Merge pull request 'issue/edgesVolume' (#59) from issue/edgesVolume into development

Reviewed-on: https://plasmalab.aero.upm.es/git/git/JGonzalez/fpakc/pulls/59

.gitignore

@@ -4,3 +4,5 @@ obj/
 doc/user_manual/
 doc/coding_style/
 json-fortran-8.2.0/
+json-fortran/
+runs/

CITATION.cff

@@ -0,0 +1,50 @@
+# This CITATION.cff file was generated with cffinit.
+# Visit https://bit.ly/cffinit to generate yours today!
+
+cff-version: 1.2.0
+title: Finite element Particle Kinetic Code
+message: >-
+  If you use this software, please cite it using the
+  metadata from this file.
+type: software
+authors:
+  - given-names: Jorge
+    family-names: Gonzalez
+    email: jorge.gonzalez@upm.es
+    affiliation: Universidad Politécnica de Madrid
+    orcid: 'https://orcid.org/0000-0001-7905-5001'
+repository-code: 'https://gitlab.com/JorgeGonz/fpakc'
+abstract: >-
+  Welcome to fpakc (Finite element PArticle Kinetic Code), a
+  modern object oriented Fortran open-source code for
+  particle simulations of plasma and gases. This code works
+  by simulating charged and neutral particles, following
+  their trajectories, collisions and boundary conditions
+  imposed by the user.
+
+  One of our aims is to make a code easy to maintain as well
+  as easy to use by a variety of reserchers and students.
+
+  This code is currenlty in very early steps of development.
+
+  The code aims to be easy to maintain and easy to use,
+  allowing its application from complex problems to easy
+  examples that can be used, for example, as teaching
+  exercises.
+
+  Parallelization techniques such as OpenMP, MPI will be
+  used to distribute the cpu load. We aim to make fpakc GPU
+  compatible in the future.
+
+  The codefpakc makes use of finite elements to generate
+  meshes in complex geometries. Particle properties are
+  deposited in the nodes and cells of the mesh. The
+  electromagnetic field, with the boundary conditions
+  imposed by the user, is solved also in this mesh.
+keywords:
+  - particle-in-cell
+  - plasma
+  - finite elements
+license: GPL-3.0
+version: beta
+date-released: '2025-10-01'

data/collisions/EL_e-Ar.dat

@@ -0,0 +1,204 @@
+# EL cross sections extracted from PROGRAM MAGBOLTZ, VERSION 7.1 JUNE 2004 www.lxcat.net/Biagi-v7.1
+# Relative energy (eV) cross section (m^2)
+ 0.000000e+0    7.100000e-20
+ 1.000000e-3    6.298400e-20
+ 2.000000e-3    5.835000e-20
+ 5.000000e-3    4.977500e-20
+ 1.000000e-2    4.113000e-20
+ 2.000000e-2    3.071300e-20
+ 5.000000e-2    1.570900e-20
+ 1.000000e-1    6.062200e-21
+ 1.092000e-1    5.117000e-21
+ 1.482000e-1    2.519100e-21
+ 1.885000e-1    1.330700e-21
+ 2.303000e-1    9.762900e-22
+ 2.735000e-1    1.139000e-21
+ 3.183000e-1    1.628900e-21
+ 3.646000e-1    2.326700e-21
+ 4.125000e-1    3.155200e-21
+ 4.622000e-1    4.064500e-21
+ 5.136000e-1    5.023100e-21
+ 5.668000e-1    6.012300e-21
+ 6.218000e-1    7.023300e-21
+ 6.788000e-1    8.054600e-21
+ 7.378000e-1    9.110500e-21
+ 7.989000e-1    1.020000e-20
+ 8.621000e-1    1.133700e-20
+ 9.275000e-1    1.253700e-20
+ 9.953000e-1    1.382100e-20
+ 1.065400e+0    1.479100e-20
+ 1.138000e+0    1.576700e-20
+ 1.213100e+0    1.677000e-20
+ 1.290900e+0    1.778100e-20
+ 1.371400e+0    1.882800e-20
+ 1.454700e+0    1.991100e-20
+ 1.541000e+0    2.107400e-20
+ 1.630300e+0    2.232400e-20
+ 1.722700e+0    2.358000e-20
+ 1.818400e+0    2.476000e-20
+ 1.917400e+0    2.598200e-20
+ 2.020000e+0    2.729100e-20
+ 2.126100e+0    2.884100e-20
+ 2.235900e+0    3.044500e-20
+ 2.349700e+0    3.210500e-20
+ 2.467400e+0    3.382400e-20
+ 2.589200e+0    3.558500e-20
+ 2.715400e+0    3.740100e-20
+ 2.845900e+0    3.928100e-20
+ 2.981100e+0    4.122700e-20
+ 3.121000e+0    4.331500e-20
+ 3.265800e+0    4.548700e-20
+ 3.415700e+0    4.773600e-20
+ 3.570900e+0    5.006300e-20
+ 3.731500e+0    5.247300e-20
+ 3.897800e+0    5.496700e-20
+ 4.069900e+0    5.775100e-20
+ 4.248100e+0    6.093800e-20
+ 4.432500e+0    6.423700e-20
+ 4.623400e+0    6.765200e-20
+ 4.821000e+0    7.118700e-20
+ 5.025600e+0    7.507600e-20
+ 5.237300e+0    7.901500e-20
+ 5.456500e+0    8.309200e-20
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+ 1.022020e+1    1.548800e-19
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+ 2.062720e+1    9.899000e-20
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+ 3.538134e+2    3.608300e-21
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+ 3.925501e+2    2.930400e-21
+ 4.063803e+2    2.789400e-21
+ 4.355158e+2    2.740800e-21
+ 4.667351e+2    2.688800e-21
+ 4.831724e+2    2.661400e-21
+ 5.001872e+2    2.633000e-21
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+ 9.005711e+2    1.965700e-21
+ 9.322543e+2    1.912900e-21
+ 9.650509e+2    1.858200e-21

data/collisions/IO_e-Ar.dat

@@ -1,34 +1,203 @@
-# H. C. Straub et. al, Physical Review A, 55,2(1995)
+# EL cross sections extracted from PROGRAM MAGBOLTZ, VERSION 7.1 JUNE 2004 www.lxcat.net/Biagi-v7.1
 # Relative energy (eV) cross section (m^2)
-17 1.700E-22
+ 1.570000e+1    0.000000e+0
-20 4.600E-21
+ 1.571000e+1    1.033000e-25
-25 1.240E-20
+ 1.574000e+1    3.631000e-23
-30 1.840E-20
+ 1.577000e+1    7.390000e-23
-35 2.260E-20
+ 1.581000e+1    1.128000e-22
-40 2.550E-20
+ 1.585000e+1    1.531000e-22
-45 2.660E-20
+ 1.589000e+1    1.948000e-22
-50 2.700E-20
+ 1.593000e+1    2.379000e-22
-55 2.690E-20
+ 1.597000e+1    2.826000e-22
-60 2.670E-20
+ 1.602000e+1    3.330000e-22
-65 2.670E-20
+ 1.606000e+1    3.914000e-22
-70 2.670E-20
+ 1.611000e+1    4.518000e-22
-75 2.660E-20
+ 1.616000e+1    5.143000e-22
-80 2.690E-20
+ 1.621000e+1    5.791000e-22
-85 2.700E-20
+ 1.627000e+1    6.461000e-22
-90 2.690E-20
+ 1.632000e+1    7.155000e-22
-95 2.670E-20
+ 1.638000e+1    7.873000e-22
-100 2.640E-20
+ 1.644000e+1    8.616000e-22
-110 2.610E-20
+ 1.650000e+1    9.386000e-22
-120 2.550E-20
+ 1.656000e+1    1.026000e-21
-140 2.450E-20
+ 1.663000e+1    1.116000e-21
-160 2.350E-20
+ 1.670000e+1    1.209000e-21
-180 2.270E-20
+ 1.677000e+1    1.306000e-21
-200 2.180E-20
+ 1.684000e+1    1.406000e-21
-225 2.100E-20
+ 1.691000e+1    1.510000e-21
-250 1.990E-20
+ 1.699000e+1    1.617000e-21
-275 1.870E-20
+ 1.707000e+1    1.733000e-21
-300 1.790E-20
+ 1.715000e+1    1.853000e-21
-350 1.630E-20
+ 1.724000e+1    1.977000e-21
-400 1.510E-20
+ 1.733000e+1    2.106000e-21
-450 1.390E-20
+ 1.742000e+1    2.239000e-21
-500 1.310E-20
+ 1.752000e+1    2.378000e-21
+ 1.762000e+1    2.526000e-21
+ 1.772000e+1    2.680000e-21
+ 1.783000e+1    2.839000e-21
+ 1.794000e+1    3.004000e-21
+ 1.805000e+1    3.175000e-21
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+ 1.829000e+1    3.540000e-21
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+ 1.868000e+1    4.146000e-21
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+ 2.013000e+1    6.498000e-21
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+ 3.111000e+1    1.888000e-20
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+ 3.346000e+2    1.862000e-20
+ 3.458000e+2    1.824000e-20
+ 3.575000e+2    1.791000e-20
+ 3.695000e+2    1.759000e-20
+ 3.820000e+2    1.727000e-20
+ 3.949000e+2    1.693000e-20
+ 4.083000e+2    1.659000e-20
+ 4.221000e+2    1.623000e-20
+ 4.364000e+2    1.585000e-20
+ 4.512000e+2    1.548000e-20
+ 4.666000e+2    1.520000e-20
+ 4.824000e+2    1.492000e-20
+ 4.989000e+2    1.462000e-20
+ 5.159000e+2    1.435000e-20
+ 5.335000e+2    1.406000e-20
+ 5.517000e+2    1.377000e-20
+ 5.706000e+2    1.347000e-20
+ 5.901000e+2    1.316000e-20
+ 6.104000e+2    1.285000e-20
+ 6.313000e+2    1.256000e-20
+ 6.530000e+2    1.226000e-20
+ 6.754000e+2    1.194000e-20
+ 6.986000e+2    1.162000e-20
+ 7.226000e+2    1.137000e-20
+ 7.475000e+2    1.112000e-20
+ 7.733000e+2    1.087000e-20
+ 7.999000e+2    1.060000e-20
+ 8.275000e+2    1.039000e-20
+ 8.561000e+2    1.018000e-20
+ 8.857000e+2    9.958000e-21
+ 9.163000e+2    9.736000e-21
+ 9.480000e+2    9.514000e-21
+ 9.808000e+2    9.285000e-21

data/collisions/IO_e-Kr.dat

@@ -0,0 +1,52 @@
+# D108525 "refs": {"B56": {"note": "CLM-R294 (1989)"}}
+# Relative energy (eV) cross section (m^2)
+1.40E+01 0
+1.62E+01 7.249E-21
+1.88E+01 1.199E-20
+2.18E+01 1.644E-20
+2.53E+01 2.1E-20
+2.94E+01 2.542E-20
+3.41E+01 2.937E-20
+3.95E+01 3.26E-20
+4.58E+01 3.499E-20
+5.32E+01 3.653E-20
+6.17E+01 3.726E-20
+7.15E+01 3.728E-20
+8.29E+01 3.671E-20
+9.62E+01 3.566E-20
+1.12E+02 3.426E-20
+1.29E+02 3.259E-20
+1.50E+02 3.075E-20
+1.74E+02 2.881E-20
+2.02E+02 2.682E-20
+2.34E+02 2.484E-20
+2.72E+02 2.289E-20
+3.15E+02 2.101E-20
+3.65E+02 1.922E-20
+4.24E+02 1.751E-20
+4.91E+02 1.592E-20
+5.70E+02 1.443E-20
+6.61E+02 1.305E-20
+7.67E+02 1.177E-20
+8.89E+02 1.06E-20
+1.03E+03 9.526E-21
+1.20E+03 8.547E-21
+1.39E+03 7.658E-21
+1.61E+03 6.851E-21
+1.87E+03 6.121E-21
+2.16E+03 5.462E-21
+2.51E+03 4.868E-21
+2.91E+03 4.334E-21
+3.38E+03 3.855E-21
+3.92E+03 3.426E-21
+4.54E+03 3.041E-21
+5.27E+03 2.698E-21
+6.11E+03 2.391E-21
+7.09E+03 2.118E-21
+8.22E+03 1.875E-21
+9.53E+03 1.658E-21
+1.11E+04 1.466E-21
+1.28E+04 1.295E-21
+1.49E+04 1.143E-21
+1.72E+04 1.009E-21
+2.00E+04 8.898E-22

data/collisions/IO_e-Li.dat

@@ -0,0 +1,148 @@
+# Rusudan I., et al., Atoms 9(4):90 2021
+# Relative energy (eV) cross section (m^2)
+5.393 1.061E-23
+6.000 5.885E-21
+7.000 1.352E-20
+8.000 1.927E-20
+9.000 2.364E-20
+10.000 2.698E-20
+11.000 2.956E-20
+12.000 3.156E-20
+13.000 3.309E-20
+14.000 3.427E-20
+15.000 3.517E-20
+16.000 3.585E-20
+17.000 3.635E-20
+18.000 3.670E-20
+19.000 3.694E-20
+20.000 3.708E-20
+21.000 3.714E-20
+22.000 3.714E-20
+23.000 3.709E-20
+24.000 3.700E-20
+25.000 3.686E-20
+26.000 3.671E-20
+27.000 3.652E-20
+28.000 3.632E-20
+29.000 3.610E-20
+30.000 3.588E-20
+31.000 3.564E-20
+32.000 3.539E-20
+33.000 3.514E-20
+34.000 3.488E-20
+35.000 3.462E-20
+36.000 3.435E-20
+37.000 3.409E-20
+38.000 3.383E-20
+39.000 3.356E-20
+40.000 3.330E-20
+41.000 3.304E-20
+42.000 3.277E-20
+43.000 3.252E-20
+44.000 3.226E-20
+45.000 3.201E-20
+46.000 3.175E-20
+47.000 3.151E-20
+48.000 3.126E-20
+49.000 3.102E-20
+50.000 3.078E-20
+51.000 3.054E-20
+52.000 3.031E-20
+53.000 3.008E-20
+54.000 2.985E-20
+55.000 2.963E-20
+56.000 2.941E-20
+57.000 2.919E-20
+58.000 2.898E-20
+59.000 2.877E-20
+60.000 2.856E-20
+61.000 2.835E-20
+62.000 2.815E-20
+63.000 2.795E-20
+64.000 2.776E-20
+65.000 2.756E-20
+66.000 2.737E-20
+67.000 2.719E-20
+68.000 2.700E-20
+69.000 2.682E-20
+70.000 2.664E-20
+71.000 2.646E-20
+72.000 2.629E-20
+73.000 2.612E-20
+74.000 2.595E-20
+75.000 2.578E-20
+76.000 2.562E-20
+77.000 2.546E-20
+78.000 2.530E-20
+79.000 2.514E-20
+80.000 2.499E-20
+81.000 2.483E-20
+82.000 2.468E-20
+83.000 2.453E-20
+84.000 2.439E-20
+85.000 2.424E-20
+86.000 2.410E-20
+87.000 2.396E-20
+88.000 2.382E-20
+89.000 2.369E-20
+90.000 2.355E-20
+91.000 2.342E-20
+92.000 2.329E-20
+93.000 2.316E-20
+94.000 2.303E-20
+95.000 2.290E-20
+96.000 2.278E-20
+97.000 2.266E-20
+98.000 2.253E-20
+99.000 2.241E-20
+100.000 2.230E-20
+101.000 2.218E-20
+102.000 2.206E-20
+103.000 2.195E-20
+104.000 2.184E-20
+105.000 2.173E-20
+106.000 2.162E-20
+107.000 2.151E-20
+108.000 2.140E-20
+109.000 2.129E-20
+110.000 2.119E-20
+111.000 2.109E-20
+112.000 2.098E-20
+113.000 2.088E-20
+114.000 2.078E-20
+115.000 2.068E-20
+116.000 2.059E-20
+117.000 2.049E-20
+118.000 2.039E-20
+119.000 2.030E-20
+120.000 2.021E-20
+121.000 2.011E-20
+122.000 2.002E-20
+123.000 1.993E-20
+124.000 1.984E-20
+125.000 1.976E-20
+126.000 1.967E-20
+127.000 1.958E-20
+128.000 1.950E-20
+129.000 1.941E-20
+130.000 1.933E-20
+131.000 1.924E-20
+132.000 1.916E-20
+133.000 1.908E-20
+134.000 1.900E-20
+135.000 1.892E-20
+136.000 1.884E-20
+137.000 1.877E-20
+138.000 1.869E-20
+139.000 1.861E-20
+140.000 1.854E-20
+141.000 1.846E-20
+142.000 1.839E-20
+143.000 1.831E-20
+144.000 1.824E-20
+145.000 1.817E-20
+146.000 1.810E-20
+147.000 1.803E-20
+148.000 1.796E-20
+149.000 1.789E-20
+150.000 1.782E-20

data/collisions/IO_e-Xe.dat

@@ -0,0 +1,52 @@
+# EL cross sections extracted from PROGRAM MAGBOLTZ, VERSION 7.1 JUNE 2004 www.lxcat.net/Biagi-v7.1
+# Relative energy (eV) cross section (m^2)
+1.21E+01 0
+1.41E+01 3.923E-21
+1.64E+01 1.194E-20
+1.91E+01 2.1E-20
+2.22E+01 2.946E-20
+2.58E+01 3.65E-20
+3.00E+01 4.185E-20
+3.49E+01 4.552E-20
+4.06E+01 4.766E-20
+4.72E+01 4.85E-20
+5.49E+01 4.828E-20
+6.39E+01 5.031E-20
+7.43E+01 5.1E-20
+8.64E+01 5.1E-20
+1.01E+02 5.032E-20
+1.17E+02 4.906E-20
+1.36E+02 4.732E-20
+1.58E+02 4.521E-20
+1.84E+02 4.283E-20
+2.14E+02 4.029E-20
+2.49E+02 3.764E-20
+2.90E+02 3.497E-20
+3.37E+02 3.233E-20
+3.92E+02 2.975E-20
+4.56E+02 2.726E-20
+5.31E+02 2.489E-20
+6.17E+02 2.266E-20
+7.18E+02 2.056E-20
+8.35E+02 1.861E-20
+9.72E+02 1.68E-20
+1.13E+03 1.514E-20
+1.32E+03 1.361E-20
+1.53E+03 1.221E-20
+1.78E+03 1.094E-20
+2.07E+03 9.781E-21
+2.41E+03 8.735E-21
+2.80E+03 7.789E-21
+3.26E+03 6.938E-21
+3.79E+03 6.171E-21
+4.41E+03 5.484E-21
+5.13E+03 4.868E-21
+5.97E+03 4.316E-21
+6.94E+03 3.824E-21
+8.07E+03 3.385E-21
+9.39E+03 2.994E-21
+1.09E+04 2.646E-21
+1.27E+04 2.336E-21
+1.48E+04 2.062E-21
+1.72E+04 1.818E-21
+2.00E+04 1.602E-21

doc/user-manual/.gitignore

@@ -6,6 +6,7 @@
 *.aux
 *.ps
 bibliography.bib.bak
+bibliography.bib.sav
 *.bbl
 *.blg
 *.out

doc/user-manual/bibliography.bib

@@ -8,6 +8,16 @@
   pages     = {3--67},
 }
 
+@article{higginson2020corrected,
+  title={A corrected method for Coulomb scattering in arbitrarily weighted particle-in-cell plasma simulations},
+  author={Higginson, Drew Pitney and Holod, Ihor and Link, Anthony},
+  journal={Journal of Computational Physics},
+  volume={413},
+  pages={109450},
+  year={2020},
+  publisher={Elsevier}
+}
+
 @Misc{gfortranURL,
   author       = {GNU Project},
   title        = {gfortran - the GNU Fortran compiler},
@@ -41,4 +51,38 @@
   howpublished = {\url{https://gmsh.info/}},
 }
 
+@Article{welford1962note,
+  author    = {Welford, BP},
+  journal   = {Technometrics},
+  title     = {Note on a method for calculating corrected sums of squares and products},
+  year      = {1962},
+  number    = {3},
+  pages     = {419--420},
+  volume    = {4},
+  publisher = {Taylor \& Francis},
+}
+
+@Article{sherlock2008monte,
+  author    = {Sherlock, Mark},
+  journal   = {Journal of Computational Physics},
+  title     = {A Monte-Carlo method for Coulomb collisions in hybrid plasma models},
+  year      = {2008},
+  number    = {4},
+  pages     = {2286--2292},
+  volume    = {227},
+  groups    = {Particle-in-cell},
+  publisher = {Elsevier},
+}
+
+@article{lemons2009small,
+  title={Small-angle Coulomb collision model for particle-in-cell simulations},
+  author={Lemons, Don S and Winske, Dan and Daughton, William and Albright, Brian},
+  journal={Journal of Computational Physics},
+  volume={228},
+  number={5},
+  pages={1391--1403},
+  year={2009},
+  publisher={Elsevier}
+}
+
 @Comment{jabref-meta: databaseType:bibtex;}

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doc/user-manual/fpakc_UserManual.tex

@@ -1,5 +1,5 @@
-\documentclass[10pt,a4paper,oneside]{book}
+\documentclass[10pt,a4paper,twoside]{book}
-\usepackage[latin1]{inputenc}
+%\usepackage[latin1]{inputenc}
 \usepackage{amsmath}
 \usepackage{amsfonts}
 \usepackage{amssymb}
@@ -10,6 +10,7 @@
 \usepackage[block=ragged,backend=bibtex]{biblatex}
 \usepackage[acronym,toc,automake]{glossaries}
 \usepackage[hidelinks]{hyperref}
+\usepackage[version=4]{mhchem}
 \hypersetup{
   breaklinks = true,                                               % Allows break links in lines
   colorlinks = true,                                               % Colours links instead of ugly boxes
@@ -21,16 +22,23 @@
     Author   = {Jorge Gonzalez}
   }
 }
+\usepackage[margin=1in]{geometry} % Reduces margins of the document
+% Allows breaking of URL in bibliography.
+\setcounter{biburllcpenalty}{7000}
+\setcounter{biburlucpenalty}{8000}
+
 \makeglossaries
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-
+\newacronym{fpakc}{fpakc}{Finite element PArticle Code}
-\newacronym{fpakc}{fpakc}{Finite Element PArticle Code}
 \newacronym{mpi}{MPI}{Message Passing Interface}
 \newacronym{gpu}{GPU}{Graphics Processing Unit}
 \newacronym{cpu}{CPU}{Central Processing Unit}
 \newacronym{json}{JSON}{JavaScript Object Notation}
 \newacronym{io}{I/O}{input/output}
+\newacronym{mcc}{MCC}{Monte-Carlo Collisions}
+\newacronym{cs}{CS}{Coulomb Scattering}
+\newacronym{vtu}{VTU}{Visualization Toolkit for unstructured grids}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \newglossaryentry{openmp}{name={OpenMP},description={Shared-memory parallelization}}
@@ -41,6 +49,7 @@
 \newglossaryentry{git}{name={Git},description={Git is a distributed version-control system for tracking changes in a set of files}}
 \newglossaryentry{gitlab}{name={GitLab},description={GitLab is a web-based lifecycle tool that provides a \Gls{git}-repository manager}}
 \newglossaryentry{gmsh}{name={Gmsh},description={A three-dimensional finite element mesh generator with built-in pre- and post-processing facilities.}}
+\newglossaryentry{gnuplot}{name={Gnuplot},description={A portable command-line driven graphing utility for Linux, OS/2, MS Windows, OSX, VMS, and many other platforms.}}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
 \bibliography{bibliography}
@@ -60,8 +69,10 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
   \chapter{Introduction}
     \section{About fpakc}
-      The \Gls{fpakc} is a simulation tool that models species in plasmas (ions, electrons and neutrals) following the trajectories of macro-particles as they move and interact between them and the boundaries of the domain.
+      The \Gls{fpakc} is a simulation tool that models species in plasma (ions, electrons and neutrals) following the trajectories of macro-particles as they move and interact between them and the boundaries of the domain.
-      The code is currently in very early steps of development and further improvements are expected very soon.
+      Particles properties are scattered into a finite element mesh in 1, 2 or three dimensions, with the possibility to choose different geometries.
+      The official repository can be found at: \url{https://gitlab.com/JorgeGonz/fpakc.git}.
+      The code is currently in the very early steps of development and further refinements are expected very soon.
     
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{Main Guidelines}
@@ -75,14 +86,14 @@
         \item \acrshort{fpakc} is coded in a \textit{understandable} way.
               This means that the code is required to be written in a clear way that is easy to understand and maintain.
               Variables and procedure names need to be self-understanding.
-              This ease the process of fixing bugs and improving the codes by a large team of developers.
+              This eases the process of fixing bugs and improving the codes by a large team of developers.
               For more information, please refer to the \acrshort{fpakc} Coding Style document.
-        \item \acrshort{fpakc} requires to be ease to use.
+        \item \acrshort{fpakc} requires being ease to use.
-              Input files are required to be in a \textit{human} format, meaning that the different options can be easily understander without constant reference to the user guide.
+              Input files are required to be in a \textit{human} format, meaning that the different options can be easily understood without constant reference to the user guide.
-              \acrshort{fpakc} is aimed to be used in a wide range of applications and by a variety of scientist: from very established ones to newcomers to the field and students.
+              \acrshort{fpakc} is aimed to be used in a wide range of applications and by various scientists: from well-established ones to newcomers to the field and also students.
       \end{enumerate}
     
-      These are foundation stones of the code and code development and should always be followed, at least for the releases in the official repository.
+      These are foundation stones of \acrshort{fpakc} and its development and should always be followed, at least for the releases in the official repository.
     
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{How to collaborate}
@@ -92,22 +103,32 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
   \chapter{Operation Scheme}
     \section{The Particle Method}
-      \acrshort{fpakc} uses macro-particles to simulate the dynamics of different plasma species (mainly ions, electrons and neutrals).
+      \Gls{fpakc} uses macro-particles to simulate the dynamics of different plasma species (mainly ions, electrons and neutrals).
-      These macro-particles represent a large amount of real particles.
+      These macro-particles could represent a large amount of real particles.
-      For now own, macro-particles will be referred as just particles by abusing of language.
+      For now own, macro-particles will be referred as just particles by abuse of language.
-      In the evolution of these particles, external forces (as the electromagnetic field), interaction between particles (as collisions) and interaction with the boundaries of the domain are included.
+      During the initiation phase, the input and mesh file(s) are reading.
+      If an initial distribution for a species is specified in the input file, particles to match that distribution are loaded into the cells.
       
-      At each time step, particles are first pushed accounting for possible acceleration by external forces.
+      The general steps performed in each iteration are:
-      Then, the cell in which the particle ends up is located.
+      \begin{enumerate}
-      If a boundary is encountered, the interaction between the particle and the boundary is calculated.
+        \item Firstly, new particles are introduced into the domain as specified in the input file.
-      Next, collisions for the particles in each cell are carried on.
+        \item Particles are then pushed, accounting for possible acceleration by external forces.
+              During this process, if a particle changes cell, it is found using the connectivity between elements.
+              If a particle encounters a boundary instead a new cell, the interaction between the boundary and the wall are computed.
+              A particle may abandon the computational domain and is no longer accounted for.
+        \item Next, collisions for the particles inside each cell are carried out.
               This may include different collision processes for each particle.
-      Finally, the particles properties are scattered into the mesh nodes.
+              Monte-Carlo collisions (elastic, ionization, charge-exchange$\ldots$) can be carried out in a specific mesh, to better adjust to the cell size required, similar to the mean-free path.
+              Although not yet implemented, Coulomb scattering will always be performed in the mesh used for scattering, which cell size should be in the order of the Debye length.
+        \item A new array containing all particles inside the numerical domain is obtained.
+        \item Finally, particle properties are scattered among the mesh nodes.
               These properties are density, momentum and the stress tensor.
-      Non-dimensional units are used for this, but output files are converted into dimensional units.
+        \item If requested, the electromagnetic field is computed.
-      If requested, the electromagnetic field is computed.
+        \item If the number of iteration requires writing output files, it is done after all steps for the particles are completed.
+      \end{enumerate}
     
-      More in depth explanation of the different steps are given in the following sections.
+      \Gls{fpakc} has the capability to configure all the behaviour of the simulation via the input file.
+      Parameters as injection, the kind of pusher used for each species, boundary conditions or collisions are user-input parameters and will be described in Chap.~\ref{ch:input_file}.
     
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{Injection of new particles}
@@ -122,100 +143,150 @@
       Particles are pushed in the selected domain.
       Velocity and position are updated according to the old particle values and the external forces.
       All the push routines for the different geometries can be found in \lstinline|moduleSolver|.
+      The pushers included in \Gls{fpakc} are:
       
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+      \begin{itemize}
-      \subsection{2D Cylindrical}
+      \item 3D Cartesian pusher.
+            Moving particles in a simple 3D Cartesian space.
+        
+      \item 2D Cylindrical.
             When a 2D cylindrical geometry is used ($z$, $r$), a Boris solver\cite{boris1970relativistic} is used to move particles accounting for the effect of the symmetry axis.
             This pusher removes the issue with particles going to infinite velocity when $r \rightarrow 0$ by pushing the particles in Cartesian space and then converting it to $r-z$ geometry.
             Velocity in the $\theta$ direction is updated for collision processes, although the dynamic in the angular direction is assumed as symmetric.
         
-        Cross-sections are read from files.
+      \item 2D Cartesian pusher.
-        These files contains two columns: one for the relative energy (in $\unit{eV}$) and another one for the cross-section (in $\unit{m^{-2}}$).
+            Moving particles in a simple 2D Cartesian space.
         
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+      \item 1D Radial pusher.
-      \subsection{1D Cartesian pusher}
+            Same implementation as 2D cylindrical pusher but direction $z$ is ignored.
 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+      \item 1D Cartesian pusher.
-      \subsection{1D Radial pusher}
+            Moving particles in a simple 1D Cartesian space. Same implementation as in 2D Cartesian but $y$ direction is ignored.
+      
+      \end{itemize}
     
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{Find new cell}      
       Once the position and velocity of the particle are updated, the new cell that contains the particle is searched.
-      This is done by a neighbor search, starting from the previous cell containing the particle.
+      This is done by a neighbour search, starting from the previous cell containing the particle.
-      In the process of finding the new cell, it is possible that a particle encounters a boundary.
+      In the process of finding the new cell, a particle might encounter a boundary.
-      When the particle interacts with the boundary, the particle may continue its life in the simulation (reflected) or might be eliminated from it (absorbed).
+      When the particle interacts with the boundary, the particle may continue its life in the simulation or might be eliminated from it.
       Once that the new cell is found or that the particle life has been terminated, the pushing is complete.
+      If a secondary mesh is used for the Monte-Carlo Collision method, the new cell in that mesh in which the particle reside is also found by the same method, although no interaction with the boundaries is accounted for this step.
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{Variable Weighting Scheme\label{sec:weightingScheme}}
-      One of the issues in particle simulations, specially for axisymmetrical cases, is that due to the disparate volume of cells, specially close to the axis, the statistics in some cells is usually poor.
+      One of the issues in particle simulations, specially for axial-symmetrical cases, is that due to the disparate volume of cells, specially close to the axis, the statistics in some cells is usually poor.
       To try to fix that, the possibility to include a Variable Weighting Scheme in the simulations is available in \Gls{fpakc}.
-      This schemes detect when a particle change cells and modify its weight accordingly.
+      These schemes detect when a particle changes cells and split it if necessary to improve statistics.
-      To avoid particles having a larger weight than the rest, particle can be split in multiple particles if weight become too large.
+      The use of a Variable Weighting Scheme is defined by the user in the input file.
+      
+      Beware that this can increase the number of particles in the simulation and increase computational time.
+    
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    \section{Interaction between species}\label{ssec:collisions}
+      For each cell, interaction among the particles in it are carried out.
+      \Gls{fpakc} distinguish between two types of interactions: \acrfull{mcc} and \acrfull{cs}.
+      \acrshort{mcc} refers to the process in which two particles interact in short range.
+      These processes include, but are not limited to: elastic collisions, ionization/recombination, charge-exchange, excitation/de-excitation\ldots
+      A secondary mesh, with cell sizes in the range of the mean-free path, can be used for this type of collision.
+      \acrshort{cs} refers to the large range interaction that a charged species suffer do to the charge of other particles.
+      The interactions between the different species is defined by the user.
+      
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+      \subsection{\acrlong{mcc}}
+        For each cell, the maximum number of collisions between particle is computed.
+        For each collision, a random pair of particles is chosen.
+        A loop over all possible collisions for the pair of particles chosen is performed.
+        If a random number is above the probability of collision for that specific type, the collision takes place.
+        If not, the next type for the particle pair is checked.
+              
+        Below are described the type of collision process implemented in \acrshort{fpakc}:
+        \begin{itemize}
+          \item Elastic.
+                In this type of collision, particles exchange energy due to hard-sphere model.
+                Total energy is conserved.
+                Resulting velocity directions are chosen from Maxwellian distribution functions.
+                This interaction is useful for short-range collisions as neutral-neutral and charged-neutral elastic collisions.
+      
+          \item Charge Exchange.
+                When an ion interacts with a neutral particle, an electron is exchanged between the two particles with no exchange of energy.
+                This is called a resonant charge-exchange.
+        
+          \item Electron Impact Ionization.
+                When the relative energy between a neutral and an electron is above the ionization threshold, there is a probability that the neutral particle will become ionized.
+                This ionization emits and additional electron
+
+          \item Recombination.
+                When an electron and an ion interact, there is a possibility for them to be recombined into a neutral particle.
+                The photons emitted by this process are not modelled yet.
+        \end{itemize}
+      
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+     \subsection{\acrlong{cs}}
+       A simple linearization of the Coulomb operator based on Ref.~\cite{sherlock2008monte} is implemented.
+       This method assumes that the species involved in the scattering process have a Maxwellian distribution.
+       The method is made to conserve momentum and kinetic energy based on the approach in Ref.~\cite{lemons2009small} for self (same species) and intra (different species) collisions.
+       
+       The user must specify the charged species that will interact together.
+       The Coulomb logarithm involved in these processes is currently set to a fix value of $10$.
+       
+       This method is not valid for situations in which the distribution functions are far from Maxwellian.
         
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{Reset of particle array}
       Once that the pushing is complete, the array of particles that remain inside the domain is copied to a new array.
       The new array containing only the particles inside the domain will be the one used in the next steps.
       In this section, particles are assigned to the list of particles inside each individual cell.
-      Unfortunately, this is done right now without parallelisation and is very CPU consuming.
+      Unfortunately, this is done right now without parallelization and is very CPU consuming.
       
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-    \section{Interaction between species}\label{ssec:collisions}
+    \section{Probing}\label{sec:probing}
-      For each cell, interaction among the particles in it are carried out.
+      As default, \gls{fpakc} outputs information of macroscopic quantities (density, velocity, temperature\ldots) in the finite element mesh.
-      The type of interaction between the different particles is defined by the user.
+      However, a lot of information can be extracted from the particle distribution function.
-      In general, the maximum number of interaction in a cell is computed.
+      Thus, a probing method is provided to extract the distribution function in a specific position.
-      For each collision, a pair of particles is selected.
-      A loop over all possible collisions for the pair of particles is performed.
-      If a random number generated is above the probability of collision for the type divided by the maximum one, the collision take place.
       
-      Collisions can change the velocity of the particles involved (elastic), create new particles (ionization-recombination) or change the type of particle (charge-exchange).
+      The particles inside a cell in which the input position is located are distributed into a 3D velocity grid.
+      The user can decide the grid width and the number of points in each direction.
+      The distribution function will be calculated and wrote with a time step decided by the user.
       
-      Below are described the type of collision process implemented between species.
+      If a particle velocity resides outside the velocity grid (in any direction), it will not be added to the tally of the distribution function.
-      
+      Due to the limitation of only considering particles in the cell, and not neighbour particles, two probes for the same species at different positions but in the same cell will output the same results.
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+      A more advance method considering distance between the particles and the probe position as well as particles in neighbour cells could be implemented to improve the statistics of the distribution function.
-      \subsection{Elastic collision}
-        In this type of collision, particles exchange energy due to hard-sphere model.
-        Total energy is conserved.
-        Resulting velocity directions are chosen from Maxwellian distribution functions.
-        This interaction is useful for short-range collisions as neutral-neutral and charged-neutral elastic collisions.
-      
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-      \subsection{Charge Exchange}
-        When an ion interacts with a neutral particle, an electron is exchanged between the two particles with no exchange of energy.
-        This is called a resonant charge-exchange.
-        
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-      \subsection{Electron Impact Ionization}
-        When the relative energy between a neutral and an electron is above the ionization threshold, there is a probability that the neutral particle will become ionized.
-        This ionization emits and additional electron
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-      \subsection{Recombination}
-        When an electron and an ion interact, there is a possibility for them to be recombined into a neutral particle.
-        The photon emitted by this process is not modeled yet.
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{Scattering}
       The properties of each particle are deposited in the nodes from the containing cell.
-      This process depend on the cell type, but in general, each node receive a proportional part of the particle properties as a function of the particle position inside the cell.
+      This process depends on the cell type, but in general, each node receives a proportional part of the particle properties as a function of the particle position inside the cell.
-      Figure \ref{fig:scatteringQuad} shows how a particle at a generic position $p(x_1, x_2)$ inside the cell is scattered to the four nodes.
+      The figure \ref{fig:scatteringQuad} shows how a particle at a generic position $p(x_1, x_2)$ inside the cell is scattered to the four nodes.
       \begin{wrapfigure}{l}{0.4\textwidth}
         \centering
         \includegraphics{figures/scatteringQuad}
         \caption{\label{fig:scatteringQuad}Example of how a particle is weighted in a quadrilateral cell.}
       \end{wrapfigure}
-      Each node receives a proportional part of the area formed by dividing the cell in for rectangles using as an additional vertex the particle position.
+      Each node receives a proportional part of the area formed by dividing the cell in for rectangles, using as an additional vertex the particle position.
       These properties are dimensionless, but they are converted to the correct units once the output is printed.
     
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{Electromagnetic field}
       WIP.
     
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    \section{Average scheme}
+      Particle-in-cell codes have an intrinsic statistical noise associated with them.
+      Although this can be reduced by increasing the number of particles, this also increases the CPU requirements of the case.
+      
+      It is quite common that most cases reach a quasi-steady state after a number of iterations and time-average results can be obtained after to improve analysis, plotting and restarting the case using these time-average results as new species backgrounds.
+      Although this is possible to do once the simulation is finished with post-processing tools, this is limited to the number of iterations printed.
+      
+      \Gls{fpakc} implements a simple average scheme that, after a start time provided by the user, scores a mean and standard deviation of all the main species properties, and the electromagnetic field.
+      This scheme is based on the Welford's online algorithm~\cite{welford1962note}.
+      The averaged data is written in the same format as the input mesh at the end of the simulation.
+
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%  
   \chapter{Installation}
     \section{Required Packages}
-      In order to properly compile \gls{fpakc}, the following packages are required.
+      To properly compile \gls{fpakc}, the following packages are required.
       \subsection{Gfortran}
         The \Gls{opensource} free compiler \Gls{gfortran}\cite{gfortranURL} from GCC is the basic way to compile \acrshort{fpakc}.
         It is distributed with all GNU/Linux distributions.
@@ -239,7 +310,7 @@
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
       \subsection{Gmsh}
         Although \Gls{gmsh}\cite{gmshURL} is not required to compile and run \Gls{fpakc}, it is the default tool to generate finite element meshes and post-processing.
-        Right now, the only \acrshort{io} format available in \Gls{fpakc} is the v2.0 .msh format.
+        Right now, the only \acrshort{io} format available in \Gls{fpakc} is the v2.0 \lstinline|.msh| format.
         
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{Installation steps}
@@ -274,7 +345,6 @@ make
       \end{lstlisting}
       to compile the code.
       If everything is correct, an executable named \textit{fpakc} will be generated.
-  
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{Running the code}
       To run a case, simply execute:
@@ -293,13 +363,13 @@ make
     
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{Mesh file}
-      \Gls{fpakc} accepts right now the version 2.0 of \Gls{gmsh} mesh format .msh in ASCII format.
+      \Gls{fpakc} accepts right now the version 2.0 of \Gls{gmsh} mesh format \lstinline|.msh| in ASCII format.
       This file contains information about the nodes, edges and volumes that define the finite element mesh used by \Gls{fpakc} to scatter particle properties and compute the self-consistent electromagnetic field.
       
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
     \section{Case file}
       The required format for the case file is \Gls{json}.
-      \Gls{json} is a case-sensitive format, so input must be written with the correct capitalisation.
+      \Gls{json} is a case-sensitive format, so input must be written with the correct capitalization.
       The basic structure and options available for the case file are explained below.
       The order of the objects and variables is irrelevant, but the structure needs to be maintained.
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -309,6 +379,10 @@ make
         \begin{itemize}
           \item \textbf{path}: Character.
                                Path for the output files. This path is also used to locate the mesh input file.
+          \item \textbf{folder}: Character.
+                                 Base name of the folder in which output files are placed.
+                                 The date and time is appended to this name.
+                                 If none is provided, only the date and time is written as the folder name.
           \item \textbf{triggerOutput}: Integer.
                                         Determines the number of iterations between writing output files for macroscopic quantities.
           \item \textbf{cpuTime}: Logical. 
@@ -323,6 +397,30 @@ make
                                   Trigger between writings is the same as in \textbf{triggerOutput}.
           \item \textbf{EMField}: Logical.
                                   Determines if the electromagnetic field is printed.
+          \item \textbf{probes}: Array of objects.
+                                 Defines the probes employed for obtaining the distribution function at specific positions.
+                                 See Sec.~\ref{sec:probing} for more information.
+                                 The object is structured as follows:
+                                 \begin{itemize}
+                                   \item \textbf{species}: Character.
+                                                           Species name as defined in \textbf{species} array.
+                                   \item \textbf{position}: Real.
+                                                            Array of dimension $3$.
+                                                            Units in $\unit{m}$.
+                                                            Indicates the position of the probing.
+                                   \item \textbf{timeStep}: Real
+                                                            Units in $\unit{s}$.
+                                                            Optional.
+                                                            Time step for output of the distribution function.
+                                                            If none is provided, the minimum time step of the case is used.
+                                   \item \textbf{velocity\_1, velocity\_2, velocity\_3}: Real.
+                                                                                         Array of dimension $2$.
+                                                                                         Velocity range (minimum-maximum) in which the distribution function will be interpolated.
+                                                                                         The subscripts 1, 2, 3 indicate the three directions of the case.
+                                   \item \textbf{points}: Integer.
+                                                          Array of dimension $3$.
+                                                          Number of points in each direction.
+                                 \end{itemize}
         \end{itemize}
       
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -330,23 +428,50 @@ make
         The object \textbf{geometry} contains information about the type of geometry, the mesh file format and the mesh filename.
         The accepted parameters are:
         \begin{itemize}
+          \item \textbf{dimension}: Integer.
+                                    Number of spatial dimensions of the geometry.
+                                    Current values are: $0$, $1$, $2$ or $3$.
+                                    Zero dimension is a fictitious volume.
+                                    Geometry used mostly to test collisional effects.
+                                    No boundary or EM field is solved.
+                                    No injection can be implemented.
+                                    Initial state must be read from file.
+                                    No mesh file is required.
+                                    The optional argument \textbf{geometry.volume} can be used to set a value for the fictitious volume.
+                                    Otherwise, the volume is set to 1 in non-dimensional units.
           \item \textbf{type}: Character.
                                Type of geometry.
                                Current accepted vaules are
                                \begin{itemize}
-                                 \item \textbf{2DCyl}: Two-dimensional grid (z-r) with symmetry axis at $r = 0$.
+                                 \item \textbf{Cart}: Cartesian coordinates.
-                                                       For \Gls{gmsh} mesh format, the coordinates $x$ and $y$ correspond to  $z$ and $r$ respectively.
+                                                      Available for \textbf{geometry.dimension} $1$, $2$ and $3$.
-                                 \item \textbf{1DCart}: One-dimensional grid (x) in Cartesian coordinates
+                                                      The coordinates $x$, $y$ and $z$ correspond to $x$, $y$ and $z$ respectively.
-                                                        For \Gls{gmsh} mesh format, the coordinates $x$ corresponds to $x$.
+                                 \item \textbf{Cyl}:  Cylindrical coordinates ($z \hyphen r$) with symmetry axis at $r = 0$.
-                                 \item \textbf{1DRad}: One-dimensional grid (r) in radial coordinates
+                                                      Only available for \textbf{geometry.dimension} $2$.
-                                                       For \Gls{gmsh} mesh format, the coordinates $x$ corresponds to $r$.
+                                                      The coordinates $x$ and $y$ correspond to  $z$ and $r$ respectively.
+                                 \item \textbf{Rad}:  One-dimensional radial space ($r$).
+                                                      Only available for \textbf{geometry.dimension} $1$.
+                                                      The coordinates $x$ corresponds to $r$.
                                \end{itemize}
           \item \textbf{meshType}: Character.
                                    Format of mesh file.
-                                   Currently, only the value \textbf{gmsh} is accepted, which makes reference to \Gls{gmsh} v2.0 output format.
+                                   The output will be written in the same format as specified here.
+                                   Accepted formats are:
+                                   \begin{itemize}
+                                     \item \textbf{gmsh2}: \Gls{gmsh} file format in version 2.0. This has to be in ASCII format.
+                                     \item \textbf{vtu}: \Gls{vtu} file format. This has to be in ASCII format.
+                                     \item \textbf{text}: Plain text file format only intended for 1D cases.
+                                                          This has to be in ASCII format and comma separated.
+                                                          The first column represents the position and the second column the physical ID of the node.
+                                                          Values have to be $1$ (left boundary), $2$ (right boundary), or $0$ (no boundary.)
+                                   \end{itemize}
           \item \textbf{meshFile}: Character.
                                    Mesh filename.
                                    This file is searched in the path \textbf{output.path} and must contain the file extension.
+          \item \textbf{volume}:   Real.
+                                   Units of $\unit{m^{-3}}$.
+                                   Used to set a fictitious volume for the $0$ dimension.
+                                   Ignored in the other cases.
         \end{itemize}
 
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -384,19 +509,72 @@ make
         \begin{itemize}
           \item \textbf{name}: Character.
                                Name of the boundary.
-          \item \textbf{type}: Character.
+          \item \textbf{physicalSurface}: Integer.
-                               Type of boundary.
+                                          Identification of the surface in the mesh file.
-                               Accepted values are:
+          \item \textbf{bType}: Array of objects of dimension 'number of species'.
+                                Per each species defined in the case, a boundary \textbf{type} needs to be provided.
+                                Accepted values for \textbf{type} are:
                                 \begin{itemize}
                                   \item \textbf{reflection}: Elastic reflection of particles.
                                   \item \textbf{absorption}: Particle is eliminated from the domain.
                                                              The particle is first moved into the edge and its properties are scattered among the edge nodes.
                                   \item \textbf{transparent}: Particle abandon the numerical domain.
-                                 \item \textbf{axis}: Identifies the symmetry axis for 2D cylindrical simulations.
+                                  \item \textbf{wallTemperature}: Reflective wall with constant temperature that exchange heat with particles.
-                                                      It has no actual function.
+                                                                  Required parameters are:
+                                                                  \begin{itemize}
+                                                                    \item \textbf{temperature}: Real.
+                                                                                                Units of $\unit{K}$.
+                                                                                                Temperature wall.
+                                                                    \item \textbf{specificHeat}: Real.
+                                                                                                 Units of $\unit{J kg^{-1} K^{-1}}$.
+                                                                                                 Specific heat capacity of the material.
+                                                                  \end{itemize}
+                                  \item \textbf{ionization}: Per each particle crossing the surface with this type of boundary, a number of ionization events are calculated.
+                                                             A pair of ion-electron is generated for each ionization event, taking as a reference a neutral background.
+                                                             The secondary electron is taken as the same type as the incident particle.
+                                                             The available input is:
+                                                             \begin{itemize}
+                                                               \item \textbf{neutral}: Object.
+                                                                                       Information about the neutral background.
+                                                                                       Required parameters are:
+                                                                                       \begin{itemize}
+                                                                                         \item \textbf{ion}: Character.
+                                                                                                             Species name of the ion generated as defined in object \textbf{species}.
+                                                                                                             Required parameter.
+                                                                                         \item \textbf{mass}: Real.
+                                                                                                              Units in $\unit{kg}$.
+                                                                                                              Mass of neutral species.
+                                                                                                              If missing, the mass of the ion is used
+                                                                                         \item \textbf{density}: Real.
+                                                                                                                 Units in $\unit{m^{-3}}$.
+                                                                                                                 Density of neutral background.
+                                                                                                                 Required parameter.
+                                                                                         \item \textbf{velocity}: Real.
+                                                                                                                  Units in $\unit{m s^{-1}}$.
+                                                                                                                  Array of dimension $3$.
+                                                                                                                  Mean velocity of neutral background.
+                                                                                                                  Required parameter.
+                                                                                         \item \textbf{temperature}: Real.
+                                                                                                                     Units in $\unit{K}$.
+                                                                                                                     Temperature of neutral background.
+                                                                                                                     Required parameter.
+                                                                                                              
+                                                                                       \end{itemize}
+                                                               \item \textbf{effectiveTime}: Real.
+                                                                                             Units in $\unit{s}$.
+                                                                                             As the particle is no longer simulated once it crossed the boundary, this time represents the effective time in which the particle produces ionization processes in the neutral background.
+                                                                                             Required parameter.
+                                                               \item \textbf{energyThreashold}: Real.
+                                                                                                Units in $\unit{eV}$.
+                                                                                                Ionization energy threshold for the simulated process.
+                                                                                                Required parameter.
+                                                               \item \textbf{crossSection}: Character.
+                                                                                            Complete path to the cross-section data for the ionization process.
+                                                                                             
+                                                             \end{itemize}
+                                  \item \textbf{axis}: Identifies the symmetry axis for 2D cylindrical simulations.
+                                                       If , for some reason, a particle interacts with this axis, it is reflected.
                                 \end{itemize}
-          \item \textbf{physicalSurface}: Integer.
-                                          Identification of the edge in the mesh file.
         \end{itemize}
       
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@@ -411,18 +589,26 @@ make
                                Type of boundary.
                                 Accepted values are:
                                \begin{itemize}
-                                 \item \textbf{dirichlet}: Elastic reflection of particles.
+                                 \item \textbf{dirichlet}: Constant value of electric potential on the surface.
+                                 \item \textbf{dirichletTime}: Constant value of the electric potential with a time variable profile.
+                                                               The value of \textbf{boundaryEM.potential} will be multiplied for the corresponding value in the file \textbf{boundaryEM.temporalProfile}.
                                 \end{itemize}
           \item \textbf{potential}: Real.
                                     Fixed potential for Dirichlet boundary condition.
           \item \textbf{physicalSurface}: Integer.
                                           Identification of the edge in the mesh file.
+          \item \textbf{temporalProfile}: Character.
+                                          Filename of the 2 column file containing the time variable profile.
+                                          File must be located in \textbf{output.path}.
+                                          The first column is the time in $\unit{s}$.
+                                          The second column is the factor that will multiply the value of the boundary.
+        
         \end{itemize}
       
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
       \subsection{inject}
         The array \textbf{inject} specifies the injection of particles from different surfaces.
-        The injection of particles need to be associated to a physicalSurface in the mesh file.
+        The injection of particles needs to be associated to a physicalSurface in the mesh file.
         Multiple injections can be associated to the same surface.
         \begin{itemize}
           \item \textbf{name}: Character.
@@ -436,26 +622,39 @@ make
                                 Available values are:
                                 \begin{itemize}
                                   \item \textbf{A}: Ampere.
-                                  \item \textbf{sccm}: Standard cubic centimeter.
+                                  \item \textbf{Am2}: Ampere per square meter.
+                                                      This value will be multiplied by the area of injection.
+                                  \item \textbf{sccm}: Standard cubic centimetre.
+                                  \item \textbf{part/s}: Particles (real) per second.
                                 \end{itemize}
           \item \textbf{v}: Real.
-                            Module of velocity vector, in $\unitfrac{m}{s}$.
+                            Units of $\unit{m s^{-1}}$.
+                            Module of velocity vector.
           \item \textbf{n}: Real.
                             Array dimension $3$.
                             Direction of injection.
-                            Norm of vector must be equal $1$.
+                            If no value is provided, the normal of the edge is used as the direction of injection.
+                            This vector is normalized to $1$ by the code.
           \item \textbf{velDist}: Character.
                                   Array dimension $3$.
                                   Type of distribution function used to obtain injected particle velocity:
                                   \begin{itemize}
                                     \item \textbf{Maxwellian}: Maxwellian distribution of temperature \textbf{T} and mean \textbf{v} times the value of \textbf{n} in the specified direction.
+                                    \item \textbf{Half-Maxwellian}: Half-Maxwellian distribution of temperature \textbf{T} and mean \textbf{v} times the value of \textbf{n} in the specified direction.
+                                                                    Only considers the positive part of the half-Maxwellian.
                                     \item \textbf{Delta}: Dirac's delta distribution function. All particles are injected with velocity \textbf{v} times the value of \textbf{n} in the specified direction.
                                   \end{itemize}
           \item \textbf{T}: Real.
+                            Units of $\unit{K}$
                             Array dimension $3$.
                             Temperature in each direction.
           \item \textbf{physicalSurface}: Integer.
                                           Identification of the edge in the mesh file.
+          \item \textbf{particlesPerEdge}: Integer.
+                                           Optional.
+                                           Number of particles to be injected by each edge in the numerical domain.
+                                           The weight of the particles for each edge will modified by the surface of the edge to ensure the right flux is injected.
+                                           If no value is provided, the number of particles to inject per edge will be calculated with the species weight and the surface of the edge respect to the total one.
         \end{itemize}        
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
       \subsection{reference}
@@ -471,29 +670,34 @@ make
           \item \textbf{radius}: Real.
                                  Reference atomic radius in $\unit{m}$.
           \item \textbf{crossSection}: Real.
-                                       Reference cross section in $\unit{m^2}$.
+                                       Reference cross-section in $\unit{m^2}$.
                                        If this value is present, radius is ignored.
         \end{itemize}
       
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-      \subsection{case}
+      \subsection{solver}
-        This object determines the simulation time, time step, pushers, weighting scheme and solver for the electromagnetic field.
+        This object determines the input parameters for the solvers used in the case, both for particle pushers and electromagnetic field.
         Accepted variables are:
         \begin{itemize}
           \item \textbf{tau}: Real.
+                              Units of $\unit{s}$.
                               Array dimension 'number of species'.
                               Defines the different time steps for each species.
                               Even if all time steps are equal, they need to be defined as an array.
-          \item \textbf{time}: Real.
+          \item \textbf{finalTime}: Real.
-                               Total simulation time in $\unit{s}$.
+                                    Units of $\unit{s}$.
+                                    Final simulation time.
+          \item \textbf{initialTime}: Real.
+                                      Units of $\unit{s}$.
+                                      Initial simulation time.
+                                      If no value is provided, the initial time is set to $\unit[0.0]{s}$.
           \item \textbf{pusher}: Character.
                                  Array dimension 'number of species'.
                                  Indicates the type of pusher used for each species:
                                  \begin{itemize}
-                                    \item \textbf{2DCylNeutral}: Pushes particles in a 2D z-r space without any external force.
+                                   \item \textbf{Neutral}: Pushes a particle without any external force.
-                                    \item \textbf{2DCylCharged}: Pushes particles in a 2D z-r space including the effect of the electrostatic field.
+                                   \item \textbf{Electrostatic}: Pushes a particle, including the effect of the electrostatic field.
-                                    \item \textbf{1DCartCharged}: Pushes particles in a 1D Cartesian space accounting the the electrostatic field.
+                                   \item \textbf{Electromagnetic}: Pushes a particle, accounting for the electromagnetic field.
-                                    \item \textbf{1DRadCharged}: Pushes particles in a 1D cylindrical space (r) accounting the the electrostatic field.
                                  \end{itemize}
           \item \textbf{WeightingScheme}: Character.
                                           Indicates the variable weighting scheme to be used in the simulation.
@@ -508,69 +712,98 @@ make
                                    If no value is supplied, no field is solved.
                                    \begin{itemize}
                                       \item \textbf{Electrostatic}: Solves the Poison equation to obtain the self-consistent electrostatic potential.
+                                      \item \textbf{ConstantB}: Assumes a constant magnetic field in all the domain.
+                                                                It solves the Poisson equation as in the \textbf{solver.EMSolver} option.
                                    \end{itemize}
-          \item \textbf{initial}: Object.
+          \item \textbf{B}: Real.
-                                  Array.
+                            Units of $\unit{T}$.
+                            Array of dimension $3$.
+                            Provides the value of constant magnetic field for the option \textbf{solver.EMSolver} \textbf{ConstantB}.
+          \item \textbf{initial}: Array of objects.
                                   Determines initial values for the species.
                                   Required values are:
                                   \begin{itemize}
-                                    \item \textbf{speciesName}: Character.
+                                    \item \textbf{species}: Character.
-                                                                Name of species.
+                                                            Name of species as defined in the object \textbf{species}.
-                                    \item \textbf{initialState}: Character.
+                                    \item \textbf{file}: Character.
-                                                                 Plain text file that contains the information about the species macroscopic properties in the grid.
+                                                         Output file from previous run used as an initial state for the species.
-                                                                 Initial particles are assumed to be Maxwellian.
+                                                         The file format must be the same as in \textbf{geometry.meshType}
-                                                                 File must be located at \textbf{output.path}.
+                                                         Initial particles are assumed to have a Maxwellian distribution.
-                                                                 The file must contain the following columns in this specific order:
+                                                         File must be located in \textbf{output.path}.
-                                                                 \begin{itemize}
+                                    \item \textbf{particlesPerCell}: Integer.
-                                                                   \item \textit{Element}: Integer. 
+                                                                     Optional.
-                                                                                           Identifier of the volume in the mesh.
+                                                                     Initial number of particles per cell.
-                                                                                           It is not required to specify empty volumes.
+                                                                     If not, the number of particles per cell will be assigned based on the species weight and the cell volume.
-                                                                   \item \textit{Density}: Real.
-                                                                                           Species density in $\unit{m^-3}$.
-                                                                   \item \textit{Velocity}: Real.
-                                                                                            Three colums representing the initial velocity in each direction.
-                                                                                            Units are $\unit{m s^-1}$.
-                                                                   \item \textit{Temperature}: Real.
-                                                                                               One column that represents the initial temperature in $\unit{K}$.
-                                                                                 
-                                                                 \end{itemize}
                                   \end{itemize}
         \end{itemize}
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+      \subsection{average}
+        This object determines the use of an average scheme.
+        If this object exists in the input file, average will be written at the end of the simulation.
+        Acceptable values are:
+        \begin{itemize}
+          \item \textbf{startTime}: Real.
+                                    Units in $\unit{s}$.
+                                    Simulation physical time in which average scheme will start to compute the mean and standard validation.
+                                    If no value is provided, the initial time is set to $\unit[0.0]{s}$.
+        \end{itemize}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
       \subsection{interactions}\label{ssec:input_interactions}
-        This object determine the different interactions among species.
+        This object determines the different interactions among species.
         Acceptable values are:
         \begin{itemize}
           \item \textbf{folderCollisions}: Character.
-                                           Indicates the path to in which the cross section tables are allocated.
+                                           Indicates the path to in which the cross-section tables are allocated.
-          \item \textbf{collisions}: Object.
+          \item \textbf{meshCollisions}: Character.
-                                     Array.
+                                         Determines a specific mesh for \acrshort{mcc} processes.
-                                     Contains the different binary collisions.
+                                         The file needs to be located in the folder \textbf{output.folder}.
+                                         If this value is not present, the mesh defined in \textbf{geometry.meshFile} is used for \acrshort{mcc}.
+                                         The format of this mesh needs to be the same as the one defined in \textbf{geometry.meshType}.
+          \item \textbf{timeStep}: Real.
+                                   Units of $\unit{s}$.
+                                   Time step to calculate MCC.
+                                   If no time is provided, the minimum time step is used.
+          \item \textbf{collisions}: Array of objects.
+                                     Contains the different short range interactions (\acrshort{mcc}).
                                      Multiple collision types can be defined for each pair of species.
                                      Each object in the array is defined by:
                                      \begin{itemize}
                                        \item \textbf{species\_i}, \textbf{species\_j}: Character.
                                                                                        Define the two species involved in the collision processes.
                                                                                        Order is indiferent.
-                                       \item \textbf{cTypes}: Object.
+                                       \item \textbf{cTypes}: Array of objects.
-                                                              Array.
                                                               Defines all the collisions between \textbf{species\_i} and \textbf{species\_j}.
                                                               Required values are:
                                                               \begin{itemize}
                                                                 \item \textbf{type}: Character.
                                                                                      Collision type.
                                                                                      Accepted values are \textbf{elastic}, \textbf{chargeExchange}, \textbf{ionization} and \textbf{recombination}.
-                                                                                     Please refer to Sec. \ref{ssec:collisions} for a description of the different collision types.
+                                                                                     Please refer to Sec.~\ref{ssec:collisions} for a description of the different collision types.
                                                                 \item \textbf{crossSection}: Character.
-                                                                                             File in \textbf{interactions.folderCollisions} that contains the cross section data as a 1D table of relative energy (in $\unit{eV}$) and cross section (in $\unit{m^-2}$).
+                                                                                             File in \textbf{interactions.folderCollisions} that contains the cross-section data as a 1D table of relative energy (in $\unit{eV}$) and cross-section (in $\unit{m^-2}$).
                                                                 \item \textbf{energyThreshold}: Real.
                                                                                                 Energy threshold of the collisional process in $\unit{eV}$.
                                                                                                 Only valid for \textbf{ionization} and \textbf{recombination} processes.
                                                                 \item \textbf{electron}: Character.
                                                                                          Name of species designed as electrons.
                                                                                          Only valid for \textbf{ionization} and \textbf{recombination} processes.
+                                                                \item \textbf{electronSecondary}: Character.
+                                                                                                  Optional.
+                                                                                                  Name of species designed as secondary electrons.
+                                                                                                  If none provided, \textbf{electron} is used.
+                                                                                                  Only valid for \textbf{ionization}.
                                                               \end{itemize}
                                      \end{itemize}
+          \item \textbf{Coulomb}: Array of objects.
+                                  Contains the information about which species must use the Coulomb linear scattering.
+                                  This method assumes a Maxwellian distribution for all species involved.
+                                  Each object in the array is defined by:
+                                  \begin{itemize}
+                                    \item \textbf{species\_i}, \textbf{species\_j}: Character.
+                                                                                    Define the two species involved in the collision processes.
+                                                                                    Order is indifferent.
+                                  
+                                  \end{itemize}
         \end{itemize}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
       \subsection{parallel}
@@ -587,22 +820,33 @@ make
                                  
         \end{itemize}
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-  \chapter{Example runs\label{ch:exampleRuns}}
+  \chapter{Example runs}\label{ch:exampleRuns}
-    \section{1D Cathode}
+    This chapter presents a description of the different example files distributed with \acrshort{fpakc}.
-      Emission from a 1D cathond in both, cartesian and radial coordinates.
+    All examples in the repository have a \lstinline|README.txt| file and a reference output.
-      Both cases insert the same amount of electrons from the minimum coordinate and have the same boundary conditions for particles and the electrostatic field.
+    Plotting of the output is done with \Gls{gnuplot} or \Gls{gmsh}.
-      This case is useful to ilustrate hoy \acrshort{fpakc} can deal with different geometries by just modifiying some parameters in the input file.
+    
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    \section{1D Emissive Cathode (1D\_Cathode)}
+      Emission from a 1D cathode in both, Cartesian and radial coordinates.
+      Both cases insert the same number of electrons from the minimum coordinate and have the same boundary conditions for particles and the electrostatic field.
+      This case is useful to illustrate how \acrshort{fpakc} can deal with different geometries by just modifying some parameters in the input file.
       The same mesh file (\lstinline|mesh.msh|) is used for both cases.
       
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-    \section{ALPHIE Grid system}
+    \section{0D \ce{Ar}-\ce{Ar+} Elastic Collision (0D\_Argon)}
-      Two-dimensional axialsymmetry case to study the counterflow of electrons and Argon ions going trhough the ALPHIE grid system.
+      Test case to check the 0D geometry that includes the elastic collision between \ce{Ar} and \ce{Ar+}.
+      Initial states are read from the \lstinline|Argon_Initial.dat| and \lstinline|Argon+_Initial.dat|.
+    
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+    \section{ALPHIE Grid system (ALPHIE\_Grid)}
+      Two-dimensional axial-symmetry case to study the counterflow of electrons and Argon ions going through the ALPHIE grid system.
       A \lstinline|mesh.geo| file is provided to easily modify the parameters of the grid system and generate a new mesh with \Gls{gmsh}.
       
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-    \section{Flow around cylinder}
+    \section{Flow around cylinder (cylFlow)}
-      Simple case of neutral Argon flow around a cylinder in a 2D axialsymmetry geometry.
+      Simple case of neutral Argon flow around a cylinder in a 2D axial-symmetry geometry.
-      Elastic collisions between argon particles are included as default.
+      Elastic collisions between argon particles are included.
+      Two cases are presented here: one in which the same mesh (\lstinline|meshSingle.msh|) for scattering and collisions is used (\lstinline|input.json|) and a second one (\lstinline|inputDualMesh.json|) in which a mesh is used for scattering (\lstinline|mesh.msh|) and a second one is used only for collisions (\lstinline|meshColl.msh|).
     
 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
   \printglossaries

makefile

@@ -6,7 +6,7 @@ SRCDIR := $(TOPDIR)/src# source folder
 # compiler
 # gfortran:
 FC := gfortran
-JSONDIR := $(TOPDIR)/json-fortran-8.2.0/build-gfortran
+JSONDIR := $(TOPDIR)/json-fortran/build-gfortran
 # ifort:
 # FC := ifort
 # JSONDIR := $(TOPDIR)/json-fortran-8.2.0/build-ifort
@@ -39,5 +39,6 @@ src.o:
 clean:
 	rm -f $(OUTPUT)
 	rm -f $(MODDIR)/*.mod
+	rm -f $(MODDIR)/*.smod
 	rm -f $(OBJDIR)/*.o
 

runs/0D_Argon/Argon+_Initial.dat

@@ -0,0 +1,2 @@
+ #        t             density                                                  velocity            pressure         temperature
+          0             1.0E+16                                      0.0E+0 0.0E+0 0.0E+0                   0              3000

runs/0D_Argon/Argon_Initial.dat

@@ -0,0 +1,2 @@
+ #        t             density                                                  velocity            pressure         temperature
+          0             1.0E+16                                      0.0E+0 0.0E+0 0.0E+0                   0               300

runs/0D_Argon/README.txt

@@ -0,0 +1,11 @@
+Example of 0D geometry.
+
+Mostly used to test collision processes.
+
+This example includes Ar and Ar+ with self-collisions for Ar and elastic collisions for AR-Ar+.
+
+Different starting temperatures for each species that end up in equilibrium.
+
+The gnuplpot script 'plot_Temperature.gp' generates a plot of the species temperatures.
+
+The result is provided in the output folder to compare if modifications to the code are made.

runs/0D_Argon/input.json

@@ -0,0 +1,49 @@
+
+{
+  "output": {
+    "path": "./runs/0D_Argon/",
+    "triggerOutput": 1,
+    "numColl": true,
+	"folder": "test"
+  },
+  "reference": {
+    "density": 1.0e16,
+    "mass": 6.633e-26,
+    "temperature": 11604.0,
+    "radius": 1.88e-10
+  },
+  "geometry": {
+    "dimension": 0,
+    "volume": 1e-11
+  },
+  "species": [
+    {"name": "Argon+", "type": "charged", "mass": 6.633e-26, "charge": 1.0, "weight": 1.0e0},
+    {"name": "Argon",  "type": "neutral", "mass": 6.633e-26,                "weight": 1.0e0}
+  ],
+  "solver": {
+    "tau":  [1.0e-3, 1.0e-3],
+    "finalTime": 1.0e0,
+    "initial": [
+      {"species": "Argon+", "file": "Argon+_Initial.dat"},
+      {"species": "Argon",  "file": "Argon_Initial.dat"}
+    ]
+  },
+  "interactions": {
+    "folderCollisions": "./data/collisions/",
+    "collisions": [
+      {"species_i": "Argon", "species_j": "Argon", 
+       "cTypes": [
+         {"type": "elastic", "crossSection": "EL_Ar-Ar.dat"}
+       ]},
+      {"species_i": "Argon+", "species_j": "Argon", 
+       "cTypes": [
+         {"type": "elastic", "crossSection": "EL_Ar-Ar.dat"}
+       ]}
+    ]
+  },
+  "parallel": {
+    "OpenMP":{
+      "nThreads": 4
+    }
+  }
+}

runs/0D_Argon/plot_Temperature.gp

@@ -0,0 +1,65 @@
+reset
+set macros
+term = 'postscript eps color enhanced'
+font = 'font "CMUSerif-Roman,20"'
+linew = 'lw 2.0'
+times='"{/Symbol \264}"'
+size_x=8.5
+size_y=5.2
+
+tmar=0.998
+bmar=0.145
+
+lmarLabel = 0.070
+
+lmar=lmarLabel+0.085
+rmar=0.97
+
+space_x=(rmar-lmar)
+
+xt_off_0=0.5
+yt_off_0=0.6
+
+set xtics nomirror offset 0.0,xt_off_0
+set mxtics 2
+
+set ytics nomirror offset yt_off_0,0.0
+set mytics 2
+
+set pointsize 1.5
+
+set style line 1  pt 4              lc rgb "#B50427" #Squares   red
+set style line 2  pt 6              lc rgb "#3B4CC1" #Circles   blue
+set style line 3  pt 1              lc rgb "#2CA02C" #Crosses   green
+set style line 4  pt 2              lc rgb "#FE7F0E" #Exes      orange
+set style line 5  pt 8              lc rgb "#D6696B" #Triangles light red
+set style line 10       lt 1 lw 2.0 lc rgb "black"   #Black solid line
+
+set terminal @term size size_x cm, size_y cm @linew @font
+
+set output "comp_temp.eps"
+
+#files
+filename1 = "OUTPUT_Argon.dat"
+filename2 = "OUTPUT_Argon+.dat"
+
+folder = 'output/'
+
+set lmargin at screen lmar 
+set rmargin at screen rmar
+
+set xrange [-0.01:1.01]
+set xtics 0.2
+set xlabel "Time (s)" offset 0.0,1.2
+
+set yrange [250:3550]
+set format y "%3.0f"
+set ytics 500
+set ylabel "Temperature (K)" offset 1.4,0.0
+
+set key width 0.5 height 0.1 spacing 1.3 samplen 0.2 box opaque font ",16"
+set key at graph 0.95, graph 0.9 right top
+
+plot folder.filename1 u ($1):($7)                                          t "Ar"     ls 1 with lines, \
+     folder.filename2 u ($1):($7)                                          t "Ar^{+}" ls 2 with lines
+

runs/1D_Cathode/README.txt

@@ -0,0 +1,8 @@
+This case is useful to explain how fpakc can work with different geometries (Cartisian and Radial in this case) using very similar input files and the same mesh.
+
+From the position to the left, electrons  are emitted at a constant rate.
+The electric potential at the left is fixed at 0.
+
+Depending on the geometry (which affects the symmetry) different distributions of the electron density and electric potential are achieved.
+
+The last iteration obtained for these cases is in the output folder.

runs/1D_Cathode/inputCart.json

@@ -5,16 +5,18 @@
     "triggerOutput": 100,
     "cpuTime": false,
     "numColl": false,
-    "EMField": true
+    "EMField": true,
+	"folder": "Cartesian_Emision"
   },
   "reference": {
     "density": 1.0e16,
     "mass": 9.109e-31,
-    "temperature": 2500.0
+    "temperature": 11604.0
   },
   "geometry": {
-    "type":     "1DCart",
+    "dimension": 1,
-    "meshType": "gmsh",
+    "type":     "Cart",
+    "meshType": "gmsh2",
     "meshFile": "mesh.msh"
   },
   "species": [
@@ -29,22 +31,21 @@
                                                 ]}
   ],
   "boundaryEM": [
-    {"name": "Cathode",  "type": "dirichlet", "potential":  -10.0, "physicalSurface": 1},
+    {"name": "Cathode",  "type": "dirichlet", "potential": 0.0, "physicalSurface": 1}
-    {"name": "Infinite", "type": "dirichlet", "potential":    0.0, "physicalSurface": 2}
   ],
   "inject": [
-    {"name": "Cathode Electron", "species": "Electron", "flow":  9.0e-5, "units": "A", "v": 27500.0, "T": [2500.0, 2500.0, 2500.0],
+    {"name": "Plasma Cat e",     "species": "Electron", "flow":  2.64e-5, "units": "A", "v": 180000.0,   "T": [ 2300.0,  2300.0,  2300.0],
                                  "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"],     "n": [ 1, 0, 0], "physicalSurface": 1}
   ],
-  "case": {
+  "solver": {
     "tau":  [1.0e-11],
-    "time": 1.0e-6,
+    "finalTime": 1.0e-8,
-    "pusher": ["1DCartCharged"],
+    "pusher": ["Electrostatic"],
     "EMSolver": "Electrostatic"
   },
   "parallel": {
     "OpenMP":{
-      "nThreads": 1
+      "nThreads": 24
     }
   }
 }

runs/1D_Cathode/inputRad.json

@@ -5,16 +5,18 @@
     "triggerOutput": 100,
     "cpuTime": false,
     "numColl": false,
-    "EMField": true
+    "EMField": true,
+	"folder": "Radial_Emission"
   },
   "reference": {
     "density": 1.0e16,
     "mass": 9.109e-31,
-    "temperature": 2500.0
+    "temperature": 11604.0
   },
   "geometry": {
-    "type":     "1DRad",
+    "dimension": 1,
-    "meshType": "gmsh",
+    "type":     "Rad",
+    "meshType": "gmsh2",
     "meshFile": "mesh.msh"
   },
   "species": [
@@ -29,22 +31,21 @@
                                                 ]}
   ],
   "boundaryEM": [
-    {"name": "Cathode",  "type": "dirichlet", "potential":  -10.0, "physicalSurface": 1},
+    {"name": "Cathode",  "type": "dirichlet", "potential": 0.0, "physicalSurface": 1}
-    {"name": "Infinite", "type": "dirichlet", "potential":    0.0, "physicalSurface": 2}
   ],
   "inject": [
-    {"name": "Cathode Electron", "species": "Electron", "flow":  9.0e-5, "units": "A", "v": 27500.0, "T": [2500.0, 2500.0, 2500.0],
+    {"name": "Plasma Cat e",     "species": "Electron", "flow":  2.64e-5, "units": "A", "v": 180000.0,   "T": [ 2300.0,  2300.0,  2300.0],
                                  "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"],     "n": [ 1, 0, 0], "physicalSurface": 1}
   ],
-  "case": {
+  "solver": {
     "tau":  [1.0e-11],
-    "time": 1.0e-6,
+    "finalTime": 1.0e-8,
-    "pusher": ["1DRadCharged"],
+    "pusher": ["Electrostatic"],
     "EMSolver": "Electrostatic"
   },
   "parallel": {
     "OpenMP":{
-      "nThreads": 1
+      "nThreads": 24
     }
   }
 }

runs/1D_Cathode/mesh.geo

@@ -0,0 +1,16 @@
+Lcell = 4e-5;
+
+x0 = 0.001;
+xf = x0 + 50.0*Lcell;
+
+Point(1) = {x0, 0, 0, 1};
+Point(2) = {xf, 0, 0, 1};
+
+Line(1) = {1, 2};
+
+Physical Point(1) = {1};
+Physical Point(2) = {2};
+
+Physical Line(1) = {1};
+
+Transfinite Line {1} = (xf-x0)/Lcell + 1 Using Progression 1;

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runs/1D_Cathode/output/Cartesian/OUTPUT_1000_Electron.msh

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runs/ALPHIE_Grid/README.txt

@@ -0,0 +1,7 @@
+Alphie grid system.
+
+The file mesh.geo can be easily modified to generate new grids to test different configurations.
+
+Two cases are provided:
+  Clasical case in which ions and electrons are input from the ionization chamber.
+  Ionization case in which ion-electron pairs are generated due to the influx of electrons using the Ionization boundary condition.

runs/ALPHIE_Grid/inputBaseCase.json

@@ -2,19 +2,20 @@
   "output": {
     "path": "./runs/ALPHIE_Grid/",
     "triggerOutput": 500,
-    "triggerCPUTime": 1,
+    "cpuTime": false,
-    "cpuTime": true,
     "numColl": false,
-    "EMField": true
+    "EMField": true,
+	"folder": "base_case"
   },
   "geometry": {
-    "type":     "2DCyl",
+    "dimension": 2,
-    "meshType": "gmsh",
+    "type":     "Cyl",
+    "meshType": "gmsh2",
     "meshFile": "mesh.msh"
   },
   "species": [
     {"name": "Argon+",   "type": "charged", "mass": 6.633e-26, "charge": 1.0, "weight": 1.0e1},
-    {"name": "Electron", "type": "charged", "mass": 9.109e-31, "charge":-1.0, "weight": 1.0e1}
+    {"name": "Electron", "type": "charged", "mass": 9.109e-31, "charge":-1.0, "weight": 1.0e2}
   ],
   "boundary": [ 
     {"name": "Ionization Chanber", "physicalSurface": 1, "bTypes": [
@@ -44,30 +45,34 @@
   ],
   "boundaryEM": [
     {"name": "Extraction Grid",    "type": "dirichlet", "potential": -150.0, "physicalSurface": 4},
-    {"name": "Acceleration Grid",  "type": "dirichlet", "potential": -600.0, "physicalSurface": 5}
+    {"name": "Acceleration Grid",  "type": "dirichlet", "potential": -600.0, "physicalSurface": 5},
+    {"name": "Ionization Chamber", "type": "dirichlet", "potential":    0.0, "physicalSurface": 1},
+    {"name": "Infinite",           "type": "dirichlet", "potential": -600.0, "physicalSurface": 2}
   ],
   "inject": [
-    {"name": "Ionization Argon+",   "species": "Argon+",   "flow": 27.0e-6, "units": "A", "v":    322.0, "T": [ 500.0,  500.0,  500.0],
+    {"name": "Ionization Argon+",   "species": "Argon+",   "flow":  1.0e-5, "units": "A", "v":   2500.0, "T": [ 500.0,  500.0,  500.0],
                                     "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [ 1, 0, 0], "physicalSurface": 1},
-    {"name": "Ionization Electron", "species": "Electron", "flow": 27.0e-6, "units": "A", "v":  87000.0, "T": [ 500.0,  500.0,  500.0],
+    {"name": "Ionization Electron", "species": "Electron", "flow":  1.0e-5, "units": "A", "v":  87000.0, "T": [30000.0, 30000.0, 30000.0],
                                     "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [ 1, 0, 0], "physicalSurface": 1},
-    {"name": "Cathode Electron",    "species": "Electron", "flow":  9.0e-5, "units": "A", "v":  87000.0, "T": [2500.0, 2500.0, 2500.0],
+    {"name": "Cathode Electron",    "species": "Electron", "flow":  1.0e-4, "units": "A", "v":  87000.0, "T": [30000.0, 30000.0, 30000.0],
                                     "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [-1, 0, 0], "physicalSurface": 2}
   ],
   "reference": {
     "density": 1.0e16,
     "mass": 9.109e-31,
-    "temperature": 2500.0
+    "temperature": 2500.0,
+    "radius": 1.88e-10
   },
-  "case": {
+  "solver": {
     "tau":  [1.0e-9, 1.0e-11],
-    "time": 2.0e-6,
+    "finalTime": 1.0e-6,
-    "pusher": ["2DCylCharged", "2DCylCharged"],
+    "pusher": ["Electrostatic", "Electrostatic"],
+    "WeightingScheme": "Volume",
     "EMSolver": "Electrostatic"
   },
   "parallel": {
     "OpenMP":{
-      "nThreads": 8
+      "nThreads": 24
     }
   }
 }

runs/ALPHIE_Grid/inputIonization_0.10mA.json

@@ -2,24 +2,26 @@
   "output": {
     "path": "./runs/ALPHIE_Grid/",
     "triggerOutput": 500,
-    "triggerCPUTime": 1,
+    "cpuTime": false,
-    "cpuTime": true,
     "numColl": false,
-    "EMField": true
+    "EMField": true,
+    "folder": "ionization_0.10mA"
   },
   "geometry": {
-    "type":     "2DCyl",
+    "dimension": 2,
-    "meshType": "gmsh",
+    "type":     "Cyl",
+    "meshType": "gmsh2",
     "meshFile": "mesh.msh"
   },
   "species": [
     {"name": "Argon+",   "type": "charged", "mass": 6.633e-26, "charge": 1.0, "weight": 1.0e1},
-    {"name": "Electron", "type": "charged", "mass": 9.109e-31, "charge":-1.0, "weight": 1.0e1}
+    {"name": "Electron", "type": "charged", "mass": 9.109e-31, "charge":-1.0, "weight": 1.0e2}
   ],
   "boundary": [ 
     {"name": "Ionization Chanber", "physicalSurface": 1, "bTypes": [
                                                            {"type": "transparent"},
-                                                           {"type": "transparent"}
+                                                           {"type": "ionization", "neutral": {"ion": "Argon+", "mass": 6.633e-26, "density": 5.0e16, "velocity": [2500, 0, 0], "temperature": 300},
+                                                                                  "effectiveTime": 5.0e-6,"energyThreshold": 15.76, "crossSection": "./data/collisions/IO_e-Ar.dat"}
                                                           ]},
     {"name": "Vacuum Chamber",     "physicalSurface": 2, "bTypes": [
                                                            {"type": "transparent"},
@@ -44,30 +46,30 @@
   ],
   "boundaryEM": [
     {"name": "Extraction Grid",    "type": "dirichlet", "potential": -150.0, "physicalSurface": 4},
-    {"name": "Acceleration Grid",  "type": "dirichlet", "potential": -600.0, "physicalSurface": 5}
+    {"name": "Acceleration Grid",  "type": "dirichlet", "potential": -600.0, "physicalSurface": 5},
+    {"name": "Ionization Chamber", "type": "dirichlet", "potential":    0.0, "physicalSurface": 1},
+    {"name": "Infinite",           "type": "dirichlet", "potential": -600.0, "physicalSurface": 2}
   ],
   "inject": [
-    {"name": "Ionization Argon+",   "species": "Argon+",   "flow": 27.0e-6, "units": "A", "v":    322.0, "T": [ 500.0,  500.0,  500.0],
+    {"name": "Cathode Electron",    "species": "Electron", "flow":  1.0e-4, "units": "A", "v":  87000.0, "T": [30000.0, 30000.0, 30000.0],
-                                    "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [ 1, 0, 0], "physicalSurface": 1},
-    {"name": "Ionization Electron", "species": "Electron", "flow": 27.0e-6, "units": "A", "v":  87000.0, "T": [ 500.0,  500.0,  500.0],
-                                    "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [ 1, 0, 0], "physicalSurface": 1},
-    {"name": "Cathode Electron",    "species": "Electron", "flow":  9.0e-5, "units": "A", "v":  87000.0, "T": [2500.0, 2500.0, 2500.0],
                                     "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [-1, 0, 0], "physicalSurface": 2}
   ],
   "reference": {
     "density": 1.0e16,
     "mass": 9.109e-31,
-    "temperature": 2500.0
+    "temperature": 2500.0,
+    "radius": 1.88e-10
   },
-  "case": {
+  "solver": {
-    "tau":  [1.0e-11, 1.0e-11],
+    "tau":  [1.0e-9, 1.0e-11],
-    "time": 2.0e-6,
+    "finalTime": 1.0e-6,
-    "pusher": ["2DCylCharged", "2DCylCharged"],
+    "pusher": ["Electrostatic", "Electrostatic"],
+    "WeightingScheme": "Volume",
     "EMSolver": "Electrostatic"
   },
   "parallel": {
     "OpenMP":{
-      "nThreads": 8
+      "nThreads": 24
     }
   }
 }

runs/ALPHIE_Grid/mesh.geo

@@ -1,12 +1,13 @@
-Lz  = 0.0100;
+zg1  = 0.0020;
-Lr  = 0.0006;
+tg1  = 0.0003;
-zg1 = 0.0025;
-tg1 = 0.0004;
 rg1  = 0.0005;
-dg  = 0.0025;
+dg   = 0.0020;
 zg2  = zg1 + tg1 + dg;
 tg2  = tg1;
 rg2  = rg1;
+zEnd = 0.0050;
+Lz   = zg2 + tg2 + zEnd;
+Lr   = rg1 + 0.0001;
 
 Lcell = 0.0001;
 
@@ -96,19 +97,19 @@ Transfinite Line {18, 19, 20, 21, 22, 6} = rg1/Lcell + 1 Using Progression 1;
 Transfinite Line {17, 15, 13, 11, 9, 7}  = (Lr-rg1)/Lcell + 1 Using Progression 1;
 
 
-#Transfinite Surface{1};
+Transfinite Surface{1};
-#Recombine Surface {1};
+Recombine Surface {1};
-#Transfinite Surface{2};
+Transfinite Surface{2};
-#Recombine Surface {2};
+Recombine Surface {2};
-#Transfinite Surface{3};
+Transfinite Surface{3};
-#Recombine Surface {3};
+Recombine Surface {3};
-#Transfinite Surface{4};
+Transfinite Surface{4};
-#Recombine Surface {4};
+Recombine Surface {4};
-#Transfinite Surface{5};
+Transfinite Surface{5};
-#Recombine Surface {5};
+Recombine Surface {5};
-#Transfinite Surface{6};
+Transfinite Surface{6};
-#Recombine Surface {6};
+Recombine Surface {6};
-#Transfinite Surface{7};
+Transfinite Surface{7};
-#Recombine Surface {7};
+Recombine Surface {7};
-#Transfinite Surface{8};
+Transfinite Surface{8};
-#Recombine Surface {8};
+Recombine Surface {8};

runs/Argon_Expansion/CX_case.json

@@ -3,11 +3,13 @@
     "path": "./runs/Argon_Expansion/",
 	"triggerOutput": 10,
 	"cpuTime": false,
-	"numColl": true
+	"numColl": true,
+	"folder": "CX_case"
   },
   "geometry": {
-    "type":     "2DCyl",
+    "dimension": 2,
-    "meshType": "gmsh",
+    "type":     "Cyl",
+    "meshType": "gmsh2",
     "meshFile": "mesh.msh"
   },
   "species": [
@@ -40,10 +42,10 @@
     "temperature": 300.0,
     "radius": 1.88e-10
   },
-  "case": {
+  "solver": {
     "tau":  [1.0e-6, 1.0e-6],
-    "time": 4.0e-3,
+    "finalTime": 4.0e-3,
-    "pusher": ["2DCylNeutral", "2DCylNeutral"],
+    "pusher": ["Neutral", "Neutral"],
     "WeightingScheme": "Volume"
   },
   "interactions": {

runs/Argon_Expansion/elastic_case.json

@@ -3,11 +3,13 @@
     "path": "./runs/Argon_Expansion/",
 	"triggerOutput": 10,
 	"cpuTime": false,
-	"numColl": false
+	"numColl": false,
+	"folder": "Elastic_case"
   },
   "geometry": {
-    "type":     "2DCyl",
+    "dimension": 2,
-    "meshType": "gmsh",
+    "type":     "Cyl",
+    "meshType": "gmsh2",
     "meshFile": "mesh.msh"
   },
   "species": [
@@ -40,10 +42,10 @@
     "temperature": 300.0,
     "radius": 1.88e-10
   },
-  "case": {
+  "solver": {
     "tau":  [1.0e-6, 1.0e-6],
-    "time": 4.0e-3,
+    "finalTime": 4.0e-3,
-    "pusher": ["2DCylNeutral", "2DCylNeutral"],
+    "pusher": ["Neutral", "Neutral"],
     "WeightingScheme": "Volume"
   },
   "interactions": {

runs/Argon_Expansion/nocoll_case.json

@@ -0,0 +1,56 @@
+{
+  "output": {
+    "path": "./runs/Argon_Expansion/",
+	"triggerOutput": 10,
+	"cpuTime": false,
+	"numColl": false,
+	"folder": "Nocoll_case"
+  },
+  "geometry": {
+    "dimension": 2,
+    "type":     "Cyl",
+    "meshType": "gmsh2",
+    "meshFile": "mesh.msh"
+  },
+  "species": [
+    {"name": "Argon",  "type": "neutral", "mass": 6.633e-26, "weight": 1.0e8,                "ion": "Argon+"},
+    {"name": "Argon+", "type": "charged", "mass": 6.633e-26, "weight": 1.0e8, "charge": 1.0, "neutral": "Argon"}
+  ],
+  "boundary": [ 
+    {"name": "Injection", "physicalSurface": 1, "bTypes": [
+                                                  {"type": "transparent"},
+                                                  {"type": "transparent"}
+                                                 ]},
+    {"name": "Exterior",  "physicalSurface": 2, "bTypes": [
+                                                  {"type": "transparent"},
+                                                  {"type": "transparent"}
+                                                 ]},
+    {"name": "Axis",      "physicalSurface": 3, "bTypes": [
+                                                  {"type": "axis"},
+                                                  {"type": "axis"}
+                                                 ]}
+  ],
+  "inject": [
+    {"name": "Exhausts Ar", "species": "Argon", "flow": 0.7, "units": "sccm",     "v": 300.0, "T": [300.0, 300.0, 300.0],
+                            "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [1, 0, 0], "physicalSurface": 1},
+    {"name": "Exhausts Ar+", "species": "Argon+", "flow": 0.3, "units": "sccm",     "v": 40000.0, "T": [300.0, 300.0, 300.0],
+                             "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [1, 0, 0], "physicalSurface": 1}
+  ],
+  "reference": {
+    "density": 1.0e19,
+    "mass": 6.633e-26,
+    "temperature": 300.0,
+    "radius": 1.88e-10
+  },
+  "solver": {
+    "tau":  [1.0e-6, 1.0e-6],
+    "finalTime": 4.0e-3,
+    "pusher": ["Neutral", "Neutral"],
+    "WeightingScheme": "Volume"
+  },
+  "parallel": {
+    "OpenMP":{
+      "nThreads": 24
+    }
+  }
+}

runs/cylFlow/README.txt

@@ -0,0 +1,7 @@
+Neutral flow around a cylinder with elastic collisions.
+
+Case with the same mesh for particle weighting and collisions and another case using the dual mesh mode, with a more refined mesh around the cylinder.
+This demostrates the capacity of fpakc to work with independent meshes for particles and collisions.
+
+CPU time is outputed.
+Gnuplot scripts for plotting the CPU time are provided.

runs/cylFlow/input.json

@@ -3,12 +3,13 @@
     "path": "./runs/cylFlow/",
 	"triggerOutput": 10,
 	"cpuTime": true,
-	"numColl": false
+	"numColl": true
   },
   "geometry": {
-    "type":     "2DCyl",
+    "dimension": 2,
-    "meshType": "gmsh",
+    "type":     "Cyl",
-    "meshFile": "mesh.msh"
+    "meshType": "gmsh2",
+    "meshFile": "meshSingle.msh"
   },
   "species": [
     {"name": "Argon",  "type": "neutral", "mass": 6.633e-26, "weight": 5.0e8}
@@ -40,11 +41,10 @@
     "temperature": 300.0,
     "radius": 1.88e-10
   },
-  "case": {
+  "solver": {
     "tau":  [5.0e-7],
-    "time":  1.0e-3,
+    "finalTime":  5.0e-4,
-    "pusher": ["2DCylNeutral"],
+    "pusher": ["Neutral"],
-    "WeightingScheme": "Volume"
   },
   "interactions": {
     "folderCollisions": "./data/collisions/",
@@ -57,7 +57,7 @@
   },
   "parallel": {
     "OpenMP":{
-      "nThreads": 8
+      "nThreads": 24
     }
   }
 }

runs/cylFlow/inputDualMesh.json

@@ -0,0 +1,65 @@
+{
+  "output": {
+    "path": "./runs/cylFlow/",
+	"triggerOutput": 10,
+	"cpuTime": true,
+	"numColl": true
+  },
+  "geometry": {
+    "dimension": 2,
+    "type":     "Cyl",
+    "meshType": "gmsh2",
+    "meshFile": "mesh.msh",
+    "meshCollisions": "meshColl.msh"
+  },
+  "species": [
+    {"name": "Argon",  "type": "neutral", "mass": 6.633e-26, "weight": 5.0e8}
+  ],
+  "boundary": [ 
+    {"name": "Injection",      "physicalSurface": 1, "bTypes": [
+                                                       {"type": "transparent"}
+                                                      ]},
+    {"name": "Chamber Walls",  "physicalSurface": 2, "bTypes": [
+                                                       {"type": "reflection"}
+                                                      ]},
+    {"name": "Exterior",       "physicalSurface": 3, "bTypes": [
+                                                       {"type": "transparent"}
+                                                      ]},
+    {"name": "Cylinder Walls", "physicalSurface": 4, "bTypes": [
+                                                       {"type": "reflection"}
+                                                      ]},
+    {"name": "Axis",           "physicalSurface": 5, "bTypes": [
+                                                       {"type": "axis"}
+                                                      ]}
+  ],
+  "inject": [
+    {"name": "Nozzle", "species": "Argon", "flow": 10.0, "units": "sccm",     "v": 300.0, "T": [300.0, 300.0, 300.0],
+                       "velDist": ["Maxwellian", "Maxwellian", "Maxwellian"], "n": [1, 0, 0], "physicalSurface": 1}
+  ],
+  "reference": {
+    "density": 1.0e20,
+    "mass": 6.633e-26,
+    "temperature": 300.0,
+    "radius": 1.88e-10
+  },
+  "solver": {
+    "tau":  [5.0e-7],
+    "finalTime":  5.0e-4,
+    "pusher": ["Neutral"],
+    "WeightingScheme": "Volume"
+  },
+  "interactions": {
+    "folderCollisions": "./data/collisions/",
+    "collisions": [
+      {"species_i": "Argon", "species_j": "Argon", 
+       "cTypes": [
+         {"type": "elastic", "crossSection": "EL_Ar-Ar.dat"}
+       ]}
+    ]
+  },
+  "parallel": {
+    "OpenMP":{
+      "nThreads": 24
+    }
+  }
+}

runs/cylFlow/mesh.geo

@@ -62,10 +62,13 @@ Physical Surface(4) = {4};
 Physical Surface(5) = {5};
 
 Transfinite Line {12, 2, 4, 6} = cyl_h/Lcell + 1 Using Progression 1;
-Transfinite Line {1, 13, 10} = cyl_s/Lcell + 1 Using Progression 1;
+Transfinite Line {10} = cyl_s/Lcell + 1 Using Progression 1;
-Transfinite Line {11, 16, 15, 7} = (dom_h - cyl_h)/Lcell + 1 Using Progression 1;
+Transfinite Line {1, 13} = cyl_s/Lcell + 1 Using Progression 0.95;
+Transfinite Line {11, 7} = (dom_h - cyl_h)/Lcell + 1 Using Progression 1;
+Transfinite Line {16,-15} = (dom_h - cyl_h)/Lcell + 1 Using Progression 0.95;
 Transfinite Line {3, 9} = cyl_l/Lcell + 1 Using Progression 1;
-Transfinite Line {5, 14, 8} = (dom_l - cyl_e)/Lcell + 1 Using Progression 1;
+Transfinite Line {8} = (dom_l - cyl_e)/Lcell + 1 Using Progression 1;
+Transfinite Line {-5, -14} = (dom_l - cyl_e)/Lcell + 1 Using Progression 0.95;
 
 Transfinite Surface{1};
 Recombine Surface {1};

runs/cylFlow/mesh.msh.opt

@@ -1,629 +0,0 @@
-General.AxesFormatX = "%.3g";
-General.AxesFormatY = "%.3g";
-General.AxesFormatZ = "%.3g";
-General.AxesLabelX = "z (m)";
-General.AxesLabelY = "r (m)";
-General.AxesLabelZ = "";
-General.BackgroundImageFileName = "";
-General.BuildOptions = " 64Bit ALGLIB Bamg Blas Blossom DIntegration Dlopen DomHex Fltk GMP Gmm[system] Hxt Hxt3D Jpeg Kbipack Lapack LinuxJoystick MathEx Mesh Metis[system] Mmg3d Mpeg NativeFileChooser Netgen ONELAB ONELABMetamodel OpenCASCADE OpenCASCADE-CAF OpenGL OpenMP OptHom Parser Plugins Png Post QuadTri Solver TetGen/BR Zlib";
-General.DefaultFileName = "untitled.geo";
-General.Display = "";
-General.ErrorFileName = ".gmsh-errors";
-General.ExecutableFileName = "/usr/bin/gmsh";
-General.FileName = "/home/jorge/PPartiC/runs/cylFlow/mesh.msh";
-General.FltkTheme = "";
-General.GraphicsFont = "Helvetica";
-General.GraphicsFontEngine = "Native";
-General.GraphicsFontTitle = "Helvetica";
-General.OptionsFileName = ".gmsh-options";
-General.RecentFile0 = "/home/jorge/PPartiC/runs/cylFlow/mesh.msh";
-General.RecentFile1 = "untitled.geo";
-General.RecentFile2 = "mesh/Neutral_Expansion_Div.geo";
-General.RecentFile3 = "mesh/Neutral_Expansion_Div.msh";
-General.RecentFile4 = "Neutral_Expansion_Div.msh";
-General.RecentFile5 = "Neutral_Expansion.geo";
-General.RecentFile6 = "Neutral_Expansion_Div.geo";
-General.RecentFile7 = "/home/jorge/Dropbox/UPMPlasmaLab/Post-Doc/Codes/PICCIL2D/PIC-FEM/Neutral_Expansion_Div.msh";
-General.RecentFile8 = "Neutral_Expansion.msh";
-General.RecentFile9 = "/home/jorge/Dropbox/UPMPlasmaLab/Post-Doc/Codes/PICCIL2D/PIC-FEM/Neutral_Expansion.msh";
-General.TextEditor = "gedit '%s'";
-General.TmpFileName = ".gmsh-tmp";
-General.Version = "4.4.1";
-General.WatchFilePattern = "";
-General.AlphaBlending = 1;
-General.Antialiasing = 0;
-General.ArrowHeadRadius = 0.12;
-General.ArrowStemLength = 0.5600000000000001;
-General.ArrowStemRadius = 0.02;
-General.Axes = 1;
-General.AxesMikado = 0;
-General.AxesAutoPosition = 1;
-General.AxesForceValue = 0;
-General.AxesMaxX = 1;
-General.AxesMaxY = 1;
-General.AxesMaxZ = 1;
-General.AxesMinX = 0;
-General.AxesMinY = 0;
-General.AxesMinZ = 0;
-General.AxesTicsX = 8;
-General.AxesTicsY = 4;
-General.AxesTicsZ = 5;
-General.AxesValueMaxX = 1;
-General.AxesValueMaxY = 1;
-General.AxesValueMaxZ = 1;
-General.AxesValueMinX = 0;
-General.AxesValueMinY = 0;
-General.AxesValueMinZ = 0;
-General.BackgroundGradient = 1;
-General.BackgroundImage3D = 0;
-General.BackgroundImagePage = 0;
-General.BackgroundImagePositionX = 0;
-General.BackgroundImagePositionY = 0;
-General.BackgroundImageWidth = -1;
-General.BackgroundImageHeight = -1;
-General.BoundingBoxSize = 0.07615773105863909;
-General.Camera = 0;
-General.CameraAperture = 40;
-General.CameraEyeSeparationRatio = 1.5;
-General.CameraFocalLengthRatio = 1;
-General.Clip0A = 1;
-General.Clip0B = 0;
-General.Clip0C = 0;
-General.Clip0D = 0;
-General.Clip1A = 0;
-General.Clip1B = 1;
-General.Clip1C = 0;
-General.Clip1D = 0;
-General.Clip2A = 0;
-General.Clip2B = 0;
-General.Clip2C = 1;
-General.Clip2D = 0;
-General.Clip3A = -1;
-General.Clip3B = 0;
-General.Clip3C = 0;
-General.Clip3D = 1;
-General.Clip4A = 0;
-General.Clip4B = -1;
-General.Clip4C = 0;
-General.Clip4D = 1;
-General.Clip5A = 0;
-General.Clip5B = 0;
-General.Clip5C = -1;
-General.Clip5D = 1;
-General.ClipFactor = 5;
-General.ClipOnlyDrawIntersectingVolume = 0;
-General.ClipOnlyVolume = 0;
-General.ClipPositionX = 650;
-General.ClipPositionY = 150;
-General.ClipWholeElements = 0;
-General.ColorScheme = 1;
-General.ConfirmOverwrite = 1;
-General.ContextPositionX = 235;
-General.ContextPositionY = 962;
-General.DetachedMenu = 0;
-General.DisplayBorderFactor = 0.2;
-General.DoubleBuffer = 1;
-General.DrawBoundingBoxes = 0;
-General.ExpertMode = 0;
-General.ExtraPositionX = 650;
-General.ExtraPositionY = 350;
-General.ExtraHeight = 100;
-General.ExtraWidth = 100;
-General.FastRedraw = 0;
-General.FieldPositionX = 650;
-General.FieldPositionY = 550;
-General.FieldHeight = 488;
-General.FieldWidth = 651;
-General.FileChooserPositionX = 200;
-General.FileChooserPositionY = 200;
-General.FltkColorScheme = 0;
-General.FontSize = -1;
-General.GraphicsFontSize = 15;
-General.GraphicsFontSizeTitle = 18;
-General.GraphicsHeight = 1003;
-General.GraphicsPositionX = 274;
-General.GraphicsPositionY = 263;
-General.GraphicsWidth = 1920;
-General.HighOrderToolsPositionX = 650;
-General.HighOrderToolsPositionY = 150;
-General.HighResolutionGraphics = 1;
-General.HighResolutionPointSizeFactor = 2;
-General.InitialModule = 0;
-General.InputScrolling = 1;
-General.Light0 = 1;
-General.Light0X = 0.65;
-General.Light0Y = 0.65;
-General.Light0Z = 1;
-General.Light0W = 0;
-General.Light1 = 0;
-General.Light1X = 0.5;
-General.Light1Y = 0.3;
-General.Light1Z = 1;
-General.Light1W = 0;
-General.Light2 = 0;
-General.Light2X = 0.5;
-General.Light2Y = 0.3;
-General.Light2Z = 1;
-General.Light2W = 0;
-General.Light3 = 0;
-General.Light3X = 0.5;
-General.Light3Y = 0.3;
-General.Light3Z = 1;
-General.Light3W = 0;
-General.Light4 = 0;
-General.Light4X = 0.5;
-General.Light4Y = 0.3;
-General.Light4Z = 1;
-General.Light4W = 0;
-General.Light5 = 0;
-General.Light5X = 0.5;
-General.Light5Y = 0.3;
-General.Light5Z = 1;
-General.Light5W = 0;
-General.LineWidth = 1;
-General.ManipulatorPositionX = 650;
-General.ManipulatorPositionY = 150;
-General.MaxX = 0.07000000000000001;
-General.MaxY = 0.03;
-General.MaxZ = 0;
-General.MenuWidth = 219;
-General.MenuHeight = 200;
-General.MenuPositionX = 400;
-General.MenuPositionY = 400;
-General.MessageFontSize = -1;
-General.MessageHeight = 300;
-General.MinX = 0;
-General.MinY = 0;
-General.MinZ = 0;
-General.MouseHoverMeshes = 0;
-General.MouseSelection = 1;
-General.MouseInvertZoom = 0;
-General.NonModalWindows = 1;
-General.NoPopup = 0;
-General.NumThreads = 1;
-General.OptionsPositionX = 827;
-General.OptionsPositionY = 541;
-General.Orthographic = 1;
-General.PluginPositionX = 58;
-General.PluginPositionY = 658;
-General.PluginHeight = 488;
-General.PluginWidth = 708;
-General.PointSize = 3;
-General.PolygonOffsetAlwaysOn = 0;
-General.PolygonOffsetFactor = 1;
-General.PolygonOffsetUnits = 1;
-General.ProgressMeterStep = 20;
-General.QuadricSubdivisions = 6;
-General.RotationX = -0;
-General.RotationY = 0;
-General.RotationZ = -0;
-General.RotationCenterGravity = 1;
-General.RotationCenterX = 0;
-General.RotationCenterY = 0;
-General.RotationCenterZ = 0;
-General.SaveOptions = 0;
-General.SaveSession = 1;
-General.ScaleX = 1;
-General.ScaleY = 1;
-General.ScaleZ = 1;
-General.Shininess = 0.4;
-General.ShininessExponent = 40;
-General.ShowModuleMenu = 1;
-General.ShowOptionsOnStartup = 0;
-General.ShowMessagesOnStartup = 0;
-General.SmallAxes = 1;
-General.SmallAxesPositionX = -60;
-General.SmallAxesPositionY = -40;
-General.SmallAxesSize = 30;
-General.StatisticsPositionX = 650;
-General.StatisticsPositionY = 150;
-General.Stereo = 0;
-General.SystemMenuBar = 1;
-General.Terminal = 0;
-General.Tooltips = 1;
-General.Trackball = 1;
-General.TrackballHyperbolicSheet = 1;
-General.TrackballQuaternion0 = 0;
-General.TrackballQuaternion1 = 0;
-General.TrackballQuaternion2 = 0;
-General.TrackballQuaternion3 = 1;
-General.TranslationX = 0;
-General.TranslationY = 0;
-General.TranslationZ = 0;
-General.VectorType = 4;
-General.Verbosity = 5;
-General.VisibilityPositionX = 1118;
-General.VisibilityPositionY = 464;
-General.ZoomFactor = 4;
-General.Color.Background = {255,255,255};
-General.Color.BackgroundGradient = {208,215,255};
-General.Color.Foreground = {85,85,85};
-General.Color.Text = {0,0,0};
-General.Color.Axes = {0,0,0};
-General.Color.SmallAxes = {0,0,0};
-General.Color.AmbientLight = {25,25,25};
-General.Color.DiffuseLight = {255,255,255};
-General.Color.SpecularLight = {255,255,255};
-Geometry.DoubleClickedPointCommand = "";
-Geometry.DoubleClickedLineCommand = "";
-Geometry.DoubleClickedSurfaceCommand = "";
-Geometry.DoubleClickedVolumeCommand = "";
-Geometry.OCCTargetUnit = "";
-Geometry.AutoCoherence = 1;
-Geometry.Clip = 0;
-Geometry.CopyMeshingMethod = 0;
-Geometry.DoubleClickedEntityTag = 0;
-Geometry.ExactExtrusion = 1;
-Geometry.ExtrudeReturnLateralEntities = 1;
-Geometry.ExtrudeSplinePoints = 5;
-Geometry.HighlightOrphans = 0;
-Geometry.LabelType = 0;
-Geometry.Light = 1;
-Geometry.LightTwoSide = 1;
-Geometry.Lines = 1;
-Geometry.LineNumbers = 0;
-Geometry.LineSelectWidth = 3;
-Geometry.LineType = 0;
-Geometry.LineWidth = 2;
-Geometry.MatchGeomAndMesh = 0;
-Geometry.MatchMeshScaleFactor = 1;
-Geometry.MatchMeshTolerance = 1e-06;
-Geometry.Normals = 0;
-Geometry.NumSubEdges = 40;
-Geometry.OCCAutoFix = 1;
-Geometry.OCCBooleanPreserveNumbering = 1;
-Geometry.OCCDisableSTL = 0;
-Geometry.OCCFixDegenerated = 0;
-Geometry.OCCFixSmallEdges = 0;
-Geometry.OCCFixSmallFaces = 0;
-Geometry.OCCImportLabels = 1;
-Geometry.OCCParallel = 0;
-Geometry.OCCScaling = 1;
-Geometry.OCCSewFaces = 0;
-Geometry.OffsetX = 0;
-Geometry.OffsetY = 0;
-Geometry.OffsetZ = 0;
-Geometry.OldCircle = 0;
-Geometry.OldRuledSurface = 0;
-Geometry.OldNewReg = 1;
-Geometry.Points = 1;
-Geometry.PointNumbers = 0;
-Geometry.PointSelectSize = 6;
-Geometry.PointSize = 4;
-Geometry.PointType = 0;
-Geometry.ReparamOnFaceRobust = 0;
-Geometry.ScalingFactor = 1;
-Geometry.OrientedPhysicals = 1;
-Geometry.SnapX = 0.1;
-Geometry.SnapY = 0.1;
-Geometry.SnapZ = 0.1;
-Geometry.Surfaces = 0;
-Geometry.SurfaceNumbers = 0;
-Geometry.SurfaceType = 0;
-Geometry.Tangents = 0;
-Geometry.Tolerance = 1e-08;
-Geometry.ToleranceBoolean = 0;
-Geometry.Transform = 0;
-Geometry.TransformXX = 1;
-Geometry.TransformXY = 0;
-Geometry.TransformXZ = 0;
-Geometry.TransformYX = 0;
-Geometry.TransformYY = 1;
-Geometry.TransformYZ = 0;
-Geometry.TransformZX = 0;
-Geometry.TransformZY = 0;
-Geometry.TransformZZ = 1;
-Geometry.Volumes = 0;
-Geometry.VolumeNumbers = 0;
-Geometry.Color.Points = {90,90,90};
-Geometry.Color.Lines = {0,0,255};
-Geometry.Color.Surfaces = {128,128,128};
-Geometry.Color.Volumes = {255,255,0};
-Geometry.Color.Selection = {255,0,0};
-Geometry.Color.HighlightZero = {255,0,0};
-Geometry.Color.HighlightOne = {255,150,0};
-Geometry.Color.HighlightTwo = {255,255,0};
-Geometry.Color.Tangents = {255,255,0};
-Geometry.Color.Normals = {255,0,0};
-Geometry.Color.Projection = {0,255,0};
-Mesh.Algorithm = 2;
-Mesh.Algorithm3D = 1;
-Mesh.AngleSmoothNormals = 30;
-Mesh.AngleToleranceFacetOverlap = 0.1;
-Mesh.AnisoMax = 9.999999999999999e+32;
-Mesh.AllowSwapAngle = 10;
-Mesh.BdfFieldFormat = 1;
-Mesh.Binary = 0;
-Mesh.BoundaryLayerFanPoints = 5;
-Mesh.CgnsImportOrder = 1;
-Mesh.CgnsConstructTopology = 0;
-Mesh.CharacteristicLengthExtendFromBoundary = 1;
-Mesh.CharacteristicLengthFactor = 1;
-Mesh.CharacteristicLengthMin = 0;
-Mesh.CharacteristicLengthMax = 1e+22;
-Mesh.CharacteristicLengthFromCurvature = 0;
-Mesh.CharacteristicLengthFromPoints = 1;
-Mesh.Clip = 0;
-Mesh.ColorCarousel = 0;
-Mesh.CompoundClassify = 1;
-Mesh.CompoundCharacteristicLengthFactor = 0.5;
-Mesh.CpuTime = 0;
-Mesh.DrawSkinOnly = 0;
-Mesh.Dual = 0;
-Mesh.ElementOrder = 1;
-Mesh.Explode = 1;
-Mesh.FlexibleTransfinite = 0;
-Mesh.NewtonConvergenceTestXYZ = 0;
-Mesh.Format = 10;
-Mesh.Hexahedra = 1;
-Mesh.HighOrderIterMax = 100;
-Mesh.HighOrderNumLayers = 6;
-Mesh.HighOrderOptimize = 0;
-Mesh.HighOrderPassMax = 25;
-Mesh.HighOrderPeriodic = 0;
-Mesh.HighOrderPoissonRatio = 0.33;
-Mesh.HighOrderPrimSurfMesh = 0;
-Mesh.HighOrderDistCAD = 0;
-Mesh.HighOrderThresholdMin = 0.1;
-Mesh.HighOrderThresholdMax = 2;
-Mesh.LabelSampling = 1;
-Mesh.LabelType = 0;
-Mesh.LcIntegrationPrecision = 1e-09;
-Mesh.Light = 1;
-Mesh.LightLines = 2;
-Mesh.LightTwoSide = 1;
-Mesh.Lines = 1;
-Mesh.LineNumbers = 0;
-Mesh.LineWidth = 1;
-Mesh.MaxNumThreads1D = 0;
-Mesh.MaxNumThreads2D = 0;
-Mesh.MaxNumThreads3D = 0;
-Mesh.MeshOnlyVisible = 0;
-Mesh.MetisAlgorithm = 1;
-Mesh.MetisEdgeMatching = 2;
-Mesh.MetisMaxLoadImbalance = -1;
-Mesh.MetisObjective = 1;
-Mesh.MetisMinConn = -1;
-Mesh.MetisRefinementAlgorithm = 2;
-Mesh.MinimumCirclePoints = 7;
-Mesh.MinimumCurvePoints = 3;
-Mesh.MshFileVersion = 4.1;
-Mesh.MedFileMinorVersion = -1;
-Mesh.MedImportGroupsOfNodes = 0;
-Mesh.MedSingleModel = 0;
-Mesh.PartitionHexWeight = -1;
-Mesh.PartitionLineWeight = -1;
-Mesh.PartitionPrismWeight = -1;
-Mesh.PartitionPyramidWeight = -1;
-Mesh.PartitionQuadWeight = -1;
-Mesh.PartitionTrihedronWeight = 0;
-Mesh.PartitionTetWeight = -1;
-Mesh.PartitionTriWeight = -1;
-Mesh.PartitionCreateTopology = 1;
-Mesh.PartitionCreatePhysicals = 1;
-Mesh.PartitionCreateGhostCells = 0;
-Mesh.PartitionSplitMeshFiles = 0;
-Mesh.PartitionTopologyFile = 0;
-Mesh.PartitionOldStyleMsh2 = 1;
-Mesh.NbHexahedra = 0;
-Mesh.NbNodes = 27248;
-Mesh.NbPartitions = 0;
-Mesh.NbPrisms = 0;
-Mesh.NbPyramids = 0;
-Mesh.NbTrihedra = 0;
-Mesh.NbQuadrangles = 26877;
-Mesh.NbTetrahedra = 0;
-Mesh.NbTriangles = 0;
-Mesh.Normals = 0;
-Mesh.NumSubEdges = 2;
-Mesh.Optimize = 1;
-Mesh.OptimizeThreshold = 0.3;
-Mesh.OptimizeNetgen = 0;
-Mesh.Points = 0;
-Mesh.PointNumbers = 0;
-Mesh.PointSize = 4;
-Mesh.PointType = 0;
-Mesh.Prisms = 1;
-Mesh.Pyramids = 1;
-Mesh.Trihedra = 1;
-Mesh.Quadrangles = 1;
-Mesh.QualityInf = 0;
-Mesh.QualitySup = 0;
-Mesh.QualityType = 2;
-Mesh.RadiusInf = 0;
-Mesh.RadiusSup = 0;
-Mesh.RandomFactor = 1e-09;
-Mesh.RandomFactor3D = 1e-12;
-Mesh.RandomSeed = 1;
-Mesh.PreserveNumberingMsh2 = 0;
-Mesh.IgnorePeriodicity = 0;
-Mesh.RecombinationAlgorithm = 1;
-Mesh.RecombineAll = 0;
-Mesh.RecombineOptimizeTopology = 5;
-Mesh.Recombine3DAll = 0;
-Mesh.Recombine3DLevel = 0;
-Mesh.Recombine3DConformity = 0;
-Mesh.RefineSteps = 10;
-Mesh.Renumber = 1;
-Mesh.SaveAll = 0;
-Mesh.SaveElementTagType = 1;
-Mesh.SaveTopology = 0;
-Mesh.SaveParametric = 0;
-Mesh.SaveGroupsOfNodes = 0;
-Mesh.ScalingFactor = 1;
-Mesh.SecondOrderExperimental = 0;
-Mesh.SecondOrderIncomplete = 0;
-Mesh.SecondOrderLinear = 0;
-Mesh.Smoothing = 1;
-Mesh.SmoothCrossField = 0;
-Mesh.CrossFieldClosestPoint = 1;
-Mesh.SmoothNormals = 0;
-Mesh.SmoothRatio = 1.8;
-Mesh.StlOneSolidPerSurface = 0;
-Mesh.StlRemoveDuplicateTriangles = 0;
-Mesh.SubdivisionAlgorithm = 0;
-Mesh.SurfaceEdges = 0;
-Mesh.SurfaceFaces = 0;
-Mesh.SurfaceNumbers = 0;
-Mesh.SwitchElementTags = 0;
-Mesh.Tangents = 0;
-Mesh.Tetrahedra = 1;
-Mesh.ToleranceEdgeLength = 0;
-Mesh.ToleranceInitialDelaunay = 1e-08;
-Mesh.Triangles = 1;
-Mesh.UnvStrictFormat = 1;
-Mesh.VolumeEdges = 1;
-Mesh.VolumeFaces = 0;
-Mesh.VolumeNumbers = 0;
-Mesh.Voronoi = 0;
-Mesh.ZoneDefinition = 0;
-Mesh.Color.Points = {0,0,255};
-Mesh.Color.PointsSup = {255,0,255};
-Mesh.Color.Lines = {0,0,0};
-Mesh.Color.Triangles = {160,150,255};
-Mesh.Color.Quadrangles = {130,120,225};
-Mesh.Color.Tetrahedra = {160,150,255};
-Mesh.Color.Hexahedra = {130,120,225};
-Mesh.Color.Prisms = {232,210,23};
-Mesh.Color.Pyramids = {217,113,38};
-Mesh.Color.Trihedra = {20,255,0};
-Mesh.Color.Tangents = {255,255,0};
-Mesh.Color.Normals = {255,0,0};
-Mesh.Color.Zero = {255,120,0};
-Mesh.Color.One = {0,255,132};
-Mesh.Color.Two = {255,160,0};
-Mesh.Color.Three = {0,255,192};
-Mesh.Color.Four = {255,200,0};
-Mesh.Color.Five = {0,216,255};
-Mesh.Color.Six = {255,240,0};
-Mesh.Color.Seven = {0,176,255};
-Mesh.Color.Eight = {228,255,0};
-Mesh.Color.Nine = {0,116,255};
-Mesh.Color.Ten = {188,255,0};
-Mesh.Color.Eleven = {0,76,255};
-Mesh.Color.Twelve = {148,255,0};
-Mesh.Color.Thirteen = {24,0,255};
-Mesh.Color.Fourteen = {108,255,0};
-Mesh.Color.Fifteen = {84,0,255};
-Mesh.Color.Sixteen = {68,255,0};
-Mesh.Color.Seventeen = {104,0,255};
-Mesh.Color.Eighteen = {0,255,52};
-Mesh.Color.Nineteen = {184,0,255};
-Solver.Executable0 = "";
-Solver.Executable1 = "";
-Solver.Executable2 = "";
-Solver.Executable3 = "";
-Solver.Executable4 = "";
-Solver.Executable5 = "";
-Solver.Executable6 = "";
-Solver.Executable7 = "";
-Solver.Executable8 = "";
-Solver.Executable9 = "";
-Solver.Name0 = "GetDP";
-Solver.Name1 = "";
-Solver.Name2 = "";
-Solver.Name3 = "";
-Solver.Name4 = "";
-Solver.Name5 = "";
-Solver.Name6 = "";
-Solver.Name7 = "";
-Solver.Name8 = "";
-Solver.Name9 = "";
-Solver.Extension0 = ".pro";
-Solver.Extension1 = "";
-Solver.Extension2 = "";
-Solver.Extension3 = "";
-Solver.Extension4 = "";
-Solver.Extension5 = "";
-Solver.Extension6 = "";
-Solver.Extension7 = "";
-Solver.Extension8 = "";
-Solver.Extension9 = "";
-Solver.OctaveInterpreter = "octave";
-Solver.PythonInterpreter = "python";
-Solver.RemoteLogin0 = "";
-Solver.RemoteLogin1 = "";
-Solver.RemoteLogin2 = "";
-Solver.RemoteLogin3 = "";
-Solver.RemoteLogin4 = "";
-Solver.RemoteLogin5 = "";
-Solver.RemoteLogin6 = "";
-Solver.RemoteLogin7 = "";
-Solver.RemoteLogin8 = "";
-Solver.RemoteLogin9 = "";
-Solver.SocketName = ".gmshsock";
-Solver.AlwaysListen = 0;
-Solver.AutoArchiveOutputFiles = 0;
-Solver.AutoCheck = 1;
-Solver.AutoLoadDatabase = 0;
-Solver.AutoSaveDatabase = 1;
-Solver.AutoMesh = 2;
-Solver.AutoMergeFile = 1;
-Solver.AutoShowViews = 2;
-Solver.AutoShowLastStep = 1;
-Solver.Plugins = 0;
-Solver.ShowInvisibleParameters = 0;
-Solver.Timeout = 5;
-PostProcessing.DoubleClickedGraphPointCommand = "";
-PostProcessing.GraphPointCommand = "";
-PostProcessing.AnimationDelay = 0.1;
-PostProcessing.AnimationCycle = 0;
-PostProcessing.AnimationStep = 1;
-PostProcessing.CombineRemoveOriginal = 1;
-PostProcessing.DoubleClickedGraphPointX = 0;
-PostProcessing.DoubleClickedGraphPointY = 0;
-PostProcessing.DoubleClickedView = 0;
-PostProcessing.ForceElementData = 0;
-PostProcessing.ForceNodeData = 0;
-PostProcessing.Format = 10;
-PostProcessing.GraphPointX = 0;
-PostProcessing.GraphPointY = 0;
-PostProcessing.HorizontalScales = 1;
-PostProcessing.Link = 0;
-PostProcessing.NbViews = 0;
-PostProcessing.Plugins = 1;
-PostProcessing.SaveInterpolationMatrices = 1;
-PostProcessing.SaveMesh = 1;
-PostProcessing.Smoothing = 0;
-Print.ParameterCommand = "Mesh.Clip=1; View.Clip=1; General.ClipWholeElements=1; General.Clip0D=Print.Parameter; SetChanged;";
-Print.Parameter = 0;
-Print.ParameterFirst = -1;
-Print.ParameterLast = 1;
-Print.ParameterSteps = 10;
-Print.Background = 0;
-Print.CompositeWindows = 0;
-Print.PgfTwoDim = 1;
-Print.PgfExportAxis = 0;
-Print.PgfHorizontalBar = 0;
-Print.DeleteTemporaryFiles = 1;
-Print.EpsBestRoot = 1;
-Print.EpsCompress = 0;
-Print.EpsLineWidthFactor = 1;
-Print.EpsOcclusionCulling = 1;
-Print.EpsPointSizeFactor = 1;
-Print.EpsPS3Shading = 0;
-Print.EpsQuality = 1;
-Print.Format = 10;
-Print.GeoLabels = 1;
-Print.GeoOnlyPhysicals = 0;
-Print.GifDither = 0;
-Print.GifInterlace = 0;
-Print.GifSort = 1;
-Print.GifTransparent = 0;
-Print.Height = -1;
-Print.JpegQuality = 100;
-Print.JpegSmoothing = 0;
-Print.PostElementary = 1;
-Print.PostElement = 0;
-Print.PostGamma = 0;
-Print.PostEta = 0;
-Print.PostSICN = 0;
-Print.PostSIGE = 0;
-Print.PostDisto = 0;
-Print.TexAsEquation = 0;
-Print.Text = 1;
-Print.X3dCompatibility = 0;
-Print.X3dPrecision = 1e-09;
-Print.X3dRemoveInnerBorders = 0;
-Print.X3dTransparency = 0;
-Print.Width = -1;

runs/cylFlow/meshColl.geo

@@ -0,0 +1,73 @@
+cl__1 = 1;
+cyl_h = 0.005;
+cyl_l = 0.02;
+cyl_s = 0.03;
+cyl_e = cyl_s + cyl_l;
+dom_h = 0.03;
+dom_l = 0.07;
+
+Lcell = 0.001;
+
+Point(1)  = {0,     0,     0, cl__1};
+Point(2)  = {cyl_s, 0,     0, cl__1};
+Point(3)  = {cyl_s, cyl_h, 0, cl__1};
+Point(4)  = {cyl_e, cyl_h, 0, cl__1};
+Point(5)  = {cyl_e, 0,     0, cl__1};
+Point(6)  = {dom_l, 0,     0, cl__1};
+Point(7)  = {dom_l, cyl_h, 0, cl__1};
+Point(8)  = {dom_l, dom_h, 0, cl__1};
+Point(9)  = {cyl_e, dom_h, 0, cl__1};
+Point(10) = {cyl_s, dom_h, 0, cl__1};
+Point(11) = {0,     dom_h, 0, cl__1};
+Point(12) = {0,     cyl_h, 0, cl__1};
+
+Line(1)  = {1,  2};
+Line(2)  = {2,  3};
+Line(3)  = {3,  4};
+Line(4)  = {4,  5};
+Line(5)  = {5,  6};
+Line(6)  = {6,  7};
+Line(7)  = {7,  8};
+Line(8)  = {8,  9};
+Line(9)  = {9,  10};
+Line(10) = {10, 11};
+Line(11) = {11, 12};
+Line(12) = {12, 1};
+Line(13) = {12, 3};
+Line(14) = {4,  7};
+Line(15) = {4,  9};
+Line(16) = {10, 3};
+
+Line Loop(1) = {1, 2, -13, 12};
+Plane Surface(1) = {1};
+Line Loop(2) = {13, -16, 10, 11};
+Plane Surface(2) = {2};
+Line Loop(3) = {3, 15, 9, 16};
+Plane Surface(3) = {3};
+Line Loop(4) = {5, 6, -14, 4};
+Plane Surface(4) = {4};
+Line Loop(5) = {14, 7, 8, -15};
+Plane Surface(5) = {5};
+
+Physical Surface(1) = {1};
+Physical Surface(2) = {2};
+Physical Surface(3) = {3};
+Physical Surface(4) = {4};
+Physical Surface(5) = {5};
+
+Transfinite Line {12, 2, 4, 6} = cyl_h/Lcell + 1 Using Progression 1;
+Transfinite Line {1, 13, 10} = cyl_s/Lcell + 1 Using Progression 1;
+Transfinite Line {11, 16, 15, 7} = (dom_h - cyl_h)/Lcell + 1 Using Progression 1;
+Transfinite Line {3, 9} = cyl_l/Lcell + 1 Using Progression 1;
+Transfinite Line {5, 14, 8} = (dom_l - cyl_e)/Lcell + 1 Using Progression 1;
+
+Transfinite Surface{1};
+Recombine Surface {1};
+Transfinite Surface{2};
+Recombine Surface {2};
+Transfinite Surface{3};
+Recombine Surface {3};
+Transfinite Surface{4};
+Recombine Surface {4};
+Transfinite Surface{5};
+Recombine Surface {5};

runs/cylFlow/meshSingle.geo

@@ -0,0 +1,79 @@
+cl__1 = 1;
+cyl_h = 0.005;
+cyl_l = 0.02;
+cyl_s = 0.03;
+cyl_e = cyl_s + cyl_l;
+dom_h = 0.03;
+dom_l = 0.07;
+
+Lcell = 0.001;
+
+Point(1)  = {0,     0,     0, cl__1};
+Point(2)  = {cyl_s, 0,     0, cl__1};
+Point(3)  = {cyl_s, cyl_h, 0, cl__1};
+Point(4)  = {cyl_e, cyl_h, 0, cl__1};
+Point(5)  = {cyl_e, 0,     0, cl__1};
+Point(6)  = {dom_l, 0,     0, cl__1};
+Point(7)  = {dom_l, cyl_h, 0, cl__1};
+Point(8)  = {dom_l, dom_h, 0, cl__1};
+Point(9)  = {cyl_e, dom_h, 0, cl__1};
+Point(10) = {cyl_s, dom_h, 0, cl__1};
+Point(11) = {0,     dom_h, 0, cl__1};
+Point(12) = {0,     cyl_h, 0, cl__1};
+
+Line(1)  = {1,  2};
+Line(2)  = {2,  3};
+Line(3)  = {3,  4};
+Line(4)  = {4,  5};
+Line(5)  = {5,  6};
+Line(6)  = {6,  7};
+Line(7)  = {7,  8};
+Line(8)  = {8,  9};
+Line(9)  = {9,  10};
+Line(10) = {10, 11};
+Line(11) = {11, 12};
+Line(12) = {12, 1};
+Line(13) = {12, 3};
+Line(14) = {4,  7};
+Line(15) = {4,  9};
+Line(16) = {10, 3};
+
+Line Loop(1) = {1, 2, -13, 12};
+Plane Surface(1) = {1};
+Line Loop(2) = {13, -16, 10, 11};
+Plane Surface(2) = {2};
+Line Loop(3) = {3, 15, 9, 16};
+Plane Surface(3) = {3};
+Line Loop(4) = {5, 6, -14, 4};
+Plane Surface(4) = {4};
+Line Loop(5) = {14, 7, 8, -15};
+Plane Surface(5) = {5};
+
+Physical Line(1) = {12, 11};
+Physical Line(2) = {10, 9, 8};
+Physical Line(3) = {7, 6};
+Physical Line(4) = {2, 3, 4};
+Physical Line(5) = {1, 5};
+
+Physical Surface(1) = {1};
+Physical Surface(2) = {2};
+Physical Surface(3) = {3};
+Physical Surface(4) = {4};
+Physical Surface(5) = {5};
+
+Transfinite Line {12, 2, 4, 6} = cyl_h/Lcell + 1 Using Progression 1;
+Transfinite Line {1, 13, 10} = cyl_s/Lcell + 1 Using Progression 1;
+Transfinite Line {11, 16, 15, 7} = (dom_h - cyl_h)/Lcell + 1 Using Progression 1;
+Transfinite Line {3, 9} = cyl_l/Lcell + 1 Using Progression 1;
+Transfinite Line {5, 14, 8} = (dom_l - cyl_e)/Lcell + 1 Using Progression 1;
+
+Transfinite Surface{1};
+Recombine Surface {1};
+Transfinite Surface{2};
+Recombine Surface {2};
+Transfinite Surface{3};
+Recombine Surface {3};
+Transfinite Surface{4};
+Recombine Surface {4};
+Transfinite Surface{5};
+Recombine Surface {5};

src/fpakc.f90

@@ -1,20 +1,22 @@
 !  FPAKC main program
 PROGRAM fpakc
-  USE moduleInput
-  USE moduleErrors
-  USE moduleInject
-  USE moduleSolver
   USE moduleCompTime
   USE moduleCaseParam
+  USE moduleInput
+  USE moduleInject
+  USE moduleSolver
+  USE moduleMesh
+  USE moduleProbe
+  USE moduleErrors
   USE OMP_LIB
   IMPLICIT NONE
 
-  ! t = time step
-  INTEGER:: t = 0
   ! arg1 = Input argument 1 (input file)
   CHARACTER(200):: arg1
   ! inputFile = path+name of input file
   CHARACTER(:), ALLOCATABLE:: inputFile
+  ! generic integer for time step
+  INTEGER:: t
 
   tStep = omp_get_wtime()
   !Gets the input file
@@ -26,8 +28,17 @@ PROGRAM fpakc
   !Reads the json configuration file
   CALL readConfig(inputFile)
 
+  !Create output folder and initial files
+  CALL initOutput(inputFile)
+
+  !Do '0' iteration
+  timeStep = tInitial
+
   !$OMP PARALLEL DEFAULT(SHARED)
   !$OMP SINGLE
+  ! Initial reset of probes
+  CALL resetProbes()
+
   CALL verboseError("Initial scatter of particles...")
   !$OMP END SINGLE
   CALL doScatter()
@@ -41,16 +52,21 @@ PROGRAM fpakc
   tStep = omp_get_wtime() - tStep
 
   !Output initial state
-  CALL doOutput(t)
+  CALL doOutput()
   CALL verboseError('Starting main loop...')
   !$OMP PARALLEL DEFAULT(SHARED) 
-  DO t = 1, tmax
+  DO t = tInitial + 1, tFinal
-    !Insert new particles and push them
     !$OMP SINGLE
     tStep = omp_get_wtime()
 
+    ! Update global time step index
+    timeStep = t
+
     !Checks if a species needs to me moved in this iteration
-    CALL solver%updatePushSpecies(t)
+    CALL solver%updatePushSpecies()
+
+    !Checks if probes need to be calculated this iteration
+    CALL resetProbes()
     tPush = omp_get_wtime()
     !$OMP END SINGLE
 
@@ -67,11 +83,26 @@ PROGRAM fpakc
     tColl = omp_get_wtime()
     !$OMP END SINGLE
 
-    CALL doCollisions()
+    IF (doMCCollisions) THEN
+      CALL meshForMCC%doCollisions()
+
+    END IF
 
     !$OMP SINGLE
     tColl = omp_get_wtime() - tColl
     
+    !Coulomb scattering
+    tCoul = omp_get_wTime()
+    !$OMP END SINGLE
+
+    IF (doCoulombScattering) THEN
+      CALL mesh%doCoulomb()
+
+    END IF
+
+    !$OMP SINGLE
+    tCoul = omp_get_wTime() - tCoul
+
     !Reset particles
     tReset = omp_get_wtime()
     !$OMP END SINGLE
@@ -98,10 +129,12 @@ PROGRAM fpakc
     !$OMP SINGLE
     tEMField = omp_get_wtime() - tEMField
 
+    CALL doAverage()
+
     tStep = omp_get_wtime() - tStep
 
     !Output data
-    CALL doOutput(t)
+    CALL doOutput()
     !$OMP END SINGLE
 
   END DO

src/makefile

@@ -1,18 +1,30 @@
-OBJECTS = $(OBJDIR)/moduleMesh.o $(OBJDIR)/moduleCompTime.o $(OBJDIR)/moduleSolver.o \
+OBJECTS = $(OBJDIR)/moduleMesh.o $(OBJDIR)/moduleMeshBoundary.o $(OBJDIR)/moduleCompTime.o \
 			  	$(OBJDIR)/moduleSpecies.o $(OBJDIR)/moduleInject.o $(OBJDIR)/moduleInput.o \
 			  	$(OBJDIR)/moduleErrors.o $(OBJDIR)/moduleList.o $(OBJDIR)/moduleOutput.o \
 			  	$(OBJDIR)/moduleBoundary.o $(OBJDIR)/moduleCaseParam.o $(OBJDIR)/moduleRefParam.o \
 			  	$(OBJDIR)/moduleCollisions.o $(OBJDIR)/moduleTable.o $(OBJDIR)/moduleParallel.o \
-			  	$(OBJDIR)/moduleEM.o $(OBJDIR)/moduleRandom.o \
+			  	$(OBJDIR)/moduleEM.o $(OBJDIR)/moduleRandom.o $(OBJDIR)/moduleMath.o \
-			  	$(OBJDIR)/moduleMeshCyl.o	$(OBJDIR)/moduleMeshCylRead.o	$(OBJDIR)/moduleMeshCylBoundary.o \
+					$(OBJDIR)/moduleProbe.o $(OBJDIR)/moduleAverage.o $(OBJDIR)/moduleCoulomb.o \
-          $(OBJDIR)/moduleMesh1DCart.o $(OBJDIR)/moduleMesh1DCartRead.o $(OBJDIR)/moduleMesh1DCartBoundary.o \
+					$(OBJDIR)/moduleMeshInoutCommon.o \
-          $(OBJDIR)/moduleMesh1DRad.o  $(OBJDIR)/moduleMesh1DRadRead.o  $(OBJDIR)/moduleMesh1DRadBoundary.o
+			  	$(OBJDIR)/moduleMeshInputVTU.o $(OBJDIR)/moduleMeshOutputVTU.o \
+			  	$(OBJDIR)/moduleMeshInputGmsh2.o $(OBJDIR)/moduleMeshOutputGmsh2.o \
+			  	$(OBJDIR)/moduleMeshInput0D.o $(OBJDIR)/moduleMeshOutput0D.o \
+				$(OBJDIR)/moduleMeshInputText.o $(OBJDIR)/moduleMeshOutputText.o \
+			  	$(OBJDIR)/moduleMesh3DCart.o \
+			  	$(OBJDIR)/moduleMesh2DCyl.o  \
+			  	$(OBJDIR)/moduleMesh2DCart.o \
+          $(OBJDIR)/moduleMesh1DRad.o  \
+          $(OBJDIR)/moduleMesh1DCart.o \
+          $(OBJDIR)/moduleMesh0D.o     \
+          $(OBJDIR)/moduleSolver.o     \
+					$(OBJDIR)/modulePusher.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 $(JSONLIB) -L/usr/local/lib -llapack -lopenblas
+	$(FC) $(FCFLAGS) -o $(TOPDIR)/$(OUTPUT) $(OBJECTS) $(OBJDIR)/$(OUTPUT).o $(JSONLIB) -L/usr/local/lib -lopenblas
 
 modules.o:
 	$(MAKE) -C modules all

src/modules/common/makefile

@@ -0,0 +1,11 @@
+OBJS = moduleCompTime.o moduleCaseParam.o moduleConstParam.o \
+			 moduleErrors.o moduleMath.o moduleParallel.o \
+			 moduleRandom.o moduleRefParam.o moduleTable.o
+
+all: $(OBJS)
+
+moduleTable.o: moduleErrors.o moduleTable.f90
+	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
+
+%.o: %.f90
+	$(FC) $(FCFLAGS) -c $< -o $(OBJDIR)/$@

src/modules/common/moduleCaseParam.f90

@@ -0,0 +1,15 @@
+!Problems of the case
+MODULE moduleCaseParam
+  !Final and initial iterations
+  INTEGER:: tFinal, tInitial = 0
+  ! Global index of current iteration
+  INTEGER:: timeStep
+  ! Time step for all species
+  REAL(8), ALLOCATABLE:: tau(:)
+  ! Minimum time step
+  REAL(8):: tauMin
+  ! Time step for Monte-Carlo Collisions
+  REAL(8):: tauColl
+
+END MODULE moduleCaseParam
+

src/modules/common/moduleCompTime.f90

@@ -0,0 +1,16 @@
+!Information to calculate computation time
+MODULE moduleCompTime
+  IMPLICIT NONE
+
+  PUBLIC
+
+  REAL(8):: tStep    = 0.D0
+  REAL(8):: tPush    = 0.D0
+  REAL(8):: tReset   = 0.D0
+  REAL(8):: tColl    = 0.D0
+  REAL(8):: tCoul    = 0.D0
+  REAL(8):: tWeight  = 0.D0
+  REAL(8):: tEMField = 0.D0
+
+END MODULE moduleCompTime
+

src/modules/common/moduleConstParam.f90

@@ -6,7 +6,8 @@ MODULE moduleConstParam
 
   REAL(8), PARAMETER:: PI  = 4.D0*DATAN(1.D0) !number pi
   REAL(8), PARAMETER:: PI2 = 2.D0*PI !2*pi
-  REAL(8), PARAMETER:: PI8 = 8.D0*PI !2*pi
+  REAL(8), PARAMETER:: PI4 = 4.D0*PI !4*pi
+  REAL(8), PARAMETER:: PI8 = 8.D0*PI !8*pi
   REAL(8), PARAMETER:: sccm2atomPerS = 4.5D17 !sccm to atom s^-1
   REAL(8), PARAMETER:: qe = 1.60217662D-19 !Elementary charge
   REAL(8), PARAMETER:: kb = 1.38064852D-23 !Boltzmann constants SI

src/modules/common/moduleMath.f90

@@ -0,0 +1,73 @@
+MODULE moduleMath
+  IMPLICIT NONE
+
+  CONTAINS
+    !Outer product of two tensors
+    PURE FUNCTION outerProduct(a,b) RESULT(s)
+      IMPLICIT NONE
+
+      REAL(8), DIMENSION(1:3), INTENT(in):: a, b
+      REAL(8):: s(1:3,1:3)
+
+      s = SPREAD(a, dim = 2, ncopies = 3)*SPREAD(b, dim = 1, ncopies = 3)
+
+    END FUNCTION outerProduct
+
+    !Cross product of two 3D vectors
+    PURE FUNCTION crossProduct(a, b) RESULT(c)
+      IMPLICIT NONE
+
+      REAL(8), DIMENSION(1:3), INTENT(in):: a, b
+      REAL(8), DIMENSION(1:3):: c
+
+      c = 0.D0
+
+      c(1) =   a(2)*b(3) - a(3)*b(2)
+      c(2) = -(a(1)*b(3) - a(3)*b(1))
+      c(3) =   a(1)*b(2) - a(2)*b(1)
+
+    END FUNCTION crossProduct
+
+    !Normalizes a 3D vector
+    PURE FUNCTION normalize(a) RESULT(b)
+      IMPLICIT NONE
+
+      REAL(8), DIMENSION(1:3), INTENT(in):: a
+      REAL(8), DIMENSION(1:3):: b
+      
+      b = a / NORM2(a)
+
+    END FUNCTION normalize
+
+    !Norm 1 of vector
+    PURE FUNCTION norm1(a) RESULT(b)
+      IMPLICIT NONE
+      REAL(8), DIMENSION(:), INTENT(in):: a
+      REAL(8):: b
+
+      b = SUM(DABS(a))
+
+    END FUNCTION norm1
+
+    PURE FUNCTION reducedMass(m_i, m_j) RESULT(rMass)
+      IMPLICIT NONE
+
+      REAL(8), INTENT(in):: m_i, m_j
+      REAL(8):: rMass
+
+      rMass = (m_i * m_j) / (m_i + m_j)
+
+    END FUNCTION
+
+    FUNCTION tensorTrace(a) RESULT(t)
+      IMPLICIT NONE
+
+      REAL(8), DIMENSION(1:3,1:3):: a
+      REAL(8):: t
+
+      t = 0.D0
+      t = a(1,1)+a(2,2)+a(3,3)
+
+    END FUNCTION tensorTrace
+
+END MODULE moduleMath

src/modules/common/moduleRandom.f90

@@ -40,30 +40,72 @@ MODULE moduleRandom
       INTEGER:: rnd
       REAL(8):: rnd01
 
-      rnd = 0.D0
+      rnd = 0
       CALL RANDOM_NUMBER(rnd01)
 
-      rnd = INT(REAL(b - a) * rnd01) + 1
+      rnd = a + FLOOR((b+1-a)*rnd01)
 
     END FUNCTION randomIntAB
 
+    !Returns a random number in a Maxwellian distribution of mean 0 and width 1 with the Box-Muller Method
+    function randomMaxwellian() result(rnd)
+      USE moduleConstParam, only: pi
+      implicit none
+
+      real(8):: rnd
+      real(8):: v1, v2, Rsquare
+
+      v1 = 0.d0
+      do while (v1 <= 0.d0)
+        v1 = random()
+
+      end do
+      v2 = random()
+
+      rnd = sqrt(-2.d0*log(v1))*cos(2*pi*v2)
+
+    end function randomMaxwellian
+
     !Returns a random number in a Maxwellian distribution of mean 0 and width 1
-    FUNCTION randomMaxwellian() RESULT(rnd)
+    FUNCTION randomHalfMaxwellian() RESULT(rnd)
-      USE moduleConstParam, ONLY: PI
       IMPLICIT NONE
 
       REAL(8):: rnd
-      REAL(8):: x, y
+      REAL(8):: x
 
       rnd = 0.D0
       x = 0.D0
       DO WHILE (x == 0.D0)
         CALL RANDOM_NUMBER(x)
       END DO
-      CALL RANDOM_NUMBER(y)
 
-      rnd = DSQRT(-2.D0*DLOG(x))*DCOS(2.D0*PI*y)
+      rnd = DSQRT(-DLOG(x))
 
-    END FUNCTION randomMaxwellian
+    END FUNCTION randomHalfMaxwellian
+
+    !Returns a random number weighted with the cumWeight array
+    FUNCTION randomWeighted(cumWeight, sumWeight) RESULT(rnd)
+      IMPLICIT NONE
+
+      REAL(8), INTENT(in):: cumWeight(1:)
+      REAL(8), INTENT(in):: sumWeight
+      REAL(8):: rnd0b
+      INTEGER:: rnd, i
+
+      rnd0b = random()
+      i = 1
+      DO 
+        IF (rnd0b <= cumWeight(i)/sumWeight) THEN
+          rnd = i
+          EXIT
+
+        ELSE
+          i = i +1
+
+        END IF
+      END DO
+      ! rnd = MINLOC(DABS(rnd0b - cumWeight), 1)
+
+    END FUNCTION randomWeighted
 
 END MODULE moduleRandom

src/modules/common/moduleRefParam.f90

@@ -1,9 +1,9 @@
 !Reference parameters
 MODULE moduleRefParam
   !Parameters that define the problem (inputs)
-  REAL(8):: n_ref, m_ref, T_ref, r_ref, debye_ref, sigma_ref
+  REAL(8):: n_ref, m_ref, T_ref, r_ref, debye_ref, sigmaVrel_ref
   !Reference parameters for non-dimensional problem
-  REAL(8):: L_ref, v_ref, ti_ref, Vol_ref, EF_ref, Volt_ref
+  REAL(8):: L_ref, v_ref, ti_ref, Vol_ref, EF_ref, Volt_ref, B_ref
 
 END MODULE moduleRefParam
 

src/modules/common/moduleTable.f90

@@ -93,7 +93,7 @@ MODULE moduleTable
         f = self%fMax
 
       ELSE
-        i = MINLOC(x - self%x, 1)
+        i = MINLOC(ABS(x - self%x), 1)
         deltaX = x - self%x(i)
         IF (deltaX < 0 ) THEN 
           i = i - 1

src/modules/init/makefile

@@ -0,0 +1,5 @@
+all: moduleInput.o
+
+%.o: %.f90
+	$(FC) $(FCFLAGS) -c $< -o $(OBJDIR)/$@
+

src/modules/makefile

@@ -1,46 +1,43 @@
+OBJS = common.o output.o mesh.o solver.o init.o \
+			 moduleBoundary.o moduleCollisions.o moduleInject.o \
+			 moduleList.o moduleProbe.o moduleCoulomb.o \
+			 moduleSpecies.o
 
-OBJS = moduleCaseParam.o moduleCompTime.o moduleList.o \
+all: $(OBJS)
-		   moduleOutput.o moduleInput.o moduleSolver.o \
-			 moduleCollisions.o moduleTable.o moduleParallel.o \
-			 moduleEM.o moduleRandom.o
 
-all: $(OBJS) mesh.o
+common.o:
+	$(MAKE) -C common all
 
-mesh.o: moduleCollisions.o moduleBoundary.o
+output.o: moduleSpecies.o common.o
+	$(MAKE) -C output all
+
+mesh.o: moduleCollisions.o moduleCoulomb.o moduleBoundary.o output.o common.o 
 	$(MAKE) -C mesh all
 
-moduleCollisions.o: moduleRandom.o moduleTable.o moduleSpecies.o moduleRefParam.o moduleConstParam.o moduleCollisions.f90
+solver.o: moduleSpecies.o moduleProbe.o common.o output.o mesh.o
+	$(MAKE) -C solver all
+
+init.o: common.o solver.o moduleInject.o
+	$(MAKE) -C init all
+
+moduleBoundary.o: common.o moduleBoundary.f90
 	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
 
-moduleInput.o: moduleParallel.o moduleRefParam.o moduleCaseParam.o moduleSolver.o moduleInject.o moduleBoundary.o moduleErrors.o moduleSpecies.o moduleInput.f90
+moduleCollisions.o: moduleList.o moduleSpecies.o common.o moduleCollisions.f90
 	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
 
-moduleInject.o: moduleRandom.o moduleSpecies.o moduleSolver.o moduleInject.f90
+moduleCoulomb.o: moduleSpecies.o common.o moduleCoulomb.f90
 	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
 
-moduleList.o: moduleSpecies.o moduleErrors.o moduleList.f90
+moduleList.o: common.o moduleSpecies.o moduleList.f90
 	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
 
-moduleOutput.o: moduleSpecies.o moduleRefParam.o moduleOutput.f90
+moduleProbe.o: mesh.o moduleProbe.f90
 	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
 
-moduleRandom.o: moduleConstParam.o moduleRandom.f90
+moduleSpecies.o: common.o moduleSpecies.f90
-	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
-
-moduleRefParam.o: moduleConstParam.o moduleRefParam.f90
-	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
-
-moduleSpecies.o: moduleErrors.o moduleCaseParam.o moduleSpecies.f90
-	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
-
-moduleSolver.o: mesh.o moduleList.o moduleEM.o moduleSpecies.o moduleRefParam.o moduleOutput.o moduleSolver.f90
-	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
-
-moduleTable.o: moduleErrors.o moduleTable.f90
-	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
-
-moduleEM.o: mesh.o moduleSpecies.o moduleEM.f90
 	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
 
 %.o: %.f90
 	$(FC) $(FCFLAGS) -c $< -o $(OBJDIR)/$@
+

src/modules/mesh/0D/makefile

@@ -0,0 +1,5 @@
+all: moduleMesh0D.o
+
+moduleMesh0D.o: moduleMesh0D.f90
+	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
+

src/modules/mesh/0D/moduleMesh0D.f90

@@ -0,0 +1,257 @@
+!moduleMesh1D: 0D mesh. No coordinates are relevant. No edges are used
+MODULE moduleMesh0D
+  USE moduleMesh
+  IMPLICIT NONE
+
+  TYPE, PUBLIC, EXTENDS(meshNode):: meshNode0D
+    INTEGER:: n1
+    CONTAINS
+      !meshNode DEFERRED PROCEDURES
+      PROCEDURE, PASS:: init           => initNode0D
+      PROCEDURE, PASS:: getCoordinates => getCoord0D
+
+  END TYPE meshNode0D
+
+  TYPE, PUBLIC, EXTENDS(meshCell):: meshCell0D
+    CLASS(meshNode), POINTER:: n1
+    CONTAINS
+      PROCEDURE, PASS::   init                => initCell0D
+      PROCEDURE, PASS::   getNodes            => getNodes0D
+      PROCEDURE, PASS::   randPos             => randPos0D
+      PROCEDURE, NOPASS:: fPsi                => fPsi0D
+      PROCEDURE, NOPASS:: dPsi                => dPsi0D
+      PROCEDURE, PASS::   partialDer          => partialDer0D
+      PROCEDURE, NOPASS:: detJac              => detJ0D
+      PROCEDURE, NOPASS:: invJac              => invJ0D
+      PROCEDURE, PASS::   gatherElectricField => gatherEF0D
+      PROCEDURE, PASS::   gatherMagneticField => gatherMF0D
+      PROCEDURE, PASS::   elemK               => elemK0D
+      PROCEDURE, PASS::   elemF               => elemF0D
+      PROCEDURE, PASS::   phy2log             => phy2log0D
+      PROCEDURE, NOPASS:: inside              => inside0D
+      PROCEDURE, PASS::   neighbourElement    => neighbourElement0D
+
+  END TYPE meshCell0D
+
+  CONTAINS
+    !NODE FUNCTIONS
+    !Init node
+    SUBROUTINE initNode0D(self, n, r)
+      USE moduleSpecies
+      USE OMP_LIB
+      IMPLICIT NONE
+
+      CLASS(meshNode0D), INTENT(out):: self
+      INTEGER, INTENT(in):: n
+      REAL(8), INTENT(in):: r(1:3) !Unused variable
+
+      self%n = n
+
+      ALLOCATE(self%output(1:nSpecies))
+
+      CALL OMP_INIT_LOCK(self%lock)
+
+    END SUBROUTINE initNode0D
+
+    !Get node coordinates
+    PURE FUNCTION getCoord0D(self) RESULT(r)
+      IMPLICIT NONE
+
+      CLASS(meshNode0D), INTENT(in):: self
+      REAL(8):: r(1:3)
+
+      r = 0.D0
+
+    END FUNCTION
+
+    !VOLUME FUNCTIONS
+    !Inits dummy 0D volume
+    SUBROUTINE initCell0D(self, n, p, nodes)
+      USE moduleRefParam
+      USE moduleSpecies
+      IMPLICIT NONE
+
+      CLASS(meshCell0D), INTENT(out):: self
+      INTEGER, INTENT(in):: n
+      INTEGER, INTENT(in):: p(:)
+      TYPE(meshNodeCont), INTENT(in), TARGET:: nodes(:)
+
+      self%n = n
+
+      self%nNodes = SIZE(p)
+
+      self%n1 => nodes(p(1))%obj
+      self%volume = 1.D0
+      self%n1%v = 1.D0
+
+      CALL OMP_INIT_LOCK(self%lock)
+
+      ALLOCATE(self%listPart_in(1:nSpecies))
+      ALLOCATE(self%totalWeight(1:nSpecies))
+
+    END SUBROUTINE initCell0D
+
+    !Get the nodes of the volume
+    PURE FUNCTION getNodes0D(self, nNodes) RESULT(n)
+      IMPLICIT NONE
+
+      CLASS(meshCell0D), INTENT(in):: self
+      INTEGER, INTENT(in):: nNodes
+      INTEGER:: n(1:nNodes)
+
+      n = self%n1%n
+
+    END FUNCTION getNodes0D
+
+    !Calculate random position inside the volume
+    FUNCTION randPos0D(self) RESULT(r)
+      IMPLICIT NONE
+
+      CLASS(meshCell0D), INTENT(in):: self
+      REAL(8):: r(1:3)
+
+      r = 0.D0
+
+    END FUNCTION randPos0D
+
+    PURE FUNCTION fPsi0D(Xi, nNodes) RESULT(fPsi)
+      IMPLICIT NONE
+
+      REAL(8), INTENT(in):: Xi(1:3)
+      INTEGER, INTENT(in):: nNodes
+      REAL(8):: fPsi(1:nNodes)
+
+      fPsi = 1.D0
+
+    END FUNCTION fPsi0D
+
+    PURE FUNCTION dPsi0D(Xi, nNodes) RESULT(dPsi)
+      IMPLICIT NONE
+
+      REAL(8), INTENT(in):: Xi(1:3)
+      INTEGER, INTENT(in):: nNodes
+      REAL(8):: dPsi(1:3,1:nNodes)
+
+      dPsi = 0.D0
+
+    END FUNCTION dPsi0D
+
+    PURE FUNCTION partialDer0D(self, nNodes, dPsi) RESULT(pDer)
+      IMPLICIT NONE
+
+      CLASS(meshCell0D), INTENT(in):: self
+      INTEGER, INTENT(in):: nNodes
+      REAL(8), INTENT(in):: dPsi(1:3,1:nNodes)
+      REAL(8):: pDer(1:3, 1:3)
+
+      pDer = 0.D0
+
+    END FUNCTION partialDer0D
+
+    PURE FUNCTION elemK0D(self, nNodes) RESULT(localK)
+      IMPLICIT NONE
+
+      CLASS(meshCell0D), INTENT(in):: self
+      INTEGER, INTENT(in):: nNodes
+      REAL(8):: localK(1:nNodes,1:nNodes)
+
+      localK = 0.D0
+
+    END FUNCTION elemK0D
+
+    PURE FUNCTION elemF0D(self, nNodes, source) RESULT(localF)
+      IMPLICIT NONE
+
+      CLASS(meshCell0D), INTENT(in):: self
+      INTEGER, INTENT(in):: nNodes
+      REAL(8), INTENT(in):: source(1:nNodes)
+      REAL(8):: localF(1:nNodes)
+
+      localF = 0.D0
+
+    END FUNCTION elemF0D
+
+    PURE FUNCTION gatherEF0D(self, Xi) RESULT(array)
+      IMPLICIT NONE
+      CLASS(meshCell0D), INTENT(in):: self
+      REAL(8), INTENT(in):: Xi(1:3)
+      REAL(8):: array(1:3)
+      REAL(8):: phi(1:1)
+
+      phi = (/ self%n1%emData%phi /)
+
+      array = -self%gatherDF(Xi, 1, phi)
+
+    END FUNCTION gatherEF0D
+
+    PURE FUNCTION gatherMF0D(self, Xi) RESULT(array)
+      IMPLICIT NONE
+      CLASS(meshCell0D), INTENT(in):: self
+      REAL(8), INTENT(in):: Xi(1:3)
+      REAL(8):: array(1:3)
+      REAL(8):: B(1:1,1:3)
+
+      B(:,1) = (/ self%n1%emData%B(1) /)
+
+      B(:,2) = (/ self%n1%emData%B(2) /)
+
+      B(:,3) = (/ self%n1%emData%B(3) /)
+
+      array = self%gatherF(Xi, 1, B)
+
+    END FUNCTION gatherMF0D
+
+    PURE FUNCTION phy2log0D(self,r) RESULT(xN) 
+      IMPLICIT NONE
+
+      CLASS(meshCell0D), INTENT(in):: self
+      REAL(8), INTENT(in):: r(1:3)
+      REAL(8):: xN(1:3)
+
+      xN = 0.D0
+
+    END FUNCTION phy2log0D
+
+    PURE FUNCTION inside0D(Xi) RESULT(ins)
+      IMPLICIT NONE
+
+      REAL(8), INTENT(in):: Xi(1:3)
+      LOGICAL:: ins
+
+      ins = .TRUE.
+
+    END FUNCTION inside0D
+
+    SUBROUTINE neighbourElement0D(self, Xi, neighbourElement)
+      IMPLICIT NONE
+
+      CLASS(meshCell0D), INTENT(in):: self
+      REAL(8), INTENT(in):: Xi(1:3)
+      CLASS(meshElement), POINTER, INTENT(out):: neighbourElement
+
+      neighbourElement => NULL()
+
+    END SUBROUTINE neighbourElement0D
+
+    !COMMON FUNCTIONS
+    PURE FUNCTION detJ0D(pDer) RESULT(dJ)
+      IMPLICIT NONE
+
+      REAL(8), INTENT(in):: pDer(1:3, 1:3)
+      REAL(8):: dJ
+
+      dJ = 0.D0
+
+    END FUNCTION detJ0D
+
+    PURE FUNCTION invJ0D(pDer) RESULT(invJ)
+      IMPLICIT NONE
+
+      REAL(8), INTENT(in):: pDer(1:3, 1:3)
+      REAL(8):: invJ(1:3,1:3)
+
+      invJ = 0.D0
+
+    END FUNCTION invJ0D
+
+END MODULE moduleMesh0D

src/modules/mesh/1DCart/makefile

@@ -1,11 +1,5 @@
-all: moduleMesh1DCart.o moduleMesh1DCartBoundary.o moduleMesh1DCartRead.o
+all: moduleMesh1DCart.o
 
 moduleMesh1DCart.o: moduleMesh1DCart.f90
 	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
 
-moduleMesh1DCartBoundary.o: moduleMesh1DCart.o moduleMesh1DCartBoundary.f90
-	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
-
-moduleMesh1DCartRead.o: moduleMesh1DCart.o moduleMesh1DCartBoundary.o moduleMesh1DCartRead.f90
-	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
-

src/modules/mesh/1DCart/moduleMesh1DCart.f90

@@ -4,12 +4,17 @@
 !              z == unused
 MODULE moduleMesh1DCart
   USE moduleMesh
+  USE moduleMeshBoundary
   IMPLICIT NONE
 
+  REAL(8), PARAMETER:: corSeg(1:3) = (/ -DSQRT(3.D0/5.D0), 0.D0,       DSQRT(3.D0/5.D0) /)
+  REAL(8), PARAMETER:: wSeg(1:3)   = (/        5.D0/9.D0 , 8.D0/9.D0,        5.D0/9.D0  /)
+
   TYPE, PUBLIC, EXTENDS(meshNode):: meshNode1DCart
     !Element coordinates
     REAL(8):: x = 0.D0
     CONTAINS
+      !meshNode DEFERRED PROCEDURES
       PROCEDURE, PASS:: init           => initNode1DCart
       PROCEDURE, PASS:: getCoordinates => getCoord1DCart
 
@@ -21,111 +26,42 @@ MODULE moduleMesh1DCart
     !Connectivity to nodes
     CLASS(meshNode), POINTER:: n1 => NULL()
     CONTAINS
+      !meshEdge DEFERRED PROCEDURES
       PROCEDURE, PASS:: init         => initEdge1DCart
       PROCEDURE, PASS:: getNodes     => getNodes1DCart
+      PROCEDURE, PASS:: intersection => intersection1DCart
       PROCEDURE, PASS:: randPos      => randPosEdge
 
   END TYPE meshEdge1DCart
 
-  !Boundary functions defined in the submodule Boundary
+  TYPE, PUBLIC, EXTENDS(meshCell):: meshCell1DCartSegm
-  INTERFACE
-    MODULE SUBROUTINE reflection(edge, part)
-      USE moduleSpecies
-      IMPLICIT NONE
-
-      CLASS(meshEdge), INTENT(inout):: edge
-      CLASS(particle), INTENT(inout):: part
-
-    END SUBROUTINE reflection
-
-    MODULE SUBROUTINE absorption(edge, part)
-      USE moduleSpecies
-      IMPLICIT NONE
-
-      CLASS(meshEdge), INTENT(inout):: edge
-      CLASS(particle), INTENT(inout):: part
-
-    END SUBROUTINE absorption
-
-    MODULE SUBROUTINE transparent(edge, part)
-      USE moduleSpecies
-      IMPLICIT NONE
-
-      CLASS(meshEdge), INTENT(inout):: edge
-      CLASS(particle), INTENT(inout):: part
-
-    END SUBROUTINE transparent
-
-    MODULE SUBROUTINE wallTemperature(edge, part)
-      USE moduleSpecies
-      IMPLICIT NONE
-
-      CLASS(meshEdge), INTENT(inout):: edge
-      CLASS(particle), INTENT(inout):: part
-
-    END SUBROUTINE wallTemperature
-
-  END INTERFACE
-
-  TYPE, PUBLIC, ABSTRACT, EXTENDS(meshVol):: meshVol1DCart
-    CONTAINS
-      PROCEDURE, PASS:: detJac => detJ1DCart
-      PROCEDURE, PASS:: invJac => invJ1DCart
-      PROCEDURE(fPsi_interface), DEFERRED, NOPASS:: fPsi
-      PROCEDURE(dPsi_interface), DEFERRED, NOPASS:: dPsi
-      PROCEDURE(partialDer_interface), DEFERRED, PASS:: partialDer
-  
-  END TYPE meshVol1DCart
-
-  ABSTRACT INTERFACE
-    PURE FUNCTION fPsi_interface(xi) RESULT(fPsi)
-      REAL(8), INTENT(in):: xi(1:3)
-      REAL(8), ALLOCATABLE:: fPsi(:)
-
-    END FUNCTION fPsi_interface
-
-    PURE FUNCTION dPsi_interface(xi) RESULT(dPsi)
-      REAL(8), INTENT(in):: xi(1:3)
-      REAL(8), ALLOCATABLE:: dPsi(:,:)
-
-    END FUNCTION dPsi_interface
-
-    PURE SUBROUTINE partialDer_interface(self, dPsi, dx)
-      IMPORT meshVol1DCart
-      CLASS(meshVol1DCart), INTENT(in):: self
-      REAL(8), INTENT(in):: dPsi(1:,1:)
-      REAL(8), INTENT(out), DIMENSION(1):: dx
-
-    END SUBROUTINE partialDer_interface
-
-  END INTERFACE
-
-  TYPE, PUBLIC, EXTENDS(meshVol1DCart):: meshVol1DCartSegm
     !Element coordinates
     REAL(8):: x(1:2)
     !Connectivity to nodes
     CLASS(meshNode), POINTER:: n1 => NULL(), n2 => NULL()
     !Connectivity to adjacent elements
-    CLASS(*), POINTER:: e1 => NULL(), e2 => NULL()
+    CLASS(meshElement), POINTER:: e1 => NULL(), e2 => NULL()
-    REAL(8):: arNodes(1:2)
     CONTAINS
-      PROCEDURE, PASS::   init        => initVol1DCartSegm
+      !meshCell DEFERRED PROCEDURES
-      PROCEDURE, PASS::   randPos     => randPos1DCartSeg
+      PROCEDURE, PASS::   init                => initCell1DCartSegm
-      PROCEDURE, PASS::   area        => areaSegm
+      PROCEDURE, PASS::   getNodes            => getNodesSegm
+      PROCEDURE, PASS::   randPos             => randPos1DCartSegm
       PROCEDURE, NOPASS:: fPsi                => fPsiSegm
       PROCEDURE, NOPASS:: dPsi                => dPsiSegm
       PROCEDURE, PASS::   partialDer          => partialDerSegm
+      PROCEDURE, NOPASS:: detJac              => detJ1DCart
+      PROCEDURE, NOPASS:: invJac              => invJ1DCart
+      PROCEDURE, PASS::   gatherElectricField => gatherEFSegm
+      PROCEDURE, PASS::   gatherMagneticField => gatherMFSegm
       PROCEDURE, PASS::   elemK               => elemKSegm
       PROCEDURE, PASS::   elemF               => elemFSegm
-      PROCEDURE, NOPASS:: weight      => weightSegm
       PROCEDURE, NOPASS:: inside              => insideSegm
-      PROCEDURE, PASS::   scatter     => scatterSegm
-      PROCEDURE, PASS::   gatherEF    => gatherEFSegm
-      PROCEDURE, PASS::   getNodes    => getNodesSegm
       PROCEDURE, PASS::   phy2log             => phy2logSegm
-      PROCEDURE, PASS::   nextElement => nextElementSegm
+      PROCEDURE, PASS::   neighbourElement    => neighbourElementSegm
+      !PARTICLUAR PROCEDURES
+      PROCEDURE, PASS, PRIVATE:: calculateVolume => volumeSegm
 
-  END TYPE meshVol1DCartSegm
+  END TYPE meshCell1DCartSegm
 
   CONTAINS
     !NODE FUNCTIONS
@@ -133,6 +69,7 @@ MODULE moduleMesh1DCart
     SUBROUTINE initNode1DCart(self, n, r)
       USE moduleSpecies
       USE moduleRefParam
+      USE OMP_LIB
       IMPLICIT NONE
 
       CLASS(meshNode1DCart), INTENT(out):: self
@@ -147,6 +84,8 @@ MODULE moduleMesh1DCart
       !Allocates output
       ALLOCATE(self%output(1:nSpecies))
 
+      CALL OMP_INIT_LOCK(self%lock)
+
     END SUBROUTINE initNode1DCart
 
     PURE FUNCTION getCoord1DCart(self) RESULT(r)
@@ -160,7 +99,7 @@ MODULE moduleMesh1DCart
     END FUNCTION getCoord1DCart
 
     !EDGE FUNCTIONS
-    !Inits edge element
+    !Init edge element
     SUBROUTINE initEdge1DCart(self, n, p, bt, physicalSurface)
       USE moduleSpecies
       USE moduleBoundary
@@ -176,12 +115,15 @@ MODULE moduleMesh1DCart
       INTEGER:: s
 
       self%n = n
+      self%nNodes = SIZE(p)
       self%n1 => mesh%nodes(p(1))%obj
       !Get element coordinates
       r1 = self%n1%getCoordinates()
 
       self%x = r1(1)
 
+      self%surface = 1.D0
+
       self%normal = (/ 1.D0, 0.D0, 0.D0 /)
 
       !Boundary index
@@ -189,23 +131,7 @@ MODULE moduleMesh1DCart
       ALLOCATE(self%fboundary(1:nSpecies))
       !Assign functions to boundary
       DO s = 1, nSpecies
-        SELECT TYPE(obj => self%boundary%bTypes(s)%obj)
+        CALL pointBoundaryFunction(self, s)
-        TYPE IS(boundaryAbsorption)
-          self%fBoundary(s)%apply => absorption
-
-        TYPE IS(boundaryReflection)
-          self%fBoundary(s)%apply => reflection
-
-        TYPE IS(boundaryTransparent)
-          self%fBoundary(s)%apply => transparent
-
-        TYPE IS(boundaryWallTemperature)
-          self%fBoundary(s)%apply => wallTemperature
-
-        CLASS DEFAULT
-          CALL criticalError("Boundary type not defined in this geometry", 'initEdge1DCart')
-
-        END SELECT
 
       END DO
 
@@ -215,18 +141,29 @@ MODULE moduleMesh1DCart
     END SUBROUTINE initEdge1DCart
 
     !Get nodes from edge
-    PURE FUNCTION getNodes1DCart(self) RESULT(n)
+    PURE FUNCTION getNodes1DCart(self, nNodes) RESULT(n)
       IMPLICIT NONE
 
       CLASS(meshEdge1DCart), INTENT(in):: self
-      INTEGER, ALLOCATABLE:: n(:)
+      INTEGER, INTENT(in):: nNodes
+      INTEGER:: n(1:nNodes)
 
-      ALLOCATE(n(1))
       n = (/ self%n1%n /)
 
     END FUNCTION getNodes1DCart
 
-    !Calculates a 'random' position in edge
+    PURE FUNCTION intersection1DCart(self, r0) RESULT(r)
+      IMPLICIT NONE
+
+      CLASS(meshEdge1DCart), INTENT(in):: self
+      REAL(8), DIMENSION(1:3), INTENT(in):: r0
+      REAL(8), DIMENSION(1:3):: r
+
+      r = (/ self%x, 0.D0, 0.D0 /)
+
+    END FUNCTION intersection1DCart
+
+    !Calculate a 'random' position in edge
     FUNCTION randPosEdge(self) RESULT(r)
       CLASS(meshEdge1DCart), INTENT(in):: self
       REAL(8):: r(1:3)
@@ -237,316 +174,420 @@ MODULE moduleMesh1DCart
 
     !VOLUME FUNCTIONS
     !SEGMENT FUNCTIONS
-    !Init segment element
+    !Init element
-    SUBROUTINE initVol1DCartSegm(self, n, p)
+    SUBROUTINE initCell1DCartSegm(self, n, p, nodes)
       USE moduleRefParam
       IMPLICIT NONE
 
-      CLASS(meshVol1DCartSegm), INTENT(out):: self
+      CLASS(meshCell1DCartSegm), INTENT(out):: self
       INTEGER, INTENT(in):: n
       INTEGER, INTENT(in):: p(:)
+      TYPE(meshNodeCont), INTENT(in), TARGET:: nodes(:)
       REAL(8), DIMENSION(1:3):: r1, r2
 
       self%n = n
-      self%n1 => mesh%nodes(p(1))%obj
+      self%nNodes = SIZE(p)
-      self%n2 => mesh%nodes(p(2))%obj
+      self%n1 => nodes(p(1))%obj
+      self%n2 => nodes(p(2))%obj
       !Get element coordinates
       r1 = self%n1%getCoordinates()
       r2 = self%n2%getCoordinates()
       self%x = (/ r1(1), r2(1) /)
 
       !Assign node volume
-      CALL self%area()
+      CALL self%calculateVolume()
-      self%n1%v = self%n1%v + self%arNodes(1)
-      self%n2%v = self%n2%v + self%arNodes(2)
-
-      self%sigmaVrelMax = sigma_ref/L_ref**2
 
       CALL OMP_INIT_LOCK(self%lock)
 
-    END SUBROUTINE initVol1DCartSegm
+      ALLOCATE(self%listPart_in(1:nSpecies))
+      ALLOCATE(self%totalWeight(1:nSpecies))
 
-    !Calculates a random position in 1D volume
+    END SUBROUTINE initCell1DCartSegm
-    FUNCTION randPos1DCartSeg(self) RESULT(r)
-      USE moduleRandom
-      IMPLICIT NONE
-
-      CLASS(meshVol1DCartSegm), INTENT(in):: self
-      REAL(8):: r(1:3)
-      REAL(8):: xii(1:3)
-      REAL(8), ALLOCATABLE:: fPsi(:)
-
-      xii(1)   = random(-1.D0, 1.D0)
-      xii(2:3) = 0.D0
-
-      fPsi = self%fPsi(xii)
-      r(1) = DOT_PRODUCT(fPsi, self%x)
-
-    END FUNCTION randPos1DCartSeg
-
-    !Computes element area
-    PURE SUBROUTINE areaSegm(self)
-      IMPLICIT NONE
-
-      CLASS(meshVol1DCartSegm), INTENT(inout):: self
-      REAL(8):: l !element length
-      REAL(8):: fPsi(1:2)
-      REAL(8):: detJ
-      REAL(8):: Xii(1:3)
-
-      self%volume  = 0.D0
-      self%arNodes = 0.D0
-      !1 point Gauss integral
-      Xii = 0.D0
-      fPsi = self%fPsi(Xii)
-      detJ = self%detJac(Xii)
-      l = 2.D0*detJ
-      self%volume  =      l
-      self%arNodes = fPsi*l
-
-    END SUBROUTINE areaSegm
-
-    !Computes element functions at point xii
-    PURE FUNCTION fPsiSegm(xi) RESULT(fPsi)
-      IMPLICIT NONE
-
-      REAL(8), INTENT(in):: xi(1:3)
-      REAL(8), ALLOCATABLE:: fPsi(:)
-
-      ALLOCATE(fPsi(1:2))
-
-      fPsi(1) = 1.D0 - xi(1)
-      fPsi(2) = 1.D0 + xi(1)
-      fPsi    = fPsi * 5.D-1
-
-    END FUNCTION fPsiSegm
-
-    !Computes element derivative shape function at Xii
-    PURE FUNCTION dPsiSegm(xi) RESULT(dPsi)
-      IMPLICIT NONE
-
-      REAL(8), INTENT(in):: xi(1:3)
-      REAL(8), ALLOCATABLE:: dPsi(:,:)
-
-      ALLOCATE(dPsi(1:1, 1:2))
-
-      dPsi(1, 1) = -5.D-1
-      dPsi(1, 2) =  5.D-1
-
-    END FUNCTION dPsiSegm
-
-    !Computes partial derivatives of coordinates
-    PURE SUBROUTINE partialDerSegm(self, dPsi, dx)
-      IMPLICIT NONE
-
-      CLASS(meshVol1DCartSegm), INTENT(in):: self
-      REAL(8), INTENT(in):: dPsi(1:,1:)
-      REAL(8), INTENT(out), DIMENSION(1):: dx
-
-      dx(1) = DOT_PRODUCT(dPsi(1,:), self%x)
-
-    END SUBROUTINE partialDerSegm
-
-    !Computes local stiffness matrix
-    PURE FUNCTION elemKSegm(self) RESULT(ke)
-      IMPLICIT NONE
-
-      CLASS(meshVol1DCartSegm), INTENT(in):: self
-      REAL(8):: ke(1:2,1:2)
-      REAL(8):: Xii(1:3)
-      REAL(8):: dPsi(1:1, 1:2)
-      REAL(8):: invJ
-
-      ke      = 0.D0
-      Xii     = (/ 0.D0, 0.D0, 0.D0 /)
-      dPsi    = self%dPsi(Xii)
-      invJ    = self%invJac(Xii, dPsi)
-      ke(1,:) = (/ dPsi(1,1)*dPsi(1,1), dPsi(1,1)*dPsi(1,2) /) 
-      ke(2,:) = (/ dPsi(1,2)*dPsi(1,1), dPsi(1,2)*dPsi(1,2) /) 
-      ke      = 2.D0*ke*invJ
-
-    END FUNCTION elemKSegm
-
-    PURE FUNCTION elemFSegm(self, source) RESULT(localF)
-      IMPLICIT NONE
-
-      CLASS(meshVol1DCartSegm), INTENT(in):: self
-      REAL(8), INTENT(in):: source(1:)
-      REAL(8), ALLOCATABLE:: localF(:)
-      REAL(8):: fPsi(1:2)
-      REAL(8):: detJ
-      REAL(8):: Xii(1:3)
-
-      Xii = 0.D0
-      fPsi = self%fPsi(Xii)
-      detJ = self%detJac(Xii)
-      ALLOCATE(localF(1:2))
-      localF = 2.D0*DOT_PRODUCT(fPsi, source)*detJ
-
-    END FUNCTION elemFSegm
-
-    PURE FUNCTION weightSegm(xi) RESULT(w)
-      IMPLICIT NONE
-
-      REAL(8), INTENT(in):: xi(1:3)
-      REAL(8):: w(1:2)
-
-      w = fPsiSegm(xi)
-
-    END FUNCTION weightSegm
-
-    PURE FUNCTION insideSegm(xi) RESULT(ins)
-      IMPLICIT NONE
-
-      REAL(8), INTENT(in):: xi(1:3)
-      LOGICAL:: ins
-
-      ins = xi(1) >=-1.D0 .AND. &
-            xi(1) <= 1.D0
-
-    END FUNCTION insideSegm
-
-    SUBROUTINE scatterSegm(self, part)
-      USE moduleOutput
-      USE moduleSpecies
-      IMPLICIT NONE
-
-      CLASS(meshVol1DCartSegm), INTENT(in):: self
-      CLASS(particle), INTENT(in):: part
-      TYPE(outputNode), POINTER:: vertex
-      REAL(8):: w_p(1:2)
-      REAL(8):: tensorS(1:3,1:3)
-
-      w_p = self%weight(part%xi)
-      tensorS = outerProduct(part%v, part%v)
-
-      vertex => self%n1%output(part%sp)
-      vertex%den          = vertex%den          + part%weight*w_p(1)
-      vertex%mom(:)       = vertex%mom(:)       + part%weight*w_p(1)*part%v(:)
-      vertex%tensorS(:,:) = vertex%tensorS(:,:) + part%weight*w_p(1)*tensorS
-
-      vertex => self%n2%output(part%sp)
-      vertex%den          = vertex%den          + part%weight*w_p(2)
-      vertex%mom(:)       = vertex%mom(:)       + part%weight*w_p(2)*part%v(:)
-      vertex%tensorS(:,:) = vertex%tensorS(:,:) + part%weight*w_p(2)*tensorS
-
-    END SUBROUTINE scatterSegm
-
-    !Gathers EF at position Xii
-    PURE FUNCTION gatherEFSegm(self, xi) RESULT(EF)
-      IMPLICIT NONE
-
-      CLASS(meshVol1DCartSegm), INTENT(in):: self
-      REAL(8), INTENT(in):: xi(1:3)
-      REAL(8):: dPsi(1, 1:2)
-      REAL(8):: phi(1:2)
-      REAL(8):: EF(1:3)
-      REAL(8):: invJ
-
-      phi = (/ self%n1%emData%phi, &
-               self%n2%emData%phi /)
-
-      dPsi  =  self%dPsi(xi)
-      invJ  =  self%invJac(xi, dPsi)
-      EF(1) = -DOT_PRODUCT(dPsi(1, :), phi)*invJ
-      EF(2) =  0.D0
-      EF(3) =  0.D0
-
-    END FUNCTION gatherEFSegm
 
     !Get nodes from 1D volume
-    PURE FUNCTION getNodesSegm(self) RESULT(n)
+    PURE FUNCTION getNodesSegm(self, nNodes) RESULT(n)
       IMPLICIT NONE
 
-      CLASS(meshVol1DCartSegm), INTENT(in):: self
+      CLASS(meshCell1DCartSegm), INTENT(in):: self
-      INTEGER, ALLOCATABLE:: n(:)
+      INTEGER, INTENT(in):: nNodes
+      INTEGER:: n(1:nNodes)
 
-      ALLOCATE(n(1:2))
       n = (/ self%n1%n, self%n2%n /)
 
     END FUNCTION getNodesSegm
 
-    PURE FUNCTION phy2logSegm(self, r) RESULT(xN)
+    !Random position in 1D volume
+    FUNCTION randPos1DCartSegm(self) RESULT(r)
+      USE moduleRandom
       IMPLICIT NONE
 
-      CLASS(meshVol1DCartSegm), INTENT(in):: self
+      CLASS(meshCell1DCartSegm), INTENT(in):: self
-      REAL(8), INTENT(in):: r(1:3)
+      REAL(8):: r(1:3)
-      REAL(8):: xN(1:3)
+      REAL(8):: Xi(1:3)
+      REAL(8):: fPsi(1:2)
 
-      xN = 0.D0
+      Xi    = 0.D0
-      xN(1) = 2.D0*(r(1) - self%x(1))/(self%x(2) - self%x(1)) - 1.D0
+      Xi(1) = random(-1.D0, 1.D0)
+
+      fPsi = self%fPsi(Xi, 2)
+
+      r    = 0.D0
+      r(1) = DOT_PRODUCT(fPsi, self%x)
+
+    END FUNCTION randPos1DCartSegm
+
+    !Compute element functions at point Xi
+    PURE FUNCTION fPsiSegm(Xi, nNodes) RESULT(fPsi)
+      IMPLICIT NONE
+
+      REAL(8), INTENT(in):: Xi(1:3)
+      INTEGER, INTENT(in):: nNodes
+      REAL(8):: fPsi(1:nNodes)
+
+      fPsi = (/ 1.D0 - Xi(1), &
+                1.D0 + Xi(1) /)
+
+      fPsi    = fPsi * 0.50D0
+
+    END FUNCTION fPsiSegm
+
+    !Derivative element function at coordinates Xi
+    PURE FUNCTION dPsiSegm(Xi, nNodes) RESULT(dPsi)
+      IMPLICIT NONE
+
+      REAL(8), INTENT(in):: Xi(1:3)
+      INTEGER, INTENT(in):: nNodes
+      REAL(8):: dPsi(1:3,1:nNodes)
+
+      dPsi = 0.D0
+
+      dPsi(1, 1:2) = (/ -5.D-1, 5.D-1 /)
+
+    END FUNCTION dPsiSegm
+
+    !Partial derivative in global coordinates
+    PURE FUNCTION partialDerSegm(self, nNodes, dPsi) RESULT(pDer)
+      IMPLICIT NONE
+
+      CLASS(meshCell1DCartSegm), INTENT(in):: self
+      INTEGER, INTENT(in):: nNodes
+      REAL(8), INTENT(in):: dPsi(1:3,1:nNodes)
+      REAL(8):: pDer(1:3, 1:3)
+
+      pDer = 0.D0
+
+      pDer(1,1) = DOT_PRODUCT(dPsi(1,1:2), self%x(1:2))
+      pDer(2,2) = 1.D0
+      pDer(3,3) = 1.D0
+
+    END FUNCTION partialDerSegm
+
+    PURE FUNCTION gatherEFSegm(self, Xi) RESULT(array)
+      IMPLICIT NONE
+      CLASS(meshCell1DCartSegm), INTENT(in):: self
+      REAL(8), INTENT(in):: Xi(1:3)
+      REAL(8):: array(1:3)
+      REAL(8):: phi(1:2)
+
+      phi = (/ self%n1%emData%phi, &
+               self%n2%emData%phi /)
+
+      array = -self%gatherDF(Xi, 2, phi)
+
+    END FUNCTION gatherEFSegm
+
+    PURE FUNCTION gatherMFSegm(self, Xi) RESULT(array)
+      IMPLICIT NONE
+      CLASS(meshCell1DCartSegm), INTENT(in):: self
+      REAL(8), INTENT(in):: Xi(1:3)
+      REAL(8):: array(1:3)
+      REAL(8):: B(1:2,1:3)
+
+      B(:,1) = (/ self%n1%emData%B(1), &
+                  self%n2%emData%B(1) /)
+
+      B(:,2) = (/ self%n1%emData%B(2), &
+                  self%n2%emData%B(2) /)
+
+      B(:,3) = (/ self%n1%emData%B(3), &
+                  self%n2%emData%B(3) /)
+
+      array = self%gatherF(Xi, 2, B)
+
+    END FUNCTION gatherMFSegm
+
+    !Compute element local stiffness matrix
+    PURE FUNCTION elemKSegm(self, nNodes) RESULT(localK)
+      IMPLICIT NONE
+
+      CLASS(meshCell1DCartSegm), INTENT(in):: self
+      INTEGER, INTENT(in):: nNodes
+      REAL(8):: localK(1:nNodes,1:nNodes)
+      REAL(8):: Xi(1:3)
+      REAL(8):: dPsi(1:3, 1:2)
+      REAL(8):: pDer(1:3, 1:3)
+      REAL(8):: invJ(1:3, 1:3), detJ
+      INTEGER:: l
+
+      localK = 0.D0
+
+      Xi = 0.D0
+      !Start 1D Gauss Quad Integral
+      DO l = 1, 3
+        Xi(1)  = corSeg(l)
+        dPsi   = self%dPsi(Xi, 2)
+        pDer   = self%partialDer(2, dPsi)
+        detJ   = self%detJac(pDer)
+        invJ   = self%invJac(pDer)
+        localK = localK + MATMUL(TRANSPOSE(MATMUL(invJ,dPsi)), &
+                                           MATMUL(invJ,dPsi))* &
+                          wSeg(l)/detJ
+
+      END DO
+
+    END FUNCTION elemKSegm
+
+    !Compute the local source vector for a force f
+    PURE FUNCTION elemFSegm(self, nNodes, source) RESULT(localF)
+      IMPLICIT NONE
+
+      CLASS(meshCell1DCartSegm), INTENT(in):: self
+      INTEGER, INTENT(in):: nNodes
+      REAL(8), INTENT(in):: source(1:nNodes)
+      REAL(8):: localF(1:nNodes)
+      REAL(8):: fPsi(1:2)
+      REAL(8):: dPsi(1:3, 1:2), pDer(1:3, 1:3)
+      REAL(8):: Xi(1:3)
+      REAL(8):: detJ, f
+      INTEGER:: l
+
+      localF = 0.D0
+
+      Xi = 0.D0
+      !Start 1D Gauss Quad Integral
+      DO l = 1, 3
+        Xi(1) = corSeg(l)
+        dPsi   = self%dPsi(Xi, 2)
+        pDer   = self%partialDer(2, dPsi)
+        detJ   = self%detJac(pDer)
+        fPsi   = self%fPsi(Xi, 2)
+        f      = DOT_PRODUCT(fPsi, source)
+        localF = localF + f*fPsi*wSeg(l)*detJ
+
+      END DO
+
+    END FUNCTION elemFSegm
+
+    PURE FUNCTION insideSegm(Xi) RESULT(ins)
+      IMPLICIT NONE
+
+      REAL(8), INTENT(in):: Xi(1:3)
+      LOGICAL:: ins
+
+      ins = Xi(1) >=-1.D0 .AND. &
+            Xi(1) <= 1.D0
+
+    END FUNCTION insideSegm
+
+    PURE FUNCTION phy2logSegm(self, r) RESULT(Xi)
+      IMPLICIT NONE
+
+      CLASS(meshCell1DCartSegm), INTENT(in):: self
+      REAL(8), INTENT(in):: r(1:3)
+      REAL(8):: Xi(1:3)
+
+      Xi = 0.D0
+
+      Xi(1) = 2.D0*(r(1) - self%x(1))/(self%x(2) - self%x(1)) - 1.D0
 
     END FUNCTION phy2logSegm
 
-    !Get next element for a logical position xi
+    !Get the next element for a logical position Xi
-    SUBROUTINE nextElementSegm(self, xi, nextElement)
+    SUBROUTINE neighbourElementSegm(self, Xi, neighbourElement)
       IMPLICIT NONE
 
-      CLASS(meshVol1DCartSegm), INTENT(in):: self
+      CLASS(meshCell1DCartSegm), INTENT(in):: self
-      REAL(8), INTENT(in):: xi(1:3)
+      REAL(8), INTENT(in):: Xi(1:3)
-      CLASS(*), POINTER, INTENT(out):: nextElement
+      CLASS(meshElement), POINTER, INTENT(out):: neighbourElement
       
-      NULLIFY(nextElement)
+      NULLIFY(neighbourElement)
-      IF     (xi(1) < -1.D0) THEN
+      IF     (Xi(1) < -1.D0) THEN
-        nextElement => self%e2
+        neighbourElement => self%e2
 
-      ELSEIF (xi(1) >  1.D0) THEN
+      ELSEIF (Xi(1) >  1.D0) THEN
-        nextElement => self%e1
+        neighbourElement => self%e1
 
       END IF
 
-    END SUBROUTINE nextElementSegm
+    END SUBROUTINE neighbourElementSegm
+
+    !Compute element volume
+    PURE SUBROUTINE volumeSegm(self)
+      IMPLICIT NONE
+
+      CLASS(meshCell1DCartSegm), INTENT(inout):: self
+      REAL(8):: Xi(1:3)
+      REAL(8):: dPsi(1:3, 1:2), pDer(1:3, 1:3)
+      REAL(8):: detJ
+      REAL(8):: fPsi(1:2)
+
+      self%volume  = 0.D0
+      !1D 1 point Gauss Quad Integral
+      Xi = 0.D0
+      dPsi = self%dPsi(Xi, 2)
+      pDer = self%partialDer(2, dPsi)
+      detJ = self%detJac(pDer)
+      fPsi = self%fPsi(Xi, 2)
+      !Compute total volume of the cell
+      self%volume  = detJ*2.D0
+      !Compute volume per node
+      self%n1%v = self%n1%v + fPsi(1)*self%volume
+      self%n2%v = self%n2%v + fPsi(2)*self%volume
+
+    END SUBROUTINE volumeSegm
 
     !COMMON FUNCTIONS FOR 1D VOLUME ELEMENTS
-    !Calculates a random position in 1D volume
+    !Compute element Jacobian determinant
-    !Computes the element Jacobian determinant
+    PURE FUNCTION detJ1DCart(pDer) RESULT(dJ)
-    PURE FUNCTION detJ1DCart(self, xi, dPsi_in) RESULT(dJ)
       IMPLICIT NONE
 
-      CLASS(meshVol1DCart), INTENT(in):: self
+      REAL(8), INTENT(in):: pDer(1:3, 1:3)
-      REAL(8), INTENT(in):: xi(1:3)
-      REAL(8), INTENT(in), OPTIONAL:: dPsi_in(1:,1:)
-      REAL(8), ALLOCATABLE:: dPsi(:,:)
       REAL(8):: dJ
-      REAL(8):: dx(1)
 
-      IF (PRESENT(dPsi_in)) THEN
+      dJ = pDer(1, 1)
-        dPsi = dPsi_in
-
-      ELSE
-        dPsi = self%dPsi(xi)
-
-      END IF
-
-      CALL self%partialDer(dPsi, dx)
-      dJ = dx(1)
 
     END FUNCTION detJ1DCart
 
-    !Computes the invers Jacobian
+    !Compute element Jacobian inverse matrix (without determinant)
-    PURE FUNCTION invJ1DCart(self, xi, dPsi_in) RESULT(invJ)
+    PURE FUNCTION invJ1DCart(pDer) RESULT(invJ)
       IMPLICIT NONE
 
-      CLASS(meshVol1DCart), INTENT(in):: self
+      REAL(8), INTENT(in):: pDer(1:3, 1:3)
-      REAL(8), INTENT(in):: xi(1:3)
+      REAL(8):: invJ(1:3,1:3)
-      REAL(8), INTENT(in), OPTIONAL:: dPsi_in(1:,1:)
-      REAL(8), ALLOCATABLE:: dPsi(:,:)
-      REAL(8):: dx(1)
-      REAL(8):: invJ
 
-      IF (PRESENT(dPsi_in)) THEN
+      invJ = 0.D0
-        dPsi = dPsi_in
 
-      ELSE
+      invJ(1, 1) = 1.D0/pDer(1, 1)
-        dPsi = self%dPsi(xi)
+      invJ(2, 2) = 1.D0
-
+      invJ(3, 3) = 1.D0
-      END IF
-
-      CALL self%partialDer(dPsi, dx)
-      invJ = 1.D0/dx(1)
 
     END FUNCTION invJ1DCart
 
+    SUBROUTINE connectMesh1DCart(self)
+      IMPLICIT NONE
+
+      CLASS(meshGeneric), INTENT(inout):: self
+      INTEGER:: e, et
+
+      DO e = 1, self%numCells
+        !Connect Cell-Cell
+        DO et = 1, self%numCells
+          IF (e /= et) THEN
+            CALL connectCellCell(self%cells(e)%obj, self%cells(et)%obj)
+
+          END IF
+
+        END DO
+
+        SELECT TYPE(self)
+        TYPE IS(meshParticles)
+          !Connect Cell-Edge
+          DO et = 1, self%numEdges
+            CALL connectCellEdge(self%cells(e)%obj, self%edges(et)%obj)
+
+          END DO
+
+      END SELECT
+
+      END DO
+
+    END SUBROUTINE connectMesh1DCart
+
+    SUBROUTINE connectCellCell(elemA, elemB)
+      IMPLICIT NONE
+
+      CLASS(meshCell), INTENT(inout):: elemA
+      CLASS(meshCell), INTENT(inout):: elemB
+
+        SELECT TYPE(elemA)
+        TYPE IS(meshCell1DCartSegm)
+          SELECT TYPE(elemB)
+          TYPE IS(meshCell1DCartSegm)
+            CALL connectSegmSegm(elemA, elemB)
+
+          END SELECT
+
+        END SELECT
+
+    END SUBROUTINE connectCellCell
+
+    SUBROUTINE connectSegmSegm(elemA, elemB)
+      IMPLICIT NONE
+
+      CLASS(meshCell1DCartSegm), INTENT(inout), TARGET:: elemA
+      CLASS(meshCell1DCartSegm), INTENT(inout), TARGET:: elemB
+
+      IF (.NOT. ASSOCIATED(elemA%e1) .AND. &
+          elemA%n2%n == elemB%n1%n) THEN
+        elemA%e1 => elemB
+        elemB%e2 => elemA
+        
+      END IF
+
+      IF (.NOT. ASSOCIATED(elemA%e2) .AND. &
+          elemA%n1%n == elemB%n2%n) THEN
+
+        elemA%e2 => elemB
+        elemB%e1 => elemA
+
+      END IF
+
+    END SUBROUTINE connectSegmSegm
+
+    SUBROUTINE connectCellEdge(elemA, elemB)
+      IMPLICIT NONE
+
+      CLASS(meshCell),  INTENT(inout):: elemA
+      CLASS(meshEdge), INTENT(inout):: elemB
+
+      SELECT TYPE(elemA)
+      TYPE IS (meshCell1DCartSegm)
+        SELECT TYPE(elemB)
+        CLASS IS(meshEdge1DCart)
+          CALL connectSegmEdge(elemA, elemB)
+
+        END SELECT
+
+      END SELECT
+
+    END SUBROUTINE connectCellEdge
+
+    SUBROUTINE connectSegmEdge(elemA, elemB)
+      IMPLICIT NONE
+
+      CLASS(meshCell1DCartSegm), INTENT(inout), TARGET:: elemA
+      CLASS(meshEdge1DCart),    INTENT(inout), TARGET:: elemB
+
+      IF (.NOT. ASSOCIATED(elemA%e1) .AND. &
+          elemA%n2%n == elemB%n1%n) THEN
+
+        elemA%e1 => elemB
+        elemB%e2 => elemA
+ 
+        !Rever the normal to point inside the domain
+        elemB%normal = - elemB%normal
+
+      END IF
+
+      IF (.NOT. ASSOCIATED(elemA%e2) .AND. &
+          elemA%n1%n == elemB%n1%n) THEN
+
+        elemA%e2 => elemB
+        elemB%e1 => elemA
+
+      END IF
+
+    END SUBROUTINE connectSegmEdge
 
 END MODULE moduleMesh1DCart
 

src/modules/mesh/1DCart/moduleMesh1DCartBoundary.f90

@@ -1,91 +0,0 @@
-SUBMODULE (moduleMesh1DCart) moduleMesh1DCartBoundary
-  USE moduleMesh1DCart
-
-  CONTAINS
-    SUBROUTINE reflection(edge, part)
-      USE moduleSpecies
-      IMPLICIT NONE
-
-      CLASS(meshEdge), INTENT(inout):: edge
-      CLASS(particle), INTENT(inout):: part
-
-      SELECT TYPE(edge)
-      TYPE IS(meshEdge1DCart)
-        part%v(1) = -part%v(1)
-        part%r(1) =  2.D0*edge%x - part%r(1)
-
-      END SELECT
-
-    END SUBROUTINE reflection
-
-    SUBROUTINE absorption(edge, part)
-      USE moduleSpecies
-      IMPLICIT NONE
-
-      CLASS(meshEdge), INTENT(inout):: edge
-      CLASS(particle), INTENT(inout):: part
-      REAL(8):: rEdge(1) !Position of particle in the edge
-      REAL(8):: d !Distance from particle to edge
-
-      SELECT TYPE(edge)
-      TYPE IS(meshEdge1DCart)
-        rEdge(1) = edge%x
-        d = DABS(part%r(1) - rEdge(1))
-
-        IF (d > 0.D0) THEN
-          part%weight = part%weight / d
-          part%r(1)   = rEdge(1)
-
-        END IF
-
-        IF (ASSOCIATED(edge%e1)) THEN
-          CALL edge%e1%scatter(part)
-
-        ELSE
-          CALL edge%e2%scatter(part)
-
-        END IF
-
-      END SELECT
-
-      part%n_in = .FALSE.
-
-    END SUBROUTINE absorption
-
-    SUBROUTINE transparent(edge, part)
-      USE moduleSpecies
-      IMPLICIT NONE
-
-      CLASS(meshEdge), INTENT(inout):: edge
-      CLASS(particle), INTENT(inout):: part
-
-      part%n_in = .FALSE.
-
-    END SUBROUTINE transparent
-
-    SUBROUTINE wallTemperature(edge, part)
-      USE moduleSpecies
-      USE moduleBoundary
-      USE moduleRandom
-      IMPLICIT NONE
-
-      CLASS(meshEdge), INTENT(inout):: edge
-      CLASS(particle), INTENT(inout):: part
-
-      !Modifies particle velocity according to wall temperature
-      SELECT TYPE(bound => edge%boundary%bTypes(part%sp)%obj)
-      TYPE IS(boundaryWallTemperature)
-        part%v(1) = part%v(1) + bound%vTh*randomMaxwellian()
-
-      END SELECT
-
-      SELECT TYPE(edge)
-      TYPE IS(meshEdge1DCart)
-        part%v(1) = -part%v(1)
-        part%r(1) =  2.D0*edge%x - part%r(1)
-
-      END SELECT
-
-    END SUBROUTINE wallTemperature
-
-END SUBMODULE moduleMesh1DCartBoundary

src/modules/mesh/1DCart/moduleMesh1DCartRead.f90

@@ -1,261 +0,0 @@
-MODULE moduleMesh1DCartRead
-  USE moduleMesh
-  USE moduleMesh1DCart
-  
-  !TODO: make this abstract to allow different mesh formats
-  TYPE, EXTENDS(meshGeneric):: mesh1DCartGeneric
-    CONTAINS
-      PROCEDURE, PASS:: init     => init1DCartMesh
-      PROCEDURE, PASS:: readMesh => readMesh1DCart
-
-  END TYPE
-
-  INTERFACE connected
-    MODULE PROCEDURE connectedVolVol, connectedVolEdge
-
-  END INTERFACE connected
-
-  CONTAINS
-    !Init 1D mesh
-    SUBROUTINE init1DCartMesh(self, meshFormat)
-      USE moduleMesh
-      USE moduleErrors
-      IMPLICIT NONE
-
-      CLASS(mesh1DCartGeneric), INTENT(out):: self
-      CHARACTER(:), ALLOCATABLE, INTENT(in):: meshFormat
-
-      SELECT CASE(meshFormat)
-      CASE ("gmsh")
-        self%printOutput => printOutputGmsh
-        self%printColl   => printCollGmsh
-        self%printEM     => printEMGmsh
-
-      CASE DEFAULT
-        CALL criticalError("Mesh type " // meshFormat // " not supported.", "init1DCart")
-        
-      END SELECT
-
-    END SUBROUTINE init1DCartMesh
-
-    !Reads 1D mesh
-    SUBROUTINE readMesh1DCart(self, filename)
-      USE  moduleBoundary
-      IMPLICIT NONE
-
-      CLASS(mesh1DCartGeneric), INTENT(inout):: self
-      CHARACTER(:), ALLOCATABLE, INTENT(in):: filename
-      REAL(8):: x
-      INTEGER:: p(1:2)
-      INTEGER:: e, et, n, eTemp, elemType, bt
-      INTEGER:: totalNumElem
-      INTEGER:: boundaryType
-
-      !Open file mesh
-      OPEN(10, FILE=TRIM(filename))
-      !Skip header
-      READ(10, *)
-      READ(10, *)
-      READ(10, *)
-      READ(10, *)
-      !Read number of nodes
-      READ(10, *) self%numNodes
-      !Allocate required matrices and vectors
-      ALLOCATE(self%nodes(1:self%numNodes))
-      ALLOCATE(self%K(1:self%numNodes, 1:self%numNodes))
-      ALLOCATE(self%IPIV(1:self%numNodes, 1:self%numNodes))
-      self%K = 0.D0
-      self%IPIV = 0
-      !Read nodes coordinates. Only relevant for x
-      DO e = 1, self%numNodes
-        READ(10, *) n, x
-        ALLOCATE(meshNode1DCart:: self%nodes(n)%obj)
-        CALL self%nodes(n)%obj%init(n, (/ x, 0.D0, 0.D0 /))
-
-      END DO
-      !Skips comments
-      READ(10, *)
-      READ(10, *)
-      !Reads the total number of elements (edges+vol)
-      READ(10, *) totalNumElem
-      self%numEdges = 0
-      DO e = 1, totalNumElem
-        READ(10, *) eTemp, elemType
-        IF (elemType == 15) THEN !15 is physical node in GMSH
-          self%numEdges = e
-
-        END IF
-
-      END DO
-
-      !Substract the number of edges to the total number of elements
-      !to obtain the number of volume elements
-      self%numVols = totalNumelem - self%numEdges
-      !Allocates arrays
-      ALLOCATE(self%edges(1:self%numEdges))
-      ALLOCATE(self%vols(1:self%numVols))
-
-      !Go back to the beginning of reading elements
-      DO e = 1, totalNumelem
-        BACKSPACE(10)
-
-      END DO
-
-      !Reads edges
-      DO e = 1, self%numEdges
-        READ(10, *) n, elemType, eTemp, boundaryType, eTemp, p(1)
-        !Associate boundary condition 
-        bt = getBoundaryId(boundaryType)
-
-        ALLOCATE(meshEdge1DCart:: self%edges(e)%obj)
-
-        CALL self%edges(e)%obj%init(n, p(1:1), bt, boundaryType)
-
-      END DO
-
-      !Read and initialize volumes
-      DO e = 1, self%numVols
-        READ(10, *) n, elemType, eTemp, eTemp, eTemp, p(1:2)
-        ALLOCATE(meshVol1DCartSegm:: self%vols(e)%obj)
-        CALL self%vols(e)%obj%init(n - self%numEdges, p(1:2))
-
-      END DO
-
-      CLOSE(10)
-
-      !Build connectivity between elements
-      DO e = 1, self%numVols
-        !Connectivity between volumes
-        DO et = 1, self%numVols
-          IF (e /= et) THEN
-            CALL connected(self%vols(e)%obj, self%vols(et)%obj)
-
-          END IF
-
-        END DO
-
-        !Connectivity betwen vols and edges
-        DO et = 1, self%numEdges
-          CALL connected(self%vols(e)%obj, self%edges(et)%obj)
-
-        END DO
-
-        !Constructs the global K matrix
-        CALL constructGlobalK(self%K, self%vols(e)%obj)
-
-      END DO
-
-    END SUBROUTINE readMesh1DCart
-
-    SUBROUTINE connectedVolVol(elemA, elemB)
-      IMPLICIT NONE
-
-      CLASS(meshVol), INTENT(inout):: elemA
-      CLASS(meshVol), INTENT(inout):: elemB
-
-        SELECT TYPE(elemA)
-        TYPE IS(meshVol1DCartSegm)
-          SELECT TYPE(elemB)
-          TYPE IS(meshVol1DCartSegm)
-            CALL connectedSegmSegm(elemA, elemB)
-
-          END SELECT
-
-        END SELECT
-
-    END SUBROUTINE connectedVolVol
-
-    SUBROUTINE connectedSegmSegm(elemA, elemB)
-      IMPLICIT NONE
-
-      CLASS(meshVol1DCartSegm), INTENT(inout), TARGET:: elemA
-      CLASS(meshVol1DCartSegm), INTENT(inout), TARGET:: elemB
-
-      IF (.NOT. ASSOCIATED(elemA%e1) .AND. &
-          elemA%n2%n == elemB%n1%n) THEN
-        elemA%e1 => elemB
-        elemB%e2 => elemA
-        
-      END IF
-
-      IF (.NOT. ASSOCIATED(elemA%e2) .AND. &
-          elemA%n1%n == elemB%n2%n) THEN
-
-        elemA%e2 => elemB
-        elemB%e1 => elemA
-
-      END IF
-
-    END SUBROUTINE connectedSegmSegm
-
-    SUBROUTINE connectedVolEdge(elemA, elemB)
-      IMPLICIT NONE
-
-      CLASS(meshVol),  INTENT(inout):: elemA
-      CLASS(meshEdge), INTENT(inout):: elemB
-
-      SELECT TYPE(elemA)
-      TYPE IS (meshVol1DCartSegm)
-        SELECT TYPE(elemB)
-        CLASS IS(meshEdge1DCart)
-          CALL connectedSegmEdge(elemA, elemB)
-
-        END SELECT
-
-      END SELECT
-
-    END SUBROUTINE connectedVolEdge
-
-    SUBROUTINE connectedSegmEdge(elemA, elemB)
-      IMPLICIT NONE
-
-      CLASS(meshVol1DCartSegm), INTENT(inout), TARGET:: elemA
-      CLASS(meshEdge1DCart),    INTENT(inout), TARGET:: elemB
-
-      IF (.NOT. ASSOCIATED(elemA%e1) .AND. &
-          elemA%n2%n == elemB%n1%n) THEN
-
-        elemA%e1 => elemB
-        elemB%e2 => elemA
-
-      END IF
-
-      IF (.NOT. ASSOCIATED(elemA%e2) .AND. &
-          elemA%n1%n == elemB%n1%n) THEN
-
-        elemA%e2 => elemB
-        elemB%e1 => elemA
-
-      END IF
-
-    END SUBROUTINE connectedSegmEdge
-
-    SUBROUTINE constructGlobalK(K, elem)
-      IMPLICIT NONE
-
-      REAL(8), INTENT(inout):: K(1:,1:)
-      CLASS(meshVol), INTENT(in):: elem
-      REAL(8):: localK(1:2,1:2)
-      INTEGER:: i, j
-      INTEGER:: n(1:2)
-
-      SELECT TYPE(elem)
-      TYPE IS(meshVol1DCartSegm)
-        localK = elem%elemK()
-        n = (/ elem%n1%n, elem%n2%n /)
-
-      CLASS DEFAULT
-        n = 0
-        localK = 0.D0
-
-      END SELECT
-      
-      DO i = 1, 2
-        DO j = 1, 2
-          K(n(i), n(j)) = K(n(i), n(j)) + localK(i, j)
-        END DO
-      END DO
-
-    END SUBROUTINE constructGlobalK
-
-END MODULE moduleMesh1DCartRead

src/modules/mesh/1DRad/makefile

@@ -1,11 +1,5 @@
-all: moduleMesh1DRad.o moduleMesh1DRadBoundary.o moduleMesh1DRadRead.o
+all: moduleMesh1DRad.o
 
 moduleMesh1DRad.o: moduleMesh1DRad.f90
 	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
 
-moduleMesh1DRadBoundary.o: moduleMesh1DRad.o moduleMesh1DRadBoundary.f90
-	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
-
-moduleMesh1DRadRead.o: moduleMesh1DRad.o moduleMesh1DRadBoundary.o moduleMesh1DRadRead.f90
-	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
-

src/modules/mesh/1DRad/moduleMesh1DRad.f90

@@ -4,12 +4,17 @@
 !              z == unused
 MODULE moduleMesh1DRad
   USE moduleMesh
+  USE moduleMeshBoundary
   IMPLICIT NONE
 
+  REAL(8), PARAMETER:: corSeg(1:3) = (/ -DSQRT(3.D0/5.D0), 0.D0,       DSQRT(3.D0/5.D0) /)
+  REAL(8), PARAMETER:: wSeg(1:3)   = (/        5.D0/9.D0 , 8.D0/9.D0,        5.D0/9.D0  /)
+
   TYPE, PUBLIC, EXTENDS(meshNode):: meshNode1DRad
     !Element coordinates
     REAL(8):: r = 0.D0
     CONTAINS
+      !meshNode DEFERRED PROCEDURES
       PROCEDURE, PASS:: init           => initNode1DRad
       PROCEDURE, PASS:: getCoordinates => getCoord1DRad
 
@@ -21,112 +26,42 @@ MODULE moduleMesh1DRad
     !Connectivity to nodes
     CLASS(meshNode), POINTER:: n1 => NULL()
     CONTAINS
+      !meshEdge DEFERRED PROCEDURES
       PROCEDURE, PASS:: init         => initEdge1DRad
       PROCEDURE, PASS:: getNodes     => getNodes1DRad
+      PROCEDURE, PASS:: intersection => intersection1DRad
       PROCEDURE, PASS:: randPos      => randPos1DRad
 
   END TYPE meshEdge1DRad
 
-  !Boundary functions defined in the submodule Boundary
+  TYPE, PUBLIC, EXTENDS(meshCell):: meshCell1DRadSegm
-  INTERFACE
-    MODULE SUBROUTINE reflection(edge, part)
-      USE moduleSpecies
-      IMPLICIT NONE
-
-      CLASS(meshEdge), INTENT(inout):: edge
-      CLASS(particle), INTENT(inout):: part
-
-    END SUBROUTINE reflection
-
-    MODULE SUBROUTINE absorption(edge, part)
-      USE moduleSpecies
-      IMPLICIT NONE
-
-      CLASS(meshEdge), INTENT(inout):: edge
-      CLASS(particle), INTENT(inout):: part
-
-    END SUBROUTINE absorption
-
-    MODULE SUBROUTINE transparent(edge, part)
-      USE moduleSpecies
-      IMPLICIT NONE
-
-      CLASS(meshEdge), INTENT(inout):: edge
-      CLASS(particle), INTENT(inout):: part
-
-    END SUBROUTINE transparent
-
-    MODULE SUBROUTINE wallTemperature(edge, part)
-      USE moduleSpecies
-      IMPLICIT NONE
-
-      CLASS(meshEdge), INTENT(inout):: edge
-      CLASS(particle), INTENT(inout):: part
-
-    END SUBROUTINE wallTemperature
-
-  END INTERFACE
-
-  TYPE, PUBLIC, ABSTRACT, EXTENDS(meshVol):: meshVol1DRad
-    CONTAINS
-      PROCEDURE, PASS:: detJac => detJ1DRad
-      PROCEDURE, PASS:: invJac => invJ1DRad
-      PROCEDURE(fPsi_interface), DEFERRED, NOPASS:: fPsi
-      PROCEDURE(dPsi_interface), DEFERRED, NOPASS:: dPsi
-      PROCEDURE(partialDer_interface), DEFERRED, PASS:: partialDer
-  
-  END TYPE meshVol1DRad
-
-  ABSTRACT INTERFACE
-    PURE FUNCTION fPsi_interface(xi) RESULT(fPsi)
-      REAL(8), INTENT(in):: xi(1:3)
-      REAL(8), ALLOCATABLE:: fPsi(:)
-
-    END FUNCTION fPsi_interface
-
-    PURE FUNCTION dPsi_interface(xi) RESULT(dPsi)
-      REAL(8), INTENT(in):: xi(1:3)
-      REAL(8), ALLOCATABLE:: dPsi(:,:)
-
-    END FUNCTION dPsi_interface
-
-    PURE SUBROUTINE partialDer_interface(self, dPsi, dx)
-      IMPORT meshVol1DRad
-
-      CLASS(meshVol1DRad), INTENT(in):: self
-      REAL(8), INTENT(in):: dPsi(1:,1:)
-      REAL(8), INTENT(out), DIMENSION(1):: dx
-
-    END SUBROUTINE partialDer_interface
-
-  END INTERFACE
-
-  TYPE, PUBLIC, EXTENDS(meshVol1DRad):: meshVol1DRadSegm
     !Element coordinates
     REAL(8):: r(1:2)
     !Connectivity to nodes
     CLASS(meshNode), POINTER:: n1 => NULL(), n2 => NULL()
     !Connectivity to adjacent elements
-    CLASS(*), POINTER:: e1 => NULL(), e2 => NULL()
+    CLASS(meshElement), POINTER:: e1 => NULL(), e2 => NULL()
-    REAL(8):: arNodes(1:2)
     CONTAINS
-      PROCEDURE, PASS::   init        => initVol1DRadSegm
+      !meshCell DEFERRED PROCEDURES
-      PROCEDURE, PASS::   randPos     => randPos1DRadSeg
+      PROCEDURE, PASS::   init                => initCell1DRadSegm
-      PROCEDURE, PASS::   area        => areaRad
+      PROCEDURE, PASS::   getNodes            => getNodesSegm
-      PROCEDURE, NOPASS:: fPsi        => fPsiRad
+      PROCEDURE, PASS::   randPos             => randPos1DRadSegm
-      PROCEDURE, NOPASS:: dPsi        => dPsiRad
+      PROCEDURE, NOPASS:: fPsi                => fPsiSegm
-      PROCEDURE, PASS::   partialDer  => partialDerRad
+      PROCEDURE, NOPASS:: dPsi                => dPsiSegm
-      PROCEDURE, PASS::   elemK       => elemKRad
+      PROCEDURE, PASS::   partialDer          => partialDerSegm
-      PROCEDURE, PASS::   elemF       => elemFRad
+      PROCEDURE, NOPASS:: detJac              => detJ1DRad
-      PROCEDURE, NOPASS:: weight      => weightRad
+      PROCEDURE, NOPASS:: invJac              => invJ1DRad
-      PROCEDURE, NOPASS:: inside      => insideRad
+      PROCEDURE, PASS::   gatherElectricField => gatherEFSegm
-      PROCEDURE, PASS::   scatter     => scatterRad
+      PROCEDURE, PASS::   gatherMagneticField => gatherMFSegm
-      PROCEDURE, PASS::   gatherEF    => gatherEFRad
+      PROCEDURE, PASS::   elemK               => elemKSegm
-      PROCEDURE, PASS::   getNodes    => getNodesRad
+      PROCEDURE, PASS::   elemF               => elemFSegm
-      PROCEDURE, PASS::   phy2log     => phy2logRad
+      PROCEDURE, NOPASS:: inside              => insideSegm
-      PROCEDURE, PASS::   nextElement => nextElementRad
+      PROCEDURE, PASS::   phy2log             => phy2logSegm
+      PROCEDURE, PASS::   neighbourElement    => neighbourElementSegm
+      !PARTICLUAR PROCEDURES
+      PROCEDURE, PASS, PRIVATE:: calculateVolume => volumeSegm
 
-  END TYPE meshVol1DRadSegm
+  END TYPE meshCell1DRadSegm
 
   CONTAINS
     !NODE FUNCTIONS
@@ -134,6 +69,7 @@ MODULE moduleMesh1DRad
     SUBROUTINE initNode1DRad(self, n, r)
       USE moduleSpecies
       USE moduleRefParam
+      USE OMP_LIB
       IMPLICIT NONE
 
       CLASS(meshNode1DRad), INTENT(out):: self
@@ -145,9 +81,11 @@ MODULE moduleMesh1DRad
       !Node volume, to be determined in mesh
       self%v = 0.D0
 
-      !Allocates output
+      !Allocate output
       ALLOCATE(self%output(1:nSpecies))
 
+      CALL OMP_INIT_LOCK(self%lock)
+
     END SUBROUTINE initNode1DRad
 
     PURE FUNCTION getCoord1DRad(self) RESULT(r)
@@ -161,7 +99,7 @@ MODULE moduleMesh1DRad
     END FUNCTION getCoord1DRad
 
     !EDGE FUNCTIONS
-    !Inits edge element
+    !Init edge element
     SUBROUTINE initEdge1DRad(self, n, p, bt, physicalSurface)
       USE moduleSpecies
       USE moduleBoundary
@@ -177,12 +115,15 @@ MODULE moduleMesh1DRad
       INTEGER:: s
 
       self%n = n
+      self%nNodes = SIZE(p)
       self%n1 => mesh%nodes(p(1))%obj
       !Get element coordinates
       r1 = self%n1%getCoordinates()
 
       self%r = r1(1)
 
+      self%surface = 1.D0
+
       self%normal = (/ 1.D0, 0.D0, 0.D0 /)
 
       !Boundary index
@@ -190,23 +131,7 @@ MODULE moduleMesh1DRad
       ALLOCATE(self%fboundary(1:nSpecies))
       !Assign functions to boundary
       DO s = 1, nSpecies
-        SELECT TYPE(obj => self%boundary%bTypes(s)%obj)
+        CALL pointBoundaryFunction(self, s)
-        TYPE IS(boundaryAbsorption)
-          self%fBoundary(s)%apply => absorption
-
-        TYPE IS(boundaryReflection)
-          self%fBoundary(s)%apply => reflection
-
-        TYPE IS(boundaryTransparent)
-          self%fBoundary(s)%apply => transparent
-
-        TYPE IS(boundaryWallTemperature)
-          self%fBoundary(s)%apply => wallTemperature
-
-        CLASS DEFAULT
-          CALL criticalError("Boundary type not defined in this geometry", 'initEdge1DRad')
-
-        END SELECT
 
       END DO
 
@@ -216,18 +141,29 @@ MODULE moduleMesh1DRad
     END SUBROUTINE initEdge1DRad
 
     !Get nodes from edge
-    PURE FUNCTION getNodes1DRad(self) RESULT(n)
+    PURE FUNCTION getNodes1DRad(self, nNodes) RESULT(n)
       IMPLICIT NONE
 
       CLASS(meshEdge1DRad), INTENT(in):: self
-      INTEGER, ALLOCATABLE:: n(:)
+      INTEGER, INTENT(in):: nNodes
+      INTEGER:: n(1:nNodes)
 
-      ALLOCATE(n(1))
       n = (/ self%n1%n /)
 
     END FUNCTION getNodes1DRad
 
-    !Calculates a 'random' position in edge
+    PURE FUNCTION intersection1DRad(self, r0) RESULT(r)
+      IMPLICIT NONE
+
+      CLASS(meshEdge1DRad), INTENT(in):: self
+      REAL(8), DIMENSION(1:3), INTENT(in):: r0
+      REAL(8), DIMENSION(1:3):: r
+
+      r = (/ self%r, 0.D0, 0.D0 /)
+
+    END FUNCTION intersection1DRad
+
+    !Calculate a 'random' position in edge
     FUNCTION randPos1DRad(self) RESULT(r)
       CLASS(meshEdge1DRad), INTENT(in):: self
       REAL(8):: r(1:3)
@@ -238,325 +174,435 @@ MODULE moduleMesh1DRad
 
     !VOLUME FUNCTIONS
     !SEGMENT FUNCTIONS
-    !Init segment element
+    !Init element
-    SUBROUTINE initVol1DRadSegm(self, n, p)
+    SUBROUTINE initCell1DRadSegm(self, n, p, nodes)
       USE moduleRefParam
       IMPLICIT NONE
 
-      CLASS(meshVol1DRadSegm), INTENT(out):: self
+      CLASS(meshCell1DRadSegm), INTENT(out):: self
       INTEGER, INTENT(in):: n
       INTEGER, INTENT(in):: p(:)
+      TYPE(meshNodeCont), INTENT(in), TARGET:: nodes(:)
       REAL(8), DIMENSION(1:3):: r1, r2
 
       self%n = n
-      self%n1 => mesh%nodes(p(1))%obj
+      self%nNodes = SIZE(p)
-      self%n2 => mesh%nodes(p(2))%obj
+      self%n1 => nodes(p(1))%obj
+      self%n2 => nodes(p(2))%obj
       !Get element coordinates
       r1 = self%n1%getCoordinates()
       r2 = self%n2%getCoordinates()
       self%r = (/ r1(1), r2(1) /)
 
       !Assign node volume
-      CALL self%area()
+      CALL self%calculateVolume()
-      self%n1%v = self%n1%v + self%arNodes(1)
-      self%n2%v = self%n2%v + self%arNodes(2)
-
-      self%sigmaVrelMax = sigma_ref/L_ref**2
 
       CALL OMP_INIT_LOCK(self%lock)
 
-    END SUBROUTINE initVol1DRadSegm
+      ALLOCATE(self%listPart_in(1:nSpecies))
+      ALLOCATE(self%totalWeight(1:nSpecies))
 
-    !Calculates a random position in 1D volume
+    END SUBROUTINE initCell1DRadSegm
-    FUNCTION randPos1DRadSeg(self) RESULT(r)
+
+    !Get nodes from 1D volume
+    PURE FUNCTION getNodesSegm(self, nNodes) RESULT(n)
+      IMPLICIT NONE
+
+      CLASS(meshCell1DRadSegm), INTENT(in):: self
+      INTEGER, INTENT(in):: nNodes
+      INTEGER:: n(1:nNodes)
+
+      n = (/ self%n1%n, self%n2%n /)
+
+    END FUNCTION getNodesSegm
+
+    !Random position in 1D volume
+    FUNCTION randPos1DRadSegm(self) RESULT(r)
       USE moduleRandom
       IMPLICIT NONE
 
-      CLASS(meshVol1DRadSegm), INTENT(in):: self
+      CLASS(meshCell1DRadSegm), INTENT(in):: self
       REAL(8):: r(1:3)
-      REAL(8):: xii(1:3)
+      REAL(8):: Xi(1:3)
-      REAL(8), ALLOCATABLE:: fPsi(:)
+      REAL(8):: fPsi(1:2)
 
-      xii(1)   = random(-1.D0, 1.D0)
+      Xi    = 0.D0
-      xii(2:3) = 0.D0
+      Xi(1) = random(-1.D0, 1.D0)
 
-      fPsi = self%fPsi(xii)
+      fPsi = self%fPsi(Xi, 2)
+
+      r    = 0.D0
       r(1) = DOT_PRODUCT(fPsi, self%r)
 
-    END FUNCTION randPos1DRadSeg
+    END FUNCTION randPos1DRadSegm
 
-    !Computes element area
+    !Compute element functions at point Xi
-    PURE SUBROUTINE areaRad(self)
+    PURE FUNCTION fPsiSegm(Xi, nNodes) RESULT(fPsi)
       IMPLICIT NONE
 
-      CLASS(meshVol1DRadSegm), INTENT(inout):: self
+      REAL(8), INTENT(in):: Xi(1:3)
-      REAL(8):: l !element length
+      INTEGER, INTENT(in):: nNodes
-      REAL(8):: fPsi(1:2)
+      REAL(8):: fPsi(1:nNodes)
-      REAL(8):: r
-      REAL(8):: detJ
-      REAL(8):: Xii(1:3)
 
-      self%volume  = 0.D0
+      fPsi = (/ 1.D0 - Xi(1), &
-      self%arNodes = 0.D0
+                1.D0 + Xi(1) /)
-      !1 point Gauss integral
-      Xii = 0.D0
-      fPsi = self%fPsi(Xii)
-      detJ = self%detJac(Xii)
-      r    = DOT_PRODUCT(fPsi, self%r)
-      l = 2.D0*detJ
-      self%volume  =      r*l
-      self%arNodes = fPsi*r*l
 
-    END SUBROUTINE areaRad
+      fPsi    = fPsi * 0.50D0
 
-    !Computes element functions at point xii
+    END FUNCTION fPsiSegm
-    PURE FUNCTION fPsiRad(xi) RESULT(fPsi)
+
+    !Derivative element function at coordinates Xi
+    PURE FUNCTION dPsiSegm(Xi, nNodes) RESULT(dPsi)
       IMPLICIT NONE
 
-      REAL(8), INTENT(in):: xi(1:3)
+      REAL(8), INTENT(in):: Xi(1:3)
-      REAL(8), ALLOCATABLE:: fPsi(:)
+      INTEGER, INTENT(in):: nNodes
+      REAL(8):: dPsi(1:3,1:nNodes)
 
-      ALLOCATE(fPsi(1:2))
+      dPsi = 0.D0
 
-      fPsi(1) = 1.D0 - xi(1)
+      dPsi(1, 1:2) = (/ -5.D-1, 5.D-1 /)
-      fPsi(2) = 1.D0 + xi(1)
-      fPsi    = fPsi * 5.D-1
 
-    END FUNCTION fPsiRad
+    END FUNCTION dPsiSegm
 
-    !Computes element derivative shape function at Xii
+    !Partial derivative in global coordinates
-    PURE FUNCTION dPsiRad(xi) RESULT(dPsi)
+    PURE FUNCTION partialDerSegm(self, nNodes, dPsi) RESULT(pDer)
       IMPLICIT NONE
 
-      REAL(8), INTENT(in):: xi(1:3)
+      CLASS(meshCell1DRadSegm), INTENT(in):: self
-      REAL(8), ALLOCATABLE:: dPsi(:,:)
+      INTEGER, INTENT(in):: nNodes
+      REAL(8), INTENT(in):: dPsi(1:3,1:nNodes)
+      REAL(8):: pDer(1:3, 1:3)
 
-      ALLOCATE(dPsi(1:1, 1:2))
+      pDer = 0.D0
 
-      dPsi(1, 1) = -5.D-1
+      pDer(1,1) = DOT_PRODUCT(dPsi(1,1:2), self%r(1:2))
-      dPsi(1, 2) =  5.D-1
+      pDer(2,2) = 1.D0
+      pDer(3,3) = 1.D0
 
-    END FUNCTION dPsiRad
+    END FUNCTION partialDerSegm
 
-    !Computes partial derivatives of coordinates
+    PURE FUNCTION gatherEFSegm(self, Xi) RESULT(array)
-    PURE SUBROUTINE partialDerRad(self, dPsi, dx)
       IMPLICIT NONE
-
+      CLASS(meshCell1DRadSegm), INTENT(in):: self
-      CLASS(meshVol1DRadSegm), INTENT(in):: self
+      REAL(8), INTENT(in):: Xi(1:3)
-      REAL(8), INTENT(in):: dPsi(1:,1:)
+      REAL(8):: array(1:3)
-      REAL(8), INTENT(out), DIMENSION(1):: dx
-
-      dx(1) = DOT_PRODUCT(dPsi(1,:), self%r)
-
-    END SUBROUTINE partialDerRad
-
-    !Computes local stiffness matrix
-    PURE FUNCTION elemKRad(self) RESULT(ke)
-      USE moduleConstParam, ONLY: PI2
-      IMPLICIT NONE
-
-      CLASS(meshVol1DRadSegm), INTENT(in):: self
-      REAL(8):: ke(1:2,1:2)
-      REAL(8):: Xii(1:3)
-      REAL(8):: dPsi(1:1, 1:2)
-      REAL(8):: invJ
-      REAL(8):: r, fPsi(1:2)
-
-      ke      = 0.D0
-      Xii     = 0.D0
-      dPsi    = self%dPsi(Xii)
-      invJ    = self%invJac(Xii, dPsi)
-      fPsi    = self%fPsi(Xii)
-      r       = DOT_PRODUCT(fPsi, self%r)
-      ke(1,:) = (/ dPsi(1,1)*dPsi(1,1), dPsi(1,1)*dPsi(1,2) /) 
-      ke(2,:) = (/ dPsi(1,2)*dPsi(1,1), dPsi(1,2)*dPsi(1,2) /) 
-      ke      = 2.D0*ke*invJ
-      ke      = ke*r*PI2
-
-    END FUNCTION elemKRad
-
-    PURE FUNCTION elemFRad(self, source) RESULT(localF)
-      USE moduleConstParam, ONLY: PI2
-      IMPLICIT NONE
-
-      CLASS(meshVol1DRadSegm), INTENT(in):: self
-      REAL(8), INTENT(in):: source(1:)
-      REAL(8), ALLOCATABLE:: localF(:)
-      REAL(8):: fPsi(1:2)
-      REAL(8):: r
-      REAL(8):: detJ
-      REAL(8):: Xii(1:3)
-
-      Xii    = 0.D0
-      fPsi   = self%fPsi(Xii)
-      detJ   = self%detJac(Xii)
-      r      = DOT_PRODUCT(fPsi,self%r)
-      ALLOCATE(localF(1:2))
-      localF = 2.D0*DOT_PRODUCT(fPsi, source)*detJ
-      localF = localF*r*PI2
-
-    END FUNCTION elemFRad
-
-    PURE FUNCTION weightRad(xi) RESULT(w)
-      IMPLICIT NONE
-
-      REAL(8), INTENT(in):: xi(1:3)
-      REAL(8):: w(1:2)
-
-      w = fPsiRad(xi)
-
-    END FUNCTION weightRad
-
-    PURE FUNCTION insideRad(xi) RESULT(ins)
-      IMPLICIT NONE
-
-      REAL(8), INTENT(in):: xi(1:3)
-      LOGICAL:: ins
-
-      ins = xi(1) >=-1.D0 .AND. &
-            xi(1) <= 1.D0
-
-    END FUNCTION insideRad
-
-    SUBROUTINE scatterRad(self, part)
-      USE moduleOutput
-      USE moduleSpecies
-      IMPLICIT NONE
-
-      CLASS(meshVol1DRadSegm), INTENT(in):: self
-      CLASS(particle), INTENT(in):: part
-      TYPE(outputNode), POINTER:: vertex
-      REAL(8):: w_p(1:2)
-      REAL(8):: tensorS(1:3,1:3)
-
-      w_p = self%weight(part%xi)
-      tensorS = outerProduct(part%v, part%v)
-
-      vertex => self%n1%output(part%sp)
-      vertex%den          = vertex%den          + part%weight*w_p(1)
-      vertex%mom(:)       = vertex%mom(:)       + part%weight*w_p(1)*part%v(:)
-      vertex%tensorS(:,:) = vertex%tensorS(:,:) + part%weight*w_p(1)*tensorS
-
-      vertex => self%n2%output(part%sp)
-      vertex%den          = vertex%den          + part%weight*w_p(2)
-      vertex%mom(:)       = vertex%mom(:)       + part%weight*w_p(2)*part%v(:)
-      vertex%tensorS(:,:) = vertex%tensorS(:,:) + part%weight*w_p(2)*tensorS
-
-    END SUBROUTINE scatterRad
-
-    !Gathers EF at position Xii
-    PURE FUNCTION gatherEFRad(self, xi) RESULT(EF)
-      IMPLICIT NONE
-
-      CLASS(meshVol1DRadSegm), INTENT(in):: self
-      REAL(8), INTENT(in):: xi(1:3)
-      REAL(8):: dPsi(1, 1:2)
       REAL(8):: phi(1:2)
-      REAL(8):: EF(1:3)
-      REAL(8):: invJ
 
       phi = (/ self%n1%emData%phi, &
                self%n2%emData%phi /)
 
-      dPsi  =  self%dPsi(xi)
+      array = -self%gatherDF(Xi, 2, phi)
-      invJ  =  self%invJac(xi, dPsi)
-      EF(1) = -DOT_PRODUCT(dPsi(1, :), phi)*invJ
-      EF(2) =  0.D0
-      EF(3) =  0.D0
 
-    END FUNCTION gatherEFRad
+    END FUNCTION gatherEFSegm
 
-    !Get nodes from 1D volume
+    PURE FUNCTION gatherMFSegm(self, Xi) RESULT(array)
-    PURE FUNCTION getNodesRad(self) RESULT(n)
+      IMPLICIT NONE
+      CLASS(meshCell1DRadSegm), INTENT(in):: self
+      REAL(8), INTENT(in):: Xi(1:3)
+      REAL(8):: array(1:3)
+      REAL(8):: B(1:2,1:3)
+
+      B(:,1) = (/ self%n1%emData%B(1), &
+                  self%n2%emData%B(1) /)
+
+      B(:,2) = (/ self%n1%emData%B(2), &
+                  self%n2%emData%B(2) /)
+
+      B(:,3) = (/ self%n1%emData%B(3), &
+                  self%n2%emData%B(3) /)
+
+      array = self%gatherF(Xi, 2, B)
+
+    END FUNCTION gatherMFSegm
+
+    !Compute element local stiffness matrix
+    PURE FUNCTION elemKSegm(self, nNodes) RESULT(localK)
+      USE moduleConstParam, ONLY: PI2
       IMPLICIT NONE
 
-      CLASS(meshVol1DRadSegm), INTENT(in):: self
+      CLASS(meshCell1DRadSegm), INTENT(in):: self
-      INTEGER, ALLOCATABLE:: n(:)
+      INTEGER, INTENT(in):: nNodes
+      REAL(8):: localK(1:nNodes,1:nNodes)
+      REAL(8):: Xi(1:3)
+      REAL(8):: dPsi(1:3, 1:2)
+      REAL(8):: pDer(1:3, 1:3)
+      REAL(8):: r
+      REAL(8):: invJ(1:3, 1:3), detJ
+      INTEGER:: l
 
-      ALLOCATE(n(1:2))
+      localK = 0.D0
-      n = (/ self%n1%n, self%n2%n /)
 
-    END FUNCTION getNodesRad
+      Xi = 0.D0
+      !Start 1D Gauss Quad Integral
+      DO l = 1, 3
+        Xi(1)  = corSeg(l)
+        dPsi   = self%dPsi(Xi, 2)
+        pDer   = self%partialDer(2, dPsi)
+        detJ   = self%detJac(pDer)
+        invJ   = self%invJac(pDer)
+        r      = self%gatherF(Xi, 2, self%r)
+        localK = localK + MATMUL(TRANSPOSE(MATMUL(invJ,dPsi)), &
+                                           MATMUL(invJ,dPsi))* &
+                          r*wSeg(l)/detJ
 
-    PURE FUNCTION phy2logRad(self, r) RESULT(xN)
+      END DO
+      localK = localK*PI2
+
+    END FUNCTION elemKSegm
+
+    !Compute the local source vector for a force f
+    PURE FUNCTION elemFSegm(self, nNodes, source) RESULT(localF)
+      USE moduleConstParam, ONLY: PI2
       IMPLICIT NONE
 
-      CLASS(meshVol1DRadSegm), INTENT(in):: self
+      CLASS(meshCell1DRadSegm), INTENT(in):: self
+      INTEGER, INTENT(in):: nNodes
+      REAL(8), INTENT(in):: source(1:nNodes)
+      REAL(8):: localF(1:nNodes)
+      REAL(8):: fPsi(1:2)
+      REAL(8):: dPsi(1:3, 1:2), pDer(1:3, 1:3)
+      REAL(8):: Xi(1:3)
+      REAL(8):: detJ, f
+      REAL(8):: r
+      INTEGER:: l
+
+      localF = 0.D0
+
+      Xi = 0.D0
+      !Start 1D Gauss Quad Integral
+      DO l = 1, 3
+        Xi(1) = corSeg(l)
+        dPsi   = self%dPsi(Xi, 2)
+        pDer   = self%partialDer(2, dPsi)
+        detJ   = self%detJac(pDer)
+        fPsi   = self%fPsi(Xi, 2)
+        r      = DOT_PRODUCT(fPsi, self%r)
+        f      = DOT_PRODUCT(fPsi, source)
+        localF = localF + r*f*fPsi*wSeg(l)*detJ
+
+      END DO
+      localF = localF*PI2
+
+    END FUNCTION elemFSegm
+
+    PURE FUNCTION insideSegm(Xi) RESULT(ins)
+      IMPLICIT NONE
+
+      REAL(8), INTENT(in):: Xi(1:3)
+      LOGICAL:: ins
+
+      ins = Xi(1) >=-1.D0 .AND. &
+            Xi(1) <= 1.D0
+
+    END FUNCTION insideSegm
+
+    PURE FUNCTION phy2logSegm(self, r) RESULT(Xi)
+      IMPLICIT NONE
+
+      CLASS(meshCell1DRadSegm), INTENT(in):: self
       REAL(8), INTENT(in):: r(1:3)
-      REAL(8):: xN(1:3)
+      REAL(8):: Xi(1:3)
 
-      xN = 0.D0
+      Xi = 0.D0
-      xN(1) = 2.D0*(r(1) - self%r(1))/(self%r(2) - self%r(1)) - 1.D0
 
-    END FUNCTION phy2logRad
+      Xi(1) = 2.D0*(r(1) - self%r(1))/(self%r(2) - self%r(1)) - 1.D0
 
-    !Get next element for a logical position xi
+    END FUNCTION phy2logSegm
-    SUBROUTINE nextElementRad(self, xi, nextElement)
+
+    !Get the next element for a logical position Xi
+    SUBROUTINE neighbourElementSegm(self, Xi, neighbourElement)
       IMPLICIT NONE
 
-      CLASS(meshVol1DRadSegm), INTENT(in):: self
+      CLASS(meshCell1DRadSegm), INTENT(in):: self
-      REAL(8), INTENT(in):: xi(1:3)
+      REAL(8), INTENT(in):: Xi(1:3)
-      CLASS(*), POINTER, INTENT(out):: nextElement
+      CLASS(meshElement), POINTER, INTENT(out):: neighbourElement
       
-      NULLIFY(nextElement)
+      NULLIFY(neighbourElement)
-      IF     (xi(1) < -1.D0) THEN
+      IF     (Xi(1) < -1.D0) THEN
-        nextElement => self%e2
+        neighbourElement => self%e2
 
-      ELSEIF (xi(1) >  1.D0) THEN
+      ELSEIF (Xi(1) >  1.D0) THEN
-        nextElement => self%e1
+        neighbourElement => self%e1
 
       END IF
 
-    END SUBROUTINE nextElementRad
+    END SUBROUTINE neighbourElementSegm
+
+    !Compute element volume
+    PURE SUBROUTINE volumeSegm(self)
+      USE moduleConstParam, ONLY: PI4
+      IMPLICIT NONE
+
+      CLASS(meshCell1DRadSegm), INTENT(inout):: self
+      REAL(8):: Xi(1:3)
+      REAL(8):: dPsi(1:3, 1:2), pDer(1:3, 1:3)
+      REAL(8):: detJ
+      REAL(8):: fPsi(1:2)
+      REAL(8):: r
+
+      self%volume  = 0.D0
+      !1D 1 point Gauss Quad Integral
+      Xi = 0.D0
+      dPsi = self%dPsi(Xi, 2)
+      pDer = self%partialDer(2, dPsi)
+      detJ = self%detJac(pDer)
+      fPsi = self%fPsi(Xi, 2)
+      r = DOT_PRODUCT(fPsi, self%r)
+      !Compute total volume of the cell
+      self%volume  = r*detJ*PI4 !2*2PI
+      !Compute volume per node
+      Xi = (/-5.D-1,  0.D0, 0.D0/)
+      r = self%gatherF(Xi, 2, self%r)
+      self%n1%v = self%n1%v + fPsi(1)*r*detJ*PI4
+      Xi = (/ 5.D-1,  0.D0, 0.D0/)
+      r = self%gatherF(Xi, 2, self%r)
+      self%n2%v = self%n2%v + fPsi(2)*r*detJ*PI4
+
+    END SUBROUTINE volumeSegm
 
     !COMMON FUNCTIONS FOR 1D VOLUME ELEMENTS
-    !Computes the element Jacobian determinant
+    !Compute element Jacobian determinant
-    PURE FUNCTION detJ1DRad(self, xi, dPsi_in) RESULT(dJ)
+    PURE FUNCTION detJ1DRad(pDer) RESULT(dJ)
       IMPLICIT NONE
 
-      CLASS(meshVol1DRad), INTENT(in):: self
+      REAL(8), INTENT(in):: pDer(1:3, 1:3)
-      REAL(8), INTENT(in):: xi(1:3)
-      REAL(8), INTENT(in), OPTIONAL:: dPsi_in(1:,1:)
-      REAL(8), ALLOCATABLE:: dPsi(:,:)
       REAL(8):: dJ
-      REAL(8):: dx(1)
 
-      IF (PRESENT(dPsi_in)) THEN
+      dJ = pDer(1, 1)
-        dPsi = dPsi_in
-
-      ELSE
-        dPsi = self%dPsi(xi)
-
-      END IF
-
-      CALL self%partialDer(dPsi, dx)
-      dJ = dx(1)
 
     END FUNCTION detJ1DRad
 
-    !Computes the invers Jacobian
+    !Compute element Jacobian inverse matrix (without determinant)
-    PURE FUNCTION invJ1DRad(self, xi, dPsi_in) RESULT(invJ)
+    PURE FUNCTION invJ1DRad(pDer) RESULT(invJ)
       IMPLICIT NONE
 
-      CLASS(meshVol1DRad), INTENT(in):: self
+      REAL(8), INTENT(in):: pDer(1:3, 1:3)
-      REAL(8), INTENT(in):: xi(1:3)
+      REAL(8):: invJ(1:3,1:3)
-      REAL(8), INTENT(in), OPTIONAL:: dPsi_in(1:,1:)
-      REAL(8), ALLOCATABLE:: dPsi(:,:)
-      REAL(8):: dx(1)
-      REAL(8):: invJ
 
-      IF (PRESENT(dPsi_in)) THEN
+      invJ = 0.D0
-        dPsi = dPsi_in
 
-      ELSE
+      invJ(1, 1) = 1.D0/pDer(1, 1)
-        dPsi = self%dPsi(xi)
+      invJ(2, 2) = 1.D0
-
+      invJ(3, 3) = 1.D0
-      END IF
-
-      CALL self%partialDer(dPsi, dx)
-      invJ = 1.D0/dx(1)
 
     END FUNCTION invJ1DRad
 
+    SUBROUTINE connectMesh1DRad(self)
+      IMPLICIT NONE
+
+      CLASS(meshGeneric), INTENT(inout):: self
+      INTEGER:: e, et
+
+      DO e = 1, self%numCells
+        !Connect Cell-Cell
+        DO et = 1, self%numCells
+          IF (e /= et) THEN
+            CALL connectCellCell(self%cells(e)%obj, self%cells(et)%obj)
+
+          END IF
+
+        END DO
+
+        SELECT TYPE(self)
+        TYPE IS(meshParticles)
+          !Connect Cell-Edge
+          DO et = 1, self%numEdges
+            CALL connectCellEdge(self%cells(e)%obj, self%edges(et)%obj)
+
+          END DO
+
+        END SELECT
+
+      END DO
+
+    END SUBROUTINE connectMesh1DRad
+
+    SUBROUTINE connectCellCell(elemA, elemB)
+      IMPLICIT NONE
+
+      CLASS(meshCell), INTENT(inout):: elemA
+      CLASS(meshCell), INTENT(inout):: elemB
+
+        SELECT TYPE(elemA)
+        TYPE IS(meshCell1DRadSegm)
+          SELECT TYPE(elemB)
+          TYPE IS(meshCell1DRadSegm)
+            CALL connectSegmSegm(elemA, elemB)
+
+          END SELECT
+
+        END SELECT
+
+    END SUBROUTINE connectCellCell
+
+    SUBROUTINE connectSegmSegm(elemA, elemB)
+      IMPLICIT NONE
+
+      CLASS(meshCell1DRadSegm), INTENT(inout), TARGET:: elemA
+      CLASS(meshCell1DRadSegm), INTENT(inout), TARGET:: elemB
+
+      IF (.NOT. ASSOCIATED(elemA%e1) .AND. &
+          elemA%n2%n == elemB%n1%n) THEN
+        elemA%e1 => elemB
+        elemB%e2 => elemA
+        
+      END IF
+
+      IF (.NOT. ASSOCIATED(elemA%e2) .AND. &
+          elemA%n1%n == elemB%n2%n) THEN
+
+        elemA%e2 => elemB
+        elemB%e1 => elemA
+
+      END IF
+
+    END SUBROUTINE connectSegmSegm
+
+    SUBROUTINE connectCellEdge(elemA, elemB)
+      IMPLICIT NONE
+
+      CLASS(meshCell),  INTENT(inout):: elemA
+      CLASS(meshEdge), INTENT(inout):: elemB
+
+      SELECT TYPE(elemA)
+      TYPE IS (meshCell1DRadSegm)
+        SELECT TYPE(elemB)
+        CLASS IS(meshEdge1DRad)
+          CALL connectSegmEdge(elemA, elemB)
+
+        END SELECT
+
+      END SELECT
+
+    END SUBROUTINE connectCellEdge
+
+    SUBROUTINE connectSegmEdge(elemA, elemB)
+      IMPLICIT NONE
+
+      CLASS(meshCell1DRadSegm), INTENT(inout), TARGET:: elemA
+      CLASS(meshEdge1DRad),    INTENT(inout), TARGET:: elemB
+
+      IF (.NOT. ASSOCIATED(elemA%e1) .AND. &
+          elemA%n2%n == elemB%n1%n) THEN
+
+        elemA%e1 => elemB
+        elemB%e2 => elemA
+
+        !Rever the normal to point inside the domain
+        elemB%normal = - elemB%normal
+
+      END IF
+
+      IF (.NOT. ASSOCIATED(elemA%e2) .AND. &
+          elemA%n1%n == elemB%n1%n) THEN
+
+        elemA%e2 => elemB
+        elemB%e1 => elemA
+
+      END IF
+
+    END SUBROUTINE connectSegmEdge
+
 END MODULE moduleMesh1DRad
 

src/modules/mesh/1DRad/moduleMesh1DRadBoundary.f90

@@ -1,93 +0,0 @@
-SUBMODULE (moduleMesh1DRad) moduleMesh1DRadBoundary
-  USE moduleMesh1DRad
-
-  CONTAINS
-    SUBROUTINE reflection(edge, part)
-      USE moduleSpecies
-      IMPLICIT NONE
-
-      CLASS(meshEdge), INTENT(inout):: edge
-      CLASS(particle), INTENT(inout):: part
-
-      SELECT TYPE(edge)
-      TYPE IS(meshEdge1DRad)
-        part%v(1) = -part%v(1)
-        part%r(1) =  2.D0*edge%r - part%r(1)
-
-      END SELECT
-
-      part%n_in = .TRUE.
-
-    END SUBROUTINE reflection
-
-    SUBROUTINE absorption(edge, part)
-      USE moduleSpecies
-      IMPLICIT NONE
-
-      CLASS(meshEdge), INTENT(inout):: edge
-      CLASS(particle), INTENT(inout):: part
-      REAL(8):: rEdge(1) !Position of particle in the edge
-      REAL(8):: d !Distance from particle to edge
-
-      SELECT TYPE(edge)
-      TYPE IS(meshEdge1DRad)
-        rEdge(1) = edge%r
-        d = DABS(part%r(1) - rEdge(1))
-
-        IF (d > 0.D0) THEN
-          part%weight = part%weight / d
-          part%r(1)   = rEdge(1)
-
-        END IF
-
-        IF (ASSOCIATED(edge%e1)) THEN
-          CALL edge%e1%scatter(part)
-
-        ELSE
-          CALL edge%e2%scatter(part)
-
-        END IF
-
-      END SELECT
-
-      part%n_in = .FALSE.
-
-    END SUBROUTINE absorption
-
-    SUBROUTINE transparent(edge, part)
-      USE moduleSpecies
-      IMPLICIT NONE
-
-      CLASS(meshEdge), INTENT(inout):: edge
-      CLASS(particle), INTENT(inout):: part
-
-      part%n_in = .FALSE.
-
-    END SUBROUTINE transparent
-
-    SUBROUTINE wallTemperature(edge, part)
-      USE moduleSpecies
-      USE moduleBoundary
-      USE moduleRandom
-      IMPLICIT NONE
-
-      CLASS(meshEdge), INTENT(inout):: edge
-      CLASS(particle), INTENT(inout):: part
-
-      !Modifies particle velocity according to wall temperature
-      SELECT TYPE(bound => edge%boundary%bTypes(part%sp)%obj)
-      TYPE IS(boundaryWallTemperature)
-        part%v(1) = part%v(1) + bound%vTh*randomMaxwellian()
-
-      END SELECT
-
-      SELECT TYPE(edge)
-      TYPE IS(meshEdge1DRad)
-        part%v(1) = -part%v(1)
-        part%r(1) =  2.D0*edge%r - part%r(1)
-
-      END SELECT
-
-    END SUBROUTINE wallTemperature
-
-END SUBMODULE moduleMesh1DRadBoundary

src/modules/mesh/1DRad/moduleMesh1DRadRead.f90

@@ -1,261 +0,0 @@
-MODULE moduleMesh1DRadRead
-  USE moduleMesh
-  USE moduleMesh1DRad
-  
-  !TODO: make this abstract to allow different mesh formats
-  TYPE, EXTENDS(meshGeneric):: mesh1DRadGeneric
-    CONTAINS
-      PROCEDURE, PASS:: init     => init1DRadMesh
-      PROCEDURE, PASS:: readMesh => readMesh1DRad
-
-  END TYPE
-
-  INTERFACE connected
-    MODULE PROCEDURE connectedVolVol, connectedVolEdge
-
-  END INTERFACE connected
-
-  CONTAINS
-    !Init 1D mesh
-    SUBROUTINE init1DRadMesh(self, meshFormat)
-      USE moduleMesh
-      USE moduleErrors
-      IMPLICIT NONE
-
-      CLASS(mesh1DRadGeneric), INTENT(out):: self
-      CHARACTER(:), ALLOCATABLE, INTENT(in):: meshFormat
-
-      SELECT CASE(meshFormat)
-      CASE ("gmsh")
-        self%printOutput => printOutputGmsh
-        self%printColl   => printCollGmsh
-        self%printEM     => printEMGmsh
-
-      CASE DEFAULT
-        CALL criticalError("Mesh type " // meshFormat // " not supported.", "init1DRad")
-        
-      END SELECT
-
-    END SUBROUTINE init1DRadMesh
-
-    !Reads 1D mesh
-    SUBROUTINE readMesh1DRad(self, filename)
-      USE  moduleBoundary
-      IMPLICIT NONE
-
-      CLASS(mesh1DRadGeneric), INTENT(inout):: self
-      CHARACTER(:), ALLOCATABLE, INTENT(in):: filename
-      REAL(8):: x
-      INTEGER:: p(1:2)
-      INTEGER:: e, et, n, eTemp, elemType, bt
-      INTEGER:: totalNumElem
-      INTEGER:: boundaryType
-
-      !Open file mesh
-      OPEN(10, FILE=TRIM(filename))
-      !Skip header
-      READ(10, *)
-      READ(10, *)
-      READ(10, *)
-      READ(10, *)
-      !Read number of nodes
-      READ(10, *) self%numNodes
-      !Allocate required matrices and vectors
-      ALLOCATE(self%nodes(1:self%numNodes))
-      ALLOCATE(self%K(1:self%numNodes, 1:self%numNodes))
-      ALLOCATE(self%IPIV(1:self%numNodes, 1:self%numNodes))
-      self%K = 0.D0
-      self%IPIV = 0
-      !Read nodes coordinates. Only relevant for x
-      DO e = 1, self%numNodes
-        READ(10, *) n, x
-        ALLOCATE(meshNode1DRad:: self%nodes(n)%obj)
-        CALL self%nodes(n)%obj%init(n, (/ x, 0.D0, 0.D0 /))
-
-      END DO
-      !Skips comments
-      READ(10, *)
-      READ(10, *)
-      !Reads the total number of elements (edges+vol)
-      READ(10, *) totalNumElem
-      self%numEdges = 0
-      DO e = 1, totalNumElem
-        READ(10, *) eTemp, elemType
-        IF (elemType == 15) THEN !15 is physical node in GMSH
-          self%numEdges = e
-
-        END IF
-
-      END DO
-
-      !Substract the number of edges to the total number of elements
-      !to obtain the number of volume elements
-      self%numVols = totalNumelem - self%numEdges
-      !Allocates arrays
-      ALLOCATE(self%edges(1:self%numEdges))
-      ALLOCATE(self%vols(1:self%numVols))
-
-      !Go back to the beginning of reading elements
-      DO e = 1, totalNumelem
-        BACKSPACE(10)
-
-      END DO
-
-      !Reads edges
-      DO e = 1, self%numEdges
-        READ(10, *) n, elemType, eTemp, boundaryType, eTemp, p(1)
-        !Associate boundary condition 
-        bt = getBoundaryId(boundaryType)
-
-        ALLOCATE(meshEdge1DRad:: self%edges(e)%obj)
-
-        CALL self%edges(e)%obj%init(n, p(1:1), bt, boundaryType)
-
-      END DO
-
-      !Read and initialize volumes
-      DO e = 1, self%numVols
-        READ(10, *) n, elemType, eTemp, eTemp, eTemp, p(1:2)
-        ALLOCATE(meshVol1DRadSegm:: self%vols(e)%obj)
-        CALL self%vols(e)%obj%init(n - self%numEdges, p(1:2))
-
-      END DO
-
-      CLOSE(10)
-
-      !Build connectivity between elements
-      DO e = 1, self%numVols
-        !Connectivity between volumes
-        DO et = 1, self%numVols
-          IF (e /= et) THEN
-            CALL connected(self%vols(e)%obj, self%vols(et)%obj)
-
-          END IF
-
-        END DO
-
-        !Connectivity betwen vols and edges
-        DO et = 1, self%numEdges
-          CALL connected(self%vols(e)%obj, self%edges(et)%obj)
-
-        END DO
-
-        !Constructs the global K matrix
-        CALL constructGlobalK(self%K, self%vols(e)%obj)
-
-      END DO
-
-    END SUBROUTINE readMesh1DRad
-
-    SUBROUTINE connectedVolVol(elemA, elemB)
-      IMPLICIT NONE
-
-      CLASS(meshVol), INTENT(inout):: elemA
-      CLASS(meshVol), INTENT(inout):: elemB
-
-        SELECT TYPE(elemA)
-        TYPE IS(meshVol1DRadSegm)
-          SELECT TYPE(elemB)
-          TYPE IS(meshVol1DRadSegm)
-            CALL connectedSegmSegm(elemA, elemB)
-
-          END SELECT
-
-        END SELECT
-
-    END SUBROUTINE connectedVolVol
-
-    SUBROUTINE connectedSegmSegm(elemA, elemB)
-      IMPLICIT NONE
-
-      CLASS(meshVol1DRadSegm), INTENT(inout), TARGET:: elemA
-      CLASS(meshVol1DRadSegm), INTENT(inout), TARGET:: elemB
-
-      IF (.NOT. ASSOCIATED(elemA%e1) .AND. &
-          elemA%n2%n == elemB%n1%n) THEN
-        elemA%e1 => elemB
-        elemB%e2 => elemA
-        
-      END IF
-
-      IF (.NOT. ASSOCIATED(elemA%e2) .AND. &
-          elemA%n1%n == elemB%n2%n) THEN
-
-        elemA%e2 => elemB
-        elemB%e1 => elemA
-
-      END IF
-
-    END SUBROUTINE connectedSegmSegm
-
-    SUBROUTINE connectedVolEdge(elemA, elemB)
-      IMPLICIT NONE
-
-      CLASS(meshVol),  INTENT(inout):: elemA
-      CLASS(meshEdge), INTENT(inout):: elemB
-
-      SELECT TYPE(elemA)
-      TYPE IS (meshVol1DRadSegm)
-        SELECT TYPE(elemB)
-        CLASS IS(meshEdge1DRad)
-          CALL connectedSegmEdge(elemA, elemB)
-
-        END SELECT
-
-      END SELECT
-
-    END SUBROUTINE connectedVolEdge
-
-    SUBROUTINE connectedSegmEdge(elemA, elemB)
-      IMPLICIT NONE
-
-      CLASS(meshVol1DRadSegm), INTENT(inout), TARGET:: elemA
-      CLASS(meshEdge1DRad),    INTENT(inout), TARGET:: elemB
-
-      IF (.NOT. ASSOCIATED(elemA%e1) .AND. &
-          elemA%n2%n == elemB%n1%n) THEN
-
-        elemA%e1 => elemB
-        elemB%e2 => elemA
-
-      END IF
-
-      IF (.NOT. ASSOCIATED(elemA%e2) .AND. &
-          elemA%n1%n == elemB%n1%n) THEN
-
-        elemA%e2 => elemB
-        elemB%e1 => elemA
-
-      END IF
-
-    END SUBROUTINE connectedSegmEdge
-
-    SUBROUTINE constructGlobalK(K, elem)
-      IMPLICIT NONE
-
-      REAL(8), INTENT(inout):: K(1:,1:)
-      CLASS(meshVol), INTENT(in):: elem
-      REAL(8):: localK(1:2,1:2)
-      INTEGER:: i, j
-      INTEGER:: n(1:2)
-
-      SELECT TYPE(elem)
-      TYPE IS(meshVol1DRadSegm)
-        localK = elem%elemK()
-        n = (/ elem%n1%n, elem%n2%n /)
-
-      CLASS DEFAULT
-        n = 0
-        localK = 0.D0
-
-      END SELECT
-      
-      DO i = 1, 2
-        DO j = 1, 2
-          K(n(i), n(j)) = K(n(i), n(j)) + localK(i, j)
-        END DO
-      END DO
-
-    END SUBROUTINE constructGlobalK
-
-END MODULE moduleMesh1DRadRead

src/modules/mesh/2DCart/makefile

@@ -0,0 +1,5 @@
+all : moduleMesh2DCart.o
+
+moduleMesh2DCart.o: moduleMesh2DCart.f90
+	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
+

src/modules/mesh/2DCyl/makefile

@@ -1,11 +1,5 @@
-all : moduleMeshCyl.o moduleMeshCylBoundary.o moduleMeshCylRead.o
+all : moduleMesh2DCyl.o
 
-moduleMeshCyl.o: moduleMeshCyl.f90
+moduleMesh2DCyl.o: moduleMesh2DCyl.f90
-	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
-
-moduleMeshCylBoundary.o: moduleMeshCyl.o moduleMeshCylBoundary.f90
-	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
-
-moduleMeshCylRead.o: moduleMeshCyl.o moduleMeshCylBoundary.o moduleMeshCylRead.f90
 	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
 

src/modules/mesh/2DCyl/moduleMeshCylBoundary.f90

@@ -1,164 +0,0 @@
-!moduleMeshCylBoundary: Boundary functions for cylindrical coordinates
-SUBMODULE (moduleMeshCyl) moduleMeshCylBoundary
-  USE moduleMeshCyl
-
-  CONTAINS
-    SUBROUTINE reflection(edge, part)
-      USE moduleSpecies
-      IMPLICIT NONE
-
-      CLASS(meshEdge), INTENT(inout):: edge
-      CLASS(particle), INTENT(inout):: part
-      REAL(8):: edgeNorm, cosT, sinT, rp(1:2), rpp(1:2), vpp(1:2)
-
-      !TODO: Try to do this without select
-      SELECT TYPE(edge)
-      TYPE IS(meshEdgeCyl)
-        edgeNorm = DSQRT((edge%r(2)-edge%r(1))**2 + (edge%z(2)-edge%z(1))**2)
-        cosT = (edge%z(2)-edge%z(1))/edgeNorm
-        sinT = DSQRT(1-cosT**2)
-
-        rp(1) = part%r(1) - edge%z(1);
-        rp(2) = part%r(2) - edge%r(1);
-
-        rpp(1) = cosT*rp(1) - sinT*rp(2)
-        rpp(2) = sinT*rp(1) + cosT*rp(2)
-        rpp(2) = -rpp(2)
-
-        vpp(1) = cosT*part%v(1) - sinT*part%v(2)
-        vpp(2) = sinT*part%v(1) + cosT*part%v(2)
-        vpp(2) = -vpp(2)
-
-        part%r(1) =  cosT*rpp(1) + sinT*rpp(2) + edge%z(1);
-        part%r(2) = -sinT*rpp(1) + cosT*rpp(2) + edge%r(1);
-        part%v(1) =  cosT*vpp(1) + sinT*vpp(2)
-        part%v(2) = -sinT*vpp(1) + cosT*vpp(2)
-
-      END SELECT
-
-      part%n_in = .TRUE.
-
-    END SUBROUTINE reflection
-
-    !Absoption in a surface
-    SUBROUTINE absorption(edge, part)
-      USE moduleSpecies
-      IMPLICIT NONE
-
-      CLASS(meshEdge), INTENT(inout):: edge
-      CLASS(particle), INTENT(inout):: part
-      REAL(8):: rEdge(1:2) !Position of particle projected to the edge
-      REAL(8):: a, b, c
-      REAL(8):: a2b2
-      REAL(8):: d !Distance from particle to edge
-
-      SELECT TYPE(edge)
-      TYPE IS(meshEdgeCyl)
-        a = (edge%z(1) - edge%z(2))
-        b = (edge%r(1) - edge%r(2))
-        c =  edge%z(1)*edge%r(2) - edge%z(2)*edge%r(1)
-
-        a2b2 = a**2 + b**2
-
-        rEdge(1) = (b*( b*part%r(1) - a*part%r(2)) - a*c)/a2b2
-        rEdge(2) = (a*(-b*part%r(1) + a*part%r(2)) - b*c)/a2b2
-
-        d = NORM2(rEdge - part%r(1:2))
-        !Reduce weight of particle by the distance to the edge and move it to the edge
-        IF (d > 0.D0) THEN
-          part%weight = part%weight / d
-          part%r(1:2) = rEdge
-
-        END IF
-
-        !Scatter particle in associated volume
-        IF (ASSOCIATED(edge%e1)) THEN
-          CALL edge%e1%scatter(part)
-
-        ELSE
-          CALL edge%e2%scatter(part)
-
-        END IF
-
-      END SELECT
-
-      !Remove particle from the domain
-      part%n_in = .FALSE.
-
-    END SUBROUTINE absorption
-
-    !Transparent boundary condition
-    SUBROUTINE transparent(edge, part)
-      USE moduleSpecies
-      IMPLICIT NONE
-
-      CLASS(meshEdge), INTENT(inout):: edge
-      CLASS(particle), INTENT(inout):: part
-
-      !Removes particle from domain
-      part%n_in = .FALSE.
-
-    END SUBROUTINE transparent
-
-    !Wall with temperature
-    SUBROUTINE wallTemperature(edge, part)
-      USE moduleSpecies
-      USE moduleBoundary
-      USE moduleRandom
-      IMPLICIT NONE
-
-      CLASS(meshEdge), INTENT(inout):: edge
-      CLASS(particle), INTENT(inout):: part
-      REAL(8):: edgeNorm, cosT, sinT, rp(1:2), rpp(1:2), vpp(1:2)
-      INTEGER:: i
-
-      !Modifies particle velocity according to wall temperature
-      SELECT TYPE(bound => edge%boundary%bTypes(part%sp)%obj)
-      TYPE IS(boundaryWallTemperature)
-        DO i = 1, 3
-          part%v(i) = part%v(i) + bound%vTh*randomMaxwellian()
-
-        END DO
-          
-      END SELECT
-
-      !Reflects particle in the edge
-      SELECT TYPE(edge)
-      TYPE IS(meshEdgeCyl)
-        edgeNorm = DSQRT((edge%r(2)-edge%r(1))**2 + (edge%z(2)-edge%z(1))**2)
-        cosT = (edge%z(2)-edge%z(1))/edgeNorm
-        sinT = DSQRT(1-cosT**2)
-
-        rp(1) = part%r(1) - edge%z(1);
-        rp(2) = part%r(2) - edge%r(1);
-
-        rpp(1) = cosT*rp(1) - sinT*rp(2)
-        rpp(2) = sinT*rp(1) + cosT*rp(2)
-        rpp(2) = -rpp(2)
-
-        vpp(1) = cosT*part%v(1) - sinT*part%v(2)
-        vpp(2) = sinT*part%v(1) + cosT*part%v(2)
-        vpp(2) = -vpp(2)
-
-        part%r(1) =  cosT*rpp(1) + sinT*rpp(2) + edge%z(1);
-        part%r(2) = -sinT*rpp(1) + cosT*rpp(2) + edge%r(1);
-        part%v(1) =  cosT*vpp(1) + sinT*vpp(2)
-        part%v(2) = -sinT*vpp(1) + cosT*vpp(2)
-
-      END SELECT
-
-      part%n_in = .TRUE.
-
-    END SUBROUTINE wallTemperature
-
-    !Symmetry axis. Dummy function
-    SUBROUTINE symmetryAxis(edge, part)
-      USE moduleSpecies
-      IMPLICIT NONE
-
-      CLASS(meshEdge), INTENT(inout):: edge
-      CLASS(particle), INTENT(inout):: part
-
-    END SUBROUTINE symmetryAxis
-
-END SUBMODULE moduleMeshCylBoundary

src/modules/mesh/2DCyl/moduleMeshCylRead.f90

@@ -1,599 +0,0 @@
-MODULE moduleMeshCylRead
-  USE moduleMesh
-  USE moduleMeshCyl
-
-  TYPE, EXTENDS(meshGeneric):: meshCylGeneric
-    CONTAINS
-      PROCEDURE, PASS:: init     => initCylMesh
-      PROCEDURE, PASS:: readMesh => readMeshCylGmsh
-
-  END TYPE
-
-  INTERFACE connected
-    MODULE PROCEDURE connectedVolVol, connectedVolEdge
-
-  END INTERFACE connected
-
-  CONTAINS
-    !Init mesh
-    SUBROUTINE initCylMesh(self, meshFormat)
-      USE moduleMesh
-      USE moduleErrors
-      IMPLICIT NONE
-
-      CLASS(meshCylGeneric), INTENT(out):: self
-      CHARACTER(:), ALLOCATABLE, INTENT(in):: meshFormat
-
-      SELECT CASE(meshFormat)
-      CASE ("gmsh")
-        self%printOutput => printOutputGmsh
-        self%printColl   => printCollGmsh
-        self%printEM     => printEMGmsh
-
-      CASE DEFAULT
-        CALL criticalError("Mesh type " // meshFormat // " not supported.", "initCylMesh")
-        
-      END SELECT
-
-    END SUBROUTINE initCylMesh
-
-    !Read mesh from gmsh file
-    SUBROUTINE readMeshCylGmsh(self, filename)
-      USE moduleBoundary
-      IMPLICIT NONE
-
-      CLASS(meshCylGeneric), INTENT(inout):: self
-      CHARACTER(:), ALLOCATABLE, INTENT(in):: filename
-      REAL(8):: r, z
-      INTEGER:: p(1:4)
-      INTEGER:: e=0, et=0, n=0, eTemp=0, elemType=0, bt = 0
-      INTEGER:: totalNumElem
-      INTEGER:: boundaryType
-
-      !Read msh
-      OPEN(10, FILE=TRIM(filename))
-      !Skip header
-      READ(10, *)
-      READ(10, *)
-      READ(10, *)
-      READ(10, *)
-      !Read number of nodes
-      READ(10, *) self%numNodes
-      !Allocate required matrices and vectors
-      ALLOCATE(self%nodes(1:self%numNodes))
-      ALLOCATE(self%K(1:self%numNodes,1:self%numNodes))
-      ALLOCATE(self%IPIV(1:self%numNodes,1:self%numNodes))
-      self%K = 0.D0
-      self%IPIV = 0
-      !Read nodes cartesian coordinates (x=z, y=r, z=null)
-      DO e=1, self%numNodes
-        READ(10, *) n, z, r
-        ALLOCATE(meshNodeCyl:: self%nodes(n)%obj)
-        CALL self%nodes(n)%obj%init(n, (/r, z, 0.D0 /))
-
-      END DO
-      !Skips comments
-      READ(10, *)
-      READ(10, *)
-      !Reads Totalnumber of elements
-      READ(10, *) TotalnumElem
-      !counts edges and volume elements
-      self%numEdges = 0
-      DO e=1, TotalnumElem
-        READ(10,*) eTemp, elemType
-        IF (elemType==1) THEN
-          self%numEdges=e
-        END IF
-      END DO
-      !Substract the number of edges to the total number of elements
-      !to obtain the number of volume elements
-      self%numVols = TotalnumElem - self%numEdges
-      !Allocates arrays
-      ALLOCATE(self%edges(1:self%numEdges))
-      ALLOCATE(self%vols(1:self%numVols))
-
-      !Go back to the beggining to read elements
-      DO e=1, totalNumElem
-        BACKSPACE(10)
-      END DO
-
-      !Reads edges
-      DO e=1, self%numEdges
-        READ(10,*) n, elemType, eTemp, boundaryType, eTemp, p(1:2)
-        !Associate boundary condition procedure.
-        bt = getBoundaryId(boundaryType)
-
-        ALLOCATE(meshEdgeCyl:: self%edges(e)%obj)
-
-        CALL self%edges(e)%obj%init(n, p(1:2), bt, boundaryType)
-
-      END DO
-
-      !Read and initialize volumes
-      DO e=1, self%numVols
-        READ(10,*) n, elemType
-        BACKSPACE(10)
-
-        SELECT CASE(elemType)
-        CASE (2)
-          !Triangular element
-          READ(10,*) n, elemType, eTemp, eTemp, eTemp, p(1:3)
-          ALLOCATE(meshVolCylTria:: self%vols(e)%obj)
-          CALL self%vols(e)%obj%init(n - self%numEdges, p(1:3))
-
-        CASE (3)
-          !Quadrilateral element
-          READ(10,*) n, elemType, eTemp, eTemp, eTemp, p(1:4)
-          ALLOCATE(meshVolCylQuad:: self%vols(e)%obj)
-          CALL self%vols(e)%obj%init(n - self%numEdges, p(1:4))
-
-        END SELECT
-
-      END DO
-
-      CLOSE(10)
-
-      !Build connectivity between elements
-      DO e = 1, self%numVols
-        !Connectivity between volumes
-        DO et = 1, self%numVols
-          IF (e /= et) THEN
-            CALL connected(self%vols(e)%obj, self%vols(et)%obj)
-
-          END IF
-        END DO
-
-        !Connectivity between vols and edges
-        DO et = 1, self%numEdges
-          CALL connected(self%vols(e)%obj, self%edges(et)%obj)
-
-        END DO
-
-        !Constructs the global K matrix
-        CALL constructGlobalK(self%K, self%vols(e)%obj)
-
-      END DO
-
-    END SUBROUTINE readMeshCylGmsh
-
-    !Selects type of elements to build connection
-    SUBROUTINE connectedVolVol(elemA, elemB)
-      IMPLICIT NONE
-
-      CLASS(meshVol), INTENT(inout):: elemA
-      CLASS(meshVol), INTENT(inout):: elemB
-
-      SELECT TYPE(elemA)
-      TYPE IS(meshVolCylQuad)
-        !Element A is a quadrilateral
-        SELECT TYPE(elemB)
-        TYPE IS(meshVolCylQuad)
-          !Element B is a quadrilateral
-          CALL connectedQuadQuad(elemA, elemB)
-
-        TYPE IS(meshVolCylTria)
-          !Element B is a triangle
-          CALL connectedQuadTria(elemA, elemB)
-
-        END SELECT
-
-      TYPE IS(meshVolCylTria)
-        !Element A is a Triangle
-        SELECT TYPE(elemB)
-        TYPE IS(meshVolCylQuad)
-          !Element B is a quadrilateral
-          CALL connectedQuadTria(elemB, elemA)
-
-        TYPE IS(meshVolCylTria)
-          !Element B is a triangle
-          CALL connectedTriaTria(elemA, elemB)
-
-        END SELECT
-
-      END SELECT
-
-    END SUBROUTINE connectedVolVol
-
-    SUBROUTINE connectedVolEdge(elemA, elemB)
-      IMPLICIT NONE
-
-      CLASS(meshVol),  INTENT(inout):: elemA
-      CLASS(meshEdge), INTENT(inout):: elemB
-
-      SELECT TYPE(elemB)
-      CLASS IS(meshEdgeCyl)
-        SELECT TYPE(elemA)
-        TYPE IS(meshVolCylQuad)
-          !Element A is a quadrilateral
-          CALL connectedQuadEdge(elemA, elemB)
-
-        TYPE IS(meshVolCylTria)
-          !Element A is a triangle
-          CALL connectedTriaEdge(elemA, elemB)
-
-        END SELECT
-
-      END SELECT
-
-    END SUBROUTINE connectedVolEdge
-
-    SUBROUTINE connectedQuadQuad(elemA, elemB)
-      IMPLICIT NONE
-
-      CLASS(meshVolCylQuad), INTENT(inout), TARGET:: elemA
-      CLASS(meshVolCylQuad), INTENT(inout), TARGET:: elemB
-
-      !Check direction 1
-      IF (.NOT. ASSOCIATED(elemA%e1) .AND. &
-          elemA%n1%n == elemB%n4%n   .AND. &
-          elemA%n2%n == elemB%n3%n) THEN
-        elemA%e1 => elemB
-        elemB%e3 => elemA
-
-      END IF
-
-      !Check direction 2
-      IF (.NOT. ASSOCIATED(elemA%e2) .AND. &
-          elemA%n2%n == elemB%n1%n   .AND. &
-          elemA%n3%n == elemB%n4%n) THEN
-        elemA%e2 => elemB
-        elemB%e4 => elemA
-
-      END IF
-
-      !Check direction 3
-      IF (.NOT. ASSOCIATED(elemA%e3) .AND. &
-          elemA%n3%n == elemB%n2%n   .AND. &
-          elemA%n4%n == elemB%n1%n) THEN
-        elemA%e3 => elemB
-        elemB%e1 => elemA
-
-      END IF
-
-      !Check direction 4
-      IF (.NOT. ASSOCIATED(elemA%e4) .AND. &
-          elemA%n4%n == elemB%n3%n   .AND. &
-          elemA%n1%n == elemB%n2%n) THEN
-        elemA%e4 => elemB
-        elemB%e2 => elemA
-
-      END IF
-
-    END SUBROUTINE connectedQuadQuad
-
-    SUBROUTINE connectedQuadTria(elemA, elemB)
-      IMPLICIT NONE
-
-      CLASS(meshVolCylQuad), INTENT(inout), TARGET:: elemA
-      CLASS(meshVolCylTria), INTENT(inout), TARGET:: elemB
-
-      !Check direction 1
-      IF (.NOT. ASSOCIATED(elemA%e1)) THEN
-        IF     (elemA%n1%n == elemB%n1%n .AND. &
-                elemA%n2%n == elemB%n3%n) THEN
-          elemA%e1 => elemB
-          elemB%e3 => elemA
-
-        ELSEIF (elemA%n1%n == elemB%n3%n .AND. &
-                elemA%n2%n == elemB%n2%n) THEN
-          elemA%e1 => elemB
-          elemB%e2 => elemA
-
-        ELSEIF (elemA%n1%n == elemB%n2%n .AND. &
-                elemA%n2%n == elemB%n1%n) THEN
-          elemA%e1 => elemB
-          elemB%e1 => elemA
-
-        END IF
-
-      END IF
-
-      !Check direction 2
-      IF (.NOT. ASSOCIATED(elemA%e2)) THEN
-        IF     (elemA%n2%n == elemB%n1%n .AND. &
-                elemA%n3%n == elemB%n3%n) THEN
-          elemA%e2 => elemB
-          elemB%e3 => elemA
-
-        ELSEIF (elemA%n2%n == elemB%n3%n .AND. &
-                elemA%n3%n == elemB%n2%n) THEN
-          elemA%e2 => elemB
-          elemB%e2 => elemA
-
-        ELSEIF (elemA%n2%n == elemB%n2%n .AND. &
-                elemA%n3%n == elemB%n1%n) THEN
-          elemA%e2 => elemB
-          elemB%e1 => elemA
-
-        END IF
-
-      END IF
-
-      !Check direction 3
-      IF (.NOT. ASSOCIATED(elemA%e3)) THEN
-        IF     (elemA%n3%n == elemB%n1%n .AND. &
-                elemA%n4%n == elemB%n3%n) THEN
-          elemA%e3 => elemB
-          elemB%e3 => elemA
-
-        ELSEIF (elemA%n3%n == elemB%n3%n .AND. &
-                elemA%n4%n == elemB%n2%n) THEN
-          elemA%e3 => elemB
-          elemB%e2 => elemA
-
-        ELSEIF (elemA%n3%n == elemB%n2%n .AND. &
-                elemA%n4%n == elemB%n1%n) THEN
-          elemA%e3 => elemB
-          elemB%e1 => elemA
-
-        END IF
-
-      END IF
-
-      !Check direction 4
-      IF (.NOT. ASSOCIATED(elemA%e4)) THEN
-        IF     (elemA%n4%n == elemB%n1%n .AND. &
-                elemA%n1%n == elemB%n3%n) THEN
-          elemA%e4 => elemB
-          elemB%e3 => elemA
-
-        ELSEIF (elemA%n4%n == elemB%n3%n .AND. &
-                elemA%n1%n == elemB%n2%n) THEN
-          elemA%e4 => elemB
-          elemB%e2 => elemA
-
-        ELSEIF (elemA%n4%n == elemB%n2%n .AND. &
-                elemA%n1%n == elemB%n1%n) THEN
-          elemA%e4 => elemB
-          elemB%e1 => elemA
-
-        END IF
-
-      END IF
-
-    END SUBROUTINE connectedQuadTria
-
-    SUBROUTINE connectedTriaTria(elemA, elemB)
-      IMPLICIT NONE
-
-      CLASS(meshVolCylTria), INTENT(inout), TARGET:: elemA
-      CLASS(meshVolCylTria), INTENT(inout), TARGET:: elemB
-
-      !Check direction 1
-      IF (.NOT. ASSOCIATED(elemA%e1)) THEN
-        IF     (elemA%n1%n == elemB%n1%n .AND. &
-                elemA%n2%n == elemB%n3%n) THEN
-          elemA%e1 => elemB
-          elemB%e3 => elemA
-
-        ELSEIF (elemA%n1%n == elemB%n2%n .AND. &
-                elemA%n2%n == elemB%n1%n) THEN
-          elemA%e1 => elemB
-          elemB%e1 => elemA
-
-        ELSEIF (elemA%n1%n == elemB%n3%n .AND. &
-                elemA%n2%n == elemB%n2%n) THEN
-          elemA%e1 => elemB
-          elemB%e2 => elemA
-
-        END IF
-
-      END IF
-
-      !Check direction 2
-      IF (.NOT. ASSOCIATED(elemA%e2)) THEN
-        IF     (elemA%n2%n == elemB%n1%n .AND. &
-                elemA%n3%n == elemB%n3%n) THEN
-          elemA%e2 => elemB
-          elemB%e3 => elemA
-
-        ELSEIF (elemA%n2%n == elemB%n2%n .AND. &
-                elemA%n3%n == elemB%n1%n) THEN
-          elemA%e2 => elemB
-          elemB%e1 => elemA
-
-        ELSEIF (elemA%n2%n == elemB%n3%n .AND. &
-                elemA%n3%n == elemB%n2%n) THEN
-          elemA%e2 => elemB
-          elemB%e2 => elemA
-
-        END IF
-
-
-      END IF
-
-      !Check direction 3
-      IF (.NOT. ASSOCIATED(elemA%e3)) THEN
-        IF     (elemA%n3%n == elemB%n1%n .AND. &
-                elemA%n1%n == elemB%n3%n) THEN
-          elemA%e3 => elemB
-          elemB%e3 => elemA
-
-        ELSEIF (elemA%n3%n == elemB%n2%n .AND. &
-                elemA%n1%n == elemB%n1%n) THEN
-          elemA%e3 => elemB
-          elemB%e1 => elemA
-
-        ELSEIF (elemA%n3%n == elemB%n3%n .AND. &
-                elemA%n1%n == elemB%n2%n) THEN
-          elemA%e3 => elemB
-          elemB%e2 => elemA
-
-        END IF
-
-
-      END IF
-
-    END SUBROUTINE connectedTriaTria
-
-    SUBROUTINE connectedQuadEdge(elemA, elemB)
-      IMPLICIT NONE
-
-      CLASS(meshVolCylQuad), INTENT(inout), TARGET:: elemA
-      CLASS(meshEdgeCyl),    INTENT(inout), TARGET:: elemB
-
-      !Check direction 1
-      IF (.NOT. ASSOCIATED(elemA%e1)) THEN
-        IF     (elemA%n1%n == elemB%n1%n .AND. &
-                elemA%n2%n == elemB%n2%n) THEN
-          elemA%e1 => elemB
-          elemB%e2 => elemA
-
-        ELSEIF (elemA%n1%n == elemB%n2%n .AND. &
-                elemA%n2%n == elemB%n1%n) THEN
-          elemA%e1 => elemB
-          elemB%e1 => elemA
-
-        END IF
-
-      END IF
-
-      !Check direction 2
-      IF (.NOT. ASSOCIATED(elemA%e2)) THEN
-        IF     (elemA%n2%n == elemB%n1%n .AND. &
-                elemA%n3%n == elemB%n2%n) THEN
-          elemA%e2 => elemB
-          elemB%e2 => elemA
-
-        ELSEIF (elemA%n2%n == elemB%n2%n .AND. &
-                elemA%n3%n == elemB%n1%n) THEN
-          elemA%e2 => elemB
-          elemB%e1 => elemA
-
-        END IF
-
-      END IF
-
-      !Check direction 3
-      IF (.NOT. ASSOCIATED(elemA%e3)) THEN
-        IF     (elemA%n3%n == elemB%n1%n .AND. &
-                elemA%n4%n == elemB%n2%n) THEN
-          elemA%e3 => elemB
-          elemB%e2 => elemA
-
-        ELSEIF (elemA%n3%n == elemB%n2%n .AND. &
-                elemA%n4%n == elemB%n1%n) THEN
-          elemA%e3 => elemB
-          elemB%e1 => elemA
-
-        END IF
-
-      END IF
-
-      !Check direction 4
-      IF (.NOT. ASSOCIATED(elemA%e4)) THEN
-        IF     (elemA%n4%n == elemB%n1%n .AND. &
-                elemA%n1%n == elemB%n2%n) THEN
-          elemA%e4 => elemB
-          elemB%e2 => elemA
-
-        ELSEIF (elemA%n4%n == elemB%n2%n .AND. &
-                elemA%n1%n == elemB%n1%n) THEN
-          elemA%e4 => elemB
-          elemB%e1 => elemA
-
-        END IF
-
-      END IF
-
-    END SUBROUTINE connectedQuadEdge
-
-    SUBROUTINE connectedTriaEdge(elemA, elemB)
-      IMPLICIT NONE
-
-      CLASS(meshVolCylTria), INTENT(inout), TARGET:: elemA
-      CLASS(meshEdgeCyl),    INTENT(inout), TARGET:: elemB
-
-      !Check direction 1
-      IF (.NOT. ASSOCIATED(elemA%e1)) THEN
-        IF     (elemA%n1%n == elemB%n1%n .AND. &
-                elemA%n2%n == elemB%n2%n) THEN
-          elemA%e1 => elemB
-          elemB%e2 => elemA
-
-        ELSEIF (elemA%n1%n == elemB%n2%n .AND. &
-                elemA%n2%n == elemB%n1%n) THEN
-          elemA%e1 => elemB
-          elemB%e1 => elemA
-
-        END IF
-
-      END IF
-
-      !Check direction 2
-      IF (.NOT. ASSOCIATED(elemA%e2)) THEN
-        IF     (elemA%n2%n == elemB%n1%n .AND. &
-                elemA%n3%n == elemB%n2%n) THEN
-          elemA%e2 => elemB
-          elemB%e2 => elemA
-
-        ELSEIF (elemA%n2%n == elemB%n2%n .AND. &
-                elemA%n3%n == elemB%n1%n) THEN
-          elemA%e2 => elemB
-          elemB%e1 => elemA
-
-        END IF
-
-      END IF
-
-      !Check direction 3
-      IF (.NOT. ASSOCIATED(elemA%e3)) THEN
-        IF     (elemA%n3%n == elemB%n1%n .AND. &
-                elemA%n1%n == elemB%n2%n) THEN
-          elemA%e3 => elemB
-          elemB%e2 => elemA
-
-        ELSEIF (elemA%n3%n == elemB%n2%n .AND. &
-                elemA%n1%n == elemB%n1%n) THEN
-          elemA%e3 => elemB
-          elemB%e1 => elemA
-
-        END IF
-
-      END IF
-
-    END SUBROUTINE connectedTriaEdge
-
-    SUBROUTINE constructGlobalK(K, elem)
-      IMPLICIT NONE
-
-      REAL(8), INTENT(inout):: K(1:,1:)
-      CLASS(meshVol), INTENT(in):: elem
-      REAL(8), ALLOCATABLE:: localK(:,:)
-      INTEGER:: nNodes, i, j
-      INTEGER, ALLOCATABLE:: n(:)
-
-      SELECT TYPE(elem)
-      TYPE IS(meshVolCylQuad)
-        nNodes = 4
-        ALLOCATE(localK(1:nNodes,1:nNodes))
-        localK = elem%elemK()
-        ALLOCATE(n(1:nNodes))
-        n = (/ elem%n1%n, elem%n2%n, &
-               elem%n3%n, elem%n4%n /)
-
-      TYPE IS(meshVolCylTria)
-        nNodes = 3
-        ALLOCATE(localK(1:nNodes,1:nNodes))
-        localK = elem%elemK()
-        ALLOCATE(n(1:nNodes))
-        n = (/ elem%n1%n, elem%n2%n, elem%n3%n /)
-
-      CLASS DEFAULT
-        nNodes = 0
-        ALLOCATE(localK(1:1, 1:1))
-        localK = 0.D0
-        ALLOCATE(n(1:1))
-        n = 0
-
-      END SELECT
-      
-      DO i = 1, nNodes
-        DO j = 1, nNodes
-          K(n(i), n(j)) = K(n(i), n(j)) + localK(i, j)
-        END DO
-      END DO
-
-    END SUBROUTINE constructGlobalK
-
-END MODULE moduleMeshCylRead

src/modules/mesh/3DCart/makefile

@@ -0,0 +1,5 @@
+all : moduleMesh3DCart.o
+
+moduleMesh3DCart.o: moduleMesh3DCart.f90
+	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
+

src/modules/mesh/3DCart/moduleMesh3DCart.f90

@@ -0,0 +1,951 @@
+!moduleMesh3DCart: 3D Cartesian coordinate system
+!                  x == x
+!                  y == y
+!                  z == z
+MODULE moduleMesh3DCart
+  USE moduleMesh
+  USE moduleMeshBoundary
+  IMPLICIT NONE
+
+  TYPE, PUBLIC, EXTENDS(meshNode):: meshNode3DCart
+    !Element coordinates
+    REAL(8):: x, y, z
+    CONTAINS
+      !meshNode DEFERRED PROCEDURES
+      PROCEDURE, PASS:: init           => initNode3DCart
+      PROCEDURE, PASS:: getCoordinates => getCoord3DCart
+
+  END TYPE meshNode3DCart
+
+  !Triangular surface element
+  TYPE, PUBLIC, EXTENDS(meshEdge):: meshEdge3DCartTria
+    !Element coordinates
+    REAL(8):: x(1:3) = 0.D0, y(1:3) = 0.D0, z(1:3) = 0.D0
+    !Connectivity to nodes
+    CLASS(meshNode), POINTER:: n1 => NULL(), n2 => NULL(), n3 => NULL()
+    CONTAINS
+      !meshEdge DEFERRED PROCEDURES
+      PROCEDURE, PASS::   init         => initEdge3DCartTria
+      PROCEDURE, PASS::   getNodes     => getNodes3DCartTria
+      PROCEDURE, PASS::   intersection => intersection3DCartTria
+      PROCEDURE, PASS::   randPos      => randPosEdgeTria
+      !PARTICULAR PROCEDURES
+      PROCEDURE, NOPASS, PRIVATE:: fPsi => fPsiEdgeTria
+
+  END TYPE meshEdge3DCartTria
+
+  !Tetrahedron volume element
+  TYPE, PUBLIC, EXTENDS(meshCell):: meshCell3DCartTetra
+    !Element Coordinates
+    REAL(8):: x(1:4) = 0.D0, y(1:4) = 0.D0, z(1:4) = 0.D0
+    !Connectivity to nodes
+    CLASS(meshNode), POINTER:: n1 => NULL(), n2 => NULL(), n3 => NULL(), n4 => NULL()
+    !Connectivity to adjacent elements
+    CLASS(meshElement), POINTER:: e1 => NULL(), e2 => NULL(), e3 => NULL(), e4 => NULL()
+    CONTAINS
+      !meshCell DEFERRED PROCEDURES
+      PROCEDURE, PASS::   init                => initCellTetra
+      PROCEDURE, PASS::   getNodes            => getNodesTetra
+      PROCEDURE, PASS::   randPos             => randPosCellTetra
+      PROCEDURE, NOPASS:: fPsi                => fPsiTetra
+      PROCEDURE, NOPASS:: dPsi                => dPsiTetra
+      PROCEDURE, PASS::   partialDer          => partialDerTetra
+      PROCEDURE, NOPASS:: detJac              => detJ3DCart
+      PROCEDURE, NOPASS:: invJac              => invJ3DCart
+      PROCEDURE, PASS::   gatherElectricField => gatherEFTetra
+      PROCEDURE, PASS::   gatherMagneticField => gatherMFTetra
+      PROCEDURE, PASS::   elemK               => elemKTetra
+      PROCEDURE, PASS::   elemF               => elemFTetra
+      PROCEDURE, NOPASS:: inside              => insideTetra
+      PROCEDURE, PASS::   phy2log             => phy2logTetra
+      PROCEDURE, PASS::   neighbourElement    => neighbourElementTetra
+      !PARTICULAR PROCEDURES
+      PROCEDURE, PASS, PRIVATE:: calculateVolume => volumeTetra
+      
+  END TYPE meshCell3DCartTetra
+
+  CONTAINS
+    !NODE FUNCTIONS
+    !Init node element
+    SUBROUTINE initNode3DCart(self, n, r)
+      USE moduleSpecies
+      USE moduleRefParam
+      USE OMP_LIB
+      IMPLICIT NONE
+
+      CLASS(meshNode3DCart), INTENT(out):: self
+      INTEGER, INTENT(in):: n
+      REAL(8), INTENT(in):: r(1:3)
+
+      self%n = n
+      self%x = r(1)/L_ref
+      self%y = r(2)/L_ref
+      self%z = r(3)/L_ref
+      !Node volume, to be determined in mesh
+      self%v = 0.D0
+
+      !Allocates output:
+      ALLOCATE(self%output(1:nSpecies))
+
+      CALL OMP_INIT_LOCK(self%lock)
+
+    END SUBROUTINE initNode3DCart
+
+    !Get coordinates from node
+    PURE FUNCTION getCoord3DCart(self) RESULT(r)
+      IMPLICIT NONE
+
+      CLASS(meshNode3DCart), INTENT(in):: self
+      REAL(8):: r(1:3)
+
+      r = (/self%x, self%y, self%z/)
+
+    END FUNCTION getCoord3DCart
+
+    !EDGE FUNCTIONS
+    !Init surface element
+    SUBROUTINE initEdge3DCartTria(self, n, p, bt, physicalSurface)
+      USE moduleSpecies
+      USE moduleBoundary
+      USE moduleErrors
+      USE moduleMath
+      USE moduleRefParam, ONLY: L_ref
+      IMPLICIT NONE
+
+      CLASS(meshEdge3DCartTria), INTENT(out):: self
+      INTEGER, INTENT(in):: n
+      INTEGER, INTENT(in):: p(:)
+      INTEGER, INTENT(in):: bt
+      INTEGER, INTENT(in):: physicalSurface
+      REAL(8), DIMENSION(1:3):: r1, r2, r3
+      REAL(8), DIMENSION(1:3):: vec1, vec2
+      INTEGER:: s
+
+      self%n = n
+      self%nNodes = SIZE(p)
+      self%n1 => mesh%nodes(p(1))%obj
+      self%n2 => mesh%nodes(p(2))%obj
+      self%n3 => mesh%nodes(p(3))%obj
+      !Get element coordinates
+      r1 = self%n1%getCoordinates()
+      r2 = self%n2%getCoordinates()
+      r3 = self%n3%getCoordinates()
+      self%x  = (/r1(1), r2(1), r3(1)/)
+      self%y  = (/r1(2), r2(2), r3(2)/)
+      self%z  = (/r1(3), r2(3), r3(3)/)
+      !Normal vector
+      vec1 = (/ self%x(2) - self%x(1), &
+                self%y(2) - self%y(1), &
+                self%z(2) - self%z(1) /)
+      vec2 = (/ self%x(3) - self%x(1), &
+                self%y(3) - self%y(1), &
+                self%z(3) - self%z(1) /)
+      self%normal = crossProduct(vec1, vec2)
+      self%normal = normalize(self%normal)
+
+      self%surface = 1.D0/L_ref**2 !TODO: FIX THIS WHEN MOVING TO 3D
+
+      !Boundary index
+      self%boundary => boundary(bt)
+      ALLOCATE(self%fBoundary(1:nSpecies))
+      !Assign functions to boundary
+      DO s = 1, nSpecies
+        CALL pointBoundaryFunction(self, s)
+
+      END DO
+
+      !Physical surface
+      self%physicalSurface = physicalSurface
+
+    END SUBROUTINE initEdge3DCartTria
+
+    !Get nodes from surface
+    PURE FUNCTION getNodes3DCartTria(self, nNodes) RESULT(n)
+      IMPLICIT NONE
+
+      CLASS(meshEdge3DCartTria), INTENT(in):: self
+      INTEGER, INTENT(in):: nNodes
+      INTEGER:: n(1:nNodes)
+
+      n = (/self%n1%n, self%n2%n, self%n3%n/)
+
+    END FUNCTION getNodes3DCartTria
+
+    !Calculate intersection between position and edge
+    PURE FUNCTION intersection3DCartTria(self, r0) RESULT(r)
+      IMPLICIT NONE
+
+      CLASS(meshEdge3DCartTria), INTENT(in):: self
+      REAL(8), INTENT(in):: r0(1:3)
+      REAL(8), DIMENSION(1:3):: r
+      REAL(8), DIMENSION(1:3):: edge0, edgeV
+      REAL(8):: tI
+
+      edge0 = (/self%x(1), self%y(1), self%z(1) /)
+      edgeV = (/self%x(2), self%y(2), self%z(2) /) - edge0
+
+      tI = DOT_PRODUCT(r0 - edge0, edgeV)/DOT_PRODUCT(edgeV, edgeV)
+
+      r = edge0 + tI*edgeV
+
+    END FUNCTION intersection3DCartTria
+
+    !Calculate a random position in the surface
+    FUNCTION randPosEdgeTria(self) RESULT(r)
+      USE moduleRandom
+      IMPLICIT NONE
+
+      CLASS(meshEdge3DCartTria), INTENT(in):: self
+      REAL(8):: r(1:3)
+      REAL(8):: Xi(1:3)
+      REAL(8):: fPsi(1:3)
+
+      Xi(1) = random( 0.D0, 1.D0)
+      Xi(2) = random( 0.D0, 1.D0 - Xi(1))
+      Xi(3) = 0.D0
+
+      fPsi = self%fPsi(Xi)
+      r = (/DOT_PRODUCT(fPsi, self%x), &
+            DOT_PRODUCT(fPsi, self%y), &
+            DOT_PRODUCT(fPsi, self%z)/)
+
+    END FUNCTION randPosEdgeTria
+
+    !Shape functions for triangular surface
+    PURE FUNCTION fPsiEdgeTria(Xi) RESULT(fPsi)
+      IMPLICIT NONE
+
+      REAL(8), INTENT(in):: Xi(1:3)
+      REAL(8):: fPsi(1:3)
+
+      fPsi(1) = 1.D0 - Xi(1) - Xi(2)
+      fPsi(2) =        Xi(1)
+      fPsi(3) =                Xi(2)
+
+    END FUNCTION fPsiEdgeTria
+
+    !VOLUME FUNCTIONS
+    !TETRA FUNCTIONS
+    !Init element
+    SUBROUTINE initCellTetra(self, n, p, nodes)
+      USE moduleRefParam
+      IMPLICIT NONE
+
+      CLASS(meshCell3DCartTetra), INTENT(out):: self
+      INTEGER, INTENT(in):: n
+      INTEGER, INTENT(in):: p(:)
+      TYPE(meshNodeCont), INTENT(in), TARGET:: nodes(:)
+      REAL(8), DIMENSION(1:3):: r1, r2, r3, r4 !Positions of each node
+
+      !Assign node index
+      self%n  = n
+
+      !Assign number of nodes of cell
+      self%nNodes = SIZE(p)
+
+      !Assign nodes to element
+      self%n1 => nodes(p(1))%obj
+      self%n2 => nodes(p(2))%obj
+      self%n3 => nodes(p(3))%obj
+      self%n4 => nodes(p(4))%obj
+      !Get element coordinates
+      r1 = self%n1%getCoordinates()
+      r2 = self%n2%getCoordinates()
+      r3 = self%n3%getCoordinates()
+      r4 = self%n4%getCoordinates()
+      self%x  = (/r1(1), r2(1), r3(1), r4(1)/)
+      self%y  = (/r1(2), r2(2), r3(2), r4(2)/)
+      self%z  = (/r1(3), r2(3), r3(3), r4(3)/)
+
+      !Computes the element volume
+      CALL self%calculateVolume()
+
+      CALL OMP_INIT_LOCK(self%lock)
+
+      ALLOCATE(self%listPart_in(1:nSpecies))
+      ALLOCATE(self%totalWeight(1:nSpecies))
+
+    END SUBROUTINE initCellTetra
+
+    !Gets node indexes from cell
+    PURE FUNCTION getNodesTetra(self, nNodes) RESULT(n)
+      IMPLICIT NONE
+
+      CLASS(meshCell3DCartTetra), INTENT(in):: self
+      INTEGER, INTENT(in):: nNodes
+      INTEGER:: n(1:nNodes)
+
+      n = (/self%n1%n, self%n2%n, self%n3%n, self%n4%n /)
+
+    END FUNCTION getNodesTetra
+
+    !Random position in cell
+    FUNCTION randPosCellTetra(self) RESULT(r)
+      USE moduleRandom
+      IMPLICIT NONE
+
+      CLASS(meshCell3DCartTetra), INTENT(in):: self
+      REAL(8):: r(1:3)
+      REAL(8):: Xi(1:3)
+      REAL(8):: fPsi(1:4)
+
+      Xi(1) = random( 0.D0, 1.D0)
+      Xi(2) = random( 0.D0, 1.D0 - Xi(1))
+      Xi(3) = random( 0.D0, 1.D0 - Xi(1) - Xi(2))
+
+      fPsi = self%fPsi(Xi, 4)
+
+      r = (/ DOT_PRODUCT(fPsi, self%x), &
+             DOT_PRODUCT(fPsi, self%y), &
+             DOT_PRODUCT(fPsi, self%z) /)
+
+    END FUNCTION randPosCellTetra
+
+    !Compute element functions in point Xi
+    PURE FUNCTION fPsiTetra(Xi, nNodes) RESULT(fPsi)
+      IMPLICIT NONE
+
+      REAL(8), INTENT(in):: Xi(1:3)
+      INTEGER, INTENT(in):: nNodes
+      REAL(8):: fPsi(1:nNodes)
+
+      fPsi(1) = 1.D0 - Xi(1) - Xi(2) - Xi(3)
+      fPsi(2) =        Xi(1)
+      fPsi(3) =                Xi(2)
+      fPsi(4) =                        Xi(3)
+
+    END FUNCTION fPsiTetra
+
+    !Compute element derivative functions in point Xi
+    PURE FUNCTION dPsiTetra(Xi, nNodes) RESULT(dPsi)
+      IMPLICIT NONE
+
+      REAL(8), INTENT(in):: Xi(1:3)
+      INTEGER, INTENT(in):: nNodes
+      REAL(8):: dPsi(1:3, 1:nNodes)
+
+      dPsi = 0.D0
+
+      dPsi(1,1:4) = (/ -1.D0, 1.D0, 0.D0, 0.D0 /)
+      dPsi(2,1:4) = (/ -1.D0, 0.D0, 1.D0, 0.D0 /)
+      dPsi(3,1:4) = (/ -1.D0, 0.D0, 0.D0, 1.D0 /)
+
+    END FUNCTION dPsiTetra
+
+    !Compute the derivatives in global coordinates
+    PURE FUNCTION partialDerTetra(self, nNodes, dPsi) RESULT(pDer)
+      IMPLICIT NONE
+
+      CLASS(meshCell3DCartTetra), INTENT(in):: self
+      INTEGER, INTENT(in):: nNodes
+      REAL(8), INTENT(in):: dPsi(1:3, 1:nNodes)
+      REAL(8):: pDer(1:3, 1:3)
+
+      pDer = 0.D0
+
+      pDer(1, 1:3) = (/ DOT_PRODUCT(dPsi(1,1:4), self%x(1:4)), &
+                        DOT_PRODUCT(dPsi(2,1:4), self%x(1:4)), &
+                        DOT_PRODUCT(dPsi(3,1:4), self%x(1:4)) /)
+
+      pDer(2, 1:3) = (/ DOT_PRODUCT(dPsi(1,1:4), self%y(1:4)), &
+                        DOT_PRODUCT(dPsi(2,1:4), self%y(1:4)), &
+                        DOT_PRODUCT(dPsi(3,1:4), self%y(1:4)) /)
+
+      pDer(3, 1:3) = (/ DOT_PRODUCT(dPsi(1,1:4), self%z(1:4)), &
+                        DOT_PRODUCT(dPsi(2,1:4), self%z(1:4)), &
+                        DOT_PRODUCT(dPsi(3,1:4), self%z(1:4)) /)
+
+    END FUNCTION partialDerTetra
+
+    !Gather electric field at position Xi
+    PURE FUNCTION gatherEFTetra(self, Xi) RESULT(array)
+      IMPLICIT NONE
+      CLASS(meshCell3DCartTetra), INTENT(in):: self
+      REAL(8), INTENT(in):: Xi(1:3)
+      REAL(8):: array(1:3)
+      REAL(8):: phi(1:4)
+
+      phi = (/ self%n1%emData%phi, &
+               self%n2%emData%phi, &
+               self%n3%emData%phi, &
+               self%n4%emData%phi /)
+
+      array = -self%gatherDF(Xi, 4, phi)
+
+    END FUNCTION gatherEFTetra
+
+    !Gather magnetic field at position Xi
+    PURE FUNCTION gatherMFTetra(self, Xi) RESULT(array)
+      IMPLICIT NONE
+      CLASS(meshCell3DCartTetra), INTENT(in):: self
+      REAL(8), INTENT(in):: Xi(1:3)
+      REAL(8):: array(1:3)
+      REAL(8):: B(1:4,1:3)
+
+      B(:,1) = (/ self%n1%emData%B(1), &
+                  self%n2%emData%B(1), &
+                  self%n3%emData%B(1), &
+                  self%n4%emData%B(1) /)
+
+      B(:,2) = (/ self%n1%emData%B(2), &
+                  self%n2%emData%B(2), &
+                  self%n3%emData%B(2), &
+                  self%n4%emData%B(2) /)
+
+      B(:,3) = (/ self%n1%emData%B(3), &
+                  self%n2%emData%B(3), &
+                  self%n3%emData%B(3), &
+                  self%n4%emData%B(3) /)
+
+      array = self%gatherF(Xi, 4, B)
+
+    END FUNCTION gatherMFTetra
+
+    !Compute cell local stiffness matrix
+    PURE FUNCTION elemKTetra(self, nNodes) RESULT(localK)
+      IMPLICIT NONE
+
+      CLASS(meshCell3DCartTetra), INTENT(in):: self
+      INTEGER, INTENT(in):: nNodes
+      REAL(8):: localK(1:nNodes,1:nNodes)
+      REAL(8):: Xi(1:3)
+      REAL(8):: fPsi(1:4), dPsi(1:3, 1:4)
+      REAL(8):: pDer(1:3, 1:3)
+      REAL(8):: invJ(1:3,1:3), detJ
+
+      localK = 0.D0
+      Xi    = 0.D0
+      !TODO: One point Gauss integral. Upgrade when possible
+      Xi     = (/ 0.25D0, 0.25D0, 0.25D0 /)
+      dPsi   = self%dPsi(Xi, 4)
+      pDer   = self%partialDer(4, dPsi)
+      detJ   = self%detJac(pDer)
+      invJ   = self%invJac(pDer)
+      fPsi = self%fPsi(Xi, 4)
+      localK = MATMUL(TRANSPOSE(MATMUL(invJ,dPsi)),MATMUL(invJ,dPsi))*1.D0/detJ
+
+    END FUNCTION elemKTetra
+
+    !Compute element local source vector
+    PURE FUNCTION elemFTetra(self, nNodes, source) RESULT(localF)
+      IMPLICIT NONE
+
+      CLASS(meshCell3DCartTetra), INTENT(in):: self
+      INTEGER, INTENT(in):: nNodes
+      REAL(8), INTENT(in):: source(1:nNodes)
+      REAL(8):: localF(1:nNodes)
+      REAL(8):: Xi(1:3)
+      REAL(8):: fPsi(1:4), dPsi(1:3, 1:4)
+      REAL(8):: pDer(1:3, 1:3)
+      REAL(8):: detJ, f
+
+      localF = 0.D0
+      Xi   = 0.D0
+      Xi   = (/ 0.25D0, 0.25D0, 0.25D0 /)
+      dPsi = self%dPsi(Xi, 4)
+      pDer = self%partialDer(4, dPsi)
+      detJ = self%detJac(pDer)
+      fPsi = self%fPsi(Xi, 4)
+      f    = DOT_PRODUCT(fPsi, source)
+      localF = f*fPsi*1.D0*detJ
+
+    END FUNCTION elemFTetra
+
+    !Check if Xi is inside the element
+    PURE FUNCTION insideTetra(Xi) RESULT(ins)
+      IMPLICIT NONE
+
+      REAL(8), INTENT(in):: Xi(1:3)
+      LOGICAL:: ins
+
+      ins =        Xi(1)                 >= 0.D0 .AND. &
+                           Xi(2)         >= 0.D0 .AND. &
+                                   Xi(3) >= 0.D0 .AND. &
+            1.D0 - Xi(1) - Xi(2) - Xi(3) >= 0.D0
+      
+    END FUNCTION insideTetra
+
+    !Transform physical coordinates to element coordinates
+    PURE FUNCTION phy2logTetra(self,r) RESULT(Xi)
+      IMPLICIT NONE
+
+      CLASS(meshCell3DCartTetra), INTENT(in):: self
+      REAL(8), INTENT(in):: r(1:3)
+      REAL(8):: Xi(1:3)
+      REAL(8):: dPsi(1:3, 1:4)
+      REAL(8):: pDer(1:3, 1:3)
+      REAL(8):: invJ(1:3, 1:3), detJ
+      REAL(8):: deltaR(1:3)
+
+      !Direct method to convert coordinates
+      Xi     = 0.D0
+      deltaR = (/r(1) - self%x(1), r(2) - self%y(1), r(3) - self%z(1) /)
+      dPsi   = self%dPsi(Xi, 4)
+      pDer   = self%partialDer(4, dPsi)
+      invJ   = self%invJac(pDer)
+      detJ   = self%detJac(pDer)
+      Xi     = MATMUL(invJ, deltaR)/detJ
+
+    END FUNCTION phy2logTetra
+    
+    !Get the neighbour cell for a logical position Xi
+    SUBROUTINE neighbourElementTetra(self, Xi, neighbourElement)
+      IMPLICIT NONE
+
+      CLASS(meshCell3DCartTetra), INTENT(in):: self
+      REAL(8), INTENT(in):: Xi(1:3)
+      CLASS(meshElement), POINTER, INTENT(out):: neighbourElement
+      REAL(8):: XiArray(1:4)
+      INTEGER:: nextInt
+
+      !TODO: Review when connectivity
+      XiArray = (/ Xi(3), 1.D0 - Xi(1) - Xi(2) - Xi(3), Xi(2), Xi(1) /)
+      nextInt = MINLOC(XiArray, 1)
+      NULLIFY(neighbourElement)
+      SELECT CASE(nextInt)
+      CASE (1)
+        neighbourElement => self%e1
+      CASE (2)
+        neighbourElement => self%e2
+      CASE (3)
+        neighbourElement => self%e3
+      CASE (4)
+        neighbourElement => self%e4
+      END SELECT
+
+    END SUBROUTINE neighbourElementTetra
+
+    !Calculate volume for triangular element
+    PURE SUBROUTINE volumeTetra(self)
+      IMPLICIT NONE
+
+      CLASS(meshCell3DCartTetra), INTENT(inout):: self
+      REAL(8):: Xi(1:3)
+      REAL(8):: detJ
+      REAL(8):: fPsi(1:4)
+      REAL(8):: dPsi(1:3, 1:4), pDer(1:3, 1:3)
+
+      self%volume = 0.D0
+      !2D 1 point Gauss Quad Integral
+      Xi = (/0.25D0, 0.25D0, 0.25D0/)
+      dPsi = self%dPsi(Xi, 4)
+      pDer = self%partialDer(4, dPsi)
+      detJ = self%detJac(pDer)
+      !Computes total volume of the cell
+      self%volume = detJ
+      !Computes volume per node
+      fPsi = self%fPsi(Xi, 4)
+      self%n1%v = self%n1%v + fPsi(1)*self%volume
+      self%n2%v = self%n2%v + fPsi(2)*self%volume
+      self%n3%v = self%n3%v + fPsi(3)*self%volume
+      self%n4%v = self%n4%v + fPsi(4)*self%volume
+
+    END SUBROUTINE volumeTetra
+
+    !COMMON FUNCTIONS FOR CARTESIAN VOLUME ELEMENTS IN 3D
+    !Compute element Jacobian determinant
+    PURE FUNCTION detJ3DCart(pDer) RESULT(dJ)
+      IMPLICIT NONE
+
+      REAL(8), INTENT(in):: pDer(1:3, 1:3)
+      REAL(8):: dJ
+
+      dJ =   pDer(1,1)*(pDer(2,2)*pDer(3,3) - pDer(2,3)*pDer(3,2)) &
+           - pDer(1,2)*(pDer(2,1)*pDer(3,3) - pDer(2,3)*pDer(3,1)) &
+           + pDer(1,3)*(pDer(2,1)*pDer(3,2) - pDer(2,2)*pDer(3,1))
+
+    END FUNCTION detJ3DCart
+
+    !Compute element Jacobian inverse matrix (without determinant)
+    PURE FUNCTION invJ3DCart(pDer) RESULT(invJ)
+      IMPLICIT NONE
+
+      REAL(8), INTENT(in):: pDer(1:3, 1:3)
+      REAL(8):: invJ(1:3,1:3)
+
+      invJ(1,1:3) =  (/ (pDer(2,2)*pDer(3,3) - pDer(2,3)*pDer(3,2)), &
+                       -(pDer(2,1)*pDer(3,3) - pDer(2,3)*pDer(3,1)), &
+                        (pDer(2,1)*pDer(3,2) - pDer(2,2)*pDer(3,1)) /)
+
+      invJ(2,1:3) = (/ -(pDer(1,2)*pDer(3,3) - pDer(1,3)*pDer(3,2)), &
+                        (pDer(1,1)*pDer(3,3) - pDer(1,3)*pDer(3,1)), &
+                       -(pDer(1,1)*pDer(3,2) - pDer(1,2)*pDer(3,1)) /)
+
+      invJ(3,1:3) =  (/ (pDer(1,2)*pDer(2,3) - pDer(1,3)*pDer(2,2)), &
+                       -(pDer(1,1)*pDer(2,3) - pDer(1,3)*pDer(2,1)), &
+                        (pDer(1,1)*pDer(2,2) - pDer(1,2)*pDer(2,1)) /)
+
+      invJ = TRANSPOSE(invJ)
+
+    END FUNCTION invJ3DCart
+
+    SUBROUTINE connectMesh3DCart(self)
+      IMPLICIT NONE
+
+      CLASS(meshGeneric), INTENT(inout):: self
+      INTEGER:: e, et
+
+      DO e = 1, self%numCells
+        !Connect Cell-Cell
+        DO et = 1, self%numCells
+          IF (e /= et) THEN
+            CALL connectCellCell(self%cells(e)%obj, self%cells(et)%obj)
+
+          END IF
+
+        END DO
+
+        SELECT TYPE(self)
+        TYPE IS(meshParticles)
+          !Connect Cell-Edge
+          DO et = 1, self%numEdges
+            CALL connectCellEdge(self%cells(e)%obj, self%edges(et)%obj)
+
+          END DO
+
+        END SELECT
+
+      END DO
+
+    END SUBROUTINE connectMesh3DCart
+
+    !Select type of elements to build connection
+    SUBROUTINE connectCellCell(elemA, elemB)
+      IMPLICIT NONE
+
+      CLASS(meshCell), INTENT(inout):: elemA
+      CLASS(meshCell), INTENT(inout):: elemB
+
+      SELECT TYPE(elemA)
+      TYPE IS(meshCell3DCartTetra)
+        !Element A is a tetrahedron
+        SELECT TYPE(elemB)
+        TYPE IS(meshCell3DCartTetra)
+          !Element B is a tetrahedron
+          CALL connectTetraTetra(elemA, elemB)
+
+        END SELECT
+
+      END SELECT
+
+    END SUBROUTINE connectCellCell
+
+    SUBROUTINE connectCellEdge(elemA, elemB)
+      IMPLICIT NONE
+
+      CLASS(meshCell),  INTENT(inout):: elemA
+      CLASS(meshEdge), INTENT(inout):: elemB
+
+      SELECT TYPE(elemB)
+      CLASS IS(meshEdge3DCartTria)
+        SELECT TYPE(elemA)
+        TYPE IS(meshCell3DCartTetra)
+          !Element A is a tetrahedron
+          CALL connectTetraEdge(elemA, elemB)
+
+        END SELECT
+
+      END SELECT
+
+    END SUBROUTINE connectCellEdge
+
+    !Checks if two sets of nodes are coincidend in any order
+    PURE FUNCTION coincidentNodes(nodesA, nodesB) RESULT(coincident)
+      IMPLICIT NONE
+
+      INTEGER, DIMENSION(1:3), INTENT(in):: nodesA, nodesB
+      LOGICAL:: coincident
+      INTEGER:: i
+
+      coincident = .FALSE.
+      DO i = 1, 3
+        IF (ANY(nodesA(i) == nodesB)) THEN
+          coincident = .TRUE.
+
+        ELSE
+          coincident = .FALSE.
+          EXIT
+
+        END IF
+
+      END DO
+
+    END FUNCTION coincidentNodes
+
+    SUBROUTINE connectTetraTetra(elemA, elemB)
+      IMPLICIT NONE
+
+      CLASS(meshCell3DCartTetra), INTENT(inout), TARGET:: elemA
+      CLASS(meshCell3DCartTetra), INTENT(inout), TARGET:: elemB
+
+      !Check surface 1
+      IF (.NOT. ASSOCIATED(elemA%e1)) THEN
+        IF     (coincidentNodes((/elemA%n1%n, elemA%n2%n, elemA%n3%n/), &
+                                (/elemB%n1%n, elemB%n2%n, elemB%n3%n/))) THEN
+
+          elemA%e1 => elemB
+          elemB%e1 => elemA
+
+        ELSEIF (coincidentNodes((/elemA%n1%n, elemA%n2%n, elemA%n3%n/), &
+                                (/elemB%n2%n, elemB%n3%n, elemB%n4%n/))) THEN
+
+          elemA%e1 => elemB
+          elemB%e2 => elemA
+
+        ELSEIF (coincidentNodes((/elemA%n1%n, elemA%n2%n, elemA%n3%n/), &
+                                (/elemB%n1%n, elemB%n2%n, elemB%n4%n/))) THEN
+
+          elemA%e1 => elemB
+          elemB%e3 => elemA
+
+        ELSEIF (coincidentNodes((/elemA%n1%n, elemA%n2%n, elemA%n3%n/), &
+                                (/elemB%n1%n, elemB%n3%n, elemB%n4%n/))) THEN
+
+          elemA%e1 => elemB
+          elemB%e4 => elemA
+
+        END IF
+
+      END IF
+
+      !Check surface 2
+      IF (.NOT. ASSOCIATED(elemA%e2)) THEN
+        IF     (coincidentNodes((/elemA%n2%n, elemA%n3%n, elemA%n4%n/), &
+                                (/elemB%n1%n, elemB%n2%n, elemB%n3%n/))) THEN
+
+          elemA%e2 => elemB
+          elemB%e1 => elemA
+
+        ELSEIF (coincidentNodes((/elemA%n2%n, elemA%n3%n, elemA%n4%n/), &
+                                (/elemB%n2%n, elemB%n3%n, elemB%n4%n/))) THEN
+
+          elemA%e2 => elemB
+          elemB%e2 => elemA
+
+        ELSEIF (coincidentNodes((/elemA%n2%n, elemA%n3%n, elemA%n4%n/), &
+                                (/elemB%n1%n, elemB%n2%n, elemB%n4%n/))) THEN
+
+          elemA%e2 => elemB
+          elemB%e3 => elemA
+
+        ELSEIF (coincidentNodes((/elemA%n2%n, elemA%n3%n, elemA%n4%n/), &
+                                (/elemB%n1%n, elemB%n3%n, elemB%n4%n/))) THEN
+
+          elemA%e2 => elemB
+          elemB%e4 => elemA
+
+        END IF
+
+      END IF
+
+      !Check surface 3
+      IF (.NOT. ASSOCIATED(elemA%e3)) THEN
+        IF     (coincidentNodes((/elemA%n1%n, elemA%n2%n, elemA%n4%n/), &
+                                (/elemB%n1%n, elemB%n2%n, elemB%n3%n/))) THEN
+
+          elemA%e3 => elemB
+          elemB%e1 => elemA
+
+        ELSEIF (coincidentNodes((/elemA%n1%n, elemA%n2%n, elemA%n4%n/), &
+                                (/elemB%n2%n, elemB%n3%n, elemB%n4%n/))) THEN
+
+          elemA%e3 => elemB
+          elemB%e2 => elemA
+
+        ELSEIF (coincidentNodes((/elemA%n1%n, elemA%n2%n, elemA%n4%n/), &
+                                (/elemB%n1%n, elemB%n2%n, elemB%n4%n/))) THEN
+
+          elemA%e3 => elemB
+          elemB%e3 => elemA
+
+        ELSEIF (coincidentNodes((/elemA%n1%n, elemA%n2%n, elemA%n4%n/), &
+                                (/elemB%n1%n, elemB%n3%n, elemB%n4%n/))) THEN
+
+          elemA%e3 => elemB
+          elemB%e4 => elemA
+
+        END IF
+
+      END IF
+
+      !Check surface 4
+      IF (.NOT. ASSOCIATED(elemA%e4)) THEN
+        IF     (coincidentNodes((/elemA%n1%n, elemA%n3%n, elemA%n4%n/), &
+                                (/elemB%n1%n, elemB%n2%n, elemB%n3%n/))) THEN
+
+          elemA%e4 => elemB
+          elemB%e1 => elemA
+
+        ELSEIF (coincidentNodes((/elemA%n1%n, elemA%n3%n, elemA%n4%n/), &
+                                (/elemB%n2%n, elemB%n3%n, elemB%n4%n/))) THEN
+
+          elemA%e4 => elemB
+          elemB%e2 => elemA
+
+        ELSEIF (coincidentNodes((/elemA%n1%n, elemA%n3%n, elemA%n4%n/), &
+                                (/elemB%n1%n, elemB%n2%n, elemB%n4%n/))) THEN
+
+          elemA%e4 => elemB
+          elemB%e3 => elemA
+
+        ELSEIF (coincidentNodes((/elemA%n1%n, elemA%n3%n, elemA%n4%n/), &
+                                (/elemB%n1%n, elemB%n3%n, elemB%n4%n/))) THEN
+
+          elemA%e4 => elemB
+          elemB%e4 => elemA
+
+        END IF
+
+      END IF
+
+    END SUBROUTINE connectTetraTetra
+
+    SUBROUTINE connectTetraEdge(elemA, elemB)
+      USE moduleMath
+      IMPLICIT NONE
+
+      CLASS(meshCell3DCartTetra), INTENT(inout), TARGET:: elemA
+      CLASS(meshEdge3DCartTria), INTENT(inout), TARGET:: elemB
+      INTEGER:: nodesEdge(1:3)
+      REAL(8), DIMENSION(1:3):: vec1, vec2
+      REAL(8):: normCell(1:3)
+
+      nodesEdge = (/ elemB%n1%n, elemB%n2%n, elemB%n3%n /)
+
+      !Check surface 1
+      IF (.NOT. ASSOCIATED(elemA%e1)) THEN
+        IF (coincidentNodes((/elemA%n1%n, elemA%n2%n, elema%n3%n/), &
+                              nodesEdge)) THEN
+
+          vec1 = (/ elemA%x(2) - elemA%x(1), &
+                    elemA%y(2) - elemA%y(1), &
+                    elemA%z(2) - elemA%z(1) /)
+          vec2 = (/ elemA%x(3) - elemA%x(1), &
+                    elemA%y(3) - elemA%y(1), &
+                    elemA%z(3) - elemA%z(1) /)
+          normCell = crossProduct(vec1, vec2)
+          normCell = normalize(normCell)
+
+          IF (DOT_PRODUCT(elemB%normal, normCell) == -1.D0) THEN
+
+            elemA%e1 => elemB
+            elemB%e1 => elemA
+
+          ELSE
+
+            elemA%e1 => elemB
+            elemB%e2 => elemA
+
+            !Revers the normal to point inside the domain
+            elemB%normal = -elemB%normal
+
+          END IF
+
+        END IF
+
+      END IF
+
+      !Check surface 2
+      IF (.NOT. ASSOCIATED(elemA%e2)) THEN
+        IF (coincidentNodes((/elemA%n2%n, elemA%n3%n, elemA%n4%n/), &
+                              nodesEdge)) THEN
+
+          vec1 = (/ elemA%x(3) - elemA%x(2), &
+                    elemA%y(3) - elemA%y(2), &
+                    elemA%z(3) - elemA%z(2) /)
+          vec2 = (/ elemA%x(4) - elemA%x(2), &
+                    elemA%y(4) - elemA%y(2), &
+                    elemA%z(4) - elemA%z(2) /)
+          normCell = crossProduct(vec1, vec2)
+          normCell = normalize(normCell)
+
+          IF (DOT_PRODUCT(elemB%normal, normCell) == -1.D0) THEN
+
+            elemA%e2 => elemB
+            elemB%e1 => elemA
+
+          ELSE
+
+            elemA%e2 => elemB
+            elemB%e2 => elemA
+
+            !Revers the normal to point inside the domain
+            elemB%normal = -elemB%normal
+
+          END IF
+
+        END IF
+
+      END IF
+
+      !Check surface 3
+      IF (.NOT. ASSOCIATED(elemA%e3)) THEN
+        IF (coincidentNodes((/elemA%n1%n, elemA%n2%n, elema%n4%n/), &
+                              nodesEdge)) THEN
+
+          vec1 = (/ elemA%x(2) - elemA%x(1), &
+                    elemA%y(2) - elemA%y(1), &
+                    elemA%z(2) - elemA%z(1) /)
+          vec2 = (/ elemA%x(4) - elemA%x(1), &
+                    elemA%y(4) - elemA%y(1), &
+                    elemA%z(4) - elemA%z(1) /)
+          normCell = crossProduct(vec1, vec2)
+          normCell = normalize(normCell)
+
+          IF (DOT_PRODUCT(elemB%normal, normCell) == -1.D0) THEN
+
+            elemA%e3 => elemB
+            elemB%e1 => elemA
+
+          ELSE
+
+            elemA%e3 => elemB
+            elemB%e2 => elemA
+
+            !Revers the normal to point inside the domain
+            elemB%normal = -elemB%normal
+
+          END IF
+
+        END IF
+
+      END IF
+
+      !Check surface 4
+      IF (.NOT. ASSOCIATED(elemA%e4)) THEN
+        IF (coincidentNodes((/elemA%n1%n, elemA%n3%n, elema%n4%n/), &
+                              nodesEdge)) THEN
+
+          vec1 = (/ elemA%x(3) - elemA%x(1), &
+                    elemA%y(3) - elemA%y(1), &
+                    elemA%z(3) - elemA%z(1) /)
+          vec2 = (/ elemA%x(4) - elemA%x(1), &
+                    elemA%y(4) - elemA%y(1), &
+                    elemA%z(4) - elemA%z(1) /)
+          normCell = crossProduct(vec1, vec2)
+          normCell = normalize(normCell)
+
+          IF (DOT_PRODUCT(elemB%normal, normCell) == -1.D0) THEN
+
+            elemA%e4 => elemB
+            elemB%e1 => elemA
+
+
+          ELSE
+
+            elemA%e4 => elemB
+            elemB%e2 => elemA
+
+            !Revers the normal to point inside the domain
+            elemB%normal = -elemB%normal
+
+          END IF
+
+        END IF
+
+      END IF
+
+    END SUBROUTINE connectTetraEdge
+
+END MODULE moduleMesh3DCart
+

src/modules/mesh/inout/0D/makefile

@@ -0,0 +1,7 @@
+all: moduleMeshInput0D.o moduleMeshOutput0D.o
+
+moduleMeshInput0D.o: moduleMeshOutput0D.o moduleMeshInput0D.f90
+	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
+
+%.o: %.f90
+	$(FC) $(FCFLAGS) -c $< -o $(OBJDIR)/$@

src/modules/mesh/inout/0D/moduleMeshInput0D.f90

@@ -0,0 +1,99 @@
+MODULE moduleMeshInput0D
+  !Creates a 0D mesh. mostly used for testing collisional processes.
+  !This mesh consists on 1 node and 1 volume in which all particles are located.
+  !No boundary conditions and no pusher should be applied to this geometry.
+  !Output should go to a single file (per species) in which each row represents an iteration.
+  !In principle, no EM field is applied.
+
+  CONTAINS
+    !Inits the 0D mesh
+    SUBROUTINE init0D(self)
+      USE moduleMesh
+      USE moduleMeshOutput0D
+      IMPLICIT NONE
+
+      CLASS(meshGeneric), INTENT(inout), TARGET:: self
+
+        IF (ASSOCIATED(meshForMCC, self)) self%printColl => printColl0D
+        SELECT TYPE(self)
+        TYPE IS(meshParticles)
+          self%printOutput => printOutput0D
+          self%printEM     => printEM0D
+          self%readInitial => readInitial0D
+
+        END SELECT
+        self%readMesh => read0D
+
+    END SUBROUTINE init0D
+
+    !Reads a 0D mesh file.
+    !No reading is actually done as the 0D mesh is a fixed one
+    SUBROUTINE read0D(self, filename)
+      USE moduleMesh
+      USE moduleMesh0D
+      IMPLICIT NONE
+
+      CLASS(meshGeneric), INTENT(inout):: self
+      CHARACTER(:), ALLOCATABLE, INTENT(in):: filename !Dummy file, not used
+      REAL(8):: r(1:3)
+
+      !Allocates one node
+      self%numNodes = 1
+      ALLOCATE(self%nodes(1:1))
+      !Allocates one volume
+      self%numCells = 1
+      ALLOCATE(self%cells(1:1))
+      !Allocates matrix K
+      SELECT TYPE(self)
+      TYPE IS(meshParticles)
+        ALLOCATE(self%K(1:1, 1:1))
+        ALLOCATE(self%IPIV(1:1, 1:1))
+        self%K = 0.D0
+        self%IPIV = 0.D0
+
+      END SELECT
+
+      !Creates the node
+      ALLOCATE(meshNode0D:: self%nodes(1)%obj)
+      r = 0.D0
+      CALL self%nodes(1)%obj%init(1, r)
+
+      !Creates the volume
+      ALLOCATE(meshCell0D:: self%cells(1)%obj)
+      CALL self%cells(1)%obj%init(1, (/ 1/), self%nodes)
+
+    END SUBROUTINE read0D
+
+    SUBROUTINE readInitial0D(filename, density, velocity, temperature)
+      IMPLICIT NONE
+
+      CHARACTER(:), ALLOCATABLE, INTENT(in):: filename
+      REAL(8), ALLOCATABLE, INTENT(out), DIMENSION(:):: density
+      REAL(8), ALLOCATABLE, INTENT(out), DIMENSION(:,:):: velocity
+      REAL(8), ALLOCATABLE, INTENT(out), DIMENSION(:):: temperature
+      REAL(8):: dummy
+      INTEGER:: stat
+
+      ALLOCATE(density(1:1))
+      ALLOCATE(velocity(1:1, 1:3))
+      ALLOCATE(temperature(1:1))
+
+      OPEN(10, file = TRIM(filename))
+      
+      !Finds the last line of data
+      stat = 0
+      DO WHILE (stat==0)
+        READ(10, *, iostat = stat)
+
+      END DO
+
+      !Go back two line
+      BACKSPACE(10)
+      BACKSPACE(10)
+
+      !Reads data
+      READ(10, *) dummy, density(1), velocity(1, 1:3), dummy, temperature(1)
+
+    END SUBROUTINE readInitial0D
+
+END MODULE moduleMeshInput0D

src/modules/mesh/inout/0D/moduleMeshOutput0D.f90

@@ -0,0 +1,78 @@
+MODULE moduleMeshOutput0D
+
+  CONTAINS
+    SUBROUTINE printOutput0D(self)
+      USE moduleMesh
+      USE moduleRefParam
+      USE moduleSpecies
+      USE moduleOutput
+      USE moduleCaseParam, ONLY: timeStep
+      IMPLICIT NONE
+
+      CLASS(meshParticles), INTENT(in):: self
+      INTEGER:: i
+      TYPE(outputFormat):: output
+      CHARACTER(:), ALLOCATABLE:: fileName
+
+      DO i = 1, nSpecies
+        fileName='OUTPUT_' // species(i)%obj%name // '.dat'
+        IF (timeStep == 0) THEN
+          OPEN(20, file = path // folder // '/' // fileName, action = 'write')
+          WRITE(20, "(A1, 14X, A5, A20, 40X, A20, 2(A20))") "#","t (s)","density (m^-3)", "velocity (m/s)", &
+                                                                        "pressure (Pa)", "temperature (K)"
+          WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
+          CLOSE(20)
+
+        END IF
+        
+        OPEN(20, file = path // folder // '/' // fileName, position = 'append', action = 'write')
+        CALL calculateOutput(self%nodes(1)%obj%output(i), output, self%nodes(1)%obj%v, species(i)%obj)
+        WRITE(20, "(7(ES20.6E3))") REAL(timeStep)*tauMin*ti_ref, output%density,    &
+                                                                 output%velocity,   &
+                                                                 output%pressure,   &
+                                                                 output%temperature
+        CLOSE(20)
+
+      END DO
+
+    END SUBROUTINE printOutput0D
+
+    SUBROUTINE printColl0D(self)
+      USE moduleMesh
+      USE moduleRefParam
+      USE moduleCaseParam
+      USE moduleCollisions
+      USE moduleOutput
+      IMPLICIT NONE
+
+      CLASS(meshGeneric), INTENT(in):: self
+      CHARACTER(:), ALLOCATABLE:: fileName
+      INTEGER:: k
+
+      fileName='OUTPUT_Collisions.dat'
+      IF (timeStep == tInitial) THEN
+        OPEN(20, file = path // folder // '/' // fileName, action = 'write')
+        WRITE(20, "(A1, 14X, A5, A20)") "#","t (s)","collisions"
+        WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
+        CLOSE(20)
+
+      END IF
+      
+      OPEN(20, file = path // folder // '/' // fileName, position = 'append', action = 'write')
+      WRITE(20, "(ES20.6E3, 10I20)") REAL(timeStep)*tauMin*ti_ref, (self%cells(1)%obj%tallyColl(k)%tally, k=1,nCollPairs)
+      CLOSE(20)
+
+    END SUBROUTINE printColl0D
+
+    SUBROUTINE printEM0D(self)
+      USE moduleMesh
+      USE moduleRefParam
+      USE moduleCaseParam
+      USE moduleOutput
+      IMPLICIT NONE
+
+      CLASS(meshParticles), INTENT(in):: self
+
+    END SUBROUTINE printEM0D
+
+END MODULE moduleMeshOutput0D

src/modules/mesh/inout/gmsh2/makefile

@@ -0,0 +1,7 @@
+all: moduleMeshInputGmsh2.o moduleMeshOutputGmsh2.o
+
+moduleMeshInputGmsh2.o: moduleMeshOutputGmsh2.o moduleMeshInputGmsh2.f90
+	$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@
+
+%.o: %.f90
+	$(FC) $(FCFLAGS) -c $< -o $(OBJDIR)/$@