From 7ee703feb0b9b4db40801643cf5d5bbc236d8b76 Mon Sep 17 00:00:00 2001
From: Antoine Cyril David Hoffmann <ahoffman@spcpc606.epfl.ch>
Date: Fri, 8 Apr 2022 13:51:33 +0200
Subject: [PATCH] xphij arrays and fort.90 + marconi batch script
---
.gitignore | 4 +-
batch_script.sh | 13 +++++++
fort.90 | 80 ++++++++++++++++++++++++++++++++++++++
src/array_mod.F90 | 3 +-
src/memory.F90 | 11 ++++--
src/moments_eq_rhs_mod.F90 | 12 +++---
src/numerics_mod.F90 | 36 +++++++++++++----
src/restarts_mod.F90 | 4 +-
wk/analysis_3D.m | 2 +-
wk/analysis_header.m | 2 +-
10 files changed, 143 insertions(+), 24 deletions(-)
create mode 100644 batch_script.sh
create mode 100644 fort.90
diff --git a/.gitignore b/.gitignore
index 963a466a..c03a3145 100644
--- a/.gitignore
+++ b/.gitignore
@@ -34,7 +34,7 @@ iCa/
*.out
src/srcinfo.h
src/srcinfo/srcinfo.h
-fort*.90
+*/fort*.90
local/
-*.sh
+*/*.sh
Gallery/
diff --git a/batch_script.sh b/batch_script.sh
new file mode 100644
index 00000000..34ffd2e7
--- /dev/null
+++ b/batch_script.sh
@@ -0,0 +1,13 @@
+#!/bin/bash
+#SBATCH --job-name=HeLaZ
+#SBATCH --time=24:00:00
+#SBATCH --nodes=1
+#SBATCH --cpus-per-task=1
+#SBATCH --ntasks-per-node=48
+#SBATCH --mem=64GB
+#SBATCH --error=err.txt
+#SBATCH --output=out.txt
+#SBATCH --account=FUA36_TSVVT422
+#SBATCH --partition=skl_fua_dbg
+module load autoload hdf5 fftw
+srun --cpu-bind=cores ./../../../bin/helaz3 2 12 2
diff --git a/fort.90 b/fort.90
new file mode 100644
index 00000000..97a73515
--- /dev/null
+++ b/fort.90
@@ -0,0 +1,80 @@
+&BASIC
+ nrun = 100000000
+ dt = 0.01
+ tmax = 200
+ maxruntime = 356400
+/
+&GRID
+ pmaxe = 4
+ jmaxe = 2
+ pmaxi = 4
+ jmaxi = 2
+ Nx = 128
+ Lx = 100
+ Ny = 128
+ Ly = 120
+ Nz = 16
+ q0 = 1.4
+ shear = 0
+ eps = 0.18
+ SG = .t.
+/
+&OUTPUT_PAR
+ nsave_0d = 200
+ nsave_1d = -1
+ nsave_2d = 200
+ nsave_3d = 200
+ nsave_5d = 2000
+ write_doubleprecision = .f.
+ write_gamma = .t.
+ write_hf = .t.
+ write_phi = .t.
+ write_Na00 = .t.
+ write_Napj = .t.
+ write_Sapj = .f.
+ write_dens = .t.
+ write_temp = .t.
+ job2load = -1
+/
+&MODEL_PAR
+ ! Collisionality
+ CLOS = 0
+ NL_CLOS = 0
+ LINEARITY = 'nonlinear'
+ KIN_E = .f.
+ mu_x = 0.0
+ mu_y = 0.0
+ mu_z = 0.2
+ mu_p = 0
+ mu_j = 0
+ nu = 0.01
+ tau_e = 1
+ tau_i = 1
+ sigma_e = 0.023338
+ sigma_i = 1
+ q_e = -1
+ q_i = 1
+ K_n = 2.22
+ K_T = 6.96
+ K_E = 0
+ GradB = 1
+ CurvB = 1
+ lambdaD = 0
+/
+&COLLISION_PAR
+ collision_model = 'DG'
+ gyrokin_CO = .true.
+ interspecies = .true.
+! mat_file = '../../../iCa/gk_sugama_P_20_J_10_N_150_kpm_8.0.h5'
+ mat_file = '../../../iCa/gk_pitchangle_8_P_20_J_10_N_150_kpm_8.0.h5'
+/
+&INITIAL_CON
+ INIT_OPT = 'ppj'
+ ACT_ON_MODES = 'donothing'
+ init_background = 0
+ init_noiselvl = 0.00005
+ iseed = 42
+/
+&TIME_INTEGRATION_PAR
+ numerical_scheme = 'RK4'
+/
diff --git a/src/array_mod.F90 b/src/array_mod.F90
index bafdc82e..841f80d2 100644
--- a/src/array_mod.F90
+++ b/src/array_mod.F90
@@ -46,7 +46,8 @@ MODULE array
REAL(dp), DIMENSION(:), ALLOCATABLE :: xnipp1j, xnipm1j, xnipp2j, xnipm2j, xnipjp1, xnipjm1
REAL(dp), DIMENSION(:,:), ALLOCATABLE :: ynipp1j, ynipm1j, ynipp1jm1, ynipm1jm1 ! mirror lin coeff for non adiab mom
REAL(dp), DIMENSION(:,:), ALLOCATABLE :: zNipm1j, zNipm1jp1, zNipm1jm1 ! mirror lin coeff for adiab mom
- REAL(dp), DIMENSION(:,:), ALLOCATABLE :: xphij, xphijp1, xphijm1
+ REAL(dp), DIMENSION(:,:), ALLOCATABLE :: xphij_e, xphijp1_e, xphijm1_e
+ REAL(dp), DIMENSION(:,:), ALLOCATABLE :: xphij_i, xphijp1_i, xphijm1_i
! Geometrical operators
! Curvature
REAL(dp), DIMENSION(:,:,:,:), ALLOCATABLE :: Ckxky ! dimensions: kx, ky, z, odd/even p
diff --git a/src/memory.F90 b/src/memory.F90
index 72d8331f..5c94ee7e 100644
--- a/src/memory.F90
+++ b/src/memory.F90
@@ -86,9 +86,14 @@ SUBROUTINE memory
CALL allocate_array( dnjs, 1,maxj+1, 1,maxj+1, 1,maxj+1)
! elect. pot. linear terms
- CALL allocate_array( xphij, ips_i,ipe_i, ijs_i,ije_i)
- CALL allocate_array( xphijp1, ips_i,ipe_i, ijs_i,ije_i)
- CALL allocate_array( xphijm1, ips_i,ipe_i, ijs_i,ije_i)
+ IF (KIN_E) THEN
+ CALL allocate_array( xphij_e, ips_e,ipe_e, ijs_e,ije_e)
+ CALL allocate_array( xphijp1_e, ips_e,ipe_e, ijs_e,ije_e)
+ CALL allocate_array( xphijm1_e, ips_e,ipe_e, ijs_e,ije_e)
+ ENDIF
+ CALL allocate_array( xphij_i, ips_i,ipe_i, ijs_i,ije_i)
+ CALL allocate_array( xphijp1_i, ips_i,ipe_i, ijs_i,ije_i)
+ CALL allocate_array( xphijm1_i, ips_i,ipe_i, ijs_i,ije_i)
! Curvature and geometry
CALL allocate_array( Ckxky, ikxs,ikxe, ikys,ikye,izgs,izge,0,1)
diff --git a/src/moments_eq_rhs_mod.F90 b/src/moments_eq_rhs_mod.F90
index 87380472..0934b533 100644
--- a/src/moments_eq_rhs_mod.F90
+++ b/src/moments_eq_rhs_mod.F90
@@ -99,9 +99,9 @@ SUBROUTINE moments_eq_rhs_e
Tmir = Tnepp1j + Tnepp1jm1 + Tnepm1j + Tnepm1jm1 + Unepm1j + Unepm1jp1 + Unepm1jm1
!! Electrical potential term
IF ( p_int .LE. 2 ) THEN ! kronecker p0 p1 p2
- Tphi = (xphij (ip,ij)*kernel_e(ij ,ikx,iky,iz,eo) &
- + xphijp1(ip,ij)*kernel_e(ij+1,ikx,iky,iz,eo) &
- + xphijm1(ip,ij)*kernel_e(ij-1,ikx,iky,iz,eo))*phi(ikx,iky,iz)
+ Tphi = (xphij_i (ip,ij)*kernel_e(ij ,ikx,iky,iz,eo) &
+ + xphijp1_i(ip,ij)*kernel_e(ij+1,ikx,iky,iz,eo) &
+ + xphijm1_i(ip,ij)*kernel_e(ij-1,ikx,iky,iz,eo))*phi(ikx,iky,iz)
ELSE
Tphi = 0._dp
ENDIF
@@ -227,9 +227,9 @@ SUBROUTINE moments_eq_rhs_i
!! Electrical potential term
IF ( p_int .LE. 2 ) THEN ! kronecker p0 p1 p2
- Tphi = (xphij (ip,ij)*kernel_i(ij ,ikx,iky,iz,eo) &
- + xphijp1(ip,ij)*kernel_i(ij+1,ikx,iky,iz,eo) &
- + xphijm1(ip,ij)*kernel_i(ij-1,ikx,iky,iz,eo))*phi(ikx,iky,iz)
+ Tphi = (xphij_i (ip,ij)*kernel_i(ij ,ikx,iky,iz,eo) &
+ + xphijp1_i(ip,ij)*kernel_i(ij+1,ikx,iky,iz,eo) &
+ + xphijm1_i(ip,ij)*kernel_i(ij-1,ikx,iky,iz,eo))*phi(ikx,iky,iz)
ELSE
Tphi = 0._dp
ENDIF
diff --git a/src/numerics_mod.F90 b/src/numerics_mod.F90
index d8e2b178..ba8d0653 100644
--- a/src/numerics_mod.F90
+++ b/src/numerics_mod.F90
@@ -227,6 +227,27 @@ SUBROUTINE compute_lin_coeff
ENDDO
!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!
!! ES linear coefficients for moment RHS !!!!!!!!!!
+ IF (KIN_E) THEN
+ DO ip = ips_e, ipe_e
+ p_int= parray_e(ip) ! Hermite degree
+ DO ij = ijs_e, ije_e
+ j_int= jarray_e(ij) ! REALof Laguerre degree
+ j_dp = REAL(j_int,dp) ! REALof Laguerre degree
+ !! Electrostatic potential pj terms
+ IF (p_int .EQ. 0) THEN ! kronecker p0
+ xphij_e(ip,ij) =+K_n + 2.*j_dp*K_T
+ xphijp1_e(ip,ij) =-K_T*(j_dp+1._dp)
+ xphijm1_e(ip,ij) =-K_T* j_dp
+ ELSE IF (p_int .EQ. 2) THEN ! kronecker p2
+ xphij_e(ip,ij) =+K_T/SQRT2
+ xphijp1_e(ip,ij) = 0._dp; xphijm1_e(ip,ij) = 0._dp;
+ ELSE
+ xphij_e(ip,ij) = 0._dp; xphijp1_e(ip,ij) = 0._dp
+ xphijm1_e(ip,ij) = 0._dp;
+ ENDIF
+ ENDDO
+ ENDDO
+ ENDIF
DO ip = ips_i, ipe_i
p_int= parray_i(ip) ! Hermite degree
DO ij = ijs_i, ije_i
@@ -234,19 +255,18 @@ SUBROUTINE compute_lin_coeff
j_dp = REAL(j_int,dp) ! REALof Laguerre degree
!! Electrostatic potential pj terms
IF (p_int .EQ. 0) THEN ! kronecker p0
- xphij(ip,ij) =+K_n + 2.*j_dp*K_T
- xphijp1(ip,ij) =-K_T*(j_dp+1._dp)
- xphijm1(ip,ij) =-K_T* j_dp
+ xphij_i(ip,ij) =+K_n + 2.*j_dp*K_T
+ xphijp1_i(ip,ij) =-K_T*(j_dp+1._dp)
+ xphijm1_i(ip,ij) =-K_T* j_dp
ELSE IF (p_int .EQ. 2) THEN ! kronecker p2
- xphij(ip,ij) =+K_T/SQRT2
- xphijp1(ip,ij) = 0._dp; xphijm1(ip,ij) = 0._dp;
+ xphij_i(ip,ij) =+K_T/SQRT2
+ xphijp1_i(ip,ij) = 0._dp; xphijm1_i(ip,ij) = 0._dp;
ELSE
- xphij(ip,ij) = 0._dp; xphijp1(ip,ij) = 0._dp
- xphijm1(ip,ij) = 0._dp;
+ xphij_i(ip,ij) = 0._dp; xphijp1_i(ip,ij) = 0._dp
+ xphijm1_i(ip,ij) = 0._dp;
ENDIF
ENDDO
ENDDO
-
END SUBROUTINE compute_lin_coeff
!******************************************************************************!
diff --git a/src/restarts_mod.F90 b/src/restarts_mod.F90
index cc69a2b1..613cf37f 100644
--- a/src/restarts_mod.F90
+++ b/src/restarts_mod.F90
@@ -72,10 +72,10 @@ CONTAINS
! Read state of system from checkpoint file
IF (KIN_E) THEN
WRITE(dset_name, "(A, '/', i6.6)") "/data/var5d/moments_e", n_
- CALL getarrnd(fidrst, dset_name, moments_e(ips_e:ipe_e, ijs_e:ije_e, ikxs:ikxe, ikys:ikye, izs:ize, 1),(/1,3/))
+ CALL getarrnd(fidrst, dset_name, moments_e(ips_e:ipe_e, ijs_e:ije_e, ikxs:ikxe, ikys:ikye, izs:ize, 1),(/1,3,5/))
ENDIF
WRITE(dset_name, "(A, '/', i6.6)") "/data/var5d/moments_i", n_
- CALL getarrnd(fidrst, dset_name, moments_i(ips_i:ipe_i, ijs_i:ije_i, ikxs:ikxe, ikys:ikye, izs:ize, 1),(/1,3/))
+ CALL getarrnd(fidrst, dset_name, moments_i(ips_i:ipe_i, ijs_i:ije_i, ikxs:ikxe, ikys:ikye, izs:ize, 1),(/1,3,5/))
CALL closef(fidrst)
diff --git a/wk/analysis_3D.m b/wk/analysis_3D.m
index a6f008af..c7a82f47 100644
--- a/wk/analysis_3D.m
+++ b/wk/analysis_3D.m
@@ -11,7 +11,7 @@ system(['mkdir -p ',MISCDIR]);
CMD = ['rsync ', LOCALDIR,'outputs* ',MISCDIR]; disp(CMD);
system(CMD);
% Load outputs from jobnummin up to jobnummax
-JOBNUMMIN = 00; JOBNUMMAX = 10;
+JOBNUMMIN = 00; JOBNUMMAX = 0;
data = compile_results(MISCDIR,JOBNUMMIN,JOBNUMMAX); %Compile the results from first output found to JOBNUMMAX if existing
diff --git a/wk/analysis_header.m b/wk/analysis_header.m
index a2017024..657b52a8 100644
--- a/wk/analysis_header.m
+++ b/wk/analysis_header.m
@@ -3,6 +3,6 @@
outfile ='';
outfile ='linear_shearless_cyclone/dbg';
% outfile ='debug/test_zpar/';
-% outfile ='shearless_cyclone/128x128x16x4x2_L_120_CTC_1.0_colless/';
+outfile ='shearless_cyclone/128x128x16x4x2_L_120_CTC_1.0/';
% outfile ='shearless_cyclone/128x128x16x4x2_L_120_CTC_0.8/';
analysis_3D
\ No newline at end of file
--
GitLab