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Commit 0cd6a38c authored by Godoy, William's avatar Godoy, William
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Merge branch 'init' into 'master' 

Add git lfs support for test data

See merge request !2
parents d690dcde 0e16d316
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.gitattributes 0 → 100644
View file @ 0cd6a38c
./test/data/AmrexCastro/hydro_tests/** filter=lfs diff=lfs merge=lfs -text
.gitignore 0 → 100644
View file @ 0cd6a38c
.buildpath
.project
src/extractor/AmrexCastro.jl
View file @ 0cd6a38c
import Glob
include("../helper/helperSystem.jl")
mutable struct AmrexCastro <: AbstractAmrex
app::String
......@@ -33,14 +34,7 @@ end
function get_dependent_variable_datasize(extractor::AmrexCastro)
findDelimiter = findlast("/",extractor.outputPrefix)
println(extractor.outputPrefix)
println(findDelimiter)
searchDirectory = extractor.outputPrefix[ 1: findDelimiter[1]-1 ]
prefix = extractor.outputPrefix[ findDelimiter[1]+1:end]
println("Search directory: ", searchDirectory, " prefix: ", prefix)
outputDirs = Glob.glob( string(prefix,"*"), searchDirectory )
outputDirs = helper_get_prefix_directories(extractor.outputPrefix)
println(outputDirs)
end
......
src/helper/helperSystem.jl 0 → 100644
View file @ 0cd6a38c
import Glob
function helper_get_prefix_directories(prefix::String)::Array{String}
findDelimiter = findlast("/",prefix)
searchDirectory = prefix[ 1: findDelimiter[1]-1 ]
print(searchDirectory)
pattern = string(prefix[ findDelimiter[1]+1:end],"*")
outputDirs = Glob.glob( pattern, searchDirectory )
return outputDirs
end
\ No newline at end of file
test/data/amrexCastro/LICENSE → test/data/AmrexCastro/LICENSE
View file @ 0cd6a38c
# COPY OF AMREX CASTRO LICENSE
Copyright (c) 2017, The Regents of the University of California,
through Lawrence Berkeley National Laboratory and the Alliance for
Sustainable Energy, LLC., through National Renewable Energy Laboratory
......
test/data/AmrexCastro/hydro_tests/Sedov/2d.cyl_in_cartcoords/case1/probin.2d.cyl_in_cartcoords 0 → 100644
View file @ 0cd6a38c
&fortin
r_init = 0.01
p_ambient = 1.d-6
exp_energy = 1.0
dens_ambient = 1.0
nsub = 10
/
&tagging
denerr = 3
dengrad = 0.01
max_denerr_lev = 3
max_dengrad_lev = 3
presserr = 3
pressgrad = 0.01
max_presserr_lev = 3
max_pressgrad_lev = 3
/
&extern
eos_assume_neutral = T
/
test/data/AmrexCastro/hydro_tests/Sedov/2d.cyl_in_cartcoords/case1/run.log 0 → 100644
View file @ 0cd6a38c
MPI initialized with 4 MPI processes
OMP initialized with 16 OMP threads
AMReX (60d291de4ffa) initialized
Starting run at 20:46:51 UTC on 2020-06-22.
Successfully read inputs file ...
Castro git describe: 20.04.1-12-g7d89c9044-dirty
AMReX git describe: 60d291de4
Microphysics git describe: 20.04
reading extern runtime parameters ...
EOS: small_temp cannot be less than the mintemp allowed by the EOS. Resetting small_temp to mintemp.
EOS: small_dens cannot be less than the mindens allowed by the EOS. Resetting small_dens to mindens.
Time in ca_set_method_params: 1.943997631e-06
1 Species:
X
0 Auxiliary Variables:
Successfully read inputs file ...
Starting to call amrex_probinit ...
Successfully run amrex_probinit
Initializing the data at level 0
Done initializing the level 0 data
...estimated hydro-limited timestep at level 0: 0.003033790465
Castro::estTimeStep (hydro-limited) at level 0: estdt = 0.003033790465
grid_places() time: 1.38292055 new finest: 1
Initializing the data at level 1
Done initializing the level 1 data
grid_places() time: 2.292115894 new finest: 2
Initializing the data at level 2
Done initializing the level 2 data
Now regridding at level lbase = 0
grid_places() time: 3.824145594 new finest: 2
Initializing the data at level 1
Done initializing the level 1 data
Initializing the data at level 2
Done initializing the level 2 data
STEP = 0 TIME = 0 : REGRID with lbase = 0
Level 1 1 grids 256 cells 25 % of domain
Level 2 1 grids 256 cells 6.25 % of domain
TIME= 0 MASS = 1
TIME= 0 XMOM = 0
TIME= 0 YMOM = 0
TIME= 0 ZMOM = 0
TIME= 0 ANG MOM X = 0
TIME= 0 ANG MOM Y = 0
TIME= 0 ANG MOM Z = 0
TIME= 0 RHO*e = 0.963634944
TIME= 0 RHO*K = 0
TIME= 0 RHO*E = 0.963634944
INITIAL GRIDS
Level 0 1 grids 256 cells 100 % of domain
Level 1 1 grids 256 cells 25 % of domain
Level 2 1 grids 256 cells 6.25 % of domain
CHECKPOINT: file = sedov_2d_cyl_in_cart_chk00000
checkPoint() time = 0.216643008 secs.
PLOTFILE: file = sedov_2d_cyl_in_cart_plt00000
Write plotfile time = 20.53022878 seconds
...estimated hydro-limited timestep at level 0: 0.003775072981
Castro::estTimeStep (hydro-limited) at level 0: estdt = 0.003775072981
...estimated hydro-limited timestep at level 1: 0.0009437682539
Castro::estTimeStep (hydro-limited) at level 1: estdt = 0.0009437682539
...estimated hydro-limited timestep at level 2: 0.000235942064
Castro::estTimeStep (hydro-limited) at level 2: estdt = 0.000235942064
[Level 0 step 1] ADVANCE with dt = 9.43768256e-06
Beginning subcycle 1 starting at time 0 with dt = 9.43768256e-06
Estimated number of subcycles remaining: 1
... Entering construct_ctu_hydro_source()
... Leaving construct_ctu_hydro_source()
Castro::construct_ctu_hydro_source() time = 0.076716001
...estimated hydro-limited timestep at level 0: 0.003773777991
Castro::estTimeStep (hydro-limited) at level 0: estdt = 0.003773777991
Subcycle completed
Subcycling complete
Zones advanced per microsecond at this level: 0.0001829721998
[Level 0 step 1] Advanced 256 cells
[Level 1 step 1] ADVANCE with dt = 4.71884128e-06
Beginning subcycle 1 starting at time 0 with dt = 4.71884128e-06
Estimated number of subcycles remaining: 1
... Entering construct_ctu_hydro_source()
... Leaving construct_ctu_hydro_source()
Castro::construct_ctu_hydro_source() time = 0.060218576
...estimated hydro-limited timestep at level 1: 0.0009431249345
Castro::estTimeStep (hydro-limited) at level 1: estdt = 0.0009431249345
Subcycle completed
Subcycling complete
Zones advanced per microsecond at this level: 0.0001838205111
[Level 1 step 1] Advanced 256 cells
[Level 2 step 1] ADVANCE with dt = 2.35942064e-06
Beginning subcycle 1 starting at time 0 with dt = 2.35942064e-06
Estimated number of subcycles remaining: 1
... Entering construct_ctu_hydro_source()
... Leaving construct_ctu_hydro_source()
Castro::construct_ctu_hydro_source() time = 0.058744209
...estimated hydro-limited timestep at level 2: 0.0002356219983
Castro::estTimeStep (hydro-limited) at level 2: estdt = 0.0002356219983
Subcycle completed
Subcycling complete
Zones advanced per microsecond at this level: 0.000180283042
[Level 2 step 1] Advanced 256 cells
[Level 2 step 2] ADVANCE with dt = 2.35942064e-06
Beginning subcycle 1 starting at time 2.35942064e-06 with dt = 2.35942064e-06
Estimated number of subcycles remaining: 1
... Entering construct_ctu_hydro_source()
... Leaving construct_ctu_hydro_source()
Castro::construct_ctu_hydro_source() time = 0.070250625
...estimated hydro-limited timestep at level 2: 0.000235191858
Castro::estTimeStep (hydro-limited) at level 2: estdt = 0.000235191858
Subcycle completed
Subcycling complete
Zones advanced per microsecond at this level: 0.0001890201521
[Level 2 step 2] Advanced 256 cells
Castro::reflux() at level 1 : time = 0.913998893
[Level 1 step 2] ADVANCE with dt = 4.71884128e-06
Beginning subcycle 1 starting at time 4.71884128e-06 with dt = 4.71884128e-06
Estimated number of subcycles remaining: 1
... Entering construct_ctu_hydro_source()
... Leaving construct_ctu_hydro_source()
Castro::construct_ctu_hydro_source() time = 0.075102265
...estimated hydro-limited timestep at level 1: 0.0009403141545
Castro::estTimeStep (hydro-limited) at level 1: estdt = 0.0009403141545
Subcycle completed
Subcycling complete
Zones advanced per microsecond at this level: 0.0001746851604
[Level 1 step 2] Advanced 256 cells
[Level 2 step 3] ADVANCE with dt = 2.35942064e-06
Beginning subcycle 1 starting at time 4.71884128e-06 with dt = 2.35942064e-06
Estimated number of subcycles remaining: 1
... Entering construct_ctu_hydro_source()
... Leaving construct_ctu_hydro_source()
Castro::construct_ctu_hydro_source() time = 0.074166295
...estimated hydro-limited timestep at level 2: 0.000234744144
Castro::estTimeStep (hydro-limited) at level 2: estdt = 0.000234744144
Subcycle completed
Subcycling complete
Zones advanced per microsecond at this level: 0.0001858576518
[Level 2 step 3] Advanced 256 cells
[Level 2 step 4] ADVANCE with dt = 2.35942064e-06
Beginning subcycle 1 starting at time 7.07826192e-06 with dt = 2.35942064e-06
Estimated number of subcycles remaining: 1
... Entering construct_ctu_hydro_source()
... Leaving construct_ctu_hydro_source()
Castro::construct_ctu_hydro_source() time = 0.071217177
...estimated hydro-limited timestep at level 2: 0.0002342862531
Castro::estTimeStep (hydro-limited) at level 2: estdt = 0.0002342862531
Subcycle completed
Subcycling complete
Zones advanced per microsecond at this level: 0.0001967017335
[Level 2 step 4] Advanced 256 cells
Castro::reflux() at level 1 : time = 0.967450156
Castro::reflux() at level 0 : time = 1.241474912
TIME= 9.43768256e-06 MASS = 1
TIME= 9.43768256e-06 XMOM = -4.935124951e-22
TIME= 9.43768256e-06 YMOM = 3.011808344e-21
TIME= 9.43768256e-06 ZMOM = 0
TIME= 9.43768256e-06 ANG MOM X = 0
TIME= 9.43768256e-06 ANG MOM Y = 0
TIME= 9.43768256e-06 ANG MOM Z = -5.302716229e-24
TIME= 9.43768256e-06 RHO*e = 0.963558447
TIME= 9.43768256e-06 RHO*K = 7.649700461e-05
TIME= 9.43768256e-06 RHO*E = 0.963634944
[STEP 1] Coarse TimeStep time: 21.60359404
[STEP 1] FAB kilobyte spread across MPI nodes: [0 ... 679]
STEP = 1 TIME = 9.43768256e-06 DT = 9.43768256e-06
...estimated hydro-limited timestep at level 0: 0.003763867994
Castro::estTimeStep (hydro-limited) at level 0: estdt = 0.003763867994
...estimated hydro-limited timestep at level 1: 0.0009381514251
Castro::estTimeStep (hydro-limited) at level 1: estdt = 0.0009381514251
...estimated hydro-limited timestep at level 2: 0.0002342862531
Castro::estTimeStep (hydro-limited) at level 2: estdt = 0.0002342862531
Castro::compute_new_dt : limiting dt at level 0
... new dt computed: 0.003763867994
... but limiting to: 1.038145082e-05 = 1.1 * 9.43768256e-06
Castro::compute_new_dt : limiting dt at level 1
... new dt computed: 0.0009381514251
... but limiting to: 5.190725408e-06 = 1.1 * 4.71884128e-06
Castro::compute_new_dt : limiting dt at level 2
... new dt computed: 0.0002342862531
... but limiting to: 2.595362704e-06 = 1.1 * 2.35942064e-06
Now regridding at level lbase = 1
grid_places() time: 2.226090154 new finest: 2
TIME = 9.43768256e-06 : REGRID with lbase = 1
Level 2 1 grids 256 cells 6.25 % of domain
[Level 0 step 2] ADVANCE with dt = 1.038145082e-05
Beginning subcycle 1 starting at time 9.43768256e-06 with dt = 1.038145082e-05
Estimated number of subcycles remaining: 1
... Entering construct_ctu_hydro_source()
... Leaving construct_ctu_hydro_source()
Castro::construct_ctu_hydro_source() time = 0.076547869
...estimated hydro-limited timestep at level 0: 0.003762485986
Castro::estTimeStep (hydro-limited) at level 0: estdt = 0.003762485986
Subcycle completed
Subcycling complete
Zones advanced per microsecond at this level: 0.000179974789
[Level 0 step 2] Advanced 256 cells
[Level 1 step 3] ADVANCE with dt = 5.190725408e-06
Beginning subcycle 1 starting at time 9.43768256e-06 with dt = 5.190725408e-06
Estimated number of subcycles remaining: 1
... Entering construct_ctu_hydro_source()
... Leaving construct_ctu_hydro_source()
Castro::construct_ctu_hydro_source() time = 0.072866906
...estimated hydro-limited timestep at level 1: 0.000937463982
Castro::estTimeStep (hydro-limited) at level 1: estdt = 0.000937463982
Subcycle completed
Subcycling complete
Zones advanced per microsecond at this level: 0.0001767969209
[Level 1 step 3] Advanced 256 cells
[Level 2 step 5] ADVANCE with dt = 2.595362704e-06
Beginning subcycle 1 starting at time 9.43768256e-06 with dt = 2.595362704e-06
Estimated number of subcycles remaining: 1
... Entering construct_ctu_hydro_source()
... Leaving construct_ctu_hydro_source()
Castro::construct_ctu_hydro_source() time = 0.067464748
...estimated hydro-limited timestep at level 2: 0.0002337753891
Castro::estTimeStep (hydro-limited) at level 2: estdt = 0.0002337753891
Subcycle completed
Subcycling complete
Zones advanced per microsecond at this level: 0.0001820054859
[Level 2 step 5] Advanced 256 cells
[Level 2 step 6] ADVANCE with dt = 2.595362704e-06
Beginning subcycle 1 starting at time 1.203304526e-05 with dt = 2.595362704e-06
Estimated number of subcycles remaining: 1
... Entering construct_ctu_hydro_source()
... Leaving construct_ctu_hydro_source()
Castro::construct_ctu_hydro_source() time = 0.082349625
...estimated hydro-limited timestep at level 2: 0.000233259245
Castro::estTimeStep (hydro-limited) at level 2: estdt = 0.000233259245
Subcycle completed
Subcycling complete
Zones advanced per microsecond at this level: 0.0001959626209
[Level 2 step 6] Advanced 256 cells
Castro::reflux() at level 1 : time = 0.949316828
[Level 1 step 4] ADVANCE with dt = 5.190725408e-06
Beginning subcycle 1 starting at time 1.462840797e-05 with dt = 5.190725408e-06
Estimated number of subcycles remaining: 1
... Entering construct_ctu_hydro_source()
... Leaving construct_ctu_hydro_source()
Castro::construct_ctu_hydro_source() time = 0.065803559
...estimated hydro-limited timestep at level 1: 0.0009344437837
Castro::estTimeStep (hydro-limited) at level 1: estdt = 0.0009344437837
Subcycle completed
Subcycling complete
Zones advanced per microsecond at this level: 0.0001880992034
[Level 1 step 4] Advanced 256 cells
[Level 2 step 7] ADVANCE with dt = 2.595362704e-06
Beginning subcycle 1 starting at time 1.462840797e-05 with dt = 2.595362704e-06
Estimated number of subcycles remaining: 1
... Entering construct_ctu_hydro_source()
... Leaving construct_ctu_hydro_source()
Castro::construct_ctu_hydro_source() time = 0.0949963
...estimated hydro-limited timestep at level 2: 0.0002327397251
Castro::estTimeStep (hydro-limited) at level 2: estdt = 0.0002327397251
Subcycle completed
Subcycling complete
Zones advanced per microsecond at this level: 0.0001764416651
[Level 2 step 7] Advanced 256 cells
[Level 2 step 8] ADVANCE with dt = 2.595362704e-06
Beginning subcycle 1 starting at time 1.722377067e-05 with dt = 2.595362704e-06
Estimated number of subcycles remaining: 1
... Entering construct_ctu_hydro_source()
... Leaving construct_ctu_hydro_source()
Castro::construct_ctu_hydro_source() time = 0.084573767
...estimated hydro-limited timestep at level 2: 0.0002322181798
Castro::estTimeStep (hydro-limited) at level 2: estdt = 0.0002322181798
Subcycle completed
Subcycling complete
Zones advanced per microsecond at this level: 0.0001837982259
[Level 2 step 8] Advanced 256 cells
Castro::reflux() at level 1 : time = 0.902958767
Castro::reflux() at level 0 : time = 1.088269677
TIME= 1.981913338e-05 MASS = 1
TIME= 1.981913338e-05 XMOM = 5.429974369e-21
TIME= 1.981913338e-05 YMOM = 1.285628476e-22
TIME= 1.981913338e-05 ZMOM = 0
TIME= 1.981913338e-05 ANG MOM X = 0
TIME= 1.981913338e-05 ANG MOM Y = 0
TIME= 1.981913338e-05 ANG MOM Z = -1.036248681e-22
TIME= 1.981913338e-05 RHO*e = 0.9633015088
TIME= 1.981913338e-05 RHO*K = 0.0003334352051
TIME= 1.981913338e-05 RHO*E = 0.963634944
[STEP 2] Coarse TimeStep time: 24.837523
[STEP 2] FAB kilobyte spread across MPI nodes: [0 ... 679]
STEP = 2 TIME = 1.981913338e-05 DT = 1.038145082e-05
...estimated hydro-limited timestep at level 0: 0.003751858582
Castro::estTimeStep (hydro-limited) at level 0: estdt = 0.003751858582
...estimated hydro-limited timestep at level 1: 0.0009321352609
Castro::estTimeStep (hydro-limited) at level 1: estdt = 0.0009321352609
...estimated hydro-limited timestep at level 2: 0.0002322181798
Castro::estTimeStep (hydro-limited) at level 2: estdt = 0.0002322181798
Castro::compute_new_dt : limiting dt at level 0
... new dt computed: 0.003751858582
... but limiting to: 1.14195959e-05 = 1.1 * 1.038145082e-05
Castro::compute_new_dt : limiting dt at level 1
... new dt computed: 0.0009321352609
... but limiting to: 5.709797949e-06 = 1.1 * 5.190725408e-06
Castro::compute_new_dt : limiting dt at level 2
... new dt computed: 0.0002322181798
... but limiting to: 2.854898974e-06 = 1.1 * 2.595362704e-06
Now regridding at level lbase = 0
grid_places() time: 3.760714687 new finest: 2
STEP = 2 TIME = 1.981913338e-05 : REGRID with lbase = 0
Level 1 1 grids 256 cells 25 % of domain
Level 2 1 grids 256 cells 6.25 % of domain
...estimated hydro-limited timestep at level 0: 0.003751858582
Castro::estTimeStep (hydro-limited) at level 0: estdt = 0.003751858582
...estimated hydro-limited timestep at level 1: 0.0009321352609
Castro::estTimeStep (hydro-limited) at level 1: estdt = 0.0009321352609
...estimated hydro-limited timestep at level 2: 0.0002322181798
Castro::estTimeStep (hydro-limited) at level 2: estdt = 0.0002322181798
[Level 0 step 3] ADVANCE with dt = 1.14195959e-05
Beginning subcycle 1 starting at time 1.981913338e-05 with dt = 1.14195959e-05
Estimated number of subcycles remaining: 1
... Entering construct_ctu_hydro_source()
... Leaving construct_ctu_hydro_source()
Castro::construct_ctu_hydro_source() time = 0.072817293
...estimated hydro-limited timestep at level 0: 0.003750388216
Castro::estTimeStep (hydro-limited) at level 0: estdt = 0.003750388216
Subcycle completed
Subcycling complete
Zones advanced per microsecond at this level: 0.0001809662484
[Level 0 step 3] Advanced 256 cells
[Level 1 step 5] ADVANCE with dt = 5.709797949e-06
Beginning subcycle 1 starting at time 1.981913338e-05 with dt = 5.709797949e-06
Estimated number of subcycles remaining: 1
... Entering construct_ctu_hydro_source()
... Leaving construct_ctu_hydro_source()
Castro::construct_ctu_hydro_source() time = 0.069199301
...estimated hydro-limited timestep at level 1: 0.0009314049416
Castro::estTimeStep (hydro-limited) at level 1: estdt = 0.0009314049416
Subcycle completed
Subcycling complete
Zones advanced per microsecond at this level: 0.000186051429
[Level 1 step 5] Advanced 256 cells
[Level 2 step 9] ADVANCE with dt = 2.854898974e-06
Beginning subcycle 1 starting at time 1.981913338e-05 with dt = 2.854898974e-06
Estimated number of subcycles remaining: 1
... Entering construct_ctu_hydro_source()
... Leaving construct_ctu_hydro_source()
Castro::construct_ctu_hydro_source() time = 0.072784835
...estimated hydro-limited timestep at level 2: 0.000231643459
Castro::estTimeStep (hydro-limited) at level 2: estdt = 0.000231643459
Subcycle completed