# | 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 14 | Line 18 | |
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 |
21 | < | #define NPTim_ENS 4 |
22 | < | #define NPTfm_ENS 5 |
21 | > | #define NVE_ENS 0 |
22 | > | #define NVT_ENS 1 |
23 | > | #define NPTi_ENS 2 |
24 | > | #define NPTf_ENS 3 |
25 | ||
24 | – | |
26 | #define FF_DUFF 0 | |
27 | #define FF_LJ 1 | |
28 | + | #define FF_EAM 2 |
29 | ||
30 | + | using namespace std; |
31 | ||
32 | SimSetup::SimSetup(){ | |
33 | + | isInfoArray = 0; |
34 | + | nInfo = 1; |
35 | + | |
36 | stamps = new MakeStamps(); | |
37 | globals = new Globals(); | |
38 | < | |
38 | > | |
39 | > | |
40 | #ifdef IS_MPI | |
41 | < | strcpy( checkPointMsg, "SimSetup creation successful" ); |
41 | > | strcpy(checkPointMsg, "SimSetup creation successful"); |
42 | MPIcheckPoint(); | |
43 | #endif // IS_MPI | |
44 | } | |
# | Line 41 | Line 48 | SimSetup::~SimSetup(){ | |
48 | delete globals; | |
49 | } | |
50 | ||
51 | < | void SimSetup::parseFile( char* fileName ){ |
51 | > | void SimSetup::setSimInfo(SimInfo* the_info, int theNinfo){ |
52 | > | info = the_info; |
53 | > | nInfo = theNinfo; |
54 | > | isInfoArray = 1; |
55 | > | } |
56 | ||
57 | + | |
58 | + | void SimSetup::parseFile(char* fileName){ |
59 | #ifdef IS_MPI | |
60 | < | if( worldRank == 0 ){ |
60 | > | if (worldRank == 0){ |
61 | #endif // is_mpi | |
62 | < | |
62 | > | |
63 | inFileName = fileName; | |
64 | < | set_interface_stamps( stamps, globals ); |
65 | < | |
64 | > | set_interface_stamps(stamps, globals); |
65 | > | |
66 | #ifdef IS_MPI | |
67 | mpiEventInit(); | |
68 | #endif | |
69 | ||
70 | < | yacc_BASS( fileName ); |
70 | > | yacc_BASS(fileName); |
71 | ||
72 | #ifdef IS_MPI | |
73 | throwMPIEvent(NULL); | |
74 | } | |
75 | < | else receiveParse(); |
75 | > | else{ |
76 | > | receiveParse(); |
77 | > | } |
78 | #endif | |
79 | ||
80 | } | |
81 | ||
82 | #ifdef IS_MPI | |
83 | void SimSetup::receiveParse(void){ | |
84 | < | |
85 | < | set_interface_stamps( stamps, globals ); |
86 | < | mpiEventInit(); |
87 | < | MPIcheckPoint(); |
73 | < | mpiEventLoop(); |
74 | < | |
84 | > | set_interface_stamps(stamps, globals); |
85 | > | mpiEventInit(); |
86 | > | MPIcheckPoint(); |
87 | > | mpiEventLoop(); |
88 | } | |
89 | ||
90 | #endif // is_mpi | |
91 | ||
92 | < | void SimSetup::createSim( void ){ |
92 | > | void SimSetup::createSim(void){ |
93 | ||
94 | < | MakeStamps *the_stamps; |
82 | < | Globals* the_globals; |
83 | < | int i, j, k, globalAtomIndex; |
84 | < | |
85 | < | int ensembleCase; |
86 | < | int ffCase; |
87 | < | |
88 | < | ensembleCase = -1; |
89 | < | ffCase = -1; |
94 | > | // gather all of the information from the Bass file |
95 | ||
96 | < | // get the stamps and globals; |
92 | < | the_stamps = stamps; |
93 | < | the_globals = globals; |
96 | > | gatherInfo(); |
97 | ||
98 | < | // set the easy ones first |
96 | < | simnfo->target_temp = the_globals->getTargetTemp(); |
97 | < | simnfo->dt = the_globals->getDt(); |
98 | < | simnfo->run_time = the_globals->getRunTime(); |
98 | > | // creation of complex system objects |
99 | ||
100 | < | // get the ones we know are there, yet still may need some work. |
101 | < | n_components = the_globals->getNComponents(); |
102 | < | strcpy( force_field, the_globals->getForceField() ); |
100 | > | sysObjectsCreation(); |
101 | ||
102 | < | if( !strcasecmp( force_field, "DUFF" )) ffCase = FF_DUFF; |
105 | < | else if( !strcasecmp( force_field, "LJ" )) ffCase = FF_LJ; |
106 | < | else{ |
107 | < | sprintf( painCave.errMsg, |
108 | < | "SimSetup Error. Unrecognized force field -> %s\n", |
109 | < | force_field ); |
110 | < | painCave.isFatal = 1; |
111 | < | simError(); |
112 | < | } |
102 | > | // check on the post processing info |
103 | ||
104 | < | // get the ensemble: |
115 | < | strcpy( ensemble, the_globals->getEnsemble() ); |
104 | > | finalInfoCheck(); |
105 | ||
106 | < | if( !strcasecmp( ensemble, "NVE" )) ensembleCase = NVE_ENS; |
107 | < | else if( !strcasecmp( ensemble, "NVT" )) ensembleCase = NVT_ENS; |
108 | < | else if( !strcasecmp( ensemble, "NPTi" ) || !strcasecmp( ensemble, "NPT") ) |
109 | < | ensembleCase = NPTi_ENS; |
121 | < | else if( !strcasecmp( ensemble, "NPTf" )) ensembleCase = NPTf_ENS; |
122 | < | else if( !strcasecmp( ensemble, "NPTim" )) ensembleCase = NPTim_ENS; |
123 | < | else if( !strcasecmp( ensemble, "NPTfm" )) ensembleCase = NPTfm_ENS; |
124 | < | else{ |
125 | < | sprintf( painCave.errMsg, |
126 | < | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
127 | < | "reverting to NVE for this simulation.\n", |
128 | < | ensemble ); |
129 | < | painCave.isFatal = 0; |
130 | < | simError(); |
131 | < | strcpy( ensemble, "NVE" ); |
132 | < | ensembleCase = NVE_ENS; |
106 | > | // initialize the system coordinates |
107 | > | |
108 | > | if (!isInfoArray){ |
109 | > | initSystemCoords(); |
110 | } | |
134 | – | strcpy( simnfo->ensemble, ensemble ); |
111 | ||
112 | + | // make the output filenames |
113 | ||
114 | < | // if( !strcasecmp( ensemble, "NPT" ) ) { |
138 | < | // the_extendedsystem = new ExtendedSystem( simnfo ); |
139 | < | // the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
140 | < | // if (the_globals->haveTargetPressure()) |
141 | < | // the_extendedsystem->setTargetPressure(the_globals->getTargetPressure()); |
142 | < | // else { |
143 | < | // sprintf( painCave.errMsg, |
144 | < | // "SimSetup error: If you use the constant pressure\n" |
145 | < | // " ensemble, you must set targetPressure.\n" |
146 | < | // " This was found in the BASS file.\n"); |
147 | < | // painCave.isFatal = 1; |
148 | < | // simError(); |
149 | < | // } |
114 | > | makeOutNames(); |
115 | ||
116 | < | // if (the_globals->haveTauThermostat()) |
152 | < | // the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
153 | < | // else if (the_globals->haveQmass()) |
154 | < | // the_extendedsystem->setQmass(the_globals->getQmass()); |
155 | < | // else { |
156 | < | // sprintf( painCave.errMsg, |
157 | < | // "SimSetup error: If you use one of the constant temperature\n" |
158 | < | // " ensembles, you must set either tauThermostat or qMass.\n" |
159 | < | // " Neither of these was found in the BASS file.\n"); |
160 | < | // painCave.isFatal = 1; |
161 | < | // simError(); |
162 | < | // } |
116 | > | // make the integrator |
117 | ||
118 | < | // if (the_globals->haveTauBarostat()) |
165 | < | // the_extendedsystem->setTauBarostat(the_globals->getTauBarostat()); |
166 | < | // else { |
167 | < | // sprintf( painCave.errMsg, |
168 | < | // "SimSetup error: If you use the constant pressure\n" |
169 | < | // " ensemble, you must set tauBarostat.\n" |
170 | < | // " This was found in the BASS file.\n"); |
171 | < | // painCave.isFatal = 1; |
172 | < | // simError(); |
173 | < | // } |
118 | > | makeIntegrator(); |
119 | ||
120 | < | // } else if ( !strcasecmp( ensemble, "NVT") ) { |
121 | < | // the_extendedsystem = new ExtendedSystem( simnfo ); |
122 | < | // the_extendedsystem->setTargetTemp(the_globals->getTargetTemp()); |
120 | > | #ifdef IS_MPI |
121 | > | mpiSim->mpiRefresh(); |
122 | > | #endif |
123 | ||
124 | < | // if (the_globals->haveTauThermostat()) |
180 | < | // the_extendedsystem->setTauThermostat(the_globals->getTauThermostat()); |
181 | < | // else if (the_globals->haveQmass()) |
182 | < | // the_extendedsystem->setQmass(the_globals->getQmass()); |
183 | < | // else { |
184 | < | // sprintf( painCave.errMsg, |
185 | < | // "SimSetup error: If you use one of the constant temperature\n" |
186 | < | // " ensembles, you must set either tauThermostat or qMass.\n" |
187 | < | // " Neither of these was found in the BASS file.\n"); |
188 | < | // painCave.isFatal = 1; |
189 | < | // simError(); |
190 | < | // } |
124 | > | // initialize the Fortran |
125 | ||
126 | < | strcpy( simnfo->mixingRule, the_globals->getMixingRule() ); |
127 | < | simnfo->usePBC = the_globals->getPBC(); |
194 | < | |
195 | < | int usesDipoles = 0; |
196 | < | switch( ffCase ){ |
126 | > | initFortran(); |
127 | > | } |
128 | ||
198 | – | case FF_DUFF: |
199 | – | the_ff = new DUFF(); |
200 | – | usesDipoles = 1; |
201 | – | break; |
129 | ||
130 | < | case FF_LJ: |
131 | < | the_ff = new LJFF(); |
132 | < | break; |
130 | > | void SimSetup::makeMolecules(void){ |
131 | > | int k; |
132 | > | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
133 | > | molInit molInfo; |
134 | > | DirectionalAtom* dAtom; |
135 | > | LinkedAssign* extras; |
136 | > | LinkedAssign* current_extra; |
137 | > | AtomStamp* currentAtom; |
138 | > | BondStamp* currentBond; |
139 | > | BendStamp* currentBend; |
140 | > | TorsionStamp* currentTorsion; |
141 | ||
142 | < | default: |
143 | < | sprintf( painCave.errMsg, |
144 | < | "SimSetup Error. Unrecognized force field in case statement.\n"); |
210 | < | painCave.isFatal = 1; |
211 | < | simError(); |
212 | < | } |
142 | > | bond_pair* theBonds; |
143 | > | bend_set* theBends; |
144 | > | torsion_set* theTorsions; |
145 | ||
214 | – | #ifdef IS_MPI |
215 | – | strcpy( checkPointMsg, "ForceField creation successful" ); |
216 | – | MPIcheckPoint(); |
217 | – | #endif // is_mpi |
146 | ||
147 | < | // get the components and calculate the tot_nMol and indvidual n_mol |
220 | < | the_components = the_globals->getComponents(); |
221 | < | components_nmol = new int[n_components]; |
222 | < | comp_stamps = new MoleculeStamp*[n_components]; |
147 | > | //init the forceField paramters |
148 | ||
149 | < | if( !the_globals->haveNMol() ){ |
225 | < | // we don't have the total number of molecules, so we assume it is |
226 | < | // given in each component |
149 | > | the_ff->readParams(); |
150 | ||
228 | – | tot_nmol = 0; |
229 | – | for( i=0; i<n_components; i++ ){ |
151 | ||
152 | < | if( !the_components[i]->haveNMol() ){ |
232 | < | // we have a problem |
233 | < | sprintf( painCave.errMsg, |
234 | < | "SimSetup Error. No global NMol or component NMol" |
235 | < | " given. Cannot calculate the number of atoms.\n" ); |
236 | < | painCave.isFatal = 1; |
237 | < | simError(); |
238 | < | } |
152 | > | // init the atoms |
153 | ||
154 | < | tot_nmol += the_components[i]->getNMol(); |
241 | < | components_nmol[i] = the_components[i]->getNMol(); |
242 | < | } |
243 | < | } |
244 | < | else{ |
245 | < | sprintf( painCave.errMsg, |
246 | < | "SimSetup error.\n" |
247 | < | "\tSorry, the ability to specify total" |
248 | < | " nMols and then give molfractions in the components\n" |
249 | < | "\tis not currently supported." |
250 | < | " Please give nMol in the components.\n" ); |
251 | < | painCave.isFatal = 1; |
252 | < | simError(); |
253 | < | |
254 | < | |
255 | < | // tot_nmol = the_globals->getNMol(); |
256 | < | |
257 | < | // //we have the total number of molecules, now we check for molfractions |
258 | < | // for( i=0; i<n_components; i++ ){ |
259 | < | |
260 | < | // if( !the_components[i]->haveMolFraction() ){ |
261 | < | |
262 | < | // if( !the_components[i]->haveNMol() ){ |
263 | < | // //we have a problem |
264 | < | // std::cerr << "SimSetup error. Neither molFraction nor " |
265 | < | // << " nMol was given in component |
266 | < | |
267 | < | } |
154 | > | double ux, uy, uz, u, uSqr; |
155 | ||
156 | < | #ifdef IS_MPI |
157 | < | strcpy( checkPointMsg, "Have the number of components" ); |
271 | < | MPIcheckPoint(); |
272 | < | #endif // is_mpi |
156 | > | for (k = 0; k < nInfo; k++){ |
157 | > | the_ff->setSimInfo(&(info[k])); |
158 | ||
159 | < | // make an array of molecule stamps that match the components used. |
160 | < | // also extract the used stamps out into a separate linked list |
159 | > | atomOffset = 0; |
160 | > | excludeOffset = 0; |
161 | > | for (i = 0; i < info[k].n_mol; i++){ |
162 | > | stampID = info[k].molecules[i].getStampID(); |
163 | ||
164 | < | simnfo->nComponents = n_components; |
165 | < | simnfo->componentsNmol = components_nmol; |
166 | < | simnfo->compStamps = comp_stamps; |
167 | < | simnfo->headStamp = new LinkedMolStamp(); |
168 | < | |
282 | < | char* id; |
283 | < | LinkedMolStamp* headStamp = simnfo->headStamp; |
284 | < | LinkedMolStamp* currentStamp = NULL; |
285 | < | for( i=0; i<n_components; i++ ){ |
164 | > | molInfo.nAtoms = comp_stamps[stampID]->getNAtoms(); |
165 | > | molInfo.nBonds = comp_stamps[stampID]->getNBonds(); |
166 | > | molInfo.nBends = comp_stamps[stampID]->getNBends(); |
167 | > | molInfo.nTorsions = comp_stamps[stampID]->getNTorsions(); |
168 | > | molInfo.nExcludes = molInfo.nBonds + molInfo.nBends + molInfo.nTorsions; |
169 | ||
170 | < | id = the_components[i]->getType(); |
171 | < | comp_stamps[i] = NULL; |
172 | < | |
173 | < | // check to make sure the component isn't already in the list |
170 | > | molInfo.myAtoms = &(info[k].atoms[atomOffset]); |
171 | > | molInfo.myExcludes = &(info[k].excludes[excludeOffset]); |
172 | > | molInfo.myBonds = new Bond * [molInfo.nBonds]; |
173 | > | molInfo.myBends = new Bend * [molInfo.nBends]; |
174 | > | molInfo.myTorsions = new Torsion * [molInfo.nTorsions]; |
175 | ||
176 | < | comp_stamps[i] = headStamp->match( id ); |
177 | < | if( comp_stamps[i] == NULL ){ |
178 | < | |
295 | < | // extract the component from the list; |
296 | < | |
297 | < | currentStamp = the_stamps->extractMolStamp( id ); |
298 | < | if( currentStamp == NULL ){ |
299 | < | sprintf( painCave.errMsg, |
300 | < | "SimSetup error: Component \"%s\" was not found in the " |
301 | < | "list of declared molecules\n", |
302 | < | id ); |
303 | < | painCave.isFatal = 1; |
304 | < | simError(); |
305 | < | } |
306 | < | |
307 | < | headStamp->add( currentStamp ); |
308 | < | comp_stamps[i] = headStamp->match( id ); |
309 | < | } |
310 | < | } |
176 | > | theBonds = new bond_pair[molInfo.nBonds]; |
177 | > | theBends = new bend_set[molInfo.nBends]; |
178 | > | theTorsions = new torsion_set[molInfo.nTorsions]; |
179 | ||
180 | < | #ifdef IS_MPI |
313 | < | strcpy( checkPointMsg, "Component stamps successfully extracted\n" ); |
314 | < | MPIcheckPoint(); |
315 | < | #endif // is_mpi |
316 | < | |
180 | > | // make the Atoms |
181 | ||
182 | + | for (j = 0; j < molInfo.nAtoms; j++){ |
183 | + | currentAtom = comp_stamps[stampID]->getAtom(j); |
184 | + | if (currentAtom->haveOrientation()){ |
185 | + | dAtom = new DirectionalAtom((j + atomOffset), |
186 | + | info[k].getConfiguration()); |
187 | + | info[k].n_oriented++; |
188 | + | molInfo.myAtoms[j] = dAtom; |
189 | ||
190 | + | ux = currentAtom->getOrntX(); |
191 | + | uy = currentAtom->getOrntY(); |
192 | + | uz = currentAtom->getOrntZ(); |
193 | ||
194 | < | // caclulate the number of atoms, bonds, bends and torsions |
194 | > | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
195 | ||
196 | < | tot_atoms = 0; |
197 | < | tot_bonds = 0; |
198 | < | tot_bends = 0; |
199 | < | tot_torsions = 0; |
326 | < | for( i=0; i<n_components; i++ ){ |
327 | < | |
328 | < | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
329 | < | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
330 | < | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
331 | < | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
332 | < | } |
196 | > | u = sqrt(uSqr); |
197 | > | ux = ux / u; |
198 | > | uy = uy / u; |
199 | > | uz = uz / u; |
200 | ||
201 | < | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
201 | > | dAtom->setSUx(ux); |
202 | > | dAtom->setSUy(uy); |
203 | > | dAtom->setSUz(uz); |
204 | > | } |
205 | > | else{ |
206 | > | molInfo.myAtoms[j] = new GeneralAtom((j + atomOffset), |
207 | > | info[k].getConfiguration()); |
208 | > | } |
209 | > | molInfo.myAtoms[j]->setType(currentAtom->getType()); |
210 | ||
336 | – | simnfo->n_atoms = tot_atoms; |
337 | – | simnfo->n_bonds = tot_bonds; |
338 | – | simnfo->n_bends = tot_bends; |
339 | – | simnfo->n_torsions = tot_torsions; |
340 | – | simnfo->n_SRI = tot_SRI; |
341 | – | simnfo->n_mol = tot_nmol; |
342 | – | |
343 | – | simnfo->molMembershipArray = new int[tot_atoms]; |
344 | – | |
211 | #ifdef IS_MPI | |
212 | ||
213 | < | // divide the molecules among processors here. |
348 | < | |
349 | < | mpiSim = new mpiSimulation( simnfo ); |
350 | < | |
351 | < | globalIndex = mpiSim->divideLabor(); |
213 | > | molInfo.myAtoms[j]->setGlobalIndex(globalIndex[j + atomOffset]); |
214 | ||
215 | < | // set up the local variables |
216 | < | |
355 | < | int localMol, allMol; |
356 | < | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
215 | > | #endif // is_mpi |
216 | > | } |
217 | ||
218 | < | int* mol2proc = mpiSim->getMolToProcMap(); |
219 | < | int* molCompType = mpiSim->getMolComponentType(); |
220 | < | |
221 | < | allMol = 0; |
222 | < | localMol = 0; |
363 | < | local_atoms = 0; |
364 | < | local_bonds = 0; |
365 | < | local_bends = 0; |
366 | < | local_torsions = 0; |
367 | < | globalAtomIndex = 0; |
218 | > | // make the bonds |
219 | > | for (j = 0; j < molInfo.nBonds; j++){ |
220 | > | currentBond = comp_stamps[stampID]->getBond(j); |
221 | > | theBonds[j].a = currentBond->getA() + atomOffset; |
222 | > | theBonds[j].b = currentBond->getB() + atomOffset; |
223 | ||
224 | + | exI = theBonds[j].a; |
225 | + | exJ = theBonds[j].b; |
226 | ||
227 | < | for( i=0; i<n_components; i++ ){ |
227 | > | // exclude_I must always be the smaller of the pair |
228 | > | if (exI > exJ){ |
229 | > | tempEx = exI; |
230 | > | exI = exJ; |
231 | > | exJ = tempEx; |
232 | > | } |
233 | > | #ifdef IS_MPI |
234 | > | tempEx = exI; |
235 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
236 | > | tempEx = exJ; |
237 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
238 | ||
239 | < | for( j=0; j<components_nmol[i]; j++ ){ |
240 | < | |
241 | < | if( mol2proc[allMol] == worldRank ){ |
242 | < | |
243 | < | local_atoms += comp_stamps[i]->getNAtoms(); |
377 | < | local_bonds += comp_stamps[i]->getNBonds(); |
378 | < | local_bends += comp_stamps[i]->getNBends(); |
379 | < | local_torsions += comp_stamps[i]->getNTorsions(); |
380 | < | localMol++; |
381 | < | } |
382 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
383 | < | simnfo->molMembershipArray[globalAtomIndex] = allMol; |
384 | < | globalAtomIndex++; |
239 | > | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
240 | > | #else // isn't MPI |
241 | > | |
242 | > | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
243 | > | #endif //is_mpi |
244 | } | |
245 | + | excludeOffset += molInfo.nBonds; |
246 | ||
247 | < | allMol++; |
248 | < | } |
249 | < | } |
250 | < | local_SRI = local_bonds + local_bends + local_torsions; |
251 | < | |
252 | < | simnfo->n_atoms = mpiSim->getMyNlocal(); |
393 | < | |
394 | < | if( local_atoms != simnfo->n_atoms ){ |
395 | < | sprintf( painCave.errMsg, |
396 | < | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
397 | < | " localAtom (%d) are not equal.\n", |
398 | < | simnfo->n_atoms, |
399 | < | local_atoms ); |
400 | < | painCave.isFatal = 1; |
401 | < | simError(); |
402 | < | } |
247 | > | //make the bends |
248 | > | for (j = 0; j < molInfo.nBends; j++){ |
249 | > | currentBend = comp_stamps[stampID]->getBend(j); |
250 | > | theBends[j].a = currentBend->getA() + atomOffset; |
251 | > | theBends[j].b = currentBend->getB() + atomOffset; |
252 | > | theBends[j].c = currentBend->getC() + atomOffset; |
253 | ||
254 | < | simnfo->n_bonds = local_bonds; |
255 | < | simnfo->n_bends = local_bends; |
256 | < | simnfo->n_torsions = local_torsions; |
407 | < | simnfo->n_SRI = local_SRI; |
408 | < | simnfo->n_mol = localMol; |
254 | > | if (currentBend->haveExtras()){ |
255 | > | extras = currentBend->getExtras(); |
256 | > | current_extra = extras; |
257 | ||
258 | < | strcpy( checkPointMsg, "Passed nlocal consistency check." ); |
259 | < | MPIcheckPoint(); |
260 | < | |
261 | < | |
262 | < | #endif // is_mpi |
263 | < | |
258 | > | while (current_extra != NULL){ |
259 | > | if (!strcmp(current_extra->getlhs(), "ghostVectorSource")){ |
260 | > | switch (current_extra->getType()){ |
261 | > | case 0: |
262 | > | theBends[j].ghost = current_extra->getInt() + atomOffset; |
263 | > | theBends[j].isGhost = 1; |
264 | > | break; |
265 | ||
266 | < | // create the atom and short range interaction arrays |
266 | > | case 1: |
267 | > | theBends[j].ghost = (int) current_extra->getDouble() + |
268 | > | atomOffset; |
269 | > | theBends[j].isGhost = 1; |
270 | > | break; |
271 | ||
272 | < | Atom::createArrays(simnfo->n_atoms); |
273 | < | the_atoms = new Atom*[simnfo->n_atoms]; |
274 | < | the_molecules = new Molecule[simnfo->n_mol]; |
275 | < | int molIndex; |
272 | > | default: |
273 | > | sprintf(painCave.errMsg, |
274 | > | "SimSetup Error: ghostVectorSource was neither a " |
275 | > | "double nor an int.\n" |
276 | > | "-->Bend[%d] in %s\n", |
277 | > | j, comp_stamps[stampID]->getID()); |
278 | > | painCave.isFatal = 1; |
279 | > | simError(); |
280 | > | } |
281 | > | } |
282 | > | else{ |
283 | > | sprintf(painCave.errMsg, |
284 | > | "SimSetup Error: unhandled bend assignment:\n" |
285 | > | " -->%s in Bend[%d] in %s\n", |
286 | > | current_extra->getlhs(), j, comp_stamps[stampID]->getID()); |
287 | > | painCave.isFatal = 1; |
288 | > | simError(); |
289 | > | } |
290 | ||
291 | < | // initialize the molecule's stampID's |
291 | > | current_extra = current_extra->getNext(); |
292 | > | } |
293 | > | } |
294 | ||
295 | + | if (!theBends[j].isGhost){ |
296 | + | exI = theBends[j].a; |
297 | + | exJ = theBends[j].c; |
298 | + | } |
299 | + | else{ |
300 | + | exI = theBends[j].a; |
301 | + | exJ = theBends[j].b; |
302 | + | } |
303 | + | |
304 | + | // exclude_I must always be the smaller of the pair |
305 | + | if (exI > exJ){ |
306 | + | tempEx = exI; |
307 | + | exI = exJ; |
308 | + | exJ = tempEx; |
309 | + | } |
310 | #ifdef IS_MPI | |
311 | < | |
311 | > | tempEx = exI; |
312 | > | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
313 | > | tempEx = exJ; |
314 | > | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
315 | ||
316 | < | molIndex = 0; |
317 | < | for(i=0; i<mpiSim->getTotNmol(); i++){ |
318 | < | |
319 | < | if(mol2proc[i] == worldRank ){ |
320 | < | the_molecules[molIndex].setStampID( molCompType[i] ); |
321 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
435 | < | the_molecules[molIndex].setGlobalIndex( i ); |
436 | < | molIndex++; |
437 | < | } |
438 | < | } |
316 | > | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
317 | > | #else // isn't MPI |
318 | > | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
319 | > | #endif //is_mpi |
320 | > | } |
321 | > | excludeOffset += molInfo.nBends; |
322 | ||
323 | < | #else // is_mpi |
324 | < | |
325 | < | molIndex = 0; |
326 | < | globalAtomIndex = 0; |
327 | < | for(i=0; i<n_components; i++){ |
328 | < | for(j=0; j<components_nmol[i]; j++ ){ |
446 | < | the_molecules[molIndex].setStampID( i ); |
447 | < | the_molecules[molIndex].setMyIndex( molIndex ); |
448 | < | the_molecules[molIndex].setGlobalIndex( molIndex ); |
449 | < | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++) { |
450 | < | simnfo->molMembershipArray[globalAtomIndex] = molIndex; |
451 | < | globalAtomIndex++; |
452 | < | } |
453 | < | molIndex++; |
454 | < | } |
455 | < | } |
456 | < | |
323 | > | for (j = 0; j < molInfo.nTorsions; j++){ |
324 | > | currentTorsion = comp_stamps[stampID]->getTorsion(j); |
325 | > | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
326 | > | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
327 | > | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
328 | > | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
329 | ||
330 | < | #endif // is_mpi |
330 | > | exI = theTorsions[j].a; |
331 | > | exJ = theTorsions[j].d; |
332 | ||
333 | + | // exclude_I must always be the smaller of the pair |
334 | + | if (exI > exJ){ |
335 | + | tempEx = exI; |
336 | + | exI = exJ; |
337 | + | exJ = tempEx; |
338 | + | } |
339 | + | #ifdef IS_MPI |
340 | + | tempEx = exI; |
341 | + | exI = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
342 | + | tempEx = exJ; |
343 | + | exJ = info[k].atoms[tempEx]->getGlobalIndex() + 1; |
344 | ||
345 | < | if( simnfo->n_SRI ){ |
346 | < | |
347 | < | Exclude::createArray(simnfo->n_SRI); |
348 | < | the_excludes = new Exclude*[simnfo->n_SRI]; |
349 | < | for( int ex=0; ex<simnfo->n_SRI; ex++) the_excludes[ex] = new Exclude(ex); |
350 | < | simnfo->globalExcludes = new int; |
467 | < | simnfo->n_exclude = simnfo->n_SRI; |
468 | < | } |
469 | < | else{ |
470 | < | |
471 | < | Exclude::createArray( 1 ); |
472 | < | the_excludes = new Exclude*; |
473 | < | the_excludes[0] = new Exclude(0); |
474 | < | the_excludes[0]->setPair( 0,0 ); |
475 | < | simnfo->globalExcludes = new int; |
476 | < | simnfo->globalExcludes[0] = 0; |
477 | < | simnfo->n_exclude = 0; |
478 | < | } |
345 | > | info[k].excludes[j + excludeOffset]->setPair(exI, exJ); |
346 | > | #else // isn't MPI |
347 | > | info[k].excludes[j + excludeOffset]->setPair((exI + 1), (exJ + 1)); |
348 | > | #endif //is_mpi |
349 | > | } |
350 | > | excludeOffset += molInfo.nTorsions; |
351 | ||
480 | – | // set the arrays into the SimInfo object |
352 | ||
353 | < | simnfo->atoms = the_atoms; |
483 | < | simnfo->molecules = the_molecules; |
484 | < | simnfo->nGlobalExcludes = 0; |
485 | < | simnfo->excludes = the_excludes; |
353 | > | // send the arrays off to the forceField for init. |
354 | ||
355 | + | the_ff->initializeAtoms(molInfo.nAtoms, molInfo.myAtoms); |
356 | + | the_ff->initializeBonds(molInfo.nBonds, molInfo.myBonds, theBonds); |
357 | + | the_ff->initializeBends(molInfo.nBends, molInfo.myBends, theBends); |
358 | + | the_ff->initializeTorsions(molInfo.nTorsions, molInfo.myTorsions, |
359 | + | theTorsions); |
360 | ||
488 | – | // get some of the tricky things that may still be in the globals |
361 | ||
362 | < | double boxVector[3]; |
491 | < | if( the_globals->haveBox() ){ |
492 | < | boxVector[0] = the_globals->getBox(); |
493 | < | boxVector[1] = the_globals->getBox(); |
494 | < | boxVector[2] = the_globals->getBox(); |
495 | < | |
496 | < | simnfo->setBox( boxVector ); |
497 | < | } |
498 | < | else if( the_globals->haveDensity() ){ |
362 | > | info[k].molecules[i].initialize(molInfo); |
363 | ||
500 | – | double vol; |
501 | – | vol = (double)tot_nmol / the_globals->getDensity(); |
502 | – | boxVector[0] = pow( vol, ( 1.0 / 3.0 ) ); |
503 | – | boxVector[1] = boxVector[0]; |
504 | – | boxVector[2] = boxVector[0]; |
364 | ||
365 | < | simnfo->setBox( boxVector ); |
366 | < | } |
367 | < | else{ |
368 | < | if( !the_globals->haveBoxX() ){ |
510 | < | sprintf( painCave.errMsg, |
511 | < | "SimSetup error, no periodic BoxX size given.\n" ); |
512 | < | painCave.isFatal = 1; |
513 | < | simError(); |
365 | > | atomOffset += molInfo.nAtoms; |
366 | > | delete[] theBonds; |
367 | > | delete[] theBends; |
368 | > | delete[] theTorsions; |
369 | } | |
515 | – | boxVector[0] = the_globals->getBoxX(); |
516 | – | |
517 | – | if( !the_globals->haveBoxY() ){ |
518 | – | sprintf( painCave.errMsg, |
519 | – | "SimSetup error, no periodic BoxY size given.\n" ); |
520 | – | painCave.isFatal = 1; |
521 | – | simError(); |
522 | – | } |
523 | – | boxVector[1] = the_globals->getBoxY(); |
524 | – | |
525 | – | if( !the_globals->haveBoxZ() ){ |
526 | – | sprintf( painCave.errMsg, |
527 | – | "SimSetup error, no periodic BoxZ size given.\n" ); |
528 | – | painCave.isFatal = 1; |
529 | – | simError(); |
530 | – | } |
531 | – | boxVector[2] = the_globals->getBoxZ(); |
532 | – | |
533 | – | simnfo->setBox( boxVector ); |
370 | } | |
371 | ||
372 | #ifdef IS_MPI | |
373 | < | strcpy( checkPointMsg, "Box size set up" ); |
373 | > | sprintf(checkPointMsg, "all molecules initialized succesfully"); |
374 | MPIcheckPoint(); | |
375 | #endif // is_mpi | |
376 | ||
377 | + | // clean up the forcefield |
378 | ||
379 | < | // initialize the arrays |
379 | > | the_ff->calcRcut(); |
380 | > | the_ff->cleanMe(); |
381 | > | } |
382 | ||
383 | < | the_ff->setSimInfo( simnfo ); |
383 | > | void SimSetup::initFromBass(void){ |
384 | > | int i, j, k; |
385 | > | int n_cells; |
386 | > | double cellx, celly, cellz; |
387 | > | double temp1, temp2, temp3; |
388 | > | int n_per_extra; |
389 | > | int n_extra; |
390 | > | int have_extra, done; |
391 | ||
392 | < | makeMolecules(); |
393 | < | simnfo->identArray = new int[simnfo->n_atoms]; |
394 | < | for(i=0; i<simnfo->n_atoms; i++){ |
395 | < | simnfo->identArray[i] = the_atoms[i]->getIdent(); |
550 | < | } |
551 | < | |
552 | < | if (the_globals->getUseRF() ) { |
553 | < | simnfo->useReactionField = 1; |
554 | < | |
555 | < | if( !the_globals->haveECR() ){ |
556 | < | sprintf( painCave.errMsg, |
557 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
558 | < | "box length for the electrostaticCutoffRadius.\n" |
559 | < | "I hope you have a very fast processor!\n"); |
560 | < | painCave.isFatal = 0; |
561 | < | simError(); |
562 | < | double smallest; |
563 | < | smallest = simnfo->boxLx; |
564 | < | if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
565 | < | if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
566 | < | simnfo->ecr = 0.5 * smallest; |
567 | < | } else { |
568 | < | simnfo->ecr = the_globals->getECR(); |
569 | < | } |
392 | > | double vel[3]; |
393 | > | vel[0] = 0.0; |
394 | > | vel[1] = 0.0; |
395 | > | vel[2] = 0.0; |
396 | ||
397 | < | if( !the_globals->haveEST() ){ |
398 | < | sprintf( painCave.errMsg, |
399 | < | "SimSetup Warning: using default value of 0.05 * the " |
400 | < | "electrostaticCutoffRadius for the electrostaticSkinThickness\n" |
401 | < | ); |
402 | < | painCave.isFatal = 0; |
403 | < | simError(); |
404 | < | simnfo->est = 0.05 * simnfo->ecr; |
405 | < | } else { |
406 | < | simnfo->est = the_globals->getEST(); |
407 | < | } |
408 | < | |
409 | < | if(!the_globals->haveDielectric() ){ |
410 | < | sprintf( painCave.errMsg, |
411 | < | "SimSetup Error: You are trying to use Reaction Field without" |
412 | < | "setting a dielectric constant!\n" |
413 | < | ); |
397 | > | temp1 = (double) tot_nmol / 4.0; |
398 | > | temp2 = pow(temp1, (1.0 / 3.0)); |
399 | > | temp3 = ceil(temp2); |
400 | > | |
401 | > | have_extra = 0; |
402 | > | if (temp2 < temp3){ |
403 | > | // we have a non-complete lattice |
404 | > | have_extra = 1; |
405 | > | |
406 | > | n_cells = (int) temp3 - 1; |
407 | > | cellx = info[0].boxL[0] / temp3; |
408 | > | celly = info[0].boxL[1] / temp3; |
409 | > | cellz = info[0].boxL[2] / temp3; |
410 | > | n_extra = tot_nmol - (4 * n_cells * n_cells * n_cells); |
411 | > | temp1 = ((double) n_extra) / (pow(temp3, 3.0) - pow(n_cells, 3.0)); |
412 | > | n_per_extra = (int) ceil(temp1); |
413 | > | |
414 | > | if (n_per_extra > 4){ |
415 | > | sprintf(painCave.errMsg, |
416 | > | "SimSetup error. There has been an error in constructing" |
417 | > | " the non-complete lattice.\n"); |
418 | painCave.isFatal = 1; | |
419 | simError(); | |
420 | } | |
421 | < | simnfo->dielectric = the_globals->getDielectric(); |
422 | < | } else { |
423 | < | if (usesDipoles) { |
424 | < | |
425 | < | if( !the_globals->haveECR() ){ |
426 | < | sprintf( painCave.errMsg, |
427 | < | "SimSetup Warning: using default value of 1/2 the smallest " |
428 | < | "box length for the electrostaticCutoffRadius.\n" |
429 | < | "I hope you have a very fast processor!\n"); |
430 | < | painCave.isFatal = 0; |
431 | < | simError(); |
432 | < | double smallest; |
433 | < | smallest = simnfo->boxLx; |
434 | < | if (simnfo->boxLy <= smallest) smallest = simnfo->boxLy; |
435 | < | if (simnfo->boxLz <= smallest) smallest = simnfo->boxLz; |
436 | < | simnfo->ecr = 0.5 * smallest; |
437 | < | } else { |
438 | < | simnfo->ecr = the_globals->getECR(); |
421 | > | } |
422 | > | else{ |
423 | > | n_cells = (int) temp3; |
424 | > | cellx = info[0].boxL[0] / temp3; |
425 | > | celly = info[0].boxL[1] / temp3; |
426 | > | cellz = info[0].boxL[2] / temp3; |
427 | > | } |
428 | > | |
429 | > | current_mol = 0; |
430 | > | current_comp_mol = 0; |
431 | > | current_comp = 0; |
432 | > | current_atom_ndx = 0; |
433 | > | |
434 | > | for (i = 0; i < n_cells ; i++){ |
435 | > | for (j = 0; j < n_cells; j++){ |
436 | > | for (k = 0; k < n_cells; k++){ |
437 | > | makeElement(i * cellx, j * celly, k * cellz); |
438 | > | |
439 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, k * cellz); |
440 | > | |
441 | > | makeElement(i * cellx, j * celly + 0.5 * celly, k * cellz + 0.5 * cellz); |
442 | > | |
443 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, k * cellz + 0.5 * cellz); |
444 | } | |
610 | – | |
611 | – | if( !the_globals->haveEST() ){ |
612 | – | sprintf( painCave.errMsg, |
613 | – | "SimSetup Warning: using default value of 5%% of the " |
614 | – | "electrostaticCutoffRadius for the " |
615 | – | "electrostaticSkinThickness\n" |
616 | – | ); |
617 | – | painCave.isFatal = 0; |
618 | – | simError(); |
619 | – | simnfo->est = 0.05 * simnfo->ecr; |
620 | – | } else { |
621 | – | simnfo->est = the_globals->getEST(); |
622 | – | } |
445 | } | |
446 | < | } |
446 | > | } |
447 | ||
448 | < | #ifdef IS_MPI |
449 | < | strcpy( checkPointMsg, "electrostatic parameters check out" ); |
628 | < | MPIcheckPoint(); |
629 | < | #endif // is_mpi |
448 | > | if (have_extra){ |
449 | > | done = 0; |
450 | ||
451 | < | if( the_globals->haveInitialConfig() ){ |
452 | < | |
453 | < | InitializeFromFile* fileInit; |
454 | < | #ifdef IS_MPI // is_mpi |
455 | < | if( worldRank == 0 ){ |
456 | < | #endif //is_mpi |
457 | < | fileInit = new InitializeFromFile( the_globals->getInitialConfig() ); |
458 | < | #ifdef IS_MPI |
459 | < | }else fileInit = new InitializeFromFile( NULL ); |
460 | < | #endif |
461 | < | fileInit->read_xyz( simnfo ); // default velocities on |
451 | > | int start_ndx; |
452 | > | for (i = 0; i < (n_cells + 1) && !done; i++){ |
453 | > | for (j = 0; j < (n_cells + 1) && !done; j++){ |
454 | > | if (i < n_cells){ |
455 | > | if (j < n_cells){ |
456 | > | start_ndx = n_cells; |
457 | > | } |
458 | > | else |
459 | > | start_ndx = 0; |
460 | > | } |
461 | > | else |
462 | > | start_ndx = 0; |
463 | ||
464 | < | delete fileInit; |
465 | < | } |
466 | < | else{ |
464 | > | for (k = start_ndx; k < (n_cells + 1) && !done; k++){ |
465 | > | makeElement(i * cellx, j * celly, k * cellz); |
466 | > | done = (current_mol >= tot_nmol); |
467 | ||
468 | < | #ifdef IS_MPI |
468 | > | if (!done && n_per_extra > 1){ |
469 | > | makeElement(i * cellx + 0.5 * cellx, j * celly + 0.5 * celly, |
470 | > | k * cellz); |
471 | > | done = (current_mol >= tot_nmol); |
472 | > | } |
473 | ||
474 | < | // no init from bass |
475 | < | |
476 | < | sprintf( painCave.errMsg, |
477 | < | "Cannot intialize a parallel simulation without an initial configuration file.\n" ); |
478 | < | painCave.isFatal; |
654 | < | simError(); |
655 | < | |
656 | < | #else |
474 | > | if (!done && n_per_extra > 2){ |
475 | > | makeElement(i * cellx, j * celly + 0.5 * celly, |
476 | > | k * cellz + 0.5 * cellz); |
477 | > | done = (current_mol >= tot_nmol); |
478 | > | } |
479 | ||
480 | < | initFromBass(); |
481 | < | |
482 | < | |
483 | < | #endif |
484 | < | } |
485 | < | |
664 | < | #ifdef IS_MPI |
665 | < | strcpy( checkPointMsg, "Successfully read in the initial configuration" ); |
666 | < | MPIcheckPoint(); |
667 | < | #endif // is_mpi |
668 | < | |
669 | < | |
670 | < | |
671 | < | |
672 | < | |
673 | < | |
674 | < | |
675 | < | #ifdef IS_MPI |
676 | < | if( worldRank == 0 ){ |
677 | < | #endif // is_mpi |
678 | < | |
679 | < | if( the_globals->haveFinalConfig() ){ |
680 | < | strcpy( simnfo->finalName, the_globals->getFinalConfig() ); |
681 | < | } |
682 | < | else{ |
683 | < | strcpy( simnfo->finalName, inFileName ); |
684 | < | char* endTest; |
685 | < | int nameLength = strlen( simnfo->finalName ); |
686 | < | endTest = &(simnfo->finalName[nameLength - 5]); |
687 | < | if( !strcmp( endTest, ".bass" ) ){ |
688 | < | strcpy( endTest, ".eor" ); |
480 | > | if (!done && n_per_extra > 3){ |
481 | > | makeElement(i * cellx + 0.5 * cellx, j * celly, |
482 | > | k * cellz + 0.5 * cellz); |
483 | > | done = (current_mol >= tot_nmol); |
484 | > | } |
485 | > | } |
486 | } | |
690 | – | else if( !strcmp( endTest, ".BASS" ) ){ |
691 | – | strcpy( endTest, ".eor" ); |
692 | – | } |
693 | – | else{ |
694 | – | endTest = &(simnfo->finalName[nameLength - 4]); |
695 | – | if( !strcmp( endTest, ".bss" ) ){ |
696 | – | strcpy( endTest, ".eor" ); |
697 | – | } |
698 | – | else if( !strcmp( endTest, ".mdl" ) ){ |
699 | – | strcpy( endTest, ".eor" ); |
700 | – | } |
701 | – | else{ |
702 | – | strcat( simnfo->finalName, ".eor" ); |
703 | – | } |
704 | – | } |
487 | } | |
706 | – | |
707 | – | // make the sample and status out names |
708 | – | |
709 | – | strcpy( simnfo->sampleName, inFileName ); |
710 | – | char* endTest; |
711 | – | int nameLength = strlen( simnfo->sampleName ); |
712 | – | endTest = &(simnfo->sampleName[nameLength - 5]); |
713 | – | if( !strcmp( endTest, ".bass" ) ){ |
714 | – | strcpy( endTest, ".dump" ); |
715 | – | } |
716 | – | else if( !strcmp( endTest, ".BASS" ) ){ |
717 | – | strcpy( endTest, ".dump" ); |
718 | – | } |
719 | – | else{ |
720 | – | endTest = &(simnfo->sampleName[nameLength - 4]); |
721 | – | if( !strcmp( endTest, ".bss" ) ){ |
722 | – | strcpy( endTest, ".dump" ); |
723 | – | } |
724 | – | else if( !strcmp( endTest, ".mdl" ) ){ |
725 | – | strcpy( endTest, ".dump" ); |
726 | – | } |
727 | – | else{ |
728 | – | strcat( simnfo->sampleName, ".dump" ); |
729 | – | } |
730 | – | } |
731 | – | |
732 | – | strcpy( simnfo->statusName, inFileName ); |
733 | – | nameLength = strlen( simnfo->statusName ); |
734 | – | endTest = &(simnfo->statusName[nameLength - 5]); |
735 | – | if( !strcmp( endTest, ".bass" ) ){ |
736 | – | strcpy( endTest, ".stat" ); |
737 | – | } |
738 | – | else if( !strcmp( endTest, ".BASS" ) ){ |
739 | – | strcpy( endTest, ".stat" ); |
740 | – | } |
741 | – | else{ |
742 | – | endTest = &(simnfo->statusName[nameLength - 4]); |
743 | – | if( !strcmp( endTest, ".bss" ) ){ |
744 | – | strcpy( endTest, ".stat" ); |
745 | – | } |
746 | – | else if( !strcmp( endTest, ".mdl" ) ){ |
747 | – | strcpy( endTest, ".stat" ); |
748 | – | } |
749 | – | else{ |
750 | – | strcat( simnfo->statusName, ".stat" ); |
751 | – | } |
752 | – | } |
753 | – | |
754 | – | #ifdef IS_MPI |
488 | } | |
756 | – | #endif // is_mpi |
757 | – | |
758 | – | // set the status, sample, and themal kick times |
759 | – | |
760 | – | if( the_globals->haveSampleTime() ){ |
761 | – | simnfo->sampleTime = the_globals->getSampleTime(); |
762 | – | simnfo->statusTime = simnfo->sampleTime; |
763 | – | simnfo->thermalTime = simnfo->sampleTime; |
764 | – | } |
765 | – | else{ |
766 | – | simnfo->sampleTime = the_globals->getRunTime(); |
767 | – | simnfo->statusTime = simnfo->sampleTime; |
768 | – | simnfo->thermalTime = simnfo->sampleTime; |
769 | – | } |
489 | ||
490 | < | if( the_globals->haveStatusTime() ){ |
491 | < | simnfo->statusTime = the_globals->getStatusTime(); |
490 | > | for (i = 0; i < info[0].n_atoms; i++){ |
491 | > | info[0].atoms[i]->setVel(vel); |
492 | } | |
493 | + | } |
494 | ||
495 | < | if( the_globals->haveThermalTime() ){ |
496 | < | simnfo->thermalTime = the_globals->getThermalTime(); |
497 | < | } |
495 | > | void SimSetup::makeElement(double x, double y, double z){ |
496 | > | int k; |
497 | > | AtomStamp* current_atom; |
498 | > | DirectionalAtom* dAtom; |
499 | > | double rotMat[3][3]; |
500 | > | double pos[3]; |
501 | ||
502 | < | // check for the temperature set flag |
502 | > | for (k = 0; k < comp_stamps[current_comp]->getNAtoms(); k++){ |
503 | > | current_atom = comp_stamps[current_comp]->getAtom(k); |
504 | > | if (!current_atom->havePosition()){ |
505 | > | sprintf(painCave.errMsg, |
506 | > | "SimSetup:initFromBass error.\n" |
507 | > | "\tComponent %s, atom %s does not have a position specified.\n" |
508 | > | "\tThe initialization routine is unable to give a start" |
509 | > | " position.\n", |
510 | > | comp_stamps[current_comp]->getID(), current_atom->getType()); |
511 | > | painCave.isFatal = 1; |
512 | > | simError(); |
513 | > | } |
514 | ||
515 | < | if( the_globals->haveTempSet() ) simnfo->setTemp = the_globals->getTempSet(); |
515 | > | pos[0] = x + current_atom->getPosX(); |
516 | > | pos[1] = y + current_atom->getPosY(); |
517 | > | pos[2] = z + current_atom->getPosZ(); |
518 | ||
519 | + | info[0].atoms[current_atom_ndx]->setPos(pos); |
520 | ||
521 | < | // make the integrator |
522 | < | |
786 | < | |
787 | < | NVT* myNVT = NULL; |
788 | < | NPTi* myNPTi = NULL; |
789 | < | NPTf* myNPTf = NULL; |
790 | < | NPTim* myNPTim = NULL; |
791 | < | NPTfm* myNPTfm = NULL; |
521 | > | if (info[0].atoms[current_atom_ndx]->isDirectional()){ |
522 | > | dAtom = (DirectionalAtom *) info[0].atoms[current_atom_ndx]; |
523 | ||
524 | < | switch( ensembleCase ){ |
524 | > | rotMat[0][0] = 1.0; |
525 | > | rotMat[0][1] = 0.0; |
526 | > | rotMat[0][2] = 0.0; |
527 | ||
528 | < | case NVE_ENS: |
529 | < | new NVE( simnfo, the_ff ); |
530 | < | break; |
528 | > | rotMat[1][0] = 0.0; |
529 | > | rotMat[1][1] = 1.0; |
530 | > | rotMat[1][2] = 0.0; |
531 | ||
532 | < | case NVT_ENS: |
533 | < | myNVT = new NVT( simnfo, the_ff ); |
534 | < | myNVT->setTargetTemp(the_globals->getTargetTemp()); |
532 | > | rotMat[2][0] = 0.0; |
533 | > | rotMat[2][1] = 0.0; |
534 | > | rotMat[2][2] = 1.0; |
535 | ||
536 | < | if (the_globals->haveTauThermostat()) |
537 | < | myNVT->setTauThermostat(the_globals->getTauThermostat()); |
536 | > | dAtom->setA(rotMat); |
537 | > | } |
538 | ||
539 | < | else { |
540 | < | sprintf( painCave.errMsg, |
808 | < | "SimSetup error: If you use the NVT\n" |
809 | < | " ensemble, you must set tauThermostat.\n"); |
810 | < | painCave.isFatal = 1; |
811 | < | simError(); |
812 | < | } |
813 | < | break; |
539 | > | current_atom_ndx++; |
540 | > | } |
541 | ||
542 | < | case NPTi_ENS: |
543 | < | myNPTi = new NPTi( simnfo, the_ff ); |
817 | < | myNPTi->setTargetTemp( the_globals->getTargetTemp()); |
542 | > | current_mol++; |
543 | > | current_comp_mol++; |
544 | ||
545 | < | if (the_globals->haveTargetPressure()) |
546 | < | myNPTi->setTargetPressure(the_globals->getTargetPressure()); |
547 | < | else { |
548 | < | sprintf( painCave.errMsg, |
549 | < | "SimSetup error: If you use a constant pressure\n" |
824 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
825 | < | painCave.isFatal = 1; |
826 | < | simError(); |
827 | < | } |
828 | < | |
829 | < | if( the_globals->haveTauThermostat() ) |
830 | < | myNPTi->setTauThermostat( the_globals->getTauThermostat() ); |
831 | < | else{ |
832 | < | sprintf( painCave.errMsg, |
833 | < | "SimSetup error: If you use an NPT\n" |
834 | < | " ensemble, you must set tauThermostat.\n"); |
835 | < | painCave.isFatal = 1; |
836 | < | simError(); |
837 | < | } |
545 | > | if (current_comp_mol >= components_nmol[current_comp]){ |
546 | > | current_comp_mol = 0; |
547 | > | current_comp++; |
548 | > | } |
549 | > | } |
550 | ||
839 | – | if( the_globals->haveTauBarostat() ) |
840 | – | myNPTi->setTauBarostat( the_globals->getTauBarostat() ); |
841 | – | else{ |
842 | – | sprintf( painCave.errMsg, |
843 | – | "SimSetup error: If you use an NPT\n" |
844 | – | " ensemble, you must set tauBarostat.\n"); |
845 | – | painCave.isFatal = 1; |
846 | – | simError(); |
847 | – | } |
848 | – | break; |
551 | ||
552 | < | case NPTf_ENS: |
553 | < | myNPTf = new NPTf( simnfo, the_ff ); |
852 | < | myNPTf->setTargetTemp( the_globals->getTargetTemp()); |
552 | > | void SimSetup::gatherInfo(void){ |
553 | > | int i; |
554 | ||
555 | < | if (the_globals->haveTargetPressure()) |
556 | < | myNPTf->setTargetPressure(the_globals->getTargetPressure()); |
856 | < | else { |
857 | < | sprintf( painCave.errMsg, |
858 | < | "SimSetup error: If you use a constant pressure\n" |
859 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
860 | < | painCave.isFatal = 1; |
861 | < | simError(); |
862 | < | } |
555 | > | ensembleCase = -1; |
556 | > | ffCase = -1; |
557 | ||
558 | < | if( the_globals->haveTauThermostat() ) |
865 | < | myNPTf->setTauThermostat( the_globals->getTauThermostat() ); |
866 | < | else{ |
867 | < | sprintf( painCave.errMsg, |
868 | < | "SimSetup error: If you use an NPT\n" |
869 | < | " ensemble, you must set tauThermostat.\n"); |
870 | < | painCave.isFatal = 1; |
871 | < | simError(); |
872 | < | } |
558 | > | // set the easy ones first |
559 | ||
560 | < | if( the_globals->haveTauBarostat() ) |
561 | < | myNPTf->setTauBarostat( the_globals->getTauBarostat() ); |
562 | < | else{ |
563 | < | sprintf( painCave.errMsg, |
564 | < | "SimSetup error: If you use an NPT\n" |
565 | < | " ensemble, you must set tauBarostat.\n"); |
880 | < | painCave.isFatal = 1; |
881 | < | simError(); |
882 | < | } |
883 | < | break; |
884 | < | |
885 | < | case NPTim_ENS: |
886 | < | myNPTim = new NPTim( simnfo, the_ff ); |
887 | < | myNPTim->setTargetTemp( the_globals->getTargetTemp()); |
560 | > | for (i = 0; i < nInfo; i++){ |
561 | > | info[i].target_temp = globals->getTargetTemp(); |
562 | > | info[i].dt = globals->getDt(); |
563 | > | info[i].run_time = globals->getRunTime(); |
564 | > | } |
565 | > | n_components = globals->getNComponents(); |
566 | ||
889 | – | if (the_globals->haveTargetPressure()) |
890 | – | myNPTim->setTargetPressure(the_globals->getTargetPressure()); |
891 | – | else { |
892 | – | sprintf( painCave.errMsg, |
893 | – | "SimSetup error: If you use a constant pressure\n" |
894 | – | " ensemble, you must set targetPressure in the BASS file.\n"); |
895 | – | painCave.isFatal = 1; |
896 | – | simError(); |
897 | – | } |
898 | – | |
899 | – | if( the_globals->haveTauThermostat() ) |
900 | – | myNPTim->setTauThermostat( the_globals->getTauThermostat() ); |
901 | – | else{ |
902 | – | sprintf( painCave.errMsg, |
903 | – | "SimSetup error: If you use an NPT\n" |
904 | – | " ensemble, you must set tauThermostat.\n"); |
905 | – | painCave.isFatal = 1; |
906 | – | simError(); |
907 | – | } |
567 | ||
568 | < | if( the_globals->haveTauBarostat() ) |
910 | < | myNPTim->setTauBarostat( the_globals->getTauBarostat() ); |
911 | < | else{ |
912 | < | sprintf( painCave.errMsg, |
913 | < | "SimSetup error: If you use an NPT\n" |
914 | < | " ensemble, you must set tauBarostat.\n"); |
915 | < | painCave.isFatal = 1; |
916 | < | simError(); |
917 | < | } |
918 | < | break; |
568 | > | // get the forceField |
569 | ||
570 | < | case NPTfm_ENS: |
921 | < | myNPTfm = new NPTfm( simnfo, the_ff ); |
922 | < | myNPTfm->setTargetTemp( the_globals->getTargetTemp()); |
570 | > | strcpy(force_field, globals->getForceField()); |
571 | ||
572 | < | if (the_globals->haveTargetPressure()) |
573 | < | myNPTfm->setTargetPressure(the_globals->getTargetPressure()); |
574 | < | else { |
575 | < | sprintf( painCave.errMsg, |
576 | < | "SimSetup error: If you use a constant pressure\n" |
577 | < | " ensemble, you must set targetPressure in the BASS file.\n"); |
578 | < | painCave.isFatal = 1; |
579 | < | simError(); |
580 | < | } |
581 | < | |
582 | < | if( the_globals->haveTauThermostat() ) |
583 | < | myNPTfm->setTauThermostat( the_globals->getTauThermostat() ); |
584 | < | else{ |
585 | < | sprintf( painCave.errMsg, |
586 | < | "SimSetup error: If you use an NPT\n" |
939 | < | " ensemble, you must set tauThermostat.\n"); |
940 | < | painCave.isFatal = 1; |
941 | < | simError(); |
942 | < | } |
572 | > | if (!strcasecmp(force_field, "DUFF")){ |
573 | > | ffCase = FF_DUFF; |
574 | > | } |
575 | > | else if (!strcasecmp(force_field, "LJ")){ |
576 | > | ffCase = FF_LJ; |
577 | > | } |
578 | > | else if (!strcasecmp(force_field, "EAM")){ |
579 | > | ffCase = FF_EAM; |
580 | > | } |
581 | > | else{ |
582 | > | sprintf(painCave.errMsg, "SimSetup Error. Unrecognized force field -> %s\n", |
583 | > | force_field); |
584 | > | painCave.isFatal = 1; |
585 | > | simError(); |
586 | > | } |
587 | ||
588 | < | if( the_globals->haveTauBarostat() ) |
945 | < | myNPTfm->setTauBarostat( the_globals->getTauBarostat() ); |
946 | < | else{ |
947 | < | sprintf( painCave.errMsg, |
948 | < | "SimSetup error: If you use an NPT\n" |
949 | < | " ensemble, you must set tauBarostat.\n"); |
950 | < | painCave.isFatal = 1; |
951 | < | simError(); |
952 | < | } |
953 | < | break; |
588 | > | // get the ensemble |
589 | ||
590 | < | default: |
591 | < | sprintf( painCave.errMsg, |
592 | < | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
593 | < | painCave.isFatal = 1; |
959 | < | simError(); |
590 | > | strcpy(ensemble, globals->getEnsemble()); |
591 | > | |
592 | > | if (!strcasecmp(ensemble, "NVE")){ |
593 | > | ensembleCase = NVE_ENS; |
594 | } | |
595 | + | else if (!strcasecmp(ensemble, "NVT")){ |
596 | + | ensembleCase = NVT_ENS; |
597 | + | } |
598 | + | else if (!strcasecmp(ensemble, "NPTi") || !strcasecmp(ensemble, "NPT")){ |
599 | + | ensembleCase = NPTi_ENS; |
600 | + | } |
601 | + | else if (!strcasecmp(ensemble, "NPTf")){ |
602 | + | ensembleCase = NPTf_ENS; |
603 | + | } |
604 | + | else{ |
605 | + | sprintf(painCave.errMsg, |
606 | + | "SimSetup Warning. Unrecognized Ensemble -> %s, " |
607 | + | "reverting to NVE for this simulation.\n", |
608 | + | ensemble); |
609 | + | painCave.isFatal = 0; |
610 | + | simError(); |
611 | + | strcpy(ensemble, "NVE"); |
612 | + | ensembleCase = NVE_ENS; |
613 | + | } |
614 | ||
615 | + | for (i = 0; i < nInfo; i++){ |
616 | + | strcpy(info[i].ensemble, ensemble); |
617 | ||
618 | < | #ifdef IS_MPI |
964 | < | mpiSim->mpiRefresh(); |
965 | < | #endif |
618 | > | // get the mixing rule |
619 | ||
620 | < | // initialize the Fortran |
620 | > | strcpy(info[i].mixingRule, globals->getMixingRule()); |
621 | > | info[i].usePBC = globals->getPBC(); |
622 | > | } |
623 | ||
624 | + | // get the components and calculate the tot_nMol and indvidual n_mol |
625 | ||
626 | < | simnfo->refreshSim(); |
627 | < | |
628 | < | if( !strcmp( simnfo->mixingRule, "standard") ){ |
629 | < | the_ff->initForceField( LB_MIXING_RULE ); |
626 | > | the_components = globals->getComponents(); |
627 | > | components_nmol = new int[n_components]; |
628 | > | |
629 | > | |
630 | > | if (!globals->haveNMol()){ |
631 | > | // we don't have the total number of molecules, so we assume it is |
632 | > | // given in each component |
633 | > | |
634 | > | tot_nmol = 0; |
635 | > | for (i = 0; i < n_components; i++){ |
636 | > | if (!the_components[i]->haveNMol()){ |
637 | > | // we have a problem |
638 | > | sprintf(painCave.errMsg, |
639 | > | "SimSetup Error. No global NMol or component NMol" |
640 | > | " given. Cannot calculate the number of atoms.\n"); |
641 | > | painCave.isFatal = 1; |
642 | > | simError(); |
643 | > | } |
644 | > | |
645 | > | tot_nmol += the_components[i]->getNMol(); |
646 | > | components_nmol[i] = the_components[i]->getNMol(); |
647 | > | } |
648 | } | |
975 | – | else if( !strcmp( simnfo->mixingRule, "explicit") ){ |
976 | – | the_ff->initForceField( EXPLICIT_MIXING_RULE ); |
977 | – | } |
649 | else{ | |
650 | < | sprintf( painCave.errMsg, |
651 | < | "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
652 | < | simnfo->mixingRule ); |
650 | > | sprintf(painCave.errMsg, |
651 | > | "SimSetup error.\n" |
652 | > | "\tSorry, the ability to specify total" |
653 | > | " nMols and then give molfractions in the components\n" |
654 | > | "\tis not currently supported." |
655 | > | " Please give nMol in the components.\n"); |
656 | painCave.isFatal = 1; | |
657 | simError(); | |
658 | } | |
659 | ||
660 | + | // set the status, sample, and thermal kick times |
661 | ||
662 | < | #ifdef IS_MPI |
663 | < | strcpy( checkPointMsg, |
664 | < | "Successfully intialized the mixingRule for Fortran." ); |
665 | < | MPIcheckPoint(); |
666 | < | #endif // is_mpi |
667 | < | } |
662 | > | for (i = 0; i < nInfo; i++){ |
663 | > | if (globals->haveSampleTime()){ |
664 | > | info[i].sampleTime = globals->getSampleTime(); |
665 | > | info[i].statusTime = info[i].sampleTime; |
666 | > | info[i].thermalTime = info[i].sampleTime; |
667 | > | } |
668 | > | else{ |
669 | > | info[i].sampleTime = globals->getRunTime(); |
670 | > | info[i].statusTime = info[i].sampleTime; |
671 | > | info[i].thermalTime = info[i].sampleTime; |
672 | > | } |
673 | ||
674 | + | if (globals->haveStatusTime()){ |
675 | + | info[i].statusTime = globals->getStatusTime(); |
676 | + | } |
677 | ||
678 | < | void SimSetup::makeMolecules( void ){ |
678 | > | if (globals->haveThermalTime()){ |
679 | > | info[i].thermalTime = globals->getThermalTime(); |
680 | > | } |
681 | ||
682 | < | int i, j, exI, exJ, tempEx, stampID, atomOffset, excludeOffset; |
683 | < | molInit info; |
684 | < | DirectionalAtom* dAtom; |
685 | < | LinkedAssign* extras; |
686 | < | LinkedAssign* current_extra; |
1002 | < | AtomStamp* currentAtom; |
1003 | < | BondStamp* currentBond; |
1004 | < | BendStamp* currentBend; |
1005 | < | TorsionStamp* currentTorsion; |
682 | > | info[i].resetIntegrator = 0; |
683 | > | if( globals->haveResetTime() ){ |
684 | > | info[i].resetTime = globals->getResetTime(); |
685 | > | info[i].resetIntegrator = 1; |
686 | > | } |
687 | ||
688 | < | bond_pair* theBonds; |
1008 | < | bend_set* theBends; |
1009 | < | torsion_set* theTorsions; |
688 | > | // check for the temperature set flag |
689 | ||
690 | < | |
691 | < | //init the forceField paramters |
690 | > | if (globals->haveTempSet()) |
691 | > | info[i].setTemp = globals->getTempSet(); |
692 | ||
693 | < | the_ff->readParams(); |
693 | > | // get some of the tricky things that may still be in the globals |
694 | ||
695 | < | |
696 | < | // init the atoms |
695 | > | double boxVector[3]; |
696 | > | if (globals->haveBox()){ |
697 | > | boxVector[0] = globals->getBox(); |
698 | > | boxVector[1] = globals->getBox(); |
699 | > | boxVector[2] = globals->getBox(); |
700 | ||
701 | < | double ux, uy, uz, u, uSqr; |
702 | < | |
703 | < | atomOffset = 0; |
704 | < | excludeOffset = 0; |
705 | < | for(i=0; i<simnfo->n_mol; i++){ |
706 | < | |
707 | < | stampID = the_molecules[i].getStampID(); |
701 | > | info[i].setBox(boxVector); |
702 | > | } |
703 | > | else if (globals->haveDensity()){ |
704 | > | double vol; |
705 | > | vol = (double) tot_nmol / globals->getDensity(); |
706 | > | boxVector[0] = pow(vol, (1.0 / 3.0)); |
707 | > | boxVector[1] = boxVector[0]; |
708 | > | boxVector[2] = boxVector[0]; |
709 | ||
710 | < | info.nAtoms = comp_stamps[stampID]->getNAtoms(); |
711 | < | info.nBonds = comp_stamps[stampID]->getNBonds(); |
712 | < | info.nBends = comp_stamps[stampID]->getNBends(); |
713 | < | info.nTorsions = comp_stamps[stampID]->getNTorsions(); |
714 | < | info.nExcludes = info.nBonds + info.nBends + info.nTorsions; |
710 | > | info[i].setBox(boxVector); |
711 | > | } |
712 | > | else{ |
713 | > | if (!globals->haveBoxX()){ |
714 | > | sprintf(painCave.errMsg, |
715 | > | "SimSetup error, no periodic BoxX size given.\n"); |
716 | > | painCave.isFatal = 1; |
717 | > | simError(); |
718 | > | } |
719 | > | boxVector[0] = globals->getBoxX(); |
720 | ||
721 | < | info.myAtoms = &the_atoms[atomOffset]; |
722 | < | info.myExcludes = &the_excludes[excludeOffset]; |
723 | < | info.myBonds = new Bond*[info.nBonds]; |
724 | < | info.myBends = new Bend*[info.nBends]; |
725 | < | info.myTorsions = new Torsion*[info.nTorsions]; |
721 | > | if (!globals->haveBoxY()){ |
722 | > | sprintf(painCave.errMsg, |
723 | > | "SimSetup error, no periodic BoxY size given.\n"); |
724 | > | painCave.isFatal = 1; |
725 | > | simError(); |
726 | > | } |
727 | > | boxVector[1] = globals->getBoxY(); |
728 | ||
729 | < | theBonds = new bond_pair[info.nBonds]; |
730 | < | theBends = new bend_set[info.nBends]; |
731 | < | theTorsions = new torsion_set[info.nTorsions]; |
732 | < | |
733 | < | // make the Atoms |
1044 | < | |
1045 | < | for(j=0; j<info.nAtoms; j++){ |
1046 | < | |
1047 | < | currentAtom = comp_stamps[stampID]->getAtom( j ); |
1048 | < | if( currentAtom->haveOrientation() ){ |
1049 | < | |
1050 | < | dAtom = new DirectionalAtom(j + atomOffset); |
1051 | < | simnfo->n_oriented++; |
1052 | < | info.myAtoms[j] = dAtom; |
1053 | < | |
1054 | < | ux = currentAtom->getOrntX(); |
1055 | < | uy = currentAtom->getOrntY(); |
1056 | < | uz = currentAtom->getOrntZ(); |
1057 | < | |
1058 | < | uSqr = (ux * ux) + (uy * uy) + (uz * uz); |
1059 | < | |
1060 | < | u = sqrt( uSqr ); |
1061 | < | ux = ux / u; |
1062 | < | uy = uy / u; |
1063 | < | uz = uz / u; |
1064 | < | |
1065 | < | dAtom->setSUx( ux ); |
1066 | < | dAtom->setSUy( uy ); |
1067 | < | dAtom->setSUz( uz ); |
729 | > | if (!globals->haveBoxZ()){ |
730 | > | sprintf(painCave.errMsg, |
731 | > | "SimSetup error, no periodic BoxZ size given.\n"); |
732 | > | painCave.isFatal = 1; |
733 | > | simError(); |
734 | } | |
735 | < | else{ |
1070 | < | info.myAtoms[j] = new GeneralAtom(j + atomOffset); |
1071 | < | } |
1072 | < | info.myAtoms[j]->setType( currentAtom->getType() ); |
1073 | < | |
1074 | < | #ifdef IS_MPI |
1075 | < | |
1076 | < | info.myAtoms[j]->setGlobalIndex( globalIndex[j+atomOffset] ); |
1077 | < | |
1078 | < | #endif // is_mpi |
1079 | < | } |
1080 | < | |
1081 | < | // make the bonds |
1082 | < | for(j=0; j<info.nBonds; j++){ |
1083 | < | |
1084 | < | currentBond = comp_stamps[stampID]->getBond( j ); |
1085 | < | theBonds[j].a = currentBond->getA() + atomOffset; |
1086 | < | theBonds[j].b = currentBond->getB() + atomOffset; |
735 | > | boxVector[2] = globals->getBoxZ(); |
736 | ||
737 | < | exI = theBonds[j].a; |
738 | < | exJ = theBonds[j].b; |
737 | > | info[i].setBox(boxVector); |
738 | > | } |
739 | > | } |
740 | ||
741 | < | // exclude_I must always be the smaller of the pair |
742 | < | if( exI > exJ ){ |
743 | < | tempEx = exI; |
744 | < | exI = exJ; |
745 | < | exJ = tempEx; |
741 | > | //setup seed for random number generator |
742 | > | int seedValue; |
743 | > | |
744 | > | if (globals->haveSeed()){ |
745 | > | seedValue = globals->getSeed(); |
746 | > | |
747 | > | if(seedValue / 1E9 == 0){ |
748 | > | sprintf(painCave.errMsg, |
749 | > | "Seed for sprng library should contain at least 9 digits\n" |
750 | > | "OOPSE will generate a seed for user\n"); |
751 | > | painCave.isFatal = 0; |
752 | > | simError(); |
753 | > | |
754 | > | //using seed generated by system instead of invalid seed set by user |
755 | > | #ifndef IS_MPI |
756 | > | seedValue = make_sprng_seed(); |
757 | > | #else |
758 | > | if (worldRank == 0){ |
759 | > | seedValue = make_sprng_seed(); |
760 | } | |
761 | + | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
762 | + | #endif |
763 | + | } |
764 | + | }//end of if branch of globals->haveSeed() |
765 | + | else{ |
766 | + | |
767 | + | #ifndef IS_MPI |
768 | + | seedValue = make_sprng_seed(); |
769 | + | #else |
770 | + | if (worldRank == 0){ |
771 | + | seedValue = make_sprng_seed(); |
772 | + | } |
773 | + | MPI_Bcast(&seedValue, 1, MPI_INT, 0, MPI_COMM_WORLD); |
774 | + | #endif |
775 | + | }//end of globals->haveSeed() |
776 | + | |
777 | + | for (int i = 0; i < nInfo; i++){ |
778 | + | info[i].setSeed(seedValue); |
779 | + | } |
780 | + | |
781 | #ifdef IS_MPI | |
782 | < | tempEx = exI; |
783 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
784 | < | tempEx = exJ; |
785 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1102 | < | |
1103 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1104 | < | #else // isn't MPI |
782 | > | strcpy(checkPointMsg, "Succesfully gathered all information from Bass\n"); |
783 | > | MPIcheckPoint(); |
784 | > | #endif // is_mpi |
785 | > | } |
786 | ||
787 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
788 | < | #endif //is_mpi |
787 | > | |
788 | > | void SimSetup::finalInfoCheck(void){ |
789 | > | int index; |
790 | > | int usesDipoles; |
791 | > | int i; |
792 | > | |
793 | > | for (i = 0; i < nInfo; i++){ |
794 | > | // check electrostatic parameters |
795 | > | |
796 | > | index = 0; |
797 | > | usesDipoles = 0; |
798 | > | while ((index < info[i].n_atoms) && !usesDipoles){ |
799 | > | usesDipoles = (info[i].atoms[index])->hasDipole(); |
800 | > | index++; |
801 | } | |
1109 | – | excludeOffset += info.nBonds; |
802 | ||
803 | < | //make the bends |
804 | < | for(j=0; j<info.nBends; j++){ |
805 | < | |
806 | < | currentBend = comp_stamps[stampID]->getBend( j ); |
807 | < | theBends[j].a = currentBend->getA() + atomOffset; |
808 | < | theBends[j].b = currentBend->getB() + atomOffset; |
809 | < | theBends[j].c = currentBend->getC() + atomOffset; |
810 | < | |
811 | < | if( currentBend->haveExtras() ){ |
812 | < | |
813 | < | extras = currentBend->getExtras(); |
814 | < | current_extra = extras; |
815 | < | |
816 | < | while( current_extra != NULL ){ |
817 | < | if( !strcmp( current_extra->getlhs(), "ghostVectorSource" )){ |
818 | < | |
819 | < | switch( current_extra->getType() ){ |
820 | < | |
821 | < | case 0: |
822 | < | theBends[j].ghost = |
823 | < | current_extra->getInt() + atomOffset; |
824 | < | theBends[j].isGhost = 1; |
825 | < | break; |
826 | < | |
1135 | < | case 1: |
1136 | < | theBends[j].ghost = |
1137 | < | (int)current_extra->getDouble() + atomOffset; |
1138 | < | theBends[j].isGhost = 1; |
1139 | < | break; |
1140 | < | |
1141 | < | default: |
1142 | < | sprintf( painCave.errMsg, |
1143 | < | "SimSetup Error: ghostVectorSource was neither a " |
1144 | < | "double nor an int.\n" |
1145 | < | "-->Bend[%d] in %s\n", |
1146 | < | j, comp_stamps[stampID]->getID() ); |
1147 | < | painCave.isFatal = 1; |
1148 | < | simError(); |
1149 | < | } |
1150 | < | } |
1151 | < | |
1152 | < | else{ |
1153 | < | |
1154 | < | sprintf( painCave.errMsg, |
1155 | < | "SimSetup Error: unhandled bend assignment:\n" |
1156 | < | " -->%s in Bend[%d] in %s\n", |
1157 | < | current_extra->getlhs(), |
1158 | < | j, comp_stamps[stampID]->getID() ); |
1159 | < | painCave.isFatal = 1; |
1160 | < | simError(); |
1161 | < | } |
1162 | < | |
1163 | < | current_extra = current_extra->getNext(); |
1164 | < | } |
803 | > | #ifdef IS_MPI |
804 | > | int myUse = usesDipoles; |
805 | > | MPI_Allreduce(&myUse, &usesDipoles, 1, MPI_INT, MPI_LOR, MPI_COMM_WORLD); |
806 | > | #endif //is_mpi |
807 | > | |
808 | > | double theEcr, theEst; |
809 | > | |
810 | > | if (globals->getUseRF()){ |
811 | > | info[i].useReactionField = 1; |
812 | > | |
813 | > | if (!globals->haveECR()){ |
814 | > | sprintf(painCave.errMsg, |
815 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
816 | > | "box length for the electrostaticCutoffRadius.\n" |
817 | > | "I hope you have a very fast processor!\n"); |
818 | > | painCave.isFatal = 0; |
819 | > | simError(); |
820 | > | double smallest; |
821 | > | smallest = info[i].boxL[0]; |
822 | > | if (info[i].boxL[1] <= smallest) |
823 | > | smallest = info[i].boxL[1]; |
824 | > | if (info[i].boxL[2] <= smallest) |
825 | > | smallest = info[i].boxL[2]; |
826 | > | theEcr = 0.5 * smallest; |
827 | } | |
828 | < | |
829 | < | if( !theBends[j].isGhost ){ |
1168 | < | |
1169 | < | exI = theBends[j].a; |
1170 | < | exJ = theBends[j].c; |
828 | > | else{ |
829 | > | theEcr = globals->getECR(); |
830 | } | |
831 | + | |
832 | + | if (!globals->haveEST()){ |
833 | + | sprintf(painCave.errMsg, |
834 | + | "SimSetup Warning: using default value of 0.05 * the " |
835 | + | "electrostaticCutoffRadius for the electrostaticSkinThickness\n"); |
836 | + | painCave.isFatal = 0; |
837 | + | simError(); |
838 | + | theEst = 0.05 * theEcr; |
839 | + | } |
840 | else{ | |
841 | < | |
1174 | < | exI = theBends[j].a; |
1175 | < | exJ = theBends[j].b; |
841 | > | theEst = globals->getEST(); |
842 | } | |
843 | < | |
844 | < | // exclude_I must always be the smaller of the pair |
845 | < | if( exI > exJ ){ |
846 | < | tempEx = exI; |
847 | < | exI = exJ; |
848 | < | exJ = tempEx; |
843 | > | |
844 | > | info[i].setEcr(theEcr, theEst); |
845 | > | |
846 | > | if (!globals->haveDielectric()){ |
847 | > | sprintf(painCave.errMsg, |
848 | > | "SimSetup Error: You are trying to use Reaction Field without" |
849 | > | "setting a dielectric constant!\n"); |
850 | > | painCave.isFatal = 1; |
851 | > | simError(); |
852 | } | |
853 | < | #ifdef IS_MPI |
1185 | < | tempEx = exI; |
1186 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
1187 | < | tempEx = exJ; |
1188 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
1189 | < | |
1190 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
1191 | < | #else // isn't MPI |
1192 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
1193 | < | #endif //is_mpi |
853 | > | info[i].dielectric = globals->getDielectric(); |
854 | } | |
855 | < | excludeOffset += info.nBends; |
855 | > | else{ |
856 | > | if (usesDipoles){ |
857 | > | if (!globals->haveECR()){ |
858 | > | sprintf(painCave.errMsg, |
859 | > | "SimSetup Warning: using default value of 1/2 the smallest " |
860 | > | "box length for the electrostaticCutoffRadius.\n" |
861 | > | "I hope you have a very fast processor!\n"); |
862 | > | painCave.isFatal = 0; |
863 | > | simError(); |
864 | > | double smallest; |
865 | > | smallest = info[i].boxL[0]; |
866 | > | if (info[i].boxL[1] <= smallest) |
867 | > | smallest = info[i].boxL[1]; |
868 | > | if (info[i].boxL[2] <= smallest) |
869 | > | smallest = info[i].boxL[2]; |
870 | > | theEcr = 0.5 * smallest; |
871 | > | } |
872 | > | else{ |
873 | > | theEcr = globals->getECR(); |
874 | > | } |
875 | ||
876 | < | for(j=0; j<info.nTorsions; j++){ |
877 | < | |
878 | < | currentTorsion = comp_stamps[stampID]->getTorsion( j ); |
879 | < | theTorsions[j].a = currentTorsion->getA() + atomOffset; |
880 | < | theTorsions[j].b = currentTorsion->getB() + atomOffset; |
881 | < | theTorsions[j].c = currentTorsion->getC() + atomOffset; |
882 | < | theTorsions[j].d = currentTorsion->getD() + atomOffset; |
883 | < | |
884 | < | exI = theTorsions[j].a; |
885 | < | exJ = theTorsions[j].d; |
876 | > | if (!globals->haveEST()){ |
877 | > | sprintf(painCave.errMsg, |
878 | > | "SimSetup Warning: using default value of 0.05 * the " |
879 | > | "electrostaticCutoffRadius for the " |
880 | > | "electrostaticSkinThickness\n"); |
881 | > | painCave.isFatal = 0; |
882 | > | simError(); |
883 | > | theEst = 0.05 * theEcr; |
884 | > | } |
885 | > | else{ |
886 | > | theEst = globals->getEST(); |
887 | > | } |
888 | ||
889 | < | // exclude_I must always be the smaller of the pair |
1209 | < | if( exI > exJ ){ |
1210 | < | tempEx = exI; |
1211 | < | exI = exJ; |
1212 | < | exJ = tempEx; |
889 | > | info[i].setEcr(theEcr, theEst); |
890 | } | |
891 | + | } |
892 | + | } |
893 | + | |
894 | #ifdef IS_MPI | |
895 | < | tempEx = exI; |
896 | < | exI = the_atoms[tempEx]->getGlobalIndex() + 1; |
897 | < | tempEx = exJ; |
898 | < | exJ = the_atoms[tempEx]->getGlobalIndex() + 1; |
899 | < | |
900 | < | the_excludes[j+excludeOffset]->setPair( exI, exJ ); |
901 | < | #else // isn't MPI |
902 | < | the_excludes[j+excludeOffset]->setPair( (exI+1), (exJ+1) ); |
903 | < | #endif //is_mpi |
895 | > | strcpy(checkPointMsg, "post processing checks out"); |
896 | > | MPIcheckPoint(); |
897 | > | #endif // is_mpi |
898 | > | } |
899 | > | |
900 | > | void SimSetup::initSystemCoords(void){ |
901 | > | int i; |
902 | > | |
903 | > | char* inName; |
904 | > | |
905 | > | (info[0].getConfiguration())->createArrays(info[0].n_atoms); |
906 | > | |
907 | > | for (i = 0; i < info[0].n_atoms; i++) |
908 | > | info[0].atoms[i]->setCoords(); |
909 | > | |
910 | > | if (globals->haveInitialConfig()){ |
911 | > | InitializeFromFile* fileInit; |
912 | > | #ifdef IS_MPI // is_mpi |
913 | > | if (worldRank == 0){ |
914 | > | #endif //is_mpi |
915 | > | inName = globals->getInitialConfig(); |
916 | > | fileInit = new InitializeFromFile(inName); |
917 | > | #ifdef IS_MPI |
918 | } | |
919 | < | excludeOffset += info.nTorsions; |
919 | > | else |
920 | > | fileInit = new InitializeFromFile(NULL); |
921 | > | #endif |
922 | > | fileInit->readInit(info); // default velocities on |
923 | ||
924 | < | |
925 | < | // send the arrays off to the forceField for init. |
924 | > | delete fileInit; |
925 | > | } |
926 | > | else{ |
927 | > | #ifdef IS_MPI |
928 | ||
929 | < | the_ff->initializeAtoms( info.nAtoms, info.myAtoms ); |
1231 | < | the_ff->initializeBonds( info.nBonds, info.myBonds, theBonds ); |
1232 | < | the_ff->initializeBends( info.nBends, info.myBends, theBends ); |
1233 | < | the_ff->initializeTorsions( info.nTorsions, info.myTorsions, theTorsions ); |
929 | > | // no init from bass |
930 | ||
931 | + | sprintf(painCave.errMsg, |
932 | + | "Cannot intialize a parallel simulation without an initial configuration file.\n"); |
933 | + | painCave.isFatal = 1;; |
934 | + | simError(); |
935 | ||
936 | < | the_molecules[i].initialize( info ); |
936 | > | #else |
937 | ||
938 | + | initFromBass(); |
939 | ||
940 | < | atomOffset += info.nAtoms; |
941 | < | delete[] theBonds; |
1241 | < | delete[] theBends; |
1242 | < | delete[] theTorsions; |
940 | > | |
941 | > | #endif |
942 | } | |
943 | ||
944 | #ifdef IS_MPI | |
945 | < | sprintf( checkPointMsg, "all molecules initialized succesfully" ); |
945 | > | strcpy(checkPointMsg, "Successfully read in the initial configuration"); |
946 | MPIcheckPoint(); | |
947 | #endif // is_mpi | |
1249 | – | |
1250 | – | // clean up the forcefield |
1251 | – | the_ff->calcRcut(); |
1252 | – | the_ff->cleanMe(); |
1253 | – | |
948 | } | |
949 | ||
1256 | – | void SimSetup::initFromBass( void ){ |
950 | ||
951 | < | int i, j, k; |
952 | < | int n_cells; |
1260 | < | double cellx, celly, cellz; |
1261 | < | double temp1, temp2, temp3; |
1262 | < | int n_per_extra; |
1263 | < | int n_extra; |
1264 | < | int have_extra, done; |
951 | > | void SimSetup::makeOutNames(void){ |
952 | > | int k; |
953 | ||
1266 | – | temp1 = (double)tot_nmol / 4.0; |
1267 | – | temp2 = pow( temp1, ( 1.0 / 3.0 ) ); |
1268 | – | temp3 = ceil( temp2 ); |
954 | ||
955 | < | have_extra =0; |
956 | < | if( temp2 < temp3 ){ // we have a non-complete lattice |
957 | < | have_extra =1; |
955 | > | for (k = 0; k < nInfo; k++){ |
956 | > | #ifdef IS_MPI |
957 | > | if (worldRank == 0){ |
958 | > | #endif // is_mpi |
959 | ||
960 | < | n_cells = (int)temp3 - 1; |
961 | < | cellx = simnfo->boxLx / temp3; |
962 | < | celly = simnfo->boxLy / temp3; |
963 | < | cellz = simnfo->boxLz / temp3; |
964 | < | n_extra = tot_nmol - ( 4 * n_cells * n_cells * n_cells ); |
965 | < | temp1 = ((double)n_extra) / ( pow( temp3, 3.0 ) - pow( n_cells, 3.0 ) ); |
966 | < | n_per_extra = (int)ceil( temp1 ); |
960 | > | if (globals->haveFinalConfig()){ |
961 | > | strcpy(info[k].finalName, globals->getFinalConfig()); |
962 | > | } |
963 | > | else{ |
964 | > | strcpy(info[k].finalName, inFileName); |
965 | > | char* endTest; |
966 | > | int nameLength = strlen(info[k].finalName); |
967 | > | endTest = &(info[k].finalName[nameLength - 5]); |
968 | > | if (!strcmp(endTest, ".bass")){ |
969 | > | strcpy(endTest, ".eor"); |
970 | > | } |
971 | > | else if (!strcmp(endTest, ".BASS")){ |
972 | > | strcpy(endTest, ".eor"); |
973 | > | } |
974 | > | else{ |
975 | > | endTest = &(info[k].finalName[nameLength - 4]); |
976 | > | if (!strcmp(endTest, ".bss")){ |
977 | > | strcpy(endTest, ".eor"); |
978 | > | } |
979 | > | else if (!strcmp(endTest, ".mdl")){ |
980 | > | strcpy(endTest, ".eor"); |
981 | > | } |
982 | > | else{ |
983 | > | strcat(info[k].finalName, ".eor"); |
984 | > | } |
985 | > | } |
986 | > | } |
987 | ||
988 | < | if( n_per_extra > 4){ |
989 | < | sprintf( painCave.errMsg, |
990 | < | "SimSetup error. There has been an error in constructing" |
991 | < | " the non-complete lattice.\n" ); |
992 | < | painCave.isFatal = 1; |
993 | < | simError(); |
988 | > | // make the sample and status out names |
989 | > | |
990 | > | strcpy(info[k].sampleName, inFileName); |
991 | > | char* endTest; |
992 | > | int nameLength = strlen(info[k].sampleName); |
993 | > | endTest = &(info[k].sampleName[nameLength - 5]); |
994 | > | if (!strcmp(endTest, ".bass")){ |
995 | > | strcpy(endTest, ".dump"); |
996 | > | } |
997 | > | else if (!strcmp(endTest, ".BASS")){ |
998 | > | strcpy(endTest, ".dump"); |
999 | > | } |
1000 | > | else{ |
1001 | > | endTest = &(info[k].sampleName[nameLength - 4]); |
1002 | > | if (!strcmp(endTest, ".bss")){ |
1003 | > | strcpy(endTest, ".dump"); |
1004 | > | } |
1005 | > | else if (!strcmp(endTest, ".mdl")){ |
1006 | > | strcpy(endTest, ".dump"); |
1007 | > | } |
1008 | > | else{ |
1009 | > | strcat(info[k].sampleName, ".dump"); |
1010 | > | } |
1011 | > | } |
1012 | > | |
1013 | > | strcpy(info[k].statusName, inFileName); |
1014 | > | nameLength = strlen(info[k].statusName); |
1015 | > | endTest = &(info[k].statusName[nameLength - 5]); |
1016 | > | if (!strcmp(endTest, ".bass")){ |
1017 | > | strcpy(endTest, ".stat"); |
1018 | > | } |
1019 | > | else if (!strcmp(endTest, ".BASS")){ |
1020 | > | strcpy(endTest, ".stat"); |
1021 | > | } |
1022 | > | else{ |
1023 | > | endTest = &(info[k].statusName[nameLength - 4]); |
1024 | > | if (!strcmp(endTest, ".bss")){ |
1025 | > | strcpy(endTest, ".stat"); |
1026 | > | } |
1027 | > | else if (!strcmp(endTest, ".mdl")){ |
1028 | > | strcpy(endTest, ".stat"); |
1029 | > | } |
1030 | > | else{ |
1031 | > | strcat(info[k].statusName, ".stat"); |
1032 | > | } |
1033 | > | } |
1034 | > | |
1035 | > | #ifdef IS_MPI |
1036 | > | |
1037 | } | |
1038 | + | #endif // is_mpi |
1039 | } | |
1040 | < | else{ |
1291 | < | n_cells = (int)temp3; |
1292 | < | cellx = simnfo->boxLx / temp3; |
1293 | < | celly = simnfo->boxLy / temp3; |
1294 | < | cellz = simnfo->boxLz / temp3; |
1295 | < | } |
1040 | > | } |
1041 | ||
1297 | – | current_mol = 0; |
1298 | – | current_comp_mol = 0; |
1299 | – | current_comp = 0; |
1300 | – | current_atom_ndx = 0; |
1042 | ||
1043 | < | for( i=0; i < n_cells ; i++ ){ |
1044 | < | for( j=0; j < n_cells; j++ ){ |
1304 | < | for( k=0; k < n_cells; k++ ){ |
1043 | > | void SimSetup::sysObjectsCreation(void){ |
1044 | > | int i, k; |
1045 | ||
1046 | < | makeElement( i * cellx, |
1307 | < | j * celly, |
1308 | < | k * cellz ); |
1046 | > | // create the forceField |
1047 | ||
1048 | < | makeElement( i * cellx + 0.5 * cellx, |
1311 | < | j * celly + 0.5 * celly, |
1312 | < | k * cellz ); |
1048 | > | createFF(); |
1049 | ||
1050 | < | makeElement( i * cellx, |
1315 | < | j * celly + 0.5 * celly, |
1316 | < | k * cellz + 0.5 * cellz ); |
1050 | > | // extract componentList |
1051 | ||
1052 | < | makeElement( i * cellx + 0.5 * cellx, |
1053 | < | j * celly, |
1054 | < | k * cellz + 0.5 * cellz ); |
1055 | < | } |
1052 | > | compList(); |
1053 | > | |
1054 | > | // calc the number of atoms, bond, bends, and torsions |
1055 | > | |
1056 | > | calcSysValues(); |
1057 | > | |
1058 | > | #ifdef IS_MPI |
1059 | > | // divide the molecules among the processors |
1060 | > | |
1061 | > | mpiMolDivide(); |
1062 | > | #endif //is_mpi |
1063 | > | |
1064 | > | // create the atom and SRI arrays. Also initialize Molecule Stamp ID's |
1065 | > | |
1066 | > | makeSysArrays(); |
1067 | > | |
1068 | > | // make and initialize the molecules (all but atomic coordinates) |
1069 | > | |
1070 | > | makeMolecules(); |
1071 | > | |
1072 | > | for (k = 0; k < nInfo; k++){ |
1073 | > | info[k].identArray = new int[info[k].n_atoms]; |
1074 | > | for (i = 0; i < info[k].n_atoms; i++){ |
1075 | > | info[k].identArray[i] = info[k].atoms[i]->getIdent(); |
1076 | } | |
1077 | } | |
1078 | + | } |
1079 | ||
1325 | – | if( have_extra ){ |
1326 | – | done = 0; |
1080 | ||
1081 | < | int start_ndx; |
1082 | < | for( i=0; i < (n_cells+1) && !done; i++ ){ |
1083 | < | for( j=0; j < (n_cells+1) && !done; j++ ){ |
1081 | > | void SimSetup::createFF(void){ |
1082 | > | switch (ffCase){ |
1083 | > | case FF_DUFF: |
1084 | > | the_ff = new DUFF(); |
1085 | > | break; |
1086 | ||
1087 | < | if( i < n_cells ){ |
1087 | > | case FF_LJ: |
1088 | > | the_ff = new LJFF(); |
1089 | > | break; |
1090 | ||
1091 | < | if( j < n_cells ){ |
1092 | < | start_ndx = n_cells; |
1093 | < | } |
1337 | < | else start_ndx = 0; |
1338 | < | } |
1339 | < | else start_ndx = 0; |
1091 | > | case FF_EAM: |
1092 | > | the_ff = new EAM_FF(); |
1093 | > | break; |
1094 | ||
1095 | < | for( k=start_ndx; k < (n_cells+1) && !done; k++ ){ |
1095 | > | default: |
1096 | > | sprintf(painCave.errMsg, |
1097 | > | "SimSetup Error. Unrecognized force field in case statement.\n"); |
1098 | > | painCave.isFatal = 1; |
1099 | > | simError(); |
1100 | > | } |
1101 | ||
1102 | < | makeElement( i * cellx, |
1103 | < | j * celly, |
1104 | < | k * cellz ); |
1105 | < | done = ( current_mol >= tot_nmol ); |
1102 | > | #ifdef IS_MPI |
1103 | > | strcpy(checkPointMsg, "ForceField creation successful"); |
1104 | > | MPIcheckPoint(); |
1105 | > | #endif // is_mpi |
1106 | > | } |
1107 | ||
1348 | – | if( !done && n_per_extra > 1 ){ |
1349 | – | makeElement( i * cellx + 0.5 * cellx, |
1350 | – | j * celly + 0.5 * celly, |
1351 | – | k * cellz ); |
1352 | – | done = ( current_mol >= tot_nmol ); |
1353 | – | } |
1108 | ||
1109 | < | if( !done && n_per_extra > 2){ |
1110 | < | makeElement( i * cellx, |
1111 | < | j * celly + 0.5 * celly, |
1112 | < | k * cellz + 0.5 * cellz ); |
1113 | < | done = ( current_mol >= tot_nmol ); |
1114 | < | } |
1109 | > | void SimSetup::compList(void){ |
1110 | > | int i; |
1111 | > | char* id; |
1112 | > | LinkedMolStamp* headStamp = new LinkedMolStamp(); |
1113 | > | LinkedMolStamp* currentStamp = NULL; |
1114 | > | comp_stamps = new MoleculeStamp * [n_components]; |
1115 | ||
1116 | < | if( !done && n_per_extra > 3){ |
1117 | < | makeElement( i * cellx + 0.5 * cellx, |
1118 | < | j * celly, |
1119 | < | k * cellz + 0.5 * cellz ); |
1120 | < | done = ( current_mol >= tot_nmol ); |
1121 | < | } |
1122 | < | } |
1116 | > | // make an array of molecule stamps that match the components used. |
1117 | > | // also extract the used stamps out into a separate linked list |
1118 | > | |
1119 | > | for (i = 0; i < nInfo; i++){ |
1120 | > | info[i].nComponents = n_components; |
1121 | > | info[i].componentsNmol = components_nmol; |
1122 | > | info[i].compStamps = comp_stamps; |
1123 | > | info[i].headStamp = headStamp; |
1124 | > | } |
1125 | > | |
1126 | > | |
1127 | > | for (i = 0; i < n_components; i++){ |
1128 | > | id = the_components[i]->getType(); |
1129 | > | comp_stamps[i] = NULL; |
1130 | > | |
1131 | > | // check to make sure the component isn't already in the list |
1132 | > | |
1133 | > | comp_stamps[i] = headStamp->match(id); |
1134 | > | if (comp_stamps[i] == NULL){ |
1135 | > | // extract the component from the list; |
1136 | > | |
1137 | > | currentStamp = stamps->extractMolStamp(id); |
1138 | > | if (currentStamp == NULL){ |
1139 | > | sprintf(painCave.errMsg, |
1140 | > | "SimSetup error: Component \"%s\" was not found in the " |
1141 | > | "list of declared molecules\n", |
1142 | > | id); |
1143 | > | painCave.isFatal = 1; |
1144 | > | simError(); |
1145 | } | |
1146 | + | |
1147 | + | headStamp->add(currentStamp); |
1148 | + | comp_stamps[i] = headStamp->match(id); |
1149 | } | |
1150 | } | |
1151 | ||
1152 | + | #ifdef IS_MPI |
1153 | + | strcpy(checkPointMsg, "Component stamps successfully extracted\n"); |
1154 | + | MPIcheckPoint(); |
1155 | + | #endif // is_mpi |
1156 | + | } |
1157 | ||
1158 | < | for( i=0; i<simnfo->n_atoms; i++ ){ |
1159 | < | simnfo->atoms[i]->set_vx( 0.0 ); |
1160 | < | simnfo->atoms[i]->set_vy( 0.0 ); |
1161 | < | simnfo->atoms[i]->set_vz( 0.0 ); |
1158 | > | void SimSetup::calcSysValues(void){ |
1159 | > | int i; |
1160 | > | |
1161 | > | int* molMembershipArray; |
1162 | > | |
1163 | > | tot_atoms = 0; |
1164 | > | tot_bonds = 0; |
1165 | > | tot_bends = 0; |
1166 | > | tot_torsions = 0; |
1167 | > | for (i = 0; i < n_components; i++){ |
1168 | > | tot_atoms += components_nmol[i] * comp_stamps[i]->getNAtoms(); |
1169 | > | tot_bonds += components_nmol[i] * comp_stamps[i]->getNBonds(); |
1170 | > | tot_bends += components_nmol[i] * comp_stamps[i]->getNBends(); |
1171 | > | tot_torsions += components_nmol[i] * comp_stamps[i]->getNTorsions(); |
1172 | } | |
1379 | – | } |
1173 | ||
1174 | < | void SimSetup::makeElement( double x, double y, double z ){ |
1174 | > | tot_SRI = tot_bonds + tot_bends + tot_torsions; |
1175 | > | molMembershipArray = new int[tot_atoms]; |
1176 | ||
1177 | < | int k; |
1178 | < | AtomStamp* current_atom; |
1179 | < | DirectionalAtom* dAtom; |
1180 | < | double rotMat[3][3]; |
1177 | > | for (i = 0; i < nInfo; i++){ |
1178 | > | info[i].n_atoms = tot_atoms; |
1179 | > | info[i].n_bonds = tot_bonds; |
1180 | > | info[i].n_bends = tot_bends; |
1181 | > | info[i].n_torsions = tot_torsions; |
1182 | > | info[i].n_SRI = tot_SRI; |
1183 | > | info[i].n_mol = tot_nmol; |
1184 | ||
1185 | < | for( k=0; k<comp_stamps[current_comp]->getNAtoms(); k++ ){ |
1185 | > | info[i].molMembershipArray = molMembershipArray; |
1186 | > | } |
1187 | > | } |
1188 | ||
1189 | < | current_atom = comp_stamps[current_comp]->getAtom( k ); |
1391 | < | if( !current_atom->havePosition() ){ |
1392 | < | sprintf( painCave.errMsg, |
1393 | < | "SimSetup:initFromBass error.\n" |
1394 | < | "\tComponent %s, atom %s does not have a position specified.\n" |
1395 | < | "\tThe initialization routine is unable to give a start" |
1396 | < | " position.\n", |
1397 | < | comp_stamps[current_comp]->getID(), |
1398 | < | current_atom->getType() ); |
1399 | < | painCave.isFatal = 1; |
1400 | < | simError(); |
1401 | < | } |
1189 | > | #ifdef IS_MPI |
1190 | ||
1191 | < | the_atoms[current_atom_ndx]->setX( x + current_atom->getPosX() ); |
1192 | < | the_atoms[current_atom_ndx]->setY( y + current_atom->getPosY() ); |
1193 | < | the_atoms[current_atom_ndx]->setZ( z + current_atom->getPosZ() ); |
1191 | > | void SimSetup::mpiMolDivide(void){ |
1192 | > | int i, j, k; |
1193 | > | int localMol, allMol; |
1194 | > | int local_atoms, local_bonds, local_bends, local_torsions, local_SRI; |
1195 | ||
1196 | < | if( the_atoms[current_atom_ndx]->isDirectional() ){ |
1196 | > | mpiSim = new mpiSimulation(info); |
1197 | ||
1198 | < | dAtom = (DirectionalAtom *)the_atoms[current_atom_ndx]; |
1198 | > | globalIndex = mpiSim->divideLabor(); |
1199 | ||
1200 | < | rotMat[0][0] = 1.0; |
1412 | < | rotMat[0][1] = 0.0; |
1413 | < | rotMat[0][2] = 0.0; |
1200 | > | // set up the local variables |
1201 | ||
1202 | < | rotMat[1][0] = 0.0; |
1203 | < | rotMat[1][1] = 1.0; |
1417 | < | rotMat[1][2] = 0.0; |
1202 | > | mol2proc = mpiSim->getMolToProcMap(); |
1203 | > | molCompType = mpiSim->getMolComponentType(); |
1204 | ||
1205 | < | rotMat[2][0] = 0.0; |
1206 | < | rotMat[2][1] = 0.0; |
1207 | < | rotMat[2][2] = 1.0; |
1205 | > | allMol = 0; |
1206 | > | localMol = 0; |
1207 | > | local_atoms = 0; |
1208 | > | local_bonds = 0; |
1209 | > | local_bends = 0; |
1210 | > | local_torsions = 0; |
1211 | > | globalAtomIndex = 0; |
1212 | ||
1213 | < | dAtom->setA( rotMat ); |
1213 | > | |
1214 | > | for (i = 0; i < n_components; i++){ |
1215 | > | for (j = 0; j < components_nmol[i]; j++){ |
1216 | > | if (mol2proc[allMol] == worldRank){ |
1217 | > | local_atoms += comp_stamps[i]->getNAtoms(); |
1218 | > | local_bonds += comp_stamps[i]->getNBonds(); |
1219 | > | local_bends += comp_stamps[i]->getNBends(); |
1220 | > | local_torsions += comp_stamps[i]->getNTorsions(); |
1221 | > | localMol++; |
1222 | > | } |
1223 | > | for (k = 0; k < comp_stamps[i]->getNAtoms(); k++){ |
1224 | > | info[0].molMembershipArray[globalAtomIndex] = allMol; |
1225 | > | globalAtomIndex++; |
1226 | > | } |
1227 | > | |
1228 | > | allMol++; |
1229 | } | |
1230 | + | } |
1231 | + | local_SRI = local_bonds + local_bends + local_torsions; |
1232 | ||
1233 | < | current_atom_ndx++; |
1233 | > | info[0].n_atoms = mpiSim->getMyNlocal(); |
1234 | > | |
1235 | > | if (local_atoms != info[0].n_atoms){ |
1236 | > | sprintf(painCave.errMsg, |
1237 | > | "SimSetup error: mpiSim's localAtom (%d) and SimSetup's" |
1238 | > | " localAtom (%d) are not equal.\n", |
1239 | > | info[0].n_atoms, local_atoms); |
1240 | > | painCave.isFatal = 1; |
1241 | > | simError(); |
1242 | } | |
1243 | ||
1244 | < | current_mol++; |
1245 | < | current_comp_mol++; |
1244 | > | info[0].n_bonds = local_bonds; |
1245 | > | info[0].n_bends = local_bends; |
1246 | > | info[0].n_torsions = local_torsions; |
1247 | > | info[0].n_SRI = local_SRI; |
1248 | > | info[0].n_mol = localMol; |
1249 | ||
1250 | < | if( current_comp_mol >= components_nmol[current_comp] ){ |
1250 | > | strcpy(checkPointMsg, "Passed nlocal consistency check."); |
1251 | > | MPIcheckPoint(); |
1252 | > | } |
1253 | ||
1254 | < | current_comp_mol = 0; |
1255 | < | current_comp++; |
1254 | > | #endif // is_mpi |
1255 | > | |
1256 | > | |
1257 | > | void SimSetup::makeSysArrays(void){ |
1258 | > | |
1259 | > | #ifndef IS_MPI |
1260 | > | int k, j; |
1261 | > | #endif // is_mpi |
1262 | > | int i, 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 | + | NVE<RealIntegrator>* myNVE = NULL; |
1346 | + | NVT<RealIntegrator>* myNVT = NULL; |
1347 | + | NPTi<NPT<RealIntegrator> >* myNPTi = NULL; |
1348 | + | NPTf<NPT<RealIntegrator> >* myNPTf = NULL; |
1349 | + | |
1350 | + | for (k = 0; k < nInfo; k++){ |
1351 | + | switch (ensembleCase){ |
1352 | + | case NVE_ENS: |
1353 | + | if (globals->haveZconstraints()){ |
1354 | + | setupZConstraint(info[k]); |
1355 | + | myNVE = new ZConstraint<NVE<RealIntegrator> >(&(info[k]), the_ff); |
1356 | + | } |
1357 | + | else{ |
1358 | + | myNVE = new NVE<RealIntegrator>(&(info[k]), the_ff); |
1359 | + | } |
1360 | + | |
1361 | + | info->the_integrator = myNVE; |
1362 | + | break; |
1363 | + | |
1364 | + | case NVT_ENS: |
1365 | + | if (globals->haveZconstraints()){ |
1366 | + | setupZConstraint(info[k]); |
1367 | + | myNVT = new ZConstraint<NVT<RealIntegrator> >(&(info[k]), the_ff); |
1368 | + | } |
1369 | + | else |
1370 | + | myNVT = new NVT<RealIntegrator>(&(info[k]), the_ff); |
1371 | + | |
1372 | + | myNVT->setTargetTemp(globals->getTargetTemp()); |
1373 | + | |
1374 | + | if (globals->haveTauThermostat()) |
1375 | + | myNVT->setTauThermostat(globals->getTauThermostat()); |
1376 | + | else{ |
1377 | + | sprintf(painCave.errMsg, |
1378 | + | "SimSetup error: If you use the NVT\n" |
1379 | + | " ensemble, you must set tauThermostat.\n"); |
1380 | + | painCave.isFatal = 1; |
1381 | + | simError(); |
1382 | + | } |
1383 | + | |
1384 | + | info->the_integrator = myNVT; |
1385 | + | break; |
1386 | + | |
1387 | + | case NPTi_ENS: |
1388 | + | if (globals->haveZconstraints()){ |
1389 | + | setupZConstraint(info[k]); |
1390 | + | myNPTi = new ZConstraint<NPTi<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1391 | + | } |
1392 | + | else |
1393 | + | myNPTi = new NPTi<NPT<RealIntegrator> >(&(info[k]), the_ff); |
1394 | + | |
1395 | + | myNPTi->setTargetTemp(globals->getTargetTemp()); |
1396 | + | |
1397 | + | if (globals->haveTargetPressure()) |
1398 | + | myNPTi->setTargetPressure(globals->getTargetPressure()); |
1399 | + | else{ |
1400 | + | sprintf(painCave.errMsg, |
1401 | + | "SimSetup error: If you use a constant pressure\n" |
1402 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1403 | + | painCave.isFatal = 1; |
1404 | + | simError(); |
1405 | + | } |
1406 | + | |
1407 | + | if (globals->haveTauThermostat()) |
1408 | + | myNPTi->setTauThermostat(globals->getTauThermostat()); |
1409 | + | else{ |
1410 | + | sprintf(painCave.errMsg, |
1411 | + | "SimSetup error: If you use an NPT\n" |
1412 | + | " ensemble, you must set tauThermostat.\n"); |
1413 | + | painCave.isFatal = 1; |
1414 | + | simError(); |
1415 | + | } |
1416 | + | |
1417 | + | if (globals->haveTauBarostat()) |
1418 | + | myNPTi->setTauBarostat(globals->getTauBarostat()); |
1419 | + | else{ |
1420 | + | sprintf(painCave.errMsg, |
1421 | + | "SimSetup error: If you use an NPT\n" |
1422 | + | " ensemble, you must set tauBarostat.\n"); |
1423 | + | painCave.isFatal = 1; |
1424 | + | simError(); |
1425 | + | } |
1426 | + | |
1427 | + | info->the_integrator = myNPTi; |
1428 | + | break; |
1429 | + | |
1430 | + | case NPTf_ENS: |
1431 | + | if (globals->haveZconstraints()){ |
1432 | + | setupZConstraint(info[k]); |
1433 | + | myNPTf = new ZConstraint<NPTf<NPT <RealIntegrator> > >(&(info[k]), the_ff); |
1434 | + | } |
1435 | + | else |
1436 | + | myNPTf = new NPTf<NPT <RealIntegrator> >(&(info[k]), the_ff); |
1437 | + | |
1438 | + | myNPTf->setTargetTemp(globals->getTargetTemp()); |
1439 | + | |
1440 | + | if (globals->haveTargetPressure()) |
1441 | + | myNPTf->setTargetPressure(globals->getTargetPressure()); |
1442 | + | else{ |
1443 | + | sprintf(painCave.errMsg, |
1444 | + | "SimSetup error: If you use a constant pressure\n" |
1445 | + | " ensemble, you must set targetPressure in the BASS file.\n"); |
1446 | + | painCave.isFatal = 1; |
1447 | + | simError(); |
1448 | + | } |
1449 | + | |
1450 | + | if (globals->haveTauThermostat()) |
1451 | + | myNPTf->setTauThermostat(globals->getTauThermostat()); |
1452 | + | else{ |
1453 | + | sprintf(painCave.errMsg, |
1454 | + | "SimSetup error: If you use an NPT\n" |
1455 | + | " ensemble, you must set tauThermostat.\n"); |
1456 | + | painCave.isFatal = 1; |
1457 | + | simError(); |
1458 | + | } |
1459 | + | |
1460 | + | if (globals->haveTauBarostat()) |
1461 | + | myNPTf->setTauBarostat(globals->getTauBarostat()); |
1462 | + | else{ |
1463 | + | sprintf(painCave.errMsg, |
1464 | + | "SimSetup error: If you use an NPT\n" |
1465 | + | " ensemble, you must set tauBarostat.\n"); |
1466 | + | painCave.isFatal = 1; |
1467 | + | simError(); |
1468 | + | } |
1469 | + | |
1470 | + | info->the_integrator = myNPTf; |
1471 | + | break; |
1472 | + | |
1473 | + | default: |
1474 | + | sprintf(painCave.errMsg, |
1475 | + | "SimSetup Error. Unrecognized ensemble in case statement.\n"); |
1476 | + | painCave.isFatal = 1; |
1477 | + | simError(); |
1478 | + | } |
1479 | + | } |
1480 | + | } |
1481 | + | |
1482 | + | void SimSetup::initFortran(void){ |
1483 | + | info[0].refreshSim(); |
1484 | + | |
1485 | + | if (!strcmp(info[0].mixingRule, "standard")){ |
1486 | + | the_ff->initForceField(LB_MIXING_RULE); |
1487 | + | } |
1488 | + | else if (!strcmp(info[0].mixingRule, "explicit")){ |
1489 | + | the_ff->initForceField(EXPLICIT_MIXING_RULE); |
1490 | + | } |
1491 | + | else{ |
1492 | + | sprintf(painCave.errMsg, "SimSetup Error: unknown mixing rule -> \"%s\"\n", |
1493 | + | info[0].mixingRule); |
1494 | + | painCave.isFatal = 1; |
1495 | + | simError(); |
1496 | + | } |
1497 | + | |
1498 | + | |
1499 | + | #ifdef IS_MPI |
1500 | + | strcpy(checkPointMsg, "Successfully intialized the mixingRule for Fortran."); |
1501 | + | MPIcheckPoint(); |
1502 | + | #endif // is_mpi |
1503 | + | } |
1504 | + | |
1505 | + | void SimSetup::setupZConstraint(SimInfo& theInfo){ |
1506 | + | int nZConstraints; |
1507 | + | ZconStamp** zconStamp; |
1508 | + | |
1509 | + | if (globals->haveZconstraintTime()){ |
1510 | + | //add sample time of z-constraint into SimInfo's property list |
1511 | + | DoubleData* zconsTimeProp = new DoubleData(); |
1512 | + | zconsTimeProp->setID(ZCONSTIME_ID); |
1513 | + | zconsTimeProp->setData(globals->getZconsTime()); |
1514 | + | theInfo.addProperty(zconsTimeProp); |
1515 | + | } |
1516 | + | else{ |
1517 | + | sprintf(painCave.errMsg, |
1518 | + | "ZConstraint error: If you use an ZConstraint\n" |
1519 | + | " , you must set sample time.\n"); |
1520 | + | painCave.isFatal = 1; |
1521 | + | simError(); |
1522 | + | } |
1523 | + | |
1524 | + | //push zconsTol into siminfo, if user does not specify |
1525 | + | //value for zconsTol, a default value will be used |
1526 | + | DoubleData* zconsTol = new DoubleData(); |
1527 | + | zconsTol->setID(ZCONSTOL_ID); |
1528 | + | if (globals->haveZconsTol()){ |
1529 | + | zconsTol->setData(globals->getZconsTol()); |
1530 | + | } |
1531 | + | else{ |
1532 | + | double defaultZConsTol = 0.01; |
1533 | + | sprintf(painCave.errMsg, |
1534 | + | "ZConstraint Waring: Tolerance for z-constraint methodl is not specified\n" |
1535 | + | " , default value %f is used.\n", |
1536 | + | defaultZConsTol); |
1537 | + | painCave.isFatal = 0; |
1538 | + | simError(); |
1539 | + | |
1540 | + | zconsTol->setData(defaultZConsTol); |
1541 | + | } |
1542 | + | theInfo.addProperty(zconsTol); |
1543 | + | |
1544 | + | //set Force Subtraction Policy |
1545 | + | StringData* zconsForcePolicy = new StringData(); |
1546 | + | zconsForcePolicy->setID(ZCONSFORCEPOLICY_ID); |
1547 | + | |
1548 | + | if (globals->haveZconsForcePolicy()){ |
1549 | + | zconsForcePolicy->setData(globals->getZconsForcePolicy()); |
1550 | + | } |
1551 | + | else{ |
1552 | + | sprintf(painCave.errMsg, |
1553 | + | "ZConstraint Warning: User does not set force Subtraction policy, " |
1554 | + | "PolicyByMass is used\n"); |
1555 | + | painCave.isFatal = 0; |
1556 | + | simError(); |
1557 | + | zconsForcePolicy->setData("BYMASS"); |
1558 | + | } |
1559 | + | |
1560 | + | theInfo.addProperty(zconsForcePolicy); |
1561 | + | |
1562 | + | //Determine the name of ouput file and add it into SimInfo's property list |
1563 | + | //Be careful, do not use inFileName, since it is a pointer which |
1564 | + | //point to a string at master node, and slave nodes do not contain that string |
1565 | + | |
1566 | + | string zconsOutput(theInfo.finalName); |
1567 | + | |
1568 | + | zconsOutput = zconsOutput.substr(0, zconsOutput.rfind(".")) + ".fz"; |
1569 | + | |
1570 | + | StringData* zconsFilename = new StringData(); |
1571 | + | zconsFilename->setID(ZCONSFILENAME_ID); |
1572 | + | zconsFilename->setData(zconsOutput); |
1573 | + | |
1574 | + | theInfo.addProperty(zconsFilename); |
1575 | + | |
1576 | + | //setup index, pos and other parameters of z-constraint molecules |
1577 | + | nZConstraints = globals->getNzConstraints(); |
1578 | + | theInfo.nZconstraints = nZConstraints; |
1579 | + | |
1580 | + | zconStamp = globals->getZconStamp(); |
1581 | + | ZConsParaItem tempParaItem; |
1582 | + | |
1583 | + | ZConsParaData* zconsParaData = new ZConsParaData(); |
1584 | + | zconsParaData->setID(ZCONSPARADATA_ID); |
1585 | + | |
1586 | + | for (int i = 0; i < nZConstraints; i++){ |
1587 | + | tempParaItem.havingZPos = zconStamp[i]->haveZpos(); |
1588 | + | tempParaItem.zPos = zconStamp[i]->getZpos(); |
1589 | + | tempParaItem.zconsIndex = zconStamp[i]->getMolIndex(); |
1590 | + | tempParaItem.kRatio = zconStamp[i]->getKratio(); |
1591 | + | |
1592 | + | zconsParaData->addItem(tempParaItem); |
1593 | + | } |
1594 | + | |
1595 | + | //check the uniqueness of index |
1596 | + | if(!zconsParaData->isIndexUnique()){ |
1597 | + | sprintf(painCave.errMsg, |
1598 | + | "ZConstraint Error: molIndex is not unique\n"); |
1599 | + | painCave.isFatal = 1; |
1600 | + | simError(); |
1601 | + | } |
1602 | + | |
1603 | + | //sort the parameters by index of molecules |
1604 | + | zconsParaData->sortByIndex(); |
1605 | + | |
1606 | + | //push data into siminfo, therefore, we can retrieve later |
1607 | + | theInfo.addProperty(zconsParaData); |
1608 | + | } |
– | Removed lines |
+ | Added lines |
< | Changed lines |
> | Changed lines |