# | Line 1 | Line 1 | |
---|---|---|
1 | + | #include <algorithm> |
2 | #include <cstdlib> | |
3 | #include <iostream> | |
4 | #include <cmath> | |
5 | + | #include <string> |
6 | ||
7 | #include "SimSetup.hpp" | |
8 | #include "parse_me.h" | |
# | Line 12 | Line 14 | |
14 | #include "mpiSimulation.hpp" | |
15 | #endif | |
16 | ||
17 | + | // some defines for ensemble and Forcefield cases |
18 | + | |
19 | + | #define NVE_ENS 0 |
20 | + | #define NVT_ENS 1 |
21 | + | #define NPTi_ENS 2 |
22 | + | #define NPTf_ENS 3 |
23 | + | #define NPTim_ENS 4 |
24 | + | #define NPTfm_ENS 5 |
25 | + | #define NVEZCONS_ENS 6 |
26 | + | |
27 | + | |
28 | + | #define FF_DUFF 0 |
29 | + | #define FF_LJ 1 |
30 | + | #define FF_EAM 2 |
31 | + | |
32 | + | using namespace std; |
33 | + | |
34 | SimSetup::SimSetup(){ | |
35 | + | |
36 | + | isInfoArray = 0; |
37 | + | nInfo = 1; |
38 | + | |
39 | stamps = new MakeStamps(); | |
40 | globals = new Globals(); | |
41 | ||
42 | + | |
43 | #ifdef IS_MPI | |
44 | strcpy( checkPointMsg, "SimSetup creation successful" ); | |
45 | MPIcheckPoint(); | |
# | Line 27 | Line 51 | SimSetup::~SimSetup(){ | |
51 | delete globals; | |
52 | } | |
53 | ||
54 | + | void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
55 | + | info = the_info; |
56 | + | nInfo = theNinfo; |
57 | + | isInfoArray = 1; |
58 | + | } |
59 | + | |
60 | + | |
61 | void SimSetup::parseFile( char* fileName ){ | |
62 | ||
63 | #ifdef IS_MPI | |
# | Line 64 | Line 95 | void SimSetup::createSim( void ){ | |
95 | ||
96 | void SimSetup::createSim( void ){ | |
97 | ||
98 | < | MakeStamps *the_stamps; |
99 | < | Globals* the_globals; |
100 | < | int i, j; |
98 | > | int i, j, k, globalAtomIndex; |
99 | > | |
100 | > | // gather all of the information from the Bass file |
101 | > | |
102 | > | gatherInfo(); |
103 | ||
104 | < | // get the stamps and globals; |
72 | < | the_stamps = stamps; |
73 | < | the_globals = globals; |
104 | > | // creation of complex system objects |
105 | ||
106 | < | // 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(); |
106 | > | sysObjectsCreation(); |
107 | ||
108 | < | // get the ones we know are there, yet still may need some work. |
109 | < | n_components = the_globals->getNComponents(); |
110 | < | strcpy( force_field, the_globals->getForceField() ); |
83 | < | strcpy( ensemble, the_globals->getEnsemble() ); |
84 | < | strcpy( simnfo->ensemble, ensemble ); |
108 | > | // check on the post processing info |
109 | > | |
110 | > | finalInfoCheck(); |
111 | ||
112 | < | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
87 | < | simnfo->usePBC = the_globals->getPBC(); |
88 | < | |
112 | > | // initialize the system coordinates |
113 | ||
114 | + | initSystemCoords(); |
115 | + | |
116 | ||
117 | < | 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 | < | } |
117 | > | // make the output filenames |
118 | ||
119 | + | makeOutNames(); |
120 | + | |
121 | + | // make the integrator |
122 | + | |
123 | + | makeIntegrator(); |
124 | + | |
125 | #ifdef IS_MPI | |
126 | < | strcpy( checkPointMsg, "ForceField creation successful" ); |
127 | < | MPIcheckPoint(); |
106 | < | #endif // is_mpi |
126 | > | mpiSim->mpiRefresh(); |
127 | > | #endif |
128 | ||
129 | < | |
129 | > | // initialize the Fortran |
130 | ||
131 | < | // 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]; |
131 | > | initFortran(); |
132 | ||
115 | – | if( !the_globals->haveNMol() ){ |
116 | – | // we don't have the total number of molecules, so we assume it is |
117 | – | // given in each component |
133 | ||
119 | – | tot_nmol = 0; |
120 | – | for( i=0; i<n_components; i++ ){ |
134 | ||
135 | < | 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 | < | } |
135 | > | } |
136 | ||
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 | – | } |
137 | ||
138 | < | #ifdef IS_MPI |
161 | < | strcpy( checkPointMsg, "Have the number of components" ); |
162 | < | MPIcheckPoint(); |
163 | < | #endif // is_mpi |
138 | > | void SimSetup::makeMolecules( void ){ |
139 | ||
140 | < | // make an array of molecule stamps that match the components used. |
141 | < | // also extract the used stamps out into a separate linked list |
140 | > | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
141 | > | molInit molInfo; |
142 | > | DirectionalAtom* dAtom; |
143 | > | LinkedAssign* extras; |
144 | > | LinkedAssign* current_extra; |
145 | > | AtomStamp* currentAtom; |
146 | > | BondStamp* currentBond; |
147 | > | BendStamp* currentBend; |
148 | > | TorsionStamp* currentTorsion; |
149 | ||
150 | < | simnfo->nComponents = n_components; |
151 | < | simnfo->componentsNmol = components_nmol; |
152 | < | simnfo->compStamps = comp_stamps; |
153 | < | simnfo->headStamp = new LinkedMolStamp(); |
150 | > | bond_pair* theBonds; |
151 | > | bend_set* theBends; |
152 | > | torsion_set* theTorsions; |
153 | > | |
154 | ||
155 | < | char* id; |
174 | < | LinkedMolStamp* headStamp = simnfo->headStamp; |
175 | < | LinkedMolStamp* currentStamp = NULL; |
176 | < | for( i=0; i<n_components; i++ ){ |
155 | > | //init the forceField paramters |
156 | ||
157 | < | id = the_components[i]->getType(); |
158 | < | comp_stamps[i] = NULL; |
157 | > | the_ff->readParams(); |
158 | > | |
159 | > | |
160 | > | // init the atoms |
161 | > | |
162 | > | double ux, uy, uz, u, uSqr; |
163 | > | |
164 | > | atomOffset = 0; |
165 | > | excludeOffset = 0; |
166 | > | for(i=0; i<info->n_mol; i++){ |
167 | ||
168 | < | // check to make sure the component isn't already in the list |
168 | > | stampID = the_molecules[i].getStampID(); |
169 | ||
170 | < | comp_stamps[i] = headStamp->match( id ); |
171 | < | if( comp_stamps[i] == NULL ){ |
170 | > | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
171 | > | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
172 | > | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
173 | > | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
174 | > | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
175 | > | |
176 | > | molInfo.myAtoms = &the_atoms[atomOffset]; |
177 | > | molInfo.myExcludes = &the_excludes[excludeOffset]; |
178 | > | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
179 | > | molInfo.myBends = new Bend*[molInfo.nBends]; |
180 | > | molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
181 | > | |
182 | > | theBonds = new bond_pair[molInfo.nBonds]; |
183 | > | theBends = new bend_set[molInfo.nBends]; |
184 | > | theTorsions = new torsion_set[molInfo.nTorsions]; |
185 | > | |
186 | > | // make the Atoms |
187 | > | |
188 | > | for(j=0; j<molInfo.nAtoms; j++){ |
189 | ||
190 | < | // extract the component from the list; |
191 | < | |
192 | < | currentStamp = the_stamps->extractMolStamp( id ); |
193 | < | if( currentStamp == NULL ){ |
194 | < | sprintf( painCave.errMsg, |
195 | < | "SimSetup error: Component \"%s\" was not found in the " |
196 | < | "list of declared molecules\n", |
197 | < | id ); |
198 | < | painCave.isFatal = 1; |
199 | < | simError(); |
190 | > | currentAtom = comp_stamps[stampID]->getAtom( j ); |
191 | > | if( currentAtom->haveOrientation() ){ |
192 | > | |
193 | > | dAtom = new DirectionalAtom(j + atomOffset); |
194 | > | info->n_oriented++; |
195 | > | molInfo.myAtoms[j] = dAtom; |
196 | > | |
197 | > | ux = currentAtom->getOrntX(); |
198 | > | uy = currentAtom->getOrntY(); |
199 | > | uz = currentAtom->getOrntZ(); |
200 | > | |
201 | > | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
202 | > | |
203 | > | u = sqrt( uSqr ); |
204 | > | ux = ux / u; |
205 | > | uy = uy / u; |
206 | > | uz = uz / u; |
207 | > | |
208 | > | dAtom->setSUx( ux ); |
209 | > | dAtom->setSUy( uy ); |
210 | > | dAtom->setSUz( uz ); |
211 | } | |
212 | < | |
213 | < | headStamp->add( currentStamp ); |
214 | < | comp_stamps[i] = headStamp->match( id ); |
215 | < | } |
216 | < | } |
202 | < | |
212 | > | else{ |
213 | > | molInfo.myAtoms[j] = new GeneralAtom(j + atomOffset); |
214 | > | } |
215 | > | molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
216 | > | |
217 | #ifdef IS_MPI | |
218 | < | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
219 | < | MPIcheckPoint(); |
218 | > | |
219 | > | molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
220 | > | |
221 | #endif // is_mpi | |
222 | < | |
222 | > | } |
223 | > | |
224 | > | // make the bonds |
225 | > | for(j=0; j<molInfo.nBonds; j++){ |
226 | > | |
227 | > | currentBond = comp_stamps[stampID]->getBond( j ); |
228 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
229 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
230 | ||
231 | + | exI = theBonds[j].a; |
232 | + | exJ = theBonds[j].b; |
233 | ||
234 | + | // exclude_I must always be the smaller of the pair |
235 | + | if( exI > exJ ){ |
236 | + | tempEx = exI; |
237 | + | exI = exJ; |
238 | + | exJ = tempEx; |
239 | + | } |
240 | + | #ifdef IS_MPI |
241 | + | tempEx = exI; |
242 | + | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
243 | + | tempEx = exJ; |
244 | + | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
245 | + | |
246 | + | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
247 | + | #else // isn't MPI |
248 | ||
249 | < | // caclulate the number of atoms, bonds, bends and torsions |
249 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
250 | > | #endif //is_mpi |
251 | > | } |
252 | > | excludeOffset += molInfo.nBonds; |
253 | ||
254 | < | tot_atoms = 0; |
255 | < | tot_bonds = 0; |
256 | < | tot_bends = 0; |
257 | < | tot_torsions = 0; |
258 | < | for( i=0; i<n_components; i++ ){ |
259 | < | |
260 | < | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
261 | < | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
262 | < | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
263 | < | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
264 | < | } |
254 | > | //make the bends |
255 | > | for(j=0; j<molInfo.nBends; j++){ |
256 | > | |
257 | > | currentBend = comp_stamps[stampID]->getBend( j ); |
258 | > | theBends[j].a = currentBend->getA() + atomOffset; |
259 | > | theBends[j].b = currentBend->getB() + atomOffset; |
260 | > | theBends[j].c = currentBend->getC() + atomOffset; |
261 | > | |
262 | > | if( currentBend->haveExtras() ){ |
263 | > | |
264 | > | extras = currentBend->getExtras(); |
265 | > | current_extra = extras; |
266 | > | |
267 | > | while( current_extra != NULL ){ |
268 | > | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
269 | > | |
270 | > | switch( current_extra->getType() ){ |
271 | > | |
272 | > | case 0: |
273 | > | theBends[j].ghost = |
274 | > | current_extra->getInt() + atomOffset; |
275 | > | theBends[j].isGhost = 1; |
276 | > | break; |
277 | > | |
278 | > | case 1: |
279 | > | theBends[j].ghost = |
280 | > | (int)current_extra->getDouble() + atomOffset; |
281 | > | theBends[j].isGhost = 1; |
282 | > | break; |
283 | > | |
284 | > | default: |
285 | > | sprintf( painCave.errMsg, |
286 | > | "SimSetup Error: ghostVectorSource was neither a " |
287 | > | "double nor an int.\n" |
288 | > | "-->Bend[%d] in %s\n", |
289 | > | j, comp_stamps[stampID]->getID() ); |
290 | > | painCave.isFatal = 1; |
291 | > | simError(); |
292 | > | } |
293 | > | } |
294 | > | |
295 | > | else{ |
296 | > | |
297 | > | sprintf( painCave.errMsg, |
298 | > | "SimSetup Error: unhandled bend assignment:\n" |
299 | > | " -->%s in Bend[%d] in %s\n", |
300 | > | current_extra->getlhs(), |
301 | > | j, comp_stamps[stampID]->getID() ); |
302 | > | painCave.isFatal = 1; |
303 | > | simError(); |
304 | > | } |
305 | > | |
306 | > | current_extra = current_extra->getNext(); |
307 | > | } |
308 | > | } |
309 | > | |
310 | > | if( !theBends[j].isGhost ){ |
311 | > | |
312 | > | exI = theBends[j].a; |
313 | > | exJ = theBends[j].c; |
314 | > | } |
315 | > | else{ |
316 | > | |
317 | > | exI = theBends[j].a; |
318 | > | exJ = theBends[j].b; |
319 | > | } |
320 | > | |
321 | > | // exclude_I must always be the smaller of the pair |
322 | > | if( exI > exJ ){ |
323 | > | tempEx = exI; |
324 | > | exI = exJ; |
325 | > | exJ = tempEx; |
326 | > | } |
327 | > | #ifdef IS_MPI |
328 | > | tempEx = exI; |
329 | > | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
330 | > | tempEx = exJ; |
331 | > | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
332 | > | |
333 | > | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
334 | > | #else // isn't MPI |
335 | > | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
336 | > | #endif //is_mpi |
337 | > | } |
338 | > | excludeOffset += molInfo.nBends; |
339 | ||
340 | < | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
340 | > | for(j=0; j<molInfo.nTorsions; j++){ |
341 | > | |
342 | > | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
343 | > | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
344 | > | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
345 | > | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
346 | > | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
347 | > | |
348 | > | exI = theTorsions[j].a; |
349 | > | exJ = theTorsions[j].d; |
350 | ||
351 | < | simnfo->n_atoms = tot_atoms; |
352 | < | simnfo->n_bonds = tot_bonds; |
353 | < | simnfo->n_bends = tot_bends; |
354 | < | simnfo->n_torsions = tot_torsions; |
355 | < | simnfo->n_SRI = tot_SRI; |
356 | < | simnfo->n_mol = tot_nmol; |
233 | < | |
234 | < | |
351 | > | // exclude_I must always be the smaller of the pair |
352 | > | if( exI > exJ ){ |
353 | > | tempEx = exI; |
354 | > | exI = exJ; |
355 | > | exJ = tempEx; |
356 | > | } |
357 | #ifdef IS_MPI | |
358 | + | tempEx = exI; |
359 | + | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
360 | + | tempEx = exJ; |
361 | + | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
362 | + | |
363 | + | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
364 | + | #else // isn't MPI |
365 | + | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
366 | + | #endif //is_mpi |
367 | + | } |
368 | + | excludeOffset += molInfo.nTorsions; |
369 | ||
370 | < | // divide the molecules among processors here. |
371 | < | |
239 | < | mpiSim = new mpiSimulation( simnfo ); |
240 | < | |
241 | < | |
370 | > | |
371 | > | // send the arrays off to the forceField for init. |
372 | ||
373 | < | globalIndex = mpiSim->divideLabor(); |
373 | > | the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
374 | > | the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
375 | > | the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
376 | > | the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
377 | ||
378 | ||
379 | + | the_molecules[i].initialize( molInfo ); |
380 | ||
247 | – | // 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++ ){ |
381 | ||
382 | < | for( j=0; j<components_nmol[i]; j++ ){ |
383 | < | |
384 | < | if( mpiSim->getMyMolStart() <= allMol && |
385 | < | allMol <= mpiSim->getMyMolEnd() ){ |
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 | < | } |
382 | > | atomOffset += molInfo.nAtoms; |
383 | > | delete[] theBonds; |
384 | > | delete[] theBends; |
385 | > | delete[] theTorsions; |
386 | } | |
274 | – | local_SRI = local_bonds + local_bends + local_torsions; |
275 | – | |
387 | ||
388 | < | simnfo->n_atoms = mpiSim->getMyNlocal(); |
389 | < | |
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 note equal.\n", |
283 | < | simnfo->n_atoms, |
284 | < | local_atoms ); |
285 | < | painCave.isFatal = 1; |
286 | < | simError(); |
287 | < | } |
288 | < | |
289 | < | 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; |
294 | < | |
295 | < | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
388 | > | #ifdef IS_MPI |
389 | > | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
390 | MPIcheckPoint(); | |
297 | – | |
298 | – | |
391 | #endif // is_mpi | |
300 | – | |
392 | ||
393 | < | // create the atom and short range interaction arrays |
393 | > | // clean up the forcefield |
394 | > | the_ff->calcRcut(); |
395 | > | the_ff->cleanMe(); |
396 | ||
397 | < | Atom::createArrays(simnfo->n_atoms); |
305 | < | the_atoms = new Atom*[simnfo->n_atoms]; |
306 | < | the_molecules = new Molecule[simnfo->n_mol]; |
397 | > | } |
398 | ||
399 | + | void SimSetup::initFromBass( void ){ |
400 | ||
401 | < | if( simnfo->n_SRI ){ |
402 | < | the_sris = new SRI*[simnfo->n_SRI]; |
403 | < | the_excludes = new int[2 * simnfo->n_SRI]; |
404 | < | simnfo->globalExcludes = new int; |
405 | < | simnfo->n_exclude = tot_SRI; |
401 | > | int i, j, k; |
402 | > | int n_cells; |
403 | > | double cellx, celly, cellz; |
404 | > | double temp1, temp2, temp3; |
405 | > | int n_per_extra; |
406 | > | int n_extra; |
407 | > | int have_extra, done; |
408 | > | |
409 | > | temp1 = (double)tot_nmol / 4.0; |
410 | > | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
411 | > | temp3 = ceil( temp2 ); |
412 | > | |
413 | > | have_extra =0; |
414 | > | if( temp2 < temp3 ){ // we have a non-complete lattice |
415 | > | have_extra =1; |
416 | > | |
417 | > | n_cells = (int)temp3 - 1; |
418 | > | cellx = info->boxL[0] / temp3; |
419 | > | celly = info->boxL[1] / temp3; |
420 | > | cellz = info->boxL[2] / temp3; |
421 | > | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
422 | > | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
423 | > | n_per_extra = (int)ceil( temp1 ); |
424 | > | |
425 | > | if( n_per_extra > 4){ |
426 | > | sprintf( painCave.errMsg, |
427 | > | "SimSetup error. There has been an error in constructing" |
428 | > | " the non-complete lattice.\n" ); |
429 | > | painCave.isFatal = 1; |
430 | > | simError(); |
431 | > | } |
432 | } | |
433 | else{ | |
434 | < | |
435 | < | the_excludes = new int[2]; |
436 | < | the_excludes[0] = 0; |
437 | < | the_excludes[1] = 0; |
320 | < | simnfo->globalExcludes = new int; |
321 | < | simnfo->globalExcludes[0] = 0; |
322 | < | |
323 | < | simnfo->n_exclude = 1; |
434 | > | n_cells = (int)temp3; |
435 | > | cellx = info->boxL[0] / temp3; |
436 | > | celly = info->boxL[1] / temp3; |
437 | > | cellz = info->boxL[2] / temp3; |
438 | } | |
439 | ||
440 | < | // set the arrays into the SimInfo object |
440 | > | current_mol = 0; |
441 | > | current_comp_mol = 0; |
442 | > | current_comp = 0; |
443 | > | current_atom_ndx = 0; |
444 | ||
445 | < | simnfo->atoms = the_atoms; |
446 | < | simnfo->sr_interactions = the_sris; |
447 | < | simnfo->nGlobalExcludes = 0; |
448 | < | simnfo->excludes = the_excludes; |
445 | > | for( i=0; i < n_cells ; i++ ){ |
446 | > | for( j=0; j < n_cells; j++ ){ |
447 | > | for( k=0; k < n_cells; k++ ){ |
448 | > | |
449 | > | makeElement( i * cellx, |
450 | > | j * celly, |
451 | > | k * cellz ); |
452 | > | |
453 | > | makeElement( i * cellx + 0.5 * cellx, |
454 | > | j * celly + 0.5 * celly, |
455 | > | k * cellz ); |
456 | > | |
457 | > | makeElement( i * cellx, |
458 | > | j * celly + 0.5 * celly, |
459 | > | k * cellz + 0.5 * cellz ); |
460 | > | |
461 | > | makeElement( i * cellx + 0.5 * cellx, |
462 | > | j * celly, |
463 | > | k * cellz + 0.5 * cellz ); |
464 | > | } |
465 | > | } |
466 | > | } |
467 | > | |
468 | > | if( have_extra ){ |
469 | > | done = 0; |
470 | ||
471 | + | int start_ndx; |
472 | + | for( i=0; i < (n_cells+1) && !done; i++ ){ |
473 | + | for( j=0; j < (n_cells+1) && !done; j++ ){ |
474 | ||
475 | < | // get some of the tricky things that may still be in the globals |
475 | > | if( i < n_cells ){ |
476 | ||
477 | + | if( j < n_cells ){ |
478 | + | start_ndx = n_cells; |
479 | + | } |
480 | + | else start_ndx = 0; |
481 | + | } |
482 | + | else start_ndx = 0; |
483 | + | |
484 | + | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
485 | + | |
486 | + | makeElement( i * cellx, |
487 | + | j * celly, |
488 | + | k * cellz ); |
489 | + | done = ( current_mol >= tot_nmol ); |
490 | + | |
491 | + | if( !done && n_per_extra > 1 ){ |
492 | + | makeElement( i * cellx + 0.5 * cellx, |
493 | + | j * celly + 0.5 * celly, |
494 | + | k * cellz ); |
495 | + | done = ( current_mol >= tot_nmol ); |
496 | + | } |
497 | + | |
498 | + | if( !done && n_per_extra > 2){ |
499 | + | makeElement( i * cellx, |
500 | + | j * celly + 0.5 * celly, |
501 | + | k * cellz + 0.5 * cellz ); |
502 | + | done = ( current_mol >= tot_nmol ); |
503 | + | } |
504 | + | |
505 | + | if( !done && n_per_extra > 3){ |
506 | + | makeElement( i * cellx + 0.5 * cellx, |
507 | + | j * celly, |
508 | + | k * cellz + 0.5 * cellz ); |
509 | + | done = ( current_mol >= tot_nmol ); |
510 | + | } |
511 | + | } |
512 | + | } |
513 | + | } |
514 | + | } |
515 | + | |
516 | + | |
517 | + | for( i=0; i<info->n_atoms; i++ ){ |
518 | + | info->atoms[i]->set_vx( 0.0 ); |
519 | + | info->atoms[i]->set_vy( 0.0 ); |
520 | + | info->atoms[i]->set_vz( 0.0 ); |
521 | + | } |
522 | + | } |
523 | + | |
524 | + | void SimSetup::makeElement( double x, double y, double z ){ |
525 | + | |
526 | + | int k; |
527 | + | AtomStamp* current_atom; |
528 | + | DirectionalAtom* dAtom; |
529 | + | double rotMat[3][3]; |
530 | + | |
531 | + | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
532 | + | |
533 | + | current_atom = comp_stamps[current_comp]->getAtom( k ); |
534 | + | if( !current_atom->havePosition() ){ |
535 | + | sprintf( painCave.errMsg, |
536 | + | "SimSetup:initFromBass error.\n" |
537 | + | "\tComponent %s, atom %s does not have a position specified.\n" |
538 | + | "\tThe initialization routine is unable to give a start" |
539 | + | " position.\n", |
540 | + | comp_stamps[current_comp]->getID(), |
541 | + | current_atom->getType() ); |
542 | + | painCave.isFatal = 1; |
543 | + | simError(); |
544 | + | } |
545 | + | |
546 | + | the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
547 | + | the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
548 | + | the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
549 | + | |
550 | + | if( the_atoms[current_atom_ndx]->isDirectional() ){ |
551 | + | |
552 | + | dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
553 | + | |
554 | + | rotMat[0][0] = 1.0; |
555 | + | rotMat[0][1] = 0.0; |
556 | + | rotMat[0][2] = 0.0; |
557 | + | |
558 | + | rotMat[1][0] = 0.0; |
559 | + | rotMat[1][1] = 1.0; |
560 | + | rotMat[1][2] = 0.0; |
561 | + | |
562 | + | rotMat[2][0] = 0.0; |
563 | + | rotMat[2][1] = 0.0; |
564 | + | rotMat[2][2] = 1.0; |
565 | + | |
566 | + | dAtom->setA( rotMat ); |
567 | + | } |
568 | + | |
569 | + | current_atom_ndx++; |
570 | + | } |
571 | + | |
572 | + | current_mol++; |
573 | + | current_comp_mol++; |
574 | + | |
575 | + | if( current_comp_mol >= components_nmol[current_comp] ){ |
576 | + | |
577 | + | current_comp_mol = 0; |
578 | + | current_comp++; |
579 | + | } |
580 | + | } |
581 | + | |
582 | + | |
583 | + | void SimSetup::gatherInfo( void ){ |
584 | + | int i,j,k; |
585 | + | |
586 | + | ensembleCase = -1; |
587 | + | ffCase = -1; |
588 | + | |
589 | + | // get the stamps and globals; |
590 | + | stamps = stamps; |
591 | + | globals = globals; |
592 | + | |
593 | + | // set the easy ones first |
594 | + | info->target_temp = globals->getTargetTemp(); |
595 | + | info->dt = globals->getDt(); |
596 | + | info->run_time = globals->getRunTime(); |
597 | + | n_components = globals->getNComponents(); |
598 | + | |
599 | + | |
600 | + | // get the forceField |
601 | + | |
602 | + | strcpy( force_field, globals->getForceField() ); |
603 | + | |
604 | + | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
605 | + | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
606 | + | else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
607 | + | else{ |
608 | + | sprintf( painCave.errMsg, |
609 | + | "SimSetup Error. Unrecognized force field -> %s\n", |
610 | + | force_field ); |
611 | + | painCave.isFatal = 1; |
612 | + | simError(); |
613 | + | } |
614 | + | |
615 | + | // get the ensemble |
616 | + | |
617 | + | strcpy( ensemble, globals->getEnsemble() ); |
618 | + | |
619 | + | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
620 | + | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
621 | + | else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
622 | + | ensembleCase = NPTi_ENS; |
623 | + | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
624 | + | else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
625 | + | else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
626 | + | else if( !strcasecmp( ensemble, "NVEZCONS")) ensembleCase = NVEZCONS_ENS; |
627 | + | else{ |
628 | + | sprintf( painCave.errMsg, |
629 | + | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
630 | + | "reverting to NVE for this simulation.\n", |
631 | + | ensemble ); |
632 | + | painCave.isFatal = 0; |
633 | + | simError(); |
634 | + | strcpy( ensemble, "NVE" ); |
635 | + | ensembleCase = NVE_ENS; |
636 | + | } |
637 | + | strcpy( info->ensemble, ensemble ); |
638 | + | |
639 | + | // get the mixing rule |
640 | + | |
641 | + | strcpy( info->mixingRule, globals->getMixingRule() ); |
642 | + | info->usePBC = globals->getPBC(); |
643 | + | |
644 | ||
645 | < | if( the_globals->haveBox() ){ |
646 | < | simnfo->box_x = the_globals->getBox(); |
647 | < | simnfo->box_y = the_globals->getBox(); |
648 | < | simnfo->box_z = the_globals->getBox(); |
645 | > | // get the components and calculate the tot_nMol and indvidual n_mol |
646 | > | |
647 | > | the_components = globals->getComponents(); |
648 | > | components_nmol = new int[n_components]; |
649 | > | |
650 | > | |
651 | > | if( !globals->haveNMol() ){ |
652 | > | // we don't have the total number of molecules, so we assume it is |
653 | > | // given in each component |
654 | > | |
655 | > | tot_nmol = 0; |
656 | > | for( i=0; i<n_components; i++ ){ |
657 | > | |
658 | > | if( !the_components[i]->haveNMol() ){ |
659 | > | // we have a problem |
660 | > | sprintf( painCave.errMsg, |
661 | > | "SimSetup Error. No global NMol or component NMol" |
662 | > | " given. Cannot calculate the number of atoms.\n" ); |
663 | > | painCave.isFatal = 1; |
664 | > | simError(); |
665 | > | } |
666 | > | |
667 | > | tot_nmol += the_components[i]->getNMol(); |
668 | > | components_nmol[i] = the_components[i]->getNMol(); |
669 | > | } |
670 | } | |
671 | < | else if( the_globals->haveDensity() ){ |
671 | > | else{ |
672 | > | sprintf( painCave.errMsg, |
673 | > | "SimSetup error.\n" |
674 | > | "\tSorry, the ability to specify total" |
675 | > | " nMols and then give molfractions in the components\n" |
676 | > | "\tis not currently supported." |
677 | > | " Please give nMol in the components.\n" ); |
678 | > | painCave.isFatal = 1; |
679 | > | simError(); |
680 | > | } |
681 | ||
682 | + | // set the status, sample, and thermal kick times |
683 | + | |
684 | + | if( globals->haveSampleTime() ){ |
685 | + | info->sampleTime = globals->getSampleTime(); |
686 | + | info->statusTime = info->sampleTime; |
687 | + | info->thermalTime = info->sampleTime; |
688 | + | } |
689 | + | else{ |
690 | + | info->sampleTime = globals->getRunTime(); |
691 | + | info->statusTime = info->sampleTime; |
692 | + | info->thermalTime = info->sampleTime; |
693 | + | } |
694 | + | |
695 | + | if( globals->haveStatusTime() ){ |
696 | + | info->statusTime = globals->getStatusTime(); |
697 | + | } |
698 | + | |
699 | + | if( globals->haveThermalTime() ){ |
700 | + | info->thermalTime = globals->getThermalTime(); |
701 | + | } |
702 | + | |
703 | + | // check for the temperature set flag |
704 | + | |
705 | + | if( globals->haveTempSet() ) info->setTemp = globals->getTempSet(); |
706 | + | |
707 | + | // get some of the tricky things that may still be in the globals |
708 | + | |
709 | + | double boxVector[3]; |
710 | + | if( globals->haveBox() ){ |
711 | + | boxVector[0] = globals->getBox(); |
712 | + | boxVector[1] = globals->getBox(); |
713 | + | boxVector[2] = globals->getBox(); |
714 | + | |
715 | + | info->setBox( boxVector ); |
716 | + | } |
717 | + | else if( globals->haveDensity() ){ |
718 | + | |
719 | double vol; | |
720 | < | vol = (double)tot_nmol / the_globals->getDensity(); |
721 | < | simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
722 | < | simnfo->box_y = simnfo->box_x; |
723 | < | simnfo->box_z = simnfo->box_x; |
720 | > | vol = (double)tot_nmol / globals->getDensity(); |
721 | > | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
722 | > | boxVector[1] = boxVector[0]; |
723 | > | boxVector[2] = boxVector[0]; |
724 | > | |
725 | > | info->setBox( boxVector ); |
726 | } | |
727 | else{ | |
728 | < | if( !the_globals->haveBoxX() ){ |
728 | > | if( !globals->haveBoxX() ){ |
729 | sprintf( painCave.errMsg, | |
730 | "SimSetup error, no periodic BoxX size given.\n" ); | |
731 | painCave.isFatal = 1; | |
732 | simError(); | |
733 | } | |
734 | < | simnfo->box_x = the_globals->getBoxX(); |
734 | > | boxVector[0] = globals->getBoxX(); |
735 | ||
736 | < | if( !the_globals->haveBoxY() ){ |
736 | > | if( !globals->haveBoxY() ){ |
737 | sprintf( painCave.errMsg, | |
738 | "SimSetup error, no periodic BoxY size given.\n" ); | |
739 | painCave.isFatal = 1; | |
740 | simError(); | |
741 | } | |
742 | < | simnfo->box_y = the_globals->getBoxY(); |
742 | > | boxVector[1] = globals->getBoxY(); |
743 | ||
744 | < | if( !the_globals->haveBoxZ() ){ |
744 | > | if( !globals->haveBoxZ() ){ |
745 | sprintf( painCave.errMsg, | |
746 | "SimSetup error, no periodic BoxZ size given.\n" ); | |
747 | painCave.isFatal = 1; | |
748 | simError(); | |
749 | } | |
750 | < | simnfo->box_z = the_globals->getBoxZ(); |
750 | > | boxVector[2] = globals->getBoxZ(); |
751 | > | |
752 | > | info->setBox( boxVector ); |
753 | } | |
754 | ||
755 | + | |
756 | + | |
757 | #ifdef IS_MPI | |
758 | < | strcpy( checkPointMsg, "Box size set up" ); |
758 | > | strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
759 | MPIcheckPoint(); | |
760 | #endif // is_mpi | |
761 | ||
762 | + | } |
763 | ||
382 | – | // initialize the arrays |
764 | ||
765 | < | the_ff->setSimInfo( simnfo ); |
765 | > | void SimSetup::finalInfoCheck( void ){ |
766 | > | int index; |
767 | > | int usesDipoles; |
768 | > | |
769 | ||
770 | < | makeAtoms(); |
387 | < | simnfo->identArray = new int[simnfo->n_atoms]; |
388 | < | for(i=0; i<simnfo->n_atoms; i++){ |
389 | < | simnfo->identArray[i] = the_atoms[i]->getIdent(); |
390 | < | } |
770 | > | // check electrostatic parameters |
771 | ||
772 | < | if( tot_bonds ){ |
773 | < | makeBonds(); |
772 | > | index = 0; |
773 | > | usesDipoles = 0; |
774 | > | while( (index < info->n_atoms) && !usesDipoles ){ |
775 | > | usesDipoles = ((info->atoms)[index])->hasDipole(); |
776 | > | index++; |
777 | } | |
778 | + | |
779 | + | #ifdef IS_MPI |
780 | + | int myUse = usesDipoles; |
781 | + | MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
782 | + | #endif //is_mpi |
783 | ||
784 | < | if( tot_bends ){ |
397 | < | makeBends(); |
398 | < | } |
784 | > | double theEcr, theEst; |
785 | ||
786 | < | if( tot_torsions ){ |
787 | < | makeTorsions(); |
788 | < | } |
789 | < | |
404 | < | |
405 | < | if (the_globals->getUseRF() ) { |
406 | < | simnfo->useReactionField = 1; |
407 | < | |
408 | < | if( !the_globals->haveECR() ){ |
786 | > | if (globals->getUseRF() ) { |
787 | > | info->useReactionField = 1; |
788 | > | |
789 | > | if( !globals->haveECR() ){ |
790 | sprintf( painCave.errMsg, | |
791 | "SimSetup Warning: using default value of 1/2 the smallest " | |
792 | "box length for the electrostaticCutoffRadius.\n" | |
# | Line 413 | Line 794 | void SimSetup::createSim( void ){ | |
794 | painCave.isFatal = 0; | |
795 | simError(); | |
796 | double smallest; | |
797 | < | smallest = simnfo->box_x; |
798 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
799 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
800 | < | simnfo->ecr = 0.5 * smallest; |
797 | > | smallest = info->boxL[0]; |
798 | > | if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
799 | > | if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
800 | > | theEcr = 0.5 * smallest; |
801 | } else { | |
802 | < | simnfo->ecr = the_globals->getECR(); |
802 | > | theEcr = globals->getECR(); |
803 | } | |
804 | ||
805 | < | if( !the_globals->haveEST() ){ |
805 | > | if( !globals->haveEST() ){ |
806 | sprintf( painCave.errMsg, | |
807 | "SimSetup Warning: using default value of 0.05 * the " | |
808 | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" | |
809 | ); | |
810 | painCave.isFatal = 0; | |
811 | simError(); | |
812 | < | simnfo->est = 0.05 * simnfo->ecr; |
812 | > | theEst = 0.05 * theEcr; |
813 | } else { | |
814 | < | simnfo->est = the_globals->getEST(); |
814 | > | theEst= globals->getEST(); |
815 | } | |
816 | + | |
817 | + | info->setEcr( theEcr, theEst ); |
818 | ||
819 | < | if(!the_globals->haveDielectric() ){ |
819 | > | if(!globals->haveDielectric() ){ |
820 | sprintf( painCave.errMsg, | |
821 | "SimSetup Error: You are trying to use Reaction Field without" | |
822 | "setting a dielectric constant!\n" | |
# | Line 441 | Line 824 | void SimSetup::createSim( void ){ | |
824 | painCave.isFatal = 1; | |
825 | simError(); | |
826 | } | |
827 | < | simnfo->dielectric = the_globals->getDielectric(); |
828 | < | } else { |
829 | < | if (simnfo->n_dipoles) { |
827 | > | info->dielectric = globals->getDielectric(); |
828 | > | } |
829 | > | else { |
830 | > | if (usesDipoles) { |
831 | ||
832 | < | if( !the_globals->haveECR() ){ |
833 | < | sprintf( painCave.errMsg, |
834 | < | "SimSetup Warning: using default value of 1/2 the smallest" |
835 | < | "box length for the electrostaticCutoffRadius.\n" |
836 | < | "I hope you have a very fast processor!\n"); |
837 | < | painCave.isFatal = 0; |
838 | < | simError(); |
839 | < | double smallest; |
840 | < | smallest = simnfo->box_x; |
841 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
842 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
843 | < | simnfo->ecr = 0.5 * smallest; |
832 | > | if( !globals->haveECR() ){ |
833 | > | sprintf( painCave.errMsg, |
834 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
835 | > | "box length for the electrostaticCutoffRadius.\n" |
836 | > | "I hope you have a very fast processor!\n"); |
837 | > | painCave.isFatal = 0; |
838 | > | simError(); |
839 | > | double smallest; |
840 | > | smallest = info->boxL[0]; |
841 | > | if (info->boxL[1] <= smallest) smallest = info->boxL[1]; |
842 | > | if (info->boxL[2] <= smallest) smallest = info->boxL[2]; |
843 | > | theEcr = 0.5 * smallest; |
844 | } else { | |
845 | < | simnfo->ecr = the_globals->getECR(); |
845 | > | theEcr = globals->getECR(); |
846 | } | |
847 | ||
848 | < | if( !the_globals->haveEST() ){ |
849 | < | sprintf( painCave.errMsg, |
850 | < | "SimSetup Warning: using default value of 5% of the" |
851 | < | "electrostaticCutoffRadius for the " |
852 | < | "electrostaticSkinThickness\n" |
853 | < | ); |
854 | < | painCave.isFatal = 0; |
855 | < | simError(); |
856 | < | simnfo->est = 0.05 * simnfo->ecr; |
848 | > | if( !globals->haveEST() ){ |
849 | > | sprintf( painCave.errMsg, |
850 | > | "SimSetup Warning: using default value of 0.05 * the " |
851 | > | "electrostaticCutoffRadius for the " |
852 | > | "electrostaticSkinThickness\n" |
853 | > | ); |
854 | > | painCave.isFatal = 0; |
855 | > | simError(); |
856 | > | theEst = 0.05 * theEcr; |
857 | } else { | |
858 | < | simnfo->est = the_globals->getEST(); |
858 | > | theEst= globals->getEST(); |
859 | } | |
860 | + | |
861 | + | info->setEcr( theEcr, theEst ); |
862 | } | |
863 | } | |
864 | ||
865 | #ifdef IS_MPI | |
866 | < | strcpy( checkPointMsg, "electrostatic parameters check out" ); |
866 | > | strcpy( checkPointMsg, "post processing checks out" ); |
867 | MPIcheckPoint(); | |
868 | #endif // is_mpi | |
869 | ||
870 | < | if( the_globals->haveInitialConfig() ){ |
870 | > | } |
871 | > | |
872 | > | void SimSetup::initSystemCoords( void ){ |
873 | > | |
874 | > | if( globals->haveInitialConfig() ){ |
875 | ||
876 | InitializeFromFile* fileInit; | |
877 | #ifdef IS_MPI // is_mpi | |
878 | if( worldRank == 0 ){ | |
879 | #endif //is_mpi | |
880 | < | fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
880 | > | fileInit = new InitializeFromFile( globals->getInitialConfig() ); |
881 | #ifdef IS_MPI | |
882 | }else fileInit = new InitializeFromFile( NULL ); | |
883 | #endif | |
884 | < | fileInit->read_xyz( simnfo ); // default velocities on |
884 | > | fileInit->readInit( info ); // default velocities on |
885 | ||
886 | delete fileInit; | |
887 | } | |
# | Line 519 | Line 909 | void SimSetup::createSim( void ){ | |
909 | MPIcheckPoint(); | |
910 | #endif // is_mpi | |
911 | ||
912 | + | } |
913 | ||
523 | – | |
524 | – | |
525 | – | |
914 | ||
915 | < | |
915 | > | void SimSetup::makeOutNames( void ){ |
916 | > | |
917 | #ifdef IS_MPI | |
918 | if( worldRank == 0 ){ | |
919 | #endif // is_mpi | |
920 | ||
921 | < | if( the_globals->haveFinalConfig() ){ |
922 | < | strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
921 | > | if( globals->haveFinalConfig() ){ |
922 | > | strcpy( info->finalName, globals->getFinalConfig() ); |
923 | } | |
924 | else{ | |
925 | < | strcpy( simnfo->finalName, inFileName ); |
925 | > | strcpy( info->finalName, inFileName ); |
926 | char* endTest; | |
927 | < | int nameLength = strlen( simnfo->finalName ); |
928 | < | endTest = &(simnfo->finalName[nameLength - 5]); |
927 | > | int nameLength = strlen( info->finalName ); |
928 | > | endTest = &(info->finalName[nameLength - 5]); |
929 | if( !strcmp( endTest, ".bass" ) ){ | |
930 | strcpy( endTest, ".eor" ); | |
931 | } | |
# | Line 544 | Line 933 | void SimSetup::createSim( void ){ | |
933 | strcpy( endTest, ".eor" ); | |
934 | } | |
935 | else{ | |
936 | < | endTest = &(simnfo->finalName[nameLength - 4]); |
936 | > | endTest = &(info->finalName[nameLength - 4]); |
937 | if( !strcmp( endTest, ".bss" ) ){ | |
938 | strcpy( endTest, ".eor" ); | |
939 | } | |
# | Line 552 | Line 941 | void SimSetup::createSim( void ){ | |
941 | strcpy( endTest, ".eor" ); | |
942 | } | |
943 | else{ | |
944 | < | strcat( simnfo->finalName, ".eor" ); |
944 | > | strcat( info->finalName, ".eor" ); |
945 | } | |
946 | } | |
947 | } | |
948 | ||
949 | // make the sample and status out names | |
950 | ||
951 | < | strcpy( simnfo->sampleName, inFileName ); |
951 | > | strcpy( info->sampleName, inFileName ); |
952 | char* endTest; | |
953 | < | int nameLength = strlen( simnfo->sampleName ); |
954 | < | endTest = &(simnfo->sampleName[nameLength - 5]); |
953 | > | int nameLength = strlen( info->sampleName ); |
954 | > | endTest = &(info->sampleName[nameLength - 5]); |
955 | if( !strcmp( endTest, ".bass" ) ){ | |
956 | strcpy( endTest, ".dump" ); | |
957 | } | |
# | Line 570 | Line 959 | void SimSetup::createSim( void ){ | |
959 | strcpy( endTest, ".dump" ); | |
960 | } | |
961 | else{ | |
962 | < | endTest = &(simnfo->sampleName[nameLength - 4]); |
962 | > | endTest = &(info->sampleName[nameLength - 4]); |
963 | if( !strcmp( endTest, ".bss" ) ){ | |
964 | strcpy( endTest, ".dump" ); | |
965 | } | |
# | Line 578 | Line 967 | void SimSetup::createSim( void ){ | |
967 | strcpy( endTest, ".dump" ); | |
968 | } | |
969 | else{ | |
970 | < | strcat( simnfo->sampleName, ".dump" ); |
970 | > | strcat( info->sampleName, ".dump" ); |
971 | } | |
972 | } | |
973 | ||
974 | < | strcpy( simnfo->statusName, inFileName ); |
975 | < | nameLength = strlen( simnfo->statusName ); |
976 | < | endTest = &(simnfo->statusName[nameLength - 5]); |
974 | > | strcpy( info->statusName, inFileName ); |
975 | > | nameLength = strlen( info->statusName ); |
976 | > | endTest = &(info->statusName[nameLength - 5]); |
977 | if( !strcmp( endTest, ".bass" ) ){ | |
978 | strcpy( endTest, ".stat" ); | |
979 | } | |
# | Line 592 | Line 981 | void SimSetup::createSim( void ){ | |
981 | strcpy( endTest, ".stat" ); | |
982 | } | |
983 | else{ | |
984 | < | endTest = &(simnfo->statusName[nameLength - 4]); |
984 | > | endTest = &(info->statusName[nameLength - 4]); |
985 | if( !strcmp( endTest, ".bss" ) ){ | |
986 | strcpy( endTest, ".stat" ); | |
987 | } | |
# | Line 600 | Line 989 | void SimSetup::createSim( void ){ | |
989 | strcpy( endTest, ".stat" ); | |
990 | } | |
991 | else{ | |
992 | < | strcat( simnfo->statusName, ".stat" ); |
992 | > | strcat( info->statusName, ".stat" ); |
993 | } | |
994 | } | |
995 | ||
996 | #ifdef IS_MPI | |
997 | } | |
998 | #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 | – | } |
999 | ||
1000 | < | if( the_globals->haveStatusTime() ){ |
625 | < | simnfo->statusTime = the_globals->getStatusTime(); |
626 | < | } |
1000 | > | } |
1001 | ||
628 | – | if( the_globals->haveThermalTime() ){ |
629 | – | simnfo->thermalTime = the_globals->getThermalTime(); |
630 | – | } |
1002 | ||
1003 | < | // check for the temperature set flag |
1003 | > | void SimSetup::sysObjectsCreation( void ){ |
1004 | ||
1005 | < | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
1005 | > | int i; |
1006 | ||
1007 | + | // create the forceField |
1008 | ||
1009 | < | // // make the longe range forces and the integrator |
1009 | > | createFF(); |
1010 | ||
1011 | < | // new AllLong( simnfo ); |
1011 | > | // extract componentList |
1012 | ||
1013 | < | if( !strcmp( force_field, "TraPPE" ) ) new Verlet( *simnfo, the_ff ); |
642 | < | if( !strcmp( force_field, "DipoleTest" ) ) new Symplectic( simnfo, the_ff ); |
643 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ) new Symplectic( simnfo, the_ff ); |
644 | < | if( !strcmp( force_field, "LJ" ) ) new Verlet( *simnfo, the_ff ); |
1013 | > | compList(); |
1014 | ||
1015 | + | // calc the number of atoms, bond, bends, and torsions |
1016 | ||
1017 | + | calcSysValues(); |
1018 | ||
1019 | < | // initialize the Fortran |
1019 | > | #ifdef IS_MPI |
1020 | > | // divide the molecules among the processors |
1021 | ||
1022 | < | simnfo->refreshSim(); |
1022 | > | mpiMolDivide(); |
1023 | > | #endif //is_mpi |
1024 | ||
1025 | < | if( !strcmp( simnfo->mixingRule, "standard") ){ |
1026 | < | the_ff->initForceField( LB_MIXING_RULE ); |
1027 | < | } |
1028 | < | else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
1029 | < | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1025 | > | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1026 | > | |
1027 | > | makeSysArrays(); |
1028 | > | |
1029 | > | // make and initialize the molecules (all but atomic coordinates) |
1030 | > | |
1031 | > | makeMolecules(); |
1032 | > | info->identArray = new int[info->n_atoms]; |
1033 | > | for(i=0; i<info->n_atoms; i++){ |
1034 | > | info->identArray[i] = the_atoms[i]->getIdent(); |
1035 | } | |
1036 | < | else{ |
1036 | > | |
1037 | > | |
1038 | > | |
1039 | > | } |
1040 | > | |
1041 | > | |
1042 | > | void SimSetup::createFF( void ){ |
1043 | > | |
1044 | > | switch( ffCase ){ |
1045 | > | |
1046 | > | case FF_DUFF: |
1047 | > | the_ff = new DUFF(); |
1048 | > | break; |
1049 | > | |
1050 | > | case FF_LJ: |
1051 | > | the_ff = new LJFF(); |
1052 | > | break; |
1053 | > | |
1054 | > | case FF_EAM: |
1055 | > | the_ff = new EAM_FF(); |
1056 | > | break; |
1057 | > | |
1058 | > | default: |
1059 | sprintf( painCave.errMsg, | |
1060 | < | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
661 | < | simnfo->mixingRule ); |
1060 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1061 | painCave.isFatal = 1; | |
1062 | simError(); | |
1063 | } | |
1064 | ||
666 | – | |
1065 | #ifdef IS_MPI | |
1066 | < | strcpy( checkPointMsg, |
669 | < | "Successfully intialized the mixingRule for Fortran." ); |
1066 | > | strcpy( checkPointMsg, "ForceField creation successful" ); |
1067 | MPIcheckPoint(); | |
1068 | #endif // is_mpi | |
1069 | + | |
1070 | } | |
1071 | ||
1072 | ||
1073 | < | void SimSetup::makeMolecules( void ){ |
1073 | > | void SimSetup::compList( void ){ |
1074 | ||
1075 | < | int i, j, exI, exJ, tempEx, stampID, atomOffset; |
678 | < | molInit info; |
679 | < | DirectionalAtom* dAtom; |
680 | < | AtomStamp* currentAtom; |
681 | < | BondStamp* currentBond; |
682 | < | BendStamp* currentBend; |
683 | < | TorsionStamp* currentTorsion; |
684 | < | |
685 | < | //init the forceField paramters |
1075 | > | int i; |
1076 | ||
1077 | < | the_ff->readParams(); |
1077 | > | comp_stamps = new MoleculeStamp*[n_components]; |
1078 | ||
1079 | + | // make an array of molecule stamps that match the components used. |
1080 | + | // also extract the used stamps out into a separate linked list |
1081 | + | |
1082 | + | info->nComponents = n_components; |
1083 | + | info->componentsNmol = components_nmol; |
1084 | + | info->compStamps = comp_stamps; |
1085 | + | info->headStamp = new LinkedMolStamp(); |
1086 | ||
1087 | < | // init the molecules |
1087 | > | char* id; |
1088 | > | LinkedMolStamp* headStamp = info->headStamp; |
1089 | > | LinkedMolStamp* currentStamp = NULL; |
1090 | > | for( i=0; i<n_components; i++ ){ |
1091 | ||
1092 | < | atomOffset = 0; |
1093 | < | for(i=0; i<simnfo->n_mol; i++){ |
1092 | > | id = the_components[i]->getType(); |
1093 | > | comp_stamps[i] = NULL; |
1094 | ||
1095 | < | stampID = the_molecules[i].getStampID(); |
1095 | > | // check to make sure the component isn't already in the list |
1096 | ||
1097 | < | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
1098 | < | 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]; |
706 | < | |
707 | < | 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++){ |
1097 | > | comp_stamps[i] = headStamp->match( id ); |
1098 | > | if( comp_stamps[i] == NULL ){ |
1099 | ||
1100 | < | currentAtom = theComponents[stampID]->getAtom( j ); |
1101 | < | if( currentAtom->haveOrientation() ){ |
1102 | < | |
1103 | < | dAtom = new DirectionalAtom(j + atomOffset); |
1104 | < | simnfo->n_oriented++; |
1105 | < | info.myAtoms[j] = dAtom; |
1106 | < | |
1107 | < | ux = currentAtom->getOrntX(); |
1108 | < | uy = currentAtom->getOrntY(); |
1109 | < | 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 ); |
1100 | > | // extract the component from the list; |
1101 | > | |
1102 | > | currentStamp = stamps->extractMolStamp( id ); |
1103 | > | if( currentStamp == NULL ){ |
1104 | > | sprintf( painCave.errMsg, |
1105 | > | "SimSetup error: Component \"%s\" was not found in the " |
1106 | > | "list of declared molecules\n", |
1107 | > | id ); |
1108 | > | painCave.isFatal = 1; |
1109 | > | simError(); |
1110 | } | |
737 | – | else{ |
738 | – | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
739 | – | } |
740 | – | info.myAtoms[j]->setType( currentAtom->getType() ); |
741 | – | |
742 | – | #ifdef IS_MPI |
1111 | ||
1112 | < | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
1113 | < | |
1112 | > | headStamp->add( currentStamp ); |
1113 | > | comp_stamps[i] = headStamp->match( id ); |
1114 | > | } |
1115 | > | } |
1116 | > | |
1117 | > | #ifdef IS_MPI |
1118 | > | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1119 | > | MPIcheckPoint(); |
1120 | #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; |
1121 | ||
756 | – | exI = theBonds[i].a; |
757 | – | exJ = theBonds[i].b; |
1122 | ||
1123 | < | // 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) |
1123 | > | } |
1124 | ||
1125 | < | #endif //is_mpi |
1125 | > | void SimSetup::calcSysValues( void ){ |
1126 | > | int i, j, k; |
1127 | > | |
1128 | > | |
1129 | > | tot_atoms = 0; |
1130 | > | tot_bonds = 0; |
1131 | > | tot_bends = 0; |
1132 | > | tot_torsions = 0; |
1133 | > | for( i=0; i<n_components; i++ ){ |
1134 | ||
1135 | + | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1136 | + | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1137 | + | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1138 | + | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1139 | } | |
1140 | ||
1141 | + | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1142 | ||
1143 | + | info->n_atoms = tot_atoms; |
1144 | + | info->n_bonds = tot_bonds; |
1145 | + | info->n_bends = tot_bends; |
1146 | + | info->n_torsions = tot_torsions; |
1147 | + | info->n_SRI = tot_SRI; |
1148 | + | info->n_mol = tot_nmol; |
1149 | + | |
1150 | + | info->molMembershipArray = new int[tot_atoms]; |
1151 | + | } |
1152 | ||
1153 | ||
1154 | + | #ifdef IS_MPI |
1155 | ||
1156 | + | void SimSetup::mpiMolDivide( void ){ |
1157 | + | |
1158 | + | int i, j, k; |
1159 | + | int localMol, allMol; |
1160 | + | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1161 | ||
1162 | + | mpiSim = new mpiSimulation( info ); |
1163 | + | |
1164 | + | globalIndex = mpiSim->divideLabor(); |
1165 | ||
1166 | + | // set up the local variables |
1167 | + | |
1168 | + | mol2proc = mpiSim->getMolToProcMap(); |
1169 | + | molCompType = mpiSim->getMolComponentType(); |
1170 | + | |
1171 | + | allMol = 0; |
1172 | + | localMol = 0; |
1173 | + | local_atoms = 0; |
1174 | + | local_bonds = 0; |
1175 | + | local_bends = 0; |
1176 | + | local_torsions = 0; |
1177 | + | globalAtomIndex = 0; |
1178 | ||
1179 | ||
1180 | + | for( i=0; i<n_components; i++ ){ |
1181 | ||
1182 | + | for( j=0; j<components_nmol[i]; j++ ){ |
1183 | + | |
1184 | + | if( mol2proc[allMol] == worldRank ){ |
1185 | + | |
1186 | + | local_atoms += comp_stamps[i]->getNAtoms(); |
1187 | + | local_bonds += comp_stamps[i]->getNBonds(); |
1188 | + | local_bends += comp_stamps[i]->getNBends(); |
1189 | + | local_torsions += comp_stamps[i]->getNTorsions(); |
1190 | + | localMol++; |
1191 | + | } |
1192 | + | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1193 | + | info->molMembershipArray[globalAtomIndex] = allMol; |
1194 | + | globalAtomIndex++; |
1195 | + | } |
1196 | ||
1197 | + | allMol++; |
1198 | + | } |
1199 | + | } |
1200 | + | local_SRI = local_bonds + local_bends + local_torsions; |
1201 | + | |
1202 | + | info->n_atoms = mpiSim->getMyNlocal(); |
1203 | + | |
1204 | + | if( local_atoms != info->n_atoms ){ |
1205 | + | sprintf( painCave.errMsg, |
1206 | + | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1207 | + | " localAtom (%d) are not equal.\n", |
1208 | + | info->n_atoms, |
1209 | + | local_atoms ); |
1210 | + | painCave.isFatal = 1; |
1211 | + | simError(); |
1212 | + | } |
1213 | ||
1214 | + | info->n_bonds = local_bonds; |
1215 | + | info->n_bends = local_bends; |
1216 | + | info->n_torsions = local_torsions; |
1217 | + | info->n_SRI = local_SRI; |
1218 | + | info->n_mol = localMol; |
1219 | ||
1220 | + | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1221 | + | MPIcheckPoint(); |
1222 | + | } |
1223 | + | |
1224 | + | #endif // is_mpi |
1225 | ||
1226 | ||
1227 | < | void SimSetup::makeAtoms( void ){ |
1227 | > | void SimSetup::makeSysArrays( void ){ |
1228 | > | int i, j, k; |
1229 | ||
798 | – | int i, j, k, index; |
799 | – | double ux, uy, uz, uSqr, u; |
800 | – | AtomStamp* current_atom; |
1230 | ||
1231 | < | DirectionalAtom* dAtom; |
803 | < | int molIndex, molStart, molEnd, nMemb, lMolIndex; |
1231 | > | // create the atom and short range interaction arrays |
1232 | ||
1233 | < | lMolIndex = 0; |
1234 | < | molIndex = 0; |
1235 | < | index = 0; |
1236 | < | for( i=0; i<n_components; i++ ){ |
809 | < | |
810 | < | for( j=0; j<components_nmol[i]; j++ ){ |
1233 | > | Atom::createArrays(info->n_atoms); |
1234 | > | the_atoms = new Atom*[info->n_atoms]; |
1235 | > | the_molecules = new Molecule[info->n_mol]; |
1236 | > | int molIndex; |
1237 | ||
1238 | < | #ifdef IS_MPI |
813 | < | if( mpiSim->getMyMolStart() <= molIndex && |
814 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
815 | < | #endif // is_mpi |
1238 | > | // initialize the molecule's stampID's |
1239 | ||
817 | – | molStart = index; |
818 | – | nMemb = comp_stamps[i]->getNAtoms(); |
819 | – | for( k=0; k<comp_stamps[i]->getNAtoms(); k++ ){ |
820 | – | |
821 | – | current_atom = comp_stamps[i]->getAtom( k ); |
822 | – | if( current_atom->haveOrientation() ){ |
823 | – | |
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++; |
859 | – | |
1240 | #ifdef IS_MPI | |
1241 | < | } |
862 | < | #endif //is_mpi |
863 | < | |
864 | < | molIndex++; |
865 | < | } |
866 | < | } |
1241 | > | |
1242 | ||
868 | – | #ifdef IS_MPI |
869 | – | for( i=0; i<mpiSim->getMyNlocal(); i++ ) the_atoms[i]->setGlobalIndex( globalIndex[i] ); |
870 | – | |
871 | – | delete[] globalIndex; |
872 | – | |
873 | – | mpiSim->mpiRefresh(); |
874 | – | #endif //IS_MPI |
875 | – | |
876 | – | the_ff->initializeAtoms(); |
877 | – | } |
878 | – | |
879 | – | void SimSetup::makeBonds( void ){ |
880 | – | |
881 | – | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
882 | – | bond_pair* the_bonds; |
883 | – | BondStamp* current_bond; |
884 | – | |
885 | – | the_bonds = new bond_pair[tot_bonds]; |
886 | – | index = 0; |
887 | – | offset = 0; |
1243 | molIndex = 0; | |
1244 | < | |
1245 | < | for( i=0; i<n_components; i++ ){ |
1246 | < | |
1247 | < | for( j=0; j<components_nmol[i]; j++ ){ |
1248 | < | |
1249 | < | #ifdef IS_MPI |
895 | < | if( mpiSim->getMyMolStart() <= molIndex && |
896 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
897 | < | #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; |
904 | < | |
905 | < | exI = the_bonds[index].a; |
906 | < | exJ = the_bonds[index].b; |
907 | < | |
908 | < | // exclude_I must always be the smaller of the pair |
909 | < | if( exI > exJ ){ |
910 | < | tempEx = exI; |
911 | < | exI = exJ; |
912 | < | exJ = tempEx; |
913 | < | } |
914 | < | |
915 | < | |
916 | < | #ifdef IS_MPI |
917 | < | |
918 | < | the_excludes[index*2] = |
919 | < | the_atoms[exI]->getGlobalIndex() + 1; |
920 | < | the_excludes[index*2 + 1] = |
921 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
922 | < | |
923 | < | #else // isn't MPI |
924 | < | |
925 | < | the_excludes[index*2] = exI + 1; |
926 | < | the_excludes[index*2 + 1] = exJ + 1; |
927 | < | // fortran index from 1 (hence the +1 in the indexing) |
928 | < | #endif //is_mpi |
929 | < | |
930 | < | // increment the index and repeat; |
931 | < | index++; |
932 | < | } |
933 | < | offset += comp_stamps[i]->getNAtoms(); |
934 | < | |
935 | < | #ifdef IS_MPI |
936 | < | } |
937 | < | #endif //is_mpi |
938 | < | |
1244 | > | for(i=0; i<mpiSim->getTotNmol(); i++){ |
1245 | > | |
1246 | > | if(mol2proc[i] == worldRank ){ |
1247 | > | the_molecules[molIndex].setStampID( molCompType[i] ); |
1248 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
1249 | > | the_molecules[molIndex].setGlobalIndex( i ); |
1250 | molIndex++; | |
1251 | < | } |
1251 | > | } |
1252 | } | |
1253 | ||
1254 | < | the_ff->initializeBonds( the_bonds ); |
944 | < | } |
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; |
1254 | > | #else // is_mpi |
1255 | ||
954 | – | |
955 | – | the_bends = new bend_set[tot_bends]; |
956 | – | index = 0; |
957 | – | offset = 0; |
1256 | molIndex = 0; | |
1257 | < | for( i=0; i<n_components; i++ ){ |
1258 | < | |
1259 | < | for( j=0; j<components_nmol[i]; j++ ){ |
1260 | < | |
1261 | < | #ifdef IS_MPI |
1262 | < | if( mpiSim->getMyMolStart() <= molIndex && |
1263 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
1264 | < | #endif // is_mpi |
1265 | < | |
968 | < | for( k=0; k<comp_stamps[i]->getNBends(); k++ ){ |
969 | < | |
970 | < | current_bend = comp_stamps[i]->getBend( k ); |
971 | < | 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 |
1257 | > | globalAtomIndex = 0; |
1258 | > | for(i=0; i<n_components; i++){ |
1259 | > | for(j=0; j<components_nmol[i]; j++ ){ |
1260 | > | the_molecules[molIndex].setStampID( i ); |
1261 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
1262 | > | the_molecules[molIndex].setGlobalIndex( molIndex ); |
1263 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1264 | > | info->molMembershipArray[globalAtomIndex] = molIndex; |
1265 | > | globalAtomIndex++; |
1266 | } | |
1064 | – | #endif //is_mpi |
1065 | – | |
1267 | molIndex++; | |
1268 | } | |
1269 | } | |
1270 | + | |
1271 | ||
1070 | – | #ifdef IS_MPI |
1071 | – | sprintf( checkPointMsg, |
1072 | – | "Successfully created the bends list.\n" ); |
1073 | – | MPIcheckPoint(); |
1272 | #endif // is_mpi | |
1075 | – | |
1273 | ||
1077 | – | the_ff->initializeBends( the_bends ); |
1078 | – | } |
1274 | ||
1275 | < | void SimSetup::makeTorsions( void ){ |
1275 | > | if( info->n_SRI ){ |
1276 | > | |
1277 | > | Exclude::createArray(info->n_SRI); |
1278 | > | the_excludes = new Exclude*[info->n_SRI]; |
1279 | > | for( int ex=0; ex<info->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
1280 | > | info->globalExcludes = new int; |
1281 | > | info->n_exclude = info->n_SRI; |
1282 | > | } |
1283 | > | else{ |
1284 | > | |
1285 | > | Exclude::createArray( 1 ); |
1286 | > | the_excludes = new Exclude*; |
1287 | > | the_excludes[0] = new Exclude(0); |
1288 | > | the_excludes[0]->setPair( 0,0 ); |
1289 | > | info->globalExcludes = new int; |
1290 | > | info->globalExcludes[0] = 0; |
1291 | > | info->n_exclude = 0; |
1292 | > | } |
1293 | ||
1294 | < | int i, j, k, index, offset, molIndex, exI, exJ, tempEx; |
1083 | < | torsion_set* the_torsions; |
1084 | < | TorsionStamp* current_torsion; |
1294 | > | // set the arrays into the SimInfo object |
1295 | ||
1296 | < | the_torsions = new torsion_set[tot_torsions]; |
1297 | < | index = 0; |
1298 | < | offset = 0; |
1299 | < | molIndex = 0; |
1090 | < | for( i=0; i<n_components; i++ ){ |
1296 | > | info->atoms = the_atoms; |
1297 | > | info->molecules = the_molecules; |
1298 | > | info->nGlobalExcludes = 0; |
1299 | > | info->excludes = the_excludes; |
1300 | ||
1301 | < | for( j=0; j<components_nmol[i]; j++ ){ |
1301 | > | the_ff->setSimInfo( info ); |
1302 | ||
1303 | < | #ifdef IS_MPI |
1095 | < | if( mpiSim->getMyMolStart() <= molIndex && |
1096 | < | molIndex <= mpiSim->getMyMolEnd() ){ |
1097 | < | #endif // is_mpi |
1303 | > | } |
1304 | ||
1305 | < | for( k=0; k<comp_stamps[i]->getNTorsions(); k++ ){ |
1305 | > | void SimSetup::makeIntegrator( void ){ |
1306 | ||
1307 | < | current_torsion = comp_stamps[i]->getTorsion( k ); |
1308 | < | the_torsions[index].a = current_torsion->getA() + offset; |
1309 | < | the_torsions[index].b = current_torsion->getB() + offset; |
1310 | < | the_torsions[index].c = current_torsion->getC() + offset; |
1311 | < | the_torsions[index].d = current_torsion->getD() + offset; |
1307 | > | NVT<RealIntegrator>* myNVT = NULL; |
1308 | > | NPTi<RealIntegrator>* myNPTi = NULL; |
1309 | > | NPTf<RealIntegrator>* myNPTf = NULL; |
1310 | > | NPTim<RealIntegrator>* myNPTim = NULL; |
1311 | > | NPTfm<RealIntegrator>* myNPTfm = NULL; |
1312 | > | ZConstraint<NVE<RealIntegrator> >* myNVEZCons = NULL; |
1313 | > | |
1314 | > | cerr << "setting integrator" <<endl; |
1315 | > | |
1316 | > | switch( ensembleCase ){ |
1317 | ||
1318 | < | exI = the_torsions[index].a; |
1319 | < | exJ = the_torsions[index].d; |
1318 | > | case NVE_ENS: |
1319 | > | new NVE<RealIntegrator>( info, the_ff ); |
1320 | > | break; |
1321 | ||
1322 | < | |
1323 | < | // exclude_I must always be the smaller of the pair |
1324 | < | if( exI > exJ ){ |
1113 | < | tempEx = exI; |
1114 | < | exI = exJ; |
1115 | < | exJ = tempEx; |
1116 | < | } |
1322 | > | case NVT_ENS: |
1323 | > | myNVT = new NVT<RealIntegrator>( info, the_ff ); |
1324 | > | myNVT->setTargetTemp(globals->getTargetTemp()); |
1325 | ||
1326 | + | if (globals->haveTauThermostat()) |
1327 | + | myNVT->setTauThermostat(globals->getTauThermostat()); |
1328 | ||
1329 | < | #ifdef IS_MPI |
1330 | < | |
1331 | < | the_excludes[(index + tot_bonds + tot_bends)*2] = |
1332 | < | the_atoms[exI]->getGlobalIndex() + 1; |
1333 | < | the_excludes[(index + tot_bonds + tot_bends)*2 + 1] = |
1334 | < | the_atoms[exJ]->getGlobalIndex() + 1; |
1335 | < | |
1336 | < | #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 | < | |
1329 | > | else { |
1330 | > | sprintf( painCave.errMsg, |
1331 | > | "SimSetup error: If you use the NVT\n" |
1332 | > | " ensemble, you must set tauThermostat.\n"); |
1333 | > | painCave.isFatal = 1; |
1334 | > | simError(); |
1335 | > | } |
1336 | > | break; |
1337 | ||
1338 | < | // increment the index and repeat; |
1339 | < | index++; |
1340 | < | } |
1137 | < | offset += comp_stamps[i]->getNAtoms(); |
1338 | > | case NPTi_ENS: |
1339 | > | myNPTi = new NPTi<RealIntegrator>( info, the_ff ); |
1340 | > | myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1341 | ||
1342 | < | #ifdef IS_MPI |
1343 | < | } |
1344 | < | #endif //is_mpi |
1342 | > | if (globals->haveTargetPressure()) |
1343 | > | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1344 | > | else { |
1345 | > | sprintf( painCave.errMsg, |
1346 | > | "SimSetup error: If you use a constant pressure\n" |
1347 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1348 | > | painCave.isFatal = 1; |
1349 | > | simError(); |
1350 | > | } |
1351 | > | |
1352 | > | if( globals->haveTauThermostat() ) |
1353 | > | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1354 | > | else{ |
1355 | > | sprintf( painCave.errMsg, |
1356 | > | "SimSetup error: If you use an NPT\n" |
1357 | > | " ensemble, you must set tauThermostat.\n"); |
1358 | > | painCave.isFatal = 1; |
1359 | > | simError(); |
1360 | > | } |
1361 | ||
1362 | < | molIndex++; |
1362 | > | if( globals->haveTauBarostat() ) |
1363 | > | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1364 | > | else{ |
1365 | > | sprintf( painCave.errMsg, |
1366 | > | "SimSetup error: If you use an NPT\n" |
1367 | > | " ensemble, you must set tauBarostat.\n"); |
1368 | > | painCave.isFatal = 1; |
1369 | > | simError(); |
1370 | } | |
1371 | < | } |
1371 | > | break; |
1372 | ||
1373 | < | the_ff->initializeTorsions( the_torsions ); |
1374 | < | } |
1373 | > | case NPTf_ENS: |
1374 | > | myNPTf = new NPTf<RealIntegrator>( info, the_ff ); |
1375 | > | myNPTf->setTargetTemp( globals->getTargetTemp()); |
1376 | ||
1377 | < | void SimSetup::initFromBass( void ){ |
1377 | > | if (globals->haveTargetPressure()) |
1378 | > | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1379 | > | else { |
1380 | > | sprintf( painCave.errMsg, |
1381 | > | "SimSetup error: If you use a constant pressure\n" |
1382 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1383 | > | painCave.isFatal = 1; |
1384 | > | simError(); |
1385 | > | } |
1386 | ||
1387 | < | int i, j, k; |
1388 | < | int n_cells; |
1389 | < | double cellx, celly, cellz; |
1155 | < | double temp1, temp2, temp3; |
1156 | < | int n_per_extra; |
1157 | < | int n_extra; |
1158 | < | int have_extra, done; |
1159 | < | |
1160 | < | temp1 = (double)tot_nmol / 4.0; |
1161 | < | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
1162 | < | temp3 = ceil( temp2 ); |
1163 | < | |
1164 | < | have_extra =0; |
1165 | < | if( temp2 < temp3 ){ // we have a non-complete lattice |
1166 | < | have_extra =1; |
1167 | < | |
1168 | < | 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 ); |
1175 | < | |
1176 | < | if( n_per_extra > 4){ |
1387 | > | if( globals->haveTauThermostat() ) |
1388 | > | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1389 | > | else{ |
1390 | sprintf( painCave.errMsg, | |
1391 | < | "SimSetup error. There has been an error in constructing" |
1392 | < | " the non-complete lattice.\n" ); |
1391 | > | "SimSetup error: If you use an NPT\n" |
1392 | > | " ensemble, you must set tauThermostat.\n"); |
1393 | painCave.isFatal = 1; | |
1394 | simError(); | |
1395 | } | |
1183 | – | } |
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 | – | } |
1396 | ||
1397 | < | current_mol = 0; |
1398 | < | current_comp_mol = 0; |
1399 | < | current_comp = 0; |
1400 | < | current_atom_ndx = 0; |
1401 | < | |
1402 | < | for( i=0; i < n_cells ; i++ ){ |
1403 | < | for( j=0; j < n_cells; j++ ){ |
1404 | < | for( k=0; k < n_cells; k++ ){ |
1199 | < | |
1200 | < | makeElement( i * cellx, |
1201 | < | j * celly, |
1202 | < | k * cellz ); |
1203 | < | |
1204 | < | makeElement( i * cellx + 0.5 * cellx, |
1205 | < | j * celly + 0.5 * celly, |
1206 | < | k * cellz ); |
1207 | < | |
1208 | < | makeElement( i * cellx, |
1209 | < | j * celly + 0.5 * celly, |
1210 | < | k * cellz + 0.5 * cellz ); |
1211 | < | |
1212 | < | makeElement( i * cellx + 0.5 * cellx, |
1213 | < | j * celly, |
1214 | < | k * cellz + 0.5 * cellz ); |
1215 | < | } |
1397 | > | if( globals->haveTauBarostat() ) |
1398 | > | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1399 | > | else{ |
1400 | > | sprintf( painCave.errMsg, |
1401 | > | "SimSetup error: If you use an NPT\n" |
1402 | > | " ensemble, you must set tauBarostat.\n"); |
1403 | > | painCave.isFatal = 1; |
1404 | > | simError(); |
1405 | } | |
1406 | < | } |
1406 | > | break; |
1407 | > | |
1408 | > | case NPTim_ENS: |
1409 | > | myNPTim = new NPTim<RealIntegrator>( info, the_ff ); |
1410 | > | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1411 | ||
1412 | < | if( have_extra ){ |
1413 | < | done = 0; |
1414 | < | |
1415 | < | int start_ndx; |
1416 | < | for( i=0; i < (n_cells+1) && !done; i++ ){ |
1417 | < | for( j=0; j < (n_cells+1) && !done; j++ ){ |
1412 | > | if (globals->haveTargetPressure()) |
1413 | > | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1414 | > | else { |
1415 | > | sprintf( painCave.errMsg, |
1416 | > | "SimSetup error: If you use a constant pressure\n" |
1417 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1418 | > | painCave.isFatal = 1; |
1419 | > | simError(); |
1420 | > | } |
1421 | > | |
1422 | > | if( globals->haveTauThermostat() ) |
1423 | > | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1424 | > | else{ |
1425 | > | sprintf( painCave.errMsg, |
1426 | > | "SimSetup error: If you use an NPT\n" |
1427 | > | " ensemble, you must set tauThermostat.\n"); |
1428 | > | painCave.isFatal = 1; |
1429 | > | simError(); |
1430 | > | } |
1431 | ||
1432 | < | if( i < n_cells ){ |
1432 | > | if( globals->haveTauBarostat() ) |
1433 | > | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1434 | > | else{ |
1435 | > | sprintf( painCave.errMsg, |
1436 | > | "SimSetup error: If you use an NPT\n" |
1437 | > | " ensemble, you must set tauBarostat.\n"); |
1438 | > | painCave.isFatal = 1; |
1439 | > | simError(); |
1440 | > | } |
1441 | > | break; |
1442 | ||
1443 | < | if( j < n_cells ){ |
1444 | < | start_ndx = n_cells; |
1445 | < | } |
1231 | < | else start_ndx = 0; |
1232 | < | } |
1233 | < | else start_ndx = 0; |
1443 | > | case NPTfm_ENS: |
1444 | > | myNPTfm = new NPTfm<RealIntegrator>( info, the_ff ); |
1445 | > | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1446 | ||
1447 | < | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
1448 | < | |
1449 | < | makeElement( i * cellx, |
1450 | < | j * celly, |
1451 | < | k * cellz ); |
1452 | < | done = ( current_mol >= tot_nmol ); |
1453 | < | |
1454 | < | if( !done && n_per_extra > 1 ){ |
1243 | < | makeElement( i * cellx + 0.5 * cellx, |
1244 | < | j * celly + 0.5 * celly, |
1245 | < | k * cellz ); |
1246 | < | done = ( current_mol >= tot_nmol ); |
1247 | < | } |
1248 | < | |
1249 | < | 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 | < | } |
1255 | < | |
1256 | < | if( !done && n_per_extra > 3){ |
1257 | < | makeElement( i * cellx + 0.5 * cellx, |
1258 | < | j * celly, |
1259 | < | k * cellz + 0.5 * cellz ); |
1260 | < | done = ( current_mol >= tot_nmol ); |
1261 | < | } |
1262 | < | } |
1263 | < | } |
1447 | > | if (globals->haveTargetPressure()) |
1448 | > | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1449 | > | else { |
1450 | > | sprintf( painCave.errMsg, |
1451 | > | "SimSetup error: If you use a constant pressure\n" |
1452 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1453 | > | painCave.isFatal = 1; |
1454 | > | simError(); |
1455 | } | |
1456 | < | } |
1456 | > | |
1457 | > | if( globals->haveTauThermostat() ) |
1458 | > | myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1459 | > | else{ |
1460 | > | sprintf( painCave.errMsg, |
1461 | > | "SimSetup error: If you use an NPT\n" |
1462 | > | " ensemble, you must set tauThermostat.\n"); |
1463 | > | painCave.isFatal = 1; |
1464 | > | simError(); |
1465 | > | } |
1466 | ||
1467 | < | |
1468 | < | for( i=0; i<simnfo->n_atoms; i++ ){ |
1469 | < | simnfo->atoms[i]->set_vx( 0.0 ); |
1270 | < | simnfo->atoms[i]->set_vy( 0.0 ); |
1271 | < | simnfo->atoms[i]->set_vz( 0.0 ); |
1272 | < | } |
1273 | < | } |
1274 | < | |
1275 | < | void SimSetup::makeElement( double x, double y, double z ){ |
1276 | < | |
1277 | < | int k; |
1278 | < | AtomStamp* current_atom; |
1279 | < | DirectionalAtom* dAtom; |
1280 | < | double rotMat[3][3]; |
1281 | < | |
1282 | < | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
1283 | < | |
1284 | < | current_atom = comp_stamps[current_comp]->getAtom( k ); |
1285 | < | if( !current_atom->havePosition() ){ |
1467 | > | if( globals->haveTauBarostat() ) |
1468 | > | myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1469 | > | else{ |
1470 | sprintf( painCave.errMsg, | |
1471 | < | "SimSetup:initFromBass error.\n" |
1472 | < | "\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() ); |
1471 | > | "SimSetup error: If you use an NPT\n" |
1472 | > | " ensemble, you must set tauBarostat.\n"); |
1473 | painCave.isFatal = 1; | |
1474 | simError(); | |
1475 | } | |
1476 | + | break; |
1477 | + | |
1478 | + | case NVEZCONS_ENS: |
1479 | + | { |
1480 | ||
1481 | < | the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1482 | < | the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1483 | < | the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
1481 | > | if(globals->haveZConsTime()){ |
1482 | > | |
1483 | > | //add sample time of z-constraint into SimInfo's property list |
1484 | > | DoubleData* zconsTimeProp = new DoubleData(); |
1485 | > | zconsTimeProp->setID("zconstime"); |
1486 | > | zconsTimeProp->setData(globals->getZConsTime()); |
1487 | > | info->addProperty(zconsTimeProp); |
1488 | > | } |
1489 | > | else{ |
1490 | > | sprintf( painCave.errMsg, |
1491 | > | "ZConstraint error: If you use an ZConstraint\n" |
1492 | > | " , you must set sample time.\n"); |
1493 | > | painCave.isFatal = 1; |
1494 | > | simError(); |
1495 | > | } |
1496 | > | |
1497 | > | if(globals->haveIndexOfAllZConsMols()){ |
1498 | > | |
1499 | > | //add index of z-constraint molecules into SimInfo's property list |
1500 | > | vector<int> tempIndex = globals->getIndexOfAllZConsMols(); |
1501 | > | sort(tempIndex.begin(), tempIndex.end()); |
1502 | > | |
1503 | > | IndexData* zconsIndex = new IndexData(); |
1504 | > | zconsIndex->setID("zconsindex"); |
1505 | > | zconsIndex->setIndexData(tempIndex); |
1506 | > | info->addProperty(zconsIndex); |
1507 | > | } |
1508 | > | else{ |
1509 | > | sprintf( painCave.errMsg, |
1510 | > | "SimSetup error: If you use an ZConstraint\n" |
1511 | > | " , you must set index of z-constraint molecules.\n"); |
1512 | > | painCave.isFatal = 1; |
1513 | > | simError(); |
1514 | > | |
1515 | > | } |
1516 | ||
1517 | < | if( the_atoms[current_atom_ndx]->isDirectional() ){ |
1517 | > | //Determine the name of ouput file and add it into SimInfo's property list |
1518 | > | //Be careful, do not use inFileName, since it is a pointer which |
1519 | > | //point to a string at master node, and slave nodes do not contain that string |
1520 | > | |
1521 | > | string zconsOutput(info->finalName); |
1522 | > | |
1523 | > | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1524 | > | |
1525 | > | StringData* zconsFilename = new StringData(); |
1526 | > | zconsFilename->setID("zconsfilename"); |
1527 | > | zconsFilename->setData(zconsOutput); |
1528 | ||
1529 | < | dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1529 | > | info->addProperty(zconsFilename); |
1530 | > | |
1531 | > | myNVEZCons = new ZConstraint<NVE<RealIntegrator> >( info, the_ff ); |
1532 | > | |
1533 | > | break; |
1534 | > | } |
1535 | > | |
1536 | > | default: |
1537 | > | sprintf( painCave.errMsg, |
1538 | > | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1539 | > | painCave.isFatal = 1; |
1540 | > | simError(); |
1541 | > | } |
1542 | ||
1543 | < | rotMat[0][0] = 1.0; |
1306 | < | rotMat[0][1] = 0.0; |
1307 | < | rotMat[0][2] = 0.0; |
1543 | > | } |
1544 | ||
1545 | < | rotMat[1][0] = 0.0; |
1310 | < | rotMat[1][1] = 1.0; |
1311 | < | rotMat[1][2] = 0.0; |
1545 | > | void SimSetup::initFortran( void ){ |
1546 | ||
1547 | < | rotMat[2][0] = 0.0; |
1548 | < | rotMat[2][1] = 0.0; |
1549 | < | rotMat[2][2] = 1.0; |
1550 | < | |
1317 | < | dAtom->setA( rotMat ); |
1318 | < | } |
1319 | < | |
1320 | < | current_atom_ndx++; |
1547 | > | info->refreshSim(); |
1548 | > | |
1549 | > | if( !strcmp( info->mixingRule, "standard") ){ |
1550 | > | the_ff->initForceField( LB_MIXING_RULE ); |
1551 | } | |
1552 | + | else if( !strcmp( info->mixingRule, "explicit") ){ |
1553 | + | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1554 | + | } |
1555 | + | else{ |
1556 | + | sprintf( painCave.errMsg, |
1557 | + | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1558 | + | info->mixingRule ); |
1559 | + | painCave.isFatal = 1; |
1560 | + | simError(); |
1561 | + | } |
1562 | ||
1323 | – | current_mol++; |
1324 | – | current_comp_mol++; |
1563 | ||
1564 | < | if( current_comp_mol >= components_nmol[current_comp] ){ |
1564 | > | #ifdef IS_MPI |
1565 | > | strcpy( checkPointMsg, |
1566 | > | "Successfully intialized the mixingRule for Fortran." ); |
1567 | > | MPIcheckPoint(); |
1568 | > | #endif // is_mpi |
1569 | ||
1328 | – | current_comp_mol = 0; |
1329 | – | current_comp++; |
1330 | – | } |
1570 | } |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |