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Scientific Software
MDANSE
Commits
35734a7b
Commit
35734a7b
authored
Jan 27, 2016
by
eric pellegrini
Browse files
Updated mvi test
parent
b6892c0b
Changes
3
Hide whitespace changes
Inline
Side-by-side
MDANSE/Framework/Jobs/McStasVirtualInstrument.py
View file @
35734a7b
...
...
@@ -48,9 +48,9 @@ from MDANSE.Externals.magnitude import magnitude
from
MDANSE.Framework.Jobs.IJob
import
IJob
from
MDANSE.MolecularDynamics.Trajectory
import
sorted_atoms
MCSTAS_UNITS_LUT
=
{
'THz'
:
magnitude
.
mg
(
1
,
"THz"
,
"meV
_
eq"
).
toval
(),
MCSTAS_UNITS_LUT
=
{
'THz'
:
magnitude
.
mg
(
1
,
"THz"
,
"meV
(fr
eq
)
"
).
toval
(),
'nm**2'
:
magnitude
.
mg
(
1
,
"nm2"
,
"b"
).
toval
(),
'inv_nm'
:
magnitude
.
mg
(
1
,
"
inv_
nm"
,
"
inv_
ang"
).
toval
()
'inv_nm'
:
magnitude
.
mg
(
1
,
"
1/
nm"
,
"
1/
ang"
).
toval
()
}
class
McStasError
(
Error
):
...
...
@@ -79,11 +79,11 @@ class McStasVirtualInstrument(IJob):
settings
[
'frames'
]
=
(
'frames'
,
{
"dependencies"
:{
'trajectory'
:
'trajectory'
}})
settings
[
'sample_coh'
]
=
(
'netcdf_input_file'
,
{
"widget"
:
'input_file'
,
"label"
:
'MDANSE Coherent Structure Factor'
,
"variables"
:[
'q'
,
'
omega
'
,
's(q,f)_total'
],
"variables"
:[
'q'
,
'
frequency
'
,
's(q,f)_total'
],
'default'
:
os
.
path
.
join
(
'..'
,
'..'
,
'..'
,
'Data'
,
'NetCDF'
,
'dcsf_prot.nc'
)})
settings
[
'sample_inc'
]
=
(
'netcdf_input_file'
,
{
"widget"
:
'input_file'
,
"label"
:
'MDANSE Incoherent Structure Factor'
,
"variables"
:[
'q'
,
'
omega
'
,
's(q,f)_total'
],
"variables"
:[
'q'
,
'
frequency
'
,
's(q,f)_total'
],
'default'
:
os
.
path
.
join
(
'..'
,
'..'
,
'..'
,
'Data'
,
'NetCDF'
,
'disf_prot.nc'
)})
settings
[
'temperature'
]
=
(
'float'
,
{
"default"
:
298.0
})
settings
[
'display'
]
=
(
'boolean'
,
{
'label'
:
'trace the 3D view of the simulation'
})
...
...
@@ -170,13 +170,13 @@ class McStasVirtualInstrument(IJob):
cmdLine
.
append
(
sqwInput
)
cmdLine
.
append
(
trace
)
cmdLine
.
extend
(
parameters
)
s
=
subprocess
.
Popen
(
" "
.
join
(
cmdLine
),
stdout
=
subprocess
.
PIPE
,
stderr
=
subprocess
.
STDOUT
,
shell
=
True
)
out
,
_
=
s
.
communicate
()
for
line
in
out
.
splitlines
():
if
"ERROR"
in
line
:
raise
McStasError
(
"An error occured during McStas run: %s"
%
line
)
raise
McStasError
(
"An error occured during McStas run: %s"
%
out
)
with
open
(
os
.
path
.
join
(
self
.
configuration
[
"options"
][
"mcstas_output_directory"
],
"mcstas_mdanse.mvi"
),
"w"
)
as
f
:
f
.
write
(
out
)
...
...
Tests/FunctionalTests/Jobs/Test_mvi.py
View file @
35734a7b
...
...
@@ -11,9 +11,9 @@ class TestMVI(UnitTest):
parameters
[
'display'
]
=
False
parameters
[
'frames'
]
=
(
0
,
10
,
1
)
parameters
[
'instrument'
]
=
'../../../Data/McStas/Instruments/Simple_ToF_Flat_Sample.out'
parameters
[
'options'
]
=
{
'ncount'
:
10000
,
'dir'
:
'/tmp/mcstas_output/
06.10
.201
5
-1
7:23
:5
3
'
}
parameters
[
'options'
]
=
{
'ncount'
:
10000
,
'dir'
:
'/tmp/mcstas_output/
27.01
.201
6
-1
4:49
:5
1
'
}
parameters
[
'output_files'
]
=
(
'/tmp/output'
,
[
'netcdf'
])
parameters
[
'parameters'
]
=
{
'beam_wavelength_Angs'
:
2.0
,
'container_thickness_m'
:
5e-05
,
'environment_radius_m'
:
0.025
,
'sample_detector_distance_m'
:
4.0
,
'container'
:
'/
users
/pellegrini/
workspace/MDANSE
/Data/McStas/Samples/Al.laz'
,
'environment_thickness_m'
:
0.002
,
'detector_height_m'
:
3.0
,
'beam_resolution_meV'
:
0.1
,
'sample_height_m'
:
0.05
,
'sample_thickness_m'
:
0.001
,
'environment'
:
'/
users
/pellegrini/
workspace/MDANSE
/Data/McStas/Samples/Al.laz'
,
'sample_width_m'
:
0.02
,
'sample_rotation_deg'
:
45.0
}
parameters
[
'parameters'
]
=
{
'beam_wavelength_Angs'
:
2.0
,
'container_thickness_m'
:
5e-05
,
'environment_radius_m'
:
0.025
,
'sample_detector_distance_m'
:
4.0
,
'container'
:
'/
home
/pellegrini/
git/mdanse
/Data/McStas/Samples/Al.laz'
,
'environment_thickness_m'
:
0.002
,
'detector_height_m'
:
3.0
,
'beam_resolution_meV'
:
0.1
,
'sample_height_m'
:
0.05
,
'sample_thickness_m'
:
0.001
,
'environment'
:
'/
home
/pellegrini/
git/mdanse
/Data/McStas/Samples/Al.laz'
,
'sample_width_m'
:
0.02
,
'sample_rotation_deg'
:
45.0
}
parameters
[
'sample_coh'
]
=
'../../../Data/NetCDF/dcsf_prot.nc'
parameters
[
'sample_inc'
]
=
'../../../Data/NetCDF/disf_prot.nc'
parameters
[
'temperature'
]
=
298.0
...
...
Tests/FunctionalTests/Jobs/Test_test.py
deleted
100755 → 0
View file @
b6892c0b
#!/usr/bin/python
import
unittest
from
Tests.UnitTests.UnitTest
import
UnitTest
from
MDANSE
import
REGISTRY
class
TestTEST
(
UnitTest
):
def
test
(
self
):
parameters
=
{}
parameters
[
'frames'
]
=
(
0
,
10
,
1
)
parameters
[
'output_files'
]
=
(
'/tmp/output'
,
[
'netcdf'
])
parameters
[
'trajectory'
]
=
'../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
job
=
REGISTRY
[
'job'
][
'test'
]()
self
.
assertNotRaises
(
job
.
run
,
parameters
,
status
=
False
)
def
suite
():
loader
=
unittest
.
TestLoader
()
s
=
unittest
.
TestSuite
()
s
.
addTest
(
loader
.
loadTestsFromTestCase
(
TestTEST
))
return
s
if
__name__
==
'__main__'
:
unittest
.
main
(
verbosity
=
2
)
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