diff --git a/Makefile b/Makefile
index d776c7daa5678172ff7fdf2d5f0461d7d9dc4133..21a929d8622fd9d4d8ba50dd9b76850caa8acce1 100644
--- a/Makefile
+++ b/Makefile
@@ -52,9 +52,9 @@ $(OBJDIR)/compute_Sapj.o $(OBJDIR)/control.o $(OBJDIR)/fourier_mod.o \
$(OBJDIR)/diagnose.o $(OBJDIR)/diagnostics_par_mod.o $(OBJDIR)/endrun.o $(OBJDIR)/fields_mod.o \
$(OBJDIR)/inital.o $(OBJDIR)/initial_par_mod.o $(OBJDIR)/main.o $(OBJDIR)/memory.o \
$(OBJDIR)/model_mod.o $(OBJDIR)/moments_eq_rhs.o $(OBJDIR)/poisson.o \
-$(OBJDIR)/ppexit.o $(OBJDIR)/ppinit.o $(OBJDIR)/prec_const_mod.o $(OBJDIR)/readinputs.o \
-$(OBJDIR)/ghosts_mod.o $(OBJDIR)/grid_mod.o $(OBJDIR)/restarts_mod.o $(OBJDIR)/stepon.o \
-$(OBJDIR)/tesend.o $(OBJDIR)/time_integration_mod.o $(OBJDIR)/utility_mod.o
+$(OBJDIR)/ppexit.o $(OBJDIR)/ppinit.o $(OBJDIR)/prec_const_mod.o $(OBJDIR)/processing_mod.o \
+$(OBJDIR)/readinputs.o $(OBJDIR)/ghosts_mod.o $(OBJDIR)/grid_mod.o $(OBJDIR)/restarts_mod.o \
+$(OBJDIR)/stepon.o $(OBJDIR)/tesend.o $(OBJDIR)/time_integration_mod.o $(OBJDIR)/utility_mod.o
$(EXEC): $(FOBJ)
$(F90) $(LDFLAGS) $(OBJDIR)/*.o $(EXTMOD) $(EXTINC) $(EXTLIBS) -o $@
@@ -86,10 +86,7 @@ $(OBJDIR)/tesend.o $(OBJDIR)/time_integration_mod.o $(OBJDIR)/utility_mod.o
$(OBJDIR)/control.o : src/control.F90 $(OBJDIR)/auxval.o $(OBJDIR)/prec_const_mod.o $(OBJDIR)/basic_mod.o $(OBJDIR)/ppexit.o $(OBJDIR)/ppinit.o $(OBJDIR)/readinputs.o $(OBJDIR)/tesend.o
$(F90) -c $(F90FLAGS) $(FPPFLAGS) $(EXTMOD) $(EXTINC) src/control.F90 -o $@
- $(OBJDIR)/fourier_mod.o : src/fourier_mod.F90 $(OBJDIR)/basic_mod.o $(OBJDIR)/prec_const_mod.o $(OBJDIR)/grid_mod.o
- $(F90) -c $(F90FLAGS) $(FPPFLAGS) $(EXTMOD) $(EXTINC) src/fourier_mod.F90 -o $@
-
- $(OBJDIR)/diagnose.o : src/diagnose.F90 $(OBJDIR)/prec_const_mod.o $(OBJDIR)/array_mod.o $(OBJDIR)/basic_mod.o $(OBJDIR)/diagnostics_par_mod.o $(OBJDIR)/fields_mod.o $(OBJDIR)/grid_mod.o $(OBJDIR)/initial_par_mod.o $(OBJDIR)/model_mod.o $(OBJDIR)/time_integration_mod.o
+ $(OBJDIR)/diagnose.o : src/diagnose.F90 $(OBJDIR)/prec_const_mod.o $(OBJDIR)/processing_mod.o $(OBJDIR)/array_mod.o $(OBJDIR)/basic_mod.o $(OBJDIR)/diagnostics_par_mod.o $(OBJDIR)/fields_mod.o $(OBJDIR)/grid_mod.o $(OBJDIR)/initial_par_mod.o $(OBJDIR)/model_mod.o $(OBJDIR)/time_integration_mod.o
$(F90) -c $(F90FLAGS) $(FPPFLAGS) $(EXTMOD) $(EXTINC) src/diagnose.F90 -o $@
$(OBJDIR)/diagnostics_par_mod.o : src/diagnostics_par_mod.F90 $(OBJDIR)/prec_const_mod.o $(OBJDIR)/basic_mod.o
@@ -101,6 +98,9 @@ $(OBJDIR)/tesend.o $(OBJDIR)/time_integration_mod.o $(OBJDIR)/utility_mod.o
$(OBJDIR)/fields_mod.o : src/fields_mod.F90 $(OBJDIR)/prec_const_mod.o
$(F90) -c $(F90FLAGS) $(FPPFLAGS) $(EXTMOD) $(EXTINC) src/fields_mod.F90 -o $@
+ $(OBJDIR)/fourier_mod.o : src/fourier_mod.F90 $(OBJDIR)/basic_mod.o $(OBJDIR)/prec_const_mod.o $(OBJDIR)/grid_mod.o
+ $(F90) -c $(F90FLAGS) $(FPPFLAGS) $(EXTMOD) $(EXTINC) src/fourier_mod.F90 -o $@
+
$(OBJDIR)/ghosts_mod.o : src/ghosts_mod.F90 $(OBJDIR)/basic_mod.o $(OBJDIR)/fields_mod.o $(OBJDIR)/grid_mod.o $(OBJDIR)/ppinit.o $(OBJDIR)/time_integration_mod.o
$(F90) -c $(F90FLAGS) $(FPPFLAGS) $(EXTMOD) $(EXTINC) src/ghosts_mod.F90 -o $@
@@ -137,6 +137,9 @@ $(OBJDIR)/tesend.o $(OBJDIR)/time_integration_mod.o $(OBJDIR)/utility_mod.o
$(OBJDIR)/prec_const_mod.o : src/prec_const_mod.F90
$(F90) -c $(F90FLAGS) $(FPPFLAGS) $(EXTMOD) $(EXTINC) src/prec_const_mod.F90 -o $@
+ $(OBJDIR)/processing_mod.o : src/processing_mod.F90 $(OBJDIR)/array_mod.o $(OBJDIR)/prec_const_mod.o $(OBJDIR)/grid_mod.o $(OBJDIR)/fields_mod.o $(OBJDIR)/basic_mod.o
+ $(F90) -c $(F90FLAGS) $(FPPFLAGS) $(EXTMOD) $(EXTINC) src/processing_mod.F90 -o $@
+
$(OBJDIR)/readinputs.o : src/readinputs.F90 $(OBJDIR)/diagnostics_par_mod.o $(OBJDIR)/initial_par_mod.o $(OBJDIR)/model_mod.o $(OBJDIR)/prec_const_mod.o $(OBJDIR)/grid_mod.o $(OBJDIR)/time_integration_mod.o
$(F90) -c $(F90FLAGS) $(FPPFLAGS) $(EXTMOD) $(EXTINC) src/readinputs.F90 -o $@
diff --git a/matlab/compile_results.m b/matlab/compile_results.m
index 74bd6379d21b14918c9af2c19b277a48cd5394ef..44065bbc397a96a3c49595241f0ecebd930ce784 100644
--- a/matlab/compile_results.m
+++ b/matlab/compile_results.m
@@ -14,35 +14,51 @@ while(CONTINUE)
% Load results of simulation #JOBNUM
load_results
% Check polynomials degrees
- sz = size(Nepj); Pe_new= sz(1); Je_new= sz(2);
- sz = size(Nipj); Pi_new= sz(1); Ji_new= sz(2);
+ Pe_new= numel(Pe); Je_new= numel(Je);
+ Pi_new= numel(Pi); Ji_new= numel(Ji);
% If a degree is larger than previous job, put them in a larger array
if (sum([Pe_new, Je_new, Pi_new, Ji_new]>[Pe_old, Je_old, Pi_old, Ji_old]) >= 1)
- tmp = Nipj_; sz = size(tmp);
- Nipj_ = zeros(cat(1,[Pi_new,Ji_new]',sz(3:end)')');
- Nipj_(1:Pi_old,1:Ji_old,:,:,:) = tmp;
- tmp = Nepj_; sz = size(tmp);
- Nepj_ = zeros(cat(1,[Pe_new,Je_new]',sz(3:end)')');
- Nepj_(1:Pe_old,1:Je_old,:,:,:) = tmp;
- tmp = Sipj_; sz = size(tmp);
- Sipj_ = zeros(cat(1,[Pi_new,Ji_new]',sz(3:end)')');
- Sipj_(1:Pi_old,1:Ji_old,:,:,:) = tmp;
- tmp = Sepj_; sz = size(tmp);
- Sepj_ = zeros(cat(1,[Pe_new,Je_new]',sz(3:end)')');
- Sepj_(1:Pe_old,1:Je_old,:,:,:) = tmp;
+ if W_NAPJ
+ tmp = Nipj_; sz = size(tmp);
+ Nipj_ = zeros(cat(1,[Pi_new,Ji_new]',sz(3:end)')');
+ Nipj_(1:Pi_old,1:Ji_old,:,:,:) = tmp;
+ tmp = Nepj_; sz = size(tmp);
+ Nepj_ = zeros(cat(1,[Pe_new,Je_new]',sz(3:end)')');
+ Nepj_(1:Pe_old,1:Je_old,:,:,:) = tmp;
+ end
+ if W_SAPJ
+ tmp = Sipj_; sz = size(tmp);
+ Sipj_ = zeros(cat(1,[Pi_new,Ji_new]',sz(3:end)')');
+ Sipj_(1:Pi_old,1:Ji_old,:,:,:) = tmp;
+ tmp = Sepj_; sz = size(tmp);
+ Sepj_ = zeros(cat(1,[Pe_new,Je_new]',sz(3:end)')');
+ Sepj_(1:Pe_old,1:Je_old,:,:,:) = tmp;
+ end
end
-
- Nipj_ = cat(5,Nipj_,Nipj);
- Nepj_ = cat(5,Nepj_,Nepj);
- Ni00_ = cat(3,Ni00_,Ni00);
- Ne00_ = cat(3,Ne00_,Ne00);
- PHI_ = cat(3,PHI_,PHI);
- Ts2D_ = cat(1,Ts2D_,Ts2D);
- Ts5D_ = cat(1,Ts5D_,Ts5D);
-
- Sipj_ = cat(5,Sipj_,Sipj);
- Sepj_ = cat(5,Sepj_,Sepj);
+
+ if W_PHI || W_NA00
+ Ts2D_ = cat(1,Ts2D_,Ts2D);
+ end
+ if W_PHI
+ PHI_ = cat(3,PHI_,PHI);
+ end
+ if W_NA00
+ Ni00_ = cat(3,Ni00_,Ni00);
+ Ne00_ = cat(3,Ne00_,Ne00);
+ end
+
+ if W_NAPJ || W_SAPJ
+ Ts5D_ = cat(1,Ts5D_,Ts5D);
+ end
+ if W_NAPJ
+ Nipj_ = cat(5,Nipj_,Nipj);
+ Nepj_ = cat(5,Nepj_,Nepj);
+ end
+ if W_SAPJ
+ Sipj_ = cat(5,Sipj_,Sipj);
+ Sepj_ = cat(5,Sepj_,Sepj);
+ end
JOBFOUND = JOBFOUND + 1;
LASTJOB = JOBNUM;
diff --git a/matlab/load_0D_data.m b/matlab/load_0D_data.m
new file mode 100644
index 0000000000000000000000000000000000000000..7c2182f1281be5310dd2245144305eb005bbb50b
--- /dev/null
+++ b/matlab/load_0D_data.m
@@ -0,0 +1,9 @@
+function [ data, time, dt ] = load_0D_data( filename, variablename )
+%LOAD_0D_DATA load a 0D variable stored in a hdf5 result file from HeLaZ
+ time = h5read(filename,'/data/var0d/time');
+ dt = h5readatt(filename,'/data/input','dt');
+ cstart= h5readatt(filename,'/data/input','start_iframe0d');
+ data = h5read(filename,['/data/var0d/',variablename]);
+
+end
+
diff --git a/matlab/load_2D_data.m b/matlab/load_2D_data.m
index f03bbaa3a0e23e209ebe32cd137b3b2ef9aa76a2..47ef91a645345a1f29fb59805dd52e90a33e9c8c 100644
--- a/matlab/load_2D_data.m
+++ b/matlab/load_2D_data.m
@@ -1,11 +1,8 @@
-function [ data, kr, kz, time, dt ] = load_2D_data( filename, variablename )
+function [ data, time, dt ] = load_2D_data( filename, variablename )
%LOAD_2D_DATA load a 2D variable stored in a hdf5 result file from HeLaZ
time = h5read(filename,'/data/var2d/time');
kr = h5read(filename,'/data/grid/coordkr');
kz = h5read(filename,'/data/grid/coordkz');
-% kr = h5read(filename,['/data/var2d/',variablename,'/coordkr']);
-% kz = h5read(filename,['/data/var2d/',variablename,'/coordkz']);
-
dt = h5readatt(filename,'/data/input','dt');
cstart= h5readatt(filename,'/data/input','start_iframe2d');
diff --git a/matlab/load_5D_data.m b/matlab/load_5D_data.m
index 87edc9b9446f37900b4f016610902967822fd301..e36d767550e9bf69000364153c4563ff4410363a 100644
--- a/matlab/load_5D_data.m
+++ b/matlab/load_5D_data.m
@@ -1,14 +1,15 @@
-function [ data, p, j, kr, kz, time, dt ] = load_5D_data( filename, variablename )
+function [ data, time, dt ] = load_5D_data( filename, variablename )
%LOAD_5D_DATA load a 5D variable stored in a hdf5 result file from HeLaZ
time = h5read(filename,'/data/var5d/time');
- p = h5read(filename,'/data/grid/coordp');
- j = h5read(filename,'/data/grid/coordj');
+ if strcmp(variablename,'moments_e') || strcmp(variablename,'Sepj')
+ p = h5read(filename,'/data/grid/coordp_e');
+ j = h5read(filename,'/data/grid/coordj_e');
+ else
+ p = h5read(filename,'/data/grid/coordp_i');
+ j = h5read(filename,'/data/grid/coordj_i');
+ end
kr = h5read(filename,'/data/grid/coordkr');
kz = h5read(filename,'/data/grid/coordkz');
-% p = h5read(filename,['/data/var5d/',variablename,'/coordp']);
-% j = h5read(filename,['/data/var5d/',variablename,'/coordj']);
-% kr = h5read(filename,['/data/var5d/',variablename,'/coordkr']);
-% kz = h5read(filename,['/data/var5d/',variablename,'/coordkz']);
dt = h5readatt(filename,'/data/input','dt');
cstart= h5readatt(filename,'/data/input','start_iframe5d');
diff --git a/matlab/load_grid_data.m b/matlab/load_grid_data.m
new file mode 100644
index 0000000000000000000000000000000000000000..431815777c1b684f2cabe20512dfb3467eb40a3d
--- /dev/null
+++ b/matlab/load_grid_data.m
@@ -0,0 +1,9 @@
+function [ pe, je, pi, ji, kr, kz ] = load_grid_data( filename )
+%LOAD_GRID_DATA stored in a hdf5 result file from HeLaZ
+ pe = h5read(filename,'/data/grid/coordp_e');
+ je = h5read(filename,'/data/grid/coordj_e');
+ pi = h5read(filename,'/data/grid/coordp_i');
+ ji = h5read(filename,'/data/grid/coordj_i');
+ kr = h5read(filename,'/data/grid/coordkr');
+ kz = h5read(filename,'/data/grid/coordkz');
+end
\ No newline at end of file
diff --git a/matlab/load_params.m b/matlab/load_params.m
index 0e47f493d87e33f4fa216db843facb4fd8c4e61b..c176b707a958f90b19e47f1168f3be2ef426a3d0 100644
--- a/matlab/load_params.m
+++ b/matlab/load_params.m
@@ -13,6 +13,12 @@ NZ = h5readatt(filename,'/data/input','nz');
L = h5readatt(filename,'/data/input','Lr');
CLOS = h5readatt(filename,'/data/input','CLOS');
MU = str2num(filename(end-18:end-14));
+W_GAMMA = h5readatt(filename,'/data/input','write_gamma') == 'y';
+W_PHI = h5readatt(filename,'/data/input','write_phi') == 'y';
+W_NA00 = h5readatt(filename,'/data/input','write_Na00') == 'y';
+W_NAPJ = h5readatt(filename,'/data/input','write_Napj') == 'y';
+W_SAPJ = h5readatt(filename,'/data/input','write_Sapj') == 'y';
+
if NON_LIN == 'y'
NON_LIN = 1;
else
diff --git a/matlab/load_results.m b/matlab/load_results.m
index 1cb6be5de7e342181193f0dc03e3f53128a61dc2..fc41f9c4f13a013dc996d153051a3ca1d61c0dac 100644
--- a/matlab/load_results.m
+++ b/matlab/load_results.m
@@ -4,12 +4,30 @@ disp(['Loading ',filename])
% Loading from output file
CPUTIME = h5readatt(filename,'/data/input','cpu_time');
DT_SIM = h5readatt(filename,'/data/input','dt');
-[Nipj, Pi, Ji, kr, kz, Ts5D, dt5D] = load_5D_data(filename, 'moments_i');
-[Nepj, Pe, Je ] = load_5D_data(filename, 'moments_e');
-[Ni00, kr, kz, Ts2D, dt2D] = load_2D_data(filename, 'Ni00');
- Ne00 = load_2D_data(filename, 'Ne00');
-PHI = load_2D_data(filename, 'phi');
+[Pe, Je, Pi, Ji, kr, kz] = load_grid_data(filename);
-% Sipj = load_5D_data(filename, 'Sipj');
-% Sepj = load_5D_data(filename, 'Sepj');
+if W_GAMMA
+ [ GGAMMA_RI, Ts0D, dt0D] = load_0D_data(filename, 'gflux_ri');
+ PGAMMA_RI = load_0D_data(filename, 'pflux_ri');
+end
+
+if W_PHI
+ [ PHI, Ts2D, dt2D] = load_2D_data(filename, 'phi');
+end
+
+if W_NA00
+ [Ni00, Ts2D, dt2D] = load_2D_data(filename, 'Ni00');
+ Ne00 = load_2D_data(filename, 'Ne00');
+end
+
+
+if W_NAPJ
+ [Nipj, Ts5D, dt5D] = load_5D_data(filename, 'moments_i');
+ [Nepj ] = load_5D_data(filename, 'moments_e');
+end
+
+if W_SAPJ
+ [Sipj, Ts5D, dt5D] = load_5D_data(filename, 'Sipj');
+ Sepj = load_5D_data(filename, 'Sepj');
+end
diff --git a/matlab/setup.m b/matlab/setup.m
index 6f42c2b2fed67f53adf8ea9068bffc55151a54e8..a0da7b856f71d639f93a4e6076366aa5b7b052e4 100644
--- a/matlab/setup.m
+++ b/matlab/setup.m
@@ -97,10 +97,15 @@ OUTPUTS.nsave_1d = -1;
OUTPUTS.nsave_2d = floor(1.0/SPS2D/DT);
OUTPUTS.nsave_5d = floor(1.0/SPS5D/DT);
OUTPUTS.nsave_cp = floor(1.0/SPSCP/DT);
-OUTPUTS.write_doubleprecision = '.false.';
-OUTPUTS.resfile0 = '''outputs''';
-OUTPUTS.rstfile0 = '''checkpoint''';
-OUTPUTS.job2load = JOB2LOAD;
+if W_DOUBLE; OUTPUTS.write_doubleprecision = '.true.'; else; OUTPUTS.write_doubleprecision = '.false.';end;
+if W_GAMMA; OUTPUTS.write_gamma = '.true.'; else; OUTPUTS.write_gamma = '.false.';end;
+if W_PHI; OUTPUTS.write_phi = '.true.'; else; OUTPUTS.write_phi = '.false.';end;
+if W_NA00; OUTPUTS.write_Na00 = '.true.'; else; OUTPUTS.write_Na00 = '.false.';end;
+if W_NAPJ; OUTPUTS.write_Napj = '.true.'; else; OUTPUTS.write_Napj = '.false.';end;
+if W_SAPJ; OUTPUTS.write_Sapj = '.true.'; else; OUTPUTS.write_Sapj = '.false.';end;
+OUTPUTS.resfile0 = '''outputs''';
+OUTPUTS.rstfile0 = '''checkpoint''';
+OUTPUTS.job2load = JOB2LOAD;
%% Create directories
if ~exist(SIMDIR, 'dir')
mkdir(SIMDIR)
diff --git a/matlab/write_fort90.m b/matlab/write_fort90.m
index 1e2f98da2a8fb75ab77763c20f26970f1a45884b..b5045f92035cfeebf40536d0158cf99a11b5dfaf 100644
--- a/matlab/write_fort90.m
+++ b/matlab/write_fort90.m
@@ -30,6 +30,11 @@ fprintf(fid,[' nsave_2d = ', num2str(OUTPUTS.nsave_2d),'\n']);
fprintf(fid,[' nsave_5d = ', num2str(OUTPUTS.nsave_5d),'\n']);
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,[' resfile0 = ', OUTPUTS.resfile0,'\n']);
fprintf(fid,[' rstfile0 = ', OUTPUTS.rstfile0,'\n']);
fprintf(fid,[' job2load = ', num2str(OUTPUTS.job2load),'\n']);
diff --git a/src/basic_mod.F90 b/src/basic_mod.F90
index 15ca6353722e2d84501a5bfe7b305a0c226eeb74..ecfb4165852ec6a37b07f6561e28396160c4c89e 100644
--- a/src/basic_mod.F90
+++ b/src/basic_mod.F90
@@ -13,6 +13,7 @@ MODULE basic
INTEGER :: comm0 ! Default communicator with a topology
INTEGER :: commp, commr ! Communicators for 1-dim cartesian subgrids of comm0
+ INTEGER :: commr_p0 ! Communicators along kr for only rank 0 on p
INTEGER :: jobnum = 0 ! Job number
INTEGER :: step = 0 ! Calculation step of this run
@@ -24,11 +25,13 @@ MODULE basic
INTEGER :: ierr ! flag for MPI error
INTEGER :: my_id ! Rank in COMM_WORLD
INTEGER :: num_procs ! number of MPI processes
- INTEGER :: num_procs_p, num_procs_kr ! Number of processes in p and r
+ INTEGER :: num_procs_p ! Number of processes in p
+ INTEGER :: num_procs_kr ! Number of processes in r
INTEGER :: rank_0, rank_p, rank_r! Ranks in comm0, commp, commr
- INTEGER :: nbr_L, nbr_R ! Left and right neighbours (along p)
- INTEGER :: nbr_T, nbr_B ! Top and bottom neighbours (along kr)
+ INTEGER :: nbr_L, nbr_R ! Left and right neighbours (along p)
+ INTEGER :: nbr_T, nbr_B ! Top and bottom neighbours (along kr)
+ INTEGER :: iframe0d ! counting the number of times 0d datasets are outputed (for diagnose)
INTEGER :: iframe1d ! counting the number of times 1d datasets are outputed (for diagnose)
INTEGER :: iframe2d ! counting the number of times 2d datasets are outputed (for diagnose)
INTEGER :: iframe3d ! counting the number of times 3d datasets are outputed (for diagnose)
diff --git a/src/diagnose.F90 b/src/diagnose.F90
index f4d9a2802236afaf410c6c918d06e3e2b78cea98..40094b6d813c60689ae2e314e151d02301ee1ec8 100644
--- a/src/diagnose.F90
+++ b/src/diagnose.F90
@@ -17,7 +17,8 @@ SUBROUTINE diagnose(kstep)
INTEGER, INTENT(in) :: kstep
INTEGER, parameter :: BUFSIZE = 2
- INTEGER :: rank, dims(1) = (/0/)
+ INTEGER :: rank = 0
+ INTEGER :: dims(1) = (/0/)
INTEGER :: cp_counter = 0
CHARACTER(len=256) :: str, fname,test_
! putarr(...,pardim=1) does not work for 2D domain decomposition
@@ -44,18 +45,6 @@ SUBROUTINE diagnose(kstep)
! Data group
CALL creatg(fidres, "/data", "data")
- CALL creatg(fidres, "/data/var2d", "2d profiles")
- CALL creatg(fidres, "/data/var5d", "5d profiles")
-
- ! Initialize counter of number of saves for each category
- IF (cstep==0) THEN
- iframe2d=0
- ENDIF
- CALL attach(fidres,"/data/var2d/" , "frames", iframe2d)
- IF (cstep==0) THEN
- iframe5d=0
- END IF
- CALL attach(fidres,"/data/var5d/" , "frames", iframe5d)
! File group
CALL creatg(fidres, "/files", "files")
@@ -96,31 +85,71 @@ SUBROUTINE diagnose(kstep)
endif
ENDIF
- ! var2d group (electro. pot., Ni00 moment)
- rank = 0
- CALL creatd(fidres, rank, dims, "/data/var2d/time", "Time t*c_s/R")
- CALL creatd(fidres, rank, dims, "/data/var2d/cstep", "iteration number")
+ ! Grid info
CALL creatg(fidres, "/data/grid", "Grid data")
CALL putarr(fidres, "/data/grid/coordkr", krarray_full(1:nkr),"kr*rho_s0", ionode=0)
CALL putarr(fidres, "/data/grid/coordkz", kzarray_full(1:nkz),"kz*rho_s0", ionode=0)
- CALL putarr(fidres, "/data/grid/coordp" , parray_e_full(1:pmaxe+1), "p_e", ionode=0)
- CALL putarr(fidres, "/data/grid/coordj" , jarray_e_full(1:jmaxe+1), "j_e", ionode=0)
+ CALL putarr(fidres, "/data/grid/coordp_e" , parray_e_full(1:pmaxe+1), "p_e", ionode=0)
+ CALL putarr(fidres, "/data/grid/coordj_e" , jarray_e_full(1:jmaxe+1), "j_e", ionode=0)
+ CALL putarr(fidres, "/data/grid/coordp_i" , parray_i_full(1:pmaxe+1), "p_i", ionode=0)
+ CALL putarr(fidres, "/data/grid/coordj_i" , jarray_i_full(1:jmaxe+1), "j_i", ionode=0)
+
+ ! var0d group (gyro transport)
+ IF (nsave_0d .GT. 0) THEN
+ CALL creatg(fidres, "/data/var0d", "0d profiles")
+ CALL creatd(fidres, rank, dims, "/data/var0d/time", "Time t*c_s/R")
+ CALL creatd(fidres, rank, dims, "/data/var0d/cstep", "iteration number")
+
+ IF (write_gamma) THEN
+ CALL creatd(fidres, rank, dims, "/data/var0d/gflux_ri", "Radial gyro ion transport")
+ CALL creatd(fidres, rank, dims, "/data/var0d/pflux_ri", "Radial part ion transport")
+ ENDIF
+ IF (cstep==0) THEN
+ iframe0d=0
+ ENDIF
+ CALL attach(fidres,"/data/var0d/" , "frames", iframe0d)
+ END IF
+
+ ! var2d group (electro. pot., Ni00 moment)
IF (nsave_2d .GT. 0) THEN
+ CALL creatg(fidres, "/data/var2d", "2d profiles")
+ CALL creatd(fidres, rank, dims, "/data/var2d/time", "Time t*c_s/R")
+ CALL creatd(fidres, rank, dims, "/data/var2d/cstep", "iteration number")
+
+ IF (write_phi) CALL creatg(fidres, "/data/var2d/phi", "phi")
+
+ IF (write_Na00) THEN
CALL creatg(fidres, "/data/var2d/Ne00", "Ne00")
CALL creatg(fidres, "/data/var2d/Ni00", "Ni00")
- CALL creatg(fidres, "/data/var2d/phi", "phi")
+ ENDIF
+
+ IF (cstep==0) THEN
+ iframe2d=0
+ ENDIF
+ CALL attach(fidres,"/data/var2d/" , "frames", iframe2d)
END IF
! var5d group (moments)
- rank = 0
- CALL creatd(fidres, rank, dims, "/data/var5d/time", "Time t*c_s/R")
- CALL creatd(fidres, rank, dims, "/data/var5d/cstep", "iteration number")
IF (nsave_5d .GT. 0) THEN
- CALL creatg(fidres, "/data/var5d/moments_e", "moments_e")
- CALL creatg(fidres, "/data/var5d/moments_i", "moments_i")
- ! CALL creatg(fidres, "/data/var5d/Sepj", "Sepj")
- ! CALL creatg(fidres, "/data/var5d/Sipj", "Sipj")
+ CALL creatg(fidres, "/data/var5d", "5d profiles")
+ CALL creatd(fidres, rank, dims, "/data/var5d/time", "Time t*c_s/R")
+ CALL creatd(fidres, rank, dims, "/data/var5d/cstep", "iteration number")
+
+ IF (write_Napj) THEN
+ CALL creatg(fidres, "/data/var5d/moments_e", "moments_e")
+ CALL creatg(fidres, "/data/var5d/moments_i", "moments_i")
+ ENDIF
+
+ IF (write_Sapj) THEN
+ CALL creatg(fidres, "/data/var5d/moments_e", "Sipj")
+ CALL creatg(fidres, "/data/var5d/moments_i", "Sepj")
+ ENDIF
+
+ IF (cstep==0) THEN
+ iframe5d=0
+ END IF
+ CALL attach(fidres,"/data/var5d/" , "frames", iframe5d)
END IF
! Add input namelist variables as attributes of /data/input, defined in srcinfo.h
@@ -130,8 +159,6 @@ SUBROUTINE diagnose(kstep)
IF (my_id .EQ. 0) WRITE(*,*) 'HOST=', HOST
WRITE(str,'(a,i2.2)') "/data/input"
-
- rank=0
CALL creatd(fidres, rank,dims,TRIM(str),'Input parameters')
CALL attach(fidres, TRIM(str), "version", VERSION) !defined in srcinfo.h
CALL attach(fidres, TRIM(str), "branch", BRANCH) !defined in srcinfo.h
@@ -140,6 +167,7 @@ SUBROUTINE diagnose(kstep)
CALL attach(fidres, TRIM(str), "host", HOST) !defined in srcinfo.h
CALL attach(fidres, TRIM(str), "start_time", time)
CALL attach(fidres, TRIM(str), "start_cstep", cstep-1)
+ CALL attach(fidres, TRIM(str), "start_iframe0d", iframe0d)
CALL attach(fidres, TRIM(str), "start_iframe2d", iframe2d)
CALL attach(fidres, TRIM(str), "start_iframe5d", iframe5d)
CALL attach(fidres, TRIM(str), "dt", dt)
@@ -149,6 +177,11 @@ SUBROUTINE diagnose(kstep)
CALL attach(fidres, TRIM(str), "Nproc", num_procs)
CALL attach(fidres, TRIM(str), "Np_p" , num_procs_p)
CALL attach(fidres, TRIM(str), "Np_kr",num_procs_kr)
+ CALL attach(fidres, TRIM(str), "write_gamma",write_gamma)
+ CALL attach(fidres, TRIM(str), "write_phi",write_phi)
+ CALL attach(fidres, TRIM(str), "write_Na00",write_Na00)
+ CALL attach(fidres, TRIM(str), "write_Napj",write_Napj)
+ CALL attach(fidres, TRIM(str), "write_Sapj",write_Sapj)
CALL grid_outputinputs(fidres, str)
@@ -242,12 +275,13 @@ END SUBROUTINE diagnose
SUBROUTINE diagnose_0d
USE basic
- USE futils, ONLY: append
+ USE futils, ONLY: append, attach, getatt
USE diagnostics_par
USE prec_const
+ USE processing
IMPLICIT NONE
-
+ ! Time measurement data
CALL append(fidres, "/profiler/Tc_rhs", tc_rhs,ionode=0)
CALL append(fidres, "/profiler/Tc_adv_field", tc_adv_field,ionode=0)
CALL append(fidres, "/profiler/Tc_poisson", tc_poisson,ionode=0)
@@ -257,6 +291,18 @@ SUBROUTINE diagnose_0d
CALL append(fidres, "/profiler/Tc_comm", tc_comm,ionode=0)
CALL append(fidres, "/profiler/Tc_step", tc_step,ionode=0)
CALL append(fidres, "/profiler/time", time,ionode=0)
+ ! Processing data
+ CALL append(fidres, "/data/var0d/time", time,ionode=0)
+ CALL append(fidres, "/data/var0d/cstep", real(cstep,dp),ionode=0)
+ CALL getatt(fidres, "/data/var0d/", "frames",iframe2d)
+ iframe0d=iframe0d+1
+ CALL attach(fidres,"/data/var0d/" , "frames", iframe0d)
+ ! Ion transport data
+ IF (write_gamma) THEN
+ CALL compute_radial_ion_transport
+ CALL append(fidres, "/data/var0d/gflux_ri",gflux_ri,ionode=0)
+ CALL append(fidres, "/data/var0d/pflux_ri",pflux_ri,ionode=0)
+ ENDIF
END SUBROUTINE diagnose_0d
@@ -282,78 +328,79 @@ SUBROUTINE diagnose_2d
iframe2d=iframe2d+1
CALL attach(fidres,"/data/var2d/" , "frames", iframe2d)
- CALL write_field2d(phi (:,:), 'phi')
+ IF (write_phi) CALL write_field2d(phi (:,:), 'phi')
- IF ( (ips_e .EQ. 1) .AND. (ips_i .EQ. 1) ) THEN
- Ne00(ikrs:ikre,ikzs:ikze) = moments_e(ips_e,1,ikrs:ikre,ikzs:ikze,updatetlevel)
- Ni00(ikrs:ikre,ikzs:ikze) = moments_i(ips_e,1,ikrs:ikre,ikzs:ikze,updatetlevel)
- ENDIF
-
- root = 0
-
- !!!!! This is a manual way to do MPI_BCAST !!!!!!!!!!!
- CALL MPI_COMM_RANK(commp,world_rank,ierr)
- CALL MPI_COMM_SIZE(commp,world_size,ierr)
+ IF (write_Na00) THEN
+ IF ( (ips_e .EQ. 1) .AND. (ips_i .EQ. 1) ) THEN
+ Ne00(ikrs:ikre,ikzs:ikze) = moments_e(ips_e,1,ikrs:ikre,ikzs:ikze,updatetlevel)
+ Ni00(ikrs:ikre,ikzs:ikze) = moments_i(ips_e,1,ikrs:ikre,ikzs:ikze,updatetlevel)
+ ENDIF
- IF (world_size .GT. 1) THEN
- !! Broadcast phi to the other processes on the same k range (communicator along p)
- IF (world_rank .EQ. root) THEN
- ! Fill the buffer
- DO ikr = ikrs,ikre
- DO ikz = ikzs,ikze
- buffer(ikr,ikz) = Ne00(ikr,ikz)
+ root = 0
+ !!!!! This is a manual way to do MPI_BCAST !!!!!!!!!!!
+ CALL MPI_COMM_RANK(commp,world_rank,ierr)
+ CALL MPI_COMM_SIZE(commp,world_size,ierr)
+
+ IF (world_size .GT. 1) THEN
+ !! Broadcast phi to the other processes on the same k range (communicator along p)
+ IF (world_rank .EQ. root) THEN
+ ! Fill the buffer
+ DO ikr = ikrs,ikre
+ DO ikz = ikzs,ikze
+ buffer(ikr,ikz) = Ne00(ikr,ikz)
+ ENDDO
ENDDO
- ENDDO
- ! Send it to all the other processes
- DO i_ = 0,num_procs_p-1
- IF (i_ .NE. world_rank) &
- CALL MPI_SEND(buffer, local_nkr * nkz , MPI_DOUBLE_COMPLEX, i_, 0, commp, ierr)
- ENDDO
- ELSE
- ! Recieve buffer from root
- CALL MPI_RECV(buffer, local_nkr * nkz , MPI_DOUBLE_COMPLEX, root, 0, commp, MPI_STATUS_IGNORE, ierr)
- ! Write it in phi
- DO ikr = ikrs,ikre
- DO ikz = ikzs,ikze
- Ne00(ikr,ikz) = buffer(ikr,ikz)
+ ! Send it to all the other processes
+ DO i_ = 0,num_procs_p-1
+ IF (i_ .NE. world_rank) &
+ CALL MPI_SEND(buffer, local_nkr * nkz , MPI_DOUBLE_COMPLEX, i_, 0, commp, ierr)
+ ENDDO
+ ELSE
+ ! Recieve buffer from root
+ CALL MPI_RECV(buffer, local_nkr * nkz , MPI_DOUBLE_COMPLEX, root, 0, commp, MPI_STATUS_IGNORE, ierr)
+ ! Write it in phi
+ DO ikr = ikrs,ikre
+ DO ikz = ikzs,ikze
+ Ne00(ikr,ikz) = buffer(ikr,ikz)
+ ENDDO
ENDDO
- ENDDO
+ ENDIF
ENDIF
- ENDIF
- CALL write_field2d(Ne00(ikrs:ikre,ikzs:ikze), 'Ne00')
+ CALL write_field2d(Ne00(ikrs:ikre,ikzs:ikze), 'Ne00')
- !!!!! This is a manual way to do MPI_BCAST !!!!!!!!!!!
- CALL MPI_COMM_RANK(commp,world_rank,ierr)
- CALL MPI_COMM_SIZE(commp,world_size,ierr)
-
- IF (world_size .GT. 1) THEN
- !! Broadcast phi to the other processes on the same k range (communicator along p)
- IF (world_rank .EQ. root) THEN
- ! Fill the buffer
- DO ikr = ikrs,ikre
- DO ikz = ikzs,ikze
- buffer(ikr,ikz) = Ni00(ikr,ikz)
+ !!!!! This is a manual way to do MPI_BCAST !!!!!!!!!!!
+ CALL MPI_COMM_RANK(commp,world_rank,ierr)
+ CALL MPI_COMM_SIZE(commp,world_size,ierr)
+
+ IF (world_size .GT. 1) THEN
+ !! Broadcast phi to the other processes on the same k range (communicator along p)
+ IF (world_rank .EQ. root) THEN
+ ! Fill the buffer
+ DO ikr = ikrs,ikre
+ DO ikz = ikzs,ikze
+ buffer(ikr,ikz) = Ni00(ikr,ikz)
+ ENDDO
ENDDO
- ENDDO
- ! Send it to all the other processes
- DO i_ = 0,num_procs_p-1
- IF (i_ .NE. world_rank) &
- CALL MPI_SEND(buffer, local_nkr * nkz , MPI_DOUBLE_COMPLEX, i_, 0, commp, ierr)
- ENDDO
- ELSE
- ! Recieve buffer from root
- CALL MPI_RECV(buffer, local_nkr * nkz , MPI_DOUBLE_COMPLEX, root, 0, commp, MPI_STATUS_IGNORE, ierr)
- ! Write it in phi
- DO ikr = ikrs,ikre
- DO ikz = ikzs,ikze
- Ni00(ikr,ikz) = buffer(ikr,ikz)
+ ! Send it to all the other processes
+ DO i_ = 0,num_procs_p-1
+ IF (i_ .NE. world_rank) &
+ CALL MPI_SEND(buffer, local_nkr * nkz , MPI_DOUBLE_COMPLEX, i_, 0, commp, ierr)
+ ENDDO
+ ELSE
+ ! Recieve buffer from root
+ CALL MPI_RECV(buffer, local_nkr * nkz , MPI_DOUBLE_COMPLEX, root, 0, commp, MPI_STATUS_IGNORE, ierr)
+ ! Write it in phi
+ DO ikr = ikrs,ikre
+ DO ikz = ikzs,ikze
+ Ni00(ikr,ikz) = buffer(ikr,ikz)
+ ENDDO
ENDDO
- ENDDO
+ ENDIF
ENDIF
- ENDIF
- CALL write_field2d(Ni00(ikrs:ikre,ikzs:ikze), 'Ni00')
+ CALL write_field2d(Ni00(ikrs:ikre,ikzs:ikze), 'Ni00')
+ ENDIF
CONTAINS
@@ -405,11 +452,15 @@ SUBROUTINE diagnose_5d
iframe5d=iframe5d+1
CALL attach(fidres,"/data/var5d/" , "frames", iframe5d)
- CALL write_field5d_e(moments_e(ips_e:ipe_e,ijs_e:ije_e,:,:,updatetlevel), 'moments_e')
- CALL write_field5d_i(moments_i(ips_i:ipe_i,ijs_i:ije_i,:,:,updatetlevel), 'moments_i')
+ IF (write_Napj) THEN
+ CALL write_field5d_e(moments_e(ips_e:ipe_e,ijs_e:ije_e,:,:,updatetlevel), 'moments_e')
+ CALL write_field5d_i(moments_i(ips_i:ipe_i,ijs_i:ije_i,:,:,updatetlevel), 'moments_i')
+ ENDIF
- ! CALL write_field5d_e(Sepj(ips_e:ipe_e,ijs_e:ije_e,:,:), 'Sepj')
- ! CALL write_field5d_i(Sipj(ips_i:ipe_i,ijs_i:ije_i,:,:), 'Sipj')
+ IF (write_Sapj) THEN
+ CALL write_field5d_e(Sepj(ips_e:ipe_e,ijs_e:ije_e,:,:), 'Sepj')
+ CALL write_field5d_i(Sipj(ips_i:ipe_i,ijs_i:ije_i,:,:), 'Sipj')
+ ENDIF
CONTAINS
diff --git a/src/diagnostics_par_mod.F90 b/src/diagnostics_par_mod.F90
index a0fb7a60afa14084d1aa0dd480b9e8fe9c1e44d4..0f743896ec319531b828ae241127f4b5cd69187b 100644
--- a/src/diagnostics_par_mod.F90
+++ b/src/diagnostics_par_mod.F90
@@ -5,7 +5,10 @@ MODULE diagnostics_par
IMPLICIT NONE
PRIVATE
- LOGICAL, PUBLIC, PROTECTED :: write_doubleprecision=.FALSE.
+ LOGICAL, PUBLIC, PROTECTED :: write_doubleprecision = .FALSE.
+ LOGICAL, PUBLIC, PROTECTED :: write_gamma
+ LOGICAL, PUBLIC, PROTECTED :: write_phi, write_Na00
+ LOGICAL, PUBLIC, PROTECTED :: write_Napj, write_Sapj
INTEGER, PUBLIC, PROTECTED :: nsave_0d , nsave_1d , nsave_2d , nsave_5d, nsave_cp
@@ -31,7 +34,8 @@ CONTAINS
IMPLICIT NONE
NAMELIST /OUTPUT_PAR/ nsave_0d , nsave_1d , nsave_2d , nsave_5d, nsave_cp
- NAMELIST /OUTPUT_PAR/ write_doubleprecision
+ NAMELIST /OUTPUT_PAR/ write_doubleprecision, write_gamma, write_phi
+ NAMELIST /OUTPUT_PAR/ write_Na00, write_Napj, write_Sapj
NAMELIST /OUTPUT_PAR/ resfile0, rstfile0, job2load
READ(lu_in,output_par)
diff --git a/src/processing_mod.F90 b/src/processing_mod.F90
new file mode 100644
index 0000000000000000000000000000000000000000..a99c56719b222c9bbffc722c125a5577facd9d33
--- /dev/null
+++ b/src/processing_mod.F90
@@ -0,0 +1,65 @@
+MODULE processing
+ ! contains the Hermite-Laguerre collision operators. Solved using COSOlver.
+ USE basic
+ USE prec_const
+ USE grid
+ implicit none
+
+ REAL(dp), PUBLIC, PROTECTED :: pflux_ri, gflux_ri
+
+ PUBLIC :: compute_radial_ion_transport
+
+CONTAINS
+
+SUBROUTINE compute_radial_ion_transport
+ USE fields, ONLY : moments_i, phi
+ USE array, ONLY : kernel_i
+ USE time_integration, ONLY : updatetlevel
+ IMPLICIT NONE
+ COMPLEX(dp) :: pflux_local, gflux_local
+ REAL(dp) :: kz_, buffer(1:2)
+ INTEGER :: i_, world_rank, world_size, root
+
+ pflux_local = 0._dp
+ gflux_local = 0._dp
+ IF(ips_i .EQ. 1) THEN
+ ! Loop to compute gamma_kr = sum_kz sum_j -i k_z Kernel_j Ni00 * phi
+ DO ikz = ikzs,ikze
+ kz_ = kzarray(ikz)
+ DO ikr = ikrs,ikre
+ gflux_local = gflux_local - &
+ imagu * kz_ * moments_i(1,1,ikr,ikz,updatetlevel) * CONJG(phi(ikr,ikz))
+ DO ij = ijs_i, ije_i
+ pflux_local = pflux_local - &
+ imagu * kz_ * kernel_i(ij,ikr,ikz) * moments_i(1,ij,ikr,ikz,updatetlevel) * CONJG(phi(ikr,ikz))
+ ENDDO
+ ENDDO
+ ENDDO
+
+ buffer(1) = REAL(gflux_local)
+ buffer(2) = REAL(pflux_local)
+
+ root = 0
+ !Gather manually among the rank_p=0 processes and perform the sum
+ gflux_ri = 0
+ pflux_ri = 0
+ IF (num_procs_kr .GT. 1) THEN
+ !! Everyone sends its local_sum to root = 0
+ IF (rank_r .NE. root) THEN
+ CALL MPI_SEND(buffer, 2 , MPI_DOUBLE_PRECISION, root, 1234, commr, ierr)
+ ELSE
+ ! Recieve from all the other processes
+ DO i_ = 0,num_procs_kr-1
+ IF (i_ .NE. rank_r) &
+ CALL MPI_RECV(buffer, 2 , MPI_DOUBLE_PRECISION, i_, 1234, commr, MPI_STATUS_IGNORE, ierr)
+ gflux_ri = gflux_ri + buffer(1)
+ pflux_ri = pflux_ri + buffer(2)
+ ENDDO
+ ENDIF
+ ENDIF
+ ENDIF
+
+
+END SUBROUTINE compute_radial_ion_transport
+
+END MODULE processing
\ No newline at end of file
diff --git a/wk/analysis_2D.m b/wk/analysis_2D.m
index a9b122602be791eb2ec67710b7e80174fa8bf692..bd544c9959a2d23a0708e33dacb398ead31f7795 100644
--- a/wk/analysis_2D.m
+++ b/wk/analysis_2D.m
@@ -104,7 +104,7 @@ PFlux_ri = zeros(1,Ns5D); % Particle flux
GFLUX_RI = real(squeeze(sum(sum(-1i*KZ.*Ni00.*conj(PHI),1),2)))*(2*pi/Nr/Nz)^2;
PFLUX_RI = real(squeeze(sum(sum(-1i*KZ.*Np_i.*conj(PHI_Ts5D),1),2)))*(2*pi/Nr/Nz)^2;
-phi_avg = zeros(1,Ns2D); % Time evol. of the norm of phi
+phi_max = zeros(1,Ns2D); % Time evol. of the norm of phi
Ne_norm = zeros(Npe,Nje,Ns5D); % Time evol. of the norm of Napj
Ni_norm = zeros(Npi,Nji,Ns5D); % .
@@ -112,7 +112,7 @@ Ddr = 1i*KR; Ddz = 1i*KZ; lapl = Ddr.^2 + Ddz.^2;
for it = 1:numel(Ts2D) % Loop over 2D arrays
NE_ = Ne00(:,:,it); NI_ = Ni00(:,:,it); PH_ = PHI(:,:,it);
- phi_avg(it) = real(squeeze(PH_(ikr0,ikz0)))/2;
+ phi_max(it) = max(max(squeeze(phi(:,:,it))));
ExB(it) = max(max(max(abs(phi(3:end,:,it)-phi(1:end-2,:,it))/(2*dr))),max(max(abs(phi(:,3:end,it)-phi(:,1:end-2,it))'/(2*dz))));
GFlux_ri(it) = sum(sum(ni00(:,:,it).*dzphi(:,:,it)))*dr*dz/Lr/Lz;
GFlux_zi(it) = sum(sum(-ni00(:,:,it).*drphi(:,:,it)))*dr*dz/Lr/Lz;
@@ -151,7 +151,7 @@ if 1
%% Time evolutions and growth rate
fig = figure; FIGNAME = ['t_evolutions',sprintf('_%.2d',JOBNUM),'_',PARAMS];
set(gcf, 'Position', [100, 100, 900, 800])
- subplot(221);
+ subplot(421);
for ip = 1:Npe
for ij = 1:Nje
plt = @(x) squeeze(x(ip,ij,:));
@@ -163,7 +163,7 @@ set(gcf, 'Position', [100, 100, 900, 800])
end
end
grid on; ylabel('$\sum_{k_r,k_z}|N_e^{pj}|$');
- subplot(222)
+ subplot(423)
for ip = 1:Npi
for ij = 1:Nji
plt = @(x) squeeze(x(ip,ij,:));
@@ -174,7 +174,14 @@ set(gcf, 'Position', [100, 100, 900, 800])
'Color',clr,'LineStyle',lstyle{1}); hold on;
end
end
- grid on; ylabel('$\sum_{k_r,k_z}|N_i^{pj}|$');
+ grid on; ylabel('$\sum_{k_r,k_z}|N_i^{pj}|$'); xlabel('$t c_s/R$')
+ subplot(222)
+ semilogy(Ts0D,GGAMMA_RI*(2*pi/Nr/Nz)^2); hold on;
+% plot(Ts2D,GFLUX_RI)
+ plot(Ts0D,PGAMMA_RI*(2*pi/Nr/Nz)^2);
+% plot(Ts5D,PFLUX_RI,'--');
+ legend(['Gyro. flux';'Part. flux']);
+ grid on; xlabel('$t c_s/R$'); ylabel('$\Gamma_{r,i}$')
subplot(223)
plot(kz,g_(1,:),'-','DisplayName','$\gamma$'); hold on;
grid on; xlabel('$k_z\rho_s$'); ylabel('$\gamma R/c_s$'); %legend('show');
@@ -185,11 +192,11 @@ set(gcf, 'Position', [100, 100, 900, 800])
plotname = '$\langle\phi\rangle_{r,z}(t)$';
clr = line_colors(min(ip,numel(line_colors(:,1))),:);
lstyle = line_styles(min(ij,numel(line_styles)));
- plot(Ts2D,phi_avg,'DisplayName',plotname,...
+ plot(Ts2D,phi_max,'DisplayName',plotname,...
'Color',clr,'LineStyle',lstyle{1}); hold on;
end
end
- grid on; xlabel('$t c_s/R$'); ylabel('$\tilde\phi_{00}/2$'); %legend('show');
+ grid on; xlabel('$t c_s/R$'); ylabel('$\max_{r,z}(\phi)$'); %legend('show');
% suptitle(['$\nu_{',CONAME,'}=$', num2str(NU), ', $\eta_B=$',num2str(ETAB)]);
save_figure
end
diff --git a/wk/local_run.m b/wk/local_run.m
index dfe9ccea17e3d27ad348abbf003d771ff9339be5..9d897ea7e55bb261a8cf79dcd5ce8044759e3c9e 100644
--- a/wk/local_run.m
+++ b/wk/local_run.m
@@ -18,13 +18,13 @@ JMAXI = 1; % Highest '' Laguerre ''
%% TIME PARAMETERS
TMAX = 100; % Maximal time unit
DT = 2e-2; % Time step
-SPS0D = 1/DT; % Sampling per time unit for profiler
+SPS0D = 1; % Sampling per time unit for profiler
SPS2D = 1/2; % Sampling per time unit for 2D arrays
SPS5D = 1/4; % Sampling per time unit for 5D arrays
SPSCP = 0; % Sampling per time unit for checkpoints/10
RESTART = 0; % To restart from last checkpoint
JOB2LOAD= 0;
-%% OPTIONS
+%% OPTIONS AND NAMING
% SIMID = ['local_eta_',num2str(ETAB),'_nu_%0.0e']; % Name of the simulation
% SIMID = sprintf(SIMID,NU);
% SIMID = 'test_init_phi'; % Name of the simulation
@@ -33,6 +33,13 @@ CO = -3; % Collision operator (0 : L.Bernstein, -1 : Full Coulomb, -2 : Do
CLOS = 0; % Closure model (0: =0 truncation, 1: semi coll, 2: Copy closure J+1 = J, P+2 = P)
KERN = 0; % Kernel model (0 : GK)
INIT_PHI= 1; % Start simulation with a noisy phi and moments
+%% OUTPUTS
+W_DOUBLE = 0;
+W_GAMMA = 1;
+W_PHI = 1;
+W_NA00 = 1;
+W_NAPJ = 1;
+W_SAPJ = 0;
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% unused
diff --git a/wk/marconi_run.m b/wk/marconi_run.m
index 92e35314a4783a068a9be1494fd9193a0f663cab..48bab70fcd2d9c2a6a35147a3e86f3f2d46f843a 100644
--- a/wk/marconi_run.m
+++ b/wk/marconi_run.m
@@ -16,29 +16,36 @@ NU = 0.1; % Collision frequency
ETAB = 0.6; % Magnetic gradient
NU_HYP = 0.1; % Hyperdiffusivity coefficient
%% GRID PARAMETERS
-N = 050; % Frequency gridpoints (Nkr = N/2)
-L = 100; % Size of the squared frequency domain
-P = 10; % Electron and Ion highest Hermite polynomial degree
-J = 01; % Electron and Ion highest Laguerre polynomial degree
+N = 200; % Frequency gridpoints (Nkr = N/2)
+L = 120; % Size of the squared frequency domain
+P = 20; % Electron and Ion highest Hermite polynomial degree
+J = 08; % Electron and Ion highest Laguerre polynomial degree
MU_P = 0; % Hermite hyperdiffusivity -mu_p*(d/dvpar)^4 f
MU_J = 0; % Laguerre hyperdiffusivity -mu_j*(d/dvperp)^4 f
%% TIME PARAMETERS
-TMAX = 50; % Maximal time unit
-DT = 2e-2; % Time step
+TMAX = 200; % Maximal time unit
+DT = 1e-2; % Time step
SPS0D = 1; % Sampling per time unit for profiler
-SPS2D = 1/2; % Sampling per time unit for 2D arrays
-SPS5D = 1/10; % Sampling per time unit for 5D arrays
+SPS2D = 1/10; % Sampling per time unit for 2D arrays
+SPS5D = 0/50; % Sampling per time unit for 5D arrays
SPSCP = 0; % Sampling per time unit for checkpoints
RESTART = 0; % To restart from last checkpoint
JOB2LOAD= 0;
%% OPTIONS
-SIMID = ['HeLaZ_v2.4_2_12_eta_',num2str(ETAB),'_nu_%0.0e']; % Name of the simulation
+SIMID = ['HeLaZ_v2.4_eta_',num2str(ETAB),'_nu_%0.0e']; % Name of the simulation
% SIMID = 'Marconi_test'; % Name of the simulation
SIMID = sprintf(SIMID,NU);
CO = -3; % Collision operator (0 : L.Bernstein, -1 : Full Coulomb, -2 : Dougherty, -3 : GK Dougherty)
CLOS = 0; % Closure model (0: =0 truncation, 1: semi coll, 2: Copy closure J+1 = J, P+2 = P)
KERN = 0; % Kernel model (0 : GK)
INIT_PHI= 1; % Start simulation with a noisy phi and moments
+%% OUTPUTS
+W_DOUBLE = 0;
+W_GAMMA = 0;
+W_PHI = 1;
+W_NA00 = 1;
+W_NAPJ = 0;
+W_SAPJ = 0;
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%% fixed parameters (for current study)