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Author SHA1 Message Date
Jorge Gonzalez
3bb5ecd06e Merge branch 'development' into 'master' 
Development

See merge request JorgeGonz/fpakc!2
 2021-01-20 15:09:58 +00:00
135 changed files with 30919 additions and 65682 deletions
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2
.gitignore vendored
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@ -4,5 +4,3 @@ obj/
doc/user_manual/
doc/coding_style/
json-fortran-8.2.0/
json-fortran/
runs/

50
CITATION.cff
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@ -1,50 +0,0 @@
# 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'

204
data/collisions/EL_e-Ar.dat
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@ -1,204 +0,0 @@
# 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
5.683400e+0 8.731200e-20
5.918300e+0 9.168100e-20
6.161400e+0 9.628400e-20
6.413100e+0 1.010900e-19
6.673600e+0 1.060800e-19
6.943300e+0 1.118000e-19
7.222400e+0 1.170000e-19
7.511400e+0 1.222000e-19
7.810500e+0 1.275900e-19
8.120100e+0 1.326900e-19
8.440600e+0 1.372100e-19
8.772400e+0 1.416500e-19
9.115800e+0 1.451600e-19
9.471300e+0 1.487100e-19
9.839300e+0 1.523900e-19
1.022020e+1 1.548800e-19
1.061450e+1 1.564600e-19
1.100000e+1 1.580000e-19
1.160000e+1 1.580000e-19
1.220000e+1 1.571000e-19
1.280380e+1 1.547800e-19
1.328890e+1 1.525600e-19
1.379110e+1 1.495700e-19
1.431090e+1 1.458200e-19
1.484890e+1 1.420600e-19
1.540590e+1 1.373500e-19
1.598240e+1 1.321600e-19
1.657920e+1 1.291500e-19
1.719700e+1 1.225700e-19
1.783650e+1 1.157400e-19
1.849840e+1 1.110100e-19
1.918370e+1 1.069000e-19
1.989300e+1 1.026400e-19
2.062720e+1 9.899000e-20
2.138720e+1 9.534100e-20
2.217390e+1 9.156500e-20
2.298830e+1 8.765600e-20
2.383130e+1 8.361000e-20
2.470400e+1 7.942100e-20
2.560730e+1 7.611800e-20
2.654230e+1 7.321900e-20
2.751020e+1 7.021800e-20
2.851210e+1 6.711300e-20
2.954920e+1 6.389700e-20
3.062280e+1 6.137900e-20
3.173410e+1 5.937900e-20
3.288440e+1 5.730800e-20
3.407520e+1 5.516500e-20
3.530780e+1 5.294600e-20
3.658370e+1 5.064900e-20
3.790450e+1 4.827200e-20
3.927170e+1 4.581100e-20
4.068690e+1 4.384700e-20
4.215190e+1 4.245600e-20
4.366840e+1 4.101500e-20
4.523810e+1 3.952400e-20
4.686300e+1 3.798000e-20
4.854500e+1 3.638200e-20
5.028610e+1 3.480000e-20
5.208840e+1 3.353800e-20
5.395410e+1 3.223200e-20
5.588530e+1 3.088000e-20
5.788440e+1 2.948100e-20
5.995370e+1 2.803200e-20
6.209570e+1 2.674300e-20
6.431310e+1 2.541200e-20
6.660830e+1 2.403500e-20
6.898420e+1 2.260900e-20
7.144360e+1 2.171100e-20
7.398940e+1 2.120200e-20
7.662470e+1 2.067500e-20
7.935260e+1 2.012900e-20
8.217640e+1 1.940100e-20
8.509940e+1 1.859800e-20
8.812510e+1 1.776600e-20
9.125710e+1 1.690400e-20
9.449930e+1 1.601300e-20
9.785530e+1 1.509000e-20
1.013293e+2 1.435400e-20
1.049254e+2 1.395800e-20
1.086478e+2 1.354900e-20
1.125011e+2 1.312500e-20
1.164898e+2 1.268600e-20
1.206186e+2 1.223200e-20
1.248925e+2 1.176200e-20
1.293167e+2 1.127500e-20
1.338963e+2 1.077100e-20
1.386368e+2 1.025000e-20
1.435440e+2 9.710200e-21
1.486236e+2 9.151400e-21
1.538817e+2 8.790400e-21
1.593245e+2 8.496500e-21
1.649587e+2 8.192200e-21
1.707908e+2 7.877300e-21
1.768279e+2 7.551300e-21
1.830772e+2 7.213800e-21
1.895461e+2 6.864500e-21
1.962423e+2 6.502900e-21
2.031738e+2 6.244500e-21
2.103489e+2 6.118900e-21
2.177762e+2 5.988900e-21
2.254644e+2 5.854400e-21
2.334229e+2 5.715100e-21
2.416610e+2 5.570900e-21
2.501886e+2 5.421700e-21
2.590160e+2 5.267200e-21
2.681535e+2 5.107300e-21
2.776121e+2 4.941800e-21
2.874032e+2 4.770400e-21
2.975383e+2 4.593100e-21
3.080295e+2 4.409500e-21
3.188895e+2 4.219400e-21
3.301311e+2 4.022700e-21
3.417678e+2 3.819100e-21
3.538134e+2 3.608300e-21
3.662823e+2 3.390100e-21
3.791894e+2 3.164200e-21
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
5.178000e+2 2.603700e-21
5.360318e+2 2.573300e-21
5.549043e+2 2.541800e-21
5.744399e+2 2.509300e-21
5.946621e+2 2.475600e-21
6.155950e+2 2.440700e-21
6.372635e+2 2.404600e-21
6.596934e+2 2.367200e-21
6.829116e+2 2.328500e-21
7.069458e+2 2.288400e-21
7.318245e+2 2.247000e-21
7.575776e+2 2.204000e-21
7.842356e+2 2.159600e-21
8.118305e+2 2.113600e-21
8.403951e+2 2.066000e-21
8.699636e+2 2.016700e-21
9.005711e+2 1.965700e-21
9.322543e+2 1.912900e-21
9.650509e+2 1.858200e-21

235
data/collisions/IO_e-Ar.dat
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@ -1,203 +1,34 @@
# EL cross sections extracted from PROGRAM MAGBOLTZ, VERSION 7.1 JUNE 2004 www.lxcat.net/Biagi-v7.1
# H. C. Straub et. al, Physical Review A, 55,2(1995)
# Relative energy (eV) cross section (m^2)
1.570000e+1 0.000000e+0
1.571000e+1 1.033000e-25
1.574000e+1 3.631000e-23
1.577000e+1 7.390000e-23
1.581000e+1 1.128000e-22
1.585000e+1 1.531000e-22
1.589000e+1 1.948000e-22
1.593000e+1 2.379000e-22
1.597000e+1 2.826000e-22
1.602000e+1 3.330000e-22
1.606000e+1 3.914000e-22
1.611000e+1 4.518000e-22
1.616000e+1 5.143000e-22
1.621000e+1 5.791000e-22
1.627000e+1 6.461000e-22
1.632000e+1 7.155000e-22
1.638000e+1 7.873000e-22
1.644000e+1 8.616000e-22
1.650000e+1 9.386000e-22
1.656000e+1 1.026000e-21
1.663000e+1 1.116000e-21
1.670000e+1 1.209000e-21
1.677000e+1 1.306000e-21
1.684000e+1 1.406000e-21
1.691000e+1 1.510000e-21
1.699000e+1 1.617000e-21
1.707000e+1 1.733000e-21
1.715000e+1 1.853000e-21
1.724000e+1 1.977000e-21
1.733000e+1 2.106000e-21
1.742000e+1 2.239000e-21
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
1.817000e+1 3.354000e-21
1.829000e+1 3.540000e-21
1.842000e+1 3.731000e-21
1.855000e+1 3.933000e-21
1.868000e+1 4.146000e-21
1.882000e+1 4.367000e-21
1.897000e+1 4.596000e-21
1.912000e+1 4.837000e-21
1.927000e+1 5.089000e-21
1.943000e+1 5.349000e-21
1.960000e+1 5.618000e-21
1.977000e+1 5.897000e-21
1.995000e+1 6.186000e-21
2.013000e+1 6.498000e-21
2.032000e+1 6.826000e-21
2.052000e+1 7.161000e-21
2.073000e+1 7.464000e-21
2.094000e+1 7.777000e-21
2.116000e+1 8.092000e-21
2.138000e+1 8.414000e-21
2.162000e+1 8.757000e-21
2.186000e+1 9.122000e-21
2.211000e+1 9.468000e-21
2.237000e+1 9.786000e-21
2.264000e+1 1.013000e-20
2.292000e+1 1.050000e-20
2.321000e+1 1.085000e-20
2.351000e+1 1.121000e-20
2.382000e+1 1.158000e-20
2.414000e+1 1.197000e-20
2.447000e+1 1.237000e-20
2.482000e+1 1.278000e-20
2.517000e+1 1.317000e-20
2.554000e+1 1.355000e-20
2.592000e+1 1.400000e-20
2.631000e+1 1.440000e-20
2.672000e+1 1.479000e-20
2.715000e+1 1.519000e-20
2.758000e+1 1.560000e-20
2.804000e+1 1.604000e-20
2.850000e+1 1.650000e-20
2.899000e+1 1.699000e-20
2.949000e+1 1.749000e-20
3.001000e+1 1.801000e-20
3.055000e+1 1.844000e-20
3.111000e+1 1.888000e-20
3.168000e+1 1.935000e-20
3.228000e+1 1.981000e-20
3.290000e+1 2.027000e-20
3.354000e+1 2.075000e-20
3.420000e+1 2.123000e-20
3.488000e+1 2.167000e-20
3.559000e+1 2.214000e-20
3.633000e+1 2.255000e-20
3.709000e+1 2.289000e-20
3.787000e+1 2.324000e-20
3.869000e+1 2.351000e-20
3.953000e+1 2.376000e-20
4.040000e+1 2.398000e-20
4.131000e+1 2.416000e-20
4.224000e+1 2.435000e-20
4.321000e+1 2.454000e-20
4.421000e+1 2.474000e-20
4.525000e+1 2.492000e-20
4.632000e+1 2.501000e-20
4.743000e+1 2.509000e-20
4.858000e+1 2.519000e-20
4.978000e+1 2.528000e-20
5.101000e+1 2.544000e-20
5.228000e+1 2.562000e-20
5.360000e+1 2.580000e-20
5.497000e+1 2.600000e-20
5.639000e+1 2.617000e-20
5.785000e+1 2.634000e-20
5.937000e+1 2.652000e-20
6.094000e+1 2.673000e-20
6.256000e+1 2.696000e-20
6.425000e+1 2.719000e-20
6.599000e+1 2.738000e-20
6.779000e+1 2.752000e-20
6.965000e+1 2.767000e-20
7.159000e+1 2.786000e-20
7.358000e+1 2.806000e-20
7.565000e+1 2.823000e-20
7.780000e+1 2.831000e-20
8.001000e+1 2.840000e-20
8.231000e+1 2.845000e-20
8.468000e+1 2.849000e-20
8.714000e+1 2.854000e-20
8.969000e+1 2.859000e-20
9.232000e+1 2.860000e-20
9.505000e+1 2.860000e-20
9.788000e+1 2.854000e-20
1.008000e+2 2.848000e-20
1.038000e+2 2.842000e-20
1.070000e+2 2.836000e-20
1.102000e+2 2.830000e-20
1.136000e+2 2.823000e-20
1.170000e+2 2.816000e-20
1.206000e+2 2.807000e-20
1.243000e+2 2.788000e-20
1.282000e+2 2.769000e-20
1.322000e+2 2.753000e-20
1.363000e+2 2.741000e-20
1.406000e+2 2.727000e-20
1.450000e+2 2.705000e-20
1.496000e+2 2.682000e-20
1.543000e+2 2.654000e-20
1.592000e+2 2.625000e-20
1.643000e+2 2.598000e-20
1.696000e+2 2.572000e-20
1.750000e+2 2.545000e-20
1.807000e+2 2.516000e-20
1.865000e+2 2.478000e-20
1.925000e+2 2.439000e-20
1.988000e+2 2.398000e-20
2.052000e+2 2.367000e-20
2.119000e+2 2.337000e-20
2.189000e+2 2.307000e-20
2.260000e+2 2.275000e-20
2.335000e+2 2.243000e-20
2.412000e+2 2.209000e-20
2.491000e+2 2.174000e-20
2.574000e+2 2.142000e-20
2.659000e+2 2.110000e-20
2.747000e+2 2.076000e-20
2.839000e+2 2.041000e-20
2.933000e+2 2.005000e-20
3.031000e+2 1.969000e-20
3.132000e+2 1.935000e-20
3.237000e+2 1.899000e-20
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
17 1.700E-22
20 4.600E-21
25 1.240E-20
30 1.840E-20
35 2.260E-20
40 2.550E-20
45 2.660E-20
50 2.700E-20
55 2.690E-20
60 2.670E-20
65 2.670E-20
70 2.670E-20
75 2.660E-20
80 2.690E-20
85 2.700E-20
90 2.690E-20
95 2.670E-20
100 2.640E-20
110 2.610E-20
120 2.550E-20
140 2.450E-20
160 2.350E-20
180 2.270E-20
200 2.180E-20
225 2.100E-20
250 1.990E-20
275 1.870E-20
300 1.790E-20
350 1.630E-20
400 1.510E-20
450 1.390E-20
500 1.310E-20

52
data/collisions/IO_e-Kr.dat
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@ -1,52 +0,0 @@
# 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

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data/collisions/IO_e-Li.dat
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@ -1,148 +0,0 @@
# 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

52
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@ -1,52 +0,0 @@
# 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

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1
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@ -6,7 +6,6 @@
*.aux
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bibliography.bib.bak
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44
doc/user-manual/bibliography.bib
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@ -8,16 +8,6 @@
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},
@ -51,38 +41,4 @@
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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%%Trailer
end
%%EOF

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@ -1,5 +1,5 @@
\documentclass[10pt,a4paper,twoside]{book}
%\usepackage[latin1]{inputenc}
\documentclass[10pt,a4paper,oneside]{book}
\usepackage[latin1]{inputenc}
\usepackage{amsmath}
\usepackage{amsfonts}
\usepackage{amssymb}
@ -10,7 +10,6 @@
\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
@ -22,23 +21,16 @@
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}}
@ -49,7 +41,6 @@
\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}
@ -69,10 +60,8 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\chapter{Introduction}
\section{About fpakc}
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.
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.
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 code is currently in very early steps of development and further improvements are expected very soon.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Main Guidelines}
@ -86,14 +75,14 @@
\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 eases the process of fixing bugs and improving the codes by a large team of developers.
This ease 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 being ease to use.
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 various scientists: from well-established ones to newcomers to the field and also students.
\item \acrshort{fpakc} requires to be 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.
\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.
\end{enumerate}
These are foundation stones of \acrshort{fpakc} and its development and should always be followed, at least for the releases in the official repository.
These are foundation stones of the code and code development and should always be followed, at least for the releases in the official repository.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{How to collaborate}
@ -103,32 +92,22 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\chapter{Operation Scheme}
\section{The Particle Method}
\Gls{fpakc} uses macro-particles to simulate the dynamics of different plasma species (mainly ions, electrons and neutrals).
These macro-particles could represent a large amount of real particles.
For now own, macro-particles will be referred as just particles by abuse of language.
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.
\acrshort{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.
For now own, macro-particles will be referred as just particles by abusing 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.
The general steps performed in each iteration are:
\begin{enumerate}
\item Firstly, new particles are introduced into the domain as specified in the input file.
\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.
At each time step, particles are first pushed accounting for possible acceleration by external forces.
Then, the cell in which the particle ends up is located.
If a boundary is encountered, the interaction between the particle and the boundary is calculated.
Next, collisions for the particles in each cell are carried on.
This may include different collision processes for each particle.
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.
Finally, the particles properties are scattered into the mesh nodes.
These properties are density, momentum and the stress tensor.
\item 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}
Non-dimensional units are used for this, but output files are converted into dimensional units.
If requested, the electromagnetic field is computed.
\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}.
More in depth explanation of the different steps are given in the following sections.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Injection of new particles}
@ -143,150 +122,100 @@
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}
\item 3D Cartesian pusher.
Moving particles in a simple 3D Cartesian space.
\item 2D Cylindrical.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\subsection{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.
\item 2D Cartesian pusher.
Moving particles in a simple 2D Cartesian space.
Cross-sections are read from files.
These files contains two columns: one for the relative energy (in $\unit{eV}$) and another one for the cross-section (in $\unit{m^{-2}}$).
\item 1D Radial pusher.
Same implementation as 2D cylindrical pusher but direction $z$ is ignored.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\subsection{1D Cartesian pusher}
\item 1D Cartesian pusher.
Moving particles in a simple 1D Cartesian space. Same implementation as in 2D Cartesian but $y$ direction is ignored.
\end{itemize}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\subsection{1D Radial pusher}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\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 neighbour search, starting from the previous cell containing the particle.
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 or might be eliminated from it.
This is done by a neighbor 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.
When the particle interacts with the boundary, the particle may continue its life in the simulation (reflected) or might be eliminated from it (absorbed).
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 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.
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.
To try to fix that, the possibility to include a Variable Weighting Scheme in the simulations is available in \Gls{fpakc}.
These schemes detect when a particle changes cells and split it if necessary to improve statistics.
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.
This schemes detect when a particle change cells and modify its weight accordingly.
To avoid particles having a larger weight than the rest, particle can be split in multiple particles if weight become too large.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\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 parallelization and is very CPU consuming.
Unfortunately, this is done right now without parallelisation and is very CPU consuming.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Probing}\label{sec:probing}
As default, \gls{fpakc} outputs information of macroscopic quantities (density, velocity, temperature\ldots) in the finite element mesh.
However, a lot of information can be extracted from the particle distribution function.
Thus, a probing method is provided to extract the distribution function in a specific position.
\section{Interaction between species}\label{ssec:collisions}
For each cell, interaction among the particles in it are carried out.
The type of interaction between the different particles is defined by the user.
In general, the maximum number of interaction in a cell is computed.
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.
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.
Collisions can change the velocity of the particles involved (elastic), create new particles (ionization-recombination) or change the type of particle (charge-exchange).
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.
Below are described the type of collision process implemented between species.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\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 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.
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.
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.
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}
To properly compile \gls{fpakc}, the following packages are required.
In order 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.
@ -310,7 +239,7 @@
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\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 \lstinline|.msh| format.
Right now, the only \acrshort{io} format available in \Gls{fpakc} is the v2.0 .msh format.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Installation steps}
@ -345,6 +274,7 @@ 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:
@ -363,13 +293,13 @@ make
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{Mesh file}
\Gls{fpakc} accepts right now the version 2.0 of \Gls{gmsh} mesh format \lstinline|.msh| in ASCII format.
\Gls{fpakc} accepts right now the version 2.0 of \Gls{gmsh} mesh format .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 capitalization.
\Gls{json} is a case-sensitive format, so input must be written with the correct capitalisation.
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.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@ -379,10 +309,6 @@ 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.
@ -397,30 +323,6 @@ 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}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@ -428,50 +330,23 @@ 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{Cart}: Cartesian coordinates.
Available for \textbf{geometry.dimension} $1$, $2$ and $3$.
The coordinates $x$, $y$ and $z$ correspond to $x$, $y$ and $z$ respectively.
\item \textbf{Cyl}: Cylindrical coordinates ($z \hyphen r$) with symmetry axis at $r = 0$.
Only available for \textbf{geometry.dimension} $2$.
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 $r$.
\item \textbf{2DCyl}: Two-dimensional grid (z-r) with symmetry axis at $r = 0$.
For \Gls{gmsh} mesh format, the coordinates $x$ and $y$ correspond to $z$ and $r$ respectively.
\item \textbf{1DCart}: One-dimensional grid (x) in Cartesian coordinates
For \Gls{gmsh} mesh format, the coordinates $x$ corresponds to $x$.
\item \textbf{1DRad}: One-dimensional grid (r) in radial coordinates
For \Gls{gmsh} mesh format, the coordinates $x$ corresponds to $r$.
\end{itemize}
\item \textbf{meshType}: Character.
Format of mesh file.
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}
Currently, only the value \textbf{gmsh} is accepted, which makes reference to \Gls{gmsh} v2.0 output format.
\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}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@ -509,72 +384,19 @@ make
\begin{itemize}
\item \textbf{name}: Character.
Name of the boundary.
\item \textbf{physicalSurface}: Integer.
Identification of the surface in the mesh file.
\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:
\item \textbf{type}: Character.
Type of boundary.
Accepted values 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{wallTemperature}: Reflective wall with constant temperature that exchange heat with particles.
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.
It has no actual function.
\end{itemize}
\item \textbf{physicalSurface}: Integer.
Identification of the edge in the mesh file.
\end{itemize}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
@ -589,26 +411,18 @@ make
Type of boundary.
Accepted values are:
\begin{itemize}
\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}.
\item \textbf{dirichlet}: Elastic reflection of particles.
\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 needs to be associated to a physicalSurface in the mesh file.
The injection of particles need 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.
@ -622,39 +436,26 @@ make
Available values are:
\begin{itemize}
\item \textbf{A}: Ampere.
\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.
\item \textbf{sccm}: Standard cubic centimeter.
\end{itemize}
\item \textbf{v}: Real.
Units of $\unit{m s^{-1}}$.
Module of velocity vector.
Module of velocity vector, in $\unitfrac{m}{s}$.
\item \textbf{n}: Real.
Array dimension $3$.
Direction of injection.
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.
Norm of vector must be equal $1$.
\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}
@ -670,34 +471,29 @@ 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{solver}
This object determines the input parameters for the solvers used in the case, both for particle pushers and electromagnetic field.
\subsection{case}
This object determines the simulation time, time step, pushers, weighting scheme and solver for the 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{finalTime}: Real.
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{time}: Real.
Total simulation time in $\unit{s}$.
\item \textbf{pusher}: Character.
Array dimension 'number of species'.
Indicates the type of pusher used for each species:
\begin{itemize}
\item \textbf{Neutral}: Pushes a particle without any external force.
\item \textbf{Electrostatic}: Pushes a particle, including the effect of the electrostatic field.
\item \textbf{Electromagnetic}: Pushes a particle, accounting for the electromagnetic field.
\item \textbf{2DCylNeutral}: Pushes particles in a 2D z-r space without any external force.
\item \textbf{2DCylCharged}: Pushes particles in a 2D z-r space including the effect of the electrostatic field.
\item \textbf{1DCartCharged}: Pushes particles in a 1D Cartesian space accounting the the electrostatic 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.
@ -712,98 +508,69 @@ 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{B}: Real.
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.
\item \textbf{initial}: Object.
Array.
Determines initial values for the species.
Required values are:
\begin{itemize}
\item \textbf{species}: Character.
Name of species as defined in the object \textbf{species}.
\item \textbf{file}: Character.
Output file from previous run used as an initial state for the species.
The file format must be the same as in \textbf{geometry.meshType}
Initial particles are assumed to have a Maxwellian distribution.
File must be located in \textbf{output.path}.
\item \textbf{particlesPerCell}: Integer.
Optional.
Initial number of particles per cell.
If not, the number of particles per cell will be assigned based on the species weight and the cell volume.
\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:
\item \textbf{speciesName}: Character.
Name of species.
\item \textbf{initialState}: Character.
Plain text file that contains the information about the species macroscopic properties in the grid.
Initial particles are assumed to be Maxwellian.
File must be located at \textbf{output.path}.
The file must contain the following columns in this specific order:
\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 $\unit[0.0]{s}$.
\item \textit{Element}: Integer.
Identifier of the volume in the mesh.
It is not required to specify empty volumes.
\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{interactions}\label{ssec:input_interactions}
This object determines the different interactions among species.
This object determine 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.
\item \textbf{meshCollisions}: Character.
Determines a specific mesh for \acrshort{mcc} processes.
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}).
Indicates the path to in which the cross section tables are allocated.
\item \textbf{collisions}: Object.
Array.
Contains the different binary collisions.
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}: Array of objects.
\item \textbf{cTypes}: Object.
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}
@ -820,33 +587,22 @@ make
\end{itemize}
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\chapter{Example runs}\label{ch:exampleRuns}
This chapter presents a description of the different example files distributed with \acrshort{fpakc}.
All examples in the repository have a \lstinline|README.txt| file and a reference output.
Plotting of the output is done with \Gls{gnuplot} or \Gls{gmsh}.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\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.
\chapter{Example runs\label{ch:exampleRuns}}
\section{1D Cathode}
Emission from a 1D cathond in both, cartesian and radial coordinates.
Both cases insert the same amount of electrons from the minimum coordinate and have the same boundary conditions for particles and the electrostatic field.
This case is useful to ilustrate hoy \acrshort{fpakc} can deal with different geometries by just modifiying some parameters in the input file.
The same mesh file (\lstinline|mesh.msh|) is used for both cases.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\section{0D \ce{Ar}-\ce{Ar+} Elastic Collision (0D\_Argon)}
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.
\section{ALPHIE Grid system}
Two-dimensional axialsymmetry case to study the counterflow of electrons and Argon ions going trhough 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 (cylFlow)}
Simple case of neutral Argon flow around a cylinder in a 2D axial-symmetry geometry.
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|).
\section{Flow around cylinder}
Simple case of neutral Argon flow around a cylinder in a 2D axialsymmetry geometry.
Elastic collisions between argon particles are included as default.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\printglossaries

3
makefile
View file

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

2
runs/0D_Argon/Argon+_Initial.dat
View file

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

2
runs/0D_Argon/Argon_Initial.dat
View file

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

11
runs/0D_Argon/README.txt
View file

@ -1,11 +0,0 @@
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.

49
runs/0D_Argon/input.json
View file

@ -1,49 +0,0 @@
{
"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
}
}
}

1002
runs/0D_Argon/output/OUTPUT_Argon+.dat
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1002
runs/0D_Argon/output/OUTPUT_Argon.dat
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1002
runs/0D_Argon/output/OUTPUT_Collisions.dat
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65
runs/0D_Argon/plot_Temperature.gp
View file

@ -1,65 +0,0 @@
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

8
runs/1D_Cathode/README.txt
View file

@ -1,8 +0,0 @@
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.

23
runs/1D_Cathode/inputCart.json
View file

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

23
runs/1D_Cathode/inputRad.json
View file

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

16
runs/1D_Cathode/mesh.geo
View file

@ -1,16 +0,0 @@
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;

20008
runs/1D_Cathode/mesh.msh
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185
runs/1D_Cathode/output/Cartesian/OUTPUT_1000_EMField.msh
View file

@ -1,185 +0,0 @@
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runs/1D_Cathode/output/Cartesian/OUTPUT_1000_Electron.msh
View file

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7
runs/ALPHIE_Grid/README.txt
View file

@ -1,7 +0,0 @@
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.

35
runs/ALPHIE_Grid/inputBaseCase.json → runs/ALPHIE_Grid/inputDiffTau.json
View file

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

40
runs/ALPHIE_Grid/inputIonization_0.10mA.json → runs/ALPHIE_Grid/inputSameTau.json
View file

@ -2,26 +2,24 @@
"output": {
"path": "./runs/ALPHIE_Grid/",
"triggerOutput": 500,
"cpuTime": false,
"triggerCPUTime": 1,
"cpuTime": true,
"numColl": false,
"EMField": true,
"folder": "ionization_0.10mA"
"EMField": true
},
"geometry": {
"dimension": 2,
"type": "Cyl",
"meshType": "gmsh2",
"type": "2DCyl",
"meshType": "gmsh",
"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": 1.0e2}
{"name": "Electron", "type": "charged", "mass": 9.109e-31, "charge":-1.0, "weight": 1.0e1}
],
"boundary": [
{"name": "Ionization Chanber", "physicalSurface": 1, "bTypes": [
{"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"}
{"type": "transparent"}
]},
{"name": "Vacuum Chamber", "physicalSurface": 2, "bTypes": [
{"type": "transparent"},
@ -46,30 +44,30 @@
],
"boundaryEM": [
{"name": "Extraction Grid", "type": "dirichlet", "potential": -150.0, "physicalSurface": 4},
{"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}
{"name": "Acceleration Grid", "type": "dirichlet", "potential": -600.0, "physicalSurface": 5}
],
"inject": [
{"name": "Cathode Electron", "species": "Electron", "flow": 1.0e-4, "units": "A", "v": 87000.0, "T": [30000.0, 30000.0, 30000.0],
{"name": "Ionization Argon+", "species": "Argon+", "flow": 27.0e-6, "units": "A", "v": 322.0, "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],
"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,
"radius": 1.88e-10
"temperature": 2500.0
},
"solver": {
"tau": [1.0e-9, 1.0e-11],
"finalTime": 1.0e-6,
"pusher": ["Electrostatic", "Electrostatic"],
"WeightingScheme": "Volume",
"case": {
"tau": [1.0e-11, 1.0e-11],
"time": 2.0e-6,
"pusher": ["2DCylCharged", "2DCylCharged"],
"EMSolver": "Electrostatic"
},
"parallel": {
"OpenMP":{
"nThreads": 24
"nThreads": 8
}
}
}

45
runs/ALPHIE_Grid/mesh.geo
View file

@ -1,13 +1,12 @@
zg1 = 0.0020;
tg1 = 0.0003;
Lz = 0.0100;
Lr = 0.0006;
zg1 = 0.0025;
tg1 = 0.0004;
rg1 = 0.0005;
dg = 0.0020;
zg2 = zg1 + tg1 + dg;
dg = 0.0025;
zg2 = zg1+tg1+dg;
tg2 = tg1;
rg2 = rg1;
zEnd = 0.0050;
Lz = zg2 + tg2 + zEnd;
Lr = rg1 + 0.0001;
Lcell = 0.0001;
@ -97,19 +96,19 @@ 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};
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};
Transfinite Surface{6};
Recombine Surface {6};
Transfinite Surface{7};
Recombine Surface {7};
Transfinite Surface{8};
Recombine Surface {8};
#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};
#Transfinite Surface{6};
#Recombine Surface {6};
#Transfinite Surface{7};
#Recombine Surface {7};
#Transfinite Surface{8};
#Recombine Surface {8};

2674
runs/ALPHIE_Grid/mesh.msh
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2839
runs/ALPHIE_Grid/output/Classic/OUTPUT_100000_Argon+.msh
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2021
runs/ALPHIE_Grid/output/Classic/OUTPUT_100000_EMField.msh
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2839
runs/ALPHIE_Grid/output/Classic/OUTPUT_100000_Electron.msh
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2839
runs/ALPHIE_Grid/output/Ionization/OUTPUT_100000_Argon+.msh
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2021
runs/ALPHIE_Grid/output/Ionization/OUTPUT_100000_EMField.msh
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2839
runs/ALPHIE_Grid/output/Ionization/OUTPUT_100000_Electron.msh
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14
runs/Argon_Expansion/CX_case.json
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@ -3,13 +3,11 @@
"path": "./runs/Argon_Expansion/",
"triggerOutput": 10,
"cpuTime": false,
"numColl": true,
"folder": "CX_case"
"numColl": true
},
"geometry": {
"dimension": 2,
"type": "Cyl",
"meshType": "gmsh2",
"type": "2DCyl",
"meshType": "gmsh",
"meshFile": "mesh.msh"
},
"species": [
@ -42,10 +40,10 @@
"temperature": 300.0,
"radius": 1.88e-10
},
"solver": {
"case": {
"tau": [1.0e-6, 1.0e-6],
"finalTime": 4.0e-3,
"pusher": ["Neutral", "Neutral"],
"time": 4.0e-3,
"pusher": ["2DCylNeutral", "2DCylNeutral"],
"WeightingScheme": "Volume"
},
"interactions": {

14
runs/Argon_Expansion/elastic_case.json → runs/Argon_Expansion/base_case.json
View file

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

56
runs/Argon_Expansion/nocoll_case.json
View file

@ -1,56 +0,0 @@
{
"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
}
}
}

7
runs/cylFlow/README.txt
View file

@ -1,7 +0,0 @@
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.

18
runs/cylFlow/input.json
View file

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

65
runs/cylFlow/inputDualMesh.json
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@ -1,65 +0,0 @@
{
"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
}
}
}

9
runs/cylFlow/mesh.geo
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@ -62,13 +62,10 @@ Physical Surface(4) = {4};
Physical Surface(5) = {5};
Transfinite Line {12, 2, 4, 6} = cyl_h/Lcell + 1 Using Progression 1;
Transfinite Line {10} = cyl_s/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 {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 {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 Line {5, 14, 8} = (dom_l - cyl_e)/Lcell + 1 Using Progression 1;
Transfinite Surface{1};
Recombine Surface {1};

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runs/cylFlow/mesh.msh
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629
runs/cylFlow/mesh.msh.opt Normal file
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@ -0,0 +1,629 @@
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;

73
runs/cylFlow/meshColl.geo
View file

@ -1,73 +0,0 @@
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};

3974
runs/cylFlow/meshColl.msh
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79
runs/cylFlow/meshSingle.geo
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@ -1,79 +0,0 @@
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};

4182
runs/cylFlow/meshSingle.msh
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8183
runs/cylFlow/output/dual/OUTPUT_1000_Argon.msh
View file

File diff suppressed because it is too large Load diff

1943
runs/cylFlow/output/dual/OUTPUT_1000_Collisions.msh
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File diff suppressed because it is too large Load diff

8183
runs/cylFlow/output/single/OUTPUT_1000_Argon.msh
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File diff suppressed because it is too large Load diff

1943
runs/cylFlow/output/single/OUTPUT_1000_Collisions.msh
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File diff suppressed because it is too large Load diff

55
src/fpakc.f90
View file

@ -1,22 +1,20 @@
! FPAKC main program
PROGRAM fpakc
USE moduleCompTime
USE moduleCaseParam
USE moduleInput
USE moduleErrors
USE moduleInject
USE moduleSolver
USE moduleMesh
USE moduleProbe
USE moduleErrors
USE moduleCompTime
USE moduleCaseParam
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
@ -28,17 +26,8 @@ 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...")
!$OMP END SINGLE
CALL doScatter()
@ -52,21 +41,16 @@ PROGRAM fpakc
tStep = omp_get_wtime() - tStep
!Output initial state
CALL doOutput()
CALL doOutput(t)
CALL verboseError('Starting main loop...')
!$OMP PARALLEL DEFAULT(SHARED)
DO t = tInitial + 1, tFinal
DO t = 1, tmax
!Insert new particles and push them
!$OMP SINGLE
tStep = omp_get_wtime()
! Update global time step index
timeStep = t
!Checks if a species needs to me moved in this iteration
CALL solver%updatePushSpecies()
!Checks if probes need to be calculated this iteration
CALL resetProbes()
CALL solver%updatePushSpecies(t)
tPush = omp_get_wtime()
!$OMP END SINGLE
@ -83,26 +67,11 @@ PROGRAM fpakc
tColl = omp_get_wtime()
!$OMP END SINGLE
IF (doMCCollisions) THEN
CALL meshForMCC%doCollisions()
END IF
CALL doCollisions()
!$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()
!$OMP END SINGLE
@ -129,12 +98,10 @@ PROGRAM fpakc
!$OMP SINGLE
tEMField = omp_get_wtime() - tEMField
CALL doAverage()
tStep = omp_get_wtime() - tStep
!Output data
CALL doOutput()
CALL doOutput(t)
!$OMP END SINGLE
END DO

24
src/makefile
View file

@ -1,30 +1,18 @@
OBJECTS = $(OBJDIR)/moduleMesh.o $(OBJDIR)/moduleMeshBoundary.o $(OBJDIR)/moduleCompTime.o \
OBJECTS = $(OBJDIR)/moduleMesh.o $(OBJDIR)/moduleCompTime.o $(OBJDIR)/moduleSolver.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)/moduleMath.o \
$(OBJDIR)/moduleProbe.o $(OBJDIR)/moduleAverage.o $(OBJDIR)/moduleCoulomb.o \
$(OBJDIR)/moduleMeshInoutCommon.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
$(OBJDIR)/moduleEM.o $(OBJDIR)/moduleRandom.o \
$(OBJDIR)/moduleMeshCyl.o $(OBJDIR)/moduleMeshCylRead.o $(OBJDIR)/moduleMeshCylBoundary.o \
$(OBJDIR)/moduleMesh1DCart.o $(OBJDIR)/moduleMesh1DCartRead.o $(OBJDIR)/moduleMesh1DCartBoundary.o \
$(OBJDIR)/moduleMesh1DRad.o $(OBJDIR)/moduleMesh1DRadRead.o $(OBJDIR)/moduleMesh1DRadBoundary.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 -lopenblas
$(FC) $(FCFLAGS) -o $(TOPDIR)/$(OUTPUT) $(OBJECTS) $(OBJDIR)/$(OUTPUT).o $(JSONLIB) -L/usr/local/lib -llapack -lopenblas
modules.o:
$(MAKE) -C modules all

11
src/modules/common/makefile
View file

@ -1,11 +0,0 @@
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 $(OBJDIR)/$@

15
src/modules/common/moduleCaseParam.f90
View file

@ -1,15 +0,0 @@
!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

16
src/modules/common/moduleCompTime.f90
View file

@ -1,16 +0,0 @@
!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

73
src/modules/common/moduleMath.f90
View file

@ -1,73 +0,0 @@
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

5
src/modules/init/makefile
View file

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

1495
src/modules/init/moduleInput.f90
View file

File diff suppressed because it is too large Load diff

51
src/modules/makefile
View file

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

5
src/modules/mesh/0D/makefile
View file

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

257
src/modules/mesh/0D/moduleMesh0D.f90
View file

@ -1,257 +0,0 @@
!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

8
src/modules/mesh/1DCart/makefile
View file

@ -1,5 +1,11 @@
all: moduleMesh1DCart.o
all: moduleMesh1DCart.o moduleMesh1DCartBoundary.o moduleMesh1DCartRead.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 $(OBJDIR)/$@

695
src/modules/mesh/1DCart/moduleMesh1DCart.f90
View file

@ -4,17 +4,12 @@
! 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
@ -26,42 +21,111 @@ 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
TYPE, PUBLIC, EXTENDS(meshCell):: meshCell1DCartSegm
!Boundary functions defined in the submodule Boundary
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(meshElement), POINTER:: e1 => NULL(), e2 => NULL()
CLASS(*), POINTER:: e1 => NULL(), e2 => NULL()
REAL(8):: arNodes(1:2)
CONTAINS
!meshCell DEFERRED PROCEDURES
PROCEDURE, PASS:: init => initCell1DCartSegm
PROCEDURE, PASS:: getNodes => getNodesSegm
PROCEDURE, PASS:: randPos => randPos1DCartSegm
PROCEDURE, PASS:: init => initVol1DCartSegm
PROCEDURE, PASS:: randPos => randPos1DCartSeg
PROCEDURE, PASS:: area => areaSegm
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:: neighbourElement => neighbourElementSegm
!PARTICLUAR PROCEDURES
PROCEDURE, PASS, PRIVATE:: calculateVolume => volumeSegm
PROCEDURE, PASS:: nextElement => nextElementSegm
END TYPE meshCell1DCartSegm
END TYPE meshVol1DCartSegm
CONTAINS
!NODE FUNCTIONS
@ -69,7 +133,6 @@ MODULE moduleMesh1DCart
SUBROUTINE initNode1DCart(self, n, r)
USE moduleSpecies
USE moduleRefParam
USE OMP_LIB
IMPLICIT NONE
CLASS(meshNode1DCart), INTENT(out):: self
@ -84,8 +147,6 @@ MODULE moduleMesh1DCart
!Allocates output
ALLOCATE(self%output(1:nSpecies))
CALL OMP_INIT_LOCK(self%lock)
END SUBROUTINE initNode1DCart
PURE FUNCTION getCoord1DCart(self) RESULT(r)
@ -99,7 +160,7 @@ MODULE moduleMesh1DCart
END FUNCTION getCoord1DCart
!EDGE FUNCTIONS
!Init edge element
!Inits edge element
SUBROUTINE initEdge1DCart(self, n, p, bt, physicalSurface)
USE moduleSpecies
USE moduleBoundary
@ -115,15 +176,12 @@ 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
@ -131,7 +189,23 @@ MODULE moduleMesh1DCart
ALLOCATE(self%fboundary(1:nSpecies))
!Assign functions to boundary
DO s = 1, nSpecies
CALL pointBoundaryFunction(self, s)
SELECT TYPE(obj => self%boundary%bTypes(s)%obj)
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
@ -141,29 +215,18 @@ MODULE moduleMesh1DCart
END SUBROUTINE initEdge1DCart
!Get nodes from edge
PURE FUNCTION getNodes1DCart(self, nNodes) RESULT(n)
PURE FUNCTION getNodes1DCart(self) RESULT(n)
IMPLICIT NONE
CLASS(meshEdge1DCart), INTENT(in):: self
INTEGER, INTENT(in):: nNodes
INTEGER:: n(1:nNodes)
INTEGER, ALLOCATABLE:: n(:)
ALLOCATE(n(1))
n = (/ self%n1%n /)
END FUNCTION getNodes1DCart
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
!Calculates a 'random' position in edge
FUNCTION randPosEdge(self) RESULT(r)
CLASS(meshEdge1DCart), INTENT(in):: self
REAL(8):: r(1:3)
@ -174,420 +237,316 @@ MODULE moduleMesh1DCart
!VOLUME FUNCTIONS
!SEGMENT FUNCTIONS
!Init element
SUBROUTINE initCell1DCartSegm(self, n, p, nodes)
!Init segment element
SUBROUTINE initVol1DCartSegm(self, n, p)
USE moduleRefParam
IMPLICIT NONE
CLASS(meshCell1DCartSegm), INTENT(out):: self
CLASS(meshVol1DCartSegm), 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%nNodes = SIZE(p)
self%n1 => nodes(p(1))%obj
self%n2 => nodes(p(2))%obj
self%n1 => mesh%nodes(p(1))%obj
self%n2 => mesh%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%calculateVolume()
CALL self%area()
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)
ALLOCATE(self%listPart_in(1:nSpecies))
ALLOCATE(self%totalWeight(1:nSpecies))
END SUBROUTINE initVol1DCartSegm
END SUBROUTINE initCell1DCartSegm
!Get nodes from 1D volume
PURE FUNCTION getNodesSegm(self, nNodes) RESULT(n)
IMPLICIT NONE
CLASS(meshCell1DCartSegm), 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 randPos1DCartSegm(self) RESULT(r)
!Calculates a random position in 1D volume
FUNCTION randPos1DCartSeg(self) RESULT(r)
USE moduleRandom
IMPLICIT NONE
CLASS(meshCell1DCartSegm), INTENT(in):: self
CLASS(meshVol1DCartSegm), INTENT(in):: self
REAL(8):: r(1:3)
REAL(8):: Xi(1:3)
REAL(8):: fPsi(1:2)
REAL(8):: xii(1:3)
REAL(8), ALLOCATABLE:: fPsi(:)
Xi = 0.D0
Xi(1) = random(-1.D0, 1.D0)
xii(1) = random(-1.D0, 1.D0)
xii(2:3) = 0.D0
fPsi = self%fPsi(Xi, 2)
r = 0.D0
fPsi = self%fPsi(xii)
r(1) = DOT_PRODUCT(fPsi, self%x)
END FUNCTION randPos1DCartSegm
END FUNCTION randPos1DCartSeg
!Compute element functions at point Xi
PURE FUNCTION fPsiSegm(Xi, nNodes) RESULT(fPsi)
!Computes element area
PURE SUBROUTINE areaSegm(self)
IMPLICIT NONE
REAL(8), INTENT(in):: Xi(1:3)
INTEGER, INTENT(in):: nNodes
REAL(8):: fPsi(1:nNodes)
CLASS(meshVol1DCartSegm), INTENT(inout):: self
REAL(8):: l !element length
REAL(8):: fPsi(1:2)
REAL(8):: detJ
REAL(8):: Xii(1:3)
fPsi = (/ 1.D0 - Xi(1), &
1.D0 + Xi(1) /)
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
fPsi = fPsi * 0.50D0
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
!Derivative element function at coordinates Xi
PURE FUNCTION dPsiSegm(Xi, nNodes) RESULT(dPsi)
!Computes element derivative shape function at Xii
PURE FUNCTION dPsiSegm(xi) RESULT(dPsi)
IMPLICIT NONE
REAL(8), INTENT(in):: Xi(1:3)
INTEGER, INTENT(in):: nNodes
REAL(8):: dPsi(1:3,1:nNodes)
REAL(8), INTENT(in):: xi(1:3)
REAL(8), ALLOCATABLE:: dPsi(:,:)
dPsi = 0.D0
ALLOCATE(dPsi(1:1, 1:2))
dPsi(1, 1:2) = (/ -5.D-1, 5.D-1 /)
dPsi(1, 1) = -5.D-1
dPsi(1, 2) = 5.D-1
END FUNCTION dPsiSegm
!Partial derivative in global coordinates
PURE FUNCTION partialDerSegm(self, nNodes, dPsi) RESULT(pDer)
!Computes partial derivatives of coordinates
PURE SUBROUTINE partialDerSegm(self, dPsi, dx)
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)
CLASS(meshVol1DCartSegm), INTENT(in):: self
REAL(8), INTENT(in):: dPsi(1:,1:)
REAL(8), INTENT(out), DIMENSION(1):: dx
pDer = 0.D0
dx(1) = DOT_PRODUCT(dPsi(1,:), self%x)
pDer(1,1) = DOT_PRODUCT(dPsi(1,1:2), self%x(1:2))
pDer(2,2) = 1.D0
pDer(3,3) = 1.D0
END SUBROUTINE partialDerSegm
END FUNCTION partialDerSegm
PURE FUNCTION gatherEFSegm(self, Xi) RESULT(array)
!Computes local stiffness matrix
PURE FUNCTION elemKSegm(self) RESULT(ke)
IMPLICIT NONE
CLASS(meshCell1DCartSegm), INTENT(in):: self
REAL(8), INTENT(in):: Xi(1:3)
REAL(8):: array(1:3)
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 /)
array = -self%gatherDF(Xi, 2, 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
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)
!Get nodes from 1D volume
PURE FUNCTION getNodesSegm(self) RESULT(n)
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
CLASS(meshVol1DCartSegm), INTENT(in):: self
INTEGER, ALLOCATABLE:: n(:)
localK = 0.D0
ALLOCATE(n(1:2))
n = (/ self%n1%n, self%n2%n /)
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 FUNCTION getNodesSegm
END DO
END FUNCTION elemKSegm
!Compute the local source vector for a force f
PURE FUNCTION elemFSegm(self, nNodes, source) RESULT(localF)
PURE FUNCTION phy2logSegm(self, r) RESULT(xN)
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
CLASS(meshVol1DCartSegm), INTENT(in):: self
REAL(8), INTENT(in):: r(1:3)
REAL(8):: Xi(1:3)
REAL(8):: xN(1:3)
Xi = 0.D0
Xi(1) = 2.D0*(r(1) - self%x(1))/(self%x(2) - self%x(1)) - 1.D0
xN = 0.D0
xN(1) = 2.D0*(r(1) - self%x(1))/(self%x(2) - self%x(1)) - 1.D0
END FUNCTION phy2logSegm
!Get the next element for a logical position Xi
SUBROUTINE neighbourElementSegm(self, Xi, neighbourElement)
!Get next element for a logical position xi
SUBROUTINE nextElementSegm(self, xi, nextElement)
IMPLICIT NONE
CLASS(meshCell1DCartSegm), INTENT(in):: self
REAL(8), INTENT(in):: Xi(1:3)
CLASS(meshElement), POINTER, INTENT(out):: neighbourElement
CLASS(meshVol1DCartSegm), INTENT(in):: self
REAL(8), INTENT(in):: xi(1:3)
CLASS(*), POINTER, INTENT(out):: nextElement
NULLIFY(neighbourElement)
IF (Xi(1) < -1.D0) THEN
neighbourElement => self%e2
NULLIFY(nextElement)
IF (xi(1) < -1.D0) THEN
nextElement => self%e2
ELSEIF (Xi(1) > 1.D0) THEN
neighbourElement => self%e1
ELSEIF (xi(1) > 1.D0) THEN
nextElement => self%e1
END IF
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
END SUBROUTINE nextElementSegm
!COMMON FUNCTIONS FOR 1D VOLUME ELEMENTS
!Compute element Jacobian determinant
PURE FUNCTION detJ1DCart(pDer) RESULT(dJ)
!Calculates a random position in 1D volume
!Computes the element Jacobian determinant
PURE FUNCTION detJ1DCart(self, xi, dPsi_in) RESULT(dJ)
IMPLICIT NONE
REAL(8), INTENT(in):: pDer(1:3, 1:3)
CLASS(meshVol1DCart), INTENT(in):: self
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)
dJ = pDer(1, 1)
IF (PRESENT(dPsi_in)) THEN
dPsi = dPsi_in
ELSE
dPsi = self%dPsi(xi)
END IF
CALL self%partialDer(dPsi, dx)
dJ = dx(1)
END FUNCTION detJ1DCart
!Compute element Jacobian inverse matrix (without determinant)
PURE FUNCTION invJ1DCart(pDer) RESULT(invJ)
!Computes the invers Jacobian
PURE FUNCTION invJ1DCart(self, xi, dPsi_in) RESULT(invJ)
IMPLICIT NONE
REAL(8), INTENT(in):: pDer(1:3, 1:3)
REAL(8):: invJ(1:3,1:3)
CLASS(meshVol1DCart), INTENT(in):: self
REAL(8), INTENT(in):: xi(1:3)
REAL(8), INTENT(in), OPTIONAL:: dPsi_in(1:,1:)
REAL(8), ALLOCATABLE:: dPsi(:,:)
REAL(8):: dx(1)
REAL(8):: invJ
invJ = 0.D0
IF (PRESENT(dPsi_in)) THEN
dPsi = dPsi_in
invJ(1, 1) = 1.D0/pDer(1, 1)
invJ(2, 2) = 1.D0
invJ(3, 3) = 1.D0
ELSE
dPsi = self%dPsi(xi)
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

91
src/modules/mesh/1DCart/moduleMesh1DCartBoundary.f90 Normal file
View file

@ -0,0 +1,91 @@
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

261
src/modules/mesh/1DCart/moduleMesh1DCartRead.f90 Normal file
View file

@ -0,0 +1,261 @@
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

8
src/modules/mesh/1DRad/makefile
View file

@ -1,5 +1,11 @@
all: moduleMesh1DRad.o
all: moduleMesh1DRad.o moduleMesh1DRadBoundary.o moduleMesh1DRadRead.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 $(OBJDIR)/$@

746
src/modules/mesh/1DRad/moduleMesh1DRad.f90
View file

@ -4,17 +4,12 @@
! 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
@ -26,42 +21,112 @@ 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
TYPE, PUBLIC, EXTENDS(meshCell):: meshCell1DRadSegm
!Boundary functions defined in the submodule Boundary
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(meshElement), POINTER:: e1 => NULL(), e2 => NULL()
CLASS(*), POINTER:: e1 => NULL(), e2 => NULL()
REAL(8):: arNodes(1:2)
CONTAINS
!meshCell DEFERRED PROCEDURES
PROCEDURE, PASS:: init => initCell1DRadSegm
PROCEDURE, PASS:: getNodes => getNodesSegm
PROCEDURE, PASS:: randPos => randPos1DRadSegm
PROCEDURE, NOPASS:: fPsi => fPsiSegm
PROCEDURE, NOPASS:: dPsi => dPsiSegm
PROCEDURE, PASS:: partialDer => partialDerSegm
PROCEDURE, NOPASS:: detJac => detJ1DRad
PROCEDURE, NOPASS:: invJac => invJ1DRad
PROCEDURE, PASS:: gatherElectricField => gatherEFSegm
PROCEDURE, PASS:: gatherMagneticField => gatherMFSegm
PROCEDURE, PASS:: elemK => elemKSegm
PROCEDURE, PASS:: elemF => elemFSegm
PROCEDURE, NOPASS:: inside => insideSegm
PROCEDURE, PASS:: phy2log => phy2logSegm
PROCEDURE, PASS:: neighbourElement => neighbourElementSegm
!PARTICLUAR PROCEDURES
PROCEDURE, PASS, PRIVATE:: calculateVolume => volumeSegm
PROCEDURE, PASS:: init => initVol1DRadSegm
PROCEDURE, PASS:: randPos => randPos1DRadSeg
PROCEDURE, PASS:: area => areaRad
PROCEDURE, NOPASS:: fPsi => fPsiRad
PROCEDURE, NOPASS:: dPsi => dPsiRad
PROCEDURE, PASS:: partialDer => partialDerRad
PROCEDURE, PASS:: elemK => elemKRad
PROCEDURE, PASS:: elemF => elemFRad
PROCEDURE, NOPASS:: weight => weightRad
PROCEDURE, NOPASS:: inside => insideRad
PROCEDURE, PASS:: scatter => scatterRad
PROCEDURE, PASS:: gatherEF => gatherEFRad
PROCEDURE, PASS:: getNodes => getNodesRad
PROCEDURE, PASS:: phy2log => phy2logRad
PROCEDURE, PASS:: nextElement => nextElementRad
END TYPE meshCell1DRadSegm
END TYPE meshVol1DRadSegm
CONTAINS
!NODE FUNCTIONS
@ -69,7 +134,6 @@ MODULE moduleMesh1DRad
SUBROUTINE initNode1DRad(self, n, r)
USE moduleSpecies
USE moduleRefParam
USE OMP_LIB
IMPLICIT NONE
CLASS(meshNode1DRad), INTENT(out):: self
@ -81,11 +145,9 @@ MODULE moduleMesh1DRad
!Node volume, to be determined in mesh
self%v = 0.D0
!Allocate output
!Allocates output
ALLOCATE(self%output(1:nSpecies))
CALL OMP_INIT_LOCK(self%lock)
END SUBROUTINE initNode1DRad
PURE FUNCTION getCoord1DRad(self) RESULT(r)
@ -99,7 +161,7 @@ MODULE moduleMesh1DRad
END FUNCTION getCoord1DRad
!EDGE FUNCTIONS
!Init edge element
!Inits edge element
SUBROUTINE initEdge1DRad(self, n, p, bt, physicalSurface)
USE moduleSpecies
USE moduleBoundary
@ -115,15 +177,12 @@ 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
@ -131,7 +190,23 @@ MODULE moduleMesh1DRad
ALLOCATE(self%fboundary(1:nSpecies))
!Assign functions to boundary
DO s = 1, nSpecies
CALL pointBoundaryFunction(self, s)
SELECT TYPE(obj => self%boundary%bTypes(s)%obj)
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
@ -141,29 +216,18 @@ MODULE moduleMesh1DRad
END SUBROUTINE initEdge1DRad
!Get nodes from edge
PURE FUNCTION getNodes1DRad(self, nNodes) RESULT(n)
PURE FUNCTION getNodes1DRad(self) RESULT(n)
IMPLICIT NONE
CLASS(meshEdge1DRad), INTENT(in):: self
INTEGER, INTENT(in):: nNodes
INTEGER:: n(1:nNodes)
INTEGER, ALLOCATABLE:: n(:)
ALLOCATE(n(1))
n = (/ self%n1%n /)
END FUNCTION getNodes1DRad
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
!Calculates a 'random' position in edge
FUNCTION randPos1DRad(self) RESULT(r)
CLASS(meshEdge1DRad), INTENT(in):: self
REAL(8):: r(1:3)
@ -174,435 +238,325 @@ MODULE moduleMesh1DRad
!VOLUME FUNCTIONS
!SEGMENT FUNCTIONS
!Init element
SUBROUTINE initCell1DRadSegm(self, n, p, nodes)
!Init segment element
SUBROUTINE initVol1DRadSegm(self, n, p)
USE moduleRefParam
IMPLICIT NONE
CLASS(meshCell1DRadSegm), INTENT(out):: self
CLASS(meshVol1DRadSegm), 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%nNodes = SIZE(p)
self%n1 => nodes(p(1))%obj
self%n2 => nodes(p(2))%obj
self%n1 => mesh%nodes(p(1))%obj
self%n2 => mesh%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%calculateVolume()
CALL self%area()
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)
ALLOCATE(self%listPart_in(1:nSpecies))
ALLOCATE(self%totalWeight(1:nSpecies))
END SUBROUTINE initVol1DRadSegm
END SUBROUTINE initCell1DRadSegm
!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)
!Calculates a random position in 1D volume
FUNCTION randPos1DRadSeg(self) RESULT(r)
USE moduleRandom
IMPLICIT NONE
CLASS(meshCell1DRadSegm), INTENT(in):: self
CLASS(meshVol1DRadSegm), INTENT(in):: self
REAL(8):: r(1:3)
REAL(8):: Xi(1:3)
REAL(8):: fPsi(1:2)
REAL(8):: xii(1:3)
REAL(8), ALLOCATABLE:: fPsi(:)
Xi = 0.D0
Xi(1) = random(-1.D0, 1.D0)
xii(1) = random(-1.D0, 1.D0)
xii(2:3) = 0.D0
fPsi = self%fPsi(Xi, 2)
r = 0.D0
fPsi = self%fPsi(xii)
r(1) = DOT_PRODUCT(fPsi, self%r)
END FUNCTION randPos1DRadSegm
END FUNCTION randPos1DRadSeg
!Compute element functions at point Xi
PURE FUNCTION fPsiSegm(Xi, nNodes) RESULT(fPsi)
!Computes element area
PURE SUBROUTINE areaRad(self)
IMPLICIT NONE
REAL(8), INTENT(in):: Xi(1:3)
INTEGER, INTENT(in):: nNodes
REAL(8):: fPsi(1:nNodes)
CLASS(meshVol1DRadSegm), INTENT(inout):: self
REAL(8):: l !element length
REAL(8):: fPsi(1:2)
REAL(8):: r
REAL(8):: detJ
REAL(8):: Xii(1:3)
fPsi = (/ 1.D0 - Xi(1), &
1.D0 + Xi(1) /)
self%volume = 0.D0
self%arNodes = 0.D0
!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
fPsi = fPsi * 0.50D0
END SUBROUTINE areaRad
END FUNCTION fPsiSegm
!Derivative element function at coordinates Xi
PURE FUNCTION dPsiSegm(Xi, nNodes) RESULT(dPsi)
!Computes element functions at point xii
PURE FUNCTION fPsiRad(xi) RESULT(fPsi)
IMPLICIT NONE
REAL(8), INTENT(in):: Xi(1:3)
INTEGER, INTENT(in):: nNodes
REAL(8):: dPsi(1:3,1:nNodes)
REAL(8), INTENT(in):: xi(1:3)
REAL(8), ALLOCATABLE:: fPsi(:)
dPsi = 0.D0
ALLOCATE(fPsi(1:2))
dPsi(1, 1:2) = (/ -5.D-1, 5.D-1 /)
fPsi(1) = 1.D0 - xi(1)
fPsi(2) = 1.D0 + xi(1)
fPsi = fPsi * 5.D-1
END FUNCTION dPsiSegm
END FUNCTION fPsiRad
!Partial derivative in global coordinates
PURE FUNCTION partialDerSegm(self, nNodes, dPsi) RESULT(pDer)
!Computes element derivative shape function at Xii
PURE FUNCTION dPsiRad(xi) RESULT(dPsi)
IMPLICIT NONE
CLASS(meshCell1DRadSegm), INTENT(in):: self
INTEGER, INTENT(in):: nNodes
REAL(8), INTENT(in):: dPsi(1:3,1:nNodes)
REAL(8):: pDer(1:3, 1:3)
REAL(8), INTENT(in):: xi(1:3)
REAL(8), ALLOCATABLE:: dPsi(:,:)
pDer = 0.D0
ALLOCATE(dPsi(1:1, 1:2))
pDer(1,1) = DOT_PRODUCT(dPsi(1,1:2), self%r(1:2))
pDer(2,2) = 1.D0
pDer(3,3) = 1.D0
dPsi(1, 1) = -5.D-1
dPsi(1, 2) = 5.D-1
END FUNCTION partialDerSegm
END FUNCTION dPsiRad
PURE FUNCTION gatherEFSegm(self, Xi) RESULT(array)
!Computes partial derivatives of coordinates
PURE SUBROUTINE partialDerRad(self, dPsi, dx)
IMPLICIT NONE
CLASS(meshCell1DRadSegm), INTENT(in):: self
REAL(8), INTENT(in):: Xi(1:3)
REAL(8):: array(1:3)
CLASS(meshVol1DRadSegm), INTENT(in):: self
REAL(8), INTENT(in):: dPsi(1:,1:)
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 /)
array = -self%gatherDF(Xi, 2, 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
END FUNCTION gatherEFRad
PURE FUNCTION gatherMFSegm(self, Xi) RESULT(array)
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
!Get nodes from 1D volume
PURE FUNCTION getNodesRad(self) RESULT(n)
IMPLICIT NONE
CLASS(meshCell1DRadSegm), 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):: r
REAL(8):: invJ(1:3, 1:3), detJ
INTEGER:: l
CLASS(meshVol1DRadSegm), INTENT(in):: self
INTEGER, ALLOCATABLE:: n(:)
localK = 0.D0
ALLOCATE(n(1:2))
n = (/ self%n1%n, self%n2%n /)
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
END FUNCTION getNodesRad
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
PURE FUNCTION phy2logRad(self, r) RESULT(xN)
IMPLICIT NONE
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
CLASS(meshVol1DRadSegm), INTENT(in):: self
REAL(8), INTENT(in):: r(1:3)
REAL(8):: Xi(1:3)
REAL(8):: xN(1:3)
Xi = 0.D0
xN = 0.D0
xN(1) = 2.D0*(r(1) - self%r(1))/(self%r(2) - self%r(1)) - 1.D0
Xi(1) = 2.D0*(r(1) - self%r(1))/(self%r(2) - self%r(1)) - 1.D0
END FUNCTION phy2logRad
END FUNCTION phy2logSegm
!Get the next element for a logical position Xi
SUBROUTINE neighbourElementSegm(self, Xi, neighbourElement)
!Get next element for a logical position xi
SUBROUTINE nextElementRad(self, xi, nextElement)
IMPLICIT NONE
CLASS(meshCell1DRadSegm), INTENT(in):: self
REAL(8), INTENT(in):: Xi(1:3)
CLASS(meshElement), POINTER, INTENT(out):: neighbourElement
CLASS(meshVol1DRadSegm), INTENT(in):: self
REAL(8), INTENT(in):: xi(1:3)
CLASS(*), POINTER, INTENT(out):: nextElement
NULLIFY(neighbourElement)
IF (Xi(1) < -1.D0) THEN
neighbourElement => self%e2
NULLIFY(nextElement)
IF (xi(1) < -1.D0) THEN
nextElement => self%e2
ELSEIF (Xi(1) > 1.D0) THEN
neighbourElement => self%e1
ELSEIF (xi(1) > 1.D0) THEN
nextElement => self%e1
END IF
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
END SUBROUTINE nextElementRad
!COMMON FUNCTIONS FOR 1D VOLUME ELEMENTS
!Compute element Jacobian determinant
PURE FUNCTION detJ1DRad(pDer) RESULT(dJ)
!Computes the element Jacobian determinant
PURE FUNCTION detJ1DRad(self, xi, dPsi_in) RESULT(dJ)
IMPLICIT NONE
REAL(8), INTENT(in):: pDer(1:3, 1:3)
CLASS(meshVol1DRad), INTENT(in):: self
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)
dJ = pDer(1, 1)
IF (PRESENT(dPsi_in)) THEN
dPsi = dPsi_in
ELSE
dPsi = self%dPsi(xi)
END IF
CALL self%partialDer(dPsi, dx)
dJ = dx(1)
END FUNCTION detJ1DRad
!Compute element Jacobian inverse matrix (without determinant)
PURE FUNCTION invJ1DRad(pDer) RESULT(invJ)
!Computes the invers Jacobian
PURE FUNCTION invJ1DRad(self, xi, dPsi_in) RESULT(invJ)
IMPLICIT NONE
REAL(8), INTENT(in):: pDer(1:3, 1:3)
REAL(8):: invJ(1:3,1:3)
CLASS(meshVol1DRad), INTENT(in):: self
REAL(8), INTENT(in):: xi(1:3)
REAL(8), INTENT(in), OPTIONAL:: dPsi_in(1:,1:)
REAL(8), ALLOCATABLE:: dPsi(:,:)
REAL(8):: dx(1)
REAL(8):: invJ
invJ = 0.D0
IF (PRESENT(dPsi_in)) THEN
dPsi = dPsi_in
invJ(1, 1) = 1.D0/pDer(1, 1)
invJ(2, 2) = 1.D0
invJ(3, 3) = 1.D0
ELSE
dPsi = self%dPsi(xi)
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

93
src/modules/mesh/1DRad/moduleMesh1DRadBoundary.f90 Normal file
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@ -0,0 +1,93 @@
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

261
src/modules/mesh/1DRad/moduleMesh1DRadRead.f90 Normal file
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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

5
src/modules/mesh/2DCart/makefile
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@ -1,5 +0,0 @@
all : moduleMesh2DCart.o
moduleMesh2DCart.o: moduleMesh2DCart.f90
$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@

1439
src/modules/mesh/2DCart/moduleMesh2DCart.f90
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File diff suppressed because it is too large Load diff

10
src/modules/mesh/2DCyl/makefile
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@ -1,5 +1,11 @@
all : moduleMesh2DCyl.o
all : moduleMeshCyl.o moduleMeshCylBoundary.o moduleMeshCylRead.o
moduleMesh2DCyl.o: moduleMesh2DCyl.f90
moduleMeshCyl.o: moduleMeshCyl.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 $(OBJDIR)/$@

1476
src/modules/mesh/2DCyl/moduleMesh2DCyl.f90
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src/modules/mesh/2DCyl/moduleMeshCyl.f90 Normal file
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src/modules/mesh/2DCyl/moduleMeshCylBoundary.f90 Normal file
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!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

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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

5
src/modules/mesh/3DCart/makefile
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@ -1,5 +0,0 @@
all : moduleMesh3DCart.o
moduleMesh3DCart.o: moduleMesh3DCart.f90
$(FC) $(FCFLAGS) -c $(subst .o,.f90,$@) -o $(OBJDIR)/$@

951
src/modules/mesh/3DCart/moduleMesh3DCart.f90
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@ -1,951 +0,0 @@
!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

7
src/modules/mesh/inout/0D/makefile
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@ -1,7 +0,0 @@
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 $(OBJDIR)/$@

99
src/modules/mesh/inout/0D/moduleMeshInput0D.f90
View file

@ -1,99 +0,0 @@
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

78
src/modules/mesh/inout/0D/moduleMeshOutput0D.f90
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@ -1,78 +0,0 @@
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

7
src/modules/mesh/inout/gmsh2/makefile
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@ -1,7 +0,0 @@
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 $(OBJDIR)/$@

375
src/modules/mesh/inout/gmsh2/moduleMeshInputGmsh2.f90
View file

@ -1,375 +0,0 @@
MODULE moduleMeshInputGmsh2
!Reads a mesh in the Gmsh v2.0 format
CONTAINS
!Init a mesh to use Gmsh2 format
SUBROUTINE initGmsh2(self)
USE moduleMesh
USE moduleMeshOutputGmsh2
IMPLICIT NONE
CLASS(meshGeneric), INTENT(inout), TARGET:: self
IF (ASSOCIATED(meshForMCC, self)) self%printColl => printCollGmsh2
SELECT TYPE(self)
TYPE IS(meshParticles)
self%printOutput => printOutputGmsh2
self%printEM => printEMGmsh2
self%readInitial => readInitialGmsh2
self%printAverage => printAverageGmsh2
END SELECT
self%readMesh => readGmsh2
END SUBROUTINE initGmsh2
!Read a Gmsh 2 format
SUBROUTINE readGmsh2(self, filename)
USE moduleMesh3DCart
USE moduleMesh2DCyl
USE moduleMesh2DCart
USE moduleMesh1DRad
USE moduleMesh1DCart
USE moduleBoundary
IMPLICIT NONE
CLASS(meshGeneric), INTENT(inout):: self
CHARACTER(:), ALLOCATABLE, INTENT(in):: filename
REAL(8):: r(1:3) !3 generic coordinates
INTEGER, ALLOCATABLE:: p(:) !Array for nodes
INTEGER:: e = 0, n = 0, eTemp = 0, elemType = 0, bt = 0
INTEGER:: totalNumElem
INTEGER:: numEdges
INTEGER:: boundaryType
!Read 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))
SELECT TYPE(self)
TYPE IS(meshParticles)
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
END SELECT
!Read the nodes information
DO e = 1, self%numNodes
READ(10, *) n, r(1), r(2), r(3)
SELECT CASE(self%dimen)
CASE(3)
ALLOCATE(meshNode3Dcart::self%nodes(n)%obj)
CASE(2)
SELECT CASE(self%geometry)
CASE("Cyl")
ALLOCATE(meshNode2DCyl:: self%nodes(n)%obj)
CASE("Cart")
ALLOCATE(meshNode2DCart:: self%nodes(n)%obj)
END SELECT
r(3) = 0.D0
CASE(1)
SELECT CASE(self%geometry)
CASE("Rad")
ALLOCATE(meshNode1DRad:: self%nodes(n)%obj)
CASE("Cart")
ALLOCATE(meshNode1DCart:: self%nodes(n)%obj)
END SELECT
r(2:3) = 0.D0
END SELECT
CALL self%nodes(n)%obj%init(n, r)
END DO
!Skip comments
READ(10, *)
READ(10, *)
!Reads total number of elements (no nodes)
READ(10, *) totalNumElem
!Count edges and volume elements
numEdges = 0
SELECT TYPE(self)
TYPE IS(meshParticles)
self%numEdges = 0
DO e = 1, totalNumElem
READ(10, *) eTemp, elemType
SELECT CASE(self%dimen)
CASE(3)
!Element type 2 is triangle in gmsh
IF (elemType == 2) self%numEdges = e
CASE(2)
!Element type 1 is segment in Gmsh
IF (elemType == 1) self%numEdges = e
CASE(1)
!Element type 15 is physical point in Gmsh
IF (elemType == 15) self%numEdges = e
END SELECT
END DO
!Substract the number of edges to the total number of elements
!to obtain the number of volume elements
self%numCells = TotalnumElem - self%numEdges
ALLOCATE(self%edges(1:self%numEdges))
numEdges = self%numEdges
!Go back to the beggining to read elements
DO e=1, totalNumElem
BACKSPACE(10)
END DO
TYPE IS(meshCollisions)
self%numCells = TotalnumElem
numEdges = 0
END SELECT
!Allocates array of cells
ALLOCATE(self%cells(1:self%numCells))
SELECT TYPE(self)
TYPE IS(meshParticles)
!Reads edges
DO e=1, self%numEdges
!Reads the edge according to the geometry
SELECT CASE(self%dimen)
CASE(3)
READ(10, *) n, elemType, eTemp, boundaryType
BACKSPACE(10)
!Associate boundary condition procedure.
bt = getBoundaryID(boundaryType)
SELECT CASE(elemType)
CASE(2)
!Triangular surface
ALLOCATE(p(1:3))
READ(10, *) n, elemType, eTemp, boundaryType, eTemp, p(1:3)
ALLOCATE(meshEdge3DCartTria:: self%edges(e)%obj)
END SELECT
CASE (2)
ALLOCATE(p(1:2))
READ(10,*) n, elemType, eTemp, boundaryType, eTemp, p(1:2)
!Associate boundary condition procedure.
bt = getBoundaryId(boundaryType)
SELECT CASE(self%geometry)
CASE("Cyl")
ALLOCATE(meshEdge2DCyl:: self%edges(e)%obj)
CASE("Cart")
ALLOCATE(meshEdge2DCart:: self%edges(e)%obj)
END SELECT
CASE(1)
ALLOCATE(p(1:1))
READ(10, *) n, elemType, eTemp, boundaryType, eTemp, p(1)
!Associate boundary condition
bt = getBoundaryId(boundaryType)
SELECT CASE(self%geometry)
CASE("Rad")
ALLOCATE(meshEdge1DRad:: self%edges(e)%obj)
CASE("Cart")
ALLOCATE(meshEdge1DCart:: self%edges(e)%obj)
END SELECT
END SELECT
CALL self%edges(e)%obj%init(n, p, bt, boundaryType)
DEALLOCATE(p)
END DO
END SELECT
!Read and initialize cells
DO e = 1, self%numCells
!Read the cell according to the geometry
SELECT CASE(self%dimen)
CASE(3)
READ(10, *) n, elemType
BACKSPACE(10)
SELECT CASE(elemType)
CASE(4)
!Tetrahedron element
ALLOCATE(p(1:4))
READ(10, *) n, elemType, eTemp, eTemp, eTemp, p(1:4)
ALLOCATE(meshCell3DCartTetra:: self%cells(e)%obj)
END SELECT
CASE(2)
SELECT CASE(self%geometry)
CASE("Cyl")
READ(10,*) n, elemType
BACKSPACE(10)
SELECT CASE(elemType)
CASE (2)
!Triangular element
ALLOCATE(p(1:3))
READ(10,*) n, elemType, eTemp, eTemp, eTemp, p(1:3)
ALLOCATE(meshCell2DCylTria:: self%cells(e)%obj)
CASE (3)
!Quadrilateral element
ALLOCATE(p(1:4))
READ(10,*) n, elemType, eTemp, eTemp, eTemp, p(1:4)
ALLOCATE(meshCell2DCylQuad:: self%cells(e)%obj)
END SELECT
CASE("Cart")
READ(10,*) n, elemType
BACKSPACE(10)
SELECT CASE(elemType)
CASE (2)
!Triangular element
ALLOCATE(p(1:3))
READ(10,*) n, elemType, eTemp, eTemp, eTemp, p(1:3)
ALLOCATE(meshCell2DCartTria:: self%cells(e)%obj)
CASE (3)
!Quadrilateral element
ALLOCATE(p(1:4))
READ(10,*) n, elemType, eTemp, eTemp, eTemp, p(1:4)
ALLOCATE(meshCell2DCartQuad:: self%cells(e)%obj)
END SELECT
END SELECT
CASE(1)
SELECT CASE(self%geometry)
CASE("Rad")
ALLOCATE(p(1:2))
READ(10, *) n, elemType, eTemp, eTemp, eTemp, p(1:2)
ALLOCATE(meshCell1DRadSegm:: self%cells(e)%obj)
CASE("Cart")
ALLOCATE(p(1:2))
READ(10, *) n, elemType, eTemp, eTemp, eTemp, p(1:2)
ALLOCATE(meshCell1DCartSegm:: self%cells(e)%obj)
END SELECT
END SELECT
CALL self%cells(e)%obj%init(n - numEdges, p, self%nodes)
DEALLOCATE(p)
END DO
CLOSE(10)
!Call mesh connectivity
CALL self%connectMesh
END SUBROUTINE readGmsh2
!Reads the initial information from an output file for an species
SUBROUTINE readInitialGmsh2(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
INTEGER:: i, e
INTEGER:: numNodes
OPEN(10, file = TRIM(filename))
!Skip first lines
DO i = 1, 11
READ(10, *)
END DO
!Reads number of nodes in file
READ(10, *) numNodes
ALLOCATE(density(1:numNodes))
ALLOCATE(velocity(1:numNodes, 1:3))
ALLOCATE(temperature(1:numNodes))
DO i = 1, numNodes
!Reads the density
READ(10, *) e, density(i)
END DO
DO i = 1, 10
READ(10, *)
END DO
DO i = 1, numNodes
!Reads the velocity
READ(10, *) e, velocity(i, 1:3)
END DO
!Skip uneccessary lines
DO i = 1, 10
READ(10, *)
END DO
!Assign density to nodes
DO i = 1, numNodes
!Skips pressure
READ(10, *)
END DO
!Skip uneccessary lines
DO i = 1, 10
READ(10, *)
END DO
!Assign density to nodes
DO i = 1, numNodes
!Skips pressure
READ(10, *) e, temperature(i)
END DO
END SUBROUTINE readInitialGmsh2
END MODULE moduleMeshInputGmsh2

320
src/modules/mesh/inout/gmsh2/moduleMeshOutputGmsh2.f90
View file

@ -1,320 +0,0 @@
MODULE moduleMeshOutputGmsh2
CONTAINS
!Header for mesh format
SUBROUTINE writeGmsh2HeaderMesh(fileID)
IMPLICIT NONE
INTEGER, INTENT(in):: fileID
WRITE(fileID, "(A)") '$MeshFormat'
WRITE(fileID, "(A)") '2.2 0 8'
WRITE(fileID, "(A)") '$EndMeshFormat'
END SUBROUTINE writeGmsh2HeaderMesh
!Node data subroutines
!Header
SUBROUTINE writeGmsh2HeaderNodeData(fileID, title, iteration, time, dimensions, nNodes)
IMPLICIT NONE
INTEGER, INTENT(in):: fileID
CHARACTER(*), INTENT(in):: title
INTEGER, INTENT(in):: iteration, dimensions, nNodes
REAL(8), INTENT(in):: time
WRITE(fileID, "(A)") '$NodeData'
WRITE(fileID, "(I10)") 1
WRITE(fileID, "(A1, A, A1)") '"' , title , '"'
WRITE(fileID, "(I10)") 1
WRITE(fileID, "(ES20.6E3)") time
WRITE(fileID, "(I10)") 3
WRITE(fileID, "(I10)") iteration
WRITE(fileID, "(I10)") dimensions
WRITE(fileID, "(I10)") nNodes
END SUBROUTINE writeGmsh2HeaderNodeData
!Footer
SUBROUTINE writeGmsh2FooterNodeData(fileID)
IMPLICIT NONE
INTEGER, INTENT(in):: fileID
WRITE(fileID, "(A)") '$EndNodeData'
END SUBROUTINE writeGmsh2FooterNodeData
!Element data subroutines
!Header
SUBROUTINE writeGmsh2HeaderElementData(fileID, title, iteration, time, dimensions, nVols)
IMPLICIT NONE
INTEGER, INTENT(in):: fileID
CHARACTER(*), INTENT(in):: title
INTEGER, INTENT(in):: iteration, dimensions, nVols
REAL(8), INTENT(in):: time
WRITE(fileID, "(A)") '$ElementData'
WRITE(fileID, "(I10)") 1
WRITE(fileID, "(A1, A, A1)") '"' , title , '"'
WRITE(fileID, "(I10)") 1
WRITE(fileID, "(ES20.6E3)") time
WRITE(fileID, "(I10)") 3
WRITE(fileID, "(I10)") iteration
WRITE(fileID, "(I10)") dimensions
WRITE(fileID, "(I10)") nVols
END SUBROUTINE writeGmsh2HeaderElementData
!Footer
SUBROUTINE writeGmsh2FooterElementData(fileID)
IMPLICIT NONE
INTEGER, INTENT(in):: fileID
WRITE(fileID, "(A)") '$EndElementData'
END SUBROUTINE writeGmsh2FooterElementData
!Prints the scattered properties of particles into the nodes
SUBROUTINE printOutputGmsh2(self)
USE moduleMesh
USE moduleRefParam
USE moduleSpecies
USE moduleOutput
USE moduleMeshInoutCommon
USE moduleCaseParam, ONLY: timeStep
IMPLICIT NONE
CLASS(meshParticles), INTENT(in):: self
INTEGER:: n, i
TYPE(outputFormat):: output(1:self%numNodes)
REAL(8):: time
CHARACTER(:), ALLOCATABLE:: fileName
time = DBLE(timeStep)*tauMin*ti_ref
DO i = 1, nSpecies
fileName = formatFileName(prefix, species(i)%obj%name, 'msh', timeStep)
WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
OPEN (60, file = path // folder // '/' // fileName)
CALL writeGmsh2HeaderMesh(60)
CALL writeGmsh2HeaderNodeData(60, species(i)%obj%name // ' density (m^-3)', timeStep, time, 1, self%numNodes)
DO n=1, self%numNodes
CALL calculateOutput(self%nodes(n)%obj%output(i), output(n), self%nodes(n)%obj%v, species(i)%obj)
WRITE(60, "(I6,ES20.6E3)") n, output(n)%density
END DO
CALL writeGmsh2FooterNodeData(60)
CALL writeGmsh2HeaderNodeData(60, species(i)%obj%name // ' velocity (m s^-1)', timeStep, time, 3, self%numNodes)
DO n=1, self%numNodes
WRITE(60, "(I6,3(ES20.6E3))") n, output(n)%velocity
END DO
CALL writeGmsh2FooterNodeData(60)
CALL writeGmsh2HeaderNodeData(60, species(i)%obj%name // ' Pressure (Pa)', timeStep, time, 1, self%numNodes)
DO n=1, self%numNodes
WRITE(60, "(I6,3(ES20.6E3))") n, output(n)%pressure
END DO
CALL writeGmsh2FooterNodeData(60)
CALL writeGmsh2HeaderNodeData(60, species(i)%obj%name // ' Temperature (K)', timeStep, time, 1, self%numNodes)
DO n=1, self%numNodes
WRITE(60, "(I6,3(ES20.6E3))") n, output(n)%temperature
END DO
CALL writeGmsh2FooterNodeData(60)
CLOSE (60)
END DO
END SUBROUTINE printOutputGmsh2
!Prints the number of collisions into the volumes
SUBROUTINE printCollGmsh2(self)
USE moduleMesh
USE moduleRefParam
USE moduleCaseParam
USE moduleCollisions
USE moduleOutput
USE moduleMeshInoutCommon
IMPLICIT NONE
CLASS(meshGeneric), INTENT(in):: self
INTEGER:: numEdges
INTEGER:: k, c
INTEGER:: n
REAL(8):: time
CHARACTER(:), ALLOCATABLE:: fileName
CHARACTER(:), ALLOCATABLE:: title
CHARACTER (LEN=2):: cString
SELECT TYPE(self)
TYPE IS(meshParticles)
numEdges = self%numEdges
TYPE IS(meshCollisions)
numEdges = 0
CLASS DEFAULT
numEdges = 0
END SELECT
IF (collOutput) THEN
time = DBLE(timeStep)*tauMin*ti_ref
fileName = formatFileName(prefix, 'Collisions', 'msh', timeStep)
WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
OPEN (60, file = path // folder // '/' // fileName)
CALL writeGmsh2HeaderMesh(60)
DO k = 1, nCollPairs
DO c = 1, interactionMatrix(k)%amount
WRITE(cString, "(I2)") c
title = '"Pair ' // interactionMatrix(k)%sp_i%name // '-' // interactionMatrix(k)%sp_j%name // ' collision ' // cString
CALL writeGmsh2HeaderElementData(60, title, timeStep, time, 1, self%numCells)
DO n=1, self%numCells
WRITE(60, "(I6,I10)") n + numEdges, self%cells(n)%obj%tallyColl(k)%tally(c)
END DO
CALL writeGmsh2FooterElementData(60)
END DO
END DO
CLOSE(60)
END IF
END SUBROUTINE printCollGmsh2
!Prints the electrostatic EM properties into the nodes and volumes
SUBROUTINE printEMGmsh2(self)
USE moduleMesh
USE moduleRefParam
USE moduleCaseParam
USE moduleOutput
USE moduleMeshInoutCommon
IMPLICIT NONE
CLASS(meshParticles), INTENT(in):: self
INTEGER:: n, e
REAL(8):: time
CHARACTER(:), ALLOCATABLE:: fileName
REAL(8):: Xi(1:3)
Xi = (/ 0.D0, 0.D0, 0.D0 /)
IF (emOutput) THEN
time = DBLE(timeStep)*tauMin*ti_ref
fileName = formatFileName(prefix, 'EMField', 'msh', timeStep)
WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
OPEN (20, file = path // folder // '/' // fileName)
CALL writeGmsh2HeaderMesh(20)
CALL writeGmsh2HeaderNodeData(20, 'Potential (V)', timeStep, time, 1, self%numNodes)
DO n=1, self%numNodes
WRITE(20, *) n, self%nodes(n)%obj%emData%phi*Volt_ref
END DO
CALL writeGmsh2FooterNodeData(20)
CALL writeGmsh2HeaderElementData(20, 'Electric Field (V m^-1)', timeStep, time, 3, self%numCells)
DO e=1, self%numCells
WRITE(20, *) e+self%numEdges, self%cells(e)%obj%gatherElectricField(Xi)*EF_ref
END DO
CALL writeGmsh2FooterElementData(20)
CALL writeGmsh2HeaderNodeData(20, 'Magnetic Field (T)', timeStep, time, 3, self%numNodes)
DO n=1, self%numNodes
WRITE(20, *) n, self%nodes(n)%obj%emData%B * B_ref
END DO
CALL writeGmsh2FooterNodeData(20)
CLOSE(20)
END IF
END SUBROUTINE printEMGmsh2
!Prints the average properties of particles into the nodes
SUBROUTINE printAverageGmsh2(self)
USE moduleMesh
USE moduleRefParam
USE moduleSpecies
USE moduleOutput
USE moduleAverage
USE moduleMeshInoutCommon
IMPLICIT NONE
CLASS(meshParticles), INTENT(in):: self
INTEGER:: n, i
TYPE(outputFormat), DIMENSION(1:self%numNodes):: outputMean, outputDeviation
CHARACTER(:), ALLOCATABLE:: fileName
INTEGER:: fileMean=10, fileDeviation=20
DO i = 1, nSpecies
fileName = formatFileName('Average_mean', species(i)%obj%name, 'msh')
WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
OPEN (fileMean, file = path // folder // '/' // fileName)
fileName = formatFileName('Average_deviation', species(i)%obj%name, 'msh')
WRITE(*, "(6X,A15,A)") "Creating file: ", fileName
OPEN (filedeviation, file = path // folder // '/' // fileName)
CALL writeGmsh2HeaderMesh(fileMean)
CALL writeGmsh2HeaderMesh(fileDeviation)
CALL writeGmsh2HeaderNodeData(fileMean, species(i)%obj%name // ' density, mean (m^-3)', 0, 0.D0, 1, self%numNodes)
CALL writeGmsh2HeaderNodeData(fileDeviation, species(i)%obj%name // ' density, sd (m^-3)', 0, 0.D0, 1, self%numNodes)
DO n=1, self%numNodes
CALL calculateOutput(averageScheme(n)%mean%output(i), outputMean(n), self%nodes(n)%obj%v, species(i)%obj)
WRITE(fileMean, "(I6,ES20.6E3)") n, outputMean(n)%density
CALL calculateOutput(averageScheme(n)%deviation%output(i), outputDeviation(n), self%nodes(n)%obj%v, species(i)%obj)
WRITE(fileDeviation, "(I6,ES20.6E3)") n, outputDeviation(n)%density
END DO
CALL writeGmsh2FooterNodeData(fileMean)
CALL writeGmsh2FooterNodeData(fileDeviation)
CALL writeGmsh2HeaderNodeData(fileMean, species(i)%obj%name // ' velocity, mean (m s^-1)', 0, 0.D0, 3, self%numNodes)
CALL writeGmsh2HeaderNodeData(fileDeviation, species(i)%obj%name // ' velocity, sd (m s^-1)', 0, 0.D0, 3, self%numNodes)
DO n=1, self%numNodes
WRITE(fileMean, "(I6,3(ES20.6E3))") n, outputMean(n)%velocity
WRITE(fileDeviation, "(I6,3(ES20.6E3))") n, outputDeviation(n)%velocity
END DO
CALL writeGmsh2FooterNodeData(fileMean)
CALL writeGmsh2FooterNodeData(fileDeviation)
CALL writeGmsh2HeaderNodeData(fileMean, species(i)%obj%name // ' Pressure, mean (Pa)', 0, 0.D0, 1, self%numNodes)
CALL writeGmsh2HeaderNodeData(fileDeviation, species(i)%obj%name // ' Pressure, sd (Pa)', 0, 0.D0, 1, self%numNodes)
DO n=1, self%numNodes
WRITE(fileMean, "(I6,3(ES20.6E3))") n, outputMean(n)%pressure
WRITE(fileDeviation, "(I6,3(ES20.6E3))") n, outputDeviation(n)%pressure
END DO
CALL writeGmsh2FooterNodeData(fileMean)
CALL writeGmsh2FooterNodeData(fileDeviation)
CALL writeGmsh2HeaderNodeData(fileMean, species(i)%obj%name // ' Temperature, mean (K)', 0, 0.D0, 1, self%numNodes)
CALL writeGmsh2HeaderNodeData(fileDeviation, species(i)%obj%name // ' Temperature, sd (K)', 0, 0.D0, 1, self%numNodes)
DO n=1, self%numNodes
WRITE(fileMean, "(I6,3(ES20.6E3))") n, outputMean(n)%temperature
WRITE(fileDeviation, "(I6,3(ES20.6E3))") n, outputDeviation(n)%temperature
END DO
CALL writeGmsh2FooterNodeData(fileMean)
CALL writeGmsh2FooterNodeData(fileDeviation)
CLOSE (fileMean)
CLOSE(fileDeviation)
END DO
END SUBROUTINE printAverageGmsh2
END MODULE moduleMeshOutputGmsh2

16
src/modules/mesh/inout/makefile
View file

@ -1,16 +0,0 @@
all: vtu.o gmsh2.o 0D.o text.o
vtu.o: moduleMeshInoutCommon.o
$(MAKE) -C vtu all
gmsh2.o:
$(MAKE) -C gmsh2 all
0D.o:
$(MAKE) -C 0D all
text.o:
$(MAKE) -C text all
%.o: %.f90
$(FC) $(FCFLAGS) -c $< -o $(OBJDIR)/$@

27
src/modules/mesh/inout/moduleMeshInoutCommon.f90
View file

@ -1,27 +0,0 @@
MODULE moduleMeshInoutCommon
CHARACTER(LEN=4):: prefix = 'Step'
CONTAINS
PURE FUNCTION formatFileName(prefix, suffix, extension, timeStep) RESULT(fileName)
USE moduleOutput
IMPLICIT NONE
CHARACTER(*), INTENT(in):: prefix, suffix, extension
INTEGER, INTENT(in), OPTIONAL:: timeStep
CHARACTER (LEN=iterationDigits):: tString
CHARACTER(:), ALLOCATABLE:: fileName
IF (PRESENT(timeStep)) THEN
WRITE(tString, iterationFormat) timeStep
fileName = prefix // '_' // tString // '_' // suffix // '.' // extension
ELSE
fileName = prefix // '_' // suffix // '.' // extension
END IF
END FUNCTION formatFileName
END MODULE moduleMeshInoutCommon

7
src/modules/mesh/inout/text/makefile
View file

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

232
src/modules/mesh/inout/text/moduleMeshInputText.f90
View file

@ -1,232 +0,0 @@
module moduleMeshInputText
!The mesh is stored as a column-wise text file.
!Aimed for simple geometries in 1D
contains
!Inits the text mesh
subroutine initText(self)
use moduleMesh
use moduleMeshOutputText
implicit none
class(meshGeneric), intent(inout), target:: self
if (associated(meshForMCC,self)) then
self%printColl => printCollText
end if
select type(self)
type is (meshParticles)
self%printOutput => printOutputText
self%printEM => printEMText
self%printAverage => printAverageText
self%readInitial => readInitialText
end select
self%readMesh => readText
end subroutine initText
!Reads the text mesh
subroutine readText(self, filename)
use moduleMesh
use moduleMesh1DCart
use moduleMesh1DRad
use moduleErrors
implicit none
class(meshGeneric), intent(inout):: self
character(:), allocatable, intent(in):: filename !Dummy file, not used
integer:: fileID, reason
character(len=256):: line
integer:: nNodes
real(8):: r(1:3) !dummy 3D coordinate
integer:: physicalID
integer:: n, c
integer, allocatable:: p(:)
integer:: bt
fileID = 10
open(fileID, file=trim(filename))
!Skip header
read(fileID, *)
!Get number of nodes
nNodes = 0
do
read(fileID, *, iostat=reason) line
if (reason > 0) then
call criticalError('Error reading mesh file', 'readText')
else if (reason < 0) then
exit
else if (len(line) > 0) then
nNodes = nNodes + 1
end if
end do
if (nNodes == 0) then
call criticalError('No nodes read in mesh file', 'readText')
end if
self%numNodes = nNodes
allocate(self%nodes(1:self%numNodes))
SELECT TYPE(self)
TYPE IS(meshParticles)
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
END SELECT
self%numCells = nNodes - 1
allocate(self%cells(1:self%numCells))
select type(self)
type is (meshParticles)
self%numEdges = 2
allocate(self%edges(1:self%numEdges))
end select
!Read the mesh now
rewind(fileID)
!Skip header
read(fileID, *)
!Allocate nodes and edges
do n = 1, self%numNodes
r = 0.D0
read(fileID, *) r(1), physicalID
select case(self%geometry)
case("Cart")
allocate(meshNode1DCart:: self%nodes(n)%obj)
case("Rad")
allocate(meshNode1DRad:: self%nodes(n)%obj)
end select
!Init nodes
call self%nodes(n)%obj%init(n, r)
!Allocate edges if required)
select type(self)
type is (meshParticles)
if ((physicalID == 1) .or. (physicalID == 2)) then
select case(self%geometry)
case("Cart")
allocate(meshEdge1DCart:: self%edges(physicalID)%obj)
case("Rad")
allocate(meshEdge1DRad:: self%edges(physicalID)%obj)
end select
allocate(p(1))
p(1) = n
bt = getBoundaryId(physicalID)
call self%edges(physicalID)%obj%init(physicalID, p, physicalID, physicalID)
deallocate(p)
end if
end select
end do
!Allocate cells
n = 1
allocate(p(1:2))
do c = 1, self%numCells
p(1) = n
n = n + 1
p(2) = n
select case(self%geometry)
case("Cart")
allocate(meshCell1DCartSegm:: self%cells(c)%obj)
case("Rad")
allocate(meshCell1DRadSegm:: self%cells(c)%obj)
end select
call self%cells(c)%obj%init(c, p, self%nodes)
end do
deallocate(p)
close(fileID)
!Call mesh connectivity
CALL self%connectMesh
end subroutine readText
subroutine readInitialText(filename, density, velocity, temperature)
use moduleErrors
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
integer:: fileID, reason
character(len=256):: line
integer:: nNodes
integer:: n
fileID = 10
open(fileID, file=trim(filename))
do
read(fileID, *, iostat=reason) line
if (reason > 0) then
call criticalError('Error reading mesh file', 'readText')
else if (reason < 0) then
exit
else if (len(line) > 0) then
nNodes = nNodes + 1
end if
end do
allocate(density(1:nNodes))
allocate(velocity(1:nNodes, 1:3))
allocate(temperature(1:nNodes))
rewind(fileID)
do n = 1, nNodes
read(fileID, *) density(n), velocity(n, 1:3), temperature(n)
end do
close(fileID)
end subroutine readInitialText
end module moduleMeshInputText

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