diff --git a/local/dirs.inc b/local/dirs.inc
index e5bbdfc75f93f2b2910bf68ab12fa81814cccdde..322f9cc956b0b0d6d9ae43f0acb0c74175497361 100644
--- a/local/dirs.inc
+++ b/local/dirs.inc
@@ -4,18 +4,29 @@ SRCDIR = $(PREFIX)/src
BINDIR = $(PREFIX)/bin
OBJDIR = $(PREFIX)/obj
LIBDIR = $(HOME)/lib
-#LIBDIR = $(HOME)/lib_gnu
MODDIR = $(PREFIX)/mod
-FMDIR = $(LIBDIR)/FM
-FUTILS_DIR = $(LIBDIR)/futils/src
-# For local install :
-HDF5_LIB = $(HDF5_ROOT)/lib
-#HDF5_LIB = /usr/local/hdf5-1.8.22/lib
-FFTW3DIR = $(LIBDIR)/fftw-3.3.10
-#LAPACKDIR = $(LIBDIR)/lapack-3.10.0
-# For marconi (use of modules):
-# -comment HDF5_LIB, FFTW3DIR and LAPACKDIR
-# -uncomment the following lines if the module are loaded
-#FFTW3DIR = $(FFTW_HOME)#mandatory
-#LAPACKDIR = $(LAPACK_HOME)#optional
+#OS environment: Linux, Marconi or MacOS
+ENVTYPE = Linux
+
+ifeq ($(ENVTYPE), Linux) #Linux env.
+ FMDIR = $(LIBDIR)/FM
+ FUTILS_DIR = $(LIBDIR)/futils/src
+ FFTW3DIR = $(LIBDIR)/fftw-3.3.10
+ LAPACKDIR = $(HOME)/lib/lapack-3.10.0
+ HDF5_LIB = $(HDF5_ROOT)/lib
+endif
+ifeq ($(ENVTYPE), Marconi) #Marconi env.
+ FMDIR = $(LIBDIR)/FM
+ FUTILS_DIR = $(LIBDIR)/futils/src
+ FFTW3DIR = $(FFTW_HOME)
+ LAPACKDIR = $(LAPACK_HOME)
+ HDF5_LIB = $(HDF5_ROOT)/lib
+endif
+ifeq ($(ENVTYPE), MacOS) #MacOS
+ FMDIR = $(LIBDIR)/FM
+ FUTILS_DIR = $(LIBDIR)/futils/src
+ FFTW3DIR = $(LIBDIR)/fftw-3.3.10
+ LAPACKDIR = /opt/homebrew/opt/lapack
+ HDF5_LIB = /usr/local/hdf5-1.8.22/lib
+endif
diff --git a/local/make.inc b/local/make.inc
index 890dcc78771ae5abbb58a70e63ca8262f8603429..5dd59b655fd3e1b68c8c90c45d4c52ae4e9fa508 100644
--- a/local/make.inc
+++ b/local/make.inc
@@ -107,7 +107,15 @@ ifeq ($(COMPTYPE), c) #cray
endif
#Flag for finding external libraries in LDIR
-EXTLIBS = $(LDIRS) -Wl,--start-group $(LIBS) -Wl,--end-group
+ifeq ($(ENVTYPE), Linux) #Linux env.
+ EXTLIBS = $(LDIRS) -Wl,--start-group $(LIBS) -Wl,--end-group
+endif
+ifeq ($(ENVTYPE), Marconi) #Linux env.
+ EXTLIBS = $(LDIRS) -Wl,--start-group $(LIBS) -Wl,--end-group
+endif
+ifeq ($(ENVTYPE), MacOS) #Linux env.
+ EXTLIBS = $(LDIRS) $(LIBS)
+endif
#Flag for finding external include files
EXTINC = $(IDIRS)
diff --git a/matlab/plot/plot_metric.m b/matlab/plot/plot_metric.m
index 5fb56042ae281f23a85fa54d7cc09f79419810fd..28e9b1c87cec3c969e6904bc1d3c52a4cf4e3d02 100644
--- a/matlab/plot/plot_metric.m
+++ b/matlab/plot/plot_metric.m
@@ -11,7 +11,13 @@ for i_ = 1:numel(names)
namae = names{i_};
geo_arrays(:,i_) = h5read(data.outfilenames{end},['/data/metric/',namae])';
end
-NPLOT = options.SHOW_FLUXSURF + options.SHOW_METRICS;
+try
+ NPLOT = options.SHOW_FLUXSURF + options.SHOW_METRICS;
+catch
+ NPLOT = 2;
+ options.SHOW_FLUXSURF = 1;
+ options.SHOW_METRICS = 1;
+end
if NPLOT > 0
fig = figure;
if options.SHOW_METRICS
diff --git a/src/diagnose.F90 b/src/diagnose.F90
index 351acccdfe1a92ebe847baf848d60892c757ca9a..8807f076fa17bd74169421b4f7907081bc8b3e26 100644
--- a/src/diagnose.F90
+++ b/src/diagnose.F90
@@ -47,6 +47,7 @@ SUBROUTINE init_outfile(comm,file0,file,fid)
USE collision, ONLY: coll_outputinputs
USE initial_par, ONLY: initial_outputinputs
USE time_integration,ONLY: time_integration_outputinputs
+ USE parallel, ONLY: parallel_outputinputs
USE futils, ONLY: creatf, creatg, creatd, attach, putfile
IMPLICIT NONE
!input
@@ -89,6 +90,7 @@ SUBROUTINE init_outfile(comm,file0,file,fid)
CALL coll_outputinputs(fid)
CALL initial_outputinputs(fid)
CALL time_integration_outputinputs(fid)
+ CALL parallel_outputinputs(fid)
! Save STDIN (input file) of this run
IF(jobnum .LE. 99) THEN
WRITE(str,'(a,i2.2)') "/files/STDIN.",jobnum
diff --git a/src/parallel_mod.F90 b/src/parallel_mod.F90
index 2d40944195d62f199e85eb36579feb47e5c86010..5f7e921db212195142d449fb9457dd6f8b24b6f6 100644
--- a/src/parallel_mod.F90
+++ b/src/parallel_mod.F90
@@ -37,7 +37,8 @@ MODULE parallel
INTEGER, DIMENSION(:), ALLOCATABLE :: rcv_zyp, dsp_zyp
PUBLIC :: ppinit, manual_0D_bcast, manual_3D_bcast, init_parallel_var, &
- gather_xyz, gather_xyz_real, gather_pjz, gather_pjxyz, exchange_ghosts_1D
+ gather_xyz, gather_xyz_real, gather_pjz, gather_pjxyz, exchange_ghosts_1D, &
+ parallel_outputinputs
CONTAINS
@@ -463,4 +464,19 @@ CONTAINS
ENDDO
END SUBROUTINE exchange_ghosts_1D
+
+ SUBROUTINE parallel_outputinputs(fid)
+ ! Write the input parameters to the results_xx.h5 file
+ USE futils, ONLY: attach, creatd
+ IMPLICIT NONE
+ INTEGER, INTENT(in) :: fid
+ CHARACTER(len=256) :: str
+ WRITE(str,'(a)') '/data/input/parallel'
+ CALL creatd(fid, 0,(/0/),TRIM(str),'MPI parallelization')
+ CALL attach(fid, TRIM(str), "num_procs", num_procs)
+ CALL attach(fid, TRIM(str), "num_procs_p", num_procs_p)
+ CALL attach(fid, TRIM(str), "num_procs_ky", num_procs_ky)
+ CALL attach(fid, TRIM(str), "num_procs_z", num_procs_z)
+ END SUBROUTINE parallel_outputinputs
+
END MODULE parallel
diff --git a/wk/benchmark_and_scan_scripts/Parisi_2020_JET_miller_eq.txt b/wk/benchmark_and_scan_scripts/Parisi_2020_JET_miller_eq.txt
new file mode 100644
index 0000000000000000000000000000000000000000..ac742f38bcb8fbe3404b6d344361ed22aace68c2
--- /dev/null
+++ b/wk/benchmark_and_scan_scripts/Parisi_2020_JET_miller_eq.txt
@@ -0,0 +1,89 @@
+2.0089285714285716, 0.08115169144580903
+2.0089285714285716, 0.3164458090928679
+2.022321428571429, 0.5245502046972632
+2.0401785714285716, 0.6873922645981467
+2.053571428571429, 0.8140486964016374
+2.0803571428571432, 0.9270900667959489
+2.1205357142857144, 1.07629013143719
+2.169642857142857, 1.2254632622279678
+2.2232142857142856, 1.3338989441930615
+2.2767857142857144, 1.419710191769015
+2.334821428571429, 1.4783586511527682
+2.3794642857142856, 1.5279977375565608
+2.4419642857142856, 1.5640082956259422
+2.5, 1.6000323206205553
+2.575892857142857, 1.626952704158586
+2.65625, 1.6357600732600728
+2.7142857142857144, 1.6355850032320616
+2.78125, 1.6308581124757588
+2.84375, 1.6125700280112039
+2.915178571428571, 1.5852052359405295
+2.9821428571428568, 1.5578539107950866
+3.0446428571428568, 1.5214662788192193
+3.1205357142857144, 1.4895631329454853
+3.1874999999999996, 1.430537599655246
+3.2499999999999996, 1.3896250808015507
+3.2946428571428568, 1.3397166558931257
+3.3660714285714284, 1.2897274294333112
+3.410714285714285, 1.23076923076923
+3.455357142857143, 1.1853856927386333
+3.504464285714285, 1.1218891402714926
+3.5535714285714284, 1.06291747468218
+3.5848214285714284, 1.0175743374272779
+3.6249999999999996, 0.9586296056884285
+3.6562499999999996, 0.8861371471665582
+3.7053571428571423, 0.790966386554621
+3.741071428571428, 0.7003609135962068
+3.7633928571428568, 0.623370502046972
+3.7857142857142856, 0.5644796380090489
+3.7991071428571423, 0.47846638655462126
+3.8080357142857135, 0.42866569704804913
+3.8169642857142856, 0.3743401206636492
+3.8258928571428568, 0.292865223012281
+3.8258928571428568, 0.22046703296703218
+3.8258928571428568, 0.16616839043309573
+3.821428571428571, 0.10283344106873438
+3.8169642857142856, 0.05307315233785759
+3.803571428571428, -0.010234863176040276
+3.7946428571428568, -0.07355634561516977
+3.7589285714285707, -0.1865707821590179
+3.741071428571428, -0.24534044386985632
+3.7187499999999996, -0.3131464124111185
+3.7053571428571423, -0.35382999353587663
+3.6696428571428568, -0.41707067442361656
+3.6339285714285707, -0.4893611290670121
+3.589285714285714, -0.5616246498599444
+3.5178571428571423, -0.6700064641241121
+3.464285714285714, -0.7377181641887531
+3.3883928571428568, -0.8189371902607199
+3.339285714285714, -0.868562809739281
+3.227678571428571, -0.9677736479207069
+3.15625, -1.0218568196509377
+3.0446428571428568, -1.0803436759319112
+2.9642857142857144, -1.1208252531781946
+2.8705357142857144, -1.1522166558931268
+2.790178571428571, -1.174598685628098
+2.7098214285714284, -1.1834060547295844
+2.633928571428571, -1.1831771170006464
+2.5625, -1.1648620986856282
+2.5, -1.1465740142210732
+2.4330357142857144, -1.1146978021978022
+2.383928571428571, -1.0693007972419737
+2.3080357142857144, -1.0011985563456152
+2.267857142857143, -0.9467787114845942
+2.2455357142857144, -0.9195620555914676
+2.21875, -0.865182611506141
+2.1875, -0.8062648136177553
+2.1651785714285716, -0.756423723335488
+2.147321428571429, -0.7111209868562811
+2.1294642857142856, -0.6522435897435896
+2.107142857142857, -0.6024024994613233
+2.09375, -0.5390136823960356
+2.075892857142857, -0.47561139840551614
+2.0625, -0.41222258134022893
+2.049107142857143, -0.3443088773971128
+2.0401785714285716, -0.28093352725705656
+2.0401785714285716, -0.22210999784529206
+2.03125, -0.14063510019392367
+2.022321428571429, -0.032010881275587266
+2.013392857142857, 0.031364468864468975
diff --git a/wk/fast_analysis.m b/wk/fast_analysis.m
index 9dcf610fc9eef151688a87fd9964da13fbaeffc5..e7c14fd1e1bd85c049d1d305e97fc81568f5b002 100644
--- a/wk/fast_analysis.m
+++ b/wk/fast_analysis.m
@@ -5,13 +5,15 @@ addpath(genpath([gyacomodir,'matlab/compute'])) % ... add
addpath(genpath([gyacomodir,'matlab/load'])) % ... add
default_plots_options
% Partition of the computer where the data have to be searched
-PARTITION='';
-
+% PARTITION='/Users/ahoffmann/gyacomo/results/paper_3/';
+PARTITION='/misc/gyacomo23_outputs/paper_3/';
%% Paper 3
-resdir = '/Users/ahoffmann/gyacomxlio/results/paper_3/DTT_rho85/3x2x192x48x32';
-% resdir = '/Users/ahoffmann/gyacomo/results/paper_3/DTT_rho85/3x2x192x48x32_NT';
-% resdir = '/Users/ahoffmann/gyacomo/results/paper_3/DTT_rho98/3x2x192x48x32';
-resdir = '/Users/ahoffmann/gyacomo/results/paper_3/DTT_rho98/3x2x192x48x32_0.25grad';
+% resdir = 'DTT_rho85/3x2x192x48x32';
+% resdir = 'DTT_rho85/3x2x192x48x32_NT';
+% resdir = 'DTT_rho98/3x2x192x48x32';
+% resdir = 'DTT_rho98/3x2x192x48x32_0.25grad';
+% resdir = 'LM_DIIID_rho95/5x3x512x92x32';
+resdir = 'LM_DIIID_rho95/3x2x512x92x32';
%%
J0 = 00; J1 = 02;
diff --git a/wk/lin_scan_script.m b/wk/lin_scan_script.m
index fa4b35099767dab82ff7919e44ed34954d95d511..8831740be18598ee3c075df149aef21272dbafd6 100644
--- a/wk/lin_scan_script.m
+++ b/wk/lin_scan_script.m
@@ -19,7 +19,7 @@ RUN = 1; % To run or just to load
RERUN = 0; % rerun if the data does not exist
default_plots_options
EXECNAME = 'gyacomo23_sp'; % single precision
-% EXECNAME = 'gyacomo23_dp'; % double precision
+%EXECNAME = 'gyacomo23_dp'; % double precision
%% Setup parameters
% run lin_DTT_AB_rho85
@@ -30,11 +30,12 @@ run lin_JET_rho97
%% Change parameters
NY = 2;
-% SIGMA_E = 0.023;
%% Scan parameters
SIMID = [SIMID,'_scan'];
P_a = [2 4 6 8];
+% P_a = 2;
ky_a = logspace(-1.5,1.5,30);
+CO = 'SG';
%% Scan loop
% arrays for the result
g_ky = zeros(numel(ky_a),numel(P_a));
@@ -47,8 +48,8 @@ for PMAX = P_a
i = 1;
for ky = ky_a
LY = 2*pi/ky;
- DT = 1e-4;%min(1e-2,1e-3/ky);
- TMAX = 10;%min(10,1.5/ky);
+ DT = 1e-5;%/(1+log(ky/0.05));%min(1e-2,1e-3/ky);
+ TMAX = 20;%min(10,1.5/ky);
DTSAVE0D = 0.1;
DTSAVE3D = 0.1;
%% RUN
@@ -64,10 +65,15 @@ for PMAX = P_a
catch
data_.outfilenames = [];
end
- if RUN && (RERUN || isempty(data_.outfilenames) || Ntime < 10)
- % system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 2 ',gyacomodir,'bin/',EXECNAME,' 1 2 1 0; cd ../../../wk'])
- system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 4 ',gyacomodir,'bin/',EXECNAME,' 1 2 2 0; cd ../../../wk'])
- % system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 6 ',gyacomodir,'bin/',EXECNAME,' 3 2 1 0; cd ../../../wk'])
+ if RUN && (RERUN || isempty(data_.outfilenames) || (Ntime < 10))
+ MVIN =['cd ../results/',SIMID,'/',PARAMS,'/;'];
+ % RUNG =['time ',mpirun,' -np 2 ',gyacomodir,'bin/',EXECNAME,' 1 2 1 0;'];
+ RUNG =['time ',mpirun,' -np 4 ',gyacomodir,'bin/',EXECNAME,' 1 2 2 0;'];
+ % RUNG =['time ',mpirun,' -np 8 ',gyacomodir,'bin/',EXECNAME,' 2 2 2 0;'];
+ % RUNG =['time ',mpirun,' -np 1 ',gyacomodir,'bin/',EXECNAME,' 1 1 1 0;'];
+ % RUNG = ['./../../../bin/gyacomo23_sp 0;'];
+ MVOUT='cd ../../../wk;';
+ system([MVIN,RUNG,MVOUT]);
end
data_ = compile_results_low_mem(data_,LOCALDIR,00,00);
[data_.PHI, data_.Ts3D] = compile_results_3D(LOCALDIR,00,00,'phi');
diff --git a/wk/load_metadata_scan.m b/wk/load_metadata_scan.m
index 6615ee538fe728c08f16c6b2eb8c78a7c284ff74..f107d4afec12cbd35cd8844c282d73a5cc056d90 100644
--- a/wk/load_metadata_scan.m
+++ b/wk/load_metadata_scan.m
@@ -15,13 +15,9 @@ addpath(genpath([gyacomodir,'matlab/load'])) % ... add% EXECNAME = 'gyacomo_1.0'
% datafname = 'lin_DTT_AB_rho85_PT_scan/16x24_ky_0.1_1_P_2_8_DGGK_0.05_be_0.0039.mat';
% datafname = 'lin_DTT_AB_rho85_PT_scan/16x24_ky_0.1_0.9_P_2_8_kN_1.33_DGGK_0.56901_be_0.0039.mat';
% datafname = 'lin_DTT_AB_rho85_PT_scan/8x24_ky_0.05_1.5_P_2_8_kN_1.33_DGGK_0.1_be_0.0039.mat';
-% datafname = 'lin_JET_rho97_scan/4x32_ky_0.01_10_P_2_8_kN_10_DGGK_0.1_be_0.0031.mat';
-% datafname = 'lin_JET_rho97_scan/4x32_ky_0.01_10_P_2_8_kN_10_DGGK_0.05_be_0.0031.mat';
-% datafname = 'lin_JET_rho97_scan/8x32_ky_0.01_10_P_2_8_kN_10_DGGK_0.05_be_0.0031.mat';
-% datafname = 'lin_JET_rho97_scan/8x32_ky_0.01_10_P_2_2_kN_10_DGGK_0.05_be_0.0031.mat';
-datafname = 'lin_JET_rho97_scan/8x32_ky_0.031623_31.6228_P_2_2_kN_10_DGGK_0.1_be_0.0031.mat';
+datafname = 'lin_JET_rho97_scan/8x32_ky_0.031623_31.6228_P_1_1_kN_31.4286_DGGK_0.1_be_0.0031.mat';
%% Chose if we filter gamma>0.05
-FILTERGAMMA = 0;
+FILTERGAMMA = 1;
%% Load data
fname = ['../results/',datafname];
@@ -29,7 +25,7 @@ d = load(fname);
gamma = real(d.data); g_err = real(d.err);
omega = imag(d.data); w_err = imag(d.err);
if FILTERGAMMA
- d.data = real(gamma).*(real(gamma)>0.025) + imag(gamma);
+ gamma = gamma.*(gamma>0.025);
end
if 0
%% Pcolor of the peak
@@ -46,7 +42,7 @@ set(gca,'YTick',1:numel(d.s2),'YTicklabel',d.s2)
colormap(jet)
colormap(bluewhitered)
clb=colorbar;
-clb.Label.String = '$\gamma c_s/R$';
+clb.Label.String = '$\gamma R/c_s$';
clb.Label.Interpreter = 'latex';
clb.Label.FontSize= 18;
end
@@ -83,7 +79,7 @@ for i = 1:numel(d.s2)
'color',colors_(i,:));
hold on;
end
-xlabel(d.s1name); ylabel('$\omega c_s/R$');title(d.title);
+xlabel(d.s1name); ylabel('$\omega R/c_s$');title(d.title);
xlim([d.s1(1) d.s1(end)]);
colormap(colors_);
diff --git a/wk/parameters/lin_JET_rho97.m b/wk/parameters/lin_JET_rho97.m
index b9f1041d170ad8d688a05a05b22427e0f80285ab..72ae55cd2c30d02fa89b8a09e4f8b8cec5816c2a 100644
--- a/wk/parameters/lin_JET_rho97.m
+++ b/wk/parameters/lin_JET_rho97.m
@@ -1,45 +1,68 @@
-% Parameters found in Parisi et al. 2020
-% Jet shot 92174
+%% Parameters found in Parisi et al. 2020
+% Jet shot 92174 parameters
+BT0 = 1.9; %[T] Toroidal field @ 2.96m
+Ip = 1.4; %[MA] Plasma current @ 2.96m
+PNBI = 17.4; %[MW] NBI power
+rhoi = 0.27; %[cm] Ion gyroradius
+R0 = 2.86; %[m] Major radius
+a = 0.91; %[m] F-T minor radius
+Rc = 2.91; %[m] ??
+rc = 0.89; %[m] ??
+m_e = 5.49e-4; %[amu] electron mass
+m_i = 2.014; %[amu] deuterium mass
+% Dimless flux-tube parameters
+nuee = 0.83; %[vti/a] e-e collision frequ.
+wTe = 42; %[a/L] e-temp. gradient length
+wTi = 11; %[a/L] i-temp. gradient length
+wNe = 10; %[a/L] dens. gradient length
+tau = 1/0.56; %Ti/Te i-e temperature ratio
+gE = 0.56; %[vti/a] ExB shearing rate
+roa = 0.9743; % r/a Flux surface position
+beta = 0.0031; % [8pi*ptot/B^2] with B = 1.99T
+% Normalization
+% v0 = vth_i = sqrt(2*Ti/mi)
+% rho0 = rho_i = vti/omegai
+% Conversion factors from GYAC to paper results
+freq_conv = a/R0 * sqrt(tau/2); % from R/c_s to a/vti
+wave_conv = sqrt(2/tau); % from rho_i to rho_s
+grad_conv = a/R0; % from R/LT to a/LT
+
%% Set simulation parameters
SIMID = 'lin_JET_rho97'; % Name of the simulation
%% Set up physical parameters
-CLUSTER.TIME = '99:00:00'; % Allocation time hh:mm:ss
NU = 0.1; % Not the true value
-TAU = 1/0.56; % e/i temperature ratio
-K_Ne = 10; % ele Density '''
-K_Te = 42; % ele Temperature '''
-K_Ni = 10; % ion Density gradient drive
-K_Ti = 11; % ion Temperature '''
-SIGMA_E = 0.0233380; % mass ratio sqrt(m_a/m_i) (correct = 0.0233380)
+TAU = tau; % i/e temperature ratio
+K_Ne = wNe/grad_conv; % ele Density '''
+K_Te = wTe/grad_conv; % ele Temperature '''
+K_Ni = wNe/grad_conv; % ion Density gradient drive
+K_Ti = wTi/grad_conv; % ion Temperature '''
+SIGMA_E = sqrt(m_e/m_i); % mass ratio sqrt(m_e/m_i) (e-H = 0.0233380)
NA = 2; % number of kinetic species
-ADIAB_E = (NA==1); % adiabatic electron model
-BETA = 0.0031; % electron plasma beta
-MHD_PD = 0;
+BETA = beta; % electron plasma beta
+MHD_PD = 1;
+CO = 'DG'; % Collision operator (LB:L.Bernstein, DG:Dougherty, SG:Sugama, LR: Lorentz, LD: Landau)
+GKCO = 1; % Gyrokinetic operator
+ABCO = 1; % INTERSPECIES collisions
+COLL_KCUT= 100; % Cutoff for collision operator
%% GEOMETRY
% GEOMETRY= 's-alpha';
GEOMETRY= 'miller';
-EPS = 0.9753*0.91/2.91; % inverse aspect ratio
-Q0 = 5.10; % safety factor
-SHEAR = 3.36; % magnetic shear
-KAPPA = 1.55; % elongation
-S_KAPPA = 0.95;
-DELTA = 0.26; % triangularity
-S_DELTA = 0.74;
-ZETA = 0; % squareness
-S_ZETA = 0;
-PARALLEL_BC = 'dirichlet'; % Boundary condition for parallel direction ('dirichlet','periodic','shearless','disconnected')
-SHIFT_Y = 0.0; % Shift in the periodic BC in z
-NPOL = 1; % Number of poloidal turns
-PB_PHASE = 0;
+EPS = a/R0; % inverse aspect ratio
+Q0 = 5.100; % safety factor
+SHEAR = 3.360; % magnetic shear
+KAPPA = 1.550; % elongation
+S_KAPPA = 0.949;
+DELTA = 0.263; % triangularity
+S_DELTA = 0.737;
%% Set up grid parameters
P = 4;
J = P/2;%P/2;
PMAX = P; % Hermite basis size
JMAX = J; % Laguerre basis size
-NX = 8; % real space x-gridpoints
-NY = 8; % real space y-gridpoints
+NX = 16; % 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/0.2; % Size of the squared frequency domain in y direction
NZ = 32; % number of perpendicular planes (parallel grid)
@@ -55,11 +78,15 @@ DTSAVE3D = 0.5; % Sampling time for 3D arrays
DTSAVE5D = 100; % Sampling time for 5D arrays
JOB2LOAD = -1; % Start a new simulation serie
+
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
+%% UNUSED PARAMETERS
+% These parameters are usually not to play with in linear runs
+
%% OPTIONS
+CLUSTER.TIME = '99:00:00'; % Allocation time hh:mm:ss
LINEARITY = 'linear'; % activate non-linearity (is cancelled if KXEQ0 = 1)
-CO = 'DG'; % Collision operator (LB:L.Bernstein, DG:Dougherty, SG:Sugama, LR: Lorentz, LD: Landau)
-GKCO = 1; % Gyrokinetic operator
-ABCO = 1; % INTERSPECIES collisions
INIT_ZF = 0; % Initialize zero-field quantities
HRCY_CLOS = 'truncation'; % Closure model for higher order moments
DMAX = -1;
@@ -67,6 +94,8 @@ NLIN_CLOS = 'truncation'; % Nonlinear closure model for higher order moments
NMAX = 0;
KERN = 0; % Kernel model (0 : GK)
INIT_OPT = 'phi'; % Start simulation with a noisy mom00/phi/allmom
+NOISE0 = 1.0e-5; % Initial noise amplitude
+BCKGD0 = 0.0e-5; % Initial background
NUMERICAL_SCHEME = 'RK4'; % Numerical integration scheme (RK2,SSPx_RK2,RK3,SSP_RK3,SSPx_RK3,IMEX_SSP2,ARK2,RK4,DOPRI5)
%% OUTPUTS
@@ -80,22 +109,25 @@ W_TEMP = 1; % Output flag for temperature
W_NAPJ = 1; % Output flag for nalphaparallel (parallel momentum of species alpha)
W_SAPJ = 0; % Output flag for saparallel (parallel current of species alpha)
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
-%% UNUSED PARAMETERS
-% These parameters are usually not to play with in linear runs
+%% Unused geometry
+ZETA = 0; % squareness
+S_ZETA = 0;
+PARALLEL_BC = 'dirichlet'; % Boundary condition for parallel direction ('dirichlet','periodic','shearless','disconnected')
+SHIFT_Y = 0.0; % Shift in the periodic BC in z
+NPOL = 1; % Number of poloidal turns
+PB_PHASE = 0;
+
+%% Diffusions
MU = 0.0; % Hyperdiffusivity coefficient
MU_X = MU; % Hyperdiffusivity coefficient in x direction
MU_Y = MU; % Hyperdiffusivity coefficient in y direction
N_HD = 4; % Degree of spatial-hyperdiffusivity
-MU_Z = 2.0; % Hyperdiffusivity coefficient in z direction
+MU_Z = 5.0; % Hyperdiffusivity coefficient in z direction
HYP_V = 'hypcoll'; % Kinetic-hyperdiffusivity model
MU_P = 0.0; % Hyperdiffusivity coefficient for Hermite
MU_J = 0.0; % Hyperdiffusivity coefficient for Laguerre
LAMBDAD = 0.0; % Lambda Debye
-NOISE0 = 1.0e-5; % Initial noise amplitude
-BCKGD0 = 0.0e-5; % Initial background
k_gB = 1.0; % Magnetic gradient strength
k_cB = 1.0; % Magnetic curvature strength
-COLL_KCUT = 1; % Cutoff for collision operator
-ADIAB_I = 0; % adiabatic ion model
\ No newline at end of file
+ADIAB_I = 0; % adiabatic ion model
+ADIAB_E = (NA==1); % adiabatic electron model
\ No newline at end of file