Changeset 41a467

Timestamp:

Nov 3, 2011, 7:44:01 PM (14 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:

ab26c3

Parents:

47d041

git-author:

Frederik Heber <heber@…> (10/27/11 15:08:36)

git-committer:

Frederik Heber <heber@…> (11/03/11 19:44:01)

Message:

LARGE: config class is now just a tiny container.

• this was loooooobg overdue. Config.cpp contained remnants from parsing pcp files and much else. Also fragmentation depended on it. Since refactoring of MoleculeListClass and the fragmentation, we don't need it anymore.
• helper functions ParseForParameters(), LoadMolecule() extracted into new module PcpParser_helper.
• config class now just contains 4 variables that are generally required (especially IsAngstroem) and they should probably remain with the world.
• removed some places where config.hpp was no unnecessarily included.
• Moved ConfigFileBuffer.* over to subfolder src/Parser/ where it rather belongs (associated with PcpParser).

Location:

src

Files:

• Actions/CommandAction/BondLengthTableAction.cpp (modified) (1 diff)
• Actions/FragmentationAction/FragmentationAction.cpp (modified) (1 diff)
• Actions/GraphAction/SubgraphDissectionAction.cpp (modified) (1 diff)
• Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp (modified) (1 diff)
• Actions/MoleculeAction/FillWithMoleculeAction.cpp (modified) (1 diff)
• Actions/MoleculeAction/SaveAdjacencyAction.cpp (modified) (1 diff)
• Actions/MoleculeAction/SaveBondsAction.cpp (modified) (1 diff)
• Actions/MoleculeAction/SuspendInWaterAction.cpp (modified) (2 diffs)
• Dynamics/MinimiseConstrainedPotential.cpp (modified) (1 diff)
• Makefile.am (modified) (2 diffs)
• Parser/ConfigFileBuffer.cpp (moved) (moved from src/ConfigFileBuffer.cpp )
• Parser/ConfigFileBuffer.hpp (moved) (moved from src/ConfigFileBuffer.hpp )
• Parser/Makefile.am (modified) (4 diffs)
• Parser/MpqcParser.cpp (modified) (1 diff)
• Parser/PcpParser.cpp (modified) (1 diff)
• Parser/PcpParser_helper.cpp (added)
• Parser/PcpParser_helper.hpp (added)
• Parser/Psi3Parser.cpp (modified) (3 diffs)
• ThermoStatContainer.cpp (modified) (1 diff)
• Thermostats/Berendsen.cpp (modified) (1 diff)
• Thermostats/GaussianThermostat.cpp (modified) (1 diff)
• Thermostats/Langevin.cpp (modified) (1 diff)
• Thermostats/NoseHoover.cpp (modified) (1 diff)
• Thermostats/Woodcock.cpp (modified) (1 diff)
• UIElements/TextUI/TextWindow.cpp (modified) (1 diff)
• config.cpp (modified) (4 diffs)
• config.hpp (modified) (2 diffs)

src/Actions/CommandAction/BondLengthTableAction.cpp

@@ -24 +24 @@
 #include "CodePatterns/MemDebug.hpp"
 
-#include "Graph/BondGraph.hpp"
-#include "config.hpp"
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
+#include "Graph/BondGraph.hpp"
 #include "World.hpp"
 

src/Actions/FragmentationAction/FragmentationAction.cpp

@@ -21 +21 @@
 
 #include "atom.hpp"
-#include "Graph/BondGraph.hpp"
-#include "config.hpp"
 #include "CodePatterns/Log.hpp"
-#include "CodePatterns/Verbose.hpp"
 #include "Fragmentation/Fragmentation.hpp"
 #include "Fragmentation/HydrogenSaturation_enum.hpp"
 #include "Graph/DepthFirstSearchAnalysis.hpp"
 #include "molecule.hpp"
-#include "Descriptors/MoleculeDescriptor.hpp"
 #include "World.hpp"
 

src/Actions/GraphAction/SubgraphDissectionAction.cpp

@@ -25 +25 @@
 #include "atom.hpp"
 #include "Bond/bond.hpp"
-#include "config.hpp"
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"

src/Actions/MoleculeAction/FillVoidWithMoleculeAction.cpp

@@ -21 +21 @@
 
 #include "atom.hpp"
-#include "Graph/BondGraph.hpp"
-#include "Tesselation/boundary.hpp"
 #include "CodePatterns/Verbose.hpp"
-#include "config.hpp"
 #include "Descriptors/MoleculeIdDescriptor.hpp"
 #include "Descriptors/MoleculeOrderDescriptor.hpp"
+#include "Graph/BondGraph.hpp"
 #include "molecule.hpp"
 #include "MoleculeListClass.hpp"
 #include "Parser/FormatParserInterface.hpp"
 #include "Parser/FormatParserStorage.hpp"
+#include "Tesselation/boundary.hpp"
 #include "World.hpp"
 

src/Actions/MoleculeAction/FillWithMoleculeAction.cpp

@@ -21 +21 @@
 
 #include "atom.hpp"
-#include "Graph/BondGraph.hpp"
-#include "Tesselation/boundary.hpp"
 #include "CodePatterns/Verbose.hpp"
-#include "config.hpp"
 #include "Descriptors/MoleculeIdDescriptor.hpp"
 #include "Descriptors/MoleculeOrderDescriptor.hpp"
+#include "Graph/BondGraph.hpp"
 #include "molecule.hpp"
 #include "MoleculeListClass.hpp"
 #include "Parser/FormatParserInterface.hpp"
 #include "Parser/FormatParserStorage.hpp"
+#include "Tesselation/boundary.hpp"
 #include "World.hpp"
 

src/Actions/MoleculeAction/SaveAdjacencyAction.cpp

@@ -20 +20 @@
 #include "CodePatterns/MemDebug.hpp"
 
-#include "Graph/BondGraph.hpp"
-#include "config.hpp"
-#include "CodePatterns/Log.hpp"
-#include "molecule.hpp"
-#include "CodePatterns/Verbose.hpp"
-#include "World.hpp"
-
 #include <iostream>
 #include <fstream>
 #include <string>
+
+#include "CodePatterns/Log.hpp"
+#include "Graph/BondGraph.hpp"
+#include "molecule.hpp"
+#include "World.hpp"
 
 #include "Actions/MoleculeAction/SaveAdjacencyAction.hpp"

src/Actions/MoleculeAction/SaveBondsAction.cpp

@@ -20 +20 @@
 #include "CodePatterns/MemDebug.hpp"
 
-#include "Graph/BondGraph.hpp"
-#include "config.hpp"
-#include "CodePatterns/Log.hpp"
-#include "molecule.hpp"
-#include "CodePatterns/Verbose.hpp"
-#include "World.hpp"
-
 #include <iostream>
 #include <fstream>
 #include <string>
+
+#include "CodePatterns/Log.hpp"
+#include "Graph/BondGraph.hpp"
+#include "molecule.hpp"
+#include "World.hpp"
 
 #include "Actions/MoleculeAction/SaveBondsAction.hpp"

src/Actions/MoleculeAction/SuspendInWaterAction.cpp

@@ -20 +20 @@
 #include "CodePatterns/MemDebug.hpp"
 
+#include "CodePatterns/Log.hpp"
 #include "Tesselation/boundary.hpp"
-#include "config.hpp"
-#include "CodePatterns/Log.hpp"
-#include "CodePatterns/Verbose.hpp"
 #include "World.hpp"
 
@@ -30 +28 @@
 
 #include "Actions/MoleculeAction/SuspendInWaterAction.hpp"
+
+class config;
 
 using namespace MoleCuilder;

src/Dynamics/MinimiseConstrainedPotential.cpp

@@ -25 +25 @@
 
 #include "atom.hpp"
-#include "config.hpp"
 #include "Element/element.hpp"
 #include "CodePatterns/enumeration.hpp"

src/Makefile.am

@@ -169 +169 @@
   Box.cpp \
   config.cpp \
-  ConfigFileBuffer.cpp \
   Formula.cpp \
   linkedcell.cpp \
@@ -193 +192 @@
   Box.hpp \
   config.hpp \
-  ConfigFileBuffer.hpp \
   Formula.hpp \
   linkedcell.hpp \

src/Parser/Makefile.am

@@ -5 +5 @@
 PARSERSOURCE = \
   Parser/ChangeTracker.cpp \
+  Parser/ConfigFileBuffer.cpp \
   Parser/FormatParser_common.cpp \
   Parser/FormatParser_Parameters.cpp \
@@ -13 +14 @@
   Parser/ParserTypes.cpp \
   Parser/PcpParser.cpp \
+  Parser/PcpParser_helper.cpp \
   Parser/PdbAtomInfoContainer.cpp \
   Parser/PdbParser.cpp \
@@ -23 +25 @@
 PARSERHEADER = \
   Parser/ChangeTracker.hpp \
+  Parser/ConfigFileBuffer.hpp \
   Parser/FormatParser.hpp \
   Parser/FormatParser_specializations_header.hpp \
@@ -37 +40 @@
   Parser/ParserTypes.undef \
   Parser/PcpParser.hpp \
+  Parser/PcpParser_helper.hpp \
   Parser/PdbAtomInfoContainer.hpp \
   Parser/PdbKey.hpp \

src/Parser/MpqcParser.cpp

@@ -28 +28 @@
 
 #include "atom.hpp"
+#include "CodePatterns/Log.hpp"
+#include "CodePatterns/toString.hpp"
 #include "config.hpp"
 #include "Element/element.hpp"
+#include "Element/periodentafel.hpp"
+#include "LinearAlgebra/Vector.hpp"
 #include "molecule.hpp"
 #include "MoleculeListClass.hpp"
-#include "CodePatterns/Log.hpp"
-#include "CodePatterns/toString.hpp"
-#include "CodePatterns/Verbose.hpp"
-#include "LinearAlgebra/Vector.hpp"
-#include "Element/periodentafel.hpp"
 #include "World.hpp"
 

src/Parser/PcpParser.cpp

@@ -23 +23 @@
 #include <iomanip>
 
-//#include "Actions/FragmentationAction/SubgraphDissectionAction.hpp"
 #include "atom.hpp"
-#include "config.hpp"
-#include "ConfigFileBuffer.hpp"
-#include "Element/element.hpp"
+#include "Box.hpp"
 #include "CodePatterns/Assert.hpp"
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
+#include "Element/element.hpp"
+#include "Element/periodentafel.hpp"
 #include "LinearAlgebra/RealSpaceMatrix.hpp"
 #include "molecule.hpp"
 #include "MoleculeListClass.hpp"
 #include "PcpParser.hpp"
-#include "Element/periodentafel.hpp"
+#include "Parser/ConfigFileBuffer.hpp"
+#include "Parser/PcpParser_helper.hpp"
 #include "ThermoStatContainer.hpp"
 #include "World.hpp"
-#include "Box.hpp"
 
 

src/Parser/Psi3Parser.cpp

@@ -28 +28 @@
 
 #include "atom.hpp"
-#include "config.hpp"
+#include "CodePatterns/Log.hpp"
+#include "CodePatterns/toString.hpp"
 #include "Element/element.hpp"
 #include "Element/periodentafel.hpp"
+#include "LinearAlgebra/Vector.hpp"
 #include "molecule.hpp"
 #include "MoleculeListClass.hpp"
-#include "CodePatterns/Log.hpp"
-#include "CodePatterns/toString.hpp"
-#include "CodePatterns/Verbose.hpp"
-#include "LinearAlgebra/Vector.hpp"
 #include "World.hpp"
 
@@ -60 +58 @@
 {}
 
-/** Load an MPQC config file into the World.
+/** Load an PSI3 config file into the World.
  * \param *file input stream
  */
@@ -155 +153 @@
 }
 
-/** Saves all atoms and data into a MPQC config file.
+/** Saves all atoms and data into a PSI3 config file.
  * \param *file output stream
  * \param atoms atoms to store

src/ThermoStatContainer.cpp

@@ -22 +22 @@
 #include <cstring>
 
-#include "ConfigFileBuffer.hpp"
-#include "config.hpp"
 #include "CodePatterns/Log.hpp"
 #include "ThermoStatContainer.hpp"
-#include "CodePatterns/Verbose.hpp"
+#include "Parser/ConfigFileBuffer.hpp"
 
 #include <Thermostats/Berendsen.hpp>

src/Thermostats/Berendsen.cpp

@@ -14 +14 @@
 
 #include "Berendsen.hpp"
+
+#include "CodePatterns/Log.hpp"
+#include "config.hpp"
 #include "Element/element.hpp"
-#include "config.hpp"
-#include "CodePatterns/Verbose.hpp"
-#include "CodePatterns/Log.hpp"
 #include "Helpers/defs.hpp"
+#include "Parser/PcpParser_helper.hpp"
 #include "ThermoStatContainer.hpp"
 #include "World.hpp"

src/Thermostats/GaussianThermostat.cpp

@@ -14 +14 @@
 
 #include "GaussianThermostat.hpp"
+
+#include "AtomSet.hpp"
 #include "CodePatterns/Log.hpp"
-#include "CodePatterns/Verbose.hpp"
+#include "config.hpp"
+#include "Element/element.hpp"
 #include "Helpers/defs.hpp"
 #include "LinearAlgebra/Vector.hpp"
-#include "AtomSet.hpp"
-#include "Element/element.hpp"
-#include "config.hpp"
+#include "Parser/PcpParser_helper.hpp"
 #include "World.hpp"
 

src/Thermostats/Langevin.cpp

@@ -14 +14 @@
 
 #include "Langevin.hpp"
+
+#include "CodePatterns/Log.hpp"
+#include "Parser/PcpParser_helper.hpp"
 #include "Element/element.hpp"
-#include "config.hpp"
-#include "CodePatterns/Verbose.hpp"
-#include "CodePatterns/Log.hpp"
 #include "Helpers/defs.hpp"
 #include "ThermoStatContainer.hpp"

src/Thermostats/NoseHoover.cpp

@@ -15 +15 @@
 #include "NoseHoover.hpp"
 
+#include "CodePatterns/Log.hpp"
+#include "config.hpp"
 #include "Element/element.hpp"
-#include "config.hpp"
-#include "CodePatterns/Verbose.hpp"
-#include "CodePatterns/Log.hpp"
 #include "Helpers/defs.hpp"
+#include "Parser/PcpParser_helper.hpp"
 #include "ThermoStatContainer.hpp"
 #include "World.hpp"

src/Thermostats/Woodcock.cpp

@@ -15 +15 @@
 #include "Woodcock.hpp"
 
+#include "CodePatterns/Log.hpp"
 #include "Element/element.hpp"
-#include "config.hpp"
-#include "CodePatterns/Verbose.hpp"
-#include "CodePatterns/Log.hpp"
 #include "Helpers/defs.hpp"
+#include "Parser/PcpParser_helper.hpp"
 #include "ThermoStatContainer.hpp"
 

src/UIElements/TextUI/TextWindow.cpp

@@ -42 +42 @@
 #include "CodePatterns/Log.hpp"
 #include "CodePatterns/Verbose.hpp"
-
-// all needed due to config::SaveAll()
-#include "config.hpp"
-#include "Element/periodentafel.hpp"
 
 // needed due to Enumerate()

src/config.cpp

@@ -19 +19 @@
 #include "CodePatterns/MemDebug.hpp"
 
-#include <stdio.h>
 #include <cstring>
-#include <iostream>
-#include <boost/tokenizer.hpp>
-#include <string>
 
-#include "atom.hpp"
-#include "Bond/bond.hpp"
-#include "Box.hpp"
-#include "CodePatterns/Info.hpp"
-#include "CodePatterns/Log.hpp"
-#include "CodePatterns/toString.hpp"
-#include "CodePatterns/Verbose.hpp"
 #include "config.hpp"
-#include "ConfigFileBuffer.hpp"
-#include "Element/element.hpp"
-#include "Element/periodentafel.hpp"
-#include "Graph/BondGraph.hpp"
-#include "Helpers/helpers.hpp"
-#include "LinearAlgebra/RealSpaceMatrix.hpp"
-#include "molecule.hpp"
-#include "MoleculeListClass.hpp"
-#include "ThermoStatContainer.hpp"
-#include "World.hpp"
+
+#include "Helpers/defs.hpp"
 
 /************************************* Functions for class config ***************************/
@@ -49 +30 @@
  */
 config::config() :
-  PsiType(0),
-  MaxPsiDouble(0),
-  PsiMaxNoUp(0),
-  PsiMaxNoDown(0),
-  MaxMinStopStep(1),
-  InitMaxMinStopStep(1),
-  ProcPEGamma(8),
-  ProcPEPsi(1),
-  configname(NULL),
+  databasepath(NULL),
+  defaultpath(NULL),
   FastParsing(false),
-  Deltat(0.01),
-  databasepath(NULL),
-  DoConstrainedMD(0),
-  MaxOuterStep(0),
-  mainname(NULL),
-  defaultpath(NULL),
-  pseudopotpath(NULL),
-  DoOutVis(0),
-  DoOutMes(1),
-  DoOutNICS(0),
-  DoOutOrbitals(0),
-  DoOutCurrent(0),
-  DoFullCurrent(0),
-  DoPerturbation(0),
-  DoWannier(0),
-  CommonWannier(0),
-  SawtoothStart(0.01),
-  VectorPlane(0),
-  VectorCut(0.),
-  UseAddGramSch(1),
-  Seed(1),
-  OutVisStep(10),
-  OutSrcStep(5),
-  MaxPsiStep(0),
-  EpsWannier(1e-7),
-  MaxMinStep(100),
-  RelEpsTotalEnergy(1e-7),
-  RelEpsKineticEnergy(1e-5),
-  MaxMinGapStopStep(0),
-  MaxInitMinStep(100),
-  InitRelEpsTotalEnergy(1e-5),
-  InitRelEpsKineticEnergy(1e-4),
-  InitMaxMinGapStopStep(0),
-  ECut(128.),
-  MaxLevel(5),
-  RiemannTensor(0),
-  LevRFactor(0),
-  RiemannLevel(0),
-  Lev0Factor(2),
-  RTActualUse(0),
-  AddPsis(0),
-  RCut(20.),
-  StructOpt(0),
   IsAngstroem(1),
-  RelativeCoord(0),
-  MaxTypes(0)
+  Deltat(0.01)
 {
-  mainname = new char[MAXSTRINGSIZE];
   defaultpath = new char[MAXSTRINGSIZE];
-  pseudopotpath = new char[MAXSTRINGSIZE];
   databasepath = new char[MAXSTRINGSIZE];
-  configname = new char[MAXSTRINGSIZE];
-  strcpy(mainname,"pcp");
-  strcpy(defaultpath,"not specified");
-  strcpy(pseudopotpath,"not specified");
-  configname[0]='\0';
+  strncpy(defaultpath,"not specified", MAXSTRINGSIZE);
 };
 
@@ -121 +45 @@
 config::~config()
 {
-  delete[](mainname);
   delete[](defaultpath);
-  delete[](pseudopotpath);
   delete[](databasepath);
-  delete[](configname);
 };
-
-/** Displays menu for editing each entry of the config file.
- * Nothing fancy here, just lots of std::cout's for the menu and a switch/case
- * for each entry of the config file structure.
- */
-void config::Edit()
-{
-  char choice;
-
-  do {
-    std::cout << "===========EDIT CONFIGURATION============================" << std::endl;
-    std::cout << " A - mainname (prefix for all runtime files)" << std::endl;
-    std::cout << " B - Default path (for runtime files)" << std::endl;
-    std::cout << " C - Path of pseudopotential files" << std::endl;
-    std::cout << " D - Number of coefficient sharing processes" << std::endl;
-    std::cout << " E - Number of wave function sharing processes" << std::endl;
-    std::cout << " F - 0: Don't output density for OpenDX, 1: do" << std::endl;
-    std::cout << " G - 0: Don't output physical data, 1: do" << std::endl;
-    std::cout << " H - 0: Don't output densities of each unperturbed orbital for OpenDX, 1: do" << std::endl;
-    std::cout << " I - 0: Don't output current density for OpenDX, 1: do" << std::endl;
-    std::cout << " J - 0: Don't do the full current calculation, 1: do" << std::endl;
-    std::cout << " K - 0: Don't do perturbation calculation to obtain susceptibility and shielding, 1: do" << std::endl;
-    std::cout << " L - 0: Wannier centres as calculated, 1: common centre for all, 2: unite centres according to spread, 3: cell centre, 4: shifted to nearest grid point" << std::endl;
-    std::cout << " M - Absolute begin of unphysical sawtooth transfer for position operator within cell" << std::endl;
-    std::cout << " N - (0,1,2) x,y,z-plane to do two-dimensional current vector cut" << std::endl;
-    std::cout << " O - Absolute position along vector cut axis for cut plane" << std::endl;
-    std::cout << " P - Additional Gram-Schmidt-Orthonormalization to stabilize numerics" << std::endl;
-    std::cout << " Q - Initial integer value of random number generator" << std::endl;
-    std::cout << " R - for perturbation 0, for structure optimization defines upper limit of iterations" << std::endl;
-    std::cout << " T - Output visual after ...th step" << std::endl;
-    std::cout << " U - Output source densities of wave functions after ...th step" << std::endl;
-    std::cout << " X - minimization iterations per wave function, if unsure leave at default value 0" << std::endl;
-    std::cout << " Y - tolerance value for total spread in iterative Jacobi diagonalization" << std::endl;
-    std::cout << " Z - Maximum number of minimization iterations" << std::endl;
-    std::cout << " a - Relative change in total energy to stop min. iteration" << std::endl;
-    std::cout << " b - Relative change in kinetic energy to stop min. iteration" << std::endl;
-    std::cout << " c - Check stop conditions every ..th step during min. iteration" << std::endl;
-    std::cout << " e - Maximum number of minimization iterations during initial level" << std::endl;
-    std::cout << " f - Relative change in total energy to stop min. iteration during initial level" << std::endl;
-    std::cout << " g - Relative change in kinetic energy to stop min. iteration during initial level" << std::endl;
-    std::cout << " h - Check stop conditions every ..th step during min. iteration during initial level" << std::endl;
-//    std::cout << " j - six lower diagonal entries of matrix, defining the unit cell" << std::endl;
-    std::cout << " k - Energy cutoff of plane wave basis in Hartree" << std::endl;
-    std::cout << " l - Maximum number of levels in multi-level-ansatz" << std::endl;
-    std::cout << " m - Factor by which grid nodes increase between standard and upper level" << std::endl;
-    std::cout << " n - 0: Don't use RiemannTensor, 1: Do" << std::endl;
-    std::cout << " o - Factor by which grid nodes increase between Riemann and standard(?) level" << std::endl;
-    std::cout << " p - Number of Riemann levels" << std::endl;
-    std::cout << " r - 0: Don't Use RiemannTensor, 1: Do" << std::endl;
-    std::cout << " s - 0: Doubly occupied orbitals, 1: Up-/Down-Orbitals" << std::endl;
-    std::cout << " t - Number of orbitals (depends pn SpinType)" << std::endl;
-    std::cout << " u - Number of SpinUp orbitals (depends on SpinType)" << std::endl;
-    std::cout << " v - Number of SpinDown orbitals (depends on SpinType)" << std::endl;
-    std::cout << " w - Number of additional, unoccupied orbitals" << std::endl;
-    std::cout << " x - radial cutoff for ewald summation in Bohrradii" << std::endl;
-    std::cout << " y - 0: Don't do structure optimization beforehand, 1: Do" << std::endl;
-    std::cout << " z - 0: Units are in Bohr radii, 1: units are in Aengstrom" << std::endl;
-    std::cout << " i - 0: Coordinates given in file are absolute, 1: ... are relative to unit cell" << std::endl;
-    std::cout << "=========================================================" << std::endl;
-    std::cout << "INPUT: " << std::endl;
-    cin >> choice;
-
-    switch (choice) {
-        case 'A': // mainname
-          std::cout << "Old: " << config::mainname << "\t new: " << std::endl;
-          cin >> config::mainname;
-          break;
-        case 'B': // defaultpath
-          std::cout << "Old: " << config::defaultpath << "\t new: " << std::endl;
-          cin >> config::defaultpath;
-          break;
-        case 'C': // pseudopotpath
-          std::cout << "Old: " << config::pseudopotpath << "\t new: " << std::endl;
-          cin >> config::pseudopotpath;
-          break;
-
-        case 'D': // ProcPEGamma
-          std::cout << "Old: " << config::ProcPEGamma << "\t new: " << std::endl;
-          cin >> config::ProcPEGamma;
-          break;
-        case 'E': // ProcPEPsi
-          std::cout << "Old: " << config::ProcPEPsi << "\t new: " << std::endl;
-          cin >> config::ProcPEPsi;
-          break;
-        case 'F': // DoOutVis
-          std::cout << "Old: " << config::DoOutVis << "\t new: " << std::endl;
-          cin >> config::DoOutVis;
-          break;
-        case 'G': // DoOutMes
-          std::cout << "Old: " << config::DoOutMes << "\t new: " << std::endl;
-          cin >> config::DoOutMes;
-          break;
-        case 'H': // DoOutOrbitals
-          std::cout << "Old: " << config::DoOutOrbitals << "\t new: " << std::endl;
-          cin >> config::DoOutOrbitals;
-          break;
-        case 'I': // DoOutCurrent
-          std::cout << "Old: " << config::DoOutCurrent << "\t new: " << std::endl;
-          cin >> config::DoOutCurrent;
-          break;
-        case 'J': // DoFullCurrent
-          std::cout << "Old: " << config::DoFullCurrent << "\t new: " << std::endl;
-          cin >> config::DoFullCurrent;
-          break;
-        case 'K': // DoPerturbation
-          std::cout << "Old: " << config::DoPerturbation << "\t new: " << std::endl;
-          cin >> config::DoPerturbation;
-          break;
-        case 'L': // CommonWannier
-          std::cout << "Old: " << config::CommonWannier << "\t new: " << std::endl;
-          cin >> config::CommonWannier;
-          break;
-        case 'M': // SawtoothStart
-          std::cout << "Old: " << config::SawtoothStart << "\t new: " << std::endl;
-          cin >> config::SawtoothStart;
-          break;
-        case 'N': // VectorPlane
-          std::cout << "Old: " << config::VectorPlane << "\t new: " << std::endl;
-          cin >> config::VectorPlane;
-          break;
-        case 'O': // VectorCut
-          std::cout << "Old: " << config::VectorCut << "\t new: " << std::endl;
-          cin >> config::VectorCut;
-          break;
-        case 'P': // UseAddGramSch
-          std::cout << "Old: " << config::UseAddGramSch << "\t new: " << std::endl;
-          cin >> config::UseAddGramSch;
-          break;
-        case 'Q': // Seed
-          std::cout << "Old: " << config::Seed << "\t new: " << std::endl;
-          cin >> config::Seed;
-          break;
-
-        case 'R': // MaxOuterStep
-          std::cout << "Old: " << config::MaxOuterStep << "\t new: " << std::endl;
-          cin >> config::MaxOuterStep;
-          break;
-        case 'T': // OutVisStep
-          std::cout << "Old: " << config::OutVisStep << "\t new: " << std::endl;
-          cin >> config::OutVisStep;
-          break;
-        case 'U': // OutSrcStep
-          std::cout << "Old: " << config::OutSrcStep << "\t new: " << std::endl;
-          cin >> config::OutSrcStep;
-          break;
-        case 'X': // MaxPsiStep
-          std::cout << "Old: " << config::MaxPsiStep << "\t new: " << std::endl;
-          cin >> config::MaxPsiStep;
-          break;
-        case 'Y': // EpsWannier
-          std::cout << "Old: " << config::EpsWannier << "\t new: " << std::endl;
-          cin >> config::EpsWannier;
-          break;
-
-        case 'Z': // MaxMinStep
-          std::cout << "Old: " << config::MaxMinStep << "\t new: " << std::endl;
-          cin >> config::MaxMinStep;
-          break;
-        case 'a': // RelEpsTotalEnergy
-          std::cout << "Old: " << config::RelEpsTotalEnergy << "\t new: " << std::endl;
-          cin >> config::RelEpsTotalEnergy;
-          break;
-        case 'b': // RelEpsKineticEnergy
-          std::cout << "Old: " << config::RelEpsKineticEnergy << "\t new: " << std::endl;
-          cin >> config::RelEpsKineticEnergy;
-          break;
-        case 'c': // MaxMinStopStep
-          std::cout << "Old: " << config::MaxMinStopStep << "\t new: " << std::endl;
-          cin >> config::MaxMinStopStep;
-          break;
-        case 'e': // MaxInitMinStep
-          std::cout << "Old: " << config::MaxInitMinStep << "\t new: " << std::endl;
-          cin >> config::MaxInitMinStep;
-          break;
-        case 'f': // InitRelEpsTotalEnergy
-          std::cout << "Old: " << config::InitRelEpsTotalEnergy << "\t new: " << std::endl;
-          cin >> config::InitRelEpsTotalEnergy;
-          break;
-        case 'g': // InitRelEpsKineticEnergy
-          std::cout << "Old: " << config::InitRelEpsKineticEnergy << "\t new: " << std::endl;
-          cin >> config::InitRelEpsKineticEnergy;
-          break;
-        case 'h': // InitMaxMinStopStep
-          std::cout << "Old: " << config::InitMaxMinStopStep << "\t new: " << std::endl;
-          cin >> config::InitMaxMinStopStep;
-          break;
-
-//        case 'j': // BoxLength
-//          std::cout << "enter lower triadiagonalo form of basis matrix" << std::endl << std::endl;
-//          double * const cell_size = World::getInstance().getDomain();
-//          for (int i=0;i<6;i++) {
-//            std::cout << "Cell size" << i << ": ";
-//            cin >> cell_size[i];
-//          }
-//          break;
-
-        case 'k': // ECut
-          std::cout << "Old: " << config::ECut << "\t new: " << std::endl;
-          cin >> config::ECut;
-          break;
-        case 'l': // MaxLevel
-          std::cout << "Old: " << config::MaxLevel << "\t new: " << std::endl;
-          cin >> config::MaxLevel;
-          break;
-        case 'm': // RiemannTensor
-          std::cout << "Old: " << config::RiemannTensor << "\t new: " << std::endl;
-          cin >> config::RiemannTensor;
-          break;
-        case 'n': // LevRFactor
-          std::cout << "Old: " << config::LevRFactor << "\t new: " << std::endl;
-          cin >> config::LevRFactor;
-          break;
-        case 'o': // RiemannLevel
-          std::cout << "Old: " << config::RiemannLevel << "\t new: " << std::endl;
-          cin >> config::RiemannLevel;
-          break;
-        case 'p': // Lev0Factor
-          std::cout << "Old: " << config::Lev0Factor << "\t new: " << std::endl;
-          cin >> config::Lev0Factor;
-          break;
-        case 'r': // RTActualUse
-          std::cout << "Old: " << config::RTActualUse << "\t new: " << std::endl;
-          cin >> config::RTActualUse;
-          break;
-        case 's': // PsiType
-          std::cout << "Old: " << config::PsiType << "\t new: " << std::endl;
-          cin >> config::PsiType;
-          break;
-        case 't': // MaxPsiDouble
-          std::cout << "Old: " << config::MaxPsiDouble << "\t new: " << std::endl;
-          cin >> config::MaxPsiDouble;
-          break;
-        case 'u': // PsiMaxNoUp
-          std::cout << "Old: " << config::PsiMaxNoUp << "\t new: " << std::endl;
-          cin >> config::PsiMaxNoUp;
-          break;
-        case 'v': // PsiMaxNoDown
-          std::cout << "Old: " << config::PsiMaxNoDown << "\t new: " << std::endl;
-          cin >> config::PsiMaxNoDown;
-          break;
-        case 'w': // AddPsis
-          std::cout << "Old: " << config::AddPsis << "\t new: " << std::endl;
-          cin >> config::AddPsis;
-          break;
-
-        case 'x': // RCut
-          std::cout << "Old: " << config::RCut << "\t new: " << std::endl;
-          cin >> config::RCut;
-          break;
-        case 'y': // StructOpt
-          std::cout << "Old: " << config::StructOpt << "\t new: " << std::endl;
-          cin >> config::StructOpt;
-          break;
-        case 'z': // IsAngstroem
-          std::cout << "Old: " << config::IsAngstroem << "\t new: " << std::endl;
-          cin >> config::IsAngstroem;
-          break;
-        case 'i': // RelativeCoord
-          std::cout << "Old: " << config::RelativeCoord << "\t new: " << std::endl;
-          cin >> config::RelativeCoord;
-          break;
-    };
-  } while (choice != 'q');
-};
-
-/** Tests whether a given configuration file adhears to old or new syntax.
- * \param *filename filename of config file to be tested
- * \param *periode pointer to a periodentafel class with all elements
- * \return 0 - old syntax, 1 - new syntax, -1 - unknown syntax
- */
-int config::TestSyntax(const char * const filename, const periodentafel * const periode) const
-{
-  int test;
-  ifstream file(filename);
-
-  // search file for keyword: ProcPEGamma (new syntax)
-  if (ParseForParameter(1,&file,"ProcPEGamma", 0, 1, 1, int_type, &test, 1, optional)) {
-    file.close();
-    return 1;
-  }
-  // search file for keyword: ProcsGammaPsi (old syntax)
-  if (ParseForParameter(1,&file,"ProcsGammaPsi", 0, 1, 1, int_type, &test, 1, optional)) {
-    file.close();
-    return 0;
-  }
-  file.close();
-  return -1;
-}
 
 /** Returns private config::IsAngstroem.
@@ -424 +57 @@
 };
 
-/** Returns private config::*defaultpath.
- * \return *defaultpath
- */
-char * config::GetDefaultPath() const
-{
-  return defaultpath;
-};
-
-
-/** Returns private config::*defaultpath.
- * \return *defaultpath
- */
-void config::SetDefaultPath(const char * const path)
-{
-  strcpy(defaultpath, path);
-};
-
-/** Loads a molecule from a ConfigFileBuffer.
- * \param *mol molecule to load
- * \param *FileBuffer ConfigFileBuffer to use
- * \param *periode periodentafel for finding elements
- * \param FastParsing whether to parse trajectories or not
- */
-void LoadMolecule(molecule * const &mol, struct ConfigFileBuffer * const &FileBuffer, const periodentafel * const periode, const bool FastParsing)
-{
-  int MaxTypes = 0;
-  const element *elementhash[MAX_ELEMENTS];
-  char name[MAXSTRINGSIZE];
-  int Z = -1;
-  int No[MAX_ELEMENTS];
-  int verbose = DoLog(4);
-  double value[3];
-
-  if (mol == NULL) {
-    ELOG(0, "Molecule is not allocated in LoadMolecule(), exit.");
-    performCriticalExit();
-  }
-
-  ParseForParameter(verbose,FileBuffer,"MaxTypes", 0, 1, 1, int_type, &(MaxTypes), 1, critical);
-  if (MaxTypes == 0) {
-    ELOG(1, "There are no atoms according to MaxTypes in this config file." << endl);
-    //performCriticalExit();
-  } else {
-    // prescan number of ions per type
-    LOG(0, "STATUS: Prescanning ions per type: " << endl);
-    int NoAtoms = 0;
-    for (int i=0; i < MaxTypes; i++) {
-      sprintf(name,"Ion_Type%i",i+1);
-      ParseForParameter(verbose,FileBuffer, (const char*)name, 0, 1, 1, int_type, &No[i], 1, critical);
-      ParseForParameter(verbose,FileBuffer, name, 0, 2, 1, int_type, &Z, 1, critical);
-      elementhash[i] = periode->FindElement(Z);
-      LOG(1, i << ". Z = " << elementhash[i]->getAtomicNumber() << " with " << No[i] << " ions.");
-      NoAtoms += No[i];
-    }
-    int repetition = -1; // which repeated keyword shall be read
-
-    // sort the lines via the LineMapping
-    sprintf(name,"Ion_Type%i",MaxTypes);
-    if (!ParseForParameter(verbose,FileBuffer, (const char*)name, 1, 1, 1, int_type, &value[0], 1, critical)) {
-      ELOG(0, "There are no atoms in the config file!" << endl);
-      performCriticalExit();
-      return;
-    }
-
-    FileBuffer->CurrentLine++;  // skip to next line
-    FileBuffer->MapIonTypesInBuffer(NoAtoms);
-    for (int i=FileBuffer->CurrentLine; i<FileBuffer->NoLines;++i) {
-      LOG(4, FileBuffer->buffer[ FileBuffer->LineMapping[i] ]);
-    }
-
-    map<int, atom *> AtomList[MaxTypes];
-    map<int, atom *> LinearList;
-    atom *neues = NULL;
-    Vector tempVector;
-    int _fixedion;
-
-    typedef boost::tokenizer<boost::char_separator<char> >
-        tokenizer;
-    boost::char_separator<char> sep("\t ");
-    ConvertTo<double> toDouble;
-    ConvertTo<int> toInt;
-
-    for (int i=0; i < MaxTypes; i++) {
-      for(int j=0;j<No[i];j++) {
-        int step = 0;
-        std::stringstream keyword_stream;
-        keyword_stream << "Ion_Type" << i+1 << "_" << j+1;
-        const std::string keyword = keyword_stream.str();
-        LOG(3, "INFO: Parsing for " << keyword << "." << std::endl);
-        while (true) {
-          const std::string line(FileBuffer->buffer[ FileBuffer->LineMapping[FileBuffer->CurrentLine] ]);
-          const std::string line_without_comment = line.substr(0,line.find("#"));
-          tokenizer tokens(line_without_comment, sep);
-          if (tokens.begin() != tokens.end()) {
-            tokenizer::iterator tok_iter = tokens.begin();
-            const std::string token = *tok_iter++;
-            if (token == keyword) {
-              LOG(3, "INFO: Found keyword " << keyword << " in line " << FileBuffer->CurrentLine << std::endl);
-              if (step == 0) {
-                neues = World::getInstance().createAtom();
-                AtomList[i][j] = neues;
-                LOG(4, "Filling LinearList [ (FileBuffer->LineMapping[" << FileBuffer->CurrentLine << "]) = " << FileBuffer->LineMapping[FileBuffer->CurrentLine] << " with " << neues << endl);
-                LinearList[ FileBuffer->LineMapping[FileBuffer->CurrentLine] ] = neues;
-                neues->setType(elementhash[i]); // find element type
-              } else
-                neues = AtomList[i][j];
-
-              // count tokens
-              size_t tokens_size = 0;
-              for (tokenizer::iterator tokiter = tokens.begin(); tokiter != tokens.end(); ++tokiter)
-                ++tokens_size;
-              LOG(3, "INFO: Line contains " << tokens_size << " tokens." << std::endl);
-              // and parse
-              tempVector.Zero();
-              if (tokens_size >= 5) { // only AtomicPosition and FixedIon
-                for (int i=0;i<NDIM;++i)
-                  tempVector[i] = toDouble(*tok_iter++);
-                neues->setPositionAtStep(step, tempVector);
-                _fixedion = toInt(*tok_iter++);
-                neues->setFixedIon(_fixedion == 1);
-                LOG(3, "INFO: Parsing AtomicPosition " << tempVector << " and FixedIon " << _fixedion << "." << std::endl);
-              }
-              tempVector.Zero();
-              if (tokens_size >= 8) { // AtomicVelocity
-                for (int i=0;i<NDIM;++i)
-                  tempVector[i] = toDouble(*tok_iter++);
-                LOG(3, "INFO: Parsing AtomicVelocity " << tempVector << "." << std::endl);
-              }
-              neues->setAtomicVelocityAtStep(step, tempVector);
-              tempVector.Zero();
-              if (tokens_size >= 11) {  // AtomicForce
-                LOG(3, "INFO: Parsing AtomicForce" << std::endl);
-                for (int i=0;i<NDIM;++i)
-                  tempVector[i] = toDouble(*tok_iter++);
-              }
-              neues->setAtomicForceAtStep(step, tempVector);
-              std::stringstream output;
-              output << "Parsed position of step " << (step+1) << ": ";
-              output << neues->getPositionAtStep(step);          // next step
-              output << "\t";
-              output << (neues->getFixedIon() ? "true" : "false");
-              output << "\t";
-              output << neues->getAtomicVelocityAtStep(step);          // next step
-              output << "\t";
-              output << neues->getAtomicForceAtStep(step);          // next step
-              LOG(2, output.str());
-
-              step++;
-            } else {
-              if ((repetition > step) || (repetition == -1))
-                repetition = step;
-              break;
-            }
-          }
-          FileBuffer->CurrentLine++;
-        }
-      }
-    }
-
-    if (repetition <= 1)  // if onyl one step, desactivate use of trajectories
-      mol->MDSteps = 0;
-    else {
-      LOG(0, "Found " << repetition << " trajectory step(s).");
-      mol->MDSteps = repetition;
-    }
-
-    // put atoms into the molecule in their original order
-    for(map<int, atom*>::iterator runner = LinearList.begin(); runner != LinearList.end(); ++runner) {
-      mol->AddAtom(runner->second);
-    }
-  }
-};
-
-/** Stores all elements of config structure from which they can be re-read.
- * \param *filename name of file
- * \param *periode pointer to a periodentafel class with all elements
- * \param *mol pointer to molecule containing all atoms of the molecule
- */
-bool config::Save(const char * const filename, const periodentafel * const periode, molecule * const mol) const
-{
-  bool result = true;
-  const RealSpaceMatrix &domain = World::getInstance().getDomain().getM();
-  ThermoStatContainer *Thermostats = World::getInstance().getThermostats();
-  ofstream * const output = new ofstream(filename, ios::out);
-  if (output != NULL) {
-    *output << "# ParallelCarParinello - main configuration file - created with molecuilder" << endl;
-    *output << endl;
-    *output << "mainname\t" << config::mainname << "\t# programm name (for runtime files)" << endl;
-    *output << "defaultpath\t" << config::defaultpath << "\t# where to put files during runtime" << endl;
-    *output << "pseudopotpath\t" << config::pseudopotpath << "\t# where to find pseudopotentials" << endl;
-    *output << endl;
-    *output << "ProcPEGamma\t" << config::ProcPEGamma << "\t# for parallel computing: share constants" << endl;
-    *output << "ProcPEPsi\t" << config::ProcPEPsi << "\t# for parallel computing: share wave functions" << endl;
-    *output << "DoOutVis\t" << config::DoOutVis << "\t# Output data for OpenDX" << endl;
-    *output << "DoOutMes\t" << config::DoOutMes << "\t# Output data for measurements" << endl;
-    *output << "DoOutOrbitals\t" << config::DoOutOrbitals << "\t# Output all Orbitals" << endl;
-    *output << "DoOutCurr\t" << config::DoOutCurrent << "\t# Ouput current density for OpenDx" << endl;
-    *output << "DoOutNICS\t" << config::DoOutNICS << "\t# Output Nucleus independent current shieldings" << endl;
-    *output << "DoPerturbation\t" << config::DoPerturbation << "\t# Do perturbation calculate and determine susceptibility and shielding" << endl;
-    *output << "DoFullCurrent\t" << config::DoFullCurrent << "\t# Do full perturbation" << endl;
-    *output << "DoConstrainedMD\t" << config::DoConstrainedMD << "\t# Do perform a constrained (>0, relating to current MD step) instead of unconstrained (0) MD" << endl;
-    *output << "Thermostat\t" << Thermostats->activeThermostat->name() << "\t";
-    *output << Thermostats->activeThermostat->writeParams();
-    *output << "\t# Which Thermostat and its parameters to use in MD case." << endl;
-    *output << "CommonWannier\t" << config::CommonWannier << "\t# Put virtual centers at indivual orbits, all common, merged by variance, to grid point, to cell center" << endl;
-    *output << "SawtoothStart\t" << config::SawtoothStart << "\t# Absolute value for smooth transition at cell border " << endl;
-    *output << "VectorPlane\t" << config::VectorPlane << "\t# Cut plane axis (x, y or z: 0,1,2) for two-dim current vector plot" << endl;
-    *output << "VectorCut\t" << config::VectorCut << "\t# Cut plane axis value" << endl;
-    *output << "AddGramSch\t" << config::UseAddGramSch << "\t# Additional GramSchmidtOrtogonalization to be safe" << endl;
-    *output << "Seed\t\t" << config::Seed << "\t# initial value for random seed for Psi coefficients" << endl;
-    *output << endl;
-    *output << "MaxOuterStep\t" << config::MaxOuterStep << "\t# number of MolecularDynamics/Structure optimization steps" << endl;
-    *output << "Deltat\t" << config::Deltat << "\t# time per MD step" << endl;
-    *output << "OutVisStep\t" << config::OutVisStep << "\t# Output visual data every ...th step" << endl;
-    *output << "OutSrcStep\t" << config::OutSrcStep << "\t# Output \"restart\" data every ..th step" << endl;
-    *output << "TargetTemp\t" << Thermostats->TargetTemp << "\t# Target temperature" << endl;
-    *output << "MaxPsiStep\t" << config::MaxPsiStep << "\t# number of Minimisation steps per state (0 - default)" << endl;
-    *output << "EpsWannier\t" << config::EpsWannier << "\t# tolerance value for spread minimisation of orbitals" << endl;
-    *output << endl;
-    *output << "# Values specifying when to stop" << endl;
-    *output << "MaxMinStep\t" << config::MaxMinStep << "\t# Maximum number of steps" << endl;
-    *output << "RelEpsTotalE\t" << config::RelEpsTotalEnergy << "\t# relative change in total energy" << endl;
-    *output << "RelEpsKineticE\t" << config::RelEpsKineticEnergy << "\t# relative change in kinetic energy" << endl;
-    *output << "MaxMinStopStep\t" << config::MaxMinStopStep << "\t# check every ..th steps" << endl;
-    *output << "MaxMinGapStopStep\t" << config::MaxMinGapStopStep << "\t# check every ..th steps" << endl;
-    *output << endl;
-    *output << "# Values specifying when to stop for INIT, otherwise same as above" << endl;
-    *output << "MaxInitMinStep\t" << config::MaxInitMinStep << "\t# Maximum number of steps" << endl;
-    *output << "InitRelEpsTotalE\t" << config::InitRelEpsTotalEnergy << "\t# relative change in total energy" << endl;
-    *output << "InitRelEpsKineticE\t" << config::InitRelEpsKineticEnergy << "\t# relative change in kinetic energy" << endl;
-    *output << "InitMaxMinStopStep\t" << config::InitMaxMinStopStep << "\t# check every ..th steps" << endl;
-    *output << "InitMaxMinGapStopStep\t" << config::InitMaxMinGapStopStep << "\t# check every ..th steps" << endl;
-    *output << endl;
-    *output << "BoxLength\t\t\t# (Length of a unit cell)" << endl;
-    *output << domain.at(0,0) << "\t" << endl;
-    *output << domain.at(1,0) << "\t" << domain.at(1,1) << "\t" << endl;
-    *output << domain.at(2,0) << "\t" << domain.at(2,1) << "\t" << domain.at(2,2) << "\t" << endl;
-    // FIXME
-    *output << endl;
-    *output << "ECut\t\t" << config::ECut << "\t# energy cutoff for discretization in Hartrees" << endl;
-    *output << "MaxLevel\t" << config::MaxLevel << "\t# number of different levels in the code, >=2" << endl;
-    *output << "Level0Factor\t" << config::Lev0Factor << "\t# factor by which node number increases from S to 0 level" << endl;
-    *output << "RiemannTensor\t" << config::RiemannTensor << "\t# (Use metric)" << endl;
-    switch (config::RiemannTensor) {
-      case 0: //UseNoRT
-        break;
-      case 1: // UseRT
-        *output << "RiemannLevel\t" << config::RiemannLevel << "\t# Number of Riemann Levels" << endl;
-        *output << "LevRFactor\t" << config::LevRFactor << "\t# factor by which node number increases from 0 to R level from" << endl;
-        break;
-    }
-    *output << "PsiType\t\t" << config::PsiType << "\t# 0 - doubly occupied, 1 - SpinUp,SpinDown" << endl;
-    // write out both types for easier changing afterwards
-  //  switch (PsiType) {
-  //    case 0:
-        *output << "MaxPsiDouble\t" << config::MaxPsiDouble << "\t# here: specifying both maximum number of SpinUp- and -Down-states" << endl;
-  //      break;
-  //    case 1:
-        *output << "PsiMaxNoUp\t" << config::PsiMaxNoUp << "\t# here: specifying maximum number of SpinUp-states" << endl;
-        *output << "PsiMaxNoDown\t" << config::PsiMaxNoDown << "\t# here: specifying maximum number of SpinDown-states" << endl;
-  //      break;
-  //  }
-    *output << "AddPsis\t\t" << config::AddPsis << "\t# Additional unoccupied Psis for bandgap determination" << endl;
-    *output << endl;
-    *output << "RCut\t\t" << config::RCut << "\t# R-cut for the ewald summation" << endl;
-    *output << "StructOpt\t" << config::StructOpt << "\t# Do structure optimization beforehand" << endl;
-    *output << "IsAngstroem\t" << config::IsAngstroem << "\t# 0 - Bohr, 1 - Angstroem" << endl;
-    *output << "RelativeCoord\t" << config::RelativeCoord << "\t# whether ion coordinates are relative (1) or absolute (0)" << endl;
-    *output << "MaxTypes\t" << mol->getElementCount() <<  "\t# maximum number of different ion types" << endl;
-    *output << endl;
-    result = result && mol->Checkout(output);
-    if (mol->MDSteps <=1 )
-      result = result && mol->Output(output);
-    else
-      result = result && mol->OutputTrajectories(output);
-    output->close();
-    output->clear();
-    delete(output);
-    return result;
-  } else {
-    ELOG(1, "Cannot open output file:" << filename);
-    return false;
-  }
-};
-
-/** Stores all elements in a MPQC input file.
- * Note that this format cannot be parsed again.
- * \param *filename name of file (without ".in" suffix!)
- * \param *mol pointer to molecule containing all atoms of the molecule
- */
-bool config::SaveMPQC(const char * const filename, const molecule * const mol) const
-{
-  Vector *center = NULL;
-  ofstream *output = NULL;
-
-  // first without hessian
-  {
-    stringstream * const fname = new stringstream;;
-    *fname << filename << ".in";
-    output = new ofstream(fname->str().c_str(), ios::out);
-    if (output == NULL) {
-      ELOG(1, "Cannot open mpqc output file:" << fname);
-      delete(fname);
-      return false;
-    }
-    *output << "% Created by MoleCuilder" << endl;
-    *output << "mpqc: (" << endl;
-    *output << "\tsavestate = no" << endl;
-    *output << "\tdo_gradient = yes" << endl;
-    *output << "\tmole<MBPT2>: (" << endl;
-    *output << "\t\tmaxiter = 200" << endl;
-    *output << "\t\tbasis = $:basis" << endl;
-    *output << "\t\tmolecule = $:molecule" << endl;
-    *output << "\t\treference<CLHF>: (" << endl;
-    *output << "\t\t\tbasis = $:basis" << endl;
-    *output << "\t\t\tmolecule = $:molecule" << endl;
-    *output << "\t\t)" << endl;
-    *output << "\t)" << endl;
-    *output << ")" << endl;
-    *output << "molecule<Molecule>: (" << endl;
-    *output << "\tunit = " << (IsAngstroem ? "angstrom" : "bohr" ) << endl;
-    *output << "\t{ atoms geometry } = {" << endl;
-    center = mol->DetermineCenterOfAll();
-    // output of atoms
-    for(molecule::const_iterator iter = mol->begin(); iter!=mol->end();++iter){
-      (*iter)->OutputMPQCLine(output,center);
-    }
-    delete(center);
-    *output << "\t}" << endl;
-    *output << ")" << endl;
-    *output << "basis<GaussianBasisSet>: (" << endl;
-    *output << "\tname = \"3-21G\"" << endl;
-    *output << "\tmolecule = $:molecule" << endl;
-    *output << ")" << endl;
-    output->close();
-    delete(output);
-    delete(fname);
-  }
-
-  // second with hessian
-  {
-    stringstream * const fname = new stringstream;
-    *fname << filename << ".hess.in";
-    output = new ofstream(fname->str().c_str(), ios::out);
-    if (output == NULL) {
-      ELOG(1, "Cannot open mpqc hessian output file:" << fname);
-      delete(fname);
-      return false;
-    }
-    *output << "% Created by MoleCuilder" << endl;
-    *output << "mpqc: (" << endl;
-    *output << "\tsavestate = no" << endl;
-    *output << "\tdo_gradient = yes" << endl;
-    *output << "\tmole<CLHF>: (" << endl;
-    *output << "\t\tmaxiter = 200" << endl;
-    *output << "\t\tbasis = $:basis" << endl;
-    *output << "\t\tmolecule = $:molecule" << endl;
-    *output << "\t)" << endl;
-    *output << "\tfreq<MolecularFrequencies>: (" << endl;
-    *output << "\t\tmolecule=$:molecule" << endl;
-    *output << "\t)" << endl;
-    *output << ")" << endl;
-    *output << "molecule<Molecule>: (" << endl;
-    *output << "\tunit = " << (IsAngstroem ? "angstrom" : "bohr" ) << endl;
-    *output << "\t{ atoms geometry } = {" << endl;
-    center = mol->DetermineCenterOfAll();
-    // output of atoms
-    for(molecule::const_iterator iter = mol->begin(); iter!=mol->end();++iter){
-      (*iter)->OutputMPQCLine(output,center);
-    }
-    delete(center);
-    *output << "\t}" << endl;
-    *output << ")" << endl;
-    *output << "basis<GaussianBasisSet>: (" << endl;
-    *output << "\tname = \"3-21G\"" << endl;
-    *output << "\tmolecule = $:molecule" << endl;
-    *output << ")" << endl;
-    output->close();
-    delete(output);
-    delete(fname);
-  }
-
-  return true;
-};
-
-/** Stores all atoms from all molecules in a PDB input file.
- * Note that this format cannot be parsed again.
- * \param *filename name of file (without ".in" suffix!)
- * \param *MolList pointer to MoleculeListClass containing all atoms
- */
-bool config::SavePDB(const char * const filename, const MoleculeListClass * const MolList) const
-{
-  int AtomNo = -1;
-  int MolNo = 0;
-  FILE *f = NULL;
-
-  char name[MAXSTRINGSIZE];
-  strncpy(name, filename, MAXSTRINGSIZE-1);
-  strncat(name, ".pdb", MAXSTRINGSIZE-(strlen(name)+1));
-  f = fopen(name, "w" );
-  if (f == NULL) {
-    ELOG(1, "Cannot open pdb output file:" << name);
-    return false;
-  }
-  fprintf(f, "# Created by MoleCuilder\n");
-
-  for (MoleculeList::const_iterator MolRunner = MolList->ListOfMolecules.begin(); MolRunner != MolList->ListOfMolecules.end(); MolRunner++) {
-    int *elementNo = new int[MAX_ELEMENTS];
-    for (int i=0;i<MAX_ELEMENTS;i++)
-      elementNo[i] = 0;
-    AtomNo = 0;
-    for (molecule::const_iterator iter = (*MolRunner)->begin(); iter != (*MolRunner)->end(); ++iter) {
-      sprintf(name, "%2s%2d",(*iter)->getType()->getSymbol().c_str(), elementNo[(*iter)->getType()->getAtomicNumber()]);
-      elementNo[(*iter)->getType()->getAtomicNumber()] = (elementNo[(*iter)->getType()->getAtomicNumber()]+1) % 100;   // confine to two digits
-      fprintf(f,
-             "ATOM %6u %-4s %4s%c%4u    %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s%2s\n",
-             (*iter)->getNr(),                /* atom serial number */
-             name,         /* atom name */
-             (*MolRunner)->name,      /* residue name */
-             'a'+(unsigned char)(AtomNo % 26),           /* letter for chain */
-             MolNo,         /* residue sequence number */
-             (*iter)->at(0),                 /* position X in Angstroem */
-             (*iter)->at(1),                 /* position Y in Angstroem */
-             (*iter)->at(2),                 /* position Z in Angstroem */
-             (double)(*iter)->getType()->getValence(),         /* occupancy */
-             (double)(*iter)->getType()->getNoValenceOrbitals(),          /* temperature factor */
-             "0",            /* segment identifier */
-             (*iter)->getType()->getSymbol().c_str(),    /* element symbol */
-             "0");           /* charge */
-      AtomNo++;
-    }
-    delete[](elementNo);
-    MolNo++;
-  }
-  fclose(f);
-
-  return true;
-};
-
-/** Stores all atoms in a PDB input file.
- * Note that this format cannot be parsed again.
- * \param *filename name of file (without ".in" suffix!)
- * \param *mol pointer to molecule
- */
-bool config::SavePDB(const char * const filename, const molecule * const mol) const
-{
-  int AtomNo = -1;
-  FILE *f = NULL;
-
-  int *elementNo = new int[MAX_ELEMENTS];
-  for (int i=0;i<MAX_ELEMENTS;i++)
-    elementNo[i] = 0;
-  char name[MAXSTRINGSIZE];
-  strncpy(name, filename, MAXSTRINGSIZE-1);
-  strncat(name, ".pdb", MAXSTRINGSIZE-(strlen(name)+1));
-  f = fopen(name, "w" );
-  if (f == NULL) {
-    ELOG(1, "Cannot open pdb output file:" << name);
-    delete[](elementNo);
-    return false;
-  }
-  fprintf(f, "# Created by MoleCuilder\n");
-
-  AtomNo = 0;
-  for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-    sprintf(name, "%2s%2d",(*iter)->getType()->getSymbol().c_str(), elementNo[(*iter)->getType()->getAtomicNumber()]);
-    elementNo[(*iter)->getType()->getAtomicNumber()] = (elementNo[(*iter)->getType()->getAtomicNumber()]+1) % 100;   // confine to two digits
-    fprintf(f,
-           "ATOM %6u %-4s %4s%c%4u    %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s%2s\n",
-           (*iter)->getNr(),                /* atom serial number */
-           name,         /* atom name */
-           mol->name,      /* residue name */
-           'a'+(unsigned char)(AtomNo % 26),           /* letter for chain */
-           0,         /* residue sequence number */
-           (*iter)->at(0),                 /* position X in Angstroem */
-           (*iter)->at(1),                 /* position Y in Angstroem */
-           (*iter)->at(2),                 /* position Z in Angstroem */
-           (double)(*iter)->getType()->getValence(),         /* occupancy */
-           (double)(*iter)->getType()->getNoValenceOrbitals(),          /* temperature factor */
-           "0",            /* segment identifier */
-           (*iter)->getType()->getSymbol().c_str(),    /* element symbol */
-           "0");           /* charge */
-    AtomNo++;
-  }
-  fclose(f);
-  delete[](elementNo);
-
-  return true;
-};
-
-/** Stores all atoms in a TREMOLO data input file.
- * Note that this format cannot be parsed again.
- * Note that TREMOLO does not like Id starting at 0, but at 1. Atoms with Id 0 are discarded!
- * \param *filename name of file (without ".in" suffix!)
- * \param *mol pointer to molecule
- */
-bool config::SaveTREMOLO(const char * const filename, const molecule * const mol) const
-{
-  ofstream *output = NULL;
-  stringstream * const fname = new stringstream;
-
-  *fname << filename << ".data";
-  output = new ofstream(fname->str().c_str(), ios::out);
-  if (output == NULL) {
-    ELOG(1, "Cannot open tremolo output file:" << fname);
-    delete(fname);
-    return false;
-  }
-
-  // scan maximum number of neighbours
-  int MaxNeighbours = 0;
-  for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-    const int count = (*iter)->getListOfBonds().size();
-    if (MaxNeighbours < count)
-      MaxNeighbours = count;
-  }
-  *output << "# ATOMDATA Id name resName resSeq x=3 Charge type neighbors=" << MaxNeighbours << endl;
-
-  for (molecule::const_iterator iter = mol->begin(); iter != mol->end(); ++iter) {
-    *output << (*iter)->getNr() << "\t";
-    *output << (*iter)->getName() << "\t";
-    *output << mol->name << "\t";
-    *output << 0 << "\t";
-    *output << (*iter)->at(0) << "\t" << (*iter)->at(1) << "\t" << (*iter)->at(2) << "\t";
-    *output << static_cast<double>((*iter)->getType()->getValence()) << "\t";
-    *output << (*iter)->getType()->getSymbol() << "\t";
-    const BondList& ListOfBonds = (*iter)->getListOfBonds();
-    for (BondList::const_iterator runner = ListOfBonds.begin();
-        runner != ListOfBonds.end();
-        runner++) {
-      *output << (*runner)->GetOtherAtom(*iter)->getNr() << "\t";
-    }
-    for(int i = ListOfBonds.size(); i < MaxNeighbours; i++)
-      *output << "-\t";
-    *output << endl;
-  }
-  output->flush();
-  output->close();
-  delete(output);
-  delete(fname);
-
-  return true;
-};
-
-/** Stores all atoms from all molecules in a TREMOLO data input file.
- * Note that this format cannot be parsed again.
- * Note that TREMOLO does not like Id starting at 0, but at 1. Atoms with Id 0 are discarded!
- * \param *filename name of file (without ".in" suffix!)
- * \param *MolList pointer to MoleculeListClass containing all atoms
- */
-bool config::SaveTREMOLO(const char * const filename, const MoleculeListClass * const MolList) const
-{
-  Info FunctionInfo(__func__);
-  ofstream *output = NULL;
-  stringstream * const fname = new stringstream;
-
-  *fname << filename << ".data";
-  output = new ofstream(fname->str().c_str(), ios::out);
-  if (output == NULL) {
-    ELOG(1, "Cannot open tremolo output file:" << fname);
-    delete(fname);
-    return false;
-  }
-
-  // scan maximum number of neighbours
-  int MaxNeighbours = 0;
-  for (MoleculeList::const_iterator MolWalker = MolList->ListOfMolecules.begin(); MolWalker != MolList->ListOfMolecules.end(); MolWalker++) {
-    for (molecule::const_iterator iter = (*MolWalker)->begin(); iter != (*MolWalker)->end(); ++iter) {
-      const int count = (*iter)->getListOfBonds().size();
-      if (MaxNeighbours < count)
-        MaxNeighbours = count;
-    }
-  }
-  *output << "# ATOMDATA Id name resName resSeq x=3 Charge type neighbors=" << MaxNeighbours << endl;
-
-  // create global to local id map
-  map<int, int> LocalNotoGlobalNoMap;
-  {
-    unsigned int MolCounter = 0;
-    int AtomNo = 1;
-    for (MoleculeList::const_iterator MolWalker = MolList->ListOfMolecules.begin(); MolWalker != MolList->ListOfMolecules.end(); MolWalker++) {
-      for(molecule::iterator AtomRunner = (*MolWalker)->begin(); AtomRunner != (*MolWalker)->end(); ++AtomRunner) {
-        LocalNotoGlobalNoMap.insert( pair<int,int>((*AtomRunner)->getId(), AtomNo++) );
-      }
-      MolCounter++;
-    }
-    ASSERT(MolCounter == MolList->ListOfMolecules.size(), "SaveTREMOLO: LocalNotoGlobalNoMap[] has not been correctly initialized for each molecule");
-  }
-
-  // write the file
-  {
-    int MolCounter = 0;
-    int AtomNo = 0;
-    for (MoleculeList::const_iterator MolWalker = MolList->ListOfMolecules.begin(); MolWalker != MolList->ListOfMolecules.end(); MolWalker++) {
-      for (molecule::const_iterator iter = (*MolWalker)->begin(); iter != (*MolWalker)->end(); ++iter) {
-        *output << LocalNotoGlobalNoMap[ (*iter)->getId() ] << "\t";
-        *output << (*iter)->getName() << "\t";
-        *output << (*MolWalker)->name << "\t";
-        *output << MolCounter+1 << "\t";
-        *output << (*iter)->at(0) << "\t" << (*iter)->at(1) << "\t" << (*iter)->at(2) << "\t";
-        *output << (double)(*iter)->getType()->getValence() << "\t";
-        *output << (*iter)->getType()->getSymbol() << "\t";
-        const BondList& ListOfBonds = (*iter)->getListOfBonds();
-        for (BondList::const_iterator runner = ListOfBonds.begin();
-            runner != ListOfBonds.end();
-            runner++) {
-          *output << LocalNotoGlobalNoMap[ (*runner)->GetOtherAtom((*iter))->getId() ] << "\t";
-        }
-        for(int i = ListOfBonds.size(); i < MaxNeighbours; i++)
-          *output << "-\t";
-        *output << endl;
-        AtomNo++;
-      }
-      MolCounter++;
-    }
-  }
-
-  // store & free
-  output->flush();
-  output->close();
-  delete(output);
-  delete(fname);
-
-  return true;
-};
-
-
-/** Tries given filename or standard on saving the config file.
- * \param *ConfigFileName name of file
- * \param *periode pointer to periodentafel structure with all the elements
- * \param *molecules list of molecules structure with all the atoms and coordinates
- */
-void config::SaveAll(char *ConfigFileName, periodentafel *periode, MoleculeListClass *molecules)
-{
-  char filename[MAXSTRINGSIZE];
-  ofstream output;
-  molecule *mol = NULL;
-
-  // first save as PDB data
-  if (ConfigFileName != NULL)
-    strcpy(filename, ConfigFileName);
-  if (output == NULL)
-    strcpy(filename,"main_pcp_linux");
-  if (SavePDB(filename, molecules))
-    LOG(0, "Saving as pdb input done.");
-  else
-    LOG(0, "Saving as pdb input failed.");
-
-  // then save as tremolo data file
-  if (ConfigFileName != NULL)
-    strcpy(filename, ConfigFileName);
-  if (output == NULL)
-    strcpy(filename,"main_pcp_linux");
-  if (SaveTREMOLO(filename, molecules))
-    LOG(0, "Saving as tremolo data input done.");
-  else
-    LOG(0, "Saving as tremolo data input failed.");
-
-  // translate each to its center and merge all molecules in MoleculeListClass into this molecule
-  int N = molecules->ListOfMolecules.size();
-  if (N != 1) { // don't do anything in case of only one molecule (shifts mol ids otherwise)
-    int *src = new int[N];
-    N=0;
-    for (MoleculeList::iterator ListRunner = molecules->ListOfMolecules.begin(); ListRunner != molecules->ListOfMolecules.end(); ListRunner++) {
-      src[N++] = (*ListRunner)->IndexNr;
-    }
-    mol = World::getInstance().createMolecule();
-    mol->SetNameFromFilename(ConfigFileName);
-    //mol->CalculateOrbitals(*this);
-    delete[](src);
-  } else {
-    if (!molecules->ListOfMolecules.empty()) {
-      mol = *(molecules->ListOfMolecules.begin());
-      mol->doCountAtoms();
-      //mol->CalculateOrbitals(*this);
-    } else {
-      ELOG(1, "There are no molecules to save!");
-    }
-  }
-
-  LOG(0, "Storing configuration ... ");
-  // get correct valence orbitals
-  if (ConfigFileName != NULL) { // test the file name
-    strcpy(filename, ConfigFileName);
-    output.open(filename, ios::trunc);
-  } else if (strlen(configname) != 0) {
-    strcpy(filename, configname);
-    output.open(configname, ios::trunc);
-    } else {
-      strcpy(filename, DEFAULTCONFIG);
-      output.open(DEFAULTCONFIG, ios::trunc);
-    }
-  output.close();
-  output.clear();
-  if (Save(filename, periode, mol))
-    LOG(0, "Saving of config file done.");
-  else
-    LOG(0, "Saving of config file failed.");
-
-  // and save to xyz file
-  if (ConfigFileName != NULL) {
-    strcpy(filename, ConfigFileName);
-    strcat(filename, ".xyz");
-    output.open(filename, ios::trunc);
-  }
-  if (output == NULL) {
-    strcpy(filename,"main_pcp_linux");
-    strcat(filename, ".xyz");
-    output.open(filename, ios::trunc);
-  }
-  if (mol->MDSteps <= 1) {
-    if (mol->OutputXYZ(&output))
-      LOG(0, "Saving of XYZ file done.");
-    else
-      LOG(0, "Saving of XYZ file failed.");
-  } else {
-    if (mol->OutputTrajectoriesXYZ(&output))
-      LOG(0, "Saving of XYZ file done.");
-    else
-      LOG(0, "Saving of XYZ file failed.");
-  }
-  output.close();
-  output.clear();
-
-  // and save as MPQC configuration
-  if (ConfigFileName != NULL)
-    strcpy(filename, ConfigFileName);
-  if (output == NULL)
-    strcpy(filename,"main_pcp_linux");
-  if (SaveMPQC(filename, mol))
-    LOG(0, "Saving as mpqc input done.");
-  else
-    LOG(0, "Saving as mpqc input failed.");
-
-  // don't destroy molecule as it contains all our atoms
-  //World::getInstance().destroyMolecule(mol);
-};
-
-/** Reads parameter from a parsed file.
- * The file is either parsed for a certain keyword or if null is given for
- * the value in row yth and column xth. If the keyword was necessity#critical,
- * then an error is thrown and the programme aborted.
- * \warning value is modified (both in contents and position)!
- * \param verbose 1 - print found value to stderr, 0 - don't
- * \param *file file to be parsed
- * \param name Name of value in file (at least 3 chars!)
- * \param sequential 1 - do not reset file pointer to begin of file, 0 - set to beginning
- *        (if file is sequentially parsed this can be way faster! However, beware of multiple values per line, as whole line is read -
- *         best approach: 0 0 0 1 (not resetted only on last value of line) - and of yth, which is now
- *         counted from this unresetted position!)
- * \param xth Which among a number of parameters it is (in grid case it's row number as grid is read as a whole!)
- * \param yth In grid case specifying column number, otherwise the yth \a name matching line
- * \param type Type of the Parameter to be read
- * \param value address of the value to be read (must have been allocated)
- * \param repetition determines, if the keyword appears multiply in the config file, which repetition shall be parsed, i.e. 1 if not multiply
- * \param critical necessity of this keyword being specified (optional, critical)
- * \return 1 - found, 0 - not found
- * \note Routine is taken from the pcp project and hack-a-slack adapted to C++
- */
-int ParseForParameter(const int verbose, ifstream * const file, const char * const name, const int sequential, const int xth, const int yth, const int type, void * value, const int repetition, const int critical) {
-  int i = 0;
-  int j = 0;  // loop variables
-  int length = 0;
-  int maxlength = -1;
-  long file_position = file->tellg(); // mark current position
-  char *dummy1 = NULL;
-  char *dummy = NULL;
-  char free_dummy[MAXSTRINGSIZE];    // pointers in the line that is read in per step
-  dummy1 = free_dummy;
-
-  //fprintf(stderr,"Parsing for %s\n",name);
-  if (repetition == 0)
-    //Error(SomeError, "ParseForParameter(): argument repetition must not be 0!");
-    return 0;
-
-  int line = 0; // marks line where parameter was found
-  int found = (type >= grid) ? 0 : (-yth + 1);  // marks if yth parameter name was found
-  while((found != repetition)) {
-    dummy1 = dummy = free_dummy;
-    do {
-      file->getline(dummy1, 256); // Read the whole line
-      if (file->eof()) {
-        if ((critical) && (found == 0)) {
-          //Error(InitReading, name);
-          fprintf(stderr,"Error:InitReading, critical %s not found\n", name);
-          exit(255);
-        } else {
-          //if (!sequential)
-          file->clear();
-          file->seekg(file_position, ios::beg);  // rewind to start position
-          return 0;
-        }
-      }
-      line++;
-    } while (dummy != NULL && dummy1 != NULL && ((dummy1[0] == '#') || (dummy1[0] == '\0'))); // skip commentary and empty lines
-
-    // C++ getline removes newline at end, thus re-add
-    if ((dummy1 != NULL) && (strchr(dummy1,'\n') == NULL)) {
-      i = strlen(dummy1);
-      dummy1[i] = '\n';
-      dummy1[i+1] = '\0';
-    }
-    //fprintf(stderr,"line %i ends at %i, newline at %i\n", line, strlen(dummy1), strchr(dummy1,'\n')-free_dummy);
-
-    if (dummy1 == NULL) {
-      if (verbose) fprintf(stderr,"Error reading line %i\n",line);
-    } else {
-      //fprintf(stderr,"Now parsing the line %i: %s\n", line, dummy1);
-    }
-    // Seek for possible end of keyword on line if given ...
-    if (name != NULL) {
-      dummy = strchr(dummy1,'\t');  // set dummy on first tab or space which ever's nearer
-      if (dummy == NULL) {
-        dummy = strchr(dummy1, ' ');  // if not found seek for space
-        while ((dummy != NULL) && ((*dummy == '\t') || (*dummy == ' ')))    // skip some more tabs and spaces if necessary
-          dummy++;
-      }
-      if (dummy == NULL) {
-        dummy = strchr(dummy1, '\n'); // set on line end then (whole line = keyword)
-        //fprintf(stderr,"Error: Cannot find tabs or spaces on line %i in search for %s\n", line, name);
-        //Error(FileOpenParams, NULL);
-      } else {
-        //fprintf(stderr,"found tab at %i\n",(char *)dummy-(char *)dummy1);
-      }
-    } else dummy = dummy1;
-    // ... and check if it is the keyword!
-    //fprintf(stderr,"name %p, dummy %i/%c, dummy1 %i/%c, strlen(name) %i\n", &name, dummy, *dummy, dummy1, *dummy1, strlen(name));
-    if ((name == NULL) || (((dummy-dummy1 >= 3) && (strncmp(dummy1, name, strlen(name)) == 0)) && ((unsigned int)(dummy-dummy1) == strlen(name)))) {
-      found++; // found the parameter!
-      //fprintf(stderr,"found %s at line %i between %i and %i\n", name, line, dummy1, dummy);
-
-      if (found == repetition) {
-        for (i=0;i<xth;i++) { // i = rows
-          if (type >= grid) {
-            // grid structure means that grid starts on the next line, not right after keyword
-            dummy1 = dummy = free_dummy;
-            do {
-              file->getline(dummy1, 256); // Read the whole line, skip commentary and empty ones
-              if (file->eof()) {
-                if ((critical) && (found == 0)) {
-                  //Error(InitReading, name);
-                  fprintf(stderr,"Error:InitReading, critical %s not found\n", name);
-                  exit(255);
-                } else {
-                  //if (!sequential)
-                  file->clear();
-                  file->seekg(file_position, ios::beg);  // rewind to start position
-                  return 0;
-                }
-              }
-              line++;
-            } while ((dummy1[0] == '#') || (dummy1[0] == '\n'));
-            if (dummy1 == NULL){
-              if (verbose) fprintf(stderr,"Error reading line %i\n", line);
-            } else {
-              //fprintf(stderr,"Reading next line %i: %s\n", line, dummy1);
-            }
-          } else { // simple int, strings or doubles start in the same line
-            while ((*dummy == '\t') || (*dummy == ' '))   // skip interjacent tabs and spaces
-              dummy++;
-          }
-          // C++ getline removes newline at end, thus re-add
-          if ((dummy1 != NULL) && (strchr(dummy1,'\n') == NULL)) {
-            j = strlen(dummy1);
-            dummy1[j] = '\n';
-            dummy1[j+1] = '\0';
-          }
-
-          int start = (type >= grid) ? 0 : yth-1 ;
-          for (j=start;j<yth;j++) { // j = columns
-            // check for lower triangular area and upper triangular area
-            if ( ((i > j) && (type == upper_trigrid)) || ((j > i) && (type == lower_trigrid))) {
-              *((double *)value) = 0.0;
-              fprintf(stderr,"%f\t",*((double *)value));
-              value = (void *)((long)value + sizeof(double));
-              //value += sizeof(double);
-            } else {
-              // otherwise we must skip all interjacent tabs and spaces and find next value
-              dummy1 = dummy;
-              dummy = strchr(dummy1, '\t'); // seek for tab or space
-              if (dummy == NULL)
-                dummy = strchr(dummy1, ' ');  // if not found seek for space
-              if (dummy == NULL) { // if still zero returned ...
-                dummy = strchr(dummy1, '\n');  // ... at line end then
-                if ((j < yth-1) && (type < 4)) {  // check if xth value or not yet
-                  if (critical) {
-                    if (verbose) fprintf(stderr,"Error: EoL at %i and still missing %i value(s) for parameter %s\n", line, yth-j, name);
-                    //return 0;
-                    exit(255);
-                    //Error(FileOpenParams, NULL);
-                  } else {
-                    //if (!sequential)
-                    file->clear();
-                    file->seekg(file_position, ios::beg);  // rewind to start position
-                    return 0;
-                  }
-                }
-              } else {
-                //fprintf(stderr,"found tab at %i\n",(char *)dummy-(char *)free_dummy);
-              }
-              if (*dummy1 == '#') {
-                // found comment, skipping rest of line
-                //if (verbose) fprintf(stderr,"Error: '#' at %i and still missing %i value(s) for parameter %s\n", line, yth-j, name);
-                if (!sequential) { // here we need it!
-                  file->seekg(file_position, ios::beg);  // rewind to start position
-                }
-                return 0;
-              }
-              //fprintf(stderr,"value from %i to %i\n",(char *)dummy1-(char *)free_dummy,(char *)dummy-(char *)free_dummy);
-              switch(type) {
-                case (row_int):
-                  *((int *)value) = atoi(dummy1);
-                  if ((verbose) && (i==0) && (j==0)) fprintf(stderr,"%s = ", name);
-                  if (verbose) fprintf(stderr,"%i\t",*((int *)value));
-                    value = (void *)((long)value + sizeof(int));
-                    //value += sizeof(int);
-                  break;
-                case(row_double):
-                case(grid):
-                case(lower_trigrid):
-                case(upper_trigrid):
-                  *((double *)value) = atof(dummy1);
-                  if ((verbose) && (i==0) && (j==0)) fprintf(stderr,"%s = ", name);
-                  if (verbose) fprintf(stderr,"%lg\t",*((double *)value));
-                  value = (void *)((long)value + sizeof(double));
-                  //value += sizeof(double);
-                  break;
-                case(double_type):
-                  *((double *)value) = atof(dummy1);
-                  if ((verbose) && (i == xth-1)) fprintf(stderr,"%s = %lg\n", name, *((double *) value));
-                  //value += sizeof(double);
-                  break;
-                case(int_type):
-                  *((int *)value) = atoi(dummy1);
-                  if ((verbose) && (i == xth-1)) fprintf(stderr,"%s = %i\n", name, *((int *) value));
-                  //value += sizeof(int);
-                  break;
-                default:
-                case(string_type):
-                  if (value != NULL) {
-                    //if (maxlength == -1) maxlength = strlen((char *)value); // get maximum size of string array
-                    maxlength = MAXSTRINGSIZE;
-                    length = maxlength > (dummy-dummy1) ? (dummy-dummy1) : maxlength; // cap at maximum
-                    strncpy((char *)value, dummy1, length);  // copy as much
-                    ((char *)value)[length] = '\0';  // and set end marker
-                    if ((verbose) && (i == xth-1)) fprintf(stderr,"%s is '%s' (%i chars)\n",name,((char *) value), length);
-                    //value += sizeof(char);
-                  } else {
-                  }
-                break;
-              }
-            }
-            while (*dummy == '\t')
-              dummy++;
-          }
-        }
-      }
-    }
-  }
-  if ((type >= row_int) && (verbose))
-    fprintf(stderr,"\n");
-  if (!sequential) {
-    file->clear();
-    file->seekg(file_position, ios::beg);  // rewind to start position
-  }
-  //fprintf(stderr, "End of Parsing\n\n");
-
-  return (found); // true if found, false if not
-}
-
-
-/** Reads parameter from a parsed file.
- * The file is either parsed for a certain keyword or if null is given for
- * the value in row yth and column xth. If the keyword was necessity#critical,
- * then an error is thrown and the programme aborted.
- * \warning value is modified (both in contents and position)!
- * \param verbose 1 - print found value to stderr, 0 - don't
- * \param *FileBuffer pointer to buffer structure
- * \param name Name of value in file (at least 3 chars!)
- * \param sequential 1 - do not reset file pointer to begin of file, 0 - set to beginning
- *        (if file is sequentially parsed this can be way faster! However, beware of multiple values per line, as whole line is read -
- *         best approach: 0 0 0 1 (not resetted only on last value of line) - and of yth, which is now
- *         counted from this unresetted position!)
- * \param xth Which among a number of parameters it is (in grid case it's row number as grid is read as a whole!)
- * \param yth In grid case specifying column number, otherwise the yth \a name matching line
- * \param type Type of the Parameter to be read
- * \param value address of the value to be read (must have been allocated)
- * \param repetition determines, if the keyword appears multiply in the config file, which repetition shall be parsed, i.e. 1 if not multiply
- * \param critical necessity of this keyword being specified (optional, critical)
- * \return 1 - found, 0 - not found
- * \note Routine is taken from the pcp project and hack-a-slack adapted to C++
- */
-int ParseForParameter(const int verbose, struct ConfigFileBuffer * const FileBuffer, const char * const name, const int sequential, const int xth, const int yth, const int type, void * value, const int repetition, const int critical) {
-  int i = 0;
-  int j = 0;  // loop variables
-  int length = 0;
-  int maxlength = -1;
-  int OldCurrentLine = FileBuffer->CurrentLine;
-  char *dummy1 = NULL;
-  char *dummy = NULL;    // pointers in the line that is read in per step
-  char *free_dummy = NULL;
-
-  if (verbose) fprintf(stderr,"Begin of Parsing for %s\n",name);
-  if (repetition == 0)
-    //Error(SomeError, "ParseForParameter(): argument repetition must not be 0!");
-    return 0;
-
-  int found = (type >= grid) ? 0 : (-yth + 1);  // marks if yth parameter name was found
-  while((found != repetition)) {
-    dummy1 = dummy = NULL;
-    do {
-      if (FileBuffer->CurrentLine < FileBuffer->NoLines)
-        free_dummy = dummy1 = FileBuffer->buffer[ FileBuffer->LineMapping[FileBuffer->CurrentLine++] ];
-      if (FileBuffer->CurrentLine >= FileBuffer->NoLines) {
-        if ((critical) && (found == 0)) {
-          //Error(InitReading, name);
-          fprintf(stderr,"Error:InitReading, critical %s not found\n", name);
-          return 0;
-        } else {
-          //fprintf(stdout,"Rewinding to OldCurrentLine due to search till end of file.\n");
-          FileBuffer->CurrentLine = OldCurrentLine; // rewind to start position
-          return 0;
-        }
-      }
-      if (dummy1 == NULL) {
-        if (verbose) fprintf(stderr,"Error reading line %i\n",FileBuffer->CurrentLine);
-      } else {
-        if (verbose) fprintf(stderr,"Now parsing the line %i: %s\n", FileBuffer->CurrentLine, dummy1);
-      }
-      //FileBuffer->CurrentLine++;
-    } while (dummy1 != NULL && ((dummy1[0] == '#') || (dummy1[0] == '\0'))); // skip commentary and empty lines
-
-    // Seek for possible end of keyword on line if given ...
-    if (name != NULL) {
-      dummy = strchr(dummy1,'\t');  // set dummy on first tab or space which ever's nearer
-      if (dummy == NULL) {
-        dummy = strchr(dummy1, ' ');  // if not found seek for space
-        while ((dummy != NULL) && ((*dummy == '\t') || (*dummy == ' ')))    // skip some more tabs and spaces if necessary
-          dummy++;
-      }
-      if (dummy == NULL) {
-        dummy = strchr(dummy1, '\n'); // set on line end then (whole line = keyword)
-        //fprintf(stderr,"Error: Cannot find tabs or spaces on line %i in search for %s\n", line, name);
-        //Error(FileOpenParams, NULL);
-      } else {
-        if (verbose) fprintf(stderr,"found tab at line %i at position %li\n",FileBuffer->CurrentLine, (char *)dummy-(char *)dummy1);
-      }
-    } else dummy = dummy1;
-    // ... and check if it is the keyword!
-    //fprintf(stderr,"name %p, dummy %i/%c, dummy1 %i/%c, strlen(name) %i\n", &name, dummy, *dummy, dummy1, *dummy1, strlen(name));
-    if ((name == NULL) || (((dummy-dummy1 >= 3) && (strncmp(dummy1, name, strlen(name)) == 0)) && ((unsigned int)(dummy-dummy1) == strlen(name)))) {
-      found++; // found the parameter!
-      if (verbose) fprintf(stderr,"found %s at line %i between %li and %li\n", name, FileBuffer->CurrentLine, (unsigned long)dummy1, (unsigned long)dummy);
-
-      if (found == repetition) {
-        for (i=0;i<xth;i++) { // i = rows
-          if (type >= grid) {
-            // grid structure means that grid starts on the next line, not right after keyword
-            dummy1 = dummy = NULL;
-            do {
-              dummy1 = FileBuffer->buffer[ FileBuffer->LineMapping[ FileBuffer->CurrentLine++] ];
-              if (FileBuffer->CurrentLine >= FileBuffer->NoLines) {
-                if ((critical) && (found == 0)) {
-                  //Error(InitReading, name);
-                  fprintf(stderr,"Error:InitReading, critical %s not found\n", name);
-                  exit(255);
-                } else {
-                  //fprintf(stdout,"Rewinding to OldCurrentLine due to search till end of line.\n");
-                  FileBuffer->CurrentLine = OldCurrentLine; // rewind to start position
-                  return 0;
-                }
-              }
-              if (dummy1 == NULL) {
-                if (verbose) fprintf(stderr,"Error reading line %i\n", FileBuffer->CurrentLine);
-              } else {
-                if (verbose) fprintf(stderr,"Reading next line %i: %s\n", FileBuffer->CurrentLine, dummy1);
-              }
-              //FileBuffer->CurrentLine++;
-            } while ((dummy1 != NULL) && ((dummy1[0] == '#') || (dummy1[0] == '\n')));
-            dummy = dummy1;
-          } else { // simple int, strings or doubles start in the same line
-            while ((*dummy == '\t') || (*dummy == ' '))  // skip interjacent tabs and spaces
-              dummy++;
-          }
-
-          for (j=((type >= grid) ? 0 : yth-1);j<yth;j++) { // j = columns
-            // check for lower triangular area and upper triangular area
-            if ( ((i > j) && (type == upper_trigrid)) || ((j > i) && (type == lower_trigrid))) {
-              *((double *)value) = 0.0;
-              fprintf(stderr,"%f\t",*((double *)value));
-              value = (void *)((long)value + sizeof(double));
-              //value += sizeof(double);
-            } else {
-              // otherwise we must skip all interjacent tabs and spaces and find next value
-              dummy1 = dummy;
-              dummy = strchr(dummy1, '\t'); // seek for tab or space
-              if (dummy == NULL)
-                dummy = strchr(dummy1, ' ');  // if not found seek for space
-              if (dummy == NULL) { // if still zero returned ...
-                dummy = strchr(dummy1, '\n'); // ... at line end then
-                if ((j < yth-1) && (type < 4)) {  // check if xth value or not yet
-                  if (critical) {
-                    if (verbose) fprintf(stderr,"Error: EoL at %i and still missing %i value(s) for parameter %s\n", FileBuffer->CurrentLine, yth-j, name);
-                    //return 0;
-                    exit(255);
-                    //Error(FileOpenParams, NULL);
-                  } else {
-                    if (!sequential) { // here we need it!
-                      //fprintf(stdout,"Rewinding to OldCurrentLine due to end of line and sequential %d.\n", sequential);
-                      FileBuffer->CurrentLine = OldCurrentLine; // rewind to start position
-                    }
-                    return 0;
-                  }
-                }
-              } else {
-                if (verbose) fprintf(stderr,"found tab at line %i at position %li\n",FileBuffer->CurrentLine, (char *)dummy-(char *)free_dummy);
-              }
-              if (*dummy1 == '#') {
-                // found comment, skipping rest of line
-                //if (verbose) fprintf(stderr,"Error: '#' at %i and still missing %i value(s) for parameter %s\n", line, yth-j, name);
-                if (!sequential) { // here we need it!
-                  //fprintf(stdout,"Rewinding to OldCurrentLine due to comment and sequential %d.\n", sequential);
-                  FileBuffer->CurrentLine = OldCurrentLine; // rewind to start position
-                }
-                return 0;
-              }
-              if (verbose) fprintf(stderr,"value from %li to %li\n",(char *)dummy1-(char *)free_dummy,(char *)dummy-(char *)free_dummy);
-              switch(type) {
-                case (row_int):
-                  *((int *)value) = atoi(dummy1);
-                  if ((verbose) && (i==0) && (j==0)) fprintf(stderr,"%s = ", name);
-                  if (verbose) fprintf(stderr,"%i\t",*((int *)value));
-                    value = (void *)((long)value + sizeof(int));
-                    //value += sizeof(int);
-                  break;
-                case(row_double):
-                case(grid):
-                case(lower_trigrid):
-                case(upper_trigrid):
-                  *((double *)value) = atof(dummy1);
-                  if ((verbose) && (i==0) && (j==0)) fprintf(stderr,"%s = ", name);
-                  if (verbose) fprintf(stderr,"%lg\t",*((double *)value));
-                  value = (void *)((long)value + sizeof(double));
-                  //value += sizeof(double);
-                  break;
-                case(double_type):
-                  *((double *)value) = atof(dummy1);
-                  if ((verbose) && (i == xth-1)) fprintf(stderr,"%s = %lg\n", name, *((double *) value));
-                  //value += sizeof(double);
-                  break;
-                case(int_type):
-                  *((int *)value) = atoi(dummy1);
-                  if ((verbose) && (i == xth-1)) fprintf(stderr,"%s = %i\n", name, *((int *) value));
-                  //value += sizeof(int);
-                  break;
-                default:
-                case(string_type):
-                  if (value != NULL) {
-                    //if (maxlength == -1) maxlength = strlen((char *)value); // get maximum size of string array
-                    maxlength = MAXSTRINGSIZE;
-                    length = maxlength > (dummy-dummy1) ? (dummy-dummy1) : maxlength; // cap at maximum
-                    strncpy((char *)value, dummy1, length); // copy as much
-                    ((char *)value)[length] = '\0'; // and set end marker
-                    if ((verbose) && (i == xth-1)) fprintf(stderr,"%s is '%s' (%i chars)\n",name,((char *) value), length);
-                    //value += sizeof(char);
-                  } else {
-                  }
-                break;
-              }
-            }
-            while (*dummy == '\t')
-              dummy++;
-          }
-        }
-      }
-    }
-  }
-  if ((type >= row_int) && (verbose)) fprintf(stderr,"\n");
-  if (!sequential) {
-    //fprintf(stdout,"Rewinding to OldCurrentLine due to sequential %d.\n", sequential);
-    FileBuffer->CurrentLine = OldCurrentLine; // rewind to start position
-  }
-  if (verbose) fprintf(stderr, "End of Parsing for %s\n\n",name);
-
-  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;
-  ThermoStatContainer *Thermostats = World::getInstance().getThermostats();
-
-  // read desired Thermostat from file along with needed additional parameters
-  if (ParseForParameter(verbose,fb,"Thermostat", 0, 1, 1, string_type, thermo, 1, optional)) {
-    Thermostats->makeActive(thermo,fb);
-  } else {
-    if ((Thermostats->TargetTemp != 0))
-      LOG(2,  "No thermostat chosen despite finite temperature MD, falling back to None.");
-    Thermostats->chooseNone();
-  }
-  delete[](thermo);
-};
-

src/config.hpp

@@ -9 +9 @@
 #define CONFIG_HPP_
 
-using namespace std;
-
-/*********************************************** includes ***********************************/
-
 // include config.h
 #ifdef HAVE_CONFIG_H
@@ -18 +14 @@
 #endif
 
-#include <string>
-
-/****************************************** forward declarations *****************************/
-
-class ConfigFileBuffer;
-class molecule;
-class MoleculeListClass;
-class periodentafel;
-
-/********************************************** declarations *******************************/
-
 /** The config file.
- * The class contains all parameters that control a dft run also functions to load and save.
+ * The class contains some general parameters.
  */
 class config {
   public:
+    config();
+    ~config();
 
-    int PsiType;
-    int MaxPsiDouble;
-    int PsiMaxNoUp;
-    int PsiMaxNoDown;
-    int MaxMinStopStep;
-    int InitMaxMinStopStep;
-    int ProcPEGamma;
-    int ProcPEPsi;
-    char *configname;
+    char *databasepath;
+    char *defaultpath;
     bool FastParsing;
+    int IsAngstroem;
     double Deltat;
 
-    char *databasepath;
-
-    int DoConstrainedMD;
-    int MaxOuterStep;
-
-  private:
-    char *mainname;
-    char *defaultpath;
-    char *pseudopotpath;
-
-    int DoOutVis;
-    int DoOutMes;
-    int DoOutNICS;
-    int DoOutOrbitals;
-    int DoOutCurrent;
-    int DoFullCurrent;
-    int DoPerturbation;
-    int DoWannier;
-    int CommonWannier;
-    double SawtoothStart;
-    int VectorPlane;
-    double VectorCut;
-    int UseAddGramSch;
-    int Seed;
-
-    int OutVisStep;
-    int OutSrcStep;
-    int MaxPsiStep;
-    double EpsWannier;
-
-    int MaxMinStep;
-    double RelEpsTotalEnergy;
-    double RelEpsKineticEnergy;
-    int MaxMinGapStopStep;
-    int MaxInitMinStep;
-    double InitRelEpsTotalEnergy;
-    double InitRelEpsKineticEnergy;
-    int InitMaxMinGapStopStep;
-
-    //double BoxLength[NDIM*NDIM];
-
-    double ECut;
-    int MaxLevel;
-    int RiemannTensor;
-    int LevRFactor;
-    int RiemannLevel;
-    int Lev0Factor;
-    int RTActualUse;
-    int AddPsis;
-
-    double RCut;
-    int StructOpt;
-    int IsAngstroem;
-    int RelativeCoord;
-    int MaxTypes;
+  bool GetIsAngstroem() const;
+};
 
 
-  public:
-  config();
-  ~config();
-
-  int TestSyntax(const char * const filename, const periodentafel * const periode) const;
-  bool Save(const char * const filename, const periodentafel * const periode, molecule * const mol) const;
-  bool SaveMPQC(const char * const filename, const molecule * const mol) const;
-  bool SavePDB(const char * const filename, const MoleculeListClass * const MolList) const;
-  bool SavePDB(const char * const filename, const molecule * const mol) const;
-  bool SaveTREMOLO(const char * const filename, const molecule * const mol) const;
-  bool SaveTREMOLO(const char * const filename, const MoleculeListClass * const MolList) const;
-
-  void SaveAll(char *ConfigFileName, periodentafel *periode, MoleculeListClass *molecules);
-
-  void Edit();
-  bool GetIsAngstroem() const;
-  char *GetDefaultPath() const;
-  void SetDefaultPath(const char * const path);
-  void ParseThermostats(class ConfigFileBuffer * const fb);
-};
-
-int ParseForParameter(const int verbose, ifstream * const file, const char * const name, const int sequential, const int xth, const int yth, const int type, void * value, const int repetition, const int critical);
-int ParseForParameter(const int verbose, struct ConfigFileBuffer * const FileBuffer, const char * const name, const int sequential, const int xth, const int yth, const int type, void * value, const int repetition, const int critical);
-void LoadMolecule(molecule * const &mol, struct ConfigFileBuffer * const &FileBuffer, const periodentafel * const periode, const bool FastParsing);
-void PrepareFileBuffer(const char * const filename, struct ConfigFileBuffer *&FileBuffer);
-
 #endif /* CONFIG_HPP_ */