From 257a31cc18b537efa542fc57c96c73e7c0cd907a Mon Sep 17 00:00:00 2001
From: Antoine Hoffmann <antoine.hoffmann@epfl.ch>
Date: Tue, 3 Oct 2023 11:49:57 +0200
Subject: [PATCH] save scripts
---
bash scripts/fort_00.90 | 107 ++++++++++++++++++
bash scripts/submit_00.cmd | 3 +-
testcases/CBC_ExBshear/fort_01.90 | 4 +-
testcases/CBC_ExBshear/std/fort_00.90 | 97 ++++++++++++++++
testcases/CBC_ExBshear/std/fort_01.90 | 97 ++++++++++++++++
testcases/CBC_ExBshear/{ => std}/fort_02.90 | 0
.../Dimits_2000_fig3_fit_to_LLNL_GK.txt | 18 +++
wk/fast_analysis.m | 13 ++-
wk/lin_run_script.m | 28 +++--
wk/parameters/lin_DIIID_LM_rho90.m | 4 +-
wk/parameters/lin_DIIID_LM_rho95.m | 6 +-
11 files changed, 350 insertions(+), 27 deletions(-)
create mode 100644 bash scripts/fort_00.90
create mode 100644 testcases/CBC_ExBshear/std/fort_00.90
create mode 100644 testcases/CBC_ExBshear/std/fort_01.90
rename testcases/CBC_ExBshear/{ => std}/fort_02.90 (100%)
create mode 100644 wk/benchmark_and_scan_scripts/Dimits_2000_fig3_fit_to_LLNL_GK.txt
diff --git a/bash scripts/fort_00.90 b/bash scripts/fort_00.90
new file mode 100644
index 00000000..183029f9
--- /dev/null
+++ b/bash scripts/fort_00.90
@@ -0,0 +1,107 @@
+&BASIC
+ nrun = 100000000
+ dt = 0.002
+ tmax = 100
+ maxruntime = 356400
+ job2load = -1
+/
+&GRID
+ pmax = 2
+ jmax = 1
+ Nx = 192
+ Lx = 90
+ Ny = 48
+ Ly = 200
+ Nz = 32
+ SG = .false.
+ Nexc = 0
+/
+&GEOMETRY
+ geom = 'miller'
+ q0 =-2.15
+ shear = 3.62
+ eps = 0.28
+ kappa = 1.53
+ s_kappa = 0.77
+ delta = 0.23
+ s_delta = 1.05
+ zeta =-0.01
+ s_zeta =-0.17
+ parallel_bc = 'dirichlet'
+ shift_y = 0
+ Npol = 1
+ PB_PHASE= .false.
+/
+&OUTPUT_PAR
+ dtsave_0d = 0.5
+ dtsave_1d = -1
+ dtsave_2d = -1
+ dtsave_3d = 5.0
+ dtsave_5d = 10
+ write_doubleprecision = .false.
+ write_gamma = .true.
+ write_hf = .true.
+ write_phi = .true.
+ write_Na00 = .true.
+ write_Napj = .true.
+ write_dens = .true.
+ write_temp = .true.
+/
+&MODEL_PAR
+LINEARITY = 'nonlinear'
+RM_LD_T_EQ= .false.
+ Na = 2
+ mu_x = 1.0
+ mu_y = 1.0
+ N_HD = 4
+ mu_z = 2.0
+ HYP_V = 'hypcoll'
+ mu_p = 0
+ mu_j = 0
+ nu = 0.5
+ k_gB = 1
+ k_cB = 1
+ lambdaD = 0
+ beta = 0.0034
+ ADIAB_E = .false.
+ ADIAB_I = .false.
+ MHD_PD = .true.
+/
+&CLOSURE_PAR
+ hierarchy_closure='truncation'
+ dmax =-1
+ nonlinear_closure='truncation'
+ nmax =0
+/
+&SPECIES
+ name_ = 'ions'
+ tau_ = 1
+ sigma_ = 1
+ q_ = 1
+ K_N_ = 1.33
+ K_T_ = 8.25
+/
+&SPECIES
+ name_ = 'electrons'
+ tau_ = 1
+ sigma_ = 0.04!0.023338
+ q_ = -1
+ K_N_ = 1.33
+ K_T_ = 12
+/
+&COLLISION_PAR
+ collision_model = 'DG'
+ GK_CO = .true.
+ INTERSPECIES = .true.
+ mat_file = '/Users/ahoffmann/gyacomo/iCa/null'
+ collision_kcut = 1
+/
+&INITIAL_CON
+ INIT_OPT = 'blob'
+ init_background = 0
+ init_noiselvl = 1e-05
+ iseed = 42
+/
+&TIME_INTEGRATION_PAR
+ numerical_scheme = 'RK4'
+/
\ No newline at end of file
diff --git a/bash scripts/submit_00.cmd b/bash scripts/submit_00.cmd
index 480ee2b3..0d1f9436 100644
--- a/bash scripts/submit_00.cmd
+++ b/bash scripts/submit_00.cmd
@@ -10,5 +10,4 @@
#SBATCH --account=FUA36_TSVVT422
#SBATCH --partition=skl_fua_dbg
#SBATCH --qos=normal
-srun --cpu-bind=cores ./gyacomo 2 24 1 0
-
+srun --cpu-bind=cores ./gyacomo 2 24 1 0
\ No newline at end of file
diff --git a/testcases/CBC_ExBshear/fort_01.90 b/testcases/CBC_ExBshear/fort_01.90
index bf5ea997..45b83533 100644
--- a/testcases/CBC_ExBshear/fort_01.90
+++ b/testcases/CBC_ExBshear/fort_01.90
@@ -57,10 +57,10 @@
HYP_V = 'hypcoll'
mu_p = 0.0
mu_j = 0.0
- nu = 1.0
+ nu = 1.00
beta = 0.0
ADIAB_E = .t.
- ExBrate = 0.01
+ ExBrate = 0.0
/
&CLOSURE
hierarchy_closure='truncation'
diff --git a/testcases/CBC_ExBshear/std/fort_00.90 b/testcases/CBC_ExBshear/std/fort_00.90
new file mode 100644
index 00000000..b26e8952
--- /dev/null
+++ b/testcases/CBC_ExBshear/std/fort_00.90
@@ -0,0 +1,97 @@
+&BASIC
+ nrun = 99999999
+ dt = 0.01
+ tmax = 50
+ maxruntime = 72000
+ job2load = -1
+/
+&GRID
+ pmax = 2
+ jmax = 1
+ Nx = 64
+ Lx = 120
+ Ny = 48
+ Ly = 120
+ Nz = 16
+ SG = .f.
+ Nexc = 0
+/
+&GEOMETRY
+ geom = 's-alpha'
+ !geom = 'miller'
+ q0 = 1.4
+ shear = 0.8
+ eps = 0.18
+ kappa = 1.0
+ s_kappa= 0.0
+ delta = 0.0
+ s_delta= 0.0
+ zeta = 0.0
+ s_zeta = 0.0
+ parallel_bc = 'dirichlet'
+ shift_y= 0.0
+/
+&DIAGNOSTICS
+ dtsave_0d = 1
+ dtsave_1d = -1
+ dtsave_2d = -1
+ dtsave_3d = 1
+ dtsave_5d = 20
+ write_doubleprecision = .f.
+ write_gamma = .t.
+ write_hf = .t.
+ write_phi = .t.
+ write_Na00 = .t.
+ write_Napj = .t.
+ write_dens = .t.
+ write_fvel = .t.
+ write_temp = .t.
+/
+&MODEL
+ LINEARITY = 'nonlinear'
+ Na = 1 ! number of species
+ mu_x = 1.0
+ mu_y = 1.0
+ N_HD = 4
+ mu_z = 1.0
+ HYP_V = 'hypcoll'
+ mu_p = 0.0
+ mu_j = 0.0
+ nu = 1.00
+ beta = 0.0
+ ADIAB_E = .t.
+ ExBrate = 0.0
+/
+&CLOSURE
+ hierarchy_closure='truncation'
+ dmax = -1
+ nonlinear_closure='truncation'
+ nmax = 0
+/
+&SPECIES
+ ! ions
+ name_ = 'ions'
+ tau_ = 1.0
+ sigma_= 1.0
+ q_ = 1.0
+ k_N_ = 2.22
+ k_T_ = 6.96
+/
+
+&COLLISION
+ collision_model = 'DG' !DG/SG/PA/LD (dougherty, sugama, pitch angle, landau)
+ GK_CO = .f.
+ INTERSPECIES = .true.
+ mat_file = 'gk_sugama_P_20_J_10_N_150_kpm_8.0.h5'
+/
+&INITIAL
+ INIT_OPT = 'blob'
+ ACT_ON_MODES = 'donothing'
+ init_background = 0.0
+ init_noiselvl = 0.005
+ iseed = 42
+/
+&TIME_INTEGRATION
+ !numerical_scheme = 'RK4'
+ numerical_scheme = 'SSP_RK3'
+/
diff --git a/testcases/CBC_ExBshear/std/fort_01.90 b/testcases/CBC_ExBshear/std/fort_01.90
new file mode 100644
index 00000000..bf5ea997
--- /dev/null
+++ b/testcases/CBC_ExBshear/std/fort_01.90
@@ -0,0 +1,97 @@
+&BASIC
+ nrun = 99999999
+ dt = 0.01
+ tmax = 100
+ maxruntime = 72000
+ job2load = 0
+/
+&GRID
+ pmax = 2
+ jmax = 1
+ Nx = 64
+ Lx = 120
+ Ny = 48
+ Ly = 120
+ Nz = 16
+ SG = .f.
+ Nexc = 0
+/
+&GEOMETRY
+ geom = 's-alpha'
+ !geom = 'miller'
+ q0 = 1.4
+ shear = 0.8
+ eps = 0.18
+ kappa = 1.0
+ s_kappa= 0.0
+ delta = 0.0
+ s_delta= 0.0
+ zeta = 0.0
+ s_zeta = 0.0
+ parallel_bc = 'dirichlet'
+ shift_y= 0.0
+/
+&DIAGNOSTICS
+ dtsave_0d = 1
+ dtsave_1d = -1
+ dtsave_2d = -1
+ dtsave_3d = 1
+ dtsave_5d = 20
+ write_doubleprecision = .f.
+ write_gamma = .t.
+ write_hf = .t.
+ write_phi = .t.
+ write_Na00 = .t.
+ write_Napj = .t.
+ write_dens = .t.
+ write_fvel = .t.
+ write_temp = .t.
+/
+&MODEL
+ LINEARITY = 'nonlinear'
+ Na = 1 ! number of species
+ mu_x = 1.0
+ mu_y = 1.0
+ N_HD = 4
+ mu_z = 1.0
+ HYP_V = 'hypcoll'
+ mu_p = 0.0
+ mu_j = 0.0
+ nu = 1.0
+ beta = 0.0
+ ADIAB_E = .t.
+ ExBrate = 0.01
+/
+&CLOSURE
+ hierarchy_closure='truncation'
+ dmax = -1
+ nonlinear_closure='truncation'
+ nmax = 0
+/
+&SPECIES
+ ! ions
+ name_ = 'ions'
+ tau_ = 1.0
+ sigma_= 1.0
+ q_ = 1.0
+ k_N_ = 2.22
+ k_T_ = 6.96
+/
+
+&COLLISION
+ collision_model = 'DG' !DG/SG/PA/LD (dougherty, sugama, pitch angle, landau)
+ GK_CO = .f.
+ INTERSPECIES = .true.
+ mat_file = 'gk_sugama_P_20_J_10_N_150_kpm_8.0.h5'
+/
+&INITIAL
+ INIT_OPT = 'blob'
+ ACT_ON_MODES = 'donothing'
+ init_background = 0.0
+ init_noiselvl = 0.005
+ iseed = 42
+/
+&TIME_INTEGRATION
+ !numerical_scheme = 'RK4'
+ numerical_scheme = 'SSP_RK3'
+/
diff --git a/testcases/CBC_ExBshear/fort_02.90 b/testcases/CBC_ExBshear/std/fort_02.90
similarity index 100%
rename from testcases/CBC_ExBshear/fort_02.90
rename to testcases/CBC_ExBshear/std/fort_02.90
diff --git a/wk/benchmark_and_scan_scripts/Dimits_2000_fig3_fit_to_LLNL_GK.txt b/wk/benchmark_and_scan_scripts/Dimits_2000_fig3_fit_to_LLNL_GK.txt
new file mode 100644
index 00000000..8e72be2d
--- /dev/null
+++ b/wk/benchmark_and_scan_scripts/Dimits_2000_fig3_fit_to_LLNL_GK.txt
@@ -0,0 +1,18 @@
+5.988372093023255, -0.020876826722338038
+6.162790697674419, 0.4384133611691041
+6.308139534883722, 0.8559498956158684
+6.482558139534884, 1.1482254697286027
+6.627906976744185, 1.4822546972860131
+6.7441860465116275, 1.7954070981210872
+6.947674418604652, 2.0668058455114835
+7.093023255813954, 2.3382045929018798
+7.151162790697676, 2.44258872651357
+7.267441860465118, 2.713987473903968
+7.38372093023256, 2.8810020876826723
+7.500000000000002, 3.0480167014613784
+7.587209302325581, 3.1941544885177464
+7.674418604651164, 3.3402922755741127
+7.790697674418606, 3.549060542797495
+7.936046511627907, 3.757828810020877
+8.13953488372093, 4.050104384133613
+8.313953488372093, 4.237995824634655
diff --git a/wk/fast_analysis.m b/wk/fast_analysis.m
index c3418eb3..09b285b8 100644
--- a/wk/fast_analysis.m
+++ b/wk/fast_analysis.m
@@ -16,7 +16,7 @@ PARTITION = '';
% resdir = 'LM_DIIID_rho95/5x3x512x92x32';
% resdir = 'LM_DIIID_rho95/3x2x512x92x32';
% resdir = '../testcases/cyclone_example';
-% resdir = '../testcases/CBC_ExBshear';
+resdir = '../testcases/CBC_ExBshear/std';
% resdir = '../results/paper_3/HM_DTT_rho98/3x2x128x64x64';
%%
J0 = 00; J1 = 10;
@@ -49,7 +49,7 @@ if 0
data.Ni00 = reshape(data.Na00(1,:,:,:,:),data.grids.Nky,data.grids.Nkx,data.grids.Nz,numel(data.Ts3D));
options.INTERP = 1;
options.POLARPLOT = 0;
-options.BWR = 1; % bluewhitered plot or gray
+options.BWR = 0; % bluewhitered plot or gray
options.CLIMAUTO = 1; % adjust the colormap auto
% options.NAME = '\phi';
% options.NAME = '\phi^{NZ}';
@@ -60,7 +60,7 @@ options.NAME = 'N_i^{00}';
% options.NAME = 'Q_x';
% options.NAME = 'n_i';
% options.NAME = 'n_i-n_e';
-options.PLAN = 'kxky';
+options.PLAN = 'xy';
% options.NAME = 'f_i';
% options.PLAN = 'sx';
options.COMP = 'avg';
@@ -85,11 +85,12 @@ options.POLARPLOT = 0;
options.AXISEQUAL = 0;
options.NORMALIZE = 0;
options.LOGSCALE = 1;
-% options.NAME = 'N_i^{00}';
-options.NAME = '\phi';
+options.CLIMAUTO = 1;
+options.NAME = 'N_i^{00}';
+% options.NAME = '\phi';
options.PLAN = 'kxky';
options.COMP = 'avg';
-options.TIME = [0 10 50 100 500];
+options.TIME = [0 100];
% options.TIME = data.Ts3D(1:2:end);
options.RESOLUTION = 256;
fig = photomaton(data,options);
diff --git a/wk/lin_run_script.m b/wk/lin_run_script.m
index eddd7273..13da10b7 100644
--- a/wk/lin_run_script.m
+++ b/wk/lin_run_script.m
@@ -25,23 +25,26 @@ EXECNAME = 'gyacomo23_dp'; % double precision
%% Setup parameters
% run lin_DTT_HM_rho85
% run lin_DTT_HM_rho98
-run lin_DIIID_LM_rho90
+% run lin_DIIID_LM_rho90
% run lin_DIIID_LM_rho95
% run lin_JET_rho97
% run lin_Entropy
-% run lin_ITG
+run lin_ITG
% run lin_KBM
%% Change parameters
-EXBRATE = 0.0; % Background ExB shear flow
-NY = 2;
-NX = 4;
-% PMAX = 4;
-% JMAX = PMAX/2;
-ky = 0.8; LY = 2*pi/ky;
-DT = 1e-4;
-TAU = 2.1;
+% EXBRATE = 0.0; % Background ExB shear flow
+NU = 0.1;
+CO = 'SG';
+GKCO = 1;
+NY = 16;
+NX = 2;
+PMAX = 4;
+JMAX = PMAX/2;
+ky = 0.1; LY = 2*pi/ky;
+% DT = 1e-4;
+% TAU = 2.1;
% SIGMA_E = 0.02;
-% TMAX = 50;
+TMAX = 25;
% DTSAVE0D = 200*DT;
% DTSAVE3D = TMAX/50;
%%-------------------------------------------------------------------------
@@ -52,7 +55,8 @@ setup
if RUN
MVIN =['cd ../results/',SIMID,'/',PARAMS,'/;'];
% RUN =['time ',mpirun,' -np 2 ',gyacomodir,'bin/',EXECNAME,' 1 2 1 0;'];
- RUN =['time ',mpirun,' -np 4 ',gyacomodir,'bin/',EXECNAME,' 1 2 2 0;'];
+ % RUN =['time ',mpirun,' -np 4 ',gyacomodir,'bin/',EXECNAME,' 1 2 2 0;'];
+ RUN =['time ',mpirun,' -np 6 ',gyacomodir,'bin/',EXECNAME,' 1 6 1 0;'];
% RUN =['time ',mpirun,' -np 8 ',gyacomodir,'bin/',EXECNAME,' 2 2 2 0;'];
% RUN =['time ',mpirun,' -np 1 ',gyacomodir,'bin/',EXECNAME,' 1 1 1 0;'];
% RUN = ['./../../../bin/gyacomo23_sp 0;'];
diff --git a/wk/parameters/lin_DIIID_LM_rho90.m b/wk/parameters/lin_DIIID_LM_rho90.m
index c8ff82e2..9995af00 100644
--- a/wk/parameters/lin_DIIID_LM_rho90.m
+++ b/wk/parameters/lin_DIIID_LM_rho90.m
@@ -20,8 +20,8 @@ P = 2;
J = P/2;%P/2;
PMAX = P; % Hermite basis size
JMAX = J; % Laguerre basis size
-NX = 2; % real space x-gridpoints
-NY = 4; % real space y-gridpoints
+NX = 4; % real space x-gridpoints
+NY = 2; % real space y-gridpoints
LX = 2*pi/0.1; % Size of the squared frequency domain in x direction
LY = 2*pi/0.3; % Size of the squared frequency domain in y direction
NZ = 32; % number of perpendicular planes (parallel grid)
diff --git a/wk/parameters/lin_DIIID_LM_rho95.m b/wk/parameters/lin_DIIID_LM_rho95.m
index 77a21328..2bd5ba9b 100644
--- a/wk/parameters/lin_DIIID_LM_rho95.m
+++ b/wk/parameters/lin_DIIID_LM_rho95.m
@@ -1,7 +1,7 @@
%% Reference values
% See Neiser et al. 2019 Gyrokinetic GENE simulations of DIII-D near-edge L-mode plasmas
%% Set simulation parameters
-SIMID = 'lin_DTT_HM_rho90'; % Name of the simulation
+SIMID = 'lin_DIIID_HM_rho90'; % Name of the simulation
%% Set up physical parameters
CLUSTER.TIME = '99:00:00'; % Allocation time hh:mm:ss
NU = 1.0; %(0.00235 in GENE)
@@ -20,7 +20,7 @@ P = 2;
J = P/2;%P/2;
PMAX = P; % Hermite basis size
JMAX = J; % Laguerre basis size
-NX = 16; % real space x-gridpoints
+NX = 6; % real space x-gridpoints
NY = 2; % real space y-gridpoints
LX = 2*pi/0.1; % Size of the squared frequency domain in x direction
LY = 2*pi/0.3; % Size of the squared frequency domain in y direction
@@ -46,7 +46,7 @@ NPOL = 1; % Number of poloidal turns
PB_PHASE = 0;
%% TIME PARAMETERS
TMAX = 15; % Maximal time unit
-DT = 1e-3; % Time step
+DT = 1e-4; % Time step
DTSAVE0D = 0.5; % Sampling time for 0D arrays
DTSAVE2D = -1; % Sampling time for 2D arrays
DTSAVE3D = 0.5; % Sampling time for 3D arrays
--
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