Commit 98f7f78f authored by eric pellegrini's avatar eric pellegrini
Browse files

repopulate MDANSE

parent 57c9ead8
...@@ -2,7 +2,11 @@ ...@@ -2,7 +2,11 @@
rm -rf ../Documentation rm -rf ../Documentation
sphinx-apidoc -o ../Documentation -F --separate -d 5 -H nMoldyn -A "B. Aoun & G. Goret & E. Pellegrini, G.R. Kneller" -V 4.0 -R 4.0 ../nMOLDYN/ setenv PYTHONPATH=/home/pellegrini/workspace/MDANSE
cp doc_utils/conf_help.py ../Documentation/conf.py
cp doc_utils/layout.html ../Documentation/_templates/ sphinx-apidoc -o . -F --separate -d 5 -H mdanse -A "G. Goret, B. Aoun & E. Pellegrini" -V 4.0 -R 4.0 ../MDANSE
sphinx-build -b htmlhelp ../Documentation ../nMOLDYN/GUI/Help/ cp conf_help.py conf.py
cp layout.html _templates/
cp nMoldyn_logo.png _static/
sphinx-build -b htmlhelp ./ ./Help/
...@@ -17,7 +17,7 @@ import sys, os ...@@ -17,7 +17,7 @@ import sys, os
# add these directories to sys.path here. If the directory is relative to the # add these directories to sys.path here. If the directory is relative to the
# documentation root, use os.path.abspath to make it absolute, like shown here. # documentation root, use os.path.abspath to make it absolute, like shown here.
sys.path.append(os.path.abspath('../nMOLDYN')) sys.path.append(os.path.abspath('../MDANSE'))
# -- General configuration ----------------------------------------------------- # -- General configuration -----------------------------------------------------
...@@ -42,7 +42,7 @@ master_doc = 'index' ...@@ -42,7 +42,7 @@ master_doc = 'index'
# General information about the project. # General information about the project.
project = u'nMoldyn' project = u'nMoldyn'
copyright = u'2014, B. Aoun & G. Goret & E. Pellegrini, G.R. Kneller' copyright = u'2014, G. Goret & B. Aoun & E. Pellegrini'
# The version info for the project you're documenting, acts as replacement for # The version info for the project you're documenting, acts as replacement for
# |version| and |release|, also used in various other places throughout the # |version| and |release|, also used in various other places throughout the
...@@ -57,10 +57,10 @@ release = '4.0' ...@@ -57,10 +57,10 @@ release = '4.0'
# for source files. # for source files.
exclude_patterns = ['Externals','_build', '**Tests**'] exclude_patterns = ['Externals','_build', '**Tests**']
html_logo = '_static/nMoldyn_logo.png' html_logo = '_static/mdanse_logo.png'
inheritance_graph_attrs = dict(size='""') inheritance_graph_attrs = dict(size='""')
inheritance_graph_attrs = dict(rankdir="TB", size='""') inheritance_graph_attrs = dict(rankdir="TB", size='""')
inheritance_node_attrs = dict(color='lightblue', style='filled') inheritance_node_attrs = dict(color='lightblue', style='filled')
...@@ -82,16 +82,13 @@ html_show_copyright = False ...@@ -82,16 +82,13 @@ html_show_copyright = False
# Output file base name for HTML help builder. # Output file base name for HTML help builder.
htmlhelp_basename = 'nMoldyndoc' htmlhelp_basename = 'mdanseDoc'
# Grouping the document tree into LaTeX files. List of tuples # Grouping the document tree into LaTeX files. List of tuples
# (source start file, target name, title, author, documentclass [howto/manual]). # (source start file, target name, title, author, documentclass [howto/manual]).
latex_documents = [
('index', 'nMoldyn.tex', u'nMoldyn Documentation',
u'B. Aoun \\& G. Goret \\& E. Pellegrini, G.R. Kneller', 'manual'),
]
#pdf_documents = [ #pdf_documents = [
# ('index', 'nMoldyn', u'nMoldyn Documentation', # ('index', 'nMoldyn', u'nMoldyn Documentation',
...@@ -100,7 +97,7 @@ latex_documents = [ ...@@ -100,7 +97,7 @@ latex_documents = [
exclude_patterns = ['nMOLDYN.Externals**', 'nMOLDYN.nMOLDYN.__pkginfo__'] exclude_patterns = ['MDANSE.Externals**', 'MDANSE.__pkginfo__']
members_to_watch = ['class'] members_to_watch = ['class']
......
...@@ -24,7 +24,7 @@ class ClassRegistry(abc.ABCMeta): ...@@ -24,7 +24,7 @@ class ClassRegistry(abc.ABCMeta):
whose keys are the |type| class attribute of the subclasses and values are the corresponding whose keys are the |type| class attribute of the subclasses and values are the corresponding
class instances. class instances.
Hence any base or child class that does not define |type| class attribute will not be registered. Hence any base or child class that does not define |type| class attribute will not be resgistered.
''' '''
__metaclass__ = _Meta __metaclass__ = _Meta
......
'''
MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
------------------------------------------------------------------------------------------
Copyright (C)
2015- Eric C. Pellegrini Institut Laue-Langevin
BP 156
6, rue Jules Horowitz
38042 Grenoble Cedex 9
France
pellegrini[at]ill.fr
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Created on Mar 23, 2015
@author: pellegrini
'''
import _abcoll import _abcoll
import ast
import copy import copy
import csv import csv
import numbers import numbers
import os import os
import xml.etree.ElementTree as etree import xml.etree.ElementTree as etree
from MMTK import Atom from MDANSE.Core.Platform import PLATFORM
from MDANSE.Core.Error import Error
from nMOLDYN import PLATFORM from MDANSE.Core.Singleton import Singleton
from nMOLDYN.Core.Error import Error
from nMOLDYN.Core.Singleton import Singleton
class ElementsDatabaseError(Error): class ElementsDatabaseError(Error):
pass pass
...@@ -138,6 +165,8 @@ class SortedCaselessDict(dict): ...@@ -138,6 +165,8 @@ class SortedCaselessDict(dict):
class ElementsDatabase(object): class ElementsDatabase(object):
__metaclass__ = Singleton
_DEFAULT_DATABASE = os.path.join(os.path.dirname(__file__), "elements_database.csv") _DEFAULT_DATABASE = os.path.join(os.path.dirname(__file__), "elements_database.csv")
_USER_DATABASE = os.path.join(PLATFORM.application_directory(), "elements_database.csv") _USER_DATABASE = os.path.join(PLATFORM.application_directory(), "elements_database.csv")
...@@ -350,10 +379,6 @@ class ElementsDatabase(object): ...@@ -350,10 +379,6 @@ class ElementsDatabase(object):
return SortedCaselessDict([(k,self[k,pname]) for k in self._data.iterkeys()]) return SortedCaselessDict([(k,self[k,pname]) for k in self._data.iterkeys()])
def get_property(self,pname):
return SortedCaselessDict([(k,self[k,pname]) for k in self._data.iterkeys()])
def get_property_settings(self,pname): def get_property_settings(self,pname):
return copy.deepcopy(self._properties[pname]) return copy.deepcopy(self._properties[pname])
...@@ -461,3 +486,4 @@ class ElementsDatabase(object): ...@@ -461,3 +486,4 @@ class ElementsDatabase(object):
f.write('mass = %s' % props["atomic_weight"]) f.write('mass = %s' % props["atomic_weight"])
f.close() f.close()
ELEMENTS = ElementsDatabase()
\ No newline at end of file
'''
MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
-----------------------------------------------------------------------
MDANSE is a library/application for the analysis of molecular dynamics simulation data.
It uses some concepts of nMolDyn program historically designed by Gerald Kneller
for the computation and decomposition of neutron scattering spectra.
-----------------------------------------------------------------------
Copyright (C)
2015- Eric C. Pellegrini Institut Laue-Langevin
BP 156
6, rue Jules Horowitz
38042 Grenoble Cedex 9
France
pellegrini[at]ill.fr
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 2.1 of the License, or (at your option) any later version.
This library is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
Lesser General Public License for more details.
You should have received a copy of the GNU Lesser General Public
License along with this library; if not, write to the Free Software
Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA
Created on Mar 23, 2015
@author: Eric C. Pellegrini
'''
from __pkginfo__ import __version__, __author__, __date__
from MDANSE.Core.ClassRegistry import ClassRegistry as REGISTRY
from MDANSE.Core.Platform import PLATFORM
from MDANSE.Data.ElementsDatabase import ELEMENTS
from MDANSE.Framework.Configurables.UserDefinable import USER_DEFINITIONS
\ No newline at end of file
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment