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Scientific Software
MDANSE
Commits
eafd3ee4
Commit
eafd3ee4
authored
Sep 29, 2015
by
eric pellegrini
Browse files
Updated the unit and functional tests according to the changes made on
MDANSE API
parent
98878138
Changes
54
Hide whitespace changes
Inline
Side-by-side
Tests/FunctionalTests/Jobs/Test_ac.py
View file @
eafd3ee4
...
...
@@ -10,7 +10,7 @@ class TestAC(UnitTest):
parameters
=
{}
parameters
[
'axis_selection'
]
=
(
'Water'
,
(
'OW'
,
'HW'
))
parameters
[
'frames'
]
=
(
0
,
10
,
1
)
parameters
[
'output_files'
]
=
(
'output'
,
[
'netcdf'
])
parameters
[
'output_files'
]
=
(
'
/tmp/
output'
,
[
'netcdf'
])
parameters
[
'per_axis'
]
=
False
parameters
[
'running_mode'
]
=
(
'monoprocessor'
,
1
)
parameters
[
'trajectory'
]
=
'../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
...
...
Tests/FunctionalTests/Jobs/Test_apm.py
View file @
eafd3ee4
...
...
@@ -11,7 +11,7 @@ class TestAPM(UnitTest):
parameters
[
'axis'
]
=
[
'a'
,
'b'
]
parameters
[
'frames'
]
=
(
0
,
10
,
1
)
parameters
[
'name'
]
=
'DMPC'
parameters
[
'output_files'
]
=
(
'output'
,
[
'netcdf'
])
parameters
[
'output_files'
]
=
(
'
/tmp/
output'
,
[
'netcdf'
])
parameters
[
'running_mode'
]
=
(
'monoprocessor'
,
1
)
parameters
[
'trajectory'
]
=
'../../../Data/Trajectories/MMTK/dmpc_in_periodic_universe.nc'
job
=
REGISTRY
[
'job'
][
'apm'
]()
...
...
Tests/FunctionalTests/Jobs/Test_btt.py
View file @
eafd3ee4
...
...
@@ -10,7 +10,7 @@ class TestBTT(UnitTest):
parameters
=
{}
parameters
[
'atom_selection'
]
=
'all'
parameters
[
'frames'
]
=
(
0
,
10
,
1
)
parameters
[
'output_files'
]
=
(
'output'
,
[
'netcdf'
])
parameters
[
'output_files'
]
=
(
'
/tmp/
output'
,
[
'netcdf'
])
parameters
[
'trajectory'
]
=
'../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
job
=
REGISTRY
[
'job'
][
'btt'
]()
self
.
assertNotRaises
(
job
.
run
,
parameters
,
status
=
False
)
...
...
Tests/FunctionalTests/Jobs/Test_castep.py
View file @
eafd3ee4
...
...
@@ -9,7 +9,7 @@ class TestCASTEP(UnitTest):
def
test
(
self
):
parameters
=
{}
parameters
[
'castep_file'
]
=
'../../../Data/Trajectories/CASTEP/PBAnew.md'
parameters
[
'output_file'
]
=
(
'output'
,
[
'netcdf'
])
parameters
[
'output_file'
]
=
(
'
/tmp/
output'
,
[
'netcdf'
])
job
=
REGISTRY
[
'job'
][
'castep'
]()
self
.
assertNotRaises
(
job
.
run
,
parameters
,
status
=
False
)
...
...
Tests/FunctionalTests/Jobs/Test_ccf.py
View file @
eafd3ee4
...
...
@@ -12,7 +12,7 @@ class TestCCF(UnitTest):
parameters
[
'frames'
]
=
(
0
,
10
,
1
)
parameters
[
'instrument_resolution'
]
=
(
'gaussian'
,
{
'mu'
:
0.0
,
'sigma'
:
10.0
})
parameters
[
'normalize'
]
=
False
parameters
[
'output_files'
]
=
(
'output'
,
[
'netcdf'
])
parameters
[
'output_files'
]
=
(
'
/tmp/
output'
,
[
'netcdf'
])
parameters
[
'q_vectors'
]
=
(
'spherical_lattice'
,
{
'width'
:
0.1
,
'n_vectors'
:
50
,
'shells'
:
(
0
,
5
,
0.1
)})
parameters
[
'running_mode'
]
=
(
'monoprocessor'
,
1
)
parameters
[
'trajectory'
]
=
'../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
...
...
Tests/FunctionalTests/Jobs/Test_charmm.py
View file @
eafd3ee4
...
...
@@ -10,7 +10,7 @@ class TestCHARMM(UnitTest):
parameters
=
{}
parameters
[
'dcd_file'
]
=
'../../../Data/Trajectories/CHARMM/2vb1.dcd'
parameters
[
'fold'
]
=
False
parameters
[
'output_file'
]
=
(
'output'
,
[
'netcdf'
])
parameters
[
'output_file'
]
=
(
'
/tmp/
output'
,
[
'netcdf'
])
parameters
[
'pdb_file'
]
=
'../../../Data/Trajectories/CHARMM/2vb1.pdb'
job
=
REGISTRY
[
'job'
][
'charmm'
]()
self
.
assertNotRaises
(
job
.
run
,
parameters
,
status
=
False
)
...
...
Tests/FunctionalTests/Jobs/Test_cn.py
View file @
eafd3ee4
...
...
@@ -10,7 +10,7 @@ class TestCN(UnitTest):
parameters
=
{}
parameters
[
'atom_selection'
]
=
'all'
parameters
[
'frames'
]
=
(
0
,
10
,
1
)
parameters
[
'output_files'
]
=
(
'output'
,
[
'netcdf'
])
parameters
[
'output_files'
]
=
(
'
/tmp/
output'
,
[
'netcdf'
])
parameters
[
'r_values'
]
=
(
0
,
10
,
1
)
parameters
[
'running_mode'
]
=
(
'monoprocessor'
,
1
)
parameters
[
'trajectory'
]
=
'../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
...
...
Tests/FunctionalTests/Jobs/Test_comt.py
View file @
eafd3ee4
...
...
@@ -11,7 +11,7 @@ class TestCOMT(UnitTest):
parameters
[
'atom_selection'
]
=
'all'
parameters
[
'frames'
]
=
(
0
,
1
,
1
)
parameters
[
'grouping_level'
]
=
'atom'
parameters
[
'output_files'
]
=
(
'output'
,
[
'netcdf'
])
parameters
[
'output_files'
]
=
(
'
/tmp/
output'
,
[
'netcdf'
])
parameters
[
'trajectory'
]
=
'../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
job
=
REGISTRY
[
'job'
][
'comt'
]()
self
.
assertNotRaises
(
job
.
run
,
parameters
,
status
=
False
)
...
...
Tests/FunctionalTests/Jobs/Test_ct.py
View file @
eafd3ee4
...
...
@@ -10,7 +10,7 @@ class TestCT(UnitTest):
parameters
=
{}
parameters
[
'atom_selection'
]
=
'all'
parameters
[
'frames'
]
=
(
0
,
10
,
1
)
parameters
[
'output_files'
]
=
(
'output'
,
[
'netcdf'
])
parameters
[
'output_files'
]
=
(
'
/tmp/
output'
,
[
'netcdf'
])
parameters
[
'trajectory'
]
=
'../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
job
=
REGISTRY
[
'job'
][
'ct'
]()
self
.
assertNotRaises
(
job
.
run
,
parameters
,
status
=
False
)
...
...
Tests/FunctionalTests/Jobs/Test_dacf.py
View file @
eafd3ee4
...
...
@@ -11,7 +11,7 @@ class TestDACF(UnitTest):
parameters
[
'atom_charges'
]
=
{
0
:
0.5
,
1
:
1.2
,
2
:
-
0.2
}
parameters
[
'atom_selection'
]
=
'atom_index 0,1,2'
parameters
[
'frames'
]
=
(
0
,
10
,
1
)
parameters
[
'output_files'
]
=
(
'output'
,
[
'netcdf'
])
parameters
[
'output_files'
]
=
(
'
/tmp/
output'
,
[
'netcdf'
])
parameters
[
'running_mode'
]
=
(
'monoprocessor'
,
1
)
parameters
[
'trajectory'
]
=
'../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
job
=
REGISTRY
[
'job'
][
'dacf'
]()
...
...
Tests/FunctionalTests/Jobs/Test_dcsf.py
View file @
eafd3ee4
...
...
@@ -11,7 +11,7 @@ class TestDCSF(UnitTest):
parameters
[
'atom_selection'
]
=
'all'
parameters
[
'frames'
]
=
(
0
,
10
,
1
)
parameters
[
'instrument_resolution'
]
=
(
'gaussian'
,
{
'mu'
:
0.0
,
'sigma'
:
10.0
})
parameters
[
'output_files'
]
=
(
'output'
,
[
'netcdf'
])
parameters
[
'output_files'
]
=
(
'
/tmp/
output'
,
[
'netcdf'
])
parameters
[
'q_vectors'
]
=
(
'spherical_lattice'
,
{
'width'
:
0.1
,
'n_vectors'
:
50
,
'shells'
:
(
0
,
5
,
0.1
)})
parameters
[
'running_mode'
]
=
(
'monoprocessor'
,
1
)
parameters
[
'trajectory'
]
=
'../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
...
...
Tests/FunctionalTests/Jobs/Test_den.py
View file @
eafd3ee4
...
...
@@ -9,7 +9,7 @@ class TestDEN(UnitTest):
def
test
(
self
):
parameters
=
{}
parameters
[
'frames'
]
=
(
0
,
10
,
1
)
parameters
[
'output_files'
]
=
(
'output'
,
[
'netcdf'
])
parameters
[
'output_files'
]
=
(
'
/tmp/
output'
,
[
'netcdf'
])
parameters
[
'running_mode'
]
=
(
'monoprocessor'
,
1
)
parameters
[
'trajectory'
]
=
'../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
job
=
REGISTRY
[
'job'
][
'den'
]()
...
...
Tests/FunctionalTests/Jobs/Test_dftb.py
View file @
eafd3ee4
...
...
@@ -8,7 +8,7 @@ class TestDFTB(UnitTest):
def
test
(
self
):
parameters
=
{}
parameters
[
'output_file'
]
=
(
'output'
,
[
'netcdf'
])
parameters
[
'output_file'
]
=
(
'
/tmp/
output'
,
[
'netcdf'
])
parameters
[
'trj_file'
]
=
'../../../Data/Trajectories/Forcite/nylon66_rho100_500K_v300K.trj'
parameters
[
'xtd_file'
]
=
'../../../Data/Trajectories/Forcite/nylon66_rho100_500K_v300K.xtd'
job
=
REGISTRY
[
'job'
][
'dftb'
]()
...
...
Tests/FunctionalTests/Jobs/Test_discover.py
View file @
eafd3ee4
...
...
@@ -9,7 +9,7 @@ class TestDISCOVER(UnitTest):
def
test
(
self
):
parameters
=
{}
parameters
[
'his_file'
]
=
'../../../Data/Trajectories/Discover/sushi.his'
parameters
[
'output_file'
]
=
(
'output'
,
[
'netcdf'
])
parameters
[
'output_file'
]
=
(
'
/tmp/
output'
,
[
'netcdf'
])
parameters
[
'xtd_file'
]
=
'../../../Data/Trajectories/Discover/sushi.xtd'
job
=
REGISTRY
[
'job'
][
'discover'
]()
self
.
assertNotRaises
(
job
.
run
,
parameters
,
status
=
False
)
...
...
Tests/FunctionalTests/Jobs/Test_disf.py
View file @
eafd3ee4
...
...
@@ -12,7 +12,7 @@ class TestDISF(UnitTest):
parameters
[
'frames'
]
=
(
0
,
10
,
1
)
parameters
[
'grouping_level'
]
=
'atom'
parameters
[
'instrument_resolution'
]
=
(
'gaussian'
,
{
'mu'
:
0.0
,
'sigma'
:
10.0
})
parameters
[
'output_files'
]
=
(
'output'
,
[
'netcdf'
])
parameters
[
'output_files'
]
=
(
'
/tmp/
output'
,
[
'netcdf'
])
parameters
[
'projection'
]
=
None
parameters
[
'q_vectors'
]
=
(
'spherical_lattice'
,
{
'width'
:
0.1
,
'n_vectors'
:
50
,
'shells'
:
(
0
,
5
,
0.1
)})
parameters
[
'running_mode'
]
=
(
'monoprocessor'
,
1
)
...
...
Tests/FunctionalTests/Jobs/Test_dl_poly.py
View file @
eafd3ee4
...
...
@@ -11,7 +11,7 @@ class TestDL_POLY(UnitTest):
parameters
[
'atom_aliases'
]
=
{}
parameters
[
'field_file'
]
=
'../../../Data/Trajectories/DL_Poly/FIELD_cumen'
parameters
[
'history_file'
]
=
'../../../Data/Trajectories/DL_Poly/HISTORY_cumen'
parameters
[
'output_file'
]
=
(
'output'
,
[
'netcdf'
])
parameters
[
'output_file'
]
=
(
'
/tmp/
output'
,
[
'netcdf'
])
parameters
[
'version'
]
=
'2'
job
=
REGISTRY
[
'job'
][
'dl_poly'
]()
self
.
assertNotRaises
(
job
.
run
,
parameters
,
status
=
False
)
...
...
Tests/FunctionalTests/Jobs/Test_dmol.py
View file @
eafd3ee4
...
...
@@ -9,7 +9,7 @@ class TestDMOL(UnitTest):
def
test
(
self
):
parameters
=
{}
parameters
[
'his_file'
]
=
'../../../Data/Trajectories/Discover/sushi.his'
parameters
[
'output_file'
]
=
(
'output'
,
[
'netcdf'
])
parameters
[
'output_file'
]
=
(
'
/tmp/
output'
,
[
'netcdf'
])
parameters
[
'xtd_file'
]
=
'../../../Data/Trajectories/Discover/sushi.xtd'
job
=
REGISTRY
[
'job'
][
'dmol'
]()
self
.
assertNotRaises
(
job
.
run
,
parameters
,
status
=
False
)
...
...
Tests/FunctionalTests/Jobs/Test_dos.py
View file @
eafd3ee4
...
...
@@ -14,7 +14,7 @@ class TestDOS(UnitTest):
parameters
[
'grouping_level'
]
=
'atom'
parameters
[
'instrument_resolution'
]
=
(
'gaussian'
,
{
'mu'
:
0.0
,
'sigma'
:
10.0
})
parameters
[
'interpolation_order'
]
=
'no interpolation'
parameters
[
'output_files'
]
=
(
'output'
,
[
'netcdf'
])
parameters
[
'output_files'
]
=
(
'
/tmp/
output'
,
[
'netcdf'
])
parameters
[
'projection'
]
=
None
parameters
[
'running_mode'
]
=
(
'monoprocessor'
,
1
)
parameters
[
'trajectory'
]
=
'../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
...
...
Tests/FunctionalTests/Jobs/Test_dp.py
View file @
eafd3ee4
...
...
@@ -12,7 +12,7 @@ class TestDP(UnitTest):
parameters
[
'axis'
]
=
'c'
parameters
[
'dr'
]
=
0.01
parameters
[
'frames'
]
=
(
0
,
10
,
1
)
parameters
[
'output_files'
]
=
(
'output'
,
[
'netcdf'
])
parameters
[
'output_files'
]
=
(
'
/tmp/
output'
,
[
'netcdf'
])
parameters
[
'running_mode'
]
=
(
'monoprocessor'
,
1
)
parameters
[
'trajectory'
]
=
'../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
parameters
[
'transmutated_atoms'
]
=
None
...
...
Tests/FunctionalTests/Jobs/Test_ecc.py
View file @
eafd3ee4
...
...
@@ -11,7 +11,7 @@ class TestECC(UnitTest):
parameters
[
'atom_selection'
]
=
'all'
parameters
[
'center_of_mass'
]
=
'all'
parameters
[
'frames'
]
=
(
0
,
10
,
1
)
parameters
[
'output_files'
]
=
(
'output'
,
[
'netcdf'
])
parameters
[
'output_files'
]
=
(
'
/tmp/
output'
,
[
'netcdf'
])
parameters
[
'trajectory'
]
=
'../../../Data/Trajectories/MMTK/waterbox_in_periodic_universe.nc'
parameters
[
'weights'
]
=
'equal'
job
=
REGISTRY
[
'job'
][
'ecc'
]()
...
...
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