox();
325	<	simnfo->box_y = the_globals->getBox();
326	<	simnfo->box_z = the_globals->getBox();
327	<	}
328	<	else if( the_globals->haveDensity() ){
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	<	double vol;
331	<	vol = (double)tot_nmol / the_globals->getDensity();
332	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
333	<	simnfo->box_y = simnfo->box_x;
334	<	simnfo->box_z = simnfo->box_x;
397	<	}
398	<	else{
399	<	if( !the_globals->haveBoxX() ){
400	<	sprintf( painCave.errMsg,
401	<	"SimSetup error, no periodic BoxX size given.\n" );
402	<	painCave.isFatal = 1;
403	<	simError();
404	<	}
405	<	simnfo->box_x = the_globals->getBoxX();
330	>	case 1:
331	>	theBends[j].ghost = (int) current_extra->getDouble() +
332	>	atomOffset;
333	>	theBends[j].isGhost = 1;
334	>	break;
335
336	<	if( !the_globals->haveBoxY() ){
337	<	sprintf( painCave.errMsg,
338	<	"SimSetup error, no periodic BoxY size given.\n" );
339	<	painCave.isFatal = 1;
340	<	simError();
341	<	}
342	<	simnfo->box_y = the_globals->getBoxY();
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	<	if( !the_globals->haveBoxZ() ){
356	<	sprintf( painCave.errMsg,
357	<	"SimSetup error, no periodic BoxZ size given.\n" );
418	<	painCave.isFatal = 1;
419	<	simError();
420	<	}
421	<	simnfo->box_z = the_globals->getBoxZ();
422	<	}
355	>	current_extra = current_extra->getNext();
356	>	}
357	>	}
358
359	+	if (theBends[j].isGhost) {
360	+
361	+	tempI = theBends[j].a;
362	+	tempJ = theBends[j].b;
363	+
364		#ifdef IS_MPI
365	<	strcpy( checkPointMsg, "Box size set up" );
366	<	MPIcheckPoint();
367	<	#endif // 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	+	} else {
374
375	<	// initialize the arrays
375	>	tempI = theBends[j].a;
376	>	tempJ = theBends[j].b;
377	>	tempK = theBends[j].c;
378	>
379	>	#ifdef 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	<	the_ff->setSimInfo( simnfo );
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	<	makeMolecules();
403	<	simnfo->identArray = new int[simnfo->n_atoms];
404	<	for(i=0; i<simnfo->n_atoms; i++){
405	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
438	<	}
439	<
440	<	if (the_globals->getUseRF() ) {
441	<	simnfo->useReactionField = 1;
442	<
443	<	if( !the_globals->haveECR() ){
444	<	sprintf( painCave.errMsg,
445	<	"SimSetup Warning: using default value of 1/2 the smallest "
446	<	"box length for the electrostaticCutoffRadius.\n"
447	<	"I hope you have a very fast processor!\n");
448	<	painCave.isFatal = 0;
449	<	simError();
450	<	double smallest;
451	<	smallest = simnfo->box_x;
452	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
453	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
454	<	simnfo->ecr = 0.5 * smallest;
455	<	} else {
456	<	simnfo->ecr        = the_globals->getECR();
457	<	}
402	>	tempI = theTorsions[j].a;
403	>	tempJ = theTorsions[j].b;
404	>	tempK = theTorsions[j].c;
405	>	tempL = theTorsions[j].d;
406
459	–	if( !the_globals->haveEST() ){
460	–	sprintf( painCave.errMsg,
461	–	"SimSetup Warning: using default value of 0.05 * the "
462	–	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
463	–	);
464	–	painCave.isFatal = 0;
465	–	simError();
466	–	simnfo->est = 0.05 * simnfo->ecr;
467	–	} else {
468	–	simnfo->est        = the_globals->getEST();
469	–	}
470	–
471	–	if(!the_globals->haveDielectric() ){
472	–	sprintf( painCave.errMsg,
473	–	"SimSetup Error: You are trying to use Reaction Field without"
474	–	"setting a dielectric constant!\n"
475	–	);
476	–	painCave.isFatal = 1;
477	–	simError();
478	–	}
479	–	simnfo->dielectric = the_globals->getDielectric();
480	–	} else {
481	–	if (simnfo->n_dipoles) {
482	–
483	–	if( !the_globals->haveECR() ){
484	–	sprintf( painCave.errMsg,
485	–	"SimSetup Warning: using default value of 1/2 the smallest"
486	–	"box length for the electrostaticCutoffRadius.\n"
487	–	"I hope you have a very fast processor!\n");
488	–	painCave.isFatal = 0;
489	–	simError();
490	–	double smallest;
491	–	smallest = simnfo->box_x;
492	–	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
493	–	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
494	–	simnfo->ecr = 0.5 * smallest;
495	–	} else {
496	–	simnfo->ecr        = the_globals->getECR();
497	–	}
498	–
499	–	if( !the_globals->haveEST() ){
500	–	sprintf( painCave.errMsg,
501	–	"SimSetup Warning: using default value of 5% of the"
502	–	"electrostaticCutoffRadius for the "
503	–	"electrostaticSkinThickness\n"
504	–	);
505	–	painCave.isFatal = 0;
506	–	simError();
507	–	simnfo->est = 0.05 * simnfo->ecr;
508	–	} else {
509	–	simnfo->est        = the_globals->getEST();
510	–	}
511	–	}
512	–	}
513	–
407		#ifdef IS_MPI
408	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
409	<	MPIcheckPoint();
410	<	#endif // is_mpi
411	<
412	<	if( the_globals->haveInitialConfig() ){
413	<
414	<	InitializeFromFile* fileInit;
415	<	#ifdef IS_MPI // is_mpi
416	<	if( worldRank == 0 ){
524	<	#endif //is_mpi
525	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
526	<	#ifdef IS_MPI
527	<	}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
529	–	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	<
539	<	sprintf( painCave.errMsg,
540	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
541	<	painCave.isFatal;
542	<	simError();
543	<
544	<	#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" );
554	<	MPIcheckPoint();
555	<	#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" );
474	<	}
475	<	else if( !strcmp( endTest, ".BASS" ) ){
476	<	strcpy( endTest, ".eor" );
477	<	}
478	<	else{
479	<	endTest = &(simnfo->finalName[nameLength - 4]);
583	<	if( !strcmp( endTest, ".bss" ) ){
584	<	strcpy( endTest, ".eor" );
585	<	}
586	<	else if( !strcmp( endTest, ".mdl" ) ){
587	<	strcpy( endTest, ".eor" );
588	<	}
589	<	else{
590	<	strcat( simnfo->finalName, ".eor" );
591	<	}
592	<	}
593	<	}
594	<
595	<	// make the sample and status out names
596	<
597	<	strcpy( simnfo->sampleName, inFileName );
598	<	char* endTest;
599	<	int nameLength = strlen( simnfo->sampleName );
600	<	endTest = &(simnfo->sampleName[nameLength - 5]);
601	<	if( !strcmp( endTest, ".bass" ) ){
602	<	strcpy( endTest, ".dump" );
603	<	}
604	<	else if( !strcmp( endTest, ".BASS" ) ){
605	<	strcpy( endTest, ".dump" );
606	<	}
607	<	else{
608	<	endTest = &(simnfo->sampleName[nameLength - 4]);
609	<	if( !strcmp( endTest, ".bss" ) ){
610	<	strcpy( endTest, ".dump" );
611	<	}
612	<	else if( !strcmp( endTest, ".mdl" ) ){
613	<	strcpy( endTest, ".dump" );
614	<	}
615	<	else{
616	<	strcat( simnfo->sampleName, ".dump" );
617	<	}
618	<	}
619	<
620	<	strcpy( simnfo->statusName, inFileName );
621	<	nameLength = strlen( simnfo->statusName );
622	<	endTest = &(simnfo->statusName[nameLength - 5]);
623	<	if( !strcmp( endTest, ".bass" ) ){
624	<	strcpy( endTest, ".stat" );
625	<	}
626	<	else if( !strcmp( endTest, ".BASS" ) ){
627	<	strcpy( endTest, ".stat" );
628	<	}
629	<	else{
630	<	endTest = &(simnfo->statusName[nameLength - 4]);
631	<	if( !strcmp( endTest, ".bss" ) ){
632	<	strcpy( endTest, ".stat" );
633	<	}
634	<	else if( !strcmp( endTest, ".mdl" ) ){
635	<	strcpy( endTest, ".stat" );
636	<	}
637	<	else{
638	<	strcat( simnfo->statusName, ".stat" );
639	<	}
640	<	}
641	<
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	<	}
482	<	#endif // is_mpi
483	<
484	<	// set the status, sample, and themal kick times
485	<
486	<	if( the_globals->haveSampleTime() ){
487	<	simnfo->sampleTime = the_globals->getSampleTime();
488	<	simnfo->statusTime = simnfo->sampleTime;
489	<	simnfo->thermalTime = simnfo->sampleTime;
490	<	}
491	<	else{
654	<	simnfo->sampleTime = the_globals->getRunTime();
655	<	simnfo->statusTime = simnfo->sampleTime;
656	<	simnfo->thermalTime = simnfo->sampleTime;
657	<	}
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	<	if( the_globals->haveStatusTime() ){
494	<	simnfo->statusTime = the_globals->getStatusTime();
495	<	}
493	>	molInfo.myRigidBodies.push_back(myRB);
494	>	info[k].rigidBodies.push_back(myRB);
495	>	}
496	>
497
498	<	if( the_globals->haveThermalTime() ){
664	<	simnfo->thermalTime = the_globals->getThermalTime();
665	<	}
498	>	//create cutoff group for molecule
499
500	<	// check for the temperature set flag
500	>	cutoffAtomSet.clear();
501	>	molInfo.myCutoffGroups.clear();
502	>
503	>	for (j = 0; j < nCutoffGroups; j++){
504
505	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
505	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
506	>	nMembers = currentCutoffGroup->getNMembers();
507
508	+	myCutoffGroup = new CutoffGroup();
509	+	myCutoffGroup->setGlobalIndex(globalGroupIndex[j + groupOffset]);
510	+
511	+	for (int cg = 0; cg < nMembers; cg++) {
512
513	<	//   // make the longe range forces and the integrator
513	>	// molI is atom numbering inside this molecule
514	>	molI = currentCutoffGroup->getMember(cg);
515
516	<	//   new AllLong( simnfo );
516	>	// tempI is atom numbering on local processor
517	>	tempI = molI + atomOffset;
518
676	–	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic(simnfo,
677	–	the_ff,
678	–	the_extendedsystem);
679	–	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo,
680	–	the_ff,
681	–	the_extendedsystem );
682	–
519		#ifdef IS_MPI
520	<	mpiSim->mpiRefresh();
520	>	globalID = info[k].atoms[tempI]->getGlobalIndex()
521	>	#else
522	>	globalID = info[k].atoms[tempI]->getIndex();
523		#endif
524
525	<	// initialize the Fortran
525	>	globalGroupMembership[globalID] = globalGroupIndex[j+groupOffset];
526
527	+	myCutoffGroup->addAtom(info[k].atoms[tempI]);
528
529	<	simnfo->refreshSim();
530	<
531	<	if( !strcmp( simnfo->mixingRule, "standard") ){
532	<	the_ff->initForceField( LB_MIXING_RULE );
533	<	}
695	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
696	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
697	<	}
698	<	else{
699	<	sprintf( painCave.errMsg,
700	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
701	<	simnfo->mixingRule );
702	<	painCave.isFatal = 1;
703	<	simError();
704	<	}
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	<	#ifdef IS_MPI
708	<	strcpy( checkPointMsg,
709	<	"Successfully intialized the mixingRule for Fortran." );
710	<	MPIcheckPoint();
711	<	#endif // is_mpi
712	<	}
537	>	//creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
538
539	+	for(j = 0; j < molInfo.nAtoms; j++){
540
541	<	void SimSetup::makeMolecules( void ){
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	>	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	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
558	<	molInit info;
719	<	DirectionalAtom* dAtom;
720	<	LinkedAssign* extras;
721	<	LinkedAssign* current_extra;
722	<	AtomStamp* currentAtom;
723	<	BondStamp* currentBond;
724	<	BendStamp* currentBend;
725	<	TorsionStamp* currentTorsion;
557	>	// After this is all set up, scan through the atoms to
558	>	// see if they can be added to the integrableObjects:
559
560	<	bond_pair* theBonds;
561	<	bend_set* theBends;
729	<	torsion_set* theTorsions;
560	>	molInfo.myIntegrableObjects.clear();
561	>
562
563	<
732	<	//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	<
737	<	// init the atoms
571	>	// if they aren't on the skip list, then they can be integrated
572
573	<	double ux, uy, uz, u, uSqr;
574	<
575	<	atomOffset = 0;
576	<	excludeOffset = 0;
577	<	for(i=0; i<simnfo->n_mol; i++){
744	<
745	<	stampID = the_molecules[i].getStampID();
746	<
747	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
748	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
749	<	info.nBends    = comp_stamps[stampID]->getNBends();
750	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
751	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
752	<
753	<	info.myAtoms = &the_atoms[atomOffset];
754	<	info.myExcludes = &the_excludes[excludeOffset];
755	<	info.myBonds = new Bond*[info.nBonds];
756	<	info.myBends = new Bend*[info.nBends];
757	<	info.myTorsions = new Torsion*[info.nTorsions];
758	<
759	<	theBonds = new bond_pair[info.nBonds];
760	<	theBends = new bend_set[info.nBends];
761	<	theTorsions = new torsion_set[info.nTorsions];
762	<
763	<	// make the Atoms
764	<
765	<	for(j=0; j<info.nAtoms; j++){
766	<
767	<	currentAtom = comp_stamps[stampID]->getAtom( j );
768	<	if( currentAtom->haveOrientation() ){
769	<
770	<	dAtom = new DirectionalAtom(j + atomOffset);
771	<	simnfo->n_oriented++;
772	<	info.myAtoms[j] = dAtom;
773	<
774	<	ux = currentAtom->getOrntX();
775	<	uy = currentAtom->getOrntY();
776	<	uz = currentAtom->getOrntZ();
777	<
778	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
779	<
780	<	u = sqrt( uSqr );
781	<	ux = ux / u;
782	<	uy = uy / u;
783	<	uz = uz / u;
784	<
785	<	dAtom->setSUx( ux );
786	<	dAtom->setSUy( uy );
787	<	dAtom->setSUz( uz );
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		}
789	–	else{
790	–	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
791	–	}
792	–	info.myAtoms[j]->setType( currentAtom->getType() );
793	–
794	–	#ifdef IS_MPI
795	–
796	–	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
797	–
798	–	#endif // is_mpi
799	–	}
800	–
801	–	// make the bonds
802	–	for(j=0; j<info.nBonds; j++){
803	–
804	–	currentBond = comp_stamps[stampID]->getBond( j );
805	–	theBonds[j].a = currentBond->getA() + atomOffset;
806	–	theBonds[j].b = currentBond->getB() + atomOffset;
579
580	<	exI = theBonds[j].a;
809	<	exJ = theBonds[j].b;
580	>	// all rigid bodies are integrated:
581
582	<	// exclude_I must always be the smaller of the pair
583	<	if( exI > exJ ){
584	<	tempEx = exI;
585	<	exI = exJ;
815	<	exJ = tempEx;
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		}
817	–	#ifdef IS_MPI
818	–	tempEx = exI;
819	–	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
820	–	tempEx = exJ;
821	–	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
822	–
823	–	the_excludes[j+excludeOffset]->setPair( exI, exJ );
824	–	#else  // isn't MPI
587
826	–	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
827	–	#endif  //is_mpi
828	–	}
829	–	excludeOffset += info.nBonds;
588
589	<	//make the bends
832	<	for(j=0; j<info.nBends; j++){
833	<
834	<	currentBend = comp_stamps[stampID]->getBend( j );
835	<	theBends[j].a = currentBend->getA() + atomOffset;
836	<	theBends[j].b = currentBend->getB() + atomOffset;
837	<	theBends[j].c = currentBend->getC() + atomOffset;
838	<
839	<	if( currentBend->haveExtras() ){
840	<
841	<	extras = currentBend->getExtras();
842	<	current_extra = extras;
843	<
844	<	while( current_extra != NULL ){
845	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
846	<
847	<	switch( current_extra->getType() ){
848	<
849	<	case 0:
850	<	theBends[j].ghost =
851	<	current_extra->getInt() + atomOffset;
852	<	theBends[j].isGhost = 1;
853	<	break;
854	<
855	<	case 1:
856	<	theBends[j].ghost =
857	<	(int)current_extra->getDouble() + atomOffset;
858	<	theBends[j].isGhost = 1;
859	<	break;
860	<
861	<	default:
862	<	sprintf( painCave.errMsg,
863	<	"SimSetup Error: ghostVectorSource was neither a "
864	<	"double nor an int.\n"
865	<	"-->Bend[%d] in %s\n",
866	<	j, comp_stamps[stampID]->getID() );
867	<	painCave.isFatal = 1;
868	<	simError();
869	<	}
870	<	}
871	<
872	<	else{
873	<
874	<	sprintf( painCave.errMsg,
875	<	"SimSetup Error: unhandled bend assignment:\n"
876	<	"    -->%s in Bend[%d] in %s\n",
877	<	current_extra->getlhs(),
878	<	j, comp_stamps[stampID]->getID() );
879	<	painCave.isFatal = 1;
880	<	simError();
881	<	}
882	<
883	<	current_extra = current_extra->getNext();
884	<	}
885	<	}
886	<
887	<	if( !theBends[j].isGhost ){
888	<
889	<	exI = theBends[j].a;
890	<	exJ = theBends[j].c;
891	<	}
892	<	else{
893	<
894	<	exI = theBends[j].a;
895	<	exJ = theBends[j].b;
896	<	}
897	<
898	<	// exclude_I must always be the smaller of the pair
899	<	if( exI > exJ ){
900	<	tempEx = exI;
901	<	exI = exJ;
902	<	exJ = tempEx;
903	<	}
904	<	#ifdef IS_MPI
905	<	tempEx = exI;
906	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
907	<	tempEx = exJ;
908	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
909	<
910	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
911	<	#else  // isn't MPI
912	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
913	<	#endif  //is_mpi
914	<	}
915	<	excludeOffset += info.nBends;
589	>	/*
590
591	<	for(j=0; j<info.nTorsions; j++){
591	>	//creat ConstraintPair.
592	>	molInfo.myConstraintPair.clear();
593
594	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
920	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
921	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
922	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
923	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
924	<
925	<	exI = theTorsions[j].a;
926	<	exJ = theTorsions[j].d;
594	>	for (j = 0; j < molInfo.nBonds; j++){
595
596	<	// exclude_I must always be the smaller of the pair
597	<	if( exI > exJ ){
598	<	tempEx = exI;
931	<	exI = exJ;
932	<	exJ = tempEx;
933	<	}
934	<	#ifdef IS_MPI
935	<	tempEx = exI;
936	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
937	<	tempEx = exJ;
938	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
939	<
940	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
941	<	#else  // isn't MPI
942	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
943	<	#endif  //is_mpi
944	<	}
945	<	excludeOffset += info.nTorsions;
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	<
601	<	// send the arrays off to the forceField for init.
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	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
607	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
608	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
609	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
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	<	the_molecules[i].initialize( info );
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	<	atomOffset += info.nAtoms;
632	<	delete[] theBonds;
633	<	delete[] theBends;
634	<	delete[] theTorsions;
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" );
654	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
655		MPIcheckPoint();
656		#endif // is_mpi
657
970	–	// clean up the forcefield
971	–	the_ff->calcRcut();
972	–	the_ff->cleanMe();
973	–
658		}
659
660	<	void SimSetup::initFromBass( void ){
977	<
660	>	void SimSetup::initFromBass(void){
661		int i, j, k;
662		int n_cells;
663		double cellx, celly, cellz;
#	Line 983 | Line 666 | void SimSetup::initFromBass( void ){
666		int n_extra;
667		int have_extra, done;
668
669	<	temp1 = (double)tot_nmol / 4.0;
670	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
671	<	temp3 = ceil( temp2 );
669	>	double vel[3];
670	>	vel[0] = 0.0;
671	>	vel[1] = 0.0;
672	>	vel[2] = 0.0;
673
674	<	have_extra =0;
675	<	if( temp2 < temp3 ){ // we have a non-complete lattice
676	<	have_extra =1;
674	>	temp1 = (double) tot_nmol / 4.0;
675	>	temp2 = pow(temp1, (1.0 / 3.0));
676	>	temp3 = ceil(temp2);
677
678	<	n_cells = (int)temp3 - 1;
679	<	cellx = simnfo->box_x / temp3;
680	<	celly = simnfo->box_y / temp3;
681	<	cellz = simnfo->box_z / temp3;
998	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
999	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1000	<	n_per_extra = (int)ceil( temp1 );
678	>	have_extra = 0;
679	>	if (temp2 < temp3){
680	>	// we have a non-complete lattice
681	>	have_extra = 1;
682
683	<	if( n_per_extra > 4){
684	<	sprintf( painCave.errMsg,
685	<	"SimSetup error. There has been an error in constructing"
686	<	" the non-complete lattice.\n" );
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 = simnfo->box_x / temp3;
702	<	celly = simnfo->box_y / temp3;
703	<	cellz = simnfo->box_z / temp3;
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;
#	Line 1019 | Line 708 | void SimSetup::initFromBass( void ){
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++ ){
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,
1027	<	j * celly,
1028	<	k * cellz );
716	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
717
718	<	makeElement( i * cellx + 0.5 * cellx,
1031	<	j * celly + 0.5 * celly,
1032	<	k * cellz );
718	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
719
720	<	makeElement( i * cellx,
1035	<	j * celly + 0.5 * celly,
1036	<	k * cellz + 0.5 * cellz );
1037	<
1038	<	makeElement( i * cellx + 0.5 * cellx,
1039	<	j * celly,
1040	<	k * cellz + 0.5 * cellz );
720	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
721		}
722		}
723		}
724
725	<	if( have_extra ){
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++ ){
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	<	if( i < n_cells ){
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( j < n_cells ){
746	<	start_ndx = n_cells;
747	<	}
748	<	else start_ndx = 0;
749	<	}
1059	<	else start_ndx = 0;
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	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
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	<	makeElement( i * cellx,
758	<	j * celly,
759	<	k * cellz );
760	<	done = ( current_mol >= tot_nmol );
761	<
762	<	if( !done && n_per_extra > 1 ){
1069	<	makeElement( i * cellx + 0.5 * cellx,
1070	<	j * celly + 0.5 * celly,
1071	<	k * cellz );
1072	<	done = ( current_mol >= tot_nmol );
1073	<	}
1074	<
1075	<	if( !done && n_per_extra > 2){
1076	<	makeElement( i * cellx,
1077	<	j * celly + 0.5 * celly,
1078	<	k * cellz + 0.5 * cellz );
1079	<	done = ( current_mol >= tot_nmol );
1080	<	}
1081	<
1082	<	if( !done && n_per_extra > 3){
1083	<	makeElement( i * cellx + 0.5 * cellx,
1084	<	j * celly,
1085	<	k * cellz + 0.5 * cellz );
1086	<	done = ( current_mol >= tot_nmol );
1087	<	}
1088	<	}
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	<
768	<	for( i=0; i<simnfo->n_atoms; i++ ){
1095	<	simnfo->atoms[i]->set_vx( 0.0 );
1096	<	simnfo->atoms[i]->set_vy( 0.0 );
1097	<	simnfo->atoms[i]->set_vz( 0.0 );
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 ){
1102	<
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	<
781	<	current_atom = comp_stamps[current_comp]->getAtom( k );
782	<	if( !current_atom->havePosition() ){
783	<	sprintf( painCave.errMsg,
784	<	"SimSetup:initFromBass error.\n"
785	<	"\tComponent %s, atom %s does not have a position specified.\n"
786	<	"\tThe initialization routine is unable to give a start"
787	<	" position.\n",
1117	<	comp_stamps[current_comp]->getID(),
1118	<	current_atom->getType() );
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	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
793	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
794	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
792	>	pos[0] = x + current_atom->getPosX();
793	>	pos[1] = y + current_atom->getPosY();
794	>	pos[2] = z + current_atom->getPosZ();
795
796	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
796	>	info[0].atoms[current_atom_ndx]->setPos(pos);
797
798	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
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;
#	Line 1140 | Line 810 | void SimSetup::makeElement( double x, double y, double
810		rotMat[2][1] = 0.0;
811		rotMat[2][2] = 1.0;
812
813	<	dAtom->setA( rotMat );
813	>	dAtom->setA(rotMat);
814		}
815
816		current_atom_ndx++;
#	Line 1149 | Line 819 | void SimSetup::makeElement( double x, double y, double
819		current_mol++;
820		current_comp_mol++;
821
822	<	if( current_comp_mol >= components_nmol[current_comp] ){
1153	<
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->getUseThermInt()) {
1024	+	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
1025	+	info[i].useThermInt = globals->getUseThermInt();
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 useThermInt 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->haveThermIntLambda() || globals->haveThermIntK()){
1044	+	sprintf(painCave.errMsg,
1045	+	"SimSetup Warning: If you want to use Thermodynamic\n"
1046	+	"\tIntegration, set useThermInt to 'true' in your .bass file.\n"
1047	+	"\tThe useThermInt keyword is 'false' by default, so your\n"
1048	+	"\tlambda and/or k values are being ignored.\n");
1049	+	painCave.isFatal = 0;
1050	+	simError();
1051	+	}
1052	+	}
1053	+
1054	+	//setup seed for random number generator
1055	+	int seedValue;
1056	+
1057	+	if (globals->haveSeed()){
1058	+	seedValue = globals->getSeed();
1059	+
1060	+	if(seedValue / 1E9 == 0){
1061	+	sprintf(painCave.errMsg,
1062	+	"Seed for sprng library should contain at least 9 digits\n"
1063	+	"OOPSE will generate a seed for user\n");
1064	+	painCave.isFatal = 0;
1065	+	simError();
1066	+
1067	+	//using seed generated by system instead of invalid seed set by user
1068	+	#ifndef IS_MPI
1069	+	seedValue = make_sprng_seed();
1070	+	#else
1071	+	if (worldRank == 0){
1072	+	seedValue = make_sprng_seed();
1073	+	}
1074	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1075	+	#endif
1076	+	}
1077	+	}//end of if branch of globals->haveSeed()
1078	+	else{
1079	+
1080	+	#ifndef IS_MPI
1081	+	seedValue = make_sprng_seed();
1082	+	#else
1083	+	if (worldRank == 0){
1084	+	seedValue = make_sprng_seed();
1085	+	}
1086	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1087	+	#endif
1088	+	}//end of globals->haveSeed()
1089	+
1090	+	for (int i = 0; i < nInfo; i++){
1091	+	info[i].setSeed(seedValue);
1092	+	}
1093	+
1094	+	#ifdef IS_MPI
1095	+	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1096	+	MPIcheckPoint();
1097	+	#endif // is_mpi
1098	+	}
1099	+
1100	+
1101	+	void SimSetup::finalInfoCheck(void){
1102	+	int index;
1103	+	int usesDipoles;
1104	+	int usesCharges;
1105	+	int i;
1106	+
1107	+	for (i = 0; i < nInfo; i++){
1108	+	// check electrostatic parameters
1109	+
1110	+	index = 0;
1111	+	usesDipoles = 0;
1112	+	while ((index < info[i].n_atoms) && !usesDipoles){
1113	+	usesDipoles = (info[i].atoms[index])->hasDipole();
1114	+	index++;
1115	+	}
1116	+	index = 0;
1117	+	usesCharges = 0;
1118	+	while ((index < info[i].n_atoms) && !usesCharges){
1119	+	usesCharges= (info[i].atoms[index])->hasCharge();
1120	+	index++;
1121	+	}
1122	+	#ifdef IS_MPI
1123	+	int myUse = usesDipoles;
1124	+	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1125	+	#endif //is_mpi
1126	+
1127	+	double theRcut, theRsw;
1128	+
1129	+	if (globals->haveRcut()) {
1130	+	theRcut = globals->getRcut();
1131	+
1132	+	if (globals->haveRsw())
1133	+	theRsw = globals->getRsw();
1134	+	else
1135	+	theRsw = theRcut;
1136	+
1137	+	info[i].setDefaultRcut(theRcut, theRsw);
1138	+
1139	+	} else {
1140	+
1141	+	the_ff->calcRcut();
1142	+	theRcut = info[i].getRcut();
1143	+
1144	+	if (globals->haveRsw())
1145	+	theRsw = globals->getRsw();
1146	+	else
1147	+	theRsw = theRcut;
1148	+
1149	+	info[i].setDefaultRcut(theRcut, theRsw);
1150	+	}
1151	+
1152	+	if (globals->getUseRF()){
1153	+	info[i].useReactionField = 1;
1154	+
1155	+	if (!globals->haveRcut()){
1156	+	sprintf(painCave.errMsg,
1157	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1158	+	"\tOOPSE will use a default value of 15.0 angstroms"
1159	+	"\tfor the cutoffRadius.\n");
1160	+	painCave.isFatal = 0;
1161	+	simError();
1162	+	theRcut = 15.0;
1163	+	}
1164	+	else{
1165	+	theRcut = globals->getRcut();
1166	+	}
1167	+
1168	+	if (!globals->haveRsw()){
1169	+	sprintf(painCave.errMsg,
1170	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1171	+	"\tOOPSE will use a default value of\n"
1172	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1173	+	painCave.isFatal = 0;
1174	+	simError();
1175	+	theRsw = 0.95 * theRcut;
1176	+	}
1177	+	else{
1178	+	theRsw = globals->getRsw();
1179	+	}
1180	+
1181	+	info[i].setDefaultRcut(theRcut, theRsw);
1182	+
1183	+	if (!globals->haveDielectric()){
1184	+	sprintf(painCave.errMsg,
1185	+	"SimSetup Error: No Dielectric constant was set.\n"
1186	+	"\tYou are trying to use Reaction Field without"
1187	+	"\tsetting a dielectric constant!\n");
1188	+	painCave.isFatal = 1;
1189	+	simError();
1190	+	}
1191	+	info[i].dielectric = globals->getDielectric();
1192	+	}
1193	+	else{
1194	+	if (usesDipoles || usesCharges){
1195	+
1196	+	if (!globals->haveRcut()){
1197	+	sprintf(painCave.errMsg,
1198	+	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1199	+	"\tOOPSE will use a default value of 15.0 angstroms"
1200	+	"\tfor the cutoffRadius.\n");
1201	+	painCave.isFatal = 0;
1202	+	simError();
1203	+	theRcut = 15.0;
1204	+	}
1205	+	else{
1206	+	theRcut = globals->getRcut();
1207	+	}
1208	+
1209	+	if (!globals->haveRsw()){
1210	+	sprintf(painCave.errMsg,
1211	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1212	+	"\tOOPSE will use a default value of\n"
1213	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1214	+	painCave.isFatal = 0;
1215	+	simError();
1216	+	theRsw = 0.95 * theRcut;
1217	+	}
1218	+	else{
1219	+	theRsw = globals->getRsw();
1220	+	}
1221	+
1222	+	info[i].setDefaultRcut(theRcut, theRsw);
1223	+
1224	+	}
1225	+	}
1226	+	}
1227	+	#ifdef IS_MPI
1228	+	strcpy(checkPointMsg, "post processing checks out");
1229	+	MPIcheckPoint();
1230	+	#endif // is_mpi
1231	+
1232	+	// clean up the forcefield
1233	+	the_ff->cleanMe();
1234	+	}
1235	+
1236	+	void SimSetup::initSystemCoords(void){
1237	+	int i;
1238	+
1239	+	char* inName;
1240	+
1241	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1242	+
1243	+	for (i = 0; i < info[0].n_atoms; i++)
1244	+	info[0].atoms[i]->setCoords();
1245	+
1246	+	if (globals->haveInitialConfig()){
1247	+	InitializeFromFile* fileInit;
1248	+	#ifdef IS_MPI // is_mpi
1249	+	if (worldRank == 0){
1250	+	#endif //is_mpi
1251	+	inName = globals->getInitialConfig();
1252	+	fileInit = new InitializeFromFile(inName);
1253	+	#ifdef IS_MPI
1254	+	}
1255	+	else
1256	+	fileInit = new InitializeFromFile(NULL);
1257	+	#endif
1258	+	fileInit->readInit(info); // default velocities on
1259	+
1260	+	delete fileInit;
1261	+	}
1262	+	else{
1263	+
1264	+	// no init from bass
1265	+
1266	+	sprintf(painCave.errMsg,
1267	+	"Cannot intialize a simulation without an initial configuration file.\n");
1268	+	painCave.isFatal = 1;;
1269	+	simError();
1270	+
1271	+	}
1272	+
1273	+	#ifdef IS_MPI
1274	+	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1275	+	MPIcheckPoint();
1276	+	#endif // is_mpi
1277	+	}
1278	+
1279	+
1280	+	void SimSetup::makeOutNames(void){
1281	+	int k;
1282	+
1283	+
1284	+	for (k = 0; k < nInfo; k++){
1285	+	#ifdef IS_MPI
1286	+	if (worldRank == 0){
1287	+	#endif // is_mpi
1288	+
1289	+	if (globals->haveFinalConfig()){
1290	+	strcpy(info[k].finalName, globals->getFinalConfig());
1291	+	}
1292	+	else{
1293	+	strcpy(info[k].finalName, inFileName);
1294	+	char* endTest;
1295	+	int nameLength = strlen(info[k].finalName);
1296	+	endTest = &(info[k].finalName[nameLength - 5]);
1297	+	if (!strcmp(endTest, ".bass")){
1298	+	strcpy(endTest, ".eor");
1299	+	}
1300	+	else if (!strcmp(endTest, ".BASS")){
1301	+	strcpy(endTest, ".eor");
1302	+	}
1303	+	else{
1304	+	endTest = &(info[k].finalName[nameLength - 4]);
1305	+	if (!strcmp(endTest, ".bss")){
1306	+	strcpy(endTest, ".eor");
1307	+	}
1308	+	else if (!strcmp(endTest, ".mdl")){
1309	+	strcpy(endTest, ".eor");
1310	+	}
1311	+	else{
1312	+	strcat(info[k].finalName, ".eor");
1313	+	}
1314	+	}
1315	+	}
1316	+
1317	+	// make the sample and status out names
1318	+
1319	+	strcpy(info[k].sampleName, inFileName);
1320	+	char* endTest;
1321	+	int nameLength = strlen(info[k].sampleName);
1322	+	endTest = &(info[k].sampleName[nameLength - 5]);
1323	+	if (!strcmp(endTest, ".bass")){
1324	+	strcpy(endTest, ".dump");
1325	+	}
1326	+	else if (!strcmp(endTest, ".BASS")){
1327	+	strcpy(endTest, ".dump");
1328	+	}
1329	+	else{
1330	+	endTest = &(info[k].sampleName[nameLength - 4]);
1331	+	if (!strcmp(endTest, ".bss")){
1332	+	strcpy(endTest, ".dump");
1333	+	}
1334	+	else if (!strcmp(endTest, ".mdl")){
1335	+	strcpy(endTest, ".dump");
1336	+	}
1337	+	else{
1338	+	strcat(info[k].sampleName, ".dump");
1339	+	}
1340	+	}
1341	+
1342	+	strcpy(info[k].statusName, inFileName);
1343	+	nameLength = strlen(info[k].statusName);
1344	+	endTest = &(info[k].statusName[nameLength - 5]);
1345	+	if (!strcmp(endTest, ".bass")){
1346	+	strcpy(endTest, ".stat");
1347	+	}
1348	+	else if (!strcmp(endTest, ".BASS")){
1349	+	strcpy(endTest, ".stat");
1350	+	}
1351	+	else{
1352	+	endTest = &(info[k].statusName[nameLength - 4]);
1353	+	if (!strcmp(endTest, ".bss")){
1354	+	strcpy(endTest, ".stat");
1355	+	}
1356	+	else if (!strcmp(endTest, ".mdl")){
1357	+	strcpy(endTest, ".stat");
1358	+	}
1359	+	else{
1360	+	strcat(info[k].statusName, ".stat");
1361	+	}
1362	+	}
1363	+
1364	+	strcpy(info[k].rawPotName, inFileName);
1365	+	nameLength = strlen(info[k].rawPotName);
1366	+	endTest = &(info[k].rawPotName[nameLength - 5]);
1367	+	if (!strcmp(endTest, ".bass")){
1368	+	strcpy(endTest, ".raw");
1369	+	}
1370	+	else if (!strcmp(endTest, ".BASS")){
1371	+	strcpy(endTest, ".raw");
1372	+	}
1373	+	else{
1374	+	endTest = &(info[k].rawPotName[nameLength - 4]);
1375	+	if (!strcmp(endTest, ".bss")){
1376	+	strcpy(endTest, ".raw");
1377	+	}
1378	+	else if (!strcmp(endTest, ".mdl")){
1379	+	strcpy(endTest, ".raw");
1380	+	}
1381	+	else{
1382	+	strcat(info[k].rawPotName, ".raw");
1383	+	}
1384	+	}
1385	+
1386	+	#ifdef IS_MPI
1387	+
1388	+	}
1389	+	#endif // is_mpi
1390	+	}
1391	+	}
1392	+
1393	+
1394	+	void SimSetup::sysObjectsCreation(void){
1395	+	int i, k;
1396	+
1397	+	// create the forceField
1398	+
1399	+	createFF();
1400	+
1401	+	// extract componentList
1402	+
1403	+	compList();
1404	+
1405	+	// calc the number of atoms, bond, bends, and torsions
1406	+
1407	+	calcSysValues();
1408	+
1409	+	#ifdef IS_MPI
1410	+	// divide the molecules among the processors
1411	+
1412	+	mpiMolDivide();
1413	+	#endif //is_mpi
1414	+
1415	+	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1416	+
1417	+	makeSysArrays();
1418	+
1419	+	// make and initialize the molecules (all but atomic coordinates)
1420	+
1421	+	makeMolecules();
1422	+
1423	+	for (k = 0; k < nInfo; k++){
1424	+	info[k].identArray = new int[info[k].n_atoms];
1425	+	for (i = 0; i < info[k].n_atoms; i++){
1426	+	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1427	+	}
1428	+	}
1429	+	}
1430	+
1431	+
1432	+	void SimSetup::createFF(void){
1433	+	switch (ffCase){
1434	+	case FF_DUFF:
1435	+	the_ff = new DUFF();
1436	+	break;
1437	+
1438	+	case FF_LJ:
1439	+	the_ff = new LJFF();
1440	+	break;
1441	+
1442	+	case FF_EAM:
1443	+	the_ff = new EAM_FF();
1444	+	break;
1445	+
1446	+	case FF_H2O:
1447	+	the_ff = new WATER();
1448	+	break;
1449	+
1450	+	default:
1451	+	sprintf(painCave.errMsg,
1452	+	"SimSetup Error. Unrecognized force field in case statement.\n");
1453	+	painCave.isFatal = 1;
1454	+	simError();
1455	+	}
1456	+
1457	+	#ifdef IS_MPI
1458	+	strcpy(checkPointMsg, "ForceField creation successful");
1459	+	MPIcheckPoint();
1460	+	#endif // is_mpi
1461	+	}
1462	+
1463	+
1464	+	void SimSetup::compList(void){
1465	+	int i;
1466	+	char* id;
1467	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1468	+	LinkedMolStamp* currentStamp = NULL;
1469	+	comp_stamps = new MoleculeStamp * [n_components];
1470	+	bool haveCutoffGroups;
1471	+
1472	+	haveCutoffGroups = false;
1473	+
1474	+	// make an array of molecule stamps that match the components used.
1475	+	// also extract the used stamps out into a separate linked list
1476	+
1477	+	for (i = 0; i < nInfo; i++){
1478	+	info[i].nComponents = n_components;
1479	+	info[i].componentsNmol = components_nmol;
1480	+	info[i].compStamps = comp_stamps;
1481	+	info[i].headStamp = headStamp;
1482	+	}
1483	+
1484	+
1485	+	for (i = 0; i < n_components; i++){
1486	+	id = the_components[i]->getType();
1487	+	comp_stamps[i] = NULL;
1488	+
1489	+	// check to make sure the component isn't already in the list
1490	+
1491	+	comp_stamps[i] = headStamp->match(id);
1492	+	if (comp_stamps[i] == NULL){
1493	+	// extract the component from the list;
1494	+
1495	+	currentStamp = stamps->extractMolStamp(id);
1496	+	if (currentStamp == NULL){
1497	+	sprintf(painCave.errMsg,
1498	+	"SimSetup error: Component \"%s\" was not found in the "
1499	+	"list of declared molecules\n",
1500	+	id);
1501	+	painCave.isFatal = 1;
1502	+	simError();
1503	+	}
1504	+
1505	+	headStamp->add(currentStamp);
1506	+	comp_stamps[i] = headStamp->match(id);
1507	+	}
1508	+
1509	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1510	+	haveCutoffGroups = true;
1511	+	}
1512	+
1513	+	for (i = 0; i < nInfo; i++)
1514	+	info[i].haveCutoffGroups = haveCutoffGroups;
1515	+
1516	+	#ifdef IS_MPI
1517	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1518	+	MPIcheckPoint();
1519	+	#endif // is_mpi
1520	+	}
1521	+
1522	+	void SimSetup::calcSysValues(void){
1523	+	int i, j;
1524	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1525	+
1526	+	int* molMembershipArray;
1527	+	CutoffGroupStamp* cg;
1528	+
1529	+	tot_atoms = 0;
1530	+	tot_bonds = 0;
1531	+	tot_bends = 0;
1532	+	tot_torsions = 0;
1533	+	tot_rigid = 0;
1534	+	tot_groups = 0;
1535	+	for (i = 0; i < n_components; i++){
1536	+	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1537	+	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1538	+	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1539	+	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1540	+	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1541	+
1542	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1543	+	atomsingroups = 0;
1544	+	for (j=0; j < ncutgroups; j++) {
1545	+	cg = comp_stamps[i]->getCutoffGroup(j);
1546	+	atomsingroups += cg->getNMembers();
1547	+	}
1548	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1549	+	tot_groups += components_nmol[i] * ngroupsinstamp;
1550	+	}
1551	+
1552	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1553	+	molMembershipArray = new int[tot_atoms];
1554	+
1555	+	for (i = 0; i < nInfo; i++){
1556	+	info[i].n_atoms = tot_atoms;
1557	+	info[i].n_bonds = tot_bonds;
1558	+	info[i].n_bends = tot_bends;
1559	+	info[i].n_torsions = tot_torsions;
1560	+	info[i].n_SRI = tot_SRI;
1561	+	info[i].n_mol = tot_nmol;
1562	+	info[i].ngroup = tot_groups;
1563	+	info[i].molMembershipArray = molMembershipArray;
1564	+	}
1565	+	}
1566	+
1567	+	#ifdef IS_MPI
1568	+
1569	+	void SimSetup::mpiMolDivide(void){
1570	+	int i, j, k;
1571	+	int localMol, allMol;
1572	+	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1573	+	int local_rigid, local_groups;
1574	+	vector<int> globalMolIndex;
1575	+	int ncutgroups, atomsingroups, ngroupsinstamp;
1576	+	CutoffGroupStamp* cg;
1577	+
1578	+	mpiSim = new mpiSimulation(info);
1579	+
1580	+	mpiSim->divideLabor();
1581	+	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1582	+	//globalMolIndex = mpiSim->getGlobalMolIndex();
1583	+
1584	+	// set up the local variables
1585	+
1586	+	mol2proc = mpiSim->getMolToProcMap();
1587	+	molCompType = mpiSim->getMolComponentType();
1588	+
1589	+	allMol = 0;
1590	+	localMol = 0;
1591	+	local_atoms = 0;
1592	+	local_bonds = 0;
1593	+	local_bends = 0;
1594	+	local_torsions = 0;
1595	+	local_rigid = 0;
1596	+	local_groups = 0;
1597	+	globalAtomCounter = 0;
1598	+
1599	+	for (i = 0; i < n_components; i++){
1600	+	for (j = 0; j < components_nmol[i]; j++){
1601	+	if (mol2proc[allMol] == worldRank){
1602	+	local_atoms += comp_stamps[i]->getNAtoms();
1603	+	local_bonds += comp_stamps[i]->getNBonds();
1604	+	local_bends += comp_stamps[i]->getNBends();
1605	+	local_torsions += comp_stamps[i]->getNTorsions();
1606	+	local_rigid += comp_stamps[i]->getNRigidBodies();
1607	+
1608	+	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1609	+	atomsingroups = 0;
1610	+	for (k=0; k < ncutgroups; k++) {
1611	+	cg = comp_stamps[i]->getCutoffGroup(k);
1612	+	atomsingroups += cg->getNMembers();
1613	+	}
1614	+	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups +
1615	+	ncutgroups;
1616	+	local_groups += ngroupsinstamp;
1617	+
1618	+	localMol++;
1619	+	}
1620	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1621	+	info[0].molMembershipArray[globalAtomCounter] = allMol;
1622	+	globalAtomCounter++;
1623	+	}
1624	+
1625	+	allMol++;
1626	+	}
1627	+	}
1628	+	local_SRI = local_bonds + local_bends + local_torsions;
1629	+
1630	+	info[0].n_atoms = mpiSim->getNAtomsLocal();
1631	+
1632	+	if (local_atoms != info[0].n_atoms){
1633	+	sprintf(painCave.errMsg,
1634	+	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1635	+	"\tlocalAtom (%d) are not equal.\n",
1636	+	info[0].n_atoms, local_atoms);
1637	+	painCave.isFatal = 1;
1638	+	simError();
1639	+	}
1640	+
1641	+	info[0].ngroup = mpiSim->getNGroupsLocal();
1642	+	if (local_groups != info[0].ngroup){
1643	+	sprintf(painCave.errMsg,
1644	+	"SimSetup error: mpiSim's localGroups (%d) and SimSetup's\n"
1645	+	"\tlocalGroups (%d) are not equal.\n",
1646	+	info[0].ngroup, local_groups);
1647	+	painCave.isFatal = 1;
1648	+	simError();
1649	+	}
1650	+
1651	+	info[0].n_bonds = local_bonds;
1652	+	info[0].n_bends = local_bends;
1653	+	info[0].n_torsions = local_torsions;
1654	+	info[0].n_SRI = local_SRI;
1655	+	info[0].n_mol = localMol;
1656	+
1657	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1658	+	MPIcheckPoint();
1659	+	}
1660	+
1661	+	#endif // is_mpi
1662	+
1663	+
1664	+	void SimSetup::makeSysArrays(void){
1665	+
1666	+	#ifndef IS_MPI
1667	+	int k, j;
1668	+	#endif // is_mpi
1669	+	int i, l;
1670	+
1671	+	Atom** the_atoms;
1672	+	Molecule* the_molecules;
1673	+
1674	+	for (l = 0; l < nInfo; l++){
1675	+	// create the atom and short range interaction arrays
1676	+
1677	+	the_atoms = new Atom * [info[l].n_atoms];
1678	+	the_molecules = new Molecule[info[l].n_mol];
1679	+	int molIndex;
1680	+
1681	+	// initialize the molecule's stampID's
1682	+
1683	+	#ifdef IS_MPI
1684	+
1685	+
1686	+	molIndex = 0;
1687	+	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1688	+	if (mol2proc[i] == worldRank){
1689	+	the_molecules[molIndex].setStampID(molCompType[i]);
1690	+	the_molecules[molIndex].setMyIndex(molIndex);
1691	+	the_molecules[molIndex].setGlobalIndex(i);
1692	+	molIndex++;
1693	+	}
1694	+	}
1695	+
1696	+	#else // is_mpi
1697	+
1698	+	molIndex = 0;
1699	+	globalAtomCounter = 0;
1700	+	for (i = 0; i < n_components; i++){
1701	+	for (j = 0; j < components_nmol[i]; j++){
1702	+	the_molecules[molIndex].setStampID(i);
1703	+	the_molecules[molIndex].setMyIndex(molIndex);
1704	+	the_molecules[molIndex].setGlobalIndex(molIndex);
1705	+	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1706	+	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1707	+	globalAtomCounter++;
1708	+	}
1709	+	molIndex++;
1710	+	}
1711	+	}
1712	+
1713	+
1714	+	#endif // is_mpi
1715	+
1716	+	info[l].globalExcludes = new int;
1717	+	info[l].globalExcludes[0] = 0;
1718	+
1719	+	// set the arrays into the SimInfo object
1720	+
1721	+	info[l].atoms = the_atoms;
1722	+	info[l].molecules = the_molecules;
1723	+	info[l].nGlobalExcludes = 0;
1724	+
1725	+	the_ff->setSimInfo(info);
1726	+	}
1727	+	}
1728	+
1729	+	void SimSetup::makeIntegrator(void){
1730	+	int k;
1731	+
1732	+	NVE<RealIntegrator>* myNVE = NULL;
1733	+	NVT<RealIntegrator>* myNVT = NULL;
1734	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1735	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1736	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1737	+
1738	+	for (k = 0; k < nInfo; k++){
1739	+	switch (ensembleCase){
1740	+	case NVE_ENS:
1741	+	if (globals->haveZconstraints()){
1742	+	setupZConstraint(info[k]);
1743	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1744	+	}
1745	+	else{
1746	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1747	+	}
1748	+
1749	+	info->the_integrator = myNVE;
1750	+	break;
1751	+
1752	+	case NVT_ENS:
1753	+	if (globals->haveZconstraints()){
1754	+	setupZConstraint(info[k]);
1755	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1756	+	}
1757	+	else
1758	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1759	+
1760	+	myNVT->setTargetTemp(globals->getTargetTemp());
1761	+
1762	+	if (globals->haveTauThermostat())
1763	+	myNVT->setTauThermostat(globals->getTauThermostat());
1764	+	else{
1765	+	sprintf(painCave.errMsg,
1766	+	"SimSetup error: If you use the NVT\n"
1767	+	"\tensemble, you must set tauThermostat.\n");
1768	+	painCave.isFatal = 1;
1769	+	simError();
1770	+	}
1771	+
1772	+	info->the_integrator = myNVT;
1773	+	break;
1774	+
1775	+	case NPTi_ENS:
1776	+	if (globals->haveZconstraints()){
1777	+	setupZConstraint(info[k]);
1778	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1779	+	}
1780	+	else
1781	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1782	+
1783	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1784	+
1785	+	if (globals->haveTargetPressure())
1786	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1787	+	else{
1788	+	sprintf(painCave.errMsg,
1789	+	"SimSetup error: If you use a constant pressure\n"
1790	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1791	+	painCave.isFatal = 1;
1792	+	simError();
1793	+	}
1794	+
1795	+	if (globals->haveTauThermostat())
1796	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1797	+	else{
1798	+	sprintf(painCave.errMsg,
1799	+	"SimSetup error: If you use an NPT\n"
1800	+	"\tensemble, you must set tauThermostat.\n");
1801	+	painCave.isFatal = 1;
1802	+	simError();
1803	+	}
1804	+
1805	+	if (globals->haveTauBarostat())
1806	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1807	+	else{
1808	+	sprintf(painCave.errMsg,
1809	+	"SimSetup error: If you use an NPT\n"
1810	+	"\tensemble, you must set tauBarostat.\n");
1811	+	painCave.isFatal = 1;
1812	+	simError();
1813	+	}
1814	+
1815	+	info->the_integrator = myNPTi;
1816	+	break;
1817	+
1818	+	case NPTf_ENS:
1819	+	if (globals->haveZconstraints()){
1820	+	setupZConstraint(info[k]);
1821	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1822	+	}
1823	+	else
1824	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1825	+
1826	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1827	+
1828	+	if (globals->haveTargetPressure())
1829	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1830	+	else{
1831	+	sprintf(painCave.errMsg,
1832	+	"SimSetup error: If you use a constant pressure\n"
1833	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1834	+	painCave.isFatal = 1;
1835	+	simError();
1836	+	}
1837	+
1838	+	if (globals->haveTauThermostat())
1839	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1840	+
1841	+	else{
1842	+	sprintf(painCave.errMsg,
1843	+	"SimSetup error: If you use an NPT\n"
1844	+	"\tensemble, you must set tauThermostat.\n");
1845	+	painCave.isFatal = 1;
1846	+	simError();
1847	+	}
1848	+
1849	+	if (globals->haveTauBarostat())
1850	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1851	+
1852	+	else{
1853	+	sprintf(painCave.errMsg,
1854	+	"SimSetup error: If you use an NPT\n"
1855	+	"\tensemble, you must set tauBarostat.\n");
1856	+	painCave.isFatal = 1;
1857	+	simError();
1858	+	}
1859	+
1860	+	info->the_integrator = myNPTf;
1861	+	break;
1862	+
1863	+	case NPTxyz_ENS:
1864	+	if (globals->haveZconstraints()){
1865	+	setupZConstraint(info[k]);
1866	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1867	+	}
1868	+	else
1869	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1870	+
1871	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1872	+
1873	+	if (globals->haveTargetPressure())
1874	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1875	+	else{
1876	+	sprintf(painCave.errMsg,
1877	+	"SimSetup error: If you use a constant pressure\n"
1878	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1879	+	painCave.isFatal = 1;
1880	+	simError();
1881	+	}
1882	+
1883	+	if (globals->haveTauThermostat())
1884	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1885	+	else{
1886	+	sprintf(painCave.errMsg,
1887	+	"SimSetup error: If you use an NPT\n"
1888	+	"\tensemble, you must set tauThermostat.\n");
1889	+	painCave.isFatal = 1;
1890	+	simError();
1891	+	}
1892	+
1893	+	if (globals->haveTauBarostat())
1894	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1895	+	else{
1896	+	sprintf(painCave.errMsg,
1897	+	"SimSetup error: If you use an NPT\n"
1898	+	"\tensemble, you must set tauBarostat.\n");
1899	+	painCave.isFatal = 1;
1900	+	simError();
1901	+	}
1902	+
1903	+	info->the_integrator = myNPTxyz;
1904	+	break;
1905	+
1906	+	default:
1907	+	sprintf(painCave.errMsg,
1908	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1909	+	painCave.isFatal = 1;
1910	+	simError();
1911	+	}
1912	+	}
1913	+	}
1914	+
1915	+	void SimSetup::initFortran(void){
1916	+	info[0].refreshSim();
1917	+
1918	+	if (!strcmp(info[0].mixingRule, "standard")){
1919	+	the_ff->initForceField(LB_MIXING_RULE);
1920	+	}
1921	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1922	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1923	+	}
1924	+	else{
1925	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1926	+	info[0].mixingRule);
1927	+	painCave.isFatal = 1;
1928	+	simError();
1929	+	}
1930	+
1931	+
1932	+	#ifdef IS_MPI
1933	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1934	+	MPIcheckPoint();
1935	+	#endif // is_mpi
1936	+	}
1937	+
1938	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1939	+	int nZConstraints;
1940	+	ZconStamp** zconStamp;
1941	+
1942	+	if (globals->haveZconstraintTime()){
1943	+	//add sample time of z-constraint  into SimInfo's property list
1944	+	DoubleData* zconsTimeProp = new DoubleData();
1945	+	zconsTimeProp->setID(ZCONSTIME_ID);
1946	+	zconsTimeProp->setData(globals->getZconsTime());
1947	+	theInfo.addProperty(zconsTimeProp);
1948	+	}
1949	+	else{
1950	+	sprintf(painCave.errMsg,
1951	+	"ZConstraint error: If you use a ZConstraint,\n"
1952	+	"\tyou must set zconsTime.\n");
1953	+	painCave.isFatal = 1;
1954	+	simError();
1955	+	}
1956	+
1957	+	//push zconsTol into siminfo, if user does not specify
1958	+	//value for zconsTol, a default value will be used
1959	+	DoubleData* zconsTol = new DoubleData();
1960	+	zconsTol->setID(ZCONSTOL_ID);
1961	+	if (globals->haveZconsTol()){
1962	+	zconsTol->setData(globals->getZconsTol());
1963	+	}
1964	+	else{
1965	+	double defaultZConsTol = 0.01;
1966	+	sprintf(painCave.errMsg,
1967	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1968	+	"\tOOPSE will use a default value of %f.\n"
1969	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1970	+	defaultZConsTol);
1971	+	painCave.isFatal = 0;
1972	+	simError();
1973	+
1974	+	zconsTol->setData(defaultZConsTol);
1975	+	}
1976	+	theInfo.addProperty(zconsTol);
1977	+
1978	+	//set Force Subtraction Policy
1979	+	StringData* zconsForcePolicy = new StringData();
1980	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1981	+
1982	+	if (globals->haveZconsForcePolicy()){
1983	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1984	+	}
1985	+	else{
1986	+	sprintf(painCave.errMsg,
1987	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1988	+	"\tOOPSE will use PolicyByMass.\n"
1989	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1990	+	painCave.isFatal = 0;
1991	+	simError();
1992	+	zconsForcePolicy->setData("BYMASS");
1993	+	}
1994	+
1995	+	theInfo.addProperty(zconsForcePolicy);
1996	+
1997	+	//set zcons gap
1998	+	DoubleData* zconsGap = new DoubleData();
1999	+	zconsGap->setID(ZCONSGAP_ID);
2000	+
2001	+	if (globals->haveZConsGap()){
2002	+	zconsGap->setData(globals->getZconsGap());
2003	+	theInfo.addProperty(zconsGap);
2004	+	}
2005	+
2006	+	//set zcons fixtime
2007	+	DoubleData* zconsFixtime = new DoubleData();
2008	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
2009	+
2010	+	if (globals->haveZConsFixTime()){
2011	+	zconsFixtime->setData(globals->getZconsFixtime());
2012	+	theInfo.addProperty(zconsFixtime);
2013	+	}
2014	+
2015	+	//set zconsUsingSMD
2016	+	IntData* zconsUsingSMD = new IntData();
2017	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
2018	+
2019	+	if (globals->haveZConsUsingSMD()){
2020	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
2021	+	theInfo.addProperty(zconsUsingSMD);
2022	+	}
2023	+
2024	+	//Determine the name of ouput file and add it into SimInfo's property list
2025	+	//Be careful, do not use inFileName, since it is a pointer which
2026	+	//point to a string at master node, and slave nodes do not contain that string
2027	+
2028	+	string zconsOutput(theInfo.finalName);
2029	+
2030	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
2031	+
2032	+	StringData* zconsFilename = new StringData();
2033	+	zconsFilename->setID(ZCONSFILENAME_ID);
2034	+	zconsFilename->setData(zconsOutput);
2035	+
2036	+	theInfo.addProperty(zconsFilename);
2037	+
2038	+	//setup index, pos and other parameters of z-constraint molecules
2039	+	nZConstraints = globals->getNzConstraints();
2040	+	theInfo.nZconstraints = nZConstraints;
2041	+
2042	+	zconStamp = globals->getZconStamp();
2043	+	ZConsParaItem tempParaItem;
2044	+
2045	+	ZConsParaData* zconsParaData = new ZConsParaData();
2046	+	zconsParaData->setID(ZCONSPARADATA_ID);
2047	+
2048	+	for (int i = 0; i < nZConstraints; i++){
2049	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
2050	+	tempParaItem.zPos = zconStamp[i]->getZpos();
2051	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
2052	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
2053	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
2054	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
2055	+	zconsParaData->addItem(tempParaItem);
2056	+	}
2057	+
2058	+	//check the uniqueness of index
2059	+	if(!zconsParaData->isIndexUnique()){
2060	+	sprintf(painCave.errMsg,
2061	+	"ZConstraint Error: molIndex is not unique!\n");
2062	+	painCave.isFatal = 1;
2063	+	simError();
2064	+	}
2065	+
2066	+	//sort the parameters by index of molecules
2067	+	zconsParaData->sortByIndex();
2068	+
2069	+	//push data into siminfo, therefore, we can retrieve later
2070	+	theInfo.addProperty(zconsParaData);
2071	+	}
2072	+
2073	+	void SimSetup::makeMinimizer(){
2074	+
2075	+	OOPSEMinimizer* myOOPSEMinimizer;
2076	+	MinimizerParameterSet* param;
2077	+	char minimizerName[100];
2078	+
2079	+	for (int i = 0; i < nInfo; i++){
2080	+
2081	+	//prepare parameter set for minimizer
2082	+	param = new MinimizerParameterSet();
2083	+	param->setDefaultParameter();
2084	+
2085	+	if (globals->haveMinimizer()){
2086	+	param->setFTol(globals->getMinFTol());
2087	+	}
2088	+
2089	+	if (globals->haveMinGTol()){
2090	+	param->setGTol(globals->getMinGTol());
2091	+	}
2092	+
2093	+	if (globals->haveMinMaxIter()){
2094	+	param->setMaxIteration(globals->getMinMaxIter());
2095	+	}
2096	+
2097	+	if (globals->haveMinWriteFrq()){
2098	+	param->setMaxIteration(globals->getMinMaxIter());
2099	+	}
2100	+
2101	+	if (globals->haveMinWriteFrq()){
2102	+	param->setWriteFrq(globals->getMinWriteFrq());
2103	+	}
2104	+
2105	+	if (globals->haveMinStepSize()){
2106	+	param->setStepSize(globals->getMinStepSize());
2107	+	}
2108	+
2109	+	if (globals->haveMinLSMaxIter()){
2110	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2111	+	}
2112	+
2113	+	if (globals->haveMinLSTol()){
2114	+	param->setLineSearchTol(globals->getMinLSTol());
2115	+	}
2116	+
2117	+	strcpy(minimizerName, globals->getMinimizer());
2118	+
2119	+	if (!strcasecmp(minimizerName, "CG")){
2120	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2121	+	}
2122	+	else if (!strcasecmp(minimizerName, "SD")){
2123	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2124	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2125	+	}
2126	+	else{
2127	+	sprintf(painCave.errMsg,
2128	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2129	+	painCave.isFatal = 0;
2130	+	simError();
2131	+
2132	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2133	+	}
2134	+	info[i].the_integrator = myOOPSEMinimizer;
2135	+
2136	+	//store the minimizer into simInfo
2137	+	info[i].the_minimizer = myOOPSEMinimizer;
2138	+	info[i].has_minimizer = true;
2139	+	}
2140	+
2141	+	}

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