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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 580 by gezelter, Wed Jul 9 13:56:36 2003 UTC vs.
Revision 1203 by gezelter, Thu May 27 18:59:17 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
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
22	–	#define FF_DUFF 0
23	–	#define FF_LJ   1
29
30	+	#define FF_DUFF  0
31	+	#define FF_LJ    1
32	+	#define FF_EAM   2
33	+	#define FF_H2O   3
34
35	+	using namespace std;
36	+
37	+	/**
38	+	* Check whether dividend is divisble by divisor or not
39	+	*/
40	+	bool isDivisible(double dividend, double divisor){
41	+	double tolerance = 0.000001;
42	+	double quotient;
43	+	double diff;
44	+	int intQuotient;
45	+
46	+	quotient = dividend / divisor;
47	+
48	+	if (quotient < 0)
49	+	quotient = -quotient;
50	+
51	+	intQuotient = int (quotient + tolerance);
52	+
53	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
54	+
55	+	if (diff <= tolerance)
56	+	return true;
57	+	else
58	+	return false;
59	+	}
60	+
61		SimSetup::SimSetup(){
62	+
63	+	initSuspend = false;
64	+	isInfoArray = 0;
65	+	nInfo = 1;
66	+
67		stamps = new MakeStamps();
68		globals = new Globals();
69	<
69	>
70	>
71		#ifdef IS_MPI
72	<	strcpy( checkPointMsg, "SimSetup creation successful" );
72	>	strcpy(checkPointMsg, "SimSetup creation successful");
73		MPIcheckPoint();
74		#endif // IS_MPI
75		}
#	Line 38 | 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();
70	<	mpiEventLoop();
71	<
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;
79	<	Globals* the_globals;
80	<	int i, j, k, globalAtomIndex;
81	<
82	<	int ensembleCase;
83	<	int ffCase;
84	<
85	<	ensembleCase = -1;
86	<	ffCase = -1;
126	>	// gather all of the information from the Bass file
127
128	<	// get the stamps and globals;
89	<	the_stamps = stamps;
90	<	the_globals = globals;
128	>	gatherInfo();
129
130	<	// set the easy ones first
93	<	simnfo->target_temp = the_globals->getTargetTemp();
94	<	simnfo->dt = the_globals->getDt();
95	<	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.
98	<	n_components = the_globals->getNComponents();
99	<	strcpy( force_field, the_globals->getForceField() );
132	>	sysObjectsCreation();
133
134	<	if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF;
102	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
103	<	else{
104	<	sprintf( painCave.errMsg,
105	<	"SimSetup Error. Unrecognized force field -> %s\n",
106	<	force_field );
107	<	painCave.isFatal = 1;
108	<	simError();
109	<	}
134	>	// check on the post processing info
135
136	<	// get the ensemble:
112	<	strcpy( ensemble, the_globals->getEnsemble() );
136	>	finalInfoCheck();
137
138	<	if( !strcasecmp( ensemble, "NVE" ))      ensembleCase = NVE_ENS;
139	<	else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS;
140	<	else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") )
141	<	ensembleCase = NPTi_ENS;
142	<	else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS;
143	<	else{
144	<	sprintf( painCave.errMsg,
121	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
122	<	"reverting to NVE for this simulation.\n",
123	<	ensemble );
124	<	painCave.isFatal = 0;
125	<	simError();
126	<	strcpy( ensemble, "NVE" );
127	<	ensembleCase = NVE_ENS;
138	>	// initialize the system coordinates
139	>
140	>	if ( !initSuspend ){
141	>	initSystemCoords();
142	>
143	>	if( !(globals->getUseInitTime()) )
144	>	info[0].currentTime = 0.0;
145		}
129	–	strcpy( simnfo->ensemble, ensemble );
146
147	+	// make the output filenames
148
149	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
150	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
151	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
152	<	//     if (the_globals->haveTargetPressure())
153	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
137	<	//     else {
138	<	//       sprintf( painCave.errMsg,
139	<	//                "SimSetup error: If you use the constant pressure\n"
140	<	//                "    ensemble, you must set targetPressure.\n"
141	<	//                "    This was found in the BASS file.\n");
142	<	//       painCave.isFatal = 1;
143	<	//       simError();
144	<	//     }
149	>	makeOutNames();
150	>
151	>	#ifdef IS_MPI
152	>	mpiSim->mpiRefresh();
153	>	#endif
154
155	<	//     if (the_globals->haveTauThermostat())
147	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
148	<	//     else if (the_globals->haveQmass())
149	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
150	<	//     else {
151	<	//       sprintf( painCave.errMsg,
152	<	//                "SimSetup error: If you use one of the constant temperature\n"
153	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
154	<	//                "    Neither of these was found in the BASS file.\n");
155	<	//       painCave.isFatal = 1;
156	<	//       simError();
157	<	//     }
155	>	// initialize the Fortran
156
157	<	//     if (the_globals->haveTauBarostat())
160	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
161	<	//     else {
162	<	//       sprintf( painCave.errMsg,
163	<	//                "SimSetup error: If you use the constant pressure\n"
164	<	//                "    ensemble, you must set tauBarostat.\n"
165	<	//                "    This was found in the BASS file.\n");
166	<	//       painCave.isFatal = 1;
167	<	//       simError();
168	<	//     }
157	>	initFortran();
158
159	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
160	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
161	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
159	>	if (globals->haveMinimizer())
160	>	// make minimizer
161	>	makeMinimizer();
162	>	else
163	>	// make the integrator
164	>	makeIntegrator();
165
166	<	//     if (the_globals->haveTauThermostat())
175	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
176	<	//     else if (the_globals->haveQmass())
177	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
178	<	//     else {
179	<	//       sprintf( painCave.errMsg,
180	<	//                "SimSetup error: If you use one of the constant temperature\n"
181	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
182	<	//                "    Neither of these was found in the BASS file.\n");
183	<	//       painCave.isFatal = 1;
184	<	//       simError();
185	<	//     }
166	>	}
167
187	–	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
188	–	simnfo->usePBC = the_globals->getPBC();
189	–
190	–	int usesDipoles = 0;
191	–	switch( ffCase ){
168
169	<	case FF_DUFF:
170	<	the_ff = new DUFF();
171	<	usesDipoles = 1;
172	<	break;
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	>	int nCutoffGroups;// number of cutoff group of a molecule defined in mdl file
189	>	set<int> cutoffAtomSet; //atoms belong to  cutoffgroup defined at mdl file
190
191	<	case FF_LJ:
192	<	the_ff = new LJFF();
193	<	break;
191	>	bond_pair* theBonds;
192	>	bend_set* theBends;
193	>	torsion_set* theTorsions;
194
195	<	default:
203	<	sprintf( painCave.errMsg,
204	<	"SimSetup Error. Unrecognized force field in case statement.\n");
205	<	painCave.isFatal = 1;
206	<	simError();
207	<	}
195	>	set<int> skipList;
196
197	<	#ifdef IS_MPI
198	<	strcpy( checkPointMsg, "ForceField creation successful" );
199	<	MPIcheckPoint();
212	<	#endif // is_mpi
197	>	double phi, theta, psi;
198	>	char* molName;
199	>	char rbName[100];
200
201	<	// get the components and calculate the tot_nMol and indvidual n_mol
215	<	the_components = the_globals->getComponents();
216	<	components_nmol = new int[n_components];
217	<	comp_stamps = new MoleculeStamp*[n_components];
201	>	//init the forceField paramters
202
203	<	if( !the_globals->haveNMol() ){
220	<	// we don't have the total number of molecules, so we assume it is
221	<	// given in each component
203	>	the_ff->readParams();
204
205	<	tot_nmol = 0;
224	<	for( i=0; i<n_components; i++ ){
205	>	// init the atoms
206
207	<	if( !the_components[i]->haveNMol() ){
208	<	// we have a problem
209	<	sprintf( painCave.errMsg,
210	<	"SimSetup Error. No global NMol or component NMol"
211	<	" given. Cannot calculate the number of atoms.\n" );
212	<	painCave.isFatal = 1;
232	<	simError();
233	<	}
207	>	int nMembers, nNew, rb1, rb2;
208	>
209	>	for (k = 0; k < nInfo; k++){
210	>	the_ff->setSimInfo(&(info[k]));
211	>
212	>	atomOffset = 0;
213
214	<	tot_nmol += the_components[i]->getNMol();
215	<	components_nmol[i] = the_components[i]->getNMol();
216	<	}
238	<	}
239	<	else{
240	<	sprintf( painCave.errMsg,
241	<	"SimSetup error.\n"
242	<	"\tSorry, the ability to specify total"
243	<	" nMols and then give molfractions in the components\n"
244	<	"\tis not currently supported."
245	<	" Please give nMol in the components.\n" );
246	<	painCave.isFatal = 1;
247	<	simError();
248	<
249	<
250	<	//     tot_nmol = the_globals->getNMol();
251	<
252	<	//   //we have the total number of molecules, now we check for molfractions
253	<	//     for( i=0; i<n_components; i++ ){
254	<
255	<	//       if( !the_components[i]->haveMolFraction() ){
256	<
257	<	//  if( !the_components[i]->haveNMol() ){
258	<	//    //we have a problem
259	<	//    std::cerr << "SimSetup error. Neither molFraction nor "
260	<	//              << " nMol was given in component
261	<
262	<	}
214	>	for (i = 0; i < info[k].n_mol; i++){
215	>	stampID = info[k].molecules[i].getStampID();
216	>	molName = comp_stamps[stampID]->getID();
217
218	<	#ifdef IS_MPI
219	<	strcpy( checkPointMsg, "Have the number of components" );
220	<	MPIcheckPoint();
221	<	#endif // is_mpi
218	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
219	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
220	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
221	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
222	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
223
224	<	// make an array of molecule stamps that match the components used.
225	<	// also extract the used stamps out into a separate linked list
224	>	nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
225	>
226	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
227
228	<	simnfo->nComponents = n_components;
229	<	simnfo->componentsNmol = components_nmol;
230	<	simnfo->compStamps = comp_stamps;
231	<	simnfo->headStamp = new LinkedMolStamp();
276	<
277	<	char* id;
278	<	LinkedMolStamp* headStamp = simnfo->headStamp;
279	<	LinkedMolStamp* currentStamp = NULL;
280	<	for( i=0; i<n_components; i++ ){
228	>	if (molInfo.nBonds > 0)
229	>	molInfo.myBonds = new Bond*[molInfo.nBonds];
230	>	else
231	>	molInfo.myBonds = NULL;
232
233	<	id = the_components[i]->getType();
234	<	comp_stamps[i] = NULL;
235	<
236	<	// check to make sure the component isn't already in the list
233	>	if (molInfo.nBends > 0)
234	>	molInfo.myBends = new Bend*[molInfo.nBends];
235	>	else
236	>	molInfo.myBends = NULL;
237
238	<	comp_stamps[i] = headStamp->match( id );
239	<	if( comp_stamps[i] == NULL ){
238	>	if (molInfo.nTorsions > 0)
239	>	molInfo.myTorsions = new Torsion *[molInfo.nTorsions];
240	>	else
241	>	molInfo.myTorsions = NULL;
242	>
243	>	theBonds = new bond_pair[molInfo.nBonds];
244	>	theBends = new bend_set[molInfo.nBends];
245	>	theTorsions = new torsion_set[molInfo.nTorsions];
246
247	<	// extract the component from the list;
291	<
292	<	currentStamp = the_stamps->extractMolStamp( id );
293	<	if( currentStamp == NULL ){
294	<	sprintf( painCave.errMsg,
295	<	"SimSetup error: Component \"%s\" was not found in the "
296	<	"list of declared molecules\n",
297	<	id );
298	<	painCave.isFatal = 1;
299	<	simError();
300	<	}
301	<
302	<	headStamp->add( currentStamp );
303	<	comp_stamps[i] = headStamp->match( id );
304	<	}
305	<	}
247	>	// make the Atoms
248
249	<	#ifdef IS_MPI
250	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
309	<	MPIcheckPoint();
310	<	#endif // is_mpi
311	<
249	>	for (j = 0; j < molInfo.nAtoms; j++){
250	>	currentAtom = comp_stamps[stampID]->getAtom(j);
251
252	+	if (currentAtom->haveOrientation()){
253	+	dAtom = new DirectionalAtom((j + atomOffset),
254	+	info[k].getConfiguration());
255	+	info[k].n_oriented++;
256	+	molInfo.myAtoms[j] = dAtom;
257
258	+	// Directional Atoms have standard unit vectors which are oriented
259	+	// in space using the three Euler angles.  We assume the standard
260	+	// unit vector was originally along the z axis below.
261
262	<	// caclulate the number of atoms, bonds, bends and torsions
262	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
263	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
264	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
265
266	<	tot_atoms = 0;
267	<	tot_bonds = 0;
268	<	tot_bends = 0;
269	<	tot_torsions = 0;
321	<	for( i=0; i<n_components; i++ ){
322	<
323	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
324	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
325	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
326	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
327	<	}
266	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
267	>
268	>	}
269	>	else{
270
271	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
271	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
272
273	<	simnfo->n_atoms = tot_atoms;
332	<	simnfo->n_bonds = tot_bonds;
333	<	simnfo->n_bends = tot_bends;
334	<	simnfo->n_torsions = tot_torsions;
335	<	simnfo->n_SRI = tot_SRI;
336	<	simnfo->n_mol = tot_nmol;
337	<
338	<	simnfo->molMembershipArray = new int[tot_atoms];
273	>	}
274
275	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
276		#ifdef IS_MPI
277
278	<	// divide the molecules among processors here.
343	<
344	<	mpiSim = new mpiSimulation( simnfo );
345	<
346	<	globalIndex = mpiSim->divideLabor();
278	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
279
280	<	// set up the local variables
281	<
350	<	int localMol, allMol;
351	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
280	>	#endif // is_mpi
281	>	}
282
283	<	int* mol2proc = mpiSim->getMolToProcMap();
284	<	int* molCompType = mpiSim->getMolComponentType();
285	<
286	<	allMol = 0;
287	<	localMol = 0;
358	<	local_atoms = 0;
359	<	local_bonds = 0;
360	<	local_bends = 0;
361	<	local_torsions = 0;
362	<	globalAtomIndex = 0;
283	>	// make the bonds
284	>	for (j = 0; j < molInfo.nBonds; j++){
285	>	currentBond = comp_stamps[stampID]->getBond(j);
286	>	theBonds[j].a = currentBond->getA() + atomOffset;
287	>	theBonds[j].b = currentBond->getB() + atomOffset;
288
289	+	tempI = theBonds[j].a;
290	+	tempJ = theBonds[j].b;
291
292	<	for( i=0; i<n_components; i++ ){
292	>	#ifdef IS_MPI
293	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
294	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
295	>	#else
296	>	exI = tempI + 1;
297	>	exJ = tempJ + 1;
298	>	#endif
299
300	<	for( j=0; j<components_nmol[i]; j++ ){
368	<
369	<	if( mol2proc[allMol] == worldRank ){
370	<
371	<	local_atoms +=    comp_stamps[i]->getNAtoms();
372	<	local_bonds +=    comp_stamps[i]->getNBonds();
373	<	local_bends +=    comp_stamps[i]->getNBends();
374	<	local_torsions += comp_stamps[i]->getNTorsions();
375	<	localMol++;
376	<	}
377	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
378	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
379	<	globalAtomIndex++;
300	>	info[k].excludes->addPair(exI, exJ);
301		}
302
303	<	allMol++;
304	<	}
305	<	}
306	<	local_SRI = local_bonds + local_bends + local_torsions;
307	<
308	<	simnfo->n_atoms = mpiSim->getMyNlocal();
388	<
389	<	if( local_atoms != simnfo->n_atoms ){
390	<	sprintf( painCave.errMsg,
391	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
392	<	" localAtom (%d) are not equal.\n",
393	<	simnfo->n_atoms,
394	<	local_atoms );
395	<	painCave.isFatal = 1;
396	<	simError();
397	<	}
303	>	//make the bends
304	>	for (j = 0; j < molInfo.nBends; j++){
305	>	currentBend = comp_stamps[stampID]->getBend(j);
306	>	theBends[j].a = currentBend->getA() + atomOffset;
307	>	theBends[j].b = currentBend->getB() + atomOffset;
308	>	theBends[j].c = currentBend->getC() + atomOffset;
309
310	<	simnfo->n_bonds = local_bonds;
311	<	simnfo->n_bends = local_bends;
312	<	simnfo->n_torsions = local_torsions;
402	<	simnfo->n_SRI = local_SRI;
403	<	simnfo->n_mol = localMol;
310	>	if (currentBend->haveExtras()){
311	>	extras = currentBend->getExtras();
312	>	current_extra = extras;
313
314	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
315	<	MPIcheckPoint();
316	<
317	<
318	<	#endif // is_mpi
319	<
314	>	while (current_extra != NULL){
315	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
316	>	switch (current_extra->getType()){
317	>	case 0:
318	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
319	>	theBends[j].isGhost = 1;
320	>	break;
321
322	<	// create the atom and short range interaction arrays
322	>	case 1:
323	>	theBends[j].ghost = (int) current_extra->getDouble() +
324	>	atomOffset;
325	>	theBends[j].isGhost = 1;
326	>	break;
327
328	<	Atom::createArrays(simnfo->n_atoms);
329	<	the_atoms = new Atom*[simnfo->n_atoms];
330	<	the_molecules = new Molecule[simnfo->n_mol];
331	<	int molIndex;
332	<
333	<	// initialize the molecule's stampID's
328	>	default:
329	>	sprintf(painCave.errMsg,
330	>	"SimSetup Error: ghostVectorSource was neither a "
331	>	"double nor an int.\n"
332	>	"-->Bend[%d] in %s\n",
333	>	j, comp_stamps[stampID]->getID());
334	>	painCave.isFatal = 1;
335	>	simError();
336	>	}
337	>	}
338	>	else{
339	>	sprintf(painCave.errMsg,
340	>	"SimSetup Error: unhandled bend assignment:\n"
341	>	"    -->%s in Bend[%d] in %s\n",
342	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
343	>	painCave.isFatal = 1;
344	>	simError();
345	>	}
346
347	+	current_extra = current_extra->getNext();
348	+	}
349	+	}
350	+
351	+	if (theBends[j].isGhost) {
352	+
353	+	tempI = theBends[j].a;
354	+	tempJ = theBends[j].b;
355	+
356		#ifdef IS_MPI
357	<
357	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
358	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
359	>	#else
360	>	exI = tempI + 1;
361	>	exJ = tempJ + 1;
362	>	#endif
363	>	info[k].excludes->addPair(exI, exJ);
364
365	<	molIndex = 0;
425	<	for(i=0; i<mpiSim->getTotNmol(); i++){
426	<
427	<	if(mol2proc[i] == worldRank ){
428	<	the_molecules[molIndex].setStampID( molCompType[i] );
429	<	the_molecules[molIndex].setMyIndex( molIndex );
430	<	the_molecules[molIndex].setGlobalIndex( i );
431	<	molIndex++;
432	<	}
433	<	}
365	>	} else {
366
367	<	#else // is_mpi
368	<
369	<	molIndex = 0;
370	<	globalAtomIndex = 0;
371	<	for(i=0; i<n_components; i++){
372	<	for(j=0; j<components_nmol[i]; j++ ){
373	<	the_molecules[molIndex].setStampID( i );
374	<	the_molecules[molIndex].setMyIndex( molIndex );
375	<	the_molecules[molIndex].setGlobalIndex( molIndex );
376	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
377	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
378	<	globalAtomIndex++;
367	>	tempI = theBends[j].a;
368	>	tempJ = theBends[j].b;
369	>	tempK = theBends[j].c;
370	>
371	>	#ifdef IS_MPI
372	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
373	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
374	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
375	>	#else
376	>	exI = tempI + 1;
377	>	exJ = tempJ + 1;
378	>	exK = tempK + 1;
379	>	#endif
380	>
381	>	info[k].excludes->addPair(exI, exK);
382	>	info[k].excludes->addPair(exI, exJ);
383	>	info[k].excludes->addPair(exJ, exK);
384	>	}
385		}
448	–	molIndex++;
449	–	}
450	–	}
451	–
386
387	<	#endif // is_mpi
387	>	for (j = 0; j < molInfo.nTorsions; j++){
388	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
389	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
390	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
391	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
392	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
393
394	+	tempI = theTorsions[j].a;
395	+	tempJ = theTorsions[j].b;
396	+	tempK = theTorsions[j].c;
397	+	tempL = theTorsions[j].d;
398
399	<	if( simnfo->n_SRI ){
400	<
401	<	Exclude::createArray(simnfo->n_SRI);
402	<	the_excludes = new Exclude*[simnfo->n_SRI];
403	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
404	<	simnfo->globalExcludes = new int;
405	<	simnfo->n_exclude = simnfo->n_SRI;
406	<	}
407	<	else{
408	<
409	<	Exclude::createArray( 1 );
467	<	the_excludes = new Exclude*;
468	<	the_excludes[0] = new Exclude(0);
469	<	the_excludes[0]->setPair( 0,0 );
470	<	simnfo->globalExcludes = new int;
471	<	simnfo->globalExcludes[0] = 0;
472	<	simnfo->n_exclude = 0;
473	<	}
399	>	#ifdef IS_MPI
400	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
401	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
402	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
403	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
404	>	#else
405	>	exI = tempI + 1;
406	>	exJ = tempJ + 1;
407	>	exK = tempK + 1;
408	>	exL = tempL + 1;
409	>	#endif
410
411	<	// set the arrays into the SimInfo object
411	>	info[k].excludes->addPair(exI, exJ);
412	>	info[k].excludes->addPair(exI, exK);
413	>	info[k].excludes->addPair(exI, exL);
414	>	info[k].excludes->addPair(exJ, exK);
415	>	info[k].excludes->addPair(exJ, exL);
416	>	info[k].excludes->addPair(exK, exL);
417	>	}
418
419	<	simnfo->atoms = the_atoms;
420	<	simnfo->molecules = the_molecules;
421	<	simnfo->nGlobalExcludes = 0;
422	<	simnfo->excludes = the_excludes;
419	>
420	>	molInfo.myRigidBodies.clear();
421	>
422	>	for (j = 0; j < molInfo.nRigidBodies; j++){
423
424	+	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
425	+	nMembers = currentRigidBody->getNMembers();
426
427	<	// get some of the tricky things that may still be in the globals
427	>	// Create the Rigid Body:
428
429	<	double boxVector[3];
486	<	if( the_globals->haveBox() ){
487	<	boxVector[0] = the_globals->getBox();
488	<	boxVector[1] = the_globals->getBox();
489	<	boxVector[2] = the_globals->getBox();
490	<
491	<	simnfo->setBox( boxVector );
492	<	}
493	<	else if( the_globals->haveDensity() ){
429	>	myRB = new RigidBody();
430
431	<	double vol;
432	<	vol = (double)tot_nmol / the_globals->getDensity();
433	<	boxVector[0] = pow( vol, ( 1.0 / 3.0 ) );
434	<	boxVector[1] = boxVector[0];
499	<	boxVector[2] = boxVector[0];
431	>	sprintf(rbName,"%s_RB_%d", molName, j);
432	>	myRB->setType(rbName);
433	>
434	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
435
436	<	simnfo->setBox( boxVector );
437	<	}
503	<	else{
504	<	if( !the_globals->haveBoxX() ){
505	<	sprintf( painCave.errMsg,
506	<	"SimSetup error, no periodic BoxX size given.\n" );
507	<	painCave.isFatal = 1;
508	<	simError();
509	<	}
510	<	boxVector[0] = the_globals->getBoxX();
436	>	// molI is atom numbering inside this molecule
437	>	molI = currentRigidBody->getMember(rb1);
438
439	<	if( !the_globals->haveBoxY() ){
440	<	sprintf( painCave.errMsg,
514	<	"SimSetup error, no periodic BoxY size given.\n" );
515	<	painCave.isFatal = 1;
516	<	simError();
517	<	}
518	<	boxVector[1] = the_globals->getBoxY();
439	>	// tempI is atom numbering on local processor
440	>	tempI = molI + atomOffset;
441
442	<	if( !the_globals->haveBoxZ() ){
443	<	sprintf( painCave.errMsg,
444	<	"SimSetup error, no periodic BoxZ size given.\n" );
523	<	painCave.isFatal = 1;
524	<	simError();
525	<	}
526	<	boxVector[2] = the_globals->getBoxZ();
442	>	// currentAtom is the AtomStamp (which we need for
443	>	// rigid body reference positions)
444	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
445
446	<	simnfo->setBox( boxVector );
447	<	}
446	>	// When we add to the rigid body, add the atom itself and
447	>	// the stamp info:
448
449	+	myRB->addAtom(info[k].atoms[tempI], currentAtom);
450	+
451	+	// Add this atom to the Skip List for the integrators
452		#ifdef IS_MPI
453	<	strcpy( checkPointMsg, "Box size set up" );
454	<	MPIcheckPoint();
455	<	#endif // is_mpi
453	>	slI = info[k].atoms[tempI]->getGlobalIndex();
454	>	#else
455	>	slI = tempI;
456	>	#endif
457	>	skipList.insert(slI);
458	>
459	>	}
460	>
461	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
462	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
463	>
464	>	tempI = currentRigidBody->getMember(rb1);
465	>	tempJ = currentRigidBody->getMember(rb2);
466	>
467	>	// Some explanation is required here.
468	>	// Fortran indexing starts at 1, while c indexing starts at 0
469	>	// Also, in parallel computations, the GlobalIndex is
470	>	// used for the exclude list:
471	>
472	>	#ifdef IS_MPI
473	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
474	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
475	>	#else
476	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
477	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
478	>	#endif
479	>
480	>	info[k].excludes->addPair(exI, exJ);
481	>
482	>	}
483	>	}
484
485	+	molInfo.myRigidBodies.push_back(myRB);
486	+	info[k].rigidBodies.push_back(myRB);
487	+	}
488	+
489
490	<	// initialize the arrays
490	>	//create cutoff group for molecule
491
492	<	the_ff->setSimInfo( simnfo );
492	>	cutoffAtomSet.clear();
493	>	molInfo.myCutoffGroups.clear();
494	>
495	>	for (j = 0; j < nCutoffGroups; j++){
496
497	<	makeMolecules();
498	<	simnfo->identArray = new int[simnfo->n_atoms];
543	<	for(i=0; i<simnfo->n_atoms; i++){
544	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
545	<	}
546	<
547	<	if (the_globals->getUseRF() ) {
548	<	simnfo->useReactionField = 1;
549	<
550	<	if( !the_globals->haveECR() ){
551	<	sprintf( painCave.errMsg,
552	<	"SimSetup Warning: using default value of 1/2 the smallest "
553	<	"box length for the electrostaticCutoffRadius.\n"
554	<	"I hope you have a very fast processor!\n");
555	<	painCave.isFatal = 0;
556	<	simError();
557	<	double smallest;
558	<	smallest = simnfo->boxLx;
559	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
560	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
561	<	simnfo->ecr = 0.5 * smallest;
562	<	} else {
563	<	simnfo->ecr        = the_globals->getECR();
564	<	}
497	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
498	>	nMembers = currentCutoffGroup->getNMembers();
499
500	<	if( !the_globals->haveEST() ){
501	<	sprintf( painCave.errMsg,
502	<	"SimSetup Warning: using default value of 0.05 * the "
503	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
504	<	);
505	<	painCave.isFatal = 0;
506	<	simError();
507	<	simnfo->est = 0.05 * simnfo->ecr;
508	<	} else {
509	<	simnfo->est        = the_globals->getEST();
510	<	}
511	<
512	<	if(!the_globals->haveDielectric() ){
513	<	sprintf( painCave.errMsg,
514	<	"SimSetup Error: You are trying to use Reaction Field without"
515	<	"setting a dielectric constant!\n"
516	<	);
517	<	painCave.isFatal = 1;
518	<	simError();
519	<	}
520	<	simnfo->dielectric = the_globals->getDielectric();
521	<	} else {
522	<	if (usesDipoles) {
523	<
524	<	if( !the_globals->haveECR() ){
525	<	sprintf( painCave.errMsg,
526	<	"SimSetup Warning: using default value of 1/2 the smallest "
527	<	"box length for the electrostaticCutoffRadius.\n"
594	<	"I hope you have a very fast processor!\n");
595	<	painCave.isFatal = 0;
596	<	simError();
597	<	double smallest;
598	<	smallest = simnfo->boxLx;
599	<	if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy;
600	<	if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz;
601	<	simnfo->ecr = 0.5 * smallest;
602	<	} else {
603	<	simnfo->ecr        = the_globals->getECR();
500	>	myCutoffGroup = new CutoffGroup();
501	>
502	>	for (int cg = 0; cg < nMembers; cg++) {
503	>
504	>	// molI is atom numbering inside this molecule
505	>	molI = currentCutoffGroup->getMember(cg);
506	>
507	>	// tempI is atom numbering on local processor
508	>	tempI = molI + atomOffset;
509	>
510	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
511	>
512	>	cutoffAtomSet.insert(tempI);
513	>	}
514	>
515	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
516	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
517	>
518	>	//creat a cutoff group for every atom  in current molecule which does not belong to cutoffgroup defined at mdl file
519	>
520	>	for(j = 0; j < molInfo.nAtoms; j++){
521	>
522	>	if(cutoffAtomSet.find(molInfo.myAtoms[j]->getIndex()) == cutoffAtomSet.end()){
523	>	myCutoffGroup = new CutoffGroup();
524	>	myCutoffGroup->addAtom(molInfo.myAtoms[j]);
525	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
526	>	}
527	>
528		}
529	+
530	+
531	+
532	+
533	+	// After this is all set up, scan through the atoms to
534	+	// see if they can be added to the integrableObjects:
535	+
536	+	molInfo.myIntegrableObjects.clear();
537
606	–	if( !the_globals->haveEST() ){
607	–	sprintf( painCave.errMsg,
608	–	"SimSetup Warning: using default value of 5%% of the "
609	–	"electrostaticCutoffRadius for the "
610	–	"electrostaticSkinThickness\n"
611	–	);
612	–	painCave.isFatal = 0;
613	–	simError();
614	–	simnfo->est = 0.05 * simnfo->ecr;
615	–	} else {
616	–	simnfo->est        = the_globals->getEST();
617	–	}
618	–	}
619	–	}
538
539	<	#ifdef IS_MPI
622	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
623	<	MPIcheckPoint();
624	<	#endif // is_mpi
539	>	for (j = 0; j < molInfo.nAtoms; j++){
540
626	–	if( the_globals->haveInitialConfig() ){
627	–
628	–	InitializeFromFile* fileInit;
629	–	#ifdef IS_MPI // is_mpi
630	–	if( worldRank == 0 ){
631	–	#endif //is_mpi
632	–	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
541		#ifdef IS_MPI
542	<	}else fileInit = new InitializeFromFile( NULL );
542	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
543	>	#else
544	>	slJ = j+atomOffset;
545		#endif
636	–	fileInit->read_xyz( simnfo ); // default velocities on
546
547	<	delete fileInit;
639	<	}
640	<	else{
547	>	// if they aren't on the skip list, then they can be integrated
548
549	<	#ifdef IS_MPI
549	>	if (skipList.find(slJ) == skipList.end()) {
550	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
551	>	info[k].integrableObjects.push_back(mySD);
552	>	molInfo.myIntegrableObjects.push_back(mySD);
553	>	}
554	>	}
555
556	<	// no init from bass
645	<
646	<	sprintf( painCave.errMsg,
647	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
648	<	painCave.isFatal;
649	<	simError();
650	<
651	<	#else
556	>	// all rigid bodies are integrated:
557
558	<	initFromBass();
558	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
559	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
560	>	info[k].integrableObjects.push_back(mySD);
561	>	molInfo.myIntegrableObjects.push_back(mySD);
562	>	}
563	>
564	>
565	>	// send the arrays off to the forceField for init.
566	>
567	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
568	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
569	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
570	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
571	>	theTorsions);
572
573	+	info[k].molecules[i].initialize(molInfo);
574
656	–	#endif
657	–	}
575
576	+	atomOffset += molInfo.nAtoms;
577	+	delete[] theBonds;
578	+	delete[] theBends;
579	+	delete[] theTorsions;
580	+	}
581	+	}
582	+
583		#ifdef IS_MPI
584	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
584	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
585		MPIcheckPoint();
586		#endif // is_mpi
587
588	+	}
589
590	<
591	<
592	<
590	>	void SimSetup::initFromBass(void){
591	>	int i, j, k;
592	>	int n_cells;
593	>	double cellx, celly, cellz;
594	>	double temp1, temp2, temp3;
595	>	int n_per_extra;
596	>	int n_extra;
597	>	int have_extra, done;
598
599	<
600	<	#ifdef IS_MPI
601	<	if( worldRank == 0 ){
602	<	#endif // is_mpi
603	<
604	<	if( the_globals->haveFinalConfig() ){
605	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
599	>	double vel[3];
600	>	vel[0] = 0.0;
601	>	vel[1] = 0.0;
602	>	vel[2] = 0.0;
603	>
604	>	temp1 = (double) tot_nmol / 4.0;
605	>	temp2 = pow(temp1, (1.0 / 3.0));
606	>	temp3 = ceil(temp2);
607	>
608	>	have_extra = 0;
609	>	if (temp2 < temp3){
610	>	// we have a non-complete lattice
611	>	have_extra = 1;
612	>
613	>	n_cells = (int) temp3 - 1;
614	>	cellx = info[0].boxL[0] / temp3;
615	>	celly = info[0].boxL[1] / temp3;
616	>	cellz = info[0].boxL[2] / temp3;
617	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
618	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
619	>	n_per_extra = (int) ceil(temp1);
620	>
621	>	if (n_per_extra > 4){
622	>	sprintf(painCave.errMsg,
623	>	"SimSetup error. There has been an error in constructing"
624	>	" the non-complete lattice.\n");
625	>	painCave.isFatal = 1;
626	>	simError();
627		}
677	–	else{
678	–	strcpy( simnfo->finalName, inFileName );
679	–	char* endTest;
680	–	int nameLength = strlen( simnfo->finalName );
681	–	endTest = &(simnfo->finalName[nameLength - 5]);
682	–	if( !strcmp( endTest, ".bass" ) ){
683	–	strcpy( endTest, ".eor" );
684	–	}
685	–	else if( !strcmp( endTest, ".BASS" ) ){
686	–	strcpy( endTest, ".eor" );
687	–	}
688	–	else{
689	–	endTest = &(simnfo->finalName[nameLength - 4]);
690	–	if( !strcmp( endTest, ".bss" ) ){
691	–	strcpy( endTest, ".eor" );
692	–	}
693	–	else if( !strcmp( endTest, ".mdl" ) ){
694	–	strcpy( endTest, ".eor" );
695	–	}
696	–	else{
697	–	strcat( simnfo->finalName, ".eor" );
698	–	}
699	–	}
700	–	}
701	–
702	–	// make the sample and status out names
703	–
704	–	strcpy( simnfo->sampleName, inFileName );
705	–	char* endTest;
706	–	int nameLength = strlen( simnfo->sampleName );
707	–	endTest = &(simnfo->sampleName[nameLength - 5]);
708	–	if( !strcmp( endTest, ".bass" ) ){
709	–	strcpy( endTest, ".dump" );
710	–	}
711	–	else if( !strcmp( endTest, ".BASS" ) ){
712	–	strcpy( endTest, ".dump" );
713	–	}
714	–	else{
715	–	endTest = &(simnfo->sampleName[nameLength - 4]);
716	–	if( !strcmp( endTest, ".bss" ) ){
717	–	strcpy( endTest, ".dump" );
718	–	}
719	–	else if( !strcmp( endTest, ".mdl" ) ){
720	–	strcpy( endTest, ".dump" );
721	–	}
722	–	else{
723	–	strcat( simnfo->sampleName, ".dump" );
724	–	}
725	–	}
726	–
727	–	strcpy( simnfo->statusName, inFileName );
728	–	nameLength = strlen( simnfo->statusName );
729	–	endTest = &(simnfo->statusName[nameLength - 5]);
730	–	if( !strcmp( endTest, ".bass" ) ){
731	–	strcpy( endTest, ".stat" );
732	–	}
733	–	else if( !strcmp( endTest, ".BASS" ) ){
734	–	strcpy( endTest, ".stat" );
735	–	}
736	–	else{
737	–	endTest = &(simnfo->statusName[nameLength - 4]);
738	–	if( !strcmp( endTest, ".bss" ) ){
739	–	strcpy( endTest, ".stat" );
740	–	}
741	–	else if( !strcmp( endTest, ".mdl" ) ){
742	–	strcpy( endTest, ".stat" );
743	–	}
744	–	else{
745	–	strcat( simnfo->statusName, ".stat" );
746	–	}
747	–	}
748	–
749	–	#ifdef IS_MPI
628		}
751	–	#endif // is_mpi
752	–
753	–	// set the status, sample, and themal kick times
754	–
755	–	if( the_globals->haveSampleTime() ){
756	–	simnfo->sampleTime = the_globals->getSampleTime();
757	–	simnfo->statusTime = simnfo->sampleTime;
758	–	simnfo->thermalTime = simnfo->sampleTime;
759	–	}
629		else{
630	<	simnfo->sampleTime = the_globals->getRunTime();
631	<	simnfo->statusTime = simnfo->sampleTime;
632	<	simnfo->thermalTime = simnfo->sampleTime;
630	>	n_cells = (int) temp3;
631	>	cellx = info[0].boxL[0] / temp3;
632	>	celly = info[0].boxL[1] / temp3;
633	>	cellz = info[0].boxL[2] / temp3;
634		}
635
636	<	if( the_globals->haveStatusTime() ){
637	<	simnfo->statusTime = the_globals->getStatusTime();
638	<	}
636	>	current_mol = 0;
637	>	current_comp_mol = 0;
638	>	current_comp = 0;
639	>	current_atom_ndx = 0;
640
641	<	if( the_globals->haveThermalTime() ){
642	<	simnfo->thermalTime = the_globals->getThermalTime();
641	>	for (i = 0; i < n_cells ; i++){
642	>	for (j = 0; j < n_cells; j++){
643	>	for (k = 0; k < n_cells; k++){
644	>	makeElement(i * cellx, j * celly, k * cellz);
645	>
646	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
647	>
648	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
649	>
650	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
651	>	}
652	>	}
653		}
654
655	<	// check for the temperature set flag
655	>	if (have_extra){
656	>	done = 0;
657
658	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
658	>	int start_ndx;
659	>	for (i = 0; i < (n_cells + 1) && !done; i++){
660	>	for (j = 0; j < (n_cells + 1) && !done; j++){
661	>	if (i < n_cells){
662	>	if (j < n_cells){
663	>	start_ndx = n_cells;
664	>	}
665	>	else
666	>	start_ndx = 0;
667	>	}
668	>	else
669	>	start_ndx = 0;
670
671	+	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
672	+	makeElement(i * cellx, j * celly, k * cellz);
673	+	done = (current_mol >= tot_nmol);
674
675	<	// make the integrator
676	<
677	<
678	<	NVT* myNVT = NULL;
679	<	switch( ensembleCase ){
675	>	if (!done && n_per_extra > 1){
676	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
677	>	k * cellz);
678	>	done = (current_mol >= tot_nmol);
679	>	}
680
681	<	case NVE_ENS:
682	<	new NVE( simnfo, the_ff );
683	<	break;
681	>	if (!done && n_per_extra > 2){
682	>	makeElement(i * cellx, j * celly + 0.5 * celly,
683	>	k * cellz + 0.5 * cellz);
684	>	done = (current_mol >= tot_nmol);
685	>	}
686
687	<	case NVT_ENS:
688	<	myNVT = new NVT( simnfo, the_ff );
689	<	myNVT->setTargetTemp(the_globals->getTargetTemp());
687	>	if (!done && n_per_extra > 3){
688	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
689	>	k * cellz + 0.5 * cellz);
690	>	done = (current_mol >= tot_nmol);
691	>	}
692	>	}
693	>	}
694	>	}
695	>	}
696
697	<	if (the_globals->haveTauThermostat())
698	<	myNVT->setTauThermostat(the_globals->getTauThermostat());
699	<	//     else if (the_globals->haveQmass())
700	<	//       myNVT->setQmass(the_globals->getQmass());
701	<	else {
702	<	sprintf( painCave.errMsg,
703	<	"SimSetup error: If you use the NVT\n"
704	<	"    ensemble, you must set either tauThermostat or qMass.\n"
705	<	"    Neither of these was found in the BASS file.\n");
697	>	for (i = 0; i < info[0].n_atoms; i++){
698	>	info[0].atoms[i]->setVel(vel);
699	>	}
700	>	}
701	>
702	>	void SimSetup::makeElement(double x, double y, double z){
703	>	int k;
704	>	AtomStamp* current_atom;
705	>	DirectionalAtom* dAtom;
706	>	double rotMat[3][3];
707	>	double pos[3];
708	>
709	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
710	>	current_atom = comp_stamps[current_comp]->getAtom(k);
711	>	if (!current_atom->havePosition()){
712	>	sprintf(painCave.errMsg,
713	>	"SimSetup:initFromBass error.\n"
714	>	"\tComponent %s, atom %s does not have a position specified.\n"
715	>	"\tThe initialization routine is unable to give a start"
716	>	" position.\n",
717	>	comp_stamps[current_comp]->getID(), current_atom->getType());
718		painCave.isFatal = 1;
719		simError();
720		}
805	–	break;
721
722	<	default:
723	<	sprintf( painCave.errMsg,
724	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
810	<	painCave.isFatal = 1;
811	<	simError();
812	<	}
722	>	pos[0] = x + current_atom->getPosX();
723	>	pos[1] = y + current_atom->getPosY();
724	>	pos[2] = z + current_atom->getPosZ();
725
726	+	info[0].atoms[current_atom_ndx]->setPos(pos);
727
728	<	#ifdef IS_MPI
729	<	mpiSim->mpiRefresh();
817	<	#endif
728	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
729	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
730
731	<	// initialize the Fortran
731	>	rotMat[0][0] = 1.0;
732	>	rotMat[0][1] = 0.0;
733	>	rotMat[0][2] = 0.0;
734
735	+	rotMat[1][0] = 0.0;
736	+	rotMat[1][1] = 1.0;
737	+	rotMat[1][2] = 0.0;
738
739	<	simnfo->refreshSim();
740	<
741	<	if( !strcmp( simnfo->mixingRule, "standard") ){
742	<	the_ff->initForceField( LB_MIXING_RULE );
739	>	rotMat[2][0] = 0.0;
740	>	rotMat[2][1] = 0.0;
741	>	rotMat[2][2] = 1.0;
742	>
743	>	dAtom->setA(rotMat);
744	>	}
745	>
746	>	current_atom_ndx++;
747		}
827	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
828	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
829	–	}
830	–	else{
831	–	sprintf( painCave.errMsg,
832	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
833	–	simnfo->mixingRule );
834	–	painCave.isFatal = 1;
835	–	simError();
836	–	}
748
749	+	current_mol++;
750	+	current_comp_mol++;
751
752	<	#ifdef IS_MPI
753	<	strcpy( checkPointMsg,
754	<	"Successfully intialized the mixingRule for Fortran." );
755	<	MPIcheckPoint();
843	<	#endif // is_mpi
752	>	if (current_comp_mol >= components_nmol[current_comp]){
753	>	current_comp_mol = 0;
754	>	current_comp++;
755	>	}
756		}
757
758
759	<	void SimSetup::makeMolecules( void ){
759	>	void SimSetup::gatherInfo(void){
760	>	int i;
761
762	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
763	<	molInit info;
851	<	DirectionalAtom* dAtom;
852	<	LinkedAssign* extras;
853	<	LinkedAssign* current_extra;
854	<	AtomStamp* currentAtom;
855	<	BondStamp* currentBond;
856	<	BendStamp* currentBend;
857	<	TorsionStamp* currentTorsion;
762	>	ensembleCase = -1;
763	>	ffCase = -1;
764
765	<	bond_pair* theBonds;
860	<	bend_set* theBends;
861	<	torsion_set* theTorsions;
765	>	// set the easy ones first
766
767	<
768	<	//init the forceField paramters
769	<
770	<	the_ff->readParams();
771	<
772	<
869	<	// init the atoms
767	>	for (i = 0; i < nInfo; i++){
768	>	info[i].target_temp = globals->getTargetTemp();
769	>	info[i].dt = globals->getDt();
770	>	info[i].run_time = globals->getRunTime();
771	>	}
772	>	n_components = globals->getNComponents();
773
871	–	double ux, uy, uz, u, uSqr;
872	–
873	–	atomOffset = 0;
874	–	excludeOffset = 0;
875	–	for(i=0; i<simnfo->n_mol; i++){
876	–
877	–	stampID = the_molecules[i].getStampID();
774
775	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
880	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
881	<	info.nBends    = comp_stamps[stampID]->getNBends();
882	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
883	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
775	>	// get the forceField
776
777	<	info.myAtoms = &the_atoms[atomOffset];
886	<	info.myExcludes = &the_excludes[excludeOffset];
887	<	info.myBonds = new Bond*[info.nBonds];
888	<	info.myBends = new Bend*[info.nBends];
889	<	info.myTorsions = new Torsion*[info.nTorsions];
777	>	strcpy(force_field, globals->getForceField());
778
779	<	theBonds = new bond_pair[info.nBonds];
780	<	theBends = new bend_set[info.nBends];
781	<	theTorsions = new torsion_set[info.nTorsions];
779	>	if (!strcasecmp(force_field, "DUFF")){
780	>	ffCase = FF_DUFF;
781	>	}
782	>	else if (!strcasecmp(force_field, "LJ")){
783	>	ffCase = FF_LJ;
784	>	}
785	>	else if (!strcasecmp(force_field, "EAM")){
786	>	ffCase = FF_EAM;
787	>	}
788	>	else if (!strcasecmp(force_field, "WATER")){
789	>	ffCase = FF_H2O;
790	>	}
791	>	else{
792	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
793	>	force_field);
794	>	painCave.isFatal = 1;
795	>	simError();
796	>	}
797	>
798	>	// get the ensemble
799	>
800	>	strcpy(ensemble, globals->getEnsemble());
801	>
802	>	if (!strcasecmp(ensemble, "NVE")){
803	>	ensembleCase = NVE_ENS;
804	>	}
805	>	else if (!strcasecmp(ensemble, "NVT")){
806	>	ensembleCase = NVT_ENS;
807	>	}
808	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
809	>	ensembleCase = NPTi_ENS;
810	>	}
811	>	else if (!strcasecmp(ensemble, "NPTf")){
812	>	ensembleCase = NPTf_ENS;
813	>	}
814	>	else if (!strcasecmp(ensemble, "NPTxyz")){
815	>	ensembleCase = NPTxyz_ENS;
816	>	}
817	>	else{
818	>	sprintf(painCave.errMsg,
819	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
820	>	"\treverting to NVE for this simulation.\n",
821	>	ensemble);
822	>	painCave.isFatal = 0;
823	>	simError();
824	>	strcpy(ensemble, "NVE");
825	>	ensembleCase = NVE_ENS;
826	>	}
827	>
828	>	for (i = 0; i < nInfo; i++){
829	>	strcpy(info[i].ensemble, ensemble);
830	>
831	>	// get the mixing rule
832	>
833	>	strcpy(info[i].mixingRule, globals->getMixingRule());
834	>	info[i].usePBC = globals->getPBC();
835	>	}
836	>
837	>	// get the components and calculate the tot_nMol and indvidual n_mol
838	>
839	>	the_components = globals->getComponents();
840	>	components_nmol = new int[n_components];
841	>
842	>
843	>	if (!globals->haveNMol()){
844	>	// we don't have the total number of molecules, so we assume it is
845	>	// given in each component
846	>
847	>	tot_nmol = 0;
848	>	for (i = 0; i < n_components; i++){
849	>	if (!the_components[i]->haveNMol()){
850	>	// we have a problem
851	>	sprintf(painCave.errMsg,
852	>	"SimSetup Error. No global NMol or component NMol given.\n"
853	>	"\tCannot calculate the number of atoms.\n");
854	>	painCave.isFatal = 1;
855	>	simError();
856	>	}
857	>
858	>	tot_nmol += the_components[i]->getNMol();
859	>	components_nmol[i] = the_components[i]->getNMol();
860	>	}
861	>	}
862	>	else{
863	>	sprintf(painCave.errMsg,
864	>	"SimSetup error.\n"
865	>	"\tSorry, the ability to specify total"
866	>	" nMols and then give molfractions in the components\n"
867	>	"\tis not currently supported."
868	>	" Please give nMol in the components.\n");
869	>	painCave.isFatal = 1;
870	>	simError();
871	>	}
872	>
873	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
874	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
875	>	sprintf(painCave.errMsg,
876	>	"Sample time is not divisible by dt.\n"
877	>	"\tThis will result in samples that are not uniformly\n"
878	>	"\tdistributed in time.  If this is a problem, change\n"
879	>	"\tyour sampleTime variable.\n");
880	>	painCave.isFatal = 0;
881	>	simError();
882	>	}
883	>
884	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
885	>	sprintf(painCave.errMsg,
886	>	"Status time is not divisible by dt.\n"
887	>	"\tThis will result in status reports that are not uniformly\n"
888	>	"\tdistributed in time.  If this is a problem, change \n"
889	>	"\tyour statusTime variable.\n");
890	>	painCave.isFatal = 0;
891	>	simError();
892	>	}
893	>
894	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
895	>	sprintf(painCave.errMsg,
896	>	"Thermal time is not divisible by dt.\n"
897	>	"\tThis will result in thermalizations that are not uniformly\n"
898	>	"\tdistributed in time.  If this is a problem, change \n"
899	>	"\tyour thermalTime variable.\n");
900	>	painCave.isFatal = 0;
901	>	simError();
902	>	}
903	>
904	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
905	>	sprintf(painCave.errMsg,
906	>	"Reset time is not divisible by dt.\n"
907	>	"\tThis will result in integrator resets that are not uniformly\n"
908	>	"\tdistributed in time.  If this is a problem, change\n"
909	>	"\tyour resetTime variable.\n");
910	>	painCave.isFatal = 0;
911	>	simError();
912	>	}
913	>
914	>	// set the status, sample, and thermal kick times
915	>
916	>	for (i = 0; i < nInfo; i++){
917	>	if (globals->haveSampleTime()){
918	>	info[i].sampleTime = globals->getSampleTime();
919	>	info[i].statusTime = info[i].sampleTime;
920	>	}
921	>	else{
922	>	info[i].sampleTime = globals->getRunTime();
923	>	info[i].statusTime = info[i].sampleTime;
924	>	}
925	>
926	>	if (globals->haveStatusTime()){
927	>	info[i].statusTime = globals->getStatusTime();
928	>	}
929	>
930	>	if (globals->haveThermalTime()){
931	>	info[i].thermalTime = globals->getThermalTime();
932	>	} else {
933	>	info[i].thermalTime = globals->getRunTime();
934	>	}
935	>
936	>	info[i].resetIntegrator = 0;
937	>	if( globals->haveResetTime() ){
938	>	info[i].resetTime = globals->getResetTime();
939	>	info[i].resetIntegrator = 1;
940	>	}
941	>
942	>	// check for the temperature set flag
943
944	<	// make the Atoms
945	<
946	<	for(j=0; j<info.nAtoms; j++){
947	<
948	<	currentAtom = comp_stamps[stampID]->getAtom( j );
949	<	if( currentAtom->haveOrientation() ){
944	>	if (globals->haveTempSet())
945	>	info[i].setTemp = globals->getTempSet();
946	>
947	>	// check for the extended State init
948	>
949	>	info[i].useInitXSstate = globals->getUseInitXSstate();
950	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
951	>
952	>	// check for thermodynamic integration
953	>	if (globals->getUseThermInt()) {
954	>	if (globals->haveThermIntLambda() && globals->haveThermIntK()) {
955	>	info[i].useThermInt = globals->getUseThermInt();
956	>	info[i].thermIntLambda = globals->getThermIntLambda();
957	>	info[i].thermIntK = globals->getThermIntK();
958
959	<	dAtom = new DirectionalAtom(j + atomOffset);
960	<	simnfo->n_oriented++;
904	<	info.myAtoms[j] = dAtom;
905	<
906	<	ux = currentAtom->getOrntX();
907	<	uy = currentAtom->getOrntY();
908	<	uz = currentAtom->getOrntZ();
909	<
910	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
911	<
912	<	u = sqrt( uSqr );
913	<	ux = ux / u;
914	<	uy = uy / u;
915	<	uz = uz / u;
916	<
917	<	dAtom->setSUx( ux );
918	<	dAtom->setSUy( uy );
919	<	dAtom->setSUz( uz );
959	>	Restraints *myRestraint = new Restraints(tot_nmol, info[i].thermIntLambda, info[i].thermIntK);
960	>	info[i].restraint = myRestraint;
961		}
962	<	else{
963	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
964	<	}
965	<	info.myAtoms[j]->setType( currentAtom->getType() );
962	>	else {
963	>	sprintf(painCave.errMsg,
964	>	"SimSetup Error:\n"
965	>	"\tKeyword useThermInt was set to 'true' but\n"
966	>	"\tthermodynamicIntegrationLambda (and/or\n"
967	>	"\tthermodynamicIntegrationK) was not specified.\n"
968	>	"\tPlease provide a lambda value and k value in your .bass file.\n");
969	>	painCave.isFatal = 1;
970	>	simError();
971	>	}
972	>	}
973	>	else if(globals->haveThermIntLambda() || globals->haveThermIntK()){
974	>	sprintf(painCave.errMsg,
975	>	"SimSetup Warning: If you want to use Thermodynamic\n"
976	>	"\tIntegration, set useThermInt to 'true' in your .bass file.\n"
977	>	"\tThe useThermInt keyword is 'false' by default, so your\n"
978	>	"\tlambda and/or k values are being ignored.\n");
979	>	painCave.isFatal = 0;
980	>	simError();
981	>	}
982	>	}
983	>
984	>	//setup seed for random number generator
985	>	int seedValue;
986	>
987	>	if (globals->haveSeed()){
988	>	seedValue = globals->getSeed();
989	>
990	>	if(seedValue / 1E9 == 0){
991	>	sprintf(painCave.errMsg,
992	>	"Seed for sprng library should contain at least 9 digits\n"
993	>	"OOPSE will generate a seed for user\n");
994	>	painCave.isFatal = 0;
995	>	simError();
996	>
997	>	//using seed generated by system instead of invalid seed set by user
998	>	#ifndef IS_MPI
999	>	seedValue = make_sprng_seed();
1000	>	#else
1001	>	if (worldRank == 0){
1002	>	seedValue = make_sprng_seed();
1003	>	}
1004	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1005	>	#endif
1006	>	}
1007	>	}//end of if branch of globals->haveSeed()
1008	>	else{
1009
1010	+	#ifndef IS_MPI
1011	+	seedValue = make_sprng_seed();
1012	+	#else
1013	+	if (worldRank == 0){
1014	+	seedValue = make_sprng_seed();
1015	+	}
1016	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
1017	+	#endif
1018	+	}//end of globals->haveSeed()
1019	+
1020	+	for (int i = 0; i < nInfo; i++){
1021	+	info[i].setSeed(seedValue);
1022	+	}
1023	+
1024		#ifdef IS_MPI
1025	<
1026	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
929	<
1025	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
1026	>	MPIcheckPoint();
1027		#endif // is_mpi
1028	<	}
932	<
933	<	// make the bonds
934	<	for(j=0; j<info.nBonds; j++){
935	<
936	<	currentBond = comp_stamps[stampID]->getBond( j );
937	<	theBonds[j].a = currentBond->getA() + atomOffset;
938	<	theBonds[j].b = currentBond->getB() + atomOffset;
1028	>	}
1029
940	–	exI = theBonds[j].a;
941	–	exJ = theBonds[j].b;
1030
1031	<	// exclude_I must always be the smaller of the pair
1032	<	if( exI > exJ ){
1033	<	tempEx = exI;
1034	<	exI = exJ;
1035	<	exJ = tempEx;
1036	<	}
1031	>	void SimSetup::finalInfoCheck(void){
1032	>	int index;
1033	>	int usesDipoles;
1034	>	int usesCharges;
1035	>	int i;
1036	>
1037	>	for (i = 0; i < nInfo; i++){
1038	>	// check electrostatic parameters
1039	>
1040	>	index = 0;
1041	>	usesDipoles = 0;
1042	>	while ((index < info[i].n_atoms) && !usesDipoles){
1043	>	usesDipoles = (info[i].atoms[index])->hasDipole();
1044	>	index++;
1045	>	}
1046	>	index = 0;
1047	>	usesCharges = 0;
1048	>	while ((index < info[i].n_atoms) && !usesCharges){
1049	>	usesCharges= (info[i].atoms[index])->hasCharge();
1050	>	index++;
1051	>	}
1052		#ifdef IS_MPI
1053	<	tempEx = exI;
1054	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1055	<	tempEx = exJ;
1056	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1053	>	int myUse = usesDipoles;
1054	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1055	>	#endif //is_mpi
1056	>
1057	>	double theRcut, theRsw;
1058	>
1059	>	if (globals->haveRcut()) {
1060	>	theRcut = globals->getRcut();
1061	>
1062	>	if (globals->haveRsw())
1063	>	theRsw = globals->getRsw();
1064	>	else
1065	>	theRsw = theRcut;
1066
1067	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
956	<	#else  // isn't MPI
1067	>	info[i].setDefaultRcut(theRcut, theRsw);
1068
1069	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1070	<	#endif  //is_mpi
1069	>	} else {
1070	>
1071	>	the_ff->calcRcut();
1072	>	theRcut = info[i].getRcut();
1073	>
1074	>	if (globals->haveRsw())
1075	>	theRsw = globals->getRsw();
1076	>	else
1077	>	theRsw = theRcut;
1078	>
1079	>	info[i].setDefaultRcut(theRcut, theRsw);
1080		}
961	–	excludeOffset += info.nBonds;
1081
1082	<	//make the bends
1083	<	for(j=0; j<info.nBends; j++){
1082	>	if (globals->getUseRF()){
1083	>	info[i].useReactionField = 1;
1084
1085	<	currentBend = comp_stamps[stampID]->getBend( j );
1086	<	theBends[j].a = currentBend->getA() + atomOffset;
1087	<	theBends[j].b = currentBend->getB() + atomOffset;
1088	<	theBends[j].c = currentBend->getC() + atomOffset;
1089	<
1090	<	if( currentBend->haveExtras() ){
1091	<
1092	<	extras = currentBend->getExtras();
974	<	current_extra = extras;
975	<
976	<	while( current_extra != NULL ){
977	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
978	<
979	<	switch( current_extra->getType() ){
980	<
981	<	case 0:
982	<	theBends[j].ghost =
983	<	current_extra->getInt() + atomOffset;
984	<	theBends[j].isGhost = 1;
985	<	break;
986	<
987	<	case 1:
988	<	theBends[j].ghost =
989	<	(int)current_extra->getDouble() + atomOffset;
990	<	theBends[j].isGhost = 1;
991	<	break;
992	<
993	<	default:
994	<	sprintf( painCave.errMsg,
995	<	"SimSetup Error: ghostVectorSource was neither a "
996	<	"double nor an int.\n"
997	<	"-->Bend[%d] in %s\n",
998	<	j, comp_stamps[stampID]->getID() );
999	<	painCave.isFatal = 1;
1000	<	simError();
1001	<	}
1002	<	}
1003	<
1004	<	else{
1005	<
1006	<	sprintf( painCave.errMsg,
1007	<	"SimSetup Error: unhandled bend assignment:\n"
1008	<	"    -->%s in Bend[%d] in %s\n",
1009	<	current_extra->getlhs(),
1010	<	j, comp_stamps[stampID]->getID() );
1011	<	painCave.isFatal = 1;
1012	<	simError();
1013	<	}
1014	<
1015	<	current_extra = current_extra->getNext();
1016	<	}
1085	>	if (!globals->haveRcut()){
1086	>	sprintf(painCave.errMsg,
1087	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1088	>	"\tOOPSE will use a default value of 15.0 angstroms"
1089	>	"\tfor the cutoffRadius.\n");
1090	>	painCave.isFatal = 0;
1091	>	simError();
1092	>	theRcut = 15.0;
1093		}
1094	<
1095	<	if( !theBends[j].isGhost ){
1020	<
1021	<	exI = theBends[j].a;
1022	<	exJ = theBends[j].c;
1094	>	else{
1095	>	theRcut = globals->getRcut();
1096		}
1097	+
1098	+	if (!globals->haveRsw()){
1099	+	sprintf(painCave.errMsg,
1100	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1101	+	"\tOOPSE will use a default value of\n"
1102	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1103	+	painCave.isFatal = 0;
1104	+	simError();
1105	+	theRsw = 0.95 * theRcut;
1106	+	}
1107		else{
1108	<
1026	<	exI = theBends[j].a;
1027	<	exJ = theBends[j].b;
1108	>	theRsw = globals->getRsw();
1109		}
1110	<
1111	<	// exclude_I must always be the smaller of the pair
1112	<	if( exI > exJ ){
1113	<	tempEx = exI;
1114	<	exI = exJ;
1115	<	exJ = tempEx;
1110	>
1111	>	info[i].setDefaultRcut(theRcut, theRsw);
1112	>
1113	>	if (!globals->haveDielectric()){
1114	>	sprintf(painCave.errMsg,
1115	>	"SimSetup Error: No Dielectric constant was set.\n"
1116	>	"\tYou are trying to use Reaction Field without"
1117	>	"\tsetting a dielectric constant!\n");
1118	>	painCave.isFatal = 1;
1119	>	simError();
1120		}
1121	<	#ifdef IS_MPI
1037	<	tempEx = exI;
1038	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1039	<	tempEx = exJ;
1040	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1041	<
1042	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1043	<	#else  // isn't MPI
1044	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1045	<	#endif  //is_mpi
1121	>	info[i].dielectric = globals->getDielectric();
1122		}
1123	<	excludeOffset += info.nBends;
1123	>	else{
1124	>	if (usesDipoles || usesCharges){
1125
1126	<	for(j=0; j<info.nTorsions; j++){
1127	<
1128	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1129	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1130	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1131	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1132	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1133	<
1057	<	exI = theTorsions[j].a;
1058	<	exJ = theTorsions[j].d;
1059	<
1060	<	// exclude_I must always be the smaller of the pair
1061	<	if( exI > exJ ){
1062	<	tempEx = exI;
1063	<	exI = exJ;
1064	<	exJ = tempEx;
1126	>	if (!globals->haveRcut()){
1127	>	sprintf(painCave.errMsg,
1128	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1129	>	"\tOOPSE will use a default value of 15.0 angstroms"
1130	>	"\tfor the cutoffRadius.\n");
1131	>	painCave.isFatal = 0;
1132	>	simError();
1133	>	theRcut = 15.0;
1134		}
1135	<	#ifdef IS_MPI
1136	<	tempEx = exI;
1137	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1138	<	tempEx = exJ;
1139	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1140	<
1141	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1142	<	#else  // isn't MPI
1143	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1144	<	#endif  //is_mpi
1135	>	else{
1136	>	theRcut = globals->getRcut();
1137	>	}
1138	>
1139	>	if (!globals->haveRsw()){
1140	>	sprintf(painCave.errMsg,
1141	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1142	>	"\tOOPSE will use a default value of\n"
1143	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1144	>	painCave.isFatal = 0;
1145	>	simError();
1146	>	theRsw = 0.95 * theRcut;
1147	>	}
1148	>	else{
1149	>	theRsw = globals->getRsw();
1150	>	}
1151	>
1152	>	info[i].setDefaultRcut(theRcut, theRsw);
1153	>
1154	>	}
1155		}
1156	<	excludeOffset += info.nTorsions;
1156	>	}
1157	>	#ifdef IS_MPI
1158	>	strcpy(checkPointMsg, "post processing checks out");
1159	>	MPIcheckPoint();
1160	>	#endif // is_mpi
1161
1162	<
1163	<	// send the arrays off to the forceField for init.
1162	>	// clean up the forcefield
1163	>	the_ff->cleanMe();
1164	>	}
1165	>
1166	>	void SimSetup::initSystemCoords(void){
1167	>	int i;
1168
1169	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1083	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1084	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1085	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1169	>	char* inName;
1170
1171	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1172
1173	<	the_molecules[i].initialize( info );
1173	>	for (i = 0; i < info[0].n_atoms; i++)
1174	>	info[0].atoms[i]->setCoords();
1175
1176	+	if (globals->haveInitialConfig()){
1177	+	InitializeFromFile* fileInit;
1178	+	#ifdef IS_MPI // is_mpi
1179	+	if (worldRank == 0){
1180	+	#endif //is_mpi
1181	+	inName = globals->getInitialConfig();
1182	+	fileInit = new InitializeFromFile(inName);
1183	+	#ifdef IS_MPI
1184	+	}
1185	+	else
1186	+	fileInit = new InitializeFromFile(NULL);
1187	+	#endif
1188	+	fileInit->readInit(info); // default velocities on
1189
1190	<	atomOffset += info.nAtoms;
1092	<	delete[] theBonds;
1093	<	delete[] theBends;
1094	<	delete[] theTorsions;
1190	>	delete fileInit;
1191		}
1192	+	else{
1193	+
1194	+	// no init from bass
1195	+
1196	+	sprintf(painCave.errMsg,
1197	+	"Cannot intialize a simulation without an initial configuration file.\n");
1198	+	painCave.isFatal = 1;;
1199	+	simError();
1200	+
1201	+	}
1202
1203		#ifdef IS_MPI
1204	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1204	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1205		MPIcheckPoint();
1206		#endif // is_mpi
1207	+	}
1208
1102	–	// clean up the forcefield
1103	–	the_ff->calcRcut();
1104	–	the_ff->cleanMe();
1209
1210	<	}
1210	>	void SimSetup::makeOutNames(void){
1211	>	int k;
1212
1108	–	void SimSetup::initFromBass( void ){
1213
1214	<	int i, j, k;
1215	<	int n_cells;
1216	<	double cellx, celly, cellz;
1217	<	double temp1, temp2, temp3;
1114	<	int n_per_extra;
1115	<	int n_extra;
1116	<	int have_extra, done;
1214	>	for (k = 0; k < nInfo; k++){
1215	>	#ifdef IS_MPI
1216	>	if (worldRank == 0){
1217	>	#endif // is_mpi
1218
1219	<	temp1 = (double)tot_nmol / 4.0;
1220	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1221	<	temp3 = ceil( temp2 );
1219	>	if (globals->haveFinalConfig()){
1220	>	strcpy(info[k].finalName, globals->getFinalConfig());
1221	>	}
1222	>	else{
1223	>	strcpy(info[k].finalName, inFileName);
1224	>	char* endTest;
1225	>	int nameLength = strlen(info[k].finalName);
1226	>	endTest = &(info[k].finalName[nameLength - 5]);
1227	>	if (!strcmp(endTest, ".bass")){
1228	>	strcpy(endTest, ".eor");
1229	>	}
1230	>	else if (!strcmp(endTest, ".BASS")){
1231	>	strcpy(endTest, ".eor");
1232	>	}
1233	>	else{
1234	>	endTest = &(info[k].finalName[nameLength - 4]);
1235	>	if (!strcmp(endTest, ".bss")){
1236	>	strcpy(endTest, ".eor");
1237	>	}
1238	>	else if (!strcmp(endTest, ".mdl")){
1239	>	strcpy(endTest, ".eor");
1240	>	}
1241	>	else{
1242	>	strcat(info[k].finalName, ".eor");
1243	>	}
1244	>	}
1245	>	}
1246
1247	<	have_extra =0;
1123	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1124	<	have_extra =1;
1247	>	// make the sample and status out names
1248
1249	<	n_cells = (int)temp3 - 1;
1250	<	cellx = simnfo->boxLx / temp3;
1251	<	celly = simnfo->boxLy / temp3;
1252	<	cellz = simnfo->boxLz / temp3;
1253	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1254	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1255	<	n_per_extra = (int)ceil( temp1 );
1249	>	strcpy(info[k].sampleName, inFileName);
1250	>	char* endTest;
1251	>	int nameLength = strlen(info[k].sampleName);
1252	>	endTest = &(info[k].sampleName[nameLength - 5]);
1253	>	if (!strcmp(endTest, ".bass")){
1254	>	strcpy(endTest, ".dump");
1255	>	}
1256	>	else if (!strcmp(endTest, ".BASS")){
1257	>	strcpy(endTest, ".dump");
1258	>	}
1259	>	else{
1260	>	endTest = &(info[k].sampleName[nameLength - 4]);
1261	>	if (!strcmp(endTest, ".bss")){
1262	>	strcpy(endTest, ".dump");
1263	>	}
1264	>	else if (!strcmp(endTest, ".mdl")){
1265	>	strcpy(endTest, ".dump");
1266	>	}
1267	>	else{
1268	>	strcat(info[k].sampleName, ".dump");
1269	>	}
1270	>	}
1271
1272	<	if( n_per_extra > 4){
1273	<	sprintf( painCave.errMsg,
1274	<	"SimSetup error. There has been an error in constructing"
1275	<	" the non-complete lattice.\n" );
1276	<	painCave.isFatal = 1;
1277	<	simError();
1272	>	strcpy(info[k].statusName, inFileName);
1273	>	nameLength = strlen(info[k].statusName);
1274	>	endTest = &(info[k].statusName[nameLength - 5]);
1275	>	if (!strcmp(endTest, ".bass")){
1276	>	strcpy(endTest, ".stat");
1277	>	}
1278	>	else if (!strcmp(endTest, ".BASS")){
1279	>	strcpy(endTest, ".stat");
1280	>	}
1281	>	else{
1282	>	endTest = &(info[k].statusName[nameLength - 4]);
1283	>	if (!strcmp(endTest, ".bss")){
1284	>	strcpy(endTest, ".stat");
1285	>	}
1286	>	else if (!strcmp(endTest, ".mdl")){
1287	>	strcpy(endTest, ".stat");
1288	>	}
1289	>	else{
1290	>	strcat(info[k].statusName, ".stat");
1291	>	}
1292	>	}
1293	>
1294	>	strcpy(info[k].rawPotName, inFileName);
1295	>	nameLength = strlen(info[k].rawPotName);
1296	>	endTest = &(info[k].rawPotName[nameLength - 5]);
1297	>	if (!strcmp(endTest, ".bass")){
1298	>	strcpy(endTest, ".raw");
1299	>	}
1300	>	else if (!strcmp(endTest, ".BASS")){
1301	>	strcpy(endTest, ".raw");
1302	>	}
1303	>	else{
1304	>	endTest = &(info[k].rawPotName[nameLength - 4]);
1305	>	if (!strcmp(endTest, ".bss")){
1306	>	strcpy(endTest, ".raw");
1307	>	}
1308	>	else if (!strcmp(endTest, ".mdl")){
1309	>	strcpy(endTest, ".raw");
1310	>	}
1311	>	else{
1312	>	strcat(info[k].rawPotName, ".raw");
1313	>	}
1314	>	}
1315	>
1316	>	#ifdef IS_MPI
1317	>
1318		}
1319	+	#endif // is_mpi
1320		}
1321	<	else{
1143	<	n_cells = (int)temp3;
1144	<	cellx = simnfo->boxLx / temp3;
1145	<	celly = simnfo->boxLy / temp3;
1146	<	cellz = simnfo->boxLz / temp3;
1147	<	}
1321	>	}
1322
1149	–	current_mol = 0;
1150	–	current_comp_mol = 0;
1151	–	current_comp = 0;
1152	–	current_atom_ndx = 0;
1323
1324	<	for( i=0; i < n_cells ; i++ ){
1325	<	for( j=0; j < n_cells; j++ ){
1156	<	for( k=0; k < n_cells; k++ ){
1324	>	void SimSetup::sysObjectsCreation(void){
1325	>	int i, k;
1326
1327	<	makeElement( i * cellx,
1159	<	j * celly,
1160	<	k * cellz );
1327	>	// create the forceField
1328
1329	<	makeElement( i * cellx + 0.5 * cellx,
1163	<	j * celly + 0.5 * celly,
1164	<	k * cellz );
1329	>	createFF();
1330
1331	<	makeElement( i * cellx,
1167	<	j * celly + 0.5 * celly,
1168	<	k * cellz + 0.5 * cellz );
1331	>	// extract componentList
1332
1333	<	makeElement( i * cellx + 0.5 * cellx,
1334	<	j * celly,
1335	<	k * cellz + 0.5 * cellz );
1336	<	}
1333	>	compList();
1334	>
1335	>	// calc the number of atoms, bond, bends, and torsions
1336	>
1337	>	calcSysValues();
1338	>
1339	>	#ifdef IS_MPI
1340	>	// divide the molecules among the processors
1341	>
1342	>	mpiMolDivide();
1343	>	#endif //is_mpi
1344	>
1345	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1346	>
1347	>	makeSysArrays();
1348	>
1349	>	// make and initialize the molecules (all but atomic coordinates)
1350	>
1351	>	makeMolecules();
1352	>
1353	>	for (k = 0; k < nInfo; k++){
1354	>	info[k].identArray = new int[info[k].n_atoms];
1355	>	for (i = 0; i < info[k].n_atoms; i++){
1356	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1357		}
1358		}
1359	+	}
1360
1177	–	if( have_extra ){
1178	–	done = 0;
1361
1362	<	int start_ndx;
1363	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1364	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1362	>	void SimSetup::createFF(void){
1363	>	switch (ffCase){
1364	>	case FF_DUFF:
1365	>	the_ff = new DUFF();
1366	>	break;
1367
1368	<	if( i < n_cells ){
1368	>	case FF_LJ:
1369	>	the_ff = new LJFF();
1370	>	break;
1371
1372	<	if( j < n_cells ){
1373	<	start_ndx = n_cells;
1374	<	}
1189	<	else start_ndx = 0;
1190	<	}
1191	<	else start_ndx = 0;
1372	>	case FF_EAM:
1373	>	the_ff = new EAM_FF();
1374	>	break;
1375
1376	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1376	>	case FF_H2O:
1377	>	the_ff = new WATER();
1378	>	break;
1379
1380	<	makeElement( i * cellx,
1381	<	j * celly,
1382	<	k * cellz );
1383	<	done = ( current_mol >= tot_nmol );
1380	>	default:
1381	>	sprintf(painCave.errMsg,
1382	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1383	>	painCave.isFatal = 1;
1384	>	simError();
1385	>	}
1386
1387	<	if( !done && n_per_extra > 1 ){
1388	<	makeElement( i * cellx + 0.5 * cellx,
1389	<	j * celly + 0.5 * celly,
1390	<	k * cellz );
1391	<	done = ( current_mol >= tot_nmol );
1205	<	}
1387	>	#ifdef IS_MPI
1388	>	strcpy(checkPointMsg, "ForceField creation successful");
1389	>	MPIcheckPoint();
1390	>	#endif // is_mpi
1391	>	}
1392
1207	–	if( !done && n_per_extra > 2){
1208	–	makeElement( i * cellx,
1209	–	j * celly + 0.5 * celly,
1210	–	k * cellz + 0.5 * cellz );
1211	–	done = ( current_mol >= tot_nmol );
1212	–	}
1393
1394	<	if( !done && n_per_extra > 3){
1395	<	makeElement( i * cellx + 0.5 * cellx,
1396	<	j * celly,
1397	<	k * cellz + 0.5 * cellz );
1398	<	done = ( current_mol >= tot_nmol );
1399	<	}
1400	<	}
1394	>	void SimSetup::compList(void){
1395	>	int i;
1396	>	char* id;
1397	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1398	>	LinkedMolStamp* currentStamp = NULL;
1399	>	comp_stamps = new MoleculeStamp * [n_components];
1400	>	bool haveCutoffGroups;
1401	>
1402	>	haveCutoffGroups = false;
1403	>
1404	>	// make an array of molecule stamps that match the components used.
1405	>	// also extract the used stamps out into a separate linked list
1406	>
1407	>	for (i = 0; i < nInfo; i++){
1408	>	info[i].nComponents = n_components;
1409	>	info[i].componentsNmol = components_nmol;
1410	>	info[i].compStamps = comp_stamps;
1411	>	info[i].headStamp = headStamp;
1412	>	}
1413	>
1414	>
1415	>	for (i = 0; i < n_components; i++){
1416	>	id = the_components[i]->getType();
1417	>	comp_stamps[i] = NULL;
1418	>
1419	>	// check to make sure the component isn't already in the list
1420	>
1421	>	comp_stamps[i] = headStamp->match(id);
1422	>	if (comp_stamps[i] == NULL){
1423	>	// extract the component from the list;
1424	>
1425	>	currentStamp = stamps->extractMolStamp(id);
1426	>	if (currentStamp == NULL){
1427	>	sprintf(painCave.errMsg,
1428	>	"SimSetup error: Component \"%s\" was not found in the "
1429	>	"list of declared molecules\n",
1430	>	id);
1431	>	painCave.isFatal = 1;
1432	>	simError();
1433		}
1434	+
1435	+	headStamp->add(currentStamp);
1436	+	comp_stamps[i] = headStamp->match(id);
1437		}
1438	+
1439	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1440	+	haveCutoffGroups = true;
1441		}
1442	+
1443	+	for (i = 0; i < nInfo; i++)
1444	+	info[i].haveCutoffGroups = haveCutoffGroups;
1445
1446	+	#ifdef IS_MPI
1447	+	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1448	+	MPIcheckPoint();
1449	+	#endif // is_mpi
1450	+	}
1451
1452	<	for( i=0; i<simnfo->n_atoms; i++ ){
1453	<	simnfo->atoms[i]->set_vx( 0.0 );
1454	<	simnfo->atoms[i]->set_vy( 0.0 );
1455	<	simnfo->atoms[i]->set_vz( 0.0 );
1452	>	void SimSetup::calcSysValues(void){
1453	>	int i, j;
1454	>	int ncutgroups, atomsingroups, ngroupsinstamp;
1455	>
1456	>	int* molMembershipArray;
1457	>	CutoffGroupStamp* cg;
1458	>
1459	>	tot_atoms = 0;
1460	>	tot_bonds = 0;
1461	>	tot_bends = 0;
1462	>	tot_torsions = 0;
1463	>	tot_rigid = 0;
1464	>	tot_groups = 0;
1465	>	for (i = 0; i < n_components; i++){
1466	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1467	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1468	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1469	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1470	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1471	>
1472	>	ncutgroups = comp_stamps[i]->getNCutoffGroups();
1473	>	atomsingroups = 0;
1474	>	for (j=0; j < ncutgroups; j++) {
1475	>	cg = comp_stamps[i]->getCutoffGroup(j);
1476	>	atomsingroups += cg->getNMembers();
1477	>	}
1478	>	ngroupsinstamp = comp_stamps[i]->getNAtoms() - atomsingroups + ncutgroups;
1479	>	tot_groups += components_nmol[i] * ngroupsinstamp;
1480		}
1481	+
1482	+	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1483	+	molMembershipArray = new int[tot_atoms];
1484	+
1485	+	for (i = 0; i < nInfo; i++){
1486	+	info[i].n_atoms = tot_atoms;
1487	+	info[i].n_bonds = tot_bonds;
1488	+	info[i].n_bends = tot_bends;
1489	+	info[i].n_torsions = tot_torsions;
1490	+	info[i].n_SRI = tot_SRI;
1491	+	info[i].n_mol = tot_nmol;
1492	+	info[i].ngroup = tot_groups;
1493	+	info[i].molMembershipArray = molMembershipArray;
1494	+	}
1495		}
1496
1497	<	void SimSetup::makeElement( double x, double y, double z ){
1497	>	#ifdef IS_MPI
1498
1499	<	int k;
1500	<	AtomStamp* current_atom;
1501	<	DirectionalAtom* dAtom;
1502	<	double rotMat[3][3];
1499	>	void SimSetup::mpiMolDivide(void){
1500	>	int i, j, k;
1501	>	int localMol, allMol;
1502	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1503	>	int local_rigid;
1504	>	vector<int> globalMolIndex;
1505
1506	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1506	>	mpiSim = new mpiSimulation(info);
1507
1508	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1509	<	if( !current_atom->havePosition() ){
1510	<	sprintf( painCave.errMsg,
1511	<	"SimSetup:initFromBass error.\n"
1512	<	"\tComponent %s, atom %s does not have a position specified.\n"
1513	<	"\tThe initialization routine is unable to give a start"
1514	<	" position.\n",
1515	<	comp_stamps[current_comp]->getID(),
1516	<	current_atom->getType() );
1517	<	painCave.isFatal = 1;
1518	<	simError();
1508	>	mpiSim->divideLabor();
1509	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1510	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1511	>
1512	>	// set up the local variables
1513	>
1514	>	mol2proc = mpiSim->getMolToProcMap();
1515	>	molCompType = mpiSim->getMolComponentType();
1516	>
1517	>	allMol = 0;
1518	>	localMol = 0;
1519	>	local_atoms = 0;
1520	>	local_bonds = 0;
1521	>	local_bends = 0;
1522	>	local_torsions = 0;
1523	>	local_rigid = 0;
1524	>	globalAtomCounter = 0;
1525	>
1526	>	for (i = 0; i < n_components; i++){
1527	>	for (j = 0; j < components_nmol[i]; j++){
1528	>	if (mol2proc[allMol] == worldRank){
1529	>	local_atoms += comp_stamps[i]->getNAtoms();
1530	>	local_bonds += comp_stamps[i]->getNBonds();
1531	>	local_bends += comp_stamps[i]->getNBends();
1532	>	local_torsions += comp_stamps[i]->getNTorsions();
1533	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1534	>	localMol++;
1535	>	}
1536	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1537	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1538	>	globalAtomCounter++;
1539	>	}
1540	>
1541	>	allMol++;
1542		}
1543	+	}
1544	+	local_SRI = local_bonds + local_bends + local_torsions;
1545
1546	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1547	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1257	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1546	>	info[0].n_atoms = mpiSim->getNAtomsLocal();
1547	>
1548
1549	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1549	>	if (local_atoms != info[0].n_atoms){
1550	>	sprintf(painCave.errMsg,
1551	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1552	>	"\tlocalAtom (%d) are not equal.\n",
1553	>	info[0].n_atoms, local_atoms);
1554	>	painCave.isFatal = 1;
1555	>	simError();
1556	>	}
1557
1558	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1558	>	info[0].n_bonds = local_bonds;
1559	>	info[0].n_bends = local_bends;
1560	>	info[0].n_torsions = local_torsions;
1561	>	info[0].n_SRI = local_SRI;
1562	>	info[0].n_mol = localMol;
1563
1564	<	rotMat[0][0] = 1.0;
1565	<	rotMat[0][1] = 0.0;
1566	<	rotMat[0][2] = 0.0;
1564	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1565	>	MPIcheckPoint();
1566	>	}
1567
1568	<	rotMat[1][0] = 0.0;
1268	<	rotMat[1][1] = 1.0;
1269	<	rotMat[1][2] = 0.0;
1568	>	#endif // is_mpi
1569
1271	–	rotMat[2][0] = 0.0;
1272	–	rotMat[2][1] = 0.0;
1273	–	rotMat[2][2] = 1.0;
1570
1571	<	dAtom->setA( rotMat );
1571	>	void SimSetup::makeSysArrays(void){
1572	>
1573	>	#ifndef IS_MPI
1574	>	int k, j;
1575	>	#endif // is_mpi
1576	>	int i, l;
1577	>
1578	>	Atom** the_atoms;
1579	>	Molecule* the_molecules;
1580	>
1581	>	for (l = 0; l < nInfo; l++){
1582	>	// create the atom and short range interaction arrays
1583	>
1584	>	the_atoms = new Atom * [info[l].n_atoms];
1585	>	the_molecules = new Molecule[info[l].n_mol];
1586	>	int molIndex;
1587	>
1588	>	// initialize the molecule's stampID's
1589	>
1590	>	#ifdef IS_MPI
1591	>
1592	>
1593	>	molIndex = 0;
1594	>	for (i = 0; i < mpiSim->getNMolGlobal(); i++){
1595	>	if (mol2proc[i] == worldRank){
1596	>	the_molecules[molIndex].setStampID(molCompType[i]);
1597	>	the_molecules[molIndex].setMyIndex(molIndex);
1598	>	the_molecules[molIndex].setGlobalIndex(i);
1599	>	molIndex++;
1600	>	}
1601		}
1602
1603	<	current_atom_ndx++;
1279	<	}
1603	>	#else // is_mpi
1604
1605	<	current_mol++;
1606	<	current_comp_mol++;
1605	>	molIndex = 0;
1606	>	globalAtomCounter = 0;
1607	>	for (i = 0; i < n_components; i++){
1608	>	for (j = 0; j < components_nmol[i]; j++){
1609	>	the_molecules[molIndex].setStampID(i);
1610	>	the_molecules[molIndex].setMyIndex(molIndex);
1611	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1612	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1613	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1614	>	globalAtomCounter++;
1615	>	}
1616	>	molIndex++;
1617	>	}
1618	>	}
1619
1284	–	if( current_comp_mol >= components_nmol[current_comp] ){
1620
1621	<	current_comp_mol = 0;
1622	<	current_comp++;
1621	>	#endif // is_mpi
1622	>
1623	>	info[l].globalExcludes = new int;
1624	>	info[l].globalExcludes[0] = 0;
1625	>
1626	>	// set the arrays into the SimInfo object
1627	>
1628	>	info[l].atoms = the_atoms;
1629	>	info[l].molecules = the_molecules;
1630	>	info[l].nGlobalExcludes = 0;
1631	>
1632	>	the_ff->setSimInfo(info);
1633		}
1634		}
1635	+
1636	+	void SimSetup::makeIntegrator(void){
1637	+	int k;
1638	+
1639	+	NVE<RealIntegrator>* myNVE = NULL;
1640	+	NVT<RealIntegrator>* myNVT = NULL;
1641	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1642	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1643	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1644	+
1645	+	for (k = 0; k < nInfo; k++){
1646	+	switch (ensembleCase){
1647	+	case NVE_ENS:
1648	+	if (globals->haveZconstraints()){
1649	+	setupZConstraint(info[k]);
1650	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1651	+	}
1652	+	else{
1653	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1654	+	}
1655	+
1656	+	info->the_integrator = myNVE;
1657	+	break;
1658	+
1659	+	case NVT_ENS:
1660	+	if (globals->haveZconstraints()){
1661	+	setupZConstraint(info[k]);
1662	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1663	+	}
1664	+	else
1665	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1666	+
1667	+	myNVT->setTargetTemp(globals->getTargetTemp());
1668	+
1669	+	if (globals->haveTauThermostat())
1670	+	myNVT->setTauThermostat(globals->getTauThermostat());
1671	+	else{
1672	+	sprintf(painCave.errMsg,
1673	+	"SimSetup error: If you use the NVT\n"
1674	+	"\tensemble, you must set tauThermostat.\n");
1675	+	painCave.isFatal = 1;
1676	+	simError();
1677	+	}
1678	+
1679	+	info->the_integrator = myNVT;
1680	+	break;
1681	+
1682	+	case NPTi_ENS:
1683	+	if (globals->haveZconstraints()){
1684	+	setupZConstraint(info[k]);
1685	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1686	+	}
1687	+	else
1688	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1689	+
1690	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1691	+
1692	+	if (globals->haveTargetPressure())
1693	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1694	+	else{
1695	+	sprintf(painCave.errMsg,
1696	+	"SimSetup error: If you use a constant pressure\n"
1697	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1698	+	painCave.isFatal = 1;
1699	+	simError();
1700	+	}
1701	+
1702	+	if (globals->haveTauThermostat())
1703	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1704	+	else{
1705	+	sprintf(painCave.errMsg,
1706	+	"SimSetup error: If you use an NPT\n"
1707	+	"\tensemble, you must set tauThermostat.\n");
1708	+	painCave.isFatal = 1;
1709	+	simError();
1710	+	}
1711	+
1712	+	if (globals->haveTauBarostat())
1713	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1714	+	else{
1715	+	sprintf(painCave.errMsg,
1716	+	"SimSetup error: If you use an NPT\n"
1717	+	"\tensemble, you must set tauBarostat.\n");
1718	+	painCave.isFatal = 1;
1719	+	simError();
1720	+	}
1721	+
1722	+	info->the_integrator = myNPTi;
1723	+	break;
1724	+
1725	+	case NPTf_ENS:
1726	+	if (globals->haveZconstraints()){
1727	+	setupZConstraint(info[k]);
1728	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1729	+	}
1730	+	else
1731	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1732	+
1733	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1734	+
1735	+	if (globals->haveTargetPressure())
1736	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1737	+	else{
1738	+	sprintf(painCave.errMsg,
1739	+	"SimSetup error: If you use a constant pressure\n"
1740	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1741	+	painCave.isFatal = 1;
1742	+	simError();
1743	+	}
1744	+
1745	+	if (globals->haveTauThermostat())
1746	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1747	+
1748	+	else{
1749	+	sprintf(painCave.errMsg,
1750	+	"SimSetup error: If you use an NPT\n"
1751	+	"\tensemble, you must set tauThermostat.\n");
1752	+	painCave.isFatal = 1;
1753	+	simError();
1754	+	}
1755	+
1756	+	if (globals->haveTauBarostat())
1757	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1758	+
1759	+	else{
1760	+	sprintf(painCave.errMsg,
1761	+	"SimSetup error: If you use an NPT\n"
1762	+	"\tensemble, you must set tauBarostat.\n");
1763	+	painCave.isFatal = 1;
1764	+	simError();
1765	+	}
1766	+
1767	+	info->the_integrator = myNPTf;
1768	+	break;
1769	+
1770	+	case NPTxyz_ENS:
1771	+	if (globals->haveZconstraints()){
1772	+	setupZConstraint(info[k]);
1773	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1774	+	}
1775	+	else
1776	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1777	+
1778	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1779	+
1780	+	if (globals->haveTargetPressure())
1781	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1782	+	else{
1783	+	sprintf(painCave.errMsg,
1784	+	"SimSetup error: If you use a constant pressure\n"
1785	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1786	+	painCave.isFatal = 1;
1787	+	simError();
1788	+	}
1789	+
1790	+	if (globals->haveTauThermostat())
1791	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1792	+	else{
1793	+	sprintf(painCave.errMsg,
1794	+	"SimSetup error: If you use an NPT\n"
1795	+	"\tensemble, you must set tauThermostat.\n");
1796	+	painCave.isFatal = 1;
1797	+	simError();
1798	+	}
1799	+
1800	+	if (globals->haveTauBarostat())
1801	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1802	+	else{
1803	+	sprintf(painCave.errMsg,
1804	+	"SimSetup error: If you use an NPT\n"
1805	+	"\tensemble, you must set tauBarostat.\n");
1806	+	painCave.isFatal = 1;
1807	+	simError();
1808	+	}
1809	+
1810	+	info->the_integrator = myNPTxyz;
1811	+	break;
1812	+
1813	+	default:
1814	+	sprintf(painCave.errMsg,
1815	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1816	+	painCave.isFatal = 1;
1817	+	simError();
1818	+	}
1819	+	}
1820	+	}
1821	+
1822	+	void SimSetup::initFortran(void){
1823	+	info[0].refreshSim();
1824	+
1825	+	if (!strcmp(info[0].mixingRule, "standard")){
1826	+	the_ff->initForceField(LB_MIXING_RULE);
1827	+	}
1828	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1829	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1830	+	}
1831	+	else{
1832	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1833	+	info[0].mixingRule);
1834	+	painCave.isFatal = 1;
1835	+	simError();
1836	+	}
1837	+
1838	+
1839	+	#ifdef IS_MPI
1840	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1841	+	MPIcheckPoint();
1842	+	#endif // is_mpi
1843	+	}
1844	+
1845	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1846	+	int nZConstraints;
1847	+	ZconStamp** zconStamp;
1848	+
1849	+	if (globals->haveZconstraintTime()){
1850	+	//add sample time of z-constraint  into SimInfo's property list
1851	+	DoubleData* zconsTimeProp = new DoubleData();
1852	+	zconsTimeProp->setID(ZCONSTIME_ID);
1853	+	zconsTimeProp->setData(globals->getZconsTime());
1854	+	theInfo.addProperty(zconsTimeProp);
1855	+	}
1856	+	else{
1857	+	sprintf(painCave.errMsg,
1858	+	"ZConstraint error: If you use a ZConstraint,\n"
1859	+	"\tyou must set zconsTime.\n");
1860	+	painCave.isFatal = 1;
1861	+	simError();
1862	+	}
1863	+
1864	+	//push zconsTol into siminfo, if user does not specify
1865	+	//value for zconsTol, a default value will be used
1866	+	DoubleData* zconsTol = new DoubleData();
1867	+	zconsTol->setID(ZCONSTOL_ID);
1868	+	if (globals->haveZconsTol()){
1869	+	zconsTol->setData(globals->getZconsTol());
1870	+	}
1871	+	else{
1872	+	double defaultZConsTol = 0.01;
1873	+	sprintf(painCave.errMsg,
1874	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1875	+	"\tOOPSE will use a default value of %f.\n"
1876	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1877	+	defaultZConsTol);
1878	+	painCave.isFatal = 0;
1879	+	simError();
1880	+
1881	+	zconsTol->setData(defaultZConsTol);
1882	+	}
1883	+	theInfo.addProperty(zconsTol);
1884	+
1885	+	//set Force Subtraction Policy
1886	+	StringData* zconsForcePolicy = new StringData();
1887	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1888	+
1889	+	if (globals->haveZconsForcePolicy()){
1890	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1891	+	}
1892	+	else{
1893	+	sprintf(painCave.errMsg,
1894	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1895	+	"\tOOPSE will use PolicyByMass.\n"
1896	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1897	+	painCave.isFatal = 0;
1898	+	simError();
1899	+	zconsForcePolicy->setData("BYMASS");
1900	+	}
1901	+
1902	+	theInfo.addProperty(zconsForcePolicy);
1903	+
1904	+	//set zcons gap
1905	+	DoubleData* zconsGap = new DoubleData();
1906	+	zconsGap->setID(ZCONSGAP_ID);
1907	+
1908	+	if (globals->haveZConsGap()){
1909	+	zconsGap->setData(globals->getZconsGap());
1910	+	theInfo.addProperty(zconsGap);
1911	+	}
1912	+
1913	+	//set zcons fixtime
1914	+	DoubleData* zconsFixtime = new DoubleData();
1915	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1916	+
1917	+	if (globals->haveZConsFixTime()){
1918	+	zconsFixtime->setData(globals->getZconsFixtime());
1919	+	theInfo.addProperty(zconsFixtime);
1920	+	}
1921	+
1922	+	//set zconsUsingSMD
1923	+	IntData* zconsUsingSMD = new IntData();
1924	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1925	+
1926	+	if (globals->haveZConsUsingSMD()){
1927	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1928	+	theInfo.addProperty(zconsUsingSMD);
1929	+	}
1930	+
1931	+	//Determine the name of ouput file and add it into SimInfo's property list
1932	+	//Be careful, do not use inFileName, since it is a pointer which
1933	+	//point to a string at master node, and slave nodes do not contain that string
1934	+
1935	+	string zconsOutput(theInfo.finalName);
1936	+
1937	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1938	+
1939	+	StringData* zconsFilename = new StringData();
1940	+	zconsFilename->setID(ZCONSFILENAME_ID);
1941	+	zconsFilename->setData(zconsOutput);
1942	+
1943	+	theInfo.addProperty(zconsFilename);
1944	+
1945	+	//setup index, pos and other parameters of z-constraint molecules
1946	+	nZConstraints = globals->getNzConstraints();
1947	+	theInfo.nZconstraints = nZConstraints;
1948	+
1949	+	zconStamp = globals->getZconStamp();
1950	+	ZConsParaItem tempParaItem;
1951	+
1952	+	ZConsParaData* zconsParaData = new ZConsParaData();
1953	+	zconsParaData->setID(ZCONSPARADATA_ID);
1954	+
1955	+	for (int i = 0; i < nZConstraints; i++){
1956	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1957	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1958	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1959	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1960	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1961	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1962	+	zconsParaData->addItem(tempParaItem);
1963	+	}
1964	+
1965	+	//check the uniqueness of index
1966	+	if(!zconsParaData->isIndexUnique()){
1967	+	sprintf(painCave.errMsg,
1968	+	"ZConstraint Error: molIndex is not unique!\n");
1969	+	painCave.isFatal = 1;
1970	+	simError();
1971	+	}
1972	+
1973	+	//sort the parameters by index of molecules
1974	+	zconsParaData->sortByIndex();
1975	+
1976	+	//push data into siminfo, therefore, we can retrieve later
1977	+	theInfo.addProperty(zconsParaData);
1978	+	}
1979	+
1980	+	void SimSetup::makeMinimizer(){
1981	+
1982	+	OOPSEMinimizer* myOOPSEMinimizer;
1983	+	MinimizerParameterSet* param;
1984	+	char minimizerName[100];
1985	+
1986	+	for (int i = 0; i < nInfo; i++){
1987	+
1988	+	//prepare parameter set for minimizer
1989	+	param = new MinimizerParameterSet();
1990	+	param->setDefaultParameter();
1991	+
1992	+	if (globals->haveMinimizer()){
1993	+	param->setFTol(globals->getMinFTol());
1994	+	}
1995	+
1996	+	if (globals->haveMinGTol()){
1997	+	param->setGTol(globals->getMinGTol());
1998	+	}
1999	+
2000	+	if (globals->haveMinMaxIter()){
2001	+	param->setMaxIteration(globals->getMinMaxIter());
2002	+	}
2003	+
2004	+	if (globals->haveMinWriteFrq()){
2005	+	param->setMaxIteration(globals->getMinMaxIter());
2006	+	}
2007	+
2008	+	if (globals->haveMinWriteFrq()){
2009	+	param->setWriteFrq(globals->getMinWriteFrq());
2010	+	}
2011	+
2012	+	if (globals->haveMinStepSize()){
2013	+	param->setStepSize(globals->getMinStepSize());
2014	+	}
2015	+
2016	+	if (globals->haveMinLSMaxIter()){
2017	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
2018	+	}
2019	+
2020	+	if (globals->haveMinLSTol()){
2021	+	param->setLineSearchTol(globals->getMinLSTol());
2022	+	}
2023	+
2024	+	strcpy(minimizerName, globals->getMinimizer());
2025	+
2026	+	if (!strcasecmp(minimizerName, "CG")){
2027	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2028	+	}
2029	+	else if (!strcasecmp(minimizerName, "SD")){
2030	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
2031	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
2032	+	}
2033	+	else{
2034	+	sprintf(painCave.errMsg,
2035	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
2036	+	painCave.isFatal = 0;
2037	+	simError();
2038	+
2039	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
2040	+	}
2041	+	info[i].the_integrator = myOOPSEMinimizer;
2042	+
2043	+	//store the minimizer into simInfo
2044	+	info[i].the_minimizer = myOOPSEMinimizer;
2045	+	info[i].has_minimizer = true;
2046	+	}
2047	+
2048	+	}

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