Commit e4e15758 authored by Remi Perenon's avatar Remi Perenon

Merge branch 'release-1.3.x'

parents 6002411b cb84004a
Pipeline #4807 passed with stages
in 24 minutes and 40 seconds
MDANSE project has been created by:
* Eric Pellegrini
MDANSE source code is currently developed by
* Eric Pellegrini
* Remi Perenon
MDANSE former contributors:
* Bachir Aoun
* Gael Goret
......@@ -4,6 +4,6 @@ SHELL ["/bin/bash", "-c"]
VOLUME builds
RUN source ./BuildServer/Unix/Debian/definitions.sh; source ./BuildServer/Unix/setup_ci.sh ; ./BuildServer/Unix/Debian/deploy.sh
RUN source ./BuildServer/Unix/Debian/definitions.sh; source ./BuildServer/Unix/setup_ci.sh ; source ./BuildServer/Unix/bionic_dependencies_modification.sh ; ./BuildServer/Unix/Debian/deploy.sh
#!/bin/bash
cd ${CI_PROJECT_DIR}
# Modifying python-vtk to python-vtk6 in CONTROL FILE
cd ${CI_PROJECT_DIR}
sed -i "s/python-vtk/python-vtk6/" BuildServer/Unix/Debian/Resources/DEBIAN/control
status=$?
if [ $status -ne 0 ]; then
echo -e "${RED}" "Failed to build/install MDANSE""${NORMAL}"
exit $status
fi
version 1.3.0
--------------
* ADDED Neutron Dynamic Total Structure Factor analysis
* ADDED User can now launch a script with qvector parameters instead of saved qvector definition
* FIXED issue #45 MSD computing on non-orthorombic universe was wrong (fixed with new mmtk version) /!\ Modifies MSD, VACF and DoS, and maybe others... /!\ Units in MMTK have slightly changed
* FIXED issue #44 An error message appeared when display, close and reopen molecular viewer and animation plugins
* FIXED issue #43 The weights are no more normalized with absolute sum /!\ Modifies at least CCF, DCSF and SSF job behavior
* FIXED issue #42 Plotter units could be inconsistent
* FIXED issue #41 Instrument resolution window froze GUI on macOS
* FIXED issue #40 MDANSE could not be used on Ubuntu Bionic systems (due to vtk dependency name)
* FIXED issue #38 Interface was frozen when jobs were launched. A delay of 2s is added at the end of jobs before suppressing the status file
version 1.2.1
--------------
* FIXED issue #39 Time scale in Gromacs converter was incorrect
......
Citing MDANSE
MDANSE: An Interactive Analysis Environment for Molecular Dynamics Simulations.
G. Goret, B. Aoun, E. Pellegrini. J Chem Inf Model. (2017) 57(1):1-5.
# **************************************************************************
#
# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
#
# @file Extensions/distance_histogram.pyx
# @brief Implements module/class/test distance_histogram
#
# @homepage https://mdanse.org
# @license GNU General Public License v3 or higher (see LICENSE)
# @copyright Institut Laue Langevin 2013-now
# @authors Scientific Computing Group at ILL (see AUTHORS)
#
# **************************************************************************
import cython
cimport numpy as np
from numpy cimport ndarray
......
# -*- coding: utf-8 -*-
#################################################
# fast calculation module of trajectory-viewer #
# Gael Goret for the Institut Laue-Langevin #
# gael.goret@ill.eu #
#################################################
# **************************************************************************
#
# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
#
# @file Extensions/fast_calculation.pyx
# @brief Implements module/class/test fast_calculation
#
# @homepage https://mdanse.org
# @license GNU General Public License v3 or higher (see LICENSE)
# @copyright Institut Laue Langevin 2013-now
# @authors Scientific Computing Group at ILL (see AUTHORS)
#
# **************************************************************************
import cython
cimport numpy as np
......@@ -37,4 +43,4 @@ def cpt_cluster_connectivity(ndarray[np.float64_t, ndim=2] coords,
bonds.append([i,j])
return bonds
\ No newline at end of file
# **************************************************************************
#
# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
#
# @file Extensions/mic_fast_calc.pyx
# @brief Implements module/class/test mic_fast_calc
#
# @homepage https://mdanse.org
# @license GNU General Public License v3 or higher (see LICENSE)
# @copyright Institut Laue Langevin 2013-now
# @authors Scientific Computing Group at ILL (see AUTHORS)
#
# **************************************************************************
cimport numpy as np
import numpy as np
from numpy cimport ndarray
......
# **************************************************************************
#
# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
#
# @file Extensions/mt_fast_calc.pyx
# @brief Implements module/class/test mt_fast_calc
#
# @homepage https://mdanse.org
# @license GNU General Public License v3 or higher (see LICENSE)
# @copyright Institut Laue Langevin 2013-now
# @authors Scientific Computing Group at ILL (see AUTHORS)
#
# **************************************************************************
import cython
cimport numpy as np
import numpy as np
......
"""
Wrappers for Qhull triangulation, plus some additional N-D geometry utilities
.. versionadded:: 0.9
# **************************************************************************
#
# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
#
# @file Extensions/qhull.pyx
# @brief Implements module/class/test qhull
#
# @homepage https://mdanse.org
# @license GNU General Public License v3 or higher (see LICENSE)
# @copyright Institut Laue Langevin 2013-now
# @authors Scientific Computing Group at ILL (see AUTHORS)
#
# **************************************************************************
"""
#
# Copyright (C) Pauli Virtanen, 2010.
#
......
# **************************************************************************
#
# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
#
# @file Extensions/sas_fast_calc.pyx
# @brief Implements module/class/test sas_fast_calc
#
# @homepage https://mdanse.org
# @license GNU General Public License v3 or higher (see LICENSE)
# @copyright Institut Laue Langevin 2013-now
# @authors Scientific Computing Group at ILL (see AUTHORS)
#
# **************************************************************************
import cython
import numpy as np
cimport numpy as np
......
# **************************************************************************
#
# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
#
# @file Extensions/sd_fast_calc.pyx
# @brief Implements module/class/test sd_fast_calc
#
# @homepage https://mdanse.org
# @license GNU General Public License v3 or higher (see LICENSE)
# @copyright Institut Laue Langevin 2013-now
# @authors Scientific Computing Group at ILL (see AUTHORS)
#
# **************************************************************************
import cython
cimport numpy as np
import numpy as np
......
# Pour compiler:
# python setup.py build_ext --inplace
# **************************************************************************
#
# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
#
# @file Extensions/setup.py
# @brief Implements module/class/test setup
#
# @homepage https://mdanse.org
# @license GNU General Public License v3 or higher (see LICENSE)
# @copyright Institut Laue Langevin 2013-now
# @authors Scientific Computing Group at ILL (see AUTHORS)
#
# **************************************************************************
import glob
import os
......
# **************************************************************************
#
# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
#
# @file Extensions/xtc/trr.pyx
# @brief Implements module/class/test trr
#
# @homepage https://mdanse.org
# @license GNU General Public License v3 or higher (see LICENSE)
# @copyright Institut Laue Langevin 2013-now
# @authors Scientific Computing Group at ILL (see AUTHORS)
#
# **************************************************************************
# cython: c_string_type=str, c_string_encoding=ascii
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
......
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# **************************************************************************
#
# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
#
# @file Extensions/xtc/xtc.pyx
# @brief Implements module/class/test xtc
#
# @homepage https://mdanse.org
# @license GNU General Public License v3 or higher (see LICENSE)
# @copyright Institut Laue Langevin 2013-now
# @authors Scientific Computing Group at ILL (see AUTHORS)
#
# **************************************************************************
# cython: c_string_type=str, c_string_encoding=ascii
##############################################################################
# MDTraj: A Python Library for Loading, Saving, and Manipulating
......
This diff is collapsed.
#!/usr/bin/env python
# **************************************************************************
#
# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
#
# @file Src/__init__.py
# @brief Implements module/class/test __init__
#
# @homepage https://mdanse.org
# @license GNU General Public License v3 or higher (see LICENSE)
# @copyright Institut Laue Langevin 2013-now
# @authors Scientific Computing Group at ILL (see AUTHORS)
#
# **************************************************************************
import cPickle
import glob
import optparse
......
#!/usr/bin/env python
# **************************************************************************
#
# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
#
# @file Src/__init__.py
# @brief Implements module/class/test __init__
#
# @homepage https://mdanse.org
# @license GNU General Public License v3 or higher (see LICENSE)
# @copyright Institut Laue Langevin 2013-now
# @authors Scientific Computing Group at ILL (see AUTHORS)
#
# **************************************************************************
if __name__ == "__main__":
from MDANSE.GUI.Apps import ElementsDatabaseEditorApp
......
#!/usr/bin/env python
# **************************************************************************
#
# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
#
# @file Src/__init__.py
# @brief Implements module/class/test __init__
#
# @homepage https://mdanse.org
# @license GNU General Public License v3 or higher (see LICENSE)
# @copyright Institut Laue Langevin 2013-now
# @authors Scientific Computing Group at ILL (see AUTHORS)
#
# **************************************************************************
if __name__ == "__main__":
from MDANSE.GUI.Apps import MainApplication
......
#!/usr/bin/env python
# **************************************************************************
#
# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
#
# @file Src/__init__.py
# @brief Implements module/class/test __init__
#
# @homepage https://mdanse.org
# @license GNU General Public License v3 or higher (see LICENSE)
# @copyright Institut Laue Langevin 2013-now
# @authors Scientific Computing Group at ILL (see AUTHORS)
#
# **************************************************************************
if __name__ == "__main__":
from MDANSE.GUI.Apps import PeriodicTableViewerApp
......
#!/usr/bin/env python
# **************************************************************************
#
# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
#
# @file Src/__init__.py
# @brief Implements module/class/test __init__
#
# @homepage https://mdanse.org
# @license GNU General Public License v3 or higher (see LICENSE)
# @copyright Institut Laue Langevin 2013-now
# @authors Scientific Computing Group at ILL (see AUTHORS)
#
# **************************************************************************
if __name__ == "__main__":
from MDANSE.GUI.Apps import PlotterApp
......
#!/usr/bin/env python
# **************************************************************************
#
# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
#
# @file Src/__init__.py
# @brief Implements module/class/test __init__
#
# @homepage https://mdanse.org
# @license GNU General Public License v3 or higher (see LICENSE)
# @copyright Institut Laue Langevin 2013-now
# @authors Scientific Computing Group at ILL (see AUTHORS)
#
# **************************************************************************
if __name__ == "__main__":
from MDANSE.GUI.Apps import UserDefinitionViewerApp
......
#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
#goret[at]ill.fr
#aoun[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 30, 2015
:author: Eric C. Pellegrini
'''
# **************************************************************************
#
# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
#
# @file Src/Core/ClassRegistry.py
# @brief Implements module/class/test ClassRegistry
#
# @homepage https://mdanse.org
# @license GNU General Public License v3 or higher (see LICENSE)
# @copyright Institut Laue Langevin 2013-now
# @authors Scientific Computing Group at ILL (see AUTHORS)
#
# **************************************************************************
import glob
import imp
import inspect
......
#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
#goret[at]ill.fr
#aoun[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.
# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
#
#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.
# @file Src/Core/Error.py
# @brief Implements module/class/test Error
#
#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 30, 2015
:author: Eric C. Pellegrini
'''
# @homepage https://mdanse.org
# @license GNU General Public License v3 or higher (see LICENSE)
# @copyright Institut Laue Langevin 2013-now
# @authors Scientific Computing Group at ILL (see AUTHORS)
#
# **************************************************************************
class Error(Exception):
'''
......
#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
#goret[at]ill.fr
#aoun[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 30, 2015
:author: Eric C. Pellegrini
'''
# **************************************************************************
#
# MDANSE: Molecular Dynamics Analysis for Neutron Scattering Experiments
#
# @file Src/Core/Platform.py
# @brief Implements module/class/test Platform
#
# @homepage https://mdanse.org
# @license GNU General Public License v3 or higher (see LICENSE)
# @copyright Institut Laue Langevin 2013-now
# @authors Scientific Computing Group at ILL (see AUTHORS)
#
# **************************************************************************
import abc
import ctypes
import datetime
......@@ -91,7 +73,17 @@ class Platform(object):
:rtype: str
'''
return os.path.join(self.package_directory(), 'Doc')
return os.path.join(self.package_directory(), 'Doc')
def jobs_launch_delay(self):
'''
Returns the delay (in seconds) for a job to launch.
This is used to determine the delay before updating the GUI and suppressing a job status file
:return: the delay (in seconds) for a job to launch
:rtype: float
'''
return 2.0
def api_path(self):
'''
......
#MDANSE : Molecular Dynamics Analysis for Neutron Scattering Experiments
#------------------------------------------------------------------------------------------
#Copyright (C)
#2015- Eric C. Pellegrini Institut Laue-Langevin