split into different tests

wk/benchmark.m

-SIMID = 'benchmark'; % Name of the simulations
-addpath(genpath('../matlab')) % ... add 
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% outputs options
-OUTPUTS.nsave_0d = 0;
-OUTPUTS.nsave_1d = 0;
-OUTPUTS.nsave_2d = 1;
-OUTPUTS.nsave_5d = 0;
-OUTPUTS.write_Ni00    = '.true.';
-OUTPUTS.write_moments = '.true.';
-OUTPUTS.write_phi     = '.true.';
-OUTPUTS.write_doubleprecision = '.true.';
-OUTPUTS.resfile0      = '''results''';
-%% Grid parameters
-GRID.pmaxe = 20;
-GRID.jmaxe = 10;
-GRID.pmaxi = 20;
-GRID.jmaxi = 10;
-GRID.nkr   = 1;
-GRID.krmin = 0.;
-GRID.krmax = 0.;
-GRID.nkz   = 1;
-GRID.kzmin = 1.0;
-GRID.kzmax = 1.0;
-%% Model parameters
-MODEL.CO      = -1;  % Collision operator (-1 = Full Coulomb, 0 = Dougherty)
-MODEL.nu      = 0.0; % collisionality nu*L_perp/Cs0
-% temperature ratio T_a/T_e
-MODEL.tau_e   = 1.0;
-MODEL.tau_i   = 1.0;
-% mass ratio sqrt(m_a/m_i)
-MODEL.sigma_e = 0.0233380;
-MODEL.sigma_i = 1.0;
-% charge q_a/e
-MODEL.q_e     =-1.0;
-MODEL.q_i     = 1.0;
-% gradients L_perp/L_x
-MODEL.eta_n   = 0.0;        % Density
-MODEL.eta_T   = 1.0;        % Temperature
-MODEL.eta_B   = 0.0;        % Magnetic
-% Debye length
-MODEL.lambdaD = 0.0;
-%% Time integration and intialization parameters
-TIME_INTEGRATION.numerical_scheme  = '''RK4''';
-BASIC.nrun                = 100000;
-BASIC.dt                  = 0.05;
-BASIC.tmax                = 100.0;
-INITIAL.initback_moments  = 0.01;
-INITIAL.initnoise_moments = 0.;
-INITIAL.iseed             = 42;
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% Write input file
-INPUT = write_fort90(OUTPUTS,GRID,MODEL,INITIAL,TIME_INTEGRATION,BASIC);
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% Run HeLaZ
-nproc = 1;
-EXEC  = ' ../bin/helaz ';
-RUN   = ['mpirun -np ' num2str(nproc)];
-CMD   = [RUN, EXEC, INPUT];
-system(CMD);
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% Run MOLI with same input parameters
-params.RK4 = 1;
-run ../matlab/MOLI_time_solver
-if params.RK4; MOLIsolvername = 'RK4';
-else;          MOLIsolvername = 'ode15i';
-end
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% Analysis and basic figures
-SAVEFIG = 1;
-filename = 'results_00.h5';
-TITLE  = [];
-TITLE = [TITLE,'$\eta_n=',num2str(MODEL.eta_n),'$, '];
-TITLE = [TITLE,'$\eta_B=',num2str(MODEL.eta_B),'$, '];
-TITLE = [TITLE,'$\eta_T=',num2str(MODEL.eta_T),'$, '];
-TITLE = [TITLE,   '$\nu=',num2str(MODEL.nu),'$, '];
-TITLE = [TITLE, '$(P,J)=(',num2str(GRID.pmaxe),',',num2str(GRID.jmaxe),')$'];
-%% Nipj
-
-moment = 'Ni00';
-
-kr       = h5read(filename,['/data/var2d/' moment '/coordkr']);
-kz       = h5read(filename,['/data/var2d/' moment '/coordkz']);
-timeNi     = h5read(filename,'/data/var2d/time');
-Nipj     = zeros(numel(timeNi),numel(kr),numel(kz));
-for it = 1:numel(timeNi)
-    tmp          = h5read(filename,['/data/var2d/', moment,'/', num2str(it,'%06d')]);
-    Nipj(it,:,:) = tmp.real + 1i * tmp.imaginary; 
-end
-
-%% phi
-timephi  = h5read(filename,'/data/var2d/time');
-kr       = h5read(filename,'/data/var2d/phi/coordkr');
-kz       = h5read(filename,'/data/var2d/phi/coordkz');
-phiHeLaZ      = zeros(numel(timephi),numel(kr),numel(kz));
-for it = 1:numel(timephi)
-    tmp         = h5read(filename,['/data/var2d/phi/' num2str(it,'%06d')]);
-    phiHeLaZ(it,:,:) = tmp.real + 1i * tmp.imaginary;
-end
-
-timephiMOLI = results.time;
-phiMOLI  = zeros(size(timephiMOLI));
-for it = 1:numel(timephiMOLI)
-    phiMOLI(it) = get_phi(results.Napj(it,:),params,options);
-end
-
-fig = figure;
-%HeLaZ results
-semilogy(timephi,abs(phiHeLaZ),'-','DisplayName','HeLaZ RK4')
-hold on
-title(TITLE);
-%MOLI results
-semilogy(timephiMOLI,abs(phiMOLI),'--','DisplayName',['MOLI ',MOLIsolvername])
-grid on
-xlabel('$t$')
-ylabel('$|\phi|$')
-legend('show')
-if SAVEFIG; FIGNAME = 'phi'; save_figure; end;
-
-
-fig = figure;
-%HeLaZ results
-x1 = timeNi;
-y1 = abs(Nipj);
-semilogy(x1,y1,'-','DisplayName','HeLaZ RK4')
-hold on
-%MOLI results
-x2 = results.time;
-y2 = abs(results.Napj(:,1));
-semilogy(x2,y2,'--','DisplayName',['MOLI ',MOLIsolvername]);
-title(TITLE);
-grid on
-legend('show')
-xlabel('$t$')
-ylabel(['$|',moment,'|$'])
-if SAVEFIG; FIGNAME = 'Ni00'; save_figure; end;
-
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\ No newline at end of file