# | Line 1 | Line 1 | |
---|---|---|
1 | + | #include <algorithm> |
2 | #include <cstdlib> | |
3 | #include <iostream> | |
4 | #include <cmath> | |
5 | + | #include <string> |
6 | + | #include <sprng.h> |
7 | ||
8 | #include "SimSetup.hpp" | |
9 | + | #include "ReadWrite.hpp" |
10 | #include "parse_me.h" | |
11 | #include "Integrator.hpp" | |
12 | #include "simError.h" | |
# | Line 12 | Line 16 | |
16 | #include "mpiSimulation.hpp" | |
17 | #endif | |
18 | ||
19 | + | // some defines for ensemble and Forcefield cases |
20 | + | |
21 | + | #define NVE_ENS 0 |
22 | + | #define NVT_ENS 1 |
23 | + | #define NPTi_ENS 2 |
24 | + | #define NPTf_ENS 3 |
25 | + | #define NPTxyz_ENS 4 |
26 | + | |
27 | + | |
28 | + | #define FF_DUFF 0 |
29 | + | #define FF_LJ 1 |
30 | + | #define FF_EAM 2 |
31 | + | |
32 | + | using namespace std; |
33 | + | |
34 | SimSetup::SimSetup(){ | |
35 | + | isInfoArray = 0; |
36 | + | nInfo = 1; |
37 | + | |
38 | stamps = new MakeStamps(); | |
39 | globals = new Globals(); | |
40 | < | |
40 | > | |
41 | > | |
42 | #ifdef IS_MPI | |
43 | < | strcpy( checkPointMsg, "SimSetup creation successful" ); |
43 | > | strcpy(checkPointMsg, "SimSetup creation successful"); |
44 | MPIcheckPoint(); | |
45 | #endif // IS_MPI | |
46 | } | |
# | Line 27 | Line 50 | SimSetup::~SimSetup(){ | |
50 | delete globals; | |
51 | } | |
52 | ||
53 | < | void SimSetup::parseFile( char* fileName ){ |
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 | #ifdef IS_MPI | |
62 | < | if( worldRank == 0 ){ |
62 | > | if (worldRank == 0){ |
63 | #endif // is_mpi | |
64 | < | |
64 | > | |
65 | inFileName = fileName; | |
66 | < | set_interface_stamps( stamps, globals ); |
67 | < | |
66 | > | set_interface_stamps(stamps, globals); |
67 | > | |
68 | #ifdef IS_MPI | |
69 | mpiEventInit(); | |
70 | #endif | |
71 | ||
72 | < | yacc_BASS( fileName ); |
72 | > | yacc_BASS(fileName); |
73 | ||
74 | #ifdef IS_MPI | |
75 | throwMPIEvent(NULL); | |
76 | } | |
77 | < | else receiveParse(); |
77 | > | else{ |
78 | > | receiveParse(); |
79 | > | } |
80 | #endif | |
81 | ||
82 | } | |
83 | ||
84 | #ifdef IS_MPI | |
85 | void SimSetup::receiveParse(void){ | |
86 | < | |
87 | < | set_interface_stamps( stamps, globals ); |
88 | < | mpiEventInit(); |
89 | < | MPIcheckPoint(); |
59 | < | mpiEventLoop(); |
60 | < | |
86 | > | set_interface_stamps(stamps, globals); |
87 | > | mpiEventInit(); |
88 | > | MPIcheckPoint(); |
89 | > | mpiEventLoop(); |
90 | } | |
91 | ||
92 | #endif // is_mpi | |
93 | ||
94 | < | void SimSetup::createSim( void ){ |
94 | > | void SimSetup::createSim(void){ |
95 | ||
96 | < | MakeStamps *the_stamps; |
68 | < | Globals* the_globals; |
69 | < | ExtendedSystem* the_extendedsystem; |
70 | < | int i, j; |
96 | > | // gather all of the information from the Bass file |
97 | ||
98 | < | // get the stamps and globals; |
73 | < | the_stamps = stamps; |
74 | < | the_globals = globals; |
98 | > | gatherInfo(); |
99 | ||
100 | < | // set the easy ones first |
77 | < | simnfo->target_temp = the_globals->getTargetTemp(); |
78 | < | simnfo->dt = the_globals->getDt(); |
79 | < | simnfo->run_time = the_globals->getRunTime(); |
100 | > | // creation of complex system objects |
101 | ||
102 | < | // get the ones we know are there, yet still may need some work. |
82 | < | n_components = the_globals->getNComponents(); |
83 | < | strcpy( force_field, the_globals->getForceField() ); |
102 | > | sysObjectsCreation(); |
103 | ||
104 | < | // get the ensemble and set up an extended system if we need it: |
86 | < | strcpy( ensemble, the_globals->getEnsemble() ); |
87 | < | if( !strcasecmp( ensemble, "NPT" ) ) { |
88 | < | the_extendedsystem = new ExtendedSystem( simnfo ); |
89 | < | the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
90 | < | if (the_globals->haveTargetPressure()) |
91 | < | the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
92 | < | else { |
93 | < | sprintf( painCave.errMsg, |
94 | < | "SimSetup error: If you use the constant pressure\n" |
95 | < | " ensemble, you must set targetPressure.\n" |
96 | < | " This was found in the BASS file.\n"); |
97 | < | painCave.isFatal = 1; |
98 | < | simError(); |
99 | < | } |
104 | > | // check on the post processing info |
105 | ||
106 | < | if (the_globals->haveTauThermostat()) |
102 | < | the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
103 | < | else if (the_globals->haveQmass()) |
104 | < | the_extendedsystem->setQmass(the_globals->getQmass()); |
105 | < | else { |
106 | < | sprintf( painCave.errMsg, |
107 | < | "SimSetup error: If you use one of the constant temperature\n" |
108 | < | " ensembles, you must set either tauThermostat or qMass.\n" |
109 | < | " Neither of these was found in the BASS file.\n"); |
110 | < | painCave.isFatal = 1; |
111 | < | simError(); |
112 | < | } |
106 | > | finalInfoCheck(); |
107 | ||
108 | < | if (the_globals->haveTauBarostat()) |
115 | < | the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
116 | < | else { |
117 | < | sprintf( painCave.errMsg, |
118 | < | "SimSetup error: If you use the constant pressure\n" |
119 | < | " ensemble, you must set tauBarostat.\n" |
120 | < | " This was found in the BASS file.\n"); |
121 | < | painCave.isFatal = 1; |
122 | < | simError(); |
123 | < | } |
108 | > | // initialize the system coordinates |
109 | ||
110 | < | } else if ( !strcasecmp( ensemble, "NVT") ) { |
111 | < | the_extendedsystem = new ExtendedSystem( simnfo ); |
127 | < | the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
110 | > | if (!isInfoArray){ |
111 | > | initSystemCoords(); |
112 | ||
113 | < | if (the_globals->haveTauThermostat()) |
114 | < | the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
131 | < | else if (the_globals->haveQmass()) |
132 | < | the_extendedsystem->setQmass(the_globals->getQmass()); |
133 | < | else { |
134 | < | sprintf( painCave.errMsg, |
135 | < | "SimSetup error: If you use one of the constant temperature\n" |
136 | < | " ensembles, you must set either tauThermostat or qMass.\n" |
137 | < | " Neither of these was found in the BASS file.\n"); |
138 | < | painCave.isFatal = 1; |
139 | < | simError(); |
140 | < | } |
141 | < | |
142 | < | } else if ( !strcasecmp( ensemble, "NVE") ) { |
143 | < | } else { |
144 | < | sprintf( painCave.errMsg, |
145 | < | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
146 | < | "reverting to NVE for this simulation.\n", |
147 | < | ensemble ); |
148 | < | painCave.isFatal = 0; |
149 | < | simError(); |
150 | < | strcpy( ensemble, "NVE" ); |
113 | > | if( !(globals->getUseInitTime()) ) |
114 | > | info[0].currentTime = 0.0; |
115 | } | |
152 | – | strcpy( simnfo->ensemble, ensemble ); |
116 | ||
117 | < | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
155 | < | simnfo->usePBC = the_globals->getPBC(); |
156 | < | |
157 | < | int usesDipoles = 0; |
158 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
159 | < | the_ff = new TraPPE_ExFF(); |
160 | < | usesDipoles = 1; |
161 | < | } |
162 | < | else if( !strcasecmp( force_field, "LJ" ) ) the_ff = new LJ_FF(); |
163 | < | else{ |
164 | < | sprintf( painCave.errMsg, |
165 | < | "SimSetup Error. Unrecognized force field -> %s\n", |
166 | < | force_field ); |
167 | < | painCave.isFatal = 1; |
168 | < | simError(); |
169 | < | } |
117 | > | // make the output filenames |
118 | ||
119 | < | #ifdef IS_MPI |
172 | < | strcpy( checkPointMsg, "ForceField creation successful" ); |
173 | < | MPIcheckPoint(); |
174 | < | #endif // is_mpi |
119 | > | makeOutNames(); |
120 | ||
121 | < | |
121 | > | // make the integrator |
122 | ||
123 | < | // get the components and calculate the tot_nMol and indvidual n_mol |
179 | < | the_components = the_globals->getComponents(); |
180 | < | components_nmol = new int[n_components]; |
181 | < | comp_stamps = new MoleculeStamp*[n_components]; |
123 | > | makeIntegrator(); |
124 | ||
125 | < | if( !the_globals->haveNMol() ){ |
126 | < | // we don't have the total number of molecules, so we assume it is |
127 | < | // given in each component |
125 | > | #ifdef IS_MPI |
126 | > | mpiSim->mpiRefresh(); |
127 | > | #endif |
128 | ||
129 | < | tot_nmol = 0; |
188 | < | for( i=0; i<n_components; i++ ){ |
129 | > | // initialize the Fortran |
130 | ||
131 | < | if( !the_components[i]->haveNMol() ){ |
132 | < | // we have a problem |
192 | < | sprintf( painCave.errMsg, |
193 | < | "SimSetup Error. No global NMol or component NMol" |
194 | < | " given. Cannot calculate the number of atoms.\n" ); |
195 | < | painCave.isFatal = 1; |
196 | < | simError(); |
197 | < | } |
131 | > | initFortran(); |
132 | > | } |
133 | ||
199 | – | tot_nmol += the_components[i]->getNMol(); |
200 | – | components_nmol[i] = the_components[i]->getNMol(); |
201 | – | } |
202 | – | } |
203 | – | else{ |
204 | – | sprintf( painCave.errMsg, |
205 | – | "SimSetup error.\n" |
206 | – | "\tSorry, the ability to specify total" |
207 | – | " nMols and then give molfractions in the components\n" |
208 | – | "\tis not currently supported." |
209 | – | " Please give nMol in the components.\n" ); |
210 | – | painCave.isFatal = 1; |
211 | – | simError(); |
212 | – | |
213 | – | |
214 | – | // tot_nmol = the_globals->getNMol(); |
215 | – | |
216 | – | // //we have the total number of molecules, now we check for molfractions |
217 | – | // for( i=0; i<n_components; i++ ){ |
218 | – | |
219 | – | // if( !the_components[i]->haveMolFraction() ){ |
220 | – | |
221 | – | // if( !the_components[i]->haveNMol() ){ |
222 | – | // //we have a problem |
223 | – | // std::cerr << "SimSetup error. Neither molFraction nor " |
224 | – | // << " nMol was given in component |
225 | – | |
226 | – | } |
134 | ||
135 | < | #ifdef IS_MPI |
136 | < | strcpy( checkPointMsg, "Have the number of components" ); |
137 | < | MPIcheckPoint(); |
138 | < | #endif // is_mpi |
135 | > | void SimSetup::makeMolecules(void){ |
136 | > | int k; |
137 | > | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
138 | > | molInit molInfo; |
139 | > | DirectionalAtom* dAtom; |
140 | > | LinkedAssign* extras; |
141 | > | LinkedAssign* current_extra; |
142 | > | AtomStamp* currentAtom; |
143 | > | BondStamp* currentBond; |
144 | > | BendStamp* currentBend; |
145 | > | TorsionStamp* currentTorsion; |
146 | ||
147 | < | // make an array of molecule stamps that match the components used. |
148 | < | // also extract the used stamps out into a separate linked list |
147 | > | bond_pair* theBonds; |
148 | > | bend_set* theBends; |
149 | > | torsion_set* theTorsions; |
150 | ||
236 | – | simnfo->nComponents = n_components; |
237 | – | simnfo->componentsNmol = components_nmol; |
238 | – | simnfo->compStamps = comp_stamps; |
239 | – | simnfo->headStamp = new LinkedMolStamp(); |
240 | – | |
241 | – | char* id; |
242 | – | LinkedMolStamp* headStamp = simnfo->headStamp; |
243 | – | LinkedMolStamp* currentStamp = NULL; |
244 | – | for( i=0; i<n_components; i++ ){ |
151 | ||
152 | < | id = the_components[i]->getType(); |
247 | < | comp_stamps[i] = NULL; |
248 | < | |
249 | < | // check to make sure the component isn't already in the list |
152 | > | //init the forceField paramters |
153 | ||
154 | < | comp_stamps[i] = headStamp->match( id ); |
252 | < | if( comp_stamps[i] == NULL ){ |
253 | < | |
254 | < | // extract the component from the list; |
255 | < | |
256 | < | currentStamp = the_stamps->extractMolStamp( id ); |
257 | < | if( currentStamp == NULL ){ |
258 | < | sprintf( painCave.errMsg, |
259 | < | "SimSetup error: Component \"%s\" was not found in the " |
260 | < | "list of declared molecules\n", |
261 | < | id ); |
262 | < | painCave.isFatal = 1; |
263 | < | simError(); |
264 | < | } |
265 | < | |
266 | < | headStamp->add( currentStamp ); |
267 | < | comp_stamps[i] = headStamp->match( id ); |
268 | < | } |
269 | < | } |
154 | > | the_ff->readParams(); |
155 | ||
271 | – | #ifdef IS_MPI |
272 | – | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
273 | – | MPIcheckPoint(); |
274 | – | #endif // is_mpi |
275 | – | |
156 | ||
157 | + | // init the atoms |
158 | ||
159 | < | |
279 | < | // caclulate the number of atoms, bonds, bends and torsions |
159 | > | double ux, uy, uz, u, uSqr; |
160 | ||
161 | < | tot_atoms = 0; |
162 | < | tot_bonds = 0; |
283 | < | tot_bends = 0; |
284 | < | tot_torsions = 0; |
285 | < | for( i=0; i<n_components; i++ ){ |
286 | < | |
287 | < | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
288 | < | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
289 | < | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
290 | < | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
291 | < | } |
161 | > | for (k = 0; k < nInfo; k++){ |
162 | > | the_ff->setSimInfo(&(info[k])); |
163 | ||
164 | < | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
164 | > | atomOffset = 0; |
165 | > | excludeOffset = 0; |
166 | > | for (i = 0; i < info[k].n_mol; i++){ |
167 | > | stampID = info[k].molecules[i].getStampID(); |
168 | ||
169 | < | simnfo->n_atoms = tot_atoms; |
170 | < | simnfo->n_bonds = tot_bonds; |
171 | < | simnfo->n_bends = tot_bends; |
172 | < | simnfo->n_torsions = tot_torsions; |
173 | < | simnfo->n_SRI = tot_SRI; |
300 | < | simnfo->n_mol = tot_nmol; |
169 | > | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
170 | > | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
171 | > | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
172 | > | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
173 | > | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
174 | ||
175 | < | |
176 | < | #ifdef IS_MPI |
175 | > | molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
176 | > | molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
177 | > | molInfo.myBonds = new Bond * [molInfo.nBonds]; |
178 | > | molInfo.myBends = new Bend * [molInfo.nBends]; |
179 | > | molInfo.myTorsions = new Torsion * [molInfo.nTorsions]; |
180 | ||
181 | < | // divide the molecules among processors here. |
182 | < | |
183 | < | mpiSim = new mpiSimulation( simnfo ); |
308 | < | |
309 | < | |
181 | > | theBonds = new bond_pair[molInfo.nBonds]; |
182 | > | theBends = new bend_set[molInfo.nBends]; |
183 | > | theTorsions = new torsion_set[molInfo.nTorsions]; |
184 | ||
185 | < | globalIndex = mpiSim->divideLabor(); |
185 | > | // make the Atoms |
186 | ||
187 | < | // set up the local variables |
188 | < | |
189 | < | int localMol, allMol; |
190 | < | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
187 | > | for (j = 0; j < molInfo.nAtoms; j++){ |
188 | > | currentAtom = comp_stamps[stampID]->getAtom(j); |
189 | > | if (currentAtom->haveOrientation()){ |
190 | > | dAtom = new DirectionalAtom((j + atomOffset), |
191 | > | info[k].getConfiguration()); |
192 | > | info[k].n_oriented++; |
193 | > | molInfo.myAtoms[j] = dAtom; |
194 | ||
195 | < | int* mol2proc = mpiSim->getMolToProcMap(); |
196 | < | int* molCompType = mpiSim->getMolComponentType(); |
197 | < | |
321 | < | allMol = 0; |
322 | < | localMol = 0; |
323 | < | local_atoms = 0; |
324 | < | local_bonds = 0; |
325 | < | local_bends = 0; |
326 | < | local_torsions = 0; |
327 | < | for( i=0; i<n_components; i++ ){ |
195 | > | ux = currentAtom->getOrntX(); |
196 | > | uy = currentAtom->getOrntY(); |
197 | > | uz = currentAtom->getOrntZ(); |
198 | ||
199 | < | for( j=0; j<components_nmol[i]; j++ ){ |
330 | < | |
331 | < | if( mol2proc[allMol] == worldRank ){ |
332 | < | |
333 | < | local_atoms += comp_stamps[i]->getNAtoms(); |
334 | < | local_bonds += comp_stamps[i]->getNBonds(); |
335 | < | local_bends += comp_stamps[i]->getNBends(); |
336 | < | local_torsions += comp_stamps[i]->getNTorsions(); |
337 | < | localMol++; |
338 | < | } |
339 | < | allMol++; |
340 | < | } |
341 | < | } |
342 | < | local_SRI = local_bonds + local_bends + local_torsions; |
343 | < | |
199 | > | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
200 | ||
201 | < | simnfo->n_atoms = mpiSim->getMyNlocal(); |
202 | < | |
203 | < | if( local_atoms != simnfo->n_atoms ){ |
204 | < | sprintf( painCave.errMsg, |
349 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
350 | < | " localAtom (%d) are not equal.\n", |
351 | < | simnfo->n_atoms, |
352 | < | local_atoms ); |
353 | < | painCave.isFatal = 1; |
354 | < | simError(); |
355 | < | } |
201 | > | u = sqrt(uSqr); |
202 | > | ux = ux / u; |
203 | > | uy = uy / u; |
204 | > | uz = uz / u; |
205 | ||
206 | < | simnfo->n_bonds = local_bonds; |
207 | < | simnfo->n_bends = local_bends; |
208 | < | simnfo->n_torsions = local_torsions; |
209 | < | simnfo->n_SRI = local_SRI; |
210 | < | simnfo->n_mol = localMol; |
206 | > | dAtom->setSUx(ux); |
207 | > | dAtom->setSUy(uy); |
208 | > | dAtom->setSUz(uz); |
209 | > | } |
210 | > | else{ |
211 | > | molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset), |
212 | > | info[k].getConfiguration()); |
213 | > | } |
214 | > | molInfo.myAtoms[j]->setType(currentAtom->getType()); |
215 | ||
216 | < | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
364 | < | MPIcheckPoint(); |
365 | < | |
366 | < | |
367 | < | #endif // is_mpi |
368 | < | |
216 | > | #ifdef IS_MPI |
217 | ||
218 | < | // create the atom and short range interaction arrays |
218 | > | molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]); |
219 | ||
220 | < | Atom::createArrays(simnfo->n_atoms); |
221 | < | the_atoms = new Atom*[simnfo->n_atoms]; |
374 | < | the_molecules = new Molecule[simnfo->n_mol]; |
375 | < | int molIndex; |
220 | > | #endif // is_mpi |
221 | > | } |
222 | ||
223 | < | // initialize the molecule's stampID's |
223 | > | // make the bonds |
224 | > | for (j = 0; j < molInfo.nBonds; j++){ |
225 | > | currentBond = comp_stamps[stampID]->getBond(j); |
226 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
227 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
228 | ||
229 | + | exI = theBonds[j].a; |
230 | + | exJ = theBonds[j].b; |
231 | + | |
232 | + | // exclude_I must always be the smaller of the pair |
233 | + | if (exI > exJ){ |
234 | + | tempEx = exI; |
235 | + | exI = exJ; |
236 | + | exJ = tempEx; |
237 | + | } |
238 | #ifdef IS_MPI | |
239 | < | |
239 | > | tempEx = exI; |
240 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
241 | > | tempEx = exJ; |
242 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
243 | ||
244 | < | molIndex = 0; |
245 | < | for(i=0; i<mpiSim->getTotNmol(); i++){ |
384 | < | |
385 | < | if(mol2proc[i] == worldRank ){ |
386 | < | the_molecules[molIndex].setStampID( molCompType[i] ); |
387 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
388 | < | molIndex++; |
389 | < | } |
390 | < | } |
244 | > | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
245 | > | #else // isn't MPI |
246 | ||
247 | < | #else // is_mpi |
248 | < | |
249 | < | molIndex = 0; |
250 | < | for(i=0; i<n_components; i++){ |
396 | < | for(j=0; j<components_nmol[i]; j++ ){ |
397 | < | the_molecules[molIndex].setStampID( i ); |
398 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
399 | < | molIndex++; |
400 | < | } |
401 | < | } |
402 | < | |
247 | > | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
248 | > | #endif //is_mpi |
249 | > | } |
250 | > | excludeOffset += molInfo.nBonds; |
251 | ||
252 | < | #endif // is_mpi |
252 | > | //make the bends |
253 | > | for (j = 0; j < molInfo.nBends; j++){ |
254 | > | currentBend = comp_stamps[stampID]->getBend(j); |
255 | > | theBends[j].a = currentBend->getA() + atomOffset; |
256 | > | theBends[j].b = currentBend->getB() + atomOffset; |
257 | > | theBends[j].c = currentBend->getC() + atomOffset; |
258 | ||
259 | + | if (currentBend->haveExtras()){ |
260 | + | extras = currentBend->getExtras(); |
261 | + | current_extra = extras; |
262 | ||
263 | < | if( simnfo->n_SRI ){ |
264 | < | |
265 | < | Exclude::createArray(simnfo->n_SRI); |
266 | < | the_excludes = new Exclude*[simnfo->n_SRI]; |
267 | < | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
268 | < | simnfo->globalExcludes = new int; |
269 | < | simnfo->n_exclude = simnfo->n_SRI; |
414 | < | } |
415 | < | else{ |
416 | < | |
417 | < | Exclude::createArray( 1 ); |
418 | < | the_excludes = new Exclude*; |
419 | < | the_excludes[0] = new Exclude(0); |
420 | < | the_excludes[0]->setPair( 0,0 ); |
421 | < | simnfo->globalExcludes = new int; |
422 | < | simnfo->globalExcludes[0] = 0; |
423 | < | simnfo->n_exclude = 0; |
424 | < | } |
263 | > | while (current_extra != NULL){ |
264 | > | if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){ |
265 | > | switch (current_extra->getType()){ |
266 | > | case 0: |
267 | > | theBends[j].ghost = current_extra->getInt() + atomOffset; |
268 | > | theBends[j].isGhost = 1; |
269 | > | break; |
270 | ||
271 | < | // set the arrays into the SimInfo object |
271 | > | case 1: |
272 | > | theBends[j].ghost = (int) current_extra->getDouble() + |
273 | > | atomOffset; |
274 | > | theBends[j].isGhost = 1; |
275 | > | break; |
276 | ||
277 | < | simnfo->atoms = the_atoms; |
278 | < | simnfo->molecules = the_molecules; |
279 | < | simnfo->nGlobalExcludes = 0; |
280 | < | simnfo->excludes = the_excludes; |
277 | > | default: |
278 | > | sprintf(painCave.errMsg, |
279 | > | "SimSetup Error: ghostVectorSource was neither a " |
280 | > | "double nor an int.\n" |
281 | > | "-->Bend[%d] in %s\n", |
282 | > | j, comp_stamps[stampID]->getID()); |
283 | > | painCave.isFatal = 1; |
284 | > | simError(); |
285 | > | } |
286 | > | } |
287 | > | else{ |
288 | > | sprintf(painCave.errMsg, |
289 | > | "SimSetup Error: unhandled bend assignment:\n" |
290 | > | " -->%s in Bend[%d] in %s\n", |
291 | > | current_extra->getlhs(), j, comp_stamps[stampID]->getID()); |
292 | > | painCave.isFatal = 1; |
293 | > | simError(); |
294 | > | } |
295 | ||
296 | + | current_extra = current_extra->getNext(); |
297 | + | } |
298 | + | } |
299 | ||
300 | < | // get some of the tricky things that may still be in the globals |
301 | < | |
302 | < | |
303 | < | if( the_globals->haveBox() ){ |
304 | < | simnfo->box_x = the_globals->getBox(); |
305 | < | simnfo->box_y = the_globals->getBox(); |
306 | < | simnfo->box_z = the_globals->getBox(); |
307 | < | } |
442 | < | else if( the_globals->haveDensity() ){ |
300 | > | if (!theBends[j].isGhost){ |
301 | > | exI = theBends[j].a; |
302 | > | exJ = theBends[j].c; |
303 | > | } |
304 | > | else{ |
305 | > | exI = theBends[j].a; |
306 | > | exJ = theBends[j].b; |
307 | > | } |
308 | ||
309 | < | double vol; |
310 | < | vol = (double)tot_nmol / the_globals->getDensity(); |
311 | < | simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
312 | < | simnfo->box_y = simnfo->box_x; |
313 | < | simnfo->box_z = simnfo->box_x; |
314 | < | } |
315 | < | else{ |
316 | < | if( !the_globals->haveBoxX() ){ |
317 | < | sprintf( painCave.errMsg, |
318 | < | "SimSetup error, no periodic BoxX size given.\n" ); |
319 | < | painCave.isFatal = 1; |
455 | < | simError(); |
456 | < | } |
457 | < | simnfo->box_x = the_globals->getBoxX(); |
309 | > | // exclude_I must always be the smaller of the pair |
310 | > | if (exI > exJ){ |
311 | > | tempEx = exI; |
312 | > | exI = exJ; |
313 | > | exJ = tempEx; |
314 | > | } |
315 | > | #ifdef IS_MPI |
316 | > | tempEx = exI; |
317 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
318 | > | tempEx = exJ; |
319 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
320 | ||
321 | < | if( !the_globals->haveBoxY() ){ |
322 | < | sprintf( painCave.errMsg, |
323 | < | "SimSetup error, no periodic BoxY size given.\n" ); |
324 | < | painCave.isFatal = 1; |
325 | < | simError(); |
326 | < | } |
465 | < | simnfo->box_y = the_globals->getBoxY(); |
321 | > | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
322 | > | #else // isn't MPI |
323 | > | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
324 | > | #endif //is_mpi |
325 | > | } |
326 | > | excludeOffset += molInfo.nBends; |
327 | ||
328 | < | if( !the_globals->haveBoxZ() ){ |
329 | < | sprintf( painCave.errMsg, |
330 | < | "SimSetup error, no periodic BoxZ size given.\n" ); |
331 | < | painCave.isFatal = 1; |
332 | < | simError(); |
333 | < | } |
473 | < | simnfo->box_z = the_globals->getBoxZ(); |
474 | < | } |
328 | > | for (j = 0; j < molInfo.nTorsions; j++){ |
329 | > | currentTorsion = comp_stamps[stampID]->getTorsion(j); |
330 | > | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
331 | > | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
332 | > | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
333 | > | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
334 | ||
335 | + | exI = theTorsions[j].a; |
336 | + | exJ = theTorsions[j].d; |
337 | + | |
338 | + | // exclude_I must always be the smaller of the pair |
339 | + | if (exI > exJ){ |
340 | + | tempEx = exI; |
341 | + | exI = exJ; |
342 | + | exJ = tempEx; |
343 | + | } |
344 | #ifdef IS_MPI | |
345 | < | strcpy( checkPointMsg, "Box size set up" ); |
346 | < | MPIcheckPoint(); |
347 | < | #endif // is_mpi |
345 | > | tempEx = exI; |
346 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
347 | > | tempEx = exJ; |
348 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
349 | ||
350 | + | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
351 | + | #else // isn't MPI |
352 | + | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
353 | + | #endif //is_mpi |
354 | + | } |
355 | + | excludeOffset += molInfo.nTorsions; |
356 | ||
482 | – | // initialize the arrays |
357 | ||
358 | < | the_ff->setSimInfo( simnfo ); |
358 | > | // send the arrays off to the forceField for init. |
359 | ||
360 | < | makeMolecules(); |
361 | < | simnfo->identArray = new int[simnfo->n_atoms]; |
362 | < | simnfo->molMembershipArray = new int[simnfo->n_atoms]; |
363 | < | for(i=0; i<simnfo->n_atoms; i++){ |
364 | < | simnfo->identArray[i] = the_atoms[i]->getIdent(); |
491 | < | } |
492 | < | for(i=0; i< simnfo->n_mol; i++) { |
493 | < | the_molecules[i].atomicRollCall(simnfo->molMembershipArray); |
494 | < | } |
495 | < | |
496 | < | if (the_globals->getUseRF() ) { |
497 | < | simnfo->useReactionField = 1; |
498 | < | |
499 | < | if( !the_globals->haveECR() ){ |
500 | < | sprintf( painCave.errMsg, |
501 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
502 | < | "box length for the electrostaticCutoffRadius.\n" |
503 | < | "I hope you have a very fast processor!\n"); |
504 | < | painCave.isFatal = 0; |
505 | < | simError(); |
506 | < | double smallest; |
507 | < | smallest = simnfo->box_x; |
508 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
509 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
510 | < | simnfo->ecr = 0.5 * smallest; |
511 | < | } else { |
512 | < | simnfo->ecr = the_globals->getECR(); |
513 | < | } |
360 | > | the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); |
361 | > | the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds); |
362 | > | the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends); |
363 | > | the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, |
364 | > | theTorsions); |
365 | ||
366 | < | if( !the_globals->haveEST() ){ |
367 | < | sprintf( painCave.errMsg, |
368 | < | "SimSetup Warning: using default value of 0.05 * the " |
369 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
370 | < | ); |
371 | < | painCave.isFatal = 0; |
372 | < | simError(); |
373 | < | simnfo->est = 0.05 * simnfo->ecr; |
523 | < | } else { |
524 | < | simnfo->est = the_globals->getEST(); |
366 | > | |
367 | > | info[k].molecules[i].initialize(molInfo); |
368 | > | |
369 | > | |
370 | > | atomOffset += molInfo.nAtoms; |
371 | > | delete[] theBonds; |
372 | > | delete[] theBends; |
373 | > | delete[] theTorsions; |
374 | } | |
375 | < | |
527 | < | if(!the_globals->haveDielectric() ){ |
528 | < | sprintf( painCave.errMsg, |
529 | < | "SimSetup Error: You are trying to use Reaction Field without" |
530 | < | "setting a dielectric constant!\n" |
531 | < | ); |
532 | < | painCave.isFatal = 1; |
533 | < | simError(); |
534 | < | } |
535 | < | simnfo->dielectric = the_globals->getDielectric(); |
536 | < | } else { |
537 | < | if (usesDipoles) { |
538 | < | |
539 | < | if( !the_globals->haveECR() ){ |
540 | < | sprintf( painCave.errMsg, |
541 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
542 | < | "box length for the electrostaticCutoffRadius.\n" |
543 | < | "I hope you have a very fast processor!\n"); |
544 | < | painCave.isFatal = 0; |
545 | < | simError(); |
546 | < | double smallest; |
547 | < | smallest = simnfo->box_x; |
548 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
549 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
550 | < | simnfo->ecr = 0.5 * smallest; |
551 | < | } else { |
552 | < | simnfo->ecr = the_globals->getECR(); |
553 | < | } |
554 | < | |
555 | < | if( !the_globals->haveEST() ){ |
556 | < | sprintf( painCave.errMsg, |
557 | < | "SimSetup Warning: using default value of 5%% of the " |
558 | < | "electrostaticCutoffRadius for the " |
559 | < | "electrostaticSkinThickness\n" |
560 | < | ); |
561 | < | painCave.isFatal = 0; |
562 | < | simError(); |
563 | < | simnfo->est = 0.05 * simnfo->ecr; |
564 | < | } else { |
565 | < | simnfo->est = the_globals->getEST(); |
566 | < | } |
567 | < | } |
568 | < | } |
375 | > | } |
376 | ||
377 | #ifdef IS_MPI | |
378 | < | strcpy( checkPointMsg, "electrostatic parameters check out" ); |
378 | > | sprintf(checkPointMsg, "all molecules initialized succesfully"); |
379 | MPIcheckPoint(); | |
380 | #endif // is_mpi | |
381 | ||
382 | < | if( the_globals->haveInitialConfig() ){ |
576 | < | |
577 | < | InitializeFromFile* fileInit; |
578 | < | #ifdef IS_MPI // is_mpi |
579 | < | if( worldRank == 0 ){ |
580 | < | #endif //is_mpi |
581 | < | fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
582 | < | #ifdef IS_MPI |
583 | < | }else fileInit = new InitializeFromFile( NULL ); |
584 | < | #endif |
585 | < | fileInit->read_xyz( simnfo ); // default velocities on |
382 | > | // clean up the forcefield |
383 | ||
384 | < | delete fileInit; |
385 | < | } |
386 | < | else{ |
384 | > | the_ff->calcRcut(); |
385 | > | the_ff->cleanMe(); |
386 | > | } |
387 | ||
388 | < | #ifdef IS_MPI |
388 | > | void SimSetup::initFromBass(void){ |
389 | > | int i, j, k; |
390 | > | int n_cells; |
391 | > | double cellx, celly, cellz; |
392 | > | double temp1, temp2, temp3; |
393 | > | int n_per_extra; |
394 | > | int n_extra; |
395 | > | int have_extra, done; |
396 | ||
397 | < | // no init from bass |
398 | < | |
399 | < | sprintf( painCave.errMsg, |
400 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
597 | < | painCave.isFatal; |
598 | < | simError(); |
599 | < | |
600 | < | #else |
397 | > | double vel[3]; |
398 | > | vel[0] = 0.0; |
399 | > | vel[1] = 0.0; |
400 | > | vel[2] = 0.0; |
401 | ||
402 | < | initFromBass(); |
402 | > | temp1 = (double) tot_nmol / 4.0; |
403 | > | temp2 = pow(temp1, (1.0 / 3.0)); |
404 | > | temp3 = ceil(temp2); |
405 | ||
406 | + | have_extra = 0; |
407 | + | if (temp2 < temp3){ |
408 | + | // we have a non-complete lattice |
409 | + | have_extra = 1; |
410 | ||
411 | < | #endif |
412 | < | } |
411 | > | n_cells = (int) temp3 - 1; |
412 | > | cellx = info[0].boxL[0] / temp3; |
413 | > | celly = info[0].boxL[1] / temp3; |
414 | > | cellz = info[0].boxL[2] / temp3; |
415 | > | n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells); |
416 | > | temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0)); |
417 | > | n_per_extra = (int) ceil(temp1); |
418 | ||
419 | < | #ifdef IS_MPI |
420 | < | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
421 | < | MPIcheckPoint(); |
422 | < | #endif // is_mpi |
423 | < | |
424 | < | |
614 | < | |
615 | < | |
616 | < | |
617 | < | |
618 | < | |
619 | < | #ifdef IS_MPI |
620 | < | if( worldRank == 0 ){ |
621 | < | #endif // is_mpi |
622 | < | |
623 | < | if( the_globals->haveFinalConfig() ){ |
624 | < | strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
419 | > | if (n_per_extra > 4){ |
420 | > | sprintf(painCave.errMsg, |
421 | > | "SimSetup error. There has been an error in constructing" |
422 | > | " the non-complete lattice.\n"); |
423 | > | painCave.isFatal = 1; |
424 | > | simError(); |
425 | } | |
626 | – | else{ |
627 | – | strcpy( simnfo->finalName, inFileName ); |
628 | – | char* endTest; |
629 | – | int nameLength = strlen( simnfo->finalName ); |
630 | – | endTest = &(simnfo->finalName[nameLength - 5]); |
631 | – | if( !strcmp( endTest, ".bass" ) ){ |
632 | – | strcpy( endTest, ".eor" ); |
633 | – | } |
634 | – | else if( !strcmp( endTest, ".BASS" ) ){ |
635 | – | strcpy( endTest, ".eor" ); |
636 | – | } |
637 | – | else{ |
638 | – | endTest = &(simnfo->finalName[nameLength - 4]); |
639 | – | if( !strcmp( endTest, ".bss" ) ){ |
640 | – | strcpy( endTest, ".eor" ); |
641 | – | } |
642 | – | else if( !strcmp( endTest, ".mdl" ) ){ |
643 | – | strcpy( endTest, ".eor" ); |
644 | – | } |
645 | – | else{ |
646 | – | strcat( simnfo->finalName, ".eor" ); |
647 | – | } |
648 | – | } |
649 | – | } |
650 | – | |
651 | – | // make the sample and status out names |
652 | – | |
653 | – | strcpy( simnfo->sampleName, inFileName ); |
654 | – | char* endTest; |
655 | – | int nameLength = strlen( simnfo->sampleName ); |
656 | – | endTest = &(simnfo->sampleName[nameLength - 5]); |
657 | – | if( !strcmp( endTest, ".bass" ) ){ |
658 | – | strcpy( endTest, ".dump" ); |
659 | – | } |
660 | – | else if( !strcmp( endTest, ".BASS" ) ){ |
661 | – | strcpy( endTest, ".dump" ); |
662 | – | } |
663 | – | else{ |
664 | – | endTest = &(simnfo->sampleName[nameLength - 4]); |
665 | – | if( !strcmp( endTest, ".bss" ) ){ |
666 | – | strcpy( endTest, ".dump" ); |
667 | – | } |
668 | – | else if( !strcmp( endTest, ".mdl" ) ){ |
669 | – | strcpy( endTest, ".dump" ); |
670 | – | } |
671 | – | else{ |
672 | – | strcat( simnfo->sampleName, ".dump" ); |
673 | – | } |
674 | – | } |
675 | – | |
676 | – | strcpy( simnfo->statusName, inFileName ); |
677 | – | nameLength = strlen( simnfo->statusName ); |
678 | – | endTest = &(simnfo->statusName[nameLength - 5]); |
679 | – | if( !strcmp( endTest, ".bass" ) ){ |
680 | – | strcpy( endTest, ".stat" ); |
681 | – | } |
682 | – | else if( !strcmp( endTest, ".BASS" ) ){ |
683 | – | strcpy( endTest, ".stat" ); |
684 | – | } |
685 | – | else{ |
686 | – | endTest = &(simnfo->statusName[nameLength - 4]); |
687 | – | if( !strcmp( endTest, ".bss" ) ){ |
688 | – | strcpy( endTest, ".stat" ); |
689 | – | } |
690 | – | else if( !strcmp( endTest, ".mdl" ) ){ |
691 | – | strcpy( endTest, ".stat" ); |
692 | – | } |
693 | – | else{ |
694 | – | strcat( simnfo->statusName, ".stat" ); |
695 | – | } |
696 | – | } |
697 | – | |
698 | – | #ifdef IS_MPI |
426 | } | |
700 | – | #endif // is_mpi |
701 | – | |
702 | – | // set the status, sample, and themal kick times |
703 | – | |
704 | – | if( the_globals->haveSampleTime() ){ |
705 | – | simnfo->sampleTime = the_globals->getSampleTime(); |
706 | – | simnfo->statusTime = simnfo->sampleTime; |
707 | – | simnfo->thermalTime = simnfo->sampleTime; |
708 | – | } |
427 | else{ | |
428 | < | simnfo->sampleTime = the_globals->getRunTime(); |
429 | < | simnfo->statusTime = simnfo->sampleTime; |
430 | < | simnfo->thermalTime = simnfo->sampleTime; |
428 | > | n_cells = (int) temp3; |
429 | > | cellx = info[0].boxL[0] / temp3; |
430 | > | celly = info[0].boxL[1] / temp3; |
431 | > | cellz = info[0].boxL[2] / temp3; |
432 | } | |
433 | ||
434 | < | if( the_globals->haveStatusTime() ){ |
435 | < | simnfo->statusTime = the_globals->getStatusTime(); |
436 | < | } |
434 | > | current_mol = 0; |
435 | > | current_comp_mol = 0; |
436 | > | current_comp = 0; |
437 | > | current_atom_ndx = 0; |
438 | ||
439 | < | if( the_globals->haveThermalTime() ){ |
440 | < | simnfo->thermalTime = the_globals->getThermalTime(); |
439 | > | for (i = 0; i < n_cells ; i++){ |
440 | > | for (j = 0; j < n_cells; j++){ |
441 | > | for (k = 0; k < n_cells; k++){ |
442 | > | makeElement(i * cellx, j * celly, k * cellz); |
443 | > | |
444 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz); |
445 | > | |
446 | > | makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz); |
447 | > | |
448 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz); |
449 | > | } |
450 | > | } |
451 | } | |
452 | ||
453 | < | // check for the temperature set flag |
453 | > | if (have_extra){ |
454 | > | done = 0; |
455 | ||
456 | < | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
456 | > | int start_ndx; |
457 | > | for (i = 0; i < (n_cells + 1) && !done; i++){ |
458 | > | for (j = 0; j < (n_cells + 1) && !done; j++){ |
459 | > | if (i < n_cells){ |
460 | > | if (j < n_cells){ |
461 | > | start_ndx = n_cells; |
462 | > | } |
463 | > | else |
464 | > | start_ndx = 0; |
465 | > | } |
466 | > | else |
467 | > | start_ndx = 0; |
468 | ||
469 | + | for (k = start_ndx; k < (n_cells + 1) && !done; k++){ |
470 | + | makeElement(i * cellx, j * celly, k * cellz); |
471 | + | done = (current_mol >= tot_nmol); |
472 | ||
473 | < | // // make the longe range forces and the integrator |
473 | > | if (!done && n_per_extra > 1){ |
474 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, |
475 | > | k * cellz); |
476 | > | done = (current_mol >= tot_nmol); |
477 | > | } |
478 | ||
479 | < | // new AllLong( simnfo ); |
479 | > | if (!done && n_per_extra > 2){ |
480 | > | makeElement(i * cellx, j * celly + 0.5 * celly, |
481 | > | k * cellz + 0.5 * cellz); |
482 | > | done = (current_mol >= tot_nmol); |
483 | > | } |
484 | ||
485 | + | if (!done && n_per_extra > 3){ |
486 | + | makeElement(i * cellx + 0.5 * cellx, j * celly, |
487 | + | k * cellz + 0.5 * cellz); |
488 | + | done = (current_mol >= tot_nmol); |
489 | + | } |
490 | + | } |
491 | + | } |
492 | + | } |
493 | + | } |
494 | ||
495 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
496 | < | new Symplectic(simnfo, the_ff, the_extendedsystem); |
495 | > | for (i = 0; i < info[0].n_atoms; i++){ |
496 | > | info[0].atoms[i]->setVel(vel); |
497 | } | |
498 | < | else if( !strcmp( force_field, "LJ" ) ){ |
737 | < | new Verlet( *simnfo, the_ff, the_extendedsystem ); |
738 | < | } |
739 | < | else { |
740 | < | std::cerr << "I'm a bug.\n"; |
741 | < | fprintf( stderr, "Ima bug. stderr %s\n", force_field); |
742 | < | } |
743 | < | #ifdef IS_MPI |
744 | < | mpiSim->mpiRefresh(); |
745 | < | #endif |
498 | > | } |
499 | ||
500 | < | // initialize the Fortran |
500 | > | void SimSetup::makeElement(double x, double y, double z){ |
501 | > | int k; |
502 | > | AtomStamp* current_atom; |
503 | > | DirectionalAtom* dAtom; |
504 | > | double rotMat[3][3]; |
505 | > | double pos[3]; |
506 | ||
507 | + | for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){ |
508 | + | current_atom = comp_stamps[current_comp]->getAtom(k); |
509 | + | if (!current_atom->havePosition()){ |
510 | + | sprintf(painCave.errMsg, |
511 | + | "SimSetup:initFromBass error.\n" |
512 | + | "\tComponent %s, atom %s does not have a position specified.\n" |
513 | + | "\tThe initialization routine is unable to give a start" |
514 | + | " position.\n", |
515 | + | comp_stamps[current_comp]->getID(), current_atom->getType()); |
516 | + | painCave.isFatal = 1; |
517 | + | simError(); |
518 | + | } |
519 | ||
520 | < | simnfo->refreshSim(); |
521 | < | |
522 | < | if( !strcmp( simnfo->mixingRule, "standard") ){ |
523 | < | the_ff->initForceField( LB_MIXING_RULE ); |
520 | > | pos[0] = x + current_atom->getPosX(); |
521 | > | pos[1] = y + current_atom->getPosY(); |
522 | > | pos[2] = z + current_atom->getPosZ(); |
523 | > | |
524 | > | info[0].atoms[current_atom_ndx]->setPos(pos); |
525 | > | |
526 | > | if (info[0].atoms[current_atom_ndx]->isDirectional()){ |
527 | > | dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx]; |
528 | > | |
529 | > | rotMat[0][0] = 1.0; |
530 | > | rotMat[0][1] = 0.0; |
531 | > | rotMat[0][2] = 0.0; |
532 | > | |
533 | > | rotMat[1][0] = 0.0; |
534 | > | rotMat[1][1] = 1.0; |
535 | > | rotMat[1][2] = 0.0; |
536 | > | |
537 | > | rotMat[2][0] = 0.0; |
538 | > | rotMat[2][1] = 0.0; |
539 | > | rotMat[2][2] = 1.0; |
540 | > | |
541 | > | dAtom->setA(rotMat); |
542 | > | } |
543 | > | |
544 | > | current_atom_ndx++; |
545 | } | |
755 | – | else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
756 | – | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
757 | – | } |
758 | – | else{ |
759 | – | sprintf( painCave.errMsg, |
760 | – | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
761 | – | simnfo->mixingRule ); |
762 | – | painCave.isFatal = 1; |
763 | – | simError(); |
764 | – | } |
546 | ||
547 | + | current_mol++; |
548 | + | current_comp_mol++; |
549 | ||
550 | < | #ifdef IS_MPI |
551 | < | strcpy( checkPointMsg, |
552 | < | "Successfully intialized the mixingRule for Fortran." ); |
553 | < | MPIcheckPoint(); |
771 | < | #endif // is_mpi |
550 | > | if (current_comp_mol >= components_nmol[current_comp]){ |
551 | > | current_comp_mol = 0; |
552 | > | current_comp++; |
553 | > | } |
554 | } | |
555 | ||
556 | ||
557 | < | void SimSetup::makeMolecules( void ){ |
557 | > | void SimSetup::gatherInfo(void){ |
558 | > | int i; |
559 | ||
560 | < | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
561 | < | molInit info; |
779 | < | DirectionalAtom* dAtom; |
780 | < | LinkedAssign* extras; |
781 | < | LinkedAssign* current_extra; |
782 | < | AtomStamp* currentAtom; |
783 | < | BondStamp* currentBond; |
784 | < | BendStamp* currentBend; |
785 | < | TorsionStamp* currentTorsion; |
560 | > | ensembleCase = -1; |
561 | > | ffCase = -1; |
562 | ||
563 | < | bond_pair* theBonds; |
788 | < | bend_set* theBends; |
789 | < | torsion_set* theTorsions; |
563 | > | // set the easy ones first |
564 | ||
565 | < | |
566 | < | //init the forceField paramters |
565 | > | for (i = 0; i < nInfo; i++){ |
566 | > | info[i].target_temp = globals->getTargetTemp(); |
567 | > | info[i].dt = globals->getDt(); |
568 | > | info[i].run_time = globals->getRunTime(); |
569 | > | } |
570 | > | n_components = globals->getNComponents(); |
571 | ||
794 | – | the_ff->readParams(); |
572 | ||
573 | < | |
797 | < | // init the atoms |
573 | > | // get the forceField |
574 | ||
575 | < | double ux, uy, uz, u, uSqr; |
800 | < | |
801 | < | atomOffset = 0; |
802 | < | excludeOffset = 0; |
803 | < | for(i=0; i<simnfo->n_mol; i++){ |
804 | < | |
805 | < | stampID = the_molecules[i].getStampID(); |
575 | > | strcpy(force_field, globals->getForceField()); |
576 | ||
577 | < | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
578 | < | info.nBonds = comp_stamps[stampID]->getNBonds(); |
579 | < | info.nBends = comp_stamps[stampID]->getNBends(); |
580 | < | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
581 | < | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
577 | > | if (!strcasecmp(force_field, "DUFF")){ |
578 | > | ffCase = FF_DUFF; |
579 | > | } |
580 | > | else if (!strcasecmp(force_field, "LJ")){ |
581 | > | ffCase = FF_LJ; |
582 | > | } |
583 | > | else if (!strcasecmp(force_field, "EAM")){ |
584 | > | ffCase = FF_EAM; |
585 | > | } |
586 | > | else{ |
587 | > | sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", |
588 | > | force_field); |
589 | > | painCave.isFatal = 1; |
590 | > | simError(); |
591 | > | } |
592 | ||
593 | < | info.myAtoms = &the_atoms[atomOffset]; |
814 | < | info.myExcludes = &the_excludes[excludeOffset]; |
815 | < | info.myBonds = new Bond*[info.nBonds]; |
816 | < | info.myBends = new Bend*[info.nBends]; |
817 | < | info.myTorsions = new Torsion*[info.nTorsions]; |
593 | > | // get the ensemble |
594 | ||
595 | < | theBonds = new bond_pair[info.nBonds]; |
820 | < | theBends = new bend_set[info.nBends]; |
821 | < | theTorsions = new torsion_set[info.nTorsions]; |
822 | < | |
823 | < | // make the Atoms |
824 | < | |
825 | < | for(j=0; j<info.nAtoms; j++){ |
826 | < | |
827 | < | currentAtom = comp_stamps[stampID]->getAtom( j ); |
828 | < | if( currentAtom->haveOrientation() ){ |
829 | < | |
830 | < | dAtom = new DirectionalAtom(j + atomOffset); |
831 | < | simnfo->n_oriented++; |
832 | < | info.myAtoms[j] = dAtom; |
833 | < | |
834 | < | ux = currentAtom->getOrntX(); |
835 | < | uy = currentAtom->getOrntY(); |
836 | < | uz = currentAtom->getOrntZ(); |
837 | < | |
838 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
839 | < | |
840 | < | u = sqrt( uSqr ); |
841 | < | ux = ux / u; |
842 | < | uy = uy / u; |
843 | < | uz = uz / u; |
844 | < | |
845 | < | dAtom->setSUx( ux ); |
846 | < | dAtom->setSUy( uy ); |
847 | < | dAtom->setSUz( uz ); |
848 | < | } |
849 | < | else{ |
850 | < | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
851 | < | } |
852 | < | info.myAtoms[j]->setType( currentAtom->getType() ); |
853 | < | |
854 | < | #ifdef IS_MPI |
855 | < | |
856 | < | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
857 | < | |
858 | < | #endif // is_mpi |
859 | < | } |
860 | < | |
861 | < | // make the bonds |
862 | < | for(j=0; j<info.nBonds; j++){ |
863 | < | |
864 | < | currentBond = comp_stamps[stampID]->getBond( j ); |
865 | < | theBonds[j].a = currentBond->getA() + atomOffset; |
866 | < | theBonds[j].b = currentBond->getB() + atomOffset; |
595 | > | strcpy(ensemble, globals->getEnsemble()); |
596 | ||
597 | < | exI = theBonds[j].a; |
598 | < | exJ = theBonds[j].b; |
597 | > | if (!strcasecmp(ensemble, "NVE")){ |
598 | > | ensembleCase = NVE_ENS; |
599 | > | } |
600 | > | else if (!strcasecmp(ensemble, "NVT")){ |
601 | > | ensembleCase = NVT_ENS; |
602 | > | } |
603 | > | else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){ |
604 | > | ensembleCase = NPTi_ENS; |
605 | > | } |
606 | > | else if (!strcasecmp(ensemble, "NPTf")){ |
607 | > | ensembleCase = NPTf_ENS; |
608 | > | } |
609 | > | else if (!strcasecmp(ensemble, "NPTxyz")){ |
610 | > | ensembleCase = NPTxyz_ENS; |
611 | > | } |
612 | > | else{ |
613 | > | sprintf(painCave.errMsg, |
614 | > | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
615 | > | "reverting to NVE for this simulation.\n", |
616 | > | ensemble); |
617 | > | painCave.isFatal = 0; |
618 | > | simError(); |
619 | > | strcpy(ensemble, "NVE"); |
620 | > | ensembleCase = NVE_ENS; |
621 | > | } |
622 | ||
623 | < | // exclude_I must always be the smaller of the pair |
624 | < | if( exI > exJ ){ |
873 | < | tempEx = exI; |
874 | < | exI = exJ; |
875 | < | exJ = tempEx; |
876 | < | } |
877 | < | #ifdef IS_MPI |
878 | < | tempEx = exI; |
879 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
880 | < | tempEx = exJ; |
881 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
882 | < | |
883 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
884 | < | #else // isn't MPI |
623 | > | for (i = 0; i < nInfo; i++){ |
624 | > | strcpy(info[i].ensemble, ensemble); |
625 | ||
626 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
887 | < | #endif //is_mpi |
888 | < | } |
889 | < | excludeOffset += info.nBonds; |
626 | > | // get the mixing rule |
627 | ||
628 | < | //make the bends |
629 | < | for(j=0; j<info.nBends; j++){ |
630 | < | |
894 | < | currentBend = comp_stamps[stampID]->getBend( j ); |
895 | < | theBends[j].a = currentBend->getA() + atomOffset; |
896 | < | theBends[j].b = currentBend->getB() + atomOffset; |
897 | < | theBends[j].c = currentBend->getC() + atomOffset; |
898 | < | |
899 | < | if( currentBend->haveExtras() ){ |
900 | < | |
901 | < | extras = currentBend->getExtras(); |
902 | < | current_extra = extras; |
903 | < | |
904 | < | while( current_extra != NULL ){ |
905 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
906 | < | |
907 | < | switch( current_extra->getType() ){ |
908 | < | |
909 | < | case 0: |
910 | < | theBends[j].ghost = |
911 | < | current_extra->getInt() + atomOffset; |
912 | < | theBends[j].isGhost = 1; |
913 | < | break; |
914 | < | |
915 | < | case 1: |
916 | < | theBends[j].ghost = |
917 | < | (int)current_extra->getDouble() + atomOffset; |
918 | < | theBends[j].isGhost = 1; |
919 | < | break; |
920 | < | |
921 | < | default: |
922 | < | sprintf( painCave.errMsg, |
923 | < | "SimSetup Error: ghostVectorSource was neither a " |
924 | < | "double nor an int.\n" |
925 | < | "-->Bend[%d] in %s\n", |
926 | < | j, comp_stamps[stampID]->getID() ); |
927 | < | painCave.isFatal = 1; |
928 | < | simError(); |
929 | < | } |
930 | < | } |
931 | < | |
932 | < | else{ |
933 | < | |
934 | < | sprintf( painCave.errMsg, |
935 | < | "SimSetup Error: unhandled bend assignment:\n" |
936 | < | " -->%s in Bend[%d] in %s\n", |
937 | < | current_extra->getlhs(), |
938 | < | j, comp_stamps[stampID]->getID() ); |
939 | < | painCave.isFatal = 1; |
940 | < | simError(); |
941 | < | } |
942 | < | |
943 | < | current_extra = current_extra->getNext(); |
944 | < | } |
945 | < | } |
946 | < | |
947 | < | if( !theBends[j].isGhost ){ |
948 | < | |
949 | < | exI = theBends[j].a; |
950 | < | exJ = theBends[j].c; |
951 | < | } |
952 | < | else{ |
953 | < | |
954 | < | exI = theBends[j].a; |
955 | < | exJ = theBends[j].b; |
956 | < | } |
957 | < | |
958 | < | // exclude_I must always be the smaller of the pair |
959 | < | if( exI > exJ ){ |
960 | < | tempEx = exI; |
961 | < | exI = exJ; |
962 | < | exJ = tempEx; |
963 | < | } |
964 | < | #ifdef IS_MPI |
965 | < | tempEx = exI; |
966 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
967 | < | tempEx = exJ; |
968 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
969 | < | |
970 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
971 | < | #else // isn't MPI |
972 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
973 | < | #endif //is_mpi |
974 | < | } |
975 | < | excludeOffset += info.nBends; |
628 | > | strcpy(info[i].mixingRule, globals->getMixingRule()); |
629 | > | info[i].usePBC = globals->getPBC(); |
630 | > | } |
631 | ||
632 | < | for(j=0; j<info.nTorsions; j++){ |
978 | < | |
979 | < | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
980 | < | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
981 | < | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
982 | < | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
983 | < | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
984 | < | |
985 | < | exI = theTorsions[j].a; |
986 | < | exJ = theTorsions[j].d; |
632 | > | // get the components and calculate the tot_nMol and indvidual n_mol |
633 | ||
634 | < | // exclude_I must always be the smaller of the pair |
635 | < | if( exI > exJ ){ |
990 | < | tempEx = exI; |
991 | < | exI = exJ; |
992 | < | exJ = tempEx; |
993 | < | } |
994 | < | #ifdef IS_MPI |
995 | < | tempEx = exI; |
996 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
997 | < | tempEx = exJ; |
998 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
999 | < | |
1000 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1001 | < | #else // isn't MPI |
1002 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1003 | < | #endif //is_mpi |
1004 | < | } |
1005 | < | excludeOffset += info.nTorsions; |
634 | > | the_components = globals->getComponents(); |
635 | > | components_nmol = new int[n_components]; |
636 | ||
1007 | – | |
1008 | – | // send the arrays off to the forceField for init. |
637 | ||
638 | < | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
639 | < | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
640 | < | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1013 | < | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
638 | > | if (!globals->haveNMol()){ |
639 | > | // we don't have the total number of molecules, so we assume it is |
640 | > | // given in each component |
641 | ||
642 | + | tot_nmol = 0; |
643 | + | for (i = 0; i < n_components; i++){ |
644 | + | if (!the_components[i]->haveNMol()){ |
645 | + | // we have a problem |
646 | + | sprintf(painCave.errMsg, |
647 | + | "SimSetup Error. No global NMol or component NMol" |
648 | + | " given. Cannot calculate the number of atoms.\n"); |
649 | + | painCave.isFatal = 1; |
650 | + | simError(); |
651 | + | } |
652 | ||
653 | < | the_molecules[i].initialize( info ); |
654 | < | |
655 | < | |
1019 | < | atomOffset += info.nAtoms; |
1020 | < | delete[] theBonds; |
1021 | < | delete[] theBends; |
1022 | < | delete[] theTorsions; |
653 | > | tot_nmol += the_components[i]->getNMol(); |
654 | > | components_nmol[i] = the_components[i]->getNMol(); |
655 | > | } |
656 | } | |
657 | + | else{ |
658 | + | sprintf(painCave.errMsg, |
659 | + | "SimSetup error.\n" |
660 | + | "\tSorry, the ability to specify total" |
661 | + | " nMols and then give molfractions in the components\n" |
662 | + | "\tis not currently supported." |
663 | + | " Please give nMol in the components.\n"); |
664 | + | painCave.isFatal = 1; |
665 | + | simError(); |
666 | + | } |
667 | ||
668 | < | #ifdef IS_MPI |
1026 | < | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1027 | < | MPIcheckPoint(); |
1028 | < | #endif // is_mpi |
668 | > | // set the status, sample, and thermal kick times |
669 | ||
670 | < | // clean up the forcefield |
671 | < | the_ff->calcRcut(); |
672 | < | the_ff->cleanMe(); |
670 | > | for (i = 0; i < nInfo; i++){ |
671 | > | if (globals->haveSampleTime()){ |
672 | > | info[i].sampleTime = globals->getSampleTime(); |
673 | > | info[i].statusTime = info[i].sampleTime; |
674 | > | info[i].thermalTime = info[i].sampleTime; |
675 | > | } |
676 | > | else{ |
677 | > | info[i].sampleTime = globals->getRunTime(); |
678 | > | info[i].statusTime = info[i].sampleTime; |
679 | > | info[i].thermalTime = info[i].sampleTime; |
680 | > | } |
681 | ||
682 | < | } |
682 | > | if (globals->haveStatusTime()){ |
683 | > | info[i].statusTime = globals->getStatusTime(); |
684 | > | } |
685 | ||
686 | < | void SimSetup::initFromBass( void ){ |
686 | > | if (globals->haveThermalTime()){ |
687 | > | info[i].thermalTime = globals->getThermalTime(); |
688 | > | } |
689 | ||
690 | < | int i, j, k; |
691 | < | int n_cells; |
692 | < | double cellx, celly, cellz; |
693 | < | double temp1, temp2, temp3; |
694 | < | int n_per_extra; |
1043 | < | int n_extra; |
1044 | < | int have_extra, done; |
690 | > | info[i].resetIntegrator = 0; |
691 | > | if( globals->haveResetTime() ){ |
692 | > | info[i].resetTime = globals->getResetTime(); |
693 | > | info[i].resetIntegrator = 1; |
694 | > | } |
695 | ||
696 | < | temp1 = (double)tot_nmol / 4.0; |
1047 | < | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
1048 | < | temp3 = ceil( temp2 ); |
696 | > | // check for the temperature set flag |
697 | ||
698 | < | have_extra =0; |
699 | < | if( temp2 < temp3 ){ // we have a non-complete lattice |
1052 | < | have_extra =1; |
698 | > | if (globals->haveTempSet()) |
699 | > | info[i].setTemp = globals->getTempSet(); |
700 | ||
701 | < | n_cells = (int)temp3 - 1; |
702 | < | cellx = simnfo->box_x / temp3; |
703 | < | celly = simnfo->box_y / temp3; |
704 | < | cellz = simnfo->box_z / temp3; |
705 | < | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
706 | < | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
707 | < | n_per_extra = (int)ceil( temp1 ); |
708 | < | |
709 | < | if( n_per_extra > 4){ |
1063 | < | sprintf( painCave.errMsg, |
1064 | < | "SimSetup error. There has been an error in constructing" |
1065 | < | " the non-complete lattice.\n" ); |
1066 | < | painCave.isFatal = 1; |
1067 | < | simError(); |
701 | > | // get some of the tricky things that may still be in the globals |
702 | > | |
703 | > | double boxVector[3]; |
704 | > | if (globals->haveBox()){ |
705 | > | boxVector[0] = globals->getBox(); |
706 | > | boxVector[1] = globals->getBox(); |
707 | > | boxVector[2] = globals->getBox(); |
708 | > | |
709 | > | info[i].setBox(boxVector); |
710 | } | |
711 | < | } |
712 | < | else{ |
713 | < | n_cells = (int)temp3; |
714 | < | cellx = simnfo->box_x / temp3; |
715 | < | celly = simnfo->box_y / temp3; |
716 | < | cellz = simnfo->box_z / temp3; |
1075 | < | } |
711 | > | else if (globals->haveDensity()){ |
712 | > | double vol; |
713 | > | vol = (double) tot_nmol / globals->getDensity(); |
714 | > | boxVector[0] = pow(vol, (1.0 / 3.0)); |
715 | > | boxVector[1] = boxVector[0]; |
716 | > | boxVector[2] = boxVector[0]; |
717 | ||
718 | < | current_mol = 0; |
719 | < | current_comp_mol = 0; |
720 | < | current_comp = 0; |
721 | < | current_atom_ndx = 0; |
718 | > | info[i].setBox(boxVector); |
719 | > | } |
720 | > | else{ |
721 | > | if (!globals->haveBoxX()){ |
722 | > | sprintf(painCave.errMsg, |
723 | > | "SimSetup error, no periodic BoxX size given.\n"); |
724 | > | painCave.isFatal = 1; |
725 | > | simError(); |
726 | > | } |
727 | > | boxVector[0] = globals->getBoxX(); |
728 | ||
729 | < | for( i=0; i < n_cells ; i++ ){ |
730 | < | for( j=0; j < n_cells; j++ ){ |
731 | < | for( k=0; k < n_cells; k++ ){ |
729 | > | if (!globals->haveBoxY()){ |
730 | > | sprintf(painCave.errMsg, |
731 | > | "SimSetup error, no periodic BoxY size given.\n"); |
732 | > | painCave.isFatal = 1; |
733 | > | simError(); |
734 | > | } |
735 | > | boxVector[1] = globals->getBoxY(); |
736 | ||
737 | < | makeElement( i * cellx, |
738 | < | j * celly, |
739 | < | k * cellz ); |
737 | > | if (!globals->haveBoxZ()){ |
738 | > | sprintf(painCave.errMsg, |
739 | > | "SimSetup error, no periodic BoxZ size given.\n"); |
740 | > | painCave.isFatal = 1; |
741 | > | simError(); |
742 | > | } |
743 | > | boxVector[2] = globals->getBoxZ(); |
744 | ||
745 | < | makeElement( i * cellx + 0.5 * cellx, |
746 | < | j * celly + 0.5 * celly, |
747 | < | k * cellz ); |
745 | > | info[i].setBox(boxVector); |
746 | > | } |
747 | > | } |
748 | ||
749 | < | makeElement( i * cellx, |
750 | < | j * celly + 0.5 * celly, |
1096 | < | k * cellz + 0.5 * cellz ); |
749 | > | //setup seed for random number generator |
750 | > | int seedValue; |
751 | ||
752 | < | makeElement( i * cellx + 0.5 * cellx, |
753 | < | j * celly, |
754 | < | k * cellz + 0.5 * cellz ); |
752 | > | if (globals->haveSeed()){ |
753 | > | seedValue = globals->getSeed(); |
754 | > | |
755 | > | if(seedValue / 1E9 == 0){ |
756 | > | sprintf(painCave.errMsg, |
757 | > | "Seed for sprng library should contain at least 9 digits\n" |
758 | > | "OOPSE will generate a seed for user\n"); |
759 | > | painCave.isFatal = 0; |
760 | > | simError(); |
761 | > | |
762 | > | //using seed generated by system instead of invalid seed set by user |
763 | > | #ifndef IS_MPI |
764 | > | seedValue = make_sprng_seed(); |
765 | > | #else |
766 | > | if (worldRank == 0){ |
767 | > | seedValue = make_sprng_seed(); |
768 | } | |
769 | + | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
770 | + | #endif |
771 | } | |
772 | + | }//end of if branch of globals->haveSeed() |
773 | + | else{ |
774 | + | |
775 | + | #ifndef IS_MPI |
776 | + | seedValue = make_sprng_seed(); |
777 | + | #else |
778 | + | if (worldRank == 0){ |
779 | + | seedValue = make_sprng_seed(); |
780 | + | } |
781 | + | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
782 | + | #endif |
783 | + | }//end of globals->haveSeed() |
784 | + | |
785 | + | for (int i = 0; i < nInfo; i++){ |
786 | + | info[i].setSeed(seedValue); |
787 | } | |
788 | ||
789 | < | if( have_extra ){ |
790 | < | done = 0; |
789 | > | #ifdef IS_MPI |
790 | > | strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n"); |
791 | > | MPIcheckPoint(); |
792 | > | #endif // is_mpi |
793 | > | } |
794 | ||
1108 | – | int start_ndx; |
1109 | – | for( i=0; i < (n_cells+1) && !done; i++ ){ |
1110 | – | for( j=0; j < (n_cells+1) && !done; j++ ){ |
795 | ||
796 | < | if( i < n_cells ){ |
796 | > | void SimSetup::finalInfoCheck(void){ |
797 | > | int index; |
798 | > | int usesDipoles; |
799 | > | int i; |
800 | ||
801 | < | if( j < n_cells ){ |
802 | < | start_ndx = n_cells; |
1116 | < | } |
1117 | < | else start_ndx = 0; |
1118 | < | } |
1119 | < | else start_ndx = 0; |
801 | > | for (i = 0; i < nInfo; i++){ |
802 | > | // check electrostatic parameters |
803 | ||
804 | < | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
804 | > | index = 0; |
805 | > | usesDipoles = 0; |
806 | > | while ((index < info[i].n_atoms) && !usesDipoles){ |
807 | > | usesDipoles = (info[i].atoms[index])->hasDipole(); |
808 | > | index++; |
809 | > | } |
810 | ||
811 | < | makeElement( i * cellx, |
812 | < | j * celly, |
813 | < | k * cellz ); |
814 | < | done = ( current_mol >= tot_nmol ); |
811 | > | #ifdef IS_MPI |
812 | > | int myUse = usesDipoles; |
813 | > | MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
814 | > | #endif //is_mpi |
815 | ||
816 | < | if( !done && n_per_extra > 1 ){ |
1129 | < | makeElement( i * cellx + 0.5 * cellx, |
1130 | < | j * celly + 0.5 * celly, |
1131 | < | k * cellz ); |
1132 | < | done = ( current_mol >= tot_nmol ); |
1133 | < | } |
816 | > | double theEcr, theEst; |
817 | ||
818 | < | if( !done && n_per_extra > 2){ |
819 | < | makeElement( i * cellx, |
1137 | < | j * celly + 0.5 * celly, |
1138 | < | k * cellz + 0.5 * cellz ); |
1139 | < | done = ( current_mol >= tot_nmol ); |
1140 | < | } |
818 | > | if (globals->getUseRF()){ |
819 | > | info[i].useReactionField = 1; |
820 | ||
821 | < | if( !done && n_per_extra > 3){ |
822 | < | makeElement( i * cellx + 0.5 * cellx, |
823 | < | j * celly, |
824 | < | k * cellz + 0.5 * cellz ); |
825 | < | done = ( current_mol >= tot_nmol ); |
826 | < | } |
827 | < | } |
821 | > | if (!globals->haveECR()){ |
822 | > | sprintf(painCave.errMsg, |
823 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
824 | > | "box length for the electrostaticCutoffRadius.\n" |
825 | > | "I hope you have a very fast processor!\n"); |
826 | > | painCave.isFatal = 0; |
827 | > | simError(); |
828 | > | double smallest; |
829 | > | smallest = info[i].boxL[0]; |
830 | > | if (info[i].boxL[1] <= smallest) |
831 | > | smallest = info[i].boxL[1]; |
832 | > | if (info[i].boxL[2] <= smallest) |
833 | > | smallest = info[i].boxL[2]; |
834 | > | theEcr = 0.5 * smallest; |
835 | } | |
836 | + | else{ |
837 | + | theEcr = globals->getECR(); |
838 | + | } |
839 | + | |
840 | + | if (!globals->haveEST()){ |
841 | + | sprintf(painCave.errMsg, |
842 | + | "SimSetup Warning: using default value of 0.05 * the " |
843 | + | "electrostaticCutoffRadius for the electrostaticSkinThickness\n"); |
844 | + | painCave.isFatal = 0; |
845 | + | simError(); |
846 | + | theEst = 0.05 * theEcr; |
847 | + | } |
848 | + | else{ |
849 | + | theEst = globals->getEST(); |
850 | + | } |
851 | + | |
852 | + | info[i].setEcr(theEcr, theEst); |
853 | + | |
854 | + | if (!globals->haveDielectric()){ |
855 | + | sprintf(painCave.errMsg, |
856 | + | "SimSetup Error: You are trying to use Reaction Field without" |
857 | + | "setting a dielectric constant!\n"); |
858 | + | painCave.isFatal = 1; |
859 | + | simError(); |
860 | + | } |
861 | + | info[i].dielectric = globals->getDielectric(); |
862 | } | |
863 | < | } |
863 | > | else{ |
864 | > | if (usesDipoles){ |
865 | > | if (!globals->haveECR()){ |
866 | > | sprintf(painCave.errMsg, |
867 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
868 | > | "box length for the electrostaticCutoffRadius.\n" |
869 | > | "I hope you have a very fast processor!\n"); |
870 | > | painCave.isFatal = 0; |
871 | > | simError(); |
872 | > | double smallest; |
873 | > | smallest = info[i].boxL[0]; |
874 | > | if (info[i].boxL[1] <= smallest) |
875 | > | smallest = info[i].boxL[1]; |
876 | > | if (info[i].boxL[2] <= smallest) |
877 | > | smallest = info[i].boxL[2]; |
878 | > | theEcr = 0.5 * smallest; |
879 | > | } |
880 | > | else{ |
881 | > | theEcr = globals->getECR(); |
882 | > | } |
883 | ||
884 | + | if (!globals->haveEST()){ |
885 | + | sprintf(painCave.errMsg, |
886 | + | "SimSetup Warning: using default value of 0.05 * the " |
887 | + | "electrostaticCutoffRadius for the " |
888 | + | "electrostaticSkinThickness\n"); |
889 | + | painCave.isFatal = 0; |
890 | + | simError(); |
891 | + | theEst = 0.05 * theEcr; |
892 | + | } |
893 | + | else{ |
894 | + | theEst = globals->getEST(); |
895 | + | } |
896 | ||
897 | < | for( i=0; i<simnfo->n_atoms; i++ ){ |
898 | < | simnfo->atoms[i]->set_vx( 0.0 ); |
899 | < | simnfo->atoms[i]->set_vy( 0.0 ); |
1157 | < | simnfo->atoms[i]->set_vz( 0.0 ); |
897 | > | info[i].setEcr(theEcr, theEst); |
898 | > | } |
899 | > | } |
900 | } | |
901 | + | |
902 | + | #ifdef IS_MPI |
903 | + | strcpy(checkPointMsg, "post processing checks out"); |
904 | + | MPIcheckPoint(); |
905 | + | #endif // is_mpi |
906 | } | |
907 | ||
908 | < | void SimSetup::makeElement( double x, double y, double z ){ |
908 | > | void SimSetup::initSystemCoords(void){ |
909 | > | int i; |
910 | ||
911 | < | int k; |
1164 | < | AtomStamp* current_atom; |
1165 | < | DirectionalAtom* dAtom; |
1166 | < | double rotMat[3][3]; |
911 | > | char* inName; |
912 | ||
913 | < | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
913 | > | (info[0].getConfiguration())->createArrays(info[0].n_atoms); |
914 | ||
915 | < | current_atom = comp_stamps[current_comp]->getAtom( k ); |
916 | < | if( !current_atom->havePosition() ){ |
917 | < | sprintf( painCave.errMsg, |
918 | < | "SimSetup:initFromBass error.\n" |
919 | < | "\tComponent %s, atom %s does not have a position specified.\n" |
920 | < | "\tThe initialization routine is unable to give a start" |
921 | < | " position.\n", |
922 | < | comp_stamps[current_comp]->getID(), |
923 | < | current_atom->getType() ); |
924 | < | painCave.isFatal = 1; |
925 | < | simError(); |
915 | > | for (i = 0; i < info[0].n_atoms; i++) |
916 | > | info[0].atoms[i]->setCoords(); |
917 | > | |
918 | > | if (globals->haveInitialConfig()){ |
919 | > | InitializeFromFile* fileInit; |
920 | > | #ifdef IS_MPI // is_mpi |
921 | > | if (worldRank == 0){ |
922 | > | #endif //is_mpi |
923 | > | inName = globals->getInitialConfig(); |
924 | > | fileInit = new InitializeFromFile(inName); |
925 | > | #ifdef IS_MPI |
926 | } | |
927 | + | else |
928 | + | fileInit = new InitializeFromFile(NULL); |
929 | + | #endif |
930 | + | fileInit->readInit(info); // default velocities on |
931 | ||
932 | < | the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
933 | < | the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
934 | < | the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
932 | > | delete fileInit; |
933 | > | } |
934 | > | else{ |
935 | > | #ifdef IS_MPI |
936 | ||
937 | < | if( the_atoms[current_atom_ndx]->isDirectional() ){ |
937 | > | // no init from bass |
938 | ||
939 | < | dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
939 | > | sprintf(painCave.errMsg, |
940 | > | "Cannot intialize a parallel simulation without an initial configuration file.\n"); |
941 | > | painCave.isFatal = 1;; |
942 | > | simError(); |
943 | ||
944 | < | rotMat[0][0] = 1.0; |
1192 | < | rotMat[0][1] = 0.0; |
1193 | < | rotMat[0][2] = 0.0; |
944 | > | #else |
945 | ||
946 | < | rotMat[1][0] = 0.0; |
1196 | < | rotMat[1][1] = 1.0; |
1197 | < | rotMat[1][2] = 0.0; |
946 | > | initFromBass(); |
947 | ||
1199 | – | rotMat[2][0] = 0.0; |
1200 | – | rotMat[2][1] = 0.0; |
1201 | – | rotMat[2][2] = 1.0; |
948 | ||
949 | < | dAtom->setA( rotMat ); |
1204 | < | } |
1205 | < | |
1206 | < | current_atom_ndx++; |
949 | > | #endif |
950 | } | |
951 | ||
952 | < | current_mol++; |
953 | < | current_comp_mol++; |
952 | > | #ifdef IS_MPI |
953 | > | strcpy(checkPointMsg, "Successfully read in the initial configuration"); |
954 | > | MPIcheckPoint(); |
955 | > | #endif // is_mpi |
956 | > | } |
957 | ||
1212 | – | if( current_comp_mol >= components_nmol[current_comp] ){ |
958 | ||
959 | < | current_comp_mol = 0; |
960 | < | current_comp++; |
959 | > | void SimSetup::makeOutNames(void){ |
960 | > | int k; |
961 | > | |
962 | > | |
963 | > | for (k = 0; k < nInfo; k++){ |
964 | > | #ifdef IS_MPI |
965 | > | if (worldRank == 0){ |
966 | > | #endif // is_mpi |
967 | > | |
968 | > | if (globals->haveFinalConfig()){ |
969 | > | strcpy(info[k].finalName, globals->getFinalConfig()); |
970 | > | } |
971 | > | else{ |
972 | > | strcpy(info[k].finalName, inFileName); |
973 | > | char* endTest; |
974 | > | int nameLength = strlen(info[k].finalName); |
975 | > | endTest = &(info[k].finalName[nameLength - 5]); |
976 | > | if (!strcmp(endTest, ".bass")){ |
977 | > | strcpy(endTest, ".eor"); |
978 | > | } |
979 | > | else if (!strcmp(endTest, ".BASS")){ |
980 | > | strcpy(endTest, ".eor"); |
981 | > | } |
982 | > | else{ |
983 | > | endTest = &(info[k].finalName[nameLength - 4]); |
984 | > | if (!strcmp(endTest, ".bss")){ |
985 | > | strcpy(endTest, ".eor"); |
986 | > | } |
987 | > | else if (!strcmp(endTest, ".mdl")){ |
988 | > | strcpy(endTest, ".eor"); |
989 | > | } |
990 | > | else{ |
991 | > | strcat(info[k].finalName, ".eor"); |
992 | > | } |
993 | > | } |
994 | > | } |
995 | > | |
996 | > | // make the sample and status out names |
997 | > | |
998 | > | strcpy(info[k].sampleName, inFileName); |
999 | > | char* endTest; |
1000 | > | int nameLength = strlen(info[k].sampleName); |
1001 | > | endTest = &(info[k].sampleName[nameLength - 5]); |
1002 | > | if (!strcmp(endTest, ".bass")){ |
1003 | > | strcpy(endTest, ".dump"); |
1004 | > | } |
1005 | > | else if (!strcmp(endTest, ".BASS")){ |
1006 | > | strcpy(endTest, ".dump"); |
1007 | > | } |
1008 | > | else{ |
1009 | > | endTest = &(info[k].sampleName[nameLength - 4]); |
1010 | > | if (!strcmp(endTest, ".bss")){ |
1011 | > | strcpy(endTest, ".dump"); |
1012 | > | } |
1013 | > | else if (!strcmp(endTest, ".mdl")){ |
1014 | > | strcpy(endTest, ".dump"); |
1015 | > | } |
1016 | > | else{ |
1017 | > | strcat(info[k].sampleName, ".dump"); |
1018 | > | } |
1019 | > | } |
1020 | > | |
1021 | > | strcpy(info[k].statusName, inFileName); |
1022 | > | nameLength = strlen(info[k].statusName); |
1023 | > | endTest = &(info[k].statusName[nameLength - 5]); |
1024 | > | if (!strcmp(endTest, ".bass")){ |
1025 | > | strcpy(endTest, ".stat"); |
1026 | > | } |
1027 | > | else if (!strcmp(endTest, ".BASS")){ |
1028 | > | strcpy(endTest, ".stat"); |
1029 | > | } |
1030 | > | else{ |
1031 | > | endTest = &(info[k].statusName[nameLength - 4]); |
1032 | > | if (!strcmp(endTest, ".bss")){ |
1033 | > | strcpy(endTest, ".stat"); |
1034 | > | } |
1035 | > | else if (!strcmp(endTest, ".mdl")){ |
1036 | > | strcpy(endTest, ".stat"); |
1037 | > | } |
1038 | > | else{ |
1039 | > | strcat(info[k].statusName, ".stat"); |
1040 | > | } |
1041 | > | } |
1042 | > | |
1043 | > | #ifdef IS_MPI |
1044 | > | |
1045 | > | } |
1046 | > | #endif // is_mpi |
1047 | } | |
1048 | } | |
1049 | + | |
1050 | + | |
1051 | + | void SimSetup::sysObjectsCreation(void){ |
1052 | + | int i, k; |
1053 | + | |
1054 | + | // create the forceField |
1055 | + | |
1056 | + | createFF(); |
1057 | + | |
1058 | + | // extract componentList |
1059 | + | |
1060 | + | compList(); |
1061 | + | |
1062 | + | // calc the number of atoms, bond, bends, and torsions |
1063 | + | |
1064 | + | calcSysValues(); |
1065 | + | |
1066 | + | #ifdef IS_MPI |
1067 | + | // divide the molecules among the processors |
1068 | + | |
1069 | + | mpiMolDivide(); |
1070 | + | #endif //is_mpi |
1071 | + | |
1072 | + | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1073 | + | |
1074 | + | makeSysArrays(); |
1075 | + | |
1076 | + | // make and initialize the molecules (all but atomic coordinates) |
1077 | + | |
1078 | + | makeMolecules(); |
1079 | + | |
1080 | + | for (k = 0; k < nInfo; k++){ |
1081 | + | info[k].identArray = new int[info[k].n_atoms]; |
1082 | + | for (i = 0; i < info[k].n_atoms; i++){ |
1083 | + | info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1084 | + | } |
1085 | + | } |
1086 | + | } |
1087 | + | |
1088 | + | |
1089 | + | void SimSetup::createFF(void){ |
1090 | + | switch (ffCase){ |
1091 | + | case FF_DUFF: |
1092 | + | the_ff = new DUFF(); |
1093 | + | break; |
1094 | + | |
1095 | + | case FF_LJ: |
1096 | + | the_ff = new LJFF(); |
1097 | + | break; |
1098 | + | |
1099 | + | case FF_EAM: |
1100 | + | the_ff = new EAM_FF(); |
1101 | + | break; |
1102 | + | |
1103 | + | default: |
1104 | + | sprintf(painCave.errMsg, |
1105 | + | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1106 | + | painCave.isFatal = 1; |
1107 | + | simError(); |
1108 | + | } |
1109 | + | |
1110 | + | #ifdef IS_MPI |
1111 | + | strcpy(checkPointMsg, "ForceField creation successful"); |
1112 | + | MPIcheckPoint(); |
1113 | + | #endif // is_mpi |
1114 | + | } |
1115 | + | |
1116 | + | |
1117 | + | void SimSetup::compList(void){ |
1118 | + | int i; |
1119 | + | char* id; |
1120 | + | LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1121 | + | LinkedMolStamp* currentStamp = NULL; |
1122 | + | comp_stamps = new MoleculeStamp * [n_components]; |
1123 | + | |
1124 | + | // make an array of molecule stamps that match the components used. |
1125 | + | // also extract the used stamps out into a separate linked list |
1126 | + | |
1127 | + | for (i = 0; i < nInfo; i++){ |
1128 | + | info[i].nComponents = n_components; |
1129 | + | info[i].componentsNmol = components_nmol; |
1130 | + | info[i].compStamps = comp_stamps; |
1131 | + | info[i].headStamp = headStamp; |
1132 | + | } |
1133 | + | |
1134 | + | |
1135 | + | for (i = 0; i < n_components; i++){ |
1136 | + | id = the_components[i]->getType(); |
1137 | + | comp_stamps[i] = NULL; |
1138 | + | |
1139 | + | // check to make sure the component isn't already in the list |
1140 | + | |
1141 | + | comp_stamps[i] = headStamp->match(id); |
1142 | + | if (comp_stamps[i] == NULL){ |
1143 | + | // extract the component from the list; |
1144 | + | |
1145 | + | currentStamp = stamps->extractMolStamp(id); |
1146 | + | if (currentStamp == NULL){ |
1147 | + | sprintf(painCave.errMsg, |
1148 | + | "SimSetup error: Component \"%s\" was not found in the " |
1149 | + | "list of declared molecules\n", |
1150 | + | id); |
1151 | + | painCave.isFatal = 1; |
1152 | + | simError(); |
1153 | + | } |
1154 | + | |
1155 | + | headStamp->add(currentStamp); |
1156 | + | comp_stamps[i] = headStamp->match(id); |
1157 | + | } |
1158 | + | } |
1159 | + | |
1160 | + | #ifdef IS_MPI |
1161 | + | strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
1162 | + | MPIcheckPoint(); |
1163 | + | #endif // is_mpi |
1164 | + | } |
1165 | + | |
1166 | + | void SimSetup::calcSysValues(void){ |
1167 | + | int i; |
1168 | + | |
1169 | + | int* molMembershipArray; |
1170 | + | |
1171 | + | tot_atoms = 0; |
1172 | + | tot_bonds = 0; |
1173 | + | tot_bends = 0; |
1174 | + | tot_torsions = 0; |
1175 | + | for (i = 0; i < n_components; i++){ |
1176 | + | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1177 | + | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1178 | + | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1179 | + | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1180 | + | } |
1181 | + | |
1182 | + | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1183 | + | molMembershipArray = new int[tot_atoms]; |
1184 | + | |
1185 | + | for (i = 0; i < nInfo; i++){ |
1186 | + | info[i].n_atoms = tot_atoms; |
1187 | + | info[i].n_bonds = tot_bonds; |
1188 | + | info[i].n_bends = tot_bends; |
1189 | + | info[i].n_torsions = tot_torsions; |
1190 | + | info[i].n_SRI = tot_SRI; |
1191 | + | info[i].n_mol = tot_nmol; |
1192 | + | |
1193 | + | info[i].molMembershipArray = molMembershipArray; |
1194 | + | } |
1195 | + | } |
1196 | + | |
1197 | + | #ifdef IS_MPI |
1198 | + | |
1199 | + | void SimSetup::mpiMolDivide(void){ |
1200 | + | int i, j, k; |
1201 | + | int localMol, allMol; |
1202 | + | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1203 | + | |
1204 | + | mpiSim = new mpiSimulation(info); |
1205 | + | |
1206 | + | globalIndex = mpiSim->divideLabor(); |
1207 | + | |
1208 | + | // set up the local variables |
1209 | + | |
1210 | + | mol2proc = mpiSim->getMolToProcMap(); |
1211 | + | molCompType = mpiSim->getMolComponentType(); |
1212 | + | |
1213 | + | allMol = 0; |
1214 | + | localMol = 0; |
1215 | + | local_atoms = 0; |
1216 | + | local_bonds = 0; |
1217 | + | local_bends = 0; |
1218 | + | local_torsions = 0; |
1219 | + | globalAtomIndex = 0; |
1220 | + | |
1221 | + | |
1222 | + | for (i = 0; i < n_components; i++){ |
1223 | + | for (j = 0; j < components_nmol[i]; j++){ |
1224 | + | if (mol2proc[allMol] == worldRank){ |
1225 | + | local_atoms += comp_stamps[i]->getNAtoms(); |
1226 | + | local_bonds += comp_stamps[i]->getNBonds(); |
1227 | + | local_bends += comp_stamps[i]->getNBends(); |
1228 | + | local_torsions += comp_stamps[i]->getNTorsions(); |
1229 | + | localMol++; |
1230 | + | } |
1231 | + | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1232 | + | info[0].molMembershipArray[globalAtomIndex] = allMol; |
1233 | + | globalAtomIndex++; |
1234 | + | } |
1235 | + | |
1236 | + | allMol++; |
1237 | + | } |
1238 | + | } |
1239 | + | local_SRI = local_bonds + local_bends + local_torsions; |
1240 | + | |
1241 | + | info[0].n_atoms = mpiSim->getMyNlocal(); |
1242 | + | |
1243 | + | if (local_atoms != info[0].n_atoms){ |
1244 | + | sprintf(painCave.errMsg, |
1245 | + | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1246 | + | " localAtom (%d) are not equal.\n", |
1247 | + | info[0].n_atoms, local_atoms); |
1248 | + | painCave.isFatal = 1; |
1249 | + | simError(); |
1250 | + | } |
1251 | + | |
1252 | + | info[0].n_bonds = local_bonds; |
1253 | + | info[0].n_bends = local_bends; |
1254 | + | info[0].n_torsions = local_torsions; |
1255 | + | info[0].n_SRI = local_SRI; |
1256 | + | info[0].n_mol = localMol; |
1257 | + | |
1258 | + | strcpy(checkPointMsg, "Passed nlocal consistency check."); |
1259 | + | MPIcheckPoint(); |
1260 | + | } |
1261 | + | |
1262 | + | #endif // is_mpi |
1263 | + | |
1264 | + | |
1265 | + | void SimSetup::makeSysArrays(void){ |
1266 | + | |
1267 | + | #ifndef IS_MPI |
1268 | + | int k, j; |
1269 | + | #endif // is_mpi |
1270 | + | int i, l; |
1271 | + | |
1272 | + | Atom** the_atoms; |
1273 | + | Molecule* the_molecules; |
1274 | + | Exclude** the_excludes; |
1275 | + | |
1276 | + | |
1277 | + | for (l = 0; l < nInfo; l++){ |
1278 | + | // create the atom and short range interaction arrays |
1279 | + | |
1280 | + | the_atoms = new Atom * [info[l].n_atoms]; |
1281 | + | the_molecules = new Molecule[info[l].n_mol]; |
1282 | + | int molIndex; |
1283 | + | |
1284 | + | // initialize the molecule's stampID's |
1285 | + | |
1286 | + | #ifdef IS_MPI |
1287 | + | |
1288 | + | |
1289 | + | molIndex = 0; |
1290 | + | for (i = 0; i < mpiSim->getTotNmol(); i++){ |
1291 | + | if (mol2proc[i] == worldRank){ |
1292 | + | the_molecules[molIndex].setStampID(molCompType[i]); |
1293 | + | the_molecules[molIndex].setMyIndex(molIndex); |
1294 | + | the_molecules[molIndex].setGlobalIndex(i); |
1295 | + | molIndex++; |
1296 | + | } |
1297 | + | } |
1298 | + | |
1299 | + | #else // is_mpi |
1300 | + | |
1301 | + | molIndex = 0; |
1302 | + | globalAtomIndex = 0; |
1303 | + | for (i = 0; i < n_components; i++){ |
1304 | + | for (j = 0; j < components_nmol[i]; j++){ |
1305 | + | the_molecules[molIndex].setStampID(i); |
1306 | + | the_molecules[molIndex].setMyIndex(molIndex); |
1307 | + | the_molecules[molIndex].setGlobalIndex(molIndex); |
1308 | + | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1309 | + | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1310 | + | globalAtomIndex++; |
1311 | + | } |
1312 | + | molIndex++; |
1313 | + | } |
1314 | + | } |
1315 | + | |
1316 | + | |
1317 | + | #endif // is_mpi |
1318 | + | |
1319 | + | |
1320 | + | if (info[l].n_SRI){ |
1321 | + | Exclude::createArray(info[l].n_SRI); |
1322 | + | the_excludes = new Exclude * [info[l].n_SRI]; |
1323 | + | for (int ex = 0; ex < info[l].n_SRI; ex++){ |
1324 | + | the_excludes[ex] = new Exclude(ex); |
1325 | + | } |
1326 | + | info[l].globalExcludes = new int; |
1327 | + | info[l].n_exclude = info[l].n_SRI; |
1328 | + | } |
1329 | + | else{ |
1330 | + | Exclude::createArray(1); |
1331 | + | the_excludes = new Exclude * ; |
1332 | + | the_excludes[0] = new Exclude(0); |
1333 | + | the_excludes[0]->setPair(0, 0); |
1334 | + | info[l].globalExcludes = new int; |
1335 | + | info[l].globalExcludes[0] = 0; |
1336 | + | info[l].n_exclude = 0; |
1337 | + | } |
1338 | + | |
1339 | + | // set the arrays into the SimInfo object |
1340 | + | |
1341 | + | info[l].atoms = the_atoms; |
1342 | + | info[l].molecules = the_molecules; |
1343 | + | info[l].nGlobalExcludes = 0; |
1344 | + | info[l].excludes = the_excludes; |
1345 | + | |
1346 | + | the_ff->setSimInfo(info); |
1347 | + | } |
1348 | + | } |
1349 | + | |
1350 | + | void SimSetup::makeIntegrator(void){ |
1351 | + | int k; |
1352 | + | |
1353 | + | NVE<RealIntegrator>* myNVE = NULL; |
1354 | + | NVT<RealIntegrator>* myNVT = NULL; |
1355 | + | NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1356 | + | NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1357 | + | NPTxyz<NPT<RealIntegrator> >* myNPTxyz = NULL; |
1358 | + | |
1359 | + | for (k = 0; k < nInfo; k++){ |
1360 | + | switch (ensembleCase){ |
1361 | + | case NVE_ENS: |
1362 | + | if (globals->haveZconstraints()){ |
1363 | + | setupZConstraint(info[k]); |
1364 | + | myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1365 | + | } |
1366 | + | else{ |
1367 | + | myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1368 | + | } |
1369 | + | |
1370 | + | info->the_integrator = myNVE; |
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 | + | else{ |
1386 | + | sprintf(painCave.errMsg, |
1387 | + | "SimSetup error: If you use the NVT\n" |
1388 | + | " ensemble, you must set tauThermostat.\n"); |
1389 | + | painCave.isFatal = 1; |
1390 | + | simError(); |
1391 | + | } |
1392 | + | |
1393 | + | info->the_integrator = myNVT; |
1394 | + | break; |
1395 | + | |
1396 | + | case NPTi_ENS: |
1397 | + | if (globals->haveZconstraints()){ |
1398 | + | setupZConstraint(info[k]); |
1399 | + | myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1400 | + | } |
1401 | + | else |
1402 | + | myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff); |
1403 | + | |
1404 | + | myNPTi->setTargetTemp(globals->getTargetTemp()); |
1405 | + | |
1406 | + | if (globals->haveTargetPressure()) |
1407 | + | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1408 | + | else{ |
1409 | + | sprintf(painCave.errMsg, |
1410 | + | "SimSetup error: If you use a constant pressure\n" |
1411 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1412 | + | painCave.isFatal = 1; |
1413 | + | simError(); |
1414 | + | } |
1415 | + | |
1416 | + | if (globals->haveTauThermostat()) |
1417 | + | myNPTi->setTauThermostat(globals->getTauThermostat()); |
1418 | + | else{ |
1419 | + | sprintf(painCave.errMsg, |
1420 | + | "SimSetup error: If you use an NPT\n" |
1421 | + | " ensemble, you must set tauThermostat.\n"); |
1422 | + | painCave.isFatal = 1; |
1423 | + | simError(); |
1424 | + | } |
1425 | + | |
1426 | + | if (globals->haveTauBarostat()) |
1427 | + | myNPTi->setTauBarostat(globals->getTauBarostat()); |
1428 | + | else{ |
1429 | + | sprintf(painCave.errMsg, |
1430 | + | "SimSetup error: If you use an NPT\n" |
1431 | + | " ensemble, you must set tauBarostat.\n"); |
1432 | + | painCave.isFatal = 1; |
1433 | + | simError(); |
1434 | + | } |
1435 | + | |
1436 | + | info->the_integrator = myNPTi; |
1437 | + | break; |
1438 | + | |
1439 | + | case NPTf_ENS: |
1440 | + | if (globals->haveZconstraints()){ |
1441 | + | setupZConstraint(info[k]); |
1442 | + | myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1443 | + | } |
1444 | + | else |
1445 | + | myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1446 | + | |
1447 | + | myNPTf->setTargetTemp(globals->getTargetTemp()); |
1448 | + | |
1449 | + | if (globals->haveTargetPressure()) |
1450 | + | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1451 | + | else{ |
1452 | + | sprintf(painCave.errMsg, |
1453 | + | "SimSetup error: If you use a constant pressure\n" |
1454 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1455 | + | painCave.isFatal = 1; |
1456 | + | simError(); |
1457 | + | } |
1458 | + | |
1459 | + | if (globals->haveTauThermostat()) |
1460 | + | myNPTf->setTauThermostat(globals->getTauThermostat()); |
1461 | + | else{ |
1462 | + | sprintf(painCave.errMsg, |
1463 | + | "SimSetup error: If you use an NPT\n" |
1464 | + | " ensemble, you must set tauThermostat.\n"); |
1465 | + | painCave.isFatal = 1; |
1466 | + | simError(); |
1467 | + | } |
1468 | + | |
1469 | + | if (globals->haveTauBarostat()) |
1470 | + | myNPTf->setTauBarostat(globals->getTauBarostat()); |
1471 | + | else{ |
1472 | + | sprintf(painCave.errMsg, |
1473 | + | "SimSetup error: If you use an NPT\n" |
1474 | + | " ensemble, you must set tauBarostat.\n"); |
1475 | + | painCave.isFatal = 1; |
1476 | + | simError(); |
1477 | + | } |
1478 | + | |
1479 | + | info->the_integrator = myNPTf; |
1480 | + | break; |
1481 | + | |
1482 | + | case NPTxyz_ENS: |
1483 | + | if (globals->haveZconstraints()){ |
1484 | + | setupZConstraint(info[k]); |
1485 | + | myNPTxyz = new ZConstraint<NPTxyz<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1486 | + | } |
1487 | + | else |
1488 | + | myNPTxyz = new NPTxyz<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1489 | + | |
1490 | + | myNPTxyz->setTargetTemp(globals->getTargetTemp()); |
1491 | + | |
1492 | + | if (globals->haveTargetPressure()) |
1493 | + | myNPTxyz->setTargetPressure(globals->getTargetPressure()); |
1494 | + | else{ |
1495 | + | sprintf(painCave.errMsg, |
1496 | + | "SimSetup error: If you use a constant pressure\n" |
1497 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1498 | + | painCave.isFatal = 1; |
1499 | + | simError(); |
1500 | + | } |
1501 | + | |
1502 | + | if (globals->haveTauThermostat()) |
1503 | + | myNPTxyz->setTauThermostat(globals->getTauThermostat()); |
1504 | + | else{ |
1505 | + | sprintf(painCave.errMsg, |
1506 | + | "SimSetup error: If you use an NPT\n" |
1507 | + | " ensemble, you must set tauThermostat.\n"); |
1508 | + | painCave.isFatal = 1; |
1509 | + | simError(); |
1510 | + | } |
1511 | + | |
1512 | + | if (globals->haveTauBarostat()) |
1513 | + | myNPTxyz->setTauBarostat(globals->getTauBarostat()); |
1514 | + | else{ |
1515 | + | sprintf(painCave.errMsg, |
1516 | + | "SimSetup error: If you use an NPT\n" |
1517 | + | " ensemble, you must set tauBarostat.\n"); |
1518 | + | painCave.isFatal = 1; |
1519 | + | simError(); |
1520 | + | } |
1521 | + | |
1522 | + | info->the_integrator = myNPTxyz; |
1523 | + | break; |
1524 | + | |
1525 | + | default: |
1526 | + | sprintf(painCave.errMsg, |
1527 | + | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1528 | + | painCave.isFatal = 1; |
1529 | + | simError(); |
1530 | + | } |
1531 | + | } |
1532 | + | } |
1533 | + | |
1534 | + | void SimSetup::initFortran(void){ |
1535 | + | info[0].refreshSim(); |
1536 | + | |
1537 | + | if (!strcmp(info[0].mixingRule, "standard")){ |
1538 | + | the_ff->initForceField(LB_MIXING_RULE); |
1539 | + | } |
1540 | + | else if (!strcmp(info[0].mixingRule, "explicit")){ |
1541 | + | the_ff->initForceField(EXPLICIT_MIXING_RULE); |
1542 | + | } |
1543 | + | else{ |
1544 | + | sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1545 | + | info[0].mixingRule); |
1546 | + | painCave.isFatal = 1; |
1547 | + | simError(); |
1548 | + | } |
1549 | + | |
1550 | + | |
1551 | + | #ifdef IS_MPI |
1552 | + | strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran."); |
1553 | + | MPIcheckPoint(); |
1554 | + | #endif // is_mpi |
1555 | + | } |
1556 | + | |
1557 | + | void SimSetup::setupZConstraint(SimInfo& theInfo){ |
1558 | + | int nZConstraints; |
1559 | + | ZconStamp** zconStamp; |
1560 | + | |
1561 | + | if (globals->haveZconstraintTime()){ |
1562 | + | //add sample time of z-constraint into SimInfo's property list |
1563 | + | DoubleData* zconsTimeProp = new DoubleData(); |
1564 | + | zconsTimeProp->setID(ZCONSTIME_ID); |
1565 | + | zconsTimeProp->setData(globals->getZconsTime()); |
1566 | + | theInfo.addProperty(zconsTimeProp); |
1567 | + | } |
1568 | + | else{ |
1569 | + | sprintf(painCave.errMsg, |
1570 | + | "ZConstraint error: If you use an ZConstraint\n" |
1571 | + | " , you must set sample time.\n"); |
1572 | + | painCave.isFatal = 1; |
1573 | + | simError(); |
1574 | + | } |
1575 | + | |
1576 | + | //push zconsTol into siminfo, if user does not specify |
1577 | + | //value for zconsTol, a default value will be used |
1578 | + | DoubleData* zconsTol = new DoubleData(); |
1579 | + | zconsTol->setID(ZCONSTOL_ID); |
1580 | + | if (globals->haveZconsTol()){ |
1581 | + | zconsTol->setData(globals->getZconsTol()); |
1582 | + | } |
1583 | + | else{ |
1584 | + | double defaultZConsTol = 0.01; |
1585 | + | sprintf(painCave.errMsg, |
1586 | + | "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1587 | + | " , default value %f is used.\n", |
1588 | + | defaultZConsTol); |
1589 | + | painCave.isFatal = 0; |
1590 | + | simError(); |
1591 | + | |
1592 | + | zconsTol->setData(defaultZConsTol); |
1593 | + | } |
1594 | + | theInfo.addProperty(zconsTol); |
1595 | + | |
1596 | + | //set Force Subtraction Policy |
1597 | + | StringData* zconsForcePolicy = new StringData(); |
1598 | + | zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1599 | + | |
1600 | + | if (globals->haveZconsForcePolicy()){ |
1601 | + | zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
1602 | + | } |
1603 | + | else{ |
1604 | + | sprintf(painCave.errMsg, |
1605 | + | "ZConstraint Warning: User does not set force Subtraction policy, " |
1606 | + | "PolicyByMass is used\n"); |
1607 | + | painCave.isFatal = 0; |
1608 | + | simError(); |
1609 | + | zconsForcePolicy->setData("BYMASS"); |
1610 | + | } |
1611 | + | |
1612 | + | theInfo.addProperty(zconsForcePolicy); |
1613 | + | |
1614 | + | //Determine the name of ouput file and add it into SimInfo's property list |
1615 | + | //Be careful, do not use inFileName, since it is a pointer which |
1616 | + | //point to a string at master node, and slave nodes do not contain that string |
1617 | + | |
1618 | + | string zconsOutput(theInfo.finalName); |
1619 | + | |
1620 | + | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1621 | + | |
1622 | + | StringData* zconsFilename = new StringData(); |
1623 | + | zconsFilename->setID(ZCONSFILENAME_ID); |
1624 | + | zconsFilename->setData(zconsOutput); |
1625 | + | |
1626 | + | theInfo.addProperty(zconsFilename); |
1627 | + | |
1628 | + | //setup index, pos and other parameters of z-constraint molecules |
1629 | + | nZConstraints = globals->getNzConstraints(); |
1630 | + | theInfo.nZconstraints = nZConstraints; |
1631 | + | |
1632 | + | zconStamp = globals->getZconStamp(); |
1633 | + | ZConsParaItem tempParaItem; |
1634 | + | |
1635 | + | ZConsParaData* zconsParaData = new ZConsParaData(); |
1636 | + | zconsParaData->setID(ZCONSPARADATA_ID); |
1637 | + | |
1638 | + | for (int i = 0; i < nZConstraints; i++){ |
1639 | + | tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1640 | + | tempParaItem.zPos = zconStamp[i]->getZpos(); |
1641 | + | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1642 | + | tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1643 | + | |
1644 | + | zconsParaData->addItem(tempParaItem); |
1645 | + | } |
1646 | + | |
1647 | + | //check the uniqueness of index |
1648 | + | if(!zconsParaData->isIndexUnique()){ |
1649 | + | sprintf(painCave.errMsg, |
1650 | + | "ZConstraint Error: molIndex is not unique\n"); |
1651 | + | painCave.isFatal = 1; |
1652 | + | simError(); |
1653 | + | } |
1654 | + | |
1655 | + | //sort the parameters by index of molecules |
1656 | + | zconsParaData->sortByIndex(); |
1657 | + | |
1658 | + | //push data into siminfo, therefore, we can retrieve later |
1659 | + | theInfo.addProperty(zconsParaData); |
1660 | + | } |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |