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 427 by mmeineke, Thu Mar 27 20:48:37 2003 UTC vs.
Revision 811 by mmeineke, Tue Oct 21 19:33:19 2003 UTC

#	Line 1 | Line 1
1	+	#include <algorithm>
2		#include <cstdlib>
3		#include <iostream>
4		#include <cmath>
5	+	#include <string>
6	+	#include <sprng.h>
7
8		#include "SimSetup.hpp"
9	+	#include "ReadWrite.hpp"
10		#include "parse_me.h"
11		#include "Integrator.hpp"
12		#include "simError.h"
#	Line 12 | Line 16 | SimSetup::SimSetup(){
16		#include "mpiSimulation.hpp"
17		#endif
18
19	+	// some defines for ensemble and Forcefield  cases
20	+
21	+	#define NVE_ENS        0
22	+	#define NVT_ENS        1
23	+	#define NPTi_ENS       2
24	+	#define NPTf_ENS       3
25	+
26	+	#define FF_DUFF 0
27	+	#define FF_LJ   1
28	+	#define FF_EAM  2
29	+
30	+	using namespace std;
31	+
32		SimSetup::SimSetup(){
33	+	isInfoArray = 0;
34	+	nInfo = 1;
35	+
36		stamps = new MakeStamps();
37		globals = new Globals();
38	<
38	>
39	>
40		#ifdef IS_MPI
41	<	strcpy( checkPointMsg, "SimSetup creation successful" );
41	>	strcpy(checkPointMsg, "SimSetup creation successful");
42		MPIcheckPoint();
43		#endif // IS_MPI
44		}
#	Line 27 | Line 48 | void SimSetup::parseFile( char* fileName ){
48		delete globals;
49		}
50
51	<	void SimSetup::parseFile( char* fileName ){
51	>	void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){
52	>	info = the_info;
53	>	nInfo = theNinfo;
54	>	isInfoArray = 1;
55	>	}
56
57	+
58	+	void SimSetup::parseFile(char* fileName){
59		#ifdef IS_MPI
60	<	if( worldRank == 0 ){
60	>	if (worldRank == 0){
61		#endif // is_mpi
62	<
62	>
63		inFileName = fileName;
64	<	set_interface_stamps( stamps, globals );
65	<
64	>	set_interface_stamps(stamps, globals);
65	>
66		#ifdef IS_MPI
67		mpiEventInit();
68		#endif
69
70	<	yacc_BASS( fileName );
70	>	yacc_BASS(fileName);
71
72		#ifdef IS_MPI
73		throwMPIEvent(NULL);
74		}
75	<	else receiveParse();
75	>	else{
76	>	receiveParse();
77	>	}
78		#endif
79
80		}
81
82		#ifdef IS_MPI
83		void SimSetup::receiveParse(void){
84	<
85	<	set_interface_stamps( stamps, globals );
86	<	mpiEventInit();
87	<	MPIcheckPoint();
59	<	mpiEventLoop();
60	<
84	>	set_interface_stamps(stamps, globals);
85	>	mpiEventInit();
86	>	MPIcheckPoint();
87	>	mpiEventLoop();
88		}
89
90		#endif // is_mpi
91
92	<	void SimSetup::createSim( void ){
92	>	void SimSetup::createSim(void){
93
94	<	MakeStamps *the_stamps;
68	<	Globals* the_globals;
69	<	int i, j;
94	>	// gather all of the information from the Bass file
95
96	<	// get the stamps and globals;
72	<	the_stamps = stamps;
73	<	the_globals = globals;
96	>	gatherInfo();
97
98	<	// set the easy ones first
76	<	simnfo->target_temp = the_globals->getTargetTemp();
77	<	simnfo->dt = the_globals->getDt();
78	<	simnfo->run_time = the_globals->getRunTime();
98	>	// creation of complex system objects
99
100	<	// get the ones we know are there, yet still may need some work.
81	<	n_components = the_globals->getNComponents();
82	<	strcpy( force_field, the_globals->getForceField() );
83	<	strcpy( ensemble, the_globals->getEnsemble() );
84	<	strcpy( simnfo->ensemble, ensemble );
100	>	sysObjectsCreation();
101
102	<	strcpy( simnfo->mixingRule, the_globals->getMixingRule() );
87	<	simnfo->usePBC = the_globals->getPBC();
88	<
102	>	// check on the post processing info
103
104	+	finalInfoCheck();
105
106	<	if( !strcmp( force_field, "TraPPE_Ex" ) ) the_ff = new TraPPE_ExFF();
92	<	else if( !strcmp( force_field, "LJ" ) ) the_ff = new LJ_FF();
93	<	else{
94	<	sprintf( painCave.errMsg,
95	<	"SimSetup Error. Unrecognized force field -> %s\n",
96	<	force_field );
97	<	painCave.isFatal = 1;
98	<	simError();
99	<	}
106	>	// initialize the system coordinates
107
108	<	#ifdef IS_MPI
109	<	strcpy( checkPointMsg, "ForceField creation successful" );
103	<	MPIcheckPoint();
104	<	#endif // is_mpi
108	>	if (!isInfoArray){
109	>	initSystemCoords();
110
111	<
111	>	if( !(globals->getUseInitTime()) )
112	>	info[0].currentTime = 0.0;
113	>	}
114
115	<	// get the components and calculate the tot_nMol and indvidual n_mol
109	<	the_components = the_globals->getComponents();
110	<	components_nmol = new int[n_components];
111	<	comp_stamps = new MoleculeStamp*[n_components];
115	>	// make the output filenames
116
117	<	if( !the_globals->haveNMol() ){
114	<	// we don't have the total number of molecules, so we assume it is
115	<	// given in each component
117	>	makeOutNames();
118
119	<	tot_nmol = 0;
118	<	for( i=0; i<n_components; i++ ){
119	>	// make the integrator
120
121	<	if( !the_components[i]->haveNMol() ){
121	<	// we have a problem
122	<	sprintf( painCave.errMsg,
123	<	"SimSetup Error. No global NMol or component NMol"
124	<	" given. Cannot calculate the number of atoms.\n" );
125	<	painCave.isFatal = 1;
126	<	simError();
127	<	}
121	>	makeIntegrator();
122
129	–	tot_nmol += the_components[i]->getNMol();
130	–	components_nmol[i] = the_components[i]->getNMol();
131	–	}
132	–	}
133	–	else{
134	–	sprintf( painCave.errMsg,
135	–	"SimSetup error.\n"
136	–	"\tSorry, the ability to specify total"
137	–	" nMols and then give molfractions in the components\n"
138	–	"\tis not currently supported."
139	–	" Please give nMol in the components.\n" );
140	–	painCave.isFatal = 1;
141	–	simError();
142	–
143	–
144	–	//     tot_nmol = the_globals->getNMol();
145	–
146	–	//   //we have the total number of molecules, now we check for molfractions
147	–	//     for( i=0; i<n_components; i++ ){
148	–
149	–	//       if( !the_components[i]->haveMolFraction() ){
150	–
151	–	//  if( !the_components[i]->haveNMol() ){
152	–	//    //we have a problem
153	–	//    std::cerr << "SimSetup error. Neither molFraction nor "
154	–	//              << " nMol was given in component
155	–
156	–	}
157	–
123		#ifdef IS_MPI
124	<	strcpy( checkPointMsg, "Have the number of components" );
125	<	MPIcheckPoint();
161	<	#endif // is_mpi
124	>	mpiSim->mpiRefresh();
125	>	#endif
126
127	<	// make an array of molecule stamps that match the components used.
164	<	// also extract the used stamps out into a separate linked list
127	>	// initialize the Fortran
128
129	<	simnfo->nComponents = n_components;
130	<	simnfo->componentsNmol = components_nmol;
168	<	simnfo->compStamps = comp_stamps;
169	<	simnfo->headStamp = new LinkedMolStamp();
170	<
171	<	char* id;
172	<	LinkedMolStamp* headStamp = simnfo->headStamp;
173	<	LinkedMolStamp* currentStamp = NULL;
174	<	for( i=0; i<n_components; i++ ){
129	>	initFortran();
130	>	}
131
176	–	id = the_components[i]->getType();
177	–	comp_stamps[i] = NULL;
178	–
179	–	// check to make sure the component isn't already in the list
132
133	<	comp_stamps[i] = headStamp->match( id );
134	<	if( comp_stamps[i] == NULL ){
135	<
136	<	// extract the component from the list;
137	<
138	<	currentStamp = the_stamps->extractMolStamp( id );
139	<	if( currentStamp == NULL ){
140	<	sprintf( painCave.errMsg,
141	<	"SimSetup error: Component \"%s\" was not found in the "
142	<	"list of declared molecules\n",
143	<	id );
192	<	painCave.isFatal = 1;
193	<	simError();
194	<	}
195	<
196	<	headStamp->add( currentStamp );
197	<	comp_stamps[i] = headStamp->match( id );
198	<	}
199	<	}
133	>	void SimSetup::makeMolecules(void){
134	>	int k;
135	>	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
136	>	molInit molInfo;
137	>	DirectionalAtom* dAtom;
138	>	LinkedAssign* extras;
139	>	LinkedAssign* current_extra;
140	>	AtomStamp* currentAtom;
141	>	BondStamp* currentBond;
142	>	BendStamp* currentBend;
143	>	TorsionStamp* currentTorsion;
144
145	<	#ifdef IS_MPI
146	<	strcpy( checkPointMsg, "Component stamps successfully extracted\n" );
147	<	MPIcheckPoint();
204	<	#endif // is_mpi
205	<
145	>	bond_pair* theBonds;
146	>	bend_set* theBends;
147	>	torsion_set* theTorsions;
148
149
150	+	//init the forceField paramters
151
152	<	// caclulate the number of atoms, bonds, bends and torsions
152	>	the_ff->readParams();
153
211	–	tot_atoms = 0;
212	–	tot_bonds = 0;
213	–	tot_bends = 0;
214	–	tot_torsions = 0;
215	–	for( i=0; i<n_components; i++ ){
216	–
217	–	tot_atoms +=    components_nmol[i] * comp_stamps[i]->getNAtoms();
218	–	tot_bonds +=    components_nmol[i] * comp_stamps[i]->getNBonds();
219	–	tot_bends +=    components_nmol[i] * comp_stamps[i]->getNBends();
220	–	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
221	–	}
154
155	<	tot_SRI = tot_bonds + tot_bends + tot_torsions;
155	>	// init the atoms
156
157	<	simnfo->n_atoms = tot_atoms;
226	<	simnfo->n_bonds = tot_bonds;
227	<	simnfo->n_bends = tot_bends;
228	<	simnfo->n_torsions = tot_torsions;
229	<	simnfo->n_SRI = tot_SRI;
230	<	simnfo->n_mol = tot_nmol;
157	>	double ux, uy, uz, u, uSqr;
158
159	<
160	<	#ifdef IS_MPI
159	>	for (k = 0; k < nInfo; k++){
160	>	the_ff->setSimInfo(&(info[k]));
161
162	<	// divide the molecules among processors here.
163	<
164	<	mpiSim = new mpiSimulation( simnfo );
165	<
239	<
162	>	atomOffset = 0;
163	>	excludeOffset = 0;
164	>	for (i = 0; i < info[k].n_mol; i++){
165	>	stampID = info[k].molecules[i].getStampID();
166
167	<	globalIndex = mpiSim->divideLabor();
167	>	molInfo.nAtoms = comp_stamps[stampID]->getNAtoms();
168	>	molInfo.nBonds = comp_stamps[stampID]->getNBonds();
169	>	molInfo.nBends = comp_stamps[stampID]->getNBends();
170	>	molInfo.nTorsions = comp_stamps[stampID]->getNTorsions();
171	>	molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions;
172
173	+	molInfo.myAtoms = &(info[k].atoms[atomOffset]);
174	+	molInfo.myExcludes = &(info[k].excludes[excludeOffset]);
175	+	molInfo.myBonds = new Bond * [molInfo.nBonds];
176	+	molInfo.myBends = new Bend * [molInfo.nBends];
177	+	molInfo.myTorsions = new Torsion * [molInfo.nTorsions];
178
179	+	theBonds = new bond_pair[molInfo.nBonds];
180	+	theBends = new bend_set[molInfo.nBends];
181	+	theTorsions = new torsion_set[molInfo.nTorsions];
182
183	<	// set up the local variables
246	<
247	<	int localMol, allMol;
248	<	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
183	>	// make the Atoms
184
185	<	int* mol2proc = mpiSim->getMolToProcMap();
186	<	int* molCompType = mpiSim->getMolComponentType();
187	<
188	<	allMol = 0;
189	<	localMol = 0;
190	<	local_atoms = 0;
191	<	local_bonds = 0;
257	<	local_bends = 0;
258	<	local_torsions = 0;
259	<	for( i=0; i<n_components; i++ ){
185	>	for (j = 0; j < molInfo.nAtoms; j++){
186	>	currentAtom = comp_stamps[stampID]->getAtom(j);
187	>	if (currentAtom->haveOrientation()){
188	>	dAtom = new DirectionalAtom((j + atomOffset),
189	>	info[k].getConfiguration());
190	>	info[k].n_oriented++;
191	>	molInfo.myAtoms[j] = dAtom;
192
193	<	for( j=0; j<components_nmol[i]; j++ ){
194	<
195	<	if( mol2proc[j] == worldRank ){
264	<
265	<	local_atoms +=    comp_stamps[i]->getNAtoms();
266	<	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	<
193	>	ux = currentAtom->getOrntX();
194	>	uy = currentAtom->getOrntY();
195	>	uz = currentAtom->getOrntZ();
196
197	<	simnfo->n_atoms = mpiSim->getMyNlocal();
278	<
279	<	if( local_atoms != simnfo->n_atoms ){
280	<	sprintf( painCave.errMsg,
281	<	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
282	<	" localAtom (%d) are not equal.\n",
283	<	simnfo->n_atoms,
284	<	local_atoms );
285	<	painCave.isFatal = 1;
286	<	simError();
287	<	}
197	>	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
198
199	<	simnfo->n_bonds = local_bonds;
200	<	simnfo->n_bends = local_bends;
201	<	simnfo->n_torsions = local_torsions;
202	<	simnfo->n_SRI = local_SRI;
293	<	simnfo->n_mol = localMol;
199	>	u = sqrt(uSqr);
200	>	ux = ux / u;
201	>	uy = uy / u;
202	>	uz = uz / u;
203
204	<	strcpy( checkPointMsg, "Passed nlocal consistency check." );
205	<	MPIcheckPoint();
206	<
207	<
204	>	dAtom->setSUx(ux);
205	>	dAtom->setSUy(uy);
206	>	dAtom->setSUz(uz);
207	>	}
208	>	else{
209	>	molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset),
210	>	info[k].getConfiguration());
211	>	}
212	>	molInfo.myAtoms[j]->setType(currentAtom->getType());
213	>
214	>	#ifdef IS_MPI
215	>
216	>	molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]);
217	>
218		#endif // is_mpi
219	<
219	>	}
220
221	<	// create the atom and short range interaction arrays
221	>	// make the bonds
222	>	for (j = 0; j < molInfo.nBonds; j++){
223	>	currentBond = comp_stamps[stampID]->getBond(j);
224	>	theBonds[j].a = currentBond->getA() + atomOffset;
225	>	theBonds[j].b = currentBond->getB() + atomOffset;
226
227	<	Atom::createArrays(simnfo->n_atoms);
228	<	the_atoms = new Atom*[simnfo->n_atoms];
306	<	the_molecules = new Molecule[simnfo->n_mol];
307	<	int molIndex;
227	>	exI = theBonds[j].a;
228	>	exJ = theBonds[j].b;
229
230	<	// initialize the molecule's stampID's
230	>	// exclude_I must always be the smaller of the pair
231	>	if (exI > exJ){
232	>	tempEx = exI;
233	>	exI = exJ;
234	>	exJ = tempEx;
235	>	}
236	>	#ifdef IS_MPI
237	>	tempEx = exI;
238	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
239	>	tempEx = exJ;
240	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
241
242	+	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
243	+	#else  // isn't MPI
244	+
245	+	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
246	+	#endif  //is_mpi
247	+	}
248	+	excludeOffset += molInfo.nBonds;
249	+
250	+	//make the bends
251	+	for (j = 0; j < molInfo.nBends; j++){
252	+	currentBend = comp_stamps[stampID]->getBend(j);
253	+	theBends[j].a = currentBend->getA() + atomOffset;
254	+	theBends[j].b = currentBend->getB() + atomOffset;
255	+	theBends[j].c = currentBend->getC() + atomOffset;
256	+
257	+	if (currentBend->haveExtras()){
258	+	extras = currentBend->getExtras();
259	+	current_extra = extras;
260	+
261	+	while (current_extra != NULL){
262	+	if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){
263	+	switch (current_extra->getType()){
264	+	case 0:
265	+	theBends[j].ghost = current_extra->getInt() + atomOffset;
266	+	theBends[j].isGhost = 1;
267	+	break;
268	+
269	+	case 1:
270	+	theBends[j].ghost = (int) current_extra->getDouble() +
271	+	atomOffset;
272	+	theBends[j].isGhost = 1;
273	+	break;
274	+
275	+	default:
276	+	sprintf(painCave.errMsg,
277	+	"SimSetup Error: ghostVectorSource was neither a "
278	+	"double nor an int.\n"
279	+	"-->Bend[%d] in %s\n",
280	+	j, comp_stamps[stampID]->getID());
281	+	painCave.isFatal = 1;
282	+	simError();
283	+	}
284	+	}
285	+	else{
286	+	sprintf(painCave.errMsg,
287	+	"SimSetup Error: unhandled bend assignment:\n"
288	+	"    -->%s in Bend[%d] in %s\n",
289	+	current_extra->getlhs(), j, comp_stamps[stampID]->getID());
290	+	painCave.isFatal = 1;
291	+	simError();
292	+	}
293	+
294	+	current_extra = current_extra->getNext();
295	+	}
296	+	}
297	+
298	+	if (!theBends[j].isGhost){
299	+	exI = theBends[j].a;
300	+	exJ = theBends[j].c;
301	+	}
302	+	else{
303	+	exI = theBends[j].a;
304	+	exJ = theBends[j].b;
305	+	}
306	+
307	+	// exclude_I must always be the smaller of the pair
308	+	if (exI > exJ){
309	+	tempEx = exI;
310	+	exI = exJ;
311	+	exJ = tempEx;
312	+	}
313		#ifdef IS_MPI
314	<
314	>	tempEx = exI;
315	>	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
316	>	tempEx = exJ;
317	>	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
318
319	<	molIndex = 0;
320	<	for(i=0; i<mpiSim->getTotNmol(); i++){
321	<
322	<	if(mol2proc[i] == worldRank ){
323	<	the_molecules[molIndex].setStampID( molCompType[i] );
324	<	molIndex++;
320	<	}
321	<	}
319	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
320	>	#else  // isn't MPI
321	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
322	>	#endif  //is_mpi
323	>	}
324	>	excludeOffset += molInfo.nBends;
325
326	<	#else // is_mpi
327	<
328	<	molIndex = 0;
329	<	for(i=0; i<n_components; i++){
330	<	for(j=0; j<components_nmol[i]; j++ ){
331	<	the_molecules[molIndex].setStampID( i );
329	<	molIndex++;
330	<	}
331	<	}
332	<
326	>	for (j = 0; j < molInfo.nTorsions; j++){
327	>	currentTorsion = comp_stamps[stampID]->getTorsion(j);
328	>	theTorsions[j].a = currentTorsion->getA() + atomOffset;
329	>	theTorsions[j].b = currentTorsion->getB() + atomOffset;
330	>	theTorsions[j].c = currentTorsion->getC() + atomOffset;
331	>	theTorsions[j].d = currentTorsion->getD() + atomOffset;
332
333	<	#endif // is_mpi
333	>	exI = theTorsions[j].a;
334	>	exJ = theTorsions[j].d;
335
336	+	// exclude_I must always be the smaller of the pair
337	+	if (exI > exJ){
338	+	tempEx = exI;
339	+	exI = exJ;
340	+	exJ = tempEx;
341	+	}
342	+	#ifdef IS_MPI
343	+	tempEx = exI;
344	+	exI = info[k].atoms[tempEx]->getGlobalIndex() + 1;
345	+	tempEx = exJ;
346	+	exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1;
347
348	<	if( simnfo->n_SRI ){
349	<	Exclude::createArray(simnfo->n_SRI);
350	<	the_excludes = new Exclude*[simnfo->n_SRI];
351	<	simnfo->globalExcludes = new int;
352	<	simnfo->n_exclude = tot_SRI;
353	<	}
343	<	else{
344	<
345	<	Exclude::createArray( 1 );
346	<	the_excludes = new Exclude*;
347	<	the_excludes[0] = new Exclude(0);
348	<	the_excludes[0]->setPair( 0,0 );
349	<	simnfo->globalExcludes = new int;
350	<	simnfo->globalExcludes[0] = 0;
351	<	simnfo->n_exclude = 0;
352	<	}
348	>	info[k].excludes[j + excludeOffset]->setPair(exI, exJ);
349	>	#else  // isn't MPI
350	>	info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1));
351	>	#endif  //is_mpi
352	>	}
353	>	excludeOffset += molInfo.nTorsions;
354
354	–	// set the arrays into the SimInfo object
355
356	<	simnfo->atoms = the_atoms;
357	<	simnfo->nGlobalExcludes = 0;
358	<	simnfo->excludes = the_excludes;
356	>	// send the arrays off to the forceField for init.
357
358	+	the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms);
359	+	the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds);
360	+	the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends);
361	+	the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions,
362	+	theTorsions);
363
361	–	// get some of the tricky things that may still be in the globals
364
365	<
364	<	if( the_globals->haveBox() ){
365	<	simnfo->box_x = the_globals->getBox();
366	<	simnfo->box_y = the_globals->getBox();
367	<	simnfo->box_z = the_globals->getBox();
368	<	}
369	<	else if( the_globals->haveDensity() ){
365	>	info[k].molecules[i].initialize(molInfo);
366
371	–	double vol;
372	–	vol = (double)tot_nmol / the_globals->getDensity();
373	–	simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) );
374	–	simnfo->box_y = simnfo->box_x;
375	–	simnfo->box_z = simnfo->box_x;
376	–	}
377	–	else{
378	–	if( !the_globals->haveBoxX() ){
379	–	sprintf( painCave.errMsg,
380	–	"SimSetup error, no periodic BoxX size given.\n" );
381	–	painCave.isFatal = 1;
382	–	simError();
383	–	}
384	–	simnfo->box_x = the_globals->getBoxX();
367
368	<	if( !the_globals->haveBoxY() ){
369	<	sprintf( painCave.errMsg,
370	<	"SimSetup error, no periodic BoxY size given.\n" );
371	<	painCave.isFatal = 1;
390	<	simError();
391	<	}
392	<	simnfo->box_y = the_globals->getBoxY();
393	<
394	<	if( !the_globals->haveBoxZ() ){
395	<	sprintf( painCave.errMsg,
396	<	"SimSetup error, no periodic BoxZ size given.\n" );
397	<	painCave.isFatal = 1;
398	<	simError();
368	>	atomOffset += molInfo.nAtoms;
369	>	delete[] theBonds;
370	>	delete[] theBends;
371	>	delete[] theTorsions;
372		}
400	–	simnfo->box_z = the_globals->getBoxZ();
373		}
374
375		#ifdef IS_MPI
376	<	strcpy( checkPointMsg, "Box size set up" );
376	>	sprintf(checkPointMsg, "all molecules initialized succesfully");
377		MPIcheckPoint();
378		#endif // is_mpi
379
380	+	// clean up the forcefield
381
382	<	// initialize the arrays
382	>	the_ff->calcRcut();
383	>	the_ff->cleanMe();
384	>	}
385
386	<	the_ff->setSimInfo( simnfo );
386	>	void SimSetup::initFromBass(void){
387	>	int i, j, k;
388	>	int n_cells;
389	>	double cellx, celly, cellz;
390	>	double temp1, temp2, temp3;
391	>	int n_per_extra;
392	>	int n_extra;
393	>	int have_extra, done;
394
395	<	makeMolecules();
396	<	simnfo->identArray = new int[simnfo->n_atoms];
397	<	for(i=0; i<simnfo->n_atoms; i++){
398	<	simnfo->identArray[i] = the_atoms[i]->getIdent();
417	<	}
418	<
419	<	if (the_globals->getUseRF() ) {
420	<	simnfo->useReactionField = 1;
421	<
422	<	if( !the_globals->haveECR() ){
423	<	sprintf( painCave.errMsg,
424	<	"SimSetup Warning: using default value of 1/2 the smallest "
425	<	"box length for the electrostaticCutoffRadius.\n"
426	<	"I hope you have a very fast processor!\n");
427	<	painCave.isFatal = 0;
428	<	simError();
429	<	double smallest;
430	<	smallest = simnfo->box_x;
431	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
432	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
433	<	simnfo->ecr = 0.5 * smallest;
434	<	} else {
435	<	simnfo->ecr        = the_globals->getECR();
436	<	}
395	>	double vel[3];
396	>	vel[0] = 0.0;
397	>	vel[1] = 0.0;
398	>	vel[2] = 0.0;
399
400	<	if( !the_globals->haveEST() ){
401	<	sprintf( painCave.errMsg,
402	<	"SimSetup Warning: using default value of 0.05 * the "
403	<	"electrostaticCutoffRadius for the electrostaticSkinThickness\n"
404	<	);
405	<	painCave.isFatal = 0;
406	<	simError();
407	<	simnfo->est = 0.05 * simnfo->ecr;
408	<	} else {
409	<	simnfo->est        = the_globals->getEST();
410	<	}
411	<
412	<	if(!the_globals->haveDielectric() ){
413	<	sprintf( painCave.errMsg,
414	<	"SimSetup Error: You are trying to use Reaction Field without"
415	<	"setting a dielectric constant!\n"
416	<	);
400	>	temp1 = (double) tot_nmol / 4.0;
401	>	temp2 = pow(temp1, (1.0 / 3.0));
402	>	temp3 = ceil(temp2);
403	>
404	>	have_extra = 0;
405	>	if (temp2 < temp3){
406	>	// we have a non-complete lattice
407	>	have_extra = 1;
408	>
409	>	n_cells = (int) temp3 - 1;
410	>	cellx = info[0].boxL[0] / temp3;
411	>	celly = info[0].boxL[1] / temp3;
412	>	cellz = info[0].boxL[2] / temp3;
413	>	n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells);
414	>	temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0));
415	>	n_per_extra = (int) ceil(temp1);
416	>
417	>	if (n_per_extra > 4){
418	>	sprintf(painCave.errMsg,
419	>	"SimSetup error. There has been an error in constructing"
420	>	" the non-complete lattice.\n");
421		painCave.isFatal = 1;
422		simError();
423		}
424	<	simnfo->dielectric = the_globals->getDielectric();
425	<	} else {
426	<	if (simnfo->n_dipoles) {
427	<
428	<	if( !the_globals->haveECR() ){
429	<	sprintf( painCave.errMsg,
430	<	"SimSetup Warning: using default value of 1/2 the smallest"
431	<	"box length for the electrostaticCutoffRadius.\n"
432	<	"I hope you have a very fast processor!\n");
433	<	painCave.isFatal = 0;
434	<	simError();
435	<	double smallest;
436	<	smallest = simnfo->box_x;
437	<	if (simnfo->box_y <= smallest) smallest = simnfo->box_y;
438	<	if (simnfo->box_z <= smallest) smallest = simnfo->box_z;
439	<	simnfo->ecr = 0.5 * smallest;
440	<	} else {
441	<	simnfo->ecr        = the_globals->getECR();
424	>	}
425	>	else{
426	>	n_cells = (int) temp3;
427	>	cellx = info[0].boxL[0] / temp3;
428	>	celly = info[0].boxL[1] / temp3;
429	>	cellz = info[0].boxL[2] / temp3;
430	>	}
431	>
432	>	current_mol = 0;
433	>	current_comp_mol = 0;
434	>	current_comp = 0;
435	>	current_atom_ndx = 0;
436	>
437	>	for (i = 0; i < n_cells ; i++){
438	>	for (j = 0; j < n_cells; j++){
439	>	for (k = 0; k < n_cells; k++){
440	>	makeElement(i * cellx, j * celly, k * cellz);
441	>
442	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz);
443	>
444	>	makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz);
445	>
446	>	makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz);
447		}
477	–
478	–	if( !the_globals->haveEST() ){
479	–	sprintf( painCave.errMsg,
480	–	"SimSetup Warning: using default value of 5% of the"
481	–	"electrostaticCutoffRadius for the "
482	–	"electrostaticSkinThickness\n"
483	–	);
484	–	painCave.isFatal = 0;
485	–	simError();
486	–	simnfo->est = 0.05 * simnfo->ecr;
487	–	} else {
488	–	simnfo->est        = the_globals->getEST();
489	–	}
448		}
449	<	}
449	>	}
450
451	<	#ifdef IS_MPI
452	<	strcpy( checkPointMsg, "electrostatic parameters check out" );
495	<	MPIcheckPoint();
496	<	#endif // is_mpi
451	>	if (have_extra){
452	>	done = 0;
453
454	<	if( the_globals->haveInitialConfig() ){
455	<
456	<	InitializeFromFile* fileInit;
457	<	#ifdef IS_MPI // is_mpi
458	<	if( worldRank == 0 ){
459	<	#endif //is_mpi
460	<	fileInit = new InitializeFromFile( the_globals->getInitialConfig() );
461	<	#ifdef IS_MPI
462	<	}else fileInit = new InitializeFromFile( NULL );
463	<	#endif
464	<	fileInit->read_xyz( simnfo ); // default velocities on
454	>	int start_ndx;
455	>	for (i = 0; i < (n_cells + 1) && !done; i++){
456	>	for (j = 0; j < (n_cells + 1) && !done; j++){
457	>	if (i < n_cells){
458	>	if (j < n_cells){
459	>	start_ndx = n_cells;
460	>	}
461	>	else
462	>	start_ndx = 0;
463	>	}
464	>	else
465	>	start_ndx = 0;
466
467	<	delete fileInit;
468	<	}
469	<	else{
467	>	for (k = start_ndx; k < (n_cells + 1) && !done; k++){
468	>	makeElement(i * cellx, j * celly, k * cellz);
469	>	done = (current_mol >= tot_nmol);
470
471	<	#ifdef IS_MPI
471	>	if (!done && n_per_extra > 1){
472	>	makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly,
473	>	k * cellz);
474	>	done = (current_mol >= tot_nmol);
475	>	}
476
477	<	// no init from bass
478	<
479	<	sprintf( painCave.errMsg,
480	<	"Cannot intialize a parallel simulation without an initial configuration file.\n" );
481	<	painCave.isFatal;
521	<	simError();
522	<
523	<	#else
477	>	if (!done && n_per_extra > 2){
478	>	makeElement(i * cellx, j * celly + 0.5 * celly,
479	>	k * cellz + 0.5 * cellz);
480	>	done = (current_mol >= tot_nmol);
481	>	}
482
483	<	initFromBass();
483	>	if (!done && n_per_extra > 3){
484	>	makeElement(i * cellx + 0.5 * cellx, j * celly,
485	>	k * cellz + 0.5 * cellz);
486	>	done = (current_mol >= tot_nmol);
487	>	}
488	>	}
489	>	}
490	>	}
491	>	}
492
493	+	for (i = 0; i < info[0].n_atoms; i++){
494	+	info[0].atoms[i]->setVel(vel);
495	+	}
496	+	}
497
498	<	#endif
499	<	}
498	>	void SimSetup::makeElement(double x, double y, double z){
499	>	int k;
500	>	AtomStamp* current_atom;
501	>	DirectionalAtom* dAtom;
502	>	double rotMat[3][3];
503	>	double pos[3];
504
505	<	#ifdef IS_MPI
506	<	strcpy( checkPointMsg, "Successfully read in the initial configuration" );
507	<	MPIcheckPoint();
508	<	#endif // is_mpi
505	>	for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){
506	>	current_atom = comp_stamps[current_comp]->getAtom(k);
507	>	if (!current_atom->havePosition()){
508	>	sprintf(painCave.errMsg,
509	>	"SimSetup:initFromBass error.\n"
510	>	"\tComponent %s, atom %s does not have a position specified.\n"
511	>	"\tThe initialization routine is unable to give a start"
512	>	" position.\n",
513	>	comp_stamps[current_comp]->getID(), current_atom->getType());
514	>	painCave.isFatal = 1;
515	>	simError();
516	>	}
517
518	+	pos[0] = x + current_atom->getPosX();
519	+	pos[1] = y + current_atom->getPosY();
520	+	pos[2] = z + current_atom->getPosZ();
521
522	<
538	<
539	<
522	>	info[0].atoms[current_atom_ndx]->setPos(pos);
523
524	<
525	<	#ifdef IS_MPI
526	<	if( worldRank == 0 ){
527	<	#endif // is_mpi
528	<
529	<	if( the_globals->haveFinalConfig() ){
530	<	strcpy( simnfo->finalName, the_globals->getFinalConfig() );
524	>	if (info[0].atoms[current_atom_ndx]->isDirectional()){
525	>	dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx];
526	>
527	>	rotMat[0][0] = 1.0;
528	>	rotMat[0][1] = 0.0;
529	>	rotMat[0][2] = 0.0;
530	>
531	>	rotMat[1][0] = 0.0;
532	>	rotMat[1][1] = 1.0;
533	>	rotMat[1][2] = 0.0;
534	>
535	>	rotMat[2][0] = 0.0;
536	>	rotMat[2][1] = 0.0;
537	>	rotMat[2][2] = 1.0;
538	>
539	>	dAtom->setA(rotMat);
540		}
549	–	else{
550	–	strcpy( simnfo->finalName, inFileName );
551	–	char* endTest;
552	–	int nameLength = strlen( simnfo->finalName );
553	–	endTest = &(simnfo->finalName[nameLength - 5]);
554	–	if( !strcmp( endTest, ".bass" ) ){
555	–	strcpy( endTest, ".eor" );
556	–	}
557	–	else if( !strcmp( endTest, ".BASS" ) ){
558	–	strcpy( endTest, ".eor" );
559	–	}
560	–	else{
561	–	endTest = &(simnfo->finalName[nameLength - 4]);
562	–	if( !strcmp( endTest, ".bss" ) ){
563	–	strcpy( endTest, ".eor" );
564	–	}
565	–	else if( !strcmp( endTest, ".mdl" ) ){
566	–	strcpy( endTest, ".eor" );
567	–	}
568	–	else{
569	–	strcat( simnfo->finalName, ".eor" );
570	–	}
571	–	}
572	–	}
573	–
574	–	// make the sample and status out names
575	–
576	–	strcpy( simnfo->sampleName, inFileName );
577	–	char* endTest;
578	–	int nameLength = strlen( simnfo->sampleName );
579	–	endTest = &(simnfo->sampleName[nameLength - 5]);
580	–	if( !strcmp( endTest, ".bass" ) ){
581	–	strcpy( endTest, ".dump" );
582	–	}
583	–	else if( !strcmp( endTest, ".BASS" ) ){
584	–	strcpy( endTest, ".dump" );
585	–	}
586	–	else{
587	–	endTest = &(simnfo->sampleName[nameLength - 4]);
588	–	if( !strcmp( endTest, ".bss" ) ){
589	–	strcpy( endTest, ".dump" );
590	–	}
591	–	else if( !strcmp( endTest, ".mdl" ) ){
592	–	strcpy( endTest, ".dump" );
593	–	}
594	–	else{
595	–	strcat( simnfo->sampleName, ".dump" );
596	–	}
597	–	}
598	–
599	–	strcpy( simnfo->statusName, inFileName );
600	–	nameLength = strlen( simnfo->statusName );
601	–	endTest = &(simnfo->statusName[nameLength - 5]);
602	–	if( !strcmp( endTest, ".bass" ) ){
603	–	strcpy( endTest, ".stat" );
604	–	}
605	–	else if( !strcmp( endTest, ".BASS" ) ){
606	–	strcpy( endTest, ".stat" );
607	–	}
608	–	else{
609	–	endTest = &(simnfo->statusName[nameLength - 4]);
610	–	if( !strcmp( endTest, ".bss" ) ){
611	–	strcpy( endTest, ".stat" );
612	–	}
613	–	else if( !strcmp( endTest, ".mdl" ) ){
614	–	strcpy( endTest, ".stat" );
615	–	}
616	–	else{
617	–	strcat( simnfo->statusName, ".stat" );
618	–	}
619	–	}
620	–
621	–	#ifdef IS_MPI
622	–	}
623	–	#endif // is_mpi
624	–
625	–	// set the status, sample, and themal kick times
626	–
627	–	if( the_globals->haveSampleTime() ){
628	–	simnfo->sampleTime = the_globals->getSampleTime();
629	–	simnfo->statusTime = simnfo->sampleTime;
630	–	simnfo->thermalTime = simnfo->sampleTime;
631	–	}
632	–	else{
633	–	simnfo->sampleTime = the_globals->getRunTime();
634	–	simnfo->statusTime = simnfo->sampleTime;
635	–	simnfo->thermalTime = simnfo->sampleTime;
636	–	}
541
542	<	if( the_globals->haveStatusTime() ){
639	<	simnfo->statusTime = the_globals->getStatusTime();
542	>	current_atom_ndx++;
543		}
544
545	<	if( the_globals->haveThermalTime() ){
546	<	simnfo->thermalTime = the_globals->getThermalTime();
545	>	current_mol++;
546	>	current_comp_mol++;
547	>
548	>	if (current_comp_mol >= components_nmol[current_comp]){
549	>	current_comp_mol = 0;
550	>	current_comp++;
551		}
552	+	}
553
646	–	// check for the temperature set flag
554
555	<	if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet();
555	>	void SimSetup::gatherInfo(void){
556	>	int i;
557
558	+	ensembleCase = -1;
559	+	ffCase = -1;
560
561	<	//   // make the longe range forces and the integrator
561	>	// set the easy ones first
562
563	<	//   new AllLong( simnfo );
563	>	for (i = 0; i < nInfo; i++){
564	>	info[i].target_temp = globals->getTargetTemp();
565	>	info[i].dt = globals->getDt();
566	>	info[i].run_time = globals->getRunTime();
567	>	}
568	>	n_components = globals->getNComponents();
569
655	–	if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff );
656	–	if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff );
570
571	+	// get the forceField
572
573	+	strcpy(force_field, globals->getForceField());
574
575	<	// initialize the Fortran
576	<
662	<	simnfo->refreshSim();
663	<
664	<	if( !strcmp( simnfo->mixingRule, "standard") ){
665	<	the_ff->initForceField( LB_MIXING_RULE );
575	>	if (!strcasecmp(force_field, "DUFF")){
576	>	ffCase = FF_DUFF;
577		}
578	<	else if( !strcmp( simnfo->mixingRule, "explicit") ){
579	<	the_ff->initForceField( EXPLICIT_MIXING_RULE );
578	>	else if (!strcasecmp(force_field, "LJ")){
579	>	ffCase = FF_LJ;
580		}
581	+	else if (!strcasecmp(force_field, "EAM")){
582	+	ffCase = FF_EAM;
583	+	}
584		else{
585	<	sprintf( painCave.errMsg,
586	<	"SimSetup Error: unknown mixing rule -> \"%s\"\n",
587	<	simnfo->mixingRule );
588	<	painCave.isFatal = 1;
675	<	simError();
585	>	sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n",
586	>	force_field);
587	>	painCave.isFatal = 1;
588	>	simError();
589		}
590
591	+	// get the ensemble
592
593	<	#ifdef IS_MPI
680	<	strcpy( checkPointMsg,
681	<	"Successfully intialized the mixingRule for Fortran." );
682	<	MPIcheckPoint();
683	<	#endif // is_mpi
684	<	}
593	>	strcpy(ensemble, globals->getEnsemble());
594
595	+	if (!strcasecmp(ensemble, "NVE")){
596	+	ensembleCase = NVE_ENS;
597	+	}
598	+	else if (!strcasecmp(ensemble, "NVT")){
599	+	ensembleCase = NVT_ENS;
600	+	}
601	+	else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){
602	+	ensembleCase = NPTi_ENS;
603	+	}
604	+	else if (!strcasecmp(ensemble, "NPTf")){
605	+	ensembleCase = NPTf_ENS;
606	+	}
607	+	else{
608	+	sprintf(painCave.errMsg,
609	+	"SimSetup Warning. Unrecognized Ensemble -> %s, "
610	+	"reverting to NVE for this simulation.\n",
611	+	ensemble);
612	+	painCave.isFatal = 0;
613	+	simError();
614	+	strcpy(ensemble, "NVE");
615	+	ensembleCase = NVE_ENS;
616	+	}
617
618	<	void SimSetup::makeMolecules( void ){
618	>	for (i = 0; i < nInfo; i++){
619	>	strcpy(info[i].ensemble, ensemble);
620
621	<	int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset;
690	<	molInit info;
691	<	DirectionalAtom* dAtom;
692	<	LinkedAssign* extras;
693	<	LinkedAssign* current_extra;
694	<	AtomStamp* currentAtom;
695	<	BondStamp* currentBond;
696	<	BendStamp* currentBend;
697	<	TorsionStamp* currentTorsion;
621	>	// get the mixing rule
622
623	<	bond_pair* theBonds;
624	<	bend_set* theBends;
625	<	torsion_set* theTorsions;
623	>	strcpy(info[i].mixingRule, globals->getMixingRule());
624	>	info[i].usePBC = globals->getPBC();
625	>	}
626
627	<
704	<	//init the forceField paramters
627	>	// get the components and calculate the tot_nMol and indvidual n_mol
628
629	<	the_ff->readParams();
629	>	the_components = globals->getComponents();
630	>	components_nmol = new int[n_components];
631
708	–
709	–	// init the atoms
632
633	<	double ux, uy, uz, u, uSqr;
634	<
635	<	atomOffset = 0;
714	<	excludeOffset = 0;
715	<	for(i=0; i<simnfo->n_mol; i++){
716	<
717	<	stampID = the_molecules[i].getStampID();
633	>	if (!globals->haveNMol()){
634	>	// we don't have the total number of molecules, so we assume it is
635	>	// given in each component
636
637	<	info.nAtoms    = comp_stamps[stampID]->getNAtoms();
638	<	info.nBonds    = comp_stamps[stampID]->getNBonds();
639	<	info.nBends    = comp_stamps[stampID]->getNBends();
640	<	info.nTorsions = comp_stamps[stampID]->getNTorsions();
641	<	info.nExcludes = info.nBonds + info.nBends + info.nTorsions;
637	>	tot_nmol = 0;
638	>	for (i = 0; i < n_components; i++){
639	>	if (!the_components[i]->haveNMol()){
640	>	// we have a problem
641	>	sprintf(painCave.errMsg,
642	>	"SimSetup Error. No global NMol or component NMol"
643	>	" given. Cannot calculate the number of atoms.\n");
644	>	painCave.isFatal = 1;
645	>	simError();
646	>	}
647
648	<	info.myAtoms = &the_atoms[atomOffset];
649	<	info.myExcludes = &the_excludes[excludeOffset];
650	<	info.myBonds = new Bond*[info.nBonds];
651	<	info.myBends = new Bend*[info.nBends];
652	<	info.myTorsions = new Torsion*[info.nTorsions];
648	>	tot_nmol += the_components[i]->getNMol();
649	>	components_nmol[i] = the_components[i]->getNMol();
650	>	}
651	>	}
652	>	else{
653	>	sprintf(painCave.errMsg,
654	>	"SimSetup error.\n"
655	>	"\tSorry, the ability to specify total"
656	>	" nMols and then give molfractions in the components\n"
657	>	"\tis not currently supported."
658	>	" Please give nMol in the components.\n");
659	>	painCave.isFatal = 1;
660	>	simError();
661	>	}
662
663	<	theBonds = new bond_pair[info.nBonds];
732	<	theBends = new bend_set[info.nBends];
733	<	theTorsions = new torsion_set[info.nTorsions];
734	<
735	<	// make the Atoms
736	<
737	<	for(j=0; j<info.nAtoms; j++){
738	<
739	<	currentAtom = comp_stamps[stampID]->getAtom( j );
740	<	if( currentAtom->haveOrientation() ){
741	<
742	<	dAtom = new DirectionalAtom(j + atomOffset);
743	<	simnfo->n_oriented++;
744	<	info.myAtoms[j] = dAtom;
745	<
746	<	ux = currentAtom->getOrntX();
747	<	uy = currentAtom->getOrntY();
748	<	uz = currentAtom->getOrntZ();
749	<
750	<	uSqr = (ux * ux) + (uy * uy) + (uz * uz);
751	<
752	<	u = sqrt( uSqr );
753	<	ux = ux / u;
754	<	uy = uy / u;
755	<	uz = uz / u;
756	<
757	<	dAtom->setSUx( ux );
758	<	dAtom->setSUy( uy );
759	<	dAtom->setSUz( uz );
760	<	}
761	<	else{
762	<	info.myAtoms[j] = new GeneralAtom(j + atomOffset);
763	<	}
764	<	info.myAtoms[j]->setType( currentAtom->getType() );
765	<
766	<	#ifdef IS_MPI
767	<
768	<	info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] );
769	<
770	<	#endif // is_mpi
771	<	}
772	<
773	<	// make the bonds
774	<	for(j=0; j<info.nBonds; j++){
775	<
776	<	currentBond = comp_stamps[stampID]->getBond( j );
777	<	theBonds[j].a = currentBond->getA() + atomOffset;
778	<	theBonds[j].b = currentBond->getB() + atomOffset;
663	>	// set the status, sample, and thermal kick times
664
665	<	exI = theBonds[i].a;
666	<	exJ = theBonds[i].b;
665	>	for (i = 0; i < nInfo; i++){
666	>	if (globals->haveSampleTime()){
667	>	info[i].sampleTime = globals->getSampleTime();
668	>	info[i].statusTime = info[i].sampleTime;
669	>	info[i].thermalTime = info[i].sampleTime;
670	>	}
671	>	else{
672	>	info[i].sampleTime = globals->getRunTime();
673	>	info[i].statusTime = info[i].sampleTime;
674	>	info[i].thermalTime = info[i].sampleTime;
675	>	}
676
677	<	// exclude_I must always be the smaller of the pair
678	<	if( exI > exJ ){
785	<	tempEx = exI;
786	<	exI = exJ;
787	<	exJ = tempEx;
788	<	}
789	<	#ifdef IS_MPI
790	<	tempEx = exI;
791	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
792	<	tempEx = exJ;
793	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
794	<
795	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
796	<	#else  // isn't MPI
797	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
798	<	#endif  //is_mpi
677	>	if (globals->haveStatusTime()){
678	>	info[i].statusTime = globals->getStatusTime();
679		}
800	–	excludeOffset += info.nBonds;
680
681	<	//make the bends
682	<	for(j=0; j<info.nBends; j++){
804	<
805	<	currentBend = comp_stamps[stampID]->getBend( j );
806	<	theBends[j].a = currentBend->getA() + atomOffset;
807	<	theBends[j].b = currentBend->getB() + atomOffset;
808	<	theBends[j].c = currentBend->getC() + atomOffset;
809	<
810	<	if( currentBend->haveExtras() ){
811	<
812	<	extras = currentBend->getExtras();
813	<	current_extra = extras;
814	<
815	<	while( current_extra != NULL ){
816	<	if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){
817	<
818	<	switch( current_extra->getType() ){
819	<
820	<	case 0:
821	<	theBends[j].ghost =
822	<	current_extra->getInt() + atomOffset;
823	<	theBends[j].isGhost = 1;
824	<	break;
825	<
826	<	case 1:
827	<	theBends[j].ghost =
828	<	(int)current_extra->getDouble() + atomOffset;
829	<	theBends[j].isGhost = 1;
830	<	break;
831	<
832	<	default:
833	<	sprintf( painCave.errMsg,
834	<	"SimSetup Error: ghostVectorSource was neiter a "
835	<	"double nor an int.\n"
836	<	"-->Bend[%d] in %s\n",
837	<	j, comp_stamps[stampID]->getID() );
838	<	painCave.isFatal = 1;
839	<	simError();
840	<	}
841	<	}
842	<
843	<	else{
844	<
845	<	sprintf( painCave.errMsg,
846	<	"SimSetup Error: unhandled bend assignment:\n"
847	<	"    -->%s in Bend[%d] in %s\n",
848	<	current_extra->getlhs(),
849	<	j, comp_stamps[stampID]->getID() );
850	<	painCave.isFatal = 1;
851	<	simError();
852	<	}
853	<
854	<	current_extra = current_extra->getNext();
855	<	}
856	<	}
857	<
858	<	if( !theBends[j].isGhost ){
859	<
860	<	exI = theBends[j].a;
861	<	exJ = theBends[j].c;
862	<	}
863	<	else{
864	<
865	<	exI = theBends[j].a;
866	<	exJ = theBends[j].b;
867	<	}
868	<
869	<	// exclude_I must always be the smaller of the pair
870	<	if( exI > exJ ){
871	<	tempEx = exI;
872	<	exI = exJ;
873	<	exJ = tempEx;
874	<	}
875	<	#ifdef IS_MPI
876	<	tempEx = exI;
877	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
878	<	tempEx = exJ;
879	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
880	<
881	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
882	<	#else  // isn't MPI
883	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
884	<	#endif  //is_mpi
681	>	if (globals->haveThermalTime()){
682	>	info[i].thermalTime = globals->getThermalTime();
683		}
886	–	excludeOffset += info.nBends;
684
685	<	for(j=0; j<info.nTorsions; j++){
686	<
687	<	currentTorsion = comp_stamps[stampID]->getTorsion( j );
688	<	theTorsions[j].a = currentTorsion->getA() + atomOffset;
892	<	theTorsions[j].b = currentTorsion->getB() + atomOffset;
893	<	theTorsions[j].c = currentTorsion->getC() + atomOffset;
894	<	theTorsions[j].d = currentTorsion->getD() + atomOffset;
895	<
896	<	exI = theTorsions[j].a;
897	<	exJ = theTorsions[j].d;
898	<
899	<	// exclude_I must always be the smaller of the pair
900	<	if( exI > exJ ){
901	<	tempEx = exI;
902	<	exI = exJ;
903	<	exJ = tempEx;
904	<	}
905	<	#ifdef IS_MPI
906	<	tempEx = exI;
907	<	exI = the_atoms[tempEx]->getGlobalIndex() + 1;
908	<	tempEx = exJ;
909	<	exJ = the_atoms[tempEx]->getGlobalIndex() + 1;
910	<
911	<	the_excludes[j+excludeOffset]->setPair( exI, exJ );
912	<	#else  // isn't MPI
913	<	the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) );
914	<	#endif  //is_mpi
685	>	info[i].resetIntegrator = 0;
686	>	if( globals->haveResetTime() ){
687	>	info[i].resetTime = globals->getResetTime();
688	>	info[i].resetIntegrator = 1;
689		}
916	–	excludeOffset += info.nTorsions;
690
691	<
919	<	// send the arrays off to the forceField for init.
691	>	// check for the temperature set flag
692
693	<	the_ff->initializeAtoms( info.nAtoms, info.myAtoms );
694	<	the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds );
923	<	the_ff->initializeBends( info.nBends, info.myBends, theBends );
924	<	the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions );
693	>	if (globals->haveTempSet())
694	>	info[i].setTemp = globals->getTempSet();
695
696	+	// get some of the tricky things that may still be in the globals
697
698	<	the_molecules[i].initialize( info );
699	<	atomOffset += info.nAtoms;
700	<	delete[] theBonds;
701	<	delete[] theBends;
702	<	delete[] theTorsions;
932	<	}
698	>	double boxVector[3];
699	>	if (globals->haveBox()){
700	>	boxVector[0] = globals->getBox();
701	>	boxVector[1] = globals->getBox();
702	>	boxVector[2] = globals->getBox();
703
704	<	// clean up the forcefield
705	<	the_ff->calcRcut();
706	<	the_ff->cleanMe();
707	<	}
704	>	info[i].setBox(boxVector);
705	>	}
706	>	else if (globals->haveDensity()){
707	>	double vol;
708	>	vol = (double) tot_nmol / globals->getDensity();
709	>	boxVector[0] = pow(vol, (1.0 / 3.0));
710	>	boxVector[1] = boxVector[0];
711	>	boxVector[2] = boxVector[0];
712
713	<	void SimSetup::initFromBass( void ){
713	>	info[i].setBox(boxVector);
714	>	}
715	>	else{
716	>	if (!globals->haveBoxX()){
717	>	sprintf(painCave.errMsg,
718	>	"SimSetup error, no periodic BoxX size given.\n");
719	>	painCave.isFatal = 1;
720	>	simError();
721	>	}
722	>	boxVector[0] = globals->getBoxX();
723
724	<	int i, j, k;
725	<	int n_cells;
726	<	double cellx, celly, cellz;
727	<	double temp1, temp2, temp3;
728	<	int n_per_extra;
729	<	int n_extra;
730	<	int have_extra, done;
724	>	if (!globals->haveBoxY()){
725	>	sprintf(painCave.errMsg,
726	>	"SimSetup error, no periodic BoxY size given.\n");
727	>	painCave.isFatal = 1;
728	>	simError();
729	>	}
730	>	boxVector[1] = globals->getBoxY();
731
732	<	temp1 = (double)tot_nmol / 4.0;
733	<	temp2 = pow( temp1, ( 1.0 / 3.0 ) );
734	<	temp3 = ceil( temp2 );
732	>	if (!globals->haveBoxZ()){
733	>	sprintf(painCave.errMsg,
734	>	"SimSetup error, no periodic BoxZ size given.\n");
735	>	painCave.isFatal = 1;
736	>	simError();
737	>	}
738	>	boxVector[2] = globals->getBoxZ();
739
740	<	have_extra =0;
741	<	if( temp2 < temp3 ){ // we have a non-complete lattice
742	<	have_extra =1;
740	>	info[i].setBox(boxVector);
741	>	}
742	>	}
743
744	<	n_cells = (int)temp3 - 1;
745	<	cellx = simnfo->box_x / temp3;
959	<	celly = simnfo->box_y / temp3;
960	<	cellz = simnfo->box_z / temp3;
961	<	n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells );
962	<	temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) );
963	<	n_per_extra = (int)ceil( temp1 );
744	>	//setup seed for random number generator
745	>	int seedValue;
746
747	<	if( n_per_extra > 4){
748	<	sprintf( painCave.errMsg,
749	<	"SimSetup error. There has been an error in constructing"
750	<	" the non-complete lattice.\n" );
751	<	painCave.isFatal = 1;
747	>	if (globals->haveSeed()){
748	>	seedValue = globals->getSeed();
749	>
750	>	if(seedValue / 1E9 == 0){
751	>	sprintf(painCave.errMsg,
752	>	"Seed for sprng library should contain at least 9 digits\n"
753	>	"OOPSE will generate a seed for user\n");
754	>	painCave.isFatal = 0;
755		simError();
756	<	}
757	<	}
756	>
757	>	//using seed generated by system instead of invalid seed set by user
758	>	#ifndef IS_MPI
759	>	seedValue = make_sprng_seed();
760	>	#else
761	>	if (worldRank == 0){
762	>	seedValue = make_sprng_seed();
763	>	}
764	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
765	>	#endif
766	>	}
767	>	}//end of if branch of globals->haveSeed()
768		else{
769	<	n_cells = (int)temp3;
770	<	cellx = simnfo->box_x / temp3;
771	<	celly = simnfo->box_y / temp3;
772	<	cellz = simnfo->box_z / temp3;
769	>
770	>	#ifndef IS_MPI
771	>	seedValue = make_sprng_seed();
772	>	#else
773	>	if (worldRank == 0){
774	>	seedValue = make_sprng_seed();
775	>	}
776	>	MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD);
777	>	#endif
778	>	}//end of globals->haveSeed()
779	>
780	>	for (int i = 0; i < nInfo; i++){
781	>	info[i].setSeed(seedValue);
782		}
783
784	<	current_mol = 0;
785	<	current_comp_mol = 0;
786	<	current_comp = 0;
787	<	current_atom_ndx = 0;
784	>	#ifdef IS_MPI
785	>	strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n");
786	>	MPIcheckPoint();
787	>	#endif // is_mpi
788	>	}
789
985	–	for( i=0; i < n_cells ; i++ ){
986	–	for( j=0; j < n_cells; j++ ){
987	–	for( k=0; k < n_cells; k++ ){
790
791	<	makeElement( i * cellx,
792	<	j * celly,
793	<	k * cellz );
791	>	void SimSetup::finalInfoCheck(void){
792	>	int index;
793	>	int usesDipoles;
794	>	int i;
795
796	<	makeElement( i * cellx + 0.5 * cellx,
797	<	j * celly + 0.5 * celly,
995	<	k * cellz );
796	>	for (i = 0; i < nInfo; i++){
797	>	// check electrostatic parameters
798
799	<	makeElement( i * cellx,
800	<	j * celly + 0.5 * celly,
801	<	k * cellz + 0.5 * cellz );
802	<
803	<	makeElement( i * cellx + 0.5 * cellx,
1002	<	j * celly,
1003	<	k * cellz + 0.5 * cellz );
1004	<	}
799	>	index = 0;
800	>	usesDipoles = 0;
801	>	while ((index < info[i].n_atoms) && !usesDipoles){
802	>	usesDipoles = (info[i].atoms[index])->hasDipole();
803	>	index++;
804		}
1006	–	}
805
806	<	if( have_extra ){
807	<	done = 0;
806	>	#ifdef IS_MPI
807	>	int myUse = usesDipoles;
808	>	MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD);
809	>	#endif //is_mpi
810
811	<	int start_ndx;
1012	<	for( i=0; i < (n_cells+1) && !done; i++ ){
1013	<	for( j=0; j < (n_cells+1) && !done; j++ ){
811	>	double theEcr, theEst;
812
813	<	if( i < n_cells ){
813	>	if (globals->getUseRF()){
814	>	info[i].useReactionField = 1;
815
816	<	if( j < n_cells ){
817	<	start_ndx = n_cells;
818	<	}
819	<	else start_ndx = 0;
820	<	}
821	<	else start_ndx = 0;
816	>	if (!globals->haveECR()){
817	>	sprintf(painCave.errMsg,
818	>	"SimSetup Warning: using default value of 1/2 the smallest "
819	>	"box length for the electrostaticCutoffRadius.\n"
820	>	"I hope you have a very fast processor!\n");
821	>	painCave.isFatal = 0;
822	>	simError();
823	>	double smallest;
824	>	smallest = info[i].boxL[0];
825	>	if (info[i].boxL[1] <= smallest)
826	>	smallest = info[i].boxL[1];
827	>	if (info[i].boxL[2] <= smallest)
828	>	smallest = info[i].boxL[2];
829	>	theEcr = 0.5 * smallest;
830	>	}
831	>	else{
832	>	theEcr = globals->getECR();
833	>	}
834
835	<	for( k=start_ndx; k < (n_cells+1) && !done; k++ ){
835	>	if (!globals->haveEST()){
836	>	sprintf(painCave.errMsg,
837	>	"SimSetup Warning: using default value of 0.05 * the "
838	>	"electrostaticCutoffRadius for the electrostaticSkinThickness\n");
839	>	painCave.isFatal = 0;
840	>	simError();
841	>	theEst = 0.05 * theEcr;
842	>	}
843	>	else{
844	>	theEst = globals->getEST();
845	>	}
846
847	<	makeElement( i * cellx,
1027	<	j * celly,
1028	<	k * cellz );
1029	<	done = ( current_mol >= tot_nmol );
847	>	info[i].setEcr(theEcr, theEst);
848
849	<	if( !done && n_per_extra > 1 ){
850	<	makeElement( i * cellx + 0.5 * cellx,
851	<	j * celly + 0.5 * celly,
852	<	k * cellz );
853	<	done = ( current_mol >= tot_nmol );
854	<	}
849	>	if (!globals->haveDielectric()){
850	>	sprintf(painCave.errMsg,
851	>	"SimSetup Error: You are trying to use Reaction Field without"
852	>	"setting a dielectric constant!\n");
853	>	painCave.isFatal = 1;
854	>	simError();
855	>	}
856	>	info[i].dielectric = globals->getDielectric();
857	>	}
858	>	else{
859	>	if (usesDipoles){
860	>	if (!globals->haveECR()){
861	>	sprintf(painCave.errMsg,
862	>	"SimSetup Warning: using default value of 1/2 the smallest "
863	>	"box length for the electrostaticCutoffRadius.\n"
864	>	"I hope you have a very fast processor!\n");
865	>	painCave.isFatal = 0;
866	>	simError();
867	>	double smallest;
868	>	smallest = info[i].boxL[0];
869	>	if (info[i].boxL[1] <= smallest)
870	>	smallest = info[i].boxL[1];
871	>	if (info[i].boxL[2] <= smallest)
872	>	smallest = info[i].boxL[2];
873	>	theEcr = 0.5 * smallest;
874	>	}
875	>	else{
876	>	theEcr = globals->getECR();
877	>	}
878
879	<	if( !done && n_per_extra > 2){
880	<	makeElement( i * cellx,
881	<	j * celly + 0.5 * celly,
882	<	k * cellz + 0.5 * cellz );
883	<	done = ( current_mol >= tot_nmol );
884	<	}
879	>	if (!globals->haveEST()){
880	>	sprintf(painCave.errMsg,
881	>	"SimSetup Warning: using default value of 0.05 * the "
882	>	"electrostaticCutoffRadius for the "
883	>	"electrostaticSkinThickness\n");
884	>	painCave.isFatal = 0;
885	>	simError();
886	>	theEst = 0.05 * theEcr;
887	>	}
888	>	else{
889	>	theEst = globals->getEST();
890	>	}
891
892	<	if( !done && n_per_extra > 3){
1046	<	makeElement( i * cellx + 0.5 * cellx,
1047	<	j * celly,
1048	<	k * cellz + 0.5 * cellz );
1049	<	done = ( current_mol >= tot_nmol );
1050	<	}
1051	<	}
892	>	info[i].setEcr(theEcr, theEst);
893		}
894		}
895		}
896
897	<
898	<	for( i=0; i<simnfo->n_atoms; i++ ){
899	<	simnfo->atoms[i]->set_vx( 0.0 );
900	<	simnfo->atoms[i]->set_vy( 0.0 );
1060	<	simnfo->atoms[i]->set_vz( 0.0 );
1061	<	}
897	>	#ifdef IS_MPI
898	>	strcpy(checkPointMsg, "post processing checks out");
899	>	MPIcheckPoint();
900	>	#endif // is_mpi
901		}
902
903	<	void SimSetup::makeElement( double x, double y, double z ){
903	>	void SimSetup::initSystemCoords(void){
904	>	int i;
905
906	<	int k;
1067	<	AtomStamp* current_atom;
1068	<	DirectionalAtom* dAtom;
1069	<	double rotMat[3][3];
906	>	char* inName;
907
908	<	for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){
908	>	(info[0].getConfiguration())->createArrays(info[0].n_atoms);
909
910	<	current_atom = comp_stamps[current_comp]->getAtom( k );
911	<	if( !current_atom->havePosition() ){
912	<	sprintf( painCave.errMsg,
913	<	"SimSetup:initFromBass error.\n"
914	<	"\tComponent %s, atom %s does not have a position specified.\n"
915	<	"\tThe initialization routine is unable to give a start"
916	<	" position.\n",
917	<	comp_stamps[current_comp]->getID(),
918	<	current_atom->getType() );
919	<	painCave.isFatal = 1;
920	<	simError();
910	>	for (i = 0; i < info[0].n_atoms; i++)
911	>	info[0].atoms[i]->setCoords();
912	>
913	>	if (globals->haveInitialConfig()){
914	>	InitializeFromFile* fileInit;
915	>	#ifdef IS_MPI // is_mpi
916	>	if (worldRank == 0){
917	>	#endif //is_mpi
918	>	inName = globals->getInitialConfig();
919	>	fileInit = new InitializeFromFile(inName);
920	>	#ifdef IS_MPI
921		}
922	+	else
923	+	fileInit = new InitializeFromFile(NULL);
924	+	#endif
925	+	fileInit->readInit(info); // default velocities on
926
927	<	the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() );
928	<	the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() );
929	<	the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() );
927	>	delete fileInit;
928	>	}
929	>	else{
930	>	#ifdef IS_MPI
931
932	<	if( the_atoms[current_atom_ndx]->isDirectional() ){
932	>	// no init from bass
933
934	<	dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx];
934	>	sprintf(painCave.errMsg,
935	>	"Cannot intialize a parallel simulation without an initial configuration file.\n");
936	>	painCave.isFatal = 1;;
937	>	simError();
938
939	<	rotMat[0][0] = 1.0;
1095	<	rotMat[0][1] = 0.0;
1096	<	rotMat[0][2] = 0.0;
939	>	#else
940
941	<	rotMat[1][0] = 0.0;
1099	<	rotMat[1][1] = 1.0;
1100	<	rotMat[1][2] = 0.0;
941	>	initFromBass();
942
1102	–	rotMat[2][0] = 0.0;
1103	–	rotMat[2][1] = 0.0;
1104	–	rotMat[2][2] = 1.0;
943
944	<	dAtom->setA( rotMat );
1107	<	}
1108	<
1109	<	current_atom_ndx++;
944	>	#endif
945		}
946
947	<	current_mol++;
948	<	current_comp_mol++;
947	>	#ifdef IS_MPI
948	>	strcpy(checkPointMsg, "Successfully read in the initial configuration");
949	>	MPIcheckPoint();
950	>	#endif // is_mpi
951	>	}
952
1115	–	if( current_comp_mol >= components_nmol[current_comp] ){
953
954	<	current_comp_mol = 0;
955	<	current_comp++;
954	>	void SimSetup::makeOutNames(void){
955	>	int k;
956	>
957	>
958	>	for (k = 0; k < nInfo; k++){
959	>	#ifdef IS_MPI
960	>	if (worldRank == 0){
961	>	#endif // is_mpi
962	>
963	>	if (globals->haveFinalConfig()){
964	>	strcpy(info[k].finalName, globals->getFinalConfig());
965	>	}
966	>	else{
967	>	strcpy(info[k].finalName, inFileName);
968	>	char* endTest;
969	>	int nameLength = strlen(info[k].finalName);
970	>	endTest = &(info[k].finalName[nameLength - 5]);
971	>	if (!strcmp(endTest, ".bass")){
972	>	strcpy(endTest, ".eor");
973	>	}
974	>	else if (!strcmp(endTest, ".BASS")){
975	>	strcpy(endTest, ".eor");
976	>	}
977	>	else{
978	>	endTest = &(info[k].finalName[nameLength - 4]);
979	>	if (!strcmp(endTest, ".bss")){
980	>	strcpy(endTest, ".eor");
981	>	}
982	>	else if (!strcmp(endTest, ".mdl")){
983	>	strcpy(endTest, ".eor");
984	>	}
985	>	else{
986	>	strcat(info[k].finalName, ".eor");
987	>	}
988	>	}
989	>	}
990	>
991	>	// make the sample and status out names
992	>
993	>	strcpy(info[k].sampleName, inFileName);
994	>	char* endTest;
995	>	int nameLength = strlen(info[k].sampleName);
996	>	endTest = &(info[k].sampleName[nameLength - 5]);
997	>	if (!strcmp(endTest, ".bass")){
998	>	strcpy(endTest, ".dump");
999	>	}
1000	>	else if (!strcmp(endTest, ".BASS")){
1001	>	strcpy(endTest, ".dump");
1002	>	}
1003	>	else{
1004	>	endTest = &(info[k].sampleName[nameLength - 4]);
1005	>	if (!strcmp(endTest, ".bss")){
1006	>	strcpy(endTest, ".dump");
1007	>	}
1008	>	else if (!strcmp(endTest, ".mdl")){
1009	>	strcpy(endTest, ".dump");
1010	>	}
1011	>	else{
1012	>	strcat(info[k].sampleName, ".dump");
1013	>	}
1014	>	}
1015	>
1016	>	strcpy(info[k].statusName, inFileName);
1017	>	nameLength = strlen(info[k].statusName);
1018	>	endTest = &(info[k].statusName[nameLength - 5]);
1019	>	if (!strcmp(endTest, ".bass")){
1020	>	strcpy(endTest, ".stat");
1021	>	}
1022	>	else if (!strcmp(endTest, ".BASS")){
1023	>	strcpy(endTest, ".stat");
1024	>	}
1025	>	else{
1026	>	endTest = &(info[k].statusName[nameLength - 4]);
1027	>	if (!strcmp(endTest, ".bss")){
1028	>	strcpy(endTest, ".stat");
1029	>	}
1030	>	else if (!strcmp(endTest, ".mdl")){
1031	>	strcpy(endTest, ".stat");
1032	>	}
1033	>	else{
1034	>	strcat(info[k].statusName, ".stat");
1035	>	}
1036	>	}
1037	>
1038	>	#ifdef IS_MPI
1039	>
1040	>	}
1041	>	#endif // is_mpi
1042	>	}
1043	>	}
1044	>
1045	>
1046	>	void SimSetup::sysObjectsCreation(void){
1047	>	int i, k;
1048	>
1049	>	// create the forceField
1050	>
1051	>	createFF();
1052	>
1053	>	// extract componentList
1054	>
1055	>	compList();
1056	>
1057	>	// calc the number of atoms, bond, bends, and torsions
1058	>
1059	>	calcSysValues();
1060	>
1061	>	#ifdef IS_MPI
1062	>	// divide the molecules among the processors
1063	>
1064	>	mpiMolDivide();
1065	>	#endif //is_mpi
1066	>
1067	>	// create the atom and SRI arrays. Also initialize Molecule Stamp ID's
1068	>
1069	>	makeSysArrays();
1070	>
1071	>	// make and initialize the molecules (all but atomic coordinates)
1072	>
1073	>	makeMolecules();
1074	>
1075	>	for (k = 0; k < nInfo; k++){
1076	>	info[k].identArray = new int[info[k].n_atoms];
1077	>	for (i = 0; i < info[k].n_atoms; i++){
1078	>	info[k].identArray[i] = info[k].atoms[i]->getIdent();
1079	>	}
1080	>	}
1081	>	}
1082	>
1083	>
1084	>	void SimSetup::createFF(void){
1085	>	switch (ffCase){
1086	>	case FF_DUFF:
1087	>	the_ff = new DUFF();
1088	>	break;
1089	>
1090	>	case FF_LJ:
1091	>	the_ff = new LJFF();
1092	>	break;
1093	>
1094	>	case FF_EAM:
1095	>	the_ff = new EAM_FF();
1096	>	break;
1097	>
1098	>	default:
1099	>	sprintf(painCave.errMsg,
1100	>	"SimSetup Error. Unrecognized force field in case statement.\n");
1101	>	painCave.isFatal = 1;
1102	>	simError();
1103	>	}
1104	>
1105	>	#ifdef IS_MPI
1106	>	strcpy(checkPointMsg, "ForceField creation successful");
1107	>	MPIcheckPoint();
1108	>	#endif // is_mpi
1109	>	}
1110	>
1111	>
1112	>	void SimSetup::compList(void){
1113	>	int i;
1114	>	char* id;
1115	>	LinkedMolStamp* headStamp = new LinkedMolStamp();
1116	>	LinkedMolStamp* currentStamp = NULL;
1117	>	comp_stamps = new MoleculeStamp * [n_components];
1118	>
1119	>	// make an array of molecule stamps that match the components used.
1120	>	// also extract the used stamps out into a separate linked list
1121	>
1122	>	for (i = 0; i < nInfo; i++){
1123	>	info[i].nComponents = n_components;
1124	>	info[i].componentsNmol = components_nmol;
1125	>	info[i].compStamps = comp_stamps;
1126	>	info[i].headStamp = headStamp;
1127	>	}
1128	>
1129	>
1130	>	for (i = 0; i < n_components; i++){
1131	>	id = the_components[i]->getType();
1132	>	comp_stamps[i] = NULL;
1133	>
1134	>	// check to make sure the component isn't already in the list
1135	>
1136	>	comp_stamps[i] = headStamp->match(id);
1137	>	if (comp_stamps[i] == NULL){
1138	>	// extract the component from the list;
1139	>
1140	>	currentStamp = stamps->extractMolStamp(id);
1141	>	if (currentStamp == NULL){
1142	>	sprintf(painCave.errMsg,
1143	>	"SimSetup error: Component \"%s\" was not found in the "
1144	>	"list of declared molecules\n",
1145	>	id);
1146	>	painCave.isFatal = 1;
1147	>	simError();
1148	>	}
1149	>
1150	>	headStamp->add(currentStamp);
1151	>	comp_stamps[i] = headStamp->match(id);
1152	>	}
1153	>	}
1154	>
1155	>	#ifdef IS_MPI
1156	>	strcpy(checkPointMsg, "Component stamps successfully extracted\n");
1157	>	MPIcheckPoint();
1158	>	#endif // is_mpi
1159	>	}
1160	>
1161	>	void SimSetup::calcSysValues(void){
1162	>	int i;
1163	>
1164	>	int* molMembershipArray;
1165	>
1166	>	tot_atoms = 0;
1167	>	tot_bonds = 0;
1168	>	tot_bends = 0;
1169	>	tot_torsions = 0;
1170	>	for (i = 0; i < n_components; i++){
1171	>	tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms();
1172	>	tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds();
1173	>	tot_bends += components_nmol[i] * comp_stamps[i]->getNBends();
1174	>	tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions();
1175	>	}
1176	>
1177	>	tot_SRI = tot_bonds + tot_bends + tot_torsions;
1178	>	molMembershipArray = new int[tot_atoms];
1179	>
1180	>	for (i = 0; i < nInfo; i++){
1181	>	info[i].n_atoms = tot_atoms;
1182	>	info[i].n_bonds = tot_bonds;
1183	>	info[i].n_bends = tot_bends;
1184	>	info[i].n_torsions = tot_torsions;
1185	>	info[i].n_SRI = tot_SRI;
1186	>	info[i].n_mol = tot_nmol;
1187	>
1188	>	info[i].molMembershipArray = molMembershipArray;
1189	>	}
1190	>	}
1191	>
1192	>	#ifdef IS_MPI
1193	>
1194	>	void SimSetup::mpiMolDivide(void){
1195	>	int i, j, k;
1196	>	int localMol, allMol;
1197	>	int local_atoms, local_bonds, local_bends, local_torsions, local_SRI;
1198	>
1199	>	mpiSim = new mpiSimulation(info);
1200	>
1201	>	globalIndex = mpiSim->divideLabor();
1202	>
1203	>	// set up the local variables
1204	>
1205	>	mol2proc = mpiSim->getMolToProcMap();
1206	>	molCompType = mpiSim->getMolComponentType();
1207	>
1208	>	allMol = 0;
1209	>	localMol = 0;
1210	>	local_atoms = 0;
1211	>	local_bonds = 0;
1212	>	local_bends = 0;
1213	>	local_torsions = 0;
1214	>	globalAtomIndex = 0;
1215	>
1216	>
1217	>	for (i = 0; i < n_components; i++){
1218	>	for (j = 0; j < components_nmol[i]; j++){
1219	>	if (mol2proc[allMol] == worldRank){
1220	>	local_atoms += comp_stamps[i]->getNAtoms();
1221	>	local_bonds += comp_stamps[i]->getNBonds();
1222	>	local_bends += comp_stamps[i]->getNBends();
1223	>	local_torsions += comp_stamps[i]->getNTorsions();
1224	>	localMol++;
1225	>	}
1226	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1227	>	info[0].molMembershipArray[globalAtomIndex] = allMol;
1228	>	globalAtomIndex++;
1229	>	}
1230	>
1231	>	allMol++;
1232	>	}
1233	>	}
1234	>	local_SRI = local_bonds + local_bends + local_torsions;
1235	>
1236	>	info[0].n_atoms = mpiSim->getMyNlocal();
1237	>
1238	>	if (local_atoms != info[0].n_atoms){
1239	>	sprintf(painCave.errMsg,
1240	>	"SimSetup error: mpiSim's localAtom (%d) and SimSetup's"
1241	>	" localAtom (%d) are not equal.\n",
1242	>	info[0].n_atoms, local_atoms);
1243	>	painCave.isFatal = 1;
1244	>	simError();
1245	>	}
1246	>
1247	>	info[0].n_bonds = local_bonds;
1248	>	info[0].n_bends = local_bends;
1249	>	info[0].n_torsions = local_torsions;
1250	>	info[0].n_SRI = local_SRI;
1251	>	info[0].n_mol = localMol;
1252	>
1253	>	strcpy(checkPointMsg, "Passed nlocal consistency check.");
1254	>	MPIcheckPoint();
1255	>	}
1256	>
1257	>	#endif // is_mpi
1258	>
1259	>
1260	>	void SimSetup::makeSysArrays(void){
1261	>
1262	>	#ifndef IS_MPI
1263	>	int k, j;
1264	>	#endif // is_mpi
1265	>	int i, l;
1266	>
1267	>	Atom** the_atoms;
1268	>	Molecule* the_molecules;
1269	>	Exclude** the_excludes;
1270	>
1271	>
1272	>	for (l = 0; l < nInfo; l++){
1273	>	// create the atom and short range interaction arrays
1274	>
1275	>	the_atoms = new Atom * [info[l].n_atoms];
1276	>	the_molecules = new Molecule[info[l].n_mol];
1277	>	int molIndex;
1278	>
1279	>	// initialize the molecule's stampID's
1280	>
1281	>	#ifdef IS_MPI
1282	>
1283	>
1284	>	molIndex = 0;
1285	>	for (i = 0; i < mpiSim->getTotNmol(); i++){
1286	>	if (mol2proc[i] == worldRank){
1287	>	the_molecules[molIndex].setStampID(molCompType[i]);
1288	>	the_molecules[molIndex].setMyIndex(molIndex);
1289	>	the_molecules[molIndex].setGlobalIndex(i);
1290	>	molIndex++;
1291	>	}
1292	>	}
1293	>
1294	>	#else // is_mpi
1295	>
1296	>	molIndex = 0;
1297	>	globalAtomIndex = 0;
1298	>	for (i = 0; i < n_components; i++){
1299	>	for (j = 0; j < components_nmol[i]; j++){
1300	>	the_molecules[molIndex].setStampID(i);
1301	>	the_molecules[molIndex].setMyIndex(molIndex);
1302	>	the_molecules[molIndex].setGlobalIndex(molIndex);
1303	>	for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){
1304	>	info[l].molMembershipArray[globalAtomIndex] = molIndex;
1305	>	globalAtomIndex++;
1306	>	}
1307	>	molIndex++;
1308	>	}
1309	>	}
1310	>
1311	>
1312	>	#endif // is_mpi
1313	>
1314	>
1315	>	if (info[l].n_SRI){
1316	>	Exclude::createArray(info[l].n_SRI);
1317	>	the_excludes = new Exclude * [info[l].n_SRI];
1318	>	for (int ex = 0; ex < info[l].n_SRI; ex++){
1319	>	the_excludes[ex] = new Exclude(ex);
1320	>	}
1321	>	info[l].globalExcludes = new int;
1322	>	info[l].n_exclude = info[l].n_SRI;
1323	>	}
1324	>	else{
1325	>	Exclude::createArray(1);
1326	>	the_excludes = new Exclude * ;
1327	>	the_excludes[0] = new Exclude(0);
1328	>	the_excludes[0]->setPair(0, 0);
1329	>	info[l].globalExcludes = new int;
1330	>	info[l].globalExcludes[0] = 0;
1331	>	info[l].n_exclude = 0;
1332	>	}
1333	>
1334	>	// set the arrays into the SimInfo object
1335	>
1336	>	info[l].atoms = the_atoms;
1337	>	info[l].molecules = the_molecules;
1338	>	info[l].nGlobalExcludes = 0;
1339	>	info[l].excludes = the_excludes;
1340	>
1341	>	the_ff->setSimInfo(info);
1342		}
1343		}
1344	+
1345	+	void SimSetup::makeIntegrator(void){
1346	+	int k;
1347	+
1348	+	NVE<RealIntegrator>* myNVE = NULL;
1349	+	NVT<RealIntegrator>* myNVT = NULL;
1350	+	NPTi<NPT<RealIntegrator> >* myNPTi = NULL;
1351	+	NPTf<NPT<RealIntegrator> >* myNPTf = NULL;
1352	+
1353	+	for (k = 0; k < nInfo; k++){
1354	+	switch (ensembleCase){
1355	+	case NVE_ENS:
1356	+	if (globals->haveZconstraints()){
1357	+	setupZConstraint(info[k]);
1358	+	myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff);
1359	+	}
1360	+	else{
1361	+	myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff);
1362	+	}
1363	+
1364	+	info->the_integrator = myNVE;
1365	+	break;
1366	+
1367	+	case NVT_ENS:
1368	+	if (globals->haveZconstraints()){
1369	+	setupZConstraint(info[k]);
1370	+	myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff);
1371	+	}
1372	+	else
1373	+	myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff);
1374	+
1375	+	myNVT->setTargetTemp(globals->getTargetTemp());
1376	+
1377	+	if (globals->haveTauThermostat())
1378	+	myNVT->setTauThermostat(globals->getTauThermostat());
1379	+	else{
1380	+	sprintf(painCave.errMsg,
1381	+	"SimSetup error: If you use the NVT\n"
1382	+	"    ensemble, you must set tauThermostat.\n");
1383	+	painCave.isFatal = 1;
1384	+	simError();
1385	+	}
1386	+
1387	+	info->the_integrator = myNVT;
1388	+	break;
1389	+
1390	+	case NPTi_ENS:
1391	+	if (globals->haveZconstraints()){
1392	+	setupZConstraint(info[k]);
1393	+	myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1394	+	}
1395	+	else
1396	+	myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff);
1397	+
1398	+	myNPTi->setTargetTemp(globals->getTargetTemp());
1399	+
1400	+	if (globals->haveTargetPressure())
1401	+	myNPTi->setTargetPressure(globals->getTargetPressure());
1402	+	else{
1403	+	sprintf(painCave.errMsg,
1404	+	"SimSetup error: If you use a constant pressure\n"
1405	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1406	+	painCave.isFatal = 1;
1407	+	simError();
1408	+	}
1409	+
1410	+	if (globals->haveTauThermostat())
1411	+	myNPTi->setTauThermostat(globals->getTauThermostat());
1412	+	else{
1413	+	sprintf(painCave.errMsg,
1414	+	"SimSetup error: If you use an NPT\n"
1415	+	"    ensemble, you must set tauThermostat.\n");
1416	+	painCave.isFatal = 1;
1417	+	simError();
1418	+	}
1419	+
1420	+	if (globals->haveTauBarostat())
1421	+	myNPTi->setTauBarostat(globals->getTauBarostat());
1422	+	else{
1423	+	sprintf(painCave.errMsg,
1424	+	"SimSetup error: If you use an NPT\n"
1425	+	"    ensemble, you must set tauBarostat.\n");
1426	+	painCave.isFatal = 1;
1427	+	simError();
1428	+	}
1429	+
1430	+	info->the_integrator = myNPTi;
1431	+	break;
1432	+
1433	+	case NPTf_ENS:
1434	+	if (globals->haveZconstraints()){
1435	+	setupZConstraint(info[k]);
1436	+	myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff);
1437	+	}
1438	+	else
1439	+	myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff);
1440	+
1441	+	myNPTf->setTargetTemp(globals->getTargetTemp());
1442	+
1443	+	if (globals->haveTargetPressure())
1444	+	myNPTf->setTargetPressure(globals->getTargetPressure());
1445	+	else{
1446	+	sprintf(painCave.errMsg,
1447	+	"SimSetup error: If you use a constant pressure\n"
1448	+	"    ensemble, you must set targetPressure in the BASS file.\n");
1449	+	painCave.isFatal = 1;
1450	+	simError();
1451	+	}
1452	+
1453	+	if (globals->haveTauThermostat())
1454	+	myNPTf->setTauThermostat(globals->getTauThermostat());
1455	+	else{
1456	+	sprintf(painCave.errMsg,
1457	+	"SimSetup error: If you use an NPT\n"
1458	+	"    ensemble, you must set tauThermostat.\n");
1459	+	painCave.isFatal = 1;
1460	+	simError();
1461	+	}
1462	+
1463	+	if (globals->haveTauBarostat())
1464	+	myNPTf->setTauBarostat(globals->getTauBarostat());
1465	+	else{
1466	+	sprintf(painCave.errMsg,
1467	+	"SimSetup error: If you use an NPT\n"
1468	+	"    ensemble, you must set tauBarostat.\n");
1469	+	painCave.isFatal = 1;
1470	+	simError();
1471	+	}
1472	+
1473	+	info->the_integrator = myNPTf;
1474	+	break;
1475	+
1476	+	default:
1477	+	sprintf(painCave.errMsg,
1478	+	"SimSetup Error. Unrecognized ensemble in case statement.\n");
1479	+	painCave.isFatal = 1;
1480	+	simError();
1481	+	}
1482	+	}
1483	+	}
1484	+
1485	+	void SimSetup::initFortran(void){
1486	+	info[0].refreshSim();
1487	+
1488	+	if (!strcmp(info[0].mixingRule, "standard")){
1489	+	the_ff->initForceField(LB_MIXING_RULE);
1490	+	}
1491	+	else if (!strcmp(info[0].mixingRule, "explicit")){
1492	+	the_ff->initForceField(EXPLICIT_MIXING_RULE);
1493	+	}
1494	+	else{
1495	+	sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n",
1496	+	info[0].mixingRule);
1497	+	painCave.isFatal = 1;
1498	+	simError();
1499	+	}
1500	+
1501	+
1502	+	#ifdef IS_MPI
1503	+	strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran.");
1504	+	MPIcheckPoint();
1505	+	#endif // is_mpi
1506	+	}
1507	+
1508	+	void SimSetup::setupZConstraint(SimInfo& theInfo){
1509	+	int nZConstraints;
1510	+	ZconStamp** zconStamp;
1511	+
1512	+	if (globals->haveZconstraintTime()){
1513	+	//add sample time of z-constraint  into SimInfo's property list
1514	+	DoubleData* zconsTimeProp = new DoubleData();
1515	+	zconsTimeProp->setID(ZCONSTIME_ID);
1516	+	zconsTimeProp->setData(globals->getZconsTime());
1517	+	theInfo.addProperty(zconsTimeProp);
1518	+	}
1519	+	else{
1520	+	sprintf(painCave.errMsg,
1521	+	"ZConstraint error: If you use an ZConstraint\n"
1522	+	" , you must set sample time.\n");
1523	+	painCave.isFatal = 1;
1524	+	simError();
1525	+	}
1526	+
1527	+	//push zconsTol into siminfo, if user does not specify
1528	+	//value for zconsTol, a default value will be used
1529	+	DoubleData* zconsTol = new DoubleData();
1530	+	zconsTol->setID(ZCONSTOL_ID);
1531	+	if (globals->haveZconsTol()){
1532	+	zconsTol->setData(globals->getZconsTol());
1533	+	}
1534	+	else{
1535	+	double defaultZConsTol = 0.01;
1536	+	sprintf(painCave.errMsg,
1537	+	"ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n"
1538	+	" , default value %f is used.\n",
1539	+	defaultZConsTol);
1540	+	painCave.isFatal = 0;
1541	+	simError();
1542	+
1543	+	zconsTol->setData(defaultZConsTol);
1544	+	}
1545	+	theInfo.addProperty(zconsTol);
1546	+
1547	+	//set Force Subtraction Policy
1548	+	StringData* zconsForcePolicy = new StringData();
1549	+	zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID);
1550	+
1551	+	if (globals->haveZconsForcePolicy()){
1552	+	zconsForcePolicy->setData(globals->getZconsForcePolicy());
1553	+	}
1554	+	else{
1555	+	sprintf(painCave.errMsg,
1556	+	"ZConstraint Warning: User does not set force Subtraction policy, "
1557	+	"PolicyByMass is used\n");
1558	+	painCave.isFatal = 0;
1559	+	simError();
1560	+	zconsForcePolicy->setData("BYMASS");
1561	+	}
1562	+
1563	+	theInfo.addProperty(zconsForcePolicy);
1564	+
1565	+	//Determine the name of ouput file and add it into SimInfo's property list
1566	+	//Be careful, do not use inFileName, since it is a pointer which
1567	+	//point to a string at master node, and slave nodes do not contain that string
1568	+
1569	+	string zconsOutput(theInfo.finalName);
1570	+
1571	+	zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz";
1572	+
1573	+	StringData* zconsFilename = new StringData();
1574	+	zconsFilename->setID(ZCONSFILENAME_ID);
1575	+	zconsFilename->setData(zconsOutput);
1576	+
1577	+	theInfo.addProperty(zconsFilename);
1578	+
1579	+	//setup index, pos and other parameters of z-constraint molecules
1580	+	nZConstraints = globals->getNzConstraints();
1581	+	theInfo.nZconstraints = nZConstraints;
1582	+
1583	+	zconStamp = globals->getZconStamp();
1584	+	ZConsParaItem tempParaItem;
1585	+
1586	+	ZConsParaData* zconsParaData = new ZConsParaData();
1587	+	zconsParaData->setID(ZCONSPARADATA_ID);
1588	+
1589	+	for (int i = 0; i < nZConstraints; i++){
1590	+	tempParaItem.havingZPos = zconStamp[i]->haveZpos();
1591	+	tempParaItem.zPos = zconStamp[i]->getZpos();
1592	+	tempParaItem.zconsIndex = zconStamp[i]->getMolIndex();
1593	+	tempParaItem.kRatio = zconStamp[i]->getKratio();
1594	+
1595	+	zconsParaData->addItem(tempParaItem);
1596	+	}
1597	+
1598	+	//check the uniqueness of index
1599	+	if(!zconsParaData->isIndexUnique()){
1600	+	sprintf(painCave.errMsg,
1601	+	"ZConstraint Error: molIndex is not unique\n");
1602	+	painCave.isFatal = 1;
1603	+	simError();
1604	+	}
1605	+
1606	+	//sort the parameters by index of molecules
1607	+	zconsParaData->sortByIndex();
1608	+
1609	+	//push data into siminfo, therefore, we can retrieve later
1610	+	theInfo.addProperty(zconsParaData);
1611	+	}

Diff Legend

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