.
diff --git a/COPYING.lesser b/COPYING.lesser
new file mode 100644
index 0000000..153d416
--- /dev/null
+++ b/COPYING.lesser
@@ -0,0 +1,165 @@
+ GNU LESSER GENERAL PUBLIC LICENSE
+ Version 3, 29 June 2007
+
+ Copyright (C) 2007 Free Software Foundation, Inc.
+ Everyone is permitted to copy and distribute verbatim copies
+ of this license document, but changing it is not allowed.
+
+
+ This version of the GNU Lesser General Public License incorporates
+the terms and conditions of version 3 of the GNU General Public
+License, supplemented by the additional permissions listed below.
+
+ 0. Additional Definitions.
+
+ As used herein, "this License" refers to version 3 of the GNU Lesser
+General Public License, and the "GNU GPL" refers to version 3 of the GNU
+General Public License.
+
+ "The Library" refers to a covered work governed by this License,
+other than an Application or a Combined Work as defined below.
+
+ An "Application" is any work that makes use of an interface provided
+by the Library, but which is not otherwise based on the Library.
+Defining a subclass of a class defined by the Library is deemed a mode
+of using an interface provided by the Library.
+
+ A "Combined Work" is a work produced by combining or linking an
+Application with the Library. The particular version of the Library
+with which the Combined Work was made is also called the "Linked
+Version".
+
+ The "Minimal Corresponding Source" for a Combined Work means the
+Corresponding Source for the Combined Work, excluding any source code
+for portions of the Combined Work that, considered in isolation, are
+based on the Application, and not on the Linked Version.
+
+ The "Corresponding Application Code" for a Combined Work means the
+object code and/or source code for the Application, including any data
+and utility programs needed for reproducing the Combined Work from the
+Application, but excluding the System Libraries of the Combined Work.
+
+ 1. Exception to Section 3 of the GNU GPL.
+
+ You may convey a covered work under sections 3 and 4 of this License
+without being bound by section 3 of the GNU GPL.
+
+ 2. Conveying Modified Versions.
+
+ If you modify a copy of the Library, and, in your modifications, a
+facility refers to a function or data to be supplied by an Application
+that uses the facility (other than as an argument passed when the
+facility is invoked), then you may convey a copy of the modified
+version:
+
+ a) under this License, provided that you make a good faith effort to
+ ensure that, in the event an Application does not supply the
+ function or data, the facility still operates, and performs
+ whatever part of its purpose remains meaningful, or
+
+ b) under the GNU GPL, with none of the additional permissions of
+ this License applicable to that copy.
+
+ 3. Object Code Incorporating Material from Library Header Files.
+
+ The object code form of an Application may incorporate material from
+a header file that is part of the Library. You may convey such object
+code under terms of your choice, provided that, if the incorporated
+material is not limited to numerical parameters, data structure
+layouts and accessors, or small macros, inline functions and templates
+(ten or fewer lines in length), you do both of the following:
+
+ a) Give prominent notice with each copy of the object code that the
+ Library is used in it and that the Library and its use are
+ covered by this License.
+
+ b) Accompany the object code with a copy of the GNU GPL and this license
+ document.
+
+ 4. Combined Works.
+
+ You may convey a Combined Work under terms of your choice that,
+taken together, effectively do not restrict modification of the
+portions of the Library contained in the Combined Work and reverse
+engineering for debugging such modifications, if you also do each of
+the following:
+
+ a) Give prominent notice with each copy of the Combined Work that
+ the Library is used in it and that the Library and its use are
+ covered by this License.
+
+ b) Accompany the Combined Work with a copy of the GNU GPL and this license
+ document.
+
+ c) For a Combined Work that displays copyright notices during
+ execution, include the copyright notice for the Library among
+ these notices, as well as a reference directing the user to the
+ copies of the GNU GPL and this license document.
+
+ d) Do one of the following:
+
+ 0) Convey the Minimal Corresponding Source under the terms of this
+ License, and the Corresponding Application Code in a form
+ suitable for, and under terms that permit, the user to
+ recombine or relink the Application with a modified version of
+ the Linked Version to produce a modified Combined Work, in the
+ manner specified by section 6 of the GNU GPL for conveying
+ Corresponding Source.
+
+ 1) Use a suitable shared library mechanism for linking with the
+ Library. A suitable mechanism is one that (a) uses at run time
+ a copy of the Library already present on the user's computer
+ system, and (b) will operate properly with a modified version
+ of the Library that is interface-compatible with the Linked
+ Version.
+
+ e) Provide Installation Information, but only if you would otherwise
+ be required to provide such information under section 6 of the
+ GNU GPL, and only to the extent that such information is
+ necessary to install and execute a modified version of the
+ Combined Work produced by recombining or relinking the
+ Application with a modified version of the Linked Version. (If
+ you use option 4d0, the Installation Information must accompany
+ the Minimal Corresponding Source and Corresponding Application
+ Code. If you use option 4d1, you must provide the Installation
+ Information in the manner specified by section 6 of the GNU GPL
+ for conveying Corresponding Source.)
+
+ 5. Combined Libraries.
+
+ You may place library facilities that are a work based on the
+Library side by side in a single library together with other library
+facilities that are not Applications and are not covered by this
+License, and convey such a combined library under terms of your
+choice, if you do both of the following:
+
+ a) Accompany the combined library with a copy of the same work based
+ on the Library, uncombined with any other library facilities,
+ conveyed under the terms of this License.
+
+ b) Give prominent notice with the combined library that part of it
+ is a work based on the Library, and explaining where to find the
+ accompanying uncombined form of the same work.
+
+ 6. Revised Versions of the GNU Lesser General Public License.
+
+ The Free Software Foundation may publish revised and/or new versions
+of the GNU Lesser General Public License from time to time. Such new
+versions will be similar in spirit to the present version, but may
+differ in detail to address new problems or concerns.
+
+ Each version is given a distinguishing version number. If the
+Library as you received it specifies that a certain numbered version
+of the GNU Lesser General Public License "or any later version"
+applies to it, you have the option of following the terms and
+conditions either of that published version or of any later version
+published by the Free Software Foundation. If the Library as you
+received it does not specify a version number of the GNU Lesser
+General Public License, you may choose any version of the GNU Lesser
+General Public License ever published by the Free Software Foundation.
+
+ If the Library as you received it specifies that a proxy can decide
+whether future versions of the GNU Lesser General Public License shall
+apply, that proxy's public statement of acceptance of any version is
+permanent authorization for you to choose that version for the
+Library.
\ No newline at end of file
diff --git a/LICENSE b/LICENSE
index 96f1555..eafa644 100644
--- a/LICENSE
+++ b/LICENSE
@@ -1,19 +1,28 @@
-Copyright (c) 2018 The Python Packaging Authority
+----------------------------------------------------
+Crystallographic Fortran Modules Library (CrysFML08)
+----------------------------------------------------
-Permission is hereby granted, free of charge, to any person obtaining a copy
-of this software and associated documentation files (the "Software"), to deal
-in the Software without restriction, including without limitation the rights
-to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-copies of the Software, and to permit persons to whom the Software is
-furnished to do so, subject to the following conditions:
+The CrysFML08 project is distributed under LGPL. In agreement with the
+Intergovernmental Convention of the ILL, this software cannot be used
+in military applications.
-The above copyright notice and this permission notice shall be included in all
-copies or substantial portions of the Software.
+Copyright (C) 2019-2020 Institut Laue-Langevin (ILL), Grenoble, FRANCE
+ Universidad de La Laguna (ULL), Tenerife, SPAIN
+ Laboratoire Leon Brillouin(LLB), Saclay, FRANCE
-THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-SOFTWARE.
+Authors: Juan Rodriguez-Carvajal (ILL)
+ Javier Gonzalez-Platas (ULL)
+ Nebil Ayape Katcho (ILL)
+
+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 3.0 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, see .
\ No newline at end of file
diff --git a/README.md b/README.md
index 5269f40..3688e86 100644
--- a/README.md
+++ b/README.md
@@ -4,12 +4,12 @@ This is a repository for testing the build process of both the fortran crystallo
### Build matrix
-| Platform / Compiler | gfortran | ifx | ifort | nagfor |
-| ------------------------- | -------- | ---------- | ------------- | ---------- |
-| Windows 10 | ✅ | ✅ | ✅ | |
-| Ubuntu 22.04 | ✅ | ✅ | ✅ | |
-| macOS 12 (Intel) | ✅ | Unsupported | ✅ | |
-| macOS 14 (Apple Silicone) | ✅ | Unsupported | Unsupported | ✅ Local |
+| Platform / Compiler | gfortran | ifx | ifort | nagfor |
+| ------------------------- | -------- | ----------- | ------------- | ---------- |
+| Windows 10 | ✅ | ✅ | ✅ | |
+| Ubuntu 22.04 | ✅ | ✅ | ✅ | |
+| macOS 12 (Intel) | ✅ | Unsupported | ✅ | |
+| macOS 14 (Apple Silicone) | ✅ | Unsupported | Unsupported | ✅ Local |
### Main steps
@@ -26,11 +26,11 @@ More details are in the [CI script](.github/workflows/main.yml).
### To run locally
-* Create and activate a python environment (_optional_)
+* Create and activate a python environment (_optional_)
```
$ python3.11 -m venv .venv
- $ source .venv/bin/activate
+ $ source .venv/bin/activate
```
* Upgrade the package installer for Python (_optional_)
@@ -38,7 +38,7 @@ More details are in the [CI script](.github/workflows/main.yml).
```
$ python -m pip install --upgrade pip
```
-
+
* Install Python dependences, including extras
```
@@ -48,7 +48,7 @@ More details are in the [CI script](.github/workflows/main.yml).
* Print possible options for creating job scripts (_optional_)
```
- $ python scripts.py --help
+ $ python scripts.py --help
```
* Create job scripts with default options
@@ -68,4 +68,3 @@ More details are in the [CI script](.github/workflows/main.yml).
```
$ scripts/main_script.sh
```
-
diff --git a/RELEASE.md b/RELEASE.md
new file mode 100644
index 0000000..0c4cdb8
--- /dev/null
+++ b/RELEASE.md
@@ -0,0 +1,5 @@
+This is the first release of the pycrysfml python library based on the new auto-generated Python API for CrysFML08 from https://code.ill.fr/scientific-software/CrysFML2008.
+
+### Features
+
+- Simulation of the powder diffraction pattern is implemented in `cfml_utilities`.
diff --git a/__init__.py b/__init__.py
new file mode 100644
index 0000000..7d61f7b
--- /dev/null
+++ b/__init__.py
@@ -0,0 +1,12 @@
+import os
+import sys
+import importlib.metadata
+
+# Set package version
+__version__ = importlib.metadata.version("pycrysfml")
+
+# Add current path to system path
+sys.path.append(os.path.dirname(__file__))
+
+# Set environment variable CRYSFML_DB to be the path to the Databases directory
+os.environ['CRYSFML_DB'] = os.path.join(os.path.dirname(__file__), 'Databases')
diff --git a/examples/.ipynb_checkpoints/srtio3-checkpoint.ipynb b/examples/.ipynb_checkpoints/srtio3-checkpoint.ipynb
new file mode 100644
index 0000000..1762369
--- /dev/null
+++ b/examples/.ipynb_checkpoints/srtio3-checkpoint.ipynb
@@ -0,0 +1,712 @@
+{
+ "cells": [
+ {
+ "cell_type": "markdown",
+ "id": "8a365a14",
+ "metadata": {
+ "pycharm": {
+ "name": "#%% md\n"
+ }
+ },
+ "source": [
+ "# Simulation of the diffraction pattern\n",
+ "This notebook shows how we can create a sample (phase) from atoms and calculate diffraction profiles using both constant wavelength and time-of-flight experiment types."
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 9,
+ "id": "9ecc4733",
+ "metadata": {
+ "ExecuteTime": {
+ "end_time": "2024-07-22T16:09:43.291492Z",
+ "start_time": "2024-07-22T16:09:43.289513Z"
+ },
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ },
+ "outputs": [],
+ "source": [
+ "from bokeh.io import output_notebook\n",
+ "from bokeh.io import show\n",
+ "from bokeh.plotting import figure\n",
+ "import copy\n",
+ "import os\n",
+ "import numpy as np\n",
+ "\n",
+ "from pycrysfml import crysfml08lib"
+ ]
+ },
+ {
+ "cell_type": "code",
+ "execution_count": 10,
+ "id": "d76d50fc",
+ "metadata": {
+ "ExecuteTime": {
+ "end_time": "2024-07-22T16:09:43.577764Z",
+ "start_time": "2024-07-22T16:09:43.571859Z"
+ },
+ "pycharm": {
+ "name": "#%%\n"
+ }
+ },
+ "outputs": [
+ {
+ "data": {
+ "text/html": [
+ " \n",
+ " \n",
+ "
\n",
+ "
Loading BokehJS ...\n",
+ "
\\n\"+\n",
+ " \"
\\n\"+\n",
+ " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n",
+ " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n",
+ " \"
\\n\"+\n",
+ " \"
\\n\"+\n",
+ " \"- re-rerun `output_notebook()` to attempt to load from CDN again, or
\\n\"+\n",
+ " \"- use INLINE resources instead, as so:
\\n\"+\n",
+ " \"
\\n\"+\n",
+ " \"
\\n\"+\n",
+ " \"from bokeh.resources import INLINE\\n\"+\n",
+ " \"output_notebook(resources=INLINE)\\n\"+\n",
+ " \"\\n\"+\n",
+ " \"
\\n\"+\n \"
\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"
\\n\"+\n \"
\\n\"+\n \"- re-rerun `output_notebook()` to attempt to load from CDN again, or
\\n\"+\n \"- use INLINE resources instead, as so:
\\n\"+\n \"
\\n\"+\n \"
\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\n",
+ "
\n",
+ "
Loading BokehJS ...\n",
+ "
\\n\"+\n",
+ " \"
\\n\"+\n",
+ " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n",
+ " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n",
+ " \"
\\n\"+\n",
+ " \"
\\n\"+\n",
+ " \"- re-rerun `output_notebook()` to attempt to load from CDN again, or
\\n\"+\n",
+ " \"- use INLINE resources instead, as so:
\\n\"+\n",
+ " \"
\\n\"+\n",
+ " \"
\\n\"+\n",
+ " \"from bokeh.resources import INLINE\\n\"+\n",
+ " \"output_notebook(resources=INLINE)\\n\"+\n",
+ " \"\\n\"+\n",
+ " \"
\\n\"+\n \"
\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"
\\n\"+\n \"
\\n\"+\n \"- re-rerun `output_notebook()` to attempt to load from CDN again, or
\\n\"+\n \"- use INLINE resources instead, as so:
\\n\"+\n \"
\\n\"+\n \"
\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"
\n",
+ "
\n",
+ "
Loading BokehJS ...\n",
+ "
\\n\"+\n",
+ " \"
\\n\"+\n",
+ " \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n",
+ " \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n",
+ " \"
\\n\"+\n",
+ " \"
\\n\"+\n",
+ " \"- re-rerun `output_notebook()` to attempt to load from CDN again, or
\\n\"+\n",
+ " \"- use INLINE resources instead, as so:
\\n\"+\n",
+ " \"
\\n\"+\n",
+ " \"
\\n\"+\n",
+ " \"from bokeh.resources import INLINE\\n\"+\n",
+ " \"output_notebook(resources=INLINE)\\n\"+\n",
+ " \"\\n\"+\n",
+ " \"
\\n\"+\n \"
\\n\"+\n \"BokehJS does not appear to have successfully loaded. If loading BokehJS from CDN, this \\n\"+\n \"may be due to a slow or bad network connection. Possible fixes:\\n\"+\n \"
\\n\"+\n \"
\\n\"+\n \"- re-rerun `output_notebook()` to attempt to load from CDN again, or
\\n\"+\n \"- use INLINE resources instead, as so:
\\n\"+\n \"
\\n\"+\n \"
\\n\"+\n \"from bokeh.resources import INLINE\\n\"+\n \"output_notebook(resources=INLINE)\\n\"+\n \"\\n\"+\n \"