From 732c9c90e5ffd8c5db2b6f55e313de3eeb103d25 Mon Sep 17 00:00:00 2001 From: Antoine Hoffmann <antoine.hoffmann@epfl.ch> Date: Tue, 25 Oct 2022 11:49:36 +0200 Subject: [PATCH] test format readme --- README.md | 81 +++++++++++++++++++++++++++---------------------------- 1 file changed, 40 insertions(+), 41 deletions(-) diff --git a/README.md b/README.md index fe6389e3..7f1e1f3e 100644 --- a/README.md +++ b/README.md @@ -17,89 +17,88 @@ along with this program. If not, see <https://www.gnu.org/licenses/>. # How to compile and run GYACOMO 1. Be sure to have correct library paths in local/dirs.inc for the different libraries, see INSTALATION.txt for a tutorial to install the required libraries. -2. Compile from /gyacomo using make, the binary will be located in /gyacomo/bin (you can also compile a debug version using make dbg) -4. The fort.90 file should contain the parameters for a typical CBC to test the compilation. One can run it by calling the executable /bin/gyacomo in the directory where the fort.90 is located. -5. It is possible to run GYACOMO in parallel using MPI: mpirun -np N ./bin/gyacomo Np Ny Nz where N=Np x Ny x Nz is the number of processes and Np Ny Nz are the parallel dimensions in Hermite polynomials, binormal direction and parallel direction, respectively -6. You can stop your simulation without corrupting the output file by creating a blank file call "mystop", using e.g. "touch mystop" in the directory where the simulation is running. (the file will be removed once read) -7. It is also possible to put simulations ID in order to chain them. The parameter Job2load allows you to tell which output file should be read in order to restart a simulation. E.g. I run a first simulation with job2load = -1, it creates a outputs_00.h5 then I create a new fort.90 which I call fort_01.90 where job2load = 0. I run then GYACOMO, indicating that I want it to read the fort_00.90 using 0 as a last argument, i.e. "./gyacomo 0" or "mpirun -np N ./gyacomo Np Ny Nz 0", which will start from the latest 5D state saved in outputs_00.h5. A new output file has also been created, output_01.h5. -8. You can obtain various plots and gifs using gyacomo/wk/gyacomo_analysis.m once the simulation is done. The directory where the results are located must be given in the scripts. It is not a function (yet...) +2. Compile from '/gyacomo' using 'make', the binary will be located in '/gyacomo/bin' (you can also compile a debug version using 'make dbg') +4. The 'fort.90' file should contain the parameters for a typical CBC to test the compilation. One can run it by calling the executable '/bin/gyacomo' in the directory where the 'fort.90' is located. +5. It is possible to run GYACOMO in parallel using MPI: 'mpirun -np N ./bin/gyacomo Np Ny Nz' where N=Np x Ny x Nz is the number of processes and Np Ny Nz are the parallel dimensions in Hermite polynomials, binormal direction and parallel direction, respectively +6. You can stop your simulation without corrupting the output file by creating a blank file call 'mystop', using e.g. 'touch mystop' in the directory where the simulation is running. (the file will be removed once read) +7. It is also possible to put simulations ID in order to chain them. The parameter 'job2load' allows you to tell which output file should be read in order to restart a simulation. E.g. I run a first simulation with 'job2load = -1', it creates a 'outputs_00.h5' then I create a new 'fort.90' which I call 'fort_01.90' where 'job2load = 0'. I run then GYACOMO, indicating that I want it to read the 'fort_00.90' using 0 as a last argument, i.e. './gyacomo 0' or 'mpirun -np N ./gyacomo Np Ny Nz 0', which will start from the latest 5D state saved in 'outputs_00.h5'. A new output file has also been created, 'outputs_01.h5'. +8. You can obtain various plots and gifs using 'gyacomo/wk/gyacomo_analysis.m' once the simulation is done. The directory where the results are located must be given in the scripts. It is not a function (yet...) // Comment : For some collision operators (Sugama and Full Coulomb) you have to run COSOlver from B.J.Frei first in order to generate the required matrices in gyacomo/iCa folder. // # Changelog 4. GYACOMO - 4.1 Miller geometry is added and benchmarked for CBC adiabatic electrons + -[] General and quantitative benchmark for Miller and edge simulations - 4.0 new naming and opening the code with GNU GPLv3 license + -[x] Miller geometry is added and benchmarked for CBC adiabatic electrons + + -[x] new naming and opening the code with GNU GPLv3 license 3. HeLaZ 3D - 3.9 HeLaZ can now evolve electromagnetic fluctuations by solving Ampere equations (benchmarked linearly) + -[x] HeLaZ can now evolve electromagnetic fluctuations by solving Ampere equations (benchmarked linearly) - 3.8 HeLaZ has been benchmarked for CBC with GENE for various gradients values (see Dimits_fig3.m) + -[x] HeLaZ has been benchmarked for CBC with GENE for various gradients values (see Dimits_fig3.m) - 3.7 The frequency plane has been transposed from positive kx to positive ky for easier implementation of shear. Also added 3D zpinch geometry + -[x] The frequency plane has been transposed from positive kx to positive ky for easier implementation of shear. Also added 3D zpinch geometry - 3.6 HeLaZ is now parallelized in p, kx and z and benchmarked for each parallel options with gbms (new molix) for linear fluxtube shearless. + -[x] HeLaZ is now parallelized in p, kx and z and benchmarked for each parallel options with gbms (new molix) for linear fluxtube shearless. - 3.5 Staggered grid for parallel odd/even coupling + -[x] Staggered grid for parallel odd/even coupling - 3.4 HeLaZ can run with adiabatic electrons now! + -[x] HeLaZ can run with adiabatic electrons now! - 3.3 HeLaZ 3D has been benchmarked in fluxtube salphaB geometry linear run with molix (B.J.Frei) code and works now for shear = 0 with periodic z BC + -[x] HeLaZ 3D has been benchmarked in fluxtube salphaB geometry linear run with molix (B.J.Frei) code and works now for shear = 0 with periodic z BC - 3.2 Stopping file procedure like in GBS is added + -[x] Stopping file procedure like in GBS is added - 3.1 Implementation of mirror force + -[x] Implementation of mirror force - 3.0 HeLaZ is now 3D and works like HeLaZ 2D if Nz = 1, the axis were renamed (r,z) -> (x,y,z) and now the parallel direction is ez. All arrays have been extended, diagnostics and analysis too. The linear coefficients are now precomputed with lin_coeff_and_geometry routines. + -[x] HeLaZ is now 3D and works like HeLaZ 2D if Nz = 1, the axis were renamed (r,z) -> (x,y,z) and now the parallel direction is ez. All arrays have been extended, diagnostics and analysis too. The linear coefficients are now precomputed with lin_coeff_and_geometry routines. 2. MPI parallel version - 2.7 Versatile interpolation of kperp for the cosolver matrices and corrections done on DGGK + -[x] Versatile interpolation of kperp for the cosolver matrices and corrections done on DGGK - 2.6 Change of collisionality normalisation (from nu_ei to nu_ii), implementation of FCGK + -[x] Change of collisionality normalisation (from nu_ei to nu_ii), implementation of FCGK - 2.5 GK cosolver collision implementation + -[x] GK cosolver collision implementation - 2.4 2D cartesian parallel (along p and kr) + -[x] 2D cartesian parallel (along p and kr) - 2.3 GK Dougherty operator + -[x] GK Dougherty operator - 2.2 Allow restart with different P,J values (results are not concluents) + -[x] Allow restart with different P,J values (results are not concluents) - 2.1 First compilable parallel version (1D parallel along kr) + -[x] First compilable parallel version (1D parallel along kr) 1. Implementation of the non linear Poisson brackets term - 1.4 Quantitative study with stationary average particle flux \Gamma_\infty - - 1.3 Linear analysis showed that a certain amount of PJ are recquired to trigger mode + -[x] Quantitative study with stationary average particle flux \Gamma_\infty - 1.2 Zonal flows are observed in a similar way to Ricci Rogers 2006 with GS2 + -[x] Linear analysis showed that a certain amount of PJ are recquired to trigger mode - 1.1 Qualitative test : find similar turbulences as Hasegawa Wakatani system with few moments + -[x] Zonal flows are observed in a similar way to Ricci Rogers 2006 with GS2 - 1.1 Methods in fourier_mod.f90 have been validated by tests on Hasegawa Wakatani system + -[x] Qualitative test : find similar turbulences as Hasegawa Wakatani system with few moments - 1.1 Methods in fourier_mod.f90 have been validated by tests on Hasegawa Wakatani system + -[x] Methods in fourier_mod.f90 have been validated by tests on Hasegawa Wakatani system - 1.0 FFTW3 has been used to treat the convolution as a product and discrete fourier transform + -[x] FFTW3 has been used to treat the convolution as a product and discrete fourier transform 0. Write MOLI matlab solver in Fortran using Monli1D as starting point - 0.6 Benchmarks now include Dougherty, Lenard-Bernstein and Full Coulomb collision operators + -[x] Benchmarks now include Dougherty, Lenard-Bernstein and Full Coulomb collision operators - 0.5 Load COSOlver matrices + -[x] Load COSOlver matrices - 0.4 Benchmark with MOLI matlab results for Z-pinch (cf. kz_linear script) + -[x] Benchmark with MOLI matlab results for Z-pinch (cf. kz_linear script) - 0.3 RK4 time solver + -[x] RK4 time solver - 0.2 implement moment hierarchy linear terms + -[x] implement moment hierarchy linear terms - 0.1 implement linear Poisson equation in fourier space + -[x] implement linear Poisson equation in fourier space - 0.0 go from 1D space to 2D fourier and from Hermite basis to Hermite-Laguerre basis - + -[x] go from 1D space to 2D fourier and from Hermite basis to Hermite-Laguerre basis -- GitLab