Changeset 43dad6

Timestamp:

Jun 12, 2010, 3:54:26 PM (15 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, 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:

1b2d30

Parents:

a3fded

Message:

Introducing (but not yet incorporated) FormatParser specializations for MPQC and PCP config files.

• new modules MpqcParser.[ch]pp and PcpParser.[ch]pp.
• class MpqcParser:
  • just a skeleton so far
• class PcpParser:
  • load and save basically adapted from config::Load and config::Save.
  • new functions OutputAtoms() and OutputElements() from molecule::Output() and molecule::CheckOut().
  • ne function ParseThermostats() - as the parsing is specific to the format it should be handled by the FormatParser, not bz ThermoStatContainer.
  • most of the variables from config placed into struct to put them into groups (for later splitting up load&save into subfunctions).
• new overload ConfigFileBuffer::InitFileBuffer() accepting streams (FormatParser works on streams, config still with filenames).
• World: new member Thermostats which contains all thermostat parameters with getter function.
• ThermoStatContainer::ParseThermostats() moved over to PcpParser and re-introduced in config.
• atom::OutputArrayIndexed() now works on ostream, not ofstream.
• molecule::Output() adapted to ostream change.

Location:

src

Files:

• ConfigFileBuffer.cpp (modified) (3 diffs)
• ConfigFileBuffer.hpp (modified) (2 diffs)
• Makefile.am (modified) (2 diffs)
• Parser/MpqcParser.cpp (added)
• Parser/MpqcParser.hpp (added)
• Parser/PcpParser.cpp (added)
• Parser/PcpParser.hpp (added)
• ThermoStatContainer.cpp (modified) (1 diff)
• World.cpp (modified) (4 diffs)
• World.hpp (modified) (3 diffs)
• atom.cpp (modified) (1 diff)
• atom.hpp (modified) (1 diff)
• config.cpp (modified) (2 diffs)
• config.hpp (modified) (1 diff)
• molecule.cpp (modified) (1 diff)

src/ConfigFileBuffer.cpp

@@ -64 +64 @@
 void ConfigFileBuffer::InitFileBuffer(const char * const filename)
 {
-  ifstream *file = NULL;
+  ifstream *file= new ifstream(filename);
+  InitFileBuffer(file);
+}
+
+void ConfigFileBuffer::InitFileBuffer(istream *file)
+{
   char line[MAXSTRINGSIZE];
 
@@ -70 +75 @@
 
   // prescan number of lines
-  file= new ifstream(filename);
-  if (file == NULL) {
-    DoeLog(1) && (eLog()<< Verbose(1) << "config file " << filename << " missing!" << endl);
+  if (file->fail()) {
+    DoeLog(1) && (eLog()<< Verbose(1) << "config file missing!" << endl);
     return;
   }
@@ -104 +108 @@
   } while((!file->eof()) && (lines < NoLines));
   DoLog(1) && (Log() << Verbose(1) << lines-1 << " lines were read into the buffer." << endl);
-
-  // close and exit
-  file->close();
-  file->clear();
-  delete(file);
 
   InitMapping();

src/ConfigFileBuffer.hpp

@@ -17 +17 @@
 #endif
 
+#include <iostream>
 
 /****************************************** forward declarations *****************************/
@@ -34 +35 @@
 
     void InitFileBuffer(const char * const filename);
+    void InitFileBuffer(std::istream *file);
     void MapIonTypesInBuffer(const int NoAtoms);
 

src/Makefile.am

@@ -88 +88 @@
   Parser/ChangeTracker.cpp \
   Parser/FormatParser.cpp \
+  Parser/MpqcParser.cpp \
+  Parser/PcpParser.cpp \
   Parser/TremoloParser.cpp \
   Parser/XyzParser.cpp
@@ -94 +96 @@
   Parser/ChangeTracker.hpp \
   Parser/FormatParser.hpp \
+  Parser/MpqcParser.hpp \
+  Parser/PcpParser.hpp \
   Parser/TremoloParser.hpp \
   Parser/XyzParser.hpp

src/ThermoStatContainer.cpp

@@ -51 +51 @@
 
 
-/** Reading of Thermostat related values from parameter file.
- * \param *fb file buffer containing the config file
- */
-void ThermoStatContainer::ParseThermostats(class ConfigFileBuffer * const fb)
-{
-  char * const thermo = new char[12];
-  const int verbose = 0;
-
-  // read desired Thermostat from file along with needed additional parameters
-  if (ParseForParameter(verbose,fb,"Thermostat", 0, 1, 1, string_type, thermo, 1, optional)) {
-    if (strcmp(thermo, ThermostatNames[0]) == 0) { // None
-      if (ThermostatImplemented[0] == 1) {
-        Thermostat = None;
-      } else {
-        DoLog(1) && (Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
-        Thermostat = None;
-      }
-    } else if (strcmp(thermo, ThermostatNames[1]) == 0) { // Woodcock
-      if (ThermostatImplemented[1] == 1) {
-        Thermostat = Woodcock;
-        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, int_type, &ScaleTempStep, 1, critical); // read scaling frequency
-      } else {
-        DoLog(1) && (Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
-        Thermostat = None;
-      }
-    } else if (strcmp(thermo, ThermostatNames[2]) == 0) { // Gaussian
-      if (ThermostatImplemented[2] == 1) {
-        Thermostat = Gaussian;
-        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, int_type, &ScaleTempStep, 1, critical); // read collision rate
-      } else {
-        DoLog(1) && (Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
-        Thermostat = None;
-      }
-    } else if (strcmp(thermo, ThermostatNames[3]) == 0) { // Langevin
-      if (ThermostatImplemented[3] == 1) {
-        Thermostat = Langevin;
-        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)) {
-          DoLog(2) && (Log() << Verbose(2) << "Extended Stochastic Thermostat detected with interpolation coefficient " << alpha << "." << endl);
-        } else {
-          alpha = 1.;
-        }
-      } else {
-        DoLog(1) && (Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
-        Thermostat = None;
-      }
-    } else if (strcmp(thermo, ThermostatNames[4]) == 0) { // Berendsen
-      if (ThermostatImplemented[4] == 1) {
-        Thermostat = Berendsen;
-        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, double_type, &TempFrequency, 1, critical); // read \tau_T
-      } else {
-        DoLog(1) && (Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
-        Thermostat = None;
-      }
-    } else if (strcmp(thermo, ThermostatNames[5]) == 0) { // Nose-Hoover
-      if (ThermostatImplemented[5] == 1) {
-        Thermostat = NoseHoover;
-        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, double_type, &HooverMass, 1, critical); // read Hoovermass
-        alpha = 0.;
-      } else {
-        DoLog(1) && (Log() << Verbose(1) << "Warning: " << ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
-        Thermostat = None;
-      }
-    } else {
-      DoLog(1) && (Log() << Verbose(1) << " Warning: thermostat name was not understood!" << endl);
-      Thermostat = None;
-    }
-  } else {
-    if ((TargetTemp != 0))
-      DoLog(2) && (Log() << Verbose(2) <<  "No thermostat chosen despite finite temperature MD, falling back to None." << endl);
-    Thermostat = None;
-  }
-  delete[](thermo);
-};
-

src/World.cpp

@@ -12 +12 @@
 #include "molecule.hpp"
 #include "periodentafel.hpp"
+#include "ThermoStatContainer.hpp"
 #include "Descriptors/AtomDescriptor.hpp"
 #include "Descriptors/AtomDescriptor_impl.hpp"
@@ -87 +88 @@
   defaultName = name;
 };
+
+class ThermoStatContainer * World::getThermostats()
+{
+  return Thermostats;
+}
+
 
 int World::getExitFlag() {
@@ -278 +285 @@
     periode(new periodentafel),
     configuration(new config),
+    Thermostats(new ThermoStatContainer),
     ExitFlag(0),
     atoms(),
@@ -303 +311 @@
   delete periode;
   delete configuration;
+  delete Thermostats;
   MoleculeSet::iterator molIter;
   for(molIter=molecules.begin();molIter!=molecules.end();++molIter){

src/World.hpp

@@ -30 +30 @@
 
 // forward declarations
-class config;
-class periodentafel;
-class MoleculeListClass;
 class atom;
-class molecule;
 class AtomDescriptor;
 class AtomDescriptor_impl;
+template<typename T> class AtomsCalculation;
+class config;
+class ManipulateAtomsProcess;
+class molecule;
 class MoleculeDescriptor;
 class MoleculeDescriptor_impl;
-class ManipulateAtomsProcess;
-template<typename T>
-class AtomsCalculation;
+class MoleculeListClass;
+class periodentafel;
+class ThermoStatContainer;
 
 /****************************************** forward declarations *****************************/
@@ -142 +142 @@
   void setDefaultName(std::string name);
 
+  /**
+   * get pointer to World's ThermoStatContainer
+   */
+  ThermoStatContainer * getThermostats();
+
   /*
    * get the ExitFlag
@@ -254 +259 @@
   static double *cell_size;
   std::string defaultName;
+  class ThermoStatContainer *Thermostats;
   int ExitFlag;
 public:

src/atom.cpp

@@ -149 +149 @@
   * \return true - \a *out present, false - \a *out is NULL
  */
-bool atom::OutputArrayIndexed(ofstream * const out, const int *ElementNo, int *AtomNo, const char *comment) const
+bool atom::OutputArrayIndexed(ostream * const out, const int *ElementNo, int *AtomNo, const char *comment) const
 {
   AtomNo[type->Z]++;  // increment number

src/atom.hpp

@@ -52 +52 @@
 
   bool OutputIndexed(ofstream * const out, const int ElementNo, const int AtomNo, const char *comment = NULL) const;
-  bool OutputArrayIndexed(ofstream * const out, const int *ElementNo, int *AtomNo, const char *comment = NULL) const;
+  bool OutputArrayIndexed(ostream * const out, const int *ElementNo, int *AtomNo, const char *comment = NULL) const;
   bool OutputXYZLine(ofstream *out) const;
   bool OutputTrajectory(ofstream * const out, const int *ElementNo, int *AtomNo, const int step) const;

src/config.cpp

@@ -614 +614 @@
   
   //TODO: This is actually sensible?: if (MaxOuterStep > 0)
-  Thermostats->ParseThermostats(FileBuffer);
+  ParseThermostats(FileBuffer);
   
   /* Namen einlesen */
@@ -2077 +2077 @@
   return (found); // true if found, false if not
 }
+
+/** Reading of Thermostat related values from parameter file.
+ * \param *fb file buffer containing the config file
+ */
+void config::ParseThermostats(class ConfigFileBuffer * const fb)
+{
+  char * const thermo = new char[12];
+  const int verbose = 0;
+
+  // read desired Thermostat from file along with needed additional parameters
+  if (ParseForParameter(verbose,fb,"Thermostat", 0, 1, 1, string_type, thermo, 1, optional)) {
+    if (strcmp(thermo, Thermostats->ThermostatNames[0]) == 0) { // None
+      if (Thermostats->ThermostatImplemented[0] == 1) {
+        Thermostats->Thermostat = None;
+      } else {
+        DoLog(1) && (Log() << Verbose(1) << "Warning: " << Thermostats->ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
+        Thermostats->Thermostat = None;
+      }
+    } else if (strcmp(thermo, Thermostats->ThermostatNames[1]) == 0) { // Woodcock
+      if (Thermostats->ThermostatImplemented[1] == 1) {
+        Thermostats->Thermostat = Woodcock;
+        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, int_type, &Thermostats->ScaleTempStep, 1, critical); // read scaling frequency
+      } else {
+        DoLog(1) && (Log() << Verbose(1) << "Warning: " << Thermostats->ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
+        Thermostats->Thermostat = None;
+      }
+    } else if (strcmp(thermo, Thermostats->ThermostatNames[2]) == 0) { // Gaussian
+      if (Thermostats->ThermostatImplemented[2] == 1) {
+        Thermostats->Thermostat = Gaussian;
+        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, int_type, &Thermostats->ScaleTempStep, 1, critical); // read collision rate
+      } else {
+        DoLog(1) && (Log() << Verbose(1) << "Warning: " << Thermostats->ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
+        Thermostats->Thermostat = None;
+      }
+    } else if (strcmp(thermo, Thermostats->ThermostatNames[3]) == 0) { // Langevin
+      if (Thermostats->ThermostatImplemented[3] == 1) {
+        Thermostats->Thermostat = Langevin;
+        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, double_type, &Thermostats->TempFrequency, 1, critical); // read gamma
+        if (ParseForParameter(verbose,fb,"Thermostat", 0, 3, 1, double_type, &Thermostats->alpha, 1, optional)) {
+          DoLog(2) && (Log() << Verbose(2) << "Extended Stochastic Thermostat detected with interpolation coefficient " << Thermostats->alpha << "." << endl);
+        } else {
+          Thermostats->alpha = 1.;
+        }
+      } else {
+        DoLog(1) && (Log() << Verbose(1) << "Warning: " << Thermostats->ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
+        Thermostats->Thermostat = None;
+      }
+    } else if (strcmp(thermo, Thermostats->ThermostatNames[4]) == 0) { // Berendsen
+      if (Thermostats->ThermostatImplemented[4] == 1) {
+        Thermostats->Thermostat = Berendsen;
+        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, double_type, &Thermostats->TempFrequency, 1, critical); // read \tau_T
+      } else {
+        DoLog(1) && (Log() << Verbose(1) << "Warning: " << Thermostats->ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
+        Thermostats->Thermostat = None;
+      }
+    } else if (strcmp(thermo, Thermostats->ThermostatNames[5]) == 0) { // Nose-Hoover
+      if (Thermostats->ThermostatImplemented[5] == 1) {
+        Thermostats->Thermostat = NoseHoover;
+        ParseForParameter(verbose,fb,"Thermostat", 0, 2, 1, double_type, &Thermostats->HooverMass, 1, critical); // read Hoovermass
+        Thermostats->alpha = 0.;
+      } else {
+        DoLog(1) && (Log() << Verbose(1) << "Warning: " << Thermostats->ThermostatNames[0] << " thermostat not implemented, falling back to None." << endl);
+        Thermostats->Thermostat = None;
+      }
+    } else {
+      DoLog(1) && (Log() << Verbose(1) << " Warning: thermostat name was not understood!" << endl);
+      Thermostats->Thermostat = None;
+    }
+  } else {
+    if ((Thermostats->TargetTemp != 0))
+      DoLog(2) && (Log() << Verbose(2) <<  "No thermostat chosen despite finite temperature MD, falling back to None." << endl);
+    Thermostats->Thermostat = None;
+  }
+  delete[](thermo);
+};
+

src/config.hpp

@@ -131 +131 @@
   char *GetDefaultPath() const;
   void SetDefaultPath(const char * const path);
+  void ParseThermostats(class ConfigFileBuffer * const fb);
 };
 

src/molecule.cpp

@@ -858 +858 @@
         ElementNo[i] = current++;
     }
-    ActOnAllAtoms( &atom::OutputArrayIndexed, output, (const int *)ElementNo, (int *)AtomNo, (const char *) NULL );
+    ActOnAllAtoms( &atom::OutputArrayIndexed, (ostream * const) output, (const int *)ElementNo, (int *)AtomNo, (const char *) NULL );
     return true;
   }