diff --git a/matlab/compile_results.m b/matlab/compile_results.m
index 50d383b3ada49c5ca740ea87839482e16f7da3a4..d0892abf007d12b5b936b7c68d74e1a9883e286f 100644
--- a/matlab/compile_results.m
+++ b/matlab/compile_results.m
@@ -71,18 +71,18 @@ while(CONTINUE)
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;
+ 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;
+% 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;
+ 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;
+% Sepj_ = zeros(cat(1,[Pe_new,Je_new]',sz(3:end)')');
+% Sepj_(1:Pe_old,1:Je_old,:,:,:,:) = tmp;
end
% If a degree is smaller than previous job, put zero to add. deg.
elseif (sum([Pe_new, Je_new, Pi_new, Ji_new]<[Pe_old, Je_old, Pi_old, Ji_old]) >= 1 && Pe_old ~= 1e9)
@@ -258,7 +258,7 @@ DATA.ikx0 = ikx0; DATA.iky0 = iky0;
DATA.Nx = Nx; DATA.Ny = Ny; DATA.Nz = Nz; DATA.Nkx = Nkx; DATA.Nky = Nky;
DATA.Pmaxe = numel(Pe); DATA.Pmaxi = numel(Pi); DATA.Jmaxe = numel(Je); DATA.Jmaxi = numel(Ji);
DATA.dir = DIRECTORY;
-DATA.localdir = ['..',DIRECTORY(20:end)];
+DATA.localdir = DIRECTORY;
DATA.param_title=['$\nu_{',DATA.CONAME,'}=$', num2str(DATA.NU), ...
', $\kappa_N=$',num2str(DATA.K_N),', $L=',num2str(DATA.L),'$, $N=',...
num2str(DATA.Nx),'$, $(P,J)=(',num2str(DATA.PMAXI),',',...
diff --git a/matlab/compute/compute_fa.m b/matlab/compute/compute_fa.m
index 3d8e4ec4ca83834a6d624f42738216601da4e375..a580a2ee399ff6db9b8102c58fe05b54d6aa2356 100644
--- a/matlab/compute/compute_fa.m
+++ b/matlab/compute/compute_fa.m
@@ -46,7 +46,7 @@ Napj_ = squeeze(Napj_);
Np = numel(parray); Nj = numel(jarray);
-FF = zeros(data.Nkx,data.Nky,numel(options.XPERP),numel(options.SPAR));
+FF = zeros(data.Nky,data.Nkx,numel(options.XPERP),numel(options.SPAR));
% FF = zeros(numel(options.XPERP),numel(options.SPAR));
FAM = FaM(SS,XX);
@@ -60,14 +60,14 @@ for ip_ = 1:Np
HLF = HH.*LL.*FAM;
for ikx = 1:data.Nkx
for iky = 1:data.Nky
- FF(ikx,iky,:,:) = squeeze(FF(ikx,iky,:,:)) + Napj_(ip_,ij_,ikx,iky)*HLF;
+ FF(iky,ikx,:,:) = squeeze(FF(iky,ikx,:,:)) + Napj_(ip_,ij_,iky,ikx)*HLF;
end
end
end
end
-% FF = (FF.*conj(FF)); %|f_a|^2
-FF = abs(FF); %|f_a|
-FF = sqrt(squeeze(mean(mean(FF,1),2))); %sqrt(<|f_a|>kx,ky)
+FF = (FF.*conj(FF)); %|f_a|^2
+% FF = abs(FF); %|f_a|
+FF = sqrt(squeeze(mean(mean(FF,1),2))); %sqrt(<|f_a|^2>kx,ky)
FF = FF./max(max(FF));
FF = FF';
% FF = FF.*conj(FF);
diff --git a/matlab/plot/show_napjz.m b/matlab/plot/show_napjz.m
index e521b944b0960889679dd4e2214dfdac3a5fed87..002bc2ebde2314c0e69fee32f3584794ca45a063 100644
--- a/matlab/plot/show_napjz.m
+++ b/matlab/plot/show_napjz.m
@@ -56,15 +56,7 @@ switch OPTIONS.PLOT_TYPE
imagesc(DATA.Ts5D,p2ja,plt(Na_ST,1:numel(p2ja)));
set(gca,'YDir','normal')
xlabel('$t$'); ylabel('$p+2j$')
- title('$\langle\sum_k |',name,'|\rangle_{p+2j=const}$')
- if DATA.K_E
- subplot(2,1,2)
- imagesc(DATA.Ts5D,p2je,plt(Ne_ST,1:numel(p2ja)));
- set(gca,'YDir','normal')
- xlabel('$t$'); ylabel('$p+2j$')
- title('$\langle\sum_k |N_e^{pj}|\rangle_{p+2j=const}$')
- suptitle(DATA.param_title);
- end
+ title(['$\langle\sum_k |',name,'|^2\rangle_{p+2j=const}$'])
case 'Tavg-1D'
t0 = OPTIONS.TIME(1);
diff --git a/matlab/process_field.m b/matlab/process_field.m
index 570965360baa1c650211d290de07a1147ca5314f..201d0a49725f55652ce61b43896c42e71daa6625 100644
--- a/matlab/process_field.m
+++ b/matlab/process_field.m
@@ -43,6 +43,10 @@ switch OPTIONS.PLAN
XNAME = '$v_\parallel$'; YNAME = '$\mu$';
[Y,X] = meshgrid(OPTIONS.XPERP,OPTIONS.SPAR);
REALP = 1; COMPDIM = 3; POLARPLOT = 0; SCALE = 0;
+ for i = 1:numel(OPTIONS.TIME)
+ [~,FRAMES(i)] =min(abs(OPTIONS.TIME(i)-DATA.Ts5D));
+ end
+ FRAMES = unique(FRAMES);
end
Xmax_ = max(max(abs(X))); Ymax_ = max(max(abs(Y)));
Lmin_ = min([Xmax_,Ymax_]);
@@ -440,13 +444,9 @@ switch OPTIONS.NAME
case 'f_i'
shift_x = @(x) x; shift_y = @(y) y;
NAME = 'fi'; OPTIONS.SPECIE = 'i';
- [~,it0_] =min(abs(OPTIONS.TIME(1)-DATA.Ts5D));
- [~,it1_]=min(abs(OPTIONS.TIME(end)-DATA.Ts5D));
- dit_ = 1;%ceil((it1_-it0_+1)/10);
- FRAMES = it0_:dit_:it1_;
- iz = 1;
- for it = 1:numel(FRAMES)
- OPTIONS.T = DATA.Ts5D(FRAMES(it));
+ for it = 1:numel(OPTIONS.TIME)
+ [~,it0_] =min(abs(OPTIONS.TIME(it)-DATA.Ts5D));
+ OPTIONS.T = DATA.Ts5D(it0_);
[~,~,FIELD(:,:,it)] = compute_fa(DATA,OPTIONS);
end
case 'f_e'
diff --git a/src/basic_mod.F90 b/src/basic_mod.F90
index ab7869f8b8e94743acf5b8d46ec0122f7c2acdca..f1d67f07028219981f609f23d3cd5ccd8b529d07 100644
--- a/src/basic_mod.F90
+++ b/src/basic_mod.F90
@@ -16,7 +16,8 @@ MODULE basic
! Communicators for 1-dim cartesian subgrids of comm0
INTEGER :: comm_p, comm_ky, comm_z
INTEGER :: rank_p, rank_ky, rank_z! Ranks
- INTEGER :: commr_p0 ! Communicators along kx for only rank 0 on p
+ INTEGER :: comm_pz, rank_pz ! 2D comm for N_a(p,j,z) output (mspfile)
+ INTEGER :: comm_kyz, rank_kyz ! 2D comm for N_a(p,j,z) output (mspfile)
INTEGER :: jobnum = 0 ! Job number
INTEGER :: step = 0 ! Calculation step of this run
@@ -80,6 +81,32 @@ CONTAINS
tc_Sapj = 0.; tc_diag = 0.; tc_checkfield = 0.
END SUBROUTINE basic_data
+
+
+ SUBROUTINE basic_outputinputs(fid, str)
+ !
+ ! Write the input parameters to the results_xx.h5 file
+ !
+ USE prec_const
+ USE futils, ONLY: attach
+ IMPLICIT NONE
+ INTEGER, INTENT(in) :: fid
+ CHARACTER(len=256), INTENT(in) :: str
+ CALL attach(fid, TRIM(str), "start_iframe0d", iframe0d)
+ CALL attach(fid, TRIM(str), "start_iframe2d", iframe2d)
+ CALL attach(fid, TRIM(str), "start_iframe3d", iframe3d)
+ CALL attach(fid, TRIM(str), "start_iframe5d", iframe5d)
+ CALL attach(fid, TRIM(str), "start_time", time)
+ CALL attach(fid, TRIM(str), "start_cstep", cstep-1)
+ CALL attach(fid, TRIM(str), "dt", dt)
+ CALL attach(fid, TRIM(str), "tmax", tmax)
+ CALL attach(fid, TRIM(str), "nrun", nrun)
+ CALL attach(fid, TRIM(str), "cpu_time", -1)
+ CALL attach(fid, TRIM(str), "Nproc", num_procs)
+ CALL attach(fid, TRIM(str), "Np_p" , num_procs_p)
+ CALL attach(fid, TRIM(str), "Np_kx",num_procs_ky)
+ CALL attach(fid, TRIM(str), "Np_z", num_procs_z)
+ END SUBROUTINE basic_outputinputs
!================================================================================
SUBROUTINE find_input_file
IMPLICIT NONE
diff --git a/src/diag_headers/diagnose_fields.h b/src/diag_headers/diagnose_fields.h
new file mode 100644
index 0000000000000000000000000000000000000000..a68cb8fbb596044e23eef10df7e648be9760fe26
--- /dev/null
+++ b/src/diag_headers/diagnose_fields.h
@@ -0,0 +1,157 @@
+SUBROUTINE diagnose_fields(kstep)
+ USE basic
+ USE grid
+ USE diagnostics_par
+ USE futils
+ USE array
+ USE model
+ USE initial_par
+ USE fields
+ USE time_integration
+ USE utility
+ USE prec_const
+ USE collision, ONLY: coll_outputinputs
+ USE geometry
+ USE processing
+ IMPLICIT NONE
+ INTEGER, INTENT(in) :: kstep
+ INTEGER, parameter :: BUFSIZE = 2
+ INTEGER :: rank = 0
+ INTEGER :: dims(1) = (/0/)
+ !____________________________________________________________________________!
+ IF ((kstep .EQ. 0)) THEN
+ ! fields result file (electro. pot., Ni00 moment, fluid moments etc.)
+ IF (nsave_3d .GT. 0) THEN
+ CALL init_outfile(comm_kyz,fldfile0,fldfile,fidfld)
+ CALL creatd(fidfld, rank, dims, "/data/time", "Time t*c_s/R")
+ CALL creatd(fidfld, rank, dims, "/data/cstep", "iteration number")
+
+ IF (write_phi) CALL creatg(fidfld, "/data/phi", "phi")
+
+ IF (write_Na00) THEN
+ IF(KIN_E)&
+ CALL creatg(fidfld, "/data/Ne00", "Ne00")
+ CALL creatg(fidfld, "/data/Ni00", "Ni00")
+ ENDIF
+
+ IF (write_dens) THEN
+ IF(KIN_E)&
+ CALL creatg(fidfld, "/data/dens_e", "dens_e")
+ CALL creatg(fidfld, "/data/dens_i", "dens_i")
+ ENDIF
+
+ IF (write_fvel) THEN
+ IF(KIN_E) THEN
+ CALL creatg(fidfld, "/data/upar_e", "upar_e")
+ CALL creatg(fidfld, "/data/uper_e", "uper_e")
+ ENDIF
+ CALL creatg(fidfld, "/data/upar_i", "upar_i")
+ CALL creatg(fidfld, "/data/uper_i", "uper_i")
+ ENDIF
+
+ IF (write_temp) THEN
+ IF(KIN_E) THEN
+ CALL creatg(fidfld, "/data/Tper_e", "Tper_e")
+ CALL creatg(fidfld, "/data/Tpar_e", "Tpar_e")
+ CALL creatg(fidfld, "/data/temp_e", "temp_e")
+ ENDIF
+ CALL creatg(fidfld, "/data/Tper_i", "Tper_i")
+ CALL creatg(fidfld, "/data/Tpar_i", "Tpar_i")
+ CALL creatg(fidfld, "/data/temp_i", "temp_i")
+ ENDIF
+
+ IF (cstep==0) THEN
+ iframe3d=0
+ ENDIF
+ CALL attach(fidfld,"/data/" , "frames", iframe3d)
+ END IF
+ ENDIF
+
+ !_____________________________________________________________________________
+ ! 2. Periodic diagnostics
+ !
+ IF (kstep .GE. 0) THEN
+
+ ! 2.2 3d profiles
+ IF (nsave_3d .GT. 0) THEN
+ IF (MOD(cstep, nsave_3d) == 0) THEN
+
+ CALL append(fidfld, "/data/time", time,ionode=0)
+ CALL append(fidfld, "/data/cstep", real(cstep,dp),ionode=0)
+ CALL getatt(fidfld, "/data/", "frames",iframe3d)
+ iframe3d=iframe3d+1
+ CALL attach(fidfld,"/data/" , "frames", iframe3d)
+
+ IF (write_phi) CALL write_field3d_kykxz(phi (ikys:ikye,ikxs:ikxe,izs:ize), 'phi')
+
+ IF (write_Na00) THEN
+ IF(KIN_E)THEN
+ IF (ips_e .EQ. 1) THEN
+ Ne00(ikys:ikye,ikxs:ikxe,izs:ize) = moments_e(ips_e,1,ikys:ikye,ikxs:ikxe,izs:ize,updatetlevel)
+ ENDIF
+ CALL write_field3d_kykxz(Ne00(ikys:ikye,ikxs:ikxe,izs:ize), 'Ne00')
+ ENDIF
+ IF (ips_i .EQ. 1) THEN
+ Ni00(ikys:ikye,ikxs:ikxe,izs:ize) = moments_i(ips_e,1,ikys:ikye,ikxs:ikxe,izs:ize,updatetlevel)
+ ENDIF
+ CALL write_field3d_kykxz(Ni00(ikys:ikye,ikxs:ikxe,izs:ize), 'Ni00')
+ ENDIF
+
+ !! Fuid moments
+ IF (write_dens .OR. write_fvel .OR. write_temp) &
+ CALL compute_fluid_moments
+
+ IF (write_dens) THEN
+ IF(KIN_E)&
+ CALL write_field3d_kykxz(dens_e(ikys:ikye,ikxs:ikxe,izs:ize), 'dens_e')
+ CALL write_field3d_kykxz(dens_i(ikys:ikye,ikxs:ikxe,izs:ize), 'dens_i')
+ ENDIF
+
+ IF (write_fvel) THEN
+ IF(KIN_E)&
+ CALL write_field3d_kykxz(upar_e(ikys:ikye,ikxs:ikxe,izs:ize), 'upar_e')
+ CALL write_field3d_kykxz(upar_i(ikys:ikye,ikxs:ikxe,izs:ize), 'upar_i')
+ IF(KIN_E)&
+ CALL write_field3d_kykxz(uper_e(ikys:ikye,ikxs:ikxe,izs:ize), 'uper_e')
+ CALL write_field3d_kykxz(uper_i(ikys:ikye,ikxs:ikxe,izs:ize), 'uper_i')
+ ENDIF
+
+ IF (write_temp) THEN
+ IF(KIN_E)&
+ CALL write_field3d_kykxz(Tpar_e(ikys:ikye,ikxs:ikxe,izs:ize), 'Tpar_e')
+ CALL write_field3d_kykxz(Tpar_i(ikys:ikye,ikxs:ikxe,izs:ize), 'Tpar_i')
+ IF(KIN_E)&
+ CALL write_field3d_kykxz(Tper_e(ikys:ikye,ikxs:ikxe,izs:ize), 'Tper_e')
+ CALL write_field3d_kykxz(Tper_i(ikys:ikye,ikxs:ikxe,izs:ize), 'Tper_i')
+ IF(KIN_E)&
+ CALL write_field3d_kykxz(temp_e(ikys:ikye,ikxs:ikxe,izs:ize), 'temp_e')
+ CALL write_field3d_kykxz(temp_i(ikys:ikye,ikxs:ikxe,izs:ize), 'temp_i')
+ ENDIF
+
+ END IF
+ END IF
+ !_____________________________________________________________________________
+ ! 3. Final diagnostics
+ ELSEIF (kstep .EQ. -1) THEN
+ ! Close diagnostic files
+ CALL mpi_barrier(MPI_COMM_WORLD, ierr)
+ CALL closef(fidfld)
+
+ END IF
+
+ CONTAINS
+ SUBROUTINE write_field3d_kykxz(field, text)
+ IMPLICIT NONE
+ COMPLEX(dp), DIMENSION(ikys:ikye,ikxs:ikxe, izs:ize), INTENT(IN) :: field
+ CHARACTER(*), INTENT(IN) :: text
+ CHARACTER(LEN=50) :: dset_name
+ WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data", TRIM(text), iframe3d
+ IF (num_procs .EQ. 1) THEN ! no data distribution
+ CALL putarr(fidfld, dset_name, field(ikys:ikye,ikxs:ikxe, izs:ize), ionode=0)
+ ELSE
+ CALL putarrnd(fidfld, dset_name, field(ikys:ikye,ikxs:ikxe, izs:ize), (/1, 3/))
+ ENDIF
+ CALL attach(fidfld, dset_name, "time", time)
+ END SUBROUTINE write_field3d_kykxz
+
+END SUBROUTINE diagnose_fields
diff --git a/src/diag_headers/diagnose_full.h b/src/diag_headers/diagnose_full.h
new file mode 100644
index 0000000000000000000000000000000000000000..5f9cc79de522ecb1a82861832dec3cf877c6c19d
--- /dev/null
+++ b/src/diag_headers/diagnose_full.h
@@ -0,0 +1,478 @@
+SUBROUTINE diagnose_full(kstep)
+USE basic
+USE grid
+USE diagnostics_par
+USE futils, ONLY: creatf, creatg, creatd, closef, putarr, putfile, attach, openf, putarrnd
+USE array
+USE model
+USE initial_par
+USE fields
+USE time_integration
+USE utility
+USE prec_const
+USE collision, ONLY: coll_outputinputs
+USE geometry
+IMPLICIT NONE
+INTEGER, INTENT(in) :: kstep
+INTEGER, parameter :: BUFSIZE = 2
+INTEGER :: rank = 0
+INTEGER :: dims(1) = (/0/)
+INTEGER :: cp_counter = 0
+CHARACTER(len=256) :: str,test_
+!____________________________________________________________________________
+! 1. Initial diagnostics
+
+IF ((kstep .EQ. 0)) THEN
+ CALL init_outfile(comm0, resfile0,resfile,fidres)
+
+ ! Profiler time measurement
+ CALL creatg(fidres, "/profiler", "performance analysis")
+ CALL creatd(fidres, 0, dims, "/profiler/Tc_rhs", "cumulative rhs computation time")
+ CALL creatd(fidres, 0, dims, "/profiler/Tc_adv_field", "cumulative adv. fields computation time")
+ CALL creatd(fidres, 0, dims, "/profiler/Tc_clos", "cumulative closure computation time")
+ CALL creatd(fidres, 0, dims, "/profiler/Tc_ghost", "cumulative communication time")
+ CALL creatd(fidres, 0, dims, "/profiler/Tc_coll", "cumulative collision computation time")
+ CALL creatd(fidres, 0, dims, "/profiler/Tc_poisson", "cumulative poisson computation time")
+ CALL creatd(fidres, 0, dims, "/profiler/Tc_Sapj", "cumulative Sapj computation time")
+ CALL creatd(fidres, 0, dims, "/profiler/Tc_checkfield", "cumulative checkfield computation time")
+ CALL creatd(fidres, 0, dims, "/profiler/Tc_diag", "cumulative sym computation time")
+ CALL creatd(fidres, 0, dims, "/profiler/Tc_process", "cumulative process computation time")
+ CALL creatd(fidres, 0, dims, "/profiler/Tc_step", "cumulative total step computation time")
+ CALL creatd(fidres, 0, dims, "/profiler/time", "current simulation time")
+
+ ! Grid info
+ CALL creatg(fidres, "/data/grid", "Grid data")
+ CALL putarr(fidres, "/data/grid/coordkx", kxarray_full, "kx*rho_s0", ionode=0)
+ CALL putarr(fidres, "/data/grid/coordky", kyarray_full, "ky*rho_s0", ionode=0)
+ CALL putarr(fidres, "/data/grid/coordz", zarray_full, "z/R", ionode=0)
+ CALL putarr(fidres, "/data/grid/coordp_e" , parray_e_full, "p_e", ionode=0)
+ CALL putarr(fidres, "/data/grid/coordj_e" , jarray_e_full, "j_e", ionode=0)
+ CALL putarr(fidres, "/data/grid/coordp_i" , parray_i_full, "p_i", ionode=0)
+ CALL putarr(fidres, "/data/grid/coordj_i" , jarray_i_full, "j_i", ionode=0)
+
+ ! Metric info
+ CALL creatg(fidres, "/data/metric", "Metric data")
+ CALL putarrnd(fidres, "/data/metric/gxx", gxx(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/gxy", gxy(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/gyy", gyy(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/gyz", gyz(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/gzz", gzz(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/hatR", hatR(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/hatZ", hatZ(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/hatB", hatB(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/gradxB", gradxB(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/gradyB", gradyB(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/gradzB", gradzB(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/Jacobian", Jacobian(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/gradz_coeff", gradz_coeff(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidres, "/data/metric/Ckxky", Ckxky(ikys:ikye,ikxs:ikxe,izs:ize,0:1), (/1, 1, 3/))
+ CALL putarrnd(fidres, "/data/metric/kernel_i", kernel_i(ijs_i:ije_i,ikys:ikye,ikxs:ikxe,izs:ize,0:1), (/ 1, 2, 4/))
+
+ ! 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 (write_hf) THEN
+ CALL creatd(fidres, rank, dims, "/data/var0d/hflux_x", "Radial part ion heat flux")
+ ENDIF
+ IF (cstep==0) THEN
+ iframe0d=0
+ ENDIF
+ CALL attach(fidres,"/data/var0d/" , "frames", iframe0d)
+ END IF
+
+
+ ! var2d group (??)
+ 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 (cstep==0) THEN
+ iframe2d=0
+ ENDIF
+ CALL attach(fidres,"/data/var2d/" , "frames", iframe2d)
+ END IF
+
+ ! var3d group (electro. pot., Ni00 moment)
+ IF (nsave_3d .GT. 0) THEN
+ CALL creatg(fidres, "/data/var3d", "3d profiles")
+ CALL creatd(fidres, rank, dims, "/data/var3d/time", "Time t*c_s/R")
+ CALL creatd(fidres, rank, dims, "/data/var3d/cstep", "iteration number")
+
+ IF (write_phi) CALL creatg(fidres, "/data/var3d/phi", "phi")
+
+ IF (write_Na00) THEN
+ IF(KIN_E)&
+ CALL creatg(fidres, "/data/var3d/Ne00", "Ne00")
+ CALL creatg(fidres, "/data/var3d/Ni00", "Ni00")
+ IF(KIN_E)&
+ CALL creatg(fidres, "/data/var3d/Nepjz", "Nepjz")
+ CALL creatg(fidres, "/data/var3d/Nipjz", "Nipjz")
+ ENDIF
+
+ IF (write_dens) THEN
+ IF(KIN_E)&
+ CALL creatg(fidres, "/data/var3d/dens_e", "dens_e")
+ CALL creatg(fidres, "/data/var3d/dens_i", "dens_i")
+ ENDIF
+
+ IF (write_fvel) THEN
+ IF(KIN_E) THEN
+ CALL creatg(fidres, "/data/var3d/upar_e", "upar_e")
+ CALL creatg(fidres, "/data/var3d/uper_e", "uper_e")
+ ENDIF
+ CALL creatg(fidres, "/data/var3d/upar_i", "upar_i")
+ CALL creatg(fidres, "/data/var3d/uper_i", "uper_i")
+ ENDIF
+
+ IF (write_temp) THEN
+ IF(KIN_E) THEN
+ CALL creatg(fidres, "/data/var3d/Tper_e", "Tper_e")
+ CALL creatg(fidres, "/data/var3d/Tpar_e", "Tpar_e")
+ CALL creatg(fidres, "/data/var3d/temp_e", "temp_e")
+ ENDIF
+ CALL creatg(fidres, "/data/var3d/Tper_i", "Tper_i")
+ CALL creatg(fidres, "/data/var3d/Tpar_i", "Tpar_i")
+ CALL creatg(fidres, "/data/var3d/temp_i", "temp_i")
+ ENDIF
+
+ IF (cstep==0) THEN
+ iframe3d=0
+ ENDIF
+ CALL attach(fidres,"/data/var3d/" , "frames", iframe3d)
+ END IF
+
+ ! var5d group (moments)
+ IF (nsave_5d .GT. 0) THEN
+ 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
+ IF(KIN_E)&
+ CALL creatg(fidres, "/data/var5d/moments_e", "moments_e")
+ CALL creatg(fidres, "/data/var5d/moments_i", "moments_i")
+ ENDIF
+
+ IF (write_Sapj) THEN
+ IF(KIN_E)&
+ 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
+ENDIF
+
+!_____________________________________________________________________________
+! 2. Periodic diagnostics
+!
+IF (kstep .GE. 0) THEN
+
+ ! 2.1 0d history arrays
+ IF (nsave_0d .GT. 0) THEN
+ IF ( MOD(cstep, nsave_0d) == 0 ) THEN
+ CALL diagnose_0d
+ END IF
+ END IF
+
+ ! 2.2 1d profiles
+ ! empty in our case
+
+ ! 2.3 2d profiles
+ ! empty in our case
+
+
+ ! 2.3 2d profiles
+ IF (nsave_3d .GT. 0) THEN
+ IF (MOD(cstep, nsave_3d) == 0) THEN
+ CALL diagnose_3d
+ END IF
+ END IF
+
+ ! 2.4 3d profiles
+ IF (nsave_5d .GT. 0 .AND. cstep .GT. 0) THEN
+ IF (MOD(cstep, nsave_5d) == 0) THEN
+ CALL diagnose_5d
+ END IF
+ END IF
+
+!_____________________________________________________________________________
+! 3. Final diagnostics
+
+ELSEIF (kstep .EQ. -1) THEN
+ CALL attach(fidres, "/data/input","cpu_time",finish-start)
+
+ ! make a checkpoint at last timestep if not crashed
+ IF(.NOT. crashed) THEN
+ IF(my_id .EQ. 0) write(*,*) 'Saving last state'
+ IF (nsave_5d .GT. 0) &
+ CALL diagnose_5d
+ ENDIF
+
+ ! Close all diagnostic files
+ CALL mpi_barrier(MPI_COMM_WORLD, ierr)
+ CALL closef(fidres)
+
+END IF
+
+END SUBROUTINE diagnose_full
+
+!!-------------- Auxiliary routines -----------------!!
+SUBROUTINE diagnose_0d
+
+ USE basic
+ USE futils, ONLY: append, attach, getatt
+ USE diagnostics_par
+ USE prec_const
+ USE processing
+ USE model, ONLY: KIN_E
+
+ 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_clos", tc_clos,ionode=0)
+ CALL append(fidres, "/profiler/Tc_ghost", tc_ghost,ionode=0)
+ CALL append(fidres, "/profiler/Tc_coll", tc_coll,ionode=0)
+ CALL append(fidres, "/profiler/Tc_poisson", tc_poisson,ionode=0)
+ CALL append(fidres, "/profiler/Tc_Sapj", tc_Sapj,ionode=0)
+ CALL append(fidres, "/profiler/Tc_checkfield",tc_checkfield,ionode=0)
+ CALL append(fidres, "/profiler/Tc_diag", tc_diag,ionode=0)
+ CALL append(fidres, "/profiler/Tc_process", tc_process,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
+ IF (write_hf) THEN
+ CALL compute_radial_heatflux
+ CALL append(fidres, "/data/var0d/hflux_x",hflux_x,ionode=0)
+ ENDIF
+END SUBROUTINE diagnose_0d
+
+SUBROUTINE diagnose_3d
+
+ USE basic
+ USE futils, ONLY: append, getatt, attach, putarrnd, putarr
+ USE fields
+ USE array
+ USE grid, ONLY: ikxs,ikxe, ikys,ikye, Nkx, Nky, local_nkx, ikx, iky, ips_e, ips_i
+ USE time_integration
+ USE diagnostics_par
+ USE prec_const
+ USE processing
+ USE model, ONLY: KIN_E
+
+ IMPLICIT NONE
+
+ INTEGER :: i_, root, world_rank, world_size
+
+ CALL append(fidres, "/data/var3d/time", time,ionode=0)
+ CALL append(fidres, "/data/var3d/cstep", real(cstep,dp),ionode=0)
+ CALL getatt(fidres, "/data/var3d/", "frames",iframe3d)
+ iframe3d=iframe3d+1
+ CALL attach(fidres,"/data/var3d/" , "frames", iframe3d)
+
+ IF (write_phi) CALL write_field3d_kykxz(phi (ikys:ikye,ikxs:ikxe,izs:ize), 'phi')
+
+ IF (write_Na00) THEN
+ IF(KIN_E)THEN
+ IF (ips_e .EQ. 1) THEN
+ Ne00(ikys:ikye,ikxs:ikxe,izs:ize) = moments_e(ips_e,1,ikys:ikye,ikxs:ikxe,izs:ize,updatetlevel)
+ ENDIF
+ CALL write_field3d_kykxz(Ne00(ikys:ikye,ikxs:ikxe,izs:ize), 'Ne00')
+ ENDIF
+ IF (ips_i .EQ. 1) THEN
+ Ni00(ikys:ikye,ikxs:ikxe,izs:ize) = moments_i(ips_e,1,ikys:ikye,ikxs:ikxe,izs:ize,updatetlevel)
+ ENDIF
+ CALL write_field3d_kykxz(Ni00(ikys:ikye,ikxs:ikxe,izs:ize), 'Ni00')
+
+ CALL compute_Napjz_spectrum
+ IF(KIN_E) &
+ CALL write_field3d_pjz_e(Nepjz(ips_e:ipe_e,ijs_e:ije_e,izs:ize), 'Nepjz')
+ CALL write_field3d_pjz_i(Nipjz(ips_i:ipe_i,ijs_i:ije_i,izs:ize), 'Nipjz')
+ ENDIF
+
+ !! Fuid moments
+ IF (write_dens .OR. write_fvel .OR. write_temp) &
+ CALL compute_fluid_moments
+
+ IF (write_dens) THEN
+ IF(KIN_E)&
+ CALL write_field3d_kykxz(dens_e(ikys:ikye,ikxs:ikxe,izs:ize), 'dens_e')
+ CALL write_field3d_kykxz(dens_i(ikys:ikye,ikxs:ikxe,izs:ize), 'dens_i')
+ ENDIF
+
+ IF (write_fvel) THEN
+ IF(KIN_E)&
+ CALL write_field3d_kykxz(upar_e(ikys:ikye,ikxs:ikxe,izs:ize), 'upar_e')
+ CALL write_field3d_kykxz(upar_i(ikys:ikye,ikxs:ikxe,izs:ize), 'upar_i')
+ IF(KIN_E)&
+ CALL write_field3d_kykxz(uper_e(ikys:ikye,ikxs:ikxe,izs:ize), 'uper_e')
+ CALL write_field3d_kykxz(uper_i(ikys:ikye,ikxs:ikxe,izs:ize), 'uper_i')
+ ENDIF
+
+ IF (write_temp) THEN
+ IF(KIN_E)&
+ CALL write_field3d_kykxz(Tpar_e(ikys:ikye,ikxs:ikxe,izs:ize), 'Tpar_e')
+ CALL write_field3d_kykxz(Tpar_i(ikys:ikye,ikxs:ikxe,izs:ize), 'Tpar_i')
+ IF(KIN_E)&
+ CALL write_field3d_kykxz(Tper_e(ikys:ikye,ikxs:ikxe,izs:ize), 'Tper_e')
+ CALL write_field3d_kykxz(Tper_i(ikys:ikye,ikxs:ikxe,izs:ize), 'Tper_i')
+ IF(KIN_E)&
+ CALL write_field3d_kykxz(temp_e(ikys:ikye,ikxs:ikxe,izs:ize), 'temp_e')
+ CALL write_field3d_kykxz(temp_i(ikys:ikye,ikxs:ikxe,izs:ize), 'temp_i')
+ ENDIF
+
+ CONTAINS
+
+ SUBROUTINE write_field3d_kykxz(field, text)
+ IMPLICIT NONE
+ COMPLEX(dp), DIMENSION(ikys:ikye,ikxs:ikxe, izs:ize), INTENT(IN) :: field
+ CHARACTER(*), INTENT(IN) :: text
+ CHARACTER(LEN=50) :: dset_name
+ WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data/var3d", TRIM(text), iframe3d
+ IF (num_procs .EQ. 1) THEN ! no data distribution
+ CALL putarr(fidres, dset_name, field(ikys:ikye,ikxs:ikxe, izs:ize), ionode=0)
+ ELSE
+ CALL putarrnd(fidres, dset_name, field(ikys:ikye,ikxs:ikxe, izs:ize), (/1, 1, 3/))
+ ENDIF
+ CALL attach(fidres, dset_name, "time", time)
+ END SUBROUTINE write_field3d_kykxz
+
+ SUBROUTINE write_field3d_pjz_i(field, text)
+ IMPLICIT NONE
+ REAL(dp), DIMENSION(ips_i:ipe_i,ijs_i:ije_i,izs:ize), INTENT(IN) :: field
+ CHARACTER(*), INTENT(IN) :: text
+ CHARACTER(LEN=50) :: dset_name
+ WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data/var3d", TRIM(text), iframe3d
+ IF (num_procs .EQ. 1) THEN ! no data distribution
+ CALL putarr(fidres, dset_name, field(ips_i:ipe_i,ijs_i:ije_i,izs:ize), ionode=0)
+ ELSE
+ CALL putarrnd(fidres, dset_name, field(ips_i:ipe_i,ijs_i:ije_i,izs:ize), (/1, 0, 3/))
+ ENDIF
+ CALL attach(fidres, dset_name, "time", time)
+ END SUBROUTINE write_field3d_pjz_i
+
+ SUBROUTINE write_field3d_pjz_e(field, text)
+ IMPLICIT NONE
+ REAL(dp), DIMENSION(ips_e:ipe_e,ijs_e:ije_e,izs:ize), INTENT(IN) :: field
+ CHARACTER(*), INTENT(IN) :: text
+ CHARACTER(LEN=50) :: dset_name
+ WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data/var3d", TRIM(text), iframe3d
+ IF (num_procs .EQ. 1) THEN ! no data distribution
+ CALL putarr(fidres, dset_name, field(ips_e:ipe_e,ijs_e:ije_e,izs:ize), ionode=0)
+ ELSE
+ CALL putarrnd(fidres, dset_name, field(ips_e:ipe_e,ijs_e:ije_e,izs:ize), (/1, 0, 3/))
+ ENDIF
+ CALL attach(fidres, dset_name, "time", time)
+ END SUBROUTINE write_field3d_pjz_e
+
+END SUBROUTINE diagnose_3d
+
+SUBROUTINE diagnose_5d
+
+ USE basic
+ USE futils, ONLY: append, getatt, attach, putarrnd
+ USE fields
+ USE array!, ONLY: Sepj, Sipj
+ USE grid, ONLY: ips_e,ipe_e, ips_i, ipe_i, &
+ ijs_e,ije_e, ijs_i, ije_i, &
+ ikxs,ikxe,ikys,ikye,izs,ize
+ USE time_integration
+ USE diagnostics_par
+ USE prec_const
+ USE model, ONLY: KIN_E
+ IMPLICIT NONE
+
+ CALL append(fidres, "/data/var5d/time", time,ionode=0)
+ CALL append(fidres, "/data/var5d/cstep", real(cstep,dp),ionode=0)
+ CALL getatt(fidres, "/data/var5d/", "frames",iframe5d)
+ iframe5d=iframe5d+1
+ CALL attach(fidres,"/data/var5d/" , "frames", iframe5d)
+
+ IF (write_Napj) THEN
+ IF(KIN_E)&
+ CALL write_field5d_e(moments_e(ips_e:ipe_e,ijs_e:ije_e,ikys:ikye,ikxs:ikxe,izs:ize,updatetlevel), 'moments_e')
+ CALL write_field5d_i(moments_i(ips_i:ipe_i,ijs_i:ije_i,ikys:ikye,ikxs:ikxe,izs:ize,updatetlevel), 'moments_i')
+ ENDIF
+
+ IF (write_Sapj) THEN
+ IF(KIN_E)&
+ CALL write_field5d_e(Sepj(ips_e:ipe_e,ijs_e:ije_e,ikys:ikye,ikxs:ikxe,izs:ize), 'Sepj')
+ CALL write_field5d_i(Sipj(ips_i:ipe_i,ijs_i:ije_i,ikys:ikye,ikxs:ikxe,izs:ize), 'Sipj')
+ ENDIF
+
+ CONTAINS
+
+ SUBROUTINE write_field5d_e(field, text)
+ USE futils, ONLY: attach, putarr, putarrnd
+ USE grid, ONLY: ips_e,ipe_e, ijs_e,ije_e, ikxs,ikxe, ikys,ikye, izs,ize
+ USE prec_const
+ IMPLICIT NONE
+
+ COMPLEX(dp), DIMENSION(ips_e:ipe_e,ijs_e:ije_e,ikys:ikye,ikxs:ikxe,izs:ize), INTENT(IN) :: field
+ CHARACTER(*), INTENT(IN) :: text
+
+ CHARACTER(LEN=50) :: dset_name
+
+ WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data/var5d", TRIM(text), iframe5d
+ IF (num_procs .EQ. 1) THEN
+ CALL putarr(fidres, dset_name, field(ips_e:ipe_e,ijs_e:ije_e,ikys:ikye,ikxs:ikxe,izs:ize), ionode=0)
+ ELSE
+ CALL putarrnd(fidres, dset_name, field(ips_e:ipe_e,ijs_e:ije_e,ikys:ikye,ikxs:ikxe,izs:ize), (/1,3,5/))
+ ENDIF
+ CALL attach(fidres, dset_name, 'cstep', cstep)
+ CALL attach(fidres, dset_name, 'time', time)
+ CALL attach(fidres, dset_name, 'jobnum', jobnum)
+ CALL attach(fidres, dset_name, 'dt', dt)
+ CALL attach(fidres, dset_name, 'iframe2d', iframe2d)
+ CALL attach(fidres, dset_name, 'iframe5d', iframe5d)
+
+ END SUBROUTINE write_field5d_e
+
+ SUBROUTINE write_field5d_i(field, text)
+ USE futils, ONLY: attach, putarr, putarrnd
+ USE grid, ONLY: ips_i,ipe_i, ijs_i,ije_i, ikxs,ikxe, ikys,ikye, izs,ize
+ USE prec_const
+ IMPLICIT NONE
+
+ COMPLEX(dp), DIMENSION(ips_i:ipe_i,ijs_i:ije_i,ikys:ikye,ikxs:ikxe,izs:ize), INTENT(IN) :: field
+ CHARACTER(*), INTENT(IN) :: text
+
+ CHARACTER(LEN=50) :: dset_name
+
+ WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data/var5d", TRIM(text), iframe5d
+ IF (num_procs .EQ. 1) THEN
+ CALL putarr(fidres, dset_name, field(ips_i:ipe_i,ijs_i:ije_i,ikys:ikye,ikxs:ikxe,izs:ize), ionode=0)
+ ELSE
+ CALL putarrnd(fidres, dset_name, field(ips_i:ipe_i,ijs_i:ije_i,ikys:ikye,ikxs:ikxe,izs:ize), (/1,3,5/))
+ ENDIF
+ CALL attach(fidres, dset_name, 'cstep', cstep)
+ CALL attach(fidres, dset_name, 'time', time)
+ CALL attach(fidres, dset_name, 'jobnum', jobnum)
+ CALL attach(fidres, dset_name, 'dt', dt)
+ CALL attach(fidres, dset_name, 'iframe2d', iframe2d)
+ CALL attach(fidres, dset_name, 'iframe5d', iframe5d)
+
+ END SUBROUTINE write_field5d_i
+END SUBROUTINE diagnose_5d
diff --git a/src/diag_headers/diagnose_gridgeom.h b/src/diag_headers/diagnose_gridgeom.h
new file mode 100644
index 0000000000000000000000000000000000000000..9ef1855c928957eeb795102eb70a28f7269b0c07
--- /dev/null
+++ b/src/diag_headers/diagnose_gridgeom.h
@@ -0,0 +1,50 @@
+SUBROUTINE diagnose_gridgeom(kstep)
+ USE basic
+ USE grid
+ USE diagnostics_par
+ USE futils, ONLY: putarr, creatg, putarrnd, closef
+ USE time_integration
+ USE prec_const
+ USE geometry
+ USE array
+ IMPLICIT NONE
+ INTEGER, INTENT(in) :: kstep
+ INTEGER, parameter :: BUFSIZE = 2
+ INTEGER :: rank = 0
+ INTEGER :: dims(1) = (/0/)
+ IF (kstep .EQ. 0) THEN
+ ! Grid info
+ CALL init_outfile(comm0,ggmfile0,ggmfile,fidggm)
+ CALL creatg(fidggm, "/data/grid", "Grid data")
+ CALL putarr(fidggm, "/data/grid/coordkx", kxarray_full, "kx*rho_s0", ionode=0)
+ CALL putarr(fidggm, "/data/grid/coordky", kyarray_full, "ky*rho_s0", ionode=0)
+ CALL putarr(fidggm, "/data/grid/coordz", zarray_full, "z/R", ionode=0)
+ CALL putarr(fidggm, "/data/grid/coordp_e" , parray_e_full, "p_e", ionode=0)
+ CALL putarr(fidggm, "/data/grid/coordj_e" , jarray_e_full, "j_e", ionode=0)
+ CALL putarr(fidggm, "/data/grid/coordp_i" , parray_i_full, "p_i", ionode=0)
+ CALL putarr(fidggm, "/data/grid/coordj_i" , jarray_i_full, "j_i", ionode=0)
+
+ ! Metric info
+ CALL creatg(fidggm, "/data/metric", "Metric data")
+ CALL putarrnd(fidggm, "/data/metric/gxx", gxx(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidggm, "/data/metric/gxy", gxy(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidggm, "/data/metric/gyy", gyy(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidggm, "/data/metric/gyz", gyz(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidggm, "/data/metric/gzz", gzz(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidggm, "/data/metric/hatR", hatR(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidggm, "/data/metric/hatZ", hatZ(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidggm, "/data/metric/hatB", hatB(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidggm, "/data/metric/gradxB", gradxB(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidggm, "/data/metric/gradyB", gradyB(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidggm, "/data/metric/gradzB", gradzB(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidggm, "/data/metric/Jacobian", Jacobian(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidggm, "/data/metric/gradz_coeff", gradz_coeff(izs:ize,0:1), (/1, 1, 1/))
+ CALL putarrnd(fidggm, "/data/metric/Ckxky", Ckxky(ikys:ikye,ikxs:ikxe,izs:ize,0:1), (/1, 1, 3/))
+ CALL putarrnd(fidggm, "/data/metric/kernel_i", kernel_i(ijs_i:ije_i,ikys:ikye,ikxs:ikxe,izs:ize,0:1), (/ 1, 2, 4/))
+ ENDIF
+ IF (kstep .EQ. -1) THEN
+ CALL mpi_barrier(MPI_COMM_WORLD, ierr)
+ CALL closef(fidggm)
+ ENDIF
+
+END SUBROUTINE diagnose_gridgeom
diff --git a/src/diag_headers/diagnose_moments.h b/src/diag_headers/diagnose_moments.h
new file mode 100644
index 0000000000000000000000000000000000000000..585822602281cbdeff42e29dbc0d3e91c958c795
--- /dev/null
+++ b/src/diag_headers/diagnose_moments.h
@@ -0,0 +1,136 @@
+SUBROUTINE diagnose_moments(kstep)
+ USE basic
+ USE grid
+ USE diagnostics_par
+ USE futils, ONLY: creatg,creatd,append,putarr,putarrnd,attach,closef,getatt
+ USE model, ONLY: KIN_E
+ USE array, ONLY: Sepj,Sipj
+ USE fields, ONLY: moments_e, moments_i
+ USE time_integration
+ USE utility
+ USE prec_const
+ IMPLICIT NONE
+ INTEGER, INTENT(in) :: kstep
+ INTEGER, parameter :: BUFSIZE = 2
+ INTEGER :: rank = 0
+ INTEGER :: dims(1) = (/0/)
+ !____________________________________________________________________________!
+ IF ((kstep .EQ. 0)) THEN
+
+ ! var5d group (moments)
+ IF (nsave_5d .GT. 0) THEN
+ CALL init_outfile(comm0, momfile0,momfile,fidmom)
+
+ CALL creatd(fidmom, rank, dims, "/data/time", "Time t*c_s/R")
+ CALL creatd(fidmom, rank, dims, "/data/cstep", "iteration number")
+
+ IF (write_Napj) THEN
+ IF(KIN_E)&
+ CALL creatg(fidmom, "/data/moments_e", "moments_e")
+ CALL creatg(fidmom, "/data/moments_i", "moments_i")
+ ENDIF
+
+ IF (write_Sapj) THEN
+ IF(KIN_E)&
+ CALL creatg(fidmom, "/data/moments_e", "Sipj")
+ CALL creatg(fidmom, "/data/moments_i", "Sepj")
+ ENDIF
+
+ IF (cstep==0) THEN
+ iframe5d=0
+ END IF
+ CALL attach(fidmom,"/data/" , "frames", iframe5d)
+ END IF
+
+ ENDIF
+
+ !_____________________________________________________________________________
+ ! 2. Periodic diagnostics
+ !
+ IF ((kstep .GE. 0) .OR. ((kstep .EQ. -1) .AND. (.NOT. CRASHED))) THEN
+
+ IF((kstep .EQ. -1) .AND. (.NOT. CRASHED .AND. (my_id .EQ. 0))) &
+ write(*,*) 'Saving last state'
+
+ ! 2.3 5d profiles
+ IF (MOD(cstep, nsave_5d) == 0) THEN
+ CALL append(fidmom, "/data/time", time,ionode=0)
+ CALL append(fidmom, "/data/cstep", real(cstep,dp),ionode=0)
+ CALL getatt(fidmom, "/data/", "frames",iframe5d)
+ iframe5d=iframe5d+1
+ CALL attach(fidmom,"/data/" , "frames", iframe5d)
+
+ IF (write_Napj) THEN
+ IF(KIN_E)&
+ CALL write_field5d_e(moments_e(ips_e:ipe_e,ijs_e:ije_e,ikys:ikye,ikxs:ikxe,izs:ize,updatetlevel), 'moments_e')
+ CALL write_field5d_i(moments_i(ips_i:ipe_i,ijs_i:ije_i,ikys:ikye,ikxs:ikxe,izs:ize,updatetlevel), 'moments_i')
+ ENDIF
+
+ IF (write_Sapj) THEN
+ IF(KIN_E)&
+ CALL write_field5d_e(Sepj(ips_e:ipe_e,ijs_e:ije_e,ikys:ikye,ikxs:ikxe,izs:ize), 'Sepj')
+ CALL write_field5d_i(Sipj(ips_i:ipe_i,ijs_i:ije_i,ikys:ikye,ikxs:ikxe,izs:ize), 'Sipj')
+ ENDIF
+ END IF
+ END IF
+ !_____________________________________________________________________________
+ ! 3. Final diagnostics
+ IF (kstep .EQ. -1) THEN
+ ! Close diagnostic files
+ CALL mpi_barrier(MPI_COMM_WORLD, ierr)
+ CALL closef(fidmom)
+ END IF
+
+ CONTAINS
+ SUBROUTINE write_field5d_e(field, text)
+ USE futils, ONLY: attach, putarr, putarrnd
+ USE grid, ONLY: ips_e,ipe_e, ijs_e,ije_e, ikxs,ikxe, ikys,ikye, izs,ize
+ USE prec_const
+ IMPLICIT NONE
+
+ COMPLEX(dp), DIMENSION(ips_e:ipe_e,ijs_e:ije_e,ikys:ikye,ikxs:ikxe,izs:ize), INTENT(IN) :: field
+ CHARACTER(*), INTENT(IN) :: text
+
+ CHARACTER(LEN=50) :: dset_name
+
+ WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data", TRIM(text), iframe5d
+ IF (num_procs .EQ. 1) THEN
+ CALL putarr(fidmom, dset_name, field(ips_e:ipe_e,ijs_e:ije_e,ikys:ikye,ikxs:ikxe,izs:ize), ionode=0)
+ ELSE
+ CALL putarrnd(fidmom, dset_name, field(ips_e:ipe_e,ijs_e:ije_e,ikys:ikye,ikxs:ikxe,izs:ize), (/1,3,5/))
+ ENDIF
+ CALL attach(fidmom, dset_name, 'cstep', cstep)
+ CALL attach(fidmom, dset_name, 'time', time)
+ CALL attach(fidmom, dset_name, 'jobnum', jobnum)
+ CALL attach(fidmom, dset_name, 'dt', dt)
+ CALL attach(fidmom, dset_name, 'iframe2d', iframe2d)
+ CALL attach(fidmom, dset_name, 'iframe5d', iframe5d)
+
+ END SUBROUTINE write_field5d_e
+
+ SUBROUTINE write_field5d_i(field, text)
+ USE futils, ONLY: attach, putarr, putarrnd
+ USE grid, ONLY: ips_i,ipe_i, ijs_i,ije_i, ikxs,ikxe, ikys,ikye, izs,ize
+ USE prec_const
+ IMPLICIT NONE
+
+ COMPLEX(dp), DIMENSION(ips_i:ipe_i,ijs_i:ije_i,ikys:ikye,ikxs:ikxe,izs:ize), INTENT(IN) :: field
+ CHARACTER(*), INTENT(IN) :: text
+
+ CHARACTER(LEN=50) :: dset_name
+
+ WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data", TRIM(text), iframe5d
+ IF (num_procs .EQ. 1) THEN
+ CALL putarr(fidmom, dset_name, field(ips_i:ipe_i,ijs_i:ije_i,ikys:ikye,ikxs:ikxe,izs:ize), ionode=0)
+ ELSE
+ CALL putarrnd(fidmom, dset_name, field(ips_i:ipe_i,ijs_i:ije_i,ikys:ikye,ikxs:ikxe,izs:ize), (/1,3,5/))
+ ENDIF
+ CALL attach(fidmom, dset_name, 'cstep', cstep)
+ CALL attach(fidmom, dset_name, 'time', time)
+ CALL attach(fidmom, dset_name, 'jobnum', jobnum)
+ CALL attach(fidmom, dset_name, 'dt', dt)
+ CALL attach(fidmom, dset_name, 'iframe2d', iframe2d)
+ CALL attach(fidmom, dset_name, 'iframe5d', iframe5d)
+
+ END SUBROUTINE write_field5d_i
+END SUBROUTINE diagnose_moments
diff --git a/src/diag_headers/diagnose_momspectrum.h b/src/diag_headers/diagnose_momspectrum.h
new file mode 100644
index 0000000000000000000000000000000000000000..36befdda16321d1172fb86b89760da2e3a2e36ee
--- /dev/null
+++ b/src/diag_headers/diagnose_momspectrum.h
@@ -0,0 +1,105 @@
+SUBROUTINE diagnose_momspectrum(kstep)
+ USE basic
+ USE grid
+ USE diagnostics_par
+ USE futils
+ USE array
+ USE model
+ USE initial_par
+ USE fields
+ USE time_integration
+ USE utility
+ USE prec_const
+ USE collision, ONLY: coll_outputinputs
+ USE geometry
+ USE processing
+ IMPLICIT NONE
+ INTEGER, INTENT(in) :: kstep
+ INTEGER, parameter :: BUFSIZE = 2
+ INTEGER :: rank = 0, frame
+ INTEGER :: dims(1) = (/0/)
+ !____________________________________________________________________________!
+ IF ((kstep .EQ. 0)) THEN
+ ! var3d group (pjz, spectrum of moments)
+ IF (nsave_3d .GT. 0) THEN
+ CALL init_outfile(comm_pz, mspfile0,mspfile,fidmsp)
+ CALL creatd(fidmsp, rank, dims, "/data/time", "Time t*c_s/R")
+ CALL creatd(fidmsp, rank, dims, "/data/cstep", "iteration number")
+
+ IF (write_Na00) THEN
+ IF(KIN_E)&
+ CALL creatg(fidmsp, "/data/Nepjz", "Nepjz")
+ CALL creatg(fidmsp, "/data/Nipjz", "Nipjz")
+ ENDIF
+
+ IF (cstep==0) THEN
+ iframe3d=0
+ ENDIF
+ CALL attach(fidmsp,"/data/" , "frames", iframe3d)
+ END IF
+
+ ENDIF
+
+ !_____________________________________________________________________________
+ ! 2. Periodic diagnostics
+ !
+ IF (kstep .GE. 0) THEN
+ ! 2.2 3d profiles
+ IF (nsave_3d .GT. 0) THEN
+ IF (MOD(cstep, nsave_3d) == 0) THEN
+ CALL append(fidmsp, "/data/time", time,ionode=0)
+ CALL append(fidmsp, "/data/cstep", real(cstep,dp),ionode=0)
+ CALL getatt(fidmsp, "/data/", "frames",frame)
+ frame=frame+1
+ CALL attach(fidmsp,"/data/" , "frames", frame)
+
+ IF (write_Na00) THEN
+ CALL compute_Napjz_spectrum
+ IF(KIN_E) &
+ CALL write_field3d_pjz_e(Nepjz(ips_e:ipe_e,ijs_e:ije_e,izs:ize), 'Nepjz', frame)
+ CALL write_field3d_pjz_i(Nipjz(ips_i:ipe_i,ijs_i:ije_i,izs:ize), 'Nipjz', frame)
+ ENDIF
+ END IF
+ END IF
+
+ !_____________________________________________________________________________
+ ! 3. Final diagnostics
+ ELSEIF (kstep .EQ. -1) THEN
+ ! Close diagnostic files
+ CALL mpi_barrier(MPI_COMM_WORLD, ierr)
+ CALL closef(fidmsp)
+
+ END IF
+
+ CONTAINS
+ SUBROUTINE write_field3d_pjz_i(field, text, frame)
+ IMPLICIT NONE
+ REAL(dp), DIMENSION(ips_i:ipe_i,ijs_i:ije_i,izs:ize), INTENT(IN) :: field
+ CHARACTER(*), INTENT(IN) :: text
+ INTEGER, INTENT(IN) :: frame
+ CHARACTER(LEN=50) :: dset_name
+ WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data", TRIM(text), frame
+ IF (num_procs .EQ. 1) THEN ! no data distribution
+ CALL putarr(fidmsp, dset_name, field(ips_i:ipe_i,ijs_i:ije_i,izs:ize), ionode=0)
+ ELSE
+ CALL putarrnd(fidmsp, dset_name, field(ips_i:ipe_i,ijs_i:ije_i,izs:ize), (/1, 3/))
+ ENDIF
+ CALL attach(fidmsp, dset_name, "time", time)
+ END SUBROUTINE write_field3d_pjz_i
+
+ SUBROUTINE write_field3d_pjz_e(field, text, frame)
+ IMPLICIT NONE
+ REAL(dp), DIMENSION(ips_e:ipe_e,ijs_e:ije_e,izs:ize), INTENT(IN) :: field
+ CHARACTER(*), INTENT(IN) :: text
+ INTEGER, INTENT(IN) :: frame
+ CHARACTER(LEN=50) :: dset_name
+ WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data", TRIM(text), frame
+ IF (num_procs .EQ. 1) THEN ! no data distribution
+ CALL putarr (fidmsp, dset_name, field(ips_e:ipe_e,ijs_e:ije_e,izs:ize), ionode=0)
+ ELSE
+ CALL putarrnd(fidmsp, dset_name, field(ips_e:ipe_e,ijs_e:ije_e,izs:ize), (/1, 3/))
+ ENDIF
+ CALL attach(fidmsp, dset_name, "time", time)
+ END SUBROUTINE write_field3d_pjz_e
+
+END SUBROUTINE diagnose_momspectrum
diff --git a/src/diag_headers/diagnose_profiler.h b/src/diag_headers/diagnose_profiler.h
new file mode 100644
index 0000000000000000000000000000000000000000..b99f67dda7826fc97b4e3a49ecea405a8b6baca4
--- /dev/null
+++ b/src/diag_headers/diagnose_profiler.h
@@ -0,0 +1,54 @@
+SUBROUTINE diagnose_profiler(kstep)
+ USE basic
+ USE diagnostics_par
+ USE futils, ONLY: creatd,creatg,append,closef
+ USE time_integration
+ USE utility
+ USE prec_const
+ IMPLICIT NONE
+ INTEGER, INTENT(in) :: kstep
+ INTEGER :: dims(1) = (/0/)
+ !____________________________________________________________________________!
+ IF ((kstep .EQ. 0)) THEN
+ CALL init_outfile(comm0, prffile0,prffile,fidprf)
+
+ ! data time measurement
+ CALL creatd(fidprf, 0, dims, "/data/Tc_rhs", "cumulative rhs computation time")
+ CALL creatd(fidprf, 0, dims, "/data/Tc_adv_field", "cumulative adv. fields computation time")
+ CALL creatd(fidprf, 0, dims, "/data/Tc_clos", "cumulative closure computation time")
+ CALL creatd(fidprf, 0, dims, "/data/Tc_ghost", "cumulative communication time")
+ CALL creatd(fidprf, 0, dims, "/data/Tc_coll", "cumulative collision computation time")
+ CALL creatd(fidprf, 0, dims, "/data/Tc_poisson", "cumulative poisson computation time")
+ CALL creatd(fidprf, 0, dims, "/data/Tc_Sapj", "cumulative Sapj computation time")
+ CALL creatd(fidprf, 0, dims, "/data/Tc_checkfield", "cumulative checkfield computation time")
+ CALL creatd(fidprf, 0, dims, "/data/Tc_diag", "cumulative sym computation time")
+ CALL creatd(fidprf, 0, dims, "/data/Tc_process", "cumulative process computation time")
+ CALL creatd(fidprf, 0, dims, "/data/Tc_step", "cumulative total step computation time")
+ CALL creatd(fidprf, 0, dims, "/data/time", "current simulation time")
+ ENDIF
+ !_____________________________________________________________________________
+ ! 2. Periodic diagnostics
+ !
+ IF (kstep .GE. 0) THEN
+ ! Time measurement data
+ CALL append(fidprf, "/data/Tc_rhs", tc_rhs,ionode=0)
+ CALL append(fidprf, "/data/Tc_adv_field", tc_adv_field,ionode=0)
+ CALL append(fidprf, "/data/Tc_clos", tc_clos,ionode=0)
+ CALL append(fidprf, "/data/Tc_ghost", tc_ghost,ionode=0)
+ CALL append(fidprf, "/data/Tc_coll", tc_coll,ionode=0)
+ CALL append(fidprf, "/data/Tc_poisson", tc_poisson,ionode=0)
+ CALL append(fidprf, "/data/Tc_Sapj", tc_Sapj,ionode=0)
+ CALL append(fidprf, "/data/Tc_checkfield",tc_checkfield,ionode=0)
+ CALL append(fidprf, "/data/Tc_diag", tc_diag,ionode=0)
+ CALL append(fidprf, "/data/Tc_process", tc_process,ionode=0)
+ CALL append(fidprf, "/data/Tc_step", tc_step,ionode=0)
+ CALL append(fidprf, "/data/time", time,ionode=0)
+ !_____________________________________________________________________________
+ ! 3. Final diagnostics
+ ELSEIF (kstep .EQ. -1) THEN
+ ! Close diagnostic files
+ CALL mpi_barrier(MPI_COMM_WORLD, ierr)
+ CALL closef(fidprf)
+
+ END IF
+END SUBROUTINE diagnose_profiler
diff --git a/src/diag_headers/diagnose_timetraces.h b/src/diag_headers/diagnose_timetraces.h
new file mode 100644
index 0000000000000000000000000000000000000000..3c688aee8c1230f1fc3292f4a4e1111dee0de34a
--- /dev/null
+++ b/src/diag_headers/diagnose_timetraces.h
@@ -0,0 +1,76 @@
+SUBROUTINE diagnose_timetraces(kstep)
+ USE basic
+ USE grid
+ USE diagnostics_par
+ USE futils
+ USE array
+ USE model
+ USE initial_par
+ USE fields
+ USE time_integration
+ USE utility
+ USE prec_const
+ USE collision, ONLY: coll_outputinputs
+ USE geometry
+ USE processing
+ IMPLICIT NONE
+ INTEGER, INTENT(in) :: kstep
+ INTEGER, parameter :: BUFSIZE = 2
+ INTEGER :: rank = 0
+ INTEGER :: dims(1) = (/0/)
+ !____________________________________________________________________________!
+ IF ((kstep .EQ. 0)) THEN
+ CALL init_outfile(comm0, ttrfile0,ttrfile,fidttr)
+
+ ! var0d group (gyro transport)
+ CALL creatd(fidttr, rank, dims, "/data/time", "Time t*c_s/R")
+ CALL creatd(fidttr, rank, dims, "/data/cstep", "iteration number")
+
+ IF (write_gamma) THEN
+ CALL creatd(fidttr, rank, dims, "/data/gflux_ri", "Radial gyro ion transport")
+ CALL creatd(fidttr, rank, dims, "/data/pflux_ri", "Radial part ion transport")
+ ENDIF
+ IF (write_hf) THEN
+ CALL creatd(fidttr, rank, dims, "/data/hflux_x", "Radial part ion heat flux")
+ ENDIF
+ IF (cstep==0) THEN
+ iframe0d=0
+ ENDIF
+ CALL attach(fidttr,"/data/" , "frames", iframe0d)
+ ENDIF
+
+ !_____________________________________________________________________________
+ ! 2. Periodic diagnostics
+ !
+ IF (kstep .GE. 0) THEN
+
+ ! 0d time traces arrays
+ IF ( MOD(cstep, nsave_0d) == 0 ) THEN
+ ! Processing data
+ CALL append(fidttr, "/data/time", time,ionode=0)
+ CALL append(fidttr, "/data/cstep", real(cstep,dp),ionode=0)
+ CALL getatt(fidttr, "/data/", "frames",iframe0d)
+ iframe0d=iframe0d+1
+ CALL attach(fidttr,"/data/" , "frames", iframe0d)
+ ! Ion transport data
+ IF (write_gamma) THEN
+ CALL compute_radial_ion_transport
+ CALL append(fidttr, "/data/gflux_ri",gflux_ri,ionode=0)
+ CALL append(fidttr, "/data/pflux_ri",pflux_ri,ionode=0)
+ ENDIF
+ IF (write_hf) THEN
+ CALL compute_radial_heatflux
+ CALL append(fidttr, "/data/hflux_x",hflux_x,ionode=0)
+ ENDIF
+ END IF
+ !_____________________________________________________________________________
+ ! 3. Final diagnostics
+ ELSEIF (kstep .EQ. -1) THEN
+ ! Close diagnostic files
+ CALL mpi_barrier(MPI_COMM_WORLD, ierr)
+ CALL closef(fidttr)
+
+ END IF
+END SUBROUTINE diagnose_timetraces
+!____________________________________________________________________________!
+! AUXILIARY ROUTINES
diff --git a/src/diagnose.F90 b/src/diagnose.F90
index ced695af71f15622c7b61d1337db50d9f213258e..894263d077b03da8c35ad6a62feff07140f65313 100644
--- a/src/diagnose.F90
+++ b/src/diagnose.F90
@@ -2,635 +2,115 @@ SUBROUTINE diagnose(kstep)
! Diagnostics, writing simulation state to disk
USE basic
- USE grid
USE diagnostics_par
- USE futils, ONLY: creatf, creatg, creatd, closef, putarr, putfile, attach, openf, putarrnd
- USE array
- USE model
- USE initial_par
- USE fields
- USE time_integration
- USE utility
- USE prec_const
- USE collision, ONLY: coll_outputinputs
- USE geometry
IMPLICIT NONE
- INCLUDE 'srcinfo.h'
-
INTEGER, INTENT(in) :: kstep
- INTEGER, parameter :: BUFSIZE = 2
- INTEGER :: rank = 0
- INTEGER :: dims(1) = (/0/)
- INTEGER :: cp_counter = 0
- CHARACTER(len=256) :: str, fname,test_
CALL cpu_time(t0_diag) ! Measuring time
- !_____________________________________________________________________________
- ! 1. Initial diagnostics
+ !! Basic diagnose loop for reading input file, displaying advancement and ending
IF ((kstep .EQ. 0)) THEN
- ! Writing output filename
- WRITE(resfile,'(a,a1,i2.2,a3)') TRIM(resfile0),'_',jobnum,'.h5'
- ! 1.1 Initial run
- ! Main output file creation
- IF (write_doubleprecision) THEN
- CALL creatf(resfile, fidres, real_prec='d', mpicomm=comm0)
- ELSE
- CALL creatf(resfile, fidres, mpicomm=comm0)
- END IF
- IF (my_id .EQ. 0) WRITE(*,'(3x,a,a)') TRIM(resfile), ' created'
-
- ! Data group
- CALL creatg(fidres, "/data", "data")
-
- ! File group
- CALL creatg(fidres, "/files", "files")
- CALL attach(fidres, "/files", "jobnum", jobnum)
-
- ! Profiler time measurement
- CALL creatg(fidres, "/profiler", "performance analysis")
- CALL creatd(fidres, 0, dims, "/profiler/Tc_rhs", "cumulative rhs computation time")
- CALL creatd(fidres, 0, dims, "/profiler/Tc_adv_field", "cumulative adv. fields computation time")
- CALL creatd(fidres, 0, dims, "/profiler/Tc_clos", "cumulative closure computation time")
- CALL creatd(fidres, 0, dims, "/profiler/Tc_ghost", "cumulative communication time")
- CALL creatd(fidres, 0, dims, "/profiler/Tc_coll", "cumulative collision computation time")
- CALL creatd(fidres, 0, dims, "/profiler/Tc_poisson", "cumulative poisson computation time")
- CALL creatd(fidres, 0, dims, "/profiler/Tc_Sapj", "cumulative Sapj computation time")
- CALL creatd(fidres, 0, dims, "/profiler/Tc_checkfield", "cumulative checkfield computation time")
- CALL creatd(fidres, 0, dims, "/profiler/Tc_diag", "cumulative sym computation time")
- CALL creatd(fidres, 0, dims, "/profiler/Tc_process", "cumulative process computation time")
- CALL creatd(fidres, 0, dims, "/profiler/Tc_step", "cumulative total step computation time")
- CALL creatd(fidres, 0, dims, "/profiler/time", "current simulation time")
-
- ! Grid info
- CALL creatg(fidres, "/data/grid", "Grid data")
- CALL putarr(fidres, "/data/grid/coordkx", kxarray_full, "kx*rho_s0", ionode=0)
- CALL putarr(fidres, "/data/grid/coordky", kyarray_full, "ky*rho_s0", ionode=0)
- CALL putarr(fidres, "/data/grid/coordz", zarray_full, "z/R", ionode=0)
- CALL putarr(fidres, "/data/grid/coordp_e" , parray_e_full, "p_e", ionode=0)
- CALL putarr(fidres, "/data/grid/coordj_e" , jarray_e_full, "j_e", ionode=0)
- CALL putarr(fidres, "/data/grid/coordp_i" , parray_i_full, "p_i", ionode=0)
- CALL putarr(fidres, "/data/grid/coordj_i" , jarray_i_full, "j_i", ionode=0)
-
- ! Metric info
- CALL creatg(fidres, "/data/metric", "Metric data")
- CALL putarrnd(fidres, "/data/metric/gxx", gxx(izs:ize,0:1), (/1, 1, 1/))
- CALL putarrnd(fidres, "/data/metric/gxy", gxy(izs:ize,0:1), (/1, 1, 1/))
- CALL putarrnd(fidres, "/data/metric/gyy", gyy(izs:ize,0:1), (/1, 1, 1/))
- CALL putarrnd(fidres, "/data/metric/gyz", gyz(izs:ize,0:1), (/1, 1, 1/))
- CALL putarrnd(fidres, "/data/metric/gzz", gzz(izs:ize,0:1), (/1, 1, 1/))
- CALL putarrnd(fidres, "/data/metric/hatR", hatR(izs:ize,0:1), (/1, 1, 1/))
- CALL putarrnd(fidres, "/data/metric/hatZ", hatZ(izs:ize,0:1), (/1, 1, 1/))
- CALL putarrnd(fidres, "/data/metric/hatB", hatB(izs:ize,0:1), (/1, 1, 1/))
- CALL putarrnd(fidres, "/data/metric/gradxB", gradxB(izs:ize,0:1), (/1, 1, 1/))
- CALL putarrnd(fidres, "/data/metric/gradyB", gradyB(izs:ize,0:1), (/1, 1, 1/))
- CALL putarrnd(fidres, "/data/metric/gradzB", gradzB(izs:ize,0:1), (/1, 1, 1/))
- CALL putarrnd(fidres, "/data/metric/Jacobian", Jacobian(izs:ize,0:1), (/1, 1, 1/))
- CALL putarrnd(fidres, "/data/metric/gradz_coeff", gradz_coeff(izs:ize,0:1), (/1, 1, 1/))
- CALL putarrnd(fidres, "/data/metric/Ckxky", Ckxky(ikys:ikye,ikxs:ikxe,izs:ize,0:1), (/1, 1, 3/))
- CALL putarrnd(fidres, "/data/metric/kernel_i", kernel_i(ijs_i:ije_i,ikys:ikye,ikxs:ikxe,izs:ize,0:1), (/ 1, 2, 4/))
-
- ! 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 (write_hf) THEN
- CALL creatd(fidres, rank, dims, "/data/var0d/hflux_x", "Radial part ion heat flux")
- ENDIF
- IF (cstep==0) THEN
- iframe0d=0
- ENDIF
- CALL attach(fidres,"/data/var0d/" , "frames", iframe0d)
- END IF
-
-
- ! var2d group (??)
- 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 (cstep==0) THEN
- iframe2d=0
- ENDIF
- CALL attach(fidres,"/data/var2d/" , "frames", iframe2d)
- END IF
-
- ! var3d group (electro. pot., Ni00 moment)
- IF (nsave_3d .GT. 0) THEN
- CALL creatg(fidres, "/data/var3d", "3d profiles")
- CALL creatd(fidres, rank, dims, "/data/var3d/time", "Time t*c_s/R")
- CALL creatd(fidres, rank, dims, "/data/var3d/cstep", "iteration number")
-
- IF (write_phi) CALL creatg(fidres, "/data/var3d/phi", "phi")
-
- IF (write_Na00) THEN
- IF(KIN_E)&
- CALL creatg(fidres, "/data/var3d/Ne00", "Ne00")
- CALL creatg(fidres, "/data/var3d/Ni00", "Ni00")
- IF(KIN_E)&
- CALL creatg(fidres, "/data/var3d/Nepjz", "Nepjz")
- CALL creatg(fidres, "/data/var3d/Nipjz", "Nipjz")
- ENDIF
-
- IF (write_dens) THEN
- IF(KIN_E)&
- CALL creatg(fidres, "/data/var3d/dens_e", "dens_e")
- CALL creatg(fidres, "/data/var3d/dens_i", "dens_i")
- ENDIF
-
- IF (write_fvel) THEN
- IF(KIN_E) THEN
- CALL creatg(fidres, "/data/var3d/upar_e", "upar_e")
- CALL creatg(fidres, "/data/var3d/uper_e", "uper_e")
- ENDIF
- CALL creatg(fidres, "/data/var3d/upar_i", "upar_i")
- CALL creatg(fidres, "/data/var3d/uper_i", "uper_i")
- ENDIF
-
- IF (write_temp) THEN
- IF(KIN_E) THEN
- CALL creatg(fidres, "/data/var3d/Tper_e", "Tper_e")
- CALL creatg(fidres, "/data/var3d/Tpar_e", "Tpar_e")
- CALL creatg(fidres, "/data/var3d/temp_e", "temp_e")
- ENDIF
- CALL creatg(fidres, "/data/var3d/Tper_i", "Tper_i")
- CALL creatg(fidres, "/data/var3d/Tpar_i", "Tpar_i")
- CALL creatg(fidres, "/data/var3d/temp_i", "temp_i")
- ENDIF
-
- IF (cstep==0) THEN
- iframe3d=0
- ENDIF
- CALL attach(fidres,"/data/var3d/" , "frames", iframe3d)
- END IF
-
- ! var5d group (moments)
- IF (nsave_5d .GT. 0) THEN
- 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
- IF(KIN_E)&
- CALL creatg(fidres, "/data/var5d/moments_e", "moments_e")
- CALL creatg(fidres, "/data/var5d/moments_i", "moments_i")
- ENDIF
-
- IF (write_Sapj) THEN
- IF(KIN_E)&
- 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
- IF (my_id .EQ. 0) WRITE(*,*) 'VERSION=', VERSION
- IF (my_id .EQ. 0) WRITE(*,*) 'BRANCH=', BRANCH
- IF (my_id .EQ. 0) WRITE(*,*) 'AUTHOR=', AUTHOR
- IF (my_id .EQ. 0) WRITE(*,*) 'HOST=', HOST
-
- WRITE(str,'(a,i2.2)') "/data/input"
- 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
- CALL attach(fidres, TRIM(str), "author", AUTHOR) !defined in srcinfo.h
- CALL attach(fidres, TRIM(str), "execdate", EXECDATE) !defined in srcinfo.h
- 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_iframe3d", iframe3d)
- CALL attach(fidres, TRIM(str), "start_iframe5d", iframe5d)
- CALL attach(fidres, TRIM(str), "dt", dt)
- CALL attach(fidres, TRIM(str), "tmax", tmax)
- CALL attach(fidres, TRIM(str), "nrun", nrun)
- CALL attach(fidres, TRIM(str), "cpu_time", -1)
- CALL attach(fidres, TRIM(str), "Nproc", num_procs)
- CALL attach(fidres, TRIM(str), "Np_p" , num_procs_p)
- CALL attach(fidres, TRIM(str), "Np_kx",num_procs_ky)
- CALL attach(fidres, TRIM(str), "write_gamma", write_gamma)
- CALL attach(fidres, TRIM(str), "write_hf", write_hf)
- 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 attach(fidres, TRIM(str), "write_dens", write_dens)
- CALL attach(fidres, TRIM(str), "write_fvel", write_fvel)
- CALL attach(fidres, TRIM(str), "write_temp", write_temp)
-
- CALL grid_outputinputs(fidres, str)
- CALL geometry_outputinputs(fidres, str)
- CALL diag_par_outputinputs(fidres, str)
- CALL model_outputinputs(fidres, str)
- CALL coll_outputinputs(fidres, str)
- CALL initial_outputinputs(fidres, str)
- CALL time_integration_outputinputs(fidres, str)
-
-
- ! Save STDIN (input file) of this run
- IF(jobnum .LE. 99) THEN
- WRITE(str,'(a,i2.2)') "/files/STDIN.",jobnum
- ELSE
- WRITE(str,'(a,i3.2)') "/files/STDIN.",jobnum
- END IF
-
- INQUIRE(unit=lu_in, name=fname)
- CLOSE(lu_in)
-
- CALL putfile(fidres, TRIM(str), TRIM(fname),ionode=0)
-
- ELSEIF((kstep .EQ. 0)) THEN
-
- IF(jobnum .LE. 99) THEN
- WRITE(resfile,'(a,a1,i2.2,a3)') TRIM(resfile0),'_',jobnum,'.h5'
- ELSE
- WRITE(resfile,'(a,a1,i3.2,a3)') TRIM(resfile0),'_',jobnum,'.h5'
- END IF
-
- CALL openf(resfile,fidres, 'D');
-
- ENDIF
-
- !_____________________________________________________________________________
- ! 2. Periodic diagnostics
- !
+ INQUIRE(unit=lu_in, name=input_fname)
+ CLOSE(lu_in)
+ ENDIF
IF (kstep .GE. 0) THEN
-
! Terminal info
IF (MOD(cstep, INT(1.0/dt)) == 0 .AND. (my_id .EQ. 0)) THEN
WRITE(*,"(F6.0,A,F6.0)") time,"/",tmax
ENDIF
-
- ! 2.1 0d history arrays
- IF (nsave_0d .GT. 0) THEN
- IF ( MOD(cstep, nsave_0d) == 0 ) THEN
- CALL diagnose_0d
- END IF
- END IF
-
- ! 2.2 1d profiles
- ! empty in our case
-
- ! 2.3 2d profiles
- ! empty in our case
-
-
- ! 2.3 2d profiles
- IF (nsave_3d .GT. 0) THEN
- IF (MOD(cstep, nsave_3d) == 0) THEN
- CALL diagnose_3d
- END IF
- END IF
-
- ! 2.4 3d profiles
- IF (nsave_5d .GT. 0 .AND. cstep .GT. 0) THEN
- IF (MOD(cstep, nsave_5d) == 0) THEN
- CALL diagnose_5d
- END IF
- END IF
-
- !_____________________________________________________________________________
- ! 3. Final diagnostics
-
ELSEIF (kstep .EQ. -1) THEN
- CALL cpu_time(finish)
- CALL attach(fidres, "/data/input","cpu_time",finish-start)
-
- ! make a checkpoint at last timestep if not crashed
- IF(.NOT. crashed) THEN
- IF(my_id .EQ. 0) write(*,*) 'Saving last state'
- IF (nsave_5d .GT. 0) &
- CALL diagnose_5d
- ENDIF
+ CALL cpu_time(finish)
! Display computational time cost
IF (my_id .EQ. 0) CALL display_h_min_s(finish-start)
-
- ! Close all diagnostic files
- CALL mpi_barrier(MPI_COMM_WORLD, ierr)
- CALL closef(fidres)
-
END IF
+ !! Specific diagnostic calls
+ ! CALL diagnose_full(kstep)
+ IF(nsave_5d .GT. 0) CALL diagnose_moments(kstep)
+ IF(nsave_3d .GT. 0) CALL diagnose_momspectrum(kstep)
+ IF(nsave_3d .GT. 0) CALL diagnose_fields(kstep)
+ IF(nsave_0d .GT. 0) CALL diagnose_profiler(kstep)
+ IF(nsave_0d .GT. 0) CALL diagnose_gridgeom(kstep)
+ IF(nsave_0d .GT. 0) CALL diagnose_timetraces(kstep)
CALL cpu_time(t1_diag); tc_diag = tc_diag + (t1_diag - t0_diag)
-END SUBROUTINE diagnose
-
-
-SUBROUTINE diagnose_0d
- USE basic
- USE futils, ONLY: append, attach, getatt
- USE diagnostics_par
- USE prec_const
- USE processing
- USE model, ONLY: KIN_E
-
- 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_clos", tc_clos,ionode=0)
- CALL append(fidres, "/profiler/Tc_ghost", tc_ghost,ionode=0)
- CALL append(fidres, "/profiler/Tc_coll", tc_coll,ionode=0)
- CALL append(fidres, "/profiler/Tc_poisson", tc_poisson,ionode=0)
- CALL append(fidres, "/profiler/Tc_Sapj", tc_Sapj,ionode=0)
- CALL append(fidres, "/profiler/Tc_checkfield",tc_checkfield,ionode=0)
- CALL append(fidres, "/profiler/Tc_diag", tc_diag,ionode=0)
- CALL append(fidres, "/profiler/Tc_process", tc_process,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
- IF (write_hf) THEN
- CALL compute_radial_heatflux
- CALL append(fidres, "/data/var0d/hflux_x",hflux_x,ionode=0)
- ENDIF
-END SUBROUTINE diagnose_0d
-
-
-SUBROUTINE diagnose_2d
-
- USE basic
- USE futils, ONLY: append, getatt, attach, putarrnd
- USE fields
- USE array
- USE grid, ONLY: ikxs,ikxe, ikys,ikye, Nkx, Nky, local_nkx, ikx, iky, ips_e, ips_i
- USE time_integration
- USE diagnostics_par
- USE prec_const
- USE processing
- USE model, ONLY: KIN_E
-
- IMPLICIT NONE
-
- COMPLEX(dp) :: buffer(ikys:ikye,ikxs:ikxe)
- INTEGER :: i_, root, world_rank, world_size
-
- CALL append(fidres, "/data/var2d/time", time,ionode=0)
- CALL append(fidres, "/data/var2d/cstep", real(cstep,dp),ionode=0)
- CALL getatt(fidres, "/data/var2d/", "frames",iframe2d)
- iframe2d=iframe2d+1
- CALL attach(fidres,"/data/var2d/" , "frames", iframe2d)
-
-CONTAINS
-
- SUBROUTINE write_field2d(field, text)
- USE futils, ONLY: attach, putarr
- USE grid, ONLY: ikxs,ikxe, ikys,ikye, Nkx, Nky, local_nkx
- USE prec_const
- USE basic, ONLY : comm_ky, num_procs_p, rank_p
- IMPLICIT NONE
-
- COMPLEX(dp), DIMENSION(ikys:ikye,ikxs:ikxe), INTENT(IN) :: field
- CHARACTER(*), INTENT(IN) :: text
- COMPLEX(dp) :: buffer_dist(ikys:ikye,ikxs:ikxe)
- COMPLEX(dp) :: buffer_full(1:Nky,1:Nkx)
- INTEGER :: scount, rcount
- CHARACTER(LEN=50) :: dset_name
-
- scount = (ikye-ikys+1) * (ikxe-ikxs+1)
- rcount = scount
-
- WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data/var2d", TRIM(text), iframe2d
- IF (num_procs .EQ. 1) THEN ! no data distribution
- CALL putarr(fidres, dset_name, field(ikys:ikye,ikxs:ikxe), ionode=0)
- ELSE
- CALL putarrnd(fidres, dset_name, field(ikys:ikye,ikxs:ikxe), (/1, 1/))
- ENDIF
- CALL attach(fidres, dset_name, "time", time)
-
- END SUBROUTINE write_field2d
-
-END SUBROUTINE diagnose_2d
-
-SUBROUTINE diagnose_3d
-
- USE basic
- USE futils, ONLY: append, getatt, attach, putarrnd, putarr
- USE fields
- USE array
- USE grid, ONLY: ikxs,ikxe, ikys,ikye, Nkx, Nky, local_nkx, ikx, iky, ips_e, ips_i
- USE time_integration
- USE diagnostics_par
- USE prec_const
- USE processing
- USE model, ONLY: KIN_E
+END SUBROUTINE diagnose
+SUBROUTINE init_outfile(comm,file0,file,fid)
+ USE diagnostics_par, ONLY : write_doubleprecision, diag_par_outputinputs, input_fname
+ USE basic, ONLY : my_id, jobnum, lu_in, basic_outputinputs
+ USE grid, ONLY : grid_outputinputs
+ USE geometry, ONLY : geometry_outputinputs
+ USE model, ONLY : model_outputinputs
+ USE collision, ONLY : coll_outputinputs
+ USE initial_par, ONLY : initial_outputinputs
+ USE time_integration,ONLY : time_integration_outputinputs
+ USE futils, ONLY : creatf, creatg, creatd, attach, putfile
IMPLICIT NONE
+ !input
+ INTEGER, INTENT(IN) :: comm
+ CHARACTER(len=256), INTENT(IN) :: file0
+ CHARACTER(len=256), INTENT(OUT) :: file
+ INTEGER, INTENT(OUT) :: fid
+ CHARACTER(len=256) :: str,fname
+ INCLUDE 'srcinfo.h'
- INTEGER :: i_, root, world_rank, world_size
-
- CALL append(fidres, "/data/var3d/time", time,ionode=0)
- CALL append(fidres, "/data/var3d/cstep", real(cstep,dp),ionode=0)
- CALL getatt(fidres, "/data/var3d/", "frames",iframe3d)
- iframe3d=iframe3d+1
- CALL attach(fidres,"/data/var3d/" , "frames", iframe3d)
-
- IF (write_phi) CALL write_field3d_kykxz(phi (ikys:ikye,ikxs:ikxe,izs:ize), 'phi')
-
- IF (write_Na00) THEN
- IF(KIN_E)THEN
- IF (ips_e .EQ. 1) THEN
- Ne00(ikys:ikye,ikxs:ikxe,izs:ize) = moments_e(ips_e,1,ikys:ikye,ikxs:ikxe,izs:ize,updatetlevel)
- ENDIF
- CALL write_field3d_kykxz(Ne00(ikys:ikye,ikxs:ikxe,izs:ize), 'Ne00')
- ENDIF
- IF (ips_i .EQ. 1) THEN
- Ni00(ikys:ikye,ikxs:ikxe,izs:ize) = moments_i(ips_e,1,ikys:ikye,ikxs:ikxe,izs:ize,updatetlevel)
- ENDIF
- CALL write_field3d_kykxz(Ni00(ikys:ikye,ikxs:ikxe,izs:ize), 'Ni00')
-
- CALL compute_Napjz_spectrum
- IF(KIN_E) &
- CALL write_field3d_pjz_e(Nepjz(ips_e:ipe_e,ijs_e:ije_e,izs:ize), 'Nepjz')
- CALL write_field3d_pjz_i(Nipjz(ips_i:ipe_i,ijs_i:ije_i,izs:ize), 'Nipjz')
- ENDIF
-
- !! Fuid moments
- IF (write_dens .OR. write_fvel .OR. write_temp) &
- CALL compute_fluid_moments
-
- IF (write_dens) THEN
- IF(KIN_E)&
- CALL write_field3d_kykxz(dens_e(ikys:ikye,ikxs:ikxe,izs:ize), 'dens_e')
- CALL write_field3d_kykxz(dens_i(ikys:ikye,ikxs:ikxe,izs:ize), 'dens_i')
- ENDIF
-
- IF (write_fvel) THEN
- IF(KIN_E)&
- CALL write_field3d_kykxz(upar_e(ikys:ikye,ikxs:ikxe,izs:ize), 'upar_e')
- CALL write_field3d_kykxz(upar_i(ikys:ikye,ikxs:ikxe,izs:ize), 'upar_i')
- IF(KIN_E)&
- CALL write_field3d_kykxz(uper_e(ikys:ikye,ikxs:ikxe,izs:ize), 'uper_e')
- CALL write_field3d_kykxz(uper_i(ikys:ikye,ikxs:ikxe,izs:ize), 'uper_i')
- ENDIF
-
- IF (write_temp) THEN
- IF(KIN_E)&
- CALL write_field3d_kykxz(Tpar_e(ikys:ikye,ikxs:ikxe,izs:ize), 'Tpar_e')
- CALL write_field3d_kykxz(Tpar_i(ikys:ikye,ikxs:ikxe,izs:ize), 'Tpar_i')
- IF(KIN_E)&
- CALL write_field3d_kykxz(Tper_e(ikys:ikye,ikxs:ikxe,izs:ize), 'Tper_e')
- CALL write_field3d_kykxz(Tper_i(ikys:ikye,ikxs:ikxe,izs:ize), 'Tper_i')
- IF(KIN_E)&
- CALL write_field3d_kykxz(temp_e(ikys:ikye,ikxs:ikxe,izs:ize), 'temp_e')
- CALL write_field3d_kykxz(temp_i(ikys:ikye,ikxs:ikxe,izs:ize), 'temp_i')
- ENDIF
-
-CONTAINS
-
- SUBROUTINE write_field3d_kykxz(field, text)
- IMPLICIT NONE
- COMPLEX(dp), DIMENSION(ikys:ikye,ikxs:ikxe, izs:ize), INTENT(IN) :: field
- CHARACTER(*), INTENT(IN) :: text
- CHARACTER(LEN=50) :: dset_name
- WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data/var3d", TRIM(text), iframe3d
- IF (num_procs .EQ. 1) THEN ! no data distribution
- CALL putarr(fidres, dset_name, field(ikys:ikye,ikxs:ikxe, izs:ize), ionode=0)
- ELSE
- CALL putarrnd(fidres, dset_name, field(ikys:ikye,ikxs:ikxe, izs:ize), (/1, 1, 3/))
- ENDIF
- CALL attach(fidres, dset_name, "time", time)
- END SUBROUTINE write_field3d_kykxz
-
- SUBROUTINE write_field3d_pjz_i(field, text)
- IMPLICIT NONE
- REAL(dp), DIMENSION(ips_i:ipe_i,ijs_i:ije_i,izs:ize), INTENT(IN) :: field
- CHARACTER(*), INTENT(IN) :: text
- CHARACTER(LEN=50) :: dset_name
- WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data/var3d", TRIM(text), iframe3d
- IF (num_procs .EQ. 1) THEN ! no data distribution
- CALL putarr(fidres, dset_name, field(ips_i:ipe_i,ijs_i:ije_i,izs:ize), ionode=0)
- ELSE
- CALL putarrnd(fidres, dset_name, field(ips_i:ipe_i,ijs_i:ije_i,izs:ize), (/1, 0, 3/))
- ENDIF
- CALL attach(fidres, dset_name, "time", time)
- END SUBROUTINE write_field3d_pjz_i
-
- SUBROUTINE write_field3d_pjz_e(field, text)
- IMPLICIT NONE
- REAL(dp), DIMENSION(ips_e:ipe_e,ijs_e:ije_e,izs:ize), INTENT(IN) :: field
- CHARACTER(*), INTENT(IN) :: text
- CHARACTER(LEN=50) :: dset_name
- WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data/var3d", TRIM(text), iframe3d
- IF (num_procs .EQ. 1) THEN ! no data distribution
- CALL putarr(fidres, dset_name, field(ips_e:ipe_e,ijs_e:ije_e,izs:ize), ionode=0)
- ELSE
- CALL putarrnd(fidres, dset_name, field(ips_e:ipe_e,ijs_e:ije_e,izs:ize), (/1, 0, 3/))
- ENDIF
- CALL attach(fidres, dset_name, "time", time)
- END SUBROUTINE write_field3d_pjz_e
-
-END SUBROUTINE diagnose_3d
-
-SUBROUTINE diagnose_5d
-
- USE basic
- USE futils, ONLY: append, getatt, attach, putarrnd
- USE fields
- USE array!, ONLY: Sepj, Sipj
- USE grid, ONLY: ips_e,ipe_e, ips_i, ipe_i, &
- ijs_e,ije_e, ijs_i, ije_i, &
- ikxs,ikxe,ikys,ikye,izs,ize
- USE time_integration
- USE diagnostics_par
- USE prec_const
- USE model, ONLY: KIN_E
- IMPLICIT NONE
-
- CALL append(fidres, "/data/var5d/time", time,ionode=0)
- CALL append(fidres, "/data/var5d/cstep", real(cstep,dp),ionode=0)
- CALL getatt(fidres, "/data/var5d/", "frames",iframe5d)
- iframe5d=iframe5d+1
- CALL attach(fidres,"/data/var5d/" , "frames", iframe5d)
-
- IF (write_Napj) THEN
- IF(KIN_E)&
- CALL write_field5d_e(moments_e(ips_e:ipe_e,ijs_e:ije_e,ikys:ikye,ikxs:ikxe,izs:ize,updatetlevel), 'moments_e')
- CALL write_field5d_i(moments_i(ips_i:ipe_i,ijs_i:ije_i,ikys:ikye,ikxs:ikxe,izs:ize,updatetlevel), 'moments_i')
- ENDIF
-
- IF (write_Sapj) THEN
- IF(KIN_E)&
- CALL write_field5d_e(Sepj(ips_e:ipe_e,ijs_e:ije_e,ikys:ikye,ikxs:ikxe,izs:ize), 'Sepj')
- CALL write_field5d_i(Sipj(ips_i:ipe_i,ijs_i:ije_i,ikys:ikye,ikxs:ikxe,izs:ize), 'Sipj')
- ENDIF
-
- CONTAINS
-
- SUBROUTINE write_field5d_e(field, text)
- USE futils, ONLY: attach, putarr, putarrnd
- USE grid, ONLY: ips_e,ipe_e, ijs_e,ije_e, ikxs,ikxe, ikys,ikye, izs,ize
- USE prec_const
- IMPLICIT NONE
-
- COMPLEX(dp), DIMENSION(ips_e:ipe_e,ijs_e:ije_e,ikys:ikye,ikxs:ikxe,izs:ize), INTENT(IN) :: field
- CHARACTER(*), INTENT(IN) :: text
-
- CHARACTER(LEN=50) :: dset_name
-
- WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data/var5d", TRIM(text), iframe5d
- IF (num_procs .EQ. 1) THEN
- CALL putarr(fidres, dset_name, field(ips_e:ipe_e,ijs_e:ije_e,ikys:ikye,ikxs:ikxe,izs:ize), ionode=0)
- ELSE
- CALL putarrnd(fidres, dset_name, field(ips_e:ipe_e,ijs_e:ije_e,ikys:ikye,ikxs:ikxe,izs:ize), (/1,3,5/))
- ENDIF
- CALL attach(fidres, dset_name, 'cstep', cstep)
- CALL attach(fidres, dset_name, 'time', time)
- CALL attach(fidres, dset_name, 'jobnum', jobnum)
- CALL attach(fidres, dset_name, 'dt', dt)
- CALL attach(fidres, dset_name, 'iframe2d', iframe2d)
- CALL attach(fidres, dset_name, 'iframe5d', iframe5d)
-
- END SUBROUTINE write_field5d_e
-
- SUBROUTINE write_field5d_i(field, text)
- USE futils, ONLY: attach, putarr, putarrnd
- USE grid, ONLY: ips_i,ipe_i, ijs_i,ije_i, ikxs,ikxe, ikys,ikye, izs,ize
- USE prec_const
- IMPLICIT NONE
-
- COMPLEX(dp), DIMENSION(ips_i:ipe_i,ijs_i:ije_i,ikys:ikye,ikxs:ikxe,izs:ize), INTENT(IN) :: field
- CHARACTER(*), INTENT(IN) :: text
-
- CHARACTER(LEN=50) :: dset_name
-
- WRITE(dset_name, "(A, '/', A, '/', i6.6)") "/data/var5d", TRIM(text), iframe5d
- IF (num_procs .EQ. 1) THEN
- CALL putarr(fidres, dset_name, field(ips_i:ipe_i,ijs_i:ije_i,ikys:ikye,ikxs:ikxe,izs:ize), ionode=0)
- ELSE
- CALL putarrnd(fidres, dset_name, field(ips_i:ipe_i,ijs_i:ije_i,ikys:ikye,ikxs:ikxe,izs:ize), (/1,3,5/))
- ENDIF
- CALL attach(fidres, dset_name, 'cstep', cstep)
- CALL attach(fidres, dset_name, 'time', time)
- CALL attach(fidres, dset_name, 'jobnum', jobnum)
- CALL attach(fidres, dset_name, 'dt', dt)
- CALL attach(fidres, dset_name, 'iframe2d', iframe2d)
- CALL attach(fidres, dset_name, 'iframe5d', iframe5d)
-
- END SUBROUTINE write_field5d_i
-
-END SUBROUTINE diagnose_5d
+ ! Writing output filename
+ WRITE(file,'(a,a1,i2.2,a3)') TRIM(file0) ,'_',jobnum,'.h5'
+ ! 1.1 Initial run
+ ! Main output file creation
+ IF (write_doubleprecision) THEN
+ CALL creatf(file, fid, real_prec='d', mpicomm=comm)
+ ELSE
+ CALL creatf(file, fid, mpicomm=comm)
+ END IF
+ IF (my_id .EQ. 0) WRITE(*,'(3x,a,a)') TRIM(file), ' created'
+ ! basic data group
+ CALL creatg(fid, "/data", "data")
+ ! File group
+ CALL creatg(fid, "/files", "files")
+ CALL attach(fid, "/files", "jobnum", jobnum)
+
+ ! Add input namelist variables as attributes of /data/input, defined in srcinfo.h
+ ! IF (my_id .EQ. 0) WRITE(*,*) 'VERSION=', VERSION
+ ! IF (my_id .EQ. 0) WRITE(*,*) 'BRANCH=', BRANCH
+ ! IF (my_id .EQ. 0) WRITE(*,*) 'AUTHOR=', AUTHOR
+ ! IF (my_id .EQ. 0) WRITE(*,*) 'HOST=', HOST
+
+ ! Add the code info and parameters to the file
+ WRITE(str,'(a,i2.2)') "/data/input"
+ CALL creatd(fid, 0,(/0/),TRIM(str),'Input parameters')
+ CALL attach(fid, TRIM(str), "version", VERSION) !defined in srcinfo.h
+ CALL attach(fid, TRIM(str), "branch", BRANCH) !defined in srcinfo.h
+ CALL attach(fid, TRIM(str), "author", AUTHOR) !defined in srcinfo.h
+ CALL attach(fid, TRIM(str), "execdate", EXECDATE) !defined in srcinfo.h
+ CALL attach(fid, TRIM(str), "host", HOST) !defined in srcinfo.h
+
+ CALL basic_outputinputs(fid,str)
+ CALL grid_outputinputs(fid, str)
+ CALL geometry_outputinputs(fid, str)
+ CALL diag_par_outputinputs(fid, str)
+ CALL model_outputinputs(fid, str)
+ CALL coll_outputinputs(fid, str)
+ CALL initial_outputinputs(fid, str)
+ CALL time_integration_outputinputs(fid, str)
+
+ ! Save STDIN (input file) of this run
+ IF(jobnum .LE. 99) THEN
+ WRITE(str,'(a,i2.2)') "/files/STDIN.",jobnum
+ ELSE
+ WRITE(str,'(a,i3.2)') "/files/STDIN.",jobnum
+ END IF
+ CALL putfile(fid, TRIM(str), TRIM(input_fname),ionode=0)
+END SUBROUTINE init_outfile
+
+!! Auxiliary routines hidden in headers
+! INCLUDE 'diag_headers/diagnose_full.h'
+INCLUDE 'diag_headers/diagnose_moments.h'
+INCLUDE 'diag_headers/diagnose_momspectrum.h'
+INCLUDE 'diag_headers/diagnose_fields.h'
+INCLUDE 'diag_headers/diagnose_profiler.h'
+INCLUDE 'diag_headers/diagnose_gridgeom.h'
+INCLUDE 'diag_headers/diagnose_timetraces.h'
diff --git a/src/diagnostics_par_mod.F90 b/src/diagnostics_par_mod.F90
index 59a7578fc1e41457ec658cd3eac8aeb5afbfdaa5..9cbe257dad638a9a99602f22d309e9491a1b2146 100644
--- a/src/diagnostics_par_mod.F90
+++ b/src/diagnostics_par_mod.F90
@@ -14,12 +14,19 @@ MODULE diagnostics_par
INTEGER, PUBLIC, PROTECTED :: nsave_0d, nsave_1d, nsave_2d, nsave_3d, nsave_5d
! HDF5 file
- CHARACTER(len=256), PUBLIC :: resfile0 = "outputs" ! Head of main result file name
- CHARACTER(len=256), PUBLIC :: resfile ! Main result file
- CHARACTER(len=256), PUBLIC :: rstfile ! restart result file
- INTEGER, PUBLIC :: job2load ! jobnum of the checkpoint to load
- INTEGER, PUBLIC :: fidres ! FID for resfile
- INTEGER, PUBLIC :: fidrst ! FID for restart file
+ CHARACTER(len=256), PUBLIC :: resfile,resfile0 = "outputs" ! Head of main result file name
+ CHARACTER(len=256), PUBLIC :: momfile,momfile0 = "moments" ! Head of the moment spectrum file (N_a(p,j,z))
+ CHARACTER(len=256), PUBLIC :: mspfile,mspfile0 = "moments_spectrum" ! Head of the moment spectrum file (N_a(p,j,z))
+ CHARACTER(len=256), PUBLIC :: fldfile,fldfile0 = "fields" ! Head of field (phi,A)
+ CHARACTER(len=256), PUBLIC :: ttrfile,ttrfile0 = "time_traces" ! Head of time traces (gamma_x,Q_x)
+ CHARACTER(len=256), PUBLIC :: ggmfile,ggmfile0 = "grid_geometry" ! Head of time traces (gamma_x,Q_x)
+ CHARACTER(len=256), PUBLIC :: prffile,prffile0 = "profiler" ! Head of time traces (gamma_x,Q_x)
+ CHARACTER(len=256), PUBLIC :: input_fname
+ CHARACTER(len=256), PUBLIC :: rstfile ! restart result file
+ INTEGER, PUBLIC :: job2load ! jobnum of the checkpoint to load
+ INTEGER, PUBLIC :: fidres,fidmsp,fidfld,fidttr ! FID for output
+ INTEGER, PUBLIC :: fidmom,fidggm, fidprf
+ INTEGER, PUBLIC :: fidrst ! FID for restart file
PUBLIC :: diag_par_readinputs, diag_par_outputinputs
@@ -44,21 +51,31 @@ CONTAINS
END SUBROUTINE diag_par_readinputs
- SUBROUTINE diag_par_outputinputs(fidres, str)
+ SUBROUTINE diag_par_outputinputs(fid, str)
!
! Write the input parameters to the results_xx.h5 file
!
USE prec_const
USE futils, ONLY: attach
IMPLICIT NONE
- INTEGER, INTENT(in) :: fidres
+ INTEGER, INTENT(in) :: fid
CHARACTER(len=256), INTENT(in) :: str
- CALL attach(fidres, TRIM(str), "write_doubleprecision", write_doubleprecision)
- CALL attach(fidres, TRIM(str), "nsave_0d", nsave_0d)
- CALL attach(fidres, TRIM(str), "nsave_1d", nsave_1d)
- CALL attach(fidres, TRIM(str), "nsave_2d", nsave_2d)
- CALL attach(fidres, TRIM(str), "nsave_5d", nsave_5d)
+ CALL attach(fid, TRIM(str), "write_doubleprecision", write_doubleprecision)
+ CALL attach(fid, TRIM(str), "nsave_0d", nsave_0d)
+ CALL attach(fid, TRIM(str), "nsave_1d", nsave_1d)
+ CALL attach(fid, TRIM(str), "nsave_2d", nsave_2d)
+ CALL attach(fid, TRIM(str), "nsave_3d", nsave_3d)
+ CALL attach(fid, TRIM(str), "nsave_5d", nsave_5d)
+ CALL attach(fid, TRIM(str), "write_gamma", write_gamma)
+ CALL attach(fid, TRIM(str), "write_hf", write_hf)
+ CALL attach(fid, TRIM(str), "write_phi", write_phi)
+ CALL attach(fid, TRIM(str), "write_Na00", write_Na00)
+ CALL attach(fid, TRIM(str), "write_Napj", write_Napj)
+ CALL attach(fid, TRIM(str), "write_Sapj", write_Sapj)
+ CALL attach(fid, TRIM(str), "write_dens", write_dens)
+ CALL attach(fid, TRIM(str), "write_fvel", write_fvel)
+ CALL attach(fid, TRIM(str), "write_temp", write_temp)
END SUBROUTINE diag_par_outputinputs
diff --git a/src/nonlinear_mod.F90 b/src/nonlinear_mod.F90
index 4d83dfc1667991e68db46a79d0f880cdf83b6d20..0fd980818adb9f96c87e59d6601715064387dd0a 100644
--- a/src/nonlinear_mod.F90
+++ b/src/nonlinear_mod.F90
@@ -74,14 +74,14 @@ SUBROUTINE compute_nonlinear
p_int = parray_e(ip)
jloope: DO ij = ijs_e, ije_e ! Loop over Laguerre moments
j_int=jarray_e(ij)
- IF((CLOS .EQ. 1) .AND. (p_int+2*j_int .LE. dmaxe)) THEN !compute
+ IF((CLOS .NE. 1) .OR. (p_int+2*j_int .LE. dmaxe)) THEN !compute
! Set non linear sum truncation
IF (NL_CLOS .EQ. -2) THEN
nmax = Jmaxe
ELSEIF (NL_CLOS .EQ. -1) THEN
nmax = Jmaxe-j_int
ELSE
- nmax = NL_CLOS
+ nmax = min(NL_CLOS,Jmaxe-j_int)
ENDIF
bracket_sum_r = 0._dp ! initialize sum over real nonlinear term
nloope: DO in = 1,nmax+1 ! Loop over laguerre for the sum
@@ -89,7 +89,7 @@ SUBROUTINE compute_nonlinear
F_cmpx(ikxs:ikxe,ikxs:ikxe) = phi(ikxs:ikxe,ikxs:ikxe,iz) * kernel_e(in, ikxs:ikxe,ikxs:ikxe, iz, eo)
! Second convolution terms
G_cmpx(ikxs:ikxe,ikxs:ikxe) = 0._dp ! initialization of the sum
- smax = MIN( (in-1)+(ij-1), jmaxe );
+ smax = MIN( (in-1)+(ij-1), Jmaxe );
DO is = 1, smax+1 ! sum truncation on number of moments
G_cmpx(ikxs:ikxe,ikxs:ikxe) = G_cmpx(ikxs:ikxe,ikxs:ikxe) + &
dnjs(in,ij,is) * moments_e(ip,is,ikxs:ikxe,ikxs:ikxe,iz,updatetlevel)
@@ -120,14 +120,14 @@ zloopi: DO iz = izs,ize
eo = MODULO(parray_i(ip),2)
jloopi: DO ij = ijs_i, ije_i ! Loop over Laguerre moments
j_int=jarray_i(ij)
- IF((CLOS .EQ. 1) .AND. (p_int+2*j_int .LE. dmaxi)) THEN !compute
+ IF((CLOS .NE. 1) .OR. (p_int+2*j_int .LE. dmaxi)) THEN !compute
! Set non linear sum truncation
IF (NL_CLOS .EQ. -2) THEN
nmax = Jmaxi
ELSEIF (NL_CLOS .EQ. -1) THEN
nmax = Jmaxi-j_int
ELSE
- nmax = NL_CLOS
+ nmax = min(NL_CLOS,Jmaxi-j_int)
ENDIF
bracket_sum_r = 0._dp ! initialize sum over real nonlinear term
nloopi: DO in = 1,nmax+1 ! Loop over laguerre for the sum
diff --git a/src/ppinit.F90 b/src/ppinit.F90
index 1a662babc6bc41ab9188b17ded43759e49d0bffc..55db146013a68d8f93ed35fe625249bdbb27d4c2 100644
--- a/src/ppinit.F90
+++ b/src/ppinit.F90
@@ -65,6 +65,10 @@ SUBROUTINE ppinit
CALL MPI_COMM_RANK(comm_ky, rank_ky, ierr)
CALL MPI_COMM_RANK(comm_z, rank_z, ierr)
+ ! 2D communicator
+ CALL MPI_CART_SUB (comm0, (/.TRUE.,.FALSE.,.TRUE./), comm_pz, ierr)
+ CALL MPI_CART_SUB (comm0, (/.FALSE.,.TRUE.,.TRUE./), comm_kyz, ierr)
+
! Find neighbours
CALL MPI_CART_SHIFT(comm0, 0, 1, nbr_L, nbr_R, ierr) !left right neighbours
CALL MPI_CART_SHIFT(comm0, 1, 1, nbr_B, nbr_T, ierr) !bottom top neighbours
diff --git a/wk/analysis_3D.m b/wk/analysis_3D.m
index f8ea45ee90443e512492db571c6abc415b2d665f..07f4a3d06a737cf8ecb857abad502c3e97de4024 100644
--- a/wk/analysis_3D.m
+++ b/wk/analysis_3D.m
@@ -42,18 +42,18 @@ if 0
% Options
options.INTERP = 0;
options.POLARPLOT = 0;
-% options.NAME = '\phi';
-options.NAME = 'N_i^{00}';
+options.NAME = '\phi';
+% options.NAME = 'N_i^{00}';
% options.NAME = 'v_y';
% options.NAME = 'n_i^{NZ}';
% options.NAME = '\Gamma_x';
% options.NAME = 'n_i';
-options.PLAN = 'kxky';
+options.PLAN = 'xy';
% options.NAME = 'f_e';
% options.PLAN = 'sx';
options.COMP = 9;
% options.TIME = dat.Ts5D;
-options.TIME = 200:1:600;
+options.TIME = 300:1:4500;
data.EPS = 0.1;
data.a = data.EPS * 2000;
create_film(data,options,'.gif')
@@ -62,7 +62,7 @@ end
if 0
%% 2D snapshots
% Options
-options.INTERP = 1;
+options.INTERP = 0;
options.POLARPLOT = 0;
options.AXISEQUAL = 1;
options.NAME = '\phi';
@@ -71,11 +71,11 @@ options.NAME = '\phi';
% options.NAME = 'T_i';
% options.NAME = '\Gamma_x';
% options.NAME = 'k^2n_e';
-options.PLAN = 'xz';
-% options.NAME = 'f_e';
+options.PLAN = 'kxky';
+% options.NAME = 'f_i';
% options.PLAN = 'sx';
options.COMP = 'avg';
-options.TIME = [260:265];
+options.TIME = [300 350 400];
data.a = data.EPS * 2e3;
fig = photomaton(data,options);
save_figure(data,fig)
@@ -100,7 +100,7 @@ if 0
options.SPAR = gene_data.vp';
options.XPERP = gene_data.mu';
options.Z = 'avg';
-options.T = 340;
+options.T = 900;
options.PLT_FCT = 'contour';
options.ONED = 0;
options.non_adiab = 1;
@@ -113,16 +113,16 @@ end
if 0
%% Hermite-Laguerre spectrum
% options.TIME = 'avg';
-options.P2J = 1;
+options.P2J = 0;
options.ST = 0;
options.PLOT_TYPE = 'space-time';
options.NORMALIZED = 0;
-options.JOBNUM = 03;
-options.TIME = [200 500];
+options.JOBNUM = 0;
+options.TIME = [300 500];
options.specie = 'i';
options.compz = 'avg';
-% fig = show_moments_spectrum(data,options);
-fig = show_napjz(data,options);
+fig = show_moments_spectrum(data,options);
+% fig = show_napjz(data,options);
save_figure(data,fig)
end
diff --git a/wk/analysis_header.m b/wk/analysis_header.m
index 5188876d351ac869d5c68bf3f20f7cd0363c5361..012bd79ef5a127ff3c433c0e7b135b93b9211238 100644
--- a/wk/analysis_header.m
+++ b/wk/analysis_header.m
@@ -5,7 +5,8 @@ helazdir = '/home/ahoffman/HeLaZ/';
outfile ='';
outfile ='';
outfile ='';
-outfile ='shearless_cyclone/128x128x16xdmax_L_120_CBC_1.0';
+% outfile ='shearless_cyclone/128x128x16xdmax_6_L_120_CBC_1.0';
+outfile ='shearless_cyclone/128x128x16xdmax_8_L_120_CBC_1.0';
% outfile ='quick_run/CLOS_1_64x64_5x3_L_120_kN_2.0_kT_0.5_nu_1e-01_SGGK';
% outfile ='pedestal/64x64x16x2x1_L_300_LnT_20_nu_0.1';
% outfile ='quick_run/32x32x16_5x3_L_300_q0_2.5_e_0.18_kN_20_kT_20_nu_1e-01_DGGK';
diff --git a/wk/gene_analysis_3D.m b/wk/gene_analysis_3D.m
index 5716569df86369e5569db594627abf3b02a7bf96..5f83d870122a18e293cae7618a640206fa649231 100644
--- a/wk/gene_analysis_3D.m
+++ b/wk/gene_analysis_3D.m
@@ -26,7 +26,7 @@ options.INTERP = 0;
options.POLARPLOT = 0;
options.AXISEQUAL = 1;
% options.NAME = 'Q_x';
-options.NAME = 'n_i';
+options.NAME = '\phi';
% options.NAME = 'T_i';
% options.NAME = '\Gamma_x';
% options.NAME = 'k^2n_e';
@@ -34,7 +34,7 @@ options.PLAN = 'xy';
% options.NAME ='f_e';
% options.PLAN = 'sx';
options.COMP = 'avg';
-options.TIME = [200];
+options.TIME = [500];
gene_data.a = data.EPS * 2000;
fig = photomaton(gene_data,options);
save_figure(gene_data,fig)
diff --git a/wk/quick_run.m b/wk/quick_run.m
index b3f5829ba476314773caf530efb6ccdc289ad775..f5a8c35d3367a5850a2ab1112a06574d467f67cd 100644
--- a/wk/quick_run.m
+++ b/wk/quick_run.m
@@ -7,7 +7,7 @@ RUN = 1; % To run or just to load
addpath(genpath('../matlab')) % ... add
default_plots_options
HELAZDIR = '/home/ahoffman/HeLaZ/';
-EXECNAME = 'helaz3.12';
+EXECNAME = 'helaz3';
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
%% Set Up parameters
CLUSTER.TIME = '99:00:00'; % allocation time hh:mm:ss
@@ -21,25 +21,25 @@ K_E = 0.0; % Electrostat '''
SIGMA_E = 0.0233380; % mass ratio sqrt(m_a/m_i) (correct = 0.0233380)
KIN_E = 0; % 1: kinetic electrons, 2: adiabatic electrons
%% GRID PARAMETERS
-PMAXE = 8; % Hermite basis size of electrons
-JMAXE = 4; % Laguerre "
-PMAXI = 8; % " ions
-JMAXI = 4; % "
+PMAXE = 4; % Hermite basis size of electrons
+JMAXE = 2; % Laguerre "
+PMAXI = 4; % " ions
+JMAXI = 2; % "
NX = 1; % real space x-gridpoints
-NY = 20; % '' y-gridpoints
-LX = 120; % Size of the squared frequency domain
-LY = 120; % Size of the squared frequency domain
-NZ = 16; % number of perpendicular planes (parallel grid)
+NY = 24; % '' y-gridpoints
+LX = 100; % Size of the squared frequency domain
+LY = 100; % Size of the squared frequency domain
+NZ = 32; % number of perpendicular planes (parallel grid)
NPOL = 1;
SG = 0; % Staggered z grids option
%% GEOMETRY
-GEOMETRY= 'Z-pinch'; % Z-pinch overwrites q0, shear and eps
-% GEOMETRY= 's-alpha';
+% GEOMETRY= 'Z-pinch'; % Z-pinch overwrites q0, shear and eps
+GEOMETRY= 's-alpha';
Q0 = 1.4; % safety factor
SHEAR = 0.0; % magnetic shear (Not implemented yet)
EPS = 0.18; % inverse aspect ratio
%% TIME PARMETERS
-TMAX = 50; % Maximal time unit
+TMAX = 10; % Maximal time unit
DT = 2e-2; % Time step
SPS0D = 1; % Sampling per time unit for 2D arrays
SPS2D = 0; % Sampling per time unit for 2D arrays
@@ -90,7 +90,7 @@ system(['rm fort*.90']);
% Run linear simulation
if RUN
system(['cd ../results/',SIMID,'/',PARAMS,'/; time mpirun -np 4 ',HELAZDIR,'bin/',EXECNAME,' 1 4 1 0; cd ../../../wk'])
-% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 2 ',HELAZDIR,'bin/',EXECNAME,' 2 1 1 0; cd ../../../wk'])
+% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 1 ',HELAZDIR,'bin/',EXECNAME,' 1 1 1 0; cd ../../../wk'])
% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 4 ',HELAZDIR,'bin/',EXECNAME,' 1 2 2 0; cd ../../../wk'])
% system(['cd ../results/',SIMID,'/',PARAMS,'/; mpirun -np 6 ',HELAZDIR,'bin/',EXECNAME,' 1 3 2 0; cd ../../../wk'])
end
@@ -104,7 +104,7 @@ JOBNUMMIN = 00; JOBNUMMAX = 00;
data = compile_results(LOCALDIR,JOBNUMMIN,JOBNUMMAX); %Compile the results from first output found to JOBNUMMAX if existing
%% Short analysis
-if 1
+if 0
%% linear growth rate (adapted for 2D zpinch and fluxtube)
trange = [0.5 1]*data.Ts3D(end);
nplots = 1;
@@ -114,12 +114,30 @@ end
if 0
%% Ballooning plot
options.time_2_plot = data.Ts3D(end);
-options.kymodes = [0.2 0.5 0.7];
+options.kymodes = [0.4 0.5 0.6];
options.normalized = 1;
options.field = 'phi';
fig = plot_ballooning(data,options);
end
+if 1
+%% Hermite-Laguerre spectrum
+% options.TIME = 'avg';
+options.P2J = 1;
+options.ST = 1;
+options.PLOT_TYPE = 'space-time';
+% options.PLOT_TYPE = 'Tavg-1D';
+% options.PLOT_TYPE = 'Tavg-2D';
+options.NORMALIZED = 0;
+options.JOBNUM = 0;
+options.TIME = [0 50];
+options.specie = 'i';
+options.compz = 'avg';
+% fig = show_moments_spectrum(data,options);
+fig = show_napjz(data,options);
+save_figure(data,fig)
+end
+
if 0
%% linear growth rate for 3D Zpinch (kz fourier transform)
trange = [0.5 1]*data.Ts3D(end);