Skip to content
Snippets Groups Projects
Commit 5b04f7e6 authored by Antoine Cyril David Hoffmann's avatar Antoine Cyril David Hoffmann
Browse files

Scripts to generate collision matrix using COSOlver given a grid

parent a143890d
No related branches found
No related tags found
No related merge requests found
Hide whitespace changes
Inline Side-by-side
matlab/COSOlver_matrices_analysis.m 0 → 100644
+ 72
− 0
View file @ 5b04f7e6
addpath(genpath('../matlab')) % ... add
%% Grid configuration
N = 10; % Frequency gridpoints (Nkr = N/2)
L = 120; % Size of the squared frequency domain
dk = 2*pi/L;
kmax = N/2*dk;
kr = dk*(0:N/2);
kz = dk*(0:N/2);
[KZ, KR]= meshgrid(kz,kr);
KPERP = sqrt(KR.^2 + KZ.^2);
kperp = reshape(KPERP,[1,numel(kr)^2]);
kperp = uniquetol(kperp,1e-14);
Nperp = numel(kperp);
COSOlver_path = '../../Documents/MoliSolver/COSOlver/';
COSOLVER.pmaxe = 10;
COSOLVER.jmaxe = 5;
COSOLVER.pmaxi = 10;
COSOLVER.jmaxi = 5;
COSOLVER.neFLR = max(5,ceil(COSOLVER.kperp^2)); % rule of thumb for sum truncation
COSOLVER.niFLR = max(5,ceil(COSOLVER.kperp^2));
COSOLVER.neFLRs = 0; % ... only for GK abel
COSOLVER.npeFLR = 0; % ... only for GK abel
COSOLVER.niFLRs = 0; % ... only for GK abel
COSOLVER.npiFLR = 0; % ... only for GK abel
COSOLVER.gk = 1;
COSOLVER.co = 3;
if 0
%% plot the kperp distribution
figure
plot(kperp)
end
%% Load the matrices
C_self_i = zeros((COSOLVER.pmaxi+1)*(COSOLVER.jmaxi+1),(COSOLVER.pmaxi+1)*(COSOLVER.jmaxi+1),Nperp);
for n_ = 1:Nperp
COSOLVER.kperp = kperp(n_);
k_string = sprintf('%0.4f',kperp(n_));
mat_file_name = ['../iCa/self_Coll_GKE_',num2str(COSOLVER.gk),'_GKI_',num2str(COSOLVER.gk),...
'_ESELF_',num2str(COSOLVER.co),'_ISELF_',num2str(COSOLVER.co),...
'_Pmaxe_',num2str(COSOLVER.pmaxe),'_Jmaxe_',num2str(COSOLVER.jmaxe),...
'_Pmaxi_',num2str(COSOLVER.pmaxi),'_Jmaxi_',num2str(COSOLVER.jmaxi),...
'_JE_12',...
'_NFLR_',num2str(COSOLVER.neFLR),...
'_kperp_',k_string,'.h5'];
tmp = h5read(mat_file_name,'/Caapj/Ceepj');
C_self_i(:,:,n_) = tmp;
end
%% Post processing
dC_self_i = diff(C_self_i,1,3);
gvar_dC = squeeze(sum(sum(abs(dC_self_i),2),1));
%% Plots
%% all coeffs evolution
figure
for ip_ = 1:COSOLVER.pmaxi+1
for ij_ = 1:COSOLVER.jmaxi+1
plot(kperp,squeeze(C_self_i(ip_,ij_,:)),'o'); hold on;
end
end
%% global matrix variation
figure;
kperpmid = 0.5*(kperp(2:end)+kperp(1:end-1));
plot(kperpmid,gvar_dC./diff(kperp)');
matlab/write_fort90_COSOlver.m 0 → 100644
+ 84
− 0
View file @ 5b04f7e6
INPUT = [COSOlver_path,'fort.90'];
fid = fopen(INPUT,'wt');
fprintf(fid,'&BASIC\n');
fprintf(fid,['pmaxe = ', num2str(COSOLVER.pmaxe),'\n']);
fprintf(fid,['jmaxe = ', num2str(COSOLVER.jmaxe),'\n']);
fprintf(fid,['pmaxi = ', num2str(COSOLVER.pmaxi),'\n']);
fprintf(fid,['jmaxi = ', num2str(COSOLVER.jmaxi),'\n']);
fprintf(fid,'JEmaxx=12\n');
fprintf(fid,'PMmaxx=16\n');
fprintf(fid,'\n');
fprintf(fid,['neFLR=',num2str(COSOLVER.neFLR),'\n']);
fprintf(fid,['neFLRs =',num2str(COSOLVER.neFLRs),'\n']);
fprintf(fid,['npeFLR=',num2str(COSOLVER.npeFLR),'\n']);
fprintf(fid,['niFLR=',num2str(COSOLVER.niFLR),'\n']);
fprintf(fid,['niFLRs=',num2str(COSOLVER.niFLRs),'\n']);
fprintf(fid,['npiFLR=',num2str(COSOLVER.npiFLR),'\n']);
fprintf(fid,'\n');
fprintf(fid,['eecolls=.true.','\n']);
fprintf(fid,['iicolls=.true.','\n']);
fprintf(fid,['eicolls=.true.','\n']);
fprintf(fid,['iecolls=.true.','\n']);
fprintf(fid,'/\n');
fprintf(fid,'\n');
fprintf(fid,'&BASIS_TRANSFORMATION_PAR\n');
fprintf(fid,['T5dir = ','''/misc/coeffs_backup/T5src/''','\n']);
fprintf(fid,['T4dir = ','''/misc/T4/NNT4_L000x200_K000x200_P000x200_J000x200/''','\n']);
fprintf(fid,'idxT4max = 30\n');
fprintf(fid,'idxT5max = 0\n');
fprintf(fid,'IFT4 = .true.\n');
fprintf(fid,'IFT5 = .false.\n');
fprintf(fid,'/\n');
fprintf(fid,'\n');
fprintf(fid,'&MODEL_PAR \n');
fprintf(fid,'nu=1\n');
fprintf(fid,'mu=0.023338\n');
fprintf(fid,'tau=1\n');
fprintf(fid,['kperp=',num2str(COSOLVER.kperp,16),'\n']);
fprintf(fid,'/\n');
fprintf(fid,'\n');
fprintf(fid,'&OPERATOR_MODEL \n');
fprintf(fid,['ETEST=', num2str(COSOLVER.co),'\n']);
fprintf(fid,['EBACK=', num2str(COSOLVER.co),'\n']);
fprintf(fid,['ITEST=', num2str(COSOLVER.co),'\n']);
fprintf(fid,['IBACK=', num2str(COSOLVER.co),'\n']);
fprintf(fid,'\n');
fprintf(fid,['ESELF=', num2str(COSOLVER.co),'\n']);
fprintf(fid,['ISELF=', num2str(COSOLVER.co),'\n']);
fprintf(fid,'\n');
fprintf(fid,['GKE = ', num2str(COSOLVER.gk),'\n']);
fprintf(fid,['GKI = ', num2str(COSOLVER.gk),'\n']);
fprintf(fid,'DKTEST = .F.\n');
fprintf(fid,'DKBACK = .F.\n');
fprintf(fid,'ADDTEST = .T.\n');
fprintf(fid,'ADDBACK = .T.\n');
fprintf(fid,'only_gk_part = .false.\n');
fprintf(fid,'only_symmetric = .false.\n');
fprintf(fid,'/\n');
fprintf(fid,'\n');
fprintf(fid,'&MPI\n');
fprintf(fid,'Nprocs_j_ii = 1\n');
fprintf(fid,'MPI_balanced = .false.\n');
fprintf(fid,'/\n');
fprintf(fid,'\n');
fprintf(fid,'&OUTPUT_PAR\n');
fprintf(fid,'OVERWRITE=.true.\n');
fprintf(fid,'nsave_ei=0\n');
fprintf(fid,'nsave_ie=0\n');
fprintf(fid,'nsave_ee=0\n');
fprintf(fid,'nsave_ii=2\n');
fprintf(fid,'ifrestart=.false.\n');
fprintf(fid,['suffix_resfile=','''''','\n']);
fprintf(fid,['outdir = ','''../../../HeLaZ/iCa''','\n']);
fprintf(fid,'/\n');
fprintf(fid,'\n');
fclose(fid);
\ No newline at end of file
wk/compute_collision_mat.m 0 → 100644
+ 81
− 0
View file @ 5b04f7e6
addpath(genpath('../matlab')) % ... add
%% Grid configuration
N = 200; % Frequency gridpoints (Nkr = N/2)
L = 120; % Size of the squared frequency domain
dk = 2*pi/L;
kmax = N/2*dk;
kr = dk*(0:N/2);
kz = dk*(0:N/2);
[KZ, KR]= meshgrid(kz,kr);
KPERP = sqrt(KR.^2 + KZ.^2);
kperp = reshape(KPERP,[1,numel(kr)^2]);
kperp = uniquetol(kperp,1e-14);
Nperp = numel(kperp);
if 0
%% plot the kperp distribution
figure
plot(kperp)
end
%% Check if the differences btw kperp is larger than naming precision
dkperp = diff(kperp);
warning = sum(dkperp<0.0002);
if warning > 0
disp('Warning : dkperp < 0.0002');
end
%%
n_ = 1;
for k_ = kperp
%% Script to run COSOlver in order to create needed collision matrices
COSOlver_path = '../../Documents/MoliSolver/COSOlver/';
COSOLVER.pmaxe = 10;
COSOLVER.jmaxe = 5;
COSOLVER.pmaxi = 10;
COSOLVER.jmaxi = 5;
COSOLVER.kperp = k_;
COSOLVER.neFLR = max(5,ceil(COSOLVER.kperp^2)); % rule of thumb for sum truncation
COSOLVER.niFLR = max(5,ceil(COSOLVER.kperp^2));
COSOLVER.neFLRs = 0; % ... only for GK abel
COSOLVER.npeFLR = 0; % ... only for GK abel
COSOLVER.niFLRs = 0; % ... only for GK abel
COSOLVER.npiFLR = 0; % ... only for GK abel
COSOLVER.gk = 1;
COSOLVER.co = 3;
% ! 0 = nothing
% ! 1 = coulomb
% ! 2 = pitch-angle (with constant coll.freq.)
% ! 3 = sugama
% ! 4 = pitch-angle with veloty dependent coll. freq.
% ! 5 = improved sugama
% ! 6 = Hirschman-Sigmar Clarke
% ! 7 = Abel (only for like species)
% ! 8 = conserving momentun pitch-angle operator (with veloty dependent coll. freq.)
% ! 9 = GK coulomb polarization term
write_fort90_COSOlver
k_string = sprintf('%0.4f',k_);
mat_file_name = ['../iCa/self_Coll_GKE_',num2str(COSOLVER.gk),'_GKI_',num2str(COSOLVER.gk),...
'_ESELF_',num2str(COSOLVER.co),'_ISELF_',num2str(COSOLVER.co),...
'_Pmaxe_',num2str(COSOLVER.pmaxe),'_Jmaxe_',num2str(COSOLVER.jmaxe),...
'_Pmaxi_',num2str(COSOLVER.pmaxi),'_Jmaxi_',num2str(COSOLVER.jmaxi),...
'_JE_12',...
'_NFLR_',num2str(COSOLVER.neFLR),...
'_kperp_',k_string,'.h5'];
if (exist(mat_file_name,'file') > 0)
disp(['Matrix available for kperp = ',k_string]);
else
cd ../../Documents/MoliSolver/COSOlver/
disp(['Matrix not found for kperp = ',k_string]);
disp([num2str(n_),'/',Nperp]
disp('computing...');
CMD = 'mpirun -np 6 bin/CO 2 2 2 > out.txt';
disp(CMD);
system(CMD);
system(CMD);
disp('..done');
cd ../../../HeLaZ/wk
end
end
\ No newline at end of file
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Please register or to comment