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 407 by mmeineke, Wed Mar 26 20:22:02 2003 UTC vs.
Revision 965 by gezelter, Mon Jan 19 21:17:39 2004 UTC

#	Line 1 | Line 1
1	<	#include <cstdlib>
1	>	#include <algorithm>
2	>	#include <stdlib.h>
3		#include <iostream>
4	<	#include <cmath>
5	<
4	>	#include <math.h>
5	>	#include <string>
6	>	#include <sprng.h>
7		#include "SimSetup.hpp"
8	+	#include "ReadWrite.hpp"
9		#include "parse_me.h"
10		#include "Integrator.hpp"
11		#include "simError.h"
#	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	+	/**
34	+	* Check whether dividend is divisble by divisor or not
35	+	*/
36	+	bool isDivisible(double dividend, double divisor){
37	+	double tolerance = 0.000001;
38	+	double quotient;
39	+	double diff;
40	+	int intQuotient;
41	+
42	+	quotient = dividend / divisor;
43	+
44	+	if (quotient < 0)
45	+	quotient = -quotient;
46	+
47	+	intQuotient = int (quotient + tolerance);
48	+
49	+	diff = fabs(fabs(dividend) - intQuotient  * fabs(divisor));
50	+
51	+	if (diff <= tolerance)
52	+	return true;
53	+	else
54	+	return false;
55	+	}
56	+
57		SimSetup::SimSetup(){
58	+
59	+	initSuspend = false;
60	+	isInfoArray = 0;
61	+	nInfo = 1;
62	+
63		stamps = new MakeStamps();
64		globals = new Globals();
65	<
65	>
66	>
67		#ifdef IS_MPI
68	<	strcpy( checkPointMsg, "SimSetup creation successful" );
68	>	strcpy(checkPointMsg, "SimSetup creation successful");
69		MPIcheckPoint();
70		#endif // IS_MPI
71		}
#	Line 27 | Line 75 | void SimSetup::parseFile( char* fileName ){
75		delete globals;
76		}
77
78	<	void SimSetup::parseFile( char* fileName ){
78	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
79	>	info = the_info;
80	>	nInfo = theNinfo;
81	>	isInfoArray = 1;
82	>	initSuspend = true;
83	>	}
84
85	+
86	+	void SimSetup::parseFile(char* fileName){
87		#ifdef IS_MPI
88	<	if( worldRank == 0 ){
88	>	if (worldRank == 0){
89		#endif // is_mpi
90	<
90	>
91		inFileName = fileName;
92	<	set_interface_stamps( stamps, globals );
93	<
92	>	set_interface_stamps(stamps, globals);
93	>
94		#ifdef IS_MPI
95		mpiEventInit();
96		#endif
97
98	<	yacc_BASS( fileName );
98	>	yacc_BASS(fileName);
99
100		#ifdef IS_MPI
101		throwMPIEvent(NULL);
102		}
103	<	else receiveParse();
103	>	else{
104	>	receiveParse();
105	>	}
106		#endif
107
108		}
109
110		#ifdef IS_MPI
111		void SimSetup::receiveParse(void){
112	<
113	<	set_interface_stamps( stamps, globals );
114	<	mpiEventInit();
115	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
112	>	set_interface_stamps(stamps, globals);
113	>	mpiEventInit();
114	>	MPIcheckPoint();
115	>	mpiEventLoop();
116		}
117
118		#endif // is_mpi
119
120	<	void SimSetup::createSim( void ){
120	>	void SimSetup::createSim(void){
121
122	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
122	>	// gather all of the information from the Bass file
123
124	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
124	>	gatherInfo();
125
126	<	// 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();
126	>	// creation of complex system objects
127
128	<	// 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 );
128	>	sysObjectsCreation();
129
130	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
130	>	// check on the post processing info
131
132	+	finalInfoCheck();
133
134	<	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	<	}
134	>	// initialize the system coordinates
135
136	<	#ifdef IS_MPI
137	<	strcpy( checkPointMsg, "ForceField creation successful" );
105	<	MPIcheckPoint();
106	<	#endif // is_mpi
136	>	if ( !initSuspend ){
137	>	initSystemCoords();
138
139	<
139	>	if( !(globals->getUseInitTime()) )
140	>	info[0].currentTime = 0.0;
141	>	}
142
143	<	// 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];
143	>	// make the output filenames
144
145	<	if( !the_globals->haveNMol() ){
116	<	// we don't have the total number of molecules, so we assume it is
117	<	// given in each component
145	>	makeOutNames();
146
147	<	tot_nmol = 0;
120	<	for( i=0; i<n_components; i++ ){
147	>	// make the integrator
148
149	<	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	<	}
149	>	makeIntegrator();
150
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	–
151		#ifdef IS_MPI
152	<	strcpy( checkPointMsg, "Have the number of components" );
153	<	MPIcheckPoint();
163	<	#endif // is_mpi
152	>	mpiSim->mpiRefresh();
153	>	#endif
154
155	<	// make an array of molecule stamps that match the components used.
166	<	// also extract the used stamps out into a separate linked list
155	>	// initialize the Fortran
156
157	<	simnfo->nComponents = n_components;
158	<	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++ ){
157	>	initFortran();
158	>	}
159
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
160
161	<	comp_stamps[i] = headStamp->match( id );
162	<	if( comp_stamps[i] == NULL ){
163	<
164	<	// extract the component from the list;
165	<
166	<	currentStamp = the_stamps->extractMolStamp( id );
167	<	if( currentStamp == NULL ){
168	<	sprintf( painCave.errMsg,
169	<	"SimSetup error: Component \"%s\" was not found in the "
170	<	"list of declared molecules\n",
171	<	id );
194	<	painCave.isFatal = 1;
195	<	simError();
196	<	}
197	<
198	<	headStamp->add( currentStamp );
199	<	comp_stamps[i] = headStamp->match( id );
200	<	}
201	<	}
161	>	void SimSetup::makeMolecules(void){
162	>	int k;
163	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
164	>	molInit molInfo;
165	>	DirectionalAtom* dAtom;
166	>	LinkedAssign* extras;
167	>	LinkedAssign* current_extra;
168	>	AtomStamp* currentAtom;
169	>	BondStamp* currentBond;
170	>	BendStamp* currentBend;
171	>	TorsionStamp* currentTorsion;
172
173	<	#ifdef IS_MPI
174	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
175	<	MPIcheckPoint();
206	<	#endif // is_mpi
207	<
173	>	bond_pair* theBonds;
174	>	bend_set* theBends;
175	>	torsion_set* theTorsions;
176
177
178	+	//init the forceField paramters
179
180	<	// caclulate the number of atoms, bonds, bends and torsions
180	>	the_ff->readParams();
181
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	–	}
182
183	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
183	>	// init the atoms
184
185	<	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;
185	>	double ux, uy, uz, u, uSqr;
186
187	<
188	<	#ifdef IS_MPI
187	>	for (k = 0; k < nInfo; k++){
188	>	the_ff->setSimInfo(&(info[k]));
189
190	<	// divide the molecules among processors here.
191	<
192	<	mpiSim = new mpiSimulation( simnfo );
193	<
241	<
190	>	atomOffset = 0;
191	>	excludeOffset = 0;
192	>	for (i = 0; i < info[k].n_mol; i++){
193	>	stampID = info[k].molecules[i].getStampID();
194
195	<	globalIndex = mpiSim->divideLabor();
195	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
196	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
197	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
198	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
199	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
200
201	+	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
202	+	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
203	+	molInfo.myBonds = new Bond * [molInfo.nBonds];
204	+	molInfo.myBends = new Bend * [molInfo.nBends];
205	+	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
206
207	+	theBonds = new bond_pair[molInfo.nBonds];
208	+	theBends = new bend_set[molInfo.nBends];
209	+	theTorsions = new torsion_set[molInfo.nTorsions];
210
211	<	// set up the local variables
248	<
249	<	int localMol, allMol;
250	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
251	<
252	<	allMol = 0;
253	<	localMol = 0;
254	<	local_atoms = 0;
255	<	local_bonds = 0;
256	<	local_bends = 0;
257	<	local_torsions = 0;
258	<	for( i=0; i<n_components; i++ ){
211	>	// make the Atoms
212
213	<	for( j=0; j<components_nmol[i]; j++ ){
214	<
215	<	if( mpiSim->getMyMolStart() <= allMol &&
216	<	allMol <= mpiSim->getMyMolEnd() ){
217	<
218	<	local_atoms +=    comp_stamps[i]->getNAtoms();
219	<	local_bonds +=    comp_stamps[i]->getNBonds();
267	<	local_bends +=    comp_stamps[i]->getNBends();
268	<	local_torsions += comp_stamps[i]->getNTorsions();
269	<	localMol++;
270	<	}
271	<	allMol++;
272	<	}
273	<	}
274	<	local_SRI = local_bonds + local_bends + local_torsions;
275	<
213	>	for (j = 0; j < molInfo.nAtoms; j++){
214	>	currentAtom = comp_stamps[stampID]->getAtom(j);
215	>	if (currentAtom->haveOrientation()){
216	>	dAtom = new DirectionalAtom((j + atomOffset),
217	>	info[k].getConfiguration());
218	>	info[k].n_oriented++;
219	>	molInfo.myAtoms[j] = dAtom;
220
221	<	simnfo->n_atoms = mpiSim->getMyNlocal();
222	<
223	<	if( local_atoms != simnfo->n_atoms ){
280	<	sprintf( painCave.errMsg,
281	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282	<	" localAtom (%d) are note equal.\n",
283	<	simnfo->n_atoms,
284	<	local_atoms );
285	<	painCave.isFatal = 1;
286	<	simError();
287	<	}
221	>	ux = currentAtom->getOrntX();
222	>	uy = currentAtom->getOrntY();
223	>	uz = currentAtom->getOrntZ();
224
225	<	simnfo->n_bonds = local_bonds;
290	<	simnfo->n_bends = local_bends;
291	<	simnfo->n_torsions = local_torsions;
292	<	simnfo->n_SRI = local_SRI;
293	<	simnfo->n_mol = localMol;
225	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
226
227	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
228	<	MPIcheckPoint();
229	<
230	<
299	<	#endif // is_mpi
300	<
227	>	u = sqrt(uSqr);
228	>	ux = ux / u;
229	>	uy = uy / u;
230	>	uz = uz / u;
231
232	<	// create the atom and short range interaction arrays
232	>	dAtom->setSUx(ux);
233	>	dAtom->setSUy(uy);
234	>	dAtom->setSUz(uz);
235	>	}
236	>	else{
237	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
238	>	info[k].getConfiguration());
239	>	}
240	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
241
242	<	Atom::createArrays(simnfo->n_atoms);
305	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
242	>	#ifdef IS_MPI
243
244	+	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
245
246	<	if( simnfo->n_SRI ){
247	<	the_sris = new SRI*[simnfo->n_SRI];
311	<	the_excludes = new int[2 * simnfo->n_SRI];
312	<	simnfo->globalExcludes = new int;
313	<	simnfo->n_exclude = tot_SRI;
314	<	}
315	<	else{
316	<
317	<	the_excludes = new int[2];
318	<	the_excludes[0] = 0;
319	<	the_excludes[1] = 0;
320	<	simnfo->globalExcludes = new int;
321	<	simnfo->globalExcludes[0] = 0;
246	>	#endif // is_mpi
247	>	}
248
249	<	simnfo->n_exclude = 1;
250	<	}
249	>	// make the bonds
250	>	for (j = 0; j < molInfo.nBonds; j++){
251	>	currentBond = comp_stamps[stampID]->getBond(j);
252	>	theBonds[j].a = currentBond->getA() + atomOffset;
253	>	theBonds[j].b = currentBond->getB() + atomOffset;
254
255	<	// set the arrays into the SimInfo object
255	>	exI = theBonds[j].a;
256	>	exJ = theBonds[j].b;
257
258	<	simnfo->atoms = the_atoms;
259	<	simnfo->sr_interactions = the_sris;
260	<	simnfo->nGlobalExcludes = 0;
261	<	simnfo->excludes = the_excludes;
258	>	// exclude_I must always be the smaller of the pair
259	>	if (exI > exJ){
260	>	tempEx = exI;
261	>	exI = exJ;
262	>	exJ = tempEx;
263	>	}
264	>	#ifdef IS_MPI
265	>	tempEx = exI;
266	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
267	>	tempEx = exJ;
268	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
269
270	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
271	+	#else  // isn't MPI
272
273	<	// get some of the tricky things that may still be in the globals
273	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
274	>	#endif  //is_mpi
275	>	}
276	>	excludeOffset += molInfo.nBonds;
277
278	<
279	<	if( the_globals->haveBox() ){
280	<	simnfo->box_x = the_globals->getBox();
281	<	simnfo->box_y = the_globals->getBox();
282	<	simnfo->box_z = the_globals->getBox();
283	<	}
342	<	else if( the_globals->haveDensity() ){
278	>	//make the bends
279	>	for (j = 0; j < molInfo.nBends; j++){
280	>	currentBend = comp_stamps[stampID]->getBend(j);
281	>	theBends[j].a = currentBend->getA() + atomOffset;
282	>	theBends[j].b = currentBend->getB() + atomOffset;
283	>	theBends[j].c = currentBend->getC() + atomOffset;
284
285	<	double vol;
286	<	vol = (double)tot_nmol / the_globals->getDensity();
287	<	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
347	<	simnfo->box_y = simnfo->box_x;
348	<	simnfo->box_z = simnfo->box_x;
349	<	}
350	<	else{
351	<	if( !the_globals->haveBoxX() ){
352	<	sprintf( painCave.errMsg,
353	<	"SimSetup error, no periodic BoxX size given.\n" );
354	<	painCave.isFatal = 1;
355	<	simError();
356	<	}
357	<	simnfo->box_x = the_globals->getBoxX();
285	>	if (currentBend->haveExtras()){
286	>	extras = currentBend->getExtras();
287	>	current_extra = extras;
288
289	<	if( !the_globals->haveBoxY() ){
290	<	sprintf( painCave.errMsg,
291	<	"SimSetup error, no periodic BoxY size given.\n" );
292	<	painCave.isFatal = 1;
293	<	simError();
294	<	}
295	<	simnfo->box_y = the_globals->getBoxY();
289	>	while (current_extra != NULL){
290	>	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
291	>	switch (current_extra->getType()){
292	>	case 0:
293	>	theBends[j].ghost = current_extra->getInt() + atomOffset;
294	>	theBends[j].isGhost = 1;
295	>	break;
296
297	<	if( !the_globals->haveBoxZ() ){
298	<	sprintf( painCave.errMsg,
299	<	"SimSetup error, no periodic BoxZ size given.\n" );
300	<	painCave.isFatal = 1;
301	<	simError();
372	<	}
373	<	simnfo->box_z = the_globals->getBoxZ();
374	<	}
297	>	case 1:
298	>	theBends[j].ghost = (int) current_extra->getDouble() +
299	>	atomOffset;
300	>	theBends[j].isGhost = 1;
301	>	break;
302
303	<	#ifdef IS_MPI
304	<	strcpy( checkPointMsg, "Box size set up" );
305	<	MPIcheckPoint();
306	<	#endif // is_mpi
303	>	default:
304	>	sprintf(painCave.errMsg,
305	>	"SimSetup Error: ghostVectorSource was neither a "
306	>	"double nor an int.\n"
307	>	"-->Bend[%d] in %s\n",
308	>	j, comp_stamps[stampID]->getID());
309	>	painCave.isFatal = 1;
310	>	simError();
311	>	}
312	>	}
313	>	else{
314	>	sprintf(painCave.errMsg,
315	>	"SimSetup Error: unhandled bend assignment:\n"
316	>	"    -->%s in Bend[%d] in %s\n",
317	>	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
318	>	painCave.isFatal = 1;
319	>	simError();
320	>	}
321
322	+	current_extra = current_extra->getNext();
323	+	}
324	+	}
325
326	<	// initialize the arrays
326	>	if (!theBends[j].isGhost){
327	>	exI = theBends[j].a;
328	>	exJ = theBends[j].c;
329	>	}
330	>	else{
331	>	exI = theBends[j].a;
332	>	exJ = theBends[j].b;
333	>	}
334
335	<	the_ff->setSimInfo( simnfo );
335	>	// exclude_I must always be the smaller of the pair
336	>	if (exI > exJ){
337	>	tempEx = exI;
338	>	exI = exJ;
339	>	exJ = tempEx;
340	>	}
341	>	#ifdef IS_MPI
342	>	tempEx = exI;
343	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
344	>	tempEx = exJ;
345	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
346
347	<	makeAtoms();
348	<	simnfo->identArray = new int[simnfo->n_atoms];
349	<	for(i=0; i<simnfo->n_atoms; i++){
350	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
351	<	}
352	<
353	<	if( tot_bonds ){
354	<	makeBonds();
355	<	}
347	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
348	>	#else  // isn't MPI
349	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
350	>	#endif  //is_mpi
351	>	}
352	>	excludeOffset += molInfo.nBends;
353	>
354	>	for (j = 0; j < molInfo.nTorsions; j++){
355	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
356	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
357	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
358	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
359	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
360
361	<	if( tot_bends ){
362	<	makeBends();
398	<	}
361	>	exI = theTorsions[j].a;
362	>	exJ = theTorsions[j].d;
363
364	<	if( tot_torsions ){
365	<	makeTorsions();
366	<	}
364	>	// exclude_I must always be the smaller of the pair
365	>	if (exI > exJ){
366	>	tempEx = exI;
367	>	exI = exJ;
368	>	exJ = tempEx;
369	>	}
370	>	#ifdef IS_MPI
371	>	tempEx = exI;
372	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
373	>	tempEx = exJ;
374	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
375
376	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
377	+	#else  // isn't MPI
378	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
379	+	#endif  //is_mpi
380	+	}
381	+	excludeOffset += molInfo.nTorsions;
382
405	–	if (the_globals->getUseRF() ) {
406	–	simnfo->useReactionField = 1;
407	–
408	–	if( !the_globals->haveECR() ){
409	–	sprintf( painCave.errMsg,
410	–	"SimSetup Warning: using default value of 1/2 the smallest "
411	–	"box length for the electrostaticCutoffRadius.\n"
412	–	"I hope you have a very fast processor!\n");
413	–	painCave.isFatal = 0;
414	–	simError();
415	–	double smallest;
416	–	smallest = simnfo->box_x;
417	–	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
418	–	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
419	–	simnfo->ecr = 0.5 * smallest;
420	–	} else {
421	–	simnfo->ecr        = the_globals->getECR();
422	–	}
383
384	<	if( !the_globals->haveEST() ){
385	<	sprintf( painCave.errMsg,
386	<	"SimSetup Warning: using default value of 0.05 * the "
387	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
388	<	);
389	<	painCave.isFatal = 0;
390	<	simError();
391	<	simnfo->est = 0.05 * simnfo->ecr;
392	<	} else {
393	<	simnfo->est        = the_globals->getEST();
384	>	// send the arrays off to the forceField for init.
385	>
386	>	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
387	>	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
388	>	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
389	>	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
390	>	theTorsions);
391	>
392	>
393	>	info[k].molecules[i].initialize(molInfo);
394	>
395	>
396	>	atomOffset += molInfo.nAtoms;
397	>	delete[] theBonds;
398	>	delete[] theBends;
399	>	delete[] theTorsions;
400		}
401	<
436	<	if(!the_globals->haveDielectric() ){
437	<	sprintf( painCave.errMsg,
438	<	"SimSetup Error: You are trying to use Reaction Field without"
439	<	"setting a dielectric constant!\n"
440	<	);
441	<	painCave.isFatal = 1;
442	<	simError();
443	<	}
444	<	simnfo->dielectric = the_globals->getDielectric();
445	<	} else {
446	<	if (simnfo->n_dipoles) {
447	<
448	<	if( !the_globals->haveECR() ){
449	<	sprintf( painCave.errMsg,
450	<	"SimSetup Warning: using default value of 1/2 the smallest"
451	<	"box length for the electrostaticCutoffRadius.\n"
452	<	"I hope you have a very fast processor!\n");
453	<	painCave.isFatal = 0;
454	<	simError();
455	<	double smallest;
456	<	smallest = simnfo->box_x;
457	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
458	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
459	<	simnfo->ecr = 0.5 * smallest;
460	<	} else {
461	<	simnfo->ecr        = the_globals->getECR();
462	<	}
463	<
464	<	if( !the_globals->haveEST() ){
465	<	sprintf( painCave.errMsg,
466	<	"SimSetup Warning: using default value of 5% of the"
467	<	"electrostaticCutoffRadius for the "
468	<	"electrostaticSkinThickness\n"
469	<	);
470	<	painCave.isFatal = 0;
471	<	simError();
472	<	simnfo->est = 0.05 * simnfo->ecr;
473	<	} else {
474	<	simnfo->est        = the_globals->getEST();
475	<	}
476	<	}
477	<	}
401	>	}
402
403		#ifdef IS_MPI
404	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
404	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
405		MPIcheckPoint();
406		#endif // is_mpi
407
408	<	if( the_globals->haveInitialConfig() ){
485	<
486	<	InitializeFromFile* fileInit;
487	<	#ifdef IS_MPI // is_mpi
488	<	if( worldRank == 0 ){
489	<	#endif //is_mpi
490	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
491	<	#ifdef IS_MPI
492	<	}else fileInit = new InitializeFromFile( NULL );
493	<	#endif
494	<	fileInit->read_xyz( simnfo ); // default velocities on
408	>	// clean up the forcefield
409
410	<	delete fileInit;
411	<	}
412	<	else{
410	>	the_ff->calcRcut();
411	>	the_ff->cleanMe();
412	>	}
413
414	<	#ifdef IS_MPI
414	>	void SimSetup::initFromBass(void){
415	>	int i, j, k;
416	>	int n_cells;
417	>	double cellx, celly, cellz;
418	>	double temp1, temp2, temp3;
419	>	int n_per_extra;
420	>	int n_extra;
421	>	int have_extra, done;
422
423	<	// no init from bass
424	<
425	<	sprintf( painCave.errMsg,
426	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
506	<	painCave.isFatal;
507	<	simError();
508	<
509	<	#else
423	>	double vel[3];
424	>	vel[0] = 0.0;
425	>	vel[1] = 0.0;
426	>	vel[2] = 0.0;
427
428	<	initFromBass();
428	>	temp1 = (double) tot_nmol / 4.0;
429	>	temp2 = pow(temp1, (1.0 / 3.0));
430	>	temp3 = ceil(temp2);
431
432	+	have_extra = 0;
433	+	if (temp2 < temp3){
434	+	// we have a non-complete lattice
435	+	have_extra = 1;
436
437	<	#endif
438	<	}
437	>	n_cells = (int) temp3 - 1;
438	>	cellx = info[0].boxL[0] / temp3;
439	>	celly = info[0].boxL[1] / temp3;
440	>	cellz = info[0].boxL[2] / temp3;
441	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
442	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
443	>	n_per_extra = (int) ceil(temp1);
444
445	<	#ifdef IS_MPI
446	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
447	<	MPIcheckPoint();
448	<	#endif // is_mpi
445	>	if (n_per_extra > 4){
446	>	sprintf(painCave.errMsg,
447	>	"SimSetup error. There has been an error in constructing"
448	>	" the non-complete lattice.\n");
449	>	painCave.isFatal = 1;
450	>	simError();
451	>	}
452	>	}
453	>	else{
454	>	n_cells = (int) temp3;
455	>	cellx = info[0].boxL[0] / temp3;
456	>	celly = info[0].boxL[1] / temp3;
457	>	cellz = info[0].boxL[2] / temp3;
458	>	}
459
460	+	current_mol = 0;
461	+	current_comp_mol = 0;
462	+	current_comp = 0;
463	+	current_atom_ndx = 0;
464
465	<
466	<
467	<
465	>	for (i = 0; i < n_cells ; i++){
466	>	for (j = 0; j < n_cells; j++){
467	>	for (k = 0; k < n_cells; k++){
468	>	makeElement(i * cellx, j * celly, k * cellz);
469
470	<
471	<	#ifdef IS_MPI
472	<	if( worldRank == 0 ){
473	<	#endif // is_mpi
474	<
532	<	if( the_globals->haveFinalConfig() ){
533	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
534	<	}
535	<	else{
536	<	strcpy( simnfo->finalName, inFileName );
537	<	char* endTest;
538	<	int nameLength = strlen( simnfo->finalName );
539	<	endTest = &(simnfo->finalName[nameLength - 5]);
540	<	if( !strcmp( endTest, ".bass" ) ){
541	<	strcpy( endTest, ".eor" );
470	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
471	>
472	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
473	>
474	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
475		}
543	–	else if( !strcmp( endTest, ".BASS" ) ){
544	–	strcpy( endTest, ".eor" );
545	–	}
546	–	else{
547	–	endTest = &(simnfo->finalName[nameLength - 4]);
548	–	if( !strcmp( endTest, ".bss" ) ){
549	–	strcpy( endTest, ".eor" );
550	–	}
551	–	else if( !strcmp( endTest, ".mdl" ) ){
552	–	strcpy( endTest, ".eor" );
553	–	}
554	–	else{
555	–	strcat( simnfo->finalName, ".eor" );
556	–	}
557	–	}
476		}
477	<
478	<	// make the sample and status out names
479	<
480	<	strcpy( simnfo->sampleName, inFileName );
481	<	char* endTest;
482	<	int nameLength = strlen( simnfo->sampleName );
483	<	endTest = &(simnfo->sampleName[nameLength - 5]);
484	<	if( !strcmp( endTest, ".bass" ) ){
485	<	strcpy( endTest, ".dump" );
486	<	}
487	<	else if( !strcmp( endTest, ".BASS" ) ){
488	<	strcpy( endTest, ".dump" );
489	<	}
490	<	else{
491	<	endTest = &(simnfo->sampleName[nameLength - 4]);
492	<	if( !strcmp( endTest, ".bss" ) ){
493	<	strcpy( endTest, ".dump" );
494	<	}
495	<	else if( !strcmp( endTest, ".mdl" ) ){
496	<	strcpy( endTest, ".dump" );
497	<	}
498	<	else{
499	<	strcat( simnfo->sampleName, ".dump" );
477	>	}
478	>
479	>	if (have_extra){
480	>	done = 0;
481	>
482	>	int start_ndx;
483	>	for (i = 0; i < (n_cells + 1) && !done; i++){
484	>	for (j = 0; j < (n_cells + 1) && !done; j++){
485	>	if (i < n_cells){
486	>	if (j < n_cells){
487	>	start_ndx = n_cells;
488	>	}
489	>	else
490	>	start_ndx = 0;
491	>	}
492	>	else
493	>	start_ndx = 0;
494	>
495	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
496	>	makeElement(i * cellx, j * celly, k * cellz);
497	>	done = (current_mol >= tot_nmol);
498	>
499	>	if (!done && n_per_extra > 1){
500	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
501	>	k * cellz);
502	>	done = (current_mol >= tot_nmol);
503	>	}
504	>
505	>	if (!done && n_per_extra > 2){
506	>	makeElement(i * cellx, j * celly + 0.5 * celly,
507	>	k * cellz + 0.5 * cellz);
508	>	done = (current_mol >= tot_nmol);
509	>	}
510	>
511	>	if (!done && n_per_extra > 3){
512	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
513	>	k * cellz + 0.5 * cellz);
514	>	done = (current_mol >= tot_nmol);
515	>	}
516	>	}
517		}
518		}
584	–
585	–	strcpy( simnfo->statusName, inFileName );
586	–	nameLength = strlen( simnfo->statusName );
587	–	endTest = &(simnfo->statusName[nameLength - 5]);
588	–	if( !strcmp( endTest, ".bass" ) ){
589	–	strcpy( endTest, ".stat" );
590	–	}
591	–	else if( !strcmp( endTest, ".BASS" ) ){
592	–	strcpy( endTest, ".stat" );
593	–	}
594	–	else{
595	–	endTest = &(simnfo->statusName[nameLength - 4]);
596	–	if( !strcmp( endTest, ".bss" ) ){
597	–	strcpy( endTest, ".stat" );
598	–	}
599	–	else if( !strcmp( endTest, ".mdl" ) ){
600	–	strcpy( endTest, ".stat" );
601	–	}
602	–	else{
603	–	strcat( simnfo->statusName, ".stat" );
604	–	}
605	–	}
606	–
607	–	#ifdef IS_MPI
519		}
609	–	#endif // is_mpi
610	–
611	–	// set the status, sample, and themal kick times
612	–
613	–	if( the_globals->haveSampleTime() ){
614	–	simnfo->sampleTime = the_globals->getSampleTime();
615	–	simnfo->statusTime = simnfo->sampleTime;
616	–	simnfo->thermalTime = simnfo->sampleTime;
617	–	}
618	–	else{
619	–	simnfo->sampleTime = the_globals->getRunTime();
620	–	simnfo->statusTime = simnfo->sampleTime;
621	–	simnfo->thermalTime = simnfo->sampleTime;
622	–	}
520
521	<	if( the_globals->haveStatusTime() ){
522	<	simnfo->statusTime = the_globals->getStatusTime();
521	>	for (i = 0; i < info[0].n_atoms; i++){
522	>	info[0].atoms[i]->setVel(vel);
523		}
524	+	}
525
526	<	if( the_globals->haveThermalTime() ){
527	<	simnfo->thermalTime = the_globals->getThermalTime();
528	<	}
526	>	void SimSetup::makeElement(double x, double y, double z){
527	>	int k;
528	>	AtomStamp* current_atom;
529	>	DirectionalAtom* dAtom;
530	>	double rotMat[3][3];
531	>	double pos[3];
532
533	<	// check for the temperature set flag
533	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
534	>	current_atom = comp_stamps[current_comp]->getAtom(k);
535	>	if (!current_atom->havePosition()){
536	>	sprintf(painCave.errMsg,
537	>	"SimSetup:initFromBass error.\n"
538	>	"\tComponent %s, atom %s does not have a position specified.\n"
539	>	"\tThe initialization routine is unable to give a start"
540	>	" position.\n",
541	>	comp_stamps[current_comp]->getID(), current_atom->getType());
542	>	painCave.isFatal = 1;
543	>	simError();
544	>	}
545
546	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
546	>	pos[0] = x + current_atom->getPosX();
547	>	pos[1] = y + current_atom->getPosY();
548	>	pos[2] = z + current_atom->getPosZ();
549
550	+	info[0].atoms[current_atom_ndx]->setPos(pos);
551
552	<	//   // make the longe range forces and the integrator
552	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
553	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
554
555	<	//   new AllLong( simnfo );
555	>	rotMat[0][0] = 1.0;
556	>	rotMat[0][1] = 0.0;
557	>	rotMat[0][2] = 0.0;
558
559	<	if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff );
560	<	if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff );
561	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
644	<	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
559	>	rotMat[1][0] = 0.0;
560	>	rotMat[1][1] = 1.0;
561	>	rotMat[1][2] = 0.0;
562
563	+	rotMat[2][0] = 0.0;
564	+	rotMat[2][1] = 0.0;
565	+	rotMat[2][2] = 1.0;
566
567	+	dAtom->setA(rotMat);
568	+	}
569
570	<	// initialize the Fortran
649	<
650	<	simnfo->refreshSim();
651	<
652	<	if( !strcmp( simnfo->mixingRule, "standard") ){
653	<	the_ff->initForceField( LB_MIXING_RULE );
570	>	current_atom_ndx++;
571		}
655	–	else if( !strcmp( simnfo->mixingRule, "explicit") ){
656	–	the_ff->initForceField( EXPLICIT_MIXING_RULE );
657	–	}
658	–	else{
659	–	sprintf( painCave.errMsg,
660	–	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
661	–	simnfo->mixingRule );
662	–	painCave.isFatal = 1;
663	–	simError();
664	–	}
572
573	+	current_mol++;
574	+	current_comp_mol++;
575
576	<	#ifdef IS_MPI
577	<	strcpy( checkPointMsg,
578	<	"Successfully intialized the mixingRule for Fortran." );
579	<	MPIcheckPoint();
671	<	#endif // is_mpi
576	>	if (current_comp_mol >= components_nmol[current_comp]){
577	>	current_comp_mol = 0;
578	>	current_comp++;
579	>	}
580		}
581
582
583	<	void SimSetup::makeMolecules( void ){
583	>	void SimSetup::gatherInfo(void){
584	>	int i;
585
586	<	int i, j, exI, exJ, tempEx, stampID, atomOffset;
587	<	molInit info;
679	<	DirectionalAtom* dAtom;
680	<	AtomStamp* currentAtom;
681	<	BondStamp* currentBond;
682	<	BendStamp* currentBend;
683	<	TorsionStamp* currentTorsion;
684	<
685	<	//init the forceField paramters
586	>	ensembleCase = -1;
587	>	ffCase = -1;
588
589	<	the_ff->readParams();
589	>	// set the easy ones first
590
591	<
592	<	// init the molecules
591	>	for (i = 0; i < nInfo; i++){
592	>	info[i].target_temp = globals->getTargetTemp();
593	>	info[i].dt = globals->getDt();
594	>	info[i].run_time = globals->getRunTime();
595	>	}
596	>	n_components = globals->getNComponents();
597
692	–	atomOffset = 0;
693	–	for(i=0; i<simnfo->n_mol; i++){
694	–
695	–	stampID = the_molecules[i].getStampID();
598
599	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
698	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
699	<	info.nBends    = comp_stamps[stampID]->getNBends();
700	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
701	<
702	<	info.myAtoms = &the_atoms[atomOffset];
703	<	info.myBonds = new Bond*[info.nBonds];
704	<	info.myBends = new Bend*[info.nBends];
705	<	info.myTorsions = new Torsions*[info.nTorsions];
599	>	// get the forceField
600
601	<	theBonds = new bond_pair[info.nBonds];
708	<	theBends = new bend_set[info.nBends];
709	<	theTorsions = new torsion_set[info.nTorsions];
710	<
711	<	// make the Atoms
712	<
713	<	for(j=0; j<info.nAtoms; j++){
714	<
715	<	currentAtom = theComponents[stampID]->getAtom( j );
716	<	if( currentAtom->haveOrientation() ){
717	<
718	<	dAtom = new DirectionalAtom(j + atomOffset);
719	<	simnfo->n_oriented++;
720	<	info.myAtoms[j] = dAtom;
721	<
722	<	ux = currentAtom->getOrntX();
723	<	uy = currentAtom->getOrntY();
724	<	uz = currentAtom->getOrntZ();
725	<
726	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
727	<
728	<	u = sqrt( uSqr );
729	<	ux = ux / u;
730	<	uy = uy / u;
731	<	uz = uz / u;
732	<
733	<	dAtom->setSUx( ux );
734	<	dAtom->setSUy( uy );
735	<	dAtom->setSUz( uz );
736	<	}
737	<	else{
738	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
739	<	}
740	<	info.myAtoms[j]->setType( currentAtom->getType() );
741	<
742	<	#ifdef IS_MPI
743	<
744	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
745	<
746	<	#endif // is_mpi
747	<	}
748	<
749	<	// make the bonds
750	<	for(j=0; j<nBonds; j++){
751	<
752	<	currentBond = comp_stamps[stampID]->getBond( j );
753	<	theBonds[j].a = currentBond->getA() + atomOffset;
754	<	theBonds[j].b = currentBond->getB() + atomOffset;
601	>	strcpy(force_field, globals->getForceField());
602
603	<	exI = theBonds[i].a;
604	<	exJ = theBonds[i].b;
603	>	if (!strcasecmp(force_field, "DUFF")){
604	>	ffCase = FF_DUFF;
605	>	}
606	>	else if (!strcasecmp(force_field, "LJ")){
607	>	ffCase = FF_LJ;
608	>	}
609	>	else if (!strcasecmp(force_field, "EAM")){
610	>	ffCase = FF_EAM;
611	>	}
612	>	else{
613	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
614	>	force_field);
615	>	painCave.isFatal = 1;
616	>	simError();
617	>	}
618
619	<	// exclude_I must always be the smaller of the pair
760	<	if( exI > exJ ){
761	<	tempEx = exI;
762	<	exI = exJ;
763	<	exJ = tempEx;
764	<	}
765	<	#ifdef IS_MPI
766	<
767	<	the_excludes[index*2] =
768	<	the_atoms[exI]->getGlobalIndex() + 1;
769	<	the_excludes[index*2 + 1] =
770	<	the_atoms[exJ]->getGlobalIndex() + 1;
771	<
772	<	#else  // isn't MPI
773	<
774	<	the_excludes[index*2] =     exI + 1;
775	<	the_excludes[index*2 + 1] = exJ + 1;
776	<	// fortran index from 1 (hence the +1 in the indexing)
619	>	// get the ensemble
620
621	<	#endif  //is_mpi
622	<
621	>	strcpy(ensemble, globals->getEnsemble());
622	>
623	>	if (!strcasecmp(ensemble, "NVE")){
624	>	ensembleCase = NVE_ENS;
625		}
626	+	else if (!strcasecmp(ensemble, "NVT")){
627	+	ensembleCase = NVT_ENS;
628	+	}
629	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
630	+	ensembleCase = NPTi_ENS;
631	+	}
632	+	else if (!strcasecmp(ensemble, "NPTf")){
633	+	ensembleCase = NPTf_ENS;
634	+	}
635	+	else if (!strcasecmp(ensemble, "NPTxyz")){
636	+	ensembleCase = NPTxyz_ENS;
637	+	}
638	+	else{
639	+	sprintf(painCave.errMsg,
640	+	"SimSetup Warning. Unrecognized Ensemble -> %s \n"
641	+	"\treverting to NVE for this simulation.\n",
642	+	ensemble);
643	+	painCave.isFatal = 0;
644	+	simError();
645	+	strcpy(ensemble, "NVE");
646	+	ensembleCase = NVE_ENS;
647	+	}
648
649	+	for (i = 0; i < nInfo; i++){
650	+	strcpy(info[i].ensemble, ensemble);
651
652	+	// get the mixing rule
653
654	+	strcpy(info[i].mixingRule, globals->getMixingRule());
655	+	info[i].usePBC = globals->getPBC();
656	+	}
657
658	+	// get the components and calculate the tot_nMol and indvidual n_mol
659
660	+	the_components = globals->getComponents();
661	+	components_nmol = new int[n_components];
662
663
664	+	if (!globals->haveNMol()){
665	+	// we don't have the total number of molecules, so we assume it is
666	+	// given in each component
667
668	+	tot_nmol = 0;
669	+	for (i = 0; i < n_components; i++){
670	+	if (!the_components[i]->haveNMol()){
671	+	// we have a problem
672	+	sprintf(painCave.errMsg,
673	+	"SimSetup Error. No global NMol or component NMol given.\n"
674	+	"\tCannot calculate the number of atoms.\n");
675	+	painCave.isFatal = 1;
676	+	simError();
677	+	}
678
679	+	tot_nmol += the_components[i]->getNMol();
680	+	components_nmol[i] = the_components[i]->getNMol();
681	+	}
682	+	}
683	+	else{
684	+	sprintf(painCave.errMsg,
685	+	"SimSetup error.\n"
686	+	"\tSorry, the ability to specify total"
687	+	" nMols and then give molfractions in the components\n"
688	+	"\tis not currently supported."
689	+	" Please give nMol in the components.\n");
690	+	painCave.isFatal = 1;
691	+	simError();
692	+	}
693
694	+	//check whether sample time, status time, thermal time and reset time are divisble by dt
695	+	if (!isDivisible(globals->getSampleTime(), globals->getDt())){
696	+	sprintf(painCave.errMsg,
697	+	"Sample time is not divisible by dt.\n"
698	+	"\tThis will result in samples that are not uniformly\n"
699	+	"\tdistributed in time.  If this is a problem, change\n"
700	+	"\tyour sampleTime variable.\n");
701	+	painCave.isFatal = 0;
702	+	simError();
703	+	}
704
705	+	if (globals->haveStatusTime() && !isDivisible(globals->getSampleTime(), globals->getDt())){
706	+	sprintf(painCave.errMsg,
707	+	"Status time is not divisible by dt.\n"
708	+	"\tThis will result in status reports that are not uniformly\n"
709	+	"\tdistributed in time.  If this is a problem, change \n"
710	+	"\tyour statusTime variable.\n");
711	+	painCave.isFatal = 0;
712	+	simError();
713	+	}
714
715	+	if (globals->haveThermalTime() && !isDivisible(globals->getThermalTime(), globals->getDt())){
716	+	sprintf(painCave.errMsg,
717	+	"Thermal time is not divisible by dt.\n"
718	+	"\tThis will result in thermalizations that are not uniformly\n"
719	+	"\tdistributed in time.  If this is a problem, change \n"
720	+	"\tyour thermalTime variable.\n");
721	+	painCave.isFatal = 0;
722	+	simError();
723	+	}
724
725	+	if (globals->haveResetTime() && !isDivisible(globals->getResetTime(), globals->getDt())){
726	+	sprintf(painCave.errMsg,
727	+	"Reset time is not divisible by dt.\n"
728	+	"\tThis will result in integrator resets that are not uniformly\n"
729	+	"\tdistributed in time.  If this is a problem, change\n"
730	+	"\tyour resetTime variable.\n");
731	+	painCave.isFatal = 0;
732	+	simError();
733	+	}
734
735	+	// set the status, sample, and thermal kick times
736
737	<	void SimSetup::makeAtoms( void ){
737	>	for (i = 0; i < nInfo; i++){
738	>	if (globals->haveSampleTime()){
739	>	info[i].sampleTime = globals->getSampleTime();
740	>	info[i].statusTime = info[i].sampleTime;
741	>	info[i].thermalTime = info[i].sampleTime;
742	>	}
743	>	else{
744	>	info[i].sampleTime = globals->getRunTime();
745	>	info[i].statusTime = info[i].sampleTime;
746	>	info[i].thermalTime = info[i].sampleTime;
747	>	}
748
749	<	int i, j, k, index;
750	<	double ux, uy, uz, uSqr, u;
751	<	AtomStamp* current_atom;
749	>	if (globals->haveStatusTime()){
750	>	info[i].statusTime = globals->getStatusTime();
751	>	}
752
753	<	DirectionalAtom* dAtom;
754	<	int molIndex, molStart, molEnd, nMemb, lMolIndex;
753	>	if (globals->haveThermalTime()){
754	>	info[i].thermalTime = globals->getThermalTime();
755	>	}
756
757	<	lMolIndex = 0;
758	<	molIndex = 0;
759	<	index = 0;
760	<	for( i=0; i<n_components; i++ ){
757	>	info[i].resetIntegrator = 0;
758	>	if( globals->haveResetTime() ){
759	>	info[i].resetTime = globals->getResetTime();
760	>	info[i].resetIntegrator = 1;
761	>	}
762
763	<	for( j=0; j<components_nmol[i]; j++ ){
763	>	// check for the temperature set flag
764	>
765	>	if (globals->haveTempSet())
766	>	info[i].setTemp = globals->getTempSet();
767
768	<	#ifdef IS_MPI
813	<	if( mpiSim->getMyMolStart() <= molIndex &&
814	<	molIndex <= mpiSim->getMyMolEnd() ){
815	<	#endif // is_mpi
768	>	// check for the extended State init
769
770	<	molStart = index;
771	<	nMemb = comp_stamps[i]->getNAtoms();
772	<	for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){
773	<
774	<	current_atom = comp_stamps[i]->getAtom( k );
775	<	if( current_atom->haveOrientation() ){
776	<
824	<	dAtom = new DirectionalAtom(index);
825	<	simnfo->n_oriented++;
826	<	the_atoms[index] = dAtom;
827	<
828	<	ux = current_atom->getOrntX();
829	<	uy = current_atom->getOrntY();
830	<	uz = current_atom->getOrntZ();
831	<
832	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
833	<
834	<	u = sqrt( uSqr );
835	<	ux = ux / u;
836	<	uy = uy / u;
837	<	uz = uz / u;
838	<
839	<	dAtom->setSUx( ux );
840	<	dAtom->setSUy( uy );
841	<	dAtom->setSUz( uz );
842	<	}
843	<	else{
844	<	the_atoms[index] = new GeneralAtom(index);
845	<	}
846	<	the_atoms[index]->setType( current_atom->getType() );
847	<	the_atoms[index]->setIndex( index );
848	<
849	<	// increment the index and repeat;
850	<	index++;
851	<	}
852	<
853	<	molEnd = index -1;
854	<	the_molecules[lMolIndex].setNMembers( nMemb );
855	<	the_molecules[lMolIndex].setStartAtom( molStart );
856	<	the_molecules[lMolIndex].setEndAtom( molEnd );
857	<	the_molecules[lMolIndex].setStampID( i );
858	<	lMolIndex++;
770	>	info[i].useInitXSstate = globals->getUseInitXSstate();
771	>	info[i].orthoTolerance = globals->getOrthoBoxTolerance();
772	>
773	>	}
774	>
775	>	//setup seed for random number generator
776	>	int seedValue;
777
778	<	#ifdef IS_MPI
778	>	if (globals->haveSeed()){
779	>	seedValue = globals->getSeed();
780	>
781	>	if(seedValue / 1E9 == 0){
782	>	sprintf(painCave.errMsg,
783	>	"Seed for sprng library should contain at least 9 digits\n"
784	>	"OOPSE will generate a seed for user\n");
785	>	painCave.isFatal = 0;
786	>	simError();
787	>
788	>	//using seed generated by system instead of invalid seed set by user
789	>	#ifndef IS_MPI
790	>	seedValue = make_sprng_seed();
791	>	#else
792	>	if (worldRank == 0){
793	>	seedValue = make_sprng_seed();
794		}
795	<	#endif //is_mpi
796	<
864	<	molIndex++;
795	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
796	>	#endif
797		}
798	+	}//end of if branch of globals->haveSeed()
799	+	else{
800	+
801	+	#ifndef IS_MPI
802	+	seedValue = make_sprng_seed();
803	+	#else
804	+	if (worldRank == 0){
805	+	seedValue = make_sprng_seed();
806	+	}
807	+	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
808	+	#endif
809	+	}//end of globals->haveSeed()
810	+
811	+	for (int i = 0; i < nInfo; i++){
812	+	info[i].setSeed(seedValue);
813		}
814
815		#ifdef IS_MPI
816	<	for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] );
817	<
818	<	delete[] globalIndex;
872	<
873	<	mpiSim->mpiRefresh();
874	<	#endif //IS_MPI
875	<
876	<	the_ff->initializeAtoms();
816	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
817	>	MPIcheckPoint();
818	>	#endif // is_mpi
819		}
820
879	–	void SimSetup::makeBonds( void ){
821
822	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
823	<	bond_pair* the_bonds;
824	<	BondStamp* current_bond;
822	>	void SimSetup::finalInfoCheck(void){
823	>	int index;
824	>	int usesDipoles;
825	>	int i;
826
827	<	the_bonds = new bond_pair[tot_bonds];
828	<	index = 0;
887	<	offset = 0;
888	<	molIndex = 0;
827	>	for (i = 0; i < nInfo; i++){
828	>	// check electrostatic parameters
829
830	<	for( i=0; i<n_components; i++ ){
830	>	index = 0;
831	>	usesDipoles = 0;
832	>	while ((index < info[i].n_atoms) && !usesDipoles){
833	>	usesDipoles = (info[i].atoms[index])->hasDipole();
834	>	index++;
835	>	}
836
892	–	for( j=0; j<components_nmol[i]; j++ ){
893	–
837		#ifdef IS_MPI
838	<	if( mpiSim->getMyMolStart() <= molIndex &&
839	<	molIndex <= mpiSim->getMyMolEnd() ){
840	<	#endif // is_mpi
898	<
899	<	for( k=0; k<comp_stamps[i]->getNBonds(); k++ ){
900	<
901	<	current_bond = comp_stamps[i]->getBond( k );
902	<	the_bonds[index].a = current_bond->getA() + offset;
903	<	the_bonds[index].b = current_bond->getB() + offset;
838	>	int myUse = usesDipoles;
839	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
840	>	#endif //is_mpi
841
842	<	exI = the_bonds[index].a;
906	<	exJ = the_bonds[index].b;
842	>	double theEcr, theEst;
843
844	<	// exclude_I must always be the smaller of the pair
845	<	if( exI > exJ ){
910	<	tempEx = exI;
911	<	exI = exJ;
912	<	exJ = tempEx;
913	<	}
844	>	if (globals->getUseRF()){
845	>	info[i].useReactionField = 1;
846
847	<
848	<	#ifdef IS_MPI
847	>	if (!globals->haveECR()){
848	>	sprintf(painCave.errMsg,
849	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
850	>	"\tOOPSE will use a default value of 15.0 angstroms"
851	>	"\tfor the electrostaticCutoffRadius.\n");
852	>	painCave.isFatal = 0;
853	>	simError();
854	>	theEcr = 15.0;
855	>	}
856	>	else{
857	>	theEcr = globals->getECR();
858	>	}
859
860	<	the_excludes[index*2] =
861	<	the_atoms[exI]->getGlobalIndex() + 1;
862	<	the_excludes[index*2 + 1] =
863	<	the_atoms[exJ]->getGlobalIndex() + 1;
860	>	if (!globals->haveEST()){
861	>	sprintf(painCave.errMsg,
862	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
863	>	"\tOOPSE will use a default value of\n"
864	>	"\t0.05 * electrostaticCutoffRadius\n"
865	>	"\tfor the electrostaticSkinThickness\n");
866	>	painCave.isFatal = 0;
867	>	simError();
868	>	theEst = 0.05 * theEcr;
869	>	}
870	>	else{
871	>	theEst = globals->getEST();
872	>	}
873
874	<	#else  // isn't MPI
875	<
876	<	the_excludes[index*2] =     exI + 1;
877	<	the_excludes[index*2 + 1] = exJ + 1;
878	<	// fortran index from 1 (hence the +1 in the indexing)
879	<	#endif  //is_mpi
880	<
881	<	// increment the index and repeat;
882	<	index++;
932	<	}
933	<	offset += comp_stamps[i]->getNAtoms();
934	<
935	<	#ifdef IS_MPI
874	>	info[i].setDefaultEcr(theEcr, theEst);
875	>
876	>	if (!globals->haveDielectric()){
877	>	sprintf(painCave.errMsg,
878	>	"SimSetup Error: No Dielectric constant was set.\n"
879	>	"\tYou are trying to use Reaction Field without"
880	>	"\tsetting a dielectric constant!\n");
881	>	painCave.isFatal = 1;
882	>	simError();
883		}
884	<	#endif //is_mpi
885	<
886	<	molIndex++;
887	<	}
884	>	info[i].dielectric = globals->getDielectric();
885	>	}
886	>	else{
887	>	if (usesDipoles){
888	>	if (!globals->haveECR()){
889	>	sprintf(painCave.errMsg,
890	>	"SimSetup Warning: No value was set for electrostaticCutoffRadius.\n"
891	>	"\tOOPSE will use a default value of 15.0 angstroms"
892	>	"\tfor the electrostaticCutoffRadius.\n");
893	>	painCave.isFatal = 0;
894	>	simError();
895	>	theEcr = 15.0;
896	>	}
897	>	else{
898	>	theEcr = globals->getECR();
899	>	}
900	>
901	>	if (!globals->haveEST()){
902	>	sprintf(painCave.errMsg,
903	>	"SimSetup Warning: No value was set for electrostaticSkinThickness.\n"
904	>	"\tOOPSE will use a default value of\n"
905	>	"\t0.05 * electrostaticCutoffRadius\n"
906	>	"\tfor the electrostaticSkinThickness\n");
907	>	painCave.isFatal = 0;
908	>	simError();
909	>	theEst = 0.05 * theEcr;
910	>	}
911	>	else{
912	>	theEst = globals->getEST();
913	>	}
914	>
915	>	info[i].setDefaultEcr(theEcr, theEst);
916	>	}
917	>	}
918		}
919	<
920	<	the_ff->initializeBonds( the_bonds );
919	>	#ifdef IS_MPI
920	>	strcpy(checkPointMsg, "post processing checks out");
921	>	MPIcheckPoint();
922	>	#endif // is_mpi
923		}
945	–
946	–	void SimSetup::makeBends( void ){
947	–
948	–	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
949	–	bend_set* the_bends;
950	–	BendStamp* current_bend;
951	–	LinkedAssign* extras;
952	–	LinkedAssign* current_extra;
924
925	+	void SimSetup::initSystemCoords(void){
926	+	int i;
927
928	<	the_bends = new bend_set[tot_bends];
956	<	index = 0;
957	<	offset = 0;
958	<	molIndex = 0;
959	<	for( i=0; i<n_components; i++ ){
928	>	char* inName;
929
930	<	for( j=0; j<components_nmol[i]; j++ ){
930	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
931
932	<	#ifdef IS_MPI
933	<	if( mpiSim->getMyMolStart() <= molIndex &&
965	<	molIndex <= mpiSim->getMyMolEnd() ){
966	<	#endif // is_mpi
932	>	for (i = 0; i < info[0].n_atoms; i++)
933	>	info[0].atoms[i]->setCoords();
934
935	<	for( k=0; k<comp_stamps[i]->getNBends(); k++ ){
936	<
937	<	current_bend = comp_stamps[i]->getBend( k );
938	<	the_bends[index].a = current_bend->getA() + offset;
972	<	the_bends[index].b = current_bend->getB() + offset;
973	<	the_bends[index].c = current_bend->getC() + offset;
974	<
975	<	if( current_bend->haveExtras() ){
976	<
977	<	extras = current_bend->getExtras();
978	<	current_extra = extras;
979	<
980	<	while( current_extra != NULL ){
981	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
982	<
983	<	switch( current_extra->getType() ){
984	<
985	<	case 0:
986	<	the_bends[index].ghost =
987	<	current_extra->getInt() + offset;
988	<	the_bends[index].isGhost = 1;
989	<	break;
990	<
991	<	case 1:
992	<	the_bends[index].ghost =
993	<	(int)current_extra->getDouble() + offset;
994	<	the_bends[index].isGhost = 1;
995	<	break;
996	<
997	<	default:
998	<	sprintf( painCave.errMsg,
999	<	"SimSetup Error: ghostVectorSource was neiter a "
1000	<	"double nor an int.\n"
1001	<	"-->Bend[%d] in %s\n",
1002	<	k, comp_stamps[i]->getID() );
1003	<	painCave.isFatal = 1;
1004	<	simError();
1005	<	}
1006	<	}
1007	<
1008	<	else{
1009	<
1010	<	sprintf( painCave.errMsg,
1011	<	"SimSetup Error: unhandled bend assignment:\n"
1012	<	"    -->%s in Bend[%d] in %s\n",
1013	<	current_extra->getlhs(),
1014	<	k, comp_stamps[i]->getID() );
1015	<	painCave.isFatal = 1;
1016	<	simError();
1017	<	}
1018	<
1019	<	current_extra = current_extra->getNext();
1020	<	}
1021	<	}
1022	<
1023	<	if( !the_bends[index].isGhost ){
1024	<
1025	<	exI = the_bends[index].a;
1026	<	exJ = the_bends[index].c;
1027	<	}
1028	<	else{
1029	<
1030	<	exI = the_bends[index].a;
1031	<	exJ = the_bends[index].b;
1032	<	}
1033	<
1034	<	// exclude_I must always be the smaller of the pair
1035	<	if( exI > exJ ){
1036	<	tempEx = exI;
1037	<	exI = exJ;
1038	<	exJ = tempEx;
1039	<	}
1040	<
1041	<
1042	<	#ifdef IS_MPI
1043	<
1044	<	the_excludes[(index + tot_bonds)*2] =
1045	<	the_atoms[exI]->getGlobalIndex() + 1;
1046	<	the_excludes[(index + tot_bonds)*2 + 1] =
1047	<	the_atoms[exJ]->getGlobalIndex() + 1;
1048	<
1049	<	#else  // isn't MPI
1050	<
1051	<	the_excludes[(index + tot_bonds)*2] =     exI + 1;
1052	<	the_excludes[(index + tot_bonds)*2 + 1] = exJ + 1;
1053	<	// fortran index from 1 (hence the +1 in the indexing)
1054	<	#endif  //is_mpi
1055	<
1056	<
1057	<	// increment the index and repeat;
1058	<	index++;
1059	<	}
1060	<	offset += comp_stamps[i]->getNAtoms();
1061	<
1062	<	#ifdef IS_MPI
1063	<	}
935	>	if (globals->haveInitialConfig()){
936	>	InitializeFromFile* fileInit;
937	>	#ifdef IS_MPI // is_mpi
938	>	if (worldRank == 0){
939		#endif //is_mpi
940	<
941	<	molIndex++;
940	>	inName = globals->getInitialConfig();
941	>	fileInit = new InitializeFromFile(inName);
942	>	#ifdef IS_MPI
943		}
944	+	else
945	+	fileInit = new InitializeFromFile(NULL);
946	+	#endif
947	+	fileInit->readInit(info); // default velocities on
948	+
949	+	delete fileInit;
950		}
951	+	else{
952	+
953	+	// no init from bass
954	+
955	+	sprintf(painCave.errMsg,
956	+	"Cannot intialize a simulation without an initial configuration file.\n");
957	+	painCave.isFatal = 1;;
958	+	simError();
959	+
960	+	}
961
962		#ifdef IS_MPI
963	<	sprintf( checkPointMsg,
1072	<	"Successfully created the bends list.\n" );
963	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
964		MPIcheckPoint();
965		#endif // is_mpi
1075	–
1076	–
1077	–	the_ff->initializeBends( the_bends );
966		}
967
1080	–	void SimSetup::makeTorsions( void ){
968
969	<	int i, j, k, index, offset, molIndex, exI, exJ, tempEx;
970	<	torsion_set* the_torsions;
1084	<	TorsionStamp* current_torsion;
969	>	void SimSetup::makeOutNames(void){
970	>	int k;
971
1086	–	the_torsions = new torsion_set[tot_torsions];
1087	–	index = 0;
1088	–	offset = 0;
1089	–	molIndex = 0;
1090	–	for( i=0; i<n_components; i++ ){
972
973	<	for( j=0; j<components_nmol[i]; j++ ){
1093	<
973	>	for (k = 0; k < nInfo; k++){
974		#ifdef IS_MPI
975	<	if( mpiSim->getMyMolStart() <= molIndex &&
976	<	molIndex <= mpiSim->getMyMolEnd() ){
1097	<	#endif // is_mpi
975	>	if (worldRank == 0){
976	>	#endif // is_mpi
977
978	<	for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){
978	>	if (globals->haveFinalConfig()){
979	>	strcpy(info[k].finalName, globals->getFinalConfig());
980	>	}
981	>	else{
982	>	strcpy(info[k].finalName, inFileName);
983	>	char* endTest;
984	>	int nameLength = strlen(info[k].finalName);
985	>	endTest = &(info[k].finalName[nameLength - 5]);
986	>	if (!strcmp(endTest, ".bass")){
987	>	strcpy(endTest, ".eor");
988	>	}
989	>	else if (!strcmp(endTest, ".BASS")){
990	>	strcpy(endTest, ".eor");
991	>	}
992	>	else{
993	>	endTest = &(info[k].finalName[nameLength - 4]);
994	>	if (!strcmp(endTest, ".bss")){
995	>	strcpy(endTest, ".eor");
996	>	}
997	>	else if (!strcmp(endTest, ".mdl")){
998	>	strcpy(endTest, ".eor");
999	>	}
1000	>	else{
1001	>	strcat(info[k].finalName, ".eor");
1002	>	}
1003	>	}
1004	>	}
1005
1006	<	current_torsion = comp_stamps[i]->getTorsion( k );
1102	<	the_torsions[index].a = current_torsion->getA() + offset;
1103	<	the_torsions[index].b = current_torsion->getB() + offset;
1104	<	the_torsions[index].c = current_torsion->getC() + offset;
1105	<	the_torsions[index].d = current_torsion->getD() + offset;
1006	>	// make the sample and status out names
1007
1008	<	exI = the_torsions[index].a;
1009	<	exJ = the_torsions[index].d;
1008	>	strcpy(info[k].sampleName, inFileName);
1009	>	char* endTest;
1010	>	int nameLength = strlen(info[k].sampleName);
1011	>	endTest = &(info[k].sampleName[nameLength - 5]);
1012	>	if (!strcmp(endTest, ".bass")){
1013	>	strcpy(endTest, ".dump");
1014	>	}
1015	>	else if (!strcmp(endTest, ".BASS")){
1016	>	strcpy(endTest, ".dump");
1017	>	}
1018	>	else{
1019	>	endTest = &(info[k].sampleName[nameLength - 4]);
1020	>	if (!strcmp(endTest, ".bss")){
1021	>	strcpy(endTest, ".dump");
1022	>	}
1023	>	else if (!strcmp(endTest, ".mdl")){
1024	>	strcpy(endTest, ".dump");
1025	>	}
1026	>	else{
1027	>	strcat(info[k].sampleName, ".dump");
1028	>	}
1029	>	}
1030
1031	<
1032	<	// exclude_I must always be the smaller of the pair
1033	<	if( exI > exJ ){
1034	<	tempEx = exI;
1035	<	exI = exJ;
1115	<	exJ = tempEx;
1116	<	}
1117	<
1118	<
1119	<	#ifdef IS_MPI
1120	<
1121	<	the_excludes[(index + tot_bonds + tot_bends)*2] =
1122	<	the_atoms[exI]->getGlobalIndex() + 1;
1123	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] =
1124	<	the_atoms[exJ]->getGlobalIndex() + 1;
1125	<
1126	<	#else  // isn't MPI
1127	<
1128	<	the_excludes[(index + tot_bonds + tot_bends)*2] =     exI + 1;
1129	<	the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = exJ + 1;
1130	<	// fortran indexes from 1 (hence the +1 in the indexing)
1131	<	#endif  //is_mpi
1132	<
1133	<
1134	<	// increment the index and repeat;
1135	<	index++;
1031	>	strcpy(info[k].statusName, inFileName);
1032	>	nameLength = strlen(info[k].statusName);
1033	>	endTest = &(info[k].statusName[nameLength - 5]);
1034	>	if (!strcmp(endTest, ".bass")){
1035	>	strcpy(endTest, ".stat");
1036		}
1037	<	offset += comp_stamps[i]->getNAtoms();
1037	>	else if (!strcmp(endTest, ".BASS")){
1038	>	strcpy(endTest, ".stat");
1039	>	}
1040	>	else{
1041	>	endTest = &(info[k].statusName[nameLength - 4]);
1042	>	if (!strcmp(endTest, ".bss")){
1043	>	strcpy(endTest, ".stat");
1044	>	}
1045	>	else if (!strcmp(endTest, ".mdl")){
1046	>	strcpy(endTest, ".stat");
1047	>	}
1048	>	else{
1049	>	strcat(info[k].statusName, ".stat");
1050	>	}
1051	>	}
1052
1053		#ifdef IS_MPI
1140	–	}
1141	–	#endif //is_mpi
1054
1143	–	molIndex++;
1055		}
1056	+	#endif // is_mpi
1057		}
1146	–
1147	–	the_ff->initializeTorsions( the_torsions );
1058		}
1059
1150	–	void SimSetup::initFromBass( void ){
1060
1061	<	int i, j, k;
1062	<	int n_cells;
1154	<	double cellx, celly, cellz;
1155	<	double temp1, temp2, temp3;
1156	<	int n_per_extra;
1157	<	int n_extra;
1158	<	int have_extra, done;
1061	>	void SimSetup::sysObjectsCreation(void){
1062	>	int i, k;
1063
1064	<	temp1 = (double)tot_nmol / 4.0;
1161	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
1162	<	temp3 = ceil( temp2 );
1064	>	// create the forceField
1065
1066	<	have_extra =0;
1165	<	if( temp2 < temp3 ){ // we have a non-complete lattice
1166	<	have_extra =1;
1066	>	createFF();
1067
1068	<	n_cells = (int)temp3 - 1;
1169	<	cellx = simnfo->box_x / temp3;
1170	<	celly = simnfo->box_y / temp3;
1171	<	cellz = simnfo->box_z / temp3;
1172	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
1173	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
1174	<	n_per_extra = (int)ceil( temp1 );
1068	>	// extract componentList
1069
1070	<	if( n_per_extra > 4){
1071	<	sprintf( painCave.errMsg,
1072	<	"SimSetup error. There has been an error in constructing"
1073	<	" the non-complete lattice.\n" );
1070	>	compList();
1071	>
1072	>	// calc the number of atoms, bond, bends, and torsions
1073	>
1074	>	calcSysValues();
1075	>
1076	>	#ifdef IS_MPI
1077	>	// divide the molecules among the processors
1078	>
1079	>	mpiMolDivide();
1080	>	#endif //is_mpi
1081	>
1082	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1083	>
1084	>	makeSysArrays();
1085	>
1086	>	// make and initialize the molecules (all but atomic coordinates)
1087	>
1088	>	makeMolecules();
1089	>
1090	>	for (k = 0; k < nInfo; k++){
1091	>	info[k].identArray = new int[info[k].n_atoms];
1092	>	for (i = 0; i < info[k].n_atoms; i++){
1093	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1094	>	}
1095	>	}
1096	>	}
1097	>
1098	>
1099	>	void SimSetup::createFF(void){
1100	>	switch (ffCase){
1101	>	case FF_DUFF:
1102	>	the_ff = new DUFF();
1103	>	break;
1104	>
1105	>	case FF_LJ:
1106	>	the_ff = new LJFF();
1107	>	break;
1108	>
1109	>	case FF_EAM:
1110	>	the_ff = new EAM_FF();
1111	>	break;
1112	>
1113	>	default:
1114	>	sprintf(painCave.errMsg,
1115	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1116		painCave.isFatal = 1;
1117		simError();
1182	–	}
1118		}
1184	–	else{
1185	–	n_cells = (int)temp3;
1186	–	cellx = simnfo->box_x / temp3;
1187	–	celly = simnfo->box_y / temp3;
1188	–	cellz = simnfo->box_z / temp3;
1189	–	}
1119
1120	<	current_mol = 0;
1121	<	current_comp_mol = 0;
1122	<	current_comp = 0;
1123	<	current_atom_ndx = 0;
1120	>	#ifdef IS_MPI
1121	>	strcpy(checkPointMsg, "ForceField creation successful");
1122	>	MPIcheckPoint();
1123	>	#endif // is_mpi
1124	>	}
1125
1196	–	for( i=0; i < n_cells ; i++ ){
1197	–	for( j=0; j < n_cells; j++ ){
1198	–	for( k=0; k < n_cells; k++ ){
1126
1127	<	makeElement( i * cellx,
1128	<	j * celly,
1129	<	k * cellz );
1127	>	void SimSetup::compList(void){
1128	>	int i;
1129	>	char* id;
1130	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1131	>	LinkedMolStamp* currentStamp = NULL;
1132	>	comp_stamps = new MoleculeStamp * [n_components];
1133
1134	<	makeElement( i * cellx + 0.5 * cellx,
1135	<	j * celly + 0.5 * celly,
1206	<	k * cellz );
1134	>	// make an array of molecule stamps that match the components used.
1135	>	// also extract the used stamps out into a separate linked list
1136
1137	<	makeElement( i * cellx,
1138	<	j * celly + 0.5 * celly,
1139	<	k * cellz + 0.5 * cellz );
1137	>	for (i = 0; i < nInfo; i++){
1138	>	info[i].nComponents = n_components;
1139	>	info[i].componentsNmol = components_nmol;
1140	>	info[i].compStamps = comp_stamps;
1141	>	info[i].headStamp = headStamp;
1142	>	}
1143
1144	<	makeElement( i * cellx + 0.5 * cellx,
1145	<	j * celly,
1146	<	k * cellz + 0.5 * cellz );
1144	>
1145	>	for (i = 0; i < n_components; i++){
1146	>	id = the_components[i]->getType();
1147	>	comp_stamps[i] = NULL;
1148	>
1149	>	// check to make sure the component isn't already in the list
1150	>
1151	>	comp_stamps[i] = headStamp->match(id);
1152	>	if (comp_stamps[i] == NULL){
1153	>	// extract the component from the list;
1154	>
1155	>	currentStamp = stamps->extractMolStamp(id);
1156	>	if (currentStamp == NULL){
1157	>	sprintf(painCave.errMsg,
1158	>	"SimSetup error: Component \"%s\" was not found in the "
1159	>	"list of declared molecules\n",
1160	>	id);
1161	>	painCave.isFatal = 1;
1162	>	simError();
1163		}
1164	+
1165	+	headStamp->add(currentStamp);
1166	+	comp_stamps[i] = headStamp->match(id);
1167		}
1168		}
1169
1170	<	if( have_extra ){
1171	<	done = 0;
1170	>	#ifdef IS_MPI
1171	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1172	>	MPIcheckPoint();
1173	>	#endif // is_mpi
1174	>	}
1175
1176	<	int start_ndx;
1177	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1224	<	for( j=0; j < (n_cells+1) && !done; j++ ){
1176	>	void SimSetup::calcSysValues(void){
1177	>	int i;
1178
1179	<	if( i < n_cells ){
1179	>	int* molMembershipArray;
1180
1181	<	if( j < n_cells ){
1182	<	start_ndx = n_cells;
1183	<	}
1184	<	else start_ndx = 0;
1185	<	}
1186	<	else start_ndx = 0;
1181	>	tot_atoms = 0;
1182	>	tot_bonds = 0;
1183	>	tot_bends = 0;
1184	>	tot_torsions = 0;
1185	>	for (i = 0; i < n_components; i++){
1186	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1187	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1188	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1189	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1190	>	}
1191
1192	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
1192	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1193	>	molMembershipArray = new int[tot_atoms];
1194
1195	<	makeElement( i * cellx,
1196	<	j * celly,
1197	<	k * cellz );
1198	<	done = ( current_mol >= tot_nmol );
1195	>	for (i = 0; i < nInfo; i++){
1196	>	info[i].n_atoms = tot_atoms;
1197	>	info[i].n_bonds = tot_bonds;
1198	>	info[i].n_bends = tot_bends;
1199	>	info[i].n_torsions = tot_torsions;
1200	>	info[i].n_SRI = tot_SRI;
1201	>	info[i].n_mol = tot_nmol;
1202
1203	<	if( !done && n_per_extra > 1 ){
1204	<	makeElement( i * cellx + 0.5 * cellx,
1205	<	j * celly + 0.5 * celly,
1245	<	k * cellz );
1246	<	done = ( current_mol >= tot_nmol );
1247	<	}
1203	>	info[i].molMembershipArray = molMembershipArray;
1204	>	}
1205	>	}
1206
1207	<	if( !done && n_per_extra > 2){
1250	<	makeElement( i * cellx,
1251	<	j * celly + 0.5 * celly,
1252	<	k * cellz + 0.5 * cellz );
1253	<	done = ( current_mol >= tot_nmol );
1254	<	}
1207	>	#ifdef IS_MPI
1208
1209	<	if( !done && n_per_extra > 3){
1210	<	makeElement( i * cellx + 0.5 * cellx,
1211	<	j * celly,
1212	<	k * cellz + 0.5 * cellz );
1213	<	done = ( current_mol >= tot_nmol );
1214	<	}
1215	<	}
1209	>	void SimSetup::mpiMolDivide(void){
1210	>	int i, j, k;
1211	>	int localMol, allMol;
1212	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1213	>
1214	>	mpiSim = new mpiSimulation(info);
1215	>
1216	>	globalIndex = mpiSim->divideLabor();
1217	>
1218	>	// set up the local variables
1219	>
1220	>	mol2proc = mpiSim->getMolToProcMap();
1221	>	molCompType = mpiSim->getMolComponentType();
1222	>
1223	>	allMol = 0;
1224	>	localMol = 0;
1225	>	local_atoms = 0;
1226	>	local_bonds = 0;
1227	>	local_bends = 0;
1228	>	local_torsions = 0;
1229	>	globalAtomIndex = 0;
1230	>
1231	>
1232	>	for (i = 0; i < n_components; i++){
1233	>	for (j = 0; j < components_nmol[i]; j++){
1234	>	if (mol2proc[allMol] == worldRank){
1235	>	local_atoms += comp_stamps[i]->getNAtoms();
1236	>	local_bonds += comp_stamps[i]->getNBonds();
1237	>	local_bends += comp_stamps[i]->getNBends();
1238	>	local_torsions += comp_stamps[i]->getNTorsions();
1239	>	localMol++;
1240	>	}
1241	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1242	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1243	>	globalAtomIndex++;
1244		}
1245	+
1246	+	allMol++;
1247		}
1248		}
1249	+	local_SRI = local_bonds + local_bends + local_torsions;
1250
1251	+	info[0].n_atoms = mpiSim->getMyNlocal();
1252
1253	<	for( i=0; i<simnfo->n_atoms; i++ ){
1254	<	simnfo->atoms[i]->set_vx( 0.0 );
1255	<	simnfo->atoms[i]->set_vy( 0.0 );
1256	<	simnfo->atoms[i]->set_vz( 0.0 );
1253	>	if (local_atoms != info[0].n_atoms){
1254	>	sprintf(painCave.errMsg,
1255	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's\n"
1256	>	"\tlocalAtom (%d) are not equal.\n",
1257	>	info[0].n_atoms, local_atoms);
1258	>	painCave.isFatal = 1;
1259	>	simError();
1260		}
1261	+
1262	+	info[0].n_bonds = local_bonds;
1263	+	info[0].n_bends = local_bends;
1264	+	info[0].n_torsions = local_torsions;
1265	+	info[0].n_SRI = local_SRI;
1266	+	info[0].n_mol = localMol;
1267	+
1268	+	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1269	+	MPIcheckPoint();
1270		}
1271
1272	<	void SimSetup::makeElement( double x, double y, double z ){
1272	>	#endif // is_mpi
1273
1277	–	int k;
1278	–	AtomStamp* current_atom;
1279	–	DirectionalAtom* dAtom;
1280	–	double rotMat[3][3];
1274
1275	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
1275	>	void SimSetup::makeSysArrays(void){
1276	>
1277	>	#ifndef IS_MPI
1278	>	int k, j;
1279	>	#endif // is_mpi
1280	>	int i, l;
1281
1282	<	current_atom = comp_stamps[current_comp]->getAtom( k );
1283	<	if( !current_atom->havePosition() ){
1284	<	sprintf( painCave.errMsg,
1287	<	"SimSetup:initFromBass error.\n"
1288	<	"\tComponent %s, atom %s does not have a position specified.\n"
1289	<	"\tThe initialization routine is unable to give a start"
1290	<	" position.\n",
1291	<	comp_stamps[current_comp]->getID(),
1292	<	current_atom->getType() );
1293	<	painCave.isFatal = 1;
1294	<	simError();
1295	<	}
1282	>	Atom** the_atoms;
1283	>	Molecule* the_molecules;
1284	>	Exclude** the_excludes;
1285
1297	–	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
1298	–	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
1299	–	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
1286
1287	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
1287	>	for (l = 0; l < nInfo; l++){
1288	>	// create the atom and short range interaction arrays
1289
1290	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
1290	>	the_atoms = new Atom * [info[l].n_atoms];
1291	>	the_molecules = new Molecule[info[l].n_mol];
1292	>	int molIndex;
1293
1294	<	rotMat[0][0] = 1.0;
1306	<	rotMat[0][1] = 0.0;
1307	<	rotMat[0][2] = 0.0;
1294	>	// initialize the molecule's stampID's
1295
1296	<	rotMat[1][0] = 0.0;
1310	<	rotMat[1][1] = 1.0;
1311	<	rotMat[1][2] = 0.0;
1296	>	#ifdef IS_MPI
1297
1313	–	rotMat[2][0] = 0.0;
1314	–	rotMat[2][1] = 0.0;
1315	–	rotMat[2][2] = 1.0;
1298
1299	<	dAtom->setA( rotMat );
1299	>	molIndex = 0;
1300	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1301	>	if (mol2proc[i] == worldRank){
1302	>	the_molecules[molIndex].setStampID(molCompType[i]);
1303	>	the_molecules[molIndex].setMyIndex(molIndex);
1304	>	the_molecules[molIndex].setGlobalIndex(i);
1305	>	molIndex++;
1306	>	}
1307		}
1308
1309	<	current_atom_ndx++;
1321	<	}
1309	>	#else // is_mpi
1310
1311	<	current_mol++;
1312	<	current_comp_mol++;
1311	>	molIndex = 0;
1312	>	globalAtomIndex = 0;
1313	>	for (i = 0; i < n_components; i++){
1314	>	for (j = 0; j < components_nmol[i]; j++){
1315	>	the_molecules[molIndex].setStampID(i);
1316	>	the_molecules[molIndex].setMyIndex(molIndex);
1317	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1318	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1319	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1320	>	globalAtomIndex++;
1321	>	}
1322	>	molIndex++;
1323	>	}
1324	>	}
1325
1326	–	if( current_comp_mol >= components_nmol[current_comp] ){
1326
1327	<	current_comp_mol = 0;
1328	<	current_comp++;
1327	>	#endif // is_mpi
1328	>
1329	>
1330	>	if (info[l].n_SRI){
1331	>	Exclude::createArray(info[l].n_SRI);
1332	>	the_excludes = new Exclude * [info[l].n_SRI];
1333	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1334	>	the_excludes[ex] = new Exclude(ex);
1335	>	}
1336	>	info[l].globalExcludes = new int;
1337	>	info[l].n_exclude = info[l].n_SRI;
1338	>	}
1339	>	else{
1340	>	Exclude::createArray(1);
1341	>	the_excludes = new Exclude * ;
1342	>	the_excludes[0] = new Exclude(0);
1343	>	the_excludes[0]->setPair(0, 0);
1344	>	info[l].globalExcludes = new int;
1345	>	info[l].globalExcludes[0] = 0;
1346	>	info[l].n_exclude = 0;
1347	>	}
1348	>
1349	>	// set the arrays into the SimInfo object
1350	>
1351	>	info[l].atoms = the_atoms;
1352	>	info[l].molecules = the_molecules;
1353	>	info[l].nGlobalExcludes = 0;
1354	>	info[l].excludes = the_excludes;
1355	>
1356	>	the_ff->setSimInfo(info);
1357		}
1358		}
1359	+
1360	+	void SimSetup::makeIntegrator(void){
1361	+	int k;
1362	+
1363	+	NVE<RealIntegrator>* myNVE = NULL;
1364	+	NVT<RealIntegrator>* myNVT = NULL;
1365	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1366	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1367	+	NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL;
1368	+
1369	+	for (k = 0; k < nInfo; k++){
1370	+	switch (ensembleCase){
1371	+	case NVE_ENS:
1372	+	if (globals->haveZconstraints()){
1373	+	setupZConstraint(info[k]);
1374	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1375	+	}
1376	+	else{
1377	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1378	+	}
1379	+
1380	+	info->the_integrator = myNVE;
1381	+	break;
1382	+
1383	+	case NVT_ENS:
1384	+	if (globals->haveZconstraints()){
1385	+	setupZConstraint(info[k]);
1386	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1387	+	}
1388	+	else
1389	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1390	+
1391	+	myNVT->setTargetTemp(globals->getTargetTemp());
1392	+
1393	+	if (globals->haveTauThermostat())
1394	+	myNVT->setTauThermostat(globals->getTauThermostat());
1395	+	else{
1396	+	sprintf(painCave.errMsg,
1397	+	"SimSetup error: If you use the NVT\n"
1398	+	"\tensemble, you must set tauThermostat.\n");
1399	+	painCave.isFatal = 1;
1400	+	simError();
1401	+	}
1402	+
1403	+	info->the_integrator = myNVT;
1404	+	break;
1405	+
1406	+	case NPTi_ENS:
1407	+	if (globals->haveZconstraints()){
1408	+	setupZConstraint(info[k]);
1409	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1410	+	}
1411	+	else
1412	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1413	+
1414	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1415	+
1416	+	if (globals->haveTargetPressure())
1417	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1418	+	else{
1419	+	sprintf(painCave.errMsg,
1420	+	"SimSetup error: If you use a constant pressure\n"
1421	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1422	+	painCave.isFatal = 1;
1423	+	simError();
1424	+	}
1425	+
1426	+	if (globals->haveTauThermostat())
1427	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1428	+	else{
1429	+	sprintf(painCave.errMsg,
1430	+	"SimSetup error: If you use an NPT\n"
1431	+	"\tensemble, you must set tauThermostat.\n");
1432	+	painCave.isFatal = 1;
1433	+	simError();
1434	+	}
1435	+
1436	+	if (globals->haveTauBarostat())
1437	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1438	+	else{
1439	+	sprintf(painCave.errMsg,
1440	+	"SimSetup error: If you use an NPT\n"
1441	+	"\tensemble, you must set tauBarostat.\n");
1442	+	painCave.isFatal = 1;
1443	+	simError();
1444	+	}
1445	+
1446	+	info->the_integrator = myNPTi;
1447	+	break;
1448	+
1449	+	case NPTf_ENS:
1450	+	if (globals->haveZconstraints()){
1451	+	setupZConstraint(info[k]);
1452	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1453	+	}
1454	+	else
1455	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1456	+
1457	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1458	+
1459	+	if (globals->haveTargetPressure())
1460	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1461	+	else{
1462	+	sprintf(painCave.errMsg,
1463	+	"SimSetup error: If you use a constant pressure\n"
1464	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1465	+	painCave.isFatal = 1;
1466	+	simError();
1467	+	}
1468	+
1469	+	if (globals->haveTauThermostat())
1470	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1471	+
1472	+	else{
1473	+	sprintf(painCave.errMsg,
1474	+	"SimSetup error: If you use an NPT\n"
1475	+	"\tensemble, you must set tauThermostat.\n");
1476	+	painCave.isFatal = 1;
1477	+	simError();
1478	+	}
1479	+
1480	+	if (globals->haveTauBarostat())
1481	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1482	+
1483	+	else{
1484	+	sprintf(painCave.errMsg,
1485	+	"SimSetup error: If you use an NPT\n"
1486	+	"\tensemble, you must set tauBarostat.\n");
1487	+	painCave.isFatal = 1;
1488	+	simError();
1489	+	}
1490	+
1491	+	info->the_integrator = myNPTf;
1492	+	break;
1493	+
1494	+	case NPTxyz_ENS:
1495	+	if (globals->haveZconstraints()){
1496	+	setupZConstraint(info[k]);
1497	+	myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1498	+	}
1499	+	else
1500	+	myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff);
1501	+
1502	+	myNPTxyz->setTargetTemp(globals->getTargetTemp());
1503	+
1504	+	if (globals->haveTargetPressure())
1505	+	myNPTxyz->setTargetPressure(globals->getTargetPressure());
1506	+	else{
1507	+	sprintf(painCave.errMsg,
1508	+	"SimSetup error: If you use a constant pressure\n"
1509	+	"\tensemble, you must set targetPressure in the BASS file.\n");
1510	+	painCave.isFatal = 1;
1511	+	simError();
1512	+	}
1513	+
1514	+	if (globals->haveTauThermostat())
1515	+	myNPTxyz->setTauThermostat(globals->getTauThermostat());
1516	+	else{
1517	+	sprintf(painCave.errMsg,
1518	+	"SimSetup error: If you use an NPT\n"
1519	+	"\tensemble, you must set tauThermostat.\n");
1520	+	painCave.isFatal = 1;
1521	+	simError();
1522	+	}
1523	+
1524	+	if (globals->haveTauBarostat())
1525	+	myNPTxyz->setTauBarostat(globals->getTauBarostat());
1526	+	else{
1527	+	sprintf(painCave.errMsg,
1528	+	"SimSetup error: If you use an NPT\n"
1529	+	"\tensemble, you must set tauBarostat.\n");
1530	+	painCave.isFatal = 1;
1531	+	simError();
1532	+	}
1533	+
1534	+	info->the_integrator = myNPTxyz;
1535	+	break;
1536	+
1537	+	default:
1538	+	sprintf(painCave.errMsg,
1539	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1540	+	painCave.isFatal = 1;
1541	+	simError();
1542	+	}
1543	+	}
1544	+	}
1545	+
1546	+	void SimSetup::initFortran(void){
1547	+	info[0].refreshSim();
1548	+
1549	+	if (!strcmp(info[0].mixingRule, "standard")){
1550	+	the_ff->initForceField(LB_MIXING_RULE);
1551	+	}
1552	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1553	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1554	+	}
1555	+	else{
1556	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1557	+	info[0].mixingRule);
1558	+	painCave.isFatal = 1;
1559	+	simError();
1560	+	}
1561	+
1562	+
1563	+	#ifdef IS_MPI
1564	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1565	+	MPIcheckPoint();
1566	+	#endif // is_mpi
1567	+	}
1568	+
1569	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1570	+	int nZConstraints;
1571	+	ZconStamp** zconStamp;
1572	+
1573	+	if (globals->haveZconstraintTime()){
1574	+	//add sample time of z-constraint  into SimInfo's property list
1575	+	DoubleData* zconsTimeProp = new DoubleData();
1576	+	zconsTimeProp->setID(ZCONSTIME_ID);
1577	+	zconsTimeProp->setData(globals->getZconsTime());
1578	+	theInfo.addProperty(zconsTimeProp);
1579	+	}
1580	+	else{
1581	+	sprintf(painCave.errMsg,
1582	+	"ZConstraint error: If you use a ZConstraint,\n"
1583	+	"\tyou must set zconsTime.\n");
1584	+	painCave.isFatal = 1;
1585	+	simError();
1586	+	}
1587	+
1588	+	//push zconsTol into siminfo, if user does not specify
1589	+	//value for zconsTol, a default value will be used
1590	+	DoubleData* zconsTol = new DoubleData();
1591	+	zconsTol->setID(ZCONSTOL_ID);
1592	+	if (globals->haveZconsTol()){
1593	+	zconsTol->setData(globals->getZconsTol());
1594	+	}
1595	+	else{
1596	+	double defaultZConsTol = 0.01;
1597	+	sprintf(painCave.errMsg,
1598	+	"ZConstraint Warning: Tolerance for z-constraint method is not specified.\n"
1599	+	"\tOOPSE will use a default value of %f.\n"
1600	+	"\tTo set the tolerance, use the zconsTol variable.\n",
1601	+	defaultZConsTol);
1602	+	painCave.isFatal = 0;
1603	+	simError();
1604	+
1605	+	zconsTol->setData(defaultZConsTol);
1606	+	}
1607	+	theInfo.addProperty(zconsTol);
1608	+
1609	+	//set Force Subtraction Policy
1610	+	StringData* zconsForcePolicy = new StringData();
1611	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1612	+
1613	+	if (globals->haveZconsForcePolicy()){
1614	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1615	+	}
1616	+	else{
1617	+	sprintf(painCave.errMsg,
1618	+	"ZConstraint Warning: No force subtraction policy was set.\n"
1619	+	"\tOOPSE will use PolicyByMass.\n"
1620	+	"\tTo set the policy, use the zconsForcePolicy variable.\n");
1621	+	painCave.isFatal = 0;
1622	+	simError();
1623	+	zconsForcePolicy->setData("BYMASS");
1624	+	}
1625	+
1626	+	theInfo.addProperty(zconsForcePolicy);
1627	+
1628	+	//Determine the name of ouput file and add it into SimInfo's property list
1629	+	//Be careful, do not use inFileName, since it is a pointer which
1630	+	//point to a string at master node, and slave nodes do not contain that string
1631	+
1632	+	string zconsOutput(theInfo.finalName);
1633	+
1634	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1635	+
1636	+	StringData* zconsFilename = new StringData();
1637	+	zconsFilename->setID(ZCONSFILENAME_ID);
1638	+	zconsFilename->setData(zconsOutput);
1639	+
1640	+	theInfo.addProperty(zconsFilename);
1641	+
1642	+	//setup index, pos and other parameters of z-constraint molecules
1643	+	nZConstraints = globals->getNzConstraints();
1644	+	theInfo.nZconstraints = nZConstraints;
1645	+
1646	+	zconStamp = globals->getZconStamp();
1647	+	ZConsParaItem tempParaItem;
1648	+
1649	+	ZConsParaData* zconsParaData = new ZConsParaData();
1650	+	zconsParaData->setID(ZCONSPARADATA_ID);
1651	+
1652	+	for (int i = 0; i < nZConstraints; i++){
1653	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1654	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1655	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1656	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1657	+
1658	+	zconsParaData->addItem(tempParaItem);
1659	+	}
1660	+
1661	+	//check the uniqueness of index
1662	+	if(!zconsParaData->isIndexUnique()){
1663	+	sprintf(painCave.errMsg,
1664	+	"ZConstraint Error: molIndex is not unique!\n");
1665	+	painCave.isFatal = 1;
1666	+	simError();
1667	+	}
1668	+
1669	+	//sort the parameters by index of molecules
1670	+	zconsParaData->sortByIndex();
1671	+
1672	+	//push data into siminfo, therefore, we can retrieve later
1673	+	theInfo.addProperty(zconsParaData);
1674	+	}

Diff Legend

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