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Scientific Software
MDANSE
Commits
b83428de
Commit
b83428de
authored
Jun 04, 2018
by
Remi Perenon
Browse files
Options
Browse Files
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Plain Diff
Replacing all output_file occurences by output_files
parent
8235f09d
Pipeline
#3840
passed with stages
in 17 minutes and 22 seconds
Changes
10
Pipelines
2
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Inline
Side-by-side
Showing
10 changed files
with
19 additions
and
22 deletions
+19
-22
MDANSE/Framework/Jobs/Castep.py
MDANSE/Framework/Jobs/Castep.py
+2
-2
MDANSE/Framework/Jobs/DCDConverter.py
MDANSE/Framework/Jobs/DCDConverter.py
+2
-2
MDANSE/Framework/Jobs/DL_POLY.py
MDANSE/Framework/Jobs/DL_POLY.py
+2
-2
MDANSE/Framework/Jobs/Discover.py
MDANSE/Framework/Jobs/Discover.py
+2
-2
MDANSE/Framework/Jobs/Forcite.py
MDANSE/Framework/Jobs/Forcite.py
+2
-2
MDANSE/Framework/Jobs/Generic.py
MDANSE/Framework/Jobs/Generic.py
+2
-2
MDANSE/Framework/Jobs/LAMMPS.py
MDANSE/Framework/Jobs/LAMMPS.py
+2
-2
MDANSE/Framework/Jobs/PDB.py
MDANSE/Framework/Jobs/PDB.py
+2
-2
MDANSE/Framework/Jobs/VASP.py
MDANSE/Framework/Jobs/VASP.py
+2
-2
Tests/FunctionalTests/Jobs/BuildJobTests.py
Tests/FunctionalTests/Jobs/BuildJobTests.py
+1
-4
No files found.
MDANSE/Framework/Jobs/Castep.py
View file @
b83428de
...
...
@@ -142,7 +142,7 @@ class CASTEPConverter(Converter):
settings
=
collections
.
OrderedDict
()
settings
[
'castep_file'
]
=
(
'input_file'
,
{
'default'
:
os
.
path
.
join
(
'..'
,
'..'
,
'..'
,
'Data'
,
'Trajectories'
,
'CASTEP'
,
'PBAnew.md'
)})
settings
[
'output_file'
]
=
(
'output_files'
,
{
'formats'
:[
"netcdf"
]})
settings
[
'output_file
s
'
]
=
(
'output_files'
,
{
'formats'
:[
"netcdf"
]})
def
initialize
(
self
):
"""
...
...
@@ -165,7 +165,7 @@ class CASTEPConverter(Converter):
self
.
_gradients
=
ParticleVector
(
self
.
_universe
)
# A MMTK trajectory is opened for writing.
self
.
_trajectory
=
Trajectory
(
self
.
_universe
,
self
.
configuration
[
'output_file'
][
'files'
][
0
],
mode
=
'w'
)
self
.
_trajectory
=
Trajectory
(
self
.
_universe
,
self
.
configuration
[
'output_file
s
'
][
'files'
][
0
],
mode
=
'w'
)
# A frame generator is created.
self
.
_snapshot
=
SnapshotGenerator
(
self
.
_universe
,
actions
=
[
TrajectoryOutput
(
self
.
_trajectory
,
[
"all"
],
0
,
None
,
1
)])
...
...
MDANSE/Framework/Jobs/DCDConverter.py
View file @
b83428de
...
...
@@ -280,7 +280,7 @@ class DCDConverter(Converter):
settings
=
collections
.
OrderedDict
()
settings
[
'pdb_file'
]
=
(
'input_file'
,{
'default'
:
os
.
path
.
join
(
'..'
,
'..'
,
'..'
,
'Data'
,
'Trajectories'
,
'CHARMM'
,
'2vb1.pdb'
)})
settings
[
'dcd_file'
]
=
(
'input_file'
,{
'default'
:
os
.
path
.
join
(
'..'
,
'..'
,
'..'
,
'Data'
,
'Trajectories'
,
'CHARMM'
,
'2vb1.dcd'
)})
settings
[
'output_file'
]
=
(
'output_files'
,
{
'formats'
:[
"netcdf"
]})
settings
[
'output_file
s
'
]
=
(
'output_files'
,
{
'formats'
:[
"netcdf"
]})
settings
[
'fold'
]
=
(
'boolean'
,
{
'default'
:
False
,
'label'
:
"Fold coordinates in to box"
})
def
initialize
(
self
):
...
...
@@ -313,7 +313,7 @@ class DCDConverter(Converter):
resolve_undefined_molecules_name
(
self
.
_universe
)
# A MMTK trajectory is opened for writing.
self
.
_trajectory
=
Trajectory
(
self
.
_universe
,
self
.
configuration
[
'output_file'
][
'files'
][
0
],
mode
=
'w'
)
self
.
_trajectory
=
Trajectory
(
self
.
_universe
,
self
.
configuration
[
'output_file
s
'
][
'files'
][
0
],
mode
=
'w'
)
# A frame generator is created.
self
.
_snapshot
=
SnapshotGenerator
(
self
.
_universe
,
actions
=
[
TrajectoryOutput
(
self
.
_trajectory
,
[
"all"
],
0
,
None
,
1
)])
...
...
MDANSE/Framework/Jobs/DL_POLY.py
View file @
b83428de
...
...
@@ -299,7 +299,7 @@ class DL_POLYConverter(Converter):
'default'
:
os
.
path
.
join
(
'..'
,
'..'
,
'..'
,
'Data'
,
'Trajectories'
,
'DL_Poly'
,
'HISTORY_cumen'
)})
settings
[
'atom_aliases'
]
=
(
'python_object'
,{
'default'
:{}})
settings
[
'version'
]
=
(
'single_choice'
,
{
'choices'
:
_HISTORY_FORMAT
.
keys
(),
'default'
:
'2'
})
settings
[
'output_file'
]
=
(
'output_files'
,
{
'formats'
:[
"netcdf"
]})
settings
[
'output_file
s
'
]
=
(
'output_files'
,
{
'formats'
:[
"netcdf"
]})
def
initialize
(
self
):
'''
...
...
@@ -338,7 +338,7 @@ class DL_POLYConverter(Converter):
# A MMTK trajectory is opened for writing.
self
.
_trajectory
=
Trajectory
(
self
.
_universe
,
self
.
configuration
[
'output_file'
][
'files'
][
0
],
mode
=
'w'
,
comment
=
self
.
_fieldFile
[
"title"
])
self
.
_trajectory
=
Trajectory
(
self
.
_universe
,
self
.
configuration
[
'output_file
s
'
][
'files'
][
0
],
mode
=
'w'
,
comment
=
self
.
_fieldFile
[
"title"
])
# A frame generator is created.
self
.
_snapshot
=
SnapshotGenerator
(
self
.
_universe
,
actions
=
[
TrajectoryOutput
(
self
.
_trajectory
,
[
"all"
],
0
,
None
,
1
)])
...
...
MDANSE/Framework/Jobs/Discover.py
View file @
b83428de
...
...
@@ -235,7 +235,7 @@ class DiscoverConverter(Converter):
settings
=
collections
.
OrderedDict
()
settings
[
'xtd_file'
]
=
(
'input_file'
,{
'default'
:
os
.
path
.
join
(
'..'
,
'..'
,
'..'
,
'Data'
,
'Trajectories'
,
'Discover'
,
'sushi.xtd'
)})
settings
[
'his_file'
]
=
(
'input_file'
,{
'default'
:
os
.
path
.
join
(
'..'
,
'..'
,
'..'
,
'Data'
,
'Trajectories'
,
'Discover'
,
'sushi.his'
)})
settings
[
'output_file'
]
=
(
'output_files'
,
{
'formats'
:[
"netcdf"
]})
settings
[
'output_file
s
'
]
=
(
'output_files'
,
{
'formats'
:[
"netcdf"
]})
def
initialize
(
self
):
'''
...
...
@@ -267,7 +267,7 @@ class DiscoverConverter(Converter):
self
.
_universe
.
foldCoordinatesIntoBox
()
# A MMTK trajectory is opened for writing.
self
.
_trajectory
=
Trajectory
(
self
.
_universe
,
self
.
configuration
[
'output_file'
][
'files'
][
0
],
mode
=
'w'
,
comment
=
self
.
_hisfile
[
"title"
])
self
.
_trajectory
=
Trajectory
(
self
.
_universe
,
self
.
configuration
[
'output_file
s
'
][
'files'
][
0
],
mode
=
'w'
,
comment
=
self
.
_hisfile
[
"title"
])
# A frame generator is created.
self
.
_snapshot
=
SnapshotGenerator
(
self
.
_universe
,
actions
=
[
TrajectoryOutput
(
self
.
_trajectory
,
[
"all"
],
0
,
None
,
1
)])
...
...
MDANSE/Framework/Jobs/Forcite.py
View file @
b83428de
...
...
@@ -285,7 +285,7 @@ class ForciteConverter(Converter):
settings
=
collections
.
OrderedDict
()
settings
[
'xtd_file'
]
=
(
'input_file'
,{
'default'
:
os
.
path
.
join
(
'..'
,
'..'
,
'..'
,
'Data'
,
'Trajectories'
,
'Forcite'
,
'nylon66_rho100_500K_v300K.xtd'
)})
settings
[
'trj_file'
]
=
(
'input_file'
,{
'default'
:
os
.
path
.
join
(
'..'
,
'..'
,
'..'
,
'Data'
,
'Trajectories'
,
'Forcite'
,
'nylon66_rho100_500K_v300K.trj'
)})
settings
[
'output_file'
]
=
(
'output_files'
,
{
'formats'
:[
"netcdf"
]})
settings
[
'output_file
s
'
]
=
(
'output_files'
,
{
'formats'
:[
"netcdf"
]})
def
initialize
(
self
):
'''
...
...
@@ -315,7 +315,7 @@ class ForciteConverter(Converter):
self
.
_forces
.
array
[:,:]
=
0.00
# A MMTK trajectory is opened for writing.
self
.
_trajectory
=
Trajectory
(
self
.
_universe
,
self
.
configuration
[
'output_file'
][
'files'
][
0
],
mode
=
'w'
,
comment
=
self
.
_trjfile
[
"title"
])
self
.
_trajectory
=
Trajectory
(
self
.
_universe
,
self
.
configuration
[
'output_file
s
'
][
'files'
][
0
],
mode
=
'w'
,
comment
=
self
.
_trjfile
[
"title"
])
# A frame generator is created.
self
.
_snapshot
=
SnapshotGenerator
(
self
.
_universe
,
actions
=
[
TrajectoryOutput
(
self
.
_trajectory
,
[
"all"
],
0
,
None
,
1
)])
...
...
MDANSE/Framework/Jobs/Generic.py
View file @
b83428de
...
...
@@ -166,7 +166,7 @@ class GenericConverter(Converter):
settings
=
collections
.
OrderedDict
()
settings
[
'gt_file'
]
=
(
'input_file'
,{
'wildcard'
:
"Generic trajectory files|*.gtf|All files|*"
,
'default'
:
os
.
path
.
join
(
'..'
,
'..'
,
'..'
,
'Data'
,
'Trajectories'
,
'Generic'
,
'test.gtf'
)})
settings
[
'output_file'
]
=
(
'output_files'
,
{
'formats'
:[
"netcdf"
]})
settings
[
'output_file
s
'
]
=
(
'output_files'
,
{
'formats'
:[
"netcdf"
]})
def
initialize
(
self
):
'''
...
...
@@ -331,7 +331,7 @@ class GenericConverter(Converter):
self
.
_dataShape
=
(
self
.
_universe
.
numberOfAtoms
(),
3
)
# A MMTK trajectory is opened for writing.
self
.
_trajectory
=
Trajectory
(
self
.
_universe
,
self
.
configuration
[
'output_file'
][
'files'
][
0
],
mode
=
'w'
)
self
.
_trajectory
=
Trajectory
(
self
.
_universe
,
self
.
configuration
[
'output_file
s
'
][
'files'
][
0
],
mode
=
'w'
)
# A frame generator is created.
self
.
_snapshot
=
SnapshotGenerator
(
self
.
_universe
,
actions
=
[
TrajectoryOutput
(
self
.
_trajectory
,
[
"all"
],
0
,
None
,
1
)])
...
...
MDANSE/Framework/Jobs/LAMMPS.py
View file @
b83428de
...
...
@@ -140,7 +140,7 @@ class LAMMPSConverter(Converter):
settings
[
'mass_tolerance'
]
=
(
'float'
,
{
'label'
:
"mass tolerance (uma)"
,
'default'
:
1.0e-5
,
'mini'
:
1.0e-9
})
settings
[
'time_step'
]
=
(
'float'
,
{
'label'
:
"time step (fs)"
,
'default'
:
1.0
,
'mini'
:
1.0e-9
})
settings
[
'n_steps'
]
=
(
'integer'
,
{
'label'
:
"number of time steps"
,
'default'
:
1
,
'mini'
:
0
})
settings
[
'output_file'
]
=
(
'output_files'
,
{
'formats'
:[
"netcdf"
]})
settings
[
'output_file
s
'
]
=
(
'output_files'
,
{
'formats'
:[
"netcdf"
]})
def
initialize
(
self
):
'''
...
...
@@ -155,7 +155,7 @@ class LAMMPSConverter(Converter):
self
.
parse_first_step
()
# A MMTK trajectory is opened for writing.
self
.
_trajectory
=
Trajectory
(
self
.
_universe
,
self
.
configuration
[
'output_file'
][
'files'
][
0
],
mode
=
'w'
)
self
.
_trajectory
=
Trajectory
(
self
.
_universe
,
self
.
configuration
[
'output_file
s
'
][
'files'
][
0
],
mode
=
'w'
)
self
.
_nameToIndex
=
dict
([(
at
.
name
,
at
.
index
)
for
at
in
self
.
_universe
.
atomList
()])
...
...
MDANSE/Framework/Jobs/PDB.py
View file @
b83428de
...
...
@@ -51,7 +51,7 @@ class PDBConverter(Converter):
settings
[
'pdb_file'
]
=
(
'input_file'
,{
'default'
:
os
.
path
.
join
(
'..'
,
'..'
,
'..'
,
'Data'
,
'Trajectories'
,
'PDB'
,
'2f58_nma.pdb'
)})
settings
[
'nb_frame'
]
=
(
'range'
,
{
'valueType'
:
int
,
'includeLast'
:
True
,
'mini'
:
0.0
,
'default'
:(
0
,
2
,
1
)})
settings
[
'time_step'
]
=
(
'float'
,
{
'mini'
:
1.0e-6
,
'default'
:
1.0
})
settings
[
'output_file'
]
=
(
'output_files'
,
{
'formats'
:[
"netcdf"
]})
settings
[
'output_file
s
'
]
=
(
'output_files'
,
{
'formats'
:[
"netcdf"
]})
def
initialize
(
self
):
"""
...
...
@@ -71,7 +71,7 @@ class PDBConverter(Converter):
self
.
_universe
.
addObject
(
pdb_config
.
createAll
(
None
,
1
))
# Open the new trajectory
self
.
_trajectory
=
Trajectory
(
self
.
_universe
,
self
.
configuration
[
'output_file'
][
'files'
][
0
],
"w"
,
"Converted from PDB"
)
self
.
_trajectory
=
Trajectory
(
self
.
_universe
,
self
.
configuration
[
'output_file
s
'
][
'files'
][
0
],
"w"
,
"Converted from PDB"
)
# Make a snapshot generator for saving.
self
.
_snapshot
=
SnapshotGenerator
(
self
.
_universe
,
actions
=
[
TrajectoryOutput
(
self
.
_trajectory
,
None
,
0
,
None
,
1
)])
...
...
MDANSE/Framework/Jobs/VASP.py
View file @
b83428de
...
...
@@ -126,7 +126,7 @@ class VASPConverter(Converter):
settings
=
collections
.
OrderedDict
()
settings
[
'xdatcar_file'
]
=
(
'input_file'
,{
'default'
:
os
.
path
.
join
(
'..'
,
'..'
,
'..'
,
'Data'
,
'Trajectories'
,
'VASP'
,
'XDATCAR_version5'
)})
settings
[
'time_step'
]
=
(
'float'
,
{
'label'
:
"time step"
,
'default'
:
1.0
,
'mini'
:
1.0e-9
})
settings
[
'output_file'
]
=
(
'output_files'
,
{
'formats'
:[
"netcdf"
]})
settings
[
'output_file
s
'
]
=
(
'output_files'
,
{
'formats'
:[
"netcdf"
]})
def
initialize
(
self
):
'''
...
...
@@ -146,7 +146,7 @@ class VASPConverter(Converter):
self
.
_universe
.
addObject
(
Atom
(
symbol
,
name
=
"%s_%d"
%
(
symbol
,
i
)))
# A MMTK trajectory is opened for writing.
self
.
_trajectory
=
Trajectory
(
self
.
_universe
,
self
.
configuration
[
'output_file'
][
'files'
][
0
],
mode
=
'w'
)
self
.
_trajectory
=
Trajectory
(
self
.
_universe
,
self
.
configuration
[
'output_file
s
'
][
'files'
][
0
],
mode
=
'w'
)
# A frame generator is created.
self
.
_snapshot
=
SnapshotGenerator
(
self
.
_universe
,
actions
=
[
TrajectoryOutput
(
self
.
_trajectory
,
[
"all"
],
0
,
None
,
1
)])
...
...
Tests/FunctionalTests/Jobs/BuildJobTests.py
View file @
b83428de
...
...
@@ -53,10 +53,7 @@ class JobFileGenerator():
temp
=
'parameters[%r] = %r
\n
'
%
(
k
,
v
)
test_string
=
test_string
+
' '
+
temp
.
replace
(
'
\\\\
'
,
'/'
)
test_string
=
test_string
+
' job = REGISTRY[%r][%r]()
\n
'
%
(
'job'
,
self
.
job
.
_type
)
test_string
=
test_string
+
' if "output_file" in parameters:
\n
'
test_string
=
test_string
+
' output_path = parameters["output_file"][0]
\n
'
test_string
=
test_string
+
' else:
\n
'
test_string
=
test_string
+
' output_path = parameters["output_files"][0]
\n
'
test_string
=
test_string
+
' output_path = parameters["output_files"][0]
\n
'
test_string
=
test_string
+
' reference_data_path = "'
+
self
.
reference_data_path
.
replace
(
'
\\
'
,
'/'
)
+
'"
\n
'
# Launch the job in monoprocessor mode and copy output file
test_string
=
test_string
+
' print "Launching job in monoprocessor mode"
\n
'
...
...
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