Input file

This should not have been a single commit.

Now we have input files.

Also, I've restructured the code and renamed modules.

.gitignore

@@ -4,3 +4,5 @@ vlaplex
 *.mod
 *.o
 *.tar.gz
+obj/
+mod/

input/input_80ns_T10.nml

@@ -0,0 +1,33 @@
+&reference
+  m_ref    = 1.9712258e-25 ! Ion mass [kg]
+  Temp_ref = 30.0          ! Plasma temperature [eV]
+  n_ref    = 1.0e24        ! Plasma density [m^-3]
+/
+
+&grid
+  r0 = 10.0e-6 ! Initial position [m]
+  rf =  2.0e-3 ! Final position [m]
+  dr =  1.0e-6 ! Spatial step [m]
+  v0 =  -80e3  ! Lower limit for velocity space [m s^-1]
+  vf =  240e3  ! Upper limit for velocity space [m s^-1]
+  nv = 301     ! Number of grid points in the velocity space
+/
+
+&time
+  t0  = 0.0    ! Initial time [s]
+  tf  = 3.0e-7 ! Final time [s]
+  cfl = 0.5    ! CFL condition (dt = CFL * dr / vf)
+/
+
+&detector
+  rCum = 1.0e-3 ! Position of the detector [m]
+/
+
+&boundary
+  filename = 'data/boundary/bc_80ns_T10.csv' ! File for boundary value
+/
+
+&Zbins
+  filename = 'data/TNZ/Sn.csv' ! File with table to get Z from Te and ne
+  ZList = 0.1, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0, 11.0, 12.0, 13.0 ! Bins of average Z
+/

input/input_80ns_T30.nml

@@ -0,0 +1,33 @@
+&reference
+  m_ref    = 1.9712258e-25 ! Ion mass [kg]
+  Temp_ref = 30.0          ! Plasma temperature [eV]
+  n_ref    = 1.0e24        ! Plasma density [m^-3]
+/
+
+&grid
+  r0 = 10.0e-6 ! Initial position [m]
+  rf =  2.0e-3 ! Final position [m]
+  dr =  1.0e-6 ! Spatial step [m]
+  v0 =  -80e3  ! Lower limit for velocity space [m s^-1]
+  vf =  240e3  ! Upper limit for velocity space [m s^-1]
+  nv = 301     ! Number of grid points in the velocity space
+/
+
+&time
+  t0  = 0.0    ! Initial time [s]
+  tf  = 3.0e-7 ! Final time [s]
+  cfl = 0.5    ! CFL condition (dt = CFL * dr / vf)
+/
+
+&detector
+  rCum = 1.0e-3 ! Position of the detector [m]
+/
+
+&boundary
+  filename = 'data/boundary/bc_80ns_T30.csv' ! File for boundary value
+/
+
+&Zbins
+  filename = 'data/TNZ/Sn.csv' ! File with table to get Z from Te and ne
+  ZList = 0.1, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0, 11.0, 12.0, 13.0 ! Bins of average Z
+/

input/input_80ns_T6.nml

@@ -0,0 +1,33 @@
+&reference
+  m_ref    = 1.9712258e-25 ! Ion mass [kg]
+  Temp_ref = 30.0          ! Plasma temperature [eV]
+  n_ref    = 1.0e24        ! Plasma density [m^-3]
+/
+
+&grid
+  r0 = 10.0e-6 ! Initial position [m]
+  rf =  2.0e-3 ! Final position [m]
+  dr =  1.0e-6 ! Spatial step [m]
+  v0 =  -80e3  ! Lower limit for velocity space [m s^-1]
+  vf =  240e3  ! Upper limit for velocity space [m s^-1]
+  nv = 301     ! Number of grid points in the velocity space
+/
+
+&time
+  t0  = 0.0    ! Initial time [s]
+  tf  = 3.0e-7 ! Final time [s]
+  cfl = 0.5    ! CFL condition (dt = CFL * dr / vf)
+/
+
+&detector
+  rCum = 1.0e-3 ! Position of the detector [m]
+/
+
+&boundary
+  filename = 'data/boundary/bc_80ns_T6.csv' ! File for boundary value
+/
+
+&Zbins
+  filename = 'data/TNZ/Sn.csv' ! File with table to get Z from Te and ne
+  ZList = 0.1, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0, 11.0, 12.0, 13.0 ! Bins of average Z
+/

input/input_80ns_T60.nml

@@ -0,0 +1,33 @@
+&reference
+  m_ref    = 1.9712258e-25 ! Ion mass [kg]
+  Temp_ref = 30.0          ! Plasma temperature [eV]
+  n_ref    = 1.0e24        ! Plasma density [m^-3]
+/
+
+&grid
+  r0 = 10.0e-6 ! Initial position [m]
+  rf =  2.0e-3 ! Final position [m]
+  dr =  1.0e-6 ! Spatial step [m]
+  v0 =  -80e3  ! Lower limit for velocity space [m s^-1]
+  vf =  240e3  ! Upper limit for velocity space [m s^-1]
+  nv = 301     ! Number of grid points in the velocity space
+/
+
+&time
+  t0  = 0.0    ! Initial time [s]
+  tf  = 3.0e-7 ! Final time [s]
+  cfl = 0.5    ! CFL condition (dt = CFL * dr / vf)
+/
+
+&detector
+  rCum = 1.0e-3 ! Position of the detector [m]
+/
+
+&boundary
+  filename = 'data/boundary/bc_80ns_T60.csv' ! File for boundary value
+/
+
+&Zbins
+  filename = 'data/TNZ/Sn.csv' ! File with table to get Z from Te and ne
+  ZList = 0.1, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0, 11.0, 12.0, 13.0 ! Bins of average Z
+/

input/input_fa_T30.nml

@@ -0,0 +1,33 @@
+&reference
+  m_ref    = 1.9712258e-25 ! Ion mass [kg]
+  Temp_ref = 30.0          ! Plasma temperature [eV]
+  n_ref    = 1.0e24        ! Plasma density [m^-3]
+/
+
+&grid
+  r0 = 10.0e-6 ! Initial position [m]
+  rf =  2.0e-3 ! Final position [m]
+  dr =  1.0e-6 ! Spatial step [m]
+  v0 =  -80e3  ! Lower limit for velocity space [m s^-1]
+  vf =  240e3  ! Upper limit for velocity space [m s^-1]
+  nv = 301     ! Number of grid points in the velocity space
+/
+
+&time
+  t0  = 0.0    ! Initial time [s]
+  tf  = 3.0e-7 ! Final time [s]
+  cfl = 0.5    ! CFL condition (dt = CFL * dr / vf)
+/
+
+&detector
+  rCum = 1.0e-3 ! Position of the detector [m]
+/
+
+&boundary
+  filename = 'data/boundary/bc_fa_T30.csv' ! File for boundary value
+/
+
+&Zbins
+  filename = 'data/TNZ/Sn.csv' ! File with table to get Z from Te and ne
+  ZList = 0.1, 3.0, 4.0, 5.0, 6.0, 7.0, 8.0, 9.0, 10.0, 11.0, 12.0, 13.0 ! Bins of average Z
+/

makefile

@@ -1,15 +1,33 @@
-all:
+# set folders
-	gfortran moduleConstantParameters.f90 -c -lopenblas -Ofast -fopenmp -Wall
+TOPDIR =  $(PWD)# top directory
-	gfortran moduleReferenceValues.f90 -c -lopenblas -Ofast -fopenmp -Wall
+MODDIR := $(TOPDIR)/mod# module folder
-	gfortran moduleOutput.f90 -c -lopenblas -Ofast -fopenmp -Wall
+OBJDIR := $(TOPDIR)/obj# object folder
-	gfortran moduleTableBC.f90 -c -lopenblas -Ofast -fopenmp -Wall
+SRCDIR := $(TOPDIR)/src# source folder
-	gfortran moduleTableTtoZ.f90 -c -lopenblas -Ofast -fopenmp -Wall
+
-	gfortran moduleTableTtoZne.f90 -c -lopenblas -Ofast -fopenmp -Wall
+# compiler
-	gfortran vlaplex.f90 moduleConstantParameters.o moduleReferenceValues.o moduleOutput.o moduleTableBC.o moduleTableTtoZ.o moduleTableTtoZne.o -lopenblas -Ofast -fopenmp -Wall -o vlaplex
+# gfortran:
+FC := gfortran
+
+# compiler flags
+# gfortran:
+FCFLAGS := -fopenmp -Ofast -J $(MODDIR) -Wall -march=native -g
+
+#Output file
+OUTPUT = vlaplex
+
+export
+
+all: $(OUTPUT)
+
+$(OUTPUT): src.o
+
+src.o:
+	@mkdir -p $(MODDIR)
+	@mkdir -p $(OBJDIR)
+	$(MAKE) -C src $(OUTPUT)
 
 clean:
-	rm -f vlaplex
+	rm -f $(OUTPUT)
-	rm -f *.mod
+	rm -f $(MODDIR)/*.mod
-	rm -f *.smod
+	rm -f $(MODDIR)/*.smod
-	rm -f *.o
+	rm -f $(OBJDIR)/*.o
-

moduleTableTtoZ.f90

@@ -1,116 +0,0 @@
-module moduleTableTtoZ
-  use constantParameters, only: dp
-
-  type:: tableTtoZ
-    real(dp):: Z_min, Z_max
-    real(dp):: Temp_min, Temp_max
-    real(dp), allocatable, dimension(:):: Temp
-    real(dp), allocatable, dimension(:):: Z
-    real(dp), allocatable, dimension(:):: Z_k
-    contains
-      procedure, pass:: init    => initTableTtoZ
-      procedure, pass:: get     => getValueTableTtoZ
-
-  end type tableTtoZ
-
-  contains
-    subroutine initTableTtoZ(self, tableFile)
-      use constantParameters, only: eV_to_K
-      use referenceValues, only: Temp_ref
-      implicit none
-
-      class(tableTtoZ), intent(inout):: self
-      character(:), allocatable, intent(in):: tableFile
-      character(100):: dummy
-      integer:: amount
-      integer:: i
-      integer:: stat
-      integer:: id = 20
-
-      open(id, file = tableFile)
-      amount = -1 ! Remove header
-      do
-        read(id, '(A)', iostat = stat) dummy
-        !If EOF or error, exit file
-        if (stat /= 0) EXIT
-        ! !Skip comment
-        ! if (index(dummy,'#') /= 0) CYCLE
-        !Add row
-        amount = amount + 1
-
-      end do
-
-      !Go bback to initial point
-      rewind(id)
-
-      !Allocate table arrays
-      allocate(self%Temp(1:amount))
-      allocate(self%Z(1:amount))
-      allocate(self%Z_k(1:amount))
-      self%Temp   = 0.0_dp
-      self%Z      = 0.0_dp
-      self%Z_k    = 0.0_dp
-
-      i = 0
-      read(id, *) ! Skip header
-      do 
-        read(id, '(A)', iostat = stat) dummy
-        !TOdo: Make this a function
-        if (stat /= 0) EXIT
-        !Add data
-        !TODO: substitute with extracting information from dummy
-        backspace(id)
-        i = i + 1
-        read(id, *) self%Temp(i), self%Z(i)
-
-      end do
-      self%Temp = self%Temp * eV_to_K / Temp_ref
-
-      close(id)
-
-      self%Temp_min    = self%Temp(1)
-      self%Temp_max    = self%Temp(amount)
-      self%Z_min    = self%Z(1)
-      self%Z_max    = self%Z(amount)
-
-      do i = 1, amount - 1
-        self%Z_k(i)    = (   self%Z(i+1) -    self%Z(i))/(self%Temp(i+1) - self%Temp(i))
-
-      end do
-
-    end subroutine initTableTtoZ
-
-    subroutine getValueTableTtoZ(self, Temp, Z)
-      implicit none
-
-      class(tableTtoZ), intent(in):: self
-      real(dp), intent(in):: Temp
-      real(dp), intent(out):: Z
-      real(dp):: delta_Temp
-      integer:: i
-
-      if     (Temp <= self%Temp_min) THEN
-        Z   = self%Z_min
-
-      elseif (Temp >= self%Temp_max) THEN
-        Z    = self%Z_max
-
-      else
-        i = minloc(abs(Temp - self%Temp), 1)
-        delta_Temp = Temp - self%Temp(i)
-        if (delta_Temp < 0 ) THEN 
-          i = i - 1
-          delta_Temp = Temp - self%Temp(i)
-          
-        end if
-
-        Z    =    self%Z(i) +    self%Z_k(i)*delta_Temp
-
-      end if
-
-    end subroutine getValueTableTtoZ
-
-
-
-end module moduleTableTtoZ
-

src/makefile

@@ -0,0 +1,16 @@
+OBJECTS = $(OBJDIR)/constantParameters.o \
+          $(OBJDIR)/input.o              \
+          $(OBJDIR)/output.o             \
+          $(OBJDIR)/referenceValues.o    \
+          $(OBJDIR)/tableBoundary.o      \
+          $(OBJDIR)/tableTNZ.o
+
+
+all: $(OUTPUT)
+
+$(OUTPUT): modules.o $(OUTPUT).f90
+	$(FC) $(FCFLAGS) -o $(OBJDIR)/$(OUTPUT).o -c $(OUTPUT).f90
+	$(FC) $(FCFLAGS) -o $(TOPDIR)/$(OUTPUT) $(OBJECTS) $(OBJDIR)/$(OUTPUT).o -lopenblas
+
+modules.o:
+	$(MAKE) -C modules all

src/modules/input.f90

@@ -0,0 +1,142 @@
+module input
+  use constantParameters, only: dp
+  implicit none
+
+  character(:), allocatable:: inputFile
+  integer:: inputFile_id, inputFile_io
+
+
+  contains
+    subroutine openInputFile()
+
+      inquire(file=inputFile, iostat=inputfile_io)
+
+      if (inputFile_io /= 0) then
+          write (*, '("Error: input file ", a, " does not exist")') inputFile
+          return
+
+      end if
+
+      open(action='read', file=inputFile, iostat=inputFile_io, newunit=inputFile_id)
+
+    end subroutine openInputFile
+
+    subroutine readReference()
+      use constantParameters, only: dp, kb, qe, eps_0, ev_to_K, cm3_to_m3, PI
+      use referenceValues
+
+      namelist /reference/ m_ref, Temp_ref, n_ref
+
+      read(nml=reference, unit=inputFile_id, iostat=inputFile_io)
+
+      ! Set reference numbers (in SI units)
+      Temp_ref = Temp_ref * eV_to_K
+      n_ref    = n_ref
+      t_ref    = sqrt(eps_0 * m_ref / (n_ref * 1.0_dp * qe**2)) ! 1.0_dp represents Z = 1 for reference values
+      u_ref    = sqrt(kb * Temp_ref / m_ref)
+      L_ref    = u_ref * t_ref
+      phi_ref  = kb * Temp_ref / qe
+
+    end subroutine readReference
+
+    subroutine readGrid(r0, rf, dr, v0, vf, nv)
+      use referenceValues, only: L_ref, u_ref
+
+      real(dp), intent(out):: r0, rf, dr
+      real(dp), intent(out):: v0, vf
+      integer,  intent(out):: nv
+      namelist /grid/ r0, rf, dr, v0, vf, nv
+
+      read(nml=grid, unit=inputFile_id, iostat=inputFile_io)
+
+      r0 = r0/L_ref
+      rf = rf/L_ref
+      dr = dr/L_ref
+
+      v0 = v0/u_ref
+      vf = vf/u_ref
+
+    end subroutine readGrid
+
+    subroutine readTime(t0, tf, CFL)
+      use referenceValues, only: t_ref
+
+      real(dp), intent(out):: t0, tf, CFL
+
+      namelist /time/ t0, tf, CFL
+
+      read(nml=time, unit=inputFile_id, iostat=inputFile_io)
+
+      t0 = t0/t_ref
+      tf = tf/t_ref
+
+    end subroutine readTime
+
+    subroutine readDetector(rCum)
+      use referenceValues, only: L_ref
+
+      real(dp), intent(out):: rCum
+      namelist /detector/ rCum
+
+      read(nml=detector, unit=inputFile_id, iostat=inputFile_io)
+
+      ! Set position to calculate cumulative sum of f (non-dimensional units)
+      rCum = rCum/L_ref
+
+    end subroutine readDetector
+
+    subroutine readBoundary(bc)
+      use tableBoundary
+
+      type(tableBC), intent(out):: bc
+      character(len=128):: filename
+      character(:), allocatable:: filename_dynamic ! Needed to pass as an argument, might delete
+      namelist /boundary/ filename
+
+      read(nml=boundary, unit=inputFile_id, iostat=inputFile_io)
+
+      filename_dynamic = trim(filename)
+
+      call bc%init(filename_dynamic)
+
+    end subroutine readBoundary
+    subroutine readZ(Zlist, nz, Tene_to_Z)
+      use tableTNZ
+      
+      real(dp), allocatable, intent(out):: Zlist(:)
+      integer, intent(out):: nz
+      type(tableTn_to_Z), intent(out):: Tene_to_Z
+      real(dp), allocatable:: ZList_dummy(:)
+      character(len=128):: filename
+      character(:), allocatable:: filename_dynamic ! Needed to pass as an argument, might delete
+      namelist /Zbins/ ZList, filename
+
+      ! List of dummy size
+      allocate(ZList(1:99))
+      ZList       = -1.0_dp
+
+      ! Read namelist
+      read(nml=Zbins, unit=inputFile_id, iostat=inputFile_io)
+
+      ! Get the real Z bins
+      nz = count(ZList > 0.0_dp)
+      allocate(ZList_dummy(1:nz))
+      ZList_dummy = ZList(1:nz)
+
+      ! Copy to final list
+      deallocate(ZList)
+      ZList = ZList_dummy
+      deallocate(ZList_dummy)
+
+      filename_dynamic = trim(filename)
+      call Tene_to_Z%init(filename_dynamic)
+
+    end subroutine readZ
+
+    subroutine closeInputFile()
+
+      close(inputFile_id)
+
+    end subroutine closeInputFile
+
+end module input

src/modules/makefile

@@ -0,0 +1,15 @@
+OBJS = constantParameters.o \
+       input.o              \
+       output.o             \
+       referenceValues.o    \
+       tableBoundary.o      \
+       tableTNZ.o
+
+all: $(OBJS)
+
+input.o: referenceValues.o tableBoundary.o tableTNZ.o input.f90
+	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
+
+%.o: %.f90
+	$(FC) $(FCFLAGS) -c $< -o $(OBJDIR)/$@
+

src/modules/referenceValues.f90

@@ -2,6 +2,7 @@ module referenceValues
   use constantParameters, only: dp
   implicit none
   
+  real(dp):: m_ref                                ! Reference values
   real(dp):: L_ref, t_ref, n_ref, u_ref, Temp_ref ! Reference values
   real(dp):: phi_ref                              ! Reference values
 

src/modules/tableBoundary.f90

@@ -1,4 +1,4 @@
-module moduleTableBC
+module tableBoundary
   use constantParameters, only: dp
 
   type:: tableBC
@@ -61,7 +61,7 @@ module moduleTableBC
       read(id, *) ! Skip header
       do 
         read(id, '(A)', iostat = stat) dummy
-        !TOdo: Make this a function
+        !TODO: Make this a function
         if (stat /= 0) EXIT
         !Add data
         !TODO: substitute with extracting information from dummy
@@ -132,5 +132,5 @@ module moduleTableBC
 
     end subroutine getValueTableBC
 
-end module moduleTableBC
+end module tableBoundary
 

src/modules/tableTNZ.f90

@@ -1,7 +1,7 @@
-module moduleTableTtoZne
+module tableTNZ
   use constantParameters, only: dp
 
-  type:: tableTtoZne
+  type:: tableTn_to_Z
     real(dp) :: Z_min, Z_max
     real(dp) :: Temp_min, Temp_max
     real(dp), allocatable, dimension(:):: Temp
@@ -12,7 +12,7 @@ module moduleTableTtoZne
       procedure, pass:: init    => initTableTtoZne
       procedure, pass:: get     => getValueTableTtoZne
 
-  end type tableTtoZne
+  end type tableTn_to_Z
 
   contains
     subroutine initTableTtoZne(self, tableFile)
@@ -20,7 +20,7 @@ module moduleTableTtoZne
       use referenceValues, only: Temp_ref, n_ref
       implicit none
 
-      class(tableTtoZne), intent(inout):: self
+      class(tableTn_to_Z), intent(inout):: self
       character(:), allocatable, intent(in):: tableFile
       character(100):: dummy
       character(len=512) :: line
@@ -110,7 +110,7 @@ module moduleTableTtoZne
     subroutine getValueTableTtoZne(self, Temp, ne, Z)
       implicit none
 
-      class(tableTtoZne), intent(in):: self
+      class(tableTn_to_Z), intent(in):: self
       real(dp), intent(in):: Temp, ne
       real(dp), intent(out):: Z
       real(dp):: delta_Temp
@@ -144,5 +144,5 @@ module moduleTableTtoZne
 
 
 
-end module moduleTableTtoZne
+end module tableTNZ
 

src/vlaplex.f90

@@ -1,37 +1,13 @@
- module eos
-   use constantParameters, only: dp
-   implicit none
-
-   private
-   public:: T_to_Z
-
-   contains
-     pure function T_to_Z(T) result(Z)
-       use constantParameters, only: eV_to_K
-       use referenceValues,    only: Temp_ref
-       implicit none
-
-       real(dp), intent(in):: T
-       real(dp):: Z
-
-      Z = 22.5 * (Temp_ref * T / eV_to_K / 100.0)**0.6
-
-     end function T_to_Z
-
-end module eos
-
 program VlaPlEx
   use constantParameters, only: dp, kb, qe, eps_0, ev_to_K, cm3_to_m3, PI
+  use input
   use output
   use referenceValues
-  use eos,                only: T_to_Z
+  use tableBoundary
-  use moduleTableBC
+  use tableTNZ
-  use moduleTableTtoZ
-  use moduleTableTtoZne
   use omp_lib
   implicit none
 
-  real(dp), parameter:: m_i     = 1.9712258e-25_dp ! Tin atom mass in kg
   real(dp), parameter:: gamma_i = 1.0_dp           ! Adiabatic coefficient for ions
   real(dp), parameter:: m_e     = 9.1093837e-31_dp ! Electron mass in kg
   real(dp), parameter:: gamma_e = 4.0_dp / 3.0_dp  ! Adiabatic coefficient for electrons
@@ -44,10 +20,10 @@ program VlaPlEx
   real(dp):: v0, vf
   real(dp), allocatable, dimension(:):: v
   real(dp):: t0, tf
+  real(dp):: CFL
   real(dp):: time
   real(dp):: dr, dv, dt
   integer::  nr, nv, nt, nz
-  integer:: nzMin, nzMax
   integer::   i, iz,  j,  t, z_inj
   integer:: j0 ! First integer of positive velocity
 
@@ -55,13 +31,8 @@ program VlaPlEx
   real(dp):: Zave_bc, Zave_bc_old ! Average charge state
   real(dp):: u_bc    ! Injection velocity
   real(dp):: n_bc    ! Injection density
-  real(dp):: c_s     ! Ion sound speed
   type(tableBC):: boundaryConditions
-  character(:), allocatable:: bc_file
+  type(tableTn_to_Z):: Tene_to_Z
-  type(tableTtoZ):: TtoZ
-  character(:), allocatable:: TtoZ_file
-  type(tableTtoZne):: TtoZne
-  character(:), allocatable:: TtoZne_file
 
   real(dp), allocatable, dimension(:,:,:):: f_i, f_i_old
   real(dp), allocatable, dimension(:):: f0   ! Boundary at r = x_0
@@ -72,7 +43,7 @@ program VlaPlEx
   real(dp), allocatable, dimension(:,:):: T_i
   real(dp), allocatable, dimension(:):: n_e
   real(dp), allocatable, dimension(:):: Zave
-  real(dp), allocatable, dimension(:):: Z_list
+  real(dp), allocatable, dimension(:):: Zlist
   real(dp), allocatable, dimension(:):: diag, diag_low, diag_high
   real(dp), allocatable, dimension(:,:):: A
   real(dp), allocatable, dimension(:):: Res
@@ -86,54 +57,48 @@ program VlaPlEx
   ! real(dp):: phiF
   integer:: k
 
+  integer:: nThreads ! number of threads for OpenMP
+
   real(dp), allocatable, dimension(:,:):: fCum_i
   real(dp):: rCum
   integer:: rCum_index
 
+  character(len=128) arg
+
+  CALL get_command_argument(1, arg)
+  if (arg == '') then
+    write (*, '(a)') "No input file provided"
+    return
+
+  end if
+  inputFile = trim(arg)
+  call openInputFile()
+  call readReference()
+  call readGrid(r0, rf, dr, v0, vf, nv)
+  call readTime(t0, tf, CFL)
+  call readDetector(rCum)
+  call readBoundary(boundaryConditions)
+  nThreads = 16
+  call readZ(Zlist, nz, Tene_to_Z)
+  call closeInputFile()
+
   ! Set number of threads
-  call omp_set_num_threads(16)
+  call omp_set_num_threads(nThreads)
 
-  ! Set reference numbers (in SI units)
+  ! Grid in the position space
-  Temp_ref = 30.0_dp * eV_to_K
-  n_ref    = 1.0e20_dp * cm3_to_m3
-  t_ref    = sqrt(eps_0 * m_i / (n_ref * 1.0_dp * qe**2)) ! 1.0_dp represents Z = 1 for reference values
-  u_ref    = sqrt(kb * Temp_ref / m_i)
-  L_ref    = u_ref * t_ref
-  phi_ref  = kb * Temp_ref / qe
-
-  ! Set input parameters (remember these have to be in non-dimensional units)
-  c_s      = sqrt(11.0_dp * gamma_i * 1.0_dp)
-  bc_file = 'bc.csv'
-  call boundaryConditions%init(bc_file)
-  TtoZ_file = 'average_TtoZ_curve.csv'
-  call TtoZ%init(TtoZ_file)
-  TtoZne_file = 'Zave_values_per_Ne.csv'
-  call TtoZne%init(TtoZne_file)
-
-  ! Set domain boundaries (non-dimensional units)
-  r0 =  10.0e-6_dp / L_ref
-  rf =   2.0e-3_dp / L_ref
-  dr =   1.0e-6_dp / L_ref
   nr = nint((rf - r0) / dr) + 1
   dr =      (rf - r0) / float(nr-1)
-
   allocate(r(1:nr))
   do i = 1, nr
     r(i) = dr * float(i-1) + r0
   end do
 
-  ! Set position to calculate cumulative sum of f (non-dimensional units)
-  rCum =  1.0e-3 / L_ref
-
   ! Index for cumulative sum
   rCum_index = minloc(abs(r - rCum), 1)
 
-  v0 =-0.5e1_dp*c_s
+  ! Grid in the velocity space
-  vf = 1.5e1_dp*c_s
+  print*, v0, vf
-  dv = 2.0e-1_dp
-  nv = nint((vf - v0) / dv) + 1
   dv = (vf - v0) / float(nv-1)
-
   allocate(v(1:nv))
   do j = 1, nv
     v(j) = dv * float(j-1) + v0
@@ -145,9 +110,7 @@ program VlaPlEx
     j0 = j0 + 1
   end if
 
-  t0 = 0.0_dp
+  dt = CFL*dr/vf
-  tf = 3.0e-7_dp / t_ref
-  dt = 5.0e-2_dp*dr/c_s
   nt = nint((tf - t0) / dt) 
   dt =      (tf - t0) / float(nt)
 
@@ -163,19 +126,12 @@ program VlaPlEx
 
   end if
 
-  write(*, '(A,ES0.4e3)') 'CFL: ', dt*vf/dr
-
-  nzMin = 3
-  nzMax = 13
-  nz    = nzMax - nzMin + 1
-  nz    = nz + 1 ! Add bin for low Z plasma
   ! Allocate vectors
   allocate(f_i(1:nz,1:nr,1:nv), f_i_old(1:nz,1:nr,1:nv))
   allocate(n_i(1:nz,1:nr))
   allocate(sum_ni(1:nr))
   allocate(u_i(1:nz,1:nr), E_i(1:nr), T_i(1:nz,1:nr))
   allocate(Zave(1:nr))
-  allocate(Z_list(1:nz))
   allocate(n_e(1:nr))
   allocate(phi(1:nr), phi_old(1:nr), E(1:nr))
   allocate(fCum_i(1:nz,1:nv))
@@ -189,10 +145,6 @@ program VlaPlEx
   n_e         = 0.0_dp
   T_e         = 0.0_dp
   Zave        = 0.0_dp
-  Z_list(1) = 0.1_dp ! Low Z bin
-  do iz = nzMin, nzMax
-    Z_list(iz-nzMin+1+1) = float(iz)
-  end do
   Zave_bc_old = 0.0_dp
   phi         = 0.0_dp
   phi_old     = 0.0_dp
@@ -246,10 +198,10 @@ program VlaPlEx
   t = 0
   call writeOutputRef()
   ! call writeOutputF(t, dt, nr, r, nv, v, f_i_old)
-  call writeOutputFCum(t, dt, nz, r(rCum_index), nv, v, fCum_i, Z_list)
+  call writeOutputFCum(t, dt, nz, r(rCum_index), nv, v, fCum_i, Zlist)
   call writeOutputPhi(t, dt, nr, r, phi, E, n_e)
-  call writeOutputMom(t, dt, nz, nr, r, n_i, u_i, T_i, Z_list)
+  call writeOutputMom(t, dt, nz, nr, r, n_i, u_i, T_i, Zlist)
-  call writeOutputZList(nz, Z_list)
+  call writeOutputZList(nz, Zlist)
 
   ! Main loop
   do t = 1, nt
@@ -258,14 +210,14 @@ program VlaPlEx
     ! Get boundary conditions for specific time
     call boundaryConditions%get(time, n_bc, u_bc, Temp_bc)
     ! Find new \bar{Z}_i based on T_e = Temp_bc and n_e = n_bc
-    call TtoZne%get(Temp_bc, n_bc, Zave_bc)
+    call Tene_to_Z%get(Temp_bc, n_bc, Zave_bc)
     ! Assign Z(T,n) to bin
-    z_inj = minloc(abs(Z_list - Zave_bc),1)
+    z_inj = minloc(abs(Zlist - Zave_bc),1)
     ! Calculate inject (sonic) speed
-    u_bc = sqrt(Z_list(z_inj)* Temp_bc)
+    u_bc = sqrt(Zlist(z_inj)* Temp_bc)
     ! Calculate ion density to inject
-    n_bc = n_bc / Z_list(z_inj)
+    n_bc = n_bc / Zlist(z_inj)
-    call writeOutputBoundary(t, dt, n_bc, u_bc, Temp_bc, Zave_bc, Z_list(z_inj))
+    call writeOutputBoundary(t, dt, n_bc, u_bc, Temp_bc, Zave_bc, Zlist(z_inj))
 
     ! f0(j0:nv) = v(j0:nv)**2 / sqrt(PI*Temp_bc**3) * exp(-(v(j0:nv) - u_bc)**2 / Temp_bc)
     f0(j0:nv) = 1.0_dp / sqrt(PI*Temp_bc) * exp(-(v(j0:nv) - u_bc)**2 / Temp_bc)
@@ -316,7 +268,7 @@ program VlaPlEx
 
       end do
       !$omp end parallel do
-      sum_ni = sum_ni + Z_list(iz) * n_i(iz,:)
+      sum_ni = sum_ni + Zlist(iz) * n_i(iz,:)
     end do
 
     ! Assume quasi-neutrality to start iterating
@@ -402,18 +354,18 @@ program VlaPlEx
       ! i = 1, v<0
       i = 1
       if (E(i) >= 0.0_dp) then
-        f_i(iz,i,2:j0-2) = f_i_old(iz,i,2:j0-2) - Z_list(iz)*E(i)*dt/dv*(f_i_old(iz,i,2:j0-2) - f_i_old(iz,i,1:j0-3))
+        f_i(iz,i,2:j0-2) = f_i_old(iz,i,2:j0-2) - Zlist(iz)*E(i)*dt/dv*(f_i_old(iz,i,2:j0-2) - f_i_old(iz,i,1:j0-3))
       else
-        f_i(iz,i,2:j0-2) = f_i_old(iz,i,2:j0-2) - Z_list(iz)*E(i)*dt/dv*(f_i_old(iz,i,3:j0-1) - f_i_old(iz,i,2:j0-2))
+        f_i(iz,i,2:j0-2) = f_i_old(iz,i,2:j0-2) - Zlist(iz)*E(i)*dt/dv*(f_i_old(iz,i,3:j0-1) - f_i_old(iz,i,2:j0-2))
 
       end if
       ! i = 2, nr-1; all v
       !$omp parallel do
       do i = 2, nr-1
         if (E(i) >= 0.0_dp) then
-          f_i(iz,i,2:nv-1) = f_i_old(iz,i,2:nv-1) - Z_list(iz)*E(i)*dt/dv*(f_i_old(iz,i,2:nv-1) - f_i_old(iz,i,1:nv-2))
+          f_i(iz,i,2:nv-1) = f_i_old(iz,i,2:nv-1) - Zlist(iz)*E(i)*dt/dv*(f_i_old(iz,i,2:nv-1) - f_i_old(iz,i,1:nv-2))
         else
-          f_i(iz,i,2:nv-1) = f_i_old(iz,i,2:nv-1) - Z_list(iz)*E(i)*dt/dv*(f_i_old(iz,i,3:nv)   - f_i_old(iz,i,2:nv-1))
+          f_i(iz,i,2:nv-1) = f_i_old(iz,i,2:nv-1) - Zlist(iz)*E(i)*dt/dv*(f_i_old(iz,i,3:nv)   - f_i_old(iz,i,2:nv-1))
 
         end if
 
@@ -422,9 +374,9 @@ program VlaPlEx
       ! i = nr, v>=0
       i = nr
       if (E(i) >= 0.0_dp) then
-        f_i(iz,i,j0+1:nv-1) = f_i_old(iz,i,j0+1:nv-1) - Z_list(iz)*E(i)*dt/dv*(f_i_old(iz,i,j0+1:nv-1) - f_i_old(iz,i,j0:nv-2))
+        f_i(iz,i,j0+1:nv-1) = f_i_old(iz,i,j0+1:nv-1) - Zlist(iz)*E(i)*dt/dv*(f_i_old(iz,i,j0+1:nv-1) - f_i_old(iz,i,j0:nv-2))
       else
-        f_i(iz,i,j0+1:nv-1) = f_i_old(iz,i,j0+1:nv-1) - Z_list(iz)*E(i)*dt/dv*(f_i_old(iz,i,j0+2:nv)   - f_i_old(iz,i,j0+1:nv-1))
+        f_i(iz,i,j0+1:nv-1) = f_i_old(iz,i,j0+1:nv-1) - Zlist(iz)*E(i)*dt/dv*(f_i_old(iz,i,j0+2:nv)   - f_i_old(iz,i,j0+1:nv-1))
 
       end if
     end do
@@ -439,10 +391,10 @@ program VlaPlEx
     end do
     ! Write output
     if (mod(t,everyOutput) == 0 .or. t == nt) then
-      ! call writeOutputF(t, dt, nz, nr, r, nv, v, f_i_old, Z_list)
+      ! call writeOutputF(t, dt, nz, nr, r, nv, v, f_i_old, Zlist)
       call writeOutputPhi(t, dt, nr, r, phi, E, n_e)
-      call writeOutputMom(t, dt, nz, nr, r, n_i, u_i, T_i, Z_list)
+      call writeOutputMom(t, dt, nz, nr, r, n_i, u_i, T_i, Zlist)
-      call writeOutputFCum(t, dt, nz, r(rCum_index), nv, v, fCum_i, Z_list)
+      call writeOutputFCum(t, dt, nz, r(rCum_index), nv, v, fCum_i, Zlist)
 
     end if