# | 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 "ReadWrite.hpp" |
9 | #include "parse_me.h" | |
10 | #include "Integrator.hpp" | |
11 | #include "simError.h" | |
# | Line 14 | Line 17 | |
17 | ||
18 | // some defines for ensemble and Forcefield cases | |
19 | ||
20 | < | #define NVE_ENS 0 |
21 | < | #define NVT_ENS 1 |
22 | < | #define NPTi_ENS 2 |
23 | < | #define NPTf_ENS 3 |
20 | > | #define NVE_ENS 0 |
21 | > | #define NVT_ENS 1 |
22 | > | #define NPTi_ENS 2 |
23 | > | #define NPTf_ENS 3 |
24 | > | #define NPTim_ENS 4 |
25 | > | #define NPTfm_ENS 5 |
26 | ||
22 | – | |
27 | #define FF_DUFF 0 | |
28 | #define FF_LJ 1 | |
29 | + | #define FF_EAM 2 |
30 | ||
31 | + | using namespace std; |
32 | ||
33 | SimSetup::SimSetup(){ | |
34 | + | |
35 | + | isInfoArray = 0; |
36 | + | nInfo = 1; |
37 | + | |
38 | stamps = new MakeStamps(); | |
39 | globals = new Globals(); | |
40 | ||
41 | + | |
42 | #ifdef IS_MPI | |
43 | strcpy( checkPointMsg, "SimSetup creation successful" ); | |
44 | MPIcheckPoint(); | |
# | Line 39 | Line 50 | SimSetup::~SimSetup(){ | |
50 | delete globals; | |
51 | } | |
52 | ||
53 | + | void SimSetup::setSimInfo( SimInfo* the_info, int theNinfo ) { |
54 | + | info = the_info; |
55 | + | nInfo = theNinfo; |
56 | + | isInfoArray = 1; |
57 | + | } |
58 | + | |
59 | + | |
60 | void SimSetup::parseFile( char* fileName ){ | |
61 | ||
62 | #ifdef IS_MPI | |
# | Line 74 | Line 92 | void SimSetup::receiveParse(void){ | |
92 | ||
93 | #endif // is_mpi | |
94 | ||
95 | < | void SimSetup::createSim( void ){ |
95 | > | void SimSetup::createSim(void){ |
96 | ||
79 | – | MakeStamps *the_stamps; |
80 | – | Globals* the_globals; |
97 | int i, j, k, globalAtomIndex; | |
98 | ||
99 | < | int ensembleCase; |
84 | < | int ffCase; |
85 | < | |
86 | < | ensembleCase = -1; |
87 | < | ffCase = -1; |
99 | > | // gather all of the information from the Bass file |
100 | ||
101 | < | // get the stamps and globals; |
90 | < | the_stamps = stamps; |
91 | < | the_globals = globals; |
101 | > | gatherInfo(); |
102 | ||
103 | < | // set the easy ones first |
94 | < | simnfo->target_temp = the_globals->getTargetTemp(); |
95 | < | simnfo->dt = the_globals->getDt(); |
96 | < | simnfo->run_time = the_globals->getRunTime(); |
103 | > | // creation of complex system objects |
104 | ||
105 | < | // get the ones we know are there, yet still may need some work. |
99 | < | n_components = the_globals->getNComponents(); |
100 | < | strcpy( force_field, the_globals->getForceField() ); |
105 | > | sysObjectsCreation(); |
106 | ||
107 | < | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
103 | < | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
104 | < | else{ |
105 | < | sprintf( painCave.errMsg, |
106 | < | "SimSetup Error. Unrecognized force field -> %s\n", |
107 | < | force_field ); |
108 | < | painCave.isFatal = 1; |
109 | < | simError(); |
110 | < | } |
107 | > | // check on the post processing info |
108 | ||
109 | < | // get the ensemble: |
113 | < | strcpy( ensemble, the_globals->getEnsemble() ); |
109 | > | finalInfoCheck(); |
110 | ||
111 | < | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
116 | < | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
117 | < | else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
118 | < | ensembleCase = NPTi_ENS; |
119 | < | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
120 | < | else{ |
121 | < | sprintf( painCave.errMsg, |
122 | < | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
123 | < | "reverting to NVE for this simulation.\n", |
124 | < | ensemble ); |
125 | < | painCave.isFatal = 0; |
126 | < | simError(); |
127 | < | strcpy( ensemble, "NVE" ); |
128 | < | ensembleCase = NVE_ENS; |
129 | < | } |
130 | < | strcpy( simnfo->ensemble, ensemble ); |
111 | > | // initialize the system coordinates |
112 | ||
113 | + | if( !isInfoArray ) initSystemCoords(); |
114 | ||
115 | < | // if( !strcasecmp( ensemble, "NPT" ) ) { |
134 | < | // the_extendedsystem = new ExtendedSystem( simnfo ); |
135 | < | // the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
136 | < | // if (the_globals->haveTargetPressure()) |
137 | < | // the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
138 | < | // else { |
139 | < | // sprintf( painCave.errMsg, |
140 | < | // "SimSetup error: If you use the constant pressure\n" |
141 | < | // " ensemble, you must set targetPressure.\n" |
142 | < | // " This was found in the BASS file.\n"); |
143 | < | // painCave.isFatal = 1; |
144 | < | // simError(); |
145 | < | // } |
115 | > | // make the output filenames |
116 | ||
117 | < | // if (the_globals->haveTauThermostat()) |
118 | < | // the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
119 | < | // else if (the_globals->haveQmass()) |
120 | < | // the_extendedsystem->setQmass(the_globals->getQmass()); |
121 | < | // else { |
122 | < | // sprintf( painCave.errMsg, |
123 | < | // "SimSetup error: If you use one of the constant temperature\n" |
124 | < | // " ensembles, you must set either tauThermostat or qMass.\n" |
125 | < | // " Neither of these was found in the BASS file.\n"); |
156 | < | // painCave.isFatal = 1; |
157 | < | // simError(); |
158 | < | // } |
117 | > | makeOutNames(); |
118 | > | |
119 | > | // make the integrator |
120 | > | |
121 | > | makeIntegrator(); |
122 | > | |
123 | > | #ifdef IS_MPI |
124 | > | mpiSim->mpiRefresh(); |
125 | > | #endif |
126 | ||
127 | < | // if (the_globals->haveTauBarostat()) |
161 | < | // the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
162 | < | // else { |
163 | < | // sprintf( painCave.errMsg, |
164 | < | // "SimSetup error: If you use the constant pressure\n" |
165 | < | // " ensemble, you must set tauBarostat.\n" |
166 | < | // " This was found in the BASS file.\n"); |
167 | < | // painCave.isFatal = 1; |
168 | < | // simError(); |
169 | < | // } |
127 | > | // initialize the Fortran |
128 | ||
129 | < | // } else if ( !strcasecmp( ensemble, "NVT") ) { |
172 | < | // the_extendedsystem = new ExtendedSystem( simnfo ); |
173 | < | // the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
129 | > | initFortran(); |
130 | ||
175 | – | // if (the_globals->haveTauThermostat()) |
176 | – | // the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
177 | – | // else if (the_globals->haveQmass()) |
178 | – | // the_extendedsystem->setQmass(the_globals->getQmass()); |
179 | – | // else { |
180 | – | // sprintf( painCave.errMsg, |
181 | – | // "SimSetup error: If you use one of the constant temperature\n" |
182 | – | // " ensembles, you must set either tauThermostat or qMass.\n" |
183 | – | // " Neither of these was found in the BASS file.\n"); |
184 | – | // painCave.isFatal = 1; |
185 | – | // simError(); |
186 | – | // } |
131 | ||
188 | – | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
189 | – | simnfo->usePBC = the_globals->getPBC(); |
190 | – | |
191 | – | int usesDipoles = 0; |
192 | – | switch( ffCase ){ |
132 | ||
133 | < | case FF_DUFF: |
195 | < | the_ff = new DUFF(); |
196 | < | usesDipoles = 1; |
197 | < | break; |
133 | > | } |
134 | ||
199 | – | case FF_LJ: |
200 | – | the_ff = new LJFF(); |
201 | – | break; |
135 | ||
136 | < | default: |
204 | < | sprintf( painCave.errMsg, |
205 | < | "SimSetup Error. Unrecognized force field in case statement.\n"); |
206 | < | painCave.isFatal = 1; |
207 | < | simError(); |
208 | < | } |
136 | > | void SimSetup::makeMolecules( void ){ |
137 | ||
138 | < | #ifdef IS_MPI |
139 | < | strcpy( checkPointMsg, "ForceField creation successful" ); |
140 | < | MPIcheckPoint(); |
141 | < | #endif // is_mpi |
138 | > | int k,l; |
139 | > | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
140 | > | molInit molInfo; |
141 | > | DirectionalAtom* dAtom; |
142 | > | LinkedAssign* extras; |
143 | > | LinkedAssign* current_extra; |
144 | > | AtomStamp* currentAtom; |
145 | > | BondStamp* currentBond; |
146 | > | BendStamp* currentBend; |
147 | > | TorsionStamp* currentTorsion; |
148 | ||
149 | < | // get the components and calculate the tot_nMol and indvidual n_mol |
150 | < | the_components = the_globals->getComponents(); |
151 | < | components_nmol = new int[n_components]; |
218 | < | comp_stamps = new MoleculeStamp*[n_components]; |
149 | > | bond_pair* theBonds; |
150 | > | bend_set* theBends; |
151 | > | torsion_set* theTorsions; |
152 | ||
153 | < | if( !the_globals->haveNMol() ){ |
154 | < | // we don't have the total number of molecules, so we assume it is |
222 | < | // given in each component |
153 | > | |
154 | > | //init the forceField paramters |
155 | ||
156 | < | tot_nmol = 0; |
225 | < | for( i=0; i<n_components; i++ ){ |
156 | > | the_ff->readParams(); |
157 | ||
158 | < | if( !the_components[i]->haveNMol() ){ |
159 | < | // we have a problem |
229 | < | sprintf( painCave.errMsg, |
230 | < | "SimSetup Error. No global NMol or component NMol" |
231 | < | " given. Cannot calculate the number of atoms.\n" ); |
232 | < | painCave.isFatal = 1; |
233 | < | simError(); |
234 | < | } |
158 | > | |
159 | > | // init the atoms |
160 | ||
161 | < | tot_nmol += the_components[i]->getNMol(); |
162 | < | components_nmol[i] = the_components[i]->getNMol(); |
163 | < | } |
239 | < | } |
240 | < | else{ |
241 | < | sprintf( painCave.errMsg, |
242 | < | "SimSetup error.\n" |
243 | < | "\tSorry, the ability to specify total" |
244 | < | " nMols and then give molfractions in the components\n" |
245 | < | "\tis not currently supported." |
246 | < | " Please give nMol in the components.\n" ); |
247 | < | painCave.isFatal = 1; |
248 | < | simError(); |
161 | > | double ux, uy, uz, u, uSqr; |
162 | > | |
163 | > | for(k=0; k<nInfo; k++){ |
164 | ||
165 | + | the_ff->setSimInfo( &(info[k]) ); |
166 | + | |
167 | + | atomOffset = 0; |
168 | + | excludeOffset = 0; |
169 | + | for(i=0; i<info[k].n_mol; i++){ |
170 | ||
171 | < | // tot_nmol = the_globals->getNMol(); |
171 | > | stampID = info[k].molecules[i].getStampID(); |
172 | > | |
173 | > | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
174 | > | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
175 | > | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
176 | > | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
177 | > | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
178 | > | |
179 | > | molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
180 | > | molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
181 | > | molInfo.myBonds = new Bond*[molInfo.nBonds]; |
182 | > | molInfo.myBends = new Bend*[molInfo.nBends]; |
183 | > | molInfo.myTorsions = new Torsion*[molInfo.nTorsions]; |
184 | > | |
185 | > | theBonds = new bond_pair[molInfo.nBonds]; |
186 | > | theBends = new bend_set[molInfo.nBends]; |
187 | > | theTorsions = new torsion_set[molInfo.nTorsions]; |
188 | ||
189 | < | // //we have the total number of molecules, now we check for molfractions |
254 | < | // for( i=0; i<n_components; i++ ){ |
189 | > | // make the Atoms |
190 | ||
191 | < | // if( !the_components[i]->haveMolFraction() ){ |
191 | > | for(j=0; j<molInfo.nAtoms; j++){ |
192 | > | |
193 | > | currentAtom = comp_stamps[stampID]->getAtom( j ); |
194 | > | if( currentAtom->haveOrientation() ){ |
195 | ||
196 | < | // if( !the_components[i]->haveNMol() ){ |
197 | < | // //we have a problem |
198 | < | // std::cerr << "SimSetup error. Neither molFraction nor " |
199 | < | // << " nMol was given in component |
196 | > | dAtom = new DirectionalAtom( (j + atomOffset), |
197 | > | info[k].getConfiguration() ); |
198 | > | info[k].n_oriented++; |
199 | > | molInfo.myAtoms[j] = dAtom; |
200 | ||
201 | + | ux = currentAtom->getOrntX(); |
202 | + | uy = currentAtom->getOrntY(); |
203 | + | uz = currentAtom->getOrntZ(); |
204 | + | |
205 | + | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
206 | + | |
207 | + | u = sqrt( uSqr ); |
208 | + | ux = ux / u; |
209 | + | uy = uy / u; |
210 | + | uz = uz / u; |
211 | + | |
212 | + | dAtom->setSUx( ux ); |
213 | + | dAtom->setSUy( uy ); |
214 | + | dAtom->setSUz( uz ); |
215 | } | |
216 | < | |
216 | > | else{ |
217 | > | molInfo.myAtoms[j] = new GeneralAtom( (j + atomOffset), |
218 | > | info[k].getConfiguration() ); |
219 | > | } |
220 | > | molInfo.myAtoms[j]->setType( currentAtom->getType() ); |
221 | > | |
222 | #ifdef IS_MPI | |
223 | < | strcpy( checkPointMsg, "Have the number of components" ); |
224 | < | MPIcheckPoint(); |
223 | > | |
224 | > | molInfo.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
225 | > | |
226 | #endif // is_mpi | |
227 | < | |
228 | < | // make an array of molecule stamps that match the components used. |
229 | < | // also extract the used stamps out into a separate linked list |
230 | < | |
273 | < | simnfo->nComponents = n_components; |
274 | < | simnfo->componentsNmol = components_nmol; |
275 | < | simnfo->compStamps = comp_stamps; |
276 | < | simnfo->headStamp = new LinkedMolStamp(); |
277 | < | |
278 | < | char* id; |
279 | < | LinkedMolStamp* headStamp = simnfo->headStamp; |
280 | < | LinkedMolStamp* currentStamp = NULL; |
281 | < | for( i=0; i<n_components; i++ ){ |
282 | < | |
283 | < | id = the_components[i]->getType(); |
284 | < | comp_stamps[i] = NULL; |
285 | < | |
286 | < | // check to make sure the component isn't already in the list |
287 | < | |
288 | < | comp_stamps[i] = headStamp->match( id ); |
289 | < | if( comp_stamps[i] == NULL ){ |
227 | > | } |
228 | > | |
229 | > | // make the bonds |
230 | > | for(j=0; j<molInfo.nBonds; j++){ |
231 | ||
232 | < | // extract the component from the list; |
233 | < | |
234 | < | currentStamp = the_stamps->extractMolStamp( id ); |
294 | < | if( currentStamp == NULL ){ |
295 | < | sprintf( painCave.errMsg, |
296 | < | "SimSetup error: Component \"%s\" was not found in the " |
297 | < | "list of declared molecules\n", |
298 | < | id ); |
299 | < | painCave.isFatal = 1; |
300 | < | simError(); |
301 | < | } |
302 | < | |
303 | < | headStamp->add( currentStamp ); |
304 | < | comp_stamps[i] = headStamp->match( id ); |
305 | < | } |
306 | < | } |
307 | < | |
308 | < | #ifdef IS_MPI |
309 | < | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
310 | < | MPIcheckPoint(); |
311 | < | #endif // is_mpi |
232 | > | currentBond = comp_stamps[stampID]->getBond( j ); |
233 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
234 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
235 | ||
236 | < | |
237 | < | |
315 | < | |
316 | < | // caclulate the number of atoms, bonds, bends and torsions |
317 | < | |
318 | < | tot_atoms = 0; |
319 | < | tot_bonds = 0; |
320 | < | tot_bends = 0; |
321 | < | tot_torsions = 0; |
322 | < | for( i=0; i<n_components; i++ ){ |
323 | < | |
324 | < | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
325 | < | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
326 | < | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
327 | < | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
328 | < | } |
329 | < | |
330 | < | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
331 | < | |
332 | < | simnfo->n_atoms = tot_atoms; |
333 | < | simnfo->n_bonds = tot_bonds; |
334 | < | simnfo->n_bends = tot_bends; |
335 | < | simnfo->n_torsions = tot_torsions; |
336 | < | simnfo->n_SRI = tot_SRI; |
337 | < | simnfo->n_mol = tot_nmol; |
236 | > | exI = theBonds[j].a; |
237 | > | exJ = theBonds[j].b; |
238 | ||
239 | < | simnfo->molMembershipArray = new int[tot_atoms]; |
240 | < | |
239 | > | // exclude_I must always be the smaller of the pair |
240 | > | if( exI > exJ ){ |
241 | > | tempEx = exI; |
242 | > | exI = exJ; |
243 | > | exJ = tempEx; |
244 | > | } |
245 | #ifdef IS_MPI | |
246 | < | |
247 | < | // divide the molecules among processors here. |
246 | > | tempEx = exI; |
247 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
248 | > | tempEx = exJ; |
249 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
250 | ||
251 | < | mpiSim = new mpiSimulation( simnfo ); |
251 | > | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
252 | > | #else // isn't MPI |
253 | ||
254 | < | globalIndex = mpiSim->divideLabor(); |
255 | < | |
256 | < | // set up the local variables |
254 | > | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
255 | > | #endif //is_mpi |
256 | > | } |
257 | > | excludeOffset += molInfo.nBonds; |
258 | > | |
259 | > | //make the bends |
260 | > | for(j=0; j<molInfo.nBends; j++){ |
261 | ||
262 | < | int localMol, allMol; |
263 | < | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
264 | < | |
265 | < | int* mol2proc = mpiSim->getMolToProcMap(); |
355 | < | int* molCompType = mpiSim->getMolComponentType(); |
262 | > | currentBend = comp_stamps[stampID]->getBend( j ); |
263 | > | theBends[j].a = currentBend->getA() + atomOffset; |
264 | > | theBends[j].b = currentBend->getB() + atomOffset; |
265 | > | theBends[j].c = currentBend->getC() + atomOffset; |
266 | ||
267 | < | allMol = 0; |
268 | < | localMol = 0; |
269 | < | local_atoms = 0; |
270 | < | local_bonds = 0; |
271 | < | local_bends = 0; |
272 | < | local_torsions = 0; |
273 | < | globalAtomIndex = 0; |
274 | < | |
275 | < | |
276 | < | for( i=0; i<n_components; i++ ){ |
277 | < | |
278 | < | for( j=0; j<components_nmol[i]; j++ ){ |
267 | > | if( currentBend->haveExtras() ){ |
268 | > | |
269 | > | extras = currentBend->getExtras(); |
270 | > | current_extra = extras; |
271 | > | |
272 | > | while( current_extra != NULL ){ |
273 | > | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
274 | > | |
275 | > | switch( current_extra->getType() ){ |
276 | > | |
277 | > | case 0: |
278 | > | theBends[j].ghost = |
279 | > | current_extra->getInt() + atomOffset; |
280 | > | theBends[j].isGhost = 1; |
281 | > | break; |
282 | > | |
283 | > | case 1: |
284 | > | theBends[j].ghost = |
285 | > | (int)current_extra->getDouble() + atomOffset; |
286 | > | theBends[j].isGhost = 1; |
287 | > | break; |
288 | > | |
289 | > | default: |
290 | > | sprintf( painCave.errMsg, |
291 | > | "SimSetup Error: ghostVectorSource was neither a " |
292 | > | "double nor an int.\n" |
293 | > | "-->Bend[%d] in %s\n", |
294 | > | j, comp_stamps[stampID]->getID() ); |
295 | > | painCave.isFatal = 1; |
296 | > | simError(); |
297 | > | } |
298 | > | } |
299 | ||
300 | < | if( mol2proc[allMol] == worldRank ){ |
301 | < | |
302 | < | local_atoms += comp_stamps[i]->getNAtoms(); |
303 | < | local_bonds += comp_stamps[i]->getNBonds(); |
304 | < | local_bends += comp_stamps[i]->getNBends(); |
305 | < | local_torsions += comp_stamps[i]->getNTorsions(); |
306 | < | localMol++; |
307 | < | } |
308 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
379 | < | simnfo->molMembershipArray[globalAtomIndex] = allMol; |
380 | < | globalAtomIndex++; |
300 | > | else{ |
301 | > | |
302 | > | sprintf( painCave.errMsg, |
303 | > | "SimSetup Error: unhandled bend assignment:\n" |
304 | > | " -->%s in Bend[%d] in %s\n", |
305 | > | current_extra->getlhs(), |
306 | > | j, comp_stamps[stampID]->getID() ); |
307 | > | painCave.isFatal = 1; |
308 | > | simError(); |
309 | } | |
310 | < | |
311 | < | allMol++; |
310 | > | |
311 | > | current_extra = current_extra->getNext(); |
312 | } | |
313 | } | |
386 | – | local_SRI = local_bonds + local_bends + local_torsions; |
314 | ||
315 | < | simnfo->n_atoms = mpiSim->getMyNlocal(); |
315 | > | if( !theBends[j].isGhost ){ |
316 | > | |
317 | > | exI = theBends[j].a; |
318 | > | exJ = theBends[j].c; |
319 | > | } |
320 | > | else{ |
321 | > | |
322 | > | exI = theBends[j].a; |
323 | > | exJ = theBends[j].b; |
324 | > | } |
325 | ||
326 | < | if( local_atoms != simnfo->n_atoms ){ |
327 | < | sprintf( painCave.errMsg, |
328 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
329 | < | " localAtom (%d) are not equal.\n", |
330 | < | simnfo->n_atoms, |
395 | < | local_atoms ); |
396 | < | painCave.isFatal = 1; |
397 | < | simError(); |
326 | > | // exclude_I must always be the smaller of the pair |
327 | > | if( exI > exJ ){ |
328 | > | tempEx = exI; |
329 | > | exI = exJ; |
330 | > | exJ = tempEx; |
331 | } | |
332 | < | |
333 | < | simnfo->n_bonds = local_bonds; |
334 | < | simnfo->n_bends = local_bends; |
335 | < | simnfo->n_torsions = local_torsions; |
336 | < | simnfo->n_SRI = local_SRI; |
337 | < | simnfo->n_mol = localMol; |
338 | < | |
339 | < | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
340 | < | MPIcheckPoint(); |
332 | > | #ifdef IS_MPI |
333 | > | tempEx = exI; |
334 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
335 | > | tempEx = exJ; |
336 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
337 | > | |
338 | > | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
339 | > | #else // isn't MPI |
340 | > | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
341 | > | #endif //is_mpi |
342 | > | } |
343 | > | excludeOffset += molInfo.nBends; |
344 | > | |
345 | > | for(j=0; j<molInfo.nTorsions; j++){ |
346 | ||
347 | + | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
348 | + | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
349 | + | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
350 | + | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
351 | + | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
352 | ||
353 | < | #endif // is_mpi |
353 | > | exI = theTorsions[j].a; |
354 | > | exJ = theTorsions[j].d; |
355 | ||
356 | < | |
357 | < | // create the atom and short range interaction arrays |
358 | < | |
359 | < | Atom::createArrays(simnfo->n_atoms); |
360 | < | the_atoms = new Atom*[simnfo->n_atoms]; |
361 | < | the_molecules = new Molecule[simnfo->n_mol]; |
418 | < | int molIndex; |
419 | < | |
420 | < | // initialize the molecule's stampID's |
421 | < | |
356 | > | // exclude_I must always be the smaller of the pair |
357 | > | if( exI > exJ ){ |
358 | > | tempEx = exI; |
359 | > | exI = exJ; |
360 | > | exJ = tempEx; |
361 | > | } |
362 | #ifdef IS_MPI | |
363 | + | tempEx = exI; |
364 | + | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
365 | + | tempEx = exJ; |
366 | + | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
367 | ||
368 | < | |
369 | < | molIndex = 0; |
370 | < | for(i=0; i<mpiSim->getTotNmol(); i++){ |
371 | < | |
372 | < | if(mol2proc[i] == worldRank ){ |
373 | < | the_molecules[molIndex].setStampID( molCompType[i] ); |
374 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
375 | < | the_molecules[molIndex].setGlobalIndex( i ); |
376 | < | molIndex++; |
377 | < | } |
378 | < | } |
368 | > | info[k].excludes[j+excludeOffset]->setPair( exI, exJ ); |
369 | > | #else // isn't MPI |
370 | > | info[k].excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
371 | > | #endif //is_mpi |
372 | > | } |
373 | > | excludeOffset += molInfo.nTorsions; |
374 | > | |
375 | > | |
376 | > | // send the arrays off to the forceField for init. |
377 | > | |
378 | > | the_ff->initializeAtoms( molInfo.nAtoms, molInfo.myAtoms ); |
379 | > | the_ff->initializeBonds( molInfo.nBonds, molInfo.myBonds, theBonds ); |
380 | > | the_ff->initializeBends( molInfo.nBends, molInfo.myBends, theBends ); |
381 | > | the_ff->initializeTorsions( molInfo.nTorsions, molInfo.myTorsions, theTorsions ); |
382 | > | |
383 | > | |
384 | > | info[k].molecules[i].initialize( molInfo ); |
385 | ||
386 | < | #else // is_mpi |
387 | < | |
388 | < | molIndex = 0; |
389 | < | globalAtomIndex = 0; |
390 | < | for(i=0; i<n_components; i++){ |
441 | < | for(j=0; j<components_nmol[i]; j++ ){ |
442 | < | the_molecules[molIndex].setStampID( i ); |
443 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
444 | < | the_molecules[molIndex].setGlobalIndex( molIndex ); |
445 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
446 | < | simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
447 | < | globalAtomIndex++; |
448 | < | } |
449 | < | molIndex++; |
386 | > | |
387 | > | atomOffset += molInfo.nAtoms; |
388 | > | delete[] theBonds; |
389 | > | delete[] theBends; |
390 | > | delete[] theTorsions; |
391 | } | |
392 | } | |
393 | < | |
394 | < | |
393 | > | |
394 | > | #ifdef IS_MPI |
395 | > | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
396 | > | MPIcheckPoint(); |
397 | #endif // is_mpi | |
398 | + | |
399 | + | // clean up the forcefield |
400 | ||
401 | + | the_ff->calcRcut(); |
402 | + | the_ff->cleanMe(); |
403 | + | |
404 | + | } |
405 | ||
406 | < | if( simnfo->n_SRI ){ |
458 | < | |
459 | < | Exclude::createArray(simnfo->n_SRI); |
460 | < | the_excludes = new Exclude*[simnfo->n_SRI]; |
461 | < | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
462 | < | simnfo->globalExcludes = new int; |
463 | < | simnfo->n_exclude = simnfo->n_SRI; |
464 | < | } |
465 | < | else{ |
466 | < | |
467 | < | Exclude::createArray( 1 ); |
468 | < | the_excludes = new Exclude*; |
469 | < | the_excludes[0] = new Exclude(0); |
470 | < | the_excludes[0]->setPair( 0,0 ); |
471 | < | simnfo->globalExcludes = new int; |
472 | < | simnfo->globalExcludes[0] = 0; |
473 | < | simnfo->n_exclude = 0; |
474 | < | } |
406 | > | void SimSetup::initFromBass( void ){ |
407 | ||
408 | < | // set the arrays into the SimInfo object |
408 | > | int i, j, k; |
409 | > | int n_cells; |
410 | > | double cellx, celly, cellz; |
411 | > | double temp1, temp2, temp3; |
412 | > | int n_per_extra; |
413 | > | int n_extra; |
414 | > | int have_extra, done; |
415 | ||
416 | < | simnfo->atoms = the_atoms; |
417 | < | simnfo->molecules = the_molecules; |
418 | < | simnfo->nGlobalExcludes = 0; |
419 | < | simnfo->excludes = the_excludes; |
416 | > | double vel[3]; |
417 | > | vel[0] = 0.0; |
418 | > | vel[1] = 0.0; |
419 | > | vel[2] = 0.0; |
420 | ||
421 | + | temp1 = (double)tot_nmol / 4.0; |
422 | + | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
423 | + | temp3 = ceil( temp2 ); |
424 | ||
425 | < | // get some of the tricky things that may still be in the globals |
425 | > | have_extra =0; |
426 | > | if( temp2 < temp3 ){ // we have a non-complete lattice |
427 | > | have_extra =1; |
428 | ||
429 | < | double boxVector[3]; |
430 | < | if( the_globals->haveBox() ){ |
431 | < | boxVector[0] = the_globals->getBox(); |
432 | < | boxVector[1] = the_globals->getBox(); |
433 | < | boxVector[2] = the_globals->getBox(); |
434 | < | |
435 | < | simnfo->setBox( boxVector ); |
493 | < | } |
494 | < | else if( the_globals->haveDensity() ){ |
429 | > | n_cells = (int)temp3 - 1; |
430 | > | cellx = info[0].boxL[0] / temp3; |
431 | > | celly = info[0].boxL[1] / temp3; |
432 | > | cellz = info[0].boxL[2] / temp3; |
433 | > | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
434 | > | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
435 | > | n_per_extra = (int)ceil( temp1 ); |
436 | ||
437 | < | double vol; |
497 | < | vol = (double)tot_nmol / the_globals->getDensity(); |
498 | < | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
499 | < | boxVector[1] = boxVector[0]; |
500 | < | boxVector[2] = boxVector[0]; |
501 | < | |
502 | < | simnfo->setBox( boxVector ); |
503 | < | } |
504 | < | else{ |
505 | < | if( !the_globals->haveBoxX() ){ |
437 | > | if( n_per_extra > 4){ |
438 | sprintf( painCave.errMsg, | |
439 | < | "SimSetup error, no periodic BoxX size given.\n" ); |
439 | > | "SimSetup error. There has been an error in constructing" |
440 | > | " the non-complete lattice.\n" ); |
441 | painCave.isFatal = 1; | |
442 | simError(); | |
443 | } | |
444 | < | boxVector[0] = the_globals->getBoxX(); |
444 | > | } |
445 | > | else{ |
446 | > | n_cells = (int)temp3; |
447 | > | cellx = info[0].boxL[0] / temp3; |
448 | > | celly = info[0].boxL[1] / temp3; |
449 | > | cellz = info[0].boxL[2] / temp3; |
450 | > | } |
451 | ||
452 | < | if( !the_globals->haveBoxY() ){ |
453 | < | sprintf( painCave.errMsg, |
454 | < | "SimSetup error, no periodic BoxY size given.\n" ); |
455 | < | painCave.isFatal = 1; |
517 | < | simError(); |
518 | < | } |
519 | < | boxVector[1] = the_globals->getBoxY(); |
452 | > | current_mol = 0; |
453 | > | current_comp_mol = 0; |
454 | > | current_comp = 0; |
455 | > | current_atom_ndx = 0; |
456 | ||
457 | < | if( !the_globals->haveBoxZ() ){ |
458 | < | sprintf( painCave.errMsg, |
459 | < | "SimSetup error, no periodic BoxZ size given.\n" ); |
460 | < | painCave.isFatal = 1; |
461 | < | simError(); |
457 | > | for( i=0; i < n_cells ; i++ ){ |
458 | > | for( j=0; j < n_cells; j++ ){ |
459 | > | for( k=0; k < n_cells; k++ ){ |
460 | > | |
461 | > | makeElement( i * cellx, |
462 | > | j * celly, |
463 | > | k * cellz ); |
464 | > | |
465 | > | makeElement( i * cellx + 0.5 * cellx, |
466 | > | j * celly + 0.5 * celly, |
467 | > | k * cellz ); |
468 | > | |
469 | > | makeElement( i * cellx, |
470 | > | j * celly + 0.5 * celly, |
471 | > | k * cellz + 0.5 * cellz ); |
472 | > | |
473 | > | makeElement( i * cellx + 0.5 * cellx, |
474 | > | j * celly, |
475 | > | k * cellz + 0.5 * cellz ); |
476 | > | } |
477 | } | |
478 | < | boxVector[2] = the_globals->getBoxZ(); |
478 | > | } |
479 | ||
480 | < | simnfo->setBox( boxVector ); |
480 | > | if( have_extra ){ |
481 | > | done = 0; |
482 | > | |
483 | > | int start_ndx; |
484 | > | for( i=0; i < (n_cells+1) && !done; i++ ){ |
485 | > | for( j=0; j < (n_cells+1) && !done; j++ ){ |
486 | > | |
487 | > | if( i < n_cells ){ |
488 | > | |
489 | > | if( j < n_cells ){ |
490 | > | start_ndx = n_cells; |
491 | > | } |
492 | > | else start_ndx = 0; |
493 | } | |
494 | + | else start_ndx = 0; |
495 | ||
496 | < | #ifdef IS_MPI |
533 | < | strcpy( checkPointMsg, "Box size set up" ); |
534 | < | MPIcheckPoint(); |
535 | < | #endif // is_mpi |
496 | > | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
497 | ||
498 | + | makeElement( i * cellx, |
499 | + | j * celly, |
500 | + | k * cellz ); |
501 | + | done = ( current_mol >= tot_nmol ); |
502 | ||
503 | < | // initialize the arrays |
503 | > | if( !done && n_per_extra > 1 ){ |
504 | > | makeElement( i * cellx + 0.5 * cellx, |
505 | > | j * celly + 0.5 * celly, |
506 | > | k * cellz ); |
507 | > | done = ( current_mol >= tot_nmol ); |
508 | > | } |
509 | ||
510 | < | the_ff->setSimInfo( simnfo ); |
510 | > | if( !done && n_per_extra > 2){ |
511 | > | makeElement( i * cellx, |
512 | > | j * celly + 0.5 * celly, |
513 | > | k * cellz + 0.5 * cellz ); |
514 | > | done = ( current_mol >= tot_nmol ); |
515 | > | } |
516 | ||
517 | < | makeMolecules(); |
518 | < | simnfo->identArray = new int[simnfo->n_atoms]; |
519 | < | for(i=0; i<simnfo->n_atoms; i++){ |
520 | < | simnfo->identArray[i] = the_atoms[i]->getIdent(); |
517 | > | if( !done && n_per_extra > 3){ |
518 | > | makeElement( i * cellx + 0.5 * cellx, |
519 | > | j * celly, |
520 | > | k * cellz + 0.5 * cellz ); |
521 | > | done = ( current_mol >= tot_nmol ); |
522 | > | } |
523 | } | |
524 | < | |
548 | < | if (the_globals->getUseRF() ) { |
549 | < | simnfo->useReactionField = 1; |
550 | < | |
551 | < | if( !the_globals->haveECR() ){ |
552 | < | sprintf( painCave.errMsg, |
553 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
554 | < | "box length for the electrostaticCutoffRadius.\n" |
555 | < | "I hope you have a very fast processor!\n"); |
556 | < | painCave.isFatal = 0; |
557 | < | simError(); |
558 | < | double smallest; |
559 | < | smallest = simnfo->boxLx; |
560 | < | if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
561 | < | if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
562 | < | simnfo->ecr = 0.5 * smallest; |
563 | < | } else { |
564 | < | simnfo->ecr = the_globals->getECR(); |
524 | > | } |
525 | } | |
526 | + | } |
527 | ||
528 | < | if( !the_globals->haveEST() ){ |
529 | < | sprintf( painCave.errMsg, |
530 | < | "SimSetup Warning: using default value of 0.05 * the " |
531 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
532 | < | ); |
533 | < | painCave.isFatal = 0; |
534 | < | simError(); |
535 | < | simnfo->est = 0.05 * simnfo->ecr; |
536 | < | } else { |
537 | < | simnfo->est = the_globals->getEST(); |
538 | < | } |
539 | < | |
540 | < | if(!the_globals->haveDielectric() ){ |
528 | > | for( i=0; i<info[0].n_atoms; i++ ){ |
529 | > | info[0].atoms[i]->setVel( vel ); |
530 | > | } |
531 | > | } |
532 | > | |
533 | > | void SimSetup::makeElement( double x, double y, double z ){ |
534 | > | |
535 | > | int k; |
536 | > | AtomStamp* current_atom; |
537 | > | DirectionalAtom* dAtom; |
538 | > | double rotMat[3][3]; |
539 | > | double pos[3]; |
540 | > | |
541 | > | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
542 | > | |
543 | > | current_atom = comp_stamps[current_comp]->getAtom( k ); |
544 | > | if( !current_atom->havePosition() ){ |
545 | sprintf( painCave.errMsg, | |
546 | < | "SimSetup Error: You are trying to use Reaction Field without" |
547 | < | "setting a dielectric constant!\n" |
548 | < | ); |
546 | > | "SimSetup:initFromBass error.\n" |
547 | > | "\tComponent %s, atom %s does not have a position specified.\n" |
548 | > | "\tThe initialization routine is unable to give a start" |
549 | > | " position.\n", |
550 | > | comp_stamps[current_comp]->getID(), |
551 | > | current_atom->getType() ); |
552 | painCave.isFatal = 1; | |
553 | simError(); | |
554 | } | |
555 | < | simnfo->dielectric = the_globals->getDielectric(); |
556 | < | } else { |
557 | < | if (usesDipoles) { |
558 | < | |
559 | < | if( !the_globals->haveECR() ){ |
560 | < | sprintf( painCave.errMsg, |
561 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
562 | < | "box length for the electrostaticCutoffRadius.\n" |
563 | < | "I hope you have a very fast processor!\n"); |
564 | < | painCave.isFatal = 0; |
565 | < | simError(); |
566 | < | double smallest; |
567 | < | smallest = simnfo->boxLx; |
568 | < | if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
569 | < | if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
570 | < | simnfo->ecr = 0.5 * smallest; |
571 | < | } else { |
572 | < | simnfo->ecr = the_globals->getECR(); |
573 | < | } |
574 | < | |
575 | < | if( !the_globals->haveEST() ){ |
576 | < | sprintf( painCave.errMsg, |
577 | < | "SimSetup Warning: using default value of 5%% of the " |
578 | < | "electrostaticCutoffRadius for the " |
611 | < | "electrostaticSkinThickness\n" |
612 | < | ); |
613 | < | painCave.isFatal = 0; |
614 | < | simError(); |
615 | < | simnfo->est = 0.05 * simnfo->ecr; |
616 | < | } else { |
617 | < | simnfo->est = the_globals->getEST(); |
618 | < | } |
555 | > | |
556 | > | pos[0] = x + current_atom->getPosX(); |
557 | > | pos[1] = y + current_atom->getPosY(); |
558 | > | pos[2] = z + current_atom->getPosZ(); |
559 | > | |
560 | > | info[0].atoms[current_atom_ndx]->setPos( pos ); |
561 | > | |
562 | > | if( info[0].atoms[current_atom_ndx]->isDirectional() ){ |
563 | > | |
564 | > | dAtom = (DirectionalAtom *)info[0].atoms[current_atom_ndx]; |
565 | > | |
566 | > | rotMat[0][0] = 1.0; |
567 | > | rotMat[0][1] = 0.0; |
568 | > | rotMat[0][2] = 0.0; |
569 | > | |
570 | > | rotMat[1][0] = 0.0; |
571 | > | rotMat[1][1] = 1.0; |
572 | > | rotMat[1][2] = 0.0; |
573 | > | |
574 | > | rotMat[2][0] = 0.0; |
575 | > | rotMat[2][1] = 0.0; |
576 | > | rotMat[2][2] = 1.0; |
577 | > | |
578 | > | dAtom->setA( rotMat ); |
579 | } | |
620 | – | } |
580 | ||
581 | < | #ifdef IS_MPI |
582 | < | strcpy( checkPointMsg, "electrostatic parameters check out" ); |
624 | < | MPIcheckPoint(); |
625 | < | #endif // is_mpi |
581 | > | current_atom_ndx++; |
582 | > | } |
583 | ||
584 | < | if( the_globals->haveInitialConfig() ){ |
585 | < | |
629 | < | InitializeFromFile* fileInit; |
630 | < | #ifdef IS_MPI // is_mpi |
631 | < | if( worldRank == 0 ){ |
632 | < | #endif //is_mpi |
633 | < | fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
634 | < | #ifdef IS_MPI |
635 | < | }else fileInit = new InitializeFromFile( NULL ); |
636 | < | #endif |
637 | < | fileInit->read_xyz( simnfo ); // default velocities on |
584 | > | current_mol++; |
585 | > | current_comp_mol++; |
586 | ||
587 | < | delete fileInit; |
640 | < | } |
641 | < | else{ |
587 | > | if( current_comp_mol >= components_nmol[current_comp] ){ |
588 | ||
589 | < | #ifdef IS_MPI |
589 | > | current_comp_mol = 0; |
590 | > | current_comp++; |
591 | > | } |
592 | > | } |
593 | ||
594 | < | // no init from bass |
594 | > | |
595 | > | void SimSetup::gatherInfo( void ){ |
596 | > | int i,j,k; |
597 | > | |
598 | > | ensembleCase = -1; |
599 | > | ffCase = -1; |
600 | > | |
601 | > | // set the easy ones first |
602 | > | |
603 | > | for( i=0; i<nInfo; i++){ |
604 | > | info[i].target_temp = globals->getTargetTemp(); |
605 | > | info[i].dt = globals->getDt(); |
606 | > | info[i].run_time = globals->getRunTime(); |
607 | > | } |
608 | > | n_components = globals->getNComponents(); |
609 | > | |
610 | > | |
611 | > | // get the forceField |
612 | > | |
613 | > | strcpy( force_field, globals->getForceField() ); |
614 | > | |
615 | > | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
616 | > | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
617 | > | else if( !strcasecmp( force_field, "EAM" )) ffCase = FF_EAM; |
618 | > | else{ |
619 | > | sprintf( painCave.errMsg, |
620 | > | "SimSetup Error. Unrecognized force field -> %s\n", |
621 | > | force_field ); |
622 | > | painCave.isFatal = 1; |
623 | > | simError(); |
624 | > | } |
625 | > | |
626 | > | // get the ensemble |
627 | > | |
628 | > | strcpy( ensemble, globals->getEnsemble() ); |
629 | > | |
630 | > | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
631 | > | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
632 | > | else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
633 | > | ensembleCase = NPTi_ENS; |
634 | > | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
635 | > | else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
636 | > | else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
637 | > | else{ |
638 | > | sprintf( painCave.errMsg, |
639 | > | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
640 | > | "reverting to NVE for this simulation.\n", |
641 | > | ensemble ); |
642 | > | painCave.isFatal = 0; |
643 | > | simError(); |
644 | > | strcpy( ensemble, "NVE" ); |
645 | > | ensembleCase = NVE_ENS; |
646 | > | } |
647 | ||
648 | < | sprintf( painCave.errMsg, |
649 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
650 | < | painCave.isFatal; |
651 | < | simError(); |
648 | > | for(i=0; i<nInfo; i++){ |
649 | > | |
650 | > | strcpy( info[i].ensemble, ensemble ); |
651 | > | |
652 | > | // get the mixing rule |
653 | > | |
654 | > | strcpy( info[i].mixingRule, globals->getMixingRule() ); |
655 | > | info[i].usePBC = globals->getPBC(); |
656 | > | } |
657 | ||
658 | < | #else |
658 | > | // get the components and calculate the tot_nMol and indvidual n_mol |
659 | > | |
660 | > | the_components = globals->getComponents(); |
661 | > | components_nmol = new int[n_components]; |
662 | ||
654 | – | initFromBass(); |
663 | ||
664 | + | if( !globals->haveNMol() ){ |
665 | + | // we don't have the total number of molecules, so we assume it is |
666 | + | // given in each component |
667 | ||
668 | < | #endif |
669 | < | } |
668 | > | tot_nmol = 0; |
669 | > | for( i=0; i<n_components; i++ ){ |
670 | ||
671 | < | #ifdef IS_MPI |
672 | < | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
673 | < | MPIcheckPoint(); |
674 | < | #endif // is_mpi |
671 | > | if( !the_components[i]->haveNMol() ){ |
672 | > | // we have a problem |
673 | > | sprintf( painCave.errMsg, |
674 | > | "SimSetup Error. No global NMol or component NMol" |
675 | > | " given. Cannot calculate the number of atoms.\n" ); |
676 | > | painCave.isFatal = 1; |
677 | > | simError(); |
678 | > | } |
679 | ||
680 | + | tot_nmol += the_components[i]->getNMol(); |
681 | + | components_nmol[i] = the_components[i]->getNMol(); |
682 | + | } |
683 | + | } |
684 | + | else{ |
685 | + | sprintf( painCave.errMsg, |
686 | + | "SimSetup error.\n" |
687 | + | "\tSorry, the ability to specify total" |
688 | + | " nMols and then give molfractions in the components\n" |
689 | + | "\tis not currently supported." |
690 | + | " Please give nMol in the components.\n" ); |
691 | + | painCave.isFatal = 1; |
692 | + | simError(); |
693 | + | } |
694 | ||
695 | < | |
667 | < | |
695 | > | // set the status, sample, and thermal kick times |
696 | ||
697 | + | for(i=0; i<nInfo; i++){ |
698 | ||
699 | < | |
700 | < | #ifdef IS_MPI |
701 | < | if( worldRank == 0 ){ |
702 | < | #endif // is_mpi |
674 | < | |
675 | < | if( the_globals->haveFinalConfig() ){ |
676 | < | strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
699 | > | if( globals->haveSampleTime() ){ |
700 | > | info[i].sampleTime = globals->getSampleTime(); |
701 | > | info[i].statusTime = info[i].sampleTime; |
702 | > | info[i].thermalTime = info[i].sampleTime; |
703 | } | |
704 | else{ | |
705 | < | strcpy( simnfo->finalName, inFileName ); |
706 | < | char* endTest; |
707 | < | int nameLength = strlen( simnfo->finalName ); |
682 | < | endTest = &(simnfo->finalName[nameLength - 5]); |
683 | < | if( !strcmp( endTest, ".bass" ) ){ |
684 | < | strcpy( endTest, ".eor" ); |
685 | < | } |
686 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
687 | < | strcpy( endTest, ".eor" ); |
688 | < | } |
689 | < | else{ |
690 | < | endTest = &(simnfo->finalName[nameLength - 4]); |
691 | < | if( !strcmp( endTest, ".bss" ) ){ |
692 | < | strcpy( endTest, ".eor" ); |
693 | < | } |
694 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
695 | < | strcpy( endTest, ".eor" ); |
696 | < | } |
697 | < | else{ |
698 | < | strcat( simnfo->finalName, ".eor" ); |
699 | < | } |
700 | < | } |
705 | > | info[i].sampleTime = globals->getRunTime(); |
706 | > | info[i].statusTime = info[i].sampleTime; |
707 | > | info[i].thermalTime = info[i].sampleTime; |
708 | } | |
709 | ||
710 | < | // make the sample and status out names |
710 | > | if( globals->haveStatusTime() ){ |
711 | > | info[i].statusTime = globals->getStatusTime(); |
712 | > | } |
713 | ||
714 | < | strcpy( simnfo->sampleName, inFileName ); |
715 | < | char* endTest; |
707 | < | int nameLength = strlen( simnfo->sampleName ); |
708 | < | endTest = &(simnfo->sampleName[nameLength - 5]); |
709 | < | if( !strcmp( endTest, ".bass" ) ){ |
710 | < | strcpy( endTest, ".dump" ); |
714 | > | if( globals->haveThermalTime() ){ |
715 | > | info[i].thermalTime = globals->getThermalTime(); |
716 | } | |
717 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
718 | < | strcpy( endTest, ".dump" ); |
719 | < | } |
720 | < | else{ |
716 | < | endTest = &(simnfo->sampleName[nameLength - 4]); |
717 | < | if( !strcmp( endTest, ".bss" ) ){ |
718 | < | strcpy( endTest, ".dump" ); |
719 | < | } |
720 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
721 | < | strcpy( endTest, ".dump" ); |
722 | < | } |
723 | < | else{ |
724 | < | strcat( simnfo->sampleName, ".dump" ); |
725 | < | } |
726 | < | } |
717 | > | |
718 | > | // check for the temperature set flag |
719 | > | |
720 | > | if( globals->haveTempSet() ) info[i].setTemp = globals->getTempSet(); |
721 | ||
722 | < | strcpy( simnfo->statusName, inFileName ); |
723 | < | nameLength = strlen( simnfo->statusName ); |
724 | < | endTest = &(simnfo->statusName[nameLength - 5]); |
725 | < | if( !strcmp( endTest, ".bass" ) ){ |
726 | < | strcpy( endTest, ".stat" ); |
722 | > | // get some of the tricky things that may still be in the globals |
723 | > | |
724 | > | double boxVector[3]; |
725 | > | if( globals->haveBox() ){ |
726 | > | boxVector[0] = globals->getBox(); |
727 | > | boxVector[1] = globals->getBox(); |
728 | > | boxVector[2] = globals->getBox(); |
729 | > | |
730 | > | info[i].setBox( boxVector ); |
731 | } | |
732 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
733 | < | strcpy( endTest, ".stat" ); |
734 | < | } |
732 | > | else if( globals->haveDensity() ){ |
733 | > | |
734 | > | double vol; |
735 | > | vol = (double)tot_nmol / globals->getDensity(); |
736 | > | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
737 | > | boxVector[1] = boxVector[0]; |
738 | > | boxVector[2] = boxVector[0]; |
739 | > | |
740 | > | info[i].setBox( boxVector ); |
741 | > | } |
742 | else{ | |
743 | < | endTest = &(simnfo->statusName[nameLength - 4]); |
744 | < | if( !strcmp( endTest, ".bss" ) ){ |
745 | < | strcpy( endTest, ".stat" ); |
743 | > | if( !globals->haveBoxX() ){ |
744 | > | sprintf( painCave.errMsg, |
745 | > | "SimSetup error, no periodic BoxX size given.\n" ); |
746 | > | painCave.isFatal = 1; |
747 | > | simError(); |
748 | } | |
749 | < | else if( !strcmp( endTest, ".mdl" ) ){ |
750 | < | strcpy( endTest, ".stat" ); |
749 | > | boxVector[0] = globals->getBoxX(); |
750 | > | |
751 | > | if( !globals->haveBoxY() ){ |
752 | > | sprintf( painCave.errMsg, |
753 | > | "SimSetup error, no periodic BoxY size given.\n" ); |
754 | > | painCave.isFatal = 1; |
755 | > | simError(); |
756 | } | |
757 | < | else{ |
758 | < | strcat( simnfo->statusName, ".stat" ); |
757 | > | boxVector[1] = globals->getBoxY(); |
758 | > | |
759 | > | if( !globals->haveBoxZ() ){ |
760 | > | sprintf( painCave.errMsg, |
761 | > | "SimSetup error, no periodic BoxZ size given.\n" ); |
762 | > | painCave.isFatal = 1; |
763 | > | simError(); |
764 | } | |
765 | + | boxVector[2] = globals->getBoxZ(); |
766 | + | |
767 | + | info[i].setBox( boxVector ); |
768 | } | |
769 | + | |
770 | + | } |
771 | ||
772 | #ifdef IS_MPI | |
773 | < | } |
773 | > | strcpy( checkPointMsg, "Succesfully gathered all information from Bass\n" ); |
774 | > | MPIcheckPoint(); |
775 | #endif // is_mpi | |
753 | – | |
754 | – | // set the status, sample, and themal kick times |
755 | – | |
756 | – | if( the_globals->haveSampleTime() ){ |
757 | – | simnfo->sampleTime = the_globals->getSampleTime(); |
758 | – | simnfo->statusTime = simnfo->sampleTime; |
759 | – | simnfo->thermalTime = simnfo->sampleTime; |
760 | – | } |
761 | – | else{ |
762 | – | simnfo->sampleTime = the_globals->getRunTime(); |
763 | – | simnfo->statusTime = simnfo->sampleTime; |
764 | – | simnfo->thermalTime = simnfo->sampleTime; |
765 | – | } |
776 | ||
777 | < | if( the_globals->haveStatusTime() ){ |
768 | < | simnfo->statusTime = the_globals->getStatusTime(); |
769 | < | } |
777 | > | } |
778 | ||
771 | – | if( the_globals->haveThermalTime() ){ |
772 | – | simnfo->thermalTime = the_globals->getThermalTime(); |
773 | – | } |
779 | ||
780 | < | // check for the temperature set flag |
780 | > | void SimSetup::finalInfoCheck( void ){ |
781 | > | int index; |
782 | > | int usesDipoles; |
783 | > | int i; |
784 | ||
785 | < | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
786 | < | |
787 | < | |
788 | < | // make the integrator |
785 | > | for(i=0; i<nInfo; i++){ |
786 | > | // check electrostatic parameters |
787 | > | |
788 | > | index = 0; |
789 | > | usesDipoles = 0; |
790 | > | while( (index < info[i].n_atoms) && !usesDipoles ){ |
791 | > | usesDipoles = (info[i].atoms[index])->hasDipole(); |
792 | > | index++; |
793 | > | } |
794 | > | |
795 | > | #ifdef IS_MPI |
796 | > | int myUse = usesDipoles; |
797 | > | MPI_Allreduce( &myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD ); |
798 | > | #endif //is_mpi |
799 | > | |
800 | > | double theEcr, theEst; |
801 | ||
802 | < | |
803 | < | NVT* myNVT = NULL; |
804 | < | switch( ensembleCase ){ |
805 | < | |
806 | < | case NVE_ENS: |
807 | < | new NVE( simnfo, the_ff ); |
808 | < | break; |
809 | < | |
810 | < | case NVT_ENS: |
811 | < | myNVT = new NVT( simnfo, the_ff ); |
812 | < | myNVT->setTargetTemp(the_globals->getTargetTemp()); |
813 | < | |
814 | < | if (the_globals->haveTauThermostat()) |
815 | < | myNVT->setTauThermostat(the_globals->getTauThermostat()); |
816 | < | // else if (the_globals->haveQmass()) |
817 | < | // myNVT->setQmass(the_globals->getQmass()); |
802 | > | if (globals->getUseRF() ) { |
803 | > | info[i].useReactionField = 1; |
804 | > | |
805 | > | if( !globals->haveECR() ){ |
806 | > | sprintf( painCave.errMsg, |
807 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
808 | > | "box length for the electrostaticCutoffRadius.\n" |
809 | > | "I hope you have a very fast processor!\n"); |
810 | > | painCave.isFatal = 0; |
811 | > | simError(); |
812 | > | double smallest; |
813 | > | smallest = info[i].boxL[0]; |
814 | > | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
815 | > | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
816 | > | theEcr = 0.5 * smallest; |
817 | > | } else { |
818 | > | theEcr = globals->getECR(); |
819 | > | } |
820 | > | |
821 | > | if( !globals->haveEST() ){ |
822 | > | sprintf( painCave.errMsg, |
823 | > | "SimSetup Warning: using default value of 0.05 * the " |
824 | > | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
825 | > | ); |
826 | > | painCave.isFatal = 0; |
827 | > | simError(); |
828 | > | theEst = 0.05 * theEcr; |
829 | > | } else { |
830 | > | theEst= globals->getEST(); |
831 | > | } |
832 | > | |
833 | > | info[i].setEcr( theEcr, theEst ); |
834 | > | |
835 | > | if(!globals->haveDielectric() ){ |
836 | > | sprintf( painCave.errMsg, |
837 | > | "SimSetup Error: You are trying to use Reaction Field without" |
838 | > | "setting a dielectric constant!\n" |
839 | > | ); |
840 | > | painCave.isFatal = 1; |
841 | > | simError(); |
842 | > | } |
843 | > | info[i].dielectric = globals->getDielectric(); |
844 | > | } |
845 | else { | |
846 | < | sprintf( painCave.errMsg, |
847 | < | "SimSetup error: If you use the NVT\n" |
848 | < | " ensemble, you must set either tauThermostat or qMass.\n" |
802 | < | " Neither of these was found in the BASS file.\n"); |
803 | < | painCave.isFatal = 1; |
804 | < | simError(); |
805 | < | } |
806 | < | break; |
807 | < | |
808 | < | default: |
846 | > | if (usesDipoles) { |
847 | > | |
848 | > | if( !globals->haveECR() ){ |
849 | sprintf( painCave.errMsg, | |
850 | < | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
851 | < | painCave.isFatal = 1; |
850 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
851 | > | "box length for the electrostaticCutoffRadius.\n" |
852 | > | "I hope you have a very fast processor!\n"); |
853 | > | painCave.isFatal = 0; |
854 | simError(); | |
855 | + | double smallest; |
856 | + | smallest = info[i].boxL[0]; |
857 | + | if (info[i].boxL[1] <= smallest) smallest = info[i].boxL[1]; |
858 | + | if (info[i].boxL[2] <= smallest) smallest = info[i].boxL[2]; |
859 | + | theEcr = 0.5 * smallest; |
860 | + | } else { |
861 | + | theEcr = globals->getECR(); |
862 | } | |
863 | + | |
864 | + | if( !globals->haveEST() ){ |
865 | + | sprintf( painCave.errMsg, |
866 | + | "SimSetup Warning: using default value of 0.05 * the " |
867 | + | "electrostaticCutoffRadius for the " |
868 | + | "electrostaticSkinThickness\n" |
869 | + | ); |
870 | + | painCave.isFatal = 0; |
871 | + | simError(); |
872 | + | theEst = 0.05 * theEcr; |
873 | + | } else { |
874 | + | theEst= globals->getEST(); |
875 | + | } |
876 | + | |
877 | + | info[i].setEcr( theEcr, theEst ); |
878 | + | } |
879 | + | } |
880 | + | } |
881 | ||
815 | – | |
882 | #ifdef IS_MPI | |
883 | < | mpiSim->mpiRefresh(); |
884 | < | #endif |
883 | > | strcpy( checkPointMsg, "post processing checks out" ); |
884 | > | MPIcheckPoint(); |
885 | > | #endif // is_mpi |
886 | ||
887 | < | // initialize the Fortran |
887 | > | } |
888 | ||
889 | + | void SimSetup::initSystemCoords( void ){ |
890 | + | int i; |
891 | + | |
892 | + | char* inName; |
893 | ||
894 | < | simnfo->refreshSim(); |
894 | > | (info[0].getConfiguration())->createArrays( info[0].n_atoms ); |
895 | > | |
896 | > | for(i=0; i<info[0].n_atoms; i++) info[0].atoms[i]->setCoords(); |
897 | ||
898 | < | if( !strcmp( simnfo->mixingRule, "standard") ){ |
899 | < | the_ff->initForceField( LB_MIXING_RULE ); |
898 | > | if( globals->haveInitialConfig() ){ |
899 | > | |
900 | > | InitializeFromFile* fileInit; |
901 | > | #ifdef IS_MPI // is_mpi |
902 | > | if( worldRank == 0 ){ |
903 | > | #endif //is_mpi |
904 | > | inName = globals->getInitialConfig(); |
905 | > | double* tempDouble = new double[1000000]; |
906 | > | fileInit = new InitializeFromFile( inName ); |
907 | > | #ifdef IS_MPI |
908 | > | }else fileInit = new InitializeFromFile( NULL ); |
909 | > | #endif |
910 | > | fileInit->readInit( info ); // default velocities on |
911 | > | |
912 | > | delete fileInit; |
913 | } | |
828 | – | else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
829 | – | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
830 | – | } |
914 | else{ | |
915 | + | |
916 | + | #ifdef IS_MPI |
917 | + | |
918 | + | // no init from bass |
919 | + | |
920 | sprintf( painCave.errMsg, | |
921 | < | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
922 | < | simnfo->mixingRule ); |
835 | < | painCave.isFatal = 1; |
921 | > | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
922 | > | painCave.isFatal; |
923 | simError(); | |
924 | + | |
925 | + | #else |
926 | + | |
927 | + | initFromBass(); |
928 | + | |
929 | + | |
930 | + | #endif |
931 | } | |
932 | < | |
839 | < | |
932 | > | |
933 | #ifdef IS_MPI | |
934 | < | strcpy( checkPointMsg, |
842 | < | "Successfully intialized the mixingRule for Fortran." ); |
934 | > | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
935 | MPIcheckPoint(); | |
936 | #endif // is_mpi | |
937 | + | |
938 | } | |
939 | ||
940 | ||
941 | < | void SimSetup::makeMolecules( void ){ |
849 | < | |
850 | < | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
851 | < | molInit info; |
852 | < | DirectionalAtom* dAtom; |
853 | < | LinkedAssign* extras; |
854 | < | LinkedAssign* current_extra; |
855 | < | AtomStamp* currentAtom; |
856 | < | BondStamp* currentBond; |
857 | < | BendStamp* currentBend; |
858 | < | TorsionStamp* currentTorsion; |
859 | < | |
860 | < | bond_pair* theBonds; |
861 | < | bend_set* theBends; |
862 | < | torsion_set* theTorsions; |
863 | < | |
941 | > | void SimSetup::makeOutNames( void ){ |
942 | ||
943 | < | //init the forceField paramters |
943 | > | int k; |
944 | ||
867 | – | the_ff->readParams(); |
868 | – | |
945 | ||
946 | < | // init the atoms |
946 | > | for(k=0; k<nInfo; k++){ |
947 | ||
948 | < | double ux, uy, uz, u, uSqr; |
949 | < | |
950 | < | atomOffset = 0; |
875 | < | excludeOffset = 0; |
876 | < | for(i=0; i<simnfo->n_mol; i++){ |
877 | < | |
878 | < | stampID = the_molecules[i].getStampID(); |
879 | < | |
880 | < | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
881 | < | info.nBonds = comp_stamps[stampID]->getNBonds(); |
882 | < | info.nBends = comp_stamps[stampID]->getNBends(); |
883 | < | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
884 | < | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
885 | < | |
886 | < | info.myAtoms = &the_atoms[atomOffset]; |
887 | < | info.myExcludes = &the_excludes[excludeOffset]; |
888 | < | info.myBonds = new Bond*[info.nBonds]; |
889 | < | info.myBends = new Bend*[info.nBends]; |
890 | < | info.myTorsions = new Torsion*[info.nTorsions]; |
891 | < | |
892 | < | theBonds = new bond_pair[info.nBonds]; |
893 | < | theBends = new bend_set[info.nBends]; |
894 | < | theTorsions = new torsion_set[info.nTorsions]; |
895 | < | |
896 | < | // make the Atoms |
897 | < | |
898 | < | for(j=0; j<info.nAtoms; j++){ |
948 | > | #ifdef IS_MPI |
949 | > | if( worldRank == 0 ){ |
950 | > | #endif // is_mpi |
951 | ||
952 | < | currentAtom = comp_stamps[stampID]->getAtom( j ); |
953 | < | if( currentAtom->haveOrientation() ){ |
902 | < | |
903 | < | dAtom = new DirectionalAtom(j + atomOffset); |
904 | < | simnfo->n_oriented++; |
905 | < | info.myAtoms[j] = dAtom; |
906 | < | |
907 | < | ux = currentAtom->getOrntX(); |
908 | < | uy = currentAtom->getOrntY(); |
909 | < | uz = currentAtom->getOrntZ(); |
910 | < | |
911 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
912 | < | |
913 | < | u = sqrt( uSqr ); |
914 | < | ux = ux / u; |
915 | < | uy = uy / u; |
916 | < | uz = uz / u; |
917 | < | |
918 | < | dAtom->setSUx( ux ); |
919 | < | dAtom->setSUy( uy ); |
920 | < | dAtom->setSUz( uz ); |
952 | > | if( globals->haveFinalConfig() ){ |
953 | > | strcpy( info[k].finalName, globals->getFinalConfig() ); |
954 | } | |
955 | else{ | |
956 | < | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
956 | > | strcpy( info[k].finalName, inFileName ); |
957 | > | char* endTest; |
958 | > | int nameLength = strlen( info[k].finalName ); |
959 | > | endTest = &(info[k].finalName[nameLength - 5]); |
960 | > | if( !strcmp( endTest, ".bass" ) ){ |
961 | > | strcpy( endTest, ".eor" ); |
962 | > | } |
963 | > | else if( !strcmp( endTest, ".BASS" ) ){ |
964 | > | strcpy( endTest, ".eor" ); |
965 | > | } |
966 | > | else{ |
967 | > | endTest = &(info[k].finalName[nameLength - 4]); |
968 | > | if( !strcmp( endTest, ".bss" ) ){ |
969 | > | strcpy( endTest, ".eor" ); |
970 | > | } |
971 | > | else if( !strcmp( endTest, ".mdl" ) ){ |
972 | > | strcpy( endTest, ".eor" ); |
973 | > | } |
974 | > | else{ |
975 | > | strcat( info[k].finalName, ".eor" ); |
976 | > | } |
977 | > | } |
978 | } | |
925 | – | info.myAtoms[j]->setType( currentAtom->getType() ); |
926 | – | |
927 | – | #ifdef IS_MPI |
979 | ||
980 | < | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
980 | > | // make the sample and status out names |
981 | ||
982 | < | #endif // is_mpi |
983 | < | } |
984 | < | |
985 | < | // make the bonds |
986 | < | for(j=0; j<info.nBonds; j++){ |
987 | < | |
937 | < | currentBond = comp_stamps[stampID]->getBond( j ); |
938 | < | theBonds[j].a = currentBond->getA() + atomOffset; |
939 | < | theBonds[j].b = currentBond->getB() + atomOffset; |
940 | < | |
941 | < | exI = theBonds[j].a; |
942 | < | exJ = theBonds[j].b; |
943 | < | |
944 | < | // exclude_I must always be the smaller of the pair |
945 | < | if( exI > exJ ){ |
946 | < | tempEx = exI; |
947 | < | exI = exJ; |
948 | < | exJ = tempEx; |
982 | > | strcpy( info[k].sampleName, inFileName ); |
983 | > | char* endTest; |
984 | > | int nameLength = strlen( info[k].sampleName ); |
985 | > | endTest = &(info[k].sampleName[nameLength - 5]); |
986 | > | if( !strcmp( endTest, ".bass" ) ){ |
987 | > | strcpy( endTest, ".dump" ); |
988 | } | |
989 | < | #ifdef IS_MPI |
990 | < | tempEx = exI; |
991 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
992 | < | tempEx = exJ; |
993 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
989 | > | else if( !strcmp( endTest, ".BASS" ) ){ |
990 | > | strcpy( endTest, ".dump" ); |
991 | > | } |
992 | > | else{ |
993 | > | endTest = &(info[k].sampleName[nameLength - 4]); |
994 | > | if( !strcmp( endTest, ".bss" ) ){ |
995 | > | strcpy( endTest, ".dump" ); |
996 | > | } |
997 | > | else if( !strcmp( endTest, ".mdl" ) ){ |
998 | > | strcpy( endTest, ".dump" ); |
999 | > | } |
1000 | > | else{ |
1001 | > | strcat( info[k].sampleName, ".dump" ); |
1002 | > | } |
1003 | > | } |
1004 | ||
1005 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1006 | < | #else // isn't MPI |
1007 | < | |
1008 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1009 | < | #endif //is_mpi |
961 | < | } |
962 | < | excludeOffset += info.nBonds; |
963 | < | |
964 | < | //make the bends |
965 | < | for(j=0; j<info.nBends; j++){ |
966 | < | |
967 | < | currentBend = comp_stamps[stampID]->getBend( j ); |
968 | < | theBends[j].a = currentBend->getA() + atomOffset; |
969 | < | theBends[j].b = currentBend->getB() + atomOffset; |
970 | < | theBends[j].c = currentBend->getC() + atomOffset; |
971 | < | |
972 | < | if( currentBend->haveExtras() ){ |
973 | < | |
974 | < | extras = currentBend->getExtras(); |
975 | < | current_extra = extras; |
976 | < | |
977 | < | while( current_extra != NULL ){ |
978 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
979 | < | |
980 | < | switch( current_extra->getType() ){ |
981 | < | |
982 | < | case 0: |
983 | < | theBends[j].ghost = |
984 | < | current_extra->getInt() + atomOffset; |
985 | < | theBends[j].isGhost = 1; |
986 | < | break; |
987 | < | |
988 | < | case 1: |
989 | < | theBends[j].ghost = |
990 | < | (int)current_extra->getDouble() + atomOffset; |
991 | < | theBends[j].isGhost = 1; |
992 | < | break; |
993 | < | |
994 | < | default: |
995 | < | sprintf( painCave.errMsg, |
996 | < | "SimSetup Error: ghostVectorSource was neither a " |
997 | < | "double nor an int.\n" |
998 | < | "-->Bend[%d] in %s\n", |
999 | < | j, comp_stamps[stampID]->getID() ); |
1000 | < | painCave.isFatal = 1; |
1001 | < | simError(); |
1002 | < | } |
1003 | < | } |
1004 | < | |
1005 | < | else{ |
1006 | < | |
1007 | < | sprintf( painCave.errMsg, |
1008 | < | "SimSetup Error: unhandled bend assignment:\n" |
1009 | < | " -->%s in Bend[%d] in %s\n", |
1010 | < | current_extra->getlhs(), |
1011 | < | j, comp_stamps[stampID]->getID() ); |
1012 | < | painCave.isFatal = 1; |
1013 | < | simError(); |
1014 | < | } |
1015 | < | |
1016 | < | current_extra = current_extra->getNext(); |
1017 | < | } |
1005 | > | strcpy( info[k].statusName, inFileName ); |
1006 | > | nameLength = strlen( info[k].statusName ); |
1007 | > | endTest = &(info[k].statusName[nameLength - 5]); |
1008 | > | if( !strcmp( endTest, ".bass" ) ){ |
1009 | > | strcpy( endTest, ".stat" ); |
1010 | } | |
1011 | < | |
1012 | < | if( !theBends[j].isGhost ){ |
1021 | < | |
1022 | < | exI = theBends[j].a; |
1023 | < | exJ = theBends[j].c; |
1011 | > | else if( !strcmp( endTest, ".BASS" ) ){ |
1012 | > | strcpy( endTest, ".stat" ); |
1013 | } | |
1014 | else{ | |
1015 | < | |
1016 | < | exI = theBends[j].a; |
1017 | < | exJ = theBends[j].b; |
1015 | > | endTest = &(info[k].statusName[nameLength - 4]); |
1016 | > | if( !strcmp( endTest, ".bss" ) ){ |
1017 | > | strcpy( endTest, ".stat" ); |
1018 | > | } |
1019 | > | else if( !strcmp( endTest, ".mdl" ) ){ |
1020 | > | strcpy( endTest, ".stat" ); |
1021 | > | } |
1022 | > | else{ |
1023 | > | strcat( info[k].statusName, ".stat" ); |
1024 | > | } |
1025 | } | |
1026 | ||
1031 | – | // exclude_I must always be the smaller of the pair |
1032 | – | if( exI > exJ ){ |
1033 | – | tempEx = exI; |
1034 | – | exI = exJ; |
1035 | – | exJ = tempEx; |
1036 | – | } |
1027 | #ifdef IS_MPI | |
1038 | – | tempEx = exI; |
1039 | – | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1040 | – | tempEx = exJ; |
1041 | – | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1042 | – | |
1043 | – | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1044 | – | #else // isn't MPI |
1045 | – | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1046 | – | #endif //is_mpi |
1028 | } | |
1029 | < | excludeOffset += info.nBends; |
1029 | > | #endif // is_mpi |
1030 | > | } |
1031 | > | } |
1032 | ||
1050 | – | for(j=0; j<info.nTorsions; j++){ |
1051 | – | |
1052 | – | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
1053 | – | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
1054 | – | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
1055 | – | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
1056 | – | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
1057 | – | |
1058 | – | exI = theTorsions[j].a; |
1059 | – | exJ = theTorsions[j].d; |
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 | < | } |
1034 | > | void SimSetup::sysObjectsCreation( void ){ |
1035 | > | |
1036 | > | int i,k; |
1037 | > | |
1038 | > | // create the forceField |
1039 | > | |
1040 | > | createFF(); |
1041 | > | |
1042 | > | // extract componentList |
1043 | > | |
1044 | > | compList(); |
1045 | > | |
1046 | > | // calc the number of atoms, bond, bends, and torsions |
1047 | > | |
1048 | > | calcSysValues(); |
1049 | > | |
1050 | #ifdef IS_MPI | |
1051 | < | tempEx = exI; |
1052 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1053 | < | tempEx = exJ; |
1054 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1055 | < | |
1056 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1057 | < | #else // isn't MPI |
1058 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1059 | < | #endif //is_mpi |
1051 | > | // divide the molecules among the processors |
1052 | > | |
1053 | > | mpiMolDivide(); |
1054 | > | #endif //is_mpi |
1055 | > | |
1056 | > | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1057 | > | |
1058 | > | makeSysArrays(); |
1059 | > | |
1060 | > | // make and initialize the molecules (all but atomic coordinates) |
1061 | > | |
1062 | > | makeMolecules(); |
1063 | > | |
1064 | > | for(k=0; k<nInfo; k++){ |
1065 | > | info[k].identArray = new int[info[k].n_atoms]; |
1066 | > | for(i=0; i<info[k].n_atoms; i++){ |
1067 | > | info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1068 | } | |
1069 | < | excludeOffset += info.nTorsions; |
1069 | > | } |
1070 | > | } |
1071 | ||
1080 | – | |
1081 | – | // send the arrays off to the forceField for init. |
1072 | ||
1073 | < | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1084 | < | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1085 | < | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1086 | < | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
1073 | > | void SimSetup::createFF( void ){ |
1074 | ||
1075 | + | switch( ffCase ){ |
1076 | ||
1077 | < | the_molecules[i].initialize( info ); |
1077 | > | case FF_DUFF: |
1078 | > | the_ff = new DUFF(); |
1079 | > | break; |
1080 | ||
1081 | + | case FF_LJ: |
1082 | + | the_ff = new LJFF(); |
1083 | + | break; |
1084 | ||
1085 | < | atomOffset += info.nAtoms; |
1086 | < | delete[] theBonds; |
1087 | < | delete[] theBends; |
1088 | < | delete[] theTorsions; |
1085 | > | case FF_EAM: |
1086 | > | the_ff = new EAM_FF(); |
1087 | > | break; |
1088 | > | |
1089 | > | default: |
1090 | > | sprintf( painCave.errMsg, |
1091 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1092 | > | painCave.isFatal = 1; |
1093 | > | simError(); |
1094 | } | |
1095 | ||
1096 | #ifdef IS_MPI | |
1097 | < | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1097 | > | strcpy( checkPointMsg, "ForceField creation successful" ); |
1098 | MPIcheckPoint(); | |
1099 | #endif // is_mpi | |
1100 | ||
1103 | – | // clean up the forcefield |
1104 | – | the_ff->calcRcut(); |
1105 | – | the_ff->cleanMe(); |
1106 | – | |
1101 | } | |
1102 | ||
1109 | – | void SimSetup::initFromBass( void ){ |
1103 | ||
1104 | < | int i, j, k; |
1112 | < | int n_cells; |
1113 | < | double cellx, celly, cellz; |
1114 | < | double temp1, temp2, temp3; |
1115 | < | int n_per_extra; |
1116 | < | int n_extra; |
1117 | < | int have_extra, done; |
1104 | > | void SimSetup::compList( void ){ |
1105 | ||
1106 | < | temp1 = (double)tot_nmol / 4.0; |
1107 | < | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
1108 | < | temp3 = ceil( temp2 ); |
1109 | < | |
1110 | < | have_extra =0; |
1111 | < | if( temp2 < temp3 ){ // we have a non-complete lattice |
1112 | < | have_extra =1; |
1113 | < | |
1114 | < | n_cells = (int)temp3 - 1; |
1115 | < | cellx = simnfo->boxLx / temp3; |
1116 | < | celly = simnfo->boxLy / temp3; |
1117 | < | cellz = simnfo->boxLz / temp3; |
1118 | < | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1119 | < | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1120 | < | n_per_extra = (int)ceil( temp1 ); |
1106 | > | int i; |
1107 | > | char* id; |
1108 | > | LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1109 | > | LinkedMolStamp* currentStamp = NULL; |
1110 | > | comp_stamps = new MoleculeStamp*[n_components]; |
1111 | > | |
1112 | > | // make an array of molecule stamps that match the components used. |
1113 | > | // also extract the used stamps out into a separate linked list |
1114 | > | |
1115 | > | for(i=0; i<nInfo; i++){ |
1116 | > | info[i].nComponents = n_components; |
1117 | > | info[i].componentsNmol = components_nmol; |
1118 | > | info[i].compStamps = comp_stamps; |
1119 | > | info[i].headStamp = headStamp; |
1120 | > | } |
1121 | > | |
1122 | ||
1123 | < | if( n_per_extra > 4){ |
1124 | < | sprintf( painCave.errMsg, |
1125 | < | "SimSetup error. There has been an error in constructing" |
1126 | < | " the non-complete lattice.\n" ); |
1127 | < | painCave.isFatal = 1; |
1128 | < | simError(); |
1123 | > | for( i=0; i<n_components; i++ ){ |
1124 | > | |
1125 | > | id = the_components[i]->getType(); |
1126 | > | comp_stamps[i] = NULL; |
1127 | > | |
1128 | > | // check to make sure the component isn't already in the list |
1129 | > | |
1130 | > | comp_stamps[i] = headStamp->match( id ); |
1131 | > | if( comp_stamps[i] == NULL ){ |
1132 | > | |
1133 | > | // extract the component from the list; |
1134 | > | |
1135 | > | currentStamp = stamps->extractMolStamp( id ); |
1136 | > | if( currentStamp == NULL ){ |
1137 | > | sprintf( painCave.errMsg, |
1138 | > | "SimSetup error: Component \"%s\" was not found in the " |
1139 | > | "list of declared molecules\n", |
1140 | > | id ); |
1141 | > | painCave.isFatal = 1; |
1142 | > | simError(); |
1143 | > | } |
1144 | > | |
1145 | > | headStamp->add( currentStamp ); |
1146 | > | comp_stamps[i] = headStamp->match( id ); |
1147 | } | |
1148 | } | |
1149 | < | else{ |
1150 | < | n_cells = (int)temp3; |
1151 | < | cellx = simnfo->boxLx / temp3; |
1152 | < | celly = simnfo->boxLy / temp3; |
1153 | < | cellz = simnfo->boxLz / temp3; |
1149 | > | |
1150 | > | #ifdef IS_MPI |
1151 | > | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
1152 | > | MPIcheckPoint(); |
1153 | > | #endif // is_mpi |
1154 | > | |
1155 | > | |
1156 | > | } |
1157 | > | |
1158 | > | void SimSetup::calcSysValues( void ){ |
1159 | > | int i, j, k; |
1160 | > | |
1161 | > | int *molMembershipArray; |
1162 | > | |
1163 | > | tot_atoms = 0; |
1164 | > | tot_bonds = 0; |
1165 | > | tot_bends = 0; |
1166 | > | tot_torsions = 0; |
1167 | > | for( i=0; i<n_components; i++ ){ |
1168 | > | |
1169 | > | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1170 | > | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1171 | > | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1172 | > | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1173 | } | |
1174 | + | |
1175 | + | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1176 | + | molMembershipArray = new int[tot_atoms]; |
1177 | + | |
1178 | + | for(i=0; i<nInfo; i++){ |
1179 | + | info[i].n_atoms = tot_atoms; |
1180 | + | info[i].n_bonds = tot_bonds; |
1181 | + | info[i].n_bends = tot_bends; |
1182 | + | info[i].n_torsions = tot_torsions; |
1183 | + | info[i].n_SRI = tot_SRI; |
1184 | + | info[i].n_mol = tot_nmol; |
1185 | + | |
1186 | + | info[i].molMembershipArray = molMembershipArray; |
1187 | + | } |
1188 | + | } |
1189 | ||
1190 | < | current_mol = 0; |
1151 | < | current_comp_mol = 0; |
1152 | < | current_comp = 0; |
1153 | < | current_atom_ndx = 0; |
1190 | > | #ifdef IS_MPI |
1191 | ||
1192 | < | for( i=0; i < n_cells ; i++ ){ |
1193 | < | for( j=0; j < n_cells; j++ ){ |
1194 | < | for( k=0; k < n_cells; k++ ){ |
1192 | > | void SimSetup::mpiMolDivide( void ){ |
1193 | > | |
1194 | > | int i, j, k; |
1195 | > | int localMol, allMol; |
1196 | > | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1197 | ||
1198 | < | makeElement( i * cellx, |
1199 | < | j * celly, |
1200 | < | k * cellz ); |
1198 | > | mpiSim = new mpiSimulation( info ); |
1199 | > | |
1200 | > | globalIndex = mpiSim->divideLabor(); |
1201 | ||
1202 | < | makeElement( i * cellx + 0.5 * cellx, |
1203 | < | j * celly + 0.5 * celly, |
1204 | < | k * cellz ); |
1202 | > | // set up the local variables |
1203 | > | |
1204 | > | mol2proc = mpiSim->getMolToProcMap(); |
1205 | > | molCompType = mpiSim->getMolComponentType(); |
1206 | > | |
1207 | > | allMol = 0; |
1208 | > | localMol = 0; |
1209 | > | local_atoms = 0; |
1210 | > | local_bonds = 0; |
1211 | > | local_bends = 0; |
1212 | > | local_torsions = 0; |
1213 | > | globalAtomIndex = 0; |
1214 | ||
1167 | – | makeElement( i * cellx, |
1168 | – | j * celly + 0.5 * celly, |
1169 | – | k * cellz + 0.5 * cellz ); |
1215 | ||
1216 | < | makeElement( i * cellx + 0.5 * cellx, |
1217 | < | j * celly, |
1218 | < | k * cellz + 0.5 * cellz ); |
1216 | > | for( i=0; i<n_components; i++ ){ |
1217 | > | |
1218 | > | for( j=0; j<components_nmol[i]; j++ ){ |
1219 | > | |
1220 | > | if( mol2proc[allMol] == worldRank ){ |
1221 | > | |
1222 | > | local_atoms += comp_stamps[i]->getNAtoms(); |
1223 | > | local_bonds += comp_stamps[i]->getNBonds(); |
1224 | > | local_bends += comp_stamps[i]->getNBends(); |
1225 | > | local_torsions += comp_stamps[i]->getNTorsions(); |
1226 | > | localMol++; |
1227 | > | } |
1228 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1229 | > | info[0].molMembershipArray[globalAtomIndex] = allMol; |
1230 | > | globalAtomIndex++; |
1231 | } | |
1232 | + | |
1233 | + | allMol++; |
1234 | } | |
1235 | } | |
1236 | + | local_SRI = local_bonds + local_bends + local_torsions; |
1237 | + | |
1238 | + | info[0].n_atoms = mpiSim->getMyNlocal(); |
1239 | + | |
1240 | + | if( local_atoms != info[0].n_atoms ){ |
1241 | + | sprintf( painCave.errMsg, |
1242 | + | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1243 | + | " localAtom (%d) are not equal.\n", |
1244 | + | info[0].n_atoms, |
1245 | + | local_atoms ); |
1246 | + | painCave.isFatal = 1; |
1247 | + | simError(); |
1248 | + | } |
1249 | ||
1250 | < | if( have_extra ){ |
1251 | < | done = 0; |
1250 | > | info[0].n_bonds = local_bonds; |
1251 | > | info[0].n_bends = local_bends; |
1252 | > | info[0].n_torsions = local_torsions; |
1253 | > | info[0].n_SRI = local_SRI; |
1254 | > | info[0].n_mol = localMol; |
1255 | ||
1256 | < | int start_ndx; |
1257 | < | for( i=0; i < (n_cells+1) && !done; i++ ){ |
1258 | < | for( j=0; j < (n_cells+1) && !done; j++ ){ |
1256 | > | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
1257 | > | MPIcheckPoint(); |
1258 | > | } |
1259 | > | |
1260 | > | #endif // is_mpi |
1261 | ||
1185 | – | if( i < n_cells ){ |
1262 | ||
1263 | < | if( j < n_cells ){ |
1264 | < | start_ndx = n_cells; |
1189 | < | } |
1190 | < | else start_ndx = 0; |
1191 | < | } |
1192 | < | else start_ndx = 0; |
1263 | > | void SimSetup::makeSysArrays( void ){ |
1264 | > | int i, j, k, l; |
1265 | ||
1266 | < | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
1266 | > | Atom** the_atoms; |
1267 | > | Molecule* the_molecules; |
1268 | > | Exclude** the_excludes; |
1269 | ||
1270 | < | makeElement( i * cellx, |
1271 | < | j * celly, |
1272 | < | k * cellz ); |
1273 | < | done = ( current_mol >= tot_nmol ); |
1270 | > | |
1271 | > | for(l=0; l<nInfo; l++){ |
1272 | > | |
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 | < | if( !done && n_per_extra > 1 ){ |
1280 | < | makeElement( i * cellx + 0.5 * cellx, |
1281 | < | j * celly + 0.5 * celly, |
1282 | < | k * cellz ); |
1283 | < | done = ( current_mol >= tot_nmol ); |
1284 | < | } |
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 | > | |
1287 | > | if(mol2proc[i] == worldRank ){ |
1288 | > | the_molecules[molIndex].setStampID( molCompType[i] ); |
1289 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
1290 | > | the_molecules[molIndex].setGlobalIndex( i ); |
1291 | > | molIndex++; |
1292 | > | } |
1293 | > | } |
1294 | > | |
1295 | > | #else // is_mpi |
1296 | > | |
1297 | > | molIndex = 0; |
1298 | > | globalAtomIndex = 0; |
1299 | > | for(i=0; i<n_components; i++){ |
1300 | > | for(j=0; j<components_nmol[i]; j++ ){ |
1301 | > | the_molecules[molIndex].setStampID( i ); |
1302 | > | the_molecules[molIndex].setMyIndex( molIndex ); |
1303 | > | the_molecules[molIndex].setGlobalIndex( molIndex ); |
1304 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
1305 | > | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1306 | > | globalAtomIndex++; |
1307 | > | } |
1308 | > | molIndex++; |
1309 | > | } |
1310 | > | } |
1311 | > | |
1312 | > | |
1313 | > | #endif // is_mpi |
1314 | ||
1208 | – | if( !done && n_per_extra > 2){ |
1209 | – | makeElement( i * cellx, |
1210 | – | j * celly + 0.5 * celly, |
1211 | – | k * cellz + 0.5 * cellz ); |
1212 | – | done = ( current_mol >= tot_nmol ); |
1213 | – | } |
1315 | ||
1316 | < | if( !done && n_per_extra > 3){ |
1317 | < | makeElement( i * cellx + 0.5 * cellx, |
1318 | < | j * celly, |
1319 | < | k * cellz + 0.5 * cellz ); |
1320 | < | done = ( current_mol >= tot_nmol ); |
1321 | < | } |
1221 | < | } |
1316 | > | if( info[l].n_SRI ){ |
1317 | > | |
1318 | > | Exclude::createArray(info[l].n_SRI); |
1319 | > | the_excludes = new Exclude*[info[l].n_SRI]; |
1320 | > | for( int ex=0; ex<info[l].n_SRI; ex++){ |
1321 | > | the_excludes[ex] = new Exclude(ex); |
1322 | } | |
1323 | + | info[l].globalExcludes = new int; |
1324 | + | info[l].n_exclude = info[l].n_SRI; |
1325 | } | |
1326 | < | } |
1326 | > | else{ |
1327 | > | |
1328 | > | Exclude::createArray( 1 ); |
1329 | > | the_excludes = new Exclude*; |
1330 | > | the_excludes[0] = new Exclude(0); |
1331 | > | the_excludes[0]->setPair( 0,0 ); |
1332 | > | info[l].globalExcludes = new int; |
1333 | > | info[l].globalExcludes[0] = 0; |
1334 | > | info[l].n_exclude = 0; |
1335 | > | } |
1336 | ||
1337 | + | // set the arrays into the SimInfo object |
1338 | ||
1339 | < | for( i=0; i<simnfo->n_atoms; i++ ){ |
1340 | < | simnfo->atoms[i]->set_vx( 0.0 ); |
1341 | < | simnfo->atoms[i]->set_vy( 0.0 ); |
1342 | < | simnfo->atoms[i]->set_vz( 0.0 ); |
1339 | > | info[l].atoms = the_atoms; |
1340 | > | info[l].molecules = the_molecules; |
1341 | > | info[l].nGlobalExcludes = 0; |
1342 | > | info[l].excludes = the_excludes; |
1343 | > | |
1344 | > | the_ff->setSimInfo( info ); |
1345 | > | |
1346 | } | |
1347 | } | |
1348 | ||
1349 | < | void SimSetup::makeElement( double x, double y, double z ){ |
1349 | > | void SimSetup::makeIntegrator( void ){ |
1350 | ||
1351 | int k; | |
1237 | – | AtomStamp* current_atom; |
1238 | – | DirectionalAtom* dAtom; |
1239 | – | double rotMat[3][3]; |
1352 | ||
1353 | < | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
1353 | > | NVT<RealIntegrator>* myNVT = NULL; |
1354 | > | NPTi<RealIntegrator>* myNPTi = NULL; |
1355 | > | NPTf<RealIntegrator>* myNPTf = NULL; |
1356 | > | NPTim<RealIntegrator>* myNPTim = NULL; |
1357 | > | NPTfm<RealIntegrator>* myNPTfm = NULL; |
1358 | > | |
1359 | > | for(k=0; k<nInfo; k++){ |
1360 | > | |
1361 | > | switch( ensembleCase ){ |
1362 | > | |
1363 | > | case NVE_ENS: |
1364 | > | if (globals->haveZconstraints()){ |
1365 | > | setupZConstraint(info[k]); |
1366 | > | new ZConstraint<NVE<RealIntegrator> >( &(info[k]), the_ff ); |
1367 | > | } |
1368 | ||
1369 | < | current_atom = comp_stamps[current_comp]->getAtom( k ); |
1370 | < | if( !current_atom->havePosition() ){ |
1369 | > | else |
1370 | > | new NVE<RealIntegrator>( &(info[k]), the_ff ); |
1371 | > | break; |
1372 | > | |
1373 | > | case NVT_ENS: |
1374 | > | if (globals->haveZconstraints()){ |
1375 | > | setupZConstraint(info[k]); |
1376 | > | myNVT = new ZConstraint<NVT<RealIntegrator> >( &(info[k]), the_ff ); |
1377 | > | } |
1378 | > | else |
1379 | > | myNVT = new NVT<RealIntegrator>( &(info[k]), the_ff ); |
1380 | > | |
1381 | > | myNVT->setTargetTemp(globals->getTargetTemp()); |
1382 | > | |
1383 | > | if (globals->haveTauThermostat()) |
1384 | > | myNVT->setTauThermostat(globals->getTauThermostat()); |
1385 | > | |
1386 | > | else { |
1387 | > | sprintf( painCave.errMsg, |
1388 | > | "SimSetup error: If you use the NVT\n" |
1389 | > | " ensemble, you must set tauThermostat.\n"); |
1390 | > | painCave.isFatal = 1; |
1391 | > | simError(); |
1392 | > | } |
1393 | > | break; |
1394 | > | |
1395 | > | case NPTi_ENS: |
1396 | > | if (globals->haveZconstraints()){ |
1397 | > | setupZConstraint(info[k]); |
1398 | > | myNPTi = new ZConstraint<NPTi<RealIntegrator> >( &(info[k]), the_ff ); |
1399 | > | } |
1400 | > | else |
1401 | > | myNPTi = new NPTi<RealIntegrator>( &(info[k]), the_ff ); |
1402 | > | |
1403 | > | myNPTi->setTargetTemp( globals->getTargetTemp() ); |
1404 | > | |
1405 | > | if (globals->haveTargetPressure()) |
1406 | > | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1407 | > | else { |
1408 | > | sprintf( painCave.errMsg, |
1409 | > | "SimSetup error: If you use a constant pressure\n" |
1410 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1411 | > | painCave.isFatal = 1; |
1412 | > | simError(); |
1413 | > | } |
1414 | > | |
1415 | > | if( globals->haveTauThermostat() ) |
1416 | > | myNPTi->setTauThermostat( globals->getTauThermostat() ); |
1417 | > | else{ |
1418 | > | sprintf( painCave.errMsg, |
1419 | > | "SimSetup error: If you use an NPT\n" |
1420 | > | " ensemble, you must set tauThermostat.\n"); |
1421 | > | painCave.isFatal = 1; |
1422 | > | simError(); |
1423 | > | } |
1424 | > | |
1425 | > | if( globals->haveTauBarostat() ) |
1426 | > | myNPTi->setTauBarostat( globals->getTauBarostat() ); |
1427 | > | else{ |
1428 | > | sprintf( painCave.errMsg, |
1429 | > | "SimSetup error: If you use an NPT\n" |
1430 | > | " ensemble, you must set tauBarostat.\n"); |
1431 | > | painCave.isFatal = 1; |
1432 | > | simError(); |
1433 | > | } |
1434 | > | break; |
1435 | > | |
1436 | > | case NPTf_ENS: |
1437 | > | if (globals->haveZconstraints()){ |
1438 | > | setupZConstraint(info[k]); |
1439 | > | myNPTf = new ZConstraint<NPTf<RealIntegrator> >( &(info[k]), the_ff ); |
1440 | > | } |
1441 | > | else |
1442 | > | myNPTf = new NPTf<RealIntegrator>( &(info[k]), the_ff ); |
1443 | > | |
1444 | > | myNPTf->setTargetTemp( globals->getTargetTemp()); |
1445 | > | |
1446 | > | if (globals->haveTargetPressure()) |
1447 | > | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1448 | > | else { |
1449 | > | sprintf( painCave.errMsg, |
1450 | > | "SimSetup error: If you use a constant pressure\n" |
1451 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1452 | > | painCave.isFatal = 1; |
1453 | > | simError(); |
1454 | > | } |
1455 | > | |
1456 | > | if( globals->haveTauThermostat() ) |
1457 | > | myNPTf->setTauThermostat( globals->getTauThermostat() ); |
1458 | > | else{ |
1459 | > | sprintf( painCave.errMsg, |
1460 | > | "SimSetup error: If you use an NPT\n" |
1461 | > | " ensemble, you must set tauThermostat.\n"); |
1462 | > | painCave.isFatal = 1; |
1463 | > | simError(); |
1464 | > | } |
1465 | > | |
1466 | > | if( globals->haveTauBarostat() ) |
1467 | > | myNPTf->setTauBarostat( globals->getTauBarostat() ); |
1468 | > | else{ |
1469 | > | sprintf( painCave.errMsg, |
1470 | > | "SimSetup error: If you use an NPT\n" |
1471 | > | " ensemble, you must set tauBarostat.\n"); |
1472 | > | painCave.isFatal = 1; |
1473 | > | simError(); |
1474 | > | } |
1475 | > | break; |
1476 | > | |
1477 | > | case NPTim_ENS: |
1478 | > | if (globals->haveZconstraints()){ |
1479 | > | setupZConstraint(info[k]); |
1480 | > | myNPTim = new ZConstraint<NPTim<RealIntegrator> >( &(info[k]), the_ff ); |
1481 | > | } |
1482 | > | else |
1483 | > | myNPTim = new NPTim<RealIntegrator>( &(info[k]), the_ff ); |
1484 | > | |
1485 | > | myNPTim->setTargetTemp( globals->getTargetTemp()); |
1486 | > | |
1487 | > | if (globals->haveTargetPressure()) |
1488 | > | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1489 | > | else { |
1490 | > | sprintf( painCave.errMsg, |
1491 | > | "SimSetup error: If you use a constant pressure\n" |
1492 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1493 | > | painCave.isFatal = 1; |
1494 | > | simError(); |
1495 | > | } |
1496 | > | |
1497 | > | if( globals->haveTauThermostat() ) |
1498 | > | myNPTim->setTauThermostat( globals->getTauThermostat() ); |
1499 | > | else{ |
1500 | > | sprintf( painCave.errMsg, |
1501 | > | "SimSetup error: If you use an NPT\n" |
1502 | > | " ensemble, you must set tauThermostat.\n"); |
1503 | > | painCave.isFatal = 1; |
1504 | > | simError(); |
1505 | > | } |
1506 | > | |
1507 | > | if( globals->haveTauBarostat() ) |
1508 | > | myNPTim->setTauBarostat( globals->getTauBarostat() ); |
1509 | > | else{ |
1510 | > | sprintf( painCave.errMsg, |
1511 | > | "SimSetup error: If you use an NPT\n" |
1512 | > | " ensemble, you must set tauBarostat.\n"); |
1513 | > | painCave.isFatal = 1; |
1514 | > | simError(); |
1515 | > | } |
1516 | > | break; |
1517 | > | |
1518 | > | case NPTfm_ENS: |
1519 | > | if (globals->haveZconstraints()){ |
1520 | > | setupZConstraint(info[k]); |
1521 | > | myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >( &(info[k]), the_ff ); |
1522 | > | } |
1523 | > | else |
1524 | > | myNPTfm = new NPTfm<RealIntegrator>( &(info[k]), the_ff ); |
1525 | > | |
1526 | > | myNPTfm->setTargetTemp( globals->getTargetTemp()); |
1527 | > | |
1528 | > | if (globals->haveTargetPressure()) |
1529 | > | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1530 | > | else { |
1531 | > | sprintf( painCave.errMsg, |
1532 | > | "SimSetup error: If you use a constant pressure\n" |
1533 | > | " ensemble, you must set targetPressure in the BASS file.\n"); |
1534 | > | painCave.isFatal = 1; |
1535 | > | simError(); |
1536 | > | } |
1537 | > | |
1538 | > | if( globals->haveTauThermostat() ) |
1539 | > | myNPTfm->setTauThermostat( globals->getTauThermostat() ); |
1540 | > | else{ |
1541 | > | sprintf( painCave.errMsg, |
1542 | > | "SimSetup error: If you use an NPT\n" |
1543 | > | " ensemble, you must set tauThermostat.\n"); |
1544 | > | painCave.isFatal = 1; |
1545 | > | simError(); |
1546 | > | } |
1547 | > | |
1548 | > | if( globals->haveTauBarostat() ) |
1549 | > | myNPTfm->setTauBarostat( globals->getTauBarostat() ); |
1550 | > | else{ |
1551 | > | sprintf( painCave.errMsg, |
1552 | > | "SimSetup error: If you use an NPT\n" |
1553 | > | " ensemble, you must set tauBarostat.\n"); |
1554 | > | painCave.isFatal = 1; |
1555 | > | simError(); |
1556 | > | } |
1557 | > | break; |
1558 | > | |
1559 | > | default: |
1560 | sprintf( painCave.errMsg, | |
1561 | < | "SimSetup:initFromBass error.\n" |
1247 | < | "\tComponent %s, atom %s does not have a position specified.\n" |
1248 | < | "\tThe initialization routine is unable to give a start" |
1249 | < | " position.\n", |
1250 | < | comp_stamps[current_comp]->getID(), |
1251 | < | current_atom->getType() ); |
1561 | > | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1562 | painCave.isFatal = 1; | |
1563 | simError(); | |
1564 | } | |
1565 | + | } |
1566 | + | } |
1567 | ||
1568 | < | the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1257 | < | the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1258 | < | the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
1568 | > | void SimSetup::initFortran( void ){ |
1569 | ||
1570 | < | if( the_atoms[current_atom_ndx]->isDirectional() ){ |
1570 | > | info[0].refreshSim(); |
1571 | > | |
1572 | > | if( !strcmp( info[0].mixingRule, "standard") ){ |
1573 | > | the_ff->initForceField( LB_MIXING_RULE ); |
1574 | > | } |
1575 | > | else if( !strcmp( info[0].mixingRule, "explicit") ){ |
1576 | > | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
1577 | > | } |
1578 | > | else{ |
1579 | > | sprintf( painCave.errMsg, |
1580 | > | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1581 | > | info[0].mixingRule ); |
1582 | > | painCave.isFatal = 1; |
1583 | > | simError(); |
1584 | > | } |
1585 | ||
1262 | – | dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1586 | ||
1587 | < | rotMat[0][0] = 1.0; |
1588 | < | rotMat[0][1] = 0.0; |
1589 | < | rotMat[0][2] = 0.0; |
1587 | > | #ifdef IS_MPI |
1588 | > | strcpy( checkPointMsg, |
1589 | > | "Successfully intialized the mixingRule for Fortran." ); |
1590 | > | MPIcheckPoint(); |
1591 | > | #endif // is_mpi |
1592 | ||
1593 | < | rotMat[1][0] = 0.0; |
1269 | < | rotMat[1][1] = 1.0; |
1270 | < | rotMat[1][2] = 0.0; |
1593 | > | } |
1594 | ||
1595 | < | rotMat[2][0] = 0.0; |
1596 | < | rotMat[2][1] = 0.0; |
1597 | < | rotMat[2][2] = 1.0; |
1595 | > | void SimSetup::setupZConstraint(SimInfo& theInfo) |
1596 | > | { |
1597 | > | int nZConstraints; |
1598 | > | ZconStamp** zconStamp; |
1599 | ||
1600 | < | dAtom->setA( rotMat ); |
1601 | < | } |
1600 | > | if(globals->haveZconstraintTime()){ |
1601 | > | |
1602 | > | //add sample time of z-constraint into SimInfo's property list |
1603 | > | DoubleData* zconsTimeProp = new DoubleData(); |
1604 | > | zconsTimeProp->setID(ZCONSTIME_ID); |
1605 | > | zconsTimeProp->setData(globals->getZconsTime()); |
1606 | > | theInfo.addProperty(zconsTimeProp); |
1607 | > | } |
1608 | > | else{ |
1609 | > | sprintf( painCave.errMsg, |
1610 | > | "ZConstraint error: If you use an ZConstraint\n" |
1611 | > | " , you must set sample time.\n"); |
1612 | > | painCave.isFatal = 1; |
1613 | > | simError(); |
1614 | > | } |
1615 | ||
1616 | < | current_atom_ndx++; |
1616 | > | //push zconsTol into siminfo, if user does not specify |
1617 | > | //value for zconsTol, a default value will be used |
1618 | > | DoubleData* zconsTol = new DoubleData(); |
1619 | > | zconsTol->setID(ZCONSTOL_ID); |
1620 | > | if(globals->haveZconsTol()){ |
1621 | > | zconsTol->setData(globals->getZconsTol()); |
1622 | } | |
1623 | + | else{ |
1624 | + | double defaultZConsTol = 0.01; |
1625 | + | sprintf( painCave.errMsg, |
1626 | + | "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1627 | + | " , default value %f is used.\n", defaultZConsTol); |
1628 | + | painCave.isFatal = 0; |
1629 | + | simError(); |
1630 | ||
1631 | < | current_mol++; |
1632 | < | current_comp_mol++; |
1631 | > | zconsTol->setData(defaultZConsTol); |
1632 | > | } |
1633 | > | theInfo.addProperty(zconsTol); |
1634 | ||
1635 | < | if( current_comp_mol >= components_nmol[current_comp] ){ |
1635 | > | //set Force Substraction Policy |
1636 | > | StringData* zconsForcePolicy = new StringData(); |
1637 | > | zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1638 | > | |
1639 | > | if(globals->haveZconsForcePolicy()){ |
1640 | > | zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
1641 | > | } |
1642 | > | else{ |
1643 | > | sprintf( painCave.errMsg, |
1644 | > | "ZConstraint Warning: User does not set force substraction policy, " |
1645 | > | "average force substraction policy is used\n"); |
1646 | > | painCave.isFatal = 0; |
1647 | > | simError(); |
1648 | > | zconsForcePolicy->setData("BYNUMBER"); |
1649 | > | } |
1650 | > | |
1651 | > | theInfo.addProperty(zconsForcePolicy); |
1652 | > | |
1653 | > | //Determine the name of ouput file and add it into SimInfo's property list |
1654 | > | //Be careful, do not use inFileName, since it is a pointer which |
1655 | > | //point to a string at master node, and slave nodes do not contain that string |
1656 | > | |
1657 | > | string zconsOutput(theInfo.finalName); |
1658 | > | |
1659 | > | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1660 | > | |
1661 | > | StringData* zconsFilename = new StringData(); |
1662 | > | zconsFilename->setID(ZCONSFILENAME_ID); |
1663 | > | zconsFilename->setData(zconsOutput); |
1664 | > | |
1665 | > | theInfo.addProperty(zconsFilename); |
1666 | > | |
1667 | > | //setup index, pos and other parameters of z-constraint molecules |
1668 | > | nZConstraints = globals->getNzConstraints(); |
1669 | > | theInfo.nZconstraints = nZConstraints; |
1670 | ||
1671 | < | current_comp_mol = 0; |
1672 | < | current_comp++; |
1671 | > | zconStamp = globals->getZconStamp(); |
1672 | > | ZConsParaItem tempParaItem; |
1673 | > | |
1674 | > | ZConsParaData* zconsParaData = new ZConsParaData(); |
1675 | > | zconsParaData->setID(ZCONSPARADATA_ID); |
1676 | > | |
1677 | > | for(int i = 0; i < nZConstraints; i++){ |
1678 | > | tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1679 | > | tempParaItem.zPos = zconStamp[i]->getZpos(); |
1680 | > | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1681 | > | tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1682 | > | |
1683 | > | zconsParaData->addItem(tempParaItem); |
1684 | } | |
1685 | + | |
1686 | + | //sort the parameters by index of molecules |
1687 | + | zconsParaData->sortByIndex(); |
1688 | + | |
1689 | + | //push data into siminfo, therefore, we can retrieve later |
1690 | + | theInfo.addProperty(zconsParaData); |
1691 | + | |
1692 | } |
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