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Scientific Software
MDANSE
Commits
da5f5a9b
Commit
da5f5a9b
authored
Nov 22, 2016
by
eric pellegrini
Browse files
Merge tag '1.0.4.rc1' into develop
version 1.0.4.rc1
parents
47847a26
5dc706f0
Pipeline
#1177
failed with stages
in 10 minutes and 42 seconds
Changes
6
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CHANGELOG
View file @
da5f5a9b
version 1.0.4.rc1
----------------
* bug fix in IWidget: the label of the configurator was not taken into account
* bug fix path_to_module function: the list of directories has to be parsed backwards
* raise an error when none or more than atom matches the mass stored in the LAMMPS config file
* modified the label for r value
version 1.0.3.e:
----------------
* bug fix relative to REGISTRY update
...
...
MDANSE/Core/ClassRegistry.py
View file @
da5f5a9b
...
...
@@ -42,13 +42,13 @@ def path_to_module(path,stop=""):
path
,
_
=
os
.
path
.
splitext
(
path
)
splittedPath
=
path
.
split
(
os
.
sep
)
try
:
idx
=
splittedPath
.
index
(
stop
)
idx
=
splittedPath
[::
-
1
]
.
index
(
stop
)
except
ValueError
:
idx
=
0
finally
:
module
=
"."
.
join
(
splittedPath
[
idx
:])
module
=
"."
.
join
(
splittedPath
[
len
(
splittedPath
)
-
1
-
idx
:])
return
module
...
...
@@ -110,14 +110,14 @@ class ClassRegistry(object):
:param packageDir: the package for which all modules should be imported
:type packageDir: str
'''
for
module
in
glob
.
glob
(
os
.
path
.
join
(
packageDir
,
'*.py'
)):
moduleDir
,
moduleFile
=
os
.
path
.
split
(
module
)
if
moduleFile
==
'__init__.py'
:
continue
# Any error that may occur here has to be caught. In such case the module is skipped.
try
:
if
macros
:
...
...
MDANSE/Framework/Jobs/DistanceHistogram.py
View file @
da5f5a9b
...
...
@@ -50,7 +50,7 @@ class DistanceHistogram(IJob):
settings
=
collections
.
OrderedDict
()
settings
[
'trajectory'
]
=
(
'mmtk_trajectory'
,{})
settings
[
'frames'
]
=
(
'frames'
,
{
'dependencies'
:{
'trajectory'
:
'trajectory'
}})
settings
[
'r_values'
]
=
(
'range'
,
{
'valueType'
:
float
,
'includeLast'
:
True
,
'mini'
:
0.0
})
settings
[
'r_values'
]
=
(
'range'
,
{
'
label'
:
'r values (nm)'
,
'
valueType'
:
float
,
'includeLast'
:
True
,
'mini'
:
0.0
})
settings
[
'atom_selection'
]
=
(
'atom_selection'
,
{
'dependencies'
:{
'trajectory'
:
'trajectory'
}})
settings
[
'atom_transmutation'
]
=
(
'atom_transmutation'
,
{
'dependencies'
:{
'trajectory'
:
'trajectory'
,
'atom_selection'
:
'atom_selection'
}})
settings
[
'weights'
]
=
(
'weights'
,{
"dependencies"
:{
"atom_selection"
:
"atom_selection"
}})
...
...
MDANSE/Framework/Jobs/LAMMPS.py
View file @
da5f5a9b
...
...
@@ -100,7 +100,12 @@ class LAMMPSConfigFile(dict):
for
j
in
range
(
1
,
self
[
"n_atom_types"
]
+
1
):
idx
,
mass
=
lines
[
i
+
j
].
strip
().
split
()
el
=
ELEMENTS
.
match_numeric_property
(
"atomic_weight"
,
float
(
mass
),
tolerance
=
1.0e-3
)
tolerance
=
1.0e-3
idx
=
int
(
idx
)
mass
=
float
(
mass
)
el
=
ELEMENTS
.
match_numeric_property
(
"atomic_weight"
,
mass
,
tolerance
=
tolerance
)
if
len
(
el
)
!=
1
:
raise
LAMMPSConfigFileError
(
"The atom %d with defined mass %f could not be assigned with a tolerance of %f. Please modify the mass in the config file to comply with MDANSE internal database"
%
(
idx
,
mass
,
tolerance
))
self
[
"elements"
][
idx
]
=
el
[
0
]
m
=
re
.
match
(
"^bonds$"
,
line
,
re
.
I
)
...
...
MDANSE/GUI/Widgets/IWidget.py
View file @
da5f5a9b
...
...
@@ -50,7 +50,7 @@ class IWidget(wx.Panel):
self
.
_configurator
=
configurator
self
.
_label
=
' '
.
join
(
name
.
capitalize
().
split
(
'_'
))
self
.
_label
=
self
.
_configurator
.
label
self
.
initialize
()
...
...
MDANSE/__pkginfo__.py
View file @
da5f5a9b
__version__
=
"1.0.
3.e
"
__version__
=
"1.0.
4.rc1
"
__date__
=
"
18
-11-2016"
__date__
=
"
22
-11-2016"
__author__
=
"Eric Pellegrini"
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