Checkpoint loading are done on output file now, bug in write 5D corrected

src/diagnose.F90

@@ -382,7 +382,12 @@ SUBROUTINE diagnose_5d
      ELSE
        CALL putarr(fidres, dset_name, field(ips_e:ipe_e,ijs_e:ije_e,ikrs:ikre,ikzs:ikze), pardim=3)
      ENDIF
-     CALL attach(fidres, dset_name, "time", time)
+     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
 
@@ -403,8 +408,13 @@ SUBROUTINE diagnose_5d
       ELSE
         CALL putarr(fidres, dset_name, field(ips_i:ipe_i,ijs_i:ije_i,ikrs:ikre,ikzs:ikze), pardim=3)
       ENDIF
-      CALL attach(fidres, dset_name, "time", time)
-
+     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

src/inital.F90

@@ -22,14 +22,14 @@ SUBROUTINE inital
   !!!!!! Set the moments arrays Nepj, Nipj !!!!!!
   ! WRITE(*,*) 'Init moments'
   IF ( RESTART ) THEN
-    CALL load_cp
+    CALL load_output
+    ! CALL load_cp
   ELSE
     CALL init_moments
     !!!!!! Set phi !!!!!!
-    IF (my_id .EQ. 0) WRITE(*,*) 'Init phi'
-    CALL poisson
   ENDIF
-
+  IF (my_id .EQ. 0) WRITE(*,*) 'Init phi'
+  CALL poisson
 
   !!!!!! Set Sepj, Sipj and dnjs coeff table !!!!!!
   IF ( NON_LIN ) THEN;
@@ -46,10 +46,6 @@ SUBROUTINE inital
     IF (my_id .EQ. 0) WRITE(*,*) '..done'
   ENDIF
 
-  ! IF (my_id .EQ. 0) WRITE(*,*) 'Set closure model..'
-  ! CALL apply_closure_model
-  ! IF (my_id .EQ. 0) WRITE(*,*) '..done'
-
 END SUBROUTINE inital
 !******************************************************************************!
 
@@ -138,6 +134,98 @@ SUBROUTINE init_moments
 END SUBROUTINE init_moments
 !******************************************************************************!
 
+!******************************************************************************!
+!!!!!!! Load moments from a previous output file
+!******************************************************************************!
+SUBROUTINE load_output
+  USE basic
+  USE futils,          ONLY: openf, closef, getarr, getatt, isgroup, isdataset
+  USE grid
+  USE fields
+  USE diagnostics_par
+  USE time_integration
+  IMPLICIT NONE
+
+  INTEGER :: rank, sz_, n_
+  INTEGER :: dims(1) = (/0/)
+  CHARACTER(LEN=50) :: dset_name
+  INTEGER :: pmaxe_cp, jmaxe_cp, pmaxi_cp, jmaxi_cp
+  COMPLEX(dp), DIMENSION(:,:,:,:), ALLOCATABLE :: moments_e_cp
+  COMPLEX(dp), DIMENSION(:,:,:,:), ALLOCATABLE :: moments_i_cp
+  ! Checkpoint filename
+  WRITE(rstfile,'(a,a1,i2.2,a3)') TRIM(resfile0),'_',job2load,'.h5'
+
+  IF (my_id .EQ. 0) WRITE(*,'(3x,a)') "Resume from ", rstfile
+  ! Open file
+  CALL openf(rstfile, fidrst,mpicomm=MPI_COMM_WORLD)
+  ! Get the checkpoint moments degrees to allocate memory
+  CALL getatt(fidrst,"/data/input/" , "pmaxe", pmaxe_cp)
+  CALL getatt(fidrst,"/data/input/" , "jmaxe", jmaxe_cp)
+  CALL getatt(fidrst,"/data/input/" , "pmaxi", pmaxi_cp)
+  CALL getatt(fidrst,"/data/input/" , "jmaxi", jmaxi_cp)
+  IF (my_id .EQ. 0) WRITE(*,*) "Pe_cp = ", pmaxe_cp
+  IF (my_id .EQ. 0) WRITE(*,*) "Je_cp = ", jmaxe_cp
+
+  ! Allocate the required size to load checkpoints moments
+  CALL allocate_array(moments_e_cp, 1,pmaxe_cp+1, 1,jmaxe_cp+1, ikrs,ikre, ikzs,ikze)
+  CALL allocate_array(moments_i_cp, 1,pmaxi_cp+1, 1,jmaxi_cp+1, ikrs,ikre, ikzs,ikze)
+  ! Find the last results of the checkpoint file by iteration
+  n_ = 1
+  WRITE(dset_name, "(A, '/', i6.6)") "/data/var5d/moments_e", n_ ! start with moments_e/000001
+  DO WHILE (isdataset(fidrst, dset_name)) ! If n_ is not a file we stop the loop
+    n_ = n_ + 1
+    WRITE(dset_name, "(A, '/', i6.6)") "/data/var5d/moments_e", n_ ! updtate file number
+  ENDDO
+  n_ = n_ - 1 ! n_ is not a file so take the previous one n_-1
+
+  ! Read state of system from checkpoint file
+  WRITE(dset_name, "(A, '/', i6.6)") "/data/var5d/moments_e", n_
+  CALL getarr(fidrst, dset_name, moments_e_cp(1:pmaxe_cp+1, 1:jmaxe_cp+1, ikrs:ikre, ikzs:ikze),pardim=3)
+  WRITE(dset_name, "(A, '/', i6.6)") "/data/var5d/moments_i", n_
+  CALL getarr(fidrst, dset_name, moments_i_cp(1:pmaxi_cp+1, 1:jmaxi_cp+1, ikrs:ikre, ikzs:ikze),pardim=3)
+
+  ! Initialize simulation moments array with checkpoints ones
+  ! (they may have a larger number of polynomials, set to 0 at the begining)
+  moments_e = 0._dp; moments_i = 0._dp
+  DO ip=1,pmaxe_cp+1 
+    DO ij=1,jmaxe_cp+1
+      DO ikr=ikrs,ikre
+        DO ikz=ikzs,ikze
+          moments_e(ip,ij,ikr,ikz,:) = moments_e_cp(ip,ij,ikr,ikz)
+        ENDDO
+      ENDDO
+    ENDDO
+  ENDDO
+
+  DO ip=1,pmaxi_cp+1
+    DO ij=1,jmaxi_cp+1
+      DO ikr=ikrs,ikre
+        DO ikz=ikzs,ikze
+          moments_i(ip,ij,ikr,ikz,:) = moments_i_cp(ip,ij,ikr,ikz)
+        ENDDO
+      ENDDO
+    ENDDO
+  ENDDO
+  ! Deallocate checkpoint arrays
+  DEALLOCATE(moments_e_cp)
+  DEALLOCATE(moments_i_cp)
+
+  ! Read time dependent attributes to continue simulation
+  CALL getatt(fidrst, dset_name, 'cstep', cstep)
+  CALL getatt(fidrst, dset_name, 'time', time)
+  CALL getatt(fidrst, dset_name, 'jobnum', jobnum)
+  jobnum = jobnum+1
+  CALL getatt(fidrst, dset_name, 'iframe2d',iframe2d)
+  CALL getatt(fidrst, dset_name, 'iframe5d',iframe5d)
+  iframe2d = iframe2d-1; iframe5d = iframe5d-1
+
+  CALL closef(fidrst)
+
+  IF (my_id .EQ. 0) WRITE(*,'(3x,a)') "Reading from restart file "//TRIM(rstfile)//" completed!"
+
+END SUBROUTINE load_output
+!******************************************************************************!
+
 !******************************************************************************!
 !!!!!!! Load moments from a previous save
 !******************************************************************************!
@@ -232,6 +320,7 @@ SUBROUTINE load_cp
 END SUBROUTINE load_cp
 !******************************************************************************!
 
+
 !******************************************************************************!
 !!!!!!! Build the Laguerre-Laguerre coupling coefficient table for nonlin
 !******************************************************************************!
@@ -287,7 +376,7 @@ SUBROUTINE evaluate_kernels
   sigmae2_taue_o2 = sigma_e**2 * tau_e/2._dp ! factor of the Kernel argument
 
   factj = 1.0 ! Start of the recursive factorial
-  DO ij = ijs_e, ije_e
+  DO ij = 1, jmaxe+1
     j_int = jarray_e(ij)
     j_dp = REAL(j_int,dp) ! REAL of degree
 
@@ -310,12 +399,21 @@ SUBROUTINE evaluate_kernels
       ENDDO
     ENDDO
   ENDDO
+  ! Kernels closure
+  DO ikr = ikrs,ikre
+    kr     = krarray(ikr)
+    DO ikz = ikzs,ikze
+      kz    = kzarray(ikz)
+      be_2  =  (kr**2 + kz**2) * sigmae2_taue_o2
+      kernel_e(ijeg_e,ikr,ikz) = be_2/(real(ijeg_e,dp))*kernel_e(ije_e,ikr,ikz)
+    ENDDO
+  ENDDO
 
   !!!!! Ion kernels !!!!!
   sigmai2_taui_o2 = sigma_i**2 * tau_i/2._dp ! (b_a/2)^2 = (kperp sqrt(2 tau_a) sigma_a/2)^2
 
   factj = 1.0 ! Start of the recursive factorial
-  DO ij = ijs_i, ije_i
+  DO ij = 1, jmaxi+1
     j_int = jarray_e(ij)
     j_dp = REAL(j_int,dp) ! REAL of degree
 
@@ -338,6 +436,14 @@ SUBROUTINE evaluate_kernels
       ENDDO
     ENDDO
   ENDDO
-
+  ! Kernels closure
+  DO ikr = ikrs,ikre
+    kr     = krarray(ikr)
+    DO ikz = ikzs,ikze
+      kz    = kzarray(ikz)
+      bi_2  =  (kr**2 + kz**2) * sigmai2_taui_o2
+      kernel_i(ijeg_i,ikr,ikz) = bi_2/(real(ijeg_i,dp))*kernel_e(ije_i,ikr,ikz)
+    ENDDO
+  ENDDO
 END SUBROUTINE evaluate_kernels
 !******************************************************************************!