Changeset ab1932 for src/config.cpp

Timestamp:

Aug 3, 2009, 8:21:05 PM (16 years ago)

Author:

Frederik Heber <heber@…>

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, Candidate_v1.7.0, 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:

03e57a

Parents:

0dbddc (diff), edb93c (diff)
Note: this is a merge changeset, the changes displayed below correspond to the merge itself.
Use the (diff) links above to see all the changes relative to each parent.

Message:

Merge branch 'TesselationRefactoring' into ConcaveHull

Conflicts:

molecuilder/src/boundary.cpp
molecuilder/src/boundary.hpp
molecuilder/src/linkedcell.cpp
molecuilder/src/linkedcell.hpp
molecuilder/src/molecules.hpp

All of Saskia Metzler's new function were transfered from boundary.cpp to tesselation.cpp and the changes due to TesselPoint, LinkedCell and so on incorporated.

File:

• src/config.cpp (modified) (10 diffs)

src/config.cpp

@@ -5 +5 @@
  */
 
-#include "molecules.hpp"
+#include "config.hpp"
 
 /******************************** Functions for class ConfigFileBuffer **********************/
@@ -276 +276 @@
 
 /** Readin of Thermostat related values from parameter file.
- * \param *source parameter file
- */
-void config::InitThermostats(ifstream *source)
+ * \param *fb file buffer containing the config file
+ */
+void config::InitThermostats(class ConfigFileBuffer *fb)
 {
   char *thermo = MallocString(12, "IonsInitRead: thermo");
@@ -284 +284 @@
 
   // read desired Thermostat from file along with needed additional parameters
-  if (ParseForParameter(verbose,source,"Thermostat", 0, 1, 1, string_type, thermo, 1, optional)) {
+  if (ParseForParameter(verbose,fb,"Thermostat", 0, 1, 1, string_type, thermo, 1, optional)) {
     if (strcmp(thermo, ThermostatNames[0]) == 0) { // None
       if (ThermostatImplemented[0] == 1) {
@@ -295 +295 @@
       if (ThermostatImplemented[1] == 1) {
         Thermostat = Woodcock;
-        ParseForParameter(verbose,source,"Thermostat", 0, 2, 1, int_type, &ScaleTempStep, 1, critical); // read scaling frequency
+        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, int_type, &ScaleTempStep, 1, critical); // read scaling frequency
       } else {
         cout << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
@@ -303 +303 @@
       if (ThermostatImplemented[2] == 1) {
         Thermostat = Gaussian;
-        ParseForParameter(verbose,source,"Thermostat", 0, 2, 1, int_type, &ScaleTempStep, 1, critical); // read collision rate
+        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, int_type, &ScaleTempStep, 1, critical); // read collision rate
       } else {
         cout << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
@@ -311 +311 @@
       if (ThermostatImplemented[3] == 1) {
         Thermostat = Langevin;
-        ParseForParameter(verbose,source,"Thermostat", 0, 2, 1, double_type, &TempFrequency, 1, critical); // read gamma
-        if (ParseForParameter(verbose,source,"Thermostat", 0, 3, 1, double_type, &alpha, 1, optional)) {
+        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, double_type, &TempFrequency, 1, critical); // read gamma
+        if (ParseForParameter(verbose,fb,"Thermostat", 0, 3, 1, double_type, &alpha, 1, optional)) {
           cout << Verbose(2) << "Extended Stochastic Thermostat detected with interpolation coefficient " << alpha << "." << endl;
         } else {
@@ -324 +324 @@
       if (ThermostatImplemented[4] == 1) {
         Thermostat = Berendsen;
-        ParseForParameter(verbose,source,"Thermostat", 0, 2, 1, double_type, &TempFrequency, 1, critical); // read \tau_T
+        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, double_type, &TempFrequency, 1, critical); // read \tau_T
       } else {
         cout << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl;
@@ -332 +332 @@
       if (ThermostatImplemented[5] == 1) {
         Thermostat = NoseHoover;
-        ParseForParameter(verbose,source,"Thermostat", 0, 2, 1, double_type, &HooverMass, 1, critical); // read Hoovermass
+        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, double_type, &HooverMass, 1, critical); // read Hoovermass
         alpha = 0.;
       } else {
@@ -704 +704 @@
     return;
   }
+  file->close();
+  delete(file);
   RetrieveConfigPathAndName(filename);
 
@@ -722 +724 @@
   double value[3];
   
-  InitThermostats(file);
+  InitThermostats(FileBuffer);
   
   /* Namen einlesen */