From 27afc84e76533c8fa63df8c8d628ad1fb0e2b53f Mon Sep 17 00:00:00 2001
From: Antoine Cyril David Hoffmann <ahoffman@spcpc606.epfl.ch>
Date: Tue, 3 Aug 2021 14:26:05 +0200
Subject: [PATCH] added shear and inverse aspect ratio as input parameters
---
matlab/setup.m | 6 +++--
matlab/write_fort90.m | 52 ++++++++++++++++++++++---------------------
src/grid_mod.F90 | 36 ++++++++++++++++--------------
wk/analysis_3D.m | 6 ++---
wk/local_run.m | 25 ++++++++++++---------
wk/marconi_run.m | 12 +++++-----
6 files changed, 73 insertions(+), 64 deletions(-)
diff --git a/matlab/setup.m b/matlab/setup.m
index dd614b74..0f6ded1f 100644
--- a/matlab/setup.m
+++ b/matlab/setup.m
@@ -9,8 +9,10 @@ GRID.Nx = N; % x grid resolution
GRID.Lx = L; % x length
GRID.Ny = N * (1-KXEQ0) + KXEQ0; % y ''
GRID.Ly = L * (1-KXEQ0); % y ''
-GRID.Nz = Nz; % z resolution
-GRID.q0 = q0; % q factor
+GRID.Nz = Nz; % z resolution
+GRID.q0 = q0; % q factor
+GRID.shear = shear; % shear
+GRID.eps = eps; % inverse aspect ratio
% Model parameters
MODEL.CO = CO; % Collision operator (0 : L.Bernstein, -1 : Full Coulomb, -2 : Dougherty)
diff --git a/matlab/write_fort90.m b/matlab/write_fort90.m
index 366ee163..311229af 100644
--- a/matlab/write_fort90.m
+++ b/matlab/write_fort90.m
@@ -7,21 +7,23 @@ fprintf(fid,'&BASIC\n');
fprintf(fid,[' nrun = ', num2str(BASIC.nrun),'\n']);
fprintf(fid,[' dt = ', num2str(BASIC.dt),'\n']);
fprintf(fid,[' tmax = ', num2str(BASIC.tmax),'\n']);
-fprintf(fid,[' RESTART = ', BASIC.RESTART,'\n']);
+fprintf(fid,[' RESTART = ', BASIC.RESTART,'\n']);
fprintf(fid,[' maxruntime = ', num2str(BASIC.maxruntime),'\n']);
fprintf(fid,'/\n');
fprintf(fid,'&GRID\n');
-fprintf(fid,[' pmaxe =', num2str(GRID.pmaxe),'\n']);
-fprintf(fid,[' jmaxe = ', num2str(GRID.jmaxe),'\n']);
-fprintf(fid,[' pmaxi = ', num2str(GRID.pmaxi),'\n']);
-fprintf(fid,[' jmaxi = ', num2str(GRID.jmaxi),'\n']);
-fprintf(fid,[' Nx = ', num2str(GRID.Nx),'\n']);
-fprintf(fid,[' Lx = ', num2str(GRID.Lx),'\n']);
-fprintf(fid,[' Ny = ', num2str(GRID.Ny),'\n']);
-fprintf(fid,[' Ly = ', num2str(GRID.Ly),'\n']);
-fprintf(fid,[' Nz = ', num2str(GRID.Nz),'\n']);
-fprintf(fid,[' q0 = ', num2str(GRID.q0),'\n']);
+fprintf(fid,[' pmaxe =', num2str(GRID.pmaxe),'\n']);
+fprintf(fid,[' jmaxe = ', num2str(GRID.jmaxe),'\n']);
+fprintf(fid,[' pmaxi = ', num2str(GRID.pmaxi),'\n']);
+fprintf(fid,[' jmaxi = ', num2str(GRID.jmaxi),'\n']);
+fprintf(fid,[' Nx = ', num2str(GRID.Nx),'\n']);
+fprintf(fid,[' Lx = ', num2str(GRID.Lx),'\n']);
+fprintf(fid,[' Ny = ', num2str(GRID.Ny),'\n']);
+fprintf(fid,[' Ly = ', num2str(GRID.Ly),'\n']);
+fprintf(fid,[' Nz = ', num2str(GRID.Nz),'\n']);
+fprintf(fid,[' q0 = ', num2str(GRID.q0),'\n']);
+fprintf(fid,[' shear = ', num2str(GRID.q0),'\n']);
+fprintf(fid,[' eps = ', num2str(GRID.q0),'\n']);
fprintf(fid,'/\n');
fprintf(fid,'&OUTPUT_PAR\n');
@@ -34,11 +36,11 @@ fprintf(fid,[' nsave_cp = ', num2str(OUTPUTS.nsave_cp),'\n']);
fprintf(fid,[' write_doubleprecision = ', OUTPUTS.write_doubleprecision,'\n']);
fprintf(fid,[' write_gamma = ', OUTPUTS.write_gamma,'\n']);
fprintf(fid,[' write_phi = ', OUTPUTS.write_phi,'\n']);
-fprintf(fid,[' write_Na00 = ', OUTPUTS.write_Na00,'\n']);
-fprintf(fid,[' write_Napj = ', OUTPUTS.write_Napj,'\n']);
-fprintf(fid,[' write_Sapj = ', OUTPUTS.write_Sapj,'\n']);
-fprintf(fid,[' write_dens = ', OUTPUTS.write_dens,'\n']);
-fprintf(fid,[' write_temp = ', OUTPUTS.write_temp,'\n']);
+fprintf(fid,[' write_Na00 = ', OUTPUTS.write_Na00,'\n']);
+fprintf(fid,[' write_Napj = ', OUTPUTS.write_Napj,'\n']);
+fprintf(fid,[' write_Sapj = ', OUTPUTS.write_Sapj,'\n']);
+fprintf(fid,[' write_dens = ', OUTPUTS.write_dens,'\n']);
+fprintf(fid,[' write_temp = ', OUTPUTS.write_temp,'\n']);
fprintf(fid,[' resfile0 = ', OUTPUTS.resfile0,'\n']);
fprintf(fid,[' rstfile0 = ', OUTPUTS.rstfile0,'\n']);
fprintf(fid,[' job2load = ', num2str(OUTPUTS.job2load),'\n']);
@@ -67,18 +69,18 @@ fprintf(fid,[' lambdaD = ', num2str(MODEL.lambdaD),'\n']);
fprintf(fid,'/\n');
fprintf(fid,'&INITIAL_CON\n');
-fprintf(fid,[' INIT_NOISY_PHI =', INITIAL.init_noisy_phi,'\n']);
-fprintf(fid,[' INIT_ZF =', num2str(INITIAL.INIT_ZF),'\n']);
-fprintf(fid,[' WIPE_TURB =', INITIAL.wipe_turb,'\n']);
-fprintf(fid,[' INIT_BLOB =', INITIAL.init_blob,'\n']);
-fprintf(fid,[' init_background =', num2str(INITIAL.init_background),'\n']);
-fprintf(fid,[' init_noiselvl =', num2str(INITIAL.init_noiselvl),'\n']);
-fprintf(fid,[' iseed =', num2str(INITIAL.iseed),'\n']);
-fprintf(fid,[' mat_file =', INITIAL.mat_file,'\n']);
+fprintf(fid,[' INIT_NOISY_PHI = ', INITIAL.init_noisy_phi,'\n']);
+fprintf(fid,[' INIT_ZF = ', num2str(INITIAL.INIT_ZF),'\n']);
+fprintf(fid,[' WIPE_TURB = ', INITIAL.wipe_turb,'\n']);
+fprintf(fid,[' INIT_BLOB = ', INITIAL.init_blob,'\n']);
+fprintf(fid,[' init_background = ', num2str(INITIAL.init_background),'\n']);
+fprintf(fid,[' init_noiselvl = ', num2str(INITIAL.init_noiselvl),'\n']);
+fprintf(fid,[' iseed = ', num2str(INITIAL.iseed),'\n']);
+fprintf(fid,[' mat_file = ', INITIAL.mat_file,'\n']);
fprintf(fid,'/\n');
fprintf(fid,'&TIME_INTEGRATION_PAR\n');
-fprintf(fid,[' numerical_scheme=', TIME_INTEGRATION.numerical_scheme,'\n']);
+fprintf(fid,[' numerical_scheme = ', TIME_INTEGRATION.numerical_scheme,'\n']);
fprintf(fid,'/');
fclose(fid);
diff --git a/src/grid_mod.F90 b/src/grid_mod.F90
index f925d1bc..42d612c1 100644
--- a/src/grid_mod.F90
+++ b/src/grid_mod.F90
@@ -82,6 +82,19 @@ MODULE grid
CONTAINS
+
+ SUBROUTINE grid_readinputs
+ ! Read the input parameters
+ USE prec_const
+ IMPLICIT NONE
+ INTEGER :: lu_in = 90 ! File duplicated from STDIN
+
+ NAMELIST /GRID/ pmaxe, jmaxe, pmaxi, jmaxi, &
+ Nx, Lx, Ny, Ly, Nz, q0, shear, eps
+ READ(lu_in,grid)
+
+ END SUBROUTINE grid_readinputs
+
SUBROUTINE init_1Dgrid_distr
! write(*,*) Nx
@@ -288,19 +301,6 @@ CONTAINS
if(my_id.EQ.0) write(*,*) '#parallel planes = ', Nz
END SUBROUTINE set_zgrid
- SUBROUTINE grid_readinputs
- ! Read the input parameters
- USE prec_const
- IMPLICIT NONE
- INTEGER :: lu_in = 90 ! File duplicated from STDIN
-
- NAMELIST /GRID/ pmaxe, jmaxe, pmaxi, jmaxi, &
- Nx, Lx, Ny, Ly, Nz, q0
- READ(lu_in,grid)
-
- END SUBROUTINE grid_readinputs
-
-
SUBROUTINE grid_outputinputs(fidres, str)
! Write the input parameters to the results_xx.h5 file
@@ -321,10 +321,12 @@ CONTAINS
CALL attach(fidres, TRIM(str), "Ly", Ly)
CALL attach(fidres, TRIM(str), "Nz", Nz)
CALL attach(fidres, TRIM(str), "q0", q0)
- CALL attach(fidres, TRIM(str), "Nkx", Nkx)
- CALL attach(fidres, TRIM(str), "Lkx", Lkx)
- CALL attach(fidres, TRIM(str), "Nky", Nky)
- CALL attach(fidres, TRIM(str), "Lky", Lky)
+ CALL attach(fidres, TRIM(str),"shear",shear)
+ CALL attach(fidres, TRIM(str), "eps", eps)
+ CALL attach(fidres, TRIM(str), "Nkx", Nkx)
+ CALL attach(fidres, TRIM(str), "Lkx", Lkx)
+ CALL attach(fidres, TRIM(str), "Nky", Nky)
+ CALL attach(fidres, TRIM(str), "Lky", Lky)
END SUBROUTINE grid_outputinputs
FUNCTION bare(p_,j_)
diff --git a/wk/analysis_3D.m b/wk/analysis_3D.m
index e146bc66..5300342d 100644
--- a/wk/analysis_3D.m
+++ b/wk/analysis_3D.m
@@ -7,10 +7,8 @@ outfile ='';
outfile ='';
outfile ='';
outfile ='';
-outfile ='';
-outfile ='';
-outfile ='HD_study/150x75_L_100_P_4_J_2_eta_0.6_nu_1e-02_DGGK_mu_3e-03';
-% outfile ='HD_study/300x150_L_100_P_2_J_1_eta_0.6_nu_5e-01_DGGK_mu_2e-03';
+outfile ='HD_study/300x150_L_100_P_2_J_1_eta_0.6_nu_5e-01_DGGK_mu_2e-03';
+% outfile ='HD_study/150x75_L_100_P_4_J_2_eta_0.6_nu_1e-02_DGGK_mu_3e-03';
BASIC.RESDIR = ['../results/',outfile,'/'];
BASIC.MISCDIR = ['/misc/HeLaZ_outputs/results/',outfile,'/'];
CMD = ['cp ', BASIC.RESDIR,'outputs* ',BASIC.MISCDIR]; disp(CMD);
diff --git a/wk/local_run.m b/wk/local_run.m
index 1574521b..c588c465 100644
--- a/wk/local_run.m
+++ b/wk/local_run.m
@@ -4,18 +4,18 @@ addpath(genpath('../matlab')) % ... add
CLUSTER.TIME = '99:00:00'; % allocation time hh:mm:ss
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% PHYSICAL PARAMETERS
-NU = 0.5; % Collision frequency
+NU = 0.1; % Collision frequency
ETAN = 1.0/0.6; % Density gradient drive (R/Ln)
-NU_HYP = 1.0;
-%% GRID PARAMETERS
-N = 300; % Frequency gridpoints (Nkx = N/2)
-L = 100; % Size of the squared frequency domain
-Nz = 1; % number of perpendicular planes (parallel grid)
-q0 = 1.0; % q factor ()
+NU_HYP = 0.1;
+%% GRID AND GEOMETRY PARAMETERS
+N = 100; % Frequency gridpoints (Nkx = N/2)
+L = 60; % Size of the squared frequency domain
+Nz = 10; % number of perpendicular planes (parallel grid)
+q0 = 1.0; % safety factor
+shear = 0.0; % magnetic shear
+eps = 0.0; % inverse aspect ratio
P = 2;
J = 1;
-MU_P = 0.0; % Hermite hyperdiffusivity -mu_p*(d/dvpar)^4 f
-MU_J = 0.0; % Laguerre hyperdiffusivity -mu_j*(d/dvperp)^4 f
%% TIME PARAMETERS
TMAX = 200; % Maximal time unit
DT = 1e-2; % Time step
@@ -32,12 +32,13 @@ JOB2LOAD= 0;
CO = 1;
CLOS = 0; % Closure model (0: =0 truncation)
NL_CLOS = 0; % nonlinear closure model (-2: nmax = jmax, -1: nmax = jmax-j, >=0 : nmax = NL_CLOS)
-SIMID = 'HD_study'; % Name of the simulation
+% SIMID = 'HD_study'; % Name of the simulation
+SIMID = 'test_3D'; % Name of the simulation
% SIMID = ['v3.0_P_',num2str(P),'_J_',num2str(J)]; % Name of the simulation
NON_LIN = 1; % activate non-linearity (is cancelled if KXEQ0 = 1)
% INIT options
INIT_ZF = 0; ZF_AMP = 0.0;
-INIT_BLOB = 1; WIPE_TURB = 1;
+INIT_BLOB = 0; WIPE_TURB = 0;
%% OUTPUTS
W_DOUBLE = 0;
W_GAMMA = 1;
@@ -68,6 +69,8 @@ TAU = 1.0; % e/i temperature ratio
ETAT = 0.0; % Temperature gradient
ETAB = 1.0; % Magnetic gradient (1.0 to set R=LB)
INIT_PHI= 1; % Start simulation with a noisy phi and moments
+MU_P = 0.0; % Hermite hyperdiffusivity -mu_p*(d/dvpar)^4 f
+MU_J = 0.0; % Laguerre hyperdiffusivity -mu_j*(d/dvperp)^4 f
%% Setup and file management
setup
system('rm fort.90');
diff --git a/wk/marconi_run.m b/wk/marconi_run.m
index 3b8f42ed..236dc473 100644
--- a/wk/marconi_run.m
+++ b/wk/marconi_run.m
@@ -2,7 +2,7 @@ clear all;
addpath(genpath('../matlab')) % ... add
SUBMIT = 1; % To submit the job automatically
% EXECNAME = 'helaz_dbg';
- EXECNAME = 'helaz_3.0';
+ EXECNAME = 'helaz_3.1';
for ETAN = [1/0.6]
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Set Up parameters
@@ -20,16 +20,16 @@ NP_KX = 24; % MPI processes along kx
%% PHYSICAL PARAMETERS
NU = 0.05; % Collision frequency
ETAN = 1.0/0.6; % Density gradient drive (R/Ln)
-NU_HYP = 1.0;
+NU_HYP = 10.0;
%% GRID PARAMETERS
N = 300; % Frequency gridpoints (Nkx = N/2)
L = 100; % Size of the squared frequency domain
Nz = 1; % number of perpendicular planes (parallel grid)
q0 = 1.0; % q factor ()
+shear = 0.0; % magnetic shear
+eps = 0.0; % inverse aspect ratio
P = 2;
J = 1;
-MU_P = 0.0; % Hermite hyperdiffusivity -mu_p*(d/dvpar)^4 f
-MU_J = 0.0; % Laguerre hyperdiffusivity -mu_j*(d/dvperp)^4 f
%% TIME PARAMETERS
TMAX = 200; % Maximal time unit
DT = 1e-2; % Time step
@@ -43,7 +43,7 @@ JOB2LOAD= 0;
%% OPTIONS AND NAMING
% Collision operator
% (0 : L.Bernstein, 1 : Dougherty, 2: Sugama, 3 : Pitch angle ; +/- for GK/DK)
-CO = 1;
+CO = 2;
CLOS = 0; % Closure model (0: =0 truncation)
NL_CLOS = 0; % nonlinear closure model (-2: nmax = jmax, -1: nmax = jmax-j, >=0 : nmax = NL_CLOS)
% SIMID = 'test_3D_marconi'; % Name of the simulation
@@ -83,6 +83,8 @@ TAU = 1.0; % e/i temperature ratio
ETAT = 0.0; % Temperature gradient
ETAB = 1.0; % Magnetic gradient (1.0 to set R=LB)
INIT_PHI= 1; % Start simulation with a noisy phi and moments
+MU_P = 0.0; % Hermite hyperdiffusivity -mu_p*(d/dvpar)^4 f
+MU_J = 0.0; % Laguerre hyperdiffusivity -mu_j*(d/dvperp)^4 f
% Compute processes distribution
Ntot = NP_P * NP_KX;
Nnodes = ceil(Ntot/48);
--
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