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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 604 by gezelter, Tue Jul 15 03:08:00 2003 UTC vs.
Revision 1157 by tim, Tue May 11 20:33:41 2004 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
12	+	#include "RigidBody.hpp"
13	+	//#include "ConjugateMinimizer.hpp"
14	+	#include "OOPSEMinimizer.hpp"
15
16		#ifdef IS_MPI
17		#include "mpiBASS.h"
#	Line 14 | Line 20
20
21		// some defines for ensemble and Forcefield  cases
22
23	<	#define NVE_ENS   0
24	<	#define NVT_ENS   1
25	<	#define NPTi_ENS  2
26	<	#define NPTf_ENS  3
27	<	#define NPTim_ENS 4
22	<	#define NPTfm_ENS 5
23	>	#define NVE_ENS        0
24	>	#define NVT_ENS        1
25	>	#define NPTi_ENS       2
26	>	#define NPTf_ENS       3
27	>	#define NPTxyz_ENS     4
28
29
30	<	#define FF_DUFF 0
31	<	#define FF_LJ   1
30	>	#define FF_DUFF  0
31	>	#define FF_LJ    1
32	>	#define FF_EAM   2
33	>	#define FF_H2O   3
34
35	+	using namespace std;
36
37	+	/**
38	+	* Check whether dividend is divisble by divisor or not
39	+	*/
40	+	bool isDivisible(double dividend, double divisor){
41	+	double tolerance = 0.000001;
42	+	double quotient;
43	+	double diff;
44	+	int intQuotient;
45	+
46	+	quotient = dividend / divisor;
47	+
48	+	if (quotient < 0)
49	+	quotient = -quotient;
50	+
51	+	intQuotient = int (quotient + tolerance);
52	+
53	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
54	+
55	+	if (diff <= tolerance)
56	+	return true;
57	+	else
58	+	return false;
59	+	}
60	+
61		SimSetup::SimSetup(){
62	+
63	+	initSuspend = false;
64	+	isInfoArray = 0;
65	+	nInfo = 1;
66	+
67		stamps = new MakeStamps();
68		globals = new Globals();
69	<
69	>
70	>
71		#ifdef IS_MPI
72	<	strcpy( checkPointMsg, "SimSetup creation successful" );
72	>	strcpy(checkPointMsg, "SimSetup creation successful");
73		MPIcheckPoint();
74		#endif // IS_MPI
75		}
#	Line 41 | Line 79 | SimSetup::~SimSetup(){
79		delete globals;
80		}
81
82	<	void SimSetup::parseFile( char* fileName ){
82	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
83	>	info = the_info;
84	>	nInfo = theNinfo;
85	>	isInfoArray = 1;
86	>	initSuspend = true;
87	>	}
88
89	+
90	+	void SimSetup::parseFile(char* fileName){
91		#ifdef IS_MPI
92	<	if( worldRank == 0 ){
92	>	if (worldRank == 0){
93		#endif // is_mpi
94	<
94	>
95		inFileName = fileName;
96	<	set_interface_stamps( stamps, globals );
97	<
96	>	set_interface_stamps(stamps, globals);
97	>
98		#ifdef IS_MPI
99		mpiEventInit();
100		#endif
101
102	<	yacc_BASS( fileName );
102	>	yacc_BASS(fileName);
103
104		#ifdef IS_MPI
105		throwMPIEvent(NULL);
106		}
107	<	else receiveParse();
107	>	else{
108	>	receiveParse();
109	>	}
110		#endif
111
112		}
113
114		#ifdef IS_MPI
115		void SimSetup::receiveParse(void){
116	<
117	<	set_interface_stamps( stamps, globals );
118	<	mpiEventInit();
119	<	MPIcheckPoint();
73	<	mpiEventLoop();
74	<
116	>	set_interface_stamps(stamps, globals);
117	>	mpiEventInit();
118	>	MPIcheckPoint();
119	>	mpiEventLoop();
120		}
121
122		#endif // is_mpi
123
124	<	void SimSetup::createSim( void ){
124	>	void SimSetup::createSim(void){
125
126	<	MakeStamps *the_stamps;
82	<	Globals* the_globals;
83	<	int i, j, k, globalAtomIndex;
84	<
85	<	int ensembleCase;
86	<	int ffCase;
87	<
88	<	ensembleCase = -1;
89	<	ffCase = -1;
126	>	// gather all of the information from the Bass file
127
128	<	// get the stamps and globals;
92	<	the_stamps = stamps;
93	<	the_globals = globals;
128	>	gatherInfo();
129
130	<	// set the easy ones first
96	<	simnfo->target_temp = the_globals->getTargetTemp();
97	<	simnfo->dt = the_globals->getDt();
98	<	simnfo->run_time = the_globals->getRunTime();
130	>	// creation of complex system objects
131
132	<	// get the ones we know are there, yet still may need some work.
101	<	n_components = the_globals->getNComponents();
102	<	strcpy( force_field, the_globals->getForceField() );
132	>	sysObjectsCreation();
133
134	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
105	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
106	<	else{
107	<	sprintf( painCave.errMsg,
108	<	"SimSetup Error. Unrecognized force field -> %s\n",
109	<	force_field );
110	<	painCave.isFatal = 1;
111	<	simError();
112	<	}
134	>	// check on the post processing info
135
136	<	// get the ensemble:
115	<	strcpy( ensemble, the_globals->getEnsemble() );
136	>	finalInfoCheck();
137
138	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
118	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
119	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
120	<	ensembleCase = NPTi_ENS;
121	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
122	<	else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS;
123	<	else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS;
124	<	else{
125	<	sprintf( painCave.errMsg,
126	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
127	<	"reverting to NVE for this simulation.\n",
128	<	ensemble );
129	<	painCave.isFatal = 0;
130	<	simError();
131	<	strcpy( ensemble, "NVE" );
132	<	ensembleCase = NVE_ENS;
133	<	}
134	<	strcpy( simnfo->ensemble, ensemble );
138	>	// initialize the system coordinates
139
140	+	if ( !initSuspend ){
141	+	initSystemCoords();
142
143	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
144	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
145	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
140	<	//     if (the_globals->haveTargetPressure())
141	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
142	<	//     else {
143	<	//       sprintf( painCave.errMsg,
144	<	//                "SimSetup error: If you use the constant pressure\n"
145	<	//                "    ensemble, you must set targetPressure.\n"
146	<	//                "    This was found in the BASS file.\n");
147	<	//       painCave.isFatal = 1;
148	<	//       simError();
149	<	//     }
143	>	if( !(globals->getUseInitTime()) )
144	>	info[0].currentTime = 0.0;
145	>	}
146
147	<	//     if (the_globals->haveTauThermostat())
152	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
153	<	//     else if (the_globals->haveQmass())
154	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
155	<	//     else {
156	<	//       sprintf( painCave.errMsg,
157	<	//                "SimSetup error: If you use one of the constant temperature\n"
158	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
159	<	//                "    Neither of these was found in the BASS file.\n");
160	<	//       painCave.isFatal = 1;
161	<	//       simError();
162	<	//     }
147	>	// make the output filenames
148
149	<	//     if (the_globals->haveTauBarostat())
150	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
166	<	//     else {
167	<	//       sprintf( painCave.errMsg,
168	<	//                "SimSetup error: If you use the constant pressure\n"
169	<	//                "    ensemble, you must set tauBarostat.\n"
170	<	//                "    This was found in the BASS file.\n");
171	<	//       painCave.isFatal = 1;
172	<	//       simError();
173	<	//     }
174	<
175	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
176	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
177	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
178	<
179	<	//     if (the_globals->haveTauThermostat())
180	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
181	<	//     else if (the_globals->haveQmass())
182	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
183	<	//     else {
184	<	//       sprintf( painCave.errMsg,
185	<	//                "SimSetup error: If you use one of the constant temperature\n"
186	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
187	<	//                "    Neither of these was found in the BASS file.\n");
188	<	//       painCave.isFatal = 1;
189	<	//       simError();
190	<	//     }
191	<
192	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
193	<	simnfo->usePBC = the_globals->getPBC();
194	<
195	<	int usesDipoles = 0;
196	<	switch( ffCase ){
197	<
198	<	case FF_DUFF:
199	<	the_ff = new DUFF();
200	<	usesDipoles = 1;
201	<	break;
202	<
203	<	case FF_LJ:
204	<	the_ff = new LJFF();
205	<	break;
206	<
207	<	default:
208	<	sprintf( painCave.errMsg,
209	<	"SimSetup Error. Unrecognized force field in case statement.\n");
210	<	painCave.isFatal = 1;
211	<	simError();
212	<	}
213	<
149	>	makeOutNames();
150	>
151		#ifdef IS_MPI
152	<	strcpy( checkPointMsg, "ForceField creation successful" );
153	<	MPIcheckPoint();
217	<	#endif // is_mpi
152	>	mpiSim->mpiRefresh();
153	>	#endif
154
155	<	// get the components and calculate the tot_nMol and indvidual n_mol
220	<	the_components = the_globals->getComponents();
221	<	components_nmol = new int[n_components];
222	<	comp_stamps = new MoleculeStamp*[n_components];
155	>	// initialize the Fortran
156
157	<	if( !the_globals->haveNMol() ){
225	<	// we don't have the total number of molecules, so we assume it is
226	<	// given in each component
157	>	initFortran();
158
159	<	tot_nmol = 0;
160	<	for( i=0; i<n_components; i++ ){
159	>	if (globals->haveMinimizer())
160	>	// make minimizer
161	>	makeMinimizer();
162	>	else
163	>	// make the integrator
164	>	makeIntegrator();
165
166	<	if( !the_components[i]->haveNMol() ){
232	<	// we have a problem
233	<	sprintf( painCave.errMsg,
234	<	"SimSetup Error. No global NMol or component NMol"
235	<	" given. Cannot calculate the number of atoms.\n" );
236	<	painCave.isFatal = 1;
237	<	simError();
238	<	}
166	>	}
167
240	–	tot_nmol += the_components[i]->getNMol();
241	–	components_nmol[i] = the_components[i]->getNMol();
242	–	}
243	–	}
244	–	else{
245	–	sprintf( painCave.errMsg,
246	–	"SimSetup error.\n"
247	–	"\tSorry, the ability to specify total"
248	–	" nMols and then give molfractions in the components\n"
249	–	"\tis not currently supported."
250	–	" Please give nMol in the components.\n" );
251	–	painCave.isFatal = 1;
252	–	simError();
253	–
254	–
255	–	//     tot_nmol = the_globals->getNMol();
256	–
257	–	//   //we have the total number of molecules, now we check for molfractions
258	–	//     for( i=0; i<n_components; i++ ){
259	–
260	–	//       if( !the_components[i]->haveMolFraction() ){
261	–
262	–	//  if( !the_components[i]->haveNMol() ){
263	–	//    //we have a problem
264	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
265	–	//              << " nMol was given in component
266	–
267	–	}
168
169	<	#ifdef IS_MPI
170	<	strcpy( checkPointMsg, "Have the number of components" );
171	<	MPIcheckPoint();
172	<	#endif // is_mpi
169	>	void SimSetup::makeMolecules(void){
170	>	int i, j, k;
171	>	int exI, exJ, exK, exL, slI, slJ;
172	>	int tempI, tempJ, tempK, tempL;
173	>	int molI;
174	>	int stampID, atomOffset, rbOffset;
175	>	molInit molInfo;
176	>	DirectionalAtom* dAtom;
177	>	RigidBody* myRB;
178	>	StuntDouble* mySD;
179	>	LinkedAssign* extras;
180	>	LinkedAssign* current_extra;
181	>	AtomStamp* currentAtom;
182	>	BondStamp* currentBond;
183	>	BendStamp* currentBend;
184	>	TorsionStamp* currentTorsion;
185	>	RigidBodyStamp* currentRigidBody;
186	>	CutoffGroupStamp* currentCutoffGroup;
187	>	CutoffGroup* myCutoffGroup;
188	>
189	>	bond_pair* theBonds;
190	>	bend_set* theBends;
191	>	torsion_set* theTorsions;
192
193	<	// make an array of molecule stamps that match the components used.
275	<	// also extract the used stamps out into a separate linked list
193	>	set<int> skipList;
194
195	<	simnfo->nComponents = n_components;
196	<	simnfo->componentsNmol = components_nmol;
197	<	simnfo->compStamps = comp_stamps;
280	<	simnfo->headStamp = new LinkedMolStamp();
281	<
282	<	char* id;
283	<	LinkedMolStamp* headStamp = simnfo->headStamp;
284	<	LinkedMolStamp* currentStamp = NULL;
285	<	for( i=0; i<n_components; i++ ){
195	>	double phi, theta, psi;
196	>	char* molName;
197	>	char rbName[100];
198
199	<	id = the_components[i]->getType();
288	<	comp_stamps[i] = NULL;
289	<
290	<	// check to make sure the component isn't already in the list
199	>	//init the forceField paramters
200
201	<	comp_stamps[i] = headStamp->match( id );
202	<	if( comp_stamps[i] == NULL ){
201	>	the_ff->readParams();
202	>
203	>	// init the atoms
204	>
205	>	int nMembers, nNew, rb1, rb2;
206	>
207	>	for (k = 0; k < nInfo; k++){
208	>	the_ff->setSimInfo(&(info[k]));
209	>
210	>	atomOffset = 0;
211	>
212	>	for (i = 0; i < info[k].n_mol; i++){
213	>	stampID = info[k].molecules[i].getStampID();
214	>	molName = comp_stamps[stampID]->getID();
215	>
216	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
217	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
218	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
219	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
220	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
221	>	molInfo.nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
222
223	<	// extract the component from the list;
223	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
224	>
225	>	if (molInfo.nBonds > 0)
226	>	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
227	>	else
228	>	molInfo.myBonds = NULL;
229	>
230	>	if (molInfo.nBends > 0)
231	>	molInfo.myBends = new (Bend *) [molInfo.nBends];
232	>	else
233	>	molInfo.myBends = NULL;
234	>
235	>	if (molInfo.nTorsions > 0)
236	>	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
237	>	else
238	>	molInfo.myTorsions = NULL;
239	>
240	>	theBonds = new bond_pair[molInfo.nBonds];
241	>	theBends = new bend_set[molInfo.nBends];
242	>	theTorsions = new torsion_set[molInfo.nTorsions];
243
244	<	currentStamp = the_stamps->extractMolStamp( id );
298	<	if( currentStamp == NULL ){
299	<	sprintf( painCave.errMsg,
300	<	"SimSetup error: Component \"%s\" was not found in the "
301	<	"list of declared molecules\n",
302	<	id );
303	<	painCave.isFatal = 1;
304	<	simError();
305	<	}
306	<
307	<	headStamp->add( currentStamp );
308	<	comp_stamps[i] = headStamp->match( id );
309	<	}
310	<	}
244	>	// make the Atoms
245
246	<	#ifdef IS_MPI
247	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
314	<	MPIcheckPoint();
315	<	#endif // is_mpi
316	<
246	>	for (j = 0; j < molInfo.nAtoms; j++){
247	>	currentAtom = comp_stamps[stampID]->getAtom(j);
248
249	+	if (currentAtom->haveOrientation()){
250	+	dAtom = new DirectionalAtom((j + atomOffset),
251	+	info[k].getConfiguration());
252	+	info[k].n_oriented++;
253	+	molInfo.myAtoms[j] = dAtom;
254
255	+	// Directional Atoms have standard unit vectors which are oriented
256	+	// in space using the three Euler angles.  We assume the standard
257	+	// unit vector was originally along the z axis below.
258
259	<	// caclulate the number of atoms, bonds, bends and torsions
259	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
260	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
261	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
262
263	<	tot_atoms = 0;
264	<	tot_bonds = 0;
265	<	tot_bends = 0;
266	<	tot_torsions = 0;
326	<	for( i=0; i<n_components; i++ ){
327	<
328	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
329	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
330	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
331	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
332	<	}
263	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
264	>
265	>	}
266	>	else{
267
268	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
268	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
269
270	<	simnfo->n_atoms = tot_atoms;
337	<	simnfo->n_bonds = tot_bonds;
338	<	simnfo->n_bends = tot_bends;
339	<	simnfo->n_torsions = tot_torsions;
340	<	simnfo->n_SRI = tot_SRI;
341	<	simnfo->n_mol = tot_nmol;
342	<
343	<	simnfo->molMembershipArray = new int[tot_atoms];
270	>	}
271
272	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
273		#ifdef IS_MPI
274
275	<	// divide the molecules among processors here.
348	<
349	<	mpiSim = new mpiSimulation( simnfo );
350	<
351	<	globalIndex = mpiSim->divideLabor();
275	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
276
277	<	// set up the local variables
278	<
355	<	int localMol, allMol;
356	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
277	>	#endif // is_mpi
278	>	}
279
280	<	int* mol2proc = mpiSim->getMolToProcMap();
281	<	int* molCompType = mpiSim->getMolComponentType();
282	<
283	<	allMol = 0;
284	<	localMol = 0;
363	<	local_atoms = 0;
364	<	local_bonds = 0;
365	<	local_bends = 0;
366	<	local_torsions = 0;
367	<	globalAtomIndex = 0;
280	>	// make the bonds
281	>	for (j = 0; j < molInfo.nBonds; j++){
282	>	currentBond = comp_stamps[stampID]->getBond(j);
283	>	theBonds[j].a = currentBond->getA() + atomOffset;
284	>	theBonds[j].b = currentBond->getB() + atomOffset;
285
286	+	tempI = theBonds[j].a;
287	+	tempJ = theBonds[j].b;
288
289	<	for( i=0; i<n_components; i++ ){
289	>	#ifdef IS_MPI
290	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
291	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
292	>	#else
293	>	exI = tempI + 1;
294	>	exJ = tempJ + 1;
295	>	#endif
296
297	<	for( j=0; j<components_nmol[i]; j++ ){
373	<
374	<	if( mol2proc[allMol] == worldRank ){
375	<
376	<	local_atoms +=    comp_stamps[i]->getNAtoms();
377	<	local_bonds +=    comp_stamps[i]->getNBonds();
378	<	local_bends +=    comp_stamps[i]->getNBends();
379	<	local_torsions += comp_stamps[i]->getNTorsions();
380	<	localMol++;
381	<	}
382	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
383	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
384	<	globalAtomIndex++;
297	>	info[k].excludes->addPair(exI, exJ);
298		}
299
300	<	allMol++;
301	<	}
302	<	}
303	<	local_SRI = local_bonds + local_bends + local_torsions;
304	<
305	<	simnfo->n_atoms = mpiSim->getMyNlocal();
393	<
394	<	if( local_atoms != simnfo->n_atoms ){
395	<	sprintf( painCave.errMsg,
396	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
397	<	" localAtom (%d) are not equal.\n",
398	<	simnfo->n_atoms,
399	<	local_atoms );
400	<	painCave.isFatal = 1;
401	<	simError();
402	<	}
300	>	//make the bends
301	>	for (j = 0; j < molInfo.nBends; j++){
302	>	currentBend = comp_stamps[stampID]->getBend(j);
303	>	theBends[j].a = currentBend->getA() + atomOffset;
304	>	theBends[j].b = currentBend->getB() + atomOffset;
305	>	theBends[j].c = currentBend->getC() + atomOffset;
306
307	<	simnfo->n_bonds = local_bonds;
308	<	simnfo->n_bends = local_bends;
309	<	simnfo->n_torsions = local_torsions;
407	<	simnfo->n_SRI = local_SRI;
408	<	simnfo->n_mol = localMol;
307	>	if (currentBend->haveExtras()){
308	>	extras = currentBend->getExtras();
309	>	current_extra = extras;
310
311	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
312	<	MPIcheckPoint();
313	<
314	<
315	<	#endif // is_mpi
316	<
311	>	while (current_extra != NULL){
312	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
313	>	switch (current_extra->getType()){
314	>	case 0:
315	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
316	>	theBends[j].isGhost = 1;
317	>	break;
318
319	<	// create the atom and short range interaction arrays
319	>	case 1:
320	>	theBends[j].ghost = (int) current_extra->getDouble() +
321	>	atomOffset;
322	>	theBends[j].isGhost = 1;
323	>	break;
324
325	<	Atom::createArrays(simnfo->n_atoms);
326	<	the_atoms = new Atom*[simnfo->n_atoms];
327	<	the_molecules = new Molecule[simnfo->n_mol];
328	<	int molIndex;
329	<
330	<	// initialize the molecule's stampID's
325	>	default:
326	>	sprintf(painCave.errMsg,
327	>	"SimSetup Error: ghostVectorSource was neither a "
328	>	"double nor an int.\n"
329	>	"-->Bend[%d] in %s\n",
330	>	j, comp_stamps[stampID]->getID());
331	>	painCave.isFatal = 1;
332	>	simError();
333	>	}
334	>	}
335	>	else{
336	>	sprintf(painCave.errMsg,
337	>	"SimSetup Error: unhandled bend assignment:\n"
338	>	"    -->%s in Bend[%d] in %s\n",
339	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
340	>	painCave.isFatal = 1;
341	>	simError();
342	>	}
343
344	+	current_extra = current_extra->getNext();
345	+	}
346	+	}
347	+
348	+	if (theBends[j].isGhost) {
349	+
350	+	tempI = theBends[j].a;
351	+	tempJ = theBends[j].b;
352	+
353		#ifdef IS_MPI
354	<
354	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
355	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
356	>	#else
357	>	exI = tempI + 1;
358	>	exJ = tempJ + 1;
359	>	#endif
360	>	info[k].excludes->addPair(exI, exJ);
361
362	<	molIndex = 0;
430	<	for(i=0; i<mpiSim->getTotNmol(); i++){
431	<
432	<	if(mol2proc[i] == worldRank ){
433	<	the_molecules[molIndex].setStampID( molCompType[i] );
434	<	the_molecules[molIndex].setMyIndex( molIndex );
435	<	the_molecules[molIndex].setGlobalIndex( i );
436	<	molIndex++;
437	<	}
438	<	}
362	>	} else {
363
364	<	#else // is_mpi
365	<
366	<	molIndex = 0;
367	<	globalAtomIndex = 0;
368	<	for(i=0; i<n_components; i++){
369	<	for(j=0; j<components_nmol[i]; j++ ){
370	<	the_molecules[molIndex].setStampID( i );
371	<	the_molecules[molIndex].setMyIndex( molIndex );
372	<	the_molecules[molIndex].setGlobalIndex( molIndex );
373	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
374	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
375	<	globalAtomIndex++;
364	>	tempI = theBends[j].a;
365	>	tempJ = theBends[j].b;
366	>	tempK = theBends[j].c;
367	>
368	>	#ifdef IS_MPI
369	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
370	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
371	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
372	>	#else
373	>	exI = tempI + 1;
374	>	exJ = tempJ + 1;
375	>	exK = tempK + 1;
376	>	#endif
377	>
378	>	info[k].excludes->addPair(exI, exK);
379	>	info[k].excludes->addPair(exI, exJ);
380	>	info[k].excludes->addPair(exJ, exK);
381	>	}
382		}
453	–	molIndex++;
454	–	}
455	–	}
456	–
383
384	<	#endif // is_mpi
384	>	for (j = 0; j < molInfo.nTorsions; j++){
385	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
386	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
387	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
388	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
389	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
390
391	+	tempI = theTorsions[j].a;
392	+	tempJ = theTorsions[j].b;
393	+	tempK = theTorsions[j].c;
394	+	tempL = theTorsions[j].d;
395
396	<	if( simnfo->n_SRI ){
397	<
398	<	Exclude::createArray(simnfo->n_SRI);
399	<	the_excludes = new Exclude*[simnfo->n_SRI];
400	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
401	<	simnfo->globalExcludes = new int;
402	<	simnfo->n_exclude = simnfo->n_SRI;
403	<	}
404	<	else{
405	<
406	<	Exclude::createArray( 1 );
472	<	the_excludes = new Exclude*;
473	<	the_excludes[0] = new Exclude(0);
474	<	the_excludes[0]->setPair( 0,0 );
475	<	simnfo->globalExcludes = new int;
476	<	simnfo->globalExcludes[0] = 0;
477	<	simnfo->n_exclude = 0;
478	<	}
396	>	#ifdef IS_MPI
397	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
398	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
399	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
400	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
401	>	#else
402	>	exI = tempI + 1;
403	>	exJ = tempJ + 1;
404	>	exK = tempK + 1;
405	>	exL = tempL + 1;
406	>	#endif
407
408	<	// set the arrays into the SimInfo object
408	>	info[k].excludes->addPair(exI, exJ);
409	>	info[k].excludes->addPair(exI, exK);
410	>	info[k].excludes->addPair(exI, exL);
411	>	info[k].excludes->addPair(exJ, exK);
412	>	info[k].excludes->addPair(exJ, exL);
413	>	info[k].excludes->addPair(exK, exL);
414	>	}
415
416	<	simnfo->atoms = the_atoms;
417	<	simnfo->molecules = the_molecules;
418	<	simnfo->nGlobalExcludes = 0;
419	<	simnfo->excludes = the_excludes;
416	>
417	>	molInfo.myRigidBodies.clear();
418	>
419	>	for (j = 0; j < molInfo.nRigidBodies; j++){
420
421	+	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
422	+	nMembers = currentRigidBody->getNMembers();
423
424	<	// get some of the tricky things that may still be in the globals
424	>	// Create the Rigid Body:
425
426	<	double boxVector[3];
491	<	if( the_globals->haveBox() ){
492	<	boxVector[0] = the_globals->getBox();
493	<	boxVector[1] = the_globals->getBox();
494	<	boxVector[2] = the_globals->getBox();
495	<
496	<	simnfo->setBox( boxVector );
497	<	}
498	<	else if( the_globals->haveDensity() ){
426	>	myRB = new RigidBody();
427
428	<	double vol;
429	<	vol = (double)tot_nmol / the_globals->getDensity();
430	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
431	<	boxVector[1] = boxVector[0];
504	<	boxVector[2] = boxVector[0];
428	>	sprintf(rbName,"%s_RB_%d", molName, j);
429	>	myRB->setType(rbName);
430	>
431	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
432
433	<	simnfo->setBox( boxVector );
434	<	}
508	<	else{
509	<	if( !the_globals->haveBoxX() ){
510	<	sprintf( painCave.errMsg,
511	<	"SimSetup error, no periodic BoxX size given.\n" );
512	<	painCave.isFatal = 1;
513	<	simError();
514	<	}
515	<	boxVector[0] = the_globals->getBoxX();
433	>	// molI is atom numbering inside this molecule
434	>	molI = currentRigidBody->getMember(rb1);
435
436	<	if( !the_globals->haveBoxY() ){
437	<	sprintf( painCave.errMsg,
519	<	"SimSetup error, no periodic BoxY size given.\n" );
520	<	painCave.isFatal = 1;
521	<	simError();
522	<	}
523	<	boxVector[1] = the_globals->getBoxY();
436	>	// tempI is atom numbering on local processor
437	>	tempI = molI + atomOffset;
438
439	<	if( !the_globals->haveBoxZ() ){
440	<	sprintf( painCave.errMsg,
441	<	"SimSetup error, no periodic BoxZ size given.\n" );
528	<	painCave.isFatal = 1;
529	<	simError();
530	<	}
531	<	boxVector[2] = the_globals->getBoxZ();
439	>	// currentAtom is the AtomStamp (which we need for
440	>	// rigid body reference positions)
441	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
442
443	<	simnfo->setBox( boxVector );
444	<	}
443	>	// When we add to the rigid body, add the atom itself and
444	>	// the stamp info:
445
446	+	myRB->addAtom(info[k].atoms[tempI], currentAtom);
447	+
448	+	// Add this atom to the Skip List for the integrators
449		#ifdef IS_MPI
450	<	strcpy( checkPointMsg, "Box size set up" );
451	<	MPIcheckPoint();
452	<	#endif // is_mpi
450	>	slI = info[k].atoms[tempI]->getGlobalIndex();
451	>	#else
452	>	slI = tempI;
453	>	#endif
454	>	skipList.insert(slI);
455	>
456	>	}
457	>
458	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
459	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
460	>
461	>	tempI = currentRigidBody->getMember(rb1);
462	>	tempJ = currentRigidBody->getMember(rb2);
463	>
464	>	// Some explanation is required here.
465	>	// Fortran indexing starts at 1, while c indexing starts at 0
466	>	// Also, in parallel computations, the GlobalIndex is
467	>	// used for the exclude list:
468	>
469	>	#ifdef IS_MPI
470	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
471	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
472	>	#else
473	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
474	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
475	>	#endif
476	>
477	>	info[k].excludes->addPair(exI, exJ);
478	>
479	>	}
480	>	}
481
482	+	molInfo.myRigidBodies.push_back(myRB);
483	+	info[k].rigidBodies.push_back(myRB);
484	+	}
485	+
486
487	<	// initialize the arrays
487	>	//creat cutoff group for molecule
488	>	molInfo.myCutoffGroups.clear();
489	>	for (j = 0; j < molInfo.nCutoffGroups; j++){
490
491	<	the_ff->setSimInfo( simnfo );
491	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
492	>	nMembers = currentCutoffGroup->getNMembers();
493
494	<	makeMolecules();
495	<	simnfo->identArray = new int[simnfo->n_atoms];
496	<	for(i=0; i<simnfo->n_atoms; i++){
549	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
550	<	}
551	<
552	<	if (the_globals->getUseRF() ) {
553	<	simnfo->useReactionField = 1;
554	<
555	<	if( !the_globals->haveECR() ){
556	<	sprintf( painCave.errMsg,
557	<	"SimSetup Warning: using default value of 1/2 the smallest "
558	<	"box length for the electrostaticCutoffRadius.\n"
559	<	"I hope you have a very fast processor!\n");
560	<	painCave.isFatal = 0;
561	<	simError();
562	<	double smallest;
563	<	smallest = simnfo->boxLx;
564	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
565	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
566	<	simnfo->ecr = 0.5 * smallest;
567	<	} else {
568	<	simnfo->ecr        = the_globals->getECR();
569	<	}
494	>	myCutoffGroup = new CutoffGroup();
495	>
496	>	for (int cg = 0; cg < nMembers; cg++) {
497
498	<	if( !the_globals->haveEST() ){
499	<	sprintf( painCave.errMsg,
500	<	"SimSetup Warning: using default value of 0.05 * the "
501	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
502	<	);
503	<	painCave.isFatal = 0;
504	<	simError();
505	<	simnfo->est = 0.05 * simnfo->ecr;
506	<	} else {
507	<	simnfo->est        = the_globals->getEST();
508	<	}
582	<
583	<	if(!the_globals->haveDielectric() ){
584	<	sprintf( painCave.errMsg,
585	<	"SimSetup Error: You are trying to use Reaction Field without"
586	<	"setting a dielectric constant!\n"
587	<	);
588	<	painCave.isFatal = 1;
589	<	simError();
590	<	}
591	<	simnfo->dielectric = the_globals->getDielectric();
592	<	} else {
593	<	if (usesDipoles) {
498	>	// molI is atom numbering inside this molecule
499	>	molI = currentCutoffGroup->getMember(cg);
500	>
501	>	// tempI is atom numbering on local processor
502	>	tempI = molI + atomOffset;
503	>
504	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
505	>	}
506	>
507	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
508	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
509
510	<	if( !the_globals->haveECR() ){
511	<	sprintf( painCave.errMsg,
512	<	"SimSetup Warning: using default value of 1/2 the smallest "
513	<	"box length for the electrostaticCutoffRadius.\n"
514	<	"I hope you have a very fast processor!\n");
515	<	painCave.isFatal = 0;
601	<	simError();
602	<	double smallest;
603	<	smallest = simnfo->boxLx;
604	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
605	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
606	<	simnfo->ecr = 0.5 * smallest;
607	<	} else {
608	<	simnfo->ecr        = the_globals->getECR();
609	<	}
510	>
511	>
512	>	// After this is all set up, scan through the atoms to
513	>	// see if they can be added to the integrableObjects:
514	>
515	>	molInfo.myIntegrableObjects.clear();
516
611	–	if( !the_globals->haveEST() ){
612	–	sprintf( painCave.errMsg,
613	–	"SimSetup Warning: using default value of 5%% of the "
614	–	"electrostaticCutoffRadius for the "
615	–	"electrostaticSkinThickness\n"
616	–	);
617	–	painCave.isFatal = 0;
618	–	simError();
619	–	simnfo->est = 0.05 * simnfo->ecr;
620	–	} else {
621	–	simnfo->est        = the_globals->getEST();
622	–	}
623	–	}
624	–	}
517
518	<	#ifdef IS_MPI
627	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
628	<	MPIcheckPoint();
629	<	#endif // is_mpi
518	>	for (j = 0; j < molInfo.nAtoms; j++){
519
631	–	if( the_globals->haveInitialConfig() ){
632	–
633	–	InitializeFromFile* fileInit;
634	–	#ifdef IS_MPI // is_mpi
635	–	if( worldRank == 0 ){
636	–	#endif //is_mpi
637	–	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
520		#ifdef IS_MPI
521	<	}else fileInit = new InitializeFromFile( NULL );
521	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
522	>	#else
523	>	slJ = j+atomOffset;
524		#endif
641	–	fileInit->read_xyz( simnfo ); // default velocities on
525
526	<	delete fileInit;
644	<	}
645	<	else{
526	>	// if they aren't on the skip list, then they can be integrated
527
528	<	#ifdef IS_MPI
528	>	if (skipList.find(slJ) == skipList.end()) {
529	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
530	>	info[k].integrableObjects.push_back(mySD);
531	>	molInfo.myIntegrableObjects.push_back(mySD);
532	>	}
533	>	}
534
535	<	// no init from bass
650	<
651	<	sprintf( painCave.errMsg,
652	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
653	<	painCave.isFatal;
654	<	simError();
655	<
656	<	#else
535	>	// all rigid bodies are integrated:
536
537	<	initFromBass();
537	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
538	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
539	>	info[k].integrableObjects.push_back(mySD);
540	>	molInfo.myIntegrableObjects.push_back(mySD);
541	>	}
542	>
543	>
544	>	// send the arrays off to the forceField for init.
545	>
546	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
547	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
548	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
549	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
550	>	theTorsions);
551
552	+	info[k].molecules[i].initialize(molInfo);
553
661	–	#endif
662	–	}
554
555	+	atomOffset += molInfo.nAtoms;
556	+	delete[] theBonds;
557	+	delete[] theBends;
558	+	delete[] theTorsions;
559	+	}
560	+	}
561	+
562		#ifdef IS_MPI
563	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
563	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
564		MPIcheckPoint();
565		#endif // is_mpi
566
567	+	// clean up the forcefield
568
569	<
671	<
672	<
569	>	if (!globals->haveRcut()){
570
571	<
572	<	#ifdef IS_MPI
573	<	if( worldRank == 0 ){
677	<	#endif // is_mpi
571	>	the_ff->calcRcut();
572	>
573	>	} else {
574
575	<	if( the_globals->haveFinalConfig() ){
576	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
575	>	the_ff->setRcut( globals->getRcut() );
576	>	}
577	>
578	>	the_ff->cleanMe();
579	>	}
580	>
581	>	void SimSetup::initFromBass(void){
582	>	int i, j, k;
583	>	int n_cells;
584	>	double cellx, celly, cellz;
585	>	double temp1, temp2, temp3;
586	>	int n_per_extra;
587	>	int n_extra;
588	>	int have_extra, done;
589	>
590	>	double vel[3];
591	>	vel[0] = 0.0;
592	>	vel[1] = 0.0;
593	>	vel[2] = 0.0;
594	>
595	>	temp1 = (double) tot_nmol / 4.0;
596	>	temp2 = pow(temp1, (1.0 / 3.0));
597	>	temp3 = ceil(temp2);
598	>
599	>	have_extra = 0;
600	>	if (temp2 < temp3){
601	>	// we have a non-complete lattice
602	>	have_extra = 1;
603	>
604	>	n_cells = (int) temp3 - 1;
605	>	cellx = info[0].boxL[0] / temp3;
606	>	celly = info[0].boxL[1] / temp3;
607	>	cellz = info[0].boxL[2] / temp3;
608	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
609	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
610	>	n_per_extra = (int) ceil(temp1);
611	>
612	>	if (n_per_extra > 4){
613	>	sprintf(painCave.errMsg,
614	>	"SimSetup error. There has been an error in constructing"
615	>	" the non-complete lattice.\n");
616	>	painCave.isFatal = 1;
617	>	simError();
618		}
682	–	else{
683	–	strcpy( simnfo->finalName, inFileName );
684	–	char* endTest;
685	–	int nameLength = strlen( simnfo->finalName );
686	–	endTest = &(simnfo->finalName[nameLength - 5]);
687	–	if( !strcmp( endTest, ".bass" ) ){
688	–	strcpy( endTest, ".eor" );
689	–	}
690	–	else if( !strcmp( endTest, ".BASS" ) ){
691	–	strcpy( endTest, ".eor" );
692	–	}
693	–	else{
694	–	endTest = &(simnfo->finalName[nameLength - 4]);
695	–	if( !strcmp( endTest, ".bss" ) ){
696	–	strcpy( endTest, ".eor" );
697	–	}
698	–	else if( !strcmp( endTest, ".mdl" ) ){
699	–	strcpy( endTest, ".eor" );
700	–	}
701	–	else{
702	–	strcat( simnfo->finalName, ".eor" );
703	–	}
704	–	}
705	–	}
706	–
707	–	// make the sample and status out names
708	–
709	–	strcpy( simnfo->sampleName, inFileName );
710	–	char* endTest;
711	–	int nameLength = strlen( simnfo->sampleName );
712	–	endTest = &(simnfo->sampleName[nameLength - 5]);
713	–	if( !strcmp( endTest, ".bass" ) ){
714	–	strcpy( endTest, ".dump" );
715	–	}
716	–	else if( !strcmp( endTest, ".BASS" ) ){
717	–	strcpy( endTest, ".dump" );
718	–	}
719	–	else{
720	–	endTest = &(simnfo->sampleName[nameLength - 4]);
721	–	if( !strcmp( endTest, ".bss" ) ){
722	–	strcpy( endTest, ".dump" );
723	–	}
724	–	else if( !strcmp( endTest, ".mdl" ) ){
725	–	strcpy( endTest, ".dump" );
726	–	}
727	–	else{
728	–	strcat( simnfo->sampleName, ".dump" );
729	–	}
730	–	}
731	–
732	–	strcpy( simnfo->statusName, inFileName );
733	–	nameLength = strlen( simnfo->statusName );
734	–	endTest = &(simnfo->statusName[nameLength - 5]);
735	–	if( !strcmp( endTest, ".bass" ) ){
736	–	strcpy( endTest, ".stat" );
737	–	}
738	–	else if( !strcmp( endTest, ".BASS" ) ){
739	–	strcpy( endTest, ".stat" );
740	–	}
741	–	else{
742	–	endTest = &(simnfo->statusName[nameLength - 4]);
743	–	if( !strcmp( endTest, ".bss" ) ){
744	–	strcpy( endTest, ".stat" );
745	–	}
746	–	else if( !strcmp( endTest, ".mdl" ) ){
747	–	strcpy( endTest, ".stat" );
748	–	}
749	–	else{
750	–	strcat( simnfo->statusName, ".stat" );
751	–	}
752	–	}
753	–
754	–	#ifdef IS_MPI
619		}
756	–	#endif // is_mpi
757	–
758	–	// set the status, sample, and themal kick times
759	–
760	–	if( the_globals->haveSampleTime() ){
761	–	simnfo->sampleTime = the_globals->getSampleTime();
762	–	simnfo->statusTime = simnfo->sampleTime;
763	–	simnfo->thermalTime = simnfo->sampleTime;
764	–	}
620		else{
621	<	simnfo->sampleTime = the_globals->getRunTime();
622	<	simnfo->statusTime = simnfo->sampleTime;
623	<	simnfo->thermalTime = simnfo->sampleTime;
621	>	n_cells = (int) temp3;
622	>	cellx = info[0].boxL[0] / temp3;
623	>	celly = info[0].boxL[1] / temp3;
624	>	cellz = info[0].boxL[2] / temp3;
625		}
626
627	<	if( the_globals->haveStatusTime() ){
628	<	simnfo->statusTime = the_globals->getStatusTime();
629	<	}
627	>	current_mol = 0;
628	>	current_comp_mol = 0;
629	>	current_comp = 0;
630	>	current_atom_ndx = 0;
631
632	<	if( the_globals->haveThermalTime() ){
633	<	simnfo->thermalTime = the_globals->getThermalTime();
634	<	}
632	>	for (i = 0; i < n_cells ; i++){
633	>	for (j = 0; j < n_cells; j++){
634	>	for (k = 0; k < n_cells; k++){
635	>	makeElement(i * cellx, j * celly, k * cellz);
636
637	<	// check for the temperature set flag
637	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
638
639	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
639	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
640
641	+	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
642	+	}
643	+	}
644	+	}
645
646	<	// make the integrator
647	<
786	<
787	<	NVT*  myNVT = NULL;
788	<	NPTi* myNPTi = NULL;
789	<	NPTf* myNPTf = NULL;
790	<	NPTim* myNPTim = NULL;
646	>	if (have_extra){
647	>	done = 0;
648
649	<	switch( ensembleCase ){
649	>	int start_ndx;
650	>	for (i = 0; i < (n_cells + 1) && !done; i++){
651	>	for (j = 0; j < (n_cells + 1) && !done; j++){
652	>	if (i < n_cells){
653	>	if (j < n_cells){
654	>	start_ndx = n_cells;
655	>	}
656	>	else
657	>	start_ndx = 0;
658	>	}
659	>	else
660	>	start_ndx = 0;
661
662	<	case NVE_ENS:
663	<	new NVE( simnfo, the_ff );
664	<	break;
662	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
663	>	makeElement(i * cellx, j * celly, k * cellz);
664	>	done = (current_mol >= tot_nmol);
665
666	<	case NVT_ENS:
667	<	myNVT = new NVT( simnfo, the_ff );
668	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
666	>	if (!done && n_per_extra > 1){
667	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
668	>	k * cellz);
669	>	done = (current_mol >= tot_nmol);
670	>	}
671
672	<	if (the_globals->haveTauThermostat())
673	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
672	>	if (!done && n_per_extra > 2){
673	>	makeElement(i * cellx, j * celly + 0.5 * celly,
674	>	k * cellz + 0.5 * cellz);
675	>	done = (current_mol >= tot_nmol);
676	>	}
677
678	<	else {
679	<	sprintf( painCave.errMsg,
680	<	"SimSetup error: If you use the NVT\n"
681	<	"    ensemble, you must set tauThermostat.\n");
682	<	painCave.isFatal = 1;
683	<	simError();
678	>	if (!done && n_per_extra > 3){
679	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
680	>	k * cellz + 0.5 * cellz);
681	>	done = (current_mol >= tot_nmol);
682	>	}
683	>	}
684	>	}
685		}
686	<	break;
686	>	}
687
688	<	case NPTi_ENS:
689	<	myNPTi = new NPTi( simnfo, the_ff );
690	<	myNPTi->setTargetTemp( the_globals->getTargetTemp());
688	>	for (i = 0; i < info[0].n_atoms; i++){
689	>	info[0].atoms[i]->setVel(vel);
690	>	}
691	>	}
692
693	<	if (the_globals->haveTargetPressure())
694	<	myNPTi->setTargetPressure(the_globals->getTargetPressure());
695	<	else {
696	<	sprintf( painCave.errMsg,
697	<	"SimSetup error: If you use a constant pressure\n"
698	<	"    ensemble, you must set targetPressure in the BASS file.\n");
824	<	painCave.isFatal = 1;
825	<	simError();
826	<	}
827	<
828	<	if( the_globals->haveTauThermostat() )
829	<	myNPTi->setTauThermostat( the_globals->getTauThermostat() );
830	<	else{
831	<	sprintf( painCave.errMsg,
832	<	"SimSetup error: If you use an NPT\n"
833	<	"    ensemble, you must set tauThermostat.\n");
834	<	painCave.isFatal = 1;
835	<	simError();
836	<	}
693	>	void SimSetup::makeElement(double x, double y, double z){
694	>	int k;
695	>	AtomStamp* current_atom;
696	>	DirectionalAtom* dAtom;
697	>	double rotMat[3][3];
698	>	double pos[3];
699
700	<	if( the_globals->haveTauBarostat() )
701	<	myNPTi->setTauBarostat( the_globals->getTauBarostat() );
702	<	else{
703	<	sprintf( painCave.errMsg,
704	<	"SimSetup error: If you use an NPT\n"
705	<	"    ensemble, you must set tauBarostat.\n");
700	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
701	>	current_atom = comp_stamps[current_comp]->getAtom(k);
702	>	if (!current_atom->havePosition()){
703	>	sprintf(painCave.errMsg,
704	>	"SimSetup:initFromBass error.\n"
705	>	"\tComponent %s, atom %s does not have a position specified.\n"
706	>	"\tThe initialization routine is unable to give a start"
707	>	" position.\n",
708	>	comp_stamps[current_comp]->getID(), current_atom->getType());
709		painCave.isFatal = 1;
710		simError();
711		}
847	–	break;
712
713	<	case NPTf_ENS:
714	<	myNPTf = new NPTf( simnfo, the_ff );
715	<	myNPTf->setTargetTemp( the_globals->getTargetTemp());
713	>	pos[0] = x + current_atom->getPosX();
714	>	pos[1] = y + current_atom->getPosY();
715	>	pos[2] = z + current_atom->getPosZ();
716
717	<	if (the_globals->haveTargetPressure())
854	<	myNPTf->setTargetPressure(the_globals->getTargetPressure());
855	<	else {
856	<	sprintf( painCave.errMsg,
857	<	"SimSetup error: If you use a constant pressure\n"
858	<	"    ensemble, you must set targetPressure in the BASS file.\n");
859	<	painCave.isFatal = 1;
860	<	simError();
861	<	}
717	>	info[0].atoms[current_atom_ndx]->setPos(pos);
718
719	<	if( the_globals->haveTauThermostat() )
720	<	myNPTf->setTauThermostat( the_globals->getTauThermostat() );
865	<	else{
866	<	sprintf( painCave.errMsg,
867	<	"SimSetup error: If you use an NPT\n"
868	<	"    ensemble, you must set tauThermostat.\n");
869	<	painCave.isFatal = 1;
870	<	simError();
871	<	}
719	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
720	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
721
722	<	if( the_globals->haveTauBarostat() )
723	<	myNPTf->setTauBarostat( the_globals->getTauBarostat() );
724	<	else{
876	<	sprintf( painCave.errMsg,
877	<	"SimSetup error: If you use an NPT\n"
878	<	"    ensemble, you must set tauBarostat.\n");
879	<	painCave.isFatal = 1;
880	<	simError();
881	<	}
882	<	break;
883	<
884	<	case NPTim_ENS:
885	<	myNPTim = new NPTim( simnfo, the_ff );
886	<	myNPTim->setTargetTemp( the_globals->getTargetTemp());
722	>	rotMat[0][0] = 1.0;
723	>	rotMat[0][1] = 0.0;
724	>	rotMat[0][2] = 0.0;
725
726	<	if (the_globals->haveTargetPressure())
727	<	myNPTim->setTargetPressure(the_globals->getTargetPressure());
728	<	else {
891	<	sprintf( painCave.errMsg,
892	<	"SimSetup error: If you use a constant pressure\n"
893	<	"    ensemble, you must set targetPressure in the BASS file.\n");
894	<	painCave.isFatal = 1;
895	<	simError();
896	<	}
897	<
898	<	if( the_globals->haveTauThermostat() )
899	<	myNPTim->setTauThermostat( the_globals->getTauThermostat() );
900	<	else{
901	<	sprintf( painCave.errMsg,
902	<	"SimSetup error: If you use an NPT\n"
903	<	"    ensemble, you must set tauThermostat.\n");
904	<	painCave.isFatal = 1;
905	<	simError();
906	<	}
726	>	rotMat[1][0] = 0.0;
727	>	rotMat[1][1] = 1.0;
728	>	rotMat[1][2] = 0.0;
729
730	<	if( the_globals->haveTauBarostat() )
731	<	myNPTim->setTauBarostat( the_globals->getTauBarostat() );
732	<	else{
733	<	sprintf( painCave.errMsg,
734	<	"SimSetup error: If you use an NPT\n"
913	<	"    ensemble, you must set tauBarostat.\n");
914	<	painCave.isFatal = 1;
915	<	simError();
730	>	rotMat[2][0] = 0.0;
731	>	rotMat[2][1] = 0.0;
732	>	rotMat[2][2] = 1.0;
733	>
734	>	dAtom->setA(rotMat);
735		}
917	–	break;
736
737	<
737	>	current_atom_ndx++;
738	>	}
739
740	<	default:
741	<	sprintf( painCave.errMsg,
742	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
743	<	painCave.isFatal = 1;
744	<	simError();
740	>	current_mol++;
741	>	current_comp_mol++;
742	>
743	>	if (current_comp_mol >= components_nmol[current_comp]){
744	>	current_comp_mol = 0;
745	>	current_comp++;
746		}
747	+	}
748
749
750	<	#ifdef IS_MPI
751	<	mpiSim->mpiRefresh();
931	<	#endif
750	>	void SimSetup::gatherInfo(void){
751	>	int i;
752
753	<	// initialize the Fortran
753	>	ensembleCase = -1;
754	>	ffCase = -1;
755
756	+	// set the easy ones first
757
758	<	simnfo->refreshSim();
759	<
760	<	if( !strcmp( simnfo->mixingRule, "standard") ){
761	<	the_ff->initForceField( LB_MIXING_RULE );
758	>	for (i = 0; i < nInfo; i++){
759	>	info[i].target_temp = globals->getTargetTemp();
760	>	info[i].dt = globals->getDt();
761	>	info[i].run_time = globals->getRunTime();
762		}
763	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
764	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
763	>	n_components = globals->getNComponents();
764	>
765	>
766	>	// get the forceField
767	>
768	>	strcpy(force_field, globals->getForceField());
769	>
770	>	if (!strcasecmp(force_field, "DUFF")){
771	>	ffCase = FF_DUFF;
772		}
773	+	else if (!strcasecmp(force_field, "LJ")){
774	+	ffCase = FF_LJ;
775	+	}
776	+	else if (!strcasecmp(force_field, "EAM")){
777	+	ffCase = FF_EAM;
778	+	}
779	+	else if (!strcasecmp(force_field, "WATER")){
780	+	ffCase = FF_H2O;
781	+	}
782		else{
783	<	sprintf( painCave.errMsg,
784	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
785	<	simnfo->mixingRule );
786	<	painCave.isFatal = 1;
949	<	simError();
783	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
784	>	force_field);
785	>	painCave.isFatal = 1;
786	>	simError();
787		}
788
789	+	// get the ensemble
790
791	<	#ifdef IS_MPI
954	<	strcpy( checkPointMsg,
955	<	"Successfully intialized the mixingRule for Fortran." );
956	<	MPIcheckPoint();
957	<	#endif // is_mpi
958	<	}
791	>	strcpy(ensemble, globals->getEnsemble());
792
793	+	if (!strcasecmp(ensemble, "NVE")){
794	+	ensembleCase = NVE_ENS;
795	+	}
796	+	else if (!strcasecmp(ensemble, "NVT")){
797	+	ensembleCase = NVT_ENS;
798	+	}
799	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
800	+	ensembleCase = NPTi_ENS;
801	+	}
802	+	else if (!strcasecmp(ensemble, "NPTf")){
803	+	ensembleCase = NPTf_ENS;
804	+	}
805	+	else if (!strcasecmp(ensemble, "NPTxyz")){
806	+	ensembleCase = NPTxyz_ENS;
807	+	}
808	+	else{
809	+	sprintf(painCave.errMsg,
810	+	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
811	+	"\treverting to NVE for this simulation.\n",
812	+	ensemble);
813	+	painCave.isFatal = 0;
814	+	simError();
815	+	strcpy(ensemble, "NVE");
816	+	ensembleCase = NVE_ENS;
817	+	}
818
819	<	void SimSetup::makeMolecules( void ){
819	>	for (i = 0; i < nInfo; i++){
820	>	strcpy(info[i].ensemble, ensemble);
821
822	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
964	<	molInit info;
965	<	DirectionalAtom* dAtom;
966	<	LinkedAssign* extras;
967	<	LinkedAssign* current_extra;
968	<	AtomStamp* currentAtom;
969	<	BondStamp* currentBond;
970	<	BendStamp* currentBend;
971	<	TorsionStamp* currentTorsion;
822	>	// get the mixing rule
823
824	<	bond_pair* theBonds;
825	<	bend_set* theBends;
826	<	torsion_set* theTorsions;
824	>	strcpy(info[i].mixingRule, globals->getMixingRule());
825	>	info[i].usePBC = globals->getPBC();
826	>	}
827
828	<
978	<	//init the forceField paramters
828	>	// get the components and calculate the tot_nMol and indvidual n_mol
829
830	<	the_ff->readParams();
830	>	the_components = globals->getComponents();
831	>	components_nmol = new int[n_components];
832
982	–
983	–	// init the atoms
833
834	<	double ux, uy, uz, u, uSqr;
835	<
836	<	atomOffset = 0;
988	<	excludeOffset = 0;
989	<	for(i=0; i<simnfo->n_mol; i++){
990	<
991	<	stampID = the_molecules[i].getStampID();
834	>	if (!globals->haveNMol()){
835	>	// we don't have the total number of molecules, so we assume it is
836	>	// given in each component
837
838	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
839	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
840	<	info.nBends    = comp_stamps[stampID]->getNBends();
841	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
842	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
838	>	tot_nmol = 0;
839	>	for (i = 0; i < n_components; i++){
840	>	if (!the_components[i]->haveNMol()){
841	>	// we have a problem
842	>	sprintf(painCave.errMsg,
843	>	"SimSetup Error. No global NMol or component NMol given.\n"
844	>	"\tCannot calculate the number of atoms.\n");
845	>	painCave.isFatal = 1;
846	>	simError();
847	>	}
848
849	<	info.myAtoms = &the_atoms[atomOffset];
850	<	info.myExcludes = &the_excludes[excludeOffset];
851	<	info.myBonds = new Bond*[info.nBonds];
852	<	info.myBends = new Bend*[info.nBends];
853	<	info.myTorsions = new Torsion*[info.nTorsions];
849	>	tot_nmol += the_components[i]->getNMol();
850	>	components_nmol[i] = the_components[i]->getNMol();
851	>	}
852	>	}
853	>	else{
854	>	sprintf(painCave.errMsg,
855	>	"SimSetup error.\n"
856	>	"\tSorry, the ability to specify total"
857	>	" nMols and then give molfractions in the components\n"
858	>	"\tis not currently supported."
859	>	" Please give nMol in the components.\n");
860	>	painCave.isFatal = 1;
861	>	simError();
862	>	}
863
864	<	theBonds = new bond_pair[info.nBonds];
865	<	theBends = new bend_set[info.nBends];
866	<	theTorsions = new torsion_set[info.nTorsions];
867	<
868	<	// make the Atoms
869	<
870	<	for(j=0; j<info.nAtoms; j++){
871	<
872	<	currentAtom = comp_stamps[stampID]->getAtom( j );
873	<	if( currentAtom->haveOrientation() ){
874	<
875	<	dAtom = new DirectionalAtom(j + atomOffset);
876	<	simnfo->n_oriented++;
877	<	info.myAtoms[j] = dAtom;
878	<
879	<	ux = currentAtom->getOrntX();
880	<	uy = currentAtom->getOrntY();
881	<	uz = currentAtom->getOrntZ();
882	<
883	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
884	<
885	<	u = sqrt( uSqr );
886	<	ux = ux / u;
887	<	uy = uy / u;
888	<	uz = uz / u;
889	<
890	<	dAtom->setSUx( ux );
891	<	dAtom->setSUy( uy );
892	<	dAtom->setSUz( uz );
893	<	}
894	<	else{
895	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
896	<	}
897	<	info.myAtoms[j]->setType( currentAtom->getType() );
864	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
865	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
866	>	sprintf(painCave.errMsg,
867	>	"Sample time is not divisible by dt.\n"
868	>	"\tThis will result in samples that are not uniformly\n"
869	>	"\tdistributed in time.  If this is a problem, change\n"
870	>	"\tyour sampleTime variable.\n");
871	>	painCave.isFatal = 0;
872	>	simError();
873	>	}
874	>
875	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
876	>	sprintf(painCave.errMsg,
877	>	"Status time is not divisible by dt.\n"
878	>	"\tThis will result in status reports that are not uniformly\n"
879	>	"\tdistributed in time.  If this is a problem, change \n"
880	>	"\tyour statusTime variable.\n");
881	>	painCave.isFatal = 0;
882	>	simError();
883	>	}
884	>
885	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
886	>	sprintf(painCave.errMsg,
887	>	"Thermal time is not divisible by dt.\n"
888	>	"\tThis will result in thermalizations that are not uniformly\n"
889	>	"\tdistributed in time.  If this is a problem, change \n"
890	>	"\tyour thermalTime variable.\n");
891	>	painCave.isFatal = 0;
892	>	simError();
893	>	}
894	>
895	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
896	>	sprintf(painCave.errMsg,
897	>	"Reset time is not divisible by dt.\n"
898	>	"\tThis will result in integrator resets that are not uniformly\n"
899	>	"\tdistributed in time.  If this is a problem, change\n"
900	>	"\tyour resetTime variable.\n");
901	>	painCave.isFatal = 0;
902	>	simError();
903	>	}
904	>
905	>	// set the status, sample, and thermal kick times
906	>
907	>	for (i = 0; i < nInfo; i++){
908	>	if (globals->haveSampleTime()){
909	>	info[i].sampleTime = globals->getSampleTime();
910	>	info[i].statusTime = info[i].sampleTime;
911	>	}
912	>	else{
913	>	info[i].sampleTime = globals->getRunTime();
914	>	info[i].statusTime = info[i].sampleTime;
915	>	}
916	>
917	>	if (globals->haveStatusTime()){
918	>	info[i].statusTime = globals->getStatusTime();
919	>	}
920	>
921	>	if (globals->haveThermalTime()){
922	>	info[i].thermalTime = globals->getThermalTime();
923	>	} else {
924	>	info[i].thermalTime = globals->getRunTime();
925	>	}
926	>
927	>	info[i].resetIntegrator = 0;
928	>	if( globals->haveResetTime() ){
929	>	info[i].resetTime = globals->getResetTime();
930	>	info[i].resetIntegrator = 1;
931	>	}
932	>
933	>	// check for the temperature set flag
934
935	<	#ifdef IS_MPI
936	<
937	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
938	<
939	<	#endif // is_mpi
940	<	}
935	>	if (globals->haveTempSet())
936	>	info[i].setTemp = globals->getTempSet();
937	>
938	>	// check for the extended State init
939	>
940	>	info[i].useInitXSstate = globals->getUseInitXSstate();
941	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
942
943	<	// make the bonds
944	<	for(j=0; j<info.nBonds; j++){
945	<
946	<	currentBond = comp_stamps[stampID]->getBond( j );
1051	<	theBonds[j].a = currentBond->getA() + atomOffset;
1052	<	theBonds[j].b = currentBond->getB() + atomOffset;
943	>	}
944	>
945	>	//setup seed for random number generator
946	>	int seedValue;
947
948	<	exI = theBonds[j].a;
949	<	exJ = theBonds[j].b;
948	>	if (globals->haveSeed()){
949	>	seedValue = globals->getSeed();
950
951	<	// exclude_I must always be the smaller of the pair
952	<	if( exI > exJ ){
953	<	tempEx = exI;
954	<	exI = exJ;
955	<	exJ = tempEx;
951	>	if(seedValue / 1E9 == 0){
952	>	sprintf(painCave.errMsg,
953	>	"Seed for sprng library should contain at least 9 digits\n"
954	>	"OOPSE will generate a seed for user\n");
955	>	painCave.isFatal = 0;
956	>	simError();
957	>
958	>	//using seed generated by system instead of invalid seed set by user
959	>	#ifndef IS_MPI
960	>	seedValue = make_sprng_seed();
961	>	#else
962	>	if (worldRank == 0){
963	>	seedValue = make_sprng_seed();
964		}
965	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
966	+	#endif
967	+	}
968	+	}//end of if branch of globals->haveSeed()
969	+	else{
970	+
971	+	#ifndef IS_MPI
972	+	seedValue = make_sprng_seed();
973	+	#else
974	+	if (worldRank == 0){
975	+	seedValue = make_sprng_seed();
976	+	}
977	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
978	+	#endif
979	+	}//end of globals->haveSeed()
980	+
981	+	for (int i = 0; i < nInfo; i++){
982	+	info[i].setSeed(seedValue);
983	+	}
984	+
985		#ifdef IS_MPI
986	<	tempEx = exI;
987	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
988	<	tempEx = exJ;
989	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1068	<
1069	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1070	<	#else  // isn't MPI
986	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
987	>	MPIcheckPoint();
988	>	#endif // is_mpi
989	>	}
990
991	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
992	<	#endif  //is_mpi
991	>
992	>	void SimSetup::finalInfoCheck(void){
993	>	int index;
994	>	int usesDipoles;
995	>	int usesCharges;
996	>	int i;
997	>
998	>	for (i = 0; i < nInfo; i++){
999	>	// check electrostatic parameters
1000	>
1001	>	index = 0;
1002	>	usesDipoles = 0;
1003	>	while ((index < info[i].n_atoms) && !usesDipoles){
1004	>	usesDipoles = (info[i].atoms[index])->hasDipole();
1005	>	index++;
1006		}
1007	<	excludeOffset += info.nBonds;
1007	>	index = 0;
1008	>	usesCharges = 0;
1009	>	while ((index < info[i].n_atoms) && !usesCharges){
1010	>	usesCharges= (info[i].atoms[index])->hasCharge();
1011	>	index++;
1012	>	}
1013	>	#ifdef IS_MPI
1014	>	int myUse = usesDipoles;
1015	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1016	>	#endif //is_mpi
1017
1018	<	//make the bends
1019	<	for(j=0; j<info.nBends; j++){
1020	<
1021	<	currentBend = comp_stamps[stampID]->getBend( j );
1022	<	theBends[j].a = currentBend->getA() + atomOffset;
1023	<	theBends[j].b = currentBend->getB() + atomOffset;
1024	<	theBends[j].c = currentBend->getC() + atomOffset;
1025	<
1026	<	if( currentBend->haveExtras() ){
1027	<
1028	<	extras = currentBend->getExtras();
1029	<	current_extra = extras;
1030	<
1090	<	while( current_extra != NULL ){
1091	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
1092	<
1093	<	switch( current_extra->getType() ){
1094	<
1095	<	case 0:
1096	<	theBends[j].ghost =
1097	<	current_extra->getInt() + atomOffset;
1098	<	theBends[j].isGhost = 1;
1099	<	break;
1100	<
1101	<	case 1:
1102	<	theBends[j].ghost =
1103	<	(int)current_extra->getDouble() + atomOffset;
1104	<	theBends[j].isGhost = 1;
1105	<	break;
1106	<
1107	<	default:
1108	<	sprintf( painCave.errMsg,
1109	<	"SimSetup Error: ghostVectorSource was neither a "
1110	<	"double nor an int.\n"
1111	<	"-->Bend[%d] in %s\n",
1112	<	j, comp_stamps[stampID]->getID() );
1113	<	painCave.isFatal = 1;
1114	<	simError();
1115	<	}
1116	<	}
1117	<
1118	<	else{
1119	<
1120	<	sprintf( painCave.errMsg,
1121	<	"SimSetup Error: unhandled bend assignment:\n"
1122	<	"    -->%s in Bend[%d] in %s\n",
1123	<	current_extra->getlhs(),
1124	<	j, comp_stamps[stampID]->getID() );
1125	<	painCave.isFatal = 1;
1126	<	simError();
1127	<	}
1128	<
1129	<	current_extra = current_extra->getNext();
1130	<	}
1018	>	double theRcut, theRsw;
1019	>
1020	>	if (globals->getUseRF()){
1021	>	info[i].useReactionField = 1;
1022	>
1023	>	if (!globals->haveRcut()){
1024	>	sprintf(painCave.errMsg,
1025	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1026	>	"\tOOPSE will use a default value of 15.0 angstroms"
1027	>	"\tfor the cutoffRadius.\n");
1028	>	painCave.isFatal = 0;
1029	>	simError();
1030	>	theRcut = 15.0;
1031		}
1032	<
1033	<	if( !theBends[j].isGhost ){
1134	<
1135	<	exI = theBends[j].a;
1136	<	exJ = theBends[j].c;
1032	>	else{
1033	>	theRcut = globals->getRcut();
1034		}
1035	+
1036	+	if (!globals->haveRsw()){
1037	+	sprintf(painCave.errMsg,
1038	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1039	+	"\tOOPSE will use a default value of\n"
1040	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1041	+	painCave.isFatal = 0;
1042	+	simError();
1043	+	theRsw = 0.95 * theRcut;
1044	+	}
1045		else{
1046	<
1140	<	exI = theBends[j].a;
1141	<	exJ = theBends[j].b;
1046	>	theRsw = globals->getRsw();
1047		}
1048	<
1049	<	// exclude_I must always be the smaller of the pair
1050	<	if( exI > exJ ){
1051	<	tempEx = exI;
1052	<	exI = exJ;
1053	<	exJ = tempEx;
1048	>
1049	>	info[i].setDefaultRcut(theRcut, theRsw);
1050	>
1051	>	if (!globals->haveDielectric()){
1052	>	sprintf(painCave.errMsg,
1053	>	"SimSetup Error: No Dielectric constant was set.\n"
1054	>	"\tYou are trying to use Reaction Field without"
1055	>	"\tsetting a dielectric constant!\n");
1056	>	painCave.isFatal = 1;
1057	>	simError();
1058		}
1059	<	#ifdef IS_MPI
1151	<	tempEx = exI;
1152	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1153	<	tempEx = exJ;
1154	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1155	<
1156	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1157	<	#else  // isn't MPI
1158	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1159	<	#endif  //is_mpi
1059	>	info[i].dielectric = globals->getDielectric();
1060		}
1061	<	excludeOffset += info.nBends;
1061	>	else{
1062	>	if (usesDipoles || usesCharges){
1063
1064	<	for(j=0; j<info.nTorsions; j++){
1065	<
1066	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1067	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1068	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1069	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1070	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1071	<
1171	<	exI = theTorsions[j].a;
1172	<	exJ = theTorsions[j].d;
1173	<
1174	<	// exclude_I must always be the smaller of the pair
1175	<	if( exI > exJ ){
1176	<	tempEx = exI;
1177	<	exI = exJ;
1178	<	exJ = tempEx;
1064	>	if (!globals->haveRcut()){
1065	>	sprintf(painCave.errMsg,
1066	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1067	>	"\tOOPSE will use a default value of 15.0 angstroms"
1068	>	"\tfor the cutoffRadius.\n");
1069	>	painCave.isFatal = 0;
1070	>	simError();
1071	>	theRcut = 15.0;
1072		}
1073	<	#ifdef IS_MPI
1074	<	tempEx = exI;
1075	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1076	<	tempEx = exJ;
1077	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1078	<
1079	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1080	<	#else  // isn't MPI
1081	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1082	<	#endif  //is_mpi
1073	>	else{
1074	>	theRcut = globals->getRcut();
1075	>	}
1076	>
1077	>	if (!globals->haveRsw()){
1078	>	sprintf(painCave.errMsg,
1079	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1080	>	"\tOOPSE will use a default value of\n"
1081	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1082	>	painCave.isFatal = 0;
1083	>	simError();
1084	>	theRsw = 0.95 * theRcut;
1085	>	}
1086	>	else{
1087	>	theRsw = globals->getRsw();
1088	>	}
1089	>
1090	>	info[i].setDefaultRcut(theRcut, theRsw);
1091	>
1092	>	}
1093		}
1094	<	excludeOffset += info.nTorsions;
1094	>	}
1095	>	#ifdef IS_MPI
1096	>	strcpy(checkPointMsg, "post processing checks out");
1097	>	MPIcheckPoint();
1098	>	#endif // is_mpi
1099	>	}
1100	>
1101	>	void SimSetup::initSystemCoords(void){
1102	>	int i;
1103
1104	<
1194	<	// send the arrays off to the forceField for init.
1104	>	char* inName;
1105
1106	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1197	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1198	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1199	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1106	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1107
1108	+	for (i = 0; i < info[0].n_atoms; i++)
1109	+	info[0].atoms[i]->setCoords();
1110
1111	<	the_molecules[i].initialize( info );
1111	>	if (globals->haveInitialConfig()){
1112	>	InitializeFromFile* fileInit;
1113	>	#ifdef IS_MPI // is_mpi
1114	>	if (worldRank == 0){
1115	>	#endif //is_mpi
1116	>	inName = globals->getInitialConfig();
1117	>	fileInit = new InitializeFromFile(inName);
1118	>	#ifdef IS_MPI
1119	>	}
1120	>	else
1121	>	fileInit = new InitializeFromFile(NULL);
1122	>	#endif
1123	>	fileInit->readInit(info); // default velocities on
1124
1125	<
1205	<	atomOffset += info.nAtoms;
1206	<	delete[] theBonds;
1207	<	delete[] theBends;
1208	<	delete[] theTorsions;
1125	>	delete fileInit;
1126		}
1127	+	else{
1128	+
1129	+	// no init from bass
1130	+
1131	+	sprintf(painCave.errMsg,
1132	+	"Cannot intialize a simulation without an initial configuration file.\n");
1133	+	painCave.isFatal = 1;;
1134	+	simError();
1135	+
1136	+	}
1137
1138		#ifdef IS_MPI
1139	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1139	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1140		MPIcheckPoint();
1141		#endif // is_mpi
1215	–
1216	–	// clean up the forcefield
1217	–	the_ff->calcRcut();
1218	–	the_ff->cleanMe();
1219	–
1142		}
1143
1222	–	void SimSetup::initFromBass( void ){
1144
1145	<	int i, j, k;
1146	<	int n_cells;
1226	<	double cellx, celly, cellz;
1227	<	double temp1, temp2, temp3;
1228	<	int n_per_extra;
1229	<	int n_extra;
1230	<	int have_extra, done;
1145	>	void SimSetup::makeOutNames(void){
1146	>	int k;
1147
1232	–	temp1 = (double)tot_nmol / 4.0;
1233	–	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1234	–	temp3 = ceil( temp2 );
1148
1149	<	have_extra =0;
1150	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1151	<	have_extra =1;
1149	>	for (k = 0; k < nInfo; k++){
1150	>	#ifdef IS_MPI
1151	>	if (worldRank == 0){
1152	>	#endif // is_mpi
1153
1154	<	n_cells = (int)temp3 - 1;
1155	<	cellx = simnfo->boxLx / temp3;
1156	<	celly = simnfo->boxLy / temp3;
1157	<	cellz = simnfo->boxLz / temp3;
1158	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1159	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1160	<	n_per_extra = (int)ceil( temp1 );
1154	>	if (globals->haveFinalConfig()){
1155	>	strcpy(info[k].finalName, globals->getFinalConfig());
1156	>	}
1157	>	else{
1158	>	strcpy(info[k].finalName, inFileName);
1159	>	char* endTest;
1160	>	int nameLength = strlen(info[k].finalName);
1161	>	endTest = &(info[k].finalName[nameLength - 5]);
1162	>	if (!strcmp(endTest, ".bass")){
1163	>	strcpy(endTest, ".eor");
1164	>	}
1165	>	else if (!strcmp(endTest, ".BASS")){
1166	>	strcpy(endTest, ".eor");
1167	>	}
1168	>	else{
1169	>	endTest = &(info[k].finalName[nameLength - 4]);
1170	>	if (!strcmp(endTest, ".bss")){
1171	>	strcpy(endTest, ".eor");
1172	>	}
1173	>	else if (!strcmp(endTest, ".mdl")){
1174	>	strcpy(endTest, ".eor");
1175	>	}
1176	>	else{
1177	>	strcat(info[k].finalName, ".eor");
1178	>	}
1179	>	}
1180	>	}
1181
1182	<	if( n_per_extra > 4){
1183	<	sprintf( painCave.errMsg,
1184	<	"SimSetup error. There has been an error in constructing"
1185	<	" the non-complete lattice.\n" );
1186	<	painCave.isFatal = 1;
1187	<	simError();
1182	>	// make the sample and status out names
1183	>
1184	>	strcpy(info[k].sampleName, inFileName);
1185	>	char* endTest;
1186	>	int nameLength = strlen(info[k].sampleName);
1187	>	endTest = &(info[k].sampleName[nameLength - 5]);
1188	>	if (!strcmp(endTest, ".bass")){
1189	>	strcpy(endTest, ".dump");
1190	>	}
1191	>	else if (!strcmp(endTest, ".BASS")){
1192	>	strcpy(endTest, ".dump");
1193	>	}
1194	>	else{
1195	>	endTest = &(info[k].sampleName[nameLength - 4]);
1196	>	if (!strcmp(endTest, ".bss")){
1197	>	strcpy(endTest, ".dump");
1198	>	}
1199	>	else if (!strcmp(endTest, ".mdl")){
1200	>	strcpy(endTest, ".dump");
1201	>	}
1202	>	else{
1203	>	strcat(info[k].sampleName, ".dump");
1204	>	}
1205	>	}
1206	>
1207	>	strcpy(info[k].statusName, inFileName);
1208	>	nameLength = strlen(info[k].statusName);
1209	>	endTest = &(info[k].statusName[nameLength - 5]);
1210	>	if (!strcmp(endTest, ".bass")){
1211	>	strcpy(endTest, ".stat");
1212	>	}
1213	>	else if (!strcmp(endTest, ".BASS")){
1214	>	strcpy(endTest, ".stat");
1215	>	}
1216	>	else{
1217	>	endTest = &(info[k].statusName[nameLength - 4]);
1218	>	if (!strcmp(endTest, ".bss")){
1219	>	strcpy(endTest, ".stat");
1220	>	}
1221	>	else if (!strcmp(endTest, ".mdl")){
1222	>	strcpy(endTest, ".stat");
1223	>	}
1224	>	else{
1225	>	strcat(info[k].statusName, ".stat");
1226	>	}
1227	>	}
1228	>
1229	>	#ifdef IS_MPI
1230	>
1231		}
1232	+	#endif // is_mpi
1233		}
1234	<	else{
1257	<	n_cells = (int)temp3;
1258	<	cellx = simnfo->boxLx / temp3;
1259	<	celly = simnfo->boxLy / temp3;
1260	<	cellz = simnfo->boxLz / temp3;
1261	<	}
1234	>	}
1235
1263	–	current_mol = 0;
1264	–	current_comp_mol = 0;
1265	–	current_comp = 0;
1266	–	current_atom_ndx = 0;
1236
1237	<	for( i=0; i < n_cells ; i++ ){
1238	<	for( j=0; j < n_cells; j++ ){
1270	<	for( k=0; k < n_cells; k++ ){
1237	>	void SimSetup::sysObjectsCreation(void){
1238	>	int i, k;
1239
1240	<	makeElement( i * cellx,
1273	<	j * celly,
1274	<	k * cellz );
1240	>	// create the forceField
1241
1242	<	makeElement( i * cellx + 0.5 * cellx,
1277	<	j * celly + 0.5 * celly,
1278	<	k * cellz );
1242	>	createFF();
1243
1244	<	makeElement( i * cellx,
1281	<	j * celly + 0.5 * celly,
1282	<	k * cellz + 0.5 * cellz );
1244	>	// extract componentList
1245
1246	<	makeElement( i * cellx + 0.5 * cellx,
1285	<	j * celly,
1286	<	k * cellz + 0.5 * cellz );
1287	<	}
1288	<	}
1289	<	}
1246	>	compList();
1247
1248	<	if( have_extra ){
1292	<	done = 0;
1248	>	// calc the number of atoms, bond, bends, and torsions
1249
1250	<	int start_ndx;
1295	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1296	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1250	>	calcSysValues();
1251
1252	<	if( i < n_cells ){
1252	>	#ifdef IS_MPI
1253	>	// divide the molecules among the processors
1254
1255	<	if( j < n_cells ){
1256	<	start_ndx = n_cells;
1302	<	}
1303	<	else start_ndx = 0;
1304	<	}
1305	<	else start_ndx = 0;
1255	>	mpiMolDivide();
1256	>	#endif //is_mpi
1257
1258	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1258	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1259
1260	<	makeElement( i * cellx,
1310	<	j * celly,
1311	<	k * cellz );
1312	<	done = ( current_mol >= tot_nmol );
1260	>	makeSysArrays();
1261
1262	<	if( !done && n_per_extra > 1 ){
1315	<	makeElement( i * cellx + 0.5 * cellx,
1316	<	j * celly + 0.5 * celly,
1317	<	k * cellz );
1318	<	done = ( current_mol >= tot_nmol );
1319	<	}
1262	>	// make and initialize the molecules (all but atomic coordinates)
1263
1264	<	if( !done && n_per_extra > 2){
1322	<	makeElement( i * cellx,
1323	<	j * celly + 0.5 * celly,
1324	<	k * cellz + 0.5 * cellz );
1325	<	done = ( current_mol >= tot_nmol );
1326	<	}
1264	>	makeMolecules();
1265
1266	<	if( !done && n_per_extra > 3){
1267	<	makeElement( i * cellx + 0.5 * cellx,
1268	<	j * celly,
1269	<	k * cellz + 0.5 * cellz );
1332	<	done = ( current_mol >= tot_nmol );
1333	<	}
1334	<	}
1335	<	}
1266	>	for (k = 0; k < nInfo; k++){
1267	>	info[k].identArray = new int[info[k].n_atoms];
1268	>	for (i = 0; i < info[k].n_atoms; i++){
1269	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1270		}
1271		}
1272	+	}
1273
1274
1275	<	for( i=0; i<simnfo->n_atoms; i++ ){
1276	<	simnfo->atoms[i]->set_vx( 0.0 );
1277	<	simnfo->atoms[i]->set_vy( 0.0 );
1278	<	simnfo->atoms[i]->set_vz( 0.0 );
1279	<	}
1345	<	}
1275	>	void SimSetup::createFF(void){
1276	>	switch (ffCase){
1277	>	case FF_DUFF:
1278	>	the_ff = new DUFF();
1279	>	break;
1280
1281	<	void SimSetup::makeElement( double x, double y, double z ){
1281	>	case FF_LJ:
1282	>	the_ff = new LJFF();
1283	>	break;
1284
1285	<	int k;
1286	<	AtomStamp* current_atom;
1287	<	DirectionalAtom* dAtom;
1352	<	double rotMat[3][3];
1285	>	case FF_EAM:
1286	>	the_ff = new EAM_FF();
1287	>	break;
1288
1289	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1289	>	case FF_H2O:
1290	>	the_ff = new WATER();
1291	>	break;
1292
1293	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1294	<	if( !current_atom->havePosition() ){
1295	<	sprintf( painCave.errMsg,
1359	<	"SimSetup:initFromBass error.\n"
1360	<	"\tComponent %s, atom %s does not have a position specified.\n"
1361	<	"\tThe initialization routine is unable to give a start"
1362	<	" position.\n",
1363	<	comp_stamps[current_comp]->getID(),
1364	<	current_atom->getType() );
1293	>	default:
1294	>	sprintf(painCave.errMsg,
1295	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1296		painCave.isFatal = 1;
1297		simError();
1298	<	}
1298	>	}
1299
1300	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1301	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1302	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1300	>	#ifdef IS_MPI
1301	>	strcpy(checkPointMsg, "ForceField creation successful");
1302	>	MPIcheckPoint();
1303	>	#endif // is_mpi
1304	>	}
1305
1373	–	if( the_atoms[current_atom_ndx]->isDirectional() ){
1306
1307	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1308	<
1309	<	rotMat[0][0] = 1.0;
1310	<	rotMat[0][1] = 0.0;
1311	<	rotMat[0][2] = 0.0;
1312	<
1313	<	rotMat[1][0] = 0.0;
1382	<	rotMat[1][1] = 1.0;
1383	<	rotMat[1][2] = 0.0;
1384	<
1385	<	rotMat[2][0] = 0.0;
1386	<	rotMat[2][1] = 0.0;
1387	<	rotMat[2][2] = 1.0;
1307	>	void SimSetup::compList(void){
1308	>	int i;
1309	>	char* id;
1310	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1311	>	LinkedMolStamp* currentStamp = NULL;
1312	>	comp_stamps = new MoleculeStamp * [n_components];
1313	>	bool haveCutoffGroups;
1314
1315	<	dAtom->setA( rotMat );
1315	>	haveCutoffGroups = false;
1316	>
1317	>	// make an array of molecule stamps that match the components used.
1318	>	// also extract the used stamps out into a separate linked list
1319	>
1320	>	for (i = 0; i < nInfo; i++){
1321	>	info[i].nComponents = n_components;
1322	>	info[i].componentsNmol = components_nmol;
1323	>	info[i].compStamps = comp_stamps;
1324	>	info[i].headStamp = headStamp;
1325	>	}
1326	>
1327	>
1328	>	for (i = 0; i < n_components; i++){
1329	>	id = the_components[i]->getType();
1330	>	comp_stamps[i] = NULL;
1331	>
1332	>	// check to make sure the component isn't already in the list
1333	>
1334	>	comp_stamps[i] = headStamp->match(id);
1335	>	if (comp_stamps[i] == NULL){
1336	>	// extract the component from the list;
1337	>
1338	>	currentStamp = stamps->extractMolStamp(id);
1339	>	if (currentStamp == NULL){
1340	>	sprintf(painCave.errMsg,
1341	>	"SimSetup error: Component \"%s\" was not found in the "
1342	>	"list of declared molecules\n",
1343	>	id);
1344	>	painCave.isFatal = 1;
1345	>	simError();
1346	>	}
1347	>
1348	>	headStamp->add(currentStamp);
1349	>	comp_stamps[i] = headStamp->match(id);
1350		}
1351
1352	<	current_atom_ndx++;
1352	>	if(comp_stamps[i]->getNCutoffGroups() > 0)
1353	>	haveCutoffGroups = true;
1354		}
1355	+
1356	+	for (i = 0; i < nInfo; i++)
1357	+	info[i].haveCutoffGroups = haveCutoffGroups;
1358
1359	<	current_mol++;
1360	<	current_comp_mol++;
1359	>	#ifdef IS_MPI
1360	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1361	>	MPIcheckPoint();
1362	>	#endif // is_mpi
1363	>	}
1364
1365	<	if( current_comp_mol >= components_nmol[current_comp] ){
1365	>	void SimSetup::calcSysValues(void){
1366	>	int i;
1367
1368	<	current_comp_mol = 0;
1369	<	current_comp++;
1368	>	int* molMembershipArray;
1369	>
1370	>	tot_atoms = 0;
1371	>	tot_bonds = 0;
1372	>	tot_bends = 0;
1373	>	tot_torsions = 0;
1374	>	tot_rigid = 0;
1375	>	for (i = 0; i < n_components; i++){
1376	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1377	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1378	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1379	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1380	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1381	>	}
1382	>
1383	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1384	>	molMembershipArray = new int[tot_atoms];
1385	>
1386	>	for (i = 0; i < nInfo; i++){
1387	>	info[i].n_atoms = tot_atoms;
1388	>	info[i].n_bonds = tot_bonds;
1389	>	info[i].n_bends = tot_bends;
1390	>	info[i].n_torsions = tot_torsions;
1391	>	info[i].n_SRI = tot_SRI;
1392	>	info[i].n_mol = tot_nmol;
1393	>
1394	>	info[i].molMembershipArray = molMembershipArray;
1395	>	}
1396	>	}
1397	>
1398	>	#ifdef IS_MPI
1399	>
1400	>	void SimSetup::mpiMolDivide(void){
1401	>	int i, j, k;
1402	>	int localMol, allMol;
1403	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1404	>	int local_rigid;
1405	>	vector<int> globalMolIndex;
1406	>
1407	>	mpiSim = new mpiSimulation(info);
1408	>
1409	>	mpiSim->divideLabor();
1410	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1411	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1412	>
1413	>	// set up the local variables
1414	>
1415	>	mol2proc = mpiSim->getMolToProcMap();
1416	>	molCompType = mpiSim->getMolComponentType();
1417	>
1418	>	allMol = 0;
1419	>	localMol = 0;
1420	>	local_atoms = 0;
1421	>	local_bonds = 0;
1422	>	local_bends = 0;
1423	>	local_torsions = 0;
1424	>	local_rigid = 0;
1425	>	globalAtomCounter = 0;
1426	>
1427	>	for (i = 0; i < n_components; i++){
1428	>	for (j = 0; j < components_nmol[i]; j++){
1429	>	if (mol2proc[allMol] == worldRank){
1430	>	local_atoms += comp_stamps[i]->getNAtoms();
1431	>	local_bonds += comp_stamps[i]->getNBonds();
1432	>	local_bends += comp_stamps[i]->getNBends();
1433	>	local_torsions += comp_stamps[i]->getNTorsions();
1434	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1435	>	localMol++;
1436	>	}
1437	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1438	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1439	>	globalAtomCounter++;
1440	>	}
1441	>
1442	>	allMol++;
1443	>	}
1444	>	}
1445	>	local_SRI = local_bonds + local_bends + local_torsions;
1446	>
1447	>	info[0].n_atoms = mpiSim->getMyNlocal();
1448	>
1449	>
1450	>	if (local_atoms != info[0].n_atoms){
1451	>	sprintf(painCave.errMsg,
1452	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1453	>	"\tlocalAtom (%d) are not equal.\n",
1454	>	info[0].n_atoms, local_atoms);
1455	>	painCave.isFatal = 1;
1456	>	simError();
1457	>	}
1458	>
1459	>	info[0].n_bonds = local_bonds;
1460	>	info[0].n_bends = local_bends;
1461	>	info[0].n_torsions = local_torsions;
1462	>	info[0].n_SRI = local_SRI;
1463	>	info[0].n_mol = localMol;
1464	>
1465	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1466	>	MPIcheckPoint();
1467	>	}
1468	>
1469	>	#endif // is_mpi
1470	>
1471	>
1472	>	void SimSetup::makeSysArrays(void){
1473	>
1474	>	#ifndef IS_MPI
1475	>	int k, j;
1476	>	#endif // is_mpi
1477	>	int i, l;
1478	>
1479	>	Atom** the_atoms;
1480	>	Molecule* the_molecules;
1481	>
1482	>	for (l = 0; l < nInfo; l++){
1483	>	// create the atom and short range interaction arrays
1484	>
1485	>	the_atoms = new Atom * [info[l].n_atoms];
1486	>	the_molecules = new Molecule[info[l].n_mol];
1487	>	int molIndex;
1488	>
1489	>	// initialize the molecule's stampID's
1490	>
1491	>	#ifdef IS_MPI
1492	>
1493	>
1494	>	molIndex = 0;
1495	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1496	>	if (mol2proc[i] == worldRank){
1497	>	the_molecules[molIndex].setStampID(molCompType[i]);
1498	>	the_molecules[molIndex].setMyIndex(molIndex);
1499	>	the_molecules[molIndex].setGlobalIndex(i);
1500	>	molIndex++;
1501	>	}
1502	>	}
1503	>
1504	>	#else // is_mpi
1505	>
1506	>	molIndex = 0;
1507	>	globalAtomCounter = 0;
1508	>	for (i = 0; i < n_components; i++){
1509	>	for (j = 0; j < components_nmol[i]; j++){
1510	>	the_molecules[molIndex].setStampID(i);
1511	>	the_molecules[molIndex].setMyIndex(molIndex);
1512	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1513	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1514	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1515	>	globalAtomCounter++;
1516	>	}
1517	>	molIndex++;
1518	>	}
1519	>	}
1520	>
1521	>
1522	>	#endif // is_mpi
1523	>
1524	>	info[l].globalExcludes = new int;
1525	>	info[l].globalExcludes[0] = 0;
1526	>
1527	>	// set the arrays into the SimInfo object
1528	>
1529	>	info[l].atoms = the_atoms;
1530	>	info[l].molecules = the_molecules;
1531	>	info[l].nGlobalExcludes = 0;
1532	>
1533	>	the_ff->setSimInfo(info);
1534		}
1535		}
1536	+
1537	+	void SimSetup::makeIntegrator(void){
1538	+	int k;
1539	+
1540	+	NVE<RealIntegrator>* myNVE = NULL;
1541	+	NVT<RealIntegrator>* myNVT = NULL;
1542	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1543	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1544	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1545	+
1546	+	for (k = 0; k < nInfo; k++){
1547	+	switch (ensembleCase){
1548	+	case NVE_ENS:
1549	+	if (globals->haveZconstraints()){
1550	+	setupZConstraint(info[k]);
1551	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1552	+	}
1553	+	else{
1554	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1555	+	}
1556	+
1557	+	info->the_integrator = myNVE;
1558	+	break;
1559	+
1560	+	case NVT_ENS:
1561	+	if (globals->haveZconstraints()){
1562	+	setupZConstraint(info[k]);
1563	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1564	+	}
1565	+	else
1566	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1567	+
1568	+	myNVT->setTargetTemp(globals->getTargetTemp());
1569	+
1570	+	if (globals->haveTauThermostat())
1571	+	myNVT->setTauThermostat(globals->getTauThermostat());
1572	+	else{
1573	+	sprintf(painCave.errMsg,
1574	+	"SimSetup error: If you use the NVT\n"
1575	+	"\tensemble, you must set tauThermostat.\n");
1576	+	painCave.isFatal = 1;
1577	+	simError();
1578	+	}
1579	+
1580	+	info->the_integrator = myNVT;
1581	+	break;
1582	+
1583	+	case NPTi_ENS:
1584	+	if (globals->haveZconstraints()){
1585	+	setupZConstraint(info[k]);
1586	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1587	+	}
1588	+	else
1589	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1590	+
1591	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1592	+
1593	+	if (globals->haveTargetPressure())
1594	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1595	+	else{
1596	+	sprintf(painCave.errMsg,
1597	+	"SimSetup error: If you use a constant pressure\n"
1598	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1599	+	painCave.isFatal = 1;
1600	+	simError();
1601	+	}
1602	+
1603	+	if (globals->haveTauThermostat())
1604	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1605	+	else{
1606	+	sprintf(painCave.errMsg,
1607	+	"SimSetup error: If you use an NPT\n"
1608	+	"\tensemble, you must set tauThermostat.\n");
1609	+	painCave.isFatal = 1;
1610	+	simError();
1611	+	}
1612	+
1613	+	if (globals->haveTauBarostat())
1614	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1615	+	else{
1616	+	sprintf(painCave.errMsg,
1617	+	"SimSetup error: If you use an NPT\n"
1618	+	"\tensemble, you must set tauBarostat.\n");
1619	+	painCave.isFatal = 1;
1620	+	simError();
1621	+	}
1622	+
1623	+	info->the_integrator = myNPTi;
1624	+	break;
1625	+
1626	+	case NPTf_ENS:
1627	+	if (globals->haveZconstraints()){
1628	+	setupZConstraint(info[k]);
1629	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1630	+	}
1631	+	else
1632	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1633	+
1634	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1635	+
1636	+	if (globals->haveTargetPressure())
1637	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1638	+	else{
1639	+	sprintf(painCave.errMsg,
1640	+	"SimSetup error: If you use a constant pressure\n"
1641	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1642	+	painCave.isFatal = 1;
1643	+	simError();
1644	+	}
1645	+
1646	+	if (globals->haveTauThermostat())
1647	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1648	+
1649	+	else{
1650	+	sprintf(painCave.errMsg,
1651	+	"SimSetup error: If you use an NPT\n"
1652	+	"\tensemble, you must set tauThermostat.\n");
1653	+	painCave.isFatal = 1;
1654	+	simError();
1655	+	}
1656	+
1657	+	if (globals->haveTauBarostat())
1658	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1659	+
1660	+	else{
1661	+	sprintf(painCave.errMsg,
1662	+	"SimSetup error: If you use an NPT\n"
1663	+	"\tensemble, you must set tauBarostat.\n");
1664	+	painCave.isFatal = 1;
1665	+	simError();
1666	+	}
1667	+
1668	+	info->the_integrator = myNPTf;
1669	+	break;
1670	+
1671	+	case NPTxyz_ENS:
1672	+	if (globals->haveZconstraints()){
1673	+	setupZConstraint(info[k]);
1674	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1675	+	}
1676	+	else
1677	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1678	+
1679	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1680	+
1681	+	if (globals->haveTargetPressure())
1682	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1683	+	else{
1684	+	sprintf(painCave.errMsg,
1685	+	"SimSetup error: If you use a constant pressure\n"
1686	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1687	+	painCave.isFatal = 1;
1688	+	simError();
1689	+	}
1690	+
1691	+	if (globals->haveTauThermostat())
1692	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1693	+	else{
1694	+	sprintf(painCave.errMsg,
1695	+	"SimSetup error: If you use an NPT\n"
1696	+	"\tensemble, you must set tauThermostat.\n");
1697	+	painCave.isFatal = 1;
1698	+	simError();
1699	+	}
1700	+
1701	+	if (globals->haveTauBarostat())
1702	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1703	+	else{
1704	+	sprintf(painCave.errMsg,
1705	+	"SimSetup error: If you use an NPT\n"
1706	+	"\tensemble, you must set tauBarostat.\n");
1707	+	painCave.isFatal = 1;
1708	+	simError();
1709	+	}
1710	+
1711	+	info->the_integrator = myNPTxyz;
1712	+	break;
1713	+
1714	+	default:
1715	+	sprintf(painCave.errMsg,
1716	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1717	+	painCave.isFatal = 1;
1718	+	simError();
1719	+	}
1720	+	}
1721	+	}
1722	+
1723	+	void SimSetup::initFortran(void){
1724	+	info[0].refreshSim();
1725	+
1726	+	if (!strcmp(info[0].mixingRule, "standard")){
1727	+	the_ff->initForceField(LB_MIXING_RULE);
1728	+	}
1729	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1730	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1731	+	}
1732	+	else{
1733	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1734	+	info[0].mixingRule);
1735	+	painCave.isFatal = 1;
1736	+	simError();
1737	+	}
1738	+
1739	+
1740	+	#ifdef IS_MPI
1741	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1742	+	MPIcheckPoint();
1743	+	#endif // is_mpi
1744	+	}
1745	+
1746	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1747	+	int nZConstraints;
1748	+	ZconStamp** zconStamp;
1749	+
1750	+	if (globals->haveZconstraintTime()){
1751	+	//add sample time of z-constraint  into SimInfo's property list
1752	+	DoubleData* zconsTimeProp = new DoubleData();
1753	+	zconsTimeProp->setID(ZCONSTIME_ID);
1754	+	zconsTimeProp->setData(globals->getZconsTime());
1755	+	theInfo.addProperty(zconsTimeProp);
1756	+	}
1757	+	else{
1758	+	sprintf(painCave.errMsg,
1759	+	"ZConstraint error: If you use a ZConstraint,\n"
1760	+	"\tyou must set zconsTime.\n");
1761	+	painCave.isFatal = 1;
1762	+	simError();
1763	+	}
1764	+
1765	+	//push zconsTol into siminfo, if user does not specify
1766	+	//value for zconsTol, a default value will be used
1767	+	DoubleData* zconsTol = new DoubleData();
1768	+	zconsTol->setID(ZCONSTOL_ID);
1769	+	if (globals->haveZconsTol()){
1770	+	zconsTol->setData(globals->getZconsTol());
1771	+	}
1772	+	else{
1773	+	double defaultZConsTol = 0.01;
1774	+	sprintf(painCave.errMsg,
1775	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1776	+	"\tOOPSE will use a default value of %f.\n"
1777	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1778	+	defaultZConsTol);
1779	+	painCave.isFatal = 0;
1780	+	simError();
1781	+
1782	+	zconsTol->setData(defaultZConsTol);
1783	+	}
1784	+	theInfo.addProperty(zconsTol);
1785	+
1786	+	//set Force Subtraction Policy
1787	+	StringData* zconsForcePolicy = new StringData();
1788	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1789	+
1790	+	if (globals->haveZconsForcePolicy()){
1791	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1792	+	}
1793	+	else{
1794	+	sprintf(painCave.errMsg,
1795	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1796	+	"\tOOPSE will use PolicyByMass.\n"
1797	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1798	+	painCave.isFatal = 0;
1799	+	simError();
1800	+	zconsForcePolicy->setData("BYMASS");
1801	+	}
1802	+
1803	+	theInfo.addProperty(zconsForcePolicy);
1804	+
1805	+	//set zcons gap
1806	+	DoubleData* zconsGap = new DoubleData();
1807	+	zconsGap->setID(ZCONSGAP_ID);
1808	+
1809	+	if (globals->haveZConsGap()){
1810	+	zconsGap->setData(globals->getZconsGap());
1811	+	theInfo.addProperty(zconsGap);
1812	+	}
1813	+
1814	+	//set zcons fixtime
1815	+	DoubleData* zconsFixtime = new DoubleData();
1816	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1817	+
1818	+	if (globals->haveZConsFixTime()){
1819	+	zconsFixtime->setData(globals->getZconsFixtime());
1820	+	theInfo.addProperty(zconsFixtime);
1821	+	}
1822	+
1823	+	//set zconsUsingSMD
1824	+	IntData* zconsUsingSMD = new IntData();
1825	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1826	+
1827	+	if (globals->haveZConsUsingSMD()){
1828	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1829	+	theInfo.addProperty(zconsUsingSMD);
1830	+	}
1831	+
1832	+	//Determine the name of ouput file and add it into SimInfo's property list
1833	+	//Be careful, do not use inFileName, since it is a pointer which
1834	+	//point to a string at master node, and slave nodes do not contain that string
1835	+
1836	+	string zconsOutput(theInfo.finalName);
1837	+
1838	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1839	+
1840	+	StringData* zconsFilename = new StringData();
1841	+	zconsFilename->setID(ZCONSFILENAME_ID);
1842	+	zconsFilename->setData(zconsOutput);
1843	+
1844	+	theInfo.addProperty(zconsFilename);
1845	+
1846	+	//setup index, pos and other parameters of z-constraint molecules
1847	+	nZConstraints = globals->getNzConstraints();
1848	+	theInfo.nZconstraints = nZConstraints;
1849	+
1850	+	zconStamp = globals->getZconStamp();
1851	+	ZConsParaItem tempParaItem;
1852	+
1853	+	ZConsParaData* zconsParaData = new ZConsParaData();
1854	+	zconsParaData->setID(ZCONSPARADATA_ID);
1855	+
1856	+	for (int i = 0; i < nZConstraints; i++){
1857	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1858	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1859	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1860	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1861	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1862	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1863	+	zconsParaData->addItem(tempParaItem);
1864	+	}
1865	+
1866	+	//check the uniqueness of index
1867	+	if(!zconsParaData->isIndexUnique()){
1868	+	sprintf(painCave.errMsg,
1869	+	"ZConstraint Error: molIndex is not unique!\n");
1870	+	painCave.isFatal = 1;
1871	+	simError();
1872	+	}
1873	+
1874	+	//sort the parameters by index of molecules
1875	+	zconsParaData->sortByIndex();
1876	+
1877	+	//push data into siminfo, therefore, we can retrieve later
1878	+	theInfo.addProperty(zconsParaData);
1879	+	}
1880	+
1881	+	void SimSetup::makeMinimizer(){
1882	+
1883	+	OOPSEMinimizer* myOOPSEMinimizer;
1884	+	MinimizerParameterSet* param;
1885	+	char minimizerName[100];
1886	+
1887	+	for (int i = 0; i < nInfo; i++){
1888	+
1889	+	//prepare parameter set for minimizer
1890	+	param = new MinimizerParameterSet();
1891	+	param->setDefaultParameter();
1892	+
1893	+	if (globals->haveMinimizer()){
1894	+	param->setFTol(globals->getMinFTol());
1895	+	}
1896	+
1897	+	if (globals->haveMinGTol()){
1898	+	param->setGTol(globals->getMinGTol());
1899	+	}
1900	+
1901	+	if (globals->haveMinMaxIter()){
1902	+	param->setMaxIteration(globals->getMinMaxIter());
1903	+	}
1904	+
1905	+	if (globals->haveMinWriteFrq()){
1906	+	param->setMaxIteration(globals->getMinMaxIter());
1907	+	}
1908	+
1909	+	if (globals->haveMinWriteFrq()){
1910	+	param->setWriteFrq(globals->getMinWriteFrq());
1911	+	}
1912	+
1913	+	if (globals->haveMinStepSize()){
1914	+	param->setStepSize(globals->getMinStepSize());
1915	+	}
1916	+
1917	+	if (globals->haveMinLSMaxIter()){
1918	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1919	+	}
1920	+
1921	+	if (globals->haveMinLSTol()){
1922	+	param->setLineSearchTol(globals->getMinLSTol());
1923	+	}
1924	+
1925	+	strcpy(minimizerName, globals->getMinimizer());
1926	+
1927	+	if (!strcasecmp(minimizerName, "CG")){
1928	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1929	+	}
1930	+	else if (!strcasecmp(minimizerName, "SD")){
1931	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1932	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1933	+	}
1934	+	else{
1935	+	sprintf(painCave.errMsg,
1936	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1937	+	painCave.isFatal = 0;
1938	+	simError();
1939	+
1940	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1941	+	}
1942	+	info[i].the_integrator = myOOPSEMinimizer;
1943	+
1944	+	//store the minimizer into simInfo
1945	+	info[i].the_minimizer = myOOPSEMinimizer;
1946	+	info[i].has_minimizer = true;
1947	+	}
1948	+
1949	+	}

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