Hydro: Export Selected Variables to VTK

Simulation Overview & Load Hydro Data

using Mera
# use compressed Mera file
path = "/Volumes/FASTStorage/Simulations/Mera-Tests/AV5CDhr/";
info = infodata(600, path)
gas = loaddata(600, path, :hydro); # load full box

[Mera]: 2025-06-28T15:06:54.435

Use datatype: hydro
Code: RAMSES
output [600] summary:
mtime: 2024-09-08T15:29:04
ctime: 2024-09-10T11:23:16.230
=======================================================
simulation time: 891.71 [Myr]
boxlen: 48.0 [kpc]
ncpu: 5120
ndim: 3
-------------------------------------------------------
amr:           true
level(s): 6 - 13 --> cellsize(s): 750.0 [pc] - 5.86 [pc]
-------------------------------------------------------
hydro:         true
hydro-variables:  7  --> (:rho, :vx, :vy, :vz, :p, :var6, :var7)
hydro-descriptor: (:density, :velocity_x, :velocity_y, :velocity_z, :pressure, :scalar_00, :scalar_01)
γ: 1.6667
-------------------------------------------------------
gravity:       true
gravity-variables: (:epot, :ax, :ay, :az)
-------------------------------------------------------
particles:     true
- Nstars:   1.353087e+06 
particle-variables: 7  --> (:vx, :vy, :vz, :mass, :family, :tag, :birth)
particle-descriptor: (:position_x, :position_y, :position_z, :velocity_x, :velocity_y, :velocity_z, :mass, :identity, :levelp, :family, :tag, :birth_time)
-------------------------------------------------------
rt:            false
clumps:           false
-------------------------------------------------------
namelist-file: ("&COOLING_PARAMS", "&HYDRO_PARAMS", "&SF_PARAMS", "&AMR_PARAMS", "&BOUNDARY_PARAMS", "&OUTPUT_PARAMS", "&POISSON_PARAMS", "&INIT_PARAMS", "&RUN_PARAMS", "&FEEDBACK_PARAMS", "&REFINE_PARAMS")
-------------------------------------------------------
timer-file:       true
compilation-file: true
makefile:         true
patchfile:        true
=======================================================

[Mera]: 2025-06-28T15:06:54.479

Open Mera-file output_00600.jld2:

domain:
xmin::xmax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]
ymin::ymax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]
zmin::zmax: 0.0 :: 1.0  	==> 0.0 [kpc] :: 48.0 [kpc]

Memory used for data table :8.63788466155529 GB
-------------------------------------------------------

Export Scalars

Standard Export

# Export full box with lmax = 9 
# -> interpolating levels 13,12,11,10, down to 9

export_vtk(
    gas,                       # loaded data
    "output01/0600_galaxy";    # prefix for outputfiles; creates folder output01 (if not existing) 
    scalars=[:rho, :T],        # load density data in cm^-3 and temperature data in Kelvin 
    scalars_unit=[:nH, :K],
    scalars_log10=true,        # apply log10 on the scalars
    positions_unit=:kpc,       # cell positions in kpc (useful in Paraview for region selection)
    lmax=9                     
);

[Mera]: 2025-06-28T15:07:40.866

Available Threads: 1
Created directory: output01
Processing levels: [6, 7, 8, 9]
Will interpolate levels [10, 11, 12, 13] down to 9
Level 6
  wrote 0600_galaxy_L6.vtu (Size: 0.0 GB)
  ✓ Level 6 completed, memory cleaned
Level 7
  wrote 0600_galaxy_L7.vtu (Size: 0.02 GB)
  ✓ Level 7 completed, memory cleaned
Level 8
  wrote 0600_galaxy_L8.vtu (Size: 0.33 GB)
  ✓ Level 8 completed, memory cleaned
Level 9
  Including higher levels for interpolation
  Interpolating down to level 9
  Unique coarse cells at level 9: 13663000 (out of max 134217728)
  → 13663000 coarse cells after interpolation
  wrote 0600_galaxy_L9.vtu (Size: 0.64 GB)
  ✓ Level 9 completed, memory cleaned
  Added block 'Level_6' to scalar VTM for 0600_galaxy_L6.vtu
  Added block 'Level_7' to scalar VTM for 0600_galaxy_L7.vtu
  Added block 'Level_8' to scalar VTM for 0600_galaxy_L8.vtu
  Added block 'Level_9' to scalar VTM for 0600_galaxy_L9.vtu
Created scalar multiblock: 0600_galaxy_scalar.vtm
  Updating scalar VTM file to reference scalar VTU files...
    - Added reference to 0600_galaxy_L6.vtu in block 'Level_6' of scalar VTM
    - Added reference to 0600_galaxy_L7.vtu in block 'Level_7' of scalar VTM
    - Added reference to 0600_galaxy_L8.vtu in block 'Level_8' of scalar VTM
    - Added reference to 0600_galaxy_L9.vtu in block 'Level_9' of scalar VTM
  Updated scalar VTM file with references to scalar VTU files at: 0600_galaxy_scalar.vtm

=== Export Summary ===
VTU files (scalars): 4
Scalar VTM: 0600_galaxy_scalar.vtm
Available scalars: rho, T, AMR_Level

readdir("output_part01")

1-element Vector{String}:
 "0600_galaxy.vtu"

# => in Paraview open the vtu file to load all level data

Export Maximum Number of Cells

# Export full box 
# -> limit the number of cells
# here: not reaching levels 11,12,13
export_vtk(
    gas,                       # loaded data
    "output03/0600_galaxy";    # prefix for outputfiles; creates folder output03 (if not existing) 
    scalars=[:rho, :T],        # load density data in cm^-3 and temperature data in Kelvin 
    scalars_unit=[:nH, :K],
    scalars_log10=true,        # apply log10 on the scalars
    positions_unit=:kpc,       # cell positions in kpc (useful in Paraview for region selection)

    lmax=10,
    max_cells=100_000          # (caps output if exceeded, prioritizing denser regions)
);

[Mera]: 2025-06-28T16:04:43.533

Available Threads: 1
Processing levels: [6, 7, 8, 9, 10]
Will interpolate levels [11, 12, 13] down to 10
Level 6
  wrote 0600_galaxy_L6.vtu (Size: 0.0 GB)
  ✓ Level 6 completed, memory cleaned
Level 7
  wrote 0600_galaxy_L7.vtu (Size: 0.02 GB)
  ✓ Level 7 completed, memory cleaned
Level 8
  wrote 0600_galaxy_L8.vtu (Size: 0.33 GB)
  ✓ Level 8 completed, memory cleaned
Level 9
  wrote 0600_galaxy_L9.vtu (Size: 0.54 GB)
  ✓ Level 9 completed, memory cleaned
Level 10
  Including higher levels for interpolation
  Interpolating down to level 10
  Unique coarse cells at level 10: 6968288 (out of max 1073741824)
  Capping output cells to 100000 (from 6968288)
  → 100000 coarse cells after interpolation
  wrote 0600_galaxy_L10.vtu (Size: 0.0 GB)
  ✓ Level 10 completed, memory cleaned
  Added block 'Level_6' to scalar VTM for 0600_galaxy_L6.vtu
  Added block 'Level_7' to scalar VTM for 0600_galaxy_L7.vtu
  Added block 'Level_8' to scalar VTM for 0600_galaxy_L8.vtu
  Added block 'Level_9' to scalar VTM for 0600_galaxy_L9.vtu
  Added block 'Level_10' to scalar VTM for 0600_galaxy_L10.vtu
Created scalar multiblock: 0600_galaxy_scalar.vtm
  Updating scalar VTM file to reference scalar VTU files...
    - Added reference to 0600_galaxy_L6.vtu in block 'Level_6' of scalar VTM
    - Added reference to 0600_galaxy_L7.vtu in block 'Level_7' of scalar VTM
    - Added reference to 0600_galaxy_L8.vtu in block 'Level_8' of scalar VTM
    - Added reference to 0600_galaxy_L9.vtu in block 'Level_9' of scalar VTM
    - Added reference to 0600_galaxy_L10.vtu in block 'Level_10' of scalar VTM
  Updated scalar VTM file with references to scalar VTU files at: 0600_galaxy_scalar.vtm

=== Export Summary ===
VTU files (scalars): 5
Scalar VTM: 0600_galaxy_scalar.vtm
Available scalars: rho, T, AMR_Level

readdir("output03")

6-element Vector{String}:
 "0600_galaxy_L10.vtu"
 "0600_galaxy_L6.vtu"
 "0600_galaxy_L7.vtu"
 "0600_galaxy_L8.vtu"
 "0600_galaxy_L9.vtu"
 "0600_galaxy_scalar.vtm"

# => in Paraview open the vtm file to load all level data

Export Scalars and Vector

# Export full box with lmax = 9 
# scalar and vector in separate files
# -> interpolating levels 13,12,11,10, down to 9

export_vtk(
    gas,                       # loaded data
    "output04/0600_galaxy";    # prefix for outputfiles; creates folder output04 (if not existing) 
    scalars=[:rho],            # load density data in cm^-3 
    scalars_unit=[:nH],
    scalars_log10=true,        # apply log10 on the scalars
    positions_unit=:kpc,       # cell positions in kpc (useful in Paraview for region selection)
    lmax=9 ,

    vector=[:vx, :vy, :vz],    # velocity components and its units
    vector_unit=:km_s,
    vector_name="velocity"     # vector name recognized by Paraview
);

[Mera]: 2025-06-28T15:35:19.707

Available Threads: 1
Created directory: output04
Processing levels: [6, 7, 8, 9]
Will interpolate levels [10, 11, 12, 13] down to 9
Level 6
  wrote 0600_galaxy_L6.vtu (Size: 0.0 GB)
  wrote 0600_galaxy_vec_L6.vtu (Size: 0.0 GB)
  ✓ Level 6 completed, memory cleaned
Level 7
  wrote 0600_galaxy_L7.vtu (Size: 0.01 GB)
  wrote 0600_galaxy_vec_L7.vtu (Size: 0.02 GB)
  ✓ Level 7 completed, memory cleaned
Level 8
  wrote 0600_galaxy_L8.vtu (Size: 0.28 GB)
  wrote 0600_galaxy_vec_L8.vtu (Size: 0.41 GB)
  ✓ Level 8 completed, memory cleaned
Level 9
  Including higher levels for interpolation
  Interpolating down to level 9
  Unique coarse cells at level 9: 13663000 (out of max 134217728)
  → 13663000 coarse cells after interpolation
  wrote 0600_galaxy_L9.vtu (Size: 0.55 GB)
  wrote 0600_galaxy_vec_L9.vtu (Size: 0.77 GB)
  ✓ Level 9 completed, memory cleaned
  Added block 'Level_6' to scalar VTM for 0600_galaxy_L6.vtu
  Added block 'Level_7' to scalar VTM for 0600_galaxy_L7.vtu
  Added block 'Level_8' to scalar VTM for 0600_galaxy_L8.vtu
  Added block 'Level_9' to scalar VTM for 0600_galaxy_L9.vtu
Created scalar multiblock: 0600_galaxy_scalar.vtm
  Updating scalar VTM file to reference scalar VTU files...
    - Added reference to 0600_galaxy_L6.vtu in block 'Level_6' of scalar VTM
    - Added reference to 0600_galaxy_L7.vtu in block 'Level_7' of scalar VTM
    - Added reference to 0600_galaxy_L8.vtu in block 'Level_8' of scalar VTM
    - Added reference to 0600_galaxy_L9.vtu in block 'Level_9' of scalar VTM
  Updated scalar VTM file with references to scalar VTU files at: 0600_galaxy_scalar.vtm
  Added block 'vec_Level_6' to vector VTM for 0600_galaxy_vec_L6.vtu
  Added block 'vec_Level_7' to vector VTM for 0600_galaxy_vec_L7.vtu
  Added block 'vec_Level_8' to vector VTM for 0600_galaxy_vec_L8.vtu
  Added block 'vec_Level_9' to vector VTM for 0600_galaxy_vec_L9.vtu
Created vector multiblock: 0600_galaxy_vector.vtm
  Updating vector VTM file to reference vector VTU files...
    - Added reference to 0600_galaxy_vec_L6.vtu in block 'vec_Level_6' of vector VTM
    - Added reference to 0600_galaxy_vec_L7.vtu in block 'vec_Level_7' of vector VTM
    - Added reference to 0600_galaxy_vec_L8.vtu in block 'vec_Level_8' of vector VTM
    - Added reference to 0600_galaxy_vec_L9.vtu in block 'vec_Level_9' of vector VTM
  Updated vector VTM file with references to vector VTU files at: 0600_galaxy_vector.vtm

=== Export Summary ===
VTU files (scalars): 4
Scalar VTM: 0600_galaxy_scalar.vtm
VTU files (vector): 4
Vector VTM: 0600_galaxy_vector.vtm
Available scalars: rho, AMR_Level
Available vector, named: velocity

readdir("output04")

10-element Vector{String}:
 "0600_galaxy_L6.vtu"
 "0600_galaxy_L7.vtu"
 "0600_galaxy_L8.vtu"
 "0600_galaxy_L9.vtu"
 "0600_galaxy_scalar.vtm"
 "0600_galaxy_vec_L6.vtu"
 "0600_galaxy_vec_L7.vtu"
 "0600_galaxy_vec_L8.vtu"
 "0600_galaxy_vec_L9.vtu"
 "0600_galaxy_vector.vtm"

# => in Paraview open
# - the vtm file to load all level data
# - open "0350_galaxy_scalar.vtm" to load multi-level scalar data
# - open  "0350_galaxy_vector.vtm"to load mjulti-level vector data
# - or open both vtm files together

Visualisation in Paraview

Volume Rendering Density

# for a test on my laptop I use lmax=8 for the full box
# and lmax=9 for the galaxy region

# Export full box with lmax = 8 
# scalar and vector in separate files
# -> interpolating levels 13,12,11,10, 9 down to 8

export_vtk(
    gas,                       # loaded data
    "output05/0600_galaxy";    # prefix for outputfiles; creates folder output05 (if not existing) 
    scalars=[:rho],            # load density data in cm^-3 
    scalars_unit=[:nH],
    scalars_log10=true,        # apply log10 on the scalars
    positions_unit=:kpc,       # cell positions in kpc (useful in Paraview for region selection)
    lmax=8 ,

    vector=[:vx, :vy, :vz],    # velocity components and its units
    vector_unit=:km_s,
    vector_name="velocity"     # vector name recognized by Paraview
);

[Mera]: 2025-06-28T15:45:52.426

Available Threads: 1
Created directory: output05
Processing levels: [6, 7, 8]
Will interpolate levels [9, 10, 11, 12, 13] down to 8
Level 6
  wrote 0600_galaxy_L6.vtu (Size: 0.0 GB)
  wrote 0600_galaxy_vec_L6.vtu (Size: 0.0 GB)
  ✓ Level 6 completed, memory cleaned
Level 7
  wrote 0600_galaxy_L7.vtu (Size: 0.01 GB)
  wrote 0600_galaxy_vec_L7.vtu (Size: 0.02 GB)
  ✓ Level 7 completed, memory cleaned
Level 8
  Including higher levels for interpolation
  Interpolating down to level 8
  Unique coarse cells at level 8: 9517504 (out of max 16777216)
  → 9517504 coarse cells after interpolation
  wrote 0600_galaxy_L8.vtu (Size: 0.39 GB)
  wrote 0600_galaxy_vec_L8.vtu (Size: 0.55 GB)
  ✓ Level 8 completed, memory cleaned
  Added block 'Level_6' to scalar VTM for 0600_galaxy_L6.vtu
  Added block 'Level_7' to scalar VTM for 0600_galaxy_L7.vtu
  Added block 'Level_8' to scalar VTM for 0600_galaxy_L8.vtu
Created scalar multiblock: 0600_galaxy_scalar.vtm
  Updating scalar VTM file to reference scalar VTU files...
    - Added reference to 0600_galaxy_L6.vtu in block 'Level_6' of scalar VTM
    - Added reference to 0600_galaxy_L7.vtu in block 'Level_7' of scalar VTM
    - Added reference to 0600_galaxy_L8.vtu in block 'Level_8' of scalar VTM
  Updated scalar VTM file with references to scalar VTU files at: 0600_galaxy_scalar.vtm
  Added block 'vec_Level_6' to vector VTM for 0600_galaxy_vec_L6.vtu
  Added block 'vec_Level_7' to vector VTM for 0600_galaxy_vec_L7.vtu
  Added block 'vec_Level_8' to vector VTM for 0600_galaxy_vec_L8.vtu
Created vector multiblock: 0600_galaxy_vector.vtm
  Updating vector VTM file to reference vector VTU files...
    - Added reference to 0600_galaxy_vec_L6.vtu in block 'vec_Level_6' of vector VTM
    - Added reference to 0600_galaxy_vec_L7.vtu in block 'vec_Level_7' of vector VTM
    - Added reference to 0600_galaxy_vec_L8.vtu in block 'vec_Level_8' of vector VTM
  Updated vector VTM file with references to vector VTU files at: 0600_galaxy_vector.vtm

=== Export Summary ===
VTU files (scalars): 3
Scalar VTM: 0600_galaxy_scalar.vtm
VTU files (vector): 3
Vector VTM: 0600_galaxy_vector.vtm
Available scalars: rho, AMR_Level
Available vector, named: velocity

readdir("output05")

8-element Vector{String}:
 "0600_galaxy_L6.vtu"
 "0600_galaxy_L7.vtu"
 "0600_galaxy_L8.vtu"
 "0600_galaxy_scalar.vtm"
 "0600_galaxy_vec_L6.vtu"
 "0600_galaxy_vec_L7.vtu"
 "0600_galaxy_vec_L8.vtu"
 "0600_galaxy_vector.vtm"

Open Scalar vtm File

Select rho array, volume rendering and apply

Choose a suitable colormap

Select value range, opazity and visualize data histogram

Change orientation, value range

# => save state

Visualize Density & Vector

# extract a small region of the galaxy
gassub = subregion(gas, :cylinder, radius=1., height=1., range_unit=:kpc, center=[23.,23.,:bc]);

[Mera]: 2025-06-28T15:51:50.842

center: [0.4791667, 0.4791667, 0.5] ==> [23.0 [kpc] :: 23.0 [kpc] :: 24.0 [kpc]]

domain:
xmin::xmax: 0.4583333 :: 0.5  	==> 22.0 [kpc] :: 24.0 [kpc]
ymin::ymax: 0.4583333 :: 0.5  	==> 22.0 [kpc] :: 24.0 [kpc]
zmin::zmax: 0.4791667 :: 0.5208333  	==> 23.0 [kpc] :: 25.0 [kpc]

Radius: 1.0 [kpc]
Height: 1.0 [kpc]
Memory used for data table :147.8594617843628 MB
-------------------------------------------------------

# Export small region with all available AMR levels
# scalar and vector in separate files

export_vtk(
    gassub,                    # loaded data
    "output06/0600_galaxy";    # prefix for outputfiles; creates folder output06 (if not existing) 
    scalars=[:rho],            # load density data in cm^-3 
    scalars_unit=[:nH],
    scalars_log10=true,        # apply log10 on the scalars
    positions_unit=:kpc,       # cell positions in kpc (useful in Paraview for region selection)

    vector=[:vx, :vy, :vz],    # velocity components and its units
    vector_unit=:km_s,
    vector_name="velocity"     # vector name recognized by Paraview
);

[Mera]: 2025-06-28T16:11:51.637

Available Threads: 1
Created directory: output06
Processing levels: [10, 11, 12, 13]
Level 10
  wrote 0600_galaxy_L10.vtu (Size: 0.0 GB)
  wrote 0600_galaxy_vec_L10.vtu (Size: 0.0 GB)
  ✓ Level 10 completed, memory cleaned
Level 11
  wrote 0600_galaxy_L11.vtu (Size: 0.01 GB)
  wrote 0600_galaxy_vec_L11.vtu (Size: 0.02 GB)
  ✓ Level 11 completed, memory cleaned
Level 12
  wrote 0600_galaxy_L12.vtu (Size: 0.02 GB)
  wrote 0600_galaxy_vec_L12.vtu (Size: 0.03 GB)
  ✓ Level 12 completed, memory cleaned
Level 13
  wrote 0600_galaxy_L13.vtu (Size: 0.03 GB)
  wrote 0600_galaxy_vec_L13.vtu (Size: 0.04 GB)
  ✓ Level 13 completed, memory cleaned
  Added block 'Level_10' to scalar VTM for 0600_galaxy_L10.vtu
  Added block 'Level_11' to scalar VTM for 0600_galaxy_L11.vtu
  Added block 'Level_12' to scalar VTM for 0600_galaxy_L12.vtu
  Added block 'Level_13' to scalar VTM for 0600_galaxy_L13.vtu
Created scalar multiblock: 0600_galaxy_scalar.vtm
  Updating scalar VTM file to reference scalar VTU files...
    - Added reference to 0600_galaxy_L10.vtu in block 'Level_10' of scalar VTM
    - Added reference to 0600_galaxy_L11.vtu in block 'Level_11' of scalar VTM
    - Added reference to 0600_galaxy_L12.vtu in block 'Level_12' of scalar VTM
    - Added reference to 0600_galaxy_L13.vtu in block 'Level_13' of scalar VTM
  Updated scalar VTM file with references to scalar VTU files at: 0600_galaxy_scalar.vtm
  Added block 'vec_Level_10' to vector VTM for 0600_galaxy_vec_L10.vtu
  Added block 'vec_Level_11' to vector VTM for 0600_galaxy_vec_L11.vtu
  Added block 'vec_Level_12' to vector VTM for 0600_galaxy_vec_L12.vtu
  Added block 'vec_Level_13' to vector VTM for 0600_galaxy_vec_L13.vtu
Created vector multiblock: 0600_galaxy_vector.vtm
  Updating vector VTM file to reference vector VTU files...
    - Added reference to 0600_galaxy_vec_L10.vtu in block 'vec_Level_10' of vector VTM
    - Added reference to 0600_galaxy_vec_L11.vtu in block 'vec_Level_11' of vector VTM
    - Added reference to 0600_galaxy_vec_L12.vtu in block 'vec_Level_12' of vector VTM
    - Added reference to 0600_galaxy_vec_L13.vtu in block 'vec_Level_13' of vector VTM
  Updated vector VTM file with references to vector VTU files at: 0600_galaxy_vector.vtm

=== Export Summary ===
VTU files (scalars): 4
Scalar VTM: 0600_galaxy_scalar.vtm
VTU files (vector): 4
Vector VTM: 0600_galaxy_vector.vtm
Available scalars: rho, AMR_Level
Available vector, named: velocity

readdir("output06")

10-element Vector{String}:
 "0600_galaxy_L10.vtu"
 "0600_galaxy_L11.vtu"
 "0600_galaxy_L12.vtu"
 "0600_galaxy_L13.vtu"
 "0600_galaxy_scalar.vtm"
 "0600_galaxy_vec_L10.vtu"
 "0600_galaxy_vec_L11.vtu"
 "0600_galaxy_vec_L12.vtu"
 "0600_galaxy_vec_L13.vtu"
 "0600_galaxy_vector.vtm"

Load Scalar

Select rho data, volume rendering, color map, choose value range

Load Vector data

Select velocity data, magnitude volume rendering

Edge-on view, apply 3D Glyphs on vector data, choose array and number of sample points

Apply streamline tracer, point cloud and its size, number of points

# => save state