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Scientific Software
MDANSE
Commits
f2fc0ead
Commit
f2fc0ead
authored
Nov 29, 2016
by
eric pellegrini
Browse files
Merge tag '1.0.4.rc4' into develop
version 1.0.4.rc4
parents
62c424a7
70af3d2b
Pipeline
#1336
passed with stages
in 11 minutes and 49 seconds
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5
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9
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CHANGELOG
View file @
f2fc0ead
version 1.0.4.rc2
version 1.0.4.rc4
----------------
* bug fix in coordination number analysis: some pairs were never taken into account
* bug fix when transmutating atoms from an atom selection different to 'all'
version 1.0.4.rc3
----------------
* bug fix in debian packager: add the python-setuptools dependency
* improved LAMMPS converter: the parsing of the config file is more tolerance in term of required keyword format
...
...
MDANSE/Framework/Configurators/AtomSelectionConfigurator.py
View file @
f2fc0ead
...
...
@@ -105,14 +105,17 @@ class AtomSelectionConfigurator(IConfigurator):
parser
=
AtomSelectionParser
(
trajConfig
[
"instance"
])
indexes
.
update
(
parser
.
parse
(
v
))
indexes
=
sorted
(
list
(
indexes
))
self
[
"flatten_indexes"
]
=
sorted
(
list
(
indexes
))
trajConfig
=
self
.
_configurable
[
self
.
_dependencies
[
'trajectory'
]]
atoms
=
sorted
(
trajConfig
[
"universe"
].
atomList
(),
key
=
operator
.
attrgetter
(
'index'
))
selectedAtoms
=
[
atoms
[
idx
]
for
idx
in
indexes
]
self
[
"selection_length"
]
=
len
(
indexes
)
self
[
"selection_length"
]
=
len
(
self
[
"flatten_indexes"
])
self
[
'indexes'
]
=
[[
idx
]
for
idx
in
self
[
"flatten_indexes"
]]
self
[
'elements'
]
=
[[
at
.
symbol
]
for
at
in
selectedAtoms
]
self
[
'indexes'
]
=
[[
idx
]
for
idx
in
indexes
]
self
[
'names'
]
=
[
at
.
symbol
for
at
in
selectedAtoms
]
self
[
'unique_names'
]
=
sorted
(
set
(
self
[
'names'
]))
self
[
'masses'
]
=
[[
ELEMENTS
[
n
,
'atomic_weight'
]]
for
n
in
self
[
'names'
]]
...
...
MDANSE/Framework/Configurators/AtomTransmutationConfigurator.py
View file @
f2fc0ead
...
...
@@ -112,12 +112,18 @@ class AtomTransmutationConfigurator(IConfigurator):
raise
ConfiguratorError
(
"the element %r is not registered in the database"
%
element
,
self
)
atomSelConfigurator
=
self
.
_configurable
[
self
.
_dependencies
[
'atom_selection'
]]
for
idx
in
selection
:
atomSelConfigurator
[
"names"
][
idx
]
=
element
atomSelConfigurator
[
"elements"
][
idx
]
=
[
element
]
try
:
idxInSelection
=
atomSelConfigurator
[
"flatten_indexes"
].
index
(
idx
)
except
ValueError
:
pass
else
:
atomSelConfigurator
[
"names"
][
idxInSelection
]
=
element
atomSelConfigurator
[
"elements"
][
idxInSelection
]
=
[
element
]
atomSelConfigurator
[
'unique_names'
]
=
sorted
(
set
(
atomSelConfigurator
[
'names'
]))
atomSelConfigurator
[
'masses'
]
=
[[
ELEMENTS
[
n
,
'atomic_weight'
]]
for
n
in
atomSelConfigurator
[
'names'
]]
def
get_information
(
self
):
'''
...
...
MDANSE/Framework/Jobs/CoordinationNumber.py
View file @
f2fc0ead
...
...
@@ -93,7 +93,8 @@ class CoordinationNumber(DistanceHistogram):
self
.
_concentrations
[
k
]
/=
nFrames
nAtomsPerElement
=
self
.
configuration
[
'atom_selection'
].
get_natoms
()
for
at1
,
at2
in
self
.
_elementsPairs
:
for
pair
in
self
.
_elementsPairs
:
at1
,
at2
=
pair
ni
=
nAtomsPerElement
[
at1
]
nj
=
nAtomsPerElement
[
at2
]
...
...
@@ -120,6 +121,7 @@ class CoordinationNumber(DistanceHistogram):
cBeta
=
self
.
_concentrations
[
pair
[
1
]]
invPair
=
pair
[::
-
1
]
print
pair
,
cnIntra
self
.
_outputData
[
"cn_intra_%s%s"
%
pair
][:]
=
self
.
averageDensity
*
cBeta
*
cnIntra
self
.
_outputData
[
"cn_inter_%s%s"
%
pair
][:]
=
self
.
averageDensity
*
cBeta
*
cnInter
self
.
_outputData
[
"cn_total_%s%s"
%
pair
][:]
=
self
.
averageDensity
*
cBeta
*
cnTotal
...
...
MDANSE/__pkginfo__.py
View file @
f2fc0ead
__version__
=
"1.0.4.rc
3
"
__version__
=
"1.0.4.rc
4
"
__date__
=
"2
8
-11-2016"
__date__
=
"2
9
-11-2016"
__author__
=
"Eric Pellegrini"
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