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 422 by mmeineke, Thu Mar 27 19:21:42 2003 UTC vs.
Revision 787 by mmeineke, Thu Sep 25 19:27:15 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6	+	#include <sprng.h>
7
8		#include "SimSetup.hpp"
9	+	#include "ReadWrite.hpp"
10		#include "parse_me.h"
11		#include "Integrator.hpp"
12		#include "simError.h"
#	Line 12 | Line 16 | SimSetup::SimSetup(){
16		#include "mpiSimulation.hpp"
17		#endif
18
19	+	// some defines for ensemble and Forcefield  cases
20	+
21	+	#define NVE_ENS        0
22	+	#define NVT_ENS        1
23	+	#define NPTi_ENS       2
24	+	#define NPTf_ENS       3
25	+
26	+	#define FF_DUFF 0
27	+	#define FF_LJ   1
28	+	#define FF_EAM  2
29	+
30	+	using namespace std;
31	+
32		SimSetup::SimSetup(){
33	+	isInfoArray = 0;
34	+	nInfo = 1;
35	+
36		stamps = new MakeStamps();
37		globals = new Globals();
38	<
38	>
39	>
40		#ifdef IS_MPI
41	<	strcpy( checkPointMsg, "SimSetup creation successful" );
41	>	strcpy(checkPointMsg, "SimSetup creation successful");
42		MPIcheckPoint();
43		#endif // IS_MPI
44		}
#	Line 27 | Line 48 | void SimSetup::parseFile( char* fileName ){
48		delete globals;
49		}
50
51	<	void SimSetup::parseFile( char* fileName ){
51	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
52	>	info = the_info;
53	>	nInfo = theNinfo;
54	>	isInfoArray = 1;
55	>	}
56
57	+
58	+	void SimSetup::parseFile(char* fileName){
59		#ifdef IS_MPI
60	<	if( worldRank == 0 ){
60	>	if (worldRank == 0){
61		#endif // is_mpi
62	<
62	>
63		inFileName = fileName;
64	<	set_interface_stamps( stamps, globals );
65	<
64	>	set_interface_stamps(stamps, globals);
65	>
66		#ifdef IS_MPI
67		mpiEventInit();
68		#endif
69
70	<	yacc_BASS( fileName );
70	>	yacc_BASS(fileName);
71
72		#ifdef IS_MPI
73		throwMPIEvent(NULL);
74		}
75	<	else receiveParse();
75	>	else{
76	>	receiveParse();
77	>	}
78		#endif
79
80		}
81
82		#ifdef IS_MPI
83		void SimSetup::receiveParse(void){
84	<
85	<	set_interface_stamps( stamps, globals );
86	<	mpiEventInit();
87	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
84	>	set_interface_stamps(stamps, globals);
85	>	mpiEventInit();
86	>	MPIcheckPoint();
87	>	mpiEventLoop();
88		}
89
90		#endif // is_mpi
91
92	<	void SimSetup::createSim( void ){
92	>	void SimSetup::createSim(void){
93
94	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
94	>	// gather all of the information from the Bass file
95
96	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
96	>	gatherInfo();
97
98	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	simnfo->run_time = the_globals->getRunTime();
98	>	// creation of complex system objects
99
100	<	// get the ones we know are there, yet still may need some work.
81	<	n_components = the_globals->getNComponents();
82	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
100	>	sysObjectsCreation();
101
102	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
102	>	// check on the post processing info
103
104	+	finalInfoCheck();
105
106	<	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
92	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
93	<	else if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
94	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
95	<	else{
96	<	sprintf( painCave.errMsg,
97	<	"SimSetup Error. Unrecognized force field -> %s\n",
98	<	force_field );
99	<	painCave.isFatal = 1;
100	<	simError();
101	<	}
106	>	// initialize the system coordinates
107
108	<	#ifdef IS_MPI
109	<	strcpy( checkPointMsg, "ForceField creation successful" );
110	<	MPIcheckPoint();
106	<	#endif // is_mpi
108	>	if (!isInfoArray){
109	>	initSystemCoords();
110	>	}
111
112	<
112	>	// make the output filenames
113
114	<	// get the components and calculate the tot_nMol and indvidual n_mol
111	<	the_components = the_globals->getComponents();
112	<	components_nmol = new int[n_components];
113	<	comp_stamps = new MoleculeStamp*[n_components];
114	>	makeOutNames();
115
116	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
116	>	// make the integrator
117
118	<	tot_nmol = 0;
120	<	for( i=0; i<n_components; i++ ){
118	>	makeIntegrator();
119
122	–	if( !the_components[i]->haveNMol() ){
123	–	// we have a problem
124	–	sprintf( painCave.errMsg,
125	–	"SimSetup Error. No global NMol or component NMol"
126	–	" given. Cannot calculate the number of atoms.\n" );
127	–	painCave.isFatal = 1;
128	–	simError();
129	–	}
130	–
131	–	tot_nmol += the_components[i]->getNMol();
132	–	components_nmol[i] = the_components[i]->getNMol();
133	–	}
134	–	}
135	–	else{
136	–	sprintf( painCave.errMsg,
137	–	"SimSetup error.\n"
138	–	"\tSorry, the ability to specify total"
139	–	" nMols and then give molfractions in the components\n"
140	–	"\tis not currently supported."
141	–	" Please give nMol in the components.\n" );
142	–	painCave.isFatal = 1;
143	–	simError();
144	–
145	–
146	–	//     tot_nmol = the_globals->getNMol();
147	–
148	–	//   //we have the total number of molecules, now we check for molfractions
149	–	//     for( i=0; i<n_components; i++ ){
150	–
151	–	//       if( !the_components[i]->haveMolFraction() ){
152	–
153	–	//  if( !the_components[i]->haveNMol() ){
154	–	//    //we have a problem
155	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
156	–	//              << " nMol was given in component
157	–
158	–	}
159	–
120		#ifdef IS_MPI
121	<	strcpy( checkPointMsg, "Have the number of components" );
122	<	MPIcheckPoint();
163	<	#endif // is_mpi
121	>	mpiSim->mpiRefresh();
122	>	#endif
123
124	<	// make an array of molecule stamps that match the components used.
166	<	// also extract the used stamps out into a separate linked list
124	>	// initialize the Fortran
125
126	<	simnfo->nComponents = n_components;
127	<	simnfo->componentsNmol = components_nmol;
170	<	simnfo->compStamps = comp_stamps;
171	<	simnfo->headStamp = new LinkedMolStamp();
172	<
173	<	char* id;
174	<	LinkedMolStamp* headStamp = simnfo->headStamp;
175	<	LinkedMolStamp* currentStamp = NULL;
176	<	for( i=0; i<n_components; i++ ){
126	>	initFortran();
127	>	}
128
178	–	id = the_components[i]->getType();
179	–	comp_stamps[i] = NULL;
180	–
181	–	// check to make sure the component isn't already in the list
129
130	<	comp_stamps[i] = headStamp->match( id );
131	<	if( comp_stamps[i] == NULL ){
132	<
133	<	// extract the component from the list;
134	<
135	<	currentStamp = the_stamps->extractMolStamp( id );
136	<	if( currentStamp == NULL ){
137	<	sprintf( painCave.errMsg,
138	<	"SimSetup error: Component \"%s\" was not found in the "
139	<	"list of declared molecules\n",
140	<	id );
194	<	painCave.isFatal = 1;
195	<	simError();
196	<	}
197	<
198	<	headStamp->add( currentStamp );
199	<	comp_stamps[i] = headStamp->match( id );
200	<	}
201	<	}
130	>	void SimSetup::makeMolecules(void){
131	>	int k;
132	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
133	>	molInit molInfo;
134	>	DirectionalAtom* dAtom;
135	>	LinkedAssign* extras;
136	>	LinkedAssign* current_extra;
137	>	AtomStamp* currentAtom;
138	>	BondStamp* currentBond;
139	>	BendStamp* currentBend;
140	>	TorsionStamp* currentTorsion;
141
142	<	#ifdef IS_MPI
143	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
144	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
142	>	bond_pair* theBonds;
143	>	bend_set* theBends;
144	>	torsion_set* theTorsions;
145
146
147	+	//init the forceField paramters
148
149	<	// caclulate the number of atoms, bonds, bends and torsions
149	>	the_ff->readParams();
150
213	–	tot_atoms = 0;
214	–	tot_bonds = 0;
215	–	tot_bends = 0;
216	–	tot_torsions = 0;
217	–	for( i=0; i<n_components; i++ ){
218	–
219	–	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
220	–	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
221	–	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
222	–	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
223	–	}
151
152	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
152	>	// init the atoms
153
154	<	simnfo->n_atoms = tot_atoms;
228	<	simnfo->n_bonds = tot_bonds;
229	<	simnfo->n_bends = tot_bends;
230	<	simnfo->n_torsions = tot_torsions;
231	<	simnfo->n_SRI = tot_SRI;
232	<	simnfo->n_mol = tot_nmol;
154	>	double ux, uy, uz, u, uSqr;
155
156	<
157	<	#ifdef IS_MPI
156	>	for (k = 0; k < nInfo; k++){
157	>	the_ff->setSimInfo(&(info[k]));
158
159	<	// divide the molecules among processors here.
160	<
161	<	mpiSim = new mpiSimulation( simnfo );
162	<
241	<
159	>	atomOffset = 0;
160	>	excludeOffset = 0;
161	>	for (i = 0; i < info[k].n_mol; i++){
162	>	stampID = info[k].molecules[i].getStampID();
163
164	<	globalIndex = mpiSim->divideLabor();
164	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
165	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
166	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
167	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
168	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
169
170	+	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
171	+	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
172	+	molInfo.myBonds = new Bond * [molInfo.nBonds];
173	+	molInfo.myBends = new Bend * [molInfo.nBends];
174	+	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
175
176	+	theBonds = new bond_pair[molInfo.nBonds];
177	+	theBends = new bend_set[molInfo.nBends];
178	+	theTorsions = new torsion_set[molInfo.nTorsions];
179
180	<	// set up the local variables
248	<
249	<	int localMol, allMol;
250	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
180	>	// make the Atoms
181
182	<	int* mol2proc = mpiSim->getMolToProcMap();
183	<	int* molCompType = mpiSim->getMolComponentType();
184	<
185	<	allMol = 0;
186	<	localMol = 0;
187	<	local_atoms = 0;
188	<	local_bonds = 0;
259	<	local_bends = 0;
260	<	local_torsions = 0;
261	<	for( i=0; i<n_components; i++ ){
182	>	for (j = 0; j < molInfo.nAtoms; j++){
183	>	currentAtom = comp_stamps[stampID]->getAtom(j);
184	>	if (currentAtom->haveOrientation()){
185	>	dAtom = new DirectionalAtom((j + atomOffset),
186	>	info[k].getConfiguration());
187	>	info[k].n_oriented++;
188	>	molInfo.myAtoms[j] = dAtom;
189
190	<	for( j=0; j<components_nmol[i]; j++ ){
191	<
192	<	if( mol2proc[j] == worldRank ){
266	<
267	<	local_atoms +=    comp_stamps[i]->getNAtoms();
268	<	local_bonds +=    comp_stamps[i]->getNBonds();
269	<	local_bends +=    comp_stamps[i]->getNBends();
270	<	local_torsions += comp_stamps[i]->getNTorsions();
271	<	localMol++;
272	<	}
273	<	allMol++;
274	<	}
275	<	}
276	<	local_SRI = local_bonds + local_bends + local_torsions;
277	<
190	>	ux = currentAtom->getOrntX();
191	>	uy = currentAtom->getOrntY();
192	>	uz = currentAtom->getOrntZ();
193
194	<	simnfo->n_atoms = mpiSim->getMyNlocal();
280	<
281	<	if( local_atoms != simnfo->n_atoms ){
282	<	sprintf( painCave.errMsg,
283	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
284	<	" localAtom (%d) are not equal.\n",
285	<	simnfo->n_atoms,
286	<	local_atoms );
287	<	painCave.isFatal = 1;
288	<	simError();
289	<	}
194	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
195
196	<	simnfo->n_bonds = local_bonds;
197	<	simnfo->n_bends = local_bends;
198	<	simnfo->n_torsions = local_torsions;
199	<	simnfo->n_SRI = local_SRI;
295	<	simnfo->n_mol = localMol;
196	>	u = sqrt(uSqr);
197	>	ux = ux / u;
198	>	uy = uy / u;
199	>	uz = uz / u;
200
201	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
202	<	MPIcheckPoint();
203	<
204	<
201	>	dAtom->setSUx(ux);
202	>	dAtom->setSUy(uy);
203	>	dAtom->setSUz(uz);
204	>	}
205	>	else{
206	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
207	>	info[k].getConfiguration());
208	>	}
209	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
210	>
211	>	#ifdef IS_MPI
212	>
213	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
214	>
215		#endif // is_mpi
216	<
216	>	}
217
218	<	// create the atom and short range interaction arrays
218	>	// make the bonds
219	>	for (j = 0; j < molInfo.nBonds; j++){
220	>	currentBond = comp_stamps[stampID]->getBond(j);
221	>	theBonds[j].a = currentBond->getA() + atomOffset;
222	>	theBonds[j].b = currentBond->getB() + atomOffset;
223
224	<	Atom::createArrays(simnfo->n_atoms);
225	<	the_atoms = new Atom*[simnfo->n_atoms];
308	<	the_molecules = new Molecule[simnfo->n_mol];
309	<	int molIndex;
224	>	exI = theBonds[j].a;
225	>	exJ = theBonds[j].b;
226
227	<	// initialize the molecule's stampID's
227	>	// exclude_I must always be the smaller of the pair
228	>	if (exI > exJ){
229	>	tempEx = exI;
230	>	exI = exJ;
231	>	exJ = tempEx;
232	>	}
233	>	#ifdef IS_MPI
234	>	tempEx = exI;
235	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
236	>	tempEx = exJ;
237	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
238
239	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
240	+	#else  // isn't MPI
241	+
242	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
243	+	#endif  //is_mpi
244	+	}
245	+	excludeOffset += molInfo.nBonds;
246	+
247	+	//make the bends
248	+	for (j = 0; j < molInfo.nBends; j++){
249	+	currentBend = comp_stamps[stampID]->getBend(j);
250	+	theBends[j].a = currentBend->getA() + atomOffset;
251	+	theBends[j].b = currentBend->getB() + atomOffset;
252	+	theBends[j].c = currentBend->getC() + atomOffset;
253	+
254	+	if (currentBend->haveExtras()){
255	+	extras = currentBend->getExtras();
256	+	current_extra = extras;
257	+
258	+	while (current_extra != NULL){
259	+	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
260	+	switch (current_extra->getType()){
261	+	case 0:
262	+	theBends[j].ghost = current_extra->getInt() + atomOffset;
263	+	theBends[j].isGhost = 1;
264	+	break;
265	+
266	+	case 1:
267	+	theBends[j].ghost = (int) current_extra->getDouble() +
268	+	atomOffset;
269	+	theBends[j].isGhost = 1;
270	+	break;
271	+
272	+	default:
273	+	sprintf(painCave.errMsg,
274	+	"SimSetup Error: ghostVectorSource was neither a "
275	+	"double nor an int.\n"
276	+	"-->Bend[%d] in %s\n",
277	+	j, comp_stamps[stampID]->getID());
278	+	painCave.isFatal = 1;
279	+	simError();
280	+	}
281	+	}
282	+	else{
283	+	sprintf(painCave.errMsg,
284	+	"SimSetup Error: unhandled bend assignment:\n"
285	+	"    -->%s in Bend[%d] in %s\n",
286	+	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
287	+	painCave.isFatal = 1;
288	+	simError();
289	+	}
290	+
291	+	current_extra = current_extra->getNext();
292	+	}
293	+	}
294	+
295	+	if (!theBends[j].isGhost){
296	+	exI = theBends[j].a;
297	+	exJ = theBends[j].c;
298	+	}
299	+	else{
300	+	exI = theBends[j].a;
301	+	exJ = theBends[j].b;
302	+	}
303	+
304	+	// exclude_I must always be the smaller of the pair
305	+	if (exI > exJ){
306	+	tempEx = exI;
307	+	exI = exJ;
308	+	exJ = tempEx;
309	+	}
310		#ifdef IS_MPI
311	<
311	>	tempEx = exI;
312	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
313	>	tempEx = exJ;
314	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
315
316	<	molIndex = 0;
317	<	for(i=0; i<mpiSim->getTotNmol(); i++){
318	<
319	<	if(mol2proc[i] == worldRank ){
320	<	the_molecules[molIndex].setStampID( molCompType[i] );
321	<	molIndex++;
322	<	}
323	<	}
316	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
317	>	#else  // isn't MPI
318	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
319	>	#endif  //is_mpi
320	>	}
321	>	excludeOffset += molInfo.nBends;
322
323	<	#else // is_mpi
324	<
325	<	molIndex = 0;
326	<	for(i=0; i<n_components; i++){
327	<	for(j=0; j<components_nmol[i]; j++ ){
328	<	the_molecules[molIndex].setStampID( i );
331	<	molIndex++;
332	<	}
333	<	}
334	<
323	>	for (j = 0; j < molInfo.nTorsions; j++){
324	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
325	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
326	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
327	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
328	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
329
330	<	#endif // is_mpi
330	>	exI = theTorsions[j].a;
331	>	exJ = theTorsions[j].d;
332
333	+	// exclude_I must always be the smaller of the pair
334	+	if (exI > exJ){
335	+	tempEx = exI;
336	+	exI = exJ;
337	+	exJ = tempEx;
338	+	}
339	+	#ifdef IS_MPI
340	+	tempEx = exI;
341	+	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
342	+	tempEx = exJ;
343	+	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
344
345	<	if( simnfo->n_SRI ){
346	<	Exclude::createArray(simnfo->n_SRI);
347	<	the_excludes = new Exclude*[simnfo->n_SRI];
348	<	simnfo->globalExcludes = new int;
349	<	simnfo->n_exclude = tot_SRI;
350	<	}
345	<	else{
346	<
347	<	Exclude::createArray( 1 );
348	<	the_excludes = new Exclude*;
349	<	the_excludes[0] = new Exclude(0);
350	<	the_excludes[0]->setPair( 0,0 );
351	<	simnfo->globalExcludes = new int;
352	<	simnfo->globalExcludes[0] = 0;
353	<	simnfo->n_exclude = 0;
354	<	}
345	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
346	>	#else  // isn't MPI
347	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
348	>	#endif  //is_mpi
349	>	}
350	>	excludeOffset += molInfo.nTorsions;
351
356	–	// set the arrays into the SimInfo object
352
353	<	simnfo->atoms = the_atoms;
359	<	simnfo->nGlobalExcludes = 0;
360	<	simnfo->excludes = the_excludes;
353	>	// send the arrays off to the forceField for init.
354
355	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
356	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
357	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
358	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
359	+	theTorsions);
360
363	–	// get some of the tricky things that may still be in the globals
361
362	<
366	<	if( the_globals->haveBox() ){
367	<	simnfo->box_x = the_globals->getBox();
368	<	simnfo->box_y = the_globals->getBox();
369	<	simnfo->box_z = the_globals->getBox();
370	<	}
371	<	else if( the_globals->haveDensity() ){
362	>	info[k].molecules[i].initialize(molInfo);
363
373	–	double vol;
374	–	vol = (double)tot_nmol / the_globals->getDensity();
375	–	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
376	–	simnfo->box_y = simnfo->box_x;
377	–	simnfo->box_z = simnfo->box_x;
378	–	}
379	–	else{
380	–	if( !the_globals->haveBoxX() ){
381	–	sprintf( painCave.errMsg,
382	–	"SimSetup error, no periodic BoxX size given.\n" );
383	–	painCave.isFatal = 1;
384	–	simError();
385	–	}
386	–	simnfo->box_x = the_globals->getBoxX();
364
365	<	if( !the_globals->haveBoxY() ){
366	<	sprintf( painCave.errMsg,
367	<	"SimSetup error, no periodic BoxY size given.\n" );
368	<	painCave.isFatal = 1;
392	<	simError();
393	<	}
394	<	simnfo->box_y = the_globals->getBoxY();
395	<
396	<	if( !the_globals->haveBoxZ() ){
397	<	sprintf( painCave.errMsg,
398	<	"SimSetup error, no periodic BoxZ size given.\n" );
399	<	painCave.isFatal = 1;
400	<	simError();
365	>	atomOffset += molInfo.nAtoms;
366	>	delete[] theBonds;
367	>	delete[] theBends;
368	>	delete[] theTorsions;
369		}
402	–	simnfo->box_z = the_globals->getBoxZ();
370		}
371
372		#ifdef IS_MPI
373	<	strcpy( checkPointMsg, "Box size set up" );
373	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
374		MPIcheckPoint();
375		#endif // is_mpi
376
377	+	// clean up the forcefield
378
379	<	// initialize the arrays
379	>	the_ff->calcRcut();
380	>	the_ff->cleanMe();
381	>	}
382
383	<	the_ff->setSimInfo( simnfo );
383	>	void SimSetup::initFromBass(void){
384	>	int i, j, k;
385	>	int n_cells;
386	>	double cellx, celly, cellz;
387	>	double temp1, temp2, temp3;
388	>	int n_per_extra;
389	>	int n_extra;
390	>	int have_extra, done;
391
392	<	makeMolecules();
393	<	simnfo->identArray = new int[simnfo->n_atoms];
394	<	for(i=0; i<simnfo->n_atoms; i++){
395	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
419	<	}
420	<
421	<	if (the_globals->getUseRF() ) {
422	<	simnfo->useReactionField = 1;
423	<
424	<	if( !the_globals->haveECR() ){
425	<	sprintf( painCave.errMsg,
426	<	"SimSetup Warning: using default value of 1/2 the smallest "
427	<	"box length for the electrostaticCutoffRadius.\n"
428	<	"I hope you have a very fast processor!\n");
429	<	painCave.isFatal = 0;
430	<	simError();
431	<	double smallest;
432	<	smallest = simnfo->box_x;
433	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
434	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
435	<	simnfo->ecr = 0.5 * smallest;
436	<	} else {
437	<	simnfo->ecr        = the_globals->getECR();
438	<	}
392	>	double vel[3];
393	>	vel[0] = 0.0;
394	>	vel[1] = 0.0;
395	>	vel[2] = 0.0;
396
397	<	if( !the_globals->haveEST() ){
398	<	sprintf( painCave.errMsg,
399	<	"SimSetup Warning: using default value of 0.05 * the "
400	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
401	<	);
402	<	painCave.isFatal = 0;
403	<	simError();
404	<	simnfo->est = 0.05 * simnfo->ecr;
405	<	} else {
406	<	simnfo->est        = the_globals->getEST();
407	<	}
408	<
409	<	if(!the_globals->haveDielectric() ){
410	<	sprintf( painCave.errMsg,
411	<	"SimSetup Error: You are trying to use Reaction Field without"
412	<	"setting a dielectric constant!\n"
413	<	);
397	>	temp1 = (double) tot_nmol / 4.0;
398	>	temp2 = pow(temp1, (1.0 / 3.0));
399	>	temp3 = ceil(temp2);
400	>
401	>	have_extra = 0;
402	>	if (temp2 < temp3){
403	>	// we have a non-complete lattice
404	>	have_extra = 1;
405	>
406	>	n_cells = (int) temp3 - 1;
407	>	cellx = info[0].boxL[0] / temp3;
408	>	celly = info[0].boxL[1] / temp3;
409	>	cellz = info[0].boxL[2] / temp3;
410	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
411	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
412	>	n_per_extra = (int) ceil(temp1);
413	>
414	>	if (n_per_extra > 4){
415	>	sprintf(painCave.errMsg,
416	>	"SimSetup error. There has been an error in constructing"
417	>	" the non-complete lattice.\n");
418		painCave.isFatal = 1;
419		simError();
420		}
421	<	simnfo->dielectric = the_globals->getDielectric();
422	<	} else {
423	<	if (simnfo->n_dipoles) {
424	<
425	<	if( !the_globals->haveECR() ){
426	<	sprintf( painCave.errMsg,
427	<	"SimSetup Warning: using default value of 1/2 the smallest"
428	<	"box length for the electrostaticCutoffRadius.\n"
429	<	"I hope you have a very fast processor!\n");
430	<	painCave.isFatal = 0;
431	<	simError();
432	<	double smallest;
433	<	smallest = simnfo->box_x;
434	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
435	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
436	<	simnfo->ecr = 0.5 * smallest;
437	<	} else {
438	<	simnfo->ecr        = the_globals->getECR();
421	>	}
422	>	else{
423	>	n_cells = (int) temp3;
424	>	cellx = info[0].boxL[0] / temp3;
425	>	celly = info[0].boxL[1] / temp3;
426	>	cellz = info[0].boxL[2] / temp3;
427	>	}
428	>
429	>	current_mol = 0;
430	>	current_comp_mol = 0;
431	>	current_comp = 0;
432	>	current_atom_ndx = 0;
433	>
434	>	for (i = 0; i < n_cells ; i++){
435	>	for (j = 0; j < n_cells; j++){
436	>	for (k = 0; k < n_cells; k++){
437	>	makeElement(i * cellx, j * celly, k * cellz);
438	>
439	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
440	>
441	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
442	>
443	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
444		}
479	–
480	–	if( !the_globals->haveEST() ){
481	–	sprintf( painCave.errMsg,
482	–	"SimSetup Warning: using default value of 5% of the"
483	–	"electrostaticCutoffRadius for the "
484	–	"electrostaticSkinThickness\n"
485	–	);
486	–	painCave.isFatal = 0;
487	–	simError();
488	–	simnfo->est = 0.05 * simnfo->ecr;
489	–	} else {
490	–	simnfo->est        = the_globals->getEST();
491	–	}
445		}
446	<	}
446	>	}
447
448	<	#ifdef IS_MPI
449	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
497	<	MPIcheckPoint();
498	<	#endif // is_mpi
448	>	if (have_extra){
449	>	done = 0;
450
451	<	if( the_globals->haveInitialConfig() ){
452	<
453	<	InitializeFromFile* fileInit;
454	<	#ifdef IS_MPI // is_mpi
455	<	if( worldRank == 0 ){
456	<	#endif //is_mpi
457	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
458	<	#ifdef IS_MPI
459	<	}else fileInit = new InitializeFromFile( NULL );
460	<	#endif
461	<	fileInit->read_xyz( simnfo ); // default velocities on
451	>	int start_ndx;
452	>	for (i = 0; i < (n_cells + 1) && !done; i++){
453	>	for (j = 0; j < (n_cells + 1) && !done; j++){
454	>	if (i < n_cells){
455	>	if (j < n_cells){
456	>	start_ndx = n_cells;
457	>	}
458	>	else
459	>	start_ndx = 0;
460	>	}
461	>	else
462	>	start_ndx = 0;
463
464	<	delete fileInit;
465	<	}
466	<	else{
464	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
465	>	makeElement(i * cellx, j * celly, k * cellz);
466	>	done = (current_mol >= tot_nmol);
467
468	<	#ifdef IS_MPI
468	>	if (!done && n_per_extra > 1){
469	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
470	>	k * cellz);
471	>	done = (current_mol >= tot_nmol);
472	>	}
473
474	<	// no init from bass
475	<
476	<	sprintf( painCave.errMsg,
477	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
478	<	painCave.isFatal;
523	<	simError();
524	<
525	<	#else
474	>	if (!done && n_per_extra > 2){
475	>	makeElement(i * cellx, j * celly + 0.5 * celly,
476	>	k * cellz + 0.5 * cellz);
477	>	done = (current_mol >= tot_nmol);
478	>	}
479
480	<	initFromBass();
480	>	if (!done && n_per_extra > 3){
481	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
482	>	k * cellz + 0.5 * cellz);
483	>	done = (current_mol >= tot_nmol);
484	>	}
485	>	}
486	>	}
487	>	}
488	>	}
489
490	+	for (i = 0; i < info[0].n_atoms; i++){
491	+	info[0].atoms[i]->setVel(vel);
492	+	}
493	+	}
494
495	<	#endif
496	<	}
495	>	void SimSetup::makeElement(double x, double y, double z){
496	>	int k;
497	>	AtomStamp* current_atom;
498	>	DirectionalAtom* dAtom;
499	>	double rotMat[3][3];
500	>	double pos[3];
501
502	<	#ifdef IS_MPI
503	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
504	<	MPIcheckPoint();
505	<	#endif // is_mpi
502	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
503	>	current_atom = comp_stamps[current_comp]->getAtom(k);
504	>	if (!current_atom->havePosition()){
505	>	sprintf(painCave.errMsg,
506	>	"SimSetup:initFromBass error.\n"
507	>	"\tComponent %s, atom %s does not have a position specified.\n"
508	>	"\tThe initialization routine is unable to give a start"
509	>	" position.\n",
510	>	comp_stamps[current_comp]->getID(), current_atom->getType());
511	>	painCave.isFatal = 1;
512	>	simError();
513	>	}
514
515	+	pos[0] = x + current_atom->getPosX();
516	+	pos[1] = y + current_atom->getPosY();
517	+	pos[2] = z + current_atom->getPosZ();
518
519	<
540	<
541	<
519	>	info[0].atoms[current_atom_ndx]->setPos(pos);
520
521	<
522	<	#ifdef IS_MPI
523	<	if( worldRank == 0 ){
524	<	#endif // is_mpi
525	<
526	<	if( the_globals->haveFinalConfig() ){
527	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
521	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
522	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
523	>
524	>	rotMat[0][0] = 1.0;
525	>	rotMat[0][1] = 0.0;
526	>	rotMat[0][2] = 0.0;
527	>
528	>	rotMat[1][0] = 0.0;
529	>	rotMat[1][1] = 1.0;
530	>	rotMat[1][2] = 0.0;
531	>
532	>	rotMat[2][0] = 0.0;
533	>	rotMat[2][1] = 0.0;
534	>	rotMat[2][2] = 1.0;
535	>
536	>	dAtom->setA(rotMat);
537		}
551	–	else{
552	–	strcpy( simnfo->finalName, inFileName );
553	–	char* endTest;
554	–	int nameLength = strlen( simnfo->finalName );
555	–	endTest = &(simnfo->finalName[nameLength - 5]);
556	–	if( !strcmp( endTest, ".bass" ) ){
557	–	strcpy( endTest, ".eor" );
558	–	}
559	–	else if( !strcmp( endTest, ".BASS" ) ){
560	–	strcpy( endTest, ".eor" );
561	–	}
562	–	else{
563	–	endTest = &(simnfo->finalName[nameLength - 4]);
564	–	if( !strcmp( endTest, ".bss" ) ){
565	–	strcpy( endTest, ".eor" );
566	–	}
567	–	else if( !strcmp( endTest, ".mdl" ) ){
568	–	strcpy( endTest, ".eor" );
569	–	}
570	–	else{
571	–	strcat( simnfo->finalName, ".eor" );
572	–	}
573	–	}
574	–	}
575	–
576	–	// make the sample and status out names
577	–
578	–	strcpy( simnfo->sampleName, inFileName );
579	–	char* endTest;
580	–	int nameLength = strlen( simnfo->sampleName );
581	–	endTest = &(simnfo->sampleName[nameLength - 5]);
582	–	if( !strcmp( endTest, ".bass" ) ){
583	–	strcpy( endTest, ".dump" );
584	–	}
585	–	else if( !strcmp( endTest, ".BASS" ) ){
586	–	strcpy( endTest, ".dump" );
587	–	}
588	–	else{
589	–	endTest = &(simnfo->sampleName[nameLength - 4]);
590	–	if( !strcmp( endTest, ".bss" ) ){
591	–	strcpy( endTest, ".dump" );
592	–	}
593	–	else if( !strcmp( endTest, ".mdl" ) ){
594	–	strcpy( endTest, ".dump" );
595	–	}
596	–	else{
597	–	strcat( simnfo->sampleName, ".dump" );
598	–	}
599	–	}
600	–
601	–	strcpy( simnfo->statusName, inFileName );
602	–	nameLength = strlen( simnfo->statusName );
603	–	endTest = &(simnfo->statusName[nameLength - 5]);
604	–	if( !strcmp( endTest, ".bass" ) ){
605	–	strcpy( endTest, ".stat" );
606	–	}
607	–	else if( !strcmp( endTest, ".BASS" ) ){
608	–	strcpy( endTest, ".stat" );
609	–	}
610	–	else{
611	–	endTest = &(simnfo->statusName[nameLength - 4]);
612	–	if( !strcmp( endTest, ".bss" ) ){
613	–	strcpy( endTest, ".stat" );
614	–	}
615	–	else if( !strcmp( endTest, ".mdl" ) ){
616	–	strcpy( endTest, ".stat" );
617	–	}
618	–	else{
619	–	strcat( simnfo->statusName, ".stat" );
620	–	}
621	–	}
622	–
623	–	#ifdef IS_MPI
624	–	}
625	–	#endif // is_mpi
626	–
627	–	// set the status, sample, and themal kick times
628	–
629	–	if( the_globals->haveSampleTime() ){
630	–	simnfo->sampleTime = the_globals->getSampleTime();
631	–	simnfo->statusTime = simnfo->sampleTime;
632	–	simnfo->thermalTime = simnfo->sampleTime;
633	–	}
634	–	else{
635	–	simnfo->sampleTime = the_globals->getRunTime();
636	–	simnfo->statusTime = simnfo->sampleTime;
637	–	simnfo->thermalTime = simnfo->sampleTime;
638	–	}
538
539	<	if( the_globals->haveStatusTime() ){
641	<	simnfo->statusTime = the_globals->getStatusTime();
539	>	current_atom_ndx++;
540		}
541
542	<	if( the_globals->haveThermalTime() ){
543	<	simnfo->thermalTime = the_globals->getThermalTime();
542	>	current_mol++;
543	>	current_comp_mol++;
544	>
545	>	if (current_comp_mol >= components_nmol[current_comp]){
546	>	current_comp_mol = 0;
547	>	current_comp++;
548		}
549	+	}
550
648	–	// check for the temperature set flag
551
552	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
552	>	void SimSetup::gatherInfo(void){
553	>	int i;
554
555	+	ensembleCase = -1;
556	+	ffCase = -1;
557
558	<	//   // make the longe range forces and the integrator
558	>	// set the easy ones first
559
560	<	//   new AllLong( simnfo );
560	>	for (i = 0; i < nInfo; i++){
561	>	info[i].target_temp = globals->getTargetTemp();
562	>	info[i].dt = globals->getDt();
563	>	info[i].run_time = globals->getRunTime();
564	>	}
565	>	n_components = globals->getNComponents();
566
657	–	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
658	–	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
659	–	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
660	–	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
567
568	+	// get the forceField
569
570	+	strcpy(force_field, globals->getForceField());
571
572	<	// initialize the Fortran
573	<
666	<	simnfo->refreshSim();
667	<
668	<	if( !strcmp( simnfo->mixingRule, "standard") ){
669	<	the_ff->initForceField( LB_MIXING_RULE );
572	>	if (!strcasecmp(force_field, "DUFF")){
573	>	ffCase = FF_DUFF;
574		}
575	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
576	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
575	>	else if (!strcasecmp(force_field, "LJ")){
576	>	ffCase = FF_LJ;
577		}
578	+	else if (!strcasecmp(force_field, "EAM")){
579	+	ffCase = FF_EAM;
580	+	}
581		else{
582	<	sprintf( painCave.errMsg,
583	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
584	<	simnfo->mixingRule );
585	<	painCave.isFatal = 1;
679	<	simError();
582	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
583	>	force_field);
584	>	painCave.isFatal = 1;
585	>	simError();
586		}
587
588	+	// get the ensemble
589
590	<	#ifdef IS_MPI
684	<	strcpy( checkPointMsg,
685	<	"Successfully intialized the mixingRule for Fortran." );
686	<	MPIcheckPoint();
687	<	#endif // is_mpi
688	<	}
590	>	strcpy(ensemble, globals->getEnsemble());
591
592	+	if (!strcasecmp(ensemble, "NVE")){
593	+	ensembleCase = NVE_ENS;
594	+	}
595	+	else if (!strcasecmp(ensemble, "NVT")){
596	+	ensembleCase = NVT_ENS;
597	+	}
598	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
599	+	ensembleCase = NPTi_ENS;
600	+	}
601	+	else if (!strcasecmp(ensemble, "NPTf")){
602	+	ensembleCase = NPTf_ENS;
603	+	}
604	+	else{
605	+	sprintf(painCave.errMsg,
606	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
607	+	"reverting to NVE for this simulation.\n",
608	+	ensemble);
609	+	painCave.isFatal = 0;
610	+	simError();
611	+	strcpy(ensemble, "NVE");
612	+	ensembleCase = NVE_ENS;
613	+	}
614
615	<	void SimSetup::makeMolecules( void ){
615	>	for (i = 0; i < nInfo; i++){
616	>	strcpy(info[i].ensemble, ensemble);
617
618	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
694	<	molInit info;
695	<	DirectionalAtom* dAtom;
696	<	LinkedAssign* extras;
697	<	LinkedAssign* current_extra;
698	<	AtomStamp* currentAtom;
699	<	BondStamp* currentBond;
700	<	BendStamp* currentBend;
701	<	TorsionStamp* currentTorsion;
702	<
703	<	//init the forceField paramters
618	>	// get the mixing rule
619
620	<	the_ff->readParams();
620	>	strcpy(info[i].mixingRule, globals->getMixingRule());
621	>	info[i].usePBC = globals->getPBC();
622	>	}
623
624	<
708	<	// init the molecules
624	>	// get the components and calculate the tot_nMol and indvidual n_mol
625
626	<	atomOffset = 0;
627	<	excludeOffset = 0;
712	<	for(i=0; i<simnfo->n_mol; i++){
713	<
714	<	stampID = the_molecules[i].getStampID();
626	>	the_components = globals->getComponents();
627	>	components_nmol = new int[n_components];
628
716	–	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
717	–	info.nBonds    = comp_stamps[stampID]->getNBonds();
718	–	info.nBends    = comp_stamps[stampID]->getNBends();
719	–	info.nTorsions = comp_stamps[stampID]->getNTorsions();
720	–	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
629
630	<	info.myAtoms = &the_atoms[atomOffset];
631	<	info.myExcludes = &the_excludes[excludeOffset];
632	<	info.myBonds = new Bond*[info.nBonds];
725	<	info.myBends = new Bend*[info.nBends];
726	<	info.myTorsions = new Torsions*[info.nTorsions];
630	>	if (!globals->haveNMol()){
631	>	// we don't have the total number of molecules, so we assume it is
632	>	// given in each component
633
634	<	theBonds = new bond_pair[info.nBonds];
635	<	theBends = new bend_set[info.nBends];
636	<	theTorsions = new torsion_set[info.nTorsions];
637	<
638	<	// make the Atoms
639	<
640	<	for(j=0; j<info.nAtoms; j++){
641	<
642	<	currentAtom = theComponents[stampID]->getAtom( j );
737	<	if( currentAtom->haveOrientation() ){
738	<
739	<	dAtom = new DirectionalAtom(j + atomOffset);
740	<	simnfo->n_oriented++;
741	<	info.myAtoms[j] = dAtom;
742	<
743	<	ux = currentAtom->getOrntX();
744	<	uy = currentAtom->getOrntY();
745	<	uz = currentAtom->getOrntZ();
746	<
747	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
748	<
749	<	u = sqrt( uSqr );
750	<	ux = ux / u;
751	<	uy = uy / u;
752	<	uz = uz / u;
753	<
754	<	dAtom->setSUx( ux );
755	<	dAtom->setSUy( uy );
756	<	dAtom->setSUz( uz );
634	>	tot_nmol = 0;
635	>	for (i = 0; i < n_components; i++){
636	>	if (!the_components[i]->haveNMol()){
637	>	// we have a problem
638	>	sprintf(painCave.errMsg,
639	>	"SimSetup Error. No global NMol or component NMol"
640	>	" given. Cannot calculate the number of atoms.\n");
641	>	painCave.isFatal = 1;
642	>	simError();
643		}
758	–	else{
759	–	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
760	–	}
761	–	info.myAtoms[j]->setType( currentAtom->getType() );
762	–
763	–	#ifdef IS_MPI
764	–
765	–	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
766	–
767	–	#endif // is_mpi
768	–	}
769	–
770	–	// make the bonds
771	–	for(j=0; j<info.nBonds; j++){
772	–
773	–	currentBond = comp_stamps[stampID]->getBond( j );
774	–	theBonds[j].a = currentBond->getA() + atomOffset;
775	–	theBonds[j].b = currentBond->getB() + atomOffset;
644
645	<	exI = theBonds[i].a;
646	<	exJ = theBonds[i].b;
645	>	tot_nmol += the_components[i]->getNMol();
646	>	components_nmol[i] = the_components[i]->getNMol();
647	>	}
648	>	}
649	>	else{
650	>	sprintf(painCave.errMsg,
651	>	"SimSetup error.\n"
652	>	"\tSorry, the ability to specify total"
653	>	" nMols and then give molfractions in the components\n"
654	>	"\tis not currently supported."
655	>	" Please give nMol in the components.\n");
656	>	painCave.isFatal = 1;
657	>	simError();
658	>	}
659
660	<	// exclude_I must always be the smaller of the pair
661	<	if( exI > exJ ){
662	<	tempEx = exI;
663	<	exI = exJ;
664	<	exJ = tempEx;
665	<	}
666	<	#ifdef IS_MPI
787	<	tempEx = exI;
788	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
789	<	tempEx = exJ;
790	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
791	<
792	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
793	<	#else  // isn't MPI
794	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
795	<	#endif  //is_mpi
660	>	// set the status, sample, and thermal kick times
661	>
662	>	for (i = 0; i < nInfo; i++){
663	>	if (globals->haveSampleTime()){
664	>	info[i].sampleTime = globals->getSampleTime();
665	>	info[i].statusTime = info[i].sampleTime;
666	>	info[i].thermalTime = info[i].sampleTime;
667		}
668	<	excludeOffset += info.nBonds;
668	>	else{
669	>	info[i].sampleTime = globals->getRunTime();
670	>	info[i].statusTime = info[i].sampleTime;
671	>	info[i].thermalTime = info[i].sampleTime;
672	>	}
673
674	<	//make the bends
675	<	for(j=0; j<info.nBends; j++){
801	<
802	<	currentBend = comp_stamps[stampID]->getBend( j );
803	<	theBends[j].a = currentBend->getA() + atomOffset;
804	<	theBends[j].b = currentBend->getB() + atomOffset;
805	<	theBends[j].c = currentBend->getC() + atomOffset;
806	<
807	<	if( currentBend->haveExtras() ){
808	<
809	<	extras = current_bend->getExtras();
810	<	current_extra = extras;
811	<
812	<	while( current_extra != NULL ){
813	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
814	<
815	<	switch( current_extra->getType() ){
816	<
817	<	case 0:
818	<	theBends[j].ghost =
819	<	current_extra->getInt() + atomOffset;
820	<	theBends[j].isGhost = 1;
821	<	break;
822	<
823	<	case 1:
824	<	theBends[j].ghost =
825	<	(int)current_extra->getDouble() + atomOffset;
826	<	theBends[j].isGhost = 1;
827	<	break;
828	<
829	<	default:
830	<	sprintf( painCave.errMsg,
831	<	"SimSetup Error: ghostVectorSource was neiter a "
832	<	"double nor an int.\n"
833	<	"-->Bend[%d] in %s\n",
834	<	j, comp_stamps[stampID]->getID() );
835	<	painCave.isFatal = 1;
836	<	simError();
837	<	}
838	<	}
839	<
840	<	else{
841	<
842	<	sprintf( painCave.errMsg,
843	<	"SimSetup Error: unhandled bend assignment:\n"
844	<	"    -->%s in Bend[%d] in %s\n",
845	<	current_extra->getlhs(),
846	<	j, comp_stamps[stampID]->getID() );
847	<	painCave.isFatal = 1;
848	<	simError();
849	<	}
850	<
851	<	current_extra = current_extra->getNext();
852	<	}
853	<	}
854	<
855	<	if( !theBends[j].isGhost ){
856	<
857	<	exI = theBends[j].a;
858	<	exJ = theBends[j].c;
859	<	}
860	<	else{
861	<
862	<	exI = theBends[j].a;
863	<	exJ = theBends[j].b;
864	<	}
865	<
866	<	// exclude_I must always be the smaller of the pair
867	<	if( exI > exJ ){
868	<	tempEx = exI;
869	<	exI = exJ;
870	<	exJ = tempEx;
871	<	}
872	<	#ifdef IS_MPI
873	<	tempEx = exI;
874	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
875	<	tempEx = exJ;
876	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
877	<
878	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
879	<	#else  // isn't MPI
880	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
881	<	#endif  //is_mpi
674	>	if (globals->haveStatusTime()){
675	>	info[i].statusTime = globals->getStatusTime();
676		}
883	–	excludeOffset += info.nBends;
677
678	<	for(j=0; j<info.nTorsions; j++){
679	<
680	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
888	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
889	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
890	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
891	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
892	<
893	<	exI = theTorsions[j].a;
894	<	exJ = theTorsions[j].d;
678	>	if (globals->haveThermalTime()){
679	>	info[i].thermalTime = globals->getThermalTime();
680	>	}
681
682	<	// exclude_I must always be the smaller of the pair
683	<	if( exI > exJ ){
684	<	tempEx = exI;
685	<	exI = exJ;
900	<	exJ = tempEx;
901	<	}
902	<	#ifdef IS_MPI
903	<	tempEx = exI;
904	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
905	<	tempEx = exJ;
906	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
907	<
908	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
909	<	#else  // isn't MPI
910	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
911	<	#endif  //is_mpi
682	>	info[i].resetIntegrator = 0;
683	>	if( globals->haveResetTime() ){
684	>	info[i].resetTime = globals->getResetTime();
685	>	info[i].resetIntegrator = 1;
686		}
913	–	excludeOffset += info.nTorsions;
687
688	<
916	<	// send the arrays off to the forceField for init.
688	>	// check for the temperature set flag
689
690	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
691	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
920	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
921	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
690	>	if (globals->haveTempSet())
691	>	info[i].setTemp = globals->getTempSet();
692
693	+	// get some of the tricky things that may still be in the globals
694
695	<	the_molecules[i].initialize( info );
696	<	atomOffset += info.nAtoms;
697	<	}
695	>	double boxVector[3];
696	>	if (globals->haveBox()){
697	>	boxVector[0] = globals->getBox();
698	>	boxVector[1] = globals->getBox();
699	>	boxVector[2] = globals->getBox();
700
701	<	// clean up the forcefield
702	<	the_ff->calcRcut();
703	<	the_ff->cleanMe();
704	<	}
701	>	info[i].setBox(boxVector);
702	>	}
703	>	else if (globals->haveDensity()){
704	>	double vol;
705	>	vol = (double) tot_nmol / globals->getDensity();
706	>	boxVector[0] = pow(vol, (1.0 / 3.0));
707	>	boxVector[1] = boxVector[0];
708	>	boxVector[2] = boxVector[0];
709
710	<	void SimSetup::initFromBass( void ){
710	>	info[i].setBox(boxVector);
711	>	}
712	>	else{
713	>	if (!globals->haveBoxX()){
714	>	sprintf(painCave.errMsg,
715	>	"SimSetup error, no periodic BoxX size given.\n");
716	>	painCave.isFatal = 1;
717	>	simError();
718	>	}
719	>	boxVector[0] = globals->getBoxX();
720
721	<	int i, j, k;
722	<	int n_cells;
723	<	double cellx, celly, cellz;
724	<	double temp1, temp2, temp3;
725	<	int n_per_extra;
726	<	int n_extra;
727	<	int have_extra, done;
721	>	if (!globals->haveBoxY()){
722	>	sprintf(painCave.errMsg,
723	>	"SimSetup error, no periodic BoxY size given.\n");
724	>	painCave.isFatal = 1;
725	>	simError();
726	>	}
727	>	boxVector[1] = globals->getBoxY();
728
729	<	temp1 = (double)tot_nmol / 4.0;
730	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
731	<	temp3 = ceil( temp2 );
729	>	if (!globals->haveBoxZ()){
730	>	sprintf(painCave.errMsg,
731	>	"SimSetup error, no periodic BoxZ size given.\n");
732	>	painCave.isFatal = 1;
733	>	simError();
734	>	}
735	>	boxVector[2] = globals->getBoxZ();
736
737	<	have_extra =0;
738	<	if( temp2 < temp3 ){ // we have a non-complete lattice
739	<	have_extra =1;
737	>	info[i].setBox(boxVector);
738	>	}
739	>	}
740
741	<	n_cells = (int)temp3 - 1;
742	<	cellx = simnfo->box_x / temp3;
953	<	celly = simnfo->box_y / temp3;
954	<	cellz = simnfo->box_z / temp3;
955	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
956	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
957	<	n_per_extra = (int)ceil( temp1 );
741	>	//setup seed for random number generator
742	>	int seedValue;
743
744	<	if( n_per_extra > 4){
745	<	sprintf( painCave.errMsg,
746	<	"SimSetup error. There has been an error in constructing"
747	<	" the non-complete lattice.\n" );
748	<	painCave.isFatal = 1;
744	>	if (globals->haveSeed()){
745	>	seedValue = globals->getSeed();
746	>
747	>	if(seedValue / 1E9 == 0){
748	>	sprintf(painCave.errMsg,
749	>	"Seed for sprng library should contain at least 9 digits\n"
750	>	"OOPSE will generate a seed for user\n");
751	>	painCave.isFatal = 0;
752		simError();
753	+
754	+	//using seed generated by system instead of invalid seed set by user
755	+	#ifndef IS_MPI
756	+	seedValue = make_sprng_seed();
757	+	#else
758	+	if (worldRank == 0){
759	+	seedValue = make_sprng_seed();
760	+	}
761	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
762	+	#endif
763		}
764	<	}
764	>	}//end of if branch of globals->haveSeed()
765		else{
766	<	n_cells = (int)temp3;
767	<	cellx = simnfo->box_x / temp3;
768	<	celly = simnfo->box_y / temp3;
769	<	cellz = simnfo->box_z / temp3;
766	>
767	>	#ifndef IS_MPI
768	>	seedValue = make_sprng_seed();
769	>	#else
770	>	if (worldRank == 0){
771	>	seedValue = make_sprng_seed();
772	>	}
773	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
774	>	#endif
775	>	}//end of globals->haveSeed()
776	>
777	>	for (int i = 0; i < nInfo; i++){
778	>	info[i].setSeed(seedValue);
779		}
780
781	<	current_mol = 0;
782	<	current_comp_mol = 0;
783	<	current_comp = 0;
784	<	current_atom_ndx = 0;
781	>	#ifdef IS_MPI
782	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
783	>	MPIcheckPoint();
784	>	#endif // is_mpi
785	>	}
786
979	–	for( i=0; i < n_cells ; i++ ){
980	–	for( j=0; j < n_cells; j++ ){
981	–	for( k=0; k < n_cells; k++ ){
787
788	<	makeElement( i * cellx,
789	<	j * celly,
790	<	k * cellz );
788	>	void SimSetup::finalInfoCheck(void){
789	>	int index;
790	>	int usesDipoles;
791	>	int i;
792
793	<	makeElement( i * cellx + 0.5 * cellx,
794	<	j * celly + 0.5 * celly,
989	<	k * cellz );
793	>	for (i = 0; i < nInfo; i++){
794	>	// check electrostatic parameters
795
796	<	makeElement( i * cellx,
797	<	j * celly + 0.5 * celly,
798	<	k * cellz + 0.5 * cellz );
799	<
800	<	makeElement( i * cellx + 0.5 * cellx,
996	<	j * celly,
997	<	k * cellz + 0.5 * cellz );
998	<	}
796	>	index = 0;
797	>	usesDipoles = 0;
798	>	while ((index < info[i].n_atoms) && !usesDipoles){
799	>	usesDipoles = (info[i].atoms[index])->hasDipole();
800	>	index++;
801		}
1000	–	}
802
803	<	if( have_extra ){
804	<	done = 0;
803	>	#ifdef IS_MPI
804	>	int myUse = usesDipoles;
805	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
806	>	#endif //is_mpi
807
808	<	int start_ndx;
1006	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1007	<	for( j=0; j < (n_cells+1) && !done; j++ ){
808	>	double theEcr, theEst;
809
810	<	if( i < n_cells ){
810	>	if (globals->getUseRF()){
811	>	info[i].useReactionField = 1;
812
813	<	if( j < n_cells ){
814	<	start_ndx = n_cells;
815	<	}
816	<	else start_ndx = 0;
817	<	}
818	<	else start_ndx = 0;
813	>	if (!globals->haveECR()){
814	>	sprintf(painCave.errMsg,
815	>	"SimSetup Warning: using default value of 1/2 the smallest "
816	>	"box length for the electrostaticCutoffRadius.\n"
817	>	"I hope you have a very fast processor!\n");
818	>	painCave.isFatal = 0;
819	>	simError();
820	>	double smallest;
821	>	smallest = info[i].boxL[0];
822	>	if (info[i].boxL[1] <= smallest)
823	>	smallest = info[i].boxL[1];
824	>	if (info[i].boxL[2] <= smallest)
825	>	smallest = info[i].boxL[2];
826	>	theEcr = 0.5 * smallest;
827	>	}
828	>	else{
829	>	theEcr = globals->getECR();
830	>	}
831
832	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
832	>	if (!globals->haveEST()){
833	>	sprintf(painCave.errMsg,
834	>	"SimSetup Warning: using default value of 0.05 * the "
835	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
836	>	painCave.isFatal = 0;
837	>	simError();
838	>	theEst = 0.05 * theEcr;
839	>	}
840	>	else{
841	>	theEst = globals->getEST();
842	>	}
843
844	<	makeElement( i * cellx,
1021	<	j * celly,
1022	<	k * cellz );
1023	<	done = ( current_mol >= tot_nmol );
844	>	info[i].setEcr(theEcr, theEst);
845
846	<	if( !done && n_per_extra > 1 ){
847	<	makeElement( i * cellx + 0.5 * cellx,
848	<	j * celly + 0.5 * celly,
849	<	k * cellz );
850	<	done = ( current_mol >= tot_nmol );
851	<	}
846	>	if (!globals->haveDielectric()){
847	>	sprintf(painCave.errMsg,
848	>	"SimSetup Error: You are trying to use Reaction Field without"
849	>	"setting a dielectric constant!\n");
850	>	painCave.isFatal = 1;
851	>	simError();
852	>	}
853	>	info[i].dielectric = globals->getDielectric();
854	>	}
855	>	else{
856	>	if (usesDipoles){
857	>	if (!globals->haveECR()){
858	>	sprintf(painCave.errMsg,
859	>	"SimSetup Warning: using default value of 1/2 the smallest "
860	>	"box length for the electrostaticCutoffRadius.\n"
861	>	"I hope you have a very fast processor!\n");
862	>	painCave.isFatal = 0;
863	>	simError();
864	>	double smallest;
865	>	smallest = info[i].boxL[0];
866	>	if (info[i].boxL[1] <= smallest)
867	>	smallest = info[i].boxL[1];
868	>	if (info[i].boxL[2] <= smallest)
869	>	smallest = info[i].boxL[2];
870	>	theEcr = 0.5 * smallest;
871	>	}
872	>	else{
873	>	theEcr = globals->getECR();
874	>	}
875
876	<	if( !done && n_per_extra > 2){
877	<	makeElement( i * cellx,
878	<	j * celly + 0.5 * celly,
879	<	k * cellz + 0.5 * cellz );
880	<	done = ( current_mol >= tot_nmol );
881	<	}
876	>	if (!globals->haveEST()){
877	>	sprintf(painCave.errMsg,
878	>	"SimSetup Warning: using default value of 0.05 * the "
879	>	"electrostaticCutoffRadius for the "
880	>	"electrostaticSkinThickness\n");
881	>	painCave.isFatal = 0;
882	>	simError();
883	>	theEst = 0.05 * theEcr;
884	>	}
885	>	else{
886	>	theEst = globals->getEST();
887	>	}
888
889	<	if( !done && n_per_extra > 3){
1040	<	makeElement( i * cellx + 0.5 * cellx,
1041	<	j * celly,
1042	<	k * cellz + 0.5 * cellz );
1043	<	done = ( current_mol >= tot_nmol );
1044	<	}
1045	<	}
889	>	info[i].setEcr(theEcr, theEst);
890		}
891		}
892		}
893
894	<
895	<	for( i=0; i<simnfo->n_atoms; i++ ){
896	<	simnfo->atoms[i]->set_vx( 0.0 );
897	<	simnfo->atoms[i]->set_vy( 0.0 );
1054	<	simnfo->atoms[i]->set_vz( 0.0 );
1055	<	}
894	>	#ifdef IS_MPI
895	>	strcpy(checkPointMsg, "post processing checks out");
896	>	MPIcheckPoint();
897	>	#endif // is_mpi
898		}
899
900	<	void SimSetup::makeElement( double x, double y, double z ){
900	>	void SimSetup::initSystemCoords(void){
901	>	int i;
902
903	<	int k;
1061	<	AtomStamp* current_atom;
1062	<	DirectionalAtom* dAtom;
1063	<	double rotMat[3][3];
903	>	char* inName;
904
905	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
905	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
906
907	<	current_atom = comp_stamps[current_comp]->getAtom( k );
908	<	if( !current_atom->havePosition() ){
909	<	sprintf( painCave.errMsg,
910	<	"SimSetup:initFromBass error.\n"
911	<	"\tComponent %s, atom %s does not have a position specified.\n"
912	<	"\tThe initialization routine is unable to give a start"
913	<	" position.\n",
914	<	comp_stamps[current_comp]->getID(),
915	<	current_atom->getType() );
916	<	painCave.isFatal = 1;
917	<	simError();
907	>	for (i = 0; i < info[0].n_atoms; i++)
908	>	info[0].atoms[i]->setCoords();
909	>
910	>	if (globals->haveInitialConfig()){
911	>	InitializeFromFile* fileInit;
912	>	#ifdef IS_MPI // is_mpi
913	>	if (worldRank == 0){
914	>	#endif //is_mpi
915	>	inName = globals->getInitialConfig();
916	>	fileInit = new InitializeFromFile(inName);
917	>	#ifdef IS_MPI
918		}
919	+	else
920	+	fileInit = new InitializeFromFile(NULL);
921	+	#endif
922	+	fileInit->readInit(info); // default velocities on
923
924	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
925	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
926	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
924	>	delete fileInit;
925	>	}
926	>	else{
927	>	#ifdef IS_MPI
928
929	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
929	>	// no init from bass
930
931	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
931	>	sprintf(painCave.errMsg,
932	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
933	>	painCave.isFatal = 1;;
934	>	simError();
935
936	<	rotMat[0][0] = 1.0;
1089	<	rotMat[0][1] = 0.0;
1090	<	rotMat[0][2] = 0.0;
936	>	#else
937
938	<	rotMat[1][0] = 0.0;
1093	<	rotMat[1][1] = 1.0;
1094	<	rotMat[1][2] = 0.0;
938	>	initFromBass();
939
1096	–	rotMat[2][0] = 0.0;
1097	–	rotMat[2][1] = 0.0;
1098	–	rotMat[2][2] = 1.0;
940
941	<	dAtom->setA( rotMat );
1101	<	}
1102	<
1103	<	current_atom_ndx++;
941	>	#endif
942		}
943
944	<	current_mol++;
945	<	current_comp_mol++;
944	>	#ifdef IS_MPI
945	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
946	>	MPIcheckPoint();
947	>	#endif // is_mpi
948	>	}
949
1109	–	if( current_comp_mol >= components_nmol[current_comp] ){
950
951	<	current_comp_mol = 0;
952	<	current_comp++;
951	>	void SimSetup::makeOutNames(void){
952	>	int k;
953	>
954	>
955	>	for (k = 0; k < nInfo; k++){
956	>	#ifdef IS_MPI
957	>	if (worldRank == 0){
958	>	#endif // is_mpi
959	>
960	>	if (globals->haveFinalConfig()){
961	>	strcpy(info[k].finalName, globals->getFinalConfig());
962	>	}
963	>	else{
964	>	strcpy(info[k].finalName, inFileName);
965	>	char* endTest;
966	>	int nameLength = strlen(info[k].finalName);
967	>	endTest = &(info[k].finalName[nameLength - 5]);
968	>	if (!strcmp(endTest, ".bass")){
969	>	strcpy(endTest, ".eor");
970	>	}
971	>	else if (!strcmp(endTest, ".BASS")){
972	>	strcpy(endTest, ".eor");
973	>	}
974	>	else{
975	>	endTest = &(info[k].finalName[nameLength - 4]);
976	>	if (!strcmp(endTest, ".bss")){
977	>	strcpy(endTest, ".eor");
978	>	}
979	>	else if (!strcmp(endTest, ".mdl")){
980	>	strcpy(endTest, ".eor");
981	>	}
982	>	else{
983	>	strcat(info[k].finalName, ".eor");
984	>	}
985	>	}
986	>	}
987	>
988	>	// make the sample and status out names
989	>
990	>	strcpy(info[k].sampleName, inFileName);
991	>	char* endTest;
992	>	int nameLength = strlen(info[k].sampleName);
993	>	endTest = &(info[k].sampleName[nameLength - 5]);
994	>	if (!strcmp(endTest, ".bass")){
995	>	strcpy(endTest, ".dump");
996	>	}
997	>	else if (!strcmp(endTest, ".BASS")){
998	>	strcpy(endTest, ".dump");
999	>	}
1000	>	else{
1001	>	endTest = &(info[k].sampleName[nameLength - 4]);
1002	>	if (!strcmp(endTest, ".bss")){
1003	>	strcpy(endTest, ".dump");
1004	>	}
1005	>	else if (!strcmp(endTest, ".mdl")){
1006	>	strcpy(endTest, ".dump");
1007	>	}
1008	>	else{
1009	>	strcat(info[k].sampleName, ".dump");
1010	>	}
1011	>	}
1012	>
1013	>	strcpy(info[k].statusName, inFileName);
1014	>	nameLength = strlen(info[k].statusName);
1015	>	endTest = &(info[k].statusName[nameLength - 5]);
1016	>	if (!strcmp(endTest, ".bass")){
1017	>	strcpy(endTest, ".stat");
1018	>	}
1019	>	else if (!strcmp(endTest, ".BASS")){
1020	>	strcpy(endTest, ".stat");
1021	>	}
1022	>	else{
1023	>	endTest = &(info[k].statusName[nameLength - 4]);
1024	>	if (!strcmp(endTest, ".bss")){
1025	>	strcpy(endTest, ".stat");
1026	>	}
1027	>	else if (!strcmp(endTest, ".mdl")){
1028	>	strcpy(endTest, ".stat");
1029	>	}
1030	>	else{
1031	>	strcat(info[k].statusName, ".stat");
1032	>	}
1033	>	}
1034	>
1035	>	#ifdef IS_MPI
1036	>
1037	>	}
1038	>	#endif // is_mpi
1039	>	}
1040	>	}
1041	>
1042	>
1043	>	void SimSetup::sysObjectsCreation(void){
1044	>	int i, k;
1045	>
1046	>	// create the forceField
1047	>
1048	>	createFF();
1049	>
1050	>	// extract componentList
1051	>
1052	>	compList();
1053	>
1054	>	// calc the number of atoms, bond, bends, and torsions
1055	>
1056	>	calcSysValues();
1057	>
1058	>	#ifdef IS_MPI
1059	>	// divide the molecules among the processors
1060	>
1061	>	mpiMolDivide();
1062	>	#endif //is_mpi
1063	>
1064	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1065	>
1066	>	makeSysArrays();
1067	>
1068	>	// make and initialize the molecules (all but atomic coordinates)
1069	>
1070	>	makeMolecules();
1071	>
1072	>	for (k = 0; k < nInfo; k++){
1073	>	info[k].identArray = new int[info[k].n_atoms];
1074	>	for (i = 0; i < info[k].n_atoms; i++){
1075	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1076	>	}
1077	>	}
1078	>	}
1079	>
1080	>
1081	>	void SimSetup::createFF(void){
1082	>	switch (ffCase){
1083	>	case FF_DUFF:
1084	>	the_ff = new DUFF();
1085	>	break;
1086	>
1087	>	case FF_LJ:
1088	>	the_ff = new LJFF();
1089	>	break;
1090	>
1091	>	case FF_EAM:
1092	>	the_ff = new EAM_FF();
1093	>	break;
1094	>
1095	>	default:
1096	>	sprintf(painCave.errMsg,
1097	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1098	>	painCave.isFatal = 1;
1099	>	simError();
1100	>	}
1101	>
1102	>	#ifdef IS_MPI
1103	>	strcpy(checkPointMsg, "ForceField creation successful");
1104	>	MPIcheckPoint();
1105	>	#endif // is_mpi
1106	>	}
1107	>
1108	>
1109	>	void SimSetup::compList(void){
1110	>	int i;
1111	>	char* id;
1112	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1113	>	LinkedMolStamp* currentStamp = NULL;
1114	>	comp_stamps = new MoleculeStamp * [n_components];
1115	>
1116	>	// make an array of molecule stamps that match the components used.
1117	>	// also extract the used stamps out into a separate linked list
1118	>
1119	>	for (i = 0; i < nInfo; i++){
1120	>	info[i].nComponents = n_components;
1121	>	info[i].componentsNmol = components_nmol;
1122	>	info[i].compStamps = comp_stamps;
1123	>	info[i].headStamp = headStamp;
1124	>	}
1125	>
1126	>
1127	>	for (i = 0; i < n_components; i++){
1128	>	id = the_components[i]->getType();
1129	>	comp_stamps[i] = NULL;
1130	>
1131	>	// check to make sure the component isn't already in the list
1132	>
1133	>	comp_stamps[i] = headStamp->match(id);
1134	>	if (comp_stamps[i] == NULL){
1135	>	// extract the component from the list;
1136	>
1137	>	currentStamp = stamps->extractMolStamp(id);
1138	>	if (currentStamp == NULL){
1139	>	sprintf(painCave.errMsg,
1140	>	"SimSetup error: Component \"%s\" was not found in the "
1141	>	"list of declared molecules\n",
1142	>	id);
1143	>	painCave.isFatal = 1;
1144	>	simError();
1145	>	}
1146	>
1147	>	headStamp->add(currentStamp);
1148	>	comp_stamps[i] = headStamp->match(id);
1149	>	}
1150	>	}
1151	>
1152	>	#ifdef IS_MPI
1153	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1154	>	MPIcheckPoint();
1155	>	#endif // is_mpi
1156	>	}
1157	>
1158	>	void SimSetup::calcSysValues(void){
1159	>	int i;
1160	>
1161	>	int* molMembershipArray;
1162	>
1163	>	tot_atoms = 0;
1164	>	tot_bonds = 0;
1165	>	tot_bends = 0;
1166	>	tot_torsions = 0;
1167	>	for (i = 0; i < n_components; i++){
1168	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1169	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1170	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1171	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1172	>	}
1173	>
1174	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1175	>	molMembershipArray = new int[tot_atoms];
1176	>
1177	>	for (i = 0; i < nInfo; i++){
1178	>	info[i].n_atoms = tot_atoms;
1179	>	info[i].n_bonds = tot_bonds;
1180	>	info[i].n_bends = tot_bends;
1181	>	info[i].n_torsions = tot_torsions;
1182	>	info[i].n_SRI = tot_SRI;
1183	>	info[i].n_mol = tot_nmol;
1184	>
1185	>	info[i].molMembershipArray = molMembershipArray;
1186	>	}
1187	>	}
1188	>
1189	>	#ifdef IS_MPI
1190	>
1191	>	void SimSetup::mpiMolDivide(void){
1192	>	int i, j, k;
1193	>	int localMol, allMol;
1194	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1195	>
1196	>	mpiSim = new mpiSimulation(info);
1197	>
1198	>	globalIndex = mpiSim->divideLabor();
1199	>
1200	>	// set up the local variables
1201	>
1202	>	mol2proc = mpiSim->getMolToProcMap();
1203	>	molCompType = mpiSim->getMolComponentType();
1204	>
1205	>	allMol = 0;
1206	>	localMol = 0;
1207	>	local_atoms = 0;
1208	>	local_bonds = 0;
1209	>	local_bends = 0;
1210	>	local_torsions = 0;
1211	>	globalAtomIndex = 0;
1212	>
1213	>
1214	>	for (i = 0; i < n_components; i++){
1215	>	for (j = 0; j < components_nmol[i]; j++){
1216	>	if (mol2proc[allMol] == worldRank){
1217	>	local_atoms += comp_stamps[i]->getNAtoms();
1218	>	local_bonds += comp_stamps[i]->getNBonds();
1219	>	local_bends += comp_stamps[i]->getNBends();
1220	>	local_torsions += comp_stamps[i]->getNTorsions();
1221	>	localMol++;
1222	>	}
1223	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1224	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1225	>	globalAtomIndex++;
1226	>	}
1227	>
1228	>	allMol++;
1229	>	}
1230	>	}
1231	>	local_SRI = local_bonds + local_bends + local_torsions;
1232	>
1233	>	info[0].n_atoms = mpiSim->getMyNlocal();
1234	>
1235	>	if (local_atoms != info[0].n_atoms){
1236	>	sprintf(painCave.errMsg,
1237	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1238	>	" localAtom (%d) are not equal.\n",
1239	>	info[0].n_atoms, local_atoms);
1240	>	painCave.isFatal = 1;
1241	>	simError();
1242	>	}
1243	>
1244	>	info[0].n_bonds = local_bonds;
1245	>	info[0].n_bends = local_bends;
1246	>	info[0].n_torsions = local_torsions;
1247	>	info[0].n_SRI = local_SRI;
1248	>	info[0].n_mol = localMol;
1249	>
1250	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1251	>	MPIcheckPoint();
1252	>	}
1253	>
1254	>	#endif // is_mpi
1255	>
1256	>
1257	>	void SimSetup::makeSysArrays(void){
1258	>
1259	>	#ifndef IS_MPI
1260	>	int k, j;
1261	>	#endif // is_mpi
1262	>	int i, l;
1263	>
1264	>	Atom** the_atoms;
1265	>	Molecule* the_molecules;
1266	>	Exclude** the_excludes;
1267	>
1268	>
1269	>	for (l = 0; l < nInfo; l++){
1270	>	// create the atom and short range interaction arrays
1271	>
1272	>	the_atoms = new Atom * [info[l].n_atoms];
1273	>	the_molecules = new Molecule[info[l].n_mol];
1274	>	int molIndex;
1275	>
1276	>	// initialize the molecule's stampID's
1277	>
1278	>	#ifdef IS_MPI
1279	>
1280	>
1281	>	molIndex = 0;
1282	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1283	>	if (mol2proc[i] == worldRank){
1284	>	the_molecules[molIndex].setStampID(molCompType[i]);
1285	>	the_molecules[molIndex].setMyIndex(molIndex);
1286	>	the_molecules[molIndex].setGlobalIndex(i);
1287	>	molIndex++;
1288	>	}
1289	>	}
1290	>
1291	>	#else // is_mpi
1292	>
1293	>	molIndex = 0;
1294	>	globalAtomIndex = 0;
1295	>	for (i = 0; i < n_components; i++){
1296	>	for (j = 0; j < components_nmol[i]; j++){
1297	>	the_molecules[molIndex].setStampID(i);
1298	>	the_molecules[molIndex].setMyIndex(molIndex);
1299	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1300	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1301	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1302	>	globalAtomIndex++;
1303	>	}
1304	>	molIndex++;
1305	>	}
1306	>	}
1307	>
1308	>
1309	>	#endif // is_mpi
1310	>
1311	>
1312	>	if (info[l].n_SRI){
1313	>	Exclude::createArray(info[l].n_SRI);
1314	>	the_excludes = new Exclude * [info[l].n_SRI];
1315	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1316	>	the_excludes[ex] = new Exclude(ex);
1317	>	}
1318	>	info[l].globalExcludes = new int;
1319	>	info[l].n_exclude = info[l].n_SRI;
1320	>	}
1321	>	else{
1322	>	Exclude::createArray(1);
1323	>	the_excludes = new Exclude * ;
1324	>	the_excludes[0] = new Exclude(0);
1325	>	the_excludes[0]->setPair(0, 0);
1326	>	info[l].globalExcludes = new int;
1327	>	info[l].globalExcludes[0] = 0;
1328	>	info[l].n_exclude = 0;
1329	>	}
1330	>
1331	>	// set the arrays into the SimInfo object
1332	>
1333	>	info[l].atoms = the_atoms;
1334	>	info[l].molecules = the_molecules;
1335	>	info[l].nGlobalExcludes = 0;
1336	>	info[l].excludes = the_excludes;
1337	>
1338	>	the_ff->setSimInfo(info);
1339		}
1340		}
1341	+
1342	+	void SimSetup::makeIntegrator(void){
1343	+	int k;
1344	+
1345	+	NVE<RealIntegrator>* myNVE = NULL;
1346	+	NVT<RealIntegrator>* myNVT = NULL;
1347	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1348	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1349	+
1350	+	for (k = 0; k < nInfo; k++){
1351	+	switch (ensembleCase){
1352	+	case NVE_ENS:
1353	+	if (globals->haveZconstraints()){
1354	+	setupZConstraint(info[k]);
1355	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1356	+	}
1357	+	else{
1358	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1359	+	}
1360	+
1361	+	info->the_integrator = myNVE;
1362	+	break;
1363	+
1364	+	case NVT_ENS:
1365	+	if (globals->haveZconstraints()){
1366	+	setupZConstraint(info[k]);
1367	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1368	+	}
1369	+	else
1370	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1371	+
1372	+	myNVT->setTargetTemp(globals->getTargetTemp());
1373	+
1374	+	if (globals->haveTauThermostat())
1375	+	myNVT->setTauThermostat(globals->getTauThermostat());
1376	+	else{
1377	+	sprintf(painCave.errMsg,
1378	+	"SimSetup error: If you use the NVT\n"
1379	+	"    ensemble, you must set tauThermostat.\n");
1380	+	painCave.isFatal = 1;
1381	+	simError();
1382	+	}
1383	+
1384	+	info->the_integrator = myNVT;
1385	+	break;
1386	+
1387	+	case NPTi_ENS:
1388	+	if (globals->haveZconstraints()){
1389	+	setupZConstraint(info[k]);
1390	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1391	+	}
1392	+	else
1393	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1394	+
1395	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1396	+
1397	+	if (globals->haveTargetPressure())
1398	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1399	+	else{
1400	+	sprintf(painCave.errMsg,
1401	+	"SimSetup error: If you use a constant pressure\n"
1402	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1403	+	painCave.isFatal = 1;
1404	+	simError();
1405	+	}
1406	+
1407	+	if (globals->haveTauThermostat())
1408	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1409	+	else{
1410	+	sprintf(painCave.errMsg,
1411	+	"SimSetup error: If you use an NPT\n"
1412	+	"    ensemble, you must set tauThermostat.\n");
1413	+	painCave.isFatal = 1;
1414	+	simError();
1415	+	}
1416	+
1417	+	if (globals->haveTauBarostat())
1418	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1419	+	else{
1420	+	sprintf(painCave.errMsg,
1421	+	"SimSetup error: If you use an NPT\n"
1422	+	"    ensemble, you must set tauBarostat.\n");
1423	+	painCave.isFatal = 1;
1424	+	simError();
1425	+	}
1426	+
1427	+	info->the_integrator = myNPTi;
1428	+	break;
1429	+
1430	+	case NPTf_ENS:
1431	+	if (globals->haveZconstraints()){
1432	+	setupZConstraint(info[k]);
1433	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1434	+	}
1435	+	else
1436	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1437	+
1438	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1439	+
1440	+	if (globals->haveTargetPressure())
1441	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1442	+	else{
1443	+	sprintf(painCave.errMsg,
1444	+	"SimSetup error: If you use a constant pressure\n"
1445	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1446	+	painCave.isFatal = 1;
1447	+	simError();
1448	+	}
1449	+
1450	+	if (globals->haveTauThermostat())
1451	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1452	+	else{
1453	+	sprintf(painCave.errMsg,
1454	+	"SimSetup error: If you use an NPT\n"
1455	+	"    ensemble, you must set tauThermostat.\n");
1456	+	painCave.isFatal = 1;
1457	+	simError();
1458	+	}
1459	+
1460	+	if (globals->haveTauBarostat())
1461	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1462	+	else{
1463	+	sprintf(painCave.errMsg,
1464	+	"SimSetup error: If you use an NPT\n"
1465	+	"    ensemble, you must set tauBarostat.\n");
1466	+	painCave.isFatal = 1;
1467	+	simError();
1468	+	}
1469	+
1470	+	info->the_integrator = myNPTf;
1471	+	break;
1472	+
1473	+	default:
1474	+	sprintf(painCave.errMsg,
1475	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1476	+	painCave.isFatal = 1;
1477	+	simError();
1478	+	}
1479	+	}
1480	+	}
1481	+
1482	+	void SimSetup::initFortran(void){
1483	+	info[0].refreshSim();
1484	+
1485	+	if (!strcmp(info[0].mixingRule, "standard")){
1486	+	the_ff->initForceField(LB_MIXING_RULE);
1487	+	}
1488	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1489	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1490	+	}
1491	+	else{
1492	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1493	+	info[0].mixingRule);
1494	+	painCave.isFatal = 1;
1495	+	simError();
1496	+	}
1497	+
1498	+
1499	+	#ifdef IS_MPI
1500	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1501	+	MPIcheckPoint();
1502	+	#endif // is_mpi
1503	+	}
1504	+
1505	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1506	+	int nZConstraints;
1507	+	ZconStamp** zconStamp;
1508	+
1509	+	if (globals->haveZconstraintTime()){
1510	+	//add sample time of z-constraint  into SimInfo's property list
1511	+	DoubleData* zconsTimeProp = new DoubleData();
1512	+	zconsTimeProp->setID(ZCONSTIME_ID);
1513	+	zconsTimeProp->setData(globals->getZconsTime());
1514	+	theInfo.addProperty(zconsTimeProp);
1515	+	}
1516	+	else{
1517	+	sprintf(painCave.errMsg,
1518	+	"ZConstraint error: If you use an ZConstraint\n"
1519	+	" , you must set sample time.\n");
1520	+	painCave.isFatal = 1;
1521	+	simError();
1522	+	}
1523	+
1524	+	//push zconsTol into siminfo, if user does not specify
1525	+	//value for zconsTol, a default value will be used
1526	+	DoubleData* zconsTol = new DoubleData();
1527	+	zconsTol->setID(ZCONSTOL_ID);
1528	+	if (globals->haveZconsTol()){
1529	+	zconsTol->setData(globals->getZconsTol());
1530	+	}
1531	+	else{
1532	+	double defaultZConsTol = 0.01;
1533	+	sprintf(painCave.errMsg,
1534	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1535	+	" , default value %f is used.\n",
1536	+	defaultZConsTol);
1537	+	painCave.isFatal = 0;
1538	+	simError();
1539	+
1540	+	zconsTol->setData(defaultZConsTol);
1541	+	}
1542	+	theInfo.addProperty(zconsTol);
1543	+
1544	+	//set Force Subtraction Policy
1545	+	StringData* zconsForcePolicy = new StringData();
1546	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1547	+
1548	+	if (globals->haveZconsForcePolicy()){
1549	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1550	+	}
1551	+	else{
1552	+	sprintf(painCave.errMsg,
1553	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1554	+	"PolicyByMass is used\n");
1555	+	painCave.isFatal = 0;
1556	+	simError();
1557	+	zconsForcePolicy->setData("BYMASS");
1558	+	}
1559	+
1560	+	theInfo.addProperty(zconsForcePolicy);
1561	+
1562	+	//Determine the name of ouput file and add it into SimInfo's property list
1563	+	//Be careful, do not use inFileName, since it is a pointer which
1564	+	//point to a string at master node, and slave nodes do not contain that string
1565	+
1566	+	string zconsOutput(theInfo.finalName);
1567	+
1568	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1569	+
1570	+	StringData* zconsFilename = new StringData();
1571	+	zconsFilename->setID(ZCONSFILENAME_ID);
1572	+	zconsFilename->setData(zconsOutput);
1573	+
1574	+	theInfo.addProperty(zconsFilename);
1575	+
1576	+	//setup index, pos and other parameters of z-constraint molecules
1577	+	nZConstraints = globals->getNzConstraints();
1578	+	theInfo.nZconstraints = nZConstraints;
1579	+
1580	+	zconStamp = globals->getZconStamp();
1581	+	ZConsParaItem tempParaItem;
1582	+
1583	+	ZConsParaData* zconsParaData = new ZConsParaData();
1584	+	zconsParaData->setID(ZCONSPARADATA_ID);
1585	+
1586	+	for (int i = 0; i < nZConstraints; i++){
1587	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1588	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1589	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1590	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1591	+
1592	+	zconsParaData->addItem(tempParaItem);
1593	+	}
1594	+
1595	+	//check the uniqueness of index
1596	+	if(!zconsParaData->isIndexUnique()){
1597	+	sprintf(painCave.errMsg,
1598	+	"ZConstraint Error: molIndex is not unique\n");
1599	+	painCave.isFatal = 1;
1600	+	simError();
1601	+	}
1602	+
1603	+	//sort the parameters by index of molecules
1604	+	zconsParaData->sortByIndex();
1605	+
1606	+	//push data into siminfo, therefore, we can retrieve later
1607	+	theInfo.addProperty(zconsParaData);
1608	+	}

Diff Legend

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