diff --git a/matlab/MOLI_kperp_scan.m b/matlab/MOLI_kperp_scan.m
index 8697f98..c3c8d4e 100644
--- a/matlab/MOLI_kperp_scan.m
+++ b/matlab/MOLI_kperp_scan.m
@@ -1,164 +1,166 @@
+%% Run MOLI for a scan in kperp
%% Move to MOLI workspace
cd ../../MoliSolver/MOLI/workspace/
%% Add paths
my_paths
%% Directories
ROOT = '/home/ahoffman/Documents/MoliSolver';
options.dirs.COSOlverdir = fullfile(ROOT,'COSOlver');
options.dirs.MOLIdir = fullfile(ROOT,'MOLI');
%% MOLI Physical and Main Parameters
% Solve DK AND/OR GK Linear Moment Hierarchy.
options.DKI = 0; % First-order DK
options.DKII = 0; % Second-order DK
options.GK = 1; % Gyrokinetic GK
options.EM = 0; % Include Electromagnetic effects (only for GK=1)
options.GD = 0; % Gyro-Drift
options.GDI = 0; % First/second order
% Solve MOLI
options.MOLI = 1; % 1 -> Solve MOLI, 0 -> off
% MOLI Solver
options.solver.solver = 3;
% MOLI Linear Fit Solver
options.LinFitSolver = 2;
%% Main parameter scan
% Closure by truncation
params.Pmaxi = GRID.pmaxi; % parallel ion Hermite moments
params.Jmaxi = GRID.jmaxi; % perpendicular ion Laguerre moments
params.Pmaxe = GRID.pmaxe; % parallel electron Hermite moments
params.Jmaxe = GRID.jmaxe; % perpendicular electron Laguerre moments
% w/wo ions
options.ions = 1; % if ions are present -> 1, 0 otherwise
% Adiabatic electrons
options.electrons = 1; % 0 -> adiabatic electrons, 1 no adiabatic electrons
% w/wo soundwaves
options.sw = 1; % 1 -> sound waves on, 0 -> put ion parallel velocity row/column to 0
%% Collision Operator Models and COSOlver Input Parameters
options.collI = MODEL.CO; % collI=-2 -> Dougherty, -1 -> COSOlver, 0 -> Lenard-Bernstein, other -> hyperviscosity exponent
options.collGK = 0; % collDKGK =1 -> GK collision operator, else DK collision operator
options.COSOlver.GKE = 0;
options.COSOlver.GKI = 0;
% COSOlver Input Parameters (if collI = -1 only)
options.COSOlver.eecolls = 1; % 1 -> electron-electron collisions, 0 -> off
options.COSOlver.iicolls = 1; % 1 -> ion-ion collisions, 0 -> off
options.COSOlver.eicolls = 1; % 1 -> electron-ion collisions (e-i) on, 0 -> off
options.COSOlver.iecolls = 1; % 1 -> ion-electron collisions (i-e) on, 0 -> off
% Collisional Coulomb sum bounds (only if collI = -1, i.e. Coulomb)
options.COSOlver.lmaxx = 10; % upper bound collision operator first sum first species
options.COSOlver.kmaxx = 10; % upper bound collision operator second sum first species
options.COSOlver.nmaxx = options.COSOlver.lmaxx; % upper bound collision operator first sum second species
options.COSOlver.qmaxx = options.COSOlver.kmaxx; % upper bound collision operator second sum second species
% Collsion FLR sum bounds
options.COSOlver.nemaxxFLR = 0; % upper bound FLR electron collision
options.COSOlver.nimaxxFLR = 0; % upper bound FLR ion collision
% Collision Operator Model
% Set electron/ion test and back-reaction model operator
%
% 0 => Coulomb Collisions
options.COSOlver.ETEST = 1; % 0 --> Buffer Operator, 1 --> Coulomb, 2 --> Lorentz
options.COSOlver.EBACK = 1;
options.COSOlver.ITEST = 1;
options.COSOlver.IBACK = 1;
options.COSOlver.ESELF = 1;
options.COSOlver.ISELF = 1;
options.COSOlver.OVERWRITE = 0; % overwrite collisional matrices even if exists
options.COSOlver.cmd = 'mpirun -np 6 ./bin/CO 2 2 2';
%% Physical Parameters
% Toroidal effects
options.magnetic = 1; % 1-> Add toroidal magnetic gradient drift resonance effects
% Physical Parameters
params.tau = MODEL.tau_i; % Ti/Te
params.nu = MODEL.nu; % electron/ion collision frequency ... only for nu/ omega_pe < nuoveromegapemax (electron plasma frequency) [See Banks et al. (2017)]
params.nuoveromegapemax = inf; % Maximum ratio between electron/ion collision frequency and electron plasma frequency [See Banks et al. (2017)]. Set to inf if not desired !!!
params.mu = MODEL.sigma_e; % sqrt(m_e/m_i)
params.kpar = 0.0; % normalized parallel wave number to the major radius
-params.kperp = GRID.kzmin; % normalized perpendicular wave number to the soundLarmor radius. Note: If ions ==0 (e.g. EPW), kperp --> b
+params.kperp = GRID.kzmin; % normalized perpendicular toroidal wave number to the soundLarmor radius. Note: If ions ==0 (e.g. EPW), kperp --> b
+params.kr = GRID.krmin; % Radial component of perpendicular vector
params.alphaD = 0.0; % (k*Debye length)^2
params.Rn = MODEL.eta_n; % Major Radius / Background density gradient length
params.RTe = MODEL.eta_T; % Major Radius * normalized kperp / Background electron temperature gradient length
params.RTi = MODEL.eta_T; % Major Radius * normalized kperp / Background ion temperature gradient length
params.Rphi = 0.0; % Major Radius * normalized kperp / Background potentiel gradient length [presence of shear] - only for GK
params.betae = 1e-6; % Electron Beta plasma.
params.rhostar = 1e-5; % sound Larmor Radius/Major Radius ~ sqrt(Te)/(R_0*B).
params.n0 = INITIAL.initback_moments; % initial density perturbation
params.gradB = MODEL.eta_B; % Magnetic field gradient
params.curvB = MODEL.eta_B; % Curvature of B
params.trappB = 0.0; % Trapping term
%% MOLI Options
% Save data in results dir
options.save = 0;
options.verbose = 0;
options.dbg = 0;
options.DR = 0; % 1 -> Solve kinetic dispersion relation,
options.KineticDR = 0; % Solve kinetic dispersion relation (Landau integral) for the given theory
% Compute the kinetic susceptibility for EPW only
options.SPTBLTY = 0;
options.nharm = 1; % Number of harmonics in disp. rel. 1 and 4
wlim = 5.0;
options.DRsolver.wr_min = -wlim; % Minimum of real part.
options.DRsolver.wr_max = wlim; % Maximum of real part.
options.DRsolver.wi_min = -wlim; % Minimum of imag part.
options.DRsolver.wi_max = wlim; % Maximum of imag part.
options.DRsolver.nw = 300; % Grid resolution
% Disp. Rel. Options
options.FLRmodel = 0; % 1 -> Truncated Laguerre, 0 -> Exact representation
options.FluidLandau = 0; % 1 -> Add Landau Fluid Closure to Fluid Dispersion Relation, 0 -> off
options.deltaLandau = 0; % 1 -> Hammet-Perkins closure on, 0 -> off
% Fluid dispersion relation
options.FluidDR = 0; % Solve annamaria's fluid equations
options.Fluid.sITGmm = 0;
% Define scan parameters
options.fscan = 1; % 1 -> peform scan over scan.list, 0-> off
options.scan.list = {'kperp'};% List of scan parameters. If empty, solve MOLI with params
options.scan.kperp.array = linspace(GRID.kzmin, GRID.kzmax, GRID.nkz);
% Time-Evolution Problem [Solver==3] ...
options.solver.TimeSolver.dt = BASIC.dt; % timestep of time evolution (R/c_s or 1/(k v/the) units)
options.solver.TimeSolver.tmax = BASIC.tmax;
options.solver.TimeSolver.Trun = BASIC.tmax; % total time to run time evolution
options.solver.TimeSolver.t_fit_min = 0.05; % Phase-Mixing fit Lower time limit
options.solver.TimeSolver.t_fit_max = 8; % Phase-Mixing fit Upper time limit
options.solver.TimeSolver.en_fit_min = 0.15; % Entropy Mode fit Lower time limit
options.solver.TimeSolver.en_fit_max = 0.3; % Entropy Mode fit Upper time limit
options.solver.TimeSolver.movie = 0; % Display movie if 1, last frame otherwise
options.solver.TimeSolver.save = 0; % 1 --> save during fscan, Warning: memory storage
%% Run MOLI
% Solve the MOLI
[results,params,options] = MOLI_Control(params,options);
%% Return to HeLaZ workspace
cd ../../../HeLaZ/wk
diff --git a/matlab/MOLI_time_solver.m b/matlab/MOLI_time_solver.m
index 0bd7d11..b2f25e3 100644
--- a/matlab/MOLI_time_solver.m
+++ b/matlab/MOLI_time_solver.m
@@ -1,162 +1,164 @@
+%% Run MOLI for a time evolution of the moments at a given kperp
%% Move to MOLI workspace
cd ../../MoliSolver/MOLI/workspace/
%% Add paths
my_paths
%% Directories
ROOT = '/home/ahoffman/Documents/MoliSolver';
options.dirs.COSOlverdir = fullfile(ROOT,'COSOlver');
options.dirs.MOLIdir = fullfile(ROOT,'MOLI');
%% MOLI Physical and Main Parameters
% Solve DK AND/OR GK Linear Moment Hierarchy.
options.DKI = 0; % First-order DK
options.DKII = 0; % Second-order DK
options.GK = 1; % Gyrokinetic GK
options.EM = 0; % Include Electromagnetic effects (only for GK=1)
options.GD = 0; % Gyro-Drift
options.GDI = 0; % First/second order
% Solve MOLI
options.MOLI = 1; % 1 -> Solve MOLI, 0 -> off
% MOLI Solver
options.solver.solver = 3;
% MOLI Linear Fit Solver
options.LinFitSolver = 0;
%% Main parameter scan
% Closure by truncation
params.Pmaxi = GRID.pmaxi; % parallel ion Hermite moments
params.Jmaxi = GRID.jmaxi; % perpendicular ion Laguerre moments
params.Pmaxe = GRID.pmaxe; % parallel electron Hermite moments
params.Jmaxe = GRID.jmaxe; % perpendicular electron Laguerre moments
% w/wo ions
options.ions = 1; % if ions are present -> 1, 0 otherwise
% Adiabatic electrons
options.electrons = 1; % 0 -> adiabatic electrons, 1 no adiabatic electrons
% w/wo soundwaves
options.sw = 1; % 1 -> sound waves on, 0 -> put ion parallel velocity row/column to 0
%% Collision Operator Models and COSOlver Input Parameters
options.collI = MODEL.CO; % collI=-2 -> Dougherty, -1 -> COSOlver, 0 -> Lenard-Bernstein, other -> hyperviscosity exponent
options.collGK = 0; % collDKGK =1 -> GK collision operator, else DK collision operator
options.COSOlver.GKE = 0;
options.COSOlver.GKI = 0;
% COSOlver Input Parameters (if collI = -1 only)
options.COSOlver.eecolls = 1; % 1 -> electron-electron collisions, 0 -> off
options.COSOlver.iicolls = 1; % 1 -> ion-ion collisions, 0 -> off
options.COSOlver.eicolls = 1; % 1 -> electron-ion collisions (e-i) on, 0 -> off
options.COSOlver.iecolls = 1; % 1 -> ion-electron collisions (i-e) on, 0 -> off
% Collisional Coulomb sum bounds (only if collI = -1, i.e. Coulomb)
options.COSOlver.lmaxx = 10; % upper bound collision operator first sum first species
options.COSOlver.kmaxx = 10; % upper bound collision operator second sum first species
options.COSOlver.nmaxx = options.COSOlver.lmaxx; % upper bound collision operator first sum second species
options.COSOlver.qmaxx = options.COSOlver.kmaxx; % upper bound collision operator second sum second species
% Collsion FLR sum bounds
options.COSOlver.nemaxxFLR = 0; % upper bound FLR electron collision
options.COSOlver.nimaxxFLR = 0; % upper bound FLR ion collision
% Collision Operator Model
% Set electron/ion test and back-reaction model operator
%
% 0 => Coulomb Collisions
options.COSOlver.ETEST = 1; % 0 --> Buffer Operator, 1 --> Coulomb, 2 --> Lorentz
options.COSOlver.EBACK = 1;
options.COSOlver.ITEST = 1;
options.COSOlver.IBACK = 1;
options.COSOlver.ESELF = 1;
options.COSOlver.ISELF = 1;
options.COSOlver.OVERWRITE = 0; % overwrite collisional matrices even if exists
options.COSOlver.cmd = 'mpirun -np 6 ./bin/CO 2 2 2';
%% Physical Parameters
% Toroidal effects
options.magnetic = 1; % 1-> Add toroidal magnetic gradient drift resonance effects
% Physical Parameters
params.tau = MODEL.tau_i; % Ti/Te
params.nu = MODEL.nu; % electron/ion collision frequency ... only for nu/ omega_pe < nuoveromegapemax (electron plasma frequency) [See Banks et al. (2017)]
params.nuoveromegapemax = inf; % Maximum ratio between electron/ion collision frequency and electron plasma frequency [See Banks et al. (2017)]. Set to inf if not desired !!!
params.mu = MODEL.sigma_e; % sqrt(m_e/m_i)
params.kpar = 0.0; % normalized parallel wave number to the major radius
-params.kperp = GRID.kzmin; % normalized perpendicular wave number to the soundLarmor radius. Note: If ions ==0 (e.g. EPW), kperp --> b
+params.kperp = GRID.kzmin; % normalized perpendicular toroidal wave number to the soundLarmor radius. Note: If ions ==0 (e.g. EPW), kperp --> b
+params.kr = GRID.krmin; % Radial component of perpendicular vector
params.alphaD = 0.0; % (k*Debye length)^2
params.Rn = MODEL.eta_n; % Major Radius / Background density gradient length
params.RTe = MODEL.eta_T; % Major Radius * normalized kperp / Background electron temperature gradient length
params.RTi = MODEL.eta_T; % Major Radius * normalized kperp / Background ion temperature gradient length
params.Rphi = 0.0; % Major Radius * normalized kperp / Background potentiel gradient length [presence of shear] - only for GK
params.betae = 1e-6; % Electron Beta plasma.
params.rhostar = 1e-5; % sound Larmor Radius/Major Radius ~ sqrt(Te)/(R_0*B).
params.n0 = INITIAL.initback_moments; % initial density perturbation
params.gradB = MODEL.eta_B; % Magnetic field gradient
params.curvB = MODEL.eta_B; % Curvature of B
params.trappB = 0.0; % Trapping term
%% MOLI Options
% Save data in results dir
options.save = 0;
options.verbose = 0;
options.dbg = 0;
options.DR = 0; % 1 -> Solve kinetic dispersion relation,
options.KineticDR = 0; % Solve kinetic dispersion relation (Landau integral) for the given theory
% Compute the kinetic susceptibility for EPW only
options.SPTBLTY = 0;
options.nharm = 1; % Number of harmonics in disp. rel. 1 and 4
wlim = 5.0;
options.DRsolver.wr_min = -wlim; % Minimum of real part.
options.DRsolver.wr_max = wlim; % Maximum of real part.
options.DRsolver.wi_min = -wlim; % Minimum of imag part.
options.DRsolver.wi_max = wlim; % Maximum of imag part.
options.DRsolver.nw = 300; % Grid resolution
% Disp. Rel. Options
options.FLRmodel = 0; % 1 -> Truncated Laguerre, 0 -> Exact representation
options.FluidLandau = 0; % 1 -> Add Landau Fluid Closure to Fluid Dispersion Relation, 0 -> off
options.deltaLandau = 0; % 1 -> Hammet-Perkins closure on, 0 -> off
% Fluid dispersion relation
options.FluidDR = 0; % Solve annamaria's fluid equations
options.Fluid.sITGmm = 0;
% Define scan parameters
options.fscan = 0; % 1 -> peform scan over scan.list, 0-> off
options.scan.list = {};% List of scan parameters. If empty, solve MOLI with params
% Time-Evolution Problem [Solver==3] ...
options.solver.TimeSolver.dt = BASIC.dt; % timestep of time evolution (R/c_s or 1/(k v/the) units)
options.solver.TimeSolver.tmax = BASIC.tmax;
options.solver.TimeSolver.Trun = BASIC.tmax; % total time to run time evolution
options.solver.TimeSolver.t_fit_min = 0.05; % Phase-Mixing fit Lower time limit
options.solver.TimeSolver.t_fit_max = 8; % Phase-Mixing fit Upper time limit
options.solver.TimeSolver.en_fit_min = 0.15; % Entropy Mode fit Lower time limit
options.solver.TimeSolver.en_fit_max = 0.3; % Entropy Mode fit Upper time limit
options.solver.TimeSolver.movie = 0; % Display movie if 1, last frame otherwise
options.solver.TimeSolver.save = 0; % 1 --> save during fscan, Warning: memory storage
%% Run MOLI
% Solve the MOLI
[results,params,options] = MOLI_Control(params,options);
%% Return to HeLaZ workspace
cd ../../../HeLaZ/wk