Changeset 437922 for src/periodentafel.cpp
- Timestamp:
- Jul 23, 2009, 12:14:13 PM (15 years ago)
- Branches:
- Action_Thermostats, Add_AtomRandomPerturbation, Add_FitFragmentPartialChargesAction, Add_RotateAroundBondAction, Add_SelectAtomByNameAction, Added_ParseSaveFragmentResults, AddingActions_SaveParseParticleParameters, Adding_Graph_to_ChangeBondActions, Adding_MD_integration_tests, Adding_ParticleName_to_Atom, Adding_StructOpt_integration_tests, AtomFragments, Automaking_mpqc_open, AutomationFragmentation_failures, Candidate_v1.5.4, Candidate_v1.6.0, Candidate_v1.6.1, ChangeBugEmailaddress, ChangingTestPorts, ChemicalSpaceEvaluator, CombiningParticlePotentialParsing, Combining_Subpackages, Debian_Package_split, Debian_package_split_molecuildergui_only, Disabling_MemDebug, Docu_Python_wait, EmpiricalPotential_contain_HomologyGraph, EmpiricalPotential_contain_HomologyGraph_documentation, Enable_parallel_make_install, Enhance_userguide, Enhanced_StructuralOptimization, Enhanced_StructuralOptimization_continued, Example_ManyWaysToTranslateAtom, Exclude_Hydrogens_annealWithBondGraph, FitPartialCharges_GlobalError, Fix_BoundInBox_CenterInBox_MoleculeActions, Fix_ChargeSampling_PBC, Fix_ChronosMutex, Fix_FitPartialCharges, Fix_FitPotential_needs_atomicnumbers, Fix_ForceAnnealing, Fix_IndependentFragmentGrids, Fix_ParseParticles, Fix_ParseParticles_split_forward_backward_Actions, Fix_PopActions, Fix_QtFragmentList_sorted_selection, Fix_Restrictedkeyset_FragmentMolecule, Fix_StatusMsg, Fix_StepWorldTime_single_argument, Fix_Verbose_Codepatterns, Fix_fitting_potentials, Fixes, ForceAnnealing_goodresults, ForceAnnealing_oldresults, ForceAnnealing_tocheck, ForceAnnealing_with_BondGraph, ForceAnnealing_with_BondGraph_continued, ForceAnnealing_with_BondGraph_continued_betteresults, ForceAnnealing_with_BondGraph_contraction-expansion, FragmentAction_writes_AtomFragments, FragmentMolecule_checks_bonddegrees, GeometryObjects, Gui_Fixes, Gui_displays_atomic_force_velocity, ImplicitCharges, IndependentFragmentGrids, IndependentFragmentGrids_IndividualZeroInstances, IndependentFragmentGrids_IntegrationTest, IndependentFragmentGrids_Sole_NN_Calculation, JobMarket_RobustOnKillsSegFaults, JobMarket_StableWorkerPool, JobMarket_unresolvable_hostname_fix, MoreRobust_FragmentAutomation, ODR_violation_mpqc_open, PartialCharges_OrthogonalSummation, PdbParser_setsAtomName, PythonUI_with_named_parameters, QtGui_reactivate_TimeChanged_changes, Recreated_GuiChecks, Rewrite_FitPartialCharges, RotateToPrincipalAxisSystem_UndoRedo, SaturateAtoms_findBestMatching, SaturateAtoms_singleDegree, StoppableMakroAction, Subpackage_CodePatterns, Subpackage_JobMarket, Subpackage_LinearAlgebra, Subpackage_levmar, Subpackage_mpqc_open, Subpackage_vmg, Switchable_LogView, ThirdParty_MPQC_rebuilt_buildsystem, TrajectoryDependenant_MaxOrder, TremoloParser_IncreasedPrecision, TremoloParser_MultipleTimesteps, TremoloParser_setsAtomName, Ubuntu_1604_changes, stable
- Children:
- d067d45
- Parents:
- 178f92
- File:
-
- 1 edited
-
src/periodentafel.cpp (modified) (12 diffs)
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src/periodentafel.cpp
r178f92 r437922 16 16 periodentafel::periodentafel() 17 17 { 18 19 20 21 22 23 18 start = new element; 19 end = new element; 20 start->previous = NULL; 21 start->next = end; 22 end->previous = start; 23 end->next = NULL; 24 24 }; 25 25 … … 29 29 periodentafel::~periodentafel() 30 30 { 31 32 33 31 CleanupPeriodtable(); 32 delete(end); 33 delete(start); 34 34 }; 35 35 … … 40 40 bool periodentafel::AddElement(element *pointer) 41 41 { 42 43 44 45 42 pointer->sort = &pointer->Z; 43 if (pointer->Z < 1 && pointer->Z >= MAX_ELEMENTS) 44 cout << Verbose(0) << "Invalid Z number!\n"; 45 return add(pointer, end); 46 46 }; 47 47 … … 52 52 bool periodentafel::RemoveElement(element *pointer) 53 53 { 54 54 return remove(pointer, start, end); 55 55 }; 56 56 … … 60 60 bool periodentafel::CleanupPeriodtable() 61 61 { 62 62 return cleanup(start,end); 63 63 }; 64 64 … … 70 70 element * periodentafel::FindElement(int Z) 71 71 { 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 72 element *walker = find(&Z, start,end); 73 if (walker == NULL) { // not found: enter and put into db 74 cout << Verbose(0) << "Element not found in database, please enter." << endl; 75 walker = new element; 76 cout << Verbose(0) << "Mass: " << endl; 77 cin >> walker->mass; 78 walker->Z = Z; 79 cout << Verbose(0) << "Atomic number: " << walker->Z << endl; 80 cout << Verbose(0) << "Name [max 64 chars]: " << endl; 81 cin >> walker->name; 82 cout << Verbose(0) << "Short form [max 3 chars]: " << endl; 83 cin >> walker->symbol; 84 periodentafel::AddElement(walker); 85 } 86 return(walker); 87 87 }; 88 88 … … 94 94 element * periodentafel::FindElement(char *shorthand) const 95 95 { 96 element *walker =periodentafel::start;97 98 99 100 101 102 96 element *walker = periodentafel::start; 97 while (walker->next != periodentafel::end) { 98 walker = walker->next; 99 if (strncmp(walker->symbol, shorthand, 3) == 0) 100 return(walker); 101 } 102 return (NULL); 103 103 }; 104 104 … … 107 107 element * periodentafel::AskElement() 108 108 { 109 110 111 112 113 114 walker = this->FindElement(Z);// give type115 116 109 element *walker = NULL; 110 int Z; 111 do { 112 cout << Verbose(0) << "Atomic number Z: "; 113 cin >> Z; 114 walker = this->FindElement(Z); // give type 115 } while (walker == NULL); 116 return walker; 117 117 }; 118 118 … … 122 122 bool periodentafel::Output(ofstream *output) const 123 123 { 124 125 126 127 128 129 130 131 132 133 124 bool result = true; 125 element *walker = start; 126 if (output != NULL) { 127 while (walker->next != end) { 128 walker = walker->next; 129 result = result && walker->Output(output); 130 } 131 return result; 132 } else 133 return false; 134 134 }; 135 135 … … 140 140 bool periodentafel::Checkout(ofstream *output, const int *checkliste) const 141 141 { 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 142 element *walker = start; 143 bool result = true; 144 int No = 1; 145 146 if (output != NULL) { 147 *output << "# Ion type data (PP = PseudoPotential, Z = atomic number)" << endl; 148 *output << "#Ion_TypeNr.\tAmount\tZ\tRGauss\tL_Max(PP)L_Loc(PP)IonMass\t# chemical name, symbol" << endl; 149 while (walker->next != end) { 150 walker = walker->next; 151 if ((walker != NULL) && (walker->Z > 0) && (walker->Z < MAX_ELEMENTS) && (checkliste[walker->Z])) { 152 walker->No = No; 153 result = result && walker->Checkout(output, No++, checkliste[walker->Z]); 154 } 155 } 156 return result; 157 } else 158 return false; 159 159 }; 160 160 … … 164 164 bool periodentafel::LoadPeriodentafel(char *path) 165 165 { 166 167 168 169 170 171 172 173 174 175 176 177 178 179 180 181 cout <<"Parsed elements:";182 183 184 185 186 187 188 189 190 191 192 193 194 195 196 197 198 199 200 201 202 203 204 205 206 207 208 209 210 211 212 213 214 215 216 217 218 219 220 221 222 223 224 225 226 227 228 229 230 231 232 233 234 235 236 237 238 239 240 241 242 243 244 245 246 247 248 249 250 251 252 253 254 255 256 257 258 259 260 261 262 263 264 265 266 267 268 269 270 271 272 273 274 275 276 277 278 279 280 281 282 283 284 285 286 287 288 289 290 291 292 293 294 295 296 297 298 166 ifstream infile; 167 double tmp; 168 element *ptr; 169 bool status = true; 170 bool otherstatus = true; 171 char filename[255]; 172 173 // fill elements DB 174 strncpy(filename, path, MAXSTRINGSIZE); 175 strncat(filename, "/", MAXSTRINGSIZE-strlen(filename)); 176 strncat(filename, STANDARDELEMENTSDB, MAXSTRINGSIZE-strlen(filename)); 177 infile.open(filename); 178 if (infile != NULL) { 179 infile.getline(header1, MAXSTRINGSIZE); 180 infile.getline(header2, MAXSTRINGSIZE); // skip first two header lines 181 cout << "Parsed elements:"; 182 while (!infile.eof()) { 183 element *neues = new element; 184 infile >> neues->name; 185 //infile >> ws; 186 infile >> neues->symbol; 187 //infile >> ws; 188 infile >> neues->period; 189 //infile >> ws; 190 infile >> neues->group; 191 //infile >> ws; 192 infile >> neues->block; 193 //infile >> ws; 194 infile >> neues->Z; 195 //infile >> ws; 196 infile >> neues->mass; 197 //infile >> ws; 198 infile >> neues->CovalentRadius; 199 //infile >> ws; 200 infile >> neues->VanDerWaalsRadius; 201 //infile >> ws; 202 infile >> ws; 203 cout << " " << neues->symbol; 204 //neues->Output((ofstream *)&cout); 205 if ((neues->Z > 0) && (neues->Z < MAX_ELEMENTS)) 206 periodentafel::AddElement(neues); 207 else { 208 cout << "Could not parse element: "; 209 neues->Output((ofstream *)&cout); 210 } 211 } 212 cout << endl; 213 infile.close(); 214 infile.clear(); 215 } else 216 status = false; 217 218 // fill valence DB per element 219 strncpy(filename, path, MAXSTRINGSIZE); 220 strncat(filename, "/", MAXSTRINGSIZE-strlen(filename)); 221 strncat(filename, STANDARDVALENCEDB, MAXSTRINGSIZE-strlen(filename)); 222 infile.open(filename); 223 if (infile != NULL) { 224 while (!infile.eof()) { 225 infile >> tmp; 226 infile >> ws; 227 infile >> FindElement((int)tmp)->Valence; 228 infile >> ws; 229 //cout << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->Valence << " valence electrons." << endl; 230 } 231 infile.close(); 232 infile.clear(); 233 } else 234 otherstatus = false; 235 236 // fill valence DB per element 237 strncpy(filename, path, MAXSTRINGSIZE); 238 strncat(filename, "/", MAXSTRINGSIZE-strlen(filename)); 239 strncat(filename, STANDARDORBITALDB, MAXSTRINGSIZE-strlen(filename)); 240 infile.open(filename); 241 if (infile != NULL) { 242 while (!infile.eof()) { 243 infile >> tmp; 244 infile >> ws; 245 infile >> FindElement((int)tmp)->NoValenceOrbitals; 246 infile >> ws; 247 //cout << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->NoValenceOrbitals << " number of singly occupied valence orbitals." << endl; 248 } 249 infile.close(); 250 infile.clear(); 251 } else 252 otherstatus = false; 253 254 // fill H-BondDistance DB per element 255 strncpy(filename, path, MAXSTRINGSIZE); 256 strncat(filename, "/", MAXSTRINGSIZE-strlen(filename)); 257 strncat(filename, STANDARDHBONDDISTANCEDB, MAXSTRINGSIZE-strlen(filename)); 258 infile.open(filename); 259 if (infile != NULL) { 260 while (!infile.eof()) { 261 infile >> tmp; 262 ptr = FindElement((int)tmp); 263 infile >> ws; 264 infile >> ptr->HBondDistance[0]; 265 infile >> ptr->HBondDistance[1]; 266 infile >> ptr->HBondDistance[2]; 267 infile >> ws; 268 //cout << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->HBondDistance[0] << " Angstrom typical distance to hydrogen." << endl; 269 } 270 infile.close(); 271 infile.clear(); 272 } else 273 otherstatus = false; 274 275 // fill H-BondAngle DB per element 276 strncpy(filename, path, MAXSTRINGSIZE); 277 strncat(filename, "/", MAXSTRINGSIZE-strlen(filename)); 278 strncat(filename, STANDARDHBONDANGLEDB, MAXSTRINGSIZE-strlen(filename)); 279 infile.open(filename); 280 if (infile != NULL) { 281 while (!infile.eof()) { 282 infile >> tmp; 283 ptr = FindElement((int)tmp); 284 infile >> ws; 285 infile >> ptr->HBondAngle[0]; 286 infile >> ptr->HBondAngle[1]; 287 infile >> ptr->HBondAngle[2]; 288 infile >> ws; 289 //cout << Verbose(3) << "Element " << (int)tmp << " has " << FindElement((int)tmp)->HBondAngle[0] << ", " << FindElement((int)tmp)->HBondAngle[1] << ", " << FindElement((int)tmp)->HBondAngle[2] << " degrees bond angle for one, two, three connected hydrogens." << endl; 290 } 291 infile.close(); 292 } else 293 otherstatus = false; 294 295 if (!otherstatus) 296 cerr << "WARNING: Something went wrong while parsing the other databases!" << endl; 297 298 return status; 299 299 }; 300 300 … … 303 303 bool periodentafel::StorePeriodentafel(char *path) const 304 304 { 305 306 307 308 309 310 311 312 313 314 315 316 317 318 319 320 321 322 323 324 325 }; 305 bool result = true; 306 ofstream f; 307 char filename[MAXSTRINGSIZE]; 308 309 strncpy(filename, path, MAXSTRINGSIZE); 310 strncat(filename, "/", MAXSTRINGSIZE-strlen(filename)); 311 strncat(filename, STANDARDELEMENTSDB, MAXSTRINGSIZE-strlen(filename)); 312 f.open(filename); 313 if (f != NULL) { 314 f << header1 << endl; 315 f << header2 << endl; 316 element *walker = periodentafel::start; 317 while (walker->next != periodentafel::end) { 318 walker = walker->next; 319 result = result && walker->Output(&f); 320 } 321 f.close(); 322 } else 323 result = false; 324 return result; 325 };
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