# | 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 NPTim_ENS 4 |
26 | + | #define NPTfm_ENS 5 |
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 | > | int i, j, k, globalAtomIndex; |
96 | ||
97 | < | MakeStamps *the_stamps; |
68 | < | Globals* the_globals; |
69 | < | ExtendedSystem* the_extendedsystem; |
70 | < | int i, j; |
97 | > | // gather all of the information from the Bass file |
98 | ||
99 | < | // get the stamps and globals; |
73 | < | the_stamps = stamps; |
74 | < | the_globals = globals; |
99 | > | gatherInfo(); |
100 | ||
101 | < | // 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(); |
101 | > | // creation of complex system objects |
102 | ||
103 | < | // 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() ); |
103 | > | sysObjectsCreation(); |
104 | ||
105 | < | // 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 | < | } |
105 | > | // check on the post processing info |
106 | ||
107 | < | 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 | < | } |
107 | > | finalInfoCheck(); |
108 | ||
109 | < | 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 | < | } |
109 | > | // initialize the system coordinates |
110 | ||
111 | < | } else if ( !strcasecmp( ensemble, "NVT") ) { |
112 | < | the_extendedsystem = new ExtendedSystem( simnfo ); |
113 | < | the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
111 | > | if (!isInfoArray){ |
112 | > | initSystemCoords(); |
113 | > | } |
114 | ||
115 | < | if (the_globals->haveTauThermostat()) |
130 | < | 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 | < | } |
115 | > | // make the output filenames |
116 | ||
117 | < | } 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" ); |
151 | < | } |
152 | < | strcpy( simnfo->ensemble, ensemble ); |
117 | > | makeOutNames(); |
118 | ||
119 | < | 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 | < | } |
119 | > | // make the integrator |
120 | ||
121 | + | makeIntegrator(); |
122 | + | |
123 | #ifdef IS_MPI | |
124 | < | strcpy( checkPointMsg, "ForceField creation successful" ); |
125 | < | MPIcheckPoint(); |
174 | < | #endif // is_mpi |
124 | > | mpiSim->mpiRefresh(); |
125 | > | #endif |
126 | ||
127 | < | |
127 | > | // initialize the Fortran |
128 | ||
129 | < | // get the components and calculate the tot_nMol and indvidual n_mol |
130 | < | the_components = the_globals->getComponents(); |
180 | < | components_nmol = new int[n_components]; |
181 | < | comp_stamps = new MoleculeStamp*[n_components]; |
129 | > | initFortran(); |
130 | > | } |
131 | ||
183 | – | if( !the_globals->haveNMol() ){ |
184 | – | // we don't have the total number of molecules, so we assume it is |
185 | – | // given in each component |
132 | ||
133 | < | tot_nmol = 0; |
134 | < | for( i=0; i<n_components; i++ ){ |
133 | > | void SimSetup::makeMolecules(void){ |
134 | > | int k, l; |
135 | > | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
136 | > | molInit molInfo; |
137 | > | DirectionalAtom* dAtom; |
138 | > | LinkedAssign* extras; |
139 | > | LinkedAssign* current_extra; |
140 | > | AtomStamp* currentAtom; |
141 | > | BondStamp* currentBond; |
142 | > | BendStamp* currentBend; |
143 | > | TorsionStamp* currentTorsion; |
144 | ||
145 | < | if( !the_components[i]->haveNMol() ){ |
146 | < | // we have a problem |
147 | < | 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 | < | } |
145 | > | bond_pair* theBonds; |
146 | > | bend_set* theBends; |
147 | > | torsion_set* theTorsions; |
148 | ||
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 | – | } |
149 | ||
150 | < | #ifdef IS_MPI |
229 | < | strcpy( checkPointMsg, "Have the number of components" ); |
230 | < | MPIcheckPoint(); |
231 | < | #endif // is_mpi |
150 | > | //init the forceField paramters |
151 | ||
152 | < | // make an array of molecule stamps that match the components used. |
234 | < | // also extract the used stamps out into a separate linked list |
152 | > | the_ff->readParams(); |
153 | ||
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++ ){ |
154 | ||
155 | < | id = the_components[i]->getType(); |
247 | < | comp_stamps[i] = NULL; |
248 | < | |
249 | < | // check to make sure the component isn't already in the list |
155 | > | // init the atoms |
156 | ||
157 | < | 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 | < | } |
157 | > | double ux, uy, uz, u, uSqr; |
158 | ||
159 | < | #ifdef IS_MPI |
160 | < | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
273 | < | MPIcheckPoint(); |
274 | < | #endif // is_mpi |
275 | < | |
159 | > | for (k = 0; k < nInfo; k++){ |
160 | > | the_ff->setSimInfo(&(info[k])); |
161 | ||
162 | + | atomOffset = 0; |
163 | + | excludeOffset = 0; |
164 | + | for (i = 0; i < info[k].n_mol; i++){ |
165 | + | stampID = info[k].molecules[i].getStampID(); |
166 | ||
167 | + | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
168 | + | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
169 | + | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
170 | + | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
171 | + | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
172 | ||
173 | < | // caclulate the number of atoms, bonds, bends and torsions |
173 | > | molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
174 | > | molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
175 | > | molInfo.myBonds = new Bond * [molInfo.nBonds]; |
176 | > | molInfo.myBends = new Bend * [molInfo.nBends]; |
177 | > | molInfo.myTorsions = new Torsion * [molInfo.nTorsions]; |
178 | ||
179 | < | tot_atoms = 0; |
180 | < | tot_bonds = 0; |
181 | < | 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 | < | } |
179 | > | theBonds = new bond_pair[molInfo.nBonds]; |
180 | > | theBends = new bend_set[molInfo.nBends]; |
181 | > | theTorsions = new torsion_set[molInfo.nTorsions]; |
182 | ||
183 | < | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
183 | > | // make the Atoms |
184 | ||
185 | < | simnfo->n_atoms = tot_atoms; |
186 | < | simnfo->n_bonds = tot_bonds; |
187 | < | simnfo->n_bends = tot_bends; |
188 | < | simnfo->n_torsions = tot_torsions; |
189 | < | simnfo->n_SRI = tot_SRI; |
190 | < | simnfo->n_mol = tot_nmol; |
185 | > | for (j = 0; j < molInfo.nAtoms; j++){ |
186 | > | currentAtom = comp_stamps[stampID]->getAtom(j); |
187 | > | if (currentAtom->haveOrientation()){ |
188 | > | dAtom = new DirectionalAtom((j + atomOffset), |
189 | > | info[k].getConfiguration()); |
190 | > | info[k].n_oriented++; |
191 | > | molInfo.myAtoms[j] = dAtom; |
192 | ||
193 | < | |
194 | < | #ifdef IS_MPI |
193 | > | ux = currentAtom->getOrntX(); |
194 | > | uy = currentAtom->getOrntY(); |
195 | > | uz = currentAtom->getOrntZ(); |
196 | ||
197 | < | // divide the molecules among processors here. |
306 | < | |
307 | < | mpiSim = new mpiSimulation( simnfo ); |
308 | < | |
309 | < | |
197 | > | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
198 | ||
199 | < | globalIndex = mpiSim->divideLabor(); |
199 | > | u = sqrt(uSqr); |
200 | > | ux = ux / u; |
201 | > | uy = uy / u; |
202 | > | uz = uz / u; |
203 | ||
204 | < | // set up the local variables |
205 | < | |
206 | < | int localMol, allMol; |
207 | < | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
204 | > | dAtom->setSUx(ux); |
205 | > | dAtom->setSUy(uy); |
206 | > | dAtom->setSUz(uz); |
207 | > | } |
208 | > | else{ |
209 | > | molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset), |
210 | > | info[k].getConfiguration()); |
211 | > | } |
212 | > | molInfo.myAtoms[j]->setType(currentAtom->getType()); |
213 | ||
214 | < | int* mol2proc = mpiSim->getMolToProcMap(); |
319 | < | int* molCompType = mpiSim->getMolComponentType(); |
320 | < | |
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++ ){ |
214 | > | #ifdef IS_MPI |
215 | ||
216 | < | for( j=0; j<components_nmol[i]; j++ ){ |
330 | < | |
331 | < | if( mol2proc[j] == 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 | < | |
216 | > | molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]); |
217 | ||
345 | – | simnfo->n_atoms = mpiSim->getMyNlocal(); |
346 | – | |
347 | – | if( local_atoms != simnfo->n_atoms ){ |
348 | – | 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 | – | } |
356 | – | |
357 | – | simnfo->n_bonds = local_bonds; |
358 | – | simnfo->n_bends = local_bends; |
359 | – | simnfo->n_torsions = local_torsions; |
360 | – | simnfo->n_SRI = local_SRI; |
361 | – | simnfo->n_mol = localMol; |
362 | – | |
363 | – | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
364 | – | MPIcheckPoint(); |
365 | – | |
366 | – | |
218 | #endif // is_mpi | |
219 | < | |
219 | > | } |
220 | ||
221 | < | // create the atom and short range interaction arrays |
221 | > | // make the bonds |
222 | > | for (j = 0; j < molInfo.nBonds; j++){ |
223 | > | currentBond = comp_stamps[stampID]->getBond(j); |
224 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
225 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
226 | ||
227 | < | Atom::createArrays(simnfo->n_atoms); |
228 | < | the_atoms = new Atom*[simnfo->n_atoms]; |
374 | < | the_molecules = new Molecule[simnfo->n_mol]; |
375 | < | int molIndex; |
227 | > | exI = theBonds[j].a; |
228 | > | exJ = theBonds[j].b; |
229 | ||
230 | < | // initialize the molecule's stampID's |
231 | < | |
230 | > | // exclude_I must always be the smaller of the pair |
231 | > | if (exI > exJ){ |
232 | > | tempEx = exI; |
233 | > | exI = exJ; |
234 | > | exJ = tempEx; |
235 | > | } |
236 | #ifdef IS_MPI | |
237 | < | |
237 | > | tempEx = exI; |
238 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
239 | > | tempEx = exJ; |
240 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
241 | ||
242 | < | molIndex = 0; |
243 | < | 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 | < | } |
242 | > | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
243 | > | #else // isn't MPI |
244 | ||
245 | < | #else // is_mpi |
246 | < | |
247 | < | molIndex = 0; |
248 | < | 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 | < | |
245 | > | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
246 | > | #endif //is_mpi |
247 | > | } |
248 | > | excludeOffset += molInfo.nBonds; |
249 | ||
250 | < | #endif // is_mpi |
250 | > | //make the bends |
251 | > | for (j = 0; j < molInfo.nBends; j++){ |
252 | > | currentBend = comp_stamps[stampID]->getBend(j); |
253 | > | theBends[j].a = currentBend->getA() + atomOffset; |
254 | > | theBends[j].b = currentBend->getB() + atomOffset; |
255 | > | theBends[j].c = currentBend->getC() + atomOffset; |
256 | ||
257 | + | if (currentBend->haveExtras()){ |
258 | + | extras = currentBend->getExtras(); |
259 | + | current_extra = extras; |
260 | ||
261 | < | if( simnfo->n_SRI ){ |
262 | < | |
263 | < | Exclude::createArray(simnfo->n_SRI); |
264 | < | the_excludes = new Exclude*[simnfo->n_SRI]; |
265 | < | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
266 | < | simnfo->globalExcludes = new int; |
267 | < | 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 | < | } |
261 | > | while (current_extra != NULL){ |
262 | > | if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){ |
263 | > | switch (current_extra->getType()){ |
264 | > | case 0: |
265 | > | theBends[j].ghost = current_extra->getInt() + atomOffset; |
266 | > | theBends[j].isGhost = 1; |
267 | > | break; |
268 | ||
269 | < | // set the arrays into the SimInfo object |
269 | > | case 1: |
270 | > | theBends[j].ghost = (int) current_extra->getDouble() + |
271 | > | atomOffset; |
272 | > | theBends[j].isGhost = 1; |
273 | > | break; |
274 | ||
275 | < | simnfo->atoms = the_atoms; |
276 | < | simnfo->molecules = the_molecules; |
277 | < | simnfo->nGlobalExcludes = 0; |
278 | < | simnfo->excludes = the_excludes; |
275 | > | default: |
276 | > | sprintf(painCave.errMsg, |
277 | > | "SimSetup Error: ghostVectorSource was neither a " |
278 | > | "double nor an int.\n" |
279 | > | "-->Bend[%d] in %s\n", |
280 | > | j, comp_stamps[stampID]->getID()); |
281 | > | painCave.isFatal = 1; |
282 | > | simError(); |
283 | > | } |
284 | > | } |
285 | > | else{ |
286 | > | sprintf(painCave.errMsg, |
287 | > | "SimSetup Error: unhandled bend assignment:\n" |
288 | > | " -->%s in Bend[%d] in %s\n", |
289 | > | current_extra->getlhs(), j, comp_stamps[stampID]->getID()); |
290 | > | painCave.isFatal = 1; |
291 | > | simError(); |
292 | > | } |
293 | ||
294 | + | current_extra = current_extra->getNext(); |
295 | + | } |
296 | + | } |
297 | ||
298 | < | // get some of the tricky things that may still be in the globals |
299 | < | |
300 | < | |
301 | < | if( the_globals->haveBox() ){ |
302 | < | simnfo->box_x = the_globals->getBox(); |
303 | < | simnfo->box_y = the_globals->getBox(); |
304 | < | simnfo->box_z = the_globals->getBox(); |
305 | < | } |
442 | < | else if( the_globals->haveDensity() ){ |
298 | > | if (!theBends[j].isGhost){ |
299 | > | exI = theBends[j].a; |
300 | > | exJ = theBends[j].c; |
301 | > | } |
302 | > | else{ |
303 | > | exI = theBends[j].a; |
304 | > | exJ = theBends[j].b; |
305 | > | } |
306 | ||
307 | < | double vol; |
308 | < | vol = (double)tot_nmol / the_globals->getDensity(); |
309 | < | simnfo->box_x = pow( vol, ( 1.0 / 3.0 ) ); |
310 | < | simnfo->box_y = simnfo->box_x; |
311 | < | simnfo->box_z = simnfo->box_x; |
312 | < | } |
313 | < | else{ |
314 | < | if( !the_globals->haveBoxX() ){ |
315 | < | sprintf( painCave.errMsg, |
316 | < | "SimSetup error, no periodic BoxX size given.\n" ); |
317 | < | painCave.isFatal = 1; |
455 | < | simError(); |
456 | < | } |
457 | < | simnfo->box_x = the_globals->getBoxX(); |
307 | > | // exclude_I must always be the smaller of the pair |
308 | > | if (exI > exJ){ |
309 | > | tempEx = exI; |
310 | > | exI = exJ; |
311 | > | exJ = tempEx; |
312 | > | } |
313 | > | #ifdef IS_MPI |
314 | > | tempEx = exI; |
315 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
316 | > | tempEx = exJ; |
317 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
318 | ||
319 | < | if( !the_globals->haveBoxY() ){ |
320 | < | sprintf( painCave.errMsg, |
321 | < | "SimSetup error, no periodic BoxY size given.\n" ); |
322 | < | painCave.isFatal = 1; |
323 | < | simError(); |
324 | < | } |
465 | < | simnfo->box_y = the_globals->getBoxY(); |
319 | > | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
320 | > | #else // isn't MPI |
321 | > | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
322 | > | #endif //is_mpi |
323 | > | } |
324 | > | excludeOffset += molInfo.nBends; |
325 | ||
326 | < | if( !the_globals->haveBoxZ() ){ |
327 | < | sprintf( painCave.errMsg, |
328 | < | "SimSetup error, no periodic BoxZ size given.\n" ); |
329 | < | painCave.isFatal = 1; |
330 | < | simError(); |
331 | < | } |
473 | < | simnfo->box_z = the_globals->getBoxZ(); |
474 | < | } |
326 | > | for (j = 0; j < molInfo.nTorsions; j++){ |
327 | > | currentTorsion = comp_stamps[stampID]->getTorsion(j); |
328 | > | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
329 | > | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
330 | > | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
331 | > | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
332 | ||
333 | + | exI = theTorsions[j].a; |
334 | + | exJ = theTorsions[j].d; |
335 | + | |
336 | + | // exclude_I must always be the smaller of the pair |
337 | + | if (exI > exJ){ |
338 | + | tempEx = exI; |
339 | + | exI = exJ; |
340 | + | exJ = tempEx; |
341 | + | } |
342 | #ifdef IS_MPI | |
343 | < | strcpy( checkPointMsg, "Box size set up" ); |
344 | < | MPIcheckPoint(); |
345 | < | #endif // is_mpi |
343 | > | tempEx = exI; |
344 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
345 | > | tempEx = exJ; |
346 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
347 | ||
348 | + | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
349 | + | #else // isn't MPI |
350 | + | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
351 | + | #endif //is_mpi |
352 | + | } |
353 | + | excludeOffset += molInfo.nTorsions; |
354 | ||
482 | – | // initialize the arrays |
355 | ||
356 | < | the_ff->setSimInfo( simnfo ); |
356 | > | // send the arrays off to the forceField for init. |
357 | ||
358 | < | makeMolecules(); |
359 | < | simnfo->identArray = new int[simnfo->n_atoms]; |
360 | < | for(i=0; i<simnfo->n_atoms; i++){ |
361 | < | simnfo->identArray[i] = the_atoms[i]->getIdent(); |
362 | < | } |
491 | < | |
492 | < | if (the_globals->getUseRF() ) { |
493 | < | simnfo->useReactionField = 1; |
494 | < | |
495 | < | if( !the_globals->haveECR() ){ |
496 | < | sprintf( painCave.errMsg, |
497 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
498 | < | "box length for the electrostaticCutoffRadius.\n" |
499 | < | "I hope you have a very fast processor!\n"); |
500 | < | painCave.isFatal = 0; |
501 | < | simError(); |
502 | < | double smallest; |
503 | < | smallest = simnfo->box_x; |
504 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
505 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
506 | < | simnfo->ecr = 0.5 * smallest; |
507 | < | } else { |
508 | < | simnfo->ecr = the_globals->getECR(); |
509 | < | } |
358 | > | the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); |
359 | > | the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds); |
360 | > | the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends); |
361 | > | the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, |
362 | > | theTorsions); |
363 | ||
364 | < | if( !the_globals->haveEST() ){ |
365 | < | sprintf( painCave.errMsg, |
366 | < | "SimSetup Warning: using default value of 0.05 * the " |
367 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
368 | < | ); |
369 | < | painCave.isFatal = 0; |
370 | < | simError(); |
371 | < | simnfo->est = 0.05 * simnfo->ecr; |
519 | < | } else { |
520 | < | simnfo->est = the_globals->getEST(); |
364 | > | |
365 | > | info[k].molecules[i].initialize(molInfo); |
366 | > | |
367 | > | |
368 | > | atomOffset += molInfo.nAtoms; |
369 | > | delete[] theBonds; |
370 | > | delete[] theBends; |
371 | > | delete[] theTorsions; |
372 | } | |
373 | < | |
523 | < | if(!the_globals->haveDielectric() ){ |
524 | < | sprintf( painCave.errMsg, |
525 | < | "SimSetup Error: You are trying to use Reaction Field without" |
526 | < | "setting a dielectric constant!\n" |
527 | < | ); |
528 | < | painCave.isFatal = 1; |
529 | < | simError(); |
530 | < | } |
531 | < | simnfo->dielectric = the_globals->getDielectric(); |
532 | < | } else { |
533 | < | if (usesDipoles) { |
534 | < | |
535 | < | if( !the_globals->haveECR() ){ |
536 | < | sprintf( painCave.errMsg, |
537 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
538 | < | "box length for the electrostaticCutoffRadius.\n" |
539 | < | "I hope you have a very fast processor!\n"); |
540 | < | painCave.isFatal = 0; |
541 | < | simError(); |
542 | < | double smallest; |
543 | < | smallest = simnfo->box_x; |
544 | < | if (simnfo->box_y <= smallest) smallest = simnfo->box_y; |
545 | < | if (simnfo->box_z <= smallest) smallest = simnfo->box_z; |
546 | < | simnfo->ecr = 0.5 * smallest; |
547 | < | } else { |
548 | < | simnfo->ecr = the_globals->getECR(); |
549 | < | } |
550 | < | |
551 | < | if( !the_globals->haveEST() ){ |
552 | < | sprintf( painCave.errMsg, |
553 | < | "SimSetup Warning: using default value of 5%% of the " |
554 | < | "electrostaticCutoffRadius for the " |
555 | < | "electrostaticSkinThickness\n" |
556 | < | ); |
557 | < | painCave.isFatal = 0; |
558 | < | simError(); |
559 | < | simnfo->est = 0.05 * simnfo->ecr; |
560 | < | } else { |
561 | < | simnfo->est = the_globals->getEST(); |
562 | < | } |
563 | < | } |
564 | < | } |
373 | > | } |
374 | ||
375 | #ifdef IS_MPI | |
376 | < | strcpy( checkPointMsg, "electrostatic parameters check out" ); |
376 | > | sprintf(checkPointMsg, "all molecules initialized succesfully"); |
377 | MPIcheckPoint(); | |
378 | #endif // is_mpi | |
379 | ||
380 | < | if( the_globals->haveInitialConfig() ){ |
572 | < | |
573 | < | InitializeFromFile* fileInit; |
574 | < | #ifdef IS_MPI // is_mpi |
575 | < | if( worldRank == 0 ){ |
576 | < | #endif //is_mpi |
577 | < | fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
578 | < | #ifdef IS_MPI |
579 | < | }else fileInit = new InitializeFromFile( NULL ); |
580 | < | #endif |
581 | < | fileInit->read_xyz( simnfo ); // default velocities on |
380 | > | // clean up the forcefield |
381 | ||
382 | < | delete fileInit; |
383 | < | } |
384 | < | else{ |
382 | > | the_ff->calcRcut(); |
383 | > | the_ff->cleanMe(); |
384 | > | } |
385 | ||
386 | < | #ifdef IS_MPI |
386 | > | void SimSetup::initFromBass(void){ |
387 | > | int i, j, k; |
388 | > | int n_cells; |
389 | > | double cellx, celly, cellz; |
390 | > | double temp1, temp2, temp3; |
391 | > | int n_per_extra; |
392 | > | int n_extra; |
393 | > | int have_extra, done; |
394 | ||
395 | < | // no init from bass |
396 | < | |
397 | < | sprintf( painCave.errMsg, |
398 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
593 | < | painCave.isFatal; |
594 | < | simError(); |
595 | < | |
596 | < | #else |
395 | > | double vel[3]; |
396 | > | vel[0] = 0.0; |
397 | > | vel[1] = 0.0; |
398 | > | vel[2] = 0.0; |
399 | ||
400 | < | initFromBass(); |
400 | > | temp1 = (double) tot_nmol / 4.0; |
401 | > | temp2 = pow(temp1, (1.0 / 3.0)); |
402 | > | temp3 = ceil(temp2); |
403 | ||
404 | + | have_extra = 0; |
405 | + | if (temp2 < temp3){ |
406 | + | // we have a non-complete lattice |
407 | + | have_extra = 1; |
408 | ||
409 | < | #endif |
410 | < | } |
409 | > | n_cells = (int) temp3 - 1; |
410 | > | cellx = info[0].boxL[0] / temp3; |
411 | > | celly = info[0].boxL[1] / temp3; |
412 | > | cellz = info[0].boxL[2] / temp3; |
413 | > | n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells); |
414 | > | temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0)); |
415 | > | n_per_extra = (int) ceil(temp1); |
416 | ||
417 | < | #ifdef IS_MPI |
418 | < | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
419 | < | MPIcheckPoint(); |
420 | < | #endif // is_mpi |
417 | > | if (n_per_extra > 4){ |
418 | > | sprintf(painCave.errMsg, |
419 | > | "SimSetup error. There has been an error in constructing" |
420 | > | " the non-complete lattice.\n"); |
421 | > | painCave.isFatal = 1; |
422 | > | simError(); |
423 | > | } |
424 | > | } |
425 | > | else{ |
426 | > | n_cells = (int) temp3; |
427 | > | cellx = info[0].boxL[0] / temp3; |
428 | > | celly = info[0].boxL[1] / temp3; |
429 | > | cellz = info[0].boxL[2] / temp3; |
430 | > | } |
431 | ||
432 | < | |
433 | < | |
434 | < | |
435 | < | |
432 | > | current_mol = 0; |
433 | > | current_comp_mol = 0; |
434 | > | current_comp = 0; |
435 | > | current_atom_ndx = 0; |
436 | ||
437 | < | |
438 | < | #ifdef IS_MPI |
439 | < | if( worldRank == 0 ){ |
440 | < | #endif // is_mpi |
441 | < | |
442 | < | if( the_globals->haveFinalConfig() ){ |
443 | < | strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
444 | < | } |
445 | < | else{ |
446 | < | strcpy( simnfo->finalName, inFileName ); |
624 | < | char* endTest; |
625 | < | int nameLength = strlen( simnfo->finalName ); |
626 | < | endTest = &(simnfo->finalName[nameLength - 5]); |
627 | < | if( !strcmp( endTest, ".bass" ) ){ |
628 | < | strcpy( endTest, ".eor" ); |
437 | > | for (i = 0; i < n_cells ; i++){ |
438 | > | for (j = 0; j < n_cells; j++){ |
439 | > | for (k = 0; k < n_cells; k++){ |
440 | > | makeElement(i * cellx, j * celly, k * cellz); |
441 | > | |
442 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz); |
443 | > | |
444 | > | makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz); |
445 | > | |
446 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz); |
447 | } | |
630 | – | else if( !strcmp( endTest, ".BASS" ) ){ |
631 | – | strcpy( endTest, ".eor" ); |
632 | – | } |
633 | – | else{ |
634 | – | endTest = &(simnfo->finalName[nameLength - 4]); |
635 | – | if( !strcmp( endTest, ".bss" ) ){ |
636 | – | strcpy( endTest, ".eor" ); |
637 | – | } |
638 | – | else if( !strcmp( endTest, ".mdl" ) ){ |
639 | – | strcpy( endTest, ".eor" ); |
640 | – | } |
641 | – | else{ |
642 | – | strcat( simnfo->finalName, ".eor" ); |
643 | – | } |
644 | – | } |
448 | } | |
449 | < | |
450 | < | // make the sample and status out names |
451 | < | |
452 | < | strcpy( simnfo->sampleName, inFileName ); |
453 | < | char* endTest; |
454 | < | int nameLength = strlen( simnfo->sampleName ); |
455 | < | endTest = &(simnfo->sampleName[nameLength - 5]); |
456 | < | if( !strcmp( endTest, ".bass" ) ){ |
457 | < | strcpy( endTest, ".dump" ); |
458 | < | } |
459 | < | else if( !strcmp( endTest, ".BASS" ) ){ |
460 | < | strcpy( endTest, ".dump" ); |
461 | < | } |
462 | < | else{ |
463 | < | endTest = &(simnfo->sampleName[nameLength - 4]); |
464 | < | if( !strcmp( endTest, ".bss" ) ){ |
465 | < | strcpy( endTest, ".dump" ); |
449 | > | } |
450 | > | |
451 | > | if (have_extra){ |
452 | > | done = 0; |
453 | > | |
454 | > | int start_ndx; |
455 | > | for (i = 0; i < (n_cells + 1) && !done; i++){ |
456 | > | for (j = 0; j < (n_cells + 1) && !done; j++){ |
457 | > | if (i < n_cells){ |
458 | > | if (j < n_cells){ |
459 | > | start_ndx = n_cells; |
460 | > | } |
461 | > | else |
462 | > | start_ndx = 0; |
463 | > | } |
464 | > | else |
465 | > | start_ndx = 0; |
466 | > | |
467 | > | for (k = start_ndx; k < (n_cells + 1) && !done; k++){ |
468 | > | makeElement(i * cellx, j * celly, k * cellz); |
469 | > | done = (current_mol >= tot_nmol); |
470 | > | |
471 | > | if (!done && n_per_extra > 1){ |
472 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, |
473 | > | k * cellz); |
474 | > | done = (current_mol >= tot_nmol); |
475 | > | } |
476 | > | |
477 | > | if (!done && n_per_extra > 2){ |
478 | > | makeElement(i * cellx, j * celly + 0.5 * celly, |
479 | > | k * cellz + 0.5 * cellz); |
480 | > | done = (current_mol >= tot_nmol); |
481 | > | } |
482 | > | |
483 | > | if (!done && n_per_extra > 3){ |
484 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, |
485 | > | k * cellz + 0.5 * cellz); |
486 | > | done = (current_mol >= tot_nmol); |
487 | > | } |
488 | > | } |
489 | } | |
664 | – | else if( !strcmp( endTest, ".mdl" ) ){ |
665 | – | strcpy( endTest, ".dump" ); |
666 | – | } |
667 | – | else{ |
668 | – | strcat( simnfo->sampleName, ".dump" ); |
669 | – | } |
490 | } | |
671 | – | |
672 | – | strcpy( simnfo->statusName, inFileName ); |
673 | – | nameLength = strlen( simnfo->statusName ); |
674 | – | endTest = &(simnfo->statusName[nameLength - 5]); |
675 | – | if( !strcmp( endTest, ".bass" ) ){ |
676 | – | strcpy( endTest, ".stat" ); |
677 | – | } |
678 | – | else if( !strcmp( endTest, ".BASS" ) ){ |
679 | – | strcpy( endTest, ".stat" ); |
680 | – | } |
681 | – | else{ |
682 | – | endTest = &(simnfo->statusName[nameLength - 4]); |
683 | – | if( !strcmp( endTest, ".bss" ) ){ |
684 | – | strcpy( endTest, ".stat" ); |
685 | – | } |
686 | – | else if( !strcmp( endTest, ".mdl" ) ){ |
687 | – | strcpy( endTest, ".stat" ); |
688 | – | } |
689 | – | else{ |
690 | – | strcat( simnfo->statusName, ".stat" ); |
691 | – | } |
692 | – | } |
693 | – | |
694 | – | #ifdef IS_MPI |
491 | } | |
696 | – | #endif // is_mpi |
697 | – | |
698 | – | // set the status, sample, and themal kick times |
699 | – | |
700 | – | if( the_globals->haveSampleTime() ){ |
701 | – | simnfo->sampleTime = the_globals->getSampleTime(); |
702 | – | simnfo->statusTime = simnfo->sampleTime; |
703 | – | simnfo->thermalTime = simnfo->sampleTime; |
704 | – | } |
705 | – | else{ |
706 | – | simnfo->sampleTime = the_globals->getRunTime(); |
707 | – | simnfo->statusTime = simnfo->sampleTime; |
708 | – | simnfo->thermalTime = simnfo->sampleTime; |
709 | – | } |
492 | ||
493 | < | if( the_globals->haveStatusTime() ){ |
494 | < | simnfo->statusTime = the_globals->getStatusTime(); |
493 | > | for (i = 0; i < info[0].n_atoms; i++){ |
494 | > | info[0].atoms[i]->setVel(vel); |
495 | } | |
496 | + | } |
497 | ||
498 | < | if( the_globals->haveThermalTime() ){ |
499 | < | simnfo->thermalTime = the_globals->getThermalTime(); |
500 | < | } |
498 | > | void SimSetup::makeElement(double x, double y, double z){ |
499 | > | int k; |
500 | > | AtomStamp* current_atom; |
501 | > | DirectionalAtom* dAtom; |
502 | > | double rotMat[3][3]; |
503 | > | double pos[3]; |
504 | ||
505 | < | // check for the temperature set flag |
505 | > | for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){ |
506 | > | current_atom = comp_stamps[current_comp]->getAtom(k); |
507 | > | if (!current_atom->havePosition()){ |
508 | > | sprintf(painCave.errMsg, |
509 | > | "SimSetup:initFromBass error.\n" |
510 | > | "\tComponent %s, atom %s does not have a position specified.\n" |
511 | > | "\tThe initialization routine is unable to give a start" |
512 | > | " position.\n", |
513 | > | comp_stamps[current_comp]->getID(), current_atom->getType()); |
514 | > | painCave.isFatal = 1; |
515 | > | simError(); |
516 | > | } |
517 | ||
518 | < | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
518 | > | pos[0] = x + current_atom->getPosX(); |
519 | > | pos[1] = y + current_atom->getPosY(); |
520 | > | pos[2] = z + current_atom->getPosZ(); |
521 | ||
522 | + | info[0].atoms[current_atom_ndx]->setPos(pos); |
523 | ||
524 | < | // // make the longe range forces and the integrator |
524 | > | if (info[0].atoms[current_atom_ndx]->isDirectional()){ |
525 | > | dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx]; |
526 | ||
527 | < | // new AllLong( simnfo ); |
527 | > | rotMat[0][0] = 1.0; |
528 | > | rotMat[0][1] = 0.0; |
529 | > | rotMat[0][2] = 0.0; |
530 | ||
531 | + | rotMat[1][0] = 0.0; |
532 | + | rotMat[1][1] = 1.0; |
533 | + | rotMat[1][2] = 0.0; |
534 | ||
535 | < | if( !strcmp( force_field, "TraPPE_Ex" ) ){ |
536 | < | new Symplectic(simnfo, the_ff, the_extendedsystem); |
537 | < | std::cerr << "called new Symplecic\n"; |
732 | < | fprintf( stderr, "called new Symplectic. stderr\n" ); |
733 | < | } |
734 | < | else if( !strcmp( force_field, "LJ" ) ){ |
735 | < | new Verlet( *simnfo, the_ff, the_extendedsystem ); |
736 | < | std::cerr << "called new Verlet\n"; |
737 | < | fprintf( stderr, "called new Verlet. stderr\n" ); |
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 |
535 | > | rotMat[2][0] = 0.0; |
536 | > | rotMat[2][1] = 0.0; |
537 | > | rotMat[2][2] = 1.0; |
538 | ||
539 | < | // initialize the Fortran |
539 | > | dAtom->setA(rotMat); |
540 | > | } |
541 | ||
542 | < | |
750 | < | simnfo->refreshSim(); |
751 | < | |
752 | < | if( !strcmp( simnfo->mixingRule, "standard") ){ |
753 | < | the_ff->initForceField( LB_MIXING_RULE ); |
542 | > | current_atom_ndx++; |
543 | } | |
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 | – | } |
544 | ||
545 | + | current_mol++; |
546 | + | current_comp_mol++; |
547 | ||
548 | < | #ifdef IS_MPI |
549 | < | strcpy( checkPointMsg, |
550 | < | "Successfully intialized the mixingRule for Fortran." ); |
551 | < | MPIcheckPoint(); |
771 | < | #endif // is_mpi |
548 | > | if (current_comp_mol >= components_nmol[current_comp]){ |
549 | > | current_comp_mol = 0; |
550 | > | current_comp++; |
551 | > | } |
552 | } | |
553 | ||
554 | ||
555 | < | void SimSetup::makeMolecules( void ){ |
555 | > | void SimSetup::gatherInfo(void){ |
556 | > | int i, j, k; |
557 | ||
558 | < | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
559 | < | molInit info; |
779 | < | DirectionalAtom* dAtom; |
780 | < | LinkedAssign* extras; |
781 | < | LinkedAssign* current_extra; |
782 | < | AtomStamp* currentAtom; |
783 | < | BondStamp* currentBond; |
784 | < | BendStamp* currentBend; |
785 | < | TorsionStamp* currentTorsion; |
558 | > | ensembleCase = -1; |
559 | > | ffCase = -1; |
560 | ||
561 | < | bond_pair* theBonds; |
788 | < | bend_set* theBends; |
789 | < | torsion_set* theTorsions; |
561 | > | // set the easy ones first |
562 | ||
563 | < | |
564 | < | //init the forceField paramters |
563 | > | for (i = 0; i < nInfo; i++){ |
564 | > | info[i].target_temp = globals->getTargetTemp(); |
565 | > | info[i].dt = globals->getDt(); |
566 | > | info[i].run_time = globals->getRunTime(); |
567 | > | } |
568 | > | n_components = globals->getNComponents(); |
569 | ||
794 | – | the_ff->readParams(); |
570 | ||
571 | < | |
797 | < | // init the atoms |
571 | > | // get the forceField |
572 | ||
573 | < | 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(); |
573 | > | strcpy(force_field, globals->getForceField()); |
574 | ||
575 | < | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
576 | < | info.nBonds = comp_stamps[stampID]->getNBonds(); |
577 | < | info.nBends = comp_stamps[stampID]->getNBends(); |
578 | < | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
579 | < | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
575 | > | if (!strcasecmp(force_field, "DUFF")){ |
576 | > | ffCase = FF_DUFF; |
577 | > | } |
578 | > | else if (!strcasecmp(force_field, "LJ")){ |
579 | > | ffCase = FF_LJ; |
580 | > | } |
581 | > | else if (!strcasecmp(force_field, "EAM")){ |
582 | > | ffCase = FF_EAM; |
583 | > | } |
584 | > | else{ |
585 | > | sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", |
586 | > | force_field); |
587 | > | painCave.isFatal = 1; |
588 | > | simError(); |
589 | > | } |
590 | ||
591 | < | 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]; |
591 | > | // get the ensemble |
592 | ||
593 | < | 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; |
593 | > | strcpy(ensemble, globals->getEnsemble()); |
594 | ||
595 | < | exI = theBonds[j].a; |
596 | < | exJ = theBonds[j].b; |
595 | > | if (!strcasecmp(ensemble, "NVE")){ |
596 | > | ensembleCase = NVE_ENS; |
597 | > | } |
598 | > | else if (!strcasecmp(ensemble, "NVT")){ |
599 | > | ensembleCase = NVT_ENS; |
600 | > | } |
601 | > | else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){ |
602 | > | ensembleCase = NPTi_ENS; |
603 | > | } |
604 | > | else if (!strcasecmp(ensemble, "NPTf")){ |
605 | > | ensembleCase = NPTf_ENS; |
606 | > | } |
607 | > | else if (!strcasecmp(ensemble, "NPTim")){ |
608 | > | ensembleCase = NPTim_ENS; |
609 | > | } |
610 | > | else if (!strcasecmp(ensemble, "NPTfm")){ |
611 | > | ensembleCase = NPTfm_ENS; |
612 | > | } |
613 | > | else{ |
614 | > | sprintf(painCave.errMsg, |
615 | > | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
616 | > | "reverting to NVE for this simulation.\n", |
617 | > | ensemble); |
618 | > | painCave.isFatal = 0; |
619 | > | simError(); |
620 | > | strcpy(ensemble, "NVE"); |
621 | > | ensembleCase = NVE_ENS; |
622 | > | } |
623 | ||
624 | < | // exclude_I must always be the smaller of the pair |
625 | < | 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 |
624 | > | for (i = 0; i < nInfo; i++){ |
625 | > | strcpy(info[i].ensemble, ensemble); |
626 | ||
627 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
887 | < | #endif //is_mpi |
888 | < | } |
889 | < | excludeOffset += info.nBonds; |
627 | > | // get the mixing rule |
628 | ||
629 | < | //make the bends |
630 | < | for(j=0; j<info.nBends; j++){ |
631 | < | |
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; |
629 | > | strcpy(info[i].mixingRule, globals->getMixingRule()); |
630 | > | info[i].usePBC = globals->getPBC(); |
631 | > | } |
632 | ||
633 | < | 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; |
633 | > | // get the components and calculate the tot_nMol and indvidual n_mol |
634 | ||
635 | < | // exclude_I must always be the smaller of the pair |
636 | < | 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; |
635 | > | the_components = globals->getComponents(); |
636 | > | components_nmol = new int[n_components]; |
637 | ||
1007 | – | |
1008 | – | // send the arrays off to the forceField for init. |
638 | ||
639 | < | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
640 | < | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
641 | < | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1013 | < | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
639 | > | if (!globals->haveNMol()){ |
640 | > | // we don't have the total number of molecules, so we assume it is |
641 | > | // given in each component |
642 | ||
643 | + | tot_nmol = 0; |
644 | + | for (i = 0; i < n_components; i++){ |
645 | + | if (!the_components[i]->haveNMol()){ |
646 | + | // we have a problem |
647 | + | sprintf(painCave.errMsg, |
648 | + | "SimSetup Error. No global NMol or component NMol" |
649 | + | " given. Cannot calculate the number of atoms.\n"); |
650 | + | painCave.isFatal = 1; |
651 | + | simError(); |
652 | + | } |
653 | ||
654 | < | the_molecules[i].initialize( info ); |
655 | < | |
656 | < | |
1019 | < | atomOffset += info.nAtoms; |
1020 | < | delete[] theBonds; |
1021 | < | delete[] theBends; |
1022 | < | delete[] theTorsions; |
654 | > | tot_nmol += the_components[i]->getNMol(); |
655 | > | components_nmol[i] = the_components[i]->getNMol(); |
656 | > | } |
657 | } | |
658 | + | else{ |
659 | + | sprintf(painCave.errMsg, |
660 | + | "SimSetup error.\n" |
661 | + | "\tSorry, the ability to specify total" |
662 | + | " nMols and then give molfractions in the components\n" |
663 | + | "\tis not currently supported." |
664 | + | " Please give nMol in the components.\n"); |
665 | + | painCave.isFatal = 1; |
666 | + | simError(); |
667 | + | } |
668 | ||
669 | < | #ifdef IS_MPI |
1026 | < | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
1027 | < | MPIcheckPoint(); |
1028 | < | #endif // is_mpi |
669 | > | // set the status, sample, and thermal kick times |
670 | ||
671 | < | // clean up the forcefield |
672 | < | the_ff->calcRcut(); |
673 | < | the_ff->cleanMe(); |
671 | > | for (i = 0; i < nInfo; i++){ |
672 | > | if (globals->haveSampleTime()){ |
673 | > | info[i].sampleTime = globals->getSampleTime(); |
674 | > | info[i].statusTime = info[i].sampleTime; |
675 | > | info[i].thermalTime = info[i].sampleTime; |
676 | > | } |
677 | > | else{ |
678 | > | info[i].sampleTime = globals->getRunTime(); |
679 | > | info[i].statusTime = info[i].sampleTime; |
680 | > | info[i].thermalTime = info[i].sampleTime; |
681 | > | } |
682 | ||
683 | < | } |
683 | > | if (globals->haveStatusTime()){ |
684 | > | info[i].statusTime = globals->getStatusTime(); |
685 | > | } |
686 | ||
687 | < | void SimSetup::initFromBass( void ){ |
687 | > | if (globals->haveThermalTime()){ |
688 | > | info[i].thermalTime = globals->getThermalTime(); |
689 | > | } |
690 | ||
691 | < | int i, j, k; |
1039 | < | int n_cells; |
1040 | < | double cellx, celly, cellz; |
1041 | < | double temp1, temp2, temp3; |
1042 | < | int n_per_extra; |
1043 | < | int n_extra; |
1044 | < | int have_extra, done; |
691 | > | // check for the temperature set flag |
692 | ||
693 | < | temp1 = (double)tot_nmol / 4.0; |
694 | < | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
1048 | < | temp3 = ceil( temp2 ); |
693 | > | if (globals->haveTempSet()) |
694 | > | info[i].setTemp = globals->getTempSet(); |
695 | ||
696 | < | have_extra =0; |
1051 | < | if( temp2 < temp3 ){ // we have a non-complete lattice |
1052 | < | have_extra =1; |
696 | > | // get some of the tricky things that may still be in the globals |
697 | ||
698 | < | n_cells = (int)temp3 - 1; |
699 | < | cellx = simnfo->box_x / temp3; |
700 | < | celly = simnfo->box_y / temp3; |
701 | < | cellz = simnfo->box_z / temp3; |
702 | < | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
1059 | < | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
1060 | < | n_per_extra = (int)ceil( temp1 ); |
698 | > | double boxVector[3]; |
699 | > | if (globals->haveBox()){ |
700 | > | boxVector[0] = globals->getBox(); |
701 | > | boxVector[1] = globals->getBox(); |
702 | > | boxVector[2] = globals->getBox(); |
703 | ||
704 | < | if( n_per_extra > 4){ |
705 | < | sprintf( painCave.errMsg, |
706 | < | "SimSetup error. There has been an error in constructing" |
707 | < | " the non-complete lattice.\n" ); |
708 | < | painCave.isFatal = 1; |
709 | < | simError(); |
704 | > | info[i].setBox(boxVector); |
705 | > | } |
706 | > | else if (globals->haveDensity()){ |
707 | > | double vol; |
708 | > | vol = (double) tot_nmol / globals->getDensity(); |
709 | > | boxVector[0] = pow(vol, (1.0 / 3.0)); |
710 | > | boxVector[1] = boxVector[0]; |
711 | > | boxVector[2] = boxVector[0]; |
712 | > | |
713 | > | info[i].setBox(boxVector); |
714 | } | |
715 | < | } |
716 | < | else{ |
717 | < | n_cells = (int)temp3; |
718 | < | cellx = simnfo->box_x / temp3; |
719 | < | celly = simnfo->box_y / temp3; |
720 | < | cellz = simnfo->box_z / temp3; |
721 | < | } |
715 | > | else{ |
716 | > | if (!globals->haveBoxX()){ |
717 | > | sprintf(painCave.errMsg, |
718 | > | "SimSetup error, no periodic BoxX size given.\n"); |
719 | > | painCave.isFatal = 1; |
720 | > | simError(); |
721 | > | } |
722 | > | boxVector[0] = globals->getBoxX(); |
723 | ||
724 | < | current_mol = 0; |
725 | < | current_comp_mol = 0; |
726 | < | current_comp = 0; |
727 | < | current_atom_ndx = 0; |
724 | > | if (!globals->haveBoxY()){ |
725 | > | sprintf(painCave.errMsg, |
726 | > | "SimSetup error, no periodic BoxY size given.\n"); |
727 | > | painCave.isFatal = 1; |
728 | > | simError(); |
729 | > | } |
730 | > | boxVector[1] = globals->getBoxY(); |
731 | ||
732 | < | for( i=0; i < n_cells ; i++ ){ |
733 | < | for( j=0; j < n_cells; j++ ){ |
734 | < | for( k=0; k < n_cells; k++ ){ |
732 | > | if (!globals->haveBoxZ()){ |
733 | > | sprintf(painCave.errMsg, |
734 | > | "SimSetup error, no periodic BoxZ size given.\n"); |
735 | > | painCave.isFatal = 1; |
736 | > | simError(); |
737 | > | } |
738 | > | boxVector[2] = globals->getBoxZ(); |
739 | ||
740 | < | makeElement( i * cellx, |
741 | < | j * celly, |
742 | < | k * cellz ); |
740 | > | info[i].setBox(boxVector); |
741 | > | } |
742 | > | } |
743 | ||
744 | < | makeElement( i * cellx + 0.5 * cellx, |
745 | < | j * celly + 0.5 * celly, |
1092 | < | k * cellz ); |
744 | > | //setup seed for random number generator |
745 | > | int seedValue; |
746 | ||
747 | < | makeElement( i * cellx, |
748 | < | j * celly + 0.5 * celly, |
1096 | < | k * cellz + 0.5 * cellz ); |
747 | > | if (globals->haveSeed()){ |
748 | > | seedValue = globals->getSeed(); |
749 | ||
750 | < | makeElement( i * cellx + 0.5 * cellx, |
751 | < | j * celly, |
752 | < | k * cellz + 0.5 * cellz ); |
750 | > | if(seedValue / 1E9 == 0){ |
751 | > | sprintf(painCave.errMsg, |
752 | > | "Seed for sprng library should contain at least 9 digits\n" |
753 | > | "OOPSE will generate a seed for user\n"); |
754 | > | painCave.isFatal = 0; |
755 | > | simError(); |
756 | > | |
757 | > | //using seed generated by system instead of invalid seed set by user |
758 | > | #ifndef IS_MPI |
759 | > | seedValue = make_sprng_seed(); |
760 | > | #else |
761 | > | if (worldRank == 0){ |
762 | > | seedValue = make_sprng_seed(); |
763 | } | |
764 | + | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
765 | + | #endif |
766 | } | |
767 | + | }//end of if branch of globals->haveSeed() |
768 | + | else{ |
769 | + | |
770 | + | #ifndef IS_MPI |
771 | + | seedValue = make_sprng_seed(); |
772 | + | #else |
773 | + | if (worldRank == 0){ |
774 | + | seedValue = make_sprng_seed(); |
775 | + | } |
776 | + | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
777 | + | #endif |
778 | + | }//end of globals->haveSeed() |
779 | + | |
780 | + | for (int i = 0; i < nInfo; i++){ |
781 | + | info[i].setSeed(seedValue); |
782 | } | |
783 | ||
784 | < | if( have_extra ){ |
785 | < | done = 0; |
784 | > | #ifdef IS_MPI |
785 | > | strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n"); |
786 | > | MPIcheckPoint(); |
787 | > | #endif // is_mpi |
788 | > | } |
789 | ||
1108 | – | int start_ndx; |
1109 | – | for( i=0; i < (n_cells+1) && !done; i++ ){ |
1110 | – | for( j=0; j < (n_cells+1) && !done; j++ ){ |
790 | ||
791 | < | if( i < n_cells ){ |
791 | > | void SimSetup::finalInfoCheck(void){ |
792 | > | int index; |
793 | > | int usesDipoles; |
794 | > | int i; |
795 | ||
796 | < | if( j < n_cells ){ |
797 | < | start_ndx = n_cells; |
1116 | < | } |
1117 | < | else start_ndx = 0; |
1118 | < | } |
1119 | < | else start_ndx = 0; |
796 | > | for (i = 0; i < nInfo; i++){ |
797 | > | // check electrostatic parameters |
798 | ||
799 | < | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
799 | > | index = 0; |
800 | > | usesDipoles = 0; |
801 | > | while ((index < info[i].n_atoms) && !usesDipoles){ |
802 | > | usesDipoles = (info[i].atoms[index])->hasDipole(); |
803 | > | index++; |
804 | > | } |
805 | ||
806 | < | makeElement( i * cellx, |
807 | < | j * celly, |
808 | < | k * cellz ); |
809 | < | done = ( current_mol >= tot_nmol ); |
806 | > | #ifdef IS_MPI |
807 | > | int myUse = usesDipoles; |
808 | > | MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
809 | > | #endif //is_mpi |
810 | ||
811 | < | 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 | < | } |
811 | > | double theEcr, theEst; |
812 | ||
813 | < | if( !done && n_per_extra > 2){ |
814 | < | makeElement( i * cellx, |
1137 | < | j * celly + 0.5 * celly, |
1138 | < | k * cellz + 0.5 * cellz ); |
1139 | < | done = ( current_mol >= tot_nmol ); |
1140 | < | } |
813 | > | if (globals->getUseRF()){ |
814 | > | info[i].useReactionField = 1; |
815 | ||
816 | < | if( !done && n_per_extra > 3){ |
817 | < | makeElement( i * cellx + 0.5 * cellx, |
818 | < | j * celly, |
819 | < | k * cellz + 0.5 * cellz ); |
820 | < | done = ( current_mol >= tot_nmol ); |
821 | < | } |
822 | < | } |
816 | > | if (!globals->haveECR()){ |
817 | > | sprintf(painCave.errMsg, |
818 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
819 | > | "box length for the electrostaticCutoffRadius.\n" |
820 | > | "I hope you have a very fast processor!\n"); |
821 | > | painCave.isFatal = 0; |
822 | > | simError(); |
823 | > | double smallest; |
824 | > | smallest = info[i].boxL[0]; |
825 | > | if (info[i].boxL[1] <= smallest) |
826 | > | smallest = info[i].boxL[1]; |
827 | > | if (info[i].boxL[2] <= smallest) |
828 | > | smallest = info[i].boxL[2]; |
829 | > | theEcr = 0.5 * smallest; |
830 | } | |
831 | + | else{ |
832 | + | theEcr = globals->getECR(); |
833 | + | } |
834 | + | |
835 | + | if (!globals->haveEST()){ |
836 | + | sprintf(painCave.errMsg, |
837 | + | "SimSetup Warning: using default value of 0.05 * the " |
838 | + | "electrostaticCutoffRadius for the electrostaticSkinThickness\n"); |
839 | + | painCave.isFatal = 0; |
840 | + | simError(); |
841 | + | theEst = 0.05 * theEcr; |
842 | + | } |
843 | + | else{ |
844 | + | theEst = globals->getEST(); |
845 | + | } |
846 | + | |
847 | + | info[i].setEcr(theEcr, theEst); |
848 | + | |
849 | + | if (!globals->haveDielectric()){ |
850 | + | sprintf(painCave.errMsg, |
851 | + | "SimSetup Error: You are trying to use Reaction Field without" |
852 | + | "setting a dielectric constant!\n"); |
853 | + | painCave.isFatal = 1; |
854 | + | simError(); |
855 | + | } |
856 | + | info[i].dielectric = globals->getDielectric(); |
857 | } | |
858 | < | } |
858 | > | else{ |
859 | > | if (usesDipoles){ |
860 | > | if (!globals->haveECR()){ |
861 | > | sprintf(painCave.errMsg, |
862 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
863 | > | "box length for the electrostaticCutoffRadius.\n" |
864 | > | "I hope you have a very fast processor!\n"); |
865 | > | painCave.isFatal = 0; |
866 | > | simError(); |
867 | > | double smallest; |
868 | > | smallest = info[i].boxL[0]; |
869 | > | if (info[i].boxL[1] <= smallest) |
870 | > | smallest = info[i].boxL[1]; |
871 | > | if (info[i].boxL[2] <= smallest) |
872 | > | smallest = info[i].boxL[2]; |
873 | > | theEcr = 0.5 * smallest; |
874 | > | } |
875 | > | else{ |
876 | > | theEcr = globals->getECR(); |
877 | > | } |
878 | ||
879 | + | if (!globals->haveEST()){ |
880 | + | sprintf(painCave.errMsg, |
881 | + | "SimSetup Warning: using default value of 0.05 * the " |
882 | + | "electrostaticCutoffRadius for the " |
883 | + | "electrostaticSkinThickness\n"); |
884 | + | painCave.isFatal = 0; |
885 | + | simError(); |
886 | + | theEst = 0.05 * theEcr; |
887 | + | } |
888 | + | else{ |
889 | + | theEst = globals->getEST(); |
890 | + | } |
891 | ||
892 | < | for( i=0; i<simnfo->n_atoms; i++ ){ |
893 | < | simnfo->atoms[i]->set_vx( 0.0 ); |
894 | < | simnfo->atoms[i]->set_vy( 0.0 ); |
1157 | < | simnfo->atoms[i]->set_vz( 0.0 ); |
892 | > | info[i].setEcr(theEcr, theEst); |
893 | > | } |
894 | > | } |
895 | } | |
896 | + | |
897 | + | #ifdef IS_MPI |
898 | + | strcpy(checkPointMsg, "post processing checks out"); |
899 | + | MPIcheckPoint(); |
900 | + | #endif // is_mpi |
901 | } | |
902 | ||
903 | < | void SimSetup::makeElement( double x, double y, double z ){ |
903 | > | void SimSetup::initSystemCoords(void){ |
904 | > | int i; |
905 | ||
906 | < | int k; |
1164 | < | AtomStamp* current_atom; |
1165 | < | DirectionalAtom* dAtom; |
1166 | < | double rotMat[3][3]; |
906 | > | char* inName; |
907 | ||
908 | < | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
908 | > | (info[0].getConfiguration())->createArrays(info[0].n_atoms); |
909 | ||
910 | < | current_atom = comp_stamps[current_comp]->getAtom( k ); |
911 | < | if( !current_atom->havePosition() ){ |
912 | < | sprintf( painCave.errMsg, |
913 | < | "SimSetup:initFromBass error.\n" |
914 | < | "\tComponent %s, atom %s does not have a position specified.\n" |
915 | < | "\tThe initialization routine is unable to give a start" |
916 | < | " position.\n", |
917 | < | comp_stamps[current_comp]->getID(), |
918 | < | current_atom->getType() ); |
919 | < | painCave.isFatal = 1; |
920 | < | simError(); |
910 | > | for (i = 0; i < info[0].n_atoms; i++) |
911 | > | info[0].atoms[i]->setCoords(); |
912 | > | |
913 | > | if (globals->haveInitialConfig()){ |
914 | > | InitializeFromFile* fileInit; |
915 | > | #ifdef IS_MPI // is_mpi |
916 | > | if (worldRank == 0){ |
917 | > | #endif //is_mpi |
918 | > | inName = globals->getInitialConfig(); |
919 | > | double* tempDouble = new double[1000000]; |
920 | > | fileInit = new InitializeFromFile(inName); |
921 | > | #ifdef IS_MPI |
922 | } | |
923 | + | else |
924 | + | fileInit = new InitializeFromFile(NULL); |
925 | + | #endif |
926 | + | fileInit->readInit(info); // default velocities on |
927 | ||
928 | < | the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
929 | < | the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
930 | < | the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
928 | > | delete fileInit; |
929 | > | } |
930 | > | else{ |
931 | > | #ifdef IS_MPI |
932 | ||
933 | < | if( the_atoms[current_atom_ndx]->isDirectional() ){ |
933 | > | // no init from bass |
934 | ||
935 | < | dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
935 | > | sprintf(painCave.errMsg, |
936 | > | "Cannot intialize a parallel simulation without an initial configuration file.\n"); |
937 | > | painCave.isFatal; |
938 | > | simError(); |
939 | ||
940 | < | rotMat[0][0] = 1.0; |
1192 | < | rotMat[0][1] = 0.0; |
1193 | < | rotMat[0][2] = 0.0; |
940 | > | #else |
941 | ||
942 | < | rotMat[1][0] = 0.0; |
1196 | < | rotMat[1][1] = 1.0; |
1197 | < | rotMat[1][2] = 0.0; |
942 | > | initFromBass(); |
943 | ||
1199 | – | rotMat[2][0] = 0.0; |
1200 | – | rotMat[2][1] = 0.0; |
1201 | – | rotMat[2][2] = 1.0; |
944 | ||
945 | < | dAtom->setA( rotMat ); |
1204 | < | } |
1205 | < | |
1206 | < | current_atom_ndx++; |
945 | > | #endif |
946 | } | |
947 | ||
948 | < | current_mol++; |
949 | < | current_comp_mol++; |
948 | > | #ifdef IS_MPI |
949 | > | strcpy(checkPointMsg, "Successfully read in the initial configuration"); |
950 | > | MPIcheckPoint(); |
951 | > | #endif // is_mpi |
952 | > | } |
953 | ||
1212 | – | if( current_comp_mol >= components_nmol[current_comp] ){ |
954 | ||
955 | < | current_comp_mol = 0; |
956 | < | current_comp++; |
955 | > | void SimSetup::makeOutNames(void){ |
956 | > | int k; |
957 | > | |
958 | > | |
959 | > | for (k = 0; k < nInfo; k++){ |
960 | > | #ifdef IS_MPI |
961 | > | if (worldRank == 0){ |
962 | > | #endif // is_mpi |
963 | > | |
964 | > | if (globals->haveFinalConfig()){ |
965 | > | strcpy(info[k].finalName, globals->getFinalConfig()); |
966 | > | } |
967 | > | else{ |
968 | > | strcpy(info[k].finalName, inFileName); |
969 | > | char* endTest; |
970 | > | int nameLength = strlen(info[k].finalName); |
971 | > | endTest = &(info[k].finalName[nameLength - 5]); |
972 | > | if (!strcmp(endTest, ".bass")){ |
973 | > | strcpy(endTest, ".eor"); |
974 | > | } |
975 | > | else if (!strcmp(endTest, ".BASS")){ |
976 | > | strcpy(endTest, ".eor"); |
977 | > | } |
978 | > | else{ |
979 | > | endTest = &(info[k].finalName[nameLength - 4]); |
980 | > | if (!strcmp(endTest, ".bss")){ |
981 | > | strcpy(endTest, ".eor"); |
982 | > | } |
983 | > | else if (!strcmp(endTest, ".mdl")){ |
984 | > | strcpy(endTest, ".eor"); |
985 | > | } |
986 | > | else{ |
987 | > | strcat(info[k].finalName, ".eor"); |
988 | > | } |
989 | > | } |
990 | > | } |
991 | > | |
992 | > | // make the sample and status out names |
993 | > | |
994 | > | strcpy(info[k].sampleName, inFileName); |
995 | > | char* endTest; |
996 | > | int nameLength = strlen(info[k].sampleName); |
997 | > | endTest = &(info[k].sampleName[nameLength - 5]); |
998 | > | if (!strcmp(endTest, ".bass")){ |
999 | > | strcpy(endTest, ".dump"); |
1000 | > | } |
1001 | > | else if (!strcmp(endTest, ".BASS")){ |
1002 | > | strcpy(endTest, ".dump"); |
1003 | > | } |
1004 | > | else{ |
1005 | > | endTest = &(info[k].sampleName[nameLength - 4]); |
1006 | > | if (!strcmp(endTest, ".bss")){ |
1007 | > | strcpy(endTest, ".dump"); |
1008 | > | } |
1009 | > | else if (!strcmp(endTest, ".mdl")){ |
1010 | > | strcpy(endTest, ".dump"); |
1011 | > | } |
1012 | > | else{ |
1013 | > | strcat(info[k].sampleName, ".dump"); |
1014 | > | } |
1015 | > | } |
1016 | > | |
1017 | > | strcpy(info[k].statusName, inFileName); |
1018 | > | nameLength = strlen(info[k].statusName); |
1019 | > | endTest = &(info[k].statusName[nameLength - 5]); |
1020 | > | if (!strcmp(endTest, ".bass")){ |
1021 | > | strcpy(endTest, ".stat"); |
1022 | > | } |
1023 | > | else if (!strcmp(endTest, ".BASS")){ |
1024 | > | strcpy(endTest, ".stat"); |
1025 | > | } |
1026 | > | else{ |
1027 | > | endTest = &(info[k].statusName[nameLength - 4]); |
1028 | > | if (!strcmp(endTest, ".bss")){ |
1029 | > | strcpy(endTest, ".stat"); |
1030 | > | } |
1031 | > | else if (!strcmp(endTest, ".mdl")){ |
1032 | > | strcpy(endTest, ".stat"); |
1033 | > | } |
1034 | > | else{ |
1035 | > | strcat(info[k].statusName, ".stat"); |
1036 | > | } |
1037 | > | } |
1038 | > | |
1039 | > | #ifdef IS_MPI |
1040 | > | |
1041 | > | } |
1042 | > | #endif // is_mpi |
1043 | } | |
1044 | } | |
1045 | + | |
1046 | + | |
1047 | + | void SimSetup::sysObjectsCreation(void){ |
1048 | + | int i, k; |
1049 | + | |
1050 | + | // create the forceField |
1051 | + | |
1052 | + | createFF(); |
1053 | + | |
1054 | + | // extract componentList |
1055 | + | |
1056 | + | compList(); |
1057 | + | |
1058 | + | // calc the number of atoms, bond, bends, and torsions |
1059 | + | |
1060 | + | calcSysValues(); |
1061 | + | |
1062 | + | #ifdef IS_MPI |
1063 | + | // divide the molecules among the processors |
1064 | + | |
1065 | + | mpiMolDivide(); |
1066 | + | #endif //is_mpi |
1067 | + | |
1068 | + | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1069 | + | |
1070 | + | makeSysArrays(); |
1071 | + | |
1072 | + | // make and initialize the molecules (all but atomic coordinates) |
1073 | + | |
1074 | + | makeMolecules(); |
1075 | + | |
1076 | + | for (k = 0; k < nInfo; k++){ |
1077 | + | info[k].identArray = new int[info[k].n_atoms]; |
1078 | + | for (i = 0; i < info[k].n_atoms; i++){ |
1079 | + | info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1080 | + | } |
1081 | + | } |
1082 | + | } |
1083 | + | |
1084 | + | |
1085 | + | void SimSetup::createFF(void){ |
1086 | + | switch (ffCase){ |
1087 | + | case FF_DUFF: |
1088 | + | the_ff = new DUFF(); |
1089 | + | break; |
1090 | + | |
1091 | + | case FF_LJ: |
1092 | + | the_ff = new LJFF(); |
1093 | + | break; |
1094 | + | |
1095 | + | case FF_EAM: |
1096 | + | the_ff = new EAM_FF(); |
1097 | + | break; |
1098 | + | |
1099 | + | default: |
1100 | + | sprintf(painCave.errMsg, |
1101 | + | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1102 | + | painCave.isFatal = 1; |
1103 | + | simError(); |
1104 | + | } |
1105 | + | |
1106 | + | #ifdef IS_MPI |
1107 | + | strcpy(checkPointMsg, "ForceField creation successful"); |
1108 | + | MPIcheckPoint(); |
1109 | + | #endif // is_mpi |
1110 | + | } |
1111 | + | |
1112 | + | |
1113 | + | void SimSetup::compList(void){ |
1114 | + | int i; |
1115 | + | char* id; |
1116 | + | LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1117 | + | LinkedMolStamp* currentStamp = NULL; |
1118 | + | comp_stamps = new MoleculeStamp * [n_components]; |
1119 | + | |
1120 | + | // make an array of molecule stamps that match the components used. |
1121 | + | // also extract the used stamps out into a separate linked list |
1122 | + | |
1123 | + | for (i = 0; i < nInfo; i++){ |
1124 | + | info[i].nComponents = n_components; |
1125 | + | info[i].componentsNmol = components_nmol; |
1126 | + | info[i].compStamps = comp_stamps; |
1127 | + | info[i].headStamp = headStamp; |
1128 | + | } |
1129 | + | |
1130 | + | |
1131 | + | for (i = 0; i < n_components; i++){ |
1132 | + | id = the_components[i]->getType(); |
1133 | + | comp_stamps[i] = NULL; |
1134 | + | |
1135 | + | // check to make sure the component isn't already in the list |
1136 | + | |
1137 | + | comp_stamps[i] = headStamp->match(id); |
1138 | + | if (comp_stamps[i] == NULL){ |
1139 | + | // extract the component from the list; |
1140 | + | |
1141 | + | currentStamp = stamps->extractMolStamp(id); |
1142 | + | if (currentStamp == NULL){ |
1143 | + | sprintf(painCave.errMsg, |
1144 | + | "SimSetup error: Component \"%s\" was not found in the " |
1145 | + | "list of declared molecules\n", |
1146 | + | id); |
1147 | + | painCave.isFatal = 1; |
1148 | + | simError(); |
1149 | + | } |
1150 | + | |
1151 | + | headStamp->add(currentStamp); |
1152 | + | comp_stamps[i] = headStamp->match(id); |
1153 | + | } |
1154 | + | } |
1155 | + | |
1156 | + | #ifdef IS_MPI |
1157 | + | strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
1158 | + | MPIcheckPoint(); |
1159 | + | #endif // is_mpi |
1160 | + | } |
1161 | + | |
1162 | + | void SimSetup::calcSysValues(void){ |
1163 | + | int i, j, k; |
1164 | + | |
1165 | + | int* molMembershipArray; |
1166 | + | |
1167 | + | tot_atoms = 0; |
1168 | + | tot_bonds = 0; |
1169 | + | tot_bends = 0; |
1170 | + | tot_torsions = 0; |
1171 | + | for (i = 0; i < n_components; i++){ |
1172 | + | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1173 | + | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1174 | + | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1175 | + | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1176 | + | } |
1177 | + | |
1178 | + | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1179 | + | molMembershipArray = new int[tot_atoms]; |
1180 | + | |
1181 | + | for (i = 0; i < nInfo; i++){ |
1182 | + | info[i].n_atoms = tot_atoms; |
1183 | + | info[i].n_bonds = tot_bonds; |
1184 | + | info[i].n_bends = tot_bends; |
1185 | + | info[i].n_torsions = tot_torsions; |
1186 | + | info[i].n_SRI = tot_SRI; |
1187 | + | info[i].n_mol = tot_nmol; |
1188 | + | |
1189 | + | info[i].molMembershipArray = molMembershipArray; |
1190 | + | } |
1191 | + | } |
1192 | + | |
1193 | + | #ifdef IS_MPI |
1194 | + | |
1195 | + | void SimSetup::mpiMolDivide(void){ |
1196 | + | int i, j, k; |
1197 | + | int localMol, allMol; |
1198 | + | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1199 | + | |
1200 | + | mpiSim = new mpiSimulation(info); |
1201 | + | |
1202 | + | globalIndex = mpiSim->divideLabor(); |
1203 | + | |
1204 | + | // set up the local variables |
1205 | + | |
1206 | + | mol2proc = mpiSim->getMolToProcMap(); |
1207 | + | molCompType = mpiSim->getMolComponentType(); |
1208 | + | |
1209 | + | allMol = 0; |
1210 | + | localMol = 0; |
1211 | + | local_atoms = 0; |
1212 | + | local_bonds = 0; |
1213 | + | local_bends = 0; |
1214 | + | local_torsions = 0; |
1215 | + | globalAtomIndex = 0; |
1216 | + | |
1217 | + | |
1218 | + | for (i = 0; i < n_components; i++){ |
1219 | + | for (j = 0; j < components_nmol[i]; j++){ |
1220 | + | if (mol2proc[allMol] == worldRank){ |
1221 | + | local_atoms += comp_stamps[i]->getNAtoms(); |
1222 | + | local_bonds += comp_stamps[i]->getNBonds(); |
1223 | + | local_bends += comp_stamps[i]->getNBends(); |
1224 | + | local_torsions += comp_stamps[i]->getNTorsions(); |
1225 | + | localMol++; |
1226 | + | } |
1227 | + | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1228 | + | info[0].molMembershipArray[globalAtomIndex] = allMol; |
1229 | + | globalAtomIndex++; |
1230 | + | } |
1231 | + | |
1232 | + | allMol++; |
1233 | + | } |
1234 | + | } |
1235 | + | local_SRI = local_bonds + local_bends + local_torsions; |
1236 | + | |
1237 | + | info[0].n_atoms = mpiSim->getMyNlocal(); |
1238 | + | |
1239 | + | if (local_atoms != info[0].n_atoms){ |
1240 | + | sprintf(painCave.errMsg, |
1241 | + | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1242 | + | " localAtom (%d) are not equal.\n", |
1243 | + | info[0].n_atoms, local_atoms); |
1244 | + | painCave.isFatal = 1; |
1245 | + | simError(); |
1246 | + | } |
1247 | + | |
1248 | + | info[0].n_bonds = local_bonds; |
1249 | + | info[0].n_bends = local_bends; |
1250 | + | info[0].n_torsions = local_torsions; |
1251 | + | info[0].n_SRI = local_SRI; |
1252 | + | info[0].n_mol = localMol; |
1253 | + | |
1254 | + | strcpy(checkPointMsg, "Passed nlocal consistency check."); |
1255 | + | MPIcheckPoint(); |
1256 | + | } |
1257 | + | |
1258 | + | #endif // is_mpi |
1259 | + | |
1260 | + | |
1261 | + | void SimSetup::makeSysArrays(void){ |
1262 | + | int i, j, k, l; |
1263 | + | |
1264 | + | Atom** the_atoms; |
1265 | + | Molecule* the_molecules; |
1266 | + | Exclude** the_excludes; |
1267 | + | |
1268 | + | |
1269 | + | for (l = 0; l < nInfo; l++){ |
1270 | + | // create the atom and short range interaction arrays |
1271 | + | |
1272 | + | the_atoms = new Atom * [info[l].n_atoms]; |
1273 | + | the_molecules = new Molecule[info[l].n_mol]; |
1274 | + | int molIndex; |
1275 | + | |
1276 | + | // initialize the molecule's stampID's |
1277 | + | |
1278 | + | #ifdef IS_MPI |
1279 | + | |
1280 | + | |
1281 | + | molIndex = 0; |
1282 | + | for (i = 0; i < mpiSim->getTotNmol(); i++){ |
1283 | + | if (mol2proc[i] == worldRank){ |
1284 | + | the_molecules[molIndex].setStampID(molCompType[i]); |
1285 | + | the_molecules[molIndex].setMyIndex(molIndex); |
1286 | + | the_molecules[molIndex].setGlobalIndex(i); |
1287 | + | molIndex++; |
1288 | + | } |
1289 | + | } |
1290 | + | |
1291 | + | #else // is_mpi |
1292 | + | |
1293 | + | molIndex = 0; |
1294 | + | globalAtomIndex = 0; |
1295 | + | for (i = 0; i < n_components; i++){ |
1296 | + | for (j = 0; j < components_nmol[i]; j++){ |
1297 | + | the_molecules[molIndex].setStampID(i); |
1298 | + | the_molecules[molIndex].setMyIndex(molIndex); |
1299 | + | the_molecules[molIndex].setGlobalIndex(molIndex); |
1300 | + | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1301 | + | info[l].molMembershipArray[globalAtomIndex] = molIndex; |
1302 | + | globalAtomIndex++; |
1303 | + | } |
1304 | + | molIndex++; |
1305 | + | } |
1306 | + | } |
1307 | + | |
1308 | + | |
1309 | + | #endif // is_mpi |
1310 | + | |
1311 | + | |
1312 | + | if (info[l].n_SRI){ |
1313 | + | Exclude::createArray(info[l].n_SRI); |
1314 | + | the_excludes = new Exclude * [info[l].n_SRI]; |
1315 | + | for (int ex = 0; ex < info[l].n_SRI; ex++){ |
1316 | + | the_excludes[ex] = new Exclude(ex); |
1317 | + | } |
1318 | + | info[l].globalExcludes = new int; |
1319 | + | info[l].n_exclude = info[l].n_SRI; |
1320 | + | } |
1321 | + | else{ |
1322 | + | Exclude::createArray(1); |
1323 | + | the_excludes = new Exclude * ; |
1324 | + | the_excludes[0] = new Exclude(0); |
1325 | + | the_excludes[0]->setPair(0, 0); |
1326 | + | info[l].globalExcludes = new int; |
1327 | + | info[l].globalExcludes[0] = 0; |
1328 | + | info[l].n_exclude = 0; |
1329 | + | } |
1330 | + | |
1331 | + | // set the arrays into the SimInfo object |
1332 | + | |
1333 | + | info[l].atoms = the_atoms; |
1334 | + | info[l].molecules = the_molecules; |
1335 | + | info[l].nGlobalExcludes = 0; |
1336 | + | info[l].excludes = the_excludes; |
1337 | + | |
1338 | + | the_ff->setSimInfo(info); |
1339 | + | } |
1340 | + | } |
1341 | + | |
1342 | + | void SimSetup::makeIntegrator(void){ |
1343 | + | int k; |
1344 | + | |
1345 | + | NVT<RealIntegrator>* myNVT = NULL; |
1346 | + | NPTi<RealIntegrator>* myNPTi = NULL; |
1347 | + | NPTf<RealIntegrator>* myNPTf = NULL; |
1348 | + | NPTim<RealIntegrator>* myNPTim = NULL; |
1349 | + | NPTfm<RealIntegrator>* myNPTfm = NULL; |
1350 | + | |
1351 | + | for (k = 0; k < nInfo; k++){ |
1352 | + | switch (ensembleCase){ |
1353 | + | case NVE_ENS: |
1354 | + | if (globals->haveZconstraints()){ |
1355 | + | setupZConstraint(info[k]); |
1356 | + | new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1357 | + | } |
1358 | + | else |
1359 | + | new NVE<RealIntegrator>(&(info[k]), the_ff); |
1360 | + | break; |
1361 | + | |
1362 | + | case NVT_ENS: |
1363 | + | if (globals->haveZconstraints()){ |
1364 | + | setupZConstraint(info[k]); |
1365 | + | myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff); |
1366 | + | } |
1367 | + | else |
1368 | + | myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff); |
1369 | + | |
1370 | + | myNVT->setTargetTemp(globals->getTargetTemp()); |
1371 | + | |
1372 | + | if (globals->haveTauThermostat()) |
1373 | + | myNVT->setTauThermostat(globals->getTauThermostat()); |
1374 | + | else{ |
1375 | + | sprintf(painCave.errMsg, |
1376 | + | "SimSetup error: If you use the NVT\n" |
1377 | + | " ensemble, you must set tauThermostat.\n"); |
1378 | + | painCave.isFatal = 1; |
1379 | + | simError(); |
1380 | + | } |
1381 | + | break; |
1382 | + | |
1383 | + | case NPTi_ENS: |
1384 | + | if (globals->haveZconstraints()){ |
1385 | + | setupZConstraint(info[k]); |
1386 | + | myNPTi = new ZConstraint<NPTi<RealIntegrator> >(&(info[k]), the_ff); |
1387 | + | } |
1388 | + | else |
1389 | + | myNPTi = new NPTi<RealIntegrator>(&(info[k]), the_ff); |
1390 | + | |
1391 | + | myNPTi->setTargetTemp(globals->getTargetTemp()); |
1392 | + | |
1393 | + | if (globals->haveTargetPressure()) |
1394 | + | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1395 | + | else{ |
1396 | + | sprintf(painCave.errMsg, |
1397 | + | "SimSetup error: If you use a constant pressure\n" |
1398 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1399 | + | painCave.isFatal = 1; |
1400 | + | simError(); |
1401 | + | } |
1402 | + | |
1403 | + | if (globals->haveTauThermostat()) |
1404 | + | myNPTi->setTauThermostat(globals->getTauThermostat()); |
1405 | + | else{ |
1406 | + | sprintf(painCave.errMsg, |
1407 | + | "SimSetup error: If you use an NPT\n" |
1408 | + | " ensemble, you must set tauThermostat.\n"); |
1409 | + | painCave.isFatal = 1; |
1410 | + | simError(); |
1411 | + | } |
1412 | + | |
1413 | + | if (globals->haveTauBarostat()) |
1414 | + | myNPTi->setTauBarostat(globals->getTauBarostat()); |
1415 | + | else{ |
1416 | + | sprintf(painCave.errMsg, |
1417 | + | "SimSetup error: If you use an NPT\n" |
1418 | + | " ensemble, you must set tauBarostat.\n"); |
1419 | + | painCave.isFatal = 1; |
1420 | + | simError(); |
1421 | + | } |
1422 | + | break; |
1423 | + | |
1424 | + | case NPTf_ENS: |
1425 | + | if (globals->haveZconstraints()){ |
1426 | + | setupZConstraint(info[k]); |
1427 | + | myNPTf = new ZConstraint<NPTf<RealIntegrator> >(&(info[k]), the_ff); |
1428 | + | } |
1429 | + | else |
1430 | + | myNPTf = new NPTf<RealIntegrator>(&(info[k]), the_ff); |
1431 | + | |
1432 | + | myNPTf->setTargetTemp(globals->getTargetTemp()); |
1433 | + | |
1434 | + | if (globals->haveTargetPressure()) |
1435 | + | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1436 | + | else{ |
1437 | + | sprintf(painCave.errMsg, |
1438 | + | "SimSetup error: If you use a constant pressure\n" |
1439 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1440 | + | painCave.isFatal = 1; |
1441 | + | simError(); |
1442 | + | } |
1443 | + | |
1444 | + | if (globals->haveTauThermostat()) |
1445 | + | myNPTf->setTauThermostat(globals->getTauThermostat()); |
1446 | + | else{ |
1447 | + | sprintf(painCave.errMsg, |
1448 | + | "SimSetup error: If you use an NPT\n" |
1449 | + | " ensemble, you must set tauThermostat.\n"); |
1450 | + | painCave.isFatal = 1; |
1451 | + | simError(); |
1452 | + | } |
1453 | + | |
1454 | + | if (globals->haveTauBarostat()) |
1455 | + | myNPTf->setTauBarostat(globals->getTauBarostat()); |
1456 | + | else{ |
1457 | + | sprintf(painCave.errMsg, |
1458 | + | "SimSetup error: If you use an NPT\n" |
1459 | + | " ensemble, you must set tauBarostat.\n"); |
1460 | + | painCave.isFatal = 1; |
1461 | + | simError(); |
1462 | + | } |
1463 | + | break; |
1464 | + | |
1465 | + | case NPTim_ENS: |
1466 | + | if (globals->haveZconstraints()){ |
1467 | + | setupZConstraint(info[k]); |
1468 | + | myNPTim = new ZConstraint<NPTim<RealIntegrator> >(&(info[k]), the_ff); |
1469 | + | } |
1470 | + | else |
1471 | + | myNPTim = new NPTim<RealIntegrator>(&(info[k]), the_ff); |
1472 | + | |
1473 | + | myNPTim->setTargetTemp(globals->getTargetTemp()); |
1474 | + | |
1475 | + | if (globals->haveTargetPressure()) |
1476 | + | myNPTim->setTargetPressure(globals->getTargetPressure()); |
1477 | + | else{ |
1478 | + | sprintf(painCave.errMsg, |
1479 | + | "SimSetup error: If you use a constant pressure\n" |
1480 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1481 | + | painCave.isFatal = 1; |
1482 | + | simError(); |
1483 | + | } |
1484 | + | |
1485 | + | if (globals->haveTauThermostat()) |
1486 | + | myNPTim->setTauThermostat(globals->getTauThermostat()); |
1487 | + | else{ |
1488 | + | sprintf(painCave.errMsg, |
1489 | + | "SimSetup error: If you use an NPT\n" |
1490 | + | " ensemble, you must set tauThermostat.\n"); |
1491 | + | painCave.isFatal = 1; |
1492 | + | simError(); |
1493 | + | } |
1494 | + | |
1495 | + | if (globals->haveTauBarostat()) |
1496 | + | myNPTim->setTauBarostat(globals->getTauBarostat()); |
1497 | + | else{ |
1498 | + | sprintf(painCave.errMsg, |
1499 | + | "SimSetup error: If you use an NPT\n" |
1500 | + | " ensemble, you must set tauBarostat.\n"); |
1501 | + | painCave.isFatal = 1; |
1502 | + | simError(); |
1503 | + | } |
1504 | + | break; |
1505 | + | |
1506 | + | case NPTfm_ENS: |
1507 | + | if (globals->haveZconstraints()){ |
1508 | + | setupZConstraint(info[k]); |
1509 | + | myNPTfm = new ZConstraint<NPTfm<RealIntegrator> >(&(info[k]), the_ff); |
1510 | + | } |
1511 | + | else |
1512 | + | myNPTfm = new NPTfm<RealIntegrator>(&(info[k]), the_ff); |
1513 | + | |
1514 | + | myNPTfm->setTargetTemp(globals->getTargetTemp()); |
1515 | + | |
1516 | + | if (globals->haveTargetPressure()) |
1517 | + | myNPTfm->setTargetPressure(globals->getTargetPressure()); |
1518 | + | else{ |
1519 | + | sprintf(painCave.errMsg, |
1520 | + | "SimSetup error: If you use a constant pressure\n" |
1521 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1522 | + | painCave.isFatal = 1; |
1523 | + | simError(); |
1524 | + | } |
1525 | + | |
1526 | + | if (globals->haveTauThermostat()) |
1527 | + | myNPTfm->setTauThermostat(globals->getTauThermostat()); |
1528 | + | else{ |
1529 | + | sprintf(painCave.errMsg, |
1530 | + | "SimSetup error: If you use an NPT\n" |
1531 | + | " ensemble, you must set tauThermostat.\n"); |
1532 | + | painCave.isFatal = 1; |
1533 | + | simError(); |
1534 | + | } |
1535 | + | |
1536 | + | if (globals->haveTauBarostat()) |
1537 | + | myNPTfm->setTauBarostat(globals->getTauBarostat()); |
1538 | + | else{ |
1539 | + | sprintf(painCave.errMsg, |
1540 | + | "SimSetup error: If you use an NPT\n" |
1541 | + | " ensemble, you must set tauBarostat.\n"); |
1542 | + | painCave.isFatal = 1; |
1543 | + | simError(); |
1544 | + | } |
1545 | + | break; |
1546 | + | |
1547 | + | default: |
1548 | + | sprintf(painCave.errMsg, |
1549 | + | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1550 | + | painCave.isFatal = 1; |
1551 | + | simError(); |
1552 | + | } |
1553 | + | } |
1554 | + | } |
1555 | + | |
1556 | + | void SimSetup::initFortran(void){ |
1557 | + | info[0].refreshSim(); |
1558 | + | |
1559 | + | if (!strcmp(info[0].mixingRule, "standard")){ |
1560 | + | the_ff->initForceField(LB_MIXING_RULE); |
1561 | + | } |
1562 | + | else if (!strcmp(info[0].mixingRule, "explicit")){ |
1563 | + | the_ff->initForceField(EXPLICIT_MIXING_RULE); |
1564 | + | } |
1565 | + | else{ |
1566 | + | sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1567 | + | info[0].mixingRule); |
1568 | + | painCave.isFatal = 1; |
1569 | + | simError(); |
1570 | + | } |
1571 | + | |
1572 | + | |
1573 | + | #ifdef IS_MPI |
1574 | + | strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran."); |
1575 | + | MPIcheckPoint(); |
1576 | + | #endif // is_mpi |
1577 | + | } |
1578 | + | |
1579 | + | void SimSetup::setupZConstraint(SimInfo& theInfo){ |
1580 | + | int nZConstraints; |
1581 | + | ZconStamp** zconStamp; |
1582 | + | |
1583 | + | if (globals->haveZconstraintTime()){ |
1584 | + | //add sample time of z-constraint into SimInfo's property list |
1585 | + | DoubleData* zconsTimeProp = new DoubleData(); |
1586 | + | zconsTimeProp->setID(ZCONSTIME_ID); |
1587 | + | zconsTimeProp->setData(globals->getZconsTime()); |
1588 | + | theInfo.addProperty(zconsTimeProp); |
1589 | + | } |
1590 | + | else{ |
1591 | + | sprintf(painCave.errMsg, |
1592 | + | "ZConstraint error: If you use an ZConstraint\n" |
1593 | + | " , you must set sample time.\n"); |
1594 | + | painCave.isFatal = 1; |
1595 | + | simError(); |
1596 | + | } |
1597 | + | |
1598 | + | //push zconsTol into siminfo, if user does not specify |
1599 | + | //value for zconsTol, a default value will be used |
1600 | + | DoubleData* zconsTol = new DoubleData(); |
1601 | + | zconsTol->setID(ZCONSTOL_ID); |
1602 | + | if (globals->haveZconsTol()){ |
1603 | + | zconsTol->setData(globals->getZconsTol()); |
1604 | + | } |
1605 | + | else{ |
1606 | + | double defaultZConsTol = 0.01; |
1607 | + | sprintf(painCave.errMsg, |
1608 | + | "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1609 | + | " , default value %f is used.\n", |
1610 | + | defaultZConsTol); |
1611 | + | painCave.isFatal = 0; |
1612 | + | simError(); |
1613 | + | |
1614 | + | zconsTol->setData(defaultZConsTol); |
1615 | + | } |
1616 | + | theInfo.addProperty(zconsTol); |
1617 | + | |
1618 | + | //set Force Substraction Policy |
1619 | + | StringData* zconsForcePolicy = new StringData(); |
1620 | + | zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1621 | + | |
1622 | + | if (globals->haveZconsForcePolicy()){ |
1623 | + | zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
1624 | + | } |
1625 | + | else{ |
1626 | + | sprintf(painCave.errMsg, |
1627 | + | "ZConstraint Warning: User does not set force substraction policy, " |
1628 | + | "PolicyByMass is used\n"); |
1629 | + | painCave.isFatal = 0; |
1630 | + | simError(); |
1631 | + | zconsForcePolicy->setData("BYMASS"); |
1632 | + | } |
1633 | + | |
1634 | + | theInfo.addProperty(zconsForcePolicy); |
1635 | + | |
1636 | + | //Determine the name of ouput file and add it into SimInfo's property list |
1637 | + | //Be careful, do not use inFileName, since it is a pointer which |
1638 | + | //point to a string at master node, and slave nodes do not contain that string |
1639 | + | |
1640 | + | string zconsOutput(theInfo.finalName); |
1641 | + | |
1642 | + | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1643 | + | |
1644 | + | StringData* zconsFilename = new StringData(); |
1645 | + | zconsFilename->setID(ZCONSFILENAME_ID); |
1646 | + | zconsFilename->setData(zconsOutput); |
1647 | + | |
1648 | + | theInfo.addProperty(zconsFilename); |
1649 | + | |
1650 | + | //setup index, pos and other parameters of z-constraint molecules |
1651 | + | nZConstraints = globals->getNzConstraints(); |
1652 | + | theInfo.nZconstraints = nZConstraints; |
1653 | + | |
1654 | + | zconStamp = globals->getZconStamp(); |
1655 | + | ZConsParaItem tempParaItem; |
1656 | + | |
1657 | + | ZConsParaData* zconsParaData = new ZConsParaData(); |
1658 | + | zconsParaData->setID(ZCONSPARADATA_ID); |
1659 | + | |
1660 | + | for (int i = 0; i < nZConstraints; i++){ |
1661 | + | tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1662 | + | tempParaItem.zPos = zconStamp[i]->getZpos(); |
1663 | + | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1664 | + | tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1665 | + | |
1666 | + | zconsParaData->addItem(tempParaItem); |
1667 | + | } |
1668 | + | |
1669 | + | //check the uniqueness of index |
1670 | + | if(!zconsParaData->isIndexUnique()){ |
1671 | + | sprintf(painCave.errMsg, |
1672 | + | "ZConstraint Error: molIndex is not unique\n"); |
1673 | + | painCave.isFatal = 1; |
1674 | + | simError(); |
1675 | + | } |
1676 | + | |
1677 | + | //sort the parameters by index of molecules |
1678 | + | zconsParaData->sortByIndex(); |
1679 | + | |
1680 | + | //push data into siminfo, therefore, we can retrieve later |
1681 | + | theInfo.addProperty(zconsParaData); |
1682 | + | } |
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