From 51b4d70e68c06e5ff1315e9c2b136f76f0b75ff7 Mon Sep 17 00:00:00 2001
From: Antoine Hoffmann <antoine.hoffmann@epfl.ch>
Date: Fri, 31 Mar 2023 15:13:39 +0200
Subject: [PATCH] add compile results low mem and changed exclusion
---
.gitignore | 10 +-
matlab/load/compile_results_3D.m | 37 +++++
matlab/load/compile_results_low_mem.m | 148 ++++++++++++++++++
.../kobayashi_2015_linear_results.m | 19 +++
4 files changed, 209 insertions(+), 5 deletions(-)
create mode 100644 matlab/load/compile_results_3D.m
create mode 100644 matlab/load/compile_results_low_mem.m
create mode 100644 testcases/matlab_testscripts/kobayashi_2015_linear_results.m
diff --git a/.gitignore b/.gitignore
index f2c5b1fc..e43fa292 100644
--- a/.gitignore
+++ b/.gitignore
@@ -40,9 +40,9 @@ local/
Gallery/
.vscode/settings.json
*figure*
-*results*
-out*
+results*
+out*
!scripts/*
-*.avi
-gyacomo
-gyacomo_dbg
+*.avi
+gyacomo
+gyacomo_dbg
diff --git a/matlab/load/compile_results_3D.m b/matlab/load/compile_results_3D.m
new file mode 100644
index 00000000..e00ddecf
--- /dev/null
+++ b/matlab/load/compile_results_3D.m
@@ -0,0 +1,37 @@
+function [field, Ts3D] = compile_results_3D(DIRECTORY,JOBNUMMIN,JOBNUMMAX,fieldname)
+CONTINUE = 1;
+JOBNUM = JOBNUMMIN; JOBFOUND = 0;
+% field
+field = [];
+Ts3D = [];
+ii = 1;
+while(CONTINUE)
+ filename = sprintf([DIRECTORY,'outputs_%.2d.h5'],JOBNUM);
+ % Check presence and jobnummax
+ if (exist(filename, 'file') == 2 && JOBNUM <= JOBNUMMAX)
+ %test if it is corrupted or currently running
+ try
+ openable = ~isempty(h5read(filename,'/data/var3d/time'));
+ catch
+ openable = 0;
+ end
+ if openable
+ % load field %%
+ [ F, T, ~] = load_3D_data(filename, fieldname);
+ field = cat(4,field,F);
+ Ts3D = cat(1,Ts3D,T);
+ ii = ii + 1;
+ JOBFOUND = JOBFOUND + 1;
+ end
+ elseif (JOBNUM > JOBNUMMAX)
+ CONTINUE = 0;
+ end
+ JOBNUM = JOBNUM + 1;
+end
+
+if(JOBFOUND == 0)
+ disp('no results found, please verify the paths');
+ return;
+end
+
+end
\ No newline at end of file
diff --git a/matlab/load/compile_results_low_mem.m b/matlab/load/compile_results_low_mem.m
new file mode 100644
index 00000000..c86518e8
--- /dev/null
+++ b/matlab/load/compile_results_low_mem.m
@@ -0,0 +1,148 @@
+function [DATA] = compile_results_low_mem(DATA,DIRECTORY,JOBNUMMIN,JOBNUMMAX)
+CONTINUE = 1;
+JOBNUM = JOBNUMMIN; JOBFOUND = 0;
+DATA.TJOB_SE = []; % Start and end times of jobs
+DATA.NU_EVOL = []; % evolution of parameter nu between jobs
+DATA.CO_EVOL = []; % evolution of CO
+DATA.MUx_EVOL = []; % evolution of parameter mu between jobs
+DATA.MUy_EVOL = []; % evolution of parameter mu between jobs
+DATA.MUz_EVOL = []; % evolution of parameter mu between jobs
+DATA.K_N_EVOL = []; %
+DATA.K_T_EVOL = []; %
+DATA.L_EVOL = []; %
+DATA.DT_EVOL = []; %
+% Low memoery cost data
+HFLUXI_ = [];
+HFLUXE_ = [];
+GGAMMAI_ = [];
+PGAMMAI_ = [];
+Ts0D_ = [];
+DATA.outfilenames = {};
+ii = 1;
+while(CONTINUE)
+ filename = sprintf([DIRECTORY,'outputs_%.2d.h5'],JOBNUM);
+ % Check presence and jobnummax
+ if (exist(filename, 'file') == 2 && JOBNUM <= JOBNUMMAX)
+ DATA.outfilenames{ii} = filename;
+ %test if it is corrupted or currently running
+ try
+ openable = ~isempty(h5read(filename,'/data/var3d/time'));
+ catch
+ openable = 0;
+ end
+ if openable
+ %% load results %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+ disp(sprintf('Loading ID %.2d (%s)',JOBNUM,filename));
+ % Loading from output file
+ CPUTIME = h5readatt(filename,'/data/input','cpu_time');
+ DT_SIM = h5readatt(filename,'/data/input/basic','dt');
+ [Pe, Je, Pi, Ji, kx, ky, z] = load_grid_data(filename);
+ W_GAMMA = strcmp(h5readatt(filename,'/data/input/diag_par','write_gamma'),'y');
+ W_HF = strcmp(h5readatt(filename,'/data/input/diag_par','write_hf' ),'y');
+ KIN_E = strcmp(h5readatt(filename,'/data/input/model', 'ADIAB_E' ),'n');
+
+ if W_GAMMA
+ [ GGAMMA_RI, Ts0D, ~] = load_0D_data(filename, 'gflux_xi');
+ PGAMMA_RI = load_0D_data(filename, 'pflux_xi');
+ GGAMMAI_ = cat(1,GGAMMAI_,GGAMMA_RI); clear GGAMMA_RI
+ PGAMMAI_ = cat(1,PGAMMAI_,PGAMMA_RI); clear PGAMMA_RI
+ end
+
+ if W_HF
+ [ HFLUX_XI, Ts0D, ~] = load_0D_data(filename, 'hflux_xi');
+ HFLUXI_ = cat(1,HFLUXI_,HFLUX_XI); clear HFLUX_XI
+ end
+
+ Ts0D_ = cat(1,Ts0D_,Ts0D);
+
+ % Evolution of simulation parameters
+ load_params
+ DATA.TJOB_SE = [DATA.TJOB_SE Ts0D(1) Ts0D(end)];
+ DATA.NU_EVOL = [DATA.NU_EVOL DATA.NU DATA.NU];
+ DATA.CO_EVOL = [DATA.CO_EVOL DATA.CO DATA.CO];
+ DATA.MUx_EVOL = [DATA.MUx_EVOL DATA.MUx DATA.MUx];
+ DATA.MUy_EVOL = [DATA.MUy_EVOL DATA.MUy DATA.MUy];
+ DATA.MUz_EVOL = [DATA.MUz_EVOL DATA.MUz DATA.MUz];
+ DATA.K_N_EVOL = [DATA.K_N_EVOL DATA.K_N DATA.K_N];
+ DATA.K_T_EVOL = [DATA.K_T_EVOL DATA.K_T DATA.K_T];
+ DATA.L_EVOL = [DATA.L_EVOL DATA.L DATA.L];
+ DATA.DT_EVOL = [DATA.DT_EVOL DATA.DT_SIM DATA.DT_SIM];
+
+ ii = ii + 1;
+ JOBFOUND = JOBFOUND + 1;
+ LASTJOB = JOBNUM;
+ end
+ elseif (JOBNUM > JOBNUMMAX)
+ CONTINUE = 0;
+ disp(['found ',num2str(JOBFOUND),' results']);
+ end
+ JOBNUM = JOBNUM + 1;
+end
+
+if(JOBFOUND == 0)
+ disp('no results found, please verify the paths');
+ return;
+else
+ %% Build grids
+
+ Nky = numel(ky);
+ if Nky > 1
+ dky = ky(2);
+ Ly = 2*pi/dky;
+ else
+ dky = 0;
+ Ly = 0;
+ end
+ [~,iky0] = min(abs(ky));
+ Ny = 2*Nky-1;
+ y = linspace(-Ly/2,Ly/2,Ny+1); y = y(1:end-1);
+
+ Nkx = numel(kx);
+ if Nkx > 1
+ dkx = kx(2);
+ Lx = 2*pi/dkx;
+ else
+ dkx = 0;
+ Lx = 0;
+ end
+ [~,ikx0] = min(abs(kx));
+ Nx = Nkx;
+ x = linspace(-Lx/2,Lx/2,Nx+1); x = x(1:end-1);
+
+ Nz = numel(z);
+
+ [KX,KY] = meshgrid(kx,ky);
+ KPERP2 = KX.^2+KY.^2;
+ %% Add everything in output structure
+ % scaling
+ DATA.scale = 1;%(1/Nx/Ny)^2;
+ % Fields
+ DATA.GGAMMA_RI = GGAMMAI_; DATA.PGAMMA_RI = PGAMMAI_; DATA.HFLUX_X = HFLUXI_;
+ if(KIN_E)
+ DATA.HFLUX_XE = HFLUXE_;
+ end
+ DATA.Ts0D = Ts0D_;
+ DATA.KIN_E=KIN_E;
+ % grids
+ DATA.Pe = Pe; DATA.Pi = Pi;
+ DATA.Je = Je; DATA.Ji = Ji;
+ DATA.kx = kx; DATA.ky = ky; DATA.z = z; DATA.Npol = -z(1)/pi;
+ DATA.x = x; DATA.y = y;
+ DATA.ikx0 = ikx0; DATA.iky0 = iky0;
+ DATA.Nx = Nx; DATA.Ny = Ny; DATA.Nz = Nz; DATA.Nkx = Nkx; DATA.Nky = Nky;
+ DATA.Pmaxe = numel(Pe); DATA.Pmaxi = numel(Pi); DATA.Jmaxe = numel(Je); DATA.Jmaxi = numel(Ji);
+ DATA.dir = DIRECTORY;
+ DATA.localdir = DIRECTORY;
+ DATA.param_title=['$\nu_{',DATA.CONAME,'}=$', num2str(DATA.NU), ...
+ ', $\kappa_{Ni}=$',num2str(DATA.K_N),', $\kappa_{Ti}=$',num2str(DATA.K_T),...
+ ', $L=',num2str(DATA.L),'$, $N=',...
+ num2str(DATA.Nx),'$, $(P,J)=(',num2str(DATA.Pi(end)),',',...
+ num2str(DATA.Ji(end)),')$,',' $\mu_{hd}=$(',num2str(DATA.MUx),...
+ ',',num2str(DATA.MUy),')'];
+ DATA.paramshort = [num2str(DATA.Pmaxi),'x',num2str(DATA.Jmaxi),'x',...
+ num2str(DATA.Nkx),'x',num2str(DATA.Nky),'x',num2str(DATA.Nz)];
+ JOBNUM = LASTJOB;
+
+ filename = sprintf([DIRECTORY,'outputs_%.2d.h5'],JOBNUM);
+end
+end
\ No newline at end of file
diff --git a/testcases/matlab_testscripts/kobayashi_2015_linear_results.m b/testcases/matlab_testscripts/kobayashi_2015_linear_results.m
new file mode 100644
index 00000000..82f33912
--- /dev/null
+++ b/testcases/matlab_testscripts/kobayashi_2015_linear_results.m
@@ -0,0 +1,19 @@
+% results for blue triangles in Kobayashi 2015
+% x_ = [0.06 0.4 0.6];
+% y_ = [0.0 0.1 0.0];
+% plot(x_,y_,'^b','DisplayName','Kobayashi et al. 2015');
+
+
+% results for red squares in Kobayashi 2015
+% x_ = [0.065 0.15 0.35];
+% y_ = [0.0 0.15 0.0];
+% plot(x_,y_,'sr','DisplayName','Kobayashi et al. 2015');
+
+
+% results for green triangles in Kobayashi 2015
+x_ = [0.06 0.5 1.8];
+y_ = [0.0 0.2 0.0];
+plot(x_,y_,'dg','DisplayName','Kobayashi et al. 2015');
+
+
+
--
GitLab