From 784baff12d6dbe5dfe1e5e04e7d7a2d8f8e8e486 Mon Sep 17 00:00:00 2001
From: Antoine Cyril David Hoffmann <ahoffman@spcpc606.epfl.ch>
Date: Fri, 19 Feb 2021 11:23:48 +0100
Subject: [PATCH] Checkpoint loading are done on output file now, bug in write
5D corrected
---
src/diagnose.F90 | 16 ++++--
src/inital.F90 | 128 +++++++++++++++++++++++++++++++++++++++++++----
2 files changed, 130 insertions(+), 14 deletions(-)
diff --git a/src/diagnose.F90 b/src/diagnose.F90
index 1b1b6c7b..da7a71cb 100644
--- a/src/diagnose.F90
+++ b/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
diff --git a/src/inital.F90 b/src/inital.F90
index d3ad1c45..cf8c4640 100644
--- a/src/inital.F90
+++ b/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
!******************************************************************************!
--
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