ViewVC Help

View File | Revision Log | Show Annotations | View Changeset | Root Listing

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

Comparing trunk/OOPSE/libmdtools/SimSetup.cpp (file contents):
Revision 558 by mmeineke, Thu Jun 19 19:21:23 2003 UTC vs.
Revision 1163 by gezelter, Wed May 12 14:30:12 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 NPT_ENS 2
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
21	–	#define FF_DUFF 0
22	–	#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 37 | 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();
69	<	mpiEventLoop();
70	<
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;
78	<	Globals* the_globals;
79	<	int i, j, k, globalAtomIndex;
80	<
81	<	int ensembleCase;
82	<	int ffCase;
83	<
84	<	ensembleCase = -1;
85	<	ffCase = -1;
126	>	// gather all of the information from the Bass file
127
128	<	// get the stamps and globals;
88	<	the_stamps = stamps;
89	<	the_globals = globals;
128	>	gatherInfo();
129
130	<	// set the easy ones first
92	<	simnfo->target_temp = the_globals->getTargetTemp();
93	<	simnfo->dt = the_globals->getDt();
94	<	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.
97	<	n_components = the_globals->getNComponents();
98	<	strcpy( force_field, the_globals->getForceField() );
132	>	sysObjectsCreation();
133
134	<	if( !strcasecmp( force_field, "DUFF" ))    ffCase = FF_DUFF;
101	<	else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ;
102	<	else{
103	<	sprintf( painCave.errMsg,
104	<	"SimSetup Error. Unrecognized force field -> %s\n",
105	<	force_field );
106	<	painCave.isFatal = 1;
107	<	simError();
108	<	}
134	>	// check on the post processing info
135
136	<	// get the ensemble:
111	<	strcpy( ensemble, the_globals->getEnsemble() );
136	>	finalInfoCheck();
137
138	<	if( !strcasecmp( ensemble, "NVE" ))      ffCase = NVE_ENS;
114	<	else if( !strcasecmp( ensemble, "NVT" )) ffCase = NVT_ENS;
115	<	else if( !strcasecmp( ensemble, "NPT" )) ffCase = NPT_ENS;
116	<	else{
117	<	sprintf( painCave.errMsg,
118	<	"SimSetup Warning. Unrecognized Ensemble -> %s, "
119	<	"reverting to NVE for this simulation.\n",
120	<	ensemble );
121	<	painCave.isFatal = 0;
122	<	simError();
123	<	strcpy( ensemble, "NVE" );
124	<	ensembleCase = NVE_ENS;
125	<	}
126	<	strcpy( simnfo->ensemble, ensemble );
138	>	// initialize the system coordinates
139
140	+	if ( !initSuspend ){
141	+	initSystemCoords();
142
143	<	//   if( !strcasecmp( ensemble, "NPT" ) ) {
144	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
145	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
132	<	//     if (the_globals->haveTargetPressure())
133	<	//       the_extendedsystem->setTargetPressure(the_globals->getTargetPressure());
134	<	//     else {
135	<	//       sprintf( painCave.errMsg,
136	<	//                "SimSetup error: If you use the constant pressure\n"
137	<	//                "    ensemble, you must set targetPressure.\n"
138	<	//                "    This was found in the BASS file.\n");
139	<	//       painCave.isFatal = 1;
140	<	//       simError();
141	<	//     }
143	>	if( !(globals->getUseInitTime()) )
144	>	info[0].currentTime = 0.0;
145	>	}
146
147	<	//     if (the_globals->haveTauThermostat())
144	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
145	<	//     else if (the_globals->haveQmass())
146	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
147	<	//     else {
148	<	//       sprintf( painCave.errMsg,
149	<	//                "SimSetup error: If you use one of the constant temperature\n"
150	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
151	<	//                "    Neither of these was found in the BASS file.\n");
152	<	//       painCave.isFatal = 1;
153	<	//       simError();
154	<	//     }
147	>	// make the output filenames
148
149	<	//     if (the_globals->haveTauBarostat())
150	<	//       the_extendedsystem->setTauBarostat(the_globals->getTauBarostat());
158	<	//     else {
159	<	//       sprintf( painCave.errMsg,
160	<	//                "SimSetup error: If you use the constant pressure\n"
161	<	//                "    ensemble, you must set tauBarostat.\n"
162	<	//                "    This was found in the BASS file.\n");
163	<	//       painCave.isFatal = 1;
164	<	//       simError();
165	<	//     }
166	<
167	<	//   } else if ( !strcasecmp( ensemble, "NVT") ) {
168	<	//     the_extendedsystem = new ExtendedSystem( simnfo );
169	<	//     the_extendedsystem->setTargetTemp(the_globals->getTargetTemp());
170	<
171	<	//     if (the_globals->haveTauThermostat())
172	<	//       the_extendedsystem->setTauThermostat(the_globals->getTauThermostat());
173	<	//     else if (the_globals->haveQmass())
174	<	//       the_extendedsystem->setQmass(the_globals->getQmass());
175	<	//     else {
176	<	//       sprintf( painCave.errMsg,
177	<	//                "SimSetup error: If you use one of the constant temperature\n"
178	<	//                "    ensembles, you must set either tauThermostat or qMass.\n"
179	<	//                "    Neither of these was found in the BASS file.\n");
180	<	//       painCave.isFatal = 1;
181	<	//       simError();
182	<	//     }
183	<
184	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
185	<	simnfo->usePBC = the_globals->getPBC();
186	<
187	<	int usesDipoles = 0;
188	<	switch( ffCase ){
189	<
190	<	case FF_DUFF:
191	<	the_ff = new DUFF();
192	<	usesDipoles = 1;
193	<	break;
194	<
195	<	case FF_LJ:
196	<	the_ff = LJFF();
197	<	break;
198	<
199	<	default:
200	<	sprintf( painCave.errMsg,
201	<	"SimSetup Error. Unrecognized force field in case statement.\n");
202	<	painCave.isFatal = 1;
203	<	simError();
204	<	}
205	<
149	>	makeOutNames();
150	>
151		#ifdef IS_MPI
152	<	strcpy( checkPointMsg, "ForceField creation successful" );
153	<	MPIcheckPoint();
209	<	#endif // is_mpi
152	>	mpiSim->mpiRefresh();
153	>	#endif
154
155	<	// get the components and calculate the tot_nMol and indvidual n_mol
212	<	the_components = the_globals->getComponents();
213	<	components_nmol = new int[n_components];
214	<	comp_stamps = new MoleculeStamp*[n_components];
155	>	// initialize the Fortran
156
157	<	if( !the_globals->haveNMol() ){
217	<	// we don't have the total number of molecules, so we assume it is
218	<	// given in each component
157	>	initFortran();
158
159	<	tot_nmol = 0;
160	<	for( i=0; i<n_components; i++ ){
159	>	if (globals->haveMinimizer())
160	>	// make minimizer
161	>	makeMinimizer();
162	>	else
163	>	// make the integrator
164	>	makeIntegrator();
165
166	<	if( !the_components[i]->haveNMol() ){
224	<	// we have a problem
225	<	sprintf( painCave.errMsg,
226	<	"SimSetup Error. No global NMol or component NMol"
227	<	" given. Cannot calculate the number of atoms.\n" );
228	<	painCave.isFatal = 1;
229	<	simError();
230	<	}
166	>	}
167
232	–	tot_nmol += the_components[i]->getNMol();
233	–	components_nmol[i] = the_components[i]->getNMol();
234	–	}
235	–	}
236	–	else{
237	–	sprintf( painCave.errMsg,
238	–	"SimSetup error.\n"
239	–	"\tSorry, the ability to specify total"
240	–	" nMols and then give molfractions in the components\n"
241	–	"\tis not currently supported."
242	–	" Please give nMol in the components.\n" );
243	–	painCave.isFatal = 1;
244	–	simError();
245	–
246	–
247	–	//     tot_nmol = the_globals->getNMol();
248	–
249	–	//   //we have the total number of molecules, now we check for molfractions
250	–	//     for( i=0; i<n_components; i++ ){
251	–
252	–	//       if( !the_components[i]->haveMolFraction() ){
253	–
254	–	//  if( !the_components[i]->haveNMol() ){
255	–	//    //we have a problem
256	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
257	–	//              << " nMol was given in component
258	–
259	–	}
168
169	<	#ifdef IS_MPI
170	<	strcpy( checkPointMsg, "Have the number of components" );
171	<	MPIcheckPoint();
172	<	#endif // is_mpi
173	<
174	<	// make an array of molecule stamps that match the components used.
175	<	// also extract the used stamps out into a separate linked list
176	<
177	<	simnfo->nComponents = n_components;
178	<	simnfo->componentsNmol = components_nmol;
179	<	simnfo->compStamps = comp_stamps;
180	<	simnfo->headStamp = new LinkedMolStamp();
169	>	void SimSetup::makeMolecules(void){
170	>	int i, j, k;
171	>	int exI, exJ, exK, exL, slI, slJ;
172	>	int tempI, tempJ, tempK, tempL;
173	>	int molI;
174	>	int stampID, atomOffset, rbOffset;
175	>	molInit molInfo;
176	>	DirectionalAtom* dAtom;
177	>	RigidBody* myRB;
178	>	StuntDouble* mySD;
179	>	LinkedAssign* extras;
180	>	LinkedAssign* current_extra;
181	>	AtomStamp* currentAtom;
182	>	BondStamp* currentBond;
183	>	BendStamp* currentBend;
184	>	TorsionStamp* currentTorsion;
185	>	RigidBodyStamp* currentRigidBody;
186	>	CutoffGroupStamp* currentCutoffGroup;
187	>	CutoffGroup* myCutoffGroup;
188
189	<	char* id;
190	<	LinkedMolStamp* headStamp = simnfo->headStamp;
191	<	LinkedMolStamp* currentStamp = NULL;
277	<	for( i=0; i<n_components; i++ ){
189	>	bond_pair* theBonds;
190	>	bend_set* theBends;
191	>	torsion_set* theTorsions;
192
193	<	id = the_components[i]->getType();
280	<	comp_stamps[i] = NULL;
281	<
282	<	// check to make sure the component isn't already in the list
193	>	set<int> skipList;
194
195	<	comp_stamps[i] = headStamp->match( id );
196	<	if( comp_stamps[i] == NULL ){
195	>	double phi, theta, psi;
196	>	char* molName;
197	>	char rbName[100];
198	>
199	>	//init the forceField paramters
200	>
201	>	the_ff->readParams();
202	>
203	>	// init the atoms
204	>
205	>	int nMembers, nNew, rb1, rb2;
206	>
207	>	for (k = 0; k < nInfo; k++){
208	>	the_ff->setSimInfo(&(info[k]));
209	>
210	>	atomOffset = 0;
211	>
212	>	for (i = 0; i < info[k].n_mol; i++){
213	>	stampID = info[k].molecules[i].getStampID();
214	>	molName = comp_stamps[stampID]->getID();
215	>
216	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
217	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
218	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
219	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
220	>	molInfo.nRigidBodies = comp_stamps[stampID]->getNRigidBodies();
221	>	molInfo.nCutoffGroups = comp_stamps[stampID]->getNCutoffGroups();
222
223	<	// extract the component from the list;
223	>	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
224	>
225	>	if (molInfo.nBonds > 0)
226	>	molInfo.myBonds = new (Bond *) [molInfo.nBonds];
227	>	else
228	>	molInfo.myBonds = NULL;
229	>
230	>	if (molInfo.nBends > 0)
231	>	molInfo.myBends = new (Bend *) [molInfo.nBends];
232	>	else
233	>	molInfo.myBends = NULL;
234	>
235	>	if (molInfo.nTorsions > 0)
236	>	molInfo.myTorsions = new (Torsion *) [molInfo.nTorsions];
237	>	else
238	>	molInfo.myTorsions = NULL;
239	>
240	>	theBonds = new bond_pair[molInfo.nBonds];
241	>	theBends = new bend_set[molInfo.nBends];
242	>	theTorsions = new torsion_set[molInfo.nTorsions];
243
244	<	currentStamp = the_stamps->extractMolStamp( id );
290	<	if( currentStamp == NULL ){
291	<	sprintf( painCave.errMsg,
292	<	"SimSetup error: Component \"%s\" was not found in the "
293	<	"list of declared molecules\n",
294	<	id );
295	<	painCave.isFatal = 1;
296	<	simError();
297	<	}
298	<
299	<	headStamp->add( currentStamp );
300	<	comp_stamps[i] = headStamp->match( id );
301	<	}
302	<	}
244	>	// make the Atoms
245
246	<	#ifdef IS_MPI
247	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
306	<	MPIcheckPoint();
307	<	#endif // is_mpi
308	<
246	>	for (j = 0; j < molInfo.nAtoms; j++){
247	>	currentAtom = comp_stamps[stampID]->getAtom(j);
248
249	+	if (currentAtom->haveOrientation()){
250	+	dAtom = new DirectionalAtom((j + atomOffset),
251	+	info[k].getConfiguration());
252	+	info[k].n_oriented++;
253	+	molInfo.myAtoms[j] = dAtom;
254
255	+	// Directional Atoms have standard unit vectors which are oriented
256	+	// in space using the three Euler angles.  We assume the standard
257	+	// unit vector was originally along the z axis below.
258
259	<	// caclulate the number of atoms, bonds, bends and torsions
259	>	phi = currentAtom->getEulerPhi() * M_PI / 180.0;
260	>	theta = currentAtom->getEulerTheta() * M_PI / 180.0;
261	>	psi = currentAtom->getEulerPsi()* M_PI / 180.0;
262
263	<	tot_atoms = 0;
264	<	tot_bonds = 0;
265	<	tot_bends = 0;
266	<	tot_torsions = 0;
318	<	for( i=0; i<n_components; i++ ){
319	<
320	<	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
321	<	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
322	<	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
323	<	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
324	<	}
263	>	dAtom->setUnitFrameFromEuler(phi, theta, psi);
264	>
265	>	}
266	>	else{
267
268	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
268	>	molInfo.myAtoms[j] = new Atom((j + atomOffset), info[k].getConfiguration());
269
270	<	simnfo->n_atoms = tot_atoms;
329	<	simnfo->n_bonds = tot_bonds;
330	<	simnfo->n_bends = tot_bends;
331	<	simnfo->n_torsions = tot_torsions;
332	<	simnfo->n_SRI = tot_SRI;
333	<	simnfo->n_mol = tot_nmol;
334	<
335	<	simnfo->molMembershipArray = new int[tot_atoms];
270	>	}
271
272	+	molInfo.myAtoms[j]->setType(currentAtom->getType());
273		#ifdef IS_MPI
274
275	<	// divide the molecules among processors here.
340	<
341	<	mpiSim = new mpiSimulation( simnfo );
342	<
343	<	globalIndex = mpiSim->divideLabor();
275	>	molInfo.myAtoms[j]->setGlobalIndex(globalAtomIndex[j + atomOffset]);
276
277	<	// set up the local variables
278	<
347	<	int localMol, allMol;
348	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
277	>	#endif // is_mpi
278	>	}
279
280	<	int* mol2proc = mpiSim->getMolToProcMap();
281	<	int* molCompType = mpiSim->getMolComponentType();
282	<
283	<	allMol = 0;
284	<	localMol = 0;
355	<	local_atoms = 0;
356	<	local_bonds = 0;
357	<	local_bends = 0;
358	<	local_torsions = 0;
359	<	globalAtomIndex = 0;
280	>	// make the bonds
281	>	for (j = 0; j < molInfo.nBonds; j++){
282	>	currentBond = comp_stamps[stampID]->getBond(j);
283	>	theBonds[j].a = currentBond->getA() + atomOffset;
284	>	theBonds[j].b = currentBond->getB() + atomOffset;
285
286	+	tempI = theBonds[j].a;
287	+	tempJ = theBonds[j].b;
288
289	<	for( i=0; i<n_components; i++ ){
289	>	#ifdef IS_MPI
290	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
291	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
292	>	#else
293	>	exI = tempI + 1;
294	>	exJ = tempJ + 1;
295	>	#endif
296
297	<	for( j=0; j<components_nmol[i]; j++ ){
365	<
366	<	if( mol2proc[allMol] == worldRank ){
367	<
368	<	local_atoms +=    comp_stamps[i]->getNAtoms();
369	<	local_bonds +=    comp_stamps[i]->getNBonds();
370	<	local_bends +=    comp_stamps[i]->getNBends();
371	<	local_torsions += comp_stamps[i]->getNTorsions();
372	<	localMol++;
373	<	}
374	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
375	<	simnfo->molMembershipArray[globalAtomIndex] = allMol;
376	<	globalAtomIndex++;
297	>	info[k].excludes->addPair(exI, exJ);
298		}
299
300	<	allMol++;
301	<	}
302	<	}
303	<	local_SRI = local_bonds + local_bends + local_torsions;
304	<
305	<	simnfo->n_atoms = mpiSim->getMyNlocal();
385	<
386	<	if( local_atoms != simnfo->n_atoms ){
387	<	sprintf( painCave.errMsg,
388	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
389	<	" localAtom (%d) are not equal.\n",
390	<	simnfo->n_atoms,
391	<	local_atoms );
392	<	painCave.isFatal = 1;
393	<	simError();
394	<	}
300	>	//make the bends
301	>	for (j = 0; j < molInfo.nBends; j++){
302	>	currentBend = comp_stamps[stampID]->getBend(j);
303	>	theBends[j].a = currentBend->getA() + atomOffset;
304	>	theBends[j].b = currentBend->getB() + atomOffset;
305	>	theBends[j].c = currentBend->getC() + atomOffset;
306
307	<	simnfo->n_bonds = local_bonds;
308	<	simnfo->n_bends = local_bends;
309	<	simnfo->n_torsions = local_torsions;
399	<	simnfo->n_SRI = local_SRI;
400	<	simnfo->n_mol = localMol;
307	>	if (currentBend->haveExtras()){
308	>	extras = currentBend->getExtras();
309	>	current_extra = extras;
310
311	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
312	<	MPIcheckPoint();
313	<
314	<
315	<	#endif // is_mpi
316	<
311	>	while (current_extra != NULL){
312	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
313	>	switch (current_extra->getType()){
314	>	case 0:
315	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
316	>	theBends[j].isGhost = 1;
317	>	break;
318
319	<	// create the atom and short range interaction arrays
319	>	case 1:
320	>	theBends[j].ghost = (int) current_extra->getDouble() +
321	>	atomOffset;
322	>	theBends[j].isGhost = 1;
323	>	break;
324
325	<	Atom::createArrays(simnfo->n_atoms);
326	<	the_atoms = new Atom*[simnfo->n_atoms];
327	<	the_molecules = new Molecule[simnfo->n_mol];
328	<	int molIndex;
329	<
330	<	// initialize the molecule's stampID's
325	>	default:
326	>	sprintf(painCave.errMsg,
327	>	"SimSetup Error: ghostVectorSource was neither a "
328	>	"double nor an int.\n"
329	>	"-->Bend[%d] in %s\n",
330	>	j, comp_stamps[stampID]->getID());
331	>	painCave.isFatal = 1;
332	>	simError();
333	>	}
334	>	}
335	>	else{
336	>	sprintf(painCave.errMsg,
337	>	"SimSetup Error: unhandled bend assignment:\n"
338	>	"    -->%s in Bend[%d] in %s\n",
339	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
340	>	painCave.isFatal = 1;
341	>	simError();
342	>	}
343
344	+	current_extra = current_extra->getNext();
345	+	}
346	+	}
347	+
348	+	if (theBends[j].isGhost) {
349	+
350	+	tempI = theBends[j].a;
351	+	tempJ = theBends[j].b;
352	+
353		#ifdef IS_MPI
354	<
354	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
355	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
356	>	#else
357	>	exI = tempI + 1;
358	>	exJ = tempJ + 1;
359	>	#endif
360	>	info[k].excludes->addPair(exI, exJ);
361
362	<	molIndex = 0;
422	<	for(i=0; i<mpiSim->getTotNmol(); i++){
423	<
424	<	if(mol2proc[i] == worldRank ){
425	<	the_molecules[molIndex].setStampID( molCompType[i] );
426	<	the_molecules[molIndex].setMyIndex( molIndex );
427	<	the_molecules[molIndex].setGlobalIndex( i );
428	<	molIndex++;
429	<	}
430	<	}
362	>	} else {
363
364	<	#else // is_mpi
365	<
366	<	molIndex = 0;
367	<	globalAtomIndex = 0;
368	<	for(i=0; i<n_components; i++){
369	<	for(j=0; j<components_nmol[i]; j++ ){
370	<	the_molecules[molIndex].setStampID( i );
371	<	the_molecules[molIndex].setMyIndex( molIndex );
372	<	the_molecules[molIndex].setGlobalIndex( molIndex );
373	<	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) {
374	<	simnfo->molMembershipArray[globalAtomIndex] = molIndex;
375	<	globalAtomIndex++;
364	>	tempI = theBends[j].a;
365	>	tempJ = theBends[j].b;
366	>	tempK = theBends[j].c;
367	>
368	>	#ifdef IS_MPI
369	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
370	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
371	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
372	>	#else
373	>	exI = tempI + 1;
374	>	exJ = tempJ + 1;
375	>	exK = tempK + 1;
376	>	#endif
377	>
378	>	info[k].excludes->addPair(exI, exK);
379	>	info[k].excludes->addPair(exI, exJ);
380	>	info[k].excludes->addPair(exJ, exK);
381	>	}
382		}
445	–	molIndex++;
446	–	}
447	–	}
448	–
383
384	<	#endif // is_mpi
384	>	for (j = 0; j < molInfo.nTorsions; j++){
385	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
386	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
387	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
388	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
389	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
390
391	+	tempI = theTorsions[j].a;
392	+	tempJ = theTorsions[j].b;
393	+	tempK = theTorsions[j].c;
394	+	tempL = theTorsions[j].d;
395
396	<	if( simnfo->n_SRI ){
397	<
398	<	Exclude::createArray(simnfo->n_SRI);
399	<	the_excludes = new Exclude*[simnfo->n_SRI];
400	<	for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex);
401	<	simnfo->globalExcludes = new int;
402	<	simnfo->n_exclude = simnfo->n_SRI;
403	<	}
404	<	else{
405	<
406	<	Exclude::createArray( 1 );
464	<	the_excludes = new Exclude*;
465	<	the_excludes[0] = new Exclude(0);
466	<	the_excludes[0]->setPair( 0,0 );
467	<	simnfo->globalExcludes = new int;
468	<	simnfo->globalExcludes[0] = 0;
469	<	simnfo->n_exclude = 0;
470	<	}
396	>	#ifdef IS_MPI
397	>	exI = info[k].atoms[tempI]->getGlobalIndex() + 1;
398	>	exJ = info[k].atoms[tempJ]->getGlobalIndex() + 1;
399	>	exK = info[k].atoms[tempK]->getGlobalIndex() + 1;
400	>	exL = info[k].atoms[tempL]->getGlobalIndex() + 1;
401	>	#else
402	>	exI = tempI + 1;
403	>	exJ = tempJ + 1;
404	>	exK = tempK + 1;
405	>	exL = tempL + 1;
406	>	#endif
407
408	<	// set the arrays into the SimInfo object
408	>	info[k].excludes->addPair(exI, exJ);
409	>	info[k].excludes->addPair(exI, exK);
410	>	info[k].excludes->addPair(exI, exL);
411	>	info[k].excludes->addPair(exJ, exK);
412	>	info[k].excludes->addPair(exJ, exL);
413	>	info[k].excludes->addPair(exK, exL);
414	>	}
415
416	<	simnfo->atoms = the_atoms;
417	<	simnfo->molecules = the_molecules;
418	<	simnfo->nGlobalExcludes = 0;
419	<	simnfo->excludes = the_excludes;
416	>
417	>	molInfo.myRigidBodies.clear();
418	>
419	>	for (j = 0; j < molInfo.nRigidBodies; j++){
420
421	+	currentRigidBody = comp_stamps[stampID]->getRigidBody(j);
422	+	nMembers = currentRigidBody->getNMembers();
423
424	<	// get some of the tricky things that may still be in the globals
424	>	// Create the Rigid Body:
425
426	<
483	<	if( the_globals->haveBox() ){
484	<	simnfo->box_x = the_globals->getBox();
485	<	simnfo->box_y = the_globals->getBox();
486	<	simnfo->box_z = the_globals->getBox();
487	<	}
488	<	else if( the_globals->haveDensity() ){
426	>	myRB = new RigidBody();
427
428	<	double vol;
429	<	vol = (double)tot_nmol / the_globals->getDensity();
430	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
431	<	simnfo->box_y = simnfo->box_x;
494	<	simnfo->box_z = simnfo->box_x;
495	<	}
496	<	else{
497	<	if( !the_globals->haveBoxX() ){
498	<	sprintf( painCave.errMsg,
499	<	"SimSetup error, no periodic BoxX size given.\n" );
500	<	painCave.isFatal = 1;
501	<	simError();
502	<	}
503	<	simnfo->box_x = the_globals->getBoxX();
428	>	sprintf(rbName,"%s_RB_%d", molName, j);
429	>	myRB->setType(rbName);
430	>
431	>	for (rb1 = 0; rb1 < nMembers; rb1++) {
432
433	<	if( !the_globals->haveBoxY() ){
434	<	sprintf( painCave.errMsg,
507	<	"SimSetup error, no periodic BoxY size given.\n" );
508	<	painCave.isFatal = 1;
509	<	simError();
510	<	}
511	<	simnfo->box_y = the_globals->getBoxY();
433	>	// molI is atom numbering inside this molecule
434	>	molI = currentRigidBody->getMember(rb1);
435
436	<	if( !the_globals->haveBoxZ() ){
437	<	sprintf( painCave.errMsg,
515	<	"SimSetup error, no periodic BoxZ size given.\n" );
516	<	painCave.isFatal = 1;
517	<	simError();
518	<	}
519	<	simnfo->box_z = the_globals->getBoxZ();
520	<	}
436	>	// tempI is atom numbering on local processor
437	>	tempI = molI + atomOffset;
438
439	<	#ifdef IS_MPI
440	<	strcpy( checkPointMsg, "Box size set up" );
441	<	MPIcheckPoint();
525	<	#endif // is_mpi
439	>	// currentAtom is the AtomStamp (which we need for
440	>	// rigid body reference positions)
441	>	currentAtom = comp_stamps[stampID]->getAtom(molI);
442
443	+	// When we add to the rigid body, add the atom itself and
444	+	// the stamp info:
445
446	<	// initialize the arrays
447	<
448	<	the_ff->setSimInfo( simnfo );
449	<
450	<	makeMolecules();
451	<	simnfo->identArray = new int[simnfo->n_atoms];
452	<	for(i=0; i<simnfo->n_atoms; i++){
453	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
454	<	}
455	<
456	<	if (the_globals->getUseRF() ) {
457	<	simnfo->useReactionField = 1;
458	<
459	<	if( !the_globals->haveECR() ){
460	<	sprintf( painCave.errMsg,
461	<	"SimSetup Warning: using default value of 1/2 the smallest "
462	<	"box length for the electrostaticCutoffRadius.\n"
463	<	"I hope you have a very fast processor!\n");
464	<	painCave.isFatal = 0;
465	<	simError();
466	<	double smallest;
467	<	smallest = simnfo->box_x;
468	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
469	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
470	<	simnfo->ecr = 0.5 * smallest;
471	<	} else {
472	<	simnfo->ecr        = the_globals->getECR();
473	<	}
474	<
475	<	if( !the_globals->haveEST() ){
476	<	sprintf( painCave.errMsg,
477	<	"SimSetup Warning: using default value of 0.05 * the "
478	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
479	<	);
480	<	painCave.isFatal = 0;
481	<	simError();
482	<	simnfo->est = 0.05 * simnfo->ecr;
483	<	} else {
566	<	simnfo->est        = the_globals->getEST();
567	<	}
568	<
569	<	if(!the_globals->haveDielectric() ){
570	<	sprintf( painCave.errMsg,
571	<	"SimSetup Error: You are trying to use Reaction Field without"
572	<	"setting a dielectric constant!\n"
573	<	);
574	<	painCave.isFatal = 1;
575	<	simError();
576	<	}
577	<	simnfo->dielectric = the_globals->getDielectric();
578	<	} else {
579	<	if (usesDipoles) {
580	<
581	<	if( !the_globals->haveECR() ){
582	<	sprintf( painCave.errMsg,
583	<	"SimSetup Warning: using default value of 1/2 the smallest "
584	<	"box length for the electrostaticCutoffRadius.\n"
585	<	"I hope you have a very fast processor!\n");
586	<	painCave.isFatal = 0;
587	<	simError();
588	<	double smallest;
589	<	smallest = simnfo->box_x;
590	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
591	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
592	<	simnfo->ecr = 0.5 * smallest;
593	<	} else {
594	<	simnfo->ecr        = the_globals->getECR();
446	>	myRB->addAtom(info[k].atoms[tempI], currentAtom);
447	>
448	>	// Add this atom to the Skip List for the integrators
449	>	#ifdef IS_MPI
450	>	slI = info[k].atoms[tempI]->getGlobalIndex();
451	>	#else
452	>	slI = tempI;
453	>	#endif
454	>	skipList.insert(slI);
455	>
456	>	}
457	>
458	>	for(rb1 = 0; rb1 < nMembers - 1; rb1++) {
459	>	for(rb2 = rb1+1; rb2 < nMembers; rb2++) {
460	>
461	>	tempI = currentRigidBody->getMember(rb1);
462	>	tempJ = currentRigidBody->getMember(rb2);
463	>
464	>	// Some explanation is required here.
465	>	// Fortran indexing starts at 1, while c indexing starts at 0
466	>	// Also, in parallel computations, the GlobalIndex is
467	>	// used for the exclude list:
468	>
469	>	#ifdef IS_MPI
470	>	exI = molInfo.myAtoms[tempI]->getGlobalIndex() + 1;
471	>	exJ = molInfo.myAtoms[tempJ]->getGlobalIndex() + 1;
472	>	#else
473	>	exI = molInfo.myAtoms[tempI]->getIndex() + 1;
474	>	exJ = molInfo.myAtoms[tempJ]->getIndex() + 1;
475	>	#endif
476	>
477	>	info[k].excludes->addPair(exI, exJ);
478	>
479	>	}
480	>	}
481	>
482	>	molInfo.myRigidBodies.push_back(myRB);
483	>	info[k].rigidBodies.push_back(myRB);
484		}
485
597	–	if( !the_globals->haveEST() ){
598	–	sprintf( painCave.errMsg,
599	–	"SimSetup Warning: using default value of 5%% of the "
600	–	"electrostaticCutoffRadius for the "
601	–	"electrostaticSkinThickness\n"
602	–	);
603	–	painCave.isFatal = 0;
604	–	simError();
605	–	simnfo->est = 0.05 * simnfo->ecr;
606	–	} else {
607	–	simnfo->est        = the_globals->getEST();
608	–	}
609	–	}
610	–	}
486
487	<	#ifdef IS_MPI
488	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
489	<	MPIcheckPoint();
615	<	#endif // is_mpi
487	>	//create cutoff group for molecule
488	>	molInfo.myCutoffGroups.clear();
489	>	for (j = 0; j < molInfo.nCutoffGroups; j++){
490
491	<	if( the_globals->haveInitialConfig() ){
492	<
493	<	InitializeFromFile* fileInit;
494	<	#ifdef IS_MPI // is_mpi
495	<	if( worldRank == 0 ){
496	<	#endif //is_mpi
497	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
491	>	currentCutoffGroup = comp_stamps[stampID]->getCutoffGroup(j);
492	>	nMembers = currentCutoffGroup->getNMembers();
493	>
494	>	myCutoffGroup = new CutoffGroup();
495	>
496	>	for (int cg = 0; cg < nMembers; cg++) {
497	>
498	>	// molI is atom numbering inside this molecule
499	>	molI = currentCutoffGroup->getMember(cg);
500	>
501	>	// tempI is atom numbering on local processor
502	>	tempI = molI + atomOffset;
503	>
504	>	myCutoffGroup->addAtom(info[k].atoms[tempI]);
505	>	}
506	>
507	>	molInfo.myCutoffGroups.push_back(myCutoffGroup);
508	>	}//end for (j = 0; j < molInfo.nCutoffGroups; j++)
509	>
510	>
511	>
512	>	// After this is all set up, scan through the atoms to
513	>	// see if they can be added to the integrableObjects:
514	>
515	>	molInfo.myIntegrableObjects.clear();
516	>
517	>
518	>	for (j = 0; j < molInfo.nAtoms; j++){
519	>
520		#ifdef IS_MPI
521	<	}else fileInit = new InitializeFromFile( NULL );
521	>	slJ = molInfo.myAtoms[j]->getGlobalIndex();
522	>	#else
523	>	slJ = j+atomOffset;
524		#endif
627	–	fileInit->read_xyz( simnfo ); // default velocities on
525
526	<	delete fileInit;
630	<	}
631	<	else{
526	>	// if they aren't on the skip list, then they can be integrated
527
528	<	#ifdef IS_MPI
528	>	if (skipList.find(slJ) == skipList.end()) {
529	>	mySD = (StuntDouble *) molInfo.myAtoms[j];
530	>	info[k].integrableObjects.push_back(mySD);
531	>	molInfo.myIntegrableObjects.push_back(mySD);
532	>	}
533	>	}
534
535	<	// no init from bass
636	<
637	<	sprintf( painCave.errMsg,
638	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
639	<	painCave.isFatal;
640	<	simError();
641	<
642	<	#else
535	>	// all rigid bodies are integrated:
536
537	<	initFromBass();
537	>	for (j = 0; j < molInfo.nRigidBodies; j++) {
538	>	mySD = (StuntDouble *) molInfo.myRigidBodies[j];
539	>	info[k].integrableObjects.push_back(mySD);
540	>	molInfo.myIntegrableObjects.push_back(mySD);
541	>	}
542	>
543	>
544	>	// send the arrays off to the forceField for init.
545	>
546	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
547	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
548	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
549	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
550	>	theTorsions);
551
552	+	info[k].molecules[i].initialize(molInfo);
553
647	–	#endif
648	–	}
554
555	+	atomOffset += molInfo.nAtoms;
556	+	delete[] theBonds;
557	+	delete[] theBends;
558	+	delete[] theTorsions;
559	+	}
560	+	}
561	+
562		#ifdef IS_MPI
563	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
563	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
564		MPIcheckPoint();
565		#endif // is_mpi
566
567	+	}
568
569	<
570	<
571	<
569	>	void SimSetup::initFromBass(void){
570	>	int i, j, k;
571	>	int n_cells;
572	>	double cellx, celly, cellz;
573	>	double temp1, temp2, temp3;
574	>	int n_per_extra;
575	>	int n_extra;
576	>	int have_extra, done;
577
578	<
579	<	#ifdef IS_MPI
580	<	if( worldRank == 0 ){
581	<	#endif // is_mpi
582	<
583	<	if( the_globals->haveFinalConfig() ){
584	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
578	>	double vel[3];
579	>	vel[0] = 0.0;
580	>	vel[1] = 0.0;
581	>	vel[2] = 0.0;
582	>
583	>	temp1 = (double) tot_nmol / 4.0;
584	>	temp2 = pow(temp1, (1.0 / 3.0));
585	>	temp3 = ceil(temp2);
586	>
587	>	have_extra = 0;
588	>	if (temp2 < temp3){
589	>	// we have a non-complete lattice
590	>	have_extra = 1;
591	>
592	>	n_cells = (int) temp3 - 1;
593	>	cellx = info[0].boxL[0] / temp3;
594	>	celly = info[0].boxL[1] / temp3;
595	>	cellz = info[0].boxL[2] / temp3;
596	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
597	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
598	>	n_per_extra = (int) ceil(temp1);
599	>
600	>	if (n_per_extra > 4){
601	>	sprintf(painCave.errMsg,
602	>	"SimSetup error. There has been an error in constructing"
603	>	" the non-complete lattice.\n");
604	>	painCave.isFatal = 1;
605	>	simError();
606		}
607	<	else{
608	<	strcpy( simnfo->finalName, inFileName );
609	<	char* endTest;
610	<	int nameLength = strlen( simnfo->finalName );
611	<	endTest = &(simnfo->finalName[nameLength - 5]);
612	<	if( !strcmp( endTest, ".bass" ) ){
613	<	strcpy( endTest, ".eor" );
607	>	}
608	>	else{
609	>	n_cells = (int) temp3;
610	>	cellx = info[0].boxL[0] / temp3;
611	>	celly = info[0].boxL[1] / temp3;
612	>	cellz = info[0].boxL[2] / temp3;
613	>	}
614	>
615	>	current_mol = 0;
616	>	current_comp_mol = 0;
617	>	current_comp = 0;
618	>	current_atom_ndx = 0;
619	>
620	>	for (i = 0; i < n_cells ; i++){
621	>	for (j = 0; j < n_cells; j++){
622	>	for (k = 0; k < n_cells; k++){
623	>	makeElement(i * cellx, j * celly, k * cellz);
624	>
625	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
626	>
627	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
628	>
629	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
630		}
676	–	else if( !strcmp( endTest, ".BASS" ) ){
677	–	strcpy( endTest, ".eor" );
678	–	}
679	–	else{
680	–	endTest = &(simnfo->finalName[nameLength - 4]);
681	–	if( !strcmp( endTest, ".bss" ) ){
682	–	strcpy( endTest, ".eor" );
683	–	}
684	–	else if( !strcmp( endTest, ".mdl" ) ){
685	–	strcpy( endTest, ".eor" );
686	–	}
687	–	else{
688	–	strcat( simnfo->finalName, ".eor" );
689	–	}
690	–	}
631		}
692	–
693	–	// make the sample and status out names
694	–
695	–	strcpy( simnfo->sampleName, inFileName );
696	–	char* endTest;
697	–	int nameLength = strlen( simnfo->sampleName );
698	–	endTest = &(simnfo->sampleName[nameLength - 5]);
699	–	if( !strcmp( endTest, ".bass" ) ){
700	–	strcpy( endTest, ".dump" );
701	–	}
702	–	else if( !strcmp( endTest, ".BASS" ) ){
703	–	strcpy( endTest, ".dump" );
704	–	}
705	–	else{
706	–	endTest = &(simnfo->sampleName[nameLength - 4]);
707	–	if( !strcmp( endTest, ".bss" ) ){
708	–	strcpy( endTest, ".dump" );
709	–	}
710	–	else if( !strcmp( endTest, ".mdl" ) ){
711	–	strcpy( endTest, ".dump" );
712	–	}
713	–	else{
714	–	strcat( simnfo->sampleName, ".dump" );
715	–	}
716	–	}
717	–
718	–	strcpy( simnfo->statusName, inFileName );
719	–	nameLength = strlen( simnfo->statusName );
720	–	endTest = &(simnfo->statusName[nameLength - 5]);
721	–	if( !strcmp( endTest, ".bass" ) ){
722	–	strcpy( endTest, ".stat" );
723	–	}
724	–	else if( !strcmp( endTest, ".BASS" ) ){
725	–	strcpy( endTest, ".stat" );
726	–	}
727	–	else{
728	–	endTest = &(simnfo->statusName[nameLength - 4]);
729	–	if( !strcmp( endTest, ".bss" ) ){
730	–	strcpy( endTest, ".stat" );
731	–	}
732	–	else if( !strcmp( endTest, ".mdl" ) ){
733	–	strcpy( endTest, ".stat" );
734	–	}
735	–	else{
736	–	strcat( simnfo->statusName, ".stat" );
737	–	}
738	–	}
739	–
740	–	#ifdef IS_MPI
632		}
742	–	#endif // is_mpi
743	–
744	–	// set the status, sample, and themal kick times
745	–
746	–	if( the_globals->haveSampleTime() ){
747	–	simnfo->sampleTime = the_globals->getSampleTime();
748	–	simnfo->statusTime = simnfo->sampleTime;
749	–	simnfo->thermalTime = simnfo->sampleTime;
750	–	}
751	–	else{
752	–	simnfo->sampleTime = the_globals->getRunTime();
753	–	simnfo->statusTime = simnfo->sampleTime;
754	–	simnfo->thermalTime = simnfo->sampleTime;
755	–	}
633
634	<	if( the_globals->haveStatusTime() ){
635	<	simnfo->statusTime = the_globals->getStatusTime();
759	<	}
634	>	if (have_extra){
635	>	done = 0;
636
637	<	if( the_globals->haveThermalTime() ){
638	<	simnfo->thermalTime = the_globals->getThermalTime();
639	<	}
637	>	int start_ndx;
638	>	for (i = 0; i < (n_cells + 1) && !done; i++){
639	>	for (j = 0; j < (n_cells + 1) && !done; j++){
640	>	if (i < n_cells){
641	>	if (j < n_cells){
642	>	start_ndx = n_cells;
643	>	}
644	>	else
645	>	start_ndx = 0;
646	>	}
647	>	else
648	>	start_ndx = 0;
649
650	<	// check for the temperature set flag
650	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
651	>	makeElement(i * cellx, j * celly, k * cellz);
652	>	done = (current_mol >= tot_nmol);
653
654	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
654	>	if (!done && n_per_extra > 1){
655	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
656	>	k * cellz);
657	>	done = (current_mol >= tot_nmol);
658	>	}
659
660	+	if (!done && n_per_extra > 2){
661	+	makeElement(i * cellx, j * celly + 0.5 * celly,
662	+	k * cellz + 0.5 * cellz);
663	+	done = (current_mol >= tot_nmol);
664	+	}
665
666	<	// make the integrator
666	>	if (!done && n_per_extra > 3){
667	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
668	>	k * cellz + 0.5 * cellz);
669	>	done = (current_mol >= tot_nmol);
670	>	}
671	>	}
672	>	}
673	>	}
674	>	}
675
676	<	switch( ensembleCase ){
676	>	for (i = 0; i < info[0].n_atoms; i++){
677	>	info[0].atoms[i]->setVel(vel);
678	>	}
679	>	}
680
681	<	case NVE_ENS:
682	<	new NVE( simnfo, the_ff );
683	<	break;
681	>	void SimSetup::makeElement(double x, double y, double z){
682	>	int k;
683	>	AtomStamp* current_atom;
684	>	DirectionalAtom* dAtom;
685	>	double rotMat[3][3];
686	>	double pos[3];
687
688	<	default:
689	<	sprintf( painCave.errMsg,
690	<	"SimSetup Error. Unrecognized ensemble in case statement.\n");
691	<	painCave.isFatal = 1;
692	<	simError();
693	<	}
688	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
689	>	current_atom = comp_stamps[current_comp]->getAtom(k);
690	>	if (!current_atom->havePosition()){
691	>	sprintf(painCave.errMsg,
692	>	"SimSetup:initFromBass error.\n"
693	>	"\tComponent %s, atom %s does not have a position specified.\n"
694	>	"\tThe initialization routine is unable to give a start"
695	>	" position.\n",
696	>	comp_stamps[current_comp]->getID(), current_atom->getType());
697	>	painCave.isFatal = 1;
698	>	simError();
699	>	}
700
701	+	pos[0] = x + current_atom->getPosX();
702	+	pos[1] = y + current_atom->getPosY();
703	+	pos[2] = z + current_atom->getPosZ();
704
705	<	#ifdef IS_MPI
787	<	mpiSim->mpiRefresh();
788	<	#endif
705	>	info[0].atoms[current_atom_ndx]->setPos(pos);
706
707	<	// initialize the Fortran
707	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
708	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
709
710	+	rotMat[0][0] = 1.0;
711	+	rotMat[0][1] = 0.0;
712	+	rotMat[0][2] = 0.0;
713
714	<	simnfo->refreshSim();
715	<
716	<	if( !strcmp( simnfo->mixingRule, "standard") ){
717	<	the_ff->initForceField( LB_MIXING_RULE );
714	>	rotMat[1][0] = 0.0;
715	>	rotMat[1][1] = 1.0;
716	>	rotMat[1][2] = 0.0;
717	>
718	>	rotMat[2][0] = 0.0;
719	>	rotMat[2][1] = 0.0;
720	>	rotMat[2][2] = 1.0;
721	>
722	>	dAtom->setA(rotMat);
723	>	}
724	>
725	>	current_atom_ndx++;
726		}
798	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
799	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
800	–	}
801	–	else{
802	–	sprintf( painCave.errMsg,
803	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
804	–	simnfo->mixingRule );
805	–	painCave.isFatal = 1;
806	–	simError();
807	–	}
727
728	+	current_mol++;
729	+	current_comp_mol++;
730
731	<	#ifdef IS_MPI
732	<	strcpy( checkPointMsg,
733	<	"Successfully intialized the mixingRule for Fortran." );
734	<	MPIcheckPoint();
814	<	#endif // is_mpi
731	>	if (current_comp_mol >= components_nmol[current_comp]){
732	>	current_comp_mol = 0;
733	>	current_comp++;
734	>	}
735		}
736
737
738	<	void SimSetup::makeMolecules( void ){
738	>	void SimSetup::gatherInfo(void){
739	>	int i;
740
741	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
742	<	molInit info;
822	<	DirectionalAtom* dAtom;
823	<	LinkedAssign* extras;
824	<	LinkedAssign* current_extra;
825	<	AtomStamp* currentAtom;
826	<	BondStamp* currentBond;
827	<	BendStamp* currentBend;
828	<	TorsionStamp* currentTorsion;
741	>	ensembleCase = -1;
742	>	ffCase = -1;
743
744	<	bond_pair* theBonds;
831	<	bend_set* theBends;
832	<	torsion_set* theTorsions;
744	>	// set the easy ones first
745
746	<
747	<	//init the forceField paramters
746	>	for (i = 0; i < nInfo; i++){
747	>	info[i].target_temp = globals->getTargetTemp();
748	>	info[i].dt = globals->getDt();
749	>	info[i].run_time = globals->getRunTime();
750	>	}
751	>	n_components = globals->getNComponents();
752
837	–	the_ff->readParams();
753
754	<
840	<	// init the atoms
754	>	// get the forceField
755
756	<	double ux, uy, uz, u, uSqr;
843	<
844	<	atomOffset = 0;
845	<	excludeOffset = 0;
846	<	for(i=0; i<simnfo->n_mol; i++){
847	<
848	<	stampID = the_molecules[i].getStampID();
756	>	strcpy(force_field, globals->getForceField());
757
758	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
759	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
760	<	info.nBends    = comp_stamps[stampID]->getNBends();
761	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
762	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
763	<
764	<	info.myAtoms = &the_atoms[atomOffset];
765	<	info.myExcludes = &the_excludes[excludeOffset];
766	<	info.myBonds = new Bond*[info.nBonds];
767	<	info.myBends = new Bend*[info.nBends];
768	<	info.myTorsions = new Torsion*[info.nTorsions];
758	>	if (!strcasecmp(force_field, "DUFF")){
759	>	ffCase = FF_DUFF;
760	>	}
761	>	else if (!strcasecmp(force_field, "LJ")){
762	>	ffCase = FF_LJ;
763	>	}
764	>	else if (!strcasecmp(force_field, "EAM")){
765	>	ffCase = FF_EAM;
766	>	}
767	>	else if (!strcasecmp(force_field, "WATER")){
768	>	ffCase = FF_H2O;
769	>	}
770	>	else{
771	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
772	>	force_field);
773	>	painCave.isFatal = 1;
774	>	simError();
775	>	}
776
777	<	theBonds = new bond_pair[info.nBonds];
778	<	theBends = new bend_set[info.nBends];
779	<	theTorsions = new torsion_set[info.nTorsions];
780	<
781	<	// make the Atoms
782	<
783	<	for(j=0; j<info.nAtoms; j++){
784	<
785	<	currentAtom = comp_stamps[stampID]->getAtom( j );
786	<	if( currentAtom->haveOrientation() ){
787	<
788	<	dAtom = new DirectionalAtom(j + atomOffset);
789	<	simnfo->n_oriented++;
790	<	info.myAtoms[j] = dAtom;
791	<
792	<	ux = currentAtom->getOrntX();
793	<	uy = currentAtom->getOrntY();
794	<	uz = currentAtom->getOrntZ();
795	<
796	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
797	<
798	<	u = sqrt( uSqr );
799	<	ux = ux / u;
800	<	uy = uy / u;
801	<	uz = uz / u;
802	<
803	<	dAtom->setSUx( ux );
804	<	dAtom->setSUy( uy );
805	<	dAtom->setSUz( uz );
777	>	// get the ensemble
778	>
779	>	strcpy(ensemble, globals->getEnsemble());
780	>
781	>	if (!strcasecmp(ensemble, "NVE")){
782	>	ensembleCase = NVE_ENS;
783	>	}
784	>	else if (!strcasecmp(ensemble, "NVT")){
785	>	ensembleCase = NVT_ENS;
786	>	}
787	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
788	>	ensembleCase = NPTi_ENS;
789	>	}
790	>	else if (!strcasecmp(ensemble, "NPTf")){
791	>	ensembleCase = NPTf_ENS;
792	>	}
793	>	else if (!strcasecmp(ensemble, "NPTxyz")){
794	>	ensembleCase = NPTxyz_ENS;
795	>	}
796	>	else{
797	>	sprintf(painCave.errMsg,
798	>	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
799	>	"\treverting to NVE for this simulation.\n",
800	>	ensemble);
801	>	painCave.isFatal = 0;
802	>	simError();
803	>	strcpy(ensemble, "NVE");
804	>	ensembleCase = NVE_ENS;
805	>	}
806	>
807	>	for (i = 0; i < nInfo; i++){
808	>	strcpy(info[i].ensemble, ensemble);
809	>
810	>	// get the mixing rule
811	>
812	>	strcpy(info[i].mixingRule, globals->getMixingRule());
813	>	info[i].usePBC = globals->getPBC();
814	>	}
815	>
816	>	// get the components and calculate the tot_nMol and indvidual n_mol
817	>
818	>	the_components = globals->getComponents();
819	>	components_nmol = new int[n_components];
820	>
821	>
822	>	if (!globals->haveNMol()){
823	>	// we don't have the total number of molecules, so we assume it is
824	>	// given in each component
825	>
826	>	tot_nmol = 0;
827	>	for (i = 0; i < n_components; i++){
828	>	if (!the_components[i]->haveNMol()){
829	>	// we have a problem
830	>	sprintf(painCave.errMsg,
831	>	"SimSetup Error. No global NMol or component NMol given.\n"
832	>	"\tCannot calculate the number of atoms.\n");
833	>	painCave.isFatal = 1;
834	>	simError();
835		}
836	<	else{
837	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
838	<	}
839	<	info.myAtoms[j]->setType( currentAtom->getType() );
836	>
837	>	tot_nmol += the_components[i]->getNMol();
838	>	components_nmol[i] = the_components[i]->getNMol();
839	>	}
840	>	}
841	>	else{
842	>	sprintf(painCave.errMsg,
843	>	"SimSetup error.\n"
844	>	"\tSorry, the ability to specify total"
845	>	" nMols and then give molfractions in the components\n"
846	>	"\tis not currently supported."
847	>	" Please give nMol in the components.\n");
848	>	painCave.isFatal = 1;
849	>	simError();
850	>	}
851	>
852	>	//check whether sample time, status time, thermal time and reset time are divisble by dt
853	>	if (globals->haveSampleTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
854	>	sprintf(painCave.errMsg,
855	>	"Sample time is not divisible by dt.\n"
856	>	"\tThis will result in samples that are not uniformly\n"
857	>	"\tdistributed in time.  If this is a problem, change\n"
858	>	"\tyour sampleTime variable.\n");
859	>	painCave.isFatal = 0;
860	>	simError();
861	>	}
862	>
863	>	if (globals->haveStatusTime() && !isDivisible(globals->getStatusTime(), globals->getDt())){
864	>	sprintf(painCave.errMsg,
865	>	"Status time is not divisible by dt.\n"
866	>	"\tThis will result in status reports that are not uniformly\n"
867	>	"\tdistributed in time.  If this is a problem, change \n"
868	>	"\tyour statusTime variable.\n");
869	>	painCave.isFatal = 0;
870	>	simError();
871	>	}
872	>
873	>	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
874	>	sprintf(painCave.errMsg,
875	>	"Thermal time is not divisible by dt.\n"
876	>	"\tThis will result in thermalizations that are not uniformly\n"
877	>	"\tdistributed in time.  If this is a problem, change \n"
878	>	"\tyour thermalTime variable.\n");
879	>	painCave.isFatal = 0;
880	>	simError();
881	>	}
882	>
883	>	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
884	>	sprintf(painCave.errMsg,
885	>	"Reset time is not divisible by dt.\n"
886	>	"\tThis will result in integrator resets that are not uniformly\n"
887	>	"\tdistributed in time.  If this is a problem, change\n"
888	>	"\tyour resetTime variable.\n");
889	>	painCave.isFatal = 0;
890	>	simError();
891	>	}
892	>
893	>	// set the status, sample, and thermal kick times
894	>
895	>	for (i = 0; i < nInfo; i++){
896	>	if (globals->haveSampleTime()){
897	>	info[i].sampleTime = globals->getSampleTime();
898	>	info[i].statusTime = info[i].sampleTime;
899	>	}
900	>	else{
901	>	info[i].sampleTime = globals->getRunTime();
902	>	info[i].statusTime = info[i].sampleTime;
903	>	}
904	>
905	>	if (globals->haveStatusTime()){
906	>	info[i].statusTime = globals->getStatusTime();
907	>	}
908	>
909	>	if (globals->haveThermalTime()){
910	>	info[i].thermalTime = globals->getThermalTime();
911	>	} else {
912	>	info[i].thermalTime = globals->getRunTime();
913	>	}
914	>
915	>	info[i].resetIntegrator = 0;
916	>	if( globals->haveResetTime() ){
917	>	info[i].resetTime = globals->getResetTime();
918	>	info[i].resetIntegrator = 1;
919	>	}
920	>
921	>	// check for the temperature set flag
922
923	<	#ifdef IS_MPI
924	<
925	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
926	<
927	<	#endif // is_mpi
928	<	}
923	>	if (globals->haveTempSet())
924	>	info[i].setTemp = globals->getTempSet();
925	>
926	>	// check for the extended State init
927	>
928	>	info[i].useInitXSstate = globals->getUseInitXSstate();
929	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
930
931	<	// make the bonds
932	<	for(j=0; j<info.nBonds; j++){
933	<
934	<	currentBond = comp_stamps[stampID]->getBond( j );
908	<	theBonds[j].a = currentBond->getA() + atomOffset;
909	<	theBonds[j].b = currentBond->getB() + atomOffset;
931	>	}
932	>
933	>	//setup seed for random number generator
934	>	int seedValue;
935
936	<	exI = theBonds[j].a;
937	<	exJ = theBonds[j].b;
936	>	if (globals->haveSeed()){
937	>	seedValue = globals->getSeed();
938
939	<	// exclude_I must always be the smaller of the pair
940	<	if( exI > exJ ){
941	<	tempEx = exI;
942	<	exI = exJ;
943	<	exJ = tempEx;
939	>	if(seedValue / 1E9 == 0){
940	>	sprintf(painCave.errMsg,
941	>	"Seed for sprng library should contain at least 9 digits\n"
942	>	"OOPSE will generate a seed for user\n");
943	>	painCave.isFatal = 0;
944	>	simError();
945	>
946	>	//using seed generated by system instead of invalid seed set by user
947	>	#ifndef IS_MPI
948	>	seedValue = make_sprng_seed();
949	>	#else
950	>	if (worldRank == 0){
951	>	seedValue = make_sprng_seed();
952		}
953	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
954	+	#endif
955	+	}
956	+	}//end of if branch of globals->haveSeed()
957	+	else{
958	+
959	+	#ifndef IS_MPI
960	+	seedValue = make_sprng_seed();
961	+	#else
962	+	if (worldRank == 0){
963	+	seedValue = make_sprng_seed();
964	+	}
965	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
966	+	#endif
967	+	}//end of globals->haveSeed()
968	+
969	+	for (int i = 0; i < nInfo; i++){
970	+	info[i].setSeed(seedValue);
971	+	}
972	+
973		#ifdef IS_MPI
974	<	tempEx = exI;
975	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
976	<	tempEx = exJ;
977	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
974	>	strcpy(checkPointMsg, "Successfully gathered all information from Bass\n");
975	>	MPIcheckPoint();
976	>	#endif // is_mpi
977	>	}
978	>
979	>
980	>	void SimSetup::finalInfoCheck(void){
981	>	int index;
982	>	int usesDipoles;
983	>	int usesCharges;
984	>	int i;
985	>
986	>	for (i = 0; i < nInfo; i++){
987	>	// check electrostatic parameters
988	>
989	>	index = 0;
990	>	usesDipoles = 0;
991	>	while ((index < info[i].n_atoms) && !usesDipoles){
992	>	usesDipoles = (info[i].atoms[index])->hasDipole();
993	>	index++;
994	>	}
995	>	index = 0;
996	>	usesCharges = 0;
997	>	while ((index < info[i].n_atoms) && !usesCharges){
998	>	usesCharges= (info[i].atoms[index])->hasCharge();
999	>	index++;
1000	>	}
1001	>	#ifdef IS_MPI
1002	>	int myUse = usesDipoles;
1003	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
1004	>	#endif //is_mpi
1005	>
1006	>	double theRcut, theRsw;
1007	>
1008	>	if (globals->haveRcut()) {
1009	>	theRcut = globals->getRcut();
1010	>
1011	>	if (globals->haveRsw())
1012	>	theRsw = globals->getRsw();
1013	>	else
1014	>	theRsw = theRcut;
1015
1016	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
927	<	#else  // isn't MPI
1016	>	info[i].setDefaultRcut(theRcut, theRsw);
1017
1018	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1019	<	#endif  //is_mpi
1018	>	} else {
1019	>
1020	>	the_ff->calcRcut();
1021	>	theRcut = info[i].getRcut();
1022	>
1023	>	if (globals->haveRsw())
1024	>	theRsw = globals->getRsw();
1025	>	else
1026	>	theRsw = theRcut;
1027	>
1028	>	info[i].setDefaultRcut(theRcut, theRsw);
1029		}
932	–	excludeOffset += info.nBonds;
1030
1031	<	//make the bends
1032	<	for(j=0; j<info.nBends; j++){
1031	>	if (globals->getUseRF()){
1032	>	info[i].useReactionField = 1;
1033
1034	<	currentBend = comp_stamps[stampID]->getBend( j );
1035	<	theBends[j].a = currentBend->getA() + atomOffset;
1036	<	theBends[j].b = currentBend->getB() + atomOffset;
1037	<	theBends[j].c = currentBend->getC() + atomOffset;
1038	<
1039	<	if( currentBend->haveExtras() ){
1040	<
1041	<	extras = currentBend->getExtras();
945	<	current_extra = extras;
946	<
947	<	while( current_extra != NULL ){
948	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
949	<
950	<	switch( current_extra->getType() ){
951	<
952	<	case 0:
953	<	theBends[j].ghost =
954	<	current_extra->getInt() + atomOffset;
955	<	theBends[j].isGhost = 1;
956	<	break;
957	<
958	<	case 1:
959	<	theBends[j].ghost =
960	<	(int)current_extra->getDouble() + atomOffset;
961	<	theBends[j].isGhost = 1;
962	<	break;
963	<
964	<	default:
965	<	sprintf( painCave.errMsg,
966	<	"SimSetup Error: ghostVectorSource was neither a "
967	<	"double nor an int.\n"
968	<	"-->Bend[%d] in %s\n",
969	<	j, comp_stamps[stampID]->getID() );
970	<	painCave.isFatal = 1;
971	<	simError();
972	<	}
973	<	}
974	<
975	<	else{
976	<
977	<	sprintf( painCave.errMsg,
978	<	"SimSetup Error: unhandled bend assignment:\n"
979	<	"    -->%s in Bend[%d] in %s\n",
980	<	current_extra->getlhs(),
981	<	j, comp_stamps[stampID]->getID() );
982	<	painCave.isFatal = 1;
983	<	simError();
984	<	}
985	<
986	<	current_extra = current_extra->getNext();
987	<	}
1034	>	if (!globals->haveRcut()){
1035	>	sprintf(painCave.errMsg,
1036	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1037	>	"\tOOPSE will use a default value of 15.0 angstroms"
1038	>	"\tfor the cutoffRadius.\n");
1039	>	painCave.isFatal = 0;
1040	>	simError();
1041	>	theRcut = 15.0;
1042		}
1043	<
1044	<	if( !theBends[j].isGhost ){
991	<
992	<	exI = theBends[j].a;
993	<	exJ = theBends[j].c;
1043	>	else{
1044	>	theRcut = globals->getRcut();
1045		}
1046	+
1047	+	if (!globals->haveRsw()){
1048	+	sprintf(painCave.errMsg,
1049	+	"SimSetup Warning: No value was set for switchingRadius.\n"
1050	+	"\tOOPSE will use a default value of\n"
1051	+	"\t0.95 * cutoffRadius for the switchingRadius\n");
1052	+	painCave.isFatal = 0;
1053	+	simError();
1054	+	theRsw = 0.95 * theRcut;
1055	+	}
1056		else{
1057	<
997	<	exI = theBends[j].a;
998	<	exJ = theBends[j].b;
1057	>	theRsw = globals->getRsw();
1058		}
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;
1059	>
1060	>	info[i].setDefaultRcut(theRcut, theRsw);
1061	>
1062	>	if (!globals->haveDielectric()){
1063	>	sprintf(painCave.errMsg,
1064	>	"SimSetup Error: No Dielectric constant was set.\n"
1065	>	"\tYou are trying to use Reaction Field without"
1066	>	"\tsetting a dielectric constant!\n");
1067	>	painCave.isFatal = 1;
1068	>	simError();
1069		}
1070	<	#ifdef IS_MPI
1008	<	tempEx = exI;
1009	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1010	<	tempEx = exJ;
1011	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1012	<
1013	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1014	<	#else  // isn't MPI
1015	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1016	<	#endif  //is_mpi
1070	>	info[i].dielectric = globals->getDielectric();
1071		}
1072	<	excludeOffset += info.nBends;
1072	>	else{
1073	>	if (usesDipoles || usesCharges){
1074
1075	<	for(j=0; j<info.nTorsions; j++){
1076	<
1077	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
1078	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
1079	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
1080	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
1081	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
1082	<
1028	<	exI = theTorsions[j].a;
1029	<	exJ = theTorsions[j].d;
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;
1075	>	if (!globals->haveRcut()){
1076	>	sprintf(painCave.errMsg,
1077	>	"SimSetup Warning: No value was set for the cutoffRadius.\n"
1078	>	"\tOOPSE will use a default value of 15.0 angstroms"
1079	>	"\tfor the cutoffRadius.\n");
1080	>	painCave.isFatal = 0;
1081	>	simError();
1082	>	theRcut = 15.0;
1083		}
1084	<	#ifdef IS_MPI
1085	<	tempEx = exI;
1086	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
1087	<	tempEx = exJ;
1088	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
1089	<
1090	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
1091	<	#else  // isn't MPI
1092	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
1093	<	#endif  //is_mpi
1084	>	else{
1085	>	theRcut = globals->getRcut();
1086	>	}
1087	>
1088	>	if (!globals->haveRsw()){
1089	>	sprintf(painCave.errMsg,
1090	>	"SimSetup Warning: No value was set for switchingRadius.\n"
1091	>	"\tOOPSE will use a default value of\n"
1092	>	"\t0.95 * cutoffRadius for the switchingRadius\n");
1093	>	painCave.isFatal = 0;
1094	>	simError();
1095	>	theRsw = 0.95 * theRcut;
1096	>	}
1097	>	else{
1098	>	theRsw = globals->getRsw();
1099	>	}
1100	>
1101	>	info[i].setDefaultRcut(theRcut, theRsw);
1102	>
1103	>	}
1104		}
1105	<	excludeOffset += info.nTorsions;
1105	>	}
1106	>	#ifdef IS_MPI
1107	>	strcpy(checkPointMsg, "post processing checks out");
1108	>	MPIcheckPoint();
1109	>	#endif // is_mpi
1110
1111	<
1112	<	// send the arrays off to the forceField for init.
1111	>	// clean up the forcefield
1112	>	the_ff->cleanMe();
1113	>	}
1114	>
1115	>	void SimSetup::initSystemCoords(void){
1116	>	int i;
1117
1118	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
1054	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
1055	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
1056	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
1118	>	char* inName;
1119
1120	+	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
1121
1122	<	the_molecules[i].initialize( info );
1122	>	for (i = 0; i < info[0].n_atoms; i++)
1123	>	info[0].atoms[i]->setCoords();
1124
1125	+	if (globals->haveInitialConfig()){
1126	+	InitializeFromFile* fileInit;
1127	+	#ifdef IS_MPI // is_mpi
1128	+	if (worldRank == 0){
1129	+	#endif //is_mpi
1130	+	inName = globals->getInitialConfig();
1131	+	fileInit = new InitializeFromFile(inName);
1132	+	#ifdef IS_MPI
1133	+	}
1134	+	else
1135	+	fileInit = new InitializeFromFile(NULL);
1136	+	#endif
1137	+	fileInit->readInit(info); // default velocities on
1138
1139	<	atomOffset += info.nAtoms;
1063	<	delete[] theBonds;
1064	<	delete[] theBends;
1065	<	delete[] theTorsions;
1139	>	delete fileInit;
1140		}
1141	+	else{
1142	+
1143	+	// no init from bass
1144	+
1145	+	sprintf(painCave.errMsg,
1146	+	"Cannot intialize a simulation without an initial configuration file.\n");
1147	+	painCave.isFatal = 1;;
1148	+	simError();
1149	+
1150	+	}
1151
1152		#ifdef IS_MPI
1153	<	sprintf( checkPointMsg, "all molecules initialized succesfully" );
1153	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
1154		MPIcheckPoint();
1155		#endif // is_mpi
1156	+	}
1157
1073	–	// clean up the forcefield
1074	–	the_ff->calcRcut();
1075	–	the_ff->cleanMe();
1158
1159	<	}
1159	>	void SimSetup::makeOutNames(void){
1160	>	int k;
1161
1079	–	void SimSetup::initFromBass( void ){
1162
1163	<	int i, j, k;
1164	<	int n_cells;
1165	<	double cellx, celly, cellz;
1166	<	double temp1, temp2, temp3;
1085	<	int n_per_extra;
1086	<	int n_extra;
1087	<	int have_extra, done;
1163	>	for (k = 0; k < nInfo; k++){
1164	>	#ifdef IS_MPI
1165	>	if (worldRank == 0){
1166	>	#endif // is_mpi
1167
1168	<	temp1 = (double)tot_nmol / 4.0;
1169	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1170	<	temp3 = ceil( temp2 );
1168	>	if (globals->haveFinalConfig()){
1169	>	strcpy(info[k].finalName, globals->getFinalConfig());
1170	>	}
1171	>	else{
1172	>	strcpy(info[k].finalName, inFileName);
1173	>	char* endTest;
1174	>	int nameLength = strlen(info[k].finalName);
1175	>	endTest = &(info[k].finalName[nameLength - 5]);
1176	>	if (!strcmp(endTest, ".bass")){
1177	>	strcpy(endTest, ".eor");
1178	>	}
1179	>	else if (!strcmp(endTest, ".BASS")){
1180	>	strcpy(endTest, ".eor");
1181	>	}
1182	>	else{
1183	>	endTest = &(info[k].finalName[nameLength - 4]);
1184	>	if (!strcmp(endTest, ".bss")){
1185	>	strcpy(endTest, ".eor");
1186	>	}
1187	>	else if (!strcmp(endTest, ".mdl")){
1188	>	strcpy(endTest, ".eor");
1189	>	}
1190	>	else{
1191	>	strcat(info[k].finalName, ".eor");
1192	>	}
1193	>	}
1194	>	}
1195
1196	<	have_extra =0;
1094	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1095	<	have_extra =1;
1196	>	// make the sample and status out names
1197
1198	<	n_cells = (int)temp3 - 1;
1199	<	cellx = simnfo->box_x / temp3;
1200	<	celly = simnfo->box_y / temp3;
1201	<	cellz = simnfo->box_z / temp3;
1202	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1203	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1204	<	n_per_extra = (int)ceil( temp1 );
1198	>	strcpy(info[k].sampleName, inFileName);
1199	>	char* endTest;
1200	>	int nameLength = strlen(info[k].sampleName);
1201	>	endTest = &(info[k].sampleName[nameLength - 5]);
1202	>	if (!strcmp(endTest, ".bass")){
1203	>	strcpy(endTest, ".dump");
1204	>	}
1205	>	else if (!strcmp(endTest, ".BASS")){
1206	>	strcpy(endTest, ".dump");
1207	>	}
1208	>	else{
1209	>	endTest = &(info[k].sampleName[nameLength - 4]);
1210	>	if (!strcmp(endTest, ".bss")){
1211	>	strcpy(endTest, ".dump");
1212	>	}
1213	>	else if (!strcmp(endTest, ".mdl")){
1214	>	strcpy(endTest, ".dump");
1215	>	}
1216	>	else{
1217	>	strcat(info[k].sampleName, ".dump");
1218	>	}
1219	>	}
1220
1221	<	if( n_per_extra > 4){
1222	<	sprintf( painCave.errMsg,
1223	<	"SimSetup error. There has been an error in constructing"
1224	<	" the non-complete lattice.\n" );
1225	<	painCave.isFatal = 1;
1226	<	simError();
1221	>	strcpy(info[k].statusName, inFileName);
1222	>	nameLength = strlen(info[k].statusName);
1223	>	endTest = &(info[k].statusName[nameLength - 5]);
1224	>	if (!strcmp(endTest, ".bass")){
1225	>	strcpy(endTest, ".stat");
1226	>	}
1227	>	else if (!strcmp(endTest, ".BASS")){
1228	>	strcpy(endTest, ".stat");
1229	>	}
1230	>	else{
1231	>	endTest = &(info[k].statusName[nameLength - 4]);
1232	>	if (!strcmp(endTest, ".bss")){
1233	>	strcpy(endTest, ".stat");
1234	>	}
1235	>	else if (!strcmp(endTest, ".mdl")){
1236	>	strcpy(endTest, ".stat");
1237	>	}
1238	>	else{
1239	>	strcat(info[k].statusName, ".stat");
1240	>	}
1241	>	}
1242	>
1243	>	#ifdef IS_MPI
1244	>
1245		}
1246	+	#endif // is_mpi
1247		}
1248	<	else{
1249	<	n_cells = (int)temp3;
1250	<	cellx = simnfo->box_x / temp3;
1251	<	celly = simnfo->box_y / temp3;
1252	<	cellz = simnfo->box_z / temp3;
1248	>	}
1249	>
1250	>
1251	>	void SimSetup::sysObjectsCreation(void){
1252	>	int i, k;
1253	>
1254	>	// create the forceField
1255	>
1256	>	createFF();
1257	>
1258	>	// extract componentList
1259	>
1260	>	compList();
1261	>
1262	>	// calc the number of atoms, bond, bends, and torsions
1263	>
1264	>	calcSysValues();
1265	>
1266	>	#ifdef IS_MPI
1267	>	// divide the molecules among the processors
1268	>
1269	>	mpiMolDivide();
1270	>	#endif //is_mpi
1271	>
1272	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1273	>
1274	>	makeSysArrays();
1275	>
1276	>	// make and initialize the molecules (all but atomic coordinates)
1277	>
1278	>	makeMolecules();
1279	>
1280	>	for (k = 0; k < nInfo; k++){
1281	>	info[k].identArray = new int[info[k].n_atoms];
1282	>	for (i = 0; i < info[k].n_atoms; i++){
1283	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1284	>	}
1285		}
1286	+	}
1287
1120	–	current_mol = 0;
1121	–	current_comp_mol = 0;
1122	–	current_comp = 0;
1123	–	current_atom_ndx = 0;
1288
1289	<	for( i=0; i < n_cells ; i++ ){
1290	<	for( j=0; j < n_cells; j++ ){
1291	<	for( k=0; k < n_cells; k++ ){
1289	>	void SimSetup::createFF(void){
1290	>	switch (ffCase){
1291	>	case FF_DUFF:
1292	>	the_ff = new DUFF();
1293	>	break;
1294
1295	<	makeElement( i * cellx,
1296	<	j * celly,
1297	<	k * cellz );
1295	>	case FF_LJ:
1296	>	the_ff = new LJFF();
1297	>	break;
1298
1299	<	makeElement( i * cellx + 0.5 * cellx,
1300	<	j * celly + 0.5 * celly,
1301	<	k * cellz );
1299	>	case FF_EAM:
1300	>	the_ff = new EAM_FF();
1301	>	break;
1302
1303	<	makeElement( i * cellx,
1304	<	j * celly + 0.5 * celly,
1305	<	k * cellz + 0.5 * cellz );
1303	>	case FF_H2O:
1304	>	the_ff = new WATER();
1305	>	break;
1306
1307	<	makeElement( i * cellx + 0.5 * cellx,
1308	<	j * celly,
1309	<	k * cellz + 0.5 * cellz );
1307	>	default:
1308	>	sprintf(painCave.errMsg,
1309	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1310	>	painCave.isFatal = 1;
1311	>	simError();
1312	>	}
1313	>
1314	>	#ifdef IS_MPI
1315	>	strcpy(checkPointMsg, "ForceField creation successful");
1316	>	MPIcheckPoint();
1317	>	#endif // is_mpi
1318	>	}
1319	>
1320	>
1321	>	void SimSetup::compList(void){
1322	>	int i;
1323	>	char* id;
1324	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1325	>	LinkedMolStamp* currentStamp = NULL;
1326	>	comp_stamps = new MoleculeStamp * [n_components];
1327	>	bool haveCutoffGroups;
1328	>
1329	>	haveCutoffGroups = false;
1330	>
1331	>	// make an array of molecule stamps that match the components used.
1332	>	// also extract the used stamps out into a separate linked list
1333	>
1334	>	for (i = 0; i < nInfo; i++){
1335	>	info[i].nComponents = n_components;
1336	>	info[i].componentsNmol = components_nmol;
1337	>	info[i].compStamps = comp_stamps;
1338	>	info[i].headStamp = headStamp;
1339	>	}
1340	>
1341	>
1342	>	for (i = 0; i < n_components; i++){
1343	>	id = the_components[i]->getType();
1344	>	comp_stamps[i] = NULL;
1345	>
1346	>	// check to make sure the component isn't already in the list
1347	>
1348	>	comp_stamps[i] = headStamp->match(id);
1349	>	if (comp_stamps[i] == NULL){
1350	>	// extract the component from the list;
1351	>
1352	>	currentStamp = stamps->extractMolStamp(id);
1353	>	if (currentStamp == NULL){
1354	>	sprintf(painCave.errMsg,
1355	>	"SimSetup error: Component \"%s\" was not found in the "
1356	>	"list of declared molecules\n",
1357	>	id);
1358	>	painCave.isFatal = 1;
1359	>	simError();
1360		}
1361	+
1362	+	headStamp->add(currentStamp);
1363	+	comp_stamps[i] = headStamp->match(id);
1364		}
1365	+
1366	+	if(comp_stamps[i]->getNCutoffGroups() > 0)
1367	+	haveCutoffGroups = true;
1368		}
1369	+
1370	+	for (i = 0; i < nInfo; i++)
1371	+	info[i].haveCutoffGroups = haveCutoffGroups;
1372
1373	<	if( have_extra ){
1374	<	done = 0;
1373	>	#ifdef IS_MPI
1374	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1375	>	MPIcheckPoint();
1376	>	#endif // is_mpi
1377	>	}
1378
1379	<	int start_ndx;
1380	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1153	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1379	>	void SimSetup::calcSysValues(void){
1380	>	int i;
1381
1382	<	if( i < n_cells ){
1382	>	int* molMembershipArray;
1383
1384	<	if( j < n_cells ){
1385	<	start_ndx = n_cells;
1386	<	}
1387	<	else start_ndx = 0;
1388	<	}
1389	<	else start_ndx = 0;
1384	>	tot_atoms = 0;
1385	>	tot_bonds = 0;
1386	>	tot_bends = 0;
1387	>	tot_torsions = 0;
1388	>	tot_rigid = 0;
1389	>	for (i = 0; i < n_components; i++){
1390	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1391	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1392	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1393	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1394	>	tot_rigid += components_nmol[i] * comp_stamps[i]->getNRigidBodies();
1395	>	}
1396	>
1397	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1398	>	molMembershipArray = new int[tot_atoms];
1399
1400	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1400	>	for (i = 0; i < nInfo; i++){
1401	>	info[i].n_atoms = tot_atoms;
1402	>	info[i].n_bonds = tot_bonds;
1403	>	info[i].n_bends = tot_bends;
1404	>	info[i].n_torsions = tot_torsions;
1405	>	info[i].n_SRI = tot_SRI;
1406	>	info[i].n_mol = tot_nmol;
1407
1408	<	makeElement( i * cellx,
1409	<	j * celly,
1410	<	k * cellz );
1169	<	done = ( current_mol >= tot_nmol );
1408	>	info[i].molMembershipArray = molMembershipArray;
1409	>	}
1410	>	}
1411
1412	<	if( !done && n_per_extra > 1 ){
1172	<	makeElement( i * cellx + 0.5 * cellx,
1173	<	j * celly + 0.5 * celly,
1174	<	k * cellz );
1175	<	done = ( current_mol >= tot_nmol );
1176	<	}
1412	>	#ifdef IS_MPI
1413
1414	<	if( !done && n_per_extra > 2){
1415	<	makeElement( i * cellx,
1416	<	j * celly + 0.5 * celly,
1417	<	k * cellz + 0.5 * cellz );
1418	<	done = ( current_mol >= tot_nmol );
1419	<	}
1414	>	void SimSetup::mpiMolDivide(void){
1415	>	int i, j, k;
1416	>	int localMol, allMol;
1417	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1418	>	int local_rigid;
1419	>	vector<int> globalMolIndex;
1420
1421	<	if( !done && n_per_extra > 3){
1422	<	makeElement( i * cellx + 0.5 * cellx,
1423	<	j * celly,
1424	<	k * cellz + 0.5 * cellz );
1425	<	done = ( current_mol >= tot_nmol );
1426	<	}
1427	<	}
1421	>	mpiSim = new mpiSimulation(info);
1422	>
1423	>	mpiSim->divideLabor();
1424	>	globalAtomIndex = mpiSim->getGlobalAtomIndex();
1425	>	//globalMolIndex = mpiSim->getGlobalMolIndex();
1426	>
1427	>	// set up the local variables
1428	>
1429	>	mol2proc = mpiSim->getMolToProcMap();
1430	>	molCompType = mpiSim->getMolComponentType();
1431	>
1432	>	allMol = 0;
1433	>	localMol = 0;
1434	>	local_atoms = 0;
1435	>	local_bonds = 0;
1436	>	local_bends = 0;
1437	>	local_torsions = 0;
1438	>	local_rigid = 0;
1439	>	globalAtomCounter = 0;
1440	>
1441	>	for (i = 0; i < n_components; i++){
1442	>	for (j = 0; j < components_nmol[i]; j++){
1443	>	if (mol2proc[allMol] == worldRank){
1444	>	local_atoms += comp_stamps[i]->getNAtoms();
1445	>	local_bonds += comp_stamps[i]->getNBonds();
1446	>	local_bends += comp_stamps[i]->getNBends();
1447	>	local_torsions += comp_stamps[i]->getNTorsions();
1448	>	local_rigid += comp_stamps[i]->getNRigidBodies();
1449	>	localMol++;
1450	>	}
1451	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1452	>	info[0].molMembershipArray[globalAtomCounter] = allMol;
1453	>	globalAtomCounter++;
1454		}
1455	+
1456	+	allMol++;
1457		}
1458		}
1459	+	local_SRI = local_bonds + local_bends + local_torsions;
1460
1461	+	info[0].n_atoms = mpiSim->getMyNlocal();
1462	+
1463
1464	<	for( i=0; i<simnfo->n_atoms; i++ ){
1465	<	simnfo->atoms[i]->set_vx( 0.0 );
1466	<	simnfo->atoms[i]->set_vy( 0.0 );
1467	<	simnfo->atoms[i]->set_vz( 0.0 );
1464	>	if (local_atoms != info[0].n_atoms){
1465	>	sprintf(painCave.errMsg,
1466	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1467	>	"\tlocalAtom (%d) are not equal.\n",
1468	>	info[0].n_atoms, local_atoms);
1469	>	painCave.isFatal = 1;
1470	>	simError();
1471		}
1472	+
1473	+	info[0].n_bonds = local_bonds;
1474	+	info[0].n_bends = local_bends;
1475	+	info[0].n_torsions = local_torsions;
1476	+	info[0].n_SRI = local_SRI;
1477	+	info[0].n_mol = localMol;
1478	+
1479	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1480	+	MPIcheckPoint();
1481		}
1482
1483	<	void SimSetup::makeElement( double x, double y, double z ){
1483	>	#endif // is_mpi
1484
1206	–	int k;
1207	–	AtomStamp* current_atom;
1208	–	DirectionalAtom* dAtom;
1209	–	double rotMat[3][3];
1485
1486	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1486	>	void SimSetup::makeSysArrays(void){
1487	>
1488	>	#ifndef IS_MPI
1489	>	int k, j;
1490	>	#endif // is_mpi
1491	>	int i, l;
1492
1493	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1494	<	if( !current_atom->havePosition() ){
1215	<	sprintf( painCave.errMsg,
1216	<	"SimSetup:initFromBass error.\n"
1217	<	"\tComponent %s, atom %s does not have a position specified.\n"
1218	<	"\tThe initialization routine is unable to give a start"
1219	<	" position.\n",
1220	<	comp_stamps[current_comp]->getID(),
1221	<	current_atom->getType() );
1222	<	painCave.isFatal = 1;
1223	<	simError();
1224	<	}
1493	>	Atom** the_atoms;
1494	>	Molecule* the_molecules;
1495
1496	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1497	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1228	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1496	>	for (l = 0; l < nInfo; l++){
1497	>	// create the atom and short range interaction arrays
1498
1499	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1499	>	the_atoms = new Atom * [info[l].n_atoms];
1500	>	the_molecules = new Molecule[info[l].n_mol];
1501	>	int molIndex;
1502
1503	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1503	>	// initialize the molecule's stampID's
1504
1505	<	rotMat[0][0] = 1.0;
1235	<	rotMat[0][1] = 0.0;
1236	<	rotMat[0][2] = 0.0;
1505	>	#ifdef IS_MPI
1506
1238	–	rotMat[1][0] = 0.0;
1239	–	rotMat[1][1] = 1.0;
1240	–	rotMat[1][2] = 0.0;
1507
1508	<	rotMat[2][0] = 0.0;
1509	<	rotMat[2][1] = 0.0;
1510	<	rotMat[2][2] = 1.0;
1508	>	molIndex = 0;
1509	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1510	>	if (mol2proc[i] == worldRank){
1511	>	the_molecules[molIndex].setStampID(molCompType[i]);
1512	>	the_molecules[molIndex].setMyIndex(molIndex);
1513	>	the_molecules[molIndex].setGlobalIndex(i);
1514	>	molIndex++;
1515	>	}
1516	>	}
1517
1518	<	dAtom->setA( rotMat );
1518	>	#else // is_mpi
1519	>
1520	>	molIndex = 0;
1521	>	globalAtomCounter = 0;
1522	>	for (i = 0; i < n_components; i++){
1523	>	for (j = 0; j < components_nmol[i]; j++){
1524	>	the_molecules[molIndex].setStampID(i);
1525	>	the_molecules[molIndex].setMyIndex(molIndex);
1526	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1527	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1528	>	info[l].molMembershipArray[globalAtomCounter] = molIndex;
1529	>	globalAtomCounter++;
1530	>	}
1531	>	molIndex++;
1532	>	}
1533		}
1534
1249	–	current_atom_ndx++;
1250	–	}
1535
1536	<	current_mol++;
1253	<	current_comp_mol++;
1536	>	#endif // is_mpi
1537
1538	<	if( current_comp_mol >= components_nmol[current_comp] ){
1538	>	info[l].globalExcludes = new int;
1539	>	info[l].globalExcludes[0] = 0;
1540	>
1541	>	// set the arrays into the SimInfo object
1542
1543	<	current_comp_mol = 0;
1544	<	current_comp++;
1543	>	info[l].atoms = the_atoms;
1544	>	info[l].molecules = the_molecules;
1545	>	info[l].nGlobalExcludes = 0;
1546	>
1547	>	the_ff->setSimInfo(info);
1548		}
1549		}
1550	+
1551	+	void SimSetup::makeIntegrator(void){
1552	+	int k;
1553	+
1554	+	NVE<RealIntegrator>* myNVE = NULL;
1555	+	NVT<RealIntegrator>* myNVT = NULL;
1556	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1557	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1558	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1559	+
1560	+	for (k = 0; k < nInfo; k++){
1561	+	switch (ensembleCase){
1562	+	case NVE_ENS:
1563	+	if (globals->haveZconstraints()){
1564	+	setupZConstraint(info[k]);
1565	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1566	+	}
1567	+	else{
1568	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1569	+	}
1570	+
1571	+	info->the_integrator = myNVE;
1572	+	break;
1573	+
1574	+	case NVT_ENS:
1575	+	if (globals->haveZconstraints()){
1576	+	setupZConstraint(info[k]);
1577	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1578	+	}
1579	+	else
1580	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1581	+
1582	+	myNVT->setTargetTemp(globals->getTargetTemp());
1583	+
1584	+	if (globals->haveTauThermostat())
1585	+	myNVT->setTauThermostat(globals->getTauThermostat());
1586	+	else{
1587	+	sprintf(painCave.errMsg,
1588	+	"SimSetup error: If you use the NVT\n"
1589	+	"\tensemble, you must set tauThermostat.\n");
1590	+	painCave.isFatal = 1;
1591	+	simError();
1592	+	}
1593	+
1594	+	info->the_integrator = myNVT;
1595	+	break;
1596	+
1597	+	case NPTi_ENS:
1598	+	if (globals->haveZconstraints()){
1599	+	setupZConstraint(info[k]);
1600	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1601	+	}
1602	+	else
1603	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1604	+
1605	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1606	+
1607	+	if (globals->haveTargetPressure())
1608	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1609	+	else{
1610	+	sprintf(painCave.errMsg,
1611	+	"SimSetup error: If you use a constant pressure\n"
1612	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1613	+	painCave.isFatal = 1;
1614	+	simError();
1615	+	}
1616	+
1617	+	if (globals->haveTauThermostat())
1618	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1619	+	else{
1620	+	sprintf(painCave.errMsg,
1621	+	"SimSetup error: If you use an NPT\n"
1622	+	"\tensemble, you must set tauThermostat.\n");
1623	+	painCave.isFatal = 1;
1624	+	simError();
1625	+	}
1626	+
1627	+	if (globals->haveTauBarostat())
1628	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1629	+	else{
1630	+	sprintf(painCave.errMsg,
1631	+	"SimSetup error: If you use an NPT\n"
1632	+	"\tensemble, you must set tauBarostat.\n");
1633	+	painCave.isFatal = 1;
1634	+	simError();
1635	+	}
1636	+
1637	+	info->the_integrator = myNPTi;
1638	+	break;
1639	+
1640	+	case NPTf_ENS:
1641	+	if (globals->haveZconstraints()){
1642	+	setupZConstraint(info[k]);
1643	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1644	+	}
1645	+	else
1646	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1647	+
1648	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1649	+
1650	+	if (globals->haveTargetPressure())
1651	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1652	+	else{
1653	+	sprintf(painCave.errMsg,
1654	+	"SimSetup error: If you use a constant pressure\n"
1655	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1656	+	painCave.isFatal = 1;
1657	+	simError();
1658	+	}
1659	+
1660	+	if (globals->haveTauThermostat())
1661	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1662	+
1663	+	else{
1664	+	sprintf(painCave.errMsg,
1665	+	"SimSetup error: If you use an NPT\n"
1666	+	"\tensemble, you must set tauThermostat.\n");
1667	+	painCave.isFatal = 1;
1668	+	simError();
1669	+	}
1670	+
1671	+	if (globals->haveTauBarostat())
1672	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1673	+
1674	+	else{
1675	+	sprintf(painCave.errMsg,
1676	+	"SimSetup error: If you use an NPT\n"
1677	+	"\tensemble, you must set tauBarostat.\n");
1678	+	painCave.isFatal = 1;
1679	+	simError();
1680	+	}
1681	+
1682	+	info->the_integrator = myNPTf;
1683	+	break;
1684	+
1685	+	case NPTxyz_ENS:
1686	+	if (globals->haveZconstraints()){
1687	+	setupZConstraint(info[k]);
1688	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1689	+	}
1690	+	else
1691	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1692	+
1693	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1694	+
1695	+	if (globals->haveTargetPressure())
1696	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1697	+	else{
1698	+	sprintf(painCave.errMsg,
1699	+	"SimSetup error: If you use a constant pressure\n"
1700	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1701	+	painCave.isFatal = 1;
1702	+	simError();
1703	+	}
1704	+
1705	+	if (globals->haveTauThermostat())
1706	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1707	+	else{
1708	+	sprintf(painCave.errMsg,
1709	+	"SimSetup error: If you use an NPT\n"
1710	+	"\tensemble, you must set tauThermostat.\n");
1711	+	painCave.isFatal = 1;
1712	+	simError();
1713	+	}
1714	+
1715	+	if (globals->haveTauBarostat())
1716	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1717	+	else{
1718	+	sprintf(painCave.errMsg,
1719	+	"SimSetup error: If you use an NPT\n"
1720	+	"\tensemble, you must set tauBarostat.\n");
1721	+	painCave.isFatal = 1;
1722	+	simError();
1723	+	}
1724	+
1725	+	info->the_integrator = myNPTxyz;
1726	+	break;
1727	+
1728	+	default:
1729	+	sprintf(painCave.errMsg,
1730	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1731	+	painCave.isFatal = 1;
1732	+	simError();
1733	+	}
1734	+	}
1735	+	}
1736	+
1737	+	void SimSetup::initFortran(void){
1738	+	info[0].refreshSim();
1739	+
1740	+	if (!strcmp(info[0].mixingRule, "standard")){
1741	+	the_ff->initForceField(LB_MIXING_RULE);
1742	+	}
1743	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1744	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1745	+	}
1746	+	else{
1747	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1748	+	info[0].mixingRule);
1749	+	painCave.isFatal = 1;
1750	+	simError();
1751	+	}
1752	+
1753	+
1754	+	#ifdef IS_MPI
1755	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1756	+	MPIcheckPoint();
1757	+	#endif // is_mpi
1758	+	}
1759	+
1760	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1761	+	int nZConstraints;
1762	+	ZconStamp** zconStamp;
1763	+
1764	+	if (globals->haveZconstraintTime()){
1765	+	//add sample time of z-constraint  into SimInfo's property list
1766	+	DoubleData* zconsTimeProp = new DoubleData();
1767	+	zconsTimeProp->setID(ZCONSTIME_ID);
1768	+	zconsTimeProp->setData(globals->getZconsTime());
1769	+	theInfo.addProperty(zconsTimeProp);
1770	+	}
1771	+	else{
1772	+	sprintf(painCave.errMsg,
1773	+	"ZConstraint error: If you use a ZConstraint,\n"
1774	+	"\tyou must set zconsTime.\n");
1775	+	painCave.isFatal = 1;
1776	+	simError();
1777	+	}
1778	+
1779	+	//push zconsTol into siminfo, if user does not specify
1780	+	//value for zconsTol, a default value will be used
1781	+	DoubleData* zconsTol = new DoubleData();
1782	+	zconsTol->setID(ZCONSTOL_ID);
1783	+	if (globals->haveZconsTol()){
1784	+	zconsTol->setData(globals->getZconsTol());
1785	+	}
1786	+	else{
1787	+	double defaultZConsTol = 0.01;
1788	+	sprintf(painCave.errMsg,
1789	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1790	+	"\tOOPSE will use a default value of %f.\n"
1791	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1792	+	defaultZConsTol);
1793	+	painCave.isFatal = 0;
1794	+	simError();
1795	+
1796	+	zconsTol->setData(defaultZConsTol);
1797	+	}
1798	+	theInfo.addProperty(zconsTol);
1799	+
1800	+	//set Force Subtraction Policy
1801	+	StringData* zconsForcePolicy = new StringData();
1802	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1803	+
1804	+	if (globals->haveZconsForcePolicy()){
1805	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1806	+	}
1807	+	else{
1808	+	sprintf(painCave.errMsg,
1809	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1810	+	"\tOOPSE will use PolicyByMass.\n"
1811	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1812	+	painCave.isFatal = 0;
1813	+	simError();
1814	+	zconsForcePolicy->setData("BYMASS");
1815	+	}
1816	+
1817	+	theInfo.addProperty(zconsForcePolicy);
1818	+
1819	+	//set zcons gap
1820	+	DoubleData* zconsGap = new DoubleData();
1821	+	zconsGap->setID(ZCONSGAP_ID);
1822	+
1823	+	if (globals->haveZConsGap()){
1824	+	zconsGap->setData(globals->getZconsGap());
1825	+	theInfo.addProperty(zconsGap);
1826	+	}
1827	+
1828	+	//set zcons fixtime
1829	+	DoubleData* zconsFixtime = new DoubleData();
1830	+	zconsFixtime->setID(ZCONSFIXTIME_ID);
1831	+
1832	+	if (globals->haveZConsFixTime()){
1833	+	zconsFixtime->setData(globals->getZconsFixtime());
1834	+	theInfo.addProperty(zconsFixtime);
1835	+	}
1836	+
1837	+	//set zconsUsingSMD
1838	+	IntData* zconsUsingSMD = new IntData();
1839	+	zconsUsingSMD->setID(ZCONSUSINGSMD_ID);
1840	+
1841	+	if (globals->haveZConsUsingSMD()){
1842	+	zconsUsingSMD->setData(globals->getZconsUsingSMD());
1843	+	theInfo.addProperty(zconsUsingSMD);
1844	+	}
1845	+
1846	+	//Determine the name of ouput file and add it into SimInfo's property list
1847	+	//Be careful, do not use inFileName, since it is a pointer which
1848	+	//point to a string at master node, and slave nodes do not contain that string
1849	+
1850	+	string zconsOutput(theInfo.finalName);
1851	+
1852	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1853	+
1854	+	StringData* zconsFilename = new StringData();
1855	+	zconsFilename->setID(ZCONSFILENAME_ID);
1856	+	zconsFilename->setData(zconsOutput);
1857	+
1858	+	theInfo.addProperty(zconsFilename);
1859	+
1860	+	//setup index, pos and other parameters of z-constraint molecules
1861	+	nZConstraints = globals->getNzConstraints();
1862	+	theInfo.nZconstraints = nZConstraints;
1863	+
1864	+	zconStamp = globals->getZconStamp();
1865	+	ZConsParaItem tempParaItem;
1866	+
1867	+	ZConsParaData* zconsParaData = new ZConsParaData();
1868	+	zconsParaData->setID(ZCONSPARADATA_ID);
1869	+
1870	+	for (int i = 0; i < nZConstraints; i++){
1871	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1872	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1873	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1874	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1875	+	tempParaItem.havingCantVel = zconStamp[i]->haveCantVel();
1876	+	tempParaItem.cantVel = zconStamp[i]->getCantVel();
1877	+	zconsParaData->addItem(tempParaItem);
1878	+	}
1879	+
1880	+	//check the uniqueness of index
1881	+	if(!zconsParaData->isIndexUnique()){
1882	+	sprintf(painCave.errMsg,
1883	+	"ZConstraint Error: molIndex is not unique!\n");
1884	+	painCave.isFatal = 1;
1885	+	simError();
1886	+	}
1887	+
1888	+	//sort the parameters by index of molecules
1889	+	zconsParaData->sortByIndex();
1890	+
1891	+	//push data into siminfo, therefore, we can retrieve later
1892	+	theInfo.addProperty(zconsParaData);
1893	+	}
1894	+
1895	+	void SimSetup::makeMinimizer(){
1896	+
1897	+	OOPSEMinimizer* myOOPSEMinimizer;
1898	+	MinimizerParameterSet* param;
1899	+	char minimizerName[100];
1900	+
1901	+	for (int i = 0; i < nInfo; i++){
1902	+
1903	+	//prepare parameter set for minimizer
1904	+	param = new MinimizerParameterSet();
1905	+	param->setDefaultParameter();
1906	+
1907	+	if (globals->haveMinimizer()){
1908	+	param->setFTol(globals->getMinFTol());
1909	+	}
1910	+
1911	+	if (globals->haveMinGTol()){
1912	+	param->setGTol(globals->getMinGTol());
1913	+	}
1914	+
1915	+	if (globals->haveMinMaxIter()){
1916	+	param->setMaxIteration(globals->getMinMaxIter());
1917	+	}
1918	+
1919	+	if (globals->haveMinWriteFrq()){
1920	+	param->setMaxIteration(globals->getMinMaxIter());
1921	+	}
1922	+
1923	+	if (globals->haveMinWriteFrq()){
1924	+	param->setWriteFrq(globals->getMinWriteFrq());
1925	+	}
1926	+
1927	+	if (globals->haveMinStepSize()){
1928	+	param->setStepSize(globals->getMinStepSize());
1929	+	}
1930	+
1931	+	if (globals->haveMinLSMaxIter()){
1932	+	param->setLineSearchMaxIteration(globals->getMinLSMaxIter());
1933	+	}
1934	+
1935	+	if (globals->haveMinLSTol()){
1936	+	param->setLineSearchTol(globals->getMinLSTol());
1937	+	}
1938	+
1939	+	strcpy(minimizerName, globals->getMinimizer());
1940	+
1941	+	if (!strcasecmp(minimizerName, "CG")){
1942	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1943	+	}
1944	+	else if (!strcasecmp(minimizerName, "SD")){
1945	+	//myOOPSEMinimizer = MinimizerFactory.creatMinimizer("", &(info[i]), the_ff, param);
1946	+	myOOPSEMinimizer = new SDMinimizer(&(info[i]), the_ff, param);
1947	+	}
1948	+	else{
1949	+	sprintf(painCave.errMsg,
1950	+	"SimSetup error: Unrecognized Minimizer, use Conjugate Gradient \n");
1951	+	painCave.isFatal = 0;
1952	+	simError();
1953	+
1954	+	myOOPSEMinimizer = new PRCGMinimizer(&(info[i]), the_ff, param);
1955	+	}
1956	+	info[i].the_integrator = myOOPSEMinimizer;
1957	+
1958	+	//store the minimizer into simInfo
1959	+	info[i].the_minimizer = myOOPSEMinimizer;
1960	+	info[i].has_minimizer = true;
1961	+	}
1962	+
1963	+	}

Diff Legend

–	Removed lines
+	Added lines
<	Changed lines
>	Changed lines