Minor changes: Rename T_e to T_e0

This should not have been a single commit.

Now we have input files.

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

.gitignore

@@ -3,3 +3,6 @@ vlaplex
 *.csv
 *.mod
 *.o
+*.tar.gz
+obj/
+mod/

AUTHORS

@@ -0,0 +1,4 @@
+# This is the list of VlaPlEx's contributors.
+
+Jorge Gonzalez
+Jop Hendrikx

COPYING

@@ -0,0 +1,674 @@
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+PURPOSE.  THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU.  SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+  16. Limitation of Liability.
+
+  IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+  17. Interpretation of Sections 15 and 16.
+
+  If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+                     END OF TERMS AND CONDITIONS
+
+            How to Apply These Terms to Your New Programs
+
+  If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+  To do so, attach the following notices to the program.  It is safest
+to attach them to the start of each source file to most effectively
+state the exclusion of warranty; and each file should have at least
+the "copyright" line and a pointer to where the full notice is found.
+
+    <one line to give the program's name and a brief idea of what it does.>
+    Copyright (C) <year>  <name of author>
+
+    This program is free software: you can redistribute it and/or modify
+    it under the terms of the GNU General Public License as published by
+    the Free Software Foundation, either version 3 of the License, or
+    (at your option) any later version.
+
+    This program is distributed in the hope that it will be useful,
+    but WITHOUT ANY WARRANTY; without even the implied warranty of
+    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+    GNU General Public License for more details.
+
+    You should have received a copy of the GNU General Public License
+    along with this program.  If not, see <https://www.gnu.org/licenses/>.
+
+Also add information on how to contact you by electronic and paper mail.
+
+  If the program does terminal interaction, make it output a short
+notice like this when it starts in an interactive mode:
+
+    <program>  Copyright (C) <year>  <name of author>
+    This program comes with ABSOLUTELY NO WARRANTY; for details type `show w'.
+    This is free software, and you are welcome to redistribute it
+    under certain conditions; type `show c' for details.
+
+The hypothetical commands `show w' and `show c' should show the appropriate
+parts of the General Public License.  Of course, your program's commands
+might be different; for a GUI interface, you would use an "about box".
+
+  You should also get your employer (if you work as a programmer) or school,
+if any, to sign a "copyright disclaimer" for the program, if necessary.
+For more information on this, and how to apply and follow the GNU GPL, see
+<https://www.gnu.org/licenses/>.
+
+  The GNU General Public License does not permit incorporating your program
+into proprietary programs.  If your program is a subroutine library, you
+may consider it more useful to permit linking proprietary applications with
+the library.  If this is what you want to do, use the GNU Lesser General
+Public License instead of this License.  But first, please read
+<https://www.gnu.org/licenses/why-not-lgpl.html>.

README.md

@@ -5,3 +5,15 @@ It solves the Vlasov equation for ions in a 1D spherical domain.
 Electrons are treated as a fluid either isothermal (Boltzmann) or polytropic.
 
 Self-consistent electric field is solved using a Newton-Raphson method to solve the Poisson equation.
+
+A 2D table linking T_e, n_e and the average Z must be provided. Examples can be found in 'data/TNZ'.
+
+Input files for different cases are in the 'input' folder.
+
+Files with the boundary conditions are provided in 'data/boundary'.
+
+Input files must specify which TNZ table and boundary file are using.
+
+To run the code execute
+
+./vlaplex <path-to-input-file>

bc_80ns_T10Z6.csv

@@ -1,5 +0,0 @@
-t (s),n (m^-3),u (m s^-1),T (eV),Z
-0.000000E-000,1.111111E+025,0.000000E+000,1.000000E+001,6.000000E+000
-8.000000E-008,1.111111E+025,0.000000E+000,1.000000E+001,6.000000E+000
-8.500000E-008,1.000000E+020,0.000000E+000,5.000000E+000,6.000000E+000
-2.000000E-006,1.000000E+020,0.000000E+000,5.000000E+000,6.000000E+000

bc_80ns_T30Z11.csv

@@ -1,5 +0,0 @@
-t (s),n (m^-3),u (m s^-1),T (eV),Z
-0.000000E-000,1.111111E+025,0.000000E+000,3.000000E+001,1.100000E+001
-8.000000E-008,1.111111E+025,0.000000E+000,3.000000E+001,1.100000E+001
-8.500000E-008,1.000000E+020,0.000000E+000,5.000000E+000,1.100000E+001
-2.000000E-006,1.000000E+020,0.000000E+000,5.000000E+000,1.100000E+001

bc_80ns_T60Z16.csv

@@ -1,5 +0,0 @@
-t (s),n (m^-3),u (m s^-1),T (eV),Z
-0.000000E-000,1.111111E+025,0.000000E+000,6.000000E+001,1.600000E+001
-8.000000E-008,1.111111E+025,0.000000E+000,6.000000E+001,1.600000E+001
-8.500000E-008,1.000000E+020,0.000000E+000,5.000000E+000,1.600000E+001
-2.000000E-006,1.000000E+020,0.000000E+000,5.000000E+000,1.600000E+001

bc_80ns_T6Z4.csv

@@ -1,5 +0,0 @@
-t (s),n (m^-3),u (m s^-1),T (eV),Z
-0.000000E-000,1.111111E+025,0.000000E+000,6.000000E+000,4.000000E+000
-8.000000E-008,1.111111E+025,0.000000E+000,6.000000E+000,4.000000E+000
-8.500000E-008,1.000000E+020,0.000000E+000,5.000000E+000,4.000000E+000
-2.000000E-006,1.000000E+020,0.000000E+000,5.000000E+000,4.000000E+000

bc_fa_T30Z11.csv

@@ -1,3 +0,0 @@
-t (s),n (m^-3),u (m s^-1),T (eV),Z
-0.000000E-000,1.111111E+025,0.000000E+000,3.000000E+001,1.100000E+001
-1.000000E-006,1.111111E+025,0.000000E+000,3.000000E+001,1.100000E+001

data/boundary/bc_80ns_T10.csv

@@ -0,0 +1,6 @@
+t (s),n (m^-3),u (m s^-1),T (eV)
+0.000000E-000,1.000000E+024,0.000000E+000,1.000000E+001
+8.000000E-008,1.000000E+024,0.000000E+000,1.000000E+001
+8.500000E-008,1.000000E+020,0.000000E+000,5.000000E-001
+1.000000E-007,1.000000E+010,0.000000E+000,5.000000E-001
+2.000000E-006,1.000000E+010,0.000000E+000,5.000000E-001

data/boundary/bc_80ns_T30.csv

@@ -0,0 +1,6 @@
+t (s),n (m^-3),u (m s^-1),T (eV)
+0.000000E-000,1.000000E+024,0.000000E+000,3.000000E+001
+8.000000E-008,1.000000E+024,0.000000E+000,3.000000E+001
+8.500000E-008,1.000000E+020,0.000000E+000,5.000000E-001
+1.000000E-007,1.000000E+010,0.000000E+000,5.000000E-001
+2.000000E-006,1.000000E+010,0.000000E+000,5.000000E-001

data/boundary/bc_80ns_T6.csv

@@ -0,0 +1,6 @@
+t (s),n (m^-3),u (m s^-1),T (eV)
+0.000000E-000,1.000000E+024,0.000000E+000,6.000000E+000
+8.000000E-008,1.000000E+024,0.000000E+000,6.000000E+000
+8.500000E-008,1.000000E+020,0.000000E+000,5.000000E-001
+1.000000E-007,1.000000E+010,0.000000E+000,5.000000E-001
+2.000000E-006,1.000000E+010,0.000000E+000,5.000000E-001

data/boundary/bc_80ns_T60.csv

@@ -0,0 +1,6 @@
+t (s),n (m^-3),u (m s^-1),T (eV)
+0.000000E-000,1.000000E+024,0.000000E+000,6.000000E+001
+8.000000E-008,1.000000E+024,0.000000E+000,6.000000E+001
+8.500000E-008,1.000000E+020,0.000000E+000,5.000000E-001
+1.000000E-007,1.000000E+010,0.000000E+000,5.000000E-001
+2.000000E-006,1.000000E+010,0.000000E+000,5.000000E-001

data/boundary/bc_fa_T30.csv

@@ -0,0 +1,3 @@
+t (s),n (m^-3),u (m s^-1),T (eV)
+0.000000E-000,1.000000E+024,0.000000E+000,3.000000E+001
+2.000000E-006,1.000000E+024,0.000000E+000,3.000000E+001

input/input_80ns_T10.nml

@@ -0,0 +1,43 @@
+&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 =  -50e3  ! Lower limit for velocity space [m s^-1]
+  vf =  250e3  ! Upper limit for velocity space [m s^-1]
+  nv = 401     ! Number of grid points in the velocity space
+/
+
+&output
+  folder = 'polytropic_80ns_T10' ! Folder name
+  outputStep = 1e-9              ! Time step for file write [s]
+/
+
+&time
+  t0  = 0.0    ! Initial time [s]
+  tf  = 2.0e-7 ! Final time [s]
+  cfl = 0.2    ! 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
+/
+
+&parallel
+  nThreads = 16 ! Number of threads for OpenMP
+/
+

input/input_80ns_T30.nml

@@ -0,0 +1,43 @@
+&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 =  -50e3  ! Lower limit for velocity space [m s^-1]
+  vf =  250e3  ! Upper limit for velocity space [m s^-1]
+  nv = 401     ! Number of grid points in the velocity space
+/
+
+&output
+  folder = 'polytropic_80ns_T30' ! Folder name
+  outputStep = 1e-9              ! Time step for file write [s]
+/
+
+&time
+  t0  = 0.0    ! Initial time [s]
+  tf  = 2.0e-7 ! Final time [s]
+  cfl = 0.2    ! 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
+/
+
+&parallel
+  nThreads = 16 ! Number of threads for OpenMP
+/
+

input/input_80ns_T6.nml

@@ -0,0 +1,43 @@
+&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 =  -50e3  ! Lower limit for velocity space [m s^-1]
+  vf =  250e3  ! Upper limit for velocity space [m s^-1]
+  nv = 401     ! Number of grid points in the velocity space
+/
+
+&output
+  folder = 'polytropic_80ns_T6'  ! Folder name
+  outputStep = 1e-9              ! Time step for file write [s]
+/
+
+&time
+  t0  = 0.0    ! Initial time [s]
+  tf  = 2.0e-7 ! Final time [s]
+  cfl = 0.2    ! 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
+/
+
+&parallel
+  nThreads = 16 ! Number of threads for OpenMP
+/
+

input/input_80ns_T60.nml

@@ -0,0 +1,43 @@
+&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 =  -50e3  ! Lower limit for velocity space [m s^-1]
+  vf =  250e3  ! Upper limit for velocity space [m s^-1]
+  nv = 401     ! Number of grid points in the velocity space
+/
+
+&output
+  folder = 'polytropic_80ns_T60' ! Folder name
+  outputStep = 1e-9              ! Time step for file write [s]
+/
+
+&time
+  t0  = 0.0    ! Initial time [s]
+  tf  = 2.0e-7 ! Final time [s]
+  cfl = 0.2    ! 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
+/
+
+&parallel
+  nThreads = 16 ! Number of threads for OpenMP
+/
+

input/input_fa_T30.nml

@@ -0,0 +1,43 @@
+&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 =  -50e3  ! Lower limit for velocity space [m s^-1]
+  vf =  250e3  ! Upper limit for velocity space [m s^-1]
+  nv = 401     ! Number of grid points in the velocity space
+/
+
+&output
+  folder = 'polytropic_fa_T30' ! Folder name
+  outputStep = 1e-9              ! Time step for file write [s]
+/
+
+&time
+  t0  = 0.0    ! Initial time [s]
+  tf  = 2.0e-7 ! Final time [s]
+  cfl = 0.2    ! 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
+/
+
+&parallel
+  nThreads = 16 ! Number of threads for OpenMP
+/
+

makefile

@@ -1,13 +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 vlaplex.f90 moduleConstantParameters.o moduleReferenceValues.o moduleOutput.o moduleTableBC.o -lopenblas -Ofast -fopenmp -Wall -o vlaplex
+
+# compiler
+# gfortran:
+FC := gfortran
+
+# compiler flags
+# gfortran:
+FCFLAGS := -fopenmp -Ofast -g -J $(MODDIR) -Wall -march=native
+
+#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
-

scripts_python/TZ_data.json

@@ -0,0 +1,641 @@
+{
+  "now": "2025-04-04T14:21:35.000Z",
+  "program": "ZVView, ver. 2021-09-16",
+  "file": "Copy of plotted data",
+  "f":"y(x)",
+  "title": "Tin Average Charge State",
+  "xAxis": "temperature",
+  "yAxis": "<Z>",
+  "xUnits": "eV",
+  "yUnits": "",
+  "xMin": 0.271593,
+  "xMax": 184099,
+  "xScale": 1,
+  "yScale": 0,
+  "funcs": [
+    {
+      "ifunc":0,
+      "fName":"Ne = 1.0E+12",
+      "numCol":1,
+      "typSoed":1,
+      "typUsi":-1,
+      "lx":36,
+      "i0x":0,
+      "i1x":35,
+      "pts":[
+	 {"x":0.5,	"y":0.032965}
+	,{"x":1,	"y":0.92671}
+	,{"x":1.5,	"y":1.6823}
+	,{"x":2,	"y":1.9381}
+	,{"x":5,	"y":3.3694}
+	,{"x":7,	"y":3.8735}
+	,{"x":10,	"y":4.1766}
+	,{"x":15,	"y":4.9651}
+	,{"x":23,	"y":6.2945}
+	,{"x":32,	"y":7.4784}
+	,{"x":52,	"y":9.4762}
+	,{"x":74,	"y":11.197}
+	,{"x":100,	"y":12.921}
+	,{"x":165,	"y":19.431}
+	,{"x":235,	"y":21.062}
+	,{"x":310,	"y":21.488}
+	,{"x":390,	"y":21.742}
+	,{"x":475,	"y":21.969}
+	,{"x":655,	"y":22.552}
+	,{"x":845,	"y":23.504}
+	,{"x":1000,	"y":24.553}
+	,{"x":1441,	"y":28.026}
+	,{"x":1925,	"y":31.867}
+	,{"x":2454,	"y":36.133}
+	,{"x":3030,	"y":38.155}
+	,{"x":3655,	"y":38.94}
+	,{"x":4331,	"y":39.397}
+	,{"x":5060,	"y":39.77}
+	,{"x":5844,	"y":40.155}
+	,{"x":6685,	"y":40.618}
+	,{"x":7585,	"y":41.202}
+	,{"x":8546,	"y":41.919}
+	,{"x":10000,	"y":43.042}
+	,{"x":20000,	"y":46.442}
+	,{"x":50000,	"y":47.852}
+	,{"x":100000,	"y":48.403}
+      ]
+    }
+    ,{
+      "ifunc":1,
+      "fName":"Ne = 1.0E+13",
+      "numCol":2,
+      "typSoed":1,
+      "typUsi":-1,
+      "lx":36,
+      "i0x":0,
+      "i1x":35,
+      "pts":[
+	 {"x":0.5,	"y":0.033255}
+	,{"x":1,	"y":1.0488}
+	,{"x":1.5,	"y":1.8974}
+	,{"x":2,	"y":1.984}
+	,{"x":5,	"y":3.4598}
+	,{"x":7,	"y":3.8851}
+	,{"x":10,	"y":4.18}
+	,{"x":15,	"y":4.9679}
+	,{"x":23,	"y":6.2958}
+	,{"x":32,	"y":7.4791}
+	,{"x":52,	"y":9.4765}
+	,{"x":74,	"y":11.197}
+	,{"x":100,	"y":12.921}
+	,{"x":165,	"y":19.431}
+	,{"x":235,	"y":21.062}
+	,{"x":310,	"y":21.488}
+	,{"x":390,	"y":21.742}
+	,{"x":475,	"y":21.969}
+	,{"x":655,	"y":22.552}
+	,{"x":845,	"y":23.504}
+	,{"x":1000,	"y":24.553}
+	,{"x":1441,	"y":28.026}
+	,{"x":1925,	"y":31.867}
+	,{"x":2454,	"y":36.133}
+	,{"x":3030,	"y":38.155}
+	,{"x":3655,	"y":38.94}
+	,{"x":4331,	"y":39.397}
+	,{"x":5060,	"y":39.77}
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+      "typUsi":-1,
+      "lx":36,
+      "i0x":0,
+      "i1x":35,
+      "pts":[
+	 {"x":0.5,	"y":8}
+	,{"x":1,	"y":8}
+	,{"x":1.5,	"y":8}
+	,{"x":2,	"y":8.0001}
+	,{"x":5,	"y":8.0069}
+	,{"x":7,	"y":8.0197}
+	,{"x":10,	"y":8.0501}
+	,{"x":15,	"y":8.1262}
+	,{"x":23,	"y":8.3073}
+	,{"x":32,	"y":7.9918}
+	,{"x":52,	"y":9.3773}
+	,{"x":74,	"y":11.177}
+	,{"x":100,	"y":12.915}
+	,{"x":165,	"y":16.245}
+	,{"x":235,	"y":23.165}
+	,{"x":310,	"y":26.987}
+	,{"x":390,	"y":29.485}
+	,{"x":475,	"y":31.555}
+	,{"x":655,	"y":35.008}
+	,{"x":845,	"y":36.799}
+	,{"x":1000,	"y":37.754}
+	,{"x":1441,	"y":39.94}
+	,{"x":1925,	"y":41.496}
+	,{"x":2454,	"y":42.632}
+	,{"x":3030,	"y":43.504}
+	,{"x":3655,	"y":44.197}
+	,{"x":4331,	"y":44.779}
+	,{"x":5060,	"y":45.238}
+	,{"x":5844,	"y":45.603}
+	,{"x":6685,	"y":45.9}
+	,{"x":7585,	"y":46.147}
+	,{"x":8546,	"y":46.365}
+	,{"x":10000,	"y":46.634}
+	,{"x":20000,	"y":47.448}
+	,{"x":50000,	"y":48.101}
+	,{"x":100000,	"y":48.558}
+      ]
+    }
+  ]
+}

scripts_python/TtoZne.py

@@ -0,0 +1,147 @@
+import json
+import numpy as np
+import matplotlib.pyplot as plt
+import csv
+import re
+import readBC
+import glob
+
+
+file_path = "TZ_data.json"
+
+with open(file_path, "r") as f:
+    data = json.load(f)
+
+T_values = {}
+
+for func in data["funcs"]:
+    for point in func["pts"]:
+        T = point["x"]
+        Z = point["y"]
+        if T not in T_values:
+            T_values[T] = []
+        T_values[T].append(Z)
+
+
+T_sorted = sorted(T_values.keys())
+Z_avg = [np.mean(T_values[T]) for T in T_sorted]
+
+
+# Save to CSV
+csv_file_path = "../average_TtoZ_curve.csv"
+with open(csv_file_path, "w", newline="") as csvfile:
+    writer = csv.writer(csvfile)
+    writer.writerow(["T", "Z_avg"])
+    writer.writerows(zip(T_sorted, Z_avg))
+
+# Plotting feature
+# plt.figure(figsize=(11, 8))
+
+# for func in data["funcs"]:
+#     fName = func["fName"]
+#     print(fName)
+#     match = re.match(r"Ne\s*=\s*([\d\.]+)E([+-]?\d+)", fName)
+#     if match:
+#         Ne, X = match.groups()
+#         formatted_label = rf"$n_e = {float(Ne):.1f} \times 10^{{{int(X)}}}$"
+#     else:
+#         formatted_label = fName  # Fallback in case of no match
+#     x = np.array([point["x"] for point in func["pts"]])
+#     y = np.array([point["y"] for point in func["pts"]])
+    # plt.plot(x, y, linestyle="--", alpha=0.6, label=formatted_label)
+
+# Plot the average curve
+# plt.errorbar(x_sorted, y_avg, y_std, capsize=3, color="black", linewidth=2, label="Average")
+# Basko = 22.5 * np.power(np.divide(x_sorted, 100.0), 0.6)
+# plt.plot(x_sorted, Basko, color="blue", linewidth=2, label="Basko's power law")
+
+# plt.xscale("log")  
+# plt.xlim([0.5, 100])
+# plt.ylim([0, 30])
+# plt.xlabel(f"Temperature ($\mathrm{{eV}}$)")
+# plt.ylabel(f"$\overline{{Z}}$")
+# plt.title(f"{data['title']}")
+# plt.legend()
+# plt.grid(True)
+# plt.savefig("TtoZ.pdf")
+# plt.show()
+
+# Collect all unique x values
+x_values = sorted(set(point["x"] for func in data["funcs"] for point in func["pts"]))
+
+# Initialize a dictionary to store y values for each Ne
+y_values_dict = {}
+
+# Process each function's data
+ne_list = []
+for func in data["funcs"]:
+    # Extract only the numerical part of Ne
+    ne_value = re.search(r"[\d\.E\+\-]+", func["fName"]).group(0)
+    ne_value = float(ne_value) * 1e6  # using conversion to m^-3
+    ne_list.append(float(ne_value))
+    y_values_dict[ne_value] = {x: None for x in x_values}
+    
+    for point in func["pts"]:
+        y_values_dict[ne_value][point["x"]] = point["y"]
+
+
+header = ["x"] + list(y_values_dict.keys())
+csv_data = []
+
+for x in x_values:
+    row = [x] + [y_values_dict[ne].get(x, "") for ne in y_values_dict]
+    csv_data.append(row)
+
+# Save to CSV
+csv_file_path = "../Zave_values_per_Ne.csv"
+with open(csv_file_path, "w", newline="") as csvfile:
+    writer = csv.writer(csvfile)
+    writer.writerow(header)  # Write heade
+    writer.writerows(csv_data)  # Write data rows
+
+
+
+
+
+# Plotting contour of T to Z per ne
+# import pandas as pd
+
+# # Define file path
+# file_path = "Zave_values_per_Ne.csv"
+
+# # Read the file and inspect its contents
+# df = pd.read_csv(file_path)
+
+# # Display the first few rows
+# df.head()
+# # Extract x values and Ne values (column headers)
+# x_values = df.iloc[:10, 0].values  # First column
+# Ne_values = np.array([float(col) for col in df.columns[1:]])  # Convert column names to float
+# # Ne_values = np.array([col for col in Ne_values])
+
+# # Extract y values as a 2D array
+# y_values = df.iloc[:10, 1:].values
+
+# # Create meshgrid for contour plot
+# X, Y = np.meshgrid(Ne_values, x_values)
+
+# # Plot contour
+# plt.figure(figsize=(8, 6))
+# cp = plt.contourf(X, Y, y_values, levels=20, cmap='viridis')
+# plt.colorbar(cp, label="Zave values")
+
+# # fileBC = glob.glob('../2025-03-10_11.23.25/bc.csv')
+# # time, n, u, T, TtoZ, Zinj = readBC.read(fileBC[0])
+# # plt.plot(n, T, color="black", linestyle="dashed", marker="o", markersize=4, label="Boundary Condition")
+# # plt.scatter(n[1], T[1], color="white", edgecolors="black", s=80, label="t = 0")  # White dot with black edge
+# # plt.scatter(n[-1], T[-1], color="cyan", edgecolors="black", s=80, label="t = end") 
+
+# # Labels and title
+# # plt.yscale("log")
+# plt.legend()
+# plt.xscale("log")  # Since Ne spans many orders of magnitude
+# plt.xlabel("Electron Density (ne)")
+# plt.ylabel("Temperature (eV)")
+# plt.title("Zave")
+# plt.savefig("Contour_Tin_Zave_BC.pdf")
+# plt.show()

scripts_python/plotBC.py

@@ -4,16 +4,17 @@ import numpy as np
 import readBC
 
 
-fileBC = glob.glob('../2025-02-10_11.14.59/bc.csv')
+paths = ['../2025-04-15_13.33.28/']
-time, n, u, T, TtoZ, Zinj = readBC.read(fileBC[0])
+time, n_i, u_i, T_i, Zinj, Z_Tne = readBC.read(paths[0] + 'bc.csv')
 
 fig, ax = plt.subplots()
 
+n_e = n_i * Zinj
 
-plt.plot(time, n / n[0] , label = f"$n_i$ ($\\times {n[0] * 1e-6} \\; cm^{{-3}})$")
+plt.plot(time, n_e / n_e[0], label = f"$n_e$ ($\\times {n_e[0] * 1e-6:.0e} \\; cm^{{-3}})$")
-plt.plot(time, T / T[0], label = f"$T  \\; (\\times{T[0]} \\; eV)$")
+plt.plot(time, T_i / T_i[0], label = f"$T  \\; (\\times{T_i[0]:.1f} \\; eV)$")
-plt.plot(time, TtoZ, label = "$Z$")
+plt.plot(time, Zinj, label = "Zinj")
-plt.plot(time, Zinj, label = "Injection species")
+#  plt.plot(time, Z_Tne, label = "Z_Tne")
 plt.semilogy()
 plt.legend()
 plt.show()

scripts_python/plotCumF.py

@@ -1,5 +1,6 @@
 import readPhi
 import readF
+import readZlist
 import matplotlib.pyplot as plt
 import glob
 import numpy as np
@@ -13,25 +14,32 @@ m_i = 1.9712e-25
 #  paths = ['../quasiNeutral_fullAblation/','../Poisson_fullAblation/', '../quasiNeutral_partialAblation/', '../Poisson_partialAblation/']
 #  paths = ['../2024-12-02_21.07.52/', '../Poisson_50ns_T30Z11/']
 #  paths = ['../2024-12-10_18.45.17/', '../Poisson_50ns_T30Z11/']
-paths = ['../2024-12-11_12.38.27/', '../Poisson_polytropic_fa_T30Z11/', '../Poisson_fa_T30Z11/']
+#  paths = ['../2024-12-11_12.38.27/', '../Poisson_polytropic_fa_T30Z11/', '../Poisson_fa_T30Z11/']
 #  paths = ['../Poisson_partialAblation/','../Poisson_partialAblation_lowerT/','../Poisson_partialAblation_lowT/','../Poisson_partialAblation_highT/']
+paths = ['../2025-04-17_14.39.34/']
 labels = [path[3:-1] for path in paths]
 
-for path, label in zip(paths, labels):
+m2s2_to_eV = m_i*0.5/e
-    filesCum_i = sorted(glob.glob(path+'time_*_fCum_i.csv'))
-    #  start = 0
-    #  end   = len(filesCum_i)
-    #  every = 20
-    #  for fileCum_i in filesCum_i[start:end+1:every]:
-        #  time, x, v, f_i = readF.read(fileCum_i)
-        #  plt.plot(v**2*m_i*0.5/e, f_i[0]*e/m_i/v, label='t = {:.1f} ns'.format(time*1e9))
 
-    time, x, v, f_i = readF.read(filesCum_i[-1])
+for path, label in zip(paths, labels):
-    plt.plot(v**2*m_i*0.5/e, f_i[0]*e/m_i/v, label=label)
+    Zlist      = readZlist.read(path+'ZList.csv')
+    filesCum_i = sorted(glob.glob(path+'time_*_fCum_i.csv'))
+    _, _, v, _ = readF.read(filesCum_i[-1])
+    sumF = np.zeros(len(v))
+    E = v**2*m2s2_to_eV
+
+    for Z in Zlist:
+        filename='time_*_Z_{:.1f}_fCum_i.csv'.format(Z)
+        filesCum_i = sorted(glob.glob(path+filename))
+        time, rCum, v, f_i = readF.read(filesCum_i[-1])
+        sumF += f_i[0]
+        plt.plot(E, 4.0*np.pi*rCum[0]**2*f_i[0]/E, label=Z)
+    plt.plot(E, 4.0*np.pi*rCum[0]**2*sumF/E, label='sum', color='k', linestyle='dashed')
+    print(time)
 
 plt.yscale('log')
-plt.ylim([1e16,5e27])
+plt.ylim([1e8,5e11])
-plt.ylabel('Sum f(e) / sqrt(e) (m^-3 eV^-1)')
+plt.ylabel('dN / dE (eV^-1)')
 plt.xscale('log')
 plt.xlim([1e0,1e4])
 plt.xlabel('e (eV)')

scripts_python/plotMom.py

@@ -1,6 +1,7 @@
 import readPhi
 import readMom
 import readF
+import readZlist
 import matplotlib.pyplot as plt
 import glob
 import numpy as np
@@ -11,29 +12,45 @@ from scipy.constants import e, k
 #  paths = ['../quasiNeutral_partialAblation/','../Poisson_partialAblation/']
 #  paths = ['../2024-10-02_14.30.44/']
 #  paths = ['../quasiNeutral_fullAblation/','../Poisson_fullAblation/']
-paths = ['../2024-12-10_18.45.17/']
+#  paths = ['../2025-04-10_11.59.02/']
+paths = ['../polytropic_80ns_T30/']
 labels = [path[3:-1] for path in paths]
 
 for path, label in zip(paths, labels):
+    Zlist      = readZlist.read(path+'ZList.csv')
     filesPhi   = sorted(glob.glob(path+'time_*_phi.csv'))
-    filesMom_i = sorted(glob.glob(path+'time_*_mom_i.csv'))
+    start = 80
-    start = 50
+    end   = 85#len(filesPhi)
-    end   = len(filesMom_i)
+    every = 1
-    every = 20
+    fig, ax = plt.subplots(3, sharex='all')
-    fig, ax = plt.subplots(4, sharex='all')
+    ax[1].set_yscale('log')
-    for fileMom_i, filePhi in zip(filesMom_i[start:end+1:every], filesPhi[start:end+1:every]):
+    ax[1].set_ylim(bottom=1e10, top=1e24)
-        time, r, phi, E, n_e         = readPhi.read(filePhi)
+    _, r, _, _, _         = readPhi.read(filesPhi[0])
-        time, r, n_i, u_i, T_i, Zave = readMom.read(fileMom_i)
+    for t in range(start,end+1,every):
+        sum_Zni = np.zeros(len(r))
+        ave_ui  = np.zeros(len(r))
+        ave_Ti  = np.zeros(len(r))
+        for Z in Zlist:
+            filename='time_*_Z_{:.1f}_mom_i.csv'.format(Z)
+            filesMom_i = sorted(glob.glob(path+filename))
+            fileMom_i = filesMom_i[t]
+            time, r, n_i, u_i, T_i, Zave = readMom.read(fileMom_i)
+            sum_Zni += Zave*n_i
+            ave_ui  += Zave*n_i*u_i
+            ave_Ti  += Zave*n_i*T_i
+
+        ave_ui = np.divide(ave_ui, sum_Zni, out=np.zeros_like(ave_ui), where=sum_Zni!=0.0)
+        ave_Ti = np.divide(ave_Ti, sum_Zni, out=np.zeros_like(ave_Ti), where=sum_Zni!=0.0)
+
+        filePhi = filesPhi[t]
+        time, r, phi, E, n_e  = readPhi.read(filePhi)
 
         ax[0].plot(r, phi, label='t = {:.1f} ns'.format(time*1e9))
         #  ax[0].plot(r, E, label='t = {:.1f} ns'.format(time*1e9))
         #  ax[0].plot(r, (Zave*n_i - n_e), label='t = {:.1f} ns'.format(time*1e9))
-        ax[1].set_yscale('log')
+        ax[1].plot(r, sum_Zni)
-        #  ax[1].set_ylim(bottom=1e16)
-        ax[1].plot(r, Zave*n_i)
         ax[1].plot(r,      n_e, color='k', linestyle='dashed')
-        ax[2].plot(r,      u_i)
+        ax[2].plot(r, ave_ui)
-        ax[3].plot(r,      T_i)
 
     ax[0].set_title(label)
     ax[0].legend()

scripts_python/readBC.py

@@ -4,12 +4,12 @@ def read(filename):
     # Get time
     df = pandas.read_csv(filename)
     time = df['t (s)'].to_numpy()
-    n = df['n (m^-3)'].to_numpy()
+    n = df['n_i (m^-3)'].to_numpy()
-    u = df['u (m s^-1)'].to_numpy()
+    u = df['u_i (m s^-1)'].to_numpy()
-    T = df['T (eV)'].to_numpy()
+    T = df['T_i (eV)'].to_numpy()
-    TtoZ = df['TtoZ'].to_numpy()
     Zinj = df['Zinj'].to_numpy()
+    Z_Tne = df['Z_Tne'].to_numpy()
 
-    return time, n, u, T, TtoZ, Zinj
+    return time, n, u, T, Zinj, Z_Tne
 
 

scripts_python/readF.py

@@ -5,9 +5,12 @@ def read(filename):
     df = pandas.read_csv(filename,skiprows=0,nrows=1)
     time = df['t (s)'].to_numpy()[0]
 
-    df = pandas.read_csv(filename,skiprows=2,nrows=1,header=None)
+    df = pandas.read_csv(filename,skiprows=2,nrows=1)
+    Z = df['Z'].to_numpy()[0]
+
+    df = pandas.read_csv(filename,skiprows=4,nrows=1,header=None)
     x = df.to_numpy()[0][1:]
-    df = pandas.read_csv(filename,skiprows=3,header=None)
+    df = pandas.read_csv(filename,skiprows=5,header=None)
     f = []
     for col in df:
         if col == 0:

scripts_python/readZlist.py

@@ -0,0 +1,10 @@
+import pandas
+
+def read(filename):
+    # Get time
+    df = pandas.read_csv(filename)
+    Zlist = df['Z_list'].to_numpy()
+
+    return Zlist
+
+

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 +1,207 @@
+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 checkIO(subroutineName)
+
+      character(len=*), intent(in):: subroutineName
+
+      if     (inputFile_io < 0) then
+        write (*, '("End-of-file found when reading in subroutine: ",a)') subroutineName
+        error stop
+
+      elseif (inputFile_io > 0) then
+        write (*, '("Error condition ", i3," found when reading in subroutine: ",a)') inputFile_io, subroutineName
+        error stop
+
+      end if
+
+      inputFile_io = 0
+
+    end subroutine checkIO
+
+    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)
+      rewind(unit=inputFile_id)
+
+      ! 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
+
+      call checkIO('readReference')
+
+    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)
+      rewind(unit=inputFile_id)
+
+      call checkIO('readGrid')
+
+      r0 = r0/L_ref
+      rf = rf/L_ref
+      dr = dr/L_ref
+
+      v0 = v0/u_ref
+      vf = vf/u_ref
+
+    end subroutine readGrid
+
+    subroutine readOutput(folder_alloc, outputStep)
+
+      character(:), allocatable, intent(out):: folder_alloc
+      real(dp), intent(out):: outputStep
+      character(len=128):: folder
+      namelist /output/ folder, outputStep
+
+      read(nml=output, unit=inputFile_id, iostat=inputFile_io)
+      rewind(unit=inputFile_id)
+
+      call checkIO('readOutput')
+
+      folder_alloc = trim(folder)
+
+    end subroutine readOutput
+
+    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)
+      rewind(unit=inputFile_id)
+
+      call checkIO('readTime')
+
+      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)
+      rewind(unit=inputFile_id)
+
+      call checkIO('readDetector')
+
+      ! 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)
+      rewind(unit=inputFile_id)
+
+      call checkIO('readBoundary')
+
+      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)
+      rewind(unit=inputFile_id)
+
+      call checkIO('readZ')
+
+      ! 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 readParallel(nThreads)
+
+      integer, intent(out):: nThreads
+      namelist /parallel/ nThreads
+
+      read(nml=parallel, unit=inputFile_id, iostat=inputFile_io)
+      rewind(unit=inputFile_id)
+
+      call checkIO('readParallel')
+
+    end subroutine readParallel
+
+    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/output.f90

@@ -13,7 +13,8 @@ module output
   integer, parameter:: dataF_id   = 30
   integer, parameter:: dataPhi_id = 40
   integer, parameter:: dataCum_id = 50
-  character(len=*), parameter :: formatInt = 'I10'
+  integer, parameter:: dataTime_id  = 60
+  character(len=*), parameter :: formatInt = 'I0'
   character(len=7), parameter:: formatFloat = 'ES0.6e3'
   character(len=3), parameter:: formatSep   = '","'
   character(len=7):: formatTime
@@ -28,15 +29,25 @@ module output
 
     end subroutine setTimeFormat
 
-    subroutine createPath()
+    function setZFormat(Z) result(ZString)
-      character(8)  :: date_now
+      real(dp), intent(in):: Z
-      character(10) :: time_now
+      character(len=4):: ZString
+
+      write(ZString, '(F4.1)') Z
+
+    end function setZFormat
+
+    subroutine createPath(folder)
+      character(8) :: date_now
+      character(10):: time_now
+      character(:), allocatable:: folder
 
       call date_and_time(date_now, time_now)
 
       !Compose the folder name
       pathOutput = date_now(1:4) // '-' // date_now(5:6) // '-' // date_now(7:8) // '_' // &
-                   time_now(1:2) // '.' // time_now(3:4) // '.' // time_now(5:6) // '/'
+                   time_now(1:2) // '.' // time_now(3:4) // '.' // time_now(5:6) // '_' // &
+                   folder        // '/'
 
       call system('mkdir ' // pathOutput)
 
@@ -56,23 +67,20 @@ module output
       character(:), allocatable:: filename
       integer:: i, j
       character(len=10):: timeString
-      character(len=10) :: ZString
+      character(len=4) :: ZString
 
       do j = 1, nz
         write (timeString, formatTime) t
-        write(ZString, '(F6.3)') Z_list(j)
+        ZString = setZFormat(Z_list(j))
-        ZString = adjustl(trim(ZString))
 
-        ZString = adjustl(ZString)
+        filename = 'time_' // trim(timeString) // '_Z_' // trim(adjustl(ZString)) // '_f_i.csv'
-        ZString = ZString(:index(ZString // '.', '.') - 1) // ZString(index(ZString, '.') + 1:)
-        filename = 'time_' // trim(timeString) // '_Z' // trim(ZString) // '_f_i.csv'
         write (*, '(A, A)') 'Writing: ', filename
 
         open(unit=dataF_id, file=pathOutput // filename)
         write(dataF_id, '(A)') "t (s)"
         write(dataF_id, '('//formatFloat//')') t*dt*t_ref
-        write(dataPhi_id, '(A)') "Z"
+        write(dataF_id, '(A)') "Z"
-        write(dataPhi_id, '('//formatFloat//')') Z_list(j)
+        write(dataF_id, '('//formatFloat//')') Z_list(j)
         write(myfmt, "(I0)") nr
         myfmt =  '(A,' // trim(myfmt) // '(' // formatSep // ',' // formatFloat // '))'
         write(dataF_id, myfmt) "v (m/s) / r (m)", r*L_ref
@@ -141,16 +149,13 @@ module output
       integer:: i
       integer:: j
       character(len=10):: timeString
-      character(len=10) :: ZString
+      character(len=4) :: ZString
 
       do j = 1, nz
         write (timeString, formatTime) t
-        write(ZString, '(F6.3)') Z_list(j)
+        ZString = setZFormat(Z_list(j))
-        ZString = adjustl(trim(ZString))
 
-        ZString = adjustl(ZString)
+        filename = 'time_' // trim(timeString) // '_Z_' // trim(adjustl(ZString)) // '_mom_i.csv'
-        ZString = ZString(:index(ZString // '.', '.') - 1) // ZString(index(ZString, '.') + 1:)
-        filename = 'time_' // trim(timeString) // '_Z' // trim(ZString) // '_mom_i.csv'
         write (*, '(A, A)') 'Writing: ', filename
 
         open(unit=dataPhi_id, file=pathOutput//filename)
@@ -162,8 +167,8 @@ module output
         do i = 1, nr
           write(dataPhi_id, '('//formatFloat//',3('//formatSep //','//formatFloat//'))') &
                             r(i)*L_ref,                                                  &
-                            n_i(j,i)*n_ref,                                                &
+                            n_i(j,i)*n_ref,                                              &
-                            u_i(j,i)*u_ref,                                                &
+                            u_i(j,i)*u_ref,                                              &
                             T_i(j,i)*Temp_ref/ev_to_K                  
 
         end do
@@ -172,13 +177,13 @@ module output
       end do
     end subroutine writeOutputMom
 
-    subroutine writeOutputBoundary(t, dt, n, u, Temp, TtoZ, Zinj)
+    subroutine writeOutputBoundary(t, dt, n, u, Temp, Z_Tne, Zinj)
       use constantParameters, only: eV_to_K
       use referenceValues,    only: t_ref, n_ref, u_ref, Temp_ref
 
       integer, intent(in):: t
       real(dp), intent(in):: dt
-      real(dp), intent(in):: n, u, Temp, TtoZ, Zinj
+      real(dp), intent(in):: n, u, Temp, Z_Tne, Zinj
       character(len=6), parameter:: filename = 'bc.csv'
       logical:: res
 
@@ -186,41 +191,61 @@ module output
       if (.not. res) then
         write (*, '(A, A)') 'Writing: ', filename
         open(unit=dataBC_id, file=pathOutput // filename, action='write', position='append')
-        write(dataBC_id, '(A,5(' // formatSep // ',A))') 't (s)', 'n (m^-3)', 'u (m s^-1)', 'T (eV)', 'TtoZ','Zinj'
+        write(dataBC_id, '(A,5(' // formatSep // ',A))') 't (s)', 'n_i (m^-3)', 'u_i (m s^-1)', 'T_i (eV)', 'Zinj','Z_Tne'
         close(dataBC_id)
 
       end if
 
       open(unit=dataBC_id, file=pathOutput // filename, action='write', position='append')
       write(dataBC_id, '(' // formatFloat // ',5('// formatSep // ',' // formatFloat // '))') &
-                        t*dt*t_ref,  n*n_ref, u*u_ref, Temp*Temp_ref/eV_to_K, TtoZ, Zinj
+                        t*dt*t_ref,  n*n_ref, u*u_ref, Temp*Temp_ref/eV_to_K, Zinj, Z_Tne
 
       close(dataBC_id)
 
     end subroutine writeOutputBoundary
 
-    subroutine writeOutputTime(t, time)
+! JG: What is this procedure?
-      integer, intent(in):: t
+!     subroutine writeOutputTime(t, time, bins)
-      real(dp), intent(in):: time
+!       integer, intent(in):: t
-      character(len=8), parameter:: filename = 'time.csv'
+!       real(dp), intent(in):: time
-      logical:: res
+!       real(dp), intent(in):: bins
+!       character(len=8), parameter:: filename = 'time.csv'
+!       logical:: res
+!
+!       inquire(file=pathOutput // filename, exist=res)
+!       if (.not. res) then
+!         write (*, '(A, A)') 'Writing: ', filename
+!         open(unit=dataTime_id, file=pathOutput // filename, action='write', position='append')
+!         write(dataTime_id, '(A,2(' // formatSep // ',A))') 'timestep', 'duration (s)', '#bins'
+!         close(dataTime_id)
+!
+!       end if
+!
+!       open(unit=dataTime_id, file=pathOutput // filename, action='write', position='append')
+!       write(dataTime_id, '(' // formatInt // ',2('// formatSep // ',' // formatFloat // '))') &
+!                         t,  time, bins
+!
+!       close(dataTime_id)
+!
+!     end subroutine writeOutputTime
 
-      inquire(file=pathOutput // filename, exist=res)
+    subroutine writeOutputZList(nz, Z_list)
-      if (.not. res) then
+      integer,  intent(in):: nz
-        write (*, '(A, A)') 'Writing: ', filename
+      real(dp), intent(in):: Z_list(1:nz)
-        open(unit=dataBC_id, file=pathOutput // filename, action='write', position='append')
+      character(:), allocatable:: filename
-        write(dataBC_id, '(A,1(' // formatSep // ',A))') 'timestep', 'duration (s)'
+      integer:: i
-        close(dataBC_id)
 
-      end if
+      filename = 'ZList.csv'
+      write (*, '(A, A)') 'Writing: ', filename
+      open(unit=dataPhi_id, file=pathOutput//filename)
+      write(dataPhi_id, '(A)') "Z_list"
+      do i = 1, nz
+        write(dataPhi_id, '('//formatFloat//')') Z_list(i)
 
-      open(unit=dataBC_id, file=pathOutput // filename, action='write', position='append')
+      end do
-      write(dataBC_id, '(' // formatInt // ',' // formatSep // ',' // formatFloat // ')') &
+      close(unit=dataPhi_id)
-                        t,  time
 
-      close(dataBC_id)
+    end subroutine writeOutputZList
-
-    end subroutine writeOutputTime
 
     subroutine writeOutputRef()
       use referenceValues,    only: t_ref, L_ref, n_ref, u_ref, Temp_ref, phi_ref
@@ -254,24 +279,21 @@ module output
       character(:), allocatable:: filename
       integer:: i, j
       character(len=10):: timeString
-      character(len=10) :: ZString
+      character(len=4) :: ZString
 
 
       do j = 1, nz
         write (timeString, formatTime) t
-        write(ZString, '(F6.3)') Z_list(j)
+        ZString = setZFormat(Z_list(j))
-        ZString = adjustl(trim(ZString))
 
-        ZString = adjustl(ZString)
+        filename = 'time_' // trim(timeString) // '_Z_' // trim(adjustl(ZString)) // '_fCum_i.csv'
-        ZString = ZString(:index(ZString // '.', '.') - 1) // ZString(index(ZString, '.') + 1:)
-        filename = 'time_' // trim(timeString) // '_Z' // trim(ZString) // '_fCum_i.csv'
         write (*, '(A, A)') 'Writing: ', filename
 
         open(unit=dataCum_id, file=pathOutput // filename)
         write(dataCum_id, '(A)') "t (s)"
         write(dataCum_id, '('//formatFloat//')') t*dt*t_ref
-        write(dataPhi_id, '(A)') "Z"
+        write(dataCum_id, '(A)') "Z"
-        write(dataPhi_id, '('//formatFloat//')') Z_list(j)
+        write(dataCum_id, '('//formatFloat//')') Z_list(j)
         write(myfmt, "(I0)") 1
         myfmt =  '(A,' // trim(myfmt) // '(' // formatSep // ',' // formatFloat // '))'
         write(dataCum_id, myfmt) "v (m/s) / r (m)", r*L_ref

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
@@ -6,10 +6,9 @@ module moduleTableBC
     real(dp):: n_min, n_max
     real(dp):: u_min, u_max
     real(dp):: Temp_min, Temp_max
-    real(dp):: Zave_min, Zave_max
     real(dp), allocatable, dimension(:):: t
-    real(dp), allocatable, dimension(:):: n, u, Temp, Zave
+    real(dp), allocatable, dimension(:):: n, u, Temp
-    real(dp), allocatable, dimension(:):: n_k, u_k, Temp_k, Zave_k
+    real(dp), allocatable, dimension(:):: n_k, u_k, Temp_k
     contains
       procedure, pass:: init    => initTableBC
       procedure, pass:: get     => getValueTableBC
@@ -48,29 +47,27 @@ module moduleTableBC
 
       !Allocate table arrays
       allocate(self%t(1:amount))
-      allocate(  self%n(1:amount),   self%u(1:amount),   self%Temp(1:amount),   self%Zave(1:amount))
+      allocate(  self%n(1:amount),   self%u(1:amount),   self%Temp(1:amount))
-      allocate(self%n_k(1:amount), self%u_k(1:amount), self%Temp_k(1:amount), self%Zave_k(1:amount))
+      allocate(self%n_k(1:amount), self%u_k(1:amount), self%Temp_k(1:amount))
       self%t      = 0.0_dp
       self%n      = 0.0_dp
       self%u      = 0.0_dp
       self%Temp   = 0.0_dp
-      self%Zave   = 0.0_dp
       self%n_k    = 0.0_dp
       self%u_k    = 0.0_dp
       self%Temp_k = 0.0_dp
-      self%Zave_k = 0.0_dp
 
       i = 0
       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
         backspace(id)
         i = i + 1
-        read(id, *) self%t(i), self%n(i), self%u(i), self%Temp(i), self%Zave(i)
+        read(id, *) self%t(i), self%n(i), self%u(i), self%Temp(i)
 
       end do
 
@@ -89,25 +86,22 @@ module moduleTableBC
       self%u_max    = self%u(amount)
       self%Temp_min = self%Temp(1)
       self%Temp_max = self%Temp(amount)
-      self%Zave_min = self%Zave(1)
-      self%Zave_max = self%Zave(amount)
 
       do i = 1, amount - 1
         self%n_k(i)    = (   self%n(i+1) -    self%n(i))/(self%t(i+1) - self%t(i))
         self%u_k(i)    = (   self%u(i+1) -    self%u(i))/(self%t(i+1) - self%t(i))
         self%Temp_k(i) = (self%Temp(i+1) - self%Temp(i))/(self%t(i+1) - self%t(i))
-        self%Zave_k(i) = (self%Zave(i+1) - self%Zave(i))/(self%t(i+1) - self%t(i))
 
       end do
 
     end subroutine initTableBC
 
-    subroutine getValueTableBC(self, t, n, u, Temp, Zave)
+    subroutine getValueTableBC(self, t, n, u, Temp)
       implicit none
 
       class(tableBC), intent(in):: self
       real(dp), intent(in):: t
-      real(dp), intent(out):: n, u, Temp, Zave
+      real(dp), intent(out):: n, u, Temp
       real(dp):: delta_t
       integer:: i
 
@@ -115,13 +109,11 @@ module moduleTableBC
         n    = self%n_min
         u    = self%u_min
         Temp = self%Temp_min
-        Zave = self%Zave_min
 
       elseif (t >= self%t_max) THEN
         n    = self%n_max
         u    = self%u_max
         Temp = self%Temp_max
-        Zave = self%Zave_max
 
       else
         i = minloc(abs(t - self%t), 1)
@@ -135,11 +127,10 @@ module moduleTableBC
         n    =    self%n(i) +    self%n_k(i)*delta_t
         u    =    self%u(i) +    self%u_k(i)*delta_t
         Temp = self%Temp(i) + self%Temp_k(i)*delta_t
-        Zave = self%Zave(i) + self%Zave_k(i)*delta_t
 
       end if
 
     end subroutine getValueTableBC
 
-end module moduleTableBC
+end module tableBoundary
 

src/modules/tableTNZ.f90

@@ -0,0 +1,155 @@
+module tableTNZ
+  use constantParameters, only: dp
+
+  type:: tableTn_to_Z
+    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
+    real(dp), allocatable, dimension(:):: ne
+    contains
+      procedure, pass:: init    => initTableTtoZne
+      procedure, pass:: get     => getValueTableTtoZne
+
+  end type tableTn_to_Z
+
+  contains
+    subroutine initTableTtoZne(self, tableFile)
+      use constantParameters, only: eV_to_K
+      use referenceValues, only: Temp_ref, n_ref
+      implicit none
+
+      class(tableTn_to_Z), intent(inout):: self
+      character(:), allocatable, intent(in):: tableFile
+      character(100):: dummy
+      character(len=512) :: line
+      character(len=20), allocatable :: ne_headers(:)
+      integer:: amount, num_ne
+      integer:: i,j
+      integer:: stat
+      integer:: id = 20
+      num_ne = 0
+
+      inquire(file=tableFile, iostat=stat)
+      if (stat /= 0) then
+          write (*, '("Error: TNZ table file ", a, " does not exist")') tableFile
+          return
+
+      end if
+
+      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)
+      read(id, '(A)', iostat = stat) dummy
+      do i = 1, len_trim(dummy)
+        if (dummy(i:i) ==  ",") num_ne = num_ne + 1
+      end do
+      allocate(ne_headers(num_ne))
+      allocate(self%ne(num_ne))
+      
+      rewind(id)
+      read(id, '(A)') line
+
+      ! Read values while skipping the first entry
+      read(line, *) dummy, (self%ne(i), i=1, num_ne)
+
+
+      ! read(id, *)  ! Skip 'x'
+      ! do i = 1, num_ne
+      !   read(dummy, *) ne_headers(i)
+      !   read(ne_headers(i), *) self%ne(i)
+      !   print *, self%ne(i)
+      ! end do
+      rewind(id)
+      
+
+      !Allocate table arrays
+      allocate(self%Temp(1:amount))
+      allocate(self%Z(1:amount, 1:num_ne))
+      allocate(self%Z_k(1:amount, 1:num_ne))
+      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, *, iostat= stat) self%Temp(i), (self%Z(i, j), j = 1, num_ne)
+
+      end do
+      self%Temp = self%Temp * eV_to_K / Temp_ref
+      self%ne = self%ne / n_ref
+
+      close(id)
+
+      self%Temp_min    = self%Temp(1)
+      self%Temp_max    = self%Temp(amount)
+      self%Z_min    = self%Z(1,1)
+      self%Z_max    = self%Z(amount,num_ne)
+      do i = 1, amount - 1
+        do j = 1, num_ne 
+          self%Z_k(i,j)    = (   self%Z(i+1,j) -    self%Z(i,j))/(self%Temp(i+1) - self%Temp(i))
+        end do
+      end do
+
+    end subroutine initTableTtoZne
+
+    subroutine getValueTableTtoZne(self, Temp, ne, Z)
+      implicit none
+
+      class(tableTn_to_Z), intent(in):: self
+      real(dp), intent(in):: Temp, ne
+      real(dp), intent(out):: Z
+      real(dp):: delta_Temp
+      integer:: i, j
+
+      j = minloc(abs(ne - self%ne), 1)
+      ! print *, "ne : ", ne
+      !  print *, "Temp : ", Temp
+
+
+      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,j) +    self%Z_k(i,j)*delta_Temp
+
+      end if
+
+    end subroutine getValueTableTtoZne
+
+
+
+end module tableTNZ
+

src/vlaplex.f90

@@ -1,46 +1,26 @@
- 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 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
   real(dp), parameter:: gamma_e_exp  =            1.0_dp /(gamma_e - 1.0_dp) ! Exponent for polytropic electrons
   real(dp), parameter:: gamma_e_dexp = (2.0_dp - gamma_e)/(gamma_e - 1.0_dp) ! Exponent for polytropic db_dphi
+  real(dp), parameter:: n_epsilon = 1.0e-16_dp
 
   real(dp):: r0, rf
   real(dp), allocatable, dimension(:):: r
   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
@@ -48,12 +28,11 @@ program VlaPlEx
   integer:: j0 ! First integer of positive velocity
 
   real(dp):: Temp_bc ! Temperature
-  real(dp):: Zave_bc ! Average charge state
+  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
 
   real(dp), allocatable, dimension(:,:,:):: f_i, f_i_old
   real(dp), allocatable, dimension(:):: f0   ! Boundary at r = x_0
@@ -64,7 +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
@@ -74,54 +53,54 @@ program VlaPlEx
   real(dp), allocatable, dimension(:):: phi, phi_old, E, db_dphi
   real(dp):: phiConv
   real(dp):: phi0
-  real(dp):: T_e
+  real(dp):: T_e0
   ! real(dp):: phiF
   integer:: k
 
+  integer:: nThreads ! number of threads for OpenMP
+
   real(dp), allocatable, dimension(:,:):: fCum_i
   real(dp):: rCum
   integer:: rCum_index
+  real(dp):: outputStep
+  character(:), allocatable:: folder
+
+  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 readParallel(nThreads)
+  call readGrid(r0, rf, dr, v0, vf, nv)
+  call readOutput(folder, outputStep)
+  call readTime(t0, tf, CFL)
+  call readDetector(rCum)
+  call readBoundary(boundaryConditions)
+  call readZ(Zlist, nz, Tene_to_Z)
+  call closeInputFile()
 
   ! Set number of threads
-  call omp_set_num_threads(8)
+  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)
-
-  ! 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 =-1.0e1_dp*c_s
+  ! Grid in the velocity space
-  vf = 2.0e1_dp*c_s
+  dv = (vf - v0) / float(nv-1)
-  dv = 1.0e-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
@@ -133,14 +112,11 @@ program VlaPlEx
     j0 = j0 + 1
   end if
 
-  t0 = 0.0_dp
+  dt = CFL*dr/vf
-  tf = 2.0e-7_dp / t_ref
-  ! tf = 1.0e1_dp * (rf - r0) / c_s
-  dt = 1.0e-2_dp*dr/c_s
   nt = nint((tf - t0) / dt) 
   dt =      (tf - t0) / float(nt)
 
-  everyOutput = nint(1.0e-9_dp/t_ref/dt)
+  everyOutput = nint(outputStep/t_ref/dt)
   if (everyOutput  == 0) then
     everyOutput = 1
 
@@ -152,34 +128,30 @@ program VlaPlEx
 
   end if
 
-  write(*, '(A,ES0.4e3)') 'CFL: ', dt*vf/dr
-
-  nz = 2
   ! 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))
-  f_i     = 0.0_dp
+  f_i         = 0.0_dp
-  f_i_old = 0.0_dp
+  f_i_old     = 0.0_dp
-  n_i     = 0.0_dp
+  n_i         = 0.0_dp
-  sum_ni   = 0.0_dp
+  sum_ni      = 0.0_dp
-  u_i     = 0.0_dp
+  u_i         = 0.0_dp
-  E_i     = 0.0_dp
+  E_i         = 0.0_dp
-  T_i     = 0.0_dp
+  T_i         = 0.0_dp
-  n_e     = 0.0_dp
+  n_e         = 0.0_dp
-  T_e     = 0.0_dp
+  T_e0        = 0.0_dp
-  Zave    = 0.0_dp
+  Zave        = 0.0_dp
-  Z_list  = (/ 6.0, 12.0 /)
+  Zave_bc_old = 0.0_dp
-  phi     = 0.0_dp
+  phi         = 0.0_dp
-  phi_old = 0.0_dp
+  phi_old     = 0.0_dp
-  E       = 0.0_dp
+  E           = 0.0_dp
-  fCum_i  = 0.0_dp
+  fCum_i      = 0.0_dp
 
   ! Allocate matrix for Poisson equation
   allocate(diag(1:nr), diag_low(1:nr-1), diag_high(1:nr-1))
@@ -223,23 +195,31 @@ program VlaPlEx
   f0 = 0.0_dp
 
   ! Output initial values
-  call createPath()
+  call createPath(folder)
   call setTimeFormat(nt)
   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, Zlist)
 
   ! Main loop
   do t = 1, nt
     time = t * dt + t0
-    call boundaryConditions%get(time, n_bc, u_bc, Temp_bc, Zave_bc)
+
-    z_inj = minloc(abs(Z_list - T_to_Z(Temp_bc)),1)
+    ! Get boundary conditions for specific time
-    Zave_bc = Z_list(z_inj)
+    call boundaryConditions%get(time, n_bc, u_bc, Temp_bc)
-    u_bc = sqrt(Zave_bc * Temp_bc)
+    ! Find new \bar{Z}_i based on T_e0 = Temp_bc and n_e = n_bc
-    call writeOutputBoundary(t, dt, n_bc, u_bc, Temp_bc, T_to_Z(Temp_bc), Zave_bc)
+    call Tene_to_Z%get(Temp_bc, n_bc, Zave_bc)
+    ! Assign Z(T,n) to bin
+    z_inj = minloc(abs(Zlist - Zave_bc),1)
+    ! Calculate inject (sonic) speed
+    u_bc = sqrt(Zlist(z_inj)* Temp_bc)
+    ! Calculate ion density to inject
+    n_bc = n_bc / Zlist(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)
@@ -249,7 +229,7 @@ program VlaPlEx
     f_i_old(z_inj,1,j0:nv) = f0
     f_i(:,1,j0:nv) = f_i_old(:,1,j0:nv)
 
-    T_e = Temp_bc
+    T_e0 = Temp_bc
 
     ! r = rf, v<0
     f_i_old(:,nr,1:j0-1) = 0.0_dp
@@ -260,32 +240,37 @@ program VlaPlEx
     sum_ni = 0.0_dp
     ! Advect in the r direction
     do iz = 1, nz
+      if (all(n_i(iz,:) < n_epsilon) .and. iz .ne. z_inj) then
+        cycle
+      end if
       !$omp parallel do
       do i = 1, nr
         ! Advect negative velocity
         if (i < nr) then
           f_i(iz,i,1:j0-1) = f_i_old(iz,i,1:j0-1) - v(1:j0-1)*dt/dr/r(i)**2*(r(i+1)**2*f_i_old(iz,i+1,1:j0-1) - &
-                                                                      r(i  )**2*f_i_old(iz,i  ,1:j0-1))
+                                                                    r(i  )**2*f_i_old(iz,i  ,1:j0-1))
         end if
         ! Advect positive velocity
         if (i >  1) then
           f_i(iz,i,j0:nv)  = f_i_old(iz,i, j0:nv) - v( j0:nv)*dt/dr/r(i)**2*(r(i  )**2*f_i_old(iz,i  , j0:nv) - &
-                                                                      r(i-1)**2*f_i_old(iz,i-1, j0:nv))
+                                                                    r(i-1)**2*f_i_old(iz,i-1, j0:nv))
         end if
 
         n_i(iz,i) = sum(f_i(iz,i,:))*dv
-        if (n_i(iz,i) > 1.0e-10_dp) then
+        if (n_i(iz,i) > n_epsilon) then
-          u_i(iz,i)  = sum(v(:)   *f_i(iz,i,:))*dv / n_i(iz,i)
+          u_i(iz,i)   = sum(v(:)   *f_i(iz,i,:))*dv / n_i(iz,i)
-          E_i(i)  = sum(v(:)**2*f_i(iz,i,:))*dv / n_i(iz,i)
+          E_i(i)      = sum(v(:)**2*f_i(iz,i,:))*dv / n_i(iz,i)
-          T_i(iz,i)  = 2.0_dp*E_i(i) - 2.0_dp*u_i(iz,i)**2
+          T_i(iz,i)   = 2.0_dp*E_i(i) - 2.0_dp*u_i(iz,i)**2
         else
-          u_i(iz,i)  = 0.0_dp
+          f_i(iz,i,:) = 0.0_dp
-          T_i(iz,i)  = 0.0_dp
+          n_i(iz,i)   = 0.0_dp
+          u_i(iz,i)   = 0.0_dp
+          T_i(iz,i)   = 0.0_dp
         end if
 
       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
@@ -323,12 +308,12 @@ program VlaPlEx
       ! phi0=phi(1) ! Neumann
 
       ! Calculate distribution of electrons
-      ! n_e = sum_ni(1) * exp((phi- phi0) / T_e) ! Isothermal (Boltzmann)
+      ! n_e = sum_ni(1) * exp((phi- phi0) / T_e0) ! Isothermal (Boltzmann)
-      n_e = sum_ni(1) * (1.0_dp + (gamma_e - 1.0_dp)/gamma_e*(phi-phi0)/T_e)**gamma_e_exp !Polytropic
+      n_e = sum_ni(1) * (1.0_dp + (gamma_e - 1.0_dp)/gamma_e*(phi-phi0)/T_e0)**gamma_e_exp !Polytropic
       ! Diagonal matrix for Newton integration scheme
-      ! db_dphi        = n_e / T_e ! Isotropic
+      ! db_dphi        = n_e / T_e0 ! Isothermal (Boltzmann)
-      db_dphi        =  sum_ni(1) / (gamma_e * T_e) * &
+      db_dphi        =  sum_ni(1) / (gamma_e * T_e0) * &
-                        (1.0_dp + (gamma_e - 1.0_dp)/gamma_e*(phi-phi0)/T_e)**gamma_e_dexp !Polytropic
+                        (1.0_dp + (gamma_e - 1.0_dp)/gamma_e*(phi-phi0)/T_e0)**gamma_e_dexp !Polytropic
 
       ! Check if the solution has converged
       phiConv = maxval(abs(Res),1)
@@ -338,8 +323,8 @@ program VlaPlEx
       end if
 
       ! ! Calculate new potential to ensure 0 current at the edge
-      ! if (n_i(nr) > 1.0e-10_dp) then
+      ! if (n_i(nr) > n_epsilon) then
-      !   phiF = phi0 + T_e * log((2.0_dp*sqrt(pi)*Zave(nr)*n_i(nr)*u_i(nr)) / (Zave(1)*n_i(1)*sqrt(m_i*T_e/m_e)))
+      !   phiF = phi0 + T_e0 * log((2.0_dp*sqrt(pi)*Zave(nr)*n_i(nr)*u_i(nr)) / (Zave(1)*n_i(1)*sqrt(m_i*T_e0/m_e)))
       !
       ! else
       !   phiF = phi(nr-5)
@@ -364,22 +349,25 @@ program VlaPlEx
     f_i_old = f_i
 
     do iz = 1, nz
+      if (all(n_i(iz,:) < n_epsilon) .and. iz .ne. z_inj) then
+        cycle
+      end if
       ! Advect in the v direction
       ! 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
 
@@ -388,9 +376,9 @@ 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
@@ -398,14 +386,17 @@ program VlaPlEx
     ! Reset values for next iteration
     f_i_old = f_i
     do iz = 1, nz
-      fCum_i(iz,:)  = fCum_i(iz,:) + f_i_old(iz,rCum_index,:)
+      if (all(n_i(iz,:) < n_epsilon) .and. iz .ne. z_inj) then
+          cycle
+      end if
+      fCum_i(iz,:)  = fCum_i(iz,:) + f_i_old(iz,rCum_index,:)*dt*(v+dv/2.0)*dv
     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