minor changes

matlab/create_gif.m

@@ -15,7 +15,7 @@ if hmax == hmin
     disp('Warning : h = hmin = hmax = const')
 else
 % Setup figure frame
-fig  = figure;
+fig  = figure('Color','white','Position', [100, 100, 400, 400]);
     pcolor(X,Y,FIELD(:,:,1)); % to set up
     colormap jet
     axis tight manual % this ensures that getframe() returns a consistent size
@@ -25,19 +25,21 @@ fig  = figure;
     in      = 1;
     nbytes = fprintf(2,'frame %d/%d',in,numel(FIELD(1,1,:)));
     for n = FRAMES % loop over selected frames
-        pclr = pcolor(X,Y,FIELD(:,:,n)); % frame plot
+        scale = max(max(abs(FIELD(:,:,n))));
+        pclr = pcolor(X,Y,FIELD(:,:,n)/scale); % frame plot
         if INTERP
             shading interp; 
         end
-        set(pclr, 'edgecolor','none');
-        caxis([min(min(FIELD(:,:,n))),max(max(FIELD(:,:,n)))]);
-        xlabel(XNAME); ylabel(YNAME); colorbar;
-        title([FIELDNAME,', $t \approx$', sprintf('%.3d',ceil(T(n)))]);
+        set(pclr, 'edgecolor','none'); axis square;
+%         caxis([min(min(FIELD(:,:,n))),max(max(FIELD(:,:,n)))]);
+        xlabel(XNAME); ylabel(YNAME); %colorbar;
+        title([FIELDNAME,', $t \approx$', sprintf('%.3d',ceil(T(n)))...
+            ,', scaling = ',sprintf('%.1e',scale)]);
         drawnow 
         % Capture the plot as an image 
         frame = getframe(fig); 
         im = frame2im(frame); 
-        [imind,cm] = rgb2ind(im,64); 
+        [imind,cm] = rgb2ind(im,32); 
         % Write to the GIF File 
         if in == 1 
           imwrite(imind,cm,GIFNAME,'gif', 'Loopcount',inf); 

matlab/create_gif_1D.m

@@ -21,7 +21,7 @@ fig  = figure;
     nbytes = fprintf(2,'frame %d/%d',in,numel(FIELD(1,1,:)));
     for n = FRAMES % loop over selected frames
         scale = max(FIELD(:,n));
-        plot(X,FIELD(:,n)/scale);
+        plot(X,FIELD(:,n)/scale,linestyle);
         ylim([YMIN,YMAX]); xlim([XMIN,XMAX]);
         title(['$t \approx$', sprintf('%.3d',ceil(T(n))), ', scaling = ',sprintf('%.1e',scale)]);
         xlabel(XNAME); ylabel(FIELDNAME);

wk/fort.90

 &BASIC
   nrun   = 100000000
-  dt     = 0.0001
-  tmax   = 20
+  dt     = 0.01
+  tmax   = 150
   RESTART = .false.
 /
 &GRID
-  pmaxe =0
-  jmaxe = 6
-  pmaxi = 0
-  jmaxi = 6
-  Nr   = 64
+  pmaxe =2
+  jmaxe = 1
+  pmaxi = 2
+  jmaxi = 1
+  Nr   = 100
   Lr = 40
-  Nz   = 64
+  Nz   = 100
   Lz = 40
   kpar = 0
 /
 &OUTPUT_PAR
   nsave_0d = 0
   nsave_1d = 0
-  nsave_2d = 10000
-  nsave_5d = 10000
+  nsave_2d = 20
+  nsave_5d = 200
   write_Na00    = .true.
   write_moments = .true.
   write_phi     = .true.
-  write_non_lin     = .false.
+  write_non_lin     = .true.
   write_doubleprecision = .true.
-  resfile0      = 'KH_lin_mode_Nz_16_A_1.25_64x32_L_40_lin_Pe_0_Je_6_Pi_0_Ji_6_nB_0_nN_0_nu_0e+00__mu_1e-04_'
-  rstfile0      = '../checkpoint/cp_KH_lin_mode_Nz_16_A_1.25_64x32_L_40_lin_Pe_0_Je_6_Pi_0_Ji_6_nB_0_nN_0_nu_0e+00__mu_1e-04_'
+  resfile0      = 'ZP_forced_sym_100x50_L_40_Pe_2_Je_1_Pi_2_Ji_1_nB_0.5_nN_1_nu_1e-02_DG_mu_5e-04_'
+  rstfile0      = '../checkpoint/cp_ZP_forced_sym_100x50_L_40_Pe_2_Je_1_Pi_2_Ji_1_nB_0.5_nN_1_nu_1e-02_DG_mu_5e-04_'
   job2load      = 0
 /
 &MODEL_PAR
   ! Collisionality
-  CO      = 0
+  CO      = -2
   DK      = .false.
-  NON_LIN = .false.
-  mu      = 0.0001
-  nu      = 0
+  NON_LIN = .true.
+  mu      = 0.0005
+  nu      = 0.01
   tau_e   = 1
   tau_i   = 1
   sigma_e = 0.023338
   sigma_i = 1
   q_e     = -1
   q_i     = 1
-  eta_n   = 0
+  eta_n   = 1
   eta_T   = 0
-  eta_B   = 0
+  eta_B   = 0.5
   lambdaD = 0
-  kr0KH   = 2.5133
-  A0KH    = 1.25
+  kr0KH   = 0
+  A0KH    = 0
 /
 &INITIAL_CON
   only_Na00         =.false.
   initback_moments  =0
-  initnoise_moments =0.0001
+  initnoise_moments =5e-05
   iseed             =42
-  selfmat_file      ='../iCa/self_Coll_GKE_0_GKI_0_ESELF_1_ISELF_1_Pmaxe_0_Jmaxe_6_Pmaxi_0_Jmaxi_6_pamaxx_10.h5'
-  eimat_file        ='../iCa/ei_Coll_GKE_0_GKI_0_ETEST_1_EBACK_1_Pmaxe_0_Jmaxe_6_Pmaxi_0_Jmaxi_6_pamaxx_10_tau_1.0000_mu_0.0233.h5'
-  iemat_file        ='../iCa/ie_Coll_GKE_0_GKI_0_ITEST_1_IBACK_1_Pmaxe_0_Jmaxe_6_Pmaxi_0_Jmaxi_6_pamaxx_10_tau_1.0000_mu_0.0233.h5'
+  selfmat_file      ='../iCa/self_Coll_GKE_0_GKI_0_ESELF_1_ISELF_1_Pmaxe_2_Jmaxe_1_Pmaxi_2_Jmaxi_1_pamaxx_10.h5'
+  eimat_file        ='../iCa/ei_Coll_GKE_0_GKI_0_ETEST_1_EBACK_1_Pmaxe_2_Jmaxe_1_Pmaxi_2_Jmaxi_1_pamaxx_10_tau_1.0000_mu_0.0233.h5'
+  iemat_file        ='../iCa/ie_Coll_GKE_0_GKI_0_ITEST_1_IBACK_1_Pmaxe_2_Jmaxe_1_Pmaxi_2_Jmaxi_1_pamaxx_10_tau_1.0000_mu_0.0233.h5'
 /
 &TIME_INTEGRATION_PAR
   numerical_scheme='RK4'