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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 843 by mmeineke, Wed Oct 29 20:41:39 2003 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"
#	Line 12 | Line 15 | SimSetup::SimSetup(){
15		#include "mpiSimulation.hpp"
16		#endif
17
18	+	// some defines for ensemble and Forcefield  cases
19	+
20	+	#define NVE_ENS        0
21	+	#define NVT_ENS        1
22	+	#define NPTi_ENS       2
23	+	#define NPTf_ENS       3
24	+	#define NPTxyz_ENS     4
25	+
26	+
27	+	#define FF_DUFF 0
28	+	#define FF_LJ   1
29	+	#define FF_EAM  2
30	+
31	+	using namespace std;
32	+
33		SimSetup::SimSetup(){
34	+
35	+	initSuspend = false;
36	+	isInfoArray = 0;
37	+	nInfo = 1;
38	+
39		stamps = new MakeStamps();
40		globals = new Globals();
41	<
41	>
42	>
43		#ifdef IS_MPI
44	<	strcpy( checkPointMsg, "SimSetup creation successful" );
44	>	strcpy(checkPointMsg, "SimSetup creation successful");
45		MPIcheckPoint();
46		#endif // IS_MPI
47		}
#	Line 27 | Line 51 | void SimSetup::parseFile( char* fileName ){
51		delete globals;
52		}
53
54	<	void SimSetup::parseFile( char* fileName ){
54	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
55	>	info = the_info;
56	>	nInfo = theNinfo;
57	>	isInfoArray = 1;
58	>	initSuspend = true;
59	>	}
60
61	+
62	+	void SimSetup::parseFile(char* fileName){
63		#ifdef IS_MPI
64	<	if( worldRank == 0 ){
64	>	if (worldRank == 0){
65		#endif // is_mpi
66	<
66	>
67		inFileName = fileName;
68	<	set_interface_stamps( stamps, globals );
69	<
68	>	set_interface_stamps(stamps, globals);
69	>
70		#ifdef IS_MPI
71		mpiEventInit();
72		#endif
73
74	<	yacc_BASS( fileName );
74	>	yacc_BASS(fileName);
75
76		#ifdef IS_MPI
77		throwMPIEvent(NULL);
78		}
79	<	else receiveParse();
79	>	else{
80	>	receiveParse();
81	>	}
82		#endif
83
84		}
85
86		#ifdef IS_MPI
87		void SimSetup::receiveParse(void){
88	<
89	<	set_interface_stamps( stamps, globals );
90	<	mpiEventInit();
91	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
88	>	set_interface_stamps(stamps, globals);
89	>	mpiEventInit();
90	>	MPIcheckPoint();
91	>	mpiEventLoop();
92		}
93
94		#endif // is_mpi
95
96	<	void SimSetup::createSim( void ){
96	>	void SimSetup::createSim(void){
97
98	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
98	>	// gather all of the information from the Bass file
99
100	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
100	>	gatherInfo();
101
102	<	// 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();
102	>	// creation of complex system objects
103
104	<	// 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 );
104	>	sysObjectsCreation();
105
106	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
106	>	// initialize the system coordinates
107
108	+	if ( !initSuspend ){
109	+	initSystemCoords();
110
111	<	if( !strcmp( force_field, "TraPPE" ) ) the_ff = new TraPPEFF();
112	<	else if( !strcmp( force_field, "DipoleTest" ) ) the_ff = new DipoleTestFF();
113	<	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	<	}
111	>	if( !(globals->getUseInitTime()) )
112	>	info[0].currentTime = 0.0;
113	>	}
114
115	<	#ifdef IS_MPI
104	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
115	>	// check on the post processing info
116
117	<
117	>	finalInfoCheck();
118
119	<	// 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];
119	>	// make the output filenames
120
121	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
121	>	makeOutNames();
122
123	<	tot_nmol = 0;
120	<	for( i=0; i<n_components; i++ ){
123	>	// make the integrator
124
125	<	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	<	}
125	>	makeIntegrator();
126
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	–
127		#ifdef IS_MPI
128	<	strcpy( checkPointMsg, "Have the number of components" );
129	<	MPIcheckPoint();
163	<	#endif // is_mpi
128	>	mpiSim->mpiRefresh();
129	>	#endif
130
131	<	// make an array of molecule stamps that match the components used.
166	<	// also extract the used stamps out into a separate linked list
131	>	// initialize the Fortran
132
133	<	simnfo->nComponents = n_components;
134	<	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++ ){
133	>	initFortran();
134	>	}
135
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
136
137	<	comp_stamps[i] = headStamp->match( id );
138	<	if( comp_stamps[i] == NULL ){
139	<
140	<	// extract the component from the list;
141	<
142	<	currentStamp = the_stamps->extractMolStamp( id );
143	<	if( currentStamp == NULL ){
144	<	sprintf( painCave.errMsg,
145	<	"SimSetup error: Component \"%s\" was not found in the "
146	<	"list of declared molecules\n",
147	<	id );
194	<	painCave.isFatal = 1;
195	<	simError();
196	<	}
197	<
198	<	headStamp->add( currentStamp );
199	<	comp_stamps[i] = headStamp->match( id );
200	<	}
201	<	}
137	>	void SimSetup::makeMolecules(void){
138	>	int k;
139	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
140	>	molInit molInfo;
141	>	DirectionalAtom* dAtom;
142	>	LinkedAssign* extras;
143	>	LinkedAssign* current_extra;
144	>	AtomStamp* currentAtom;
145	>	BondStamp* currentBond;
146	>	BendStamp* currentBend;
147	>	TorsionStamp* currentTorsion;
148
149	<	#ifdef IS_MPI
150	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
151	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
149	>	bond_pair* theBonds;
150	>	bend_set* theBends;
151	>	torsion_set* theTorsions;
152
153
154	+	//init the forceField paramters
155
156	<	// caclulate the number of atoms, bonds, bends and torsions
156	>	the_ff->readParams();
157
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	–	}
158
159	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
159	>	// init the atoms
160
161	<	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;
161	>	double ux, uy, uz, u, uSqr;
162
163	<
164	<	#ifdef IS_MPI
163	>	for (k = 0; k < nInfo; k++){
164	>	the_ff->setSimInfo(&(info[k]));
165
166	<	// divide the molecules among processors here.
167	<
168	<	mpiSim = new mpiSimulation( simnfo );
169	<
241	<
166	>	atomOffset = 0;
167	>	excludeOffset = 0;
168	>	for (i = 0; i < info[k].n_mol; i++){
169	>	stampID = info[k].molecules[i].getStampID();
170
171	<	globalIndex = mpiSim->divideLabor();
171	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
172	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
173	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
174	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
175	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
176
177	+	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
178	+	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
179	+	molInfo.myBonds = new Bond * [molInfo.nBonds];
180	+	molInfo.myBends = new Bend * [molInfo.nBends];
181	+	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
182
183	+	theBonds = new bond_pair[molInfo.nBonds];
184	+	theBends = new bend_set[molInfo.nBends];
185	+	theTorsions = new torsion_set[molInfo.nTorsions];
186
187	<	// set up the local variables
248	<
249	<	int localMol, allMol;
250	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
187	>	// make the Atoms
188
189	<	int* mol2proc = mpiSim->getMolToProcMap();
190	<	int* molCompType = mpiSim->getMolComponentType();
191	<
192	<	allMol = 0;
193	<	localMol = 0;
194	<	local_atoms = 0;
195	<	local_bonds = 0;
259	<	local_bends = 0;
260	<	local_torsions = 0;
261	<	for( i=0; i<n_components; i++ ){
189	>	for (j = 0; j < molInfo.nAtoms; j++){
190	>	currentAtom = comp_stamps[stampID]->getAtom(j);
191	>	if (currentAtom->haveOrientation()){
192	>	dAtom = new DirectionalAtom((j + atomOffset),
193	>	info[k].getConfiguration());
194	>	info[k].n_oriented++;
195	>	molInfo.myAtoms[j] = dAtom;
196
197	<	for( j=0; j<components_nmol[i]; j++ ){
198	<
199	<	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	<
197	>	ux = currentAtom->getOrntX();
198	>	uy = currentAtom->getOrntY();
199	>	uz = currentAtom->getOrntZ();
200
201	<	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	<	}
201	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
202
203	<	simnfo->n_bonds = local_bonds;
204	<	simnfo->n_bends = local_bends;
205	<	simnfo->n_torsions = local_torsions;
206	<	simnfo->n_SRI = local_SRI;
295	<	simnfo->n_mol = localMol;
203	>	u = sqrt(uSqr);
204	>	ux = ux / u;
205	>	uy = uy / u;
206	>	uz = uz / u;
207
208	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
209	<	MPIcheckPoint();
210	<
211	<
212	<	#endif // is_mpi
213	<
208	>	dAtom->setSUx(ux);
209	>	dAtom->setSUy(uy);
210	>	dAtom->setSUz(uz);
211	>	}
212	>	else{
213	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
214	>	info[k].getConfiguration());
215	>	}
216	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
217
218	<	// create the atom and short range interaction arrays
218	>	#ifdef IS_MPI
219
220	<	Atom::createArrays(simnfo->n_atoms);
307	<	the_atoms = new Atom*[simnfo->n_atoms];
308	<	the_molecules = new Molecule[simnfo->n_mol];
309	<	int molIndex;
220	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
221
222	<	// initialize the molecule's stampID's
222	>	#endif // is_mpi
223	>	}
224
225	+	// make the bonds
226	+	for (j = 0; j < molInfo.nBonds; j++){
227	+	currentBond = comp_stamps[stampID]->getBond(j);
228	+	theBonds[j].a = currentBond->getA() + atomOffset;
229	+	theBonds[j].b = currentBond->getB() + atomOffset;
230	+
231	+	exI = theBonds[j].a;
232	+	exJ = theBonds[j].b;
233	+
234	+	// exclude_I must always be the smaller of the pair
235	+	if (exI > exJ){
236	+	tempEx = exI;
237	+	exI = exJ;
238	+	exJ = tempEx;
239	+	}
240		#ifdef IS_MPI
241	<
241	>	tempEx = exI;
242	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
243	>	tempEx = exJ;
244	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
245
246	<	molIndex = 0;
247	<	for(i=0; i<mpiSim->getTotNmol(); i++){
318	<
319	<	if(mol2proc[i] == worldRank ){
320	<	the_molecules[molIndex].setStampID( molCompType[i] );
321	<	molIndex++;
322	<	}
323	<	}
246	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
247	>	#else  // isn't MPI
248
249	<	#else // is_mpi
250	<
251	<	molIndex = 0;
252	<	for(i=0; i<n_components; i++){
329	<	for(j=0; j<components_nmol[i]; j++ ){
330	<	the_molecules[molIndex].setStampID( i );
331	<	molIndex++;
332	<	}
333	<	}
334	<
249	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
250	>	#endif  //is_mpi
251	>	}
252	>	excludeOffset += molInfo.nBonds;
253
254	<	#endif // is_mpi
254	>	//make the bends
255	>	for (j = 0; j < molInfo.nBends; j++){
256	>	currentBend = comp_stamps[stampID]->getBend(j);
257	>	theBends[j].a = currentBend->getA() + atomOffset;
258	>	theBends[j].b = currentBend->getB() + atomOffset;
259	>	theBends[j].c = currentBend->getC() + atomOffset;
260
261	+	if (currentBend->haveExtras()){
262	+	extras = currentBend->getExtras();
263	+	current_extra = extras;
264
265	<	if( simnfo->n_SRI ){
266	<	Exclude::createArray(simnfo->n_SRI);
267	<	the_excludes = new Exclude*[simnfo->n_SRI];
268	<	simnfo->globalExcludes = new int;
269	<	simnfo->n_exclude = tot_SRI;
270	<	}
271	<	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	<	}
265	>	while (current_extra != NULL){
266	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
267	>	switch (current_extra->getType()){
268	>	case 0:
269	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
270	>	theBends[j].isGhost = 1;
271	>	break;
272
273	<	// set the arrays into the SimInfo object
273	>	case 1:
274	>	theBends[j].ghost = (int) current_extra->getDouble() +
275	>	atomOffset;
276	>	theBends[j].isGhost = 1;
277	>	break;
278
279	<	simnfo->atoms = the_atoms;
280	<	simnfo->nGlobalExcludes = 0;
281	<	simnfo->excludes = the_excludes;
279	>	default:
280	>	sprintf(painCave.errMsg,
281	>	"SimSetup Error: ghostVectorSource was neither a "
282	>	"double nor an int.\n"
283	>	"-->Bend[%d] in %s\n",
284	>	j, comp_stamps[stampID]->getID());
285	>	painCave.isFatal = 1;
286	>	simError();
287	>	}
288	>	}
289	>	else{
290	>	sprintf(painCave.errMsg,
291	>	"SimSetup Error: unhandled bend assignment:\n"
292	>	"    -->%s in Bend[%d] in %s\n",
293	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
294	>	painCave.isFatal = 1;
295	>	simError();
296	>	}
297
298	+	current_extra = current_extra->getNext();
299	+	}
300	+	}
301
302	<	// get some of the tricky things that may still be in the globals
302	>	if (!theBends[j].isGhost){
303	>	exI = theBends[j].a;
304	>	exJ = theBends[j].c;
305	>	}
306	>	else{
307	>	exI = theBends[j].a;
308	>	exJ = theBends[j].b;
309	>	}
310
311	<
312	<	if( the_globals->haveBox() ){
313	<	simnfo->box_x = the_globals->getBox();
314	<	simnfo->box_y = the_globals->getBox();
315	<	simnfo->box_z = the_globals->getBox();
316	<	}
317	<	else if( the_globals->haveDensity() ){
311	>	// exclude_I must always be the smaller of the pair
312	>	if (exI > exJ){
313	>	tempEx = exI;
314	>	exI = exJ;
315	>	exJ = tempEx;
316	>	}
317	>	#ifdef IS_MPI
318	>	tempEx = exI;
319	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
320	>	tempEx = exJ;
321	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
322
323	<	double vol;
324	<	vol = (double)tot_nmol / the_globals->getDensity();
325	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
326	<	simnfo->box_y = simnfo->box_x;
327	<	simnfo->box_z = simnfo->box_x;
328	<	}
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();
323	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
324	>	#else  // isn't MPI
325	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
326	>	#endif  //is_mpi
327	>	}
328	>	excludeOffset += molInfo.nBends;
329
330	<	if( !the_globals->haveBoxY() ){
331	<	sprintf( painCave.errMsg,
332	<	"SimSetup error, no periodic BoxY size given.\n" );
333	<	painCave.isFatal = 1;
334	<	simError();
335	<	}
394	<	simnfo->box_y = the_globals->getBoxY();
330	>	for (j = 0; j < molInfo.nTorsions; j++){
331	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
332	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
333	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
334	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
335	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
336
337	<	if( !the_globals->haveBoxZ() ){
338	<	sprintf( painCave.errMsg,
339	<	"SimSetup error, no periodic BoxZ size given.\n" );
340	<	painCave.isFatal = 1;
341	<	simError();
337	>	exI = theTorsions[j].a;
338	>	exJ = theTorsions[j].d;
339	>
340	>	// exclude_I must always be the smaller of the pair
341	>	if (exI > exJ){
342	>	tempEx = exI;
343	>	exI = exJ;
344	>	exJ = tempEx;
345	>	}
346	>	#ifdef IS_MPI
347	>	tempEx = exI;
348	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
349	>	tempEx = exJ;
350	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
351	>
352	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
353	>	#else  // isn't MPI
354	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
355	>	#endif  //is_mpi
356	>	}
357	>	excludeOffset += molInfo.nTorsions;
358	>
359	>
360	>	// send the arrays off to the forceField for init.
361	>
362	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
363	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
364	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
365	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
366	>	theTorsions);
367	>
368	>
369	>	info[k].molecules[i].initialize(molInfo);
370	>
371	>
372	>	atomOffset += molInfo.nAtoms;
373	>	delete[] theBonds;
374	>	delete[] theBends;
375	>	delete[] theTorsions;
376		}
402	–	simnfo->box_z = the_globals->getBoxZ();
377		}
378
379		#ifdef IS_MPI
380	<	strcpy( checkPointMsg, "Box size set up" );
380	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
381		MPIcheckPoint();
382		#endif // is_mpi
383
384	+	// clean up the forcefield
385
386	<	// initialize the arrays
386	>	the_ff->calcRcut();
387	>	the_ff->cleanMe();
388	>	}
389
390	<	the_ff->setSimInfo( simnfo );
390	>	void SimSetup::initFromBass(void){
391	>	int i, j, k;
392	>	int n_cells;
393	>	double cellx, celly, cellz;
394	>	double temp1, temp2, temp3;
395	>	int n_per_extra;
396	>	int n_extra;
397	>	int have_extra, done;
398
399	<	makeMolecules();
400	<	simnfo->identArray = new int[simnfo->n_atoms];
401	<	for(i=0; i<simnfo->n_atoms; i++){
402	<	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	<	}
399	>	double vel[3];
400	>	vel[0] = 0.0;
401	>	vel[1] = 0.0;
402	>	vel[2] = 0.0;
403
404	<	if( !the_globals->haveEST() ){
405	<	sprintf( painCave.errMsg,
406	<	"SimSetup Warning: using default value of 0.05 * the "
407	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
408	<	);
409	<	painCave.isFatal = 0;
410	<	simError();
411	<	simnfo->est = 0.05 * simnfo->ecr;
412	<	} else {
413	<	simnfo->est        = the_globals->getEST();
414	<	}
415	<
416	<	if(!the_globals->haveDielectric() ){
417	<	sprintf( painCave.errMsg,
418	<	"SimSetup Error: You are trying to use Reaction Field without"
419	<	"setting a dielectric constant!\n"
420	<	);
404	>	temp1 = (double) tot_nmol / 4.0;
405	>	temp2 = pow(temp1, (1.0 / 3.0));
406	>	temp3 = ceil(temp2);
407	>
408	>	have_extra = 0;
409	>	if (temp2 < temp3){
410	>	// we have a non-complete lattice
411	>	have_extra = 1;
412	>
413	>	n_cells = (int) temp3 - 1;
414	>	cellx = info[0].boxL[0] / temp3;
415	>	celly = info[0].boxL[1] / temp3;
416	>	cellz = info[0].boxL[2] / temp3;
417	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
418	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
419	>	n_per_extra = (int) ceil(temp1);
420	>
421	>	if (n_per_extra > 4){
422	>	sprintf(painCave.errMsg,
423	>	"SimSetup error. There has been an error in constructing"
424	>	" the non-complete lattice.\n");
425		painCave.isFatal = 1;
426		simError();
427		}
428	<	simnfo->dielectric = the_globals->getDielectric();
429	<	} else {
430	<	if (simnfo->n_dipoles) {
431	<
432	<	if( !the_globals->haveECR() ){
433	<	sprintf( painCave.errMsg,
434	<	"SimSetup Warning: using default value of 1/2 the smallest"
435	<	"box length for the electrostaticCutoffRadius.\n"
436	<	"I hope you have a very fast processor!\n");
437	<	painCave.isFatal = 0;
438	<	simError();
439	<	double smallest;
440	<	smallest = simnfo->box_x;
441	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
442	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
443	<	simnfo->ecr = 0.5 * smallest;
444	<	} else {
445	<	simnfo->ecr        = the_globals->getECR();
428	>	}
429	>	else{
430	>	n_cells = (int) temp3;
431	>	cellx = info[0].boxL[0] / temp3;
432	>	celly = info[0].boxL[1] / temp3;
433	>	cellz = info[0].boxL[2] / temp3;
434	>	}
435	>
436	>	current_mol = 0;
437	>	current_comp_mol = 0;
438	>	current_comp = 0;
439	>	current_atom_ndx = 0;
440	>
441	>	for (i = 0; i < n_cells ; i++){
442	>	for (j = 0; j < n_cells; j++){
443	>	for (k = 0; k < n_cells; k++){
444	>	makeElement(i * cellx, j * celly, k * cellz);
445	>
446	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
447	>
448	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
449	>
450	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
451		}
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	–	}
452		}
453	<	}
453	>	}
454
455	<	#ifdef IS_MPI
456	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
497	<	MPIcheckPoint();
498	<	#endif // is_mpi
455	>	if (have_extra){
456	>	done = 0;
457
458	<	if( the_globals->haveInitialConfig() ){
459	<
460	<	InitializeFromFile* fileInit;
461	<	#ifdef IS_MPI // is_mpi
462	<	if( worldRank == 0 ){
463	<	#endif //is_mpi
464	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
465	<	#ifdef IS_MPI
466	<	}else fileInit = new InitializeFromFile( NULL );
467	<	#endif
468	<	fileInit->read_xyz( simnfo ); // default velocities on
458	>	int start_ndx;
459	>	for (i = 0; i < (n_cells + 1) && !done; i++){
460	>	for (j = 0; j < (n_cells + 1) && !done; j++){
461	>	if (i < n_cells){
462	>	if (j < n_cells){
463	>	start_ndx = n_cells;
464	>	}
465	>	else
466	>	start_ndx = 0;
467	>	}
468	>	else
469	>	start_ndx = 0;
470
471	<	delete fileInit;
472	<	}
473	<	else{
471	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
472	>	makeElement(i * cellx, j * celly, k * cellz);
473	>	done = (current_mol >= tot_nmol);
474
475	<	#ifdef IS_MPI
475	>	if (!done && n_per_extra > 1){
476	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
477	>	k * cellz);
478	>	done = (current_mol >= tot_nmol);
479	>	}
480
481	<	// no init from bass
482	<
483	<	sprintf( painCave.errMsg,
484	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
485	<	painCave.isFatal;
523	<	simError();
524	<
525	<	#else
481	>	if (!done && n_per_extra > 2){
482	>	makeElement(i * cellx, j * celly + 0.5 * celly,
483	>	k * cellz + 0.5 * cellz);
484	>	done = (current_mol >= tot_nmol);
485	>	}
486
487	<	initFromBass();
487	>	if (!done && n_per_extra > 3){
488	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
489	>	k * cellz + 0.5 * cellz);
490	>	done = (current_mol >= tot_nmol);
491	>	}
492	>	}
493	>	}
494	>	}
495	>	}
496
497	+	for (i = 0; i < info[0].n_atoms; i++){
498	+	info[0].atoms[i]->setVel(vel);
499	+	}
500	+	}
501
502	<	#endif
503	<	}
502	>	void SimSetup::makeElement(double x, double y, double z){
503	>	int k;
504	>	AtomStamp* current_atom;
505	>	DirectionalAtom* dAtom;
506	>	double rotMat[3][3];
507	>	double pos[3];
508
509	<	#ifdef IS_MPI
510	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
511	<	MPIcheckPoint();
512	<	#endif // is_mpi
509	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
510	>	current_atom = comp_stamps[current_comp]->getAtom(k);
511	>	if (!current_atom->havePosition()){
512	>	sprintf(painCave.errMsg,
513	>	"SimSetup:initFromBass error.\n"
514	>	"\tComponent %s, atom %s does not have a position specified.\n"
515	>	"\tThe initialization routine is unable to give a start"
516	>	" position.\n",
517	>	comp_stamps[current_comp]->getID(), current_atom->getType());
518	>	painCave.isFatal = 1;
519	>	simError();
520	>	}
521
522	+	pos[0] = x + current_atom->getPosX();
523	+	pos[1] = y + current_atom->getPosY();
524	+	pos[2] = z + current_atom->getPosZ();
525
526	<
540	<
541	<
526	>	info[0].atoms[current_atom_ndx]->setPos(pos);
527
528	<
529	<	#ifdef IS_MPI
545	<	if( worldRank == 0 ){
546	<	#endif // is_mpi
547	<
548	<	if( the_globals->haveFinalConfig() ){
549	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
550	<	}
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	<	}
528	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
529	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
530
531	<	if( the_globals->haveStatusTime() ){
532	<	simnfo->statusTime = the_globals->getStatusTime();
533	<	}
531	>	rotMat[0][0] = 1.0;
532	>	rotMat[0][1] = 0.0;
533	>	rotMat[0][2] = 0.0;
534
535	<	if( the_globals->haveThermalTime() ){
536	<	simnfo->thermalTime = the_globals->getThermalTime();
537	<	}
535	>	rotMat[1][0] = 0.0;
536	>	rotMat[1][1] = 1.0;
537	>	rotMat[1][2] = 0.0;
538
539	<	// check for the temperature set flag
539	>	rotMat[2][0] = 0.0;
540	>	rotMat[2][1] = 0.0;
541	>	rotMat[2][2] = 1.0;
542
543	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
543	>	dAtom->setA(rotMat);
544	>	}
545
546	<
653	<	//   // make the longe range forces and the integrator
654	<
655	<	//   new AllLong( simnfo );
656	<
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 );
661	<
662	<
663	<
664	<	// initialize the Fortran
665	<
666	<	simnfo->refreshSim();
667	<
668	<	if( !strcmp( simnfo->mixingRule, "standard") ){
669	<	the_ff->initForceField( LB_MIXING_RULE );
546	>	current_atom_ndx++;
547		}
671	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
672	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
673	–	}
674	–	else{
675	–	sprintf( painCave.errMsg,
676	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
677	–	simnfo->mixingRule );
678	–	painCave.isFatal = 1;
679	–	simError();
680	–	}
548
549	+	current_mol++;
550	+	current_comp_mol++;
551
552	<	#ifdef IS_MPI
553	<	strcpy( checkPointMsg,
554	<	"Successfully intialized the mixingRule for Fortran." );
555	<	MPIcheckPoint();
687	<	#endif // is_mpi
552	>	if (current_comp_mol >= components_nmol[current_comp]){
553	>	current_comp_mol = 0;
554	>	current_comp++;
555	>	}
556		}
557
558
559	<	void SimSetup::makeMolecules( void ){
559	>	void SimSetup::gatherInfo(void){
560	>	int i;
561
562	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
563	<	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
562	>	ensembleCase = -1;
563	>	ffCase = -1;
564
565	<	the_ff->readParams();
565	>	// set the easy ones first
566
567	<
568	<	// init the molecules
567	>	for (i = 0; i < nInfo; i++){
568	>	info[i].target_temp = globals->getTargetTemp();
569	>	info[i].dt = globals->getDt();
570	>	info[i].run_time = globals->getRunTime();
571	>	}
572	>	n_components = globals->getNComponents();
573
710	–	atomOffset = 0;
711	–	excludeOffset = 0;
712	–	for(i=0; i<simnfo->n_mol; i++){
713	–
714	–	stampID = the_molecules[i].getStampID();
574
575	<	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;
575	>	// get the forceField
576
577	<	info.myAtoms = &the_atoms[atomOffset];
723	<	info.myExcludes = &the_excludes[excludeOffset];
724	<	info.myBonds = new Bond*[info.nBonds];
725	<	info.myBends = new Bend*[info.nBends];
726	<	info.myTorsions = new Torsions*[info.nTorsions];
577	>	strcpy(force_field, globals->getForceField());
578
579	<	theBonds = new bond_pair[info.nBonds];
580	<	theBends = new bend_set[info.nBends];
581	<	theTorsions = new torsion_set[info.nTorsions];
582	<
583	<	// make the Atoms
584	<
585	<	for(j=0; j<info.nAtoms; j++){
586	<
587	<	currentAtom = theComponents[stampID]->getAtom( j );
588	<	if( currentAtom->haveOrientation() ){
589	<
590	<	dAtom = new DirectionalAtom(j + atomOffset);
591	<	simnfo->n_oriented++;
592	<	info.myAtoms[j] = dAtom;
593	<
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 );
757	<	}
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;
579	>	if (!strcasecmp(force_field, "DUFF")){
580	>	ffCase = FF_DUFF;
581	>	}
582	>	else if (!strcasecmp(force_field, "LJ")){
583	>	ffCase = FF_LJ;
584	>	}
585	>	else if (!strcasecmp(force_field, "EAM")){
586	>	ffCase = FF_EAM;
587	>	}
588	>	else{
589	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
590	>	force_field);
591	>	painCave.isFatal = 1;
592	>	simError();
593	>	}
594
595	<	exI = theBonds[i].a;
778	<	exJ = theBonds[i].b;
595	>	// get the ensemble
596
597	<	// exclude_I must always be the smaller of the pair
781	<	if( exI > exJ ){
782	<	tempEx = exI;
783	<	exI = exJ;
784	<	exJ = tempEx;
785	<	}
786	<	#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
796	<	}
797	<	excludeOffset += info.nBonds;
597	>	strcpy(ensemble, globals->getEnsemble());
598
599	<	//make the bends
600	<	for(j=0; j<info.nBends; j++){
601	<
602	<	currentBend = comp_stamps[stampID]->getBend( j );
603	<	theBends[j].a = currentBend->getA() + atomOffset;
604	<	theBends[j].b = currentBend->getB() + atomOffset;
605	<	theBends[j].c = currentBend->getC() + atomOffset;
606	<
607	<	if( currentBend->haveExtras() ){
608	<
609	<	extras = current_bend->getExtras();
610	<	current_extra = extras;
611	<
612	<	while( current_extra != NULL ){
613	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
614	<
615	<	switch( current_extra->getType() ){
616	<
617	<	case 0:
618	<	theBends[j].ghost =
619	<	current_extra->getInt() + atomOffset;
620	<	theBends[j].isGhost = 1;
621	<	break;
622	<
623	<	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
882	<	}
883	<	excludeOffset += info.nBends;
599	>	if (!strcasecmp(ensemble, "NVE")){
600	>	ensembleCase = NVE_ENS;
601	>	}
602	>	else if (!strcasecmp(ensemble, "NVT")){
603	>	ensembleCase = NVT_ENS;
604	>	}
605	>	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
606	>	ensembleCase = NPTi_ENS;
607	>	}
608	>	else if (!strcasecmp(ensemble, "NPTf")){
609	>	ensembleCase = NPTf_ENS;
610	>	}
611	>	else if (!strcasecmp(ensemble, "NPTxyz")){
612	>	ensembleCase = NPTxyz_ENS;
613	>	}
614	>	else{
615	>	sprintf(painCave.errMsg,
616	>	"SimSetup Warning. Unrecognized Ensemble -> %s, "
617	>	"reverting to NVE for this simulation.\n",
618	>	ensemble);
619	>	painCave.isFatal = 0;
620	>	simError();
621	>	strcpy(ensemble, "NVE");
622	>	ensembleCase = NVE_ENS;
623	>	}
624
625	<	for(j=0; j<info.nTorsions; j++){
626	<
887	<	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;
625	>	for (i = 0; i < nInfo; i++){
626	>	strcpy(info[i].ensemble, ensemble);
627
628	<	// exclude_I must always be the smaller of the pair
897	<	if( exI > exJ ){
898	<	tempEx = exI;
899	<	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
912	<	}
913	<	excludeOffset += info.nTorsions;
628	>	// get the mixing rule
629
630	<
631	<	// send the arrays off to the forceField for init.
917	<
918	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
919	<	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 );
922	<
923	<
924	<	the_molecules[i].initialize( info );
925	<	atomOffset += info.nAtoms;
630	>	strcpy(info[i].mixingRule, globals->getMixingRule());
631	>	info[i].usePBC = globals->getPBC();
632		}
633
634	<	// clean up the forcefield
929	<	the_ff->calcRcut();
930	<	the_ff->cleanMe();
931	<	}
634	>	// get the components and calculate the tot_nMol and indvidual n_mol
635
636	<	void SimSetup::initFromBass( void ){
636	>	the_components = globals->getComponents();
637	>	components_nmol = new int[n_components];
638
935	–	int i, j, k;
936	–	int n_cells;
937	–	double cellx, celly, cellz;
938	–	double temp1, temp2, temp3;
939	–	int n_per_extra;
940	–	int n_extra;
941	–	int have_extra, done;
639
640	<	temp1 = (double)tot_nmol / 4.0;
641	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
642	<	temp3 = ceil( temp2 );
640	>	if (!globals->haveNMol()){
641	>	// we don't have the total number of molecules, so we assume it is
642	>	// given in each component
643
644	<	have_extra =0;
645	<	if( temp2 < temp3 ){ // we have a non-complete lattice
646	<	have_extra =1;
644	>	tot_nmol = 0;
645	>	for (i = 0; i < n_components; i++){
646	>	if (!the_components[i]->haveNMol()){
647	>	// we have a problem
648	>	sprintf(painCave.errMsg,
649	>	"SimSetup Error. No global NMol or component NMol"
650	>	" given. Cannot calculate the number of atoms.\n");
651	>	painCave.isFatal = 1;
652	>	simError();
653	>	}
654
655	<	n_cells = (int)temp3 - 1;
656	<	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 );
958	<
959	<	if( n_per_extra > 4){
960	<	sprintf( painCave.errMsg,
961	<	"SimSetup error. There has been an error in constructing"
962	<	" the non-complete lattice.\n" );
963	<	painCave.isFatal = 1;
964	<	simError();
655	>	tot_nmol += the_components[i]->getNMol();
656	>	components_nmol[i] = the_components[i]->getNMol();
657		}
658		}
659		else{
660	<	n_cells = (int)temp3;
661	<	cellx = simnfo->box_x / temp3;
662	<	celly = simnfo->box_y / temp3;
663	<	cellz = simnfo->box_z / temp3;
660	>	sprintf(painCave.errMsg,
661	>	"SimSetup error.\n"
662	>	"\tSorry, the ability to specify total"
663	>	" nMols and then give molfractions in the components\n"
664	>	"\tis not currently supported."
665	>	" Please give nMol in the components.\n");
666	>	painCave.isFatal = 1;
667	>	simError();
668		}
669
670	<	current_mol = 0;
975	<	current_comp_mol = 0;
976	<	current_comp = 0;
977	<	current_atom_ndx = 0;
670	>	// set the status, sample, and thermal kick times
671
672	<	for( i=0; i < n_cells ; i++ ){
673	<	for( j=0; j < n_cells; j++ ){
674	<	for( k=0; k < n_cells; k++ ){
672	>	for (i = 0; i < nInfo; i++){
673	>	if (globals->haveSampleTime()){
674	>	info[i].sampleTime = globals->getSampleTime();
675	>	info[i].statusTime = info[i].sampleTime;
676	>	info[i].thermalTime = info[i].sampleTime;
677	>	}
678	>	else{
679	>	info[i].sampleTime = globals->getRunTime();
680	>	info[i].statusTime = info[i].sampleTime;
681	>	info[i].thermalTime = info[i].sampleTime;
682	>	}
683
684	<	makeElement( i * cellx,
685	<	j * celly,
686	<	k * cellz );
684	>	if (globals->haveStatusTime()){
685	>	info[i].statusTime = globals->getStatusTime();
686	>	}
687
688	<	makeElement( i * cellx + 0.5 * cellx,
689	<	j * celly + 0.5 * celly,
690	<	k * cellz );
688	>	if (globals->haveThermalTime()){
689	>	info[i].thermalTime = globals->getThermalTime();
690	>	}
691
692	<	makeElement( i * cellx,
693	<	j * celly + 0.5 * celly,
694	<	k * cellz + 0.5 * cellz );
695	<
995	<	makeElement( i * cellx + 0.5 * cellx,
996	<	j * celly,
997	<	k * cellz + 0.5 * cellz );
998	<	}
692	>	info[i].resetIntegrator = 0;
693	>	if( globals->haveResetTime() ){
694	>	info[i].resetTime = globals->getResetTime();
695	>	info[i].resetIntegrator = 1;
696		}
697	+
698	+	// check for the temperature set flag
699	+
700	+	if (globals->haveTempSet())
701	+	info[i].setTemp = globals->getTempSet();
702	+
703		}
704	+
705	+	//setup seed for random number generator
706	+	int seedValue;
707
708	<	if( have_extra ){
709	<	done = 0;
708	>	if (globals->haveSeed()){
709	>	seedValue = globals->getSeed();
710
711	<	int start_ndx;
712	<	for( i=0; i < (n_cells+1) && !done; i++ ){
713	<	for( j=0; j < (n_cells+1) && !done; j++ ){
714	<
715	<	if( i < n_cells ){
711	>	if(seedValue / 1E9 == 0){
712	>	sprintf(painCave.errMsg,
713	>	"Seed for sprng library should contain at least 9 digits\n"
714	>	"OOPSE will generate a seed for user\n");
715	>	painCave.isFatal = 0;
716	>	simError();
717
718	<	if( j < n_cells ){
719	<	start_ndx = n_cells;
720	<	}
721	<	else start_ndx = 0;
722	<	}
723	<	else start_ndx = 0;
718	>	//using seed generated by system instead of invalid seed set by user
719	>	#ifndef IS_MPI
720	>	seedValue = make_sprng_seed();
721	>	#else
722	>	if (worldRank == 0){
723	>	seedValue = make_sprng_seed();
724	>	}
725	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
726	>	#endif
727	>	}
728	>	}//end of if branch of globals->haveSeed()
729	>	else{
730	>
731	>	#ifndef IS_MPI
732	>	seedValue = make_sprng_seed();
733	>	#else
734	>	if (worldRank == 0){
735	>	seedValue = make_sprng_seed();
736	>	}
737	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
738	>	#endif
739	>	}//end of globals->haveSeed()
740
741	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
741	>	for (int i = 0; i < nInfo; i++){
742	>	info[i].setSeed(seedValue);
743	>	}
744
745	<	makeElement( i * cellx,
746	<	j * celly,
747	<	k * cellz );
748	<	done = ( current_mol >= tot_nmol );
745	>	#ifdef IS_MPI
746	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
747	>	MPIcheckPoint();
748	>	#endif // is_mpi
749	>	}
750
1025	–	if( !done && n_per_extra > 1 ){
1026	–	makeElement( i * cellx + 0.5 * cellx,
1027	–	j * celly + 0.5 * celly,
1028	–	k * cellz );
1029	–	done = ( current_mol >= tot_nmol );
1030	–	}
751
752	<	if( !done && n_per_extra > 2){
753	<	makeElement( i * cellx,
754	<	j * celly + 0.5 * celly,
755	<	k * cellz + 0.5 * cellz );
1036	<	done = ( current_mol >= tot_nmol );
1037	<	}
752	>	void SimSetup::finalInfoCheck(void){
753	>	int index;
754	>	int usesDipoles;
755	>	int i;
756
757	<	if( !done && n_per_extra > 3){
758	<	makeElement( i * cellx + 0.5 * cellx,
759	<	j * celly,
760	<	k * cellz + 0.5 * cellz );
761	<	done = ( current_mol >= tot_nmol );
762	<	}
763	<	}
757	>	for (i = 0; i < nInfo; i++){
758	>	// check electrostatic parameters
759	>
760	>	index = 0;
761	>	usesDipoles = 0;
762	>	while ((index < info[i].n_atoms) && !usesDipoles){
763	>	usesDipoles = (info[i].atoms[index])->hasDipole();
764	>	index++;
765	>	}
766	>
767	>	#ifdef IS_MPI
768	>	int myUse = usesDipoles;
769	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
770	>	#endif //is_mpi
771	>
772	>	double theEcr, theEst;
773	>
774	>	if (globals->getUseRF()){
775	>	info[i].useReactionField = 1;
776	>
777	>	if (!globals->haveECR()){
778	>	sprintf(painCave.errMsg,
779	>	"SimSetup Warning: using default value of 1/2 the smallest "
780	>	"box length for the electrostaticCutoffRadius.\n"
781	>	"I hope you have a very fast processor!\n");
782	>	painCave.isFatal = 0;
783	>	simError();
784	>	double smallest;
785	>	smallest = info[i].boxL[0];
786	>	if (info[i].boxL[1] <= smallest)
787	>	smallest = info[i].boxL[1];
788	>	if (info[i].boxL[2] <= smallest)
789	>	smallest = info[i].boxL[2];
790	>	theEcr = 0.5 * smallest;
791		}
792	+	else{
793	+	theEcr = globals->getECR();
794	+	}
795	+
796	+	if (!globals->haveEST()){
797	+	sprintf(painCave.errMsg,
798	+	"SimSetup Warning: using default value of 0.05 * the "
799	+	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
800	+	painCave.isFatal = 0;
801	+	simError();
802	+	theEst = 0.05 * theEcr;
803	+	}
804	+	else{
805	+	theEst = globals->getEST();
806	+	}
807	+
808	+	info[i].setDefaultEcr(theEcr, theEst);
809	+
810	+	if (!globals->haveDielectric()){
811	+	sprintf(painCave.errMsg,
812	+	"SimSetup Error: You are trying to use Reaction Field without"
813	+	"setting a dielectric constant!\n");
814	+	painCave.isFatal = 1;
815	+	simError();
816	+	}
817	+	info[i].dielectric = globals->getDielectric();
818		}
819	+	else{
820	+	if (usesDipoles){
821	+	if (!globals->haveECR()){
822	+	sprintf(painCave.errMsg,
823	+	"SimSetup Warning: using default value of 1/2 the smallest "
824	+	"box length for the electrostaticCutoffRadius.\n"
825	+	"I hope you have a very fast processor!\n");
826	+	painCave.isFatal = 0;
827	+	simError();
828	+	double smallest;
829	+	smallest = info[i].boxL[0];
830	+	if (info[i].boxL[1] <= smallest)
831	+	smallest = info[i].boxL[1];
832	+	if (info[i].boxL[2] <= smallest)
833	+	smallest = info[i].boxL[2];
834	+	theEcr = 0.5 * smallest;
835	+	}
836	+	else{
837	+	theEcr = globals->getECR();
838	+	}
839	+
840	+	if (!globals->haveEST()){
841	+	sprintf(painCave.errMsg,
842	+	"SimSetup Warning: using default value of 0.05 * the "
843	+	"electrostaticCutoffRadius for the "
844	+	"electrostaticSkinThickness\n");
845	+	painCave.isFatal = 0;
846	+	simError();
847	+	theEst = 0.05 * theEcr;
848	+	}
849	+	else{
850	+	theEst = globals->getEST();
851	+	}
852	+
853	+	info[i].setDefaultEcr(theEcr, theEst);
854	+	}
855	+	}
856		}
857
858	+	#ifdef IS_MPI
859	+	strcpy(checkPointMsg, "post processing checks out");
860	+	MPIcheckPoint();
861	+	#endif // is_mpi
862	+	}
863
864	<	for( i=0; i<simnfo->n_atoms; i++ ){
865	<	simnfo->atoms[i]->set_vx( 0.0 );
866	<	simnfo->atoms[i]->set_vy( 0.0 );
867	<	simnfo->atoms[i]->set_vz( 0.0 );
864	>	void SimSetup::initSystemCoords(void){
865	>	int i;
866	>
867	>	char* inName;
868	>
869	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
870	>
871	>	for (i = 0; i < info[0].n_atoms; i++)
872	>	info[0].atoms[i]->setCoords();
873	>
874	>	if (globals->haveInitialConfig()){
875	>	InitializeFromFile* fileInit;
876	>	#ifdef IS_MPI // is_mpi
877	>	if (worldRank == 0){
878	>	#endif //is_mpi
879	>	inName = globals->getInitialConfig();
880	>	fileInit = new InitializeFromFile(inName);
881	>	#ifdef IS_MPI
882	>	}
883	>	else
884	>	fileInit = new InitializeFromFile(NULL);
885	>	#endif
886	>	fileInit->readInit(info); // default velocities on
887	>
888	>	delete fileInit;
889		}
890	+	else{
891	+	#ifdef IS_MPI
892	+
893	+	// no init from bass
894	+
895	+	sprintf(painCave.errMsg,
896	+	"Cannot intialize a parallel simulation without an initial configuration file.\n");
897	+	painCave.isFatal = 1;;
898	+	simError();
899	+
900	+	#else
901	+
902	+	initFromBass();
903	+
904	+
905	+	#endif
906	+	}
907	+
908	+	#ifdef IS_MPI
909	+	strcpy(checkPointMsg, "Successfully read in the initial configuration");
910	+	MPIcheckPoint();
911	+	#endif // is_mpi
912		}
913
1058	–	void SimSetup::makeElement( double x, double y, double z ){
914
915	+	void SimSetup::makeOutNames(void){
916		int k;
1061	–	AtomStamp* current_atom;
1062	–	DirectionalAtom* dAtom;
1063	–	double rotMat[3][3];
917
1065	–	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
918
919	<	current_atom = comp_stamps[current_comp]->getAtom( k );
920	<	if( !current_atom->havePosition() ){
921	<	sprintf( painCave.errMsg,
922	<	"SimSetup:initFromBass error.\n"
923	<	"\tComponent %s, atom %s does not have a position specified.\n"
924	<	"\tThe initialization routine is unable to give a start"
925	<	" position.\n",
926	<	comp_stamps[current_comp]->getID(),
927	<	current_atom->getType() );
919	>	for (k = 0; k < nInfo; k++){
920	>	#ifdef IS_MPI
921	>	if (worldRank == 0){
922	>	#endif // is_mpi
923	>
924	>	if (globals->haveFinalConfig()){
925	>	strcpy(info[k].finalName, globals->getFinalConfig());
926	>	}
927	>	else{
928	>	strcpy(info[k].finalName, inFileName);
929	>	char* endTest;
930	>	int nameLength = strlen(info[k].finalName);
931	>	endTest = &(info[k].finalName[nameLength - 5]);
932	>	if (!strcmp(endTest, ".bass")){
933	>	strcpy(endTest, ".eor");
934	>	}
935	>	else if (!strcmp(endTest, ".BASS")){
936	>	strcpy(endTest, ".eor");
937	>	}
938	>	else{
939	>	endTest = &(info[k].finalName[nameLength - 4]);
940	>	if (!strcmp(endTest, ".bss")){
941	>	strcpy(endTest, ".eor");
942	>	}
943	>	else if (!strcmp(endTest, ".mdl")){
944	>	strcpy(endTest, ".eor");
945	>	}
946	>	else{
947	>	strcat(info[k].finalName, ".eor");
948	>	}
949	>	}
950	>	}
951	>
952	>	// make the sample and status out names
953	>
954	>	strcpy(info[k].sampleName, inFileName);
955	>	char* endTest;
956	>	int nameLength = strlen(info[k].sampleName);
957	>	endTest = &(info[k].sampleName[nameLength - 5]);
958	>	if (!strcmp(endTest, ".bass")){
959	>	strcpy(endTest, ".dump");
960	>	}
961	>	else if (!strcmp(endTest, ".BASS")){
962	>	strcpy(endTest, ".dump");
963	>	}
964	>	else{
965	>	endTest = &(info[k].sampleName[nameLength - 4]);
966	>	if (!strcmp(endTest, ".bss")){
967	>	strcpy(endTest, ".dump");
968	>	}
969	>	else if (!strcmp(endTest, ".mdl")){
970	>	strcpy(endTest, ".dump");
971	>	}
972	>	else{
973	>	strcat(info[k].sampleName, ".dump");
974	>	}
975	>	}
976	>
977	>	strcpy(info[k].statusName, inFileName);
978	>	nameLength = strlen(info[k].statusName);
979	>	endTest = &(info[k].statusName[nameLength - 5]);
980	>	if (!strcmp(endTest, ".bass")){
981	>	strcpy(endTest, ".stat");
982	>	}
983	>	else if (!strcmp(endTest, ".BASS")){
984	>	strcpy(endTest, ".stat");
985	>	}
986	>	else{
987	>	endTest = &(info[k].statusName[nameLength - 4]);
988	>	if (!strcmp(endTest, ".bss")){
989	>	strcpy(endTest, ".stat");
990	>	}
991	>	else if (!strcmp(endTest, ".mdl")){
992	>	strcpy(endTest, ".stat");
993	>	}
994	>	else{
995	>	strcat(info[k].statusName, ".stat");
996	>	}
997	>	}
998	>
999	>	#ifdef IS_MPI
1000	>
1001	>	}
1002	>	#endif // is_mpi
1003	>	}
1004	>	}
1005	>
1006	>
1007	>	void SimSetup::sysObjectsCreation(void){
1008	>	int i, k;
1009	>
1010	>	// create the forceField
1011	>
1012	>	createFF();
1013	>
1014	>	// extract componentList
1015	>
1016	>	compList();
1017	>
1018	>	// calc the number of atoms, bond, bends, and torsions
1019	>
1020	>	calcSysValues();
1021	>
1022	>	#ifdef IS_MPI
1023	>	// divide the molecules among the processors
1024	>
1025	>	mpiMolDivide();
1026	>	#endif //is_mpi
1027	>
1028	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1029	>
1030	>	makeSysArrays();
1031	>
1032	>	// make and initialize the molecules (all but atomic coordinates)
1033	>
1034	>	makeMolecules();
1035	>
1036	>	for (k = 0; k < nInfo; k++){
1037	>	info[k].identArray = new int[info[k].n_atoms];
1038	>	for (i = 0; i < info[k].n_atoms; i++){
1039	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1040	>	}
1041	>	}
1042	>	}
1043	>
1044	>
1045	>	void SimSetup::createFF(void){
1046	>	switch (ffCase){
1047	>	case FF_DUFF:
1048	>	the_ff = new DUFF();
1049	>	break;
1050	>
1051	>	case FF_LJ:
1052	>	the_ff = new LJFF();
1053	>	break;
1054	>
1055	>	case FF_EAM:
1056	>	the_ff = new EAM_FF();
1057	>	break;
1058	>
1059	>	default:
1060	>	sprintf(painCave.errMsg,
1061	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1062		painCave.isFatal = 1;
1063		simError();
1064	+	}
1065	+
1066	+	#ifdef IS_MPI
1067	+	strcpy(checkPointMsg, "ForceField creation successful");
1068	+	MPIcheckPoint();
1069	+	#endif // is_mpi
1070	+	}
1071	+
1072	+
1073	+	void SimSetup::compList(void){
1074	+	int i;
1075	+	char* id;
1076	+	LinkedMolStamp* headStamp = new LinkedMolStamp();
1077	+	LinkedMolStamp* currentStamp = NULL;
1078	+	comp_stamps = new MoleculeStamp * [n_components];
1079	+
1080	+	// make an array of molecule stamps that match the components used.
1081	+	// also extract the used stamps out into a separate linked list
1082	+
1083	+	for (i = 0; i < nInfo; i++){
1084	+	info[i].nComponents = n_components;
1085	+	info[i].componentsNmol = components_nmol;
1086	+	info[i].compStamps = comp_stamps;
1087	+	info[i].headStamp = headStamp;
1088	+	}
1089	+
1090	+
1091	+	for (i = 0; i < n_components; i++){
1092	+	id = the_components[i]->getType();
1093	+	comp_stamps[i] = NULL;
1094	+
1095	+	// check to make sure the component isn't already in the list
1096	+
1097	+	comp_stamps[i] = headStamp->match(id);
1098	+	if (comp_stamps[i] == NULL){
1099	+	// extract the component from the list;
1100	+
1101	+	currentStamp = stamps->extractMolStamp(id);
1102	+	if (currentStamp == NULL){
1103	+	sprintf(painCave.errMsg,
1104	+	"SimSetup error: Component \"%s\" was not found in the "
1105	+	"list of declared molecules\n",
1106	+	id);
1107	+	painCave.isFatal = 1;
1108	+	simError();
1109	+	}
1110	+
1111	+	headStamp->add(currentStamp);
1112	+	comp_stamps[i] = headStamp->match(id);
1113		}
1114	+	}
1115
1116	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1117	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1118	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1116	>	#ifdef IS_MPI
1117	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1118	>	MPIcheckPoint();
1119	>	#endif // is_mpi
1120	>	}
1121
1122	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1122	>	void SimSetup::calcSysValues(void){
1123	>	int i;
1124
1125	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1125	>	int* molMembershipArray;
1126
1127	<	rotMat[0][0] = 1.0;
1128	<	rotMat[0][1] = 0.0;
1129	<	rotMat[0][2] = 0.0;
1127	>	tot_atoms = 0;
1128	>	tot_bonds = 0;
1129	>	tot_bends = 0;
1130	>	tot_torsions = 0;
1131	>	for (i = 0; i < n_components; i++){
1132	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1133	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1134	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1135	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1136	>	}
1137
1138	<	rotMat[1][0] = 0.0;
1139	<	rotMat[1][1] = 1.0;
1094	<	rotMat[1][2] = 0.0;
1138	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1139	>	molMembershipArray = new int[tot_atoms];
1140
1141	<	rotMat[2][0] = 0.0;
1142	<	rotMat[2][1] = 0.0;
1143	<	rotMat[2][2] = 1.0;
1141	>	for (i = 0; i < nInfo; i++){
1142	>	info[i].n_atoms = tot_atoms;
1143	>	info[i].n_bonds = tot_bonds;
1144	>	info[i].n_bends = tot_bends;
1145	>	info[i].n_torsions = tot_torsions;
1146	>	info[i].n_SRI = tot_SRI;
1147	>	info[i].n_mol = tot_nmol;
1148
1149	<	dAtom->setA( rotMat );
1149	>	info[i].molMembershipArray = molMembershipArray;
1150	>	}
1151	>	}
1152	>
1153	>	#ifdef IS_MPI
1154	>
1155	>	void SimSetup::mpiMolDivide(void){
1156	>	int i, j, k;
1157	>	int localMol, allMol;
1158	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1159	>
1160	>	mpiSim = new mpiSimulation(info);
1161	>
1162	>	globalIndex = mpiSim->divideLabor();
1163	>
1164	>	// set up the local variables
1165	>
1166	>	mol2proc = mpiSim->getMolToProcMap();
1167	>	molCompType = mpiSim->getMolComponentType();
1168	>
1169	>	allMol = 0;
1170	>	localMol = 0;
1171	>	local_atoms = 0;
1172	>	local_bonds = 0;
1173	>	local_bends = 0;
1174	>	local_torsions = 0;
1175	>	globalAtomIndex = 0;
1176	>
1177	>
1178	>	for (i = 0; i < n_components; i++){
1179	>	for (j = 0; j < components_nmol[i]; j++){
1180	>	if (mol2proc[allMol] == worldRank){
1181	>	local_atoms += comp_stamps[i]->getNAtoms();
1182	>	local_bonds += comp_stamps[i]->getNBonds();
1183	>	local_bends += comp_stamps[i]->getNBends();
1184	>	local_torsions += comp_stamps[i]->getNTorsions();
1185	>	localMol++;
1186	>	}
1187	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1188	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1189	>	globalAtomIndex++;
1190	>	}
1191	>
1192	>	allMol++;
1193		}
1194	+	}
1195	+	local_SRI = local_bonds + local_bends + local_torsions;
1196
1197	<	current_atom_ndx++;
1197	>	info[0].n_atoms = mpiSim->getMyNlocal();
1198	>
1199	>	if (local_atoms != info[0].n_atoms){
1200	>	sprintf(painCave.errMsg,
1201	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1202	>	" localAtom (%d) are not equal.\n",
1203	>	info[0].n_atoms, local_atoms);
1204	>	painCave.isFatal = 1;
1205	>	simError();
1206		}
1207
1208	<	current_mol++;
1209	<	current_comp_mol++;
1208	>	info[0].n_bonds = local_bonds;
1209	>	info[0].n_bends = local_bends;
1210	>	info[0].n_torsions = local_torsions;
1211	>	info[0].n_SRI = local_SRI;
1212	>	info[0].n_mol = localMol;
1213
1214	<	if( current_comp_mol >= components_nmol[current_comp] ){
1214	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1215	>	MPIcheckPoint();
1216	>	}
1217
1218	<	current_comp_mol = 0;
1219	<	current_comp++;
1218	>	#endif // is_mpi
1219	>
1220	>
1221	>	void SimSetup::makeSysArrays(void){
1222	>
1223	>	#ifndef IS_MPI
1224	>	int k, j;
1225	>	#endif // is_mpi
1226	>	int i, l;
1227	>
1228	>	Atom** the_atoms;
1229	>	Molecule* the_molecules;
1230	>	Exclude** the_excludes;
1231	>
1232	>
1233	>	for (l = 0; l < nInfo; l++){
1234	>	// create the atom and short range interaction arrays
1235	>
1236	>	the_atoms = new Atom * [info[l].n_atoms];
1237	>	the_molecules = new Molecule[info[l].n_mol];
1238	>	int molIndex;
1239	>
1240	>	// initialize the molecule's stampID's
1241	>
1242	>	#ifdef IS_MPI
1243	>
1244	>
1245	>	molIndex = 0;
1246	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1247	>	if (mol2proc[i] == worldRank){
1248	>	the_molecules[molIndex].setStampID(molCompType[i]);
1249	>	the_molecules[molIndex].setMyIndex(molIndex);
1250	>	the_molecules[molIndex].setGlobalIndex(i);
1251	>	molIndex++;
1252	>	}
1253	>	}
1254	>
1255	>	#else // is_mpi
1256	>
1257	>	molIndex = 0;
1258	>	globalAtomIndex = 0;
1259	>	for (i = 0; i < n_components; i++){
1260	>	for (j = 0; j < components_nmol[i]; j++){
1261	>	the_molecules[molIndex].setStampID(i);
1262	>	the_molecules[molIndex].setMyIndex(molIndex);
1263	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1264	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1265	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1266	>	globalAtomIndex++;
1267	>	}
1268	>	molIndex++;
1269	>	}
1270	>	}
1271	>
1272	>
1273	>	#endif // is_mpi
1274	>
1275	>
1276	>	if (info[l].n_SRI){
1277	>	Exclude::createArray(info[l].n_SRI);
1278	>	the_excludes = new Exclude * [info[l].n_SRI];
1279	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1280	>	the_excludes[ex] = new Exclude(ex);
1281	>	}
1282	>	info[l].globalExcludes = new int;
1283	>	info[l].n_exclude = info[l].n_SRI;
1284	>	}
1285	>	else{
1286	>	Exclude::createArray(1);
1287	>	the_excludes = new Exclude * ;
1288	>	the_excludes[0] = new Exclude(0);
1289	>	the_excludes[0]->setPair(0, 0);
1290	>	info[l].globalExcludes = new int;
1291	>	info[l].globalExcludes[0] = 0;
1292	>	info[l].n_exclude = 0;
1293	>	}
1294	>
1295	>	// set the arrays into the SimInfo object
1296	>
1297	>	info[l].atoms = the_atoms;
1298	>	info[l].molecules = the_molecules;
1299	>	info[l].nGlobalExcludes = 0;
1300	>	info[l].excludes = the_excludes;
1301	>
1302	>	the_ff->setSimInfo(info);
1303	>	}
1304	>	}
1305	>
1306	>	void SimSetup::makeIntegrator(void){
1307	>	int k;
1308	>
1309	>	NVE<RealIntegrator>* myNVE = NULL;
1310	>	NVT<RealIntegrator>* myNVT = NULL;
1311	>	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1312	>	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1313	>	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1314	>
1315	>	for (k = 0; k < nInfo; k++){
1316	>	switch (ensembleCase){
1317	>	case NVE_ENS:
1318	>	if (globals->haveZconstraints()){
1319	>	setupZConstraint(info[k]);
1320	>	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1321	>	}
1322	>	else{
1323	>	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1324	>	}
1325	>
1326	>	info->the_integrator = myNVE;
1327	>	break;
1328	>
1329	>	case NVT_ENS:
1330	>	if (globals->haveZconstraints()){
1331	>	setupZConstraint(info[k]);
1332	>	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1333	>	}
1334	>	else
1335	>	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1336	>
1337	>	myNVT->setTargetTemp(globals->getTargetTemp());
1338	>
1339	>	if (globals->haveTauThermostat())
1340	>	myNVT->setTauThermostat(globals->getTauThermostat());
1341	>	else{
1342	>	sprintf(painCave.errMsg,
1343	>	"SimSetup error: If you use the NVT\n"
1344	>	"    ensemble, you must set tauThermostat.\n");
1345	>	painCave.isFatal = 1;
1346	>	simError();
1347	>	}
1348	>
1349	>	info->the_integrator = myNVT;
1350	>	break;
1351	>
1352	>	case NPTi_ENS:
1353	>	if (globals->haveZconstraints()){
1354	>	setupZConstraint(info[k]);
1355	>	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1356	>	}
1357	>	else
1358	>	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1359	>
1360	>	myNPTi->setTargetTemp(globals->getTargetTemp());
1361	>
1362	>	if (globals->haveTargetPressure())
1363	>	myNPTi->setTargetPressure(globals->getTargetPressure());
1364	>	else{
1365	>	sprintf(painCave.errMsg,
1366	>	"SimSetup error: If you use a constant pressure\n"
1367	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1368	>	painCave.isFatal = 1;
1369	>	simError();
1370	>	}
1371	>
1372	>	if (globals->haveTauThermostat())
1373	>	myNPTi->setTauThermostat(globals->getTauThermostat());
1374	>	else{
1375	>	sprintf(painCave.errMsg,
1376	>	"SimSetup error: If you use an NPT\n"
1377	>	"    ensemble, you must set tauThermostat.\n");
1378	>	painCave.isFatal = 1;
1379	>	simError();
1380	>	}
1381	>
1382	>	if (globals->haveTauBarostat())
1383	>	myNPTi->setTauBarostat(globals->getTauBarostat());
1384	>	else{
1385	>	sprintf(painCave.errMsg,
1386	>	"SimSetup error: If you use an NPT\n"
1387	>	"    ensemble, you must set tauBarostat.\n");
1388	>	painCave.isFatal = 1;
1389	>	simError();
1390	>	}
1391	>
1392	>	info->the_integrator = myNPTi;
1393	>	break;
1394	>
1395	>	case NPTf_ENS:
1396	>	if (globals->haveZconstraints()){
1397	>	setupZConstraint(info[k]);
1398	>	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1399	>	}
1400	>	else
1401	>	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1402	>
1403	>	myNPTf->setTargetTemp(globals->getTargetTemp());
1404	>
1405	>	if (globals->haveTargetPressure())
1406	>	myNPTf->setTargetPressure(globals->getTargetPressure());
1407	>	else{
1408	>	sprintf(painCave.errMsg,
1409	>	"SimSetup error: If you use a constant pressure\n"
1410	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1411	>	painCave.isFatal = 1;
1412	>	simError();
1413	>	}
1414	>
1415	>	if (globals->haveTauThermostat())
1416	>	myNPTf->setTauThermostat(globals->getTauThermostat());
1417	>
1418	>	else{
1419	>	sprintf(painCave.errMsg,
1420	>	"SimSetup error: If you use an NPT\n"
1421	>	"    ensemble, you must set tauThermostat.\n");
1422	>	painCave.isFatal = 1;
1423	>	simError();
1424	>	}
1425	>
1426	>	if (globals->haveTauBarostat())
1427	>	myNPTf->setTauBarostat(globals->getTauBarostat());
1428	>
1429	>	else{
1430	>	sprintf(painCave.errMsg,
1431	>	"SimSetup error: If you use an NPT\n"
1432	>	"    ensemble, you must set tauBarostat.\n");
1433	>	painCave.isFatal = 1;
1434	>	simError();
1435	>	}
1436	>
1437	>	info->the_integrator = myNPTf;
1438	>	break;
1439	>
1440	>	case NPTxyz_ENS:
1441	>	if (globals->haveZconstraints()){
1442	>	setupZConstraint(info[k]);
1443	>	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1444	>	}
1445	>	else
1446	>	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1447	>
1448	>	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1449	>
1450	>	if (globals->haveTargetPressure())
1451	>	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1452	>	else{
1453	>	sprintf(painCave.errMsg,
1454	>	"SimSetup error: If you use a constant pressure\n"
1455	>	"    ensemble, you must set targetPressure in the BASS file.\n");
1456	>	painCave.isFatal = 1;
1457	>	simError();
1458	>	}
1459	>
1460	>	if (globals->haveTauThermostat())
1461	>	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1462	>	else{
1463	>	sprintf(painCave.errMsg,
1464	>	"SimSetup error: If you use an NPT\n"
1465	>	"    ensemble, you must set tauThermostat.\n");
1466	>	painCave.isFatal = 1;
1467	>	simError();
1468	>	}
1469	>
1470	>	if (globals->haveTauBarostat())
1471	>	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1472	>	else{
1473	>	sprintf(painCave.errMsg,
1474	>	"SimSetup error: If you use an NPT\n"
1475	>	"    ensemble, you must set tauBarostat.\n");
1476	>	painCave.isFatal = 1;
1477	>	simError();
1478	>	}
1479	>
1480	>	info->the_integrator = myNPTxyz;
1481	>	break;
1482	>
1483	>	default:
1484	>	sprintf(painCave.errMsg,
1485	>	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1486	>	painCave.isFatal = 1;
1487	>	simError();
1488	>	}
1489		}
1490		}
1491	+
1492	+	void SimSetup::initFortran(void){
1493	+	info[0].refreshSim();
1494	+
1495	+	if (!strcmp(info[0].mixingRule, "standard")){
1496	+	the_ff->initForceField(LB_MIXING_RULE);
1497	+	}
1498	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1499	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1500	+	}
1501	+	else{
1502	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1503	+	info[0].mixingRule);
1504	+	painCave.isFatal = 1;
1505	+	simError();
1506	+	}
1507	+
1508	+
1509	+	#ifdef IS_MPI
1510	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1511	+	MPIcheckPoint();
1512	+	#endif // is_mpi
1513	+	}
1514	+
1515	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1516	+	int nZConstraints;
1517	+	ZconStamp** zconStamp;
1518	+
1519	+	if (globals->haveZconstraintTime()){
1520	+	//add sample time of z-constraint  into SimInfo's property list
1521	+	DoubleData* zconsTimeProp = new DoubleData();
1522	+	zconsTimeProp->setID(ZCONSTIME_ID);
1523	+	zconsTimeProp->setData(globals->getZconsTime());
1524	+	theInfo.addProperty(zconsTimeProp);
1525	+	}
1526	+	else{
1527	+	sprintf(painCave.errMsg,
1528	+	"ZConstraint error: If you use an ZConstraint\n"
1529	+	" , you must set sample time.\n");
1530	+	painCave.isFatal = 1;
1531	+	simError();
1532	+	}
1533	+
1534	+	//push zconsTol into siminfo, if user does not specify
1535	+	//value for zconsTol, a default value will be used
1536	+	DoubleData* zconsTol = new DoubleData();
1537	+	zconsTol->setID(ZCONSTOL_ID);
1538	+	if (globals->haveZconsTol()){
1539	+	zconsTol->setData(globals->getZconsTol());
1540	+	}
1541	+	else{
1542	+	double defaultZConsTol = 0.01;
1543	+	sprintf(painCave.errMsg,
1544	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1545	+	" , default value %f is used.\n",
1546	+	defaultZConsTol);
1547	+	painCave.isFatal = 0;
1548	+	simError();
1549	+
1550	+	zconsTol->setData(defaultZConsTol);
1551	+	}
1552	+	theInfo.addProperty(zconsTol);
1553	+
1554	+	//set Force Subtraction Policy
1555	+	StringData* zconsForcePolicy = new StringData();
1556	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1557	+
1558	+	if (globals->haveZconsForcePolicy()){
1559	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1560	+	}
1561	+	else{
1562	+	sprintf(painCave.errMsg,
1563	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1564	+	"PolicyByMass is used\n");
1565	+	painCave.isFatal = 0;
1566	+	simError();
1567	+	zconsForcePolicy->setData("BYMASS");
1568	+	}
1569	+
1570	+	theInfo.addProperty(zconsForcePolicy);
1571	+
1572	+	//Determine the name of ouput file and add it into SimInfo's property list
1573	+	//Be careful, do not use inFileName, since it is a pointer which
1574	+	//point to a string at master node, and slave nodes do not contain that string
1575	+
1576	+	string zconsOutput(theInfo.finalName);
1577	+
1578	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1579	+
1580	+	StringData* zconsFilename = new StringData();
1581	+	zconsFilename->setID(ZCONSFILENAME_ID);
1582	+	zconsFilename->setData(zconsOutput);
1583	+
1584	+	theInfo.addProperty(zconsFilename);
1585	+
1586	+	//setup index, pos and other parameters of z-constraint molecules
1587	+	nZConstraints = globals->getNzConstraints();
1588	+	theInfo.nZconstraints = nZConstraints;
1589	+
1590	+	zconStamp = globals->getZconStamp();
1591	+	ZConsParaItem tempParaItem;
1592	+
1593	+	ZConsParaData* zconsParaData = new ZConsParaData();
1594	+	zconsParaData->setID(ZCONSPARADATA_ID);
1595	+
1596	+	for (int i = 0; i < nZConstraints; i++){
1597	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1598	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1599	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1600	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1601	+
1602	+	zconsParaData->addItem(tempParaItem);
1603	+	}
1604	+
1605	+	//check the uniqueness of index
1606	+	if(!zconsParaData->isIndexUnique()){
1607	+	sprintf(painCave.errMsg,
1608	+	"ZConstraint Error: molIndex is not unique\n");
1609	+	painCave.isFatal = 1;
1610	+	simError();
1611	+	}
1612	+
1613	+	//sort the parameters by index of molecules
1614	+	zconsParaData->sortByIndex();
1615	+
1616	+	//push data into siminfo, therefore, we can retrieve later
1617	+	theInfo.addProperty(zconsParaData);
1618	+	}

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